@article {pmid40586834, year = {2025}, author = {Moisa, MB and Roba, ZR and Purohit, S and Deribew, KT and Gemeda, DO}, title = {Evaluating the impact of land use and land cover change on soil moisture variability using GIS and remote sensing technology in southwestern Ethiopia.}, journal = {Environmental monitoring and assessment}, volume = {197}, number = {7}, pages = {824}, pmid = {40586834}, issn = {1573-2959}, mesh = {Ethiopia ; *Soil/chemistry ; *Remote Sensing Technology ; *Environmental Monitoring/methods ; Geographic Information Systems ; Agriculture ; Climate Change ; Conservation of Natural Resources ; Water/analysis ; Ecosystem ; Forests ; }, abstract = {Soil moisture dynamics are critical for agriculture, water resources, and climate resilience in Ethiopia, influencing crop yields, water availability, and ecosystem health. Assessing soil moisture variability in relation to land use and cover (LULC) changes is essential for effective ecosystem conservation and climate change adaptation, ensuring sustainable development and resilience to environmental challenges. This study examines the impact of LULC changes on soil moisture variability in Southwestern Ethiopia over 30 years (1994-2024). Utilizing Landsat Thematic Mapper (1994), Enhanced Thematic Mapper Plus (2004), and Operational Land Imager/Thermal Infrared Sensor (2024) data, LULC changes were analyzed using supervised classification approach with the Maximum Likelihood Algorithm. The classification process was conducted using ERDAS Imagine 2015 software. In addition, vegetation health and soil moisture dynamics were assessed through the Normalized Difference Vegetation Index (NDVI) and the Normalized Difference Moisture Index (NDMI). Results reveal a significant increase in cultivated land from 3595.2 km[2] (42.0%) to 6183.3 km[2] (72.2%), with a corresponding decrease in forest cover from 3119.2 km[2] (36.4%) to 2030.4 km[2] (23.7%).This significant shift indicates intensive agricultural expansion at the expense of forest cover, highlighting increased land conversion pressures. NDVI values dropped from 0.71 in 1994 to 0.52 in 2024, this decline in NDVI values signifies a substantial reduction in vegetation cover and density over the 30-year period. The NDMI results indicated a decrease in peak moisture levels and average soil moisture, emphasizing a growing trend of intensified dryness. This soil moisture decline is attributed to factors such as reduced precipitation, increased evaporation, and changes in LULC. The conversion of forest land to cultivation led to a significant decrease in NDMI values, reflecting a reduction in soil moisture due to the loss of forest cover and increased evapotranspiration from agricultural activities. A strong correlation (R[2] = 0.98) between NDVI and NDMI highlights that higher vegetation cover is associated with higher soil moisture. Therefore, the study highlights the profound impact of land use and land cover changes on soil moisture, underscoring the urgent need for sustainable land management practices. These practices are critical to combat environmental degradation, improve soil moisture retention, and bolster ecosystem resilience, ensuring a sustainable and climate-resilient future.}, } @article {pmid40585004, year = {2025}, author = {Boyes, D and Crowley, LM and Boyes, C and , and , and , and , and , and , and , }, title = {The genome sequence of the Uncertain moth, Hoplodrina octogenaria (Goeze, 1781).}, journal = {Wellcome open research}, volume = {10}, number = {}, pages = {201}, pmid = {40585004}, issn = {2398-502X}, abstract = {We present a genome assembly from a male specimen of Hoplodrina octogenaria (Uncertain moth; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence has a total length of 476.65 megabases. Most of the assembly (99.98%) is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled, with a length of 15.93 kilobases.}, } @article {pmid40578867, year = {2025}, author = {Topalian, N and Fagherazzi, G and Perchoux, C}, title = {Daily mobility, activity and environmental determinants of stress in ecological momentary assessment (EMA) and GPS studies: a scoping review protocol.}, journal = {BMJ open}, volume = {15}, number = {6}, pages = {e091509}, pmid = {40578867}, issn = {2044-6055}, mesh = {Humans ; Scoping Review as Topic ; *Ecological Momentary Assessment ; *Geographic Information Systems ; *Stress, Psychological ; Research Design ; *Activities of Daily Living ; Environment ; }, abstract = {INTRODUCTION: Stress is omnipresent in our everyday lives and a key risk factor for our physical and mental health. Yet little is known about the impact of geographic life environments, linked to our daily activities and mobility patterns, on our momentary and daily stress levels.We propose this review to gather evidence on the spatio-temporal determinants of momentary or daily stress in studies using ecological momentary assessment (EMA) or experience sampling methods (ESM) in addition to global positioning systems (GPS) tracking. We will focus on the spatio-temporal definition and modelling of environmental exposures accounting for participant daily activities and mobility patterns and their association with stress.

METHODS AND ANALYSIS: This scoping review will follow the Preferred Reporting Items for Systematic Reviews and Meta-Analyses framework for scoping reviews (2018). We will search the PubMed/Medline, Web of Science, PsycInfo and Scopus databases. We will include papers using EMA or ESM and GPS measuring chronic, daily or momentary stress as an outcome; these methods are also referred to as geographically-explicit ecological momentary assessment.Articles published from January 2000-June 2025 will be screened. Two independent reviewers will screen titles and abstracts to agree on the inclusion of articles. No geographical or population limitation will be imposed.

ETHICS AND DISSEMINATION: This study is a scoping review based on previously published and publicly available literature. It does not involve the collection of primary data, human participants, or the processing of personal or sensitive information. Therefore, ethical approval is not required in accordance with institutional and international research ethics guidelines. The results will be submitted in peer-reviewed journals and presented at international conferences.}, } @article {pmid40578201, year = {2025}, author = {Son, HF and Hwang, S and Kim, Y and Ahn, JH and Ko, JK and Gong, G and Um, Y and Park, JH and Park, HJ and Lee, SM}, title = {Enzymatic depolymerization of polyethylene using a small laccase and its potential for bio-upcycling.}, journal = {Journal of hazardous materials}, volume = {495}, number = {}, pages = {139021}, doi = {10.1016/j.jhazmat.2025.139021}, pmid = {40578201}, issn = {1873-3336}, abstract = {Polyethylene (PE) plastics present significant environmental challenges due to their recalcitrant nature and widespread usage. This study explores the biological degradation of PE using a novel enzyme, small laccase from Amycolatopsis sp. ATCC 39116 (ASLAC). Among four selected laccases, ASLAC demonstrated the highest biomass production using PE as a carbon source when expressed by Yarrowia lipolytica. Surface analysis of PE films treated with purified ASLAC, using scanning electron microscopy (SEM) and atomic force microscopy (AFM), revealed substantial degradation of the material. The degradation products were successfully utilized by Y. lipolytica, underscoring its potential for converting PE into bioenergy. Structural analysis and molecular docking simulations revealed that the substrate binding site of ASLAC, characterized by a hydrophobic planner configuration, is highly optimized for binding and cleaving PE polymers. This unique structure distinguishes it from other laccases with narrower or obstructed binding sites. Phylogenetic analysis of 311 small laccase sequences classified ASLAC into the Type-Ia subgroup, which exhibited superior potential for PE degradation. This study establishes ASLAC as a promising biocatalyst for sustainable PE management, providing a foundation for future applications in bioremediation and polymer upcycling.}, } @article {pmid40432231, year = {2025}, author = {Tian, XC and Nie, S and Domingues, D and Rossi Paschoal, A and Jiang, LB and Mao, JF}, title = {PlantLncBoost: key features for plant lncRNA identification and significant improvement in accuracy and generalization.}, journal = {The New phytologist}, volume = {247}, number = {3}, pages = {1538-1549}, doi = {10.1111/nph.70211}, pmid = {40432231}, issn = {1469-8137}, support = {2022YFD2200103//National Key R&D Program of China/ ; 32171816//National Natural Science Foundation of China/ ; ZR2022YQ23//Natural Science Fund for Excellent Young Scholars of Shandong Province/ ; 2025A1515012969//Guangdong Basic and Applied Basic Research Foundation/ ; #440412/2022-6//Conselho Nacional de Desenvolvimento Científico e Tecnológico - CNPq/ ; Project: NAPI Bioinformatica #66.2021//Fundação Araucária/ ; }, mesh = {*RNA, Long Noncoding/genetics ; *RNA, Plant/genetics ; *Computational Biology/methods ; Algorithms ; *Plants/genetics ; RNA, Messenger/genetics ; *Software ; Open Reading Frames/genetics ; }, abstract = {Long noncoding RNAs (lncRNAs) are critical regulators of numerous biological processes in plants. Nevertheless, their identification is challenging due to the low sequence conservation across various species. Existing computational methods for lncRNA identification often face difficulties in generalizing across diverse plant species, highlighting the need for more robust and versatile identification models. Here, we present PlantLncBoost, a novel computational tool designed to improve the generalization in plant lncRNA identification. By integrating advanced gradient boosting algorithms with comprehensive feature selection, our approach achieves both high accuracy and generalizability. We conducted an extensive analysis of 1662 features and identified three key features - ORF coverage, complex Fourier average, and atomic Fourier amplitude - that effectively distinguish lncRNAs from mRNAs. We assessed the performance of PlantLncBoost using comprehensive datasets from 20 plant species. The model exhibited exceptional performance, with an accuracy of 96.63%, a sensitivity of 98.42%, and a specificity of 94.93%, significantly outperforming existing tools. Further analysis revealed that the features we selected effectively capture the differences between lncRNAs and mRNAs across a variety of plant species. PlantLncBoost represents a significant advancement in plant lncRNA identification. It is freely accessible on GitHub (https://github.com/xuechantian/PlantLncBoost) and has been integrated into a comprehensive analysis pipeline, Plant-LncRNA-pipeline v.2 (https://github.com/xuechantian/Plant-LncRNA-pipeline-v2).}, } @article {pmid40167332, year = {2025}, author = {Curto, M and Veríssimo, A and Riccioni, G and Santos, CD and Ribeiro, F and Jentoft, S and Alves, MJ and Gante, HF}, title = {Improving Whole Biodiversity Monitoring and Discovery With Environmental DNA Metagenomics.}, journal = {Molecular ecology resources}, volume = {25}, number = {6}, pages = {e14105}, doi = {10.1111/1755-0998.14105}, pmid = {40167332}, issn = {1755-0998}, support = {CEEC/0482/2020//Fundação para a Ciência e a Tecnologia/ ; DL 57/2016/CP1440/CP1646/CT0001//Fundação para a Ciência e a Tecnologia/ ; LA/P/0069/2020//Fundação para a Ciência e a Tecnologia/ ; PTDC/BIA-CBI/31644/2017//Fundação para a Ciência e a Tecnologia/ ; UID/04292/2020//Fundação para a Ciência e a Tecnologia/ ; UID/BIA/00329/2020//Fundação para a Ciência e a Tecnologia/ ; UIDP/50027/2020//Fundação para a Ciência e a Tecnologia/ ; LA/P/0048/2020//Fundação para a Ciência e a Tecnologia/ ; 857251//Horizon 2020 Framework Programme/ ; STG/21/044//KU Leuven/ ; }, mesh = {*Metagenomics/methods ; *Biodiversity ; *DNA, Environmental/genetics ; *Computational Biology/methods ; DNA Barcoding, Taxonomic/methods ; Metagenome ; }, abstract = {Environmental DNA (eDNA) metagenomics sequences all DNA molecules present in environmental samples and has the potential of identifying virtually any organism from which they are derived. However, due to unacceptable levels of false positives and negatives, this approach is underexplored as a tool for biodiversity monitoring across the tree of life, particularly for non-microscopic eukaryotes. We present SeqIDist, a framework that combines multilocus BLAST matches against several reference databases followed by an analysis of sequence identity distribution patterns to disentangle false positives while revealing new biodiversity and increasing the accuracy of metagenomic approaches. We tested SeqIDist on an eDNA metagenomic dataset from a riverine site and compared the results to those obtained with an eDNA metabarcoding approach for benchmarking purposes. We start by characterising the biological community (~2000 taxa) across the tree of life at low taxonomic levels and show that eDNA metagenomics has a higher sensitivity than eDNA metabarcoding in discovering new diversity. We show that limited representation of whole genome sequences in reference databases can lead to false positives. For non-microscopic eukaryotes, eDNA metagenomic data often consist of a few sparse, anonymous sequences scattered across the genome, making metagenome assembly methods unfeasible. Finally, we infer eDNA source and residency time using read length distributions as a measure of decay status. The higher accuracy of SeqIDist opens the discussion of the potential of eDNA metagenomics for archived samples and its implementation in long-term biodiversity monitoring at a planetary scale.}, } @article {pmid40125978, year = {2025}, author = {Bailey, N and Stevison, L and Samuk, K}, title = {Correcting for Bias in Estimates of θ w and Tajima's D From Missing Data in Next-Generation Sequencing.}, journal = {Molecular ecology resources}, volume = {25}, number = {6}, pages = {e14104}, doi = {10.1111/1755-0998.14104}, pmid = {40125978}, issn = {1755-0998}, support = {R35GM147501/GM/NIGMS NIH HHS/United States ; R35GM147501/GM/NIGMS NIH HHS/United States ; }, mesh = {*High-Throughput Nucleotide Sequencing/methods ; *Genetics, Population/methods ; *Genetic Variation ; Software ; *Computational Biology/methods ; Bias ; }, abstract = {Population genetic analyses use information from the site frequency spectrum to infer evolutionary processes. Two summary statistics, Watterson's estimator (θ w) of genetic diversity, and Tajima's D , used for detecting non-neutral evolution, are among the most frequently computed statistics utilising this information. However, missing information in genomic data, particularly as encoded in the Variant Call Format (VCF), can bias these estimates, leading to incorrect evolutionary inferences. We assessed the impact of missing data on the estimation of these statistics using various population genetic software packages (VCFtools, PopGenome, pegas and scikit-allel). By simulating neutral genomic data with varying levels of missing genotypes and sites, we found consistent underestimation of θ w across programs. We found a consequent bias in estimates of Tajima's D , though the direction varied by software. We developed and implemented correction methods as functions in an update of the popular pixy software, significantly reducing these biases. Our findings highlight the need for accurate data handling in population genomics to avoid misinterpretations of evolutionary phenomena.}, } @article {pmid40087979, year = {2025}, author = {Van den Wyngaert, S and Cerbin, S and Garzoli, L and Grossart, HP and Gsell, AS and Kraberg, A and Lepère, C and Neuhauser, S and Stupar, M and Tarallo, A and Cunliffe, M and Gachon, C and Gavrilović, A and Masigol, H and Rasconi, S and Selmeczy, GB and Schmeller, DS and Scholz, B and Timoneda, N and Trbojević, I and Wilk-Woźniak, E and Reñé, A}, title = {ParAquaSeq, a Database of Ecologically Annotated rRNA Sequences Covering Zoosporic Parasites Infecting Aquatic Primary Producers in Natural and Industrial Systems.}, journal = {Molecular ecology resources}, volume = {25}, number = {6}, pages = {e14099}, doi = {10.1111/1755-0998.14099}, pmid = {40087979}, issn = {1755-0998}, support = {PID2020-112978GB-I00//Ministerio de Ciencia, Innovación y Universidades/ ; CA20125//European Cooperation in Science and Technology/ ; 451-03-66/2024-03/200178//Ministarstvo Prosvete, Nauke i Tehnološkog Razvoja/ ; 239548-051//RANNIS Icelandic Research Fund/ ; 340659//Research Council of Finland/ ; 346387//Research Council of Finland/ ; 101086521//European Commission/ ; IR0000005//European Commission/ ; NKFIH KKP 144068//National Laboratory for Water Science and Water Security/ ; RRF-2.3.1-21-2022-00008//National Laboratory for Water Science and Water Security/ ; Y0801-B16//Austrian Science Fund/ ; //AXA Research Fund/ ; ANR-21-BIRE-0002-01//Agence Nationale de la Recherche/ ; 101052342//Biodiversa+/ ; CIR-01_00028//Italian Ministry of University and Research/ ; GR1540/33-1//Deutsche Forschungsgemeinschaft/ ; GR1540/47-1//Deutsche Forschungsgemeinschaft/ ; GR1540/48-1//Deutsche Forschungsgemeinschaft/ ; GR1540/51-1//Deutsche Forschungsgemeinschaft/ ; CEX2019-000928-S//AEI/ ; }, mesh = {*Aquatic Organisms/parasitology ; *RNA, Ribosomal/genetics ; Microalgae/parasitology ; *Parasites/genetics/classification ; *Databases, Genetic ; }, abstract = {Amplicon sequencing tools such as metabarcoding are commonly used for thorough characterisation of microbial diversity in natural samples. They mostly rely on the amplification of conserved universal markers, mainly ribosomal genes, allowing the taxonomic assignment of barcodes. However, linking taxonomic classification with functional traits is not straightforward and requires knowledge of each taxonomic group to confidently assign taxa to a given functional trait. Zoosporic parasites are highly diverse and yet understudied, with many undescribed species and host associations. However, they can have important impacts on host populations in natural ecosystems (e.g., controlling harmful algal blooms), as well as on industrial-scale algae production, e.g. aquaculture, causing their collapse or economic losses. Here, we present ParAquaSeq, a curated database of available molecular ribosomal sequences belonging to zoosporic parasites infecting aquatic vascular plants, macroalgae and photosynthetic microorganisms, i.e. microalgae and cyanobacteria. These sequences are aligned with ancillary data and other information currently available, including details on their hosts, occurrence, culture availability and associated bibliography. The database includes 1131 curated sequences from marine, freshwater and industrial or artificial environments, and belonging to 13 different taxonomic groups, including Chytridiomycota, Oomycota, Phytomyxea, and Syndiniophyceae. The curated database will allow a comprehensive analysis of zoosporic parasites in molecular datasets to answer questions related to their occurrence and distribution in natural communities. Especially through meta-analysis, the database serves as a valuable tool for developing effective mitigation and sustainable management strategies in the algae biomass industry, but it will also help to identify knowledge gaps for future research.}, } @article {pmid40079420, year = {2025}, author = {Jurburg, SD}, title = {Short Read Lengths Recover Ecological Patterns in 16S rRNA Gene Amplicon Data.}, journal = {Molecular ecology resources}, volume = {25}, number = {6}, pages = {e14102}, doi = {10.1111/1755-0998.14102}, pmid = {40079420}, issn = {1755-0998}, mesh = {*RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification ; *Metagenomics/methods ; Microbiota ; Animals ; *DNA Barcoding, Taxonomic/methods ; Biodiversity ; Computational Biology/methods ; Sequence Analysis, DNA/methods ; }, abstract = {16S rRNA gene metabarcoding, the study of amplicon sequences of the 16S rRNA gene from mixed environmental samples, is an increasingly popular and accessible method for assessing bacterial communities across a wide range of environments. As metabarcoding sequence data archives continue to grow, data reuse will likely become an important source of novel insights into the ecology of microbes. While recent work has demonstrated the benefits of longer read lengths for the study of microbial communities from 16S rRNA gene segments, no studies have explored the use of shorter (< 200 bp) read lengths in the context of data reuse. Nevertheless, this information is essential to improve the reuse and comparability of metabarcoding data across existing datasets. This study reanalyzed nine 16S rRNA datasets targeting aquatic, animal-associated and soil microbiomes, and evaluated how processing the sequence data across a range of read lengths affected the resulting taxonomic assignments, biodiversity metrics and differential (i.e., before-after treatment) analyses. Short read lengths successfully recovered ecological patterns and allowed for the use of more sequences. Limited increases in resolution were observed beyond 150 bp reads across environments. Furthermore, abundance-weighted diversity metrics (e.g., Inverse Simpson index, Morisita-Horn dissimilarities or weighted Unifrac distances) were more robust to variation in read lengths. Read lengths alone contributed to consistent increases in the total number of ASVs detected, highlighting the need to consider metabarcoding-derived diversity estimates within the context of the bioinformatics parameters selected. This study provides evidence-based guidelines for the processing of short reads.}, } @article {pmid40051336, year = {2025}, author = {Birchard, K and Boccia, C and Lounder, H and Colston-Nepali, L and Friesen, VL}, title = {Popfinder: A Highly Effective Artificial Neural Network Package for Genetic Population Assignment.}, journal = {Molecular ecology resources}, volume = {25}, number = {6}, pages = {e14096}, doi = {10.1111/1755-0998.14096}, pmid = {40051336}, issn = {1755-0998}, support = {//Environment and Climate Change Canada/ ; }, mesh = {*Neural Networks, Computer ; Animals ; *Genetics, Population/methods ; *Computational Biology/methods ; *Software ; *Birds/genetics/classification ; }, abstract = {The ability to assign biological samples to source populations with high accuracy and precision based on genetic variation is important for numerous applications from ecological studies through wildlife conservation to epidemiology. However, population assignment when genetic differentiation is low is challenging, and methods to address this problem are lacking. The application of artificial neural networks to population assignment using genomic data is highly promising. Here we present popfinder: a new, easy-to-use Python-based artificial neural network pipeline for genetic population assignment. We tested popfinder both with simulated genetic data from populations connected by varying levels of gene flow and with reduced-representation sequence data for three species of seabirds with weak to no population genetic structure. Popfinder was able to assign individuals to their source populations with high accuracy, precision and recall in most cases, including both simulated and empirical data sets, except in the empirical data set with the weakest population structure, where the comparator programs also performed poorly. Compared to other available software, popfinder was slower on the simulated data sets due to hyperparameter tuning and the fact that it does not reduce the dimensionality of the data set; however, all programs ran in seconds on empirical data sets. Additionally, popfinder provides a perturbation ranking method to help develop optimised SNP panels for genetic population assignment and is designed to be user-friendly. Finally, we caution users of all assignment programs to watch both for leakage of data during model training, which can lead to overfitting and inflation of performance metrics, and for unequal detection probabilities.}, } @article {pmid40577234, year = {2025}, author = {Roberts, T and Hanan, NP}, title = {Sapflow Database Reveals Density-Dependent Competition Among Woody Plants at Global Scale.}, journal = {Ecology letters}, volume = {28}, number = {6}, pages = {e70167}, pmid = {40577234}, issn = {1461-0248}, support = {DEB 2025166//National Science Foundation/ ; //New Mexico Space Consortium/ ; }, mesh = {Databases, Factual ; *Water/metabolism ; Ecosystem ; *Trees/physiology ; }, abstract = {Though limiting resources differ among systems, water is limiting in most arid and many mesic systems, potentially allowing for direct measurement of competition by measurement of water uptake. Sapflow measurements provide a direct measure of water movement through plant stems, but, to our knowledge, sapflow has never been used to study density dependence and competition at large (regional or global) scales. Here, we examine a global database of sapflow measurements, the SapFluxNet database, for signs of density-dependent competition for water. We find that plant-level water uptake decreases with increasing competition from neighbours (specifically, neighbourhood basal area). Further analysis demonstrates that global-scale variability in annual sapflow can be largely explained (R[2] = 0.522) by the combination of average vapour pressure and neighbourhood summed basal area. This analysis provides a rare quantification of plant competition for a limiting resource inferred directly via measurements of resource acquisition (i.e., sapflow).}, } @article {pmid40573089, year = {2025}, author = {Suarez, C and Adibi, S}, title = {Integrating Traditional Nutritional Wisdom into Digital Nutrition Platforms: Toward Culturally Adaptive and Inclusive Health Technologies.}, journal = {Nutrients}, volume = {17}, number = {12}, pages = {}, pmid = {40573089}, issn = {2072-6643}, mesh = {Humans ; *Biomedical Technology/methods ; Culture ; *Digital Technology ; Health Knowledge, Attitudes, Practice ; *Nutritional Sciences ; }, abstract = {Background/Objectives: Traditional nutritional knowledge, shaped by centuries of cultural and ecological adaptation, offers holistic and sustainable dietary frameworks that remain highly relevant to modern health challenges. However, current digital nutrition platforms often fail to reflect this diversity, relying instead on standardized models with limited cultural sensitivity. This paper aims to explore how traditional nutritional wisdom can be integrated into digital health platforms to promote more inclusive and effective approaches to personalized nutrition. Methods: This perspective paper employs a cultural adaptation framework to analyze the integration of traditional food knowledge into digital contexts. Drawing from interdisciplinary research across nutrition science, anthropology, digital health and implementation science, we utilize the Knowledge-to-Action (KTA) Framework and the PEN-3 Cultural Model to structure our analysis. A systematic scoping review of literature published between 2010 and 2025 was conducted to identify integration challenges and opportunities. Additionally, we analyzed case studies of three traditional dietary systems (Argentina, Italy and Japan) and evaluated five leading digital nutrition platforms for their degree of cultural inclusivity, using qualitative comparative methods. Results: The analysis highlights significant challenges in adapting traditional knowledge to digital formats, including standardization barriers, contextual loss and technological limitations. However, successful integration initiatives demonstrate that through participatory design, flexible data architectures and culturally-informed algorithms, traditional food systems can be meaningfully represented. Our proposed four-phase integration framework-documentation, digital adaptation, implementation and evaluation-provides a structured approach for developers and researchers. Conclusions: Bridging traditional nutrition with digital platforms represents a vital opportunity to enhance personalization and preserve food heritage while improving health outcomes for diverse populations. This integration requires interdisciplinary collaboration, user-centered design processes and ethical approaches that respect cultural ownership and context.}, } @article {pmid40571921, year = {2025}, author = {Demsash, AW and Abebe, R and Gezimu, W and Kitil, GW and Tizazu, MA and Lambebo, A and Bekele, F and Alemu, SS and Jarso, MH and Dube, GN and Wedajo, LF and Purohit, S and Kalayou, MH}, title = {Correction: Data-driven machine learning algorithm model for pneumonia prediction and determinant factor stratification among children aged 6-23 months in Ethiopia.}, journal = {BMC infectious diseases}, volume = {25}, number = {1}, pages = {808}, pmid = {40571921}, issn = {1471-2334}, } @article {pmid40562960, year = {2025}, author = {Habibie, MI and Hariyanto, and Arifandri, R and Qonita, Z and Kricella, P and Khoirudin, MH and Fuadi, NMR and Shabrina, N and Gutami, NI and Sadiah, S and Kartikasari, D and Widodo, MMA and Waluyo, and Binaruno, FA and Ismoyo, K}, title = {A comparative study of fully automatic and semi-automatic methods for oil spill detection using Sentinel-1 data.}, journal = {Environmental monitoring and assessment}, volume = {197}, number = {7}, pages = {808}, pmid = {40562960}, issn = {1573-2959}, mesh = {*Petroleum Pollution/analysis/statistics & numerical data ; *Environmental Monitoring/methods ; *Water Pollutants, Chemical/analysis ; Machine Learning ; Indonesia ; Geographic Information Systems ; Neural Networks, Computer ; }, abstract = {The oil spill detection and assessment study conducted in the Banten Province of Indonesia involves the application of Sentinel-1 satellite data and machine learning tools in the year 2024. Synthetic Aperture Radar (SAR) data were used with VV polarization to observe the surface characteristics, using an oil spill threshold of - 25 dB to differentiate clean water from the oil spill based on low backscatter intensity. After desiring image processing and binary masking applications on the data that improve visibility of the oil spill-affected zones, vectorization was conducted for integration into geographic information systems (GIS). A temporal analysis indicated high variability across the spill sizes with an extreme peak on May 16 (79.686 km[2]) and July 3 (41.593 km[2]), which are likely dictated by the weather and oceanographic conditions plus the ship traffic of that time. Wind pattern analysis via ERA5 reanalysis data presented more insight into spill dispersion dynamics. Three machine learning classifiers were applied toward oil spill detection, namely Artificial Neural Networks (ANN), Random Forest (RF), and Extreme Gradient Boosting (XGBoost). Performance metrics indicate the ANN outperformed in discriminative ability (AUC = 0.92), while RF was highly accurate (99.01%) and precise (99.02%). This clearly demonstrates the viability of using an integrated approach of remote sensing, advanced image processing, and supervised learning for environmental monitoring and provides important information for minimizing ecological impacts and optimizing disaster response plans for maritime areas. Such an integrated scheme calls for advanced technology to combat ecological threats in maritime areas and provides crucial evidence toward ongoing interventions to protect and manage marine ecosystems and the associated local communities.}, } @article {pmid40561147, year = {2025}, author = {Impalli, I and Bergland, E and Saad-Roy, CM and Grenfell, BT and Levin, SA and Larsson, DGJ and Laxminarayan, R}, title = {Optimal sampling frequency and site selection for wastewater and environmental surveillance of infectious pathogens: A value of information assessment.}, journal = {PLoS computational biology}, volume = {21}, number = {6}, pages = {e1013190}, pmid = {40561147}, issn = {1553-7358}, mesh = {Humans ; *Wastewater/microbiology ; *Environmental Monitoring/methods ; Animals ; Computational Biology ; *Communicable Diseases/epidemiology ; Computer Simulation ; Disease Outbreaks ; Sensitivity and Specificity ; }, abstract = {Wastewater and environmental surveillance (WES) is a promising method of detecting infectious diseases in human and animal populations and offers significant advantages over traditional surveillance methods in the early detection of outbreaks. However, WES involves financial and human resources, and public policy decisions must determine whether the benefits of WES outweigh the costs, particularly in low-resource areas. The selection of surveillance sites, sampling frequency, and test sensitivity and specificity are crucial determinants of WES effectiveness and cost-efficiency. We created an analytical model and numerical simulations of disease arrival, spread, and WES strategies to determine the optimal sampling frequency for two interacting patches, each represented by a different sampling site. We show that it is optimal to test in one patch more frequently than it is to test in both patches less frequently if the patches are sufficiently interactive, surveillance is of sufficient sensitivity and specificity, and setup costs are substantial. In our value of information (VOI) assessment, the net value of surveillance information for both patches is non-monotonic with respect to the degree of patch interaction. Increased mixing between the patches allows for quicker surveillance detection but is worse for overall infection burden. Overall, optimizing the value of surveillance information for all patches being surveilled requires coordination and deliberate selection of surveillance sites and sampling frequencies. This paper provides a VOI assessment of WES to determine the optimal number of sites and sampling frequency at a high level of abstraction, leaving opportunity to adapt the model to specific pathogens and populations as needed. Our findings can inform the cost-efficient implementation of WES for infectious diseases, particularly in resource-constrained settings.}, } @article {pmid40561027, year = {2025}, author = {Otte, A and Wohlrab, S and Moritz, F and Müller, C and Janouškovec, J and Michálek, J and Cembella, A and Voss, D and Wang, X and Tebben, J and Larsen, TO and Edvardsen, B and Schmitt-Kopplin, P and John, U}, title = {High-resolution multiomics links nutrients and mixotrophy to toxicity in a harmful bloom of the haptophyte Chrysochromulina leadbeateri.}, journal = {Science advances}, volume = {11}, number = {26}, pages = {eadv3390}, pmid = {40561027}, issn = {2375-2548}, mesh = {*Harmful Algal Bloom ; *Haptophyta/metabolism/genetics/growth & development ; *Nutrients/metabolism ; Polyketide Synthases/metabolism/genetics ; Multiomics ; }, abstract = {Harmful algal blooms (HABs) of the toxigenic haptophyte Chrysochromulina are known to cause fish mortalities and collateral ecosystem damage. The ichthyotoxic mechanisms are poorly understood but likely dependent on toxigenesis by polyketide synthases (PKSs). We hypothesize that induction of PKS activity facilitates mixotrophic behavior during nutrient-depleted bloom conditions. To identify potential in situ stimuli for growth, toxigenicity, and bloom persistence, we compared environmental factors and biological processes identified by metaomics to Chrysochromulina leadbeateri HABs between two fjords in northern Norway. We identified the polyketide ichthyotoxin leadbeaterin-1 from the C. leadbeateri bloom and found potentially associated candidate PKS genes of which most were higher expressed at bloom stations. A relative depletion of inorganic nitrogen and phosphate during the bloom was correlated with higher expression of genes involved in endocytosis, autophagy, and lysosomal activity. Mixotrophy is evidently a compensatory nutritional strategy coupled to induction of toxigenesis and other metabolomic processes as biotic factors linked to Chrysochromulina bloom dynamics.}, } @article {pmid40299786, year = {2025}, author = {Xiao, Y and Elmasry, M and Bai, JDK and Chen, A and Chen, Y and Jackson, B and Johnson, JO and Prasanna, P and Chen, C and Damaghi, M}, title = {Eco-Evolutionary Guided Pathomic Analysis Detects Biomarkers to Predict Ductal Carcinoma In Situ Upstaging.}, journal = {Cancer research}, volume = {85}, number = {13}, pages = {2537-2547}, doi = {10.1158/0008-5472.CAN-24-2070}, pmid = {40299786}, issn = {1538-7445}, support = {U01CA261841//National Institutes of Health (NIH)/ ; R01CA272601//National Institutes of Health (NIH)/ ; R01CA249016//National Institutes of Health (NIH)/ ; R01CA297843//National Institutes of Health (NIH)/ ; R21CA258493-02S1//National Institutes of Health (NIH)/ ; R01GM148970//National Institute of General Medical Sciences (NIGMS)/ ; }, mesh = {Humans ; Female ; *Breast Neoplasms/pathology/metabolism/diagnosis/genetics ; *Biomarkers, Tumor/metabolism/analysis ; *Carcinoma, Intraductal, Noninfiltrating/pathology/metabolism/diagnosis/genetics ; Tumor Microenvironment ; Retrospective Studies ; Neoplasm Staging ; Disease Progression ; Middle Aged ; Prognosis ; }, abstract = {UNLABELLED: Cancers evolve in a dynamic ecosystem. Thus, characterizing the ecological dynamics of cancer is crucial to understanding cancer evolution, which can lead to the discovery of biomarkers to predict disease progression. Ductal carcinoma in situ (DCIS) is an early-stage breast cancer characterized by abnormal epithelial cell growth confined within the milk ducts, and biomarkers are needed to predict which cases will progress to aggressive disease. In this study, we showed that ecological analysis of hypoxia and acidosis biomarkers can significantly improve prediction of DCIS upstaging. Quantitative analyses were performed on immunohistologic images from a retrospective cohort of DCIS specimens collected from biopsy samples. First, an eco-evolutionary designed approach was developed to define habitats in the tumor intraductal microenvironment based on oxygen diffusion distance. Then, cancer cells with metabolic phenotypes attributed to their habitats were identified, including a hypoxia-responding CA9+ phenotype and an acid-adapted LAMP2b+ phenotype. Whereas these markers have traditionally shown limited, if any, predictive capabilities for DCIS progression when analyzed from an ecological perspective, their power to differentiate between non-upstaged and upstaged DCIS increased significantly. Additionally, the distribution of distinct niches with specific spatial patterns of these biomarkers predicted patient upstaging. The niches were characterized by pattern analysis of both cellular and spatial features. A random forest classifier that was trained and underwent a five-fold validation on the biopsy cohort achieved an AUC of 0.74 for predicting clinical outcome. These results affirm the importance of tumor ecological features in eco-evolutionary-designed approaches for biomarker discovery.

SIGNIFICANCE: Evolutionary dynamics of the various niches composing the tumor ecosystem can be harnessed for predicting cancer progression, demonstrating how eco-evolutionary-designed approaches can guide biomarkers discovery studies in the era of digital pathology. This article is part of a special series: Driving Cancer Discoveries with Computational Research, Data Science, and Machine Learning/AI.}, } @article {pmid39810621, year = {2025}, author = {Gottlieb, E and Gupta, S and Gahan, L and Raymann, RJ and Watson, NF}, title = {Social jetlag decreases across the lifespan: A prospective big data analysis of objective sleep metrics.}, journal = {Journal of sleep research}, volume = {34}, number = {4}, pages = {e14433}, doi = {10.1111/jsr.14433}, pmid = {39810621}, issn = {1365-2869}, mesh = {Humans ; Female ; Male ; Middle Aged ; *Jet Lag Syndrome/physiopathology ; Adult ; *Sleep/physiology ; Prospective Studies ; Big Data ; Polysomnography ; Aged ; Longitudinal Studies ; Self Report ; Retirement ; Caffeine ; Age Factors ; Circadian Rhythm/physiology ; Cross-Sectional Studies ; }, abstract = {Changes in social zeitgebers across the lifespan affect the interaction between biological and social clocks, potentially contributing to social jetlag. Extant literature suggests a reduction in social jetlag given declining social obligations occurring after retirement, but is limited to self-reported methods and cross-sectional designs. Leveraging longitudinal and ecologically valid data from consumer sleep technology, we analysed objective sleep data from 2439 users of the polysomnography-validated SleepScore mobile application, encompassing 500,415 total nights recorded. We examined the relationship between age as a continuous variable, age as a proxy for retirement status, and social jetlag. Additional linear models were employed to assess the effect of self-reported chronotype, average reported daily caffeine, alcohol and stress on social jetlag. There was a significant negative association between overall age and social jetlag (β = -0.64, t = -9.90, p < 0.001, effect size = 0.040), such that every 1-year increase in age corresponded with a 0.64-min reduction in social jetlag. The inclusion of self-reported chronotype, stress, caffeine and alcohol increased the explanatory power of our models slightly, but the effect of age remained consistent (β = -0.642, t = -8.91, p < 0.001, effect size = 0.046). Retirement-aged individuals exhibited nearly 50% less reduction in social jetlag than pre-retirement (30.6 ± 48.2 min versus post-retirement: 15.8 ± 41.6 min, p < 0.0001). While social jetlag after retirement was most pronounced for strong evening chronotypes (β = -0.41, t = -2.876, p = 0.004, effect size = -0.4276), pairwise comparisons revealed no statistically significant differences in the slopes between chronotypes (p > 0.05). Thus, social jetlag decreases across the lifespan, and its reduction appears to be amplified post-retirement even after accounting for behavioural factors.}, } @article {pmid40559311, year = {2025}, author = {Liang, X and Yu, S and Meng, B and Ju, Y and Wang, S and Wang, Y}, title = {Machine-Learning-Guided Design of Nanostructured Metal Oxide Photoanodes for Photoelectrochemical Water Splitting: From Material Discovery to Performance Optimization.}, journal = {Nanomaterials (Basel, Switzerland)}, volume = {15}, number = {12}, pages = {}, pmid = {40559311}, issn = {2079-4991}, support = {LH2022B019//Heilongjiang Provincial Natural Science Foundation of China/ ; }, abstract = {The rational design of photoanode materials is pivotal for advancing photoelectrochemical (PEC) water splitting toward sustainable hydrogen production. This review highlights recent progress in the machine learning (ML)-assisted development of nanostructured metal oxide photoanodes, focusing on bridging materials discovery and device-level performance optimization. We first delineate the fundamental physicochemical criteria for efficient photoanodes, including suitable band alignment, visible-light absorption, charge carrier mobility, and electrochemical stability. Conventional strategies such as nanostructuring, elemental doping, and surface/interface engineering are critically evaluated. We then discuss the integration of ML techniques-ranging from high-throughput density functional theory (DFT)-based screening to experimental data-driven modeling-for accelerating the identification of promising oxides (e.g., BiVO4, Fe2O3, WO3) and optimizing key parameters such as dopant selection, morphology, and catalyst interfaces. Particular attention is given to surrogate modeling, Bayesian optimization, convolutional neural networks, and explainable AI approaches that enable closed-loop synthesis-experiment-ML frameworks. ML-assisted performance prediction and tandem device design are also addressed. Finally, current challenges in data standardization, model generalizability, and experimental validation are outlined, and future perspectives are proposed for integrating ML with automated platforms and physics-informed modeling to facilitate scalable PEC material development for clean energy applications.}, } @article {pmid40558602, year = {2025}, author = {Mpuhua, CAM and Souza, OF and Daboin, BEG and Bezerra, IMP and Na Blei, M and Sarti, TD and Silva, VEBD and Abreu, LC}, title = {Proportional Stroke Mortality in Espírito Santo, Brazil: A 20-Year Joinpoint Regression Study.}, journal = {Epidemiologia (Basel, Switzerland)}, volume = {6}, number = {2}, pages = {}, pmid = {40558602}, issn = {2673-3986}, support = {001/2025//Fapes. Fundação de Amparo à Pesquisa do Estado do Espírito Santo, Brazil./ ; }, abstract = {Introduction: Stroke is one of the leading causes of death and disability worldwide. In Brazil, it remains the primary cause of mortality among adults. Although overall stroke mortality rates have declined, the absolute number of stroke incidents, deaths, and years of life loss continues to rise, particularly in developing and underdeveloped countries. Objective: The aim of this study was to analyze trends in stroke mortality across different age groups and both sexes in Espírito Santo, Brazil, from 2000 to 2021. Methods: This ecological time series study utilized secondary data from Espírito Santo, Brazil, from 2000 to 2021. Mortality data, categorized by sex and age group, were obtained from the Department of Informatics of the Unified Health System (DATASUS) database. Stroke-related mortality included deaths recorded under the International Classification of Diseases, 10th Revision (ICD-10) codes for subarachnoid hemorrhage (I60), intracerebral hemorrhage (I61), cerebral infarction (I63), and stroke not specified as hemorrhagic or ischemic (I64). Temporal trends in stroke mortality were assessed using joinpoint regression analysis. Results: From 2000 to 2021, there was a significant reduction in proportional mortality from stroke, with an overall decrease of -3.7% (p < 0.001). When analyzed by sex, the decline was -3.0% (p < 0.001) for males and -3.9% (p < 0.001) for females. The most significant decrease in proportional mortality was observed in the 50 to 59 age group, with an average annual percentage change of -4.9% (p < 0.001). The 30 to 39 age group exhibited the smallest decline, with an average annual percentage change of -2.4% (p < 0.001). No significant segments were observed in the 40 to 49, 60 to 69, and 70 to 79 age groups during the study period. Conclusions: This study identified a notable decline in stroke-related proportional mortality in the adult population of Espírito Santo between 2000 and 2021. While males had a higher absolute number of deaths, females exhibited a higher proportional mortality rate, underscoring the need for targeted preventive measures and effective acute stroke treatment, particularly among men.}, } @article {pmid40556364, year = {2025}, author = {Peat, GM and Hill, JC and Yu, D and Wathall, S and Parry, E and Bailey, J and Stevenson, K and Thompson, C and Wilkie, R and Dziedzic, K and Jordan, KP and , }, title = {Local variation in musculoskeletal pain consultation rates in primary care: findings from an ecologic study in Staffordshire.}, journal = {Primary health care research & development}, volume = {26}, number = {}, pages = {e52}, pmid = {40556364}, issn = {1477-1128}, mesh = {Humans ; *Musculoskeletal Pain/epidemiology/therapy ; Male ; Female ; *Primary Health Care/statistics & numerical data ; Middle Aged ; Adult ; England/epidemiology ; *Referral and Consultation/statistics & numerical data ; Aged ; Prevalence ; Chronic Pain/epidemiology ; Self Report ; Young Adult ; Adolescent ; }, abstract = {Variation between general practices in the rate of consultations for musculoskeletal pain conditions may signal important differences in access to primary care, perceived usefulness, or available alternative sources of care; however, it might also just reflect differences in underlying 'need' between practices' registered populations. In a study of 30 general practices in Staffordshire, we calculated the proportion of adults consulting for a musculoskeletal pain condition, then examined this in relation to selected practice and population characteristics, including the estimated prevalence of self-reported musculoskeletal problems and chronic pain in each practices' registered population. Between September 2021 and July 2022, 18,388 adults were consulted for a musculoskeletal pain condition. After controlling for length of recruitment, time of year, and age-sex structure, the proportion consulting varied up to two-fold between practices but was not strongly associated with the prevalence of self-reported long-term musculoskeletal problems, chronic pain, and high-impact chronic pain.}, } @article {pmid40554807, year = {2025}, author = {Poulin-Laprade, D and Broadbent, J and Biot-Pelletier, D and Kraemer, S and Griffiths, EJ and Kumar, A and Li, XZ and Carrillo, CD and Zaheer, R and McAllister, TA and Kullik, S and Liebana, E and Ricker, N and Langlois, A and Reid-Smith, R and Faucher, SP and Flores-Vargas, G and Bédard, É and Summers, JK and Jarocki, V and Thongthum, T and Carson, CA}, title = {Requirements and Considerations for Effective Implementation of Integrated One Health Antimicrobial Resistance Research.}, journal = {Canadian journal of microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1139/cjm-2024-0194}, pmid = {40554807}, issn = {1480-3275}, abstract = {The One Health (OH) approach recognizes the interconnectedness of the health of people, animals, plants/crops and ecosystems, and is central to addressing antimicrobial resistance (AMR). The 7th Environmental Dimension of Antimicrobial Resistance Conference (EDAR7), held in Montreal in May 2024, exemplified this approach by convening international experts and stakeholders to discuss AMR research and policy progress. EDAR7 workshop #8 focused on 1) barriers to establishing effective OH AMR research programs, 2) gaps in OH AMR research priorities, and 3) potential solutions/approaches or 'tools' to ensure programs develop in accordance with OH principles and generate insightful data that maximizes limited resources. Key workshop outcomes included identifying critical principles for OH AMR research programs and highlighting the pivotal role of sustainable data management strategies. Additionally, the importance of considering AMR policy and risk assessment needs when planning and designing research was emphasized. Discussions explored specific tools and approaches that support the standardized and harmonized collection and analysis of data, and associated challenges of integrating genomics data into current risk assessments and models. Synthesis of the workshop's discussions outlined critical considerations that interdisciplinary OH AMR research programs and networks should prioritize to enhance the impact of their outputs.}, } @article {pmid40552042, year = {2025}, author = {Mu, YQ and Song, JB and Zhao, M and Ren, P and Liu, HY and Huang, X}, title = {Integrative omics analysis of plant-microbe synergies in petroleum pollution remediation.}, journal = {PeerJ}, volume = {13}, number = {}, pages = {e19396}, pmid = {40552042}, issn = {2167-8359}, mesh = {Biodegradation, Environmental ; *Medicago sativa/microbiology/metabolism/genetics ; Metabolomics ; *Petroleum Pollution ; *Petroleum/metabolism ; *Soil Pollutants/metabolism ; Rhizosphere ; RNA, Ribosomal, 16S/genetics ; Soil Microbiology ; Hydrocarbons/metabolism ; Plant Roots/microbiology/metabolism ; Transcriptome ; Multiomics ; }, abstract = {As the petrochemical industry continues to advance, the exacerbation of ecological imbalance and environmental degradation due to petroleum pollution is increasingly pronounced. The synergistic interaction between plants and microorganisms are pivotal in the degradation of petroleum hydrocarbons; however, the underlying degradation mechanisms are not yet fully understood. This study aims to contribute to understanding these mechanisms by employing a multi-omics approach, integrating transcriptomics, 16S rRNA gene sequencing, and metabolomics, to analyze key differential genes, dominant microbial strains, and root-secreted metabolites involved in petroleum hydrocarbon degradation in alfalfa. Our findings revealed that several stress-related genes are upregulated in alfalfa contaminated with petroleum hydrocarbon. Moreover, Pseudomonas, Rhodococcus, and Brevundimonas were identified as dominant species in the rhizosphere microbiome. Metabolomics analysis identified pantothenic acid, malic acid, and ascorbic acid as critical metabolites that enhance hydrocarbon degradation. Application of pantothenic acid in oil-contaminated soil increased the degradation rate by approximately 10% compared to other treatments. These results highlight the potential of alfalfa-based phytoremediation strategies and offer a novel perspective for improving the efficiency of soil decontamination. Further research is needed to validate the scalability of these strategies for practical applications.}, } @article {pmid40413976, year = {2025}, author = {Bai, Z and Zhang, D and Zhang, S and Li, T and Wang, G and Xu, X and Pan, X and Zhong, Q and Zhou, W and Pu, Y and Jia, Y}, title = {Integrating multi-omics and biomarkers to reveal the stress mechanisms of high fluoride on earthworms.}, journal = {Journal of hazardous materials}, volume = {494}, number = {}, pages = {138706}, doi = {10.1016/j.jhazmat.2025.138706}, pmid = {40413976}, issn = {1873-3336}, mesh = {Animals ; *Oligochaeta/drug effects/metabolism/genetics ; Reactive Oxygen Species/metabolism ; Biomarkers/metabolism ; Oxidative Stress/drug effects ; *Soil Pollutants/toxicity ; *Fluorides/toxicity ; Apoptosis/drug effects ; Multiomics ; }, abstract = {Excessive fluorine accumulation poses a significant threat to soil ecology and even human health, yet its impact on soil fauna, especially earthworms, remains poorly understood. This study employed multi-omics and biomarkers to investigate high fluorine-induced biochemical changes that cause tissue damages in Eisenia fetida. The results demonstrated that earthworms exhibited obvious damage with fluorine addition exceeding 200 mg kg[-1], with stress levels escalating as fluorine contents increased. Further analysis of the underlying mechanisms revealed that fluorine could upregulate genes encoding mitochondrial respiratory chain complexes I-III and downregulate those for IV-V, leading to reactive oxygen species (ROS) accumulation despite antioxidant system activation. The resulting ROS interfered with deoxyribonucleoside triphosphate synthesis, prompting homologous recombination as the main DNA repair mechanism. Additionally, fluorine-induced ROS also attacked and disrupted protein and lipid related metabolisms ultimately causing oxidative damages. These cumulative oxidative damages from high fluorine contents subsequently triggered autophagy or apoptosis, resulting in tissue ulceration and epithelial exfoliation. Therefore, high fluorine could threaten earthworms by inducing ROS accumulation and subsequent biomolecule damages.}, } @article {pmid40398052, year = {2025}, author = {Guo, Z and Li, J and Hu, J and An, G and Wang, C}, title = {Deciphering the joint intracellular and extracellular regulatory strategies of toxigenic Microcystis to achieve intraspecific competitive advantage: An integrated multi-omics analysis with novel allelochemicals identified.}, journal = {Water research}, volume = {283}, number = {}, pages = {123774}, doi = {10.1016/j.watres.2025.123774}, pmid = {40398052}, issn = {1879-2448}, mesh = {*Microcystis/metabolism ; *Pheromones ; Microcystins ; Proteomics ; Metabolomics ; Multiomics ; }, abstract = {Global increase in Microcystis-dominated cyanobacterial blooms (MCBs) severely threatens ecological and human health. Intraspecific interaction between microcystin (MC)-producing (MC[+]) Microcystis and co-existing MC-free (MC[-]) Microcystis influences the relative abundance of MC[+]Microcystis, ultimately determining the toxicity and hazard of MCBs. However, specific allelochemicals driving this interaction and underlying molecular mechanisms remain unclear. This study confirmed that intraspecific interaction promoted the competitive advantage of MC[+]Microcystis over MC[-]Microcystis and unveiled the joint intracellular and extracellular regulatory strategies of MC[+]Microcystis based on proteomics-metabolomics analyses and biochemical validation. Intracellularly, MC[+]Microcystis enhanced pentose phosphate pathway and lipid and fatty acid biosynthesis to maintain cellular functions and membrane stability, but inhibited glycolysis, tricarboxylic acid cycle, and protein biosynthesis to optimize energy utilization for growth and proliferation. Extracellularly, MC[+]Microcystis released allelochemicals, including cytidine diphosphate-diacylglycerol and N-acyl-homoserine lactones, to inhibit MC[-]Microcystis growth by 13.53% and 16.39%, respectively, thereby achieving its competitive advantage. In contrast, MC[-]Microcystis exhibited the suppressed photosynthesis and oxidative phosphorylation, imbalanced anti-inflammatory responses, nucleic acid degradation, and membrane damage, resulting in its competitive disadvantage in co-culture. These findings provide new insights into the competitive dynamics between MC[+] and MC[-]Microcystis, and their involved implications for aquatic ecosystem health.}, } @article {pmid40393297, year = {2025}, author = {Yang, H and Zhou, J and Zhou, J}, title = {Integrated multi-omics and DNA stable-isotope probing approaches to reveal soil-ryegrass response to ionic rare earth mineral ammonium-lead contamination.}, journal = {Journal of hazardous materials}, volume = {494}, number = {}, pages = {138658}, doi = {10.1016/j.jhazmat.2025.138658}, pmid = {40393297}, issn = {1873-3336}, mesh = {*Lolium/drug effects/metabolism/growth & development/genetics ; *Soil Pollutants/toxicity ; *Lead/toxicity ; Plant Roots/drug effects/metabolism/growth & development ; Soil/chemistry ; *Ammonium Compounds/toxicity ; Oxidative Stress/drug effects ; Nitrogen/metabolism ; Nitrogen Isotopes ; Multiomics ; }, abstract = {The extensive use of ammonium (NH4[+]) sulfate in ionic rare earth mining has resulted in soil contamination with NH4[+] and lead (Pb), posing significant challenges for ecological restoration. Here, multi-omics and DNA stable-isotope probing (DNA-SIP) approaches were utilized to investigate soil nitrogen cycling and the molecular response of ryegrass (Lolium perenne L.) to NH4[+] (180-720 mg kg[-1])-Pb[2+] (207-828 mg kg[-1]) co-contamination. A synergistic interaction between NH4[+] and Pb[2+] was observed, significantly inhibited ryegrass growth, and induced oxidative stress and mitochondrial swelling. The EC50 toxicity thresholds were 383 mg kg[-1] for NH4[+] and 512 mg kg[-1] for Pb. The Integrated Biomarker Response (IBRv2) model elucidated the synergistic toxic effects. Transcriptomic and metabolomic analyses indicated that ryegrass roots enhanced carbon metabolism and antioxidant response pathways related to stress tolerance. Galactose metabolism and lysine degradation were identified as key pathways associated with stress response. Co-contamination with NH4[+] and Pb[2+] reduced ryegrass root [15]N-total nitrogen (TN) by 30 % while increasing soil [15]N-NH4[+] residue by 95 % and decreasing [15]N-microbial biomass nitrogen (MBN) by 59 %, compared to NH4[+] single contamination. DNA-SIP analysis revealed that ryegrass cultivation under NH4[+]- Pb[2+] co-contamination increased the abundance of plant growth-promoting rhizobacteria (Dyella), acid-tolerant nitrogen (Acidibacter), and sulfur-cycling taxa (Desulfosporosinus). The presence of raffinose and chlorogenic acid in ryegrass root metabolites was associated with shifts in the structure and composition of using NH4[+] active microbial taxa. These findings provide valuable insights into plant-soil-microbe interactions under multi-pollutant stress and offer practical strategies for phytoremediation and ecological restoration in areas affected by mining.}, } @article {pmid40327938, year = {2025}, author = {Wang, H and Xie, G and Zhang, Z and Han, J and Zhang, Y and Xu, T and Yin, D}, title = {PFHxA and PFHxS promote breast cancer progression in 3D culture: MEX3C-associated immune infiltration revealed by bioinformatics and machine learning.}, journal = {Journal of hazardous materials}, volume = {494}, number = {}, pages = {138458}, doi = {10.1016/j.jhazmat.2025.138458}, pmid = {40327938}, issn = {1873-3336}, mesh = {Humans ; Machine Learning ; Cell Line, Tumor ; Female ; *Fluorocarbons/toxicity ; Computational Biology ; Cell Movement/drug effects ; Cell Proliferation/drug effects ; *RNA-Binding Proteins/genetics/metabolism ; Tumor Microenvironment/drug effects ; *Triple Negative Breast Neoplasms/immunology/pathology/genetics ; *Sulfonic Acids/toxicity ; Disease Progression ; }, abstract = {Per- and polyfluoroalkyl substances (PFAS) are persistent environmental contaminants with widespread use and bioaccumulative potential. Short-chain PFAS such as perfluorohexanoic acid (PFHxA) and perfluorohexane sulfonate (PFHxS) have been introduced as safer alternatives to long-chain PFAS, yet their toxicological impacts remain poorly defined. In this study, we employed a 3D Gelatin methacryloyl (GelMA) hydrogel model to mimic the tumor microenvironment and investigated the effects of PFHxA and PFHxS on triple-negative breast cancer (TNBC) progression. At environmentally relevant concentrations (0.1-10 μM), both compounds significantly enhanced proliferation, migration, and invasion of MDA-MB-231 cells. Transcriptomic and machine learning analyses identified MEX3C as a key gene upregulated by PFAS exposure. Gene set enrichment analysis (GSEA) revealed activation of the PI3K-AKT-mTOR signaling pathway, which was further supported by siRNA-mediated knockdown of MEX3C, leading to a marked reduction in the expression levels of phosphorylated PI3K, AKT, and mTOR proteins. Furthermore, immune cell co-culture experiments showed that MDA-MB-231 cells with high MEX3C expression promoted M2 macrophage polarization, suppressed M1 polarization, and enhanced macrophage chemotactic activity, the immunomodulatory effects were significantly attenuated upon MEX3C knockdown. These findings establish MEX3C as a central mediator of PFAS-induced tumor progression and immune remodeling. This study provides mechanistic insight into the carcinogenic potential of emerging short-chain PFAS and underscores the need for stricter regulation to safeguard public health.}, } @article {pmid40550119, year = {2025}, author = {Kang, B and Park, MK and Kim, JI and Yoon, S and Heo, SJ and Kang, C and Lee, S and Choi, Y and Hong, D}, title = {Exploring Factors Related to Social Isolation Among Older Adults in the Predementia Stage Using Ecological Momentary Assessments and Actigraphy: Machine Learning Approach.}, journal = {Journal of medical Internet research}, volume = {27}, number = {}, pages = {e69379}, doi = {10.2196/69379}, pmid = {40550119}, issn = {1438-8871}, mesh = {Humans ; *Machine Learning ; Aged ; *Social Isolation ; Female ; Male ; *Actigraphy ; Loneliness ; *Ecological Momentary Assessment ; Aged, 80 and over ; *Dementia ; Cognitive Dysfunction ; }, abstract = {BACKGROUND: As the global population ages, the economic burden of dementia continues to rise. Social isolation-which includes limited social interaction and feelings of loneliness-negatively affects cognitive function and is a significant risk factor for dementia. Individuals with subjective cognitive decline and mild cognitive impairment represent predementia stages in which functional decline may still be reversible. Therefore, identifying factors related to social isolation in these at-risk groups is crucial, as early detection and intervention can help mitigate the risk of further cognitive decline.

OBJECTIVE: This study aims to develop and validate machine learning models to identify and explore factors related to social interaction frequency and loneliness levels among older adults in the predementia stage.

METHODS: The study included 99 community-dwelling older adults aged 65 years and above in the predementia stage. Social interaction frequency and loneliness levels were assessed 4 times daily using mobile ecological momentary assessment over a 2-week period. Actigraphy data were categorized into 4 domains: sleep quantity, sleep quality, physical movement, and sedentary behavior. Demographic and health-related survey data collected at baseline were also included in the analysis. Machine learning models, including logistic regression, random forest, Gradient Boosting Machine, and Extreme Gradient Boosting, were used to explore factors associated with low social interaction frequency and high levels of loneliness.

RESULTS: Of the 99 participants, 43 were classified into the low social interaction frequency group, and 37 were classified into the high loneliness level group. The random forest model was the most suitable for exploring factors associated with low social interaction frequency (accuracy 0.849; precision 0.837; specificity 0.857; and area under the receiver operating characteristic curve 0.935). The Gradient Boosting Machine model performed best for identifying factors related to high loneliness levels (accuracy 0.838; precision 0.871; specificity 0.784; and area under the receiver operating characteristic curve 0.887).

CONCLUSIONS: This study demonstrated the potential of machine learning-based exploratory models, using data collected from mobile ecological momentary assessment and wearable actigraphy, to detect vulnerable groups in terms of social interaction frequency and loneliness levels among older adults with subjective cognitive decline and mild cognitive impairment. Our findings highlight physical movement as a key factor associated with low social interaction frequency, and sleep quality as a key factor related to loneliness. These results suggest that social interaction frequency and loneliness may operate through distinct mechanisms. Ultimately, this approach may contribute to preventing cognitive and physical decline in older adults at high risk of dementia.

RR2-10.1177/20552076241269555.}, } @article {pmid40548332, year = {2025}, author = {Pita, L and Maldonado, M and Koutsouveli, V and Riesgo, A and Hentschel, U and Oatley, G and Sinclair, E and Aunin, E and Gettle, N and Santos, C and Paulini, M and Niu, H and McKenna, V and O'Brien, R and , and , and , and , and , }, title = {The chromosomal genome sequence of the kidney sponge, Chondrosia reniformis Nardo, 1847, and its associated microbial metagenome sequences.}, journal = {Wellcome open research}, volume = {10}, number = {}, pages = {283}, pmid = {40548332}, issn = {2398-502X}, abstract = {We present a genome assembly from a specimen of Chondrosia reniformis (kidney sponge; Porifera; Demospongiae; Chondrillida; Chondrillidae). The genome sequence has a total length of 117.37 megabases. Most of the assembly (99.98%) is scaffolded into 14 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 17.45 kilobases in length. Several symbiotic bacterial genomes were assembled as MAGs. Gene annotation of the host organism assembly on Ensembl identified 17,340 protein-coding genes. The metagenome of the specimen was also assembled and 53 binned bacterial genomes were identified, including 40 high-quality MAGs that were representative of a typical high microbial abundance sponge and included three candiate phyla (Poribacteria, Latescibacteria, Binatota).}, } @article {pmid40544059, year = {2025}, author = {Moloney, ME and Moga, DC and Grandner, M and Schoenberg, N}, title = {"No rest for me tonight": A social-ecological exploration of insomnia in rural Appalachian women.}, journal = {Sleep health}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.sleh.2025.04.009}, pmid = {40544059}, issn = {2352-7226}, abstract = {OBJECTIVES: Insomnia disproportionally affects women and is prevalent among rural Appalachian adults at higher rates than in the general US population. Given the strong, bi-directional relationship between sleep and health, a better understanding of insomnia in this health-disparate population is critical. The present study focused on the sex (females), gender (women), and age group (45+) at highest insomnia risk and explores the social determinants of sleep that contributed to insomnia.

METHODS: Semistructured telephone interviews were conducted to understand factors associated with insomnia among rural Appalachian women who self-reported insomnia symptoms ≥3 nights per week for ≥3months. Interviews were recorded with permission and transcribed. We used a multistage, inductive and deductive coding process aided by NVIVO 12.0 software.

RESULTS: Participants were 46 cisgender women in rural Appalachia who met the criteria for insomnia. The social-ecological model was our interpretative framework. Findings illuminate individual (e.g., rumination, menopause, pain, depression), social (e.g., family roles, grief, caregiving, financial concerns), and societal (e.g., gender norms, technology use) factors that likely contribute to insomnia among middle-aged rural Appalachian women.

CONCLUSIONS: Across levels of the social-ecological model, factors of female sex (e.g., menopause) and gendered behaviors, roles, and norms (e.g., caregiving close and extended kin) played a central role in the precipitation and perpetuation of insomnia in this population. Attending to the regional cultural norms of heightened self-sufficiency, domestic work, and inter-generational familial care may aid healthcare providers and policy makers aiming to address insomnia among rural Appalachian women as well as other rural populations.}, } @article {pmid40541223, year = {2025}, author = {Kamgno, J and Adeleke, M and Basáñez, MG and Coulibaly, Y and de Souza, DK and Debrah, LB and Debrah, AY and Diggle, PJ and Nana-Djeunga, HC and Domché, A and Gass, K and Hoerauf, A and Hopkins, A and Klion, A and Mackenzie, CD and Mwingira, U and Njenga, SM and Nutman, TB and Nwane, P and Stolk, WA and Unnasch, TR and Kelly-Hope, LA}, title = {Vector-borne helminthiases: a road map for current and future research to support control and elimination in sub-Saharan Africa.}, journal = {The Lancet. Infectious diseases}, volume = {}, number = {}, pages = {}, doi = {10.1016/S1473-3099(25)00084-2}, pmid = {40541223}, issn = {1474-4457}, } @article {pmid40537580, year = {2025}, author = {Sahana, S and Sarkar, J and Mandal, S and Chatterjee, I and Dhar, S and Datta, S and Mondal, S}, title = {Multi-omics approaches: transforming the landscape of natural product isolation.}, journal = {Functional & integrative genomics}, volume = {25}, number = {1}, pages = {132}, pmid = {40537580}, issn = {1438-7948}, mesh = {*Biological Products/isolation & purification/metabolism ; *Proteomics/methods ; *Genomics/methods ; *Metabolomics/methods ; Transcriptome ; Drug Discovery/methods ; Humans ; Multiomics ; }, abstract = {The field of natural product (NPs) discovery has significantly evolved with the advent of multi-omics approaches, encompassing genomics, transcriptomics, proteomics, and metabolomics. This review highlighting targeted isolation strategies and the comprehensive applications of omics in investigating natural products. Omics technologies, including genomics, transcriptomics, proteomics, and metabolomics, have emerged as powerful tools that revolutionize the traditional methods of natural product discovery. This review delves into the integration of multi-omics technology in the isolation and discovery of natural product. Omics applications in natural product investigation have revolutionized the field by enabling high-throughput screening, rapid identification of novel compounds, and understanding the complex interactions within biological systems. For instance, metabolomics gives insights into the metabolic profiles of organisms under different conditions, aiding in the discovery of unique NPs with potential therapeutic applications. Genomics has facilitated the mining of microbial genomes for biosynthetic gene clusters, leading to the discovery of new antibiotics and carcinopreventive agents. Transcriptomics and proteomics provide insights into gene expression and protein synthesis, revealing the dynamics of NPs biosynthesis under various conditions. Despite these limitations, the future prospects of multi-omics in natural product discovery are promising. Advances in omics technologies, coupled with machine learning and artificial intelligence, are expected to enhance data integration and predictive modeling, accelerating the discovery and development of innovative drugs. Furthermore, the continuous improvement in analytical techniques and the establishment of comprehensive databases will facilitate the identification and characterization of NPs, ultimately contributing to the development of new therapeutic agents. Collaborative efforts across disciplines and the integration of environmental and ecological data will further enhance our understanding of NP biosynthesis and lead to more effective and sustainable drug discovery strategies.}, } @article {pmid40536912, year = {2025}, author = {Vilela-Estrada, AL and Villarreal-Zegarra, D and Mayo-Puchoc, N and Holt, N and Flórez-Varela, Á and Fung, C and Ariza-Salazar, K and Carbonetti, FL and Flores, S and Carbonel, A and Olivar, N and Gomez-Restrepo, C and Brusco, LI and Priebe, S and Diez-Canseco, F}, title = {Fluctuations in Daily Happiness and Nervousness Based on Depressive and Anxious Symptoms in Adolescents or Young Adults Across 3 Latin American Cities: Experience Sampling Study.}, journal = {JMIR formative research}, volume = {9}, number = {}, pages = {e65732}, pmid = {40536912}, issn = {2561-326X}, mesh = {Humans ; Male ; Adolescent ; Female ; *Happiness ; Young Adult ; *Anxiety/psychology/epidemiology ; *Depression/psychology/epidemiology ; Quality of Life/psychology ; Latin America/epidemiology ; Argentina ; Cities ; Ecological Momentary Assessment ; }, abstract = {BACKGROUND: Experience sampling methods (ESMs) have been used in clinical research to collect data on emotional and behavioral states in real-life contexts among different populations. Although the use of ESMs in mental health has increased, it has not been applied to larger samples of young people in disadvantaged urban settings.

OBJECTIVE: This study aimed to determine the extent to which mood status scores (happiness and nervousness) vary during a week, as a function of having or not having symptoms of depression or anxiety, in a sample of adolescents and young adults in the cities of Buenos Aires, Bogotá, and Lima. A secondary objective was to identify factors associated with mood scores, including sociodemographics, quality of life, and daily activities.

METHODS: This study was part of the Building Resilience and Resources to Reduce Mental Distress in Young People in Latin America research program, which focuses on mental health resources for young people. Participants (n=143) aged 15-24 years completed daily ESM assessments over a week using the mobile app, resulting in 5246 reports. Data were analyzed using descriptive analyses with 2-tailed t tests and chi-square tests, and multilevel linear regression was used to examine associations between depressive or anxiety symptoms, mood variability, and factors influencing mean mood. Finally, Spearman correlation assessed the relationship between happiness and nervousness.

RESULTS: The analysis revealed that depressive or anxiety symptoms were not significantly associated with increased variability in mood scores (happiness P=.40 and nervousness P=.84). However, males exhibited greater variability in happiness and nervousness scores (P<.001) than females. Additionally, young people showed higher variability in nervousness than adolescents (P=.02). Regarding average happiness scores, young adults reported higher average happiness than adolescents (β=.604; P=.003). Engaging in structured activities (eg, sports, music lessons, and dance classes) was associated with increased happiness (β=.266; P=.01). In contrast, instrumental activities (eg, cleaning, shopping, meal preparation, or taking medication; β=-.144; P=.02) and work-related tasks (β=-.205; P=.01) were linked to lower happiness and higher nervousness (β=.387; P<.001). Quality of life was positively correlated with happiness (β=.486; P<.001) and negatively correlated with nervousness (β=-.273; P=.005). Finally, as for average scores, a strong negative correlation was found between happiness and nervousness (rs=-0.92; P<.001). The simple multilevel analysis showed that for each point of happiness, nervousness decreased by 0.45 points (95% CI -0.48 to -0.42; t3=-41.7; P<.001; SE 0.01).

CONCLUSIONS: Our study reveals that depressive and anxiety symptoms do not significantly affect the variability in predicted happiness and nervousness scores. However, we observed that demographic factors, such as gender and age, play a role in emotional variability.}, } @article {pmid40531985, year = {2025}, author = {Priorelli, M and Stoianov, IP and Pezzulo, G}, title = {Embodied decisions as active inference.}, journal = {PLoS computational biology}, volume = {21}, number = {6}, pages = {e1013180}, pmid = {40531985}, issn = {1553-7358}, mesh = {*Decision Making/physiology ; Humans ; Computational Biology ; Choice Behavior/physiology ; }, abstract = {Decision-making is often conceptualized as a serial process, during which sensory evidence is accumulated for the choice alternatives until a certain threshold is reached, at which point a decision is made and an action is executed. This decide-then-act perspective has successfully explained various facets of perceptual and economic decisions in the laboratory, in which action dynamics are usually irrelevant to the choice. However, living organisms often face another class of decisions-called embodied decisions-that require selecting between potential courses of actions to be executed timely in a dynamic environment, e.g., for a lion, deciding which gazelle to chase and how fast to do so. Studies of embodied decisions reveal two aspects of goal-directed behavior in stark contrast to the serial view. First, that decision and action processes can unfold in parallel; second, that action-related components, such as the motor costs associated with selecting a particular choice alternative or required to "change mind" between choice alternatives, exert a feedback effect on the decision taken. Here, we show that these signatures of embodied decisions emerge naturally in active inference-a framework that simultaneously optimizes perception and action, according to the same (free energy minimization) imperative. We show that optimizing embodied choices requires a continuous feedback loop between motor planning (where beliefs about choice alternatives guide action dynamics) and motor inference (where action dynamics finesse beliefs about choice alternatives). Furthermore, our active inference simulations reveal the normative character of embodied decisions in ecological settings - namely, achieving an effective balance between a high accuracy and a low risk of missing valid opportunities.}, } @article {pmid40502073, year = {2025}, author = {Chen, H and Shu, J and Mudappathi, R and Li, E and Wang, P and Bergsagel, L and Yang, P and Sun, Z and Zhao, L and Shi, C and Townsend, JP and Maley, C and Liu, L}, title = {Competing Subclones and Fitness Diversity Shape Tumor Evolution Across Cancer Types.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {40502073}, issn = {2692-8205}, abstract = {Intratumor heterogeneity arises from ongoing somatic evolution complicating cancer diagnosis, prognosis, and treatment. Here we present TEATIME (estimating evolutionary events through single-timepoint sequencing), a novel computational framework that models tumors as mixtures of two competing cell populations: an ancestral clone with baseline fitness and a derived subclone with elevated fitness. Using cross-sectional bulk sequencing data, TEATIME estimates mutation rates, timing of subclone emergence, relative fitness, and number of generations of growth. To quantify intratumor fitness asymmetries, we introduce a novel metric-fitness diversity-which captures the imbalance between competing cell populations and serves as a measure of functional intratumor heterogeneity. Applying TEATIME to 33 tumor types from The Cancer Genome Atlas, we revealed divergent as well as convergent evolutionary patterns. Notably, we found that immune-hot microenvironments constraint subclonal expansion and limit fitness diversity. Moreover, we detected temporal dependencies in mutation acquisition, where early driver mutations in ancestral clones epistatically shape the fitness landscape, predisposing specific subclones to selective advantages. These findings underscore the importance of intratumor competition and tumor-microenvironment interactions in shaping evolutionary trajectories, driving intratumor heterogeneity. Lastly, we demonstrate that TEATIME-derived evolutionary parameters and fitness diversity offer novel prognostic insights across multiple cancer types.}, } @article {pmid40527897, year = {2025}, author = {Basava, K and Alam, MNU and Roberts, L and Martinet, K and Cherry, P and García-Verdugo, H and Román-Palacios, C}, title = {Mapping nonhuman cultures with the Animal Culture Database.}, journal = {Scientific data}, volume = {12}, number = {1}, pages = {1019}, pmid = {40527897}, issn = {2052-4463}, mesh = {Animals ; *Databases, Factual ; *Behavior, Animal ; *Social Behavior ; }, abstract = {Socially transmitted behaviors are widespread across the animal kingdom, yet there is a lack of comprehensive datasets documenting their distribution and ecological significance. Knowledge of animal behavioral traditions could be essential for understanding many species' responses to anthropogenic disturbances and further enhancing conservation efforts. Here, we introduce the first open-access database that synthesizes data on animal cultural behaviors and traditions. The Animal Culture Database (ACDB) contains descriptions of 128 behaviors including forms of vocal communication, migration, predator defense, foraging practices, habitat alteration, play, mating displays, and other social behaviors for an initial sample of 61 species. In addition to offering an open-access resource for researchers, educators, and conservationists, the ACDB represents a step toward recognizing the role of social learning in animal populations.}, } @article {pmid40524951, year = {2025}, author = {Jánošíková, R and Tulis, F and Baláž, I and Eccard, JA and Mazza, V}, title = {Range expansion during recolonization: what does animal personality have to do with it?.}, journal = {Behavioral ecology : official journal of the International Society for Behavioral Ecology}, volume = {36}, number = {4}, pages = {araf053}, pmid = {40524951}, issn = {1045-2249}, abstract = {At the edge of an ongoing expansion, pioneer individuals encounter novel ecological and evolutionary pressures that may not be experienced by conspecifics settled in long-colonized areas. Consistent behavioral differences among conspecifics (animal personality) may be important determinants of individuals' successful colonization of novel environments and range expansion. By enhancing an individual's ability to find food and shelter as well as increasing its capacity to navigate novel environments, behavioral traits such as exploration and risk-taking are thus expected to be more highly expressed in populations undergoing expansion than in established populations. We investigated among-individual variation in behaviors associated to risk-taking and exploratory tendencies in populations of small mammals during different stages of the colonization process. Using a standardized behavioral test in the field, we quantified exploration and boldness of striped field mice (Apodemus agrarius, N = 95) from six subpopulations from Germany, where they are established, and in Slovakia, where a recolonization of the area is currently in progress, and in control species bank voles (Myodes glareolus, N = 76) that shared the same habitats but were long-established at all sites. Striped field mice in the expanding populations were significantly slower in exploring the open field arena, while showing comparable levels of risk taking compared to conspecifics from established populations. No difference in behavior was detected between the populations of bank voles. Our results suggest that a slow exploration strategy might play an advantageous role in expansion processes of small mammal populations.}, } @article {pmid40524188, year = {2025}, author = {Perillo, VL and Nute, M and Sapoval, N and Curry, KD and Golia, L and Yin, Y and Ogilvie, HA and Nakhleh, L and Segarra, S and Bhaya, D and Cuadrado, DG and Treangen, TJ}, title = {A survey of computational approaches for characterizing microbial interactions in microbial mats.}, journal = {Genome biology}, volume = {26}, number = {1}, pages = {168}, pmid = {40524188}, issn = {1474-760X}, support = {EF-2126387//National Science Foundation/ ; BBSRC-NSF/BIO #1921429//National Science Foundation/ ; NSF#2125965//National Science Foundation/ ; PICT 2020-302//Fondo para la Investigación Científica y Tecnológica/ ; Pampa Azul A8 Programa "Investigación//Ministerio de Ciencia, Tecnología e Innovación/ ; Desarrollo e Innovación en Ciencias del Mar"//Ministerio de Ciencia, Tecnología e Innovación/ ; Proposal 503441//Joint Genome Institute/ ; proposal: 10.46936/10.25585/60001132//Joint Genome Institute/ ; }, mesh = {*Microbial Interactions ; *Computational Biology/methods ; *Microbiota ; Ecosystem ; Bacteria/genetics/metabolism ; }, abstract = {In this review, we use microbial mat communities as a general model system to highlight the strengths and limitations of current computational methods for analyzing interactions between members of microbial ecosystems. We describe the factors that make this environment have such a high degree of interaction, and we explore different categories of both laboratory and computational tools for studying these interactions. For each tool, we describe efforts to apply them to microbial mats in the past and, in the process, argue that genome-scale metabolic models have breakthrough potential for modeling microbial interactions in microbial mats.}, } @article {pmid40523168, year = {2025}, author = {Barfuss, W and Flack, J and Gokhale, CS and Hammond, L and Hilbe, C and Hughes, E and Leibo, JZ and Lenaerts, T and Leonard, N and Levin, S and Madhushani Sehwag, U and McAvoy, A and Meylahn, JM and Santos, FP}, title = {Collective cooperative intelligence.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {122}, number = {25}, pages = {e2319948121}, doi = {10.1073/pnas.2319948121}, pmid = {40523168}, issn = {1091-6490}, abstract = {Cooperation at scale is critical for achieving a sustainable future for humanity. However, achieving collective, cooperative behavior-in which intelligent actors in complex environments jointly improve their well-being-remains poorly understood. Complex systems science (CSS) provides a rich understanding of collective phenomena, the evolution of cooperation, and the institutions that can sustain both. Yet, much of the theory in this area fails to fully consider individual-level complexity and environmental context-largely for the sake of tractability and because it has not been clear how to do so rigorously. These elements are well captured in multiagent reinforcement learning (MARL), which has recently put focus on cooperative (artificial) intelligence. However, typical MARL simulations can be computationally expensive and challenging to interpret. In this perspective, we propose that bridging CSS and MARL affords new directions forward. Both fields can complement each other in their goals, methods, and scope. MARL offers CSS concrete ways to formalize cognitive processes in dynamic environments. CSS offers MARL improved qualitative insight into emergent collective phenomena. We see this approach as providing the necessary foundations for a proper science of collective, cooperative intelligence. We highlight work that is already heading in this direction and discuss concrete steps for future research.}, } @article {pmid40520149, year = {2025}, author = {Maldonado, M and Pita, L and Hentschel, U and Erpenbeck, D and Oatley, G and Sinclair, E and Aunin, E and Gettle, N and Santos, C and Paulini, M and Niu, H and McKenna, V and O'Brien, R and , and , and , and , and , }, title = {The chromosomal genome sequence of the sponge Crambe crambe (Schmidt, 1862) and its associated microbial metagenome sequences.}, journal = {Wellcome open research}, volume = {10}, number = {}, pages = {275}, pmid = {40520149}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual Crambe crambe (Porifera; Demospongiae; Poecilosclerida; Crambeidae). The host genome sequence is 143.20 megabases in span. Most of the assembly is scaffolded into 18 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 19.53 kilobases in length. Several symbiotic prokaryotic genomes were assembled as MAGs, including two relevant sponge symbionts, the Candidatus Beroebacter blanensis/ AqS2 clade (Tethybacterales, Gammaproteobacteria) of LMA sponges, and the widely distributed archaeal Nitrosopumilus sp. clade.}, } @article {pmid40519052, year = {2025}, author = {Hilbert, A and Klotz, U and Sadeghi, S and Juarascio, AS and Kirsten, T}, title = {Smartphone-Supported Cognitive-Behavioral Therapy in Binge-Eating Disorder: An Exploratory Randomized Trial.}, journal = {The International journal of eating disorders}, volume = {}, number = {}, pages = {}, doi = {10.1002/eat.24479}, pmid = {40519052}, issn = {1098-108X}, support = {3/2019//Roland Ernst Foundation for Healthcare/ ; }, abstract = {OBJECTIVE: To assess the feasibility of a smartphone app delivering just-in-time adaptive interventions as an adjunct to cognitive-behavioral therapy (CBT) adapted to binge-eating disorder (BED), estimate its effects assuming superiority over CBT alone, and document safety and target engagement.

METHOD: A single-center, assessor-blinded, parallel feasibility study randomized adults aged 18-65 years with full-syndrome or subthreshold BED to smartphone-supported CBT (SmartCBT) or standard CBT (DRKS00024597). Both arms received 16 individual 50-min CBT sessions over 4 months. Assessments were conducted at baseline (T0), midtreatment (T1), posttreatment (T2), and 3-month follow-up (T3). Feasibility was determined regarding recruitment, attrition, dropout, adherence, assessment completion, app use, and acceptance. Further, eating disorder symptoms, mental and physical health, weight management behavior, safety, and target engagement (i.e., skill use) were assessed.

RESULTS: Over a 7-month recruitment period, 28 of 50 eligible volunteers were included and randomized 1:1 to SmartCBT or CBT. In the modified intent-to-treat sample (N = 25; SmartCBT: 13, CBT: 12), the feasibility of SmartCBT was further supported regarding attrition, dropout, adherence, treatment completion, app use, and acceptance; however, assessment completion was moderate. Clinical improvements were found in both arms, but differential results were affected by baseline differences and moderate assessment completion in the SmartCBT arm. Safety was documented, and support for target engagement was found.

CONCLUSIONS: This exploratory study provides evidence for the feasibility of app-supported CBT for BED. With few procedural refinements, the protocol can be used in a confirmatory randomized-controlled trial with long-term follow-up to evaluate efficacy and determine treatment mechanisms.

TRIAL REGISTRATION: German Clinical Trials Register, https://www.drks.de, DRKS00024597.}, } @article {pmid40502560, year = {2025}, author = {Gontjes, KJ and Singh, A and Sansom, SE and Boyko, JD and Smith, SA and Lautenbach, E and Snitkin, E}, title = {Phylogenetic context of antibiotic resistance provides insights into the dynamics of resistance emergence and spread.}, journal = {medRxiv : the preprint server for health sciences}, volume = {}, number = {}, pages = {}, pmid = {40502560}, abstract = {BACKGROUND: To ameliorate the antibiotic resistance crisis, the drivers of resistance emergence (i.e., de novo evolution) and resistance spread (i.e., cross-transmission) must be better understood.

METHODS: Whole-genome sequencing and susceptibility testing were performed on clinical carbapenem-resistant Klebsiella pneumoniae isolates collected from August 2014 to July 2015 across 12 hospitals. Ancestral state reconstruction partitioned patients with resistant strains into those that likely acquired resistance via de novo evolution or cross-transmission. Logistic regression was used to evaluate the associations between patient characteristics/exposures and these two pathways: resistance due to predicted within-host emergence of resistance, and resistance due to predicted cross-transmission. This framework is available in the user-friendly R package, phyloAMR (https://github.com/kylegontjes/phyloAMR).

RESULTS: Phylogenetic analysis of 386 epidemic lineage carbapenem-resistant Klebsiella pneumoniae sequence type 258 isolates revealed differences in the relative contribution of de novo evolution and cross-transmission to the burden of resistance to five antibiotics. Clade-specific variations in rates of resistance emergence and their frequency and magnitude of spread were detected for each antibiotic. Phylogenetically-informed regression modeling identified distinct clinical risk factors associated with each pathway. Exposure to the cognate antibiotic was an independent risk factor for resistance emergence (trimethoprim-sulfamethoxazole, colistin, and beta-lactam/beta-lactamase inhibitors) and resistance spread (trimethoprim-sulfamethoxazole, amikacin, and colistin). In addition to antibiotic exposures, comorbidities (e.g., stage IV+ decubitus ulcers) and indwelling devices (e.g., gastrostomy tubes) were detected as unique risk factors for resistance spread.

CONCLUSIONS: Phylogenetic contextualization generated insights and hypotheses into how bacterial genetic background, patient characteristics, and clinical practices influence the emergence and spread of antibiotic resistance.}, } @article {pmid40489355, year = {2025}, author = {Valverde, S and Vidiella, B and Martínez-Redondo, GI and Duran-Nebreda, S and Fernández, R and Bombarely, A and Rojas, AM and Bentley, RA}, title = {Structural Changes in Gene Ontology Reveal Modular and Complex Representations of Biological Function.}, journal = {Molecular biology and evolution}, volume = {42}, number = {6}, pages = {}, doi = {10.1093/molbev/msaf148}, pmid = {40489355}, issn = {1537-1719}, support = {PID2020-117822GB-I00//AEI/ ; PID2021-127503OB-I00//AEI/ ; PCI2022-132936//Swedish Environmental Protection Agency/ ; }, mesh = {*Gene Ontology/trends ; Computational Biology/methods ; }, abstract = {The Gene Ontology is a central resource for representing biological knowledge, yet its internal structure is often treated as static-or as a black box-in computational analyses. Here, we examine 15 years of Gene Ontology evolution using network-based methods, revealing that Gene Ontology changes not only through incremental growth but also through punctuated, curator-driven restructuring. In particular, we document a major reorganization of the Cellular Component branch in 2019, where broad "part" terms were removed and the ontology was modularized into distinct domains for anatomical entities and protein-containing complexes. Semantic modularity aligns Gene Ontology with emerging frameworks such as the Common Anatomy Reference Ontology and Gene Ontology-Causal Activity Modeling, but also disrupts similarity metrics that rely solely on hierarchical proximity. More broadly, the restructuring of the cellular components branch consolidates a shift toward treating Gene Ontology as a multi-layer semantic network-a transformation rooted in a decade-long process of scientific and social consensus across institutions. These findings underscore the need for version-aware, multi-layer models to ensure reproducibility and interpretability-and to better represent biological function across compositional, spatial, and regulatory dimensions as ontologies continue to evolve.}, } @article {pmid40518659, year = {2025}, author = {Gurung, S and Lee, CM and Weon, HY and Han, SR and Oh, TJ}, title = {Comparative Genome Analysis of Three Halobacillus Strains Isolated From Saline Environments Reveal Potential Salt Tolerance and Algicidal Mechanisms.}, journal = {Environmental microbiology reports}, volume = {17}, number = {3}, pages = {e70121}, pmid = {40518659}, issn = {1758-2229}, support = {RS-2024-00441423//The Bio & Medical Technology Development Program of the National Research Foundation (NRF) funded by the Korean government (MSIT)/ ; }, mesh = {*Salt Tolerance/genetics ; *Genome, Bacterial ; Harmful Algal Bloom ; Phylogeny ; *Bacillaceae/genetics/isolation & purification/physiology/classification ; Computational Biology ; Genomics ; }, abstract = {Harmful algal blooms (HABs) pose a significant global threat to water ecosystems, prompting extensive research into their inhibition and control strategies. This study presents genomic and bioinformatic analyses to investigate the algicidal potential and elucidate the survival mechanisms in harsh conditions of newly identified Halobacillus species three strains (SSTM10-2[T], SSBR10-3[T], and SSHM10-5[T]) isolated from saline environments. Moreover, genomic and bioinformatic analyses were conducted to elucidate their survival mechanisms in harsh conditions. Moreover, comparative genomic analysis revealed a diverse set of orthologous genes, with a core genome primarily associated with metabolism and information processing. Pangenome analysis highlighted accessory and unique genes potentially involved in environmental adaptation and stress response. Functional annotation using KEGG pathways identified genes linked to xenobiotic compound degradation, stress tolerance, and salt adaptation. Additionally, the study elucidated potential mechanisms underlying algicidal activity, implicating Carbohydrate-Active enZYmes (CAZymes), cytochrome P450 oxidases (CYP), and quorum sensing (QS) systems. Finally, analysis of KEGG pathways related to microcystin degradation suggested the strains' capacity to mitigate HABs. Thus, this research enhances understanding of the genomic diversity, phylogeny, and functional characteristics of Halobacillus species, offering insights into their ecological roles and potential applications in biotechnology and environmental management.}, } @article {pmid40512727, year = {2025}, author = {Clauss, M and Roller, M and Bertelsen, MF and Rudolf von Rohr, C and Müller, DWH and Schiffmann, C and Kummrow, M and Encke, D and Ferreira, S and Duvall, ES and Maré, C and Abraham, AJ}, title = {Reply to Ferraro et al.: Breed-and-feed reflects inevitable trade-offs between individual longevity and population sustainability.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {122}, number = {26}, pages = {e2509145122}, doi = {10.1073/pnas.2509145122}, pmid = {40512727}, issn = {1091-6490}, } @article {pmid40508665, year = {2025}, author = {Jiao, Y and Miao, X and Wang, L and Hong, S and Gao, Y and Wang, X}, title = {The Engineered Synthesis and Enhancement of Nitrogen and Chlorine Co-Doped Fluorescent Carbon Dots for the Sensitive Detection of Quercetin.}, journal = {Materials (Basel, Switzerland)}, volume = {18}, number = {11}, pages = {}, pmid = {40508665}, issn = {1996-1944}, support = {202303021221041, 202203021212443//Fundamental Research Program of Shanxi Province/ ; 22408259//Young Scientists Fund of the National Natural Science Foundation of China/ ; 2023M743771//China Postdoctoral Science Foundation/ ; SXBYKY2022076//Shanxi Province doctoral graduates and postdoctoral researchers come to work in Shanxi Province to reward the fund scientific research project/ ; 2021L029//Science and technology innovation project of colleges and universities in Shanxi Province/ ; }, abstract = {Flavonoid alcohols, particularly quercetin, as emerging antioxidants, demand advanced detection methodologies to comprehensively explore and evaluate their potential environmental and health risks. In this study, nitrogen-chlorine co-doped carbon dots (N, Cl-CDs), featuring an extended wavelength emission at 625 nm, were synthesized via the reaction of 4-chloro-1,2-phenylenediamine with polyethyleneimine. The engineered N, Cl-CDs exhibit superior photostability, exceptional aqueous dispersibility, and anti-interference capability in complex matrices. Leveraging static electron transfer mechanisms, the N, Cl-CDs demonstrate selective fluorescence quenching toward quercetin with an ultralow detection limit of 60.42 nM. Validation through rigorous spiked recovery assays in apple peel and red wine has been proficiently performed with satisfactory accuracy, highlighting the significant prospect of the constructed N, Cl-CDs for quercetin identification in real samples. This study provides valuable insights into the analytical determination of flavonoid compounds in complex environmental matrices, highlighting the potential of N, Cl-CDs for environmental and food safety monitoring.}, } @article {pmid40505380, year = {2025}, author = {Borics, G and Lerf, V and Falucskai, J and B-Béres, V and Kisantal, T and Tóth, I and T-Krasznai, E and Stanković, I and Görgényi, J and Lukács, Á and Várbíró, G}, title = {Projected area calculation for microalgae using three-dimensional models.}, journal = {Water research}, volume = {284}, number = {}, pages = {123951}, doi = {10.1016/j.watres.2025.123951}, pmid = {40505380}, issn = {1879-2448}, abstract = {Light acquisition and sinking properties of microalgae fundamentally affect how species perform in aquatic environments. Both properties are the function of their projected area (Ā), a crucial morphological trait of microalgae. Despite their importance, species-specific Ā values have not been computed for microalgae. The reason for this is that although using an analytical approach Ā can be calculated for every convex shape, a vast majority of planktic algae are concave and currently not known how to calculate the projected area of concave shapes. Applying shape-realistic 3D models of microalgae and a novel numerical approach combined with computer simulation, we calculated the projected area for more than 800 microalgae. Validating this approach using convex shapes and the analytical Ā = surface area/4 formula we found, that the proposed method achieves less than 5 % estimation bias. We also studied how Ā values of species can be predicted by easy-to-measure morphological metrics (such as Gald/width ratio, compactness, relative surface area extension, relative elongation, surface area constant, volume constant). We have found that the metrics do not show a sufficiently close relationship with the projected area to allow us to estimate species-specific Ā values. We demonstrated that the morphological differences among species can result in up to 6-fold differences in Ā values for the same volume. Spindle-form, filamentous species and loosely packed coenobia are the most efficient adaptations to maximize Ā. This study provides an innovative methodology and a huge dataset containing Ā values of 844 planktic freshwater microalgae. Although the dataset contains species only for the Pannonian and Dinaric ecoregions, because of the cosmopolitan nature of planktic algae it can be used for other ecoregions. Species-specific projected area values multiplied by cell counts give a new metric that characterizes the shading property of the given phytoplankton assemblage and enables us to better understand the changes in light availability and study the vertical processes in the water.}, } @article {pmid40505009, year = {2025}, author = {Yang, S and Zhang, X and Jin, LN and Fang, M and Gu, AZ and Li, D and Chen, J}, title = {Unveiling Phase-Dependent Genotoxicity of Organic Pollutants in Gaseous and Aqueous Forms.}, journal = {Environmental science & technology}, volume = {59}, number = {24}, pages = {12048-12059}, doi = {10.1021/acs.est.5c01852}, pmid = {40505009}, issn = {1520-5851}, mesh = {tert-Butylhydroperoxide/toxicity ; Water ; Gases ; Organic Chemicals ; }, abstract = {Organic pollutants exist in various physical states within the natural environment, yet it remains unclear how their physical states influence their toxicity characteristics. This study investigated the phase-dependent genotoxicity and combined effects of two organic compounds, tert-butyl hydroperoxide (TBHP) and dimethyl sulfate (DES), in both gaseous and aqueous phases. Given the substantial differences in concentrations for the same compound in gaseous and aqueous environments, we constructed the complete multitoxic and dose-response curves for gene induction in both phases, covering environmentally relevant concentrations. Under the same stress conditions, the genotoxicity of gaseous TBHP was 158.21 ± 33.17% of that of its aqueous form, while gaseous DES exhibited 260.56 ± 12.63% of the genotoxicity of its aqueous form. Notably, while no formation of new reaction products were observed, aqueous-phase mixtures exhibited greater complexity and higher toxicity compared to their gaseous counterparts. These differences were attributed to variations in molecular energy states, free radical generation and diffusion, molecular interaction pathways, and chemical reactivity between the two phases. By elucidating the mechanisms underlying these disparities, this study highlights the critical role of physical states in evaluating the toxicity and risks associated with gaseous organic chemicals.}, } @article {pmid40497295, year = {2025}, author = {Taylor, BA and Slater, GP and Stolle, E and Dorey, J and Buchmann, G and Oldroyd, BP and Gloag, R and Harpur, BA}, title = {Multi-Omic Analysis Reveals Population Differentiation and Signatures of Social Evolution in Tetragonula Stingless Bees.}, journal = {Molecular ecology}, volume = {34}, number = {13}, pages = {e17823}, doi = {10.1111/mec.17823}, pmid = {40497295}, issn = {1365-294X}, support = {DE220100466//Australian Research Council/ ; LT0056/2022-L//Human Frontier Science Program/ ; }, mesh = {Animals ; Bees/genetics ; *Genetics, Population ; *Social Evolution ; Male ; Genome, Insect ; Selection, Genetic ; Australia ; Female ; Social Behavior ; Multiomics ; }, abstract = {Stingless bees in the genus Tetragonula are social insects with a fully sterile worker caste, and are therefore well-placed to provide insights into the genomic changes associated with 'superorganismal' life histories. Here we assemble the genome of Tetragonula carbonaria and characterise the population structure and divergence of both T. carbonaria and its cryptic congener T. hockingsi in eastern Australia, revealing three distinct populations for T. carbonaria and two partially differentiated subpopulations for T. hockingsi. We then combine our genomic results with RNA-seq data from different T. carbonaria castes (queens, males, workers) to test two hypotheses about genomic adaptations in social insects: the 'Relaxed Constraint' hypothesis, which predicts indirect, and therefore relaxed, selection on worker-biased genes; and the 'Adapted Worker' hypothesis, which predicts intensified positive selection on worker genes due to their evolutionarily novel functions. Although we do not find a direct signal of either weaker purifying selection or elevated positive selection in worker-biased genes based on deviations from neutral expectations of nucleotide change between the two species, other evidence does support a model of relaxed selection on worker-biased genes: such genes show higher nucleotide diversity and greater interspecies divergence than queen-biased genes. We also find that differentially caste-biased genes exhibit distinct patterns of length, GC content and evolutionary origin. These findings, which converge with patterns found in other social insects, support the hypothesis that social evolution produces distinct signatures in the genome. Overall, Tetragonula bees emerge as a valuable model for studying the genomic basis of social complexity in insects.}, } @article {pmid40493719, year = {2025}, author = {Campbell, AM and Kula, AC and Jabaily, RS and Oberle, B and Sidoti, B and Capaldi, A and Bodine, EN}, title = {Predicting potential recovery of the endangered bromeliad Tillandsia utriculata: An agent-based modeling approach.}, journal = {PLoS computational biology}, volume = {21}, number = {6}, pages = {e1013157}, pmid = {40493719}, issn = {1553-7358}, mesh = {Animals ; *Endangered Species ; *Weevils/physiology ; *Models, Biological ; *Bromeliaceae/physiology/parasitology ; Predatory Behavior ; Florida ; Female ; Computational Biology ; Computer Simulation ; Population Dynamics ; Introduced Species ; }, abstract = {Invasive pests and pathogens are a major driver of biodiversity loss. Some rare species may persist through rapid evolution to tolerate or escape new threats, but representing the underlying ecological and evolutionary processes at the appropriate scale is analytically and computationally challenging. Tillandsia utriculata has been classified as endangered in Florida where its population has decreased significantly due to predation by the invasive Mexican weevil Metamasius callizona. Adult female weevils deposit their eggs in leaves of epiphytic bromeliads, preferentially ovipositing in the largest rosettes. Once the eggs hatch, the larvae consume the core of the rosette, often leading to pre-reproductive death. During the past three decades of predation, the T. utriculata population has shifted to initiating the production of inflorescences (to commence its single attempt at sexual reproduction) at smaller rosette sizes. Importantly, the rosette size at induction is correlated with the number of seeds produced. We have constructed an agent-based model to simulate the dynamics of a Florida T. utriculata population over many generations where the minimum rosettes size required to initiate inflorescence production (minimum size of induction or MSI), is an inherited trait. We use the model to explore how predation may have shifted the population's genetic composition and the impact this has on population viability. Our results show that larger germination rates are required for population viability when weevils are present. Parameter uncertainty analysis revealed that in the presence of weevil predation, only a population with a very high germination rate and a short period of predation would sustain its population for 100 years with sizes similar to simulations without weevil predation. Furthermore, uncertainty analysis showed that the mean MSI of the population decreased over a 100-year period without weevil predation, and this trend was exacerbated by the presence of weevil predation.}, } @article {pmid40458985, year = {2025}, author = {Carné, A and Vieites, DR and van den Burg, MP}, title = {In Vouchers We (Hope to) Trust: Unveiling Hidden Errors in GenBank's Tetrapod Taxonomic Foundations.}, journal = {Molecular ecology}, volume = {34}, number = {13}, pages = {e17812}, doi = {10.1111/mec.17812}, pmid = {40458985}, issn = {1365-294X}, support = {10.13039/501100011033//Ministerio de Ciencia, Innovación y Universidades, Agencia Estatal de Investigación./ ; }, mesh = {Animals ; *Databases, Nucleic Acid/standards ; Sequence Analysis, DNA ; Phylogeny ; DNA Barcoding, Taxonomic ; }, abstract = {Genetic repositories are invaluable resources foundational to various biological disciplines. While their data and metadata reliability are essential for robust research outcomes, numerous studies have highlighted data quality and consistency issues. Here, we detect and quantify errors at the most fundamental level by analysing the congruence of sequences derived from the same genetic marker and specimen voucher across tetrapods. Our analysis reveals that 32% of re-sequenced vouchers (with identical field or museum numbers) yield unequal sequences, ranging from a few mutations to significant divergences (0.06%-33.95%). These divergences may result from sample misidentification, labelling errors, fidelity disparities between sequencing methods, or contamination at various stages of the research process. Our findings demonstrate errors within GenBank at its most basal level and suggest that, although undetectable, a similar error rate likely exists in non-re-sequenced data. These previously overlooked errors are concerning because they arise from replicated experiments, which are uncommon, and raise serious questions about the reliability of non-re-sequenced specimens. Such errors can compromise the accuracy of biodiversity assessments (e.g., taxonomic assessment, eDNA and barcoding), phylogenetic analyses and conservation planning by artificially inflating the intraspecific divergence or misidentifying (to-be-described) species. Additionally, the accuracy of large-scale biological studies that rely on such data can be compromised. Our concerning results call for protocols ensuring sample traceability to the specimens or tissues during the whole process of data generation, analysis and deposition in a database. We propose a third-party annotation system for individual GenBank records that would allow flagging common errors and alert both the original submitter and all users to potential problems without modifying the original records.}, } @article {pmid40156461, year = {2025}, author = {Sharma, G and Deuis, JR and Jia, X and Crawford, T and Rahnama, S and Undheim, EAB and Vetter, I and Chin, YK and Mobli, M}, title = {Refining the NaV1.7 pharmacophore of a class of venom-derived peptide inhibitors via a combination of in silico screening and rational engineering.}, journal = {FEBS letters}, volume = {599}, number = {12}, pages = {1717-1732}, pmid = {40156461}, issn = {1873-3468}, support = {FTl10100925//Australian Research Council/ ; DE160101142//Australian Research Council/ ; APP1102267//National Health and Medical Research Council/ ; APP1080405//National Health and Medical Research Council/ ; 2017086//National Health and Medical Research Council/ ; APP1034958//National Health and Medical Research Council/ ; //University of Queensland/ ; 101039862/ERC_/European Research Council/International ; }, mesh = {*NAV1.7 Voltage-Gated Sodium Channel/chemistry/metabolism/genetics ; Humans ; *Peptides/chemistry/pharmacology ; Animals ; *Voltage-Gated Sodium Channel Blockers/chemistry/pharmacology ; Structure-Activity Relationship ; Amino Acid Sequence ; Computer Simulation ; Protein Engineering ; *Scorpion Venoms/chemistry/pharmacology ; Computational Biology ; Pharmacophore ; }, abstract = {Ion channels are among the main targets of venom peptides. Extensive functional screening has identified a number of these peptides as modulators of the voltage-gated sodium channel subtype NaV1.7, a potential target for the treatment of chronic pain. In this study, we used a bioinformatic approach that can automatically identify NaV1.7 gating modifier toxins from sequence information alone. The method further enables the incorporation of evolutionarily accessible sequence space in structure-activity relationship studies. The in silico method identified a putative NaV1.7 inhibitor, μ-theraphotoxin Cg4a, which we produced recombinantly and confirmed as a NaV1.7 inhibitor. Using structural and mutagenesis studies, we propose an improved definition of the pharmacophore of this class of NaV1.7 inhibitors, aiding future in silico screening and classification of NaV1.7 inhibitors.}, } @article {pmid40504830, year = {2025}, author = {Negeri, BG and Xiuguang, B and Moisa, MB}, title = {Assessment of potential land suitability for rainfed wheat production using GIS and multi criteria decision analysis in the Southwestern parts of Ethiopia.}, journal = {PloS one}, volume = {20}, number = {6}, pages = {e0324540}, pmid = {40504830}, issn = {1932-6203}, mesh = {*Triticum/growth & development ; Ethiopia ; *Geographic Information Systems ; Rain ; Soil/chemistry ; *Decision Support Techniques ; *Agriculture/methods ; Crops, Agricultural/growth & development ; }, abstract = {Wheat production in Ethiopia is vital for improving food security, boosting the national economy, and achieving self-sufficiency in food consumption. The present study aims to assess the potential land suitability for rainfed wheat (Triticum aestivum L.) production by using Geographic Information System and multi criteria decision analysis in southwestern parts of Ethiopia. Biophysical data, including land use and land cover (LULC), soil drainage, soil texture, soil depth, proximity to markets and roads, land surface temperature, slope, rainfall, and elevation, were used. In addition, different software tools, such as ArcGIS 10.3, ERDAS Imagine 2015, IDRISI Selva 17, and ArcSWAT were applied. The results revealed that approximately 177.1 km[2] (1.3%) of the study area was classified as highly suitable, 5375.2 km[2] (38.2%) as moderately suitable, 7,246.0 km[2] (51.5%) as marginally suitable, and 1235.1 km[2] (8.8%) as currently not suitable for rainfed wheat cultivation. Furthermore, out of the 23 districts analyzed, Sayo Nole and Bedelle Zuriya were identified as highly suitable for wheat production, with an area of 32.7km2 and 23.3km2 respectively. Therefore, the study recommends that future study research investigate additional other ecological parameters, such as soil PH, lime, gypsum, salinity, alkalinity and socio-economic data, which were not included in the present study.}, } @article {pmid40504771, year = {2025}, author = {Augustijn, HE and Reitz, ZL and Zhang, L and Boot, JA and Elsayed, SS and Challis, GL and Medema, MH and van Wezel, GP}, title = {Genome mining based on transcriptional regulatory networks uncovers a novel locus involved in desferrioxamine biosynthesis.}, journal = {PLoS biology}, volume = {23}, number = {6}, pages = {e3003183}, pmid = {40504771}, issn = {1545-7885}, mesh = {*Deferoxamine ; *Gene Regulatory Networks ; Gene Expression Regulation, Bacterial ; *Streptomyces coelicolor/genetics/metabolism ; *Genome, Bacterial ; Multigene Family ; Bacterial Proteins/genetics/metabolism ; Operon ; Computational Biology ; Iron/metabolism ; Data Mining ; }, abstract = {Bacteria produce a plethora of natural products that are in clinical, agricultural and biotechnological use. Genome mining has uncovered millions of biosynthetic gene clusters (BGCs) that encode their biosynthesis, the vast majority of them lacking a clear product or function. Thus, a major challenge is to predict the bioactivities of the molecules these BGCs specify, and how to elicit their expression. Here, we present an innovative strategy whereby we harness the power of regulatory networks combined with global gene expression patterns to predict BGC functions. Bioinformatic analysis of all genes predicted to be controlled by the iron master regulator DmdR1 combined with co-expression data, led to identification of the novel operon desJGH that plays a key role in the biosynthesis of the iron overload drug desferrioxamine (DFO) B in Streptomyces coelicolor. Deletion of either desG or desH strongly reduces the biosynthesis of DFO B, while that of DFO E is enhanced. DesJGH most likely act by changing the balance between the DFO precursors. Our work shows the power of harnessing regulation-based genome mining to functionally prioritize BGCs, accelerating the discovery of novel bioactive molecules.}, } @article {pmid40123484, year = {2025}, author = {Poulin, R}, title = {To bin or not to bin: why parasite abundance data should not be lumped into categories for statistical analysis.}, journal = {Parasitology}, volume = {152}, number = {3}, pages = {338-345}, doi = {10.1017/S003118202500040X}, pmid = {40123484}, issn = {1469-8161}, mesh = {Animals ; *Host-Parasite Interactions ; *Parasites/physiology ; *Parasitology/methods ; Data Interpretation, Statistical ; *Parasitic Diseases/parasitology ; }, abstract = {The impact of macroparasites on their hosts is proportional to the number of parasites per host, or parasite abundance. Abundance values are count data, i.e. integers ranging from 0 to some maximum number, depending on the host-parasite system. When using parasite abundance as a predictor in statistical analysis, a common approach is to bin values, i.e. group hosts into infection categories based on abundance, and test for differences in some response variable (e.g. a host trait) among these categories. There are well-documented pitfalls associated with this approach. Here, I use a literature review to show that binning abundance values for analysis has been used in one-third of studies published in parasitological journals over the past 15 years, and half of the studies in ecological and behavioural journals, often without any justification. Binning abundance data into arbitrary categories has been much more common among studies using experimental infections than among those using naturally infected hosts. I then use simulated data to demonstrate that true and significant relationships between parasite abundance and host traits can be missed when abundance values are binned for analysis, and vice versa that when there is no underlying relationship between abundance and host traits, analysis of binned data can create a spurious one. This holds regardless of the prevalence of infection or the level of parasite aggregation in a host sample. These findings argue strongly for the practice of binning abundance data as a predictor variable to be abandoned in favour of more appropriate analytical approaches.}, } @article {pmid40504102, year = {2025}, author = {Roces, V and Cañal, MJ and Mateo, JL and Valledor, L}, title = {Pra-GE-ATLAS: Empowering Pinus radiata stress and breeding research through a multi-omics database.}, journal = {Journal of integrative plant biology}, volume = {}, number = {}, pages = {}, doi = {10.1111/jipb.13944}, pmid = {40504102}, issn = {1744-7909}, support = {FPU18/02953//Ministerio de Universidades/ ; PID2019-107107GB-I00//Ministerio de Ciencia e Innovación/ ; }, abstract = {In recent decades, research on model organisms has significantly increased our understanding of core biological processes in plant science. However, this focus has created a substantial knowledge bottleneck due to the limited phylogenetic and ecological spectrum covered. Gymnosperms, especially conifers, represent a molecular and ecological diversity hotspot among seed plants. Despite their importance, research on these species is notably underrepresented, primarily due to a slower pace of investigation resulting from a lack of community-based resources and databases. To fill this gap, we developed the P(inus)ra(diata)-G(ene)E(xpression) (Pra-GE)-ATLAS, which consists of several tools and two main modules: transcriptomics and proteomics, presented in this work for the forestry commercial and stress-sensitive species Pinus radiata. We have summarized and centralized all the available information to provide a comprehensive view of the gene expression landscape. To illustrate how applications of the database lead to new biological insights, we have integrated multiple regulatory layers across tissues and stressors. While stress favors the retention of small introns, harmonized alternative splicing analyses reveal that genes with conifers' iconic large introns tend to be under constitutive regulation. Furthermore, the degree of convergence between stressors differed between regulatory layers, with proteomic responses remaining highly distinctive even through intergenerational memory tolerance. Overall, the Pra-GE-ATLAS aims to narrow the distance between angiosperms and gymnosperms resources, deepening our understanding of how characteristic pine features have evolved. Pra-GE-ATLAS DB is available at: http://pra-ge-atlas.valmei.es.}, } @article {pmid40498870, year = {2025}, author = {Wu, X and Liu, J and Hou, Y}, title = {Data and methods for assessing urban green infrastructure using GIS: A systematic review.}, journal = {PloS one}, volume = {20}, number = {6}, pages = {e0324906}, pmid = {40498870}, issn = {1932-6203}, mesh = {*Geographic Information Systems ; Humans ; Sustainable Development ; Cities ; *City Planning/methods ; Ecosystem ; *Conservation of Natural Resources/methods ; }, abstract = {Comprehensive and visual assessments utilizing Geographic Information Systems (GIS) offer an empirical foundation for the planning, construction, and optimization of Urban Green Infrastructure (UGI), effectively promoting its sustainable development. A comprehensive review of this field clarifies the research methods, application scope, trends, and challenges associated with using GIS to advance UGI development. This study synthesizes research findings from the Science Citation Index (SCI) and Social Science Citation Index (SSCI) within the Web of Science (WOS) database, as well as from the Scopus database, for the period from January 1, 2020, to June 30, 2024. The initial dataset included 640 articles from WOS and 952 articles from Scopus. After removing 1,572 duplicates and irrelevant studies, the final selection consisted of 20 articles. The integration of both WOS and Scopus databases ensures a comprehensive capture of current trends and limitations in GIS-based UGI assessments. This study centers on the scope, data sources, theoretical models, analyses, and objectives of GIS-based UGI assessments. The research indicates that over the past five years, GIS-based UGI assessments have primarily focused on areas such as accessibility, ecosystem service potential, resilience, and environmental justice, in addition to non-ecological aspects such as social benefits and aesthetics. While the integration of diverse data and analytical indicators into GIS has enhanced assessment comprehensiveness, and AI technologies have deepened data analysis, field research with urban residents remains crucial, underscoring the importance of inclusiveness in the study. This study also reveals a significant increase in interdisciplinarity in GIS-based assessments of UGI. The integration of assessment methods from ecology, computer science, urban planning, sociology, aesthetics, and other disciplines demonstrates that research in this field has fully considered ecological, social, economic, and humanistic factors, thereby more comprehensively reflecting the integrated needs of sustainable urban development.}, } @article {pmid40498755, year = {2025}, author = {Morrison, ES and Pandolfi, GP and Aguillon, SM and Ali, JR and Archard, O and Baldassarre, DT and Baquero, I and Bennett, KFP and Bonney, KM and Bryant, R and Catanach, RM and Catanach, TA and Chavoshan, I and Davis, SN and Goodman, BD and Gulson-Castillo, ER and Hack, M and Hudon, J and Leighton, GM and Long, KM and Ma, Z and McCoy, DE and McLaughlin, JF and Rueda Moreno, G and Mota, TM and Noguchi, L and Nwigwe, U and Pegan, T and Provost, KL and Rasband, SA and Salter, JF and Silvernail, LC and Simard, JA and Skeen, HR and Soto-Patiño, J and Suh, YH and Wang, Q and Warshauer, ME and Yan, S and Zalinski, B and Zhao, Z and Shultz, AJ}, title = {AvianLexiconAtlas: A database of descriptive categories of English-language bird names around the world.}, journal = {PloS one}, volume = {20}, number = {6}, pages = {e0325890}, pmid = {40498755}, issn = {1932-6203}, mesh = {*Birds/classification ; Animals ; *Language ; *Terminology as Topic ; *Databases, Factual ; Humans ; }, abstract = {Common names of species are important for communicating with the general public. In principle, these names should provide an accessible way to engage with and identify species. The common names of species have historically been labile without standard guidelines, even within a language. Currently, there is no systematic assessment of how often common names communicate identifiable and biologically relevant characteristics about species. This is a salient issue in ornithology, where common names are used more often than scientific names for species of birds in written and spoken English, even by professional researchers. To gain a better understanding of the types of terminology used in the English-language common names of bird species, a group of 85 professional ornithologists and non-professional contributors classified unique descriptors in the common names of all recognized species of birds. In the AvianLexiconAtlas database produced by this work, each species' common name is assigned to one of ten categories associated with aspects of avian biology, ecology, or human culture. Across 10,906 species of birds, 89% have names describing the biology of the species, while the remaining 11% of species have names derived from human cultural references, human names, or local non-English languages. Species with common names based on features of avian biology are more likely to be related to each other or be from the same geographic region. The crowdsourced data collection also revealed that many common names contain specialized or historic terminology unknown to many of the data collectors, and we include these terms in a glossary and gazetteer alongside the dataset. The AvianLexiconAtlas can be used as a quantitative resource to assess the state of terminology in English-language common names of birds. Future research using the database can shed light on historical approaches to nomenclature and how people engage with species through their names.}, } @article {pmid40253884, year = {2025}, author = {Wang, X and Zhao, C and Huang, G and Liu, H and Zhu, X and Huang, J}, title = {Quantifying leachate discharge and assessing environmental risks of gully-type coal-based solid waste dumps in small watersheds: A refined hydrological modeling approach for mitigation strategies.}, journal = {Water research}, volume = {282}, number = {}, pages = {123655}, doi = {10.1016/j.watres.2025.123655}, pmid = {40253884}, issn = {1879-2448}, mesh = {*Water Pollutants, Chemical/analysis ; *Coal ; Environmental Monitoring/methods ; Models, Theoretical ; Hydrology ; Risk Assessment ; *Solid Waste/analysis ; *Refuse Disposal ; }, abstract = {Rainfall-induced leaching from extensive coal-based solid waste storage results in a long-term risk to watershed's water quality and safety. The leachate carries heavy metals and other contaminants, which migrate and accumulate through the watershed, leading to a persistent deterioration of downstream water environment. However, the lack of systematic research on the release, accumulation, and spatial-scale migration dynamics of leachate limits effective management of diffused leachate pollutions. This study presents a novel cross-scale coupling framework which integrates multi-source remote sensing data with Soil and Water Assessment Tool (SWAT) model, employing a strategy that transfers parameters from large basins to accurately quantify the hydrological processes in coal waste sub-basins. Additionally, a comprehensive analysis is performed on the hydrological characteristics, leachate generation, and watershed migration dynamics in gangue dump sub-watersheds, providing a new methodological framework for managing mining-related leachate pollution. The large basin model demonstrated strong performance (R[2] = 0.79, NSE = 0.66 for calibration; R[2] = 0.74, NSE = 0.59 for verification), while the sub-basin model exhibited excellent accuracy (R[2] = 0.94, NSE = 0.92 for calibration; R[2] = 0.81, NSE = 0.77 for verification). High-resolution drone data estimated the annual leachate production to be 3366.87 m[3]. Simulations revealed that leachate migration peaks in the summer months (July to September), significantly increasing downstream pollution risks. Risk assessments indicate that vegetation in land restoration areas reduces leachate production and migration via evapotranspiration and other processes. This study provides an adaptable methodological framework for managing mining-related leachate pollution and highlights the critical importance of optimal reclamation strategies for mitigating pollution and restoring degraded landscapes.}, } @article {pmid40494636, year = {2025}, author = {Yaling, H and Shasha, C and Mengyao, L and Wenhui, L and Yan, G and Mengjiao, L and Qian, Z and Siyuan, Z and Diao, Z and Xinhui, L and Lei, Z and Qiong, Z and Ziqiang, Y and Yandong, X and Gaihua, Z and Yin, J}, title = {Phosphate-solubilizing function of Pediococcus pentosaceus PSM16 and its underlying mechanism.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0049125}, doi = {10.1128/spectrum.00491-25}, pmid = {40494636}, issn = {2165-0497}, abstract = {Phosphorus is a crucial nutrient for plant growth, but only a limited quantity is typically accessible in the soil for plants to absorb directly. Phosphate-solubilizing bacteria (PSB) can convert inorganic phosphorus compounds into forms that are more readily usable for plant nutrition. Our previous research has verified the function of Pediococcus pentosaceus PSM16 in degrading phytic acid. On this basis, we further explored the phosphorus-solubilizing capacity of PSM16 and evaluated its potential for practical application in this study. The results indicated that PSM16 significantly enhanced phosphorus utilization, not only enriching the environment with bioavailable phosphorus but also lowering the environmental pH and conductivity. These changes are instrumental in enhancing soil fertility, providing favorable conditions for plant growth, and stimulating seed germination. Through whole-genome sequencing of PSM16, we have identified key genes associated with the production of acid phosphatase. Specifically, the genes of GM000834, GM000917, GM000925, and GM000974 are implicated in PSM16's phosphorus solubilization function, likely through the production of phosphatase enzymes. Moreover, we have discovered that the phosphatases T.fus-QOS58989.1, A.cae-WP_156200763, M.the-SNW17984, N.gly-GGP12115, T.chr-SDQ48339.1, and T.chr-SDQ90039.1 are homologous to the aforementioned proteins and are present in compost, as confirmed by our informatics analysis. This presence in compost suggests their potential for real-world agricultural applications. This research presents promising candidate strains for the development of phosphorus-degrading bacterial agents, which could increase the efficiency of phosphorus fertilizers and contribute to sustainable agricultural practices. This strategy is not only effective but also environmentally benign and cost-effective, offering a valuable contribution to the field of agricultural biotechnology.IMPORTANCEThis study sheds light on the transformative power of the PSM16 strain, a paragon of phosphorus solubilization that adeptly converts inert phosphorus into a form that is readily absorbed by plants. In this way, it not only elevates the levels of available phosphorus in the environment but also enriches the soil fertility, supporting the healthy growth of plants. The strategic application of PSM16 in tandem with phosphorus fertilizers promises to enhance the utilization rates of these fertilizers, reinforcing sustainable agricultural initiatives and alleviating the environmental pressures caused by excessive application. In addition, the study has uncovered a trove of strains that hold promise for the development of safe dephosphorylating bacterial agents. These agents are poised to deliver an economical, efficient, and eco-friendly alternative, encapsulating a commitment to agricultural advancement that is both responsible and resourceful.}, } @article {pmid40489617, year = {2025}, author = {van Ittersum, MK and Alimagham, S and Silva, JV and Adjei-Nsiah, S and Baijukya, FP and Bala, A and Chikowo, R and Grassini, P and de Groot, HLE and Nshizirungu, A and Mahamane Soulé, A and Sulser, TB and Taulya, G and Amor Tenorio, F and Tesfaye, K and Yuan, S and van Loon, MP}, title = {Prospects for cereal self-sufficiency in sub-Saharan Africa.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {122}, number = {24}, pages = {e2423669122}, doi = {10.1073/pnas.2423669122}, pmid = {40489617}, issn = {1091-6490}, support = {INV-030103/GATES/Gates Foundation/United States ; INV-005431/GATES/Gates Foundation/United States ; INV-018444//Nederlandse Organisatie voor Wetenschappelijk Onderzoek (NWO)/ ; }, mesh = {Africa South of the Sahara ; *Edible Grain/growth & development ; *Food Supply ; Humans ; *Agriculture/methods/trends ; Climate Change ; *Crops, Agricultural/growth & development ; Zea mays/growth & development ; Millets/growth & development ; }, abstract = {Sub-Saharan Africa (SSA) has the world's largest projected increase in demand for food. Increased dependence on imports makes SSA vulnerable to geopolitical and economic risks, while further expansion of agricultural land is environmentally harmful. Cereals, in particular, maize, millet, rice, sorghum, and wheat, take nearly 50% of the cropland and 43% of the calories and proteins consumed in the region. Demand is projected to double until 2050. Here, we assess recent developments in cereal self-sufficiency and provide outlooks until 2050 under different intensification, area expansion, and climate change scenarios. We use detailed data for ten countries. Cereal self-sufficiency increased between 2010 and 2020 from 84 to 92% despite the 29% population increase. The production increase was achieved by increased yields per hectare (44%), area expansion (34%), and a shift from millet to the higher yielding maize (22%). Outlooks for 2050 are less pessimistic than earlier assessments because of the larger 2020 baseline area, higher shares of maize and somewhat less steep projected population increase. Yet, to halt further area expansion, a drastic trend change in annual yield increase from the present 20 to 58 kg ha[-1] y[-1] is needed to achieve cereal self-sufficiency. While such yield increases have been achieved elsewhere and are feasible given the yield potentials in SSA, they require structural changes and substantial agronomic, socioeconomic, and political investments. We estimate that amounts of added nitrogen need to at least triple to achieve such yield improvements, but it is essential that this comes with improved context-specific agronomy.}, } @article {pmid40478826, year = {2025}, author = {Flynn, KJ and Morozov, AY}, title = {Resource acquisition in diel cycles and the cost of growing quickly.}, journal = {PLoS computational biology}, volume = {21}, number = {6}, pages = {e1013132}, doi = {10.1371/journal.pcbi.1013132}, pmid = {40478826}, issn = {1553-7358}, mesh = {*Models, Biological ; *Microalgae/growth & development/metabolism/physiology ; Computer Simulation ; Carbon/metabolism ; Biomass ; Computational Biology ; *Circadian Rhythm/physiology ; Carbon Cycle/physiology ; }, abstract = {Many organisms, notably phototrophs, routinely acquire resources over only a fraction of the day. They have to balance their main period of initial biosynthesis against cell cycle events. Because of their short generation times, this challenge is especially acute for the planktonic microalgae that perform 50% of global C-fixation. Empirical evidence indicates that microalgal day-average growth is a function of the ability to acquire resources rapidly when available, retaining initial products of assimilation to support growth. A fundamental question arises over the optimal physiological configuration to support such activity. Here, we applied computer simulations implementing a development of the quota concept, in which the internal limiting resource is itself C, ratioed against total organism C-biomass. The model comprises metabolite and core pools of carbon C (MC and CC, respectively), with growth modulated by MC/(MC + CC); MC supports growth of CC in the absence of concurrent resource acquisition. Dynamic feedback interactions from the relative size of MC controls resource acquisition. The model reproduces the general pattern of growth at different light:day fraction (LD), and of afternoon-depression of C-fixation. We explored the efficiency of the physiological cell configuration to locate optimal configurations at different combinations of maximum growth rates (Umax) and LD values across plausible parameter values for microalgae. While the optimum maximum resource acquisition rate deployed during the L phase scales with Umax/LD, the maximum size of the metabolite pool scales to LD/DV, where DV is division time (i.e. Umax/Ln(2)). Accordingly, we conclude that faster growing organisms carry a penalty limiting their geographic spread to latitudes and seasons where LD is high. Larger, vacuolated organisms (such as diatoms), having a bigger metabolite compartment, may be at an advantage in such situations.}, } @article {pmid40474615, year = {2025}, author = {Amador, LG and Ramirez-Parada, TH and Park, IW and Mazer, SJ and Ellison, AM and O'Brien, M and Sokol, ER and Smith, CA and Davis, CC and Record, S}, title = {Bridging data silos to holistically model plant macrophenology.}, journal = {The New phytologist}, volume = {}, number = {}, pages = {}, doi = {10.1111/nph.70249}, pmid = {40474615}, issn = {1469-8137}, support = {1556768//Division of Environmental Biology/ ; 2105903//Division of Environmental Biology/ ; 2105907//Division of Environmental Biology/ ; 2105932//Division of Environmental Biology/ ; 22425//Maine Agricultural and Forest Experiment Station/ ; 2223103//Division of Biological Infrastructure/ ; 2223104//Division of Biological Infrastructure/ ; }, abstract = {Phenological response to global climate change can impact ecosystem functions. There are various data sources from which spatiotemporal and taxonomic phenological data may be obtained: mobilized herbaria, community science initiatives, observatory networks, and remote sensing. However, analyses conducted to date have generally relied on single sources of these data. Siloed treatment of data in analyses may be due to the lack of harmonization across different data sources that offer partially nonoverlapping information and are often complementary. Such treatment precludes a deeper understanding of phenological responses at varying macroecological scales. Here, we describe a detailed vision for the harmonization of phenological data, including the direct integration of disparate sources of phenological data using a common schema. Specifically, we highlight existing methods for data harmonization that can be applied to phenological data: data design patterns, metadata standards, and ontologies. We describe how harmonized data from multiple sources can be integrated into analyses using existing methods and discuss the use of automated extraction techniques. Data harmonization is not a new concept in ecology, but the harmonization of phenological data is overdue. We aim to highlight the need for better data harmonization, providing a roadmap for how harmonized phenological data may fill gaps while simultaneously being integrated into analyses.}, } @article {pmid40449428, year = {2025}, author = {Hussain, M and Ullah, K and Tayyab, M and Ullah, S and Shah, AA and Zhang, J and Tong, Z and Liu, X and Rahman, ZU}, title = {Data-driven multi-hazard susceptibility and community perceptions assessment using a mixed-methods approach.}, journal = {Journal of environmental management}, volume = {388}, number = {}, pages = {126009}, doi = {10.1016/j.jenvman.2025.126009}, pmid = {40449428}, issn = {1095-8630}, mesh = {Humans ; Floods ; Pakistan ; Surveys and Questionnaires ; Perception ; Climate Change ; Disaster Planning ; Landslides ; Geographic Information Systems ; }, abstract = {Assessing multi-hazard susceptibility and understanding community insights are important for effective disaster risk management; however, limited research has been conducted to study these aspects together. This study uses a data-driven approach to assess multi-hazard susceptibility and community perceptions, aiming to deepen climate change mitigation strategies. We employed a two-stage framework in Eastern Hindukush, Pakistan, which is based on machine learning, remote sensing, geographical information systems, and index-based methods. In the first stage, flood and landslide inventories were generated, and predictive factors were analyzed using logistic regression, resulting in an integrated multi-hazard susceptibility map. In the second stage, a survey of 410 household heads assessed community risk perception, communication, and preparedness, using a structured questionnaire with 28 Likert-scale indicators, and a composite index was calculated. The findings indicate that 25.81 % and 35.43 % of the study area are susceptible to flooding and landslides, respectively, with 15.07 % vulnerable to both hazards concurrently. On the other hand, the community is generally aware of flood and landslide risks; however, there are significant gaps in coping abilities and preparedness, including insufficient insurance coverage and training. Moreover, socioeconomic challenges, such as limited access to information and low trust in local authorities, further complicate disaster preparedness efforts. This study provides a holistic framework for identifying multi-hazard hotspots and assessing community perceptions, facilitating targeted interventions to enhance disaster preparedness and resilience in the region.}, } @article {pmid40468364, year = {2025}, author = {Pan, X and Shan, Z and Tian, X and Niu, Y and Liu, Y and Li, Z and Li, Y and Huang, Y and Ye, J}, title = {Evaluating conservation gaps of China's national key protected wild plants: insights from county-level distribution data.}, journal = {BMC biology}, volume = {23}, number = {1}, pages = {156}, pmid = {40468364}, issn = {1741-7007}, support = {202206193000001//Shenzhen Science and Technology Program/ ; 20220816162653003//Shenzhen Science and Technology Program/ ; 32270233//National Natural Science Foundation of China/ ; 32200177//National Natural Science Foundation of China/ ; 2022YFF0802300//National Key Research Development Program of China/ ; 2023BSZR014//Doctoral Research Foundation of Jiangxi University of Chinese Medicine/ ; Jiangxi Traditional Chinese Medicine Comprehensive Word No. 3 (2024)//Construction of National Heritage Studio for Old Medicine Workers/ ; }, mesh = {*Conservation of Natural Resources ; China ; *Endangered Species ; *Plants/classification ; Biodiversity ; Databases, Factual ; }, abstract = {BACKGROUND: The National Key Protected Wild Plants (NKPWPs) list serves as China's primary legal framework for plant diversity protection, with the species categorized into Level I (critically endangered, strictly protected) and Level II (lower risk but still requiring protection). However, the geographical distribution of these species and gaps in their conservation remain elusive due to the limited availability of data on species distribution. Thus, to address these gaps and support precise conservation, we developed a county-level distribution database for the NKPWP species using information primarily sourced from literature. Using this database, we elucidated the geographical distribution patterns of NKPWPs and identified the gaps in both in situ and ex situ conservation.

RESULTS: The NKPWPs analyzed in the study included 1,128 plant species. We compiled a county-level distribution database for these species with 30,397 records. Detailed analysis of this data revealed that these species were concentrated in the mountainous regions of southern China, including the Eastern Himalaya-Hengduan Mountains, south Yunnan, the Yunnan-Guizhou-Guangxi border, and the Wuling Mountains. Among the 1,118 embryophyte species of the checklist, 1,060 (94.81%) were found conserved in situ, 681 (60.91%) were found conserved ex situ, and 660 (59.03%) through both approaches. Besides, species with a higher threat level and limited distribution range exhibited lower conservation coverage in both ex situ and in situ approaches; 37 species received no conservation (3.31%).

CONCLUSIONS: The county-level distribution database developed in this study comprehensively depicts the geographical distribution patterns of NKPWP in China, offering valuable data for planning species conservation and providing a foundational framework for addressing the existing gaps in their conservation across China. This database will ultimately support targeted conservation and resource allocation to protect plant diversity effectively. We also suggest adopting an integrated evaluation approach for conservation strategies in other areas, globally, or for other biological groups.}, } @article {pmid40465754, year = {2025}, author = {Duan, Z and Wang, G and Hu, J and Yu, T and Chen, S and Zhang, Y and Wang, Y and Liu, H and Zhao, X and Chen, H}, title = {Spatiotemporal dynamics of northern Caspian shorelines (1985-2023) and implications for coastal management: Lessons from the Aral Sea.}, journal = {PloS one}, volume = {20}, number = {6}, pages = {e0325546}, pmid = {40465754}, issn = {1932-6203}, mesh = {Oceans and Seas ; *Conservation of Natural Resources ; Spatio-Temporal Analysis ; Ecosystem ; Geographic Information Systems ; Biodiversity ; }, abstract = {Dynamic changes to the northern Caspian Sea shoreline have significant ecological implications, including impacts to biodiversity and the surrounding environment. This study employs Landsat datasets, historical records, and geographic information systems (GIS) to quantitatively analyze spatiotemporal variations along the northern Caspian Sea coastline from 1985 to 2023. The findings demonstrate pronounced cyclic variations in the Caspian Sea's water level. Compared to 1930, the water level decreased by 2.6 m by 2023, with 1935 marking the onset of a significant downward trend. From 1995 to 2023, a pronounced decline in the water level at a rate of 6.1 cm/year was observed. Multiscale temporal oscillations in water levels revealed periodic rises and falls with cycles ranging from 6-8 years to 10-16 years. Due to the broad and shallow morphology of the northern Caspian Sea, fluctuations in water level have resulted in significant displacements of the northern coastline. Between 1985 and 2023, the shoreline length decreased by 262 km, which is equivalent to a 17% reduction. The intensity of the coastline length index reached a critical point during from 2010 to 2015, after which it declined sharply by 3.67. By 2023, the coastline had shifted seaward by 1.33 × 10[4] km2 relative to that in 1985. This continuous retreat of the shoreline poses a severe threat to the ecological stability of the northern Caspian Sea. If the trend persists, then the disappearance of the eastern basin of the South Aral Sea may be replicated in the northern Caspian Sea by 2100. These findings provide critical insights for formulating effective coastal management strategies and conservation initiatives.}, } @article {pmid40463795, year = {2025}, author = {Petrou, E and Davies, H and Aoun, M and Radford, AD and Singleton, D and Noble, PM and Killick, DR}, title = {First opinion practice electronic health records are a useful source of descriptions of medication errors.}, journal = {Frontiers in veterinary science}, volume = {12}, number = {}, pages = {1560652}, pmid = {40463795}, issn = {2297-1769}, abstract = {BACKGROUND: Medication error (MedE) is a leading global cause of harm in human healthcare with significance both in patient morbidity and mortality, and consequent legal and financial issues. Despite this, MedEs are a poorly explored area in veterinary medicine. Research has so far focussed on survey work and errors spontaneously reported to third parties, such as professional indemnity providers.

AIM: Determine if MedEs can be successfully identified in first opinion electronic health records (EHRs).

ANIMALS: EHRs pertaining to animals treated in UK first opinion practice.

MATERIALS AND METHODS: Regular expressions (REGEX) were designed (with assistance from a domain expert) to identify explicit reference to MedEs in the SAVSNET EHR dataset. Identified MedEs were then classified by the linear sequence of medication therapy, the degree of harm caused, the role of the person who made the error, and the medication type involved.

RESULTS: In total, 6,665 EHRs were identified by the REGEX, of which a random 2,847 were manually reviewed, with 1,023 (35.9%) matching the MedEs case definition. Of these MedEs, 29.5% (n = 302) caused mild harm to the patient, 2.8% (n = 27) moderate harm and 0.2% (n = 2) severe harm. MedEs were most frequent during the "drug administered" phase (51.4%) and within this phase, "dosing errors" were most common (68.1%). The most common medication types, associated with "drug administered" phase MedEs were vaccinations (27.1%) and non-steroidal anti-inflammatory drugs (19.0%).

CONCLUSION: EHRs are a useful source of data on MedEs. MedEs are a common cause of patient harm in veterinary practice. The data provided here highlights drug classes at higher risk of problems for which mitigating action and/or education interventions are indicated.}, } @article {pmid40463267, year = {2025}, author = {Brook, JBH and Salo, T and Luo, AC and Bagautdinova, J and Rush, S and Alexander-Bloch, AF and Baller, EB and Calkins, ME and Cieslak, M and Cooper, EC and Detre, JA and Elliot, MA and Fair, DA and Freedman, P and Gehrman, PR and Gur, RC and Gur, RE and Klein, A and Laney, N and Laumann, TO and Mehta, K and Merikangas, K and Milham, MP and Mitchell, JA and Moore, TM and Nelson, SM and Ruparel, K and Sevchik, BL and Shanmugan, S and Shou, H and Taso, M and White, LK and Wolf, DH and Tisdall, MD and Roalf, DR and Satterthwaite, TD}, title = {An open, fully-processed data resource for studying mood and sleep variability in the developing brain.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {40463267}, issn = {2692-8205}, abstract = {Brain development during adolescence and early adulthood coincides with shifts in emotion regulation and sleep. Despite this, few existing datasets simultaneously characterize affective dynamics, sleep variation, and multimodal measures of brain development. Here, we describe the study protocol and initial release (n = 10) of an open data resource of neuroimaging paired with densely sampled behavioral measures in adolescents and young adults. All participants complete multi-echo functional MRI, compressed-sensing diffusion MRI, and advanced arterial spin-labeled MRI. Behavioral measures include ecological momentary assessment, actigraphy, extensive cognitive assessments, and detailed clinical phenotyping focused on emotion regulation. Raw and processed data are openly available without a data use agreement and will be regularly updated as accrual continues. Together, this resource will accelerate research on the links between mood, sleep, and brain development.}, } @article {pmid40455595, year = {2025}, author = {Fetters, AM and Cantalupo, PG and Robles, MTS and Pipas, JM and Ashman, TL}, title = {Sharing Pollinators and Viruses: Virus Diversity of Pollen in a Co-Flowering Community.}, journal = {Integrative and comparative biology}, volume = {}, number = {}, pages = {}, doi = {10.1093/icb/icaf073}, pmid = {40455595}, issn = {1557-7023}, abstract = {Co-flowering plant species frequently share pollinators, flower-inhabiting bacteria, and fungi, but whether pollen-associated viruses are shared is unknown. Given that pollen-associated viruses are sexually transmitted diseases, their diversity is expected to increase with pollinator sharing. We conducted a metagenomic study to identify pollen-associated viruses from 18 co-flowering plant species to determine whether 1) life history, floral traits, or pollination generalism were associated with viral richness, and 2) plants shared pollen-associated viruses. We demonstrated that pollination generalism influences pollen-associated virus richness and the extent of pollen virus sharing between plant species. We also revealed that perenniality, multiple flowers, and bilateral floral symmetry were associated with high pollen viral richness locally, confirming and extending patterns observed previously at a continental scale. Our results highlight the importance of plant-pollinator interactions as drivers of plant-viral interaction diversity.}, } @article {pmid40450230, year = {2025}, author = {Leung, WKC and Yau, CYC and Lam, SC}, title = {Facilitators, barriers, and recommendations for mobile health applications among Chinese older populations: a scoping review.}, journal = {BMC geriatrics}, volume = {25}, number = {1}, pages = {396}, pmid = {40450230}, issn = {1471-2318}, support = {CRG2023/01//Tung Wah College/ ; CRG2023/01//Tung Wah College/ ; }, mesh = {Aged ; Aged, 80 and over ; Humans ; Middle Aged ; China ; *COVID-19/epidemiology ; *Mobile Applications ; *Telemedicine ; East Asian People ; }, abstract = {BACKGROUND: Mobile health (mHealth) applications have become indispensable in people's daily lives and are now incorporated into a multitude of healthcare services. However, due to inappropriate designs and ineffective promotional strategies, the rates of uptake and continued use of mHealth applications in older adults are usually low. Given that recent evidence has reported distinct mHealth adoption patterns between Chinese and non-Chinese populations, the aim of this scoping review was to map relevant evidence on the end-user perceptions and age-appropriate recommendations for interface design, persuasive features, and promotional strategies among Chinese older adults.

METHODS: All primary studies conducted in Chinese older people aged 60 + years, including quantitative, qualitative, and mixed methods research, examining end-user perceptions (e.g., motivators, barriers, and design) of mHealth applications were considered eligible for inclusion. Four electronic databases (PubMed, CINAHL, PsycINFO, and Medline) were searched from their inceptions through 31 May 2024. A narrative approach was adopted for data analyses relevant to the study aim.

RESULTS: A total of 23 studies (n = 8,203) were included. End-user perceptions (facilitators and barriers) of older people were narratively synthesized according to the socio-ecological model (individual/product, interpersonal, community, and societal). In Chinese deaf and hard-of-hearing older adults, the lack of proficiency in mastering operations of smartphone, Internet, and mHealth applications greatly jeopardized their communication with family or friends, accessibility to online medical consultations, and access to public places amidst COVID-19 pandemic. Recommended interface designs were categorized into various aspects of functional impairments (vision, manual dexterity, and cognition) of elderly users. Seven promotional strategies were also highlighted, whereas more than half of the studies recommended education measures (e.g., personalized family/peer- or health professional-led training program) and technical support (e.g., face-to-face instructions, detailed manual instructions, and timely consultation services). Other recommendations included increased publicity, co-creation, and supportive government policies.

CONCLUSION: This review synthesizes the existing relevant evidence and hence provides age-friendly recommendations for interface designs, persuasive features, and promotional strategies in Chinese older populations. Overall, this study empirically offers actionable guidelines for mHealth developers to meet the multifaceted needs of older people.}, } @article {pmid40443799, year = {2025}, author = {Broad, GR and Lees, DC and Boyes, D and , and , and , and , and , and , and , and , }, title = {The genome sequence of the Straw-barred Pearl moth, Pyrausta despicata Scopoli, 1763.}, journal = {Wellcome open research}, volume = {10}, number = {}, pages = {151}, pmid = {40443799}, issn = {2398-502X}, abstract = {We present a genome assembly from a male specimen of Pyrausta despicata (Straw-barred Pearl; Arthropoda; Insecta; Lepidoptera; Crambidae). The genome sequence has a total length of 481.83 megabases. Most of the assembly (99.61%) is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled, with a length of 15.29 kilobases.}, } @article {pmid40442647, year = {2025}, author = {Maździarz, M and Zając, S and Paukszto, Ł and Sawicki, J}, title = {RSCUcaller: an R package for analyzing differences in relative synonymous codon usage (RSCU).}, journal = {BMC bioinformatics}, volume = {26}, number = {1}, pages = {141}, pmid = {40442647}, issn = {1471-2105}, support = {2024/53/N/NZ8/02829//The National Science Center Kraków, Poland/ ; 12.610.002-110//University of Warmia and Mazury in Olsztyn/ ; }, mesh = {*Codon Usage ; *Software ; *Codon ; *Computational Biology/methods ; }, abstract = {BACKGROUND: Synonymous codon usage bias, a significant factor in gene expression and genome evolution, was extensively studied in genomics and molecular biology. Although the genetic code is universal, significant variations in synonymous codon usage have been observed among and within organisms. This bias was linked to various factors, including gene expression levels, tRNA abundance, protein structure, and environmental adaptation. Relative Synonymous Codon Usage (RSCU), a normalized measure, was used to quantify this bias. By analyzing RSCU values, researchers uncovered patterns and trends related to the underlying mechanisms driving codon usage bias.

RESULTS: We present an R package named RSCUcaller designed for the analysis of coding nucleotide sequences at the level of relative synonymous codon usage (RSCU). The package enables both visualization of data and the performance of advanced statistical analyses. RSCUcaller accepts as input a multi-fasta file containing coding sequences (CDS) and an accompanying description table. Alternatively, the user may provide separate fasta files for each sequence along with the corresponding table. The program merges the provided sequences and calculates RSCU values for each. Implemented visualization features include creating heatmaps and dendrograms based on these heatmaps. Furthermore, the package allows for the presentation of data in the form of histograms. The calculated RSCU values can also be used to create matrices that can be subjected to further analysis by the user. RSCUcaller offers the functionality of correlation analysis between any two organisms. Additionally, to compare the frequency of amino acid occurrence between different groups of sequences, statistical tests have been implemented.

CONCLUSIONS: RSCUcaller enabled comparative RSCU analysis between coding sequences of different organisms or individuals of the same species. It facilitated visualization and statistical analysis among codons and user-defined groups. The RSCUcaller package is available at https://github.com/Mordziarz/RSCUcaller under the GPL-3 license.}, } @article {pmid40442224, year = {2025}, author = {Sun, Y and Meng, W and Wang, F and Han, H and Sui, M and Jian, Z}, title = {Spatio-temporal evolution and coupling relationship between biodiversity and urbanization in the areas along the Yellow River of Shandong province.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {18876}, pmid = {40442224}, issn = {2045-2322}, support = {20221830//cultivation platform for integrating production, science, and education jointly built by Shandong Province and Peking University/ ; 42301320//National Natural Science Fund of China/ ; }, mesh = {*Biodiversity ; *Urbanization ; China ; *Rivers ; Spatio-Temporal Analysis ; Ecosystem ; Conservation of Natural Resources ; Sustainable Development ; }, abstract = {Mastering the coupling relationship and driving mechanism between urbanization and biodiversity is of great significance to ecological protection and regional sustainable development. The study took areas along the Yellow River of Shandong province (AYRSP) as the study area, which have the most rich and unique biodiversity resources in the whole basin. First, this study constructed a new indicator system of biodiversity based on remote-sensing data from species, ecosystem, and landscape to monitor and evaluate the spatial heterogeneity. The result was quantified by the proportion of key biodiversity areas, based on Sustainable Development Goal 15.1.2 from The United Nations. Then, the urbanization system was evaluated based on panel data. At last, the coordination relationship, lead-lag type between biodiversity and urbanization, and key influencing factors of coupling system at the county scale in 2015-2021 were identified by combining multiple models. The results demonstrated that the biodiversity level was gradually declining, with a distribution pattern of "low in the western, and high in mid-southern and eastern regions." The AYRSP still faced certain challenges in the sustainable development of biodiversity. The coupling coordination degree between biodiversity and urbanization showed an increasing trend with continuous improvement in the urbanization level. Only two counties were types of biodiversity-urbanization synchronous development. The results of grey relation degree model indicated that most of indicators were above 0.6 and the urbanization had a significant impact on the coupling system. This study established the evaluation system for biodiversity and urbanization at the small scale, which could provide theoretical reference for the sustainable development of county-level administrative region.}, } @article {pmid40441709, year = {2025}, author = {Dang, T and Fuji, Y and Kumaishi, K and Usui, E and Kobori, S and Sato, T and Narukawa, M and Toda, Y and Sakurai, K and Yamasaki, Y and Tsujimoto, H and Hirai, MY and Ichihashi, Y and Iwata, H}, title = {I-SVVS: integrative stochastic variational variable selection to explore joint patterns of multi-omics microbiome data.}, journal = {Briefings in bioinformatics}, volume = {26}, number = {3}, pages = {}, pmid = {40441709}, issn = {1477-4054}, support = {JP21J21850//JSPS KAKENHI/ ; JPMJCR1602//JST-CREST Program/ ; JPMJMI120C7//JST-Mirai Program/ ; JPMJAN23D1//JST ALCA-Next Program/ ; }, mesh = {*Microbiota ; Mice ; Animals ; Humans ; Stochastic Processes ; Bayes Theorem ; Glycine max/microbiology ; *Metabolomics/methods ; Algorithms ; *Computational Biology/methods ; Metabolome ; Cluster Analysis ; Multiomics ; }, abstract = {High-dimensional multi-omics microbiome data play an important role in elucidating microbial community interactions with their hosts and environment in critical diseases and ecological changes. Although Bayesian clustering methods have recently been used for the integrated analysis of multi-omics data, no method designed to analyze multi-omics microbiome data has been proposed. In this study, we propose a novel framework called integrative stochastic variational variable selection (I-SVVS), which is an extension of stochastic variational variable selection for high-dimensional microbiome data. The I-SVVS approach addresses a specific Bayesian mixture model for each type of omics data, such as an infinite Dirichlet multinomial mixture model for microbiome data and an infinite Gaussian mixture model for metabolomic data. This approach is expected to reduce the computational time of the clustering process and improve the accuracy of the clustering results. Additionally, I-SVVS identifies a critical set of representative variables in multi-omics microbiome data. Three datasets from soybean, mice, and humans (each set integrated microbiome and metabolome) were used to demonstrate the potential of I-SVVS. The results indicate that I-SVVS achieved improved accuracy and faster computation compared to existing methods across all test datasets. It effectively identified key microbiome species and metabolites characterizing each cluster. For instance, the computational analysis of the soybean dataset, including 377 samples with 16 943 microbiome species and 265 metabolome features, was completed in 2.18 hours using I-SVVS, compared to 2.35 days with Clusternomics and 1.12 days with iClusterPlus. The software for this analysis, written in Python, is freely available at https://github.com/tungtokyo1108/I-SVVS.}, } @article {pmid40440249, year = {2025}, author = {Guevara Rodríguez, DM and Pichihua Grandez, JD and Dianderas, FV and Del Carmen Sara, J}, title = {Incidence of cerebrovascular disease in Peru from 2015 to 2023.}, journal = {PLOS global public health}, volume = {5}, number = {5}, pages = {e0004559}, pmid = {40440249}, issn = {2767-3375}, abstract = {Cerebrovascular disease (stroke) is one of the leading causes of mortality and disability worldwide, particularly in low- and middle-income countries. This study aims to estimate the incidence of stroke in Peru between 2015 and 2023 using national hospital discharge data provided by the National Health Superintendency. We conducted a mixed ecological study using records of stroke cases reported across various healthcare systems, including the Ministry of Health, Social Security, and private entities. Hospitalizations were categorized according to ICD-10 codes (I60-I64) and stratified by age, sex, and region. Incidence rates were calculated using population projections from the National Institute of Statistics and Informatics. A total of 89,776 hospital discharges for stroke were analyzed, yielding an incidence rate of 3.11 per 10,000 persons over the study period, with a predominance in men and individuals over 60 years of age. Cerebral infarction was the most common diagnosis, particularly among those over 40 years old. Incidence varied significantly across regions, with Lima and Callao consistently exceeding the national average. The results highlight disparities in healthcare access and the need for targeted public health interventions. Our findings provide a 9-year overview of stroke in Peru, offering evidence to estimate hospital bed demand and prioritize preventive and management strategies-particularly in regions with higher vulnerability.}, } @article {pmid40381407, year = {2025}, author = {Lei, L and Sha, W and Liu, Q and Liu, S and Zhou, Y and Li, R and Duan, Y and Fu, S and Li, H and Liao, R and Li, L and Zhou, R and Zhou, C and Liu, H}, title = {Hepatotoxic effects of exposure to different concentrations of Dibutyl phthalate (DBP) in Schizothorax prenanti: Insights from a multi-omics analysis.}, journal = {Aquatic toxicology (Amsterdam, Netherlands)}, volume = {285}, number = {}, pages = {107390}, doi = {10.1016/j.aquatox.2025.107390}, pmid = {40381407}, issn = {1879-1514}, mesh = {*Dibutyl Phthalate/toxicity ; Animals ; *Liver/drug effects/pathology/metabolism ; *Water Pollutants, Chemical/toxicity ; *Cyprinidae/physiology ; Oxidative Stress/drug effects ; Multiomics ; }, abstract = {Dibutyl phthalate (DBP) is one of the most widely used phthalate esters (PAEs) that raise increasing ecotoxicological concerns due to their harmful effects on living organisms and ecosystems. Recently, while PAEs pollution in the Yangtze River has attracted significant attention, little research has been conducted on the impact of PAEs stress on S. prenanti, an endemic and valuable species in the Yangtze River. In this study, one control group (C-L) and three experimental groups: T1-L (3 µg/L), T2-L (30 µg/L), and T3-L (300 µg/L) were established with reference to the DBP concentration in the environment. For the first time, we investigated the effects of DBP stress on the liver of S. prenanti using histomorphological, physiological, and biochemical indexes, as well as a joint multi-omics analysis. The results revealed that compared to the C-L group, liver structural damage and stress were not significant in the environmental concentration group (T1-L) and the number of differential genes and differential metabolites were lower. However, as DBP stress concentration increased, the liver damage became severe, with significant vacuolation and hemolysis observed in the T2-L and T3-L groups. The TUNEL assay revealed a significant increase in the number of apoptotic cells along with a notable rise in differential genes and metabolites in the T2-L and T3-L groups. Oxidative stress markers (T-AOC, SOD, CAT, and GSH-PX) were also significantly higher in the T2-L and T3-L groups. RNA-Seq analysis showed that the protein processing in the endoplasmic reticulum pathway was most significantly -enriched differential gene pathway shared by both C-L vs T2-L and C-L vs T3-L, with most of the genes in this pathway showing significant up-regulation. This suggests that the protein processing in the endoplasmic reticulum pathway may play a key role in protecting the liver from injuries caused by high DBP stress. Interestingly, C XI, C XII, C XIII, C XIV and C XV in the chemical carcinogenesis - reactive oxygen species pathway were significantly down-regulated in the T2-L and T3-L groups based on combined transcriptomic and metabolomic analyses, suggesting that DBP causes liver injury by disrupting mitochondria. This comprehensive histomorphometric and multi-omics study demonstrated that the current DBP concentration in the habitat of S. prenanti in the upper reaches of the Yangtze River temporarily causes less liver damage. However, with increasing of DBP concentration, DBP could still cause serious liver damage to S. prenanti. This study provides a new mechanistic understanding of the liver response mechanism of S. prenanti under different concentrations of DBP stress and offers basic data for the ecological protection of the Yangtze River.}, } @article {pmid40288322, year = {2025}, author = {Zhou, H and Wu, Z and Wang, X and Jiang, L and Sun, H and Li, H and Yan, Z and Wang, Y and Yao, X and Zhang, C and Tang, J}, title = {6PPD-quinone exposure induces oxidative damage and physiological disruption in Eisenia fetida: An integrated analysis of phenotypes, multi-omics, and intestinal microbiota.}, journal = {Journal of hazardous materials}, volume = {493}, number = {}, pages = {138334}, doi = {10.1016/j.jhazmat.2025.138334}, pmid = {40288322}, issn = {1873-3336}, mesh = {*Oligochaeta/drug effects/physiology/metabolism ; Animals ; *Gastrointestinal Microbiome/drug effects ; *Soil Pollutants/toxicity ; *Oxidative Stress/drug effects ; *Phenylenediamines/toxicity ; Phenotype ; Reactive Oxygen Species/metabolism ; Metabolomics ; Transcriptome/drug effects ; Multiomics ; Benzoquinones ; }, abstract = {The environmental prevalence of the tire wear-derived emerging pollutant N-(1,3-dimethylbutyl)-N'-phenyl-p-phenylenediamine-quinone (6PPD-Q) has increasingly raised public concern. However, knowledge of the adverse effects of 6PPD-Q on soil fauna is scarce. In this study, we elucidated its impact on soil fauna, specifically on the earthworm Eisenia fetida. Our investigation encompassed phenotypic, multi-omics, and microbiota analyses to assess earthworm responses to a gradient of 6PPD-Q contamination (10, 100, 1000, and 5000 μg/kg dw soil). Post-28-day exposure, 6PPD-Q was found to bioaccumulate in earthworms, triggering reactive oxygen species production and consequent oxidative damage to coelomic and intestinal tissues. Transcriptomic and metabolomic profiling revealed several physiological perturbations, including inflammation, immune dysfunction, metabolic imbalances, and genetic toxicity. Moreover, 6PPD-Q perturbed the intestinal microbiota, with high dosages significantly suppressing microbial functions linked to metabolism and information processing (P < 0.05). These alterations were accompanied by increased mortality and weight loss in the earthworms. Specifically, at an environmental concentration of 6PPD-Q (1000 μg/kg), we observed a substantial reduction in survival rate and physiological disruptions. This study provides important insights into the environmental hazards of 6PPD-Q to soil biota and reveals the underlying toxicological mechanisms, underscoring the need for further research to mitigate its ecological footprint.}, } @article {pmid40233751, year = {2025}, author = {McKenzie, PF and Berardi, AE and Hopkins, R}, title = {Delayed flowering phenology of red-flowering plants in response to hummingbird migration.}, journal = {Current biology : CB}, volume = {35}, number = {9}, pages = {2175-2182.e3}, pmid = {40233751}, issn = {1879-0445}, support = {R35 GM142742/GM/NIGMS NIH HHS/United States ; }, mesh = {*Birds ; Animals ; *Flowers/growth & development/physiology ; Animal Migration ; Pollination ; North America ; Datasets as Topic ; Seasons ; Pigmentation ; Time Factors ; *Magnoliopsida/physiology ; Crowdsourcing ; }, abstract = {The radiation of angiosperms is marked by a phenomenal diversity of floral size, shape, color, scent, and reward.[1][,][2][,][3][,][4] The multi-dimensional response to selection to optimize pollination has generated correlated suites of these floral traits across distantly related species, known as "pollination syndromes."[5][,][6][,][7][,][8][,][9] The ability to test the broad utility of pollination syndromes and expand upon the generalities of these syndromes is constrained by limited trait data, creating a need for new approaches that can integrate vast, unstructured records from community-science platforms. Here, we compile the largest North American flower color dataset to date, using GPT-4 with Vision to classify color in over 11,000 species across more than 1.6 million iNaturalist observations. We discover that red- and orange-flowering species (classic "hummingbird pollination" colors) bloom later in eastern North America compared with other colors, corresponding to the arrival of migratory hummingbirds. Our findings reveal how seasonal flowering phenology, in addition to floral color and morphology, can contribute to the hummingbird pollination syndrome in regions where these pollinators are migratory. Our results highlight phenology as an underappreciated dimension of pollination syndromes and underscore the utility of integrating artificial intelligence with community-science data. The potential breadth of analysis offered by community-science datasets, combined with emerging data extraction techniques, could accelerate discoveries about the evolutionary and ecological drivers of biological diversity.}, } @article {pmid40435619, year = {2025}, author = {Matuszewska, D and Kiedrzyńska, E and Jóźwik, A and Kiedrzyński, M}, title = {An analysis of catchment factors associated with heavy metal export into the Baltic Sea and nature-based solutions aimed at its limitation.}, journal = {Journal of hazardous materials}, volume = {494}, number = {}, pages = {138727}, doi = {10.1016/j.jhazmat.2025.138727}, pmid = {40435619}, issn = {1873-3336}, abstract = {The aim of the article was to determine the shares of individual Baltic countries participating in the inflow of metal loads to the Baltic Sea and identify patterns of similarity between these countries regarding the causes of heavy metal load generation. The analyses used HELCOM and EUROSTAT data. The findings indicate that Finland and Sweden generate the highest total loads of heavy metals flowing in through rivers. However, Lithuania and Finland are distinguished by high metal loads calculated per km[2] of catchment area. Clustering countries in terms of their similarity in the heavy metal loads provided to the Baltic resulted in three groups. Finland and Lithuania generates the highest mean loads of cadmium, chromium, nickel and zinc per unit area [kg/km[2]/year]. Estonia and Latvia generates the highest mean annual loads of lead, mercury and copper. Poland, Germany and Sweden generates the lowest heavy metal loads. Multidimensional data analysis showed a strong correlation between aquaculture production in the Baltic Sea catchment area, the number of cattle, beef, mutton, pigs, poultry, and meat produced from them, the amount of waste, trucks, cereal production, the use of nitrogen fertilizers, and the loads of heavy metals reaching the Baltic Sea with river waters. Therefore, there is a need for continuous monitoring of the loads and transfer of heavy metals to the Baltic Sea, and for activities aimed at eliminating them from the environment. For this purpose, Nature-Based Solutions can be used, as they represent inexpensive, nature-friendly methods for removing pollutants from surface waters.}, } @article {pmid39890763, year = {2025}, author = {Kuru, A and Yüzer, MA and Yüzer, AŞ and Güney, BG and Yüzer, ME}, title = {Integrated site selection model for industrial areas: case study for İnegöl furniture industry.}, journal = {Environmental science and pollution research international}, volume = {32}, number = {8}, pages = {4771-4793}, pmid = {39890763}, issn = {1614-7499}, mesh = {*Interior Design and Furnishings ; *Industry ; Noise ; Odorants/analysis ; Environmental Monitoring ; Socioeconomic Factors ; Geographic Information Systems ; *Environment ; }, abstract = {Industrial activities in the central area have adverse effects such as noise, odor, and traffic congestion. Simultaneously, due to changing technological and economic advances, existing industrial areas cannot meet the needs, spatial inadequacies obstruct competition, and production capacity decreases. Decentralizing industrial activities from urban centers are ecologically and economically necessary. Various elements on a macro and micro scale need to be considered to select suitable sites for new industrial areas. Natural, socioeconomic, and built environment features must be examined to ensure sustainability. The objective of this study is to develop an integrated industrial site location model that considers the needs of authorities and industrial stakeholders, as well as economic and ecological sustainability for the İnegöl district, one of Turkey's leading settlements in the furniture industry. Thirty-seven criteria were evaluated using GIS based multi-criteria decision making methods. The criteria were defined through spatial analysis, expert opinions, and in-depth interviews with industry and local government representatives. Using weighted linear combination process the five sub-regions exhibiting the lowest economic costs and the least environmental degradation have been identified. Advantages and disadvantages were identified through the use of sketches and comparisons between the sub-regions. A decision support system was developed for local and central government institutions to be used in industrial site selection processes.}, } @article {pmid40435606, year = {2025}, author = {Guo, J and Xie, Y and Dou, X and Qi, W and Liao, Y and Cao, X and Peng, J and Liu, H}, title = {Combining source identification and risk assessment to uncover spatial risk patterns in an agricultural lake.}, journal = {Journal of environmental management}, volume = {387}, number = {}, pages = {125966}, doi = {10.1016/j.jenvman.2025.125966}, pmid = {40435606}, issn = {1095-8630}, mesh = {*Lakes ; Agriculture ; *Environmental Monitoring/methods ; Risk Assessment ; Geologic Sediments ; Water Pollutants, Chemical/analysis ; Polycyclic Aromatic Hydrocarbons/analysis ; Metals, Heavy/analysis ; Bayes Theorem ; Water Quality ; Rivers ; }, abstract = {Pollutant source identification and risk assessment underpin environmental management, necessitating innovative methods for both pollution source identification and comprehensive evaluation to enhance management efficiency. In this study, we developed a novel integrated framework that combines Bayesian isotope mixing, positive matrix factorization (PMF), random forest, and spatial autocorrelation for multi-pollutant source identification and risk assessment. The Bayesian isotope mixing model revealed that fertilizers accounted for 61 % of the nitrate in the lake and 46 % of the nitrate in the river. Furthermore, PMF analysis indicated that polycyclic aromatic hydrocarbons (PAHs) in sediments and soil were primarily sourced from vehicular emissions (32 %), while heavy metals (40 %) were mainly from vehicular emissions and agricultural activities. Using a comprehensive pollution assessment framework for water and sediment quality, we found that water quality ranged from "medium" to "excellent", and sediment quality ranged from "good" to "excellent". Among various evaluation indices, CODMn, As, F[-], TP, Pb, and Zn were pivotal in determining comprehensive water quality. Key indices for sediment quality evaluation included Flua, BaP, BaA, Pyr, Ant, Pb, and As, primarily sourced from automobile emissions and agricultural activities. Spatial autocorrelation analysis demonstrated a spatial relationship between water quality and sediment quality, covering 43 % of the area. High-pollution areas (13 %) were concentrated around natural river inlets, while low-pollution zones (17 %) were located near ecological water replenishment river inlets. This underscores the significant influence of inflowing water quality on sediment conditions. This study highlights the development of a comprehensive pollution assessment framework to evaluate sediment and soil pollution, as well as to identify high-risk zones of compound pollution in water and sediment. Furthermore, the framework's universal applicability for agricultural lake systems enables the identification of high-risk zones through water-sediment interaction analysis.}, } @article {pmid40435494, year = {2025}, author = {Berger, M and Ehlers, JP and Nitsche, J}, title = {Aligning With the Goals of the Planetary Health Concept Regarding Ecological Sustainability and Digital Health: Scoping Review.}, journal = {Journal of medical Internet research}, volume = {27}, number = {}, pages = {e71795}, doi = {10.2196/71795}, pmid = {40435494}, issn = {1438-8871}, mesh = {*Telemedicine ; Climate Change ; Humans ; Global Health ; Delivery of Health Care ; Artificial Intelligence ; Digital Health ; }, abstract = {BACKGROUND: Climate change, driven by greenhouse gas emissions, threatens human health and biodiversity. While the digitalization of health care, including telemedicine and artificial intelligence, offers sustainability benefits, it also raises concerns about energy use and electronic waste. Balancing these factors is key to a sustainable health care future.

OBJECTIVE: The objective of this review was to examine the extent to which digitalization in the health care sector influences environmental sustainability. Specifically, it aimed to assess how digitalization can contribute to reducing the health care sector's impact on global climate change. From these findings, conclusions were drawn regarding the extent to which digitalization aligns with the objectives of the Planetary Health movement and how these 2 movements may mutually reinforce each other.

METHODS: A scoping review guided by the PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) 2020 guidelines using databases such as PubMed and Scopus was conducted, and 58 quantitative studies from 2009 to 2024 were analyzed for environmental, social, and economic outcomes aligned with Planetary Health goals.

RESULTS: This review analyzed 58 studies on the environmental impact of digitalization in health care primarily focusing on telemedicine, which was examined in 91% (53/58) of the studies. Most studies (56/58, 97%) quantified transport-related emissions avoided through digitalization, with some also assessing emissions from health care facilities, medical equipment, and energy consumption. Findings indicated that telemedicine significantly reduces carbon dioxide emissions, with total avoided emissions amounting to approximately 830 million kg. A substantial proportion of the studies (36/58, 62%) focused on social aspects, highlighting factors such as patient satisfaction, time efficiency, and overall convenience. In addition, economic considerations were analyzed in 48% (28/58) of the studies, emphasizing cost reductions and resource optimization. However, only 12% (7/58) of the studies evaluated the full life cycle impact of digital technologies, highlighting the need for further research on their long-term environmental sustainability.

CONCLUSIONS: This review calls for further research beyond telemedicine, advocating for life cycle analyses and actionable strategies for a sustainable digitalization in health care systems. The Planetary Health framework is highlighted as a guide for ensuring sustainable digital transformation in health care.}, } @article {pmid39892263, year = {2025}, author = {Yang, W and Liu, Y and Shao, H and Iravani, M and Yu, Z and Weber, M}, title = {Developing a cloud-based WebGIS tool for communicating integrated ecosystem services assessment modeling to conservation stakeholders.}, journal = {Journal of environmental management}, volume = {375}, number = {}, pages = {124372}, doi = {10.1016/j.jenvman.2025.124372}, pmid = {39892263}, issn = {1095-8630}, mesh = {*Cloud Computing ; *Geographic Information Systems ; Ecosystem ; *Agriculture/economics/methods/statistics & numerical data ; *Conservation of Natural Resources/economics/methods/statistics & numerical data ; Environmental Monitoring ; Models, Statistical ; Farms/economics/statistics & numerical data ; Cost-Effectiveness Analysis ; Alberta ; Agroecology/economics/methods/statistics & numerical data ; Stakeholder Participation ; Hydrology ; }, abstract = {Various modeling efforts have been conducted to evaluate ecosystem services (ES) of agricultural conservation practices but typically these models are too complex for conservation stakeholders to use. This research developed a cloud-based WebGIS tool for communicating integrated ES modeling to conservation stakeholders. The integrated ES modeling was developed by linking farm economic, watershed hydrologic, and soil carbon modeling within a spatial optimization framework for identifying conservation practices to minimize economic costs subject to multiple ES targets including water quality and soil carbon improvement benefits. The WebGIS tool, named "Ecosystem Services Assessment Tool" (ESAT), has a suite of functions to visualize watershed characteristics, summarize the effectiveness of existing agricultural conservation practices, examine the cost, effectiveness, and cost-effectiveness of future agricultural conservation practices, and further, identify optimal sets of conservation practices for achieving cost-effectiveness. The study area for the integrated ES modeling and WebGIS tool development was the 4,820-km[2] Modeste watershed in Alberta, Canada. The ESAT application demonstrated its functionalities to support decision making, particularly in identifying cost-effective conservation practices for achieving sediment, phosphorus or nitrogen reduction, or soil carbon increase target. In the research, conservation stakeholders including municipal and provincial governments, conservation management agencies, and NGOs were actively engaged in data collection, modeling development, WebGIS tool development, and training for the use of the WebGIS tool. Conservation stakeholders assessed that the ESAT is a very useful tool for supporting decision making in agri-environmental programs. However, the WebGIS tool can be further simplified and streamlined to improve the user-friendliness of the ESAT.}, } @article {pmid37732396, year = {2025}, author = {Lajmi, A and Glinka, F and Privman, E}, title = {Optimizing ddRAD sequencing for population genomic studies with ddgRADer.}, journal = {Molecular ecology resources}, volume = {25}, number = {5}, pages = {e13870}, doi = {10.1111/1755-0998.13870}, pmid = {37732396}, issn = {1755-0998}, support = {2017319//US-Israel Binational Science Foundation/ ; }, mesh = {*Sequence Analysis, DNA/methods ; *Genetics, Population/methods ; *Software ; *Computational Biology/methods ; *Genomics/methods ; *High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; }, abstract = {Double-digest Restriction-site Associated DNA sequencing (ddRADseq) is widely used to generate genomic data for non-model organisms in evolutionary and ecological studies. Along with affordable paired-end sequencing, this method makes population genomic analyses more accessible. However, multiple factors should be considered when designing a ddRADseq experiment, which can be challenging for new users. The generated data often suffer from substantial read overlaps and adaptor contamination, severely reducing sequencing efficiency and affecting data quality. Here, we analyse diverse datasets from the literature and carry out controlled experiments to understand the effects of enzyme choice and size selection on sequencing efficiency. The empirical data reveal that size selection is imprecise and has limited efficacy. In certain scenarios, a substantial proportion of short fragments pass below the lower size-selection cut-off resulting in low sequencing efficiency. However, enzyme choice can considerably mitigate inadvertent inclusion of these shorter fragments. A simple model based on these experiments is implemented to predict the number of genomic fragments generated after digestion and size selection, number of SNPs genotyped, number of samples that can be multiplexed and the expected sequencing efficiency. We developed ddgRADer - http://ddgrader.haifa.ac.il/ - a user-friendly webtool and incorporated these calculations to aid in ddRADseq experimental design while optimizing sequencing efficiency. This tool can also be used for single enzyme protocols such as Genotyping-by-Sequencing. Given user-defined study goals, ddgRADer recommends enzyme pairs and allows users to compare and choose enzymes and size-selection criteria. ddgRADer improves the accessibility and ease of designing ddRADseq experiments and increases the probability of success of the first population genomic study conducted in labs with no prior experience in genomics.}, } @article {pmid37526650, year = {2025}, author = {Robledo-Ruiz, DA and Austin, L and Amos, JN and Castrejón-Figueroa, J and Harley, DKP and Magrath, MJL and Sunnucks, P and Pavlova, A}, title = {Easy-to-use R functions to separate reduced-representation genomic datasets into sex-linked and autosomal loci, and conduct sex assignment.}, journal = {Molecular ecology resources}, volume = {25}, number = {5}, pages = {e13844}, doi = {10.1111/1755-0998.13844}, pmid = {37526650}, issn = {1755-0998}, support = {//Australian Government Department of Education/ ; DP180102359//Australian Research Council/ ; DP210102275//Australian Research Council/ ; LP160100482//Australian Research Council/ ; //Department of Biodiversity, Conservation and Attractions (Western Australia)/ ; //Department of Environment, Land, Water and Planning (Victoria)/ ; //Diversity Arrays Technology/ ; //Ecological Society of Australia Incorporated/ ; //Environment, Planning & Sustainable Development Directorate (ACT)/ ; //Monash University Faculty of Science/ ; //Revive & Restore/ ; //Zoos Victoria/ ; }, mesh = {Animals ; Birds/genetics ; *Genomics/methods ; Male ; *Sex Determination Processes ; *Computational Biology/methods ; Female ; Mammals/genetics ; *Software ; Sex Chromosomes/genetics ; }, abstract = {Identifying sex-linked markers in genomic datasets is important because their presence in supposedly neutral autosomal datasets can result in incorrect estimates of genetic diversity, population structure and parentage. However, detecting sex-linked loci can be challenging, and available scripts neglect some categories of sex-linked variation. Here, we present new R functions to (1) identify and separate sex-linked loci in ZW and XY sex determination systems and (2) infer the genetic sex of individuals based on these loci. We tested these functions on genomic data for two bird and one mammal species and compared the biological inferences made before and after removing sex-linked loci using our function. We found that our function identified autosomal loci with ≥98.8% accuracy and sex-linked loci with an average accuracy of 87.8%. We showed that standard filters, such as low read depth and call rate, failed to remove up to 54.7% of sex-linked loci. This led to (i) overestimation of population FIS by up to 24%, and the number of private alleles by up to 8%; (ii) wrongly inferring significant sex differences in heterozygosity; (iii) obscuring genetic population structure and (iv) inferring ~11% fewer correct parentages. We discuss how failure to remove sex-linked markers can lead to incorrect biological inferences (e.g. sex-biased dispersal and cryptic population structure) and misleading management recommendations. For reduced-representation datasets with at least 15 known-sex individuals of each sex, our functions offer convenient resources to remove sex-linked loci and to sex the remaining individuals (freely available at https://github.com/drobledoruiz/conservation_genomics).}, } @article {pmid37357835, year = {2025}, author = {Chi, L and Zhang, X and Xue, Y and Chen, H}, title = {fastHaN: a fast and scalable program for constructing haplotype network for large-sample sequences.}, journal = {Molecular ecology resources}, volume = {25}, number = {5}, pages = {e13829}, doi = {10.1111/1755-0998.13829}, pmid = {37357835}, issn = {1755-0998}, support = {2021YFC0863400//National Key Research and Development Program of China/ ; 2021YFC2301305//National Key Research and Development Program of China/ ; 2020YFC0847000//National Key Research and Development Program of China/ ; KJZ-SW-L14//the Key Program of Chinese Academy of Sciences/ ; }, mesh = {*Haplotypes ; *Software ; *Computational Biology/methods ; Algorithms ; *Sequence Analysis, DNA/methods ; }, abstract = {Haplotype networks can be used to demonstrate the genealogical relationships of DNA sequences within species, and thus are widely applied in population genetics, molecular ecology, epidemiology and evolutionary studies. However, existing programs become computationally infeasible as the sample size increases. Here, we present fastHaN, an efficient and scalable program suitable for constructing haplotype networks for large samples. On a data set with the haplotype length of 30 kb, the Median Joining Network (MJN) algorithm implemented by fastHaN is 3000 times faster than PopART and 70 times faster than NETWORK in single-threaded mode. The implementation of the Templeton-Crandall-Sing (TCS) algorithm is 100 times faster than PopART and 5800 times faster than the TCS software. Moreover, fastHaN also enables multi-threaded mode with scalability. The source code is freely available on https://github.com/ChenHuaLab/fastHaN/. A web-based version is also available on https://ngdc.cncb.ac.cn/haplotype/.}, } @article {pmid36458971, year = {2025}, author = {Huang, K and Li, W and Yang, B and Wang, D and He, S and Shen, Y and Ao, J and Li, Y and Cui, Y and Kong, Y and Li, W and Li, N and Dunn, DW and Li, B}, title = {vcfpop: Performing population genetics analyses for autopolyploids and aneuploids based on next-generation sequencing data sets.}, journal = {Molecular ecology resources}, volume = {25}, number = {5}, pages = {e13744}, doi = {10.1111/1755-0998.13744}, pmid = {36458971}, issn = {1755-0998}, support = {XDB31020302//Strategic Priority Research Program of the Chinese Academy of Sciences/ ; 31730104//National Natural Science Foundation of China/ ; 31770411//National Natural Science Foundation of China/ ; 32070453//National Natural Science Foundation of China/ ; 32170515//National Natural Science Foundation of China/ ; 2021KJXX-026//Innovation Capability Support Program of Shaanxi/ ; }, mesh = {*Software ; *Polyploidy ; *Genetics, Population/methods ; *High-Throughput Nucleotide Sequencing/methods ; *Computational Biology/methods ; *Plants/genetics ; }, abstract = {Polyploids are cells or organisms with a genome consisting of more than two sets of homologous chromosomes. Polyploid plants have important traits that facilitate speciation and are thus often model systems for evolutionary, molecular ecology and agricultural studies. However, due to their unusual mode of inheritance and double-reduction, diploid models of population genetic analysis cannot properly be applied to autopolyploids. To overcome this problem, we developed a software package entitled vcfpop to perform a variety of population genetic analyses for autopolyploids, such as parentage analysis, analysis of molecular variance, principal coordinates analysis, hierarchical clustering analysis and Bayesian clustering. We used three data sets to evaluate the capability of vcfpop to analyse large data sets on a desktop computer. This software is freely available at http://github.com/huangkang1987/vcfpop.}, } @article {pmid40433986, year = {2024}, author = {He, Y and Mulqueeney, JM and Watt, EC and Salili-James, A and Barber, NS and Camaiti, M and Hunt, ESE and Kippax-Chui, O and Knapp, A and Lanzetti, A and Rangel-de Lázaro, G and McMinn, JK and Minus, J and Mohan, AV and Roberts, LE and Adhami, D and Grisan, E and Gu, Q and Herridge, V and Poon, STS and West, T and Goswami, A}, title = {Opportunities and Challenges in Applying AI to Evolutionary Morphology.}, journal = {Integrative organismal biology (Oxford, England)}, volume = {6}, number = {1}, pages = {obae036}, pmid = {40433986}, issn = {2517-4843}, abstract = {Artificial intelligence (AI) is poised to revolutionize many aspects of science, including the study of evolutionary morphology. While classical AI methods such as principal component analysis and cluster analysis have been commonplace in the study of evolutionary morphology for decades, recent years have seen increasing application of deep learning to ecology and evolutionary biology. As digitized specimen databases become increasingly prevalent and openly available, AI is offering vast new potential to circumvent long-standing barriers to rapid, big data analysis of phenotypes. Here, we review the current state of AI methods available for the study of evolutionary morphology, which are most developed in the area of data acquisition and processing. We introduce the main available AI techniques, categorizing them into 3 stages based on their order of appearance: (1) machine learning, (2) deep learning, and (3) the most recent advancements in large-scale models and multimodal learning. Next, we present case studies of existing approaches using AI for evolutionary morphology, including image capture and segmentation, feature recognition, morphometrics, and phylogenetics. We then discuss the prospectus for near-term advances in specific areas of inquiry within this field, including the potential of new AI methods that have not yet been applied to the study of morphological evolution. In particular, we note key areas where AI remains underutilized and could be used to enhance studies of evolutionary morphology. This combination of current methods and potential developments has the capacity to transform the evolutionary analysis of the organismal phenotype into evolutionary phenomics, leading to an era of "big data" that aligns the study of phenotypes with genomics and other areas of bioinformatics.}, } @article {pmid40378593, year = {2025}, author = {Broel, N and Daumüller, F and Ali, A and Lemanschick, J and Maibach, K and Mewe, C and Bunk, B and Spröer, C and Baschien, C and Zorn, H and Schlüter, H and Rühl, M and Janssen, S and Gand, M}, title = {Unravelling the enzymatic wood decay repertoire of Cerrena zonata: A multi-omics approach.}, journal = {Microbiological research}, volume = {298}, number = {}, pages = {128214}, doi = {10.1016/j.micres.2025.128214}, pmid = {40378593}, issn = {1618-0623}, mesh = {Lignin/metabolism ; *Wood/metabolism/microbiology ; Fungal Proteins/genetics/metabolism ; Glycoside Hydrolases/metabolism/genetics ; Peroxidases/metabolism/genetics ; Laccase/metabolism/genetics ; Biomass ; *Basidiomycota/enzymology/genetics/metabolism ; Genomics ; Gene Expression Profiling ; Genome, Fungal ; Proteomics ; Hydrolysis ; Multiomics ; }, abstract = {Lignocellulosic biomass (LCB), such as wheat straw, bagasse, or wood, is a cost-effective, sustainable carbon source but remains challenging to utilize due to the recalcitrance of lignin, which hinders efficient carbohydrate hydrolysis. Effective LCB degradation demands a wide range of enzymes, and commercial enzyme cocktails often require physical or chemical pretreatments. A fully enzymatic degradation could drastically improve the efficiency of these processes. Basidiomycota fungi naturally possess diverse enzymes suited for LCB breakdown. The white-rot fungus Cerrena zonata, a member of the phylum Basidiomycota, was analyzed for its Carbohydrate-Active Enzymes (CAZymes) using a multi-omics approach. Genomic and transcriptomic analyses of C. zonata identified 20,816 protein-encoding genes, including 487 CAZymes (2.3 %). Cultivating C. zonata with and without LCB addition revealed a total of 147 proteins, of which 36 were CAZymes (13 auxiliary activities (AA), 3 carbohydrate esterases, and 20 glycoside hydrolases). In accordance, laccase, manganese peroxidase (MnP) as well as versatile peroxidase (VP) activities were detected in the fungal culture supernatants. Furthermore, relevant enzymes were visualized via zymography. Consistent with these results, five putative peroxidases (AA2) and three putative laccases (AA1_1) were identified in all -omics dimensions. Further structure and sequence analysis of AA2 proteins supports that two proteins were classified as VPs and three as MnPs, based on their active and Mn[2 +] binding sites. In summary, C. zonata possesses a broad enzyme spectrum expressed under varied conditions, highlighting its potential for identifying efficient lignin-degrading enzymes for enzymatic pretreatment of food industry side streams and other LCBs.}, } @article {pmid39856573, year = {2025}, author = {Sun, Z and Zhang, F and Zhong, N and Zhou, K and Tang, J}, title = {Genome sequence resources for three strains of the genus Clonostachys.}, journal = {BMC genomic data}, volume = {26}, number = {1}, pages = {8}, pmid = {39856573}, issn = {2730-6844}, support = {No. 2022AH051346 and No. KJ2021A0676//the Key Natural Science Research Projects in Anhui Universities/ ; No. KJTS2022002; No. KJTS2022003//Science and Technology Innovation Capability Enhancement Projects in Fuyang National Agricultural Sci-Tech Park/ ; No. 2022AH020081//Natural Science Foundation of Universities of Anhui Province for Distinguished Young Project/ ; No. 2020KYQD0023//The Fuyang Normal University Research Project/ ; [2023]13//Biological and Medical Sciences of Applied Summit Nurturing Disciplines in Anhui Province, Anhui Education Secretary Department/ ; }, mesh = {*Ascomycota/classification/genetics ; Datasets as Topic ; Genome, Fungal ; Molecular Sequence Annotation ; Biological Control Agents ; }, abstract = {OBJECTIVE: Clonostachys, a genus with rich morphological and ecological diversity in Bionectriaceae, has a wide distribution among diverse habitats. Several studies have reported Clonostachys fungi as effective biological agents against multiple fungal plant pathogens. To clarify the diversity and biocontrol mechanisms of the Clonostachys fungi, this study was undertaken to sequence and assemble the genomes of two C. chloroleuca and one C. rhizophaga.

DATA DESCRIPTION: Here, we performed genomic sequencing of three strains of genus Clonostachys collected from the China General Microbiological Culture Collection Center (CGMCC) using Illumina HiSeq 2500 sequencing technology. Whole genome analysis indicated that their genomes consist of 58,484,224 bp with a GC content of 48.58%, 58,114,960 bp with a GC content of 47.74% and 58,450,453 bp with a GC content of 48.58%, respectively. BUSCO analysis of the genome assembly indicated that the completeness of these genomes was at least 98%. In summary, these datasets provide a valuable resource for ongoing studies that include further exploration of biological function, marker development, enhanced biological control ability of Clonostachys fungi, and population diversity.}, } @article {pmid40432488, year = {2025}, author = {Min, J and Kim, B and Park, Y and Son, Y and Park, W}, title = {Bacterial cell wall synthesis and recycling: new antimicrobial targets and vaccine development.}, journal = {Critical reviews in microbiology}, volume = {}, number = {}, pages = {1-20}, doi = {10.1080/1040841X.2025.2510250}, pmid = {40432488}, issn = {1549-7828}, abstract = {Almost all bacteria have peptidoglycan (PG) components that are essential for virulence and are absent in humans, making them a top-priority target for antibiotics and vaccines. The rise of multidrug-resistant bacteria (MRB) necessitates urgent expansion of our arsenal of inhibitors targeting the PG cell wall. This review addresses our understanding of PG biosynthesis and recycling processes, emphasizing the need to identify novel target proteins and redesign existing PG-targeted antimicrobial peptides. Building on our understanding of cell wall biochemistry and biogenesis derived from Escherichia coli, we also aim to compare and elucidate the cell wall processes in other pathogens, such as Acinetobacter baumannii and Salmonella Typhimurium, where knowledge remains incomplete. We cover in detail the distinct roles of PG-related proteins in Gram-negative bacteria, strategies to block PG biosynthesis/recycling pathways, and their potential as novel antibiotic targets to address the growing challenge of antibiotic resistance. Finally, we review the application of rigorous immuno-informatics analysis and several immune filters to construct epitope-specific vaccines displaying PG-related proteins on the surface of outer membrane vesicles (OMVs), aiming to combat MRB proliferation.}, } @article {pmid40431635, year = {2025}, author = {Rodrigues, GVP and Santos, JPN and Ferreira, LYM and Conceição, LBA and Porto, JAM and Aguiar, ERGR}, title = {Theobroma cacao Virome: Exploring Public RNA-Seq Data for Viral Discovery and Surveillance.}, journal = {Viruses}, volume = {17}, number = {5}, pages = {}, pmid = {40431635}, issn = {1999-4915}, support = {Financial Code 001//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)/ ; //Conselho Nacional de Pesquisa Científica (CNPq)/ ; }, mesh = {*Cacao/virology ; *Virome/genetics ; Plant Diseases/virology ; RNA-Seq ; Computational Biology/methods ; Phylogeny ; *Plant Viruses/genetics/classification/isolation & purification ; Genome, Viral ; Badnavirus/genetics/isolation & purification/classification ; Microbiota ; }, abstract = {Cocoa (Theobroma cacao L.) is a major agricultural commodity, essential for the global chocolate industry and the livelihoods of millions of farmers. However, viral diseases pose a significant threat to cocoa production, with Badnavirus species causing severe losses in Africa. Despite its economic importance, the overall virome of T. cacao remains poorly characterized, limiting our understanding of viral diversity and potential disease interactions. This study aims to assess the cocoa-associated virome by analyzing 109 publicly available RNA-seq libraries from nine BioProjects, covering diverse conditions and geographic regions. We implemented a comprehensive bioinformatics pipeline integrating multiple viral sequence enrichment steps, a hybrid assembly strategy using different assemblers, and sequence similarity searches against NCBI non-redundant databases. Our approach identified ten putative novel viruses associated with the cocoa microbiome and a novel Badnavirus species. These findings provide new insights into the viral landscape of T. cacao, characterizing the diversity of cacao-associated viruses and their potential ecological roles. Expanding the catalog of viruses associated with cocoa plants not only enhances our understanding of plant-virus-microbiome interactions but also contributes to the development of more effective disease surveillance and management strategies, ultimately supporting sustainable cocoa production.}, } @article {pmid40427823, year = {2025}, author = {Santos, AFB and Nunes, M and Filipa-Silva, A and Pimentel, V and Pingarilho, M and Abrantes, P and Miranda, MNS and Crespo, MTB and Abecasis, AB and Parreira, R and Seabra, SG}, title = {Wastewater Metavirome Diversity: Exploring Replicate Inconsistencies and Bioinformatic Tool Disparities.}, journal = {International journal of environmental research and public health}, volume = {22}, number = {5}, pages = {}, pmid = {40427823}, issn = {1660-4601}, support = {PTDC/CTA AMB/29586/2017//Fundação para a Ciência e Tecnologia, Portugal 568 through projects AgriWWAter/ ; 706, Internalproject IBETXplore 2017//VirusFreeWater/ ; GHTM- UID/04413/2020//Internal exploratory Project WasteWaterVir/ ; LA/P/0117/2020//LA-REAL/ ; }, mesh = {*Wastewater/virology ; *Computational Biology/methods ; *Virome ; Portugal ; *Metagenomics/methods ; *Viruses/classification/isolation & purification/genetics ; }, abstract = {This study investigates viral composition in wastewater through metagenomic analysis, evaluating the performance of four bioinformatic tools-Genome Detective, CZ.ID, INSaFLU-TELEVIR and Trimmomatic + Kraken2-on samples collected from four sites in each of two wastewater treatment plants (WWTPs) in Lisbon, Portugal in April 2019. From each site, we collected and processed separately three replicates and one pool of nucleic acids extracted from the replicates. A total of 32 samples were processed using sequence-independent single-primer amplification (SISPA) and sequenced on an Illumina MiSeq platform. Across the 128 sample-tool combinations, viral read counts varied widely, from 3 to 288,464. There was a lack of consistency between replicates and their pools in terms of viral abundance and diversity, revealing the heterogeneity of the wastewater matrix and the variability in sequencing effort. There was also a difference between software tools highlighting the impact of tool selection on community profiling. A positive correlation between crAssphage and human pathogens was found, supporting crAssphage as a proxy for public health surveillance. A custom Python pipeline automated viral identification report processing, taxonomic assignments and diversity calculations, streamlining analysis and ensuring reproducibility. These findings emphasize the importance of sequencing depth, software tool selection and standardized pipelines in advancing wastewater-based epidemiology.}, } @article {pmid40334559, year = {2025}, author = {Semcesen, PO and Wells, MG and Sherlock, C and Gutierrez, RF and Rochman, CM}, title = {Wind driven transport of macroplastic debris in a large urban harbour measured by GPS-tracked drifters.}, journal = {Marine pollution bulletin}, volume = {217}, number = {}, pages = {118034}, doi = {10.1016/j.marpolbul.2025.118034}, pmid = {40334559}, issn = {1879-3363}, mesh = {*Wind ; *Plastics/analysis ; *Environmental Monitoring/methods ; Ontario ; Geographic Information Systems ; }, abstract = {The transport pathways of floating plastic debris in Toronto Harbour, Ontario, Canada, were assessed using a series of GPS-tracked drifter bottles. The drifter trajectories were largely controlled by winds, and they could traverse the 2 km wide harbour within a day. The average ratio of drifter speed to wind speed (the wind factor) is consistent with values of 2-5 % used in modelling dispersion of marine debris. However, significant variability in wind factors meant some drifters travelled 2-5 times faster than expected in small waterbodies (Toronto Harbour), and as much as 7 times faster in large waterbodies (Lake Ontario). Importantly, based on our calculated wind factor equations and the coincident accumulation of our drifters with real plastic debris, we can justify the use of wind factors when studying plastic debris transport. Most (75 %) of the drifters that were released in the harbour, stayed within the harbour, accumulating downwind. However, 14 of all 66 drifters escaped Toronto Harbour, where ∼70 % escaped through the West Gap while ∼30 % escaped via the Outer Harbour. One drifter made a 290 km journey across Lake Ontario in a period of 14 days, demonstrating that Toronto is a potential source of plastic debris throughout Lake Ontario.}, } @article {pmid40426056, year = {2025}, author = {Charest, J and Loebenstein, P and Mach, RL and Mach-Aigner, AR}, title = {FunFEA: an R package for fungal functional enrichment analysis.}, journal = {BMC bioinformatics}, volume = {26}, number = {1}, pages = {138}, pmid = {40426056}, issn = {1471-2105}, mesh = {*Genome, Fungal ; *Software ; Molecular Sequence Annotation/methods ; *Fungi/genetics ; Gene Ontology ; Databases, Genetic ; Genomics/methods ; Computational Biology/methods ; }, abstract = {BACKGROUND: The functional annotation of fungal genomes is critical for understanding their biological processes and ecological roles. While existing tools support functional enrichment analysis from publicly available annotations of well-established model organisms, few are tailored to the specific needs of the fungal research community. Furthermore, many tools struggle with processing functional annotations of novel species, for which no publicly available functional annotations are yet available.

RESULTS: FunFEA is an R package designed for functional enrichment analysis of fungal genomes. It supports COG/KOG (Clusters of Orthologous Genes), GO (Gene Ontology), and KEGG (Kyoto Encyclopedia of Genes and Genomes) annotations, and generates background frequency models from publicly available annotations for overrepresentation analysis, within a set of experimentally defined genes or proteins. Additionally, FunFEA can process eggNOG-mapper annotations, thus enabling functional enrichment analysis of novel genomes. The package offers a suite of tools for generation of background frequency models, functional enrichment analysis, as well as visualization of enriched functional categories. On release, the package includes precomputed models for 65 commonly used fungal strains in academic research and strains listed on the WHO fungal priority pathogens list.

CONCLUSIONS: FunFEA fills a critical need for a specialized tool in fungal genomics, providing valuable insights into fungal biology. Additionally, its ability to process eggNOG-mapper annotations makes it an essential resource for researchers, helping to drive further exploration of fungal functional diversity and pathways and derive biological insights from novel genomes.}, } @article {pmid40425680, year = {2025}, author = {Péter, SA and Gallo, T and Mullinax, J and Roess, A and Palomo-Munoz, G and Anderson, T}, title = {Integrating human mobility and animal movement data reveals complex space-use between humans and white-tailed deer in urban environments.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {18588}, pmid = {40425680}, issn = {2045-2322}, support = {AP23OA000000C003//Animal and Plant Health Inspection Service/ ; AP23OA000000C003//Animal and Plant Health Inspection Service/ ; AP23OA000000C003//Animal and Plant Health Inspection Service/ ; AP23OA000000C003//Animal and Plant Health Inspection Service/ ; AP23OA000000C003//Animal and Plant Health Inspection Service/ ; AP23OA000000C003//Animal and Plant Health Inspection Service/ ; }, mesh = {Animals ; *Deer/physiology ; Humans ; Zoonoses/transmission ; Animals, Wild ; Ecosystem ; Maryland ; Cities ; Wasting Disease, Chronic/transmission ; COVID-19/transmission/epidemiology/virology ; SARS-CoV-2 ; Geographic Information Systems ; }, abstract = {Human expansion into wildlife habitats has increased the need to understand human-wildlife interactions, necessitating interdisciplinary approaches to assess zoonotic disease transmission risks and public health impacts. This study integrated fine-grained human foot traffic data with hourly GPS data from 38 white-tailed deer (Odocoileus virginianus), a species linked to SARS-CoV-2, brucella, and chronic wasting disease, in Howard County, Maryland. We explored spatial and temporal overlap between human and deer activity over 24 months (2018-2019) across a hexagonal tessellation with metrics like hourly popularity and visit counts. Negative binomial models were fitted to the visit counts of each deer and humans per tessellation area, using landscape features as predictors. A separate deer-only model included commercial human activity as another predictor. Spatial analysis showed deer and humans sharing spaces in the study area, with results indicating deer using more populated residential areas and areas with commercial activity. Temporal analysis showed deer avoiding commercial spaces during daytime but using them in late evening and early morning. These findings highlight the complex space use between species and the importance of integrating detailed human mobility and animal movement data when managing wildlife-human conflict and zoonotic disease transmission, particularly in urban areas with a high probability of deer-human interactions.}, } @article {pmid40425079, year = {2025}, author = {Mambully, S and Ramesh, V and Rani, S and Khatoon, M and Jayashree, A and Patil, AV and Palavesam, A and Sengupta, PP and Patil, SS and Suresh, KP}, title = {Genotype Patterns and Evolutionary Rates: Uncovering Japanese Encephalitis Virus Spread Across Asia's Climate Regions.}, journal = {Acta tropica}, volume = {}, number = {}, pages = {107676}, doi = {10.1016/j.actatropica.2025.107676}, pmid = {40425079}, issn = {1873-6254}, abstract = {Japanese Encephalitis Virus (JEV) is a highly endemic zoonotic virus, consistently found in Asia and parts of the Western Pacific, and it's a major cause of human encephalitis. JEV belongs to a family of antigenically related viruses such as West Nile Virus (WNV), Murray Valley encephalitis virus (MVEV), and Aichi Lake Fever Virus (ALFV) and is transmitted by mosquitoes. Persistent outbreaks of the disease necessitate detailed studies to understand their transmission dynamics and develop effective prevention strategies. This study explores the evolutionary dynamics and spatial transmission of JEV, concentrating on the envelope protein (E) structural gene sequences obtained from across Asia's diverse climatic regions. Evolutionary modeling of the JEV E gene revealed a higher evolutionary rate in tropical regions compared to temperate regions, with nucleotide substitution rates estimated at 1.12 × 10[-3] per site per year for tropical regions and 5.284 × 10[-4] for temperate regions. The time to the most recent common ancestor (tMRCA) was traced to 1796 from Korea for temperate regions, and 1865 from Indonesia for tropical regions. Among the five genotypes of JEV, Genotype I (GI) and III (GIII) were established all over Southeast Asia; moreover, GI revealed a higher evolutionary rate, reflecting its adaptability to diverse ecological niches. The phylogeographic analysis highlighted significant contributions to virus diffusion by China, Korea, and Japan in temperate zones and by Vietnam in tropical zones. By analyzing genetic sequences from various regions and time periods, this study delivered valuable intuitions into transmission pathways. The findings highlighted the necessity of ongoing surveillance and evolutionary monitoring to track the spread and emergence of novel variations of JEV, which are crucial not just for managing JEV outbreaks but also for guiding immunization programs and public health initiatives.}, } @article {pmid40419494, year = {2025}, author = {Jucker, T and Fischer, FJ and Chave, J and Coomes, DA and Caspersen, J and Ali, A and Loubota Panzou, GJ and Feldpausch, TR and Falster, D and Usoltsev, VA and Jackson, TD and Adu-Bredu, S and Alves, LF and Aminpour, M and Angoboy Ilondea, B and Anten, NPR and Antin, C and Askari, Y and Ayyappan, N and Banin, LF and Barbier, N and Battles, JJ and Beeckman, H and Bocko, YE and Bond-Lamberty, B and Bongers, F and Bowers, S and van Breugel, M and Chantrain, A and Chaudhary, R and Dai, J and Dalponte, M and Dimobe, K and Domec, JC and Doucet, JL and Dupuy Rada, JM and Duursma, RA and Enríquez, M and van Ewijk, KY and Farfán-Rios, W and Fayolle, A and Ferretti, M and Forni, E and Forrester, DI and Gilani, H and Godlee, JL and Haeni, M and Hall, JS and He, JK and Hemp, A and Hernández-Stefanoni, JL and Higgins, SI and Holdaway, RJ and Hussain, K and Hutley, LB and Ichie, T and Iida, Y and Jiang, HS and Joshi, PR and Kaboli, H and Kazempour Larsary, M and Kenzo, T and Kloeppel, BD and Kohyama, TS and Kunwar, S and Kuyah, S and Kvasnica, J and Lin, S and Lines, ER and Liu, H and Lorimer, C and Loumeto, JJ and Malhi, Y and Marshall, PL and Mattsson, E and Matula, R and Meave, JA and Mensah, S and Mi, X and Momo, ST and Moncrieff, GR and Mora, F and Muñoz, R and Nissanka, SP and Nur Hajar, ZS and O'Hara, KL and Pearce, S and Pelissier, R and Peri, PL and Ploton, P and Poorter, L and Pour, MJ and Pourbabaei, H and Ribeiro, SC and Ryan, C and Sanaei, A and Sanger, J and Schlund, M and Sellan, G and Shenkin, A and Sonké, B and Sterck, FJ and Svátek, M and Takagi, K and Trugman, AT and Vadeboncoeur, MA and Valipour, A and Vanderwel, MC and Vovides, AG and Waldner, P and Wang, W and Wang, LQ and Wirth, C and Woods, M and Xiang, W and de Aquino Ximenes, F and Xu, Y and Yamada, T and Zavala, MA and Zimmermann, NE}, title = {The global spectrum of tree crown architecture.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {4876}, pmid = {40419494}, issn = {2041-1723}, support = {NE/S01537X/1//RCUK | Natural Environment Research Council (NERC)/ ; }, mesh = {*Trees/anatomy & histology/physiology/classification ; Ecosystem ; *Plant Stems/anatomy & histology ; Photosynthesis ; Climate ; Biological Evolution ; Phylogeny ; }, abstract = {Trees can differ enormously in their crown architectural traits, such as the scaling relationships between tree height, crown width and stem diameter. Yet despite the importance of crown architecture in shaping the structure and function of terrestrial ecosystems, we lack a complete picture of what drives this incredible diversity in crown shapes. Using data from 374,888 globally distributed trees, we explore how climate, disturbance, competition, functional traits, and evolutionary history constrain the height and crown width scaling relationships of 1914 tree species. We find that variation in height-diameter scaling relationships is primarily controlled by water availability and light competition. Conversely, crown width is predominantly shaped by exposure to wind and fire, while also covarying with functional traits related to mechanical stability and photosynthesis. Additionally, we identify several plant lineages with highly distinctive stem and crown forms, such as the exceedingly slender dipterocarps of Southeast Asia, or the extremely wide crowns of legume trees in African savannas. Our study charts the global spectrum of tree crown architecture and pinpoints the processes that shape the 3D structure of woody ecosystems.}, } @article {pmid40417563, year = {2024}, author = {Foreman, MA and Ross, A and Burgess, APH and Myneni, S and Franklin, A}, title = {Barriers and Facilitators of Digital Health Use for Self-Management of Hypertensive Disorders by Black Pregnant Women.}, journal = {AMIA ... Annual Symposium proceedings. AMIA Symposium}, volume = {2024}, number = {}, pages = {433-442}, pmid = {40417563}, issn = {1942-597X}, mesh = {Humans ; Female ; Pregnancy ; *Self-Management ; *Black or African American ; *Hypertension, Pregnancy-Induced/therapy/ethnology ; Adult ; Interviews as Topic ; Telemedicine ; Digital Health ; White ; }, abstract = {Although digital health tools are increasingly common for managing health conditions, these applications are often developed without consideration of differences across user populations. A reproducible framework is needed to support tailoring applications to include cultural considerations, potentially leading to better adoption and more effective use. As a first step, this study captures a snapshot of Black women's barriers and facilitators in using digital health products for self-management of hypertensive disorders of pregnancy (HDP). One-on-one semi-structured interviews were conducted with 17 Black pregnant women with HDP. We established a unique model for cultural tailoring with these experiences using Black feminist theory and the CDC's Social-Ecological Model (SEM). 38 themes across the four levels of SEM were found through grounded theory. These themes can inform the feature development of a digital health intervention. Future work will instantiate and validate a framework that provides theoretical constructs for developing culturally tailored digital health interventions.}, } @article {pmid40359589, year = {2025}, author = {Silva, MKP and Nicoleti, VYU and Rodrigues, BDPP and Araujo, ASF and Ellwanger, JH and de Almeida, JM and Lemos, LN}, title = {Exploring deep learning in phage discovery and characterization.}, journal = {Virology}, volume = {609}, number = {}, pages = {110559}, doi = {10.1016/j.virol.2025.110559}, pmid = {40359589}, issn = {1096-0341}, mesh = {*Deep Learning ; *Bacteriophages/genetics/isolation & purification/classification ; Metagenomics/methods ; Computational Biology/methods ; Genome, Viral ; Neural Networks, Computer ; Metagenome ; Algorithms ; }, abstract = {Bacteriophages, or bacterial viruses, play diverse ecological roles by shaping bacterial populations and also hold significant biotechnological and medical potential, including the treatment of infections caused by multidrug-resistant bacteria. The discovery of novel bacteriophages using large-scale metagenomic data has been accelerated by the accessibility of deep learning (Artificial Intelligence), the increased computing power of graphical processing units (GPUs), and new bioinformatics tools. This review addresses the recent revolution in bacteriophage research, ranging from the adoption of neural network algorithms applied to metagenomic data to the use of pre-trained language models, such as BERT, which have improved the reconstruction of viral metagenome-assembled genomes (vMAGs). This article also discusses the main aspects of bacteriophage biology using deep learning, highlighting the advances and limitations of this approach. Finally, prospects of deep-learning-based metagenomic algorithms and recommendations for future investigations are described.}, } @article {pmid40258091, year = {2025}, author = {Hashem, I and Wang, J and Van Impe, JFM}, title = {A Discretized Overlap Resolution Algorithm (DORA) for resolving spatial overlaps in individual-based models of microbes.}, journal = {PLoS computational biology}, volume = {21}, number = {4}, pages = {e1012974}, doi = {10.1371/journal.pcbi.1012974}, pmid = {40258091}, issn = {1553-7358}, mesh = {*Algorithms ; *Models, Biological ; Computational Biology/methods ; Computer Simulation ; Biofilms/growth & development ; }, abstract = {Individual-based modeling (IbM) is an instrumental tool for simulating spatial microbial growth, with applications in both microbial ecology and biochemical engineering. Unlike Cellular Automata (CA), which use a fixed grid of cells with predefined rules for interactions, IbMs model the individual behaviors of cells, allowing complex population dynamics to emerge. IbMs require more detailed modeling of individual interactions, which introduces significant computational challenges, particularly in resolving spatial overlaps between cells. Traditionally, this is managed using arrays or kd-trees, which require numerous pairwise comparisons and become inefficient as population size increases. To address this bottleneck, we introduce the Discretized Overlap Resolution Algorithm (DORA), which employs a grid-based framework to efficiently manage overlaps. By discretizing the simulation space further and assigning circular cells to specific grid units, DORA transforms the computationally intensive pairwise comparison process into a more efficient grid-based operation. This approach significantly reduces the computational load, particularly in simulations with large cell populations. Our evaluation of DORA, through simulations of microbial colonies and biofilms under varied nutrient conditions, demonstrates its superior computational efficiency and ability to accurately capture microbial growth dynamics compared to conventional methods. DORA's grid-based strategy enables the modeling of densely populated microbial communities within practical computational timeframes, thereby expanding the scope and applicability of individual-based modeling.}, } @article {pmid40416669, year = {2025}, author = {Gaievskyi, S and Delfrate, N and Ragazzoni, L and Bahattab, A}, title = {Use of multi-criteria decision analysis (MCDA) to support decision-making during health emergencies: a scoping review.}, journal = {Frontiers in public health}, volume = {13}, number = {}, pages = {1584026}, pmid = {40416669}, issn = {2296-2565}, mesh = {Humans ; *Decision Support Techniques ; *Decision Making ; *Emergencies ; }, abstract = {BACKGROUND: The mismatch between the health needs of populations affected by emergencies and resources devoted to response is projected to further increase. Making the response more effective is one of the solutions to meet the growing needs. Multi-criteria decision analysis (MCDA) has been successfully used to increase effectiveness in various fields by supporting decision-making. However, no review of its application to all-hazard health emergencies has been done to date.

METHODS: A review of peer-reviewed English-language articles published since 2004 was conducted in May 2024 using Scopus, PubMed and Web of Science databases. The review focused on the empirical application of MCDA to support decision-making during health emergencies. The review was guided by the Joanna Briggs Institute methodology for scoping reviews and adhered to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses extension for Scoping Reviews. Quantitative data were analyzed using summary statistics and qualitative data were analyzed using content analysis.

RESULTS: Seventy-one articles were included after screening. The articles described the MCDA application to support a variety of decision problems related to health emergency management. However, the technique was mostly applied to infectious hazards management and only seldom to other hazards. The review also found a lack of standardized methodology for identifying alternatives and criteria, weighting, computation of model output, methods of dealing with uncertainty, and stakeholder engagement.

CONCLUSION: The review provides an overview of the current use of the MCDA approach to support decision-making in health emergency management and informs areas of future development. The review emphasizes that while MCDA is already used for infectious hazards, it is underutilized for other types of health emergencies. Developing tailored MCDA approaches for health emergencies, including defining evaluation criteria and stakeholder engagement, may improve uptake of the technique and benefit the efforts to meet the growing health needs of the population affected by emergencies, https://osf.io/6kd5s/.}, } @article {pmid40344154, year = {2025}, author = {Babič, J and Kunavar, T and Oztop, E and Kawato, M}, title = {Success-efficient/failure-safe strategy for hierarchical reinforcement motor learning.}, journal = {PLoS computational biology}, volume = {21}, number = {5}, pages = {e1013089}, doi = {10.1371/journal.pcbi.1013089}, pmid = {40344154}, issn = {1553-7358}, mesh = {Humans ; *Reinforcement, Psychology ; *Learning/physiology ; Male ; Female ; Computational Biology ; Movement/physiology ; Adult ; Young Adult ; Psychomotor Performance/physiology ; Motor Skills/physiology ; }, abstract = {Our study explores how ecological aspects of motor learning enhance survival by improving movement efficiency and mitigating injury risks during task failures. Traditional motor control theories mainly address isolated body movements and often overlook these ecological factors. We introduce a novel computational motor control approach, incorporating ecological fitness and a strategy that alternates between success-driven movement efficiency and failure-driven safety, akin to win-stay/lose-shift tactics. In our experiments, participants performed squat-to-stand movements under novel force perturbations. They adapted effectively through various adaptive motor control mechanisms to avoid falls, reducing failure rates rapidly. The results indicate a high-level ecological controller in human motor learning that switches objectives between safety and movement efficiency, depending on failure or success. This approach is supported by policy learning, internal model adaptation, and adaptive feedback control. Our findings offer a comprehensive perspective on human motor control, integrating risk management in a hierarchical reinforcement learning framework for real-world environments.}, } @article {pmid40091604, year = {2025}, author = {Tu, M and Liu, N and He, ZS and Dong, XM and Gao, TY and Zhu, A and Yang, JB and Zhang, SB}, title = {Integrative omics reveals mechanisms of biosynthesis and regulation of floral scent in Cymbidium tracyanum.}, journal = {Plant biotechnology journal}, volume = {23}, number = {6}, pages = {2162-2181}, doi = {10.1111/pbi.70025}, pmid = {40091604}, issn = {1467-7652}, support = {202403AC100032//Key Research and Development Program of Yunnan Province/ ; YNWR-CYJS-2020-023//High-level Talent Support Plan of Yunnan Province/ ; XDB31000000//Strategic Priority Research Program of the Chinese Academy of Sciences/ ; 32170393//National Natural Science Foundation of China/ ; 2024YFF1306703//National Key Research and Development Program of China/ ; 202201AU070123//Yunnan Fundamental Research Project/ ; 202301AT070306//Yunnan Fundamental Research Project/ ; }, mesh = {*Flowers/metabolism/genetics ; *Orchidaceae/genetics/metabolism ; *Odorants/analysis ; Terpenes/metabolism ; Gene Expression Regulation, Plant ; Transcriptome ; Volatile Organic Compounds/metabolism ; Genomics ; Plant Proteins/metabolism/genetics ; Multiomics ; }, abstract = {Flower scent is a crucial determiner in pollinator attraction and a significant horticultural trait in ornamental plants. Orchids, which have long been of interest in evolutionary biology and horticulture, exhibit remarkable diversity in floral scent type and intensity. However, the mechanisms underlying floral scent biosynthesis and regulation in orchids remain largely unexplored. In this study, we focus on floral scent in Cymbidium tracyanum, a wild species known for its strong floral fragrance and as a primary breeding parent of commercial Cymbidium hybrids. We present a chromosome-level genome assembly of C. tracyanum, totaling 3.79 Gb in size. Comparative genomic analyses reveal significant expansion of gene families associated with terpenoid biosynthesis and related metabolic pathways in C. tracyanum. Integrative analysis of genomic, volatolomic and transcriptomic data identified terpenoids as the predominant volatile components in the flowers of C. tracyanum. We characterized the spatiotemporal patterns of these volatiles and identified CtTPS genes responsible for volatile terpenoid biosynthesis, validating their catalytic functions in vitro. Dual-luciferase reporter assays, yeast one-hybrid assays and EMSA experiments confirmed that CtTPS2, CtTPS3, and CtTPS8 could be activated by various transcription factors (i.e., CtAP2/ERF1, CtbZIP1, CtMYB2, CtMYB3 and CtAP2/ERF4), thereby regulating the production of corresponding monoterpenes and sesquiterpenes. Our study elucidates the biosynthetic and regulatory mechanisms of floral scent in C. tracyanum, which is of great significance for the breeding of fragrant Cymbidium varieties and understanding the ecological adaptability of orchids. This study also highlights the importance of integrating multi-omics data in deciphering key horticultural traits in orchids.}, } @article {pmid40415801, year = {2025}, author = {Yang, P and Wang, X and Yang, J and Yan, B and Sheng, H and Li, Y and Yang, Y and Wang, J}, title = {AI-Driven Multiscale Study on the Mechanism of Polygonati Rhizoma in Regulating Immune Function in STAD.}, journal = {ACS omega}, volume = {10}, number = {19}, pages = {19770-19796}, pmid = {40415801}, issn = {2470-1343}, abstract = {Polygonati Rhizoma, a traditional Chinese medicine, has demonstrated immunomodulatory and anticancer properties, yet its precise mechanisms in stomach adenocarcinoma (STAD) remain underexplored. This study aims to uncover the multitarget mechanisms of Polygonati Rhizoma in regulating the tumor immune microenvironment in STAD using artificial intelligence (AI)-driven network pharmacology, bioinformatics, and single-cell RNA sequencing, offering new insights into its immunotherapeutic potential. This study harnessed the power of AI to unravel the molecular mechanisms underlying Polygonati Rhizoma's effects. AI-driven methodologies screened 38 putative constituents, retaining 8 based on ADME criteria. Machine Learning algorithms predicted potential targets, which were cross-referenced with 5,569 immune-related genes from GeneCards, revealing 52 immune-associated targets. Differential expression analysis of the STAD data set identified 18 overlapping DEGs with prognostic significance and immune cell infiltration correlations. Key targets (AKT1, TP53, PTGS2 and VEGFA) emerged as central nodes in the network, with AI-assisted molecular docking confirming strong binding affinities, particularly between diosgenin and these core proteins. Molecular dynamics simulations further validated these interactions. Single-cell RNA sequencing revealed distinct target-gene expression patterns across malignant, stromal, and immune cell subsets in digestive-system tumors. In vitro, Polygonati Rhizoma extract significantly inhibited HGC-27 cell viability and increased intracellular ROS levels. These findings underscore the critical role of AI in integrating multiscale analyses, unveiling a multitarget immunomodulatory and antitumor mechanism for Polygonati Rhizoma in STAD, and providing a foundation for future preclinical and clinical studies.}, } @article {pmid40414987, year = {2025}, author = {Jia, L and Liu, Z and Li, Y}, title = {Spatiotemporal dynamics of rural settlement evolution in Guangdong Province, China.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {18244}, pmid = {40414987}, issn = {2045-2322}, support = {23BDJ019//National Planning Office of Philosophy and Social Science/ ; 23BDJ019//National Planning Office of Philosophy and Social Science/ ; }, mesh = {China ; *Rural Population/statistics & numerical data ; Humans ; *Urbanization/trends ; Spatio-Temporal Analysis ; *Population Dynamics ; Socioeconomic Factors ; Industrial Development ; Geographic Information Systems ; }, abstract = {This study analyzes the spatiotemporal dynamics of rural settlement evolution in Guangdong Province, China, examining their transformation amid rapid urbanization and industrialization over the past 20 years. Rural settlements serve as primary spatial carriers for production and living activities, embodying multiple functions including production, living, ecological, and cultural aspects. Using GIS-based analytical tools, including landscape pattern indices, average nearest neighbor index, kernel density estimation, and geographical detector methods, we examined settlement evolution patterns and their driving factors. Results show a continuous decline in settlement numbers, while patch areas exhibited a U-shaped trend of decreasing then increasing. Settlement patterns shifted from "reduction" to "integration", with intensifying spatial agglomeration over time. The Pearl River Delta and Eastern Guangdong regions followed similar trajectories, reflecting the impact of urbanization and industrialization on rural development. Multiple factors, including natural conditions, socioeconomic variables, and locational accessibility, drove these changes. The spatial distribution of rural settlements demonstrates an overall trend of agglomeration, which has gradually intensified over time, leading to significant variations in settlement density across different regions. The findings reveal significant regional disparities and temporal changes in settlement patterns, highlighting the complex interplay between rural transformation and urban development. This research contributes to understanding rural transformation processes in developing countries and emphasizes the need for differentiated approaches in spatial planning and rural revitalization strategies to address the challenges of disordered land expansion and population hollowing while promoting sustainable rural development.}, } @article {pmid40414334, year = {2025}, author = {Dou, X and Liu, Q and Fan, Q and Guo, J and Qi, W}, title = {Comprehensive Analysis of Common Heavy Metals in the Yellow River Over 20 Years: Spatiotemporal distribution, Migration Characteristics, Traceability, and Potential Risk Evaluation.}, journal = {Environmental research}, volume = {}, number = {}, pages = {121931}, doi = {10.1016/j.envres.2025.121931}, pmid = {40414334}, issn = {1096-0953}, abstract = {Heavy metal pollution posed a great threat to the global aquatic ecological environment, especially in the Yellow River where the utilization rate of water resources was as high as 80%. This study addressed the spatiotemporal distribution, sources, and ecological risks of seven heavy metals (As, Cd, Cr, Cu, Ni, Pb, Zn) in the Yellow River by analyzing historical data collected from 2000 to 2020. The annual heavy metal fluxes increased from Qinghai to Henan section, then decreased from Henan to Shandong section. Similarly, concentrations of Cu, Ni, Pb, and Zn peaked in the sediments of the Henan section. These trends might be attributed to the interception effects of the Xiaolangdi and Sanmenxia Dams. The annual fluxes from 2016-2020 increased by an average of 162.6% compared to that from 2011-2015, likely reflecting the impact of ongoing economic growth (33.36%) and SS increase (69.68%). The annual fluxes of SS demonstrated a significant correlation with all heavy metal fluxes, underscoring their role as a critical transport medium in aquatic ecosystem. The fluxes of Cd and Pb were most strongly influenced by human factors. While most metals in surface water present negligible risks to aquatic life, Cd in sediments presents a considerable ecological threat. Furthermore, the highest potential ecological risk index (RI) was observed in the river sections in Gansu and Inner Mongolia, mainly due to Cd, which contributed up to 85.87%. The findings establish a fundamental framework for safeguarding the aquatic ecosystem of the Yellow River and managing its heavy metal contamination.}, } @article {pmid40413228, year = {2025}, author = {Fan, J and Zhang, Y and Nie, X and Liu, Y and Wei, S and Peng, H and Li, H and Zhang, M and Ning, L and Wang, S and Qin, L and Zheng, Y and Xing, Y}, title = {Comprehensive curation and validation of genomic datasets for chestnut.}, journal = {Scientific data}, volume = {12}, number = {1}, pages = {860}, pmid = {40413228}, issn = {2052-4463}, mesh = {*Fagaceae/genetics ; *Genome, Plant ; Genomics ; Databases, Genetic ; Molecular Sequence Annotation ; Data Curation ; }, abstract = {The Chinese chestnut (Castanea mollissima) stands out as a plant with significant ecological and economic value, excellent nutritional quality and natural resistance to pests and diseases. Recent strides in high-throughput techniques have enabled the continuous accumulation of genomic data on chestnuts, presenting a promising future for genetic research and advancing traits in this species. To facilitate the accessibility and utility of this data, we have curated and analyzed a collection of genomic datasets for eight Castanea species, including functional annotations, 213 RNA-Seq samples, and 330 resequencing samples. These datasets are publicly available on Figshare and are also available through other platforms such as GEO and EVA, providing a valuable resource for researchers studying Castanea genetics, functional genomics, and evolutionary biology. Furthermore, the datasets are integrated into the Castanea Genome Database (CGD, http://castaneadb.net), which serves as a complementary platform, offering advanced data mining and analysis tools, including BLAST, Batch Query, GO/KEGG Enrichment Analysis, and Synteny Viewer, to enhance the usability of the curated datasets.}, } @article {pmid40412934, year = {2025}, author = {Zhu, Q and Cai, Y and Hu, Z}, title = {Effects of bactericides and sulphate reducing bacteria addition on acidification and microbial community structure of newly produced coal gangue.}, journal = {Journal of environmental sciences (China)}, volume = {156}, number = {}, pages = {311-320}, doi = {10.1016/j.jes.2024.06.024}, pmid = {40412934}, issn = {1001-0742}, mesh = {*Coal ; Sulfates/metabolism ; *Bacteria/metabolism ; Hydrogen-Ion Concentration ; *Microbiota ; *Soil Microbiology ; }, abstract = {Microbiologically driven acidic pollution of coal gangue has become a major environmental problem in coal gangue dumps in coal mining areas. Addition of bactericides and sulphate reducing bacteria (SRB) is an effective means to control the acidic pollution of coal gangue, but their mechanism of action has not been fully investigated. By adding bactericide, SRB and bactericide-SRB to the newly produced coal gangue, respectively, the effects of these treatments on the microbial community structure were observed. Changes in pH and electrical conductivity (EC) of the gangue leaching solution, as well as the microbial community composition and functional abundance on the gangue surface were analysed by leaching simulation experiments and 16S rRNA sequencing. The results showed that (1) the addition of bactericide-SRB was the most effective treatment to elevate pH before 8 d, while the addition of SRB performed best after 22 d (2) The addition of bactericide and SRB drastically changed the microbial community structure on the gangue surface. Simultaneous addition of both had the best inhibitory effect on pathogenic bacteria and Thiobacillus. (3) All three treatments promote higher abundance of genes related to nitrogen cycling, but reflected in different gene functions. Microorganisms with sulfate respiration function in the experimental group all showed different increases. The abundance of other sulfur cycle genes decreased substantially. However, Human Pathogens All had higher abundance than control check (CK) in each treatment, which may indicate that the addition of either bactericides or SRB increases the risk of microbial pathogenicity to humans.}, } @article {pmid40410961, year = {2025}, author = {Zhang, L and Zhang, L and Gao, S and Huang, C and Dai, Q}, title = {Structural balance and evolution of cooperation in a population with hybrid interactions.}, journal = {Physical review. E}, volume = {111}, number = {4-1}, pages = {044309}, doi = {10.1103/PhysRevE.111.044309}, pmid = {40410961}, issn = {2470-0053}, abstract = {This study explores the evolution of cooperation in populations with mixed pairwise and three-body interactions, investigating the impact of higher-order interaction density ρ and individual interaction preference α. Our results reveal that sparse higher-order interactions markedly boost cooperation, exhibiting two critical phase transitions as ρ changes. These transitions underscore the delicate equilibrium needed for optimal cooperation, as excessive higher-order interactions can diminish returns. The preference parameter α significantly influences cooperation sustainability, with intermediate values maximizing cooperative outcomes, particularly when the temptation to defect r is not strong. Crucially, our findings demonstrate that hybrid social dilemmas structurally encode emergent cooperation pathways that are unattainable within homogeneous interaction frameworks, emphasizing the importance of modeling mixed interactions to capture real-world complexity. These insights offer valuable guidance for designing systems aimed at promoting cooperative behavior across social, ecological, and artificial domains.}, } @article {pmid40408306, year = {2025}, author = {Bukat, A and Bukowicki, M and Bykowski, M and Kuczkowska, K and Nowakowski, S and Śliwińska, A and Kowalewska, Ł}, title = {GRANA: An AI-based tool for accelerating chloroplast grana nanomorphology analysis using hybrid intelligence.}, journal = {Plant physiology}, volume = {}, number = {}, pages = {}, doi = {10.1093/plphys/kiaf212}, pmid = {40408306}, issn = {1532-2548}, abstract = {Grana are fundamental structural units of the intricate chloroplast membrane network. Investigating their nanomorphology is essential for understanding photosynthetic efficiency regulation. Here, we present GRANA (Graphical Recognition and Analysis of Nanostructural Assemblies), an AI-enhanced, user-friendly software tool that recognizes grana on thylakoid network electron micrographs and generates a complex set of their structural parameters. GRANA employs three artificial neural networks of different architectures and binds them in a one-click workflow. Its output is designed to facilitate hybrid intelligence analysis, securing fast and reliable results from large datasets. The GRANA tool is over 100 times faster compared with currently used manual approaches. As a proof of concept, we have successfully applied GRANA software to diverse grana structures across different land plant species grown under various conditions, demonstrating the wide range of potential applications for our software. GRANA tool supports large-scale analysis of grana nanomorphological features, facilitating advancements in photosynthesis-oriented studies.}, } @article {pmid40408146, year = {2025}, author = {Fontanarrosa, P and Clare, C and Fedorec, AJH and Barnes, CP}, title = {MIMIC: a Python package for simulating, inferring, and predicting microbial community interactions and dynamics.}, journal = {Bioinformatics (Oxford, England)}, volume = {41}, number = {5}, pages = {}, doi = {10.1093/bioinformatics/btaf174}, pmid = {40408146}, issn = {1367-4811}, support = {BB/W013770/1//Bioengineered Cells & Systems/ ; BB/T008709/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {*Software ; *Microbiota ; Bayes Theorem ; *Computational Biology/methods ; *Microbial Interactions ; Machine Learning ; Computer Simulation ; }, abstract = {SUMMARY: The study of microbial communities is vital for understanding their impact on environmental, health, and technological domains. The Modelling and Inference of MICrobiomes Project (MIMIC) introduces a Python package designed to advance the simulation, inference, and prediction of microbial community interactions and dynamics. Addressing the complex nature of microbial ecosystems, MIMIC integrates a suite of mathematical models, including previously used approaches such as Generalized Lotka-Volterra (gLV), Gaussian Processes (GP), and Vector Autoregression (VAR) plus newly developed models for integrating multi-omic data, to offer a versatile framework for analyzing microbial dynamics. By leveraging Bayesian inference and machine learning techniques, MIMIC provides the ability to infer the dynamics of microbial communities from empirical data, facilitating a deeper understanding of their complex biological processes, unveiling possible unknown ecological interactions, and enabling the design of microbial communities. Such insights could help to advance microbial ecology research, optimizing biotechnological applications, and contribute to environmental sustainability and public health strategies. MIMIC is designed for flexibility and ease of use, aiming to support researchers and practitioners in microbial ecology and microbiome research.

MIMIC is freely available under the MIT License at https://github.com/ucl-cssb/MIMIC. It is implemented in Python (version 3.7 or higher) and is compatible with Windows, macOS, and Linux operating systems. MIMIC depends on standard Python libraries including NumPy, SciPy, and PyMC. Comprehensive examples and tutorials (including the main text demonstrations) are provided as Jupyter notebooks in the examples/directory and at the MIMIC Docs website, along with detailed installation instructions and real-world data use cases. The software will remain freely available for at least two years following publication. A code snapshot for this publication is also available at Zenodo: https://doi.org/10.5281/zenodo.15149003.}, } @article {pmid40407930, year = {2025}, author = {Bate, JB and Dagamac, NHA}, title = {Wallow land suitability assessment using GIS-based multicriteria decision-making framework.}, journal = {Environmental monitoring and assessment}, volume = {197}, number = {6}, pages = {668}, pmid = {40407930}, issn = {1573-2959}, mesh = {*Geographic Information Systems ; *Conservation of Natural Resources/methods ; Animals ; *Environmental Monitoring/methods ; Ecosystem ; Philippines ; Decision Making ; Biodiversity ; }, abstract = {Protected areas are the frontlines of biodiversity conservation, featuring critical landscapes and microhabitats that are fitted for the survival of the organisms that have restricted populations. The determination of land suitability and habitat connectivity in these protected areas are important for species with specialized adaptive behavior that requires favorable conditions to survive. The Bubalus mindorensis is a critically endangered bovine of the Philippines which utilizes mud or water puddles to address heat stress through body submersion, known as wallowing. With Mts. Iglit-Baco National Park (MIBNP) harboring the largest remaining subpopulation of the tamaraw, the preservation of its natural landscapes is critical for tamaraw survival. Here, the potential wallows in MIBNP were determined using the weighted overlay analysis (WOA) assisted by the analytical hierarchy process (AHP). Using environmental variables that were influential to the creation of wallows, an equal-weighed scenario and an AHP-assisted scenario wallow suitability map was generated. Moderate and highly suitable areas were found at the north-central portion of the mountain, coinciding with the current and future conservation zones of the tamaraw, whereas low suitable areas dominate the other half, aggregating at the corners due to build areas and agriculture. The result of the study provides supplementary information in constructing future conservation strategies for an endemic species with global importance, particularly in its possible range expansion within the park. Furthermore, this study provides a framework for future conservation efforts, which helps in the management of critical landscapes for species with specialized adaptive behaviors through GIS-based multicriteria decision-making.}, } @article {pmid40407563, year = {2025}, author = {Araujo, ACB and Souza, OF and Kersanach, BB and Mozzer, JSC and Feitosa, VL and Brandão, VA and Alencar, FEC and Oliveira, NS and Silva, AVBD and Abreu, LC}, title = {Trends in Congenital Syphilis Incidence and Mortality in Brazil's Southeast Region: A Time-Series Analysis (2008-2022).}, journal = {Epidemiologia (Basel, Switzerland)}, volume = {6}, number = {2}, pages = {}, pmid = {40407563}, issn = {2673-3986}, support = {182023//Fundação de Amparo à Pesquisa do Espírito Santo/ ; }, abstract = {Congenital syphilis (CS) is an important infectious cause of miscarriage, stillbirth, and neonatal morbidity and mortality. Despite the advances in diagnosis and treatment, CS continues to challenge health systems with increasing incidence and mortality rates in recent years worldwide. Given this, the present study aims to comparatively analyze the temporal trends in CS incidence and mortality in Brazil's Southeast Region from 2008 to 2022. This is an ecological time-series study using secondary data on congenital syphilis from the states of Espírito Santo, Minas Gerais, Rio de Janeiro, and São Paulo. The data was extracted from the Brazilian Health System Informatics Department. Incidence and mortality rates were calculated per 100,000 live births. Joinpoint regression models were employed to identify trends in annual percentage change and average annual percentage change with 95% confidence intervals. The temporal trend of CS incidence in Brazil's Southeast Region increased 12.8% between 2008 and 2022. Minas Gerais, São Paulo, Espírito Santo, and Rio de Janeiro showed increasing temporal trends of 21.4%, 14.1%, 14.0%, and 10.9%, respectively. The temporal trend of CS mortality in Brazil's Southeast Region rose 11.9% between 2008 and 2022. Minas Gerais, São Paulo, and Rio de Janeiro exhibited increasing mortality temporal trends of 21.9%, 20.8%, and 10.1%, respectively. In contrast, Espírito Santo showed reduced mortality, with no deaths in 2021 and 2022. The temporal trend of CS incidence increased in all states of Brazil's Southeast Region between 2008 and 2022, highlighting the need to reassess control measures. The temporal trend of CS mortality also increased during the same period, except in Espírito Santo. Considering that CS is preventable with adequate prenatal care and low-cost measures, these findings can serve as instruments to support strengthening public health policies.}, } @article {pmid40407387, year = {2025}, author = {Wang, M and Chen, X and Liu, M and Luo, H and Zhang, S and Guo, J and Wang, J and Zhou, L and Zhang, N and Li, H and Wang, C and Li, L and Wang, Z and Wang, H and Guo, Z and Li, Y and Wang, Y}, title = {Decoding herbal combination models through systematic strategies: insights from target information and traditional Chinese medicine clinical theory.}, journal = {Briefings in bioinformatics}, volume = {26}, number = {3}, pages = {}, pmid = {40407387}, issn = {1477-4054}, support = {2021CXGC010509//2021 Shandong Provincial Key RD Program (Major Technological Innovation Project)/ ; 2022ZDYF0410//Key RD Projects of Ningxia Hui Nationality Autonomous Region in 2022/ ; }, mesh = {*Medicine, Chinese Traditional/methods ; *Drugs, Chinese Herbal/therapeutic use/pharmacology ; Humans ; Arthritis, Rheumatoid/drug therapy ; Databases, Factual ; Animals ; }, abstract = {Traditional Chinese medicine (TCM) utilizes intricate herbal formulations that exemplify the principles of compatibility and synergy. However, the rapid proliferation of herbal data has resulted in redundant information, complicating the understanding of their potential mechanisms. To address this issue, we first established a comprehensive database that encompasses 992 herbs, 18 681 molecules, and 2168 targets. Consequently, we implemented a multi-network strategy based on a core information screening method to elucidate the highly intertwined relationships among the targets of various herbs and to refine herbal target information. Within a non-redundant network framework, separation and overlap analysis demonstrated that the networking of herbs preserves essential clinical information, including their properties, meridians, and therapeutic classifications. Furthermore, two notable trends emerged from the statistical analyses of classical TCM formulas: the separation of herbs and the overlap between herbs and diseases. This phenomenon is termed the herbal combination model (HCM), validated through statistical analyses of two representative case studies: the common cold and rheumatoid arthritis. Additionally, in vivo and in vitro experiments with the new formula YanChuanQin (YanHuSuo-Corydalis Rhizoma, ChuanWu-Aconiti Radix, and QinJiao-Gentianae Macrophyllae Radix) for acute gouty arthritis further support the HCM. Overall, this computational method provides a systematic network strategy for exploring herbal combinations in complex and poorly understood diseases from a non-redundant perspective.}, } @article {pmid40341906, year = {2025}, author = {Shoemaker, WR and Sánchez, Á and Grilli, J}, title = {Macroecological patterns in experimental microbial communities.}, journal = {PLoS computational biology}, volume = {21}, number = {5}, pages = {e1013044}, doi = {10.1371/journal.pcbi.1013044}, pmid = {40341906}, issn = {1553-7358}, mesh = {*Models, Biological ; *Ecology/methods ; Biodiversity ; Ecosystem ; *Microbiota/physiology ; Computational Biology ; }, abstract = {Ecology has historically benefited from the characterization of statistical patterns of biodiversity within and across communities, an approach known as macroecology. Within microbial ecology, macroecological approaches have identified universal patterns of diversity and abundance that can be captured by effective models. Experimentation has simultaneously played a crucial role, as the advent of high-replication community time-series has allowed researchers to investigate underlying ecological forces. However, there remains a gap between experiments performed in the laboratory and macroecological patterns documented in natural systems, as we do not know whether these patterns can be recapitulated in the lab and whether experimental manipulations produce macroecological effects. This work aims at bridging the gap between experimental ecology and macroecology. Using high-replication time-series, we demonstrate that microbial macroecological patterns observed in nature exist in a laboratory setting, despite controlled conditions, and can be unified under the Stochastic Logistic Model of growth (SLM). We found that demographic manipulations (e.g., migration) impact observed macroecological patterns. By modifying the SLM to incorporate said manipulations alongside experimental details (e.g., sampling), we obtain predictions that are consistent with macroecological outcomes. By combining high-replication experiments with ecological models, microbial macroecology can be viewed as a predictive discipline.}, } @article {pmid40407023, year = {2025}, author = {Pang, D and Zhu, R and Zhao, H and Wang, T}, title = {Probabilistic exponential family inverse regression and its applications.}, journal = {Biometrics}, volume = {81}, number = {2}, pages = {}, doi = {10.1093/biomtc/ujaf065}, pmid = {40407023}, issn = {1541-0420}, support = {12222111//National Natural Science Foundation of China/ ; 12331009//National Natural Science Foundation of China/ ; }, mesh = {Humans ; Algorithms ; Computer Simulation ; *Models, Statistical ; Regression Analysis ; Likelihood Functions ; *Biometry/methods ; Data Interpretation, Statistical ; }, abstract = {Rapid advances in high-throughput sequencing technologies have led to the fast accumulation of high-dimensional data, which is harnessed for understanding the implications of various factors on human disease and health. While dimension reduction plays an essential role in high-dimensional regression and classification, existing methods often require the predictors to be continuous, making them unsuitable for discrete data, such as presence-absence records of species in community ecology and sequencing reads in single-cell studies. To identify and estimate sufficient reductions in regressions with discrete predictors, we introduce probabilistic exponential family inverse regression (PrEFIR), assuming that, given the response and a set of latent factors, the predictors follow one-parameter exponential families. We show that the low-dimensional reductions result not only from the response variable but also from the latent factors. We further extend the latent factor modeling framework to the double exponential family by including an additional parameter to account for the dispersion. This versatile framework encompasses regressions with all categorical or a mixture of categorical and continuous predictors. We propose the method of maximum hierarchical likelihood for estimation, and develop a highly parallelizable algorithm for its computation. The effectiveness of PrEFIR is demonstrated through simulation studies and real data examples.}, } @article {pmid40406849, year = {2025}, author = {Han, Y and Cai, J and Chen, Y and Zhang, Y and Jin, LN and Chen, T and Li, J and Zhang, G and Chen, J}, title = {Concurrent Formation of Low-Maturity EC and BrC in Biomass and Coal Burning: O-PAH as a Precursor.}, journal = {Environmental science & technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.4c13299}, pmid = {40406849}, issn = {1520-5851}, abstract = {Black carbon (BC) significantly influences climate change through light absorption. Traditional emission inventories equate BC with elemental carbon (EC) and overlook the variability in its properties across sources, leading to uncertainties in climate predictions. This study shows that EC from solid fuel combustion contains substantial low-maturity EC (char), whose emissions increase alongside the light absorption of soluble organic carbon (OC) as the fuel aromaticity rises. Concurrently, the abundance of oxygenated polycyclic aromatic hydrocarbons (O-PAHs) in soluble OC also increases. This suggests that char and brown carbon (BrC) share similar formation pathways with O-PAHs as key precursors. Time-resolved analysis during combustion cycles revealed a significant positive correlation between O-PAHs, the light absorption of soluble OC, and char emissions, further supporting this shared pathway. The nonbonding orbitals in BrC and char facilitate n → π* transitions in the visible region, which are more wavelength-dependent than the π → π* transition in high-maturity EC (soot). This study highlights char as a light-absorbing intermediate, influencing light absorption of EC emitted from solid fuel combustion. These insights into the formation pathways and optical properties of carbonaceous aerosols enhance our understanding of their climate impacts and underscore the need to differentiate between char and soot in climate models to improve accuracy.}, } @article {pmid40404926, year = {2025}, author = {Pringle, S and Dallimer, M and Goddard, MA and Le Goff, LK and Hart, E and Langdale, SJ and Fisher, JC and Abad, SA and Ancrenaz, M and Angeoletto, F and Auat Cheein, F and Austen, GE and Bailey, JJ and Baldock, KCR and Banin, LF and Banks-Leite, C and Barau, AS and Bashyal, R and Bates, AJ and Bicknell, JE and Bielby, J and Bosilj, P and Bush, ER and Butler, SJ and Carpenter, D and Clements, CF and Cully, A and Davies, KF and Deere, NJ and Dodd, M and Drinkwater, R and Driscoll, DA and Dutilleux, G and Dyrmann, M and Edwards, DP and Farhadinia, MS and Faruk, A and Field, R and Fletcher, RJ and Foster, CW and Fox, R and Francksen, RM and Franco, AMA and Gainsbury, AM and Gardner, CJ and Giorgi, I and Griffiths, RA and Hamaza, S and Hanheide, M and Hayward, MW and Hedblom, M and Helgason, T and Heon, SP and Hughes, KA and Hunt, ER and Ingram, DJ and Jackson-Mills, G and Jowett, K and Keitt, TH and Kloepper, LN and Kramer-Schadt, S and Labisko, J and Labrosse, F and Lawson, J and Lecomte, N and de Lima, RF and Littlewood, NA and Marshall, HH and Masala, GL and Maskell, LC and Matechou, E and Mazzolai, B and McConnell, A and Melbourne, BA and Miriyev, A and Nana, ED and Ossola, A and Papworth, S and Parr, CL and Payo-Payo, A and Perry, G and Pettorelli, N and Pillay, R and Potts, SG and Prendergast-Miller, MT and Qie, L and Rolley-Parnell, P and Rossiter, SJ and Rowcliffe, M and Rumble, H and Sadler, JP and Sandom, CJ and Sanyal, A and Schrodt, F and Sethi, SS and Shabrani, A and Siddall, R and Smith, SC and Snep, RPH and Soulsbury, CD and Stanley, MC and Stephens, PA and Stephenson, PJ and Struebig, MJ and Studley, M and Svátek, M and Tang, G and Taylor, NK and Umbers, KDL and Ward, RJ and White, PJC and Whittingham, MJ and Wich, S and Williams, CD and Yakubu, IB and Yoh, N and Zaidi, SAR and Zmarz, A and Zwerts, JA and Davies, ZG}, title = {Opportunities and challenges for monitoring terrestrial biodiversity in the robotics age.}, journal = {Nature ecology & evolution}, volume = {}, number = {}, pages = {}, pmid = {40404926}, issn = {2397-334X}, abstract = {With biodiversity loss escalating globally, a step change is needed in our capacity to accurately monitor species populations across ecosystems. Robotic and autonomous systems (RAS) offer technological solutions that may substantially advance terrestrial biodiversity monitoring, but this potential is yet to be considered systematically. We used a modified Delphi technique to synthesize knowledge from 98 biodiversity experts and 31 RAS experts, who identified the major methodological barriers that currently hinder monitoring, and explored the opportunities and challenges that RAS offer in overcoming these barriers. Biodiversity experts identified four barrier categories: site access, species and individual identification, data handling and storage, and power and network availability. Robotics experts highlighted technologies that could overcome these barriers and identified the developments needed to facilitate RAS-based autonomous biodiversity monitoring. Some existing RAS could be optimized relatively easily to survey species but would require development to be suitable for monitoring of more 'difficult' taxa and robust enough to work under uncontrolled conditions within ecosystems. Other nascent technologies (for instance, new sensors and biodegradable robots) need accelerated research. Overall, it was felt that RAS could lead to major progress in monitoring of terrestrial biodiversity by supplementing rather than supplanting existing methods. Transdisciplinarity needs to be fostered between biodiversity and RAS experts so that future ideas and technologies can be codeveloped effectively.}, } @article {pmid40404775, year = {2025}, author = {Wang, J and Xu, Y and Zhu, H and Chen, C and Zhao, Y and Wang, Y}, title = {CheloniansTraits: a comprehensive trait database of global turtles and tortoises.}, journal = {Scientific data}, volume = {12}, number = {1}, pages = {840}, pmid = {40404775}, issn = {2052-4463}, support = {32271734//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {*Turtles/anatomy & histology ; Animals ; Databases, Factual ; Biological Evolution ; Life History Traits ; Conservation of Natural Resources ; }, abstract = {Turtles and tortoises (chelonians) possess a variety of ecological characteristics, including long lifespans and protective shells, which have enabled them to survive and adapt to environmental challenges since the Triassic period. However, many characteristics of chelonians have turned into disadvantages for their populations in the Anthropocene. Currently, there remains a lack of comprehensive data on the morphological, life-history, and ecological characteristics of all chelonians on a global scale. Consequently, our study aims to collect a complete trait database of global chelonians (CheloniansTraits), which may help bridge the knowledge gap regarding the identity and ecology of global chelonians and thereby aiding future conservation endeavors. We compiled 69 trait data for all 358 recognized chelonian species, utilizing ~2,000 literature sources, covering 33 morphological, 21 life-history, 7 ecological traits, and 8 conservation information. This database serves as a uniquely valuable resource for exploring evolutionary, biogeographical, and ecological inquiries related to chelonians, as well as elucidating key aspects of ecological strategy variation among species.}, } @article {pmid40404082, year = {2025}, author = {Zhang, S and Qiang, J and Liu, H and Zhou, J and Li, J and Chen, J and Ding, Q and Qian, K}, title = {An efficient and precise (micro)plastic identification method: feature infrared spectra extraction based on EIS-VIP-CARS and ANN modeling.}, journal = {Environmental research}, volume = {}, number = {}, pages = {121916}, doi = {10.1016/j.envres.2025.121916}, pmid = {40404082}, issn = {1096-0953}, abstract = {Understanding microplastics' (MPs) ecological impact necessitates their precise identification. To address the issue of the competitive adaptive reweighted sampling (CARS) algorithm extracting numerous feature wavenumber points (FWPs) that often miss transmittance peaks (TPs), resulting in high computational load and low accuracy in artificial neural network (ANN) models, this study introduces a novel approach. Initially, the equal interval sampling (EIS) method is employed to capture the main information of the full spectra. Subsequently, the variable importance in projection (VIP) is innovatively integrated into the CARS to formulate the EIS-VIP-CARS method for extracting feature spectra (FS). Using 20 typical MPs as the subjects, this study compares the identification performance of ANN models using full-spectra, EIS, CARS, EIS-CARS, VIP-CARS, and EIS-VIP-CARS. The results show that VIP-CARS extracts 128 FWPs, a reduction of 49.41% compared to CARS. Moreover, the distribution of these FWPs is more concentrated around the TPs and their vicinity. The accuracy of MPs by the ANN model based on VIP-CARS is generally higher than that of CARS. EIS-VIP-CARS extracts 55 FWPs, representing a reduction of 58.65% and 57.03% compared to EIS and VIP-CARS, respectively. The overall distribution of these points closely aligns with the distribution of functional groups. The ANN model based on EIS-VIP-CARS can achieve a similar accuracy for MPs as the model based on EIS, both greater than 99%, demonstrating good generalization ability. The accuracies of the MNN and convolutional neural network (CNN) models are higher than those of the SNN model, but the modeling time is longer. The ANN model established using the EIS-VIP-CARS is an efficient and precise approach for the identification of MPs in infrared spectroscopy. This study provides technical references for the research on the environmental behavior of MPs and is also of significant importance for the classification and management of plastic waste.}, } @article {pmid40403917, year = {2025}, author = {Wang, H and Lei, W and Wu, M and Guo, J and He, S and Shen, N and Li, C and Wang, L}, title = {Spatial distribution and ecological risks of neonicotinoids in surface waters of Eastern China.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {378}, number = {}, pages = {126507}, doi = {10.1016/j.envpol.2025.126507}, pmid = {40403917}, issn = {1873-6424}, abstract = {Over the past two decades, neonicotinoid insecticides (NNIs) have been extensively used in agricultural activities. Due to its high-water solubility, NNIs are primarily found in surface waters, contaminating them and posing significant ecological risks. However complex watershed environments pose challenges in elucidating the pollution characteristics and ecological risks of NNIs in large-scale waters. This study focused on typical surface waters in Eastern China, exploring the spatial characteristics, driving factors, and ecological risks of NNIs. The total concentration of NNIs (Σ8NNIs) ranges from 2.3 ng/L to 1377.8 ng/L. This concentration range exceeded the European water environment toxicity thresholds, with 86 of the sites surpassing the chronic toxicity threshold (8.3 ng/L) and 14 of the sites exceeding the acute toxicity threshold (200 ng/L). Thiamethoxam (THIA), imidacloprid (IMI), and dinotefuran (DIN) were detected with high rates and concentrations. Spatially, the Σ8NNIs in the Yangtze River (YZ, 140.0 ng/L) are significantly higher than in the north of Beijing-Hangzhou Grand Canal (BHN, 62.8 ng/L), Taihu Lake (TH, 36.6 ng/L), and Taihu Basin (THB, 21.9 ng/L). Moreover, Σ8NNIs in the south of Beijing-Hangzhou Grand Canal (BHS, 326.5 ng/L) are significantly higher than in BHN (62.8 ng/L). The spatial distribution of NNI components indicated that DIN and THIA dominated in YZ (37 %), THIA (34 %) and DIN (20 %) in BHN, IMI (53 %) in BHS, DIN (53 %) in TH, and THIA (49 %) and DIN (31 %) in THB. Correlation analysis and linear mixed modeling identified land use, pH, and dissolved oxygen (DO) as significant factors influencing the occurrence of NNIs, with DO emerging as a crucial element. The species sensitivity distribution (SSD) results showed the acute and chronic toxicity thresholds of NNIs for 5 % of aquatic species were 716 ng/L and 166 ng/L respectively with 19 sites exceeding the chronic toxicity threshold and 1 sites surpassing the acute toxicity threshold.}, } @article {pmid40402004, year = {2025}, author = {Brunk, KM and Kramer, HA and Peery, MZ and Kahl, S and Wood, CM}, title = {Assessing spatial variability and efficacy of surrogate species at an ecosystem scale.}, journal = {Conservation biology : the journal of the Society for Conservation Biology}, volume = {}, number = {}, pages = {e70058}, doi = {10.1111/cobi.70058}, pmid = {40402004}, issn = {1523-1739}, support = {//Arthur Vining Davis Foundations/ ; FKZ 01|S22072//German Federal Ministry of Education and Research/ ; //Josh Holshuh/ ; //University of Wisconsin's Office of the Vice Chancellor for Research/ ; 20-ECOF20-0017//NASA Biodiversity and Ecological Forecasting Program/ ; //National Park Service/ ; 19-RP-NEU-043//California Climate Investment Forest Health Research Program/ ; FKZ 67KI31040E//German Federal Ministry of Environment, Nature Conservation, and Nuclear Safety/ ; //USDA Forest Service Region 5/ ; }, abstract = {Preserving biodiversity is a central goal of conservation, but, in practice, monitoring biodiversity often involves assessing population trends for one or a handful of species that are presumed proxies for biodiversity. Despite the popularity of surrogate species strategies, the links between biodiversity and surrogate species are rarely tested, especially across the broad spatial scales at which they are applied. We quantitatively evaluated a prominent surrogate species strategy across 25,000 km[2] of California's Sierra Nevada, an ecosystem undergoing substantial forest loss due to changing fire regimes and climate. We used passive acoustic monitoring and multispecies occupancy models to quantify pairwise co-occurrence among 6 indicator species and much of the avian community (63 species). We found that 95% of the sampled avian community had a positive association with at least one indicator species and that latitude played an important role in shaping co-occurrence for many species. Our work provides an important test of a long-standing conservation tool, suggests that a well-chosen suite of surrogate species can represent the occurrence patterns of a large portion of the rest of the community, and demonstrates the importance of explicitly considering the spatial scale over which surrogate species are effective.}, } @article {pmid40399277, year = {2025}, author = {Petit, MJ and Flory, C and Gu, Q and Fares, M and Lamont, D and Score, A and Davies, K and Bell-Sakyi, L and Scaturro, P and Brennan, B and Kohl, A}, title = {Multi-omics analysis of SFTS virus infection in Rhipicephalus microplus cells reveals antiviral tick factors.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {4732}, pmid = {40399277}, issn = {2041-1723}, support = {MC_UU_00034/5//RCUK | Medical Research Council (MRC)/ ; SC 314/2-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 210462/Z/18/Z//Wellcome Trust (Wellcome)/ ; TICKITS 890970//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; MC_UU_12014/8//RCUK | Medical Research Council (MRC)/ ; /WT_/Wellcome Trust/United Kingdom ; MC_UU_00034/4//RCUK | Medical Research Council (MRC)/ ; }, mesh = {Animals ; *Rhipicephalus/virology/genetics/immunology ; Cell Line ; Proteomics/methods ; Virus Replication ; *Phlebovirus/physiology/genetics ; Transcriptome ; Host-Pathogen Interactions/genetics ; RNA Helicases/metabolism/genetics ; Proteome ; *Severe Fever with Thrombocytopenia Syndrome/virology ; Gene Expression Profiling ; Multiomics ; }, abstract = {The increasing prevalence of tick-borne arboviral infections worldwide necessitates advanced control strategies, particularly those targeting vectors, to mitigate the disease burden. However, the cellular interactions between arboviruses and ticks, especially for negative-strand RNA viruses, remain largely unexplored. Here, we employ a proteomics informed by transcriptomics approach to elucidate the cellular response of the Rhipicephalus microplus-derived BME/CTVM6 cell line to severe fever with thrombocytopenia syndrome virus (SFTSV) infection. We generate the de novo transcriptomes and proteomes of SFTSV- and mock-infected tick cells, identifying key host responses and regulatory pathways. Additionally, interactome analysis of the viral nucleoprotein (N) integrated host responses with viral replication and dsRNA-mediated gene silencing screen reveals two anti-SFTSV effectors: the N interacting RNA helicases DHX9 and UPF1. Collectively, our results provide insights into the antiviral responses of R. microplus vector cells and highlight critical SFTSV restriction factors, while enriching transcriptomic and proteomic resources for future research.}, } @article {pmid40397662, year = {2025}, author = {Li, S and Zou, J and Wu, J and Sun, B and Zhao, M and Liu, D and Cheng, Q and Tan, H and Ma, J}, title = {New Insights into Natural Polyphenol-Enhanced Fe(III)/Peracetic Acid System under Acidic pH Conditions: The Overlooked Role of Coexisting Hydrogen Peroxide.}, journal = {Environmental science & technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.5c01622}, pmid = {40397662}, issn = {1520-5851}, abstract = {Natural polyphenols have been extensively utilized as reducing agents to enhance contaminant degradation in the Fe(III)/peracetic acid (PAA) system. However, the roles of coexisting hydrogen peroxide (H2O2) remain insufficiently explored. This study, using protocatechuic acid (PCA) as a representative natural polyphenol, demonstrated that contaminant removal within the PCA/Fe(III)/PAA system under acidic pH conditions exhibited two kinetic stages: an initial rapid stage driven by PAA, followed by a slower stage driven by H2O2. The presence of H2O2 facilitated the complete degradation (100%) of contaminants even at low concentrations (<1.0 μM). Interestingly, these two stages contributed differently to various contaminants' degradation. Mechanistic investigations revealed that Fe(IV) was the major reactive species (RSs) for contaminant degradation during the PAA stage, while [•]OH dominated during the H2O2 stage. In brief, H2O2 enriched the generation pathways and types of RSs. Notably, besides PCA itself, the reaction intermediates (i.e., phenoxy radicals) formed during the reaction between PCA and RSs also played a key role in reducing Fe(III), which explained why the PCA/Fe(III)/PAA system was able to maintain sufficient Fe(II) to further interact with H2O2. Overall, this study highlighted the synergistic role of coexisting H2O2 and provided valuable insights for optimizing various contaminants' degradation in actual waters using PAA-based Fenton-like systems.}, } @article {pmid40393855, year = {2025}, author = {Zhivkoplias, E and da Silva, JM and Blasiak, R}, title = {How transdisciplinarity can help biotech-driven biodiversity research.}, journal = {Trends in biotechnology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tibtech.2025.04.008}, pmid = {40393855}, issn = {1879-3096}, abstract = {The Kunming-Montreal Global Biodiversity Framework marks a significant step toward conserving genetic diversity on a global scale. Sequencing advancements have broadened biodiversity studies by enabling the mapping of species distributions, increasing understanding of ecological interactions, and monitoring genetic diversity. However, these tools are hindered by inequalities and biases, particularly in biodiversity-rich developing countries. To navigate these challenges, we propose strategies using the existing biotechnological toolbox to make biodiversity data more accessible and useful for research and development. This includes increasing funding for database curation, improving metadata standards, addressing inequalities in technological capacity, and supporting holistic capacity-building programmes. Implementing these strategies can unlock new opportunities for biodiversity research aligned with sustainable development principles and can contribute to improved conservation outcomes.}, } @article {pmid40393068, year = {2025}, author = {Williams, CM and Scelza, BA and Slack, SD and Font-Porterias, N and Al-Hindi, DR and Mathias, RA and Watson, H and Barnes, KC and Lange, E and Johnson, RK and Gignoux, CR and Ramachandran, S and Henn, BM}, title = {A rapid accurate approach to inferring pedigrees in endogamous populations.}, journal = {Genetics}, volume = {}, number = {}, pages = {}, doi = {10.1093/genetics/iyaf094}, pmid = {40393068}, issn = {1943-2631}, abstract = {Accurate reconstruction of pedigrees from genetic data remains a challenging problem. Many relationship categories (e.g. half-sibships versus avuncular) can be difficult to distinguish without external information. Pedigree inference algorithms are often trained on European-descent families in urban locations. Thus, existing methods tend to perform poorly in endogamous populations for which there may be reticulations within the pedigrees and elevated haplotype sharing. We present a simple, rapid algorithm which initially uses only high-confidence first-degree relationships to seed a machine learning step based on summary statistics of identity-by-descent (IBD) sharing. One of these statistics, our ``haplotype score'', is novel and can be used to: (1) distinguish half-sibling pairs from avuncular or grandparent-grandchildren pairs; and (2) assign individuals to ancestor versus descendant generation. We test our approach in a sample of ∼700 individuals from northern Namibia, sampled from an endogamous population called the Himba. Due to a culture of concurrent relationships in the Himba, there is a high proportion of half-sibships. We accurately identify first through fourth-degree relationships and distinguish between various second-degree relationships: half-sibships, avuncular pairs, and grandparent-grandchildren. We further validate our approach in a second African-descent dataset, the Barbados Asthma Genetics Study (BAGS), and a European-descent founder population from Quebec. Accurate reconstruction of relatives facilitates estimation of allele frequencies, tracing allele trajectories, improved phasing, heritability and other population genomic questions.}, } @article {pmid40389091, year = {2025}, author = {Narita, M and Matsugaki, R and Muramatsu, K and Fushimi, K and Matsuda, S}, title = {Obesity and risk of post-operative pneumonia among older adult patients with hip fracture: an obesity paradox.}, journal = {Clinical nutrition ESPEN}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.clnesp.2025.05.020}, pmid = {40389091}, issn = {2405-4577}, abstract = {BACKGROUND & AIM: Hip fracture is a condition with a high incidence among older adults and is associated with a high post-operative mortality rate. Post-operative pneumonia is one of the most important risk factors for mortality, making its prevention essential. In recent years, reports on obesity paradoxes have increasingly been documented. Therefore, this study aimed to investigate the relationship between body mass index (BMI) and the risk of developing post-operative pneumonia using a large database.

METHOD: We included 407,203 patients aged 75 years or older who underwent surgery for hip fracture between 2014 and 2018 using Diagnosis Procedure Combination data, a healthcare reimbursement system. Patients were classified into six BMI categories: <16.0, 16.0-16.9, 17.0-18.4, 18.5-24.9, 25.0-29.9, and ≥30 kg/m[2]. Multilevel logistic regression analysis was performed based on BMI 18.5-24.9 kg/m[2] to determine odds ratios for post-operative pneumonia.

RESULTS: The data of 332,768 patients were included in the final analysis. Those with BMI <18.5 kg/m[2] demonstrated significantly higher odds of developing post-operative pneumonia compared to those with BMI between 18.5-24.9 kg/m[2], BMI <16.0 kg/m[2] (adjusted odds ratio [AOR: 2.14, 95% confidence interval [CI: 2.01-2.27 p<0.001); BMI 16.0-16.9 kg/m[2] (AOR: 1.57, 95% CI: 1.46-1.69, p<0.001); and BMI 17.0-18.4 kg/m[2] (AOR: 1.31, 95% CI: 1.24-1.39, p<0.001). Conversely, patients with BMI 25.0-29.9 kg/m[2] showed a risk of post-operative pneumonia compared to the other groups (AOR: 0.83, 95% CI: 0.76-0.91, p<0.001). Notably, a J-curve relationship was observed between BMI and the incidence of post-operative pneumonia.

CONCLUSION: Patients with higher BMI had a lower risk of developing post-operative pneumonia, revealing the presence of an obesity paradox between hip fracture and post-operative pneumonia. Patients with low BMI are at a higher risk and may benefit from enhanced preventive measures to mitigate the risk of pneumonia.}, } @article {pmid40386950, year = {2025}, author = {Cordeiro, AL and Cusack, DF and Guerrero-Ramírez, N and Norby, RJ and Toro, L and Wong, MY and Wright, SJ and Cabugao, KGM and Andersen, KM and Fuchslueger, L and Iversen, CM and Soper, F and Ghimire, OP and Lugli, LF and Miron, AC and Valverde-Barrantes, O and Arnaud, M and Batterman, SA and Dietterich, LH and Lee, MY and Weemstra, M and Yaffar, D and Addo-Danso, SD and Pierick, K and Bridges, R and Easton, C and Felsing, I and Gonçalves, NB and Krudop, R and McKinzie, MR and Perbohner, J and Pozzoli-Oropeza, AN and Samaniego, M and Smilor, AW and Vargas, IS and Webb, L and Powers, JS and McCormack, ML}, title = {TropiRoot 1.0: Database of tropical root characteristics across environments.}, journal = {Ecology}, volume = {106}, number = {5}, pages = {e70074}, doi = {10.1002/ecy.70074}, pmid = {40386950}, issn = {1939-9170}, mesh = {*Plant Roots/physiology/anatomy & histology ; *Tropical Climate ; *Databases, Factual ; Ecosystem ; Biodiversity ; }, abstract = {Tropical ecosystems contain the world's largest biodiversity of vascular plants. Yet, our understanding of tropical functional diversity and its contribution to global diversity patterns is constrained by data availability. This discrepancy underscores an urgent need to bridge data gaps by incorporating comprehensive tropical root data into global datasets. Here, we provide a database of tropical root characteristics. This new database, TropiRoot 1.0, will be instrumental in evaluating an array of hypotheses pertaining to root functional ecology and plant biogeography, both within the tropics and relative to other global biomes. The data compilation was conducted by the TropiRoot Initiative, in partnership with the Fine-Root Ecology Database (FRED) and the Global Root Trait (GRooT) database, Colorado State University (CSU) and the Smithsonian Tropical Research Institute (STRI). Literature search and data extraction were conducted between 2020 and 2024. Literature was identified using Web of Science, Scopus, and complemented using the expert knowledge of members of TropiRoot. To provide broad environmental and geographical distributions, literature searches included root characteristics (traits) across global change drivers, natural gradients, and from different continents. We adopted FRED standardized data columns and streamlined the format to enhance accessibility for data extraction across various user groups. This optimized framework resulted in a smaller, yet comprehensive datasheet. To make the database compatible with other global root trait initiatives, column identification was standardized following the codes provided by FRED. These efforts culminated in data extracted from 104 new sources, resulting in more than 8000 rows of data (either species or community data). Most of the data in TropiRoot 1.0 include root characteristics such as root biomass, morphology, root dynamics, mass fraction, architecture, anatomy, physiology, and root chemistry. This initiative represents a 30% increase in the currently available data for tropical roots in FRED. TropiRoot 1.0 contains root characteristics from 25 different countries, where seven are located in Asia, six in South America, five in Central America and the Caribbean, four in Africa, two in North America, and 1 in Oceania. Due to the volume of data, when ancillary data were available, including soil data, these data were either extracted and included in the database or its availability was recorded in an additional column. Multiple contributors checked the entries for outliers during the collation process to ensure data quality. For text-based observations, we examined all cells to ensure that their content relates to their specific categories. For numerical observations, we ordered each numerical value from least to greatest and plotted the values, checking apparent outliers against the data in their respective sources and correcting or removing incorrect or impossible values. Some data (soil and aboveground) have different columns for the same variable presented in different units, including originally published units, but root characteristics data had units converted to match those reported in FRED. By filling a gap from global databases, TropiRoot 1.0 expands our knowledge of otherwise so far underrepresented regions and our ability to assess global trends. This advancement can be used to improve tropical forest representation in vegetation models. The data are freely available and should be cited when used.}, } @article {pmid40386543, year = {2025}, author = {Ramos, E and Schweizer, M and Wu, MY and Sahli, C and Latt, C and Lunak, M and Crochet, PA and Salzburger, W and Meier, J and Marques, DA and , and , and , and , and , }, title = {The genome sequence of the Yellow-legged Gull, Larus michahellis Naumann, 1840.}, journal = {Wellcome open research}, volume = {10}, number = {}, pages = {129}, pmid = {40386543}, issn = {2398-502X}, abstract = {We present a genome assembly from a female specimen of Larus michahellis (Yellow-legged Gull; Chordata; Aves; Charadriiformes; Laridae). The genome sequence has a total length of 1,405.56 megabases. Most of the assembly (90.55%) is scaffolded into 35 chromosomal pseudomolecules, including the W and Z sex chromosomes. The mitochondrial genome has also been assembled and is 16.79 kilobases in length.}, } @article {pmid40379663, year = {2025}, author = {Iminjili, V and Crowther, A and Fisher, MT and Kay, A and Roberts, P and Goldstein, S and Boivin, N and Fernandes, R}, title = {A dataset of scientific dates from archaeological sites in eastern Africa spanning 5000 BCE to 1800 CE.}, journal = {Scientific data}, volume = {12}, number = {1}, pages = {801}, pmid = {40379663}, issn = {2052-4463}, mesh = {*Archaeology ; Africa, Eastern ; History, Ancient ; History, 18th Century ; Humans ; }, abstract = {Large collections of archaeological spatiotemporal data can reveal past cultural and demographic trends, land use strategies, and processes of environmental adaptation. Within Africa, archaeological Big Data can contribute to the study of the spread of agriculture, domesticated species, and specific artefacts and technologies, as well as their ecological impacts. Although reviews addressing these topics are available for different parts of the continent, existing mid-late Holocene archaeology datasets have yet to be compiled into a central, open-access, standardized informatic-oriented dataset. Here we present Wanyika, a dataset of scientific dates from archaeological sites in eastern Africa spanning almost 7 millennia, from ~5000 BCE to 1800 CE. This dataset compiles published scientific dates and associated botanical, faunal, iron, and ceramic finds from sites in Kenya, Tanzania, the Comoros Islands, and Madagascar. The records also include data for megafauna extinctions in Madagascar. We describe the spatiotemporal coverage of the dataset, how the data were collected, the structure of the dataset, and the applied quality control measures.}, } @article {pmid40378227, year = {2025}, author = {Ha, MK and Postovskaya, A and Kuznetsova, M and Meysman, P and Van Deuren, V and Van Ierssel, S and De Reu, H and Schippers, J and Peeters, K and Besbassi, H and Heyndrickx, L and Willems, B and Mariën, J and Bartholomeus, E and Vercauteren, K and Beutels, P and Van Damme, P and Lion, E and Vlieghe, E and Laukens, K and Coenen, S and Naesens, R and Ariën, KK and Ogunjimi, B}, title = {Celluloepidemiology-A paradigm for quantifying infectious disease dynamics on a population level.}, journal = {Science advances}, volume = {11}, number = {20}, pages = {eadt2926}, pmid = {40378227}, issn = {2375-2548}, mesh = {Humans ; *COVID-19/epidemiology/immunology/virology ; *SARS-CoV-2/immunology ; T-Lymphocytes/immunology ; Machine Learning ; Receptors, Antigen, T-Cell/immunology/metabolism ; Flow Cytometry ; *Communicable Diseases/epidemiology/immunology ; }, abstract = {To complement serology as a tool in public health interventions, we introduced the "celluloepidemiology" paradigm where we leveraged pathogen-specific T cell responses at a population level to advance our epidemiological understanding of infectious diseases, using SARS-CoV-2 as a model. Applying flow cytometry and machine learning on data from more than 500 individuals, we showed that the number of T cells with positive expression of functional markers not only could distinguish patients who recovered from COVID-19 from controls and pre-COVID donors but also identify previously unrecognized asymptomatic patients from mild, moderate, and severe recovered patients. The celluloepidemiology approach was uniquely capable to differentiate health care worker groups with different SARS-CoV-2 exposures from each other. T cell receptor (TCR) profiling strengthened our analysis by revealing that SARS-CoV-2-specific TCRs were more abundant in patients than in controls. We believe that adding data on T cell reactivity will complement serology and augment the value of infection morbidity modeling for populations.}, } @article {pmid40376739, year = {2025}, author = {Arnold, LE and Hendrix, K and Pan, X and Vollebregt, MA and Yu, M and Kerson, C and Arns, M and Hatsu, IE and DeBeus, R and Hollway, J and Roley-Roberts, ME}, title = {Lifestyle Effects in a Randomized Controlled Trial of Neurofeedback for Attention-Deficit/Hyperactivity Disorder.}, journal = {Journal of child and adolescent psychopharmacology}, volume = {}, number = {}, pages = {}, doi = {10.1089/cap.2025.0019}, pmid = {40376739}, issn = {1557-8992}, abstract = {Objectives/Background: Multiple factors influence symptom severity in Attention Deficit/Hyperactivity Disorder (ADHD). We examined four of these: diet, sleep hygiene, exercise, and lighting, in the International Collaborative ADHD Neurofeedback (ICAN) randomized clinical trial, which found large significant improvement with both active neurofeedback and control condition without treatment difference. Methods: A total of 142 participants aged 7-10 had breakfast and lunch intake and exercise recorded at each neurofeedback session. Parents completed the Children's Sleep Habits Questionnaire (CSHQ). Parents and teachers rated inattention on Conners3. Lifestyle changes were correlated with inattention changes. Results: At baseline, CSHQ correlated with parent-rated inattention (r = 0.17, p = 0.04), and length of sleep correlated with teacher-rated inattention (r = 0.20, p = 0.03). From baseline to treatment end food group variety (p = 0.029, d = 0.22) and sleep problems (p < 0.0001, d = -0.49) improved significantly, exercise time and protein intake marginally (p = 0.06 - 0.08). Parent-rated inattention improvement correlated with CSHQ improvement (Rho = 0.26, p = 0.002) and marginally with protein intake increase (Rho = 0.18, p = 0.06). The three components of the light-emitting-diode (LED)-induced circadian pathway hypothesis were significant. Conclusions: Most measures improved, but few significantly. How much they impact classroom attention remains unclear. Although parent ratings of inattention improvement correlated with sleep problems improvement, composited parent/teacher ratings (primary outcome) did not. The circadian pathway hypothesis associated with LED lighting was supported. These findings warrant further studies examining the role sleep hygiene can play in improving ADHD symptoms. Meanwhile, attention to sleep hygiene seems appropriate in any treatment plan for ADHD.}, } @article {pmid40371923, year = {2025}, author = {Cirino, T and Pinto, L and Iwan, M and Dougha, A and Lučić, B and Kraljević, A and Navoyan, Z and Tevosyan, A and Yeghiazaryan, H and Khondkaryan, L and Abelyan, N and Atoyan, V and Babayan, N and Iwashita, Y and Kimura, K and Komasaka, T and Shishido, K and Nakamura, T and Asada, M and Jain, S and Zakharov, AV and Wang, H and Liu, W and Chupakhin, V and Uesawa, Y}, title = {Consensus Modeling Strategies for Predicting Transthyretin Binding Affinity from Tox24 Challenge Data.}, journal = {Chemical research in toxicology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.chemrestox.5c00018}, pmid = {40371923}, issn = {1520-5010}, abstract = {Transthyretin (TTR) is a key transporter of the thyroid hormone thyroxine, and chemicals that bind to TTR, displacing the hormone, can disrupt the endocrine system, even at low concentrations. This study evaluates computational modeling strategies developed during the Tox24 Challenge, using a data set of 1512 compounds tested for TTR binding affinity. Individual models from nine top-performing teams were analyzed for performance and uncertainty using regression metrics and applicability domains (AD). Consensus models were developed by averaging predictions across these models, with and without consideration of their ADs. While applying AD constraints in individual models generally improved external prediction accuracy (at the expense of reduced chemical space coverage), it had limited additional benefit for consensus models. Results showed that consensus models outperformed individual models, achieving a root-mean-square error (RMSE) of 19.8% on the test set, compared to an average RMSE of 20.9% for the nine individual models. Outliers consistently identified in several of these models indicate potential experimental artifacts and/or activity cliffs, requiring further investigation. Substructure importance analysis revealed that models prioritized different chemical features, and consensus averaging harmonized these divergent perspectives. These findings highlight the value of consensus modeling in improving predictive performance and addressing model limitations. Future work should focus on expanding chemical space coverage and refining experimental data sets to support public health protection.}, } @article {pmid40371524, year = {2025}, author = {Li, YH and Zhang, Y}, title = {[Wilderness network construction in Lincang City of Yunnan Province, Southwest China based on landscape connectivity].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {36}, number = {4}, pages = {1233-1243}, doi = {10.13287/j.1001-9332.202504.026}, pmid = {40371524}, issn = {1001-9332}, mesh = {China ; *Conservation of Natural Resources/methods ; *Ecosystem ; Geographic Information Systems ; *Wilderness ; Cities ; *Environment Design ; Models, Theoretical ; *City Planning ; }, abstract = {Constructing wilderness networks based on landscape connectivity is crucial for wilderness conservation. We calculated the continuous spectrum of the wilderness with GIS, identified wilderness sources with morphological spatial pattern analysis (MSPA), constructed wilderness corridors and networks and extracted wilderness strategic points with minimum cumulative resistance model (MCR) and circuit theory. We further analyzed the characte-ristics of the wilderness network, and proposed wilderness protection strategies and ecological planning suggestions for Lincang City. Results showed that wilderness was mainly distributed at 1000-2500 m elevation, with a spatial pattern of more in the south and east, less in the north and west in Lincang City. Grade 3 wilderness covered 55% of the total area, indicating high quality of the study area. Based on the MSPA analysis, we found 27 wilderness sources, most of which were distributed in the eastern and southern areas such as Linxiang and Cangyuan. The western and northern such as Fengqing and Yongde had fewer wilderness sources. There were 63 wilderness corridors in the wilderness network, including 16 important corridors and 47 general corridors. There were 186 strategic points in the wilderness network, including 53 wilderness nodes and 133 barrier points. We constructed the wilderness network of Lincang based in the identified wilderness source areas and extracted wilderness corridors, which had the advantages of high stability, strong resistance to interference, efficient connectivity. Finally, we proposed the "three-zone as a whole" protection strategy and ecological planning suggestions, which had referential value for establishing an ecological security pattern in Lincang City and the practicalization of wilderness protection in China.}, } @article {pmid40371522, year = {2025}, author = {Dong, WZ and Su, WC and Gou, R and Zhou, HY and Liu, DY}, title = {[Spatial and temporal evolution of ecological risk in Guizhou Province, China from the perspective of ecosystem services and ecosystem health].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {36}, number = {4}, pages = {1211-1221}, doi = {10.13287/j.1001-9332.202504.021}, pmid = {40371522}, issn = {1001-9332}, mesh = {China ; *Ecosystem ; *Conservation of Natural Resources ; Risk Assessment ; Rivers ; Spatio-Temporal Analysis ; Geographic Information Systems ; *Environmental Monitoring/methods ; Ecology ; Models, Theoretical ; }, abstract = {Guizhou Province is an important ecological barrier in the upper reaches of the Yangtze River and the Pearl River. Karst landform in Guizhou is developed, with fragile ecological background. The ecological risk assessment and control of Karst landform are of great significance to ecological security and sustainable development of southwest China and the upper reaches of those two rivers. Based on the InVEST model and vigor-organization-resi-lience model, we quantitatively evaluated the ecosystem services and ecosystem health and constructed the ecological risk assessment model of Guizhou Province. With the help of GIS technology, spatial autocorrelation analysis method and gravity center migration model, we analyzed the spatial and temporal variations of ecological risk in Guizhou Province from 2000 to 2020. The results showed that ecosystem services in Guizhou Province increased from 2000 to 2020, with an annual average growth rate of 0.3%. The ecosystem health status was generally well and showed a good trend, and the annual average growth rate of ecosystem health was 12.6%. The ecological risk was dominated by medium ecological risk. The proportion of extremely low ecological risk area and low ecological risk area increased, the proportion of medium and above ecological risk area decreased, and the overall ecological risk showed a downward trend. The low ecological risk areas were mainly located in the south and southeast of Guizhou Province, while the high ecological risk areas were distributed in the central, western and northern parts of Guizhou Province. The global Moran's I of ecological risk in 2000, 2005, 2010, 2015, and 2020 were 0.856, 0.836, 0.844, 0.804, and 0.768, respectively, indicating that the positive correlation of ecological risk in spatial distribution, but the spatial correlation and spatial agglomeration characteristics were weakened. During the study period, the centroid and trajectory of ecological risk in Guizhou Province were consistent with the distribution area of its corresponding ecological risk. From 2000 to 2020, the spatial distribution pattern of ecological risk in Guizhou Pro-vince was relatively stable. With the evolution of time, the dispersion of spatial distribution of extremely high ecological risk and low ecological risk increased. Ecological risk assessment based on ecosystem services and ecosystem health would provide scientific basis for regional ecological risk management and control.}, } @article {pmid40369670, year = {2025}, author = {Wu, B and Luo, D and Yue, Y and Yan, H and He, M and Ma, X and Zhao, B and Xu, B and Zhu, J and Wang, J and Jia, J and Sun, M and Xie, Z and Wang, X and Huang, L}, title = {New insights into the cold tolerance of upland switchgrass by integrating a haplotype-resolved genome and multi-omics analysis.}, journal = {Genome biology}, volume = {26}, number = {1}, pages = {128}, pmid = {40369670}, issn = {1474-760X}, support = {2021YFYZ0013//Sichuan Province Research Grant/ ; SCCXTD-2020-16//Modern Agricultural Industry System Sichuan Forage Innovation Team/ ; 32071867//National Natural Science Foundation of China/ ; }, mesh = {*Panicum/genetics/physiology ; *Haplotypes ; *Genome, Plant ; *Cold-Shock Response/genetics ; Ecotype ; Gene Expression Regulation, Plant ; Genome-Wide Association Study ; Cold Temperature ; Gene Expression Profiling ; Plant Proteins/genetics/metabolism ; Transcriptome ; Multiomics ; }, abstract = {BACKGROUND: Switchgrass (Panicum virgatum L.) is a bioenergy and forage crop. Upland switchgrass exhibits superior cold tolerance compared to the lowland ecotype, but the underlying molecular mechanisms remain unclear.

RESULTS: Here, we present a high-quality haplotype-resolved genome of the upland ecotype "Jingji31." We then conduct multi-omics analysis to explore the mechanism underlying its cold tolerance. By comparative transcriptome analysis of the upland and lowland ecotypes, we identify many genes with ecotype-specific differential expression, particularly members of the cold-responsive (COR) gene family, under cold stress. Notably, AFB1, ATL80, HOS10, and STRS2 gene families show opposite expression changes between the two ecotypes. Based on the haplotype-resolved genome of "Jingji31," we detect more cold-induced allele-specific expression genes in the upland ecotype than in the lowland ecotype, and these genes are significantly enriched in the COR gene family. By genome-wide association study, we detect an association signal related to the overwintering rate, which overlaps with a selective sweep region containing a cytochrome P450 gene highly expressed under cold stress. Heterologous overexpression of this gene in rice alleviates leaf chlorosis and wilting under cold stress. We also verify that expression of this gene is suppressed by a structural variation in the promoter region.

CONCLUSIONS: Based on the high-quality haplotype-resolved genome and multi-omics analysis of upland switchgrass, we characterize candidate genes responsible for cold tolerance. This study advances our understanding of plant cold tolerance, which provides crop breeding for improved cold tolerance.}, } @article {pmid40369175, year = {2025}, author = {Barroux, M and Househam, J and Lakatos, E and Ronel, T and Baker, AM and Salié, H and Mossner, M and Smith, K and Kimberley, C and Nowinski, S and Berner, A and Gunasri, V and Borgmann, M and Liffers, S and Jansen, M and Caravagna, G and Steiger, K and Slotta-Huspenina, J and Weichert, W and Zapata, L and Giota, E and Lorenzen, S and Alberstmeier, M and Chain, B and Friess, H and Bengsch, B and Schmid, RM and Siveke, JT and Quante, M and Graham, TA}, title = {Evolutionary and immune microenvironment dynamics during neoadjuvant treatment of esophageal adenocarcinoma.}, journal = {Nature cancer}, volume = {}, number = {}, pages = {}, pmid = {40369175}, issn = {2662-1347}, abstract = {Locally advanced esophageal adenocarcinoma remains difficult to treat and the ecological and evolutionary dynamics responsible for resistance and recurrence are incompletely understood. Here, we performed longitudinal multiomic analysis of patients with esophageal adenocarcinoma in the MEMORI trial. Multi-region multi-timepoint whole-exome and paired transcriptome sequencing was performed on 27 patients before, during and after neoadjuvant treatment. We found major transcriptomic changes during treatment with upregulation of immune, stromal and oncogenic pathways. Genetic data revealed that clonal sweeps through treatment were rare. Imaging mass cytometry and T cell receptor sequencing revealed remodeling of the tumor microenvironment during treatment. The presence of genetic immune escape, a less-cytotoxic T cell phenotype and a lack of clonal T cell expansions were linked to poor treatment response. In summary, there were widespread transcriptional and environmental changes through treatment, with limited clonal replacement, suggestive of phenotypic plasticity.}, } @article {pmid40368894, year = {2025}, author = {Yi, S and Li, X and Liu, Y and Dong, X and Tu, W}, title = {A sub-meter resolution urban surface albedo dataset for 34 U.S. cities based on deep learning.}, journal = {Scientific data}, volume = {12}, number = {1}, pages = {789}, pmid = {40368894}, issn = {2052-4463}, support = {2314709//National Science Foundation (NSF)/ ; }, abstract = {Surface albedo is a key determinant of urban heat islands, which modulates the amount of solar energy absorbed or reflected by urban surfaces, influencing microclimate and thermal comfort. However, high-resolution albedo is usually not available, which makes the understanding of the urban thermal environment at hyperlocal difficult. This study presents the first high-resolution urban albedo maps for 34 major U.S. cities using advanced deep learning models and multisource remote sensing data. By differentiating between impervious and pervious surfaces using a combination of NAIP imagery, roof albedo data, building footprints, land cover classifications, and Sentinel-2 imagery, this work achieves sub-meter resolution in albedo mapping. Employing U-Net for impervious surface classification along with impervious (ISA) and pervious surface albedo (PSA) prediction, these models were validated in selected cities, with ISA showing an R[2] of 0.9028 and MAE of 0.0057, and PSA demonstrating an R[2] of 0.9538 and MAE of 0.0027, highlighting the precision and reliability. The datasets, made publicly available, offer essential insights for urban planning and environmental monitoring.}, } @article {pmid40365044, year = {2025}, author = {Ogba, P and Baumann, A and Alabi, T and Archer, N and Eniojukan, J and Ibhawoh, B and DiLiberto, DD}, title = {Enhancing IPTp-SP uptake: Community and stakeholder recommendations for improving access and utilisation - insights from a study in Bayelsa-Nigeria.}, journal = {MalariaWorld journal}, volume = {16}, number = {}, pages = {9}, pmid = {40365044}, issn = {2214-4374}, abstract = {BACKGROUND: Malaria remains a major global health challenge, disproportionately affecting pregnant women and children. In Nigeria, malaria in pregnancy contributes to 70.5% of maternal morbidity and 41.1% of maternal mortality. Recognising these risks, the World Health Organization recommends intermittent preventive treatment with sulfadoxine-pyrimethamine (IPTp-SP) as a key strategy for malaria in pregnancy prevention. However, despite its proven effectiveness, pregnant women's uptake of IPTp-SP remains unacceptably low. This study presents participant-driven recommendations to enhance IPTp-SP uptake, structured within the socio-ecological framework.

MATERIALS AND METHODS: This study employed an exploratory descriptive qualitative approach to examine the community-level contextual factors influencing IPTp-SP uptake. Data were collected from 53 participants in two communities in Bayelsa, Nigeria. Individual interviews were conducted with 17 key stakeholders (spouses, mothers-in-law, religious leaders, community leaders, and traditional birth attendants) and 6 focus group discussions with 36 pregnant women. Data management and coding were conducted using NVivo 14 QSR International software, following an inductive-deductive thematic analysis approach.

RESULTS: Participants proposed multi-level interventions to address barriers to IPTp-SP uptake at the individual, interpersonal, community, and healthcare system levels. Key recommendations include: Community-wide education campaigns to raise awareness of IPTp-SP's benefits; comprehensive training for healthcare providers to enhance their knowledge and prescription of IPTp-SP; integration of traditional birth attendants into the formal healthcare system; community-level distribution of IPTp-SP to improve access for pregnant women who do not attend antenatal care; government intervention to ensure the functionality of health centers; addressing workforce shortages, and guaranteeing a consistent supply of IPTp-SP.

CONCLUSION: These evidence-based, participant-driven recommendations offer a holistic and scalable strategy to improve pregnant women's uptake of IPTp-SP in Nigeria and other malaria-endemic regions. Implementing these recommendations can strengthen malaria prevention efforts, improve maternal and child health outcomes, and support broader public health initiatives.}, } @article {pmid40197051, year = {2025}, author = {Shamash, M and Sinha, A and Maurice, CF}, title = {Improving gut virome comparisons using predicted phage host information.}, journal = {mSystems}, volume = {10}, number = {5}, pages = {e0136424}, doi = {10.1128/msystems.01364-24}, pmid = {40197051}, issn = {2379-5077}, mesh = {*Bacteriophages/genetics/classification/physiology ; *Virome/genetics ; Humans ; *Gastrointestinal Microbiome/genetics ; Animals ; Mice ; Feces/virology/microbiology ; Metagenomics/methods ; Computational Biology/methods ; Bacteria/virology ; }, abstract = {UNLABELLED: The human gut virome is predominantly made up of bacteriophages (phages), viruses that infect bacteria. Metagenomic studies have revealed that phages in the gut are highly individual specific and dynamic. These features make it challenging to perform meaningful cross-study comparisons. While several taxonomy frameworks exist to group phages and improve these comparisons, these strategies provide little insight into the potential effects phages have on their bacterial hosts. Here, we propose the use of predicted phage host families (PHFs) as a functionally relevant, qualitative unit of phage classification to improve these cross-study analyses. We first show that bioinformatic predictions of phage hosts are accurate at the host family level by measuring their concordance to Hi-C sequencing-based predictions in human and mouse fecal samples. Next, using phage host family predictions, we determined that PHFs reduce intra- and interindividual ecological distances compared to viral contigs in a previously published cohort of 10 healthy individuals, while simultaneously improving longitudinal virome stability. Lastly, by reanalyzing a previously published metagenomics data set with >1,000 samples, we determined that PHFs are prevalent across individuals and can aid in the detection of inflammatory bowel disease-specific virome signatures. Overall, our analyses support the use of predicted phage hosts in reducing between-sample distances and providing a biologically relevant framework for making between-sample virome comparisons.

IMPORTANCE: The human gut virome consists mainly of bacteriophages (phages), which infect bacteria and show high individual specificity and variability, complicating cross-study comparisons. Furthermore, existing taxonomic frameworks offer limited insight into their interactions with bacterial hosts. In this study, we propose using predicted phage host families (PHFs) as a higher-level classification unit to enhance functional cross-study comparisons. We demonstrate that bioinformatic predictions of phage hosts align with Hi-C sequencing results at the host family level in human and mouse fecal samples. We further show that PHFs reduce ecological distances and improve virome stability over time. Additionally, reanalysis of a large metagenomics data set revealed that PHFs are widespread and can help identify disease-specific virome patterns, such as those linked to inflammatory bowel disease.}, } @article {pmid40361718, year = {2025}, author = {Nițescu, M and Nedelescu, MM and Moroşan, E and Simionescu, AA and Furtunescu, FL and Ştefănescu, BE and Tusaliu, M and Panaitescu, E and Stanciu, AM and Stoian, IM}, title = {Assessment of Food Safety Knowledge and Practices Among Medical Students.}, journal = {Foods (Basel, Switzerland)}, volume = {14}, number = {9}, pages = {}, pmid = {40361718}, issn = {2304-8158}, abstract = {Food safety is an important requirement for protecting human health worldwide. In particular, medical students' education on food safety is essential for them as future physicians, and university education is the first step in acquiring this knowledge. We performed an online survey with 1277 respondents among medical students to assess knowledge, attitudes, and practices (KAPs) related to food safety regarding microbiological contamination. Our findings showed that more than half of the respondents presented a low level of food safety knowledge, with a score between 11-60 points, and only 6% managed to score between 81 and 100 points, which was considered a high level of knowledge. On the contrary, we found that most participants had a high level of good practice: 58% scored more than 25 points, 39% had an average level of good practice (scoring between 21 and 25 points), and 3% of respondents had a low level of good practice (scoring below 21 points). We also noticed a statistically significant difference between total scores of preclinical and clinical years of study among medical students (p = 0.005) regarding food safety knowledge. The frequency of cooking was positively correlated with the level of food safety knowledge, but not with food safety practices. Our study shows that better knowledge on food safety is needed among medical students. Improving knowledge and awareness of food safety in relation to microbiological contamination is a good way to protect themselves and to promote the correct food safety knowledge and measures among their patients.}, } @article {pmid40361012, year = {2025}, author = {Barkan, R and Cooke, I and Watson, SA and Strugnell, JM}, title = {Synthesis of transcriptomic studies reveals a core response to heat stress in abalone (genus Haliotis).}, journal = {BMC genomics}, volume = {26}, number = {1}, pages = {474}, pmid = {40361012}, issn = {1471-2164}, mesh = {Animals ; *Gastropoda/genetics/physiology ; *Heat-Shock Response/genetics ; *Gene Expression Profiling ; *Transcriptome ; Computational Biology/methods ; }, abstract = {BACKGROUND: As climate change causes marine heat waves to become more intense and frequent, marine species increasingly suffer from heat stress. This stress can result in reduced growth, disrupted breeding cycles, vulnerability to diseases and pathogens, and increased mortality rates. Abalone (genus Haliotis) are an ecologically significant group of marine gastropods and are among the most highly valued seafood products. However, heat stress events have had devastating impacts on both farmed and wild populations. Members of this genus are among the most susceptible marine species to climate change impacts, with over 40% of all abalone species listed as threatened with extinction. This has motivated researchers to explore the genetics linked to heat stress in abalone. A substantial portion of publicly available studies has employed transcriptomic approaches to investigate abalone genetic response to heat stress. However, to date, no meta-analysis has been conducted to determine the common response to heat stress (i.e. the core response) across the genus. This study uses a standardized bioinformatic pipeline to reanalyze and compare publicly available RNA-seq datasets from different heat stress studies on abalone.

RESULTS: Nine publicly available RNA-seq datasets from nine different heat-stress studies on abalone from seven different abalone species and three hybrids were included in the meta-analysis. We identified a core set of 74 differentially expressed genes (DEGs) in response to heat stress in at least seven out of nine studies. This core set of DEGs mainly included genes associated with alternative splicing, heat shock proteins (HSPs), Ubiquitin-Proteasome System (UPS), and other protein folding and protein processing pathways.

CONCLUSIONS: The detection of a consistent set of genes that respond to heat stress across various studies, despite differences in experimental design (e.g. stress intensity, species studied-geographical distribution, preferred temperature range, etc.), strengthens our proposal that these genes are key elements of the heat stress response in abalone. The identification of the core response to heat stress in abalone lays an important foundation for future research. Ultimately, this study will aid conservation efforts and aquaculture through the identification of resilient populations, genetic-based breeding programs, possible manipulations such as early exposure to stress, gene editing and the use of immunostimulants to enhance thermal tolerance.}, } @article {pmid40357641, year = {2025}, author = {Pourmohsenin, B and Wiese, A and Ziemert, N}, title = {AutoMLST2: a web server for phylogeny and microbial taxonomy.}, journal = {Nucleic acids research}, volume = {}, number = {}, pages = {}, doi = {10.1093/nar/gkaf397}, pmid = {40357641}, issn = {1362-4962}, support = {101000794//H2020-FNR-11-2020: SECRETED/ ; TTU09.717//German Center for Infection Research/ ; 390838134//Cluster of Excellence: EXC 2124: Controlling Microbes to Fight Infection/ ; }, abstract = {Accurate and accessible phylogenetic analysis is essential for understanding microbial taxonomy and evolution, which are integral to microbiology, ecology, and drug discovery, yet it remains a challenging task. AutoMLST2 (https://automlst2.ziemertlab.com) is a web server designed to facilitate automated phylogenetic reconstruction and microbial taxonomy analysis for bacterial and archaeal genomes. It builds on the foundation of AutoMLST, which remains widely used due to its user-friendly interface compared to similar tools. Given its continued popularity and utility, we have enhanced AutoMLST to leverage newer reference databases and computational tools. AutoMLST2 integrates the Genome Taxonomy Database, extends support to archaeal genomes, and improves analytical flexibility. Key improvements include more customizable processing modes, containerization to prevent queue accumulations, and parallel computing for large-scale studies. By incorporating up-to-date databases and workflows, AutoMLST2 continues to provide an accessible and efficient platform for researchers in microbiology, evolutionary ecology, and natural product discovery.}, } @article {pmid40344895, year = {2025}, author = {Kičić, M and Scheuer, S and Korpilo, S and Vuletić, D and Seletković, A and Haase, D and Krajter Ostoić, S}, title = {Relationships between urban green space types, cultural ecosystem services and disservices - a Public Participation Geographic Information System study in Zagreb, Croatia.}, journal = {The Science of the total environment}, volume = {981}, number = {}, pages = {179549}, doi = {10.1016/j.scitotenv.2025.179549}, pmid = {40344895}, issn = {1879-1026}, mesh = {Croatia ; *Geographic Information Systems ; Cities ; *Ecosystem ; *Conservation of Natural Resources/methods ; *Community Participation ; Humans ; *Parks, Recreational ; }, abstract = {Urban green spaces are important providers of ecosystem services in cities, however cultural ecosystem services remain difficult to quantify. Different types of urban green spaces provide various cultural ecosystem services and differ in how they are perceived and utilized by citizens. In this study, we used a Public Participation GIS (PPGIS) survey to collect data on citizens' perceptions and use of cultural ecosystem services and disservices provided by different types of urban green spaces in Zagreb, Croatia. We collected spatial data from 384 respondents on the perceived provision of 19 different attributes of cultural ecosystem services and disservices in 20 defined types of urban green spaces. We used descriptive statistics, spatial metrics, multivariate analysis and visualization techniques to explore and explain 5757 spatial points collected with the PPGIS questionnaire. Results confirm the importance of parks and forests but also that the water elements and greenery around residential buildings serve as important urban green space for providing benefits for citizens of Zagreb. Based on results presented, cultural ecosystem services are perceived as more important than disservices but in some places both co-exist. Our study builds on current literature by providing a systematic, city-wide assessment of cultural ecosystem services related to different types of urban green spaces, while advancing the availability of methods for their quantification.}, } @article {pmid40194740, year = {2025}, author = {Nieman, DC and Sakaguchi, CA and Williams, JC and Lawson, J and Lambirth, KC and Omar, AM and Mulani, FA and Zhang, Q}, title = {Gut Prevotella copri abundance linked to elevated post-exercise inflammation.}, journal = {Journal of sport and health science}, volume = {14}, number = {}, pages = {101039}, doi = {10.1016/j.jshs.2025.101039}, pmid = {40194740}, issn = {2213-2961}, abstract = {PURPOSE: This study aimed to examine the linkage between gut microbiome taxa and exercise-induced inflammation.

METHODS: Twenty-five cyclists provided 4 stool samples during a 10-week period and cycled vigorously for 2.25 h at 67% maximal oxygen uptake (VO2max) in a laboratory setting. Blood samples were collected pre- and post-exercise, with additional samples collected at 1.5-h, 3-h, and 24-h post exercise. Primary outcomes included stool microbiome composition and alpha diversity via whole genome shotgun (WGS) sequencing (averaged from 4 stool samples) and a targeted panel of 75 plasma oxylipins. A total of 5719 taxa were identified, and the 339 that were present in more than 20% of stool samples were used in the analysis. Alpha diversity was calculated by evenness, and the Analysis of Composition of Microbiomes (ANCOM) differential abundance analysis was performed using Quantitative Insights Into Microbial Ecology-2 (QIIME2). A composite variable was calculated from 8 pro-inflammatory oxylipins generated from arachidonic acid (ARA) and cytochrome P-450 (CYP).

RESULTS: ARA-CYP oxylipins were significantly elevated for at least 3-h post-exercise (p < 0.001); they were strongly and positively related to Prevotella copri (P. copri) abundance (R[2] = 0.676, p < 0.001) and negatively related to gut microbiome alpha diversity (R[2] = 0.771, p < 0.001).

CONCLUSION: This analysis revealed for the first time a novel, positive relationship between gut microbiome P. copri abundance in cyclists and post-exercise pro-inflammatory oxylipins. These data demonstrate that about two-thirds of the wide variance in inflammation following prolonged and intensive exercise is largely explained by the abundance of a single gut bacterial species: P. copri.}, } @article {pmid40147302, year = {2025}, author = {Keneally, C and Chilton, D and Dornan, TN and Kidd, SP and Gaget, V and Toomes, A and Lassaline, C and Petrovski, R and Wood, L and Brookes, JD}, title = {Multi-omics reveal microbial succession and metabolomic adaptations to flood in a hypersaline coastal lagoon.}, journal = {Water research}, volume = {280}, number = {}, pages = {123511}, doi = {10.1016/j.watres.2025.123511}, pmid = {40147302}, issn = {1879-2448}, mesh = {*Floods ; Salinity ; RNA, Ribosomal, 16S/genetics ; Geologic Sediments/microbiology ; Metabolomics ; Microbiota ; Multiomics ; }, abstract = {Microorganisms drive essential biogeochemical processes in aquatic ecosystems and are sensitive to both salinity and hydrological changes. As climate change and anthropogenic activities alter hydrology and salinity worldwide, understanding microbial ecology and metabolism becomes increasingly important for managing aquatic ecosystems. Biogeochemical processes were investigated on sediment microbial communities during a significant flood event in the hypersaline Coorong lagoon, South Australia (the largest in the Murray-Darling Basin since 1956). Samples from six sites across a salinity gradient were collected before and during flooding in 2022. To assess changes in microbial taxonomy and metabolic function, 16S rRNA amplicon sequencing was employed alongside untargeted liquid chromatography-mass spectrometry (LC-MS) to assess changes in microbial taxonomy and metabolic function. Results showed a decrease in microbial richness and diversity during flooding, especially in hypersaline conditions. Pre-flood communities were enriched with osmolyte-degrading and methanogenic taxa, alongside osmoprotectant metabolites, such as glycine betaine and choline. Flood conditions favored taxa such as Halanaerobiaceae and Beggiatoaceae, inducing inferred metagenomic shifts indicative of sulfur cycling and nitrogen reduction pathways, while also enriching a greater diversity of metabolites including Gly-Phe dipeptides and guanine. This study demonstrates that integrating metabolomics with microbial community analysis enhances understanding of ecosystem responses to disturbance. These findings suggest microbial communities rapidly change in response to salinity reductions while maintaining key biogeochemical functions. Such insights are valuable for ecosystem management and predictive modelling under environmental stressors such as flooding.}, } @article {pmid40352255, year = {2025}, author = {Seminar, KB and Damayanthi, E and Priandana, K and Imantho, H and Ligar, BW and Seminar, AU and Krishnajaya, AD and Aditya, MR and Suherman, MIH and Fillah, IF}, title = {AI-based system for food and beverage selection towards precision nutrition in Indonesian restaurants.}, journal = {Frontiers in nutrition}, volume = {12}, number = {}, pages = {1590523}, pmid = {40352255}, issn = {2296-861X}, abstract = {The complexity surrounding food selection is attributable to the variability in foods, restaurants, and diners. The diversity of foods, where each dish may have a unique recipe across different restaurants, needs to be accounted for in personalized nutrition. However, personalized food selection poses a combinatorial challenge in selecting the most suitable food at a specific restaurant. The key question is how a diner visiting a particular restaurant can be assisted in selecting optimal foods and beverages based on factors such as sex, age, height, weight, and history of non-communicable diseases (NCDs). In this study, a genetic algorithm (GA) is used to develop a system that can address this issue in the context of Indonesian restaurants. In this system, a database with data on registered diners and foods is maintained. Foods comprise staple foods, side dishes, vegetables, and beverages, each containing its energy and nutrient content for a given restaurant. The nutritional adequacy of a single meal is determined by comparing the energy and nutrient content of the menu with the diner's nutritional needs. The novelty of the proposed system lies in combining scientific nutritional data with individual diner profiles for the selection of the best meal for a diner. This system differs from the existing food recommender applications in Indonesia, which typically do not consider specific diners, personalized nutrition, and NCD history. The proposed system is the first developed application prototype for Indonesian restaurants to overcome the inefficiency of the existing applications. In this study, the structure and chromosome content of the food, its corresponding energy and nutrient contents, and GA operators such as crossover, mutation, and tournament selection for determining the best meal using the defined fitness functions are discussed. The proposed system has been tested at Karimata Restaurant and proved to be highly suitable for the ultimate goal of meal selection for individual diners with different needs, and it can be replicated at other restaurants. Furthermore, user-centered evaluation has revealed that the system (a) increases nutritional understanding and health awareness; (b) is easy to use with comprehensive functions; and (c) promotes user satisfaction with personalized recommendations.}, } @article {pmid40351335, year = {2024}, author = {Li, S and Fan, C and Kargarandehkordi, A and Sun, Y and Slade, C and Jaiswal, A and Benzo, RM and Phillips, KT and Washington, P}, title = {Monitoring Substance Use with Fitbit Biosignals: A Case Study on Training Deep Learning Models Using Ecological Momentary Assessments and Passive Sensing.}, journal = {AI (Basel, Switzerland)}, volume = {5}, number = {4}, pages = {2725-2738}, pmid = {40351335}, issn = {2673-2688}, support = {U54 GM138062/GM/NIGMS NIH HHS/United States ; }, abstract = {Substance use disorders affect 17.3% of Americans. Digital health solutions that use machine learning to detect substance use from wearable biosignal data can eventually pave the way for real-time digital interventions. However, difficulties in addressing severe between-subject data heterogeneity have hampered the adaptation of machine learning approaches for substance use detection, necessitating more robust technological solutions. We tested the utility of personalized machine learning using participant-specific convolutional neural networks (CNNs) enhanced with self-supervised learning (SSL) to detect drug use. In a pilot feasibility study, we collected data from 9 participants using Fitbit Charge 5 devices, supplemented by ecological momentary assessments to collect real-time labels of substance use. We implemented a baseline 1D-CNN model with traditional supervised learning and an experimental SSL-enhanced model to improve individualized feature extraction under limited label conditions. Results: Among the 9 participants, we achieved an average area under the receiver operating characteristic curve score across participants of 0.695 for the supervised CNNs and 0.729 for the SSL models. Strategic selection of an optimal threshold enabled us to optimize either sensitivity or specificity while maintaining reasonable performance for the other metric. Conclusion: These findings suggest that Fitbit data have the potential to enhance substance use monitoring systems. However, the small sample size in this study limits its generalizability to diverse populations, so we call for future research that explores SSL-powered personalization at a larger scale.}, } @article {pmid40348945, year = {2025}, author = {Chen, J and Liu, J and Liu, S and Li, Z and Gao, C and Wang, Z and Huang, S and Jiang, Z and Yang, H}, title = {Multiomics reveals the synergistic response of gut microbiota and spider A. ventricosus to lead and cadmium toxicity.}, journal = {Bulletin of environmental contamination and toxicology}, volume = {114}, number = {5}, pages = {77}, pmid = {40348945}, issn = {1432-0800}, support = {32001205//National Natural Science Foundation of China/ ; 2023JJ30299//Natural Science Foundation of Hunan Province/ ; 2019JJ50236//Natural Science Foundation of Hunan Province/ ; }, mesh = {Animals ; *Cadmium/toxicity ; *Gastrointestinal Microbiome/drug effects ; *Lead/toxicity ; *Spiders/physiology/drug effects ; Metagenomics ; Multiomics ; }, abstract = {The potential crosstalk between the host and gut microbiota (GM) under heavy metal compound pollution remains unexplored. Herein, using comprehensive analysis of metagenomics, metabolomics, behavioral analysis, and cell morphology to investigate the causal relationship between GM and host responses to cadmium (Cd) and lead (Pb) toxicities. Results indicate that Pb and Cd pollution, alone or together, hinder spider predatory behavior and change the composition and function of GM. Combined exposure reduces protein and exogenous compound metabolism, while single exposure affects energy and lipid metabolism. Gut microbiota helps spider antioxidant activity by increasing glutathione, lipoic acid, and L-cysteine. Oxidative damage, increased Enterobacteriaceae (Salmonella), and lipopolysaccharide (LPS) may harm the midgut barrier. Upregulation of choline and acetylcholine, and downregulation of spermidine, may initiate neurotoxicity. Inhibiting actinomycetes might boost sodium gallate for detoxifying single contaminants. Combined pollution detoxification may involve downregulation of indole synthesis metabolic bacteria, tryptophan, indole metabolites, cytochrome P450 (CYP450), and an increase in Desulfobulbia could remove heavy metals and reduce oxidative stress. Combined pollution has a synergistic effect, making the toxicity of multiple pollutants greater than their individual effects, impacting metal resistance genes (MRGs), and antibiotic resistance ontology (AROs) which used for classifying and describing antibiotic resistance, midgut barrier integrity, oxidative stress, and detoxification. The results help to elucidate the interplay of GM and host's reactions, and aid in monitoring and bioremediation of heavy metal pollution.}, } @article {pmid40346497, year = {2025}, author = {Sigwart, JD and Wong, NLWS and González, VL and Machado, FM and Greve, C and Schell, T and Chen, Z}, title = {Genome of the enigmatic watering-pot shell and morphological adaptations for anchoring in sediment.}, journal = {BMC genomics}, volume = {26}, number = {1}, pages = {460}, pmid = {40346497}, issn = {1471-2164}, mesh = {Animals ; *Bivalvia/genetics/anatomy & histology/classification ; Phylogeny ; *Genome ; *Animal Shells/anatomy & histology ; *Geologic Sediments ; *Adaptation, Physiological/genetics ; *Genomics/methods ; }, abstract = {BACKGROUND: In this study, we present the first chromosome-scale genome of Verpa penis (Linnaeus, 1758), and the first for the bivalve clade Anomalodesmata. The present study has two separate foci. Primarily, we provide the genetic resource to bridge further studies from genome to phenome and propose hypotheses to guide future empirical investigations. Secondarily, based on morphology, we outline a conceptual exploration to address their adaptation. Watering-pot shells have been called "the weirdest bivalves" for their fused tubular shell resembling the spout of a watering can. This adventitious tube arose twice convergently in clavagelloidean bivalves. However, previous literature has never provided a convincing adaptive pathway.

RESULTS: The genome assembly of V. penis was about 507 Mb, with contig N50 of 5.33 Mb, and has 96.5% of sequences anchored onto 19 pseudochromosomes. Phylogenomic analyses of this new genome in context of other bivalves confirms the placement for Anomalodesmata as sister to the clade Imparidentia. Contrary to expectations from its highly modified body plan, there is no evidence of chromosome reduction compared to the ancestral karyotype of heterodont bivalves (1 N = 19). Drawing on established principles from engineering as well as morphology, the thought experiment about the adventitious tube seeks to extend current understanding by exploring parallels with other built structures. A new hypothesis explains one possible interpretation of the adaptive significance of this body form: it is potentially structurally optimised for vertical stability in relatively soft sediments, with parallels to the engineering principles of a suction anchor.

CONCLUSIONS: While the conclusions presented here on morphological interpretations are theoretical, this serves as a foundation for further empirical validation and refinement. Our study offers new insights to a long-standing mystery in molluscan body forms and provides genomic resources that are relevant to understanding molluscan evolution, biomineralisation, and biomimetic design.}, } @article {pmid40346072, year = {2025}, author = {Bosso, L and Saviano, S and Abagnale, M and Bellardini, D and Bolinesi, F and Botte, V and Buondonno, A and Carotenuto, Y and Casotti, R and Chiusano, ML and Cipolletta, F and Conversano, F and De Domenico, F and Del Gaizo, G and Donnarumma, V and Furia, M and Iudicone, D and Kokoszka, F and Laface, F and Licandro, P and Mangoni, O and Margiotta, F and Mazzocchi, MG and Miralto, M and Montresor, M and Pansera, M and Pedà, C and Percopo, I and Raffini, F and Russo, L and Romeo, T and Saggiomo, M and Sarno, D and Trano, AC and Vannini, J and Vargiu, M and Zampicinini, G and Zingone, A and Cianelli, D and D'Alelio, D}, title = {GIS-based integration of marine data for assessment and management of a highly anthropized coastal area.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {16200}, pmid = {40346072}, issn = {2045-2322}, mesh = {Italy ; *Geographic Information Systems ; *Environmental Monitoring/methods ; Ecosystem ; Humans ; *Conservation of Natural Resources ; Oceans and Seas ; Animals ; Food Chain ; }, abstract = {Monitoring coastal marine environments by evaluating and comparing their chemical, physical, biological, and anthropogenic components is essential for ecological assessment and socio-economic development. In this study, we conducted an integrated multivariate analysis to assess the descriptors of the Marine Strategy Framework Directive at a regional scale in the Tyrrhenian Sea (Italy), with a specific focus on the densely populated coastal zone of the Campania region. Physical, chemical, and biological data were collected and analyzed in 22 sampling sites during three oceanographic surveys in the Gulf of Gaeta (GoG), Naples (GoN), and Salerno (GoS) in autumn 2020. Our results indicated that these three gulfs were distinct overall, with GoN being more divergent and heterogeneous than GoG and GoS. The marine area studied in the GoN had more favorable hydrographic and trophic conditions and food web characteristics, except for the mesozooplankton biomass, and was closer to socio-economic factors compared to the GoS and GoG. Our analysis helped us find the key ecological features that define different sub-regions and connect them to social and economic factors, including human activities. We highlighted the relevance of primary and secondary variables in terms of the comprehensive ecological assessment of a marine area and its impact on specific socio-economic activities. These findings support the need to describe and integrate multiple descriptors at the spatial scale.}, } @article {pmid40345178, year = {2025}, author = {O'Callaghan, ME and Casey, M and Pearl, D and Hickey, O and Fosse, A and Sigurðsson, SE and Savage, DW and Vehviläinen-Julkunen, K and Bykachev, K and Parviainen, A and Parker, H and Condell, J and Leavey, G and Hart, N and Weihe, P and Petersen, MS and Glynn, L}, title = {COVID-19 open data: An ecological study and international collaboration examining pandemic trends in Northern Periphery arctic countries.}, journal = {Health informatics journal}, volume = {31}, number = {2}, pages = {14604582251315588}, doi = {10.1177/14604582251315588}, pmid = {40345178}, issn = {1741-2811}, mesh = {Humans ; *COVID-19/epidemiology/mortality ; Arctic Regions/epidemiology ; *International Cooperation ; *Pandemics ; SARS-CoV-2 ; }, abstract = {Objectives: In the early stages of the COVID-19 pandemic, evidence generation lagged behind public health responses. This study describes an international collaboration of frontline clinicians who used open data describing COVID-19 trends to generate "practice-based evidence". Methods: Open data resources from nine Northern Periphery and Arctic (NPA) countries were harnessed using the open-source programming language 'R' and our collaborations analyses and insights were published on a public-facing website. The website's visualisations guided teleconference discussions from September 2020 to March 2021, focusing on contextualizing national responses, especially in rural regions. Results: This project facilitated shared learning from COVID-19 trends and highlighted key aspects of national responses. Notably, rural NPA regions experienced less COVID-19 cases and mortality in the first year of the pandemic. Conclusion: This international collaborative effort, driven by open data analysis, provided a platform to share real-world insights. The study offers a potential template for future pandemics and emphasises the importance of sustaining open data resources, including granular data like excess mortality, for effective pandemic learning.}, } @article {pmid40344217, year = {2025}, author = {Schindler, Z and Larysch, E and Fornoff, F and Kröner, K and Obladen, N and Klein, AM and Seifert, T and Vonderach, C and Morhart, C}, title = {Flower power: Modeling floral resources of wild cherry (Prunus avium L.) for bee pollinators based on 3D data.}, journal = {Ecology}, volume = {106}, number = {5}, pages = {e70103}, pmid = {40344217}, issn = {1939-9170}, support = {2819NA071//Bundesministerium für Ernährung und Landwirtschaft/ ; }, mesh = {*Pollination/physiology ; *Flowers/physiology ; Animals ; Bees/physiology ; *Models, Biological ; *Prunus avium/physiology ; }, abstract = {Pollinator declines pose a threat to ecosystems and food production. Agriculture contributes to, but also suffers from, the erosion of pollination services. Our study explores the potential of trees in agricultural landscapes to support pollinators by providing floral resources. Our overarching objective is the quantification of floral resources produced by wild cherry (Prunus avium L.) that can be used by flower-visiting and pollinating insects such as bees. Using an innovative approach, we combine pollen measurements with manual counts of flowers on branches and 3D data derived from terrestrial laser scanning. This approach allows us to scale up flower numbers from branches to entire trees. The derived models for estimating the probability of flower occurrence (R[2] c = 0.52, R[2] m = 0.50) and the number of flowers per branch (R[2] c = 0.88, R[2] m = 0.84), as well as the number of flowers per tree (R[2] = 0.83), show good model fits with only a small set of predictors. The model fits indicate that, at the branch level, predicting flowering probability is more challenging than predicting flower abundance. We found differences in the number of flowers per branch in different crown sections, suggesting that floral resources are heterogeneously distributed. Furthermore, we demonstrate that the number of flowers per tree increases exponentially with tree dimension (stem diameter, crown volume). Therefore, large trees provide disproportionately more floral resources than small trees and are particularly worthy of conservation efforts. For example, our models estimate that a single tree with a stem diameter of 25 cm carries 195,535 flowers (95% CI: 159,991-237,318), thus providing about 57 cm[3] (95% CI: 32-88 cm[3]) of pollen and producing 170 g (95% CI: 48-345 g) nectar sugar per 24 h. This amount of pollen is sufficient to rear, for example, 5202 larvae (95% CI: 2886-8022) of Lasioglossum laticeps, a common and generalist sweat bee of cherry trees. In contrast, a smaller tree with a stem diameter of 10 cm provides only 8% of these resources. In conclusion, we demonstrate how our results contribute to the broader single-large-or-several-small debate in nature conservation by highlighting the value of large trees. Additionally, we show how information gathered at the branch level may be nondestructively upscaled to entire trees.}, } @article {pmid40344046, year = {2025}, author = {Ramihangihajason, TA and Weber, JL and Rakotondraompiana, S and Roger, E and Faramalala, MH and Rakotoniaina, S}, title = {Natural capital accounting as a decision support tool for environmental management of a protected area in Madagascar.}, journal = {PloS one}, volume = {20}, number = {5}, pages = {e0321948}, pmid = {40344046}, issn = {1932-6203}, mesh = {Madagascar ; *Conservation of Natural Resources/methods ; Ecosystem ; Biodiversity ; Forests ; Animals ; *Decision Support Techniques ; Humans ; Birds ; }, abstract = {Ecosystem change affects the availability of resources and services provided by nature. Ecosystem Natural capital accounting helps track these changes and supports better decision-making for managing the environment. This approach aims to assess changes in the stocks and flows of natural resources and the possibility to integrate them into economic and political decisions. The protected area of Mahavavy-Kinkony Complex, in North-Western of Madagascar, was chosen to implement this approach due to its many types of ecosystems as well as important reserves of threatened birds. In five years (2013-2018), we have observed a reduction in woodland cover (forest and mangrove) due to both regulated and illegal logging, linked to urban expansion and increasing of human pressure. This loss of woodland compromises not only biodiversity but also the capacity of ecosystems to provide ecosystem services. At the same time, the silting up of surface waters is compromising water quality and the health of aquatic ecosystems. In addition, the increase in agricultural land at the expense of forested areas raises concerns about the continuing degradation of natural ecosystems. All of these changes can be observed inside local socio-ecological landscape type. Each socio-ecological landscape type shows the potential variation in the production of ecosystem services.}, } @article {pmid40343940, year = {2025}, author = {Longo, L and Veronese, M and Cagnato, C and Sorrentino, G and Tetruashvili, A and Belfer-Cohen, A and Jakeli, N and Meshveliani, T and Meneghetti, M and Zoleo, A and Marcomini, A and Artioli, G and Badetti, E and Hardy, K}, title = {Direct evidence for processing Isatis tinctoria L., a non-nutritional plant, 32-34,000 years ago.}, journal = {PloS one}, volume = {20}, number = {5}, pages = {e0321262}, pmid = {40343940}, issn = {1932-6203}, mesh = {*Plant Leaves/chemistry/ultrastructure ; Humans ; *Isatis/chemistry/anatomy & histology ; Spectrum Analysis, Raman ; Spectroscopy, Fourier Transform Infrared ; Archaeology ; History, Ancient ; }, abstract = {Recovering evidence for the intentional use of plants in the Palaeolithic is challenging due to their perishable nature as, unlike chipped stone or bone artefacts, plant remains are rarely preserved. This has created a paradigm for the Palaeolithic in which plants seldom feature, resulting in a partial and skewed perspective; in fact, plants were as essential to human life then as they are today. Here, we combine morphological and spectroscopic analyses (µ-Raman, µ-FTIR) to provide robust multiscale physical and biomolecular evidence for the deliberate pounding and grinding of Isatis tinctoria L. leaves 34-32,000 years ago. The leaf epidermis fragments were found entrapped in the topography of the used surface of unmodified pebbles, in association with use-wear traces. Although their bitter taste renders them essentially inedible, the leaves have well-recognised medicinal properties and contain indigotin precursors, the chromophore responsible for the blue colour of woad, a plant-based dye that is insoluble in water. We used a stringent approach to contamination control and biomolecular analysis to provide evidence for a new perspective on human behaviour, and the applied technical and ecological knowledge that is likely to have prevailed in the Upper Palaeolithic. Whether this plant was used as a colourant, as medicine, or indeed for both remains unknown, but offers a new perspective on the fascinating possibilities of non-edible plant use.}, } @article {pmid40343039, year = {2025}, author = {Cuenca, PR and Souza, FN and do Nascimento, RC and da Silva, AG and Eyre, MT and Santana, JO and de Oliveira, DS and de Souza, EVR and Palma, FAG and de Carvalho Santiago, DC and Dos Santos Ribeiro, P and Read, JM and Cremonese, C and Costa, F and Giorgi, E}, title = {Using step selection functions to analyse human mobility using telemetry data in infectious disease epidemiology: a case study of leptospirosis.}, journal = {medRxiv : the preprint server for health sciences}, volume = {}, number = {}, pages = {}, pmid = {40343039}, abstract = {Human movement plays a critical role in the transmission of infectious diseases, especially those with environmental drivers like leptospirosis-a zoonotic bacterial infection linked to mud and water contact. Using GPS loggers, we collected detailed telemetry data to understand how fine-scale movements can be analysed in the context of an infectious disease. We recruited individuals living in urban slums in Salvador, Brazil to analyse how they interact with environmental risk factors such as domestic rubbish piles, open sewers, and a local stream. We aimed to identify differences in movement patterns inside the study areas by gender, age, and leptospirosis serological status. Step-selection functions, a spatio-temporal model used in animal movement ecology, estimated selection coefficients to represent the likelihood of movement toward specific environmental factors. With 124 participants wearing GPS devices for 24 to 48 hours, recording locations every 35 seconds during active daytime hours, we segmented movements into morning, midday, afternoon, and evening. Our results suggested women moved closer to the central stream and farther from open sewers compared to men, while serologically positive individuals avoided open sewers. This study introduces a novel method for analysing human telemetry data in infectious disease research, providing critical insights for targeted interventions.}, } @article {pmid40339581, year = {2025}, author = {Pekar, JE and Lytras, S and Ghafari, M and Magee, AF and Parker, E and Wang, Y and Ji, X and Havens, JL and Katzourakis, A and Vasylyeva, TI and Suchard, MA and Hughes, AC and Hughes, J and Rambaut, A and Robertson, DL and Dellicour, S and Worobey, M and Wertheim, JO and Lemey, P}, title = {The recency and geographical origins of the bat viruses ancestral to SARS-CoV and SARS-CoV-2.}, journal = {Cell}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.cell.2025.03.035}, pmid = {40339581}, issn = {1097-4172}, abstract = {The emergence of SARS-CoV in 2002 and SARS-CoV-2 in 2019 led to increased sampling of sarbecoviruses circulating in horseshoe bats. Employing phylogenetic inference while accounting for recombination of bat sarbecoviruses, we find that the closest-inferred bat virus ancestors of SARS-CoV and SARS-CoV-2 existed less than a decade prior to their emergence in humans. Phylogeographic analyses show bat sarbecoviruses traveled at rates approximating their horseshoe bat hosts and circulated in Asia for millennia. We find that the direct ancestors of SARS-CoV and SARS-CoV-2 are unlikely to have reached their respective sites of emergence via dispersal in the bat reservoir alone, supporting interactions with intermediate hosts through wildlife trade playing a role in zoonotic spillover. These results can guide future sampling efforts and demonstrate that viral genomic regions extremely closely related to SARS-CoV and SARS-CoV-2 were circulating in horseshoe bats, confirming their importance as the reservoir species for SARS viruses.}, } @article {pmid40338955, year = {2025}, author = {Benjamin, JR and Neibauer, J and Anthony, H and Vazquez, J and Rawhouser, A and Dunham, JB}, title = {A partner-driven decision support model to inform the reintroduction of bull trout.}, journal = {PloS one}, volume = {20}, number = {5}, pages = {e0323427}, pmid = {40338955}, issn = {1932-6203}, mesh = {Animals ; *Trout/physiology ; *Conservation of Natural Resources/methods ; Ecosystem ; *Decision Support Techniques ; Decision Making ; }, abstract = {Assessments of species reintroductions involve a series of complex decisions that include human perspectives and ecological contexts. Here, we present a reintroduction assessment involving bull trout (Salvelinus confluentus) using a structured decision-making process. We approached this assessment by engaging partners representing public utilities, government agencies, and Tribes with shared interests in a potential reintroduction. These individuals identified objectives, decision alternatives, and ecological scenarios that were incorporated into a co-produced simulation-based model of potential reintroduction outcomes. The model included mathematical representations of habitat availability, life history expression, and assumptions regarding constraints on potential bull trout populations. Within each recipient stream, partners chose to explore a wide range of decision alternatives and simulated scenarios affecting reintroduction success. Results suggested that 1) reintroductions using eggs or adults were most optimal, 2) adding more individuals resulted in diminishing returns, 3) access to migratory habitat could improve success, and 4) the diversity of opportunities for life history expression led to improved reintroduction opportunities. In addition, modeled scenarios indicated some recipient streams consistently produced lower abundance of reintroduced bull trout. This work contributes a novel example to a growing portfolio of reintroduction assessments that may inform future conservation for bull trout and many other species facing similar challenges.}, } @article {pmid40335533, year = {2025}, author = {Pakulnicka, J and Kruk, M}, title = {Water beetle networks differences and migration between natural lakes and post-exploitation water bodies.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {15898}, pmid = {40335533}, issn = {2045-2322}, mesh = {Animals ; *Coleoptera/physiology ; *Lakes ; Ecosystem ; *Animal Migration ; Biodiversity ; }, abstract = {Water deficits are a serious problem around the world, which also affects young landscapes, where lakes are most abundant. This poses a threat to many habitats and biological diversity found here. The relationships between species in the ecological networks of lakes at different stages of development and in nearby post-exploitation water bodies remain poorly understood. To better understand the functioning of beetle communities in different ecosystems, we created five network models that we subjected to graph analysis. By analysing the general attributes of the network (number of neighbours, shortest path, characteristic path length, clustering coefficient, network centralisation, network density and network heterogeneity) and those related to the nodes (NCC-Node Closeness Centrality, NBC-Node Betweenness Centrality, NDC-Node Degree Centrality) and to the edges (EBC-Edge Betweenness Centrality and correlations between the biomass of species as nodes), we were able to determine the role of each species in the networks and the relationships between the species. We then used the machine learning ensemble modelling XGBoost-SHAP to identify species that are particularly important in migrations between water bodies and to assess the direction and strength of migrations using Shapley values. Our analyses are based on faunal material from 25 lakes (mesotrophic, eutrophic, dystrophic) and 31-post-exploitation water bodies (clay pits and gravel pits) in northern Poland, in the Masurian Lake District. We found a total of 169 species representing different ecological and functional components. We have shown that the structures of the network between the biomass of species in the analysed five water types differ significantly. The highest value for network density was recorded in eutrophic lakes and clay ponds, the lowest in dystrophic lakes. In eutrophic lakes these are mainly eurybionts, in clay pits-rheophiles and in gravel pits-argilophiles and tyrphophiles. The relationship between the species with the highest NBC and EBC values is particularly important in order to maintain the stability of the network. The periphery of the network usually consists of larger predators that do not compete with each other. By analysing the migration directions of beetles between different ecosystems, we were able to demonstrate a greater affinity of the beetle fauna, especially the argilophiles (e.g. Scarodytes halensis and Laccobius minutus) inhabiting gravel pits, to dystrophic lakes. The beetles in clay pits originate mainly from mesotrophic lakes. These are mainly rheophiles, mostly weakly flying species, such as: Haliplus fluviatilis, Haliplus fulvus, Ilybius fenestratus, Hygrotus vericolor and Haliplus flavicollis. These species are important for the stability of ecological networks in the studied lake types. Their movements between the ecosystems studied in turn contribute to the functional connectivity between the individual lakes, which ensures the stabilisation of biotic relationships at the landscape level. At the same time, they generally also indicate the optimisation of environmental conditions in post-exploitation water bodies, which makes them potential substitute habitats for natural lakes.}, } @article {pmid40324147, year = {2025}, author = {Gilpin, W}, title = {Optimization hardness constrains ecological transients.}, journal = {PLoS computational biology}, volume = {21}, number = {5}, pages = {e1013051}, pmid = {40324147}, issn = {1553-7358}, mesh = {*Ecosystem ; *Models, Biological ; Computer Simulation ; Computational Biology ; Biological Evolution ; }, abstract = {Living systems operate far from equilibrium, yet few general frameworks provide global bounds on biological transients. In high-dimensional biological networks like ecosystems, long transients arise from the separate timescales of interactions within versus among subcommunities. Here, we use tools from computational complexity theory to frame equilibration in complex ecosystems as the process of solving an analogue optimization problem. We show that functional redundancies among species in an ecosystem produce difficult, ill-conditioned problems, which physically manifest as transient chaos. We find that the recent success of dimensionality reduction methods in describing ecological dynamics arises due to preconditioning, in which fast relaxation decouples from slow solving timescales. In evolutionary simulations, we show that selection for steady-state species diversity produces ill-conditioning, an effect quantifiable using scaling relations originally derived for numerical analysis of complex optimization problems. Our results demonstrate the physical toll of computational constraints on biological dynamics.}, } @article {pmid40132265, year = {2025}, author = {Gu, J and Shen, Y and Guo, L and Chen, Z and Zhou, D and Ji, G and Gu, A}, title = {Investigation of the mechanisms of liver injury induced by emamectin benzoate exposure at environmental concentrations in zebrafish: A multi-omics approach to explore the role of the gut-liver axis.}, journal = {Journal of hazardous materials}, volume = {491}, number = {}, pages = {138008}, doi = {10.1016/j.jhazmat.2025.138008}, pmid = {40132265}, issn = {1873-3336}, mesh = {Animals ; Zebrafish ; *Ivermectin/analogs & derivatives/toxicity ; *Liver/drug effects/metabolism/pathology ; Gastrointestinal Microbiome/drug effects ; *Chemical and Drug Induced Liver Injury/metabolism/pathology/etiology ; *Water Pollutants, Chemical/toxicity ; Metabolomics ; Lipid Metabolism/drug effects ; *Insecticides/toxicity ; RNA, Ribosomal, 16S/genetics ; Multiomics ; }, abstract = {Emamectin benzoate (EMB) is a lipophilic pesticide that enters aquatic systems and adversely affects non-target organisms. This study investigated the long-term effects of EMB on zebrafish, exposing them to concentrations of 0, 0.1, 1, and 10 μg/L from the 4-hour post-fertilization (hpf) embryo stage to the 120-day post-fertilisation (dpf) adult stage. We found that exposure to 1 μg/L EMB induced liver damage, manifested as impaired liver function (elevated aspartate aminotransferase (AST) and alanine aminotransferase (ALT)), histopathological damage (lipid accumulation), as well as inflammatory and oxidative damage, with a dose - dependent effect. Non-targeted metabolomic analysis revealed an increase in lipid molecules in the liver, affecting the pathways related to glycerophospholipid metabolism. In addition, EMB exposure resulted in damage to the intestinal barrier and inflammatory responses in zebrafish. 16S rRNA sequencing demonstrated that EMB exposure resulted in notable alterations in the gut microbiota composition. Notably, the abundance of Plesiomonas and Cetobacterium increased in the EMB exposure group and exhibited a positive correlation with the majority of liver lipid metabolites. In contrast, reductions in Muribaculaceae and Alloprevotella were negatively correlated. The results of this study indicate that long-term exposure to EMB disrupts the gut microbiota, leading to the dysregulation of hepatic phospholipid metabolism. These findings provide new insights into the health risks associated with EMB and highlight its potential threats to higher organisms, including mammals.}, } @article {pmid40117176, year = {2025}, author = {Zielińska, K and Udekwu, KI and Rudnicki, W and Frolova, A and Łabaj, PP}, title = {Healthy microbiome-moving towards functional interpretation.}, journal = {GigaScience}, volume = {14}, number = {}, pages = {}, pmid = {40117176}, issn = {2047-217X}, support = {2020/38/E/NZ2/00598//NCN/ ; PLG/2023/016234//Jagiellonian University in Krakow/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Inflammatory Bowel Diseases/microbiology ; *Metagenomics/methods ; Dysbiosis/microbiology ; Phylogeny ; *Microbiota ; Principal Component Analysis ; Computational Biology/methods ; }, abstract = {BACKGROUND: Microbiome-based disease prediction has significant potential as an early, noninvasive marker of multiple health conditions linked to dysbiosis of the human gut microbiota, thanks in part to decreasing sequencing and analysis costs. Microbiome health indices and other computational tools currently proposed in the field often are based on a microbiome's species richness and are completely reliant on taxonomic classification. A resurgent interest in a metabolism-centric, ecological approach has led to an increased understanding of microbiome metabolic and phenotypic complexity, revealing substantial restrictions of taxonomy-reliant approaches.

FINDINGS: In this study, we introduce a new metagenomic health index developed as an answer to recent developments in microbiome definitions, in an effort to distinguish between healthy and unhealthy microbiomes, here in focus, inflammatory bowel disease (IBD). The novelty of our approach is a shift from a traditional Linnean phylogenetic classification toward a more holistic consideration of the metabolic functional potential underlining ecological interactions between species. Based on well-explored data cohorts, we compare our method and its performance with the most comprehensive indices to date, the taxonomy-based Gut Microbiome Health Index (GMHI), and the high-dimensional principal component analysis (hiPCA) methods, as well as to the standard taxon- and function-based Shannon entropy scoring. After demonstrating better performance on the initially targeted IBD cohorts, in comparison with other methods, we retrain our index on an additional 27 datasets obtained from different clinical conditions and validate our index's ability to distinguish between healthy and disease states using a variety of complementary benchmarking approaches. Finally, we demonstrate its superiority over the GMHI and the hiPCA on a longitudinal COVID-19 cohort and highlight the distinct robustness of our method to sequencing depth.

CONCLUSIONS: Overall, we emphasize the potential of this metagenomic approach and advocate a shift toward functional approaches to better understand and assess microbiome health as well as provide directions for future index enhancements. Our method, q2-predict-dysbiosis (Q2PD), is freely available (https://github.com/Kizielins/q2-predict-dysbiosis).}, } @article {pmid40017036, year = {2025}, author = {Han, Y and Du, Q and Dai, Y and Gu, S and Lei, M and Liu, W and Zhang, W and Zhu, M and Feng, L and Si, H and Liu, J and Zan, Y}, title = {EasyOmics: A graphical interface for population-scale omics data association, integration, and visualization.}, journal = {Plant communications}, volume = {6}, number = {5}, pages = {101293}, doi = {10.1016/j.xplc.2025.101293}, pmid = {40017036}, issn = {2590-3462}, mesh = {*Software ; *Genomics/methods ; Genome-Wide Association Study ; *Computational Biology/methods ; User-Computer Interface ; Computer Graphics ; Quantitative Trait Loci ; Proteomics ; Metabolomics ; }, abstract = {The rapid growth of population-scale whole-genome resequencing, RNA sequencing, bisulfite sequencing, and metabolomic and proteomic profiling has led quantitative genetics into the era of big omics data. Association analyses of omics data, such as genome-, transcriptome-, proteome-, and methylome-wide association studies, along with integrative analyses of multiple omics datasets, require various bioinformatics tools, which rely on advanced programming skills and command-line interfaces and thus pose challenges for wet-lab biologists. Here, we present EasyOmics, a stand-alone R Shiny application with a user-friendly interface that enables wet-lab biologists to perform population-scale omics data association, integration, and visualization. The toolkit incorporates multiple functions designed to meet the increasing demand for population-scale omics data analyses, including data quality control, heritability estimation, genome-wide association analysis, conditional association analysis, omics quantitative trait locus mapping, omics-wide association analysis, omics data integration, and visualization. A wide range of publication-quality graphs can be prepared in EasyOmics by pointing and clicking. EasyOmics is a platform-independent software that can be run under all operating systems, with a docker container for quick installation. It is freely available to non-commercial users at Docker Hub https://hub.docker.com/r/yuhan2000/easyomics.}, } @article {pmid38319551, year = {2025}, author = {Fuller, TJ and Lambert, DN and DiClemente, RJ and Wingood, GM}, title = {Reach and Capacity of Black Protestant Health Ministries as Sites of Community-Wide Health Promotion: A Qualitative Social Ecological Model Examination.}, journal = {Journal of racial and ethnic health disparities}, volume = {12}, number = {2}, pages = {887-898}, pmid = {38319551}, issn = {2196-8837}, mesh = {Adult ; Female ; Humans ; Male ; Middle Aged ; *Black or African American/statistics & numerical data/psychology ; Georgia ; *Health Promotion/organization & administration ; Interviews as Topic ; *Protestantism ; Qualitative Research ; Secondary Data Analysis ; }, abstract = {Black communities in the Southeast United States experience a disproportionate burden of illness and disease. To address this inequity, public health practitioners are partnering with Black Protestant churches to deliver health promotion interventions. Yet, the reach of these programs beyond the organizational level of the Social Ecological Model (SEM) is not well defined. Thus, the aim of this study is to understand Black Protestant church leaders' and members' perceptions about the capacity of their ministries to reach into their communities, beyond their congregations, as providers or hosts of health education or promotion interventions. From 20 Black Protestant churches in Atlanta, GA, 92 church leaders and members participated in semi-structured interviews. Grounded theory guided data analysis and a diverse team coded the interviews. Most participating churches had health ministries. Participants saw the boundaries between their churches at the organizational level of the SEM and the broader Black community to be porous. Those who described their "community" as being broader than their congregation also tended to describe community-wide health promotion their church engaged in. They described church-based health fairs as a strategy to promote engagement in their communities. Some participants, particularly those in a health-related profession, discussed visions of how to utilize their church as a site for community-wide health promotion. We suggest these participants may be boundary leaders who can build relationships between public health professionals, pastors, and congregants. Based on the findings, we suggest that church-based health fairs may be effective sites of community-wide health promotion.}, } @article {pmid40333133, year = {2025}, author = {Niculescu, AG and Mitache, MM and Grumezescu, AM and Chifiriuc, MC and Mihai, MM and Tantu, MM and Tantu, AC and Popa, LG and Grigore, GA and Cristian, RE and Popa, MI and Vrancianu, CO}, title = {From Microbial Ecology to Clinical Challenges: The Respiratory Microbiome's Role in Antibiotic Resistance.}, journal = {Pathogens (Basel, Switzerland)}, volume = {14}, number = {4}, pages = {}, pmid = {40333133}, issn = {2076-0817}, support = {CNFIS-FDI-2024-F-0484 INOVEX//University of Bucharest/ ; Pillar III, Component C9/Investment no. 8 (I8) - contract CF 68//; Ministry of Research, Innovation and Digitalization through the National Recovery and Resilience Plan (PNRR) of Romania/ ; project no. 23020101, Contract no. 7N from 3 January 2023//The core program within the National Research Development and Innovation Plan, 2022-2027', carried out with the support of the Ministry of Research, Innovation and Digitalization (MCID)/ ; }, mesh = {Humans ; *Microbiota/drug effects ; Anti-Bacterial Agents/pharmacology/therapeutic use ; *Respiratory Tract Infections/microbiology/drug therapy ; *Drug Resistance, Microbial ; Probiotics ; *Drug Resistance, Bacterial ; *Respiratory System/microbiology ; }, abstract = {Antibiotic resistance represents a growing public health threat, with airborne drug-resistant strains being especially alarming due to their ease of transmission and association with severe respiratory infections. The respiratory microbiome plays a pivotal role in maintaining respiratory health, influencing the dynamics of antibiotic resistance among airborne pathogenic microorganisms. In this context, this review proposes the exploration of the complex interplay between the respiratory microbiota and antimicrobial resistance, highlighting the implications of microbiome diversity in health and disease. Moreover, strategies to mitigate antibiotic resistance, including stewardship programs, alternatives to traditional antibiotics, probiotics, microbiota restoration techniques, and nanotechnology-based therapeutic interventions, are critically presented, setting an updated framework of current management options. Therefore, through a better understanding of respiratory microbiome roles in antibiotic resistance, alongside emerging therapeutic strategies, this paper aims to shed light on how the global health challenges posed by multi-drug-resistant pathogens can be addressed.}, } @article {pmid40319682, year = {2025}, author = {Hwang, H and Kim, D and Kim, S and Kim, JY and Kim, ES and Yang, T and Lee, N and Piao, Y and Park, BJ and Lee, DK}, title = {Optimizing urban green spaces using a decision-support model for carbon sequestration and ecological connectivity.}, journal = {Journal of environmental management}, volume = {384}, number = {}, pages = {125058}, doi = {10.1016/j.jenvman.2025.125058}, pmid = {40319682}, issn = {1095-8630}, mesh = {*Carbon Sequestration ; *Decision Support Techniques ; Cities ; *Conservation of Natural Resources/methods ; Ecosystem ; }, abstract = {Urban green spaces (UGSs) are vital for enhancing urban ecological health and resident well-being. However, their diverse functions need to be balanced based on spatial limitations and varying stakeholder preferences. Integrated planning approaches are needed to exploit the multiple benefits of UGSs. This study introduces a multi-objective decision-support model designed to optimize UGS planning by simultaneously addressing carbon sequestration, ecological connectivity, and cost constraints. The model incorporates the non-dominated sorting genetic algorithm II to identify Pareto-optimal solutions for tailored decision-making strategies that balance different priorities. The model indicated that ecological connectivity can be improved by 7.57 % while meeting carbon-reduction and budgetary targets. The model effectively balanced trade-offs, underscoring the importance of both the quantity and strategic placement of green space. This decision-support framework empowers decision-makers to rapidly simulate and validate optimal scenarios, effectively balance competing objectives, and provide a scientific basis through verifiable feedback, ultimately promoting the development of sustainable urban environments.}, } @article {pmid40273607, year = {2025}, author = {Nkoh, JN and Ye, T and Shang, C and Li, C and Tu, J and Li, S and Wu, Z and Chen, P and Hussain, Q and Esemu, SN}, title = {Deciphering the mechanisms for preferential tolerance of Escherichia coli BL21 to Cd(II) over Cu(II) and Ni(II): A combined physiological, biochemical, and multiomics perspective.}, journal = {Ecotoxicology and environmental safety}, volume = {297}, number = {}, pages = {118195}, doi = {10.1016/j.ecoenv.2025.118195}, pmid = {40273607}, issn = {1090-2414}, mesh = {*Escherichia coli/drug effects/physiology/metabolism ; *Cadmium/toxicity ; *Nickel/toxicity ; *Copper/toxicity ; Oxidative Stress/drug effects ; Escherichia coli Proteins/metabolism/genetics ; Hydrogen Peroxide/metabolism ; Multiomics ; }, abstract = {Environmental pollution severely affects ecological functions/health, and nondegradable pollutants such as heavy metals (HMs) cause significant damage to living organisms. Escherichia coli is one of the most studied life forms, and its response to oxidative stress is driven by a complex ensemble of mechanisms driven by transcriptomic-level adjustments. However, the magnitude of the physiological, metabolic, and biochemical alterations and their relationships with transcriptomic changes remain unclear. Studying the growth of E. coli in Cd-, Cu-, and Ni-polluted media at pH 5.0, we observed that (i) downregulation of the alkyl hydroperoxide complex, glutathione reductase, and glutathione S-transferase by Cd inhibited H2O2 degradation, and the accumulated H2O2 was respectively 2.7, 1.7, and 2.4 times greater than that in the control, Cu, and Ni treatments; (ii) Zn-associated resistance protein (ZraP) was the major scavenger of Cd, with a 140.7-fold increase in its expression; (iii) the P-type Cu[+] transporter (CopA), multicopper oxidase (CueO), and heteromultimeric transport system (CusCBAF) controlled the excretion and detoxification of Cu; (iv) the Cd[2+]/Zn[2+]/Pb[2+]-exporting P-type ATPase (ZntA) and transcriptional activator ZntR were the major transporters of Ni; (v) Cd upregulated biofilm formation and synthesis of secondary metabolites more than Cu and Ni, which resulted in increased adsorption and improved tolerance; and (vi) the activity of superoxide dismutase in Cu-spiked cells was 153.2 %, 141.7 %, and 172.7 % higher and corresponded to 85.7 %, 524.5 %, and 491.5 % lower O2[●][-] in the control, Cd-, and Ni-spiked cells, respectively. This study reveals E. coli's preferential tolerance mechanisms to Cd rather than Cu and Ni and demonstrates mechanisms for its survival in highly polluted environments.}, } @article {pmid40332368, year = {2025}, author = {Zheng, K and Feng, Y and Liu, R and Zhang, Y and Fan, D and Zhong, K and Tang, X and Zhang, Q and Cao, S}, title = {Bioinformatics Analysis Reveals the Evolutionary Characteristics of the Phoebe bournei ARF Gene Family and Its Expression Patterns in Stress Adaptation.}, journal = {International journal of molecular sciences}, volume = {26}, number = {8}, pages = {}, pmid = {40332368}, issn = {1422-0067}, mesh = {*Gene Expression Regulation, Plant ; *Stress, Physiological/genetics ; Phylogeny ; *Evolution, Molecular ; *Computational Biology/methods ; *Plant Proteins/genetics/metabolism ; *Transcription Factors/genetics/metabolism ; *Multigene Family ; *Adaptation, Physiological/genetics ; *Poaceae/genetics ; Indoleacetic Acids/metabolism ; Promoter Regions, Genetic ; }, abstract = {Auxin response factors (ARFs) are pivotal transcription factors that regulate plant growth, development, and stress responses. Yet, the genomic characteristics and functions of ARFs in Phoebe bournei remain undefined. In this study, 25 PbARF genes were identified for the first time across the entire genome of P. bournei. Phylogenetic analysis categorized these genes into five subfamilies, with members of each subfamily displaying similar conserved motifs and gene structures. Notably, Classes III and V contained the largest number of members. Collinearity analysis suggested that segmental duplication events were the primary drivers of PbARF gene family expansion. Structural analysis revealed that all PbARF genes possess a conserved B3 binding domain and an auxin response element, while additional motifs varied among different classes. Promoter cis-acting element analysis revealed that PbARF genes are extensively involved in hormonal responses-particularly to abscisic acid and jasmonic acid and abiotic stresses-as well as abiotic stresses, including heat, drought, light, and dark. Tissue-specific expression analysis showed that PbARF25, PbARF23, PbARF19, PbARF22, and PbARF20 genes (class III), and PbARF18 and PbARF11 genes (class V) consistently exhibited high expression levels in the five tissues. In addition, five representative PbARF genes were analyzed using qRT-PCR. The results demonstrated significant differences in the expression of PbARF genes under various abiotic stress conditions (drought, salt stress, light, and dark), indicating their important roles in stress response. This study laid a foundation for elucidating the molecular evolution mechanism of ARF genes in P. bournei and for determining the candidate genes for stress-resistance breeding.}, } @article {pmid40331936, year = {2025}, author = {Li, H and Wang, R and Pan, J and Chen, J and Hao, X}, title = {Bioinformatics Analysis of the Glutamate-Gated Chloride Channel Family in Bursaphelenchus xylophilus.}, journal = {International journal of molecular sciences}, volume = {26}, number = {8}, pages = {}, pmid = {40331936}, issn = {1422-0067}, support = {202403//Key Laboratory of National Forestry and Grassland Administration on Prevention and Control Technology of Pine Wilt Disease/ ; 202401BD070001-115//Yunnan Fundamental Research Projects/ ; LXXK-2023M06, LXXK-2024Z04//Southwest Forestry University Forestry major in Yunnan Province First-Class Construction Discipline/ ; }, mesh = {*Chloride Channels/genetics/metabolism/chemistry ; Animals ; *Computational Biology/methods ; Phylogeny ; *Tylenchida/genetics/metabolism ; Multigene Family ; Amino Acid Sequence ; }, abstract = {Glutamate-gated chloride channels (GluCls), a class of ion channels found in the nerve and muscle cells of invertebrates, are involved in vital life processes. Bursaphelenchus xylophilus, the pathogen of pine wilt disease, has induced major economic and ecological losses in invaded areas of Asia and Europe. We identified 33 GluCls family members by sequence alignment analysis. A subsequent bioinformatic analysis revealed the physicochemical properties, protein structure, and gene expression patterns in different developmental stages. The results showed that GluCls genes are distributed across all six chromosomes of B. xylophilus. These proteins indicated a relatively conserved structure by NCBI-conserved domains and InterPro analysis. A gene structure analysis revealed that GluCls genes consist of 5 to 14 exons. Expression pattern analysis revealed BxGluCls were extensively involved in the development of second instar larvae of B. xylophilus. Furthermore, BxGluCls15, BxGluCls25, and BxGluCls28 were mainly associated with the development of eggs of B. xylophilus. BxGluCls12, BxGluCls18, and BxGluCls32 were predominantly linked to nematode resistance and adaptation. Investigation the structure and expression patterns of BxGluCls is crucial to understand the developmental trends of B. xylophilus. It also helps identify molecular targets for the development of biopesticides or drugs designed to control this nematode.}, } @article {pmid40053042, year = {2025}, author = {Duarte, T and Martin, GM and Anjos-Santos, D and Pessacq, P}, title = {Unraveling Plecoptera Diversity in Two Protected Areas of Argentine Patagonia.}, journal = {Anais da Academia Brasileira de Ciencias}, volume = {97}, number = {1}, pages = {e20240085}, doi = {10.1590/0001-3765202520240085}, pmid = {40053042}, issn = {1678-2690}, mesh = {Animals ; Argentina ; *Biodiversity ; *Neoptera/classification ; Forests ; Population Density ; Cluster Analysis ; *Animal Distribution ; *Insecta/classification ; Conservation of Natural Resources ; Parks, Recreational ; Geographic Information Systems ; }, abstract = {The Plecoptera taxonomy in Patagonia is well-documented, yet their distribution remains poorly understood, hindering comprehensive ecological and biogeographical studies. This study enhances knowledge of stonefly distribution in two Patagonian national parks: Nahuel Huapi and Los Alerces. Extensive fieldwork, georeferenced species records, and geographic information system data integration were conducted. Species richness was calculated using polygons (0.1° x 0.1° pixels) across ecoregions, with species indexed from rare to ubiquitous. Cluster analyses revealed faunal affinities across ecosystem complexes, and richness estimators (Jack1, Jack2, and Chao2) highlighted knowledge gaps. Results showed uneven species distribution, with the highest richness polygon (n = 19) in Los Alerces. The Northern Moist Forests hosted the most species, followed by the Transitional Cypress-Beech Forests. The rarest species were also found in these two complexes, as well as the Ecotone Steppe-Forest. Cluster analysis revealed strong affinities between the Northern Moist Forests of Nahuel Huapi and Ecotone Steppe-Forest. Richness estimators suggested up to 23 undocumented species. Though much remains to be learned about Plecoptera distribution in Patagonia, this study emphasizes the critical role of national parks in conserving biodiversity and provides a foundation for future conservation strategies, identifying new taxa records, including southernmost distributions.}, } @article {pmid40045055, year = {2025}, author = {Shi, J and Gong, J and Zhang, Y and Kan, G}, title = {Spatiotemporal change in ecological quality of the Qinghai-Tibetan Plateau based on an improved remote sensing ecological index and Google Earth Engine platform.}, journal = {Environmental monitoring and assessment}, volume = {197}, number = {4}, pages = {355}, pmid = {40045055}, issn = {1573-2959}, mesh = {*Remote Sensing Technology ; *Environmental Monitoring/methods ; *Ecosystem ; China ; Tibet ; Spatio-Temporal Analysis ; Conservation of Natural Resources ; Geographic Information Systems ; }, abstract = {The Qinghai-Tibetan Plateau (QTP) serves as a vital ecological security barrier in China and globally. Evaluating changes in ecological quality on the QTP provides critical insights for regional conservation initiatives. This study, tailored to the unique characteristics of the region, develops an Improved Remote Sensing Ecological Index (IRSEI) framework by integrating Gross Primary Productivity (GPP) with the Normalized Difference Vegetation Index (NDVI), humidity (WET), Land Surface Temperature (LST), and the Negative Drought Index (NDBSI). This comprehensive index aims to provide a more precise assessment of the environmental quality of the alpine ecosystem. It investigates spatial and temporal variations in ecological quality across the QTP, as well as within individual geographic subregions from 2000 to 2020. The first principal component accounts for an average variance of 63.69%. Over the past 20 years, the spatial distribution pattern of IRSEI on the QTP has shown lower values in the northwest, higher values in the southeast, and predominantly poor grades throughout the region. The mean trend coefficient for IRSEI was 0.002, indicating a gradual improvement in ecological quality on the QTP over time. Among 11 influencing factors examined, NDVI and GPP exhibit significant positive correlation with ecological quality, with q statistics of 0.942 and 0.932, respectively, underscoring the substantial impact of vegetation cover on ecosystem quality. These findings provide a robust theoretical foundation for supporting ecological management, restoration efforts, and the evaluation of ecological restoration within the QTP, thereby promoting ecosystem balance.}, } @article {pmid40329811, year = {2025}, author = {Yang, Y and Liu, X and Wu, J and Svenning, JC and Liu, J and Shrestha, N}, title = {A comprehensive county-level distribution database of alien and invasive plants in China.}, journal = {Ecology}, volume = {106}, number = {5}, pages = {e70084}, pmid = {40329811}, issn = {1939-9170}, support = {2022YFC2601100//National Key Research and Development Program of China/ ; DNRF173//Danmarks Grundforskningsfond/ ; }, mesh = {*Introduced Species ; China ; *Plants/classification ; *Databases, Factual ; Biodiversity ; }, abstract = {Over the past half century, international trade and exchange have continued to increase in China, resulting in the widespread introduction of alien plant species. The accumulation of these alien species has accelerated invasion events, posing serious threats to local ecological security and economic development. Comprehensive and accurate species distribution records are extremely important for early detection, understanding dispersal dynamics, and supporting various management strategies and research initiatives. However, biodiversity databases, both global and local, often lack comprehensive and high-resolution distribution data for alien invasive plant species (AIPs). This limitation is particularly evident in China, where local databases typically provide coarse spatial data, often restricted to the provincial level, leading to a substantial underestimation of the actual distribution of AIPs. Here, we fill this gap by creating the most comprehensive distribution database for AIPs in China at a much finer spatial resolution. By integrating 73,469 distribution records from China's online herbarium, biodiversity databases, flora, published literature, and 173,396 georeferenced records from GBIF, we built the county-level distribution database for 400 AIPs and report for the first time their presence in 2684 administrative counties in China (92.5% of the total counties). Notably, our database provides 2.58 times more distribution records than global biodiversity data repositories such as GBIF and also includes the earliest introduction dates for each AIP. The temporal range of the records spans from 1607 to 2023, capturing over 400 years of AIP presence in China. These rigorously quality-controlled georeferenced data can be used to examine the dynamics and influencing factors of plant invasions in China. They can also serve as the most updated data reference for policy makers in designing effective AIP management policies in China. We encourage users to cite this data paper when utilizing the data, and there are no restrictions on its use for non-commercial purposes.}, } @article {pmid40294093, year = {2025}, author = {Williams, B and Balvanera, SM and Sethi, SS and Lamont, TAC and Jompa, J and Prasetya, M and Richardson, L and Chapuis, L and Weschke, E and Hoey, A and Beldade, R and Mills, SC and Haguenauer, A and Zuberer, F and Simpson, SD and Curnick, D and Jones, KE}, title = {Unlocking the soundscape of coral reefs with artificial intelligence: pretrained networks and unsupervised learning win out.}, journal = {PLoS computational biology}, volume = {21}, number = {4}, pages = {e1013029}, pmid = {40294093}, issn = {1553-7358}, mesh = {*Coral Reefs ; Animals ; Acoustics ; *Unsupervised Machine Learning ; *Artificial Intelligence ; Ecosystem ; Algorithms ; Neural Networks, Computer ; Computational Biology ; Fishes/physiology ; Machine Learning ; Environmental Monitoring/methods ; }, abstract = {Passive acoustic monitoring can offer insights into the state of coral reef ecosystems at low-costs and over extended temporal periods. Comparison of whole soundscape properties can rapidly deliver broad insights from acoustic data, in contrast to detailed but time-consuming analysis of individual bioacoustic events. However, a lack of effective automated analysis for whole soundscape data has impeded progress in this field. Here, we show that machine learning (ML) can be used to unlock greater insights from reef soundscapes. We showcase this on a diverse set of tasks using three biogeographically independent datasets, each containing fish community (high or low), coral cover (high or low) or depth zone (shallow or mesophotic) classes. We show supervised learning can be used to train models that can identify ecological classes and individual sites from whole soundscapes. However, we report unsupervised clustering achieves this whilst providing a more detailed understanding of ecological and site groupings within soundscape data. We also compare three different approaches for extracting feature embeddings from soundscape recordings for input into ML algorithms: acoustic indices commonly used by soundscape ecologists, a pretrained convolutional neural network (P-CNN) trained on 5.2 million hrs of YouTube audio, and CNN's which were trained on each individual task (T-CNN). Although the T-CNN performs marginally better across tasks, we reveal that the P-CNN offers a powerful tool for generating insights from marine soundscape data as it requires orders of magnitude less computational resources whilst achieving near comparable performance to the T-CNN, with significant performance improvements over the acoustic indices. Our findings have implications for soundscape ecology in any habitat.}, } @article {pmid40329386, year = {2025}, author = {Hou, L and Zhao, Z and Steger-Mähnert, B and Jiao, N and Herndl, GJ and Zhang, Y}, title = {Microbial metabolism in laboratory reared marine snow as revealed by a multi-omics approach.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {114}, pmid = {40329386}, issn = {2049-2618}, support = {42206098//National Natural Science Foundation of China-China Academy of General Technology Joint Fund for Basic Research/ ; 42125603//National Natural Science Foundation of China-China Academy of General Technology Joint Fund for Basic Research/ ; MELRS2327//State Key Laboratory of Marine Environmental Science/ ; I4978-B//Austrian Science Fund/ ; }, mesh = {*Snow/microbiology ; Gammaproteobacteria/metabolism/genetics/classification ; Metagenomics/methods ; Metagenome ; *Seawater/microbiology ; *Microbiota ; *Bacteria/classification/metabolism/genetics/isolation & purification ; Phytoplankton/microbiology/metabolism ; Multiomics ; }, abstract = {BACKGROUND: Marine snow represents an organic matter-rich habitat and provides substrates for diverse microbial populations in the marine ecosystem. However, the functional diversity and metabolic interactions within the microbial community inhabiting marine snow remain largely underexplored, particularly for specific metabolic pathways involved in marine snow degradation. Here, we used a multi-omics approach to explore the microbial response to laboratory-reared phytoplankton-derived marine snow.

RESULTS: Our results demonstrated a dramatic shift in both taxonomic and functional profiles of the microbial community after the formation of phytoplankton-derived marine snow using a rolling tank system. The changes in microbial metabolic processes were more pronounced in the metaproteome than in the metagenome in response to marine snow. Fast-growing taxa within the Gammaproteobacteria were the most dominant group at both the metagenomic and metaproteomic level. These Gammaproteobacteria possessed a variety of carbohydrate-active enzymes (CAZymes) and transporters facilitating substrate cleavage and uptake, respectively. Analysis of metagenome-assembled genomes (MAGs) revealed that the response to marine snow amendment was primarily mediated by Alteromonas, Vibrio, and Thalassotalea. Among these, Alteromonas exclusively expressing auxiliary activities 2 (AA2) of the CAZyme subfamily were abundant in both the free-living (FL) and marine snow-attached (MA) microbial communities. Thus, Alteromonas likely played a pivotal role in the degradation of marine snow. The enzymes of AA2 produced by these Alteromonas MAGs are capable of detoxifying peroxide intermediates generated during the breakdown of marine snow into smaller poly- and oligomers, providing available substrates for other microorganisms within the system. In addition, Vibrio and Thalassotalea MAGs exhibited distinct responses to these hydrolysis products of marine snow in different size fractions, suggesting a distinct niche separation. Although chemotaxis proteins were found to be enriched in the proteome of all three MAGs, differences in transporter proteins were identified as the primary factor contributing to the niche separation between these two groups. Vibrio in the FL fraction predominantly utilized ATP-binding cassette transporters (ABCTs), while Thalassotalea MAGs in the MA fraction primarily employed TonB-dependent outer membrane transporters (TBDTs).

CONCLUSIONS: Our findings shed light on the essential metabolic interactions within marine snow-degrading microbial consortia, which employ complementary physiological mechanisms and survival strategies to effectively scavenge marine snow. This work advances our understanding of the fate of marine snow and the role of microbes in carbon sequestration in the ocean. Video Abstract.}, } @article {pmid40328721, year = {2025}, author = {Zhang, H and Wen, T and Wang, Z and Zhao, X and Wu, H and Xiang, P and Ma, Y}, title = {[Multi-omics analysis of hormesis effect of lanthanum chloride on carotenoid synthesis in Rhodotorula mucilaginosa].}, journal = {Sheng wu gong cheng xue bao = Chinese journal of biotechnology}, volume = {41}, number = {4}, pages = {1631-1648}, doi = {10.13345/j.cjb.240537}, pmid = {40328721}, issn = {1872-2075}, mesh = {*Lanthanum/pharmacology ; *Rhodotorula/metabolism/drug effects/genetics ; *Carotenoids/metabolism ; *Hormesis/drug effects ; Fermentation ; Multiomics ; }, abstract = {Hormesis effect has been observed in the secondary metabolite synthesis of microorganisms induced by rare earth elements. However, the underlying molecular mechanism remains unclear. To analyze the molecular mechanism of the regulatory effect of Rhodotorula mucilaginosa in the presence of lanthanum chloride, different concentrations of lanthanum chloride were added to the fermentation medium of Rhodotorula mucilaginosa, and the carotenoid content was subsequently measured. It was found that the concentrations of La[3+] exerting the promotional and inhibitory effects were 0-100 mg/L and 100-400 mg/L, respectively. Furthermore, the expression of 33 genes and the synthesis of 55 metabolites were observed to be up-regulated, while the expression of 85 genes and the synthesis of 123 metabolites were found to be down-regulated at the concentration range of the promotional effect. Notably, the expression of carotenoid synthesis-related genes except AL1 was up-regulated. Additionally, the content of β-carotene, lycopene, and astaxanthin demonstrated increases of 10.74%, 5.02%, and 3.22%, respectively. The expression of 5 genes and the synthesis of 91 metabolites were up-regulated, while the expression of 35 genes and the synthesis of 138 metabolites were down-regulated at the concentration range of the inhibitory effect. Meanwhile, the content of β-carotene, lycopene, and astaxanthin decreased by 21.73%, 34.81%, and 35.51%, respectively. In summary, appropriate concentrations of rare earth ions can regulate the synthesis of secondary metabolites by modulating the activities of various enzymes involved in metabolic pathways, thereby exerting the hormesis effect. The findings of this study not only contribute to our comprehension for the mechanism of rare earth elements in organisms but also offer a promising avenue for the utilization of rare earth elements in diverse fields, including agriculture, pharmaceuticals, and healthcare.}, } @article {pmid40325107, year = {2025}, author = {Pitogo, KME and Meneses, CG and Flores, ABA and Saavedra, AJL and Amarga, AKS and Angeles, MD and Lucañas, CC and Decena, SCP and Venturina, REL and Fidelino, JS and Pantinople, D and Cabañas, AJC and Herr, MW and Bernstein, JM and Chan, KO and Sanguila, MB and Mallari, NA and Brown, RM and Supsup, CE}, title = {Caught in statistical noise: pitfalls of a unidimensional approach to understanding biodiversity-conflict relationships.}, journal = {npj biodiversity}, volume = {4}, number = {1}, pages = {17}, pmid = {40325107}, issn = {2731-4243}, } @article {pmid40324092, year = {2025}, author = {Compton, ZT and Vincze, O and Mellon, W and Tollis, M and Abegglen, L and Schiffman, JD and Giraudeau, M and Boddy, AM and Maley, CC}, title = {Paradoxical indeed.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {122}, number = {19}, pages = {e2504512122}, doi = {10.1073/pnas.2504512122}, pmid = {40324092}, issn = {1091-6490}, support = {T32 CA272303/CA/NCI NIH HHS/United States ; U54 CA217376/CA/NCI NIH HHS/United States ; }, } @article {pmid40323496, year = {2025}, author = {Oyelayo, EA and Taiwo, TJ and Oyelude, SO and Alao, JO}, title = {The global impact of industrialisation and climate change on antimicrobial resistance: assessing the role of Eco-AMR Zones.}, journal = {Environmental monitoring and assessment}, volume = {197}, number = {6}, pages = {625}, pmid = {40323496}, issn = {1573-2959}, mesh = {*Industrial Development ; *Drug Resistance, Microbial/genetics ; *Climate Change ; Temperature ; Environmental Monitoring ; Genes, Microbial ; Computational Biology ; Anti-Bacterial Agents ; }, abstract = {This study examines the relationship between industrialisation, climate change, and antimicrobial resistance (AMR) gene prevalence. Data analysis from the top 20 highly industrialised and the top 20 least industrialised nations revealed that industrial activities significantly contribute to global warming, with temperature increases of up to 2 °C observed in highly industrialised regions. These environmental changes influence the distribution and evolution of AMR genes, as rising temperatures can affect bacterial resistance in a manner similar to antibiotics. Through a bioinformatics approach, a marked disparity in AMR gene frequencies was observed between highly industrialised and less industrialised nations, with developed countries reporting higher frequencies due to extensive antibiotic use and advanced monitoring systems. 'Eco-AMR Zones' is proposed as a solution to specialised areas by promoting sustainable industrial practices, enforcing pollution controls, and regulating antibiotic use to mitigate AMR's environmental and public health impacts. These zones, supported by collaboration across various sectors, offer a promising approach to preserving antibiotic effectiveness and reducing environmental degradation. The study emphasises the importance of integrated global strategies that address both the ecological and public health challenges posed by AMR, advocating for sustainable practices, international collaboration, and ongoing research to combat the evolving threats of climate change and antimicrobial resistance.}, } @article {pmid40112992, year = {2025}, author = {Wei, L and Luo, Z and Wu, X and Liu, C and Shi, Y and Zhang, Q and Chen, M and Qin, W}, title = {Multi-omics analysis provided insights into the fruit softening of postharvest okra under carboxymethyl chitosan treatment.}, journal = {International journal of biological macromolecules}, volume = {307}, number = {Pt 3}, pages = {142149}, doi = {10.1016/j.ijbiomac.2025.142149}, pmid = {40112992}, issn = {1879-0003}, mesh = {*Chitosan/analogs & derivatives/pharmacology ; *Fruit/drug effects/metabolism/genetics ; *Abelmoschus/genetics/metabolism/drug effects ; Gene Expression Regulation, Plant/drug effects ; Transcriptome/drug effects ; *Metabolomics/methods ; Metabolome/drug effects ; Gene Expression Profiling ; Pectins/metabolism ; Multiomics ; }, abstract = {To understand the potential regulatory mechanism of carboxymethyl chitosan (CMCS) treatment on postharvest softening of okra, a joint analysis of physiologic index, transcriptome and metabolome was used. The results showed that CMCS could delay the deterioration of the apparent quality of okra and reduce the degradation of chlorophyll. CMCS can reduce the accumulation of WSP and CSP and the decrease of NSP, and inhibit the enzyme activities of pectin degradation (PE, PG, PL). The results of metabolic pathways related to quality and texture showed that CMCS could increase the metabolic level of pentose phosphate pathway (PPP), inhibit the expression of membrane lipid degradation-related genes, and balance the expression of antioxidant-related genes. Ethylene and abscisic acid (ABA) are two important phytohormones. CMCS down-regulates the biosynthesis of ethylene and increases the expression of ABA. The combined analysis of transcriptome and metabolome showed that CMCS could significantly up-regulate flavonoid biosynthesis metabolites and transcriptional expression levels. Cellulose and pectin are important polymers to maintain the rigidity of okra cell wall. CMCS treatment can slow down the accumulation of cellulose by regulating the expression of DEGs related to cellulose synthesis (CesA) and degradation (EGase). CMCS slowed down the degradation of pectin by down-regulating the expression of pectin degradation-related genes. These results indicate that the quality of okra is deteriorated and the fruit is softened during cold storage. CMCS treatment can improve the nutritional quality of okra and slow down its texture decline. In this study, the regulatory effect of CMCS on softening and quality deterioration of okra during cold storage was discussed at the molecular level, which provided a reference for improving the quality of postharvest okra.}, } @article {pmid40089216, year = {2025}, author = {Torres-Roman, JS and Quispe-Vicuña, C and Benavente-Casas, A and Julca-Marin, D and Rios-Garcia, W and Challapa-Mamani, MR and Rio-Muñiz, LD and Ybaseta-Medina, J}, title = {Trends in stroke mortality in Latin America and the Caribbean from 1997 to 2020 and predictions to 2035: An analysis of gender, and geographical disparities.}, journal = {Journal of stroke and cerebrovascular diseases : the official journal of National Stroke Association}, volume = {34}, number = {6}, pages = {108286}, doi = {10.1016/j.jstrokecerebrovasdis.2025.108286}, pmid = {40089216}, issn = {1532-8511}, mesh = {Humans ; Latin America/epidemiology ; Female ; Male ; *Stroke/mortality/diagnosis ; Caribbean Region/epidemiology ; Risk Factors ; Sex Factors ; Middle Aged ; Sex Distribution ; Time Factors ; Databases, Factual ; Aged ; Adult ; *Health Status Disparities ; Age Distribution ; Forecasting ; Risk Assessment ; Age Factors ; Young Adult ; Aged, 80 and over ; }, abstract = {BACKGROUND: Stroke is a leading cause of death and disability globally, with significant public health implications. In Latin America, while mortality rates have declined, the number of stroke cases has increased due to prevalent risk factors like high blood pressure and obesity. Unlike Europe, recent trends in stroke mortality in this region remain underreported.

OBJECTIVE: This study evaluates stroke mortality rates in Latin America Latin American and Caribbean (LAC) countries from 1997 to 2020 and predictions to 2035.

METHODS: This ecological observational study utilized mortality data from the World Health Organization database. Trends were analyzed using Joinpoint regression to evaluate the annual percent change (APC) by sex and country. Predicted mortality rates through 2035 were calculated using the Nordpred package in R. Changes in stroke mortality were assessed by disentangling the effects of population growth, aging, and risk factor modifications, based on age-specific rates and projections. Results were presented as absolute case numbers and relative percentages.

RESULTS: From 1997 to 2020, twelve countries presented significant reductions in stroke mortality rates for men in LAC, the main ones being Chile (-4.2 %), El Salvador (-4.2 %), and Puerto Rico (-4.0 %). Thirteen countries reported a reduction in their mortality for women, mainly in Puerto Rico (-4.3 %), Chile (-3.7 %), Argentina, El Salvador, and Uruguay (-3.5 %). By 2035, an increase in deaths among men and women is expected, mainly due to the increase in population structure and size. However, a decrease in the mortality rate will be reported, mainly due to the reduction of risk factors.

CONCLUSION: Our final findings show a reduction in stroke mortality trends in LAC countries between 1997 and 2020, due to creating public awareness about vascular risk factors by authorities and the implementation of effective health policies. By 2035, an overall increase in mortality is expected, mainly due to population change in each country.}, } @article {pmid40102961, year = {2025}, author = {Hinojosa-Alvarez, S and Mendoza-Portillo, V and Chavez-Santoscoy, RA and Hernández-Pérez, J and Felix-Ceniceros, A and Magallón-Gayón, E and Mar-Silva, AF and Ochoa-Zavala, M and Díaz-Jaimes, P}, title = {The draft genome assembly of the cosmopolitan pelagic fish dolphinfish Coryphaena hippurus.}, journal = {G3 (Bethesda, Md.)}, volume = {15}, number = {5}, pages = {}, doi = {10.1093/g3journal/jkaf059}, pmid = {40102961}, issn = {2160-1836}, support = {CF-2023-G-493//Consejo Nacional de Humanidades, Ciencias y Tecnologías/ ; }, mesh = {Animals ; *Genome ; Molecular Sequence Annotation ; *Genomics/methods ; *Perciformes/genetics ; Sequence Analysis, DNA ; High-Throughput Nucleotide Sequencing ; *Fishes/genetics ; Whole Genome Sequencing ; Computational Biology/methods ; }, abstract = {For the first time, the complete genome assembly of the dolphinfish (Coryphaena hippurus), a tropical cosmopolitan species with commercial fishing importance was sequenced. Using a combination of Illumina and Nanopore sequencing technologies, a draft genome of 497.8 Mb was assembled into 6,044 contigs, with an N50 of 200.9 kb and a BUSCO genome completeness score of 89%. This high-quality genome assembly provides a valuable resource to study adaptive evolutionary processes and supports conservation and management strategies for this ecologically and economically significant species.}, } @article {pmid40319413, year = {2025}, author = {Wang, Y and Mao, Z and Yu, J and Feng, B and Zhang, Z and Zhong, L and Tang, Y}, title = {Construction of risk management system for polluted sites in coal industry clusters.}, journal = {Environmental geochemistry and health}, volume = {47}, number = {6}, pages = {195}, pmid = {40319413}, issn = {1573-2983}, mesh = {*Coal Industry ; *Risk Management/methods ; China ; *Coal ; *Environmental Pollution/prevention & control/statistics & numerical data ; Soil/chemistry ; Groundwater/chemistry ; Environmental Restoration and Remediation ; Environmental Monitoring ; Risk Assessment ; Decision Making, Organizational ; *Coal Mining ; Decision Making, Computer-Assisted ; Algorithms ; *Environmental Pollutants/analysis ; }, abstract = {Coal has always been the main source of energy in China, accounting for more than 60% of primary energy production and consumption. As a result of coal mining, coal industry agglomerations such as mining, coal chemical industry, and so on have been gradually formed, and there are many types of industries in the agglomerations, complex sources of pollutants, and sensitive soil and water environments, and all kinds of industrial sites and solid waste dumps of coal-related industries may pollute the soil and groundwater, and have a certain impact on the ecological environment. However, at present, there is a lack of a targeted region-wide pollution risk management technology system for the polluted sites in the agglomeration area, therefore, it is particularly important to construct a scientific and complete soil-groundwater risk management system and propose more targeted and effective control strategies for the polluted sites in the coal industry agglomeration area. Based on the domestic and international experience and historical data, this paper takes the coal industry cluster area as the research object classifies the land in the area according to the land use type into construction land, agricultural land, and another ecological land, and carries out the risk zoning and grading based on the dosage-effect model and the potential ecological hazard index method respectively, assesses the appropriateness, feasibility, and necessity of the implementation of risk control for the polluted plots, and then designs and develops a risk control decision-making framework by using the hierarchical analysis method. Hierarchical analysis was used to design and develop a decision-making framework for risk management, and finally, the optimal risk management and remediation strategy was proposed based on the AHP + TOPSIS algorithm, which combined with the contaminated land conditions to propose a suitable solution.}, } @article {pmid40318965, year = {2025}, author = {Lucca, E and Kofinas, D and Avellán, T and Kleemann, J and Mooren, CE and Blicharska, M and Teutschbein, C and Sperotto, A and Sušnik, J and Milliken, S and Fader, M and Đorđević, D and Dašić, T and Vasilić, V and Taiwo, B and Baubekova, A and Pineda-Martos, R and Spyropoulou, A and Baganz, GFM and El Jeitany, J and Oral, HV and Merheb, M and Castelli, G and Pagano, A and Sambo, B and Suškevičs, M and Arnold, M and Rađenović, T and Psomas, A and Masia, S and La Jeunesse, I and Amorocho-Daza, H and Das, SS and Bresci, E and Munaretto, S and Brouwer, F and Laspidou, C}, title = {Corrigendum to "Integrating 'nature' in the water-energy-food nexus: Current perspectives and future directions" [Science of The Total Environment, Volume 966, 2025, 178600].}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {179482}, doi = {10.1016/j.scitotenv.2025.179482}, pmid = {40318965}, issn = {1879-1026}, } @article {pmid40318638, year = {2025}, author = {Aguilar-Gómez, D and Bejder, J and Graae, J and Ko, Y and Vaughn, A and Clement, K and Tristani-Firouzi, M and Lee, JY and Nordsborg, NB and Nielsen, R and Ilardo, M}, title = {Genetic and training adaptations in the Haenyeo divers of Jeju, Korea.}, journal = {Cell reports}, volume = {}, number = {}, pages = {115577}, doi = {10.1016/j.celrep.2025.115577}, pmid = {40318638}, issn = {2211-1247}, abstract = {Natural selection and relative isolation have shaped the genetics and physiology of unique human populations from Greenland to Tibet. Another such population is the Haenyeo, the all-female Korean divers renowned for their remarkable diving abilities in frigid waters. Apnea diving induces considerable physiological strain, particularly in females diving throughout pregnancy. In this study, we explore the hypothesis that breath-hold diving has shaped physiological and genetic traits in the Haenyeo. We identified pronounced bradycardia during diving, a likely training effect. We paired natural selection and genetic association analyses to investigate adaptive genetic variation that may mitigate the effects of diving on pregnancy through an associated reduction of diastolic blood pressure. Finally, we identified positively selected variation in a gene previously associated with cold water tolerance, which may contribute to reduced hypothermia susceptibility. These findings highlight the importance of traditional diving populations for understanding genetic and physiological adaptation.}, } @article {pmid40318544, year = {2025}, author = {Gomes, MLS and Cestari, VRF and Florêncio, RS and Yamamura, M and Santos, JO and Sales, LBF and Silva, RR and Oriá, MOB}, title = {Spatial-temporal analysis of cervical cancer screening and social and health indicators in Brazil.}, journal = {Public health}, volume = {243}, number = {}, pages = {105747}, doi = {10.1016/j.puhe.2025.105747}, pmid = {40318544}, issn = {1476-5616}, abstract = {OBJECTIVE: To identify the spatial-temporal patterns of cervical cancer (CC) screening in Brazil from 2013 to 2022 and its relationship with social and health indicators.

STUDY DESIGN: This ecological study uses data from the Cancer Information System (SISCAN) of the Brazilian Unified Health System's Department of Informatics.

METHODS: The study analyzed women aged 25 to 64 who underwent CC screening in 5570 municipalities across Brazil. Global Moran's I and the Local Index of Spatial Autocorrelation (LISA) were employed to investigate clustering. The purely spatial scan statistic technique was used for spatial cluster detection. Temporal trends were assessed using joinpoint regression. GeoDa, SaTScan, GWR, and QGIS software were used for the analysis.

RESULTS: The global clustering analysis of CC screening proportions revealed significant spatial autocorrelation (Moran's I = 0.530). Clusters of municipalities with low screening rates were significantly observed in the Northern (Amapá, Amazonas, Rondônia, Roraima) and Northeastern (Piauí, Pernambuco) regions. The Gini Index (β = -2.60), the Municipal Human Development Index (MHDI) (β = -10.5), and the Social Vulnerability Index (SVI) (β = -9.14) showed negative associations. Conversely, Family Health Strategy (FHS) coverage (β = 2.18) demonstrated a positive impact on screening rates. In terms of temporal trends, the screening proportion gradually increased from 5.4 % in 2014 to 10.5 % in 2022.

CONCLUSION: Areas with a high risk of low CC screening rates were identified in the Northern and Northeastern regions of Brazil, which are characterized by socioeconomic and demographic disparities, vulnerabilities, and inequalities.}, } @article {pmid40317095, year = {2025}, author = {Seizer, L and Pascher, A and Branz, S and Schmitt, N and Löchner, J and Schuller, BW and Rohleder, N and Renner, TJ}, title = {Bridging acute and chronic stress effects on inflammation: protocol for a mixed-methods intensive longitudinal study.}, journal = {BMC psychology}, volume = {13}, number = {1}, pages = {464}, pmid = {40317095}, issn = {2050-7283}, mesh = {Humans ; Longitudinal Studies ; *Stress, Psychological/metabolism/immunology/complications ; *Inflammation/metabolism/psychology/immunology ; Saliva/chemistry ; Male ; Female ; Young Adult ; Chronic Disease ; Adult ; Ecological Momentary Assessment ; Biomarkers/metabolism ; Cytokines/metabolism ; Research Design ; }, abstract = {Acute stress triggers adaptive physiological responses-including transient increases in inflammatory cytokines-while chronic stress is associated with sustained inflammatory activity that may underlie the development of various disorders. Despite extensive research on each stress type individually, the transition and interaction between them remain underexplored. This study aims to address this gap by employing an intensive longitudinal measurement burst design. Healthy university students will be recruited and monitored over three one-week assessment bursts, spaced by three-month breaks. Participants will complete ecological momentary assessments four times daily, recording their emotional states, stress experiences, and daily incidents. Simultaneously, saliva samples will be collected at matching time points to measure biomarkers of immune and stress system activity. In addition, daily audio diaries will provide qualitative context through advanced speech analysis techniques. Data will be analyzed using a multi-level modeling approach to differentiate within-person dynamics from between-person variability, accounting for potential moderators. The findings are expected to shed light on how repeated acute stressors transition into chronic stress and how chronic stress burden may influence acute stress responses.}, } @article {pmid39937595, year = {2025}, author = {Royaux, C and Mihoub, JB and Jossé, M and Pelletier, D and Norvez, O and Reecht, Y and Fouilloux, A and Rasche, H and Hiltemann, S and Batut, B and Marc, E and Seguineau, P and Massé, G and Amossé, A and Bissery, C and Lorrilliere, R and Martin, A and Bas, Y and Virgoulay, T and Chambon, V and Arnaud, E and Michon, E and Urfer, C and Trigodet, E and Delannoy, M and Loïs, G and Julliard, R and Grüning, B and Le Bras, Y and , }, title = {Guidance framework to apply best practices in ecological data analysis: lessons learned from building Galaxy-Ecology.}, journal = {GigaScience}, volume = {14}, number = {}, pages = {}, pmid = {39937595}, issn = {2047-217X}, support = {2020-1-NL01-KA203-064717//European Union/ ; //Agence Nationale de la Recherche/ ; //Muséum National d'Histoire Naturelle/ ; //Ministry of Higher Education and Research/ ; }, mesh = {*Ecology/methods/standards ; *Software ; *Data Analysis ; Reproducibility of Results ; *Computational Biology/methods/standards ; }, abstract = {Numerous conceptual frameworks exist for best practices in research data and analysis (e.g., Open Science and FAIR principles). In practice, there is a need for further progress to improve transparency, reproducibility, and confidence in ecology. Here, we propose a practical and operational framework for researchers and experts in ecology to achieve best practices for building analytical procedures from individual research projects to production-level analytical pipelines. We introduce the concept of atomization to identify analytical steps that support generalization by allowing us to go beyond single analyses. The term atomization is employed to convey the idea of single analytical steps as "atoms" composing an analytical procedure. When generalized, "atoms" can be used in more than a single case analysis. These guidelines were established during the development of the Galaxy-Ecology initiative, a web platform dedicated to data analysis in ecology. Galaxy-Ecology allows us to demonstrate a way to reach higher levels of reproducibility in ecological sciences by increasing the accessibility and reusability of analytical workflows once atomized and generalized.}, } @article {pmid40316929, year = {2025}, author = {Demsash, AW and Abebe, R and Gezimu, W and Kitil, GW and Tizazu, MA and Lembebo, A and Bekele, F and Alemu, SS and Jarso, MH and Dube, G and Wedajo, LF and Purohit, S and Kalayou, MH}, title = {Data-driven machine learning algorithm model for pneumonia prediction and determinant factor stratification among children aged 6-23 months in Ethiopia.}, journal = {BMC infectious diseases}, volume = {25}, number = {1}, pages = {647}, pmid = {40316929}, issn = {1471-2334}, mesh = {Humans ; Ethiopia/epidemiology ; Infant ; *Pneumonia/epidemiology/diagnosis ; *Machine Learning ; Female ; Male ; Algorithms ; Risk Factors ; }, abstract = {INTRODUCTION: Pneumonia is the leading cause of child morbidity and mortality and accounts for 5.6 million under-five child deaths. Pneumonia has a significant impact on the quality of life, the country's economy, and the survival of children. Therefore, this study aimed to develop data-driven predictive model using machine learning algorithms to predict pneumonia and stratify the determinant factors among children aged 6-23 months in Ethiopia.

METHODS: A total of 2035 samples of children were used from the 2016 Ethiopian Demographic and Health Survey dataset. Jupyter Notebook from Anaconda Navigators was used for data management and analysis. Important libraries such as Pandas, Seaborn, and Numpy were imported from Python. The data was pre-processed into a training and testing dataset with a 4:1 ratio, and tenfold cross-validation was used to reduce bias and enhance the models' performance. Six machine learning algorithms were used for model building and comparison, and confusion matrix elements were used to evaluate the performance of each algorithm. Principal component analysis and heatmap function were used for correlation detection between features. Feature importance score was used to identify and stratify the most important predictors of pneumonia.

RESULTS: From 2035 total samples, 16.6%, 20.1%, and 24.2% of children had short rapid breath, fever, and cough respectively. The overall magnitude of pneumonia among children aged 6-23 months was 31.3% based on the 2016 EDHS report. A random forest algorithm is the relatively best performance model to predict pneumonia and stratify its determinates with 91.3% accuracy. The health facility visits, child sex, initiation of breastfeeding, birth interval, birth weight, husbands' education, women's age, and region, are the top eight important predictors of pneumonia among children with important scores of more than 5% to 20% respectively.

CONCLUSIONS: Random forest is the best model to predict pneumonia and stratify its determinant factors. The implications of this study are profound for advanced research methodology, tailored to promote effective health interventions such as lifestyle modification and behavioral intervention, based on individuals' unique features, specifically for stakeholders to take proactive childcare interventions. The study would serve as pioneering evidence for future research, and researchers are recommended to use deep learning algorithms to enhance prediction accuracy.}, } @article {pmid40307287, year = {2025}, author = {Wu, J and He, D and Wang, Y and Liu, S and Du, Y and Wang, H and Tan, S and Zhang, D and Xie, J}, title = {An integrated transcriptome, metabolome, and microbiome dataset of Populus under nutrient-poor conditions.}, journal = {Scientific data}, volume = {12}, number = {1}, pages = {717}, pmid = {40307287}, issn = {2052-4463}, mesh = {*Metabolome ; *Microbiota ; Nutrients ; Plant Roots/microbiology/metabolism ; *Populus/microbiology/genetics/metabolism ; Rhizosphere ; RNA, Ribosomal, 16S/genetics ; Soil Microbiology ; *Transcriptome ; Datasets as Topic ; }, abstract = {The rhizosphere microbiota recruited by plants contributes significantly to maintaining host productivity and resisting stress. However, the genetic mechanisms by which plants regulate this recruitment process remain largely unclear. Here, we generated a comprehensive dataset, including 27 root transcriptomes, 27 root metabolomes, and 54 bulk or rhizosphere soil 16S rRNA amplicons across nine poplar species from four sections grown in nutrient-poor natural soil, along with eleven growth phenotype data. We provided a thorough description of this dataset, followed by a comprehensive co-expression network analysis example that broke down the wall of the four-way relationship between plant gene-metabolite-microbe-phenotype, thus identifying the links between plant gene expression, metabolite accumulation, growth behavior, and rhizosphere microbiome variation under nutrient-poor conditions. Overall, this dataset enhances our understanding of plant and microbe interactions, offering valuable strategies and novel insights for resolving how plants regulate rhizosphere microbial compositions and functions, thereby improving host fitness, which will benefit future research.}, } @article {pmid40314555, year = {2025}, author = {Yu, Z and Li, S and Yang, W and Chen, J and Rahman, MA and Wang, C and Ma, W and Yao, X and Xiong, J and Xu, C and Zhou, Y and Chen, J and Huang, K and Gao, X and Fensholt, R and Weng, Q and Zhou, W}, title = {Enhancing Climate-Driven Urban Tree Cooling with Targeted Nonclimatic Interventions.}, journal = {Environmental science & technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.4c14275}, pmid = {40314555}, issn = {1520-5851}, abstract = {Urban trees play a pivotal role in mitigating heat, yet the global determinants and patterns of their cooling efficiency (CE) remain elusive. Here, we quantify the diel CE of 229 cities across four climatic zones and employ a machine-learning model to assess the influence of variables on CE. We found that for every 10% increase in tree cover, surface temperatures are reduced by 0.25 °C during the day and 0.04 °C at night. Trees in humid regions exhibit the highest daytime CE, while those in arid zones demonstrate the greatest cooling effect at night. This can be explained by the difference in canopy density between the humid and arid zones. During the day, the high canopy density in the humid zone converts more solar radiation into latent heat flux. At night, the low canopy density in the arid zone intercepts less longwave radiation, which favors surface cooling. While climatic factors contribute nearly twice as much to CE as nonclimatic ones, our findings suggest that optimizing CE is possible by managing variables within specific thresholds due to their nonlinear effects. For instance, we revealed that in arid regions, an impervious surface coverage of approximately 60% is optimal, whereas in humid areas, reducing it to around 40% maximizes cooling benefits. These insights underscore the need for targeted management of nonclimatic factors to sustain tree cooling benefits and offer practical guidance for designing climate-resilient, nature-based urban strategies.}, } @article {pmid40312707, year = {2025}, author = {Ketchaji, A and Fokam, J and Assah, F and Ateba, F and Wandji, ML and Pamen, JNB and Djoko, GRP and Seugnou, CDN and Kah, E and Atangana, AF and Ateudjieu, J}, title = {The impact of short message service reminders or peer home visits on adherence to antiretroviral therapy and viral load suppression among HIV-Infected adolescents in Cameroon: a randomized controlled trial.}, journal = {AIDS research and therapy}, volume = {22}, number = {1}, pages = {49}, pmid = {40312707}, issn = {1742-6405}, mesh = {Humans ; *HIV Infections/drug therapy/virology ; Adolescent ; Female ; Cameroon/epidemiology ; Male ; *Viral Load/drug effects ; *Text Messaging ; *House Calls ; Young Adult ; *Medication Adherence ; *Anti-HIV Agents/therapeutic use ; *Reminder Systems ; Peer Group ; }, abstract = {BACKGROUND: Adherence to antiretroviral therapy (ART) and viral load suppression (VLS) constitute one of the key challenges to control human immunodeficiency virus (HIV), especially during adolescence. This trial aimed at assessing the impact of short message services (SMS) or peer home visits (PHV) on adherence to ART and VL suppression among adolescents living with HIV (ALWHIV) in Cameroon.

METHODS: A randomized controlled trial (RCT) was conducted from July 2018 to February 2019 at the Mother and Child Center of the Chantal Biya Foundation in Yaounde. Eligible ALWHIV (15-19 years), with a fully disclosed HIV status, with availability of phone and guardian's consent, were randomly assigned to receive either daily SMS or bi-weekly PHV for a six-months period. The control-group received standard of care according to the national guidelines. Study investigators and participants were not blinded to the interventions group allocation, and no adverse events or side effects were observed. Adjusted logistic regression was used to assess the impact of interventions on outcomes. The study was approved by The Pan-African Clinical Trials Registry with PACTR201904582515723 at (www.pactr.org).

RESULTS: Adherence to ART increased in the PHV (aRR: 4.3; 95% CI: 2.2-8.3; p < 0.001) and SMS (aRR: 3.1, 95% CI: 2.1-5.3; p < 0.001) groups compared to the control-group. Likewise, VL suppression was higher in PHV (aRR: 2.1; 95% CI: 1.9-7.5 p < 0.001) and SMS (aRR: 3.2; 95% CI: 1.8-5.4; p < 0.001) groups compared to the control-group. Based on CI, both interventions showed similar benefits on improving adherence and VLS.

CONCLUSIONS: Among ALHIV, SMS or PHV contribute substantially to improving adherence and VL suppression among ALWHIV. Implementing such strategies would support efforts in eliminating pediatric AIDS in low- and middle-income countries.}, } @article {pmid40120189, year = {2025}, author = {Sun, Q and Li, D and He, Y and Ping, Q and Wang, L and Li, Y}, title = {Improved anaerobic digestion of waste activated sludge under ammonia stress by nanoscale zero-valent iron/peracetic acid pretreatment and hydrochar regulation: Insights from multi-omics analyses.}, journal = {Water research}, volume = {279}, number = {}, pages = {123497}, doi = {10.1016/j.watres.2025.123497}, pmid = {40120189}, issn = {1879-2448}, mesh = {*Sewage ; *Ammonia ; Anaerobiosis ; Iron/chemistry ; Methane ; *Peracetic Acid/chemistry ; Multiomics ; }, abstract = {This study developed a novel strategy combining a nanoscale zero-valent iron (nZVI)/peracetic acid (PAA) pretreatment and hydrochar regulation to enhance anaerobic digestion of waste activated sludge (WAS) under ammonia-stressed conditions. The strategy significantly enhanced methane production at ammonia concentrations below 3000 mg/L, with the regulation groups (AN3000/REG) achieving a 50.1 % increase in cumulative methane yield. Metagenomic analysis demonstrated a 14.2 % enrichment of key functional microorganisms, including syntrophic fatty acid-oxidizing bacteria and hydrogenotrophic methanogens, in the AN3000/REG groups. Some of them promote the conversion of butyrate and valerate to acetate through the upregulation of key genes in the fatty acid β-oxidation pathway, thereby supplying sufficient substrates for acetoclastic methanogenesis. Beyond enhancing acetoclastic methanogenesis, the AN3000/REG groups exhibited significant upregulation of other metabolic pathways, with a 34.2 % increase in syntrophic acetate oxidation-hydrogenotrophic methanogenesis genes and a 17.1 % increase in methanol/methylotrophic methanogenesis-related genes. These findings were further validated by the metatranscriptomic and metaproteomic combination analyses. Furthermore, the AN3000/REG groups exhibited a significant enhancement in direct interspecies electron transfer, with functional microbes (e.g., Geobacter, Methanosarcina, and Methanobacterium), pili, and cytochrome c showing significant increases of 1.38-fold, 12.7-fold, and 5.6-fold, respectively. This might be due to the synergistic effects of nZVI and hydrochar in the regulation groups. Additionally, metabolomic analyses revealed that the regulation strategy improved the microbial adaptability to ammonia stress by modulating metabolic products, such as alkaloids. Our study not only provides a promising strategy for alleviating ammonia inhibition during the anaerobic digestion of WAS but also provides a strong basis for understanding the underlying mechanism under ammonia-stressed conditions.}, } @article {pmid39871222, year = {2025}, author = {Diongue, FB and Faye, A and Loucoubar, C and Sougou, NM and Sy, I and Tall, A and Ndiaye, Y and Sarr, SC}, title = {Situational analysis of the quality of maternal, child, and adolescent health data in the health districts of Thiès, Mbour, Kédougou, and Saraya in Senegal.}, journal = {BMC public health}, volume = {25}, number = {1}, pages = {337}, pmid = {39871222}, issn = {1471-2458}, mesh = {Senegal ; Humans ; Adolescent ; Female ; *Data Accuracy ; Child ; *Health Information Systems/standards ; *Child Health/statistics & numerical data ; *Adolescent Health/statistics & numerical data ; Qualitative Research ; Lot Quality Assurance Sampling ; *Maternal Health ; }, abstract = {INTRODUCTION: In Senegal, the Routine Health Information System (RHIS) captures the majority of data from the Ministry of Health and Social Action (MHSA) public structures and very little health data from the private sector and other ministerial departments. Quality data strengthens the validity and reliability of research results. Common areas of data quality include accuracy, completeness, consistency, credibility, and timeliness. The work aims to assess the quality of routine maternal, child, and adolescent health data in Senegal.

MATERIALS AND METHODS: A mixed quantitative and qualitative design was chosen in four health districts, including Thiès, Mbour, Kédougou, and Saraya. The study included functional health structures that produce maternal, child, and adolescent health data. For the quantitative part, a descriptive and analytical study was carried out. Lot Quality Assurance Sampling (LQAS) was used as the sampling method. Data were collected using Performance of Routine Information Systems Management (PRISM) data collection tools and the ODK application and analyzed (univariate and bivariate) using R and Stata with an alpha risk of 5%. The following data quality indicators (accuracy, completeness, and promptness) were estimated. An exploratory case study and purposive sampling supported the qualitative part by implementing individual interviews.

RESULTS: The study showed an accuracy ratio of 1 in the intervention districts, a difference in the control districts, and a disparity in the transmission of guidelines between districts (inter- and intra-region). The average level of completeness was 0.64 (+/- 0.44) for all regions combined, with no significant difference between districts. The promptness rate for Kédougou, Saraya, Thiès, and Mbour districts was 81%, 75.9%, 72.2%, and 86.7%, respectively. Between 40% and 60% of facilities in each district carried out self-assessments. Data collection tools were considered to be numerous. A large number of tools were easy to use. The recording space was appreciated. On the other hand, the length of the forms was little or not appreciated by the providers. Few of the providers in the 4 districts had been trained to record data in DHIS2.

CONCLUSION: Assessment of data quality in the districts studied shows shortcomings in terms of completeness and timeliness. Many factors influence the SMEA data quality situation, including knowledge or application of RHIS policies, standards, and protocols, perception of the importance of RHIS, ease of use of data collection tools, training of providers, and diversity of data production sources.}, } @article {pmid40307720, year = {2025}, author = {Moreau, SJM and Marchal, L and Boulain, H and Musset, K and Labas, V and Tomas, D and Gauthier, J and Drezen, JM}, title = {Multi-omic approach to characterize the venom of the parasitic wasp Cotesia congregata (Hymenoptera: Braconidae).}, journal = {BMC genomics}, volume = {26}, number = {1}, pages = {431}, pmid = {40307720}, issn = {1471-2164}, support = {ANR-12-ADAP-0001//Agence Nationale de la Recherche/ ; ANR-12-ADAP-0001//Agence Nationale de la Recherche/ ; ANR-12-ADAP-0001//Agence Nationale de la Recherche/ ; ANR-12-ADAP-0001//Agence Nationale de la Recherche/ ; ANR-12-ADAP-0001//Agence Nationale de la Recherche/ ; ANR-12-ADAP-0001//Agence Nationale de la Recherche/ ; SMHART project 35069//European Regional Development Fund/ ; SMHART project 35069//European Regional Development Fund/ ; }, mesh = {Animals ; *Wasps/genetics/virology/metabolism ; *Wasp Venoms/genetics/metabolism/chemistry ; Female ; *Proteomics/methods ; Insect Proteins/genetics/metabolism/chemistry ; Multiomics ; }, abstract = {BACKGROUND: Cotesia congregata is a parasitoid Hymenoptera belonging to the Braconidae family and carrying CCBV (Cotesia congregata Bracovirus), an endosymbiotic polydnavirus. CCBV virus is considered as the main virulence factor of this species, which has raised questions, over the past thirty years, about the potential roles of venom in the parasitic interaction between C. congregata and its host, Manduca sexta (Lepidoptera: Sphingidae). To investigate C. congregata venom composition, we identified genes overexpressed in the venom glands (VGs) compared to ovaries, analyzed the protein composition of this fluid and performed a detailed analysis of conserved domains of these proteins.

RESULTS: Of the 14 140 known genes of the C. congregata genome, 659 genes were significantly over-expressed (with 10-fold or higher changes in expression) in the VGs of female C. congregata, compared with the ovaries. We identified 30 proteins whose presence was confirmed in venom extracts by proteomic analyses. Twenty-four of these were produced as precursor molecules containing a predicted signal peptide. Six of the proteins lacked a predicted signal peptide, suggesting that venom production in C. congregata also involves non-canonical secretion mechanisms. We have also analysed 18 additional proteins and peptides of interest whose presence in venom remains uncertain, but which could play a role in VG function.

CONCLUSIONS: Our results show that the venom of C. congregata not only contains proteins (including several enzymes) homologous to well-known venomous compounds, but also original proteins that appear to be specific to this species. This exhaustive study sheds a new light on this venom composition, the molecular diversity of which was unexpected. These data pave the way for targeted functional analyses and to better understand the evolutionary mechanisms that have led to the formation of the venomous arsenals we observe today in parasitoid insects.}, } @article {pmid39849009, year = {2025}, author = {Calderón-Osorno, M and Rojas-Villalta, D and Lejzerowicz, F and Cortés, J and Arias-Andres, M and Rojas-Jimenez, K}, title = {The influence of depth on the global deep-sea plasmidome.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {2959}, pmid = {39849009}, issn = {2045-2322}, support = {SIA 0483-21//Universidad Nacional de Costa Rica/ ; C1455//Vicerrectoría de Investigacion de la Universidad Costa Rica/ ; C2650//Vicerrectoría de Investigacion de la Universidad Costa Rica/ ; C3509//Vicerrectoría de Investigacion de la Universidad Costa Rica/ ; }, mesh = {*Plasmids/genetics ; *Metagenome ; *Seawater/microbiology ; Ecosystem ; Gammaproteobacteria/genetics ; Alphaproteobacteria/genetics ; Oceans and Seas ; Bacteria/genetics ; Computational Biology/methods ; Indian Ocean ; }, abstract = {Plasmids play a crucial role in facilitating genetic exchange and enhancing the adaptability of microbial communities. Despite their importance, environmental plasmids remain understudied, particularly those in fragile and underexplored ecosystems such as the deep-sea. In this paper we implemented a bioinformatics pipeline to study the composition, diversity, and functional attributes of plasmid communities (plasmidome) in 81 deep-sea metagenomes from the Tara and Malaspina expeditions, sampled from the Pacific, Atlantic, and Indian Oceans at depths ranging from 270 to 4005 m. We observed an association between depth and plasmid traits, with the 270-1000 m range (mesopelagic samples) exhibiting the highest number of plasmids and the largest plasmid sizes. Plasmids of Alphaproteobacteria and Gammaproteobacteria were predominant across the oceans, particularly in this depth range, which also showed the highest species diversity and abundance of metabolic pathways, including aromatic compound degradation. Surprisingly, relatively few antibiotic resistance genes were found in the deep-sea ecosystem, with most being found in the mesopelagic layer. These included classes such as beta-lactamase, biocide resistance, and aminoglycosides. Our study also identified the MOBP and MOBQ relaxase families as prevalent across various taxonomic classes. This research underscores the importance of studying the plasmidome independently from the chromosomal context. Our limited understanding of the deep-sea's microbial ecology, especially its plasmidome, necessitates caution in human activities like mining. Such activities could have unforeseen impacts on this largely unexplored ecosystem.}, } @article {pmid40306212, year = {2025}, author = {Nica, I and Georgescu, I}, title = {The ecological impact of agricultural production on CO2 emissions in India: Pathways to sustainable agriculture.}, journal = {Journal of environmental management}, volume = {384}, number = {}, pages = {125548}, doi = {10.1016/j.jenvman.2025.125548}, pmid = {40306212}, issn = {1095-8630}, abstract = {This study examines the relationship between CO2 emissions and agricultural production in India from 1990 to 2023, using an Autoregressive Distributed Lag (ARDL) model. Key agricultural indicators analyzed include the Food Production Index (FPI), Cereal Production (CP), Livestock Production Index (LPI), and the value added by Agriculture, Forestry, and Fishing (AFF). The results show that on the long run, a 1 % increase in FPI leads to a 7.86 unit increase in CO2 emissions per capita, while a 1 % increase in livestock production results in a 3.28 unit decrease in CO2 emissions per capita. In the short run, a similar increase in food production and livestock production also influences CO2 emissions, with notable but varying impacts over time. These findings underline the environmental trade-offs between food security and CO2 emissions, emphasizing the need for sustainable agricultural practices. This research contributes to existing literature by utilizing a broad set of agricultural indicators and robust ARDL analysis to examine both short- and long-term effects, providing a more comprehensive understanding of agricultural sustainability. The study was prompted by India's rapid agricultural growth, driven by its growing population and economic expansion, which has raised significant environmental concerns. Unlike prior research that often takes a generalized or global approach, this study offers an India-specific analysis that captures the country's distinct socio-economic and ecological conditions. By focusing on nationally relevant agricultural indicators and sustainability challenges, the research provides context-sensitive insights that can support effective and targeted policy design. The findings highlight the importance of policies that align agricultural productivity with sustainability, supporting the UN Sustainable Development Goals on climate action and food security.}, } @article {pmid40305182, year = {2025}, author = {Uemura, NA and Nakane, D}, title = {Type IV Pili in Thermophilic Bacteria: Mechanisms and Ecological Implications.}, journal = {Biomolecules}, volume = {15}, number = {4}, pages = {}, pmid = {40305182}, issn = {2218-273X}, support = {24KJ1131//Japan Society for the Promotion of Science/ ; 21K07020//Japan Society for the Promotion of Science/ ; 22H05066//Japan Society for the Promotion of Science/ ; }, mesh = {*Fimbriae, Bacterial/metabolism/physiology ; *Thermus thermophilus/metabolism/physiology/genetics ; }, abstract = {Type IV pili (T4P) machinery is critical for bacterial surface motility, protein secretion, and DNA uptake. This review highlights the ecological significance of T4P-dependent motility in Thermus thermophilus, a thermophilic bacterium isolated from hot springs. Unlike swimming motility, the T4P machinery enables bacteria to move over two-dimensional surfaces through repeated cycles of extension and retraction of pilus filaments. Notably, T. thermophilus exhibits upstream-directed migration under shear stress, known as rheotaxis, which appears to represent an adaptive strategy unique to thermophilic bacteria thriving in rapid water flows. Furthermore, T4P contributes to the capture of DNA and phages, indicating their multifunctionality in natural environments. Understanding the T4P dynamics provides insights into bacterial survival and evolution in extreme habitats.}, } @article {pmid40303041, year = {2024}, author = {McDuie, F and T Overton, C and A Lorenz, A and L Matchett, E and L Mott, A and A Mackell, D and T Ackerman, J and De La Cruz, SEW and Patil, VP and Prosser, DJ and Takekawa, JY and Orthmeyer, DL and Pitesky, ME and Díaz-Muñoz, SL and Riggs, BM and Gendreau, J and Reed, ET and Petrie, MJ and Williams, CK and Buler, JJ and Hardy, MJ and Ladman, BS and Legagneux, P and Bêty, J and Thomas, PJ and Rodrigue, J and Lefebvre, J and Casazza, ML}, title = {Mitigating Risk: Predicting H5N1 Avian Influenza Spread with an Empirical Model of Bird Movement.}, journal = {Transboundary and emerging diseases}, volume = {2024}, number = {}, pages = {5525298}, pmid = {40303041}, issn = {1865-1682}, mesh = {Animals ; *Influenza in Birds/epidemiology/virology/transmission/prevention & control ; *Influenza A Virus, H5N1 Subtype/physiology ; *Animal Migration ; Birds ; Geographic Information Systems ; Disease Outbreaks/veterinary ; Animals, Wild ; }, abstract = {Understanding timing and distribution of virus spread is critical to global commercial and wildlife biosecurity management. A highly pathogenic avian influenza virus (HPAIv) global panzootic, affecting ~600 bird and mammal species globally and over 83 million birds across North America (December 2023), poses a serious global threat to animals and public health. We combined a large, long-term waterfowl GPS tracking dataset (16 species) with on-ground disease surveillance data (county-level HPAIv detections) to create a novel empirical model that evaluated spatiotemporal exposure and predicted future spread and potential arrival of HPAIv via GPS tracked migratory waterfowl through 2022. Our model was effective for wild waterfowl, but predictions lagged HPAIv detections in poultry facilities and among some highly impacted nonmigratory species. Our results offer critical advance warning for applied biosecurity management and planning and demonstrate the importance and utility of extensive multispecies tracking to highlight potential high-risk disease spread locations and more effectively manage outbreaks.}, } @article {pmid39852552, year = {2025}, author = {Yang, H and Luo, X and Shang, Z and Li, K and Cai, J and Chen, Y and Xin, L and Ju, J}, title = {Metabolic Blockade-Based Genome Mining of Malbranchea circinata SDU050: Discovery of Diverse Secondary Metabolites.}, journal = {Marine drugs}, volume = {23}, number = {1}, pages = {}, pmid = {39852552}, issn = {1660-3397}, support = {U2106207//National Natural Science Foundation of China/ ; 2022YFC2804100//National Key Research and Development Program of China/ ; 22037006//National Natural Science Foundation of China/ ; SYS202205//Shandong Laboratory Program/ ; }, mesh = {*Anti-Bacterial Agents/pharmacology/isolation & purification ; *Secondary Metabolism/genetics ; Multigene Family ; Polyketide Synthases/genetics/metabolism ; Biosynthetic Pathways/genetics ; Methicillin-Resistant Staphylococcus aureus/drug effects ; Genome, Fungal ; Microbial Sensitivity Tests ; Gram-Positive Bacteria/drug effects ; Staphylococcus aureus/drug effects ; Bacillus subtilis/drug effects ; *Ascomycota/genetics/metabolism ; Isocoumarins/pharmacology ; Computational Biology ; Geologic Sediments/microbiology ; }, abstract = {Malbranchea circinata SDU050, a fungus derived from deep-sea sediment, is a prolific producer of diverse secondary metabolites. Genome sequencing revealed the presence of at least 69 biosynthetic gene clusters (BGCs), including 30 encoding type I polyketide synthases (PKSs). This study reports the isolation and identification of four classes of secondary metabolites from wild-type M. circinata SDU050, alongside five additional metabolite classes, including three novel cytochalasins (7-9), obtained from a mutant strain through the metabolic blockade strategy. Furthermore, bioinformatic analysis of the BGC associated with the isocoumarin sclerin (1) enabled the deduction of its biosynthetic pathway based on gene function predictions. Bioactivity assays demonstrated that sclerin (1) and (-)-mycousnine (10) exhibited weak antibacterial activity against Gram-positive bacteria such as Staphylococcus aureus, methicillin-resistant Staphylococcus aureus (MRSA), and Bacillus subtilis. These findings underscore the chemical diversity and biosynthetic potential of M. circinata SDU050 and highlight an effective strategy for exploring marine fungal metabolites.}, } @article {pmid40303815, year = {2023}, author = {Wielgus, E and Klamm, A and Conraths, FJ and Dormann, CF and Henrich, M and Kronthaler, F and Heurich, M}, title = {First-Passage Time Analysis Based on GPS Data Offers a New Approach to Estimate Restricted Zones for the Management of Infectious Diseases in Wildlife: A Case Study Using the Example of African Swine Fever.}, journal = {Transboundary and emerging diseases}, volume = {2023}, number = {}, pages = {4024083}, pmid = {40303815}, issn = {1865-1682}, mesh = {Animals ; *African Swine Fever/prevention & control/epidemiology/transmission ; *Geographic Information Systems ; Swine ; Animals, Wild ; *Sus scrofa ; Germany/epidemiology ; Female ; Disease Outbreaks/veterinary/prevention & control ; Male ; African Swine Fever Virus ; }, abstract = {An essential part of any disease containment and eradication policy is the implementation of restricted zones, but determining the appropriate size of these zones can be challenging for managers. We designed a new method, based on animal movement, to help assess how large restricted zones should be after a spontaneous outbreak to successfully control infectious diseases in wildlife. Our approach uses first-passage time (FPT) analysis and Cox proportional hazard (CPH) models to calculate and compare the risk of an animal leaving different-sized areas. We illustrate our approach using the example of the African swine fever (ASF) virus and its wild pig reservoir host species, the wild boar (Sus scrofa), and we investigate the feasibility of applying this method to other systems. Using GPS data from 57 wild boar living in the Hainich National Park, Germany, we calculate the time spent by each individual in areas of different sizes using FPT analysis. We apply CPH models on the derived data to compare the risk of leaving areas of different sizes and to assess the effects of season and the sex of the wild boar on the risk of leaving. We conduct survival analyses to estimate the risk of leaving an area over time. Our results indicate that the risk of leaving an area decreases exponentially by 10% for each 100 m increase in radius size so that the differences were more pronounced for small sizes. Furthermore, the probability of leaving increases exponentially with time. Wild boar had a similar risk of leaving an area of a given size throughout the year, except in spring and winter, when females had a much lower risk of leaving. Our findings are in agreement with the literature on wild boar movement, further validating our method, and repeated analyses with location data resampled at different rates gave similar results. Our results may be applicable only to our study area, but they demonstrate the applicability of the proposed method to any ecosystem where wild boar populations are likely to be infected with ASF and where restricted zones should be established accordingly. The outlined approach relies solely on the analysis of movement data and provides a useful tool to determine the optimal size of restricted zones. It can also be applied to future outbreaks of other diseases.}, } @article {pmid40298711, year = {2025}, author = {Prado, SI and Novais, MAP}, title = {Acute viral bronchiolitis in Brazil: characteristics of length of stay and hospital costs.}, journal = {Ciencia & saude coletiva}, volume = {30}, number = {4}, pages = {e07402023}, doi = {10.1590/1413-81232025304.07402023}, pmid = {40298711}, issn = {1678-4561}, mesh = {Humans ; Brazil ; Infant ; Retrospective Studies ; *Length of Stay/statistics & numerical data/economics ; Acute Disease ; Child, Preschool ; *Hospitalization/economics/statistics & numerical data ; *Bronchiolitis, Viral/economics/therapy/epidemiology ; *Hospital Costs/statistics & numerical data ; Longitudinal Studies ; Male ; Female ; National Health Programs/economics ; }, abstract = {The objective of the study was to evaluate the length of stay in pediatric hospitalizations for acute viral bronchiolitis in the Brazilian Health System (SUS) and the costs of hospitalizations. This was a quantitative, observational, and ecological study, based on a retrospective and longitudinal analysis of data from the Department of Informatics of the Unified Health System (DATASUS; 2012-2021) using descriptive statistics and Tukey's paired test. Regarding the mean value of AIH/HAA Hospital Admission Authorization, among the regions, the high costs of hospitalizations are located more frequent in the Southeast region and the lowest proportion is directed to the corresponds to the North region. In the length of hospital stay among the regions, the shortest mean stay was identified in the Central West region (2.5 days) and the greatest stay in the Northeast region (3.1 days). Considering the age group of one year of life, its representativeness was 57% when compared to the age group of 1-4 years (43%). The fragility of the implementation of primary public policies in the prevention of bronchiolitis contributes to high hospital costs and significant economic impacts on the national healthcare system.}, } @article {pmid39969985, year = {2025}, author = {Zhang, J and Gao, X and Liang, C and Zhang, M and Zhang, S}, title = {Spatiotemporal pattern evolution analysis of ecological networks based on morphological spatial pattern analysis: a case study of Ningbo City, China.}, journal = {Integrated environmental assessment and management}, volume = {21}, number = {3}, pages = {540-554}, doi = {10.1093/inteam/vjaf027}, pmid = {39969985}, issn = {1551-3793}, support = {202148/WT_/Wellcome Trust/United Kingdom ; }, mesh = {China ; *Environmental Monitoring/methods ; Spatio-Temporal Analysis ; *Ecosystem ; Cities ; *Conservation of Natural Resources/methods ; Geographic Information Systems ; Biodiversity ; Urbanization ; }, abstract = {The exponential expansion of urban areas has precipitated a concomitant deterioration in the natural environment. Constructing ecological networks is vital in improving landscape connectivity, protecting biodiversity, and maintaining regional sustainable development. Ningbo, China, was set as the research area. Geographic information system and morphological spatial pattern analysis (MSPA) were used to determine the ecological source area. Subsequently, the corridor design model Linkage Mapper was used to ascertain and assess the linkages between the designated ecological source areas. The results showed that from 2000-2020, there was a large-scale change in land use type in Ningbo, with increasing complexity of patches and landscape fragmentation. The ecological sources of the three periods in Ningbo were primarily situated in the western, southern, and Hangzhou Bay coastal regions, exhibiting an uneven distribution in the eastern and western areas. The number of primary ecological corridors in Ningbo underwent a significant reduction, from 26 to 17, between the years 2000-2020. In terms of the distribution of ecological corridors, the primary corridors were concentrated in the central, southern, and western regions of the study area in 2000. By 2020, however, the primary ecological corridors within the study region were distributed mainly in a southerly direction. The interaction between north and south ecological sources was weakened, which adversely affected the species spread and ecosystem stability. After optimization, 12 ecological corridors and four ecological nodes were incorporated into Ningbo, 67 ecological breakpoints were identified, and four stepping stone patches were added. The study used spatiotemporal change trends, including land use type and landscape pattern, to examine the ecological network of Ningbo. In conclusion, the proposed optimization strategy is aligned with the current urban development context, offering a particularly pertinent reference point for Ningbo's ecological protection initiatives.}, } @article {pmid40297776, year = {2025}, author = {Schwarzerova, J and Olesova, D and Jureckova, K and Kvasnicka, A and Kostoval, A and Friedecky, D and Sekora, J and Pomenkova, J and Provaznik, V and Popelinsky, L and Weckwerth, W}, title = {Enhanced metabolomic predictions using concept drift analysis: identification and correction of confounding factors.}, journal = {Bioinformatics advances}, volume = {5}, number = {1}, pages = {vbaf073}, pmid = {40297776}, issn = {2635-0041}, abstract = {MOTIVATION: The increasing use of big data and optimized prediction methods in metabolomics requires techniques aligned with biological assumptions to improve early symptom diagnosis. One major challenge in predictive data analysis is handling confounding factors-variables influencing predictions but not directly included in the analysis.

RESULTS: Detecting and correcting confounding factors enhances prediction accuracy, reducing false negatives that contribute to diagnostic errors. This study reviews concept drift detection methods in metabolomic predictions and selects the most appropriate ones. We introduce a new implementation of concept drift analysis in predictive classifiers using metabolomics data. Known confounding factors were confirmed, validating our approach and aligning it with conventional methods. Additionally, we identified potential confounding factors that may influence biomarker analysis, which could introduce bias and impact model performance.

Based on biological assumptions supported by detected concept drift, these confounding factors were incorporated into correction of prediction algorithms to enhance their accuracy. The proposed methodology has been implemented in Semi-Automated Pipeline using Concept Drift Analysis for improving Metabolomic Predictions (SAPCDAMP), an open-source workflow available at https://github.com/JanaSchwarzerova/SAPCDAMP.}, } @article {pmid40295976, year = {2025}, author = {Liberati, F and Pose Marino, TM and Bottoni, P and Canestrelli, D and Castrignanò, T}, title = {HPC-T-Assembly: a pipeline for de novo transcriptome assembly of large multi-specie datasets.}, journal = {BMC bioinformatics}, volume = {26}, number = {1}, pages = {113}, pmid = {40295976}, issn = {1471-2105}, mesh = {*Software ; *Transcriptome ; *Gene Expression Profiling/methods ; Sequence Analysis, RNA/methods ; Computational Biology/methods ; Databases, Genetic ; RNA-Seq/methods ; }, abstract = {BACKGROUND: Recent years have seen a substantial increase in RNA-seq data production, with this technique becoming the primary approach for gene expression studies across a wide range of non-model organisms. The majority of these organisms lack a well-annotated reference genome to serve as a basis for studying differentially expressed genes (DEGs). As an alternative cost-effective protocol to using a reference genome, the assembly of RNA-seq raw reads is performed to produce what is referred to as a 'de novo transcriptome,' serving as a reference for subsequent DEGs' analysis. This assembly step for conventional DEGs analysis pipelines for non-model organisms is a computationally expensive task. Furthermore, the complexity of the de novo transcriptome assembly workflows poses a challenge for researchers in implementing best-practice techniques and the most recent software versions, particularly when applied to various organisms of interest.

RESULTS: To address computational challenges in transcriptomic analyses of non-model organisms, we present HPC-T-Assembly, a tool for de novo transcriptome assembly from RNA-seq data on high-performance computing (HPC) infrastructures. It is designed for straightforward setup via a Web-oriented interface, allowing analysis configuration for several species. Once configuration data is provided, the entire parallel computing software for assembly is automatically generated and can be launched on a supercomputer with a simple command line. Intermediate and final outputs of the assembly pipeline include additional post-processing steps, such as assembly quality control, ORF prediction, and transcript count matrix construction.

CONCLUSION: HPC-T-Assembly allows users, through a user-friendly Web-oriented interface, to configure a run for simultaneous assemblies of RNA-seq data from multiple species. The parallel pipeline, launched on HPC infrastructures, significantly reduces computational load and execution times, enabling large-scale transcriptomic and meta-transcriptomics analysis projects.}, } @article {pmid40295704, year = {2024}, author = {Grunnill, M and Eshaghi, A and Damodaran, L and Nagra, S and Gharouni, A and Braukmann, T and Clark, S and Peci, A and Isabel, S and Banh, P and Plessis, LD and Murall, CL and Colijn, C and Mubareka, S and Hasso, M and Bahl, J and Mostafa, HH and Gubbay, JB and Patel, SN and Wu, J and Duvvuri, VR}, title = {Inferring enterovirus D68 transmission dynamics from the genomic data of two 2022 North American outbreaks.}, journal = {Npj viruses}, volume = {2}, number = {1}, pages = {34}, pmid = {40295704}, issn = {2948-1767}, abstract = {Enterovirus D68 (EV-D68) has emerged as a significant cause of acute respiratory illness in children globally, notably following its extensive outbreak in North America in 2014. A recent outbreak of EV-D68 was observed in Ontario, Canada, from August to October 2022. Our phylogenetic analysis revealed a notable genetic similarity between the Ontario outbreak and a concurrent outbreak in Maryland, USA. Utilizing Bayesian phylodynamic modeling on whole genome sequences (WGS) from both outbreaks, we determined the median peak time-varying reproduction number (Rt) to be 2.70, 95% HPD (1.76, 4.08) in Ontario and 2.10, 95% HPD (1.41, 3.17) in Maryland. The Rt trends in Ontario closely matched those derived via EpiEstim using reported case numbers. Our study also provides new insights into the median infection duration of EV-D68, estimated at 7.94 days, 95% HPD (4.55, 12.8) in Ontario and 10.8 days, 95% HPD (5.85, 18.6) in Maryland, addressing the gap in the existing literature surrounding EV-D68's infection period. We observed that the estimated Time since the Most Recent Common Ancestor (TMRCA) and the epidemic's origin coincided with the easing of COVID-19 related social contact restrictions in both areas. This suggests that the relaxation of non-pharmaceutical interventions, initially implemented to control COVID-19, may have inadvertently facilitated the spread of EV-D68. These findings underscore the effectiveness of phylodynamic methods in public health, demonstrating their broad application from local to global scales and underscoring the critical role of pathogen genomic data in enhancing public health surveillance and outbreak characterization.}, } @article {pmid40245036, year = {2025}, author = {Hu, J and Weber, JN and Fuess, LE and Steinel, NC and Bolnick, DI and Wang, M}, title = {A spectral framework to map QTLs affecting joint differential networks of gene co-expression.}, journal = {PLoS computational biology}, volume = {21}, number = {4}, pages = {e1012953}, pmid = {40245036}, issn = {1553-7358}, mesh = {*Quantitative Trait Loci/genetics ; *Gene Regulatory Networks/genetics ; Animals ; Computational Biology/methods ; *Chromosome Mapping/methods ; Phenotype ; Genotype ; Models, Genetic ; Gene Expression Profiling/methods ; }, abstract = {Studying the mechanisms underlying the genotype-phenotype association is crucial in genetics. Gene expression studies have deepened our understanding of the genotype → expression → phenotype mechanisms. However, traditional expression quantitative trait loci (eQTL) methods often overlook the critical role of gene co-expression networks in translating genotype into phenotype. This gap highlights the need for more powerful statistical methods to analyze genotype → network → phenotype mechanism. Here, we develop a network-based method, called spectral network quantitative trait loci analysis (snQTL), to map quantitative trait loci affecting gene co-expression networks. Our approach tests the association between genotypes and joint differential networks of gene co-expression via a tensor-based spectral statistics, thereby overcoming the ubiquitous multiple testing challenges in existing methods. We demonstrate the effectiveness of snQTL in the analysis of three-spined stickleback (Gasterosteus aculeatus) data. Compared to conventional methods, our method snQTL uncovers chromosomal regions affecting gene co-expression networks, including one strong candidate gene that would have been missed by traditional eQTL analyses. Our framework suggests the limitation of current approaches and offers a powerful network-based tool for functional loci discoveries.}, } @article {pmid39808116, year = {2024}, author = {Zárate, A and Díaz-González, L and Taboada, B}, title = {VirDetect-AI: a residual and convolutional neural network-based metagenomic tool for eukaryotic viral protein identification.}, journal = {Briefings in bioinformatics}, volume = {26}, number = {1}, pages = {}, pmid = {39808116}, issn = {1477-4054}, mesh = {*Metagenomics/methods ; *Neural Networks, Computer ; *Viral Proteins/genetics ; Humans ; *Eukaryota/virology ; *Viruses/genetics ; Genome, Viral ; Artificial Intelligence ; Computational Biology/methods ; Metagenome ; Convolutional Neural Networks ; }, abstract = {This study addresses the challenging task of identifying viruses within metagenomic data, which encompasses a broad array of biological samples, including animal reservoirs, environmental sources, and the human body. Traditional methods for virus identification often face limitations due to the diversity and rapid evolution of viral genomes. In response, recent efforts have focused on leveraging artificial intelligence (AI) techniques to enhance accuracy and efficiency in virus detection. However, existing AI-based approaches are primarily binary classifiers, lacking specificity in identifying viral types and reliant on nucleotide sequences. To address these limitations, VirDetect-AI, a novel tool specifically designed for the identification of eukaryotic viruses within metagenomic datasets, is introduced. The VirDetect-AI model employs a combination of convolutional neural networks and residual neural networks to effectively extract hierarchical features and detailed patterns from complex amino acid genomic data. The results demonstrated that the model has outstanding results in all metrics, with a sensitivity of 0.97, a precision of 0.98, and an F1-score of 0.98. VirDetect-AI improves our comprehension of viral ecology and can accurately classify metagenomic sequences into 980 viral protein classes, hence enabling the identification of new viruses. These classes encompass an extensive array of viral genera and families, as well as protein functions and hosts.}, } @article {pmid40293859, year = {2025}, author = {Wastler, HM and Cowan, HR and Breitborde, NJK and Tabares, JV and Yu, M and Pan, X and Boettner, B and Browning, C and Bryan, CJ}, title = {Ecological Momentary Assessment of Emotion Regulation and Suicidal Ideation in First-Episode Psychosis.}, journal = {Schizophrenia bulletin}, volume = {}, number = {}, pages = {}, doi = {10.1093/schbul/sbaf042}, pmid = {40293859}, issn = {1745-1701}, support = {YIG-0-184-20//American Foundation for Suicide Prevention/ ; }, abstract = {Individuals with first-episode psychosis (FEP) are at increased risk for suicide, though few studies have examined the extent to which emotion regulation abnormalities contribute to this risk. The current study sought to address this gap by examining which stages of emotion regulation (ie, identification, selection, implementation) are related to suicidal ideation among individuals with FEP. Forty-one participants completed 28 days of ecological momentary assessment to assess suicidal ideation, negative affect, and emotion regulation in real-time. Results indicated that all 3 stages of emotion regulation were related to suicidal ideation in FEP. Specifically, within-person emotion regulation interacted with between-person negative affect to predict concurrent suicidal ideation (identification stage). Additionally, decreased use of adaptive strategies and increased use of maladaptive strategies were associated with more severe suicidal ideation (selection stage). Finally, decreased emotion regulation effectiveness was associated with more severe suicidal ideation (implementation stage). These findings suggest that emotion regulation difficulties might contribute to the high rates of suicide risk among individuals with FEP. Additional research is needed to determine whether these emotion regulation difficulties are unique to FEP or if they also appear in other high-risk groups.}, } @article {pmid40292360, year = {2025}, author = {Andersen, ZJ and Badyda, A and Tzivian, L and Dzhambov, AM and Paunovic, K and Savic, S and Jacquemin, B and Dragic, N}, title = {Air pollution inequalities in Europe: A deeper understating of challenges in Eastern Europe and pathways forward towards closing the gap between East and West.}, journal = {Environmental epidemiology (Philadelphia, Pa.)}, volume = {9}, number = {3}, pages = {e383}, pmid = {40292360}, issn = {2474-7882}, } @article {pmid40292044, year = {2025}, author = {Edelson, JB and Huang, J and Wang, Z and Tam, V and Lefktowitz, D and O'Connor, MJ and White, R and Ha, L and Wittlieb-Weber, CA and Rossano, JW and Lin, K and Cousino, MK and Lane-Fall, M and O'Byrne, ML}, title = {Identifying the determinants of health-related quality of life in children after heart transplant.}, journal = {JHLT open}, volume = {8}, number = {}, pages = {100250}, pmid = {40292044}, issn = {2950-1334}, abstract = {BACKGROUND: Pediatric heart transplant (PHT) recipients have impaired health-related quality of life (HRQOL) that is not fully explained by cardiac limitations. Environment is known to influence HRQOL in other chronic disease populations but is less understood in PHT. Understanding the determinants of HRQOL is a necessary step in identifying high-risk groups and designing actionable interventions.

METHODS: This cross-sectional study includes 8- to 18-year heart transplant (HT) recipients and their families. Generalized estimating equations were used to evaluate the associations of individual characteristics (diagnosis, pulmonary capillary wedge pressure [PCWP], cardiac index [CI]), microenvironment (parent education level, financial security, parental stress [PSI], assessment of child anxiety) and macroenvironment [Child Opportunity Index (COI)] with HRQOL.

RESULTS: Of 31 participants, 32% self-identified as Black, and 40% had congenital heart disease. On cardiac catheterization, 61% had a CI ≥3 liter/min/m[2] and PCWP ≤10 mm Hg. Most households had ≥1 parent who had completed college (58%); 28% of households expressed difficulty paying bills. The PSI showed elevated parental stress [64.5 (interquartile range [IQR] 52.0, 77.8)], while the COI was low [73.0 (IQR 44.5, 89.0)] as was HRQOL [Pediatric Quality of Life 4.0 Core Scales 71.7 (IQR 64.2-82.5), Pediatric Cardiac Quality of Life Index 61.8 (IQR 55.7-74.8)]. Higher parental stress (p = 0.036), higher parental perception of child anxiety (p = 0.058), lower Max VO2 (p = 0.059), and higher PCWP (p = 0.006) were independently associated with worse quality of life.

CONCLUSIONS: HRQOL in children after heart transplant is reduced and determined not only by traditional measures of cardiovascular function, but also by patient psychology and their household environment, highlighting the utility of using an adapted ecological systems framework to understand HRQOL.}, } @article {pmid40287834, year = {2025}, author = {Mohanty, A and Srinivasan, A and Udupaa, P and Catchpoole, D}, title = {Multiomics and tumor banking: comprehensive plaforms- integrating cancer diversity, biomarker discovery and personalised cancer care in India.}, journal = {Human molecular genetics}, volume = {}, number = {}, pages = {}, doi = {10.1093/hmg/ddaf033}, pmid = {40287834}, issn = {1460-2083}, abstract = {Biobanks are innovative biomedical research infrastructures that play a crucial role in advancing cancer research by supporting investigations into the etiology, progression, and therapeutic interventions of the disease. Biobanks have significantly contributed to personalized medicine by providing high-quality bio specimen resources and expertise in tissue handling, essential for understanding the interplay of genetic, ecological, and lifestyle factors on cancer biology, human health, and mortality. By linking bio specimens with clinical, pathological, and epidemiological data, biobanks are central in the discovery and development of cancer therapeutics through biomarkers. In this review, the importance of managing biobanks as integral parts of data generation and analytics continuum driving precision medicine is pointed out. The advent of multi-OMICS analytics, combined with artificial intelligence, systems biology, and deep machine learning, has elevated the importance of bio banking human bio specimens as not only a biological resource but also an informatics asset. Here, we examine the impact of bio banking in facilitating translational, bench-to-bedside cancer research, with a focus on multi-OMICS data-driven biomarker discovery and precision oncology. In addition, we discuss one of the major innovations in biobank management: the hub-and-spoke model. This centralized system leverages core expertise and resources while collecting bio specimens from diverse geographic regions, thereby capturing the heterogeneity of cancer biology. The hub-and-spoke approach is particularly advantageous for countries like India, characterized by vast geographic and demographic diversity. It ensures complete coverage of the different types of cancers, disease stages, and population groups in addressing the complexity and diversity of cancer biology.}, } @article {pmid39724139, year = {2024}, author = {Stephens, JL and Fraga, LAO and Ferreira, JA and De Mondesert, L and Kitron, U and Clennon, JA and Fairley, JK}, title = {Spatial associations of Hansen's disease and schistosomiasis in endemic regions of Minas Gerais, Brazil.}, journal = {PLoS neglected tropical diseases}, volume = {18}, number = {12}, pages = {e0012682}, pmid = {39724139}, issn = {1935-2735}, mesh = {Humans ; Brazil/epidemiology ; *Leprosy/epidemiology ; *Endemic Diseases ; Female ; Male ; Spatial Analysis ; Adult ; Incidence ; Adolescent ; Middle Aged ; Young Adult ; Child ; Geographic Information Systems ; Animals ; *Schistosomiasis mansoni/epidemiology ; *Schistosomiasis/epidemiology ; Child, Preschool ; Aged ; }, abstract = {BACKGROUND: Brazil has the second highest case count of Hansen's disease (leprosy, HD), but factors contributing to transmission in highly endemic areas of the country remain unclear. Recent studies have shown associations of helminth infection and leprosy, supporting a biological plausibility for increased leprosy transmission in areas with helminths. However, spatial analyses of the overlap of these infections are limited. Therefore, we aimed to spatially analyze these two diseases in a co-endemic area of Minas Gerais, Brazil, in order to identify potential epidemiologic associations.

METHODS: An ecological study using public health surveillance records and census data was conducted to investigate whether the occurrence of HD -and specifically multibacillary (MB) disease- was associated with the presence of schistosomiasis in a community of 41 municipalities in eastern Minas Gerais, Brazil from 2011 to 2015. Multivariate logistic regression and spatial cluster analyses using geographic information systems (GIS) were performed.

RESULTS: The average annual incidence of HD in the study area was 35.3 per 100,000 while Schistosoma mansoni average annual incidence was 26 per 100,000. Both HD and schistosomiasis were spatially distributed showing significant clustering across the study area. Schistosomiasis was present in 10.4% of the tracts with HD and thirteen high-high clusters of local bivariate autocorrelation for HD and schistosomiasis cases were identified. A multivariate non-spatial analysis found that census tracts with MB disease were more likely to have schistosomiasis when adjusted for population density, household density, and household income (aOR = 1.7, 95% CI 1.0, 2.7). This remained significant when accounting for spatial correlation (aOR = 1.1, 95% CI (1.0, 1.2)).

CONCLUSION: We found clustering of both HD and schistosomiasis in this area with some statistically significant overlap of multibacillary HD with S. mansoni infection. Not only did we provide an effective approach to study the epidemiology of two endemic neglected tropical diseases with geographic spatial analyses, we highlight the need for further clinical and translational studies to study the potential epidemiologic associations uncovered.}, } @article {pmid40287826, year = {2025}, author = {Gerhardt, K and Ruiz-Perez, CA and Rodriguez-R, LM and Jain, C and Tiedje, JM and Cole, JR and Konstantinidis, KT}, title = {FastAAI: efficient estimation of genome average amino acid identity and phylum-level relationships using tetramers of universal proteins.}, journal = {Nucleic acids research}, volume = {53}, number = {8}, pages = {}, pmid = {40287826}, issn = {1362-4962}, support = {DBI1356288NSF//NSF/ ; }, mesh = {Phylogeny ; *Genome, Bacterial ; *Software ; *Bacteria/genetics/classification ; *Amino Acids/genetics ; *Computational Biology/methods ; }, abstract = {Estimation of whole-genome relatedness and taxonomic identification are two important bioinformatics tasks in describing environmental or clinical microbiomes. The genome-aggregate Average Nucleotide Identity is routinely used to derive the relatedness of closely related (species level) microbial and viral genomes, but it is not appropriate for more divergent genomes. Average Amino-acid Identity (AAI) can be used in the latter cases, but no current AAI implementation can efficiently compare thousands of genomes. Here we present FastAAI, a tool that estimates whole-genome pairwise relatedness using shared tetramers of universal proteins in a matter of microseconds, providing a speedup of up to 5 orders of magnitude when compared with current methods for calculating AAI or alternative whole-genome metrics. Further, FastAAI resolves distantly related genomes related at the phylum level with comparable accuracy to the phylogeny of ribosomal RNA genes, substantially improving on a known limitation of current AAI implementations. Our analysis of the resulting AAI matrices also indicated that bacterial lineages predominantly evolve gradually, rather than showing bursts of diversification, and that AAI thresholds to define classes, orders, and families are generally elusive. Therefore, FastAAI uniquely expands the toolbox for microbiome analysis and allows it to scale to millions of genomes.}, } @article {pmid40287646, year = {2025}, author = {He, L and Zou, Q and Wang, Y}, title = {metaTP: a meta-transcriptome data analysis pipeline with integrated automated workflows.}, journal = {BMC bioinformatics}, volume = {26}, number = {1}, pages = {111}, pmid = {40287646}, issn = {1471-2105}, support = {62102269//National Natural Science Foundation of China/ ; }, mesh = {Workflow ; *Software ; *Gene Expression Profiling/methods ; *Computational Biology/methods ; *Transcriptome ; Microbiota/genetics ; Humans ; }, abstract = {BACKGROUND: The accessibility of sequencing technologies has enabled meta-transcriptomic studies to provide a deeper understanding of microbial ecology at the transcriptional level. Analyzing omics data involves multiple steps that require the use of various bioinformatics tools. With the increasing availability of public microbiome datasets, conducting meta-analyses can reveal new insights into microbiome activity. However, the reproducibility of data is often compromised due to variations in processing methods for sample omics data. Therefore, it is essential to develop efficient analytical workflows that ensure repeatability, reproducibility, and the traceability of results in microbiome research.

RESULTS: We developed metaTP, a pipeline that integrates bioinformatics tools for analyzing meta-transcriptomic data comprehensively. The pipeline includes quality control, non-coding RNA removal, transcript expression quantification, differential gene expression analysis, functional annotation, and co-expression network analysis. To quantify mRNA expression, we rely on reference indexes built using protein-coding sequences, which help overcome the limitations of database analysis. Additionally, metaTP provides a function for calculating the topological properties of gene co-expression networks, offering an intuitive explanation for correlated gene sets in high-dimensional datasets. The use of metaTP is anticipated to support researchers in addressing microbiota-related biological inquiries and improving the accessibility and interpretation of microbiota RNA-Seq data.

CONCLUSIONS: We have created a conda package to integrate the tools into our pipeline, making it a flexible and versatile tool for handling meta-transcriptomic sequencing data. The metaTP pipeline is freely available at: https://github.com/nanbei45/metaTP .}, } @article {pmid40286849, year = {2025}, author = {Bartas, M and Petrovič, M and Brázda, V and Trenz, O and Ďurčanský, A and Štastný, J}, title = {CpX Hunter web tool allows high-throughput identification of CpG, CpA, CpT, and CpC islands: A case study in Drosophila genome.}, journal = {The Journal of biological chemistry}, volume = {}, number = {}, pages = {108537}, doi = {10.1016/j.jbc.2025.108537}, pmid = {40286849}, issn = {1083-351X}, abstract = {With continuous advances in DNA sequencing methods, accessibility to high-quality genomic information for all living organisms is ever increasing. However, to interpret this information effectively and formulate hypotheses, users often require higher level programming skills. Therefore, the generation of web-based tools is becoming increasingly popular. CpG island regions in genomes are often found in gene promoters and are prone to DNA methylation; with their methylation status determining if a gene is expressed. Notably, understanding the biological impact of CpX modifications on genomic regulation is becoming increasingly important as these modifications have been associated with diseases such as cancer and neurodegeneration. However, there is currently no easy-to-use scalable tool to detect and quantify CpX islands in full genomes. We have developed a Java-based web server for CpX island analyses that benefits from the DNA Analyzer Web server environment and overcomes several limitations. For a pilot demonstration study, we selected a well-described model organism Drosophila melanogaster. Subsequent analysis of obtained CpX islands revealed several interesting and previously undescribed phenomena. One of them is the fact, that nearly half of long CpG islands were located on chromosome X, and that long CpA and CpT islands were significantly overrepresented at the subcentromeric regions of autosomes (chr2 and chr3) and also on chromosome Y. Wide genome overlays of predicted CpX islands revealed their co-occurrence with various (epi)genomics features comprising cytosine methylations, accessible chromatin, transposable elements, or binding of transcription factors and other proteins. CpX Hunter is freely available as a web tool at: https://bioinformatics.ibp.cz/#/analyse/cpg.}, } @article {pmid40286830, year = {2025}, author = {Yu, X and Yao, R and Yao, R and Jin, X and Huang, J and Liang, Q and Jin, LN and Sun, J}, title = {Mechanistic understanding of the toxic effects of tri-n-butyl phosphate (TnBP) and tricresyl phosphate (TCP) to Escherichia coli: Evidence from alterations in biomarker expression and perturbations of the metabolic network.}, journal = {Comparative biochemistry and physiology. Toxicology & pharmacology : CBP}, volume = {}, number = {}, pages = {110211}, doi = {10.1016/j.cbpc.2025.110211}, pmid = {40286830}, issn = {1532-0456}, abstract = {Tri-n-butyl phosphate (TnBP) and tricresyl phosphate (TCP), emerging flame retardants and plasticizers, have garnered increasing attention due to their potential risks to ecosystem. A few researches regarding the toxicological mechanisms of TnBP and TCP had been performed, while molecular-level toxic effects of them and metabolic response using microbial models are the lack of relevant investigation. Thus, we investigated the cytotoxicity, oxidative stress response, and metabolic response in E. coli exposed to TnBP and TCP. Exposure to them significantly increased the activities of antioxidant enzymes, indicating activation of the antioxidant defense system. Excessive accumulation of reactive oxygen species (ROS) triggered various biological events, including a reduction in membrane potential (MP), decrease of adenosine triphosphatase (ATPase) activity, and increased malondialdehyde (MDA) content. These findings suggested that oxidative damage compromised membrane proteins function, membrane stability, and intracellular homeostasis. GC-MS and LC-MS-based metabolomics analyses revealed that TnBP and TCP strongly disrupted multiple metabolic pathways, including carbohydrate metabolism, nucleotide metabolism, lipid metabolism, beta-alanine metabolism, pyruvate metabolism and oxidative phosphorylation. These disruptions highlighted the inhibitory effects on molecular functions and metabolic processes. Notably, lipids biomarkers e.g., PC(11:0/16:0), PA(17:1(9Z)/18:2(9Z,12Z)), PE(17:0/14:1(9Z)), and LysoPE(0:0/18:1(11Z)) were significantly altered, verifying that the regulation of lipid-associated metabolite synthesis plays a protective role in maintaining cellular membrane function. In summary, this study enhances our understanding of TnBP and TCP toxicity in E. coli, providing novel insights into their toxicological mechanisms at molecular and network levels. These findings underscore the ecological risks posed by organophosphate flame retardants in aquatic ecosystem.}, } @article {pmid38163964, year = {2025}, author = {Bhardwaj, N and S, S and Tripathi, N and Kumar, S and Lal, UR and G, R and Guru, SK and Jain, SK}, title = {Mahamanalactone A, a new triterpenoid from Dysoxylum malabaricum bark: a case study for rapid identification of new metabolites via LC-HRMS profiling and database mining strategy.}, journal = {Natural product research}, volume = {39}, number = {9}, pages = {2438-2443}, doi = {10.1080/14786419.2023.2298721}, pmid = {38163964}, issn = {1478-6427}, mesh = {Humans ; *Triterpenes/chemistry/isolation & purification/pharmacology ; *Plant Bark/chemistry ; Cell Line, Tumor ; *Antineoplastic Agents, Phytogenic/chemistry/pharmacology/isolation & purification ; Chromatography, Liquid ; Molecular Structure ; Mass Spectrometry ; *Meliaceae/chemistry ; Data Mining ; Plant Extracts/chemistry ; }, abstract = {In this recent investigation, the focus centred on exploring the potential phytoconstituents within the bark of Dysoxylum malabaricum. A profiling strategy employing LC-HRMS (Liquid Chromatography-High Resolution Mass Spectrometry) was implemented for the rapid identification of compounds from the bark extract. The crude extract underwent fractionation, resulting in the isolation of four previously known compounds (1-4) and a novel cycloartane triterpenoid named Mahamanalactone A (5). Compound 5 represents a cycloartane triterpenoid with a modified ring-A, featuring £-caprolactone fusion at positions 4 and 5, distinguishing it from other reported compounds where £-caprolactone is typically fused at positions 3 and 4. Cytotoxicity assessment revealed that the newly identified compound 5 exhibited a moderate cytotoxic profile (IC50 29 to 78 µM) against a panel of cancer cell lines.}, } @article {pmid40284070, year = {2025}, author = {Lu, F and Yi, B and Qin, K and Bu, ZJ}, title = {Long-Term Nitrogen Addition Eliminates the Cooling Effect on Climate in a Temperate Peatland.}, journal = {Plants (Basel, Switzerland)}, volume = {14}, number = {8}, pages = {}, pmid = {40284070}, issn = {2223-7747}, support = {U23A2003//National Natural Science Foundation of China/ ; 42407354//National Natural Science Foundation of China/ ; 42371050//National Natural Science Foundation of China/ ; 20210402032GH//Jilin Provincial Science and Technology Development Pro-ject/ ; 20230203002SF//Jilin Provincial Science and Technology Development Pro-ject/ ; JP230021//Fundamental Research Funds for the Central Universities/ ; }, abstract = {Peatlands play a crucial role in global carbon (C) sequestration, but their response to long-term nitrogen (N) deposition remains uncertain. This study investigates the effects of 12 years of simulated N addition on CO2 and CH4 fluxes in a temperate peatland through in situ monitoring. The results demonstrate that long-term N addition significantly reduces net ecosystem exchange (NEE), shifting the peatland from a C sink to a C source. This transition is primarily driven by a decline in aboveground plant productivity, as Sphagnum mosses were suppressed and even experienced mortality, while graminoid plants thrived under elevated N conditions. Although graminoid cover increased, it did not compensate for the GPP loss caused by Sphagnum decline. Instead, it further increased CH4 emissions. These findings suggest that sustained N input may diminish the C sequestration function of peatlands, significantly weakening their global cooling effect.}, } @article {pmid40278529, year = {2025}, author = {Fabio, RA and Semino, M and Perina, M and Martini, M and Riccio, E and Pili, G and Pani, D and Chessa, M}, title = {Virtual Reality as a Tool for Upper Limb Rehabilitation in Rett Syndrome: Reducing Stereotypies and Improving Motor Skills.}, journal = {Pediatric reports}, volume = {17}, number = {2}, pages = {}, pmid = {40278529}, issn = {2036-749X}, abstract = {BACKGROUND/OBJECTIVES: Rett Syndrome (RTT) is a rare neurodevelopmental disorder that causes the loss of motor, communicative, and cognitive skills. While no cure exists, rehabilitation plays a crucial role in improving quality of life. Virtual Reality (VR) has shown promise in enhancing motor function and reducing stereotypic behaviors in RTT. This study aims to assess the impact of VR training on upper limb motor skills in RTT patients, focusing on reaching and hand-opening tasks, as well as examining its role in motivation and engagement during rehabilitation.

METHODS: Twenty RTT patients (aged 5-33) were randomly assigned to an experimental group (VR training) and a control group (standard rehabilitation). Pre- and post-tests evaluated motor skills and motivation in both VR and real-world contexts. The VR training involved 40 sessions over 8 weeks, focusing on fine motor tasks. Non-parametric statistical methods were used to analyze the data.

RESULTS: Results indicated significant improvements in the experimental group for motor parameters, including reduced stereotypy intensity and frequency, faster response times, and increased correct performance. These improvements were consistent across VR and ecological conditions. Moreover, attention time increased, while the number of aids required decreased, highlighting enhanced engagement and independence. However, motivation levels remained stable throughout the sessions.

CONCLUSIONS: This study demonstrates the potential of VR as a tool for RTT rehabilitation, addressing both motor and engagement challenges. Future research should explore the customization of VR environments to maximize the generalization of skills and sustain motivation over extended training periods.}, } @article {pmid40277515, year = {2025}, author = {Kargarandehkordi, A and Li, S and Lin, K and Phillips, KT and Benzo, RM and Washington, P}, title = {Fusing Wearable Biosensors with Artificial Intelligence for Mental Health Monitoring: A Systematic Review.}, journal = {Biosensors}, volume = {15}, number = {4}, pages = {}, pmid = {40277515}, issn = {2079-6374}, support = {MedRes_2023_00002689//Hawai'i Community Foundation/ ; 2406251//U.S. National Science Foundation/ ; 1U54GM138062-02A1/NH/NIH HHS/United States ; U54 GM138062/GM/NIGMS NIH HHS/United States ; U54GM138062/GM/NIGMS NIH HHS/United States ; }, mesh = {*Wearable Electronic Devices ; *Biosensing Techniques ; Humans ; *Artificial Intelligence ; *Mental Health ; Monitoring, Physiologic ; Heart Rate ; }, abstract = {The development of digital instruments for mental health monitoring using biosensor data from wearable devices can enable remote, longitudinal, and objective quantitative benchmarks. To survey developments and trends in this field, we conducted a systematic review of artificial intelligence (AI) models using data from wearable biosensors to predict mental health conditions and symptoms. Following PRISMA guidelines, we identified 48 studies using a variety of wearable and smartphone biosensors including heart rate, heart rate variability (HRV), electrodermal activity/galvanic skin response (EDA/GSR), and digital proxies for biosignals such as accelerometry, location, audio, and usage metadata. We observed several technical and methodological challenges across studies in this field, including lack of ecological validity, data heterogeneity, small sample sizes, and battery drainage issues. We outline several corresponding opportunities for advancement in the field of AI-driven biosensing for mental health.}, } @article {pmid40276974, year = {2025}, author = {Blin, K and Shaw, S and Vader, L and Szenei, J and Reitz, ZL and Augustijn, HE and Cediel-Becerra, JDD and de Crécy-Lagard, V and Koetsier, RA and Williams, SE and Cruz-Morales, P and Wongwas, S and Segurado Luchsinger, AE and Biermann, F and Korenskaia, A and Zdouc, MM and Meijer, D and Terlouw, BR and van der Hooft, JJJ and Ziemert, N and Helfrich, EJN and Masschelein, J and Corre, C and Chevrette, MG and van Wezel, GP and Medema, MH and Weber, T}, title = {antiSMASH 8.0: extended gene cluster detection capabilities and analyses of chemistry, enzymology, and regulation.}, journal = {Nucleic acids research}, volume = {}, number = {}, pages = {}, doi = {10.1093/nar/gkaf334}, pmid = {40276974}, issn = {1362-4962}, support = {NNF20CC0035580//Novo Nordisk Foundation/ ; //Microbial Secondary Metabolites/ ; DNRF137//Danish National Research Foundation/ ; MSC 101072485//Horizon Europe Programme/ ; 101000392//Horizon 2020/ ; KICH1.LWV04.21.013//NWO/ ; 101055020//ERC/ ; RM1GM145426/NH/NIH HHS/United States ; TTU09.716//German Center for Infection Research/ ; //The Royal Thai Government/ ; 504947087//German Research Foundation/ ; //Hessian Ministry for Science and the Arts/ ; //Translational Biodiversity Genomics/ ; I008520N//FWO/ ; }, abstract = {Microorganisms synthesize small bioactive compounds through their secondary or specialized metabolism. Those compounds play an important role in microbial interactions and soil health, but are also crucial for the development of pharmaceuticals or agrochemicals. Over the past decades, advancements in genome sequencing have enabled the identification of large numbers of biosynthetic gene clusters directly from microbial genomes. Since its inception in 2011, antiSMASH (https://antismash.secondarymetabolites.org/), has become the leading tool for detecting and characterizing these gene clusters in bacteria and fungi. This paper introduces version 8 of antiSMASH, which has increased the number of detectable cluster types from 81 to 101, and has improved analysis support for terpenoids and tailoring enzymes, as well as improvements in the analysis of modular enzymes like polyketide synthases and nonribosomal peptide synthetases. These modifications keep antiSMASH up-to-date with developments in the field and extend its overall predictive capabilities for natural product genome mining.}, } @article {pmid40275196, year = {2025}, author = {Li, Q}, title = {Assessing and adjusting for bias in ecological analysis using multiple sample datasets.}, journal = {BMC medical research methodology}, volume = {25}, number = {1}, pages = {112}, pmid = {40275196}, issn = {1471-2288}, mesh = {Humans ; Bias ; Kenya ; *Ecology/methods ; *Datasets as Topic ; Health Surveys ; Models, Statistical ; Data Interpretation, Statistical ; Computer Simulation ; }, abstract = {BACKGROUND: Ecological analysis utilizes group-level aggregate measures to investigate the complex relationships between individuals or groups and their environment. Despite its extensive applications across various disciplines, this approach remains susceptible to several biases, including ecological fallacy.

METHODS: Our study identified another significant source of bias in ecological analysis when using multiple sample datasets, a common practice in fields such as public health and medical research. We show this bias is proportional to the sampling fraction used during data collection. We propose two adjustment methods to address this bias: one that directly accounts for the sampling fraction and another based on measurement error models. The effectiveness of these adjustments is evaluated through formal mathematical derivations, simulations, and empirical analysis using data from the 2014 Kenya Demographic and Health Survey.

RESULTS: Our findings reveal that the sampling fraction bias can lead to significant underestimation of true relationships when using aggregate measures from multiple sample datasets. Both adjustment methods effectively mitigate this bias, with the measurement-error-adjusted estimator showing particular robustness in real-world applications. The results highlight the importance of accounting for sampling fraction bias in ecological analyses to ensure accurate inference.

CONCLUSION: Beyond the ecological fallacy uncovered by Robinson's seminar work, our research identified another critical bias in ecological analysis that is likely just as prevalent and consequential. The proposed adjustment methods provide potential tools for researchers to adjust for this bias, thereby improving the validity of ecological inferences. This study underscores the need for caution when pooling aggregate measures from multiple sample datasets and offers potential solutions to enhance the reliability of ecological analyses in various research domains.

CLINICAL TRIAL NUMBER: Not applicable.}, } @article {pmid40275133, year = {2025}, author = {Antala, M and Kovar, M and Sporinová, L and Filacek, A and Juszczak, R and Zivcak, M and Shomali, A and Prasad, R and Brestic, M and Rastogi, A}, title = {Correction: High-throughput phenotyping of buckwheat (Fagopyrum esculentum Moench.) genotypes under water stress: exploring drought resistance for sustainable agriculture.}, journal = {BMC plant biology}, volume = {25}, number = {1}, pages = {517}, doi = {10.1186/s12870-025-06560-4}, pmid = {40275133}, issn = {1471-2229}, } @article {pmid40273274, year = {2025}, author = {Chen, N}, title = {The impact of the rural digital economy on China's new-type urbanization.}, journal = {PloS one}, volume = {20}, number = {4}, pages = {e0321663}, doi = {10.1371/journal.pone.0321663}, pmid = {40273274}, issn = {1932-6203}, mesh = {China ; *Urbanization/trends ; *Rural Population ; Humans ; *Economic Development/trends ; Agriculture ; }, abstract = {The Chinese government is vigorously implementing the rural revitalization strategy and accelerating the process of new-type urbanization. The rapid development of the rural digital economy has emerged as a new driving force for new-type urbanization. This study aims to explore how the rural digital economy impacts China's new-type urbanization from direct, heterogeneous, and indirect perspectives. Using the provincial-level panel data in China from 2014 to 2022, a mixed-methods approach is employed for the empirical research. The CRITIC and Entropy TOPSIS are used to assess the comprehensive development level and temporal characteristics of the rural digital economy and new-type urbanization. Moreover, a global-local auto-correlation analysis is carried out to depict the spatial distribution of the two variables. Subsequently, a two-way fixed effects model is constructed to verify the direct impact of the rural digital economy on new-type urbanization, as well as its structural and spatial heterogeneity characteristics. Finally, an mediating effect model is established to explore the impact paths through which the rural digital economy impacts new-type urbanization. The results show that the rural digital economy has significantly promoted new-type urbanization. Specifically, rural digital infrastructure, digital transformation of agriculture, agricultural production service informatization have a significant positive effect, while the role of rural life digitization is not significant. The rural digital economy has more significant positive impact on population agglomeration and economic growth, followed by social public service, but has no significant impact on ecological environmental protection and urban-rural coordination. Additionally, the qualitative analysis identifies geographical region, poverty, demographic structure and social equality as notable influencing factors in this impact. Further mechanism analysis result indicates that the rural digital economy impacts new-type urbanization through rural human capital improvement, agricultural economic growth and rural industrial structure upgrading. This research contributes to the existing body of knowledge by providing the practical path of rural development to promote new-type urbanization in the context of the digital economy, also clarifies the weak points and key links in this process. It also highlights the need for further research into the institutional factors that influence this relationship to enhances the policy applicability.}, } @article {pmid39475336, year = {2025}, author = {Menssen, M and Dammann, M and Fneish, F and Ellenberger, D and Schaarschmidt, F}, title = {Prediction Intervals for Overdispersed Poisson Data and Their Application in Medical and Pre-Clinical Quality Control.}, journal = {Pharmaceutical statistics}, volume = {24}, number = {2}, pages = {e2447}, pmid = {39475336}, issn = {1539-1612}, mesh = {Humans ; *Quality Control ; Poisson Distribution ; Monte Carlo Method ; Algorithms ; Computer Simulation ; Models, Statistical ; Multiple Sclerosis ; Data Interpretation, Statistical ; }, abstract = {In pre-clinical and medical quality control, it is of interest to assess the stability of the process under monitoring or to validate a current observation using historical control data. Classically, this is done by the application of historical control limits (HCL) graphically displayed in control charts. In many applications, HCL are applied to count data, for example, the number of revertant colonies (Ames assay) or the number of relapses per multiple sclerosis patient. Count data may be overdispersed, can be heavily right-skewed and clusters may differ in cluster size or other baseline quantities (e.g., number of petri dishes per control group or different length of monitoring times per patient). Based on the quasi-Poisson assumption or the negative-binomial distribution, we propose prediction intervals for overdispersed count data to be used as HCL. Variable baseline quantities are accounted for by offsets. Furthermore, we provide a bootstrap calibration algorithm that accounts for the skewed distribution and achieves equal tail probabilities. Comprehensive Monte-Carlo simulations assessing the coverage probabilities of eight different methods for HCL calculation reveal, that the bootstrap calibrated prediction intervals control the type-1-error best. Heuristics traditionally used in control charts (e.g., the limits in Shewhart c- or u-charts or the mean ± 2 SD) fail to control a pre-specified coverage probability. The application of HCL is demonstrated based on data from the Ames assay and for numbers of relapses of multiple sclerosis patients. The proposed prediction intervals and the algorithm for bootstrap calibration are publicly available via the R package predint.}, } @article {pmid40273037, year = {2025}, author = {Wu, KC and Belza, B and Berry, D and Lewis, F and Zaslavsky, O and Hartzler, A}, title = {UTI risk factors in older people living with dementia: A conceptual framework and a scoping review.}, journal = {Dementia (London, England)}, volume = {}, number = {}, pages = {14713012251326129}, doi = {10.1177/14713012251326129}, pmid = {40273037}, issn = {1741-2684}, abstract = {Background and Aims: UTIs greatly impact hospitalization rates for people living with dementia. This study aims to craft a framework through a scoping review, assessing UTI symptoms, risk factors, and non-pharmacological prevention strategies in older people living with dementia. Research Design and Methods: Our scoping review followed PRISMA-ScR guidelines, exploring databases (PubMed, CINAHL, Embase, Web of Science) for topics like geriatric care, urinary tract issues published from January 1977 to April 2023. Two reviewers assessed data, organizing it using the Social-Ecological Model to construct the UTI Prevention (UTIP) framework. Results: The literature review scrutinized 1394 articles, selecting 14 through rigorous evaluation. It detailed demographic characteristics, synthesized UTI symptoms, 14 risk factors, and seven outcomes for older people living with dementia. Moreover, it outlined ten preventive domains and proposed a comprehensive UTI Prevention (UTIP) framework spanning individual, relational, community, and societal levels. This framework aims to prevent UTIs among older people living with dementia, integrating risk factors and outcomes to bolster effective prevention strategies for this population. Discussion and Implications: The review introduced a UTIP framework, and non-pharmacological preventive measures tailored for elderly people living with dementia. However, some factors in the framework require further validation to strengthen their associations with outcomes. Preventive measures from studies had limitations like small sample sizes, bias risks, and inconsistent findings. Future research should prioritize robust randomized trials with strong statistical power, strict criteria, and consistent individual-level interventions to boost outcome reliability and validity. Such efforts will enhance the credibility of findings and contribute significantly to refining preventive strategies for this vulnerable population.}, } @article {pmid40266389, year = {2025}, author = {Xinyi, B and Qingbiao, G and Songbo, W and Jin, L and Jiren, X}, title = {Identifying the spatio-temporal evolution and driving mechanisms of ecosystem service value in high groundwater table coal mining areas.}, journal = {Environmental monitoring and assessment}, volume = {197}, number = {5}, pages = {581}, pmid = {40266389}, issn = {1573-2959}, support = {No. 2024cx2152//the Graduate Innovation Fund Project of Anhui University of Science and Technology/ ; 2024cxcysj094//the Provincial graduate student innovation and entrepreneurship practice project/ ; NO. KSXTJC202401//Engineering Research Center of Mining Area Environmental And Disaster Cooperative Monitoring (Anhui University of Science and Technology)/ ; No. 52274164//the Natural Science Foundation of China/ ; No. 2308085Y31//the Anhui Provincial Natural Science Foundation/ ; No. 2022QNRC001//the Young Elite Scientists Sponsorship Program by CAST/ ; No. GJNY-21-41-15//the Open Fund of State Key Laboratory of Water Resource Protection and Utilization in Coal Mining/ ; }, mesh = {*Coal Mining ; *Environmental Monitoring ; *Ecosystem ; *Groundwater/chemistry ; *Conservation of Natural Resources/methods ; Spatio-Temporal Analysis ; China ; }, abstract = {In coal mining areas with high groundwater tables, surface subsidence has emerged as a non-negligible phenomenon, stemming from long-term coal mining activities. Employing the Huainan mining area as an exemplar, this research meticulously examines the temporal and spatial attributes of ecosystem service value (ESV) across distinct timeframes of 2005, 2010, 2015, and 2020, utilizing the refined equivalent factor approach in conjunction with spatial analysis methodologies. To delve into the primary forces driving the observed changes, the optimal parameter-based geographical detector (OPGD) model is subsequently utilized as a tool for analysis. Lastly, the study delves into the trade-offs and synergies existing between four exemplary services at the grid level, utilizing Spearman correlation coefficient and bivariate spatial autocorrelation. The findings suggest that: (1) From 2005 to 2020, the total ESV in the Huainan mining area demonstrated a general increasing tendency, primarily attributed to the increase in waters. (2) Throughout the research period, the ecosystem service functions in the coal mining area all exhibited relatively significant hydrological regulation and waste treatment capabilities. (3) Vegetation factors significantly influenced the ESV in the Huainan mining area. (4) The Huainan mining area predominantly exhibited synergistic effects among ecosystem services, with the most pronounced synergy occurring between cultural services (CS) and regulating services (RS). All services were transitioning towards an enhanced trend of synergistic effects. (5) Significant spatial variations are present in the observed trade-offs and synergies among diverse ecosystem services. The aforementioned research findings will provide scientific theoretical guidance for rational mining activities and ecological environmental governance in coal mining areas.}, } @article {pmid40263346, year = {2025}, author = {Yamamoto, PK and Takasuka, K and Mori, M and Masuda, T and Kono, N}, title = {Non-invasive molecular species identification using spider silk proteomics.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {13844}, pmid = {40263346}, issn = {2045-2322}, support = {23K21203//Japan Society for the Promotion of Science/ ; }, mesh = {Animals ; *Spiders/genetics/classification/metabolism ; *Proteomics/methods ; *Silk/chemistry/genetics/metabolism ; Species Specificity ; Amino Acid Sequence ; Computational Biology/methods ; DNA Barcoding, Taxonomic/methods ; }, abstract = {Accurate species identification is essential in biology, ecology, medicine, and agriculture, yet traditional methods relying on morphological characteristics often fail due to phenotypic plasticity and cryptic species. These limitations are particularly pronounced in small organisms with minimal distinguishing features. DNA barcoding has become a popular alternative; however, it requires invasive tissue sampling, making it unsuitable for delicate or rare organisms like insects and spiders. To address this challenge, we propose a non-invasive molecular method using proteomic analysis focused on species-specific protein sequences in spider silk, offering a viable solution for species identification without harming specimens. We developed a universal silk-dissolving method, followed by sequence similarity analysis to classify species into those identifiable at the species level and those distinguishable only to a group of closely related species. A bioinformatics pipeline was established to analyze peptide sequences, achieving 96% accuracy across 15 spider species, even in the presence of contaminants. This technique complements DNA barcoding and can be extended to other organisms producing biological materials. It holds promise in pest management, medical diagnostics, and improving public health by enabling accurate species identification without invasive procedures.}, } @article {pmid40259303, year = {2025}, author = {Yano, KM and Zucchi, P and Novais, MAP}, title = {Psychiatric hospitalizations in the Unified Health System: an observational study on hospitalization rates from 2012 to 2023.}, journal = {BMC public health}, volume = {25}, number = {1}, pages = {1463}, pmid = {40259303}, issn = {1471-2458}, support = {2022/10716-2//São Paulo State Research Foundation (FAPESP)/ ; }, mesh = {Humans ; *Hospitalization/trends/statistics & numerical data ; Brazil/epidemiology ; Female ; Male ; Adult ; Middle Aged ; Adolescent ; *Mental Disorders/therapy/epidemiology ; Aged ; Young Adult ; Aged, 80 and over ; Child ; Infant ; Child, Preschool ; *National Health Programs/statistics & numerical data ; Infant, Newborn ; }, abstract = {BACKGROUND: Psychiatric care in Brazil is based on the National Mental Health Policy and is aligned with the guidelines of the Brazilian Unified Health System. It is based on the preeminence of care in the extra-hospital context over the hospital context. Hospital admissions should occur solely when extra-hospital resources prove insufficient for the proper management of the mental health condition.

METHOD: It refers to a time series investigation of a descriptive, ecological, and observational nature. We used publicly available hospital admissions data from the Brazilian Unified Health System's Department of Informatics. The study looked at information on diseases in ICD-10 group V that affected both men and women aged 0 to 80 or older, from 2012 to 2023. The information was analyzed using the statistical software SPSS 20.0, as well as Jointpoint, through permutation tests, with the aim of evaluating the temporal trend of hospitalization and mortality rates. The joinpoint regression model used a log-linear method to set up a series of connected lines on a logarithmic scale and the Monte Carlo permutation method to figure out the direction or statistical significance. A significance level of 5% was established for the execution of all statistical tests.

RESULTS: Overall, a trend of reduction in psychiatric hospitalization rates was observed. However, these trends exhibited fluctuations when analyzed in isolation with respect to the type of disorder, gender, and age group. In contrast to the general trend, the number of hospitalizations for affective disorders and disorders linked to stress and somatization went up. This was especially true between 2021 and 2023, when the number of hospitalizations for other disorders went down more significantly. The predominance of hospitalizations in the male gender was significant. However, the trends of decrease were less pronounced in the male group, especially regarding hospitalizations associated with alcohol and other substance use, which draws attention to the hospitalization rates of the female sex. As it relates to dementias, the national picture shows that hospitalizations are going down, and most of the patients are women and older adults or people who are very old. However, an analysis of the state scenario showed that hospitalizations went up for adults, more than for the elderly combined, with more men than women.

CONCLUSION: the results achieved in this research confirm the findings, both nationally and internationally. Studies have shown that investments made through the National Mental Health Policy and the effects of Covid-19 led to a drop in the number of people admitted to psychiatric hospitals. This was because of the restructuring of the care model, which meant that hospitalizations had to be prioritized to meet the needs of Covid-19, which hurt people with mental disorders.}, } @article {pmid40208899, year = {2025}, author = {Minier, L and Rouch, J and Sabbagh, B and Bertucci, F and Parmentier, E and Lecchini, D and Sèbe, F and Mathevon, N and Emonet, R}, title = {Visualization and quantification of coral reef soundscapes using CoralSoundExplorer software.}, journal = {PLoS computational biology}, volume = {21}, number = {4}, pages = {e1012050}, doi = {10.1371/journal.pcbi.1012050}, pmid = {40208899}, issn = {1553-7358}, mesh = {*Coral Reefs ; *Software ; Animals ; Acoustics ; Anthozoa/physiology ; Sound ; Machine Learning ; Computational Biology ; Polynesia ; Ecosystem ; *Environmental Monitoring/methods ; }, abstract = {Despite hosting some of the highest concentrations of biodiversity and providing invaluable goods and services in the oceans, coral reefs are under threat from global change and other local human impacts. Changes in living ecosystems often induce changes in their acoustic characteristics, but despite recent efforts in passive acoustic monitoring of coral reefs, rapid measurement and identification of changes in their soundscapes remains a challenge. Here we present the new open-source software CoralSoundExplorer, which is designed to study and monitor coral reef soundscapes. CoralSoundExplorer uses machine learning approaches and is designed to eliminate the need to extract conventional acoustic indices. To demonstrate CoralSoundExplorer's functionalities, we use and analyze a set of recordings from three coral reef sites, each with different purposes (undisturbed site, tourist site and boat site), located on the island of Bora-Bora in French Polynesia. We explain the CoralSoundExplorer analysis workflow, from raw sounds to ecological results, detailing and justifying each processing step. We detail the software settings, the graphical representations used for visual exploration of soundscapes and their temporal dynamics, along with the analysis methods and metrics proposed. We demonstrate that CoralSoundExplorer is a powerful tool for identifying disturbances affecting coral reef soundscapes, combining visualizations of the spatio-temporal distribution of sound recordings with new quantification methods to characterize soundscapes at different temporal scales.}, } @article {pmid40173380, year = {2025}, author = {Zagorščak, M and Abdelhakim, L and Rodriguez-Granados, NY and Široká, J and Ghatak, A and Bleker, C and Blejec, A and Zrimec, J and Novák, O and Pěnčík, A and Baebler, Š and Perez Borroto, L and Schuy, C and Županič, A and Afjehi-Sadat, L and Wurzinger, B and Weckwerth, W and Pompe Novak, M and Knight, MR and Strnad, M and Bachem, C and Chaturvedi, P and Sonnewald, S and Sasidharan, R and Panzarová, K and Gruden, K and Teige, M}, title = {Integration of multi-omics data and deep phenotyping provides insights into responses to single and combined abiotic stress in potato.}, journal = {Plant physiology}, volume = {197}, number = {4}, pages = {}, doi = {10.1093/plphys/kiaf126}, pmid = {40173380}, issn = {1532-2548}, support = {//H2020-SFS-2019-2/ ; P4-0165//Slovenian Research Agency/ ; //Ministry of Education, Youth and Sports of the Czech Republic/ ; CZ.02.1.01/0.0/0.0/16_026/0008446//European Regional Development Fund-Project/ ; }, mesh = {*Solanum tuberosum/physiology/genetics/metabolism ; *Stress, Physiological/genetics ; Phenotype ; Droughts ; Proteomics ; Metabolomics ; Gene Expression Regulation, Plant ; Transcriptome ; Plant Leaves/physiology ; Plant Tubers ; Multiomics ; }, abstract = {Potato (Solanum tuberosum) is highly water and space efficient but susceptible to abiotic stresses such as heat, drought, and flooding, which are severely exacerbated by climate change. Our understanding of crop acclimation to abiotic stress, however, remains limited. Here, we present a comprehensive molecular and physiological high-throughput profiling of potato (Solanum tuberosum, cv. Désirée) under heat, drought, and waterlogging applied as single stresses or in combinations designed to mimic realistic future scenarios. Stress responses were monitored via daily phenotyping and multi-omics analyses of leaf samples comprising proteomics, targeted transcriptomics, metabolomics, and hormonomics at several timepoints during and after stress treatments. Additionally, critical metabolites of tuber samples were analyzed at the end of the stress period. We performed integrative multi-omics data analysis using a bioinformatic pipeline that we established based on machine learning and knowledge networks. Waterlogging produced the most immediate and dramatic effects on potato plants, interestingly activating ABA responses similar to drought stress. In addition, we observed distinct stress signatures at multiple molecular levels in response to heat or drought and to a combination of both. In response to all treatments, we found a downregulation of photosynthesis at different molecular levels, an accumulation of minor amino acids, and diverse stress-induced hormones. Our integrative multi-omics analysis provides global insights into plant stress responses, facilitating improved breeding strategies toward climate-adapted potato varieties.}, } @article {pmid40253432, year = {2025}, author = {Kelliher, JM and Aljumaah, M and Bordenstein, SR and Brister, JR and Chain, PSG and Dundore-Arias, JP and Emerson, JB and Fernandes, VMC and Flores, R and Gonzalez, A and Hansen, ZA and Hatcher, EL and Jackson, SA and Kellogg, CA and Madupu, R and Miller, CML and Mirzayi, C and Moustafa, AM and Mungall, C and Oliver, A and Pariente, N and Pett-Ridge, J and Record, S and Reji, L and Reysenbach, AL and Rich, VI and Richardson, L and Schriml, LM and Shabman, RS and Sierra, MA and Sullivan, MB and Sundaramurthy, P and Thibault, KM and Thompson, LR and Tighe, S and Vereen, E and Eloe-Fadrosh, EA}, title = {Microbiome data management in action workshop: Atlanta, GA, USA, June 12-13, 2024.}, journal = {Environmental microbiome}, volume = {20}, number = {1}, pages = {40}, pmid = {40253432}, issn = {2524-6372}, support = {2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; }, abstract = {Microbiome research is revolutionizing human and environmental health, but the value and reuse of microbiome data are significantly hampered by the limited development and adoption of data standards. While several ongoing efforts are aimed at improving microbiome data management, significant gaps still remain in terms of defining and promoting adoption of consensus standards for these datasets. The Strengthening the Organization and Reporting of Microbiome Studies (STORMS) guidelines for human microbiome research have been endorsed and successfully utilized by many research organizations, publishers, and funding agencies, and have been recognized as a consensus community standard. No equivalent effort has occurred for environmental, synthetic, and non-human host-associated microbiomes. To address this growing need within the microbiome research community, we convened the Microbiome Data Management in Action Workshop (June 12-13, 2024, in Atlanta, GA, USA), to bring together key decision makers in microbiome science including researchers, publishers, funders, and data repositories. The 50 attendees, representing the diverse and interdisciplinary nature of microbiome research, discussed recent progress and challenges, and brainstormed actionable recommendations and paths forward for coordinated environmental microbiome data management and the modifications necessary for the STORMS guidelines to be applied to environmental, non-human host, and synthetic microbiomes. The outcomes of this workshop will form the basis of a formalized data management roadmap to be implemented across the field. These best practices will drive scientific innovation now and in years to come as these data continue to be used not only in targeted reanalyses but in large-scale models and machine learning efforts.}, } @article {pmid40249863, year = {2025}, author = {Wu, Q and Cheng, S and Zhang, W and Zhao, J and Zhang, L and Lv, M and Ma, J and Ding, J and Wang, S and Zheng, X and Gao, J and Liu, R and Yin, Y and Shi, J and Qu, G and Jiang, G}, title = {Heterogeneous Single-Cell Distribution of Trace-Level Metal Mixtures in Tetrahymena thermophila Using Mass Cytometry.}, journal = {Environmental science & technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.4c12818}, pmid = {40249863}, issn = {1520-5851}, abstract = {The uptake of heavy metals by unicellular organisms can lead to the bioaccumulation of these metals in higher organisms, detrimentally affecting organismal health and ultimately impacts the ecosystems. By studying the uptake and accumulation of heavy metals in unicellular organisms, we gain insights into potential risks associated with low-dose heavy metal exposure in aquatic environments. Thus, to investigate the accumulation characteristics of Mo, Ag, Cd, Sn, Sb, Hg, Tl, and Pb mixtures in single Tetrahymena thermophila cells, we developed a label-free approach for the simultaneous absolute quantification of multiple metals in a single cell using mass cytometry. Our results demonstrated the dynamic changes in metal concentrations in T. thermophila, and the competition between metals in uptake and excretory pathways resulted in heterogeneous accumulation and bioconcentration of these metals. Additionally, our findings revealed the limited capacity of T. thermophila to excrete Cd and Hg, suggesting a higher risk for T. thermophila cells when exposed to Cd and Hg over an extended period. Therefore, the current study provides valuable data for a more comprehensive understanding of the impact of low-dose heavy metals on aquatic ecosystems.}, } @article {pmid40188731, year = {2025}, author = {Li, Y and Huang, S and Jiang, S and Yang, L and Huang, J and Yang, Q and Jiang, Z and Shi, J and Ma, Z and Li, E and Zhou, F}, title = {Multi-omics insights into antioxidant and immune responses in Penaeus monodon under ammonia-N, low salinity, and combined stress.}, journal = {Ecotoxicology and environmental safety}, volume = {295}, number = {}, pages = {118156}, doi = {10.1016/j.ecoenv.2025.118156}, pmid = {40188731}, issn = {1090-2414}, mesh = {Animals ; *Penaeidae/immunology/physiology/drug effects ; *Ammonia/toxicity ; Salinity ; *Antioxidants/metabolism ; *Water Pollutants, Chemical/toxicity ; Oxidative Stress ; Gastrointestinal Microbiome/drug effects ; Metabolomics ; Stress, Physiological ; Transcriptome ; Nitrogen/toxicity ; Multiomics ; }, abstract = {Ammonia nitrogen and salinity are critical environmental factors that significantly impact marine organisms and present substantial threats to Penaeus monodon species within aquaculture systems. This study utilized a comprehensive multi-omics approach, encompassing transcriptomics, metabolomics, and gut microbiome analysis, to systematically examine the biological responses of shrimp subjected to low salinity, ammonia nitrogen stress, and their combined conditions. Metabolomic analysis demonstrated that exposure to ammonia nitrogen stress markedly influenced the concentrations of antioxidant-related metabolites, such as glutathione, suggesting that shrimp mitigate oxidative stress by augmenting their antioxidant capacity. The transcriptomic analysis revealed an upregulation of genes linked to energy metabolism and immune responses and antioxidant enzymes. Concurrently, gut microbiome analysis demonstrated that ammonia nitrogen stress resulted in a marked increase in Vibrio populations and a significant decrease in Photobacterium, indicating that alterations in microbial community structure are intricately associated with the shrimp stress response. A comprehensive analysis further indicated that the combined stressors of ammonia nitrogen and salinity exert a synergistic effect on the immune function and physiological homeostasis of shrimp by modulating antioxidant metabolic pathways and gut microbial communities. These findings provide critical systematic data for elucidating the mechanisms through which ammonia nitrogen and salinity influence marine ecosystems, offering substantial implications for environmental protection and ecological management.}, } @article {pmid40248649, year = {2025}, author = {Boyes, D and Januszczak, I and , and , and , and , and , and , and , and , and Mitchell, R}, title = {The genome sequence of the Warted Knot-Horn moth, Acrobasis repandana Fabricius, 1798.}, journal = {Wellcome open research}, volume = {10}, number = {}, pages = {50}, pmid = {40248649}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual female specimen of Acrobasis repandana (Warted Knot-Horn moth; Arthropoda; Insecta; Lepidoptera; Pyralidae). The genome sequence has a total length of 620.40 megabases. Most of the assembly (99.78%) is scaffolded into 32 chromosomal pseudomolecules, including the Z and W sex chromosomes. The mitochondrial genome has also been assembled and is 15.21 kilobases in length. Gene annotation of this assembly on Ensembl identified 11,522 protein-coding genes.}, } @article {pmid40247661, year = {2025}, author = {Abraham, AJ and Duvall, ES and Doughty, CE and Riond, B and Ortmann, S and Terranova, M and le Roux, E and Clauss, M}, title = {Sodium Retention in Large Herbivores: Physiological Insights and Zoogeochemical Consequences.}, journal = {Journal of experimental zoology. Part A, Ecological and integrative physiology}, volume = {}, number = {}, pages = {}, doi = {10.1002/jez.2924}, pmid = {40247661}, issn = {2471-5646}, support = {//A.J.A. acknowledges Horizon Europe Marie Skłodowska-Curie Actions Grant Agreement No. 101062339./ ; }, abstract = {The assimilation, retention, and release of nutrients by animals fundamentally shapes their physiology and contributions to ecological processes (e.g., zoogeochemistry). Yet, information on the transit of nutrients through the bodies of large mammals remains scarce. Here, we examined how sodium (Na), a key element for animal health and ecosystem functioning, travels differently through fecal and urinary systems of cows (Bos taurus) and horses (Equus ferus caballus). We provided a large dose of Na and compared its timing of release in feces and urine to that of nonabsorbable markers. Na excretion by urine occurred approximately twice as fast as excretion by feces, yet both were shorter than indigestible particle markers. These differences correspond to rapid absorption of Na in the upper gastrointestinal tract and transport by blood to the kidneys (urine Na excretion) or resecretion of Na into the lower intestinal tract (fecal Na excretion). Interestingly, for cows, we found a second peak of Na excretion in urine and feces > 96 h after dosage. This result may indicate that surplus Na can be rapidly absorbed and stored in specific body cells (e.g., skin), from which it is later released. Using a propagule dispersal model, we found that the distance of cattle- and horse-driven nutrient dispersal by urine was 31% and 36% less than the fecal pathway and 60% and 41% less than the particle marker pathway, which is commonly used to estimate nutrient dispersal. Future physiological and zoogeochemical studies should resolve different pathways of nutrient retention and release from large mammals.}, } @article {pmid40247093, year = {2025}, author = {Yang, J and Chen, YN and Fang, CY and Li, Y and Ke, HQ and Guo, RQ and Xiang, P and Xiao, YL and Zhang, LW and Liu, H}, title = {Investigating immune cell infiltration and gene expression features in pterygium pathogenesis.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {13352}, pmid = {40247093}, issn = {2045-2322}, support = {ZKF2024042//National clinical key specialty ophthalmology open foundation/ ; ZKF2024041//National clinical key specialty ophthalmology open foundation/ ; 202208535051//China Scholarship Council/ ; 81860171//National Natural Science Foundation of China/ ; 82460201//National Natural Science Foundation of China/ ; 202205AC160016//Yunnan Young and middle-aged Academic and technical leader Project/ ; L2019029//Yunnan Provincial Health Committee Training program for leading medical talents/ ; YDYXJJ2024-0003//Yunnan University Medical Research Foundation/ ; }, mesh = {Humans ; *Pterygium/genetics/immunology/pathology ; Gene Expression Profiling ; Computational Biology/methods ; Conjunctiva/pathology/metabolism/immunology ; Transcriptome ; *Gene Expression Regulation ; Biomarkers/metabolism ; }, abstract = {Pterygium is a prevalent ocular disease characterized by abnormal conjunctival tissue proliferation, significantly impacting patients' quality of life. However, the underlying molecular mechanisms driving pterygium pathogenesis remain inadequately understood. This study aimed to investigate gene expression changes following pterygium excision and their association with immune cell infiltration. Clinical samples of pterygium and adjacent relaxed conjunctival tissue were collected for transcriptomic analysis using RNA sequencing combined with bioinformatics approaches. Machine learning algorithms, including LASSO, SVM-RFE, and Random Forest, were employed to identify potential diagnostic biomarkers. GO, KEGG, GSEA, and GSVA were utilized for enrichment analysis. Single-sample GSEA was employed to analyze immune infiltration. The GSE2513 and GSE51995 datasets from the GEO database, along with clinical samples, were selected for validation analysis. Differentially expressed genes (DEGs) were identified from the PRJNA1147595 and GSE2513 datasets, revealing 2437 DEGs and 172 differentially regulated genes (DRGs), respectively. There were 52 co-DEGs shared by both datasets, and four candidate biomarkers (FN1, SPRR1B, SERPINB13, EGR2) with potential diagnostic value were identified through machine learning algorithms. Single-sample GSEA demonstrated increased Th2 cell infiltration and decreased CD8 + T cell presence in pterygium tissues, suggesting a crucial role of the immune microenvironment in pterygium pathogenesis. Analysis of the GSE51995 dataset and qPCR results revealed significantly higher expression levels of FN1 and SPRR1B in pterygium tissues compared to conjunctival tissues, but SERPINB13 and EGR2 expression levels were not statistically significant. Furthermore, we identified four candidate drugs targeting the two feature genes FN1 and SPRR1B. This study provides valuable insights into the molecular characteristics and immune microenvironment of pterygium. The identification of potential biomarkers FN1 and SPRR1B highlights their significance in pterygium pathogenesis and lays a foundation for further exploration aimed at integrating these findings into clinical practice.}, } @article {pmid40163742, year = {2025}, author = {Ghassemi Nedjad, C and Bolteau, M and Bourneuf, L and Paulevé, L and Frioux, C}, title = {Seed2LP: seed inference in metabolic networks for reverse ecology applications.}, journal = {Bioinformatics (Oxford, England)}, volume = {41}, number = {4}, pages = {}, doi = {10.1093/bioinformatics/btaf140}, pmid = {40163742}, issn = {1367-4811}, support = {//French National Research Agency/ ; }, mesh = {*Metabolic Networks and Pathways ; *Software ; *Computational Biology/methods ; Models, Biological ; Algorithms ; }, abstract = {MOTIVATION: A challenging problem in microbiology is to determine nutritional requirements of microorganisms and culture them, especially for the microbial dark matter detected solely with culture-independent methods. The latter foster an increasing amount of genomic sequences that can be explored with reverse ecology approaches to raise hypotheses on the corresponding populations. Building upon genome-scale metabolic networks (GSMNs) obtained from genome annotations, metabolic models predict contextualized phenotypes using nutrient information.

RESULTS: We developed the tool Seed2LP, addressing the inverse problem of predicting source nutrients, or seeds, from a GSMN and a metabolic objective. The originality of Seed2LP is its hybrid model, combining a scalable and discrete Boolean approximation of metabolic activity, with the numerically accurate flux balance analysis (FBA). Seed inference is highly customizable, with multiple search and solving modes, exploring the search space of external and internal metabolites combinations. Application to a benchmark of 107 curated GSMNs highlights the usefulness of a logic modelling method over a graph-based approach to predict seeds, and the relevance of hybrid solving to satisfy FBA constraints. Focusing on the dependency between metabolism and environment, Seed2LP is a computational support contributing to address the multifactorial challenge of culturing possibly uncultured microorganisms.

Seed2LP is available on https://github.com/bioasp/seed2lp.}, } @article {pmid40246854, year = {2025}, author = {He, B and Zhang, H and Qin, T and Shi, B and Wang, Q and Dong, W}, title = {A simultaneous EEG and eye-tracking dataset for remote sensing object detection.}, journal = {Scientific data}, volume = {12}, number = {1}, pages = {651}, pmid = {40246854}, issn = {2052-4463}, support = {42230103//National Science Foundation of China | Key Programme/ ; }, mesh = {*Electroencephalography ; Humans ; *Eye-Tracking Technology ; *Remote Sensing Technology ; Artificial Intelligence ; }, abstract = {We introduce the EEGET-RSOD, a simultaneous electroencephalography (EEG) and eye-tracking dataset for remote sensing object detection. This dataset contains EEG and eye-tracking data when 38 remote sensing experts located specific objects in 1,000 remote sensing images within a limited time frame. This task reflects the typical cognitive processes associated with human visual search and object identification in remote sensing imagery. To our knowledge, EEGET-RSOD is the first publicly available dataset to offer synchronized eye-tracking and EEG data for remote sensing images. This dataset will not only advance the study of human visual cognition in real-world environment, but also bridge the gap between human cognition and artificial intelligence, enhancing the interpretability and reliability of AI models in geospatial applications.}, } @article {pmid40245396, year = {2025}, author = {Melia, R and Musacchio Schafer, K and Rogers, ML and Wilson-Lemoine, E and Joiner, TE}, title = {The Application of AI to Ecological Momentary Assessment Data in Suicide Research: Systematic Review.}, journal = {Journal of medical Internet research}, volume = {27}, number = {}, pages = {e63192}, doi = {10.2196/63192}, pmid = {40245396}, issn = {1438-8871}, mesh = {Humans ; *Ecological Momentary Assessment ; *Artificial Intelligence ; *Suicide ; *Suicidal Ideation ; }, abstract = {BACKGROUND: Ecological momentary assessment (EMA) captures dynamic processes suitable to the study of suicidal ideation and behaviors. Artificial intelligence (AI) has increasingly been applied to EMA data in the study of suicidal processes.

OBJECTIVE: This review aims to (1) synthesize empirical research applying AI strategies to EMA data in the study of suicidal ideation and behaviors; (2) identify methodologies and data collection procedures used, suicide outcomes studied, AI applied, and results reported; and (3) develop a standardized reporting framework for researchers applying AI to EMA data in the future.

METHODS: PsycINFO, PubMed, Scopus, and Embase were searched for published articles applying AI to EMA data in the investigation of suicide outcomes. The PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) guidelines were used to identify studies while minimizing bias. Quality appraisal was performed using CREMAS (adapted STROBE [Strengthening the Reporting of Observational Studies in Epidemiology] Checklist for Reporting Ecological Momentary Assessment Studies).

RESULTS: In total, 1201 records were identified across databases. After a full-text review, 12 (1%) articles, comprising 4398 participants, were included. In the application of AI to EMA data to predict suicidal ideation, studies reported mean area under the curve (0.74-0.86), sensitivity (0.64-0.81), specificity (0.73-0.86), and positive predictive values (0.72-0.77). Studies met between 4 and 13 of the 16 recommended CREMAS reporting standards, with an average of 7 items met across studies. Studies performed poorly in reporting EMA training procedures and treatment of missing data.

CONCLUSIONS: Findings indicate the promise of AI applied to self-report EMA in the prediction of near-term suicidal ideation. The application of AI to EMA data within suicide research is a burgeoning area hampered by variations in data collection and reporting procedures. The development of an adapted reporting framework by the research team aims to address this.

TRIAL REGISTRATION: Open Science Framework (OSF); https://doi.org/10.17605/OSF.IO/NZWUJ and PROSPERO CRD42023440218; https://www.crd.york.ac.uk/PROSPERO/view/CRD42023440218.}, } @article {pmid40240877, year = {2025}, author = {Li, W and Chu, C and Zhang, T and Sun, H and Wang, S and Liu, Z and Wang, Z and Li, H and Li, Y and Zhang, X and Geng, Z and Wang, Y and Li, Y and Zhang, H and Fan, W and Wang, Y and Xu, X and Cheng, L and Zhang, D and Xiong, Y and Li, H and Zhou, B and Guan, Q and Deng, CH and Han, Y and Ma, H and Han, Z}, title = {Pan-genome analysis reveals the evolution and diversity of Malus.}, journal = {Nature genetics}, volume = {}, number = {}, pages = {}, pmid = {40240877}, issn = {1546-1718}, support = {CARS-27//Earmarked Fund for China Agriculture Research System/ ; 32172522//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32422077//National Natural Science Foundation of China (National Science Foundation of China)/ ; 2019M661344//China Postdoctoral Science Foundation/ ; }, abstract = {Malus Mill., a genus of temperate perennial trees with great agricultural and ecological value, has diversified through hybridization, polyploidy and environmental adaptation. Limited genomic resources for wild Malus species have hindered the understanding of their evolutionary history and genetic diversity. We sequenced and assembled 30 high-quality Malus genomes, representing 20 diploids and 10 polyploids across major evolutionary lineages and geographical regions. Phylogenomic analyses revealed ancient gene duplications and conversions, while six newly defined genome types, including an ancestral type shared by polyploid species, facilitated the detection of strong signals for extensive introgressions. The graph-based pan-genome captured shared and species-specific structural variations, facilitating the development of a molecular marker for apple scab resistance. Our pipeline for analyzing selective sweep identified a mutation in MdMYB5 having reduced cold and disease resistance during domestication. This study advances Malus genomics, uncovering genetic diversity and evolutionary insights while enhancing breeding for desirable traits.}, } @article {pmid40179878, year = {2025}, author = {Li, Y and Liu, X and Guo, L and Han, K and Fang, S and Wan, X and Wang, D and Xu, X and Jiang, L and Fan, G and Xu, M}, title = {SpaGRN: Investigating spatially informed regulatory paths for spatially resolved transcriptomics data.}, journal = {Cell systems}, volume = {16}, number = {4}, pages = {101243}, doi = {10.1016/j.cels.2025.101243}, pmid = {40179878}, issn = {2405-4720}, mesh = {Animals ; *Transcriptome/genetics ; *Gene Expression Profiling/methods ; Humans ; *Gene Regulatory Networks/genetics ; Drosophila/genetics ; Computational Biology/methods ; }, abstract = {Cells spatially organize into distinct cell types or functional domains through localized gene regulatory networks. However, current spatially resolved transcriptomics analyses fail to integrate spatial constraints and proximal cell influences, limiting the mechanistic understanding of tissue organization. Here, we introduce SpaGRN, a statistical framework that reconstructs cell-type- or functional-domain-specific, dynamic, and spatial regulons by coupling intracellular spatial regulatory causality with extracellular signaling path information. Benchmarking across synthetic and real datasets demonstrates SpaGRN's superior precision over state-of-the-art tools in identifying context-dependent regulons. Applied to diverse spatially resolved transcriptomics platforms (Stereo-seq, STARmap, MERFISH, CosMx, Slide-seq, and 10x Visium), complex cancerous samples, and 3D datasets of developing Drosophila embryos and larvae, SpaGRN not only provides a versatile toolkit for decoding receptor-mediated spatial regulons but also reveals spatiotemporal regulatory mechanisms underlying organogenesis and inflammation.}, } @article {pmid40238767, year = {2025}, author = {Rodrigues, RDS and Cionek, VM and Barreto, AS and Branco, JO}, title = {Seabird strandings on the Brazilian coast: What influences spatial and temporal patterns?.}, journal = {PloS one}, volume = {20}, number = {4}, pages = {e0317335}, doi = {10.1371/journal.pone.0317335}, pmid = {40238767}, issn = {1932-6203}, mesh = {Animals ; Brazil ; *Animal Migration/physiology ; *Birds/physiology ; Seasons ; Spatio-Temporal Analysis ; Ecosystem ; Biodiversity ; }, abstract = {Seabirds exhibit physiological adaptations that allow them to forage in the marine environment and undertake long-distance migrations during non-reproductive periods. As a result, they face various natural and anthropogenic pressures, which can lead to extreme fatigue and even death. Stranded bodies that float in the sea can wash ashore, providing valuable ecological information. This study aimed to analyze seabird strandings along the south and southeast coasts of Brazil between 2016 and 2019, focusing on spatiotemporal and potential environmental and anthropogenic influences. Using data from the Santos Basin Beach Monitoring Project, we calculated ecological indices of abundance, richness, and diversity for the entire seabird community and separately by migratory behavior (resident, southern migratory, northern migratory). Statistical modeling revealed a strong decreasing trend in strandings from south to north, with higher events on the southern coast (Santa Catarina and Paraná) and lower on the southeast coast (São Paulo). Resident species and northern migratory species showed peak strandings in spring, while southern migratory peaked in winter. These spatial and temporal patterns reflected birds' home ranges, reproductive cycles, and migratory behaviors. Environmental variables influenced strandings differently depending on species migration behavior and ecological indices, highlighting the role of oceanographic processes in carcass drift and the impact of climatic events on species mortality. This study is the first to demonstrate a spatiotemporal pattern of seabird strandings on the Brazilian coast, providing valuable insights into seabird dynamics in the Santos Basin and offering important data for conservation efforts.}, } @article {pmid40238239, year = {2025}, author = {Sutori, S and Eliasson, ET and Mura, F and Ortiz, V and Catrambonephd, V and Hadlaczky, G and Todorov, I and Alfeo, AL and Cardi, V and Cimino, MGCA and Mioni, G and Raya, MA and Valenza, G and Carli, V and Gentili, C}, title = {Acceptability, Usability, and Insights Into Cybersickness Levels of a Novel Virtual Reality Environment for the Evaluation of Depressive Symptoms: Exploratory Observational Study.}, journal = {JMIR formative research}, volume = {9}, number = {}, pages = {e68132}, doi = {10.2196/68132}, pmid = {40238239}, issn = {2561-326X}, mesh = {Humans ; *Virtual Reality ; Male ; Female ; Adult ; *Depression/diagnosis/psychology ; Young Adult ; Italy ; Surveys and Questionnaires ; User-Computer Interface ; Pilot Projects ; Self Report ; }, abstract = {BACKGROUND: There is a clear need for enhanced mental health assessment, depressive symptom (DS) evaluation being no exception. A promising approach to this aim is using virtual reality (VR), which entails the potential of adding a wider set of assessment domains with enhanced ecological validity. However, whilst several studies have used VR for both diagnostic and treatment purposes, its acceptance, in particular how exposure to virtual environments affects populations with psychiatric conditions remains unknown.

OBJECTIVE: This study aims to report on the acceptability, usability, and cybersickness levels of a pilot VR environment designed for the purpose of differentiating between individuals with DSs.

METHODS: The exploratory study, conducted in Italy, included 50 healthy controls and 50 young adults with mild-to-moderate DSs (without the need for a formal diagnosis). The study used an observational design with approximately 30 minutes of VR exposure followed by a self-report questionnaire battery. The battery included a questionnaire based on the Theoretical Framework of Acceptability, the System Usability Scale as well as the Simulator Sickness Questionnaire.

RESULTS: Results indicate that the majority found VR acceptable for the purposes of mental health screening and treatment. However, for diagnostics, there was a clear preference for VR to be used by mental health professionals as a supplementary tool, as opposed to a stand-alone solution. In practice, following exposure to the pilot VR environment, generally, good levels of acceptability and usability were reported, but areas in need of improvement were identified (such as self-efficacy). Self-reported cybersickness levels were comparable to literature averages but were considerably higher among those with DSs.

CONCLUSIONS: These findings raise questions about the potential interplay between underlying somatic symptoms of depression and VR-induced cybersickness and call for more attention from the scientific community both in terms of methodology as well as potential clinical and theoretical implications. Conclusively, user support indicates a potential for VR to aid mental health assessment, but further research is needed to understand how exposure to virtual environments might affect populations with varying severity and other forms of psychiatric symptoms.

RR2-10.1186/ISRCTN16396369.}, } @article {pmid40235568, year = {2025}, author = {Davies, H and Noble, PJ and Fins, IS and Pinchbeck, G and Singleton, D and Pirmohamed, M and Killick, D}, title = {Developing electronic health records as a source of real-world data for veterinary pharmacoepidemiology.}, journal = {Frontiers in veterinary science}, volume = {12}, number = {}, pages = {1550468}, pmid = {40235568}, issn = {2297-1769}, abstract = {Spontaneous reporting of adverse events (AEs) by veterinary professionals and the public is the cornerstone of post-marketing safety surveillance for veterinary medicinal products (VMPs). However, studies suggest that most veterinary AEs remain unreported. Veterinary medicine regulators, including the United Kingdom Veterinary Medicines Directorate and the European Medicines Agency, have included the exploration of big data utilization to support pharmacovigilance efforts in their regulatory strategies. In this study, we describe the application of veterinary electronic healthcare records (EHRs) from the SAVSNET veterinary first opinion informatics system to conduct pharmacoepidemiological analyses. Five VMP-AE pairs were selected for investigation in a proof-of-concept study, where drug exposure was identified from semi-structured treatment data and AEs from the unstructured free-text clinical narrative. Dictionaries were developed to identify AEs based on standard terminology. The precision of these dictionaries improved when they were expanded using word vectorization and expert opinion. A key strength of first-opinion EHR datasets is their ability to enable cohort studies and facilitate calculations of absolute incidence and relative risk. Thus, we demonstrate that unstructured free-text clinical narratives can be used to identify outcomes for veterinary pharmacoepidemiological studies and, consequently, support and expand pharmacovigilance efforts based on spontaneous AE reports.}, } @article {pmid40232549, year = {2025}, author = {Xu, F and Jiang, C and Liu, Q and Yang, R and Li, W and Wei, Y and Bao, L and Tong, H}, title = {Source identification of polycyclic aromatic hydrocarbons (PAHs) in river sediments within a hilly agricultural watershed of Southwestern China: an integrated study based on Pb isotopes and PMF method.}, journal = {Environmental geochemistry and health}, volume = {47}, number = {5}, pages = {174}, pmid = {40232549}, issn = {1573-2983}, support = {NO. 2023YFC3705904//National Key Research and Development Plan of China/ ; NO. 2023YFC3705904//National Key Research and Development Plan of China/ ; NO. 2021-043//Stationing Point Tracking Research of Ecological Barrier Construction in the upper Yangtze River of Sichuan Province/ ; NO. 2021-043//Stationing Point Tracking Research of Ecological Barrier Construction in the upper Yangtze River of Sichuan Province/ ; NO. 41977169//National Natural Science Foundation of China/ ; NO. 41977169//National Natural Science Foundation of China/ ; SKLGP2022Z009//State Key Laboratory of Geohazard Prevention and Geoenvironment Protection Independent Research Project/ ; SKLGP2022Z009//State Key Laboratory of Geohazard Prevention and Geoenvironment Protection Independent Research Project/ ; }, mesh = {China ; *Polycyclic Aromatic Hydrocarbons/analysis ; *Geologic Sediments/chemistry/analysis ; *Rivers/chemistry ; *Water Pollutants, Chemical/analysis ; *Environmental Monitoring/methods ; *Lead/analysis ; Agriculture ; Isotopes/analysis ; Geographic Information Systems ; }, abstract = {Polycyclic aromatic hydrocarbons (PAHs) in sediments represent a pervasive environmental issue that poses significant ecological risks. This study employed a combination of geographic information systems, diagnostic ratios, correlation analysis, Pb isotope ratios, and positive matrix factorization (PMF) to elucidate the potential sources of 16 priority PAHs in river sediments from a hilly agricultural watershed in Southwestern China. The results indicated that PAHs concentrations ranged from 55.9 to 6083.5 ng/g, with a mean value of 1582.1 ± 1528.9 ng/g, reflecting high levels of contamination throughout the watershed. The predominant class of PAHs identified was high molecular weight (HMW) PAHs. Diagnostic ratios and correlation analysis suggested that the presence of PHAs is likely attributed primarily to emissions from industrial dust and combustion of coal and petroleum. Furthermore, correlation analysis revealed a significant association between Pb and PAHs, indicating potential shared sources for both pollutants. Additionally, Pb isotopic analysis demonstrated that aerosols may be the primary contributor to Pb accumulation within this environment. Given the similarity in origins between Pb and PAHs, it can be inferred that PAHs predominantly originate from aerosols associated with coal combustion, industrial dust emissions, and vehicle exhaust. This inference is further supported by PMF results which yielded consistent findings with those derived from Pb isotopes analysis. Moreover, PMF estimated three major sources contributing 57.63%, 23.57%, and 18.80%, respectively. These findings provide novel insights into identifying the sources of PAHs in river sediments within hilly agricultural watersheds in Southwest China, thereby establishing a scientific foundation for enhancing environmental quality in agricultural regions.}, } @article {pmid40198742, year = {2025}, author = {Choi, H and Lee, CH}, title = {The impact of climate change on ecology of tick associated with tick-borne diseases.}, journal = {PLoS computational biology}, volume = {21}, number = {4}, pages = {e1012903}, doi = {10.1371/journal.pcbi.1012903}, pmid = {40198742}, issn = {1553-7358}, mesh = {*Climate Change ; *Tick-Borne Diseases/transmission/epidemiology/prevention & control ; Animals ; *Ticks/physiology ; Humans ; *Models, Biological ; Population Dynamics ; Computational Biology ; }, abstract = {Infectious diseases have caused significant economic and human losses worldwide. Growing concerns exist regarding climate change potentially exacerbating the spread of these diseases, particularly those transmitted by vectors such as ticks and mosquitoes. Tick-borne diseases, such as Severe Fever with Thrombocytopenia Syndrome (SFTS), can be particularly detrimental to elderly and immunocompromised individuals. This study utilizes a mathematical modeling approach to predict changes in tick populations under climate change scenarios, incorporating tick ecology and climate-sensitive parameters. Sensitivity analysis is performed to investigate the factors influencing tick population dynamics. The study further explores effective tick control strategies and their cost-effectiveness in the context of climate change. The findings indicate that the efficacy of tick population reduction varies greatly depending on the timing of control measure implementation and the effectiveness of the control strategies exhibits a strong dependence on the duration of implementation. Furthermore, as climate change intensifies, tick populations are projected to increase, leading to a rise in control costs and SFTS cases. In light of these findings, identifying and implementing appropriate control measures to manage tick populations under climate change will be increasingly crucial.}, } @article {pmid40229317, year = {2025}, author = {Sabadel, AJM and Riekenberg, P and Ayala-Diaz, M and Belk, MC and Bennett, J and Bode, A and Bury, SJ and Dabouineau, L and Delgado, J and Finucci, B and García-Seoane, R and Giari, L and Henkens, J and IJsseldijk, LL and Joling, T and Kerr-Hislop, O and MacLeod, CD and Meyer, L and McGill, RAR and Negro, E and Quillfeldt, P and Reed, C and Roberts, C and Sayyaf Dezfuli, B and Schmidt, O and Sturbois, A and Suchomel, AD and Thieltges, DW and van der Lingen, CD and van der Meer, MTJ and Viana, IG and Weston, M and Willis, TJ and Filion, A}, title = {Establishing a comprehensive host-parasite stable isotope database to unravel trophic relationships.}, journal = {Scientific data}, volume = {12}, number = {1}, pages = {623}, pmid = {40229317}, issn = {2052-4463}, support = {CAWX2207//Ministry of Business, Innovation and Employment (MBIE)/ ; }, mesh = {*Host-Parasite Interactions ; Animals ; Nitrogen Isotopes/analysis ; Carbon Isotopes ; *Databases, Factual ; Sulfur Isotopes/analysis ; *Parasites ; }, abstract = {Over the past decades, stable isotopes have been infrequently used to characterise host-parasite trophic relationships. This is because we have not yet identified consistent patterns in stable isotope values between parasites and their host tissues across species, which are crucial for understanding host-parasite dynamics. To address this, we initiated a worldwide collaboration to establish a unique database of stable isotope values of novel host-parasite pairs, effectively doubling the existing data in published literature. This database includes nitrogen, carbon, and sulphur stable isotope values. We present 3213 stable isotope data entries, representing 586 previously unpublished host-parasite pairs. Additionally, while existing literature was particularly limited in sulphur isotope values, we tripled information on this crucial element. By publishing unreported host-parasite pairs from previously unsampled areas of the world and using appropriate host tissues, our dataset stands unparalleled. We anticipate that end-users will utilise our database to uncover generalisable patterns, deepening our understanding of the complexities of parasite-host relationships and driving future research efforts in stable isotope parasitology.}, } @article {pmid40229216, year = {2025}, author = {Zhang, X and Lu, B and Jin, LN and Yang, S and Wang, C and Tai, J and Li, D and Chen, J}, title = {Emission Dynamics and Public Health Implications of Airborne Pathogens and Antimicrobial Resistance from Urban Waste Collection Facilities.}, journal = {Environmental science & technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.4c12108}, pmid = {40229216}, issn = {1520-5851}, abstract = {Airborne pathogens and antimicrobial resistance (AMR) present significant global health threats. Household waste collection facilities (WCFs), crucial initial nodes in urban waste management systems, have been understudied in regards to their role in emitting these hazards. This study investigated the abundance, composition, sources, driving mechanisms, and health risks associated with pathogens and AMR originating from WCFs in a major city, using culture-based analysis, high-throughput sequencing, and health risk modeling, respectively. The atmospheric escape rates of culturable bacteria (43.4%), fungi (71.7%), and antibiotic-resistant bacteria (ARB) (43.7%) were estimated based on the concentration differences between the interior and exterior of the WCFs by using SourceTracker2 analysis. Health risk assessments showed that annual infection risks for waste-handling workers ranged from 0.194 to 0.489, far exceeding the World Health Organization's acceptable limit of 10[-4]. Community exposure risks were notable up to 220 m downwind from WCFs, marking the maximum extent of pathogen dispersion. Our analysis suggests that approximately 6.3% of the megacity's area (equivalent to 400 km[2]) is within potential risk zones influenced by WCF emissions. These results underscore the critical need to evaluate and mitigate the public health risks posed by airborne pathogens and AMR emitted from WCFs in megacities globally.}, } @article {pmid40227267, year = {2025}, author = {Cassaro, A and Pacelli, C and Fanelli, G and Baqué, M and Maturilli, A and Leo, P and Lelli, V and de Vera, JP and Onofri, S and Timperio, A}, title = {Biomarker Preservation in Antarctic Sandstones after Prolonged Space Exposure Outside the International Space Station During the ESA EXPOSE-E Lichens and Fungi Experiment.}, journal = {Astrobiology}, volume = {}, number = {}, pages = {}, doi = {10.1089/ast.2024.0068}, pmid = {40227267}, issn = {1557-8070}, abstract = {A primary aim of current and future space exploration missions is the detection and identification of chemical and biological indicators of life, namely biomarkers, on Mars. The Mars Sample Return NASA-ESA program will bring to Earth samples of martian soil, acquired from up to 7 cm depth. The ESA Rosalind Franklin rover will search for signs of life in the subsurface (down to a depth of 2 meters), given the highly radioactive conditions on Mars' surface, which are not ideal for life as we know it and for the preservation of its traces. In the frame of the Lichens and Fungi Experiment, small fragments of Antarctic sandstones colonized by cryptoendolithic microbial communities were exposed to space and simulated martian conditions in low Earth orbit for 18 months, aboard the EXPOSE-E payload. Through the use of Raman and infrared spectroscopies, as well as a metabolomic approach, we aimed to detect organic compounds in a quartz mineral matrix. The results show that pigments, such as melanin, carotenoids, and chlorophyll, lipids, and amino acids, maintained their stability within minerals under simulated martian conditions in space, which makes them ideal biomarkers for the exploration of putative life on Mars.}, } @article {pmid40226649, year = {2024}, author = {Tamm, J and Takano, K and Just, L and Ehring, T and Rosenkranz, T and Kopf-Beck, J}, title = {Ecological Momentary Assessment versus Weekly Questionnaire Assessment of Change in Depression.}, journal = {Depression and anxiety}, volume = {2024}, number = {}, pages = {9191823}, pmid = {40226649}, issn = {1520-6394}, mesh = {Humans ; *Ecological Momentary Assessment ; Male ; Female ; Adult ; Middle Aged ; Surveys and Questionnaires/standards ; *Depression/diagnosis/therapy ; *Outcome Assessment, Health Care/methods ; Reproducibility of Results ; Pessimism/psychology ; Psychiatric Status Rating Scales ; Rumination, Cognitive ; }, abstract = {OBJECTIVE: Ecological momentary assessment (EMA) is increasingly used to monitor depressive symptoms in clinical trials, but little is known about the comparability of its outcomes to those of clinical interviews and questionnaires. In our study, we administered EMA and questionnaires to measure change in depressive symptoms and repetitive negative thinking (RNT) in a clinical trial and investigated (a) the size of intervention effects associated with both techniques and (b) their validity in predicting clinical interview outcomes (i.e., global functioning).

MATERIALS AND METHODS: Seventy-one depressed patients were randomly assigned to one of three psychological interventions. The EMA comprised a concise item set (four items per scale) and was administered three times per day during a 7-week intervention period. Conversely, questionnaires were assessed weekly (WQA), encompassing their full sets of items of depressive symptoms and RNT.

RESULTS: While EMA excelled in detecting significant intervention effects, WQA demonstrated greater strength in predicting clinician ratings of global functioning. Additionally, we observed significant differences in time effects (slopes) between the two techniques. WQA scores decreased steeper over time and were more extreme, e.g., higher at baseline and lower postintervention, than EMA scores.

CONCLUSIONS: Although clinical interviews, questionnaires, and EMA outcomes are related, they assess changes in depression differently. EMA may be more sensitive to intervention effects, but all three methods harbor potential bias, raising validity and reliability questions. Therefore, to enhance the validity and reliability of clinical trial assessments, we emphasize the importance of EMA approaches that combine subjective self-reports with objectively measured behavioral markers. This trial is registered with osf.io/9fuhn.}, } @article {pmid40223273, year = {2025}, author = {Yang, SY and Han, SM and Lee, JY and Kim, KS and Lee, JE and Lee, DW}, title = {Advancing Gut Microbiome Research: The Shift from Metagenomics to Multi-Omics and Future Perspectives.}, journal = {Journal of microbiology and biotechnology}, volume = {35}, number = {}, pages = {e2412001}, doi = {10.4014/jmb.2412.12001}, pmid = {40223273}, issn = {1738-8872}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Metagenomics/methods/trends ; *Metabolomics/methods ; *Genomics/methods ; Proteomics/methods ; Precision Medicine ; Host Microbial Interactions ; Multiomics ; }, abstract = {The gut microbiome, a dynamic and integral component of human health, has co-evolved with its host, playing essential roles in metabolism, immunity, and disease prevention. Traditional microbiome studies, primarily focused on microbial composition, have provided limited insights into the functional and mechanistic interactions between microbiota and their host. The advent of multi-omics technologies has transformed microbiome research by integrating genomics, transcriptomics, proteomics, and metabolomics, offering a comprehensive, systems-level understanding of microbial ecology and host-microbiome interactions. These advances have propelled innovations in personalized medicine, enabling more precise diagnostics and targeted therapeutic strategies. This review highlights recent breakthroughs in microbiome research, demonstrating how these approaches have elucidated microbial functions and their implications for health and disease. Additionally, it underscores the necessity of standardizing multi-omics methodologies, conducting large-scale cohort studies, and developing novel platforms for mechanistic studies, which are critical steps toward translating microbiome research into clinical applications and advancing precision medicine.}, } @article {pmid40222989, year = {2025}, author = {Mu, K and Wang, Z and Tang, J and Zhang, J and Han, W}, title = {The satisfaction of ecological environment in sports public services by artificial intelligence and big data.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {12748}, pmid = {40222989}, issn = {2045-2322}, mesh = {Humans ; *Artificial Intelligence ; *Big Data ; *Sports ; Surveys and Questionnaires ; Neural Networks, Computer ; *Personal Satisfaction ; }, abstract = {In order to gain a more accurate understanding and enhance the relationship between the fitness ecological environment and artificial intelligence (AI)-driven sports public services, this study combines a Convolutional Neural Network (CNN) approach based on residual modules and attention mechanisms with the SERVQUAL evaluation model. The method employed involves the analysis of big data collected from questionnaire surveys, literature reviews, and interviews. This study critically examines the impact of advanced AI technologies on residents' satisfaction with the fitness ecological environment in sports public services and conducts theoretical analysis of the obtained data. The results show that the quality of sports public services empowered by AI significantly influences residents' satisfaction with the fitness ecological environment, such as running, swimming, ball games and other sports with high requirements for sports service quality and ecological environment. Only the good public sports service quality matching with them can meet the needs of the ecological environment for fitness, and stimulate the enthusiasm of the people for fitness. The study also shows that swimming, running and all kinds of ball games account for the largest proportion of all sports. To sum up, the satisfaction of residents' fitness ecological environment is greatly affected by the quality of public sports services, which is mainly reflected in the good and perfect sports environment and facilities that can provide residents with a wealth of fitness options, greatly improving the sports ecological environment. This study is helpful to realize the relationship between sports public service and sports ecological environment. It contributes to understanding the role of AI and deep learning in enhancing the correlation between sports public service and the ecological environment of sports.}, } @article {pmid39031316, year = {2025}, author = {Chakraborty, K and Saha, S and Mandal, D}, title = {Hydrological modelling using SWAT for the assessment of streamflow dynamics in the Ganga River basin.}, journal = {Environmental science and pollution research international}, volume = {32}, number = {16}, pages = {10258-10278}, doi = {10.1007/s11356-024-34385-5}, pmid = {39031316}, issn = {1614-7499}, mesh = {*Rivers ; Hydrology ; *Models, Theoretical ; *Environmental Monitoring/methods ; Geographic Information Systems ; *Water Movements ; Rain ; }, abstract = {Growing concerns over water availability arise from the problems of population growth, rapid industrialization, and human interferences, necessitating accurate streamflow estimation at the river basin scale. It is extremely challenging to access stream flow data of a transboundary river at a spatio-temporal scale due to data unavailability caused by water conflicts for assessing the water availability.Primarily, this estimation is done using rainfall-runoff models. The present study addresses this challenge by applying the soil and water assessment tool (SWAT) for hydrological modelling, utilizing high-resolution geospatial inputs. Hydrological modelling using remote sensing and GIS (Geographic Information System) through this model is initiated to assess the water availability in the Ganga River basin at different locations. The outputs are calibrated and validated using the observed station data from Global Runoff Data Centre (GRDC). To check the performance of the model, Nash-Sutcliffe efficiency (NSE), percent bias (PBIAS), coefficient of determination (R[2]), and RSR efficacy measures are initiated in ten stations using the observed and simulated stream flow data. The R[2] values of eight stations range from 0.82 to 0.93, reflecting the efficacy of the model in rainfall-runoff modelling. Moreover, the results obtained from this hydrological modelling can serve as valuable resources for water resource planners and geographers for future reference.}, } @article {pmid40218748, year = {2025}, author = {Meng, J and Wang, Y and Liu, W and Yang, X and He, P}, title = {Research on the Development of an Inland Lake Bathymetry Estimation Model Based on Multispectral Data.}, journal = {Sensors (Basel, Switzerland)}, volume = {25}, number = {7}, pages = {}, pmid = {40218748}, issn = {1424-8220}, support = {41901285//the National Natural Science Foundation of China/ ; }, abstract = {Lakes play a crucial role in regional economic development and ecological construction. The variation in lake water depth has a direct impact on local economic activities, such as agriculture, livestock farming, and fisheries, as well as the stability of hydrological conditions and water ecology. In response to the lack of unified evaluation in the application of remote sensing water-depth estimation models for inland lakes, this study systematically compares the performance of numerical models and machine learning models for water-depth estimation in inland lakes. A machine learning-based water-depth estimation model construction methodology suitable for inland lakes is proposed. This study introduces an innovative approach by integrating machine learning techniques with multispectral remote sensing data, improving the accuracy and applicability of water-depth estimation models for inland lakes. The results show the following: (1) The machine learning models based on random forest (RF), BP neural networks (BP), and AdaBoost demonstrate better performance (R[2] = 0.88, 0.72, and 0.61; MAE = 0.12 m, 0.24 m, and 0.31 m; RMSE = 0.32 m, 0.48 m, and 0.57 m) compared to the multi-band logarithmic ratio (MLR) model (R[2] = 0.59; MAE = 0.32 m; RMSE = 0.58 m); (2) the machine learning water-depth estimation model constructed based on this methodology exhibits improved precision (R[2] = 0.92, 0.89, and 0.80; MAE = 0.11 m, 0.17 m, and 0.25 m; RMSE = 0.25 m, 0.30 m, and 0.41 m). This suggests that the methodology is more suitable for the estimation of water depth in medium- and small-sized lakes; (3) The machine learning model developed in this study, combined with multispectral remote sensing imagery, achieves the accuracy required for the evaluation of water depths for practical water resources. This model enables the rapid acquisition of high-precision underwater three-dimensional topographic maps, providing more accurate and timely hydrological data support for lake water resource management.}, } @article {pmid40213769, year = {2025}, author = {Yi, S and Liu, Y and Wu, Q and Zhao, D and Li, Z and Peng, X and Liao, G and Wang, S}, title = {Glycosylation of oral bacteria in modulating adhesion and biofilm formation.}, journal = {Journal of oral microbiology}, volume = {17}, number = {1}, pages = {2486650}, pmid = {40213769}, issn = {2000-2297}, abstract = {BACKGROUND: Glycosylation is a ubiquitous biochemical process that covalently attaches glycans to proteins or lipids, which plays a pivotal role in modulating the structure and function of these biomolecules. This post-translational modification is prevalent in living organisms and intricately regulates various biological processes, including signaling transduction, recognition, and immune responses. In the oral environment, bacteria ingeniously use glycosylation to enhance their adhesion to oral surfaces, which is a key step in biofilm formation and subsequent development. This adhesion process is intimately associated with the onset and progression of oral diseases, including dental caries and periodontal disease.

OBJECTIVE: This review aims to describe the types and mechanisms of glycosylation in oral bacteria, and to understand the role of glycosylation in the adhesion, biofilm formation and virulence of oral bacteria.

METHODS: We reviewed articles on glycosylation in a variety of oral bacteria.

CONCLUSION: In cariogenic bacteria and periodontopathic pathogens, glycosylation facilitates adhesion and subsequent biofilm maturation on tooth surface.   Distinct glycosylation patterns in oral bacteria shape biofilm structure and function, influencing microbial interactions and community stability.   Pathogen-specific glycosylation signatures enhance virulence and ecological competitiveness, contributing to disease progression. Glycosylation plays a critical role in bacterial virulence and community  interactions, with significant implications for oral health and disease development.}, } @article {pmid40213351, year = {2025}, author = {Fehér, ÁM and Bajory, Z and Czimbalmos, N and Burián, K and Lázár, A and Rárosi, F and Köves, B}, title = {Single-dose vs prolonged antibiotic prophylaxis of fosfomycin for transrectal prostate biopsy: a single-center prospective, randomized, controlled trial.}, journal = {Prostate international}, volume = {13}, number = {1}, pages = {28-33}, pmid = {40213351}, issn = {2287-8882}, abstract = {BACKGROUND: Transrectal prostate biopsy is a commonly performed urological procedure in which antibiotic prophylaxis is recommended. Fluoroquinolone-type antibiotics are no longer acceptable in the EU. Fosfomycin-trometamol may be used, but there is no evidence regarding its ideal dose and administration time.

METHODS: Patients who underwent prostate biopsy between 2021 and 2023 were evaluated prospectively. 204 patients were randomized into two arms: 102 patients (Arm A) received a single-dose of fosfomycin-trometamol one hour before surgery, and 102 patients (Arm B) received one additional dose of fosfomycin-trometamol 48 hours after the first dose. Urine tests and questionnaires were administered during the postoperative period and the subsequent four weeks to identify any symptoms, infectious, or other complications.

RESULTS: There was no statistical difference in the rate of asymptomatic bacteriuria (4.90% (5) vs. 8.82% (9), P = 0.27) symptomatic urinary tract infection (0% (0) vs. 1.96% (2), P = 0.50), or febrile urinary tract infection (0% (0) vs. 0.98% (1), P = 1) between the groups. Only hematuria was significantly more common in Arm B (6.86% (7) vs. 16.67% (17), P = 0.03), whereas other complications did not differ significantly. There was no statistical difference in hospitalization (0.98% (1) vs. 2.94 (3), P = 0.62) or mortality rate (0 % (0) vs. 0.98% (1), P = 1). Sub-group analysis of previous antibiotic users showed no difference in terms of complications.

CONCLUSION: There is no significant difference in infectious complications between single-dose and prolonged prophylaxis of fosfomycin-trometamol for transrectal prostate biopsy. A single-dose of fosfomycin one hour before biopsy is an ideal choice with a better ecological impact compared with prolonged antibiotic prophylaxis for transrectal prostate biopsy.}, } @article {pmid40211980, year = {2025}, author = {Elena Schmitz, J and Rahmann, S}, title = {A comprehensive review and evaluation of species richness estimation.}, journal = {Briefings in bioinformatics}, volume = {26}, number = {2}, pages = {}, doi = {10.1093/bib/bbaf158}, pmid = {40211980}, issn = {1477-4054}, mesh = {*Biodiversity ; Computer Simulation ; Animals ; Computational Biology/methods ; Algorithms ; }, abstract = {MOTIVATION: The statistical problem of estimating the total number of distinct species in a population (or distinct elements in a multiset), given only a small sample, occurs in various areas, ranging from the unseen species problem in ecology to estimating the diversity of immune repertoires. Accurately estimating the true richness from very small samples is challenging, in particular for highly diverse populations with many rare species. Depending on the application, different estimation strategies have been proposed that incorporate explicit or implicit assumptions about either the species distribution or about the sampling process. These methods are scattered across the literature, and an extensive overview of their assumptions, methodology, and performance is currently lacking.

RESULTS: We comprehensively review and evaluate a variety of existing methods on real and simulated data with different compositions of rare and abundant species. Our evaluation shows that, depending on species composition, different methods provide the most accurate richness estimates. Simple methods based on the observed number of singletons yield accurate asymptotic lower bounds for several of the tested simulated species compositions, but tend to underestimate the true richness for heterogeneous populations and small samples containing 1% to 5% of the population. When the population size is known, upsampling (extrapolating) estimators such as PreSeq and RichnEst yield accurate estimates of the total species richness in a sample that is up to 10 times larger than the observed sample.

AVAILABILITY: Source code for data simulation and richness estimation is available at https://gitlab.com/rahmannlab/speciesrichness.}, } @article {pmid40205052, year = {2025}, author = {Yoo, D and Rhie, A and Hebbar, P and Antonacci, F and Logsdon, GA and Solar, SJ and Antipov, D and Pickett, BD and Safonova, Y and Montinaro, F and Luo, Y and Malukiewicz, J and Storer, JM and Lin, J and Sequeira, AN and Mangan, RJ and Hickey, G and Monfort Anez, G and Balachandran, P and Bankevich, A and Beck, CR and Biddanda, A and Borchers, M and Bouffard, GG and Brannan, E and Brooks, SY and Carbone, L and Carrel, L and Chan, AP and Crawford, J and Diekhans, M and Engelbrecht, E and Feschotte, C and Formenti, G and Garcia, GH and de Gennaro, L and Gilbert, D and Green, RE and Guarracino, A and Gupta, I and Haddad, D and Han, J and Harris, RS and Hartley, GA and Harvey, WT and Hiller, M and Hoekzema, K and Houck, ML and Jeong, H and Kamali, K and Kellis, M and Kille, B and Lee, C and Lee, Y and Lees, W and Lewis, AP and Li, Q and Loftus, M and Loh, YHE and Loucks, H and Ma, J and Mao, Y and Martinez, JFI and Masterson, P and McCoy, RC and McGrath, B and McKinney, S and Meyer, BS and Miga, KH and Mohanty, SK and Munson, KM and Pal, K and Pennell, M and Pevzner, PA and Porubsky, D and Potapova, T and Ringeling, FR and Rocha, JL and Ryder, OA and Sacco, S and Saha, S and Sasaki, T and Schatz, MC and Schork, NJ and Shanks, C and Smeds, L and Son, DR and Steiner, C and Sweeten, AP and Tassia, MG and Thibaud-Nissen, F and Torres-González, E and Trivedi, M and Wei, W and Wertz, J and Yang, M and Zhang, P and Zhang, S and Zhang, Y and Zhang, Z and Zhao, SA and Zhu, Y and Jarvis, ED and Gerton, JL and Rivas-González, I and Paten, B and Szpiech, ZA and Huber, CD and Lenz, TL and Konkel, MK and Yi, SV and Canzar, S and Watson, CT and Sudmant, PH and Molloy, E and Garrison, E and Lowe, CB and Ventura, M and O'Neill, RJ and Koren, S and Makova, KD and Phillippy, AM and Eichler, EE}, title = {Complete sequencing of ape genomes.}, journal = {Nature}, volume = {}, number = {}, pages = {}, pmid = {40205052}, issn = {1476-4687}, abstract = {The most dynamic and repetitive regions of great ape genomes have traditionally been excluded from comparative studies[1-3]. Consequently, our understanding of the evolution of our species is incomplete. Here we present haplotype-resolved reference genomes and comparative analyses of six ape species: chimpanzee, bonobo, gorilla, Bornean orangutan, Sumatran orangutan and siamang. We achieve chromosome-level contiguity with substantial sequence accuracy (<1 error in 2.7 megabases) and completely sequence 215 gapless chromosomes telomere-to-telomere. We resolve challenging regions, such as the major histocompatibility complex and immunoglobulin loci, to provide in-depth evolutionary insights. Comparative analyses enabled investigations of the evolution and diversity of regions previously uncharacterized or incompletely studied without bias from mapping to the human reference genome. Such regions include newly minted gene families in lineage-specific segmental duplications, centromeric DNA, acrocentric chromosomes and subterminal heterochromatin. This resource serves as a comprehensive baseline for future evolutionary studies of humans and our closest living ape relatives.}, } @article {pmid40048849, year = {2025}, author = {Bargheet, A and Noordzij, HT and Ponsero, AJ and Jian, C and Korpela, K and Valles-Colomer, M and Debelius, J and Kurilshikov, A and Pettersen, VK}, title = {Dynamics of gut resistome and mobilome in early life: a meta-analysis.}, journal = {EBioMedicine}, volume = {114}, number = {}, pages = {105630}, pmid = {40048849}, issn = {2352-3964}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Infant ; Metagenomics/methods ; Infant, Newborn ; Anti-Bacterial Agents/pharmacology/therapeutic use ; Metagenome ; Female ; Interspersed Repetitive Sequences ; *Drug Resistance, Bacterial/genetics ; Computational Biology/methods ; }, abstract = {BACKGROUND: The gut microbiota of infants harbours a higher proportion of antibiotic resistance genes (ARGs) compared to adults, even in infants never exposed to antibiotics. Our study aims to elucidate this phenomenon by analysing how different perinatal factors influence the presence of ARGs, mobile genetic elements (MGEs), and their bacterial hosts in the infant gut.

METHODS: We searched MEDLINE and Embase up to April 3rd, 2023, for studies reporting infant cohorts with shotgun metagenomic sequencing of stool samples. The systematic search identified 14 longitudinal infant cohorts from 10 countries across three continents, featuring publicly available sequencing data with corresponding metadata. For subsequent integrative bioinformatic analyses, we used 3981 high-quality metagenomic samples from 1270 infants and 415 mothers.

FINDINGS: We identified distinct trajectories of the resistome and mobilome associated with birth mode, gestational age, antibiotic use, and geographical location. Geographical variation was exemplified by differences between cohorts from Europe, Southern Africa, and Northern America, which showed variation in both diversity and abundance of ARGs. On the other hand, we did not detect a significant impact of breastfeeding on the infants' gut resistome. More than half of detected ARGs co-localised with plasmids in key bacterial hosts, such as Escherichia coli and Enterococcus faecalis. These ARG-associated plasmids were gradually lost during infancy. We also demonstrate that E. coli role as a primary modulator of the infant gut resistome and mobilome is facilitated by its increased abundance and strain diversity compared to adults.

INTERPRETATION: Birth mode, gestational age, antibiotic exposure, and geographical location significantly influence the development of the infant gut resistome and mobilome. A reduction in E. coli relative abundance over time appears as a key factor driving the decrease in both resistome and plasmid relative abundance as infants grow.

FUNDING: Centre for Advanced Study in Oslo, Norway. Centre for New Antibacterial Strategies through the Tromsø Research Foundation, Norway.}, } @article {pmid40169791, year = {2025}, author = {Ding, DY and Tang, Z and Zhu, B and Ren, H and Shalek, AK and Tibshirani, R and Nolan, GP}, title = {Quantitative characterization of tissue states using multiomics and ecological spatial analysis.}, journal = {Nature genetics}, volume = {57}, number = {4}, pages = {910-921}, pmid = {40169791}, issn = {1546-1718}, mesh = {Humans ; *Spatial Analysis ; *Genomics/methods ; Single-Cell Analysis/methods ; Multiomics ; }, abstract = {The spatial organization of cells in tissues underlies biological function, and recent advances in spatial profiling technologies have enhanced our ability to analyze such arrangements to study biological processes and disease progression. We propose MESA (multiomics and ecological spatial analysis), a framework drawing inspiration from ecological concepts to delineate functional and spatial shifts across tissue states. MESA introduces metrics to systematically quantify spatial diversity and identify hot spots, linking spatial patterns to phenotypic outcomes, including disease progression. Furthermore, MESA integrates spatial and single-cell multiomics data to facilitate an in-depth, molecular understanding of cellular neighborhoods and their spatial interactions within tissue microenvironments. Applying MESA to diverse datasets demonstrates additional insights it brings over prior methods, including newly identified spatial structures and key cell populations linked to disease states. Available as a Python package, MESA offers a versatile framework for quantitative decoding of tissue architectures in spatial omics across health and disease.}, } @article {pmid40200522, year = {2025}, author = {Dsouza, N and Cohen, E and Ossebaard, H and van Meurs, H and Sijm-Eeken, M}, title = {The Ecological Footprint of Gynecology: Lessons from Dutch Hospitals and Implications for Future Healthcare Management.}, journal = {Studies in health technology and informatics}, volume = {323}, number = {}, pages = {424-428}, doi = {10.3233/SHTI250125}, pmid = {40200522}, issn = {1879-8365}, mesh = {Netherlands ; *Gynecology/organization & administration ; Humans ; Quality Improvement/organization & administration ; Female ; Models, Organizational ; }, abstract = {In 2023, global temperatures reached record-breaking highs, highlighting the urgent need for climate action. Healthcare is responsible for 4-8% of global carbon emissions, contributing to global warming and impacting the health of billions of people. Within healthcare, gynecology has a significant ecological footprint due to its high volume and broad range of care services. However, little is known on how gynecology departments' management structures, information systems and processes can be optimized to reduce the ecological footprint of this specialty. Therefore, a sustainability maturity model based on Donabedian's structure-process-outcome model for quality improvement was used to assess sustainability performance in two gynecology practices with different organizational structures (centralized vs. decentralized). Maturity model scores and interview findings were analyzed to extract lessons and recommendations for optimizing sustainability within gynecology. As the first assessment of its kind, this study provides a foundation for healthcare management seeking to improve environmental performance in gynecological care.}, } @article {pmid40200140, year = {2025}, author = {Antala, M and Kovar, M and Sporinová, L and Filacek, A and Juszczak, R and Zivcak, M and Shomali, A and Prasad, R and Brestic, M and Rastogi, A}, title = {High-throughput phenotyping of buckwheat (Fagopyrum esculentum Moench.) genotypes under water stress: exploring drought resistance for sustainable agriculture.}, journal = {BMC plant biology}, volume = {25}, number = {1}, pages = {444}, pmid = {40200140}, issn = {1471-2229}, support = {23-04221 L//Grantová Agentura České Republiky/ ; 731013//Horizon 2020 Framework Programme/ ; 2021/43/I/NZ9/01356//Narodowym Centrum Nauki/ ; BWS/BIL/2022/1/00120//Narodowa Agencja Wymiany Akademickiej/ ; }, mesh = {*Fagopyrum/genetics/physiology/growth & development ; Genotype ; *Droughts ; Phenotype ; Dehydration ; Crops, Agricultural/genetics/physiology ; Agriculture ; Stress, Physiological ; Plant Breeding ; Drought Resistance ; }, abstract = {BACKGROUND: As global agriculture faces the challenge of climate change, characterized by longer and more severe drought episodes, there is an increasing need for crop diversification and improved plant breeding. Buckwheat is one of the climate-resilient candidates for future important crops with remarkable adaptability to various biotic and abiotic stresses. As an underbred crop, a large number of genotypes should be assessed for the breeding of superior plants. Therefore, this study investigates the response of various buckwheat genotypes to water stress by high-throughput phenotyping and auxiliary plant physiology measurements.

RESULTS: We assessed six buckwheat genotypes from different regions under mild and severe water stress, focusing on morphological and physiological changes to understand drought tolerance mechanisms. Our findings revealed that reallocation of assimilated carbon from growth to secondary metabolite production is a common response to drought stress. Among the genotypes tested, Panda emerged as the most drought-resistant, with its morphology remaining the most stable under mild water stress and its ability to rapidly accumulate protective pigments in response to drought. Silver Hull also demonstrated resilience, maintaining its aboveground biomass under mild water stress at levels comparable to the control group. Additionally, the response magnitude to drought stress was linked to the biomass production potential of the genotypes, which was higher for those from warmer regions (Bhutan, Zimbabwe) and lower for those from colder regions (Poland, Canada).

CONCLUSION: The diversity in genotypic responses highlights the significant role of genetic variability in shaping drought resistance strategies in buckwheat. This research not only enhances our understanding of buckwheat's physiological responses to water stress but also holds promise for developing drought-resistant buckwheat varieties. These advancements are crucial for promoting sustainable agriculture in the face of climate change.}, } @article {pmid40200134, year = {2025}, author = {Hu, X and Pan, L and Fu, C and Zhu, Q and Hao, J and Wang, X and Nawaz, M and Qu, J and Zhang, J and Chen, Y and Zong, J and Liao, L and Tang, M and Wang, Z}, title = {A multi-omics analysis reveals candidate genes for Cd tolerance in Paspalum vaginatum.}, journal = {BMC plant biology}, volume = {25}, number = {1}, pages = {441}, pmid = {40200134}, issn = {1471-2229}, support = {No.321RC475//Hainan Natural Science Foundation high-level Talents Project/ ; No.321RC475//Hainan Natural Science Foundation high-level Talents Project/ ; ZDYF2023XDNY078//the Hainan Province Science and Technology Special Fund/ ; XTCX2022STC10//Collaborative Innovation Center Project of Ecological Civilization in Hainan University/ ; KJRC2023C21//Innovational Fund for Scientific and Technological Personnel of Hainan Province/ ; No.32060409//the National Natural Science Foundation of China/ ; XTCX2022NYB08//Collaborative Innovation Center Project of Nanfan and High-Efficiency Tropical Agriculture in Hainan University/ ; }, mesh = {*Cadmium/toxicity ; *Paspalum/genetics/drug effects/metabolism/physiology ; Genome-Wide Association Study ; *Genes, Plant ; Gene Expression Regulation, Plant ; Multiomics ; }, abstract = {Cadmium (Cd) pollution in the farmland has become a serious global issue threatening both human health and plant biomass production. Seashore paspalum (Paspalum vaginatum Sw.), a halophytic turfgrass, has been recognized as a Cd-tolerant species. However, the underlying genetic basis of natural variations in Cd tolerance still remains unknown. This study is possibly the first to apply genome-wide association studies (GWAS) and selective sweep analysis to identify potential Cd stress-responsive genes in P. vaginatum. We identified a total of 89 candidate genes and 656 putative selective sweeps regions. Based on the correlation analysis of differentially expressed metabolites (DEMs) and differentially expressed genes (DEGs), we identified the 55 key genes associated with metabolic changes induced by Cd treatment as the Cd tolerance-related genes. These genes showed significantly higher expression in Cd-tolerant accessions as compared to Cd-susceptive accessions. Therefore, our multi-omics study revealed the molecular and genetic basis of Cd tolerance, which may help develop Cd tolerant crop varieties.}, } @article {pmid40199921, year = {2025}, author = {Chaudhary, VB and Nokes, LF and González, JB and Cooper, PO and Katula, AM and Mares, EC and Pehim Limbu, S and Robinson, JN and Aguilar-Trigueros, CA}, title = {TraitAM, a global spore trait database for arbuscular mycorrhizal fungi.}, journal = {Scientific data}, volume = {12}, number = {1}, pages = {588}, pmid = {40199921}, issn = {2052-4463}, support = {DEB-2205650//National Science Foundation (NSF)/ ; Feodor Lynen Fellowship//Alexander von Humboldt-Stiftung (Alexander von Humboldt Foundation)/ ; }, mesh = {*Mycorrhizae/genetics ; *Spores, Fungal ; Phylogeny ; Symbiosis ; Databases, Factual ; }, abstract = {Knowledge regarding organismal traits supports a better understanding of the relationship between form and function and can be used to predict the consequences of environmental stressors on ecological and evolutionary processes. Most plants on Earth form symbioses with mycorrhizal fungi, but our ability to make trait-based inferences for these fungi is limited due to a lack of publicly available trait data. Here, we present TraitAM, a comprehensive database of multiple spore traits for all described species of the most common group of mycorrhizal fungi, the arbuscular mycorrhizal (AM) fungi (subphylum Glomeromycotina). Trait data for 344 species were mined from original species descriptions and used to calculate newly developed fungal trait metrics that can be employed to explore both intra- and inter-specific variation in traits. TraitAM also includes an updated phylogenetic tree that can be used to conduct phylogenetically-informed multivariate analyses of AM fungal traits. TraitAM will aid our further understanding of the biology, ecology, and evolution of these globally widespread, symbiotic fungi.}, } @article {pmid40198914, year = {2025}, author = {Holmqvist, S and Kaplan, M and Chaturvedi, R and Shou, H and Giovannetti, T}, title = {Longitudinal and Combined Smartwatch and Ecological Momentary Assessment in Racially Diverse Older Adults: Feasibility, Adherence, and Acceptability Study.}, journal = {JMIR human factors}, volume = {12}, number = {}, pages = {e69952}, doi = {10.2196/69952}, pmid = {40198914}, issn = {2292-9495}, mesh = {Humans ; *Ecological Momentary Assessment/statistics & numerical data ; Male ; Aged ; Female ; Feasibility Studies ; Middle Aged ; *Patient Compliance/statistics & numerical data ; Aged, 80 and over ; Longitudinal Studies ; *Smartphone ; *Mobile Applications ; *Cognitive Dysfunction/diagnosis ; *Wearable Electronic Devices/statistics & numerical data ; }, abstract = {BACKGROUND: Due to the rising prevalence of Alzheimer disease and related dementias, easily deployable tools to quantify risk are needed. Smartphones and smartwatches enable unobtrusive and continuous monitoring, but there is limited information regarding the feasibility, adherence, and acceptability of digital data collection among racially diverse older adults.

OBJECTIVE: This paper examined the feasibility, adherence, and acceptability of a 4-week combined smartwatch monitoring and ecological momentary assessment (EMA) study in a racially diverse sample of older adults.

METHODS: A total of 44 older adults (aged ≥55 y) with either mild cognitive impairment or healthy cognition completed an informed consent comprehension quiz, baseline cognitive testing, training regarding digital data collection, and questionnaires. Participants were instructed to wear a Garmin Vivosmart 4 smartwatch for 23 h/d for 4 weeks, sync 2 smartphone apps (Garmin and Labfront) daily, and complete a daily EMA survey with automated prompts for surveys and charging. Training time, smartwatch adherence (eg, wear time), daily EMA survey response rate, and performance on the consent quiz were quantified. Associations between feasibility and adherence metrics and participant factors were evaluated. Self-reported usability of the apps and smartwatch was collected at study end.

RESULTS: Consent comprehension quiz scores were high (mean 97.33%, SD 6.86% correct), and training sessions lasted on average 17.93 (SD 6.89) minutes. During the 4-week study, participants wore the smartwatch for an average of 21 h/d (SD 1.53) and showed an average response rate of 94% (SD 9.58%) to daily EMA surveys. In unadjusted bivariate analyses, age, race, and cognition were associated with feasibility and adherence measures, but only age and race remained significant in multivariate models. After accounting for all participant factors, older age was a significant predictor of longer training time, and Black race was a significant predictor of lower daily wear time. On the usability survey, all participants (45/45, 100%) indicated willingness to participate in future smartwatch studies, >80% (37/45) had a positive experience, and >90% (41/45) were satisfied with smartphone app syncing.

CONCLUSIONS: Smartwatch monitoring, requiring daily wear, smartphone syncing, and daily EMA survey completion, is highly feasible in older adults because adherence to daily wear and EMA surveys was high, as was general satisfaction on usability surveys. Although older participants may require more training on smartwatch and smartphone procedures and automated prompting during the study period, longitudinal monitoring with the Garmin Vivosmart 4 smartwatch and Labfront app is acceptable and feasible for collecting nearly continuous data in Black and White older adults, including those with mild cognitive impairment and those without.}, } @article {pmid40198416, year = {2025}, author = {Huan, F and Gao, S and Gu, Y and Ni, L and Wu, M and Li, Y and Liu, M and Yang, Y and Xiao, A and Liu, G}, title = {Molecular Allergology: Epitope Discovery and Its Application for Allergen-Specific Immunotherapy of Food Allergy.}, journal = {Clinical reviews in allergy & immunology}, volume = {68}, number = {1}, pages = {37}, pmid = {40198416}, issn = {1559-0267}, support = {32472449//the grant from the National Natural Science Foundation of China/ ; 32472449//the grant from the National Natural Science Foundation of China/ ; 32472449//the grant from the National Natural Science Foundation of China/ ; 32472449//the grant from the National Natural Science Foundation of China/ ; 32472449//the grant from the National Natural Science Foundation of China/ ; 32472449//the grant from the National Natural Science Foundation of China/ ; 32472449//the grant from the National Natural Science Foundation of China/ ; 32472449//the grant from the National Natural Science Foundation of China/ ; 32472449//the grant from the National Natural Science Foundation of China/ ; 32472449//the grant from the National Natural Science Foundation of China/ ; 2022YFF1100103//the grant from the National Key R&D Program of China/ ; 2022YFF1100103//the grant from the National Key R&D Program of China/ ; 2022YFF1100103//the grant from the National Key R&D Program of China/ ; 2022YFF1100103//the grant from the National Key R&D Program of China/ ; 2022YFF1100103//the grant from the National Key R&D Program of China/ ; 2022YFF1100103//the grant from the National Key R&D Program of China/ ; 2022YFF1100103//the grant from the National Key R&D Program of China/ ; 2022YFF1100103//the grant from the National Key R&D Program of China/ ; 2022YFF1100103//the grant from the National Key R&D Program of China/ ; 2022YFF1100103//the grant from the National Key R&D Program of China/ ; }, mesh = {Humans ; *Food Hypersensitivity/therapy/immunology ; *Allergens/immunology/chemistry/genetics ; *Desensitization, Immunologic/methods ; Animals ; *Epitopes, T-Lymphocyte/immunology ; *Epitopes, B-Lymphocyte/immunology ; *Epitopes/immunology ; Computational Biology ; Epitope Mapping ; }, abstract = {The prevalence of food allergy continues to rise, posing a significant burden on health and quality of life. Research on antigenic epitope identification and hypoallergenic agent design is advancing allergen-specific immunotherapy (AIT). This review focuses on food allergens from the perspective of molecular allergology, provides an overview of integration of bioinformatics and experimental validation for epitope identification, highlights hypoallergenic agents designed based on epitope information, and offers a valuable guidance to the application of hypoallergenic agents in AIT. With the development of molecular allergology, the characterization of the amino acid sequence and structure of the allergen at the molecular level facilitates T-/B-cell epitope identification. Alignment of the identified epitopes in food allergens revealed that the amino acid sequence of T-/B-cell epitopes barely overlapped, providing crucial data to design allergen molecules as a promising form for treating (FA) food allergy. Manipulating antigenic epitopes can reduce the allergenicity of allergens to obtain hypoallergenic agents, thereby minimizing the severe side effects associated with AIT. Currently, hypoallergenic agents are mainly developed through synthetic epitope peptides, genetic engineering, or food processing methods based on the identified epitope. New strategies such as DNA vaccines, signaling molecules coupling, and nanoparticles are emerging to improve efficiency. Although significant progress has been made in designing hypoallergenic agents for AIT, the challenge in clinical translation is to determine the appropriate dose and duration of treatment to induce long-term immune tolerance.}, } @article {pmid40196448, year = {2025}, author = {Rotstein, NM and Cohen, ZD and Welborn, A and Zbozinek, TD and Akre, S and Jones, KG and Null, KE and Pontanares, J and Sanchez, KL and Flanagan, DC and Halavi, SE and Kittle, E and McClay, MG and Bui, AAT and Narr, KL and Welsh, RC and Craske, MG and Kuhn, TP}, title = {Investigating low intensity focused ultrasound pulsation in anhedonic depression-A randomized controlled trial.}, journal = {Frontiers in human neuroscience}, volume = {19}, number = {}, pages = {1478534}, pmid = {40196448}, issn = {1662-5161}, abstract = {INTRODUCTION: Anhedonic depression is a subtype of depression characterized by deficits in reward processing. This subtype of depression is associated with higher suicide risk and longer depressive episodes, underscoring the importance of effective treatments. Anhedonia has also been found to correlate with alterations in activity in several subcortical regions, including the caudate head and nucleus accumbens. Low intensity focused ultrasound pulsation (LIFUP) is an emerging technology that enables non-invasive stimulation of these subcortical regions, which were previously only accessible with surgically-implanted electrodes.

METHODS: This double-blinded, sham-controlled study aims to investigate the effects of LIFUP to the left caudate head and right nucleus accumbens in participants with anhedonic depression. Participants in this protocol will undergo three sessions of LIFUP over the span of 5-9 days. To investigate LIFUP-related changes, this 7-week protocol collects continuous digital phenotyping data, an array of self-report measures of depression, anhedonia, and other psychopathology, and magnetic resonance imaging (MRI) before and after the LIFUP intervention. Primary self-report outcome measures include Ecological Momentary Assessment, the Positive Valence Systems Scale, and the Patient Health Questionnaire. Primary imaging measures include magnetic resonance spectroscopy and functional MRI during reward-based tasks and at rest. Digital phenotyping data is collected with an Apple Watch and participants' personal iPhones throughout the study, and includes information about sleep, heart rate, and physical activity.

DISCUSSION: This study is the first to investigate the effects of LIFUP to the caudate head or nucleus accumbens in depressed subjects. Furthermore, the data collected for this protocol covers a wide array of potentially affected modalities. As a result, this protocol will help to elucidate potential impacts of LIFUP in individuals with anhedonic depression.}, } @article {pmid39218423, year = {2025}, author = {Morris, JS}, title = {Tracking vaccine effectiveness in an evolving pandemic, countering misleading hot takes and epidemiologic fallacies.}, journal = {American journal of epidemiology}, volume = {194}, number = {4}, pages = {898-907}, doi = {10.1093/aje/kwae280}, pmid = {39218423}, issn = {1476-6256}, mesh = {Humans ; *COVID-19 Vaccines/immunology ; *Vaccine Efficacy ; *COVID-19/prevention & control/epidemiology ; *Pandemics/prevention & control ; SARS-CoV-2/immunology ; Social Media ; Bias ; }, abstract = {With the emergence of Omicron during the pandemic and the establishment of antibody waning over time, vaccine effectiveness, especially against infection, declined sharply from the original levels seen after the initial rollout. However, studies have demonstrated that they still provided substantial protection vs severe/fatal disease even with Omicron and after waning. Social media has been rife with reports claiming vaccines provided no benefit and some even claiming they made things worse, often driven by simple presentations of raw observational data using erroneous arguments involving epidemiologic fallacies including the base rate fallacy, Simpson's paradox, and the ecological fallacy and ignoring the extensive bias especially from confounding that is an inherent feature of these data. Similar fallacious arguments have been made by some in promoting vaccination policies, as well. Generally, vaccine effectiveness cannot be accurately estimated from raw population summaries but instead require rigorous, careful studies using epidemiologic designs and statistical analysis tools attempting to adjust for key confounders and sources of bias. This article summarizes what aggregated evidence across studies reveals about effectiveness of the mRNA vaccines as the pandemic has evolved, chronologically summarized with emerging variants and highlighting some of the fallacies and flawed arguments feeding social media-based claims that have obscured society's collective understanding.}, } @article {pmid40186616, year = {2025}, author = {Chen, L and Guo, Y and López-Güell, K and Ma, J and Dong, Y and Xie, J and Alhambra, DP}, title = {Immunity Debt for Seasonal Influenza After the COVID-19 Pandemic and as a Result of Nonpharmaceutical Interventions: An Ecological Analysis and Cohort Study.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {}, number = {}, pages = {e2410513}, doi = {10.1002/advs.202410513}, pmid = {40186616}, issn = {2198-3844}, support = {82373593//National Natural Science Foundation of China/ ; }, abstract = {Non-pharmaceutical interventions (NPIs) during the COVID-19 pandemic significantly reduced influenza transmission. This study explores the hypothesis of "immunity debt" which suggests increased vulnerability to influenza following reduced exposure during the pandemic. World Health Organization aggregated data on influenza from 116 countries and its association with NPI intensity as measured by the COVID-19 Stringency Index is analyzed. Where individual-level data available (France, the United Kingdom, Spain, Italy, Belgium, and Romania), the analyses of influenza monthly rates in six European countries (France, the United Kingdom, Spain, Italy, Belgium, and Romania) are replicated. The results indicate globally a 46.3% (95%CI: 15.79-70.78%) reduction in influenza cases during COVID-19 restrictions in the winter season, followed by a 131.7% (95%CI: 34.95-255.78%) increase in the first postrelaxation winter and a 161.2% (95%CI: 31.88-382.16%) increase in the summer as compared to the predicted level based on historical influenza epidemic trends. In addition, a positive association between the Stringency Index and post-relaxation influenza surge is observed globally (R[2] = 0.14-0.17) and replicated regionally. The findings support the population immunity debt hypothesis for influenza and call for proactive preparations against its consequences in future pandemics.}, } @article {pmid39689860, year = {2025}, author = {Wu, Z and Huang, Z and Tang, N and Wang, K and Bian, C and Li, D and Kuraki, V and Schmid, F}, title = {Research on Sports Injury Rehabilitation Detection Based on IoT Models for Digital Health Care.}, journal = {Big data}, volume = {13}, number = {2}, pages = {144-160}, doi = {10.1089/big.2023.0134}, pmid = {39689860}, issn = {2167-647X}, mesh = {Humans ; *Internet of Things ; *Athletic Injuries/rehabilitation/diagnosis ; Delivery of Health Care ; Telemedicine ; Digital Health ; }, abstract = {Physical therapists specializing in sports rehabilitation detection help injured athletes recover from their wounds and avoid further harm. Sports rehabilitators treat not just commonplace sports injuries but also work-related musculoskeletal injuries, discomfort, and disorders. Sensor-equipped Internet of Things (IoT) monitors the real-time location of medical equipment such as scooters, cardioverters, nebulizer treatments, oxygenation pumps, or other monitor gear. Analysis of medicine deployment across sites is possible in real time. Health care delivery based on digital technology to improve access, affordability, and sustainability of medical treatment is known as digital health care. The challenging characteristics of such sports injury rehabilitation for digital health care are playing position, game strategies, and cybersecurity. Hence, in this research, health care IoT-enabled body area networks (HIoT-BAN) have been designed to improve sports injury rehabilitation detection for digital health care. The health care sector may benefit significantly from IoT adoption since it allows for enhanced patient safety; health care investment management includes controlling the hospital's pharmaceutical stock and monitoring the heat and humidity levels. Digital health describes a group of programmers made to aid health care delivery, whether by assisting with clinical decision-making or streamlining back-end operations in health care institutions. A HIoT-BAN effectively predicts the rise in sports injury rehabilitation detection with faster digital health care based on IoT. The research concludes that the HIoT-BAN effectively indicates sports injury rehabilitation detection for digital health care. The experimental analysis of HIoT-BAN outperforms the IoT method in terms of performance, accuracy, prediction ratio, and mean square error rate.}, } @article {pmid40185844, year = {2025}, author = {Amin, NU and Islam, F and Umar, M and Muhammad, W and Rahman, SU and Gaafar, AZ and Shah, TA and Dauelbait, M and Bourhia, M}, title = {Evaluation of crop phenology using remote sensing and decision support system for agrotechnology transfer.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {11582}, pmid = {40185844}, issn = {2045-2322}, mesh = {*Remote Sensing Technology/methods ; *Crops, Agricultural/growth & development ; Biomass ; *Agriculture/methods ; *Decision Support Techniques ; Plant Leaves/growth & development ; Seasons ; }, abstract = {The decision support system for agro-technology transfer (DSSAT) is a worldwide crop modeling platform used for crops growth, yield, leaf area index (LAI), and biomass estimation under varying climatic, soil and management conditions. This study integrates DSSAT with satellite remote sensing (RS) data to estimates canopy state variables like LAI and biomass. For LAI estimation, Moderate Resolution Imaging Spectroradiometer (MODIS) product (MCD15A3H for LAI and MOD17A2 / MOD17A3 products for biomass) are used. Field data for Sheikhupura district is provided by National Agriculture Research Council (NARC) and used for the calibration and validation of the model. The results indicate strong agreement between the DSSAT and RS derived estimates. Correlation coefficients (R[2]) for LAI varied from 0.82 to 0.90, while for biomass ranged from 0.92 to 0.99 over two farms and two growing seasons (2012-2014). The index of agreement (D-index) ranged from 0.79 to 0.96 across the two farms and two growing seasons (2012-2014) affirming the model's durability. However, the biomass estimated from RS data is underestimated due to saturation phenomenon in the optical RS. The performance metrics, comprising the coefficient of residual mass (CRM) and normalized root mean square error (nRMSE), further substantiate the approach utilized. This study will help decision and policymakers and researchers to apply geospatial techniques for the sustainable agriculture practices.}, } @article {pmid40181527, year = {2025}, author = {Mills, MB and Shenkin, A and Wilkes, P and Disney, M and Page, S and Berrio, JC and Kaduk, J and Malhi, Y and Robert, R and Nilus, R and Riutta, T}, title = {Investigating the accuracy of tropical woody stem CO2 efflux estimates: scaling methods, and vertical and diel variation.}, journal = {The New phytologist}, volume = {}, number = {}, pages = {}, doi = {10.1111/nph.70122}, pmid = {40181527}, issn = {1469-8137}, support = {CA20118//European Cooperation in Science and Technology/ ; PRA 11.23//Royal Geographical Society/ ; NE/P011780/1//Natural Environment Research Council/ ; NE/Y006216/1//National Centre for Earth Observation/ ; NE/S007350/1//Central England NERC Training Alliance/ ; }, abstract = {Stem CO2 efflux (EA) significantly contributes to autotrophic and ecosystem respiration in tropical forests, but field methodologies often introduce biases and uncertainty. This study evaluates these biases and their impact on scaling EA at the stand-level. Diel and vertical patterns of EA were investigated, along with the accuracy of estimating stem surface area from allometric equations vs terrestrial light dection and ranging (LiDAR) scanning (TLS) in Maliau Basin Conservation Area, Sabah, Malaysian Borneo. Diel EA exhibited no uniform pattern due to inter-tree variability, but results suggest measuring EA before 15:00 h. EA was significantly higher on buttresses and above the first major branching point, but vertical variations in EA did not impact stand-level EA when stem surface area was accurately estimated. Allometric equations underestimated total stem surface area by c. 40% compared with TLS, but applying a site-specific correction factor yielded a similar stand-level EA and total stem surface area to TLS. This study provides guidance for measuring EA in the field and suggests that measuring at one time point and one height along the stem can produce accurate results if conducted using the correct time frame and if stem surface area is accurately estimated.}, } @article {pmid40180992, year = {2025}, author = {González, AL and Merder, J and Andraczek, K and Brose, U and Filipiak, M and Harpole, WS and Hillebrand, H and Jackson, MC and Jochum, M and Leroux, SJ and Nessel, MP and Onstein, RE and Paseka, R and Perry, GLW and Rugenski, A and Sitters, J and Sperfeld, E and Striebel, M and Zandona, E and Aymes, JC and Blanckaert, A and Bluhm, SL and Doi, H and Eisenhauer, N and Farjalla, VF and Hood, J and Kratina, P and Labonne, J and Lovelock, CE and Moody, EK and Mozsár, A and Nash, L and Pollierer, MM and Potapov, A and Romero, GQ and Roussel, JM and Scheu, S and Scheunemann, N and Seeber, J and Steinwandter, M and Susanti, WI and Tiunov, A and Dézerald, O}, title = {StoichLife: A Global Dataset of Plant and Animal Elemental Content.}, journal = {Scientific data}, volume = {12}, number = {1}, pages = {569}, pmid = {40180992}, issn = {2052-4463}, support = {DFG HI848/26-2//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; FOR 5000//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; DFG 493345801//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; FZT 118, 202548816//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; FZT 118, 202548816//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; RGPIN-2020-04132//Canadian Network for Research and Innovation in Machining Technology, Natural Sciences and Engineering Research Council of Canada (NSERC Canadian Network for Research and Innovation in Machining Technology)/ ; 310119/2018-9//Ministry of Science, Technology and Innovation | Conselho Nacional de Desenvolvimento Científico e Tecnológico (National Council for Scientific and Technological Development)/ ; 310119/2018-9//Ministry of Science, Technology and Innovation | Conselho Nacional de Desenvolvimento Científico e Tecnológico (National Council for Scientific and Technological Development)/ ; NAF\R2\180791//Royal Society/ ; DP0986179//Department of Education and Training | Australian Research Council (ARC)/ ; DP160103669//Department of Education and Training | Australian Research Council (ARC)/ ; 22-14-00363)//Russian Science Foundation (RSF)/ ; }, mesh = {*Plants/chemistry ; Animals ; Ecosystem ; Phosphorus/analysis ; Nitrogen/analysis ; Carbon/analysis ; }, abstract = {The elemental content of life is a key trait shaping ecology and evolution, yet organismal stoichiometry has largely been studied on a case-by-case basis. This limitation has hindered our ability to identify broad patterns and mechanisms across taxa and ecosystems. To address this, we present StoichLife, a global dataset of 28,049 records from 5,876 species spanning terrestrial, freshwater, and marine realms. Compiled from published and unpublished sources, StoichLife documents elemental content and stoichiometric ratios (%C, %N, %P, C:N, C:P, and N:P) for individual plants and animals. The dataset is standardized and, where available, includes information on taxonomy, habitat, body mass (for animals), geography, and environmental conditions such as temperature, solar radiation, and nutrient availability. By providing an unprecedented breadth of organismal stoichiometry, StoichLife enables the exploration of global patterns, ecological and evolutionary drivers, and context-dependent variations. This resource advances our understanding of the chemical makeup of life and its responses to environmental change, supporting progress in ecological stoichiometry and related fields.}, } @article {pmid39936183, year = {2025}, author = {Brait, N and Hackl, T and Lequime, S}, title = {detectEVE: Fast, Sensitive and Precise Detection of Endogenous Viral Elements in Genomic Data.}, journal = {Molecular ecology resources}, volume = {25}, number = {4}, pages = {e14083}, doi = {10.1111/1755-0998.14083}, pmid = {39936183}, issn = {1755-0998}, mesh = {*Computational Biology/methods ; *Genomics/methods ; *Software ; Genome, Viral ; *Viruses/genetics ; Sensitivity and Specificity ; }, abstract = {Endogenous viral elements (EVEs) are fragments of viral genomic material embedded within the host genome. Retroviruses contribute to the majority of EVEs because of their genomic integration during their life cycle; however, the latter can also arise from non-retroviral RNA or DNA viruses, then collectively known as non-retroviral (nr) EVEs. Detecting nrEVEs poses challenges because of their sequence and genomic structural diversity, contributing to the scarcity of specific tools designed for nrEVEs detection. Here, we introduce detectEVE, a user-friendly and open-source tool designed for the accurate identification of nrEVEs in genomic assemblies. detectEVE deviates from other nrEVE detection pipelines, which usually classify sequences in a more rigid manner as either virus-associated or not. Instead, we implemented a scaling system assigning confidence scores to hits in protein sequence similarity searches, using bit score distributions and search hints related to various viral characteristics, allowing for higher sensitivity and specificity. Our benchmarking shows that detectEVE is computationally efficient and accurate, as well as considerably faster than existing approaches, because of its resource-efficient parallel execution. Our tool can help to fill current gaps in both host-associated fields and virus-related studies. This includes (i) enhancing genome annotations with metadata for EVE loci, (ii) conducting large-scale paleo-virological studies to explore deep viral evolutionary histories, and (iii) aiding in the identification of actively expressed EVEs in transcriptomic data, reducing the risk of misinterpretations between exogenous viruses and EVEs.}, } @article {pmid39925235, year = {2025}, author = {Shi, T and Gao, Z and Zhang, Y and Rausher, MD and Chen, J}, title = {A Strategy of Assessing Gene Copy Number Differentiation Between Populations Using Ultra-Fast De Novo Assembly of Next-Generation Sequencing Data.}, journal = {Molecular ecology resources}, volume = {25}, number = {4}, pages = {e14080}, doi = {10.1111/1755-0998.14080}, pmid = {39925235}, issn = {1755-0998}, support = {31570220//National Natural Science Foundation of China/ ; 31870208//National Natural Science Foundation of China/ ; 32170240//National Natural Science Foundation of China/ ; KFJ-BRP-007-009//Biological Resources Program, CAS/ ; }, mesh = {*High-Throughput Nucleotide Sequencing/methods ; *DNA Copy Number Variations ; *Computational Biology/methods ; *Genetics, Population/methods ; *Gene Dosage ; Sequence Analysis, DNA/methods ; }, abstract = {Gene duplication and loss play pivotal roles in the evolutionary dynamics of genomes, contributing to species phenotypic diversity and adaptation. However, detecting copy number variations (CNVs) in homoploid populations and newly-diverged species using short reads from next-generation sequencing (NGS) with traditional methods can often be challenging due to uneven read coverage caused by variations in GC content and the presence of repetitive sequences. To address these challenges, we developed a novel pipeline, ST4gCNV, which leverages ultra-fast de novo assemblies of NGS data to detect gene-specific CNVs between populations. The pipeline effectively reduces the variance of read coverage due to technical factors such as GC bias, providing a reliable CNV detection with a minimum sequencing depth of 10. We successfully apply ST4gCNV to the resequencing analysis of homoploid species Nelumbo nucifera and Nelumbo lutea (lotus). We reveal significant CNV-driven differentiation between these species, particularly in genes related to petal colour diversity such as those involved in the anthocyanin pathway. By highlighting the extensive gene duplication and loss events in Nelumbo, our study demonstrates the utility of ST4gCNV in population genomics and underscores its potential of integrating genomic CNV analysis with traditional SNP-based resequencing analysis.}, } @article {pmid39801085, year = {2025}, author = {Anderson, EC and Giglio, RM and DeSaix, MG and Smyser, TJ}, title = {gscramble: Simulation of Admixed Individuals Without Reuse of Genetic Material.}, journal = {Molecular ecology resources}, volume = {25}, number = {4}, pages = {e14069}, doi = {10.1111/1755-0998.14069}, pmid = {39801085}, issn = {1755-0998}, support = {//National Wildlife Research Center/ ; //Southwest Fisheries Science Center/ ; }, mesh = {*Computer Simulation ; *Computational Biology/methods ; *Genetics, Population/methods ; Genotype ; *Software ; }, abstract = {While a best practice for evaluating the behaviour of genetic clustering algorithms on empirical data is to conduct parallel analyses on simulated data, these types of simulation techniques often involve sampling genetic data with replacement. In this paper we demonstrate that sampling with replacement, especially with large marker sets, inflates the perceived statistical power to correctly assign individuals (or the alleles that they carry) back to source populations-a phenomenon we refer to as resampling-induced, spurious power inflation (RISPI). To address this issue, we present gscramble, a simulation approach in R for creating biologically informed individual genotypes from empirical data that: (1) samples alleles from populations without replacement and (2) segregates alleles based on species-specific recombination rates. This framework makes it possible to simulate admixed individuals in a way that respects the physical linkage between markers on the same chromosome and which does not suffer from RISPI. This is achieved in gscramble by allowing users to specify pedigrees of varying complexity in order to simulate admixed genotypes, segregating and tracking haplotype blocks from different source populations through those pedigrees, and then sampling-using a variety of permutation schemes-alleles from empirical data into those haplotype blocks. We demonstrate the functionality of gscramble with both simulated and empirical data sets and highlight additional uses of the package that users may find valuable.}, } @article {pmid40180917, year = {2025}, author = {Schmitz, MA and Dimonaco, NJ and Clavel, T and Hitch, TCA}, title = {Lineage-specific microbial protein prediction enables large-scale exploration of protein ecology within the human gut.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {3204}, pmid = {40180917}, issn = {2041-1723}, support = {460129525//Massachusetts Department of Fish and Game (DFG)/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Metagenome/genetics ; *Metagenomics/methods ; *Bacterial Proteins/genetics/metabolism ; *Bacteria/genetics/classification/metabolism ; Phylogeny ; Computational Biology/methods ; }, abstract = {Microbes use a range of genetic codes and gene structures, yet these are often ignored during metagenomic analysis. This causes spurious protein predictions, preventing functional assignment which limits our understanding of ecosystems. To resolve this, we developed a lineage-specific gene prediction approach that uses the correct genetic code based on the taxonomic assignment of genetic fragments, removes incomplete protein predictions, and optimises prediction of small proteins. Applied to 9634 metagenomes and 3594 genomes from the human gut, this approach increased the landscape of captured expressed microbial proteins by 78.9%, including previously hidden functional groups. Optimised small protein prediction captured 3,772,658 small protein clusters, which form an improved microbial protein catalogue of the human gut (MiProGut). To enable the ecological study of a protein's prevalence and association with host parameters, we developed InvestiGUT, a tool which integrates both the protein sequences and sample metadata. Accurate prediction of proteins is critical to providing a functional understanding of microbiomes, enhancing our ability to study interactions between microbes and hosts.}, } @article {pmid40179423, year = {2025}, author = {Dejeante, R and Valeix, M and Chamaillé-Jammes, S}, title = {Do Mixed-Species Groups Travel as One? An Investigation on Large African Herbivores Monitored Using Animal-Borne Video Collars.}, journal = {The American naturalist}, volume = {205}, number = {4}, pages = {451-458}, doi = {10.1086/734410}, pmid = {40179423}, issn = {1537-5323}, mesh = {Animals ; Video Recording ; *Herbivory ; *Giraffes/physiology ; *Equidae/physiology ; *Antelopes/physiology ; Social Behavior ; Geographic Information Systems ; Ecosystem ; }, abstract = {AbstractAlthough prey foraging in mixed-species groups benefit from a reduced risk of predation, whether heterospecific groupmates move together in the landscape, and more generally to what extent mixed-species groups remain cohesive over time and space, remains unknown. Here, we used GPS collars with video cameras to investigate the movements of plains zebras (Equus quagga) in mixed-species groups. Blue wildebeest (Connochaetes taurinus), impalas (Aepyceros melampus), and giraffes (Giraffa camelopardalis) commonly form mixed-species groups with zebras in savanna ecosystems. We found that zebras adjust their movement decisions solely on the basis of the presence of giraffes, being more likely to move in zebra-giraffe herds, and this was correlated with a higher cohesion of such groups. Additionally, zebras moving with giraffes spent more time grazing, suggesting that zebras benefit from foraging in the proximity of giraffes. Our results provide new insights into animal movements in mixed-species groups, contributing to a better consideration of mutualism in movement ecology.}, } @article {pmid40179162, year = {2025}, author = {Davín, AA and Woodcroft, BJ and Soo, RM and Morel, B and Murali, R and Schrempf, D and Clark, JW and Álvarez-Carretero, S and Boussau, B and Moody, ERR and Szánthó, LL and Richy, E and Pisani, D and Hemp, J and Fischer, WW and Donoghue, PCJ and Spang, A and Hugenholtz, P and Williams, TA and Szöllősi, GJ}, title = {A geological timescale for bacterial evolution and oxygen adaptation.}, journal = {Science (New York, N.Y.)}, volume = {388}, number = {6742}, pages = {eadp1853}, doi = {10.1126/science.adp1853}, pmid = {40179162}, issn = {1095-9203}, mesh = {*Oxygen/metabolism ; Phylogeny ; *Biological Evolution ; Oxidation-Reduction ; *Bacteria/metabolism/classification/genetics ; Machine Learning ; Photosynthesis ; Adaptation, Physiological ; Cyanobacteria/genetics/metabolism ; }, abstract = {Microbial life has dominated Earth's history but left a sparse fossil record, greatly hindering our understanding of evolution in deep time. However, bacterial metabolism has left signatures in the geochemical record, most conspicuously the Great Oxidation Event (GOE). We combine machine learning and phylogenetic reconciliation to infer ancestral bacterial transitions to aerobic lifestyles, linking them to the GOE to calibrate the bacterial time tree. Extant bacterial phyla trace their diversity to the Archaean and Proterozoic, and bacterial families prior to the Phanerozoic. We infer that most bacterial phyla were ancestrally anaerobic and adopted aerobic lifestyles after the GOE. However, in the cyanobacterial ancestor, aerobic metabolism likely predated the GOE, which may have facilitated the evolution of oxygenic photosynthesis.}, } @article {pmid40178345, year = {2025}, author = {Riobueno-Naylor, A and Gomez, I and Quan, S and Hutt Vater, C and Montes, M and Hoskova, B and Lai, BS}, title = {Methods for integrating public datasets: insights from youth disaster mental health research.}, journal = {European journal of psychotraumatology}, volume = {16}, number = {1}, pages = {2481699}, doi = {10.1080/20008066.2025.2481699}, pmid = {40178345}, issn = {2000-8066}, mesh = {Humans ; Adolescent ; *Disasters ; United States/epidemiology ; *Mental Health/statistics & numerical data ; Male ; Female ; *Depression/epidemiology ; *Datasets as Topic ; Databases, Factual ; }, abstract = {Introduction: Weather-related disasters pose significant risks to youth mental health. Exposure to multiple disasters is becoming more common; however, the effects of such exposure remain understudied. This study demonstrates the application of integrative data approaches and FAIR (Findable, Accessible, Interoperable, Reusable) data principles to evaluate the relationship between cumulative disaster exposure and youth depression and suicidality in the United States, taking into account contextual factors across levels of social ecology.Methods: We combined data from five public sources, including the Youth Risk Behavior Surveillance System (YRBS), Federal Emergency Management Agency (FEMA), United States Census Bureau, Center for Homeland Defense and Security School Shooting Safety Compendium, and Global Terrorism Database. The integrative dataset included 415,701 youth from 37 districts across the United States who completed the YRBS between 1999 and 2021. The YRBS served as the core dataset.Results: This data note highlights strategies for harmonizing diverse data formats, addressing geographic and temporal inconsistencies, and validating integrated datasets. Automated data cleaning and visualization techniques enhance accuracy and efficiency. Planning for sensitivity analyses before data cleaning is recommended to improve the data integration process and enhance the robustness of findings.Discussion: This integrative approach demonstrates how leveraging FAIR principles can advance trauma research by facilitating large-scale analyses of complex public health questions. The methods provide a replicable framework for examining population-level impacts of phenomena and highlight opportunities for expanding trauma research.}, } @article {pmid40175550, year = {2025}, author = {Pärtel, M and Tamme, R and Carmona, CP and Riibak, K and Moora, M and Bennett, JA and Chiarucci, A and Chytrý, M and de Bello, F and Eriksson, O and Harrison, S and Lewis, RJ and Moles, AT and Öpik, M and Price, JN and Amputu, V and Askarizadeh, D and Atashgahi, Z and Aubin, I and Azcárate, FM and Barrett, MD and Bashirzadeh, M and Bátori, Z and Beenaerts, N and Bergholz, K and Birkeli, K and Biurrun, I and Blanco-Moreno, JM and Bloodworth, KJ and Boisvert-Marsh, L and Boldgiv, B and Brancalion, PHS and Brearley, FQ and Brown, C and Bueno, CG and Buffa, G and Cahill, JF and Campos, JA and Cangelmi, G and Carbognani, M and Carcaillet, C and Cerabolini, BEL and Chevalier, R and Clavel, JS and Costa, JM and Cousins, SAO and Čuda, J and Dairel, M and Dalle Fratte, M and Danilova, A and Davison, J and Deák, B and Del Vecchio, S and Dembicz, I and Dengler, J and Dolezal, J and Domene, X and Dvorsky, M and Ejtehadi, H and Enrico, L and Epikhin, D and Eskelinen, A and Essl, F and Fan, G and Fantinato, E and Fazlioglu, F and Fernández-Pascual, E and Ferrara, A and Fidelis, A and Fischer, M and Flagmeier, M and Forte, TGW and Fraser, LH and Fujinuma, J and Furquim, FF and Garris, B and Garris, HW and Giorgis, MA and Giusso Del Galdo, G and González-Robles, A and Good, MK and Guardiola, M and Guarino, R and Guerrero, I and Guillemot, J and Güler, B and Guo, Y and Haesen, S and Hejda, M and Heleno, RH and Høye, TT and Hrivnák, R and Huang, Y and Hunter, JT and Iakushenko, D and Ibáñez, R and Ingerpuu, N and Irl, SDH and Janíková, E and Jansen, F and Jeltsch, F and Jentsch, A and Jiménez-Alfaro, B and Jõks, M and Jouri, MH and Karami, S and Katal, N and Kelemen, A and Khairullin, BI and Khuroo, AA and Komatsu, KJ and Konečná, M and Kook, E and Korell, L and Koroleva, N and Korznikov, KA and Kozhevnikova, MV and Kozub, Ł and Laanisto, L and Lager, H and Lanta, V and Lasagno, RG and Lembrechts, JJ and Li, L and Lisner, A and Liu, H and Liu, K and Liu, X and Lucas-Borja, ME and Ludewig, K and Lukács, K and Luther-Mosebach, J and Macek, P and Marignani, M and Michalet, R and Miglécz, T and Moeslund, JE and Moeys, K and Montesinos, D and Moreno-Jiménez, E and Moysiyenko, I and Mucina, L and Muñoz-Rojas, M and Murillo, RA and Nambahu, SM and Neuenkamp, L and Normand, S and Nowak, A and Nuche, P and Oja, T and Onipchenko, VG and Pachedjieva, KL and Paganeli, B and Peco, B and Peralta, AML and Pérez-Haase, A and Peri, PL and Petraglia, A and Peyre, G and Plaza-Álvarez, PA and Plue, J and Prentice, HC and Prokhorov, VE and Radujković, D and Rahmanian, S and Reitalu, T and Ristow, M and Robin, AA and Robles, AB and Rodríguez Ginart, DA and Román, R and Roos, RE and Rosati, L and Sádlo, J and Salimbayeva, K and Sánchez de Dios, R and Sanchir, K and Sattler, C and Scasta, JD and Schmiedel, U and Schrader, J and Schultz, NL and Sellan, G and Serra-Diaz, JM and Silan, G and Skálová, H and Skobel, N and Sonkoly, J and Štajerová, K and Svitková, I and Świerszcz, S and Tanentzap, AJ and Tanentzap, FM and Tarifa, R and Tejero, P and Tekeev, DK and Tholin, M and Thormodsæter, RS and Tian, Y and Tokaryuk, A and Tölgyesi, C and Tomaselli, M and Tordoni, E and Török, P and Tóthmérész, B and Toussaint, A and Touzard, B and Trindade, DPF and Tsakalos, JL and Türkiş, S and Valencia, E and Valerio, M and Valkó, O and Van Meerbeek, K and Vandvik, V and Villellas, J and Virtanen, R and Vítková, M and Vojík, M and von Hessberg, A and von Oppen, J and Wagner, V and Wan, JZ and Wang, CJ and Wani, SA and Weiss, L and Wevill, T and Xiao, S and Zárate Martínez, O and Zobel, M}, title = {Global impoverishment of natural vegetation revealed by dark diversity.}, journal = {Nature}, volume = {}, number = {}, pages = {}, pmid = {40175550}, issn = {1476-4687}, abstract = {Anthropogenic biodiversity decline threatens the functioning of ecosystems and the many benefits they provide to humanity[1]. As well as causing species losses in directly affected locations, human influence might also reduce biodiversity in relatively unmodified vegetation if far-reaching anthropogenic effects trigger local extinctions and hinder recolonization. Here we show that local plant diversity is globally negatively related to the level of anthropogenic activity in the surrounding region. Impoverishment of natural vegetation was evident only when we considered community completeness: the proportion of all suitable species in the region that are present at a site. To estimate community completeness, we compared the number of recorded species with the dark diversity-ecologically suitable species that are absent from a site but present in the surrounding region[2]. In the sampled regions with a minimal human footprint index, an average of 35% of suitable plant species were present locally, compared with less than 20% in highly affected regions. Besides having the potential to uncover overlooked threats to biodiversity, dark diversity also provides guidance for nature conservation. Species in the dark diversity remain regionally present, and their local populations might be restored through measures that improve connectivity between natural vegetation fragments and reduce threats to population persistence.}, } @article {pmid40173850, year = {2025}, author = {Vivien, R and Martin, P}, title = {Maintaining taxonomic accuracy in genetic databases: A duty for taxonomists-Reanalysis of the DNA sequences from Mercan et al. (2024) on the genus Potamothrix (Annelida, Clitellata) in Turkish lakes.}, journal = {Zootaxa}, volume = {5575}, number = {4}, pages = {555-562}, doi = {10.11646/zootaxa.5575.4.5}, pmid = {40173850}, issn = {1175-5334}, mesh = {Turkey ; Animals ; Lakes ; Phylogeny ; *Databases, Genetic/standards ; *Databases, Nucleic Acid/standards ; Sequence Analysis, DNA ; *Polychaeta/classification/genetics ; }, abstract = {Public DNA sequence databases such as GenBank are widely used for identification of organisms in ecological and taxonomic studies. It is important that these public databases contain as few mistakes as possible and that any errors detected in these databases are reported. Here, we reanalyzed the COI sequences of Mercan et al. (2024) and showed that they were mistakenly considered by these authors as belonging to different populations (haplotypes) within the species Potamothrix hammoniensis (Tubificinae). We found that they corresponded to four distinct Tubificinae lineages (species), Pothamothrix alatus paravanicus, Potamothrix bavaricus, Tubifex sp. and Potamothrix sp. Despite these identification errors, the data from Mercan et al. (2024) remain interesting as they provide new information on the diversity of the genus Potamothrix in Turkey. Prompt measures must be taken to correct these errors and prevent them from being detrimental to future studies.}, } @article {pmid40111995, year = {2025}, author = {Eales, O and Shearer, FM and McCaw, JM}, title = {How immunity shapes the long-term dynamics of influenza H3N2.}, journal = {PLoS computational biology}, volume = {21}, number = {3}, pages = {e1012893}, pmid = {40111995}, issn = {1553-7358}, mesh = {Humans ; *Influenza, Human/immunology/epidemiology/transmission/virology ; *Influenza A Virus, H3N2 Subtype/immunology/genetics ; Computational Biology ; *Models, Immunological ; Adult ; Aged ; Middle Aged ; Adolescent ; }, abstract = {Since its emergence in 1968, influenza A H3N2 has caused yearly epidemics in temperate regions. While infection confers immunity against antigenically similar strains, new antigenically distinct strains that evade existing immunity regularly emerge ('antigenic drift'). Immunity at the individual level is complex, depending on an individual's lifetime infection history. An individual's first infection with influenza typically elicits the greatest response with subsequent infections eliciting progressively reduced responses ('antigenic seniority'). The combined effect of individual-level immune responses and antigenic drift on the epidemiological dynamics of influenza are not well understood. Here we develop an integrated modelling framework of influenza transmission, immunity, and antigenic drift to show how individual-level exposure, and the build-up of population level immunity, shape the long-term epidemiological dynamics of H3N2. Including antigenic seniority in the model, we observe that following an initial decline after the pandemic year, the average annual attack rate increases over the next 80 years, before reaching an equilibrium, with greater increases in older age-groups. Our analyses suggest that the average attack rate of H3N2 is still in a growth phase. Further increases, particularly in the elderly, may be expected in coming decades, driving an increase in healthcare demand due to H3N2 infections.}, } @article {pmid39880083, year = {2025}, author = {Vande Moortele, T and Verschaffelt, P and Huang, Q and Doncheva, NT and Holstein, T and Jachmann, C and Dawyndt, P and Martens, L and Mesuere, B and Van Den Bossche, T}, title = {PathwayPilot: A User-Friendly Tool for Visualizing and Navigating Metabolic Pathways.}, journal = {Molecular & cellular proteomics : MCP}, volume = {24}, number = {3}, pages = {100918}, pmid = {39880083}, issn = {1535-9484}, mesh = {*Software ; *Metabolic Networks and Pathways ; Humans ; *Proteomics/methods ; Gastrointestinal Microbiome ; User-Computer Interface ; Proteome/metabolism ; *Computational Biology/methods ; Caloric Restriction ; }, abstract = {Metaproteomics, the study of collective proteomes in environmental communities, plays a crucial role in understanding microbial functionalities affecting ecosystems and human health. Pathway analysis offers structured insights into the biochemical processes within these communities. However, no existing tool effectively combines pathway analysis with peptide- or protein-level data. We here introduce PathwayPilot, a web-based application designed to improve metaproteomic data analysis by integrating pathway analysis with peptide- and protein-level data, filling a critical gap in current metaproteomics bioinformatics tools. By allowing users to compare functional annotations across different samples or multiple organisms within a sample, PathwayPilot provides valuable insights into microbial functions. In the re-analysis of a study examining the effects of caloric restriction on gut microbiota, the tool successfully identified shifts in enzyme expressions linked to short-chain fatty acid biosynthesis, aligning with its original findings. PathwayPilot's user-friendly interface and robust capabilities make it a significant advancement in metaproteomics, with the potential for widespread application in microbial ecology and health sciences. All code is open source under the Apache2 license and is available at https://pathwaypilot.ugent.be.}, } @article {pmid39609363, year = {2025}, author = {Xu, S and Akhatayeva, Z and Liu, J and Feng, X and Yu, Y and Badaoui, B and Esmailizadeh, A and Kantanen, J and Amills, M and Lenstra, JA and Johansson, AM and Coltman, DW and Liu, GE and Curik, I and Orozco-terWengel, P and Paiva, SR and Zinovieva, NA and Zhang, L and Yang, J and Liu, Z and Wang, Y and Yu, Y and Li, M}, title = {Genetic advancements and future directions in ruminant livestock breeding: from reference genomes to multiomics innovations.}, journal = {Science China. Life sciences}, volume = {68}, number = {4}, pages = {934-960}, pmid = {39609363}, issn = {1869-1889}, mesh = {Animals ; *Livestock/genetics ; *Genomics/methods ; *Breeding/methods ; *Ruminants/genetics ; *Genome ; Phenotype ; Multiomics ; }, abstract = {Ruminant livestock provide a rich source of products, such as meat, milk, and wool, and play a critical role in global food security and nutrition. Over the past few decades, genomic studies of ruminant livestock have provided valuable insights into their domestication and the genetic basis of economically important traits, facilitating the breeding of elite varieties. In this review, we summarize the main advancements for domestic ruminants in reference genome assemblies, population genomics, and the identification of functional genes or variants for phenotypic traits. These traits include meat and carcass quality, reproduction, milk production, feed efficiency, wool and cashmere yield, horn development, tail type, coat color, environmental adaptation, and disease resistance. Functional genomic research is entering a new era with the advancements of graphical pangenomics and telomere-to-telomere (T2T) gap-free genome assembly. These advancements promise to improve our understanding of domestication and the molecular mechanisms underlying economically important traits in ruminant livestock. Finally, we provide new perspectives and future directions for genomic research on ruminant genomes. We suggest how ever-increasing multiomics datasets will facilitate future studies and molecular breeding in livestock, including the potential to uncover novel genetic mechanisms underlying phenotypic traits, to enable more accurate genomic prediction models, and to accelerate genetic improvement programs.}, } @article {pmid40175491, year = {2025}, author = {Zhang, H and Guo, G and Li, H and Wang, T and Ni, J and Meng, H}, title = {A new numerical method for calculating residual deformation in mined-out areas considering water-rock interaction and its application.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {11207}, pmid = {40175491}, issn = {2045-2322}, support = {2023YFC3804201//National Key R&D Program of China/ ; }, abstract = {Globally, extensive land regions have fallen victim to coal mining subsidence, rendering the reuse of goaf sites a crucial concern. The residual deformation amount of these sites is the linchpin for determining their reusability. Presently, numerical computations of residual deformation in goafs, which overlook water-rock coupling, breed significant errors, posing severe threats to the safety of on-site structures. To remedy the situation, this research hinges on the mechanical experiment results of fractured rock masses under water-rock interaction within the goaf. By leveraging an embedded programming language, it pinpoints the irregular damage range of overlying strata due to water-rock effects. Then, corresponding mechanical parameters are allocated to the surrounding rocks at diverse spatial positions, with the erosive impact of water-soaked coal pillars also factored in. This gives rise to a novel numerical method that more precisely gauges groundwater's influence on strata movement and surface subsidence. Using the 01 working face of a Shandong mine as a practical backdrop, the new method verifies its reliability and accuracy. When contrasted with traditional approaches, be it neglecting water filling or assuming full saturation in the goaf, it slashes the calculation error by 20%, furnishing new approaches for residual deformation calculation and novel perspectives for evaluating site stability under complex geological conditions.}, } @article {pmid40171521, year = {2025}, author = {Boyes, D and Hutchinson, F and Crowley, LM and , and , and , and , and , and , and , }, title = {The genome sequence of the Large Birch Bell moth, Large Birch Roller, Epinotia brunnichana (Linnaeus, 1767).}, journal = {Wellcome open research}, volume = {10}, number = {}, pages = {101}, pmid = {40171521}, issn = {2398-502X}, abstract = {We present a genome assembly from a female Epinotia brunnichana (Large Birch Bell, Large Birch Roller; Arthropoda; Insecta; Lepidoptera; Tortricidae). The genome sequence has a total length of 943.10 megabases. Most of the assembly (99.68%) is scaffolded into 29 chromosomal pseudomolecules, including the W and Z sex chromosomes. The mitochondrial genome has also been assembled and is 15.7 kilobases in length. Gene annotation of this assembly on Ensembl identified 12,003 protein-coding genes.}, } @article {pmid40170100, year = {2025}, author = {Sato, K and Watanabe, S and Noda, T and Koizumi, T and Yoda, K and Watanabe, YY and Sakamoto, KQ and Isokawa, T and Yoshida, MA and Aoki, K and Takahashi, A and Iwata, T and Nishizawa, H and Maekawa, T and Kawabe, R and Watanuki, Y}, title = {Biologging intelligent Platform (BiP): an integrated and standardized platform for sharing, visualizing, and analyzing biologging data.}, journal = {Movement ecology}, volume = {13}, number = {1}, pages = {23}, pmid = {40170100}, issn = {2051-3933}, abstract = {Sharing biologging data can facilitate collaborative research and biological conservation by providing maps showing animals' distribution and movements. It is a critical social mission to preserve not only horizontal position data, but also behavioral data such as diving depth, flight altitude, speed, and acceleration, as well as physiological data such as body temperature, along with related metadata, ensuring their preservation for future generation. Moreover, although biologging was initially developed in the field of biology, it now contributes to diverse fields such as meteorology and oceanography, leading to expanded opportunities for secondary data utilization. In light of social and academic requirements, we developed "Biologging intelligent Platform (BiP)", which adheres to internationally recognized standards for sensor data and metadata storage. As a result, BiP not only stores sensor data along with metadata but also standardizes this information to facilitate secondary data analysis, facilitating broader applications of biologging data across various disciplines. By visiting the website (https://www.bip-earth.com) and completing the user registration, data owners can interactively upload sensor data, input metadata associated with individual animals, devices, and deployments, standardize data formats, and choose between open and private settings for sharing data. Anyone interested in utilizing the data can access metadata and visualized route maps, irrespective of the data's open or private status. Users can freely download open datasets that are available under the CC BY 4.0 license, which permits copying, redistribution, and modification while adhering to the metadata's credit requirements. To use private datasets, users can contact the data owner to request permission. A unique feature of BiP is the Online Analytical Processing (OLAP) tools that calculate environmental parameters, such as surface currents, ocean winds, and waves from data collected by animals. Algorithms published in some previous studies are integrated into the OLAP which can estimate the environmental and behavioral parameters. To enhance data accessibility, BiP allows users to search for datasets using the DOI of the paper in which the data was used. We believe that linking with other databases for data exchange and multi-repository storage could enhance the sustainability of the data itself.}, } @article {pmid39934999, year = {2025}, author = {De Moor, D and Skelton, M and , and Amici, F and Arlet, ME and Balasubramaniam, KN and Ballesta, S and Berghänel, A and Berman, CM and Bernstein, SK and Bhattacharjee, D and Bliss-Moreau, E and Brotcorne, F and Butovskaya, M and Campbell, LAD and Carosi, M and Chatterjee, M and Cooper, MA and Cowl, VB and De la O, C and De Marco, A and Dettmer, AM and Dhawale, AK and Erinjery, JJ and Evans, CL and Fischer, J and García-Nisa, I and Giraud, G and Hammer, R and Hansen, MF and Holzner, A and Kaburu, S and Konečná, M and Kumara, HN and Larrivaz, M and Leca, JB and Legrand, M and Lehmann, J and Li, JH and Lezé, AS and MacIntosh, A and Majolo, B and Maréchal, L and Marty, PR and Massen, JJM and Maulany, RI and McCowan, B and McFarland, R and Merieau, P and Meunier, H and Micheletta, J and Mishra, PS and Sah, SAM and Molesti, S and Morrow, KS and Müller-Klein, N and Ngakan, PO and Palagi, E and Petit, O and Pflüger, LS and di Sorrentino, EP and Raghaven, R and Raimbault, G and Ram, S and Reichard, UH and Riley, EP and Rincon, AV and Ruppert, N and Sadoughi, B and Santhosh, K and Schino, G and Sheeran, LK and Silk, JB and Singh, M and Sinha, A and Sosa, S and Stribos, MS and Sueur, C and Tiddi, B and Tkaczynski, PJ and Trebouet, F and Widdig, A and Whitehouse, J and Wooddell, LJ and Xia, DP and von Fersen, L and Young, C and Schülke, O and Ostner, J and Neumann, C and Duboscq, J and Brent, LJN}, title = {MacaqueNet: Advancing comparative behavioural research through large-scale collaboration.}, journal = {The Journal of animal ecology}, volume = {94}, number = {4}, pages = {519-534}, doi = {10.1111/1365-2656.14223}, pmid = {39934999}, issn = {1365-2656}, support = {864461//H2020 European Research Council/ ; LSC-AF2023_03//Leibniz ScienceCampus EEGA/ ; }, mesh = {Animals ; *Behavioral Research/methods ; Macaca/physiology ; Behavior, Animal ; Databases, Factual ; Social Behavior ; }, abstract = {There is a vast and ever-accumulating amount of behavioural data on individually recognised animals, an incredible resource to shed light on the ecological and evolutionary drivers of variation in animal behaviour. Yet, the full potential of such data lies in comparative research across taxa with distinct life histories and ecologies. Substantial challenges impede systematic comparisons, one of which is the lack of persistent, accessible and standardised databases. Big-team approaches to building standardised databases offer a solution to facilitating reliable cross-species comparisons. By sharing both data and expertise among researchers, these approaches ensure that valuable data, which might otherwise go unused, become easier to discover, repurpose and synthesise. Additionally, such large-scale collaborations promote a culture of sharing within the research community, incentivising researchers to contribute their data by ensuring their interests are considered through clear sharing guidelines. Active communication with the data contributors during the standardisation process also helps avoid misinterpretation of the data, ultimately improving the reliability of comparative databases. Here, we introduce MacaqueNet, a global collaboration of over 100 researchers (https://macaquenet.github.io/) aimed at unlocking the wealth of cross-species data for research on macaque social behaviour. The MacaqueNet database encompasses data from 1981 to the present on 61 populations across 14 species and is the first publicly searchable and standardised database on affiliative and agonistic animal social behaviour. We describe the establishment of MacaqueNet, from the steps we took to start a large-scale collective, to the creation of a cross-species collaborative database and the implementation of data entry and retrieval protocols. We share MacaqueNet's component resources: an R package for data standardisation, website code, the relational database structure, a glossary and data sharing terms of use. With all these components openly accessible, MacaqueNet can act as a fully replicable template for future endeavours establishing large-scale collaborative comparative databases.}, } @article {pmid39760247, year = {2025}, author = {Lee, CE and Messer, LF and Wattiez, R and Matallana-Surget, S}, title = {Decoding Microbial Plastic Colonisation: Multi-Omic Insights Into the Fast-Evolving Dynamics of Early-Stage Biofilms.}, journal = {Proteomics}, volume = {25}, number = {7}, pages = {e202400208}, doi = {10.1002/pmic.202400208}, pmid = {39760247}, issn = {1615-9861}, support = {//Joint UKRI Natural Environment Research Council (NERC) and National Research Foundation (NRF) Singapore/ ; NE/V009621/1//UKRI NERC/NRF/ ; NRF-SEAP-2020-0001//UKRI NERC/NRF/ ; NE/S007342/1//NERC Scottish Universities Partnership for Environmental Research (SUPER) Doctoral Training Partnership (DTP)/ ; }, mesh = {*Biofilms/growth & development ; *Bacterial Proteins/metabolism/genetics ; Proteomics/methods ; Plastics/metabolism ; Proteome/metabolism/analysis ; Bacteria/genetics/metabolism/classification ; Microbiota/genetics/physiology ; Metagenome/genetics ; Polyethylene/metabolism ; Metagenomics/methods ; Multiomics ; }, abstract = {Marine plastispheres represent dynamic microhabitats where microorganisms colonise plastic debris and interact. Metaproteomics has provided novel insights into the metabolic processes within these communities; however, the early metabolic interactions driving the plastisphere formation remain unclear. This study utilised metaproteomic and metagenomic approaches to explore early plastisphere formation on low-density polyethylene (LDPE) over 3 (D3) and 7 (D7) days, focusing on microbial diversity, activity and biofilm development. In total, 2948 proteins were analysed, revealing dominant proteomes from Pseudomonas and Marinomonas, with near-complete metagenome-assembled genomes (MAGs). Pseudomonas dominated at D3, whilst at D7, Marinomonas, along with Acinetobacter, Vibrio and other genera became more prevalent. Pseudomonas and Marinomonas showed high expression of reactive oxygen species (ROS) suppression proteins, associated with oxidative stress regulation, whilst granule formation, and alternative carbon utilisation enzymes, also indicated nutrient limitations. Interestingly, 13 alkanes and other xenobiotic degradation enzymes were expressed by five genera. The expression of toxins, several type VI secretion system (TVISS) proteins, and biofilm formation proteins by Pseudomonas indicated their competitive advantage against other taxa. Upregulated metabolic pathways relating to substrate transport also suggested enhanced nutrient cross-feeding within the more diverse biofilm community. These insights enhance our understanding of plastisphere ecology and its potential for biotechnological applications.}, } @article {pmid39660842, year = {2025}, author = {Xu, C and Song, LY and Li, J and Zhang, LD and Guo, ZJ and Ma, DN and Dai, MJ and Li, QH and Liu, JY and Zheng, HL}, title = {MangroveDB: A Comprehensive Online Database for Mangroves Based on Multi-Omics Data.}, journal = {Plant, cell & environment}, volume = {48}, number = {5}, pages = {2950-2962}, doi = {10.1111/pce.15318}, pmid = {39660842}, issn = {1365-3040}, support = {//This work was supported by the Natural Science Foundation of China (NSFC) (32171740, 31870581); the National Key Research and Development Program of China (2017YFC0506102)/ ; }, mesh = {*Databases, Genetic ; Transcriptome ; Avicennia/genetics ; Gene Expression Profiling ; Computational Biology/methods ; Multiomics ; }, abstract = {Mangroves are dominant flora of intertidal zones along tropical and subtropical coastline around the world that offer important ecological and economic value. Recently, the genomes of mangroves have been decoded, and massive omics data were generated and deposited in the public databases. Reanalysis of multi-omics data can provide new biological insights excluded in the original studies. However, the requirements for computational resource and lack of bioinformatics skill for experimental researchers limit the effective use of the original data. To fill this gap, we uniformly processed 942 transcriptome data, 386 whole-genome sequencing data, and provided 13 reference genomes and 40 reference transcriptomes for 53 mangroves. Finally, we built an interactive web-based database platform MangroveDB (https://github.com/Jasonxu0109/MangroveDB), which was designed to provide comprehensive gene expression datasets to facilitate their exploration and equipped with several online analysis tools, including principal components analysis, differential gene expression analysis, tissue-specific gene expression analysis, GO and KEGG enrichment analysis. MangroveDB not only provides query functions about genes annotation, but also supports some useful visualization functions for analysis results, such as volcano plot, heatmap, dotplot, PCA plot, bubble plot, population structure, and so on. In conclusion, MangroveDB is a valuable resource for the mangroves research community to efficiently use the massive public omics datasets.}, } @article {pmid40168108, year = {2025}, author = {Wang, TY and Wu, YW and Lu, HJ and Liao, TY and Tai, JH and Huang, SP and Wang, FY and Yu, TH and Ting, CT and Chaw, SM and Wang, HY}, title = {Chromosome-Level Genome Assembly of the Loach Goby Rhyacichthys aspro Offers Insights Into Gobioidei Evolution.}, journal = {Molecular ecology resources}, volume = {}, number = {}, pages = {e14110}, doi = {10.1111/1755-0998.14110}, pmid = {40168108}, issn = {1755-0998}, support = {23-23//Biodiversity Research Center, Academia Sinica/ ; MOST 102-2311-B-001-019//National Science and Technology Council/ ; MOST 108-2621-B-001-002//National Science and Technology Council/ ; MOST 109-2311-B-002-023-MY3//National Science and Technology Council/ ; 113L7223//National Taiwan University/ ; }, abstract = {The percomorph fish clade Gobioidei is a suborder that comprises over 2200 species distributed in nearly all aquatic habitats. To understand the genetics underlying their species diversification, we sequenced and annotated the genome of the loach goby, Rhyacichthys aspro, an early-diverging group, and compared it with nine additional Gobioidei species. Within Gobioidei, the loach goby possesses the smallest genome at 594 Mb, and a rise in species diversity from early-diverging to more recently diverged lineages is mirrored by enlarged genomes and a higher presence of transposable elements (TEs), particularly DNA transposons. These DNA transposons are enriched in genic and regulatory regions and their copy number increase is strongly correlated with substitution rate, suggesting that DNA repair after transposon excision/insertion leads to nearby mutations. Consequently, the proliferation of DNA transposons might be the crucial driver of Gobioidei diversification and adaptability. The loach goby genome also points to mechanisms of ecological adaptation. It contains relatively few genes for lateral line development but an overrepresentation of synaptic function genes, with genes putatively under selection linked to synapse organisation and calcium signalling, implicating a sensory system distinct from other Gobioidei species. We also see an overabundance of genes involved in neurocranium development and renal function, adaptations likely connected to its flat morphology suited for strong currents and an amphidromous life cycle. Comparative analyses with hill-stream loaches and the European eel reveal convergent adaptations in body shape and saltwater balance. These findings shed new light on the loach goby's survival mechanisms and the broader evolutionary trends within Gobioidei.}, } @article {pmid40165685, year = {2025}, author = {Gu, Y and Meng, L and Wang, Y and Wu, Z and Pan, Y and Zhao, Y and Detto, M and Wu, J}, title = {Uncovering the role of solar radiation and water stress factors in constraining decadal intra-site spring phenology variability in diverse ecosystems across the Northern Hemisphere.}, journal = {The New phytologist}, volume = {}, number = {}, pages = {}, doi = {10.1111/nph.70104}, pmid = {40165685}, issn = {1469-8137}, support = {#2017804//Carbon Mitigation Initiative of Princeton University and NSF grant/ ; //HKU Seed Funding for Strategic Interdisciplinary Research Scheme/ ; #17305321//Hong Kong Research Grant Council General Research Fund/ ; #C5062-21GF//Hong Kong Research Grant Council Collaborative Research Fund/ ; #31922090//National Natural Science Foundation of China/ ; //Innovation and Technology Fund (funding support to State Key Laboratories of Agrobiotechnology)/ ; //HKU Science Faculty RAE Improvement Fund 2023-24/ ; }, abstract = {The spring phenology has advanced significantly over recent decades with climate change, impacting large-scale biogeochemical cycles, climate feedback, and other essential ecosystem processes. Although numerous prognostic models have been developed for spring phenology, regional analyses of the optimality (OPT) strategy model that incorporate environmental variables beyond temperature and photoperiod remain lacking. We investigated the roles of solar radiation (SR) and three water stress factors (precipitation (P), soil moisture, and vapor pressure deficit (VPD)) on spring phenology from 1982 to 2015 using the OPT model with Global Inventory Modeling and Mapping Studies NDVI3g dataset and environmental data from TerraClimate, CRU_TS, and Global Land Data Assimilation System across the Northern Hemisphere (> 30°N). Our results show that SR and water stress factors significantly impacted intrasite decadal spring phenology variability, with water stress factors dominant in grassland ecosystems while SR dominated in the rest of the ecosystem types. Enhanced models incorporating SR (OPT-S) and VPD (OPT-VPD) outperformed the original OPT model, likely due to improved representation of the adaptive strategy of spring phenology to optimize photosynthetic carbon gain while minimizing frost risk. Our research enhances the understanding of the key environmental drivers influencing decadal spring phenology variation in the Northern Hemisphere and contributes to more accurate forecasts of ecological responses to global environmental change.}, } @article {pmid40155956, year = {2025}, author = {van Kessel, SAM and Wielders, CCH and Schoffelen, AF and Verbon, A}, title = {Enhancing antimicrobial resistance surveillance and research: a systematic scoping review on the possibilities, yield and methods of data linkage studies.}, journal = {Antimicrobial resistance and infection control}, volume = {14}, number = {1}, pages = {25}, pmid = {40155956}, issn = {2047-2994}, mesh = {Humans ; *Drug Resistance, Bacterial ; Anti-Bacterial Agents/pharmacology/therapeutic use ; Antimicrobial Stewardship ; Information Storage and Retrieval ; }, abstract = {BACKGROUND: Surveillance data on antimicrobial resistance (AMR) determinants such as antibiotic use, prevalence of AMR, antimicrobial stewardship, and infection prevention and control are mostly analysed and reported separately, although they are inextricably linked to each other. The impact of surveillance and research can be enhanced by linking these data. This systematic scoping review aims to summarize the studies that link AMR data and evaluate whether they yield new results, implications, or recommendations for practice.

METHODS: For this review, data linkage is defined as the process of linking records, from at least two independent data sources on either (I) at least two AMR determinants or (II) one AMR determinant and one or more general population characteristics. Data linkage should be performed on the level of a certain entity which, in the context of this review, can encompass persons, healthcare institutes, geographical regions or countries. A systematic literature search was performed on February 7th 2025 in Embase.com, PubMed and Scopus to identify AMR data linkage studies.

RESULTS: Forty-eight articles were included in our review. Most data linkage studies used two data sources, and most studies were published in the last 5 years (n = 23 in 2020-2024). A predominance of studies linked data on geographical location, and thirteen studies linked data on individual patient level. Findings demonstrate that the majority of studies (43/48) had added value and provided recommendations for clinical practice and future policies or had suggestions for further research and surveillance. Additionally, data linkage studies appeared to be suitable for hypothesis generating. Several limitations were identified. Most studies had ecological designs, which are prone to ecological fallacy and unobserved confounding, making it hard to establish causality.

CONCLUSION: This systematic scoping review showed that AMR data linkage studies are increasingly performed. They have potential to gain a more comprehensive understanding of AMR dynamics by generating hypotheses, assisting in optimisation of surveillance, and interpretation of data in the context of guideline/policy development. To increase the added value of data linkage, more studies should be performed to improve knowledge on methodological approaches, data access, data management, and governance issues.

CLINICAL TRIAL NUMBER: Not applicable.}, } @article {pmid40036964, year = {2025}, author = {Jyoti, J and Hütt, MT}, title = {Evaluating changes in attractor sets under small network perturbations to infer reliable microbial interaction networks from abundance patterns.}, journal = {Bioinformatics (Oxford, England)}, volume = {41}, number = {4}, pages = {}, doi = {10.1093/bioinformatics/btaf095}, pmid = {40036964}, issn = {1367-4811}, mesh = {*Algorithms ; Humans ; *Microbial Interactions ; Microbiota ; Computational Biology/methods ; }, abstract = {MOTIVATION: Inferring microbial interaction networks from microbiome data is a core task of computational ecology. An avenue of research to create reliable inference methods is based on a stylized view of microbiome data, starting from the assumption that the presences and absences of microbiomes, rather than the quantitative abundances, are informative about the underlying interaction network. With this starting point, inference algorithms can be based on the notion of attractors (asymptotic states) in Boolean networks. Boolean network framework offers a computationally efficient method to tackle this problem. However, often existing algorithms operating under a Boolean network assumption, fail to provide networks that can reproduce the complete set of initial attractors (abundance patterns). Therefore, there is a need for network inference algorithms capable of reproducing the initial stable states of the system.

RESULTS: We study the change of attractors in Boolean threshold dynamics on signed undirected graphs under small changes in network architecture and show, how to leverage these relationships to enhance network inference algorithms. As an illustration of this algorithmic approach, we analyse microbial abundance patterns from stool samples of humans with inflammatory bowel disease (IBD), with colorectal cancer and from healthy individuals to study differences between the interaction networks of the three conditions. The method reveals strong diversity in IBD interaction networks. The networks are first partially deduced by an earlier inference method called ESABO, then we apply the new algorithm developed here, EDAME, to this result to generate a network that comes nearest to satisfying the original attractors.

Implementation code is freely available at https://github.com/Jojo6297/edame.git.}, } @article {pmid40086783, year = {2025}, author = {Yang, JZ and Li, JH and Liu, JL and Zhou, AD and Wang, H and Xie, XL and Zhang, KK and Wang, Q}, title = {Multiomics analysis revealed the effects of polystyrene nanoplastics at different environmentally relevant concentrations on intestinal homeostasis.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {372}, number = {}, pages = {126050}, doi = {10.1016/j.envpol.2025.126050}, pmid = {40086783}, issn = {1873-6424}, mesh = {Animals ; Mice ; *Polystyrenes/toxicity ; *Homeostasis/drug effects ; *Gastrointestinal Microbiome/drug effects ; Microplastics/toxicity ; Nanoparticles/toxicity ; Male ; Mice, Inbred C57BL ; Colon/drug effects ; Intestines/drug effects ; Multiomics ; }, abstract = {Nanoplastics pollution is a global issue, with the digestive tract being one of the first affected organs, requiring further research on its impact on intestinal health. This study involved orally exposing mice to polystyrene nanoplastics (PS-NPs) at doses of 0.1, 0.5, or 2.5 mg/d for 42 days. The effects on intestinal health were thoroughly assessed via microbiomics, metabolomics, transcriptomics, and molecular biology. Our study demonstrated that the administration of all three doses of PS-NPs resulted in increased colonic permeability, heightened colonic and peripheral inflammation, reduced levels of antimicrobial peptides, and shortened colonic length. These effects may be attributed to a reduction in the abundance of probiotic bacteria, such as Clostridia_UCG-014, Roseburia, and Akkermansia, alongside an increase in the abundance of the pathogenic bacterium Desulfovibrionaceae induced by PS-NPs. Furthermore, we underscored the crucial role of histidine metabolism in PS-NPs-induced colonic injury, characterized by a significant reduction of L-histidine, which is closely related to microbial ecological dysregulation. Corresponding to microbiota deterioration and metabolic dysregulation, transcriptome analysis revealed that PS-NPs may disrupt colonic immune homeostasis by activating the TLR4/MyD88/NF-κB/NLRP3 signaling pathway. In conclusion, this study provided novel insights into the mechanisms by which PS-NPs disrupt intestinal homeostasis through integrated multiomics analysis, revealing critical molecular pathway and providing a scientific basis for future risk assessment of nanoplastics exposure.}, } @article {pmid40155652, year = {2025}, author = {Rehbein, M and Escobari, B and Fischer, S and Güntsch, A and Haas, B and Matheisen, G and Perschl, T and Wieshuber, A and Engel, T}, title = {Quantitative and qualitative Data on historical Vertebrate Distributions in Bavaria 1845.}, journal = {Scientific data}, volume = {12}, number = {1}, pages = {525}, pmid = {40155652}, issn = {2052-4463}, support = {442032008//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 442032008//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 442032008//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 442032008//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 442032008//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; }, mesh = {*Vertebrates ; Germany ; Animals ; *Biodiversity ; History, 19th Century ; Ecosystem ; Conservation of Natural Resources ; Forests ; }, abstract = {Archival collections contain an underutilized wealth of biodiversity data, encapsulated in government files and other historical documents. In 1845, the Bavarian government conducted a comprehensive national survey on the occurrence of 44 selected vertebrate species across the country. The detailed expert responses from 119 forestry offices, totalling 520 handwritten pages, have been preserved in the Bavarian State Archives. In this study, we digitized, annotated, geographically referenced, and published these historical records, making them widely available as data for research and conservation planning. Our dataset, openly accessible through the Global Biodiversity Information Facility (GBIF) and Zenodo, contains 5,467 species occurrence records from 1845. Besides the binary presence/absence data, we have also published the original textual survey responses, which contain rich qualitative information, such as species abundances, population trends, habitats, forest management practices, and human-nature relationships. This information can be further processed and interpreted to address a range of questions in historical and contemporary ecology.}, } @article {pmid40144399, year = {2021}, author = {Boyes, D and Holland, PWH and , and , and , and , and , and , }, title = {The genome sequence of the poplar hawk-moth, Laothoe populi (Linnaeus, 1758).}, journal = {Wellcome open research}, volume = {6}, number = {}, pages = {237}, pmid = {40144399}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual female Laothoe populi (the poplar hawk-moth; Arthropoda; Insecta; Lepidoptera; Sphingidae). The genome sequence is 576 megabases in span. Most of the assembly is scaffolded into 29 chromosomal pseudomolecules, with the W and Z sex chromosome assembled.}, } @article {pmid40143245, year = {2025}, author = {Culot, A and Abriat, G and Furlong, KP}, title = {High-Performance Genome Annotation for a Safer and Faster-Developing Phage Therapy.}, journal = {Viruses}, volume = {17}, number = {3}, pages = {}, doi = {10.3390/v17030314}, pmid = {40143245}, issn = {1999-4915}, mesh = {*Genome, Viral ; *Bacteriophages/genetics/classification ; *Molecular Sequence Annotation ; *Computational Biology/methods ; *Phage Therapy/methods ; Humans ; }, abstract = {Phage therapy, which uses phages to decrease bacterial load in an ecosystem, introduces a multitude of gene copies (bacterial and phage) into said ecosystem. While it is widely accepted that phages have a significant impact on ecology, the mechanisms underlying their impact are not well understood. It is therefore paramount to understand what is released in the said ecosystem, to avoid alterations with difficult-to-predict-but potentially huge-consequences. An in-depth annotation of therapeutic phage genomes is therefore essential. Currently, the average published phage genome has only 20-30% functionally annotated genes, which represents a hurdle to overcome to deliver safe phage therapy, for both patients and the environment. This study aims to compare the effectiveness of manual versus automated phage genome annotation methods. Twenty-seven phage genomes were annotated using SEA-PHAGE and Rime Bioinformatics protocols. The structural (gene calling) and functional annotation results were compared. The results suggest that during the structural annotation step, the SEA-PHAGE method was able to identify an average of 1.5 more genes per phage (typically a frameshift gene) and 5.3 gene start sites per phage. Despite this difference, the impact on functional annotation appeared to be limited: on average, 1.2 genes per phage had erroneous functions, caused by the structural annotation. Rime Bioinformatics' tool (rTOOLS, v2) performed better at assigning functions, especially where the SEA-PHAGE methods assigned hypothetical proteins: 7.0 genes per phage had a better functional annotation on average, compared to SEA PHAGE's 1.7. The method comparison detailed in this article indicate that (1) manual structural annotation is marginally superior to rTOOLS automated structural annotation; (2) rTOOLS automated functional annotation is superior to manual functional annotation. Previously, the only way to obtain a high-quality annotation was by using manual protocols, such as SEA-PHAGES. In the relatively new field of phage therapy, which requires support to advance, manual work can be problematic due to its high cost. Rime Bioinformatics' rTOOLS software allows for time and money to be saved by providing high-quality genome annotations that are comparable to manual results, enabling a safer and faster-developing phage therapy.}, } @article {pmid40140737, year = {2025}, author = {Tahir Ul Qamar, M and Fatima, K and Rao, MJ and Tang, Q and Sadaqat, M and Ding, B and Chen, LL and Zhu, XT}, title = {Comparative genomics profiling of Citrus species reveals the diversity and disease responsiveness of the GLP pangenes family.}, journal = {BMC plant biology}, volume = {25}, number = {1}, pages = {388}, pmid = {40140737}, issn = {1471-2229}, mesh = {*Citrus/genetics ; *Multigene Family ; *Genome, Plant ; Genomics ; Plant Diseases/genetics/microbiology ; Plant Proteins/genetics/metabolism ; Genetic Variation ; Phylogeny ; Genes, Plant ; Gene Expression Regulation, Plant ; Disease Resistance/genetics ; }, abstract = {Citrus is an important nutritional fruit globally; however, its yield is affected by various stresses. This study presents the draft pangenome of Citrus, developed using 11 species to examine their genetic diversity and identify members of the germin-like proteins (GLPs) gene family involved in disease responsiveness. The developed sequence-based pangenome contains 954 Mb sequence and 74,755 genes. The comparative genomics analysis revealed the presence-absence variations (PAVs) among the Citrus genomes and species-specific protein-coding genes. Gene-based pangenome analysis revealed 4,936 new genes missing in the reference genome and highlighted the core and shell genes with putative functions in stress regulation. The pangenome-wide identification of GLP gene family members indicated the intraspecies diversity among the members across 11 genomes by analyzing their gene structure, motifs, and chromosomal distribution patterns. The synteny and evolutionary constraints analyses of Citrus GLPs provide detailed evidence of their evolutionary conservation and divergence. Further, the interaction, functional enrichment, and promoter analysis revealed their involvement in abiotic-, biotic-stress, signaling, and development-related pathways. The expression patterns of C. sinensis GLPs were studied in Huanglongbing (HLB) and Citrus canker disease. Several genes including CsGLPs1-2 and CsGLPs8-4 showed changes in expression patterns under both disease conditions. The qRT-PCR analysis revealed that these two genes were highly expressed in leaves infected with HLB disease across seven HLB-tolerant and susceptible citrus species. This Citrus pangenome and pangenes family study offers a comprehensive resource and new insights into the structural and functional diversity, identifying candidate genes that are important for future research to understand the stress-responsive mechanisms in Citrus.}, } @article {pmid40139213, year = {2025}, author = {Tam, CC and Young, SD and Harrison, S and Li, X and Litwin, AH}, title = {Theory-Based Social Media Intervention for Nonmedical Use of Prescription Opioids in Young Adults: Protocol for a Randomized Controlled Trial.}, journal = {JMIR research protocols}, volume = {14}, number = {}, pages = {e65847}, doi = {10.2196/65847}, pmid = {40139213}, issn = {1929-0748}, mesh = {Humans ; *Social Media ; Young Adult ; Male ; Female ; Analgesics, Opioid ; Adult ; Adolescent ; Opioid-Related Disorders/psychology ; }, abstract = {BACKGROUND: The nonmedical use of prescription opioids (NMUPO) in young adults in the United States is concerning and is robustly influenced by many psychosocial factors. Given the advantages of flexibility, wide coverage, and real-time responses and assessment, using social media appears to be a promising and innovative approach to delivering psychosocial intervention to young adults. However, few theory-based social media interventions are available for NMUPO targeting this at-risk population.

OBJECTIVE: Guided by the information-motivation-behavioral skills model, the proposed research aims to address critical gaps by theoretically exploring psychosocial content associated with NMUPO among young adults via formative assessment. These findings will then be used to develop and evaluate the feasibility and preliminary efficacy of a peer-led social media intervention to reduce NMUPO among young adults.

METHODS: The proposed study will comprise serial research activities. First, formative research will be conducted through semistructured interviews among 30 young adults engaged in NMUPO. Qualitative data will be synthesized using a pragmatic approach for identifying psychosocial content associated with NMUPO. Second, qualitative findings will be used for developing a peer-led social media intervention to reduce NMUPO among young adults by integrating promising psychotherapy principles and incorporating them with well-trained recovery coaches. Third, the social media intervention will be evaluated through a 12-week randomized controlled trial among 70 young adults (n=35, 50% in the intervention group and control group) engaged in NMUPO via mixed methods, including pre- and postintervention surveys, social media paradata (eg, time-series reactions to posts) collection, and ecological momentary assessment during the intervention. The control group will not receive an intervention but will complete the pre- and postintervention surveys. The primary outcomes will be feasibility, usability, and acceptability, while the secondary outcomes will be psychosocial and behavioral measures, such as past-3-month NMUPO, intention, psychological distress, self-efficacy, resilience, and coping strategies.

RESULTS: The proposed study was funded in May 2024. Social media campaigns have received responses from a total of 379 individuals, with 24 (6.3%) identified as eligible. As of February 10, 2025, we have completed formative interviews with 8 eligible participants.

CONCLUSIONS: The proposed study will be one of the first efforts to develop and deliver a theory-based peer-led intervention on social media, incorporating empirical findings on the psychosocial mechanism of NMUPO. The findings of the proposed study will provide valuable insights into opioid risk reduction for young adults through an innovative approach. If the tested trial is found to be feasible, the proposed study will contribute to future scaled-up and fully powered psychosocial interventions among young adults and other key populations at risk for NMUPO.

TRIAL REGISTRATION: ClincialTrials.gov NCT06469749; https://clinicaltrials.gov/study/NCT06469749.

DERR1-10.2196/65847.}, } @article {pmid40139065, year = {2025}, author = {Sfriso, AA and Juhmani, AS and Tomio, Y and Wedyan, M and Cunsolo, F and Forlani, G and Sfriso, A and Ferretti, G and Coltorti, M and Munari, C and Mistri, M}, title = {Microbial dynamics in seagrass restoration: Unveiling hidden indicators of ecological success.}, journal = {Marine environmental research}, volume = {208}, number = {}, pages = {107089}, doi = {10.1016/j.marenvres.2025.107089}, pmid = {40139065}, issn = {1879-0291}, abstract = {Seagrass transplantation significantly alters sediment microbial communities, shaping their composition and metabolic functions. One year after Zostera marina transplantation, the microbial community structure and functions at the recipient site began shifting toward those of the donor site. Key microbial taxa associated with seagrass meadow sediment, such as Firmicutes (Hungateiclostridiaceae, Defluviitaleaceae) and Campylobacterota (Sulfurovum), increased in abundance, correlating with sediment organic matter content and carbon availability. Four functional groups were identified, each with distinct metabolic roles: (1) Opportunistic Anaerobic Degraders, (2) Seagrass-Driven Carbon Recyclers, (3) Anaerobic Fermenters and Hydrocarbon Recyclers and (4) Oxygen-Linked Carbon and Sulfur Cyclers. The sediments of transplanted Z. marina meadows exhibited increased cellulolysis and aerobic chemoheterotrophy, along with a reduction in nitrogen metabolism one year post transplant. Despite these microbial shifts, sediment isotopic signatures remained indicative of algal biomass, suggesting an incomplete transition toward a mature seagrass environment. Multivariate analysis further confirmed that the microbial community at the recipient site had not yet fully converged with that of the donor meadow, indicating that complete sediment maturation may require longer timescales. These findings demonstrate that microbial community composition and functional annotations serve as early indicators of seagrass restoration success. Long-term monitoring is essential to track ecosystem recovery and assess the stabilization of sediment conditions.}, } @article {pmid40136166, year = {2025}, author = {Ferrari, YAC and Jesus, CVF and Batista, JFC and Silva, BEBD and Cavalcante, AB and Lima, CA}, title = {Secular trend of cervical cancer mortality in Brazil and regions.}, journal = {Ciencia & saude coletiva}, volume = {30}, number = {3}, pages = {e09962023}, doi = {10.1590/1413-81232025303.09962023}, pmid = {40136166}, issn = {1678-4561}, mesh = {Brazil/epidemiology ; Humans ; Female ; *Uterine Cervical Neoplasms/mortality ; Adult ; Middle Aged ; Mortality/trends ; Young Adult ; Aged ; Adolescent ; National Health Programs/organization & administration/trends ; }, abstract = {The scope of this study was to describe the secular trend of cervical cancer mortality in Brazil and its various regions from 1980 to 2021. It involved a populational and ecological study, based on data available at the Department of Informatics of the Unified Health System, using codes 180 and C53. Crude rates, age-specific rates, and age-standardized rates were calculated for the Brazilian and world population. The Average Annual Percent Change (AAPC) was obtained by trend analysis using the Joinpoint Regression Program, with a significance level of 0.05 and 95% confidence intervals (95%CI). There were 171,793 deaths from cervical cancer. In Brazil (AAPC -0.3; CI95%-1.0; 0.4), North (AAPC 0.6; 95%CI -0.1; 1.3) and South (AAPC 0.0; 95%CI -0.5; 0.5) the trends were stationary, increasing in the Northeast (AAPC 0.6; 95%CI 0.3; 0.8) and in the Midwest (AAPC -1.3; 95%CI -1.5; -1.1), and decreasing in the Southeast (AAPC -0.9; 95%CI -1.4; -0.5). Regional differences indicate that public policies need to be improved regarding women's access to a health system that offers adequate prevention, screening and treatment through management strategies that include the most vulnerable population.}, } @article {pmid40133528, year = {2025}, author = {Pekar, JE and Wang, Y and Wang, JC and Shao, Y and Taki, F and Forgione, LA and Amin, H and Clabby, T and Johnson, K and Torian, LV and Braunstein, SL and Pathela, P and Omoregie, E and Hughes, S and Suchard, MA and Vasylyeva, TI and Lemey, P and Wertheim, JO}, title = {Transmission dynamics of the 2022 mpox epidemic in New York City.}, journal = {Nature medicine}, volume = {}, number = {}, pages = {}, pmid = {40133528}, issn = {1546-170X}, support = {AI135992//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; AI153044//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; AI135995//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; AI153044//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; AI135995//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; AI153044//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; AI135995//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; AI135992//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; PS21-2102//U.S. Department of Health & Human Services | Centers for Disease Control and Prevention (CDC)/ ; PS21-2102//U.S. Department of Health & Human Services | Centers for Disease Control and Prevention (CDC)/ ; PS21-2102//U.S. Department of Health & Human Services | Centers for Disease Control and Prevention (CDC)/ ; PS21-2102//U.S. Department of Health & Human Services | Centers for Disease Control and Prevention (CDC)/ ; PS21-2102//U.S. Department of Health & Human Services | Centers for Disease Control and Prevention (CDC)/ ; PS21-2102//U.S. Department of Health & Human Services | Centers for Disease Control and Prevention (CDC)/ ; PS21-2102//U.S. Department of Health & Human Services | Centers for Disease Control and Prevention (CDC)/ ; PS21-2102//U.S. Department of Health & Human Services | Centers for Disease Control and Prevention (CDC)/ ; PS21-2102//U.S. Department of Health & Human Services | Centers for Disease Control and Prevention (CDC)/ ; PS21-2102//U.S. Department of Health & Human Services | Centers for Disease Control and Prevention (CDC)/ ; PS21-2102//U.S. Department of Health & Human Services | Centers for Disease Control and Prevention (CDC)/ ; }, abstract = {The 2022 global mpox epidemic was caused by transmission of MPXV clade IIb, lineage B.1 through sexual contact networks, with New York City (NYC) experiencing the first and largest outbreak in the United States. By performing phylogeographic analysis of MPXV genomes sampled from 757 individuals in NYC between April 2022 and April 2023, and 3,287 MPXV genomes sampled around the world, we identify over 200 introductions of MPXV into NYC with at least 84 leading to onward transmission. These infections primarily occurred among men who have sex with men, transgender women and nonbinary individuals. Through a comparative analysis with HIV in NYC, we find that both MPXV and HIV genomic cluster sizes are best fit by scale-free distributions, and that people in MPXV clusters are more likely to have previously received an HIV diagnosis and be a member of a recently growing HIV transmission cluster. We model MPXV transmission through sexual contact networks and show that highly connected individuals would be disproportionately infected at the start of an epidemic, which would likely result in the exhaustion of the most densely connected parts of the network, and, therefore, explain the rapid expansion and decline of the NYC outbreak. By coupling the genomic epidemiology of MPXV and HIV with epidemic modeling, we demonstrate that the transmission dynamics of MPXV in NYC can be understood by general principles of sexually transmitted pathogens.}, } @article {pmid40132633, year = {2025}, author = {Liu, X and Milesi, E and Fontsere, C and Owens, HL and Heinsohn, R and Gilbert, MTP and Crates, R and Nogués-Bravo, D and Morales, HE}, title = {Time-lagged genomic erosion and future environmental risks in a bird on the brink of extinction.}, journal = {Proceedings. Biological sciences}, volume = {292}, number = {2043}, pages = {20242480}, doi = {10.1098/rspb.2024.2480}, pmid = {40132633}, issn = {1471-2954}, support = {//The European Molecular Biology Organization/ ; //Mohamed bin Zayed Species Conservation Fund/ ; //Danish National Research Foundation/ ; /ERC_/European Research Council/International ; 25925//Villum Fonden/ ; }, mesh = {Animals ; *Endangered Species ; *Extinction, Biological ; Conservation of Natural Resources ; Ecosystem ; Genomics ; Biodiversity ; Genetic Variation ; Australia ; Birds/genetics ; Passeriformes/genetics/physiology ; }, abstract = {Global biodiversity is rapidly declining due to habitat degradation and genomic erosion, highlighting the urgent need to monitor endangered species and their genetic health. Temporal genomics and ecological modelling offer finer resolution than single-time-point measurements, providing a comprehensive view of species' recent and future trajectories. We investigated genomic erosion and environmental suitability in the critically endangered regent honeyeater (Anthochaera phrygia) by sequencing whole genomes of historical and modern specimens and building multi-temporal species distribution models (SDMs) across the last century. The species has declined from hundreds of thousands of individuals to fewer than 300 over the past 100 years. SDMs correctly predicted known patterns of local extinction in southeast Australia. Our demographic reconstructions revealed a gradual population decline from 2000 to 2500 years ago, sharply accelerating in the last 500 years due to climate variability and habitat loss. Despite this substantial demographic collapse, the regent honeyeater has lost only 9% of its genetic diversity, with no evidence of inbreeding or connectivity loss. Also, it exhibits higher diversity than many other threatened bird species. Forward-in-time genomic simulations indicate that this time lag between population decline and genetic diversity loss conceals the risk of ongoing genomic erosion into a future of rapidly degrading environmental suitability. Our work underscores the need for targeted conservation efforts and continuous genetic monitoring to prevent species extinction.}, } @article {pmid40096239, year = {2025}, author = {Dinnage, R and Kleineberg, M}, title = {Generative AI extracts ecological meaning from the complex three dimensional shapes of bird bills.}, journal = {PLoS computational biology}, volume = {21}, number = {3}, pages = {e1012887}, pmid = {40096239}, issn = {1553-7358}, mesh = {Animals ; *Birds/anatomy & histology ; *Imaging, Three-Dimensional/methods ; *Artificial Intelligence ; Beak/anatomy & histology ; Computational Biology ; Deep Learning ; }, abstract = {Data on the three dimensional shape of organismal morphology is becoming increasingly available, and forms part of a new revolution in high-throughput phenomics that promises to help understand ecological and evolutionary processes that influence phenotypes at unprecedented scales. However, in order to meet the potential of this revolution we need new data analysis tools to deal with the complexity and heterogeneity of large-scale phenotypic data such as 3D shapes. In this study we explore the potential of generative Artificial Intelligence to help organize and extract meaning from complex 3D data. Specifically, we train a deep representational learning method known as DeepSDF on a dataset of 3D scans of the bills of 2,020 bird species. The model is designed to learn a continuous vector representation of 3D shapes, along with a 'decoder' function, that allows the transformation from this vector space to the original 3D morphological space. We find that approach successfully learns coherent representations: particular directions in latent space are associated with discernible morphological meaning (such as elongation, flattening, etc.). More importantly, learned latent vectors have ecological meaning as shown by their ability to predict the trophic niche of the bird each bill belongs to with a high degree of accuracy. Unlike existing 3D morphometric techniques, this method has very little requirements for human supervised tasks such as landmark placement, increasing it accessibility to labs with fewer labour resources. It has fewer strong assumptions than alternative dimension reduction techniques such as PCA. Once trained, 3D morphology predictions can be made from latent vectors very computationally cheaply. The trained model has been made publicly available and can be used by the community, including for finetuning on new data, representing an early step toward developing shared, reusable AI models for analyzing organismal morphology.}, } @article {pmid40136165, year = {2025}, author = {Aquino, ÉC and Borowicc, SL and Alves-Souza, SN and Teixeira, RA and Ishitani, LH and Malta, DC and Morais Neto, OL}, title = {Distribution of garbage codes in the Mortality Information System, Brazil, 2000 to 2020.}, journal = {Ciencia & saude coletiva}, volume = {30}, number = {3}, pages = {e09442023}, doi = {10.1590/1413-81232025303.09442023}, pmid = {40136165}, issn = {1678-4561}, mesh = {Brazil/epidemiology ; Humans ; *Information Systems/statistics & numerical data/standards ; *Cause of Death/trends ; Linear Models ; Mortality/trends ; Time Factors ; }, abstract = {The analysis of the causes of death is essential to understand the main problems that affect the health level of the population of a region or country. The garbage codes (GC) provide little useful information about causes of death. This study aims to identify the proportion of GC among the deaths registered and to analyze their temporal distribution in Brazil from 2000 to 2020. It's an ecological time-series study of the evolution of the proportion of GC in Brazil. Time series analysis was performed using segmented linear regression models (joinpoint). Between 2000 and 2020, 39.9% of deaths that occurred in Brazil were coded with GC. Between 2000 and 2007, there was a continuous and persistent reduction in the proportion of GC (APC -2.1; P < 0.001). Between 2007 and 2015, there continued to be a reduction, albeit to a lesser extent (APC = -0.7; P = 0.013). Between 2015 and 2018, there was no significant trend of the proportion of GC (APC = -2.3; P = 0.172), which persisted from 2018 (APC 3.2; P < 0.079). Although a reduction in the proportion of GC in Brazil was observed until 2018, this trend did not persist after that year. Reducing the proportion of GC allows managers to plan health policies more adequately for the population.}, } @article {pmid40073274, year = {2025}, author = {Aucello, R and Pernice, S and Tortarolo, D and Calogero, RA and Herrera-Rincon, C and Ronchi, G and Geuna, S and Cordero, F and Lió, P and Beccuti, M}, title = {UnifiedGreatMod: a new holistic modelling paradigm for studying biological systems on a complete and harmonious scale.}, journal = {Bioinformatics (Oxford, England)}, volume = {41}, number = {3}, pages = {}, pmid = {40073274}, issn = {1367-4811}, support = {//Ministero dell'Univerisita' e della Ricerca/ ; }, mesh = {*Models, Biological ; Humans ; Software ; Escherichia coli/metabolism ; Systems Biology/methods ; Computational Biology/methods ; Computer Simulation ; }, abstract = {MOTIVATION: Computational models are crucial for addressing critical questions about systems evolution and deciphering system connections. The pivotal feature of making this concept recognizable from the biological and clinical community is the possibility of quickly inspecting the whole system, bearing in mind the different granularity levels of its components. This holistic view of system behaviour expands the evolution study by identifying the heterogeneous behaviours applicable, e.g. to the cancer evolution study.

RESULTS: To address this aspect, we propose a new modelling paradigm, UnifiedGreatMod, which allows modellers to integrate fine-grained and coarse-grained biological information into a unique model. It enables functional studies by combining the analysis of the system's multi-level stable states with its fluctuating conditions. This approach helps to investigate the functional relationships and dependencies among biological entities. This is achieved, thanks to the hybridization of two analysis approaches that capture a system's different granularity levels. The proposed paradigm was then implemented into the open-source, general modelling framework GreatMod, in which a graphical meta-formalism is exploited to simplify the model creation phase and R languages to define user-defined analysis workflows. The proposal's effectiveness was demonstrated by mechanistically simulating the metabolic output of Escherichia coli under environmental nutrient perturbations and integrating a gene expression dataset. Additionally, the UnifiedGreatMod was used to examine the responses of luminal epithelial cells to Clostridium difficile infection.

GreatMod https://qbioturin.github.io/epimod/, epimod_FBAfunctions https://github.com/qBioTurin/epimod_FBAfunctions, first case study E. coli  https://github.com/qBioTurin/Ec_coli_modelling, second case study C. difficile  https://github.com/qBioTurin/EpiCell_CDifficile.}, } @article {pmid40125538, year = {2025}, author = {Broad, GR and Holt, S and Sivess, L and Boyes, D and , and , and , and , and , and , and , and , }, title = {The genome sequence of the Scorched Wing moth, Plagodis dolabraria (Linnaeus, 1767).}, journal = {Wellcome open research}, volume = {10}, number = {}, pages = {111}, doi = {10.12688/wellcomeopenres.23761.1}, pmid = {40125538}, issn = {2398-502X}, abstract = {We present a genome assembly from a male specimen of Plagodis dolabraria (Scorched Wing; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence has a total length of 939.07 megabases. Most of the assembly (99.59%) is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 16.97 kilobases in length.}, } @article {pmid40121238, year = {2025}, author = {Kelliher, JM and Rodriguez, FE and Johnson, LYD and Roux, S and Smith, M and Clum, A and Lynch, W and Bias, CH and Finks, SS and Keenum, I and Kiledal, EA and Lin, HA and Longley, R and McDonald, R and Pitot, TM and Rodríguez-Ramos, J and Shen, J and Sprockett, DD and Swift, J and Yadav, A and Eloe-Fadrosh, EA}, title = {Quantifying the impact of workshops promoting microbiome data standards and data stewardship.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {9887}, pmid = {40121238}, issn = {2045-2322}, support = {The work conducted by the National Microbiome Data Collaborative (https://ror.org/05cwx3318) is supported by the Genomic Science Program in the U.S. Department of Energy, Office of Science, Office of Biological and Environmental Research (BER) under contract numbers DE-AC02-05CH11231 (LBNL), 89233218CNA000001 (LANL), and DE-AC05-76RL01830 (PNNL).//U.S. Department of Energy/ ; }, mesh = {*Microbiota ; Humans ; Surveys and Questionnaires ; Research Personnel ; }, abstract = {The field of microbiome research continues to grow at a rapid pace, with multi-omics approaches becoming widely used to interrogate diverse microbiome samples. However, due to lagging awareness and implementation of standards and data stewardship, many datasets are produced that are not comparable, reproducible, or reusable. In 2021, the National Microbiome Data Collaborative launched its Ambassador Program, which utilizes a community-learning model to annually train a cohort of early-career researchers in microbiome data stewardship best practices. These Ambassadors then host workshops and other events to communicate these themes to their respective microbiome research communities. To quantify the impact of this learning model for promoting awareness of and experience with microbiome data, we conducted a survey of workshop participants from events hosted by the 2023 Ambassador cohort. The 2023 cohort of 13 National Microbiome Data Collaborative Ambassadors collectively hosted 21 events, reaching over 550 researchers. The Ambassadors distributed an anonymous post-workshop survey to their event participants to quantify the effectiveness of the training materials, the workshop format, and the thematic content. From the 21 events, survey results were successfully collected for 15 of those events from a total of 122 researchers. Overall, 122 participants working with a range of microbiome types and from a variety of institutions responded to the survey and reported overwhelmingly positive experiences with the workshop content and materials, with 98% of respondents reporting that they gained knowledge from the event. Participants across the events also reported an increase in their post-workshop understanding of metadata standards, principles for microbiome data management and reporting, and the importance of standardization in microbiome data processing. Participants also expressed a willingness to apply what they learned about microbiome data stewardship to their own research. The results of this study demonstrate the effectiveness of hands-on workshops and community-learning for communicating data stewardship best practices to microbiome researchers. The lessons learned and details about the implementation of this cohort-based learning model contained herein are intended to assist other groups in their efforts to create or improve similar learning strategies.}, } @article {pmid40121181, year = {2025}, author = {Eaton, WD and McGee, KM and Glahn, A and Lemenze, A and Soteropoulos, P}, title = {Use of a logging road in a Costa Rican forest changes the composition and stability of soil microbial decomposer communities, and the conversion of organic carbon into biomass.}, journal = {Journal of applied microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1093/jambio/lxaf075}, pmid = {40121181}, issn = {1365-2672}, abstract = {AIMS: The effects of a tropical forest logging road on soil C and N, and the compositions of Actinobacteria, Acidobacteria, and wood rot/lignin-degrading fungal (WRT/LD) decomposer communities were evaluated.

METHODS AND RESULTS: Soils from a healthy Costa Rican old growth forest before Hurricane Otto and from an adjacent, recently formed logging road built after Hurricane Otto were collected over 4 years and assessed for C and N metrics, and characteristics of the 3 decomposer communities determined by Illumina amplicon sequencing methods. The Logging Road negatively impacted the soil total organic C, respiration, biomass C, qCO2, and total N, while the Actinobacterial and Acidobacterial communities changed from stable compositions of copiotrophic taxa in the rich forest soil to stable compositions of oligotrophic taxa in the poor logging road soil, and the wood rot/lignin degrading (WRT/LD) community changed from stable compositions of copiotrophic taxa in the forest soils to an unstable community of oligotrophic taxa with almost no overlap in genera between Logging Road soils.

CONCLUSIONS: The logging road negatively influenced 3 decomposer communities and associated C and N metrics, with the two bacterial communities taxonomically stabilizing, but the fungal community taxonomically diverging into an unstable composition over time. Monitoring efforts are on-going to provide local forest land managers with potential indicators of soil ecosystem damage and recovery.}, } @article {pmid40121109, year = {2025}, author = {Hanly, J and Anon, and Perret, J and Khan, A}, title = {Disability in ecology and evolution.}, journal = {Trends in ecology & evolution}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tree.2025.02.005}, pmid = {40121109}, issn = {1872-8383}, } @article {pmid40120582, year = {2025}, author = {Pinkert, S and Reuber, V and Krug, LM and Heidrich, L and Rehling, F and Brandl, R and Farwig, N}, title = {Burrowing facilitated the survival of mammals in harsh and fluctuating climates.}, journal = {Current biology : CB}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.cub.2025.02.064}, pmid = {40120582}, issn = {1879-0445}, abstract = {Species' ability to cope with climatic instability varies greatly, influenced by factors such as dispersal, physiological adaptations, and phylogenetic conservatism. Here, we investigate how burrowing behavior, a key component of species' endurance strategies and ecosystem functioning, shaped the contemporary patterns of species richness and range size as well as the diversification of mammalian lineages. Analyzing 4,407 terrestrial mammal species, excluding bats, combined with novel trait data on 3,096 species, we reveal contrasting responses to climatic factors between burrowing and non-burrowing species. Burrowing lineages are disproportionately species-rich at lower temperatures and productivity. Both range size and species richness steeply increase with climate seasonality in burrowing species as opposed to non-burrowing species. The proportion of burrowing species increases with latitude, with regions above 20°, especially those exhibiting greater Pleistocene temperature changes, being almost exclusively composed of burrowing species. Trait conservatism, higher net diversification rates, and Eocene peak diversification provide the evolutionary context for these contemporary patterns, underscoring the role of burrowing for mammalian radiations into temperate climates. Moreover, the lower extinction rate of burrowing species and peak diversification at the Cretaceous-Paleogene (K-Pg) boundary support the longstanding hypothesis that burrowing behavior promoted survival during the "impact winter" that marks the replacement of non-avian dinosaurs by mammals. Our study highlights the potential of readily available trait information for understanding the ecological and evolutionary processes that shape species distributions through space and time. The careful integration of divergent environmental constraints bears vast improvements for forecasts of species' responses to climatic changes and global models of biodiversity patterns.}, } @article {pmid40049043, year = {2025}, author = {Huang, JN and Gao, CC and Ren, HY and Wen, B and Wang, ZN and Gao, JZ and Chen, ZZ}, title = {Multi-omics association pattern between gut microbiota and host metabolism of a filter-feeding fish in situ exposed to microplastics.}, journal = {Environment international}, volume = {197}, number = {}, pages = {109360}, doi = {10.1016/j.envint.2025.109360}, pmid = {40049043}, issn = {1873-6750}, mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Microplastics ; *Water Pollutants, Chemical/metabolism/toxicity ; *Carps/microbiology ; Liver/metabolism ; Zebrafish ; Multiomics ; }, abstract = {Microplastics (MPs) are widespread in water environments and can affect gut microbiota and host metabolism of fish, but whether changes in host metabolism under MPs are mediated by gut microbiota remains unclear. Here, silver carp, a filter-feeding fish with important ecological functions, was in-situ exposure to environmentally relevant MPs. Multi-omics analysis and fecal microbiota transplantation were used to reveal the metabolic responses of carp along gut-liver-muscle axis. After three months of in situ exposure to MPs, community structure of gut microbiota of carp was reshaped, and five dominate phyla were significantly changed, including increased Cyanobacteria, Chloroflexi and Planctomycetota but decreased Firmicutes and Fusobacteriota. Weighted gene co-expression network analysis was further performed between these phyla and liver transcription spectrum, showing that the hub gene module contained up-regulated hppD, maiA and plg and activated ubiquinone and other terpenoid-quinone biosynthesis and phenylalanine metabolism. By fecal microbiota transplantation, the key gene module associated with core microbiota phyla of carp was verified in germ-free zebrafish. Interestingly, up-regulated hppD, maiA and plg and enriched phenylalanine metabolism were also observed in this module. Subsequently, metabolome performed in carp liver also shared activated phenylalanine metabolism, including increased trans-cinnamic acid and L-tyrosine. Furthermore, high-associated mapping showed that the differentially expressed metabolites (gamma-aminobutyric acid, ornithine and L-serine) related to amino acid metabolism in carp muscle were significantly accompanied with increased L-tyrosine in its liver. Overall, MPs exposure could change gut microbiome of silver carp and alter host metabolism especially amino acid metabolism along the gut-liver-muscle axis.}, } @article {pmid39833389, year = {2025}, author = {Schroeder, MW and Frumkin, MR and Mace, RA}, title = {Proof-of-concept for integrating multimodal digital health assessments into lifestyle interventions for older adults with dementia risk factors.}, journal = {Journal of behavioral medicine}, volume = {48}, number = {2}, pages = {373-384}, pmid = {39833389}, issn = {1573-3521}, support = {1 K23 AG075257-01/AG/NIA NIH HHS/United States ; 1 K23 AG075257-01/AG/NIA NIH HHS/United States ; }, mesh = {Humans ; Aged ; Female ; Male ; *Actigraphy/instrumentation ; *Dementia/psychology/therapy ; *Ecological Momentary Assessment ; *Mindfulness ; Pilot Projects ; Life Style ; Middle Aged ; Risk Factors ; Proof of Concept Study ; Aged, 80 and over ; Sleep ; Digital Health ; }, abstract = {Multimodal digital health assessments overcome the limitations of patient-reported outcomes by allowing for continuous and passive monitoring but remain underutilized in older adult lifestyle interventions for brain health. Therefore, we aim to (1) report ecological momentary assessment (EMA) and ActiGraph adherence among older adults during a lifestyle intervention; and (2) use dynamic data collected via EMA and ActiGraph to examine person-specific patterns of mindfulness, steps, and sleep throughout the intervention. We analyzed EMA and ActiGraph data from a pilot study of the 8-week My Healthy Brain program (N = 10) lifestyle group for older adults (60+) with subjective cognitive decline. EMA adherence metrics included proportion of EMA completed and the proportion of days with at least 10 mindfulness minutes. ActiGraph GT9X adherence metrics included the number of valid wear days (≥ 7 h) and the number of days participants achieved their step goal. We used linear mixed-effects models to examine person-specific patterns of step count, sleep efficiency, and mindfulness practice. On average, participants completed 39 of the 49 possible EMAs (80%) during the program. ActiGraph adherence was slightly higher than EMA (M = 61.40 days, 87.71%). Participants achieved the daily mindfulness goal (10 min/day) and step goal on 46.32% and 55.10% of days, respectively. Dynamic data revealed that on average, participant step counts increased by approximately 16.5 steps per day (b = 16.495, p = 0.002). However, some participants exhibited no changes while improvements made by other participants returned to baseline levels of activity. There was substantial heterogeneity in trajectories of mindfulness practice and sleep efficiency. EMA and ActiGraph are feasible for older adults enrolled in dementia risk reduction lifestyle interventions. Future studies are needed to better understand how mechanisms of lifestyle behaviors captured by EMA and ActiGraph are related to cognitive outcomes in older adults.}, } @article {pmid38582819, year = {2025}, author = {Li, M and Wu, L and Shi, Y and Wu, L and Afzal, F and Jia, Y and Huang, Y and Hu, B and Chen, J and Huang, J}, title = {Bioinformatics and Functional Analysis of OsASMT1 Gene in Response to Abiotic Stress.}, journal = {Biochemical genetics}, volume = {63}, number = {2}, pages = {1527-1540}, pmid = {38582819}, issn = {1573-4927}, support = {2023NSFSC1270//The Sichuan Natural Science Foundation Project/ ; SKL-KF202316//The Open Project Program of State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China/ ; }, mesh = {*Stress, Physiological ; *Computational Biology/methods ; *Oryza/genetics/metabolism ; *Plant Proteins/genetics/metabolism ; *Gene Expression Regulation, Plant ; Sodium Chloride/pharmacology ; Salt Stress ; }, abstract = {The study aimed to elucidate the functional characteristics of OsASMT1 gene under copper (Cu) or sodium chloride (NaCl) stress. Bioinformatics scrutiny unveiled that OsASMT1 is situated on chromosome 9. Its protein architecture, comprising dimerization and methyltransferase domains, showed significant similarities to OsASMT2 and OsASMT3. High expression in roots and panicles, along with abiotic stress putative cis-regulatory elements in the promoter, indicated potential stress responsiveness. Real-time quantitative PCR confirmed OsASMT1 induction under Cu and NaCl stress in rice. Surprisingly, yeast expressing OsASMT1 did not exhibit enhanced resistance to abiotic stresses. The results of subcellular localization analysis indicated that OsASMT1 plays a role in the cytoplasm. While OsASMT1 responded to Cu and NaCl stress in rice, its heterologous expression in yeast failed to confer abiotic stress resistance, highlighting the need for further investigation of its functional implications.}, } @article {pmid40115327, year = {2025}, author = {Hesson, JC and Haba, Y and McBride, CS and Sheerin, E and Mathers, TC and Paulini, M and Pointon, DB and Torrance, JW and Sadasivan Baby, C and Wood, JMD and , and , and McCarthy, SA and Lawniczak, MKN and Makunin, A}, title = {A chromosomal reference genome sequence for the northern house mosquito, Culex pipiens form pipiens, Linnaeus, 1758.}, journal = {Wellcome open research}, volume = {10}, number = {}, pages = {107}, pmid = {40115327}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual female Culex pipiens sensu stricto (the northern house mosquito; Arthropoda; Insecta; Diptera; Culicidae), from a wild population in Sweden. The genome sequence is 533 megabases in span. Most of the assembly is scaffolded into three chromosomal pseudomolecules. The complete mitochondrial genome was also assembled and is 15.6 kilobases in length.}, } @article {pmid40108281, year = {2025}, author = {Dong, J and Dai, W and Xu, J and Zhang, H and Li, Y and Xie, F}, title = {Impact and elastic modulus of coal mining on terrestrial ecosystems.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {9454}, pmid = {40108281}, issn = {2045-2322}, support = {CSC202306420029//China Scholarship Council/ ; Lumeidike (2022) No.14//Key Research Projects of Shandong Bureau of Coal Geology/ ; }, abstract = {The energy consumption structure is gradually evolving into a "diversified energy structure" against the backdrop of the global implementation of energy-saving and low-carbon policies. Coal, as the main energy source in China, is difficult to change in the short term, given the characteristics of China's energy and resource endowments, as well as the actual social and economic development at the present stage. Nevertheless, coal mining inevitably leads to a range of ecological issues. Identifying the impact of coal mining on terrestrial ecosystems and adopting resilient recovery measures are crucial prerequisites for advancing green coal mining efforts and attaining carbon peaking and carbon neutrality goals. Using China's open-pit coal mining as a case study: (1) the research examines the fundamental attributes and evolving patterns of spatial distribution among these mines within the country. Furthermore, it delineates the life cycle stages and distinctive features of the five principal open-pit coal mines. The life cycle of a coal mining area is divided into four distinct development phases: the initial phase, the accelerated phase, the stable phase, and the declining phase. The spatial relationship between the life cycle stages of coal mining and ecosystem succession is elucidated by examining the evolutionary types of ecosystems within coal mine area. In the accelerated and stable development phase, the adverse effects of coal mining on the ecosystem are in a long-term increasing trend, causing the key elements of the ecosystem to gradually surpass their threshold values. The ecosystem is out of balance, severely damaged, and gradually undergoing degradation or extreme degradation. The types of ecological succession in coal mining areas can be categorized as follows: terrestrial succession leading to a new terrestrial ecosystem, terrestrial to aquatic ecosystem transitions, or the development of an amphibious symbiotic ecosystem. (2) The research quantitatively assessed the impact of surface coal mining on terrestrial ecosystems by utilizing remote sensing data in conjunction with coal production information. In 2022, the affected areas of the five major open-pit coal mines due to coal mining activities amounted to approximately 0.02% of China's total land area. Meanwhile, the nationwide affected areas of all open-pit coal mines combined reached to approximately 0.13% of China's land area. Open-pit coal mining activities have a significant impact on the surface. (3) By incorporating the ecological resilience theory, we establish a model for the ecosystem's elastic modulus in coal mining areas, taking into account landscape diversity, vegetation coverage, land type, and climate factors, which are based on the concepts of elastic strength and elastic limit. A conceptual model for recognizing ecological thresholds in coal mining areas is developed by incorporating the comprehensive integrity index of the ecosystem. The comprehensive integrity of the ecosystem within a coal mining area undergoes significant alterations as it crosses three distinct ecological thresholds: the elastic point, the yield point, and the mutational point. There should be a corresponding constant (or constant interval) at the three ecological thresholds of ecosystem resilience, the elastic point, the yield point, and the mutational point, which is closely related to the scale of mining operations, mining technology, and the service life in coal mining areas. The established models for identifying ecological thresholds and the resilience modulus degree serve as both theoretical references and practical bases for managing the progress and trends of ecosystem changes during coal resource extraction, making ecological restoration in coal mine areas more target-oriented and specific.}, } @article {pmid40108248, year = {2025}, author = {Mammides, C and Ieronymidou, C and Papadopoulos, H}, title = {An ecoacoustic dataset collected on the island of Cyprus in the Mediterranean Basin biodiversity hotspot.}, journal = {Scientific data}, volume = {12}, number = {1}, pages = {461}, pmid = {40108248}, issn = {2052-4463}, support = {101090273//European Commission (EC)/ ; }, mesh = {Cyprus ; *Biodiversity ; Animals ; *Acoustics ; Vocalization, Animal ; Mediterranean Region ; Islands ; }, abstract = {There is growing interest in using novel technologies for large-scale biodiversity monitoring. Passive acoustic monitoring (PAM) represents a promising approach for surveying vocalizing animals. However, further development of PAM methods is needed to improve their accuracy. The availability of extensive ecoacoustic datasets from biodiverse areas can facilitate this development. In this study, we present a large ecoacoustic dataset (1.58 TB) collected at sixty-one study sites on the island of Cyprus between March and May 2023. The dataset comprises >313,000 audio files, representing over 5,200 hours of recordings. It can be used for a range of applications, such as developing and refining species identification algorithms, acoustic indices, and protocols for processing acoustic data to exclude non-focal sounds, e.g., those produced by human activities. It can also be used to explore fundamental ecological questions. To facilitate its use, the complete dataset has been made available on the Hugging Face repository and the ARBIMON platform, operated by Rainforest Connection[TM], which offers a range of free tools for ecoacoustic analyses.}, } @article {pmid40067093, year = {2025}, author = {Zhang, G and Ristola, P and Su, H and Kumar, B and Zhang, B and Hu, Y and Elliot, MG and Drobot, V and Zhu, J and Staal, J and Larralde, M and Wang, S and Yi, Y and Yu, H}, title = {BioArchLinux: community-driven fresh reproducible software repository for life sciences.}, journal = {Bioinformatics (Oxford, England)}, volume = {41}, number = {3}, pages = {}, doi = {10.1093/bioinformatics/btaf106}, pmid = {40067093}, issn = {1367-4811}, mesh = {*Software ; *Computational Biology/methods ; *Biological Science Disciplines/methods ; Programming Languages ; Reproducibility of Results ; }, abstract = {MOTIVATION: The BioArchLinux project was initiated to address challenges in bioinformatics software reproducibility and freshness. Relying on Arch Linux's user-driven ecosystem, we aim to create a comprehensive and continuously updated repository for life sciences research.

RESULTS: BioArchLinux provides a PKGBUILD-based system for seamless software packaging and maintenance, enabling users to access the latest bioinformatics tools across multiple programming languages. The repository includes Docker images, Windows Subsystem for Linux (WSL) support, and Junest for nonroot environments, enhancing accessibility across platforms. Although being developed and maintained by a small core team, BioArchLinux is a fast-growing bioinformatics repository that offers a participatory and community-driven environment.

The repository, documentation, and tools are freely available at https://bioarchlinux.org and https://github.com/BioArchLinux. Users and developers are encouraged to contribute and expand this open-source initiative.}, } @article {pmid40102624, year = {2025}, author = {Rank, M and Kather, A and Wilke, D and Steib-Bauert, M and Kern, WV and Röder, I and de With, K}, title = {Limitations of estimating antibiotic resistance using German hospital consumption data - a comprehensive computational analysis.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {9244}, pmid = {40102624}, issn = {2045-2322}, mesh = {Germany/epidemiology ; Humans ; *Anti-Bacterial Agents/therapeutic use/pharmacology ; *Hospitals ; Drug Resistance, Microbial ; Drug Resistance, Bacterial ; Neural Networks, Computer ; }, abstract = {For almost a century, antibiotics have played an important role in the treatment of infectious diseases. However, the efficacy of these very drugs is now threatened by the development of resistances, which pose major challenges to medical professionals and decision-makers. Thereby, the consumption of antibiotics in hospitals is an important driver that can be targeted directly. To illuminate the relation between consumption and resistance depicts a very important step in this procedure. With the help of comprehensive ecological and clinical data, we applied a variety of different computational approaches ranging from classical linear regression to artificial neural networks to analyze antibiotic resistance in Germany. These mathematical and statistical models demonstrate that the amount and particularly the structure of currently available data sets lead to contradictory results and do, therefore, not allow for profound conclusions. More effort and attention on both data collection and distribution is necessary to overcome this problem. In particular, our results suggest that at least monthly or quarterly antibiotic use and resistance data at the department and ward level for each hospital (including application route and type of specimen) are needed to reliably determine the extent to which antibiotic consumption influences resistance development.}, } @article {pmid39066964, year = {2025}, author = {Árvay, J and Hauptvogl, M and Demková, L and Jančo, I and Jakabová, S and Mleczek, M}, title = {GIS-based Visualization of Elemental Distribution in Neoboletus Luridiformis Fruiting Body.}, journal = {Biological trace element research}, volume = {203}, number = {4}, pages = {2271-2283}, pmid = {39066964}, issn = {1559-0720}, support = {1/0602/22//Vedecká Grantová Agentúra MŠVVaŠ SR a SAV/ ; }, mesh = {*Fruiting Bodies, Fungal/chemistry/metabolism ; Trace Elements/analysis ; Geographic Information Systems ; Agaricales/chemistry/metabolism ; }, abstract = {The fruiting body of Neoboletus luridiformis (Scarletina bolete) mushroom was used to determine the level of bioconcentration and subsequent distribution of seventeen elements (Ag, Al, Ba, Ca, Cd, Cr, Cu, Fe, K, Mg, Mn, Na, Ni, Pb, Se, Sr, and Zn). A two-centimeter-thick vertical section of the entire fruit body was divided into 101 partial sub-samples where the contents of the studied elements were determined using ICP OES. The actual distribution of the elements in the fruiting body profile was visualized using a GIS interpolation method resulting in distribution maps. The study provides valuable insights into the distribution patterns of 17 elements within the fruiting body of N. luridiformis. Based on the visualization of the elemental content, the determined elements can be divided into three categories. Elements accumulated primarily (i) in the cap (Al, Ag, Ca, Cd, Cu, Fe, K, Mg, Ni, and Zn), (ii) in the stipe (Ba, Mn, Na, Pb, and Se), and (iii) elements with non-specific distribution (Cr and Sr). Since such detailed information supported by graphical visualization has not been published to date, the information in this study will help to better understand the accumulation and distribution of elements within the fruiting bodies of wild as well as cultivated mushroom species.}, } @article {pmid40099017, year = {2025}, author = {Sivell, O and Sivell, D and Mitchell, R and Webb, J and , and , and , and , and , and , and , }, title = {The genome sequence of the Small Red Damselfly, Ceriagrion tenellum (de Villers, 1789).}, journal = {Wellcome open research}, volume = {10}, number = {}, pages = {79}, pmid = {40099017}, issn = {2398-502X}, abstract = {We present a genome assembly from a male specimen of Ceriagrion tenellum (Small Red Damselfly; Arthropoda; Insecta; Odonata; Coenagrionidae). The genome sequence has a total length of 2,077.00 megabases. Most of the assembly (99.28%) is scaffolded into 14 chromosomal pseudomolecules, including the X sex chromosome. The mitochondrial genome has also been assembled and is 17.21 kilobases in length.}, } @article {pmid39938845, year = {2025}, author = {Rakkannan, G and Mohanty, AK and Das, II and Nayak, S and Sahoo, L and Kumar, R and Rasal, A and Rather, MA and Ahmad, I and Sundaray, JK}, title = {Triflumezopyrim induced oxidative stress, DNA damage and apoptosis on Labeo rohita: Insights from Bioinformatics, Histopathological and Molecular approaches.}, journal = {International journal of biological macromolecules}, volume = {304}, number = {Pt 2}, pages = {140911}, doi = {10.1016/j.ijbiomac.2025.140911}, pmid = {39938845}, issn = {1879-0003}, mesh = {Animals ; *Oxidative Stress/drug effects ; *DNA Damage/drug effects ; *Apoptosis/drug effects ; Computational Biology/methods ; Carps/metabolism/genetics ; Water Pollutants, Chemical/toxicity ; Molecular Docking Simulation ; Cyprinidae ; 8-Hydroxy-2'-Deoxyguanosine/metabolism ; Liver/drug effects/pathology/metabolism ; }, abstract = {Triflumezopyrim is a novel mesoionic pesticide used in Asian rice fields to control brown plant hopper, which can reach aquatic environments through drift during application or surface runoff. Thus, this study aimed to investigate the effect of chronic exposure of sub-lethal concentrations of triflumezopyrim (2.468 ppm, 1.480 ppm, and 0.740 ppm) on freshwater carp, Labeo rohita.This study encompassed a multi-pronged approach, including molecular docking studies to elucidate the interactions between triflumezopyrim and selected proteins, an assessment of 8-OHdG (8-hydroxy-2-deoxyguanosine) activity to gauge DNA damage, histopathological examinations to identify cellular alterations, and expression of genes involved in oxidative stress, DNA repair, and apoptosis in L. rohita. We observed dose-dependent responses in 8-OHdG activity and the expression of select genes, with higher concentrations of triflumezopyrim yielding more pronounced transcriptional alterations. Notably, histopathological examinations of liver and brain tissues vividly portrayed the impact of triflumezopyrim on L. rohita. These findings contribute to the assessment of biological toxicity and the environmental footprint left by chemical pollutants such as triflumezopyrim. The study emphasizes the crucial role of monitoring histopathological alterations, 8-OHdG activity and gene expression changes as potential biomarkers for assessing exposures to triflumezopyrim. This research provides valuable insights into the ecological implications of triflumezopyrim in aquatic ecosystems.}, } @article {pmid24192328, year = {2013}, author = {Weston, ED and Whitfield, DP and Travis, JM and Lambin, X}, title = {When do young birds disperse? Tests from studies of golden eagles in Scotland.}, journal = {BMC ecology}, volume = {13}, number = {}, pages = {42}, pmid = {24192328}, issn = {1472-6785}, mesh = {*Animal Distribution ; Animals ; Geographic Information Systems ; Raptors/*physiology ; Scotland ; }, abstract = {BACKGROUND: Dispersal comprises three broad stages - departure from the natal or breeding locations, subsequent travel, and settlement. These stages are difficult to measure, and vary considerably between sexes, age classes, individuals and geographically. We used tracking data from 24 golden eagles, fitted with long-lived GPS satellite transmitters as nestlings, which we followed during their first year. We estimated the timing of emigration from natal sites using ten previously published methods. We propose and evaluate two new methods. The first of these uses published ranging distances of parents as a measure of the natal home range, with the requirement that juveniles must exceed it for a minimum of 10 days (a literature-based measure of the maximum time that a juvenile can survive without food from its parents). The second method uses the biggest difference in the proportion of locations inside and outside of the natal home range smoothed over a 30 day period to assign the point of emigration. We used the latter as the standard against which we compared the ten published methods.

RESULTS: The start of golden eagle dispersal occurred from 39 until 250 days after fledging (based on method 12). Previously published methods provided very different estimates of the point of emigration with a general tendency for most to apparently assign it prematurely. By contrast the two methods we proposed provided very similar estimates for the point of emigration that under visual examination appeared to fit the definition of emigration much better.

CONCLUSIONS: We have used simple methods to decide when an individual has dispersed - they are rigorous and repeatable. Despite one method requiring much more information, both methods provided robust estimates for when individuals emigrated at the start of natal dispersal. Considerable individual variation in recorded behaviour appears to account for the difficulty capturing the point of emigration and these results demonstrate the potential pitfalls associated with species exhibiting complex dispersal behaviour. We anticipate that coupled with the rapidly increasing availability of tracking data, our new methods will, for at least some species, provide a far simpler and more biologically representative approach to determine the timing of emigration.}, } @article {pmid23587026, year = {2013}, author = {Hardisty, A and Roberts, D and , and Addink, W and Aelterman, B and Agosti, D and Amaral-Zettler, L and Ariño, AH and Arvanitidis, C and Backeljau, T and Bailly, N and Belbin, L and Berendsohn, W and Bertrand, N and Caithness, N and Campbell, D and Cochrane, G and Conruyt, N and Culham, A and Damgaard, C and Davies, N and Fady, B and Faulwetter, S and Feest, A and Field, D and Garnier, E and Geser, G and Gilbert, J and Grosche, and Grosser, D and Hardisty, A and Herbinet, B and Hobern, D and Jones, A and de Jong, Y and King, D and Knapp, S and Koivula, H and Los, W and Meyer, C and Morris, RA and Morrison, N and Morse, D and Obst, M and Pafilis, E and Page, LM and Page, R and Pape, T and Parr, C and Paton, A and Patterson, D and Paymal, E and Penev, L and Pollet, M and Pyle, R and von Raab-Straube, E and Robert, V and Roberts, D and Robertson, T and Rovellotti, O and Saarenmaa, H and Schalk, P and Schaminee, J and Schofield, P and Sier, A and Sierra, S and Smith, V and van Spronsen, E and Thornton-Wood, S and van Tienderen, P and van Tol, J and Tuama, ÉÓ and Uetz, P and Vaas, L and Vignes Lebbe, R and Vision, T and Vu, D and De Wever, A and White, R and Willis, K and Young, F}, title = {A decadal view of biodiversity informatics: challenges and priorities.}, journal = {BMC ecology}, volume = {13}, number = {}, pages = {16}, pmid = {23587026}, issn = {1472-6785}, mesh = {Animals ; *Biodiversity ; Computational Biology/*instrumentation/*methods ; Ecosystem ; Humans ; Information Dissemination ; }, abstract = {Biodiversity informatics plays a central enabling role in the research community's efforts to address scientific conservation and sustainability issues. Great strides have been made in the past decade establishing a framework for sharing data, where taxonomy and systematics has been perceived as the most prominent discipline involved. To some extent this is inevitable, given the use of species names as the pivot around which information is organised. To address the urgent questions around conservation, land-use, environmental change, sustainability, food security and ecosystem services that are facing Governments worldwide, we need to understand how the ecosystem works. So, we need a systems approach to understanding biodiversity that moves significantly beyond taxonomy and species observations. Such an approach needs to look at the whole system to address species interactions, both with their environment and with other species.It is clear that some barriers to progress are sociological, basically persuading people to use the technological solutions that are already available. This is best addressed by developing more effective systems that deliver immediate benefit to the user, hiding the majority of the technology behind simple user interfaces. An infrastructure should be a space in which activities take place and, as such, should be effectively invisible.This community consultation paper positions the role of biodiversity informatics, for the next decade, presenting the actions needed to link the various biodiversity infrastructures invisibly and to facilitate understanding that can support both business and policy-makers. The community considers the goal in biodiversity informatics to be full integration of the biodiversity research community, including citizens' science, through a commonly-shared, sustainable e-infrastructure across all sub-disciplines that reliably serves science and society alike.}, } @article {pmid23497177, year = {2013}, author = {Tonk, L and Bongaerts, P and Sampayo, EM and Hoegh-Guldberg, O}, title = {SymbioGBR: a web-based database of Symbiodinium associated with cnidarian hosts on the Great Barrier Reef.}, journal = {BMC ecology}, volume = {13}, number = {}, pages = {7}, pmid = {23497177}, issn = {1472-6785}, mesh = {Animals ; Anthozoa/*microbiology ; Australia ; *Coral Reefs ; DNA, Ribosomal Spacer/genetics ; *Databases, Genetic ; Dinoflagellida/classification/*genetics ; Genetic Markers ; Internet ; Sequence Analysis, DNA ; Symbiosis ; User-Computer Interface ; }, abstract = {BACKGROUND: The algal endosymbionts (genus Symbiodinium) associated with scleractinian corals (and other reef invertebrates) have received a lot of research attention in the past decade, particularly as certain host-symbiont associations appear more affected by increasing seawater temperatures than others. With the rapid accumulation of information on the diversity of Symbiodinium, it is becoming increasingly difficult to compare newly acquired Symbiodinium data with existing data to detect patterns of host-symbiont specificity on broader spatial scales. The lack of a general consensus on the classification of Symbiodinium species coupled with the variety of different markers used to identify the genus Symbiodinium (ITS1, ITS2, LSU D1/D2, chloroplast 23S rDNA and psbA minicircle) further complicate direct comparison.

DESCRIPTION: The SymbioGBR database compiles all currently available Symbiodinium sequences and associated host information of data collected from the Great Barrier Reef into a single relational database that is accessible via a user-friendly, searchable web-based application (http://www.SymbioGBR.org). SymbioGBR allows users to query Symbiodinium types or sequences sourced from various genetic markers (e.g. ITS1, ITS2, LSU D1/D2 and chloroplast 23S) and invertebrate host species to explore their reported associations. In addition, as the database includes sequence information of multiple genetic markers, it allows cross-referencing between conventional (e.g. ITS2 region) and novel markers that exhibit low intragenomic variability (e.g. psbA region). Finally, the database is based on the collection details of individual specimens. Such host-symbiont associations can be assessed quantitatively and viewed in relation to their environmental and geographic context.

CONCLUSIONS: The SymbioGBR database provides a comprehensive overview of Symbiodinium diversity and host-associations on the Great Barrier Reef. It provides a quick, user-friendly means to compare newly acquired data on Symbiodinium (e.g. raw sequences or characterized Symbiodinium types) with previous data on the diversity of invertebrate host-symbiont associations on the GBR. The inclusion of psbAncr sequence information allows for validation of widely used ITS1/ITS2 markers and their ability to accurately identify relevant sequences. Most importantly, centralization of sequence information from multiple genetic markers will aid the classification of Symbiodinium species diversity and allow researchers to easily compare patterns of host-Symbiodinium associations.}, } @article {pmid23173946, year = {2012}, author = {Renaud, AK and Savage, J and Adamowicz, SJ}, title = {DNA barcoding of Northern Nearctic Muscidae (Diptera) reveals high correspondence between morphological and molecular species limits.}, journal = {BMC ecology}, volume = {12}, number = {}, pages = {24}, pmid = {23173946}, issn = {1472-6785}, mesh = {Animals ; Cluster Analysis ; *DNA Barcoding, Taxonomic ; *Databases, Genetic ; Female ; Genes, Insect ; Male ; Muscidae/*classification/genetics ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {BACKGROUND: Various methods have been proposed to assign unknown specimens to known species using their DNA barcodes, while others have focused on using genetic divergence thresholds to estimate "species" diversity for a taxon, without a well-developed taxonomy and/or an extensive reference library of DNA barcodes. The major goals of the present work were to: a) conduct the largest species-level barcoding study of the Muscidae to date and characterize the range of genetic divergence values in the northern Nearctic fauna; b) evaluate the correspondence between morphospecies and barcode groupings defined using both clustering-based and threshold-based approaches; and c) use the reference library produced to address taxonomic issues.

RESULTS: Our data set included 1114 individuals and their COI sequences (951 from Churchill, Manitoba), representing 160 morphologically-determined species from 25 genera, covering 89% of the known fauna of Churchill and 23% of the Nearctic fauna. Following an iterative process through which all specimens belonging to taxa with anomalous divergence values and/or monophyly issues were re-examined, identity was modified for 9 taxa, including the reinstatement of Phaonia luteva (Walker) stat. nov. as a species distinct from Phaonia errans (Meigen). In the post-reassessment data set, no distinct gap was found between maximum pairwise intraspecific distances (range 0.00-3.01%) and minimum interspecific distances (range: 0.77-11.33%). Nevertheless, using a clustering-based approach, all individuals within 98% of species grouped with their conspecifics with high (>95%) bootstrap support; in contrast, a maximum species discrimination rate of 90% was obtained at the optimal threshold of 1.2%. DNA barcoding enabled the determination of females from 5 ambiguous species pairs and confirmed that 16 morphospecies were genetically distinct from named taxa. There were morphological differences among all distinct genetic clusters; thus, no cases of cryptic species were detected.

CONCLUSIONS: Our findings reveal the great utility of building a well-populated, species-level reference barcode database against which to compare unknowns. When such a library is unavailable, it is still possible to obtain a fairly accurate (within ~10%) rapid assessment of species richness based upon a barcode divergence threshold alone, but this approach is most accurate when the threshold is tuned to a particular taxon.}, } @article {pmid23095476, year = {2012}, author = {Sherwood, AR and Wang, N and Carlile, AL and Neumann, JM and Wolfgruber, TK and Presting, GG}, title = {The Hawaiian Freshwater Algal Database (HfwADB): a laboratory LIMS and online biodiversity resource.}, journal = {BMC ecology}, volume = {12}, number = {}, pages = {22}, pmid = {23095476}, issn = {1472-6785}, mesh = {*Biodiversity ; *Chlorophyta ; *Clinical Laboratory Information Systems ; *Cyanobacteria ; *Databases, Factual ; *Diatoms ; Fresh Water ; Hawaii ; Internet ; *Rhodophyta ; User-Computer Interface ; }, abstract = {BACKGROUND: Biodiversity databases serve the important role of highlighting species-level diversity from defined geographical regions. Databases that are specially designed to accommodate the types of data gathered during regional surveys are valuable in allowing full data access and display to researchers not directly involved with the project, while serving as a Laboratory Information Management System (LIMS). The Hawaiian Freshwater Algal Database, or HfwADB, was modified from the Hawaiian Algal Database to showcase non-marine algal specimens collected from the Hawaiian Archipelago by accommodating the additional level of organization required for samples including multiple species.

DESCRIPTION: The Hawaiian Freshwater Algal Database is a comprehensive and searchable database containing photographs and micrographs of samples and collection sites, geo-referenced collecting information, taxonomic data and standardized DNA sequence data. All data for individual samples are linked through unique 10-digit accession numbers ("Isolate Accession"), the first five of which correspond to the collection site ("Environmental Accession"). Users can search online for sample information by accession number, various levels of taxonomy, habitat or collection site. HfwADB is hosted at the University of Hawaii, and was made publicly accessible in October 2011. At the present time the database houses data for over 2,825 samples of non-marine algae from 1,786 collection sites from the Hawaiian Archipelago. These samples include cyanobacteria, red and green algae and diatoms, as well as lesser representation from some other algal lineages.

CONCLUSIONS: HfwADB is a digital repository that acts as a Laboratory Information Management System for Hawaiian non-marine algal data. Users can interact with the repository through the web to view relevant habitat data (including geo-referenced collection locations) and download images of collection sites, specimen photographs and micrographs, and DNA sequences. It is publicly available at http://algae.manoa.hawaii.edu/hfwadb/.}, } @article {pmid21929792, year = {2011}, author = {Gonzalez, SC and Soto-Centeno, JA and Reed, DL}, title = {Population distribution models: species distributions are better modeled using biologically relevant data partitions.}, journal = {BMC ecology}, volume = {11}, number = {}, pages = {20}, pmid = {21929792}, issn = {1472-6785}, mesh = {Animals ; Geographic Information Systems ; Mice/genetics/*physiology ; *Models, Biological ; *Population Dynamics ; ROC Curve ; Southeastern United States ; Statistics as Topic ; }, abstract = {BACKGROUND: Predicting the geographic distribution of widespread species through modeling is problematic for several reasons including high rates of omission errors. One potential source of error for modeling widespread species is that subspecies and/or races of species are frequently pooled for analyses, which may mask biologically relevant spatial variation within the distribution of a single widespread species. We contrast a presence-only maximum entropy model for the widely distributed oldfield mouse (Peromyscus polionotus) that includes all available presence locations for this species, with two composite maximum entropy models. The composite models either subdivided the total species distribution into four geographic quadrants or by fifteen subspecies to capture spatially relevant variation in P. polionotus distributions.

RESULTS: Despite high Area Under the ROC Curve (AUC) values for all models, the composite species distribution model of P. polionotus generated from individual subspecies models represented the known distribution of the species much better than did the models produced by partitioning data into geographic quadrants or modeling the whole species as a single unit.

CONCLUSIONS: Because the AUC values failed to describe the differences in the predictability of the three modeling strategies, we suggest using omission curves in addition to AUC values to assess model performance. Dividing the data of a widespread species into biologically relevant partitions greatly increased the performance of our distribution model; therefore, this approach may prove to be quite practical and informative for a wide range of modeling applications.}, } @article {pmid17900366, year = {2007}, author = {Blundell, AG and Burkey, TV}, title = {A database of schemes that prioritize sites and species based on their conservation value: focusing business on biodiversity.}, journal = {BMC ecology}, volume = {7}, number = {}, pages = {10}, pmid = {17900366}, issn = {1472-6785}, mesh = {Animals ; *Biodiversity ; Birds ; Conservation of Natural Resources/*methods ; *Databases, Factual ; Plants ; Wetlands ; }, abstract = {BACKGROUND: Biodiversity offsets are conservation projects used mainly by business to counterbalance the environmental impacts of their operations, with the aim of achieving a net neutral or even beneficial outcome for biodiversity. Companies considering offsets need to know: (1) if there are areas of such biological importance that no impact is acceptable, and outside of these no-go areas, (2) the relative importance of biodiversity in the impacted site versus the site(s) proposed for protection, to ensure that the offset is of equal or greater status than that lost through the company's operations. We compiled a database of 40 schemes that use various methods to assess conservation priorities, and we examined if the schemes would allow companies to answer the above questions.

DESCRIPTION: Overall, schemes tend to be designed to guide conservation organizations in their own priority setting or they categorize species based on conservation status. Generally, the schemes do not provide all the necessary information for offsets because they operate at a broad spatial scale or with low spatial resolution, which make it difficult to assess sites at the project level. Furthermore, most schemes do not explicitly incorporate threat, which we consider key to assessing whether offsets protect habitats or species that would otherwise be lost (i.e., provide additionality). The schemes are useful, however, for identifying the major conservation issues in different ecosystems around the globe.

CONCLUSION: Companies can proceed by first avoiding, reducing, and mitigating impacts, and then using existing schemes to identify i) no-go areas and ii) appropriate offsets to compensate for any unavoidable loss in biodiversity. If existing schemes are inadequate, then companies should use integrated conservation planning techniques to define offset options within the region of their operations.}, } @article {pmid17144922, year = {2006}, author = {Johnson, K and Neville, TB and Neville, P}, title = {GIS habitat analysis for lesser prairie-chickens in southeastern New Mexico.}, journal = {BMC ecology}, volume = {6}, number = {}, pages = {18}, pmid = {17144922}, issn = {1472-6785}, mesh = {Agriculture ; Animals ; *Conservation of Natural Resources ; *Ecosystem ; *Galliformes ; *Geographic Information Systems ; Herbicides ; New Mexico ; }, abstract = {BACKGROUND: We conducted Geographic Information System (GIS) habitat analyses for lesser prairie-chicken (LPCH, Tympanuchus pallidicinctus) conservation planning. The 876,799 ha study area included most of the occupied habitat for the LPCH in New Mexico. The objectives were to identify and quantify: 1. suitable LPCH habitat in New Mexico, 2. conversion of native habitats, 3. potential for habitat restoration, and 4. unsuitable habitat available for oil and gas activities.

RESULTS: We found 16% of suitable habitat (6% of the study area) distributed in 13 patches of at least 3,200 ha and 11% of suitable habitat (4% of the study area) distributed in four patches over 7,238 ha. The area converted from native vegetation types comprised 17% of the study area. Ninety-five percent of agricultural conversion occurred on private lands in the northeastern corner of the study area. Most known herbicide-related conversions (82%) occurred in rangelands in the western part of the study area, on lands managed primarily by the US Bureau of Land Management (BLM). We identified 88,190 ha (10% of the study area) of habitats with reasonable restoration potential. Sixty-two percent of the primary population area (PPA) contained occupied, suitable, or potentially suitable habitat, leaving 38% that could be considered for oil and gas development.

CONCLUSION: Although suitable LPCH habitat appears at first glance to be abundant in southeastern New Mexico, only a fraction of apparently suitable vegetation types constitute quality habitat. However, we identified habitat patches that could be restored through mesquite control or shin-oak reintroduction. The analysis also identified areas of unsuitable habitat with low restoration potential that could be targeted for oil and gas exploration, in lieu of occupied, high-quality habitats. Used in combination with GIS analysis and current LPCH population data, the habitat map represents a powerful conservation and management tool.}, } @article {pmid40088887, year = {2025}, author = {Hartley, GA and Okhovat, M and Hoyt, SJ and Fuller, E and Pauloski, N and Alexandre, N and Alexandrov, I and Drennan, R and Dubocanin, D and Gilbert, DM and Mao, Y and McCann, C and Neph, S and Ryabov, F and Sasaki, T and Storer, JM and Svendsen, D and Troy, W and Wells, J and Core, L and Stergachis, A and Carbone, L and O'Neill, RJ}, title = {Centromeric transposable elements and epigenetic status drive karyotypic variation in the eastern hoolock gibbon.}, journal = {Cell genomics}, volume = {}, number = {}, pages = {100808}, doi = {10.1016/j.xgen.2025.100808}, pmid = {40088887}, issn = {2666-979X}, abstract = {Great apes have maintained a stable karyotype with few large-scale rearrangements; in contrast, gibbons have undergone a high rate of chromosomal rearrangements coincident with rapid centromere turnover. Here, we characterize fully assembled centromeres in the eastern hoolock gibbon, Hoolock leuconedys (HLE), finding a diverse group of transposable elements (TEs) that differ from the canonical alpha-satellites found across centromeres of other apes. We find that HLE centromeres contain a CpG methylation centromere dip region, providing evidence that this epigenetic feature is conserved in the absence of satellite arrays. We uncovered a variety of atypical centromeric features, including protein-coding genes and mismatched replication timing. Further, we identify duplications and deletions in HLE centromeres that distinguish them from other gibbons. Finally, we observed differentially methylated TEs, topologically associated domain boundaries, and segmental duplications at chromosomal breakpoints, and thus propose that a combination of multiple genomic attributes with propensities for chromosome instability shaped gibbon centromere evolution.}, } @article {pmid40087683, year = {2025}, author = {Mbuba, E and Mañas-Chavernas, N and Moore, SJ and Ruzige, PD and Kobe, D and Moore, J and Philipo, R and Kisoka, N and Pontiggia, G and Chacky, F and Mwalimu, CD and Cattin, PC and Wolleb, J and Sandkuehler, R and Ross, A}, title = {Estimating the hole surface area of insecticide-treated nets using image analysis, manual hole counting and exact hole measurements.}, journal = {Malaria journal}, volume = {24}, number = {1}, pages = {82}, pmid = {40087683}, issn = {1475-2875}, mesh = {*Image Processing, Computer-Assisted/methods ; *Insecticide-Treated Bednets/statistics & numerical data ; Mosquito Control/methods ; Animals ; Insecticides ; }, abstract = {BACKGROUND: The physical integrity of insecticidal-treated nets (ITNs) is important for creating a barrier against host-seeking mosquitoes and, therefore, influences people's perception of the net's effectiveness and their willingness to use it. Monitoring the physical integrity of ITNs over time provides information for replenishment schedules and purchasing decisions. Currently, the assessment of physical integrity of ITNs is conducted by manually counting holes and estimating their size to class the net as functional or not. This approach is laborious to routinely conduct during field surveys of ITNs. Automated image analysis may provide a rapid assessment of the physical integrity of ITNs but it is not known if the images can capture sufficient information. As a first step, this study aimed to assess the agreement between estimated hole surface areas derived from (1) manually segmented images, (2) manual hole counting compared to (3) ground truth obtained by calibrated close-up shots of individual holes.

METHODS: The physical integrity of 75 ITNs purposely selected from an ongoing study was assessed by manual hole counting, image analysis and ground truth. For the image analysis, a graphical user interface was developed and used for the segmentation of holes visible in photographs taken from each side of the net. The hole surface area was then computed from this data. The agreement between the estimates from image analysis and manual hole counting was compared to the ground truth using the Bland-Altman method.

RESULTS: There was substantial agreement between the manually segmented image analysis estimates and the ground truth hole surface areas. The overall bias was small, with a mean ratio of the hole surface area from image analysis to the ground truth of 0.70, and the 95% limits of agreement ranging from 0.35 to 1.38. Manual hole counting underestimated the hole surface area compared to the ground truth, particularly among nets with holes above 10 cm in diameter.

CONCLUSION: Images coupled with manual segmentation contain sufficient information to calculate hole surface area. This lays the groundwork for incorporating automatic hole detection, and then assessing whether this method will offer a fast and objective method for routine assessment of physical integrity of ITNs. While the WHO method underestimated the hole surface area, it remains useful in classifying nets as either serviceable or too torn because the cut-off is specific to this method.}, } @article {pmid40086213, year = {2025}, author = {Dong, L and Mu, L and Huang, X}, title = {Exploring lipid remodeling and antioxidant responses in Chlorella pyrenoidosa exposed to streptomycin sulfate stress.}, journal = {Food chemistry}, volume = {478}, number = {}, pages = {143565}, doi = {10.1016/j.foodchem.2025.143565}, pmid = {40086213}, issn = {1873-7072}, abstract = {Microalgae, particularly Chlorella pyrenoidosa, are valuable for bioactive compounds and biofuel production, but antibiotic use in large-scale cultivation can impact growth and biochemical productivity. This study examines the physiological and molecular responses of C. pyrenoidosa to streptomycin sulfate (STRS) stress. STRS exposure significantly reduced cell density (15.31 × 10[6] to 11.20 × 10[6] cells/mL, p < 0.001) and photosynthetic efficiency (Fv/fm from 0.45 to 0.15). Multi-omics analysis revealed a dual adaptive strategy: (1) activation of antioxidant defenses, including upregulated superoxide dismutase (SOD, 19-fold) and ascorbate peroxidase (APX, 32-fold); (2) lipid remodeling, with increased α-linolenic acid (ALA) content (17.43 % to 21.25 %, p < 0.001) due to β-oxidation downregulation. These findings enhance understanding of microalgal stress adaptation and highlight potential applications in biofuel and food/feed industries. Future studies should optimize genetic and cultivation strategies to enhance these adaptive traits while ensuring ecological sustainability.}, } @article {pmid40074806, year = {2025}, author = {Tang, Y and Hu, H and Chen, S and Hao, B and Xu, X and Zhu, H and Zhan, W and Zhang, T and Hu, H and Chen, G}, title = {Multi-omics analysis revealed the novel role of NQO1 in microenvironment, prognosis and immunotherapy of hepatocellular carcinoma.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {8591}, pmid = {40074806}, issn = {2045-2322}, support = {24B0413//the Scientific Research Project of the Hunan Provincial Department of Education/ ; 2024JJ7455//Natural Science Foundation of Hunan Province/ ; 20224310NHYCG04//University of South China Clinical Research 4310 Program/ ; 20224310NHYCG01//University of South China Clinical Research 4310 Program/ ; 82473965//National Natural Science Foundation of China/ ; 2023JJ50156//the Natural Science Foundation of Hunan Province/ ; 202250045223//Science and technology innovation Program of Hengyang City/ ; ZYYD2024CG17//Central Government Guided Local Science and Technology Development Fund Project in Xinjiang Uygur Autonomous Region/ ; 2024WK4008//Hunan Province Innovation Ecological Construction Plan Science and Technology Assistance Project in Xinjiang Uygur Autonomous Region/ ; SYTG-Y202429//Health Technology Promotion Project in Xinjiang Uygur Autonomous Region/ ; }, mesh = {*Carcinoma, Hepatocellular/therapy/genetics/immunology/pathology ; *NAD(P)H Dehydrogenase (Quinone)/genetics/metabolism ; Humans ; *Liver Neoplasms/therapy/genetics/immunology/pathology ; *Tumor Microenvironment/immunology ; Prognosis ; *Immunotherapy/methods ; Gene Expression Regulation, Neoplastic ; Biomarkers, Tumor/genetics ; Male ; Female ; Nomograms ; Tumor-Associated Macrophages/immunology/metabolism ; Middle Aged ; Multiomics ; }, abstract = {NAD(P)H dehydrogenase quinone 1 (NQO1) is overexpressed in various cancers and is strongly associated with an immunosuppressive microenvironment and poor prognosis. In this study, we explored the role of NQO1 in the microenvironment, prognosis and immunotherapy of Hepatocellular carcinoma (HCC) using multi-omics analysis and machine learning. The results revealed that NQO1 was significantly overexpressed in HCC cells. NQO1[+]HCC cells were correlated with poor prognosis and facilitated tumor-associated macrophages (TAMs) polarization to M2 macrophages. We identified core NQO1-related genes (NRGs) and developed the NRGs-related risk-scores in hepatocellular carcinoma (NRSHC). The comprehensive nomogram integrating NRSHC, age, and pathological tumor-node-metastasis (pTNM) Stage achieved an area under the curve (AUC) above 0.7, demonstrating its accuracy in predicting survival outcomes and immunotherapy responses of HCC patients. High-risk patients exhibited worse prognoses but greater sensitivity to immunotherapy. Additionally, a web-based prediction tool was designed to enhance clinical utility. In conclusion, NQO1 may play a critical role in M2 polarization and accelerates HCC progression. The NRSHC model and accompanying tools offer valuable insights for personalized HCC treatment.}, } @article {pmid40074756, year = {2025}, author = {Wei, P and Song, Y and Tian, R and Wang, Y and Chen, J and Yuan, Z and Zhou, W}, title = {CaecilianTraits, an individual level trait database of Caecilians worldwide.}, journal = {Scientific data}, volume = {12}, number = {1}, pages = {428}, pmid = {40074756}, issn = {2052-4463}, support = {32170445//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {*Amphibians/classification ; Animals ; *Databases, Factual ; Biodiversity ; Biological Evolution ; }, abstract = {Functional traits differ among species, which determine the ecological niche a species occupies and its ability to adapt to environment. However, differences in traits also exist at intraspecific level. Such variations shape differences in individual survival capabilities. Investigating intraspecific differences of functional traits is important for ecology, evolutionary biology and biodiversity conservation. Individual trait-based approaches have been applied in plant ecology. But for animals, most databases only provide data at the species level. In this study, we presented a global database of morphological traits for caecilians (Amphibia, Gymnophiona) at both species and individual level. Caecilians are a unique group of amphibians characterized by their secretive habits, which have limited our understanding of this taxon. We compiled the most comprehensive database covering 218 out of 222 known species, with 215 of them have individual level data. This database will facilitate research in the ecology, evolutionary biology, conservation biology, and taxonomy of caecilians. Furthermore, this dataset can be utilized to test ecological and evolutionary hypotheses at the individual level.}, } @article {pmid40070804, year = {2025}, author = {Vršanský, P and Sendi, H and Kotulová, J and Szwedo, J and Havelcová, M and Palková, H and Vršanská, L and Sakala, J and Puškelová, L and Golej, M and Biroň, A and Peyrot, D and Quicke, D and Néraudeau, D and Uher, P and Maksoud, S and Azar, D}, title = {Jurassic Park approached: a coccid from Kimmeridgian cheirolepidiacean Aintourine Lebanese amber.}, journal = {National science review}, volume = {12}, number = {3}, pages = {nwae200}, pmid = {40070804}, issn = {2053-714X}, abstract = {With the exception of a fly and a mite from the Triassic of Italy, all Mesozoic amber arthropods are from the Cretaceous. Late Jurassic Lebanese amber from Aintourine revealed a completely preserved adult coccid male (wing length 0.8 mm), Jankotejacoccus libanogloria gen. et sp. n., the earliest record of a plant sucking scale insect. Associated plant material included the cheirolepidiaceans Protopodocarpoxylon, Brachyphyllum and Classostrobus, plus Classopolis pollen, suggesting a forested temporary swamp habitat with ferns, tree ferns, water ferns, tall araucarian and ginkgoacean trees and shrubs. (Sub)tropic lateritic soil with vegetation debris underwent incomplete microbial decomposition in an anoxic water environment of peat swamp development. Strata-associated marine organisms support the Kimmeridgian age revealed by zircons. The discovery opens a new field of research in Jurassic amber fossils.}, } @article {pmid40069723, year = {2025}, author = {Pieroni, A and Zocchi, DM and Alrhmoun, M and Sulaiman, N and Bavorova, M and Sõukand, R}, title = {Not "just necessity"? Two-x-eco-cultural dilemmas and the ethnobiological importance of the informal grannies' markets in Moldova.}, journal = {Journal of ethnobiology and ethnomedicine}, volume = {21}, number = {1}, pages = {17}, pmid = {40069723}, issn = {1746-4269}, support = {714874/ERC_/European Research Council/International ; 714874/ERC_/European Research Council/International ; 714874/ERC_/European Research Council/International ; }, mesh = {Moldova ; Humans ; Female ; *Commerce ; Food Supply ; Conservation of Natural Resources ; Middle Aged ; Agriculture ; Rural Population ; Culture ; Anthropology, Cultural ; Aged ; Biodiversity ; }, abstract = {Informal food markets, particularly those managed by (elderly) women in post-communist Eastern Europe, represent a biocultural phenomenon of profound significance since globalisation and increasingly strict legal frameworks often threaten these reservoirs of biocultural food heritage. In the fall of 2022 and 2023, a preliminary field study was conducted by visiting the informal markets of six Moldovan centres: Chișinău, Orhei, Bălți, Călărași, Comrat, and Taraclia, and conversing with approximately 40 mid-aged and elderly sellers. We argue that these markets are crucial in sustaining small-scale farming, preserving biodiversity, and maintaining a connection between urban communities and rural communities and, ultimately, between these rural citizens and their nature, keeping small-scale family farming and domestic traditional gastronomic activities alive. By trading fresh, homegrown, and homemade food and goods (including handicrafts), these mid-aged and elderly vendors support local economies, promote environmental sustainability, and safeguard traditional ecological knowledge and cultural heritage. This paper explores how grannies' markets contribute to biocultural diversity and sustainable food practices, especially amid the country's recent turbulent political, socioeconomic, and demographic challenges. The analysis advocates for the survival rights of these ecological, economic, and cultural (2-x-eco-cultural) refugia and invites ethnobiologists, food studies and cultural heritage scholars, rural sociologists, and agricultural economists to defend the biocultural diversity of informal food markets, moving them from an "out of necessity" status to a solid pillar of a possible future, new, family farming and small-scale ecological and gastronomic (conscientious) tourism. Policymakers should protect and enhance these informal spaces, especially the socioecological farming systems behind them, as essential socioeconomic and environmental assets. They should emphasise their importance as hubs for biological diversity, cultural preservation, community cohesion, and ecological sustainability.}, } @article {pmid40066908, year = {2025}, author = {Weeks, F and Myerson, R and Gangnon, R and Dykema, J and Cornelius, C and Green, T}, title = {Intrapartum Care Experiences Associated With Postpartum Visit Attendance.}, journal = {Birth (Berkeley, Calif.)}, volume = {}, number = {}, pages = {}, doi = {10.1111/birt.12910}, pmid = {40066908}, issn = {1523-536X}, support = {//Wisconsin Alumni Research Foundation/ ; }, abstract = {INTRODUCTION: The postpartum visit is an important opportunity to prevent pregnancy-related morbidity and mortality; however, about 1 in 10 birthing people do not attend this visit. Intrapartum care experiences are an understudied factor that may contribute to postpartum healthcare engagement.

MATERIALS AND METHODS: We analyze data from a novel survey supplement on intrapartum care experiences administered to a probability-based population sample of people who have recently given birth through the Wisconsin Pregnancy Risk Assessment Monitoring System.

RESULTS: In regression models adjusting for a robust set of individual characteristics and birth hospital clustering, we find that lower provider responsiveness during intrapartum care is associated with increased odds of forgoing the postpartum visit (aOR 1.4, 95% CI 1.0-2.0).

DISCUSSION: The quality of care received during the birth hospitalization may shape how birthing people feel about health care providers and their willingness to attend future visits. Experiences of care during the intrapartum period may contribute to future health care utilization. Improving these experiences is an opportunity to promote long-term health.}, } @article {pmid40064850, year = {2025}, author = {Roman, J and Abraham, AJ and Kiszka, JJ and Costa, DP and Doughty, CE and Friedlaender, A and Hückstädt, LA and Marcondes, M and Wetsel, E and Pershing, AJ}, title = {Migrating baleen whales transport high-latitude nutrients to tropical and subtropical ecosystems.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {2125}, pmid = {40064850}, issn = {2041-1723}, mesh = {Animals ; *Animal Migration/physiology ; *Ecosystem ; *Whales/physiology/metabolism ; *Nutrients/metabolism ; Tropical Climate ; Seasons ; Nitrogen/metabolism ; Biomass ; Female ; }, abstract = {Baleen whales migrate from productive high-latitude feeding grounds to usually oligotrophic tropical and subtropical reproductive winter grounds, translocating limiting nutrients across ecosystem boundaries in their bodies. Here, we estimate the latitudinal movement of nutrients through carcasses, placentas, and urea for four species of baleen whales that exhibit clear annual migration, relying on spatial data from publicly available databases, present and past populations, and measurements of protein catabolism and other sources of nitrogen from baleen whales and other marine mammals. Migrating gray, humpback, and North Atlantic and southern right whales convey an estimated 3784 tons N yr[-1] and 46,512 tons of biomass yr[-1] to winter grounds, a flux also known as the "great whale conveyor belt"; these numbers might have been three times higher before commercial whaling. We discuss how species recovery might help restore nutrient movement by whales in global oceans and increase the resilience and adaptative capacity of recipient ecosystems.}, } @article {pmid40064777, year = {2025}, author = {Crespo-Bellido, A and Martin, DP and Duffy, S}, title = {Recombination Analysis of Geminiviruses Using Recombination Detection Program (RDP).}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2912}, number = {}, pages = {125-143}, pmid = {40064777}, issn = {1940-6029}, mesh = {*Geminiviridae/genetics ; *Recombination, Genetic ; Software ; Algorithms ; Sequence Alignment ; Genome, Viral ; Evolution, Molecular ; Computational Biology/methods ; Phylogeny ; }, abstract = {Geminiviruses are recombination-prone, and characterizing this evolutionary process within their genomes is a frequent goal of researchers. RDP is a stand-alone Windows program combining many algorithms that detect and characterize recombination. It has been widely used by the geminivirus community (and beyond). Here we describe the use of RDP4 and RDP5 for analysis of geminiviral nucleotide sequences including: (i) obtaining a reasonable dataset for analysis, (ii) making a credible multiple sequence alignment and (iii) analyzing an alignment with RDP on that alignment. RDP to both characterize recombination events and to produce statistically recombination-free datasets for other molecular evolution analyses.}, } @article {pmid40063696, year = {2025}, author = {Smith, LB and Ahlich, E and Lang, B and Bollepalli, S and Prioleau, T and Bartolome, A and Hughes Lansing, A and Rancourt, D}, title = {Glycemic variability and weight-focused eating behaviors among adolescents and young adults with type 1 diabetes†.}, journal = {Journal of pediatric psychology}, volume = {}, number = {}, pages = {}, doi = {10.1093/jpepsy/jsaf009}, pmid = {40063696}, issn = {1465-735X}, support = {//Dexcom, Inc/ ; }, abstract = {OBJECTIVE: Type 1 diabetes (T1D) disease management and associated glycemic fluctuations can disrupt experiences of hunger and satiety, which may increase risk for disordered eating behaviors. Glycemic variability may be a useful trigger for just-in-time interventions for disordered eating behaviors. In this exploratory study, we hypothesized that two metrics of glycemic variability would be associated with greater hunger and predict eating behaviors for weight loss or maintenance in adolescents and young adults with T1D.

METHODS: Individuals with T1D were recruited from a university diabetes clinic (N = 34; 50% female, Mage = 19.53 years, MHbA1c = 7.98%; 29% Hispanic/Latinx; 79% White). Participants wore a blinded continuous glucose monitor for 5 days, and completed ecological momentary assessments (four prompts per day) that included measures of hunger and eating behaviors for weight loss or maintenance purposes. Generalized and linear mixed models were used to test hypotheses.

RESULTS: Approximately 30% of participants were at risk for an eating disorder based on Diabetes Eating Problem Survey-Revised scores. Greater glycemic variability did not predict hunger, but was associated with increased odds of endorsing any eating behavior for weight loss or maintenance purposes within-person (ps<.05). Greater hunger was associated with increased odds of endorsing disordered eating behavior within-person (p<.05).

CONCLUSIONS: This exploratory study provides some preliminary evidence that times of greater hunger and glycemic variability may be when individuals with T1D may be at higher risk of engaging in behaviors to lose or maintain weight.}, } @article {pmid39823836, year = {2025}, author = {Li, Z and Meng, C and Azad, MAK and Zhu, Q and Lin, W and Cui, Y and Lan, W and He, Q and Kong, X}, title = {Effects of the Salvia miltiorrhiza, Ligustrum lucidum, and Taraxacum mongolicum ultra-fine powder formula on meat quality of aged layers by multi-omics.}, journal = {Poultry science}, volume = {104}, number = {2}, pages = {104783}, pmid = {39823836}, issn = {1525-3171}, mesh = {*Taraxacum/chemistry ; Animals ; *Ligustrum/chemistry ; *Salvia miltiorrhiza/chemistry ; *Meat/analysis ; *Drugs, Chinese Herbal/pharmacology/administration & dosage/chemistry ; *Diet/veterinary ; *Animal Feed/analysis ; *Dietary Supplements/analysis ; *Chickens/physiology ; Female ; Powders/chemistry ; Aging/drug effects ; Multiomics ; }, abstract = {This study was aimed to identify the targets of 1% ultra-fine Chinese medicine formula (UCMF, 0.5% Salvia miltiorrhiza Bge. + 0.25% Ligustrum lucidum Ait. + 0.25% Taraxacum mongolicum Hand.-Mazz.) in delaying aging and explore its impacts on meat quality of aged layers. The effective components of the above three Chinese herbs were screened, and the network pharmacology analysis identified 91 common targets and enriched pathways between herbs and aging. The results showed that cellular response to chemical stimulus, response to oxidative stress, and response to oxygen-containing compound pathways were crucial for UCMF to resist aging. Further in vivo analyses confirmed that UCMF supplementation enhanced the antioxidant function in breast muscles of aged layers by upregulating (P < 0.05) the SOD2 gene expression. Meanwhile, UCMF supplementation reduced (P < 0.05) yellowness (b* value) and drip loss while enhancing (P < 0.05) cooked meat percentage of aged layers. For the health lipid indices in breast muscles, UCMF supplementation increased (P < 0.05) polyunsaturated fatty acids/saturated fatty acids and hypocholesterolemic/hypercholesterolemic ratios and decreased (P < 0.05) the thrombogenic index. The UCMF supplementation optimized the cecal microbiota of aged layers by enhancing the relative abundance of Firmicutes and reducing the relative abundances of Bacteroidetes and Spirochaetes (P < 0.05), which may be related to improving meat quality. In conclusion, dietary UCMF supplementation may be an effective strategy for improving antioxidant function and the meat quality of aged layers.}, } @article {pmid39752826, year = {2025}, author = {Zhao, X and Jiang, WY and Liu, JJ and Yan, WJ and Zhang, YH and Zhang, Z and Zhang, PD}, title = {Unraveling the impact of PFOA toxicity on Zostera marina using a multi-omics approach: Insights from growth, physiological, transcriptomic, and metabolomic signatures.}, journal = {Journal of hazardous materials}, volume = {486}, number = {}, pages = {137024}, doi = {10.1016/j.jhazmat.2024.137024}, pmid = {39752826}, issn = {1873-3336}, mesh = {*Caprylates/toxicity ; *Water Pollutants, Chemical/toxicity ; *Transcriptome/drug effects ; *Zosteraceae/genetics/drug effects/metabolism ; *Fluorocarbons/toxicity ; *Metabolomics ; Photosynthesis/drug effects ; Gene Expression Profiling ; Multiomics ; }, abstract = {Perfluorooctanoic acid (PFOA), an anthropogenic organic pollutant known for its persistence, resistance to degradation, and toxicity, has raised significant concerns about its potential ecological impacts. Zostera marina, a common submerged seagrass species in temperate offshore areas, is highly vulnerable to pollutant stressors. However, the impact of PFOA on Z. marina remains unclear. In this study, Z. marina was exposed to different concentrations of PFOA (0, 0.5, 1, 5, 10, and 20 μg/L) for 14 days. We subsequently assessed survival rates, growth patterns, physiological indices, transcriptomic profiles, and metabolomic characteristics. The results revealed dose-dependent PFOA accumulation in Z. marina tissues and significant growth inhibition. Furthermore, exposure to PFOA resulted in a significant reduction in photosynthetic pigment content (IBRv2 indices: 2.78-10.29) and elevated enzyme activity (IBRv2 indices: 2.90-8.96). Transcriptomic analysis identified 1511 differentially expressed genes associated with 11 KEGG pathways predominantly affected by PFOA exposure. Weighted gene co-expression network analysis highlighted the crucial role of the hydroxyphenylpyruvate reductase (hppr) gene in antioxidant defense mechanisms and detoxification processes against PFOA-induced stress. Metabolomics identified 412 differentially expressed metabolites, mainly consisting of flavonoids, organic acids, and lipids. In summary, PFOA exposure resulted in the down-regulation of gene expression related to photosynthesis and energy metabolism while also affecting metabolite synthesis. The response of Z. marina to PFOA stress involves modulation of the cytoskeletal dynamics and signal transduction pathways, as well as activation of a suite of genes and metabolites to initiate defense mechanisms.}, } @article {pmid39724715, year = {2025}, author = {Zhang, L and Du, Y and Li, Y and Wang, T and Pan, Y and Xue, X and Mu, X and Qiu, J and Qian, Y}, title = {Mitochondrial mechanism of florfenicol-induced nonalcoholic fatty liver disease in zebrafish using multi-omics technology.}, journal = {Journal of hazardous materials}, volume = {486}, number = {}, pages = {136958}, doi = {10.1016/j.jhazmat.2024.136958}, pmid = {39724715}, issn = {1873-3336}, mesh = {Animals ; *Zebrafish ; *Non-alcoholic Fatty Liver Disease/chemically induced/metabolism/pathology ; *Thiamphenicol/analogs & derivatives/toxicity ; *Anti-Bacterial Agents/toxicity ; Mitochondria/drug effects/metabolism ; Oxidative Stress/drug effects ; Liver/drug effects/metabolism/pathology ; Metabolomics ; Water Pollutants, Chemical/toxicity ; Energy Metabolism/drug effects ; Lipidomics ; Multiomics ; }, abstract = {Florfenicol (FF), a third-generation chloramphenicol antibiotic widely used in food-producing animals, has become a "pseudopersistent" environmental contaminant, raising concerns about its potential ecological and human health impacts. However, its bioaccumulation behavior and hepatotoxic mechanisms remain poorly understood. This study aims to address these gaps with a 28-day exposure experiment in adult zebrafish at 0.05 and 0.5 mg/L FF. Multiomic analyses (metabolomics, lipidomics, and transcriptomics), combined with histological and mitochondrial function assessments, were employed. Higher bioaccumulation was observed at 0.05 mg/L, potentially due to metabolic saturation at higher concentrations. Histological analysis revealed significant hepatic steatosis (>5 % steatosis area), indicative of moderate nonalcoholic fatty liver disease (NAFLD). Multiomic data demonstrated global dysregulation in energy metabolism, including marked alterations in lipids (accumulation of toxic sphingolipids, excessive fatty acids, and acylglycerol), amino acids, tricarboxylic acid cycle intermediates, and nucleotides. Crucially, mitochondrial dysfunction was identified as a central mechanism, with impaired respiratory chain activities, adenosine triphosphate depletion, elevated reactive oxygen species, and oxidative stress promoting NAFLD progression. These findings highlight mitochondrial impairment and oxidative stress as key drivers of FF-induced hepatotoxicity, providing novel insights into its toxicological mechanisms and emphasizing the ecological risks posed by antibiotic pollution in aquatic systems.}, } @article {pmid40062320, year = {2025}, author = {Boyes, D and Davis, J and , and , and , and , and , and , }, title = {The genome sequence of the Sandy Carpet moth, Perizoma flavofasciatum (Thunberg, 1792).}, journal = {Wellcome open research}, volume = {10}, number = {}, pages = {40}, pmid = {40062320}, issn = {2398-502X}, abstract = {We present a genome assembly from a male specimen of Perizoma flavofasciatum (Sandy Carpet; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence has a total length of 369.30 megabases. Most of the assembly (99.88%) is scaffolded into 30 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 16.61 kilobases in length. Gene annotation of this assembly on Ensembl identified 11,915 protein-coding genes.}, } @article {pmid40062319, year = {2025}, author = {Boyes, D and Boyes, C and , and , and , and , and , and , and , }, title = {The genome sequence of the Alder Moth, Acronicta alni (Linnaeus, 1767).}, journal = {Wellcome open research}, volume = {10}, number = {}, pages = {68}, pmid = {40062319}, issn = {2398-502X}, abstract = {We present a genome assembly from a male Acronicta alni (Alder Moth; Arthropoda; Insecta; Lepidoptera; Noctuidae). The assembly contains two haplotypes with total lengths of 470.37 megabases and 472.86 megabases. Most of haplotype 1 (98.95%) is scaffolded into 31 chromosomal pseudomolecules, including the Z chromosome. Haplotype 2 was assembled to scaffold level. The mitochondrial genome has also been assembled and is 15.38 kilobases in length.}, } @article {pmid40061226, year = {2025}, author = {Ab Kadir, MA and Abdul Manaf, R and Mokhtar, SA and Ismail, LI}, title = {Identifying leptospirosis hotspots in Selangor: uncovering climatic connections using remote sensing and developing a predictive model.}, journal = {PeerJ}, volume = {13}, number = {}, pages = {e18851}, pmid = {40061226}, issn = {2167-8359}, mesh = {*Leptospirosis/epidemiology ; Humans ; Cross-Sectional Studies ; Malaysia/epidemiology ; *Remote Sensing Technology/methods ; *Geographic Information Systems ; Male ; Female ; Adult ; Adolescent ; Incidence ; Machine Learning ; Middle Aged ; Child ; Young Adult ; Climate Change ; Aged ; Rain ; Child, Preschool ; }, abstract = {BACKGROUND: Leptospirosis is an endemic disease in countries with tropical climates such as South America, Southern Asia, and Southeast Asia. There has been an increase in leptospirosis incidence in Malaysia from 1.45 to 25.94 cases per 100,000 population between 2005 and 2014. With increasing incidence in Selangor, Malaysia, and frequent climate change dynamics, a study on the disease hotspot areas and their association with the hydroclimatic factors could enhance disease surveillance and public health interventions.

METHODS: This ecological cross-sectional study utilised a geographic information system (GIS) and remote sensing techniques to analyse the spatiotemporal distribution of leptospirosis in Selangor from 2011 to 2019. Laboratory-confirmed leptospirosis cases (n = 1,045) were obtained from the Selangor State Health Department. Using ArcGIS Pro, spatial autocorrelation analysis (Moran's I) and Getis-Ord Gi* (hotspot analysis) was conducted to identify hotspots based on the monthly aggregated cases for each subdistrict. Satellite-derived rainfall and land surface temperature (LST) data were acquired from NASA's Giovanni EarthData website and processed into monthly averages. These data were integrated into ArcGIS Pro as thematic layers. Machine learning algorithms, including support vector machine (SVM), Random Forest (RF), and light gradient boosting machine (LGBM) were employed to develop predictive models for leptospirosis hotspot areas. Model performance was then evaluated using cross-validation and metrics such as accuracy, precision, sensitivity, and F1-score.

RESULTS: Moran's I analysis revealed a primarily random distribution of cases across Selangor, with only 20 out of 103 observed having a clustered distribution. Meanwhile, hotspot areas were mainly scattered in subdistricts throughout Selangor with clustering in the central region. Machine learning analysis revealed that the LGBM algorithm had the best performance scores compared to having a cross-validation score of 0.61, a precision score of 0.16, and an F1-score of 0.23. The feature importance score indicated river water level and rainfall contributes most to the model.

CONCLUSIONS: This GIS-based study identified a primarily sporadic occurrence of leptospirosis in Selangor with minimal spatial clustering. The LGBM algorithm effectively predicted leptospirosis hotspots based on the analysed hydroclimatic factors. The integration of GIS and machine learning offers a promising framework for disease surveillance, facilitating targeted public health interventions in areas at high risk for leptospirosis.}, } @article {pmid40055331, year = {2025}, author = {Guerrero, PC and Contador, T and Díaz, A and Escobar, C and Orlando, J and Marín, C and Medina, P}, title = {Southern Islands Vascular Flora (SIVFLORA) dataset: A global plant database from Southern Ocean islands.}, journal = {Scientific data}, volume = {12}, number = {1}, pages = {397}, pmid = {40055331}, issn = {2052-4463}, mesh = {*Biodiversity ; *Islands ; *Plants ; Databases, Factual ; Ecosystem ; Climate Change ; Oceans and Seas ; }, abstract = {The Southern Islands Vascular Flora (SIVFLORA) dataset is a globally significant, open-access resource that compiles essential biodiversity data on vascular plants from islands across the Southern Ocean. The SIVFLORA dataset was generated through five steps: study area delimitation, compiling the dataset, validating and harmonizing taxonomy, structuring dataset attributes, and establishing file format and open access. Covering major taxonomic divisions, SIVFLORA offers a comprehensive overview of plant occurrences, comprising 14,589 records representing 886 species, 95 families, and 42 orders. This dataset documents that 58.62% of the taxa are native, 9.61% are endemic, and 31.77% are alien species. The Falkland/Malvinas Archipelago, the most species-rich, contrast sharply with less diverse islands like the South Orkney Archipelago. SIVFLORA serves as a taxonomically harmonized, interoperable resource for investigating plant diversity patterns, ecosystem responses to climate change in extreme environments, island biogeography, endemism, and the effects of anthropogenic pressures on Southern Ocean flora.}, } @article {pmid40055329, year = {2025}, author = {Ferrer-Paris, JR and Sánchez-Mercado, A and Cornwell, WK and Ooi, M and Tozer, M and Mackenzie, BDE and Woodward, R and Denham, AJ and Auld, TD and Keith, DA}, title = {Fire ecology database for documenting plant responses to fire events in Australia.}, journal = {Scientific data}, volume = {12}, number = {1}, pages = {399}, pmid = {40055329}, issn = {2052-4463}, mesh = {*Databases, Factual ; *Fires ; *Plants ; Biodiversity ; Australia ; New South Wales ; }, abstract = {An understanding of fire-response traits is essential for predicting how fire regimes structure plant communities and for informing fire management strategies for biodiversity conservation. Quantification of these traits is complex, encompassing several levels of data abstraction scaling up from field observations of individuals, to general categories of species responses. We developed the Fire Ecology Database to accommodate this complexity. Its conceptual framework is underpinned by a flexible data pipeline enabling links between fire-related trait data and event information at individual, population, and community levels. Key features include: (a) concise and documented trait and method vocabularies; (b) documented uncertainty in observations and aggregation; and (c) documented origin of data including field observations, laboratory experiments, and expert elicitation. We demonstrated application of our framework using data from new field surveys and existing data sets in New South Wales, Australia. The database includes 14 traits for 6,287 plant species derived from 8,936 field work records from 2007 to 2018, 7,054 field records from surveys after 2019, and 48,306 records from 301 existing sources.}, } @article {pmid40054299, year = {2025}, author = {Guarischi, M and Montagnani, E and Catalano, G and Saligari, E and Signorini, S and Gori, M}, title = {From motion to interaction: How multisensory information shapes motor behaviors in children with visual impairment.}, journal = {Research in developmental disabilities}, volume = {159}, number = {}, pages = {104956}, doi = {10.1016/j.ridd.2025.104956}, pmid = {40054299}, issn = {1873-3379}, abstract = {BACKGROUND: The ability to move independently enables children to develop perceptual, cognitive, and social interaction skills. Concerning this, vision holds a key role. As a result, children with visual impairment (VI) might be more challenged in their ability to move within their surroundings and interact with their caregivers.

AIM: This study investigated whether the use of multisensory stimuli could influence the motor exploration of children with VI and shape their interaction with the caregivers. For this, the present work examined the variability of children's motor trajectory and the distance between children and caregivers in a setting with and without multisensory cues.

METHODS AND PROCEDURES: A Motion Capture System was used within an ecological playroom environment. The Strange Situation paradigm was simplified and adapted by placing three TechARMs in the corners of the playroom to deliver audio-visual stimuli, used instead of the stranger.

OUTCOMES AND RESULTS: Children with VI showed larger variability within their motor trajectory and kept a shorter distance from the caregivers when multisensory cues were introduced in the playroom.

CONCLUSIONS AND IMPLICATIONS: Multisensory signals were considered unusual and influenced the kinematic parameters. Motor control of the environment was achieved by managing attention flexibility. WHAT DOES THIS PAPER ADD?: This study enriches available evidence about the study of motor and social interaction in children with VI, highlighting how multisensory stimuli could either support or hinder social and motor behaviors. Moreover, enhancing ecological validity could drive progress in the development and application of technological devices to clinical and research setting.}, } @article {pmid40045231, year = {2025}, author = {Agyapong, D and Propster, JR and Marks, J and Hocking, TD}, title = {Cross-validation for training and testing co-occurrence network inference algorithms.}, journal = {BMC bioinformatics}, volume = {26}, number = {1}, pages = {74}, pmid = {40045231}, issn = {1471-2105}, support = {2125088//National Science Foundation/ ; 2125088//National Science Foundation/ ; 2125088//National Science Foundation/ ; 2125088//National Science Foundation/ ; }, mesh = {*Algorithms ; *Microbiota ; Computational Biology/methods ; Bacteria/genetics/classification ; }, abstract = {BACKGROUND: Microorganisms are found in almost every environment, including soil, water, air and inside other organisms, such as animals and plants. While some microorganisms cause diseases, most of them help in biological processes such as decomposition, fermentation and nutrient cycling. Much research has been conducted on the study of microbial communities in various environments and how their interactions and relationships can provide insight into various diseases. Co-occurrence network inference algorithms help us understand the complex associations of micro-organisms, especially bacteria. Existing network inference algorithms employ techniques such as correlation, regularized linear regression, and conditional dependence, which have different hyper-parameters that determine the sparsity of the network. These complex microbial communities form intricate ecological networks that are fundamental to ecosystem functioning and host health. Understanding these networks is crucial for developing targeted interventions in both environmental and clinical settings. The emergence of high-throughput sequencing technologies has generated unprecedented amounts of microbiome data, necessitating robust computational methods for network inference and validation.

RESULTS: Previous methods for evaluating the quality of the inferred network include using external data, and network consistency across sub-samples, both of which have several drawbacks that limit their applicability in real microbiome composition data sets. We propose a novel cross-validation method to evaluate co-occurrence network inference algorithms, and new methods for applying existing algorithms to predict on test data. Our method demonstrates superior performance in handling compositional data and addressing the challenges of high dimensionality and sparsity inherent in real microbiome datasets. The proposed framework also provides robust estimates of network stability.

CONCLUSIONS: Our empirical study shows that the proposed cross-validation method is useful for hyper-parameter selection (training) and comparing the quality of inferred networks between different algorithms (testing). This advancement represents a significant step forward in microbiome network analysis, providing researchers with a reliable tool for understanding complex microbial interactions. The method's applicability extends beyond microbiome studies to other fields where network inference from high-dimensional compositional data is crucial, such as gene regulatory networks and ecological food webs. Our framework establishes a new standard for validation in network inference, potentially accelerating discoveries in microbial ecology and human health.}, } @article {pmid39749403, year = {2025}, author = {Bougiouri, K}, title = {Mind the Gap: A Neural Network Framework for Imputing Genotypes in Non-Model Species.}, journal = {Molecular ecology resources}, volume = {25}, number = {3}, pages = {e14066}, doi = {10.1111/1755-0998.14066}, pmid = {39749403}, issn = {1755-0998}, mesh = {*Neural Networks, Computer ; *Genotype ; Genotyping Techniques/methods ; Haplotypes/genetics ; Computational Biology/methods ; Sequence Analysis, DNA/methods ; }, abstract = {Reduced representation sequencing (RRS) has proven to be a cost-effective solution for sequencing subsets of the genome in non-model species for large-scale studies. However, the targeted nature of RRS approaches commonly introduces large amounts of missing data, leading to reduced statistical power and biased estimates in downstream analyses. Genotype imputation, the statistical inference of missing sites across the genome, is a powerful alternative to overcome the caveats associated with missing sites. Typically, genotype imputation requires the presence of a reference panel of haplotypes, however, this is not always feasible for non-model species. In this issue of Molecular Ecology Resources, Mora-Márquez et al. (2024) develop gtImputation, an unsupervised machine learning imputation tool with an interactive GUI, which leverages information from the underlying data structure itself, without the need for a reference panel. They showcase that their method performs equally well and even surpasses existing haplotype-clustering and unsupervised machine learning algorithms, particularly for sites with low minor allele frequency (MAF) and for data sets with strong underlying population structure. This innovative framework adds to the ongoing efforts to expand the applicability of imputation to non-model species, offering the opportunity to apply varied types of analyses requiring dense sets of markers, while also maintaining lower sequencing costs.}, } @article {pmid39739202, year = {2025}, author = {Bard, NW and Davies, TJ and Cronk, QCB}, title = {Teknonaturalist: A Snakemake Pipeline for Assessing Fungal Diversity From Plant Genome Bycatch.}, journal = {Molecular ecology resources}, volume = {25}, number = {3}, pages = {e14056}, doi = {10.1111/1755-0998.14056}, pmid = {39739202}, issn = {1755-0998}, support = {RGPIN-2019-04041//Natural Sciences and Engineering Research Council of Canada/ ; RGPIN-2020-04439//Natural Sciences and Engineering Research Council of Canada/ ; }, mesh = {*Fungi/genetics/classification/isolation & purification ; *Genome, Plant/genetics ; DNA, Ribosomal Spacer/genetics ; Plants/microbiology ; DNA, Fungal/genetics ; Endophytes/genetics/classification/isolation & purification ; DNA Barcoding, Taxonomic/methods ; Computational Biology/methods ; Sequence Analysis, DNA/methods ; }, abstract = {Relatively little is known of the host associations and compatibility of fungal plant pathogens and endophytes. Publicly available plant genomic DNA can be mined to detect incidental fungal DNA, but taxonomic assignment can be challenging due to short lengths and variable discriminative power among different genomic regions and taxa. Here, we introduce a computationally lightweight and accessible Snakemake pipeline for rapid detection and classification (identification and assignment to taxonomic rank) of pathogenic and endophytic fungi (and other fungi associated with plants) that targets the internal transcribed spacer (ITS) region, a fungal barcode standard. We include methods for maximising query sequence length, which gives higher support for ITS1 and ITS2 taxonomic classifications by extending to other fragments of the ITS region and providing taxon-specific local cut-off and confidence scores. We demonstrate our pipeline with a case study using public genomic sequence data for six diverse plant species, including four species within Betula, an ecologically and economically important broadleaved forest tree genus, a shrub and a grass. Our pipeline classified fungi within minutes to a few hours per host individual, with 204 different fungal genera identified at high confidence (≥ 70%). Our pipeline detected and classified pathogenic and endophytic genera known to associate with Betula, and many others with no prior record of association. Our pipeline, leveraging existing sequence data, has several potential applications, including detecting cryptic fungal pathogens and helping characterise the endophytic fungal microbiome, bioprospecting commercially useful fungal species, and determining the plant host range of fungi.}, } @article {pmid39611246, year = {2025}, author = {Armstrong, EE and Li, C and Campana, MG and Ferrari, T and Kelley, JL and Petrov, DA and Solari, KA and Mooney, JA}, title = {A Pipeline and Recommendations for Population and Individual Diagnostic SNP Selection in Non-Model Species.}, journal = {Molecular ecology resources}, volume = {25}, number = {3}, pages = {e14048}, doi = {10.1111/1755-0998.14048}, pmid = {39611246}, issn = {1755-0998}, mesh = {*Polymorphism, Single Nucleotide ; *Genetics, Population/methods ; Genotyping Techniques/methods ; Computational Biology/methods ; Animals ; }, abstract = {Despite substantial reductions in the cost of sequencing over the last decade, genetic panels remain relevant due to their cost-effectiveness and flexibility across a variety of sample types. In particular, single nucleotide polymorphism (SNP) panels are increasingly favoured for conservation applications. SNP panels are often used because of their adaptability, effectiveness with low-quality samples, and cost-efficiency for population monitoring and forensics. However, the selection of diagnostic SNPs for population assignment and individual identification can be challenging. The consequences of poor SNP selection are under-powered panels, inaccurate results, and monetary loss. Here, we develop a novel and user-friendly SNP selection pipeline (mPCRselect) that can be used to select SNPs for population assignment and/or individual identification. mPCRselect allows any researcher, who has sufficient SNP-level data, to design a successful and cost-effective SNP panel for a diploid species of conservation concern.}, } @article {pmid39552382, year = {2025}, author = {Beemelmanns, A and Bouchard, R and Michaelides, S and Normandeau, E and Jeon, HB and Chamlian, B and Babin, C and Hénault, P and Perrot, O and Harris, LN and Zhu, X and Fraser, D and Bernatchez, L and Moore, JS}, title = {Development of SNP Panels from Low-Coverage Whole Genome Sequencing (lcWGS) to Support Indigenous Fisheries for Three Salmonid Species in Northern Canada.}, journal = {Molecular ecology resources}, volume = {25}, number = {3}, pages = {e14040}, doi = {10.1111/1755-0998.14040}, pmid = {39552382}, issn = {1755-0998}, support = {//Genome Canada/ ; //Génome Québec/ ; //Ontario Genomics/ ; NST-1718-0036//Polar Knowledge Canada/ ; //Natural Sciences and Engineering Research Council of Canada (NSERC)/ ; IT16149//Mitacs/ ; //Fisheries and Oceans Canada (DFO)/ ; //Ressources Aquatiques Québec (RAQ)/ ; }, mesh = {Animals ; *Polymorphism, Single Nucleotide ; *Fisheries ; *Salmonidae/genetics/classification ; Whole Genome Sequencing/methods ; Genotyping Techniques/methods ; Genotype ; Trout/genetics/classification ; Canada ; Genetics, Population/methods ; Nunavut ; Quebec ; Northwest Territories ; Computational Biology/methods ; }, abstract = {Single nucleotide polymorphism (SNP) panels are powerful tools for assessing the genetic population structure and dispersal of fishes and can enhance management practices for commercial, recreational and subsistence mixed-stock fisheries. Arctic Char (Salvelinus alpinus), Brook Trout (Salvelinus fontinalis) and Lake Whitefish (Coregonus clupeaformis) are among the most harvested and consumed fish species in Northern Indigenous communities in Canada, contributing significantly to food security, culture, tradition and economy. However, genetic resources supporting Indigenous fisheries have not been widely accessible to northern communities (e.g. Inuit, Cree, Dene). Here, we developed Genotyping-in-Thousands by sequencing (GT-seq) panels for population assignment and mixed-stock analyses of three salmonids, to support fisheries stewardship or co-management in Northern Canada. Using low-coverage Whole Genome Sequencing data from 418 individuals across source populations in Cambridge Bay (Nunavut), Great Slave Lake (Northwest Territories), James Bay (Québec) and Mistassini Lake (Québec), we developed a bioinformatic SNP filtering workflow to select informative SNP markers from genotype likelihoods. These markers were then used to design GT-seq panels, thus enabling high-throughput genotyping for these species. The three GT-seq panels yielded an average of 413 autosomal loci and were validated using 525 individuals with an average assignment accuracy of 83%. Thus, these GT-seq panels are powerful tools for assessing population structure and quantifying the relative contributions of populations/stocks in mixed-stock fisheries across multiple regions. Interweaving genomic data derived from these tools with Traditional Ecological Knowledge will ensure the sustainable harvest of three culturally important salmonids in Indigenous communities, contributing to food security programmes and the economy in Northern Canada.}, } @article {pmid39545396, year = {2025}, author = {Li, J and Gao, Y and Shu, G and Chen, X and Zhu, J and Zheng, S and Chen, T}, title = {HMicroDB: A Comprehensive Database of Herpetofaunal Microbiota With a Focus on Host Phylogeny, Physiological Traits, and Environment Factors.}, journal = {Molecular ecology resources}, volume = {25}, number = {3}, pages = {e14046}, doi = {10.1111/1755-0998.14046}, pmid = {39545396}, issn = {1755-0998}, support = {2021YFF1201300//National Key Research and Development Program of China/ ; 2021YFF1201303//National Key Research and Development Program of China/ ; 2022YFC2703105//National Key Research and Development Program of China/ ; 2023M731976//Postdoctoral Research Foundation of China/ ; }, mesh = {*Microbiota/genetics ; Animals ; *Phylogeny ; *Amphibians/microbiology ; *Symbiosis/genetics ; Reptiles/microbiology ; Host Microbial Interactions/genetics ; Databases, Factual ; }, abstract = {Symbiotic microbiota strongly impact host physiology. Amphibians and reptiles occupy a pivotal role in the evolutionary history of Animalia, and they are of significant ecological, economic, and scientific value. Many prior studies have found that symbiotic microbiota in herpetofaunal species are closely associated with host phylogeny, physiological traits, and environmental factors; however, insufficient integrated databases hinder researchers from querying, accessing, and reanalyzing these resources. To rectify this, we built the first herpetofaunal microbiota database (HMicroDB; https://herpdb.com/) that integrates 11,697 microbiological samples from 337 host species (covering 23 body sites and associated with 23 host phenotypic or environmental factors), and we identified 11,084 microbial taxa by consistent annotation. The standardised analysis process, cross-dataset integration, user-friendly interface, and interactive visualisation make the HMicroDB a powerful resource for researchers to search, browse, and explore the relationships between symbiotic microbiota, hosts, and environment. This facilitates research in host-microbiota coevolution, biological conservation, and resource utilisation.}, } @article {pmid40044867, year = {2025}, author = {Aguirre-Gutiérrez, J and Rifai, SW and Deng, X and Ter Steege, H and Thomson, E and Corral-Rivas, JJ and Guimaraes, AF and Muller, S and Klipel, J and Fauset, S and Resende, AF and Wallin, G and Joly, CA and Abernethy, K and Adu-Bredu, S and Alexandre Silva, C and de Oliveira, EA and Almeida, DRA and Alvarez-Davila, E and Asner, GP and Baker, TR and Benchimol, M and Bentley, LP and Berenguer, E and Blanc, L and Bonal, D and Bordin, K and Borges de Lima, R and Both, S and Cabezas Duarte, J and Cardoso, D and de Lima, HC and Cavalheiro, L and Cernusak, LA and Dos Santos Prestes, NCC and da Silva Zanzini, AC and da Silva, RJ and Dos Santos Alves da Silva, R and de Andrade Iguatemy, M and De Sousa Oliveira, TC and Dechant, B and Derroire, G and Dexter, KG and Rodrigues, DJ and Espírito-Santo, M and Silva, LF and Domingues, TF and Ferreira, J and Simon, MF and Girardin, CAJ and Hérault, B and Jeffery, KJ and Kalpuzha Ashtamoorthy, S and Kavidapadinjattathil Sivadasan, A and Klitgaard, B and Laurance, WF and Dan, ML and Magnusson, WE and Campos-Filho, EM and Manoel Dos Santos, R and Manzatto, AG and Silveira, M and Marimon-Junior, BH and Martin, RE and Vieira, DLM and Metzker, T and Milliken, W and Moonlight, P and Moraes de Seixas, MM and Morandi, PS and Muscarella, R and Nava-Miranda, MG and Nyirambangutse, B and Silva, JO and Oliveras Menor, I and Francisco Pena Rodrigues, PJ and Pereira de Oliveira, C and Pereira Zanzini, L and Peres, CA and Punjayil, V and Quesada, CA and Réjou-Méchain, M and Riutta, T and Rivas-Torres, G and Rosa, C and Salinas, N and Bergamin, RS and Marimon, BS and Shenkin, A and Silva Rodrigues, PM and Figueiredo, AES and Garcia, QS and Spósito, T and Storck-Tonon, D and Sullivan, MJP and Svátek, M and Vieira Santiago, WT and Arn Teh, Y and Theruvil Parambil Sivan, P and Nascimento, MT and Veenendaal, E and Zo-Bi, IC and Dago, MR and Traoré, S and Patacca, M and Badouard, V and de Padua Chaves E Carvalho, S and White, LJT and Zhang-Zheng, H and Zibera, E and Zwerts, JA and Burslem, DFRP and Silman, M and Chave, J and Enquist, BJ and Barlow, J and Phillips, OL and Coomes, DA and Malhi, Y}, title = {Canopy functional trait variation across Earth's tropical forests.}, journal = {Nature}, volume = {}, number = {}, pages = {}, pmid = {40044867}, issn = {1476-4687}, abstract = {Tropical forest canopies are the biosphere's most concentrated atmospheric interface for carbon, water and energy[1,2]. However, in most Earth System Models, the diverse and heterogeneous tropical forest biome is represented as a largely uniform ecosystem with either a singular or a small number of fixed canopy ecophysiological properties[3]. This situation arises, in part, from a lack of understanding about how and why the functional properties of tropical forest canopies vary geographically[4]. Here, by combining field-collected data from more than 1,800 vegetation plots and tree traits with satellite remote-sensing, terrain, climate and soil data, we predict variation across 13 morphological, structural and chemical functional traits of trees, and use this to compute and map the functional diversity of tropical forests. Our findings reveal that the tropical Americas, Africa and Asia tend to occupy different portions of the total functional trait space available across tropical forests. Tropical American forests are predicted to have 40% greater functional richness than tropical African and Asian forests. Meanwhile, African forests have the highest functional divergence-32% and 7% higher than that of tropical American and Asian forests, respectively. An uncertainty analysis highlights priority regions for further data collection, which would refine and improve these maps. Our predictions represent a ground-based and remotely enabled global analysis of how and why the functional traits of tropical forest canopies vary across space.}, } @article {pmid40041564, year = {2025}, author = {Zhang, J and Qian, H and Wang, X}, title = {An online version and some updates of R package U.Taxonstand for standardizing scientific names in plant and animal species.}, journal = {Plant diversity}, volume = {47}, number = {1}, pages = {166-168}, pmid = {40041564}, issn = {2468-2659}, abstract = {•We present 'U.Taxonstand Online', a user-friendly web application for scientific name matching of both plants and animals.•U.Taxonstand Online provides a solution for the users with limited abilities of programming and data mining.•We add several new functions to clean and format the data for R package U.Taxonstand.}, } @article {pmid40038315, year = {2025}, author = {Chen, Y and Chen, S and Tao, J and Li, M and Wang, W and Chen, M and Fang, X and Kong, L and Wang, Y and Pereira, O and Zhang, C}, title = {Multi-omic stock of surface ocean microbiome built by monthly, weekly and daily sampling in Dapeng Bay, China.}, journal = {Scientific data}, volume = {12}, number = {1}, pages = {378}, pmid = {40038315}, issn = {2052-4463}, support = {32393974//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42321004//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42321004//National Natural Science Foundation of China (National Science Foundation of China)/ ; 92351301//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32393974//National Natural Science Foundation of China (National Science Foundation of China)/ ; 92351301//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32393974//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42321004//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42321004//National Natural Science Foundation of China (National Science Foundation of China)/ ; 92351301//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32393974//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42321004//National Natural Science Foundation of China (National Science Foundation of China)/ ; 92351301//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32393974//National Natural Science Foundation of China (National Science Foundation of China)/ ; RCBS20221008093229035//Shenzhen Science and Technology Innovation Commission/ ; 92351301//École Nationale d'Ingénieurs de Saint-Etienne (National Engineering School of Saint-Étienne)/ ; }, mesh = {China ; *Microbiota ; *Archaea/genetics ; *Bacteria/genetics/classification ; *Bays ; Seawater/microbiology ; Metagenome ; Multiomics ; }, abstract = {The coastal ocean is the dynamic interface where terrestrial, atmospheric, and marine systems converge, acting as a hotspot for microbial activity, which underpins the intricate web of carbon and nitrogen cycling. Dapeng Bay, a typical semi-enclosed bay along the southern coastline of China, is strongly influenced by monsoon climates and human activities. Despite its ecological importance, long-term observations and investigations into the microbial community structure in this region are notably lacking. To address this gap, we conducted a two-year continuous sampling from May 2021 to June 2023 to explore shifts in nearshore surface microbial communities and assess the long-term effects of environmental stressors. This study presents comprehensive amplicon, metagenomic, and metatranscriptomic information. We identified 3,600 amplicon sequence variants and recovered 1,216 high-quality metagenome-assembled MAGs, representing 17 bacterial and 3 archaeal phyla. Additionally, 587 MAGs were correlated with transcriptional activity, comprising 539 bacterial and 48 archaeal populations. This dataset is anticipated to provide a multi-dimensional perspective, enhancing our understanding of the complexity, dynamics, and adaptability of microbial communities in coastal environments.}, } @article {pmid39990470, year = {2025}, author = {Edwards, SV and Fang, B and Khost, D and Kolyfetis, GE and Cheek, RG and DeRaad, DA and Chen, N and Fitzpatrick, JW and McCormack, JE and Funk, WC and Ghalambor, CK and Garrison, E and Guarracino, A and Li, H and Sackton, TB}, title = {Comparative population pangenomes reveal unexpected complexity and fitness effects of structural variants.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {39990470}, issn = {2692-8205}, support = {R01 GM123489/GM/NIGMS NIH HHS/United States ; R01 HG011485/HG/NHGRI NIH HHS/United States ; R35 GM133412/GM/NIGMS NIH HHS/United States ; U01 DA047638/DA/NIDA NIH HHS/United States ; }, abstract = {Structural variants (SVs) are widespread in vertebrate genomes, yet their evolutionary dynamics remain poorly understood. Using 45 long-read de novo genome assemblies and pangenome tools, we analyze SVs within three closely related species of North American jays (Aphelocoma, scrub-jays) displaying a 60-fold range in effective population size. We find rapid evolution of genome architecture, including ~100 Mb variation in genome size driven by dynamic satellite landscapes with unexpectedly long (> 10 kb) repeat units and widespread variation in gene content, influencing gene expression. SVs exhibit slightly deleterious dynamics modulated by variant length and population size, with strong evidence of adaptive fixation only in large populations. Our results demonstrate how population size shapes the distribution of SVs and the importance of pangenomes to characterizing genomic diversity.}, } @article {pmid40034275, year = {2025}, author = {Veneros, J and Hansen, AJ and Jantz, P and Roberts, D and Noguera-Urbano, E and García, L}, title = {Analysis of changes in temperature and precipitation in South American countries and ecoregions: Comparison between reference conditions and three representative concentration pathways for 2050.}, journal = {Heliyon}, volume = {11}, number = {4}, pages = {e42459}, pmid = {40034275}, issn = {2405-8440}, abstract = {Climate change is a global concern, and its impact on environmental variables such as temperature and annual precipitation is unknown spatially in the desert, andes, and rainforest ecoregions of Peru, Ecuador, and Colombia. In this study, we conducted a general review of climate drivers for South America (SA) and explored climate data using the GCM compareR package (General Circulation Models) and average ensembles for temperature and precipitation. Our results showed that all GCMs demonstrated increases in the annual mean temperature (BIO1) and in the mean temperature of the driest quarter (BIO9) for Peru, Ecuador, and Colombia for 2050 in three RCPs (2.6, 4.5, and 8.5). Also, most of the GCMs showed increases in the annual precipitation (BIO12) and the precipitation in the driest quarter (BIO17). We conducted non-parametric tests (Kruskal-Wallis Test) to assess if the medians of temperature and precipitation in the three ecoregions are equal for both the baseline and the climate change scenarios. We rejected the null hypothesis that the medians are equal for both temperatures and precipitation in the baseline vs. 2050 RCPs (2.6, 4.5, and 8.5). A spatial analysis was conducted to visualize the variations in temperature and precipitation between the RCPs versus the baseline, and the spatial variation at the country or ecoregion level can be observed. The annual mean temperature (°C) or annual precipitation (mm) divided by its standard deviation for each ecoregion (M metric) was analyzed to see how much the average temperature or the annual precipitation is relatively large compared to the variability or dispersion of temperatures or precipitation respectively; the average temperature and the annual precipitation for the baseline and the three RCPs are relatively large and associated with the variability or dispersion of their temperatures in the Napo moist forest compared to the other ecoregions. Our study provides important insights into the potential impacts of climate change on these ecosystems. Prospects in the Napo moist forest ecoregion, where significant changes in temperature and humidity have already occurred, and new species have invaded or evolved in the western Amazon rainforest, are particularly highlighted and reflected in terms of risk mitigation, ecosystem restoration, surveillance, and monitoring.}, } @article {pmid40033715, year = {2025}, author = {Gorné, LD and Hendry, AP and Pelletier, F and Sanderson, S and Correa, C and Arias, C and Beausoleil, MO and Boisjoly, M and Crispo, E and Berner, D and De León, LF and DiBattista, JD and Haines, GE and Haller, BC and Kinnison, MT and Muttalib, S and McKellar, AE and O'Dea, RE and Reyes-Corral, WD and Ritchot, Y and Oke, KB and Wood, ZT and Farrugia, T and Gotanda, KM}, title = {PROCEED v6.1: Phenotypic rates of change evolutionary and ecological database.}, journal = {Ecology}, volume = {106}, number = {3}, pages = {e70009}, doi = {10.1002/ecy.70009}, pmid = {40033715}, issn = {1939-9170}, support = {//Natural Sciences and Engineering Research Council of Canada/ ; //Le Fonds Québécois de la Recherche sur la Nature et les Technologies/ ; //McGill University/ ; //National Science Foundation/ ; //Brock University/ ; }, mesh = {*Biological Evolution ; Animals ; *Phenotype ; *Databases, Factual ; Ecosystem ; }, abstract = {Populations must continuously respond to environmental change or risk extinction. These responses can be measured as phenotypic rates of change, which allow researchers to predict their contemporary evolutionary responses. In 1999, a database of phenotypic rates of change in wild populations was compiled. Since then, researchers have used (and expanded) this database to examine the phenotypic responses as a function of the features of the study system (i.e., the population or set of populations, of a given species, that experienced a specific driver or disturbance), the measured traits, and methodological approaches. Therefore, PROCEED (Phenotypic Rates of Change Evolutionary and Ecological Database) is an ongoing compilation of rates of phenotypic change, typically calculated as Haldanes and Darwins, published in peer-reviewed literature (but also including data from theses and technical reports). Studies in this database measure the intraspecific change in quantitative (continuous or discrete) traits and report either the time elapsed from the onset of environmental novelty, or reference a historical or biological event reported in other sources (e.g., a mine opening or a well-documented biological invasion). Included studies either follow a single population through time (allochronic design) or compare two or more populations that diverged at a known time (synchronic design). Some included studies account for the total phenotypic variability in the field (i.e., phenotypic studies), while others employed common-garden or other quantitative genetic approaches to account for the heritable component of the phenotypic change (i.e., genetic studies). PROCEED includes systems in both natural and experimental conditions, provided that reproduction was not manipulated (i.e., artificial selection experiments were excluded). In the included experimental systems, the environment of the focal populations was manipulated (e.g., an herbivory exclusion experiment, where the type and load of herbivory are manipulated) but the studies did not deliberately select for trait values in the study population (e.g., the plant height). PROCEED does not include systems where the phenotypic change is presumably due to interspecific hybridization, polyploidy, or other chromosomal alterations. Here, we present the most recently updated PROCEED (Version 6.1). This new, curated version has 9263 records (n) collated from 326 studies, 1801 systems, and 428 species. The database includes records belonging to mammals (n = 686), birds (n = 1475), reptiles (n = 96), amphibians (n = 23), fishes (n = 3671), invertebrates (n = 1141, mostly arthropods), and plants (n = 2171). The maximum elapsed time between the environmental change and the sampling is 500 years but is typically less than 100 years (third quartile 89.5; median 45 years). The database also includes a set of variables describing biological and methodological aspects of the study system and measured traits, along with features of the sampling design in the primary source of information. This new version of PROCEED also includes a time series dataset comprising a subset of records included in the general dataset. These are allochronic studies with three or more sampling times throughout the entire study period. The time series dataset contains 655 time series (s)-belonging to 61 studies, from 156 systems, and 77 species-including mammals (s = 140), birds (s = 77), reptiles (s = 4), amphibians (s = 8), fishes (s = 404), and plants (s = 22). The data are released under a Creative Commons CC0 1.0 Universal Public Domain Dedication license.}, } @article {pmid38995706, year = {2024}, author = {Dietrich, SW and Ma, W and Ding, Y and Watanabe, KH and Zelinski, MB and Sluka, JP}, title = {MOTHER-DB: A Database for Sharing Nonhuman Ovarian Histology Images.}, journal = {IEEE/ACM transactions on computational biology and bioinformatics}, volume = {21}, number = {6}, pages = {2598-2603}, pmid = {38995706}, issn = {1557-9964}, support = {P51 OD011092/OD/NIH HHS/United States ; }, mesh = {Female ; *Databases, Factual ; *Ovary/pathology ; Animals ; Metadata ; Information Dissemination/methods ; Image Processing, Computer-Assisted/methods ; Computational Biology/methods ; }, abstract = {The goal of the Multispecies Ovary Tissue Histology Electronic Repository (MOTHER) project is to establish a collection of nonhuman ovary histology images for multiple species as a resource for researchers and educators. An important component of sharing scientific data is the inclusion of the contextual metadata that describes the data. MOTHER extends the Ecological Metadata Language (EML) for documenting research data, leveraging its data provenance and usage license with the inclusion of metadata for ovary histology images. The design of the MOTHER metadata includes information on the donor animal, including reproductive cycle status, the slide and its preparation. MOTHER also extends the ezEML tool, called ezEML+MOTHER, for the specification of the metadata. The design of the MOTHER database (MOTHER-DB) captures the metadata about the histology images, providing a searchable resource for discovering relevant images. MOTHER also defines a curation process for the ingestion of a collection of images and its metadata, verifying the validity of the metadata before its inclusion in the MOTHER collection. A Web search provides the ability to identify relevant images based on various characteristics in the metadata itself, such as genus and species, using filters.}, } @article {pmid40030035, year = {2025}, author = {Jin, J and Zhang, R and Li, J and Gao, F and Liao, Z and Yu, Y and Wang, Y and Bucci, D and Xiao, M and Ma, R and Ma, Q and Gao, S and Lio, J and Novais, F and Huang, SC and Zhu, J and Ghoneim, H and Wen, H and Li, Z and Sun, N and Xin, G}, title = {The NAE1-mediated neddylation operates as an essential post-translational modification checkpoint for effector CD8[+] T cells.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {122}, number = {10}, pages = {e2424061122}, doi = {10.1073/pnas.2424061122}, pmid = {40030035}, issn = {1091-6490}, support = {1R01CA269984//HHS | NIH | National Cancer Institute (NCI)/ ; CCR231013713//Susan G. Komen (SGK)/ ; RSG-23-1036499-01//American Cancer Society (ACS)/ ; }, mesh = {*CD8-Positive T-Lymphocytes/immunology/metabolism ; Humans ; *Protein Processing, Post-Translational ; Animals ; Mice ; *NEDD8 Protein/metabolism/genetics ; Ubiquitin-Activating Enzymes/metabolism/genetics ; NFATC Transcription Factors/metabolism/genetics ; Lymphocyte Activation ; Receptors, Antigen, T-Cell/metabolism ; Colonic Neoplasms/immunology/metabolism/genetics/pathology ; Signal Transduction ; Mice, Inbred C57BL ; }, abstract = {Optimal activation of CD8+ T cells is crucial for immunity-mediated destruction of cancer, requiring a substantial amount of proteins involved in metabolism, proliferation, and effector function. Despite extensive studies emphasizing the role of transcriptional regulation in this process, paired transcriptomic and proteomic analyses reveal that the RNA profile is poorly correlated with protein levels. This discrepancy underscores the importance of post-translational modifications (PTMs) in controlling protein abundance during activation. However, the impact of PTMs on the CD8+ T cell protein dynamic remains underexplored. We identify that neddylation, a recently discovered PTM, is activated in response to T cell receptor (TCR) stimulation and enriched in effector CD8+ T cells from colon cancer patients. Mechanistically, we found the rate-limiting enzyme of neddylation, neural precursor cell expressed developmentally down-regulated protein 8 activating enzyme E1 (NAE1), is induced by the NFATc1, a critical transcription factor downstream of TCR signaling. Our observation revealed that genetic ablation of NAE1 significantly disturbed the proteomic landscape related to activation and mitochondrial function. As a result, CD8+ T cells lacking NAE1 exhibited severely compromised activation, proliferation, and survival, which was accompanied by impaired mitochondrial function. Consistently, deletion of NAE1 in CD8+ T cells abolished their antitumor function and promoted tumor progression. By contrast, the overexpression of NAE1 significantly improved the function of tumor-infiltrating CD8+ T cells. Overall, we uncovered neddylation, a previously underappreciated PTM, as a proteomic checkpoint for CD8+ T cell activation. Enforced expression of NAE1 offers promising therapeutic potential for boosting the antitumor CD8+ T cell responses.}, } @article {pmid40029426, year = {2025}, author = {Zhang, J and Wang, Q and Gao, H and Qi, Q and He, W and Li, J and Yao, S and Li, W}, title = {Ecological suitability distribution of hop based on MaxEnt modeling.}, journal = {Environmental monitoring and assessment}, volume = {197}, number = {4}, pages = {346}, pmid = {40029426}, issn = {1573-2959}, mesh = {China ; *Environmental Monitoring ; *Humulus/growth & development ; *Ecosystem ; Geographic Information Systems ; Climate ; Soil/chemistry ; }, abstract = {Hop has been widely utilized in both food production and traditional medicine owing to their distinctive flavor and various pharmacological effects. In recent years, the increasing demand for hop has led to their cultivation in many regions across China. However, hops require specific ecological conditions, including climate, soil, precipitation, and temperature, which significantly affect their distribution and growth. To facilitate the standardization and scientific cultivation of hops, it is essential to clarify the distribution of their ecological suitability. In this study, we collected data from 95 hops distribution locations and 115 ecological factors to determine the areas suitable for hops cultivation using the Maximum Entropy (MaxEnt) model and Geographic Information System (GIS). The highly suitable areas are primarily located in the northwestern part of the Xinjiang Uygur Autonomous Region, the eastern part of Gansu Province, Shaanxi Province, the southwestern part of Shanxi Province, and parts of Ningxia Hui Autonomous Region and Yunnan Province. These findings provide valuable guidance for the scientific cultivation of hops, ensuring the efficient use of ecological resources and promoting sustainable cultivation practices.}, } @article {pmid40028932, year = {2025}, author = {Eisaguirre, JM and Lohman, MG and Frye, GG and Johnson, HE and Riecke, TV and Williams, PJ}, title = {Estimating Spatially Explicit Survival and Mortality Risk From Telemetry Data With Thinned Point Process Models.}, journal = {Ecology letters}, volume = {28}, number = {3}, pages = {e70092}, doi = {10.1111/ele.70092}, pmid = {40028932}, issn = {1461-0248}, support = {//U.S. Geological Survey/ ; //National Science Foundation Graduate Research Fellowship Program/ ; //Institute for Wetland and Waterfowl Research Bonnycastle Fellowship for Wetland and Waterfowl Research/ ; }, mesh = {Animals ; *Telemetry ; Alaska ; Ecosystem ; Models, Biological ; Mortality ; Geographic Information Systems ; }, abstract = {Mortality risk for animals often varies spatially and can be linked to how animals use landscapes. While numerous studies collect telemetry data on animals, the focus is typically on the period when animals are alive, even though there is important information that could be gleaned about mortality risk. We introduce a thinned spatial point process (SPP) modelling framework that couples relative abundance and space use with a mortality process to formally treat the occurrence of mortality events across the landscape as a spatial process. We show how this model can be embedded in a hierarchical statistical framework and fit to telemetry data to make inferences about how spatial covariates drive both space use and mortality risk. We apply the method to two data sets to study the effects of roads and habitat on spatially explicit mortality risk: (1) VHF telemetry data collected for willow ptarmigan in Alaska, and (2) hourly GPS telemetry data collected for black bears in Colorado. These case studies demonstrate the applicability of this method for different species and data types, making it broadly useful in enabling inferences about the mechanisms influencing animal survival and spatial population processes while formally treating survival as a spatial process, especially as the development and implementation of joint analyses continue to progress.}, } @article {pmid40028774, year = {2025}, author = {Fuzessy, L and Pizo, MA}, title = {NeoFrugivory: A comprehensive database for frugivory interactions and functional traits in the Neotropics.}, journal = {Ecology}, volume = {106}, number = {3}, pages = {e70049}, doi = {10.1002/ecy.70049}, pmid = {40028774}, issn = {1939-9170}, support = {2023/12469-5//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 21/02943-6//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 151167/2023-0//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 304742/2019-8//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; }, mesh = {Animals ; *Fruit/physiology ; Vertebrates/physiology ; Databases, Factual ; Tropical Climate ; Plants/classification ; Feeding Behavior ; Herbivory ; Ecosystem ; }, abstract = {Frugivory plays a crucial role in shaping Neotropical ecosystems, influencing plant dispersal, community dynamics, and ecosystem function. Despite its ecological significance, a systematic understanding of frugivore-fruit interactions spanning the entire Neotropical realm has been lacking. Therefore, we compiled the NeoFrugivory database, which addresses this gap by synthesizing data from a wide range of sources, including peer-reviewed literature, field studies, and existing databases. NeoFrugivory represents a comprehensive compilation of 10,175 unique frugivory interactions across the Neotropical region, the most diverse in terms of vertebrate frugivores, and consolidates information from 419 studies spanning from 1967 to 2023. It includes 2375 plant species and 758 terrestrial vertebrate species. In addition to documenting frugivory interactions, NeoFrugivory includes information on functional traits for both plants and vertebrates, such as body mass, diet, fruit morphology, and seed characteristics. The database encompasses diverse terrestrial vertebrate taxa, including species belonging to taxonomic groups such as Primates, Chiroptera, Birds, Artiodactyla/Perissodactyla, Reptilia, Carnivora, Marsupialia, and Rodentia. By providing a centralized repository of frugivory interactions, NeoFrugivory facilitates comprehensive analyses of ecological networks, evolutionary patterns, and ecosystem dynamics across the Neotropics, and NeoFrugivory provides a unique resource for researchers interested in exploring the intricate dynamics of plant-animal frugivory interactions in the Neotropics. This database enables researchers to explore the ecological roles of different frugivore taxa, identify keystone species, assess the resilience of mutualistic networks, and evaluate the impacts of environmental change on fruit-frugivore interactions. Furthermore, NeoFrugivory serves as a valuable resource for conservation practitioners, supporting the design and implementation of targeted conservation strategies aimed at preserving biodiversity and ecosystem function in the Neotropical region. Overall, NeoFrugivory represents a significant advancement in our understanding of frugivory dynamics in the Neotropics and provides a foundation for future research and conservation efforts in this ecologically diverse and critically important region. There are no copyright restrictions on the data; this paper should be cited when data are used in publications.}, } @article {pmid40027489, year = {2025}, author = {Bai, D and Chen, T and Xun, J and Ma, C and Luo, H and Yang, H and Cao, C and Cao, X and Cui, J and Deng, YP and Deng, Z and Dong, W and Dong, W and Du, J and Fang, Q and Fang, W and Fang, Y and Fu, F and Fu, M and Fu, YT and Gao, H and Ge, J and Gong, Q and Gu, L and Guo, P and Guo, Y and Hai, T and Liu, H and He, J and He, ZY and Hou, H and Huang, C and Ji, S and Jiang, C and Jiang, GL and Jiang, L and Jin, LN and Kan, Y and Kang, D and Kou, J and Lam, KL and Li, C and Li, C and Li, F and Li, L and Li, M and Li, X and Li, Y and Li, ZT and Liang, J and Lin, Y and Liu, C and Liu, D and Liu, F and Liu, J and Liu, T and Liu, T and Liu, X and Liu, Y and Liu, B and Liu, M and Lou, W and Luan, Y and Luo, Y and Lv, H and Ma, T and Mai, Z and Mo, J and Niu, D and Pan, Z and Qi, H and Shi, Z and Song, C and Sun, F and Sun, Y and Tian, S and Wan, X and Wang, G and Wang, H and Wang, H and Wang, H and Wang, J and Wang, J and Wang, K and Wang, L and Wang, SK and Wang, X and Wang, Y and Xiao, Z and Xing, H and Xu, Y and Yan, SY and Yang, L and Yang, S and Yang, Y and Yao, X and Yousuf, S and Yu, H and Lei, Y and Yuan, Z and Zeng, M and Zhang, C and Zhang, C and Zhang, H and Zhang, J and Zhang, N and Zhang, T and Zhang, YB and Zhang, Y and Zhang, Z and Zhou, M and Zhou, Y and Zhu, C and Zhu, L and Zhu, Y and Zhu, Z and Zou, H and Zuo, A and Dong, W and Wen, T and Chen, S and Li, G and Gao, Y and Liu, YX}, title = {EasyMetagenome: A user-friendly and flexible pipeline for shotgun metagenomic analysis in microbiome research.}, journal = {iMeta}, volume = {4}, number = {1}, pages = {e70001}, pmid = {40027489}, issn = {2770-596X}, abstract = {Shotgun metagenomics has become a pivotal technology in microbiome research, enabling in-depth analysis of microbial communities at both the high-resolution taxonomic and functional levels. This approach provides valuable insights of microbial diversity, interactions, and their roles in health and disease. However, the complexity of data processing and the need for reproducibility pose significant challenges to researchers. To address these challenges, we developed EasyMetagenome, a user-friendly pipeline that supports multiple analysis methods, including quality control and host removal, read-based, assembly-based, and binning, along with advanced genome analysis. The pipeline also features customizable settings, comprehensive data visualizations, and detailed parameter explanations, ensuring its adaptability across a wide range of data scenarios. Looking forward, we aim to refine the pipeline by addressing host contamination issues, optimizing workflows for third-generation sequencing data, and integrating emerging technologies like deep learning and network analysis, to further enhance microbiome insights and data accuracy. EasyMetageonome is freely available at https://github.com/YongxinLiu/EasyMetagenome.}, } @article {pmid40023237, year = {2025}, author = {Munteanu, A and Bortolini, M and Feltracco, M and Alterio, A and Cairns, WRL and Turetta, C and Barbaro, E and Barbante, C and Gambaro, A and Azzaro, M}, title = {Contamination by benzothiazoles in the Arctic: first evidence in the seawater of the Greenland Sea.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {}, number = {}, pages = {125943}, doi = {10.1016/j.envpol.2025.125943}, pmid = {40023237}, issn = {1873-6424}, abstract = {Benzothiazoles (BTHs), used in industrial chemistry, consumer products, and pharmaceuticals, are emerging contaminants due to their environmental presence and toxicological risks to aquatic life and human health. However, their environmental fate in seawater remains poorly investigated. This study reports for the first time the occurrence and distribution of six BTHs in the sub-Arctic seawater of the Greenland Sea. Using solid-phase extraction combined with ultrahigh performance liquid chromatography tandem mass spectrometry, total BTHs were detected at concentrations ranging from 0.2 to 1043 ng L[-1]. Benzothiazole, 2-hydroxy-benzothiazole, 2-methylthio-benzothiazole, and 2-methyl-benzothiazole exhibited higher mean concentrations (355 ± 335, 114 ± 80, 34 ± 7, 15 ± 8 ng L[-1], respectively) compared to 2-thiocyanomethylthio-benzothiazole (0.5 ± 0.9 ng L[-1]) and 2-amino-benzothiazole (0.3 ± 0.2 ng L[-1]). Local emissions and both short- and long-range transport may account for BTHs presence in the Greenland Sea. The spatial distribution of BTHs along the 75° N transect and in the water column appears influenced by the Greenland Sea Gyre circulation and deep convection processes. Total BTHs distribution showed no significant differences between superficial and water column concentrations or between the outermost and innermost transect zones, as determined by the Mann-Whitney test, although concentrations were generally higher in the zone influenced by the Norwegian Atlantic Current. The ecological risks of BTHs, assessed using the risk quotient methodology, indicate a low threat to aquatic life. This research underscores the need for monitoring BTHs in the Arctic to understand their sources, transport, and environmental fate, providing a foundation for future studies.}, } @article {pmid40022802, year = {2025}, author = {Wang, H and Liu, C and Li, L and Kong, Y and Akbar, A and Zhou, X}, title = {High-precision inversion of urban river water quality via integration of riparian spatial structures and river spectral signatures.}, journal = {Water research}, volume = {278}, number = {}, pages = {123378}, doi = {10.1016/j.watres.2025.123378}, pmid = {40022802}, issn = {1879-2448}, abstract = {With the ongoing process of urbanization, it poses challenges to the monitoring of water quality in urban rivers. The mainstream methods for remote sensing water quality monitoring rely on the optical characteristics of water to achieve water quality inversion, while overlooking the correlation between water quality and riparian zones. The spatial arrangement and scale fluctuation of the riparian zones exert a substantial influence on water quality as it serves as an intermediary region connecting riverine and terrestrial ecosystems. Therefore, this study firstly employed unmanned aerial vehicle (UAV)-borne multispectral remote sensing technology to capture the subtle variations in urban river water quality and obtain detailed spatial information of the riparian zone. The Liang-Kleeman information flow was subsequently employed to quantitatively assess the causal responses of the spatial composition of riparian zone to water quality parameters across various spatial scales. Finally, we developed a hierarchical ensemble learning model for water quality assessment by integrating the spatial characteristics of the riparian zone with the spectral properties of the water body. The result demonstrates that this model accurately delineated water quality grades for three key parameters: ammonia nitrogen (NH3N), chemical oxygen demand (COD), and total phosphorus (TP), achieving accuracies of 94.87 %, 92.31 %, and 89.74 %, respectively. Our study presents a water quality inversion method for urban rivers, which holds significant guidance for the monitoring and management of urban rivers and contributes to further promoting the sustainable development of cities.}, } @article {pmid39974046, year = {2025}, author = {Slack, SD and Esquinca, E and Arehart, CH and Boorgula, MP and Szczesny, B and Romero, A and Campbell, M and Chavan, S and Rafaels, N and Watson, H and Landis, RC and Hansel, NN and Rotimi, CN and Olopade, CO and Figueiredo, CA and Ober, C and Liu, AH and Kenny, EE and Kammers, K and Ruczinski, I and Taub, MA and Daya, M and Gignoux, CR and Kechris, K and Barnes, KC and Mathias, RA and Johnson, RK}, title = {Prediction and Characterization of Genetically Regulated Expression of Target Tissues in Asthma.}, journal = {medRxiv : the preprint server for health sciences}, volume = {}, number = {}, pages = {}, pmid = {39974046}, support = {R01 AI132476/AI/NIAID NIH HHS/United States ; R01 HL104608/HL/NHLBI NIH HHS/United States ; }, abstract = {BACKGROUND: Genetic control of gene expression in asthma-related tissues is not well-characterized, particularly for African-ancestry populations, limiting advancement in our understanding of the increased prevalence and severity of asthma in those populations.

OBJECTIVE: To create novel transcriptome prediction models for asthma tissues (nasal epithelium and CD4+ T cells) and apply them in transcriptome-wide association study (TWAS) to discover candidate asthma genes.

METHODS: We developed and validated gene expression prediction databases for unstimulated CD4+ T cells (CD4+T) and nasal epithelium using an elastic net framework. Combining these with existing prediction databases (N=51), we performed TWAS of 9,284 individuals of African-ancestry to identify tissue-specific and cross-tissue candidate genes for asthma. For detailed Methods, please see the Supplemental Methods.

RESULTS: Novel databases for CD4+T and nasal epithelial gene expression prediction contain 8,351 and 10,296 genes, respectively, including four asthma loci (SCGB1A1, MUC5AC, ZNF366, LTC4S) not predictable with existing public databases. Prediction performance was comparable to existing databases and was most accurate for populations sharing ancestry with the training set (e.g. African ancestry). From TWAS, we identified 17 candidate causal asthma genes (adjusted P<0.1), including genes with tissue-specific (IL33 in nasal epithelium) and cross-tissue (CCNC and FBXW7) effects.

CONCLUSIONS: Expression of IL33, CCNC, and FBXW7 may affect asthma risk in African ancestry populations by mediating inflammatory responses. The addition of CD4+T and nasal epithelium prediction databases to the public sphere will improve ancestry representation and power to detect novel gene-trait associations from TWAS.}, } @article {pmid40025088, year = {2025}, author = {Kim, SY and Cheon, S and Park, C and Soh, HY}, title = {Integrating DNA metabarcoding and morphological analysis improves marine zooplankton biodiversity assessment.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {7283}, pmid = {40025088}, issn = {2045-2322}, support = {RS-2018-KS181192//Korea Institute of Marine Science & Technology Promotion (KIMST) funded by the Ministry of Oceans and Fisheries, Korea/ ; RS-2018-KS181192//Korea Institute of Marine Science & Technology Promotion (KIMST) funded by the Ministry of Oceans and Fisheries, Korea/ ; No. RS-2024-00442775)//Global-Learning & Academic research institution for Master's · PhD students, and Postdocs (LAMP) Program of the National Research Foundation of Korea (NRF) grant funded by the Ministry of Education/ ; Grant number: 2018-3416//Chonnam National University/ ; }, mesh = {Animals ; *Zooplankton/genetics/classification ; *DNA Barcoding, Taxonomic/methods ; *Biodiversity ; *Copepoda/genetics/classification ; Ecosystem ; China ; Oceans and Seas ; Aquatic Organisms/genetics/classification ; }, abstract = {Marine copepod communities play crucial roles in ocean ecosystems. However, their accurate assessment remains challenging due to taxonomic complexities. This study combines morphological and DNA metabarcoding approaches to evaluate copepod diversity and community structure in the northern East China Sea. Zooplankton samples were collected from 10 stations along a coastal-offshore gradient in August 2019. Morphological analysis identified 34 species from 25 genera, while DNA metabarcoding detected 31 species from 20 genera. Both methods revealed distinct coastal and offshore assemblages, with Paracalanus parvus s.l. as the dominant species across all stations. A significant positive correlation was found between morphology-based individual counts and metabarcoding sequence reads (Spearman's Rho = 0.58, p < 0.001), improving at the genus level (Rho = 0.70, p < 0.001). Redundancy analysis revealed that salinity, temperature, and phytoplankton density significantly influenced copepod distribution. Although both approaches captured similar broad-scale patterns, they provided complementary insights into community structure. Morphological identification was more effective for detecting Cyclopoida diversity, whereas DNA metabarcoding had greater sensitivity for specific Calanoid species. This study underscores the value of integrating traditional and molecular methods for marine biodiversity assessment, especially in the context of global environmental changes.}, } @article {pmid40021550, year = {2025}, author = {Post, AK and Richardson, AD}, title = {Predicting end-of-season timing across diverse North American grasslands.}, journal = {Oecologia}, volume = {207}, number = {3}, pages = {44}, pmid = {40021550}, issn = {1432-1939}, support = {EF-1065029//National Science Foundation/ ; EF-1702697//National Science Foundation/ ; DESC0016011//U.S. Department of Energy/ ; }, mesh = {*Grassland ; *Seasons ; *Climate Change ; North America ; Ecosystem ; }, abstract = {Climate change is altering the timing of seasonal vegetation cycles (phenology), with cascading consequences on larger ecosystem processes. Therefore, understanding the drivers of vegetation phenology is critical to predicting ecological impacts of climate change. While numerous phenology models exist to predict the timing of the start of the growing season (SOS), there are fewer end-of-season (EOS) models, and most perform poorly in grasslands, since they were made for forests. Our objective was to develop an improved EOS grassland phenology model. We used repeat digital imagery from the PhenoCam Network to extract EOS dates for 44 diverse North American grassland sites (212 site-years) that we fit to 20 new and 3 existing EOS models. All new EOS models (RMSE = 22-33 days between observed and predicted dates) performed substantially better than existing ones (RMSE = 43-46 days). The top model predicted EOS after surpassing a threshold of either accumulated cold temperatures or dryness, but only after a certain number of days following SOS. Including SOS date improved all model fits, indicating a strong correlation between start- and end-of-season timing. Model performance was further improved by independently optimizing parameters for six distinct climate regions (RMSE = 4-19 days). While the best model varied slightly by region, most included similar drivers as the top all-sites model. Thus, across diverse grassland sites, EOS is influenced by both weather (temperature, moisture) and SOS timing. Incorporating these new EOS models into Earth System Models should improve predictions of grassland dynamics and associated ecosystem processes.}, } @article {pmid39955977, year = {2025}, author = {Otay, EN and Uzun, P and Üstün, A}, title = {Multifactorial risk mapping of oil spill accidents for emergency response areas at regional, national and international scales.}, journal = {Marine pollution bulletin}, volume = {213}, number = {}, pages = {117670}, doi = {10.1016/j.marpolbul.2025.117670}, pmid = {39955977}, issn = {1879-3363}, mesh = {*Petroleum Pollution ; Risk Assessment ; Geographic Information Systems ; Turkey ; Environmental Monitoring/methods ; Risk Management ; Accidents/statistics & numerical data ; }, abstract = {Quantification and mapping of oil spill risk are essential for emergency response and mitigation of marine accidents. Large-scale risk management involves geographical identification of hazards and sensitivities in coastal and offshore regions. In this study, a multifactorial oil spill risk model was developed on a national scale by determining the frequency (probability) and sensitivity (severity) of marine and coastal accidents. Seven accident frequency and 51 sensitivity factors were investigated within the Turkish Emergency Response Area (TERA) of 660,908 km[2]. Hydrographical, meteorological, oceanographical, and maritime conditions were analyzed to calculate accident frequency. The sensitive areas were mapped using the geographical distribution of ecologic, social, and economic assets. Using data analytics, digital maps of accident frequency, sensitivity and risk were produced in a GIS grid of 21,410 cells with 3NM resolution. Accident hotspots were identified from scalable frequency maps showing regions of high accident probability. Sensitivity factors were analyzed from environmental, social, and economic vulnerabilities. Using their geographic distribution, a sensitivity map was generated and hotspots were identified. Frequency and sensitivity indices were combined to obtain the grid-based high-resolution oil spill risk map on a scalable GIS platform. High-risk areas were identified for future research on oil spill simulations and emergency response plans. The methodology may help scientists and environmental experts develop regional, national, and global risk assessment tools. The outcomes within the TERA may serve as planning and decision support tools for lawmakers, environmental experts, and oil spill response professionals to manage oil pollution risk across the TERA.}, } @article {pmid40016792, year = {2025}, author = {Mendoza, JN and Prūse, B and Ciriaco, A and Mendoza, A and Ciriaco, H and Buen, C and Pua, JJ and Primavera, F and Mattalia, G and Sõukand, R}, title = {Correction: Fishery and ecology-related knowledge about plants among fishing communities along Laguna Lake, Philippines.}, journal = {Journal of ethnobiology and ethnomedicine}, volume = {21}, number = {1}, pages = {11}, doi = {10.1186/s13002-025-00763-7}, pmid = {40016792}, issn = {1746-4269}, } @article {pmid40014700, year = {2025}, author = {Chen, Z and Baeza, JA and Chen, C and Gonzalez, MT and González, VL and Greve, C and Kocot, KM and Arbizu, PM and Moles, J and Schell, T and Schwabe, E and Sun, J and Wong, NLWS and Yap-Chiongco, M and Sigwart, JD}, title = {A genome-based phylogeny for Mollusca is concordant with fossils and morphology.}, journal = {Science (New York, N.Y.)}, volume = {387}, number = {6737}, pages = {1001-1007}, doi = {10.1126/science.ads0215}, pmid = {40014700}, issn = {1095-9203}, mesh = {Animals ; *Phylogeny ; *Mollusca/genetics/classification/anatomy & histology ; *Genome ; *Fossils ; }, abstract = {Extreme morphological disparity within Mollusca has long confounded efforts to reconstruct a stable backbone phylogeny for the phylum. Familiar molluscan groups-gastropods, bivalves, and cephalopods-each represent a diverse radiation with myriad morphological, ecological, and behavioral adaptations. The phylum further encompasses many more unfamiliar experiments in animal body-plan evolution. In this work, we reconstructed the phylogeny for living Mollusca on the basis of metazoan BUSCO (Benchmarking Universal Single-Copy Orthologs) genes extracted from 77 (13 new) genomes, including multiple members of all eight classes with two high-quality genome assemblies for monoplacophorans. Our analyses confirm a phylogeny proposed from morphology and show widespread genomic variation. The flexibility of the molluscan genome likely explains both historic challenges with their genomes and their evolutionary success.}, } @article {pmid40012989, year = {2024}, author = {Boyes, D and Holland, PWH and , and , and , and , and , and , and , }, title = {The genome sequence of the Olive Crescent, Trisateles emortualis (Denis & Schiffermüller, 1775).}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {178}, pmid = {40012989}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual male Trisateles emortualis (the Olive Crescent; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 565.5 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 16.01 kilobases in length. Gene annotation of this assembly on Ensembl identified 13,176 protein coding genes.}, } @article {pmid40012987, year = {2024}, author = {McGregor, AP and Sumner-Rooney, L and Burkmar, R and Schoenauer, A and , and , and , and , and , and , and , }, title = {The genome sequence of the silver stretch spider, Tetragnatha montana (Simon, 1874) (Araneae: Tetragnathidae).}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {288}, pmid = {40012987}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual female Tetragnatha montana (the silver stretch spider; Arthropoda; Arachnida; Araneae; Tetragnathidae). The genome sequence is 784.7 megabases in span. Most of the assembly is scaffolded into 13 chromosomal pseudomolecules, including the X sex chromosome. The mitochondrial genome has also been assembled and is 15.49 kilobases in length.}, } @article {pmid40011724, year = {2025}, author = {Brodie, JF and Mohd-Azlan, J and Chen, C and Wearn, OR and Deith, MCM and Ball, JGC and Slade, EM and Burslem, DFRP and Teoh, SW and Williams, PJ and Nguyen, A and Moore, JH and Goetz, SJ and Burns, P and Jantz, P and Hakkenberg, CR and Kaszta, Z and Cushman, S and Coomes, D and Helmy, OE and Reynolds, G and Rodríguez, JP and Jetz, W and Luskin, MS}, title = {Reply to: Causal claims, causal assumptions and protected area impact.}, journal = {Nature}, volume = {638}, number = {8052}, pages = {E42-E44}, pmid = {40011724}, issn = {1476-4687}, } @article {pmid40011233, year = {2025}, author = {Dos Santos, AP and da Silva Junior, AX and Nery, LM and Gomes, G and Toniolo, BP and da Cunha E Silva, DC and Lourenço, RW}, title = {Random forest algorithm applied to model soil textural classification in a river basin.}, journal = {Environmental monitoring and assessment}, volume = {197}, number = {3}, pages = {330}, pmid = {40011233}, issn = {1573-2959}, mesh = {*Soil/chemistry ; *Environmental Monitoring/methods ; *Rivers/chemistry ; *Algorithms ; Agriculture ; Machine Learning ; Geographic Information Systems ; Conservation of Natural Resources/methods ; Random Forest ; }, abstract = {The proportion of sand, silt, and clay defines soil texture, significantly influencing agricultural and ecological practices. However, conventional classification methods are costly and limit evaluation frequency and scope. In contrast, machine learning algorithms, such as random forest, provide a more efficient solution for accurate soil texture predictions. This study aims to address this knowledge gap by integrating geoprocessing, precision agriculture, and machine learning to classify soil texture in the Sorocabuçu River Basin (SRB), predominantly agricultural. Twenty-seven sampling points were selected based on topography and land use, ensuring the representativeness of area variations and the reliability of classification. Granulometric analysis was performed using the pipette method to separate sand, silt, and clay. The data were spatially interpolated using geographic information system (GIS) techniques. Soil texture was classified using the random forest algorithm, trained on 70% of the data and tested on 30%, evaluating overall accuracy, kappa index, sensitivity, and specificity. Fifty trees (ntree) and four features per split (ntry) were used, considering the variability of parameters to ensure satisfactory results. The varied spatial distribution of clay, along with high levels of sand and silt, suggests greater vulnerability to erosion without conservation management practices. The random forest model achieved an out-of-bag (OOB) error of 2.78%, a kappa index of 0.88, and an overall accuracy of 0.92, demonstrating excellent predictive capacity. The variability of sand was essential, but the Sandy Clay Loam (SCL) class posed challenges due to its intermediate characteristics between sand and clay, resulting in classification overlaps. This integrated methodology enhances understanding of soil structure in the SRB and provides a foundation for future research and practical applications, supporting food security and environmental sustainability. The model can be applied in other locations and agricultural contexts. In homogeneous soils, the method can be improved through the application of machine learning algorithms to enhance accuracy.}, } @article {pmid39742992, year = {2025}, author = {Kim, DH and Kim, Y}, title = {Factors Associated With Habitual Drug Use Among Adolescents: A Secondary Data Analysis.}, journal = {Asian nursing research}, volume = {19}, number = {1}, pages = {78-85}, doi = {10.1016/j.anr.2024.12.006}, pmid = {39742992}, issn = {2093-7482}, mesh = {Humans ; Adolescent ; Female ; Male ; Republic of Korea/epidemiology ; *Substance-Related Disorders/epidemiology ; *Adolescent Behavior/psychology ; Risk Factors ; Risk-Taking ; Prevalence ; Cross-Sectional Studies ; Secondary Data Analysis ; }, abstract = {PURPOSE: Drug use during adolescence can have lasting health consequences, and understanding the factors that contribute to drug use is essential for effective prevention. This study aimed to identify the factors influencing habitual drug use among South Korean adolescents. It employed Bronfenbrenner's ecological model to examine personal, familial, school-related, and social factors.

METHODS: The study analyzed data from the 19th Korea Youth Risk Behavior Survey for 41,928 students from 1st grade of middle school to 3rd grade of high school. Data analysis involved cross-tabulation and logistic regression for complex samples.

RESULTS: The prevalence of habitual drug use was 1.4%. Significant personal factors included smoking [adjusted odds ratio (aOR) = 2.61], alcohol consumption (aOR = 1.55), sexual intercourse (aOR = 1.45), smartphone overdependence (high-risk group aOR = 2.04, potential risk group aOR = 1.31), suicidal ideation (aOR = 2.66), depressed mood (aOR = 1.87), and loneliness (aOR = 1.88). Significant family factors included non-cohabitation with family (aOR = 1.86) and both parents being foreign-born (aOR = 3.36). Experience of violence (aOR = 2.95) was also a significant factor.

CONCLUSION: This study highlights the need for an integrated approach to prevent adolescent drug use by addressing adolescents' personal behaviors, family dynamics, and school environments. Prevention programs should account for the influence of multiple systems on habitual drug use. School and community nurses should adopt a comprehensive, multi-dimensional strategy that involves families, schools, and communities to prevent adolescent drug use. Additionally, there is a need to develop family-centered and culturally sensitive drug prevention programs for adolescents.}, } @article {pmid39297890, year = {2025}, author = {Daich Varela, M and Sanders Villa, A and Pontikos, N and Crossland, MD and Michaelides, M}, title = {Digital health and wearable devices for retinal disease monitoring.}, journal = {Graefe's archive for clinical and experimental ophthalmology = Albrecht von Graefes Archiv fur klinische und experimentelle Ophthalmologie}, volume = {263}, number = {2}, pages = {279-289}, pmid = {39297890}, issn = {1435-702X}, support = {206619/Z/17/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Humans ; *Wearable Electronic Devices ; *Telemedicine/instrumentation ; *Retinal Diseases/diagnosis/therapy/physiopathology ; Monitoring, Physiologic/instrumentation/methods ; Artificial Intelligence ; Digital Health ; }, abstract = {Digital health is wielding a growing influence across all areas of healthcare, encompassing various facets such as telemedicine, artificial intelligence (AI), and electronic healthcare records. In Ophthalmology, digital health innovations can be broadly divided into four categories: (i) self-monitoring home devices and apps, (ii) virtual and augmented reality visual aids, (iii) AI software, and (iv) wearables. Wearable devices can work in the background, collecting large amounts of objective data while we do our day-to-day activities, which may be ecologically more valid and meaningful to patients than that acquired in traditional hospital settings. They can be a watch, wristband, piece of clothing, glasses, cane, smartphone in our pocket, earphones, or any other device with a sensor that we carry with us. Focusing on retinal diseases, a key challenge in developing novel therapeutics has been to prove a meaningful benefit in patients' lives and the creation of objective patient-centred endpoints in clinical trials. In this review, we will discuss wearable devices collecting different aspects of visual behaviour, visual field, central vision, and functional vision, as well as their potential implementation as outcome measures in research/clinical trial settings. The healthcare landscape is facing a paradigm shift. Clinicians have a key role of collaborating with the development and fine-tuning of digital health innovations, as well as identifying opportunities where they can be leveraged to enhance our understanding of retinal diseases and improve patient outcomes.}, } @article {pmid40007820, year = {2024}, author = {Grieco, F and Parisi, S and Simmenroth, A and Eichinger, M and Zirkel, J and König, S and Jünger, J and Geck, E and Schwienhorst-Stich, EM}, title = {Planetary health education in undergraduate medical education in Germany: results from structured interviews and an online survey within the national PlanetMedEd Project.}, journal = {Frontiers in medicine}, volume = {11}, number = {}, pages = {1507515}, pmid = {40007820}, issn = {2296-858X}, abstract = {BACKGROUND: In light of the accumulating evidence, awareness and urgency to act upon the three planetary crises - climate change, biodiversity loss, and pollution - the concept of Planetary Health underscores their profound implications for health and promotes actionable solutions to advance both wellbeing and ecological sustainability. Despite (inter)national calls to integrate Planetary Health into health workers' curricula, the current status of Planetary Health Education in undergraduate medical education in Germany is unclear. This study therefore aimed (a) to assess the current implementation of Planetary Health in undergraduate medical education in Germany and (b) to explore its characteristics as a foundation to develop evidence-informed recommendations for mainstreaming Planetary Health Education in medical schools in Germany.

METHODS: The study comprised structured interviews followed by an online survey, both targeting all 39 medical schools in Germany. In 2021, structured interviews were conducted with students, educators and deanery staff at medical schools. In 2023, educators and deanery staff participated in an online survey based on the findings from the interviews.

FINDINGS: In total, 80% of the 39 medical schools participated in the interviews, while 90% took part in the online survey. Based on integrated findings, 35 medical schools (90%) offered Planetary Health Education, with a median of two educational activities, including both stand-alone courses and lectures integrated into other courses. Despite an overall increase since winter semester 2021/2022, most educational activities were electives and not part of the mandatory curriculum. Innovative educational approaches and learning objectives differed significantly between mandatory and elective formats. In contrast to mandatory educational activities, student involvement was reported for the majority of electives and was significantly associated with transformative learning objectives.

INTERPRETATION: Despite a steady rise in teaching activities, mandatory Planetary Health Education remains insufficiently integrated into undergraduate medical education in Germany. Key criteria defining high-quality Planetary Health Education, such as innovative educational approaches, practical skills, and transformative learning, were primarily reflected in electives, that reach only a minority of students. To adequately equip the future healthcare workforce, the current barriers to successfully integrating Planetary Health into medical education must be systematically addressed and overcome.}, } @article {pmid40007688, year = {2025}, author = {Boyes, D and Lees, DC and Coates, BS and , and , and , and , and , and , and , and , }, title = {The genome sequence of the European Corn Borer, Ostrinia nubilalis Hübner, 1796.}, journal = {Wellcome open research}, volume = {10}, number = {}, pages = {12}, pmid = {40007688}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual female specimen of Ostrinia nubilalis (European Corn Borer; Arthropoda; Insecta; Lepidoptera; Crambidae). The genome sequence has a total length of 495.50 megabases. Most of the assembly (99.87%) is scaffolded into 32 chromosomal pseudomolecules, including the Z and W sex chromosomes. The mitochondrial genome has also been assembled and is 15.24 kilobases in length. Gene annotation of this assembly on Ensembl identified 16,780 protein-coding genes.}, } @article {pmid40007687, year = {2025}, author = {Boyes, D and Lewis, OT and , and , and , and , and , and , and , }, title = {The genome sequence of Red Underwing, Catocala nupta Linnaeus, 1767.}, journal = {Wellcome open research}, volume = {10}, number = {}, pages = {36}, pmid = {40007687}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual female specimen of Catocala nupta (Red Underwing; Arthropoda; Insecta; Lepidoptera; Erebidae). The genome sequence has a total length of 930.40 megabases. Most of the assembly (99.82%) is scaffolded into 32 chromosomal pseudomolecules, including the W and Z sex chromosomes. The mitochondrial genome has also been assembled and is 15.57 kilobases in length. Gene annotation of this assembly on Ensembl identified 13,889 protein-coding genes.}, } @article {pmid40004070, year = {2025}, author = {Brzhozovskiy, AG and Semenov, SD and Zherebker, AY and Bugrova, AE and Yurova, MN and Zhernov, YV and Kovaleva, OA and Semenov, AL and Abroskin, DP and Kruglov, SS and Fedoros, EI and Kononikhin, AS and Nikolaev, EN}, title = {Hepatoprotective Activity of Nature-Derived Polyphenols Studied by Mass Spectrometry Based Multi-OMICS Approach.}, journal = {International journal of molecular sciences}, volume = {26}, number = {4}, pages = {}, doi = {10.3390/ijms26041604}, pmid = {40004070}, issn = {1422-0067}, support = {22-75-10140//Russian Science Foundation/ ; }, mesh = {Animals ; *Polyphenols/pharmacology ; Mice ; *Metabolomics/methods ; *Carbon Tetrachloride ; *Mice, Inbred BALB C ; *Protective Agents/pharmacology/chemistry ; Liver/drug effects/metabolism ; Mass Spectrometry/methods ; Proteomics/methods ; Pueraria/chemistry ; Metabolome/drug effects ; Plant Extracts/pharmacology/chemistry ; Male ; Proteome/drug effects/metabolism ; Multiomics ; }, abstract = {The aim of this study was to examine the hepatoprotective activity of multicomponent mixtures of natural origin in the BALB/C mouse model, with subacute liver failure (SALF) induced by the administration of toxin carbon tetrachloride (CCl4). The hepatoprotective activity of activated hydrolytic lignin (BP-Cx-1), humic acid peloids (HA), and isoflavones from kudzu Pueraria lobata roots (IFL) was evaluated using mass spectrometry (MS)-based omics technologies. Our MS-based approach revealed new insights into the molecular mechanisms of the hepatoprotective activity of multicomponent mixtures of natural origin. Significant differences were observed in the proteome and metabolome profiles of the urine and liver of BALB/c mice with SALF between a control group with CCl4 administration, intact controls, and groups receiving potential hepatoprotectors of natural origin (BP-Cx-1, HA, IFL). Proteomic and metabolomics analyses demonstrated that among the hepatoprotectors, IFL possessed the highest hepatoprotective potential, which correlated well with the relative effectiveness of the drugs recorded during in vitro studies. These results correlate with the relative effectiveness of the drugs recorded in previous in vitro and in vivo studies. The leading IFL activity may be attributed to a higher content of active polyphenolic components compared to heterogeneous HA and BP-Cx-1. Enrichment with active components by fractionation is a direction that can be explored for developing hepatoprotective agents based on natural complex polyphenols.}, } @article {pmid39996333, year = {2025}, author = {Medeiros, W and Kralova, S and Oliveira, V and Ziemert, N and Sehnal, L}, title = {Antarctic bacterial natural products: from genomic insights to drug discovery.}, journal = {Natural product reports}, volume = {}, number = {}, pages = {}, doi = {10.1039/d4np00045e}, pmid = {39996333}, issn = {1460-4752}, abstract = {Covering: up to the end of 2024Microbial life dominates the extreme continent Antarctica, playing a pivotal role in ecosystem functioning and serving as a reservoir of specialized metabolites known as natural products (NPs). NPs not only contribute to microbial adaptation to harsh conditions but also modulate microbial community structure. Long-term isolation and environmental pressures have shaped the genomes of Antarctic bacteria, suggesting that they also encode unique NPs. Since NPs are also an important source of drugs, we argue that investigating Antarctic bacterial NPs is essential not only for understanding their ecological role and evolution, but also for discovering new chemical structures, biosynthetic mechanisms, and potential new drugs. Yet, despite advances in omics technologies and increased scientific activities in Antarctica, relatively few new bacterial NPs have been discovered. The lack of systematic research activities focused on the exploration of Antarctic bacteria and their NPs constitutes a big problem considering the climate change issue, to which ecosystems in polar regions are the most sensitive areas on the Earth. Here, we highlight the currently available data on Antarctic bacteria, their biosynthetic potential, and the successful NP discoveries, while addressing the challenges in NP research and advocating for systematic, collaborative efforts aligned with the Antarctic Treaty System and the Antarctic Conservation Biogeographic Regions.}, } @article {pmid39995465, year = {2025}, author = {Huang, J and Bibri, SE and Keel, P}, title = {Generative spatial artificial intelligence for sustainable smart cities: A pioneering large flow model for urban digital twin.}, journal = {Environmental science and ecotechnology}, volume = {24}, number = {}, pages = {100526}, pmid = {39995465}, issn = {2666-4984}, abstract = {Rapid urbanization, alongside escalating resource depletion and ecological degradation, underscores the critical need for innovative urban development solutions. In response, sustainable smart cities are increasingly turning to cutting-edge technologies-such as Generative Artificial Intelligence (GenAI), Foundation Models (FMs), and Urban Digital Twin (UDT) frameworks-to transform urban planning and design practices. These transformative tools provide advanced capabilities to analyze complex urban systems, optimize resource management, and enable evidence-based decision-making. Despite recent progress, research on integrating GenAI and FMs into UDT frameworks remains scant, leaving gaps in our ability to capture complex urban flows and multimodal dynamics essential to achieving environmental sustainability goals. Moreover, the lack of a robust theoretical foundation and real-world operationalization of these tools hampers comprehensive modeling and practical adoption. This study introduces a pioneering Large Flow Model (LFM), grounded in a robust foundational framework and designed with GenAI capabilities. It is specifically tailored for integration into UDT systems to enhance predictive analytics, adaptive learning, and complex data management functionalities. To validate its applicability and relevance, the Blue City Project in Lausanne City is examined as a case study, showcasing the ability of the LFM to effectively model and analyze urban flows-namely mobility, goods, energy, waste, materials, and biodiversity-critical to advancing environmental sustainability. This study highlights how the LFM addresses the spatial challenges inherent in current UDT frameworks. The LFM demonstrates its novelty in comprehensive urban modeling and analysis by completing impartial city data, estimating flow data in new locations, predicting the evolution of flow data, and offering a holistic understanding of urban dynamics and their interconnections. The model enhances decision-making processes, supports evidence-based planning and design, fosters integrated development strategies, and enables the development of more efficient, resilient, and sustainable urban environments. This research advances both the theoretical and practical dimensions of AI-driven, environmentally sustainable urban development by operationalizing GenAI and FMs within UDT frameworks. It provides sophisticated tools and valuable insights for urban planners, designers, policymakers, and researchers to address the complexities of modern cities and accelerate the transition towards sustainable urban futures.}, } @article {pmid39995103, year = {2025}, author = {Campbell, IH and Needham, N and Grossi, H and Kamenska, I and Luz, S and Sheehan, S and Thompson, G and Thrippleton, MJ and Gibbs, MC and Leitao, J and Moses, T and Burgess, K and Rigby, BP and Simpson, SA and McIntosh, E and Brown, R and Meadowcroft, B and Creasy, F and Mitchell-Grigorjeva, M and Norrie, J and McLellan, A and Fisher, C and Zieliński, T and Gaggioni, G and Campbell, H and Smith, DJ}, title = {A pilot study of a ketogenic diet in bipolar disorder: clinical, metabolic and magnetic resonance spectroscopy findings.}, journal = {BJPsych open}, volume = {11}, number = {2}, pages = {e34}, doi = {10.1192/bjo.2024.841}, pmid = {39995103}, issn = {2056-4724}, abstract = {BACKGROUND: Preliminary evidence suggests that a ketogenic diet may be effective for bipolar disorder.

AIMS: To assess the impact of a ketogenic diet in bipolar disorder on clinical, metabolic and magnetic resonance spectroscopy outcomes.

METHOD: Euthymic individuals with bipolar disorder (N = 27) were recruited to a 6- to 8-week single-arm open pilot study of a modified ketogenic diet. Clinical, metabolic and MRS measures were assessed before and after the intervention.

RESULTS: Of 27 recruited participants, 26 began and 20 completed the ketogenic diet. For participants completing the intervention, mean body weight fell by 4.2 kg (P < 0.001), mean body mass index fell by 1.5 kg/m[2] (P < 0.001) and mean systolic blood pressure fell by 7.4 mmHg (P < 0.041). The euthymic participants had average baseline and follow-up assessments consistent with them being in the euthymic range with no statistically significant changes in Affective Lability Scale-18, Beck Depression Inventory and Young Mania Rating Scale. In participants providing reliable daily ecological momentary assessment data (n = 14), there was a positive correlation between daily ketone levels and self-rated mood (r = 0.21, P < 0.001) and energy (r = 0.19 P < 0.001), and an inverse correlation between ketone levels and both impulsivity (r = -0.30, P < 0.001) and anxiety (r = -0.19, P < 0.001). From the MRS measurements, brain glutamate plus glutamine concentration decreased by 11.6% in the anterior cingulate cortex (P = 0.025) and fell by 13.6% in the posterior cingulate cortex (P = <0.001).

CONCLUSIONS: These findings suggest that a ketogenic diet may be clinically useful in bipolar disorder, for both mental health and metabolic outcomes. Replication and randomised controlled trials are now warranted.}, } @article {pmid39909332, year = {2025}, author = {Cheng, Z and He, Y and Wang, N and Wu, L and Xu, J and Shi, J}, title = {Uncovering soil amendment-induced genomic and functional divergence in soybean rhizosphere microbiomes during cadmium-contaminated soil remediation: Novel insights from field multi-omics.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {368}, number = {}, pages = {125787}, doi = {10.1016/j.envpol.2025.125787}, pmid = {39909332}, issn = {1873-6424}, mesh = {*Cadmium/metabolism ; *Glycine max/genetics/microbiology/metabolism ; *Rhizosphere ; *Soil Pollutants/metabolism ; *Soil Microbiology ; *Microbiota ; Soil/chemistry ; Biodegradation, Environmental ; Bacteria/genetics/metabolism ; Metagenomics ; Metagenome ; Multiomics ; }, abstract = {Soil amendments exhibit great potential in reducing cadmium (Cd) bioavailability and its accumulation in crop grains, but their practical implications on microbial characteristics (genomic traits and ecological functions) remain unclear. The objective of this study was to combine metagenomics and metatranscriptomics to track the dynamics of bacterial and viral communities in the soybean rhizosphere during the remediation of Cd-contaminated soil using a commercial Mg-Ca-Si conditioner (CMC), applied at low and high (975 kg ha[-1] and 1950 kg ha[-1]) rates under field conditions. Application of CMC increased the average size and decreased the guanine-cytosine (GC) content of microbial genomes, which were strongly shaped by soil pH and available Cd (ACd). Gene and transcript abundances analysis indicated that CMC promoted the enrichment of Alphaproteobacterial metagenome-assembled genomes (MAGs) carrying czcC gene encoding Cd efflux and dsbB gene encoding disulfide bond oxidoreductase. These genes are closely related to Cd resistance and exhibited notable (p < 0.05) increased expression in CMC-treated soils. Additionally, low and high CMC addition significantly increased viral alpha diversity by 5.7% and 9.6%, and viral activity by 3.3% and 7.8%, respectively, in comparison to the control. Temperate viruses were predicted as the major group (64%) and actively linked to the dominant host, and CMC amendment increased host metabolism and adaptability by enhancing (p < 0.05) the abundance and transcriptional activity of virus-encoded auxiliary metabolic genes (AMGs) involved in heavy metal resistance (ABC transport), sulfur cycling (cysH), and host metabolism (galE and queD) through "piggyback-the-winner" strategy. Structural equation modeling further revealed that CMC application influences Cd accumulation in soybean grains through its direct and indirect effects on soil properties and rhizosphere microbiomes, and highlighted the potential role of rhizosphere viruses in agricultural soil remediation.}, } @article {pmid39882857, year = {2025}, author = {Grettenberger, C and Gold, DA and Brown, CT}, title = {Distribution of early-branching Cyanobacteriia and the potential habitats that gave rise to the earliest oxygenic phototrophs.}, journal = {mSphere}, volume = {10}, number = {2}, pages = {e0101324}, doi = {10.1128/msphere.01013-24}, pmid = {39882857}, issn = {2379-5042}, mesh = {*Cyanobacteria/genetics/classification/metabolism ; *Oxygen/metabolism ; *Ecosystem ; *Photosynthesis ; Phototrophic Processes ; Biological Evolution ; Computational Biology/methods ; Phylogeny ; Metagenome ; }, abstract = {The evolution of oxygenic photosynthesis in the Cyanobacteria was one of the most transformative events in Earth history, eventually leading to the oxygenation of Earth's atmosphere. However, it is difficult to understand how the earliest Cyanobacteria functioned or evolved on early Earth in part because we do not understand their ecology, including the environments in which they lived. Here, we use a cutting-edge bioinformatics tool to survey nearly 500,000 metagenomes for relatives of the taxa that likely bookended the evolution of oxygenic photosynthesis to identify the modern environments in which these organisms live. Ancestral state reconstruction suggests that the common ancestors of these organisms lived in terrestrial (soil and/or freshwater) environments. This restricted distribution may have increased the lag between the evolution of oxygenic photosynthesis and the oxygenation of Earth's atmosphere.IMPORTANCECyanobacteria generate oxygen as part of their metabolism and are responsible for the rise of oxygen in Earth's atmosphere over two billion years ago. However, we do not know how long this process may have taken. To help constrain how long this process would have taken, it is necessary to understand where the earliest Cyanobacteria may have lived. Here, we use a cutting-edge bioinformatics tool called branch water to examine the environments where modern Cyanobacteria and their relatives live to constrain those inhabited by the earliest Cyanobacteria. We find that these species likely lived in non-marine environments. This indicates that the rise of oxygen may have taken longer than previously believed.}, } @article {pmid39240386, year = {2025}, author = {Han, S and Hogue, W}, title = {Assessing Human Influence and Vegetative Dune Dynamics on Barrier Islands via Satellite Raster Classification.}, journal = {Environmental management}, volume = {75}, number = {3}, pages = {524-537}, pmid = {39240386}, issn = {1432-1009}, mesh = {Alabama ; *Islands ; Humans ; *Conservation of Natural Resources/methods ; *Ecosystem ; Mississippi ; Satellite Imagery ; Geographic Information Systems ; Climate Change ; Environmental Monitoring/methods ; }, abstract = {Barrier islands support ecological diversity and offshore ecosystems and provide critical protection to coastal communities. Climate change has intensified the frequency and severity of hurricanes affecting these islands, leading to ongoing erosion. The primary goal of this study was to explore the relationship between human intervention such as development and construction and the vegetative dune systems on Gulf Coast barrier islands in Alabama and Mississippi, USA. This research employed two decades of satellite images of three neighboring barrier islands and employed GIS raster classification to track changes in the vegetative dune system in terms of: (1) dune coverage (surface area of the vegetation), (2) vegetative maturity (vegetation type), and (3) stability (fluctuations in the vegetative coverage over time). Time series and trend analyses were used to compare the results for three neighboring islands. The findings show that Dauphin Island, which features both commercial facilities and vacation homes, exhibited a decrease in total area over time, and had the lowest percentage of vegetative dune coverage and highest level of vegetative fluctuation. In contrast, Petit Bois and Horn Islands, which remain untouched by human activity, displayed significantly higher levels of vegetative maturity and coverage and comparatively less fluctuation. This research provides a foundation for those advocating for dune restoration strategies, development limitations, and conservation regulations as nature-based infrastructure solutions to combat erosion on barrier islands and serves as a point of entry for future inquiries in the field of environmental management.}, } @article {pmid39990132, year = {2025}, author = {Keet, JH and Hui, C}, title = {One-hectare fine-scale dataset of a fynbos plant community in the Cape Floristic Region.}, journal = {Data in brief}, volume = {59}, number = {}, pages = {111334}, pmid = {39990132}, issn = {2352-3409}, abstract = {Cape fynbos, which forms part of the Cape Floristic Region (CFR) of South Africa, a global biodiversity hotspot, is renowned for its high levels of plant species endemism and diversity. This extraordinary ecosystem, characterised by nutrient-poor soils and fire-adapted vegetation, is a treasure trove of endemic flora. However, this fragile system faces increasing threats from habitat loss, climate change, and invasive species. Pristine fynbos, naturally high in plant diversity and which forms a large part of the CFR, presents an ideal opportunity to gather fine-scale data on community assembly patterns. Most fynbos vegetation surveys use a plot size of about 100 m[2], with no spatial structures within plots to demarcate individual subplots. Here, a groundbreaking dataset is presented that fully covers 1-hectare of pristine fynbos, systematically gridded into 50 × 50 subplots, each measuring 2 × 2 m, arranged evenly within a square-shaped survey site. Each plot was assigned a unique Y-X coordinate combination. For each plot, all plant species present were recorded, along with their total percentage covers and maximum height values. Total percentage covers were also recorded for bare soil, rock, and termite mounds. This dataset provides a valuable contribution to the field of fynbos ecology, as well as plant community ecology in general, and establishes a benchmark for future one-hectare surveys of similar fynbos vegetation types, delineating the fine-scale composition and structure of fynbos in the CFR. The dataset will be useful for a wide audience, including community and spatial ecologists, plant and environmental scientists, and biodiversity informaticians and statistical ecologists, offering ideal data for testing new metrics of diversity and compositional turnover.}, } @article {pmid39989610, year = {2024}, author = {Liu, C and Downey, RJ and Salminen, JS and Rojas, SA and Richer, N and Pliner, EM and Hwang, J and Cruz-Almeida, Y and Manini, TM and Hass, CJ and Seidler, RD and Clark, DJ and Ferris, DP}, title = {Electrical brain activity during human walking with parametric variations in terrain unevenness and walking speed.}, journal = {Imaging neuroscience (Cambridge, Mass.)}, volume = {2}, number = {}, pages = {}, pmid = {39989610}, issn = {2837-6056}, abstract = {Mobile brain imaging with high-density electroencephalography (EEG) can provide insight into the cortical processes involved in complex human walking tasks. While uneven terrain is common in the natural environment and poses challenges to human balance control, there is limited understanding of the supraspinal processes involved with traversing uneven terrain. The primary objective of this study was to quantify electrocortical activity related to parametric variations in terrain unevenness for neurotypical young adults. We used high-density EEG to measure brain activity when 32 young adults walked on a novel custom-made uneven terrain treadmill surface with four levels of difficulty at a walking speed tailored to each participant. We identified multiple brain regions associated with uneven terrain walking. Alpha (8 - 13 Hz) and beta (13 - 30 Hz) spectral power decreased in the sensorimotor and posterior parietal areas with increasing terrain unevenness while theta (4 - 8 Hz) power increased in the mid/posterior cingulate area with terrain unevenness. We also found that within stride spectral power fluctuations increased with terrain unevenness. Our secondary goal was to investigate the effect of parametric changes in walking speed (0.25 m/s, 0.5 m/s, 0.75 m/s, 1.0 m/s) to differentiate the effects of walking speed from uneven terrain. Our results revealed that electrocortical activities only changed substantially with speed within the sensorimotor area but not in other brain areas. Together, these results indicate there are distinct cortical processes contributing to the control of walking over uneven terrain versus modulation of walking speed on smooth, flat terrain. Our findings increase our understanding of cortical involvement in an ecologically valid walking task and could serve as a benchmark for identifying deficits in cortical dynamics that occur in people with mobility deficits.}, } @article {pmid39918865, year = {2025}, author = {Astill Wright, L and Moore, M and Reeves, S and Vallejos, EP and Morriss, R}, title = {Improving the Utility, Safety, and Ethical Use of a Passive Mood-Tracking App for People With Bipolar Disorder Using Coproduction: Qualitative Focus Group Study.}, journal = {JMIR formative research}, volume = {9}, number = {}, pages = {e65140}, pmid = {39918865}, issn = {2561-326X}, mesh = {Humans ; *Bipolar Disorder/psychology/therapy ; *Focus Groups ; Male ; Female ; Adult ; Middle Aged ; *Mobile Applications ; *Qualitative Research ; Affect ; }, abstract = {BACKGROUND: Coproduction with users of new digital technology, such as passive mood monitoring, is likely to improve its utility, safety, and successful implementation via improved design and consideration of how such technology fits with their daily lives. Mood-monitoring interventions are commonly used by people with bipolar disorder (BD) and have promising potential for digitization using novel technological methods.

OBJECTIVE: This study aims to explore how a passive behavioral monitoring platform, Remote Assessment of Disease and Relapse, would meet the needs of people with BD by specifically considering purpose and function, diversity of need, personal preference, essential components and potential risks, and harms and mitigation strategies through an iterative coproduction process.

METHODS: A total of 17 people with BD were recruited via national charities. We conducted 3 web-based focus groups as a part of an iterative coproduction process in line with responsible research and innovation principles and with consideration of clinical challenges associated with BD. Data were analyzed thematically. Results were cross-checked by someone with lived experience of BD.

RESULTS: Focus groups were transcribed and analyzed using thematic analysis. Six themes were identified as follows: (1) the purpose of using the app, (2) desired features, (3) when to use the app, (4) risks of using the app, (5) sharing with family and friends, and (6) sharing with health care professionals.

CONCLUSIONS: People with BD who are interested in using passive technology to monitor their mood wish to do so for a wide variety of purposes, identifying several preferences and potential risks. Principally, people with BD wished to use this novel technology to aid them in self-managing their BD with greater insight and a better understanding of potential triggers. We discuss key features that may aid this functionality and purpose, including crisis plans and sharing with others. Future development of passive mood-monitoring technologies should not assume that the involvement of formal mental health services is desired.}, } @article {pmid39987271, year = {2025}, author = {Wuyun, D and Sun, L and Chen, Z and Li, Y and Han, M and Shi, Z and Ren, T and Zhao, H}, title = {A 10-meter resolution dataset of abandoned and reclaimed cropland from 2016 to 2023 in Inner Mongolia, China.}, journal = {Scientific data}, volume = {12}, number = {1}, pages = {317}, pmid = {39987271}, issn = {2052-4463}, abstract = {Amid growing global food security concerns and frequent armed conflicts, real-time monitoring of abandoned cropland is essential for strategic planning and crisis management. This study develops a method to map abandoned cropland accurately, crucial for maintaining the food supply chain and ecological balance. Utilizing Sentinel-1/2 satellite data, we employed multi-feature stacking and machine learning to create the ARCC10-IM (Abandoned and Reclaimed Cropland Classification at 10-meter resolution in Inner Mongolia) dataset, which tracks annual cropland activity. A novel temporal segmentation algorithm was developed to extract cropland abandonment and reclamation patterns annually, using sliding time windows over several years. This research differentiates cropland states-active cultivation, unstable fallowing, continuous abandonment, and reclamation-providing continuous, regional-scale maps with 10-meter resolution. ARCC10-IM is crucial for land planning, environmental monitoring, and agricultural management in arid areas like Inner Mongolia, enhancing decision-making and technology in land use tracking.}, } @article {pmid39986902, year = {2025}, author = {Lee, S and Kaufmann, CN and Lippi, CA and Ryan, SJ and Guo, Y}, title = {Untreated insomnia as a contributor to geographic disparities in risk for Alzheimer's disease and related dementias.}, journal = {Sleep health}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.sleh.2025.01.002}, pmid = {39986902}, issn = {2352-7226}, } @article {pmid39842565, year = {2025}, author = {Zheng, JY and Jiang, G and Gao, FH and Ren, SN and Zhu, CY and Xie, J and Li, Z and Yin, W and Xia, X and Li, Y and Wang, HL}, title = {MCTASmRNA: A deep learning framework for alternative splicing events classification.}, journal = {International journal of biological macromolecules}, volume = {300}, number = {}, pages = {139941}, doi = {10.1016/j.ijbiomac.2025.139941}, pmid = {39842565}, issn = {1879-0003}, mesh = {*Deep Learning ; *Alternative Splicing/genetics ; RNA, Messenger/genetics ; Humans ; Animals ; Computational Biology/methods ; Software ; }, abstract = {Alternative splicing (AS) plays crucial post-transcriptional gene function regulation roles in eukaryotic. Despite progress in studying AS at the RNA level, existing methods for AS event identification face challenges such as inefficiency, lengthy processing times, and limitations in capturing the complexity of RNA sequences. To overcome these challenges, we evaluated 10 AS detection tools and selected rMATS for dataset construction. We then developed a multi-scale convolutional and Transformer-based model (MCTASmRNA) to classify AS events in mRNA sequences without relying on a reference genome. To handle the problem of large intra-class and small inter-class difference in AS event sequences, we incorporated an efficient channel attention mechanism and designed a new joint loss function to optimize MCTASmRNA training. MCTASmRNA outperformed baseline models, with an accuracy improvement and exhibited enhanced cross-species generalizability. This model provides valuable support for AS research across different organisms. Future work will focus on optimizing and expanding the model to further explore the complex mechanisms underlying AS.}, } @article {pmid39982558, year = {2025}, author = {Li, L and Gupta, A and Zhu, C and Xu, K and Watanabe, Y and Tanaka, M and Seki, M and Mochida, K and Kanno, Y and Seo, M and Nguyen, KH and Tran, CD and Chu, HD and Yin, H and Jia, KP and Tran, LP and Yin, X and Li, W}, title = {Strigolactone and karrikin receptors regulate phytohormone biosynthetic and catabolic processes.}, journal = {Plant cell reports}, volume = {44}, number = {3}, pages = {60}, pmid = {39982558}, issn = {1432-203X}, support = {XDA28110100//State Key Laboratory of Microbial Resources, Chinese Academy of Sciences/ ; 2022YFD1500505//National Key Research and Development Program of China/ ; 32370321//Natural Science Foundation of Jilin Province/ ; }, mesh = {*Plant Growth Regulators/metabolism ; *Lactones/metabolism ; *Arabidopsis/genetics/metabolism ; *Gene Expression Regulation, Plant ; *Arabidopsis Proteins/metabolism/genetics ; *Indoleacetic Acids/metabolism ; *Pyrans/metabolism ; *Cyclopentanes/metabolism ; *Furans/metabolism ; Oxylipins/metabolism ; Gibberellins/metabolism ; Abscisic Acid/metabolism ; Cytokinins/metabolism ; Receptors, Cell Surface/metabolism/genetics ; Salicylic Acid/metabolism ; Signal Transduction ; Mutation ; Gene Expression Profiling ; }, abstract = {Karrikin plays a more critical role in affecting the homeostasis of ABA and cytokinins, while strigolactones play a more critical role in influencing the homeostasis of jasmonic acid and gibberellins. Strigolactones (SLs) and karrikins (KARs) regulate plant growth and development through their crosstalk, and through the crosstalk between them and other phytohormones, such as abscisic acid (ABA) and auxin. However, how SL and KAR signaling pathways influence the levels of other phytohormones is still unknown. Here, we performed a comparative transcriptome analysis of the Arabidopsis thaliana double mutant dwarf14 karrikin-insensitive 2 (d14 kai2), deficient in SL and KAR perception, and the wild-type (WT) using their rosette leaves. Ten gene ontology terms related to phytohormones were enriched with differentially expressed genes derived from the 'd14 kai2 vs WT' comparison. Our data revealed that the levels of auxin, ABA and salicylic acid (SA) were higher in d14 and kai2 single and d14 kai2 mutant plants than in WT, which was consistent with the results of previous investigations. In contrast, the levels of cytokinins (CKs) were found to be lower in all single and double mutants than in WT. The levels of active gibberellins were lower in d14 and d14 kai2 mutants than in WT, while they were comparable in kai2 and WT plants. Similarly, the levels of jasmonic acid (JA) were lower in d14 and d14 kai2 plants, but higher in kai2 plants than in WT. Both transcriptome and qRT-PCR analyses indicated that SL and KAR signaling pathways affect the levels of auxin, SA, CKs, gibberellin 4 (GA4) and ABA by influencing the expression of their biosynthetic (in case of auxin, SA, GA4 and CKs) and catabolic (in case of ABA) genes. Collectively, our data demonstrated that KAI2 plays a more critical role in the homeostasis of ABA and CKs, while D14 plays a more critical role in the homeostasis of JA and gibberellins. Findings of this study indicate a complex and broad crosstalk among various phytohormones in plants, which can be considered for future exogenous applications and hormone engineering.}, } @article {pmid39982516, year = {2025}, author = {Elkin-Frankston, S and McIntyre, J and Brunyé, TT and Gardony, AL and Hancock, CL and O'Donovan, MP and Bode, VG and Miller, EL}, title = {Beyond boundaries: a location-based toolkit for quantifying group dynamics in diverse contexts.}, journal = {Cognitive research: principles and implications}, volume = {10}, number = {1}, pages = {10}, pmid = {39982516}, issn = {2365-7464}, support = {W911QY1920003//U.S. Army Combat Capabilities Development Command Soldier Center/ ; 1934553//National Science Foundation/ ; 1931978//National Science Foundation/ ; }, mesh = {Humans ; *Group Processes ; *Military Personnel ; Geographic Information Systems ; Social Behavior ; Movement/physiology ; Models, Theoretical ; Group Dynamics ; }, abstract = {Existing toolkits for analyzing movement dynamics in animal ecology primarily focus on individual or group behavior in habitats without predefined boundaries, while methods for studying human activity often cater to bounded environments, such as team sports played on defined fields. This leaves a gap in tools for modeling and analyzing human group dynamics in large-scale, unbounded, or semi-constrained environments. Examples of such contexts include tourist groups, cycling teams, search and rescue teams, and military units. To address this issue, we survey existing methods and metrics for characterizing individual and collective movement in humans and animals. Using a rich GPS dataset from groups of military personnel engaged in a foot march, we develop a comprehensive, general-purpose toolkit for quantifying group dynamics using location-based metrics during goal-directed movement in open environments. This toolkit includes a repository of Python functions for extracting and analyzing movement data, integrating cognitive factors such as decision-making, situational awareness, and group coordination. By extending location-based analytics to non-traditional domains, this toolkit enhances the understanding of collective movement, group behavior, and emergent properties shaped by cognitive processes. To demonstrate its practical utility, we present a use case utilizing metrics derived from the foot march data to predict group performance during a subsequent strategic and tactical exercise, highlighting the influence of cognitive and decision-making behaviors on team effectiveness.}, } @article {pmid39982380, year = {2025}, author = {Blumenstiel, JP and Kingan, SB and Garrigan, D and Hill, T and Vedanayagam, J}, title = {Nested likelihood-ratio testing of the nonsynonymous:synonymous ratio suggests greater adaptation in the piRNA machinery of Drosophila melanogaster compared with Drosophila ananassae and Drosophila willistoni, two species with higher repeat content.}, journal = {G3 (Bethesda, Md.)}, volume = {}, number = {}, pages = {}, doi = {10.1093/g3journal/jkaf017}, pmid = {39982380}, issn = {2160-1836}, support = {1413532//NSF MCB/ ; P20GM103638//NIH-NIGMS/COBRE/ ; P20GM103418//NIH-NIGMS/KINBRE/ ; //University of Kansas/ ; DEB1209536//NSF-DDIG/ ; R00GM137077//NIH-NIGMS/ ; //University of Texas at San Antonio/ ; //KU Medical Center Genome Sequencing Facility/ ; NIH U54 HD090216/GF/NIH HHS/United States ; UL1TR002366//Frontiers CTSA/ ; }, abstract = {Numerous studies have revealed a signature of strong adaptive evolution in the piwi-interacting RNA (piRNA) machinery of Drosophila melanogaster, but the cause of this pattern is not understood. Several hypotheses have been proposed. One hypothesis is that transposable element (TE) families and the piRNA machinery are co-evolving under an evolutionary arms race, perhaps due to antagonism by TEs against the piRNA machinery. A related, though not co-evolutionary, hypothesis is that recurrent TE invasion drives the piRNA machinery to adapt to novel TE strategies. A third hypothesis is that ongoing fluctuation in TE abundance leads to adaptation in the piRNA machinery that must constantly adjust between sensitivity for detecting new elements and specificity to avoid the cost of off-target gene silencing. Rapid evolution of the piRNA machinery may also be driven independently of TEs, and instead from other functions such as the role of piRNAs in suppressing sex-chromosome meiotic drive. We sought to evaluate the impact of TE abundance on adaptive evolution of the piRNA machinery in D. melanogaster and 2 species with higher repeat content-Drosophila ananassae and Drosophila willistoni. This comparison was achieved by employing a likelihood-based hypothesis testing framework based on the McDonald-Kreitman test. We show that we can reject a faster rate of adaptive evolution in the piRNA machinery of these 2 species. We propose that the high rate of adaptation in D. melanogaster is either driven by a recent influx of TEs that have occurred during range expansion or selection on other functions of the piRNA machinery.}, } @article {pmid39981105, year = {2025}, author = {Plaitano, EG and McNeish, D and Bartels, SM and Bell, K and Dallery, J and Grabinski, M and Kiernan, M and Lavoie, HA and Lemley, SM and Lowe, MR and MacKinnon, DP and Metcalf, SA and Onken, L and Prochaska, JJ and Sand, CL and Scherer, EA and Stoeckel, LE and Xie, H and Marsch, LA}, title = {Adherence to a digital therapeutic mediates the relationship between momentary self-regulation and health risk behaviors.}, journal = {Frontiers in digital health}, volume = {7}, number = {}, pages = {1467772}, pmid = {39981105}, issn = {2673-253X}, abstract = {INTRODUCTION: Smoking, obesity, and insufficient physical activity are modifiable health risk behaviors. Self-regulation is one fundamental behavior change mechanism often incorporated within digital therapeutics as it varies momentarily across time and contexts and may play a causal role in improving these health behaviors. However, the role of momentary self-regulation in achieving behavior change has been infrequently examined. Using a novel momentary self-regulation scale, this study examined how targeting self-regulation through a digital therapeutic impacts adherence to the therapeutic and two different health risk behavioral outcomes.

METHODS: This prospective interventional study included momentary data for 28 days from 50 participants with obesity and binge eating disorder and 50 participants who smoked regularly. An evidence-based digital therapeutic, called Laddr™, provided self-regulation behavior change tools. Participants reported on their momentary self-regulation via ecological momentary assessments and health risk behaviors were measured as steps taken from a physical activity tracker and breathalyzed carbon monoxide. Medical regimen adherence was assessed as daily Laddr usage. Bayesian dynamic mediation models were used to examine moment-to-moment mediation effects between momentary self-regulation subscales, medical regimen adherence, and behavioral outcomes.

RESULTS: In the binge eating disorder sample, the perseverance [β 1 = 0.17, 95% CI = (0.06, 0.45)] and emotion regulation [β 1 = 0.12, 95% CI = (0.03, 0.27)] targets of momentary self-regulation positively predicted Laddr adherence on the following day, and higher Laddr adherence was subsequently a positive predictor of steps taken the same day for both perseverance [β 2 = 0.335, 95% CI = (0.030, 0.717)] and emotion regulation [β 2 = 0.389, 95% CI = (0.080, 0.738)]. In the smoking sample, the perseverance target of momentary self-regulation positively predicted Laddr adherence on the following day [β = 0.91, 95% CI = (0.60, 1.24)]. However, higher Laddr adherence was not a predictor of CO values on the same day [β 2 = -0.09, 95% CI = (-0.24, 0.09)].

CONCLUSIONS: This study provides evidence that a digital therapeutic targeting self-regulation can modify the relationships between momentary self-regulation, medical regimen adherence, and behavioral health outcomes. Together, this work demonstrated the ability to digitally assess the transdiagnostic mediating effect of momentary self-regulation on medical regimen adherence and pro-health behavioral outcomes.

CLINICAL TRIAL REGISTRATION: ClinicalTrials.gov, identifier (NCT03774433).}, } @article {pmid39980689, year = {2025}, author = {Su, Z and Liu, L and Zhang, J and Guo, J and Wang, G and Zeng, X}, title = {A scientometric visualization analysis of the gut microbiota and gestational diabetes mellitus.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1485560}, pmid = {39980689}, issn = {1664-302X}, abstract = {BACKGROUND: The prevalence of gestational diabetes mellitus (GDM), a condition that is widespread globally, is increasing. The relationship between the gut microbiota and GDM has been a subject of research for nearly two decades, yet there has been no bibliometric analysis of this correlation. This study aimed to use bibliometrics to explore the relationship between the gut microbiota and GDM, highlighting emerging trends and current research hotspots in this field.

RESULTS: A total of 394 papers were included in the analysis. China emerged as the preeminent nation in terms of the number of publications on the subject, with 128 papers (32.49%), whereas the United States had the most significant impact, with 4,874 citations. The University of Queensland emerged as the most prolific institution, contributing 18 publications. Marloes Dekker Nitert was the most active author with 16 publications, and Omry Koren garnered the most citations, totaling 154. The journal Nutrients published the most studies (28 publications, 7.11%), whereas PLoS One was the most commonly co-cited journal, with a total of 805 citations. With respect to keywords, research focuses can be divided into 4 clusters, namely, "the interrelationship between the gut microbiota and pregnancy, childbirth," "the relationship between adverse metabolic outcomes and GDM," "the gut microbiota composition and metabolic mechanisms" and "microbiota and ecological imbalance." Key areas of focus include the interactions between the gut microbiota and individuals with GDM, as well as the formation and inheritance of the gut microbiota. Increasing attention has been given to the impact of probiotic supplementation on metabolism and pregnancy outcomes in GDM patients. Moreover, ongoing research is exploring the potential of the gut microbiota as a biomarker for GDM. These topics represent both current and future directions in this field.

CONCLUSION: This study provides a comprehensive knowledge map of the gut microbiota and GDM, highlights key research areas, and outlines potential future directions.}, } @article {pmid39980161, year = {2025}, author = {Smith, AR and Mueller, ER and Lewis, CE and Markland, A and Smerdon, C and Smith, AL and Sutcliffe, S and Wyman, JF and Low, LK and Miller, JM and , }, title = {Assessment of Environmental, Sociocultural, and Physiological Influences on Women's Toileting Decisions and Behaviors Using "Where I Go": Pilot Study of a Mobile App.}, journal = {JMIR mHealth and uHealth}, volume = {13}, number = {}, pages = {e56533}, doi = {10.2196/56533}, pmid = {39980161}, issn = {2291-5222}, mesh = {Humans ; Female ; *Mobile Applications/standards/statistics & numerical data ; Adult ; Pilot Projects ; Middle Aged ; Aged ; Aged, 80 and over ; Urination/physiology ; Decision Making ; Surveys and Questionnaires ; }, abstract = {BACKGROUND: Little is known about women's decisions around toileting for urination and how those decisions influence moment-to-moment behaviors to manage bladder needs. The new smartphone app "Where I Go" captures such nuanced and granular data in real-world environments.

OBJECTIVE: This study aims to describe participant engagement with "Where I Go", variation in novel parameters collected, and readiness for the data collection tool's use in population-based studies.

METHODS: "Where I Go" has three components: (1) real-time data, (2) short look-back periods (3-4 h), and (3) event location (GPS recorded at each interaction). The sample size was 44 women. Recording of real-time toileting events and responding to look-back questions was measured over 2 days of data collection. The participant's self-entered location descriptions and the automatic GPS recordings were compared.

RESULTS: A total of 44 women with an average age of 44 (range 21-85) years interacted with the app. Real-time reporting of at least 1 toileting event per day was high (38/44, 86%, on day 1 and 40/44, 91%, on day 2) with a median of 5 (IQR 3-7 on day 1 and IQR 3-8 on day 2) toileting events recorded each day. Toileting most commonly occurred at home (85/140, 61%, on day 1 and 129/171, 75%, on day 2) due to a need to go (114/140, 66%, on day 1 and 153/171, 74%, on day 2). The most common reasons for delaying toileting were "work duties" (33/140, 21%, on day 1 and 21/171, 11%, on day 2) and "errands or traveling" (19/140, 12%, on day 1 and 19/171, 10%, on day 2). Response to at least 1 look-back notification was similarly high (41/44, 93%, on day 1 and 42/44, 95%, on day 2), with number of responses higher on average on day 2 compared with day 1 (mean on day 1=3.2, 95% CI 3.0-3.5; mean on day 2=4.3, 95% CI 3.9-4.7; P<.001). Median additional toileting events reported on the look-back survey were 1 (IQR 1-2) and 2 (IQR 1-2) on days 1 and 2, respectively. Overall concordance between self-reported location recording and GPS was 76% (188/247). Participants reported lower urge ratings when at home versus away when reporting real-time toileting (median rating 61, IQR 41-84 vs 72, IQR 56-98), and daily fluid intake showed a small to medium positive correlation with toileting frequency (day 1 r=0.3, day 2 r=0.24). Toileting frequency reported in "Where I Go" showed a small positive correlation with the frequency item from the International Consultation on Incontinence Questionnaire (r=0.31 with day 1 toileting frequency and r=0.21 with day 2 toileting frequency).

CONCLUSIONS: "Where I Go" has potential to increase the understanding of factors that affect women's toileting decisions and long-term bladder health. We anticipate its use as a data collection tool in population-based studies.}, } @article {pmid39900590, year = {2025}, author = {Chen, Y and Zheng, L and Ma, J and Zhu, H and Gan, Y}, title = {The Mediating Role of Meaning-Making in the Relationship Between Mental Time Travel and Positive Emotions in Stress-Related Blogs: Big Data Text Analysis Research.}, journal = {Journal of medical Internet research}, volume = {27}, number = {}, pages = {e63407}, doi = {10.2196/63407}, pmid = {39900590}, issn = {1438-8871}, mesh = {Humans ; *Stress, Psychological/psychology ; *Emotions ; *Big Data ; *Blogging ; Social Media ; }, abstract = {BACKGROUND: Given the ubiquity of stress, a key focus of stress research is exploring how to better coexist with stress.

OBJECTIVE: This study conducted text analysis on stress-related Weibo posts using a web crawler to investigate whether these posts contained positive emotions, as well as elements of mental time travel and meaning-making. A mediation model of mental time travel, meaning-making, and positive emotions was constructed to examine whether meaning-making triggered by mental time travel can foster positive emotions under stress.

METHODS: Using Python 3.8, the original public data from active Weibo users were crawled, yielding 331,711 stress-related posts. To avoid false positives, these posts were randomly divided into two large samples for cross-validation (sample 1: n=165,374; sample 2: n=166,337). Google's natural language processing application programming interface was used for word segmentation, followed by text and mediation analysis using the Chinese psychological analysis system "Wenxin." A mini-meta-analysis of the mediation path coefficients was conducted. Text analysis identified mental time travel words, meaning-making words, and positive emotion words in stress-related posts.

RESULTS: The constructed mediation model of mental time travel words (time words), meaning-making words (causal and insightful words), and positive poststress emotions validated positive adaptation following stress. A mini-meta-analysis of two different mediation models constructed in the two subsamples indicated a stable mediation effect across the 2 random subsamples. The combined effect size (B) obtained was .013 (SE 0.003, 95% CI 0.007-0.018; P<.001), demonstrating that meaning-making triggered by mental time travel in stress-related blog posts can predict positive emotions under stress.

CONCLUSIONS: Individuals can adapt positively to stress by engaging in meaning-making processes that are triggered by mental time travel and reflected in their social media posts. The study's mediation model confirmed that mental time travel leads to meaning-making, which fosters positive emotional responses to stress. Mental time travel serves as a psychological strategy to facilitate positive adaptation to stressful situations.}, } @article {pmid39975655, year = {2025}, author = {Gutiérrez, ME and Lahoz-Beltrá, R and Donayre-Torres, AJ}, title = {Editorial: Towards the embedding of artificial intelligence into synthetic organisms: engineering intelligence in microorganisms.}, journal = {Frontiers in genetics}, volume = {16}, number = {}, pages = {1562092}, doi = {10.3389/fgene.2025.1562092}, pmid = {39975655}, issn = {1664-8021}, } @article {pmid39973193, year = {2025}, author = {Beltran, RS and Kilpatrick, AM and Adamczak, SK and Beumer, LT and Czapanskiy, MF and Davidson, SC and McLean, BS and Mueller, T and Payne, AR and Soria, CD and Weeks, BC and Williams, TM and Salguero-Gómez, R}, title = {Integrating animal tracking and trait data to facilitate global ecological discoveries.}, journal = {The Journal of experimental biology}, volume = {228}, number = {Suppl_1}, pages = {}, doi = {10.1242/jeb.247981}, pmid = {39973193}, issn = {1477-9145}, support = {IOS 2052497//National Science Foundation/ ; //Office of Naval Research/ ; //David and Lucile Packard Foundation/ ; //Arnold and Mabel Beckman Foundation/ ; //Elysea Fund/ ; NE/X013766/1//Natural Environment Research Council/ ; 101044740//European Union/ ; //University of California/ ; 80NSSC21K1182/NASA/NASA/United States ; }, mesh = {Animals ; *Ecology/methods ; Databases, Factual ; Animal Migration ; Big Data ; }, abstract = {Understanding animal movement is at the core of ecology, evolution and conservation science. Big data approaches for animal tracking have facilitated impactful synthesis research on spatial biology and behavior in ecologically important and human-impacted regions. Similarly, databases of animal traits (e.g. body size, limb length, locomotion method, lifespan) have been used for a wide range of comparative questions, with emerging data being shared at the level of individuals and populations. Here, we argue that the proliferation of both types of publicly available data creates exciting opportunities to unlock new avenues of research, such as spatial planning and ecological forecasting. We assessed the feasibility of combining animal tracking and trait databases to develop and test hypotheses across geographic, temporal and biological allometric scales. We identified multiple research questions addressing performance and distribution constraints that could be answered by integrating trait and tracking data. For example, how do physiological (e.g. metabolic rates) and biomechanical traits (e.g. limb length, locomotion form) influence migration distances? We illustrate the potential of our framework with three case studies that effectively integrate trait and tracking data for comparative research. An important challenge ahead is the lack of taxonomic and spatial overlap in trait and tracking databases. We identify critical next steps for future integration of tracking and trait databases, with the most impactful being open and interlinked individual-level data. Coordinated efforts to combine trait and tracking databases will accelerate global ecological and evolutionary insights and inform conservation and management decisions in our changing world.}, } @article {pmid39973045, year = {2025}, author = {Panayi, P and Contreras, A and Peters, E and Bentall, R and Hardy, A and Berry, K and Sellwood, W and Dudley, R and Longden, E and Underwood, R and Steel, C and Jafari, H and Mason, L and Varese, F}, title = {A temporal network analysis of complex post-traumatic stress disorder and psychosis symptoms.}, journal = {Psychological medicine}, volume = {55}, number = {}, pages = {e43}, doi = {10.1017/S0033291725000030}, pmid = {39973045}, issn = {1469-8978}, support = {2488414//Economic and Social Research Council/ ; NIHR128623//Health Technology Assessment Programme/ ; //NIHR Maudsley Biomedical Research Centre/ ; }, mesh = {Humans ; *Stress Disorders, Post-Traumatic/physiopathology ; *Psychotic Disorders/physiopathology ; Adult ; Male ; Female ; Middle Aged ; Ecological Momentary Assessment ; Young Adult ; Self Concept ; Comorbidity ; }, abstract = {BACKGROUND: Symptoms of complex post-traumatic stress disorder (cPTSD) may play a role in the maintenance of psychotic symptoms. Network analyses have shown interrelationships between post-traumatic sequelae and psychosis, but the temporal dynamics of these relationships in people with psychosis and a history of trauma remain unclear. We aimed to explore, using network analysis, the temporal order of relationships between symptoms of cPTSD (i.e. core PTSD and disturbances of self-organization [DSOs]) and psychosis in the flow of daily life.

METHODS: Participants with psychosis and comorbid PTSD (N = 153) completed an experience-sampling study involving multiple daily assessments of psychosis (paranoia, voices, and visions), core PTSD (trauma-related intrusions, avoidance, hyperarousal), and DSOs (emotional dysregulation, interpersonal difficulties, negative self-concept) over six consecutive days. Multilevel vector autoregressive modeling was used to estimate three complementary networks representing different timescales.

RESULTS: Our between-subjects network suggested that, on average over the testing period, most cPTSD symptoms related to at least one positive psychotic symptom. Many average relationships persist in the contemporaneous network, indicating symptoms of cPTSD and psychosis co-occur, especially paranoia with hyperarousal and negative self-concept. The temporal network suggested that paranoia reciprocally predicted, and was predicted by, hyperarousal, negative self-concept, and emotional dysregulation from moment to moment. cPTSD did not directly relate to voices in the temporal network.

CONCLUSIONS: cPTSD and positive psychosis symptoms mutually maintain each other in trauma-exposed people with psychosis via the maintenance of current threat, consistent with cognitive models of PTSD. Current threat, therefore, represents a valuable treatment target in phased-based trauma-focused psychosis interventions.}, } @article {pmid39969100, year = {2025}, author = {Miller, L and Beaney, T and Hope, R and Cunningham, M and Robotham, JV and Pouwels, KB and Costelloe, CE}, title = {General practice antibiotic prescriptions attributable to respiratory syncytial virus by age and antibiotic class: an ecological analysis of the English population.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {}, number = {}, pages = {}, doi = {10.1093/jac/dkaf043}, pmid = {39969100}, issn = {1460-2091}, support = {MRF-145-0004-TPG-AVISO//Medical Research Foundation National PhD Training Programme in Antimicrobial Resistance Research/ ; //National Institute for Health and Care Research (NIHR) Royal Marsden/ ; //Institute of Cancer Research Biomedical Research Centre/ ; 2016-10-95//NIHR/ ; //National Institute for Health Research Health Protection Research Unit/ ; //Healthcare Associated Infections and Antimicrobial Resistance/ ; //University of Oxford/ ; NIHR200915//UK Health Security Agency (UKHSA)/ ; /WT_/Wellcome Trust/United Kingdom ; }, abstract = {BACKGROUND: Respiratory syncytial virus (RSV) may contribute to a substantial volume of antibiotic prescriptions in primary care. However, data on the type of antibiotics prescribed for such infections are only available for children <5 years in the UK. Understanding the contribution of RSV to antibiotic prescribing would facilitate predicting the impact of RSV preventative measures on antibiotic use and resistance. The objective of this study was to estimate the proportion of antibiotic prescriptions in English general practice attributable to RSV by age and antibiotic class.

METHODS: Generalized additive models examined associations between weekly counts of general practice antibiotic prescriptions and laboratory-confirmed respiratory infections from 2015 to 2018, adjusting for temperature, practice holidays and remaining seasonal confounders. We used general practice records from the Clinical Practice Research Datalink and microbiology tests for RSV, influenza, rhinovirus, adenovirus, parainfluenza, human metapneumovirus, Mycoplasma pneumoniae and Streptococcus pneumoniae from England's Second Generation Surveillance System.

RESULTS: An estimated 2.1% of antibiotics were attributable to RSV, equating to an average of 640 000 prescriptions annually. Of these, adults ≥75 years contributed to the greatest volume, with an annual average of 149 078 (95% credible interval: 93 733-206 045). Infants 6-23 months had the highest average annual rate at 6580 prescriptions per 100 000 individuals (95% credible interval: 4522-8651). Most RSV-attributable antibiotic prescriptions were penicillins, macrolides or tetracyclines. Adults ≥65 years had a wider range of antibiotic classes associated with RSV compared with younger age groups.

CONCLUSIONS: Interventions to reduce the burden of RSV, particularly in older adults, could complement current strategies to reduce antibiotic use in England.}, } @article {pmid39968615, year = {2025}, author = {Klarevas-Irby, JA and Nyaguthii, B and Farine, DR}, title = {Moving as a group imposes constraints on the energetic efficiency of movement.}, journal = {Proceedings. Biological sciences}, volume = {292}, number = {2041}, pages = {20242760}, doi = {10.1098/rspb.2024.2760}, pmid = {39968615}, issn = {1471-2954}, support = {//Centre for the Advanced Study of Collective Behaviour/ ; //Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; //Association for the Study of Animal Behaviour/ ; //H2020 European Research Council/ ; //Max Planck Society/ ; //Deutsche Forschungsgemeinschaft/ ; //Max Planck-Yale Center for Biodiversity Movement and Global Change/ ; }, mesh = {Animals ; *Energy Metabolism ; *Galliformes/physiology ; Social Behavior ; Movement ; Female ; Geographic Information Systems ; }, abstract = {Movement is a key part of life for many species. In solitary animals, the energetic costs of movement can be mitigated through energetically efficient strategies that produce faster, straighter movements. However, little is known about whether moving as part of a collective enhances or limits the ability of individual group members to express such strategies. Drawing on 6 years of population-level, high-resolution (1 Hz) GPS tracking of group-living vulturine guineafowl (Acryllium vulturinum), we detected 886 events from 94 tagged individuals where their groups made large, range-shifting displacements in response to changing environmental conditions. We contrasted these movements with data from 94 similarly large displacement events by 19 lone, dispersing individuals. Our results suggest that individuals in groups can significantly reduce their energetic cost of transport when making large displacements (15.3% more efficient relative to their normal daily ranging) by increasing the speed and straightness of their movements. However, even during their most efficient movements, individuals in groups could not achieve or maintain comparable increases in speed to lone individuals, resulting in significantly limited efficiency gains (35.7% less efficient than solitary individuals). Overall, this study provides evidence for a substantial energetic cost arising from collective movement.}, } @article {pmid39963945, year = {2025}, author = {Giglio, VJ and Adelir-Alves, J and Balzaretti Merino, N and Bravo-Olivas, ML and Camp, EF and Casoli, E and Chávez-Dagostino, RM and Ferretti, E and Fraser, D and Grillo, AC and Jiménez-Guiérrez, S and Leite, KL and Lucrezi, S and Luiz, OJ and Luna-Pérez, B and McBride, J and Milanese, M and Moity, N and Pinheiro, JV and Renfro, B and Roche, R and Saliba, BM and Sara, A and Schiavetti, A and Toso, Y and Valle-Pérez, C and Ferreira, CEL}, title = {DiverReef: A global database of the behavior of recreational divers and their interactions with reefs over 20 years.}, journal = {Ecology}, volume = {106}, number = {2}, pages = {e4519}, doi = {10.1002/ecy.4519}, pmid = {39963945}, issn = {1939-9170}, support = {17/22273-0//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 111.210/2014//Fundação Carlos Chagas Filho de Amparo à Pesquisa do Estado do Rio de Janeiro/ ; }, mesh = {*Diving/physiology ; *Coral Reefs ; *Databases, Factual ; *Recreation ; Animals ; Humans ; Male ; Female ; Time Factors ; }, abstract = {Recreational diving is an important activity in reef environments worldwide, providing income and employment for coastal communities and connecting visiting divers to these ecosystems promoting conservation and stewardship. However, if poorly managed, diving has the potential to cause detrimental effects on benthic communities via mechanical damage caused by physical contact of divers with the reef, often in the form of unintentional fin kicks resulting from poor buoyancy. Understanding diver-reef interaction patterns is important to elucidate the potential impacts of diving tourism on the reef biota. The DiverReef database provides the first public dataset on the underwater behavior of recreational divers in shallow reef environments (<25 m depth) globally and their interactions with the reef seascape and/or reef benthic sessile organisms. The dataset comprises 20 years of data (2004-2023) by observing the behavior of 2311 recreational divers in nine countries at 19 diving destinations and 176 diving sites; 93% of the observations were in marine protected areas. The data were collected through on-site observations of divers' behavior during tourism activities and their physical interactions with the reef structure and/or benthic sessile reef organisms. Observers discreetly followed divers and recorded their behavior and interactions with the reef over set periods. Interactions were described as "contact" or "damage," the latter referring to when physical damage to a benthic organism or the reef structure was observed. Besides behavior, observers also recorded data on the type of diving activity (scuba or snorkeling), profiles of the divers (gender and experience), use of cameras by the divers, visibility, type of reef formation, and marine protection status of the dive site. The authors of this research expect that the data provided will be useful in advancing knowledge of how divers interact with reefs and in developing strategies to mitigate the potential detrimental effects of the diving industry on reef biota. Part of the data has already been used in reports and scientific articles. This dataset can be freely used for noncommercial purposes; we request that users of these data cite this data paper in all publications resulting from the use of this dataset.}, } @article {pmid39963041, year = {2025}, author = {Lima-Cordón, R and Mohabir, JT and Sooklall, M and Zurita, AM and Shieh, M and Knox, C and Gobran, S and Johnson, Z and Laws, M and Panchal, R and Niles-Robin, R and Cox, H and Grillet, ME and Moreno, JE and Herrera, S and Quinones, M and Early, AM and Tennessen, JA and Neafsey, DE}, title = {A Short-Read Amplicon Sequencing Protocol and Bioinformatic Pipeline for Ecological Surveillance of Dipteran Disease Vectors.}, journal = {Molecular ecology resources}, volume = {}, number = {}, pages = {e14088}, doi = {10.1111/1755-0998.14088}, pmid = {39963041}, issn = {1755-0998}, support = {INV-009416/GATES/Bill & Melinda Gates Foundation/United States ; U19AI110818//National Institute of Allergy and Infectious Diseases, National Institutes of Health, Department of Health and Human Services/ ; }, abstract = {Vector control remains an important strategy worldwide to prevent human infection with pathogens transmitted by arthropods. Vector control strategies rely on accurate identification of vector taxa along with vector-specific biological indicators such as feeding ecology, infection prevalence and insecticide resistance. Multiple 'DNA barcoding' protocols have been published over the past several decades to support these applications, generally relying on informal manual approaches such as BLAST to assign taxonomic identity to the resulting sequences. We present a standardised informatic pipeline for analysis of DNA barcoding data from dipteran vectors, VecTreeID, that uses short-read amplicon sequencing (AmpSeq) coupled with sequence similarity assessment (BLAST) and an evolutionary placement algorithm (EPA-ng) to achieve vector taxonomic identification, capture bionomic features (blood and plant meal sources), determine Plasmodium infection status (for anopheline mosquitoes) and detect target-site insecticide resistance mutations. The VecTreeID pipeline provides uncertainty in assignment through identifications at varying levels of taxonomic rank, a feature missing from many approaches to DNA barcoding, but important given gaps and labelling problems in public sequence databases. We validated an Illumina-based implementation of VecTreeID on laboratory and field samples, and find that the blood meal amplicons can detect vertebrate DNA sequences up to 36 h post-feeding, and that short-read sequencing data are capable of sensitively detecting minor sequences in DNA mixtures representing multi-species blood or nectar meals. This high-throughput VecTreeID approach empowers researchers and public health professionals to survey and control arthropod disease vectors consistently and effectively.}, } @article {pmid39960184, year = {2025}, author = {Ferdousee, S and Alam, MS and Hwangbo, M and Kim, J}, title = {Visualizing Methane-Cycling Microbial Dynamics in Coastal Wetlands.}, journal = {Journal of visualized experiments : JoVE}, volume = {}, number = {215}, pages = {}, doi = {10.3791/67715}, pmid = {39960184}, issn = {1940-087X}, mesh = {*Wetlands ; *Methane/metabolism ; Texas ; Geographic Information Systems ; }, abstract = {Coastal wetlands are the largest biotic source of methane, where methanogens convert organic matter into methane and methanotrophs oxidize methane, thus playing a critical role in regulating the methane cycle. The wetlands in South Texas, which are subject to frequent weather events, fluctuating salinity levels, and anthropogenic activities due to climate change, influence methane cycling. Despite the ecological importance of these processes, methane cycling in South Texas coastal wetlands remains insufficiently explored. To address this gap, we developed and optimized a method for detecting genes related to methanogens and methanotrophs, including mcrA as a biomarker for methanogens and pmoA1, pmoA2, and mmoX as biomarkers for methanotrophs. Additionally, this study aimed to visualize the spatial and temporal distribution patterns of methanogen and methanotroph abundance utilizing the geographic information system (GIS) software ArcGIS Pro. The integration of these molecular techniques with advanced geospatial visualization provided critical insights into the spatial and temporal distribution of methanogen and methanotroph communities across South Texas wetlands. Thus, the methodology established in this study offers a robust framework for mapping microbial dynamics in wetlands, enhancing our understanding of methane cycling under varying environmental conditions, and supporting broader ecological and environmental change studies.}, } @article {pmid39957502, year = {2025}, author = {Latini, L and Burini, G and Mazza, V and Grignani, G and De Donno, R and Bello, E and Tricarico, E and Malavasi, S and Nascetti, G and Canestrelli, D and Carere, C}, title = {Early-life environment shapes claw bilateral asymmetry in the European lobster (Homarus gammarus).}, journal = {Biology open}, volume = {}, number = {}, pages = {}, doi = {10.1242/bio.061901}, pmid = {39957502}, issn = {2046-6390}, support = {//Universite degli Studi della Tuscia/ ; //Universite degli Studi di Firenze/ ; //Universite Ca' Foscari Venezia/ ; }, abstract = {Developmental plasticity refers to an organism's ability to adjust its development in response to changing environmental conditions, leading to changes in behaviour, physiology, or morphology. This adaptability is crucial for survival and helps organisms to cope with environmental challenges throughout their lives. Understanding the mechanisms underlying developmental plasticity, particularly how environmental and ontogenetic factors shape functional traits, is fundamental for both evolutionary biology and conservation efforts. In this study we investigated the effects of early-life environmental conditions on the development of claw asymmetry in juvenile European lobsters (Homarus gammarus, N=244), a functional trait essential for survival and ecological success. Juveniles were randomly divided between four different rearing conditions characterized by the presence or absence of physical enrichments (e.g., substrate and shelters), which were introduced at different developmental stages in separated groups to assess the timing and nature of their effect. Results revealed that exposure to substrate alone, without additional stimuli, consistently promoted claw asymmetry, regardless of the timing of its introduction, while the 6th developmental stage emerged as the critical period for claw differentiation. By identifying the environmental factors that influence developmental outcomes in lobsters, and the timing of these effects, this study improves our understanding of developmental plasticity and offers valuable insights for optimizing conservation aquaculture and reintroduction strategies.}, } @article {pmid39955351, year = {2025}, author = {Yang, Y and Yang, Y and Yang, S and Zhang, J}, title = {Pollution control mechanism of national water network with water quality differences based on differential game and case study.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {5588}, pmid = {39955351}, issn = {2045-2322}, support = {51679089//National Nature Science Foundation of China/ ; 51679089//National Nature Science Foundation of China/ ; 51679089//National Nature Science Foundation of China/ ; 51679089//National Nature Science Foundation of China/ ; GXJD004//Intelligent Water Conservancy Project of the Discipline Innovation Introduction Base of Henan Province, China/ ; GXJD004//Intelligent Water Conservancy Project of the Discipline Innovation Introduction Base of Henan Province, China/ ; GXJD004//Intelligent Water Conservancy Project of the Discipline Innovation Introduction Base of Henan Province, China/ ; GXJD004//Intelligent Water Conservancy Project of the Discipline Innovation Introduction Base of Henan Province, China/ ; }, abstract = {The construction of the national water network optimizes water resource allocation but also causes a redistribution of pollutants due to water quality differences, posing urgent challenges for water pollution management. Taking the South-to-North Water Diversion Project and Yangtze-to-Hanjiang River Water Diversion Project (YHRWDP) as an example and considering the pressure brought by the redistribution of pollutants to the polluting enterprises (PE) and water diversion enterprises (WDE) situated in areas where pollution is aggravated, a differential game model of pollution control among the central government, water-supply area (WSA), PE and WDE is constructed based on the cost-sharing mechanism. The results show that: (1) The pressure coefficient has an apparent negative correlation with the effort level of the affected subject. (2) An increase in the amount of pollution elimination per unit of pollution control effort of WSA and PE will lead to their own investment in more efforts to improve the ecology of the basin, thus benefiting all participants in the system. (3) The cost-sharing rate of the central government on the WSA of the YHRWDP, the PE, and the WDE is influenced by several factors, which shows a stable monotonically increasing or decreasing relation. The results are an useful supplement to the research on natural river pollution control, and can also provide a reference for designing pollution control mechanisms of national water network.}, } @article {pmid39952648, year = {2025}, author = {Siddiqui, JA and Fan, R and Liu, Y and Syed, AH and Benlin, Y and Chu, Q and Ding, Z and Ghani, MI and Liu, X and Wakil, W and Liu, DD and Chen, X and Cernava, T and Smagghe, G}, title = {The larval gut of Spodoptera frugiperda harbours culturable bacteria with metabolic versatility after insecticide exposure.}, journal = {Insect molecular biology}, volume = {}, number = {}, pages = {}, doi = {10.1111/imb.12983}, pmid = {39952648}, issn = {1365-2583}, support = {32360705//National Natural Science Foundation of China/ ; 31960555//National Natural Science Foundation of China/ ; GCC[2023]070//Guizhou Provincial Science and Technology Program/ ; HZJD[2022]001//Guizhou Provincial Science and Technology Program/ ; 2019-1410//Guizhou Provincial Science and Technology Program/ ; [2023]1-4//Guiyang Science and Technology Program/ ; D20023//Program for Introducing Talents to Chinese Universities/ ; }, abstract = {Spodoptera frugiperda (fall armyworm) poses a substantial risk to crops worldwide, resulting in considerable economic damage. The gut microbiota of insects plays crucial roles in digestion, nutrition, immunity, growth and, sometimes, the degradation of insecticides. The current study examines the effect of synthetic insecticides on the gut microbiome of third instar S. frugiperda larvae using both culture-dependent techniques and 16S rRNA gene sequencing for bacterial community profiling and diversity analysis. In untreated larvae, the sequencing approach revealed a diverse microbiome dominated by the phyla Firmicutes, Proteobacteria and Bacteroidota, with key genera including Bacteroides, Faecalibacterium and Pelomonas. In parallel, 323 bacterial strains were isolated and assigned to the orders Bacillales, Burkholderiales, Enterobacterales, Flavobacteriales, Lactobacillales, Micrococcales, Neisseriaies, Pseudomonadales, Sphingobacteriales and Xanthomonadales. The prevailing culturable species included Serratia marcescens, Klebsiella variicola and Enterobacter quasiroggenkampii. Treatment with sublethal concentrations of three insecticides (broflanilide, spinosad and indoxacarb) caused significant changes in gut microbiome diversity and composition. Treated larvae showed a shift towards increased Proteobacteria abundance and decreased Firmicutes. Specifically, Acinetobacter and Rhodococcus were dominant in treated samples. Functional predictions highlighted significant metabolic versatility involving nutrient processing, immune response, detoxification, xenobiotic metabolism, and stress response, suggesting microbial adaptation to insecticide exposure. Network correlation analysis highlighted disrupted microbial interactions and altered community structures under insecticide treatment. These findings enhance our understanding of how insecticides impact the gut microbiota in S. frugiperda and may inform future strategies for managing pest resistance through microbiome-based approaches.}, } @article {pmid39952543, year = {2025}, author = {Chaemsaithong, P and Romero, R and Pongchaikul, P and Warintaksa, P and Mongkolsuk, P and Bhuwapathanapun, M and Kotchompoo, K and Nimsamer, P and Kruasuwan, W and Amnuaykiatlert, O and Vivithanaporn, P and Meyyazhagan, A and Awonuga, A and Settacomkul, R and Singhsnaeh, A and Laolerd, W and Santanirand, P and Thaipisuttikul, I and Wongsurawat, T and Jenjaroenpun, P}, title = {The rapid diagnosis of intraamniotic infection with nanopore sequencing.}, journal = {American journal of obstetrics and gynecology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.ajog.2025.02.011}, pmid = {39952543}, issn = {1097-6868}, abstract = {BACKGROUND: Intraamniotic infection (defined as intraamniotic inflammation with microorganisms) is an important cause of the preterm labor syndrome. Methods for the detection of microorganisms in amniotic fluid are culture and/or polymerase chain reaction. However, both methods take time, and results are rarely available for clinical decision-making. Nanopore sequencing technology offers real-time, long-read sequencing that can produce rapid results.

OBJECTIVES: To determine 1) the diagnostic performance of the 16S rDNA nanopore sequencing method for the identification of microorganisms in patients with intraamniotic inflammation; and 2) the relationship between microbial burden and the intensity of the amniotic fluid inflammatory response.

STUDY DESIGN: We performed a prospective cohort study that included singleton pregnancies presenting with symptoms of preterm labor with intact membranes or of preterm prelabor rupture of the membranes. Amniotic fluid samples were obtained for the evaluation of bacteria in the amniotic cavity using cultivation and polymerase chain reaction-based 16S Sanger sequencing methods. Participants were classified into 4 groups according to the results of an amniotic fluid culture, 16S Sanger sequencing, and an amniotic fluid interleukin-6 concentration: 1) no intraamniotic infection and intraamniotic inflammation (interleukin-6 <2.6 ng/mL and no microorganisms in the amniotic cavity determined by culture or 16S Sanger sequencing); 2) microbial invasion of the amniotic cavity without intraamniotic inflammation, defined by the presence of bacteria detected by culture or 16S Sanger sequencing; 3) sterile intraamniotic inflammation (interleukin-6 ≥2.6 ng/mL without microbial invasion of the amniotic cavity); and 4) intraamniotic infection (interkeukin-6 ≥2.6 ng/mL with microbial invasion of the amniotic cavity). Patients who underwent a midtrimester amniocentesis, had no intraamniotic infection or intraamniotic inflammation, and delivered at term represented the control group. 16S rDNA nanopore sequencing was performed and the diagnostic indices for the identification of intraamniotic infection were determined. Bioinformatic analysis was carried out to identify microorganisms, and a read count of at least 100 or a read count exceeding that of the background species from the control group, along with a relative abundance of no less than 1%, was used.

RESULTS: 1) 16S nanopore sequencing had a sensitivity of 88.9% (8/9), specificity of 95.4% (41/43), positive predictive value of 80.0% (8/10), negative predictive value of 97.6% (41/42), positive likelihood ratio of 19.1 (95% CI, 4.8-75.4), negative likelihood ratio of 0.1 (95% CI, 0.02-0.7), and an accuracy of 94.2% (49/52) for the identification of intraamniotic infection [prevalence, 17% (9/52)]; 2) the microbial load determined by 16S nanopore sequencing had a strong positive correlation with the intensity of an intraamniotic inflammatory response (amniotic fluid interleukin-6 concentration; Spearman's correlation 0.9; p = 0.002); and 3) a subgroup of patients with intraamniotic inflammation did not have bacteria determined by culture, Sanger sequencing, or nanopore 16S, thus confirming the existence of sterile intraamniotic inflammation.

CONCLUSION: 16S nanopore sequencing has high diagnostic indices, predictive values, likelihood ratios, and accuracy in the diagnosis of intraamniotic infection.}, } @article {pmid39952461, year = {2025}, author = {Shi, W and Lu, P and Yang, H and Han, J and Wang, Q}, title = {Quantifying the relative importance of natural and human factors on vegetation dynamics in China's western frontiers during 2010-2021.}, journal = {Environmental research}, volume = {}, number = {}, pages = {121120}, doi = {10.1016/j.envres.2025.121120}, pmid = {39952461}, issn = {1096-0953}, abstract = {Vegetation is a core component of terrestrial ecosystems, thus understanding the drivers of its dynamics is crucial for ecological conservation and management, especially in regions rich in natural resources but ecologically fragile. Here, we examined vegetation cover changes in China's western frontiers and quantified the relative importance of key drivers of vegetation dynamics. First, we employed the Dimidiate Pixel Model (DPM) via Google Earth Engine (GEE) to estimate fractional vegetation cover (FVC), followed by trend analysis using the Theil-Sen median and Mann-Kendall methods to examine FVC dynamics from 2010 to 2021. Next, we applied the optimal parameter-based geographic detector (OPGD) to further assess the impact of natural (ie., temperature, precipitation, and elevation) and human (ie., land use and population density) factors on FVC. Our results revealed that approximately 61.26% of the vegetation-covered regions in China's western frontiers have shown improvement. In Xinjiang, population density, land use, and precipitation were the primary drivers of FVC changes, with Q values exceeding 0.20. In Xizang, precipitation, elevation, temperature, and land use changes were the dominant drivers, with Q values greater than 0.30. Furthermore, interactions between natural and human factors significantly influenced FVC variation. Our findings have the potential to provide references for promoting sustainable vegetation management in western China.}, } @article {pmid39823671, year = {2025}, author = {Liu, T and Wang, M and Wang, M and Xiong, Q and Jia, L and Ma, W and Sui, S and Wu, W and Guo, X}, title = {Identification of the primary pollution sources and dominant influencing factors of soil heavy metals using a random forest model optimized by genetic algorithm coupled with geodetector.}, journal = {Ecotoxicology and environmental safety}, volume = {290}, number = {}, pages = {117731}, doi = {10.1016/j.ecoenv.2025.117731}, pmid = {39823671}, issn = {1090-2414}, mesh = {*Soil Pollutants/analysis ; *Metals, Heavy/analysis ; China ; *Environmental Monitoring/methods ; *Algorithms ; Geographic Information Systems ; Soil/chemistry ; Risk Assessment ; Environmental Pollution/analysis/statistics & numerical data ; Monte Carlo Method ; Principal Component Analysis ; Random Forest ; }, abstract = {Identifying and quantifying the dominant factors influencing heavy metal (HM) pollution sources are essential for maintaining soil ecological health and implementing effective pollution control measures. This study analyzed soil HM samples from 53 different land use types in Jiaozuo City, Henan Province, China. Pollution sources were identified using Absolute Principal Component Score (APCS), with 8 anthropogenic factors, 9 natural factors, and 4 soil physicochemical properties mapped using Geographic Information System (GIS) kernel density estimation. Geodetector and a genetic algorithm optimized random forest model (GA-RF) were employed to quantify the dominant factors and precisely identify pollution sources. A Monte Carlo model was further applied to assess source-oriented health risk probabilities across age groups in the study area. The results revealed three principal components representing pollution sources, with contribution rates of 47.2 %, 33.3 %, and 19.5 %, respectively. For pollution source 1, industrial activities were dominant, with factory density (27.7 %) and distance from the factory (36.3 %) identified as the main factors. Cr, Cu, Mn, and Ni had high loads in this source. Pollution source 2, a combination of natural and transportation influences, was primarily affected by the normalized difference vegetation index (NDVI, 37.8 %), road network density (16.8 %), and proximity to roads (15.3 %). Pollution source 3 was linked to agricultural activities, with cultivated land density (CLD) contributing 39.1 %. As exhibited a high load (91.1 %) in this source, with an exceedance rate of 93 % in cultivated soil, a moderate enrichment factor of 2.33, and a strong ecological risk index of 615.72, making it the most polluted metal in the area. The source-oriented Health Risk Assessment (HRA) showed that agricultural activities contributed 88.7 % to the carcinogenic risk from As in cultivated land. Overall, 99.3 % of the population faced an acceptable cancer risk level. Unlike traditional source apportionment methods, the GA-RF model effectively quantified the contributions of specific influencing factors (e.g., factory density) to pollution sources, rather than merely estimating the percentage contributions of the sources themselves. This approach provides a novel perspective for HM source apportionment under complex environmental conditions.}, } @article {pmid39742640, year = {2025}, author = {Zhang, H and Dong, S and Shan, H and Yang, C and Wang, F}, title = {Application of the DEB-TKTD model with multi-omics data: Prediction of life history traits of Chinese mitten crab (Eriocheir sinensis) under different salinities.}, journal = {Ecotoxicology and environmental safety}, volume = {290}, number = {}, pages = {117635}, doi = {10.1016/j.ecoenv.2024.117635}, pmid = {39742640}, issn = {1090-2414}, mesh = {Animals ; *Brachyura/physiology/drug effects/growth & development/genetics ; *Salinity ; *Aquaculture ; Life History Traits ; Reproduction/drug effects ; Fresh Water ; Female ; Oxidative Stress ; Water Pollutants, Chemical/toxicity ; Osmoregulation ; Multiomics ; }, abstract = {Saline-alkaline aquaculture plays a crucial role in the ecological restoration of saline soils, yet high water salinity can significantly restrict the growth of cultured organisms. The Chinese mitten crab (Eriocheir sinensis) is typically farmed in freshwater, to evaluate the effects of salinity stress on these crabs, this study conducted laboratory aquaculture experiments at salinities of ≤ 0.5 (freshwater), 6, 12, and 18 ‰. Regular data on crab survival and growth were collected over 35 days. Subsequently, tissues including the eyestalk, posterior gill, hepatopancreas, and ovary were sampled from crabs in both the freshwater control group and the 18 ‰ salinity treatment group for transcriptional and metabolomic analysis. The omics data were used to ascertain the physiological mode of action (pMoA) affected by salinity in the crabs. A dynamic energy budget toxicokinetic-toxicodynamic (DEB-TKTD) model was built based on these pMoAs to predict the life history traits of crabs across different salinities, including survival, growth, and reproduction. The omics results indicated that at 18 ‰, the osmoregulatory capacity and oxidative stress resistance were enhanced, and vitellogenin synthesis was stimulated. This suggests that the two pMoAs involved increasing maintenance costs and reallocating energy between soma and reproduction. DEB-TKTD model predictions fit well with the observed data, with high R[2] values (0.9704 for survival, 0.9842 for carapace width, and 0.9283 for reproduction) and low NRMSE (0.0093, 0.1175, and 0.0778, respectively). The predictions indicate that after 60 days, survival rates under salinities of 6, 12, and 18 ‰ decreased by 35.7 %, 56.7 %, and 66.2 %, respectively, compared to freshwater conditions. Growth in carapace width was similarly affected, with reductions of 21.5 %, 42.3 %, and 62.5 %, respectively. The maturation process was accelerated for crabs in saline conditions, with puberty achieved at 45, 36, and 31 days, compared to the freshwater group that had not matured. Furthermore, the LC50 for salinity decreased from 9.07 ‰ (95 % CI: 7.33-10.15 ‰) at 35 days to 4.59 ‰ (95 % CI: 3.12-5.83 ‰) at 60 days. The findings of this study indicate the significant impact of salinity on the survival, growth, and maturation of Chinese mitten crabs by altering maintenance costs and energy allocation. The DEB-TKTD model, informed by omics data, accurately predicts the life history traits of crabs under saline stress. This approach provides an innovative tool for ecological toxicological research in the aquaculture environment.}, } @article {pmid39730187, year = {2025}, author = {Yan, M and Andersen, TO and Pope, PB and Yu, Z}, title = {Probing the eukaryotic microbes of ruminants with a deep-learning classifier and comprehensive protein databases.}, journal = {Genome research}, volume = {35}, number = {2}, pages = {368-378}, doi = {10.1101/gr.279825.124}, pmid = {39730187}, issn = {1549-5469}, mesh = {Animals ; *Ruminants/microbiology ; *Deep Learning ; *Fungi/genetics/classification ; Rumen/microbiology/parasitology ; Databases, Protein ; Metagenome ; Metagenomics/methods ; Eukaryota/genetics/classification ; Gastrointestinal Microbiome ; Computational Biology/methods ; }, abstract = {Metagenomics, particularly genome-resolved metagenomics, have significantly deepened our understanding of microbes, illuminating their taxonomic and functional diversity and roles in ecology, physiology, and evolution. However, eukaryotic populations within various microbiomes, including those in the mammalian gastrointestinal (GI) tract, remain relatively underexplored in metagenomic studies owing to the lack of comprehensive reference genome databases and robust bioinformatic tools. The GI tract of ruminants, particularly the rumen, contains a high eukaryotic biomass but a relatively low diversity of ciliates and fungi, which significantly impacts feed digestion, methane emissions, and rumen microbial ecology. In the present study, we developed GutEuk, a bioinformatics tool that improves upon the currently available Tiara and EukRep in accurately identifying eukaryotic sequences from metagenomes. GutEuk is optimized for high precision across different sequence lengths. It can also distinguish fungal and protozoal sequences, further elucidating their unique ecological, physiological, and nutritional impacts. GutEuk was shown to facilitate comprehensive analyses of protozoa and fungi within more than 1000 rumen metagenomes, revealing a greater genomic diversity among protozoa than previously documented. We further curated several ruminant eukaryotic protein databases, significantly enhancing our ability to distinguish the functional roles of ruminant fungi and protozoa from those of prokaryotes. Overall, the newly developed package GutEuk and its associated databases create new opportunities for the in-depth study of GI tract eukaryotes.}, } @article {pmid39891349, year = {2025}, author = {Wang, Y and Li, J and Chiu, TP and Gompel, N and Rohs, R}, title = {DNAdesign: feature-aware in silico design of synthetic DNA through mutation.}, journal = {Bioinformatics (Oxford, England)}, volume = {41}, number = {2}, pages = {}, doi = {10.1093/bioinformatics/btaf052}, pmid = {39891349}, issn = {1367-4811}, support = {RGP0021/2018//Human Frontier Science Program/ ; }, mesh = {*DNA/chemistry/genetics ; *Mutation ; *Software ; Nucleic Acid Conformation ; Binding Sites ; Computer Simulation ; Sequence Analysis, DNA/methods ; Computational Biology/methods ; }, abstract = {MOTIVATION: DNA sequence and shape readout represent different modes of protein-DNA recognition. Current tools lack the functionality to simultaneously consider alterations in different readout modes caused by sequence mutations. DNAdesign is a web-based tool to compare and design mutations based on both DNA sequence and shape characteristics. Users input a wild-type sequence, select sites to introduce mutations and choose a set of DNA shape parameters for mutation design.

RESULTS: DNAdesign utilizes Deep DNAshape to provide ultra-fast predictions of DNA shape based on extended k-mers and offers multiple encoding methods for nucleotide sequences, including the physicochemical encoding of DNA through their functional groups in the major and minor groove. DNAdesign provides all mutation candidates along the sequence and shape dimensions, with interactive visualization comparing each candidate with the wild-type DNA molecule. DNAdesign provides an approach to studying gene regulation and applications in synthetic biology, such as the design of synthetic enhancers and transcription factor binding sites.

The DNAdesign webserver and documentation are freely accessible at https://dnadesign.usc.edu.}, } @article {pmid39623597, year = {2024}, author = {Félix, CR and Navarro, HMC and Landell, MF}, title = {The Hidden Global Diversity of the Yeast Genus Carlosrosaea: A Biodiversity Databases Perspective.}, journal = {Yeast (Chichester, England)}, volume = {41}, number = {11-12}, pages = {658-667}, doi = {10.1002/yea.3986}, pmid = {39623597}, issn = {1097-0061}, support = {//This work was supported by Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq, number of grants 475378/2013-0, 312889/2021-6 and 311553/2018-4), Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) and Fundação de amparo a Pesquisa de Alagoas (FAPEAL). This work is also part of the project "INCT Yeasts: Biodiversity, preservation and biotechnological innovation", funded by Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq), grant #406564/2022-1./ ; }, mesh = {*Biodiversity ; Phylogeny ; Saccharomycetales/classification/genetics/isolation & purification ; Databases, Factual ; }, abstract = {Biodiversity gaps in microorganisms, such as yeasts, blur our understanding of microbial diversity, introducing biases in their biogeography, ecology, and taxonomy. The genus Carlosrosaea is a potential plant growth booster, yet it is still a little-known yeast group. Considering that databases like GBIF and GenBank are powerful tools for exploring biodiversity data, we aimed to map the geographic distribution, ecological patterns, and taxonomic potential of the genus Carlosrosaea. We found 176 records of the genus, with about 70% associated with plant material, mostly leaves. Furthermore, 55% of the records pertained to the tropical region and only 12% to the temperate. The data indicates the existence of more than a dozen possible new species of the genus, cataloged yet undescribed. This study advances our understanding of the geographic, ecological, and taxonomic aspects of Carlosrosaea. It also highlights how public databases and literature reviews provide accessible ways to analyze information about microbial groups with limited data.}, } @article {pmid39949385, year = {2023}, author = {Lohse, K and , and , and , and Vila, R and , }, title = {The genome sequence of the Common Blue, Polyommatus icarus (Rottemburg, 1775).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {72}, pmid = {39949385}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual male Polyommatus icarus (the Common Blue; Arthropoda; Insecta; Lepidoptera; Lycaenidae). The genome sequence is 512 megabases in span. Most of the assembly is scaffolded into 23 chromosomal pseudomolecules, including the assembled Z chromosome. The mitochondrial genome has also been assembled and is 15.6 kilobases long. Gene annotation of this assembly on Ensembl identified 13,350 protein-coding genes.}, } @article {pmid39948527, year = {2025}, author = {Rakshasa-Loots, AM and Steyn, C and Swiffen, D and Marwick, KFM and Semple, RK and Reynolds, RM and Burgess, K and Lawrie, SM and Lightman, SL and Luz, S and Smith, DJ}, title = {Metabolic biomarkers of clinical outcomes in severe mental illness (METPSY): protocol for a prospective observational study in the Hub for metabolic psychiatry.}, journal = {BMC psychiatry}, volume = {25}, number = {1}, pages = {122}, pmid = {39948527}, issn = {1471-244X}, support = {MR/Z503563/1/MRC_/Medical Research Council/United Kingdom ; }, abstract = {People with severe mental illness have high rates of obesity, type 2 diabetes, and cardiovascular disease. Emerging evidence suggests that metabolic dysfunction may be causally linked to the risk of severe mental illness. However, more research is needed to identify reliable metabolic markers which may have an impact on mental health outcomes, and to determine the mechanisms behind their impact. In the METPSY research study, we will investigate the relationship between metabolic markers and clinical outcomes of severe mental illness in young adults. We will recruit 120 young adults aged 16-25 years living in Scotland with major depressive disorder, bipolar disorder, schizophrenia, or no severe mental illness (controls) for a prospective observational study. We will assess clinical symptoms at three in-person visits (baseline, 6 months, and 12 months) using the Structured Clinical Interview for DSM-5, and collect blood samples at each of these visits for agnostic profiling of metabolic biomarkers through an untargeted metabolomic screen, using the rapid hydrophilic interaction liquid chromatography ion mobility mass spectrometry method (RHIMMS). Participants will also complete remote assessments at 3 and 9 months after the baseline visit: Ecological Momentary Assessments to measure mental health, wrist actigraphy to measure rhythms of rest and activity, and continuous glucose monitoring to measure metabolic changes. Throughout the 12-month enrolment period, we will also measure objective markers of sleep using a radar sleep monitor (Somnofy). Using advanced statistical techniques and machine learning analysis, we will seek to better understand the mechanisms linking metabolic health with mental health in young adults with schizophrenia, bipolar disorder, and severe depression. Clinical trial number: Not applicable.}, } @article {pmid39945053, year = {2025}, author = {Tittes, S and Lorant, A and McGinty, SP and Holland, JB and de Jesus Sánchez-González, J and Seetharam, A and Tenaillon, M and Ross-Ibarra, J}, title = {The population genetics of convergent adaptation in maize and teosinte is not locally restricted.}, journal = {eLife}, volume = {12}, number = {}, pages = {}, doi = {10.7554/eLife.92405}, pmid = {39945053}, issn = {2050-084X}, support = {1822330//National Science Foundation/ ; 1238014//National Science Foundation/ ; CA-D-PLS-2066-H 548//U.S. Department of Agriculture/ ; }, mesh = {*Zea mays/genetics/physiology ; *Adaptation, Physiological/genetics ; *Genetics, Population ; Genetic Variation ; Selection, Genetic ; }, abstract = {What is the genetic architecture of local adaptation and what is the geographic scale over which it operates? We investigated patterns of local and convergent adaptation in five sympatric population pairs of traditionally cultivated maize and its wild relative teosinte (Zea mays subsp. parviglumis). We found that signatures of local adaptation based on the inference of adaptive fixations and selective sweeps are frequently exclusive to individual populations, more so in teosinte compared to maize. However, for both maize and teosinte, selective sweeps are also frequently shared by several populations, and often between subspecies. We were further able to infer that selective sweeps were shared among populations most often via migration, though sharing via standing variation was also common. Our analyses suggest that teosinte has been a continued source of beneficial alleles for maize, even after domestication, and that maize populations have facilitated adaptation in teosinte by moving beneficial alleles across the landscape. Taken together, our results suggest local adaptation in maize and teosinte has an intermediate geographic scale, one that is larger than individual populations but smaller than the species range.}, } @article {pmid39943576, year = {2025}, author = {Cleveland, P and Morrison, A}, title = {Sông Sài Gòn: Extreme Plastic Pollution Pathways in Riparian Waterways.}, journal = {Sensors (Basel, Switzerland)}, volume = {25}, number = {3}, pages = {}, doi = {10.3390/s25030937}, pmid = {39943576}, issn = {1424-8220}, support = {2023//Annual Award, School of Future Environments, Auckland University of Techolology/ ; }, mesh = {*Plastics ; *Rivers/chemistry ; *Environmental Monitoring/methods ; Vietnam ; Water Pollutants, Chemical/analysis ; Water Pollution/analysis ; Geographic Information Systems ; Ecosystem ; }, abstract = {Plastic pollution in waterways poses a significant global challenge, largely stemming from land-based sources and subsequently transported by rivers to marine environments. With a substantial percentage of marine plastic waste originating from land-based sources, comprehending the trajectory and temporal experience of single-use plastic bottles assumes paramount importance. This project designed, developed, and released a plastic pollution tracking device, coinciding with Vietnam's annual Plastic Awareness Month. By mapping the plastic tracker's journey through the Saigon River, this study generated high-fidelity data for comprehensive analysis and bolstered public awareness through regular updates on the Re-Think Plastics Vietnam website. The device, equipped with technologies such as drone flight controller, open-source software, embedded computing, and cellular networking effectively captured GPS position, track, and localized conditions experienced by the plastic bottle tracker on its journey. This amalgamation of data contributes to the understanding of plastic pollution behaviors and serves as a data set for future initiatives aimed at plastic prevention in the ecologically sensitive Mekong Delta. By illuminating the transportation of single-use plastic bottles in the riparian waterways of Ho Chi Minh City and beyond, this study plays a role in collective efforts to understand plastic pollution and preserve aquatic ecosystems. By deploying a GPS-enabled plastic tracker, this study provides novel, high-resolution empirical data on plastic transport in urban tidal systems. These findings contribute to improving waste interception strategies and informing environmental policies aimed at reducing plastic accumulation in critical retention zones.}, } @article {pmid39939924, year = {2025}, author = {Lorková, Z and Cimermanová, M and Piknová, M and Adhvaryu, S and Pristaš, P and Kisková, J}, title = {Environmental impact on the genome shaping of putative new Streptomyces species.}, journal = {BMC microbiology}, volume = {25}, number = {1}, pages = {72}, pmid = {39939924}, issn = {1471-2180}, support = {VEGA 1/0779/21//Grant Agency of the Ministry of Education, Science, Research and Sport, Slovak Republic and the Slovak Academy of Sciences/ ; }, mesh = {*Streptomyces/genetics/classification/metabolism/isolation & purification ; *Genome, Bacterial/genetics ; *Phylogeny ; *Metals, Heavy/metabolism ; Siderophores/metabolism ; Multigene Family ; Poland ; Secondary Metabolism/genetics ; Adaptation, Physiological/genetics ; Mining ; Computational Biology/methods ; }, abstract = {BACKGROUND: The bacterial evolution and the emergence of new species are likely influenced by multiple forces, including long-term environmental pressure such as living in extreme conditions. In this study, the genomes of two potentially new Streptomyces species isolated from a former mine heap in Tarnowskie Góry in Poland, were analyzed.

RESULTS: A bioinformatic approach revealed notable phylogenetic and metabolic differences between the studied Streptomyces strains, despite originating from the same environment. While both strains are characterized by genetic features common to actinomycetes, additional unique biosynthetic gene clusters were also predicted in their genomes. The comparative genomic analysis with other Streptomyces spp. revealed a high conservation in heavy metal adaptive mechanisms, indicating a preadaptation to extreme conditions. The difference observed in the cad and mer operons could be attributed to the specific adaptations to heavy metal contamination. The high metal tolerance of examined strains was also confirmed by an agar dilution assay in the presence of several heavy metals. The confirmed siderophore production represents an additional mechanism allowing streptomycetes to survive in extreme conditions. On the other hand, both of studied genomes show significant differences in energy acquisition processes and the production of putative novel secondary metabolites. The isolates showed these differences not only among themselves but also compared to other Streptomyces species, indicating their uniqueness.

CONCLUSIONS: Our results demonstrate that extreme environmental conditions can lead to the development of various adaptation mechanisms in the Streptomyces spp. Furthermore, the results indicate that diverse Streptomyces species have developed conserved adaptation mechanisms against the heavy metals under extreme conditions, indicating the emergence of preadaptations that allow bacteria to respond rapidly to polluted environments and evolve their genomes accordingly up to the evolution of new species.}, } @article {pmid38452336, year = {2024}, author = {Vacchi, L and Zirone, E and Strina, V and Cavaletti, G and Ferrarese, C}, title = {Mobile Applications to Support Multiple Sclerosis Communities: The Post-COVID-19 Scenario.}, journal = {Telemedicine journal and e-health : the official journal of the American Telemedicine Association}, volume = {30}, number = {6}, pages = {e1615-e1628}, doi = {10.1089/tmj.2023.0515}, pmid = {38452336}, issn = {1556-3669}, mesh = {Humans ; Access to Information ; COVID-19/epidemiology/prevention & control ; *Digital Health/trends ; Health Knowledge, Attitudes, Practice ; Italy/epidemiology ; *Mobile Applications/trends ; *Multiple Sclerosis/diagnosis/therapy ; Social Networking ; *Telemedicine/trends ; }, abstract = {Introduction: The increase in the use of mobile apps since the COVID-19 pandemic, even among people with multiple sclerosis (PwMS) and health care providers (HCPs), has enabled access to reliable information, symptoms monitoring and management, and social connections. The pandemic has undoubtedly contributed to the acceleration of the "digital revolution." But how far has it progressed for the MS communities? Methods: Italian Google Play and App Store were queried, selecting MS-specific apps in English or Italian language and usable by a wide public. Results: Fifty-four (n = 54) MS-specific apps were identified; most were PwMS-oriented (83%), free of charge (94%), and in English language (76%). The 45 PwMS-oriented apps focused on increasing MS knowledge (71%), tracking symptoms (33%), and promoting networking with peers or HCPs (38%). The 13 HCPs-oriented tools addressed education and updates on MS (62%), disease assessment and management (54%), and research (15%). Google Search tool was also queried to find non-MS-specific apps to fulfill some unmet domains (as sleep, pain, sexual or mental health). Twenty-four additional apps were listed to provide a valuable contribution. Conclusion: The "digital revolution" led to increasingly customized tools for PwMS, especially as m-health or social-networking apps. However, apps to support other specific MS-relevant domains, appealing HCPs-oriented apps, and specific mobile tools for MS caregivers are still lacking. The absence of data assessing the usability and quality of MS apps in ecologically contexts leads to not reliable conclusions about potential benefits. A strong dialogue between MS communities and the digital industry is encouraged to fill this gap.}, } @article {pmid39938295, year = {2025}, author = {Zhuo, W and Wu, N and Shi, R and Cui, Y and Zhang, C and Liu, S and Zhu, F and Zhang, B and Liu, P}, title = {Assessing the impacts of reclamation and invasion on ecological dynamics of coastal wetland vegetation in the Yangtze Estuary from 1985 to 2019:A case study of Chongming Island, China.}, journal = {Journal of environmental management}, volume = {376}, number = {}, pages = {124505}, doi = {10.1016/j.jenvman.2025.124505}, pmid = {39938295}, issn = {1095-8630}, abstract = {The distribution of coastal wetland vegetation is influenced by biological invasions, human reclamations and climate changes, which continually reshape vegetation structures. However, limited attention has been given to the impact of biological invasion on native vegetation and tidal wetlands. This study focuses on the wetlands of Chongming Island, employing a multi-feature dataset combining spectral, phenological, and temporal information on the Google Earth Engine (GEE) platform. Using the Random Forest (RF) classification method, we analyzed annual vegetation distribution changes and examined the distinct effects of natural and anthropogenic factors. The research results indicate that: (1) From 1985 to 2019, the total area of Chongming Island expanded, while wetland vegetation decreased due to embankment construction and island connection projects. (2) The total area of wetland vegetation on Chongming Island dropped to its lowest point in 2002 (3812.76 ha), and then gradually recovered. (3) Human reclamation was the primary driver of vegetation changes from 1985 to 1995. (4) Vegetation distribution in Dongtan was influenced by both human and natural factors, whereas Beiliuyao affected by the invasion and expansion of the S. alterniflor. These findings provide valuable insights into the drivers of long-term vegetation distribution changes, offering essential data and theoretical support for sustainable development and management of Chongming Island's ecosystems.}, } @article {pmid39936843, year = {2025}, author = {Kim, KK and Backonja, U}, title = {Digital health equity frameworks and key concepts: a scoping review.}, journal = {Journal of the American Medical Informatics Association : JAMIA}, volume = {}, number = {}, pages = {}, doi = {10.1093/jamia/ocaf017}, pmid = {39936843}, issn = {1527-974X}, support = {//The MITRE Innovation Program/ ; //MITRE Corporation/ ; }, abstract = {OBJECTIVES: Digital health equity, the opportunity for all to engage with digital health tools to support good health outcomes, is an emerging priority across the world. The field of digital health equity would benefit from a comprehensive and systematic understanding of digital health, digital equity, and health equity, with a focus on real-world applications. We conducted a scoping review to identify and describe published frameworks and concepts relevant to digital health equity interventions.

MATERIALS AND METHODS: We conducted a scoping review of published peer-reviewed literature guided by the PRISMA Extension for Scoping Reviews. We searched 5 databases for frameworks related to or applied to digital health or equity interventions. Using deductive and inductive approaches, we analyzed frameworks and concepts based on the socio-ecological model.

RESULTS: Of the 910 publications initially identified, we included 44 (4.8%) publications in our review that described 42 frameworks that sought to explain the ecosystem of digital and/or health equity, but none were comprehensive. From the frameworks we identified 243 concepts grouped into 43 categories including characteristics of individuals, communities, and organizations; societal context; perceived value of the intervention by and impacts on individuals, community members, and the organization; partnerships; and access to digital health services, in-person services, digital services, and data and information, among others.

DISCUSSION: We suggest a consolidated definition of digital health equity, highlight illustrative frameworks, and suggest concepts that may be needed to enhance digital health equity intervention development and evaluation.

CONCLUSION: The expanded understanding of frameworks and relevant concepts resulting from this study may inform communities and stakeholders who seek to achieve digital inclusion and digital health equity.}, } @article {pmid39936690, year = {2025}, author = {Krefer, LT and Oliveira, WF}, title = {[Reformulations in the national mental health policy: analysis of assistance data in the period from 2012 to 2022].}, journal = {Ciencia & saude coletiva}, volume = {30}, number = {2}, pages = {e13372023}, doi = {10.1590/1413-81232025302.13372023}, pmid = {39936690}, issn = {1678-4561}, mesh = {Brazil ; Humans ; *Health Policy ; *Mental Health Services/organization & administration ; *Hospitals, Psychiatric/organization & administration/statistics & numerical data ; Longitudinal Studies ; *Deinstitutionalization/trends ; Primary Health Care/organization & administration ; Mental Health ; Ambulatory Care/statistics & numerical data ; Health Care Reform ; Health Information Systems/organization & administration ; }, abstract = {This article aims to analyze data on care in the field of public mental healthcare in Brazil from 2012 to 2022, corresponding to the years before and after the implementation of the New Mental Health Policy. For this purpose, quantitative methodology, of the longitudinal ecological study type, was used. Data was extracted for the period from 2012 to 2022. The sources used were Health Information Systems. The data was compiled into time series and analyzed using descriptive statistical techniques. The results pointed to the enhancement of outpatient services and a decrease in the expansion of Psychosocial Care Centers and Primary Care facilities after 2017, indicating compliance with the New Policy guidelines to deprioritize territorial and community-based services. The number of psychiatric hospitals showed little variation for the entire period, indicating not only alignment with the strengthening of hospital institutions indicated in the New Policy, but also weaknesses in the deinstitutionalization policy of the period prior to 2017. This study concludes that the effects of the changes in national policies on the organization, management and execution of the health system can be seen, but at the same time there is continuity in various aspects.}, } @article {pmid39889433, year = {2025}, author = {Shukla, S and Khan, R and Chrzanowski, Ł and Vagliasindi, FGA and Roccaro, P}, title = {Advancing sustainable agriculture through multi-omics profiling of biosolids for safe application: A review.}, journal = {Journal of environmental management}, volume = {375}, number = {}, pages = {124292}, doi = {10.1016/j.jenvman.2025.124292}, pmid = {39889433}, issn = {1095-8630}, mesh = {*Agriculture/methods ; Soil/chemistry ; Wastewater/chemistry ; Multiomics ; }, abstract = {Biosolids, derived from wastewater treatment processes, are valuable resources for soil amendment in agriculture due to their nutrient-rich composition. However, various contaminants of concern (CEC) such as pharmaceuticals, per-and poly-fluoroalkyl substances, endocrine disruptive chemicals, surfactants, pathogens, nanoplastics, and microplastics, are also reported in biosolids. The use of biosolids for agriculture may introduce these CEC into the soil, which raises concerns about their environmental and human health impacts. Moreover, the presence of pathogens (Escherichia coli, Salmonella sp., Shigella, Giardia, Rotavirus, etc.) even after treatment calls for microbial profiling of biosolids, especially in developing countries. Multi-omics approaches can be used as powerful tools for characterizing microbial communities and highlighting metabolic pathways. Moreover, these approaches also help in predicting the ecological and agronomic effects of biosolids application in agricultural soils. This review discusses the advantages and challenges of using biosolids in agriculture, considering the range of different CEC reported in biosolids. Moreover, the current legislation for the use of biosolids in agriculture is also presented, highlighting the limitations with respect to guidelines for emerging contaminants in biosolids. Furthermore, the role of the multi-omics approach in biosolids management, focusing on genomics, transcriptomics, proteomics, and metabolomics is also assessed. Multi-omics also allows for real-time monitoring, ensuring continuous optimization of biosolids towards changing environmental conditions. This dynamic approach not only enhances the safe use, but also enhances the sustainability of waste management practices, minimizing the negative effects. Finally, the future research directions for integrating the multi-omics approach into biosolid management practices are also suggested. The need for updating the legislative framework, continued innovation to promote sustainable and robust agricultural systems, bringing the process closer to the principles of a circular bioeconomy is also empahasized.}, } @article {pmid39854904, year = {2025}, author = {Ghimire, SR and Schumacher, B and Swanson, S and Hall, R and Hall, ES and Zambrana, J and Johnston, JM}, title = {Assessing riparian functioning condition for improved ecosystem services: A case study of the Back Creek watershed (Virginia, USA).}, journal = {Journal of environmental management}, volume = {375}, number = {}, pages = {124154}, doi = {10.1016/j.jenvman.2025.124154}, pmid = {39854904}, issn = {1095-8630}, mesh = {*Ecosystem ; *Rivers ; Virginia ; *Environmental Monitoring/methods ; Water Quality ; Conservation of Natural Resources ; Hydrology ; Geographic Information Systems ; }, abstract = {Riparian functioning condition refers to a rating and description of the current ecological status of a reach of a riparian ecosystem in consideration of its potential hydrology, vegetation, and geomorphology. Reach rating options are Proper Functioning Condition (PFC), Functional-At-Risk (FAR), Non-Functional, and apparent or monitored trends. We assessed the functioning condition of flowing riverbank areas of Back Creek located in Virginia (USA) following a PFC protocol developed by the U.S. Department of the Interior and the U.S. Department of Agriculture. The PFC protocol involves 17 qualitative assessment items that address three categories of attributes (hydrology, vegetation, and geomorphology); each is answered as "yes", "no," or "not applicable" with an explanation. We discussed key PFC items driving stream water quality contextualizing the previously modeled riparian buffer zones and ecosystem services tradeoffs in the Back Creek watershed published by U.S. Environmental Protection Agency. Using the remote sensing data in the Geographic Information System, we delineated and characterized 26 Back Creek reaches of 41.1 km length. We also analyzed the 38-year (1981-2018) daily datasets of the precipitation, surface runoff, temperature, soil moisture pattern, and vegetation types for the watershed. Then, we conducted the PFC assessments using field reconnaissance of 10 reaches, 19.3 km of the Back Creek. The field assessments concluded that 52% of the assessed length of Back Creek was in PFC, attributed to diverse vegetation, maintained channel characteristics, floodplain accessibility (where appropriate), and balanced water and sediment loading supplied by individual headwater streams to the Back Creek. 48% of the assessed length was in FAR condition due to land use changes and urban road network. This study provides an exemplar of nonpoint source (diffused pollution generated by land runoff) methodology for identifying key riparian functioning issues and assessing effectiveness of the non-point source best management practice programs.}, } @article {pmid39848196, year = {2025}, author = {Wang, S and Liping, Y and Arif, M}, title = {Evolutionary analysis of ecological-production-living space-carrying capacity in tourism-centric traditional villages in Guangxi, China.}, journal = {Journal of environmental management}, volume = {375}, number = {}, pages = {124182}, doi = {10.1016/j.jenvman.2025.124182}, pmid = {39848196}, issn = {1095-8630}, mesh = {China ; *Tourism ; Humans ; Conservation of Natural Resources ; Geographic Information Systems ; Ecology ; }, abstract = {The carrying capacity of ecological-production-living space (EPLS) is pivotal to the development of traditional villages and the optimization of their tourism industries. However, research on tourism-centric traditional villages in China remains limited. This study addresses this gap by examining EPLS carrying capacity in tourism-focused villages in Guangxi, China. Using remote sensing imagery of Chengyang Bazhai (CYBZ) along with data on local tourism and socio-economic development, the study classifies different types of EPLS and establishes a comprehensive indicator system. Geographic information system spatial analysis, combined with grey correlation analysis, was employed to assess the evolution of EPLS carrying capacity and its influencing factors in CYBZ. The findings indicate that between 2006 and 2015, the overall carrying capacity of EPLS experienced a decline. While the carrying capacity of production spaces remained relatively stable, ecological and living spaces saw notable decreases. However, from 2015 to 2021, EPLS carrying capacity increased substantially. The most substantial growth was observed in Pingyan Village, followed by Chengyang Village, with Pingfu Village exhibiting the smallest improvement. The expansion of the tourism industry has significantly influenced the evolution of EPLS carrying capacity in CYBZ, creating a greater need for strategic future planning. Optimal EPLS and durable tourism development require continuous enhancements in EPLS capacity, reductions in negative interactions between carrying capacity and tourism growth, as well as ecological revitalization. This study contributes to the existing literature by enhancing EPLS carrying capacity understanding. It offers theoretical guidance for its optimization in Chengyang and practical insights into sustainable tourism development in similar regions.}, } @article {pmid39294488, year = {2024}, author = {Zhang, WH and Gao, JW and Lau, CC and Jiang, ZF and Yeong, YS and Mok, WJ and Zhou, W}, title = {Effects of different trophic conditions on total fatty acids, amino acids, pigment and gene expression profiles in Euglena gracilis.}, journal = {World journal of microbiology & biotechnology}, volume = {40}, number = {10}, pages = {325}, pmid = {39294488}, issn = {1573-0972}, support = {22zxbtsn00020//Tianjin Municipal Science and Technology Bureau/ ; }, mesh = {*Euglena gracilis/genetics/growth & development/metabolism/ultrastructure ; *Gene Expression Profiling ; *Amino Acids/metabolism ; *Fatty Acids/metabolism ; *Pigments, Biological/metabolism ; Biomass ; Gene Ontology ; Gene Expression Regulation, Developmental ; Heterotrophic Processes ; }, abstract = {Euglena gracilis is a unique microalga that lacks a cell wall and is able to grow under different trophic culture conditions. In this study, cell growth, biomass production, and changes in the ultrastructure of E. gracilis cells cultivated photoautotrophically, mixotrophically, and under sequential-heterotrophy-photoinduction (SHP) were assessed. Mixotrophy induced the highest cell growth and biomass productivity (6.27 ± 0.59 mg/L/d) in E. gracilis, while the highest content of fatty acids, 2.69 ± 0.04% of dry cell weight (DCW) and amino acids, 38.16 ± 0.08% of DCW was obtained under SHP condition. E. gracilis also accumulated significantly higher saturated fatty acids and lower unsaturated fatty acids when cultivated under SHP condition. Transcriptomic analysis showed that the expression of photosynthetic genes (PsbA, PsbC, F-type ATPase alpha and beta) was lower, carbohydrate and protein synthetic genes (glnA, alg14 and fba) were expressed higher in SHP-culture cells when compared to other groups. Different trophic conditions also induced changes in the cell ultrastructure, where paramylon and starch granules were more abundant in SHP-cultured cells. The findings generated in this study illustrated that aerobic SHP cultivation of E. gracilis possesses great potential in human and animal feed applications.}, } @article {pmid39934908, year = {2025}, author = {Wang, L and Simopoulos, CMA and Serrana, JM and Ning, Z and Li, Y and Sun, B and Yuan, J and Figeys, D and Li, L}, title = {PhyloFunc: phylogeny-informed functional distance as a new ecological metric for metaproteomic data analysis.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {50}, pmid = {39934908}, issn = {2049-2618}, support = {201906015034//China Scholarship Council/ ; TECHNOMISE Program//Natural Sciences and Engineering Research Council of Canada/ ; TECHNOMISE Program//Natural Sciences and Engineering Research Council of Canada/ ; 32370050//National Natural Science Foundation of China/ ; }, abstract = {BACKGROUND: Beta-diversity is a fundamental ecological metric for exploring dissimilarities between microbial communities. On the functional dimension, metaproteomics data can be used to quantify beta-diversity to understand how microbial community functional profiles vary under different environmental conditions. Conventional approaches to metaproteomic functional beta-diversity often treat protein functions as independent features, ignoring the evolutionary relationships among microbial taxa from which different proteins originate. A more informative functional distance metric that incorporates evolutionary relatedness is needed to better understand microbiome functional dissimilarities.

RESULTS: Here, we introduce PhyloFunc, a novel functional beta-diversity metric that incorporates microbiome phylogeny to inform on metaproteomic functional distance. Leveraging the phylogenetic framework of weighted UniFrac distance, PhyloFunc innovatively utilizes branch lengths to weigh between-sample functional distances for each taxon, rather than differences in taxonomic abundance as in weighted UniFrac. Proof of concept using a simulated toy dataset and a real dataset from mouse inoculated with a synthetic gut microbiome and fed different diets show that PhyloFunc successfully captured functional compensatory effects between phylogenetically related taxa. We further tested a third dataset of complex human gut microbiomes treated with five different drugs to compare PhyloFunc's performance with other traditional distance methods. PCoA and machine learning-based classification algorithms revealed higher sensitivity of PhyloFunc in microbiome responses to paracetamol. We provide PhyloFunc as an open-source Python package (available at https://pypi.org/project/phylofunc/), enabling efficient calculation of functional beta-diversity distances between a pair of samples or the generation of a distance matrix for all samples within a dataset.

CONCLUSIONS: Unlike traditional approaches that consider metaproteomics features as independent and unrelated, PhyloFunc acknowledges the role of phylogenetic context in shaping the functional landscape in metaproteomes. In particular, we report that PhyloFunc accounts for the functional compensatory effect of taxonomically related species. Its effectiveness, ecological relevance, and enhanced sensitivity in distinguishing group variations are demonstrated through the specific applications presented in this study. Video Abstract.}, } @article {pmid39931107, year = {2024}, author = {Boyes, D and Murray, C and , and , and , and , and , and , and , }, title = {The genome sequence of the Bird-cherry Ermine moth, Yponomeuta evonymella (Linnaeus, 1758).}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {618}, pmid = {39931107}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual female Yponomeuta evonymella (the Bird-cherry Ermine; Arthropoda; Insecta; Lepidoptera; Yponomeutidae). The genome sequence has a total length of 572.70 megabases. Most of the assembly is scaffolded into 32 chromosomal pseudomolecules, including the trivalent sex chromosomes Z 1, Z 2 and W. The mitochondrial genome has also been assembled and is 16.16 kilobases in length.}, } @article {pmid39899595, year = {2025}, author = {McKenzie-Smith, GC and Wolf, SW and Ayroles, JF and Shaevitz, JW}, title = {Capturing continuous, long timescale behavioral changes in Drosophila melanogaster postural data.}, journal = {PLoS computational biology}, volume = {21}, number = {2}, pages = {e1012753}, doi = {10.1371/journal.pcbi.1012753}, pmid = {39899595}, issn = {1553-7358}, mesh = {Animals ; *Drosophila melanogaster/physiology ; *Behavior, Animal/physiology ; *Locomotion/physiology ; *Circadian Rhythm/physiology ; *Posture/physiology ; Computational Biology ; Deep Learning ; Grooming/physiology ; Female ; Male ; }, abstract = {Animal behavior spans many timescales, from short, seconds-scale actions to daily rhythms over many hours to life-long changes during aging. To access longer timescales of behavior, we continuously recorded individual Drosophila melanogaster at 100 frames per second for up to 7 days at a time in featureless arenas on sucrose-agarose media. We use the deep learning framework SLEAP to produce a full-body postural dataset for 47 individuals resulting in nearly 2 billion pose instances. We identify stereotyped behaviors such as grooming, proboscis extension, and locomotion and use the resulting ethograms to explore how the flies' behavior varies across time of day and days in the experiment. We find distinct daily patterns in all stereotyped behaviors, adding specific information about trends in different grooming modalities, proboscis extension duration, and locomotion speed to what is known about the D. melanogaster circadian cycle. Using our holistic measurements of behavior, we find that the hour after dawn is a unique time point in the flies' daily pattern of behavior, and that the behavioral composition of this hour tracks well with other indicators of health such as locomotion speed and the fraction of time spend moving vs. resting. The method, data, and analysis presented here give us a new and clearer picture of D. melanogaster behavior across timescales, revealing novel features that hint at unexplored underlying biological mechanisms.}, } @article {pmid39793648, year = {2025}, author = {Ji, G and Wang, Y and Lu, Z and Long, G and Xu, C}, title = {Associations between ambient benzene and stroke, and the mediating role of accelerated biological aging: Findings from the UK biobank.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {367}, number = {}, pages = {125656}, doi = {10.1016/j.envpol.2025.125656}, pmid = {39793648}, issn = {1873-6424}, mesh = {*Benzene ; Humans ; United Kingdom ; Male ; *Stroke/epidemiology/chemically induced ; Middle Aged ; Female ; *Environmental Exposure/statistics & numerical data ; *Air Pollutants/analysis ; Aged ; *Aging ; *Biological Specimen Banks ; Adult ; Cohort Studies ; Risk Factors ; UK Biobank ; }, abstract = {Benzene can cause respiratory diseases. However, the associations between benzene and stroke are unclear. A total of 13,116 patients with stroke and 377,120 controls from the UK Biobank were included. The benzene exposure concentrations were matched on the basis of the address information of each participant via a data form from the UK Department for Environment, Food and Rural Affairs. Weighted Cox regression was used to investigate the association between benzene and stroke risk. The polygenic risk score (PRS) was used to observe the joint effects of benzene exposure and genetic factors on stroke risk. We conducted a mediation analysis to investigate the mediating role of accelerated biological aging in this cohort study. After adjusting for covariates, every 1 μg/m[3] increase in benzene exposure increased the risk of stroke by 70%, which may be mediated by accelerated biological aging. The population with high benzene exposure concentrations and high PRSs had a 44% greater risk of stroke than did those with low benzene exposure concentrations and low PRSs. Benzene exposure and the PRS have joint effects on the risk of stroke. Benzene exposure was associated with stroke risk, possibly through increased biological aging, and the PRS modified this association.}, } @article {pmid39929026, year = {2025}, author = {Song, J and Zhou, S and Kwan, MP and Song, G and Long, J and Song, W}, title = {The time-lagged effect of noise exposure on noise annoyance: The role of temporal, spatial and social contexts.}, journal = {Social science & medicine (1982)}, volume = {368}, number = {}, pages = {117817}, doi = {10.1016/j.socscimed.2025.117817}, pmid = {39929026}, issn = {1873-5347}, abstract = {While some research has examined the time-lagged effect of restorative soundscape in specific contexts (e.g., parks), how the time-lagged effect of noise annoyance during people's daily activities may vary across different temporal, spatial, and social contexts remains largely unknown. To address this research gap, we utilized Ecological Momentary Assessment (EMA) data to measure people's real-time noise annoyance and activity diary data to assess their time-lagged noise annoyance. Real-time noise exposure was captured by portable noise sensors. We employed fixed effects ordered panel logistic regression to examine the effects of different thresholds of noise levels on people's time-lagged noise annoyance, and how it varied across different temporal, spatial, and social contexts. The results indicated that: (1) there were significant time-lagged effects between participants' real-time noise exposure and their time-lagged noise annoyance; (2) participants' time-lagged noise annoyance associated with an activity was influenced by its temporal, spatial, and social contexts, particularly on weekdays; (3) participants' time-lagged noise annoyance was significantly associated with measured noise levels, with the highest coefficient for 65 dB, followed by 70 dB; and (4) there were significant interaction effects between noise levels and temporal-spatial-social contexts on participants' time-lagged noise annoyance (particularly when noise levels exceeded 70 dB). These findings enhance our understanding and have crucial implications for the implementation of noise control policies, which should consider not only noise levels but also the time-lagged effects of noise, particularly on weekdays, at outdoor recreational activity sites, as well as the potential vulnerabilities of individuals experiencing noise exposure in isolation.}, } @article {pmid39928107, year = {2025}, author = {Güneri, FD and Karaarslan, F and Özen, H and Odabaşi, E}, title = {Medical mud-pack treatment with different temperatures in patients with knee osteoarthritis.}, journal = {International journal of biometeorology}, volume = {}, number = {}, pages = {}, pmid = {39928107}, issn = {1432-1254}, abstract = {To compare the effects of medical mud-pack (MMP) treatments applied at different temperatures on the pain and joint functions of patients with knee osteoarthritis (KOA). Kellgren Lawrence (KL) stage 3 or 4 KOA patients were included and randomized into three groups. Patients in groups 1, 2, and 3 took MMP treatment to both knees at 39 °C, 42 °C, and 45 °C, respectively. The treatment was performed for 12 days (only weekdays) and was 30 min long per day. The same blinded physician evaluated the patients at baseline and at the end of the treatment. The assessments were done before and after the intervention. The primary outcome was to achieve a minimal clinically important improvement (MCII) for KOA (decrease of at least 19 mm (-40.8%) on the VAS for pain, a decrease of 18.3 mm (-39%) on the patient's global assessment (PGA), and/or a decrease of at least 9.1 points (-26%) on the Western Ontario and McMaster Universities Osteoarthritis Index function subscale (WOMAC-FS). Secondary outcomes were pain (VAS), patient's global assessment (VAS), physician's global assessment (VAS), Western Ontario and McMaster Universities Osteoarthritis Index (WOMAC), Patient's health state, Patient Acceptable Symptom State (PASS). 217 patients were analyzed. Groups 1, 2, and 3 had 68, 81,68 patients, respectively. The MCII measurement revealed that MMP treatment did not show a significant difference between groups 2 and 3 (p > 0.05). Also, it was observed that more patients in groups 2 and 3 reached the MCII compared to group 1 (p < 0.001). For the secondary outcomes, significant improvements were observed within-group evaluations for each of the three groups (p < 0.001). Between groups comparisons, the improvements at the end of the treatment were found to be superior for group 2 and group 3 compared to group 1 (p < 0.001). There was no statistically significant difference between groups 2 and 3 for any parameters (p > 0.05). The number of patients who achieved the PASS was statistically lower for group 1 compared to groups 2 and 3 (p < 0.001). We observed significant improvements in all groups after treatment. The main result, as measured by MCII, suggests that MMP treatments at 42-45 °C is more effective than at 39 °C in managing severe KOA patients' pain and functional status. We found no significant difference in pain and joint function improvement between 42 °C and 45 °C after MMP.}, } @article {pmid39899643, year = {2025}, author = {Hozé, N and Pons-Salort, M and Metcalf, CJE and White, M and Salje, H and Cauchemez, S}, title = {RSero: A user-friendly R package to reconstruct pathogen circulation history from seroprevalence studies.}, journal = {PLoS computational biology}, volume = {21}, number = {2}, pages = {e1012777}, doi = {10.1371/journal.pcbi.1012777}, pmid = {39899643}, issn = {1553-7358}, mesh = {Seroepidemiologic Studies ; Humans ; *Software ; *Bayes Theorem ; Computational Biology/methods ; Computer Simulation ; Disease Outbreaks/statistics & numerical data ; Communicable Diseases/epidemiology/transmission ; }, abstract = {Population-based serological surveys are a key tool in epidemiology to characterize the level of population immunity and reconstruct the past circulation of pathogens. A variety of serocatalytic models have been developed to estimate the force of infection (FOI) (i.e., the rate at which susceptible individuals become infected) from age-stratified seroprevalence data. However, few tool currently exists to easily implement, combine, and compare these models. Here, we introduce an R package, Rsero, that implements a series of serocatalytic models and estimates the FOI from age-stratified seroprevalence data using Bayesian methods. The package also contains a series of features to perform model comparison and visualise model fit. We introduce new serocatalytic models of successive outbreaks and extend existing models of seroreversion to any transmission model. The different features of the package are illustrated with simulated and real-life data. We show we can identify the correct epidemiological scenario and recover model parameters in different epidemiological settings. We also show how the package can support serosurvey study design in a variety of epidemic situations. This package provides a standard framework to epidemiologists and modellers to study the dynamics of past pathogen circulation from cross-sectional serological survey data.}, } @article {pmid38866716, year = {2024}, author = {Brock, MT and Morrison, HG and Maignien, L and Weinig, C}, title = {Impacts of sample handling and storage conditions on archiving physiologically active soil microbial communities.}, journal = {FEMS microbiology letters}, volume = {371}, number = {}, pages = {}, doi = {10.1093/femsle/fnae044}, pmid = {38866716}, issn = {1574-6968}, support = {IOS-1444571//NSF/ ; }, mesh = {*Specimen Handling ; *Soil Microbiology ; *Microbiota ; *Preservation, Biological ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, RNA ; Data Curation ; Phylogeny ; Biodiversity ; Principal Component Analysis ; }, abstract = {Soil microbial communities are fundamental to ecosystem processes and plant growth, yet community composition is seasonally and successionally dynamic, which interferes with long-term iterative experimentation of plant-microbe interactions. We explore how soil sample handling (e.g. filtering) and sample storage conditions impact the ability to revive the original, physiologically active, soil microbial community. We obtained soil from agricultural fields in Montana and Oklahoma, USA and samples were sieved to 2 mm or filtered to 45 µm. Sieved and filtered soil samples were archived at -20°C or -80°C for 50 days and revived for 2 or 7 days. We extracted DNA and the more transient RNA pools from control and treatment samples and characterized microbial communities using 16S amplicon sequencing. Filtration and storage treatments significantly altered soil microbial communities, impacting both species richness and community composition. Storing sieved soil at -20°C did not alter species richness and resulted in the least disruption to the microbial community composition in comparison to nonarchived controls as characterized by RNA pools from soils of both sites. Filtration significantly altered composition but not species richness. Archiving sieved soil at -20°C could allow for long-term and repeated experimentation on preserved physiologically active microbial communities.}, } @article {pmid39923474, year = {2025}, author = {Lucca, E and Kofinas, D and Avellán, T and Kleemann, J and Mooren, CE and Blicharska, M and Teutschbein, C and Sperotto, A and Sušnik, J and Milliken, S and Fader, M and Đorđević, D and Dašić, T and Vasilić, V and Taiwo, B and Baubekova, A and Pineda-Martos, R and Spyropoulou, A and Baganz, GFM and El Jeitany, J and Oral, HV and Merheb, M and Castelli, G and Pagano, A and Sambo, B and Suškevičs, M and Arnold, M and Rađenović, T and Psomas, A and Masia, S and La Jeunesse, I and Amorocho-Daza, H and Das, SS and Bresci, E and Munaretto, S and Brouwer, F and Laspidou, C}, title = {Integrating "nature" in the water-energy-food Nexus: Current perspectives and future directions.}, journal = {The Science of the total environment}, volume = {966}, number = {}, pages = {178600}, doi = {10.1016/j.scitotenv.2025.178600}, pmid = {39923474}, issn = {1879-1026}, abstract = {Integrated approaches for managing natural resources are said to meet increasing demand for water, energy, and food, while maintaining the integrity of ecosystems, and ensuring equitable access to resources. The Water-Energy-Food (WEF) Nexus has been proposed as a cross-sectoral approach to manage trade-offs and exploit synergies that arise among these sectors. Although not initially included as a component of the Nexus, the role of nature in sustaining the water, energy, and food sectors and in regulating their interrelationships is increasingly recognised by Nexus researchers and practitioners. To converge existing approaches that integrate nature into the WEF Nexus and suggest a common framework, we - an interdisciplinary group of natural resources management researchers and systems thinkers from the European research network NEXUSNET COST Action - followed a collaborative process of knowledge creation combining literature review, elicitation of expert opinion and collaborative writing. Our results reveal a multiplicity of concepts utilised in the literature to represent, partially or fully, "nature" in the Nexus, such as "environment", "ecosystems", "ecosystem services", "social-ecological systems", and "biodiversity". Disparity was also found in the role attributed to nature, represented by three key paradigms: (1) ecosystems as the fourth component of an expanded Nexus, i.e., the WEF-Ecosystems (WEFE) Nexus; (2) ecosystems as a foundational layer to the Nexus; and (3) the WEF Nexus as a central component of social-ecological systems (SES). By creating a hybrid approach that brings together the benefits of the respective paradigms, we present a forward-looking WEFE Nexus conceptualisation. This paradigm expands the mutual interlinkages among water, energy and food to the entirety of SES, thus acknowledging the social-ecological processes that are affected by and affect the WEF Nexus. The results of this collaborative research effort intend to provide researchers and stakeholders with means to better understand and ultimately manage Nexus issues towards a transformative change.}, } @article {pmid39923291, year = {2025}, author = {de Melo, LRS and Dos Santos Pereira, J and Melo, MS and Andrade, LA and Bezerra-Santos, M and Lima, CA and Dos Santos, AD}, title = {Spatial and temporal dynamic of colorectal cancer mortality in Brazil: A nationwide population-based study of four decades (1980-2021).}, journal = {Cancer epidemiology}, volume = {95}, number = {}, pages = {102766}, doi = {10.1016/j.canep.2025.102766}, pmid = {39923291}, issn = {1877-783X}, abstract = {BACKGROUND: Regardless of being preventable through screening strategies and prompt diagnosis, deaths from colorectal cancer (CRC) still represent a serious public health concern in Brazil, with more than 20 thousand deaths annually. Herein, we aimed to assess the temporal trends and spatiotemporal patterns of CRC mortality in all Brazilian states.

METHODS: An ecological study using temporal and spatial analysis techniques on deaths due to CRC as the underlying cause in Brazil from 1980 to 2021 was conducted. Death certificate and population data were provided by the Department of Informatics of the Unified Health System (DATASUS) and by the Brazilian Institute of Geography and Statistics (IBGE), respectively.

RESULTS: A total of 395,782 deaths from CRC were recorded in this period and most of them were in female (205,479; 51.92 %), ≥ 65 years old (233,059; 58.89 %), diagnosed with malignant neoplasm of the colon (212,277; 53.63 %), with 1-7 years of education (157.564; 39.81 %), married (192.276; 48.58 %), hospital as place of death (331.393; 83.73 %) and white (212.666; 65.07 %). Moreover, there was an increasing temporal trend in the Northeast region (APC: 2.6; p < 0.05), men (APC: 1.5; p < 0.05) and 45-64 years old (APC: 1.2; p < 0.05). Also, the spatial analysis showed positive spatial autocorrelation in all periods, with the South and Southeast regions presenting the highest concentration of high-risk clusters CRC deaths. Nevertheless, high-risk clusters were also observed in capitals and municipalities in metropolitan regions in the Northeast region.

CONCLUSIONS: In general, a temporal and spatial expansion of CRC mortality has been observed in Brazil over the last few decades.}, } @article {pmid39921816, year = {2025}, author = {Asuako, PAG and Stojan, R and Bock, O and Mack, M and Voelcker-Rehage, C}, title = {Multitasking: does task-switching add to the effect of dual-tasking on everyday-like driving behavior?.}, journal = {Cognitive research: principles and implications}, volume = {10}, number = {1}, pages = {5}, pmid = {39921816}, issn = {2365-7464}, support = {SPP 1772//Deutsche Forschungsgemeinschaft/ ; }, mesh = {Humans ; Female ; Young Adult ; Male ; Adult ; *Automobile Driving ; Adolescent ; *Psychomotor Performance/physiology ; *Multitasking Behavior/physiology ; *Executive Function/physiology ; Reaction Time/physiology ; Attention/physiology ; }, abstract = {It is well established that performing multiple tasks simultaneously (dual-tasking) or sequentially (task-switching) degrades performance on one or both tasks. However, it is unknown whether task-switching adds to the effects of dual-tasking in a single setup. We investigated this in a simulated everyday-like car driving scenario. We expected an additive effect of task-switching on dual-tasking, leading to a stronger deterioration of driving performance due to the increased cognitive load required to handle multiple task-sets. Forty-five young adults aged 18 to 30 years (age: 23.62 ± 2.51, 28 females) were instructed to follow a lead car driving at a constant speed of 70 km/h through a rural landscape while concurrently performing additional tasks. The additional tasks were typing and arguing, in response to stimuli presented visually or auditorily. The tasks were presented either in separate blocks or in intermixed order (conditions: repetitive vs. switching). Driving performance was assessed by use of the average velocity and the standard deviation of lateral position, and performance in the additional tasks was assessed by reaction time. Linear-mixed effect models revealed better performance in the repetitive, compared to the switch condition only for the standard deviation of the lateral lane position while performing the additional typing task. This provides limited evidence for the view that task-switching adds to the challenges of dual-tasking. We therefore posit that already dual-tasking alone involves processing demands that are not substantially increased by adding switching demands.}, } @article {pmid39615103, year = {2025}, author = {Sha, J and Liu, X and Wang, H and Song, X and Bao, M and Yu, Q and Wen, G and Wei, M}, title = {Status and habitat suitability evaluation: A case study of the typical temperate seagrass beds in the Bohai Sea, China.}, journal = {Marine environmental research}, volume = {204}, number = {}, pages = {106873}, doi = {10.1016/j.marenvres.2024.106873}, pmid = {39615103}, issn = {1879-0291}, mesh = {*Ecosystem ; China ; *Environmental Monitoring/methods ; *Conservation of Natural Resources ; Oceans and Seas ; Geographic Information Systems ; }, abstract = {Seagrass beds serve crucial ecological functions, yet they are facing a severe decline necessitating immediate conservation and restoration efforts. Current assessments of seagrass habitat suitability are insufficient, thus hindering the restoration effects. This study used a combination of field surveys and satellite remote sensing to conduct a three-year monitoring of typical temperate seagrass beds in the Caofeidian and Xingcheng areas of the Bohai Sea. The relationships between seagrass community factors and environmental factors were investigated using Spearman correlation analysis, BIOENV analysis, and redundancy analysis (RDA). Subsequently, the weights of each environmental factor were determined using the Analytic Hierarchy Process (AHP), leading to the development of the Habitat Suitability Index (HSI). Seagrass habitat suitability maps for Caofeidian and Xingcheng areas were then generated using Geographic Information System (GIS). The results indicate that both seagrass ecosystems degraded during the study period, which coincided with a decreasing trend in habitat suitability shown by the suitability maps. This study provides a methodology for seagrass bed habitat suitability assessment, thereby contributing to the conservation and restoration of these vital ecosystems.}, } @article {pmid39917311, year = {2025}, author = {Lysholm, S and Chaters, GL and Di Bari, C and Hughes, EC and Huntington, B and Rushton, J and Thomas, L}, title = {A framework for quantifying the multisectoral burden of animal disease to support decision making.}, journal = {Frontiers in veterinary science}, volume = {12}, number = {}, pages = {1476505}, pmid = {39917311}, issn = {2297-1769}, abstract = {Animal diseases have wide-ranging impacts in multiple societal arenas, including agriculture, public health and the environment. These diseases cause significant economic losses for farmers, disrupt food security and present zoonotic risks to human populations. Additionally, they contribute to antimicrobial resistance and a range of environmental issues such as greenhouse gas emissions. The societal and ecological costs of livestock diseases are frequently underrepresented or unaddressed in policy decisions and resource allocations. Social cost-benefit analysis (SCBA) offers a comprehensive framework to evaluate the broad impacts of animal diseases across different sectors. This approach aligns with the One Health concept, which seeks to integrate and optimize the health of humans, animals and the environment. Traditional economic evaluations often focus narrowly on profit maximization within the livestock sector, neglecting wider externalities such as public health and environmental impacts. In contrast, SCBA takes a multi-sectoral whole-system view, considering multiple factors to guide public and private sector investments toward maximizing societal benefits. This paper discusses three separate sector specific (Animal health, Human health, Environmental health) methodologies for quantifying the burden of animal diseases. It then discusses how these estimates can be combined to generate multisectoral estimates of the impacts of animal diseases on human societies and the environment using monetary values. Finally this paper explores how this framework can support the evaluation of interventions from a One Health perspective though SCBA. This integrated assessment framework supports informed decision-making and resource allocation, ultimately contributing to improved public health outcomes, enhanced animal welfare, and greater environmental sustainability.}, } @article {pmid39567690, year = {2025}, author = {Borton, MA and McGivern, BB and Willi, KR and Woodcroft, BJ and Mosier, AC and Singleton, DM and Bambakidis, T and Pelly, A and Daly, RA and Liu, F and Freiburger, A and Edirisinghe, JN and Faria, JP and Danczak, R and Leleiwi, I and Goldman, AE and Wilkins, MJ and Hall, EK and Pennacchio, C and Roux, S and Eloe-Fadrosh, EA and Good, SP and Sullivan, MB and Wood-Charlson, EM and Miller, CS and Ross, MRV and Henry, CS and Crump, BC and Stegen, JC and Wrighton, KC}, title = {A functional microbiome catalogue crowdsourced from North American rivers.}, journal = {Nature}, volume = {637}, number = {8044}, pages = {103-112}, pmid = {39567690}, issn = {1476-4687}, support = {P30 CA046934/CA/NCI NIH HHS/United States ; }, mesh = {*Crowdsourcing ; *Microbiota/genetics ; *Rivers/microbiology ; United States ; Water Microbiology ; Transcriptome ; Carbon Cycle ; Metagenome ; Databases, Factual ; }, abstract = {Predicting elemental cycles and maintaining water quality under increasing anthropogenic influence requires knowledge of the spatial drivers of river microbiomes. However, understanding of the core microbial processes governing river biogeochemistry is hindered by a lack of genome-resolved functional insights and sampling across multiple rivers. Here we used a community science effort to accelerate the sampling, sequencing and genome-resolved analyses of river microbiomes to create the Genome Resolved Open Watersheds database (GROWdb). GROWdb profiles the identity, distribution, function and expression of microbial genomes across river surface waters covering 90% of United States watersheds. Specifically, GROWdb encompasses microbial lineages from 27 phyla, including novel members from 10 families and 128 genera, and defines the core river microbiome at the genome level. GROWdb analyses coupled to extensive geospatial information reveals local and regional drivers of microbial community structuring, while also presenting foundational hypotheses about ecosystem function. Building on the previously conceived River Continuum Concept[1], we layer on microbial functional trait expression, which suggests that the structure and function of river microbiomes is predictable. We make GROWdb available through various collaborative cyberinfrastructures[2,3], so that it can be widely accessed across disciplines for watershed predictive modelling and microbiome-based management practices.}, } @article {pmid39915771, year = {2025}, author = {Gould, E and Fraser, HS and Parker, TH and Nakagawa, S and Griffith, SC and Vesk, PA and Fidler, F and Hamilton, DG and Abbey-Lee, RN and Abbott, JK and Aguirre, LA and Alcaraz, C and Aloni, I and Altschul, D and Arekar, K and Atkins, JW and Atkinson, J and Baker, CM and Barrett, M and Bell, K and Bello, SK and Beltrán, I and Berauer, BJ and Bertram, MG and Billman, PD and Blake, CK and Blake, S and Bliard, L and Bonisoli-Alquati, A and Bonnet, T and Bordes, CNM and Bose, APH and Botterill-James, T and Boyd, MA and Boyle, SA and Bradfer-Lawrence, T and Bradham, J and Brand, JA and Brengdahl, MI and Bulla, M and Bussière, L and Camerlenghi, E and Campbell, SE and Campos, LLF and Caravaggi, A and Cardoso, P and Carroll, CJW and Catanach, TA and Chen, X and Chik, HYJ and Choy, ES and Christie, AP and Chuang, A and Chunco, AJ and Clark, BL and Contina, A and Covernton, GA and Cox, MP and Cressman, KA and Crotti, M and Crouch, CD and D'Amelio, PB and de Sousa, AA and Döbert, TF and Dobler, R and Dobson, AJ and Doherty, TS and Drobniak, SM and Duffy, AG and Duncan, AB and Dunn, RP and Dunning, J and Dutta, T and Eberhart-Hertel, L and Elmore, JA and Elsherif, MM and English, HM and Ensminger, DC and Ernst, UR and Ferguson, SM and Fernandez-Juricic, E and Ferreira-Arruda, T and Fieberg, J and Finch, EA and Fiorenza, EA and Fisher, DN and Fontaine, A and Forstmeier, W and Fourcade, Y and Frank, GS and Freund, CA and Fuentes-Lillo, E and Gandy, SL and Gannon, DG and García-Cervigón, AI and Garretson, AC and Ge, X and Geary, WL and Géron, C and Gilles, M and Girndt, A and Gliksman, D and Goldspiel, HB and Gomes, DGE and Good, MK and Goslee, SC and Gosnell, JS and Grames, EM and Gratton, P and Grebe, NM and Greenler, SM and Griffioen, M and Griffith, DM and Griffith, FJ and Grossman, JJ and Güncan, A and Haesen, S and Hagan, JG and Hager, HA and Harris, JP and Harrison, ND and Hasnain, SS and Havird, JC and Heaton, AJ and Herrera-Chaustre, ML and Howard, TJ and Hsu, BY and Iannarilli, F and Iranzo, EC and Iverson, ENK and Jimoh, SO and Johnson, DH and Johnsson, M and Jorna, J and Jucker, T and Jung, M and Kačergytė, I and Kaltz, O and Ke, A and Kelly, CD and Keogan, K and Keppeler, FW and Killion, AK and Kim, D and Kochan, DP and Korsten, P and Kothari, S and Kuppler, J and Kusch, JM and Lagisz, M and Lalla, KM and Larkin, DJ and Larson, CL and Lauck, KS and Lauterbur, ME and Law, A and Léandri-Breton, DJ and Lembrechts, JJ and L'Herpiniere, K and Lievens, EJP and de Lima, DO and Lindsay, S and Luquet, M and MacLeod, R and Macphie, KH and Magellan, K and Mair, MM and Malm, LE and Mammola, S and Mandeville, CP and Manhart, M and Manrique-Garzon, LM and Mäntylä, E and Marchand, P and Marshall, BM and Martin, CA and Martin, DA and Martin, JM and Martinig, AR and McCallum, ES and McCauley, M and McNew, SM and Meiners, SJ and Merkling, T and Michelangeli, M and Moiron, M and Moreira, B and Mortensen, J and Mos, B and Muraina, TO and Murphy, PW and Nelli, L and Niemelä, P and Nightingale, J and Nilsonne, G and Nolazco, S and Nooten, SS and Novotny, JL and Olin, AB and Organ, CL and Ostevik, KL and Palacio, FX and Paquet, M and Parker, DJ and Pascall, DJ and Pasquarella, VJ and Paterson, JH and Payo-Payo, A and Pedersen, KM and Perez, G and Perry, KI and Pottier, P and Proulx, MJ and Proulx, R and Pruett, JL and Ramananjato, V and Randimbiarison, FT and Razafindratsima, OH and Rennison, DJ and Riva, F and Riyahi, S and Roast, MJ and Rocha, FP and Roche, DG and Román-Palacios, C and Rosenberg, MS and Ross, J and Rowland, FE and Rugemalila, D and Russell, AL and Ruuskanen, S and Saccone, P and Sadeh, A and Salazar, SM and Sales, K and Salmón, P and Sánchez-Tójar, A and Santos, LP and Santostefano, F and Schilling, HT and Schmidt, M and Schmoll, T and Schneider, AC and Schrock, AE and Schroeder, J and Schtickzelle, N and Schultz, NL and Scott, DA and Scroggie, MP and Shapiro, JT and Sharma, N and Shearer, CL and Simón, D and Sitvarin, MI and Skupien, FL and Slinn, HL and Smith, GP and Smith, JA and Sollmann, R and Whitney, KS and Still, SM and Stuber, EF and Sutton, GF and Swallow, B and Taff, CC and Takola, E and Tanentzap, AJ and Tarjuelo, R and Telford, RJ and Thawley, CJ and Thierry, H and Thomson, J and Tidau, S and Tompkins, EM and Tortorelli, CM and Trlica, A and Turnell, BR and Urban, L and Van de Vondel, S and van der Wal, JEM and Van Eeckhoven, J and van Oordt, F and Vanderwel, KM and Vanderwel, MC and Vanderwolf, KJ and Vélez, J and Vergara-Florez, DC and Verrelli, BC and Vieira, MV and Villamil, N and Vitali, V and Vollering, J and Walker, J and Walker, XJ and Walter, JA and Waryszak, P and Weaver, RJ and Wedegärtner, REM and Weller, DL and Whelan, S and White, RL and Wolfson, DW and Wood, A and Yanco, SW and Yen, JDL and Youngflesh, C and Zilio, G and Zimmer, C and Zimmerman, GM and Zitomer, RA}, title = {Same data, different analysts: variation in effect sizes due to analytical decisions in ecology and evolutionary biology.}, journal = {BMC biology}, volume = {23}, number = {1}, pages = {35}, pmid = {39915771}, issn = {1741-7007}, abstract = {Although variation in effect sizes and predicted values among studies of similar phenomena is inevitable, such variation far exceeds what might be produced by sampling error alone. One possible explanation for variation among results is differences among researchers in the decisions they make regarding statistical analyses. A growing array of studies has explored this analytical variability in different fields and has found substantial variability among results despite analysts having the same data and research question. Many of these studies have been in the social sciences, but one small "many analyst" study found similar variability in ecology. We expanded the scope of this prior work by implementing a large-scale empirical exploration of the variation in effect sizes and model predictions generated by the analytical decisions of different researchers in ecology and evolutionary biology. We used two unpublished datasets, one from evolutionary ecology (blue tit, Cyanistes caeruleus, to compare sibling number and nestling growth) and one from conservation ecology (Eucalyptus, to compare grass cover and tree seedling recruitment). The project leaders recruited 174 analyst teams, comprising 246 analysts, to investigate the answers to prespecified research questions. Analyses conducted by these teams yielded 141 usable effects (compatible with our meta-analyses and with all necessary information provided) for the blue tit dataset, and 85 usable effects for the Eucalyptus dataset. We found substantial heterogeneity among results for both datasets, although the patterns of variation differed between them. For the blue tit analyses, the average effect was convincingly negative, with less growth for nestlings living with more siblings, but there was near continuous variation in effect size from large negative effects to effects near zero, and even effects crossing the traditional threshold of statistical significance in the opposite direction. In contrast, the average relationship between grass cover and Eucalyptus seedling number was only slightly negative and not convincingly different from zero, and most effects ranged from weakly negative to weakly positive, with about a third of effects crossing the traditional threshold of significance in one direction or the other. However, there were also several striking outliers in the Eucalyptus dataset, with effects far from zero. For both datasets, we found substantial variation in the variable selection and random effects structures among analyses, as well as in the ratings of the analytical methods by peer reviewers, but we found no strong relationship between any of these and deviation from the meta-analytic mean. In other words, analyses with results that were far from the mean were no more or less likely to have dissimilar variable sets, use random effects in their models, or receive poor peer reviews than those analyses that found results that were close to the mean. The existence of substantial variability among analysis outcomes raises important questions about how ecologists and evolutionary biologists should interpret published results, and how they should conduct analyses in the future.}, } @article {pmid39910401, year = {2025}, author = {Fatima, M and Butt, I and MohammadEbrahimi, S and Kiani, B and Gruebner, O}, title = {Spatiotemporal clusters of acute respiratory infections associated with socioeconomic, meteorological, and air pollution factors in South Punjab, Pakistan.}, journal = {BMC public health}, volume = {25}, number = {1}, pages = {469}, pmid = {39910401}, issn = {1471-2458}, abstract = {BACKGROUND: In Pakistan, acute respiratory infections (ARI) continue to be a major public health problem. However, there is still a lack of scholarly work regarding different environmental and socioeconomic influencing factors and how they interact with respiratory infections. Furthermore, we do not know much about geographic variation in this context. Therefore, our study examines the ecological-level spatial and temporal patterns of acute respiratory infection incidence (ARI) and their geographic relationship with selected socio-economic, meteorological, and air pollution factors in Pakistan.

METHODS: We applied the spatiotemporal scan statistics to examine the purely temporal, spatial, and spatiotemporal clusters of ARI in South Punjab, Pakistan for five years (2016-2020). Generalized Linear Model (GLM) and geographically weighted regression (GWR) were also applied to model the linear and non-linear spatial relationships between selected variables and ARI.

RESULTS: Our results indicate that in the central and northern regions of Pakistan, two spatial clusters of ARI were present, accounting for 28.5% of the total cases. A spatiotemporal cluster with a relative risk of 1.57 was discovered in the northeastern area. The results obtained from the season-based GLM highlighted the significance of climatic factors (temperature, fog, dust storms) and air pollutants (NO2) in influencing ARI incidence, while socio-economic variables (rural population, literacy) had limited impact. In addition, GWR revealed that the relationships between predictors and ARI incidence varied across locations, emphasizing the importance of considering local settings. Season-based non-stationary GLM revealed a multifaceted interaction among socio-economic, meteorological, and air pollution factors.

CONCLUSIONS: Our study provides evidence about environmental and socio-economic factors significantly associated with ARI incidence. In addition, this study provides the first baseline of ARI cases in Pakistan to plan for intervention and adaptation strategies and may be replicated in other regions of comparable settings worldwide.}, } @article {pmid39907430, year = {2025}, author = {Hebert, JD and Tang, YJ and Szamecz, M and Andrejka, L and Lopez, SS and Petrov, DA and Boross, G and Winslow, MM}, title = {Combinatorial in vivo genome editing identifies widespread epistasis and an accessible fitness landscape during lung tumorigenesis.}, journal = {Molecular biology and evolution}, volume = {}, number = {}, pages = {}, doi = {10.1093/molbev/msaf023}, pmid = {39907430}, issn = {1537-1719}, abstract = {Lung adenocarcinoma, the most common subtype of lung cancer, is genomically complex, with tumors containing tens to hundreds of non-synonymous mutations. However, little is understood about how genes interact with each other to enable the evolution of cancer in vivo, largely due to a lack of methods for investigating genetic interactions in a high-throughput and quantitative manner. Here, we employed a novel platform to generate tumors with inactivation of pairs of ten diverse tumor suppressor genes within an autochthonous mouse model of oncogenic KRAS-driven lung cancer. By quantifying the fitness of tumors with every single and double mutant genotype, we show that most tumor suppressor genetic interactions exhibited negative epistasis, with diminishing returns on tumor fitness. In contrast, Apc inactivation showed positive epistasis with the inactivation of several other genes, including synergistic effects on tumor fitness in combination with Lkb1 or Nf1 inactivation. Sign epistasis was extremely rare, suggesting a surprisingly accessible fitness landscape during lung tumorigenesis. These findings expand our understanding of the evolutionary interactions that drive tumorigenesis in vivo.}, } @article {pmid39906497, year = {2025}, author = {Palande, S and Arsenault, J and Basurto-Lozada, P and Bleich, A and Brown, BNI and Buysse, SF and Connors, NA and Das Adhikari, S and Dobson, KC and Guerra-Castillo, FX and Guerrero-Carrillo, MF and Harlow, S and Herrera-Orozco, H and Hightower, AT and Izquierdo, P and Jacobs, M and Johnson, NA and Leuenberger, W and Lopez-Hernandez, A and Luckie-Duque, A and Martínez-Avila, C and Mendoza-Galindo, EJ and Plancarte, DC and Schuster, JM and Shomer, H and Sitar, SC and Steensma, AK and Thomson, JE and Villaseñor-Amador, D and Waterman, R and Webster, BM and Whyte, M and Zorilla-Azcué, S and Montgomery, BL and Husbands, AY and Krishnan, A and Percival, S and Munch, E and VanBuren, R and Chitwood, DH and Rougon-Cardoso, A}, title = {Expression-based machine learning models for predicting plant tissue identity.}, journal = {Applications in plant sciences}, volume = {13}, number = {1}, pages = {e11621}, pmid = {39906497}, issn = {2168-0450}, abstract = {PREMISE: The selection of Arabidopsis as a model organism played a pivotal role in advancing genomic science. The competing frameworks to select an agricultural- or ecological-based model species were rejected, in favor of building knowledge in a species that would facilitate genome-enabled research.

METHODS: Here, we examine the ability of models based on Arabidopsis gene expression data to predict tissue identity in other flowering plants. Comparing different machine learning algorithms, models trained and tested on Arabidopsis data achieved near perfect precision and recall values, whereas when tissue identity is predicted across the flowering plants using models trained on Arabidopsis data, precision values range from 0.69 to 0.74 and recall from 0.54 to 0.64.

RESULTS: The identity of belowground tissue can be predicted more accurately than other tissue types, and the ability to predict tissue identity is not correlated with phylogenetic distance from Arabidopsis. k-nearest neighbors is the most successful algorithm, suggesting that gene expression signatures, rather than marker genes, are more valuable to create models for tissue and cell type prediction in plants.

DISCUSSION: Our data-driven results highlight that the assertion that knowledge from Arabidopsis is translatable to other plants is not always true. Considering the current landscape of abundant sequencing data, we should reevaluate the scientific emphasis on Arabidopsis and prioritize plant diversity.}, } @article {pmid39611775, year = {2025}, author = {Andorf, CM and Ross-Ibarra, J and Seetharam, AS and Hufford, MB and Woodhouse, MR}, title = {A unified VCF dataset from nearly 1,500 diverse maize accessions and resources to explore the genomic landscape of maize.}, journal = {G3 (Bethesda, Md.)}, volume = {15}, number = {2}, pages = {}, doi = {10.1093/g3journal/jkae281}, pmid = {39611775}, issn = {2160-1836}, support = {5030-21000-072-00-D//US. Department of Agriculture, Agricultural Research Service/ ; //Corn Insects and Crop Genetics Research Unit in Ames, Iowa/ ; //Iowa State University/ ; //SCINet/ ; 0201-88888-003-000D//AI Center of Excellence of the USDA Agricultural Research Service/ ; CA-D-PLS-2066-H//USDA/ ; }, mesh = {*Zea mays/genetics ; *Genome, Plant ; *Polymorphism, Single Nucleotide ; *Genomics/methods ; *Databases, Genetic ; Software ; Molecular Sequence Annotation ; Linkage Disequilibrium ; Genotype ; Genetic Variation ; }, abstract = {Efforts to capture and analyze maize nucleotide diversity have ranged widely in scope, but differences in reference genome version and software algorithms used in these efforts inhibit comparison, and these data are generally not available in an easy-to-use visualization platform for quick access and analysis. To address these issues, The Maize Genetics and Genomics Database has collaborated with maize researchers to offer variant data from a diverse set of 1,498 inbred lines, traditional varieties, and teosintes through a standardized variant-calling pipeline against version 5 of the B73 reference genome. The output was filtered for mapping quality, completeness, and linkage disequilibrium, and annotated based on variant effects relative to the B73 RefGen_v5 gene annotations. MaizeGDB has also updated a web tool, SNPversity 2.0, to filter, visualize, and download genotype sets based on genomic locations and accessions of interest, and added external datasets to demonstrate SNPversity 2.0's broad usage. MaizeGDB plans to host annual updates of these resources as additional resequencing data become available, with plans to expand to all publicly available sequence data.}, } @article {pmid39904391, year = {2025}, author = {Mihaljevic, JR and Páez, DJ}, title = {Systematic shifts in the variation among host individuals must be considered in climate-disease theory.}, journal = {Proceedings. Biological sciences}, volume = {292}, number = {2040}, pages = {20242515}, doi = {10.1098/rspb.2024.2515}, pmid = {39904391}, issn = {1471-2954}, support = {//Exxon Valdez Oil Spill Trustee Council/ ; //Division of Environmental Biology/ ; }, mesh = {*Climate Change ; Animals ; *Host-Pathogen Interactions ; Temperature ; Population Dynamics ; Models, Biological ; Disease Susceptibility ; }, abstract = {To make more informed predictions of host-pathogen interactions under climate change, studies have incorporated the thermal performance of host, vector and pathogen traits into disease models to quantify effects on average transmission rates. However, this body of work has omitted the fact that variation in susceptibility among individual hosts affects disease spread and long-term patterns of host population dynamics. Furthermore, and especially for ectothermic host species, variation in susceptibility is likely to be plastic, influenced by variables such as environmental temperature. For example, as host individuals respond idiosyncratically to temperature, this could affect the population-level variation in susceptibility, such that there may be predictable functional relationships between variation in susceptibility and temperature. Quantifying the relationship between temperature and among-host trait variation will therefore be critical for predicting how climate change and disease will interact to influence host-pathogen population dynamics. Here, we use a model to demonstrate how short-term effects of temperature on the distribution of host susceptibility can drive epidemic characteristics, fluctuations in host population sizes and probabilities of host extinction. Our results emphasize that more research is needed in disease ecology and climate biology to understand the mechanisms that shape individual trait variation, not just trait averages.}, } @article {pmid39903560, year = {2025}, author = {Thomas, GWC and Hughes, JJ and Kumon, T and Berv, JS and Nordgren, CE and Lampson, M and Levine, M and Searle, JB and Good, JM}, title = {The genomic landscape, causes, and consequences of extensive phylogenomic discordance in murine rodents.}, journal = {Genome biology and evolution}, volume = {}, number = {}, pages = {}, doi = {10.1093/gbe/evaf017}, pmid = {39903560}, issn = {1759-6653}, abstract = {A species tree is a central concept in evolutionary biology whereby a single branching phylogeny reflects relationships among species. However, the phylogenies of different genomic regions often differ from the species tree. Although tree discordance is widespread in phylogenomic studies, we still lack a clear understanding of how variation in phylogenetic patterns is shaped by genome biology or the extent to which discordance may compromise comparative studies. We characterized patterns of phylogenomic discordance across the murine rodents - a large and ecologically diverse group that gave rise to the laboratory mouse and rat model systems. Combining recently published linked-read genome assemblies for seven murine species with other available rodent genomes, we first used ultra-conserved elements (UCEs) to infer a robust time-calibrated species tree. We then used whole genomes to examine finer-scale patterns of discordance across ∼12 million years of divergence. We found that proximate chromosomal regions tended to have more similar phylogenetic histories. There was no clear relationship between local tree similarity and recombination rates in house mice, but we did observe a correlation between recombination rates and average similarity to the species tree. We also detected a strong influence of linked selection whereby purifying selection at UCEs led to appreciably less discordance. Finally, we show that assuming a single species tree can result in substantial deviation from the results with gene trees when testing for positive selection under different models. Collectively, our results highlight the complex relationship between phylogenetic inference and genome biology and underscore how failure to account for this complexity can mislead comparative genomic studies.}, } @article {pmid39745426, year = {2025}, author = {Gulyaeva, A and Liu, L and Garmaeva, S and Kruk, M and Weersma, RK and Harmsen, HJM and Zhernakova, A}, title = {Identification and characterization of Faecalibacterium prophages rich in diversity-generating retroelements.}, journal = {Microbiology spectrum}, volume = {13}, number = {2}, pages = {e0106624}, doi = {10.1128/spectrum.01066-24}, pmid = {39745426}, issn = {2165-0497}, mesh = {*Prophages/genetics/isolation & purification ; *Retroelements ; Humans ; *Metagenomics ; Genome, Viral/genetics ; Gastrointestinal Microbiome ; Computational Biology/methods ; Host Specificity ; Bacteriophages/genetics/classification/isolation & purification/physiology ; Genome, Bacterial/genetics ; Phylogeny ; Genetic Variation ; }, abstract = {Metagenomics has revealed the incredible diversity of phages within the human gut. However, very few of these phages have been subjected to in-depth experimental characterization. One promising method of obtaining novel phages for experimental characterization is through induction of the prophages integrated into the genomes of cultured gut bacteria. Here, we developed a bioinformatic approach to prophage identification that builds on prophage genomic properties, existing prophage-detecting software, and publicly available virome sequencing data. We applied our approach to 22 strains of bacteria belonging to the genus Faecalibacterium, resulting in identification of 15 candidate prophages, and validated the approach by demonstrating the activity of five prophages from four of the strains. The genomes of three active phages were identical or similar to those of known phages, while the other two active phages were not represented in the Viral RefSeq database. Four of the active phages possessed a diversity-generating retroelement (DGR), and one retroelement had two variable regions. DGRs of two phages were active at the time of the induction experiments, as evidenced by nucleotide variation in sequencing reads. We also predicted that the host range of two active phages may include multiple bacterial species. Finally, we noted that four phages were less prevalent in the metagenomes of inflammatory bowel disease patients compared to a general population cohort, a difference mainly explained by differences in the abundance of the host bacteria. Our study highlights the utility of prophage identification and induction for unraveling phage molecular mechanisms and ecological interactions.IMPORTANCEWhile hundreds of thousands of phage genomes have been discovered in metagenomics studies, only a few of these phages have been characterized experimentally. Here, we explore phage characterization through bioinformatic identification of prophages in genomes of cultured bacteria, followed by prophage induction. Using this approach, we detect the activity of five prophages in four strains of commensal gut bacteria Faecalibacterium. We further note that four of the prophages possess diversity-generating retroelements implicated in rapid mutation of phage genome loci associated with phage-host and phage-environment interactions and analyze the intricate patterns of retroelement activity. Our study highlights the potential of prophage characterization for elucidating complex molecular mechanisms employed by the phages.}, } @article {pmid39900973, year = {2025}, author = {Vysakh, VG and Sukumaran, S and Sebastian, W and Gopalakrishnan, A}, title = {The transcriptomic footprint of Mytella strigata: de novo transcriptome assembly of a major invasive species.}, journal = {Scientific data}, volume = {12}, number = {1}, pages = {201}, pmid = {39900973}, issn = {2052-4463}, mesh = {*Introduced Species ; Animals ; *Transcriptome ; Mytilidae/genetics ; South America ; Gene Ontology ; Molecular Sequence Annotation ; }, abstract = {Mytella strigata, a potentially invasive species native to South America, is rapidly spreading across various aquatic ecosystems around the globe, posing a threat to native mussels. This study presents the first comprehensive de novo transcriptome assembly of M. strigata. We generated 254 million reads, which were processed and assembled using the Trinity assembler, resulting in 60362 transcripts with an N50 of 1,578 bp and over 93-98% completeness, as confirmed by BUSCO analysis with multiple ortho-datasets. A number of databases were used for functional annotation, including UniProt, KEGG, Reactome, InterPro, and eggNOG. Gene Ontology and pathway analyses identified transcripts associated with key biological processes, including those associated with cell signalling, metabolism, stress responses, cancer pathways, and immune regulation. This dataset enriches the bivalve database by advancing the understanding of the adaptive success and evolutionary resilience of this invasive species. The present study provides a fundamental framework for future research on the ecological and evolutionary impacts of this invasive species.}, } @article {pmid39899630, year = {2025}, author = {Sheen, JK and Kennedy-Shaffer, L and Levy, MZ and Metcalf, CJE}, title = {Design of field trials for the evaluation of transmissible vaccines in animal populations.}, journal = {PLoS computational biology}, volume = {21}, number = {2}, pages = {e1012779}, doi = {10.1371/journal.pcbi.1012779}, pmid = {39899630}, issn = {1553-7358}, mesh = {Animals ; *Vaccines/immunology ; Vaccination/methods ; Computational Biology ; Sample Size ; Research Design ; }, abstract = {Vaccines which can transmit from vaccinated to unvaccinated animals may be especially useful for increasing immunity in hard to reach populations or in populations where achieving high coverage is logistically infeasible. However, gauging the public health utility for future use of such transmissible vaccines and assessing their risk-benefit tradeoff, given their potential for unintended evolution, hinges on accurate estimates of their indirect protective effect. Here, we establish the conditions under which a two-stage randomized field trial can characterize the protective effects of a transmissible vaccine relative to a traditional vaccine. We contrast the sample sizes required to adequately power these trials when the vaccine is weakly and strongly transmissible. We also identify how required sample sizes change based on the characteristics of host ecology such as the overdispersion of the contact structure of the population, as well as the efficacy of the vaccine and timing of vaccination. Our results indicate the range of scenarios where two-stage randomized field trial designs are feasible and appropriate to capture the protective effects of transmissible vaccines. Our estimates identify the protective benefit of using transmissible vaccines compared to traditional vaccines, and thus can be used to weigh against evolutionary risks.}, } @article {pmid39897903, year = {2025}, author = {Doshi, P and Klas, M and Kyzek, S and Zahoranová, A and Šerá, B}, title = {Investigating the effect of plasma activated water on entomopathogenic nematodes under laboratory conditions.}, journal = {Heliyon}, volume = {11}, number = {2}, pages = {e42038}, pmid = {39897903}, issn = {2405-8440}, abstract = {Entomopathogenic nematodes are currently being tested for their efficiency in controlling several insect pests. In recent years, non-thermal plasma has been investigated as a state-of-the-art technology for its disinfection/decontamination properties on the seed surface. In addition, it is also used to induce seed germination. In this investigation, the effect of plasma activated water (PAW) was tested on three EPN species, namely Steinernema feltiae Filipjev (1934), S. carpocapsae Weiser (1955), and Heterorhabditis bacteriophora Poinar (1976). Seven different PAW prepared at different treatment times, that is, (1s, 3s, 5s, 10s, 20s, 60s, 90s) were tested directly on the three selected nematode species. Distilled water was used as a control treatment (0s). In the case of H. bacteriophora, significantly higher mortality was observed in PAW preparation times of 5, 10, 20, 60 and 90s compared to the control. In the case of S. feltiae, significantly high mortality was observed for PAW preparation times of 10, 20, 60 and 90s. However, S. carpocapsae was found to have the least sensitivity against all PAW treatments, with a maximum mortality of 14 % (<20 %), indicating the potential synergy between PAW and EPNs. The possibility of combined treatments in the context of integrated pest management is presented and discussed.}, } @article {pmid39897842, year = {2025}, author = {Loukili, I and Laamrani, A and El Ghorfi, M and El Moutak, S and Ghafiri, A}, title = {Monitoring land changes at an open mine site using remote sensing and multi-spectral indices.}, journal = {Heliyon}, volume = {11}, number = {2}, pages = {e41845}, pmid = {39897842}, issn = {2405-8440}, abstract = {This study investigates the growth of mining activities in Benguerir, one of Morocco's largest and fastest-growing phosphate mines and a global leader in phosphate production, using remote sensing and ancillary data. The study examines spatio-temporal changes in land use and land cover (LULC) within this phosphate mining city to analyze the impacts of mining on agricultural areas, built-up lands, and water bodies over time. A series of images from 1984 to 2021 were processed in to assess patterns of change within the city. Five LULC maps were generated using supervised classification with the maximum likelihood method, providing detailed insights into both urban and non-urban transformations during the study period. Classification quality was evaluated using accuracy assessment and the Kappa index. Additionally, multi-spectral indices, including the Normalized Difference Vegetation Index (NDVI), Normalized Difference Water Index (NDWI), and Normalized Difference Built-up Index (NDBI), were simulated and analyzed across four intervals. The results reveal significant variations in LULC and ecological indices over time, which are associated with mining activities, water stress, urban sprawl, and socio-economic changes in the region.These results provide a valuable means for decision-makers and planners to effectively manage the spaces and lands in the future.}, } @article {pmid39897809, year = {2025}, author = {Milling, M and Rampp, SDN and Triantafyllopoulos, A and Plaza, MP and Brunner, JO and Traidl-Hoffmann, C and Schuller, BW and Damialis, A}, title = {Automating airborne pollen classification: Identifying and interpreting hard samples for classifiers.}, journal = {Heliyon}, volume = {11}, number = {2}, pages = {e41656}, pmid = {39897809}, issn = {2405-8440}, abstract = {Deep-learning-based classification of pollen grains has been a major driver towards automatic monitoring of airborne pollen. Yet, despite an abundance of available datasets, little effort has been spent to investigate which aspects pose the biggest challenges to the (often black-box- resembling) pollen classification approaches. To shed some light on this issue, we conducted a sample-level difficulty analysis based on the likelihood for one of the largest automatically-generated datasets of pollen grains on microscopy images and investigated the reason for which certain airborne samples and specific pollen taxa pose particular problems to deep learning algorithms. It is here concluded that the main challenges lie in A) the (partly) co-occurring of multiple pollen grains in a single image, B) the occlusion of specific markers through the 2D capturing of microscopy images, and C) for some taxa, a general lack of salient, unique features. Our code is publicly available under https://github.com/millinma/SDPollen.}, } @article {pmid39897501, year = {2025}, author = {Fuster-Calvo, A and Valentin, S and Tamayo, WC and Gravel, D}, title = {Evaluating the feasibility of automating dataset retrieval for biodiversity monitoring.}, journal = {PeerJ}, volume = {13}, number = {}, pages = {e18853}, pmid = {39897501}, issn = {2167-8359}, mesh = {*Biodiversity ; *Databases, Factual ; Feasibility Studies ; Information Storage and Retrieval/methods ; Algorithms ; Quebec ; Conservation of Natural Resources/methods ; }, abstract = {AIM: Effective management strategies for conserving biodiversity and mitigating the impacts of global change rely on access to comprehensive and up-to-date biodiversity data. However, manual search, retrieval, evaluation, and integration of this information into databases present a significant challenge to keeping pace with the rapid influx of large amounts of data, hindering its utility in contemporary decision-making processes. Automating these tasks through advanced algorithms holds immense potential to revolutionize biodiversity monitoring.

INNOVATION: In this study, we investigate the potential for automating the retrieval and evaluation of biodiversity data from Dryad and Zenodo repositories. We have designed an evaluation system based on various criteria, including the type of data provided and its spatio-temporal range, and applied it to manually assess the relevance for biodiversity monitoring of datasets retrieved through an application programming interface (API). We evaluated a supervised classification to identify potentially relevant datasets and investigate the feasibility of automatically ranking the relevance. Additionally, we applied the same appraoch on a scientific literature source, using data from Semantic Scholar for reference. Our evaluation centers on the database utilized by a national biodiversity monitoring system in Quebec, Canada.

MAIN CONCLUSIONS: We retrieved 89 (55%) relevant datasets for our database, showing the value of automated dataset search in repositories. Additionally, we find that scientific publication sources offer broader temporal coverage and can serve as conduits guiding researchers toward other valuable data sources. Our automated classification system showed moderate performance in detecting relevant datasets (with an F-score up to 0.68) and signs of overfitting, emphasizing the need for further refinement. A key challenge identified in our manual evaluation is the scarcity and uneven distribution of metadata in the texts, especially pertaining to spatial and temporal extents. Our evaluative framework, based on predefined criteria, can be adopted by automated algorithms for streamlined prioritization, and we make our manually evaluated data publicly available, serving as a benchmark for improving classification techniques.}, } @article {pmid39808665, year = {2025}, author = {Fonseca, LL and Böttcher, L and Mehrad, B and Laubenbacher, RC}, title = {Optimal control of agent-based models via surrogate modeling.}, journal = {PLoS computational biology}, volume = {21}, number = {1}, pages = {e1012138}, doi = {10.1371/journal.pcbi.1012138}, pmid = {39808665}, issn = {1553-7358}, mesh = {*Algorithms ; *Computational Biology/methods ; Humans ; Computer Simulation ; Systems Analysis ; Models, Biological ; }, abstract = {This paper describes and validates an algorithm to solve optimal control problems for agent-based models (ABMs). For a given ABM and a given optimal control problem, the algorithm derives a surrogate model, typically lower-dimensional, in the form of a system of ordinary differential equations (ODEs), solves the control problem for the surrogate model, and then transfers the solution back to the original ABM. It applies to quite general ABMs and offers several options for the ODE structure, depending on what information about the ABM is to be used. There is a broad range of applications for such an algorithm, since ABMs are used widely in the life sciences, such as ecology, epidemiology, and biomedicine and healthcare, areas where optimal control is an important purpose for modeling, such as for medical digital twin technology.}, } @article {pmid39889380, year = {2025}, author = {Weeks, F and Myerson, R and Gangnon, R and Dykema, J and Cornelius, C and Green, T}, title = {Racial disparities in intrapartum care experiences and birth hospital characteristics.}, journal = {Social science & medicine (1982)}, volume = {367}, number = {}, pages = {117720}, doi = {10.1016/j.socscimed.2025.117720}, pmid = {39889380}, issn = {1873-5347}, abstract = {Policymakers and researchers have posited intrapartum care as a potential mediator of racial inequities in perinatal outcomes. However, few studies have measured patient-centered quality of intrapartum care or explored differences by race. To address this gap, we developed a survey supplement using cognitive interviewing and administered it to a probability-based race-stratified random sample of people who recently gave birth in Wisconsin in 2020, including oversamples of non-Hispanic Black and Indigenous birthing people. We estimate overall and race-specific prevalences of intrapartum care experiences and use survey-weighted mixed effects ordinal and logistic regression to estimate differences in intrapartum care experiences by race/ethnicity and hospital characteristics. We find significant racial differences in the population prevalence of negative experiences of intrapartum care providers, including disrespect, lack of responsiveness, inclusion in decision-making about care, and pressure to use epidural analgesia. In unadjusted models, both non-Hispanic Indigenous (American Indian/Alaska Native) and non-Hispanic Black respondents had higher odds (than non-Hispanic White birthing people) of reporting several negative intrapartum experiences, including feeling disrespected by providers and experiencing a lower level of care team responsiveness. In adjusted models, Indigenous respondents had significantly higher odds of reporting that intrapartum care providers withheld information, showed disrespect, and were less responsive. Giving birth at a low birth-volume hospital was associated with higher odds of reporting greater participation in decision-making. CONCLUSION: While all birthing people are entitled to respectful and person-centered care, in practice, Indigenous and Black birthing persons are more likely than their white counterparts to endure negative intrapartum experiences including disrespect and lack of responsiveness to their needs. Equitable implementation of person-centered care principles will require concerted efforts to institutionalize practices that preserve patient dignity and autonomy.}, } @article {pmid39888239, year = {2025}, author = {Giles, EC and González, VL and Carimán, P and Leiva, C and Suescún, AV and Lemer, S and Guillemin, ML and Ortiz-Barrientos, D and Saenz-Agudelo, P}, title = {Comparative Genomics Points to Ecological Drivers of Genomic Divergence Among Intertidal Limpets.}, journal = {Molecular ecology resources}, volume = {}, number = {}, pages = {e14075}, doi = {10.1111/1755-0998.14075}, pmid = {39888239}, issn = {1755-0998}, support = {2190878//BECA CONICYT-PCHA/Doctorado Nacional Chile/2019/ ; 1190710//Fondo Nacional de Desarrollo Científico y Tecnológico/ ; OIA-1946352//National Science Foundation NSF-EPSCoR/ ; }, abstract = {Comparative genomic studies of closely related taxa are important for our understanding of the causes of divergence on a changing Earth. This being said, the genomic resources available for marine intertidal molluscs are limited and currently, there are few publicly available high-quality annotated genomes for intertidal species and for molluscs in general. Here we report transcriptome assemblies for six species of Patellogastropoda and genome assemblies and annotations for three of these species (Scurria scurra, Scurria viridula and Scurria zebrina). Comparative analysis using these genomic resources suggest that and recently diverging lineages (10-20 Mya) have experienced similar amounts of contractions and expansions but across different gene families. Furthermore, differences among recently diverged species are reflected in variation in the amount of coding and noncoding material in genomes, such as amount of repetitive elements and lengths of transcripts and introns and exons. Additionally, functional ontologies of species-specific and duplicated genes together with demographic inference support the finding that recent divergence among members of the genus Scurria aligns with their unique ecological characteristics. Overall, the resources presented here will be valuable for future studies of adaptation in molluscs and in intertidal habitats as a whole.}, } @article {pmid39854567, year = {2025}, author = {Moody, NM and Williams, CM and Ramachandran, S and Fuxjager, MJ}, title = {Social mates dynamically coordinate aggressive behavior to produce strategic territorial defense.}, journal = {PLoS computational biology}, volume = {21}, number = {1}, pages = {e1012740}, doi = {10.1371/journal.pcbi.1012740}, pmid = {39854567}, issn = {1553-7358}, mesh = {Animals ; Female ; Male ; *Aggression/physiology ; *Territoriality ; Birds/physiology ; Computational Biology ; Social Behavior ; Behavior, Animal/physiology ; Sexual Behavior, Animal/physiology ; }, abstract = {Negotiating social dynamics among allies and enemies is a complex problem that often requires individuals to tailor their behavioral approach to a specific situation based on environmental and/or social factors. One way to make these contextual adjustments is by arranging behavioral output into intentional patterns. Yet, few studies explore how behavioral patterns vary across a wide range of contexts, or how allies might interlace their behavior to produce a coordinated response. Here, we investigate the possibility that resident female and male downy woodpeckers guard their breeding territories from conspecific intruders by deploying defensive behavior in context-specific patterns. To study whether this is the case, we use correlation networks to reveal how suites of agonistic behavior are interrelated. We find that residents do organize their defense into definable patterns, with female and male social mates deploying their behaviors non-randomly in a correlated fashion. We then employ spectral clustering analyses to further distill these responses into distinct behavioral motifs. Our results show that this population of woodpeckers adjusts the defensive motifs deployed according to threat context. When we combine this approach with behavioral transition analyses, our results reveal that pair coordination is a common feature of territory defense in this species. However, if simulated intruders are less threatening, residents are more likely to defend solo, where only one bird deploys defensive behaviors. Overall, our study supports the hypothesis that nonhuman animals can pattern their behavior in a strategic and coordinated manner, while demonstrating the power of systems approaches for analyzing multiagent behavioral dynamics.}, } @article {pmid38112302, year = {2025}, author = {Marques, PH and Rodrigues, TCV and Santos, EH and Bleicher, L and Aburjaile, FF and Martins, FS and Oliveira, CJF and Azevedo, V and Tiwari, S and Soares, S}, title = {Design of a multi-epitope vaccine (vme-VAC/MST-1) against cholera and vibriosis based on reverse vaccinology and immunoinformatics approaches.}, journal = {Journal of biomolecular structure & dynamics}, volume = {43}, number = {4}, pages = {1788-1803}, doi = {10.1080/07391102.2023.2293256}, pmid = {38112302}, issn = {1538-0254}, mesh = {*Cholera/prevention & control/immunology ; *Computational Biology/methods ; Humans ; *Cholera Vaccines/immunology ; *Vaccinology/methods ; Epitopes, T-Lymphocyte/immunology/chemistry ; Epitopes/immunology/chemistry ; Epitopes, B-Lymphocyte/immunology/chemistry ; Vibrio Infections/prevention & control/immunology ; Molecular Docking Simulation ; Immunoinformatics ; }, abstract = {Vibriosis and cholera are serious diseases distributed worldwide and caused by six marine bacteria of the Vibrio genus. Thousands of deaths occur each year due to these illnesses, necessitating the development of new preventive measures. Presently, the existing cholera vaccine demonstrates an effectiveness of approximately 60%. Here we describe a new multi-epitope vaccine, 'vme-VAC/MST-1' based on vaccine targets identified by reverse vaccinology and epitopes predicted by immunoinformatics, two currently effective tools for predicting new vaccines for bacterial pathogens. The vaccine was designed to combat vibriosis and cholera by incorporating epitopes predicted for CTL, HTL, and B cells. These epitopes were identified from six vaccine targets revealed through subtractive genomics, combined with reverse vaccinology, and were further filtered using immunoinformatics approaches based on their predicted immunogenicity. To construct the vaccine, 28 epitopes (24 CTL/B and 4 HTL/B) were linked to the sequence of the cholera toxin B subunit adjuvant. In silico analyses indicate that the resulting immunogen is stable, soluble, non-toxic, and non-allergenic. Furthermore, it exhibits no homology to the host and demonstrates a strong capacity to elicit innate, B-cell, and T-cell immune responses. Our analysis suggests that it is likely to elicit immune reactions mediated through the TLR5 pathway, as evidenced by the molecular docking of the vaccine with the receptor, which revealed high affinity and a favorable reaction. Thus, vme-VAC/MST-1 is predicted to be a safe and effective solution against pathogenic Vibrio spp. However, further experimental analyses are required to measure the vaccine's effects In vivo.Communicated by Ramaswamy H. Sarma.}, } @article {pmid39834325, year = {2025}, author = {Chen, L and Xu, Z and He, Y and Zhang, X and Li, L and Zhu, R and Zhang, Z and Lin, H and Hong, G}, title = {Multiomics Analysis Reveals Key Targeted Metabolic Pathways Underlying the Hormesis and Detrimental Effects of Enrofloxacin on Rice Plants.}, journal = {Journal of agricultural and food chemistry}, volume = {73}, number = {4}, pages = {2678-2695}, doi = {10.1021/acs.jafc.4c09001}, pmid = {39834325}, issn = {1520-5118}, mesh = {*Oryza/metabolism/growth & development/drug effects/genetics/chemistry ; *Enrofloxacin/metabolism ; *Hormesis/drug effects ; *Metabolic Networks and Pathways/drug effects ; Anti-Bacterial Agents/pharmacology ; Plant Proteins/genetics/metabolism ; Gene Expression Regulation, Plant/drug effects ; Multiomics ; }, abstract = {Fluoroquinolone antibiotic enrofloxacin (ENR) is frequently detected in agricultural environments. The hormesis and detrimental effects of ENR on crops have been extensively observed. However, the molecular mechanisms underlying these crops' responses to ENR remain limited. Here, integrated physiological, transcriptomic, and metabolomic analysis revealed the key metabolic pathway responses underlying the ENR-induced effects on rice. The results showed that ENR mainly affected three metabolic pathways: 'biosynthesis of amino acids', "tryptophan metabolism", and 'phenylpropanoid/flavonoid biosynthesis'. A low level of ENR treatment promoted root elongation and enhanced the antioxidant capacity by increasing the phytohormone gibberellin A3 and the flavonol quercetin-3-O-neohesperidoside, respectively. However, the high dose of ENR significantly stimulated ROS production, inhibited photosynthesis, and ultimately impaired plant growth. In response to high ENR toxicity, plants accumulated more quercetin derivatives as antioxidants and produced defense-related substances, such as N-hydroxytryptamine, indole-3-acetonitrile, and jasmonic acid, to combat biotic stress. In conclusion, this study provides new insights into the molecular mechanism accounting for the ecological effects of antibiotic pollution in farmland.}, } @article {pmid39874571, year = {2025}, author = {Sahandi Far, M and Fischer, JM and Senge, S and Rathmakers, R and Meissner, T and Schneble, D and Narava, M and Eickhoff, SB and Dukart, J}, title = {Cross-Platform Ecological Momentary Assessment App (JTrack-EMA+): Development and Usability Study.}, journal = {Journal of medical Internet research}, volume = {27}, number = {}, pages = {e51689}, doi = {10.2196/51689}, pmid = {39874571}, issn = {1438-8871}, mesh = {Humans ; *Ecological Momentary Assessment ; *Mobile Applications ; Smartphone ; }, abstract = {BACKGROUND: Traditional in-clinic methods of collecting self-reported information are costly, time-consuming, subjective, and often limited in the quality and quantity of observation. However, smartphone-based ecological momentary assessments (EMAs) provide complementary information to in-clinic visits by collecting real-time, frequent, and longitudinal data that are ecologically valid. While these methods are promising, they are often prone to various technical obstacles. However, despite the potential of smartphone-based EMAs, they face technical obstacles that impact adaptability, availability, and interoperability across devices and operating systems. Deficiencies in these areas can contribute to selection bias by excluding participants with unsupported devices or limited digital literacy, increase development and maintenance costs, and extend deployment timelines. Moreover, these limitations not only impede the configurability of existing solutions but also hinder their adoption for addressing diverse clinical challenges.

OBJECTIVE: The primary aim of this research was to develop a cross-platform EMA app that ensures a uniform user experience and core features across various operating systems. Emphasis was placed on maximizing the integration and adaptability to various study designs, all while maintaining strict adherence to security and privacy protocols. JTrack-EMA+ was designed and implemented per the FAIR (findable, accessible, interpretable, and reusable) principles in both its architecture and data management layers, thereby reducing the burden of integration for clinicians and researchers.

METHODS: JTrack-EMA+ was built using the Flutter framework, enabling it to run seamlessly across different platforms. This platform comprises two main components. JDash (Research Centre Jülich, Institute of Neuroscience and Medicine, Brain and Behaviour [INM-7]) is an online management tool created using Python (Python Software Foundation) with the Django (Django Software Foundation) framework. This online dashboard offers comprehensive study management tools, including assessment design, user administration, data quality control, and a reminder casting center. The JTrack-EMA+ app supports a wide range of question types, allowing flexibility in assessment design. It also has configurable assessment logic and the ability to include supplementary materials for a richer user experience. It strongly commits to security and privacy and complies with the General Data Protection Regulations to safeguard user data and ensure confidentiality.

RESULTS: We investigated our platform in a pilot study with 480 days of follow-up to assess participants' compliance. The 6-month average compliance was 49.3%, significantly declining (P=.004) from 66.7% in the first month to 42% in the sixth month.

CONCLUSIONS: The JTrack-EMA+ platform prioritizes platform-independent architecture, providing an easy entry point for clinical researchers to deploy EMA in their respective clinical studies. Remote and home-based assessments of EMA using this platform can provide valuable insights into patients' daily lives, particularly in a population with limited mobility or inconsistent access to health care services.}, } @article {pmid39813804, year = {2025}, author = {Ahmad, S and Peng, X and Ashraf, A and Yin, D and Chen, Z and Ahmed, R and Israr, M and Jia, H}, title = {Building resilient urban drainage systems by integrated flood risk index for evidence-based planning.}, journal = {Journal of environmental management}, volume = {374}, number = {}, pages = {124130}, doi = {10.1016/j.jenvman.2025.124130}, pmid = {39813804}, issn = {1095-8630}, mesh = {*Floods ; *Cities ; Geographic Information Systems ; Climate Change ; Risk Management/methods ; Urbanization ; Risk Assessment ; }, abstract = {Urban flooding poses a significant risk to cities worldwide, exacerbated by increasing urbanization and climate change. Effective flood risk management requires comprehensive assessments considering the complex interaction of social, economic, and environmental factors. This study developed an innovative Urban Flood Risk Index (FRI) to quantify and assess flood risk at the sub-catchment level, providing a tool for evidence-based planning and resilient infrastructure development. This study integrates Geographic Information System (GIS), Storm Water Management Model (SWMM), Analytic Hierarchy Process (AHP), and the Pressure-State-Response (PSR) framework. The FRI incorporates seven pressure and state indicators and three response indicators weighted by expert judgment. The FRI was calculated by combining the weighted sub-indices, classifying flood risk into five levels. Results showed that 51% of the study area experienced high pressure, with 26% facing very-high pressure. The state index indicated that 55% of the area falls under a moderate state, while 21% exhibits a high state. Importantly, the response index highlighted the effectiveness of Low Impact Development (LID) practices, with 20% of the area showing high to very-high response levels. The integrated FRI demonstrated an overall moderate flood risk level for maximum sub-catchments, emphasizing the positive impact of LID practices in mitigating flood risk despite existing pressures and system limitations. This evidence-based assessment provides a valuable tool for sub-catchment level flood risk assessment. It empowers decision-makers to prioritize investments, target interventions, and develop adaptive strategies to enhance urban resilience in a changing climate.}, } @article {pmid39809974, year = {2025}, author = {Jia, W and Chan, JC and Wong, TY and Fisher, EB}, title = {Diabetes in China: epidemiology, pathophysiology and multi-omics.}, journal = {Nature metabolism}, volume = {7}, number = {1}, pages = {16-34}, pmid = {39809974}, issn = {2522-5812}, mesh = {Humans ; China/epidemiology ; *Diabetes Mellitus/epidemiology ; Risk Factors ; Prevalence ; Metabolomics ; Multiomics ; }, abstract = {Although diabetes is now a global epidemic, China has the highest number of affected people, presenting profound public health and socioeconomic challenges. In China, rapid ecological and lifestyle shifts have dramatically altered diabetes epidemiology and risk factors. In this Review, we summarize the epidemiological trends and the impact of traditional and emerging risk factors on Chinese diabetes prevalence. We also explore recent genetic, metagenomic and metabolomic studies of diabetes in Chinese, highlighting their role in pathogenesis and clinical management. Although heterogeneity across these multidimensional areas poses major analytic challenges in classifying patterns or features, they have also provided an opportunity to increase the accuracy and specificity of diagnosis for personalized treatment and prevention. National strategies and ongoing research are essential for improving diabetes detection, prevention and control, and for personalizing care to alleviate societal impacts and maintain quality of life.}, } @article {pmid39648557, year = {2025}, author = {Huang, Y and Wang, T and Li, Y and Wang, Z and Cai, X and Chen, J and Li, R and Li, X}, title = {In Vitro-to-In Vivo Extrapolation on Lung Toxicity Induced by Metal Oxide Nanoparticles via Data-Mining.}, journal = {Environmental science & technology}, volume = {59}, number = {3}, pages = {1673-1682}, doi = {10.1021/acs.est.4c06186}, pmid = {39648557}, issn = {1520-5851}, mesh = {*Lung/drug effects/pathology ; Animals ; *Metal Nanoparticles/toxicity ; Mice ; *Oxides/toxicity ; Data Mining ; Humans ; }, abstract = {While in silico analyses are commonly employed for chemical risk assessments, predicting chronic lung toxicity induced by engineered nanoparticles (ENMs) in vivo still faces many challenges due to complex interactions at multiple nanobio interfaces. In this study, we developed a rigorous method to compile published evidence on the in vivo lung toxicity of metal oxide nanoparticles (MeONPs) and revealed previously overlooked in vitro-to-in vivo extrapolation (IVIVE) relationships. A comprehensive multidimensional data set containing 1102 in vivo data points, 75 pulmonary toxicological biomarkers, and 20 features (covering in vitro effects, physicochemical properties, and exposure conditions) was constructed. An IVIVE approach that related effects at the cellular level to in vivo lung toxicity in rodent model was established with prediction accuracy reaching 89 and 80% in training and test sets. Experimental validation was conducted by testing chronic lung fibrosis of 8 new MeONPs in 32 independent mice, with prediction accuracy reaching 88%. The IVIVE model indicated that the proinflammatory cytokine IL-1β in THP-1 cells could serve as an in vitro marker to predict lung toxicity. The IVIVE model showed great promise for minimizing unnecessary animal tests and understanding toxicological mechanisms.}, } @article {pmid39871100, year = {2025}, author = {Terauds, A and Lee, JR and Wauchope, HS and Raymond, B and Bergstrom, DM and Convey, P and Mason, C and Patterson, CR and Robinson, SA and Van de Putte, A and Watts, D and Chown, SL}, title = {The biodiversity of ice-free Antarctica database.}, journal = {Ecology}, volume = {106}, number = {1}, pages = {e70000}, doi = {10.1002/ecy.70000}, pmid = {39871100}, issn = {1939-9170}, support = {n°FR/36/AN1/AntaBIS(EU-LifeWatch)//Belgian Science Policy Office/ ; n°RT/23/ADVANCE//Belgian Science Policy Office/ ; //Royal Commission for the Exhibition of 1851 Research Fellowship/ ; SRIEAS-SR200100005//Australian Research Council/ ; //Securing Antarctica's Environmental Future/ ; AAS 4296//Australian Antarctic Division/ ; AAS 4297//Australian Antarctic Division/ ; }, abstract = {Antarctica is one of Earth's most untouched, inhospitable, and poorly known regions. Although knowledge of its biodiversity has increased over recent decades, a diverse, wide-ranging, and spatially explicit compilation of the biodiversity that inhabits Antarctica's permanently ice-free areas is unavailable. This absence hinders both Antarctic biodiversity research and the integration of Antarctica in global biodiversity-related studies. Fundamental and applied research on biodiversity patterns, ecological structure and function, and options for conservation are reliant on spatially resolved, taxonomically consistent observations. Such information is especially important for modern, data-driven biodiversity science, in both Antarctica and globally, and forms the backbone of biodiversity informatics, reflected, for example, in the Darwin Core Standard used by the Global Biodiversity Information Facility. Biodiversity data are also essential to fulfill the conservation requirements for Antarctica, as set out in the Protocol on Environmental Protection to the Antarctic Treaty and inform the design of systematic surveys to address biodiversity and ecological knowledge gaps, for both specific taxa and ecosystems. Such surveys are key requirements for understanding and mitigating the impacts of environmental change on the region's biodiversity. Here, we address these requirements through the public release of The Biodiversity of Ice-free Antarctica Database. In 2008, we extracted a subset of biodiversity records only from terrestrial ice-free areas from the Scientific Committee on Antarctic Research (SCAR) Antarctic Biodiversity Database. We have subsequently added thousands of records from a range of sources: checking, and where necessary (and possible), correcting the spatial location, clarifying, cross-referencing, and harmonizing taxonomy with globally recognized sources, and documenting the original source of records. The Biodiversity of Ice-free Antarctica Database spans the early 1800s to 2019 (with most records collected after 1950) and represents the most comprehensive consolidation of Antarctic ice-free biodiversity occurrence data yet compiled into a single database. The Biodiversity of Ice-free Antarctica Database contains 35,654 records of 1890 species in over 800 genera across six kingdoms and spans all Antarctic Conservation Biogeographic Regions. These data are released under a CC BY Attribution License (http://creativecommons.org/licenses/by/4.0/).}, } @article {pmid39870942, year = {2025}, author = {Lazaro, A and Tiago, I and Mendes, J and Ribeiro, J and Bernardes, A and Oliveira, F and Regateiro, F and Caramelo, F and Silva, H}, title = {Sleeve Gastrectomy and Gastric Bypass Impact in Patient's Metabolic, Gut Microbiome, and Immuno-inflammatory Profiles-A Comparative Study.}, journal = {Obesity surgery}, volume = {}, number = {}, pages = {}, pmid = {39870942}, issn = {1708-0428}, abstract = {BACKGROUND: Bariatric surgery is the most long-term effective treatment option for severe obesity. The role of gut microbiome (GM) in either the development of obesity or in response to obesity management strategies has been a matter of debate. This study aims to compare the impact of two of the most popular procedures, sleeve gastrectomy (SG) and Roux-en-Y gastric bypass (GB), on metabolic syndrome parameters and gut bacterial microbiome and in systemic immuno-inflammatory response.

METHODS: A prospective observational study enrolled 24 patients with severe obesity, 14 underwent SG and 10 GB. Evaluations before (0 M) and 6 months (6 M) after surgical procedures included clinical and biochemical parameters, expression of 17 immuno-inflammatory genes in peripheral blood leukocytes, and assessment of gut microbiome profile using 16 s rRNA next-generation sequencing approach. Statistical significance was set to a p value < 0.05 with an FDR < 0.1.

RESULTS: A significant and similar decrease in weight-associated parameters and for most metabolic markers was achieved with both surgeries. Considering the gut microbiome in the whole study population, there was an increase in alpha diversity at family-level taxa. Beta diversity between SG and GB at 6 M showed near significant differences (p = 0.042) at genus levels. Analysis of the relative abundance of individual taxonomic groups highlighted differences between pre- and post-surgical treatment and between both approaches, namely, a higher representation of family Enterobacteriaceae and genera Veillonella and Enterobacteriaceae_unclassified after GB. Increased expression of immune-inflammatory genes was observed mainly for SG patients.

CONCLUSIONS: We conclude that SG and GB have similar clinical and metabolic outcomes but different impacts in the gut bacterial microbiome. Results also suggest reactivation of immune response after bariatric surgery.}, } @article {pmid39870652, year = {2025}, author = {Koizumi, T and Suzuki, K and Mizuki, I and Kumaishi, K and Ichihashi, Y}, title = {A quantitative prediction method utilizing whole omics data for biosensing.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {1928}, pmid = {39870652}, issn = {2045-2322}, support = {21J00762//Japan Society for the Promotion of Science/ ; Technologies for Smart Bio-industry and Agriculture//the Cabinet Office, Goverment of Japan/ ; }, mesh = {*Biosensing Techniques/methods ; *Biomarkers ; Transcriptome ; Humans ; Metabolomics/methods ; Gene Regulatory Networks ; Genomics/methods ; Computational Biology/methods ; Metabolome ; Microbiota/genetics ; Gene Expression Profiling/methods ; }, abstract = {Omics data provide a plethora of quantifiable information that can potentially be used to identify biomarkers targeting the physiological processes and ecological phenomena of organisms. However, omics data have not been fully utilized because current prediction methods in biomarker construction are susceptible to data multidimensionality and noise. We developed OmicSense, a quantitative prediction method that uses a mixture of Gaussian distributions as the probability distribution, yielding the most likely objective variable predicted for each biomarker. Our benchmark test using a transcriptome dataset revealed that OmicSense achieves accurate and robust prediction against background noise without overfitting. Weighted gene co-expression network analysis revealed that OmicSense preferentially utilized hub nodes of the network, indicating the interpretability of the method. Application of OmicSense to single-cell transcriptome, metabolome, and microbiome datasets confirmed high prediction performance (r > 0.8), suggesting applicability to diverse scientific fields. Given the recent rapidly expanding availability of omics data, the developed prediction tool OmicSense, can accelerate the use of omics data as a "biosensor" based on an assemblage of potential biomarkers.}, } @article {pmid39870651, year = {2025}, author = {Ridgway, J and Wesner, J}, title = {A global dataset of freshwater fish trophic interactions.}, journal = {Scientific data}, volume = {12}, number = {1}, pages = {160}, pmid = {39870651}, issn = {2052-4463}, mesh = {Animals ; *Fishes ; *Fresh Water ; Food Chain ; Diet/veterinary ; Predatory Behavior ; Databases, Factual ; }, abstract = {Freshwater management and research frequently rely on trophic data to manage freshwater fishes, yet it is difficult to perform a simple search of dietary information for any one species. FishBase represents the largest effort to organize freshwater dietary data into a singular, navigable dataset. Nonetheless, FishBase excludes a large portion of the ecological literature because it was developed before the creation of most modern scientific search engines. Our project, TroPhish, builds upon FishBase by digitizing over 100 years of data from the fish predation literature. Data from 1,106 published papers, theses, dissertations, and government reports were filtered, scanned in through third-party software (Able2Extract), reorganized, and consolidated with FishBase to form a unified dataset. This dataset contains 54,750 observations of data on 4,571 unique dietary samples, representing 9% (982) of all freshwater fish species and 43% (111) of all freshwater fish families. Fish species and family representation varied by continent, ranging from 3-32% and 34-75%, respectively. Users are encouraged to submit errors or additional data through GitHub's fork and pull model.}, } @article {pmid39869900, year = {2025}, author = {Yeom, JW and Kim, H and Pack, SP and Lee, HJ and Cheong, T and Cho, CH}, title = {Exploring the Psychological and Physiological Insights Through Digital Phenotyping by Analyzing the Discrepancies Between Subjective Insomnia Severity and Activity-Based Objective Sleep Measures: Observational Cohort Study.}, journal = {JMIR mental health}, volume = {12}, number = {}, pages = {e67478}, doi = {10.2196/67478}, pmid = {39869900}, issn = {2368-7959}, mesh = {Humans ; Middle Aged ; Male ; *Sleep Initiation and Maintenance Disorders/physiopathology/psychology/diagnosis ; Female ; Adult ; *Severity of Illness Index ; Aged ; Cohort Studies ; *Wearable Electronic Devices ; Young Adult ; Ecological Momentary Assessment ; Sleep/physiology ; Exercise/psychology/physiology ; Self Report ; }, abstract = {BACKGROUND: Insomnia is a prevalent sleep disorder affecting millions worldwide, with significant impacts on daily functioning and quality of life. While traditionally assessed through subjective measures such as the Insomnia Severity Index (ISI), the advent of wearable technology has enabled continuous, objective sleep monitoring in natural environments. However, the relationship between subjective insomnia severity and objective sleep parameters remains unclear.

OBJECTIVE: This study aims to (1) explore the relationship between subjective insomnia severity, as measured by ISI scores, and activity-based objective sleep parameters obtained through wearable devices; (2) determine whether subjective perceptions of insomnia align with objective measures of sleep; and (3) identify key psychological and physiological factors contributing to the severity of subjective insomnia complaints.

METHODS: A total of 250 participants, including both individuals with and without insomnia aged 19-70 years, were recruited from March 2023 to November 2023. Participants were grouped based on ISI scores: no insomnia, mild, moderate, and severe insomnia. Data collection involved subjective assessments through self-reported questionnaires and objective measurements using wearable devices (Fitbit Inspire 3) that monitored sleep parameters, physical activity, and heart rate. The participants also used a smartphone app for ecological momentary assessment, recording daily alcohol consumption, caffeine intake, exercise, and stress. Statistical analyses were used to compare groups on subjective and objective measures.

RESULTS: Results indicated no significant differences in general sleep structure (eg, total sleep time, rapid eye movement sleep time, and light sleep time) among the insomnia groups (mild, moderate, and severe) as classified by ISI scores (all P>.05). Interestingly, the no insomnia group had longer total awake times and lower sleep quality compared with the insomnia groups. Among the insomnia groups, no significant differences were observed regarding sleep structure (all P>.05), suggesting similar sleep patterns regardless of subjective insomnia severity. There were significant differences among the insomnia groups in stress levels, dysfunctional beliefs about sleep, and symptoms of restless leg syndrome (all P≤.001), with higher severity associated with higher scores in these factors. Contrary to expectations, no significant differences were observed in caffeine intake (P=.42) and alcohol consumption (P=.07) between the groups.

CONCLUSIONS: The findings demonstrate a discrepancy between subjective perceptions of insomnia severity and activity-based objective sleep parameters, suggesting that factors beyond sleep duration and quality may contribute to subjective sleep complaints. Psychological factors, such as stress, dysfunctional sleep beliefs, and symptoms of restless legs syndrome, appear to play significant roles in the perception of insomnia severity. These results highlight the importance of considering both subjective and objective assessments in the evaluation and treatment of insomnia and suggest potential avenues for personalized treatment strategies that address both psychological and physiological aspects of sleep disturbances.

TRIAL REGISTRATION: Clinical Research Information Service KCT0009175; https://cris.nih.go.kr/cris/search/detailSearch.do?seq=26133.}, } @article {pmid39868965, year = {2025}, author = {Grikscheit, K and Berger, A and Rabenau, H and Kohmer, N and Appel, KS and Scherer, M and Bals, R and Blaschke, S and Hamprecht, A and Hopff, SM and Krefting, D and Meybohm, P and Nürnberger, C and Heuschmann, P and Pley, C and Nunes de Miranda, SM and Dahl, E and Jensen, B and Illig, T and Anton, G and Vehreschild, JJ and Ciesek, S}, title = {Occurrence and clinical correlates of SARS-CoV-2 viremia in two German patient cohorts.}, journal = {Emerging microbes & infections}, volume = {}, number = {}, pages = {2459137}, doi = {10.1080/22221751.2025.2459137}, pmid = {39868965}, issn = {2222-1751}, abstract = {Viremia defined as detectable SARS-CoV-2 RNA in the blood is a potential marker of disease severity and prognosis in COVID-19 patients. Here, we determined the frequency of viremia in serum of two independent COVID-19 patient cohorts within the German National Pandemic Cohort Network (German: Nationales Pandemie Kohorten Netzwerk, NAPKON) with diagnostic RT-PCR against SARS-CoV-2. A cross-sectional cohort with 1,122 COVID-19 patients (German: Sektorenuebergreifende Platform, SUEP) and 299 patients recruited in a high-resolution platform with patients at high risk to develop severe courses (German: Hochaufloesende Plattform, HAP) were tested for viremia. Our study also involved a comprehensive analysis and association of serological, diagnostic and clinical parameters of the NAPKON medical dataset. Prevalence of viremia at the recruitment visit was 12,8% (SUEP) and 13% (HAP) respectively. Serological analysis revealed that viremic patients had lower levels of SARS-CoV-2 specific antibodies as well as lower neutralizing antibodies compared to aviremic patients. Viremia was associated with severity (<0.0001 SUEP; 0.002 HAP) and mortality of COVID-19 (both cohorts <0.0001) compared to aviremic patients. While rare, viremia was also detected in patients with mild disease (0.7%). In patients of the SUEP cohort with acute kidney disease (p = 0.0099) and hematooncological conditions (p = 0.0091), viremia was detected more frequently. Compared to the aviremic group, treatment with immunomodulating drugs as well as elevated levels of inflammatory markers in the blood was more frequent in the viremic group. In conclusion, our analysis revealed that detectable viremia correlates with hyperinflammatory conditions and higher risk for severe COVID-19 disease.}, } @article {pmid39830079, year = {2024}, author = {Couch, J and Arnaout, R and Arnaout, R}, title = {Beyond Size and Class Balance: Alpha as a New Dataset Quality Metric for Deep Learning.}, journal = {ArXiv}, volume = {}, number = {}, pages = {}, pmid = {39830079}, issn = {2331-8422}, support = {R01 AI148747/AI/NIAID NIH HHS/United States ; R01 HL150394/HL/NHLBI NIH HHS/United States ; }, abstract = {In deep learning, achieving high performance on image classification tasks requires diverse training sets. However, the current best practice-maximizing dataset size and class balance-does not guarantee dataset diversity. We hypothesized that, for a given model architecture, model performance can be improved by maximizing diversity more directly. To test this hypothesis, we introduce a comprehensive framework of diversity measures from ecology that generalizes familiar quantities like Shannon entropy by accounting for similarities among images. (Size and class balance emerge as special cases.) Analyzing thousands of subsets from seven medical datasets showed that the best correlates of performance were not size or class balance but A -"big alpha"-a set of generalized entropy measures interpreted as the effective number of image-class pairs in the dataset, after accounting for image similarities. One of these, A 0 , explained 67% of the variance in balanced accuracy, vs. 54% for class balance and just 39% for size. The best pair of measures was size-plus- A 1 (79%), which outperformed size-plus-class-balance (74%). Subsets with the largest A 0 performed up to 16% better than those with the largest size (median improvement, 8%). We propose maximizing A as a way to improve deep learning performance in medical imaging.}, } @article {pmid39866757, year = {2023}, author = {Gudelj Rakić, J and Maksimović, M and Vlajinac, H and Janković, J and Vukašinović, D and Marinković, J}, title = {TRENDS IN OVERWEIGHT AND OBESITY AMONG SERBIAN ADULT POPULATION 2000-2013.}, journal = {Acta clinica Croatica}, volume = {62}, number = {4}, pages = {605-614}, pmid = {39866757}, issn = {1333-9451}, mesh = {Humans ; Male ; Serbia/epidemiology ; Female ; Adult ; *Obesity/epidemiology ; *Overweight/epidemiology ; Prevalence ; Middle Aged ; *Body Mass Index ; Cross-Sectional Studies ; Health Surveys ; Young Adult ; Aged ; }, abstract = {The aim of the study was to determine changes in body mass index (BMI) and in the prevalence of overweight and obesity in Serbian adult population. Data for this study were obtained from three National Health Interview Surveys, carried out as cross-sectional, nationally representative surveys in 2000, 2006 and 2013. The values of p for trends of sociodemographic and health related behavioral characteristics, of BMI distribution, and of overweight and obesity prevalence were determined by univariate and multivariate linear and logistic regression analyses, with year of survey as a continuous variable. The mean values of BMI and standard deviations in surveys were 26.09±3.92, 26.28±4.02 and 26.87±4.33 in men, and 25.91±5.25, 25.77±5.22 and 26.35±5.58 in women, respectively (trend p<0.001 both). The prevalence of obesity was 14.3%, 16.5% and 21.4% in men, and 20.0%, 19.7% and 23.3% in women, respectively (trend p<0.001 both). The prevalence of overweight did not change significantly during the observed period. In conclusion, the prevalence of obesity showed an increasing trend in both men and women, demanding targeted public health interventions.}, } @article {pmid39865039, year = {2024}, author = {Alekseeva, AO and Zolotovskaia, MA and Sorokin, MI and Suntsova, MV and Zakharova, GS and Pugacheva, PA and Tinkov, AA and Korobeinikova, TV and Sekacheva, MI and Poddubskaya, EV and Skalny, AV and Kushlinskii, NE and Buzdin, AA}, title = {The First Multiomics Association Study of Trace Element and Mineral Concentration and RNA Sequencing Profiles in Human Cancers.}, journal = {Biochemistry. Biokhimiia}, volume = {89}, number = {12}, pages = {2274-2286}, doi = {10.1134/S0006297924120150}, pmid = {39865039}, issn = {1608-3040}, mesh = {Humans ; *Trace Elements/metabolism/analysis ; Minerals/metabolism ; Sequence Analysis, RNA ; Neoplasms/genetics/metabolism ; Male ; Colorectal Neoplasms/genetics/metabolism ; Female ; Gene Expression Profiling ; Multiomics ; }, abstract = {Integration of various types of omics data is an important trend in contemporary molecular oncology. In this regard, high-throughput analysis of trace and essential elements in cancer biosamples is an emerging field that has not yet been sufficiently addressed. For the first time, we simultaneously obtained gene expression profiles (RNA sequencing) and essential and trace element profiles (inductively coupled plasma mass spectrometry) for a set of human cancer samples. The biosamples were formalin-fixed, paraffin-embedded primary tumor tissue blocks: 67 for colorectal cancer patients and 18 for other solid cancer types (16 types). Mass spectrometry profiles were obtained for 45 chemical elements: Ag, Al, As, Au, B, Ba, Be, Bi, Ca, Cd, Co, Cr, Cu, Fe, Ga, Ge, Hg, I, K, La, Li, Mg, Mn, Mo, Na, Ni, P, Pb, Pd, Pt, Rb, Sb, Sc, Se, Si, Sn, Sr, Te, Ti, Tl, Zn, U, V, W, and Zr. The expression levels were profiled for 36,596 known human genes, and the activation levels were assessed for 10,520 human intracellular molecular pathways. For the concentrations of essential elements Ca, Cu, Fe, K, Mg, Na, P, and Zn we detected statistically significant correlations on both gene expression and pathway activation levels for both colorectal cancer samples and at the pan-cancer level. In total, 222/137, 122/220, 1/0, 239/186, 71/44, 1/0, 354/294, 69/82 gene/pathway biomarkers were detected for Ca, Cu, Fe, K, Mg, Na, P, and Zn, respectively. We believe that this first-in-class database provided here will be valuable for multiomics cancer research.}, } @article {pmid39860723, year = {2025}, author = {Dewmini, H and Meedeniya, D and Perera, C}, title = {Elephant Sound Classification Using Deep Learning Optimization.}, journal = {Sensors (Basel, Switzerland)}, volume = {25}, number = {2}, pages = {}, doi = {10.3390/s25020352}, pmid = {39860723}, issn = {1424-8220}, mesh = {*Elephants/physiology ; *Deep Learning ; Animals ; *Vocalization, Animal/physiology ; *Bayes Theorem ; Sound Spectrography/methods ; Sound ; Algorithms ; }, abstract = {Elephant sound identification is crucial in wildlife conservation and ecological research. The identification of elephant vocalizations provides insights into the behavior, social dynamics, and emotional expressions, leading to elephant conservation. This study addresses elephant sound classification utilizing raw audio processing. Our focus lies on exploring lightweight models suitable for deployment on resource-costrained edge devices, including MobileNet, YAMNET, and RawNet, alongside introducing a novel model termed ElephantCallerNet. Notably, our investigation reveals that the proposed ElephantCallerNet achieves an impressive accuracy of 89% in classifying raw audio directly without converting it to spectrograms. Leveraging Bayesian optimization techniques, we fine-tuned crucial parameters such as learning rate, dropout, and kernel size, thereby enhancing the model's performance. Moreover, we scrutinized the efficacy of spectrogram-based training, a prevalent approach in animal sound classification. Through comparative analysis, the raw audio processing outperforms spectrogram-based methods. In contrast to other models in the literature that primarily focus on a single caller type or binary classification that identifies whether a sound is an elephant voice or not, our solution is designed to classify three distinct caller-types namely roar, rumble, and trumpet.}, } @article {pmid39856257, year = {2025}, author = {Gulakhmadov, A and Chen, X and Gulahmadov, N and Rizwan, M and Gulakhmadov, M and Nadeem, MU and Rakhimova, M and Liu, T}, title = {Modeling of historical and future changes in temperature and precipitation in the Panj River Basin in Central Asia under the CMIP5 RCP and CMIP6 SSP scenarios.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {3037}, pmid = {39856257}, issn = {2045-2322}, support = {42150410393//Research Fund for International Scientists of the National Natural Science Foundation of China/ ; 42150410393//Research Fund for International Scientists of the National Natural Science Foundation of China/ ; 42150410393//Research Fund for International Scientists of the National Natural Science Foundation of China/ ; 2023000137//Tianshan Talent Training Program of Xinjiang Uygur Autonomous region/ ; 2023000137//Tianshan Talent Training Program of Xinjiang Uygur Autonomous region/ ; 42230708/42361144887//National Natural Science Foundation of China/ ; 42230708/42361144887//National Natural Science Foundation of China/ ; GJTD-2020-14//K.C. Wong Education Foundation/ ; GJTD-2020-14//K.C. Wong Education Foundation/ ; HZXM20225001MI//Joint CAS-MPG Research Project/ ; HZXM20225001MI//Joint CAS-MPG Research Project/ ; }, abstract = {This study examines the complexities of climate modeling, specifically in the Panj River Basin (PRB) in Central Asia, to evaluate the transition from CMIP5 to CMIP6 models. The research aimed to identify differences in historical simulations and future predictions of rainfall and temperature, examining the accuracy of eight General Circulation Models (GCMs) used in both CMIP5 (RCP4.5 and 8.5) and CMIP6 (SSP2-4.5 and 5-8.5). The evaluation metrics demonstrated that the GCMs have a high level of accuracy in reproducing maximum temperature (Tmax) with a correlation coefficient of 0.96. The models also performed well in replicating minimum temperature (Tmin) with a correlation coefficient of 0.94. This suggests that the models have improved modeling capabilities in both CMIPs. The performance of Max Plank Institute (MPI) across all variables in CMIP6 models was exceptional. Within the CMIP5 domain, Geophysical Fluid Dynamics (GFDL) demonstrated outstanding skill in reproducing maximum temperature (Tmax) and precipitation (KGE 0.58 and 0.34, respectively), while (Institute for Numerical Mathematics) INMCM excelled in replicating minimum temperature (Tmin) (KGE 0.28). The uncertainty analysis revealed a significant improvement in the CMIP6 precipitation bias bands, resulting in a more precise depiction of diverse climate zones compared to CMIP5. Both CMIPs consistently tended to underestimate Tmax in the Csa zone and overestimate it in the Bwk zone throughout all months. Nevertheless, the CMIP6 models demonstrated a significant decrease in uncertainty, especially in ensemble simulations, suggesting improvements in forecasting PRB climate dynamics. The projections revealed a complex story, as the CMIP6 models predict a relatively small increase in temperature and a simultaneous drop in precipitation. This indicates a trend towards more uniform temperature patterns across different areas. Nevertheless, the precipitation forecasts exhibited increased variability, highlighting the intricate interaction of climate dynamics in the PRB area under the impact of global warming scenarios. Hydrological components in global climate models can be further improved and developed with the theoretical reference provided by this study.}, } @article {pmid39854555, year = {2025}, author = {Zhou, J and Johnson, VC and Shi, J and Tan, ML and Zhang, F}, title = {Multi-scenario land use change simulation and spatial-temporal evolution of carbon storage in the Yangtze River Delta region based on the PLUS-InVEST model.}, journal = {PloS one}, volume = {20}, number = {1}, pages = {e0316255}, doi = {10.1371/journal.pone.0316255}, pmid = {39854555}, issn = {1932-6203}, mesh = {China ; *Rivers ; *Conservation of Natural Resources/methods ; *Carbon/metabolism/analysis ; Models, Theoretical ; Carbon Sequestration ; Ecosystem ; Spatio-Temporal Analysis ; Computer Simulation ; Humans ; Agriculture/methods ; }, abstract = {Influenced by urban expansion, population growth, and various socio-economic activities, land use in the Yangtze River Delta (YRD) area has undergone prominent changes. Modifications in land use have resulted in adjustments to ecological structures, leading to subsequent fluctuations in carbon storage. This study focuses on YRD region and analyzes the characteristics of land use changes in the area using land use data from 2000 to 2020, with a 10-year interval. Utilizing InVEST Model's Carbon Storage module in combination with PLUS model (patch-generating land use simulation), we simulated and projected future land use patterns and carbon storage across YRD region under five scenarios including natural development (ND), urban development (UD), ecological protection (EP), cropland protection (CP), and balanced development (BD). Upon comparing carbon storage levels predicted for 2030 under the five scenarios with those in 2020, carbon stocks decrease in the initial four scenarios and then increase in the fifth scenario. In the initial four declining scenarios, CP scenario had the least reduction in carbon storage, followed by EP scenario. The implementation of policies aimed at safeguarding cropland and preserving ecological integrity can efficaciously curtail the expansion of developed land into woodland and cropland, enhance the structure of land use, and mitigate the loss of carbon storage.}, } @article {pmid39854538, year = {2025}, author = {Katchali, M and Richard, E and Tonnang, HEZ and Tanga, CM and Beesigamukama, D and Senagi, K}, title = {Mathematical and computational modeling for organic and insect frass fertilizer production: A systematic review.}, journal = {PloS one}, volume = {20}, number = {1}, pages = {e0292418}, doi = {10.1371/journal.pone.0292418}, pmid = {39854538}, issn = {1932-6203}, mesh = {*Fertilizers/analysis ; Animals ; *Insecta ; Models, Theoretical ; Agriculture/methods ; Computer Simulation ; }, abstract = {Organic fertilizers have been identified as a sustainable agricultural practice that can enhance productivity and reduce environmental impact. Recently, the European Union defined and accepted insect frass as an innovative and emerging organic fertilizer. In the wider domain of organic fertilizers, mathematical and computational models have been developed to optimize their production and application conditions. However, with the advancement in policies and regulations, modelling has shifted towards efficiencies in the deployment of these technologies. Therefore, this paper reviews and critically analyzes the recent developments in the mathematical and computation modeling that have promoted various organic fertilizer products including insect frass. We reviewed a total of 35 studies and discussed the methodologies, benefits, and challenges associated with the use of these models. The results show that mathematical and computational modeling can improve the efficiency and effectiveness of organic fertilizer production, leading to improved agricultural productivity and reduced environmental impact. Mathematical models such as simulation, regression, dynamics, and kinetics have been applied while computational data driven machine learning models such as random forest, support vector machines, gradient boosting, and artificial neural networks have also been applied as well. These models have been used in quantifying nutrients concentration/release, effects of nutrients in agro-production, and fertilizer treatment. This paper also discusses prospects for the use of these models, including the development of more comprehensive and accurate models and integration with emerging technologies such as Internet of Things.}, } @article {pmid39853577, year = {2025}, author = {Pierrat, ZA and Magney, TS and Richardson, WP and Runkle, BRK and Diehl, JL and Yang, X and Woodgate, W and Smith, WK and Johnston, MR and Ginting, YRS and Koren, G and Albert, LP and Kibler, CL and Morgan, BE and Barnes, M and Uscanga, A and Devine, C and Javadian, M and Meza, K and Julitta, T and Tagliabue, G and Dannenberg, MP and Antala, M and Wong, CYS and Santos, ALD and Hufkens, K and Marrs, JK and Stovall, AEL and Liu, Y and Fisher, JB and Gamon, JA and Cawse-Nicholson, K}, title = {Proximal remote sensing: an essential tool for bridging the gap between high-resolution ecosystem monitoring and global ecology.}, journal = {The New phytologist}, volume = {}, number = {}, pages = {}, doi = {10.1111/nph.20405}, pmid = {39853577}, issn = {1469-8137}, support = {//National Research Council Postdoctoral Research Associateship Program/ ; 2020/37/B/ST10/01213//National Science Centre of Poland/ ; //TVL E-13 work contract at the Climate Monitoring Group of the University of Bonn/ ; //The LEMONTREE project by E. Schmidt and W. Schmidt/ ; 1926090//National Science Foundation/ ; 2044818//National Science Foundation/ ; 2131853//National Science Foundation/ ; IOS-2005574 OPP-2023205//National Science Foundation/ ; 80NSSC20K1805/NASA/NASA/United States ; 80NSSC21K1002/NASA/NASA/United States ; 80NSSC21K1639/NASA/NASA/United States ; 80NSSC21K1707/NASA/NASA/United States ; 80NSSC23K0109/NASA/NASA/United States ; 80NSSC23K0309/NASA/NASA/United States ; 80NSSC24K0135/NASA/NASA/United States ; NNH20ZDA001N-BIODIV/NASA/NASA/United States ; DE190101182//Australian Research Council/ ; }, abstract = {A new proliferation of optical instruments that can be attached to towers over or within ecosystems, or 'proximal' remote sensing, enables a comprehensive characterization of terrestrial ecosystem structure, function, and fluxes of energy, water, and carbon. Proximal remote sensing can bridge the gap between individual plants, site-level eddy-covariance fluxes, and airborne and spaceborne remote sensing by providing continuous data at a high-spatiotemporal resolution. Here, we review recent advances in proximal remote sensing for improving our mechanistic understanding of plant and ecosystem processes, model development, and validation of current and upcoming satellite missions. We provide current best practices for data availability and metadata for proximal remote sensing: spectral reflectance, solar-induced fluorescence, thermal infrared radiation, microwave backscatter, and LiDAR. Our paper outlines the steps necessary for making these data streams more widespread, accessible, interoperable, and information-rich, enabling us to address key ecological questions unanswerable from space-based observations alone and, ultimately, to demonstrate the feasibility of these technologies to address critical questions in local and global ecology.}, } @article {pmid39843543, year = {2025}, author = {Gioiosa, S and Gasparini, S and Presutti, C and Rinaldi, A and Castrignanò, T and Mannironi, C}, title = {Integrated gene expression and alternative splicing analysis in human and mouse models of Rett syndrome.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {2778}, pmid = {39843543}, issn = {2045-2322}, support = {GJC22071//Cariplo Telethon Alliance/ ; }, mesh = {*Rett Syndrome/genetics ; Humans ; Animals ; *Alternative Splicing ; Mice ; *Disease Models, Animal ; *Methyl-CpG-Binding Protein 2/genetics/metabolism ; Gene Expression Profiling ; Gene Expression Regulation ; Computational Biology/methods ; Mutation ; }, abstract = {Mutations of the MECP2 gene lead to Rett syndrome (RTT), a rare developmental disease causing severe intellectual and physical disability. How the loss or defective function of MeCP2 mediates RTT is still poorly understood. MeCP2 is a global gene expression regulator, acting at transcriptional and post-transcriptional levels. Little attention has been given so far to the contribution of alternative splicing (AS) dysregulation to RTT pathophysiology. To perform a comparative analysis of publicly available RNA sequencing (RNA-seq) studies and generate novel data resources for AS, we explored 100 human datasets and 130 mouse datasets from Mecp2-mutant models, processing data for gene expression and alternative splicing. Our comparative analysis across studies indicates common species-specific differentially expressed genes (DEGs) and differentially alternatively spliced (DAS) genes. Human and mouse dysregulated genes are involved in two main functional categories: cell-extracellular matrix adhesion regulation and synaptic functions, the first category more significantly enriched in human datasets. Our extensive bioinformatics study indicates, for the first time, a significant dysregulation of AS in human RTT datasets, suggesting the crucial contribution of altered RNA processing to the pathophysiology of RTT.}, } @article {pmid39841777, year = {2025}, author = {Cardoso, ADRO and Ferreira, ACG and Rabahi, MF}, title = {Asthma-related deaths in Brazil: data from an ecological study.}, journal = {Jornal brasileiro de pneumologia : publicacao oficial da Sociedade Brasileira de Pneumologia e Tisilogia}, volume = {50}, number = {6}, pages = {e20240296}, doi = {10.36416/1806-3756/e20240296}, pmid = {39841777}, issn = {1806-3756}, mesh = {Humans ; Brazil/epidemiology ; *Asthma/mortality/epidemiology ; Male ; Female ; Middle Aged ; Adult ; *Hospitalization/statistics & numerical data ; Young Adult ; Adolescent ; Child ; Sex Distribution ; Age Distribution ; Child, Preschool ; Aged ; Infant ; Sex Factors ; Age Factors ; Cause of Death ; Time Factors ; }, abstract = {OBJECTIVE: The aim of this study was to present epidemiological data on hospitalizations and deaths related to asthma in Brazil over the past 11 years.

METHODS: An ecological study was conducted on asthma-related hospitalizations and mortality in Brazil from 2013 to 2023, using data extracted from the Department of Informatics of the Brazilian Unified Health System and the Mortality Information System.

RESULTS: Asthma-related deaths showed an increasing trend during the analyzed period. A surge in deaths was observed in 2022 compared to 2014 (difference between means = 56.08 ± 19.7; 95% CI = 15.2-96.9). The mean number of deaths was higher among females, with their rate remaining stable, while the rate for males increased. Individuals aged >60 years accounted for approximately 65% of all asthma-related deaths from 2013 to 2023, with a strong direct correlation observed between age and the number of deaths, regardless of sex. During the same period, the total number of asthma-related hospitalizations in Brazil showed a declining trend, decreasing from 134,322 in 2013 to 87,707 in 2023.

CONCLUSION: Over the past 11 years, asthma-related deaths have increased in Brazil, with the majority occurring among females. Older individuals accounted for most asthma-related deaths, and a positive correlation was observed between age and the number of deaths.}, } @article {pmid39840283, year = {2024}, author = {Yan, B and Nam, Y and Li, L and Deek, RA and Li, H and Ma, S}, title = {Recent advances in deep learning and language models for studying the microbiome.}, journal = {Frontiers in genetics}, volume = {15}, number = {}, pages = {1494474}, pmid = {39840283}, issn = {1664-8021}, abstract = {Recent advancements in deep learning, particularly large language models (LLMs), made a significant impact on how researchers study microbiome and metagenomics data. Microbial protein and genomic sequences, like natural languages, form a language of life, enabling the adoption of LLMs to extract useful insights from complex microbial ecologies. In this paper, we review applications of deep learning and language models in analyzing microbiome and metagenomics data. We focus on problem formulations, necessary datasets, and the integration of language modeling techniques. We provide an extensive overview of protein/genomic language modeling and their contributions to microbiome studies. We also discuss applications such as novel viromics language modeling, biosynthetic gene cluster prediction, and knowledge integration for metagenomics studies.}, } @article {pmid39838963, year = {2024}, author = {Guan, J and Ji, Y and Peng, C and Zou, W and Tang, X and Shang, J and Sun, Y}, title = {GOPhage: protein function annotation for bacteriophages by integrating the genomic context.}, journal = {Briefings in bioinformatics}, volume = {26}, number = {1}, pages = {}, doi = {10.1093/bib/bbaf014}, pmid = {39838963}, issn = {1477-4054}, support = {11209823//City University of Hong Kong/ ; }, mesh = {*Bacteriophages/genetics ; *Genome, Viral ; *Molecular Sequence Annotation ; *Viral Proteins/genetics/metabolism ; Genomics/methods ; Computational Biology/methods ; Software ; }, abstract = {Bacteriophages are viruses that target bacteria, playing a crucial role in microbial ecology. Phage proteins are important in understanding phage biology, such as virus infection, replication, and evolution. Although a large number of new phages have been identified via metagenomic sequencing, many of them have limited protein function annotation. Accurate function annotation of phage proteins presents several challenges, including their inherent diversity and the scarcity of annotated ones. Existing tools have yet to fully leverage the unique properties of phages in annotating protein functions. In this work, we propose a new protein function annotation tool for phages by leveraging the modular genomic structure of phage genomes. By employing embeddings from the latest protein foundation models and Transformer to capture contextual information between proteins in phage genomes, GOPhage surpasses state-of-the-art methods in annotating diverged proteins and proteins with uncommon functions by 6.78% and 13.05% improvement, respectively. GOPhage can annotate proteins lacking homology search results, which is critical for characterizing the rapidly accumulating phage genomes. We demonstrate the utility of GOPhage by identifying 688 potential holins in phages, which exhibit high structural conservation with known holins. The results show the potential of GOPhage to extend our understanding of newly discovered phages.}, } @article {pmid39558756, year = {2025}, author = {Paris, JR and King, RA and Ferrer Obiol, J and Shaw, S and Lange, A and Bourret, V and Hamilton, PB and Rowe, D and Laing, LV and Farbos, A and Moore, K and Urbina, MA and van Aerle, R and Catchen, JM and Wilson, RW and Bury, NR and Santos, EM and Stevens, JR}, title = {The Genomic Signature and Transcriptional Response of Metal Tolerance in Brown Trout Inhabiting Metal-Polluted Rivers.}, journal = {Molecular ecology}, volume = {34}, number = {1}, pages = {e17591}, pmid = {39558756}, issn = {1365-294X}, support = {BB/K003240/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; //University of Exeter/ ; WT097835MF/WT_/Wellcome Trust/United Kingdom ; Charityno.1135007,Companyno.06545646//Westcountry Rivers Trust, UK/ ; WT101650MA/WT_/Wellcome Trust/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; //Environment Agency, UK/ ; }, mesh = {*Genome ; *Transcription, Genetic/drug effects ; *Adaptation, Physiological/drug effects/genetics ; *Rivers ; *Water Pollutants, Chemical/toxicity ; *Salmon/genetics/physiology ; Gene Expression Profiling ; Gene Expression Regulation/drug effects ; *Metals/toxicity ; United Kingdom ; Genetic Loci ; Gene Library ; Metagenomics ; Organ Specificity/drug effects ; Gene Ontology ; Animals ; }, abstract = {Industrial pollution is a major driver of ecosystem degradation, but it can also act as a driver of contemporary evolution. As a result of intense mining activity during the Industrial Revolution, several rivers across the southwest of England are polluted with high concentrations of metals. Despite the documented negative impacts of ongoing metal pollution, brown trout (Salmo trutta L.) survive and thrive in many of these metal-impacted rivers. We used population genomics, transcriptomics, and metal burdens to investigate the genomic and transcriptomic signatures of potential metal tolerance. RADseq analysis of six populations (originating from three metal-impacted and three control rivers) revealed strong genetic substructuring between impacted and control populations. We identified selection signatures at 122 loci, including genes related to metal homeostasis and oxidative stress. Trout sampled from metal-impacted rivers exhibited significantly higher tissue concentrations of cadmium, copper, nickel and zinc, which remained elevated after 11 days in metal-free water. After depuration, we used RNAseq to quantify gene expression differences between metal-impacted and control trout, identifying 2042 differentially expressed genes (DEGs) in the gill, and 311 DEGs in the liver. Transcriptomic signatures in the gill were enriched for genes involved in ion transport processes, metal homeostasis, oxidative stress, hypoxia, and response to xenobiotics. Our findings reveal shared genomic and transcriptomic pathways involved in detoxification, oxidative stress responses and ion regulation. Overall, our results demonstrate the diverse effects of metal pollution in shaping both neutral and adaptive genetic variation, whilst also highlighting the potential role of constitutive gene expression in promoting metal tolerance.}, } @article {pmid39833495, year = {2025}, author = {Akar, SE and Nwachukwu, W and Adewuyi, OS and Ahumibe, AA and Akanimo, I and Okunromade, O and Babatunde, O and Ihekweazu, C and Hitachi, M and Kato, K and Takamatsu, Y and Hirayama, K and Kaneko, S}, title = {Epidemiology of Yellow Fever in Nigeria: Analysis of Climatic, Ecological, Socio-Demographic, and Clinical Factors Associated with Viral Positivity Among Suspected Cases Using National Surveillance Data, 2017-2023.}, journal = {Journal of epidemiology and global health}, volume = {15}, number = {1}, pages = {2}, pmid = {39833495}, issn = {2210-6014}, mesh = {Humans ; Nigeria/epidemiology ; *Yellow Fever/epidemiology ; Male ; Female ; Adolescent ; Retrospective Studies ; Adult ; Middle Aged ; Young Adult ; Child ; Child, Preschool ; Infant ; Climate ; Disease Outbreaks/statistics & numerical data ; Yellow fever virus ; Risk Factors ; Socioeconomic Factors ; Sociodemographic Factors ; Population Surveillance/methods ; }, abstract = {BACKGROUND: Since its resurgence in 2017, Yellow fever (YF) outbreaks have continued to occur in Nigeria despite routine immunization and the implementation of several reactive mass vaccinations. Nigeria, Africa's most populous endemic country, is considered a high-priority country for implementing the End Yellow fever Epidemics strategy.

METHODS: This retrospective analysis described the epidemiological profile, trends, and factors associated with Yellow fever viral positivity in Nigeria. We conducted a multivariable binary logistic regression analysis to identify factors associated with YF viral positivity.

RESULTS: Of 16,777 suspected cases, 8532(50.9%) had laboratory confirmation with an overall positivity rate of 6.9%(585). Predictors of YFV positivity were the Jos Plateau, Derived/Guinea Savanah, and the Freshwater/Lowland rainforest compared to the Sahel/Sudan Savannah; dry season compared to rainy season; the hot dry or humid compared to the temperate, dry cool/humid climatic zone; 2019, 2020, 2021, 2022, and 2023 epidemic years compared to compared to 2017; first, third, and fourth quarters compared to the second; male sex compared to female; age group > = 15 years compared to < 15 years; working in outdoor compared to indoor settings; having traveled within the last two weeks; being of unknown vaccination status compared to being vaccinated; and vomiting.

CONCLUSION: Ecological, climatic, and socio-demographic characteristics are drivers of YF outbreaks in Nigeria, and public health interventions need to target these factors to halt local epidemics and reduce the risk of international spread. Inadequate vaccination coverage alone may not account for the recurrent outbreaks of YF in Nigeria.}, } @article {pmid39833104, year = {2024}, author = {Liu, F and Zhao, Z and Liu, Y}, title = {PHPGAT: predicting phage hosts based on multimodal heterogeneous knowledge graph with graph attention network.}, journal = {Briefings in bioinformatics}, volume = {26}, number = {1}, pages = {}, doi = {10.1093/bib/bbaf017}, pmid = {39833104}, issn = {1477-4054}, support = {62303193//National Natural Science Foundation of China/ ; 20230101064JC//Natural Science Foundation of Jilin Province, China/ ; }, mesh = {*Bacteriophages/genetics ; Algorithms ; Software ; Computational Biology/methods ; Host-Pathogen Interactions/genetics ; Bacteria/virology/genetics ; Phage Therapy ; }, abstract = {Antibiotic resistance poses a significant threat to global health, making the development of alternative strategies to combat bacterial pathogens increasingly urgent. One such promising approach is the strategic use of bacteriophages (or phages) to specifically target and eradicate antibiotic-resistant bacteria. Phages, being among the most prevalent life forms on Earth, play a critical role in maintaining ecological balance by regulating bacterial communities and driving genetic diversity. Accurate prediction of phage hosts is essential for successfully applying phage therapy. However, existing prediction models may not fully encapsulate the complex dynamics of phage-host interactions in diverse microbial environments, indicating a need for improved accuracy through more sophisticated modeling techniques. In response to this challenge, this study introduces a novel phage-host prediction model, PHPGAT, which leverages a multimodal heterogeneous knowledge graph with the advanced GATv2 (Graph Attention Network v2) framework. The model first constructs a multimodal heterogeneous knowledge graph by integrating phage-phage, host-host, and phage-host interactions to capture the intricate connections between biological entities. GATv2 is then employed to extract deep node features and learn dynamic interdependencies, generating context-aware embeddings. Finally, an inner product decoder is designed to compute the likelihood of interaction between a phage and host pair based on the embedding vectors produced by GATv2. Evaluation results using two datasets demonstrate that PHPGAT achieves precise phage host predictions and outperforms other models. PHPGAT is available at https://github.com/ZhaoZMer/PHPGAT.}, } @article {pmid39832988, year = {2025}, author = {Shimels, T and Kantelhardt, EJ and Assefa, M and Fenta, TG}, title = {Spatiotemporal dynamics and prevention strategies of cervical cancer incidence in Addis Ababa, Ethiopia: an ecological study.}, journal = {BMJ open}, volume = {15}, number = {1}, pages = {e089521}, doi = {10.1136/bmjopen-2024-089521}, pmid = {39832988}, issn = {2044-6055}, mesh = {Humans ; Ethiopia/epidemiology ; *Uterine Cervical Neoplasms/epidemiology/prevention & control ; Female ; Incidence ; Adult ; Middle Aged ; *Spatio-Temporal Analysis ; Young Adult ; Bayes Theorem ; Aged ; Geographic Information Systems ; Adolescent ; Papillomavirus Vaccines ; }, abstract = {OBJECTIVE: This study analysed the spatial and temporal patterns of cervical cancer incidence in Addis Ababa from 2012 to 2021.

DESIGN: An ecological study was conducted from 1 September to 30 November 2023 to examine the spatiotemporal trends of cervical cancer incidence.

SETTING: The research was conducted in Addis Ababa, the capital city of Ethiopia.

PARTICIPANTS: Included were all patients with clinically and/or histopathologically confirmed diagnoses of cervical cancer.

DATA ANALYSIS: The study employed advanced analytical tools including R programming, Quantum Geographic Information System V.3.36.0, GeoDa V.1.2.2 and System for Automated Geoscientific Analyses GIS V.9.3.2. Techniques such as Bayesian empirical testing with a block weighting matrix for hotspot identification, Global Moran's I for spatial autocorrelation, nearest neighbour imputation and universal Kriging interpolation were used to manage data gaps. Joinpoint trend analysis and direct age-standardised incidence rate (ASIR) using the Segi's World standard population was applied to compare trends across subcities. A statistical significance threshold was set at p<0.05.

RESULTS: Between 2012 and 2021, a total of 2435 new cervical cancer cases were recorded in the Addis Ababa City Population-based Cancer Registry, with significant spatial clustering observed in Nifas Silk Lafto, Bole, Kirkos as well as parts of Gulele and Yeka sub cities (z score>1.96) in 2018. The citywide age-standardised incidence rate varied from 19 to 26 cases per 100 000 women-years during 2013 and 2016, respectively. Subcity trends varied significantly, with increases and decreases noted in Akaki Kality and Kolfe Keraniyo over different periods while Bole subcity showed modest increase at 4.2% APC (95% CI: 0.6% to 7.9%; p=0.026).

CONCLUSION: The study highlights substantial fluctuations in ASIR and significant geographic disparities in cervical cancer throughout Addis Ababa. To address these challenges, the implementation of school-based human papillomavirus vaccination programmes, alongside targeted interventions, active campaigns and sustained surveillance, is critical. These strategies are essential to effectively reduce the cervical cancer burden and improve health outcomes in the community.}, } @article {pmid39832144, year = {2024}, author = {Ištoňová, M and Dorko, E and Knap, V and Stehlíková, B and Murgová, A and Ondová, P and Rimárová, K}, title = {Assessment of depressive disorders and states of anxiety in patients following cerebrovascular accidents in connection with health care provision.}, journal = {Central European journal of public health}, volume = {32}, number = {Supplement}, pages = {18-24}, pmid = {39832144}, issn = {1210-7778}, mesh = {Humans ; Female ; Male ; Middle Aged ; Aged ; Slovakia/epidemiology ; Aged, 80 and over ; *Stroke/epidemiology/psychology ; Anxiety/epidemiology ; Depressive Disorder/epidemiology ; Surveys and Questionnaires ; Depression/epidemiology ; Anxiety Disorders/epidemiology ; }, abstract = {OBJECTIVE: Anxiety and depression in patients following cerebrovascular accidents are among frequently occurring complications of the medical condition. The consequences affect personal, family, professional, and social life. They cause severe functional and cognitive impairments, limit the ability to perform normal daily activities, which can result in complete disability. The aim of the study was to monitor the occurrence of anxiety and depression in patients following cerebrovascular accidents hospitalized in neurological departments in the region of eastern Slovakia.

METHODS: A total of 101 patients following cerebrovascular accidents, aged from 48-86 years, were included in the descriptive study. Demographic and clinical data were obtained from patients and from medical records. We determined the occurrence of anxiety disorders, depression and emotional distress in patients following cerebrovascular accidents using a standardized Hospital Anxiety and Depression Scale (HADS) questionnaire.

RESULTS: Data analysis confirms a high incidence of anxiety in the HADS-A subscale (9.23 ± 4.13) and depression in the HADS-D subscale (9.09 ± 4.43) during the hospitalization phase of the disease. It demonstrates the pathological occurrence of anxiety states in 37%, depression in 36%, emotional distress in 36%, and a serious degree of combination of pathological values of the anxiety subscale and the depression subscale in 27% of patients. The existence of a strong positive correlation between anxiety and depression indicators was confirmed.

CONCLUSION: The results confirm a high prevalence of anxiety and depression in the acute phase of the disease. The findings indicate that patients recovering from cerebrovascular accidents not only face physical difficulties and loss of independence but also struggle with anxiety and depression, which can negatively impact and slow their recovery. Given the high frequency of these psychological conditions, further research is needed to enhance the quality and effectiveness of care provided to patients with cerebrovascular accidents.}, } @article {pmid39832137, year = {2025}, author = {Iobbi, V and Parisi, V and Giacomini, M and De Riccardis, F and Brun, P and Núñez-Pons, L and Drava, G and Giordani, P and Monti, MC and Poggi, R and Murgia, Y and De Tommasi, N and Bisio, A}, title = {Sesterterpenoids: sources, structural diversity, biological activity, and data management.}, journal = {Natural product reports}, volume = {}, number = {}, pages = {}, doi = {10.1039/d4np00041b}, pmid = {39832137}, issn = {1460-4752}, abstract = {Reviewing the literature published up to October 2024.Sesterterpenoids are one of the most chemically diverse and biologically promising subgroup of terpenoids, the largest family of secondary metabolites. The present review article summarizes more than seven decades of studies on isolation and characterization of more than 1600 structurally novel sesterterpenoids, supplemented by biological, pharmacological, ecological, and geographic distribution data. All the information have been implemented in eight tables available on the web and a relational database https://sesterterpenoids.unige.net/. The interface has two sections, one open to the public for reading only and the other, protected by an authentication mechanism, for timely updating of published results.}, } @article {pmid39830898, year = {2025}, author = {Gartler, S and Scheer, J and Meyer, A and Abass, K and Bartsch, A and Doloisio, N and Falardeau, J and Hugelius, G and Irrgang, A and Haukur Ingimundarson, J and Jungsberg, L and Lantuit, H and Nymand Larsen, J and Lodi, R and Martin, VS and Mercer, L and Nielsen, D and Overduin, P and Povoroznyuk, O and Rautio, A and Schweitzer, P and Speetjens, NJ and Tomaškovičová, S and Timlin, U and Vanderlinden, JP and Vonk, J and Westerveld, L and Ingeman-Nielsen, T}, title = {A transdisciplinary, comparative analysis reveals key risks from Arctic permafrost thaw.}, journal = {Communications earth & environment}, volume = {6}, number = {1}, pages = {21}, doi = {10.1038/s43247-024-01883-w}, pmid = {39830898}, issn = {2662-4435}, abstract = {Permafrost thaw poses diverse risks to Arctic environments and livelihoods. Understanding the effects of permafrost thaw is vital for informed policymaking and adaptation efforts. Here, we present the consolidated findings of a risk analysis spanning four study regions: Longyearbyen (Svalbard, Norway), the Avannaata municipality (Greenland), the Beaufort Sea region and the Mackenzie River Delta (Canada) and the Bulunskiy District of the Sakha Republic (Russia). Local stakeholders' and scientists' perceptions shaped our understanding of the risks as dynamic, socionatural phenomena involving physical processes, key hazards, and societal consequences. Through an inter- and transdisciplinary risk analysis based on multidirectional knowledge exchanges and thematic network analysis, we identified five key hazards of permafrost thaw. These include infrastructure failure, disruption of mobility and supplies, decreased water quality, challenges for food security, and exposure to diseases and contaminants. The study's novelty resides in the comparative approach spanning different disciplines, environmental and societal contexts, and the transdisciplinary synthesis considering various risk perceptions.}, } @article {pmid39826720, year = {2025}, author = {Akhoon, BA and Qiao, Q and Stewart, A and Chen, J and Rodriguez Lopez, CM and Corbin, KR}, title = {Pangenomic analysis of the bacterial cellulose-producing genera Komagataeibacter and Novacetimonas.}, journal = {International journal of biological macromolecules}, volume = {}, number = {}, pages = {139980}, doi = {10.1016/j.ijbiomac.2025.139980}, pmid = {39826720}, issn = {1879-0003}, abstract = {Bacterial cellulose (BC) holds significant commercial potential due to its unique structural and chemical properties, making it suitable for applications in electronics, medicine, and pharmaceuticals. However, large-scale BC production remains limited by challenges in bacterial performance. In this study, we compared 79 microbial genomes from three genera-Komagataeibacter, Novacetimonas, and Gluconacetobacter-to investigate their pangenomes, genetic diversity, and evolutionary relationships. Through comparative genomic and phylogenetic analyses, we identified distinct genome compositions and evolutionary patterns that differ from previous reports. The role of horizontal gene transfer (HGT) in shaping the genetic diversity and adaptability of these bacteria was also explored. Key determinants in BC production, such as variations in the bacterial cellulose biosynthesis (bcs) operon, carbohydrate uptake genes, and carbohydrate-active enzymes, were examined. Additionally, several biosynthetic gene clusters (BGCs), including Linocin M18 and sactipeptides, which encode for antimicrobial peptides known as bacteriocins, were identified. These findings reveal new aspects of the genetic diversity in cellulose-producing bacteria and present a comprehensive genomic toolkit that will support future efforts to optimize BC production and improve microbial performance for commercial applications.}, } @article {pmid39817434, year = {2025}, author = {Blum, J and Brüll, M and Hengstler, JG and Dietrich, DR and Gruber, AJ and Dipalo, M and Kraushaar, U and Mangas, I and Terron, A and Fritsche, E and Marx-Stoelting, P and Hardy, B and Schepky, A and Escher, S and Hartung, T and Landsiedel, R and Odermatt, A and Sachana, M and Koch, K and Dönmez, A and Masjosthusmann, S and Bothe, K and Schildknecht, S and Beilmann, M and Beltman, JB and Fitzpatrick, S and Mangerich, A and Rehm, M and Tangianu, S and Zickgraf, FM and Kamp, H and Burger, G and van de Water, B and Kleinstreuer, N and White, A and Leist, M}, title = {The long way from raw data to NAM-based information: Overview on data layers and processing steps.}, journal = {ALTEX}, volume = {42}, number = {1}, pages = {167-180}, doi = {10.14573/altex.2412171}, pmid = {39817434}, issn = {1868-8551}, abstract = {Toxicological test methods generate raw data and provide instructions on how to use these to determine a final outcome such as a classification of test compounds as hits or non-hits. The data processing pipeline provided in the test method description is often highly complex. Usually, multiple layers of data, ranging from a machine-generated output to the final hit definition, are considered. Transition between each of these layers often requires several data processing steps. As changes in any of these processing steps can impact the final output of new approach methods (NAMs), the processing pipeline is an essential part of a NAM description and should be included in reporting templates such as the ToxTemp. The same raw data, processed in different ways, may result in different final outcomes that may affect the readiness status and regulatory acceptance of the NAM, as an altered output can affect robustness, performance, and relevance. Data management, pro­cessing, and interpretation are therefore important elements of a comprehensive NAM definition. We aim to give an overview of the most important data levels to be considered during the devel­opment and application of a NAM. In addition, we illustrate data processing and evaluation steps between these data levels. As NAMs are increasingly standard components of the spectrum of toxi­cological test methods used for risk assessment, awareness of the significance of data processing steps in NAMs is crucial for building trust, ensuring acceptance, and fostering the reproducibility of NAM outcomes.}, } @article {pmid39652873, year = {2025}, author = {Naderian, M and Norland, K and Schaid, DJ and Kullo, IJ}, title = {Development and Evaluation of a Comprehensive Prediction Model for Incident Coronary Heart Disease Using Genetic, Social, and Lifestyle-Psychological Factors: A Prospective Analysis of the UK Biobank.}, journal = {Annals of internal medicine}, volume = {178}, number = {1}, pages = {1-10}, doi = {10.7326/ANNALS-24-00716}, pmid = {39652873}, issn = {1539-3704}, mesh = {Humans ; Male ; United Kingdom/epidemiology ; Middle Aged ; *Coronary Disease/epidemiology ; Female ; Prospective Studies ; Risk Assessment ; *Life Style ; Risk Factors ; Incidence ; Social Determinants of Health ; Machine Learning ; UK Biobank ; }, abstract = {BACKGROUND: Clinical risk calculators for coronary heart disease (CHD) do not include genetic, social, and lifestyle-psychological risk factors.

OBJECTIVE: To improve CHD risk prediction by developing and evaluating a prediction model that incorporated a polygenic risk score (PRS) and a polysocial score (PSS), the latter including social determinants of health and lifestyle-psychological factors.

DESIGN: Cohort study.

SETTING: United Kingdom.

PARTICIPANTS: UK Biobank participants recruited between 2006 and 2010.

MEASUREMENTS: Incident CHD (myocardial infarction and/or coronary revascularization); 10-year clinical risk based on pooled cohort equations (PCE), Predicting Risk of cardiovascular disease EVENTs (PREVENT), and QRISK3; PRS (Polygenic Score Catalog identification: PGS000018) for CHD (PRSCHD); and PSSCHD from 100 related covariates. Machine-learning and time-to-event analyses and model performance indices.

RESULTS: In 388 224 participants (age, 55.5 [SD, 8.1] years; 42.5% men; 94.9% White), the hazard ratio for 1 SD increase in PSSCHD for incident CHD was 1.43 (95% CI, 1.38 to 1.49; P < 0.001) and for 1 SD increase in PRSCHD was 1.59 (CI, 1.53 to 1.66, P < 0.001). Non-White persons had higher PSSCHD than White persons. The effects of PSSCHD and PRSCHD on CHD were independent and additive. At a 10-year CHD risk threshold of 7.5%, adding PSSCHD and PRSCHD to PCE reclassified 12% of participants, with 1.86 times higher CHD risk in the up- versus down-reclassified persons and showed superior performance compared with PCE as reflected by improved net benefit while maintaining good calibration relative to the clinical risk calculators. Similar results were seen when incorporating PSSCHD and PRSCHD into PREVENT and QRISK3.

LIMITATION: A predominantly White cohort; possible healthy participant effect and ecological fallacy.

CONCLUSION: A PSSCHD was associated with incident CHD and its joint modeling with PRSCHD improved the performance of clinical risk calculators.

PRIMARY FUNDING SOURCE: National Human Genome Research Institute.}, } @article {pmid39830091, year = {2023}, author = {Boyes, D and Eljounaidi, K and , and , and , and , and , and , }, title = {The genome sequence of the Beautiful Golden Y, Autographa pulchrina (Haworth, 1809).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {375}, doi = {10.12688/wellcomeopenres.19840.1}, pmid = {39830091}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual female Autographa pulchrina (the Beautiful Golden Y; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 426.2 megabases in span. Most of the assembly is scaffolded into 32 chromosomal pseudomolecules, including the Z and W sex chromosomes. The mitochondrial genome has also been assembled and is 15.25 kilobases in length. Gene annotation of this assembly on Ensembl identified 12,916 protein coding genes.}, } @article {pmid39825388, year = {2025}, author = {Burthe, SJ and Kumbar, B and Schäfer, SM and Purse, BV and Vanak, AT and Balakrishnan, N and Hassall, R and Hoti, SL and Narayanaswamy, D and Potadar, S and Rahman, M and Chanda, MM}, title = {First evidence of transovarial transmission of Kyasanur Forest disease virus in Haemaphysalis and Rhipicephalus ticks in the wild.}, journal = {Parasites & vectors}, volume = {18}, number = {1}, pages = {14}, pmid = {39825388}, issn = {1756-3305}, support = {MR/T029846/1//Global Challenges Research Fund/ ; MR/T029846/1//Global Challenges Research Fund/ ; MR/T029846/1//Global Challenges Research Fund/ ; MR/T029846/1//Global Challenges Research Fund/ ; MR/T029846/1//Global Challenges Research Fund/ ; MR/P024335/1//Global Challenges Research Fund/ ; MR/T029846/1//Global Challenges Research Fund/ ; MR/T029846/1//Global Challenges Research Fund/ ; MR/T029846/1//Global Challenges Research Fund/ ; MR/P024335/1//Global Challenges Research Fund/ ; MR/T029846/1//Global Challenges Research Fund/ ; MR/T029846/1//Global Challenges Research Fund/ ; }, mesh = {Animals ; Female ; *Encephalitis Viruses, Tick-Borne/physiology/isolation & purification/genetics ; *Kyasanur Forest Disease/transmission/virology ; India/epidemiology ; *Larva/virology ; *Rhipicephalus/virology ; *Ixodidae/virology ; Arachnid Vectors/virology ; }, abstract = {BACKGROUND: Kyasanur forest disease virus (KFDV) is a tick-borne flavivirus causing debilitating and potentially fatal disease in people in the Western Ghats region of India. The transmission cycle is complex, involving multiple vector and host species, but there are significant gaps in ecological knowledge. Empirical data on pathogen-vector-host interactions and incrimination have not been updated since the last century, despite significant local changes in land use and the expansion of KFD to new areas. Mathematical models predict that transovarial transmission, whereby adult female ticks pass KFDV infections to their offspring, plays an important role in the persistence of KFD, but this has not been shown in the wild. Here we set out to establish whether transovarial transmission of KFDV was occurring under natural field conditions by assessing whether host-seeking larvae were positive for KFDV.

METHODS: Ticks were sampled by dragging and flagging across a broad range of habitats within the agro-forest matrix at 49 sites in two districts: Shivamogga, Karnataka and Wayanad, Kerala (September 2018-March 2019), and larvae were tested for KFDV by PCR.

RESULTS: In total, larval ticks from 7 of the 49 sites sampled tested positive for KFDV, indicating that transovarial transmission is occurring. Of the 13 KFDV-positive larval samples, 3 came from around houses and gardens, 5 from crops (3 from harvested rice paddy and 2 from areca plantation), 1 from teak plantation and 4 (2 from 1 transect) from forests. Five different tick species were found to have KFDV-positive larvae: Haemaphysalis spinigera, H. bispinosa, Rhipicephalus annulatus, R. microplus and an unidentifiable species of Haemaphysalis (no close match in GenBank).

CONCLUSIONS: Our empirical confirmation of transovarial transmission has important implications for understanding and predicting KFD dynamics, suggesting that ticks may act as a reservoir for KFDV. Moreover, small mammals and cattle may play crucial roles in transmission if small mammals are the main hosts for larvae infected via transovarial transmission, and cattle support large numbers of infected female adult ticks. This first report of transovarial transmission of KFDV, and within a hitherto undescribed range of vectors and habitats, will help disease managers improve KFD surveillance and mitigation strategies, ultimately leading to communities becoming more resilient to the risk of this tick-transmitted disease.}, } @article {pmid39441382, year = {2025}, author = {Canzler, S and Schubert, K and Rolle-Kampczyk, UE and Wang, Z and Schreiber, S and Seitz, H and Mockly, S and Kamp, H and Haake, V and Huisinga, M and Bergen, MV and Buesen, R and Hackermüller, J}, title = {Evaluating the performance of multi-omics integration: a thyroid toxicity case study.}, journal = {Archives of toxicology}, volume = {99}, number = {1}, pages = {309-332}, pmid = {39441382}, issn = {1432-0738}, support = {C5 - XomeTox//European Chemical Industry Council/ ; 101057014//HORIZON EUROPE Framework Programme/ ; }, mesh = {Animals ; *Thyroid Gland/drug effects/pathology ; *Propylthiouracil/toxicity ; Rats ; Metabolomics ; Proteomics ; Transcriptome/drug effects ; Male ; Genomics ; Risk Assessment ; Female ; Antithyroid Agents/toxicity ; Rats, Sprague-Dawley ; Proteome/metabolism ; Multiomics ; }, abstract = {Multi-omics data integration has been repeatedly discussed as the way forward to more comprehensively cover the molecular responses of cells or organisms to chemical exposure in systems toxicology and regulatory risk assessment. In Canzler et al. (Arch Toxicol 94(2):371-388. https://doi.org/10.1007/s00204-020-02656-y), we reviewed the state of the art in applying multi-omics approaches in toxicological research and chemical risk assessment. We developed best practices for the experimental design of multi-omics studies, omics data acquisition, and subsequent omics data integration. We found that multi-omics data sets for toxicological research questions were generally rare, with no data sets comprising more than two omics layers adhering to these best practices. Due to these limitations, we could not fully assess the benefits of different data integration approaches or quantitatively evaluate the contribution of various omics layers for toxicological research questions. Here, we report on a multi-omics study on thyroid toxicity that we conducted in compliance with these best practices. We induced direct and indirect thyroid toxicity through Propylthiouracil (PTU) and Phenytoin, respectively, in a 28-day plus 14-day recovery oral rat toxicity study. We collected clinical and histopathological data and six omics layers, including the long and short transcriptome, proteome, phosphoproteome, and metabolome from plasma, thyroid, and liver. We demonstrate that the multi-omics approach is superior to single-omics in detecting responses at the regulatory pathway level. We also show how combining omics data with clinical and histopathological parameters facilitates the interpretation of the data. Furthermore, we illustrate how multi-omics integration can hint at the involvement of non-coding RNAs in post-transcriptional regulation. Also, we show that multi-omics facilitates grouping, and we assess how much information individual and combinations of omics layers contribute to this approach.}, } @article {pmid39822595, year = {2024}, author = {Boyes, D and , and , and , and , and , and , and , }, title = {The genome sequence of the Poplar Grey moth, Subacronicta megacephala (Denis & Schiffermüller, 1775).}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {696}, doi = {10.12688/wellcomeopenres.23371.1}, pmid = {39822595}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual male Subacronicta megacephala (Poplar Grey moth; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence has a total length of 424.20 megabases. Most of the assembly (99.02%) is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.35 kilobases in length. Gene annotation of this assembly on Ensembl identified 18,189 protein-coding genes.}, } @article {pmid39822261, year = {2025}, author = {Proença Neto, MA and De Sousa, MPA}, title = {Pytaxon: A Python software for resolving and correcting taxonomic names in biodiversity data.}, journal = {Biodiversity data journal}, volume = {13}, number = {}, pages = {e138257}, doi = {10.3897/BDJ.13.e138257}, pmid = {39822261}, issn = {1314-2828}, abstract = {BACKGROUND: The standardisation and correction of taxonomic names in large biodiversity databases remain persistent challenges for researchers, as errors in species names can compromise ecological analyses, land-use planning and conservation efforts, particularly when inaccurate data are shared on global biodiversity portals.

NEW INFORMATION: We present pytaxon, a Python software designed to resolve and correct taxonomic names in biodiversity data by leveraging the Global Names Verifier (GNV) API and employing fuzzy matching techniques to suggest corrections for discrepancies and nomenclatural inconsistencies. The pytaxon offers both a Command Line Interface (CLI) and a Graphical User Interface (GUI), ensuring accessibility to users with different levels of computing expertise. Tests on spreadsheets derived from datasets published in the Global Biodiversity Information Facility (GBIF) demonstrated its effectiveness in identifying and resolving taxonomic errors. By mitigating the propagation of inaccuracies from researchers' datasets to global biodiversity databases, pytaxon supports more reliable conservation decisions and robust scientific investigations. Its contributions enhance data integrity and promote informed biodiversity management in a rapidly evolving global environment.}, } @article {pmid39821365, year = {2025}, author = {Zhang, D and Cai, Y and Sun, Y and Zeng, P and Wang, W and Wang, W and Jiang, X and Lian, Y}, title = {A Real-World Disproportionality Analysis of Histamine H2-Receptors Antagonists (Famotidine): A Pharmacovigilance Study Based on Spontaneous Reports in the FDA Adverse Event Reporting System.}, journal = {Drug development research}, volume = {86}, number = {1}, pages = {e70045}, doi = {10.1002/ddr.70045}, pmid = {39821365}, issn = {1098-2299}, support = {//This study was funded by the National Natural Science Foundation of China (Grant No: 82303109), the Natural Science Foundation of Fujian Province, China (Grant No: 2022J05299), Cross-Strait Postdoctoral Exchange Funding Program of Fujian Province, China (Grant No: 2021B002)./ ; }, mesh = {Humans ; *Famotidine/adverse effects ; *Adverse Drug Reaction Reporting Systems/statistics & numerical data ; United States/epidemiology ; *Histamine H2 Antagonists/adverse effects ; *Pharmacovigilance ; *United States Food and Drug Administration ; Female ; Male ; Adult ; Middle Aged ; Aged ; Adolescent ; Young Adult ; Child ; Child, Preschool ; Drug-Related Side Effects and Adverse Reactions/epidemiology ; Databases, Factual ; Infant ; }, abstract = {Famotidine is an H2 receptor antagonist and is currently used on a large scale in gastroenterology. However, Famotidine may also cause severe toxicity to organ systems, including the blood system, digestive system, and urinary system. The objective of this study was to scientifically and systematically investigate the adverse events (AEs) of Famotidine in the real world through the FDA Adverse Event Reporting System (FAERS) database. A disproportionality analysis was used to quantify the signals of AEs associated with Famotidine in FAERS data from the first quarter of 2004 to the first quarter of 2023. The clinical features, onset time, oral and intravenous administration and severe consequences of Famotidine induced AEs were further analyzed. Among the four tests, we found several AEs that were not mentioned in the drug label. For example, abdominal pain upper, abdominal discomfort, dyspepsia, liver disorder, gastrooesophageal reflux disease, and rhabdomyolysis. These AEs are consistent with the drug instructions. Interestingly, we found several unreported AEs, such as: cerebral infarction, hypocalcaemia, hallucination, visual, hypomagnesaemia, hypoparathyroidism, diabetes insipidus, vulvovaginal candidiasis, retro-orbital neoplasm, neuroblastoma recurrent, and malignant cranial nerve neoplasm. Most of our findings are consistent with clinical observations and drug labels, and we also found possible new and unexpected AEs signals, which suggest the need for prospective clinical studies to confirm these results and explain their relationships. Our findings provide valuable evidence for further safety studies.}, } @article {pmid39423319, year = {2025}, author = {Tian, Y and Yang, L and Ding, S and Zhang, D and Yuan, L and Liu, Z and Hu, QN}, title = {BioTRY: A Comprehensive Knowledge Base for Titer, Rate, and Yield of Biosynthesis.}, journal = {ACS synthetic biology}, volume = {14}, number = {1}, pages = {285-289}, doi = {10.1021/acssynbio.4c00347}, pmid = {39423319}, issn = {2161-5063}, mesh = {*Synthetic Biology/methods ; *Knowledge Bases ; Databases, Factual ; Software ; Computational Biology/methods ; }, abstract = {Synthetic biology is rapidly evolving into a data-intensive science that increasingly relies on massive data sets; one of its applications is the evaluation of the economic viability of fermentation processes. However, the key economic indicators, namely titer, rate, and yield (TRY), which respectively reflect the downstream processing, reactor size, and raw material costs, are not well captured in bioinformatics databases. In this paper, we present BioTRY, an intuitive and user-friendly tool that contains >5,000 biochemicals and >3,800 strains, along with over 52,000 corresponding TRY entries with original references. It is freely available at http://www.synbiohealth.cn/biotry. To our knowledge, BioTRY is the first available database on biosynthesis TRY data from original research. We anticipate that BioTRY will become a useful tool that aids researchers and decision-makers in understanding the current development state of biosynthesis and allows them to foresee potential prospects and applications for biosynthesis.}, } @article {pmid38383603, year = {2025}, author = {Nevers, Y and Warwick Vesztrocy, A and Rossier, V and Train, CM and Altenhoff, A and Dessimoz, C and Glover, NM}, title = {Quality assessment of gene repertoire annotations with OMArk.}, journal = {Nature biotechnology}, volume = {43}, number = {1}, pages = {124-133}, pmid = {38383603}, issn = {1546-1696}, mesh = {*Software ; *Molecular Sequence Annotation ; *Proteome/genetics ; Animals ; Databases, Protein ; Genomics/methods ; }, abstract = {In the era of biodiversity genomics, it is crucial to ensure that annotations of protein-coding gene repertoires are accurate. State-of-the-art tools to assess genome annotations measure the completeness of a gene repertoire but are blind to other errors, such as gene overprediction or contamination. We introduce OMArk, a software package that relies on fast, alignment-free sequence comparisons between a query proteome and precomputed gene families across the tree of life. OMArk assesses not only the completeness but also the consistency of the gene repertoire as a whole relative to closely related species and reports likely contamination events. Analysis of 1,805 UniProt Eukaryotic Reference Proteomes with OMArk demonstrated strong evidence of contamination in 73 proteomes and identified error propagation in avian gene annotation resulting from the use of a fragmented zebra finch proteome as a reference. This study illustrates the importance of comparing and prioritizing proteomes based on their quality measures.}, } @article {pmid39814778, year = {2025}, author = {Gómez-Gras, D and Linares, C and Viladrich, N and Zentner, Y and Grinyó, J and Gori, A and McFadden, CS and Fabricius, KE and Madin, JS}, title = {The Octocoral Trait Database: a global database of trait information for octocoral species.}, journal = {Scientific data}, volume = {12}, number = {1}, pages = {82}, pmid = {39814778}, issn = {2052-4463}, mesh = {*Anthozoa/classification ; Animals ; *Databases, Factual ; *Coral Reefs ; Biodiversity ; Ecosystem ; }, abstract = {Trait-based approaches are revolutionizing our understanding of high-diversity ecosystems by providing insights into the principles underlying key ecological processes, such as community assembly, species distribution, resilience, and the relationship between biodiversity and ecosystem functioning. In 2016, the Coral Trait Database advanced coral reef science by centralizing trait information for stony corals (i.e., Subphylum Anthozoa, Class Hexacorallia, Order Scleractinia). However, the absence of trait data for soft corals, gorgonians, and sea pens (i.e., Class Octocorallia) limits our understanding of ecosystems where these organisms are significant members and play pivotal roles. To address this gap, we introduce the Octocoral Trait Database, a global, open-source database of curated trait data for octocorals. This database houses species- and individual-level data, complemented by contextual information that provides a relevant framework for analyses. The inaugural dataset, OctocoralTraits v2.2, contains over 97,500 global trait observations across 98 traits and over 3,500 species. The database aims to evolve into a steadily growing, community-led resource that advances future marine science, with a particular emphasis on coral reef research.}, } @article {pmid39813953, year = {2025}, author = {Knight, ME and Farkas, K and Wade, M and Webster, G and Pass, DA and Perry, W and Kille, P and Singer, A and Jones, DL}, title = {Wastewater-based analysis of antimicrobial resistance at UK airports: Evaluating the potential opportunities and challenges.}, journal = {Environment international}, volume = {195}, number = {}, pages = {109260}, doi = {10.1016/j.envint.2025.109260}, pmid = {39813953}, issn = {1873-6750}, abstract = {With 40 million annual passenger flights, airports are key hubs for microbial communities from diverse geographic origins to converge, mix, and distribute. Wastewater derived from airports and aircraft represent both a potential route for the global dispersion of antimicrobial resistant (AMR) organisms and an under-utilised resource for strengthening global AMR surveillance. This study investigates the abundance and diversity of antimicrobial resistance genes (ARGs) in wastewater samples collected from airport terminals (n = 132), aircraft (n = 25), and a connected wastewater treatment plant (n = 11) at three international airports in the UK (London Heathrow, Edinburgh and Bristol). A total of 76 ARGs were quantified using high throughput qPCR (HT-qPCR) while a subset of samples (n = 30) was further analysed by metagenomic sequencing. Our findings reveal that aircraft wastewater resistomes were compositionally distinct from those observed at airport terminals, despite their similar diversity. Notably, flights originating from Asia and Africa carried a higher number of unique ARGs compared to those from Europe and North America. However, clustering of the ARG profile displayed no overall association with geography. Edinburgh terminal and pumping station wastewater had compositionally comparable resistomes to that of the connected urban wastewater treatment plant, though further research is needed to determine the relative contributions of the local population and international travellers. This study provides the first comprehensive investigation of AMR in wastewater from both aircraft and terminals across multiple international airports. Our results highlight aircraft wastewater as a potential route for cross-border AMR transmission and a valuable tool for global AMR surveillance. However, the findings also underscore the limitations and need for standardised approaches for AMR monitoring in airport environments, to effectively mitigate the global spread of AMR and enhance public health surveillance strategies.}, } @article {pmid39813347, year = {2025}, author = {Gu, S and Shao, Z and Qu, Z and Zhu, S and Shao, Y and Zhang, D and Allen, R and He, R and Shao, J and Xiong, G and Jousset, A and Friman, VP and Wei, Z and Kümmerli, R and Li, Z}, title = {Siderophore synthetase-receptor gene coevolution reveals habitat- and pathogen-specific bacterial iron interaction networks.}, journal = {Science advances}, volume = {11}, number = {3}, pages = {eadq5038}, doi = {10.1126/sciadv.adq5038}, pmid = {39813347}, issn = {2375-2548}, mesh = {*Iron/metabolism ; *Siderophores/metabolism ; *Evolution, Molecular ; Ecosystem ; Pseudomonas/genetics/metabolism ; Bacterial Proteins/genetics/metabolism ; Genome, Bacterial ; Ligases/metabolism/genetics ; Humans ; Computational Biology/methods ; Bacterial Outer Membrane Proteins ; Receptors, Cell Surface ; }, abstract = {Bacterial social interactions play crucial roles in various ecological, medical, and biotechnological contexts. However, predicting these interactions from genome sequences is notoriously difficult. Here, we developed bioinformatic tools to predict whether secreted iron-scavenging siderophores stimulate or inhibit the growth of community members. Siderophores are chemically diverse and can be stimulatory or inhibitory depending on whether bacteria have or lack corresponding uptake receptors. We focused on 1928 representative Pseudomonas genomes and developed an experimentally validated coevolution algorithm to match encoded siderophore synthetases to corresponding receptor groups. We derived community-level iron interaction networks to show that siderophore-mediated interactions differ across habitats and lifestyles. Specifically, dense networks of siderophore sharing and competition were observed among environmental and nonpathogenic species, while small, fragmented networks occurred among human-associated and pathogenic species. Together, our sequence-to-ecology approach empowers the analyses of social interactions among thousands of bacterial strains and offers opportunities for targeted intervention to microbial communities.}, } @article {pmid39809329, year = {2025}, author = {Amino, K and Hirakawa, T and Yago, M and Matsuo, T}, title = {Dorsoventral comparison of intraspecific variation in the butterfly wing pattern using a convolutional neural network.}, journal = {Biology letters}, volume = {21}, number = {1}, pages = {20240446}, doi = {10.1098/rsbl.2024.0446}, pmid = {39809329}, issn = {1744-957X}, support = {//ACT-X/ ; //Japan Society for the Promotion of Science/ ; }, mesh = {Animals ; *Butterflies/anatomy & histology/genetics ; *Wings, Animal/anatomy & histology ; *Neural Networks, Computer ; *Sex Characteristics ; Male ; Female ; Species Specificity ; Biological Mimicry ; }, abstract = {Butterfly wing patterns exhibit notable differences between the dorsal and ventral surfaces, and morphological analyses of them have provided insights into the ecological and behavioural characteristics of wing patterns. Conventional methods for dorsoventral comparisons are constrained by the need for homologous patches or shared features between two surfaces, limiting their applicability across species. We used a convolutional neural network (CNN)-based analysis, which can compare images of the two surfaces without focusing on homologous patches or features, to detect dorsoventral bias in two types of intraspecific variation: sexual dimorphism and mimetic polymorphism. Using specimen images of 29 species, we first showed that the level of sexual dimorphism calculated by CNN-based analysis corresponded well with traditional assessments of sexual dissimilarity, demonstrating the validity of the method. Dorsal biases were widely detected in sexual dimorphism, suggesting that the conventional hypothesis of dorsally biased sexual selection can be supported in a broader range of species. In contrast, mimetic polymorphism showed no such bias, indicating the importance of both surfaces in mimicry. Our study demonstrates the potential versatility of CNN in comparing wing patterns between the two surfaces, while elucidating the relationship between dorsoventrally different selections and dorsoventral biases in intraspecific variations.}, } @article {pmid39807382, year = {2024}, author = {Smith, SD and Geraghty, EM and Rivas, AL and Fasina, FO and Kosoy, M and Malania, L and Hoogesteijn, AL and Fair, JM}, title = {Multidimensional perspectives of geo-epidemiology: from interdisciplinary learning and research to cost-benefit oriented decision-making.}, journal = {Frontiers in public health}, volume = {12}, number = {}, pages = {1492426}, pmid = {39807382}, issn = {2296-2565}, mesh = {Humans ; *Cost-Benefit Analysis ; *Decision Making ; Epidemiology/education ; Geographic Information Systems ; Learning ; }, abstract = {Research typically promotes two types of outcomes (inventions and discoveries), which induce a virtuous cycle: something suspected or desired (not previously demonstrated) may become known or feasible once a new tool or procedure is invented and, later, the use of this invention may discover new knowledge. Research also promotes the opposite sequence-from new knowledge to new inventions. This bidirectional process is observed in geo-referenced epidemiology-a field that relates to but may also differ from spatial epidemiology. Geo-epidemiology encompasses several theories and technologies that promote inter/transdisciplinary knowledge integration, education, and research in population health. Based on visual examples derived from geo-referenced studies on epidemics and epizootics, this report demonstrates that this field may extract more (geographically related) information than simple spatial analyses, which then supports more effective and/or less costly interventions. Actual (not simulated) bio-geo-temporal interactions (never captured before the emergence of technologies that analyze geo-referenced data, such as geographical information systems) can now address research questions that relate to several fields, such as Network Theory. Thus, a new opportunity arises before us, which exceeds research: it also demands knowledge integration across disciplines as well as novel educational programs which, to be biomedically and socially justified, should demonstrate cost-effectiveness. Grounded on many bio-temporal-georeferenced examples, this report reviews the literature that supports this hypothesis: novel educational programs that focus on geo-referenced epidemic data may help generate cost-effective policies that prevent or control disease dissemination.}, } @article {pmid39806613, year = {2024}, author = {Shen, A and Ye, J and Zhao, H and Qiang, W and Zhao, H and Huang, Y and Zhou, Y and Wang, Y and Li, X and Zhang, Z and Bian, J and Zhang, L and Wu, P and Wang, Y and Lu, Q}, title = {Risk factors and prediction model of breast cancer-related lymphoedema in a Chinese cancer centre: a prospective cohort study protocol.}, journal = {BMJ open}, volume = {14}, number = {12}, pages = {e089769}, doi = {10.1136/bmjopen-2024-089769}, pmid = {39806613}, issn = {2044-6055}, mesh = {Humans ; Female ; Prospective Studies ; China/epidemiology ; Risk Factors ; *Breast Neoplasms/complications/surgery ; *Breast Cancer Lymphedema/epidemiology/etiology ; Incidence ; Risk Assessment ; Middle Aged ; Adult ; Lymphedema/epidemiology/etiology ; Research Design ; East Asian People ; }, abstract = {INTRODUCTION: Lymphoedema is a distressing and long-term complication for breast cancer survivors. However, the reported incidence of lymphoedema varies, and its risk factors remain underexplored. Currently, a well-established risk prediction model is still lacking. This study aims to describe the rationale, objectives, protocol and baseline characteristics of a prospective cohort study focused on examining the incidence and risk factors of breast cancer-related lymphoedema (BCRL), as well as developing a risk prediction model.

METHODS AND ANALYSIS: This study is an ongoing single-centre prospective observational cohort study recruiting 1967 patients with breast cancer scheduled for surgery treatment in northern China between 15 February 2022 and 21 June 2023. Assessments will be conducted presurgery and at 1, 3, 6, 12, 18, 24, 30 and 36 months postsurgery. Bilateral limb circumferences will be measured by patients at home or by researchers at the outpatient clinics during follow-up visits. The diagnosis of lymphoedema is based on a relative limb volume increase of ≥10% from the preoperative assessment. Self-reported symptoms will be assessed to assist in diagnosis. Potential risk factors are classified into innate personal traits, behavioural lifestyle, interpersonal networks, socioeconomic status and macroenvironmental factors, based on health ecology model. Data collection, storage and management were conducted using the online 'H6WORLD' data management platform. Survival analysis using the Kaplan-Meier estimate will determine the incidence of BCRL. Risk factors of BCRL will be analysed using log-rank test and COX-LASSO regression. Traditional COX regression analysis and seven common survival analysis machine learning algorithms (COX, CARST, RSF, GBSM, XGBS, SSVM and SANN) will be employed for model construction and validation.

ETHICS AND DISSEMINATION: The study protocol was approved by the Biomedical Ethics Committee of Peking University (IRB00001052-21124) and the Research Ethics Committee of Tianjin Medical University Cancer Institute and Hospital (bc2023013). The results of this study will be published in peer-reviewed journals and will be presented at several research conferences.

TRIAL REGISTRATION NUMBER: ChiCTR2200057083.}, } @article {pmid39671935, year = {2025}, author = {Paulukonis, EA and Purucker, ST}, title = {Spatiotemporally derived agricultural field delineations for species effects assessments and environmental decision support.}, journal = {The Science of the total environment}, volume = {958}, number = {}, pages = {177967}, doi = {10.1016/j.scitotenv.2024.177967}, pmid = {39671935}, issn = {1879-1026}, mesh = {*Agriculture/methods ; *Environmental Monitoring/methods ; Crops, Agricultural ; Pesticides/analysis ; Risk Assessment/methods ; Decision Support Techniques ; United States ; Geographic Information Systems ; Ecosystem ; }, abstract = {Rural landscapes are strongly defined by the spatial distribution of agricultural fields. GIS layers that capture this information have much utility in many decision support contexts, particularly with regards to the intersection of agricultural pesticide use and endangered species habitat. The United States Department of Agriculture's Cropland Data Layer (CDL) is a georeferenced, annual resource that often serves a crucial role in pesticide risk-related decision support applications. However, CDL agriculture timeseries data are not mapped to explicit field boundaries, contributing to increased uncertainty regarding differentiated crop type spatial homogeneity and geographic extent, inherently adding complexity to multi-temporal crop monitoring and analyses efforts. We describe the development and testing of an approach for field delineation based on timeseries information from the 2008-2021 CDL at spatial scales relevant for endangered species risk assessment. We validate and test the approach against quantitative crop information and contextualize the outputs as part of a case study reconstructing past agricultural pesticide exposures to non-target species to demonstrate the utility of the method for ecological risk assessment decision support. The approach resulted in delineated field unit boundaries that effectively incorporated the unmodified CDL crop type generalized spatial distribution patterns; derived metrics closely corresponded with reported crop metrics for landscapes with proportionally significant agriculture use. When modified to reflect areas of mixed/small crop acreages, the method can provide a useful framework for large-scale field delineation of the CDL, which can complement ongoing environmental risk assessment and conservation efforts in agricultural landscapes.}, } @article {pmid39584487, year = {2025}, author = {Daru, BH}, title = {A global database of butterfly species native distributions.}, journal = {Ecology}, volume = {106}, number = {1}, pages = {e4462}, doi = {10.1002/ecy.4462}, pmid = {39584487}, issn = {1939-9170}, support = {2345994//National Science Foundation/ ; 2416314//National Science Foundation/ ; }, mesh = {*Butterflies/physiology ; Animals ; *Animal Distribution ; Databases, Factual ; Species Specificity ; Ecosystem ; }, abstract = {Butterflies represent a diverse group of insects, playing key ecosystem roles such as pollination and their larval form engage in herbivory. Despite their importance, comprehensive global distribution data for butterfly species are lacking. This lack of comprehensive global data has hindered many large-scale questions in ecology, evolutionary biology, and conservation at the regional and global scales. Here, I use an integrative workflow that combines occurrence records, alpha hull polygons, species' dispersal capacity, and natural habitat and environmental variables within a framework of species distribution models to generate species-level native distributions for butterflies at a global scale in the contemporary period. The database releases native range maps for 10,372 extant species of butterflies at a spatial grain resolution of 5 arcmin (~10 km). This database has the potential to allow unprecedented large-scale analyses in ecology, biogeography, and conservation of butterflies. The maps are available in the WGS84 coordinate reference system (EPSG:4326 code) and stored as vector polygons in the GEOPACKAGE format for maximum compression, allowing easy data manipulation using a standard computer. I additionally provide each species' spatial raster. All maps and R scripts are open access and available for download in Dryad and Zenodo, respectively, and are guided by FAIR (Findable, Accessible, Interoperable, and Reusable) data principles. By making these data available to the scientific community, I aim to advance the sharing of biological data to stimulate more comprehensive research in ecology, biogeography, and conservation of butterflies.}, } @article {pmid39805953, year = {2025}, author = {Daruka, L and Czikkely, MS and Szili, P and Farkas, Z and Balogh, D and Grézal, G and Maharramov, E and Vu, TH and Sipos, L and Juhász, S and Dunai, A and Daraba, A and Számel, M and Sári, T and Stirling, T and Vásárhelyi, BM and Ari, E and Christodoulou, C and Manczinger, M and Enyedi, MZ and Jaksa, G and Kovács, K and van Houte, S and Pursey, E and Pintér, L and Haracska, L and Kintses, B and Papp, B and Pál, C}, title = {ESKAPE pathogens rapidly develop resistance against antibiotics in development in vitro.}, journal = {Nature microbiology}, volume = {}, number = {}, pages = {}, pmid = {39805953}, issn = {2058-5276}, abstract = {Despite ongoing antibiotic development, evolution of resistance may render candidate antibiotics ineffective. Here we studied in vitro emergence of resistance to 13 antibiotics introduced after 2017 or currently in development, compared with in-use antibiotics. Laboratory evolution showed that clinically relevant resistance arises within 60 days of antibiotic exposure in Escherichia coli, Klebsiella pneumoniae, Acinetobacter baumannii and Pseudomonas aeruginosa, priority Gram-negative ESKAPE pathogens. Resistance mutations are already present in natural populations of pathogens, indicating that resistance in nature can emerge through selection of pre-existing bacterial variants. Functional metagenomics showed that mobile resistance genes to antibiotic candidates are prevalent in clinical bacterial isolates, soil and human gut microbiomes. Overall, antibiotic candidates show similar susceptibility to resistance development as antibiotics currently in use, and the corresponding resistance mechanisms overlap. However, certain combinations of antibiotics and bacterial strains were less prone to developing resistance, revealing potential narrow-spectrum antibacterial therapies that could remain effective. Finally, we develop criteria to guide efforts in developing effective antibiotic candidates.}, } @article {pmid39763978, year = {2024}, author = {Palma-Martínez, MJ and Posadas-García, YS and López-Ángeles, BE and Quiroz-López, C and Lewis, ACF and Bird, KA and Lasisi, T and Zaidi, AA and Sohail, M}, title = {The multi-scale complexity of human genetic variation beyond continental groups.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {39763978}, issn = {2692-8205}, support = {K99 HG012809/HG/NHGRI NIH HHS/United States ; R00 GM137076/GM/NIGMS NIH HHS/United States ; }, abstract = {Traditional clustering and visualization approaches in human genetics often operate under frameworks that assume inherent, discrete groupings[1,2]. These methods can inadvertently simplify multifaceted relationships, functioning to entrench the idea of typological groups[3]. We introduce a network-based pipeline and visualization tool grounded in relational thinking[4], which constructs networks from a variety of genetic similarity metrics. We identify communities at multiple resolutions, departing from typological models of analysis and interpretation that categorize individuals into a (predefined) number of sets. We applied our pipeline to a dataset merged from the 1000 Genomes and Human Genome Diversity Project[5], revealing the limitations of traditional groupings and capturing the complexities introduced by demographic events and evolutionary processes. This method embraces the context-specificity of genetic similarities that are salient depending on the question, markers of interest, and study individuals. Different numbers of communities are revealed depending on the resolution chosen and metric used, underscoring a fluid spectrum of genetic relationships and challenging the notion of universal categorization. We provide a web application (https://sohail-lab.shinyapps.io/GG-NC/) for interactive visualization and engagement with these intricate genetic landscapes.}, } @article {pmid39799926, year = {2025}, author = {Fridman, M and Krasko, O and Veyalkin, I}, title = {The incidence trends of papillary thyroid carcinoma in Belarus during the post-Chernobyl epoch.}, journal = {Cancer epidemiology}, volume = {95}, number = {}, pages = {102745}, doi = {10.1016/j.canep.2025.102745}, pmid = {39799926}, issn = {1877-783X}, abstract = {BACKGROUND: The increase of papillary thyroid cancer (PTC) rate among children who were exposed to post-Chernobyl 131-I release was reported only four years after the accident, first in Belarus where the heaviest fallout happened. The evolution of the occurrence of thyroid carcinoma based on the age-period-cohort analysis and the effects of age, period, and birth cohort on time trends aimed to reveal if post-Chernobyl follicular cells irradiation still has been impacting on incidence rate of papillary thyroid carcinoma nowadays.

METHODS: The Belarusian Cancer Registry was used to identify patients with PTC diagnosed during the years 1980-2019. The incidence trends were analysed using Join-point regression software.

RESULTS: The highest peak of age-specific incidence curve was shown during the years 1980-2001 in the age group of 15-19 years old that was associated also with short-latency cases of post-Chernobyl PTC. This is the same age group that demonstrated significant growth of the incidence rate during the years 2006-2019, largely because of the increasing number of non-exposed patients with PTC (p < 0.001). Influence of post-Chernobyl exposure also can be seen in the young adults age-groups of patients (for 20-24 years old during the years 1980-2003 and 2013-2019, p < 0.001; for 25-29 years old during the years 1980-1999 and 1999-2011, p < 0.001).

CONCLUSION: After the Chernobyl accident, epidemiological waves that reflect the age shift of the group of children exposed to 131-I have consistently emerged. Currently, the incidence rate continues to increase only in the cohort of patients aged 20-44 years.}, } @article {pmid39798660, year = {2025}, author = {Li, J and Lu, Y and Chen, X and Wang, L and Cao, Z and Lei, H and Zhang, Z and Wang, P and Sun, B}, title = {Seasonal variation of microbial community and diversity in the Taiwan Strait sediments.}, journal = {Environmental research}, volume = {}, number = {}, pages = {120809}, doi = {10.1016/j.envres.2025.120809}, pmid = {39798660}, issn = {1096-0953}, abstract = {Human activities and ocean currents in the Taiwan Strait exhibit significant seasonal variation, yet the response of marine microbes to ocean changes under anthropogenic and climatic stress remains unclear. Using 16S rRNA gene amplicon sequencing, we investigated the spatiotemporal dynamics and functional variations of microbial communities in sediment samples. Our findings revealed distinct seasonal patterns in microbial diversity and composition. Proteobacteria, Desulfobacterota, and Crenarchaeota dominated at the phylum level, while Candidatus Nitrosopumilus, Woeseia, and Subgroup 10 were prevalent at the genus level. Iron concentrations, heavy metals and C/N ratio were primary factors influencing microbial communities during specific seasons, whereas sulfur content, temperature fluctuations, and heavy metals shaped the entire microbial structure and diversity. Core microbial groups, including Desulfobulbus, Subgroup 10, Unidentified Latescibacterota, and Sumerlaea, played essential roles in regulating community structure and functional transitions. Marker species, such as Aliidiomarina sanyensis, Spirulina platensis, Croceimarina litoralis and Sulfuriflexus mobilis, acted as seasonal indicators. Bacteria exhibited survival strategy akin to higher organisms, encompassing process of synthesis, growth, dormancy, and disease resistance throughout the seasonal cycle. Core microbial groups and marker species in specific seasons can serve as indicators for monitoring and assessing the health of the Taiwan Strait ecosystem.}, } @article {pmid39794649, year = {2025}, author = {Mohammad, L and Bandyopadhyay, J and Mondal, I and Altuwaijri, HA and Khatun, S and Hossain, SKA and Juliev, M}, title = {Assessing cropping system dynamics over three decades: remote sensing and GIS insights in Murshidabad-Jiaganj Block.}, journal = {Environmental monitoring and assessment}, volume = {197}, number = {2}, pages = {164}, pmid = {39794649}, issn = {1573-2959}, mesh = {*Environmental Monitoring/methods ; *Remote Sensing Technology ; *Agriculture/methods ; *Geographic Information Systems ; Crops, Agricultural/growth & development ; Seasons ; }, abstract = {Agriculture is a significant contributor to the country's economic development. We used multiple Landsat images from 1990 to 2021 in the Murshidabad-Jiaganj Block to assess changes in the agricultural system and their underlying causes. The Rabi season saw a 10.99% growth in agrarian regions from 1990 to 2000 and an 8.86% increase in 2010, yet it declined by 28.12% in 2021. During the summer, the cultivated lands diminished by 26.63%, 19.43%, and 19.64%, while in the Kharif season, they declined by 21.78%, 15.68%, and 11.99% from 1990 in the years 2000, 2010, and 2021, respectively. The agricultural area had 36.82%, 34.16%, and 19.01% increases between 1990 and 2021, respectively. Regarding direction, farmland acreage decreased in all zones except the SSE, which had a 0.95% increase. Mono-, double-, and triple-cropping systems have decreased in area, while multi-cropping systems have experienced increases of 43.51%, 4.50%, and 18.49% in 1990-2021, respectively. The multi-cropping system has a good correlation with all agroclimatic factors. The reduction of irrigated lands post-2009 significantly affected the agriculture system. The fall in agricultural employment in recent decades is attributable to migration seeking higher-paying occupations. The advancement of accurate remote sensing-based modeling is crucial for mitigating food security risks, particularly those posed by climate change, and informing policy decisions.}, } @article {pmid39794678, year = {2025}, author = {Sasia, I and Bueno, G and Etxano, I}, title = {Amalur EIS: a system for calculating the environmental impacts of industrial sites from E-PRTR records.}, journal = {Environmental monitoring and assessment}, volume = {197}, number = {2}, pages = {163}, pmid = {39794678}, issn = {1573-2959}, support = {IT 1567-22 Ekopol Research Group (UPV/EHU)//Department of Education of the Basque Government/ ; IT 1567-22 Ekopol Research Group (UPV/EHU)//Department of Education of the Basque Government/ ; IT 1567-22 Ekopol Research Group (UPV/EHU)//Department of Education of the Basque Government/ ; }, mesh = {*Environmental Monitoring/methods ; Climate Change ; Environment ; Europe ; Databases, Factual ; Industry ; Environmental Pollutants/analysis ; Environmental Pollution/statistics & numerical data ; }, abstract = {This article presents Amalur EIS (https://www.amalur-eis.eus/), an Environmental Information System that estimates environmental impacts using data sourced from the European Pollutant Release and Transfer Register database (E-PRTR). The system uses data on the releases into land, air and water of 31,556 European industrial facilities for the period 2007-2021. Amalur EIS calculates environmental impacts of industrial releases using 31 life cycle impact assessment methods (LCIA) and covering 78 of the 91 pollutants regulated by the PRTR Protocol. The system has been constructed using a two-layer software infrastructure: (i) a data layer supported by a relational database built in Postgres and (ii) a presentation layer built in Tableau, so it provides user-friendly access to the information. For an illustrative analysis of the tool, the EF 3.0 LCIA method recommended by the European Commission was used, including normalisation and weighting steps for a better comparison. The analysis concludes that the climate change impact category contributes the most (68.6%) to the total impacts, while the largest contributor from an economic activity perspective is the energy sector (59.5%). Geographically, both elements coincide in the German regions of Düsseldorf, Köln and Brandenburg, resulting in the concentration of the largest impacts at the European regional level. In fact, Germany is the country with the highest impact (20.3% of total). Beyond this analysis, Amalur EIS is poised to be a valuable tool for tracking the transition towards sustainability, particularly in Europe.}, } @article {pmid39793033, year = {2025}, author = {Clauss, M and Roller, M and Bertelsen, MF and Rudolf von Rohr, C and Müller, DWH and Schiffmann, C and Kummrow, M and Encke, D and Ferreira, S and Duvall, ES and Maré, C and Abraham, AJ}, title = {Zoos must embrace animal death for education and conservation.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {122}, number = {1}, pages = {e2414565121}, doi = {10.1073/pnas.2414565121}, pmid = {39793033}, issn = {1091-6490}, support = {101062339//EC | Horizon Europe | Excellent Science | HORIZON EUROPE Marie Sklodowska-Curie Actions (MSCA)/ ; }, } @article {pmid39792995, year = {2025}, author = {Soeishi, T and Nakata, A and Nagata, T and Akutsu, S and Tondokoro, T and Inoue, Y and Katsumura, F and Kikunaga, K}, title = {Predicting depressive symptoms and psychological distress by circulating inflammatory mediators: A 16-month prospective study in Japanese white-collar employees.}, journal = {Journal of occupational and environmental medicine}, volume = {}, number = {}, pages = {}, doi = {10.1097/JOM.0000000000003307}, pmid = {39792995}, issn = {1536-5948}, abstract = {OBJECTIVE: Although increasing evidence suggests that depression/distress involves inflammatory processes, its potential sex differences and the temporal directions for this association remain elusive.

METHODS: We examined the temporal association between serum inflammatory mediators and depression/distress as measured by the Center for Epidemiologic Studies Depression Scale (CES-D) and the Kessler Psychological Distress Scale (K6), in non-depressed working men and women (n = 61 and 43, respectively) by a 16-month prospective design.

RESULTS: Fully-adjusted partial correlation analyses revealed that in men, a lower IFN-γ predicted subsequent increases in CES-D and K6 scores, while a higher TNF-α predicted increased K6 scores. In women, a higher IFN-γ predicted a subsequent increase in the CES-D score. CES-D and K6 scores did not predict inflammatory mediators at follow-up.

CONCLUSIONS: The finding suggests that inflammatory activation precedes depression/distress with distinct sex differences.}, } @article {pmid39792790, year = {2025}, author = {Kherroubi Garcia, I and Erdmann, C and Gesing, S and Barton, M and Cadwallader, L and Hengeveld, G and Kirkpatrick, CR and Knight, K and Lemmen, C and Ringuette, R and Zhan, Q and Harrison, M and Mac Gabhann, F and Meyers, N and Osborne, C and Till, C and Brenner, P and Buys, M and Chen, M and Lee, A and Papin, J and Rao, Y}, title = {Ten simple rules for good model-sharing practices.}, journal = {PLoS computational biology}, volume = {21}, number = {1}, pages = {e1012702}, doi = {10.1371/journal.pcbi.1012702}, pmid = {39792790}, issn = {1553-7358}, mesh = {*Information Dissemination/methods ; Humans ; *Computational Biology ; Computer Simulation ; }, abstract = {Computational models are complex scientific constructs that have become essential for us to better understand the world. Many models are valuable for peers within and beyond disciplinary boundaries. However, there are no widely agreed-upon standards for sharing models. This paper suggests 10 simple rules for you to both (i) ensure you share models in a way that is at least "good enough," and (ii) enable others to lead the change towards better model-sharing practices.}, } @article {pmid39789290, year = {2025}, author = {Sağlam, S and Özdemir, E and Özden, Ö and Makineci, E and Özkan, UY and Bingöl, D and Güzelçimen, F}, title = {The effects of some chemical compounds on the sound absorbing ability of tree bark.}, journal = {Biologia futura}, volume = {}, number = {}, pages = {}, pmid = {39789290}, issn = {2676-8607}, abstract = {Tree bark is an important natural polymer for sound absorption. The main components in the bark of different tree species are polymers with high molecular weight such as cellulose, hemicellulose, and lignin. The aim of this study is to determine the noise reduction coefficient (NRC), lignin, alcohol-benzene solubility (ABS), carbon (C), and nitrogen (N) contents in samples taken from the bark of different tree species-black locust (Robinia pseudoacacia), narrow-leaved ash (Fraxinus angustifolia), stone pine (Pinus pinea), silver lime (Tilia tomentosa), sweet chestnut (Castanea sativa), sessile oak (Quercus petraea), and maritime pine (Pinus pinaster) and to investigate the relationship between these chemical properties and sound absorption measurements. Tree species showed a statistically significant difference in terms of all measured variables. In the correlation matrix obtained as a result of the analysis, only ABS showed a significant and the highest positive correlation with the NRC, with a correlation coefficient of r = 0.812. ABS in bark is seen as the most important chemical factor regarding sound retention, indicating the abundance of extractives in barks of different tree species. An investigation into the relationship between sound retention and different extractive substance and contents of different extractive substances in bark is recommended for further studies.}, } @article {pmid39789035, year = {2025}, author = {Li, F and Xia, H and Miao, J and Yang, J}, title = {Changes of the ecological environment status in villages under the background of traditional village preservation: a case study in Enshi Tujia and Miao Autonomous Prefecture.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {1504}, pmid = {39789035}, issn = {2045-2322}, support = {42271318//National Natural Science Foundation of China/ ; }, mesh = {*Conservation of Natural Resources/methods ; *Ecosystem ; China ; Humans ; Rural Population ; Geographic Information Systems ; }, abstract = {The preservation of Chinese traditional villages plays a crucial role in promoting the sustainable development of rural natural, cultural, and ecological environments. It is also a key strategy for achieving rural revitalization. Current research on traditional villages predominantly focuses on the realm of cultural landscapes, with an emphasis on preserving the cultural ecological value of these communities. In comparison, discussions on the quality of the ecological environment of villages from the perspectives of natural environment, economic environment, and the social organizational environment within regional development are relatively scarce. Our study employed GIS and RS technology and refers to the Technical Criterion for Ecosystem Status Evaluation. Several sub-indices of the ecological environment status, including the biological richness index, vegetation coverage index, water network density index, and land stress index, were selected to construct an ecological environment assessment model. This model was used to analyze the spatial-temporal changes in the ecological environment status of each county, county-level city, and traditional village within the jurisdiction of Enshi Tujia and Miao Autonomous Prefecture and its surrounding areas from 2010 to 2020. The study quantitatively evaluated the ecological environment status of each county, county-level city, and village in Enshi before and after the implementation of traditional village preservation policies. Through comparative analysis, the study revealed the impact of these policies on the natural ecological environment of the study area. The results indicated the following: (1) From 2010 to 2020, the ecological index (EI) values in the villages of Enshi Prefecture exhibited a similar trend to the EI values in the respective counties and county-level cities they are located in, although significant differences in magnitude of change were observed. (2) The EI values in the counties, county-level cities, and villages demonstrated greater variation in the latter five years of the decade (2015-2020) compared to the previous five years (2010-2015). (3) In 2020, the EI value of the villages experienced more significant changes compared to 2010, whereas the overall EI value of the counties and county-level cities showed less pronounced changes. The findings of this study suggest that the traditional village preservation policies implemented in Enshi Prefecture have both positive and negative impacts on the ecological environment of the surrounding areas of protected villages, and these impacts become increasingly evident over time. By comparing and analyzing the ecological changes in the surrounding areas of traditional villages in Enshi Prefecture with the overall ecological changes in the respective counties and county-level cities, our study employs quantitative analytical methods to delve into the impact of traditional village conservation policies on the natural ecological environment. It assesses the effects of policy implementation on the natural ecological environment of traditional villages, analyzing both the positive and negative impacts brought about by the execution of these policies, with the aim of effectively guiding the natural ecological conditions of traditional villages towards a more healthy trajectory of development.}, } @article {pmid39788970, year = {2025}, author = {Sánchez-Jardón, L and Hernández de Diego, A and Mackenzie, R and Villodre, M and Arnaiz-Schmitz, C and Schmitz, MF and Acosta-Gallo, B}, title = {Bryophyte literature records database of Aysén, Chilean sub-Antarctic ecoregion.}, journal = {Scientific data}, volume = {12}, number = {1}, pages = {36}, pmid = {39788970}, issn = {2052-4463}, mesh = {*Bryophyta ; Chile ; *Biodiversity ; Antarctic Regions ; Ecosystem ; Databases, Factual ; }, abstract = {The Chilean sub-Antarctic ecoregion hosts the largest expanse of temperate forests, wetlands and peatlands, as well as the largest proportion of protected areas in the southern hemisphere. Bryophytes are highly diverse and ecologically essential in sub-Antarctic ecosystems and are considered as biodiversity loss indicators caused by the current socio-ecological crisis. However, knowledge about their biodiversity is rather limited. Integrating the available information on bryophyte diversity in regional platforms such as SIB-Aysén can be useful to acknowledge their ecological importance and remarkable biodiversity. This article integrates 345 records of 273 bryophyte taxa known in the region of Aysén and emphasizes the need to include citizen science as a tool to increase observations in lesser-known taxonomic groups.}, } @article {pmid39787642, year = {2024}, author = {Aanes, H and Vigeland, MD and Star, B and Gilfillan, GD and Mattingsdal, M and Trøan, S and Strand, M and Eide, LM and Hanssen, EN}, title = {Heating up three cold cases in Norway using investigative genetic genealogy.}, journal = {Forensic science international. Genetics}, volume = {76}, number = {}, pages = {103217}, doi = {10.1016/j.fsigen.2024.103217}, pmid = {39787642}, issn = {1878-0326}, abstract = {With the advent of commercial DNA databases, investigative genetic genealogy (IGG) has emerged as a powerful forensic tool, rivalling the impact of STR analyses, introduced four decades ago. IGG has been frequently applied in the US and tested in other countries, but never in Norway. Here, we apply IGG to three cold criminal cases and successfully identify the donor of the DNA in two of these cases. Our findings suggest that when combined with phenotypic prediction and case information, IGG holds substantial potential for resolving both active and cold cases in Norway. This potential is amplified by the digitalization of archives and the transparent and structured nature of society in Norway. Additionally, the databases exhibit sufficient representation to yield matches with distant relatives. Moreover, this work has uncovered a series of lingering research questions spanning the entire workflow from DNA extraction to genealogy research. Finally, we highlight the possibility that more insights can be gleaned from genetic profiles, for instance using an accurate age prediction method. The results show that IGG can be successfully applied in Norway, having reached a level of maturity that enables identification of unknown individuals in cases where DNA is accessible.}, } @article {pmid39787194, year = {2025}, author = {Bantie, GM and Tadege, M and Nigussie, TZ and Woya, AA and Tekile, AK and Melese, AA and Ayalew, S and Beyene, BB and Wubetu, GY}, title = {Regional disparities of full pentavalent vaccine uptake and the determinants in Ethiopia: Mapping and spatial analysis using the EDHS data.}, journal = {PloS one}, volume = {20}, number = {1}, pages = {e0312514}, doi = {10.1371/journal.pone.0312514}, pmid = {39787194}, issn = {1932-6203}, mesh = {Humans ; Ethiopia ; Infant ; Female ; Adult ; *Spatial Analysis ; Male ; *Vaccination/statistics & numerical data ; Diphtheria-Tetanus-Pertussis Vaccine/administration & dosage ; Hepatitis B Vaccines/administration & dosage ; Young Adult ; Immunization Programs/statistics & numerical data ; Middle Aged ; Haemophilus Vaccines ; Adolescent ; Vaccination Coverage/statistics & numerical data ; Vaccines, Combined ; }, abstract = {BACKGROUND: The full pentavalent (DPT-HepB-Hib) vaccination is the main strategy to prevent five communicable diseases in early childhood, especially in countries with huge communicable disease burdens like Ethiopia. Exploring spatial distributions and determinants of full pentavalent vaccination status in minor ecological areas in Ethiopia is crucial for creating targeted immunization campaigns and monitoring the advancement of accomplishing sustainable development goals. This study aimed to investigate the spatial disparities and determinants of full pentavalent vaccination among 12-23-month-old children in Ethiopia.

METHOD: The data on pentavalent vaccine uptake was found in the Ethiopian Health and Demographic Survey (EDHS, 2019). A two-stage cluster sampling method was applied to collect the EDHS data. The enumeration area was the primary sample unit while the household served as the secondary sampling unit. The geographical variations of full pentavalent vaccine uptake were explored using Quantum Geographic Information System (QGIS) software. The significant predictors of full pentavalent vaccination were identified using a simple logistic regression model through R version 4.1 software.

RESULT: The national full pentavalent vaccine uptake was 59.2%. The spatial distribution of full pentavalent vaccine uptake was not uniform in Ethiopia. Spatial cluster analysis revealed that most of low coverage regions for full pentavalent vaccine uptake were Afar, Somali, and Harari. The regions with the highest and lowest rates of vaccine uptake were Tigray and Harari region, respectively. Maternal age of 35-49 years (AOR = 3.42; 95% CI: 1.99, 5.87), and 25-34 years (AOR = 1.55; 95% CI: 1.17, 2.19), primary education attended (AOR = 1.51; 95%CI: 1.07, 2.11), richness wealth index (AOR = 1.96; 95% CI: 1.40, 2.75), birth order of 1-3 (AOR = 1.88; 95% CI: 1.19, 2.96), and delivery in the health facility (AOR = 3.41: 95% CI: 2.52, 4.61) were the determinants of full pentavalent vaccine uptake in Ethiopia.

CONCLUSION: Ethiopia's full pentavalent vaccine uptake was far lower than the global target. Older maternal age, maternal education, wealth index, birth order, and giving birth in a health facility were the determinants of full pentavalent vaccine uptake. Special attention should be given to Afar, Somali, and Harari regions, to strengthen the vaccine uptake. Moreover, improved socioeconomic status and getting maternal health services during delivery are necessary to enhance vaccine uptake.}, } @article {pmid39750058, year = {2024}, author = {Jain, S and Srinivasan, R and Helton, TJ and Karthikeyan, R}, title = {TXSELECT: a web-based decision support system for regional assessment of potential E. coli loads using a spatially explicit approach.}, journal = {Journal of environmental science and health. Part A, Toxic/hazardous substances & environmental engineering}, volume = {59}, number = {10}, pages = {550-561}, doi = {10.1080/10934529.2024.2445953}, pmid = {39750058}, issn = {1532-4117}, mesh = {*Escherichia coli/isolation & purification ; Texas ; *Internet ; Environmental Monitoring/methods ; Water Microbiology ; Decision Support Techniques ; }, abstract = {Bacterial source characterization and allocation are imperative to watershed planning and identifying best management practices. The Spatially Explicit Load Enrichment Calculation Tool (SELECT) has been extensively utilized in watershed protection plans to evaluate the potential bacteria loads and sources in impaired watersheds. However, collecting data, compiling inputs, and spatially mapping sources can be arduous, time-intensive, expensive, and iterative until potential bacteria loads are appropriately allocated to sources based on stakeholder recommendations. We developed a web-based decision support system (DSS), TXSELECT (https://tx.select.tamu.edu), providing a user-friendly interface to run the SELECT model on Texas watersheds. The DSS includes pre-determined watershed-specific inputs that can be readily adjusted within the interface based on user preference and stakeholder recommendations, obviating the necessity for expensive GIS tools and data extraction. To illustrate the applications of TXSELECT, we implemented it in the entire coverage area to identify the potential hotspots and source contributions for Escherichia coli at a regional scale. Median potential E. coli loads were significantly higher in subwatersheds not supporting recreation use. Overall, the large-scale application of SELECT has the potential to aid in prioritizing management measures in watersheds that are less frequently monitored but could have an elevated risk of impairment.}, } @article {pmid39560426, year = {2025}, author = {Zhu, H-H and Liu, M-M and Boekhout, T and Wang, Q-M}, title = {Improvement of a MALDI-TOF database for the reliable identification of Candidozyma auris (formally Candida auris) and related species.}, journal = {Microbiology spectrum}, volume = {13}, number = {1}, pages = {e0144424}, pmid = {39560426}, issn = {2165-0497}, mesh = {*Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/methods ; Humans ; *Candidiasis/microbiology/diagnosis ; Candida auris/chemistry/isolation & purification/classification ; Databases, Factual ; Mycological Typing Techniques/methods ; Candida/classification/isolation & purification/chemistry ; }, abstract = {UNLABELLED: Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) is a promising technique for the rapid identification microorganisms. The aim of this study was to create a new database for the accurate identification of Candidozyma auris (formerly known as Candida auris) and 11 species of the Candidozyma haemuli species complex, including C. chanthaburiensis, C. duobushaemuli, C. haemuli, C. heveicola, C. khanbhai, C. konsanensis, C. metrosideri, C. ohialehuae, C. pseudohaemuli, C. ruelliae, and C. vulturna. Seventy-one Candidozyma isolates from different national institutions were studied. Thirty-seven strains were used to create a MALDI-TOF (microTyper MS) database using the formic acid extraction method. The validation of this database was performed with 34 other strains of the genus Candidozyma, and the result was compared with the identification results when using DBRs v1.0.0.4 (Tianrui, China). Our library allowed a 100% identification of the evaluated strains with all strains showing log scores of >2.0. Repeatability and reproducibility tests result showed a coefficient of variation of the log score values of less than 5%. The MALDI-TOF MS system can identify C. auris and related species quickly and accurately. This method will play a crucial role in accurately diagnosing infectious agents of the genus Candidozyma in clinical practice.

IMPORTANCE: Importance Candidozyma auris, also known as Candida auris, has quickly spread across the world, and prompt identification of C. auris from infected individuals is critical. However, a standard identification method is lacking for the identification of C. auris in clinical and public health laboratories. To make matters worse, its biochemical assimilation profile was found to be similar to that of closely related and even no-related species, leading to frequent misidentification. To improve diagnostics of this and closely related species, we created a database of reference mass spectra resulting in the efficient and correct identification of all Candidozyma species by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). Moreover, potential pathogenic species of Candidozyma can be effectively identified by MALDI-TOF MS, and differentiated from non-clinically relevant phylogenetic relatives. Thus, MALDI-TOF MS may help expedite laboratory diagnosis and treatment of C. auris and related species of clinical importance and help the clinician to decide on early treatment.}, } @article {pmid39304763, year = {2025}, author = {Pakkir Shah, AK and Walter, A and Ottosson, F and Russo, F and Navarro-Diaz, M and Boldt, J and Kalinski, JJ and Kontou, EE and Elofson, J and Polyzois, A and González-Marín, C and Farrell, S and Aggerbeck, MR and Pruksatrakul, T and Chan, N and Wang, Y and Pöchhacker, M and Brungs, C and Cámara, B and Caraballo-Rodríguez, AM and Cumsille, A and de Oliveira, F and Dührkop, K and El Abiead, Y and Geibel, C and Graves, LG and Hansen, M and Heuckeroth, S and Knoblauch, S and Kostenko, A and Kuijpers, MCM and Mildau, K and Papadopoulos Lambidis, S and Portal Gomes, PW and Schramm, T and Steuer-Lodd, K and Stincone, P and Tayyab, S and Vitale, GA and Wagner, BC and Xing, S and Yazzie, MT and Zuffa, S and de Kruijff, M and Beemelmanns, C and Link, H and Mayer, C and van der Hooft, JJJ and Damiani, T and Pluskal, T and Dorrestein, P and Stanstrup, J and Schmid, R and Wang, M and Aron, A and Ernst, M and Petras, D}, title = {Statistical analysis of feature-based molecular networking results from non-targeted metabolomics data.}, journal = {Nature protocols}, volume = {20}, number = {1}, pages = {92-162}, pmid = {39304763}, issn = {1750-2799}, support = {EXC 2124//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; }, mesh = {*Metabolomics/methods ; Chromatography, Liquid/methods ; Software ; Tandem Mass Spectrometry/methods ; Data Interpretation, Statistical ; }, abstract = {Feature-based molecular networking (FBMN) is a popular analysis approach for liquid chromatography-tandem mass spectrometry-based non-targeted metabolomics data. While processing liquid chromatography-tandem mass spectrometry data through FBMN is fairly streamlined, downstream data handling and statistical interrogation are often a key bottleneck. Especially users new to statistical analysis struggle to effectively handle and analyze complex data matrices. Here we provide a comprehensive guide for the statistical analysis of FBMN results, focusing on the downstream analysis of the FBMN output table. We explain the data structure and principles of data cleanup and normalization, as well as uni- and multivariate statistical analysis of FBMN results. We provide explanations and code in two scripting languages (R and Python) as well as the QIIME2 framework for all protocol steps, from data clean-up to statistical analysis. All code is shared in the form of Jupyter Notebooks (https://github.com/Functional-Metabolomics-Lab/FBMN-STATS). Additionally, the protocol is accompanied by a web application with a graphical user interface (https://fbmn-statsguide.gnps2.org/) to lower the barrier of entry for new users and for educational purposes. Finally, we also show users how to integrate their statistical results into the molecular network using the Cytoscape visualization tool. Throughout the protocol, we use a previously published environmental metabolomics dataset for demonstration purposes. Together, the protocol, code and web application provide a complete guide and toolbox for FBMN data integration, cleanup and advanced statistical analysis, enabling new users to uncover molecular insights from their non-targeted metabolomics data. Our protocol is tailored for the seamless analysis of FBMN results from Global Natural Products Social Molecular Networking and can be easily adapted to other mass spectrometry feature detection, annotation and networking tools.}, } @article {pmid39778451, year = {2025}, author = {Lausch, A and Selsam, P and Heege, T and von Trentini, F and Almeroth, A and Borg, E and Klenke, R and Bumberger, J}, title = {Monitoring and modelling landscape structure, land use intensity and landscape change as drivers of water quality using remote sensing.}, journal = {The Science of the total environment}, volume = {960}, number = {}, pages = {178347}, doi = {10.1016/j.scitotenv.2024.178347}, pmid = {39778451}, issn = {1879-1026}, abstract = {The interactions between landscape structure, land use intensity (LUI), climate change, and ecological processes significantly impact hydrological processes, affecting water quality. Monitoring these factors is crucial for understanding their influence on water quality. Remote sensing (RS) provides a continuous, standardized approach to capture landscape structures, LUI, and landscape changes over long-term time series. In this study, RS-based indicators from Landsat data (2018-2021) were used to assess landscape structure, LUI, and land use change for a study area in northern Germany, applying the ESIS/Imalys tool. These indicators were then used to model and predict water quality (Chla) in 119 standing waters. Various machine learning methods, including Generalised Linear Models, Support Vector Machines, Deep Learning, Decision Trees, Random Forest, and Gradient Boosted Trees, were tested. The Random Forest model performed best, with a correlation of 0.744 ± 0.11. Indicators related to landscape structure, such as diversity_mean (0.376) and relation_mean (0.292), had the highest global correlation weights, while LUI and land use change indicators like NirV2_mean (0.369) and NirV_regme (0.284) were also significant. All indicators and their effects on water quality (Chla) are discussed in detail. The study highlights the potential of the ESIS/Imalys tool for quantifying landscape structure, LUI, and land use change with RS to model and predict water quality and suggests directions for future model improvements by incorporating additional influencing factors.}, } @article {pmid39777935, year = {2025}, author = {Mond, L and Geyer, S and Tetzlaff, J and Weißenborn, K and Schneider, J and Epping, J}, title = {More Drugs and Fewer Strokes? Time Trends in CVD Medication and Incidence of Stroke With German Health Insurance Data.}, journal = {Pharmacoepidemiology and drug safety}, volume = {34}, number = {1}, pages = {e70077}, doi = {10.1002/pds.70077}, pmid = {39777935}, issn = {1099-1557}, support = {//Allgemeine Ortskrankenkasse Niedersachsen/ ; GE 1167/15-1//Deutsche Forschungsgemeinschaft/ ; GE 1167/19-1//Deutsche Forschungsgemeinschaft/ ; }, mesh = {Humans ; Germany/epidemiology ; Female ; Male ; Incidence ; Middle Aged ; Aged ; *Stroke/epidemiology/prevention & control ; Adult ; Aged, 80 and over ; *Cardiovascular Diseases/epidemiology/prevention & control ; Young Adult ; Adolescent ; *Insurance, Health/statistics & numerical data ; Prevalence ; Cardiovascular Agents/therapeutic use/adverse effects ; Age Factors ; Time Factors ; Databases, Factual ; }, abstract = {BACKGROUND: Successful prevention of cardiovascular diseases (CVD) may reduce the burden of diseases. Preventive medication is an important measure to decrease the risks of cardiovascular events, in particular myocardial infarction and stroke. The aim of this study is to analyze the prevalence of CVD preventive medication in Germany over time with respect to sex and age and to compare it with the temporal development of strokes.

METHODS: The study is based on statutory health insurance claims data from the AOK Niedersachsen (AOKN) covering the years 2005-2018. The study population comprises all AOKN insured persons aged 18 years and older (N = 2 088 495). Age-standardized time trends of the prevalence of CVD preventive medication and incidence of stroke were calculated for men and women in different age groups. After that, the relationship of both measures was examined in an ecological correlation.

RESULTS: We found a clear increase in medication prevalence over time. In 2018, about 35% of the total population and about 85% of those over 85 years of age received CVD preventive medication. At the same time, age-standardized incidence rates of ischemic stroke were decreasing slightly. The ecological correlation showed a negative association between medication prevalence and stroke incidence especially in the higher age groups.

CONCLUSION: High correlation coefficients indicate that higher medication prevalence could be linked to better population health. Further research is needed to draw conclusions about the effects of increasing medicalization, including adverse risks and side effects at the population level.}, } @article {pmid39776539, year = {2024}, author = {Chandel, N and Maile, A and Shrivastava, S and Verma, AK and Thakur, V}, title = {Establishment and perturbation of human gut microbiome: common trends and variations between Indian and global populations.}, journal = {Gut microbiome (Cambridge, England)}, volume = {5}, number = {}, pages = {e8}, doi = {10.1017/gmb.2024.6}, pmid = {39776539}, issn = {2632-2897}, abstract = {Human gut microbial species are crucial for dietary metabolism and biosynthesis of micronutrients. Digested products are utilised by the host as well as several gut bacterial species. These species are influenced by various factors such as diet, age, geographical location, and ethnicity. India is home to the largest human population in the world. It is spread across diverse ecological and geographical locations. With variable dietary habits and lifestyles, Indians have unique gut microbial composition. This review captures contrasting and common trends of gut bacterial community establishment in infants (born through different modes of delivery), and how that bacterial community manifests itself along infancy, through old age between Indian and global populations. Because dysbiosis of the gut community structure is associated with various diseases, this review also highlights the common and unique bacterial species associated with various communicable as well as noncommunicable diseases such as diarrhoea, amoebiasis, malnutrition, type 2 diabetes, obesity, colorectal cancer, inflammatory bowel disease, and gut inflammation and damage to the brain in the global and Indian population.}, } @article {pmid39776261, year = {2025}, author = {Nolasco, M and Balzarini, M}, title = {Assessment of temporal aggregation of Sentinel-2 images on seasonal land cover mapping and its impact on landscape metrics.}, journal = {Environmental monitoring and assessment}, volume = {197}, number = {2}, pages = {142}, pmid = {39776261}, issn = {1573-2959}, mesh = {*Environmental Monitoring/methods ; *Ecosystem ; *Seasons ; Satellite Imagery ; Geographic Information Systems ; }, abstract = {Landscape metrics (LM) play a crucial role in fields such as urban planning, ecology, and environmental research, providing insights into the ecological and functional dynamics of ecosystems. However, in dynamic systems, generating thematic maps for LM analysis poses challenges due to the substantial data volume required and issues such as cloud cover interruptions. The aim of this study was to compare the accuracy of land cover maps produced by three temporal aggregation methods: median reflectance, maximum normalised difference vegetation index (NDVI), and a two-date image stack using Sentinel-2 (S2) and then to analyse their implications for LM calculation. The Google Earth Engine platform facilitated data filtering, image selection, and aggregation. A random forest algorithm was employed to classify five land cover classes across ten sites, with classification accuracy assessed using global measurements and the Kappa index. LM were then quantified. The analysis revealed that S2 data provided a high-quality, cloud-free dataset suitable for analysis, ensuring a minimum of 25 cloud-free pixels over the study period. The two-date and median methods exhibited superior land cover classification accuracy compared to the max NDVI method. In particular, the two-date method resulted in lower fragmentation-heterogeneity and complexity metrics in the resulting maps compared to the median and max NDVI methods. Nevertheless, the median method holds promise for integration into operational land cover mapping programmes, particularly for larger study areas exceeding the width of S2 swath coverage. We find patch density combined with conditional entropy to be particularly useful metrics for assessing fragmentation and configuration complexity.}, } @article {pmid39771200, year = {2024}, author = {Sedmáková, D and Jaloviar, P and Mišíková, O and Šumichrast, L and Slováčková, B and Kucbel, S and Vencurik, J and Bosela, M and Sedmák, R}, title = {Small Gap Dynamics in High Mountain Central European Spruce Forests-The Role of Standing Dead Trees in Gap Formation.}, journal = {Plants (Basel, Switzerland)}, volume = {13}, number = {24}, pages = {}, doi = {10.3390/plants13243502}, pmid = {39771200}, issn = {2223-7747}, support = {APVV-21-0199//Slovak Research and Development Agency/ ; APVV-19-0183//Slovak Research and Development Agency/ ; APVV-20-0408//Slovak Research and Development Agency/ ; 1/0515/23//The Ministry of Education, Science, Research and Sport of the Slovak Republic/ ; }, abstract = {Gap dynamics are driving many important processes in the development of temperate forest ecosystems. What remains largely unknown is how often the regeneration processes initialized by endogenous mortality of dominant and co-dominant canopy trees take place. We conducted a study in the high mountain forests of the Central Western Carpathians, naturally dominated by the Norway spruce. Based on the repeated forest inventories in two localities, we quantified the structure and amount of deadwood, as well as the associated mortality of standing dead canopy trees. We determined the basic specific gravity of wood and anatomical changes in the initial phase of wood decomposition. The approach for estimating the rate of gap formation and the number of canopy trees per unit area needed for intentional gap formation was formulated based on residence time analysis of three localities. The initial phase of gap formation (standing dead tree in the first decay class) had a narrow range of residence values, with a 90-95% probability that gap age was less than 10 or 13 years. Correspondingly, a relatively constant absolute number of 12 and 13 canopy spruce trees per hectare died standing in 10 years, with a mean diameter reaching 50-58 cm. Maximum diameters trees (70-80 cm) were represented by 1-4 stems per hectare. The values of the wood-specific gravity of standing trees were around 0.370-0.380 g.cm[-3], and varied from 0.302 to 0.523 g.cm[-3]. Microscopically, our results point out that gap formation is a continuous long-lasting process, starting while canopy trees are living. We observed early signs of wood degradation and bacteria, possibly associated with bark beetles, that induce a strong effect when attacking living trees with vigorous defenses. New information about the initial phase of gap formation has provided a basis for the objective proposal of intervals and intensities of interventions, designed to promote a diversified structure and the long-term ecological stability of the mountain spruce stands in changing climate conditions.}, } @article {pmid39656924, year = {2025}, author = {Bastian, FB and Cammarata, AB and Carsanaro, S and Detering, H and Huang, WT and Joye, S and Niknejad, A and Nyamari, M and Mendes de Farias, T and Moretti, S and Tzivanopoulou, M and Wollbrett, J and Robinson-Rechavi, M}, title = {Bgee in 2024: focus on curated single-cell RNA-seq datasets, and query tools.}, journal = {Nucleic acids research}, volume = {53}, number = {D1}, pages = {D878-D885}, pmid = {39656924}, issn = {1362-4962}, support = {//University of Lausanne/ ; U01CA215010/GF/NIH HHS/United States ; //Service de la Santé Publique, Canton de Vaud/ ; U01 CA215010/CA/NCI NIH HHS/United States ; 31003A_173048/SNSF_/Swiss National Science Foundation/Switzerland ; 863410//Horizon 2020 - Research and Innovation Framework Programme/ ; //swissuniversities Programme Open Science/ ; //SIB Swiss Institute of Bioinformatics/ ; }, mesh = {Animals ; *Single-Cell Analysis/methods ; *RNA-Seq/methods ; *Software ; *Databases, Genetic ; Humans ; Internet ; Molecular Sequence Annotation ; Gene Expression Profiling/methods ; Data Curation ; Single-Cell Gene Expression Analysis ; }, abstract = {Bgee (https://www.bgee.org/) is a database to retrieve and compare gene expression patterns in multiple animal species. Expression data are integrated and made comparable between species thanks to consistent data annotation and processing. In the past years, we have integrated single-cell RNA-sequencing expression data into Bgee through careful curation of public datasets in multiple species. We have fully integrated this new technology along with the wealth of other data existing in Bgee. As a result, Bgee can now provide one definitive answer all the way to the cell resolution about a gene's expression pattern, comparable between species. We have updated our programmatic access tools to adapt to these changes accordingly. We have introduced a new web interface, providing detailed access to our annotations and expression data. It enables users to retrieve data, e.g. for specific organs, cell types or developmental stages, and leverages ontology reasoning to build powerful queries. Finally, we have expanded our species count from 29 to 52, emphasizing fish species critical for vertebrate genome studies, species of agronomic and veterinary importance and nonhuman primates.}, } @article {pmid39475188, year = {2025}, author = {Kemmler, E and Lemfack, MC and Goede, A and Gallo, K and Toguem, SMT and Ahmed, W and Millberg, I and Preissner, S and Piechulla, B and Preissner, R}, title = {mVOC 4.0: a database of microbial volatiles.}, journal = {Nucleic acids research}, volume = {53}, number = {D1}, pages = {D1692-D1696}, pmid = {39475188}, issn = {1362-4962}, support = {Pi153/36-1//German Research Foundation/ ; //University of Rostock/ ; 428445448//Food allergy and tolerance (FOOD@)/ ; }, mesh = {*Volatile Organic Compounds/metabolism/chemistry ; *Bacteria/metabolism/genetics ; Microbiota ; Metabolomics/methods ; Databases, Factual ; Humans ; Metabolome ; Terpenes/metabolism/chemistry ; Databases, Chemical ; }, abstract = {Metabolomic microbiome research has become an important topic for understanding agricultural, ecological as well as health correlations. Only the determination of both the non-volatile and the volatile organic compound (mVOC) production by microorganisms allows a holistic view for understanding the complete potential of metabolomes and metabolic capabilities of bacteria. In the recent past, more and more bacterial headspaces and culture media were analyzed, leading to an accumulation of about 3500 mVOCs in the updated mVOC 4.0 database, including compounds synthesized by the newly discovered non-canonical terpene pathway. Approximately 10% of all mVOCs can be assigned with a biological function, some mVOCs have the potential to impact agriculture in the future (e.g. eco-friendly pesticides) or animal and human health care. mVOC 4.0 offers various options for exploring extensively annotated mVOC data from different perspectives, including improved mass spectrometry matching. The mVOC 4.0 database includes literature searches with additional relevant keywords, making it the most up-to-date and comprehensive publicly available mVOC platform at: http://bioinformatics.charite.de/mvoc.}, } @article {pmid39470715, year = {2025}, author = {Miao, Z and Ren, Y and Tarabini, A and Yang, L and Li, H and Ye, C and Liti, G and Fischer, G and Li, J and Yue, JX}, title = {ScRAPdb: an integrated pan-omics database for the Saccharomyces cerevisiae reference assembly panel.}, journal = {Nucleic acids research}, volume = {53}, number = {D1}, pages = {D852-D863}, pmid = {39470715}, issn = {1362-4962}, support = {32070592//National Natural Science Foundation of China/ ; 2022A1515010717//Guangdong Basic and Applied Basic Research Foundation/ ; 2019QN01Y183//Guangdong Pearl River Talents Program/ ; YTP-SYSUCC-0042//Sun Yat-sen University Cancer Center/ ; 24qnpy293//Fundamental Research Funds for the Central Universities/ ; }, mesh = {*Saccharomyces cerevisiae/genetics/metabolism ; *Genome, Fungal ; *Databases, Genetic ; *Genomics/methods ; Telomere/genetics ; Molecular Sequence Annotation ; Proteomics ; Multiomics ; }, abstract = {As a unicellular eukaryote, the budding yeast Saccharomyces cerevisiae strikes a unique balance between biological complexity and experimental tractability, serving as a long-standing classic model for both basic and applied studies. Recently, S. cerevisiae further emerged as a leading system for studying natural diversity of genome evolution and its associated functional implication at population scales. Having high-quality comparative and functional genomics data are critical for such efforts. Here, we exhaustively expanded the telomere-to-telomere (T2T) S. cerevisiae reference assembly panel (ScRAP) that we previously constructed for 142 strains to cover high-quality genome assemblies and annotations of 264 S. cerevisiae strains from diverse geographical and ecological niches and also 33 outgroup strains from all the other Saccharomyces species complex. We created a dedicated online database, ScRAPdb (https://www.evomicslab.org/db/ScRAPdb/), to host this expanded pangenome collection. Furthermore, ScRAPdb also integrates an array of population-scale pan-omics atlases (pantranscriptome, panproteome and panphenome) and extensive data exploration toolkits for intuitive genomics analyses. All curated data and downstream analysis results can be easily downloaded from ScRAPdb. We expect ScRAPdb to become a highly valuable platform for the yeast community and beyond, leading to a pan-omics understanding of the global genetic and phenotypic diversity.}, } @article {pmid39761773, year = {2025}, author = {Banakar, SN and Karan, R and Prasanna Kumar, MK and Venkateshbabu, G and Harish, J and Patil, SS and Chandrashekar, BS and Mahesh, HB and Devanna, P and Manjunatha, C and Vamsidharreddy, N and Pallavi, KN and Sarangi, AN and Vaidya, K and Guru Murthy, DS}, title = {Unveiling Fusarium falciforme: Genome sequencing of a Novel wilt causing pathogen in Subabul (Leucaena leucocephala L.) in India.}, journal = {Microbial pathogenesis}, volume = {}, number = {}, pages = {107281}, doi = {10.1016/j.micpath.2025.107281}, pmid = {39761773}, issn = {1096-1208}, abstract = {Subabul (Leucaena leucocephala L.) is a leguminous species often referred to as the "miracle tree," it provides numerous ecosystem services and exhibits robust ecological characteristics. However, the infection caused by phytopathogenic fungi is poorly understood in Subabul. Therefore, this study provides comprehensive insights into the molecular and genomic characteristics of Fusarium falciforme, the causal agent of wilt disease in Subabul (Leucaena leucocephala). Pathogen isolation from infected samples, followed by morpho-molecular characterization through DNA sequencing of key markers (ITS, LSU, TEF1α) and phylogenetic analysis, confirmed the identity of F. falciforme. Host range analysis demonstrated the pathogen's ability to infect additional leguminous crops, including chickpea (Cicer arietinum) and soybean (Glycine max). A complete genome assembly revealed a genome size of 59.19 Mb, comprising 18,853 protein-coding genes. Comparative genomic analysis elucidated evolutionary relationships with other Fusarium species, while functional annotation identified critical virulence factors, such as polyketide synthases, ABC transporters, and secretory proteins, which facilitate host tissue invasion. These findings enhance the understanding of F. falciforme pathogenicity, enabling improved diagnostic tools and management strategies for controlling wilt disease in Subabul and related legumes.}, } @article {pmid39761073, year = {2025}, author = {Sangeetha, S and Sajeev, S and Hamza, MK and Shome, BR and Raisen, C and Holmes, MA and Sivaraman, GK}, title = {Whole-Genome Sequencing of Antimicrobial Resistant Klebsiella quasipneumoniae, a Novel Sequence Type 5655 from Retail Fish Market, Assam, India.}, journal = {Foodborne pathogens and disease}, volume = {}, number = {}, pages = {}, doi = {10.1089/fpd.2023.0017}, pmid = {39761073}, issn = {1556-7125}, abstract = {Klebsiella quasipneumoniae is a recently described species that can be differentiated from Klebsiella pneumoniae. However, in clinical settings, they are frequently misidentified as K. pneumoniae. In this study, our objective was to conduct genomic characterization and bioinformatics analysis of K. quasipneumoniae subsp. quasipneumoniae (KpII-A) isolated from a sample obtained from a retail fish market in Assam, India. Notably, this particular isolate was identified as K. pneumoniae when identified using BD Pheonix™ M50 (BD Difco, USA). This represents a serious pitfall of conventional microbiological methods for distinguishing between K. pneumoniae and K. quasipneumoniae. In this connection, identifying differences in nuclear gene content is key to avoid misidentification. The isolate was confirmed to be KpII-A using species identification by Mash Screen and whole-genome sequencing by the Illumina platform. We report the draft genome sequence of this strain, comprising of 53 contigs with an average GC content of 58.11%. The annotation revealed 5,095 protein coding sequences, 69 tRNA genes, and 4 rRNA genes. The isolated strain acknowledges the presence of oqxA, oqxB, fosA, and blaOKP-A-3 antimicrobial resistance genes (ARGs). Additionally two phage genomes were detected in contigs 3 and 19 of the bacterial genome. Based on the multilocus sequence typing and genome sequencing, the isolate was identified as a novel sequence type, ST5655, within the species K. quasipneumoniae under the phylogroup KpII-A. The presence of antimicrobial resistance genes in KpII-A, isolated from retail fish samples, raises concerns regarding transmission across barriers in ecological niches and possible transmission to consumers. Given that fish may serve as a potential vehicle for ARG transmission, our findings are highly relevant and paramount to human health. Moreover, our study supports the robustness of the sequence-based microbial identification.}, } @article {pmid39753746, year = {2025}, author = {Allegretti, E and D'Innocenzo, G and Coco, MI}, title = {The Visual Integration of Semantic and Spatial Information of Objects in Naturalistic Scenes (VISIONS) database: attentional, conceptual, and perceptual norms.}, journal = {Behavior research methods}, volume = {57}, number = {1}, pages = {42}, pmid = {39753746}, issn = {1554-3528}, support = {PTDC/PSI-ESP/30958/2017//Fundação para a Ciência e a Tecnologia/ ; LISBOA-01-0145-FEDER-0309//Fundação para a Ciência e a Tecnologia/ ; }, mesh = {Humans ; *Semantics ; *Attention/physiology ; Female ; Adult ; Male ; Young Adult ; *Space Perception/physiology ; *Visual Perception/physiology ; Databases, Factual ; Eye-Tracking Technology ; Adolescent ; }, abstract = {The complex interplay between low- and high-level mechanisms governing our visual system can only be fully understood within ecologically valid naturalistic contexts. For this reason, in recent years, substantial efforts have been devoted to equipping the scientific community with datasets of realistic images normed on semantic or spatial features. Here, we introduce VISIONS, an extensive database of 1136 naturalistic scenes normed on a wide range of perceptual and conceptual norms by 185 English speakers across three levels of granularity: isolated object, whole scene, and object-in-scene. Each naturalistic scene contains a critical object systematically manipulated and normed regarding its semantic consistency (e.g., a toothbrush vs. a flashlight in a bathroom) and spatial position (i.e., left, right). Normative data are also available for low- (i.e., clarity, visual complexity) and high-level (i.e., name agreement, confidence, familiarity, prototypicality, manipulability) features of the critical object and its embedding scene context. Eye-tracking data during a free-viewing task further confirms the experimental validity of our manipulations while theoretically demonstrating that object semantics is acquired in extra-foveal vision and used to guide early overt attention. To our knowledge, VISIONS is the first database exhaustively covering norms about integrating objects in scenes and providing several perceptual and conceptual norms of the two as independently taken. We expect VISIONS to become an invaluable image dataset to examine and answer timely questions above and beyond vision science, where a diversity of perceptual, attentive, mnemonic, or linguistic processes could be explored as they develop, age, or become neuropathological.}, } @article {pmid38979368, year = {2024}, author = {Xiao, Y and Elmasry, M and Bai, JDK and Chen, A and Chen, Y and Jackson, B and Johnson, JO and Gillies, RJ and Prasanna, P and Chen, C and Damaghi, M}, title = {Eco-evolutionary Guided Pathomics Analysis to Predict DCIS Upstaging.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {38979368}, issn = {2692-8205}, support = {P30 CA076292/CA/NCI NIH HHS/United States ; R01 CA249016/CA/NCI NIH HHS/United States ; R01 CA272601/CA/NCI NIH HHS/United States ; U01 CA261841/CA/NCI NIH HHS/United States ; }, abstract = {Cancers evolve in a dynamic ecosystem. Thus, characterizing cancer's ecological dynamics is crucial to understanding cancer evolution and can lead to discovering novel biomarkers to predict disease progression. Ductal carcinoma in situ (DCIS) is an early-stage breast cancer characterized by abnormal epithelial cell growth confined within the milk ducts. In this study, we show that ecological habitat analysis of hypoxia and acidosis biomarkers can significantly improve prediction of DCIS upstaging. First, we developed a novel eco-evolutionary designed approach to define habitats in the tumor intraductal microenvironment based on oxygen diffusion distance. Then, we identified cancer cells with metabolic phenotypes attributed to their habitat conditions, such as the expression of CA9 indicating hypoxia responding phenotype, and LAMP2b indicating the acid adaptation. Traditionally these markers have shown limited predictive capabilities for DCIS upstaging, if any. However, when analyzed from an ecological perspective, their power to differentiate between pure DCIS and upstaged DCIS increased significantly. Second, using eco-evolutionary guided computational and digital pathology techniques, we discovered distinct niches with spatial patterns of these biomarkers and used the distribution of such niches to predict patient upstaging. The niches patterns were characterized by pattern analysis of both cellular and spatial features. With a 5-fold validation on the biopsy cohort, we trained a random forest classifier to achieve the area under curve (AUC) of 0.74. Our results affirm the importance of using eco-evolutionary-designed approaches in biomarkers discovery studies in the era of digital pathology by demonstrating the role of tumor ecological habitats and niches.}, } @article {pmid39753915, year = {2025}, author = {Davidson, SC and Cagnacci, F and Newman, P and Dettki, H and Urbano, F and Desmet, P and Bajona, L and Bryant, E and Carneiro, APB and Dias, MP and Fujioka, E and Gambin, D and Hoenner, X and Hunter, C and Kato, A and Kot, CY and Kranstauber, B and Lam, CH and Lepage, D and Naik, H and Pye, JD and Sequeira, AMM and Tsontos, VM and van Loon, E and Vo, D and Rutz, C}, title = {Establishing bio-logging data collections as dynamic archives of animal life on Earth.}, journal = {Nature ecology & evolution}, volume = {}, number = {}, pages = {}, pmid = {39753915}, issn = {2397-334X}, support = {80NSSC21K1182//National Aeronautics and Space Administration (NASA)/ ; Fellowship at Fondation IméRA//Institut de Recherche pour le Développement (French Research Institute for Development)/ ; CN00000033//Ministero dell'Istruzione, dell'Università e della Ricerca (Ministry of Education, University and Research)/ ; LifeWatch//Fonds Wetenschappelijk Onderzoek (Research Foundation Flanders)/ ; DP210103091//Department of Education and Training | Australian Research Council (ARC)/ ; GBMF9881//Gordon and Betty Moore Foundation (Gordon E. and Betty I. Moore Foundation)/ ; NGS-82515R-20//National Geographic Society/ ; }, abstract = {Rapid growth in bio-logging-the use of animal-borne electronic tags to document the movements, behaviour, physiology and environments of wildlife-offers opportunities to mitigate biodiversity threats and expand digital natural history archives. Here we present a vision to achieve such benefits by accounting for the heterogeneity inherent to bio-logging data and the concerns of those who collect and use them. First, we can enable data integration through standard vocabularies, transfer protocols and aggregation protocols, and drive their wide adoption. Second, we need to develop integrated data collections on standardized data platforms that support data preservation through public archiving and strategies that ensure long-term access. We outline pathways to reach these goals, highlighting the need for resources to govern community data standards and guide data mobilization efforts. We propose the launch of a community-led coordinating body and provide recommendations for how stakeholders-including government data centres, museums and those who fund, permit and publish bio-logging work-can support these efforts.}, } @article {pmid39753264, year = {2025}, author = {Aguirre Vergara, F and Pinker, I and Fischer, A and Seuring, T and Tichomirowa, MA and de Beaufort, C and Kamp, SM and Fagherazzi, G and Aguayo, GA}, title = {Readiness of adults with type 1 diabetes and diabetes caregivers for diabetes distress monitoring using a voice-based digital health solution: insights from the PsyVoice mixed methods study.}, journal = {BMJ open}, volume = {15}, number = {1}, pages = {e088424}, doi = {10.1136/bmjopen-2024-088424}, pmid = {39753264}, issn = {2044-6055}, abstract = {OBJECTIVES: Diabetes distress can negatively affect the well-being of individuals with type 1 diabetes (T1D). Voice-based (VB) technology can be used to develop inexpensive and ecological tools for managing diabetes distress. This study explored the competencies to engage with digital health services, needs and preferences of individuals with T1D or caring for a child with this condition regarding VB technology to inform the tailoring of a co-designed tool for supporting diabetes distress management.

DESIGN: We used a mixed methods design. We performed a qualitative reflexive thematic analysis of semistructured interviews of people living with T1D or caring for a child with T1D, complemented by quantitative analysis (descriptive statistics).

SETTING: 12 adults living with T1D who attended diabetes centres or cared for a child with this condition participated in semistructured interviews to collect opinions about voice technology. They also responded to three questionnaires on sociodemographics and diabetes management, diabetes distress and e-health literacy.

OUTCOME MEASURES: Main: Patient experiences and perceptions derived from the coded transcriptions of interview data. Secondary: Quantitative data generated from Socio-Demographic and Diabetes Management questionnaire; Problem Areas in Diabetes Scale and e-Health Literacy Questionnaire.

RESULTS: Five major themes were generated from the participants' interview responses: (1) Experience of T1D, (2) Barriers to VB technology use, (3) Facilitators of VB technology, (4) Expectations of VB technology management in T1D, (5) Role of healthcare professionals in implementing VB technology for T1D. Most participants expressed a favourable view of voice technology for diabetes distress management. Trust in technology and healthcare professionals emerged as the predominant sentiment, with participants' current device type impacting anticipated barriers to adopting new technologies.

CONCLUSION: The results highlighted positive participant views towards VB technology. Device use, previous experience and health professional endorsement were influential facilitators of novel VB digital health solutions. Further research involving younger people with T1D could further contribute to the successful development of these tools.

TRIAL REGISTRATION NUMBER: ClinicalTrials.gov, NCT05517772.}, } @article {pmid39749768, year = {2025}, author = {Fifield, K and Veerakanjana, K and Hodsoll, J and Kuntsi, J and Tye, C and Simblett, S}, title = {Completion Rates of Smart Technology Ecological Momentary Assessment (EMA) in Populations With a Higher Likelihood of Cognitive Impairment: A Systematic Review and Meta-Analysis.}, journal = {Assessment}, volume = {}, number = {}, pages = {10731911241306364}, doi = {10.1177/10731911241306364}, pmid = {39749768}, issn = {1552-3489}, abstract = {Ecological Momentary Assessment using smartphone technology (smart EMA) has grown substantially over the last decade. However, little is known about the factors associated with completion rates in populations who have a higher likelihood of cognitive impairment. A systematic review of Smart EMA studies in populations who have a higher likelihood of cognitive impairment was carried out (PROSPERO; ref no CRD42022375829). Smartphone EMA studies in neurological, neurodevelopmental and neurogenetic conditions were included. Six databases were searched, and bias was assessed using Egger's test. Completion rates and moderators were analyzed using meta-regression. Fifty-five cohorts were included with 18 cohorts reporting confirmed cognitive impairment. In the overall cohort, the completion rate was 74.4% and EMA protocol characteristics moderated completion rates. Participants with cognitive impairment had significantly lower completion rates compared with those without (p = .021). There were no significant moderators in the cognitive impairment group. Limitations included significant methodological issues in reporting of completion rates, sample characteristics, and associations with completion and dropout rates. These findings conclude that smart EMA is feasible for people with cognitive impairment. Future research should focus on the efficacy of using smart EMA within populations with cognitive impairment to develop an appropriate methodological evidence base.}, } @article {pmid39747897, year = {2025}, author = {Petrovic, M and Salovic, B and Tomic, A and Jesic-Petrovic, T and Matejic, A and Radovic, I and Babic, S and Korugic, A and Jelovac, D and Mikovic, N and Jakovljevic, S and Pelemis, S and Dimitrijevic, M and Milovanovic, J and Jotic, A and Trivic, A and Dimitrijevic, A and Bulatovic, S and Dudvarski, Z and Soldatovic, I and Ilic-Zivojinovic, J}, title = {Functional assessment of cancer therapy - head & neck (FACT-HN) translation and validation in Serbian.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {298}, pmid = {39747897}, issn = {2045-2322}, mesh = {Humans ; *Head and Neck Neoplasms/therapy/psychology ; Male ; Serbia ; Female ; *Quality of Life ; Middle Aged ; *Psychometrics/methods ; Surveys and Questionnaires ; Aged ; Reproducibility of Results ; Adult ; Translations ; }, abstract = {This study aimed to translate and validate the Functional Assessment of Cancer Therapy - Head & Neck (FACT-HN) in a Serbian-speaking population, assessing its psychometric properties and utility in evaluating the quality of life in head and neck cancer patients. The research focuses on determining the translated questionnaire's reliability, validity, and cultural relevance. A total of 106 Serbian-speaking head and neck cancer patients completed the translated FACT-HN, along with other validated instruments, including the EORTC QLQ-C30, EORTC QLQ-HN43, CES-D, and GAD-7. The translation followed a standard internationally accepted procedure. Psychometric analyses were conducted using confirmatory and exploratory factor analysis, Pearson correlations, and reliability measures such as Cronbach's alpha and intraclass correlation coefficients. The Serbian version of the FACT-HN showed excellent internal consistency across all subscales, with Cronbach's alpha ranging from 0.70 to 0.89. Confirmatory factor analysis confirmed the five-factor structure. Strong correlations were observed between the FACT-HN and other validated QoL measures, particularly with the EORTC QLQ-C30 and EORTC QLQ-HN43. Convergent validity was satisfactory for all components except the Social Well-Being component. The Serbian version of the FACT-HN is a valid and reliable tool for assessing the quality of life in head and neck cancer patients. It provides a comprehensive assessment of physical, social, emotional, and functional well-being, making it valuable for clinical and research applications in Serbian-speaking populations. Further research is needed to assess its sensitivity to longitudinal treatment-related changes.}, } @article {pmid39747514, year = {2025}, author = {Liu, X and Tan, Y and Dong, J and Wu, J and Wang, X and Sun, Z}, title = {Assessing habitat selection parameters of Arabica coffee using BWM and BCM methods based on GIS.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {8}, pmid = {39747514}, issn = {2045-2322}, support = {51979133//National Natural Science Foundation of China/ ; 202301AS070030//Yunnan Fundamental Research Projects/ ; 202302AE090024//Yunnan Major Science and Technology Special Plan/ ; }, mesh = {*Ecosystem ; *Geographic Information Systems ; *Coffea/growth & development ; China ; Coffee ; Climate ; Decision Making ; Conservation of Natural Resources/methods ; Soil/chemistry ; }, abstract = {Arabica coffee, as one of the world's three native coffee species, requires rational planning for its growing areas to ensure ecological and sustainable agricultural development. This study aims to establish a decision-making framework using Geographic Information Systems (GIS) and Multi-Criteria Decision-Making (MCDM), with a focus on assessing the habitat suitability of Arabica coffee in Yunnan Province, China. The impacts of climate, topography, soil, and socio-economic factors were considered by selecting 13 criteria through correlation analysis. Indicator weights were determined using the Best-Worst Method (BWM), while weighted processing was conducted using the Base-Criterion Method (BCM). Sensitivity analysis was performed to verify the accuracy and stability of the model. Additionally, several decision models were evaluated to investigate regionalizing Arabica coffee habitats in Yunnan. The results highlighted that minimum temperature during the coldest month is crucial for evaluation purposes. The BWM-GIS model identified suitable areas comprising 13.55% of the total area as most suitable, 27.46% as suitable, and 59.00% as unsuitable, whereas corresponding values for the BCM-GIS model were 9.97%, 30.43%, and 59.59%. Despite employing different decision-making methods, both models yielded similar and consistent results. The suitable areas mainly encompass Dehong, Pu'er, Lincang, Xishuangbanna, Baoshan, southern Chuxiong, eastern Honghe, southern Yuxi, and parts of Wenshan. BWM-GIS achieved an area under curve (AUC) value of 0.891, while BCM-GIS obtained an AUC value of 0.890, indicating the stability and reliability of the models. Among them, the evaluation process of BCM-GIS was simpler and more realistic. Therefore, it has high feasibility and practical value in practical application. The findings from this study provide a significant scientific foundation for optimizing Yunnan Province.}, } @article {pmid39373541, year = {2025}, author = {Zuo, YW and Quan, MH and Liu, GH and Zhang, X and Long, NN and You, SQ and Peng, Y and Deng, HP}, title = {Multi-Omics Analysis Reveals Molecular Responses of Alkaloid Content Variations in Lycoris aurea Across Different Locations.}, journal = {Plant, cell & environment}, volume = {48}, number = {2}, pages = {953-964}, doi = {10.1111/pce.15187}, pmid = {39373541}, issn = {1365-3040}, support = {//This study was supported by General Program of the Chongqing Natural Science Foundation and National Natural Science Foundation of China./ ; }, mesh = {*Lycoris/metabolism/genetics ; *Alkaloids/metabolism ; Gene Expression Regulation, Plant ; Metabolomics ; Transcriptome ; Soil Microbiology ; Protein Interaction Maps ; Gene Expression Profiling ; Photosynthesis ; Metabolome ; Genes, Plant ; Multiomics ; }, abstract = {Lycoris aurea, celebrated for its visually striking flowers and significant medicinal value due to the presence of alkaloids such as lycorine and galanthamine, has intricate yet poorly understood regulatory mechanisms. This study provides a detailed examination of the transcriptomic, metabolomic and ecological dynamics of L. aurea, aiming to elucidate the underlying molecular mechanisms of alkaloid biosynthesis. Our comparative analysis across different ecological settings highlighted key genes involved in alkaloid biosynthesis, such as genes encoding aldehyde dehydrogenase and norbelladine 4'-O-methyltransferase, which were distinctively increased in the high alkaloids-producing group. We identified a total of 6871 differentially expressed genes and 915 metabolites involved in pathways like terpenoid backbone biosynthesis, phenylalanine, tyrosine and tryptophan biosynthesis. Protein interaction network analysis revealed significant upregulation of photosynthesis, photosystem and photosynthetic membrane pathways in the alkaloids-producing region. Furthermore, our research delineated the interactions among soil microbial communities, genes and plant and soil biochemical properties, noting that bacterial populations correlate with soil properties that favour the activation of metabolic pathways essential for alkaloid production. Collectively, this study advances our understanding of the genetic and metabolic alkaloid biosynthesis pathways in L. aurea, shedding light on the complex interactions that govern alkaloid production.}, } @article {pmid39746011, year = {2025}, author = {Wohltjen, S and Colón, YI and Zhu, Z and Miller, K and Huang, WC and Mutlu, B and Li, Y and Niedenthal, PM}, title = {Uniting theory and data: the promise and challenge of creating an honest model of facial expression.}, journal = {Cognition & emotion}, volume = {}, number = {}, pages = {1-15}, doi = {10.1080/02699931.2024.2446945}, pmid = {39746011}, issn = {1464-0600}, abstract = {People routinely use facial expressions to communicate successfully and to regulate other's behaviour, yet modelling the form and meaning of these facial behaviours has proven surprisingly complex. One reason for this difficulty may lie in an over-reliance on the assumptions inherent in existing theories of facial expression - specifically that (1) there is a putative set of facial expressions that signal an internal state of emotion, (2) patterns of facial movement have been empirically linked to the prototypical emotions in this set, and (3) static, non-social, posed images from convenience samples are adequate to validate the first two assumptions. These assumptions have guided the creation of datasets, which are then used to train unrepresentative computational models of facial expression. In this article, we discuss existing theories of facial expression and review how they have shaped current facial expression recognition tools. We then discuss the resources that are available to help researchers build a more ecologically valid model of facial expressions.}, } @article {pmid39736019, year = {2024}, author = {Kobzeva, K and Ivenkov, M and Gromov, R and Bushueva, O}, title = {HSP90 Family Members, Their Regulators and Ischemic Stroke Risk: A Comprehensive Molecular-Genetics and Bioinformatics Analysis.}, journal = {Frontiers in bioscience (Scholar edition)}, volume = {16}, number = {4}, pages = {19}, doi = {10.31083/j.fbs1604019}, pmid = {39736019}, issn = {1945-0524}, support = {22-15-00288//Russian Science Foundation/ ; }, mesh = {Humans ; *Polymorphism, Single Nucleotide ; *HSP90 Heat-Shock Proteins/genetics/metabolism ; *Ischemic Stroke/genetics ; Male ; Female ; Middle Aged ; *Computational Biology ; Aged ; *Genetic Predisposition to Disease ; Russia/epidemiology ; Risk Factors ; Case-Control Studies ; Heat Shock Transcription Factors/genetics/metabolism ; }, abstract = {BACKGROUND: Disruptions in proteostasis are recognized as key drivers in cerebro- and cardiovascular disease progression. Heat shock proteins (HSPs), essential for maintaining protein stability and cellular homeostasis, are pivotal in neuroperotection. Consequently, deepening the understanding the role of HSPs in ischemic stroke (IS) risk is crucial for identifying novel therapeutic targets and advancing neuroprotective strategies.

AIM: Our objective was to examine the potential correlation between single nucleotide polymorphisms (SNPs) in genes that encode members of the Heat shock protein 90 (HSP90), small heat shock proteins (HSPB), and heat shock factors (HSF) families, and the risk and clinical characteristics of IS.

METHODS: 953 IS patients and 1265 controls from Central Russia were genotyped for nine SNPs in genes encoding HSP90AA1, HSFs, and HSPBs using the MassArray-4 system and probe-based polymerase chain reaction (PCR).

RESULTS: In smokers, SNP rs1133026 HSPB8 increased the risk of IS (risk allele A, odds ratio (OR) = 1.43, 95% Confidence Interval (CI) 1.02-2.02, p = 0.035), and rs556439 HSF2 increased the brain infarct size (risk allele A, p = 0.02). In non-smokers, SNPs rs4279640 HSF1 (protective allele T, OR = 0.58, 95% CI 0.37-0.92, p = 0.02) and rs4264324 HSP90AA1 (protective allele C, OR = 0.11, 95% CI 0.01-0.78, p = 0.001) lowered the risk of recurrent stroke; SNP rs7303637 HSPB8 increased the age of onset of IS (protective allele T, p = 0.04). In patients with body mass index (BMI) ≥25, SNPs rs556439 HSF2 (risk allele A, OR = 1.33, 95% CI 1.04-1.69, p = 0.02) and rs549302 HSF2 (risk allele G, OR = 1.34, 95% CI 1.02-1.75, p = 0.03) were linked to a higher risk of IS.

CONCLUSIONS: The primary molecular mechanisms through which the studied SNPs contribute to IS pathogenesis were found to be the regulation of cell death, inflammatory and oxidative stress responses.}, } @article {pmid39730727, year = {2024}, author = {Kato, H}, title = {Daily walking time effects of the opening of a multifunctional facility "ONIKURU" using propensity score matching and GPS tracking techniques.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {31047}, pmid = {39730727}, issn = {2045-2322}, support = {24K17421//Japan Society for the Promotion of Science/ ; }, mesh = {Humans ; Female ; *Walking/physiology ; Male ; Adult ; *Geographic Information Systems ; *Propensity Score ; Middle Aged ; Young Adult ; Exercise/physiology ; Adolescent ; Environment Design ; Time Factors ; Smartphone ; }, abstract = {Urban design focused on improving walkability has received attention as a method of increasing physical activity among the population. However, only a few studies have examined the effect of walking time of opening multifunctional facilities as an architecture-scale intervention. This study aimed to clarify the effect of opening a multifunctional facility on residents' daily walking time. In addition, this study analyzed the gender and age subgroups. The natural experiment was conducted using the case of the Ibaraki City Cultural and Childcare Complex "ONIKURU," a public multifunctional facility. This study used GPS-trajectory data based on GPS tracking techniques, which is anonymized location data for smartphone users. The causal relationship was analyzed using propensity score matching and difference-in-differences analysis. The results showed that the opening of ONIKURU significantly increased the average walking time of visitors to 3.165 [- 1.697, 8.027] min/day compared with that of non-visitors. Specifically, visitors' average daily walking time improved to a level comparable to that of non-visitors after the opening of ONIKURU. In addition, opening ONIKURU significantly increased female young adults' average walking time to 3.385 [- 4.906, 11.676] min/day. Therefore, this study provides theoretical contributions to a health-promoting built environment significantly affecting walking at an architecture-scale intervention.}, } @article {pmid39729740, year = {2024}, author = {Gupta, AK and Ravikumar, K and Gopal, V and Begum, N and Tabassum, and Sangeetha, S and Narendran, P and Shankar, D}, title = {A trans-disciplinary agro-ecology strategy to grow medicinal plants.}, journal = {Journal of Ayurveda and integrative medicine}, volume = {16}, number = {1}, pages = {100985}, doi = {10.1016/j.jaim.2024.100985}, pmid = {39729740}, issn = {0975-9476}, abstract = {The scope of the emerging field of Ayurvedic-biology visualized thus far is confined to studies on dimensions pertaining to clinical and experimental pharmacology, basic trans-disciplinary science and drug design. However, given the multiple facets of classical Ayurveda knowledge system, its application in the field of organic agriculture perhaps also needs to be urgently explored. The urgency is due to the growing public acceptance of Ayurveda as a preferred clinical choice for well-being and disease management. The turnover of the sector across manufacturing and health services is estimated to be around Rs.1,00,000 crores per annum. Medicinal plants today and in the coming decade will therefore be required in large volumes and given that their applications are solely for enhancing health of humans, livestock (Pashu Ayurveda) and crops (Vriksh Ayurveda), it is imperative that they be cultivated in an organic manner employing the fusion of best available inter-cultural knowledge. The Ayurvedic subjects relevant for organic agriculture are Desh vichar, Dravya guna Shastra and Vriksh Ayurveda. From the perspective of modern biology subjects like soil micro biome, genetics, plant physiology and the natural geographical distribution of species are relevant. It must be stated at the very outset that this article is largely theoretical. While experiments in Vriksh Ayurveda have been attempted on a small scale, the fusion of Ayurveda and biology for improving organic agriculture of medicinal plants has thus far not been systematically explored.}, } @article {pmid39727132, year = {2024}, author = {Xin, PY and Tian, T and Zhang, ML and Han, WZ and Song, YT}, title = {[Assessment of habitat quality changes and driving factors in Jilin Province based on InVEST model and geodetector].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {35}, number = {10}, pages = {2853-2860}, doi = {10.13287/j.1001-9332.202410.026}, pmid = {39727132}, issn = {1001-9332}, mesh = {China ; *Ecosystem ; *Conservation of Natural Resources ; *Models, Theoretical ; Environmental Monitoring ; Forests ; Trees/growth & development ; Geographic Information Systems ; }, abstract = {Jilin Province is an important ecological security barrier in Northeast China as it is located at the junction of the Northeast forest belts and the northern sand prevention belts. In recent years, Jilin Province has actively carried out ecological protection and restoration projects, resulting in a continuous improvement trend for the overall ecological environment. However, the evolution patterns and mechanisms of habitat quality are largely unkown. We applied the InVEST model and geographic detector method to analyze the changes in habitat quality and evaluate the main driving factors from 2000 to 2020. The results showed that the average habitat quality in Jilin Province showed a slight downward trend, and that the spatial heterogeneity characteristics of habitat quality in east and west gradually increased. The degree of habitat degradation presented a single nuclear radiation pattern centered on Changchun City. Vegetation factors and terrain factors were the first and secondary causes of spatial heterogeneity of habitat quality, respectively. The average habitat quality within the eco-redline of Jilin Province was showing an increasing trend year by year, which was consistent with the overall distribution of regions with extremely high habitat quality levels. There was a local spatial dislocation (the phenomenon of extremely high habitat quality levels not within the eco-redline) in the eastern part of Jilin Province. Our results could provide reference basis for ecosystem protection and the spatial pattern optimization.}, } @article {pmid39727130, year = {2024}, author = {Jia, J and Su, X and Zhang, J and Lu, CL and Zhang, MY and Li, X and Dong, YG and Ren, HC}, title = {[Land use changes and driving forces of landslide area in Tongwei County, Gansu Province, Northwest China from 1985 to 2020.].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {35}, number = {10}, pages = {2833-2841}, doi = {10.13287/j.1001-9332.202410.020}, pmid = {39727130}, issn = {1001-9332}, mesh = {China ; *Landslides ; *Conservation of Natural Resources ; *Crops, Agricultural/growth & development ; Ecosystem ; Trees/growth & development ; Forests ; Grassland ; Environmental Monitoring/methods ; Disasters ; Geographic Information Systems ; Poaceae/growth & development ; }, abstract = {Accurately analyzing the type of land use and change characteristics of disaster damage in landslide areas is of great significance to scientifically promote the optimization of regional land use pattern and disaster prevention and mitigation. We analyzed the characteristic parameters of landslides as well as the characteristics and driving factors of land use change from 1985 to 2020 in Tongwei County, Gansu Province, using ALOS DEM data and 1985-2020 land use data, GIS spatial analysis, land-use dynamic attitude, transfer matrix, and Geodetector. The results showed that a total of 1012 landslide samples were identified, characterized by medium elevation, gentle gradient, low elevation difference, short length, and small size. During 1985-2020, landslide area land use types were cropland, woodland, grassland, bare land and impervious surface, dominated by grassland and cropland. During 2015-2020, each category of single land use dynamic attitude reached the largest, with the value of cropland, grassland, woodland, bare land, and the combined land use being 3.1%, 3.0%, 10.9%, 20.0%, 1.5%, respectively. During the study period, land use change was dominated by cropland and grassland, with a total reduction of 4.39 km[2] in cultivated land area, which was converted into grassland and forest. There was no change in bare land and impervious surfaces. We investigated the driving factors of land use change across 2000-2005 and 2015-2020. Slope and normalized difference vegetation index had a stronger explanatory power for land use change during 2000-2005, while slope, population density and total population had a stronger explanatory power during 2015-2020. The land use mode of regional individual landslide tended to be unified, and the increase of grassland enhanced the vegetation cover of the region. The findings would provide a scientific basis for the development and reuse of disaster damaged land and ecological restoration.}, } @article {pmid39720717, year = {2024}, author = {Luo, Z and Zhou, F and Jiang, S and Huang, J and Yang, L and Yang, Q and Shi, J and Li, E and Ma, Z and Li, Y}, title = {Immune and physiological responses in Penaeus monodon to ammonia-N stress: a multi-omics approach.}, journal = {Frontiers in immunology}, volume = {15}, number = {}, pages = {1510887}, pmid = {39720717}, issn = {1664-3224}, mesh = {Animals ; *Penaeidae/immunology ; *Ammonia/metabolism ; *Stress, Physiological/immunology ; *Oxidative Stress ; Transcriptome ; Metabolomics ; Immunity, Innate ; Gene Expression Profiling ; Nitrogen/metabolism ; Aquaculture ; Biomarkers ; Hepatopancreas/immunology/metabolism ; Multiomics ; }, abstract = {Ammonia-N stress is a significant environmental factor that adversely affects the health and productivity of aquaculture species. This study investigates the effects of ammonia-N stress on the shrimp Penaeus monodon through a combination of biochemical, histological, transcriptomic, and metabolomic analyses. Shrimp were exposed to ammonia-N stress for 12 and 96 hours, and key markers of oxidative stress, nitrogen metabolism, immune response, and overall health were assessed. The results showed that prolonged ammonia-N exposure causes significant hepatopancreatic damage, including atrophy and deformation. Transcriptomic analysis revealed significant changes in gene expression related to apoptosis, immune response, and key metabolic pathways, with particular emphasis on the disruption of innate immune signaling and defense mechanisms. Metabolomic analysis identified disruptions in nucleotide turnover, antioxidant defenses, and fundamental metabolic processes. These findings suggest that ammonia-N stress induces a multifaceted stress response in shrimp, involving oxidative stress, immune activation, and metabolic disturbances. Understanding these immune-related and metabolic mechanisms provides valuable insights into the molecular responses of crustaceans to environmental stress, laying the foundation for assessing the ecological risk of ammonia-N and identifying potential immunological biomarkers for monitoring and mitigating its adverse effects in aquaculture systems.}, } @article {pmid39719706, year = {2024}, author = {Zhang, AN and Gaston, JM and Cárdenas, P and Zhao, S and Gu, X and Alm, EJ}, title = {CRISPR-Cas spacer acquisition is a rare event in human gut microbiome.}, journal = {Cell genomics}, volume = {}, number = {}, pages = {100725}, doi = {10.1016/j.xgen.2024.100725}, pmid = {39719706}, issn = {2666-979X}, abstract = {Host-parasite relationships drive the evolution of both parties. In microbe-phage dynamics, CRISPR functions as an adaptive defense mechanism, updating immunity via spacer acquisition. Here, we investigated these interactions within the human gut microbiome, uncovering low frequencies of spacer acquisition at an average rate of one spacer every ∼2.9 point mutations using isolates' whole genomes and ∼2.7 years using metagenome time series. We identified a highly prevalent CRISPR array in Bifidobacterium longum spreading via horizontal gene transfer (HGT), with six spacers found in various genomic regions in 15 persons from the United States and Europe. These spacers, targeting two prominent Bifidobacterium phages, comprised 76% of spacer occurrence of all spacers targeting these phages in all B. longum populations. This result suggests that HGT of an entire CRISPR-Cas system introduced three times more spacers than local CRISPR-Cas acquisition in B. longum. Overall, our findings identified key ecological and evolutionary factors in prokaryote adaptive immunity.}, } @article {pmid39718830, year = {2024}, author = {Kicsiny, R and Hufnagel, L and Lóczi, L and Székely, L and Varga, Z}, title = {Modeling the Mutation and Competition of Certain Nutrient-Producing Protocells by Means of Specific Turing Machines.}, journal = {Artificial life}, volume = {}, number = {}, pages = {1-29}, doi = {10.1162/artl_a_00463}, pmid = {39718830}, issn = {1530-9185}, abstract = {It is very important to model the behavior of protocells as basic lifelike artificial organisms more and more accurately from the level of genomes to the level of populations. A better understanding of basic protocell communities may help us in describing more complex ecological systems accurately. In this article, we propose a new comprehensive, bilevel mathematical model of a community of three protocell species (one generalist and two specialists). The aim is to achieve a model that is as basic/fundamental as possible while already displaying mutation, selection, and complex population dynamics phenomena (like competitive exclusion and keystone species). At the microlevel of genetic codes, the protocells and their mutations are modeled with Turing machines (TMs). The specialists arise from the generalist by means of mutation. Then the species are put into a common habitat, where, at the macrolevel of populations, they have to compete for the available nutrients, a part of which they themselves can produce. Because of different kinds of mutations, the running times of the species as TMs (algorithms) are different. This feature is passed on to the macrolevel as different reproduction times. At the macrolevel, a discrete-time dynamic model describes the competition. The model displays complex lifelike behavior known from population ecology, including the so-called competitive exclusion principle and the effect of keystone species. In future works, the bilevel model will have a good chance of serving as a simple and useful tool for studying more lifelike phenomena (like evolution) in their pure/abstract form.}, } @article {pmid39717656, year = {2024}, author = {Nguyen, TTT and de A Santiago, ALCM and Hallsworth, JE and Cordeiro, TRL and Voigt, K and Kirk, PM and Crous, PW and Júnior, MAM and Elsztein, C and Lee, HB}, title = {New Mucorales from opposite ends of the world.}, journal = {Studies in mycology}, volume = {109}, number = {}, pages = {273-321}, pmid = {39717656}, issn = {0166-0616}, abstract = {The Mucorales is a group of ancient fungi with global distribution. In the current study we accessed mucoralean fungi isolated from two countries on opposite sides of the Earth and in different hemispheres: South Korea and Brazil. Mucorales isolates were obtained from freshwater, soil, invertebrates, and fruit seeds and identified using phenotypic techniques combined with the DNA sequence data. These analyses revealed 15 new species including one that we affiliated to a newly proposed genus, Neofennellomyces. Names proposed for these 15 new species are Absidia cheongyangensis, A. fluvii, A. kunryangriensis, A. paracylindrospora, A. tarda, A. variiprojecta, A. variispora, Backusella varians, Mucor albicolonia, M. aurantiacus, M. cryophilus, M. glutinatus, M. paraorantomantidis, M. timomeni, and Neofennellomyces jeongsukae. Of these new species, 12 were isolated from South Korea: A. cheongyangensis, A. fluvii, A. kunryangriensis, A. paracylindrospora, B. varians, M. albicolonia, M. aurantiacus, M. cryophilus, M. glutinatus, M. paraorantomantidis, M. timomeni, and N. jeongsukae, and three from Brazil: A. tarda, A. variiprojecta, and A. variispora. Niche specificity of these fungi is discussed including newly recorded invertebrate hosts and a new geographic distribution for species of Backusella, Circinella, Cunninghamella, and Mucor. Given these findings, we provide an inventory of Mucorales. Taxonomic novelties: New genus: Neofennellomyces Hyang B. Lee & T.T.T. Nguyen. New species: Absidia cheongyangensis Hyang B. Lee & T.T.T. Nguyen, Absidia fluvii Hyang B. Lee, A.L. Santiago, P.M. Kirk, K. Voigt & T.T.T. Nguyen, Absidia kunryangriensis Hyang B. Lee & T.T.T. Nguyen, Absidia paracylindrospora Hyang B. Lee & T.T.T. Nguyen, Absidia tarda T.R.L. Cordeiro, Hyang B. Lee & A.L. Santiago, Absidia variiprojecta T.R.L. Cordeiro & A.L. Santiago, Absidia variispora T.R.L. Cordeiro & A.L. Santiago, Backusella varians Hyang B. Lee & T.T.T. Nguyen, Mucor aurantiacus Hyang B. Lee & T.T.T. Nguyen, Mucor cryophilus Hyang B. Lee & T.T.T. Nguyen, Mucor albicolonia Hyang B. Lee & T.T.T. Nguyen, Mucor glutinatus Hyang B. Lee & T.T.T. Nguyen, Mucor paraorantomantidis Hyang B. Lee & T.T.T. Nguyen, Mucor timomeni Hyang B. Lee & T.T.T. Nguyen, Neofennellomyces jeongsukae Hyang B. Lee & T.T.T. Nguyen. Citation: Nguyen TTT, de A. Santiago ALCM, Hallsworth JE, Cordeiro TRL, Voigt K, Kirk PM, Crous PW, Júnior MAM, Elsztein C, Lee HB (2024). New Mucorales from opposite ends of the world. Studies in Mycology 109: 273-321. doi: 10.3114/sim.2024.109.04.}, } @article {pmid39717508, year = {2025}, author = {Wang, T and Campbell, C and Stockdale, AJ and Todd, S and McIntyre, K and Frankland, A and Jaworski, J and Glampson, B and Papadimitriou, D and Mercuri, L and Mayer, E and Jones, CR and Salih, H and Roadknight, G and Little, S and Noble, T and Várnai, KA and Davis, C and Heinson, AI and George, M and Borca, F and English, L and Romão, L and Ramlakhan, D and , and Woods, K and Davies, J and Nastouli, E and Khakoo, SI and Gelson, W and Cooke, GS and Barnes, E and Matthews, PC}, title = {Distinct virologic trajectories in chronic hepatitis B identify heterogeneity in response to nucleos(t)ide analogue therapy.}, journal = {JHEP reports : innovation in hepatology}, volume = {7}, number = {1}, pages = {101229}, pmid = {39717508}, issn = {2589-5559}, abstract = {BACKGROUND & AIMS: The dynamics of HBV viral load (VL) in patients with chronic hepatitis B (CHB) on nucleos(t)ide analogue (NA) treatment and its relationship with liver disease are poorly understood. We aimed to study longitudinal VL patterns and their associations with CHB clinical outcomes.

METHODS: Utilising large scale, routinely collected electronic health records from six centres in England, collated by the National Institute for Health and Care Research Health Informatics Collaborative (NIHR HIC), we applied latent class mixed models to investigate VL trajectory patterns in adults receiving NA treatment. We assessed associations of VL trajectory with alanine transaminase, and with liver fibrosis/cirrhosis.

RESULTS: We retrieved data from 1,885 adults on NA treatment (median follow-up 6.2 years, IQR 3.7-9.3 years), with 21,691 VL measurements (median 10 per patient, IQR 5-17). Five VL classes were identified from the derivation cohort (n = 1,367, discrimination: 0.93, entropy: 0.90): class 1 'long term suppression' (n = 827, 60.5%), class 2 'timely virological suppression' (n = 254, 18.6%), class 3 'persistent moderate viraemia' (n = 140, 10.2%), class 4 'persistent high-level viraemia' (n = 44, 3.2%), and class 5 'slow virological suppression' (n = 102, 7.5%). The model demonstrated a discrimination of 0.93 and entropy of 0.88 for the validation cohort (n = 518). Alanine transaminase decreased variably over time in VL-suppressed groups (classes 1, 2, 5; all p <0.001), but did not significantly improve in those with persistent viraemia (classes 3, 4). Patients in class 5 had twofold increased hazards of fibrosis/cirrhosis compared with class 1 (adjusted hazard ratio, 2.00; 95% CI, 1.33-3.02).

CONCLUSIONS: Heterogeneity exists in virological response to NA therapy in CHB patients, with over 20% showing potentially suboptimal responses. Slow virological suppression is associated with liver disease progression.

IMPACT AND IMPLICATIONS: Treatment recommendations for people living with chronic hepatitis B virus (HBV) infection are becoming less stringent, meaning that more of the population will be eligible to receive therapy with nucleos(t)ide analogue agents. We explored outcomes of HBV treatment in a large UK dataset, describing different responses to treatment, and showing that the viral load is not completely suppressed after 1 year in about one in five cases, associated with an increased risk of liver complications. As treatment is rolled out more widely, patients and clinicians need to be aware of the potential for incomplete virologic responses. The findings can support the identification of high-risk individuals, improve early fibrosis and cirrhosis prediction, guide monitoring and preventive interventions, and support public health elimination goals.}, } @article {pmid39716198, year = {2024}, author = {Mendoza, JN and Prūse, B and Ciriaco, A and Mendoza, A and Ciriaco, H and Buen, C and Pua, JJ and Primavera, F and Mattalia, G and Sõukand, R}, title = {Fishery and ecology-related knowledge about plants among fishing communities along Laguna Lake, Philippines.}, journal = {Journal of ethnobiology and ethnomedicine}, volume = {20}, number = {1}, pages = {108}, pmid = {39716198}, issn = {1746-4269}, mesh = {*Fisheries ; Philippines ; *Ethnobotany ; Humans ; *Knowledge ; *Conservation of Natural Resources ; *Lakes ; Ecosystem ; Fishes ; Animals ; Ecology ; Female ; Male ; Middle Aged ; Adult ; Plants ; }, abstract = {BACKGROUND: Ethnobotanical knowledge about plant roles in fisheries is crucial for sustainable resource management. Local ecological knowledge helps understand dynamics of the lake ecosystem. Fishers use plants based on availability and characteristics while adapting to the changes in the environment. Studying fishery related uses of plants and algae and the challenges interconnected with them from local perspectives can provide insights into their beneficial uses and impacts to the ecosystem.

METHODS: The study investigates the botanical knowledge of three fishing villages in Laguna Lake or Laguna de Bay (LB), Philippines, including Buhangin, Sampiruhan, and Mabato-Azufre, each with varying degrees of industrialization. The ethnobotanical study, which gathered 27 interviews between June 2022 and July 2024, included plant collection with the help of local collaborators, including local fishers as research guides.

RESULTS: Fishers in LB highlighted positive and negative plant-fishing interactions. The most frequently mentioned plant applications were fish habitat and fish hiding places. Fish food, spawning sites, conservation, and a number of challenges such as navigational concerns and aquaculture fish deaths had been previously reported in local use reports. The remaining observations provide new insights into plant-fishing interactions, including indicators of food quality and food sources for fish, the decrease in the action of waves, and how plants help in improving the quality of the water.

CONCLUSION: These results highlight that the knowledge of fishers regarding the ecosystem in which they conduct their fishing activities provides baseline information about the positive and negative relationships between plants and fishing activities in the region, which is vital for further understanding its biodiversity and ecosystem interactions. It is crucial to consider fisher knowledge and involve them as equal partners in conservation efforts of LB.}, } @article {pmid39716000, year = {2025}, author = {Chunduri, JR and Sagar, SP}, title = {Insect Brain Proteomics: A Case Study of Periplaneta americana.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2884}, number = {}, pages = {99-118}, pmid = {39716000}, issn = {1940-6029}, mesh = {Animals ; *Periplaneta/metabolism ; *Proteomics/methods ; *Brain/metabolism ; *Insect Proteins/metabolism/analysis ; *Proteome ; Chromatography, Liquid/methods ; Mass Spectrometry/methods ; Computational Biology/methods ; }, abstract = {Insects are known invertebrate species with economic, ecological, pathological, and medicinal value, as well as closely associated with human populations. Entomophagy and entomotherapy are future promising prospects largely attributable to the abundant availability, high protein content, and climatic sustainability of insects. In particular, the insect brain is an important system with a secluded, compact, and protective exoskeleton. It is immunologically privileged and capable of producing a robust immune response against pathogens. It is also a source of materials that initiate key activity throughout the body. Proteomic interrogation of Periplaneta americana enables understanding the role of this insect in the fields of food and pharmacology. Proximate analyses of P. americana highlights its richness in proteins. Here we perform a simple proteomic analysis to study the brain proteome of P. americana. The processes applied during the study include gel-based isolation and separation of proteins, followed by NanoLC-MS (Orbitrap) analyses and bioinformatic interrogation of the data. The results demonstrated that this insect proteome comprises antimicrobial proteins, allergens, and proteins required for metabolic processes.}, } @article {pmid39713561, year = {2024}, author = {Blair, ME and Noguera-Urbano, EA and Ochoa-Quintero, JM and Paz, A and Lopez-Gallego, C and Echeverry-Galvis, MÁ and Zuloaga, J and Rodríguez, P and Lemus-Mejia, L and Ersts, P and López-Lozano, DF and Aiello-Lammens, ME and Arango, HM and Buitrago, L and Chang Triguero, S and Cruz-Rodríguez, CA and Díaz-Nieto, JF and Escobar, D and Grisales-Betancur, V and Johnson, BA and Kass, JM and Londoño-Murcia, MC and Merow, C and Muñoz-Rodríguez, CJ and Olaya-Rodríguez, MH and Parra, JL and Pinilla-Buitrago, GE and Roach, NS and Rojas-Soto, O and Roncancio-Duque, N and Suárez-Valencia, E and Urbina-Cardona, JN and Velásquez-Tibatá, J and Zapata-Martinez, CA and Anderson, RP}, title = {Software codesign between end users and developers to enhance utility for biodiversity conservation.}, journal = {Bioscience}, volume = {74}, number = {12}, pages = {867-873}, pmid = {39713561}, issn = {0006-3568}, abstract = {Creating software tools that address the needs of a wide range of decision-makers requires the inclusion of differing perspectives throughout the development process. Software tools for biodiversity conservation often fall short in this regard, partly because broad decision-maker needs may exceed the toolkits of single research groups or even institutions. We show that participatory, collaborative codesign enhances the utility of software tools for better decision-making in biodiversity conservation planning, as demonstrated by our experiences developing a set of integrated tools in Colombia. Specifically, we undertook an interdisciplinary, multi-institutional collaboration of ecological modelers, software engineers, and a diverse profile of potential end users, including decision-makers, conservation practitioners, and biodiversity experts. We leveraged and modified common paradigms of software production, including codesign and agile development, to facilitate collaboration through all stages (including conceptualization, development, testing, and feedback) to ensure the accessibility and applicability of the new tools to inform decision-making for biodiversity conservation planning.}, } @article {pmid39710433, year = {2024}, author = {Yuan, H and Hicks, P and Ahmadian, M and Johnson, KA and Valtadoros, L and Krishnan, A}, title = {Annotating publicly-available samples and studies using interpretable modeling of unstructured metadata.}, journal = {Briefings in bioinformatics}, volume = {26}, number = {1}, pages = {}, pmid = {39710433}, issn = {1477-4054}, support = {2328140//National Science Foundation/ ; }, mesh = {*Metadata ; *Natural Language Processing ; *Machine Learning ; Humans ; Computational Biology/methods ; Proteomics/methods ; Vocabulary, Controlled ; }, abstract = {Reusing massive collections of publicly available biomedical data can significantly impact knowledge discovery. However, these public samples and studies are typically described using unstructured plain text, hindering the findability and further reuse of the data. To combat this problem, we propose txt2onto 2.0, a general-purpose method based on natural language processing and machine learning for annotating biomedical unstructured metadata to controlled vocabularies of diseases and tissues. Compared to the previous version (txt2onto 1.0), which uses numerical embeddings as features, this new version uses words as features, resulting in improved interpretability and performance, especially when few positive training instances are available. Txt2onto 2.0 uses embeddings from a large language model during prediction to deal with unseen-yet-relevant words related to each disease and tissue term being predicted from the input text, thereby explaining the basis of every annotation. We demonstrate the generalizability of txt2onto 2.0 by accurately predicting disease annotations for studies from independent datasets, using proteomics and clinical trials as examples. Overall, our approach can annotate biomedical text regardless of experimental types or sources. Code, data, and trained models are available at https://github.com/krishnanlab/txt2onto2.0.}, } @article {pmid39709508, year = {2024}, author = {De Wint, FC and Nicholson, S and Koid, QQ and Zahra, S and Chestney-Claassen, G and Seelan, JSS and Xie, J and Xing, S and Fayle, TM and Haelewaters, D}, title = {Introducing a global database of entomopathogenic fungi and their host associations.}, journal = {Scientific data}, volume = {11}, number = {1}, pages = {1418}, pmid = {39709508}, issn = {2052-4463}, support = {2023 Student Mobility Grant to F.C.D.W.//EC | Erasmus+/ ; Senior Postdoctoral Fellowship 1206024N to D.H.//Fonds Wetenschappelijk Onderzoek (Research Foundation Flanders)/ ; }, mesh = {*Insecta/microbiology ; Animals ; *Databases, Factual ; *Hypocreales ; Host Specificity ; Biodiversity ; }, abstract = {Pathogens significantly influence natural and agricultural ecosystems, playing a crucial role in the regulation of species populations and maintaining biodiversity. Entomopathogenic fungi (EF), particularly within the Hypocreales order, exemplify understudied pathogens that infect insects and other arthropods globally. Despite their ecological importance, comprehensive data on EF host specificity and geographical distribution are lacking. To address this, we present EntomoFun 1.0, an open-access database centralizing global records of EF-insect associations in Hypocreales. This database includes 1,791 records detailing EF species, insect host taxa, countries of occurrence, life stages of hosts, and information sources. EntomoFun 1.0 is constructed based on 600 literature sources, as well as herbarium specimens of the Royal Botanical Gardens, Kew. This database is intended to test hypotheses, identify knowledge gaps, and stimulate future research. Contents of the EntomoFun 1.0 database are visualized with a global map, taxonomic chart, bipartite community network, and graphs.}, } @article {pmid39709502, year = {2024}, author = {Jakobsson, M and Mohammad, R and Karlsson, M and Salas-Romero, S and Vacek, F and Heinze, F and Bringensparr, C and Castro, CF and Johnson, P and Kinney, J and Cardigos, S and Bogonko, M and Accettella, D and Amblas, D and An, L and Bohan, A and Brandt, A and Bünz, S and Canals, M and Casamor, JL and Coakley, B and Cornish, N and Danielson, S and Demarte, M and Di Franco, D and Dickson, ML and Dorschel, B and Dowdeswell, JA and Dreutter, S and Fremand, AC and Hall, JK and Hally, B and Holland, D and Hong, JK and Ivaldi, R and Knutz, PC and Krawczyk, DW and Kristofferson, Y and Lastras, G and Leck, C and Lucchi, RG and Masetti, G and Morlighem, M and Muchowski, J and Nielsen, T and Noormets, R and Plaza-Faverola, A and Prescott, MM and Purser, A and Rasmussen, TL and Rebesco, M and Rignot, E and Rysgaard, S and Silyakova, A and Snoeijs-Leijonmalm, P and Sørensen, A and Straneo, F and Sutherland, DA and Tate, AJ and Travaglini, P and Trenholm, N and van Wijk, E and Wallace, L and Willis, JK and Wood, M and Zimmermann, M and Zinglersen, KB and Mayer, L}, title = {The International Bathymetric Chart of the Arctic Ocean Version 5.0.}, journal = {Scientific data}, volume = {11}, number = {1}, pages = {1420}, pmid = {39709502}, issn = {2052-4463}, abstract = {Knowledge about seafloor depth, or bathymetry, is crucial for various marine activities, including scientific research, offshore industry, safety of navigation, and ocean exploration. Mapping the central Arctic Ocean is challenging due to the presence of perennial sea ice, which limits data collection to icebreakers, submarines, and drifting ice stations. The International Bathymetric Chart of the Arctic Ocean (IBCAO) was initiated in 1997 with the goal of updating the Arctic Ocean bathymetric portrayal. The project team has since released four versions, each improving resolution and accuracy. Here, we present IBCAO Version 5.0, which offers a resolution four times as high as Version 4.0, with 100 × 100 m grid cells compared to 200 × 200 m. Over 25% of the Arctic Ocean is now mapped with individual depth soundings, based on a criterion that considers water depth. Version 5.0 also represents significant advancements in data compilation and computing techniques. Despite these improvements, challenges such as sea-ice cover and political dynamics still hinder comprehensive mapping.}, } @article {pmid39707199, year = {2024}, author = {Zhang, M and Sun, Y and Lan, Y and Cheng, L and Lv, Z and Han, M and Yang, L}, title = {Multiomics joint analysis reveals the potential mechanism of differences in the taproot thickening between cultivated ginseng and mountain-cultivated ginseng.}, journal = {BMC genomics}, volume = {25}, number = {1}, pages = {1228}, pmid = {39707199}, issn = {1471-2164}, support = {20230204001YY//the Key Research and Development Projects of Jilin Province Science and Technology Development Plan/ ; 20200504002YY//the Major Projects of Jilin Province Science and Technology Development Plan/ ; CARS-21//the National Modern Agricultural Industrial Technology System Fund Project/ ; }, mesh = {*Panax/genetics/growth & development/metabolism ; *Plant Roots/genetics/growth & development/metabolism ; Gene Expression Profiling ; Gene Expression Regulation, Plant ; Transcriptome ; Metabolomics ; Starch/metabolism ; Sucrose/metabolism ; Phenotype ; Genomics ; Multiomics ; }, abstract = {Panax ginseng is an important medicinal plant in China and is classified into two types: cultivated ginseng (CFCG) and mountain-cultivated ginseng (MCG). The two types of genetic varieties are the same, but the growth environments and management practices are different, resulting in substantial differences in their taproot morphology. Currently, there is a paucity of research on the internal mechanisms that regulate the phenotypic differences between cultivated ginseng and mountain-cultivated ginseng. In this study, we explored the potential mechanisms underlying their phenotypic differences using transcriptomic and metabolomic techniques. The results indicate that the taproot thickening of CFCG was significantly greater than that of MCG. Compared with MCG-4, MCG-10, and MCG-18, the diameters of the taproots of CFCG-4 increased by 158.96, 81.57, and 43.21%, respectively. Additionally, the contents of sucrose and starch in the taproot, as well as TRA and DHZR, were markedly elevated. Transcriptome analysis revealed that compared with MCG of different age groups, genes associated with starch and sucrose metabolism pathways (PgSUS1, PgSPS1, PgSPS3, and PgglgC1) were significantly upregulated in CFCG-4, whereas genes involved in the phenylpropanoid biosynthesis pathway (PgPER3, PgPER51, and PgPER12) were significantly downregulated in CFCG-4. This imbalance in the metabolic pathways suggests that these genes play crucial roles in ginseng taproot thickening. PgbHLH130 and PgARF18 may be key regulators of transcriptional changes in these pathways. These findings elucidate the molecular mechanisms governing ginseng taproot thickening, and have important implications for enhancing the overall quality and value of ginseng.}, } @article {pmid39703500, year = {2024}, author = {Townsend, HA and Rosenberger, KJ and Vanderlinden, LA and Inamo, J and Zhang, F}, title = {Evaluating methods for integrating single-cell data and genetics to understand inflammatory disease complexity.}, journal = {Frontiers in immunology}, volume = {15}, number = {}, pages = {1454263}, pmid = {39703500}, issn = {1664-3224}, mesh = {*Single-Cell Analysis/methods ; Humans ; *Genome-Wide Association Study ; Inflammation/genetics ; Arthritis, Rheumatoid/genetics/immunology ; Polymorphism, Single Nucleotide ; Genetic Predisposition to Disease ; Colitis, Ulcerative/genetics/immunology ; Algorithms ; Sequence Analysis, RNA/methods ; }, abstract = {BACKGROUND: Understanding genetic underpinnings of immune-mediated inflammatory diseases is crucial to improve treatments. Single-cell RNA sequencing (scRNA-seq) identifies cell states expanded in disease, but often overlooks genetic causality due to cost and small genotyping cohorts. Conversely, large genome-wide association studies (GWAS) are commonly accessible.

METHODS: We present a 3-step robust benchmarking analysis of integrating GWAS and scRNA-seq to identify genetically relevant cell states and genes in inflammatory diseases. First, we applied and compared the results of three recent algorithms, based on pathways (scGWAS), single-cell disease scores (scDRS), or both (scPagwas), according to accuracy/sensitivity and interpretability. While previous studies focused on coarse cell types, we used disease-specific, fine-grained single-cell atlases (183,742 and 228,211 cells) and GWAS data (Ns of 97,173 and 45,975) for rheumatoid arthritis (RA) and ulcerative colitis (UC). Second, given the lack of scRNA-seq for many diseases with GWAS, we further tested the tools' resolution limits by differentiating between similar diseases with only one fine-grained scRNA-seq atlas. Lastly, we provide a novel evaluation of noncoding SNP incorporation methods by testing which enabled the highest sensitivity/accuracy of known cell-state calls.

RESULTS: We first found that single-cell based tools scDRS and scPagwas called superior numbers of supported cell states that were overlooked by scGWAS. While scGWAS and scPagwas were advantageous for gene exploration, scDRS effectively accounted for batch effect and captured cellular heterogeneity of disease-relevance without single-cell genotyping. For noncoding SNP integration, we found a key trade-off between statistical power and confidence with positional (e.g. MAGMA) and non-positional approaches (e.g. chromatin-interaction, eQTL). Even when directly incorporating noncoding SNPs through 5' scRNA-seq measures of regulatory elements, non disease-specific atlases gave misleading results by not containing disease-tissue specific transcriptomic patterns. Despite this criticality of tissue-specific scRNA-seq, we showed that scDRS enabled deconvolution of two similar diseases with a single fine-grained scRNA-seq atlas and separate GWAS. Indeed, we identified supported and novel genetic-phenotype linkages separating RA and ankylosing spondylitis, and UC and crohn's disease. Overall, while noting evolving single-cell technologies, our study provides key findings for integrating expanding fine-grained scRNA-seq, GWAS, and noncoding SNP resources to unravel the complexities of inflammatory diseases.}, } @article {pmid39701966, year = {2024}, author = {Oskolkov, N and Sandionigi, A and Götherström, A and Canini, F and Turchetti, B and Zucconi, L and Mimmo, T and Buzzini, P and Borruso, L}, title = {Unraveling the ancient fungal DNA from the Iceman gut.}, journal = {BMC genomics}, volume = {25}, number = {1}, pages = {1225}, pmid = {39701966}, issn = {1471-2164}, mesh = {*DNA, Ancient/analysis ; Humans ; *DNA, Fungal/genetics ; Metagenomics/methods ; Gastrointestinal Microbiome/genetics ; Gastrointestinal Tract/microbiology ; Mummies/microbiology ; Computational Biology/methods ; Fungi/genetics/classification ; }, abstract = {BACKGROUND: Fungal DNA is rarely reported in metagenomic studies of ancient samples. Although fungi are essential for their interactions with all kingdoms of life, limited information is available about ancient fungi. Here, we explore the possibility of the presence of ancient fungal species in the gut of Ötzi, the Iceman, a naturally mummified human found in the Tyrolean Alps (border between Italy and Austria).

METHODS: A robust bioinformatic pipeline has been developed to detect and authenticate fungal ancient DNA (aDNA) from muscle, stomach, small intestine, and large intestine samples.

RESULTS: We revealed the presence of ancient DNA associated with Pseudogymnoascus genus, with P. destructans and P. verrucosus as possible species, which were abundant in the stomach and small intestine and absent in the large intestine and muscle samples.

CONCLUSION: We suggest that Ötzi may have consumed these fungi accidentally, likely in association with other elements of his diet, and they persisted in his gut after his death due to their adaptability to harsh and cold environments. This suggests the potential co-occurrence of ancient humans with opportunistic fungal species and proposes and validates a conservative bioinformatic approach for detecting and authenticating fungal aDNA in historical metagenomic samples.}, } @article {pmid39700981, year = {2024}, author = {Wong, SY and Machado-de-Lima, NM and Wilkins, D and Zhang, E and Ferrari, BC}, title = {Fine-scale landscape heterogeneity drives microbial community structure at Robinson Ridge, East Antarctica.}, journal = {The Science of the total environment}, volume = {958}, number = {}, pages = {177964}, doi = {10.1016/j.scitotenv.2024.177964}, pmid = {39700981}, issn = {1879-1026}, abstract = {Life at Robinson Ridge, located in the Windmill Islands region of East Antarctica, is susceptible to a changing climate. At this site, responses of the vegetation communities and moss-beds have been well researched, but corresponding information for microbial counterparts is still lacking. To bridge this knowledge gap, we established baseline data for monitoring the environmental drivers shaping the soil microbial community on the local 'hillslope' scale. Using triplicate 300-m long transects encompassing a hillslope with wind-exposed arid soils near the top, and snowmelt-sustained-moss beds at the bottom, we assessed the fine-scale heterogeneity of the soil environmental and microbial properties. Moist, low-lying, and vegetated soils exhibited higher soil fertility and unique biodiversity, with taxa adapted to thrive in moist conditions (i.e., Tardigrada, Phragmoplastophyta, Chloroflexi) and those that have previously demonstrated strong specificity for moss species (i.e., Fibrobacterota, Mucoromycota and Cyanobacteria) dominating. In contrast, elevated soils with limited moisture and nutrients were dominated by metabolically diverse phyla like Actinobacteriota and Ascomycota. Significant differences in microbial communities were observed at both hillslope (50-300 m) and fine spatial scales, as small as 0.1 m. Vertical heterogeneity was observed with higher abundances of Cyanobacteria and micro-algae in surfaces compared to subsoil, potentially indicating early biocrust formation. Stochastic and deterministic processes governing phylogenetic assembly were linked to soil positional groups and microbial domains rather than soil depth. Gradient Forest modeling identified critical environmental thresholds, such as ammonia, manganese, and sulphur, responsible for drastic community changes following level alterations. This reinforces the existence of strong niche preferences and distinct distribution patterns within the local microbial communities. This study highlights the need for finer-scale investigations considering site topography to better understand the relationship between environmental drivers and local microbiota. Ultimately, these insights enable us to understand environmental drivers and predict Antarctic ecosystem responses, helping safeguard this fragile environment.}, } @article {pmid39700412, year = {2024}, author = {Duan, HN and Hearne, G and Polikar, R and Rosen, GL}, title = {The Naïve Bayes Classifier ++ for Metagenomic Taxonomic Classification-Query Evaluation.}, journal = {Bioinformatics (Oxford, England)}, volume = {}, number = {}, pages = {}, doi = {10.1093/bioinformatics/btae743}, pmid = {39700412}, issn = {1367-4811}, abstract = {MOTIVATION: This study examines the query performance of the NBC ++ (Incremental Naive Bayes Classifier) program for variations in canonicality, k-mer size, databases, and input sample data size. We demonstrate that both NBC ++ and Kraken2 are influenced by database depth, with macro measures improving as depth increases. However, fully capturing the diversity of life, especially viruses, remains a challenge.

RESULTS: NBC ++ can competitively profile the superkingdom content of metagenomic samples using a small training database. NBC ++ spends less time training and can use a fraction of the memory than Kraken2 but at the cost of long querying time. Major NBC ++ enhancements include accommodating canonical k-mer storage (leading to significant storage savings) and adaptable and optimized memory allocation that accelerates query analysis and enables the software to be run on nearly any system. Additionally, the output now includes log-likelihood values for each training genome, providing users with valuable confidence information.

AVAILABILITY: Source code and Dockerfile are available at http://github.com/EESI/Naive_Bayes.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online, and databases are available at Zenodo records #11657719 and #11643985.}, } @article {pmid39695923, year = {2024}, author = {Zhang, Z and Li, Q and Li, H and Wei, S and Yu, W and Peng, Z and Wei, F and Zhou, W}, title = {Integrative multi-omics analysis reveals the contribution of neoVTX genes to venom diversity of Synanceia verrucosa.}, journal = {BMC genomics}, volume = {25}, number = {1}, pages = {1210}, pmid = {39695923}, issn = {1471-2164}, support = {2023YFF1304900//Ministry of Science and Technology of the People's Republic of China/ ; 2024A1515013196//Science and Technology Department of Guangdong Province/ ; SLYJ2023B4004//Guangdong Forestry Administration/ ; GML2020GD0804//PI Project of Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou)/ ; GML2022GD0804//PI Project of Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou)/ ; 32222014//National Natural Science Foundation of China/ ; 2021YFF0502804//Ministry of Science and Technology of China/ ; }, mesh = {Animals ; *Transcriptome ; Fish Venoms/genetics/chemistry ; Genomics/methods ; Proteomics ; Proteome ; Alternative Splicing ; Fishes/genetics ; Phylogeny ; Gene Expression Profiling ; Multiomics ; }, abstract = {BACKGROUND: Animal venom systems are considered as valuable model for investigating the molecular mechanisms underlying phenotypic evolution. Stonefish are the most venomous and dangerous fish because of severe human envenomation and occasionally fatalities, whereas the genomic background of their venom has not been fully explored compared with that in other venomous animals.

RESULTS: In this study, we followed modern venomic pipelines to decode the Synanceia verrucosa venom components. A catalog of 478 toxin genes was annotated based on our assembled chromosome-level genome. Integrative analysis of the high-quality genome, the transcriptome of the venom gland, and the proteome of crude venom revealed mechanisms underlying the venom complexity in S. verrucosa. Six tandem-duplicated neoVTX subunit genes were identified as the major source for the neoVTX protein production. Further isoform sequencing revealed massive alternative splicing events with a total of 411 isoforms demonstrated by the six genes, which further contributed to the venom diversity. We then characterized 12 dominantly expressed toxin genes in the venom gland, and 11 of which were evidenced to produce the venom protein components, with the neoVTX proteins as the most abundant. Other major venom proteins included a presumed CRVP, Kuntiz-type serine protease inhibitor, calglandulin protein, and hyaluronidase. Besides, a few of highly abundant non-toxin proteins were also characterized and they were hypothesized to function in housekeeping or hemostasis maintaining roles in the venom gland. Notably, gastrotropin like non-toxin proteins were the second highest abundant proteins in the venom, which have not been reported in other venomous animals and contribute to the unique venom properties of S. verrucosa.

CONCLUSIONS: The results identified the major venom composition of S. verrucosa, and highlighted the contribution of neoVTX genes to the diversity of venom composition through tandem-duplication and alternative splicing. The diverse neoVTX proteins in the venom as lethal particles are important for understanding the adaptive evolution of S. verrucosa. Further functional studies are encouraged to exploit the venom components of S. verrucosa for pharmaceutical innovation.}, } @article {pmid39695260, year = {2024}, author = {Ma, X and Zheng, G and Xu, C and Moskal, LM and Gong, P and Guo, Q and Huang, H and Li, X and Liang, X and Pang, Y and Wang, C and Xie, H and Yu, B and Zhao, B and Zhou, Y}, title = {A global product of 150-m urban building height based on spaceborne lidar.}, journal = {Scientific data}, volume = {11}, number = {1}, pages = {1387}, pmid = {39695260}, issn = {2052-4463}, support = {42171340//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, abstract = {Urban building height, as a fundamental 3D urban structural feature, has far-reaching applications. However, creating readily available datasets of recent urban building heights with fine spatial resolutions and global coverage remains a challenging task. Here, we provide a 150-m global urban building heights dataset around 2020 by combining the spaceborne lidar (Global Ecosystem Dynamics Investigation, GEDI), multi-sourced data (Landsat-8, Sentinel-2, and Sentinel-1), and topographic data. The validation results revealed that the GEDI-estimated building height samples were effective compared to the reference data (Pearson's r = 0.81, RMSE = 3.58 m). The mapping product also demonstrated good performance, as indicated by its strong correlation with the reference data (Pearson's r = 0.71, RMSE = 4.73 m). Compared with the currently existing datasets, it holds the ability to provide a spatial resolution (150 m) with a great level of inherent details about the spatial heterogeneity and flexibility of updating using the GEDI samples as inputs. This product will boost future urban studies across many fields, including environmental, ecological, and social sciences.}, } @article {pmid39694720, year = {2024}, author = {Reynolds, SA and Beery, S and Burgess, N and Burgman, M and Butchart, SHM and Cooke, SJ and Coomes, D and Danielsen, F and Di Minin, E and Durán, AP and Gassert, F and Hinsley, A and Jaffer, S and Jones, JPG and Li, BV and Mac Aodha, O and Madhavapeddy, A and O'Donnell, SAL and Oxbury, WM and Peck, L and Pettorelli, N and Rodríguez, JP and Shuckburgh, E and Strassburg, B and Yamashita, H and Miao, Z and Sutherland, WJ}, title = {The potential for AI to revolutionize conservation: a horizon scan.}, journal = {Trends in ecology & evolution}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tree.2024.11.013}, pmid = {39694720}, issn = {1872-8383}, abstract = {Artificial Intelligence (AI) is an emerging tool that could be leveraged to identify the effective conservation solutions demanded by the urgent biodiversity crisis. We present the results of our horizon scan of AI applications likely to significantly benefit biological conservation. An international panel of conservation scientists and AI experts identified 21 key ideas. These included species recognition to uncover 'dark diversity', multimodal models to improve biodiversity loss predictions, monitoring wildlife trade, and addressing human-wildlife conflict. We consider the potential negative impacts of AI adoption, such as AI colonialism and loss of essential conservation skills, and suggest how the conservation field might adapt to harness the benefits of AI while mitigating its risks.}, } @article {pmid39692459, year = {2024}, author = {Shitindo, M}, title = {Interactions between wild pigs and the spread of disease.}, journal = {eLife}, volume = {13}, number = {}, pages = {}, pmid = {39692459}, issn = {2050-084X}, mesh = {Animals ; *Animals, Wild ; Swine ; Swine Diseases ; Geographic Information Systems ; Humans ; }, abstract = {Tracking wild pigs with GPS devices reveals how their social interactions could influence the spread of disease, offering new strategies for protecting agriculture, wildlife, and human health.}, } @article {pmid39691468, year = {2024}, author = {Winders, S and Yoo, L and Heitkemper, M and Kamp, K}, title = {Multilevel Factors and Sleep in Adults With Inflammatory Bowel Disease: A Qualitative Study.}, journal = {Crohn's & colitis 360}, volume = {6}, number = {4}, pages = {otae075}, pmid = {39691468}, issn = {2631-827X}, abstract = {BACKGROUND: This study aimed to describe the patient-reported factors that impact sleep among individuals with inflammatory bowel disease (IBD), aligning with the Social Ecological Model of Sleep. This addresses the gap in IBD sleep research, which predominantly focuses on individual-level factors and their impact on sleep.

METHODS: Adults (ages 18-65) with IBD were recruited online through ResearchMatch in June 2023. Participants filled out survey questions on their demographic characteristics, health history, sleep, and IBD-related symptoms. Content analysis was conducted on 2 open-ended questions about factors that impacted their sleep.

RESULTS: This analysis included 163 adults with IBD (M = 39 years of age, 76.7% White, 91.4% non-Hispanic or Latino, 66.9% female, and 83.4% active IBD) who answered open-ended questions with comments about their sleep. Most participants indicated an individual-level factor impacted their sleep quality (85.3%, n = 139), categorized into 5 subthemes: Mental health, health, behavior and choices, physiology, and attitudes. Additionally, participants (43.6%, n = 71) mentioned social-level factors divided into 7 subthemes: Family, work, home, neighborhood, social network, and school. A smaller group of participants (17.2%, n = 28) mentioned societal-level factors designated into 4 subthemes: Natural environment and geography, technology, 24/7 society, and economics.

CONCLUSIONS: This study highlights the need for tailored sleep interventions for those with IBD that consider not only disease activity but also mental health, family, work, and the natural environment. IBD clinics should prioritize sleep health using an interdisciplinary approach to holistically address the unique needs of those with IBD.}, } @article {pmid39689854, year = {2024}, author = {Radice, VZ and Hernández-Agreda, A and Pérez-Rosales, G and Booker, R and Bellworthy, J and Broadribb, M and Carpenter, GE and Diaz, C and Eckert, RJ and Foster, NL and Gijsbers, JC and Gress, E and Laverick, JH and Micaroni, V and Pierotti, M and Rouzé, H and Stevenson, A and Sturm, AB and Bongaerts, P}, title = {Recent trends and biases in mesophotic ecosystem research.}, journal = {Biology letters}, volume = {20}, number = {12}, pages = {20240465}, pmid = {39689854}, issn = {1744-957X}, mesh = {*Ecosystem ; Animals ; Oceans and Seas ; Research/trends ; Anthozoa/physiology ; Bias ; Databases, Factual ; }, abstract = {Mesophotic ecosystems (approx. 30-150 m) represent a significant proportion of the world's oceans yet have long remained understudied due to challenges in accessing these deeper depths. Owing to advances in underwater technologies and a growing scientific and management interest, there has been a major expansion in research of both (sub)tropical mesophotic coral ecosystems and temperate mesophotic ecosystems. Here, we characterize the recent global trends in mesophotic research through an updated release of the 'mesophotic.org' database (www.mesophotic.org) where we reviewed and catalogued 1500 scientific publications. In doing so, we shed light on four major research biases: a gross imbalance in (a) the geographical spread of research efforts, differences in (b) the focal depth range and (c) research fields associated with study organisms and research platforms, and (d) the lack of temporal studies. Overall, we are optimistic about the future of mesophotic research and hope that by highlighting current trends and imbalances, we can raise awareness and stimulate discussion on the future directions of this emerging field.}, } @article {pmid39689059, year = {2024}, author = {Bernadou, A and Jeanson, R}, title = {Randomness as a driver of inactivity in social groups.}, journal = {PLoS computational biology}, volume = {20}, number = {12}, pages = {e1012668}, pmid = {39689059}, issn = {1553-7358}, mesh = {Animals ; *Ants/physiology ; *Social Behavior ; Behavior, Animal/physiology ; Models, Biological ; Bees/physiology ; Computational Biology ; Computer Simulation ; Social Group ; }, abstract = {Social insects, such as ants and bees, are known for their highly efficient and structured colonies. Division of labour, in which each member of the colony has a specific role, is considered to be one major driver of their ecological success. However, empirical evidence has accumulated showing that many workers, sometimes more than half, remain idle in insect societies. Several hypotheses have been put forward to explain these patterns, but none provides a consensual explanation. Task specialisation exploits inter-individual variations, which are mainly influenced by genetic factors beyond the control of the colony. As a result, individuals may also differ in the efficiency with which they perform tasks. In this context, we aimed to test the hypothesis that colonies generate a large number of individuals in order to recruit only the most efficient to perform tasks, at the cost of producing and maintaining a fraction of workers that remain inactive. We developed a model to explore the conditions under which variations in the scaling of workers' production and maintenance costs, along with activity costs, allow colonies to sustain a fraction of inactive workers. We sampled individual performances according to different random distributions in order to simulate the variability associated with worker efficiency. Our results show that the inactivity of part of the workforce can be beneficial for a wide range of parameters if it allows colonies to select the most efficient workers. In decentralised systems such as insect societies, we suggest that inactivity is a by-product of the random processes associated with the generation of individuals whose performance levels cannot be controlled.}, } @article {pmid39688289, year = {2024}, author = {Bao, Y and Jia, F and Geng, Y and Song, G and Xu, R and Wang, H and Mu, Y and Tong, HHY and Zhang, F and Guo, J}, title = {Uncovering the Differed Susceptibility of Fusarium oxysporum (Fo32931 and FocII5) to Fungicide Phenamacril: From Computational and Experimental Perspectives.}, journal = {Journal of agricultural and food chemistry}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.jafc.4c07865}, pmid = {39688289}, issn = {1520-5118}, abstract = {Fo32931 and FoCII5 are two subtypes of Fusarium oxysporum (Fo), a pathogenic filamentous fungus. Phenamacril (PHA), a Fusarium-specific fungicide that targets myosin I, exhibits significant hyphal growth inhibition in Fo32931 but shows weak resistance in FocII5, despite only two amino acid differences in the PHA-binding pocket of myosin I. In this study, we aim to elucidate the molecular basis for the differential sensitivity ofF. oxysporum myosin I variants (FoMyoI[32931] and FoMyoI[cII5]) to phenamacril through computational methods and biochemical validation. The results suggest that phenamacril functions as an allosteric inhibitor for FoMyoI[32931], inhibiting the large oscillation of the converter lever domain (CLD) upon ATP binding and promoting the opening of the outer cleft, further impairing protein function. PHA significantly reduced the coupling between the CLD, especially the converter, and the catalytic center, diminishing the response of the CLD to the motor domain in FoMyoI[32931]. From the residue mutation experiment, we found that the S418T substitution in FoMyoI[cII5] is the key to the reduced phenamacril sensitivity of FocII5. According to the microscale thermophoresis (MST) assay and pocket conformation analysis, the S418T mutation disturbs the orientation of pocket residues, especially Lys537, leading to a looser pocket and reduced interaction between Lys537 and phenamacril, which lowers the binding affinity of FoMyoI[cII5] for phenamacril. These findings provide deeper insights into the reasons for the lower sensitivity of FoCII5 to phenamacril from both molecular and structural perspectives and will also guide the design of novel inhibitors against resistant Fusarium spp., like FoCII5.}, } @article {pmid39684926, year = {2024}, author = {Liu, R and Zhang, P and Bai, J and Zhong, Z and Shan, Y and Cheng, Z and Zhang, Q and Guo, Q and Zhang, H and Zhang, B}, title = {Integrated Transcriptomic and Proteomic Analyses of Antler Growth and Ossification Mechanisms.}, journal = {International journal of molecular sciences}, volume = {25}, number = {23}, pages = {}, pmid = {39684926}, issn = {1422-0067}, support = {23CB063 and 24CE-BGS-09//Beijing Academy of Science and Technology Financial Support Projects/ ; }, mesh = {*Antlers/growth & development/metabolism ; Animals ; *Osteogenesis/genetics ; *Deer/genetics/growth & development ; *Transcriptome ; *Proteomics/methods ; Proteome/metabolism ; Gene Expression Profiling ; Gene Expression Regulation, Developmental ; Computational Biology/methods ; }, abstract = {Antlers are the sole mammalian organs capable of continuous regeneration. This distinctive feature has evolved into various biomedical models. Research on mechanisms of antler growth, development, and ossification provides valuable insights for limb regeneration, cartilage-related diseases, and cancer mechanisms. Here, ribonucleic acid sequencing (RNA-seq) and four-dimensional data-independent acquisition (4D DIA) technologies were employed to examine gene and protein expression differences among four tissue layers of the Chinese milu deer antler: reserve mesenchyme (RM), precartilage (PC), transition zone (TZ), cartilage (CA). Overall, 4611 differentially expressed genes (DEGs) and 2388 differentially expressed proteins (DEPs) were identified in the transcriptome and proteome, respectively. Among the 828 DEGs common to both omics approaches, genes from the collagen, integrin, and solute carrier families, and signaling molecules were emphasized for their roles in the regulation of antler growth, development, and ossification. Bioinformatics analysis revealed that in addition to being regulated by vascular and nerve regeneration pathways, antler growth and development are significantly influenced by numerous cancer-related signaling pathways. This indicates that antler growth mechanisms may be similar to those of cancer cell proliferation and development. This study lays a foundation for future research on the mechanisms underlying the rapid growth and ossification of antlers.}, } @article {pmid39684378, year = {2024}, author = {Zhang, KL and Leng, YN and Hao, RR and Zhang, WY and Li, HF and Chen, MX and Zhu, FY}, title = {Adaptation of High-Altitude Plants to Harsh Environments: Application of Phenotypic-Variation-Related Methods and Multi-Omics Techniques.}, journal = {International journal of molecular sciences}, volume = {25}, number = {23}, pages = {}, pmid = {39684378}, issn = {1422-0067}, support = {KYCX24_1376//Postgraduate Research & Practice Innovation Program of Jiangsu Province/ ; 2023ZD0405602//STI 2030－Major Projects/ ; CX (21)2023//Jiangsu Agricultural Science and Technology Innovation Fund/ ; BK20240668//Basic Research Program of Jiangsu Province/ ; }, mesh = {*Altitude ; *Metabolomics/methods ; *Plants/metabolism/genetics ; *Proteomics/methods ; *Adaptation, Physiological ; *Genomics/methods ; *Phenotype ; Plant Physiological Phenomena ; Acclimatization ; Transcriptome ; Multiomics ; }, abstract = {High-altitude plants face extreme environments such as low temperature, low oxygen, low nutrient levels, and strong ultraviolet radiation, causing them to adopt complex adaptation mechanisms. Phenotypic variation is the core manifestation of ecological adaptation and evolution. Many plants have developed a series of adaptive strategies through long-term natural selection and evolution, enabling them to survive and reproduce under such harsh conditions. This article reviews the techniques and methods used in recent years to study the adaptive evolution of high-altitude plants, including transplantation techniques, genomics, transcriptomics, proteomics, and metabolomics techniques, and their applications in high-altitude plant adaptive evolution. Transplantation technology focuses on phenotypic variation, which refers to natural variations in morphological, physiological, and biochemical characteristics, exploring their key roles in nutrient utilization, photosynthesis optimization, and stress-resistance protection. Multiple omics technologies, including genomics, transcriptomics, proteomics, and metabolomics, have revealed genes, regulatory pathways, and metabolic networks associated with phenotypic variations at the genetic and molecular levels. At the same time, the limitations and deficiencies of current technologies used to study plant adaptation to high-altitude environments were discussed. In addition, we propose future improvements to existing technologies and advocate for the integration of different technologies at multiple levels to study the molecular mechanisms of plant adaptation to high-altitude environments, thus providing insights for future research in this field.}, } @article {pmid39683090, year = {2024}, author = {Chaligava, O and Zinicovscaia, I and Peshkova, A and Yushin, N and Frontasyeva, M and Vergel, K and Nurkassimova, M and Cepoi, L}, title = {Major and Trace Airborne Elements and Ecological Risk Assessment: Georgia Moss Survey 2019-2023.}, journal = {Plants (Basel, Switzerland)}, volume = {13}, number = {23}, pages = {}, pmid = {39683090}, issn = {2223-7747}, abstract = {The study, carried out as part of the International Cooperative Program on Effects of Air Pollution on Natural Vegetation and Crops, involved collecting 95 moss samples across the territory of Georgia during the period from 2019 to 2023. Primarily samples of Hypnum cupressiforme were selected, with supplementary samples of Abietinella abietina, Pleurozium schreberi, and Hylocomium splendens in cases of the former's absence. The content of 14 elements (Al, Ba, Cd, Co, Cr, Cu, Fe, Mn, Ni, Pb, S, Sr, V, and Zn) was detected using Inductively Coupled Plasma Atomic Emission Spectroscopy (ICP-AES), while the Hg content was determined using a Direct Mercury Analyzer. To identify any relationships between chemical elements and to depict their sources, multivariate statistics was applied. Principal component analysis identified three main components: PC1 (geogenic, 43.4%), PC2 (anthropogenic, 13.3%), and PC3 (local anomalies, 8.5%). The results were compared with the first moss survey conducted in Georgia in the period from 2014 to 2017, offering insights into temporal trends of air quality. Utilizing GIS, a spatial map illustrating pollution levels across Georgia, based on the Pollution Load Index, was generated. The Potential Environmental Risk Index emphasized significant risks associated with mercury and cadmium at several locations. The study highlights the utility of moss biomonitoring in assessing air pollution and identifying hotspots of contamination. The findings from this study could be beneficial for future biomonitoring research in areas with varying physical and geographical conditions.}, } @article {pmid39679384, year = {2024}, author = {Khosravi, M and Mojtabaeian, SM and Sarvestani, MA}, title = {A Systematic Review on the Outcomes of Climate Change in the Middle-Eastern Countries: The Catastrophes of Yemen and Syria.}, journal = {Environmental health insights}, volume = {18}, number = {}, pages = {11786302241302270}, pmid = {39679384}, issn = {1178-6302}, abstract = {The Middle East is facing serious climate change challenges, rendering it as one of the most affected regions worldwide. This paper aimed to investigate the outcomes of climate change in the Middle East. In 2024, a qualitative study was conducted employing a methodology that integrated systematic review for data collection and thematic analysis for data analysis. Such integration of the approaches provided valuable insights into the findings within the literature in a comprehensive and categorized format. PubMed, Scopus, ProQuest, and the Cochrane Database of Systematic Reviews were searched for relevant studies published between 2000 and 2024. The quality of these studies was assessed using the AACODS (Accuracy, Coverage, Objectivity, Date, Significance) checklist. The data extracted from the included studies underwent a thematic analysis utilizing Braun and Clarke's methodology. After completing the screening process, a total of 93 papers were deemed suitable for inclusion in the study. The quality assessment of these selected studies demonstrated a notably high standard, particularly in terms of authority, accuracy, coverage, objectivity, and significance. Moreover, minimal levels of bias were observed within the included studies. Subsequent thematic analysis of the findings from the systematic review identified 6 overarching themes: "Human Health Outcomes," "Animal Health Outcomes," "Plant Health Outcomes," "Ecological Outcomes," "Economic Outcomes," and "Political Outcomes." The study revealed ecological outcomes as the most prevalent consequences of climate change in the Middle East, including alterations in habitat distribution, temperature increase, water scarcity, and more. The outcomes seemed to be interconnected, exacerbating each other. Yemen and Syria had faced severe consequences, leading to political unrest and humanitarian crises in which Yemen ranking among the most water-stressed nations globally, while Syria contending with millions of displaced individuals living in dire conditions.}, } @article {pmid39675288, year = {2024}, author = {Mu, X and Chen, C and Fan, Q and Zhang, W and Liu, F and Guo, J and Qi, W and Liu, H}, title = {Removal and ecological impact of sulfamethoxazole and N-acetyl sulfamethoxazole in mesocosmic wetlands dominated by submerged plants: Plant tolerance, microbial response, and nitrogen transformation.}, journal = {The Science of the total environment}, volume = {958}, number = {}, pages = {178034}, doi = {10.1016/j.scitotenv.2024.178034}, pmid = {39675288}, issn = {1879-1026}, abstract = {Sulfamethoxazole (SMX) and its human metabolite N-acetylsulfamethoxazole (N-SMX) are frequently detected in aquatic environments, posing potential threats to freshwater ecosystem health. Constructed wetlands are pivotal for wastewater treatment, with plant species serving as key determinants of pollutant removal efficiency. In this study, wetlands dominated by three submerged plants (Myriophyllum verticillatum, Vallisneria spiralis, Hydrilla verticillata) were respectively constructed to investigate the removal of SMX and N-SMX, and the impact on wetland ecology regarding plant tolerance, microbial response, and nitrogen transformation. Results showed that wetlands removed N-SMX (82.3-99.8 %) more effectively than SMX (54.3-80.2 %), with the wetland dominated by Myriophyllum verticillatum showing the highest removal efficiency. However, high concentrations (5 mg/L) of SMX and N-SMX significantly reduced NH4[+]-N and TN removal (p < 0.05), accompanied by shifts in microbial communities, especially a decreased abundance of Proteobacteria and key nitrogen-transforming genes. A total of 22 different ARGs (antibiotic resistance genes) were detected. SMX significantly increased the relative abundance of sulfonamide resistance genes (sul1, sul2) (p < 0.05), while major denitrifying genera, such as Thiobacillus, which were not the primary hosts of these genes, showed a significant negative correlation with sul1 and sul2 (p < 0.05). This study provides a reference for ecological remediation of wetlands in response to antibiotic contamination.}, } @article {pmid39656857, year = {2024}, author = {Alvarado, M and Gómez-Navajas, JA and Blázquez-Muñoz, MT and Gómez-Molero, E and Fernández-Sánchez, S and Eraso, E and Munro, CA and Valentín, E and Mateo, E and de Groot, PWJ}, title = {The good, the bad, and the hazardous: comparative genomic analysis unveils cell wall features in the pathogen Candidozyma auris typical for both baker's yeast and Candida.}, journal = {FEMS yeast research}, volume = {24}, number = {}, pages = {}, pmid = {39656857}, issn = {1567-1364}, support = {PID2020-117983RB-I00//Agencia Estatal de Investigación/ ; SBPLY/23/180225/000029//UCLM/ ; //European Regional Development Fund/ ; JDC2023-051226-I//European Social Fund Plus/ ; }, mesh = {*Cell Wall/metabolism ; *Saccharomyces cerevisiae/genetics/metabolism ; Computational Biology ; Genomics ; Candida auris/genetics/metabolism/drug effects ; beta-Glucans/metabolism ; Genome, Fungal ; Fungal Proteins/genetics/metabolism ; Glycosylphosphatidylinositols/metabolism/genetics ; Candida albicans/genetics/pathogenicity ; Candida/genetics/metabolism/pathogenicity ; }, abstract = {The drug-resistant pathogenic yeast Candidozyma auris (formerly named Candida auris) is considered a critical health problem of global importance. As the cell wall plays a crucial role in pathobiology, here we performed a detailed bioinformatic analysis of its biosynthesis in C. auris and related Candidozyma haemuli complex species using Candida albicans and Saccharomyces cerevisiae as references. Our data indicate that the cell wall architecture described for these reference yeasts is largely conserved in Candidozyma spp.; however, expansions or reductions in gene families point to subtle alterations, particularly with respect to β--1,3--glucan synthesis and remodeling, phosphomannosylation, β-mannosylation, and glycosylphosphatidylinositol (GPI) proteins. In several aspects, C. auris holds a position in between C. albicans and S. cerevisiae, consistent with being classified in a separate genus. Strikingly, among the identified putative GPI proteins in C. auris are adhesins typical for both Candida (Als and Hyr/Iff) and Saccharomyces (Flo11 and Flo5-like flocculins). Further, 26 putative C. auris GPI proteins lack homologs in Candida genus species. Phenotypic analysis of one such gene, QG37_05701, showed mild phenotypes implicating a role associated with cell wall β-1,3-glucan. Altogether, our study uncovered a wealth of information relevant for the pathogenicity of C. auris as well as targets for follow-up studies.}, } @article {pmid39671449, year = {2024}, author = {Celiker, E and Woodrow, C and Guadayol, Ò and Davranoglou, LR and Schlepütz, CM and Mortimer, B and Taylor, GK and Humphries, S and Montealegre-Z, F}, title = {Mechanical network equivalence between the katydid and mammalian inner ears.}, journal = {PLoS computational biology}, volume = {20}, number = {12}, pages = {e1012641}, pmid = {39671449}, issn = {1553-7358}, mesh = {Animals ; *Ear, Inner/anatomy & histology/physiology ; *Mammals/physiology ; *Hearing/physiology ; Computer Simulation ; Insecta/physiology ; Computational Biology ; Models, Biological ; Cochlea/physiology/anatomy & histology ; X-Ray Microtomography ; }, abstract = {Mammalian hearing operates on three basic steps: 1) sound capturing, 2) impedance conversion, and 3) frequency analysis. While these canonical steps are vital for acoustic communication and survival in mammals, they are not unique to them. An equivalent mechanism has been described for katydids (Insecta), and it is unique to this group among invertebrates. The katydid inner ear resembles an uncoiled cochlea, and has a length less than 1 mm. Their inner ears contain the crista acustica, which holds tonotopically arranged sensory cells for frequency mapping via travelling waves. The crista acustica is located on a curved triangular surface formed by the dorsal wall of the ear canal. While empirical recordings show tonotopic vibrations in the katydid inner ear for frequency analysis, the biophysical mechanism leading to tonotopy remains elusive due to the small size and complexity of the hearing organ. In this study, robust numerical simulations are developed for an in silico investigation of this process. Simulations are based on the precise katydid inner ear geometry obtained by synchrotron-based micro-computed tomography, and empirically determined inner ear fluid properties for an accurate representation of the underlying mechanism. We demonstrate that the triangular structure below the hearing organ drives the tonotopy and travelling waves in the inner ear, and thus has an equivalent role to the mammalian basilar membrane. This reveals a stronger analogy between the inner ear basic mechanical networks of two organisms with ancient evolutionary differences and independent phylogenetic histories.}, } @article {pmid39671336, year = {2024}, author = {Karim, AAJ and Mahmud, MZ and Khan, R}, title = {Advanced vision transformers and open-set learning for robust mosquito classification: A novel approach to entomological studies.}, journal = {PLoS computational biology}, volume = {20}, number = {12}, pages = {e1012654}, pmid = {39671336}, issn = {1553-7358}, mesh = {Animals ; *Culicidae/classification ; *Deep Learning ; *Computational Biology/methods ; Entomology/methods ; Mosquito Vectors/classification ; Humans ; Algorithms ; Neural Networks, Computer ; }, abstract = {Mosquito-related diseases pose a significant threat to global public health, necessitating efficient and accurate mosquito classification for effective surveillance and control. This work presents an innovative approach to mosquito classification by leveraging state-of-the-art vision transformers and open-set learning techniques. A novel framework has been introduced that integrates Transformer-based deep learning models with comprehensive data augmentation and preprocessing methods, enabling robust and precise identification of ten mosquito species. The Swin Transformer model achieves the best performance for traditional closed-set learning with 99.60% accuracy and 0.996 F1 score. The lightweight MobileViT technique attains an almost equivalent accuracy of 98.90% with significantly reduced parameters and model complexities. Next, the applied deep learning models' adaptability and generalizability in a static environment have been enhanced by using new classes of data samples during the inference stage that have not been included in the training set. The proposed framework's ability to handle unseen classes like insects similar to mosquitoes, even humans, through open-set learning further enhances its practical applicability employing the OpenMax technique and Weibull distribution. The traditional CNN model, Xception, outperforms the latest transformer with higher accuracy and F1 score for open-set learning. The study's findings highlight the transformative potential of advanced deep-learning architectures in entomology, providing a strong groundwork for future research and development in mosquito surveillance and vector control. The implications of this work extend beyond mosquito classification, offering valuable insights for broader ecological and environmental monitoring applications.}, } @article {pmid39670410, year = {2025}, author = {Alipio, K and García-Colón, J and Boscarino, N and Fox, K}, title = {Indigenous Data Sovereignty, Circular Systems, and Solarpunk Solutions for a Sustainable Future.}, journal = {Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing}, volume = {30}, number = {}, pages = {717-733}, pmid = {39670410}, issn = {2335-6936}, mesh = {*Artificial Intelligence ; *Computational Biology ; Humans ; Cloud Computing/statistics & numerical data ; Sustainable Development ; Indigenous Peoples/statistics & numerical data ; Conservation of Natural Resources ; }, abstract = {Recent advancements in Artificial Intelligence (AI) and data center infrastructure have brought the global cloud computing market to the forefront of conversations about sustainability and energy use. Current policy and infrastructure for data centers prioritize economic gain and resource extraction, inherently unsustainable models which generate massive amounts of energy and heat waste. Our team proposes the formation of policy around earth-friendly computation practices rooted in Indigenous models of circular systems of sustainability. By looking to alternative systems of sustainability rooted in Indigenous values of aloha 'āina, or love for the land, we find examples of traditional ecological knowledge (TEK) that can be imagined alongside Solarpunk visions for a more sustainable future. One in which technology works with the environment, reusing electronic waste (e-waste) and improving data life cycles.}, } @article {pmid39664868, year = {2024}, author = {Boyes, D and Zilli, A and , and , and , and , and , and , and , }, title = {The genome sequence of the Grey Shoulder-knot, Lithophane ornitopus (Hufnagel, 1766).}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {214}, pmid = {39664868}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual male Lithophane ornitopus (the Grey Shoulder-knot; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 508.6 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.33 kilobases in length. Gene annotation of this assembly on Ensembl identified 18,397 protein coding genes.}, } @article {pmid39664717, year = {2024}, author = {Baker, KS and Millerand, F}, title = {The Incremental Growth of Data Infrastructure in Ecology (1980-2020).}, journal = {Ecology and evolution}, volume = {14}, number = {12}, pages = {e70444}, pmid = {39664717}, issn = {2045-7758}, abstract = {After decades of growth, a research community's network information system and data repository were transformed to become a national data management office and a major element of data infrastructure for ecology and the environmental sciences. Developing functional data infrastructures is key to the support of ongoing Open Science and Open Data efforts. This example of data infrastructure growth contrasts with the top-down development typical of many digital initiatives. The trajectory of this network information system evolved within a collaborative, long-term ecological research community. This particular community is funded to conduct ecological research while collective data management is also carried out across its geographically dispersed study sites. From this longitudinal ethnography, we describe an Incremental Growth Model that includes a sequence of six relatively stable phases where each phase is initiated by a rapid response to a major pivotal event. Exploring these phases and the roles of data workers provides insight into major characteristics of digital growth. Further, a transformation in assumptions about data management is reported for each phase. Investigating the growth of a community information system over four decades as it becomes data infrastructure reveals details of its social, technical, and institutional dynamics. In addition to addressing how digital data infrastructure characteristics change, this study also considers when the growth of data infrastructure begins.}, } @article {pmid39663400, year = {2024}, author = {Carter, KR and Cavaleri, MA and Atkin, OK and Bahar, NHA and Cheesman, AW and Choury, Z and Crous, KY and Doughty, CE and Dusenge, ME and Ely, KS and Evans, JR and Fonseca da Silva, J and Mau, AC and Medlyn, BE and Meir, P and Norby, RJ and Read, J and Reed, SC and Reich, PB and Rogers, A and Serbin, SP and Slot, M and Schwartz, EC and Tribuzy, ES and Uddling, J and Vårhammar, A and Walker, AP and Winter, K and Wood, TE and Wu, J}, title = {Photosynthetic responses to temperature across the tropics: a meta-analytic approach.}, journal = {Annals of botany}, volume = {}, number = {}, pages = {}, doi = {10.1093/aob/mcae206}, pmid = {39663400}, issn = {1095-8290}, abstract = {BACKGROUND AND AIMS: Tropical forests exchange more carbon dioxide (CO2) with the atmosphere than any other terrestrial biome. Yet, uncertainty in the projected carbon balance over the next century is roughly three-times greater for the tropics than other ecosystems. Our limited knowledge of tropical plant physiological responses, including photosynthetic, to climate change is a substantial source of uncertainty in our ability to forecast the global terrestrial carbon sink.

METHODS: We used a meta-analytic approach, focusing on tropical photosynthetic temperature responses, to address this knowledge gap. Our dataset, gleaned from 18 independent studies, included leaf-level light saturated photosynthetic (Asat) temperature responses from 108 woody species, with additional temperature parameters (35 species) and rates (250 species) of both maximum rates of electron transport (Jmax) and Rubisco carboxylation (Vcmax). We investigated how these parameters responded to mean annual temperature (MAT), temperature variability, aridity, and elevation, as well as also how responses differed among successional strategy, leaf habit, and light environment.

KEY RESULTS: Optimum temperatures for Asat (ToptA) and Jmax (ToptJ) increased with MAT but not for Vcmax (ToptV). Although photosynthetic rates were higher for "light" than "shaded" leaves, light conditions did not generate differences in temperature response parameters. ToptA did not differ with successional strategy, but early successional species had ~4 °C wider thermal niches than mid/late species. Semi-deciduous species had ~1 °C higher ToptA than broadleaf evergreen. Most global modeling efforts consider all tropical forests as a single "broadleaf evergreen" functional type, but our data show that tropical species with different leaf habits display distinct temperature responses that should be included in modeling efforts.

CONCLUSIONS: This novel research will inform modeling efforts to quantify tropical ecosystem carbon cycling and provide more accurate representations of how these key ecosystems will respond to altered temperature patterns in the face of climate warming.}, } @article {pmid39660611, year = {2024}, author = {Mortzfeld, BM and Bhattarai, SK and Bucci, V}, title = {Novel class IIb microcins show activity against Gram-negative ESKAPE and plant pathogens.}, journal = {eLife}, volume = {13}, number = {}, pages = {}, pmid = {39660611}, issn = {2050-084X}, support = {R01 AG075283/AG/NIA NIH HHS/United States ; 457837076//Deutsche Forschungsgemeinschaft/ ; W81XWH2020013//Congressionally Directed Medical Research Programs/ ; 1R01AG075283-01A1/NH/NIH HHS/United States ; }, mesh = {*Bacteriocins/pharmacology/genetics/metabolism ; *Enterobacteriaceae/drug effects/genetics ; *Anti-Bacterial Agents/pharmacology ; Gram-Negative Bacteria/drug effects/genetics ; Plant Diseases/microbiology ; Microbial Sensitivity Tests ; }, abstract = {Interspecies interactions involving direct competition via bacteriocin production play a vital role in shaping ecological dynamics within microbial ecosystems. For instance, the ribosomally produced siderophore bacteriocins, known as class IIb microcins, affect the colonization of host-associated pathogenic Enterobacteriaceae species. Notably, to date, only five of these antimicrobials have been identified, all derived from specific Escherichia coli and Klebsiella pneumoniae strains. We hypothesized that class IIb microcin production extends beyond these specific compounds and organisms. With a customized informatics-driven approach, screening bacterial genomes in public databases with BLAST and manual curation, we have discovered 12 previously unknown class IIb microcins in seven additional Enterobacteriaceae species, encompassing phytopathogens and environmental isolates. We introduce three novel clades of microcins (MccW, MccX, and MccZ), while also identifying eight new variants of the five known class IIb microcins. To validate their antimicrobial potential, we heterologously expressed these microcins in E. coli and demonstrated efficacy against a variety of bacterial isolates, including plant pathogens from the genera Brenneria, Gibbsiella, and Rahnella. Two newly discovered microcins exhibit activity against Gram-negative ESKAPE pathogens, i.e., Acinetobacter baumannii or Pseudomonas aeruginosa, providing the first evidence that class IIb microcins can target bacteria outside of the Enterobacteriaceae family. This study underscores that class IIb microcin genes are more prevalent in the microbial world than previously recognized and that synthetic hybrid microcins can be a viable tool to target clinically relevant drug-resistant pathogens. Our findings hold significant promise for the development of innovative engineered live biotherapeutic products tailored to combat these resilient bacteria.}, } @article {pmid39657789, year = {2024}, author = {Zdouc, MM and Blin, K and Louwen, NLL and Navarro, J and Loureiro, C and Bader, CD and Bailey, CB and Barra, L and Booth, TJ and Bozhüyük, KAJ and Cediel-Becerra, JDD and Charlop-Powers, Z and Chevrette, MG and Chooi, YH and D'Agostino, PM and de Rond, T and Del Pup, E and Duncan, KR and Gu, W and Hanif, N and Helfrich, EJN and Jenner, M and Katsuyama, Y and Korenskaia, A and Krug, D and Libis, V and Lund, GA and Mantri, S and Morgan, KD and Owen, C and Phan, CS and Philmus, B and Reitz, ZL and Robinson, SL and Singh, KS and Teufel, R and Tong, Y and Tugizimana, F and Ulanova, D and Winter, JM and Aguilar, C and Akiyama, DY and Al-Salihi, SAA and Alanjary, M and Alberti, F and Aleti, G and Alharthi, SA and Rojo, MYA and Arishi, AA and Augustijn, HE and Avalon, NE and Avelar-Rivas, JA and Axt, KK and Barbieri, HB and Barbosa, JCJ and Barboza Segato, LG and Barrett, SE and Baunach, M and Beemelmanns, C and Beqaj, D and Berger, T and Bernaldo-Agüero, J and Bettenbühl, SM and Bielinski, VA and Biermann, F and Borges, RM and Borriss, R and Breitenbach, M and Bretscher, KM and Brigham, MW and Buedenbender, L and Bulcock, BW and Cano-Prieto, C and Capela, J and Carrion, VJ and Carter, RS and Castelo-Branco, R and Castro-Falcón, G and Chagas, FO and Charria-Girón, E and Chaudhri, AA and Chaudhry, V and Choi, H and Choi, Y and Choupannejad, R and Chromy, J and Donahey, MSC and Collemare, J and Connolly, JA and Creamer, KE and Crüsemann, M and Cruz, AA and Cumsille, A and Dallery, JF and Damas-Ramos, LC and Damiani, T and de Kruijff, M and Martín, BD and Sala, GD and Dillen, J and Doering, DT and Dommaraju, SR and Durusu, S and Egbert, S and Ellerhorst, M and Faussurier, B and Fetter, A and Feuermann, M and Fewer, DP and Foldi, J and Frediansyah, A and Garza, EA and Gavriilidou, A and Gentile, A and Gerke, J and Gerstmans, H and Gomez-Escribano, JP and González-Salazar, LA and Grayson, NE and Greco, C and Gomez, JEG and Guerra, S and Flores, SG and Gurevich, A and Gutiérrez-García, K and Hart, L and Haslinger, K and He, B and Hebra, T and Hemmann, JL and Hindra, H and Höing, L and Holland, DC and Holme, JE and Horch, T and Hrab, P and Hu, J and Huynh, TH and Hwang, JY and Iacovelli, R and Iftime, D and Iorio, M and Jayachandran, S and Jeong, E and Jing, J and Jung, JJ and Kakumu, Y and Kalkreuter, E and Kang, KB and Kang, S and Kim, W and Kim, GJ and Kim, H and Kim, HU and Klapper, M and Koetsier, RA and Kollten, C and Kovács, ÁT and Kriukova, Y and Kubach, N and Kunjapur, AM and Kushnareva, AK and Kust, A and Lamber, J and Larralde, M and Larsen, NJ and Launay, AP and Le, NT and Lebeer, S and Lee, BT and Lee, K and Lev, KL and Li, SM and Li, YX and Licona-Cassani, C and Lien, A and Liu, J and Lopez, JAV and Machushynets, NV and Macias, MI and Mahmud, T and Maleckis, M and Martinez-Martinez, AM and Mast, Y and Maximo, MF and McBride, CM and McLellan, RM and Bhatt, KM and Melkonian, C and Merrild, A and Metsä-Ketelä, M and Mitchell, DA and Müller, AV and Nguyen, GS and Nguyen, HT and Niedermeyer, THJ and O'Hare, JH and Ossowicki, A and Ostash, BO and Otani, H and Padva, L and Paliyal, S and Pan, X and Panghal, M and Parade, DS and Park, J and Parra, J and Rubio, MP and Pham, HT and Pidot, SJ and Piel, J and Pourmohsenin, B and Rakhmanov, M and Ramesh, S and Rasmussen, MH and Rego, A and Reher, R and Rice, AJ and Rigolet, A and Romero-Otero, A and Rosas-Becerra, LR and Rosiles, PY and Rutz, A and Ryu, B and Sahadeo, LA and Saldanha, M and Salvi, L and Sánchez-Carvajal, E and Santos-Medellin, C and Sbaraini, N and Schoellhorn, SM and Schumm, C and Sehnal, L and Selem, N and Shah, AD and Shishido, TK and Sieber, S and Silviani, V and Singh, G and Singh, H and Sokolova, N and Sonnenschein, EC and Sosio, M and Sowa, ST and Steffen, K and Stegmann, E and Streiff, AB and Strüder, A and Surup, F and Svenningsen, T and Sweeney, D and Szenei, J and Tagirdzhanov, A and Tan, B and Tarnowski, MJ and Terlouw, BR and Rey, T and Thome, NU and Torres Ortega, LR and Tørring, T and Trindade, M and Truman, AW and Tvilum, M and Udwary, DW and Ulbricht, C and Vader, L and van Wezel, GP and Walmsley, M and Warnasinghe, R and Weddeling, HG and Weir, ANM and Williams, K and Williams, SE and Witte, TE and Rocca, SMW and Yamada, K and Yang, D and Yang, D and Yu, J and Zhou, Z and Ziemert, N and Zimmer, L and Zimmermann, A and Zimmermann, C and van der Hooft, JJJ and Linington, RG and Weber, T and Medema, MH}, title = {MIBiG 4.0: advancing biosynthetic gene cluster curation through global collaboration.}, journal = {Nucleic acids research}, volume = {}, number = {}, pages = {}, doi = {10.1093/nar/gkae1115}, pmid = {39657789}, issn = {1362-4962}, support = {KICH1.LWV04.21.013//NWO/ ; 101000392//Horizon 2020/ ; OSF.23.1.044//NWO Open Science Project 'BiG-CODEC'/ ; 547394769//German Research Foundation/ ; //University of Sydney/ ; NNF22OC0078997//Novo Nodisk Foundation/ ; IM230100154//Australian Research Council Industry Fellowship/ ; //Hans Fischer Society/ ; //UK Government Department for Environment, Food & Rural Affairs (DEFRA) Global Centre on Biodiversity for the Climate/ ; EP/X03142X/1//United Kingdom Research and Innovation/ ; 101072485//Horizon Europe Marie Skłodowska-Curie/ ; //Indonesia Endowment Fund for Education Agency (LPDP)/ ; 106/IV/KS/11/2023//National Research and Innovation Agency/ ; 027/E5/PG.02.00.PL/2024//Ministry of Education/ ; MR/W011247/1//UKRI Future Leaders Fellowship/ ; 101117891-MeDiSyn//ERC Starting/ ; ANR-22-CE44-0011-01 UMISYN//Agence Nationale de la Recherche/ ; BB/X010953/1//Growing Health Institute Strategic Programme/ ; //Department of Biotechnology/ ; //National Agri-Food Biotechnology Institute/ ; 101087181//EU/ ; 212747/SNSF_/Swiss National Science Foundation/Switzerland ; 2021YFA0909500//National Key Research and Development Program of China/ ; 32170080//National Natural Science Foundation of China/ ; //Shanghai Pilot Program for Basic Research - Shanghai Jiao Tong University/ ; 21K06336//KAKENHI/ ; 21/07038-0//São Paulo Research Foundation/ ; VI.Veni.202.130//NWO Talent/ ; MR/V022334/1//UKRI Future Leaders Fellowship/ ; 222676//USDA Evans-Allen Research/ ; F32AT011475/AT/NCCIH NIH HHS/United States ; DGE 21-46756//National Science Foundation Graduate Research Fellowship/ ; //University of Illinois/ ; 802736//European Union Horizon 2020/ ; 735867//Consejo Nacional de Ciencia y Tecnología/ ; //NWO Merian/ ; BB/T007222/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; 101066127//European Union/ ; RYC2020-029240-I//Ministerio de Ciencia, Innovación y Universidades/ ; K12 GM068524/GM/NIGMS NIH HHS/United States ; //HZI POF IV Cooperativity and Creativity Project Call/ ; //Alexander von Humboldt-Stiftung/ ; EXC-2124/1-09.029_0//Cluster of Excellence: Controlling Microbes to Fight Infection/ ; NRF-2020R1A6A1A03044512//Korean Government (MSIT)/ ; 2022R1C1C2004118//National Research Foundation of Korea/ ; NE/T010959/1//Signals in the Soil/ ; CZIF2022-007203//Chan Zuckerberg Initiative Foundation/ ; 495740318//German Research Foundation/ ; ANR-24-CE20-7299-01//Agence Nationale de la Recherche/ ; ANR-17-EUR-0007//EUR Saclay Plant Sciences-SPS/ ; 101072485//European Union's Horizon/ ; //European Regional Development Fund/ ; 802736//European Union's Horizon 2020/ ; EP/X03142X/1//United Kingdom Research and Innovation/ ; //Swiss Federal Government/ ; PS00349981//Fulbright/ ; 398967434-TRR 261//Deutsche Forschungsgemeinschaft/ ; DM60066//Italian Ministry of Research/ ; 1229222N//Research Foundation-Flanders (FWO)/ ; R01-GM146224/GM/NIGMS NIH HHS/United States ; NA22NOS4200050//NERRS/ ; BB/V005723/2//BBSRC/ ; 1347411//CONAHCYT/ ; T32GM136583/NH/NIH HHS/United States ; 101130799//European Union's Horizon/ ; CFB 2.0//Novo Nordisk Foundation/ ; //Basic Science Research Program/ ; NRF-RS-2024-00352229//Ministry of Science and ICT/ ; NRF 2018R1A5A2023127//Korea Government (MSIT)/ ; //Werner Siemens Foundation/ ; OCENW.XL21.XL21.088//NWO-XL/ ; DNRF137//Danish National Research Foundation/ ; NNF19SA0059360//Novo Nordisk Foundation INTERACT/ ; CBET-2032243//U.S. National Science Foundation/ ; //Delta Stewardship Council Delta Science Program/ ; //European Union's Horizon 2020 Research/ ; 852600//Innovation Program ERC St/ ; 101072485//European Union's Horizon Europe/ ; //Conahcyt Mexico International PhD Studentship/ ; //Strathclyde University Global Research Scholarship/ ; 3141-00013A//Innovation Fund Denmark/ ; K445/2022//Leibniz Association/ ; 23/01956-2//São Paulo Research Foundation/ ; DGE 2241144//NSF GRFP/ ; 024.004.014//MiCRop Consortium/ ; CF22-1239//Carlsberg Foundation/ ; 102022750//SINTEF/ ; 102029187//SEP AGREE/ ; 102024676-14//POS BIOINFO 2024/ ; 101106349//Marie Sklodowska-Curie/ ; 57/0009//Ministry of Education and Science of Ukraine/ ; //National Research Fund of Ukraine/ ; DE-AC02-05CH11231//U.S. Department of Energy/ ; //German Academic Scholarship Foundation/ ; OCENW.GROOT.2019.063//NWO-XL/ ; //Department of Biotechnology/ ; //University Grants Commission/ ; PROYEXCEL_00012//Spanish "Junta de Andalucía"/ ; GNT2021638//National Health and Medical Research Council/ ; DP230102668//Australian Research Council Discovery Project/ ; 101000794//SECRETed EU Project Horizon 2020/ ; 865738/ERC_/European Research Council/International ; T32-GM136629//Chemical-Biology Interface Training/ ; DGE 21-46756//National Science Foundation Graduate Research Fellowship/ ; 101055020-COMMUNITY//ERC Advanced/ ; 757173//Consejo Nacional de Ciencia y Tecnología/ ; //Horizon Europe Marie Skłodowska-Curie Actions Postdoctoral Fellowship/ ; 101099528//European Innovation Council/ ; 10062709//UK Innovation Funding Agency (UKRI)/ ; //Swedish Pharmaceutical Society PostDoc/ ; 205320_219638/SNSF_/Swiss National Science Foundation/Switzerland ; //Saarland University/ ; BB/X01097X/1//BBSRC Institute Strategic Program/ ; AUFF-E-2022-9-42//AUFF/ ; 101055020-COMMUNITY//ERC Advanced/ ; NNF22OC0079021//Novo Nordisk Foundation Postdoctoral Fellowship/ ; //Natural Science and Research Council of Canada/ ; TTU 09.826//German Center for Infection Research/ ; 10.55776/P 34036//Austrian Science Fund/ ; //Natural Sciences and Engineering Research Council of Canada Discovery/ ; DNRF137//Danish National Research Foundation CeMiSt/ ; }, abstract = {Specialized or secondary metabolites are small molecules of biological origin, often showing potent biological activities with applications in agriculture, engineering and medicine. Usually, the biosynthesis of these natural products is governed by sets of co-regulated and physically clustered genes known as biosynthetic gene clusters (BGCs). To share information about BGCs in a standardized and machine-readable way, the Minimum Information about a Biosynthetic Gene cluster (MIBiG) data standard and repository was initiated in 2015. Since its conception, MIBiG has been regularly updated to expand data coverage and remain up to date with innovations in natural product research. Here, we describe MIBiG version 4.0, an extensive update to the data repository and the underlying data standard. In a massive community annotation effort, 267 contributors performed 8304 edits, creating 557 new entries and modifying 590 existing entries, resulting in a new total of 3059 curated entries in MIBiG. Particular attention was paid to ensuring high data quality, with automated data validation using a newly developed custom submission portal prototype, paired with a novel peer-reviewing model. MIBiG 4.0 also takes steps towards a rolling release model and a broader involvement of the scientific community. MIBiG 4.0 is accessible online at https://mibig.secondarymetabolites.org/.}, } @article {pmid39653494, year = {2024}, author = {Lee, HB and Nguyen, TTT and Noh, SJ and Kim, DH and Kang, KH and Kim, SJ and Kirk, PM and Avery, SV and Medina, A and Hallsworth, JE}, title = {Aspergillus ullungdoensis sp. nov., Penicillium jeongsukae sp. nov., and other fungi from Korea.}, journal = {Fungal biology}, volume = {128}, number = {8 Pt B}, pages = {2479-2492}, doi = {10.1016/j.funbio.2024.05.014}, pmid = {39653494}, issn = {1878-6146}, mesh = {Republic of Korea ; *Phylogeny ; *Penicillium/isolation & purification/classification/genetics ; DNA, Fungal/genetics ; Soil Microbiology ; Aspergillus/isolation & purification/classification/genetics ; Sequence Analysis, DNA ; Cluster Analysis ; DNA, Ribosomal Spacer/genetics/chemistry ; }, abstract = {Eurotiales fungi are thought to be distributed worldwide but there is a paucity of information about their occurrence on diverse substrates or hosts and at specific localities. Some of the Eurotiales, including Aspergillus and Penicillium species, produce an array of secondary metabolites of use for agricultural, medicinal, and pharmaceutical applications. Here, we carried out a survey of the Eurotiales in South Korea, focusing on soil, freshwater, and plants (dried persimmon fruits and seeds of Perilla frutescens, known commonly as shiso). We obtained 11 species that-based on morphology, physiology, and multi-locus (ITS, BenA, CaM, and RPB2) phylogenetic analyses-include two new species, Aspergillus ullungdoensis sp. nov. and Penicillium jeongsukae sp. nov., and nine species that were known, but previously not described in South Korea, Aspergillus aculeatinus, Aspergillus aurantiacoflavus, Aspergillus croceiaffinis, Aspergillus pseudoviridinutans, Aspergillus uvarum, Penicillium ferraniaense, Penicillium glaucoroseum, Penicillium sajarovii, and one, Penicillium charlesii, that was isolated from previously unknown host, woodlouse (Porcellio scaber). We believe that biodiversity survey and identifying new species can contribute to set a baseline for future changes in the context of humanitarian crises such as climate change.}, } @article {pmid39652754, year = {2024}, author = {Pillay, R and Watson, JEM and Hansen, AJ and Burns, P and Virnig, ALS and Supples, C and Armenteras, D and González-Del-Pliego, P and Aragon-Osejo, J and A Jantz, P and Ervin, J and Goetz, SJ and Venter, O}, title = {Global rarity of high-integrity tropical rainforests for threatened and declining terrestrial vertebrates.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {121}, number = {51}, pages = {e2413325121}, pmid = {39652754}, issn = {1091-6490}, support = {NNX17AG51G/NASA/NASA/United States ; NNL15AA03/NASA/NASA/United States ; 80NSSC18K0338/NASA/NASA/United States ; }, mesh = {*Rainforest ; Animals ; *Biodiversity ; *Vertebrates/physiology ; *Conservation of Natural Resources/methods ; Tropical Climate ; Endangered Species ; Ecosystem ; }, abstract = {Structurally intact native forests free from major human pressures are vitally important habitats for the persistence of forest biodiversity. However, the extent of such high-integrity forest habitats remaining for biodiversity is unknown. Here, we quantify the amount of high-integrity tropical rainforests, as a fraction of total forest cover, within the geographic ranges of 16,396 species of terrestrial vertebrates worldwide. We found up to 90% of the humid tropical ranges of forest-dependent vertebrates was encompassed by forest cover. Concerningly, however, merely 25% of these remaining rainforests are of high integrity. Forest-dependent species that are threatened and declining and species with small geographic ranges have disproportionately low proportions of high-integrity forest habitat left. Our work brings much needed attention to the poor quality of much of the forest estate remaining for biodiversity across the humid tropics. The targeted preservation of the world's remaining high-integrity tropical rainforests that are currently unprotected is a critical conservation priority that may help alleviate the biodiversity crisis in these hyperdiverse and irreplaceable ecosystems. Enhanced efforts worldwide to preserve tropical rainforest integrity are essential to meet the targets of the Convention on Biological Diversity's 2022 Kunming-Montreal Global Biodiversity Framework which aims to achieve near zero loss of high biodiversity importance areas (including ecosystems of high integrity) by 2030.}, } @article {pmid39649625, year = {2024}, author = {Boyes, D and Crowley, LC and Hutchinson, F and Wawman, DC and , and , and , and , and , and , and , }, title = {The genome sequence of the Broad-barred Knot-horn, Acrobasis consociella (Hübner, 1813).}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {429}, pmid = {39649625}, issn = {2398-502X}, abstract = {We present a genome assembly from one female Acrobasis consociella (the Broad-barred Knot-horn; Arthropoda; Insecta; Lepidoptera; Pyralidae). The genome sequence is 598.4 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z and W sex chromosomes. The mitochondrial genome has also been assembled and is 15.22 kilobases in length.}, } @article {pmid39647412, year = {2024}, author = {He, T and Xie, J and Jin, L and Zhao, J and Zhang, X and Liu, H and Li, XD}, title = {Seasonal dynamics of the phage-bacterium linkage and associated antibiotic resistome in airborne PM2.5 of urban areas.}, journal = {Environment international}, volume = {194}, number = {}, pages = {109155}, doi = {10.1016/j.envint.2024.109155}, pmid = {39647412}, issn = {1873-6750}, mesh = {*Bacteriophages/genetics ; *Particulate Matter ; China ; *Bacteria/genetics/drug effects ; *Seasons ; Humans ; Air Microbiology ; Cities ; Drug Resistance, Microbial/genetics ; Anti-Bacterial Agents/pharmacology ; Air Pollutants/analysis ; Metagenomics ; Drug Resistance, Bacterial/genetics ; Microbiota ; }, abstract = {Inhalable microorganisms in airborne fine particulate matter (PM2.5), including bacteria and phages, are major carriers of antibiotic resistance genes (ARGs) with strong ecological linkages and potential health implications for urban populations. A full-spectrum study on ARG carriers and phage-bacterium linkages will shed light on the environmental processes of antibiotic resistance from airborne dissemination to the human lung microbiome. Our metagenomic study reveals the seasonal dynamics of phage communities in PM2.5, their impacts on clinically important ARGs, and potential implications for the human respiratory microbiome in selected cities of China. Gene-sharing network comparisons show that air harbours a distinct phage community connected to human- and water-associated viromes, with 57 % of the predicted hosts being potential bacterial pathogens. The ARGs of common antibiotics, e.g., peptide and tetracycline, dominate both the antibiotic resistome associated with bacteria and phages in PM2.5. Over 60 % of the predicted hosts of vARG-carrying phages are potential bacterial pathogens, and about 67 % of these hosts have not been discovered as direct carriers of the same ARGs. The profiles of ARG-carrying phages are distinct among urban sites, but show a significant enrichment in abundance, diversity, temperate lifestyle, and matches of CRISPR (short for 'clustered regularly interspaced short palindromic repeats') to identified bacterial genomes in winter and spring. Moreover, phages putatively carry 52 % of the total mobile genetic element (MGE)-ARG pairs with a unique 'flu season' pattern in urban areas. This study highlights the role that phages play in the airborne dissemination of ARGs and their delivery of ARGs to specific opportunistic pathogens in human lungs, independent of other pathways of horizontal gene transfer. Natural and anthropogenic stressors, particularly wind speed, UV index, and level of ozone, potentially explained over 80 % of the seasonal dynamics of phage-bacterial pathogen linkages on antibiotic resistance. Therefore, understanding the phage-host linkages in airborne PM2.5, the full-spectrum of antibiotic resistomes, and the potential human pathogens involved, will be of benefit to protect human health in urban areas.}, } @article {pmid39644634, year = {2024}, author = {Xie, Y and Guo, J and Fan, Q and Huang, S and Qi, W and Cao, X and Peng, J and Chen, Y and Chen, M}, title = {High-density sampling reveals the occurrence, levels and transport flux of 15 polycyclic aromatic hydrocarbons derivatives (PAHs-d) along the Yangtze River.}, journal = {The Science of the total environment}, volume = {958}, number = {}, pages = {177907}, doi = {10.1016/j.scitotenv.2024.177907}, pmid = {39644634}, issn = {1879-1026}, abstract = {Polycyclic aromatic hydrocarbons derivatives (PAHs-d) have higher toxicity levels compared to its parent polycyclic aromatic hydrocarbons (PPAHs). Their partitioning in different media and large-scale transport patterns in rivers remain largely unknown. This study investigated the occurrence of 15 PAHs-d and 19 PPAHs in water and suspended particulate matter (SPM) of the Yangtze River between 2019 and 2020. The range of Σ15PAHs-d concentrations was 20.54 to 2010.03 ng·L[-1] in water and 0.62 to 29.80 μg·g[-1] in SPM. The primary PAHs-d components were 2,6-dimethylnaphthalene, 2-methylnaphthalene, and anthraquinone. The range of Σ19PPAHs concentrations in water and SPM was 34.89 to 739.53 ng·L[-1] and 0.37 to 204.62 μg·g[-1], respectively. And low-ring PAHs-d and PPAHs were more prevalent in water than SPM. Partitioning behaviors indicated that PAHs-d and PPAHs were more readily partitioned into water and SPM during normal and dry periods, respectively. The concentrations of PAHs-d saw significant changes in their spatial distribution, which rose in water and reduced in SPM in downstream of the Three Gorges Dam. This is due to the dam's blocking effect on sediment transport. Positive matrix factorization source analysis revealed biomass combustion upstream and vehicle emissions downstream as primary sources, shaped by the evolving energy consumption patterns of urban areas situated around the Yangtze River. The annual fluxes of PAHs-d in water and SPM of the Yangtze River were 90.40 t·yr[-1] and 11.95 t·yr[-1], representing 88.3 % and 11.7 % of the overall PAHs-d fluxes, respectively. The total fluxes of PAHs-d and PPAHs in water and SPM tended to increase spatially along the river, with growth rates exceeding 76 and 24 times, respectively. Interception within the Three Gorges Reservoir area has resulted in the differences in the concentration and transport distribution of PAHs-d and PPAHs upstream and downstream, which play important roles in reducing PAHs-d and PPAHs entry into the sea. Future studies on PAHs-d in Yangtze River basin tributaries and estuaries are essential.}, } @article {pmid39643871, year = {2024}, author = {Zhang, W and Jin, Z and Huang, R and Huang, W and Li, L and He, Y and Zhou, J and Tian, C and Xiao, L and Li, P and Quan, M and Zhang, D and Du, Q}, title = {Multi-omics analysis reveals genetic architecture and local adaptation of coumarins metabolites in Populus.}, journal = {BMC plant biology}, volume = {24}, number = {1}, pages = {1170}, pmid = {39643871}, issn = {1471-2229}, support = {No. 2021ZD0008//Major Science and Technology project of Inner Mongolia Autonomous Region/ ; No. 2021ZD0008//Major Science and Technology project of Inner Mongolia Autonomous Region/ ; No. 6212021//Project of the Natural Science Foundation of Beijing Municipality/ ; QNTD202305//Fundamental Research Funds for Central Universities of the Central South University/ ; }, mesh = {*Populus/genetics/metabolism ; *Coumarins/metabolism ; *Polymorphism, Single Nucleotide ; *Quantitative Trait Loci ; Adaptation, Physiological/genetics ; Gene Expression Regulation, Plant ; Genes, Plant ; Multiomics ; }, abstract = {BACKGROUND: Accumulation of coumarins plays key roles in response to immune and abiotic stress in plants, but the genetic adaptation basis of controlling coumarins in perennial woody plants remain unclear.

RESULTS: We detected 792 SNPs within 334 genes that were significantly associated with the phenotypic variations of 15 single-metabolic traits and multiple comprehensive index, such as principal components (PCs) of coumarins metabolites. Expression quantitative trait locus mapping uncovered that 337 eQTLs associated with the expression levels of 132 associated genes. Selective sweep revealed 55 candidate genes have potential selective signature among three geographical populations, highlighting that the coumarins biosynthesis have been encountered forceful local adaptation. Furthermore, we constructed a genetic network of seven candidate genes that coordinately regulate coumarins biosynthesis, revealing the multiple regulatory patterns affecting coumarins accumulation in Populus tomentosa. Validation of candidate gene variations in a drought-tolerated population and DUF538 heterologous transformation experiments verified the function of candidate genes and their roles in adapting to the different geographical conditions in poplar.

CONCLUSIONS: Our study uncovered the genetic regulation of the coumarins metabolic biosynthesis of Populus, and offered potential clues for drought-tolerance evaluation and regional improvement in woody plants.}, } @article {pmid39642727, year = {2024}, author = {Mendrik, F and Hackney, CR and Cumming, VM and Waller, C and Hak, D and Dorrell, R and Hung, NN and Parsons, DR}, title = {The transport and vertical distribution of microplastics in the Mekong River, SE Asia.}, journal = {Journal of hazardous materials}, volume = {484}, number = {}, pages = {136762}, doi = {10.1016/j.jhazmat.2024.136762}, pmid = {39642727}, issn = {1873-3336}, abstract = {Rivers are primary vectors of plastic debris to oceans, but sources, transport mechanisms, and fate of fluvial microplastics (<5 mm) remain poorly understood, impeding accurate predictions of microplastic flux, ecological risk and socio-economic impacts. We report on microplastic concentrations, characteristics and dynamics in the Mekong River, one of the world's largest and polluting rivers, in Cambodia and Vietnam. Sampling throughout the water column at multiple localities detected an average of 24 microplastics m[-3] (0.073 mg l[-1]). Concentrations increased downstream from rural Kampi, Cambodia (344 km from river mouth; 2 microplastics m[-3,] 0.006 mg l[-1]), to Can Tho, Vietnam (83 km from river mouth; 64 microplastics m[-3], 0.182 mg l[-1]) with most microplastics being fibres (53 %), followed by fragments (44 %) and the most common polymer being polyethylene terephthalate (PET) or polyester. Pathways of microplastic pollution are expected to be from urban wastewater highlighting the need for improved wastewater treatment in this region. On average, 86 % of microplastics are transported within the water column and consequently we identified an optimum sampling depth capturing a representative flux value, highlighting that sampling only the water surface substantially biases microplastic concentration predictions. Additionally, microplastic abundance does not linearly follow discharge changes during annual monsoonal floods or mirror siliciclastic sediment transport, as microplastic concentrations decrease rapidly during higher monsoon flows. The findings reveal complex microplastic transport in large rivers and call for improved sampling methods and predictive models to better assess environmental risk and guide policy.}, } @article {pmid39642364, year = {2024}, author = {Lee, TY and Chen, CH and Chen, IM and Chen, HC and Liu, CM and Wu, SI and Hsiao, CK and Kuo, PH}, title = {Dynamic Bidirectional Associations Between Global Positioning System Mobility and Ecological Momentary Assessment of Mood Symptoms in Mood Disorders: Prospective Cohort Study.}, journal = {Journal of medical Internet research}, volume = {26}, number = {}, pages = {e55635}, pmid = {39642364}, issn = {1438-8871}, mesh = {Humans ; *Geographic Information Systems ; *Ecological Momentary Assessment ; Prospective Studies ; Male ; Adult ; Female ; Middle Aged ; *Mood Disorders/psychology ; Smartphone/statistics & numerical data ; Affect ; Mobile Applications ; }, abstract = {BACKGROUND: Although significant research has explored the digital phenotype in mood disorders, the time-lagged and bidirectional relationship between mood and global positioning system (GPS) mobility remains relatively unexplored. Leveraging the widespread use of smartphones, we examined correlations between mood and behavioral changes, which could inform future scalable interventions and personalized mental health monitoring.

OBJECTIVE: This study aims to investigate the bidirectional time lag relationships between passive GPS data and active ecological momentary assessment (EMA) data collected via smartphone app technology.

METHODS: Between March 2020 and May 2022, we recruited 45 participants (mean age 42.3 years, SD 12.1 years) who were followed up for 6 months: 35 individuals diagnosed with mood disorders referred by psychiatrists and 10 healthy control participants. This resulted in a total of 5248 person-days of data. Over 6 months, we collected 2 types of smartphone data: passive data on movement patterns with nearly 100,000 GPS data points per individual and active data through EMA capturing daily mood levels, including fatigue, irritability, depressed, and manic mood. Our study is limited to Android users due to operating system constraints.

RESULTS: Our findings revealed a significant negative correlation between normalized entropy (r=-0.353; P=.04) and weekly depressed mood as well as between location variance (r=-0.364; P=.03) and depressed mood. In participants with mood disorders, we observed bidirectional time-lagged associations. Specifically, changes in homestay were positively associated with fatigue (β=0.256; P=.03), depressed mood (β=0.235; P=.01), and irritability (β=0.149; P=.03). A decrease in location variance was significantly associated with higher depressed mood the following day (β=-0.015; P=.009). Conversely, an increase in depressed mood was significantly associated with reduced location variance the next day (β=-0.869; P<.001). These findings suggest a dynamic interplay between mood symptoms and mobility patterns.

CONCLUSIONS: This study demonstrates the potential of utilizing active EMA data to assess mood levels and passive GPS data to analyze mobility behaviors, with implications for managing disease progression in patients. Monitoring location variance and homestay can provide valuable insights into this process. The daily use of smartphones has proven to be a convenient method for monitoring patients' conditions. Interventions should prioritize promoting physical movement while discouraging prolonged periods of staying at home.}, } @article {pmid39642189, year = {2024}, author = {Graham, AL and Regoes, RR}, title = {Dose-dependent interaction of parasites with tiers of host defense predicts "wormholes" that prolong infection at intermediate inoculum sizes.}, journal = {PLoS computational biology}, volume = {20}, number = {12}, pages = {e1012652}, pmid = {39642189}, issn = {1553-7358}, mesh = {*Host-Parasite Interactions/immunology ; Animals ; Computational Biology ; Parasites/physiology/immunology ; Immunity, Innate ; Models, Biological ; }, abstract = {Immune responses are induced by parasite exposure and can in turn reduce parasite burden. Despite such apparently simple rules of engagement, key drivers of within-host dynamics, including dose-dependence of defense and infection duration, have proven difficult to predict. Here, we model how varied inoculating doses interact with multi-tiered host defenses at a site of inoculation, by confronting barrier, innate, and adaptive tiers with replicating and non-replicating parasites across multiple orders of magnitude of dose. We find that, in general, intermediate parasite doses generate infections of longest duration because they are sufficient in number to breach barrier defenses, but insufficient to strongly induce subsequent tiers of defense. These doses reveal "wormholes" in defense from which parasites might profit: Deviation from the hypothesis of independent action, which postulates that each parasite has an independent probability of establishing infection, may therefore be widespread. Interestingly, our model predicts local maxima of duration at two doses-one for each tier transition. While some empirical evidence is consistent with nonlinear dose-dependencies, testing the predicted dynamics will require finer-scale dose variation than experiments usually incorporate. Our results help explain varied infection establishment and duration among differentially-exposed hosts and elucidate evolutionary pressures that shape both virulence and defense.}, } @article {pmid39642168, year = {2024}, author = {Champion, C and Momal, R and Le Chatelier, E and Sola, M and Mariadassou, M and Berland, M}, title = {OneNet-One network to rule them all: Consensus network inference from microbiome data.}, journal = {PLoS computational biology}, volume = {20}, number = {12}, pages = {e1012627}, pmid = {39642168}, issn = {1553-7358}, mesh = {*Computational Biology/methods ; Humans ; *Microbiota/physiology ; *Algorithms ; *Gastrointestinal Microbiome/physiology ; Microbial Interactions/physiology ; }, abstract = {Modeling microbial interactions as sparse and reproducible networks is a major challenge in microbial ecology. Direct interactions between the microbial species of a biome can help to understand the mechanisms through which microbial communities influence the system. Most state-of-the art methods reconstruct networks from abundance data using Gaussian Graphical Models, for which several statistically grounded and computationnally efficient inference approaches are available. However, the multiplicity of existing methods, when applied to the same dataset, generates very different networks. In this article, we present OneNet, a consensus network inference method that combines seven methods based on stability selection. This resampling procedure is used to tune a regularization parameter by computing how often edges are selected in the networks. We modified the stability selection framework to use edge selection frequencies directly and combine them in the inferred network to ensure that only reproducible edges are included in the consensus. We demonstrated on synthetic data that our method generally led to slightly sparser networks while achieving much higher precision than any single method. We further applied the method to gut microbiome data from liver-cirrothic patients and demonstrated that the resulting network exhibited a microbial guild that was meaningful in terms of human health.}, } @article {pmid39638881, year = {2024}, author = {Vojteková, J and Janizadeh, S and Vojtek, M and Tirpáková, A and Ruttkay, M and Petrovič, F}, title = {Prediction of potential occurrence of historical objects with defensive function in Slovakia using machine learning approach.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {30350}, pmid = {39638881}, issn = {2045-2322}, support = {033UKF-4/2023//Kultúrna a Edukacná Grantová Agentúra MŠVVaŠ SR/ ; }, abstract = {In this article, we aim at the prediction of possible locations of already defunct historical objects with a defensive function (HODFs) in Slovakia, which have not been found and documented so far, using three machine learning methods. Specifically, we used the support vector machine, k-nearest neighbors, and random forest algorithms, which were trained based on the following five factors influencing the possible occurrence of HODFs: elevation, distance from a river, distance from a settlement, lithological rock type, and type of representative geoecosystems. Training and testing datasets were based on a database of already documented 605 HODFs, which were divided into 70% of training samples and 30% of testing samples. All of the three models reached the AUC-ROC value over 0.74 based on the testing dataset. The best performance was recorded by the random forest predictive model with the AUC-ROC value equal to 0.79. The results of the random forest model were also validated with the recently documented HODFs via the archeological research.}, } @article {pmid39636475, year = {2024}, author = {Ganie, PA and Posti, R and Bharti, VS and Sehgal, VK and Sarma, D and Pandey, PK}, title = {Erosion landscape characterization in the Himalayan basin: insights from geospatial data and multi-criteria evaluation.}, journal = {Environmental monitoring and assessment}, volume = {197}, number = {1}, pages = {29}, pmid = {39636475}, issn = {1573-2959}, mesh = {India ; *Environmental Monitoring ; *Rivers/chemistry ; *Geographic Information Systems ; Soil Erosion ; Conservation of Natural Resources ; Hydrology ; }, abstract = {In regions characterized by mountainous landscapes, such as watersheds with high elevations, steep inclines, and rugged terrains, there exists an inherent susceptibility to water-induced soil erosion. This susceptibility underscores the importance of identifying areas prone to erosion to mitigate the loss of valuable natural resources and ensure their preservation over time. In response to this need, the current research employed a combination of four multi-criteria decision-making (MCDM) models, namely TOPSIS-AHP, VIKOR-AHP, ARAS-AHP, and CODAS-AHP, for the identification of areas susceptible to soil erosion within the Himalayan River basin of Nandakini, Uttarakhand, India. This identification was facilitated through the utilization of remote sensing and geospatial technologies. The study considered a total of 19 prioritization parameters that included morphological, topo-hydrological, climatic, and environmental factors specific to the Nandakini catchment for the purpose of prioritization modeling. The adoption of morphometric parameters in depicting the geological structures and hydrodynamic behavior of the river basin proves to be a crucial approach in locales where hydrological data may be scarce. The investigation delineated twenty watersheds within the catchment by employing SRTM DEM, SOI toposheets, and Geographic Information Systems (GIS), calculating the catchment's total area to be approximately 540.98 km[2]. The analysis determined that the catchment is classified as a 6th-order catchment, exhibiting mainly a sub-dendritic to dendritic drainage pattern. It was identified that the catchment is vulnerable to flooding and subsequent gully erosion due to the slow movement of surface runoff. Furthermore, the catchment's elongated shape and the compactness coefficient suggest a delayed peak runoff. The drainage texture ranged from very coarse to coarse, and the relief characteristics highlighted that the watersheds within the catchment possess a high relief ratio, thereby increasing their erosion vulnerability. Topo-hydrological indices revealed significant topographic variability and spatial differences in water availability and erosion potential across the basin. The efficacy of the MCDM models was evaluated through the Spearman's correlation coefficient test, alongside indices of intensity and percentage of change, to validate the findings. The ARAS-AHP and CODAS-AHP models were found to exhibit superior efficiency and higher accuracy relative to the other methods assessed. The insights gained from the ARAS-AHP and CODAS-AHP models are instrumental in the development of strategies for sustainable catchment management plans and inform decision-making processes regarding water resources management within the catchment.}, } @article {pmid39635120, year = {2024}, author = {Qiu, Y and He, Z and Yu, X and Jia, G and Wang, Y}, title = {Analysis of factors influencing groundwater drought in the Loess zone of China.}, journal = {iScience}, volume = {27}, number = {10}, pages = {110929}, pmid = {39635120}, issn = {2589-0042}, abstract = {Understanding the characteristics and factors influencing groundwater resources is important for regional water resources management. The Gravity Recovery and Climate Experiment (GRACE)-based groundwater conditions were used to analyze the spatiotemporal characteristics of and the factors influencing groundwater storage (GWS) distribution in the Loess zone of the Yellow River Basin. The results revealed that the spatiotemporal distribution of GWS anomalies in the Loess zone of China was best explained by the first three components of the empirical orthogonal function (EOF), representing 85.6% of the total variance. The normalized difference vegetation index (NDVI) was significantly correlated with groundwater drought (p < 0.05). In addition, NDVI and evapotranspiration (ET) were the dominant factors influencing groundwater drought. NDVI was the dominant influencing factor in 67% and 80% of the total study area between 2002-2014 and 2015-2021, respectively. This study provides important guidance for a future ecological restoration plan in the Loess zone.}, } @article {pmid39627996, year = {2024}, author = {Rodman, KC and Bradford, JB and Formanack, AM and Fulé, PZ and Huffman, DW and Kolb, TE and Miller-Ter Kuile, AT and Normandin, DP and Ogle, K and Pedersen, RJ and Schlaepfer, DR and Stoddard, MT and Waltz, AEM}, title = {Restoration treatments enhance tree growth and alter climatic constraints during extreme drought.}, journal = {Ecological applications : a publication of the Ecological Society of America}, volume = {}, number = {}, pages = {e3072}, doi = {10.1002/eap.3072}, pmid = {39627996}, issn = {1051-0761}, support = {22-DG-11030000-012//U.S. Forest Service/ ; }, abstract = {The frequency and severity of drought events are predicted to increase due to anthropogenic climate change, with cascading effects across forested ecosystems. Management activities such as forest thinning and prescribed burning, which are often intended to mitigate fire hazard and restore ecosystem processes, may also help promote tree resistance to drought. However, it is unclear whether these treatments remain effective during the most severe drought conditions or whether their impacts differ across environmental gradients. We used tree-ring data from a system of replicated, long-term (>20 years) experiments in the southwestern United States to evaluate the effects of forest restoration treatments (i.e., evidence-based thinning and burning) on annual growth rates (i.e., basal area increment; BAI) of ponderosa pine (Pinus ponderosa), a broadly distributed and heavily managed species in western North America. The study sites were established at the onset of the most extreme drought event in at least 1200 years and span much of the climatic niche of Rocky Mountain ponderosa pine. Across sites, tree-level BAI increased due to treatment, where trees in treated units grew 133.1% faster than trees in paired, untreated units. Likewise, trees in treated units grew an average of 85.6% faster than their pre-treatment baseline levels (1985 to ca. 2000), despite warm, dry conditions in the post-treatment period (ca. 2000-2018). Variation in the local competitive environment promoted variation in BAI, and larger trees were the fastest-growing individuals, irrespective of treatment. Tree thinning and prescribed fire altered the climatic constraints on growth, decreasing the effects of belowground moisture availability and increasing the effects of atmospheric evaporative demand over multi-year timescales. Our results illustrate that restoration treatments can enhance tree-level growth across sites spanning ponderosa pine's climatic niche, even during recent, extreme drought events. However, shifting climatic constraints, combined with predicted increases in evaporative demand in the southwestern United States, suggest that the beneficial effects of such treatments on tree growth may wane over the upcoming decades.}, } @article {pmid39627652, year = {2024}, author = {Peltier, DMP and Carbone, MS and Ogle, K and Koch, GW and Richardson, AD}, title = {Decades-old carbon reserves are widespread among tree species, constrained only by sapwood longevity.}, journal = {The New phytologist}, volume = {}, number = {}, pages = {}, doi = {10.1111/nph.20310}, pmid = {39627652}, issn = {1469-8137}, support = {149//Save the Redwoods League/ ; 1936205//Division of Integrative Organismal Systems/ ; 2053337//Division of Integrative Organismal Systems/ ; 1832218//Division of Environmental Biology/ ; 2213599//Division of Environmental Biology/ ; }, abstract = {Carbon reserves are distributed throughout plant cells allowing past photosynthesis to fuel current metabolism. In trees, comparing the radiocarbon (Δ[14]C) of reserves to the atmospheric bomb spike can trace reserve ages. We synthesized Δ[14]C observations of stem reserves in nine tree species, fitting a new process model of reserve building. We asked how the distribution, mixing, and turnover of reserves vary across trees and species. We also explored how stress (drought and aridity) and disturbance (fire and bark beetles) perturb reserves. Given sufficient sapwood, young (< 1 yr) and old (20-60+ yr) reserves were simultaneously present in single trees, including 'prebomb' reserves in two conifers. The process model suggested that most reserves are deeply mixed (30.2 ± 21.7 rings) and then respired (2.7 ± 3.5-yr turnover time). Disturbance strongly increased Δ[14]C mean ages of reserves (+15-35 yr), while drought and aridity effects on mixing and turnover were species-dependent. Fire recovery in Sequoia sempervirens also appears to involve previously unobserved outward mixing of old reserves. Deep mixing and rapid turnover indicate most photosynthate is rapidly metabolized. Yet ecological variation in reserve ages is enormous, perhaps driven by stress and disturbance. Across species, maximum reserve ages appear primarily constrained by sapwood longevity, and thus old reserves are probably widespread.}, } @article {pmid39624726, year = {2024}, author = {Tian, T and Zhang, X and Zhang, F and Huang, X and Li, M and Quan, Z and Wang, W and Lei, J and Wang, Y and Liu, Y and Wang, JH}, title = {Harnessing AI for advancing pathogenic microbiology: a bibliometric and topic modeling approach.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1510139}, pmid = {39624726}, issn = {1664-302X}, abstract = {INTRODUCTION: The integration of artificial intelligence (AI) in pathogenic microbiology has accelerated research and innovation. This study aims to explore the evolution and trends of AI applications in this domain, providing insights into how AI is transforming research and practice in pathogenic microbiology.

METHODS: We employed bibliometric analysis and topic modeling to examine 27,420 publications from the Web of Science Core Collection, covering the period from 2010 to 2024. These methods enabled us to identify key trends, research areas, and the geographical distribution of research efforts.

RESULTS: Since 2016, there has been an exponential increase in AI-related publications, with significant contributions from China and the USA. Our analysis identified eight major AI application areas: pathogen detection, antibiotic resistance prediction, transmission modeling, genomic analysis, therapeutic optimization, ecological profiling, vaccine development, and data management systems. Notably, we found significant lexical overlaps between these areas, especially between drug resistance and vaccine development, suggesting an interconnected research landscape.

DISCUSSION: AI is increasingly moving from laboratory research to clinical applications, enhancing hospital operations and public health strategies. It plays a vital role in optimizing pathogen detection, improving diagnostic speed, treatment efficacy, and disease control, particularly through advancements in rapid antibiotic susceptibility testing and COVID-19 vaccine development. This study highlights the current status, progress, and challenges of AI in pathogenic microbiology, guiding future research directions, resource allocation, and policy-making.}, } @article {pmid39622961, year = {2024}, author = {Jeong, D and Hyun, JY and Marchenkova, T and Matiukhina, D and Cho, S and Lee, J and Kim, DY and Li, Y and Darman, Y and Min, MS and Bardyuk, V and Lee, Y and Pandey, P and Lee, H}, title = {Genetic insights and conservation strategies for Amur tigers in Southwest Primorye Russia.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {29985}, pmid = {39622961}, issn = {2045-2322}, support = {550-20190003//Ministry of Environment of the Republic of Korea, Convention on Biological Diversity under Bio-Bridge Initiative/ ; 550-20190003//Ministry of Environment of the Republic of Korea, Convention on Biological Diversity under Bio-Bridge Initiative/ ; 550-20190003//Ministry of Environment of the Republic of Korea, Convention on Biological Diversity under Bio-Bridge Initiative/ ; 550-20190003//Ministry of Environment of the Republic of Korea, Convention on Biological Diversity under Bio-Bridge Initiative/ ; 550-20190003//Ministry of Environment of the Republic of Korea, Convention on Biological Diversity under Bio-Bridge Initiative/ ; 550-20190003//Ministry of Environment of the Republic of Korea, Convention on Biological Diversity under Bio-Bridge Initiative/ ; 550-20190003//Ministry of Environment of the Republic of Korea, Convention on Biological Diversity under Bio-Bridge Initiative/ ; 550-20190003//Ministry of Environment of the Republic of Korea, Convention on Biological Diversity under Bio-Bridge Initiative/ ; 5260-20190100//Brain Korea-21 programme/ ; 5260-20200100//Brain Korea-21 programme/ ; A0449-2020010//Brain Korea-21 programme/ ; 5260-20190100//Brain Korea-21 programme/ ; 5260-20200100//Brain Korea-21 programme/ ; A0449-2020010//Brain Korea-21 programme/ ; 5260-20190100//Brain Korea-21 programme/ ; 5260-20200100//Brain Korea-21 programme/ ; A0449-2020010//Brain Korea-21 programme/ ; Building Tumen River Corridor for Tigers and leopards: Genetic diversity of tigers and leopards using non-invasive technique 2022-2023//Tiger and Leopard Conservation Fund in Korea/ ; Building Tumen River Corridor for Tigers and leopards: Genetic diversity of tigers and leopards using non-invasive technique 2022-2023//Tiger and Leopard Conservation Fund in Korea/ ; Building Tumen River Corridor for Tigers and leopards: Genetic diversity of tigers and leopards using non-invasive technique 2022-2023//Tiger and Leopard Conservation Fund in Korea/ ; }, mesh = {Animals ; *Tigers/genetics ; *Conservation of Natural Resources ; *Genetic Variation ; *Microsatellite Repeats/genetics ; Male ; Female ; *DNA, Mitochondrial/genetics ; Russia ; Genetics, Population ; Population Density ; }, abstract = {Southwest Primorye hosts approximately 9% of the remaining wild Amur tiger population and represents hope for the revival of tigers in Northeast China and the Korean peninsula. Decades of conservation efforts have led to a significant increase in population size, from less than 10 individuals surviving in the region in 1996 to multiple folds today. However, while the population size has recovered since the mid-1900s, the effects of genetic depletion on evolutionary potential are not easily reversed. In this study, a non-invasive genetic analysis of the Amur tiger subpopulation in Southwest Primorye was conducted using microsatellite loci and mitochondrial genes to estimate genetic diversity, relatedness, and determine the impact of historical demographic dynamics. A total of 32 individuals (16 males, 15 females, and 1 unidentified sex) were identified, and signs of bottlenecks were detected, reflecting past demographic events. Low genetic variation observed in mitochondrial DNA also revealed genetic depletion within the population. Most individuals were found to be closely related to each other, raising concerns about inbreeding given the small population size and somewhat isolated environment from the main population in Sikhote-Alin. These findings emphasize the urgent need to establish ecological corridors to neighboring areas to restore genetic diversity and ensure the conservation of the Amur tiger population in Southwest Primorye.}, } @article {pmid39622813, year = {2024}, author = {Monadjem, A and Montauban, C and Webala, PW and Laverty, TM and Bakwo-Fils, EM and Torrent, L and Tanshi, I and Kane, A and Rutrough, AL and Waldien, DL and Taylor, PJ}, title = {African bat database: curated data of occurrences, distributions and conservation metrics for sub-Saharan bats.}, journal = {Scientific data}, volume = {11}, number = {1}, pages = {1309}, pmid = {39622813}, issn = {2052-4463}, mesh = {*Chiroptera/classification/physiology ; Animals ; Africa South of the Sahara ; *Conservation of Natural Resources ; *Databases, Factual ; Ecosystem ; Animal Distribution ; }, abstract = {Accurate knowledge of species distributions is foundational for effective conservation efforts. Bats are a diverse group of mammals, with important roles in ecosystem functioning. However, our understanding of bats and their ecological importance is hindered by poorly defined ranges, mostly as a result of under-recording. This issue is exacerbated in Africa by the ongoing rapid discovery of new species, both de novo and splits of existing species, and by inaccessibility to museum specimens that are mostly hosted outside of the continent. Here we present the African bat database - a curated set of 17,285 unique locality records of all 266 species of bats from sub-Saharan Africa, vouched for by specimens and/or genetic sequencing, and aligned with current taxonomy. Based on these records, we also present Maxent-based distribution models and calculate the IUCN Red List metrics for Extent of Occurrence and Area of Occupancy. This database and online visualization tool provide an important open-source resource and is expected to significantly advance studies in ecology, and aid in bat conservation.}, } @article {pmid39622351, year = {2024}, author = {Nishimura, H and Nawa, N and Ogawa, T and Fushimi, K and Schwartz, BS and Fujiwara, T}, title = {Projections of future heat-related emergency hospitalizations for asthma under climate and demographic change scenarios: A Japanese nationwide time-series analysis.}, journal = {Environmental research}, volume = {266}, number = {}, pages = {120498}, doi = {10.1016/j.envres.2024.120498}, pmid = {39622351}, issn = {1096-0953}, abstract = {BACKGROUND: There is growing concern about climate impacts on human health. However, empirical evidence is lacking regarding future projections of heat-related asthma hospitalizations. This study aimed to project excess emergency hospitalizations for heat-related asthma exacerbation in Japan.

METHODS: Using Japanese nationwide administrative data from 2011 to 2019, we conducted an ecological time-series quasi-Poisson regression analysis to estimate the heat-related relative risk of emergency hospitalization for asthma over a lag of 0-3 days during the warm season (June to September). Heat exposure was defined as the region-specific daily mean temperature exceeding the locally defined minimum morbidity temperature percentile (MMP). Heat-related excess hospitalizations for asthma were projected under future climate and demographic change scenarios based on Shared Socioeconomic Pathways (SSPs).

RESULTS: We identified 75,829 emergency hospitalizations for asthma. The heat-related relative risk of hospitalization was 1.22 (95% confidence interval (CI): 1.12-1.33) at the 99th percentile temperature relative to the MMP, with the highest estimates for cases aged 0-14 years. Heat-related excess hospitalizations were projected to increase by 6.78 (95%CI: 5.84-7.67) times in 2091-2099 versus 2011-2019 along SSP5-8.5 when constant population structure was assumed. The increasing trend persisted even when the future population decline was considered (4.19 (95%CI: 3.53-4.85) times in 2091-2099 versus 2011-2019 under SSP5-8.5).

CONCLUSION: Future heat-related impacts on asthma exacerbation are expected to increase in Japan toward the end of this century, even when the future demographic change is considered. Our projections will contribute to resilient health systems adapting to ongoing climate change.}, } @article {pmid39621910, year = {2024}, author = {Alfaro-Sánchez, R and Richardson, AD and Smith, SL and Johnstone, JF and Turetsky, MR and Cumming, SG and Le Moine, JM and Baltzer, JL}, title = {Permafrost instability negates the positive impact of warming temperatures on boreal radial growth.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {121}, number = {50}, pages = {e2411721121}, pmid = {39621910}, issn = {1091-6490}, support = {15879//Aurora Research Institute (ARI)/ ; permafrost monitoring in the Mackenzie River Valley//Canadian Government | Natural Resources Canada (NRCan)/ ; MZ2021//María Zambrano program/ ; Small Research 2021 - SR21/1291//British Ecological Society (BES)/ ; Environmental Studies Research Fund and Cumulative Impacts Monitoring Program (Project 170)//Environment and Natural Resources, Northwest Territories (ENR, NWT)/ ; Discovery Grant support//Canadian Government | NSERC | RES'EAU-WaterNET/ ; Bonanza Creek LTER DEB-2224776//National Science Foundation (NSF)/ ; }, mesh = {*Permafrost ; *Trees/growth & development ; Temperature ; Taiga ; Global Warming ; Climate Change ; Forests ; }, abstract = {Climate warming can alleviate temperature and nutrient constraints on tree growth in boreal regions, potentially enhancing boreal productivity. However, in permafrost environments, warming also disrupts the physical foundation on which trees grow, leading to leaning trees or "drunken" forests. Tree leaning might reduce radial growth, undermining potential benefits of warming. Here, we found widespread radial growth reductions in southern latitude boreal forests since the 1980s. At mid latitudes, radial growth increased from ~1980 to ~2000 but showed recent signs of decline afterward. Increased growth was evident since the 1980 s at higher latitudes, where radial growth appears to be temperature limited. However, recent changes in permafrost stability, and the associated increased frequency of tree leaning events, emerged as a significant stressor, leading to reduced radial growth in boreal trees at the highest latitudes, where permafrost is extensive. We showed that trees growing in unstable permafrost sites allocated more nonstructural carbohydrate reserves to offset leaning which compromised radial growth and potential carbon uptake benefits of warming. This higher allocation of resources in drunken trees is needed to build the high-density reaction wood, rich in lignin, that is required to maintain a vertical position. With continued climate warming, we anticipate widespread reductions in radial growth in boreal forests, leading to lower carbon sequestration. These findings enhance our understanding of how climate warming and indirect effects, such as ground instability caused by warming permafrost, will affect boreal forest productivity in the future.}, } @article {pmid39621775, year = {2024}, author = {Osiecka, AN and Bryndza, P and Briefer, EF and Wojczulanis-Jakubas, K}, title = {Long distance calls: Negligible information loss of little auk social vocalisations due to high frequency propagation losses.}, journal = {PLoS computational biology}, volume = {20}, number = {12}, pages = {e1011961}, doi = {10.1371/journal.pcbi.1011961}, pmid = {39621775}, issn = {1553-7358}, mesh = {Animals ; *Vocalization, Animal/physiology ; Sound Spectrography/methods ; Computational Biology ; Acoustics ; Social Behavior ; }, abstract = {How well does the information contained in vocal signals travel through the environment? To assess the efficiency of information transfer in little auk (Alle alle, an Arctic seabird) calls over distance, we selected two of the social call types with the highest potential for individuality coding. Using available recordings of known individuals, we calculated the apparent source levels, with apparent maximum peak sound pressure level (ASPL) of 63 dB re 20 μPa at 1 m for both call types. Further, we created a sound attenuation model using meteorological data collected in the vicinity of the little auk colony in Hornsund, Spitsbergen. Using this model, we modelled the calls to reflect higher frequency filtering and sound level loss occurring during spherical spreading in perfect local conditions, down to the putative hearing threshold of the species, calculated to equal ASPL of signals "propagated" to roughly one kilometre. Those modelled calls were then used in a permuted discriminant function analysis, support vector machine models, and linear models of Beecher's information statistic, to investigate whether transmission loss will affect the retention of individual information of the signal. Calls could be correctly classified to individuals above chance level independently of the distance, down to and over the putative physiological hearing threshold. Interestingly, the information capacity of the signal did not decrease with its filtering and attenuation. While this study touches on signal properties purely and cannot provide evidence of the actual use by the animals, it shows that little auk signals can theoretically travel long distances with negligible information loss, and supports the hypothesis that vocalisations could facilitate long-distance communication in the species.}, } @article {pmid39618809, year = {2024}, author = {Boyes, D and Young, MR and , and , and , and , and , and , and , }, title = {The genome sequence of the Straw Grass-veneer moth, Agriphila straminella (Denis & Schiffermüller), 1775.}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {433}, pmid = {39618809}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual male Straw Grass-veneer moth, Agriphila straminella (Arthropoda; Insecta; Lepidoptera; Crambidae). The genome sequence has a length of 511.50 megabases. Most of the assembly is scaffolded into 26 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.36 kilobases in length. Gene annotation of this assembly on Ensembl identified 12,087 protein-coding genes.}, } @article {pmid39616400, year = {2024}, author = {Asaaga, FA and Shakeer, I and Sriram, A and Chhotaria, K and Dutta, S and Narayanaswamy, D and Amankwaa, G and Chanda, MM and Hoti, SL and Young, JC and Purse, BV}, title = {Ties that bind: understanding One Health networks and participation for zoonoses prevention and control in India.}, journal = {One health outlook}, volume = {6}, number = {1}, pages = {24}, pmid = {39616400}, issn = {2524-4655}, abstract = {BACKGROUND: Cross-sectoral collaborations as exemplified by the One Health approach, are widely endorsed as pragmatic avenues for addressing zoonotic diseases, but operationalisation remain limited in low-and-middle income countries (LMICs). Complexities and competing interests and agendas of key stakeholders and the underlying politico-administrative context can all shape outcomes of collaborative arrangements. Evidence is building that organised collaborations are complex political initiatives where different objectives; individual and institutional agendas need to be reconciled to incentivise collaborations.

METHODS: Drawing on a qualitative network analysis of published sources on 'One Health' stakeholders supplemented with 26 multi-scale (national-state-district level) key-informant interviews (including policymakers, disease managers and public health experts), this paper characterises the fragmented and complex characteristics of institutional networks involved in zoonoses prevention and control in India.

RESULTS: Our results highlight how the local socio-political and institutional contexts interact to modulate how and when collaborations occur (or not), the associated contingencies and stakeholder innovations in circumventing existing barriers (e.g. competing interests, distrust between actors, departmental bureaucracy) to cross-sector collaborations and zoonoses management. Aside from principal actors negotiating common ground in some instance, they also capitalised on political/institutional pressure to subtly 'manipulate' their subordinates as a way of fostering collaboration, especially in instances when the institutional and political stakes are high.

CONCLUSION: Altogether our findings suggest that cross-sectoral collaborations are by-product of political and institutional tinkering as long as individual actors and institutional interests converge and these dynamics must be embraced to embed meaningful and sustainable collaborations in local socio-political and administrative contexts.}, } @article {pmid39612036, year = {2024}, author = {Ma, D and Huang, Q and Wang, Q and Xu, H and Yan, Y}, title = {Detection of spatiotemporal changes in eco-environmental quality based on RSEI and SG filtering and its driving force analysis: a case study in Sichuan Province, China.}, journal = {Environmental monitoring and assessment}, volume = {196}, number = {12}, pages = {1274}, pmid = {39612036}, issn = {1573-2959}, support = {ZR2020MD025//Natural Science Foundation of Shandong Province/ ; 42171435//National Natural Science Foundation of China/ ; }, mesh = {China ; *Environmental Monitoring/methods ; *Remote Sensing Technology ; Forests ; Ecosystem ; Grassland ; Conservation of Natural Resources/methods ; }, abstract = {Landsat images were extracted using Google Earth Engine (GEE) platform and optimized by Savitzky-Golay (SG) filtering. The Remote Sensing Ecological Index (RSEI) method was used to analyze the eco-environmental quality in Sichuan Province in recent 20 years. In addition, Theil-Sen median method and Mann-Kendall (MK) test were used to test the change trend of eco-environmental quality. Furthermore, drivers were evaluated by partial correlation analysis, 2D scatter plots, and t tests. The results showed that (1) in the past 20 years, the eco-environmental quality of Sichuan Province was on the rise, and the eco-environmental quality in the western region was better than that in the eastern region. The eco-environmental quality was positively correlated with forest and grassland types, and negatively correlated with cultivated land and urban and rural construction land types. (2) The eco-environmental quality of Sichuan Province is linearly correlated with the digital elevation model, but poorly correlated with slope and slope direction. In the range of slope 0° ~ 9° and southeast direction, the eco-environmental quality is the worst. (3) The eco-environmental quality of Sichuan Province was most significantly affected by soil moisture and sunshine hours. The study can help us to understand and assess the health of ecosystems in Sichuan Province, provide a scientific basis for protecting and improving the environment, and guide the formulation and implementation of environmental protection policies.}, } @article {pmid39609505, year = {2024}, author = {Alvarez-Mamani, E and Buettner, F and Beltran-Castanon, CA and Ibanez, AJ}, title = {Exploratory analysis of metabolic changes using mass spectrometry data and graph embeddings.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {29570}, pmid = {39609505}, issn = {2045-2322}, support = {No. 174-2020-FONDECYT "Doctoral Programs in Peruvian Universities"//Consejo Nacional de Ciencia, Tecnología e Innovación Tecnológica (CONCYTEC), and Fondo Nacional de Desarrollo Científico, Tecnológico y de Innovación Tecnológica (FONDECYT)/ ; "The Max Planck Partner Group" (Max Planck Institute for Chemical Ecology-Jena)//Max-Planck-Gesellschaft/ ; "The Max Planck Partner Group" (Max Planck Institute for Chemical Ecology-Jena)//Max-Planck-Gesellschaft/ ; Nº PE501086715-2024- PROCIENCIA)//CONCYTEC-Prociencia convocatoria E041-2024-01/ ; }, mesh = {*Metabolomics/methods ; *Mass Spectrometry/methods ; *Algorithms ; *Data Mining/methods ; Humans ; Deep Learning ; Metabolic Networks and Pathways ; Metabolome ; }, abstract = {Mass spectrometry (MS)-based metabolomics analysis is a powerful tool, but it comes with its own set of challenges. The MS workflow involves multiple steps before its interpretation in what is denominate data mining. Data mining consists of a two-step process. First, the MS data is ordered, arranged, and presented for filtering before being analyzed. Second, the filtered and reduced data are analyzed using statistics to remove further variability. This holds true particularly for MS-based untargeted metabolomics studies, which focused on understanding fold changes in metabolic networks. Since the task of filtering and identifying changes from a large dataset is challenging, automated techniques for mining untargeted MS-based metabolomic data are needed. The traditional statistics-based approach tends to overfilter raw data, which may result in the removal of relevant data and lead to the identification of fewer metabolomic changes. This limitation of the traditional approach underscores the need for a new method. In this work, we present a novel deep learning approach using node embeddings (powered by GNNs), edge embeddings, and anomaly detection algorithm to analyze the data generated by mass spectrometry (MS)-based metabolomics called GEMNA (Graph Embedding-based Metabolomics Network Analysis), for example for an untargeted volatile study on Mentos candy, the data clusters produced by GEMNA were better than the ones used traditional tools, i.e., GEMNA has [Formula: see text], vs. the traditional approach has [Formula: see text].}, } @article {pmid39606930, year = {2024}, author = {Whyte, M and Wambui, KM and Musenge, E}, title = {Nigeria's malaria prevalence in 2015: a geospatial, exploratory district-level approach.}, journal = {Geospatial health}, volume = {19}, number = {2}, pages = {}, doi = {10.4081/gh.2024.1243}, pmid = {39606930}, issn = {1970-7096}, mesh = {Humans ; Nigeria/epidemiology ; *Malaria/epidemiology ; Prevalence ; Child, Preschool ; Infant ; *Spatial Analysis ; Female ; Male ; *Geographic Information Systems ; Socioeconomic Factors ; Adult ; Adolescent ; Child ; Middle Aged ; Young Adult ; }, abstract = {This study used data from the second Nigeria Malaria Indicator Survey (NMIS) conducted in 2015 to investigate the spatial distribution of malaria prevalence in the country and identify its associated factors. Nigeria is divided into 36 states with 109 senatorial districts, most of which are affected by malaria, a major cause of morbidity and mortality in children under five years of age. We carried out an ecological study with analysis at the senatorial district level. A malaria prevalence map was produced combining geographic information systems data from the Nigeria Malaria Indicator Survey (NMIS) of 2015 with shape files from an open data-sharing platform. Spatial autoregressive models were fitted using a set of key covariates. Malaria prevalence in children under-five was highest in Kebbi South senatorial district (70.6%). It was found that poorest wealth index (β = 0.10 (95% CI: 0.01, 0.20), p = 0.04), mothers having only secondary level of education (β = 0.78 (95% CI: 0.05, 1.51), p = 0.04) and households without mosquito bed nets (β = 0.21 (95% CI: 0.02, 0.39), p = 0.03) were all significantly associated with higher malaria prevalence. Moran's I (54.81, p<0.001) showed spatial dependence of malaria prevalence across contiguous districts and spatial autoregressive modelling demonstrated significant spill-over effect of malaria prevalence. Maps produced in this study provide a useful graphical representation of the spatial distribution of malaria prevalence based on NMIS-2015 data. Clustering of malaria prevalence in certain areas further highlights the need for sustained malaria elimination interventions across affected regions in order to break the chain of transmission.}, } @article {pmid39602490, year = {2024}, author = {Soares, R and Azevedo, L and Vasconcelos, V and Pratas, D and Sousa, SF and Carneiro, J}, title = {Machine Learning-Driven Discovery and Database of Cyanobacteria Bioactive Compounds: A Resource for Therapeutics and Bioremediation.}, journal = {Journal of chemical information and modeling}, volume = {64}, number = {24}, pages = {9576-9593}, doi = {10.1021/acs.jcim.4c00995}, pmid = {39602490}, issn = {1549-960X}, mesh = {*Cyanobacteria/metabolism ; *Machine Learning ; *Biodegradation, Environmental ; *Drug Discovery ; Molecular Docking Simulation ; Databases, Factual ; Databases, Chemical ; Humans ; Software ; }, abstract = {Cyanobacteria strains have the potential to produce bioactive compounds that can be used in therapeutics and bioremediation. Therefore, compiling all information about these compounds to consider their value as bioresources for industrial and research applications is essential. In this study, a searchable, updated, curated, and downloadable database of cyanobacteria bioactive compounds was designed, along with a machine-learning model to predict the compounds' targets of newly discovered molecules. A Python programming protocol obtained 3431 cyanobacteria bioactive compounds, 373 unique protein targets, and 3027 molecular descriptors. PaDEL-descriptor, Mordred, and Drugtax software were used to calculate the chemical descriptors for each bioactive compound database record. The biochemical descriptors were then used to determine the most promising protein targets for human therapeutic approaches and environmental bioremediation using the best machine learning (ML) model. The creation of our database, coupled with the integration of computational docking protocols, represents an innovative approach to understanding the potential of cyanobacteria bioactive compounds. This resource, adhering to the findability, accessibility, interoperability, and reuse of digital assets (FAIR) principles, is an excellent tool for pharmaceutical and bioremediation researchers. Moreover, its capacity to facilitate the exploration of specific compounds' interactions with environmental pollutants is a significant advancement, aligning with the increasing reliance on data science and machine learning to address environmental challenges. This study is a notable step forward in leveraging cyanobacteria for both therapeutic and ecological sustainability.}, } @article {pmid39600916, year = {2021}, author = {Boyes, D and Crowley, LM and , and , and , and , and , and , }, title = {The genome sequence of the harlequin ladybird, Harmonia axyridis (Pallas, 1773).}, journal = {Wellcome open research}, volume = {6}, number = {}, pages = {300}, pmid = {39600916}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual female Harmonia axyridis (the harlequin ladybird; Arthropoda; Insecta; Coleoptera; Coccinellidae). The genome sequence is 426 megabases in span. The majority (99.98%) of the assembly is scaffolded into 8 chromosomal pseudomolecules, with the X sex chromosome assembled.}, } @article {pmid39599286, year = {2024}, author = {Toghan, A and Alduaij, OK and Sanad, MMS and Elessawy, NA}, title = {Scalable Engineering of 3D Printing Filaments Derived from Recycling of Plastic Drinking Water Bottle and Glass Waste.}, journal = {Polymers}, volume = {16}, number = {22}, pages = {}, pmid = {39599286}, issn = {2073-4360}, support = {IMSIU-RG23086//Deanship of Scientific Research at Imam Mohammad Ibn Saud Islamic University/ ; }, abstract = {The most significant challenge that the world is currently facing is the development of beneficial industrial applications for solid waste. A novel strategy was implemented to produce a composite with varying loadings of glass waste nanoparticles (GWNP) in 5, 10, and 15 wt.% with recycled polyethylene terephthalate drinking water bottle waste (RPET). This strategy was based on glass and drinking water bottle waste. An analysis was conducted to evaluate the performance of the composite as filaments for 3D printer applications. This study evaluated the effect of GWNP addition on the chemical structure, thermal and mechanical characteristics of the composite. The Fourier Transform Infrared (FTIR) spectra of the filament composites and RPET composites exhibited similarities. However, the mechanical strength and thermal stability of the filament composites were enhanced due to the increased GWNP content. Furthermore, the results indicated that the filament developed could be utilized for 3D printing, as demonstrated by the successful fabrication of the filament composite, including 5 wt.% GWNP, using a 3D printer pen. The production of filaments using GWNP and RPET matrix presents a cost-effective, high-yield, and ecologically beneficial alternative. The present study may pave the way for the future advancement and utilization of 3D printing filaments by treating hazardous waste and using more ecologically friendly materials in design applications.}, } @article {pmid39597377, year = {2024}, author = {Maślanka, P and Korycki, R}, title = {Material, Aerodynamic, and Operational Aspects of Single-Skin Paraglider.}, journal = {Materials (Basel, Switzerland)}, volume = {17}, number = {22}, pages = {}, pmid = {39597377}, issn = {1996-1944}, abstract = {The operating comfort of a paraglider is created by the aerodynamic parameters as well as the mass and packing volume of the wing. A classic paraglider has upper and lower covers. To reduce the material and manufacturing costs as well as protect the environment, it is possible to introduce a single-skin wing. This article conducts an analysis of a single-skin paraglider covered only with upper panels, whereas the lower cover is applied only at the leading and trailing edges. The analysis is theoretically oriented; aerodynamic and structural calculations were performed using the ANSYS environment. The single-skin structure was evaluated in terms of the predicted behavior during flight and the material's deformation under the influence of a specified pressure and the overloads acting on it. The results show that developing these structures may influence the creation of models with comparable aerodynamic characteristics to traditional ones. Additionally, the reduced masses and packing volumes of difficult-to-degrade materials are strongly correlated with saving costs and an ecological approach. No corresponding studies were found in the available literature. Thus, this presented analysis may result in a greater understanding and application of this paraglider type.}, } @article {pmid39596552, year = {2024}, author = {Signore, IA and Donoso, G and Bocchieri, P and Tobar-Calfucoy, EA and Yáñez, CE and Carvajal-Silva, L and Silva, AX and Otth, C and Cappelli, C and Valenzuela Jorquera, H and Zapata-Contreras, D and Espinosa-Parrilla, Y and Zúñiga-Pacheco, P and Fuentes-Guajardo, M and Monardes-Ramírez, VA and Kochifas Velasquez, P and Muñoz, CA and Dorador, C and García-Araya, J and Campillay-Véliz, CP and Echeverria, C and Santander, RA and Cerpa, LC and Martínez, MF and Quiñones, LA and Lamoza Galleguillos, ER and Saez Hidalgo, J and Nova-Lamperti, E and Sanhueza, S and Giacaman, A and Acosta-Jamett, G and Verdugo, C and Plaza, A and Verdugo, C and Selman, C and Verdugo, RA and Colombo, A}, title = {The Chilean COVID-19 Genomics Network Biorepository: A Resource for Multi-Omics Studies of COVID-19 and Long COVID in a Latin American Population.}, journal = {Genes}, volume = {15}, number = {11}, pages = {}, pmid = {39596552}, issn = {2073-4425}, support = {ANID COVID0961, ANID COVID0789, ANID COVID1005, ANID COVID0585, ACT210085, FONDECYT 1170446, FONDECYT 1211480//Agencia Nacional de Investigación y Desarrollo/ ; MAG1995//Ministry of Education/ ; RED21193//Interuniversity Center for Healthy Aging/ ; VRID220.085.041-INI//University of Concepción/ ; }, mesh = {Humans ; *COVID-19/genetics/virology/epidemiology ; Chile ; *Biological Specimen Banks ; *Genomics/methods ; *SARS-CoV-2/genetics ; Male ; Female ; Adult ; Middle Aged ; Aged ; Latin America ; Multiomics ; }, abstract = {Although a lack of diversity in genetic studies is an acknowledged obstacle for personalized medicine and precision public health, Latin American populations remain particularly understudied despite their heterogeneity and mixed ancestry. This gap extends to COVID-19 despite its variability in susceptibility and clinical course, where ethnic background appears to influence disease severity, with non-Europeans facing higher hospitalization rates. In addition, access to high-quality samples and data is a critical issue for personalized and precision medicine, and it has become clear that the solution lies in biobanks. The creation of the Chilean COVID-19 Biorepository reported here addresses these gaps, representing the first nationwide multicentric Chilean initiative. It operates under rigorous biobanking standards and serves as one of South America's largest COVID cohorts. A centralized harmonization strategy was chosen and included unified standard operating procedures, a sampling coding system, and biobanking staff training. Adults with confirmed SARS-CoV-2 infection provided broad informed consent. Samples were collected to preserve blood, plasma, buffy coat, and DNA. Quality controls included adherence to the standard preanalytical code, incident reporting, and DNA concentration and absorbance ratio 260/280 assessments. Detailed sociodemographic, health, medication, and preexisting condition data were gathered. In five months, 2262 participants were enrolled, pseudonymized, and sorted by disease severity. The average Amerindian ancestry considering all participant was 44.0% [SD 15.5%], and this value increased to 61.2% [SD 19.5%] among those who self-identified as Native South Americans. Notably, 279 participants self-identified with one of 12 ethnic groups. High compliance (>90%) in all assessed quality controls was achieved. Looking ahead, our team founded the COVID-19 Genomics Network (C19-GenoNet) focused on identifying genetic factors influencing SARS-CoV-2 outcomes. In conclusion, this bottom-up collaborative effort aims to promote the integration of Latin American populations into global genetic research and welcomes collaborations supporting this endeavor. Interested parties are invited to explore collaboration opportunities through our catalog, accessible online.}, } @article {pmid39595758, year = {2024}, author = {Aras, SG and Runyon, JR and Kazman, JB and Thayer, JF and Sternberg, EM and Deuster, PA}, title = {Is Greener Better? Quantifying the Impact of a Nature Walk on Stress Reduction Using HRV and Saliva Cortisol Biomarkers.}, journal = {International journal of environmental research and public health}, volume = {21}, number = {11}, pages = {}, pmid = {39595758}, issn = {1660-4601}, support = {XX//The Institute for Integrative Health and Nature Sacred/ ; }, mesh = {Humans ; *Hydrocortisone/analysis/metabolism ; *Saliva/chemistry ; *Walking/physiology ; *Heart Rate/physiology ; Male ; Adult ; Female ; *Biomarkers/analysis/metabolism ; Stress, Psychological/metabolism/physiopathology ; Affect/physiology ; Stress, Physiological/physiology ; Young Adult ; Nature ; Middle Aged ; }, abstract = {The physiological impact of walking in nature was quantified via continuous heart rate variability (HRV), pre- and post-walk saliva cortisol measures, and self-reported mood and mindfulness scores for N = 17 participants who walked "The Green Road" at Walter Reed National Military Medical Center in Bethesda, Maryland. For N = 15 of the participants, HRV analysis revealed two main groups: group one individuals had a 104% increase (mean) in the root mean square standard deviation (RMSSD) and a 47% increase (mean) in the standard deviation of NN values (SDNN), indicating an overall reduction in physiological stress from walking the Green Road, and group two individuals had a decrease (mean) of 42% and 31% in these respective HRV metrics, signaling an increase in physiological stresses. Post-walk self-reported scores for vigor and mood disturbance were more robust for the Green Road than for a comparable urban road corridor and showed that a higher HRV during the walk was associated with improved overall mood. Saliva cortisol was lower after taking a walk for all participants, and it showed that walking the Green Road elicited a significantly larger reduction in cortisol of 53%, on average, when compared with 37% of walking along an urban road. It was also observed that the order in which individuals walked the Green Road and urban road also impacted their cortisol responses, with those walking the urban road before the Green Road showing a substantial reduction in cortisol, suggesting a possible attenuation effect of walking the Green Road first. These findings provide quantitative data demonstrating the stress-reducing effects of being in nature, thus supporting the health benefit value of providing access to nature more broadly in many settings.}, } @article {pmid39594004, year = {2024}, author = {Alrhmoun, M and Sulaiman, N and Haq, SM and Abidullah, S and Prakofjewa, J and Krigas, N and Pieroni, A and Sõukand, R}, title = {Is Boiling Bitter Greens a Legacy of Ancient Crete? Contemporary Foraging in the Minoan Refugium of the Lasithi Plateau.}, journal = {Foods (Basel, Switzerland)}, volume = {13}, number = {22}, pages = {}, pmid = {39594004}, issn = {2304-8158}, support = {N/A//University of Gastronomic Sciences, Pollenzo, Italy/ ; N/A//Department of Environmental Sciences, Informatics, and Statistics, Ca' Foscari Uni-versity of Venice, Italy/ ; }, abstract = {Wild greens (WGs) play a significant role in Mediterranean diets (MDs), reflecting botanical and cultural diversities, mainly influenced by a complex conglomerate of local human ecologies. This study investigates local ecological knowledge (LEK) linked to traditional gathering and consumption of WGs in the Lasithi Plateau of eastern Crete, where human genetic studies one decade ago showed very peculiar patterns, hypothesising that the Minoan civilisation took refuge there before it disappeared. A field ethnobotanical study was conducted to document the diversity of WGs and their detailed local culinary uses in the Lasithi area by interviewing 31 study participants. Fifty-nine folk taxa (species and subspecies) were recorded, corresponding to fifty-eight botanical taxa. A quotation index was measured to assess the cultural significance of WGs in the study areas; logistic regression analysis was adopted to understand the impact of sensory classifications of WGs and their local cooking methods. Lasithi's foraging showed a notable prevalence of bitter-tasting WGs, which play a central role in local cognition and culinary practices. This bitterness aspect of WGs, potentially influenced by cultural preferences and genetic factors, probably suggests a connection to the ancient Lasithi's inhabitants, i.e., Minoan dietary habits. We found that bitterness is the predominant sensory attribute in Lasithi, characterising 45.76% of the WGs. These findings underscore the complex interplay between local ecologies and biodiversity, LEK, and dietary traditions, highlighting the importance of WGs in understanding the evolution of foraging and plant culinary diversities across the Mediterranean.}, } @article {pmid39592922, year = {2024}, author = {Das, VA and Gautam, B and Yadav, PK and Varadwaj, PK and Wadhwa, G and Singh, S}, title = {Computational approach to identify novel genomic features conferring high fitness in Bacillus atrophaeus CNY01 and Bacillus velezensis AK-0 associated with plant growth promotion (PGP) in apple.}, journal = {BMC plant biology}, volume = {24}, number = {1}, pages = {1127}, pmid = {39592922}, issn = {1471-2229}, mesh = {*Bacillus/genetics/physiology ; *Malus/microbiology/genetics ; *Genome, Bacterial ; Genetic Fitness ; Genomics/methods ; Genomic Islands ; Computational Biology/methods ; }, abstract = {A comparative genomic analysis approach provides valuable information about genetic variations and evolutionary relationships among microorganisms, aiding not only in the identification of functional genes responsible for traits such as pathogenicity, antibiotic resistance, and metabolic capabilities but also in enhancing our understanding of microbial genomic diversity and their ecological roles, such as supporting plant growth promotion, thereby enabling the development of sustainable strategies for agriculture. We used two strains from different Bacillus species, Bacillus velezensis AK-0 and Bacillus atrophaeus CNY01, which have previously been reported to have PGP activity in apple, and performed comparative genomic analysis to understand their evolutionary process and obtain a mechanistic understanding of their plant growth-promoting activity. We identified genomic features such as mobile genetic elements (MGEs) that encode key proteins involved in the survival, adaptation and growth of these bacterial strains. The presence of genomic islands and intact prophage DNA in Bacillus atrophaeus CNY01 and Bacillus velezensis AK-0 suggests that horizontal gene transfer has contributed to their diversification and acquisition of adaptive traits, enhancing their evolutionary advantage. We also identified novel DNA motifs that are associated with key physiological processes and metabolic pathways.}, } @article {pmid39591252, year = {2024}, author = {Baradaran, M and Salabi, F and Mahdavinia, M and Mohammadi, E and Vazirianzadeh, B and Avella, I and Kazemi, SM and Lüddecke, T}, title = {ScorpDb: A Novel Open-Access Database for Integrative Scorpion Toxinology.}, journal = {Toxins}, volume = {16}, number = {11}, pages = {}, pmid = {39591252}, issn = {2072-6651}, mesh = {*Scorpion Venoms/chemistry ; *Scorpions ; Animals ; Humans ; Databases, Factual ; Scorpion Stings/drug therapy ; Databases, Protein ; }, abstract = {Scorpion stings are a significant public health concern globally, particularly in tropical and subtropical regions. Scorpion venoms contain a diverse array of bioactive peptides, and different scorpion species around the world typically exhibit varying venom profiles, resulting in a wide range of envenomation symptoms. Despite their harmful effects, scorpion venom peptides hold immense potential for drug development due to their unique characteristics. Therefore, the establishment of a comprehensive database that catalogs scorpions along with their known venom peptides and proteins is imperative in furthering research efforts in this research area. We hereby present ScorpDb, a novel database that offers convenient access to data related to different scorpion species, the peptides and proteins found in their venoms, and the symptoms they can cause. To this end, the ScorpDb database has been primarily advanced to accommodate data on the Iranian scorpion fauna. From there, we propose future community efforts to include a larger diversity of scorpions and scorpion venom components. ScorpDb holds the promise to become a valuable resource for different professionals from a variety of research fields, like toxinologists, arachnologists, and pharmacologists. The database is available at https://www.scorpdb.com/.}, } @article {pmid39591213, year = {2024}, author = {Roman-Ramos, H and Ho, PL}, title = {Current Technologies in Snake Venom Analysis and Applications.}, journal = {Toxins}, volume = {16}, number = {11}, pages = {}, pmid = {39591213}, issn = {2072-6651}, support = {2017/18398-1//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 309741/2023-8//National Council for Scientific and Technological Development/ ; }, mesh = {*Snake Venoms/chemistry ; Animals ; *Proteomics ; Humans ; Genomics ; Computational Biology ; Snakes ; }, abstract = {This comprehensive review explores the cutting-edge advancements in snake venom research, focusing on the integration of proteomics, genomics, transcriptomics, and bioinformatics. Highlighting the transformative impact of these technologies, the review delves into the genetic and ecological factors driving venom evolution, the complex molecular composition of venoms, and the regulatory mechanisms underlying toxin production. The application of synthetic biology and multi-omics approaches, collectively known as venomics, has revolutionized the field, providing deeper insights into venom function and its therapeutic potential. Despite significant progress, challenges such as the functional characterization of toxins and the development of cost-effective antivenoms remain. This review also discusses the future directions of venom research, emphasizing the need for interdisciplinary collaborations and new technologies (mRNAs, cryo-electron microscopy for structural determinations of toxin complexes, synthetic biology, and other technologies) to fully harness the biomedical potential of venoms and toxins from snakes and other animals.}, } @article {pmid39589804, year = {2024}, author = {Arias, M and Behrendt, L and Dreßler, L and Raka, A and Perrier, C and Elias, M and Gomez, D and Renoult, JP and Tedore, C}, title = {Testing the equivalency of human "predators" and deep neural networks in the detection of cryptic moths.}, journal = {Journal of evolutionary biology}, volume = {}, number = {}, pages = {}, doi = {10.1093/jeb/voae146}, pmid = {39589804}, issn = {1420-9101}, abstract = {Researchers have shown growing interest in using deep neural networks (DNNs) to efficiently test the effects of perceptual processes on the evolution of color patterns and morphologies. Whether this is a valid approach remains unclear, as it is unknown whether the relative detectability of ecologically relevant stimuli to DNNs actually matches that of biological neural networks. To test this, we compare image classification performance by humans and six DNNs (AlexNet, VGG-16, VGG-19, ResNet-18, SqueezeNet, and GoogLeNet) trained to detect artificial moths on tree trunks. Moths varied in their degree of crypsis, conferred by different sizes and spatial configurations of transparent wing elements. Like humans, four of six DNN architectures found moths with larger transparent elements harder to detect. However, humans and only one DNN architecture (GoogLeNet) found moths with transparent elements touching one side of the moth's outline harder to detect than moths with untouched outlines. When moths were small, the camouflaging effect of transparent elements touching the moth's outline was reduced for DNNs but enhanced for humans. Prey size can thus interact with camouflage type in opposing directions in humans and DNNs, which warrants a deeper investigation of size interactions with a broader range of stimuli. Overall, our results suggest that humans and DNNs responses had some similarities, but not enough to justify the widespread use of DNNs for studies of camouflage.}, } @article {pmid39586965, year = {2024}, author = {Gianicolo, E and Russo, A and Di Staso, R and Ronckers, CM and Schmidtmann, I and Wollschläger, D and Blettner, M}, title = {A municipality-specific analysis to investigate persistent increased incidence rates of childhood leukaemia near the nuclear power plant of Krümmel in Germany.}, journal = {European journal of epidemiology}, volume = {39}, number = {12}, pages = {1373-1378}, pmid = {39586965}, issn = {1573-7284}, mesh = {Humans ; Germany/epidemiology ; Child ; *Nuclear Power Plants ; Incidence ; Male ; Child, Preschool ; Female ; *Leukemia/epidemiology ; Adolescent ; Infant ; *Registries ; Leukemia, Radiation-Induced/epidemiology ; Infant, Newborn ; Cities/epidemiology ; Environmental Exposure/adverse effects/statistics & numerical data ; Risk Factors ; }, abstract = {Increased incidence rates for childhood leukaemia have been reported in municipalities close to the nuclear power plant (NPP) Krümmel (Geesthacht, Germany). Methodological challenges arise when analysing this association at ecological level. They include the use of an appropriate reference population, unstable estimates of standardised incidence ratios (SIRs), and the potential role of prevailing winds. The aim of our study is to address these challenges. The German Childhood Cancer Registry provided data on leukaemia in children under 15 years (2004-2019). The German Federal Statistical Office provided the population data. The study region included all municipalities with ≥ 75% surface area within 50 kms from the Krümmel NPP. We calculated SIRs using national and regional reference rates. Smoothed incidence relative rates (IRRs) were calculated and mapped to check for potential patterns associated with prevailing winds. Overall 356 cases of childhood leukaemia were observed in the study region (321 municipalities) during 2004-2019. SIRs based on national reference rates show nearly no difference to those calculated using the regional rates as reference. Increased SIR and IRR were observed in Geesthacht (observed-cases = eight; SIR = 2.29; 95% confidence interval: 0.99-4.51. IRR = 1.80; 95% credibility interval: 0.88-2.79). The analysis of the IRR map does not show patterns associated with prevailing winds. Using a regional population as the reference, we found evidence that there may still be an increased risk for childhood leukaemia in Geesthacht. However, IRR estimates are uncertain and credibility intervals are compatible with the absence of elevated risk. The persistent evidence of risk of childhood leukaemia in Geesthacht warrants further epidemiological surveillance.}, } @article {pmid39585857, year = {2024}, author = {Adderley-Heron, K and Chow-Fraser, P}, title = {Unsupervised classification of Blanding's turtle (Emydoidea blandingii) behavioural states from multi-sensor biologger data.}, journal = {PloS one}, volume = {19}, number = {11}, pages = {e0314291}, pmid = {39585857}, issn = {1932-6203}, mesh = {Animals ; *Turtles/physiology/classification ; Female ; Male ; *Behavior, Animal/physiology ; Accelerometry ; Markov Chains ; Geographic Information Systems ; Nesting Behavior/physiology ; }, abstract = {Classifying animal behaviors in their natural environments is both challenging and ecologically important, but the use of biologgers with multiple sensors has significantly advanced this research beyond the capabilities of traditional methods alone. Here, we show how biologgers containing an integrated tri-axial accelerometer, GPS logger and immersion sensor were used to infer behavioural states of a cryptic, freshwater turtle, the Blanding's turtle (Emydoidea blandingii). Biologgers were attached to three males and five females that reside in two undisturbed coastal marshes in northeastern Georgian Bay (Ontario, Canada) between May and July 2023. Raw acceleration values were separated into static and dynamic acceleration and subsequently used to calculate overall dynamic body acceleration (ODBA) and pitch. The unsupervised Hidden Markov Model (HMM) successfully differentiated five behavioural states as follows: active in water, resting in water, active out of water, resting in water, and nesting. Overall accuracy of the classification was 93.8%, and except for nesting (79%), all other behaviours were above 92%. There were significant differences in daily activity budgets between male and female turtles, with females spending a greater proportion of time active out of water, and inactive out of the water, while males spent a greater proportion of time active in water. These differences were likely a result of large seasonal life-history requirements such as nesting and mate finding. Accurate classification of behavioural states is important for researchers to understand fine-scale activities carried out during the active season and how environmental variables may influence the behaviours of turtles in their natural habitats.}, } @article {pmid39585479, year = {2024}, author = {Sahak, AS and Karsli, F and Saraj, MA}, title = {Evaluating the impact of urban sprawl on the urban ecological status using GIS and remote sensing from 2000 to 2021: a case study of Herat City, Afghanistan.}, journal = {Environmental monitoring and assessment}, volume = {196}, number = {12}, pages = {1246}, pmid = {39585479}, issn = {1573-2959}, mesh = {*Geographic Information Systems ; *Remote Sensing Technology ; *Environmental Monitoring/methods ; *Urbanization ; *Cities ; Afghanistan ; Conservation of Natural Resources/methods ; Ecosystem ; }, abstract = {Urbanization often incurs environmental costs, as fertile agricultural and forested lands are converted into urban areas. Herat City is currently undergoing significant urban transformation. This research aims to assess the impact of urban sprawl on Herat City's urban ecological status during 2000, 2013, and 2021, using GIS and remote sensing. The urban expansion intensity index was used to measure urban sprawl. The Mean Remote Sensing Ecological Index (MRSEI), integrating known granulation entropy (KGE) and comprehensive distance-based ranking (COBRA) algorithms, was utilized to evaluate urban ecological status. The random forest (RF) supervised machine learning-based algorithm was used to classify the study area into four categories (Built-up, Bare-land, Water, and Vegetation). Findings indicate rapid development from 2000 to 2013, followed by moderate expansion until 2021. Urban ecological quality degradation is observed in various directions over time, with the southeast consistently demonstrating excellent status. Interestingly, while good and excellent urban ecological status decreases over two decades, poor and very poor conditions improve. The research underscores an inverse relationship between urban expansion intensity and ecological status, highlighting the need for improved strategies to mitigate environmental decline. These findings will inform Afghan governmental bodies and international organizations, enabling them to better address resource consumption, ecological disruptions, social inequalities, and foster sustainable development.}, } @article {pmid39583330, year = {2024}, author = {Hakkenberg, CR and Clark, ML and Bailey, T and Burns, P and Goetz, SJ}, title = {Ladder fuels rather than canopy volumes consistently predict wildfire severity even in extreme topographic-weather conditions.}, journal = {Communications earth & environment}, volume = {5}, number = {1}, pages = {721}, pmid = {39583330}, issn = {2662-4435}, abstract = {Drivers of forest wildfire severity include fuels, topography and weather. However, because only fuels can be actively managed, quantifying their effects on severity has become an urgent research priority. Here we employed GEDI spaceborne lidar to consistently assess how pre-fire forest fuel structure affected wildfire severity across 42 California wildfires between 2019-2021. Using a spatial-hierarchical modeling framework, we found a positive concave-down relationship between GEDI-derived fuel structure and wildfire severity, marked by increasing severity with greater fuel loads until a decline in severity in the tallest and most voluminous forest canopies. Critically, indicators of canopy fuel volumes (like biomass and height) became decoupled from severity patterns in extreme topographic and weather conditions (slopes >20°; winds > 9.3 m/s). On the other hand, vertical continuity metrics like layering and ladder fuels more consistently predicted severity in extreme conditions - especially ladder fuels, where sparse understories were uniformly associated with lower severity levels. These results confirm that GEDI-derived fuel estimates can overcome limitations of optical imagery and airborne lidar for quantifying the interactive drivers of wildfire severity. Furthermore, these findings have direct implications for designing treatment interventions that target ladder fuels versus entire canopies and for delineating wildfire risk across topographic and weather conditions.}, } @article {pmid39581005, year = {2024}, author = {Tinsley, E and Froidevaux, JSP and Jones, G}, title = {The location of solar farms within England's ecological landscape: Implications for biodiversity conservation.}, journal = {Journal of environmental management}, volume = {372}, number = {}, pages = {123372}, doi = {10.1016/j.jenvman.2024.123372}, pmid = {39581005}, issn = {1095-8630}, mesh = {*Biodiversity ; England ; *Conservation of Natural Resources ; *Ecosystem ; Solar Energy ; Farms ; Geographic Information Systems ; Ecology ; Agriculture ; }, abstract = {A global energy transition to using sustainable renewable sources is being driven by global agreements. Simultaneously there is a call for increased biodiversity conservation. This creates a green-green dilemma, where the expansion of renewables could lead to the demise of biodiversity if not carefully assessed, managed and monitored. Recognition of the dilemma is central to the development of Sustainable Development Goals. It is therefore important to understand whether renewable energy sources such as solar farms are being sited in areas where they have minimal impact on biodiversity. If solar farms were sited with minimal impacts on biodiversity, we hypothesised that they would be less likely to be sited close to ecologically sensitive areas than near random points. We used Geographic Information System methods to explore the density of solar photovoltaic (PV) farms in England and assessed their siting relative to sensitive ecological features, including priority habitat types, designated sites, and land conservation initiatives. We compared the area of 25 sensitive ecological features around solar farms and random points across three spatial scales (100 m, 1000 m, and 6000 m radius scales). Solar farms were distributed throughout England, with the highest concentration in South West England. Solar sites were primarily surrounded by habitats with anthropogenic influences, such as agricultural and urban settings. Priority habitats, such as woodland, grassland, wetland and heathland, were more extensive around random points across spatial scales (except for woodland at the largest scale). Most designated sites were significantly more extensive around random points. We conclude that, under current planning regulations, solar sites in England are being placed appropriately with regard to sensitive ecological habitats, and are often sited in areas already impacted by farming and development. Adaptive planning should be implemented to ensure that the evolving research around biodiversity and solar farms is incorporated into decision making, and monitoring is completed across the lifespan of solar farms to assess impacts and effective mitigation.}, } @article {pmid39580513, year = {2024}, author = {Li, J and Weckwerth, W and Waldherr, S}, title = {Network structure and fluctuation data improve inference of metabolic interaction strengths with the inverse Jacobian.}, journal = {NPJ systems biology and applications}, volume = {10}, number = {1}, pages = {137}, pmid = {39580513}, issn = {2056-7189}, support = {201806010428//China Scholarship Council (CSC)/ ; }, mesh = {Humans ; *Algorithms ; *Metabolic Networks and Pathways/genetics ; *Breast Neoplasms/metabolism/genetics ; *Metabolomics/methods ; Cell Line, Tumor ; Models, Biological ; Computational Biology/methods ; Female ; Systems Biology/methods ; }, abstract = {Based on high-throughput metabolomics data, the recently introduced inverse differential Jacobian algorithm can infer regulatory factors and molecular causality within metabolic networks close to steady-state. However, these studies assumed perturbations acting independently on each metabolite, corresponding to metabolic system fluctuations. In contrast, emerging evidence puts forward internal network fluctuations, particularly from gene expression fluctuations, leading to correlated perturbations on metabolites. Here, we propose a novel approach that exploits these correlations to quantify relevant metabolic interactions. By integrating enzyme-related fluctuations in the construction of an appropriate fluctuation matrix, we are able to exploit the underlying reaction network structure for the inverse Jacobian algorithm. We applied this approach to a model-based artificial dataset for validation, and to an experimental breast cancer dataset with two different cell lines. By highlighting metabolic interactions with significantly changed interaction strengths, the inverse Jacobian approach identified critical dynamic regulation points which are confirming previous breast cancer studies.}, } @article {pmid39578727, year = {2024}, author = {Ang'ang'o, LM and Herren, JK and Tastan Bishop, Ö}, title = {Bioinformatics analysis of the Microsporidia sp. MB genome: a malaria transmission-blocking symbiont of the Anopheles arabiensis mosquito.}, journal = {BMC genomics}, volume = {25}, number = {1}, pages = {1132}, pmid = {39578727}, issn = {1471-2164}, mesh = {*Anopheles/microbiology/parasitology/genetics ; Animals ; *Microsporidia/genetics ; *Symbiosis ; *Computational Biology/methods ; *Genome, Fungal ; Malaria/transmission ; Phylogeny ; Mosquito Vectors/microbiology/genetics ; Genomics/methods ; RNA Interference ; }, abstract = {BACKGROUND: The use of microsporidia as a disease-transmission-blocking tool has garnered significant attention. Microsporidia sp. MB, known for its ability to block malaria development in mosquitoes, is an optimal candidate for supplementing malaria vector control methods. This symbiont, found in Anopheles mosquitoes, can be transmitted both vertically and horizontally with minimal effects on its mosquito host. Its genome, recently sequenced from An. arabiensis, comprises a compact 5.9 Mbp.

RESULTS: Here, we analyze the Microsporidia sp. MB genome, highlighting its major genomic features, gene content, and protein function. The genome contains 2247 genes, predominantly encoding enzymes. Unlike other members of the Enterocytozoonida group, Microsporidia sp. MB has retained most of the genes in the glycolytic pathway. Genes involved in RNA interference (RNAi) were also identified, suggesting a mechanism for host immune suppression. Importantly, meiosis-related genes (MRG) were detected, indicating potential for sexual reproduction in this organism. Comparative analyses revealed similarities with its closest relative, Vittaforma corneae, despite key differences in host interactions.

CONCLUSION: This study provides an in-depth analysis of the newly sequenced Microsporidia sp. MB genome, uncovering its unique adaptations for intracellular parasitism, including retention of essential metabolic pathways and RNAi machinery. The identification of MRGs suggests the possibility of sexual reproduction, offering insights into the symbiont's evolutionary strategies. Establishing a reference genome for Microsporidia sp. MB sets the foundation for future studies on its role in malaria transmission dynamics and host-parasite interactions.}, } @article {pmid39576832, year = {2024}, author = {Devadhasan, A and Kolodny, O and Carja, O}, title = {Competition for resources can reshape the evolutionary properties of spatial structure.}, journal = {PLoS computational biology}, volume = {20}, number = {11}, pages = {e1012542}, pmid = {39576832}, issn = {1553-7358}, support = {R35 GM147445/GM/NIGMS NIH HHS/United States ; T32 EB009403/EB/NIBIB NIH HHS/United States ; }, mesh = {*Ecosystem ; Humans ; *Biological Evolution ; Computational Biology ; Mutation ; Models, Biological ; Computer Simulation ; }, abstract = {Many evolving ecosystems have spatial structures that can be conceptualized as networks, with nodes representing individuals or homogeneous subpopulations and links the patterns of spread between them. Prior models of evolution on networks do not take ecological niche differences and eco-evolutionary interplay into account. Here, we combine a resource competition model with evolutionary graph theory to study how heterogeneous topological structure shapes evolutionary dynamics under global frequency-dependent ecological interactions. We find that the addition of ecological competition for resources can produce a reversal of roles between amplifier and suppressor networks for deleterious mutants entering the population. We show that this effect is a nonlinear function of ecological niche overlap and discuss intuition for the observed dynamics using simulations and analytical approximations. We use these theoretical results together with spatial representations from imaging data to show that, for ductal carcinoma, where tumor growth is highly spatially constrained, with cells confined to a tree-like network of ducts, the topological structure can lead to higher rates of deleterious mutant hitchhiking with metabolic driver mutations, compared to tumors characterized by different spatial topologies.}, } @article {pmid39570994, year = {2024}, author = {Madden, WG and Jin, W and Lopman, B and Zufle, A and Dalziel, B and E Metcalf, CJ and Grenfell, BT and Lau, MSY}, title = {Deep neural networks for endemic measles dynamics: Comparative analysis and integration with mechanistic models.}, journal = {PLoS computational biology}, volume = {20}, number = {11}, pages = {e1012616}, pmid = {39570994}, issn = {1553-7358}, mesh = {*Measles/epidemiology ; Humans ; *Neural Networks, Computer ; *Disease Outbreaks/statistics & numerical data ; *Endemic Diseases/statistics & numerical data ; England/epidemiology ; Wales/epidemiology ; Computational Biology ; Forecasting/methods ; Epidemiological Models ; }, abstract = {Measles is an important infectious disease system both for its burden on public health and as an opportunity for studying nonlinear spatio-temporal disease dynamics. Traditional mechanistic models often struggle to fully capture the complex nonlinear spatio-temporal dynamics inherent in measles outbreaks. In this paper, we first develop a high-dimensional feed-forward neural network model with spatial features (SFNN) to forecast endemic measles outbreaks and systematically compare its predictive power with that of a classical mechanistic model (TSIR). We illustrate the utility of our model using England and Wales measles data from 1944-1965. These data present multiple modeling challenges due to the interplay between metapopulations, seasonal trends, and nonlinear dynamics related to demographic changes. Our results show that while the TSIR model yields similarly performant short-term (1 to 2 biweeks ahead) forecasts for highly populous cities, our neural network model (SFNN) consistently achieves lower root mean squared error (RMSE) across other forecasting windows. Furthermore, we show that our spatial-feature neural network model, without imposing mechanistic assumptions a priori, can uncover gravity-model-like spatial hierarchy of measles spread in which major cities play an important role in driving regional outbreaks. We then turn our attention to integrative approaches that combine mechanistic and machine learning models. Specifically, we investigate how the TSIR can be utilized to improve a state-of-the-art approach known as Physics-Informed-Neural-Networks (PINN) which explicitly combines compartmental models and neural networks. Our results show that the TSIR can facilitate the reconstruction of latent susceptible dynamics, thereby enhancing both forecasts in terms of mean absolute error (MAE) and parameter inference of measles dynamics within the PINN. In summary, our results show that appropriately designed neural network-based models can outperform traditional mechanistic models for short to long-term forecasts, while simultaneously providing mechanistic interpretability. Our work also provides valuable insights into more effectively integrating machine learning models with mechanistic models to enhance public health responses to measles and similar infectious disease systems.}, } @article {pmid39570888, year = {2024}, author = {Cuesta-Aguirre, DR and Malgosa, A and Santos, C}, title = {An easy-to-use pipeline to analyze amplicon-based Next Generation Sequencing results of human mitochondrial DNA from degraded samples.}, journal = {PloS one}, volume = {19}, number = {11}, pages = {e0311115}, pmid = {39570888}, issn = {1932-6203}, mesh = {*DNA, Mitochondrial/genetics ; Humans ; *High-Throughput Nucleotide Sequencing/methods ; Sequence Analysis, DNA/methods ; Computational Biology/methods ; Software ; Forensic Genetics/methods ; DNA, Ancient/analysis ; }, abstract = {Genome and transcriptome examinations have become more common due to Next-Generation Sequencing (NGS), which significantly increases throughput and depth coverage while reducing costs and time. Mitochondrial DNA (mtDNA) is often the marker of choice in degraded samples from archaeological and forensic contexts, as its higher number of copies can improve the success of the experiment. Among other sequencing strategies, amplicon-based NGS techniques are currently being used to obtain enough data to be analyzed. There are some pipelines designed for the analysis of ancient mtDNA samples and others for the analysis of amplicon data. However, these pipelines pose a challenge for non-expert users and cannot often address both ancient and forensic DNA particularities and amplicon-based sequencing simultaneously. To overcome these challenges, a user-friendly bioinformatic tool was developed to analyze the non-coding region of human mtDNA from degraded samples recovered in archaeological and forensic contexts. The tool can be easily modified to fit the specifications of other amplicon-based NGS experiments. A comparative analysis between two tools, MarkDuplicates from Picard and dedup parameter from fastp, both designed for duplicate removal was conducted. Additionally, various thresholds of PMDtools, a specialized tool designed for extracting reads affected by post-mortem damage, were used. Finally, the depth coverage of each amplicon was correlated with its level of damage. The results obtained indicated that, for removing duplicates, dedup is a better tool since retains more non-repeated reads, that are removed by MarkDuplicates. On the other hand, a PMDS = 1 in PMDtools was the threshold that allowed better differentiation between present-day and ancient samples, in terms of damage, without losing too many reads in the process. These two bioinformatic tools were added to a pipeline designed to obtain both haplotype and haplogroup of mtDNA. Furthermore, the pipeline presented in the present study generates information about the quality and possible contamination of the sample. This pipeline is designed to automatize mtDNA analysis, however, particularly for ancient samples, some manual analyses may be required to fully validate results since the amplicons that used to be more easily recovered were the ones that had fewer reads with damage, indicating that special care must be taken for poor recovered samples.}, } @article {pmid39569566, year = {2024}, author = {Sung, ML and León, C and Reisman, JI and Gordon, KS and Kerns, RD and Li, W and Liu, W and Mitra, A and Yu, H and Becker, WC}, title = {Disparities in Receipt of Medications for Opioid Use Disorder Before and During the COVID-19 Pandemic in the US Veterans Health Administration.}, journal = {Substance use & addiction journal}, volume = {}, number = {}, pages = {29767342241293334}, doi = {10.1177/29767342241293334}, pmid = {39569566}, issn = {2976-7350}, abstract = {BACKGROUND: Populations disproportionately impacted by the opioid epidemic are less likely to receive medications for opioid use disorder (MOUD; OUD). The COVID-19 pandemic exacerbated these disparities. We performed an ecological survey of subpopulations to compare differences in MOUD receipt among Veterans with OUD before versus during the pandemic.

METHODS: Using 2 cross-sections of 2 time periods of national Veterans Health Administration electronic health record data, we calculated proportions of Veterans with any MOUD receipt by demographics, Elixhauser comorbidity index, and natural language processing (NLP)-derived substance use and social determinants of health in each time period. We evaluated differences in MOUD receipt before and during the pandemic by patient characteristics using Chi-square and Cohen's h for effect size.

RESULTS: Among 62 195 patients with OUD before the pandemic, the proportion prescribed MOUD increased from 46.5% before to 47.5% (P = .0003) during the pandemic. Statistically significant increased receipt of MOUD was observed for patients who were ≥55 years, men, White, with Elixhauser comorbidity indices of 2 and ≥5, and with NLP-derived indicators of substance use. There was a decrease that did not achieve statistical significance in MOUD receipt from before to during the pandemic for patients who were women, Black, Latinx, and food insecure.

CONCLUSIONS: The proportions of patients with OUD prescribed MOUD increased from before to during the pandemic. However, Veterans who were women, Black, Latinx, and food insecure did not experience these increases. These patients may benefit from interventions such as targeted outreach efforts to improve MOUD engagement to reduce OUD harms.}, } @article {pmid39569448, year = {2024}, author = {Yu, Y and Edelson, M and Pham, A and Pekar, JE and Johnson, B and Post, K and Kuo, TT}, title = {Distributed, immutable, and transparent biomedical limited data set request management on multi-capacity network.}, journal = {Journal of the American Medical Informatics Association : JAMIA}, volume = {}, number = {}, pages = {}, doi = {10.1093/jamia/ocae288}, pmid = {39569448}, issn = {1527-974X}, support = {R01EB031030//U.S. National Institutes of Health/ ; }, abstract = {OBJECTIVE: Our study aimed to expedite data sharing requests of Limited Data Sets (LDS) through the development of a streamlined platform that allows distributed, immutable management of network activities, provides transparent and intuitive auditing of data access history, and systematically evaluated it on a multi-capacity network setting for meaningful efficiency metrics.

MATERIALS AND METHODS: We developed a blockchain-based system with six types of smart contracts to automate the LDS sharing process among major stakeholders. Our workflow included metadata initialization, access-request processing, and audit-log querying. We evaluated our system using synthetic data on three machines with varying specifications to emulate real-world scenarios. The data employed included ∼1000 researcher requests and ∼360 000 log queries.

RESULTS: On average, it took ∼2.5 s to register and respond to a researcher access request. The average runtime for an audit-log query with non-empty output was ∼3 ms. The runtime metrics at each institution showed general trends affiliated with their computational capacity.

DISCUSSION: Our system can reduce the LDS sharing request time from potentially hours to seconds, while enhancing data access transparency in a multi-institutional setting. There were variations in performance across sites that could be attributed to differences in hardware specifications. The performance gains became marginal beyond certain hardware thresholds, pointing to the influence of external factors such as network speeds.

CONCLUSION: Our blockchain-based system can potentially accelerate clinical research by strengthening the data access process, expediting access and delivery of data links, increasing transparency with clear audit trails, and reinforcing trust in medical data management. Our smart contracts are available at: https://github.com/graceyufei/LDS-Request-Management.}, } @article {pmid39568559, year = {2024}, author = {Boyes, D and Hutchinson, F and Crowley, LM and Boyes, C and , and , and , and , and , and , and , }, title = {The genome sequence of the Silver-barred Sober moth, Aproaerema taeniolella (Zeller, 1839).}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {500}, pmid = {39568559}, issn = {2398-502X}, abstract = {We present a genome assembly of a female Silver-barred Sober moth Aproaerema taeniolella (Arthropoda; Insecta; Lepidoptera; Gelechiidae). The genome sequence has a length of 636.60 megabases. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.19 kilobases in length. Gene annotation of this assembly on Ensembl identified 22,274 protein-coding genes.}, } @article {pmid39564491, year = {2024}, author = {Zhang, Y and Wang, M and Huang, M and Zhao, J}, title = {Innovative strategies and challenges mosquito-borne disease control amidst climate change.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1488106}, pmid = {39564491}, issn = {1664-302X}, abstract = {The revival of the transmission dynamics of mosquito-borne diseases grants striking challenges to public health intensified by climate change worldwide. This inclusive review article examines multidimensional strategies and challenges linked to climate change and the epidemiology of mosquito-borne diseases such as malaria, dengue, Zika, chikungunya, and yellow fever. It delves into how the biology, pathogenic dynamics, and vector distribution of mosquitoes are influenced by continuously rising temperatures, modified rainfall patterns, and extreme climatic conditions. We also highlighted the high likelihood of malaria in Africa, dengue in Southeast Asia, and blowout of Aedes in North America and Europe. Modern predictive tools and developments in surveillance, including molecular gears, Geographic Information Systems (GIS), and remote sensing have boosted our capacity to predict epidemics. Integrated data management techniques and models based on climatic conditions provide a valuable understanding of public health planning. Based on recent data and expert ideas, the objective of this review is to provide a thoughtful understanding of existing landscape and upcoming directions in the control of mosquito-borne diseases regarding changing climate. This review determines emerging challenges and innovative vector control strategies in the changing climatic conditions to ensure public health.}, } @article {pmid39563951, year = {2024}, author = {Sivell, O and Hawkes, WLS and , and , and , and , and , and , and , }, title = {The genome sequence of the silvery leafcutter bee, Megachile leachella Curtis, 1828.}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {415}, pmid = {39563951}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual female Megachile leachella (the silvery leafcutter bee; Arthropoda; Insecta; Hymenoptera; Megachilidae). The genome sequence is 573.0 megabases in span. Most of the assembly is scaffolded into 16 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 21.04 kilobases in length.}, } @article {pmid39563229, year = {2024}, author = {Toth, AL and Wyatt, CDR and Masonbrink, RE and Geist, KS and Fortune, R and Scott, SB and Favreau, E and Rehan, SM and Sumner, S and Gardiner, MM and Sivakoff, FS}, title = {New genomic resources inform transcriptomic responses to heavy metal toxins in the common Eastern bumble bee Bombus impatiens.}, journal = {BMC genomics}, volume = {25}, number = {1}, pages = {1106}, pmid = {39563229}, issn = {1471-2164}, support = {20176701326595//USDA National Institute of Food and Agriculture/ ; 1929239//NSF DEB-NERC/ ; }, mesh = {Animals ; Bees/genetics/drug effects ; *Metals, Heavy/toxicity ; *Transcriptome ; Genomics/methods ; Molecular Sequence Annotation ; Gene Expression Profiling ; Genome, Insect ; Toxins, Biological/genetics ; }, abstract = {BACKGROUND: The common Eastern bumble bee Bombus impatiens is native to North America and is the main commercially reared pollinator in the Americas. There has been extensive research on this species related to its social biology, applied pollination, and genetics. The genome of this species was previously sequenced using short-read technology, but recent technological advances provide an opportunity for substantial improvements. This species is common in agricultural and urban environments, and heavy metal contaminants produced by industrial processes can negatively impact it. To begin to identify possible mechanisms underlying responses to these toxins, we used RNA-sequencing to examine how exposure to a cocktail of four heavy metals at field-realistic levels from industrial areas affected B. impatiens worker gene expression.

RESULTS: PacBio long-read sequencing resulted in 544x coverage of the genome, and HiC technology was used to map chromatin contacts. Using Juicer and manual curation, the genome was scaffolded into 18 main pseudomolecules, representing a high quality, chromosome-level assembly. The sequenced genome size is 266.6 Mb and BRAKER3 annotation produced 13,938 annotated genes. The genome and annotation show high completeness, with ≥ 96% of conserved Eukaryota and Hymenoptera genes present in both the assembly and annotated genes. RNA sequencing of heavy metal exposed workers revealed 603 brain and 34 fat body differentially expressed genes. In the brain, differentially expressed genes had biological functions related to chaperone activity and protein folding.

CONCLUSIONS: Our data represent a large improvement in genomic resources for this important model species-with 10% more genome coverage than previously available, and a high-quality assembly into 18 chromosomes, the expected karyotype for this species. The new gene annotation added 777 new genes. Altered gene expression in response to heavy metal exposure suggests a possible mechanism for how these urban toxins are negatively impacting bee health, specifically by altering protein folding in the brain. Overall, these data are useful as a general high quality genomic resource for this species, and provide insight into mechanisms underlying tissue-specific toxicological responses of bumble bees to heavy metals.}, } @article {pmid39561196, year = {2024}, author = {Konzen, E and Delahay, RJ and Hodgson, DJ and McDonald, RA and Brooks Pollock, E and Spencer, SEF and McKinley, TJ}, title = {Efficient modelling of infectious diseases in wildlife: A case study of bovine tuberculosis in wild badgers.}, journal = {PLoS computational biology}, volume = {20}, number = {11}, pages = {e1012592}, pmid = {39561196}, issn = {1553-7358}, mesh = {Animals ; *Mustelidae/microbiology ; *Tuberculosis, Bovine/epidemiology/transmission/diagnosis ; Cattle ; *Animals, Wild/microbiology ; United Kingdom/epidemiology ; Models, Biological ; Mycobacterium bovis ; Computational Biology/methods ; Disease Reservoirs/microbiology/veterinary ; Ireland/epidemiology ; }, abstract = {Bovine tuberculosis (bTB) has significant socio-economic and welfare impacts on the cattle industry in parts of the world. In the United Kingdom and Ireland, disease control is complicated by the presence of infection in wildlife, principally the European badger. Control strategies tend to be applied to whole populations, but better identification of key sources of transmission, whether individuals or groups, could help inform more efficient approaches. Mechanistic transmission models can be used to better understand key epidemiological drivers of disease spread and identify high-risk individuals and groups if they can be adequately fitted to observed data. However, this is a significant challenge, especially within wildlife populations, because monitoring relies on imperfect diagnostic test information, and even under systematic surveillance efforts (such as capture-mark-recapture sampling) epidemiological events are only partially observed. To this end we develop a stochastic compartmental model of bTB transmission, and fit this to individual-level data from a unique > 40-year longitudinal study of 2,391 badgers using a recently developed individual forward filtering backward sampling algorithm. Modelling challenges are further compounded by spatio-temporal meta-population structures and age-dependent mortality. We develop a novel estimator for the individual effective reproduction number that provides quantitative evidence for the presence of superspreader badgers, despite the population-level effective reproduction number being less than one. We also infer measures of the hidden burden of infection in the host population through time; the relative likelihoods of competing routes of transmission; effective and realised infectious periods; and longitudinal measures of diagnostic test performance. This modelling framework provides an efficient and generalisable way to fit state-space models to individual-level data in wildlife populations, which allows identification of high-risk individuals and exploration of important epidemiological questions about bTB and other wildlife diseases.}, } @article {pmid39556417, year = {2024}, author = {Helgeson, SA and Mudgalkar, RM and Jacobs, KA and Lee, AS and Sanghavi, D and Moreno Franco, P and Brooks, IS and , }, title = {Association Between X/Twitter and Prescribing Behavior During the COVID-19 Pandemic: Retrospective Ecological Study.}, journal = {JMIR infodemiology}, volume = {4}, number = {}, pages = {e56675}, pmid = {39556417}, issn = {2564-1891}, support = {U24 TR002306/TR/NCATS NIH HHS/United States ; }, mesh = {Humans ; Retrospective Studies ; *Hydroxychloroquine/therapeutic use ; *Social Media ; United States/epidemiology ; *COVID-19/epidemiology ; *Practice Patterns, Physicians' ; Pandemics ; COVID-19 Drug Treatment ; Male ; Female ; Middle Aged ; SARS-CoV-2/drug effects ; }, abstract = {BACKGROUND: Social media has become a vital tool for health care providers to quickly share information. However, its lack of content curation and expertise poses risks of misinformation and premature dissemination of unvalidated data, potentially leading to widespread harmful effects due to the rapid and large-scale spread of incorrect information.

OBJECTIVE: We aim to determine whether social media had an undue association with the prescribing behavior of hydroxychloroquine, using the COVID-19 pandemic as the setting.

METHODS: In this retrospective study, we gathered the use of hydroxychloroquine in 48 hospitals in the United States between January and December 2020. Social media data from X/Twitter was collected using Brandwatch, a commercial aggregator with access to X/Twitter's data, and focused on mentions of "hydroxychloroquine" and "Plaquenil." Tweets were categorized by sentiment (positive, negative, or neutral) using Brandwatch's sentiment analysis tool, with results classified by date. Hydroxychloroquine prescription data from the National COVID Cohort Collaborative for 2020 was used. Granger causality and linear regression models were used to examine relationships between X/Twitter mentions and prescription trends, using optimum time lags determined via vector auto-regression.

RESULTS: A total of 581,748 patients with confirmed COVID-19 were identified. The median daily number of positive COVID-19 cases was 1318.5 (IQR 1005.75-1940.3). Before the first confirmed COVID-19 case, hydroxychloroquine was prescribed at a median rate of 559 (IQR 339.25-728.25) new prescriptions per day. A day-of-the-week effect was noted in both prescriptions and case counts. During the pandemic in 2020, hydroxychloroquine prescriptions increased significantly, with a median of 685.5 (IQR 459.75-897.25) per day, representing a 22.6% rise from baseline. The peak occurred on April 2, 2020, with 3411 prescriptions, a 397.6% increase. Hydroxychloroquine mentions on X/Twitter peaked at 254,770 per day on April 5, 2020, compared to a baseline of 9124 mentions per day before January 21, 2020. During this study's period, 3,823,595 total tweets were recorded, with 10.09% (n=386,115) positive, 37.87% (n=1,448,030) negative, and 52.03% (n=1,989,450) neutral sentiments. A 1-day lag was identified as the optimal time for causal association between tweets and hydroxychloroquine prescriptions. Univariate analysis showed significant associations across all sentiment types, with the largest impact from positive tweets. Multivariate analysis revealed only neutral and negative tweets significantly affected next-day prescription rates.

CONCLUSIONS: During the first year of the COVID-19 pandemic, there was a significant association between X/Twitter mentions and the number of prescriptions of hydroxychloroquine. This study showed that X/Twitter has an association with the prescribing behavior of hydroxychloroquine. Clinicians need to be vigilant about their potential unconscious exposure to social media as a source of medical knowledge, and health systems and organizations need to be more diligent in identifying expertise, source, and quality of evidence when shared on social media platforms.}, } @article {pmid39555185, year = {2024}, author = {Yang, D and Hashizume, M and Tobías, A and Honda, Y and Roye, D and Oh, J and Dang, TN and Kim, Y and Abrutzky, R and Guo, Y and Tong, S and Coelho, MSZS and Saldiva, PHN and Lavigne, E and Correa, PM and Ortega, NV and Osorio, S and Kyselý, J and Urban, A and Orru, H and Indermitte, E and Jaakkola, J and Ryti, N and Pascal, M and Huber, V and Schneider, A and Katsouyanni, K and Analitis, A and Entezari, A and Mayvaneh, F and Goodman, P and Zeka, A and Michelozzi, P and de'Donato, F and Alahmad, B and Diaz, MH and la Cruz Valencia, C and Overcenco, A and Houthuijs, D and Ameling, C and Rao, S and Nunes, B and Madureira, J and Holo-Bâc, IH and Scovronick, N and Acquaotta, F and Kim, H and Lee, W and Íñiguez, C and Forsberg, B and Vicedo-Cabrera, AM and Ragettli, MS and Guo, YL and Pan, SC and Li, S and Sera, F and Zanobetti, A and Schwartz, J and Armstrong, B and Gasparrini, A and Chung, Y}, title = {Temporal change in minimum mortality temperature under changing climate: A multicountry multicommunity observational study spanning 1986-2015.}, journal = {Environmental epidemiology (Philadelphia, Pa.)}, volume = {8}, number = {5}, pages = {e334}, pmid = {39555185}, issn = {2474-7882}, support = {MR/R013349/1/MRC_/Medical Research Council/United Kingdom ; MR/V034162/1/MRC_/Medical Research Council/United Kingdom ; }, abstract = {BACKGROUND: The minimum mortality temperature (MMT) or MMT percentile (MMTP) is an indicator of population susceptibility to nonoptimum temperatures. MMT and MMTP change over time; however, the changing directions show region-wide heterogeneity. We examined the heterogeneity of temporal changes in MMT and MMTP across multiple communities and in multiple countries.

METHODS: Daily time-series data for mortality and ambient mean temperature for 699 communities in 34 countries spanning 1986-2015 were analyzed using a two-stage meta-analysis. First, a quasi-Poisson regression was employed to estimate MMT and MMTP for each community during the designated subperiods. Second, we pooled the community-specific temporally varying estimates using mixed-effects meta-regressions to examine temporal changes in MMT and MMTP in the entire study population, as well as by climate zone, geographical region, and country.

RESULTS: Temporal increases in MMT and MMTP from 19.5 °C (17.9, 21.1) to 20.3 °C (18.5, 22.0) and from the 74.5 (68.3, 80.6) to 75.0 (71.0, 78.9) percentiles in the entire population were found, respectively. Temporal change was significantly heterogeneous across geographical regions (P < 0.001). Temporal increases in MMT were observed in East Asia (linear slope [LS] = 0.91, P = 0.02) and South-East Asia (LS = 0.62, P = 0.05), whereas a temporal decrease in MMT was observed in South Europe (LS = -0.46, P = 0.05). MMTP decreased temporally in North Europe (LS = -3.45, P = 0.02) and South Europe (LS = -2.86, P = 0.05).

CONCLUSIONS: The temporal change in MMT or MMTP was largely heterogeneous. Population susceptibility in terms of optimum temperature may have changed under a warming climate, albeit with large region-dependent variations.}, } @article {pmid39549265, year = {2024}, author = {Rayamajhi, N and Rivera-Colón, AG and Minhas, BF and Cheng, CC and Catchen, JM}, title = {The genome of the cryopelagic Antarctic bald notothen, Trematomus borchgrevinki.}, journal = {G3 (Bethesda, Md.)}, volume = {}, number = {}, pages = {}, doi = {10.1093/g3journal/jkae267}, pmid = {39549265}, issn = {2160-1836}, abstract = {The Antarctic bald notothen, Trematomus borchgrevinki (family Nototheniidae) occupies a high latitude, ice-laden environment and represents an extreme example of cold-specialization among fishes. We present the first, high quality, chromosome-scale genome of a female T. borchgrevinki individual comprised of 23 putative chromosomes, the largest of which is 65 megabasepairs (Mbp) in length. The total length of the genome 935.13 Mbp, composed of 2,094 scaffolds, with a scaffold N50 of 42.67 Mbp. Annotation yielded 22,192 protein coding genes while 54.75% of the genome was occupied by repetitive elements; an analysis of repeats demonstrated that an expansion occurred in recent time. Conserved synteny analysis revealed that the genome architecture of T. borchgrevinki is largely maintained with other members of the notothenioid clade, although several significant translocations and inversions are present, including the fusion of orthologous chromosomes 8 and 11 into a single element. This genome will serve as a cold-specialized model for comparisons to other members of the notothenioid adaptive radiation.}, } @article {pmid39548719, year = {2024}, author = {Chen, Y and Gao, Y and Zhang, Z and Zhan, A}, title = {Multi-Omics Inform Invasion Risks Under Global Climate Change.}, journal = {Global change biology}, volume = {30}, number = {11}, pages = {e17588}, doi = {10.1111/gcb.17588}, pmid = {39548719}, issn = {1365-2486}, support = {2022GDASZH-2022010106//GDAS Special Project of Science and Technology Development/ ; 2024A1515010914//Guangdong Basic and Applied Basic Research Foundation/ ; 42106098//National Natural Science Foundation of China/ ; 32061143012//National Natural Science Foundation of China/ ; 42276126//National Natural Science Foundation of China/ ; 32371753//National Natural Science Foundation of China/ ; }, mesh = {*Climate Change ; *Introduced Species ; *Genomics ; Urochordata/genetics ; Epigenomics ; Adaptation, Physiological/genetics ; Animals ; Multiomics ; }, abstract = {Global climate change is exacerbating biological invasions; however, the roles of genomic and epigenomic variations and their interactions in future climate adaptation remain underexplored. Using the model invasive ascidian Botryllus schlosseri across the Northern Hemisphere, we investigated genomic and epigenomic responses to future climates and developed a framework to assess future invasion risks. We employed generalized dissimilarity modeling and gradient forest analyses to assess genomic and epigenomic offsets under climate change. Our results showed that populations with genomic maladaptation did not geographically overlap with those experiencing epigenomic maladaptation, suggesting that genomic and epigenomic variations play complementary roles in adaptation to future climate conditions. By integrating genomic and epigenomic offsets into the genome-epigenomic index, we predicted that populations with lower index values were less maladapted, indicating a higher risk of future invasions. Native populations exhibited lower offsets than invasive populations, suggesting greater adaptive potentials and higher invasion risks under future climate change scenarios. These results highlight the importance of incorporating multi-omics data into predictive models to study future climate (mal)adaptation and assess invasion risks under global climate change.}, } @article {pmid39548060, year = {2024}, author = {Conrad, RE and Brink, CE and Viver, T and Rodriguez-R, LM and Aldeguer-Riquelme, B and Hatt, JK and Venter, SN and Rossello-Mora, R and Amann, R and Konstantinidis, KT}, title = {Microbial species and intraspecies units exist and are maintained by ecological cohesiveness coupled to high homologous recombination.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {9906}, pmid = {39548060}, issn = {2041-1723}, support = {1831582//NSF | BIO | Division of Environmental Biology (DEB)/ ; }, mesh = {*Homologous Recombination ; *Escherichia coli/genetics/classification ; Genome, Bacterial ; Microbiota/genetics ; Evolution, Molecular ; Gene Flow ; Phylogeny ; Computational Biology/methods ; }, abstract = {Recent genomic analyses have revealed that microbial communities are predominantly composed of persistent, sequence-discrete species and intraspecies units (genomovars), but the mechanisms that create and maintain these units remain unclear. By analyzing closely-related isolate genomes from the same or related samples and identifying recent recombination events using a novel bioinformatics methodology, we show that high ecological cohesiveness coupled to frequent-enough and unbiased (i.e., not selection-driven) horizontal gene flow, mediated by homologous recombination, often underlie these diversity patterns. Ecological cohesiveness was inferred based on greater similarity in temporal abundance patterns of genomes of the same vs. different units, and recombination was shown to affect all sizable segments of the genome (i.e., be genome-wide) and have two times or greater impact on sequence evolution than point mutations. These results were observed in both Salinibacter ruber, an environmental halophilic organism, and Escherichia coli, the model gut-associated organism and an opportunistic pathogen, indicating that they may be more broadly applicable to the microbial world. Therefore, our results represent a departure compared to previous models of microbial speciation that invoke either ecology or recombination, but not necessarily their synergistic effect, and answer an important question for microbiology: what a species and a subspecies are.}, } @article {pmid39547957, year = {2024}, author = {Kwon, EJ and Lee, H and Shin, U and Kim, ES and Myung, K and Kim, J and Park, JH and Kim, K and Lee, Y and Oh, CK and Kim, YH}, title = {Ionizing radiation inhibits zebrafish embryo hatching through induction of tissue inhibitors of metalloproteinases (TIMPs) expression.}, journal = {The FEBS journal}, volume = {291}, number = {24}, pages = {5470-5485}, doi = {10.1111/febs.17318}, pmid = {39547957}, issn = {1742-4658}, support = {IBS-R022-D1//Institute for Basic Science/ ; RS-2023-00223591//National Research Foundation of Korea/ ; RS-2023-00301938//National Research Foundation of Korea/ ; RS-2024-00439078//National Research Foundation of Korea/ ; //KREONET/ ; }, mesh = {Animals ; *Zebrafish/genetics/embryology/metabolism ; *Radiation, Ionizing ; *Tissue Inhibitor of Metalloproteinases/metabolism/genetics ; *Gene Expression Regulation, Developmental/radiation effects ; *Embryo, Nonmammalian/radiation effects/metabolism ; Zebrafish Proteins/genetics/metabolism ; }, abstract = {Ionizing radiation (IR) has garnered growing attention because of its biological effects on aquatic organisms and humans. Here, we identify the most impacted organs and uncover the molecular mechanisms causing the changes in the context of vertebrate development using single-cell RNA sequencing. Alterations in cellular composition and biological functions were explored using transcriptomic profiling of zebrafish embryos exposed to 5 Gy. Single-cell RNA sequencing analyses unveiled notable shifts in the proportions of brain/central nervous system and hatching gland clusters. Although IR exposure led to increased expression of hatching enzymes, a significant but mild delay in hatching was observed following 5 Gy IR exposure. Gene Ontology analysis showed an increased expression of tissue inhibitors of metalloproteinases (TIMPs), known as matrix metalloproteinase inhibitors, which was confirmed via whole-mount in situ hybridization. Correlation analysis linked TIMPs to transcription factors cebpb and cebpd, which were significantly correlated post-IR exposure. Although no morphological changes were observed in some organs, including the brain, the study reveals substantial alterations in developing vertebrates. Notably, despite increased hatching enzymes, elevated TIMPs in the hatching gland suggest a regulatory mechanism impacting hatching activity. This research contributes to comprehending the ecological repercussions of IR exposure, emphasizing the importance of safety measures for aquatic ecosystems and overall environmental health.}, } @article {pmid39546825, year = {2025}, author = {Meyer, A and Ndiaye, B and Larkins, A and Chaters, G and Gilbert, W and Huntington, B and Ilboudo, G and Dione, M and Jemberu, WT and Diouf, MN and Fall, AG and Fall, M and Lo, M and Rushton, J}, title = {Economic assessment of animal disease burden in Senegalese small ruminants.}, journal = {Preventive veterinary medicine}, volume = {234}, number = {}, pages = {106382}, doi = {10.1016/j.prevetmed.2024.106382}, pmid = {39546825}, issn = {1873-1716}, mesh = {Animals ; Senegal/epidemiology ; *Goat Diseases/economics/epidemiology ; *Goats ; Sheep ; *Sheep Diseases/economics/epidemiology ; Cost of Illness ; Animal Husbandry/economics/methods ; }, abstract = {Small ruminant production in sub-Saharan Africa is limited by a range of constraints, including animal health issues. This study aimed at estimating the impact of these issues on the small ruminant production in Senegal in a holistic manner, using an approach developed by the Global Burden of Animal Diseases (GBADs) programme. The estimation focused on the mixed crop-livestock system, representing a large proportion (>60 %) of the small ruminant population in the country. It was based on existing data collected via a systematic literature review, acquisition of secondary datasets from local stakeholders, and expert elicitation. A dynamic population model was used to calculate the gross margin of the sector under both the current health constraints and an ideal health state, where animals are not exposed to causes of morbidity and mortality. The difference between the current and ideal health scenarios, termed the Animal Health Loss Envelope (AHLE), provides a quantitative measure of the farm-level cost of disease in the system. The all-cause AHLE was estimated at 292 billion FCFA (468 million USD, with 95 % prediction interval 216 - 366 billion FCFA) per year for 2022, for a population of 8.8 million animals. The contribution of Peste des Petits Ruminants (PPR) was modelled separately, as an example of attributing part of the AHLE to a specific disease cause. PPR was estimated to contribute 5 % of the total AHLE. The animal disease burden experienced by Senegalese livestock keepers was largely due to loss in animals and production, with relatively small amounts of animal health expenditure. Implementation of this study contributed to the further development of the GBADs approach. Such estimates can support decision making at all levels, from investment decisions at the international level to local disease awareness campaigns targeting livestock keepers.}, } @article {pmid39545367, year = {2024}, author = {Heuck, MK and Powell, JR and Kath, J and Birnbaum, C and Frew, A}, title = {Evaluating the Usefulness of the C-S-R Framework for Understanding AM Fungal Responses to Climate Change in Agroecosystems.}, journal = {Global change biology}, volume = {30}, number = {11}, pages = {e17566}, doi = {10.1111/gcb.17566}, pmid = {39545367}, issn = {1365-2486}, support = {DE220100479//Australian Research Council (ARC) Discovery Early Career Researcher Award (DECRA)/ ; FT190100590//Australian Research Council Future Fellowship/ ; }, mesh = {*Climate Change ; *Mycorrhizae/physiology ; *Agriculture ; *Ecosystem ; Symbiosis ; }, abstract = {Arbuscular mycorrhizal (AM) fungi play a key role in terrestrial ecosystems by forming symbiotic relationships with plants and may confer benefits for sustainable agriculture, by reducing reliance on harmful fertiliser and pesticide inputs and enhancing plant resilience against insect herbivores. Despite their ecological importance, critical gaps in understanding AM fungal ecology limit predictions of their responses to global change in agroecosystems. However, predicting climate change impacts on AM fungi is important for maintaining crop productivity and ecosystem stability. Efforts to classify AM fungi based on functional traits, such as the competitor, stress-tolerator, ruderal (C-S-R) framework, aim to address these gaps but face challenges due to the obligate symbiotic nature of the fungi. As the framework is still widely used, we evaluate its applicability in predicting global change impacts on AM fungal communities in agroecosystems. Chagnon's adaptation of the C-S-R framework for AM fungi aligns with some study outcomes (e.g., under the context of water limitation) but faces challenges when used in complex climate change scenarios, varying agricultural conditions and/or extreme climatic conditions. The reliance on a limited dataset to classify AM fungal families further limits accurate predictions of AM fungal community dynamics. Trait data collection could support a nuanced understanding of AM fungi and leveraging AM fungal databases could streamline data management and analysis, enhancing efforts to clarify AM fungal responses to environmental change and guide ecosystem management practices. Thus, while the C-S-R framework holds promise, it requires additional AM fungal trait data for validation and improvement of its predictive power. Conclusively, before designing experiments based on life-history strategies and developing new frameworks tailored to AM fungi a critical first step is to gain a comprehensive understanding of their traits.}, } @article {pmid39543597, year = {2024}, author = {Rajovic, N and Grubor, N and Cirkovic, A and Maheswaran, R and Bath, PA and Green, D and Bellantuono, I and Milicevic, O and Kanazir, S and Miljus, D and Zivkovic, S and Vidojevic, D and Mickovski, N and Rakocevic, I and Ivanovic, I and Mladenovic, A and Goyder, E and Milic, N}, title = {Insights into relationship of environmental inequalities and multimorbidity: a population-based study.}, journal = {Environmental health : a global access science source}, volume = {23}, number = {1}, pages = {99}, pmid = {39543597}, issn = {1476-069X}, support = {200110/WT_/Wellcome Trust/United Kingdom ; 200110/WT_/Wellcome Trust/United Kingdom ; 200110/WT_/Wellcome Trust/United Kingdom ; 200110/WT_/Wellcome Trust/United Kingdom ; 200007//Ministry of Science, Innovation and Technological Development of the Republic of Serbia/ ; 200007//Ministry of Science, Innovation and Technological Development of the Republic of Serbia/ ; 200110/WT_/Wellcome Trust/United Kingdom ; 164294//UKRI Global Challenges Research Fund/ ; 164294//UKRI Global Challenges Research Fund/ ; 164294//UKRI Global Challenges Research Fund/ ; 164294//UKRI Global Challenges Research Fund/ ; 164294//UKRI Global Challenges Research Fund/ ; 164294//UKRI Global Challenges Research Fund/ ; 164294//UKRI Global Challenges Research Fund/ ; 164294//UKRI Global Challenges Research Fund/ ; 164294//UKRI Global Challenges Research Fund/ ; 164294//UKRI Global Challenges Research Fund/ ; 164294//UKRI Global Challenges Research Fund/ ; 164294//UKRI Global Challenges Research Fund/ ; 164294//UKRI Global Challenges Research Fund/ ; 164294//UKRI Global Challenges Research Fund/ ; 164294//UKRI Global Challenges Research Fund/ ; }, mesh = {Humans ; Middle Aged ; *Multimorbidity ; Adult ; Male ; Female ; Serbia/epidemiology ; Aged ; Young Adult ; *Air Pollutants/analysis ; Adolescent ; Environmental Exposure/adverse effects ; Air Pollution/analysis/adverse effects ; Prevalence ; Water Quality ; Socioeconomic Factors ; }, abstract = {BACKGROUND: Substantial inequalities in the overall prevalence and patterns of multimorbidity have been widely reported, but the causal mechanisms are complex and not well understood. This study aimed to identify common patterns of multimorbidity in Serbia and assess their relationship with air pollutant concentrations and water quality indicators.

METHODS: This ecological study was conducted on a nationally representative sample of the Serbian population. Data were obtained from the European Health Interview (EHIS) Survey, a periodic study designed to assess population health using widely recognized standardized instruments. The study included 13,069 participants aged 15 and older, randomly selected through a multistage stratified sampling design. Multimorbidity was defined as having two or more self-reported diagnoses of chronic non-communicable diseases. Latent class analysis (LCA) was performed to identify clusters of multimorbidity. Concentrations of particulate matter (PM10), sulfur dioxide (SO2), nitrogen dioxide (NO2), carbon monoxide (CO), and ozone (O3), as well as water quality indicators, were obtained from the Serbian Environmental Protection Agency.

RESULTS: The overall prevalence of multimorbidity was 33.4% [32.6%-34.2%]. Six latent classes of multimorbidity were identified: Healthy, Multicondition, Cardiovascular, Metabolic syndrome, Respiratory, and Musculoskeletal. Annual increases in PM10 and SO2 concentrations, as well as daily increases in O3 concentrations, significantly raised the odds of having multimorbidity (OR = 1.02, 95% CI 1.02-1.03; OR = 1.01, 95% CI 1.00-1.02 and OR = 1.03, 95% CI 1.02-1.03, respectively). A pattern of increased risk was observed with rising levels of water contamination. Exposure to physico-chemical, microbiological and combined contamination was associated with a 3.92%, 5.17% and 5.54% higher probability, respectively, of having multiple chronic conditions. There was strong evidence that air pollutants, as well as chemical and microbial water contamination, were significantly associated with higher odds of the most common clusters of multimorbidity identified by LCA.

CONCLUSION: There is compelling evidence of an association between multimorbidity and environmental pollution, suggesting that exposure to air pollutants and water contaminants may contribute to disease accumulation and help explain geographically and socioeconomically patterned inequalities. These findings underscore the need for extensive studies that simultaneously measure both multimorbidity and pollution to explore their complex interrelationships.}, } @article {pmid39543483, year = {2024}, author = {Rzehak, T and Praeg, N and Galla, G and Seeber, J and Hauffe, HC and Illmer, P}, title = {Comparison of commonly used software pipelines for analyzing fungal metabarcoding data.}, journal = {BMC genomics}, volume = {25}, number = {1}, pages = {1085}, pmid = {39543483}, issn = {1471-2164}, mesh = {*DNA Barcoding, Taxonomic/methods ; *Fungi/genetics/classification ; *Software ; Animals ; Cattle ; Computational Biology/methods ; Feces/microbiology ; Soil Microbiology ; }, abstract = {BACKGROUND: Metabarcoding targeting the internal transcribed spacer (ITS) region is commonly used to characterize fungal communities of various environments. Given their size and complexity, raw ITS sequences are necessarily processed and quality-filtered with bioinformatic pipelines. However, such pipelines are not yet standardized, especially for fungal communities, and those available may produce contrasting results. While some pipelines cluster sequences based on a specified percentage of base pair similarity into operational taxonomic units (OTUs), others utilize denoising techniques to infer amplicon sequencing variants (ASVs). While ASVs are now considered a more accurate representation of taxonomic diversity for prokaryote communities based on 16S rRNA amplicon sequencing, the applicability of this method for fungal ITS sequences is still debated.

RESULTS: Here we compared the performance of two commonly used pipelines DADA2 (inferring ASVs) and mothur (clustering OTUs) on fungal metabarcoding sequences originating from two different environmental sample types (fresh bovine feces and pasture soil). At a 99% OTU similarity threshold, mothur consistently identified a higher fungal richness compared to DADA2. In addition, mothur generated homogenous relative abundances across multiple technical replicates (n = 18), while DADA2 results for the same replicates were highly heterogeneous.

CONCLUSIONS: Our study highlights a potential pipeline-associated bias in fungal metabarcoding data analysis of environmental samples. Based on the homogeneity of relative abundances across replicates and the capacity to detect OTUs/ASVs, we suggest using OTU clustering with a similarity of 97% as the most appropriate option for processing fungal metabarcoding data.}, } @article {pmid39541885, year = {2024}, author = {Wang, G and Li, X and Deng, J and Cao, J and Meng, H and Dong, J and Zhang, H}, title = {Assessing soil cadmium quality standards for different land use types: A global synthesis.}, journal = {Journal of hazardous materials}, volume = {480}, number = {}, pages = {136450}, doi = {10.1016/j.jhazmat.2024.136450}, pmid = {39541885}, issn = {1873-3336}, abstract = {The contamination of cadmium (Cd) in soil has become an increasingly serious issue worldwide, presenting significant risks to human health, crop safety, and ecosystems. Despite its importance, there is a lack of standardized soil threshold values for use in regulating exposure to Cd-contaminated surface soil. By synthesizing soil environmental standards for Cd from 61 countries and 75 regions, this study analyzed and categorized these standards by land use types. The distribution of Cd quality standards among various countries was determined, based on available data primarily from the United States, Canada, Europe, Australia, and China. The established soil Cd quality standards were also determined for different land types, including lands for agricultural, residential, industrial, construction, commercial uses, and parks/green spaces. Using the ecological environment criteria - species sensitivity distribution (ECC-SSD) model, Cd levels were analyzed across different land use types, and it was determined that a log-logistic distribution was the best fitted model. Our findings indicated that soil Cd quality standards ranged from 0.11 to 5.20 mg/kg for agricultural land, 1.25 to 171.51 mg/kg for residential land, and 2.58 to 1845.26 mg/kg for industrial land, all within the 5-95 % percentile range. The 5 % hazard concentration (HC5) value was recommended as the latest national quality standards for each land type. This comprehensive assessment of global soil Cd quality standards provides valuable insight for decision-makers tasked with effectively managing and mitigating Cd pollution in soil.}, } @article {pmid39539549, year = {2024}, author = {Pappa, T and Rivas, AL and Iandiorio, MJ and Hoogesteijn, AL and Fair, JM and Rojas Gil, AP and Burriel, AR and Bagos, PG and Chatzipanagiotou, S and Ioannidis, A}, title = {Personalized, disease-stage specific, rapid identification of immunosuppression in sepsis.}, journal = {Frontiers in immunology}, volume = {15}, number = {}, pages = {1430972}, pmid = {39539549}, issn = {1664-3224}, mesh = {Humans ; *Sepsis/immunology/mortality/blood/diagnosis ; Male ; Female ; Middle Aged ; Aged ; *Precision Medicine ; Leukocyte Count ; Biomarkers/blood ; Aged, 80 and over ; Adult ; Immunosuppression Therapy ; }, abstract = {INTRODUCTION: Data overlapping of different biological conditions prevents personalized medical decision-making. For example, when the neutrophil percentages of surviving septic patients overlap with those of non-survivors, no individualized assessment is possible. To ameliorate this problem, an immunological method was explored in the context of sepsis.

METHODS: Blood leukocyte counts and relative percentages as well as the serum concentration of several proteins were investigated with 4072 longitudinal samples collected from 331 hospitalized patients classified as septic (n=286), non-septic (n=43), or not assigned (n=2). Two methodological approaches were evaluated: (i) a reductionist alternative, which analyzed variables in isolation; and (ii) a non-reductionist version, which examined interactions among six (leukocyte-, bacterial-, temporal-, personalized-, population-, and outcome-related) dimensions.

RESULTS: The reductionist approach did not distinguish outcomes: the leukocyte and serum protein data of survivors and non-survivors overlapped. In contrast, the non-reductionist alternative differentiated several data groups, of which at least one was only composed of survivors (a finding observable since hospitalization day 1). Hence, the non-reductionist approach promoted personalized medical practices: every patient classified within a subset associated with 100% survival subset was likely to survive. The non-reductionist method also revealed five inflammatory or disease-related stages (provisionally named 'early inflammation, early immunocompetence, intermediary immuno-suppression, late immuno-suppression, or other'). Mortality data validated these labels: both 'suppression' subsets revealed 100% mortality, the 'immunocompetence' group exhibited 100% survival, while the remaining sets reported two-digit mortality percentages. While the 'intermediary' suppression expressed an impaired monocyte-related function, the 'late' suppression displayed renal-related dysfunctions, as indicated by high concentrations of urea and creatinine.

DISCUSSION: The data-driven differentiation of five data groups may foster early and non-overlapping biomedical decision-making, both upon admission and throughout their hospitalization. This approach could evaluate therapies, at personalized level, earlier. To ascertain repeatability and investigate the dynamics of the 'other' group, additional studies are recommended.}, } @article {pmid39537861, year = {2024}, author = {Noria, SF and Pratt, KJ and Abdel-Rasoul, M and Diaz, K and Shalash, B and Abul-Khoudoud, D and Needleman, B and Magallanes, M}, title = {The impact of social determinants of health (SDOH) on completing bariatric surgery at a single academic institution.}, journal = {Surgical endoscopy}, volume = {}, number = {}, pages = {}, pmid = {39537861}, issn = {1432-2218}, abstract = {BACKGROUND: Underutilization of bariatric surgery is multifactorial. This study aimed to understand the association of SDOH on not achieving surgery.

METHODS: 1081 applications for primary MBS from January-December 2021 were stratified into those that completed surgery (COM; n = 415), in progress > 1-year (IP; n = 107), dropped out (DO; n = 379), and never started (NS; n = 180). Using the American-Community-Survey results (2015-2020) and patient zip-codes, population differences in 4-domains of SDOH (demographic/social/housing/economic) were examined between COM versus the other groups. Additionally, using institutional MBSAQIP and EMR data, patient-specific differences in comorbidities were evaluated for COM versus IP/DO. Univariate analysis using Kruskal-Wallis, chi-squared/Fisher's exact tests were used for continuous and/or categorical variables. For patient-level analysis multinomial logistic regression was used to determine predictors of not achieving surgery. Hypothesis testing was conducted at an overall 5 percent type-I error rate (alpha = 0.05) and Bonferroni's method was used to adjust for multiple comparisons.

RESULTS: Compared to COM, IP-patients resided in zip-codes characterized by fewer married people (43% vs 46%; p = 0.019), lower education levels (49% vs 43%; p = 0.048), more households where rent was > 50% of household income (10% vs 8%, p = 0.002), and households below the poverty line (17.6% vs 14.5%, p = 0.017). At the patient-level, IP were more likely to be male (27.9% vs 14.9%; p = 0.014), publicly insured (44.9% vs 28.4%; p = 0.004), Black (35.5% vs 22.2%; p = 0.006), an active smoker (8.9% vs 2.2%; p = 0.018), have a higher BMI (49.6 vs 47.6; p = 0.01), and coronary intervention (5.8% vs 1.7%, p = 0.034). Comparison of COM vs DO was similar for both phases. Multinomial multivariable logistic regression demonstrated higher BMI (OR = 1.03,[CI]:1.01-1.05, p = 0.001), males (OR = 1.9,[CI]:1.09-3.32, p = 0.024), smoking (OR = 4.58,[CI]:1.74-12.02, p = 0.002), and Medicaid (OR = 2.16,[CI]:1.33-3.49, p = 0.002) independently predicted not achieving surgery.

CONCLUSION: Patient-level data demonstrated social not clinical factors predicted surgery completion. Given zip-codes characterizing the IP/DO groups had a greater prevalence of social risk, more attention needs to be directed patient-level social risks.}, } @article {pmid39537735, year = {2024}, author = {Ki, J and Lee, JM and Lee, W and Kim, JH and Jin, H and Jung, S and Lee, J}, title = {Dual-encoder architecture for metal artifact reduction for kV-cone-beam CT images in head and neck cancer radiotherapy.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {27907}, pmid = {39537735}, issn = {2045-2322}, support = {NRF-2020R1F1A1073430//National Research Foundation of Korea/ ; NRF-2021R1F1A1057818//National Research Foundation of Korea/ ; HI21C1161//Korea Health Industry Development Institute/ ; RS-2020-II201336//Ministry of Science and ICT, South Korea/ ; }, mesh = {*Cone-Beam Computed Tomography/methods ; Humans ; *Head and Neck Neoplasms/radiotherapy/diagnostic imaging ; *Artifacts ; *Metals/chemistry ; Deep Learning ; Image Processing, Computer-Assisted/methods ; Radiotherapy Planning, Computer-Assisted/methods ; Radiotherapy Dosage ; Phantoms, Imaging ; }, abstract = {During a radiotherapy (RT) course, geometrical variations of target volumes, organs at risk, weight changes (loss/gain), tumor regression and/or progression can significantly affect the treatment outcome. Adaptive RT has become the effective methods along with technical advancements in imaging modalities including cone-beam computed tomography (CBCT). Planning CT (pCT) can be modified via deformable image registration (DIR), which is applied to the pair of pCT and CBCT. However, the artifact existed in both pCT and CBCT is a vulnerable factor in DIR. The dose calculation on CBCT is also suggested. Missing information due to the artifacts hinders the accurate dose calculation on CBCT. In this study, we aim to develop a deep learning-based metal artifact reduction (MAR) model to reduce the metal artifacts in CBCT for head and neck cancer RT. To train the proposed MAR model, we synthesized the kV-CBCT images including metallic implants, with and without metal artifacts (simulated image data pairs) through sinogram image handling process. We propose the deep learning architecture which focuses on both artifact removal and reconstruction of anatomic structure using a dual-encoder architecture. We designed four single-encoder models and three dual-encoder models based on UNet (for an artifact removal) and FusionNet (for a tissue restoration). Each single-encoder model contains either UNet or FusionNet, while the dual-encoder models have both UNet and FusionNet architectures. In the dual-encoder models, we implemented different feature fusion methods, including simple addition, spatial attention, and spatial/channel wise attention. Among the models, a dual-encoder model with spatial/channel wise attention showed the highest scores in terms of peak signal-to-noise ratio, mean squared error, structural similarity index, and Pearson correlation coefficient. CBCT images from 34 head and neck cancer patients were used to test the developed models. The dual-encoder model with spatial/channel wise attention showed the best results in terms of artifact index. By using the proposed model to CBCT, one can achieve more accurate synthetic pCT for head and neck patients as well as better tissue recognition and structure delineation for CBCT image itself.}, } @article {pmid39537340, year = {2024}, author = {Di Battista, V and Danielsen, PH and Gajewicz-Skretna, A and Kedziorski, A and Seiffert, SB and Ma-Hock, L and Berthing, T and Mortensen, A and Sundermann, A and Skjolding, LM and Vogel, U and Baun, A and Wohlleben, W}, title = {Oxide-Perovskites for Automotive Catalysts Biotransform and Induce Multicomponent Clearance and Hazard.}, journal = {ACS nano}, volume = {18}, number = {47}, pages = {32672-32693}, pmid = {39537340}, issn = {1936-086X}, mesh = {*Oxides/chemistry ; Animals ; Catalysis ; *Lanthanum/chemistry ; Rats ; Mice ; Calcium Compounds/chemistry ; Titanium/chemistry ; Automobiles ; Male ; Biotransformation ; Surface Properties ; Lung/metabolism/drug effects ; }, abstract = {Oxide-perovskites designed for automotive catalysts contain multiple metal elements whose presence is crucial to achieving the targeted performance. They are highly stable in exhaust operating conditions; however, little is known about their stability under physiological conditions. As some of the metallic components are hazardous to humans and the environment, perovskite benefits in cleaner air must be balanced with risks in a Safe and Sustainable Design (SSbD) approach. New approach methodologies (NAMs), including in chemico and in silico methods, were used for testing hazards and benefits, including catalytic activity and tolerance for temporary excess of oxygen under dynamic driving conditions. The composition and surface properties of six different lanthanum-based oxide-perovskites compromised their stability under lung physiological conditions, influencing the oxidative damage of the particles and the bioacessibility of leaching metals. We found consistent biotransformation of the oxide-perovskite materials at pH 4.5. The leached lanthanum ions, but not other metals, respeciated into lanthanum phosphate nanoparticles, which increased the overall oxidative damage in additive synergy. The NAM results in the presented SSbD approach were challenged by in vivo studies in rats and mice, which confirmed multicomponent clearance from lungs into urine and supported the comparative ranking of effects against well-characterized spinel materials. Among the perovskites, the version with reduced nickel content and doped with palladium offered the best SSbD balance, despite not improving the conventional benchmark catalytic performance and related sustainability benefits. Redesign by industry may be necessary to better fulfill all SSbD dimensions.}, } @article {pmid39536186, year = {2024}, author = {Corrêa-do-Nascimento, GS and Galvão, C and Leite, GR}, title = {Investigating the distribution of a rare Colombo-Venezuelan kissing bug, Rhodnius neivai, Lent, 1953, using geographical information system-based analyses.}, journal = {Memorias do Instituto Oswaldo Cruz}, volume = {119}, number = {}, pages = {e240106}, pmid = {39536186}, issn = {1678-8060}, mesh = {Animals ; *Rhodnius ; *Geographic Information Systems ; Colombia ; *Insect Vectors/classification ; *Animal Distribution ; Venezuela ; Chagas Disease/transmission ; Ecosystem ; }, abstract = {BACKGROUND: Rhodnius neivai, a kissing bug found in the dry regions of Colombia and Venezuela, has limited documented occurrences. While it is not deemed a significant vector for Chagas disease, distributional and ecological studies are essential in monitoring species domiciliation and shedding light on the evolutionary aspects of the Rhodniini tribe.

OBJECTIVES: The study aims to provide a detailed revision of R. neivai distribution and evaluate general spatial data quality for ecological niche modelling (ENM). It will also provide the first published ENM for the species, which may aid species sampling and future analytical improvement.

METHODS: Registers and other spatial information were gathered by literature review; data georeferencing, preliminary geographical investigations, and model editing were conducted in GIS platforms; ENMs were built using R and explored the uncertainty of parameters and algorithms.

FINDINGS: Twenty four unique sites were identified, unearthing 17 previously uncovered records. Data lacks robust spatial and temporal precision; however, ENMs had acceptable validations. The models present some variation in suitability but with objective areas for sampling effort.

MAIN CONCLUSIONS: Rhodnius neivai distribution is better explained by conditions that characterise dry ecotypes, but further sampling is essential to improve modelling and advance with ecological and evolutive matters.}, } @article {pmid39536049, year = {2024}, author = {Zhao, Y and Cordero, OX and Tikhonov, M}, title = {Linear-regression-based algorithms can succeed at identifying microbial functional groups despite the nonlinearity of ecological function.}, journal = {PLoS computational biology}, volume = {20}, number = {11}, pages = {e1012590}, pmid = {39536049}, issn = {1553-7358}, mesh = {*Algorithms ; Linear Models ; *Ecosystem ; *Computational Biology/methods ; Models, Biological ; Microbiota/physiology ; Nonlinear Dynamics ; }, abstract = {Microbial communities play key roles across diverse environments. Predicting their function and dynamics is a key goal of microbial ecology, but detailed microscopic descriptions of these systems can be prohibitively complex. One approach to deal with this complexity is to resort to coarser representations. Several approaches have sought to identify useful groupings of microbial species in a data-driven way. Of these, recent work has claimed some empirical success at de novo discovery of coarse representations predictive of a given function using methods as simple as a linear regression, against multiple groups of species or even a single such group (the ensemble quotient optimization (EQO) approach). Modeling community function as a linear combination of individual species' contributions appears simplistic. However, the task of identifying a predictive coarsening of an ecosystem is distinct from the task of predicting the function well, and it is conceivable that the former could be accomplished by a simpler methodology than the latter. Here, we use the resource competition framework to design a model where the "correct" grouping to be discovered is well-defined, and use synthetic data to evaluate and compare three regression-based methods, namely, two proposed previously and one we introduce. We find that regression-based methods can recover the groupings even when the function is manifestly nonlinear; that multi-group methods offer an advantage over a single-group EQO; and crucially, that simpler (linear) methods can outperform more complex ones.}, } @article {pmid39530726, year = {2024}, author = {Toledo, MJL and Zawadzki, MJ and Scott, SB and Johnson, JA and Marcusson-Clavertz, D and Kim, J and Lanza, S and Almeida, DM and Sliwinski, MJ and Smyth, JM}, title = {Exploring the Utility of a Real-Time Approach to Characterising Within-Person Fluctuations in Everyday Stress Responses.}, journal = {Stress and health : journal of the International Society for the Investigation of Stress}, volume = {40}, number = {6}, pages = {e3501}, pmid = {39530726}, issn = {1532-2998}, support = {/NH/NIH HHS/United States ; /NH/NIH HHS/United States ; }, mesh = {Humans ; Female ; Male ; *Stress, Psychological/psychology ; Adult ; *Ecological Momentary Assessment ; Middle Aged ; Aged ; }, abstract = {Few studies have measured components of stress responses in real time-an essential step in designing just-in-time interventions targeting moments of risk. Using ecological momentary assessment (EMA), we characterised stress response components to everyday stressors, including reactivity (the response following a stressor), recovery (the return towards baseline), and pile-up (the accumulation of stressors) (RRPs) by quantifying the dynamics of response indicators (i.e., subjective stress, negative affect, and perseverative cognition). To determine the utility of these novel measures in capturing and characterising acute moments of the stress response, this study evaluated the proportion of variance in RRPs attributed to (1) between-person, (2) between-days, and (3) within-day (momentary) levels. Healthy adults (n = 123; aged 35-65, 79% women, 91% non-Hispanic White) participated in a 14-day study assessing stress response via EMA 6 times a day. RRPs were constructed from 10,065 EMA reports. Multilevel models with moments nested within days nested within persons were used to partition variance in the RRPs. Reactivity and recovery indicators captured the most variation within-days (i.e., across moments; range 76%-80% and 87%-89%, respectively), with small amounts of variance between-person. For pile-up, variation was mostly observed between-days (range 60%-63%) and between-persons (range 27%-31%). In contrast, raw measures of stress response reflected substantial between-person (range 32%-54%) and within-day (range 34%-53%) variance. These results demonstrated that a person-specific approach to measuring stress response components (i.e., RRPs) can capture the dynamic within-person variation in stress response, as it occurs in real time, making it well-suited for use in novel just-in-time interventions targeting moments of risk.}, } @article {pmid39526854, year = {2024}, author = {Tan, X and Xue, F and Zhang, C and Wang, T}, title = {mbDriver: identifying driver microbes in microbial communities based on time-series microbiome data.}, journal = {Briefings in bioinformatics}, volume = {25}, number = {6}, pages = {}, pmid = {39526854}, issn = {1477-4054}, support = {12331009//National Natural Science Foundation of China/ ; }, mesh = {Humans ; *Microbiota ; Computational Biology/methods ; Algorithms ; Gastrointestinal Microbiome ; }, abstract = {Alterations in human microbial communities are intricately linked to the onset and progression of diseases. Identifying the key microbes driving these community changes is crucial, as they may serve as valuable biomarkers for disease prevention, diagnosis, and treatment. However, there remains a need for further research to develop effective methods for addressing this critical task. This is primarily because defining the driver microbe requires consideration not only of each microbe's individual contributions but also their interactions. This paper introduces a novel framework, called mbDriver, for identifying driver microbes based on microbiome abundance data collected at discrete time points. mbDriver comprises three main components: (i) data preprocessing of time-series abundance data using smoothing splines based on the negative binomial distribution, (ii) parameter estimation for the generalized Lotka-Volterra (gLV) model using regularized least squares, and (iii) quantification of each microbe's contribution to the community's steady state by manipulating the causal graph implied by gLV equations. The performance of nonparametric spline-based denoising and regularized least squares estimation is comprehensively evaluated on simulated datasets, demonstrating superiority over existing methods. Furthermore, the practical applicability and effectiveness of mbDriver are showcased using a dietary fiber intervention dataset and an ulcerative colitis dataset. Notably, driver microbes identified in the dietary fiber intervention dataset exhibit significant effects on the abundances of short-chain fatty acids, while those identified in the ulcerative colitis dataset show a significant correlation with metabolism-related pathways.}, } @article {pmid39526196, year = {2024}, author = {Boyes, D and Crowley, LM and Boyes, C and , and , and , and , and , and , and , }, title = {The genome sequence of the Pale November moth, Epirrita christyi (Allen, 1906).}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {540}, pmid = {39526196}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual female Pale November moth, Epirrita christyi (Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence has a total length of 474.20 megabases. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.99 kilobases in length. Gene annotation of this assembly on Ensembl identified 16,983 protein-coding genes.}, } @article {pmid39521320, year = {2024}, author = {Coelho, LA and Gonzalez, CLR and Tammurello, C and Campus, C and Gori, M}, title = {Hand and foot overestimation in visually impaired human adults.}, journal = {Neuroscience}, volume = {563}, number = {}, pages = {74-83}, doi = {10.1016/j.neuroscience.2024.10.055}, pmid = {39521320}, issn = {1873-7544}, mesh = {Humans ; Female ; Male ; Adult ; *Hand ; *Foot ; Middle Aged ; *Blindness/physiopathology/psychology ; Visually Impaired Persons/psychology ; Body Image/psychology ; Young Adult ; Sex Characteristics ; }, abstract = {Previous research has shown that visual impairment results in reduced audio, tactile and proprioceptive ability. One hypothesis is that these issues arise from inaccurate body representations. Few studies have investigated metric body representations in a visually impaired population. We designed an ecologically valid behavioural task in which visually impaired adults haptically explored various sized gloves or shoes. They were asked to indicate if they perceived each clothing item as bigger than the size of their hand or foot. In the post-hoc analyses we fit psychometric curves to the data to extract the point of subjective equality. We then compared the results to age/sex matched controls. We hypothesized the blind participants body representations should be more distorted. Because previous research has shown that females are more likely to overestimate body size, we predicted sex differences in the sighted participants. However, because blind adults have no exposure to visual ideals of body size, we predicted that there would be no sex differences. Our results showed thatblind participants overestimated their hands and feetto a similar degree. Sighted controls overestimated their hands significantly more than their feet. Taken together, our results partially support our hypothesis and suggest that visual deprivation, even for short periods result in hand size overestimation.}, } @article {pmid39520764, year = {2025}, author = {Rodriguez-Caturla, MY and Margalho, LP and Graça, JS and Pia, AKR and Xavier, VL and Noronha, MF and Cabral, L and Lemos-Junior, WJF and Castillo, CJC and SantˈAna, AS}, title = {Bacterial dynamics and volatile metabolome changes of vacuum-packaged beef with different pH during chilled storage.}, journal = {International journal of food microbiology}, volume = {427}, number = {}, pages = {110955}, doi = {10.1016/j.ijfoodmicro.2024.110955}, pmid = {39520764}, issn = {1879-3460}, mesh = {*Volatile Organic Compounds/analysis/metabolism ; Hydrogen-Ion Concentration ; Vacuum ; Cattle ; Animals ; *Red Meat/microbiology ; *Food Packaging/methods ; *Food Microbiology ; *Food Storage ; Bacteria/metabolism/growth & development/classification/genetics/isolation & purification ; Metabolome ; Brazil ; RNA, Ribosomal, 16S/genetics ; }, abstract = {This study aimed to assess the growth of spoilage bacteria in Brazilian vacuum-packed beef across different pH ranges (5.4-5.8, 5.8-6.1, ≥6.1) stored at temperatures of 0 °C, 4 °C, and 7 °C. Additionally, the research sought to identify predominant spoilage bacteria at the genus level using 16S rDNA gene sequencing and analyze the principal volatile organic compounds (VOCs) produced by this microbiota through HS-SPME/GC-MS. Lactic acid bacteria (LAB) consistently exhibited counts exceeding 6.0 Log CFU/g, regardless of temperature and pH conditions. The bacterial diversity in the meat samples reflected the influence of slaughterhouse environments, with Pseudomonas and Serratia remaining dominant across different cuts and pH levels. Post-storage, variations in pH and temperature modulated the initial bacterial diversity, leading to a reduction in diversity and an increase in LAB such as Lactobacillus, Lactococcus, Leuconostoc, and Carnobacterium. Notably, these changes were observed within pH ranges of 5.4-5.8 and 5.8-6.1, irrespective of beef cuts and storage temperatures. Based on high throughput sequencing and VOCS, correlation analysis revealed a relationship between the growth of specific spoilage microorganisms under vacuum conditions and the presence of VOCs such as alcohols (e.g., 1-propanol, 2-methyl-) and ketones (e.g., 2-nonanone, 2-octanone, 2-heptanone), identifying them as potential indicators of spoilage bacteria growth.}, } @article {pmid39516498, year = {2024}, author = {Weistuch, C and Murgas, KA and Zhu, J and Norton, L and Dill, KA and Tannenbaum, AR and Deasy, JO}, title = {Normal tissue transcriptional signatures for tumor-type-agnostic phenotype prediction.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {27230}, pmid = {39516498}, issn = {2045-2322}, support = {BCRF-17-193//Breast Cancer Research Foundation/ ; W911NF2210292//Army Research Office/ ; FA9550-20-1-0029//Air Force Office of Scientific Research/ ; R01-AG048769/GF/NIH HHS/United States ; R01 AG048769/AG/NIA NIH HHS/United States ; }, mesh = {Humans ; *Transcriptome ; *Phenotype ; *Gene Expression Regulation, Neoplastic ; Female ; Neoplasms/genetics/pathology/metabolism ; Gene Expression Profiling ; Breast Neoplasms/genetics/pathology/metabolism ; }, abstract = {Cancer transcriptional patterns reflect both unique features and shared hallmarks across diverse cancer types, but whether differences in these patterns are sufficient to characterize the full breadth of tumor phenotype heterogeneity remains an open question. We hypothesized that these shared transcriptomic signatures reflect repurposed versions of functional tasks performed by normal tissues. Starting with normal tissue transcriptomic profiles, we use non-negative matrix factorization to derive six distinct transcriptomic phenotypes, called archetypes, which combine to describe both normal tissue patterns and variations across a broad spectrum of malignancies. We show that differential enrichment of these signatures correlates with key tumor characteristics, including overall patient survival and drug sensitivity, independent of clinically actionable DNA alterations. Additionally, we show that in HR+/HER2- breast cancers, metastatic tumors adopt transcriptomic signatures consistent with the invaded tissue. Broadly, our findings suggest that cancer often arrogates normal tissue transcriptomic characteristics as a component of both malignant progression and drug response. This quantitative framework provides a strategy for connecting the diversity of cancer phenotypes and could potentially help manage individual patients.}, } @article {pmid39512488, year = {2024}, author = {Lewis, JH and Kojima, H and Suenaga, M and Petsopoulos, D and Fujisawa, Y and Truong, XL and Warren, DL}, title = {The era of cybertaxonomy: X-ray microtomography reveals cryptic diversity and concealed cuticular sculpture in Aphanerostethus Voss, 1957 (Coleoptera, Curculionidae).}, journal = {ZooKeys}, volume = {1217}, number = {}, pages = {1-45}, pmid = {39512488}, issn = {1313-2989}, abstract = {Weevils represent one of the most speciose and economically important animal clades, but remain poorly studied across much of the Oriental Region. Here, an integrative revision of the Oriental, flightless genus Aphanerostethus Voss, 1957 (Curculionidae: Molytinae) based on X-ray microtomography, multi-gene DNA barcoding (CO1, Cytb, 16S), and traditional morphological techniques (light microscopy, dissections) is presented. Twelve new species, namely, A.armatus Lewis & Kojima, sp. nov., A.bifidus Kojima & Lewis, sp. nov., A.darlingi Lewis, sp. nov., A.decoratus Lewis & Kojima, sp. nov., A.falcatus Kojima, Lewis & Fujisawa, sp. nov., A.incurvatus Kojima & Lewis, sp. nov., A.japonicus Lewis & Kojima, sp. nov., A.magnus Lewis & Kojima, sp. nov., A.morimotoi Kojima & Lewis, sp. nov., A.nudus Lewis & Kojima, sp. nov., A.spinosus Lewis & Kojima, sp. nov., and A.taiwanus Lewis, Fujisawa & Kojima, sp. nov. are described from Japan, Taiwan, Vietnam, and Malaysia. A neotype is designated for A.vannideki Voss, 1957. The hitherto monotypic genus Darumazo Morimoto & Miyakawa, 1985, syn. nov. is synonymized under Aphanerostethus based on new morphological data and Aphanerostethusdistinctus (Morimoto & Miyakawa, 1985), comb. nov. is transferred accordingly. X-ray microtomography is successfully used to explore for stable interspecific differences in cuticular, internal and micro morphology. Remarkable species-specific sexual dimorphism in the metatibial uncus is described in seven of the newly described Aphanerostethus species and the evolution of this character is discussed.}, } @article {pmid39511491, year = {2024}, author = {Tang, Y and Tian, C and Yao, D and Yang, S and Shi, L and Yi, L and Peng, Q}, title = {Community assembly and potential function analysis of the endophyte in Eucommia ulmoides.}, journal = {BMC microbiology}, volume = {24}, number = {1}, pages = {460}, pmid = {39511491}, issn = {1471-2180}, mesh = {*Endophytes/genetics/metabolism/classification/physiology/isolation & purification ; *Eucommiaceae/microbiology ; *Ascomycota/genetics/growth & development/physiology ; *Bacteria/classification/genetics/metabolism/isolation & purification ; High-Throughput Nucleotide Sequencing ; Iridoid Glucosides/metabolism ; Basidiomycota/genetics/physiology ; Symbiosis ; Fungi/classification/genetics/isolation & purification/metabolism/physiology ; Computational Biology ; }, abstract = {Endophytes play a pivotal role in protecting host plants from both biotic and abiotic stresses, promoting the production of active components (AC) and plant growth. However, the succession of the endophyte community in Eucommia ulmoides (E. ulmoides), particularly the community assembly and function, has not been extensively investigated. In this study, we employed high-throughput sequencing and bioinformatics tools to analyze endophyte diversity across different tree ages, parts, and periods. We examined the population differences, correlations, community assembly mechanisms, and functional roles of these endophytes. Functional predictions via PICRUSt2 revealed that most endophytic fungal functions were linked to biosynthesis, with significant differences in biosynthetic functional abundance across parts and periods. In contrast, the metabolic activity of endophytic bacteria remained stable across different periods and parts. Correlation analysis further confirmed a strong positive relationship between ACs and certain endophytic fungi. Among them, the fungal phyla Ascomycota and Basidiomycota were identified as key contributors to the metabolism of chlorogenic acid (CA), while Aucubin was significantly positively correlated with several endophytic bacteria. These findings provide valuable insights into the functional roles and community assembly mechanism of E. ulmoides endophytes, as well as their symbiotic relationships.}, } @article {pmid39507254, year = {2024}, author = {Flores, M and Ho, E and Ly, C and Ceberio, N and Guardado, M and Felix, K and Thorner, HM and Paunovich, M and Godek, C and Kalaydjian, C and Rohlfs, RV}, title = {Decreased accuracy of forensic DNA mixture analysis for groups with lower genetic diversity.}, journal = {iScience}, volume = {27}, number = {11}, pages = {111067}, pmid = {39507254}, issn = {2589-0042}, support = {T32 GM148332/GM/NIGMS NIH HHS/United States ; }, abstract = {Forensic investigation of DNA samples from multiple contributors has become commonplace. These complex analyses use statistical frameworks accounting for multiple levels of uncertainty in allelic contributions from different individuals, particularly for samples containing few molecules of DNA. These methods have been thoroughly tested along some axes of variation, but less attention has been paid to accuracy across human genetic variation. Here, we quantify the accuracy of DNA mixture analysis over 83 human groups. We find higher false inclusion rates for mixtures with more contributors and for groups with lower genetic diversity. Even for three-contributor mixtures where two contributors are known and the reference group is correctly specified, false inclusion rates are 1e-5 or higher for 36 out of 83 groups. This means that, depending on multiple testing, some false inclusions may be expected. These false positives could be lessened with more selective and conservative use of DNA mixture analysis.}, } @article {pmid39503522, year = {2024}, author = {Campelo, F and de Oliveira, ALG and Reis-Cunha, J and Fraga, VG and Bastos, PH and Ashford, J and Ekárt, A and Adelino, TER and Silva, MVF and de Melo Iani, FC and de Jesus, ACP and Bartholomeu, DC and de Souza Trindade, G and Fujiwara, RT and Bueno, LL and Lobo, FP}, title = {Phylogeny-aware linear B-cell epitope predictor detects targets associated with immune response to orthopoxviruses.}, journal = {Briefings in bioinformatics}, volume = {25}, number = {6}, pages = {}, pmid = {39503522}, issn = {1477-4054}, support = {BIP-00123-23//FAPEMIG/ ; INCT-406441/2022-7//Brazilian National Institutes of Science and Technology/ ; RED-00067-23//Rede Mineira de Imunobiológicos/ ; APQ-4035/17//State of Minas Gerais Research Support Foundation/ ; 310311/2023-3//National Council for Scientific and Technological Development/ ; 405249/2022-5//MCTI/Brazil/ ; MR/T016019/1//UK Medical Research Council/ ; //EPSRC/UK/ ; }, mesh = {*Phylogeny ; Humans ; *Epitopes, B-Lymphocyte/immunology ; Orthopoxvirus/immunology/genetics ; Computational Biology/methods ; Vaccinia virus/immunology/genetics ; Mpox (monkeypox) ; }, abstract = {We introduce a phylogeny-aware framework for predicting linear B-cell epitope (LBCE)-containing regions within proteins. Our approach leverages evolutionary information by using a taxonomic scaffold to build models trained on hierarchically structured data. The resulting models present performance equivalent or superior to generalist methods, despite using simpler features and a fraction of the data volume required by current state-of-the-art predictors. This allows the utilization of available data for major pathogen lineages to facilitate the prediction of LBCEs for emerging infectious agents. We demonstrate the efficacy of our approach by predicting new LBCEs in the monkeypox (MPXV) and vaccinia viruses. Experimental validation of selected targets using sera from infected patients confirms the presence of LBCEs, including candidates for the differential serodiagnosis of recent MPXV infections. These results point to the use of phylogeny-aware predictors as a useful strategy to facilitate the targeted development of immunodiagnostic tools.}, } @article {pmid39501271, year = {2024}, author = {Sijm-Eeken, M and Ossebaard, HC and Čaluković, A and Temme, B and Peute, LW and Jaspers, MW}, title = {Linking theory and practice to advance sustainable healthcare: the development of maturity model version 1.0.}, journal = {BMC health services research}, volume = {24}, number = {1}, pages = {1350}, pmid = {39501271}, issn = {1472-6963}, mesh = {Humans ; *Delivery of Health Care/organization & administration ; Climate Change ; Sustainable Development ; Conservation of Natural Resources/methods ; Models, Theoretical ; Models, Organizational ; }, abstract = {BACKGROUND: Climate change and increased awareness of planetary health have made reducing ecological footprints a priority for healthcare organizations. However, improving healthcare's environmental impact remains difficult. Numerous researchers argue these difficulties are caused by healthcare's environmental impact being multidimensional, influenced throughout the healthcare chain, and often has downstream consequences that are hard to identify or to measure. Even though existing research describes many successful approaches to reduce healthcare's environmental impact, a robust multidimensional framework to assess this impact is lacking. This research aims at developing a maturity model for sustainable healthcare that could be used for self-assessment by healthcare professionals to identify improvement actions and for sharing best practices in environmental sustainability.

METHODS: A design-oriented approach for maturity model development was combined with an expert panel and six case studies to develop, refine and expand the maturity model for environmentally sustainable healthcare.

RESULTS: A maturity model was developed containing four domains: 'Governance', 'Organization Structures', 'Processes', and 'Outcomes and Control'. Applying the model in real-world environments demonstrated the model's understandability, ease of use, usefulness, practicality and ability to identify improvement actions for environmental sustainability in healthcare organizations.

CONCLUSIONS: This study found that healthcare practitioners could apply the maturity model developed and tested in this study in several hours without training to help them gain valuable insights into the environment footprint of the healthcare setting they worked in. Systematically implementing the model developed in this study could help address the urgent need to mitigate the substantial environmental impact of healthcare. These implementations can help evaluate and improve the maturity model.}, } @article {pmid39497067, year = {2024}, author = {Moeller, AH and Dillard, BA and Goldman, SL and Real, MVF and Sprockett, DD}, title = {Removal of sequencing adapter contamination improves microbial genome databases.}, journal = {BMC genomics}, volume = {25}, number = {1}, pages = {1033}, pmid = {39497067}, issn = {1471-2164}, mesh = {Animals ; *Databases, Genetic ; DNA Contamination ; Genome, Microbial ; Humans ; Sequence Analysis, DNA/methods ; High-Throughput Nucleotide Sequencing/methods ; Cattle ; Mice ; Swine ; }, abstract = {Advances in assembling microbial genomes have led to growth of reference genome databases, which have been transformative for applied and basic microbiome research. Here we show that published microbial genome databases from humans, mice, cows, pigs, fish, honeybees, and marine environments contain significant sequencing-adapter contamination that systematically reduces assembly accuracy and contiguousness. By removing the adapter-contaminated ends of contiguous sequences and reassembling MGnify reference genomes, we improve the quality of assemblies in these databases.}, } @article {pmid39494195, year = {2024}, author = {Boyes, D and Boyes, C and , and , and , and , and , and , and , }, title = {The genome sequence of the Case-bearing Clothes moth, Tinea pellionella (Linnaeus, 1758).}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {119}, pmid = {39494195}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual female Tinea pellionella (the Case-bearing Clothes moth; Arthropoda; Insecta; Lepidoptera; Tineidae). The genome sequence is 245.3 megabases in span. Most of the assembly is scaffolded into 30 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 25.86 kilobases in length. Gene annotation of this assembly on Ensembl identified 13,811 protein coding genes.}, } @article {pmid39493766, year = {2024}, author = {Chakraborty, H and Chakraborty, HJ and Das, BK and Maity, J}, title = {Age-specific changes in the serum proteome of female anadromous, hilsa Tenualosa ilisha: a comparative analysis across developmental stages.}, journal = {Frontiers in immunology}, volume = {15}, number = {}, pages = {1448627}, pmid = {39493766}, issn = {1664-3224}, mesh = {Female ; *Proteome ; Animals ; Proteomics/methods ; Tandem Mass Spectrometry ; Protein Interaction Maps ; Computational Biology/methods ; Age Factors ; Chromatography, Liquid ; Blood Proteins/metabolism ; Fishes/genetics/blood ; Aging/blood/immunology ; }, abstract = {INTRODUCTION: The proteome profile of the female Tenualosa ilisha (Hamilton, 1822), a species of great ecological and economic importance, across various age groups was investigated to comprehend the functional dynamics of the serum proteome for conservation and aquaculture, as well as sustain the population.

METHODS: Advanced liquid chromatography-tandem mass spectrometry LC-MS/MS-based proteomic data were analysed and submitted to the ProteomeXchange Consortium via PRIDE (PRoteomics IDEntifications database). Bioinformatics analysis of serum proteome have been done and it showed different proteins associated with GO Gene Ontology () terms, and the genes associated with enriched KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways (such as phagosome, mTOR, Apelin signalling pathways, herpes simplex virus) implicated in immune responses.

RESULTS: The expression levels of important immunological proteins, such as those involved in cellular defence and inflammatory responses, were significantly different age-dependently. In this study, we annotated 952, 494, 415, and 282 proteins in year classes IV, III, II, and I Hilsa, respectively, and analysed their Protein-Protein Interaction (PPI) networks based on their functional characteristics. From year classes I to IV, new proteins appeared and were more than three-fold. Notably, class I hilsa displayed a lower abundance of proteins than class IV hilsa.

DISCUSSION: This is the first study, to the best of our knowledge, to report the analysis of the serum proteome of hilsa at different developmental stages, and the results can help improve the understanding of the mechanisms underlying the different changes in protein enrichment during migration in hilsa. This analysis also offers crucial insights into the immune system for hilsa conservation and management.}, } @article {pmid39493638, year = {2024}, author = {Reuken, PA and Besteher, B and Bleidorn, J and Brockmann, D and Finke, K and Freytag, A and Lehmann-Pohl, K and Lemhöfer, C and Mikolajczyk, R and Puta, C and Scherag, A and Wiedermann, M and Zippel-Schultz, B and Stallmach, A}, title = {Web-based telemedicine approach for treatment of post-COVID-19 in Thuringia (WATCH).}, journal = {Digital health}, volume = {10}, number = {}, pages = {20552076241291748}, pmid = {39493638}, issn = {2055-2076}, abstract = {OBJECTIVE: After infection with SARS-CoV-2, a substantial proportion of patients develop long-lasting sequelae. These sequelae include fatigue (potentially as severe as that seen in ME/CFS cases), cognitive dysfunction, and psychiatric symptoms. Because the pathophysiology of these sequelae remains unclear, existing therapeutic concepts address the symptoms through pacing strategies, cognitive training, and psychological therapy.

METHODS: Here, we present a protocol for a digital multimodal structured intervention addressing common symptoms through three intervention modules: BRAIN, BODY, and SOUL. This intervention includes an assessment conducted via a mobile "post-COVID-19 bus" near the patient's home, as well as the use of wearable devices and mobile applications to support pacing strategies and collection of data, including ecological momentary assessment.

RESULTS: We will focus on physical component subscore of the SF36 as Quality of Life parameter as the primary outcome parameter for WATCH to take into account the holistic approach that is necessary for care of post-COVID patients.

CONCLUSION: In the current project, we present a protocol for a holistic and multimodal structured therapeutic concept which is easily accessible, and scalable for post-COVID patients.}, } @article {pmid39488960, year = {2024}, author = {Tayyab, M and Hussain, M and Zhang, J and Ullah, S and Tong, Z and Rahman, ZU and Al-Aizari, AR and Al-Shaibah, B}, title = {Leveraging GIS-based AHP, remote sensing, and machine learning for susceptibility assessment of different flood types in peshawar, Pakistan.}, journal = {Journal of environmental management}, volume = {371}, number = {}, pages = {123094}, doi = {10.1016/j.jenvman.2024.123094}, pmid = {39488960}, issn = {1095-8630}, mesh = {*Floods ; Pakistan ; *Machine Learning ; *Geographic Information Systems ; Algorithms ; Remote Sensing Technology ; }, abstract = {Due to its diverse topography, Pakistan faces different types of floods each year, which cause substantial physical, environmental, and socioeconomic damage. However, the susceptibility of specific regions to different flood types remains unexplored. To the best of our knowledge for the first time, this study employed an integrated approach by leveraging a GIS-based Analytical Hierarchy Process (AHP), remote sensing, and machine learning (ML) algorithms, to assess susceptibility to three different types of flooding in Peshawar, Pakistan. The study first evaluated the degree of susceptibility to riverine, urban, and flash floods using the GIS-based AHP technique, and then employed ML models, (i.e., specifically Random Forest [RF] and Extreme Gradient Boosting [XG-Boost] to analyze multi-type flood susceptibility in the study region. The performance of the ML models was also evaluated, and the XG-Boost model outperforms RF, demonstrating a higher correlation coefficient (R[2] = 0.561-0.922) and lower mean absolute error (MAE = 0.042-0.354), and root-mean-square error (RMSE = 0.119-0.415) for both training and testing datasets. The superior performance of the XG-Boost was further confirmed by the higher value of the area under the curve (AUC) values, which is relatively higher (0.87) than that of the AHP (0.70) and RF (0.86) models. Based on the relative best performance, the XG-Boost model was chosen for further susceptibility assessment of different types of floods, and the generated flood susceptibility maps revealed that 20.9% of the total area is susceptible to riverine flooding, while 30.27% and 48.68% of the total area is susceptible to urban and flash flooding, respectively. The study's findings are significant, offering valuable insights for relevant stakeholders in guiding future flood risk management and sustainable land use plans in the study area.}, } @article {pmid39480949, year = {2024}, author = {Goldshtein, A and Chen, X and Amichai, E and Boonman, A and Harten, L and Yinon, O and Orchan, Y and Nathan, R and Toledo, S and Couzin, ID and Yovel, Y}, title = {Acoustic cognitive map-based navigation in echolocating bats.}, journal = {Science (New York, N.Y.)}, volume = {386}, number = {6721}, pages = {561-567}, doi = {10.1126/science.adn6269}, pmid = {39480949}, issn = {1095-9203}, mesh = {Animals ; Acoustics ; *Chiroptera/physiology ; *Cognition ; *Echolocation ; Geographic Information Systems ; Homing Behavior ; *Spatial Navigation ; }, abstract = {Bats are known for their ability to use echolocation for obstacle avoidance and orientation. However, the extent to which bats utilize their highly local and directional echolocation for kilometer-scale navigation is unknown. In this study, we translocated wild Kuhl's pipistrelle bats and tracked their homing abilities while manipulating their visual, magnetic, and olfactory sensing and accurately tracked them using a new reverse GPS system. We show that bats can identify their location after translocation and conduct several-kilometer map-based navigation using solely echolocation. This proposition was further supported by a large-scale echolocation model disclosing how bats use environmental acoustic information to perform acoustic cognitive map-based navigation. We also demonstrate that navigation is improved when using both echolocation and vision.}, } @article {pmid39480880, year = {2024}, author = {Silva, GAA and Harder, AM and Kirksey, KB and Mathur, S and Willoughby, JR}, title = {Detectability of runs of homozygosity is influenced by analysis parameters and population-specific demographic history.}, journal = {PLoS computational biology}, volume = {20}, number = {10}, pages = {e1012566}, pmid = {39480880}, issn = {1553-7358}, mesh = {*Homozygote ; *Genetics, Population/methods ; *Inbreeding ; Animals ; Models, Genetic ; Computational Biology/methods ; Humans ; Computer Simulation ; Polymorphism, Single Nucleotide/genetics ; }, abstract = {Wild populations are increasingly threatened by human-mediated climate change and land use changes. As populations decline, the probability of inbreeding increases, along with the potential for negative effects on individual fitness. Detecting and characterizing runs of homozygosity (ROHs) is a popular strategy for assessing the extent of individual inbreeding present in a population and can also shed light on the genetic mechanisms contributing to inbreeding depression. Here, we analyze simulated and empirical datasets to demonstrate the downstream effects of program selection and long-term demographic history on ROH inference, leading to context-dependent biases in the results. Through a sensitivity analysis we evaluate how various parameter values impact ROH-calling results, highlighting its utility as a tool for parameter exploration. Our results indicate that ROH inferences are sensitive to factors such as sequencing depth and ROH length distribution, with bias direction and magnitude varying with demographic history and the programs used. Estimation biases are particularly pronounced at lower sequencing depths, potentially leading to either underestimation or overestimation of inbreeding. These results are particularly important for the management of endangered species, as underestimating inbreeding signals in the genome can substantially undermine conservation initiatives. We also found that small true ROHs can be incorrectly lumped together and called as longer ROHs, leading to erroneous inference of recent inbreeding. To address these challenges, we suggest using a combination of ROH detection tools and ROH length-specific inferences, along with sensitivity analysis, to generate robust and context-appropriate population inferences regarding inbreeding history. We outline these recommendations for ROH estimation at multiple levels of sequencing effort, which are typical of conservation genomics studies.}, } @article {pmid39480818, year = {2024}, author = {Ramesh, S and Rapp, S and Tapias Gomez, J and Levine, B and Tapias-Gomez, D and Chung, D and Truong, Z}, title = {Reference Sequence Browser: An R application with a user-friendly GUI to rapidly query sequence databases.}, journal = {PloS one}, volume = {19}, number = {10}, pages = {e0309707}, pmid = {39480818}, issn = {1932-6203}, mesh = {*User-Computer Interface ; *Software ; *DNA Barcoding, Taxonomic/methods ; Databases, Genetic ; Databases, Nucleic Acid ; Web Browser ; }, abstract = {Land managers, researchers, and regulators increasingly utilize environmental DNA (eDNA) techniques to monitor species richness, presence, and absence. In order to properly develop a biological assay for eDNA metabarcoding or quantitative PCR, scientists must be able to find not only reference sequences (previously identified sequences in a genomics database) that match their target taxa but also reference sequences that match non-target taxa. Determining which taxa have publicly available sequences in a time-efficient and accurate manner currently requires computational skills to search, manipulate, and parse multiple unconnected DNA sequence databases. Our team iteratively designed a Graphic User Interface (GUI) Shiny application called the Reference Sequence Browser (RSB) that provides users efficient and intuitive access to multiple genetic databases regardless of computer programming expertise. The application returns the number of publicly accessible barcode markers per organism in the NCBI Nucleotide, BOLD, or CALeDNA CRUX Metabarcoding Reference Databases. Depending on the database, we offer various search filters such as min and max sequence length or country of origin. Users can then download the FASTA/GenBank files from the RSB web tool, view statistics about the data, and explore results to determine details about the availability or absence of reference sequences.}, } @article {pmid39483086, year = {2024}, author = {Behera, BP and Naik, H and Konkimalla, VB}, title = {Peptaloid: A Comprehensive Database for Exploring Peptide Alkaloid.}, journal = {Journal of chemical information and modeling}, volume = {64}, number = {22}, pages = {8387-8395}, doi = {10.1021/acs.jcim.4c01667}, pmid = {39483086}, issn = {1549-960X}, mesh = {*Peptides/chemistry ; *Alkaloids/chemistry/pharmacology ; Databases, Protein ; Machine Learning ; Databases, Factual ; Humans ; }, abstract = {Peptaloid is the first dedicated database for peptide alkaloid molecules, a unique class of naturally derived compounds known for their structural diversity and significant biological activities. Despite their promising potential in drug discovery and therapeutic development, research on peptide alkaloids has been limited by the absence of a comprehensive and centralized resource. Fragmented data across various sources have posed a significant challenge, underscoring the need for a specialized database to facilitate more efficient research and application. Peptaloid addresses this critical gap by providing a database with over 161,000 peptide alkaloid entries, each detailed with structural, physicochemical, and pharmacological properties. By leveraging advanced computational tools and machine learning, Peptaloid generates ADMET profiles, aiding in identifying and optimizing therapeutic candidates. Designed for versatility, the database supports various applications beyond drug discovery, including ecology and material sciences. Peptaloid (as a specialized database for peptide alkaloids) will play a crucial role in innovation and collaboration across scientific disciplines. Peptaloid is accessible at https://peptaloid.niser.ac.in.}, } @article {pmid39481332, year = {2025}, author = {Yao, M and Ren, A and Yang, X and Chen, L and Wang, X and van der Meer, W and van Loosdrecht, MCM and Liu, G and Pabst, M}, title = {Unveiling the influence of heating temperature on biofilm formation in shower hoses through multi-omics.}, journal = {Water research}, volume = {268}, number = {Pt B}, pages = {122704}, doi = {10.1016/j.watres.2024.122704}, pmid = {39481332}, issn = {1879-2448}, mesh = {*Biofilms ; Proteomics ; Heating ; Metagenomics ; Hot Temperature ; Metagenome ; Multiomics ; }, abstract = {Shower systems provide unique environments that are conducive to biofilm formation and the proliferation of pathogens. The water heating temperature is a delicate decision that can impact microbial growth, balancing safety and energy consumption. This study investigated the impact of different heating temperatures (39 °C, 45 °C, 51 °C and 58 °C) on the shower hose biofilm (exposed to a final water temperature of 39 °C) using controlled full-scale shower setups. Whole metagenome sequencing and metaproteomics were employed to unveil the microbial composition and protein expression profiles. Overall, the genes and enzymes associated with disinfectant resistance and biofilm formation appeared largely unaffected. However, metagenomic analysis revealed a sharp decline in the number of total (86,371 to 34,550) and unique genes (32,279 to 137) with the increase in hot water temperature, indicating a significant reduction of overall microbial complexity. None of the unique proteins were detected in the proteomics experiments, suggesting smaller variation among biofilms on the proteome level compared to genomic data. Furthermore, out of 43 pathogens detected by metagenomics, only 5 could actually be detected by metaproteomics. Most interestingly, our study indicates that 45 °C heating temperature may represent an optimal balance. It minimizes active biomass (ATP) and reduces the presence of pathogens while saving heating energy. Our study offered new insights into the impact of heating temperature on shower hose biofilm formation and proposed optimal parameters that ensure biosafety while conserving energy.}, } @article {pmid39477106, year = {2024}, author = {Manzanedo, RD and Chin, ARO and Ettinger, AK and Pederson, N and Pradhan, K and Guiterman, CH and Su, J and Baumgarten, F and Hille Ris Lambers, J}, title = {Moving ecological tree-ring big data forwards: Limitations, data integration, and multidisciplinarity.}, journal = {The Science of the total environment}, volume = {955}, number = {}, pages = {177244}, doi = {10.1016/j.scitotenv.2024.177244}, pmid = {39477106}, issn = {1879-1026}, mesh = {*Ecology ; *Big Data ; *Trees ; *Databases, Factual ; Environmental Monitoring/methods ; Forests ; Ecosystem ; }, abstract = {In recent years, tree-ring databases have emerged as a remarkable resource for ecological research, allowing us to address ecological questions at unprecedented temporal and spatial scales. However, concerns regarding big tree-ring data limitations and risks have also surfaced, leading to questions about their potential to be representative of long-term forest responses. Here, we highlight three paths of action to improve on tree-ring databases in ecology: 1) Implementing consistent bias analyses in large dendroecological databases and promoting community-driven data to address data limitations, 2) Encouraging the integration of tree-ring data with other ecological datasets, and 3) Promoting theory-driven, mechanistic dendroecological research. These issues are increasingly important for tackling pressing cross-disciplinary research questions. Finally, although we focus here on tree ring databases, these points apply broadly across many aggregative databases in ecology.}, } @article {pmid39475652, year = {2024}, author = {Chala, D and Endresen, D and Demissew, S and Slaughter, LA and Johnsen, EB and Stenseth, NC}, title = {Stop using racist, unethical, and inappropriate names in taxonomy.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {121}, number = {45}, pages = {e2415490121}, pmid = {39475652}, issn = {1091-6490}, } @article {pmid39473806, year = {2024}, author = {Ayadi, H and Elbéji, A and Despotovic, V and Fagherazzi, G}, title = {Digital Vocal Biomarker of Smoking Status Using Ecological Audio Recordings: Results from the Colive Voice Study.}, journal = {Digital biomarkers}, volume = {8}, number = {1}, pages = {159-170}, pmid = {39473806}, issn = {2504-110X}, abstract = {INTRODUCTION: The complex health, social, and economic consequences of tobacco smoking underscore the importance of incorporating reliable and scalable data collection on smoking status and habits into research across various disciplines. Given that smoking impacts voice production, we aimed to develop a gender and language-specific vocal biomarker of smoking status.

METHODS: Leveraging data from the Colive Voice study, we used statistical analysis methods to quantify the effects of smoking on voice characteristics. Various voice feature extraction methods combined with machine learning algorithms were then used to produce a gender and language-specific (English and French) digital vocal biomarker to differentiate smokers from never-smokers.

RESULTS: A total of 1,332‬ participants were included after propensity score matching (mean age = 43.6 [13.65], 64.41% are female, 56.68% are English speakers, 50% are smokers and 50% are never-smokers). We observed differences in voice features distribution: for women, the fundamental frequency F0, the formants F1, F2, and F3 frequencies and the harmonics-to-noise ratio were lower in smokers compared to never-smokers (p < 0.05) while for men no significant disparities were noted between the two groups. The accuracy and AUC of smoking status prediction reached 0.71 and 0.76, respectively, for the female participants, and 0.65 and 0.68, respectively, for the male participants.

CONCLUSION: We have shown that voice features are impacted by smoking. We have developed a novel digital vocal biomarker that can be used in clinical and epidemiological research to assess smoking status in a rapid, scalable, and accurate manner using ecological audio recordings.}, } @article {pmid39473051, year = {2024}, author = {Wang, Y and Chen, J and Ni, Y and Liu, Y and Gao, X and Tse, MA and Panagiotou, G and Xu, A}, title = {Exercise-changed gut mycobiome as a potential contributor to metabolic benefits in diabetes prevention: an integrative multi-omics study.}, journal = {Gut microbes}, volume = {16}, number = {1}, pages = {2416928}, pmid = {39473051}, issn = {1949-0984}, mesh = {Humans ; *Gastrointestinal Microbiome ; Male ; *Exercise ; Middle Aged ; *Mycobiome ; *Fungi/classification/genetics/isolation & purification ; *Feces/microbiology ; Proteomics ; Prediabetic State/microbiology/metabolism ; Metabolomics ; Bacteria/classification/isolation & purification/genetics/metabolism ; Adult ; Diabetes Mellitus, Type 2/microbiology/prevention & control ; Metagenomics ; Multiomics ; }, abstract = {BACKGROUND: The importance of gut microbes in mediating the benefits of lifestyle intervention is increasingly recognized. However, compared to the bacterial microbiome, the role of intestinal fungi in exercise remains elusive. With our established randomized controlled trial of exercise intervention in Chinese males with prediabetes (n = 39, ClinicalTrials.gov:NCT03240978), we investigated the dynamics of human gut mycobiome and further interrogated their associations with exercise-elicited outcomes using multi-omics approaches.

METHODS: Clinical variations and biological samples were collected before and after training. Fecal fungal composition was analyzed using the internal transcribed spacer 2 (ITS2) sequencing and integrated with paired shotgun metagenomics, untargeted metabolomics, and Olink proteomics.

RESULTS: Twelve weeks of exercise training profoundly promoted fungal ecological diversity and intrakingdom connection. We further identified exercise-responsive genera with potential metabolic benefits, including Verticillium, Sarocladium, and Ceratocystis. Using multi-omics approaches, we elucidated comprehensive associations between changes in gut mycobiome and exercise-shaped metabolic phenotypes, bacterial microbiome, and circulating metabolomics and proteomics profiles. Furthermore, a machine-learning algorithm built using baseline microbial signatures and clinical characteristics predicted exercise responsiveness in improvements of insulin sensitivity, with an area under the receiver operating characteristic (AUROC) of 0.91 (95% CI: 0.85-0.97) in the discovery cohort and of 0.79 (95% CI: 0.74-0.86) in the independent validation cohort (n = 30).

CONCLUSIONS: Our findings suggest that intense exercise training significantly remodels the human fungal microbiome composition. Changes in gut fungal composition are associated with the metabolic benefits of exercise, indicating gut mycobiome is a possible molecular transducer of exercise. Moreover, baseline gut fungal signatures predict exercise responsiveness for diabetes prevention, highlighting that targeting the gut mycobiome emerges as a prospective strategy in tailoring personalized training for diabetes prevention.}, } @article {pmid39472185, year = {2024}, author = {Orr, MC and Albert, G and Hughes, AC and Koludarov, I and Luo, A and Qiao, H and Wang, MQ and Chesters, D and Zhu, CD}, title = {Dark data limit the biological sciences.}, journal = {Science bulletin}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.scib.2024.10.021}, pmid = {39472185}, issn = {2095-9281}, } @article {pmid39470965, year = {2024}, author = {Sandin, P and Baard, P and Bülow, W and Helgesson, G}, title = {Authorship and Citizen Science: Seven Heuristic Rules.}, journal = {Science and engineering ethics}, volume = {30}, number = {6}, pages = {53}, pmid = {39470965}, issn = {1471-5546}, support = {2019-00548//Svenska Forskningsrådet Formas/ ; }, mesh = {*Authorship/standards ; Humans ; *Citizen Science/ethics ; *Heuristics ; *Guidelines as Topic ; *Ethics, Research ; *Publishing/ethics/standards ; Editorial Policies ; Research Personnel/ethics ; Volunteers ; Social Responsibility ; }, abstract = {Citizen science (CS) is an umbrella term for research with a significant amount of contributions from volunteers. Those volunteers can occupy a hybrid role, being both 'researcher' and 'subject' at the same time. This has repercussions for questions about responsibility and credit, e.g. pertaining to the issue of authorship. In this paper, we first review some existing guidelines for authorship and their applicability to CS. Second, we assess the claim that the guidelines from the International Committee of Medical Journal Editors (ICMJE), known as 'the Vancouver guidelines', may lead to exclusion of deserving citizen scientists as authors. We maintain that the idea of including citizen scientists as authors is supported by at least two arguments: transparency and fairness. Third, we argue that it might be plausible to include groups as authors in CS. Fourth and finally, we offer a heuristic list of seven recommendations to be considered when deciding about whom to include as an author of a CS publication.}, } @article {pmid39470730, year = {2024}, author = {Bağcı, C and Nuhamunada, M and Goyat, H and Ladanyi, C and Sehnal, L and Blin, K and Kautsar, SA and Tagirdzhanov, A and Gurevich, A and Mantri, S and von Mering, C and Udwary, D and Medema, MH and Weber, T and Ziemert, N}, title = {BGC Atlas: a web resource for exploring the global chemical diversity encoded in bacterial genomes.}, journal = {Nucleic acids research}, volume = {}, number = {}, pages = {}, doi = {10.1093/nar/gkae953}, pmid = {39470730}, issn = {1362-4962}, support = {161L0284C//Federal Ministry of Research and Education (BMBF)/ ; TTU09.716//German Centre for Infection Research (DZIF)/ ; NNF20CC0035580//Novo Nordisk Foundation/ ; //Saarland University/ ; //National Agri-Food Biotechnology Institute/ ; 101064285//Horizon Europe-Research and Innovation Framework Programme/ ; //Office of Science/ ; DE-AC02-05CH11231//Department of Energy/ ; }, abstract = {Secondary metabolites are compounds not essential for an organism's development, but provide significant ecological and physiological benefits. These compounds have applications in medicine, biotechnology and agriculture. Their production is encoded in biosynthetic gene clusters (BGCs), groups of genes collectively directing their biosynthesis. The advent of metagenomics has allowed researchers to study BGCs directly from environmental samples, identifying numerous previously unknown BGCs encoding unprecedented chemistry. Here, we present the BGC Atlas (https://bgc-atlas.cs.uni-tuebingen.de), a web resource that facilitates the exploration and analysis of BGC diversity in metagenomes. The BGC Atlas identifies and clusters BGCs from publicly available datasets, offering a centralized database and a web interface for metadata-aware exploration of BGCs and gene cluster families (GCFs). We analyzed over 35 000 datasets from MGnify, identifying nearly 1.8 million BGCs, which were clustered into GCFs. The analysis showed that ribosomally synthesized and post-translationally modified peptides are the most abundant compound class, with most GCFs exhibiting high environmental specificity. We believe that our tool will enable researchers to easily explore and analyze the BGC diversity in environmental samples, significantly enhancing our understanding of bacterial secondary metabolites, and promote the identification of ecological and evolutionary factors shaping the biosynthetic potential of microbial communities.}, } @article {pmid39469132, year = {2024}, author = {Bernstein, JM and Bautista, JB and Clores, MA and Brown, RM and Ruane, S and Sanguila, MB and Alis-Besenio, MGJ and Pejo, CLF and Cuesta, MA}, title = {Using mangrove and field observation data to identify fine-scale species distributions: a case study in bockadams (Serpentes: Homalopsidae: Cerberus).}, journal = {Royal Society open science}, volume = {11}, number = {10}, pages = {240483}, pmid = {39469132}, issn = {2054-5703}, abstract = {Characterization of species distributions is a fundamental challenge in biodiversity science, with particular significance for downstream evolutionary studies, conservation efforts, field-based faunal studies and estimates of species diversity. Checklists and phylogenetic studies often focus on poorly known, rare taxa with limited ranges. However, studies of widely distributed, ecologically important species that are abundant in their preferred microhabitats are also important for systematics and local conservation efforts, but less often studied. We collected novel natural history data during fieldwork (2019-2023) for Philippine populations of bockadams (Homalopsidae: Cerberus), one of the most abundant vertebrates in Southeast Asian aquatic systems. Considered a coastal snake, many studies report Cerberus inland. We report the frequency of encounters of Cerberus schneiderii, and the IUCN data-deficient, Philippine-endemic Cerberus microlepis during six expeditions (62 days; 1041 person-hours). We report new occurrence data for 69 C. schneiderii and 6 C. microlepis for coastal and inland populations, water measurements and dietary observations. Regression analyses and ecological niche models show the importance of coastal and mangrove habitats for Cerberus. Our study is the most comprehensive assessment of Philippine Cerberus populations to date and provides critical baseline natural history data for downstream research on widespread and range-restricted species of Southeast Asian snakes.}, } @article {pmid39469049, year = {2024}, author = {Chávez-Luzanía, RA and Ortega-Urquieta, ME and Aguilera-Ibarra, J and Morales-Sandoval, PH and Hernández-Coss, JA and González-Vázquez, LA and Jara-Morales, VB and Arredondo-Márquez, SH and Olea-Félix, MJ and de Los Santos-Villalobos, S}, title = {Transdisciplinary approaches for the study of cyanobacteria and cyanotoxins.}, journal = {Current research in microbial sciences}, volume = {7}, number = {}, pages = {100289}, pmid = {39469049}, issn = {2666-5174}, abstract = {Cyanobacteria, ancient aerobic and photoautotrophic prokaryotes, thrive in diverse ecosystems due to their extensive morphological and physiological adaptations. They play crucial roles in aquatic ecosystems as primary producers and resource providers but also pose significant ecological and health risks through blooms that produce harmful toxins, called cyanotoxins. The taxonomic affiliation of cyanobacteria has evolved from morphology-based methods to genomic analysis, which offers detailed structural and physiological insights that are essential for accurate taxonomic affiliation and monitoring. However, challenges posed by uncultured species have been extrapolated to the detection and quantification of cyanotoxins. Current advances in molecular biology and informatics improve the precision of monitoring and allow the analysis of groups of genes related to toxin production, providing crucial information for environmental biosafety and public health. Unfortunately, public genomic databases heavily underrepresent cyanobacteria, which limits the understanding of their diversity and metabolic capabilities. Despite the increasing availability of cyanobacterial genome sequences, research is still largely focused on a few model strains, narrowing the scope of genetic and metabolic studies. The challenges posed by cyanobacterial blooms and cyanotoxins necessitate improved molecular, cultivation, and polyphasic techniques for comprehensive classification and quantification, highlighting the need for advanced genomic approaches to better understand and manage cyanobacteria and toxins. This review explores the application of transdisciplinary approaches for the study of cyanobacteria and cyanotoxins focused on diversity analysis, population quantification, and cyanotoxin monitoring, emphasizing their genomic resources and their potential in the genomic mining of toxin-related genes.}, } @article {pmid39467848, year = {2024}, author = {Büttiker, P and Boukherissa, A and Weissenberger, S and Ptacek, R and Anders, M and Raboch, J and Stefano, GB}, title = {Cognitive Impact of Neurotropic Pathogens: Investigating Molecular Mimicry through Computational Methods.}, journal = {Cellular and molecular neurobiology}, volume = {44}, number = {1}, pages = {72}, pmid = {39467848}, issn = {1573-6830}, mesh = {Humans ; *Molecular Mimicry ; Computational Biology/methods ; Cognition/physiology ; Protein Binding ; Amino Acid Sequence ; Viral Proteins/metabolism/chemistry ; Models, Molecular ; }, abstract = {Neurotropic pathogens, notably, herpesviruses, have been associated with significant neuropsychiatric effects. As a group, these pathogens can exploit molecular mimicry mechanisms to manipulate the host central nervous system to their advantage. Here, we present a systematic computational approach that may ultimately be used to unravel protein-protein interactions and molecular mimicry processes that have not yet been solved experimentally. Toward this end, we validate this approach by replicating a set of pre-existing experimental findings that document the structural and functional similarities shared by the human cytomegalovirus-encoded UL144 glycoprotein and human tumor necrosis factor receptor superfamily member 14 (TNFRSF14). We began with a thorough exploration of the Homo sapiens protein database using the Basic Local Alignment Search Tool (BLASTx) to identify proteins sharing sequence homology with UL144. Subsequently, we used AlphaFold2 to predict the independent three-dimensional structures of UL144 and TNFRSF14. This was followed by a comprehensive structural comparison facilitated by Distance-Matrix Alignment and Foldseek. Finally, we used AlphaFold-multimer and PPIscreenML to elucidate potential protein complexes and confirm the predicted binding activities of both UL144 and TNFRSF14. We then used our in silico approach to replicate the experimental finding that revealed TNFRSF14 binding to both B- and T-lymphocyte attenuator (BTLA) and glycoprotein domain and UL144 binding to BTLA alone. This computational framework offers promise in identifying structural similarities and interactions between pathogen-encoded proteins and their host counterparts. This information will provide valuable insights into the cognitive mechanisms underlying the neuropsychiatric effects of viral infections.}, } @article {pmid39466727, year = {2024}, author = {Charniga, K and Park, SW and Akhmetzhanov, AR and Cori, A and Dushoff, J and Funk, S and Gostic, KM and Linton, NM and Lison, A and Overton, CE and Pulliam, JRC and Ward, T and Cauchemez, S and Abbott, S}, title = {Best practices for estimating and reporting epidemiological delay distributions of infectious diseases.}, journal = {PLoS computational biology}, volume = {20}, number = {10}, pages = {e1012520}, pmid = {39466727}, issn = {1553-7358}, mesh = {Humans ; *Communicable Diseases/epidemiology ; *Disease Outbreaks/statistics & numerical data ; Models, Statistical ; Computational Biology/methods ; Epidemiological Models ; }, abstract = {Epidemiological delays are key quantities that inform public health policy and clinical practice. They are used as inputs for mathematical and statistical models, which in turn can guide control strategies. In recent work, we found that censoring, right truncation, and dynamical bias were rarely addressed correctly when estimating delays and that these biases were large enough to have knock-on impacts across a large number of use cases. Here, we formulate a checklist of best practices for estimating and reporting epidemiological delays. We also provide a flowchart to guide practitioners based on their data. Our examples are focused on the incubation period and serial interval due to their importance in outbreak response and modeling, but our recommendations are applicable to other delays. The recommendations, which are based on the literature and our experience estimating epidemiological delay distributions during outbreak responses, can help improve the robustness and utility of reported estimates and provide guidance for the evaluation of estimates for downstream use in transmission models or other analyses.}, } @article {pmid39464503, year = {2023}, author = {Weir, JC and , and , and , and , and , and , and Boyes, D}, title = {The genome sequence of the Vapourer moth, Orgyia antiqua (Linnaeus, 1758).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {314}, pmid = {39464503}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual male Orgyia antiqua specimen (the Vapourer moth; Arthropoda; Insecta; Lepidoptera; Erebidae). The genome sequence is 480.1 megabases in span. Most of the assembly is scaffolded into 14 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.4 kilobases in length. Gene annotation of this assembly on Ensembl identified 12,475 protein coding genes.}, } @article {pmid39464235, year = {2022}, author = {Boyes, D and , and , and , and , and , and Lewin, T and , }, title = {The genome sequence of the acorn piercer, Pammene fasciana (Linnaeus, 1761).}, journal = {Wellcome open research}, volume = {7}, number = {}, pages = {258}, pmid = {39464235}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual male Pammene fasciana (acorn piercer; Arthropoda; Insecta; Lepidoptera; Tortricidae). The genome sequence is 564 megabases in span. Most of the assembly (99.94%) is scaffolded into 28 chromosomal pseudomolecules with the Z sex chromosome assembled. The complete mitochondrial genome was also assembled and is 16.4 kilobases in length. Gene annotation of this assembly on Ensembl identified 21,224 protein-coding genes.}, } @article {pmid39461044, year = {2024}, author = {Wu, Y and Wei, C and Zhang, Y and Gu, C and Fang, Y}, title = {Investigating intrinsic and situational predictors of depression among older adults: An analysis of the CHARLS database.}, journal = {Asian journal of psychiatry}, volume = {102}, number = {}, pages = {104279}, doi = {10.1016/j.ajp.2024.104279}, pmid = {39461044}, issn = {1876-2026}, mesh = {Humans ; Female ; Male ; Aged ; Middle Aged ; Aged, 80 and over ; *Depression/epidemiology ; Databases, Factual ; China/epidemiology ; Risk Factors ; Follow-Up Studies ; Depressive Disorder/epidemiology ; Chronic Disease ; }, abstract = {BACKGROUND: This study aimed to investigate the intrinsic and situational predictors of depression under the health ecological model.

METHODS: Two waves (2011 and 2013) of survey data were collected from the CHARLS. A total of 5845 older adults (≧60) were included, and depression was defined as CESD-10 score ≧10. Random forest combined with interpretable methods were utilized to select important predictors of depression. Multilevel logit model was used to examine the associations of intrinsic and situational predictors with depression.

RESULTS: After a 2-year follow up, 1822 individuals (31.17 %) developed depression. Interpretable analyses showed that both intrinsic and situational variables were predictive for depression. Multilevel logit model showed that age, gender, number of chronic diseases, number of pain areas, life satisfaction, and toilet distance were significantly associated with depression.

CONCLUSION: Both intrinsic and situational factors were found to be associated with depression among community older population, highlighting their significance for early prevention from the perspective of public health.}, } @article {pmid39460934, year = {2024}, author = {Frazer, SA and Baghbanzadeh, M and Rahnavard, A and Crandall, KA and Oakley, TH}, title = {Discovering genotype-phenotype relationships with machine learning and the Visual Physiology Opsin Database (VPOD).}, journal = {GigaScience}, volume = {13}, number = {}, pages = {}, pmid = {39460934}, issn = {2047-217X}, support = {DEB-2153773//National Science Foundation/ ; }, mesh = {*Machine Learning ; *Opsins/genetics/metabolism ; Animals ; *Phenotype ; *Databases, Genetic ; Genetic Association Studies ; Genotype ; Humans ; Mutation ; }, abstract = {BACKGROUND: Predicting phenotypes from genetic variation is foundational for fields as diverse as bioengineering and global change biology, highlighting the importance of efficient methods to predict gene functions. Linking genetic changes to phenotypic changes has been a goal of decades of experimental work, especially for some model gene families, including light-sensitive opsin proteins. Opsins can be expressed in vitro to measure light absorption parameters, including λmax-the wavelength of maximum absorbance-which strongly affects organismal phenotypes like color vision. Despite extensive research on opsins, the data remain dispersed, uncompiled, and often challenging to access, thereby precluding systematic and comprehensive analyses of the intricate relationships between genotype and phenotype.

RESULTS: Here, we report a newly compiled database of all heterologously expressed opsin genes with λmax phenotypes that we call the Visual Physiology Opsin Database (VPOD). VPOD_1.0 contains 864 unique opsin genotypes and corresponding λmax phenotypes collected across all animals from 73 separate publications. We use VPOD data and deepBreaks to show regression-based machine learning (ML) models often reliably predict λmax, account for nonadditive effects of mutations on function, and identify functionally critical amino acid sites.

CONCLUSION: The ability to reliably predict functions from gene sequences alone using ML will allow robust exploration of molecular-evolutionary patterns governing phenotype, will inform functional and evolutionary connections to an organism's ecological niche, and may be used more broadly for de novo protein design. Together, our database, phenotype predictions, and model comparisons lay the groundwork for future research applicable to families of genes with quantifiable and comparable phenotypes.}, } @article {pmid39460811, year = {2024}, author = {Hasan, A and Ibrahim, M and Alonazi, WB and Yu, R and Li, B}, title = {Pangenome analysis of five representative Tropheryma whipplei strains following multiepitope-based vaccine design via immunoinformatic approaches.}, journal = {Molecular genetics and genomics : MGG}, volume = {299}, number = {1}, pages = {101}, pmid = {39460811}, issn = {1617-4623}, mesh = {Humans ; *Tropheryma/genetics/immunology ; *Bacterial Vaccines/immunology/genetics ; Whipple Disease/immunology/microbiology/genetics ; Computational Biology/methods ; Bacterial Proteins/genetics/immunology ; Genome, Bacterial ; Epitopes/immunology/genetics ; Vaccine Development ; Immunodominant Epitopes/immunology/genetics ; Proteomics/methods ; Proteome/genetics/immunology ; }, abstract = {Whipple disease caused by Tropheryma whipplei a gram-positive bacterium is a systemic disorder that impacts not only the gastrointestinal tract but also the vascular system, joints, central nervous system, and cardiovascular system. Due to the lack of an approved vaccine, this study aimed to utilize immunoinformatic approaches to design multiepitope -based vaccine by utilizing the proteomes of five representative T. whipplei strains. The genomes initially comprised a total of 4,844 proteins ranging from 956 to 1012 proteins per strain. We collected 829 nonredundant lists of core proteins, that were shared among all the strains. Following subtractive proteomics, one extracellular protein, WP_033800108.1, a WhiB family transcriptional regulator, was selected for the chimeric-based multiepitope vaccine. Five immunodominant epitopes were retrieved from the WhiB family transcriptional regulator protein, indicating MHC-I and MHC-II with a global population coverage of 70.61%. The strong binding affinity, high solubility, nontoxicity, nonallergenic properties and high antigenicity scores make the selected epitopes more appropriate. Integration of the epitopes into a chimeric vaccine was carried out by applying appropriate adjuvant molecules and linkers, leading to the vaccine construct having enhanced immunogenicity and successfully eliciting both innate and adaptive immune responses. Moreover, the abilityof the vaccine to bind TLR4, a core innate immune receptor, was confirmed. Molecular dynamics simulations have also revealed the promising potential stability of the designed vaccine at 400 ns. In summary, we have designed a potential vaccine construct that has the ability not only to induce targeted immunogenicity for one strain but also for global T. whipplei strains. This study proposes a potential universal vaccine, reducing Whipple's disease risk and laying the groundwork for future research on multi-strain pathogens.}, } @article {pmid39454020, year = {2024}, author = {Wong, R and Matulewicz, RS and Talwar, R and Shoenbill, KA and Goldstein, AO and Bjurlin, MA}, title = {Increased tobacco taxation associated with decreased consumption and bladder cancer incidence.}, journal = {Urology practice}, volume = {}, number = {}, pages = {101097UPJ0000000000000743}, doi = {10.1097/UPJ.0000000000000743}, pmid = {39454020}, issn = {2352-0787}, abstract = {PURPOSE: The temporal relationship between smoking exposure and bladder cancer (BC) diagnosis remains ill-defined. This study aims to cross-correlate and temporally associate changes in United States (US) tobacco tax and consumption with BC incidence.

METHODS: US tobacco consumption, tobacco tax data, and BC incidence rates from 1975-2019 were retrieved. A cross-correlation lag time for tobacco tax and consumption on BC incidence was calculated while controlling for national health expenditure. Proxied lag weighted semi-log linear models to determine the rate of change in BC incidence rates associated with a 1% change in tobacco tax percentages on a national and state level.

RESULTS: A 1% increase in tobacco tax was associated with a 1.77% decrease in BC incidence over a 6-year period (R[2]=0.9687, p=0.00044). 22 states had a statistically significant decline in BC incidences correlated with increasing tobacco taxation. Reduction in BC incidence >0.5% were observed in states along the Western and Eastern US borders. Montana, Utah, Nebraska, Arkansas, and Tennessee did not have decreasing BC incidences from tobacco tax increases. California had the most drastic decline in BC incidence (1.98%). Nationally, tobacco consumption decrease in 1 pack per capita was associated with a 0.47% decrease in BC incidence over a 28-year period (R[2]=0.984, p=0.00011).

CONCLUSION: Declining US tobacco consumption may indicate significant reduction in BC incidence through 2047. Primary prevention through adaptation of state-legislated tax changes may contribute to a reduction in BC incidence in states lying within the Central US. A national tobacco tax initative can be considered given the improvement in population health.}, } @article {pmid39449983, year = {2023}, author = {Boyes, D and Holland, PWH and , and , and , and , and , and , }, title = {The genome sequence of the Currant Clearwing moth, Synanthedon tipuliformis (Clerck, 1759).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {300}, pmid = {39449983}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual male Synanthedon tipuliformis (the Currant Clearwing; Arthropoda; Insecta; Lepidoptera; Sesiidae). The genome sequence is 295.8 megabases in span. Most of the assembly (99.98%) is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 27.05 kilobases in length. Gene annotation of this assembly on Ensembl identified 11,878 protein-coding genes.}, } @article {pmid39448189, year = {2024}, author = {Konečný, L and Peterková, K}, title = {Unveiling the peptidases of parasites from the office chair - The endothelin-converting enzyme case study.}, journal = {Advances in parasitology}, volume = {126}, number = {}, pages = {1-52}, doi = {10.1016/bs.apar.2024.05.003}, pmid = {39448189}, issn = {2163-6079}, mesh = {Animals ; *Computational Biology ; Endothelin-Converting Enzymes/genetics ; Schistosoma mansoni/enzymology/genetics ; Humans ; Peptide Hydrolases/genetics/metabolism ; Proteomics ; }, abstract = {The emergence of high-throughput methodologies such as next-generation sequencing and proteomics has necessitated significant advancements in biological databases and bioinformatic tools, therefore reshaping the landscape of research into parasitic peptidases. In this review we outline the development of these resources along the -omics technologies and their transformative impact on the field. Apart from extensive summary of general and specific databases and tools, we provide a general pipeline on how to use these resources effectively to identify candidate peptidases from these large datasets and how to gain as much information about them as possible without leaving the office chair. This pipeline is then applied in an illustrative case study on the endothelin-converting enzyme 1 homologue from Schistosoma mansoni and attempts to highlight the contemporary capabilities of bioinformatics. The case study demonstrate how such approach can aid to hypothesize enzyme functions and interactions through computational analysis alone effectively and emphasizes how such virtual investigations can guide and optimize subsequent wet lab experiments therefore potentially saving precious time and resources. Finally, by showing what can be achieved without traditional wet laboratory methods, this review provides a compelling narrative on the use of bioinformatics to bridge the gap between big data and practical research applications, highlighting the key role of these technologies in furthering our understanding of parasitic diseases.}, } @article {pmid39446479, year = {2024}, author = {Oliveira, J and Aires Dias, J and Correia, R and Pinheiro, R and Reis, V and Sousa, D and Agostinho, D and Simões, M and Castelo-Branco, M}, title = {Exploring Immersive Multimodal Virtual Reality Training, Affective States, and Ecological Validity in Healthy Firefighters: Quasi-Experimental Study.}, journal = {JMIR serious games}, volume = {12}, number = {}, pages = {e53683}, pmid = {39446479}, issn = {2291-9279}, abstract = {BACKGROUND: Firefighters face stressful life-threatening events requiring fast decision-making. To better prepare for those situations, training is paramount, but errors in real-life training can be harmful. Virtual reality (VR) simulations provide the desired realism while enabling practice in a secure and controlled environment. Firefighters' affective states are also crucial as they are a higher-risk group.

OBJECTIVE: To assess the impact on affective states of 2 simulated immersive experiences in a sample of healthy firefighters (before, during, and after the simulation), we pursued a multivariate approach comprising cognitive performance, situational awareness, depression, anxiety, stress, number of previous adverse events experienced, posttraumatic stress disorder (PTSD) severity, and emotions. The efficacy and ecological validity of an innovative VR haptic system were also tested, exploring its impact on performance.

METHODS: In collaboration with the Portuguese National Fire Service School, we exposed 22 healthy firefighters to 2 immersive scenarios using the FLAIM Trainer VR system (neutral and arousing scenarios) while recording physiological data in a quasi-experimental study. Baseline cognitive performance, depression, anxiety, stress, number of adverse events, and severity of PTSD symptoms were evaluated. Positive and negative affective states were measured before, between, and after each scenario. Situational awareness, sense of presence, ecological validity, engagement, and negative effects resulting from VR immersion were tested.

RESULTS: Baseline positive affect score was high (mean 32.4, SD 7.2) and increased after the VR tasks (partial η[2]=0.52; Greenhouse-Geisser F1.82,32.78=19.73; P<.001). Contrarily, mean negative affect score remained low (range 11.0-11.9) throughout the study (partial η[2]=0.02; Greenhouse-Geisser F2.13,38.4=0.39; P=.69). Participants' feedback on the VR sense of presence was also positive, reporting a high sense of physical space (mean score 3.9, SD 0.8), ecological validity (mean score 3.8, SD 0.6), and engagement (mean score 3.8, SD 0.6). Engagement was related to the number of previously experienced adverse events (r=0.49; P=.02) and positive affect (after the last VR task; r=0.55; P=.02). Conversely, participants reported few negative effects (mean score 1.7, SD 0.6). The negative effects correlated positively with negative affect (after the last VR task; r=0.53; P=.03); and avoidance (r=0.73; P<.001), a PTSD symptom, controlling for relevant baseline variables. Performance related to situational awareness was positive (mean 46.4, SD 34.5), although no relation was found to metacognitively perceived situational awareness (r=-0.12; P=.59).

CONCLUSIONS: We show that VR is an effective alternative to in-person training as it was considered ecologically valid and engaging while promoting positive emotions, with few negative repercussions. This corroborates the use of VR to test firefighters' performance and situational awareness. Further research is needed to ascertain that firefighters with PTSD symptomatology are not negatively affected by VR. This study favors the use of VR training and provides new insights on its emotional and cognitive impact on the trainee.}, } @article {pmid39445720, year = {2024}, author = {Compton, ZT and Mellon, W and Harris, VK and Rupp, S and Mallo, D and Kapsetaki, SE and Wilmot, M and Kennington, R and Noble, K and Baciu, C and Ramirez, LN and Peraza, A and Martins, B and Sudhakar, S and Aksoy, S and Furukawa, G and Vincze, O and Giraudeau, M and Duke, EG and Spiro, S and Flach, E and Davidson, H and Li, CI and Zehnder, A and Graham, TA and Troan, BV and Harrison, TM and Tollis, M and Schiffman, JD and Aktipis, CA and Abegglen, LM and Maley, CC and Boddy, AM}, title = {Cancer Prevalence across Vertebrates.}, journal = {Cancer discovery}, volume = {}, number = {}, pages = {OF1-OF18}, doi = {10.1158/2159-8290.CD-24-0573}, pmid = {39445720}, issn = {2159-8290}, support = {P01 CA091955/CA/NCI NIH HHS/United States ; OTKA K143421//Agence Nationale de la Recherche (ANR)/ ; U54 CA217376/CA/NCI NIH HHS/United States ; ADHS18-198847//Arizona Biomedical Research Commission (ABRC)/ ; U2C CA233254/CA/NCI NIH HHS/United States ; //Hyundai Hope On Wheels (Hope On Wheels)/ ; BC132057//Congressionally Directed Medical Research Programs (CDMRP)/ ; R01 CA140657/CA/NCI NIH HHS/United States ; R21 CA257980/CA/NCI NIH HHS/United States ; T32 CA272303/CA/NCI NIH HHS/United States ; COVER ANR-23-CE02-0019//Agence Nationale de la Recherche (ANR)/ ; }, abstract = {Cancer is pervasive across multicellular species, but what explains the differences in cancer prevalence across species? Using 16,049 necropsy records for 292 species spanning three clades of tetrapods (amphibians, sauropsids, and mammals), we found that neoplasia and malignancy prevalence increases with adult mass (contrary to Peto's paradox) and somatic mutation rate but decreases with gestation time. The relationship between adult mass and malignancy prevalence was only apparent when we controlled for gestation time. Evolution of cancer susceptibility appears to have undergone sudden shifts followed by stabilizing selection. Outliers for neoplasia prevalence include the common porpoise (<1.3%), the Rodrigues fruit bat (<1.6%), the black-footed penguin (<0.4%), ferrets (63%), and opossums (35%). Discovering why some species have particularly high or low levels of cancer may lead to a better understanding of cancer syndromes and novel strategies for the management and prevention of cancer. Significance: Evolution has discovered mechanisms for suppressing cancer in a wide variety of species. By analyzing veterinary necropsy records, we can identify species with exceptionally high or low cancer prevalence. Discovering the mechanisms of cancer susceptibility and resistance may help improve cancer prevention and explain cancer syndromes.}, } @article {pmid39442119, year = {2024}, author = {Castro-Nunes, P and Palmieri, P and Bellas, H and Soares, A and Viana, J and Carvalho, PVR and Jatobá, A}, title = {Effects of pay for performance in primary care in an under-registration scenario.}, journal = {Revista de saude publica}, volume = {58}, number = {}, pages = {44}, pmid = {39442119}, issn = {1518-8787}, mesh = {Humans ; *Primary Health Care/economics ; Brazil ; *Reimbursement, Incentive/economics ; Female ; National Health Programs/economics ; }, abstract = {OBJECTIVE: To propose a method for detecting and analyzing under-registration and highlight its potential financial effect in view of the implementation of the Previne Brasil Program.

METHODS: An ecological study was carried out to analyze cytopathological exams in programmatic area 3.1 in the municipality of Rio de Janeiro. The data was collected from the Departamento de Informática do Sistema Único de Saúde (DATASUS - Department of Informatics of the Unified Health System) database, including information on reports from outsourced cytopathology laboratories and those available in the Sistema de Informação em Saúde para a Atenção Básica (SISAB - Health Information System for Primary Care) and the Sistema de Informação do Câncer do Colo do Útero (SISCOLO - Cervical Cancer Information System) of DATASUS/Ministry of Health.

RESULTS: The estimated under-registrations per health unit totaled 108,511 exams in the last two years in the programmatic area 3.1 area, which corresponds to an estimated total of R$ 435,129.00 that would have been foregone if the Previne Brasil Program had been in place during the period studied.

CONCLUSION: The article's main contribution lies in the presentation of empirical evidence of the potential effects of under-registration on Primary Health Care financing. In addition, there are two other significant findings - firstly, it highlights weaknesses in the process of recording health information inherent to vulnerable regions; secondly, it indicates a vicious circle potentially fueled by sudden changes in Primary Health Care funding conditions, in addition to potential consequences for other levels of care.}, } @article {pmid39440963, year = {2024}, author = {Wang, Y and Sun, Y and Huang, K and Gao, Y and Lin, Y and Yuan, B and Wang, X and Xu, G and Nussio, LG and Yang, F and Ni, K}, title = {Multi-omics analysis reveals the core microbiome and biomarker for nutrition degradation in alfalfa silage fermentation.}, journal = {mSystems}, volume = {9}, number = {11}, pages = {e0068224}, pmid = {39440963}, issn = {2379-5077}, support = {32171686//MOST | National Natural Science Foundation of China (NSFC)/ ; }, mesh = {*Medicago sativa/microbiology/metabolism ; *Silage/microbiology ; *Fermentation ; *Microbiota/genetics ; Animals ; Biomarkers/metabolism ; Bacteria/genetics/metabolism/classification/isolation & purification ; Metagenomics/methods ; High-Throughput Nucleotide Sequencing ; Cattle ; Multiomics ; }, abstract = {UNLABELLED: Alfalfa (Medicago sativa L.) is one of the most extensively cultivated forage crops globally, and its nutritional quality critically influences the productivity of dairy cows. Silage fermentation is recognized as a crucial technique for the preservation of fresh forage, ensuring the retention of its vital nutrients. However, the detailed microbial components and their functions in silage fermentation are not fully understood. This study integrated large-scale microbial culturing with high-throughput sequencing to thoroughly examine the microbial community structure in alfalfa silage and explored the potential pathways of nutritional degradation via metagenomic analysis. The findings revealed an enriched microbial diversity in silage, indicated by the identification of amplicon sequence variants. Significantly, the large-scale culturing approach recovered a considerable number of unique microbes undetectable by high-throughput sequencing. Predominant genera, such as Lactiplantibacillus, Leuconostoc, Lentilactobacillus, Weissella, and Liquorilactobacillus, were identified based on their abundance and prevalence. Additionally, genes associated with Enterobacteriaceae were discovered, which might be involved in pathways leading to the production of ammonia-N and butyric acid. Overall, this study offers a comprehensive insight into the microbial ecology of silage fermentation and provides valuable information for leveraging microbial consortia to enhance fermentation quality.

IMPORTANCE: Silage fermentation is a microbial-driven anaerobic process that efficiently converts various substrates into nutrients readily absorbable and metabolizable by ruminant animals. This study, integrating culturomics and metagenomics, has successfully identified core microorganisms involved in silage fermentation, including those at low abundance. This discovery is crucial for the targeted cultivation of specific microorganisms to optimize fermentation processes. Furthermore, our research has uncovered signature microorganisms that play pivotal roles in nutrient metabolism, significantly advancing our understanding of the intricate relationships between microbial communities and nutrient degradation during silage fermentation.}, } @article {pmid39439296, year = {2025}, author = {Rosche, C and Broennimann, O and Novikov, A and Mrázová, V and Boiko, GV and Danihelka, J and Gastner, MT and Guisan, A and Kožić, K and Lehnert, M and Müller-Schärer, H and Nagy, DU and Remelgado, R and Ronikier, M and Selke, JA and Shiyan, NM and Suchan, T and Thoma, AE and Zdvořák, P and Mráz, P}, title = {Herbarium specimens reveal a cryptic invasion of polyploid Centaurea stoebe in Europe.}, journal = {The New phytologist}, volume = {245}, number = {1}, pages = {392-405}, pmid = {39439296}, issn = {1469-8137}, mesh = {*Centaurea/genetics/physiology ; Europe ; *Polyploidy ; *Introduced Species ; Phylogeography ; Ecosystem ; Diploidy ; }, abstract = {Numerous plant species are expanding their native ranges due to anthropogenic environmental change. Because cytotypes of polyploid complexes often show similar morphologies, there may be unnoticed range expansions (i.e. cryptic invasions) of one cytotype into regions where only the other cytotype is native. We critically revised herbarium specimens of diploid and tetraploid Centaurea stoebe, collected across Europe between 1790 and 2023. Based on their distribution in natural and relict habitats and phylogeographic data, we estimated the native ranges of both cytotypes. Diploids are native across their entire European range, whereas tetraploids are native only to South-Eastern Europe and have recently expanded their range toward Central Europe. The proportion of tetraploids has exponentially increased over time in their expanded but not in their native range. This cryptic invasion predominantly occurred in ruderal habitats and enlarged the climatic niche of tetraploids toward a more oceanic climate. We conclude that spatio-temporally explicit assessments of range shifts, habitat preferences and niche evolution can improve our understanding of cryptic invasions. We also emphasize the value of herbarium specimens for accurate estimation of species´ native ranges, with fundamental implications for the design of research studies and the assessment of biodiversity trends.}, } @article {pmid39438357, year = {2024}, author = {Little, AJ and Matthee, CA and Ueckermann, EA and Horak, IG and Hui, C and Matthee, S}, title = {Host and habitat shape ectoparasite diversity on Mastomys natalensis and Mastomys coucha (Muridae).}, journal = {Parasitology}, volume = {151}, number = {8}, pages = {769-783}, pmid = {39438357}, issn = {1469-8161}, support = {R01 AI136832/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; *Rodent Diseases/parasitology/epidemiology ; *Ecosystem ; *Murinae/parasitology ; Male ; *Ectoparasitic Infestations/parasitology/veterinary ; Female ; Host-Parasite Interactions ; Mites/physiology/classification ; Siphonaptera/classification/physiology ; Biodiversity ; Ticks/classification/physiology ; }, abstract = {Mastomys natalensis and M. coucha are commensal rodent species endemic to Africa. A recent taxonomic revision within Mastomys leaves the parasite–host list of M. natalensis questionable and that of M. coucha incomplete. The current study aimed to develop a better understanding of the ectoparasite diversity associated with the 2 distinct but closely related rodent species and to explore the influence of host and habitat type on ectoparasite infestations. Between 2014 and 2020, 590 rodents were trapped in 3 habitat types (village, agriculture and natural) across a wildlife-human/domestic animal interface. In total 48 epifaunistic species (45 ectoparasitic and 3 predatory) represented by 29 genera from 4 taxonomic groups (fleas, lice, mites and ticks) were recorded. Only 50% of the epifauna were shared between the 2 rodent species, with mites the most speciose taxon in both host species. The abundance of epifaunistic individuals, and also those of mites and fleas, were significantly higher on male M. natalensis, while ticks were significantly higher on reproductively active M. natalensis. For both rodent species, infestations by most epifaunistic taxa (on M. natalensis) and some taxa (on M. coucha) were significantly lower in the village as opposed to the less disturbed agricultural and natural habitat types. The study highlights the importance of host life history, even in closely related rodent species, in shaping parasite profiles and a loss of parasite diversity in more extreme anthropogenic habitats.}, } @article {pmid39436938, year = {2024}, author = {Rocha, U and Kasmanas, JC and Toscan, R and Sanches, DS and Magnusdottir, S and Saraiva, JP}, title = {Simulation of 69 microbial communities indicates sequencing depth and false positives are major drivers of bias in prokaryotic metagenome-assembled genome recovery.}, journal = {PLoS computational biology}, volume = {20}, number = {10}, pages = {e1012530}, pmid = {39436938}, issn = {1553-7358}, mesh = {*Metagenome/genetics ; *Microbiota/genetics ; *Computer Simulation ; Metagenomics/methods ; High-Throughput Nucleotide Sequencing/methods ; Sequence Analysis, DNA/methods ; Computational Biology/methods ; Bacteria/genetics/classification ; Genome, Bacterial/genetics ; }, abstract = {We hypothesize that sample species abundance, sequencing depth, and taxonomic relatedness influence the recovery of metagenome-assembled genomes (MAGs). To test this hypothesis, we assessed MAG recovery in three in silico microbial communities composed of 42 species with the same richness but different sample species abundance, sequencing depth, and taxonomic distribution profiles using three different pipelines for MAG recovery. The pipeline developed by Parks and colleagues (8K) generated the highest number of MAGs and the lowest number of true positives per community profile. The pipeline by Karst and colleagues (DT) showed the most accurate results (~ 92%), outperforming the 8K and Multi-Metagenome pipeline (MM) developed by Albertsen and collaborators. Sequencing depth influenced the accurate recovery of genomes when using the 8K and MM, even with contrasting patterns: the MM pipeline recovered more MAGs found in the original communities when employing sequencing depths up to 60 million reads, while the 8K recovered more true positives in communities sequenced above 60 million reads. DT showed the best species recovery from the same genus, even though close-related species have a low recovery rate in all pipelines. Our results highlight that more bins do not translate to the actual community composition and that sequencing depth plays a role in MAG recovery and increased community resolution. Even low MAG recovery error rates can significantly impact biological inferences. Our data indicates that the scientific community should curate their findings from MAG recovery, especially when asserting novel species or metabolic traits.}, } @article {pmid39436510, year = {2024}, author = {Zinicovscaia, I and Chernyagina, O and Chaligava, O and Yushin, N and Devyatova, E and Grozov, D}, title = {Moss biomonitoring in areas affected by ashfalls of Shiveluch volcano (Kamchatka).}, journal = {Environmental science and pollution research international}, volume = {31}, number = {52}, pages = {61730-61739}, pmid = {39436510}, issn = {1614-7499}, mesh = {*Bryophyta/chemistry ; *Volcanic Eruptions ; *Environmental Monitoring/methods ; *Biological Monitoring ; Air Pollutants/analysis ; }, abstract = {The moss bag technique was applied on Kamchatka to assess the effect of Shiveluch volcano on the air quality. Moss bags were exposed in settlements located at different distances from the volcano and affected by ashfall to varying degrees. The inductively coupled plasma optical emission spectrometry was used for the determination of the content of Al, Ba, Co, Cd, Cr, Cu, Fe, Mn, P, Pb, Sr, S, V, and Zn in both exposed and unexposed moss samples. Relative accumulation factor revealed enrichment of mosses exposed in the area affected by ashfall with Al, Cr, V, and Zn. Correlation and principal component analysis allowed to identify elements of volcanogenic, geogenic, and anthropogenic origin. Ecological risk values less than 150 indicate low potential ecological risk in the region. Active moss biomonitoring can be considered a cheap and efficient tool for in-depth study of the influence of volcanic activity on air quality on the peninsula.}, } @article {pmid39435526, year = {2025}, author = {Kan-Lingwood, NY and Sagi, L and Mazie, S and Shahar, N and Zecherle Bitton, L and Templeton, A and Rubenstein, D and Bouskila, A and Bar-David, S}, title = {Genotyping Error Detection and Customised Filtration for SNP Datasets.}, journal = {Molecular ecology resources}, volume = {25}, number = {1}, pages = {e14033}, doi = {10.1111/1755-0998.14033}, pmid = {39435526}, issn = {1755-0998}, support = {2011384//United States-Israel Binational Science Foundation/ ; }, mesh = {*Polymorphism, Single Nucleotide ; *Genotyping Techniques/methods ; Animals ; Genotype ; Computational Biology/methods ; }, abstract = {A major challenge in analysing single-nucleotide polymorphism (SNP) genotype datasets is detecting and filtering errors that bias analyses and misinterpret ecological and evolutionary processes. Here, we present a comprehensive method to estimate and minimise genotyping error rates (deviations from the 'true' genotype) in any SNP datasets using triplicates (three repeats of the same sample) in a four-step filtration pipeline. The approach involves: (1) SNP filtering by missing data; (2) SNP filtering by error rates; (3) sample filtering by missing data and (4) detection of recaptured individuals by using estimated SNP error rates. The modular pipeline is provided in an R script that allows customised adjustments. We demonstrate the applicability of the method using non-invasive sampling from the Asiatic wild ass (Equus hemionus) population in Israel. We genotyped 756 samples using 625 SNPs, of which 255 were triplicates of 85 samples. The average SNP error rate, calculated based on the number of mismatching genotypes across triplicates before filtration, was 0.0034 and was reduced to 0.00174 following filtration. Evaluating genetic distance (GD) and relatedness (r) between triplicates before and after filtration (expected to be at the minimum and maximum respectively) showed a significant reduction in the average GD, from 58.1 to 25.3 (p = 0.0002) and a significant increase in relatedness, from r = 0.98 to r = 0.991 (p = 0.00587). We demonstrate how error rate estimation enhances recapture detection and improves genotype quality.}, } @article {pmid39434036, year = {2024}, author = {Li, C and Zhang, X and Zhao, L and Liu, S}, title = {Multi-omics profiling reveals the molecular mechanisms of H2O2-induced detrimental effects on Thamnaconus septentrionalis.}, journal = {BMC genomics}, volume = {25}, number = {1}, pages = {984}, pmid = {39434036}, issn = {1471-2164}, mesh = {Animals ; *Hydrogen Peroxide/metabolism ; Fishes/metabolism/genetics ; Transcriptome/drug effects ; Gene Expression Profiling ; Metabolomics ; Signal Transduction/drug effects ; Metabolome/drug effects ; Multiomics ; }, abstract = {BACKGROUND: Hydrogen peroxide (H2O2), a novel water treatment agent, can be used for disinfection, water quality adjustment, and disease prevention, while excessive H2O2 can injure farm animals, even leading to death. Hydrogen peroxide is a recommended disinfectant and bactericide for treating gill diseases and vibriosis in the greenfin horse-faced filefish Thamnaconus septentrionalis. However, its cumulative effect, toxic molecular mechanism and relevant signal transduction/metabolic networks in marine fishes are largely unknown.

RESULTS: We employed a multi-omics approach to investigate the detrimental effects of 50 mg/L H2O2 exposure (2 h/d) on filefish for 2 d, 4 d, and 6 d. Transcriptome sequencing showed that differentially expressed genes (DEGs) were mainly classified into functions such as signal transduction, nervous system, liver and bile acid metabolism, energy metabolism, cell adhesion and communication, inflammation and immune response. Metabolomic analysis found that the significantly changed metabolites (SCMs) were involved in phenylalanine metabolism, inflammatory mediator regulation, linoleic acid metabolism, and necroptosis. The main SCMs were cholic acid, carnitine C12:1, dimethylmalonic acid, glutamic acid, L-lactic acid, shikimic acid, 2-methylsuccinic acid, and others. Moreover, H2O2-induced oxidative stress also disturbs the balance of the gut microbiota, altering the microbial composition and affecting digestive processes.

CONCLUSIONS: Integrated multiomics analysis revealed that H2O2-induced detrimental impacts include mucosal damage, inflammatory and immune responses, altered energy metabolism, and gut microbiota disorders. These findings offer novel insights into the harmful effects and signal transduction/metabolic pathways triggered by H2O2 exposure in marine fishes.}, } @article {pmid39432055, year = {2025}, author = {Zhao, L and Henriksen, RA and Ramsøe, A and Nielsen, R and Korneliussen, TS}, title = {Revisiting the Briggs Ancient DNA Damage Model: A Fast Maximum Likelihood Method to Estimate Post-Mortem Damage.}, journal = {Molecular ecology resources}, volume = {25}, number = {1}, pages = {e14029}, pmid = {39432055}, issn = {1755-0998}, support = {CF19-0712//Carlsberg Foundation/ ; CF20-0071//Carlsberg Foundation/ ; R302-2018-2155//Lundbeck Foundation/ ; }, mesh = {*DNA, Ancient/analysis ; DNA Damage ; Sequence Analysis, DNA/methods ; Likelihood Functions ; High-Throughput Nucleotide Sequencing/methods ; Computational Biology/methods ; Humans ; }, abstract = {One essential initial step in the analysis of ancient DNA is to authenticate that the DNA sequencing reads are actually from ancient DNA. This is done by assessing if the reads exhibit typical characteristics of post-mortem damage (PMD), including cytosine deamination and nicks. We present a novel statistical method implemented in a fast multithreaded programme, ngsBriggs that enables rapid quantification of PMD by estimation of the Briggs ancient damage model parameters (Briggs parameters). Using a multinomial model with maximum likelihood fit, ngsBriggs accurately estimates the parameters of the Briggs model, quantifying the PMD signal from single and double-stranded DNA regions. We extend the original Briggs model to capture PMD signals for contemporary sequencing platforms and show that ngsBriggs accurately estimates the Briggs parameters across a variety of contamination levels. Classification of reads into ancient or modern reads, for the purpose of decontamination, is significantly more accurate using ngsBriggs than using other methods available. Furthermore, ngsBriggs is substantially faster than other state-of-the-art methods. ngsBriggs offers a practical and accurate method for researchers seeking to authenticate ancient DNA and improve the quality of their data.}, } @article {pmid39430511, year = {2024}, author = {Shamrat, FMJM and Idna Idris, MY and Zhou, X and Khalid, M and Sharmin, S and Sharmin, Z and Ahmed, K and Moni, MA}, title = {PollenNet: A novel architecture for high precision pollen grain classification through deep learning and explainable AI.}, journal = {Heliyon}, volume = {10}, number = {19}, pages = {e38596}, pmid = {39430511}, issn = {2405-8440}, abstract = {Pollen grains play a critical role in environmental, agricultural, and allergy research despite their tiny dimensions. The accurate classification of pollen grains remains a significant challenge, mainly attributable to their intricate structures and the extensive diversity of species. Traditional methods often lack accuracy and effectiveness, prompting the need for advanced solutions. This study introduces a novel deep learning framework, PollenNet, designed to tackle the intricate challenge of pollen grain image classification. The efficiency of PollenNet is thoroughly evaluated through stratified 5-fold cross-validation, comparing it with cutting-edge methods to demonstrate its superior performance. A comprehensive data preparation phase is conducted, including removing duplicates and low-quality images, applying Non-local Means Denoising for noise reduction, and Gamma correction to adjust image brightness. Furthermore, Explainable AI (XAI) is utilized to enhance the interpretability of the model, while Receiver Operating Characteristic (ROC) curve analysis serves as a quantitative method for evaluating the model's capabilities. PollenNet demonstrates superior performance when compared to existing models, with an accuracy of 98.45 %, precision of 98.20 %, specificity of 98.40 %, recall of 98.30 %, and f1-score of 98.25 %. The model also maintains low Mean Squared Error (0.03) and Mean Absolute Error (0.02) rates. The ROC curve analysis, the low False Positive Rate (0.016), and the False Negative Rate (0.017) highlight the reliability and dependability of the model. This study significantly improves the efficacy of classifying pollen grains, indicating an important advancement in the application of deep learning for ecological research.}, } @article {pmid39429633, year = {2024}, author = {Boyes, D and Holland, PWH and , and , and , and , and , and , and , }, title = {The genome sequence of the Hebrew Character, Orthosia gothica (Linnaeus, 1758).}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {90}, pmid = {39429633}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual female Orthosia gothica (the Hebrew character; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 1,065.1 megabases in span. Most of the assembly is scaffolded into 37 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.38 kilobases in length. Gene annotation of this assembly on Ensembl identified 13,691 protein coding genes.}, } @article {pmid39429632, year = {2024}, author = {Li, R and Li, J and Lopez, JV and Oatley, G and Clayton-Lucey, IA and Sinclair, E and Aunin, E and Gettle, N and Santos, C and Paulini, M and Niu, H and McKenna, V and O'Brien, R and , and , and , and , and , }, title = {The genome sequence of the smooth giant clam, Tridacna derasa Röding, 1798.}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {375}, pmid = {39429632}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual Tridacna derasa (the smooth giant clam; Mollusca; Bivalvia;Cardiida; Cardiidae). The genome sequence is 1,060.2 megabases in span. Most of the assembly is scaffolded into 18 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 24.95 kilobases in length. Gene annotation of this assembly on Ensembl identified 19,638 protein coding genes.}, } @article {pmid39424895, year = {2024}, author = {Melo, MS and Lima, SVMA and Dos Santos, AD and Ribeiro, CJN and Júnior, PAB and Silva, TKS and de Resende, LT and Corrêa, F and Migowski, A and Schiffman, M and Rodriguez, AC and Ribeiro, A and Raiol, T}, title = {Temporal trends, spatial and spatiotemporal clusters of cervical cancer mortality in Brazil from 2000 to 2021.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {24436}, pmid = {39424895}, issn = {2045-2322}, support = {Grant number GEREB-Fiocruz/CNPq 440204/2019-4.//Oswaldo Cruz Foundation (Fiocruz) and National Council for Scientific and Technological Development (CNPq)/ ; }, mesh = {Humans ; Female ; Brazil/epidemiology ; *Uterine Cervical Neoplasms/mortality/epidemiology ; Adult ; Middle Aged ; *Spatio-Temporal Analysis ; Aged ; Young Adult ; Adolescent ; Mortality/trends ; }, abstract = {Cervical cancer, despite being preventable through primary and secondary prevention strategies, remains one of the leading causes of morbidity and mortality among women in Brazil. This study aimed to analyze the temporal, spatial, and space-time patterns of cervical cancer mortality in Brazil. An ecological study was conducted using temporal, spatial, and space-time analysis techniques, using death certificates with cervical cancer as the underlying cause or associated condition among females in Brazil from 2000 to 2021. Death certificate and population data were provided by the Department of Health Informatics of the Unified Health System (DATASUS) and the Brazilian Institute of Geography and Statistics (IBGE), respectively. A total of 123,306 deaths associated with cervical cancer among women were registered during the study period. A rising trend in mortality was detected since 2014 onwards, after 14 years of decline. Particularly, an increase in mortality was observed among the younger age groups, and in the North and Northeast regions regardless of age. Heterogeneity in the spatial distribution of cervical cancer mortality was observed, with high mortality clusters around the country, but mostly concentrated in the North and Northeast regions. These findings suggest a need and an opportunity to develop efficient and effective health policies targeting those regions and groups of women at higher risk which in turn will allow for fast and significant reductions in cervical cancer mortality in Brazil.}, } @article {pmid39421415, year = {2024}, author = {Ion, MC and Bloomer, CC and Bărăscu, TI and Oficialdegui, FJ and Shoobs, NF and Williams, BW and Scheers, K and Clavero, M and Grandjean, F and Collas, M and Baudry, T and Loughman, Z and Wright, JJ and Ruokonen, TJ and Chucholl, C and Guareschi, S and Koese, B and Banyai, ZM and Hodson, J and Hurt, M and Kaldre, K and Lipták, B and Fetzner, JW and Cancellario, T and Weiperth, A and Birzaks, J and Trichkova, T and Todorov, M and Balalaikins, M and Griffin, B and Petko, ON and Acevedo-Alonso, A and D'Elía, G and Śliwińska, K and Alekhnovich, A and Choong, H and South, J and Whiterod, N and Zorić, K and Haase, P and Soto, I and Brady, DJ and Haubrock, PJ and Torres, PJ and Şadrin, D and Vlach, P and Kaya, C and Woo Jung, S and Kim, JY and Vermeersch, XHC and Bonk, M and Guiaşu, R and Harlioğlu, MM and Devlin, J and Kurtul, I and Błońska, D and Boets, P and Masigol, H and Cabe, PR and Jussila, J and Vrålstad, T and Beresford, DV and Reid, SM and Patoka, J and Strand, DA and Tarkan, AS and Steen, F and Abeel, T and Harwood, M and Auer, S and Kelly, S and Giantsis, IA and Maciaszek, R and Alvanou, MV and Aksu, Ö and Hayes, DM and Kawai, T and Tricarico, E and Chakandinakira, A and Barnett, ZC and Kudor, ŞG and Beda, AE and Vîlcea, L and Mizeranschi, AE and Neagul, M and Licz, A and Cotoarbă, AD and Petrusek, A and Kouba, A and Taylor, CA and Pârvulescu, L}, title = {World of Crayfish™: a web platform towards real-time global mapping of freshwater crayfish and their pathogens.}, journal = {PeerJ}, volume = {12}, number = {}, pages = {e18229}, pmid = {39421415}, issn = {2167-8359}, mesh = {Animals ; *Astacoidea/microbiology ; *Fresh Water ; Aphanomyces ; Internet ; Ecosystem ; Databases, Factual ; }, abstract = {Freshwater crayfish are amongst the largest macroinvertebrates and play a keystone role in the ecosystems they occupy. Understanding the global distribution of these animals is often hindered due to a paucity of distributional data. Additionally, non-native crayfish introductions are becoming more frequent, which can cause severe environmental and economic impacts. Management decisions related to crayfish and their habitats require accurate, up-to-date distribution data and mapping tools. Such data are currently patchily distributed with limited accessibility and are rarely up-to-date. To address these challenges, we developed a versatile e-portal to host distributional data of freshwater crayfish and their pathogens (using Aphanomyces astaci, the causative agent of the crayfish plague, as the most prominent example). Populated with expert data and operating in near real-time, World of Crayfish™ is a living, publicly available database providing worldwide distributional data sourced by experts in the field. The database offers open access to the data through specialized standard geospatial services (Web Map Service, Web Feature Service) enabling users to view, embed, and download customizable outputs for various applications. The platform is designed to support technical enhancements in the future, with the potential to eventually incorporate various additional features. This tool serves as a step forward towards a modern era of conservation planning and management of freshwater biodiversity.}, } @article {pmid39420601, year = {2024}, author = {Li, Z and Zhang, Y and Peng, B and Qin, S and Zhang, Q and Chen, Y and Chen, C and Bao, Y and Zhu, Y and Hong, Y and Liu, B and Liu, Q and Xu, L and Chen, X and Ma, X and Wang, H and Xie, L and Yao, Y and Deng, B and Li, J and De, B and Chen, Y and Wang, J and Li, T and Liu, R and Tang, Z and Cao, J and Zuo, E and Mei, C and Zhu, F and Shao, C and Wang, G and Sun, T and Wang, N and Liu, G and Ni, JQ and Liu, Y}, title = {A novel interpretable deep learning-based computational framework designed synthetic enhancers with broad cross-species activity.}, journal = {Nucleic acids research}, volume = {52}, number = {21}, pages = {13447-13468}, pmid = {39420601}, issn = {1362-4962}, support = {2021YFF1200500//China National Key R&D Program/ ; 32070595//National Natural Science Foundation of China/ ; 20221250020//Ministry of Science and Technology/ ; 20181300988//National Natural Science Foundation of China/ ; }, mesh = {*Enhancer Elements, Genetic ; Animals ; *Deep Learning ; Drosophila melanogaster/genetics ; Drosophila/genetics ; Humans ; Computational Biology/methods ; Gene Expression Regulation ; }, abstract = {Enhancers play a critical role in dynamically regulating spatial-temporal gene expression and establishing cell identity, underscoring the significance of designing them with specific properties for applications in biosynthetic engineering and gene therapy. Despite numerous high-throughput methods facilitating genome-wide enhancer identification, deciphering the sequence determinants of their activity remains challenging. Here, we present the DREAM (DNA cis-Regulatory Elements with controllable Activity design platforM) framework, a novel deep learning-based approach for synthetic enhancer design. Proficient in uncovering subtle and intricate patterns within extensive enhancer screening data, DREAM achieves cutting-edge sequence-based enhancer activity prediction and highlights critical sequence features implicating strong enhancer activity. Leveraging DREAM, we have engineered enhancers that surpass the potency of the strongest enhancer within the Drosophila genome by approximately 3.6-fold. Remarkably, these synthetic enhancers exhibited conserved functionality across species that have diverged more than billion years, indicating that DREAM was able to learn highly conserved enhancer regulatory grammar. Additionally, we designed silencers and cell line-specific enhancers using DREAM, demonstrating its versatility. Overall, our study not only introduces an interpretable approach for enhancer design but also lays out a general framework applicable to the design of other types of cis-regulatory elements.}, } @article {pmid39419226, year = {2024}, author = {Liu, J and Zhu, M and Shi, X and Hui, C and Sun, Y and Zhang, R and Jin, D and Li, Z and Chen, H and Zhao, Z}, title = {Cascading impacts of nitrogen deposition on soil microbiome and herbivore communities in desert steppes.}, journal = {The Science of the total environment}, volume = {955}, number = {}, pages = {176892}, doi = {10.1016/j.scitotenv.2024.176892}, pmid = {39419226}, issn = {1879-1026}, mesh = {*Nitrogen ; *Soil Microbiology ; *Microbiota/drug effects ; *Herbivory ; Animals ; *Insecta/physiology ; Desert Climate ; Soil/chemistry ; Biodiversity ; Grassland ; Ecosystem ; China ; }, abstract = {Human activities in the last century have intensified global nitrogen deposition, resulting in the degradation of ecosystem function and loss of biodiversity worldwide. Nitrogen addition is a crucial method for examining the effects of atmospheric nitrogen deposition on species composition and structure of soil microbiome and biotic community, as exogenous nitrogen inputs can trigger cascading effects on ecosystem functions. In a 6-year experiment, we evaluated the impact of nitrogen addition on soil microbial-plant-insect systems in desert steppes. Our results show that nitrogen addition significantly altered soil microbial composition and ecological function, leading to a decrease in nitrogen-fixing bacteria and an increase in saprophytic fungi. High levels of nitrogen addition increased total plant biomass while decreasing species diversity. Additionally, high nitrogen addition levels suppressed below-ground biomass of gramineae and legumes compared to low nitrogen addition. Nitrogen addition also increased herbivore abundance by altering insect community structure, particularly benefiting chewing pests over sucking pests, thus heightening the risk of biological disasters through trophic cascading effects. Consequently, excessive nitrogen addition may destabilize desert steppe ecosystems by disturbing soil microbial-plant-insect interactions, hindering the maintenance of biotic community diversity and steppe productivity.}, } @article {pmid39417898, year = {2024}, author = {Khalaf, SMH and Alqahtani, MSM and Ali, MRM and Abdelalim, ITI and Hodhod, MS}, title = {Modeling climate-related global risk maps of rice bacterial blight caused by Xanthomonas oryzae (Ishiyama 1922) using geographical information system (GIS).}, journal = {Environmental monitoring and assessment}, volume = {196}, number = {11}, pages = {1064}, pmid = {39417898}, issn = {1573-2959}, mesh = {*Xanthomonas ; *Oryza/microbiology ; *Climate Change ; *Plant Diseases/microbiology/statistics & numerical data ; *Geographic Information Systems ; Environmental Monitoring ; Climate ; }, abstract = {Rice is a critical staple crop that feeds more than half of the world's population. Still, its production confronts various biotic risks, notably the severe bacterial blight disease produced by Xanthomonas oryzae. Understanding the possible effects of climate change on the geographic distribution of this virus is critical to ensuring food security. This work used ecological niche modeling and the Maxent algorithm to create future risk maps for the range of X. oryzae under several climate change scenarios between 2050 and 2070. The model was trained using 93 occurrence records of X. oryzae and five critical bioclimatic variables. It has an excellent predictive performance, with an AUC of 0.889. The results show that X. oryzae's potential geographic range and habitat suitability are expected to increase significantly under low (RCP2.6) and high (RCP8.5) emission scenarios. Key climatic drivers allowing this development include increased yearly precipitation, precipitation during the wettest quarter, and the wettest quarter's mean temperature. These findings are consistent with broader research revealing that climate change is allowing many plant diseases and other dangerous microbes to spread across the globe. Integrating these spatial predictions with data on host susceptibility, agricultural practices, and socioeconomic vulnerabilities can help to improve targeted surveillance, preventative, and management methods for reducing the growing threat of bacterial blight to rice production. Proactive, multidisciplinary efforts to manage the changing disease dynamics caused by climate change will be critical to assuring global food security in the future decades.}, } @article {pmid39417330, year = {2024}, author = {Kershenbaum, A and Akçay, Ç and Babu-Saheer, L and Barnhill, A and Best, P and Cauzinille, J and Clink, D and Dassow, A and Dufourq, E and Growcott, J and Markham, A and Marti-Domken, B and Marxer, R and Muir, J and Reynolds, S and Root-Gutteridge, H and Sadhukhan, S and Schindler, L and Smith, BR and Stowell, D and Wascher, CAF and Dunn, JC}, title = {Automatic detection for bioacoustic research: a practical guide from and for biologists and computer scientists.}, journal = {Biological reviews of the Cambridge Philosophical Society}, volume = {}, number = {}, pages = {}, doi = {10.1111/brv.13155}, pmid = {39417330}, issn = {1469-185X}, support = {//A*MIDEX/ ; //Cambridge Centre for Data-Driven Discovery/ ; //African Institute for Mathematical Sciences/ ; NE/W005468/1//Natural Environment Research Council/ ; //Global Affairs Canada/ ; ANR-20-CE23-0012-01 MIM//Agence Nationale de la Recherche/ ; ANR-20-CHIA-0014//Agence Nationale de la Recherche/ ; ANR-16-CONV-0002//Institute of Convergence ILCB/ ; //International Development Research Centre/ ; }, abstract = {Recent years have seen a dramatic rise in the use of passive acoustic monitoring (PAM) for biological and ecological applications, and a corresponding increase in the volume of data generated. However, data sets are often becoming so sizable that analysing them manually is increasingly burdensome and unrealistic. Fortunately, we have also seen a corresponding rise in computing power and the capability of machine learning algorithms, which offer the possibility of performing some of the analysis required for PAM automatically. Nonetheless, the field of automatic detection of acoustic events is still in its infancy in biology and ecology. In this review, we examine the trends in bioacoustic PAM applications, and their implications for the burgeoning amount of data that needs to be analysed. We explore the different methods of machine learning and other tools for scanning, analysing, and extracting acoustic events automatically from large volumes of recordings. We then provide a step-by-step practical guide for using automatic detection in bioacoustics. One of the biggest challenges for the greater use of automatic detection in bioacoustics is that there is often a gulf in expertise between the biological sciences and the field of machine learning and computer science. Therefore, this review first presents an overview of the requirements for automatic detection in bioacoustics, intended to familiarise those from a computer science background with the needs of the bioacoustics community, followed by an introduction to the key elements of machine learning and artificial intelligence that a biologist needs to understand to incorporate automatic detection into their research. We then provide a practical guide to building an automatic detection pipeline for bioacoustic data, and conclude with a discussion of possible future directions in this field.}, } @article {pmid39415784, year = {2024}, author = {Lohse, K and Vila, R and Hayward, A and Laetsch, DR and Harnqvist, S and , and , and , and , and , }, title = {The genome sequence of the Essex Skipper butterfly, Thymelicus lineola (Ochsenheimer, 1808).}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {452}, pmid = {39415784}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual female Essex Skipper butterfly, Thymelicus lineola (Arthropoda; Insecta; Lepidoptera; Hesperiidae). The genome sequence spans 511.80 megabases. Most of the assembly is scaffolded into 30 chromosomal pseudomolecules, including the Z and W sex chromosomes. The mitochondrial genome has also been assembled and is 17.24 kilobases in length.}, } @article {pmid39414803, year = {2024}, author = {Lončarević, N and Liu, U and Stefanaki, A and Carapeto, A and Ensslin, A and Meade, C and Metzing, D and Peci, D and Fantinato, E and Colling, G and Pankova, H and Akmane, I and Tsvetkov, IN and Sibik, J and Szitár, K and Van Meerbeek, K and Daco, L and Boudagher, M and Klisz, M and Walczak, M and Evju, M and Lužnik, M and Kiehn, M and Sarginci, M and Aksoy, N and Koçer, N and Barazani, O and Anastasiu, P and Stroh, P and Vit, P and Vergeer, P and Puchałka, R and Kahale, R and Godefroid, S and Lanfranco, S and Parpan, T and Kull, T and Rašomavičius, V and Fišer, Ž and Glasnović, P}, title = {Database of European vascular plants red lists as a contribution to more coherent plant conservation.}, journal = {Scientific data}, volume = {11}, number = {1}, pages = {1138}, pmid = {39414803}, issn = {2052-4463}, support = {R25 CA018201/CA/NCI NIH HHS/United States ; CA18201//European Cooperation in Science and Technology (COST)/ ; }, mesh = {Europe ; *Databases, Factual ; *Conservation of Natural Resources ; *Plants/classification ; Biodiversity ; }, abstract = {We introduce the database of European vascular plant red lists, a compilation of red list categories designated to taxa during in-country conservation assessments. Version 1.0 of the database is a standalone static dataset with open access in an end-user friendly format. Its aim is to fulfil the objectives of European Cooperation in Science and Technology (COST) Action 18201, ConservePlants. The database synthesizes data across 42 red lists from 41 countries, with participation of 39 out of a total of 44 European countries and two additional Mediterranean countries. The database contains 51,109 records representing 21,481 original taxonomic names with 37 different red list categories. During data harmonisation, 20,312 of the original taxonomic names were assigned to 17,873 unique accepted taxonomic names with scientific authorships across 184 families, 1650 genera and 15,593 species; and red list categories were standardised to 13 unique categories. We see this database as a source of information in diverse plant conservation activities and suitable for various stakeholders.}, } @article {pmid39409485, year = {2024}, author = {Jechow, A and Bumberger, J and Palm, B and Remmler, P and Schreck, G and Ogashawara, I and Kiel, C and Kohnert, K and Grossart, HP and Singer, GA and Nejstgaard, JC and Wollrab, S and Berger, SA and Hölker, F}, title = {Characterizing and Implementing the Hamamatsu C12880MA Mini-Spectrometer for Near-Surface Reflectance Measurements of Inland Waters.}, journal = {Sensors (Basel, Switzerland)}, volume = {24}, number = {19}, pages = {}, pmid = {39409485}, issn = {1424-8220}, support = {Leibniz Competition No. K45/2017 (CONNECT-Connectivity and synchronization of lake ecosystems in space and time)//Leibniz Association/ ; IGB Frontiers project (2017)//Leibniz Institute of Freshwater Ecology and Inland Fisheries/ ; }, abstract = {In recent decades, inland water remote sensing has seen growing interest and very strong development. This includes improved spatial resolution, increased revisiting times, advanced multispectral sensors and recently even hyperspectral sensors. However, inland waters are more challenging than oceanic waters due to their higher complexity of optically active constituents and stronger adjacency effects due to their small size and nearby vegetation and built structures. Thus, bio-optical modeling of inland waters requires higher ground-truthing efforts. Large-scale ground-based sensor networks that are robust, self-sufficient, non-maintenance-intensive and low-cost could assist this otherwise labor-intensive task. Furthermore, most existing sensor systems are rather expensive, precluding their employability. Recently, low-cost mini-spectrometers have become widely available, which could potentially solve this issue. In this study, we analyze the characteristics of such a mini-spectrometer, the Hamamatsu C12880MA, and test it regarding its application in measuring water-leaving radiance near the surface. Overall, the measurements performed in the laboratory and in the field show that the system is very suitable for the targeted application.}, } @article {pmid39407030, year = {2024}, author = {Mc Cartney, AM and Formenti, G and Mouton, A and De Panis, D and Marins, LS and Leitão, HG and Diedericks, G and Kirangwa, J and Morselli, M and Salces-Ortiz, J and Escudero, N and Iannucci, A and Natali, C and Svardal, H and Fernández, R and De Pooter, T and Joris, G and Strazisar, M and Wood, JMD and Herron, KE and Seehausen, O and Watts, PC and Shaw, F and Davey, RP and Minotto, A and Fernández, JM and Böhne, A and Alegria, C and Alioto, T and Alves, PC and Amorim, IR and Aury, JM and Backstrom, N and Baldrian, P and Baltrunaite, L and Barta, E and BedHom, B and Belser, C and Bergsten, J and Bertrand, L and Bilandija, H and Binzer-Panchal, M and Bista, I and Blaxter, M and Borges, PAV and Dias, GB and Bosse, M and Brown, T and Bruggmann, R and Buena-Atienza, E and Burgin, J and Buzan, E and Cariani, A and Casadei, N and Chiara, M and Chozas, S and Čiampor, F and Crottini, A and Cruaud, C and Cruz, F and Dalen, L and De Biase, A and Del Campo, J and Delic, T and Dennis, AB and Derks, MFL and Diroma, MA and Djan, M and Duprat, S and Eleftheriadi, K and Feulner, PGD and Flot, JF and Forni, G and Fosso, B and Fournier, P and Fournier-Chambrillon, C and Gabaldon, T and Garg, S and Gissi, C and Giupponi, L and Gomez-Garrido, J and González, J and Grilo, ML and Grüning, B and Guerin, T and Guiglielmoni, N and Gut, M and Haesler, MP and Hahn, C and Halpern, B and Harrison, PW and Heintz, J and Hindrikson, M and Höglund, J and Howe, K and Hughes, GM and Istace, B and Cock, MJ and Janžekovič, F and Jonsson, ZO and Joye-Dind, S and Koskimäki, JJ and Krystufek, B and Kubacka, J and Kuhl, H and Kusza, S and Labadie, K and Lähteenaro, M and Lantz, H and Lavrinienko, A and Leclère, L and Lopes, RJ and Madsen, O and Magdelenat, G and Magoga, G and Manousaki, T and Mappes, T and Marques, JP and Redondo, GIM and Maumus, F and McCarthy, SA and Megens, HJ and Melo-Ferreira, J and Mendes, SL and Montagna, M and Moreno, J and Mosbech, MB and Moura, M and Musilova, Z and Myers, E and Nash, WJ and Nater, A and Nicholson, P and Niell, M and Nijland, R and Noel, B and Noren, K and Oliveira, PH and Olsen, RA and Ometto, L and Oomen, RA and Ossowski, S and Palinauskas, V and Palsson, S and Panibe, JP and Pauperio, J and Pavlek, M and Payen, E and Pawlowska, J and Pellicer, J and Pesole, G and Pimenta, J and Pippel, M and Pirttilä, AM and Poulakakis, N and Rajan, J and M C Rego, R and Resendes, R and Resl, P and Riesgo, A and Rodin-Morch, P and Soares, AER and Fernandes, CR and Romeiras, MM and Roxo, G and Rüber, L and Ruiz-Lopez, MJ and Saarma, U and da Silva, LP and Sim-Sim, M and Soler, L and Sousa, VC and Santos, CS and Spada, A and Stefanovic, M and Steger, V and Stiller, J and Stöck, M and Struck, TH and Sudasinghe, H and Tapanainen, R and Tellgren-Roth, C and Trindade, H and Tukalenko, Y and Urso, I and Vacherie, B and Van Belleghem, SM and Van Oers, K and Vargas-Chavez, C and Velickovic, N and Vella, N and Vella, A and Vernesi, C and Vicente, S and Villa, S and Pettersson, OV and Volckaert, FAM and Voros, J and Wincker, P and Winkler, S and Ciofi, C and Waterhouse, RM and Mazzoni, CJ}, title = {Author Correction: The European Reference Genome Atlas: piloting a decentralised approach to equitable biodiversity genomics.}, journal = {npj biodiversity}, volume = {3}, number = {1}, pages = {31}, doi = {10.1038/s44185-024-00065-3}, pmid = {39407030}, issn = {2731-4243}, } @article {pmid39404811, year = {2024}, author = {Litavský, J and Majzlan, O and Langraf, V and Žarnovičan, H}, title = {Influence of habitat management and selected environmental parameters on the ground-living communities of harvestmen (Opiliones) in the historical park in Rusovce (Slovakia).}, journal = {Environmental monitoring and assessment}, volume = {196}, number = {11}, pages = {1056}, pmid = {39404811}, issn = {1573-2959}, support = {No. 1/0007/21//Slovak Grant Agency of the Ministry of Education, Science, Research and Sport of the Slovak Republic/ ; No. 1/0007/21//Slovak Grant Agency of the Ministry of Education, Science, Research and Sport of the Slovak Republic/ ; No. 1/0255/23//Slovak Grant Agency of the Ministry of Education, Science, Research and Sport of the Slovak Republic/ ; }, mesh = {*Ecosystem ; *Parks, Recreational ; *Environmental Monitoring ; Animals ; Slovakia ; Biodiversity ; Arachnida ; Conservation of Natural Resources/methods ; Forests ; Microclimate ; }, abstract = {City parks serve as valuable refuges for invertebrates in the urban environment, which are constantly exposed to human influence caused by management practices in the parks. Many harvestman species are suitable bioindicators for monitoring ecological change; however, their effective use in environmental assessment necessitates to expand the insufficient knowledge of ecological environmental specificities of their communities. We studied the diversity and dynamics of harvestman (Opiliones) communities in the historical park in Rusovce, situated in the southwestern part of Bratislava (Slovakia). Seven study sites were investigated, representing areas subjected to different management practices. The research was conducted from March 2019 to April 2020, using pitfall traps. We evaluated the impact of microclimatic variables (soil and air temperature), environmental characteristics (plant diversity and cover of vegetation layers, age of forest stands, thickness of the litter layer), and management practices on the structure of harvestman communities. The study revealed the response of specific harvestman species to temperature variations, emphasizing the importance of microclimatic conditions. Environmental variables, such as the richness of plant species in the shrub layer, the cover of the herb and shrub vegetation layers, and the age of the forest stands, were identified as key factors that influence the dispersal of harvestman species. Furthermore, management practices, especially the presence of monoculture tree plantations, significantly affected the species composition of harvestmen. Examining the sensitivity of Opiliones, important bioindicators, to these factors is crucial for implementing effective conservation strategies in urban green spaces and anthropogenically influenced ecosystems.}, } @article {pmid39403498, year = {2024}, author = {Hung, RJ and Low, I and Yeh, HC and Wang, PY and Chen, YS and Chen, LF}, title = {Feedback matters: EEG correlates of empathy involved in the naturalistic communication of emotions.}, journal = {Heliyon}, volume = {10}, number = {19}, pages = {e38574}, pmid = {39403498}, issn = {2405-8440}, abstract = {Empathy involves the processing of complex information related to dynamic interactions between the empathizer and target. One neural signature of empathy is the suppression of electroencephalographic mu rhythm (8-13 Hz) over the sensorimotor region. It is important to consider that few researchers have studied the effects of empathizer feedback on empathy and its underlying neural mechanism, and most previous research has lacked ecological validity due to standardized emotional stimuli and constraints on the experiment environment. Our objective in this study was to investigate the means by which empathizer feedback influences one's own empathy in naturalistic social situations. Our results revealed that empathizer feedback decreases empathic accuracy but does not affect the emotional contagion nor the emotional intensity of the empathizer. We also found that the ability to accurately infer sadness is hindered by empathizer feedback. Empathizers presented lower alpha activity in the sensorimotor cortical areas only while receiving sad narratives and not providing feedback. This study contributes to the emerging research on the influence of empathizer feedback in naturalistic social settings.}, } @article {pmid39403309, year = {2024}, author = {Sivell, O and Sivell, D and Webb, JA and Mitchell, R and Ashworth, M and , and , and , and , and , and , and , }, title = {The genome sequence of the acalyptrate fly Dryomyza anilis Fallén, 1820.}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {440}, pmid = {39403309}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual male acalyptrate fly Dryomyza anilis (Arthropoda; Insecta; Diptera; Dryomyzidae). The genome sequence has a total length of 656.60 megabases. Most of the assembly is scaffolded into 7 chromosomal pseudomolecules, including the X and Y sex chromosomes. The mitochondrial genome has also been assembled and is 16.48 kilobases in length.}, } @article {pmid39401552, year = {2024}, author = {Yan, X and Zhao, Z and Feng, S and Zhang, Y and Wang, Z and Li, Z}, title = {Multi-omics analysis reveal the fall armyworm Spodoptera frugiperda tolerate high temperature by mediating chitin-related genes.}, journal = {Insect biochemistry and molecular biology}, volume = {174}, number = {}, pages = {104192}, doi = {10.1016/j.ibmb.2024.104192}, pmid = {39401552}, issn = {1879-0240}, mesh = {Animals ; *Spodoptera/genetics/growth & development/metabolism/physiology ; *Chitin/metabolism ; Hot Temperature ; Larva/genetics/growth & development/metabolism ; CRISPR-Cas Systems ; Insect Proteins/metabolism/genetics ; Thermotolerance ; Transcriptome ; RNA Interference ; Multiomics ; }, abstract = {Climate change facilitates the rapid invasion of agricultural pests, threatening global food security. The fall armyworm Spodoptera frugiperda is a highly polyphagous migratory pest tolerant to high temperatures, allowing its proliferation in harsh thermal environments. We aimed to demonstrate mechanisms of its high-temperature tolerance, particularly transcriptional and metabolic regulation, which are poorly understood. To achieve the aim, we examined the impact and mechanism of heat events on S. frugiperda by using multiple approaches: ecological measurements, transcriptomics, metabolomics, RNAi, and CRISPR/Cas9 technology. We observed that several physiological indices (larval survival rate, larval period, pupation rate, pupal weight, eclosion rate, and average fecundity) decreased as the temperature increased, with the 32 °C treatment displaying a significant difference from the control group at 26 °C. Significantly upregulated expression of genes encoding endochitinase and chitin deacetylase was observed in the chitin-binding, extracellular region, and carbohydrate metabolic process GO terms of hemolymph, fat body, and brain, exhibiting a tissue-specific pattern. Significantly enriched pathways (e.g., cutin, suberin, and wax biosynthesis; oxidative phosphorylation and cofactor biosynthesis; diverse amino acid biosynthesis and degradation; carbon metabolism; and energy metabolism), all of which are essential for S. frugiperda larvae to tolerate temperature, were found in metabolites that were expressed differently. Successful RNA interference targeting of the three chitin-related genes reduced gene expression levels and larval survival rate. Knockout of the endochitinase gene by using the CRISPR/Cas9 system significantly reduced the relative gene expression and increased sensitivity to high-temperature exposure. On the basis of our findings, theoretical foundations for understanding the high-temperature tolerance of S. frugiperda populations and latent genetic control strategies were established.}, } @article {pmid39401366, year = {2024}, author = {Posch, BC and Bush, SE and Koepke, DF and Schuessler, A and Anderegg, LLD and Aparecido, LMT and Blonder, BW and Guo, JS and Kerr, KL and Moran, ME and Cooper, HF and Doughty, CE and Gehring, CA and Whitham, TG and Allan, GJ and Hultine, KR}, title = {Intensive leaf cooling promotes tree survival during a record heatwave.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {121}, number = {43}, pages = {e2408583121}, pmid = {39401366}, issn = {1091-6490}, support = {IOS-2140427//NSF (NSF)/ ; IOS-2140428//NSF (NSF)/ ; IOS-2140429//NSF (NSF)/ ; IOS-2003205//NSF (NSF)/ ; IOS-2216855//NSF (NSF)/ ; DEB-1340852//NSF (NSF)/ ; DEB-1340856//NSF (NSF)/ ; DEB-2017895//NSF (NSF)/ ; }, mesh = {*Plant Leaves/physiology ; *Populus/physiology/genetics ; *Trees/physiology/genetics ; *Water ; Soil ; Genotype ; Extreme Heat ; Hot Temperature ; Ecosystem ; }, abstract = {Increasing heatwaves are threatening forest ecosystems globally. Leaf thermal regulation and tolerance are important for plant survival during heatwaves, though the interaction between these processes and water availability is unclear. Genotypes of the widely distributed foundation tree species Populus fremontii were studied in a controlled common garden during a record summer heatwave-where air temperature exceeded 48 °C. When water was not limiting, all genotypes cooled leaves 2 to 5 °C below air temperatures. Homeothermic cooling was disrupted for weeks following a 72-h reduction in soil water, resulting in leaf temperatures rising 3 °C above air temperature and 1.3 °C above leaf thresholds for physiological damage, despite the water stress having little effect on leaf water potentials. Tradeoffs between leaf thermal safety and hydraulic safety emerged but, regardless of water use strategy, all genotypes experienced significant leaf mortality following water stress. Genotypes from warmer climates showed greater leaf cooling and less leaf mortality after water stress in comparison with genotypes from cooler climates. These results illustrate how brief soil water limitation disrupts leaf thermal regulation and potentially compromises plant survival during extreme heatwaves, thus providing insight into future scenarios in which ecosystems will be challenged with extreme heat and unreliable soil water access.}, } @article {pmid39399683, year = {2024}, author = {Martin, C and Gitter, A and Anantharaman, K}, title = {Protein Set Transformer: A protein-based genome language model to power high diversity viromics.}, journal = {Research square}, volume = {}, number = {}, pages = {}, pmid = {39399683}, issn = {2693-5015}, support = {R35 GM143024/GM/NIGMS NIH HHS/United States ; }, abstract = {Exponential increases in microbial and viral genomic data demand transformational advances in scalable, generalizable frameworks for their interpretation. Standard homology-based functional analyses are hindered by the rapid divergence of microbial and especially viral genomes and proteins that significantly decreases the volume of usable data. Here, we present Protein Set Transformer (PST), a protein-based genome language model that models genomes as sets of proteins without considering sparsely available functional labels. Trained on >100k viruses, PST outperformed other homology- and language model-based approaches for relating viral genomes based on shared protein content. Further, PST demonstrated protein structural and functional awareness by clustering capsid-fold-containing proteins with known capsid proteins and uniquely clustering late gene proteins within related viruses. Our data establish PST as a valuable method for diverse viral genomics, ecology, and evolutionary applications. We posit that the PST framework can be a foundation model for microbial genomics when trained on suitable data.}, } @article {pmid39399250, year = {2024}, author = {Arliyani, I and Noori, MT and Ammarullah, MI and Tangahu, BV and Mangkoedihardjo, S and Min, B}, title = {Constructed wetlands combined with microbial fuel cells (CW-MFCs) as a sustainable technology for leachate treatment and power generation.}, journal = {RSC advances}, volume = {14}, number = {44}, pages = {32073-32100}, pmid = {39399250}, issn = {2046-2069}, abstract = {The physical and chemical treatment processes of leachate are not only costly but can also possibly produce harmful by products. Constructed wetlands (CW) has been considered a promising alternative technology for leachate treatment due to less demand for energy, economic, ecological benefits, and simplicity of operations. Various trends and approaches for the application of CW for leachate treatment have been discussed in this review along with offering an informatics peek of the recent innovative developments in CW technology and its perspectives. In addition, coupling CW with microbial fuel cells (MFCs) has proven to produce renewable energy (electricity) while treating contaminants in leachate wastewaters (CW-MFC). The combination of CW-MFC is a promising bio electrochemical that plays symbiotic among plant microorganisms in the rhizosphere of an aquatic plant that convert sun electricity is transformed into bioelectricity with the aid of using the formation of radical secretions, as endogenous substrates, and microbial activity. Several researchers study and try to find out the application of CW-MFC for leachate treatment, along with this system and performance. Several key elements for the advancement of CW-MFC technology such as bioelectricity, reactor configurations, plant species, and electrode materials, has been comprehensively discussed and future research directions were suggested for further improving the performance. Overall, CW-MFC may offer an eco-friendly approach to protecting the aquatic environment and come with built-in advantages for visual appeal and animal habitats using natural materials such as gravel, soil, electroactive bacteria, and plants under controlled condition.}, } @article {pmid39398940, year = {2024}, author = {Boyes, D and Hutchinson, F and Crowley, LM and Holland, PWH and , and , and , and , and , and , and , }, title = {The genome sequence of the Common Flat-body moth, Agonopterix heracliana Linnaeus, 1758.}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {329}, pmid = {39398940}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual male Agonopterix heracliana (the Common Flat-body; Arthropoda; Insecta; Lepidoptera; Depressariidae). The genome sequence is 539.1 megabases in span. Most of the assembly is scaffolded into 30 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.36 kilobases in length.}, } @article {pmid39398938, year = {2024}, author = {Li, R and Li, J and Lemer, S and Lopez, JV and Oatley, G and Sinclair, E and Clayton-Lucey, IA and Aunin, E and Gettle, N and Santos, C and Paulini, M and Niu, H and McKenna, V and O'Brien, R and , and , and , and , and , }, title = {The genome sequence of the heart cockle, Fragum sueziense (Issel, 1869).}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {366}, pmid = {39398938}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual Fragum sueziense (the heart cockle; Mollusca; Bivalvia; Cardiida; Cardiidae). The genome sequence is 1,206.1 megabases in span. Most of the assembly is scaffolded into 19 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 92.77 kilobases in length. Gene annotation of this assembly on Ensembl identified 70,309 protein-coding genes.}, } @article {pmid39398937, year = {2024}, author = {Boyes, D and Crowley, LM and Morley, LM and , and , and , and , and , and , and , }, title = {The genome sequence of the Green Oak Leaf Roller, Tortrix viridana (Linnaeus, 1758).}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {260}, pmid = {39398937}, issn = {2398-502X}, abstract = {We present a genome assembly from a female Tortrix viridana (the Green Oak Leaf Roller; Arthropoda; Insecta; Lepidoptera; Tortricidae). The genome sequence is 456.6 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z and W sex chromosomes. The mitochondrial genome has also been assembled and is 16.43 kilobases in length.}, } @article {pmid39396151, year = {2025}, author = {Burger, J and Gochfeld, M and Brown, KG and Cortes, M and Ng, K and Kosson, D}, title = {Using the National Land Cover Database as an indicator of shrub-steppe habitat: comparing two large United States federal lands with surrounding regions.}, journal = {Journal of toxicology and environmental health. Part A}, volume = {88}, number = {1}, pages = {1-19}, doi = {10.1080/15287394.2024.2412659}, pmid = {39396151}, issn = {1528-7394}, mesh = {*Ecosystem ; *Conservation of Natural Resources ; Idaho ; Washington ; Databases, Factual ; United States ; Grassland ; Environmental Monitoring/methods ; }, abstract = {There is a need to assess whether ecological resources are being protected on large, federal lands. The aim of this study was to present a methodology which consistently and transparently determines whether two large Department of Energy (U.S. DOE) facilities have protected valuable ecological lands on their sites compared to the surrounding region. The National Land Cover Database (2019) was used to examine the % shrub-scrub (shrub-steppe) and other habitats on the DOE's Hanford Site (HS, Washington) and on the Idaho National Laboratory (INL), compared to a 10-km and 30-km diameter band of land surrounding each site. On both sites, over 95% is in shrub-scrub or grassland, compared to the surrounding region. Approximately 70% of 10 km and 30-km bands around INL, and less than 50% of land surrounding HS is located in these two habitat types. INL has preserved a significantly higher % shrub/scrub habitat than HS, but INL allows grazing on 60% of its land. HS has preserved a significantly higher % grassland than INL but no grazing on site is present. The methodology presented may be used to compare key ecological habitat types such as grasslands, forest, and desert among sites in different parts of the country. This methodology enables managers, resource trustees, and the public to (1) make remediation decisions that protect resources, (2) assess whether landowners and managers have adequately characterized and protected environmental resources on their sites, and (3) whether landowners and managers have protected the integrity of that land as well as its climax vegetation.}, } @article {pmid39395210, year = {2025}, author = {Pachade, S and Porwal, P and Kokare, M and Deshmukh, G and Sahasrabuddhe, V and Luo, Z and Han, F and Sun, Z and Qihan, L and Kamata, SI and Ho, E and Wang, E and Sivajohan, A and Youn, S and Lane, K and Chun, J and Wang, X and Gu, Y and Lu, S and Oh, YT and Park, H and Lee, CY and Yeh, H and Cheng, KW and Wang, H and Ye, J and He, J and Gu, L and Müller, D and Soto-Rey, I and Kramer, F and Arai, H and Ochi, Y and Okada, T and Giancardo, L and Quellec, G and Mériaudeau, F}, title = {RFMiD: Retinal Image Analysis for multi-Disease Detection challenge.}, journal = {Medical image analysis}, volume = {99}, number = {}, pages = {103365}, doi = {10.1016/j.media.2024.103365}, pmid = {39395210}, issn = {1361-8423}, mesh = {Humans ; *Retinal Diseases/diagnostic imaging ; Image Interpretation, Computer-Assisted/methods ; Deep Learning ; Fundus Oculi ; Datasets as Topic ; Diabetic Retinopathy/diagnostic imaging ; Databases, Factual ; }, abstract = {In the last decades, many publicly available large fundus image datasets have been collected for diabetic retinopathy, glaucoma, and age-related macular degeneration, and a few other frequent pathologies. These publicly available datasets were used to develop a computer-aided disease diagnosis system by training deep learning models to detect these frequent pathologies. One challenge limiting the adoption of a such system by the ophthalmologist is, computer-aided disease diagnosis system ignores sight-threatening rare pathologies such as central retinal artery occlusion or anterior ischemic optic neuropathy and others that ophthalmologists currently detect. Aiming to advance the state-of-the-art in automatic ocular disease classification of frequent diseases along with the rare pathologies, a grand challenge on "Retinal Image Analysis for multi-Disease Detection" was organized in conjunction with the IEEE International Symposium on Biomedical Imaging (ISBI - 2021). This paper, reports the challenge organization, dataset, top-performing participants solutions, evaluation measures, and results based on a new "Retinal Fundus Multi-disease Image Dataset" (RFMiD). There were two principal sub-challenges: disease screening (i.e. presence versus absence of pathology - a binary classification problem) and disease/pathology classification (a 28-class multi-label classification problem). It received a positive response from the scientific community with 74 submissions by individuals/teams that effectively entered in this challenge. The top-performing methodologies utilized a blend of data-preprocessing, data augmentation, pre-trained model, and model ensembling. This multi-disease (frequent and rare pathologies) detection will enable the development of generalizable models for screening the retina, unlike the previous efforts that focused on the detection of specific diseases.}, } @article {pmid39395131, year = {2024}, author = {Atesoglu, A and Ayyildiz, E and Karakaya, I and Bulut, FS and Serengil, Y}, title = {Land cover and drought risk assessment in Türkiye's mountain regions using neutrosophic decision support system.}, journal = {Environmental monitoring and assessment}, volume = {196}, number = {11}, pages = {1046}, pmid = {39395131}, issn = {1573-2959}, mesh = {*Droughts ; *Environmental Monitoring/methods ; *Climate Change ; Risk Assessment ; Ecosystem ; Turkey ; Decision Support Techniques ; Remote Sensing Technology ; Conservation of Natural Resources/methods ; }, abstract = {Earth observation (EO) provides dynamic scientific methods for tracking and defining ecological parameters in mountainous regions. Open-source platforms are frequently utilized in this context to efficiently collect and evaluate spatial data. In this study, we used Collect Earth (CE), an open-source land monitoring platform, to reveal and assess land cover, land cover change, and relevant ecological parameters such as drought risk. Mountain ecosystems were subject to an evaluation for the first time by combining remote sensing with a hybridization of Decision-Making Trial and Evaluation Laboratory (DEMATEL), analytic hierarchy process (AHP), and Technique for Order of Preference by Similarity to Ideal Solution (TOPSIS) for neutrosophic sets in risk assessment problems of several connected criteria. The high and dispersed high alpine environment of Türkiye accommodates land with relatively less human influence, making it suitable to observe climate change impacts. In the framework of the study, we evaluated more than two decades (2000-2022) of land use and land cover (LULC) changes in the mountain regions of the country. Using nine identified ecological parameters, we also evaluated drought risk. The parameters included were the LULC classes and their change, elevation, slope, aspect, precipitation, temperature, normalized difference vegetation index (NDVI), water deficit, and evapotranspiration (ET). The risk map we produced revealed a high to very high drought risk for almost throughout the Türkiye's mountainous areas. We concluded that integrating geospatial techniques with hybridization is promising for mapping drought risk, helping policymakers prepare effective drought mitigation measures to reasonably adapt to climate change impacts.}, } @article {pmid39392918, year = {2024}, author = {Kopania, EEK and Thomas, GWC and Hutter, CR and Mortimer, SME and Callahan, CM and Roycroft, E and Achmadi, AS and Breed, WG and Clark, NL and Esselstyn, JA and Rowe, KC and Good, JM}, title = {Sperm competition intensity shapes divergence in both sperm morphology and reproductive genes across murine rodents.}, journal = {Evolution; international journal of organic evolution}, volume = {79}, number = {1}, pages = {11-27}, pmid = {39392918}, issn = {1558-5646}, support = {DEB-1754096//National Science Foundation/ ; R01-HG009299/HG/NHGRI NIH HHS/United States ; R01-HD073439//National Institute of Child Health and Human Development/ ; }, mesh = {Animals ; Male ; *Spermatozoa/physiology ; Mice/genetics ; *Evolution, Molecular ; *Testis/anatomy & histology ; Phylogeny ; Selection, Genetic ; Sexual Selection ; Spermatogenesis/genetics ; Murinae/genetics/physiology ; Rats ; Reproduction/genetics ; }, abstract = {It remains unclear how variation in the intensity of sperm competition shapes phenotypic and molecular evolution across clades. Mice and rats in the subfamily Murinae are a rapid radiation exhibiting incredible diversity in sperm morphology and production. We combined phenotypic and genomic data to perform phylogenetic comparisons of male reproductive traits and genes across 78 murine species. We identified several shifts towards smaller relative testes mass (RTM), presumably reflecting reduced sperm competition. Several sperm traits were associated with RTM, suggesting that mating system evolution selects for convergent suites of traits related to sperm competitive ability. We predicted that sperm competition would also drive more rapid molecular divergence in species with large testes. Contrary to this, we found that many spermatogenesis genes evolved more rapidly in species with smaller RTM due to relaxed purifying selection. While some reproductive genes evolved rapidly under recurrent positive selection, relaxed selection played a greater role in underlying rapid evolution in small testes species. Our work demonstrates that postcopulatory sexual selection can impose strong purifying selection shaping the evolution of male reproduction and that broad patterns of molecular evolution may help identify genes that contribute to male fertility.}, } @article {pmid39390673, year = {2024}, author = {Udaondo, Z and Ramos, JL and Abram, K}, title = {Unraveling the genomic diversity of the Pseudomonas putida group: exploring taxonomy, core pangenome, and antibiotic resistance mechanisms.}, journal = {FEMS microbiology reviews}, volume = {48}, number = {6}, pages = {}, pmid = {39390673}, issn = {1574-6976}, support = {PID2021-123469OB-I00//Plan Nacional sobre Drogas/ ; }, mesh = {*Pseudomonas putida/genetics/classification/drug effects ; *Genome, Bacterial/genetics ; *Genetic Variation ; Drug Resistance, Bacterial/genetics ; Genomics ; Phylogeny ; Anti-Bacterial Agents/pharmacology ; }, abstract = {The genus Pseudomonas is characterized by its rich genetic diversity, with over 300 species been validly recognized. This reflects significant progress made through sequencing and computational methods. Pseudomonas putida group comprises highly adaptable species that thrive in diverse environments and play various ecological roles, from promoting plant growth to being pathogenic in immunocompromised individuals. By leveraging the GRUMPS computational pipeline, we scrutinized 26 363 genomes labeled as Pseudomonas in the NCBI GenBank, categorizing all Pseudomonas spp. genomes into 435 distinct species-level clusters or cliques. We identified 224 strains deposited under the taxonomic identifier "Pseudomonas putida" distributed within 31 of these species-level clusters, challenging prior classifications. Nine of these 31 cliques contained at least six genomes labeled as "Pseudomonas putida" and were analysed in depth, particularly clique_1 (P. alloputida) and clique_2 (P. putida). Pangenomic analysis of a set of 413 P. putida group strains revealed over 2.2 million proteins and more than 77 000 distinct protein families. The core genome of these 413 strains includes 2226 protein families involved in essential biological processes. Intraspecific genetic homogeneity was observed within each clique, each possessing a distinct genomic identity. These cliques exhibit distinct core genes and diverse subgroups, reflecting adaptation to specific environments. Contrary to traditional views, nosocomial infections by P. alloputida, P. putida, and P. monteilii have been reported, with strains showing varied antibiotic resistance profiles due to diverse mechanisms. This review enhances the taxonomic understanding of key P. putida group species using advanced population genomics approaches and provides a comprehensive understanding of their genetic diversity, ecological roles, interactions, and potential applications.}, } @article {pmid39390511, year = {2024}, author = {Li, Y and Thomas, GWC and Richards, S and Waterhouse, RM and Zhou, X and Pfrender, ME}, title = {Rapid evolution of mitochondrion-related genes in haplodiploid arthropods.}, journal = {BMC biology}, volume = {22}, number = {1}, pages = {229}, pmid = {39390511}, issn = {1741-7007}, mesh = {Animals ; *Evolution, Molecular ; *Arthropods/genetics ; *Genes, Mitochondrial/genetics ; Phylogeny ; Haploidy ; Diploidy ; Oxidative Phosphorylation ; Cell Nucleus/genetics ; }, abstract = {BACKGROUND: Mitochondrial genes and nuclear genes cooperate closely to maintain the functions of mitochondria, especially in the oxidative phosphorylation (OXPHOS) pathway. However, mitochondrial genes among arthropod lineages have dramatic evolutionary rate differences. Haplodiploid arthropods often show fast-evolving mitochondrial genes. One hypothesis predicts that the small effective population size of haplodiploid species could enhance the effect of genetic drift leading to higher substitution rates in mitochondrial and nuclear genes. Alternatively, positive selection or compensatory changes in nuclear OXPHOS genes could lead to the fast-evolving mitochondrial genes. However, due to the limited number of arthropod genomes, the rates of evolution for nuclear genes in haplodiploid species, besides hymenopterans, are largely unknown. To test these hypotheses, we used data from 76 arthropod genomes, including 5 independently evolved haplodiploid lineages, to estimate the evolutionary rates and patterns of gene family turnover of mitochondrial and nuclear genes.

RESULTS: We show that five haplodiploid lineages tested here have fast-evolving mitochondrial genes and fast-evolving nuclear genes related to mitochondrial functions, while nuclear genes not related to mitochondrion showed no significant evolutionary rate differences. Among hymenopterans, bees and ants show faster rates of molecular evolution in mitochondrial genes and mitochondrion-related nuclear genes than sawflies and wasps. With genome data, we also find gene family expansions and contractions in mitochondrion-related genes of bees and ants.

CONCLUSIONS: Our results reject the small population size hypothesis in haplodiploid species. A combination of positive selection and compensatory changes could lead to the observed patterns in haplodiploid species. The elevated evolutionary rates in OXPHOS complex 2 genes of bees and ants suggest a unique evolutionary history of social hymenopterans.}, } @article {pmid39387871, year = {2024}, author = {Smith, SJ and Cummins, SF and Motti, CA and Wang, T}, title = {A mass spectrometry database for the identification of marine animal saponin-related metabolites.}, journal = {Analytical and bioanalytical chemistry}, volume = {416}, number = {29}, pages = {6893-6907}, pmid = {39387871}, issn = {1618-2650}, mesh = {*Saponins/analysis/metabolism ; Animals ; *Aquatic Organisms/chemistry/metabolism ; *Mass Spectrometry/methods ; Databases, Factual ; }, abstract = {Saponins encompass a diverse group of naturally occurring glycoside molecules exhibiting amphiphilic properties and a broad range of biological activities. There is a resurgence of interest in those saponins produced by marine organisms based on their potential therapeutic benefits, application in food products and most recently their potential involvement in intra- and inter-species chemical communication. The continual advancements in liquid chromatography techniques and mass spectrometry technologies have allowed for greater detection rates, as well as improved isolation and elucidation of saponins. These factors have significantly contributed to the expansion in the catalogue of known saponin structures isolated from marine invertebrates; however, there currently exists no specific chemical library resource to accelerate the discovery process. In this study, a Marine Animal Saponin Database (MASD v1.0) has been developed to serve as a valuable chemical repository for known marine saponin-related data, including chemical formula, molecular mass and biological origin of nearly 1000 secondary metabolites associated with saponins produced by marine invertebrates. We demonstrate its application with an exemplar asteroid extract (Acanthaster cf. solaris, also known as crown-of-thorns starfish; COTS), identifying saponins from the MASD v1.0 that have been previously reported from COTS, as well as 21 saponins isolated from multiple other related asteroid species. This database will help facilitate future research endeavours, aiding researchers in exploring the vast chemical diversity of saponins produced by marine organisms and providing ecological insights, and the realisation of their potential for various applications, including as pharmaceuticals.}, } @article {pmid39386964, year = {2024}, author = {Martin, SH and Lohse, K and Ebdon, S and Mackintosh, A and , and , and , and , and , }, title = {The genome sequence of the Pearl-bordered Fritillary, Boloria euphrosyne (Linnaeus, 1758).}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {267}, pmid = {39386964}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual male Boloria euphrosyne (the Pearl-bordered Fritillary; Arthropoda; Insecta; Lepidoptera; Nymphalidae). The genome sequence is 400.4 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.17 kilobases in length. Gene annotation of this assembly on Ensembl identified 19,138 protein coding genes.}, } @article {pmid39385455, year = {2024}, author = {Wu, H and Li, Q and Wu, JC}, title = {Bioinformatics-aided function exploration of GH29 fucosidases from human gut Parabacteroides.}, journal = {Glycobiology}, volume = {34}, number = {12}, pages = {}, doi = {10.1093/glycob/cwae086}, pmid = {39385455}, issn = {1460-2423}, support = {2023GDASZH-2023010102//GDAS' Project of Science and Technology Development/ ; SL2023A04J01435//Guangzhou Basic and Applied Basic Research Foundation/ ; 2022A1515110917//Guangdong Basic and Applied Basic Research Foundation/ ; 32302033//National Natural Science Foundation of China/ ; 2023A04J1494//Guangzhou Basic and Applied Basic Research Foundation/ ; 2022GDASZH-2022010110//GDAS' Project of Science and Technology Development/ ; }, mesh = {Humans ; *alpha-L-Fucosidase/metabolism/genetics/chemistry ; *Computational Biology ; Gastrointestinal Microbiome ; Bacteroidetes/enzymology/genetics ; Polysaccharides/metabolism/chemistry ; Substrate Specificity ; Mucins/metabolism/chemistry ; }, abstract = {Gut microbes produce α-l-fucosidases critical for utilizing human milk oligosaccharides, mucosal and dietary glycans. Although gut Parabacteroides have garnered attention for their impact on host health and disease, their CAZymes remain poorly studied. CAZome analysis of eleven gut Parabacteroides type strains revealed their capacity to degrade mucin O-glycans. Their abundance of GH29 fucosidases caught our attention, and we predicted the functional profiles of 46 GH29 fucosidases using in silico approaches. Our findings showed diverse linkages specificities and species-specific distributions, with over half of GH29 enzymes functioning as α1,3/4 fucosidases, essential for acting on Lewis antigen epitopes of mucin O-glycans. We further enzymatically validated 4 novel GH29 sequences from poorly characterized groups. PgoldGH29A (cluster37GH29BERT, GH29:75.1CUPP) does not act on tested natural substrates. PgoldGH29B (cluster1GH29BERT, GH29:84.1CUPP) functions as a strict α1,3/4 fucosidase. PgoldGH29C (cluster14GH29BERT, GH29:29.1CUPP) displays unprecedented substrate specificity for α1,2/3/4 disaccharides. PgoldGH29D (cluster4GH29BERT, GH29:6.2CUPP) acts on α1,2/3/4/6 linkages similar to enzymes from GH29:6.1CUPP but prefers disaccharides over trisaccharides. These results suggest that PgoldGH29B and PgoldGH29D can contribute to mucin O-glycan degradation via their α1,3/4 and α1,2 fucosidase activity, respectively, while the natural substrates of PgoldGH29A and PgoldGH29C may be irrelevant to host-glycans. These insights enhance our understanding of the ecological niches inhabited by gut Parabacteroides and may guide similar exploration in other intriguing gut microbial species.}, } @article {pmid39381069, year = {2024}, author = {Boyes, D and Lees, DC and Sims, I and Phillips, D and Boyes, C and , and , and , and , and , and , and , and , }, title = {The genome sequence of the Yellow-dotted Stilt, Euspilapteryx auroguttella Stephens, 1835.}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {226}, pmid = {39381069}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual male Euspilapteryx auroguttella (the Yellow-dotted Stilt; Arthropoda; Insecta; Lepidoptera; Gracillariidae). The genome sequence is 331.9 megabases in span. Most of the assembly is scaffolded into 30 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 16.94 kilobases in length.}, } @article {pmid39379720, year = {2024}, author = {Klopper, A}, title = {GPS tracking reveals how hares shape lynx populations.}, journal = {Nature}, volume = {634}, number = {8033}, pages = {301}, doi = {10.1038/d41586-024-03272-x}, pmid = {39379720}, issn = {1476-4687}, mesh = {Animals ; *Geographic Information Systems ; *Lynx/physiology ; Population Density ; Population Dynamics ; Alaska ; *Predatory Behavior ; *Hares/physiology ; }, } @article {pmid39376700, year = {2024}, author = {Chelliah, DS and Ray, AE and Zhang, E and Terauds, A and Ferrari, BC}, title = {The Vestfold Hills are alive: characterising microbial and environmental dynamics in Old Wallow, eastern Antarctica.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1443491}, pmid = {39376700}, issn = {1664-302X}, abstract = {Old Wallow is an underexplored, hyper-arid coastal desert in Antarctica's Vestfold Hills. Situated near an elephant seal wallow, we examined how stochastic nutrient inputs from the seal wallow affect soil communities amid environmental changes along a spatially explicit sampling transect. We hypothesized that nutrient levels would be elevated due to proximity to the seal wallow, influencing community distributions. While the soil bacterial and eukaryotic communities at the phylum level were similar to other terrestrial environments, analysis at class and family levels revealed a dominance of unclassified taxa that are often linked to marine environments. Elevated nutrient concentrations (NO3 [-], SO4 [2-], SO3) were found at Old Wallow, with conductivity and Cl[-] levels up to 10-fold higher at the lowest elevation soils, correlating with significantly (p < 0.05) higher abundances of halophilic (Halomonadaceace) and uncultivated lineages (Ca Actinomarinales, unclassified Bacillariophyta and unclassified Opisthonkonta). An improved Gradient Forest model was used to quantify microbial responses to 26 soil gradients at OW, revealing variable responses to environmental predictors and identifying critical environmental thresholds or drivers of community turnover. Major tipping points were projected for eukaryotes with SO4 [2-], pH, and SO3, and for bacteria with moisture, Na2O, and Cl[-]. Thus, the Old Wallow ecosystem is primarily shaped by salt, sulphate, and moisture and is dominated by uncultivated taxa, which may be sensitive to environmental changes once critical tipping points are reached. This study provides critical baseline data for future regional monitoring under threats of environmental change.}, } @article {pmid39374677, year = {2024}, author = {Ikeda, T and Cooray, U and Matsugaki, R and Suzuki, Y and Takagi, M and Muramatsu, K and Fushimi, K and Murakami, M and Osaka, K and Matsuda, S}, title = {Associations of hypothetical early intensive in-hospital rehabilitation with activities of daily living after hip fracture surgery in patients with and without dementia: emulating a randomized controlled trial using medical claims data.}, journal = {Journal of clinical epidemiology}, volume = {176}, number = {}, pages = {111550}, doi = {10.1016/j.jclinepi.2024.111550}, pmid = {39374677}, issn = {1878-5921}, mesh = {Humans ; *Hip Fractures/surgery/rehabilitation ; Female ; Male ; *Dementia/rehabilitation ; Aged ; *Activities of Daily Living ; Japan ; Aged, 80 and over ; Middle Aged ; Hospitalization/statistics & numerical data ; Recovery of Function ; }, abstract = {OBJECTIVES: To investigate the impact of early intensive in-hospital rehabilitation, initiated within 2 days of surgery and lasting up to 7 days, on the recovery of activities of daily living in patients with and without dementia.

STUDY DESIGN AND SETTING: Medical claims data from 925 hospitals in Japan were analyzed. We enrolled patients aged ≥50 years who underwent hip fracture surgery within 2 days of admission between April 1, 2018, and December 31, 2019. Low- (20 minutes per day starting on day 2), highest- (60 minutes per day starting on day 1), and gradually increasing (20 minutes on day 1, 40 minutes on days 2-4, and 60 minutes per day thereafter) intensity regimens were used as exposures. The outcomes were Barthel Index (BI) scores at 14 and 30 days postoperatively. For per-protocol analysis, a target trial emulation framework with the sequential doubly robust estimator was used.

RESULTS: Among patients without dementia (N = 11,461), no significant differences in BI scores were observed at 14 days postoperatively across regimens. At 30 days postoperatively, significant differences in BI scores were noted between highest- and low-intensity regimens and between gradually increasing intensity and low-intensity regimens, with additive BI scores of 15.2 (95% CI, 10.7-19.7) and 14.7 (95% CI, 9.2-20.2), respectively. In patients with dementia (N = 14,302), significant differences in BI scores were noted at 14 days postoperatively between highest- and low-intensity regimens and between gradually increasing intensity and low-intensity regimens, with additive BI scores of 8.7 (95% CI, 5.2-12.2) and 10.7 (95% CI, 5.8-15.6), respectively. At 30 days postoperatively, a significant difference in BI scores was observed between gradually increasing intensity and low-intensity regimens, with an additive BI score of 17.9 (95% CI, 11.3-24.5).

CONCLUSION: Early intensive in-hospital rehabilitation is highly relevant and beneficial for dementia patients.}, } @article {pmid39373887, year = {2024}, author = {Dittrich, SP and Adithya, S and Ajith, Y and Athira, N and Athira, KS and Safeer, MS and Preena, P and Aishwarya, A and Athira, K and Nisha, AR and Devi, G and Mäder, M and Beena, V and Jacob, SS}, title = {Parasite diversity among domestic goats of tropical monsoon climatic zone in India.}, journal = {Parasitology research}, volume = {123}, number = {10}, pages = {342}, pmid = {39373887}, issn = {1432-1955}, support = {IN-ME_BI-5550//Deutscher Akademischer Austauschdienst/ ; SRG/2022/000837//Science and Engineering Research Board/ ; SRG/2022/000837//Science and Engineering Research Board/ ; }, mesh = {Animals ; *Goats/parasitology ; India/epidemiology ; *Goat Diseases/parasitology/epidemiology ; *Tropical Climate ; Phylogeny ; Parasitic Diseases, Animal/parasitology/epidemiology ; Parasites/classification/isolation & purification/genetics ; Biodiversity ; }, abstract = {Among different climatic zones in India, the tropical monsoon region comprises a diverse ecosystem characterized by the endemic nature of several parasites including certain emerging and re-emerging vector-borne pathogens of humans, whereas a systematic investigation of the occurrence of different parasites among domestic goats in this area is not yet explored. The goal of the present study is to explore the parasite diversity focusing on molecular identification of vector-borne hemoparasites and its health impacts on domestic goats reared in the tropical monsoon climate zone of Kerala, India. Among 227 goats presented to the Teaching Veterinary Clinical Complex (TVCC) in the monsoon months of 2023, thirty animals were recruited for the study. The animals were screened for the presence of different hemoparasites (Anaplasma spp., Theileria spp., and Babesia spp.), ectoparasites (ticks, lice, and fleas), and gastrointestinal (GI) parasites (hookworms, threadworms, tapeworms, whipworms, and coccidia). The isolated hemoparasites were further characterized by sequencing and phylogenetic analysis. The correlation studies to elucidate the association between the occurrence of different parasites and clinical manifestations (hyperthermia, pallor of mucous membrane, circulatory failure, respiratory signs, neurological instability, and GI signs), blood picture (anemia, leukopenia, thrombocytopenia), demographics (sex and age), and treatment history (hemoparasitic therapy, ectoparasiticidal application, and prophylactic deworming) were conducted. The co-infection status of these parasites was also evaluated. A substantial portion of the goats in the study group was found to be affected by vector-borne hemoparasitic diseases and their arthropod vectors or GI parasites or both. This can be attributed to the constantly warm and humid climate of the region, which is favorable for the survival and growth of different life cycle stages of these parasites and vectors. A strategic parasitic disease surveillance-cum-control program is the need of the hour for ensuring climate resilience and profitable goat farming in the region.}, } @article {pmid39373528, year = {2024}, author = {Ros-Rocher, N}, title = {The evolution of multicellularity and cell differentiation symposium: bridging evolutionary cell biology and computational modelling using emerging model systems.}, journal = {Biology open}, volume = {13}, number = {10}, pages = {}, pmid = {39373528}, issn = {2046-6390}, support = {101106415//European Union's Horizon Europe research and innovation funding program/ ; //Institute Pasteur: Institut Pasteur; Baylor College of Medicine/ ; }, mesh = {*Cell Differentiation/genetics ; *Biological Evolution ; Animals ; Computational Biology/methods ; Humans ; Cell Biology ; Models, Biological ; Computer Simulation ; Genomics/methods ; }, abstract = {'The evolution of multicellularity and cell differentiation' symposium, organized as part of the EuroEvoDevo 2024 meeting on June 25-28th in Helsinki (Finland), addressed recent advances on the molecular and mechanistic basis for the evolution of multicellularity and cell differentiation in eukaryotes. The symposium involved over 100 participants and brought together 10 speakers at diverse career stages. Talks covered various topics at the interface of developmental biology, evolutionary cell biology, comparative genomics, computational biology, and ecology using animal, protist, algal and mathematical models. This symposium offered a unique opportunity for interdisciplinary dialog among researchers working on different systems, especially in promoting collaborations and aligning strategies for studying emerging model species. Moreover, it fostered opportunities to promote early career researchers in the field and opened discussions of ongoing work and unpublished results. In this Meeting Review, we aim to promote the research, capture the spirit of the meeting, and present key topics discussed within this dynamic, growing and open community.}, } @article {pmid39373052, year = {2024}, author = {Xie, X and Gui, L and Qiao, B and Wang, G and Huang, S and Zhao, Y and Sun, S}, title = {Deep learning in template-free de novo biosynthetic pathway design of natural products.}, journal = {Briefings in bioinformatics}, volume = {25}, number = {6}, pages = {}, pmid = {39373052}, issn = {1477-4054}, support = {2572022BD04//Fundamental Research Funds for the Central Universities/ ; 62001088//National Natural Science Foundation of China/ ; }, mesh = {*Biological Products/metabolism ; *Deep Learning ; *Biosynthetic Pathways ; Algorithms ; Computational Biology/methods ; Humans ; }, abstract = {Natural products (NPs) are indispensable in drug development, particularly in combating infections, cancer, and neurodegenerative diseases. However, their limited availability poses significant challenges. Template-free de novo biosynthetic pathway design provides a strategic solution for NP production, with deep learning standing out as a powerful tool in this domain. This review delves into state-of-the-art deep learning algorithms in NP biosynthesis pathway design. It provides an in-depth discussion of databases like Kyoto Encyclopedia of Genes and Genomes (KEGG), Reactome, and UniProt, which are essential for model training, along with chemical databases such as Reaxys, SciFinder, and PubChem for transfer learning to expand models' understanding of the broader chemical space. It evaluates the potential and challenges of sequence-to-sequence and graph-to-graph translation models for accurate single-step prediction. Additionally, it discusses search algorithms for multistep prediction and deep learning algorithms for predicting enzyme function. The review also highlights the pivotal role of deep learning in improving catalytic efficiency through enzyme engineering, which is essential for enhancing NP production. Moreover, it examines the application of large language models in pathway design, enzyme discovery, and enzyme engineering. Finally, it addresses the challenges and prospects associated with template-free approaches, offering insights into potential advancements in NP biosynthesis pathway design.}, } @article {pmid39367377, year = {2024}, author = {Qiao, L and Zhang, C and Zhang, M and Jiang, H and Shi, Y and Zhang, W and Mei, Y and Li, Y and Wang, H}, title = {High-risk spatiotemporal patterns of leprosy in the southeastern region of Yunnan province from 2010 to 2022: an analysis at the township level.}, journal = {BMC public health}, volume = {24}, number = {1}, pages = {2707}, pmid = {39367377}, issn = {1471-2458}, support = {82103748//National Natural Science Foundation of China/ ; 81972950//National Natural Science Foundation of China/ ; }, mesh = {Humans ; *Leprosy/epidemiology ; China/epidemiology ; Female ; Male ; *Spatio-Temporal Analysis ; Adult ; Middle Aged ; *Geographic Information Systems ; Adolescent ; Young Adult ; Aged ; Child ; Risk Factors ; }, abstract = {BACKGROUND: Despite being preventable and curable, leprosy remains endemic in some undeveloped regions, including China. Wenshan Zhuang and Miao Autonomous Prefecture (Wenshan prefecture) currently bears the highest leprosy burden in China. In this ecological study, we aimed to analyze the epidemiological characteristics as well as identify and visualize the high-risk townships of Wenshan prefecture using the most updated leprosy data from 2010 to 2022.

METHODS: Geographical information system combined with spatial scan statistics was used for newly detected leprosy cases abstracted from the Leprosy Management Information System in China. Global Moran's I index was used to uncover the spatial pattern of leprosy at the township level. Spatial scan statistics, encompassing purely temporal, purely spatial, spatial variation in temporal trends, and space-time analysis, were implemented for detecting the risk clusters.

RESULTS: Between 2010 and 2022, Wenshan prefecture detected 532 new leprosy cases, comprising 352 (66.17%) males and 180 (33.83%) females. The aggregated time primarily occurred between October 2010 and March 2014. The distribution pattern of newly detected leprosy cases was spatially clustered. We identified four high-risk spatial clusters encompassing 54.51% of the new cases. Furthermore, spatial variation in temporal trends highlighted one cluster as a potential high-risk area. Finally, two space-time clusters were detected, and the most likely cluster was predominantly located in the central and northwest regions of Wenshan prefecture, spanning from January 2010 to September 2013.

CONCLUSIONS: In this ecology study, we characterized the epidemiological features and temporal and spatial patterns of leprosy in Wenshan prefecture using the most recent leprosy data between 2010 and 2022. Our findings offer scientific insights into the epidemiological profiles and spatiotemporal dynamics of leprosy in Wenshan prefecture. Clinicians and policymakers should pay particular attention to the identified clusters for the prevention and control of leprosy.}, } @article {pmid39367017, year = {2024}, author = {Zhou, M and Guo, F}, title = {Mechanism and spatial spillover effect of digital economy on common prosperity in the Yellow River Basin of China.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {23086}, pmid = {39367017}, issn = {2045-2322}, support = {41801105//National Natural Science Foundation of China/ ; 2022RW040//Shandong Province Higher Education Youth Innovation Technology Support Program/ ; 23CGLJ15//Shandong Province Social Science Planning and Research Project/ ; }, abstract = {The digital economy has emerged as a new trend in economic development and has profoundly influenced the process of achieving common prosperity. However, current research on the correlation between the digital economy and common prosperity from the perspective of a river basin still needs to be strengthened. Based on this, the present study first theoretically elaborates the conceptual meanings of "digital economy" and "common prosperity", as well as the mechanism by which the digital economy empowers common prosperity. Subsequently, a scientifically-constructed performance evaluation index system for the digital economy and common prosperity is established. Considering the Yellow River Basin as an empirical case study area, this study investigates the mechanism and spatial spillover effects of the digital economy in empowering common prosperity from 2005 to 2020. The research findings reveal that: (1) The Yellow River Basin exhibits a basin characteristic with downstream > midstream > upstream areas regarding the level of common prosperity and digital economy. It indicates that a distinct spatial correlation exists between the two factors. However, the ongoing decrease in both high-level and very high-level areas reflects the lengthy and challenging journey of enhancing the quality and efficiency of the digital economy in empowering common prosperity. (2) The digital economy not only directly impacts common prosperity, but also fosters its development through spatial spillover effects. Among the control factors, informatization and housing levels have a major stimulating effect. (3) There exists a clear regional heterogeneity in how the digital economy affects common prosperity in the Yellow River Basin. Specifically, common prosperity of downstream cities is significantly impacted by the digital economy. The spatial spillover effects of the digital economy on common prosperity exhibit a pronounced "neighborhood as a moat" characteristic. (4) The digital economy facilitates the achievement of shared prosperity through the implementation of mechanisms centered on sharing, affluence, and sustainability. These research findings illuminate the empowering mechanisms and spatial spillover pathways of the digital economy in promoting shared prosperity, aligning with national strategies for ecological conservation and high-quality development in the Yellow River Basin.}, } @article {pmid39364368, year = {2024}, author = {Bullion, CM and Bahlai, CA}, title = {Data gap or biodiversity gap? Evaluating apparent spatial biases in community science observations of Odonata in the east-central United States.}, journal = {PeerJ}, volume = {12}, number = {}, pages = {e18115}, pmid = {39364368}, issn = {2167-8359}, mesh = {Animals ; *Biodiversity ; *Odonata ; Humans ; Bias ; United States ; Databases, Factual ; }, abstract = {Odonates (dragonflies and damselflies) have become popular study organisms for insect-based climate studies, due to the taxon's strong sensitivity to environmental conditions, and an enthusiastic following by community scientists due to their charismatic appearance and size. Where formal records of this taxon can be limited, public efforts have provided nearly 1,500,000 open-sourced odonate records through online databases, making real-time spatio-temporal monitoring more feasible. While these databases can be extensive, concerns regarding these public endeavors have arisen from a variety of sources: records may be biased by human factors (ex: density, technological access) which may cause erroneous interpretations. Indeed, records of odonates in the east-central US documented in the popular database iNaturalist bear striking patterns corresponding to political boundaries and other human activities. We conducted a 'ground-truthing' study using a structured sampling method to examine these patterns in an area where community science reports indicated variable abundance, richness, and diversity which appeared to be linked to observation biases. Our observations were largely consistent with patterns recorded by community scientists, suggesting these databases were indeed capturing representative biological trends and raising further questions about environmental drivers in the observed data gaps.}, } @article {pmid39363544, year = {2024}, author = {Panayi, P and Peters, E and Bentall, R and Hardy, A and Berry, K and Sellwood, W and Dudley, R and Longden, E and Underwood, R and Steel, C and Jafari, H and Emsley, R and Mason, L and Elliott, R and Varese, F}, title = {Complex PTSD symptoms predict positive symptoms of psychosis in the flow of daily life.}, journal = {Psychological medicine}, volume = {54}, number = {12}, pages = {1-12}, pmid = {39363544}, issn = {1469-8978}, support = {NIHR128623//Health Technology Assessment Programme/ ; NIHR130971//Efficacy and Mechanism Evaluation Programme/ ; N/A//NIHR Maudsley Biomedical Research Centre/ ; }, abstract = {BACKGROUND: Post-traumatic stress disorder (PTSD) has been shown to predict psychotic symptomology. However, few studies have examined the relative contribution of PTSD compared to broader post-traumatic sequelae in maintaining psychosis. Complex PTSD (cPTSD), operationalized using ICD-11 criteria, includes core PTSD (intrusions, avoidance, hyperarousal) as well as additional "disturbances of self-organisation" (DSO; emotional dysregulation, interpersonal difficulties, negative self-concept) symptoms, more likely to be associated with complex trauma histories. It was hypothesized that DSOs would be associated with positive psychotic symptoms (paranoia, voices, and visions) in daily life, over and above core PTSD symptoms.

METHODS: This study (N = 153) employed a baseline subsample of the Study of Trauma And Recovery (STAR), a clinical sample of participants with comorbid post-traumatic stress and psychosis symptoms. Core PTSD, DSO and psychosis symptoms were assessed up to 10 times per day at quasi-random intervals over six consecutive days using Experience Sampling Methodology.

RESULTS: DSOs within the preceding 90 min predicted paranoia, voices, and visions at subsequent moments. These relationships persisted when controlling for core PTSD symptoms within this timeframe, which were themselves significant. The associations between DSOs and paranoia but not voices or visions, were significantly stronger than those between psychosis and core PTSD symptoms.

CONCLUSIONS: Consistent with an affective pathway to psychosis, the findings suggest that DSOs may be more important than core PTSD symptoms in maintaining psychotic experiences in daily life among people with comorbid psychosis and cPTSD, and indicate the potential importance of addressing broad post-traumatic sequelae in trauma-focused psychosis interventions.}, } @article {pmid39363203, year = {2024}, author = {Viana, PAB and Tschoeke, DA and de Moraes, L and Santos, LA and Barral-Netto, M and Khouri, R and Ramos, PIP and Meirelles, PM}, title = {Design and implementation of a metagenomic analytical pipeline for respiratory pathogen detection.}, journal = {BMC research notes}, volume = {17}, number = {1}, pages = {291}, pmid = {39363203}, issn = {1756-0500}, support = {2023-PPI-007//Rockefeller Foundation/ ; }, mesh = {*Metagenomics/methods ; Humans ; *Respiratory Tract Infections/microbiology/diagnosis ; Metagenome/genetics ; Computational Biology/methods ; Reproducibility of Results ; Nasopharynx/microbiology/virology ; }, abstract = {OBJECTIVE: We developed an in-house bioinformatics pipeline to improve the detection of respiratory pathogens in metagenomic sequencing data. This pipeline addresses the need for short-time analysis, high accuracy, scalability, and reproducibility in a high-performance computing environment.

RESULTS: We evaluated our pipeline using ninety synthetic metagenomes designed to simulate nasopharyngeal swab samples. The pipeline successfully identified 177 out of 204 respiratory pathogens present in the compositions, with an average processing time of approximately 4 min per sample (processing 1 million paired-end reads of 150 base pairs). For the estimation of all the 470 taxa included in the compositions, the pipeline demonstrated high accuracy, identifying 420 and achieving a correlation of 0.9 between their actual and predicted relative abundances. Among the identified taxa, 27 were significantly underestimated or overestimated, including only three clinically relevant pathogens. We also validated the pipeline by applying it to a clinical dataset from a study on metagenomic pathogen characterization in patients with acute respiratory infections and successfully identified all pathogens responsible for the diagnosed infections. These findings underscore the pipeline's effectiveness in pathogen detection and highlight its potential utility in respiratory pathogen surveillance.}, } @article {pmid39362872, year = {2024}, author = {Fu, SW and Feng, MC and Chi, PW and Ding, TS}, title = {Combining citizen science data and literature to build a traits dataset of Taiwan's birds.}, journal = {Scientific data}, volume = {11}, number = {1}, pages = {1076}, pmid = {39362872}, issn = {2052-4463}, mesh = {Animals ; Taiwan ; *Birds ; *Citizen Science ; *Ecosystem ; Databases, Factual ; }, abstract = {Trait-based methodologies are gaining traction in the field of ecology, providing deeper insights into ecosystem structure and functions. To this end, trait databases tailored to specific taxonomic groups have become foundational. In Taiwan, the collaborative efforts of avian researchers and dedicated citizen scientists have led to the compilation of a vast array of data. This includes web-sourced images from social media, spatial distribution records from eBird, and morphological metrics from banded birds and specimens. Enriched by peer-reviewed literature, we have meticulously assembled a comprehensive trait dataset encompassing 454 bird species across 73 families. This dataset covers a wide range of traits, including foraging ecology, morphological characteristics, territorial behaviors, breeding attributes, and the roles of bird species in ecosystem regulation. As an invaluable resource, this dataset lays the foundation for in-depth exploration of functional diversity, trait-based community ecology, ecosystem function, and critical insights needed to shape conservation strategies.}, } @article {pmid39362167, year = {2024}, author = {Fardullah, M and Hossain, MT and Islam, MS and Islam, MR and Rahman, MR and Akther, K and Uddin, A and Morshed, S and Sultana, N and Alam, MA and Bahadur, NM and Robel, FN}, title = {Occurrence and spatial distribution of microplastics in water and sediments of Hatiya Island, Bangladesh and their risk assessment.}, journal = {Journal of environmental management}, volume = {370}, number = {}, pages = {122697}, doi = {10.1016/j.jenvman.2024.122697}, pmid = {39362167}, issn = {1095-8630}, mesh = {*Microplastics/analysis ; Risk Assessment ; Bangladesh ; *Environmental Monitoring ; *Water Pollutants, Chemical/analysis ; Geologic Sediments/chemistry/analysis ; Islands ; }, abstract = {This research has evaluated the MPs distribution, characteristics, and potential threats of MPs in surface water and sediments from Hatiya Island. The results showed that the abundance of MPs was 139 ± 44 items/m[3] in surface water and 493 ± 80 items/kg dw in sediments, indicating higher levels of MPs contamination in sediment samples. Fibers were the predominant kind of microplastics, and microscopic sizes (0.3-1.5 mm) MPs were generally more frequent and largely present in both the surface water and sediments. Fourier-transform infrared spectroscopy (FTIR) confirmed that polyethylene terephthalate was the major polymer component of microplastics in surface water, whereas polyethylene was the most abundant polymer in sediments. MPs contamination risk was examined based on multiple risk assessment models. Nemerow pollution index (NPI) and pollutant load index (PLI) show minimal pollution levels of MPs. But potential hazard index (PHI), potential ecological risk factor (Er), and potential ecological risk index (RI), indicate severe MPs contamination due to the presence of polyurethane, polycarbonate, polyvinyl chloride, epoxy that were hazardous MPs and exhibited a critical concern for MPs risk. These statistics will help to understand the environmental difficulties generated by MPs and which hazard is waiting for mankind in the future.}, } @article {pmid39360250, year = {2024}, author = {Soni, N and Eyre, MT and Souza, FN and Diggle, PJ and Ko, AI and Begon, M and Pickup, R and Childs, JE and Khalil, H and Carvalho-Pereira, TSA and Pertile, AC and Carvalho, M and de Oliveira, D and Nery, N and Giorgi, E and Costa, F}, title = {Disentangling the influence of reservoir abundance and pathogen shedding on zoonotic spillover of the Leptospira agent in urban informal settlements.}, journal = {Frontiers in public health}, volume = {12}, number = {}, pages = {1447592}, pmid = {39360250}, issn = {2296-2565}, mesh = {Animals ; Humans ; *Leptospirosis/epidemiology/microbiology/transmission ; *Leptospira/isolation & purification ; *Disease Reservoirs/microbiology ; Brazil/epidemiology ; Rats ; *Zoonoses/microbiology ; Male ; Female ; Adult ; Bacterial Shedding ; Longitudinal Studies ; Middle Aged ; Risk Factors ; Urban Population/statistics & numerical data ; Adolescent ; Young Adult ; }, abstract = {Rats are major reservoirs for pathogenic Leptospira, the bacteria causing leptospirosis, particularly in urban informal settlements. However, the impact of variation in rat abundance and pathogen shedding rates on spillover transmission to humans remains unclear. This study aimed to investigate how spatial variation in reservoir abundance and pathogen pressure affect Leptospira spillover transmission to humans in a Brazilian urban informal settlement. A longitudinal eco-epidemiological study was conducted from 2013 to 2014 to characterize the spatial distribution of rat abundance and Leptospira shedding rates in rats and determine the association with human infection risk in a cohort of 2,206 community residents. Tracking plates and live-trapping were used to measure rat abundance and quantify rat shedding status and load. In parallel, four sequential biannual serosurveys were used to identify human Leptospira infections. To evaluate the role of shedding on human risk, we built three statistical models for: (1) the relative abundance of rats, (2) the shedding rate by individual rats, and (3) human Leptospira infection, in which "total shedding", obtained by multiplying the predictions from those two models, was used as a risk factor. We found that Leptospira shedding was associated with older and sexually mature rats and varied spatially and temporally-higher at valley bottoms and with seasonal rainfall (December to March). The point estimate for "total shedding" by rat populations was positive, i.e., Leptospira infection risk increased with total shedding, but the association was not significant [odds ratio (OR) = 1.1; 95% confidence interval (CI): 0.9, 1.4]. This positive trend was mainly driven by rat abundance, rather than individual rat shedding (OR = 1.8; 95% CI: 0.6, 5.4 vs. OR = 1.0; 95% CI: 0.7, 1.4]. Infection risk was higher in areas with more vegetative land cover (OR = 2.4; 95% CI: 1.2, 4.8), and when floodwater entered the house (OR = 2.4; 95% CI: 1.6, 3.4). Our findings indicate that environmental and hydrological factors play a more significant role in Leptospira spillover than rat associated factors. Furthermore, we developed a novel approach combining several models to elucidate complex links between animal reservoir abundance, pathogen shedding and environmental factors on zoonotic spillover in humans that can be extended to other environmentally transmitted diseases.}, } @article {pmid39359327, year = {2023}, author = {Boyes, D and Boyes, C and , and , and , and , and , and , }, title = {The genome sequence of the Crescent Plume, Marasmarcha lunaedactyla (Haworth, 1811).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {431}, pmid = {39359327}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual female Marasmarcha lunaedactyla (the Crescent Plume; Arthropoda; Insecta; Lepidoptera; Pterophoridae). The genome sequence is 771.1 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the W and Z sex chromosomes. The mitochondrial genome has also been assembled and is 16.43 kilobases in length. Gene annotation of this assembly on Ensembl identified 21,571 protein coding genes.}, } @article {pmid39355992, year = {2024}, author = {Auffret, AG and Ladouceur, E and Haussmann, NS and Daouti, E and Elumeeva, TG and Kačergytė, I and Knape, J and Kotowska, D and Low, M and Onipchenko, VG and Paquet, M and Rubene, D and Plue, J}, title = {A global database of soil seed bank richness, density, and abundance.}, journal = {Ecology}, volume = {105}, number = {11}, pages = {e4438}, doi = {10.1002/ecy.4438}, pmid = {39355992}, issn = {1939-9170}, mesh = {*Seed Bank ; *Soil ; *Databases, Factual ; *Biodiversity ; *Seeds ; Ecosystem ; Plants/classification ; }, abstract = {A soil seed bank is the collective name for viable seeds that are stored naturally in the soil. At the species or population level, the ability to form a seed bank represents a strategy for (re)colonization following a disturbance or other change in the local environmental conditions. At the community level, seed banks are thought to buffer local diversity during periods of environmental change and are often studied in relation to the potential for passive habitat restoration. The role that seed banks play in plant population and community dynamics, as well as their importance in the agricultural sector, means that they have been widely studied in ecological research. This database is the result of a comprehensive literature search, including all seed bank studies from the Web of Science from which data could be extracted, as well as an additional search of the Russian language literature. The database contains information on the species richness, seed density, and/or seed abundance in 3096 records from at least 1929 locations across the world's seven continents, extracted from 1442 studies published between 1940 and 2020. Records are grouped into five broad habitat categories (aquatic, arable, forest, grassland-including shrubland-and wetland), including information relating to habitat degradation from, or restoration to other habitats (total 14 combinations). Sampling protocols were also extracted for each record, and the database was extensively checked for errors. The location of each record was then used to extract summary climate data and biome classification from external published databases. The database has several potential uses. The large geographical spread relative to many other global biodiversity datasets is relevant for investigating patterns of diversity in biogeographical or macroecological contexts. Habitat type and status (intact, degraded, and restored) can be used to provide insights for biodiversity conservation, while the potential effects of sampling method and effort can be used to inform optimized data collection for future seed bank studies. This database is released under the CC-BY license.}, } @article {pmid39354608, year = {2024}, author = {Navratilova, HF and Whetton, AD and Geifman, N}, title = {Artificial intelligence driven definition of food preference endotypes in UK Biobank volunteers is associated with distinctive health outcomes and blood based metabolomic and proteomic profiles.}, journal = {Journal of translational medicine}, volume = {22}, number = {1}, pages = {881}, pmid = {39354608}, issn = {1479-5876}, support = {202205080261//Lembaga Pengelola Dana Pendidikan/ ; }, mesh = {Humans ; *Food Preferences ; United Kingdom ; Male ; Female ; *Biological Specimen Banks ; Middle Aged ; *Proteomics/methods ; *Metabolomics ; *Artificial Intelligence ; Metabolome ; Adult ; Aged ; Surveys and Questionnaires ; Health ; UK Biobank ; }, abstract = {BACKGROUND: Specific food preferences can determine an individual's dietary patterns and therefore, may be associated with certain health risks and benefits.

METHODS: Using food preference questionnaire (FPQ) data from a subset comprising over 180,000 UK Biobank participants, we employed Latent Profile Analysis (LPA) approach to identify the main patterns or profiles among participants. blood biochemistry across groups/profiles was compared using the non-parametric Kruskal-Wallis test. We applied the Limma algorithm for differential abundance analysis on 168 metabolites and 2923 proteins, and utilized the Database for Annotation, Visualization and Integrated Discovery (DAVID) to identify enriched biological processes and pathways. Relative risks (RR) were calculated for chronic diseases and mental conditions per group, adjusting for sociodemographic factors.

RESULTS: Based on their food preferences, three profiles were termed: the putative Health-conscious group (low preference for animal-based or sweet foods, and high preference for vegetables and fruits), the Omnivore group (high preference for all foods), and the putative Sweet-tooth group (high preference for sweet foods and sweetened beverages). The Health-conscious group exhibited lower risk of heart failure (RR = 0.86, 95%CI 0.79-0.93) and chronic kidney disease (RR = 0.69, 95%CI 0.65-0.74) compared to the two other groups. The Sweet-tooth group had greater risk of depression (RR = 1.27, 95%CI 1.21-1.34), diabetes (RR = 1.15, 95%CI 1.01-1.31), and stroke (RR = 1.22, 95%CI 1.15-1.31) compared to the other two groups. Cancer (overall) relative risk showed little difference across the Health-conscious, Omnivore, and Sweet-tooth groups with RR of 0.98 (95%CI 0.96-1.01), 1.00 (95%CI 0.98-1.03), and 1.01 (95%CI 0.98-1.04), respectively. The Health-conscious group was associated with lower levels of inflammatory biomarkers (e.g., C-reactive Protein) which are also known to be elevated in those with common metabolic diseases (e.g., cardiovascular disease). Other markers modulated in the Health-conscious group, ketone bodies, insulin-like growth factor-binding protein (IGFBP), and Growth Hormone 1 were more abundant, while leptin was less abundant. Further, the IGFBP pathway, which influences IGF1 activity, may be significantly enhanced by dietary choices.

CONCLUSIONS: These observations align with previous findings from studies focusing on weight loss interventions, which include a reduction in leptin levels. Overall, the Health-conscious group, with preference to healthier food options, has better health outcomes, compared to Sweet-tooth and Omnivore groups.}, } @article {pmid39352141, year = {2024}, author = {Coclet, C and Camargo, AP and Roux, S}, title = {MVP: a modular viromics pipeline to identify, filter, cluster, annotate, and bin viruses from metagenomes.}, journal = {mSystems}, volume = {9}, number = {10}, pages = {e0088824}, pmid = {39352141}, issn = {2379-5077}, mesh = {*Metagenome/genetics ; *Genome, Viral/genetics ; *Metagenomics/methods ; *Viruses/genetics/classification/isolation & purification ; Software ; Virome/genetics ; Computational Biology/methods ; Molecular Sequence Annotation ; }, abstract = {While numerous computational frameworks and workflows are available for recovering prokaryote and eukaryote genomes from metagenome data, only a limited number of pipelines are designed specifically for viromics analysis. With many viromics tools developed in the last few years alone, it can be challenging for scientists with limited bioinformatics experience to easily recover, evaluate quality, annotate genes, dereplicate, assign taxonomy, and calculate relative abundance and coverage of viral genomes using state-of-the-art methods and standards. Here, we describe Modular Viromics Pipeline (MVP) v.1.0, a user-friendly pipeline written in Python and providing a simple framework to perform standard viromics analyses. MVP combines multiple tools to enable viral genome identification, characterization of genome quality, filtering, clustering, taxonomic and functional annotation, genome binning, and comprehensive summaries of results that can be used for downstream ecological analyses. Overall, MVP provides a standardized and reproducible pipeline for both extensive and robust characterization of viruses from large-scale sequencing data including metagenomes, metatranscriptomes, viromes, and isolate genomes. As a typical use case, we show how the entire MVP pipeline can be applied to a set of 20 metagenomes from wetland sediments using only 10 modules executed via command lines, leading to the identification of 11,656 viral contigs and 8,145 viral operational taxonomic units (vOTUs) displaying a clear beta-diversity pattern. Further, acting as a dynamic wrapper, MVP is designed to continuously incorporate updates and integrate new tools, ensuring its ongoing relevance in the rapidly evolving field of viromics. MVP is available at https://gitlab.com/ccoclet/mvp and as versioned packages in PyPi and Conda.IMPORTANCEThe significance of our work lies in the development of Modular Viromics Pipeline (MVP), an integrated and user-friendly pipeline tailored exclusively for viromics analyses. MVP stands out due to its modular design, which ensures easy installation, execution, and integration of new tools and databases. By combining state-of-the-art tools such as geNomad and CheckV, MVP provides high-quality viral genome recovery and taxonomy and host assignment, and functional annotation, addressing the limitations of existing pipelines. MVP's ability to handle diverse sample types, including environmental, human microbiome, and plant-associated samples, makes it a versatile tool for the broader microbiome research community. By standardizing the analysis process and providing easily interpretable results, MVP enables researchers to perform comprehensive studies of viral communities, significantly advancing our understanding of viral ecology and its impact on various ecosystems.}, } @article {pmid39352117, year = {2024}, author = {Gu, S and Shao, Y and Rehm, K and Bigler, L and Zhang, D and He, R and Xu, R and Shao, J and Jousset, A and Friman, VP and Bian, X and Wei, Z and Kümmerli, R and Li, Z}, title = {Feature sequence-based genome mining uncovers the hidden diversity of bacterial siderophore pathways.}, journal = {eLife}, volume = {13}, number = {}, pages = {}, pmid = {39352117}, issn = {2050-084X}, support = {No. 2021YFF1200500//National Key Research and Development Program of China/ ; No. 42107140//National Natural Science Foundation of China/ ; No.41922053//National Natural Science Foundation of China/ ; No. 32071255//National Natural Science Foundation of China/ ; No. T2321001//National Natural Science Foundation of China/ ; No. BX2021012//National Postdoctoral Program for Innovative Talents/ ; no. 310030_212266/SNSF_/Swiss National Science Foundation/Switzerland ; }, mesh = {*Siderophores/metabolism/genetics ; *Genome, Bacterial ; *Pseudomonas/genetics/metabolism ; *Computational Biology/methods ; Metabolic Networks and Pathways/genetics ; Phylogeny ; Oligopeptides/metabolism/genetics ; Secondary Metabolism/genetics ; Iron/metabolism ; }, abstract = {Microbial secondary metabolites are a rich source for pharmaceutical discoveries and play crucial ecological functions. While tools exist to identify secondary metabolite clusters in genomes, precise sequence-to-function mapping remains challenging because neither function nor substrate specificity of biosynthesis enzymes can accurately be predicted. Here, we developed a knowledge-guided bioinformatic pipeline to solve these issues. We analyzed 1928 genomes of Pseudomonas bacteria and focused on iron-scavenging pyoverdines as model metabolites. Our pipeline predicted 188 chemically different pyoverdines with nearly 100% structural accuracy and the presence of 94 distinct receptor groups required for the uptake of iron-loaded pyoverdines. Our pipeline unveils an enormous yet overlooked diversity of siderophores (151 new structures) and receptors (91 new groups). Our approach, combining feature sequence with phylogenetic approaches, is extendable to other metabolites and microbial genera, and thus emerges as powerful tool to reconstruct bacterial secondary metabolism pathways based on sequence data.}, } @article {pmid39351379, year = {2024}, author = {Leavy, OC and Russell, RJ and Harrison, EM and Lone, NI and Kerr, S and Docherty, AB and Sheikh, A and Richardson, M and Elneima, O and Greening, NJ and Harris, VC and Houchen-Wolloff, L and McAuley, HJC and Saunders, RM and Sereno, M and Shikotra, A and Singapuri, A and Aul, R and Beirne, P and Bolton, CE and Brown, JS and Choudhury, G and Diar Bakerly, N and Easom, N and Echevarria, C and Fuld, J and Hart, N and Hurst, JR and Jones, M and Parekh, D and Pfeffer, P and Rahman, NM and Rowland-Jones, S and Shah, AM and Wootton, DG and Jolley, C and Thompson, AAR and Chalder, T and Davies, MJ and De Soyza, A and Geddes, JR and Greenhalf, W and Heller, S and Howard, L and Jacob, J and Jenkins, RG and Lord, JM and Man, WD and McCann, GP and Neubauer, S and Openshaw, PJM and Porter, J and Rowland, MJ and Scott, JT and Semple, MG and Singh, SJ and Thomas, D and Toshner, M and Lewis, K and Heaney, LG and Briggs, A and Zheng, B and Thorpe, M and Quint, JK and Chalmers, JD and Ho, LP and Horsley, A and Marks, M and Poinasamy, K and Raman, B and Wain, LV and Brightling, CE and Evans, RA}, title = {1-year health outcomes associated with systemic corticosteroids for COVID-19: a longitudinal cohort study.}, journal = {ERJ open research}, volume = {10}, number = {5}, pages = {}, pmid = {39351379}, issn = {2312-0541}, abstract = {BACKGROUND: In patients with coronavirus disease 2019 (COVID-19) requiring supplemental oxygen, dexamethasone reduces acute severity and improves survival, but longer-term effects are unknown. We hypothesised that systemic corticosteroid administration during acute COVID-19 would be associated with improved health-related quality of life (HRQoL) 1 year after discharge.

METHODS: Adults admitted to hospital between February 2020 and March 2021 for COVID-19 and meeting current guideline recommendations for dexamethasone treatment were included using two prospective UK cohort studies (Post-hospitalisation COVID-19 and the International Severe Acute Respiratory and emerging Infection Consortium). HRQoL, assessed by the EuroQol-Five Dimensions-Five Levels utility index (EQ-5D-5L UI), pre-hospital and 1 year after discharge were compared between those receiving corticosteroids or not after propensity weighting for treatment. Secondary outcomes included patient-reported recovery, physical and mental health status, and measures of organ impairment. Sensitivity analyses were undertaken to account for survival and selection bias.

FINDINGS: Of the 1888 participants included in the primary analysis, 1149 received corticosteroids. There was no between-group difference in EQ-5D-5L UI at 1 year (mean difference 0.004, 95% CI -0.026-0.034). A similar reduction in EQ-5D-5L UI was seen at 1 year between corticosteroid exposed and nonexposed groups (mean±sd change -0.12±0.22 versus -0.11±0.22). Overall, there were no differences in secondary outcome measures. After sensitivity analyses modelled using a cohort of 109 318 patients admitted to hospital with COVID-19, EQ-5D-5L UI at 1 year remained similar between the two groups.

INTERPRETATION: Systemic corticosteroids for acute COVID-19 have no impact on the large reduction in HRQoL 1 year after hospital discharge. Treatments to address the persistent reduction in HRQoL are urgently needed.}, } @article {pmid39351031, year = {2024}, author = {Wei, C and Cai, Y and Liu, J and Guo, Y and Wu, X and He, X and Hu, D}, title = {Factors influencing user's health information discernment abilities in online health communities: based on SEM and fsQCA.}, journal = {Frontiers in public health}, volume = {12}, number = {}, pages = {1379094}, pmid = {39351031}, issn = {2296-2565}, mesh = {Humans ; Surveys and Questionnaires ; Female ; Male ; Adult ; *Internet ; Consumer Health Information ; Latent Class Analysis ; Information Seeking Behavior ; Fuzzy Logic ; Young Adult ; Middle Aged ; }, abstract = {INTRODUCTION: Online health communities have become the main source for people to obtain health information. However, the existence of poor-quality health information, misinformation, and rumors in online health communities increases the challenges in governing information quality. It not only affects users' health decisions but also undermines social stability. It is of great significance to explore the factors that affect users' ability to discern information in online health communities.

METHODS: This study integrated the Stimulus-Organism-Response Theory, Information Ecology Theory and the Mindsponge Theory to constructed a model of factors influencing users' health information discernment abilities in online health communities. A questionnaire was designed based on the variables in the model, and data was collected. Utilizing Structural Equation Modeling (SEM) in conjunction with fuzzy-set Qualitative Comparative Analysis (fsQCA), the study analyzed the complex causal relationships among stimulus factors, user perception, and the health information discernment abilities.

RESULTS: The results revealed that the dimensions of information, information environment, information technology, and information people all positively influenced health information discernment abilities. Four distinct configurations were identified as triggers for users' health information discernment abilities. The core conditions included information source, informational support, technological security, technological facilitation, and perceived risk. It was also observed that information quality and emotional support can act as substitutes for one another, as can informational support and emotional support.

DISCUSSION: This study provides a new perspective to study the influencing factors of health information discernment abilities of online health community users. It can provide experiences and references for online health community information services, information resource construction and the development of users' health information discernment abilities.}, } @article {pmid39349447, year = {2024}, author = {Zhou, L and Wu, S and Chen, Y and Huang, R and Cheng, B and Mao, Q and Liu, T and Liu, Y and Zhao, K and Pan, H and Yu, C and Gao, X and Luo, L and Zhang, Q}, title = {Multi-omics analyzes of Rosa gigantea illuminate tea scent biosynthesis and release mechanisms.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {8469}, pmid = {39349447}, issn = {2041-1723}, mesh = {*Rosa/genetics/metabolism ; *Volatile Organic Compounds/metabolism ; *Odorants/analysis ; *Genome, Plant ; *Gene Expression Regulation, Plant ; Gene Regulatory Networks ; Genomics/methods ; Eugenol/analogs & derivatives/metabolism ; Plant Proteins/genetics/metabolism ; Pollination ; Multiomics ; }, abstract = {Rose is an important ornamental crop cultivated globally for perfume production. However, our understanding of the mechanisms underlying scent production and molecular breeding for fragrance is hindered by the lack of a reference genome for tea roses. We present the first complete telomere-to-telomere (T2T) genome of Rosa gigantea, with high quality (QV > 60), including detailed characterization of the structural features of repetitive regions. The expansion of genes associated with phenylpropanoid biosynthesis may account for the unique tea scent. We uncover the release rhythm of aromatic volatile organic compounds and their gene regulatory networks through comparative genomics and time-ordered gene co-expression networks. Analyzes of eugenol homologs demonstrate how plants attract pollinators using specialized phenylpropanoids in specific tissues. This study highlights the conservation and utilization of genetic diversity from wild endangered species through multi-omics approaches, providing a scientific foundation for enhancing rose fragrance via de novo domestication.}, } @article {pmid39346055, year = {2024}, author = {Knobloch, S and Salimi, F and Buaya, A and Ploch, S and Thines, M}, title = {RAPiD: a rapid and accurate plant pathogen identification pipeline for on-site nanopore sequencing.}, journal = {PeerJ}, volume = {12}, number = {}, pages = {e17893}, pmid = {39346055}, issn = {2167-8359}, mesh = {*Nanopore Sequencing/methods ; Metagenomics/methods ; Plant Diseases/microbiology ; Bacteria/genetics/isolation & purification/classification ; Sequence Analysis, DNA/methods ; Fungi/genetics/isolation & purification/classification ; Plants/microbiology ; Computational Biology/methods ; }, abstract = {Nanopore sequencing technology has enabled the rapid, on-site taxonomic identification of samples from anything and anywhere. However, sequencing errors, inadequate databases, as well as the need for bioinformatic expertise and powerful computing resources, have hampered the widespread use of the technology for pathogen identification in the agricultural sector. Here we present RAPiD, a lightweight and accurate real-time taxonomic profiling pipeline. Compared to other metagenomic profilers, RAPiD had a higher classification precision achieved through the use of a curated, non-redundant database of common agricultural pathogens and extensive quality filtering of alignments. On a fungal, bacterial and mixed mock community RAPiD was the only pipeline to detect all members of the communities. We also present a protocol for in-field sample processing enabling pathogen identification from plant sample to sequence within 3 h using low-cost equipment. With sequencing costs continuing to decrease and more high-quality reference genomes becoming available, nanopore sequencing provides a viable method for rapid and accurate pathogen identification in the field. A web implementation of the RAPiD pipeline for real-time analysis is available at https://agrifuture.senckenberg.de.}, } @article {pmid39345378, year = {2024}, author = {McDaniel, JH and Patel, V and Olson, ND and He, HJ and He, Z and Cole, KD and Schmitt, A and Sikkink, K and Sedlazeck, FJ and Doddapaneni, H and Jhangiani, SN and Muzny, DM and Gingras, MC and Mehta, H and Paulin, LF and Hastie, AR and Yu, HC and Weigman, V and Rojas, A and Kennedy, K and Remington, J and Gonzalez, I and Sudkamp, M and Wiseman, K and Lajoie, BR and Levy, S and Jain, M and Akeson, S and Narzisi, G and Steinsnyder, Z and Reeves, C and Shelton, J and Kingan, SB and Lambert, C and Bayabyan, P and Wenger, AM and McLaughlin, IJ and Adamson, A and Kingsley, C and Wescott, M and Kim, Y and Paten, B and Park, J and Violich, I and Miga, KH and Gardner, J and McNulty, B and Rosen, G and McCoy, R and Brundu, F and Sayyari, E and Scheffler, K and Truong, S and Catreux, S and Hannah, LC and Lipson, D and Benjamin, H and Iremadze, N and Soifer, I and Eacker, S and Wood, M and Cross, E and Husar, G and Gross, S and Vernich, M and Kolmogorov, M and Ahmad, T and Keskus, A and Bryant, A and Thibaud-Nissen, F and Trow, J and Proszynski, J and Hirschberg, JW and Ryon, K and Mason, CE and Wagner, J and Xiao, C and Liss, AS and Zook, JM}, title = {Development and extensive sequencing of a broadly-consented Genome in a Bottle matched tumor-normal pair.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {39345378}, issn = {2692-8205}, support = {R35 GM133747/GM/NIGMS NIH HHS/United States ; OT2 OD034190/OD/NIH HHS/United States ; U01 CA253405/CA/NCI NIH HHS/United States ; R01 HG011274/HG/NHGRI NIH HHS/United States ; U24 HG011853/HG/NHGRI NIH HHS/United States ; }, abstract = {The Genome in a Bottle Consortium (GIAB), hosted by the National Institute of Standards and Technology (NIST), is developing new matched tumor-normal samples, the first to be explicitly consented for public dissemination of genomic data and cell lines. Here, we describe a comprehensive genomic dataset from the first individual, HG008, including DNA from an adherent, epithelial-like pancreatic ductal adenocarcinoma (PDAC) tumor cell line and matched normal cells from duodenal and pancreatic tissues. Data for the tumor-normal matched samples comes from thirteen distinct state-of-the-art whole genome measurement technologies, including high depth short and long-read bulk whole genome sequencing (WGS), single cell WGS, and Hi-C, and karyotyping. These data will be used by the GIAB Consortium to develop matched tumor-normal benchmarks for somatic variant detection. We expect these data to facilitate innovation for whole genome measurement technologies, de novo assembly of tumor and normal genomes, and bioinformatic tools to identify small and structural somatic mutations. This first-of-its-kind broadly consented open-access resource will facilitate further understanding of sequencing methods used for cancer biology.}, } @article {pmid39345343, year = {2024}, author = {Halpern, B and Vörös, J and Mc Cartney, AM and Formenti, G and Mouton, A and , and , and , and , }, title = {The genome sequence of the Hungarian meadow viper, Vipera ursinii rakosiensis Méhely, 1893.}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {404}, pmid = {39345343}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual female Vipera ursinii rakosiensis (the Hungarian meadow viper; Chordata; Lepidosauria; Squamata; Viperidae). The genome sequence is 1,625.0 megabases in span. Most of the assembly is scaffolded into 19 chromosomal pseudomolecules, including the W and Z sex chromosomes. The mitochondrial genome has also been assembled and is 17.38 kilobases in length.}, } @article {pmid39343505, year = {2024}, author = {Eneli, I and Heeren, FAN and Cason-Wilkerson, RL and Pratt, KJ}, title = {Metabolic and Bariatric Surgery for Adolescents.}, journal = {Pediatric clinics of North America}, volume = {71}, number = {5}, pages = {981-998}, doi = {10.1016/j.pcl.2024.06.007}, pmid = {39343505}, issn = {1557-8240}, mesh = {Humans ; Adolescent ; *Bariatric Surgery/methods ; *Pediatric Obesity/surgery ; Obesity, Morbid/surgery/psychology ; Gastrectomy/methods ; }, abstract = {Obesity is a chronic, complex, and multifactorial disease. Currently, approximately 6% have severe obesity with higher rates seen among racial/ethnic minority subgroups and in rural communities. Severe obesity is associated with cardiometabolic, psychologic, and musculoskeletal comorbidities. Metabolic and bariatric surgery is an effective treatment option for adolescents endorsed by major pediatric organizations. The most common procedure is the vertical sleeve gastrectomy. Pre-operative evaluation includes an in-depth medical, nutrition, physical activity and psychosocial assessment, with a care plan developed by a multidicplinary team with the adolescent and caregiver. The post-operative plan should include monitoring for surgical complications, weight regain, micronutrient deficiencies, psychologic challenges, and transition to adult care.}, } @article {pmid39341239, year = {2024}, author = {Adomako, MO and Jin, L and Li, C and Liu, J and Adu, D and Seshie, VI and Yu, FH}, title = {Mechanisms underpinning microplastic effects on the natural climate solutions of wetland ecosystems.}, journal = {The Science of the total environment}, volume = {954}, number = {}, pages = {176491}, doi = {10.1016/j.scitotenv.2024.176491}, pmid = {39341239}, issn = {1879-1026}, abstract = {Wetland ecosystems are vital carbon dioxide (CO2) sinks, offering significant nature-based solutions for global climate mitigation. However, the recent influx of microplastic (MP) into wetlands substantially impacts key drivers (e.g., plants and microorganisms) underpinning these wetland functions. While MP-induced greenhouse gas (GHG) emissions and effects on soil organic carbon (SOC) mineralization potentially threaten the long-term wetland C-climate feedbacks, the exact mechanisms and linkage are unclear. This review provides a conceptual framework to elaborate on the interplay between MPs, wetland ecosystems, and the atmospheric milieu. We also summarize published studies that validate possible MP impacts on natural climate solutions of wetlands, as well as provide extensive elaboration on underlying mechanisms. We briefly highlight the relationships between MP influx, wetland degradation, and climate change and conclude by identifying key gaps for future research priorities. Globally, plastic production, MP entry into aquatic systems, and wetland degradation-related emissions are predicted to increase. This means that MP-related emissions and wetland-climate feedback should be addressed in the context of the UN Paris Climate Agreement on net-zero emissions by 2050. This overview serves as a wake-up call on the alarming impacts of MPs on wetland ecosystems and urges a global reconsideration of nature-based solutions in the context of climate mitigation.}, } @article {pmid39340701, year = {2024}, author = {Gang, J and Ping, Y and Du, C}, title = {Anti-Magnaporthe oryzae Activity of Streptomyces bikiniensis HD-087 In Vitro and Bioinformatics Analysis of Polyketide Synthase Gene pksL.}, journal = {Current microbiology}, volume = {81}, number = {11}, pages = {379}, pmid = {39340701}, issn = {1432-0991}, support = {32172468//National Natural Science Foundation of China/ ; }, mesh = {*Polyketide Synthases/genetics/metabolism ; *Streptomyces/genetics/metabolism/enzymology ; *Computational Biology ; *Multigene Family ; Bacterial Proteins/genetics/metabolism ; Erythromycin/pharmacology ; Antifungal Agents/pharmacology/metabolism ; Polyketides/metabolism/pharmacology ; Anti-Bacterial Agents/pharmacology ; Molecular Docking Simulation ; Ascomycota ; }, abstract = {Streptomyces bikiniensis HD-087 is capable of synthesizing various antimicrobial substances to counter the detrimental effects of hazardous microorganisms. To elucidate whether it produces polyketide antibiotics and the synthesis mechanism of antibiotic substances, the metabolites and related genes of S. bikiniensis HD-087 were analyzed through LC-MS, anti-Magnaporthe oryzae activity detection, and bioinformatics approaches. The result indicated that the strain HD-087 could produce erythromycin, a polyketide antibiotic. The inhibitory zones of the fermentation supernatant of strain HD-087 and methanol solution of erythromycin extract against M. oryzae were 40.84 ± 0.68 mm and 33.18 ± 0.81 mm, respectively. The IC50 value of erythromycin extract for inhibiting spore germination of erythromycin extract was 220.43 μg/mL. There are two polyketide synthesis gene clusters in the genome of strain HD-087, namely t1pks-nrps and t3pks-lantipeptide-t1pks-nrps. The key gene pksL in the t3pks-lantipeptide-t1pks-nrps gene cluster was predicted. The results suggested that it encodes a stable, hydrophilic, and acidic protein, mainly composed of α-helix and random coil. The PksL protein contains dehydrogenase (DH), ketone reductase (KR), acyl carrier protein (ACP), and ketone synthase (KS) domains. Moreover, it can form interaction networks with 11 proteins containing domains, such as polyketide synthase and ACP synthase. The molecular docking between PksL and acetyl-CoA is stable and strong, suggesting that PksL protein could catalyze the synthesis of polyketides with CoA as a substrate. This study provides a theoretical basis for further exploring the polyketides synthesis mechanism and developing antifungal metabolites in S. bikiniensis HD-087.}, } @article {pmid39337302, year = {2024}, author = {Romano Spica, V and Volpini, V and Valeriani, F and Carotenuto, G and Arcieri, M and Platania, S and Castrignanò, T and Clementi, ME and Michetti, F}, title = {In Silico Predicting the Presence of the S100B Motif in Edible Plants and Detecting Its Immunoreactive Materials: Perspectives for Functional Foods, Dietary Supplements and Phytotherapies.}, journal = {International journal of molecular sciences}, volume = {25}, number = {18}, pages = {}, pmid = {39337302}, issn = {1422-0067}, mesh = {*Dietary Supplements ; *S100 Calcium Binding Protein beta Subunit/metabolism ; *Functional Food ; *Plants, Edible/chemistry ; Computer Simulation ; Amino Acid Motifs ; Phytotherapy/methods ; Computational Biology/methods ; Humans ; Fruit/chemistry/metabolism ; Phylogeny ; Plant Proteins/metabolism ; }, abstract = {The protein S100B is a part of the S100 protein family, which consists of at least 25 calcium-binding proteins. S100B is highly conserved across different species, supporting important biological functions. The protein was shown to play a role in gut microbiota eubiosis and is secreted in human breast milk, suggesting a physiological trophic function in newborn development. This study explores the possible presence of the S100B motif in plant genomes, and of S100B-like immunoreactive material in different plant extracts, opening up potential botanical uses for dietary supplementation. To explore the presence of the S100B motif in plants, a bioinformatic workflow was used. In addition, the immunoreactivity of S100B from vegetable and fruit samples was tested using an ELISA assay. The S100B motif was expected in silico in the genome of different edible plants belonging to the Viridiplantae clade, such as Durio zibethinus or Malus domestica and other medicinal species. S100B-like immunoreactive material was also detected in samples from fruits or leaves. The finding of S100B-like molecules in plants sheds new light on their role in phylogenesis and in the food chain. This study lays the foundation to elucidate the possible beneficial effects of plants or derivatives containing the S100B-like principle and their potential use in nutraceuticals.}, } @article {pmid39332349, year = {2024}, author = {Sun, Q and Zhang, Z and Ping, Q and Wang, L and Li, Y}, title = {Insight into using multi-omics analysis to elucidate nitrogen removal mechanisms in a novel improved constructed rapid infiltration system: Functional gene and metabolite signatures.}, journal = {Water research}, volume = {267}, number = {}, pages = {122502}, doi = {10.1016/j.watres.2024.122502}, pmid = {39332349}, issn = {1879-2448}, mesh = {*Nitrogen/metabolism ; *Wastewater/chemistry ; Waste Disposal, Fluid/methods ; Denitrification ; Nitrification ; Metabolomics ; Metagenomics ; Ammonium Compounds/metabolism ; Multiomics ; }, abstract = {In this study, a laboratory-scale improved constructed rapid infiltration (imCRI) system with non-saturated and saturated layers was constructed, and corn cobs as solid carbon source were added to the saturated layer to enhance the removal of nitrogen. Combined analyses of metagenomics and metabolomics were conducted to elucidate the nitrogen removal mechanism in the imCRI system. The results showed that the hydraulic load significantly influenced the treatment performance of the imCRI system, and a hydraulic load of 1.25 m[3]/(m[2]⋅d) was recommended. Under optimal conditions, the imCRI system using simulated wastewater achieved average removal efficiencies of 97.8 % for chemical oxygen demand, 85.7 % for total nitrogen (TN), and 97.6 % for ammonia nitrogen. Metagenomic and metabolomic analyses revealed that besides nitrification and denitrification, dissimilatory nitrate reduction to ammonium (DNRA), anammox, etc., are also involved in nitrogen metabolism in the imCRI system. Although nitrification was the predominant pathway in the non-saturated layer, aerobic denitrification also occurred, accounting for 22.59 % of the TN removal. In the saturated layer, nitrogen removal was attributed to synergistic effects of denitrification, DNRA and anammox. Moreover, correlation analysis among nitrogen removal, functional genes and metabolites suggested that metabolites related to the tricarboxylic acid cycle generated from the glycolysis of corn cobs provided sufficient energy for denitrification. Our results can offer a promising technology for decentralized wastewater treatment with stringent nitrogen removal requirements, and provide a foundation for understanding the underlying nitrogen transformation and removal mechanism.}, } @article {pmid39331699, year = {2024}, author = {Yang, Z and Shan, Y and Liu, X and Chen, G and Pan, Y and Gou, Q and Zou, J and Chang, Z and Zeng, Q and Yang, C and Kong, J and Sun, Y and Li, S and Zhang, X and Wu, WC and Li, C and Peng, H and Holmes, EC and Guo, D and Shi, M}, title = {VirID: Beyond Virus Discovery-An Integrated Platform for Comprehensive RNA Virus Characterization.}, journal = {Molecular biology and evolution}, volume = {41}, number = {10}, pages = {}, pmid = {39331699}, issn = {1537-1719}, support = {82341118//National Natural Science Foundation of China/ ; 2022A1515011854//Natural Science Foundation of Guangdong Province of China/ ; JCYJ20210324124414040//Shenzhen Science and Technology Program/ ; //Hong Kong Innovation and Technology Fund (ITF/ ; GZNL2023A01001//Major Project of Guangzhou National Laboratory/ ; 2019ZT08Y464//Guangdong Province "Pearl River Talent Plan" Innovation, Entrepreneurship Team Project/ ; ZDSYS20220606100803007//Fund of Shenzhen Key Laboratory/ ; GNT2017197//NHMRC (Australia) Investigator Award/ ; //Innovation and Technology Commission, Hong Kong Special Administrative Region, China/ ; }, mesh = {*RNA Viruses/genetics ; *Software ; *Metagenomics/methods ; *Phylogeny ; Humans ; RNA-Dependent RNA Polymerase/genetics ; Computational Biology/methods ; }, abstract = {RNA viruses exhibit vast phylogenetic diversity and can significantly impact public health and agriculture. However, current bioinformatics tools for viral discovery from metagenomic data frequently generate false positive virus results, overestimate viral diversity, and misclassify virus sequences. Additionally, current tools often fail to determine virus-host associations, which hampers investigation of the potential threat posed by a newly detected virus. To address these issues we developed VirID, a software tool specifically designed for the discovery and characterization of RNA viruses from metagenomic data. The basis of VirID is a comprehensive RNA-dependent RNA polymerase database to enhance a workflow that includes RNA virus discovery, phylogenetic analysis, and phylogeny-based virus characterization. Benchmark tests on a simulated data set demonstrated that VirID had high accuracy in profiling viruses and estimating viral richness. In evaluations with real-world samples, VirID was able to identify RNA viruses of all types, but also provided accurate estimations of viral genetic diversity and virus classification, as well as comprehensive insights into virus associations with humans, animals, and plants. VirID therefore offers a robust tool for virus discovery and serves as a valuable resource in basic virological studies, pathogen surveillance, and early warning systems for infectious disease outbreaks.}, } @article {pmid39331660, year = {2024}, author = {Pasqualini, J and Facchin, S and Rinaldo, A and Maritan, A and Savarino, E and Suweis, S}, title = {Emergent ecological patterns and modelling of gut microbiomes in health and in disease.}, journal = {PLoS computational biology}, volume = {20}, number = {9}, pages = {e1012482}, pmid = {39331660}, issn = {1553-7358}, mesh = {Humans ; *Gastrointestinal Microbiome/physiology/genetics ; Models, Biological ; Computational Biology ; Dysbiosis/microbiology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Recent advancements in next-generation sequencing have revolutionized our understanding of the human microbiome. Despite this progress, challenges persist in comprehending the microbiome's influence on disease, hindered by technical complexities in species classification, abundance estimation, and data compositionality. At the same time, the existence of macroecological laws describing the variation and diversity in microbial communities irrespective of their environment has been recently proposed using 16s data and explained by a simple phenomenological model of population dynamics. We here investigate the relationship between dysbiosis, i.e. in unhealthy individuals there are deviations from the "regular" composition of the gut microbial community, and the existence of macro-ecological emergent law in microbial communities. We first quantitatively reconstruct these patterns at the species level using shotgun data, and addressing the consequences of sampling effects and statistical errors on ecological patterns. We then ask if such patterns can discriminate between healthy and unhealthy cohorts. Concomitantly, we evaluate the efficacy of different statistical generative models, which incorporate sampling and population dynamics, to describe such patterns and distinguish which are expected by chance, versus those that are potentially informative about disease states or other biological drivers. A critical aspect of our analysis is understanding the relationship between model parameters, which have clear ecological interpretations, and the state of the gut microbiome, thereby enabling the generation of synthetic compositional data that distinctively represent healthy and unhealthy individuals. Our approach, grounded in theoretical ecology and statistical physics, allows for a robust comparison of these models with empirical data, enhancing our understanding of the strengths and limitations of simple microbial models of population dynamics.}, } @article {pmid39331576, year = {2024}, author = {Qiao, B and Wang, S and Hou, M and Chen, H and Zhou, Z and Xie, X and Pang, S and Yang, C and Yang, F and Zou, Q and Sun, S}, title = {Identifying nucleotide-binding leucine-rich repeat receptor and pathogen effector pairing using transfer-learning and bilinear attention network.}, journal = {Bioinformatics (Oxford, England)}, volume = {40}, number = {10}, pages = {}, doi = {10.1093/bioinformatics/btae581}, pmid = {39331576}, issn = {1367-4811}, support = {62273086//National Natural Science Foundation of China/ ; }, mesh = {*Deep Learning ; *NLR Proteins/metabolism ; *Computational Biology/methods ; Algorithms ; }, abstract = {MOTIVATION: Nucleotide-binding leucine-rich repeat (NLR) family is a class of immune receptors capable of detecting and defending against pathogen invasion. They have been widely used in crop breeding. Notably, the correspondence between NLRs and effectors (CNE) determines the applicability and effectiveness of NLRs. Unfortunately, CNE data is very scarce. In fact, we've found a substantial 91 291 NLRs confirmed via wet experiments and bioinformatics methods but only 387 CNEs are recognized, which greatly restricts the potential application of NLRs.

RESULTS: We propose a deep learning algorithm called ProNEP to identify NLR-effector pairs in a high-throughput manner. Specifically, we conceptualized the CNE prediction task as a protein-protein interaction (PPI) prediction task. Then, ProNEP predicts the interaction between NLRs and effectors by combining the transfer learning with a bilinear attention network. ProNEP achieves superior performance against state-of-the-art models designed for PPI predictions. Based on ProNEP, we conduct extensive identification of potential CNEs for 91 291 NLRs. With the rapid accumulation of genomic data, we expect that this tool will be widely used to predict CNEs in new species, advancing biology, immunology, and breeding.

The ProNEP is available at http://nerrd.cn/#/prediction. The project code is available at https://github.com/QiaoYJYJ/ProNEP.}, } @article {pmid39328967, year = {2024}, author = {Dey, B and Ferdous, J and Ahmed, R}, title = {Comprehensive stomata image dataset of Sundarbans Mangrove and Ratargul Swamp forest tree species in Bangladesh.}, journal = {Data in brief}, volume = {57}, number = {}, pages = {110908}, pmid = {39328967}, issn = {2352-3409}, abstract = {Plants' leaf stomata are crucial for various scientific research, including identifying species, studying ecology, conserving ecosystems, improving agriculture, and advancing the field of deep learning. This dataset, containing 1083 images, encompasses 11 species from two distinct locations in Bangladesh: nine from the Sundarbans mangrove forest and two from the Ratargul Swamp Forest. It is a valuable tool for refining machine learning algorithms that specialize in detecting stomata and categorizing species accurately. Researchers can explore a deeper understanding of plant physiology, adaptation mechanisms, and environmental interactions by employing pattern recognition, deep learning, and feature extraction techniques. Additionally, this dataset could be a potential tool for enhancing research in macroscopic metamaterials, extending its impact beyond traditional biological studies into interdisciplinary fields of technology and material science.}, } @article {pmid39326744, year = {2024}, author = {Wang, Y and Feng, Z and Ghani, MI and Wang, Q and Zeng, L and Yang, X and Zhang, X and Chen, C and Li, S and Cao, P and Chen, X and Cernava, T}, title = {Co-exposure to microplastics and soil pollutants significantly exacerbates toxicity to crops: Insights from a global meta and machine-learning analysis.}, journal = {The Science of the total environment}, volume = {954}, number = {}, pages = {176490}, doi = {10.1016/j.scitotenv.2024.176490}, pmid = {39326744}, issn = {1879-1026}, mesh = {*Soil Pollutants/toxicity ; *Microplastics/toxicity ; *Crops, Agricultural ; *Machine Learning ; Environmental Monitoring/methods ; Soil/chemistry ; Environmental Pollution/statistics & numerical data ; }, abstract = {Environmental contamination of microplastics (MPs) is ubiquitous worldwide, and co-contamination of arable soils with MPs and other pollutants is of increasing concern, and may lead to unexpected consequences on crop production. However, the overall implications of this combined effect, whether beneficial or detrimental, remain a subject of current debate. Here, we conducted a global meta and machine-learning analysis to evaluate the effects of co-exposure to MPs and other pollutants on crops, utilizing 3346 biological endpoints derived from 68 different studies. Overall, compared with control groups that only exposure to conventional soil contaminants, co-exposure significantly exacerbated toxicity to crops, particularly with MPs intensifying adverse effects on crop morphology, oxidative damage, and photosynthetic efficiency. Interestingly, our analysis demonstrated a significant reduction in the accumulation of pollutants in the crop due to the presence of MPs. In addition, the results revealed that potential adverse effects were primarily associated with crop species, MPs mass concentration, and exposure duration. Our study reaffirms the substantial consequences of MPs as emerging pollutants on crops within the context of integrated pollution, providing novel insights into improving sustainability in agro-ecosystems.}, } @article {pmid39326182, year = {2024}, author = {Li, D and Ping, Q and Mo, R and Guo, W and Zhang, S and Wang, L and Li, Y}, title = {Revealing synergistic mechanisms of biochar-assisted microbial electrolysis cells in enhancing the anaerobic digestion performance of waste activated sludge: Extracellular polymeric substances characterization, enzyme activity assay, and multi-omics analysis.}, journal = {Water research}, volume = {267}, number = {}, pages = {122501}, doi = {10.1016/j.watres.2024.122501}, pmid = {39326182}, issn = {1879-2448}, mesh = {*Sewage/microbiology ; Anaerobiosis ; *Extracellular Polymeric Substance Matrix/metabolism ; Charcoal/chemistry ; Waste Disposal, Fluid/methods ; Electrolysis ; Methane/metabolism ; Multiomics ; }, abstract = {Although biochar (BC)-assisted microbial electrolysis cells (MEC) has been shown to improve anaerobic digestion (AD) performance of waste activated sludge (WAS), the underlying mechanisms remain unclear. This study conducted an in-depth investigation into the mechanism based on analyses of extracellular polymeric substances (EPS) characteristics, enzyme activities and multi-omics. The results showed that compared with the control group, methane production improved by 16.73 %, 21.32 %, and 29.37 % in the BC, MEC, and BC-assisted MEC (BC-MEC) groups, respectively. The reconfiguration of the protein secondary structure increased the hydrophobicity of the EPS, thereby promoting microbial aggregation. In addition, partial least-squares path modeling (PLS-PM) and mantel test based on the enzyme activity and multi-omics analyses revealed that the promotional effect of MEC on the hydrolysis of WAS was superior to that of BC, while BC was more advantageous in promoting electron transfer and biofilm formation regulated by quorum sensing. The synergistic effects of BC and MEC were exemplified in the BC-MEC group. g_norank_Aminicenantales responsible for the hydrolysis of WAS was enriched (29.6 %), and the activities of hydrolytic enzymes including α-glucosidases and proteases were increased by 29.1 % and 43.6 %, respectively. Further, the expressions of genes related to acyl homoserine lactones (AHLs) and diffusible signal factor (DSF) in quorum sensing systems, as well as the genes related to hydrogenase involved in electron transfer (mbhJKL, hyfB-JR, hypA-F, and hoxFHUY), were up-regulated in the BC-MEC group. This facilitated electron transfer and microbial communication, consequently enhancing methane production. This research significantly advances the understanding of the mechanism by which BC-assisted MEC enhances AD performance and provides valuable insights into strategies for improving energy recovery from WAS.}, } @article {pmid39325874, year = {2024}, author = {Zhu, Y and Chen, G and Sun, Y}, title = {VirTAXA: enhancing RNA virus taxonomic classification with remote homology search and tree-based validation.}, journal = {Bioinformatics (Oxford, England)}, volume = {40}, number = {10}, pages = {}, pmid = {39325874}, issn = {1367-4811}, support = {11206819//City University of Hong Kong, Hong Kong Research Grants Council/ ; //Hong Kong Innovation and Technology Fund/ ; }, mesh = {*RNA Viruses/genetics/classification ; *Software ; RNA, Viral/genetics ; Phylogeny ; Sequence Analysis, RNA/methods ; Genome, Viral ; Algorithms ; Computational Biology/methods ; }, abstract = {SUMMARY: RNA viruses are ubiquitous across a broad spectrum of ecosystems. Therefore, beyond their significant implications for public health, RNA viruses are also key players in ecological processes. High-through sequencing has accelerated the discovery of RNA viruses. Nevertheless, many of these viruses lack taxonomic annotation, posing a challenge to functional inference and evolutionary study. In particular, virus classification at the genus level remains difficult due to the limited reference data and ambiguous boundaries between some closely related genera. We introduce VirTAXA, a robust classification tool that combines remote homology search and tree-based validation to enhance the genus-level taxonomic classification of RNA viruses. VirTAXA is able to predict the genus label of an assembled viral contig and provide evidence type for each prediction. It achieves comparable accuracy to state-of-the-art methods while assigning genus labels to a greater number of sequences. Specifically, on the Global Ocean RNA metatranscriptomic data, VirTAXA can assign genus labels for 18% more contigs than the second-best classification tool. Furthermore, we demonstrated that VirTAXA can be conveniently extended to other types of viruses.

The source code and data of VirTAXA are available via https://github.com/JudithEllyn/VirTAXA.}, } @article {pmid39323974, year = {2022}, author = {Boyes, D and Crowley, LM and , and , and , and , and , and Skojec, C and Plotkin, D and Kawahara, AY and , }, title = {The genome sequence of the 6-spot burnet, Zygaena filipendulae (Linnaeus, 1758).}, journal = {Wellcome open research}, volume = {7}, number = {}, pages = {197}, pmid = {39323974}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual female Zygaena filipendulae (6-spot burnet; Arthropoda; Insecta; Lepidoptera; Zygaenidae). The genome sequence is 365.9 megabases in span. The majority of the assembly (99.99%) is scaffolded into 31 chromosomal pseudomolecules, with the W and Z sex chromosomes assembled. The complete mitochondrial genome was also assembled and is 15.6 kilobases in length. Gene annotation of this assembly on Ensembl has identified 12,493 protein coding genes.}, } @article {pmid39323166, year = {2024}, author = {Lin, ML and Hu, ZQ and Peng, WH and Ye, WL and Zhang, CL and Huang, XR and Chen, S and Gui, HR}, title = {[Pollution Assessment and Source Apportionment of Heavy Metals in the Surrounding Soil of Typical Mining Areas in Tongling, Anhui Province].}, journal = {Huan jing ke xue= Huanjing kexue}, volume = {45}, number = {9}, pages = {5494-5505}, doi = {10.13227/j.hjkx.202307274}, pmid = {39323166}, issn = {0250-3301}, abstract = {To study the level of heavy metal pollution and ecological risks in the soil around typical mining areas in Tongling, a total of 150 soil samples were collected from the study area. The content characteristics of 10 elements, namely, As, Cd, Cr, Cu, Hg, Mn, Ni, Pb, Fe, and Zn, in the soils were analyzed. Methods including enrichment factor, the geo-accumulation index, single-factor pollution index, Nemero comprehensive pollution index, and potential ecological risk index were used to evaluate the pollution status of heavy metals in the soil of the study area. The pollution sources of heavy metals in the soil were also analyzed using correlation analysis, cluster analysis, and principal component analysis. The results showed that except for Cr and Fe, the average contents of the other eight heavy metal elements were higher than the soil background values in the study area. Pb, Zn, As, Cu, and Cd had a high degree of variation and were significantly affected by external interference. The spatial distribution showed that both Cr and Ni showed a decreasing trend from the edge to the central region, whereas the other eight heavy metals showed a decreasing trend from the central region to the surrounding areas. The pollution level of Cd and Cu in the soil of the research area was relatively severe. The overall ecological risk was at a medium to low level. Cd and Hg were the main contributing factors. As, Cd, Cu, Fe, Mn, Pb, and Zn mainly came from agricultural, industrial, and transportation sources, whereas Cr and Ni were mainly from natural sources. However, the sources of Hg were relatively complex. The research results can provide a scientific basis for the prevention and control of soil heavy metal pollution in metal mining areas, as well as the remediation of mine pollution.}, } @article {pmid39321538, year = {2024}, author = {Cao, J and Lei, Y and Li, W and Jiang, X and Li, M}, title = {Coupled digital visualization and multi-omics uncover neurobehavioral dysfunction in zebrafish induced by resorcinol bis(diphenylphosphate).}, journal = {Environment international}, volume = {192}, number = {}, pages = {109023}, doi = {10.1016/j.envint.2024.109023}, pmid = {39321538}, issn = {1873-6750}, mesh = {Animals ; *Zebrafish/physiology ; Water Pollutants, Chemical/toxicity ; Blood-Brain Barrier/drug effects ; Resorcinols/toxicity ; Brain/drug effects/metabolism ; Behavior, Animal/drug effects ; Gastrointestinal Microbiome/drug effects ; Multiomics ; }, abstract = {Resorcinol bis(diphenylphosphate) (RDP) is an emerging pollutant that has been frequently detected in aquatic environments, although its toxicity is poorly characterized. To understand how RDP affects the neural system, two-month-old zebrafish were exposed to RDP at concentrations of 0.1 and 10 μg/L for 60 days. Following exposure, behavioral assessments were conducted, revealing the emergence of anxiety-like symptoms and memory deficits among the adult fish exposed to RDP, especially at the higher concentration. The increased blood-brain barrier (BBB) permeability (4.67-5.58-fold higher than the control group), reduced expression of tight junction proteins and the rapid brain RDP bioaccumulation (15.63 ± 2.34 ng/g wet weight) indicated the neurotoxicity of RDP. Excess reactive oxygen species synthesis (2.20-2.50-fold) was induced by RDP, leading to mitochondrial dysfunction and decreased production of neurotransmitters in the brain, specifically serotonin (5-HT; 16.3 %) and dopamine (DA; 18.1 %). Metabolomic analysis revealed that the low-toxicity RDP dose up-regulated lipid-related metabolites, while the high-toxicity dose up-regulated arachidonic acid metabolism and disrupted amino acid metabolism, including tryptophan and tyrosine metabolism related to dopaminergic and serotonergic pathways. The dysregulation of genes in various cellular processes was identified by transcriptomics, mainly involved in cell adhesion molecules and gap junctions, and oxidative phosphorylation, which were directly associated with BBB permeability and oxidative stress, respectively. Correlation analysis of microbiome-metabolite-host links built a mechanistic hypothesis for alterations in gut microbiota (Actinobacteriota and Proteobacteria) induced by high-dose RDP leading to the alteration of tryptophan, tyrosine, and arachidonic acid metabolism, decreasing the production of 5-HT and DA through the gut-brain axis. This study provides valuable insights into the mechanism underlying RDP-induced neurotoxicity in zebrafish, which can inform ecological risk assessments.}, } @article {pmid39320588, year = {2024}, author = {Oroud, IM}, title = {The implications of climate change on freshwater resources in the arid and semiarid Mediterranean environments using hydrological modeling, GIS tools, and remote sensing.}, journal = {Environmental monitoring and assessment}, volume = {196}, number = {10}, pages = {979}, pmid = {39320588}, issn = {1573-2959}, mesh = {*Climate Change ; *Environmental Monitoring/methods ; *Hydrology ; *Remote Sensing Technology ; *Geographic Information Systems ; Fresh Water/chemistry ; Groundwater/chemistry ; Models, Theoretical ; Mediterranean Region ; Desert Climate ; Water Resources ; }, abstract = {Precipitation partitioning in arid and semiarid environments is not well understood due to scanty precipitation, its temporal distribution, and the lack/absence of adequate measurements of the hydrometeorological components. Simulation methods have the potential to bridge the data gap, thereby providing a window to estimate the water balance components. The present investigation evaluates the water balance components of a typical watershed situated in the southeastern Mediterranean for the period 1979 through 2019 using daily meteorological data and a grid spacing of 250 m. Generated runoff results were commensurate with corresponding values obtained using the SWAT model. Computed groundwater recharge is also compatible with recharge values calculated using the chloride mass balance method. Results show that average runoff and groundwater recharge for the entire period was ⁓24 mm a[-1] and 19 mm a[-1], giving a precipitation ratio of 9.5% and 7.5%, respectively. Substantial interannual variability in the water balance components was observed during the study period which reflected the significant precipitation fluctuations typifying the Eastern Mediterranean. Results show that the period extending from 1998/1999 through 2018/2019 witnessed an 18% drop in annual precipitation, while surface runoff and groundwater recharge experienced a reduction of ⁓34% and ⁓67%, respectively. Although groundwater recharge is a complex function of numerous meteorological and geological factors, the NDVI can provide an excellent indicator of groundwater recharge in marginal Mediterranean environments. This is highly beneficial in areas where climate records are scanty or absent. The presented results emphasize the significant impacts of global warming and aridification on the future availability of water resources in the semiarid marginal climates in the Eastern Mediterranean and point out clearly that water resources in this area will become scarcer, leading to multiple security threats at national and regional levels.}, } @article {pmid39313745, year = {2024}, author = {Dabrowski, JK and Yang, EJ and Crofts, SJC and Hillary, RF and Simpson, DJ and McCartney, DL and Marioni, RE and Kirschner, K and Latorre-Crespo, E and Chandra, T}, title = {Probabilistic inference of epigenetic age acceleration from cellular dynamics.}, journal = {Nature aging}, volume = {4}, number = {10}, pages = {1493-1507}, pmid = {39313745}, issn = {2662-8465}, support = {/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Humans ; *Epigenesis, Genetic ; *Aging/genetics ; *DNA Methylation ; CpG Islands/genetics ; Genome-Wide Association Study ; Aged ; Female ; Male ; Middle Aged ; Models, Statistical ; }, abstract = {The emergence of epigenetic predictors was a pivotal moment in geroscience, propelling the measurement and concept of biological aging into a quantitative era; however, while current epigenetic clocks show strong predictive power, they are data-driven in nature and are not based on the underlying biological mechanisms driving methylation dynamics. We show that predictions of these clocks are susceptible to several confounding non-age-related phenomena that make interpretation of these estimates and associations difficult. To address these limitations, we developed a probabilistic model describing methylation transitions at the cellular level. Our approach reveals two measurable components, acceleration and bias, which directly reflect perturbations of the underlying cellular dynamics. Acceleration is the proportional increase in the speed of methylation transitions across CpG sites, whereas bias corresponds to global changes in methylation levels. Using data from 15,900 participants from the Generation Scotland study, we develop a robust inference framework and show that these are two distinct processes confounding current epigenetic predictors. Our results show improved associations of acceleration and bias with physiological traits known to impact healthy aging, such as smoking and alcohol consumption, respectively. Furthermore, a genome-wide association study of epigenetic age acceleration identified seven genomic loci.}, } @article {pmid39312537, year = {2024}, author = {Malamud, J and Guloksuz, S and van Winkel, R and Delespaul, P and De Hert, MAF and Derom, C and Thiery, E and Jacobs, N and Rutten, BPF and Huys, QJM}, title = {Characterizing the dynamics, reactivity and controllability of moods in depression with a Kalman filter.}, journal = {PLoS computational biology}, volume = {20}, number = {9}, pages = {e1012457}, pmid = {39312537}, issn = {1553-7358}, support = {/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Humans ; *Affect/physiology ; *Depression/physiopathology ; *Computational Biology ; Algorithms ; Ecological Momentary Assessment ; Psychometrics/methods ; Male ; Female ; }, abstract = {BACKGROUND: Mood disorders involve a complex interplay between multifaceted internal emotional states, and complex external inputs. Dynamical systems theory suggests that this interplay between aspects of moods and environmental stimuli may hence determine key psychopathological features of mood disorders, including the stability of mood states, the response to external inputs, how controllable mood states are, and what interventions are most likely to be effective. However, a comprehensive computational approach to all these aspects has not yet been undertaken.

METHODS: Here, we argue that the combination of ecological momentary assessments (EMA) with a well-established dynamical systems framework-the humble Kalman filter-enables a comprehensive account of all these aspects. We first introduce the key features of the Kalman filter and optimal control theory and their relationship to aspects of psychopathology. We then examine the psychometric and inferential properties of combining EMA data with Kalman filtering across realistic scenarios. Finally, we apply the Kalman filter to a series of EMA datasets comprising over 700 participants with and without symptoms of depression.

RESULTS: The results show a naive Kalman filter approach performs favourably compared to the standard vector autoregressive approach frequently employed, capturing key aspects of the data better. Furthermore, it suggests that the depressed state involves alterations to interactions between moods; alterations to how moods responds to external inputs; and as a result an alteration in how controllable mood states are. We replicate these findings qualitatively across datasets and explore an extension to optimal control theory to guide therapeutic interventions.

CONCLUSIONS: Mood dynamics are richly and profoundly altered in depressed states. The humble Kalman filter is a well-established, rich framework to characterise mood dynamics. Its application to EMA data is valid; straightforward; and likely to result in substantial novel insights both into mechanisms and treatments.}, } @article {pmid39309423, year = {2023}, author = {Boyes, D and Blaxter, ML and , and , and , and , and , and , }, title = {The genome sequence of the Beautiful Hook-tip, Laspeyria flexula (Denis & Schiffermüller, 1775).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {529}, pmid = {39309423}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual male Laspeyria flexula (the Beautiful Hook-tip; Arthropoda; Insecta; Lepidoptera; Erebidae). The genome sequence is 450.9 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.58 kilobases in length. Gene annotation of this assembly on Ensembl identified 13,281 protein coding genes.}, } @article {pmid39309224, year = {2024}, author = {Boyes, D and Lees, DC and Wawman, DC and , and , and , and , and , and , and , and , }, title = {The genome sequence of the Blue-bordered Carpet moth Plemyria rubiginata (Denis & Schiffermüller) 1775.}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {271}, pmid = {39309224}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual female Plemyria rubiginata (the Blue-bordered Carpet moth; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 356.2 megabases in span. Most of the assembly is scaffolded into 30 chromosomal pseudomolecules, including the Z and W sex chromosomes. The mitochondrial genome has also been assembled and is 17.64 kilobases in length.}, } @article {pmid39309222, year = {2024}, author = {Boyes, D and Wawman, DC and , and , and , and , and , and , and , }, title = {The genome sequence of the Figure of Eighty moth Tethea ocularis Linnaeus, 1767.}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {348}, pmid = {39309222}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual male Tethea ocularis (the Figure of Eighty; Arthropoda; Insecta; Lepidoptera; Drepanidae). The genome sequence is 339.1 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.28 kilobases in length.}, } @article {pmid39304543, year = {2024}, author = {Hossen, MF and Sultana, N}, title = {Landscape transition-induced ecological risk modeling using GIS and remote sensing techniques: a case of Saint Martin Island, Bangladesh.}, journal = {Environmental monitoring and assessment}, volume = {196}, number = {10}, pages = {964}, pmid = {39304543}, issn = {1573-2959}, mesh = {Bangladesh ; *Environmental Monitoring/methods ; *Remote Sensing Technology ; *Geographic Information Systems ; *Conservation of Natural Resources ; *Islands ; *Ecosystem ; Risk Assessment/methods ; Humans ; Bayes Theorem ; }, abstract = {Uncontrolled human activity and nature are causing the deterioration of Saint Martin Island, Bangladesh's only tropical island, necessitating sustainable land use strategies and ecological practices. Therefore, the present study measures the land use/cover transition from 1974 to 2021, predicts 2032 and 2042, and constructs the spatiotemporal features of the Landscape Ecological Risk Index based on land use changes. The study utilized Maximum Likelihood Classification (MLC) on Landsat images from 1974, 1988, 2001, 2013, and Sentinel 2B in 2021, achieving ≥ 80% accuracy. The MLP-MC approach was also used to predict 2032 and 2042 LULC change patterns. The eco-risk index was developed using landscape disturbance and vulnerability indices, Bayesian Kriging interpolation, and spatial autocorrelations to indicate spatial clustering. The research found that settlements increased from 2.06 to 28.62 ha between 1974 and 2021 and would cover 41.22 ha in 2042, causing considerable losses in agricultural areas, waterbodies, sand, coral reefs, and vegetation. The area under study showed a more uniform and homogenous environment as Shannon's diversity and evenness scores decreased. The ecological risk of Saint Martin Island increased from 4.31 to 31.05 ha between 1974 and 2042 due to natural and human factors like erosion, tidal bores, population growth, coral mining, habitat destruction, and intensive agricultural practices and tourism, primarily in Nazrul Para, Galachipa, and Western Dakhin Para. The findings will benefit St. Martin Island stakeholders and policymakers by providing insights into current and potential landscape changes and land eco-management.}, } @article {pmid39303692, year = {2024}, author = {Crits-Christoph, A and Levy, JI and Pekar, JE and Goldstein, SA and Singh, R and Hensel, Z and Gangavarapu, K and Rogers, MB and Moshiri, N and Garry, RF and Holmes, EC and Koopmans, MPG and Lemey, P and Peacock, TP and Popescu, S and Rambaut, A and Robertson, DL and Suchard, MA and Wertheim, JO and Rasmussen, AL and Andersen, KG and Worobey, M and Débarre, F}, title = {Genetic tracing of market wildlife and viruses at the epicenter of the COVID-19 pandemic.}, journal = {Cell}, volume = {187}, number = {19}, pages = {5468-5482.e11}, pmid = {39303692}, issn = {1097-4172}, support = {U19 AI135995/AI/NIAID NIH HHS/United States ; R01 AI153044/AI/NIAID NIH HHS/United States ; T15 LM011271/LM/NLM NIH HHS/United States ; T32 AI007244/AI/NIAID NIH HHS/United States ; 75N93021C00015/AI/NIAID NIH HHS/United States ; /WT_/Wellcome Trust/United Kingdom ; U01 AI151812/AI/NIAID NIH HHS/United States ; R01 AI135992/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; *COVID-19/epidemiology/virology ; *SARS-CoV-2/genetics/isolation & purification ; *Animals, Wild/virology ; *Phylogeny ; Humans ; Pandemics ; }, abstract = {Zoonotic spillovers of viruses have occurred through the animal trade worldwide. The start of the COVID-19 pandemic was traced epidemiologically to the Huanan Seafood Wholesale Market. Here, we analyze environmental qPCR and sequencing data collected in the Huanan market in early 2020. We demonstrate that market-linked severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genetic diversity is consistent with market emergence and find increased SARS-CoV-2 positivity near and within a wildlife stall. We identify wildlife DNA in all SARS-CoV-2-positive samples from this stall, including species such as civets, bamboo rats, and raccoon dogs, previously identified as possible intermediate hosts. We also detect animal viruses that infect raccoon dogs, civets, and bamboo rats. Combining metagenomic and phylogenetic approaches, we recover genotypes of market animals and compare them with those from farms and other markets. This analysis provides the genetic basis for a shortlist of potential intermediate hosts of SARS-CoV-2 to prioritize for serological and viral sampling.}, } @article {pmid39301440, year = {2024}, author = {Morales, HE and Groombridge, JJ and Tollington, S and Henshaw, S and Tatayah, V and Ruhomaun, K and van Oosterhout, C and Gilbert, MTP and , and , and , and , }, title = {The genome sequence of the Mauritius parakeet, Alexandrinus eques (formerly Psittacula eques) (A.Newton & E. Newton, 1876).}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {378}, pmid = {39301440}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual male Alexandrinus eques, formerly Psittacula eques (the Mauritius Parakeet; Chordata; Aves; Psittaciformes; Psittacidae). The genome sequence is 1203.8 megabases in span. Most of the assembly is scaffolded into 35 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 18.86 kilobases in length.}, } @article {pmid39295890, year = {2023}, author = {Boyes, D and Januszczak, I and , and , and , and , and , and , }, title = {The genome sequence of the Lunar-spotted Pinion, Cosmia pyralina (Denis & Schiffermüller, 1775).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {545}, pmid = {39295890}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual male Cosmia pyralina (the Lunar-spotted Pinion; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 803.3 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.39 kilobases in length. Gene annotation of this assembly on Ensembl identified 19,901 protein coding genes.}, } @article {pmid39294496, year = {2024}, author = {Khaliq, AM and Rajamohan, M and Saeed, O and Mansouri, K and Adil, A and Zhang, C and Turk, A and Carstens, JL and House, M and Hayat, S and Nagaraju, GP and Pappas, SG and Wang, YA and Zyromski, NJ and Opyrchal, M and Lee, KP and O'Hagan, H and El Rayes, B and Masood, A}, title = {Spatial transcriptomic analysis of primary and metastatic pancreatic cancers highlights tumor microenvironmental heterogeneity.}, journal = {Nature genetics}, volume = {56}, number = {11}, pages = {2455-2465}, pmid = {39294496}, issn = {1546-1718}, mesh = {Humans ; *Tumor Microenvironment/genetics ; *Pancreatic Neoplasms/genetics/pathology ; *Carcinoma, Pancreatic Ductal/genetics/pathology ; *Transcriptome ; *Neoplasm Metastasis/genetics ; Gene Expression Regulation, Neoplastic ; Gene Expression Profiling/methods ; Female ; }, abstract = {Although the spatial, cellular and molecular landscapes of resected pancreatic ductal adenocarcinoma (PDAC) are well documented, the characteristics of its metastatic ecology remain elusive. By applying spatially resolved transcriptomics to matched primary and metastatic PDAC samples, we discovered a conserved continuum of fibrotic, metabolic and immunosuppressive spatial ecotypes across anatomical regions. We observed spatial tumor microenvironment heterogeneity spanning beyond that previously appreciated in PDAC. Through comparative analysis, we show that the spatial ecotypes exhibit distinct enrichment between primary and metastatic sites, implying adaptability to the local environment for survival and progression. The invasive border ecotype exhibits both pro-tumorigenic and anti-tumorigenic cell-type enrichment, suggesting a potential immunotherapy target. The ecotype heterogeneity across patients emphasizes the need to map individual patient landscapes to develop personalized treatment strategies. Collectively, our findings provide critical insights into metastatic PDAC biology and serve as a valuable resource for future therapeutic exploration and molecular investigations.}, } @article {pmid39292721, year = {2024}, author = {Bastien, GE and Cable, RN and Batterbee, C and Wing, AJ and Zaman, L and Duhaime, MB}, title = {Virus-host interactions predictor (VHIP): Machine learning approach to resolve microbial virus-host interaction networks.}, journal = {PLoS computational biology}, volume = {20}, number = {9}, pages = {e1011649}, pmid = {39292721}, issn = {1553-7358}, mesh = {*Machine Learning ; Humans ; *Viruses/genetics ; *Computational Biology/methods ; *Host-Pathogen Interactions/genetics/physiology ; Host Microbial Interactions/genetics/physiology ; }, abstract = {Viruses of microbes are ubiquitous biological entities that reprogram their hosts' metabolisms during infection in order to produce viral progeny, impacting the ecology and evolution of microbiomes with broad implications for human and environmental health. Advances in genome sequencing have led to the discovery of millions of novel viruses and an appreciation for the great diversity of viruses on Earth. Yet, with knowledge of only "who is there?" we fall short in our ability to infer the impacts of viruses on microbes at population, community, and ecosystem-scales. To do this, we need a more explicit understanding "who do they infect?" Here, we developed a novel machine learning model (ML), Virus-Host Interaction Predictor (VHIP), to predict virus-host interactions (infection/non-infection) from input virus and host genomes. This ML model was trained and tested on a high-value manually curated set of 8849 virus-host pairs and their corresponding sequence data. The resulting dataset, 'Virus Host Range network' (VHRnet), is core to VHIP functionality. Each data point that underlies the VHIP training and testing represents a lab-tested virus-host pair in VHRnet, from which meaningful signals of viral adaptation to host were computed from genomic sequences. VHIP departs from existing virus-host prediction models in its ability to predict multiple interactions rather than predicting a single most likely host or host clade. As a result, VHIP is able to infer the complexity of virus-host networks in natural systems. VHIP has an 87.8% accuracy rate at predicting interactions between virus-host pairs at the species level and can be applied to novel viral and host population genomes reconstructed from metagenomic datasets.}, } @article {pmid39292164, year = {2024}, author = {Sakai, K and Nagata, T and Mori, T and Inoue, S and Fujiwara, H and Odagami, K and Adi, NP and Tatemichi, M and Mori, K}, title = {Research topics in occupational medicine, 1990-2022: A text-mining-applied bibliometric study.}, journal = {Scandinavian journal of work, environment & health}, volume = {50}, number = {7}, pages = {567-576}, pmid = {39292164}, issn = {1795-990X}, support = {240801-01//Industrial Disease Clinical Research Grants from the Ministry of Health, Labor and Welfare/ ; }, mesh = {*Bibliometrics ; *Data Mining ; Humans ; *Occupational Medicine ; Occupational Health ; }, abstract = {OBJECTIVE: Occupational health has been influenced by societal and industrial changes. This study aimed to clarify topic trends in occupational health research in 1990-2022.

METHODS: We conducted a text-mining-adjusted bibliometric study using research titles in occupational health. Data on research titles and the years of publication were collected from 26 peer-reviewed journals on PubMed. Using morphological and correspondence analyses in text mining, we structured research topics into multiple categories and visualized the relationship between all categories and publication years. Statistical analyses were conducted using the text mining software - KH Coder 3.0.

RESULTS: We obtained 48 645 articles containing 714 890 words in their titles. The research topics were classified into 4 categories and 17 subcategories, of which those of occupations; countries; non-intervention; psychosocial factors; lifestyle factors; safety; symptoms; therapy and care; and productivity have recently shown an increasing trend. In contrast, the subcategories of risk, chemical factors, disease, and organ damage showed decreasing trends. Chemical factors, which were the main topics in the 1990s, included risk, organ damage, and disease. Productivity, the main topic in the 2020s, co-occurred with lifestyle factors, symptoms, and intervention.

CONCLUSIONS: Focal areas in occupational-health research shift according to societal trends. Occupational-health research has primarily analyzed issues in developed countries with capitalist values and may not have sufficiently covered issues in developing countries. It is imperative for policymakers and public funding bodies to determine priorities for investigation in the field.}, } @article {pmid39292040, year = {2024}, author = {Vasconcelos, NM and Bernal, RTI and Souza, JB and Bordoni, PHC and Stein, C and Coll, CVN and Murray, J and Malta, DC}, title = {Underreporting of violence against women: an analysis of two data sources.}, journal = {Ciencia & saude coletiva}, volume = {29}, number = {10}, pages = {e07732023}, doi = {10.1590/1413-812320242910.07732023}, pmid = {39292040}, issn = {1678-4561}, mesh = {Humans ; Brazil/epidemiology ; Female ; Adult ; Young Adult ; Adolescent ; *Sex Offenses/statistics & numerical data ; Middle Aged ; Health Surveys ; Gender-Based Violence/statistics & numerical data ; Information Systems/statistics & numerical data ; Information Sources ; }, abstract = {This article aims to estimate the underreporting of violence against women (VAW) in the Notifiable Diseases Information System (SINAN), based on data from the National Survey of Health (NSH), in Brazil and subnational units (SU). This work was an ecological study using SINAN and NSH, both from 2019. In SINAN, reports of sexual, physical, and psychological VAW, aged 18 years or older, were selected. In the NSH, women of the same age group who reported psychological, physical, or sexual violence, and who had sought health care due to consequences of the violence were selected. SINAN underreporting was calculated in reference to the NSH's estimated population, for Brazil and each SU. Underreporting of VAW in Brazil was 98.5%, 75.9%, and 89.4% for psychological, physical, and sexual violence, respectively. The North and Northeast states presented the lowest reporting rates among the states. VAW in Brazil is highly underreported by the health sector, showing the need for adequate training of health professionals to recognize situations of violence and raise awareness of the importance of reporting.}, } @article {pmid39290666, year = {2024}, author = {Guclu, C and Luk, CL and Ashton, LA and Abbas, S and Boyle, MJW}, title = {Beta diversity subcomponents of plant species turnover and nestedness reveal drivers of community assembly in a regenerating subtropical forest.}, journal = {Ecology and evolution}, volume = {14}, number = {9}, pages = {e70233}, pmid = {39290666}, issn = {2045-7758}, abstract = {Secondary forests represent a significant proportion of global forest cover, with over 70% of forests in East Asia classified as regenerating. While succession has been studied extensively in temperate systems, trajectories of subtropical succession remain poorly characterized in highly disturbed, urban-adjacent forests. Investigating the additive beta diversity components of turnover and nestedness may reveal community assembly mechanisms driving secondary succession. The present study investigates plant community assembly along a successional gradient from 7 to 70 years following the onset of succession in secondary subtropical forests in Hong Kong, China. Plant survey data for 28 plots were analysed, generating additive Simpsons turnover and nestedness beta diversity metrics. Dissimilarity matrices were generated and modelled as a function of environmental matrices including forest plant community age (years following onset of secondary succession), inter-community distance (metres), and soil moisture saturation (%) across three elevational bands using generalized dissimilarity models. Nonmetric multidimensional scaling of plant communities was conducted with Bray-Curtis dissimilarity matrices. Inter-community distance and successional age differentially influenced plant species turnover between lowland and Montane forest types. Models of nestedness found that plot age and soil moisture saturation were significant drivers of nestedness patterns in plant communities across elevational classes. Turnover represented a higher proportion of Sorensen beta diversity than nestedness, while ANOSIM found significant differentiation between plant communities at different successional stages. Turnover patterns suggest a deterministic model of community assembly, with strong patterns of species replacement between communities at fine spatial scales and successional stages, as well as clear compositional shifts between lowland and montane forest types. NMDS analysis and functional compositional assessments suggested a transition from early successional communities with a high proportion of shrub species, to later successional communities with a higher proportion of tree species, with an increase in species turnover with greater age dissimilarity.}, } @article {pmid39290433, year = {2024}, author = {Castrillo, M and Aguilar, F and García-Díaz, D}, title = {Dataset on sub-daily vertical profiles of physicochemical parameters and chlorophyll concentration in El Val reservoir, together with its daily meteorological data, storage state and downstream flow (2018-2022).}, journal = {Data in brief}, volume = {57}, number = {}, pages = {110839}, pmid = {39290433}, issn = {2352-3409}, abstract = {The dataset addressed in this article contains parameters about El Val reservoir (province of Zaragoza, Spain). It includes physicochemical variables, the water level, the stored water volume, its meteorological conditions and the flow rate of its effluent, the Queiles River, a few metres downstream of the dam. The El Val reservoir stores water from the Val River, but it also receives water from the Queiles River through a pipeline and from several ravines. The dam releases on the Queiles River, which is a tributary of the Ebro River (the second one in Spain in length and discharge rate). A multiparametric probe (aquaDam, Adasa Systems), hanging from a structure located in the dam, every 6 h makes a vertical profile taking the measurements at each metre of depth from the surface to approximately 573 m above sea level (m.a.s.l.), in other words, between 2 and 3 m above the bottom outlet. This probe collects data of water temperature, pH, ORP, conductivity, dissolved oxygen, turbidity and chlorophyll concentration. Meteorological data are collected in the nearest weather station, located in the municipality of Los Fayos which is about 500 m downstream of the dam. These include daily accumulated precipitation, daily maximum and average solar irradiance, daily maximum, minimum and average air temperature and daily average wind speed. The water level and volume of stored water and the flow rate of the Queiles River are collected in the El Val monitoring station and the Queiles River gauge station respectively, and are also provided on a daily basis. These data are useful to feed deterministic, data driven or hybrid hydrological models with different purposes, like the identification of the impact of meteorological conditions on the physicochemical properties of the reservoir as well as the assessment of different management strategies in the reservoir. This is a data article that additionally supports the work published in Ecological Informatics [1] where the use of common and readily available open data is promoted through its use to feed data driven models, in particular to infer the depth of the thermocline in reservoirs that are periodically or permanently thermally stratified. In that article a dataset derived from the one presented in this article is used.}, } @article {pmid39290364, year = {2024}, author = {Boyes, D and Holland, PWH and , and , and , and , and , and , and , }, title = {The genome sequence of the Red Chestnut moth, Cerastis rubricosa (Schiffermüller, 1775).}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {88}, pmid = {39290364}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual male Cerastis rubricosa (the Red Chestnut moth; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 678.7 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.39 kilobases in length. Gene annotation of this assembly on Ensembl identified 18,784 protein coding genes.}, } @article {pmid39290036, year = {2024}, author = {Monreal-Di Bello, M and González-Bermejo, D and Castillo-Cano, B and Rodriguez-Pascual, A and Montero-Corominas, D}, title = {Impact of Regulatory Interventions on Ulipristal Acetate 5 mg (Esmya) Use in Spain: An Interrupted Time-Series Analysis.}, journal = {Pharmacoepidemiology and drug safety}, volume = {33}, number = {9}, pages = {e70004}, doi = {10.1002/pds.70004}, pmid = {39290036}, issn = {1099-1557}, support = {//Spanish Agency on Medicines and Medical Devices (AEMPS)/ ; }, mesh = {Humans ; Spain/epidemiology ; *Norpregnadienes/administration & dosage/adverse effects/therapeutic use ; *Interrupted Time Series Analysis ; Female ; Databases, Factual ; Electronic Health Records/statistics & numerical data ; Risk Evaluation and Mitigation ; Male ; Adult ; Middle Aged ; }, abstract = {PURPOSE: Since late 2017, the use of ulipristal acetate 5 mg (UPA; Proprietary name: Esmya) has been under review in the European Union, due to an emerging hepatic risk. In February 2018 and in July 2018, the Spanish Agency of Medicines and Medical Devices and the marketing authorization holder put two risk minimization measures (RMM) in place, in order to inform about new safety information and to mitigate this risk. This study aims to assess RMM effectiveness in Spain, by performing an interrupted time-series (ITS) analyses, between 2014 and 2019.

METHOD: Two quasi-experimental ITS analyses to examine the use of UPA before and after the RMM release were performed: (a) an ecological study using aggregated data from a drug consumption database; and (b) a study using primary healthcare data gathered from electronic clinical records.

RESULTS: Regulatory interventions were associated with an immediate and significant decrease level of DID (the number of DDD dispensed per 100 000 inhabitants and day) and incidence. The DID was 70% less than expected 12 months after the interventions. This value was 59% for the incidence. However, a change in the slope was not observed and the use started rising again in the last segment of the study period.

CONCLUSION: Despite RMM had an immediate strong impact on UPA use, the last segment upward trend in the long-term might have been affected by the lack of comparable therapeutic alternatives. Further studies should be performed to confirm the increase trend observed and analyze subsequent measures and additional data.}, } @article {pmid39289538, year = {2024}, author = {Mc Cartney, AM and Formenti, G and Mouton, A and De Panis, D and Marins, LS and Leitão, HG and Diedericks, G and Kirangwa, J and Morselli, M and Salces-Ortiz, J and Escudero, N and Iannucci, A and Natali, C and Svardal, H and Fernández, R and De Pooter, T and Joris, G and Strazisar, M and Wood, JMD and Herron, KE and Seehausen, O and Watts, PC and Shaw, F and Davey, RP and Minotto, A and Fernández, JM and Böhne, A and Alegria, C and Alioto, T and Alves, PC and Amorim, IR and Aury, JM and Backstrom, N and Baldrian, P and Baltrunaite, L and Barta, E and BedHom, B and Belser, C and Bergsten, J and Bertrand, L and Bilandija, H and Binzer-Panchal, M and Bista, I and Blaxter, M and Borges, PAV and Dias, GB and Bosse, M and Brown, T and Bruggmann, R and Buena-Atienza, E and Burgin, J and Buzan, E and Cariani, A and Casadei, N and Chiara, M and Chozas, S and Čiampor, F and Crottini, A and Cruaud, C and Cruz, F and Dalen, L and De Biase, A and Del Campo, J and Delic, T and Dennis, AB and Derks, MFL and Diroma, MA and Djan, M and Duprat, S and Eleftheriadi, K and Feulner, PGD and Flot, JF and Forni, G and Fosso, B and Fournier, P and Fournier-Chambrillon, C and Gabaldon, T and Garg, S and Gissi, C and Giupponi, L and Gomez-Garrido, J and González, J and Grilo, ML and Grüning, B and Guerin, T and Guiglielmoni, N and Gut, M and Haesler, MP and Hahn, C and Halpern, B and Harrison, PW and Heintz, J and Hindrikson, M and Höglund, J and Howe, K and Hughes, GM and Istace, B and Cock, MJ and Janžekovič, F and Jonsson, ZO and Joye-Dind, S and Koskimäki, JJ and Krystufek, B and Kubacka, J and Kuhl, H and Kusza, S and Labadie, K and Lähteenaro, M and Lantz, H and Lavrinienko, A and Leclère, L and Lopes, RJ and Madsen, O and Magdelenat, G and Magoga, G and Manousaki, T and Mappes, T and Marques, JP and Redondo, GIM and Maumus, F and McCarthy, SA and Megens, HJ and Melo-Ferreira, J and Mendes, SL and Montagna, M and Moreno, J and Mosbech, MB and Moura, M and Musilova, Z and Myers, E and Nash, WJ and Nater, A and Nicholson, P and Niell, M and Nijland, R and Noel, B and Noren, K and Oliveira, PH and Olsen, RA and Ometto, L and Oomen, RA and Ossowski, S and Palinauskas, V and Palsson, S and Panibe, JP and Pauperio, J and Pavlek, M and Payen, E and Pawlowska, J and Pellicer, J and Pesole, G and Pimenta, J and Pippel, M and Pirttilä, AM and Poulakakis, N and Rajan, J and M C Rego, R and Resendes, R and Resl, P and Riesgo, A and Rodin-Morch, P and Soares, AER and Fernandes, CR and Romeiras, MM and Roxo, G and Rüber, L and Ruiz-Lopez, MJ and Saarma, U and da Silva, LP and Sim-Sim, M and Soler, L and Sousa, VC and Santos, CS and Spada, A and Stefanovic, M and Steger, V and Stiller, J and Stöck, M and Struck, TH and Sudasinghe, H and Tapanainen, R and Tellgren-Roth, C and Trindade, H and Tukalenko, Y and Urso, I and Vacherie, B and Van Belleghem, SM and Van Oers, K and Vargas-Chavez, C and Velickovic, N and Vella, N and Vella, A and Vernesi, C and Vicente, S and Villa, S and Pettersson, OV and Volckaert, FAM and Voros, J and Wincker, P and Winkler, S and Ciofi, C and Waterhouse, RM and Mazzoni, CJ}, title = {The European Reference Genome Atlas: piloting a decentralised approach to equitable biodiversity genomics.}, journal = {npj biodiversity}, volume = {3}, number = {1}, pages = {28}, pmid = {39289538}, issn = {2731-4243}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {A genomic database of all Earth's eukaryotic species could contribute to many scientific discoveries; however, only a tiny fraction of species have genomic information available. In 2018, scientists across the world united under the Earth BioGenome Project (EBP), aiming to produce a database of high-quality reference genomes containing all ~1.5 million recognized eukaryotic species. As the European node of the EBP, the European Reference Genome Atlas (ERGA) sought to implement a new decentralised, equitable and inclusive model for producing reference genomes. For this, ERGA launched a Pilot Project establishing the first distributed reference genome production infrastructure and testing it on 98 eukaryotic species from 33 European countries. Here we outline the infrastructure and explore its effectiveness for scaling high-quality reference genome production, whilst considering equity and inclusion. The outcomes and lessons learned provide a solid foundation for ERGA while offering key learnings to other transnational, national genomic resource projects and the EBP.}, } @article {pmid39287883, year = {2024}, author = {Stolz, BJ and Dhesi, J and Bull, JA and Harrington, HA and Byrne, HM and Yoon, IHR}, title = {Relational Persistent Homology for Multispecies Data with Application to the Tumor Microenvironment.}, journal = {Bulletin of mathematical biology}, volume = {86}, number = {11}, pages = {128}, pmid = {39287883}, issn = {1522-9602}, support = {EP/R018472/1//EPSRC/ ; EP/R018472/1, EP/K041096/1, EP/R005125/1, EP/T001968/1//EPSRC/ ; EP/R018472/1//EPSRC/ ; EP/R018472/1//EPSRC/ ; RGF EA 201074, UF150238//Royal Society/ ; CTRQQR-2021/100002/CRUK_/Cancer Research UK/United Kingdom ; }, mesh = {*Tumor Microenvironment/immunology ; Humans ; *Mathematical Concepts ; *Models, Biological ; *Neoplasms/pathology/immunology ; Computer Simulation ; Computational Biology ; Macrophages/immunology/pathology ; }, abstract = {Topological data analysis (TDA) is an active field of mathematics for quantifying shape in complex data. Standard methods in TDA such as persistent homology (PH) are typically focused on the analysis of data consisting of a single entity (e.g., cells or molecular species). However, state-of-the-art data collection techniques now generate exquisitely detailed multispecies data, prompting a need for methods that can examine and quantify the relations among them. Such heterogeneous data types arise in many contexts, ranging from biomedical imaging, geospatial analysis, to species ecology. Here, we propose two methods for encoding spatial relations among different data types that are based on Dowker complexes and Witness complexes. We apply the methods to synthetic multispecies data of a tumor microenvironment and analyze topological features that capture relations between different cell types, e.g., blood vessels, macrophages, tumor cells, and necrotic cells. We demonstrate that relational topological features can extract biological insight, including the dominant immune cell phenotype (an important predictor of patient prognosis) and the parameter regimes of a data-generating model. The methods provide a quantitative perspective on the relational analysis of multispecies spatial data, overcome the limits of traditional PH, and are readily computable.}, } @article {pmid39287032, year = {2024}, author = {Meaume, S and Senet, P and Thomé, B and Aragno, VA and Serge, B and Fortin, S and Boucley, I and Michon-Pasturel, U and Colboc, H}, title = {Impact of primary dressings on healing of venous leg ulcers: a French cohort study from the healthcare insurance database.}, journal = {Journal of wound care}, volume = {33}, number = {9}, pages = {678-686}, doi = {10.12968/jowc.2024.0189}, pmid = {39287032}, issn = {0969-0700}, mesh = {Humans ; Female ; Male ; *Wound Healing ; France ; *Varicose Ulcer/therapy/economics ; Aged ; *Bandages/economics ; Middle Aged ; Cohort Studies ; Databases, Factual ; Aged, 80 and over ; Insurance, Health/statistics & numerical data ; Treatment Outcome ; Health Care Costs/statistics & numerical data ; }, abstract = {OBJECTIVE: Multicomponent bandages (MCBs) are recommended by the French Authority for Health (Haute Autorité de Santé) as first-line treatment for venous leg ulcers (VLUs). A first analysis of the data collected from the French administrative healthcare database (Système National des Données de Santé (SNDS)) on 25,255 patients with a VLU supported superiority of MCBs versus short stretch bandages when considering the healing outcomes and costs associated with closure of these wounds. The aim of this study was to assess how beneficial the primary dressing (technology lipido-colloid nano-oligosaccharide factor (TLC NOSF) or control dressing group (CDG)) could be, when used in combination with MCBs in the treatment of VLUs.

METHOD: Data from the SNDS were collected for patients meeting the following inclusion criteria: treatment for a VLU with MCBs and with the same dressing type (TLC-NOSF or CDG) during the whole treatment period. Healing outcomes were documented on the global cohorts and propensity score-matched cohorts. The mean healthcare cost and the ecological impact were calculated for those patients healed within the study period.

RESULTS: In total, 12,507 patients met the criteria for treatment with both MCBs and TLC-NOSF dressings (n=1134) versus MCBs and CDG (n=11,373); with 1134 and 2268 patients per group following propensity score matching. Healing outcomes were favourable for the TLC-NOSF group in the global cohort and were enhanced in the propensity score-matched cohorts. At every point of the analysis, the adjusted healing rates were significantly higher in the TLC-NOSF group than in the CDG group (p<0.001). In the propensity score-matched cohorts (n=3402), the healing rate at three months was 52% in the TLC-NOSF group versus 37% in the CDG group (p<0.001). The median healing time was 87 days versus 125.5 days in the TLC-NOSF and CDG groups, respectively (p<0.0001). TLC-NOSF dressings significantly reduced the average treatment cost per healed ulcer (€2099) by 23.7% compared with dressings without TLC-NOSF (€2751) (p<0.001), as well as the resources used.

CONCLUSION: This SNDS analysis confirms, in the largest real-life study performed in VLU management, the superiority of the TLC-NOSF dressings versus those not impregnated with the NOSF compound. Better clinical outcomes associated with cost savings and a positive ecological impact support the combination of MCBs and TLC-NOSF dressings and should be considered as an optimal standard of care for the global management of VLUs. These outcomes reinforce the current positions of the international guidelines on the use of NOSF impregnated dressings (UrgoStart range; Laboratoires Urgo, France) in this pathology.}, } @article {pmid39283951, year = {2024}, author = {Amaral, AS and Devos, DP}, title = {The neglected giants: Uncovering the prevalence and functional groups of huge proteins in proteomes.}, journal = {PLoS computational biology}, volume = {20}, number = {9}, pages = {e1012459}, pmid = {39283951}, issn = {1553-7358}, mesh = {*Proteome/metabolism ; Databases, Protein ; Computational Biology ; Proteins/metabolism/chemistry ; Humans ; Proteomics/methods ; Bacteria/metabolism/genetics ; Animals ; }, abstract = {An often-overlooked aspect of biology is formed by the outliers of the protein length distribution, specifically those proteins with more than 5000 amino acids, which we refer to as huge proteins (HPs). By examining UniprotKB, we discovered more than 41 000 HPs throughout the tree of life, with the majority found in eukaryotes. Notably, the phyla with the highest propensity for HPs are Apicomplexa and Fornicata. Moreover, we observed that certain bacteria, such as Elusimicrobiota or Planctomycetota, have a higher tendency for encoding HPs, even more than the average eukaryote. To investigate if these macro-polypeptides represent "real" proteins, we explored several indirect metrics. Additionally, orthology analyses reveals thousands of clusters of homologous sequences of HPs, revealing functional groups related to key cellular processes such as cytoskeleton organization and functioning as chaperones or as E3-ubiquitin ligases in eukaryotes. In the case of bacteria, the major clusters have functions related to non-ribosomomal peptide synthesis/polyketide synthesis, followed by pathogen-host attachment or recognition surface proteins. Further exploration of the annotations for each HPs supported the previously identified functional groups. These findings underscore the need for further investigation of the cellular and ecological roles of these HPs and their potential impact on biology and biotechnology.}, } @article {pmid39283104, year = {2024}, author = {Tedim, AP and Almeida-Santos, AC and Lanza, VF and Novais, C and Coque, TM and Freitas, AR and Peixe, L and , }, title = {Bacteriocin distribution patterns in Enterococcus faecium and Enterococcus lactis: bioinformatic analysis using a tailored genomics framework.}, journal = {Applied and environmental microbiology}, volume = {90}, number = {10}, pages = {e0137624}, pmid = {39283104}, issn = {1098-5336}, support = {EXPL/SAU-INF/0261/2021, UIDP/04378/2020, UIDB/04378/2020, LA/P/0140/2020, UI/BD/151317/2021//MCTES | Fundação para a Ciência e a Tecnologia (FCT)/ ; }, mesh = {*Bacteriocins/genetics/metabolism ; *Enterococcus faecium/genetics/metabolism/drug effects ; *Genomics ; *Computational Biology ; Genome, Bacterial ; Anti-Bacterial Agents/pharmacology ; Enterococcus/genetics/metabolism/drug effects ; }, abstract = {UNLABELLED: Multidrug-resistant Enterococcus faecium strains represent a major concern due to their ability to thrive in diverse environments and cause life-threatening infections. While antimicrobial resistance and virulence mechanisms have been extensively studied, the contribution of bacteriocins to E. faecium's adaptability remains poorly explored. E. faecium, within the Bacillota phylum, is a prominent bacteriocin producer. Here, we developed a tailored database of 76 Bacillota bacteriocins (217 sequences, including 40 novel bacteriocins) and applied it to uncover bacteriocin distribution patterns in 997 quality-filtered E. faecium and Enterococcus lactis (former E. faecium clade B) genomes. Curated using computational pipelines and literature mining, our database demonstrates superior precision versus leading public tools in identifying diverse bacteriocins. Distinct bacteriocin profiles emerged between E. faecium and E. lactis, highlighting species-specific adaptations. E. faecium strains from hospitalized patients were significantly enriched in bacteriocins as enterocin A and bacteriocins 43 (or T8), AS5, and AS11. These bacteriocin genes were strongly associated with antibiotic resistance, particularly vancomycin and ampicillin, and Inc18 rep2_pRE25-derivative plasmids, classically associated with vancomycin resistance transposons. Such bacteriocin arsenal likely enhances the adaptability and competitive fitness of E. faecium in the nosocomial environment. By combining a novel tailored database, whole-genome sequencing, and epidemiological data, our work elucidates meaningful connections between bacteriocin determinants, antimicrobial resistance, mobile genetic elements, and ecological origins in E. faecium and provides a framework for elucidating bacteriocin landscapes in other organisms. Characterizing species- and strain-level differences in bacteriocin profiles may reveal determinants of ecological adaptation, and translating these discoveries could further inform strategies to exploit bacteriocins against high-risk clones.

IMPORTANCE: This work significantly expands the knowledge on the understudied bacteriocin diversity in opportunistic enterococci, revealing their contribution in the adaptation to different environments. It underscores the importance of placing increased emphasis on genetic platforms carrying bacteriocins as well as on cryptic plasmids that often exclusively harbor bacteriocins since bacteriocin production can significantly contribute to plasmid maintenance, potentially facilitating their stable transmission across generations. Further characterization of strain-level bacteriocin landscapes could inform strategies to combat high-risk clones. Overall, these insights provide a framework for unraveling the therapeutic and biotechnological potential of bacteriocins.}, } @article {pmid39277496, year = {2024}, author = {van der Feltz-Cornelis, CM and Turk, F and Sweetman, J and Khunti, K and Gabbay, M and Shepherd, J and Montgomery, H and Strain, WD and Lip, GYH and Wootton, D and Watkins, CL and Cuthbertson, DJ and Williams, N and Banerjee, A}, title = {Corrigendum to "Prevalence of mental health conditions and brain fog in people with long COVID: A systematic review and meta-analysis" [General Hospital Psychiatry volume 88 (2024)10-22 10.1016/j.genhosppsych.2024.02.009].}, journal = {General hospital psychiatry}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.genhosppsych.2024.09.006}, pmid = {39277496}, issn = {1873-7714}, } @article {pmid39275913, year = {2024}, author = {Takada, K and Nakagawa, S and Kryukov, K and Ozawa, M and Watanabe, T}, title = {Metagenomic analysis of the gut microbiota of hooded cranes (Grus monacha) on the Izumi plain in Japan.}, journal = {FEBS open bio}, volume = {14}, number = {12}, pages = {1972-1984}, pmid = {39275913}, issn = {2211-5463}, support = {//Crane Conservation by the City of Izumi/ ; //Tokyo Biochemical Research Foundation/ ; JPMJCR20H6//Core Research for Evolutional Science and Technology/ ; //2020 Tokai University School of Medicine Research Aid/ ; 22gm1610010h0001//Japan Agency for Medical Research and Development/ ; JP223fa627002h//Japan Agency for Medical Research and Development/ ; //Takeda Science Foundation/ ; 16H06429//Japan Society for the Promotion of Science/ ; 16H06434//Japan Society for the Promotion of Science/ ; 16K21723//Japan Society for the Promotion of Science/ ; 19H04843//Japan Society for the Promotion of Science/ ; 19fk0108171//Japan Society for the Promotion of Science/ ; 21J01036//Japan Society for the Promotion of Science/ ; 22K15469//Japan Society for the Promotion of Science/ ; JP19fk0108113//Japan Society for the Promotion of Science/ ; JP22H02521//Japan Society for the Promotion of Science/ ; }, mesh = {Animals ; Japan ; *Gastrointestinal Microbiome/genetics ; *Birds/microbiology/virology ; *Metagenomics/methods ; Feces/microbiology ; Bacteria/genetics/classification/isolation & purification ; High-Throughput Nucleotide Sequencing ; Metagenome/genetics ; }, abstract = {Recent advances in DNA sequencing technology have dramatically improved our understanding of the gut microbiota of various animal species. However, research on the gut microbiota of birds lags behind that of many other vertebrates, and information about the gut microbiota of wild birds such as migratory waterfowl is particularly lacking. Because the ecology of migratory waterfowl (e.g., lifestyle, diet, physiological characteristics) differs from that of other birds, the gut microbiota of migratory waterfowl likely also differs, but much is still unknown. The hooded crane (Grus monacha) is an important representative migratory waterbird species and is listed as endangered on the International Union for Conservation of Nature and Natural Resources Red List of Threatened Species. In this study, we analyzed the bacterial and viral microbiota in the gut of hooded cranes by using deep sequencing data from fecal samples of hooded cranes that winter on the Izumi plain in Japan, and found that Cetobacterium, Clupeiformes, and Pbunavirus were clearly present in the fecal samples of hooded cranes. These findings advance our understanding of the ecology of hooded cranes.}, } @article {pmid39274728, year = {2024}, author = {Sąsiadek-Andrzejczak, E and Maras, P and Kozicki, M}, title = {Flexible and Ecological Cotton-Based Dosimeter for 2D UV Surface Dose Distribution Measurements.}, journal = {Materials (Basel, Switzerland)}, volume = {17}, number = {17}, pages = {}, pmid = {39274728}, issn = {1996-1944}, abstract = {This work presents a 2D radiochromic dosimeter for ultraviolet (UV) radiation measurements, based on cotton fabric volume-modified with nitroblue tetrazolium chloride (NBT) as a radiation-sensitive compound. The developed dosimeter is flexible, which allows it to adapt to various shapes and show a color change from yellowish to purple-brown during irradiation. The intensity of the color change depends on the type of UV radiation and is the highest for UVC (253.7 nm). It has been shown that the developed dosimeters (i) can be used for UVC radiation dose measurements in the range of up to 10 J/cm[2]; (ii) can be measured in 2D using a flatbed scanner; and (iii) can have the obtained images after scanning be filtered with a medium filter to improve their quality by reducing noise from the fabric structure. The developed cotton-NBT dosimeters can measure UVC-absorbed radiation doses on objects of various shapes, and when combined with a dedicated computer software package and a data processing method, they form a comprehensive system for measuring dose distributions for objects with complex shapes. The developed system can also serve as a comprehensive method for assessing the quality and control of UV radiation sources used in various industrial processes.}, } @article {pmid39273837, year = {2024}, author = {Gatina, E and Zinicovscaia, I and Yushin, N and Chaligava, O and Frontasyeva, M and Sharipova, A}, title = {Assessment of the Atmospheric Deposition of Potentially Toxic Elements Using Moss Pleurozium schreberi in an Urban Area: The Perm (Perm Region, Russia) Case Study.}, journal = {Plants (Basel, Switzerland)}, volume = {13}, number = {17}, pages = {}, pmid = {39273837}, issn = {2223-7747}, abstract = {Assessment of air quality in urban areas is very important because pollutants affect both the environment and human health. In Perm (Russia), a moss biomonitoring method was used to assess the level of air pollution. The concentrations of 15 elements in 87 samples of moss Pleurozium schreberi in the city territory were determined using a direct mercury analyzer and an inductively coupled plasma atomic emission spectroscopy. Using factor and correlation analyses, the grouping of elements and their relationship with emission sources were established. The main sources of emissions of potentially toxic elements are the transportation (road and rail), metallurgical, and chemical industries. The level of atmospheric air pollution was assessed by calculating the environmental risk index, pollutant load index, and pollution coefficient. Based on the values of the pollution index, the level of atmospheric air pollution in Perm varies from unpolluted to highly polluted, with moderate environmental risk.}, } @article {pmid39273245, year = {2024}, author = {Damarov, IS and Korbolina, EE and Rykova, EY and Merkulova, TI}, title = {Multi-Omics Analysis Revealed the rSNPs Potentially Involved in T2DM Pathogenic Mechanism and Metformin Response.}, journal = {International journal of molecular sciences}, volume = {25}, number = {17}, pages = {}, pmid = {39273245}, issn = {1422-0067}, support = {23-15-00113//Russian Science Foundation/ ; }, mesh = {Humans ; *Metformin/pharmacology/therapeutic use ; *Diabetes Mellitus, Type 2/genetics/drug therapy/metabolism ; *Polymorphism, Single Nucleotide ; *Genome-Wide Association Study ; Hypoglycemic Agents/therapeutic use/pharmacology ; Quantitative Trait Loci ; Computational Biology/methods ; Leukocytes, Mononuclear/metabolism/drug effects ; Gene Expression Regulation/drug effects ; Promoter Regions, Genetic ; Multiomics ; }, abstract = {The goal of our study was to identify and assess the functionally significant SNPs with potentially important roles in the development of type 2 diabetes mellitus (T2DM) and/or their effect on individual response to antihyperglycemic medication with metformin. We applied a bioinformatics approach to identify the regulatory SNPs (rSNPs) associated with allele-asymmetric binding and expression events in our paired ChIP-seq and RNA-seq data for peripheral blood mononuclear cells (PBMCs) of nine healthy individuals. The rSNP outcomes were analyzed using public data from the GWAS (Genome-Wide Association Studies) and Genotype-Tissue Expression (GTEx). The differentially expressed genes (DEGs) between healthy and T2DM individuals (GSE221521), including metformin responders and non-responders (GSE153315), were searched for in GEO RNA-seq data. The DEGs harboring rSNPs were analyzed using the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG). We identified 14,796 rSNPs in the promoters of 5132 genes of human PBMCs. We found 4280 rSNPs to associate with both phenotypic traits (GWAS) and expression quantitative trait loci (eQTLs) from GTEx. Between T2DM patients and controls, 3810 rSNPs were detected in the promoters of 1284 DEGs. Based on the protein-protein interaction (PPI) network, we identified 31 upregulated hub genes, including the genes involved in inflammation, obesity, and insulin resistance. The top-ranked 10 enriched KEGG pathways for these hubs included insulin, AMPK, and FoxO signaling pathways. Between metformin responders and non-responders, 367 rSNPs were found in the promoters of 131 DEGs. Genes encoding transcription factors and transcription regulators were the most widely represented group and many were shown to be involved in the T2DM pathogenesis. We have formed a list of human rSNPs that add functional interpretation to the T2DM-association signals identified in GWAS. The results suggest candidate causal regulatory variants for T2DM, with strong enrichment in the pathways related to glucose metabolism, inflammation, and the effects of metformin.}, } @article {pmid39271937, year = {2024}, author = {Hansen, AJ and Burns, P and Ervin, J and Goetz, SJ and Hansen, M and Venter, O and Watson, JEM and Jantz, PA and Virnig, ALS and Barnett, K and Pillay, R and Atkinson, S and Supples, C and Rodríguez-Buritica, S and Armenteras, D}, title = {Author Correction: A policy-driven framework for conserving the best of Earth's remaining moist tropical forests.}, journal = {Nature ecology & evolution}, volume = {8}, number = {12}, pages = {2336}, doi = {10.1038/s41559-024-02557-8}, pmid = {39271937}, issn = {2397-334X}, } @article {pmid39271747, year = {2024}, author = {Shin, S and Baker, AJ and Enk, J and McKenna, DD and Foquet, B and Vandergast, AG and Weissman, DB and Song, H}, title = {Orthoptera-specific target enrichment (OR-TE) probes resolve relationships over broad phylogenetic scales.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {21377}, pmid = {39271747}, issn = {2045-2322}, support = {DEB-1937815//National Science Foundation/ ; IOS-1253493//National Science Foundation/ ; DEB-1064082//National Science Foundation/ ; Hatch Grant TEX0-2-6584//U.S. Department of Agriculture/ ; }, mesh = {Animals ; *Phylogeny ; *Orthoptera/genetics/classification ; Transcriptome/genetics ; Computational Biology/methods ; DNA Probes/genetics ; Evolution, Molecular ; }, abstract = {Phylogenomic data are revolutionizing the field of insect phylogenetics. One of the most tenable and cost-effective methods of generating phylogenomic data is target enrichment, which has resulted in novel phylogenetic hypotheses and revealed new insights into insect evolution. Orthoptera is the most diverse insect order within polyneoptera and includes many evolutionarily and ecologically interesting species. Still, the order as a whole has lagged behind other major insect orders in terms of transitioning to phylogenomics. In this study, we developed an Orthoptera-specific target enrichment (OR-TE) probe set from 80 transcriptomes across Orthoptera. The probe set targets 1828 loci from genes exhibiting a wide range of evolutionary rates. The utility of this new probe set was validated by generating phylogenomic data from 36 orthopteran species that had not previously been subjected to phylogenomic studies. The OR-TE probe set captured an average of 1037 loci across the tested taxa, resolving relationships across broad phylogenetic scales. Our detailed documentation of the probe design and bioinformatics process is intended to facilitate the widespread adoption of this tool.}, } @article {pmid39269993, year = {2024}, author = {Golumbeanu, M and Briët, O and Champagne, C and Lemant, J and Winkel, M and Zogo, B and Gerhards, M and Sinka, M and Chitnis, N and Penny, M and Pothin, E and Smith, T}, title = {AnophelesModel: An R package to interface mosquito bionomics, human exposure and intervention effects with models of malaria intervention impact.}, journal = {PLoS computational biology}, volume = {20}, number = {9}, pages = {e1011609}, pmid = {39269993}, issn = {1553-7358}, mesh = {Animals ; Humans ; *Malaria/transmission/prevention & control ; *Anopheles/physiology ; *Mosquito Vectors/physiology ; *Mosquito Control/methods ; *Software ; Computational Biology ; Models, Biological ; }, abstract = {In recent decades, field and semi-field studies of malaria transmission have gathered geographic-specific information about mosquito ecology, behaviour and their sensitivity to interventions. Mathematical models of malaria transmission can incorporate such data to infer the likely impact of vector control interventions and hence guide malaria control strategies in various geographies. To facilitate this process and make model predictions of intervention impact available for different geographical regions, we developed AnophelesModel. AnophelesModel is an online, open-access R package that quantifies the impact of vector control interventions depending on mosquito species and location-specific characteristics. In addition, it includes a previously published, comprehensive, curated database of field entomological data from over 50 Anopheles species, field data on mosquito and human behaviour, and estimates of vector control effectiveness. Using the input data, the package parameterizes a discrete-time, state transition model of the mosquito oviposition cycle and infers species-specific impacts of various interventions on vectorial capacity. In addition, it offers formatted outputs ready to use in downstream analyses and by other models of malaria transmission for accurate representation of the vector-specific components. Using AnophelesModel, we show how the key implications for intervention impact change for various vectors and locations. The package facilitates quantitative comparisons of likely intervention impacts in different geographical settings varying in vector compositions, and can thus guide towards more robust and efficient malaria control recommendations. The AnophelesModel R package is available under a GPL-3.0 license at https://github.com/SwissTPH/AnophelesModel.}, } @article {pmid39269992, year = {2024}, author = {O'Meara, BC and Beaulieu, JM}, title = {Noise leads to the perceived increase in evolutionary rates over short time scales.}, journal = {PLoS computational biology}, volume = {20}, number = {9}, pages = {e1012458}, pmid = {39269992}, issn = {1553-7358}, mesh = {*Computational Biology/methods ; Models, Genetic ; Biological Evolution ; Evolution, Molecular ; Animals ; Models, Statistical ; Humans ; }, abstract = {Across a variety of biological datasets, from genomes to conservation to the fossil record, evolutionary rates appear to increase toward the present or over short time scales. This has long been seen as an indication of processes operating differently at different time scales, even potentially as an indicator of a need for new theory connecting macroevolution and microevolution. Here we introduce a set of models that assess the relationship between rate and time and demonstrate that these patterns are statistical artifacts of time-independent errors present across ecological and evolutionary datasets, which produce hyperbolic patterns of rates through time. We show that plotting a noisy numerator divided by time versus time leads to the observed hyperbolic pattern; in fact, randomizing the amount of change over time generates patterns functionally identical to observed patterns. Ignoring errors can not only obscure true patterns but create novel patterns that have long misled scientists.}, } @article {pmid39267994, year = {2024}, author = {Boyes, D and Broad, GR and Holland, PWH and , and , and , and , and , and , and , }, title = {The genome sequence of the Oak Nycteoline moth, Nycteola revayana (Scopoli, 1772).}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {258}, pmid = {39267994}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual male Nycteola revayana (the Oak Nycteoline moth; Arthropoda; Insecta; Lepidoptera; Nolidae). The genome sequence is 621.0 megabases in span. Most of the assembly is scaffolded into 26 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.25 kilobases in length. Gene annotation of this assembly on Ensembl identified 19,235 protein-coding genes.}, } @article {pmid39266599, year = {2024}, author = {He, H and Boehringer, T and Schäfer, B and Heppell, K and Beck, C}, title = {Analyzing spatio-temporal dynamics of dissolved oxygen for the River Thames using superstatistical methods and machine learning.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {21288}, pmid = {39266599}, issn = {2045-2322}, support = {VH-NG-1727//Helmholtz Association and the Networking Fund/ ; }, abstract = {By employing superstatistical methods and machine learning, we analyze time series data of water quality indicators for the River Thames (UK). The indicators analyzed include dissolved oxygen, temperature, electrical conductivity, pH, ammonium, turbidity, and rainfall, with a specific focus on the dynamics of dissolved oxygen. After detrending, the probability density functions of dissolved oxygen fluctuations exhibit heavy tails that are effectively modeled using q-Gaussian distributions. Our findings indicate that the multiplicative Empirical Mode Decomposition method stands out as the most effective detrending technique, yielding the highest log-likelihood in nearly all fittings. We also observe that the optimally fitted width parameter of the q-Gaussian shows a negative correlation with the distance to the sea, highlighting the influence of geographical factors on water quality dynamics. In the context of same-time prediction of dissolved oxygen, regression analysis incorporating various water quality indicators and temporal features identify the Light Gradient Boosting Machine as the best model. SHapley Additive exPlanations reveal that temperature, pH, and time of year play crucial roles in the predictions. Furthermore, we use the Transformer, a state-of-the-art machine learning model, to forecast dissolved oxygen concentrations. For long-term forecasting, the Informer model consistently delivers superior performance, achieving the lowest Mean Absolute Error (0.15) and Symmetric Mean Absolute Percentage Error (21.96%) with the 192 historical time steps that we used. This performance is attributed to the Informer's ProbSparse self-attention mechanism, which allows it to capture long-range dependencies in time-series data more effectively than other machine learning models. It effectively recognizes the half-life cycle of dissolved oxygen, with particular attention to critical periods such as morning to early afternoon, late evening to early morning, and key intervals between the 16th and 26th quarter-hours of the previous half-day. Our findings provide valuable insights for policymakers involved in ecological health assessments, aiding in accurate predictions of river water quality and the maintenance of healthy aquatic ecosystems.}, } @article {pmid39264951, year = {2024}, author = {Pfennig, T and Kullmann, E and Zavřel, T and Nakielski, A and Ebenhöh, O and Červený, J and Bernát, G and Matuszyńska, AB}, title = {Shedding light on blue-green photosynthesis: A wavelength-dependent mathematical model of photosynthesis in Synechocystis sp. PCC 6803.}, journal = {PLoS computational biology}, volume = {20}, number = {9}, pages = {e1012445}, pmid = {39264951}, issn = {1553-7358}, mesh = {*Photosynthesis/physiology ; *Synechocystis/metabolism/physiology ; *Light ; *Models, Biological ; Computational Biology ; Carbon Dioxide/metabolism ; Carbon Cycle/physiology ; Phycobilisomes/metabolism ; Computer Simulation ; }, abstract = {Cyanobacteria hold great potential to revolutionize conventional industries and farming practices with their light-driven chemical production. To fully exploit their photosynthetic capacity and enhance product yield, it is crucial to investigate their intricate interplay with the environment including the light intensity and spectrum. Mathematical models provide valuable insights for optimizing strategies in this pursuit. In this study, we present an ordinary differential equation-based model for the cyanobacterium Synechocystis sp. PCC 6803 to assess its performance under various light sources, including monochromatic light. Our model can reproduce a variety of physiologically measured quantities, e.g. experimentally reported partitioning of electrons through four main pathways, O2 evolution, and the rate of carbon fixation for ambient and saturated CO2. By capturing the interactions between different components of a photosynthetic system, our model helps in understanding the underlying mechanisms driving system behavior. Our model qualitatively reproduces fluorescence emitted under various light regimes, replicating Pulse-amplitude modulation (PAM) fluorometry experiments with saturating pulses. Using our model, we test four hypothesized mechanisms of cyanobacterial state transitions for ensemble of parameter sets and found no physiological benefit of a model assuming phycobilisome detachment. Moreover, we evaluate metabolic control for biotechnological production under diverse light colors and irradiances. We suggest gene targets for overexpression under different illuminations to increase the yield. By offering a comprehensive computational model of cyanobacterial photosynthesis, our work enhances the basic understanding of light-dependent cyanobacterial behavior and sets the first wavelength-dependent framework to systematically test their producing capacity for biocatalysis.}, } @article {pmid39264914, year = {2024}, author = {Zhang, K and Cao, Y and Guo, X and Kong, F and Sun, H and Jing, T and Zhan, Y and Qi, F}, title = {Comparative transcriptome analysis of differentially expressed genes and pathways in male and female flowers of Fraxinus mandshurica.}, journal = {PloS one}, volume = {19}, number = {9}, pages = {e0308013}, pmid = {39264914}, issn = {1932-6203}, mesh = {*Flowers/genetics/metabolism/growth & development ; *Gene Expression Regulation, Plant ; *Gene Expression Profiling ; *Fraxinus/genetics ; *Transcriptome ; Signal Transduction/genetics ; Plant Proteins/genetics/metabolism ; Gene Ontology ; Genes, Plant ; }, abstract = {Fraxinus mandshurica Rupr. (F. mandshurica) is a dioecious tree species with important ecological and application values. To delve deeper into the regulatory pathways and genes responsible for male and female flowers in F. mandshurica, we conducted transcriptome sequencing on male and female flowers at four distinct stages. The analysis revealed that the female database generated 38,319,967 reads while the male database generated 43,320,907 reads, resulting in 2930 differentially expressed genes with 1441 were up-regulated and 1489 down-regulated in males compared to females. Following an analysis of Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG), four distinct pathways (hormone signal transduction, energy metabolism, flavonoid biosynthesis, and photoperiod) linked to female and male flowers were identified. Subsequently, qRT-PCR verification revealed that FmAUX/IAA, FmEIN3, and FmA-ARR genes in hormone signal transduction pathway are related to female flower development. Meanwhile, FmABF genes in hormone signal transduction pathway, FmGS and FmGDH genes in energy metabolism pathway, FmFLS genes in flavonoid biosynthesis pathway, and FmCaM, FmCRY, and FmPKA genes in photoperiod pathway are related to male flower development. This study was the first to analyze the transcriptome of male and female flowers of F. mandshurica, providing a reference for the developmental pathways and gene expression levels of male and female plants.}, } @article {pmid39264239, year = {2024}, author = {Silva, M and Capps, S and London, JK}, title = {Community-Engaged Research and the Use of Open Access ToxVal/ToxRef In Vivo Databases and New Approach Methodologies (NAM) to Address Human Health Risks From Environmental Contaminants.}, journal = {Birth defects research}, volume = {116}, number = {9}, pages = {e2395}, pmid = {39264239}, issn = {2472-1727}, support = {P30 ES023513/ES/NIEHS NIH HHS/United States ; }, mesh = {Humans ; *Environmental Pollutants ; *Databases, Factual ; Risk Assessment/methods ; Environmental Exposure/adverse effects ; United States ; United States Environmental Protection Agency ; Pesticides/adverse effects/toxicity ; }, abstract = {BACKGROUND: The paper analyzes opportunities for integrating Open access resources (Abstract Sifter, US EPA and NTP Toxicity Value and Toxicity Reference [ToxVal/ToxRefDB]) and New Approach Methodologies (NAM) integration into Community Engaged Research (CEnR).

METHODS: CompTox Chemicals Dashboard and Integrated Chemical Environment with in vivo ToxVal/ToxRef and NAMs (in vitro) databases are presented in three case studies to show how these resources could be used in Pilot Projects involving Community Engaged Research (CEnR) from the University of California, Davis, Environmental Health Sciences Center.

RESULTS: Case #1 developed a novel assay methodology for testing pesticide toxicity. Case #2 involved detection of water contaminants from wildfire ash and Case #3 involved contaminants on Tribal Lands. Abstract Sifter/ToxVal/ToxRefDB regulatory data and NAMs could be used to screen/prioritize risks from exposure to metals, PAHs and PFAS from wildfire ash leached into water and to investigate activities of environmental toxins (e.g., pesticides) on Tribal lands. Open access NAMs and computational tools can apply to detection of sensitive biological activities in potential or known adverse outcome pathways to predict points of departure (POD) for comparison with regulatory values for hazard identification. Open access Systematic Empirical Evaluation of Models or biomonitoring exposures are available for human subpopulations and can be used to determine bioactivity (POD) to exposure ratio to facilitate mitigation.

CONCLUSIONS: These resources help prioritize chemical toxicity and facilitate regulatory decisions and health protective policies that can aid stakeholders in deciding on needed research. Insights into exposure risks can aid environmental justice and health equity advocates.}, } @article {pmid39263387, year = {2024}, author = {Deeleman-Reinhold, CL and Addink, W and Miller, JA}, title = {The genera Chrysillaand Phintelloidesrevisited with the description of a new species (Araneae, Salticidae) using digital specimen DOIs and nanopublications.}, journal = {Biodiversity data journal}, volume = {12}, number = {}, pages = {e129438}, pmid = {39263387}, issn = {1314-2828}, abstract = {BACKGROUND: Two Southeast Asian spider collections: that of Frances and John Murphy, now in the Manchester University Museum and the Deeleman collection, now at the Naturalis Biodiversity Center in Leiden constituted the basis of this analysis of Chrysilla Thorell, 1887 and related genera. The latter collection also includes many thousands of spiders obtained by canopy fogging for an ecological project in Borneo by A. Floren.

NEW INFORMATION: Some incongruences within the genera of the tribe Chrysillini are disentangled. The transfer of C.jesudasi Caleb & Mathai, 2014 from Chrysilla as type species of Phintelloides Kanesharatnam & Benjamin, 2019, based on analysis of molecular data is validated by morphology. An interesting new species known only from the forest canopy in Borneo, Phintelloidesscandens sp. nov, is described based on both male and female specimens. Distinguishing chrysilline genera is mostly based on traditional somatic characters, e.g., habitus, carapace and abdomen patterns, mouthparts, and genital organs. The utility of two character systems for distinguishing chrysilline genera is highlighted: 1) the presence of a flexible, articulating embolic tegular branch (etb) in combination with the conformation of the characteristic construction of the epigyne in Chrysilla and Phintelloides; 2) presence of red colour on carapace and abdomen of live males and females, in combination with abundant blue/violet/white iridescent scales such as inChrysilla and Siler. The red colour usually gets lost in alcohol, hampering species identification of alcohol material. The genera Chrysilla andPhintelloidesare redefined. Specimens of the heretofore unknown female of Chrysilla deelemani Prószyński & Deeleman-Reinhold, 2010 are described. The male and female ofChrysillalauta and male of C.volupe are redescribed. The genus Chrysilla is diagnosed and discriminated from PhintellaBösenberg & Strand, 1906, SilerSimon, 1889, Phintelloides Kanesharatnam & Benjamin, 2019 andProszynskiaKanesharatnam & Benjamin, 2019. The structure of the female genital organ of Phintelloidesflavumi Kanesharatnam & Benjamin, 2019 is scrutinized and the generic placement of Phintelloides is discussed. Males and females of one of the most variable species, Phintelloidesversicolor (C. L. Koch, 1846) are redescribed.Phintelloidesmunita(Bösenberg & Strand, 1906) is removed from synonymy with P.versicolor. Phintellaleucaspis Simon 1903 (male, Sumatra) is synonymized withP.versicolor.Biodiversity data are increasingly reliant on digital infrastructure. By linking physical specimens to digital representations of their associated data, we can lower barriers to information flow. Here we demonstrate a workflow whereby persistent identifiers (PIDs) in the form of DOIs issued by DataCite are assigned to specimens. Recognized taxa are identified by their catalog of life identifier, or by registration in ZooBank where no catalog of life identifier is available. We demonstrate the use of nanopublications, creating a series of machine readable, scientifically meaningful assertions regarding the provenance and identification of cited specimens. All human agents associated with the specimen data are linked to a persistent identifier issued by either ORCiD or Wikidata.}, } @article {pmid39262445, year = {2023}, author = {Borry, M and Forsythe, A and Andrades Valtueña, A and Hübner, A and Ibrahim, A and Quagliariello, A and White, AE and Kocher, A and Vågene, ÅJ and Bartholdy, BP and Spurīte, D and Ponce-Soto, GY and Neumann, G and Huang, IT and Light, I and Velsko, IM and Jackson, I and Frangenberg, J and Serrano, JG and Fumey, J and Özdoğan, KT and Blevins, KE and Daly, KG and Lopopolo, M and Moraitou, M and Michel, M and van Os, M and Bravo-Lopez, MJ and Sarhan, MS and Dagtas, ND and Oskolkov, N and Smith, OS and Lebrasseur, O and Rozwalak, P and Eisenhofer, R and Wasef, S and Ramachandran, SL and Vanghi, V and Warinner, C and Fellows Yates, JA}, title = {Facilitating accessible, rapid, and appropriate processing of ancient metagenomic data with AMDirT.}, journal = {F1000Research}, volume = {12}, number = {}, pages = {926}, pmid = {39262445}, issn = {2046-1402}, support = {T32 GM139782/GM/NIGMS NIH HHS/United States ; }, mesh = {*Metagenomics/methods ; Humans ; *Metadata ; High-Throughput Nucleotide Sequencing/methods ; Software ; Metagenome ; Computational Biology/methods ; DNA, Ancient/analysis ; }, abstract = {BACKGROUND: Access to sample-level metadata is important when selecting public metagenomic sequencing datasets for reuse in new biological analyses. The Standards, Precautions, and Advances in Ancient Metagenomics community (SPAAM, https://spaam-community.org) has previously published AncientMetagenomeDir, a collection of curated and standardised sample metadata tables for metagenomic and microbial genome datasets generated from ancient samples. However, while sample-level information is useful for identifying relevant samples for inclusion in new projects, Next Generation Sequencing (NGS) library construction and sequencing metadata are also essential for appropriately reprocessing ancient metagenomic data. Currently, recovering information for downloading and preparing such data is difficult when laboratory and bioinformatic metadata is heterogeneously recorded in prose-based publications.

METHODS: Through a series of community-based hackathon events, AncientMetagenomeDir was updated to provide standardised library-level metadata of existing and new ancient metagenomic samples. In tandem, the companion tool 'AMDirT' was developed to facilitate rapid data filtering and downloading of ancient metagenomic data, as well as improving automated metadata curation and validation for AncientMetagenomeDir.

RESULTS: AncientMetagenomeDir was extended to include standardised metadata of over 6000 ancient metagenomic libraries. The companion tool 'AMDirT' provides both graphical- and command-line interface based access to such metadata for users from a wide range of computational backgrounds. We also report on errors with metadata reporting that appear to commonly occur during data upload and provide suggestions on how to improve the quality of data sharing by the community.

CONCLUSIONS: Together, both standardised metadata reporting and tooling will help towards easier incorporation and reuse of public ancient metagenomic datasets into future analyses.}, } @article {pmid39257810, year = {2024}, author = {Hartley, GA and Okhovat, M and Hoyt, SJ and Fuller, E and Pauloski, N and Alexandre, N and Alexandrov, I and Drennan, R and Dubocanin, D and Gilbert, DM and Mao, Y and McCann, C and Neph, S and Ryabov, F and Sasaki, T and Storer, JM and Svendsen, D and Troy, W and Wells, J and Core, L and Stergachis, A and Carbone, L and O'Neill, RJ}, title = {Centromeric transposable elements and epigenetic status drive karyotypic variation in the eastern hoolock gibbon.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {39257810}, issn = {2692-8205}, support = {P51 OD011092/OD/NIH HHS/United States ; R01 GM123312/GM/NIGMS NIH HHS/United States ; R01 HG007352/HG/NHGRI NIH HHS/United States ; R01 HG010333/HG/NHGRI NIH HHS/United States ; }, abstract = {Great apes have maintained a stable karyotype with few large-scale rearrangements; in contrast, gibbons have undergone a high rate of chromosomal rearrangements coincident with rapid centromere turnover. Here we characterize assembled centromeres in the Eastern hoolock gibbon, Hoolock leuconedys (HLE), finding a diverse group of transposable elements (TEs) that differ from the canonical alpha satellites found across centromeres of other apes. We find that HLE centromeres contain a CpG methylation centromere dip region, providing evidence this epigenetic feature is conserved in the absence of satellite arrays; nevertheless, we report a variety of atypical centromeric features, including protein-coding genes and mismatched replication timing. Further, large structural variations define HLE centromeres and distinguish them from other gibbons. Combined with differentially methylated TEs, topologically associated domain boundaries, and segmental duplications at chromosomal breakpoints, we propose that a "perfect storm" of multiple genomic attributes with propensities for chromosome instability shaped gibbon centromere evolution.}, } @article {pmid39257624, year = {2024}, author = {Lohse, K and Vila, R and Hayward, A and , and , and , and , and , }, title = {The genome sequence of the Lulworth Skipper, Thymelicus acteon (Rottemburg, 1775).}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {266}, pmid = {39257624}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual male Thymelicus acteon (the Lulworth Skipper; Arthropoda; Insecta; Lepidoptera; Hesperiidae). The genome sequence is 537.0 megabases in span. Most of the assembly is scaffolded into 28 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 17.08 kilobases in length. Gene annotation of this assembly on Ensembl identified 12,813 protein-coding genes.}, } @article {pmid39257623, year = {2024}, author = {Boyes, D and Januszczak, I and Lees, DC and , and , and , and , and , and , and , }, title = {The genome sequence of the White-pinion Spotted, Lomographa bimaculata (Fabricius, 1775).}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {96}, pmid = {39257623}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual male Lomographa bimaculata (the White-pinion Spotted; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 554.7 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 16.66 kilobases in length. Gene annotation of this assembly on Ensembl identified 12,749 protein coding genes.}, } @article {pmid39257281, year = {2024}, author = {Calabrese, JM and Schüler, L and Fu, X and Gawel, E and Zozmann, H and Bumberger, J and Quaas, M and Wolf, G and Attinger, S}, title = {A novel, scenario-based approach to comparing non-pharmaceutical intervention strategies across nations.}, journal = {Journal of the Royal Society, Interface}, volume = {21}, number = {218}, pages = {20240301}, pmid = {39257281}, issn = {1742-5662}, support = {//Helmholtz-Gemeinschaft/ ; //Bundesministerium für Bildung und Forschung/ ; //Sächsisches Staatsministerium für Wissenschaft und Kunst/ ; }, mesh = {*COVID-19/epidemiology/prevention & control ; Humans ; New Zealand/epidemiology ; Switzerland/epidemiology ; Germany/epidemiology ; *SARS-CoV-2 ; Pandemics/prevention & control ; }, abstract = {Comparing COVID-19 response strategies across nations is a key step in preparing for future pandemics. Conventional comparisons, which rank individual non-pharmaceutical intervention (NPI) effects, are limited by: (i) a focus on epidemiological outcomes; (ii) NPIs typically being applied as packages of interventions; and (iii) different political, economic and social conditions among nations. Here, we develop a coupled epidemiological-behavioural-macroeconomic model that can transfer NPI effects from a reference nation to a focal nation. This approach quantifies epidemiological, behavioural and economic outcomes while accounting for both packaged NPIs and differing conditions among nations. As a first proof of concept, we take Germany as our focal nation during Spring 2020, and New Zealand and Switzerland as reference nations with contrasting NPI strategies. Our results suggest that, while New Zealand's more aggressive strategy would have yielded modest epidemiological gains in Germany, it would have resulted in substantially higher economic costs while dramatically reducing social contacts. In contrast, Switzerland's more lenient strategy would have prolonged the first wave in Germany, but would also have increased relative costs. More generally, these findings indicate that our approach can provide novel, multifaceted insights on the efficacy of pandemic response strategies, and therefore merits further exploration and development.}, } @article {pmid39255632, year = {2024}, author = {Amenu, K and Daborn, C and Huntington, B and Knight-Jones, T and Rushton, J and Grace, D}, title = {Prioritization, resource allocation and utilization of decision support tools in animal health: Results of qualitative interviews with experts.}, journal = {Preventive veterinary medicine}, volume = {233}, number = {}, pages = {106333}, doi = {10.1016/j.prevetmed.2024.106333}, pmid = {39255632}, issn = {1873-1716}, mesh = {Animals ; *Resource Allocation ; Decision Support Techniques ; Health Priorities ; Decision Making ; Animal Husbandry/methods ; Surveys and Questionnaires ; }, abstract = {A follow up to an online questionnaire survey (in a kind of a sequential study design), qualitative assessment was made on the views of selected animal health experts on disease prioritization methods, resource allocation and use of decision-support tools. This was done through in-depth interviews with experts working for national or international organizations and sectors. A semi-structured question guide was formulated based on the information generated in the online questionnaire and a systematic content analysis of animal and human health manuals for disease prioritization and resource allocation. In-depth, one-on-one, online interviews on the process of disease prioritization, animal health decision-making, types of prioritization tools and aspects of improvements in the tools were conducted during March and April 2022 with 20 expert informants. Prioritization approaches reported by experts were either single criterion-based or multiple criteria-based. Experts appreciated the single-criterion-based approach (quantitative) for its objectivity in contrast to multicriteria prioritization approaches which were criticized for their subjectivity. Interviews with the experts revealed a perceived lack of quality and reliable data to inform disease prioritization, especially in smallholder livestock production systems. It was found that outputs of disease prioritization exercises do not generally directly influence resource allocation in animal health and highlighted the paucity of funding for animal health compared to other agricultural sectors. The experts considered that the available decision-support tools in animal health need improvement in terms of data visualization for interpretation, management decision making and advocacy. Further recommendations include minimizing subjective biases by increasing the availability and quality of data and improving the translation of disease prioritization outputs into actions and the resources to deliver those actions. DATA AVAILABILITY STATEMENT: The data can be obtained from the corresponding author upon request.}, } @article {pmid39255272, year = {2024}, author = {Sylla, A and Chevillon, C and Djidjiou-Demasse, R and Seydi, O and Campos, CAV and Dogbe, M and Fast, KM and Pechal, JL and Rakestraw, A and Scott, ME and Sandel, MW and Jordan, H and Benbow, ME and Guégan, JF}, title = {Understanding the transmission of bacterial agents of sapronotic diseases using an ecosystem-based approach: A first spatially realistic metacommunity model.}, journal = {PLoS computational biology}, volume = {20}, number = {9}, pages = {e1012435}, pmid = {39255272}, issn = {1553-7358}, mesh = {Humans ; *Ecosystem ; Mycobacterium ulcerans/pathogenicity ; Buruli Ulcer/transmission/microbiology ; Models, Biological ; Computational Biology ; Animals ; }, abstract = {Pathogens such as bacteria, fungi and viruses are important components of soil and aquatic communities, where they can benefit from decaying and living organic matter, and may opportunistically infect human and animal hosts. One-third of human infectious diseases is constituted by sapronotic disease agents that are natural inhabitants of soil or aquatic ecosystems. They are capable of existing and reproducing in the environment outside of the host for extended periods of time. However, as ecological research on sapronosis is infrequent and epidemiological models are even rarer, very little information is currently available. Their importance is overlooked in medical and veterinary research, as well as the relationships between free environmental forms and those that are pathogenic. Here, using dynamical models in realistic aquatic metacommunity systems, we analyze sapronosis transmission, using the human pathogen Mycobacterium ulcerans that is responsible for Buruli ulcer. We show that the persistence of bacilli in aquatic ecosystems is driven by a seasonal upstream supply, and that the attachment and development of cells to aquatic living forms is essential for such pathogen persistence and population dynamics. Our work constitutes the first set of metacommunity models of sapronotic disease transmission, and is highly flexible for adaptation to other types of sapronosis. The importance of sapronotic agents on animal and human disease burden needs better understanding and new models of sapronosis disease ecology to guide the management and prevention of this important group of pathogens.}, } @article {pmid39255143, year = {2024}, author = {Jiang, W and Windl, M and Tag, B and Sarsenbayeva, Z and Mayer, S}, title = {An Immersive and Interactive VR Dataset to Elicit Emotions.}, journal = {IEEE transactions on visualization and computer graphics}, volume = {30}, number = {11}, pages = {7343-7353}, doi = {10.1109/TVCG.2024.3456202}, pmid = {39255143}, issn = {1941-0506}, mesh = {Humans ; *Emotions/physiology ; *Virtual Reality ; Female ; Male ; *Computer Graphics ; Adult ; Young Adult ; User-Computer Interface ; Databases, Factual ; Video Recording ; }, abstract = {Images and videos are widely used to elicit emotions; however, their visual appeal differs from real-world experiences. With virtual reality becoming more realistic, immersive, and interactive, we envision virtual environments to elicit emotions effectively, rapidly, and with high ecological validity. This work presents the first interactive virtual reality dataset to elicit emotions. We created five interactive virtual environments based on corresponding validated 360° videos and validated their effectiveness with 160 participants. Our results show that our virtual environments successfully elicit targeted emotions. Compared with the existing methods using images or videos, our dataset allows virtual reality researchers and practitioners to integrate their designs effectively with emotion elicitation settings in an immersive and interactive way.}, } @article {pmid39253482, year = {2024}, author = {Mortzfeld, BM and Bhattarai, SK and Bucci, V}, title = {Expanding the toolbox: Novel class IIb microcins show activity against Gram-negative ESKAPE and plant pathogens.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2023.12.05.570296}, pmid = {39253482}, issn = {2692-8205}, abstract = {Interspecies interactions involving direct competition via bacteriocin production play a vital role in shaping ecological dynamics within microbial ecosystems. For instance, the ribosomally-produced siderophore bacteriocins, known as class IIb microcins, affect the colonization of host-associated pathogenic Enterobacteriaceae species. Notably, to date, only five of these antimicrobials have been identified, all derived from specific Escherichia coli and Klebsiella pneumoniae strains. We hypothesized that class IIb microcin production extends beyond these specific compounds and organisms. With a customized informatics-driven approach, screening bacterial genomes in public databases with BLAST and manual curation, we have discovered twelve previously unknown class IIb microcins in seven additional Enterobacteriaceae species, encompassing phytopathogens and environmental isolates. We introduce three novel clades of microcins (MccW, MccX, and MccZ), while also identifying eight new variants of the five known class IIb microcins. To validate their antimicrobial potential, we heterologously expressed these microcins in E. coli and demonstrated efficacy against a variety of bacterial isolates, including plant pathogens from the genera Brenneria, Gibbsiella, and Rahnella . Two newly discovered microcins exhibit activity against Gram-negative ESKAPE pathogens, i.e. Acinetobacter baumannii or Pseudomonas aeruginosa , providing the first evidence that class IIb microcins can target bacteria outside of the Enterobacteriaceae family. This study underscores that class IIb microcin genes are more prevalent in the microbial world than previously recognized and that synthetic hybrid microcins can be a viable tool to target clinically relevant drug-resistant pathogens. Our findings hold significant promise for the development of innovative engineered live biotherapeutic products tailored to combat these resilient bacteria.}, } @article {pmid39250076, year = {2024}, author = {Zancolli, G and von Reumont, BM and Anderluh, G and Caliskan, F and Chiusano, ML and Fröhlich, J and Hapeshi, E and Hempel, BF and Ikonomopoulou, MP and Jungo, F and Marchot, P and de Farias, TM and Modica, MV and Moran, Y and Nalbantsoy, A and Procházka, J and Tarallo, A and Tonello, F and Vitorino, R and Zammit, ML and Antunes, A}, title = {Web of venom: exploration of big data resources in animal toxin research.}, journal = {GigaScience}, volume = {13}, number = {}, pages = {}, pmid = {39250076}, issn = {2047-217X}, support = {//European Cooperation in Science and Technology/ ; //Fundação para a Ciência e a Tecnologia/ ; }, mesh = {Animals ; *Venoms ; *Internet ; *Computational Biology/methods ; *Big Data ; Databases, Factual ; }, abstract = {Research on animal venoms and their components spans multiple disciplines, including biology, biochemistry, bioinformatics, pharmacology, medicine, and more. Manipulating and analyzing the diverse array of data required for venom research can be challenging, and relevant tools and resources are often dispersed across different online platforms, making them less accessible to nonexperts. In this article, we address the multifaceted needs of the scientific community involved in venom and toxin-related research by identifying and discussing web resources, databases, and tools commonly used in this field. We have compiled these resources into a comprehensive table available on the VenomZone website (https://venomzone.expasy.org/10897). Furthermore, we highlight the challenges currently faced by researchers in accessing and using these resources and emphasize the importance of community-driven interdisciplinary approaches. We conclude by underscoring the significance of enhancing standards, promoting interoperability, and encouraging data and method sharing within the venom research community.}, } @article {pmid39244927, year = {2024}, author = {Ibrahim, AS and Kuuire, V and Kepe, T}, title = {On mapping urban community resilience: Land use vulnerability, coping and adaptive strategies in Ghana.}, journal = {Journal of environmental management}, volume = {370}, number = {}, pages = {122426}, doi = {10.1016/j.jenvman.2024.122426}, pmid = {39244927}, issn = {1095-8630}, mesh = {Ghana ; *Floods ; Humans ; *Cities ; Climate Change ; Urban Population ; Geographic Information Systems ; }, abstract = {Cities across the globe are prioritizing resilience in the wake of increasing climate change-related disasters. About 44% of these disasters are floods and their manifestation in cities is more pronounced, threatening urban social, ecological, and economic systems. This study draws on community resilience and participatory GIS, to examine land use vulnerability to flooding and local coping and adaptive strategies to achieve resilience. Using Ghana as a case study, the results show that participatory mapping offers community resilience benefits by providing context to community resilience challenges and potentials, enabling a deeper understanding of socio-environmental coupling that contributes to flood vulnerability and builds on community adaptive strategies through harnessing local community knowledge. We identified that topography, poor drainage and road network, rainfall variability, residents' land use practices, and land use planning conundrum drive disparities in land use vulnerability to flooding. Participants underscored the necessity of critical urban infrastructure in facilitating community adaptability to floods. The findings indicate that socio-spatial inequities threaten urban community resilience, especially in increasingly cosmopolitan urban contexts, by putting the marginalized urban population in a more vulnerable position. We recommend the prioritization of recognitional equity in community resilience planning efforts to allow for the targeting of resilient interventions that reflect and respect social differentiation in the urban environment so that outcomes will not exacerbate or generate new urban socio-spatial inequalities.}, } @article {pmid39242865, year = {2023}, author = {Karakulak, A and Tepe, B and Dimitrova, R and Abdelrahman, M and Akaliyski, P and Alaseel, R and Alkamali, YA and Amin, A and Lizarzaburu Aguinaga, DA and Andres, A and Aruta, JJBR and Assiotis, M and Avanesyan, H and Ayub, N and Bacikova-Sleskova, M and Baikanova, R and Bakkar, B and Bartoluci, S and Benitez, D and Bodnar, I and Bolatov, A and Borchet, J and Bosnar, K and Broche-Pérez, Y and Buzea, C and Cassibba, R and Carbonell, MM and Chen, BB and Dimitrovska, GR and Công Doanh, D and Dominguez Espinosa, ADC and Edine, WG and Ferenczi, N and Fernández-Morales, R and Gaete, J and Gan, Y and Giolo, S and Giordani, RCF and Friehs, MT and Gindi, S and Gjoneska, B and Godoy, JC and Del Pilar Grazioso, M and Hancheva, C and Hapunda, G and Hihara, S and Husain, MS and Islam, MS and Janovská, A and Javakhishvili, N and Jovanović, V and Kabir, RS and Abdul Kadir, NB and Karl, J and Katović, D and Kauyzbay, Z and Kawashima, TD and Kazmierczak, M and Khanna, R and Khosla, M and Klicperová-Baker, M and Kozina, A and Krauss, SE and Landabur, R and Lefringhausen, K and Lewandowska-Walter, A and Liang, YH and Makashvili, A and Malik, S and Manrique-Millones, D and Mastrotheodoros, S and McGrath, B and Mechili, EA and Mejía, M and Mhizha, S and Michalek-Kwiecien, J and Miconi, D and Mohsen, F and Moreta-Herrera, R and Muhl, C and Muradyan, M and Musso, P and Naterer, A and Nemat, A and Neto, F and Neto, J and Palacio, LMA and Okati-Aliabad, H and Orellana, CI and Orellana, LM and Mishra, SK and Park, J and Pavlova, I and Peralta, E and Petrytsa, P and Pišot, S and Prot, F and Rasia, J and Rivera, R and Riyanti, BPD and Samekin, A and Seisembekov, T and Serapinas, D and Silletti, F and Sharma, P and Shukla, S and Skrzypińska, K and Šolcová, IP and Solomontos-Kountouri, O and Stanciu, A and Stefenel, D and Steinmetz, LCL and Stogianni, M and Stuart, J and Sudarnoto, LF and Sugimura, K and Sultana, S and Suryani, AO and Tair, E and Tavitian-Elmadjan, L and Thome, LD and Uka, F and Valickienė, RP and Walter, B and Wendt, GW and Yang, PJ and Yıldırım, E and Yu, Y and Yunes, MAM and Zanoni da Silva, M and Rudnev, M}, title = {Trust in government moderates the association between fear of COVID-19 as well as empathic concern and preventive behaviour.}, journal = {Communications psychology}, volume = {1}, number = {1}, pages = {43}, pmid = {39242865}, issn = {2731-9121}, abstract = {With the COVID-19 pandemic, behavioural scientists aimed to illuminate reasons why people comply with (or not) large-scale cooperative activities. Here we investigated the motives that underlie support for COVID-19 preventive behaviours in a sample of 12,758 individuals from 34 countries. We hypothesized that the associations of empathic prosocial concern and fear of disease with support towards preventive COVID-19 behaviours would be moderated by trust in the government. Results suggest that the association between fear of disease and support for COVID-19 preventive behaviours was strongest when trust in the government was weak (both at individual- and country-level). Conversely, the association with empathic prosocial concern was strongest when trust in the government was high, but this moderation was only found at individual-level scores of governmental trust. We discuss how motivations may be shaped by socio-cultural context, and outline how findings may contribute to a better understanding of collective action during global crises.}, } @article {pmid39242702, year = {2023}, author = {Santangeli, A and Haukka, A and Morris, W and Arkkila, S and Delhey, K and Kempenaers, B and Valcu, M and Dale, J and Lehikoinen, A and Mammola, S}, title = {What drives our aesthetic attraction to birds?.}, journal = {npj biodiversity}, volume = {2}, number = {1}, pages = {20}, pmid = {39242702}, issn = {2731-4243}, abstract = {In the Anthropocene, the era when the imprint of humans on nature is pervasive across the planet, it is of utmost importance to understand human relationships with other species. The aesthetics of nature, and of species, is one of the values that plays a role in shaping human-nature relationships. Birds are ubiquitous across the world. The beauty of birds exerts a powerful tug on human emotions, and bird-rich areas attract scores of eco-tourists. People naturally find some birds more beautiful or interesting than others, but we currently lack a global understanding of the specifics of what makes a species aesthetically attractive. Here, we used a global citizen-science database on bird attractiveness covering nearly all extant bird species, to show that there are specific visual features that drive our aesthetic appeal for some bird species over others. First, our aesthetic attraction is highest for smaller birds with specific, vivid colors (e.g., blue and red, and departing from brown-grey) and extreme ornaments (a long crest or tail). Second, our aesthetic attraction is highest for species with broad ranges, possibly because such species may be more familiar to us. The features that make us attracted to a particular bird strongly align with broad human visual aesthetic preferences in modern society. Unveiling the visual features underpinning our aesthetic attraction to birds is a critical step towards optimizing conservation (e.g., via conservation marketing) and education campaigns, and leverage the cultural ecosystem service potential of birds.}, } @article {pmid39240878, year = {2024}, author = {Shipley, ON and Dabrowski, AJ and Bowen, GJ and Hayden, B and Pauli, JN and Jordan, C and Anderson, L and Bailey, A and Bataille, CP and Cicero, C and Close, HG and Cook, C and Cook, JA and Desai, AR and Evaristo, J and Filley, TR and France, CAM and Jackson, AL and Kim, SL and Kopf, S and Loisel, J and Manlick, PJ and McFarlin, JM and McMeans, BC and O'Connell, TC and Pilaar Birch, SE and Putman, AL and Semmens, BX and Stantis, C and Stricker, CA and Szejner, P and Trammell, TLE and Uhen, MD and Weintraub-Leff, S and Wooller, MJ and Williams, JW and Yarnes, CT and Vander Zanden, HB and Newsome, SD}, title = {Design, development, and implementation of IsoBank: A centralized repository for isotopic data.}, journal = {PloS one}, volume = {19}, number = {9}, pages = {e0295662}, pmid = {39240878}, issn = {1932-6203}, mesh = {*Databases, Factual ; *Metadata ; Isotopes ; Internet ; }, abstract = {Stable isotope data have made pivotal contributions to nearly every discipline of the physical and natural sciences. As the generation and application of stable isotope data continues to grow exponentially, so does the need for a unifying data repository to improve accessibility and promote collaborative engagement. This paper provides an overview of the design, development, and implementation of IsoBank (www.isobank.org), a community-driven initiative to create an open-access repository for stable isotope data implemented online in 2021. A central goal of IsoBank is to provide a web-accessible database supporting interdisciplinary stable isotope research and educational opportunities. To achieve this goal, we convened a multi-disciplinary group of over 40 analytical experts, stable isotope researchers, database managers, and web developers to collaboratively design the database. This paper outlines the main features of IsoBank and provides a focused description of the core metadata structure. We present plans for future database and tool development and engagement across the scientific community. These efforts will help facilitate interdisciplinary collaboration among the many users of stable isotopic data while also offering useful data resources and standardization of metadata reporting across eco-geoinformatics landscapes.}, } @article {pmid39239169, year = {2024}, author = {Boyes, D and Holland, PWH and , and , and , and , and , and , and , }, title = {The genome sequence of the Elephant Hawk-moth, Deilephila elpenor (Linnaeus, 1758).}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {104}, pmid = {39239169}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual female Deilephila elpenor (the Elephant Hawk-moth; Arthropoda; Insecta; Lepidoptera; Sphingidae). The genome sequence is 414.1 megabases in span. Most of the assembly is scaffolded into 30 chromosomal pseudomolecules, including the Z and W sex chromosomes. The mitochondrial genome has also been assembled and is 15.37 kilobases in length. Gene annotation of this assembly on Ensembl identified 11,748 protein coding genes.}, } @article {pmid39235751, year = {2025}, author = {Lemée, P and Bridier, A}, title = {Bioinformatic Pipeline for Profiling Foodborne Bacterial Ecology and Resistome from Short-Read Metagenomics.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2852}, number = {}, pages = {289-309}, pmid = {39235751}, issn = {1940-6029}, mesh = {*Metagenomics/methods ; *Computational Biology/methods ; *Food Microbiology/methods ; *Bacteria/genetics ; *High-Throughput Nucleotide Sequencing/methods ; Metagenome ; Microbiota/genetics ; }, abstract = {Next-generation sequencing revolutionized food safety management these last years providing access to a huge quantity of valuable data to identify, characterize, and monitor bacterial pathogens on the food chain. Shotgun metagenomics emerged as a particularly promising approach as it enables in-depth taxonomic profiling and functional investigation of food microbial communities. In this chapter, we provide a comprehensive step-by-step bioinformatical workflow to characterize bacterial ecology and resistome composition from metagenomic short-reads obtained by shotgun sequencing.}, } @article {pmid39233902, year = {2024}, author = {Boyes, D and Holland, PWH and , and , and , and , and , and , and , }, title = {The genome sequence of the Green Silver-lines, Pseudoips prasinana (Linnaeus, 1758).}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {117}, pmid = {39233902}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual female Pseudoips prasinana (the Green Silver-lines; Arthropoda; Insecta; Lepidoptera; Nolidae). The genome sequence is 1,125.7 megabases in span. Most of the assembly is scaffolded into 33 chromosomal pseudomolecules, including the Z and W sex chromosomes. The mitochondrial genome has also been assembled and is 15.23 kilobases in length. Gene annotation of this assembly on Ensembl identified 20,065 protein coding genes.}, } @article {pmid39233899, year = {2024}, author = {Boyes, D and Holland, PWH and , and , and , and , and , and , and , }, title = {The genome sequence of the Scarlet Tiger moth, Callimorpha dominula (Linnaeus, 1758).}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {31}, pmid = {39233899}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual male Callimorpha dominula (the Scarlet Tiger moth; Arthropoda; Insecta; Lepidoptera; Erebidae). The genome sequence is 658.1 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.45 kilobases in length. Gene annotation of this assembly on Ensembl identified 20,234 protein coding genes.}, } @article {pmid39233418, year = {2024}, author = {Li, X and Zhang, LY and Wu, C}, title = {Vegetation changes and influencing factors in different watersheds of Henan Province based on GEE and geographic detectors.}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {35}, number = {7}, pages = {1887-1896}, doi = {10.13287/j.1001-9332.202407.021}, pmid = {39233418}, issn = {1001-9332}, mesh = {China ; *Rivers ; *Ecosystem ; *Environmental Monitoring/methods ; Conservation of Natural Resources ; Plant Development ; Geographic Information Systems ; Plants ; }, abstract = {Clarifying vegetation changes and the driving factors can provide references for ecological restoration and sustainable social development. We analyzed vegetation distribution and trend changes in Henan Province and its basin zoning (Haihe River basin zoning, Yellow River basin zoning, Huaihe River basin zoning, Yangtze River basin zoning), with fractional vegetation cover data from 2000 to 2020 based on the Google Earth Engine platform, and by combining Theil-Sen Median trend analysis, Mann-Kendall test, and Hurst index. We also utilized factor detection and factor interaction to explore the individual and mutual influences of natural and anthropogenic factors on vegetation at different scales. The results showed that the fractional vegetation cover (FVC) in Henan Province exhibited a distribution pattern of higher coverage in the south and lower in the north during the study period, predominantly characterized by moderate to high vegetation coverage. The Yangtze River basin zoning had the highest coverage. FVC in Henan Province and its zoning exhibited a consistent pattern of fluctuating upward trends, with all areas showing significant improvement. Particularly, the Yangtze River basin zoning had the largest area of improvement. According to the Hurst index, apart from the possibility of continued improvement in the Huaihe River basin zoning, other zoning would be likely to shift from improvement to degradation in the future. Vegetation changes in Henan Province and its zoning were the result of combined effects of anthropogenic and natural factors, with the influence of these factors changing over time and the dominant factors varying by region. Anthropogenic factors such as land use/cover type and nighttime lighting had a stronger impact on vegetation than natural factors like elevation, slope, and annual mean low temperature. The interaction between factors, particularly between anthropogenic and natural factors, exhibited a nonlinear enhancing pattern.}, } @article {pmid39233286, year = {2024}, author = {Long, XB and Yao, CR and Li, SY and Zhang, JG and Lu, ZJ and Ma, DD and Jiang, YX and Ying, GG and Shi, WJ}, title = {Multiomics analysis reveal the impact of 17α-Ethinylestradiol on mortality in juvenile zebrafish.}, journal = {Comparative biochemistry and physiology. Toxicology & pharmacology : CBP}, volume = {286}, number = {}, pages = {110027}, doi = {10.1016/j.cbpc.2024.110027}, pmid = {39233286}, issn = {1532-0456}, mesh = {Animals ; *Zebrafish ; *Ethinyl Estradiol/toxicity ; *Water Pollutants, Chemical/toxicity ; Endocrine Disruptors/toxicity ; Transcriptome/drug effects ; Multiomics ; }, abstract = {17α-Ethinylestradiol (EE2) is known for its endocrine-disrupting effects on embryonic and adult fish. However, its impact on juvenile zebrafish has not been well established. In this study, juvenile zebrafish were exposed to EE2 at concentrations of 5 ng/L (low dose, L), 10 ng/L (medium dose, M), and 50 ng/L (high dose, H) from 21 days post-fertilization (dpf) to 49 dpf. We assessed their growth, development, behavior, transcriptome, and metabolome. The findings showed that the survival rate in the EE2-H group was 66.8 %, with all surviving fish displaying stunted growth and swollen, transparent abdomens by 49 dpf. Moreover, severe organ deformities were observed in the gills, kidneys, intestines, and heart of fish in both the EE2-H and EE2-M groups. Co-expression analysis of mRNA and lncRNA revealed that EE2 downregulated the transcription of key genes involved in the cell cycle, DNA replication, and Fanconi anemia signaling pathways. Additionally, metabolomic analysis indicated that EE2 influenced metabolism and development-related signaling pathways. These pathways were also significantly identified based on the genes regulated by lncRNA. Consequently, EE2 induced organ deformities and mortality in juvenile zebrafish by disrupting signaling pathways associated with development and metabolism. The results of this study offer new mechanistic insights into the adverse effects of EE2 on juvenile zebrafish based on multiomics analysis. The juvenile zebrafish are highly sensitive to EE2 exposure, which is not limited to adult and embryonic stages. It is a potential model for studying developmental toxicity.}, } @article {pmid39233066, year = {2024}, author = {Wen, J and Chuai, X and Xiang, A and Liu, Y and Wang, T and Luo, Y and Miao, L and Zhang, L and Li, J and Zhao, R}, title = {Re-identifying farmland carbon neutrality gap under a new carbon counting and the framework of regional interactions in China.}, journal = {The Science of the total environment}, volume = {952}, number = {}, pages = {175996}, doi = {10.1016/j.scitotenv.2024.175996}, pmid = {39233066}, issn = {1879-1026}, abstract = {The farmland ecosystem, with its numerous material cycles and energy flows, is an important part of the carbon cycle in terrestrial ecosystems. Focusing on the carbon neutrality of farmland is meaningful for mitigating global warming and serving national low-carbon strategies. This study enriches the carbon accounting items of farmland and establishes a new research framework to check the carbon neutrality of farmland from the aspect of regional interactions and, subsequently, the inequality among China's provinces. The results revealed that there is still a great gap in the capability of China[']s farmland to reach carbon neutrality, with a gap value of up to 10,503 × 10[4] t C. All of the provinces presented net carbon emissions, and the per unit area carbon neutrality gaps showed spatial regularity decreasing from the coastal regions to the inland areas. Anthropogenic carbon emissions on farmland played a dominant role compared with soil organic carbon. Five provinces had reduced interior-regional carbon emissions through grain trade, and the amounts were especially high for developed regions, such as Guangdong, Zhejiang, Beijing, Shanghai and Jiangsu. Sixteen provinces gained external carbon emissions through trade; these were the less developed regions located mainly in the north, such as Inner Mongolia, Hebei, Jilin, Heilongjiang and Xinjiang. Under regional inequality, 15 provinces added to the net amount of the carbon emissions generated in external regions, with China's megacities adding the highest percentage, especially Beijing, with 389.95 % compared with its original emissions. Inequality showed that most provinces had a moderate status. Sichuan and Hunan experienced weak advantages, and six provinces had disadvantages. Therefore, constructing compensation and trade-based rights and responsibilities traceability mechanisms is important.}, } @article {pmid39230451, year = {2024}, author = {Hendrix, JG and Robitaille, AL and Kusch, JM and Webber, QMR and Vander Wal, E}, title = {Faithful pals and familiar locales: differentiating social and spatial site fidelity during reproduction.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {379}, number = {1912}, pages = {20220525}, pmid = {39230451}, issn = {1471-2970}, support = {//Natural Sciences and Engineering Research Council of Canada/ ; }, mesh = {Animals ; Female ; *Reproduction ; *Reindeer/physiology ; Newfoundland and Labrador ; Social Behavior ; Geographic Information Systems ; }, abstract = {Site fidelity-the tendency to reuse familiar spaces-is expected to improve fitness. Familiarity with the local environment is particularly crucial when resource demands or predation risk are high. Consequently, site fidelity often peaks during reproduction when energetic costs are high and offspring are vulnerable. For many species, the environment they experience is not solely a function of geography but also of the social environment. Social fidelity, the selection for familiar social environments, could constitute an independent or parallel strategy to spatial fidelity when considering behaviour at the spatial-social interface. Using global positioning system locations from caribou across Newfoundland, we tested whether females selected calving sites based on proximity to familiar conspecifics, in addition to geographical (spatial) fidelity. These strategies were synergistic, not alternative, and correlated across the population but more variable within individuals. We also tested whether either form of fidelity affected reproductive success. We failed to detect an effect of spatial or social fidelity on reproductive success in this population. Nevertheless, given the association between social and spatial fidelity and the demonstrated fitness consequences of site fidelity in other systems, familiar conspecifics and the potential benefits these social partners provide may be an underappreciated component driving site fidelity.This article is part of the theme issue 'The spatial-social interface: a theoretical and empirical integration'.}, } @article {pmid39229001, year = {2024}, author = {Obbard, DJ and , and , and , and , and , and , }, title = {The genome sequence of a drosophilid fruit fly, Drosophila limbata von Roser 1840.}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {365}, pmid = {39229001}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual male Drosophila limbata (drosophilid fruit fly; Arthropoda; Insecta; Diptera; Drosophilidae). The genome sequence is 233.5 megabases in span. Most of the assembly is scaffolded into 6 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 16.09 kilobases in length.}, } @article {pmid39226337, year = {2024}, author = {Rahman, AU and Tikhonov, G and Oksanen, J and Rossi, T and Ovaskainen, O}, title = {Accelerating joint species distribution modelling with Hmsc-HPC by GPU porting.}, journal = {PLoS computational biology}, volume = {20}, number = {9}, pages = {e1011914}, pmid = {39226337}, issn = {1553-7358}, mesh = {*Algorithms ; *Computational Biology/methods ; *Software ; Models, Biological ; Machine Learning ; Computer Graphics ; Models, Statistical ; Humans ; }, abstract = {Joint species distribution modelling (JSDM) is a widely used statistical method that analyzes combined patterns of all species in a community, linking empirical data to ecological theory and enhancing community-wide prediction tasks. However, fitting JSDMs to large datasets is often computationally demanding and time-consuming. Recent studies have introduced new statistical and machine learning techniques to provide more scalable fitting algorithms, but extending these to complex JSDM structures that account for spatial dependencies or multi-level sampling designs remains challenging. In this study, we aim to enhance JSDM scalability by leveraging high-performance computing (HPC) resources for an existing fitting method. Our work focuses on the Hmsc R-package, a widely used JSDM framework that supports the integration of various dataset types into a single comprehensive model. We developed a GPU-compatible implementation of its model-fitting algorithm using Python and the TensorFlow library. Despite these changes, our enhanced framework retains the original user interface of the Hmsc R-package. We evaluated the performance of the proposed implementation across various model configurations and dataset sizes. Our results show a significant increase in model fitting speed for most models compared to the baseline Hmsc R-package. For the largest datasets, we achieved speed-ups of over 1000 times, demonstrating the substantial potential of GPU porting for previously CPU-bound JSDM software. This advancement opens promising opportunities for better utilizing the rapidly accumulating new biodiversity data resources for inference and prediction.}, } @article {pmid39225619, year = {2024}, author = {Liu, Z and Sun, Y and Li, Y and Ma, A and Willaims, NF and Jahanbahkshi, S and Hoyd, R and Wang, X and Zhang, S and Zhu, J and Xu, D and Spakowicz, D and Ma, Q and Liu, B}, title = {An Explainable Graph Neural Framework to Identify Cancer-Associated Intratumoral Microbial Communities.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {11}, number = {41}, pages = {e2403393}, pmid = {39225619}, issn = {2198-3844}, support = {2020YFA0712400//National Key Research and Development Program of China/ ; 62272270//National Nature Science Foundation of China/ ; 11931008//National Nature Science Foundation of China/ ; ZR2023JQ002//Shandong Provincial Natural Science Foundation for Distinguished Young Scholars/ ; }, mesh = {Mice ; *Microbiota ; Animals ; *Neoplasms/microbiology ; *Neural Networks, Computer ; Humans ; Reproducibility of Results ; Disease Models, Animal ; }, abstract = {Microbes are extensively present among various cancer tissues and play critical roles in carcinogenesis and treatment responses. However, the underlying relationships between intratumoral microbes and tumors remain poorly understood. Here, a MIcrobial Cancer-association Analysis using a Heterogeneous graph transformer (MICAH) to identify intratumoral cancer-associated microbial communities is presented. MICAH integrates metabolic and phylogenetic relationships among microbes into a heterogeneous graph representation. It uses a graph transformer to holistically capture relationships between intratumoral microbes and cancer tissues, which improves the explainability of the associations between identified microbial communities and cancers. MICAH is applied to intratumoral bacterial data across 5 cancer types and 5 fungi datasets, and its generalizability and reproducibility are demonstrated. After experimentally testing a representative observation using a mouse model of tumor-microbe-immune interactions, a result consistent with MICAH's identified relationship is observed. Source tracking analysis reveals that the primary known contributor to a cancer-associated microbial community is the organs affected by the type of cancer. Overall, this graph neural network framework refines the number of microbes that can be used for follow-up experimental validation from thousands to tens, thereby helping to accelerate the understanding of the relationship between tumors and intratumoral microbiomes.}, } @article {pmid39224879, year = {2023}, author = {Boyes, D and Mulley, JF and , and , and , and , and , and , }, title = {The genome sequence of the Small Emerald, Hemistola chrysoprasaria (Esper, 1795).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {441}, pmid = {39224879}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual male Hemistola chrysoprasaria (the Small Emerald; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 438.2 megabases in span. Most of the assembly is scaffolded into 30 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.63 kilobases in length. Gene annotation of this assembly on Ensembl identified 17,512 protein coding genes.}, } @article {pmid39224768, year = {2024}, author = {Jentoft, S and Tørresen, OK and Tooming-Klunderud, A and Skage, M and Kollias, S and Jakobsen, KS and , and , and , and , and , }, title = {The genome sequence of the Atlantic cod, Gadus morhua (Linnaeus, 1758).}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {189}, pmid = {39224768}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual male Gadus morhua (the Atlantic cod; Chordata; Actinopteri; Gadiformes; Gadidae). The genome sequence is 669.9 megabases in span. Most of the assembly is scaffolded into 23 chromosomal pseudomolecules. Gene annotation of this assembly on Ensembl identified 23,515 protein coding genes.}, } @article {pmid39224703, year = {2024}, author = {Shi, Y and Zhang, W and Li, L and Wu, W and Li, M and Xiao, K and Wang, K and Sheng, Z and Xie, F and Wang, X and Shi, X and Tong, Y and Xie, L}, title = {Evaluation of phage-based decontamination in respiratory intensive care unit environments using ddPCR and 16S rRNA targeted sequencing techniques.}, journal = {Frontiers in cellular and infection microbiology}, volume = {14}, number = {}, pages = {1442062}, pmid = {39224703}, issn = {2235-2988}, mesh = {*RNA, Ribosomal, 16S/genetics ; *Klebsiella pneumoniae/virology/genetics ; *Intensive Care Units ; *Decontamination/methods ; *Bacteriophages/genetics ; Humans ; Polymerase Chain Reaction/methods ; Cross Infection/prevention & control/microbiology ; Disinfectants/pharmacology ; Klebsiella Infections/prevention & control/microbiology ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: Klebsiella pneumoniae is a major cause of hospital-acquired infections (HAIs), primarily spread through environmental contamination in hospitals. The effectiveness of current chemical disinfectants is waning due to emerging resistance, which poses environmental hazards and fosters new resistance in pathogens. Developing environmentally friendly and effective disinfectants against multidrug-resistant organisms is increasingly important.

METHODS: This study developed a bacteriophage cocktail targeting two common carbapenem-resistant Klebsiella pneumoniae (CRKP) strains, ST11 KL47 and ST11 KL64. The cocktail was used as an adjunctive disinfectant in a hospital's respiratory intensive care unit (RICU) via ultrasonic nebulization. Digital PCR was used to quantify CRKP levels post-intervention. The microbial community composition was analyzed via 16S rRNA sequencing to assess the intervention's impact on overall diversity.

RESULTS: The phage cocktail significantly reduced CRKP levels within the first 24 hours post-treatment. While a slight increase in pathogen levels was observed after 24 hours, they remained significantly lower than those treated with conventional disinfectants. 16S rRNA sequencing showed a decrease in the target pathogens' relative abundance, while overall species diversity remained stable, confirming that phages selectively target CRKP without disrupting ecological balance.

DISCUSSION: The findings highlight the efficacy and safety of phage-based biocleaners as a sustainable alternative to conventional disinfectants. Phages selectively reduce multidrug-resistant pathogens while preserving microbial diversity, making them a promising tool for infection control.}, } @article {pmid39222768, year = {2024}, author = {Yushin, N and Jakhu, R and Chaligava, O and Grozdov, D and Zinicovscaia, I}, title = {Evaluation of the potentially toxic elements and radionuclides in the soil sample of Novaya Zemlya in the Arctic Circle.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {361}, number = {}, pages = {124871}, doi = {10.1016/j.envpol.2024.124871}, pmid = {39222768}, issn = {1873-6424}, mesh = {Arctic Regions ; *Soil/chemistry ; Russia ; Environmental Monitoring/methods ; Soil Pollutants/analysis ; Thorium/analysis ; Cesium Radioisotopes/analysis ; Soil Pollutants, Radioactive/analysis ; Radiation Monitoring/methods ; Animals ; Birds ; Radioisotopes/analysis ; Radium ; }, abstract = {The study presented here elucidate the concentrations of radionuclides and potentially toxic elements in the soil samples around the Novaya Zemlya in the Russian Arctic zone, determined using HPGe gamma spectrometry, inductively coupled plasma optical emission spectrometry and direct mercury analyzer. The average detected concentrations for [226]Ra, [232]Th, [40]K, [235]U and [137]Cs were 36.40, 46.06, 768, 2.06 and 4.71 Bq/kg, respectively. At many sampling sites, the concentrations of potentially toxic elements (Zn, Cu, Pb, Cd, Ni, and Cr) were higher than the natural levels. Positive Matrix Factorization analysis revealed the contribution of oil dumps (32%), natural sources (16%), bird colonies (32%) and atmospheric deposition (20%) for elevated elements content. In the case of radionuclides, the natural occurring contamination (38%) was primary source followed by dumped material (32%) and bird colonies (30%). The radiological risk from radionuclides was relatively high, yet still under permissible levels. For potentially toxic elements, Fe was predominant non-carcinogenic pollutant and Ni emerged as major carcinogenic contaminant. Keeping in view the high content of some elements, future studies are required to keep the human and ecological risk low, and to establish scientific grounds for the contribution of settled bird species. The findings of the study advance the present knowledge about the contamination of the study area and lays the path for further effort.}, } @article {pmid39222062, year = {2024}, author = {Acheampong, DA and Jenjaroenpun, P and Wongsurawat, T and Kurilung, A and Pomyen, Y and Kandel, S and Kunadirek, P and Chuaypen, N and Kusonmano, K and Nookaew, I}, title = {CAIM: coverage-based analysis for identification of microbiome.}, journal = {Briefings in bioinformatics}, volume = {25}, number = {5}, pages = {}, pmid = {39222062}, issn = {1477-4054}, support = {P20 GM125503/GM/NIGMS NIH HHS/United States ; R01 CA143130/CA/NCI NIH HHS/United States ; P20GM125503//National Institute of General Medical Sciences of the National Institutes of Health/ ; R01CA143130/NH/NIH HHS/United States ; }, mesh = {Humans ; *Microbiota/genetics ; *Metagenomics/methods ; Computational Biology/methods ; Metagenome ; High-Throughput Nucleotide Sequencing/methods ; Software ; Algorithms ; Sequence Analysis, DNA/methods ; }, abstract = {Accurate taxonomic profiling of microbial taxa in a metagenomic sample is vital to gain insights into microbial ecology. Recent advancements in sequencing technologies have contributed tremendously toward understanding these microbes at species resolution through a whole shotgun metagenomic approach. In this study, we developed a new bioinformatics tool, coverage-based analysis for identification of microbiome (CAIM), for accurate taxonomic classification and quantification within both long- and short-read metagenomic samples using an alignment-based method. CAIM depends on two different containment techniques to identify species in metagenomic samples using their genome coverage information to filter out false positives rather than the traditional approach of relative abundance. In addition, we propose a nucleotide-count-based abundance estimation, which yield lesser root mean square error than the traditional read-count approach. We evaluated the performance of CAIM on 28 metagenomic mock communities and 2 synthetic datasets by comparing it with other top-performing tools. CAIM maintained a consistently good performance across datasets in identifying microbial taxa and in estimating relative abundances than other tools. CAIM was then applied to a real dataset sequenced on both Nanopore (with and without amplification) and Illumina sequencing platforms and found high similarity of taxonomic profiles between the sequencing platforms. Lastly, CAIM was applied to fecal shotgun metagenomic datasets of 232 colorectal cancer patients and 229 controls obtained from 4 different countries and 44 primary liver cancer patients and 76 controls. The predictive performance of models using the genome-coverage cutoff was better than those using the relative-abundance cutoffs in discriminating colorectal cancer and primary liver cancer patients from healthy controls with a highly confident species markers.}, } @article {pmid39222055, year = {2024}, author = {Xu, C and Wang, JC and Sun, L and Zhuang, LH and Guo, ZJ and Ding, QS and Ma, DN and Song, LY and Li, J and Tang, HC and Zhu, XY and Zheng, HL}, title = {Genome-Wide Identification of Pentatricopeptide Repeat (PPR) Gene Family and Multi-Omics Analysis Provide New Insights Into the Albinism Mechanism of Kandelia obovata Propagule Leaves.}, journal = {Plant, cell & environment}, volume = {47}, number = {12}, pages = {5498-5510}, doi = {10.1111/pce.15132}, pmid = {39222055}, issn = {1365-3040}, support = {//This study was supported by the Natural Science Foundation of China (NSFC) (32171740, 31870581) and the National Key Research and Development Program of China (2017YFC0506102)./ ; }, mesh = {*Plant Leaves/genetics/metabolism ; *Genome-Wide Association Study ; *Plant Proteins/genetics/metabolism ; Multigene Family ; RNA Editing/genetics ; Rhizophoraceae/genetics/physiology ; Phylogeny ; Gene Expression Regulation, Plant ; Gene Expression Profiling ; Genes, Plant ; Genome, Plant ; Multiomics ; }, abstract = {Pentatricopeptide repeat (PPR) gene family constitutes one of the largest gene families in plants, which mainly participate in RNA editing and RNA splicing of organellar RNAs, thereby affecting the organellar development. Recently, some evidence elucidated the important roles of PPR proteins in the albino process of plant leaves. However, the functions of PPR genes in the woody mangrove species have not been investigated. In this study, using a typical true mangrove Kandelia obovata, we systematically identified 298 PPR genes and characterized their general features and physicochemical properties, including evolutionary relationships, the subcellular localization, PPR motif type, the number of introns and PPR motifs, and isoelectric point, and so forth. Furthermore, we combined genome-wide association studies (GWAS) and transcriptome analysis to identify the genetic architecture and potential PPR genes associated with propagule leaves colour variations of K. obovata. As a result, we prioritized 16 PPR genes related to the albino phenotype using different strategies, including differentially expressed genes analysis and genetic diversity analysis. Further analysis discovered two genes of interest, namely Maker00002998 (PLS-type) and Maker00003187 (P-type), which were differentially expressed genes and causal genes detected by GWAS analysis. Moreover, we successfully predicted downstream target chloroplast genes (rps14, rpoC1 and rpoC2) bound by Maker00002998 PPR proteins. The experimental verification of RNA editing sites of rps14, rpoC1, and rpoC2 in our previous study and the verification of interaction between Maker00002998 and rps14 transcript using in vitro RNA pull-down assays revealed that Maker00002998 PPR protein might be involved in the post-transcriptional process of chloroplast genes. Our result provides new insights into the roles of PPR genes in the albinism mechanism of K. obovata propagule leaves.}, } @article {pmid39221663, year = {2024}, author = {Crawford, AD and Slavin, R and Tabar, M and Radhakrishnan, K and Wang, M and Estrada, A and McGrath, JM}, title = {Methodological approaches in developing and implementing digital health interventions amongst underserved women.}, journal = {Public health nursing (Boston, Mass.)}, volume = {41}, number = {6}, pages = {1612-1621}, doi = {10.1111/phn.13410}, pmid = {39221663}, issn = {1525-1446}, mesh = {Humans ; Female ; *Telemedicine ; Texas ; Vulnerable Populations ; Women's Health ; Medically Underserved Area ; Artificial Intelligence ; Adult ; Mobile Applications ; Digital Health ; }, abstract = {BACKGROUND: Minority populations are utilizing mobile health applications more frequently to access health information. One group that may benefit from using mHealth technology is underserved women, specifically those on community supervision.

OBJECTIVE: Discuss methodological approaches for navigating digital health strategies to address underserved women's health disparities.

Using an intersectional lens, we identified strategies for conducting research using digital health technology and artificial intelligence amongst the underserved, particularly those with community supervision.

We explore (1) methodological approaches that combine traditional research methods with precision medicine, digital phenotyping, and ecological momentary assessment; (2) implications for artificial intelligence; and (3) ethical considerations with data collection, storage, and engagement.

DISCUSSION: Researchers must address gendered differences related to health, social, and economic disparities concurrently with an unwavering focus on the protection of human subjects when addressing the unique needs of underserved women while utilizing digital health methodologies.

PUBLIC CONTRIBUTION: Women on community supervision in South Central Texas helped inform the design of JUN, the mHealth app we reported in the case exemplar. JUN is named after the Junonia shell, a native shell to South Texas, which means strength, power, and self-sufficiency, like the participants in our preliminary studies.}, } @article {pmid39221442, year = {2024}, author = {Morales, HE and Norris, K and Henshaw, S and Tatayah, V and Ruhomaun, K and van Oosterhout, C and Groombridge, JJ and Gilbert, MTP and , and , and , and , }, title = {The genome sequence of the Mauritius kestrel, Falco punctatus (Temminck, 1821).}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {312}, pmid = {39221442}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual male Falco punctatus (the Mauritius kestrel; Chordata; Aves; Falconiformes; Falconidae). The genome sequence is 1,279.3 megabases in span. Most of the assembly is scaffolded into 23 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 17.34 kilobases in length.}, } @article {pmid39219129, year = {2024}, author = {Xie, Z and Hu, D and Jiang, F and Fu, X and Li, R and Zheng, D and Zhao, L and Xu, J and Yuan, X and Bao, Y and Zhou, H and Wang, B and Wang, Q}, title = {Assessment of urban flood resilience based on the socio-ecological composite index model: a case study in Wuhua District, Kunming City, China.}, journal = {Water science and technology : a journal of the International Association on Water Pollution Research}, volume = {89}, number = {2}, pages = {252-270}, doi = {10.2166/wst.2023.413}, pmid = {39219129}, issn = {0273-1223}, mesh = {China ; *Floods ; *Cities ; Models, Theoretical ; Geographic Information Systems ; Socioeconomic Factors ; }, abstract = {Global climate change and rapid urbanization have increased the frequency of flooding, making urban flood resilience a critical objective. This article introduces a methodology for assessing urban flood resilience, utilizing a social-ecological synthesis index that integrates geographical and temporal data with Geographic Information System (GIS). The study focuses on ten administrative subdistricts in Wuhua District, Kunming City, China, and selects 18 social-ecological indicators. These indicators, chosen from social and ecological perspectives, are weighted using the entropy weight method to determine their significance in the assessment system. By combining scores for each subdistrict, the study quantifies flood resilience and creates a spatial distribution map using ArcGIS. Key findings reveal that out of the ten administrative subdistricts, five in Wuhua District, particularly in the core urban area of Kunming, demonstrate strong overall flood resilience. Influenced by social-ecological indicators, there is significant spatial differentiation in flood resilience within Wuhua District, with a decreasing trend radiating from the city center to areas farther from the urban core. The research indicates that regions with well-established transportation infrastructure, a wide distribution of government institutions, improved water management facilities, and a substantial population with higher education levels contribute significantly to enhancing urban flood resilience.}, } @article {pmid39209912, year = {2024}, author = {Yuan, R and Qu, Q and Lu, Z and Geng, X and Tian, S and Jin, Y and Gong, J and Ye, X and Tang, P and Chen, X}, title = {A chromosome-level genome assembly of the gall maker pest inquiline, Diomorus aiolomorphi Kamijo (Hymenoptera: Torymidae).}, journal = {Scientific data}, volume = {11}, number = {1}, pages = {944}, pmid = {39209912}, issn = {2052-4463}, support = {32070467//National Natural Science Foundation of China (National Science Foundation of China)/ ; 31920103005//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {Animals ; Chromosomes, Insect ; Genome Size ; *Genome, Insect ; *Hymenoptera/genetics ; Wasps/parasitology ; Datasets as Topic ; }, abstract = {Diomorus aiolomorphi Kamijo (Hymenoptera: Torymidae) is an inquiline of gall maker Aiolomorphus rhopaloides Walker (Hymenoptera: Eurytomidae). They are of significant economic significance and predominantly inhabit bamboo forest. So far, only four scaffold-level genomes have been published for the family Torymidae. In this study, we present a high-quality genome assembly of D. aiolomorphi at the chromosome level, achieved through the integration of Nanopore (ONT) long-read, Illumina pair-end DNA short-read, and High-through Chromosome Conformation Capture (Hi-C) sequencing methods. The final assembly was 1,084.56 Mb in genome size, with 1,083.41 Mb (99.89%) assigned to five pseudochromosomes. The scaffold N50 length reached 224.87 Mb, and the complete Benchmarking Universal Single-Copy Orthologs (BUSCO) score was 97.3%. The genome contained 762.12 Mb of repetitive elements, accounting for 70.27% of the total genome size. A total of 18,011 protein-coding genes were predicted, with 17,829 genes being functionally annotated. The high-quality genome assembly of D. aiolomorphi presented in this study will serve as a valuable genomic resource for future research on parasitoid wasps. The results of this study may also contribute to the development of biological control strategies for pest management in bamboo forests, enhancing ecological balance and economic sustainability.}, } @article {pmid39209853, year = {2024}, author = {Mi, J and Jing, X and Ma, C and Yang, Y and Li, Y and Zhang, Y and Long, R and Zheng, H}, title = {Massive expansion of the pig gut virome based on global metagenomic mining.}, journal = {NPJ biofilms and microbiomes}, volume = {10}, number = {1}, pages = {76}, pmid = {39209853}, issn = {2055-5008}, mesh = {Animals ; Swine ; *Virome/genetics ; *Metagenomics/methods ; *Gastrointestinal Microbiome ; *Viruses/genetics/classification/isolation & purification ; *Genome, Viral ; Data Mining ; Metagenome ; Phylogeny ; }, abstract = {The pig gut virome plays a vital role in the gut microbial ecosystem of pigs. However, a comprehensive understanding of their diversity and a reference database for the virome are currently lacking. To address this gap, we established a Pig Virome Database (PVD) that comprised of 5,566,804 viral contig sequences from 4650 publicly available gut metagenomic samples using a pipeline designated "metav". By clustering sequences, we identified 48,299 viral operational taxonomic units (vOTUs) genomes of at least medium quality, of which 92.83% of which were not found in existing major databases. The majority of vOTUs were identified as Caudoviricetes (72.21%). The PVD database contained a total of 2,362,631 protein-coding genes across the above medium-quality vOTUs genomes that can be used to explore the functional potential of the pig gut virome. These findings highlight the extensive diversity of viruses in the pig gut and provide a pivotal reference dataset for forthcoming research concerning the pig gut virome.}, } @article {pmid39213392, year = {2024}, author = {Du, Q and Zhang, Z and Yang, W and Zhou, X and Zhou, N and Wu, C and Bao, J}, title = {CBGDA: a manually curated resource for gene-disease associations based on genome-wide CRISPR.}, journal = {Database : the journal of biological databases and curation}, volume = {2024}, number = {}, pages = {}, pmid = {39213392}, issn = {1758-0463}, support = {31971162 32071275 U20A20410//National Nature Science Foundation of China/ ; 31971162 32071275 U20A20410//National Nature Science Foundation of China/ ; }, mesh = {Humans ; *Databases, Genetic ; *Data Curation/methods ; Genome-Wide Association Study/methods ; Genetic Predisposition to Disease ; Clustered Regularly Interspaced Short Palindromic Repeats/genetics ; CRISPR-Cas Systems ; Disease/genetics ; }, abstract = {The field of understanding the association between genes and diseases is rapidly expanding, making it challenging for researchers to keep up with the influx of new publications and genetic datasets. Fortunately, there are now several regularly updated databases available that focus on cataloging gene-disease relationships. The development of the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-Cas9 system has revolutionized the field of gene editing, providing a highly efficient, accurate, and reliable method for exploring gene-disease associations. However, currently, there is no resource specifically dedicated to collecting and integrating the latest experimentally supported gene-disease association data derived from genome-wide CRISPR screening. To address this gap, we have developed the CRISPR-Based Gene-Disease Associations (CBGDA) database, which includes over 200 manually curated gene-disease association data derived from genome-wide CRISPR screening studies. Through CBGDA, users can explore gene-disease association data derived from genome-wide CRISPR screening, gaining insights into the expression patterns of genes in different diseases, associated chemical data, and variant information. This provides a novel perspective on understanding the associations between genes and diseases. What is more, CBGDA integrates data from several other databases and resources, enhancing its comprehensiveness and utility. In summary, CBGDA offers a fresh perspective and comprehensive insights into the research on gene-disease associations. It fills the gap by providing a dedicated resource for accessing up-to-date, experimentally supported gene-disease association data derived from genome-wide CRISPR screening. Database URL: http://cbgda.zhounan.org/main.}, } @article {pmid39213378, year = {2024}, author = {Wang, M and Li, Z and Wang, H and Zhao, J and Zhang, Y and Lin, K and Zheng, S and Feng, Y and Zhang, Y and Teng, W and Tong, Y and Zhang, W and Xue, Y and Mao, H and Li, H and Zhang, B and Rasheed, A and Bhavani, S and Liu, C and Ling, HQ and Hu, YQ and Zhang, Y}, title = {A Quantitative Computational Framework for Allopolyploid Single-Cell Data Integration and Core Gene Ranking in Development.}, journal = {Molecular biology and evolution}, volume = {41}, number = {9}, pages = {}, pmid = {39213378}, issn = {1537-1719}, support = {//National Natural Science Foundation of China/ ; //National Key R&D Program of China/ ; //Yangfan Project of Shanghai Science and Technology Commission/ ; //State Key Laboratory of Genetic Engineering/ ; //State Key Laboratory of Crop Gene Exploration and Utilization in Southwest/ ; //State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology/ ; //Shanghai Key Laboratory of Agricultural Genetics and Breeding/ ; }, mesh = {*Single-Cell Analysis/methods ; *Polyploidy ; Animals ; Computational Biology/methods ; }, abstract = {Polyploidization drives regulatory and phenotypic innovation. How the merger of different genomes contributes to polyploid development is a fundamental issue in evolutionary developmental biology and breeding research. Clarifying this issue is challenging because of genome complexity and the difficulty in tracking stochastic subgenome divergence during development. Recent single-cell sequencing techniques enabled probing subgenome-divergent regulation in the context of cellular differentiation. However, analyzing single-cell data suffers from high error rates due to high dimensionality, noise, and sparsity, and the errors stack up in polyploid analysis due to the increased dimensionality of comparisons between subgenomes of each cell, hindering deeper mechanistic understandings. In this study, we develop a quantitative computational framework, called "pseudo-genome divergence quantification" (pgDQ), for quantifying and tracking subgenome divergence directly at the cellular level. Further comparing with cellular differentiation trajectories derived from single-cell RNA sequencing data allows for an examination of the relationship between subgenome divergence and the progression of development. pgDQ produces robust results and is insensitive to data dropout and noise, avoiding high error rates due to multiple comparisons of genes, cells, and subgenomes. A statistical diagnostic approach is proposed to identify genes that are central to subgenome divergence during development, which facilitates the integration of different data modalities, enabling the identification of factors and pathways that mediate subgenome-divergent activity during development. Case studies have demonstrated that applying pgDQ to single-cell and bulk tissue transcriptomic data promotes a systematic and deeper understanding of how dynamic subgenome divergence contributes to developmental trajectories in polyploid evolution.}, } @article {pmid39209112, year = {2024}, author = {Ji, N and Kumar, A and Joe, W and Kuriyan, R and Sethi, V and Finkelstein, JL and Mehta, S}, title = {Prevalence and Correlates of Double and Triple Burden of Malnutrition Among Children and Adolescents in India: The Comprehensive National Nutrition Survey.}, journal = {The Journal of nutrition}, volume = {154}, number = {10}, pages = {2932-2947}, doi = {10.1016/j.tjnut.2024.08.021}, pmid = {39209112}, issn = {1541-6100}, mesh = {Humans ; India/epidemiology ; Adolescent ; Child ; Female ; Male ; Prevalence ; *Nutrition Surveys ; Child, Preschool ; *Malnutrition/epidemiology ; Nutritional Status ; Young Adult ; Overnutrition/epidemiology ; Socioeconomic Factors ; Child Nutrition Disorders/epidemiology ; }, abstract = {BACKGROUND: Limited information on the co-prevalence of undernutrition, micronutrient deficiencies, overnutrition, and abnormal levels of noncommunicable disease biomarkers at the same time in children and adolescents in India hinders efforts to comprehensively address their health.

OBJECTIVES: This study aimed to examine the prevalence and correlates of double burden of malnutrition (DBM) and triple burden of malnutrition (TBM) among children and adolescents (5-19 y) to inform policies and programs.

METHODS: A total of 17,599 children (5-9 y) and 16,184 adolescents (10-19 y) with available biomarker data from the Comprehensive National Nutrition Survey were included. Malnutrition was defined based on either undernutrition based on anthropometry, overnutrition/abnormal metabolic markers, and anemia/micronutrient deficiency. DBM was defined as the coexistence of any 2 forms of malnutrition. DBM+ was defined as the coexistence of undernutrition and/or micronutrient deficiency along with overnutrition. TBM was defined as having the coexistence of all 3 forms of malnutrition. The prevalence of DBM, DBM+, and TBM was estimated accounting for probabilistic selection. We used mixed-effect binomial regression to determine correlates of DBM/TBM in children and adolescents separately.

RESULTS: The prevalence of DBM, DBM+, and TBM was 50.8%, 37.2%, and 14.4%, respectively, in children and 53.4%, 36.1%, and 12.7%, respectively, in adolescents. The prevalence of DBM+ was significantly higher in girls compared to in boys in the 5-9 y age group. In children, being in a disadvantaged caste group, having a lower wealth index, having inadequate diet diversity, having no maternal schooling, and having a recent history of acute illness were associated with DBM. In adolescents, being in a disadvantaged caste group, maternal occupation, and lower paternal age were correlated with DBM. A similar set of variables was associated with TBM in both age groups.

CONCLUSIONS: The prevalence of DBM and TBM is substantial in children and adolescents in India and varies across states. Socioeconomic factors and acute illness were the main correlates for DBM and TBM.}, } @article {pmid39208288, year = {2024}, author = {Ishigohoka, J and Bascón-Cardozo, K and Bours, A and Fuß, J and Rhie, A and Mountcastle, J and Haase, B and Chow, W and Collins, J and Howe, K and Uliano-Silva, M and Fedrigo, O and Jarvis, ED and Pérez-Tris, J and Illera, JC and Liedvogel, M}, title = {Distinct patterns of genetic variation at low-recombining genomic regions represent haplotype structure.}, journal = {Evolution; international journal of organic evolution}, volume = {78}, number = {12}, pages = {1916-1935}, doi = {10.1093/evolut/qpae117}, pmid = {39208288}, issn = {1558-5646}, support = {MFFALIMN0001//The Max Planck Society/ ; 395940726//Magnetoreception and Navigation in Vertebrates/ ; 407495230//DFG Research Infrastructure/ ; 423957469//Next Generation Sequencing Competence Network/ ; 1ZIAHG200398//Intramural Research Program of the NHGRI/ ; //Spanish Ministry of Science/ ; //Innovation and Universities/ ; PGC2018-097575-B-I00//The European Regional Development Fund/ ; }, mesh = {Animals ; *Haplotypes ; *Recombination, Genetic ; *Genetic Variation ; *Songbirds/genetics ; Selection, Genetic ; Genome ; }, abstract = {Genomic regions sometimes show patterns of genetic variation distinct from the genome-wide population structure. Such deviations have often been interpreted to represent effects of selection. However, systematic investigation of whether and how non-selective factors, such as recombination rates, can affect distinct patterns has been limited. Here, we associate distinct patterns of genetic variation with reduced recombination rates in a songbird, the Eurasian blackcap (Sylvia atricapilla), using a new reference genome assembly, whole-genome resequencing data and recombination maps. We find that distinct patterns of genetic variation reflect haplotype structure at genomic regions with different prevalence of reduced recombination rate across populations. At low-recombining regions shared in most populations, distinct patterns reflect conspicuous haplotypes segregating in multiple populations. At low-recombining regions found only in a few populations, distinct patterns represent variance among cryptic haplotypes within the low-recombining populations. With simulations, we confirm that these distinct patterns evolve neutrally by reduced recombination rate, on which the effects of selection can be overlaid. Our results highlight that distinct patterns of genetic variation can emerge through evolutionary reduction of local recombination rate. The recombination landscape as an evolvable trait therefore plays an important role determining the heterogeneous distribution of genetic variation along the genome.}, } @article {pmid39208193, year = {2024}, author = {Naser, AY}, title = {Insights into hospitalization pattern for drug, medicament, and biological substance poisoning, adverse effect, and underdosing in Australia: An ecological study between 1998 and 2019.}, journal = {PloS one}, volume = {19}, number = {8}, pages = {e0309362}, pmid = {39208193}, issn = {1932-6203}, mesh = {Humans ; *Hospitalization/statistics & numerical data/trends ; Australia/epidemiology ; Female ; Male ; Adult ; Middle Aged ; Adolescent ; Aged ; Child ; Young Adult ; Poisoning/epidemiology ; Child, Preschool ; Infant ; Drug-Related Side Effects and Adverse Reactions/epidemiology ; Aged, 80 and over ; Databases, Factual ; }, abstract = {BACKGROUND: Drug, medicament, and biological substance poisoning, adverse effects, and underdosing are significant public health concerns. Gaining insight into the patterns and trends in hospitalizations caused by these occurrences is essential for the development of preventative initiatives, optimization of treatment regimens, and improvement of patient safety. The aim of this study is to examine the trend of hospitalisation related to poisoning by, adverse effect of and underdosing of drugs, medicaments and biological substances in Australia between 1998 and 2019.

METHODS: This is an ecological descriptive study that examined hospitalisation related to poisoning by, adverse effect of and underdosing of drugs, medicaments and biological substances in Australia between 1998 and 2019. A nationwide hospital admissions database was used for this study.

RESULTS: Between 1998 and 2019, a total of 683,869 hospital admission episodes were recorded in Australia. The overall annual number of hospital admissions for various reasons increased by 20.5% from 29,854 in 1998 to 35,960 in 2019, representing a decrease in hospital admission rate of 10.6% [from 158.69 (95% CI 156.90-160.49) in 1998 to 141.91 (95% CI 140.44-143.37) in 2019 per 100,000 persons, trend test, p<0.05]. Overnight-stay admissions accounted for 69.2% of the total number of hospital admissions, and 30.8% were same-day admissions. Rates of same-day hospital admission decreased by 13.3% [from 50.55 (95%CI 49.54-51.57) in 1998 to 43.81 (95%CI 43.00-44.63) in 2019 per 100,000 persons]. Rates of overnight-stay hospital admission decreased by 11.1% [from 108.14 (95%CI 106.66-109.63) in 1998 to 96.17 (95%CI 94.96-97.38) in 2019 per 100,000 persons]. Admissions related to antiepileptic, sedative-hypnotic and antiparkinsonism drugs was the most prevalent hospital admissions type accounting for 26.8%. Females were responsible for 418,751 hospital admission episodes, representing 61.5% of the total number of hospital admission.

CONCLUSION: This study found that while the overall annual number of admissions increased, the rate of admission decreased over the same period. The most common reasons for admissions were antiepileptic, sedative-hypnotic, and anti-parkinsonism drugs. The study also noted increases in admissions related to anaesthetics, therapeutic gases, hormones, and their synthetic substitutes. These findings suggest a concerning rise in the suboptimal use of these medications. In order to combat the increasing incidence of this type of admissions, it is imperative to strengthen public awareness initiatives on medicine safety and abuse.}, } @article {pmid39205176, year = {2024}, author = {Vanslembrouck, A and Jansen, S and De Witte, J and Janssens, C and Vereecken, S and Helms, M and Lange, U and Lühken, R and Schmidt-Chanasit, J and Heitmann, A and Müller, R}, title = {Larval Competition between Aedes and Culex Mosquitoes Carries over to Higher Arboviral Infection during Their Adult Stage.}, journal = {Viruses}, volume = {16}, number = {8}, pages = {}, pmid = {39205176}, issn = {1999-4915}, support = {G0G2319N//BiodivERsA/ ; CA17108//European Cooperation in Science and Technology/ ; 653316//European Union's Horizon 2020 research and innovation program/ ; Dubois-Brigué scholarship//Doctor Albert Dubois Foundation for tropical pathology/ ; }, mesh = {Animals ; *Culex/virology/growth & development ; *Aedes/virology/growth & development/physiology ; *Larva/virology ; *Mosquito Vectors/virology/growth & development ; Arbovirus Infections/transmission/virology ; Arboviruses/physiology ; West Nile virus/physiology ; Female ; Chikungunya virus/physiology ; Encephalitis Virus, Japanese/physiology ; }, abstract = {The common house mosquito (Culex pipiens) is a native vector for West Nile virus (WNV). Invasive species like the tiger mosquito (Aedes albopictus) and Asian bush mosquito (Aedes japonicus) are rapidly spreading through Europe, posing a major threat as vectors for dengue, chikungunya (CHIKV), and Japanese encephalitis virus (JEV). These mosquitoes share a similar ecological niche as larvae, but the carry-over effects of aquatic larval interactions to the terrestrial adult stage remain largely unknown and their medical relevance requires further investigation. This study examines the context dependency of larval interactions among Aedes albopictus, Aedes japonicus, and Culex pipiens. The survival, development time, growth, and energetic storage were measured in different European populations within density-response (intraspecific) experiments and replacement (interspecific) experiments at 20 °C and 26 °C. Overall, Ae. japonicus was the weakest competitor, while competition between Ae. albopictus and Cx. pipiens varied with temperature. Adults emerging from this larval competition were infected as follows: Culex pipiens with WNV, Ae. albopictus with CHIKV, and Ae. japonicus with JEV. While no JEV infection was observed, mosquitoes experiencing interspecific interactions during their larval stages exhibited higher infection rates and viral RNA titers for CHIKV and WNV. This increased susceptibility to viral infection after larval competition suggests a higher risk of arbovirus transmission in co-occurring populations.}, } @article {pmid39202353, year = {2024}, author = {Maltseva, PY and Plotnitskaya, NA and Krivoruchko, AV and Beletskiy, AV and Rakitin, AL and Mardanov, AV and Ivshina, IB}, title = {Bioinformatics Analysis of the Genome of Rhodococcus rhodochrous IEGM 1362, an (-)-Isopulegol Biotransformer.}, journal = {Genes}, volume = {15}, number = {8}, pages = {}, pmid = {39202353}, issn = {2073-4425}, support = {24-14-20015//the Russian Science Foundation/ ; }, mesh = {*Rhodococcus/genetics/metabolism ; *Genome, Bacterial ; *Computational Biology/methods ; *Biotransformation/genetics ; Cytochrome P-450 Enzyme System/genetics/metabolism ; Monoterpenes/metabolism ; }, abstract = {A genome of Rhodococcus rhodochrous IEGM 1362 was sequenced and annotated. This strain can transform monoterpene alcohol (-)-isopulegol with the formation of two novel pharmacologically promising metabolites. Nine genes encoding cytochrome P450, presumably involved in (-)-isopulegol transformation, were found in the genome of R. rhodochrous IEGM 1362. Primers and PCR conditions for their detection were selected. The obtained data can be used for the further investigation of genes encoding enzymes involved in monoterpene biotransformation.}, } @article {pmid39202178, year = {2024}, author = {de Llanza Varona, M and Martínez, M}, title = {Synergy Makes Direct Perception Inefficient.}, journal = {Entropy (Basel, Switzerland)}, volume = {26}, number = {8}, pages = {}, pmid = {39202178}, issn = {1099-4300}, support = {PID2021-127046NA-I00//Ministerio de Ciencia, Innovación y Universidades/ ; CEX2021-001169-M MCIN/AEI/10.13039/501100011033)//Ministerio de Ciencia, Innovación y Universidades/ ; 2021-SGR-00276//Government of Catalonia/ ; }, abstract = {A typical claim in anti-representationalist approaches to cognition such as ecological psychology or radical embodied cognitive science is that ecological information is sufficient for guiding behavior. According to this view, affordances are immediately perceptually available to the agent (in the so-called "ambient energy array"), so sensory data does not require much further inner processing. As a consequence, mental representations are explanatorily idle: perception is immediate and direct. Here we offer one way to formalize this direct-perception claim and identify some important limits to it. We argue that the claim should be read as saying that successful behavior just implies picking out affordance-related information from the ambient energy array. By relying on the Partial Information Decomposition framework, and more concretely on its development of the notion of synergy, we show that in multimodal perception, where various energy arrays carry affordance-related information, the "just pick out affordance-related information" approach is very inefficient, as it is bound to miss all synergistic components. Efficient multimodal information combination requires transmitting sensory-specific (and not affordance-specific) information to wherever it is that the various information streams are combined. The upshot is that some amount of computation is necessary for efficient affordance reconstruction.}, } @article {pmid39198944, year = {2024}, author = {Wang, HT and Li, HY and Lu, QW and He, SL}, title = {[Determination of eight neonicotinoid pesticides in wastewater by solid phase extraction combined with liquid chromatography-tandem mass spectrometry].}, journal = {Se pu = Chinese journal of chromatography}, volume = {42}, number = {9}, pages = {856-865}, pmid = {39198944}, issn = {1872-2059}, mesh = {*Tandem Mass Spectrometry/methods ; *Solid Phase Extraction/methods ; *Wastewater/chemistry/analysis ; *Neonicotinoids/analysis ; *Water Pollutants, Chemical/analysis ; Chromatography, Liquid/methods ; *Nitro Compounds/analysis ; Thiamethoxam/analysis ; Guanidines/analysis ; Thiazoles/analysis ; Pesticides/analysis ; Thiazines/analysis ; Oxazines/analysis ; }, abstract = {Neonicotinoid pesticides are a relatively new class of pesticides that have garnered significant attention owing to their potential ecological risks to nontarget organisms. A method combining solid phase extraction with liquid chromatography-tandem mass spectrometry (SPE-LC-MS/MS) was developed for the rapid and accurate detection of eight neonicotinoid pesticides (dinotefuran, E-nitenpyram, thiamethoxam, clothianidin, imidacloprid, imidaclothiz, acetamiprid, and thiacloprid) in wastewater. The chromatographic mobile phase and MS parameters were selected, and a single-factor method was used to determine the optimal column type, extraction volume, sample loading speed, and pH for SPE. The optimal parameters were as follows: column type, HLB column (500 mg/6 mL); sample extraction volume, 500 mL; sample loading speed, 10 mL/min; and sample pH, 6-8. The matrix effects of the wastewater samples were reduced by optimizing the chromatographic gradient-elution program, examining the dilution factor of the samples, and using the isotope internal standard calibration method. Prior to analysis, the wastewater samples were diluted 5-fold with ultrapure water for pretreatment. Subsequently, 2 mmol/L ammonium acetate aqueous solution containing 0.1% (v/v) formic acid and methanol was used as mobile phases for gradient elution on a ZORBAX Eclipse Plus C18 column (100 mm×2.1 mm, 1.8 μm). The samples were quantified using positive-ion multiple reaction monitoring (MRM) mode for 10 min. Imidacloprid-d4 was used as the isotope internal standard. The SPE process was further optimized by applying response surface methodology to select the type and mass of rinsing and elution solvents. The optimal pretreatment of the SPE column included rinsing with 10% methanol aqueous solution and elution with methanol-acetonitrile (1∶1, v/v) mixture (7 mL). The eight neonicotinoid pesticides showed satisfactory linearity within the relevant range, with linear correlation coefficients (r) all greater than 0.9990. The method detection limits (MDLs) ranged from 0.2 to 1.2 ng/L, and the method quantification limits (MQLs) ranged from 0.8 to 4.8 ng/L. The average recoveries of the eight neonicotinoid pesticides were in the range of 82.6%-94.2% at three spiked levels, with relative standard deviations (RSDs) ranging from 3.9% to 9.4%. Finally, the optimized method was successfully applied to analyze wastewater samples collected from four sewage treatment plants. The results indicated that the eight neonicotinoid pesticides could be generally detected at concentrations ranging from not detected (ND) to 256 ng/L. The developed method has a low MDL and high accuracy, rendering it a suitable choice for the trace detection of the eight neonicotinoid pesticides in wastewater when compared with other similar methods. The proposed method can be utilized to monitor the environmental impact and assess the potential risks of neonicotinoid pesticides in wastewater, thus promoting the protection of nontarget organisms and the sustainable use of these pesticides in agriculture.}, } @article {pmid39198489, year = {2024}, author = {Chanda, MM and Campbell, L and Walke, H and Salzer, JS and Hemadri, D and Patil, SS and Purse, BV and Shivachandra, SB}, title = {A thirty-year time series analyses identifies coherence between oscillations in Anthrax outbreaks and El Niño in Karnataka, India.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {19928}, pmid = {39198489}, issn = {2045-2322}, mesh = {*Anthrax/epidemiology ; India/epidemiology ; *Disease Outbreaks ; Animals ; *El Nino-Southern Oscillation ; Bayes Theorem ; Bacillus anthracis/isolation & purification/pathogenicity ; Humans ; Livestock/microbiology ; }, abstract = {Anthrax is an economically important zoonotic disease affecting both livestock and humans. The disease is caused by a spore forming bacterium, Bacillus anthracis, and is considered endemic to the state of Karnataka, India. It is critical to quantify the role of climatic factors in determining the temporal pattern of anthrax outbreaks, so that reliable forecasting models can be developed. These models will aid in establishing public health surveillance and guide strategic vaccination programs, which will reduce the economic loss to farmers, and prevent the spill-over of anthrax from livestock to humans. In this study, correlation and coherence between time series of anthrax outbreaks in livestock (1987-2016) and meteorological variables and Sea Surface Temperature anomalies (SST) were identified using a combination of cross-correlation analyses, spectral analyses (wavelets and empirical mode decomposition) and further quantified using a Bayesian time series regression model accounting for temporal autocorrelation. Monthly numbers of anthrax outbreaks were positively associated with a lagged effect of rainfall and wet day frequency. Long-term periodicity in anthrax outbreaks (approximately 6-8 years) was coherent with the periodicity in SST anomalies and outbreak numbers increased with decrease in SST anomalies. These findings will be useful in planning long-term anthrax prevention and control strategies in Karnataka state of India.}, } @article {pmid39198479, year = {2024}, author = {Zhu, J and Li, Z and Yang, J and Yu, K and Zhang, D and Zhong, J}, title = {Ecological space management and control zoning of Giant Panda National Park from the perspective of ecosystem services and land use.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {19951}, pmid = {39198479}, issn = {2045-2322}, support = {GJGY2020-ZD002//Key Project of National Park Research Center, Key Social Science Research Base of Sichuan Province, "National Park Natural Ecosystem Service Function Importance Evaluation and Protection Policy Research"/ ; ZDJS202303//Chengdu University of Technology "Double First-Class" initiative Construction Philosophy and Social Sciences Key Construction Project/ ; }, mesh = {Animals ; Bayes Theorem ; Carbon Sequestration ; China ; Computer Simulation ; *Conservation of Natural Resources/legislation & jurisprudence/methods ; Conservation of Water Resources ; Datasets as Topic ; *Ecosystem ; *Parks, Recreational/legislation & jurisprudence/organization & administration/standards ; Probability ; Soil ; *Ursidae ; Ecology/legislation & jurisprudence/methods/organization & administration ; }, abstract = {Since China proposed building a national park system in 2017, the establishment of a planning system for nature reserves, with national parks as the main body, is being actively promoted around the country. Among them, scientific ecological space management and control zoning (ESMCZ) is an important link in maintaining the ecological stability of national parks. How to zone national parks and how to improve the precision of zoning has become a new task for national parks. Therefore, this study takes the Giant Panda National Park as the study area, takes ecosystem services and land use/cover change as the research perspective, integrates the InVEST model, PLUS model and bayes belief network (BBN) model, and builds a set of ecological space management and control zoning (ESMCZ) spatial zoning framework based on raster scale, dividing the study area into strictly protected zone, ecological buffer zone, ecological control zone and controlled development zone. The results showed that: (1) The study area showed an increasing trend in water conservation, soil conservation and carbon storage from 2005 to 2020, and the habitat quality index was generally high. The spatial heterogeneity of ecosystem services in the study area was significant, and the effect of a single factor on ecosystem services was most pronounced. (2) Large variation in area for different land uses under natural development scenarios and ecological protection scenarios. In both scenarios, the area of cultivated land, the area of grassland and the area of unused land decrease relative to 2020, and the area of forested land, the area of water and the area of constructed land increase relative to 2020. (3) The Giant Panda National Park is divided into strictly protected zone, ecological buffer zone, ecological control zone and control development zone, of which the strictly protected zone have the largest area and the best ecosystem background condition, and the control development zone have the smallest area and the worst ecosystem background condition. (4) The ecological space management and control zoning (ESMCZ) framework provides a more refined method for the secondary zoning of nature reserves such as the Giant Panda National Park, which is valuable for the implementation of zoning and categorization management for ecological conservation in the Giant Panda National Park.}, } @article {pmid39196880, year = {2024}, author = {Tsigeman, E and Zemliak, V and Likhanov, M and Papageorgiou, KA and Kovas, Y}, title = {AI can see you: Machiavellianism and extraversion are reflected in eye-movements.}, journal = {PloS one}, volume = {19}, number = {8}, pages = {e0308631}, pmid = {39196880}, issn = {1932-6203}, mesh = {Humans ; *Eye Movements/physiology ; Male ; Female ; Adolescent ; *Extraversion, Psychological ; *Machine Learning ; *Machiavellianism ; Surveys and Questionnaires ; Algorithms ; Personality/physiology ; Eye-Tracking Technology ; }, abstract = {INTRODUCTION: Recent studies showed an association between personality traits and individual patterns of visual behaviour in laboratory and other settings. The current study extends previous research by measuring multiple personality traits in natural settings; and by comparing accuracy of prediction of multiple machine learning algorithms.

METHODS: Adolescent participants (N = 35) completed personality questionnaires (Big Five Inventory and Short Dark Triad Questionnaire) and visited an interactive museum while their eye movements were recorded with head-mounted eye tracking. To predict personality traits the eye-movement data was analysed using eight machine-learning methods: Random Forest, Adaboost, Naive Bayes, Support Vector Machine, Logistic Regression, k Nearest Neighbours, Decision Tree and a three-layer Perceptron.

RESULTS AND DISCUSSION: Extracted eye movement features introduced to machine learning algorithms predicted personality traits with above 33% chance accuracy (34%-48%). This result is comparable to previous ecologically valid studies, but lower than in laboratory-based research. Better prediction was achieved for Machiavellianism and Extraversion compared to other traits (10 and 9 predictions above the chance level by different algorithms from different parts of the recording). Conscientiousness, Narcissism and Psychopathy were not reliably predicted from eye movements. These differences in predictability across traits might be explained by differential activation of different traits in different situations, such as new vs. familiar, exciting vs. boring, and complex vs. simple settings. In turn, different machine learning approaches seem to be better at capturing specific gaze patterns (e.g. saccades), associated with specific traits evoked by the situation. Further research is needed to gain better insights into trait-situation-algorithm interactions.}, } @article {pmid39193916, year = {2024}, author = {Spöri, Y and Flot, JF}, title = {Haxe as a Swiss knife for bioinformatic applications: the SeqPHASE case story.}, journal = {Briefings in bioinformatics}, volume = {25}, number = {5}, pages = {}, pmid = {39193916}, issn = {1477-4054}, support = {T.0078.23//Fonds de la Recherche Scientifique - FNRS/ ; }, mesh = {*Computational Biology/methods ; *Programming Languages ; *Software ; }, abstract = {Haxe is a general purpose, object-oriented programming language supporting syntactic macros. The Haxe compiler is well known for its ability to translate the source code of Haxe programs into the source code of a variety of other programming languages including Java, C++, JavaScript, and Python. Although Haxe is more and more used for a variety of purposes, including games, it has not yet attracted much attention from bioinformaticians. This is surprising, as Haxe allows generating different versions of the same program (e.g. a graphical user interface version in JavaScript running in a web browser for beginners and a command-line version in C++ or Python for increased performance) while maintaining a single code, a feature that should be of interest for many bioinformatic applications. To demonstrate the usefulness of Haxe in bioinformatics, we present here the case story of the program SeqPHASE, written originally in Perl (with a CGI version running on a server) and published in 2010. As Perl+CGI is not desirable anymore for security purposes, we decided to rewrite the SeqPHASE program in Haxe and to host it at Github Pages (https://eeg-ebe.github.io/SeqPHASE), thereby alleviating the need to configure and maintain a dedicated server. Using SeqPHASE as an example, we discuss the advantages and disadvantages of Haxe's source code conversion functionality when it comes to implementing bioinformatic software.}, } @article {pmid39193399, year = {2024}, author = {Boyes, D and Crowley, LM and Hutchinson, F and Wawman, DC and , and , and , and , and , and , and , }, title = {The genome sequence of the Lesser Yellow Underwing, Noctua comes Hübner, 1813.}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {200}, pmid = {39193399}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual female Noctua comes (the Lesser Yellow Underwing; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 540.7 megabases in span. Most of the assembly is scaffolded into 32 chromosomal pseudomolecules, including the W and Z sex chromosomes. The mitochondrial genome has also been assembled and is 15.37 kilobases in length. Gene annotation of this assembly on Ensembl identified 18,001 protein coding genes.}, } @article {pmid39193313, year = {2024}, author = {Kang, B and Ma, J and Jeong, I and Yoon, S and Kim, JI and Heo, SJ and Oh, SS}, title = {Behavioral marker-based predictive modeling of functional status for older adults with subjective cognitive decline and mild cognitive impairment: Study protocol.}, journal = {Digital health}, volume = {10}, number = {}, pages = {20552076241269555}, pmid = {39193313}, issn = {2055-2076}, abstract = {OBJECTIVE: This study describes a research protocol for a behavioral marker-based predictive model that examines the functional status of older adults with subjective cognitive decline and mild cognitive impairment.

METHODS: A total of 130 older adults aged ≥65 years with subjective cognitive decline or mild cognitive impairment will be recruited from the Dementia Relief Centers or the Community Service Centers. Data on behavioral and psychosocial markers (e.g. physical activity, mobility, sleep/wake patterns, social interaction, and mild behavioral impairment) will be collected using passive wearable actigraphy, in-person questionnaires, and smartphone-based ecological momentary assessments. Two follow-up assessments will be performed at 12 and 24 months after baseline. Mixed-effect machine learning models: MErf, MEgbm, MEmod, and MEctree, and standard machine learning models without random effects [random forest, gradient boosting machine] will be employed in our analyses to predict functional status over time.

RESULTS: The results of this study will be fundamental for developing tailored digital interventions that apply deep learning techniques to behavioral data to predict, identify, and aid in the management of functional decline in older adults with subjective cognitive decline and mild cognitive impairment. These older adults are considered the optimal target population for preventive interventions and will benefit from such tailored strategies.

CONCLUSIONS: Our study will contribute to the development of self-care interventions that utilize behavioral data and machine learning techniques to provide automated analyses of the functional decline of older adults who are at risk for dementia.}, } @article {pmid39193090, year = {2023}, author = {Boyes, D and Lewis, OT and , and , and , and , and , and , }, title = {The genome sequence of the Small Angle Shades, Euplexia lucipara (Linnaeus, 1758).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {509}, pmid = {39193090}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual male Euplexia lucipara (the Small Angle Shades; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 661.8 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.37 kilobases in length. Gene annotation of this assembly on Ensembl identified 20,395 protein coding genes.}, } @article {pmid39192185, year = {2024}, author = {Donthu, R and Marcelino, JAP and Giordano, R and Tao, Y and Weber, E and Avalos, A and Band, M and Akraiko, T and Chen, SC and Reyes, MP and Hao, H and Ortiz-Alvarado, Y and Cuff, CA and Claudio, EP and Soto-Adames, F and Smith-Pardo, AH and Meikle, WG and Evans, JD and Giray, T and Abdelkader, FB and Allsopp, M and Ball, D and Morgado, SB and Barjadze, S and Correa-Benitez, A and Chakir, A and Báez, DR and Chavez, NHM and Dalmon, A and Douglas, AB and Fraccica, C and Fernández-Marín, H and Galindo-Cardona, A and Guzman-Novoa, E and Horsburgh, R and Kence, M and Kilonzo, J and Kükrer, M and Le Conte, Y and Mazzeo, G and Mota, F and Muli, E and Oskay, D and Ruiz-Martínez, JA and Oliveri, E and Pichkhaia, I and Romane, A and Sanchez, CG and Sikombwa, E and Satta, A and Scannapieco, AA and Stanford, B and Soroker, V and Velarde, RA and Vercelli, M and Huang, Z}, title = {HBeeID: a molecular tool that identifies honey bee subspecies from different geographic populations.}, journal = {BMC bioinformatics}, volume = {25}, number = {1}, pages = {278}, pmid = {39192185}, issn = {1471-2105}, support = {PRSTRT # 2020-00081//Puerto Rico Science, Technology and Research Trust, United States of America/ ; PRSTRT # 2020-00081//Puerto Rico Science, Technology and Research Trust, United States of America/ ; USDA-APHIS #AP20PPQS & T00C009//United States Dept. of Agriculture - Animal and Plant Health Inspection Service (APHIS), United States of America/ ; USDA-APHIS #AP20PPQS & T00C009//United States Dept. of Agriculture - Animal and Plant Health Inspection Service (APHIS), United States of America/ ; NSF-OISE #1545803//National Science Foundation, United States of America/ ; }, mesh = {Bees/genetics/classification ; Animals ; *Polymorphism, Single Nucleotide/genetics ; Genomics/methods ; }, abstract = {BACKGROUND: Honey bees are the principal commercial pollinators. Along with other arthropods, they are increasingly under threat from anthropogenic factors such as the incursion of invasive honey bee subspecies, pathogens and parasites. Better tools are needed to identify bee subspecies. Genomic data for economic and ecologically important organisms is increasing, but in its basic form its practical application to address ecological problems is limited.

RESULTS: We introduce HBeeID a means to identify honey bees. The tool utilizes a knowledge-based network and diagnostic SNPs identified by discriminant analysis of principle components and hierarchical agglomerative clustering. Tests of HBeeID showed that it identifies African, Americas-Africanized, Asian, and European honey bees with a high degree of certainty even when samples lack the full 272 SNPs of HBeeID. Its prediction capacity decreases with highly admixed samples.

CONCLUSION: HBeeID is a high-resolution genomic, SNP based tool, that can be used to identify honey bees and screen species that are invasive. Its flexible design allows for future improvements via sample data additions from other localities.}, } @article {pmid39188222, year = {2024}, author = {Koracevic, G and Stojanovic, M and Zdravkovic, M and Lovic, D and Simic, D and Mladenovic, K}, title = {Proposal of a Modified Classification of Hypertensive Crises: Urgency, Impending Emergency, and Emergency.}, journal = {Current vascular pharmacology}, volume = {22}, number = {3}, pages = {180-186}, pmid = {39188222}, issn = {1875-6212}, mesh = {Humans ; *Hypertension/diagnosis/physiopathology/drug therapy/classification ; *Antihypertensive Agents/therapeutic use/adverse effects ; Risk Assessment ; Risk Factors ; *Blood Pressure/drug effects ; *Emergencies ; Prognosis ; Predictive Value of Tests ; Decision Support Techniques ; Clinical Decision-Making ; Hypertensive Crisis ; }, abstract = {Systemic arterial hypertension (HTN) is the main cause of morbidity and mortality, and HTN crises contribute significantly to an unfavourable clinical course. For decades, HTN crises have been dichotomized into hypertensive emergency (HTN-E) and hypertensive urgency (HTN-U). The main difference between the two is the presence of acute hypertension-mediated organ damage (HMOD) - if HMOD is present, HTN crisis is HTN-E; if not, it is HTN-U. Patients with HTN-E are in a life-threatening situation. They are hospitalized and receive antihypertensive drugs intravenously (IV). On the other hand, patients with HTN-U are usually not hospitalized and receive their antihypertensives orally. We suggest a modification of the current risk stratification scheme for patients with HTN crises. The new category would be the intermediate risk group, more precisely the 'impending HTN-E' group, with a higher risk in comparison to HTN-U and a lower risk than HTN-E. 'Impending HMOD' means that HMOD has not occurred (yet), and the prognosis is, therefore, better than in patients with ongoing HMOD. There are three main reasons to classify patients as having impending HTN-E: excessively elevated BP, high-risk comorbidities, and ongoing bleeding/high bleeding risk. Their combinations are probable. This approach may enable us to prevent some HTNEs by avoiding acute HMOD using a timely blood pressure treatment. This treatment should be prompt but controlled.}, } @article {pmid39186487, year = {2024}, author = {Raj, U and Banerjee, A and Ray, S and Bhattacharya, S}, title = {Structure of higher-order interactions in social-ecological networks through Q-analysis of their neighbourhood and clique complex.}, journal = {PloS one}, volume = {19}, number = {8}, pages = {e0306409}, pmid = {39186487}, issn = {1932-6203}, mesh = {*Ecosystem ; Humans ; Models, Theoretical ; Madagascar ; Algorithms ; Social Networking ; Social Support ; Agriculture ; }, abstract = {This paper studies higher-order interactions in social-ecological networks, which formally represent interactions within the social and ecological units of an ecosystem. Many real-world social ecosystems exhibit not only pairwise interactions but also higher-order interactions among their units. Therefore, the conventional graph-theoretic description of networks falls short of capturing these higher-order interactions due to the inherent limitations of the graph definition. In this work, a mathematical framework for capturing the higher-order interactions of a social-ecological system has been given by incorporating notions from combinatorial algebraic topology. In order to achieve this, two different simplicial complexes, the clique and the neighbourhood complex, have been constructed from a pairwise social-ecological network. As a case study, the Q-analysis and a structural study of the interactions in the rural agricultural system of southern Madagascar have been done at various structural levels denoted by q. The results obtained by calculating all the structural vectors for both simplicial complexes, along with exciting results about the participation of facets of the clique complex at different q-levels, have been discussed. This work also establishes significant theorems concerning the dimension of the neighbourhood complex and clique complex obtained from the parent pairwise network.}, } @article {pmid39185327, year = {2024}, author = {Panyushkina, IP and Jull, AJT and Molnár, M and Varga, T and Kontul', I and Hantemirov, R and Kukarskih, V and Sljusarenko, I and Myglan, V and Livina, V}, title = {The timing of the ca-660 BCE Miyake solar-proton event constrained to between 664 and 663 BCE.}, journal = {Communications earth & environment}, volume = {5}, number = {1}, pages = {454}, pmid = {39185327}, issn = {2662-4435}, abstract = {Extreme solar energetic particle events, known as Miyake events, are rare phenomena observed by cosmogenic isotopes, with only six documented. The timing of the ca. 660 BCE Miyake event remains undefined until now. Here, we assign its occurrence to 664-663 BCE through new radiocarbon measurements in gymnosperm larch tree rings from arctic-alpine biomes (Yamal and Altai). Using a 22-box carbon cycle model and Bayesian statistics, we calculate the radiocarbon production rate during the event that is 3.2-4.8 times higher than the average solar modulation, and comparable to the 774-775 CE solar-proton event. The prolonged radiocarbon signature manifests a 12‰ rise over two years. The non-uniform signal in the tree rings is likely driven by the low rate of CO2 gas exchange between the trees and the ambient atmosphere, and the high residence time of radiocarbon in the post-event stratosphere. We caution about using the event's pronounced signature for precise single-year-dating.}, } @article {pmid39184546, year = {2024}, author = {Yuan, H and Mancuso, CA and Johnson, K and Braasch, I and Krishnan, A}, title = {Computational strategies for cross-species knowledge transfer and translational biomedicine.}, journal = {ArXiv}, volume = {}, number = {}, pages = {}, pmid = {39184546}, issn = {2331-8422}, support = {R01 OD011116/OD/NIH HHS/United States ; R35 GM128765/GM/NIGMS NIH HHS/United States ; }, abstract = {Research organisms provide invaluable insights into human biology and diseases, serving as essential tools for functional experiments, disease modeling, and drug testing. However, evolutionary divergence between humans and research organisms hinders effective knowledge transfer across species. Here, we review state-of-the-art methods for computationally transferring knowledge across species, primarily focusing on methods that utilize transcriptome data and/or molecular networks. We introduce the term "agnology" to describe the functional equivalence of molecular components regardless of evolutionary origin, as this concept is becoming pervasive in integrative data-driven models where the role of evolutionary origin can become unclear. Our review addresses four key areas of information and knowledge transfer across species: (1) transferring disease and gene annotation knowledge, (2) identifying agnologous molecular components, (3) inferring equivalent perturbed genes or gene sets, and (4) identifying agnologous cell types. We conclude with an outlook on future directions and several key challenges that remain in cross-species knowledge transfer.}, } @article {pmid39181462, year = {2024}, author = {de Vries, P}, title = {ECOTOXr: An R package for reproducible and transparent retrieval of data from EPA's ECOTOX database.}, journal = {Chemosphere}, volume = {364}, number = {}, pages = {143078}, doi = {10.1016/j.chemosphere.2024.143078}, pmid = {39181462}, issn = {1879-1298}, mesh = {*United States Environmental Protection Agency ; *Databases, Factual ; *Software ; United States ; Ecotoxicology/methods ; Risk Assessment/methods ; Reproducibility of Results ; }, abstract = {The US EPA ECOTOX database provides key ecotoxicological data that are crucial in environmental risk assessment. It can be used for computational predictions of toxicity or indications of hazard in a wide range of situations. There is no standardised or formalised method for extracting and subsetting data from the database for these purposes. Consequently, results in such meta-analyses are difficult to reproduce. The present study introduces the software package ECOTOXr, which provides the means to formalise data retrieval from the ECOTOX database in the R scripting language. Three cases are presented to evaluate the performance of the package in relation to earlier data extractions and searches on the website. These cases demonstrate that the package can reproduce data sets relatively well. Furthermore, they illustrate how future studies can further improve traceability and reproducibility by applying the package and adhering to some simple guidelines. This contributes to the FAIR principles, credibility and acceptance of research that uses data from the ECOTOX database.}, } @article {pmid39181078, year = {2024}, author = {Wei, Q and Yin, Y and Tong, Q and Gong, Z and Shi, Y}, title = {Multi-omics analysis of excessive nitrogen fertilizer application: Assessing environmental damage and solutions in potato farming.}, journal = {Ecotoxicology and environmental safety}, volume = {284}, number = {}, pages = {116916}, doi = {10.1016/j.ecoenv.2024.116916}, pmid = {39181078}, issn = {1090-2414}, mesh = {*Solanum tuberosum/microbiology ; *Fertilizers ; *Nitrogen/analysis ; *Soil Microbiology ; Transcriptome ; Metabolome/drug effects ; Agriculture/methods ; Metagenomics ; Soil/chemistry ; Multiomics ; }, abstract = {Potatoes (Solanum tuberosum L.) are the third largest food crop globally and are pivotal for global food security. Widespread N fertilizer waste in potato cultivation has caused diverse environmental issues. This study employed microbial metagenomic sequencing to analyze the causes behind the declining N use efficiency (NUE) and escalating greenhouse gas emissions resulting from excessive N fertilizer application. Addressing N fertilizer inefficiency through breeding has emerged as a viable solution for mitigating overuse in potato cultivation. In this study, transcriptome and metabolome analyses were applied to identify N fertilizer-responsive genes. Metagenomic sequencing revealed that excessive N fertilizer application triggered alterations in the population dynamics of 11 major bacterial phyla, consequently affecting soil microbial functions, particularly N metabolism pathways and bacterial secretion systems. Notably, the enzyme levels associated with NO3[-] increased, and those associated with NO and N2O increased. Furthermore, excessive N fertilizer application enhanced soil virulence factors and increased potato susceptibility to diseases. Transcriptome and metabolome sequencing revealed significant impacts of excessive N fertilizer use on lipid and amino acid metabolism pathways. Weighted gene co‑expression network analysis (WGCNA) was adopted to identify two genes associated with N fertilizer response: PGSC0003DMG400021157 and PGSC0003DMG400009544.}, } @article {pmid39180071, year = {2024}, author = {Zhuang, M and Qiao, C and Han, L and Bi, Y and Cao, M and Wang, S and Guo, L and Pang, R and Xie, H}, title = {Multi-omics analyses reveal the responses of wheat (Triticum aestivum L.) and rhizosphere bacterial community to nano(micro)plastics stress.}, journal = {Journal of nanobiotechnology}, volume = {22}, number = {1}, pages = {507}, pmid = {39180071}, issn = {1477-3155}, support = {2023YFD1400902//National Key Research and Development Program of China/ ; J210019//Beijing Municipal Natural Science Foundation/ ; C2021204190//Natural Science Foundation of Hebei Province/ ; 21JCZXJC00110//Natural Science Foundation of Tianjin Municipality/ ; }, mesh = {*Triticum ; *Rhizosphere ; *Bacteria/genetics/metabolism/drug effects ; *Microplastics ; *Soil Microbiology ; Nanoparticles/chemistry ; Stress, Physiological ; Microbiota ; Soil Pollutants ; Particle Size ; Polystyrenes/chemistry ; Multiomics ; }, abstract = {The pervasive existence of nanoplastics (NPs) and microplastics (MPs) in soil has become a worldwide environmental concern. N/MPs exist in the environment in a variety of forms, sizes, and concentrations, while multi-omics studies on the comprehensive impact of N/MPs with different properties (e.g. type and size) on plants remain limited. Therefore, this study utilized multi-omics analysis methods to investigate the effects of three common polymers [polyethylene-NPs (PE-NPs, 50 nm), PE-MPs (PE-MPs, 10 μm), and polystyrene-MPs (PS-MPs, 10 μm)] on the growth and stress response of wheat, as well as the rhizosphere microbial community at two concentrations (0.05 and 0.5 g/kg). PS and PE exhibited different effects for the same particle size and concentration. PE-NPs had the most severe stress effects, resulting in reduced rhizosphere bacteria diversity, plant biomass, and antioxidant enzyme activity while increasing beneficial bacteria richness. N/MPs altered the expression of nitrogen-, phosphorus-, and sulfur-related functional genes in rhizosphere bacteria, thereby affecting photosynthesis, as well as metabolite and gene levels in wheat leaves. Partial least squares pathway models (PLSPMs) indicated that concentration, size, and type play important roles in the impact of N/MPs on the plant ecological environment, which could have essential implications for assessing the environmental risk of N/MPs.}, } @article {pmid39178805, year = {2024}, author = {Bravo-Ortiz, MA and Guevara-Navarro, E and Holguín-García, SA and Rivera-Garcia, M and Cardona-Morales, O and Ruz, GA and Tabares-Soto, R}, title = {SpectroCVT-Net: A convolutional vision transformer architecture and channel attention for classifying Alzheimer's disease using spectrograms.}, journal = {Computers in biology and medicine}, volume = {181}, number = {}, pages = {109022}, doi = {10.1016/j.compbiomed.2024.109022}, pmid = {39178805}, issn = {1879-0534}, mesh = {*Alzheimer Disease/classification/physiopathology/diagnosis ; Humans ; *Electroencephalography/methods ; *Signal Processing, Computer-Assisted ; Male ; Female ; Databases, Factual ; Aged ; }, abstract = {Dementia arises from various brain-affecting diseases and injuries, with Alzheimer's disease being the most prevalent, impacting around 55 million people globally. Current clinical diagnosis often relies on biomarkers indicative of Alzheimer's distinctive features. Electroencephalography (EEG) serves as a cost-effective, user-friendly, and safe biomarker for early Alzheimer's detection. This study utilizes EEG signals processed with Short-Time Fourier Transform (STFT) to generate spectrograms, facilitating visualization of EEG signal properties. Leveraging the Brainlat database, we propose SpectroCVT-Net, a novel convolutional vision transformer architecture incorporating channel attention mechanisms. SpectroCVT-Net integrates convolutional and attention mechanisms to capture local and global dependencies within spectrograms. Comprising feature extraction and classification stages, the model enhances Alzheimer's disease classification accuracy compared to transfer learning methods, achieving 92.59 ± 2.3% accuracy across Alzheimer's, healthy controls, and behavioral variant frontotemporal dementia (bvFTD). This article introduces a new architecture and evaluates its efficacy with unconventional data for Alzheimer's diagnosis, contributing: SpectroCVT-Net, tailored for EEG spectrogram classification without reliance on transfer learning; a convolutional vision transformer (CVT) module in the classification stage, integrating local feature extraction with attention heads for global context analysis; Grad-CAM analysis for network decision insight, identifying critical layers, frequencies, and electrodes influencing classification; and enhanced interpretability through spectrograms, illuminating key brain wave contributions to Alzheimer's, frontotemporal dementia, and healthy control classifications, potentially aiding clinical diagnosis and management.}, } @article {pmid39178313, year = {2024}, author = {Du, J and Liu, W and Li, M and Li, Z and Li, X and Dai, Y and Liu, G and Wang, X and Zhu, P and Gladyshev, VN and Zhou, X}, title = {Comparative time-series multi-omics analyses suggest H1.2 involvement in anoxic adaptation and cancer resistance.}, journal = {PLoS biology}, volume = {22}, number = {8}, pages = {e3002778}, pmid = {39178313}, issn = {1545-7885}, mesh = {Animals ; Mice ; *Histones/metabolism ; Humans ; Neoplasms/genetics/metabolism/pathology ; Mole Rats/genetics ; Hypoxia-Inducible Factor 1, alpha Subunit/metabolism/genetics ; Proteomics/methods ; Fibroblasts/metabolism ; Autophagy/genetics ; Adaptation, Physiological/genetics ; Transcriptome/genetics ; Cell Hypoxia/genetics ; Cell Line, Tumor ; Signal Transduction ; Multiomics ; }, abstract = {The naked mole rat (NMR), Heterocephalus glaber, is known as the longest-lived rodent and is extraordinarily resistant to hypoxia and cancer. Here, both NMR embryonic fibroblasts (NEFs) and their mouse counterparts (MEFs) were subjected to anoxic conditions (0% O2, 5% CO2). A combination of comparative transcriptomics and proteomics was then employed to identify differentially expressed genes (DEGs). Notably, we observed distinct levels of histone H1.2 (encoded by HIST1H1C) accumulation between NEFs and MEFs. Subsequent mechanistic analyses showed that higher H1.2 expression in NEFs was associated with the lower expression of its inhibitor, PARP1. Additionally, we discovered that H1.2 can directly interact with HIF-1α PAS domains, thereby promoting the expression of HIF-1α through facilitating the dimerization with HIF-1β. The overexpression of H1.2 was also found to trigger autophagy and to suppress the migration of cancer cells, as well as the formation of xenograft tumors, via the NRF2/P62 signaling pathway. Moreover, an engineered H1.2 knock-in mouse model exhibited significantly extended survival in hypoxic conditions (4% O2) and showed a reduced rate of tumor formation. Collectively, our results indicate a potential mechanistic link between H1.2 and the dual phenomena of anoxic adaptation and cancer resistance.}, } @article {pmid39176874, year = {2024}, author = {Knak, AK and Roheger, M and Wulff, A}, title = {Challenges in Daily Computerized Assessment of Cognitive Functions of Post-COVID Patients.}, journal = {Studies in health technology and informatics}, volume = {316}, number = {}, pages = {1950-1954}, doi = {10.3233/SHTI240815}, pmid = {39176874}, issn = {1879-8365}, mesh = {Humans ; *COVID-19 ; Cognitive Dysfunction ; Diagnosis, Computer-Assisted/methods ; SARS-CoV-2 ; Fatigue ; Post-Acute COVID-19 Syndrome ; Cognition ; }, abstract = {While it would be quite helpful to learn more about the daily fluctuations of fatigue and cognitive impairments of post-COVID patients, their condition can make investigating these especially challenging. By discussing these issues with post-COVID patients and clinical practitioners, we identified six challenges that specifically apply to daily computerized assessment of cognitive functions of post-COVID patients. We proposed solutions for each of the challenges which can be summarized as offering a carefully planned and flexible study design to participants and monitoring their well-being throughout the assessments. We argue that when the proposed precautions are taken, it is feasible to conduct a study that will generate valuable insights into the trajectories of (cognitive) post-COVID symptoms.}, } @article {pmid39176504, year = {2024}, author = {Kokolakis, S and Kokinou, E and Chronaki, C and Moen, A and Datta, G}, title = {Earth Observation and Geoinformatics to Monitoring the Environmental Status of Urban Streams Inextricably Linked to People's Mental Health.}, journal = {Studies in health technology and informatics}, volume = {316}, number = {}, pages = {1560-1564}, doi = {10.3233/SHTI240716}, pmid = {39176504}, issn = {1879-8365}, mesh = {*Environmental Monitoring/methods ; Humans ; *Mental Health ; Rivers ; Geographic Information Systems ; Cities ; }, abstract = {The general condition of urban watercourses is inextricably linked to ecological balance and public health (physical and mental well-being). Given the vulnerability of these systems to climate change and human pollution, this work aims to demonstrate the effective use of environmental indicators to: a) rapidly assess soil and water conditions near urban streams and b) highlight the importance of geoinformatics and earth observation supported by ground-based techniques. There is a great need for new technology and methods for spatial and temporal monitoring and further quantification of environmental quality in urban streams and the land surrounding them to sensitize policymakers and the public to the environmental degradation of these exceptional habitats and to further protect people's mental health.}, } @article {pmid39173171, year = {2024}, author = {Barahona, M and Alegría, A and Amstein, C and Cárcamo, M and Barahona, M}, title = {Epidemiology of high-energy trauma in Chile: An ecological analysis using public registries.}, journal = {Medwave}, volume = {24}, number = {7}, pages = {e2929}, doi = {10.5867/medwave.2024.07.2929}, pmid = {39173171}, issn = {0717-6384}, mesh = {Chile/epidemiology ; Humans ; *Accidents, Traffic/statistics & numerical data/mortality ; Male ; Adult ; *Databases, Factual ; *Registries ; Female ; Young Adult ; Middle Aged ; *Multiple Trauma/epidemiology/mortality ; Wounds and Injuries/epidemiology/mortality ; Public Health ; Sex Distribution ; Adolescent ; Age Distribution ; World Health Organization ; Aged ; }, abstract = {High-energy trauma is defined as severe organic injuries resulting from events that generate a large amount of kinetic, electrical, or thermal energy. It represents a significant public health concern, accounting for 10% of global mortality. This article aims to describe the epidemiology of high-energy trauma in Chile. Specifically, it seeks to compare the mortality rate per 100 000 inhabitants among member countries of the World Health Organization (WHO), provide a descriptive analysis of notifications under the Explicit Health Guarantees (GES) for the health issue of polytraumatized patients, and analyze the trend in the mortality rate due to external causes in Chile. This study employs an ecological design using three open-access databases. First, the WHO database on deaths from traffic accidents in 2019 was used. Then, the GES database was consulted for the "Polytraumatized" issue between 2018 and 2022. Finally, the Chilean Department of Health Statistics database on causes of death between 1997 and 2020 was utilized. In 2019, Chile ranked in the middle regarding the mortality rate per 100 000 inhabitants due to traffic accidents. GES notifications for polytrauma predominantly involved men aged 20 to 40 years and those affiliated with the public health system, highlighting a primary focus for prevention efforts. Mortality from accidents showed a decreasing trend, with significant structural changes identified in 2000 and 2007.}, } @article {pmid39170344, year = {2024}, author = {D, S and Vellaturi, G and Shaik Ibrahim, SH and Molugu, S and Desanamukula, VS and Kocherla, R and Vatambeti, R}, title = {Enhanced deep learning models for automatic fish species identification in underwater imagery.}, journal = {Heliyon}, volume = {10}, number = {15}, pages = {e35217}, pmid = {39170344}, issn = {2405-8440}, abstract = {Underwater cameras are crucial in marine ecology, but their data management needs automatic species identification. This study proposes a two-stage deep learning approach. First, the Unsharp Mask Filter (UMF) preprocesses images. Then, an enhanced region-based fully convolutional network (R-FCN) detects fish using two-order integrals for position-sensitive score maps and precise region of interest (PS-Pr-RoI) pooling for accuracy. The second stage integrates ShuffleNetV2 with the Squeeze and Excitation (SE) module, forming the Improved ShuffleNetV2 model, enhancing classification focus. Hyperparameters are optimized with the Enhanced Northern Goshawk Optimization Algorithm (ENGO). The improved R-FCN model achieves 99.94 % accuracy, 99.58 % precision and recall, and a 99.27 % F-measure on the Fish4knowledge dataset. Similarly, the ENGO-based ShuffleNetV2 model, evaluated on the same dataset, shows 99.93 % accuracy, 99.19 % precision, 98.29 % recall, and a 98.71 % F-measure, highlighting its superior classification accuracy.}, } @article {pmid39169276, year = {2024}, author = {Arcioni, L and Arcieri, M and Martino, JD and Liberati, F and Bottoni, P and Castrignanò, T}, title = {HPC-T-Annotator: an HPC tool for de novo transcriptome assembly annotation.}, journal = {BMC bioinformatics}, volume = {25}, number = {1}, pages = {272}, pmid = {39169276}, issn = {1471-2105}, support = {B87G22000450001//Ministry of University and Research, Italy/ ; }, mesh = {*Software ; *Transcriptome/genetics ; *Molecular Sequence Annotation/methods ; Gene Expression Profiling/methods ; Computational Biology/methods ; Databases, Genetic ; }, abstract = {BACKGROUND: The availability of transcriptomic data for species without a reference genome enables the construction of de novo transcriptome assemblies as alternative reference resources from RNA-Seq data. A transcriptome provides direct information about a species' protein-coding genes under specific experimental conditions. The de novo assembly process produces a unigenes file in FASTA format, subsequently targeted for the annotation. Homology-based annotation, a method to infer the function of sequences by estimating similarity with other sequences in a reference database, is a computationally demanding procedure.

RESULTS: To mitigate the computational burden, we introduce HPC-T-Annotator, a tool for de novo transcriptome homology annotation on high performance computing (HPC) infrastructures, designed for straightforward configuration via a Web interface. Once the configuration data are given, the entire parallel computing software for annotation is automatically generated and can be launched on a supercomputer using a simple command line. The output data can then be easily viewed using post-processing utilities in the form of Python notebooks integrated in the proposed software.

CONCLUSIONS: HPC-T-Annotator expedites homology-based annotation in de novo transcriptome assemblies. Its efficient parallelization strategy on HPC infrastructures significantly reduces computational load and execution times, enabling large-scale transcriptome analysis and comparison projects, while its intuitive graphical interface extends accessibility to users without IT skills.}, } @article {pmid39167718, year = {2024}, author = {Zass, L and Mwapagha, LM and Louis-Jacques, AF and Allali, I and Mulindwa, J and Kiran, A and Hanachi, M and Souiai, O and Mulder, N and Oduaran, OH}, title = {Advancing microbiome research through standardized data and metadata collection: introducing the Microbiome Research Data Toolkit.}, journal = {Database : the journal of biological databases and curation}, volume = {2024}, number = {}, pages = {}, pmid = {39167718}, issn = {1758-0463}, support = {U24 HG009780/HG/NHGRI NIH HHS/United States ; 1U24HG009780/NH/NIH HHS/United States ; }, mesh = {*Metadata ; *Microbiota ; Humans ; Databases, Factual ; }, abstract = {Microbiome research has made significant gains with the evolution of sequencing technologies. Ensuring comparability between studies and enhancing the findability, accessibility, interoperability and reproducibility of microbiome data are crucial for maximizing the value of this growing body of research. Addressing the challenges of standardized metadata reporting, collection and curation, the Microbiome Working Group of the Human Hereditary and Health in Africa (H3Africa) consortium aimed to develop a comprehensive solution. In this paper, we present the Microbiome Research Data Toolkit, a versatile tool designed to standardize microbiome research metadata, facilitate MIxS-MIMS and PhenX reporting, standardize prospective collection of participant biological and lifestyle data, and retrospectively harmonize such data. This toolkit enables past, present and future microbiome research endeavors to collaborate effectively, fostering novel collaborations and accelerating knowledge discovery in the field. Database URL: https://doi.org/10.25375/uct.24218999.v2.}, } @article {pmid39162518, year = {2024}, author = {Hu, D and Zhang, T and He, S and Pu, T and Yin, Y and Hu, Y}, title = {Mining metagenomic data to gain a new insight into the gut microbial biosynthetic potential in placental mammals.}, journal = {Microbiology spectrum}, volume = {12}, number = {10}, pages = {e0086424}, pmid = {39162518}, issn = {2165-0497}, support = {32370552//MOST | National Natural Science Foundation of China (NSFC)/ ; 32070414,32325010//MOST | National Natural Science Foundation of China (NSFC)/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; *Metagenomics ; *Mammals/microbiology ; *Metagenome ; *Multigene Family ; Bacteria/genetics/classification/metabolism ; Polyketides/metabolism ; Data Mining ; Biological Products/metabolism ; Female ; Biosynthetic Pathways/genetics ; }, abstract = {Mammals host a remarkable diversity and abundance of gut microbes. Biosynthetic gene clusters (BGCs) in microbial genomes encode biologically active chemical products and play an important role in microbe-host interactions. Traditionally, the exploration of gut microbial metabolic functions has relied on the pure culture method. However, given the limited amounts of microbes being cultivated, insights into the metabolism of gut microbes in mammals continued to be very limited. In this study, we adopted a computational pipeline for mining the metagenomic data (named taxonomy-guided identification of biosynthetic gene clusters, TaxiBGC) to identify experimentally verified BGCs in 373 metagenomes across 53 mammalian species in an unbiased manner. We demonstrated that polyketides (PKs) and nonribosomal peptides (NRPs) are representative of mammals, and the products derived from them were associated with cell-cell communication and resistance to inflammation. Large carnivores had the highest number of BGCs, followed by large herbivores and small mammals. We also observed that the large mammals had more common BGCs that aid in the biosynthesis of a variety of natural products. However, small mammals not only had fewer BGCs but were also unique to each species. Our results provide novel insights into the mining of metagenomic data sets to identify active BGCs and their products across mammals.IMPORTANCEThe gut microbes host numerous biosynthetic gene clusters (BGCs) that biosynthesize natural products and impact the host's physiology. Historically, our understanding of BGCs in mammalian gut microbes was largely based on studies on cultured isolates; however, only a small fraction of mammal-associated microbes have been investigated. The biochemical diversity of the mammalian gut microbiota is poorly understood. Metagenomic sequencing contains data from a vast number of organisms and provides information on the total gene content of communities. Unfortunately, the existing BGC prediction tools are designed for individual microbial genomes. Recently, a BGC prediction tool called the taxonomy-guided identification of biosynthetic gene clusters (TaxiBGC) that directly mine the metagenome was developed. To gain new insights into the microbial metabolism, we used TaxiBGC to predict BGCs from 373 metagenomes across 53 mammalian species representing seven orders. Our findings elucidate the functional activities of complex microbial communities in the gut.}, } @article {pmid39161242, year = {2024}, author = {Setyawati, I and Husaini, AF and Setiawan, AG and Artika, IM and Ambarsari, L and Nurcholis, W and Vidilaseris, K and Kurniatin, PA}, title = {Structural Classification Insights Into the Plant Defensive Peptides.}, journal = {Proteins}, volume = {92}, number = {12}, pages = {1413-1427}, doi = {10.1002/prot.26736}, pmid = {39161242}, issn = {1097-0134}, support = {102/E5/PG.02.00.PL/2023//Ministry of Education, Culture, Research, and Technology, Republic of Indonesia/ ; }, mesh = {*Phylogeny ; *Plant Proteins/chemistry/genetics/metabolism ; *Plants/metabolism/chemistry ; *Databases, Protein ; Evolution, Molecular ; Amino Acid Sequence ; Models, Molecular ; }, abstract = {This study presents a structural phylogenetic analysis of plant defensive peptides, revealing their evolutionary relationships, structural diversification, and functional adaptations. Utilizing a robust dataset comprising both experimental and predicted structures sourced from the RCSB Protein Data Bank and AlphaFold DB, we constructed a detailed phylogenetic tree to elucidate the distinct evolutionary paths of plant defensive peptide families. Our findings showcase the evolutionary intricacies of defensive peptides, highlighting their diversity and the conservation of key structural motifs critical to their antimicrobial or defensive functions. The results also underscore the adaptive significance of defensive peptides in plant evolution, highlighting their roles in responding to ecological pressures and pathogen interactions.}, } @article {pmid39155119, year = {2024}, author = {Reitz, ZL}, title = {Predicting metallophore structure and function through genome mining.}, journal = {Methods in enzymology}, volume = {702}, number = {}, pages = {371-401}, doi = {10.1016/bs.mie.2024.06.007}, pmid = {39155119}, issn = {1557-7988}, mesh = {*Genomics/methods ; Genome, Bacterial ; Computational Biology/methods ; Siderophores/metabolism/chemistry/genetics ; Data Mining/methods ; }, abstract = {Metallophores are small molecule chelators that many microbes use to obtain trace metals from their environment. Through genome mining, where genomes are scanned for metallophore biosynthesis genes, one can not only identify which organisms are likely to produce a metallophore, but also predict the metallophore structure, thus preventing undesired reisolation of known compounds and accelerating characterization. Furthermore, the presence of accessory genes for the transport, utilization, and regulation can suggest the biological function and fate of a metallophore. Modern, user-friendly tools have made powerful genomic analyses accessible to scientists with no bioinformatics experience, but these tools are often not utilized to their full potential. This chapter provides an introduction to metallophore genomics and demonstrates how to use the free, publicly available antiSMASH platform to infer metallophore function and structure.}, } @article {pmid39154763, year = {2024}, author = {Lin, X and Sun, B and Wang, P and Zhao, M and Liu, D and Zhang, Q and Wu, B and Liu, D}, title = {Enhanced low-concentration phosphate adsorption using magnetic UiO-66@Fe3O4 composite with potential linker exchange.}, journal = {Chemosphere}, volume = {364}, number = {}, pages = {143126}, doi = {10.1016/j.chemosphere.2024.143126}, pmid = {39154763}, issn = {1879-1298}, mesh = {Adsorption ; *Phosphates/chemistry ; *Water Pollutants, Chemical/chemistry ; Water Purification/methods ; Metal-Organic Frameworks/chemistry ; Ferric Compounds/chemistry ; Magnetics ; Phthalic Acids ; }, abstract = {A magnetic FenUiO-66 adsorbent was created to achieve high phosphate adsorption capacity. The incorporation of Fe3O4 facilitated the precipitation and growth of UiO-66 during crystallization, resulting in a shift towards a multilayer heterogeneous distribution of adsorption sites. The increased Fe3O4 content notably enhanced the magnetic properties of FenUiO-66, while negligibly affecting its adsorption performance. The Fe1.5UiO-66 demonstrated exceptional phosphate adsorption capacity (136.54 mg/g), outstanding selectivity, and sustained reusability, with an 80% removal efficiency after nine cycles of treating actual water. The mechanism of phosphate adsorption by FenUiO-66 involved electrostatic attraction, ligand exchange, and linker exchange. Notably, while linker exchange significantly contributed to high adsorption capacity, it resulted in irreversible damage to the FenUiO-66 crystal. These unequivocal findings will serve as a solid foundation for further research and underline the critical role of linkers in the process of phosphate adsorption.}, } @article {pmid39154477, year = {2024}, author = {Bai, Z and He, Y and Hu, G and Cheng, L and Wang, M}, title = {Microplastics at an environmentally relevant dose enhance mercury toxicity in a marine copepod under multigenerational exposure: Multi-omics perspective.}, journal = {Journal of hazardous materials}, volume = {478}, number = {}, pages = {135529}, doi = {10.1016/j.jhazmat.2024.135529}, pmid = {39154477}, issn = {1873-3336}, mesh = {Animals ; *Copepoda/drug effects ; *Mercury/toxicity ; *Water Pollutants, Chemical/toxicity ; *Microplastics/toxicity ; Reproduction/drug effects ; Apoptosis/drug effects ; Proteomics ; Multiomics ; }, abstract = {Here, we subjected the marine copepod Tigriopus japonicus to environmentally-relevant concentrations of microplastics (MPs) and mercury (Hg) for three generations (F0-F2) to investigate their physiological and molecular responses. Hg accumulation and phenotypic traits were measured in each generation, with multi-omics analysis conducted in F2. The results showed that MPs insignificantly impacted the copepod's development and reproduction, however, which were significantly compromised by Hg exposure. Interestingly, MPs significantly increased Hg accumulation and consequently aggravated this metal toxicity in T. japonicus, demonstrating their carrier role. Multi-omics analysis indicated that Hg pollution produced numerous toxic events, e.g., induction of apoptosis, damage to cell/organ morphogenesis, and disordered energy metabolism, ultimately resulting in retarded development and decreased fecundity. Importantly, MPs enhanced Hg toxicity mainly via increased oxidative apoptosis, compromised cell/organ morphogenesis, and energy depletion. Additionally, phosphoproteomic analysis revealed extensive regulation of the above processes, and also impaired neuron activity under combined MPs and Hg exposure. These alterations adversely affected development and reproduction of T. japonicus. Overall, our findings should offer novel molecular insights into the response of T. japonicus to long-term exposure to MPs and Hg, with a particular emphasis on the carrier role of MPs on Hg toxicity.}, } @article {pmid39151562, year = {2024}, author = {Rahimian, M and Panahi, B}, title = {Metagenome sequence data mining for viral interaction studies: Review on progress and prospects.}, journal = {Virus research}, volume = {349}, number = {}, pages = {199450}, pmid = {39151562}, issn = {1872-7492}, mesh = {*Metagenomics/methods ; *Metagenome ; *Viruses/genetics/classification ; *Computational Biology/methods ; *Data Mining ; *High-Throughput Nucleotide Sequencing ; Humans ; Animals ; }, abstract = {Metagenomics has been greatly accelerated by the development of next-generation sequencing (NGS) technologies, which allow scientists to discover and describe novel microorganisms without the need for conventional culture techniques. Examining integrative bioinformatics methods used in viral interaction research, this study highlights metagenomic data from various contexts. Accurate viral identification depends on high-purity genetic material extraction, appropriate NGS platform selection, and sophisticated bioinformatics tools like VirPipe and VirFinder. The efficiency and precision of metagenomic analysis are further improved with the advent of AI-based techniques. The diversity and dynamics of viral communities are demonstrated by case studies from a variety of environments, emphasizing the seasonal and geographical variations that influence viral populations. In addition to speeding up the discovery of new viruses, metagenomics offers thorough understanding of virus-host interactions and their ecological effects. This review provides a promising framework for comprehending the complexity of viral communities and their interactions with hosts, highlighting the transformational potential of metagenomics and bioinformatics in viral research.}, } @article {pmid39147186, year = {2024}, author = {Song, J and Zhou, S and Zou, D and Kwan, MP and Cai, J and Lu, J}, title = {Non-linear associations between noise level and people's short-term noise annoyance in different activity contexts.}, journal = {Environmental research}, volume = {260}, number = {}, pages = {119772}, doi = {10.1016/j.envres.2024.119772}, pmid = {39147186}, issn = {1096-0953}, mesh = {Humans ; Male ; Female ; Adult ; *Noise/adverse effects ; Young Adult ; Ecological Momentary Assessment ; Environmental Exposure ; Middle Aged ; Noise, Transportation/adverse effects ; Geographic Information Systems ; Nonlinear Dynamics ; }, abstract = {Recent research has become increasingly interested in the on-linear associations between noise levels and people's short-term noise annoyance. However, there has been limited investigation into measuring short-term noise annoyance and how different activity contexts may affect these non-linear associations. To address this research gap, this study measured people's short-term noise annoyance using real-time Ecological Momentary Assessment (EMA) data and the Day Reconstruction Method's (DRM) recalled data. Corresponding noise levels were captured using Global Positioning Systems and portable noise sensors. Employing the Shapley additive explanations method, we examined the non-linear associations between noise level and people's real-time and recalled noise annoyance across different activity contexts. The results indicated that 1) People had greater sensitivity to noise levels in real-time annoyance (non-linear association threshold: 60 dB) compared to recalled annoyance, which had a higher non-linear association threshold of 70 dB. 2) The non-linear associations between noise level and people's real-time/recalled noise annoyance varied between different activity contexts. People tended to be more sensitive to noise in real-time annoyance than recalled annoyance on travel routes and at workplaces. 3) Among the factors examined, the contribution of noise level varied across activity contexts. Noise level contributed more significantly to people's real-time noise annoyance in outdoor recreational sites and on travel routes. These findings enhance our understanding of the non-linear association between noise level and people's short-term noise annoyance, moving beyond the linear paradigm. Policymakers should consider the non-linear relationships and different activity contexts when implementing noise control measures.}, } @article {pmid39146704, year = {2024}, author = {Li, G and Wu, M and Xiao, Y and Tong, Y and Li, S and Qian, H and Zhao, T}, title = {Multi-omics reveals the ecological and biological functions of Enterococcus mundtii in the intestine of lepidopteran insects.}, journal = {Comparative biochemistry and physiology. Part D, Genomics & proteomics}, volume = {52}, number = {}, pages = {101309}, doi = {10.1016/j.cbd.2024.101309}, pmid = {39146704}, issn = {1878-0407}, mesh = {Animals ; *Bombyx/microbiology/genetics ; *Enterococcus/genetics ; *Gastrointestinal Microbiome ; *Intestines/microbiology ; Proteomics ; Symbiosis ; Multiomics ; }, abstract = {Insect guts offer unique habitats for microbial colonization, with gut bacteria potentially offering numerous benefits to their hosts. Although Enterococcus has emerged as one of the predominant gut commensal bacteria in insects, its establishment in various niches within the gut has not been characterized well. In this study, Enterococcus mundtii was inoculated into the silkworm (Bombyx mori L.) to investigate its biological functions. Genome-based analysis revealed that its successful colonization is related to adherence genes (ebpA, ebpC, efaA, srtC, and scm). This bacterium did not alter the activities of related metabolic enzymes or the intestinal barrier function. However, significant changes in the gene expressions levels of Att2, CecA, and Lys suggest potential adaptive mechanisms of host immunity to symbiotic E. mundtii. Moreover, 16S metagenomics analysis revealed a significant increase in the relative abundance of E. mundtii in the intestines of silkworms following inoculation. The intestinal microbiome displayed marked heterogeneity, an elevated gut microbiome health index, a reduced microbial dysbiosis index, and low potential pathogenicity in the treatment group. Additionally, E. mundtii enhanced the breakdown of carbohydrates in host intestines. Overall, E. mundtii serves as a beneficial microbe for insects, promoting intestinal homeostasis by providing competitive advantage. This characteristic helps E. mundtii dominate complex microbial environments and remain prevalent across Lepidoptera, likely fostering long-term symbiosis between the both parties. The present study contributes to clarifying the niche of E. mundtii in the intestine of lepidopteran insects and further reveals its potential roles in their insect hosts.}, } @article {pmid39146377, year = {2024}, author = {Nuismer, SL and Basinski, AJ and Schreiner, CL and Eskew, EA and Fichet-Calvet, E and Remien, CH}, title = {Quantifying the risk of spillover reduction programs for human health.}, journal = {PLoS computational biology}, volume = {20}, number = {8}, pages = {e1012358}, pmid = {39146377}, issn = {1553-7358}, support = {R01 GM122079/GM/NIGMS NIH HHS/United States ; }, mesh = {Humans ; Animals ; *Computer Simulation ; *Zoonoses/transmission/epidemiology/prevention & control/virology ; Computational Biology ; Public Health ; Lassa Fever/epidemiology/prevention & control/transmission ; Disease Outbreaks/prevention & control/statistics & numerical data ; Risk Assessment ; Africa, Western/epidemiology ; }, abstract = {Reducing spillover of zoonotic pathogens is an appealing approach to preventing human disease and minimizing the risk of future epidemics and pandemics. Although the immediate human health benefit of reducing spillover is clear, over time, spillover reduction could lead to counterintuitive negative consequences for human health. Here, we use mathematical models and computer simulations to explore the conditions under which unanticipated consequences of spillover reduction can occur in systems where the severity of disease increases with age at infection. Our results demonstrate that, because the average age at infection increases as spillover is reduced, programs that reduce spillover can actually increase population-level disease burden if the clinical severity of infection increases sufficiently rapidly with age. If, however, immunity wanes over time and reinfection is possible, our results reveal that negative health impacts of spillover reduction become substantially less likely. When our model is parameterized using published data on Lassa virus in West Africa, it predicts that negative health outcomes are possible, but likely to be restricted to a small subset of populations where spillover is unusually intense. Together, our results suggest that adverse consequences of spillover reduction programs are unlikely but that the public health gains observed immediately after spillover reduction may fade over time as the age structure of immunity gradually re-equilibrates to a reduced force of infection.}, } @article {pmid39146316, year = {2024}, author = {He, YJ and Liao, H and Yang, G and Qiu, W and Xuan, R and Zheng, G and Xu, B and Yang, X and Magnuson, JT and Schlenk, D and Zheng, C}, title = {Perfluorohexanesulfonic Acid (PFHxS) Impairs Lipid Homeostasis in Zebrafish Larvae through Activation of PPARα.}, journal = {Environmental science & technology}, volume = {58}, number = {37}, pages = {16258-16268}, doi = {10.1021/acs.est.4c03053}, pmid = {39146316}, issn = {1520-5851}, mesh = {Animals ; *Zebrafish ; *Larva/drug effects/metabolism ; *Homeostasis ; *PPAR alpha/metabolism ; Lipid Metabolism/drug effects ; Fluorocarbons ; Sulfonic Acids ; }, abstract = {Perfluorohexanesulfonic acid (PFHxS), an emerging short-chain per- and polyfluoroalkyl substance, has been frequently detected in aquatic environments. Adverse outcome pathway studies have shown that perfluorinated compounds impair lipid homeostasis through peroxisome proliferator activated receptors (PPARs). However, many of these studies were performed at high concentrations and may thus be a result of overt toxicity. To better characterize the molecular and key events of PFHxS to biota, early life-stage zebrafish (Danio rerio) were exposed to concentrations detected in the environment (0.01, 0.1, 1, and 10 μg/L). Lipidomic and transcriptomic evaluations were integrated to predict potential molecular targets. PFHxS significantly impaired lipid homeostasis by the dysregulation of glycerophospholipids, fatty acyls, glycerolipids, sphingolipids, prenol lipids, and sterol lipids. Informatic analyses of the lipidome and transcriptome indicated alterations of the PPAR signaling pathway, with downstream changes to retinol, linoleic acid, and glycerophospholipid metabolism. To assess the role of PPARs, potential binding of PFHxS to PPARs was predicted and animals were coexposed to a PPAR antagonist (GW6471). Molecular simulation indicated PFHxS had a 27.1% better binding affinity than oleic acid, an endogenous agonist of PPARα. Antagonist coexposures rescued impaired glycerophosphocholine concentrations altered by PFHxS. These data indicate PPARα activation may be an important molecular initiating event for PFHxS.}, } @article {pmid39145536, year = {2024}, author = {Pipes, L and Nielsen, R}, title = {A rapid phylogeny-based method for accurate community profiling of large-scale metabarcoding datasets.}, journal = {eLife}, volume = {13}, number = {}, pages = {}, pmid = {39145536}, issn = {2050-084X}, support = {BIO180028//Pittsburgh Supercomputing Center/ ; 1R01GM138634-01/GM/NIGMS NIH HHS/United States ; 1K99GM144747-01/GM/NIGMS NIH HHS/United States ; BIO180028//Advanced Cyberinfrastructure Coordination Ecosystem: Services & Support/ ; R01 GM138634/GM/NIGMS NIH HHS/United States ; K99 GM144747/GM/NIGMS NIH HHS/United States ; }, mesh = {*Phylogeny ; *DNA Barcoding, Taxonomic/methods ; Computational Biology/methods ; DNA, Environmental/genetics ; Metagenomics/methods ; High-Throughput Nucleotide Sequencing/methods ; }, abstract = {Environmental DNA (eDNA) is becoming an increasingly important tool in diverse scientific fields from ecological biomonitoring to wastewater surveillance of viruses. The fundamental challenge in eDNA analyses has been the bioinformatical assignment of reads to taxonomic groups. It has long been known that full probabilistic methods for phylogenetic assignment are preferable, but unfortunately, such methods are computationally intensive and are typically inapplicable to modern next-generation sequencing data. We present a fast approximate likelihood method for phylogenetic assignment of DNA sequences. Applying the new method to several mock communities and simulated datasets, we show that it identifies more reads at both high and low taxonomic levels more accurately than other leading methods. The advantage of the method is particularly apparent in the presence of polymorphisms and/or sequencing errors and when the true species is not represented in the reference database.}, } @article {pmid39145283, year = {2023}, author = {Boyes, D and Skojec, C and Kawahara, AY and , and , and , and , and , and , }, title = {The genome sequence of the Buff Footman, Eilema depressum (Esper, 1787).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {342}, pmid = {39145283}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual male Eilema depressum (the Buff Footman; Arthropoda; Insecta; Lepidoptera; Erebidae). The genome sequence is 622.0 megabases in span. Most of the assembly is scaffolded into 30 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.46 kilobases in length. Gene annotation of this assembly on Ensembl identified 20,038 protein coding genes.}, } @article {pmid39143756, year = {2024}, author = {Bauer, IE and Davies, MA and Bona, KA and Hararuk, O and Shaw, CH and Thompson, DK and Kurz, WA and Webster, KL and Garneau, M and McLaughlin, JW and Packalen, MS and Prystupa, E and Sanderson, NK and Tarnocai, C}, title = {Peat profile database from peatlands in Canada.}, journal = {Ecology}, volume = {105}, number = {10}, pages = {e4398}, doi = {10.1002/ecy.4398}, pmid = {39143756}, issn = {1939-9170}, support = {//Government of Canada (Expanding Market Opportunities Program)/ ; }, mesh = {Canada ; *Soil/chemistry ; Databases, Factual ; Ecosystem ; }, abstract = {Peatlands cover approximately 12% of the Canadian landscape and play an important role in the carbon cycle through their centennial- to millennial-scale storage of carbon under waterlogged and anoxic conditions. In recognizing the potential of these ecosystems as natural climate solutions and therefore the need to include them in national greenhouse gas inventories, the Canadian Model for Peatlands module (CaMP v. 2.0) was developed by the Canadian Forest Service. Model parameterization included compiling peat profiles across Canada to calibrate peat decomposition rates from different peatland types, to define typical bulk density profiles, and to describe the hydrological (i.e., water table) response of peatlands to climatic changes. A total of 1217 sites were included in the dataset from published and unpublished sources. The CORESITES table contains site location and summary data for each profile, as well as an estimate of total carbon mass per unit area (in megagrams of C per hectare). Total carbon mass per unit area at each location was calculated using bulk density and carbon content through each profile. The PROFILES table contains data for depth (in centimeters), bulk density (in grams per cubic meter), ash and carbon content (in percentage), and material descriptions for contiguous samples through each peat profile. Data gaps for bulk density and C content were filled using interpolation, regression trees, and assigned values based on material description and/or soil classification to allow for the estimation of total carbon mass per unit area. A subset of the sites (N = 374) also have pH and pore water trace-elemental geochemistry data and are found in the WATER table. The REFERENCES table contains the full citation of each source of the data and is linked to each core location through the SOURCEDATA table. The LOOKUP table defines codes in the database that required more space that what was sufficient in the metadata tables. The data can be accessed on Open Government Canada and will be useful for future work on carbon stock mapping and ecosystem modeling. All metadata and data are provided © Her Majesty the Queen in Right of Canada, 2023 and information contained in this publication may be reproduced for personal or public noncommercial purposes with attribution, whereas commercial reproduction and distribution are prohibited except with written permission from NRCan; complete details are noted in the Supporting Information file Metadata S1 (see Class III.B.3: Copyright restrictions).}, } @article {pmid39140146, year = {2024}, author = {Yang, F and Han, QL and Zhao, WD and Zhao, Y}, title = {EC number prediction of protein sequences based on combination of hierarchical and global features.}, journal = {Yi chuan = Hereditas}, volume = {46}, number = {8}, pages = {661-669}, doi = {10.16288/j.yczz.24-102}, pmid = {39140146}, issn = {0253-9772}, mesh = {*Computational Biology/methods ; Amino Acid Sequence ; Proteins/chemistry ; Algorithms ; Sequence Analysis, Protein/methods ; Enzymes/chemistry/metabolism ; }, abstract = {The identification of enzyme functions plays a crucial role in understanding the mechanisms of biological activities and advancing the development of life sciences. However, existing enzyme EC number prediction methods did not fully utilize protein sequence information and still had shortcomings in identification accuracy. To address this issue, we proposed an EC number prediction network using hierarchical features and global features (ECPN-HFGF). This method first utilized residual networks to extract generic features from protein sequences, and then employed hierarchical feature extraction modules and global feature extraction modules to further extract hierarchical and global features of protein sequences. Subsequently, the prediction results of both feature types were combined, and a multitask learning framework was utilized to achieve accurate prediction of enzyme EC numbers. Experimental results indicated that the ECPN-HFGF method performed best in the task of predicting EC numbers for protein sequences, achieving macro F1 and micro F1 scores of 95.5% and 99.0%, respectively. The ECPN-HFGF method effectively combined hierarchical and global features of protein sequences, allowing for rapid and accurate EC number prediction. Compared to current commonly used methods, this method offers significantly higher prediction accuracy, providing an efficient approach for the advancement of enzymology research and enzyme engineering applications.}, } @article {pmid39139763, year = {2023}, author = {Boyes, D and Boyes, C and , and , and , and , and , and , }, title = {The genome sequence of the Acer Sober, Anarsia innoxiella (Gregersen & Karsholt, 2017).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {357}, pmid = {39139763}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual female Anarsia innoxiella (the Acer Sober; Arthropoda; Insecta; Lepidoptera; Gelechiidae). The genome sequence is 302.9 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z and W sex chromosomes. The mitochondrial genome has also been assembled and is 15.25 kilobases in length.}, } @article {pmid39139615, year = {2024}, author = {Boyes, D and Boyes, C and , and , and , and , and , and , and , }, title = {The genome sequence of the Crescent Groundling, Teleiodes luculella (Hübner, 1813).}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {143}, pmid = {39139615}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual male Teleiodes luculella (the Crescent Groundling; Arthropoda; Insecta; Lepidoptera; Gelechiidae). The genome sequence is 454.5 megabases in span. Most of the assembly is scaffolded into 30 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.32 kilobases in length. Gene annotation of this assembly on Ensembl identified 19,943 protein coding genes.}, } @article {pmid39139614, year = {2024}, author = {Boyes, D and Crowley, LM and McCulloch, J and Boyes, C and , and , and , and , and , and , and , }, title = {The genome sequence of the Elm Groundling moth, Carpatolechia fugitivella (Zeller, 1839).}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {211}, pmid = {39139614}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual male Carpatolechia fugitivella (the Elm Groundling; Arthropoda; Insecta; Lepidoptera; Gelechiidae). The genome sequence is 493.1 megabases in span. Most of the assembly is scaffolded into 30 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.26 kilobases in length. Gene annotation of this assembly on Ensembl identified 12,721 protein coding genes.}, } @article {pmid39137474, year = {2024}, author = {Tanaka, S and Uraguchi, K and Suzuki, E and Matsumoto, N and Tsumura, M and Fujimoto, S and Miyamoto, S and Yorifuji, T and Ando, M}, title = {Survey of pharyngeal foreign bodies in Japan: An ecological study using the nationwide claims data.}, journal = {International journal of pediatric otorhinolaryngology}, volume = {184}, number = {}, pages = {112055}, doi = {10.1016/j.ijporl.2024.112055}, pmid = {39137474}, issn = {1872-8464}, mesh = {Humans ; *Foreign Bodies/epidemiology ; Japan/epidemiology ; Female ; Male ; Child ; Child, Preschool ; Adolescent ; Infant ; Adult ; *Pharynx ; Young Adult ; Feeding Behavior ; Middle Aged ; Incidence ; Databases, Factual ; Seasons ; Aged ; Sex Distribution ; Age Distribution ; }, abstract = {OBJECTIVE: Pharyngeal foreign bodies (PFBs) are a prevalent disease affected by food culture and dietary habits, with fish bones as the leading cause. Most studies were limited to specific regions, and a nationwide survey was not conducted in Japan. In this ecological study, we aimed to conduct a nationwide analysis of outpatient PFB cases in Japan over three years, focusing on seasonal trends, sex- and age-stratified cases, and regional differences.

METHODS: We used the National Database of Health Insurance Claims and Specific Health Checkups of Japan open data from April 2019 to March 2022. The case data were analyzed by month, age, sex, and prefecture. Additionally, we calculated the standardized claim ratios (SCRs) for each prefecture and investigated the association between dietary habits, food culture, and SCR of PFBs using a two-level linear regression model.

RESULTS: We analyzed a total of 164,337 outpatient PFB cases in Japan, revealing an average incidence rate of 45.6 per 100,000 persons. The seasonal trend revealed a peak in July each year from 2019 to 2021, confirming seasonality in PFB incidents. Children reported a higher incidence rate. Living west of Japan and expenditure on fish and shellfish had a strongly positive association with the SCR of PFBs.

CONCLUSION: Our nationwide survey reveals that, even within Japan, there were regional variations influenced by food culture and dietary habits. The data showed that PFB incidence was higher among children, highlighting the need for preventive education.

LEVEL OF EVIDENCE: Level 3.}, } @article {pmid39133313, year = {2024}, author = {Kuchař, M and Kotěrová, AP and Morávek, A and Santos, F and Harnádková, K and Henyš, P and Cunha, E and Brůžek, J}, title = {Correction to: Automatic variable extraction from 3D coxal bone models for sex estimation using the DSP2 method.}, journal = {International journal of legal medicine}, volume = {138}, number = {6}, pages = {2739}, doi = {10.1007/s00414-024-03311-2}, pmid = {39133313}, issn = {1437-1596}, } @article {pmid39132840, year = {2024}, author = {Vale, FF and Roberts, RJ and Kobayashi, I and Camargo, MC and Rabkin, CS and , }, title = {Gene content, phage cycle regulation model and prophage inactivation disclosed by prophage genomics in the Helicobacter pylori Genome Project.}, journal = {Gut microbes}, volume = {16}, number = {1}, pages = {2379440}, pmid = {39132840}, issn = {1949-0984}, support = {P30 DK058404/DK/NIDDK NIH HHS/United States ; R03 CA167773/CA/NCI NIH HHS/United States ; K22 CA226395/CA/NCI NIH HHS/United States ; P01 CA116087/CA/NCI NIH HHS/United States ; R01 DK062813/DK/NIDDK NIH HHS/United States ; K07 CA125588/CA/NCI NIH HHS/United States ; P01 CA028842/CA/NCI NIH HHS/United States ; K08 CA252635/CA/NCI NIH HHS/United States ; R01 CA077955/CA/NCI NIH HHS/United States ; R01 CA190612/CA/NCI NIH HHS/United States ; U54 GM133807/GM/NIGMS NIH HHS/United States ; P30 CA068485/CA/NCI NIH HHS/United States ; I01 CX002171/CX/CSRD VA/United States ; R01 ES010178/ES/NIEHS NIH HHS/United States ; R01 DK058587/DK/NIDDK NIH HHS/United States ; }, mesh = {*Helicobacter pylori/genetics/virology ; *Prophages/genetics/physiology ; *Genome, Bacterial ; Humans ; *Phylogeny ; *Genomics ; Helicobacter Infections/microbiology ; }, abstract = {Prophages can have major clinical implications through their ability to change pathogenic bacterial traits. There is limited understanding of the prophage role in ecological, evolutionary, adaptive processes and pathogenicity of Helicobacter pylori, a widespread bacterium causally associated with gastric cancer. Inferring the exact prophage genomic location and completeness requires complete genomes. The international Helicobacter pylori Genome Project (HpGP) dataset comprises 1011 H. pylori complete clinical genomes enriched with epigenetic data. We thoroughly evaluated the H. pylori prophage genomic content in the HpGP dataset. We investigated population evolutionary dynamics through phylogenetic and pangenome analyses. Additionally, we identified genome rearrangements and assessed the impact of prophage presence on bacterial gene disruption and methylome. We found that 29.5% (298) of the HpGP genomes contain prophages, of which only 32.2% (96) were complete, minimizing the burden of prophage carriage. The prevalence of H. pylori prophage sequences was variable by geography and ancestry, but not by disease status of the human host. Prophage insertion occasionally results in gene disruption that can change the global bacterial epigenome. Gene function prediction allowed the development of the first model for lysogenic-lytic cycle regulation in H. pylori. We have disclosed new prophage inactivation mechanisms that appear to occur by genome rearrangement, merger with other mobile elements, and pseudogene accumulation. Our analysis provides a comprehensive framework for H. pylori prophage biological and genomics, offering insights into lysogeny regulation and bacterial adaptation to prophages.}, } @article {pmid39131439, year = {2024}, author = {Menger, J and Magagna, B and Henle, K and Harpke, A and Frenzel, M and Rick, J and Wiltshire, K and Grimm-Seyfarth, A}, title = {FAIR-EuMon: a FAIR-enabling resource for biodiversity monitoring schemes.}, journal = {Biodiversity data journal}, volume = {12}, number = {}, pages = {e125132}, pmid = {39131439}, issn = {1314-2828}, abstract = {BACKGROUND: Within the scope of the Helmholtz Metadata Collaboration (HMC), the ADVANCE project - Advanced metadata standards for biodiversity survey and monitoring data: supporting of research and conservation - aimed at supporting rich metadata generation with interoperable metadata standards and semantic artefacts that facilitate data access, integration and reuse across terrestrial, freshwater and marine realms. HMC's mission is to facilitate the discovery, access, machine-readability, and reuse of research data across and beyond the Helmholtz Association.

NEW INFORMATION: We revised, adapted and expanded existing metadata schemas, vocabularies and thesauri to build a FAIR metadata schema and a metadata entry form built on it for users to provide their metadata instances focused on biodiversity monitoring data. The schema is FAIR because it is both machine-interpretable and follows domain-relevant community standards. This report provides a general overview of the project results and instructions on how to access, re-use and complete the metadata form.}, } @article {pmid39131363, year = {2024}, author = {Martin, C and Gitter, A and Anantharaman, K}, title = {Protein Set Transformer: A protein-based genome language model to power high diversity viromics.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {39131363}, issn = {2692-8205}, support = {R35 GM143024/GM/NIGMS NIH HHS/United States ; }, abstract = {Exponential increases in microbial and viral genomic data demand transformational advances in scalable, generalizable frameworks for their interpretation. Standard homology-based functional analyses are hindered by the rapid divergence of microbial and especially viral genomes and proteins that significantly decreases the volume of usable data. Here, we present Protein Set Transformer (PST), a protein-based genome language model that models genomes as sets of proteins without considering sparsely available functional labels. Trained on >100k viruses, PST outperformed other homology- and language model-based approaches for relating viral genomes based on shared protein content. Further, PST demonstrated protein structural and functional awareness by clustering capsid-fold-containing proteins with known capsid proteins and uniquely clustering late gene proteins within related viruses. Our data establish PST as a valuable method for diverse viral genomics, ecology, and evolutionary applications. We posit that the PST framework can be a foundation model for microbial genomics when trained on suitable data.}, } @article {pmid39131277, year = {2024}, author = {Yoo, D and Rhie, A and Hebbar, P and Antonacci, F and Logsdon, GA and Solar, SJ and Antipov, D and Pickett, BD and Safonova, Y and Montinaro, F and Luo, Y and Malukiewicz, J and Storer, JM and Lin, J and Sequeira, AN and Mangan, RJ and Hickey, G and Anez, GM and Balachandran, P and Bankevich, A and Beck, CR and Biddanda, A and Borchers, M and Bouffard, GG and Brannan, E and Brooks, SY and Carbone, L and Carrel, L and Chan, AP and Crawford, J and Diekhans, M and Engelbrecht, E and Feschotte, C and Formenti, G and Garcia, GH and de Gennaro, L and Gilbert, D and Green, RE and Guarracino, A and Gupta, I and Haddad, D and Han, J and Harris, RS and Hartley, GA and Harvey, WT and Hiller, M and Hoekzema, K and Houck, ML and Jeong, H and Kamali, K and Kellis, M and Kille, B and Lee, C and Lee, Y and Lees, W and Lewis, AP and Li, Q and Loftus, M and Loh, YHE and Loucks, H and Ma, J and Mao, Y and Martinez, JFI and Masterson, P and McCoy, RC and McGrath, B and McKinney, S and Meyer, BS and Miga, KH and Mohanty, SK and Munson, KM and Pal, K and Pennell, M and Pevzner, PA and Porubsky, D and Potapova, T and Ringeling, FR and Roha, JL and Ryder, OA and Sacco, S and Saha, S and Sasaki, T and Schatz, MC and Schork, NJ and Shanks, C and Smeds, L and Son, DR and Steiner, C and Sweeten, AP and Tassia, MG and Thibaud-Nissen, F and Torres-González, E and Trivedi, M and Wei, W and Wertz, J and Yang, M and Zhang, P and Zhang, S and Zhang, Y and Zhang, Z and Zhao, SA and Zhu, Y and Jarvis, ED and Gerton, JL and Rivas-González, I and Paten, B and Szpiech, ZA and Huber, CD and Lenz, TL and Konkel, MK and Yi, SV and Canzar, S and Watson, CT and Sudmant, PH and Molloy, E and Garrison, E and Lowe, CB and Ventura, M and O'Neill, RJ and Koren, S and Makova, KD and Phillippy, AM and Eichler, EE}, title = {Complete sequencing of ape genomes.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {39131277}, issn = {2692-8205}, support = {R01 MH120295/MH/NIMH NIH HHS/United States ; UH3 AG064706/AG/NIA NIH HHS/United States ; R35 GM146886/GM/NIGMS NIH HHS/United States ; R01 HG010329/HG/NHGRI NIH HHS/United States ; R01 AG056169/AG/NIA NIH HHS/United States ; R01 GM123312/GM/NIGMS NIH HHS/United States ; T15 LM007093/LM/NLM NIH HHS/United States ; U24 HG007497/HG/NHGRI NIH HHS/United States ; R01 HG002385/HG/NHGRI NIH HHS/United States ; P20 GM139769/GM/NIGMS NIH HHS/United States ; U24 HG010263/HG/NHGRI NIH HHS/United States ; R35 GM133747/GM/NIGMS NIH HHS/United States ; P51 OD011092/OD/NIH HHS/United States ; R56 AG056169/AG/NIA NIH HHS/United States ; P01 AI152999/AI/NIAID NIH HHS/United States ; R35 HG011332/HG/NHGRI NIH HHS/United States ; R35 GM133600/GM/NIGMS NIH HHS/United States ; U19 AG023122/AG/NIA NIH HHS/United States ; R01 HG007352/HG/NHGRI NIH HHS/United States ; R35 GM142916/GM/NIGMS NIH HHS/United States ; R01 HG010169/HG/NHGRI NIH HHS/United States ; U41 HG007234/HG/NHGRI NIH HHS/United States ; R35 GM146926/GM/NIGMS NIH HHS/United States ; R35 GM151945/GM/NIGMS NIH HHS/United States ; }, abstract = {We present haplotype-resolved reference genomes and comparative analyses of six ape species, namely: chimpanzee, bonobo, gorilla, Bornean orangutan, Sumatran orangutan, and siamang. We achieve chromosome-level contiguity with unparalleled sequence accuracy (<1 error in 500,000 base pairs), completely sequencing 215 gapless chromosomes telomere-to-telomere. We resolve challenging regions, such as the major histocompatibility complex and immunoglobulin loci, providing more in-depth evolutionary insights. Comparative analyses, including human, allow us to investigate the evolution and diversity of regions previously uncharacterized or incompletely studied without bias from mapping to the human reference. This includes newly minted gene families within lineage-specific segmental duplications, centromeric DNA, acrocentric chromosomes, and subterminal heterochromatin. This resource should serve as a definitive baseline for all future evolutionary studies of humans and our closest living ape relatives.}, } @article {pmid39129912, year = {2023}, author = {Boyes, D and Hutchinson, F and , and , and , and , and , and , }, title = {The genome sequence of the Brown Rustic, Charanyca ferruginea (Esper, 1785).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {547}, pmid = {39129912}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual female Charanyca ferruginea (the Brown Rustic; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 854.6 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z and W sex chromosomes. The mitochondrial genome has also been assembled and is 15.36 kilobases in length. Gene annotation of this assembly on Ensembl identified 23,126 protein coding genes.}, } @article {pmid39127755, year = {2024}, author = {Pekár, S}, title = {Datasets of traits of zodariid spiders (Araneae: Zodariidae).}, journal = {Scientific data}, volume = {11}, number = {1}, pages = {862}, pmid = {39127755}, issn = {2052-4463}, mesh = {*Spiders/classification/anatomy & histology/physiology ; Animals ; Ecosystem ; Databases, Factual ; Australia ; }, abstract = {Species traits are essential for inferences on ecology and the evolution of organisms. Spiders are the most abundant and diversified terrestrial predators, playing an important role in a range of ecosystem services. Here, I present datasetse on all traits of zodariid spiders, which are known to be free-living ground-dwellers occurring on all continents (except Antarctica) with the highest species diversity in Australia. I collated the data from published resources. The datasets includes nearly 100 000 trait records on all (90) genera and almost all species (1249) of the family. The majority of the 88 traits collected are morphometric, followed by those relating to ecology, reproduction, and physiology. Morphometric traits were available for the majority of species. Other trait classes were only available for some species. I provide a standardized classification of selected categorical traits (habitat, microhabitat, retreat type, circadian activity, prey, primary defensive, and predators). This is the first complete database of traits of a whole spider family, which is available through the World Spider Trait database.}, } @article {pmid39122728, year = {2024}, author = {Hixon, SW and Fernandes, R and Andriamahaihavana, A and Baden, AL and Blanco, MB and Caulier, G and Dammhahn, M and Eeckhaut, I and Eppley, TM and Frédérich, B and Ganzhorn, JU and Garbaras, A and Gibson, D and Goodman, SM and Irwin, M and Kelley, EA and Michel, LN and Lepoint, G and Loudon, JE and Mittelheiser, L and Rakotondranary, J and Rasamisoa, DC and Rasolofonirina, R and Ratovonamana, Y and Razafindramanana, J and Reisdorff, C and Sponheimer, M and Terrana, L and Vasey, N and Crowley, BE}, title = {Introducing IsoMad, a compilation of isotopic datasets for Madagascar.}, journal = {Scientific data}, volume = {11}, number = {1}, pages = {857}, pmid = {39122728}, issn = {2052-4463}, mesh = {Madagascar ; *Databases, Factual ; Animals ; Carbon Isotopes/analysis ; Nitrogen Isotopes/analysis ; }, abstract = {We present the first open-access, island-wide isotopic database (IsoMad) for modern biologically relevant materials collected on Madagascar within the past 150 years from both terrestrial and nearshore marine environments. Isotopic research on the island has increasingly helped with biological studies of endemic organisms, including evaluating foraging niches and investigating factors that affect the spatial distribution and abundance of species. The IsoMad database should facilitate future work by making it easy for researchers to access existing data (even for those who are relatively unfamiliar with the literature) and identify both research gaps and opportunities for using various isotope systems to answer research questions. We also hope that this database will encourage full data reporting in future publications.}, } @article {pmid39122322, year = {2024}, author = {Martín, G and Erinjery, JJ and Ediriweera, D and Goldstein, E and Somaweera, R and de Silva, HJ and Lalloo, DG and Iwamura, T and Murray, KA}, title = {Effects of global change on snakebite envenoming incidence up to 2050: a modelling assessment.}, journal = {The Lancet. Planetary health}, volume = {8}, number = {8}, pages = {e533-e544}, pmid = {39122322}, issn = {2542-5196}, mesh = {*Snake Bites/epidemiology ; Incidence ; Sri Lanka/epidemiology ; Humans ; *Climate Change ; Models, Theoretical ; Forecasting ; Animals ; Snakes ; }, abstract = {BACKGROUND: Human activities are driving climate, land cover, and population change (global change), and shifting the baseline geographical distribution of snakebite. The interacting effects of global change on snakes and communities at risk of snakebite are poorly understood, limiting capacity to anticipate and manage future changes in snakebite risk.

METHODS: In this modelling study, we projected how global change will affect snakebite envenoming incidence in Sri Lanka, as a model system that has a high incidence of snakebite. We used the shared socioeconomic pathway (SSP) scenario analysis framework to integrate forecasts across the domains of: climate change (historical trend from WorldClim plus three underlying regional circulation models [RCMs] in the Coordinated Regional Downscaling Experiment-South Asia repository, with two emissions pathways [representative concentration pathways RCP4.5 and RCP8.5]); land cover change (Dyna-CLUE model); and human population density change (based on Gridded Population of the World data) from Jan 1, 2010 to Dec 31, 2050. Forecasts were integrated under three different development scenarios: a sustainability pathway (SSP1 and no further emissions), a middle-of-the-road pathway (SSP2 and RCP4.5), and a fossil-fuelled pathway (SSP5 and RCP8.5). For SSP2 and SSP5, we nested three different RCMs (CNRM-CM5, GFDL-CCM3, and MPI-ESM-LR; mean averaged to represent consensus) to account for variability in climate predictions. Data were used as inputs to a mechanistic model that predicted snakebite envenoming incidence based on human-snake contact patterns.

FINDINGS: From 2010 to 2050, at the national level, envenoming incidence in Sri Lanka was projected to decrease by 12·0-23·0%, depending on the scenario. The rate of decrease in envenoming incidence was higher in SSP5-RCP8.5 than in SSP1 and SSP2-RCP4.5. Change in envenoming incidence was heterogenous across the country. In SSP1, incidence decreased in urban areas expected to have population growth, and with land cover changes towards anthropised classes. In SSP2-RCP4.5 and SSP5-RCP8.5, most areas were projected to have decreases in incidence (SSP5-RCP8.5 showing the largest area with incidence reductions), while areas such as the central highlands and the north of the country showed localised increases. In the model, decreases occurred with human population growth, land use change towards anthropised classes (potentially shifting occupational risk factors), and decreasing abundance of some snake species, potentially due to global warming and reduced climatic and habitat suitability, with displacement of some snake species.

INTERPRETATION: Snakebite envenoming incidence was projected to decrease overall in the coming decades in Sri Lanka, but with an apparent emerging conflict with sustainability objectives. Therefore, efforts to mitigate snakebite envenoming incidence will need to consider the potential impacts of sustainability interventions, particularly related to climate and land use change and in areas where increases in incidence are projected. In view of global change, neglected tropical diseases and public health issues related to biodiversity, such as snakebite, should be managed collaboratively by both environment and health stakeholders.

FUNDING: UK Medical Research Council.}, } @article {pmid39116194, year = {2024}, author = {Guseva, K and Mohrlok, M and Alteio, L and Schmidt, H and Pollak, S and Kaiser, C}, title = {Bacteria face trade-offs in the decomposition of complex biopolymers.}, journal = {PLoS computational biology}, volume = {20}, number = {8}, pages = {e1012320}, pmid = {39116194}, issn = {1553-7358}, mesh = {Biopolymers/metabolism/chemistry ; *Bacteria/metabolism/enzymology ; Models, Biological ; Computational Biology ; }, abstract = {Although depolymerization of complex carbohydrates is a growth-limiting bottleneck for microbial decomposers, we still lack understanding about how the production of different types of extracellular enzymes affect individual microbes and in turn the performance of whole decomposer communities. In this work we use a theoretical model to evaluate the potential trade-offs faced by microorganisms in biopolymer decomposition which arise due to the varied biochemistry of different depolymerizing enzyme classes. We specifically consider two broad classes of depolymerizing extracellular enzymes, which are widespread across microbial taxa: exo-enzymes that cleave small units from the ends of polymer chains and endo-enzymes that act at random positions generating degradation products of varied sizes. Our results demonstrate a fundamental trade-off in the production of these enzymes, which is independent of system's complexity and which appears solely from the intrinsically different temporal depolymerization dynamics. As a consequence, specialists that produce either exo- or only endo-enzymes limit their growth to high or low substrate conditions, respectively. Conversely, generalists that produce both enzymes in an optimal ratio expand their niche and benefit from the synergy between the two enzymes. Finally, our results show that, in spatially-explicit environments, consortia composed of endo- and exo-specialists can only exist under oligotrophic conditions. In summary, our analysis demonstrates that the (evolutionary or ecological) selection of a depolymerization pathway will affect microbial fitness under low or high substrate conditions, with impacts on the ecological dynamics of microbial communities. It provides a possible explanation why many polysaccharide degraders in nature show the genetic potential to produce both of these enzyme classes.}, } @article {pmid39114815, year = {2023}, author = {Lohse, K and Ebdon, S and Mackintosh, A and Martin, S and Saccheri, IJ and Bourn, NAD and Vila, R and , and , and , and , }, title = {The genome sequence of the Arctic Skipper, Carterocephalus palaemon (Pallas, 1771).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {369}, pmid = {39114815}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual male Carterocephalus palaemon (the Arctic Skipper; Arthropoda; Insecta; Lepidoptera; Hesperiidae). The genome sequence is 394.5 megabases in span. The whole assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.78 kilobases in length. Gene annotation of this assembly on Ensembl identified 17,032 protein coding genes.}, } @article {pmid39114490, year = {2024}, author = {Butlin, R and Mérot, C and , and , and , and , and , }, title = {The genome sequence of a kelp fly, Coelopa pilipes Haliday, 1838.}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {197}, pmid = {39114490}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual male Coelopa pilipes (kelp fly; Arthropoda; Insecta; Diptera; Coelopidae). The genome sequence is 263.0 megabases in span. Most of the assembly is scaffolded into 7 chromosomal pseudomolecules, including the X and Y sex chromosomes. The mitochondrial genome has also been assembled and is 16.86 kilobases in length.}, } @article {pmid39112823, year = {2024}, author = {Darabi, H and Bazhdar, Y and Ehsani, AH}, title = {Modeling the spatial relationship between landscape services and vulnerability assessment.}, journal = {Environmental monitoring and assessment}, volume = {196}, number = {9}, pages = {797}, pmid = {39112823}, issn = {1573-2959}, mesh = {*Geographic Information Systems ; *Environmental Monitoring/methods ; *Conservation of Natural Resources ; *Ecosystem ; Iran ; Remote Sensing Technology ; Models, Theoretical ; Spatial Analysis ; }, abstract = {Even though many studies have been thus far devoted to landscape services (LS) or vulnerability assessment (VA) alone, the relationship between these two concepts has been less investigated. The current study attempts to model the spatial relationship between LS and VA in the Tarhan area (west of Iran). For this purpose, a combination of the analytic hierarchy process (AHP), remote sensing (RS), and geographic information system (GIS) techniques are applied to assess vulnerability. Variogram models and geostatistical simulations are used for mapping and evaluating landscape services. Moreover, the geographically weighted regression (GWR) is operated to predict the relationship between LS and VA. The results indicate that landform and socioeconomic variables are also two main factors shaping variations in VA. As well, the levels of services provided in the possible landscape are affected by the vulnerability. The assessment accordingly establishes that natural and cultural values have significant effects on services, in terms of their spatial distribution and nature. Exploring the relationship between LS and VA correspondingly depicts that VA has a direct influence on the capacity and entity of LS provision (adjusted R[2] = 0.67). The outcomes of the study provide a foundation for nature management and conservation, although it is less able to analyze the trade-off between ecosystem degradation and future development trends. The nexus of LS and future ecological processes in an integrated system can be thus the subject of further research.}, } @article {pmid39109333, year = {2024}, author = {Boyes, D and Mulhair, PO and , and , and , and , and , and , and , }, title = {The genome sequence of the Beautiful China-mark moth Nymphula nitidulata (Hufnagel, 1767).}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {135}, pmid = {39109333}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual female Nymphula nitidulata (the Beautiful China-mark moth; Arthropoda; Insecta; Lepidoptera; Crambidae). The genome sequence is 635.8 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z and W sex chromosomes. The mitochondrial genome has also been assembled and is 15.36 kilobases in length. Gene annotation of this assembly on Ensembl identified 20,031 protein coding genes.}, } @article {pmid39109332, year = {2024}, author = {Boyes, D and Boyes, C and , and , and , and , and , and , and , }, title = {The genome sequence of the Brown Ash Ermine moth, Zelleria hepariella Stainton, 1849.}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {242}, pmid = {39109332}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from a male Zelleria hepariella (the Brown Ash Ermine; Arthropoda; Insecta; Lepidoptera; Yponomeutidae). The genome sequence is 428.8 megabases in span. Most of the assembly is scaffolded into 19 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 16.31 kilobases in length. Gene annotation of this assembly on Ensembl identified 15,718 protein coding genes.}, } @article {pmid39108663, year = {2023}, author = {Taylor, SC and Crowley, LM and Luker, S and Harvey, M and , and , and , and , and , and , and , }, title = {The genome sequence of the Downland Villa bee-fly, Villa cingulata (Meigen, 1804).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {526}, pmid = {39108663}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual male Villa cingulata (the Downland Villa bee-fly; Arthropoda; Insecta; Diptera; Bombyliidae). The genome sequence is 412.6 megabases in span. Most of the assembly is scaffolded into 10 chromosomal pseudomolecules, including the X and Y sex chromosomes. The mitochondrial genome has also been assembled and is 22.43 kilobases in length.}, } @article {pmid39103962, year = {2024}, author = {Prakofjewa, J and Sartori, M and Kalle, R and Łuczaj, Ł and Karbarz, M and Mattalia, G and Šarka, P and Prūse, B and Stryamets, N and Anegg, M and Kuznetsova, N and Kolosova, V and Belichenko, O and Aziz, MA and Pieroni, A and Sõukand, R}, title = {"But how true that is, I do not know": the influence of written sources on the medicinal use of fungi across the western borderlands of the former Soviet Union.}, journal = {IMA fungus}, volume = {15}, number = {1}, pages = {22}, pmid = {39103962}, issn = {2210-6340}, support = {714874//HORIZON EUROPE European Research Council/ ; }, abstract = {Fungi have been used for medicinal purposes for many centuries. This study, based on 35 historical written sources and 581 in-depth semi-structured interviews from eight countries in the western borderlands of the former Soviet Union, investigates the medicinal use of fungi by local communities. We compared the taxa and uses obtained from fieldwork and historical sources with works that advocated fungi use within Soviet herbals, representing the centralised medical system. During fieldwork, we identified eight locally used fungi and one lichen. The highest numbers of medicinal uses were documented in Russia, Estonia and Ukraine. Studies published before the Soviet era listed 21 fungal taxa and one lichen species used in the study region. However, only six of these taxa were mentioned as used by people in our field studies (Amanita muscaria, Boletus edulis, Lycoperdon, Morchella, Phallus impudicus and Cetraria islandica). Notably, these same six taxa were consistently endorsed in Soviet herbals. Of the remaining three taxa recorded in the fieldwork, none were mentioned in historical written sources. However, they were promoted either in Soviet herbals (Inonotus obliquus, Kombucha) or later popular publications (Cantharellus cibarius). This highlights the significant influence of written sources on the use of fungi for medicinal purposes within the studied local communities.}, } @article {pmid39103035, year = {2024}, author = {Shi, C and Cheng, L and Yu, Y and Chen, S and Dai, Y and Yang, J and Zhang, H and Chen, J and Geng, N}, title = {Multi-omics integration analysis: Tools and applications in environmental toxicology.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {360}, number = {}, pages = {124675}, doi = {10.1016/j.envpol.2024.124675}, pmid = {39103035}, issn = {1873-6424}, mesh = {*Environmental Pollutants/toxicity ; *Ecotoxicology/methods ; *Proteomics ; Genomics ; Metabolomics ; Animals ; Humans ; Multiomics ; }, abstract = {Nowadays, traditional single-omics study is not enough to explain the causality between molecular alterations and toxicity endpoints for environmental pollutants. With the development of high-throughput sequencing technology and high-resolution mass spectrometry technology, the integrative analysis of multi-omics has become an efficient strategy to understand holistic biological mechanisms and to uncover the regulation network in specific biological processes. This review summarized sample preparation methods, integration analysis tools and the application of multi-omics integration analyses in environmental toxicology field. Currently, omics methods have been widely applied being as the sensitivity of early biological response, especially for low-dose and long-term exposure to environmental pollutants. Integrative omics can reveal the overall changes of genes, proteins, and/or metabolites in the cells, tissues or organisms, which provide new insights into revealing the overall toxicity effects, screening the toxic targets, and exploring the underlying molecular mechanism of pollutants.}, } @article {pmid39102402, year = {2024}, author = {Saad-Roy, CM and Morris, SE and Boots, M and Baker, RE and Lewis, BL and Farrar, J and Marathe, MV and Graham, AL and Levin, SA and Wagner, CE and Metcalf, CJE and Grenfell, BT}, title = {Impact of waning immunity against SARS-CoV-2 severity exacerbated by vaccine hesitancy.}, journal = {PLoS computational biology}, volume = {20}, number = {8}, pages = {e1012211}, pmid = {39102402}, issn = {1553-7358}, support = {U01 CK000555/CK/NCEZID CDC HHS/United States ; }, mesh = {Humans ; *COVID-19/immunology/prevention & control/epidemiology ; *SARS-CoV-2/immunology ; *COVID-19 Vaccines/immunology ; Vaccination Hesitancy/statistics & numerical data ; Severity of Illness Index ; Vaccination/statistics & numerical data ; Pandemics/prevention & control ; Computational Biology ; }, abstract = {The SARS-CoV-2 pandemic has generated a considerable number of infections and associated morbidity and mortality across the world. Recovery from these infections, combined with the onset of large-scale vaccination, have led to rapidly-changing population-level immunological landscapes. In turn, these complexities have highlighted a number of important unknowns related to the breadth and strength of immunity following recovery or vaccination. Using simple mathematical models, we investigate the medium-term impacts of waning immunity against severe disease on immuno-epidemiological dynamics. We find that uncertainties in the duration of severity-blocking immunity (imparted by either infection or vaccination) can lead to a large range of medium-term population-level outcomes (i.e. infection characteristics and immune landscapes). Furthermore, we show that epidemiological dynamics are sensitive to the strength and duration of underlying host immune responses; this implies that determining infection levels from hospitalizations requires accurate estimates of these immune parameters. More durable vaccines both reduce these uncertainties and alleviate the burden of SARS-CoV-2 in pessimistic outcomes. However, heterogeneity in vaccine uptake drastically changes immune landscapes toward larger fractions of individuals with waned severity-blocking immunity. In particular, if hesitancy is substantial, more robust vaccines have almost no effects on population-level immuno-epidemiology, even if vaccination rates are compensatorily high among vaccine-adopters. This pessimistic scenario for vaccination heterogeneity arises because those few individuals that are vaccine-adopters are so readily re-vaccinated that the duration of vaccinal immunity has no appreciable consequences on their immune status. Furthermore, we find that this effect is heightened if vaccine-hesitants have increased transmissibility (e.g. due to riskier behavior). Overall, our results illustrate the necessity to characterize both transmission-blocking and severity-blocking immune time scales. Our findings also underline the importance of developing robust next-generation vaccines with equitable mass vaccine deployment.}, } @article {pmid39102091, year = {2024}, author = {Kuchař, M and Pilmann Kotěrová, A and Morávek, A and Santos, F and Harnádková, K and Henyš, P and Cunha, E and Brůžek, J}, title = {Automatic variable extraction from 3D coxal bone models for sex estimation using the DSP2 method.}, journal = {International journal of legal medicine}, volume = {138}, number = {6}, pages = {2647-2658}, pmid = {39102091}, issn = {1437-1596}, mesh = {Humans ; *Sex Determination by Skeleton/methods ; Male ; Female ; *Pelvic Bones/diagnostic imaging ; *Algorithms ; *Imaging, Three-Dimensional ; *Forensic Anthropology/methods ; Adult ; Middle Aged ; Aged ; Young Adult ; Portugal ; Aged, 80 and over ; }, abstract = {Thanks to technical progress and the availability of virtual data, sex estimation methods as part of a biological profile are undergoing an inevitable evolution. Further reductions in subjectivity, but potentially also in measurement errors, can be brought by approaches that automate the extraction of variables. Such automatization also significantly accelerates and facilitates the specialist's work. The aim of this study is (1) to apply a previously proposed algorithm (Kuchař et al. 2021) to automatically extract 10 variables used for the DSP2 sex estimation method, and (2) to test the robustness of the new automatic approach in a current heterogeneous population. For the first aim, we used a sample of 240 3D scans of pelvic bones from the same individuals, which were measured manually for the DSP database. For the second aim a sample of 108 pelvic bones from the New Mexico Decedent Image Database was used. The results showed high agreement between automatic and manual measurements with rTEM below 5% for all dimensions except two. The accuracy of final sex estimates based on all 10 variables was excellent (error rate 0.3%). However, we observed a higher number of undetermined individuals in the Portuguese sample (25% of males) and the New Mexican sample (36.5% of females). In conclusion, the procedure for automatic dimension extraction was successfully applied both to a different type of data and to a heterogeneous population.}, } @article {pmid39101049, year = {2024}, author = {Boyes, D and Lees, DC and Holland, PWH and , and , and , and , and , and , and , and , }, title = {The genome sequence of the Oak Beauty, Biston strataria (Hufnagel, 1767).}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {35}, pmid = {39101049}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual male Biston strataria (the Oak Beauty; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 424.0 megabases in span. Most of the assembly is scaffolded into 16 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.61 kilobases in length. Gene annotation of this assembly on Ensembl identified 18,406 protein coding genes.}, } @article {pmid39100235, year = {2024}, author = {Ciach, MA and Pawłowska, J and Górecki, P and Muszewska, A}, title = {The interkingdom horizontal gene transfer in 44 early diverging fungi boosted their metabolic, adaptive, and immune capabilities.}, journal = {Evolution letters}, volume = {8}, number = {4}, pages = {526-538}, pmid = {39100235}, issn = {2056-3744}, abstract = {Numerous studies have been devoted to individual cases of horizontally acquired genes in fungi. It has been shown that such genes expand the hosts' metabolic capabilities and contribute to their adaptations as parasites or symbionts. Some studies have provided an extensive characterization of the horizontal gene transfer (HGT) in Dikarya. However, in the early diverging fungi (EDF), a similar characterization is still missing. In order to fill this gap, we have designed a computational pipeline to obtain a statistical sample of reliable HGT events with a low false discovery rate. We have analyzed 44 EDF proteomes and identified 829 xenologs in fungi ranging from Chytridiomycota to Mucoromycota. We have identified several patterns and statistical properties of EDF HGT. We show that HGT is driven by bursts of gene exchange and duplication, resulting in highly divergent numbers and molecular properties of xenologs between fungal lineages. Ancestrally aquatic fungi are generally more likely to acquire foreign genetic material than terrestrial ones. Endosymbiotic bacteria can be a source of useful xenologs, as exemplified by NOD-like receptors transferred to Mortierellomycota. Closely related fungi have similar rates of intronization of xenologs. Posttransfer gene fusions and losses of protein domains are common and may influence the encoded proteins' functions. We argue that there is no universal approach for HGT identification and inter- and intra-kingdom transfers require tailored identification methods. Our results help to better understand how and to what extent HGT has shaped the metabolic, adaptive, and immune capabilities of fungi.}, } @article {pmid39099847, year = {2024}, author = {Kapsetaki, SE and Compton, ZT and Dolan, J and Harris, VΚ and Mellon, W and Rupp, SM and Duke, EG and Harrison, TM and Aksoy, S and Giraudeau, M and Vincze, O and McGraw, KJ and Aktipis, A and Tollis, M and Boddy, AΜ and Maley, CC}, title = {Life history traits and cancer prevalence in birds.}, journal = {Evolution, medicine, and public health}, volume = {12}, number = {1}, pages = {105-116}, pmid = {39099847}, issn = {2050-6201}, support = {R01 CA140657/CA/NCI NIH HHS/United States ; }, abstract = {BACKGROUND AND OBJECTIVES: Cancer is a disease that affects nearly all multicellular life, including the broad and diverse taxa of Aves. While little is known about the factors that contribute to cancer risk across Aves, life history trade-offs may explain some of this variability in cancer prevalence. We predict birds with high investment in reproduction may have a higher likelihood of developing cancer. In this study, we tested whether life history traits are associated with cancer prevalence in 108 species of birds.

METHODOLOGY: We obtained life history data from published databases and cancer data from 5,729 necropsies from 108 species of birds across 24 taxonomic orders from 25 different zoological facilities. We performed phylogenetically controlled regression analyses between adult body mass, lifespan, incubation length, clutch size, sexually dimorphic traits, and both neoplasia and malignancy prevalence. We also compared the neoplasia and malignancy prevalence of female and male birds.

RESULTS: Providing support for a life history trade-off between somatic maintenance and reproduction, we found a positive relationship between clutch size and cancer prevalence across Aves. There was no significant association with body mass, lifespan, incubation length, sexual dimorphism, and cancer.

CONCLUSIONS AND IMPLICATIONS: Life history theory presents an important framework for understanding differences in cancer defenses across various species. These results suggest a trade-off between reproduction and somatic maintenance, where Aves with small clutch sizes get less cancer.}, } @article {pmid39099645, year = {2023}, author = {Obbard, DJ and , and , and , and , }, title = {The genome sequence of a drosophilid fruit fly, Chymomyza fuscimana (Drosophilidae) (Zetterstedt, 1838).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {477}, pmid = {39099645}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual male Chymomyza fuscimana (drosophilid fruit fly; Arthropoda; Insecta; Diptera; Drosophilidae). The genome sequence is 338.0 megabases in span. Most of the assembly is scaffolded into 5 chromosomal pseudomolecules, including the X and Y sex chromosomes. The mitochondrial genome has also been assembled and is 16.47 kilobases in length.}, } @article {pmid39092794, year = {2024}, author = {Ma, X and Huete, A and Liu, Y and Zhu, X and Nguyen, H and Miura, T and Chen, M and Li, X and Asrar, G}, title = {A holistic big data approach to understand and manage increasing pollen-induced respiratory allergies under global change.}, journal = {Global change biology}, volume = {30}, number = {8}, pages = {e17451}, doi = {10.1111/gcb.17451}, pmid = {39092794}, issn = {1365-2486}, support = {1027576//National Institute of Food and Agriculture/ ; DP210100347//Australian Research Council/ ; 42171305//National Natural Science Foundation of China/ ; }, mesh = {*Pollen/immunology ; *Big Data ; *Climate Change ; Humans ; Respiratory Hypersensitivity/etiology ; }, } @article {pmid39092001, year = {2024}, author = {Boyes, D and Holland, PWH and , and , and , and , and , and , and , }, title = {The genome sequence of the Orange-tailed Clearwing, Synanthedon andrenaeformis (Laspeyres, 1801).}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {160}, pmid = {39092001}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual male Synanthedon andrenaeformis (the Orange-tailed Clearwing; Arthropoda; Insecta; Lepidoptera; Sesiidae). The genome sequence is 348.4 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 16.65 kilobases in length. Gene annotation of this assembly on Ensembl identified 12,867 protein coding genes.}, } @article {pmid39090383, year = {2024}, author = {Manubens-Gil, L and Zhou, Z and Chen, H and Ramanathan, A and Liu, X and Liu, Y and Bria, A and Gillette, T and Ruan, Z and Yang, J and Radojević, M and Zhao, T and Cheng, L and Qu, L and Liu, S and Bouchard, KE and Gu, L and Cai, W and Ji, S and Roysam, B and Wang, CW and Yu, H and Sironi, A and Iascone, DM and Zhou, J and Bas, E and Conde-Sousa, E and Aguiar, P and Li, X and Li, Y and Nanda, S and Wang, Y and Muresan, L and Fua, P and Ye, B and He, HY and Staiger, JF and Peter, M and Cox, DN and Simonneau, M and Oberlaender, M and Jefferis, G and Ito, K and Gonzalez-Bellido, P and Kim, J and Rubel, E and Cline, HT and Zeng, H and Nern, A and Chiang, AS and Yao, J and Roskams, J and Livesey, R and Stevens, J and Liu, T and Dang, C and Guo, Y and Zhong, N and Tourassi, G and Hill, S and Hawrylycz, M and Koch, C and Meijering, E and Ascoli, GA and Peng, H}, title = {Author Correction: BigNeuron: a resource to benchmark and predict performance of algorithms for automated tracing of neurons in light microscopy datasets.}, journal = {Nature methods}, volume = {21}, number = {10}, pages = {1959}, doi = {10.1038/s41592-024-02395-3}, pmid = {39090383}, issn = {1548-7105}, } @article {pmid39089617, year = {2024}, author = {Chen, SH and Chen, CH and Lin, HC and Yeh, SA and Hwang, TL and Chen, PJ}, title = {Drug repurposing of cyclin-dependent kinase inhibitors for neutrophilic acute respiratory distress syndrome and psoriasis.}, journal = {Journal of advanced research}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jare.2024.07.026}, pmid = {39089617}, issn = {2090-1224}, abstract = {BACKGROUND: Neutrophilic inflammation, characterized by dysregulated neutrophil activation, triggers a variety of inflammatory responses such as chemotactic infiltration, oxidative bursts, degranulation, neutrophil extracellular traps (NETs) formation, and delayed turnover. This type of inflammation is pivotal in the pathogenesis of acute respiratory distress syndrome (ARDS) and psoriasis. Despite current treatments, managing neutrophil-associated inflammatory symptoms remains a significant challenge.

AIM OF REVIEW: This review emphasizes the role of cyclin-dependent kinases (CDKs) in neutrophil activation and inflammation. It aims to highlight the therapeutic potential of repurposing CDK inhibitors to manage neutrophilic inflammation, particularly in ARDS and psoriasis. Additionally, it discusses the necessary precautions for the clinical application of these inhibitors due to potential off-target effects and the need for dose optimization.

CDKs regulate key neutrophilic functions, including chemotactic responses, degranulation, NET formation, and apoptosis. Repurposing CDK inhibitors, originally developed for cancer treatment, shows promise in controlling neutrophilic inflammation. Clinical anticancer drugs, palbociclib and ribociclib, have demonstrated efficacy in treating neutrophilic ARDS and psoriasis by targeting off-label pathways, phosphoinositide 3-kinase (PI3K) and phosphodiesterase 4 (PDE4), respectively. While CDK inhibitors offer promising therapeutic benefits, their clinical repurposing requires careful consideration of off-target effects and dose optimization. Further exploration and clinical trials are necessary to ensure their safety and efficacy in treating inflammatory conditions.}, } @article {pmid39086664, year = {2023}, author = {Boyes, D and Eljounaidi, K and , and , and , and , and , and , }, title = {The genome sequence of the Rose-flounced Tabby, Endotricha flammealis (Denis & Schiffermüller, 1775).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {516}, pmid = {39086664}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual female Endotricha flammealis (the Rose-flounced Tabby; Arthropoda; Insecta; Lepidoptera; Pyralidae). The genome sequence is 473.9 megabases in span. Most of the assembly is scaffolded into 32 chromosomal pseudomolecules, including the W and Z sex chromosomes. The mitochondrial genome has also been assembled and is 15.23 kilobases in length. Gene annotation of this assembly on Ensembl identified 17,578 protein coding genes.}, } @article {pmid39083325, year = {2024}, author = {Webb, EK and Stevens, JS and Ely, TD and Lebois, LAM and van Rooij, SJH and Bruce, SE and House, SL and Beaudoin, FL and An, X and Neylan, TC and Clifford, GD and Linnstaedt, SD and Germine, LT and Bollen, KA and Rauch, SL and Haran, JP and Storrow, AB and Lewandowski, C and Musey, PI and Hendry, PL and Sheikh, S and Jones, CW and Punches, BE and Swor, RA and Murty, VP and Hudak, LA and Pascual, JL and Seamon, MJ and Datner, EM and Pearson, C and Peak, DA and Domeier, RM and Rathlev, NK and O'Neil, BJ and Sergot, P and Sanchez, LD and Joormann, J and Pizzagalli, DA and Harte, SE and Kessler, RC and Koenen, KC and Ressler, KJ and McLean, SA and Harnett, NG}, title = {Neighborhood Resources Associated With Psychological Trajectories and Neural Reactivity to Reward After Trauma.}, journal = {JAMA psychiatry}, volume = {81}, number = {11}, pages = {1090-1100}, pmid = {39083325}, issn = {2168-6238}, support = {K01 MH129828/MH/NIMH NIH HHS/United States ; }, mesh = {Humans ; *Stress Disorders, Post-Traumatic/physiopathology/diagnostic imaging ; Female ; Male ; *Reward ; Adult ; *Magnetic Resonance Imaging ; *Resilience, Psychological ; Longitudinal Studies ; *Residence Characteristics ; Middle Aged ; Young Adult ; Brain/physiopathology/diagnostic imaging ; Survivors/psychology ; }, abstract = {IMPORTANCE: Research on resilience after trauma has often focused on individual-level factors (eg, ability to cope with adversity) and overlooked influential neighborhood-level factors that may help mitigate the development of posttraumatic stress disorder (PTSD).

OBJECTIVE: To investigate whether an interaction between residential greenspace and self-reported individual resources was associated with a resilient PTSD trajectory (ie, low/no symptoms) and to test if the association between greenspace and PTSD trajectory was mediated by neural reactivity to reward.

As part of a longitudinal cohort study, trauma survivors were recruited from emergency departments across the US. Two weeks after trauma, a subset of participants underwent functional magnetic resonance imaging during a monetary reward task. Study data were analyzed from January to November 2023.

EXPOSURES: Residential greenspace within a 100-m buffer of each participant's home address was derived from satellite imagery and quantified using the Normalized Difference Vegetation Index and perceived individual resources measured by the Connor-Davidson Resilience Scale (CD-RISC).

MAIN OUTCOME AND MEASURES: PTSD symptom severity measured at 2 weeks, 8 weeks, 3 months, and 6 months after trauma. Neural responses to monetary reward in reward-related regions (ie, amygdala, nucleus accumbens, orbitofrontal cortex) was a secondary outcome. Covariates included both geocoded (eg, area deprivation index) and self-reported characteristics (eg, childhood maltreatment, income).

RESULTS: In 2597 trauma survivors (mean [SD] age, 36.5 [13.4] years; 1637 female [63%]; 1304 non-Hispanic Black [50.2%], 289 Hispanic [11.1%], 901 non-Hispanic White [34.7%], 93 non-Hispanic other race [3.6%], and 10 missing/unreported [0.4%]), 6 PTSD trajectories (resilient, nonremitting high, nonremitting moderate, slow recovery, rapid recovery, delayed) were identified through latent-class mixed-effect modeling. Multinominal logistic regressions revealed that for individuals with higher CD-RISC scores, greenspace was associated with a greater likelihood of assignment in a resilient trajectory compared with nonremitting high (Wald z test = -3.92; P < .001), nonremitting moderate (Wald z test = -2.24; P = .03), or slow recovery (Wald z test = -2.27; P = .02) classes. Greenspace was also associated with greater neural reactivity to reward in the amygdala (n = 288; t277 = 2.83; adjusted P value = 0.02); however, reward reactivity did not differ by PTSD trajectory.

CONCLUSIONS AND RELEVANCE: In this cohort study, greenspace and self-reported individual resources were significantly associated with PTSD trajectories. These findings suggest that factors at multiple ecological levels may contribute to the likelihood of resiliency to PTSD after trauma.}, } @article {pmid39082646, year = {2024}, author = {Mallawaarachchi, V and Wickramarachchi, A and Xue, H and Papudeshi, B and Grigson, SR and Bouras, G and Prahl, RE and Kaphle, A and Verich, A and Talamantes-Becerra, B and Dinsdale, EA and Edwards, RA}, title = {Solving genomic puzzles: computational methods for metagenomic binning.}, journal = {Briefings in bioinformatics}, volume = {25}, number = {5}, pages = {}, pmid = {39082646}, issn = {1477-4054}, support = {RC2 DK116713/DK/NIDDK NIH HHS/United States ; /NH/NIH HHS/United States ; DP220102915//Australian Research Council/ ; RC2DK116713/DK/NIDDK NIH HHS/United States ; }, mesh = {*Metagenomics/methods ; Computational Biology/methods ; Metagenome ; Algorithms ; Genomics/methods ; }, abstract = {Metagenomics involves the study of genetic material obtained directly from communities of microorganisms living in natural environments. The field of metagenomics has provided valuable insights into the structure, diversity and ecology of microbial communities. Once an environmental sample is sequenced and processed, metagenomic binning clusters the sequences into bins representing different taxonomic groups such as species, genera, or higher levels. Several computational tools have been developed to automate the process of metagenomic binning. These tools have enabled the recovery of novel draft genomes of microorganisms allowing us to study their behaviors and functions within microbial communities. This review classifies and analyzes different approaches of metagenomic binning and different refinement, visualization, and evaluation techniques used by these methods. Furthermore, the review highlights the current challenges and areas of improvement present within the field of research.}, } @article {pmid39082518, year = {2024}, author = {Cabral, BVB and Sousa, GJB and Cordeiro, LI and Maranhão, TA and Pereira, MLD}, title = {Temporal Pattern and Spatial Distribution of Tuberculosis Prevalence Associated with Multimorbidity in Brazil.}, journal = {Revista da Sociedade Brasileira de Medicina Tropical}, volume = {57}, number = {}, pages = {e00408}, pmid = {39082518}, issn = {1678-9849}, mesh = {Humans ; Brazil/epidemiology ; Prevalence ; *Tuberculosis/epidemiology ; *Spatio-Temporal Analysis ; Male ; *Multimorbidity ; Female ; Adult ; Middle Aged ; Chronic Disease/epidemiology ; Socioeconomic Factors ; }, abstract = {BACKGROUND: Four main chronic conditions may be involved in the tuberculosis pathogenic process and/or clinical evolution: HIV/AIDS, diabetes mellitus, mental illness, and Chronic Obstructive Pulmonary Disease. This study aimed to determine the spatiotemporal pattern of tuberculosis (TB) associated with multimorbidity in Brazil.

METHODS: Ecological study use data from the Notifiable Diseases Information System (SINAN), collected from the electronic portal of the Department of Informatics of the SUS (DATASUS). These data included TB cases that were reported between 2007 and 2021 and were associated with two or more chronic clinical health conditions (multimorbidity).

RESULTS: A total of 7,795 cases of TB associated with multimorbidity were recorded, with an average growth trend of 4.6% per year (95% Confidence Interval (CI): 3.3-5.9; p<0.001) and higher growth in the first temporal segment (2007 to 2011) (8.9%; 95%CI: 4.2-13.9; p=0.002). The spatial analysis, after Bayesian smoothing, highlighted the main municipalities states of the study, namely: São Paulo (19.8%; n = 297), Porto Alegre (23.6%; n = 354), and Rio de Janeiro (44.8%; n = 672). The proportion of extremely poor (β=-0.002), the bolsa família program (β=0.002), the average per-person income (β=0.001), and the percentage of the population living in households with a density of more than 2 people per bedroom (β=0.001) were related to chronic health conditions.

CONCLUSIONS: These findings will stimulate public action to manage this situation. However, as this is still a recent topic in the literature, we encourage the development of studies on the synergistic characteristics of TB and other clinical conditions.}, } @article {pmid39082244, year = {2024}, author = {Farrell, MJ and Le Guillarme, N and Brierley, L and Hunter, B and Scheepens, D and Willoughby, A and Yates, A and Mideo, N}, title = {The changing landscape of text mining: a review of approaches for ecology and evolution.}, journal = {Proceedings. Biological sciences}, volume = {291}, number = {2027}, pages = {20240423}, pmid = {39082244}, issn = {1471-2954}, support = {//Natural Sciences and Engineering Research Council of Canada/ ; }, mesh = {*Data Mining ; *Ecology/methods ; *Biological Evolution ; *Natural Language Processing ; Machine Learning ; }, abstract = {In ecology and evolutionary biology, the synthesis and modelling of data from published literature are commonly used to generate insights and test theories across systems. However, the tasks of searching, screening, and extracting data from literature are often arduous. Researchers may manually process hundreds to thousands of articles for systematic reviews, meta-analyses, and compiling synthetic datasets. As relevant articles expand to tens or hundreds of thousands, computer-based approaches can increase the efficiency, transparency and reproducibility of literature-based research. Methods available for text mining are rapidly changing owing to developments in machine learning-based language models. We review the growing landscape of approaches, mapping them onto three broad paradigms (frequency-based approaches, traditional Natural Language Processing and deep learning-based language models). This serves as an entry point to learn foundational and cutting-edge concepts, vocabularies, and methods to foster integration of these tools into ecological and evolutionary research. We cover approaches for modelling ecological texts, generating training data, developing custom models and interacting with large language models and discuss challenges and possible solutions to implementing these methods in ecology and evolution.}, } @article {pmid39081076, year = {2024}, author = {Levy, O and Shahar, S}, title = {Artificial Intelligence for Climate Change Biology: From Data Collection to Predictions.}, journal = {Integrative and comparative biology}, volume = {64}, number = {3}, pages = {953-974}, doi = {10.1093/icb/icae127}, pmid = {39081076}, issn = {1557-7023}, support = {300/22//Israeli Science Foundation/ ; NGS-84241T-21//National Geographic Society/ ; IOS-1754949//National Science Foundation/ ; }, mesh = {*Climate Change ; *Artificial Intelligence ; Animals ; Big Data ; Microclimate ; Data Collection/methods ; }, abstract = {In the era of big data, ecological research is experiencing a transformative shift, yet big-data advancements in thermal ecology and the study of animal responses to climate conditions remain limited. This review discusses how big data analytics and artificial intelligence (AI) can significantly enhance our understanding of microclimates and animal behaviors under changing climatic conditions. We explore AI's potential to refine microclimate models and analyze data from advanced sensors and camera technologies, which capture detailed, high-resolution information. This integration can allow researchers to dissect complex ecological and physiological processes with unprecedented precision. We describe how AI can enhance microclimate modeling through improved bias correction and downscaling techniques, providing more accurate estimates of the conditions that animals face under various climate scenarios. Additionally, we explore AI's capabilities in tracking animal responses to these conditions, particularly through innovative classification models that utilize sensors such as accelerometers and acoustic loggers. For example, the widespread usage of camera traps can benefit from AI-driven image classification models to accurately identify thermoregulatory responses, such as shade usage and panting. AI is therefore instrumental in monitoring how animals interact with their environments, offering vital insights into their adaptive behaviors. Finally, we discuss how these advanced data-driven approaches can inform and enhance conservation strategies. In particular, detailed mapping of microhabitats essential for species survival under adverse conditions can guide the design of climate-resilient conservation and restoration programs that prioritize habitat features crucial for biodiversity resilience. In conclusion, the convergence of AI, big data, and ecological science heralds a new era of precision conservation, essential for addressing the global environmental challenges of the 21st century.}, } @article {pmid39080706, year = {2024}, author = {Hamamoto, K and Mizuyama, M and Nishijima, M and Maeda, A and Gibu, K and Poliseno, A and Iguchi, A and Reimer, JD}, title = {Diversity, composition and potential roles of sedimentary microbial communities in different coastal substrates around subtropical Okinawa Island, Japan.}, journal = {Environmental microbiome}, volume = {19}, number = {1}, pages = {54}, pmid = {39080706}, issn = {2524-6372}, support = {20H00653//Japan Society for the Promotion of Science/ ; }, abstract = {BACKGROUND: Marine benthic prokaryotic communities play crucial roles in material recycling within coastal environments, including coral reefs. Coastal sedimentary microbiomes are particularly important as potential reservoirs of symbiotic, beneficial, and pathogenic bacteria in coral reef environments, and therefore presumably play a core role in local ecosystem functioning. However, there is a lack of studies comparing different environments with multiple sites on the island scale, particularly studies focusing on prokaryotic communities, as previous investigations have focused mainly on a single site or on specific environmental conditions. In our study, we collected coastal sediments from seven sites around Okinawa Island, Japan, including three different benthic types; sandy bottoms, seagrass meadows, and hard substratum with living scleractinian corals. We then used metabarcoding to identify prokaryotic compositions and estimate enzymes encoded by genes to infer their functions.

RESULTS: The results showed that the three substrata had significantly different prokaryotic compositions. Seagrass meadow sites exhibited significantly higher prokaryotic alpha-diversity compared to sandy bottom sites. ANCOM analysis revealed that multiple bacterial orders were differentially abundant within each substratum. At coral reef sites, putative disease- and thermal stress-related opportunistic bacteria such as Rhodobacterales, Verrucomicrobiales, and Cytophagales were comparatively abundant, while seagrass meadow sites abundantly harbored Desulfobacterales, Steroidobacterales and Chromatiales, which are common bacterial orders in seagrass meadows. According to our gene-coded enzyme analyses the numbers of differentially abundant enzymes were highest in coral reef sites. Notably, superoxide dismutase, an important enzyme for anti-oxidative stress in coral tissue, was abundant at coral sites. Our results provide a list of prokaryotes to look into in each substrate, and further emphasize the importance of considering the microbiome, especially when focusing on environmental conservation.

CONCLUSION: Our findings prove that prokaryotic metabarcoding is capable of capturing compositional differences and the diversity of microbial communities in three different environments. Furthermore, several taxa were suggested to be differentially more abundant in specific environments, and gene-coded enzymic compositions also showed possible differences in ecological functions. Further study, in combination with field observations and temporal sampling, is key to achieving a better understanding of the interactions between the local microbiome and the surrounding benthic community.}, } @article {pmid39079269, year = {2024}, author = {Tian, Y and Liu, Y and Yue, L and Zhao, X and Zhou, Q and Uwaremwe, C and Wang, Y and Chen, G and Sha, Y and Zhang, Y and Wang, R}, title = {Multi-omics analysis reveals the effects of three application modes of plant growth promoting microbes biofertilizer on potato (Solanum tuberosum L.) growth under alkaline loess conditions.}, journal = {Microbiological research}, volume = {287}, number = {}, pages = {127855}, doi = {10.1016/j.micres.2024.127855}, pmid = {39079269}, issn = {1618-0623}, mesh = {*Solanum tuberosum/microbiology/growth & development ; *Fertilizers/analysis ; *Soil Microbiology ; Bacillus amyloliquefaciens/growth & development ; Transcriptome ; Plant Tubers/microbiology/growth & development ; Microbiota ; Soil/chemistry ; Metabolome ; Rhizosphere ; Sucrose/metabolism ; Plant Development ; Metabolomics/methods ; Multiomics ; }, abstract = {Potato is an important crop due to its high contents of starch, protein, and various vitamins and minerals. Biofertilizers are composed of plant growth promoting microbes (PGPMs) which are essential for improving the growth and resistance of potato. However, little information has focused on the modes of inoculation of biofertilizers on plant growth and microecology. This study aims to reveal the response mechanism of the potato to three modes of inoculation of biofertilizers all containing PGPM Bacillus amyloliquefaciens EZ99, i.e. scattered mode of 5 kg/ha biofertilizer (M5), soaking seed tubers with dissolved 5 kg/ha biofertilizer (MZG), and scattered mode of 3 kg/ha biofertilizer + 2 kg/ha sucrose (MY34) in alkaline loess field through multi-omics analysis of transcriptome, metabolome and microbiome. The physiological result revealed that two application modes of equal amount of biofertilizer M5 and MZG significantly improved the growth and yield of potatoes. Furthermore, the transcriptome of potato exhibited sets of differentially expressed genes enriched in photosynthesis, sugar metabolism, and phenylpropanoid biosynthesis among the three modes, with the M5 mode exhibiting overall up-regulation of 828 genes. Based on the untargeted metabolomic analysis of potato tuber, M5 mode significantly accumulated sucrose, while MZG and MY34 mode significantly accumulated the stress metabolites euchrenone b6 and mannobiose, respectively. Besides, the microbial structure of potato rhizosphere showed that the diversity of bacteria and fungi was similar in all soils, but their abundances varied significantly. Specifically, beneficial Penicillium was enriched in M5 and MZG soils, whereas MY34 soil accumulated potential pathogens Plectosphaerella and saccharophilic Mortierella. Collectively, these e findings highlight that MZG is the most effective mode to promote potato growth and stimulate rhizosphere effect. The present study not only encourages sustainable agriculture through agroecological practices, but also provides broad prospects for the application of PGPM biofertilizer in staple foods.}, } @article {pmid39075558, year = {2024}, author = {Pinheiro-Junior, EL and Alirahimi, E and Peigneur, S and Isensee, J and Schiffmann, S and Erkoc, P and Fürst, R and Vilcinskas, A and Sennoner, T and Koludarov, I and Hempel, BF and Tytgat, J and Hucho, T and von Reumont, BM}, title = {Diversely evolved xibalbin variants from remipede venom inhibit potassium channels and activate PKA-II and Erk1/2 signaling.}, journal = {BMC biology}, volume = {22}, number = {1}, pages = {164}, pmid = {39075558}, issn = {1741-7007}, support = {2016/04761-4//São Paulo Research Foundation/ ; GOC2319 N//F.W.O.-Vlaanderen/ ; GOA4919 N//F.W.O.-Vlaanderen/ ; G0E7120N//F.W.O.-Vlaanderen/ ; PDM/19/164//KU Leuven funding/ ; CA19144 EUVEN//EU COST Action/ ; }, mesh = {Animals ; *Potassium Channels/metabolism/genetics ; MAP Kinase Signaling System/drug effects ; Phylogeny ; Mice ; Cyclic AMP-Dependent Protein Kinases/metabolism/genetics ; Evolution, Molecular ; Humans ; Arthropod Venoms/chemistry ; }, abstract = {BACKGROUND: The identification of novel toxins from overlooked and taxonomically exceptional species bears potential for various pharmacological applications. The remipede Xibalbanus tulumensis, an underwater cave-dwelling crustacean, is the only crustacean for which a venom system has been described. Its venom contains several xibalbin peptides that have an inhibitor cysteine knot (ICK) scaffold.

RESULTS: Our screenings revealed that all tested xibalbin variants particularly inhibit potassium channels. Xib1 and xib13 with their eight-cysteine domain similar to spider knottins also inhibit voltage-gated sodium channels. No activity was noted on calcium channels. Expanding the functional testing, we demonstrate that xib1 and xib13 increase PKA-II and Erk1/2 sensitization signaling in nociceptive neurons, which may initiate pain sensitization. Our phylogenetic analysis suggests that xib13 either originates from the common ancestor of pancrustaceans or earlier while xib1 is more restricted to remipedes. The ten-cysteine scaffolded xib2 emerged from xib1, a result that is supported by our phylogenetic and machine learning-based analyses.

CONCLUSIONS: Our functional characterization of synthesized variants of xib1, xib2, and xib13 elucidates their potential as inhibitors of potassium channels in mammalian systems. The specific interaction of xib2 with Kv1.6 channels, which are relevant to treating variants of epilepsy, shows potential for further studies. At higher concentrations, xib1 and xib13 activate the kinases PKA-II and ERK1/2 in mammalian sensory neurons, suggesting pain sensitization and potential applications related to pain research and therapy. While tested insect channels suggest that all probably act as neurotoxins, the biological function of xib1, xib2, and xib13 requires further elucidation. A novel finding on their evolutionary origin is the apparent emergence of X. tulumensis-specific xib2 from xib1. Our study is an important cornerstone for future studies to untangle the origin and function of these enigmatic proteins as important components of remipede but also other pancrustacean and arthropod venoms.}, } @article {pmid39074140, year = {2024}, author = {Melo, D and Pallares, LF and Ayroles, JF}, title = {Reassessing the modularity of gene co-expression networks using the Stochastic Block Model.}, journal = {PLoS computational biology}, volume = {20}, number = {7}, pages = {e1012300}, pmid = {39074140}, issn = {1553-7358}, support = {R01 ES029929/ES/NIEHS NIH HHS/United States ; R35 GM124881/GM/NIGMS NIH HHS/United States ; }, mesh = {*Drosophila melanogaster/genetics ; Animals ; *Gene Regulatory Networks/genetics ; *Stochastic Processes ; *Algorithms ; *Computational Biology/methods ; Models, Genetic ; Gene Expression Profiling/methods ; }, abstract = {Finding communities in gene co-expression networks is a common first step toward extracting biological insight from these complex datasets. Most community detection algorithms expect genes to be organized into assortative modules, that is, groups of genes that are more associated with each other than with genes in other groups. While it is reasonable to expect that these modules exist, using methods that assume they exist a priori is risky, as it guarantees that alternative organizations of gene interactions will be ignored. Here, we ask: can we find meaningful communities without imposing a modular organization on gene co-expression networks, and how modular are these communities? For this, we use a recently developed community detection method, the weighted degree corrected stochastic block model (SBM), that does not assume that assortative modules exist. Instead, the SBM attempts to efficiently use all information contained in the co-expression network to separate the genes into hierarchically organized blocks of genes. Using RNAseq gene expression data measured in two tissues derived from an outbred population of Drosophila melanogaster, we show that (a) the SBM is able to find ten times as many groups as competing methods, that (b) several of those gene groups are not modular, and that (c) the functional enrichment for non-modular groups is as strong as for modular communities. These results show that the transcriptome is structured in more complex ways than traditionally thought and that we should revisit the long-standing assumption that modularity is the main driver of the structuring of gene co-expression networks.}, } @article {pmid39071792, year = {2023}, author = {Falk, S and Gorše, I and , and , and , and , and , and , }, title = {The genome sequence of the hawkweed Cheilosia, Cheilosia urbana (Meigen, 1822).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {311}, pmid = {39071792}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual female Cheilosia urbana (the hawkweed Cheilosia; Arthropoda; Insecta; Diptera; Syrphidae). The genome sequence is 546.9 megabases in span. Most of the assembly is scaffolded into 5 chromosomal pseudomolecules, including the X sex chromosome. The mitochondrial genome has also been assembled and is 17.08 kilobases in length.}, } @article {pmid39069513, year = {2024}, author = {Xu, R and Xu, C and Li, Z and Zheng, T and Yu, W and Yang, C}, title = {Boundary guidance network for medical image segmentation.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {17345}, pmid = {39069513}, issn = {2045-2322}, support = {2019YFC0117800//National Key Research and Development Program of China/ ; }, mesh = {Humans ; *Urinary Bladder Neoplasms/diagnostic imaging/pathology ; Image Processing, Computer-Assisted/methods ; Deep Learning ; Magnetic Resonance Imaging/methods ; Tomography, X-Ray Computed/methods ; Neural Networks, Computer ; Algorithms ; Cystoscopy/methods ; Image Interpretation, Computer-Assisted/methods ; }, abstract = {Accurate segmentation of the tumor area is crucial for the treatment and prognosis of patients with bladder cancer. Cystoscopy is the gold standard for diagnosing bladder tumors. However, The vast majority of current work uses deep learning to identify and segment tumors from CT and MRI findings, and rarely involves cystoscopy findings. Accurately segmenting bladder tumors remains a great challenge due to their diverse morphology and fuzzy boundaries. In order to solve the above problems, this paper proposes a medical image segmentation network with boundary guidance called boundary guidance network. This network combines local features extracted by CNNs and long-range dependencies between different levels inscribed by Parallel ViT, which can capture tumor features more effectively. The Boundary extracted module is designed to extract boundary features and utilize the boundary features to guide the decoding process. Foreground-background dual-channel decoding is performed by boundary integrated module. Experimental results on our proposed new cystoscopic bladder tumor dataset (BTD) show that our method can efficiently perform accurate segmentation of tumors and retain more boundary information, achieving an IoU score of 91.3%, a Hausdorff Distance of 10.43, an mAP score of 85.3%, and a F1 score of 94.8%. On BTD and three other public datasets, our model achieves the best scores compared to state-of-the-art methods, which proves the effectiveness of our model for common medical image segmentation.}, } @article {pmid39068884, year = {2024}, author = {Fan, Q and Huang, S and Guo, J and Xie, Y and Chen, M and Chen, Y and Qi, W and Liu, H and Jia, Z and Hu, H and Qu, J}, title = {Spatiotemporal distribution and transport flux of organophosphate esters in the sediment of the Yangtze River.}, journal = {Journal of hazardous materials}, volume = {477}, number = {}, pages = {135312}, doi = {10.1016/j.jhazmat.2024.135312}, pmid = {39068884}, issn = {1873-3336}, abstract = {The Yangtze River Basin is an important area for organophosphate esters (OPEs) consumption and emission. Studies proved high OPE detection in Yangtze River water, but there is limited information about the spatiotemporal distribution and transport flux of OPEs in sediment. The present study investigated 16 OPEs in sediment from upstream to mid-downstream of the Yangtze River. The mean concentration of OPEs was 84.30 ng/g, and alkyl-OPEs was the primary component. Great specific surface area and high content of organic carbon significantly increased OPE concentration in Three Gorges Reservoir (TGR) by physical adsorption and chemical bonds (p < 0.05), making TGR the most contaminated area in mainstream. No significant differences in OPE constituents were found in seasonal distribution. Four potential sources of OPEs were identified by principal component analysis and self-organizing maps, and traffic emissions were the dominant source for OPEs. The hazard quotient model results indicated that aryl-OPEs showed moderate risks in the mainstream of Yangtze River, alkyl-OPEs and Cl-OPEs showed low risks. TGR was a significant sink of OPEs in Yangtze River and buried 7.41 tons of OPEs in 2020, a total of 14.87 tons of OPE were transported into the sea by sediment.}, } @article {pmid39066932, year = {2024}, author = {Seldeslachts, A and Maurstad, MF and Øyen, JP and Undheim, EAB and Peigneur, S and Tytgat, J}, title = {Exploring oak processionary caterpillar induced lepidopterism (Part 1): unveiling molecular insights through transcriptomics and proteomics.}, journal = {Cellular and molecular life sciences : CMLS}, volume = {81}, number = {1}, pages = {311}, pmid = {39066932}, issn = {1420-9071}, support = {GOC2319N, GOA4919N, and G0E7120N//Fonds Wetenschappelijk Onderzoek/ ; 12W7822N//Fonds Wetenschappelijk Onderzoek/ ; 1S51521N and 1S51523N//Fonds Wetenschappelijk Onderzoek/ ; CA19144 EUVEN//European Cooperation in Science and Technology/ ; FRIPRO-YRT Fellowship no. 287462//Norwegian Research Council/ ; 101039862//H2020 European Research Council/ ; }, mesh = {Animals ; *Proteomics/methods ; *Transcriptome ; *Moths/genetics ; Arthropod Venoms ; Larva/metabolism ; Quercus ; Gene Expression Profiling ; Allergens/immunology ; Insect Proteins/genetics/metabolism ; Proteome/metabolism ; Computational Biology/methods ; }, abstract = {Lepidopterism, a skin inflammation condition caused by direct or airborne exposure to irritating hairs (setae) from processionary caterpillars, is becoming a significant public health concern. Recent outbreaks of the oak processionary caterpillar (Thaumetopoea processionea) have caused noteworthy health and economic consequences, with a rising frequency expected in the future, exacerbated by global warming promoting the survival of the caterpillar. Current medical treatments focus on symptom relief due to the lack of an effective therapy. While the source is known, understanding the precise causes of symptoms remain incomplete understood. In this study, we employed an advanced method to extract venom from the setae and identify the venom components through high-quality de novo transcriptomics, venom proteomics, and bioinformatic analysis. A total of 171 venom components were identified, including allergens, odorant binding proteins, small peptides, enzymes, enzyme inhibitors, and chitin biosynthesis products, potentially responsible for inflammatory and allergic reactions. This work presents the first comprehensive proteotranscriptomic database of T. processionea, contributing to understanding the complexity of lepidopterism. Furthermore, these findings hold promise for advancing therapeutic approaches to mitigate the global health impact of T. processionea and related caterpillars.}, } @article {pmid39060281, year = {2024}, author = {Khaki, JJ and Meiring, JE and Thindwa, D and Henrion, MYR and Jere, TM and Msuku, H and , and Heyderman, RS and Gordon, MA and Giorgi, E}, title = {Modelling Salmonella Typhi in high-density urban Blantyre neighbourhood, Malawi, using point pattern methods.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {17164}, pmid = {39060281}, issn = {2045-2322}, support = {106158/Z/14/Z/WT_/Wellcome Trust/United Kingdom ; 617 OPP1141321//Bill and Melinda Gates Foundation/ ; }, mesh = {Humans ; *Typhoid Fever/epidemiology/microbiology ; *Salmonella typhi/isolation & purification ; Adolescent ; Child ; Malawi/epidemiology ; Adult ; Child, Preschool ; Male ; Female ; Young Adult ; Incidence ; Infant ; Risk Factors ; Sanitation ; Urban Population ; }, abstract = {Salmonella Typhi is a human-restricted pathogen that is transmitted by the faecal-oral route and causative organism of typhoid fever. Using health facility data from 2016 to 2020, this study focuses on modelling the spatial variation in typhoid risk in Ndirande township in Blantyre. To pursue this objective, we developed a marked inhomogeneous Poisson process model that allows us to incorporate both individual-level and environmental risk factors. The results from our analysis indicate that typhoid cases are spatially clustered, with the incidence decreasing by 54% for a unit increase in the water, sanitation, and hygiene (WASH) score. Typhoid intensity was also higher in children aged below 18 years than in adults. However, our results did not show evidence of a strong temporal variation in typhoid incidence. We also discuss the inferential benefits of using point pattern models to characterise the spatial variation in typhoid risk and outline possible extensions of the proposed modelling framework.}, } @article {pmid39060268, year = {2024}, author = {Tagliaferro, S and Maio, S and Pirona, F and Stanisci, I and Sarno, G and Silvi, P and Kermenidou, M and Papaioannou, N and Perchard, R and Prpic, I and Polanska, K and Jerzynska, J and Ramos, E and Rovira, J and Belmonte, J and Snoj Tratnik, JS and Horvat, M and Kocman, D and Spiric, Z and Zickella, J and Fasola, S and La Grutta, S and Malizia, V and Montalbano, L and , and , and Baldacci, S and Annesi-Maesano, I}, title = {Assessing external exposome by implementing an Environmental Data Management System using Open Data.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {17142}, pmid = {39060268}, issn = {2045-2322}, support = {603946//European Commission/ ; }, mesh = {Humans ; Male ; Female ; *Exposome ; Environmental Exposure ; Data Management ; Environmental Monitoring/methods ; Europe ; Aged, 80 and over ; Cities ; Aged ; }, abstract = {Due to the increasing importance of exposome in environmental epidemiology, feasibility and usefulness of an Environmental Data Management System (EDMS) using Open Data was evaluated. The EDMS includes data from 10 European cities (Celje (Slovenia), Łódź (Poland), Manchester (UK), Palermo (Italy), Paris (France), Porto (Portugal), Regensburg (Germany), Reus (Spain), Rijeka (Croatia), Thessaloniki (Greece)) about external non-specific and specific exposome factors at the city or country level (2017-2020). Findings showed that the highest values of life expectancy were in Reus females (86 years) and Palermo males (81 years). UK had the highest obesity rate (28%), Croatia the highest prescribed drug consumption (62%), Greece and Portugal the highest smoking rates (37%, 42%) and daily alcohol consumption (21%), respectively. The most polluted cities were Thessaloniki for PM10 (38 µg/m[3]), Łódź for PM2.5 (25 µg/m[3]), Porto for NO2 (62 µg/m[3]) and Rijeka for O3 (92 µg/m[3]). Thessaloniki had the highest grey space (98%) and Łódź the highest cumulative amount of pollen (39,041 p/m[3]). The highest daily noise levels ≥ 55 dB was in Reus (81% to traffic) and Regensburg (21% to railway). In drinking water, arsenic had the highest value in Thessaloniki (6.4 µg/L), boron in Celje (24 mg/L) and lead in Paris (46.7 µg/L). Portugal and Greece showed the highest pesticide residues in food (7%). In conclusion, utilizing open-access databases enables the translation of research findings into actionable strategies for public health interventions.}, } @article {pmid39059890, year = {2024}, author = {Tikhomirov, L and Semmler, C and McCradden, M and Searston, R and Ghassemi, M and Oakden-Rayner, L}, title = {Medical artificial intelligence for clinicians: the lost cognitive perspective.}, journal = {The Lancet. Digital health}, volume = {6}, number = {8}, pages = {e589-e594}, doi = {10.1016/S2589-7500(24)00095-5}, pmid = {39059890}, issn = {2589-7500}, mesh = {*Artificial Intelligence ; Humans ; *Clinical Decision-Making/methods ; Cognition ; Decision Support Systems, Clinical ; Radiology ; }, abstract = {The development and commercialisation of medical decision systems based on artificial intelligence (AI) far outpaces our understanding of their value for clinicians. Although applicable across many forms of medicine, we focus on characterising the diagnostic decisions of radiologists through the concept of ecologically bounded reasoning, review the differences between clinician decision making and medical AI model decision making, and reveal how these differences pose fundamental challenges for integrating AI into radiology. We argue that clinicians are contextually motivated, mentally resourceful decision makers, whereas AI models are contextually stripped, correlational decision makers, and discuss misconceptions about clinician-AI interaction stemming from this misalignment of capabilities. We outline how future research on clinician-AI interaction could better address the cognitive considerations of decision making and be used to enhance the safety and usability of AI models in high-risk medical decision-making contexts.}, } @article {pmid39057817, year = {2024}, author = {Chanda, MM and Purse, BV and Sedda, L and Benz, D and Prasad, M and Reddy, YN and Yarabolu, KR and Byregowda, SM and Carpenter, S and Prasad, G and Rogers, DJ}, title = {Bluetongue Risk Map for Vaccination and Surveillance Strategies in India.}, journal = {Pathogens (Basel, Switzerland)}, volume = {13}, number = {7}, pages = {}, pmid = {39057817}, issn = {2076-0817}, support = {BB/H009167/1//BBSRC, DFID, Scottish government/ ; }, abstract = {Bluetongue virus (BTV, Sedoreoviridae: Orbivirus) causes an economically important disease, namely, bluetongue (BT), in domestic and wild ruminants worldwide. BTV is endemic to South India and has occurred with varying severity every year since the virus was first reported in 1963. BT can cause high morbidity and mortality to sheep flocks in this region, resulting in serious economic losses to subsistence farmers, with impacts on food security. The epidemiology of BTV in South India is complex, characterized by an unusually wide diversity of susceptible ruminant hosts, multiple vector species biting midges (Culicoides spp., Diptera: Ceratopogonidae), which have been implicated in the transmission of BTV and numerous co-circulating virus serotypes and strains. BT presence data (1997-2011) for South India were obtained from multiple sources to develop a presence/absence model for the disease. A non-linear discriminant analysis (NLDA) was carried out using temporal Fourier transformed variables that were remotely sensed as potential predictors of BT distribution. Predictive performance was then characterized using a range of different accuracy statistics (sensitivity, specificity, and Kappa). The top ten variables selected to explain BT distribution were primarily thermal metrics (land surface temperature, i.e., LST, and middle infrared, i.e., MIR) and a measure of plant photosynthetic activity (the Normalized Difference Vegetation Index, i.e., NDVI). A model that used pseudo-absence points, with three presence and absence clusters each, outperformed the model that used only the recorded absence points and showed high correspondence with past BTV outbreaks. The resulting risk maps may be suitable for informing disease managers concerned with vaccination, prevention, and control of BT in high-risk areas and for planning future state-wide vector and virus surveillance activities.}, } @article {pmid39056317, year = {2024}, author = {Stulberg, EL and Lisabeth, L and Schneider, ALC and Skolarus, L and Kershaw, KN and Zheutlin, AR and Harris, BRE and Sarpong, D and Wong, KH and Sheth, KN and de Havenon, A}, title = {Correlations of Socioeconomic and Clinical Determinants with United States County-Level Stroke Prevalence.}, journal = {Annals of neurology}, volume = {96}, number = {4}, pages = {739-744}, doi = {10.1002/ana.27039}, pmid = {39056317}, issn = {1531-8249}, support = {R01 NS107463/NH/NIH HHS/United States ; 1R38HL167282-01/HI/NHLBI NIH HHS/United States ; R01MD016178/NS/NINDS NIH HHS/United States ; R01NS110721/NS/NINDS NIH HHS/United States ; HT9425-23-1-0981//Department of Defense/ ; R01 HL152741/NH/NIH HHS/United States ; R01 HL156906/NH/NIH HHS/United States ; //American Heart Association/American Stroke Association/ ; U24NS107136/NS/NINDS NIH HHS/United States ; R01EB301114/NS/NINDS NIH HHS/United States ; R01NR018335/NS/NINDS NIH HHS/United States ; /MD/NIMHD NIH HHS/United States ; /AG/NIA NIH HHS/United States ; R01NS130189/NS/NINDS NIH HHS/United States ; U24NS129500/NS/NINDS NIH HHS/United States ; W81XWH-21-1-0590//Department of Defense/ ; K23NS123340/NS/NINDS NIH HHS/United States ; R38 HL167282/HL/NHLBI NIH HHS/United States ; U24NS107215/NS/NINDS NIH HHS/United States ; R01 NS038916/NH/NIH HHS/United States ; U01NS106513/NS/NINDS NIH HHS/United States ; UG3NS130228/NS/NINDS NIH HHS/United States ; K23NS105924/NS/NINDS NIH HHS/United States ; }, mesh = {Humans ; *Stroke/epidemiology ; United States/epidemiology ; Prevalence ; Socioeconomic Factors ; Risk Factors ; Social Class ; Male ; Female ; Adult ; Middle Aged ; Health Services Accessibility ; Aged ; }, abstract = {Socioeconomic status (SES) is a multi-faceted theoretical construct associated with stroke risk and outcomes. Knowing which SES measures best correlate with population stroke metrics would improve its accounting in observational research and inform interventions. Using the Centers for Disease Control and Prevention's (CDC) Population Level Analysis and Community Estimates (PLACES) and other publicly available databases, we conducted an ecological study comparing correlations of different United States county-level SES, health care access and clinical risk factor measures with age-adjusted stroke prevalence. The prevalence of adults living below 150% of the federal poverty level most strongly correlated with stroke prevalence compared to other SES and non-SES measures (correlation coefficient = 0.908, R[2] = 0.825; adjusted partial correlation coefficient: 0.589, R[2] = 0.347). ANN NEUROL 2024;96:739-744.}, } @article {pmid39056051, year = {2024}, author = {Navarro-Farfán, MDM and García-Romero, L and Martínez-Cinco, MA and Domínguez-Sánchez, C and Sánchez-Quispe, ST}, title = {Methodology for the assessment of poor-data water resources.}, journal = {PeerJ}, volume = {12}, number = {}, pages = {e17755}, pmid = {39056051}, issn = {2167-8359}, mesh = {*Water Resources ; Models, Theoretical ; Hydrology/methods ; Environmental Monitoring/methods ; }, abstract = {Surface hydrologic modeling becomes a problem when insufficient spatial and temporal information is available. It is common to have useful modeling periods of less than 15 years. The purpose of this work is to develop a methodology that allows the selection of meteorological and hydrometric stations that are suitable for modeling when information is scarce in the area. Based on the scarcity of data, a series of statistical tests are proposed to eliminate stations according to a decision-making process. Although the number of stations decreases drastically, the information used is reliable and of adequate quality, ensuring less uncertainty in the surface simulation models. Individual basin modeling can be carried out considering the poor data. The transfer of parameters can be applied through the nesting of basins to have information distributed over an extensive area. Therefore, temporally and spatially extended modeling can be achieved with information that preserves statistical parameters over time. If data management and validation is performed, the modeled watersheds are well represented; if this is not done, only 26% to 50% of the runoff is represented.}, } @article {pmid39053536, year = {2024}, author = {He, M and Cui, J and Yi, Y and Chen, HW and Zhang, Q and Li, L and Huang, L and Hong, S}, title = {Vegetation increases global climate vulnerability risk by shifting climate zones in response to rising atmospheric CO2.}, journal = {The Science of the total environment}, volume = {949}, number = {}, pages = {174810}, doi = {10.1016/j.scitotenv.2024.174810}, pmid = {39053536}, issn = {1879-1026}, mesh = {*Carbon Dioxide/analysis ; *Climate Change ; *Ecosystem ; Atmosphere/chemistry ; }, abstract = {Global climate zones are experiencing widespread shifts with ongoing rise in atmospheric CO2, influencing vegetation growth and shifting its distributions to challenge ecosystem structure and function, posing threats on ecological and societal safety. However, how rising atmospheric CO2 affects the pace of global climate zone shifts is highly uncertain. More attentions are urgently required to understand the underlying mechanisms and quantifications of regional climate vulnerability in response to rising CO2. In this study, we employ nine Earth system models from CMIP6 to investigate global climate zone shifts with rising CO2, unravel the effects of vegetation physiological response (PHY), and categorize climate vulnerable regions depending on the extent of climate zone shifts. We find that climate zone shifts over half of the global land area, 16.8% of which is contributed by PHY at 4 × CO2. Intriguingly, besides warming, PHY-induced precipitation changes and their interactions with warming dominate about two-fifths of PHY-forced shifts, providing potential direction for model improvement in future predictions of climate zone shifts. Aided with PHY effects, 4 × CO2 imposes substantial climate zone shifts over about one-fifth of the global land area, suggesting substantial changes in local climate and ecosystem structure and functions. Hence, those regions would experience strong climate vulnerability, and face high risk of climate extremes, water scarcity and food production. Our results quantitatively identify the vulnerable regions and unravel the underlying drivers, providing scientific insights to prioritize conservation and restoration efforts to ensure ecological and social safety globally.}, } @article {pmid39051209, year = {2024}, author = {de Souza, OF and Araújo, ACB and Vieira, LB and Bachur, JA and Lopez, AGP and Gonçalves, TG and de Abreu, LC}, title = {Sex Disparity in Stroke Mortality among Adults: A Time Series Analysis in the Greater Vitoria Region, Brazil (2000-2021).}, journal = {Epidemiologia (Basel, Switzerland)}, volume = {5}, number = {3}, pages = {402-410}, pmid = {39051209}, issn = {2673-3986}, abstract = {The disparity between the sexes in stroke mortality has been demonstrated in people from different locations. The objective of this study was to analyze the disparity between sexes in stroke mortality in adults in the metropolitan area of Greater Vitoria between 2000 and 2021. Ecological time series design was conducted with a database of the Brazilian Health System Informatics Department. The annual percentage change and average annual percentage change were calculated through joinpoint regression. Pairwise comparisons using parallelism and coincidence tests were applied to compare temporal trends between men and women. Men had higher mortality rates in most years between 2000 and 2021. In contrast, women had higher proportional mortality values in all years evaluated from 2000 to 2021. The paired comparison revealed a disparity between the sexes in the proportional mortality time series (parallelism test: p = 0.003; coincidence test: p < 0.001). However, the time series of the mortality rates showed no disparity between the sexes (parallelism test: p = 0.114; coincidence test: p = 0.093). From 2000 to 2021, there was a disparity in proportional mortality from stroke between the sexes of the population in the metropolitan area of Greater Vitoria, Brazil. However, the time series of mortality rates between the sexes did not reveal any disparity in the study period.}, } @article {pmid39050029, year = {2024}, author = {Kryukov, K and Nakahama, N and Kuraku, S}, title = {Genome assembly catalog for species in the Japanese Red List: unlocking endangered biodiversity through genomic inventory.}, journal = {F1000Research}, volume = {13}, number = {}, pages = {583}, pmid = {39050029}, issn = {2046-1402}, mesh = {Animals ; *Biodiversity ; *Endangered Species ; Genome ; *Genomics/methods ; Japan ; }, abstract = {Improvements in DNA sequencing technology are allowing the dramatic increase of whole genome data for a wide variety of species. Such genome sequence data can assist the monitoring of intraspecific genetic diversity, but is often lacking for threatened species. In this project, we focused on the national Red List, a catalog of extinct and threatened species, issued by the Japanese government. We combined the data included in it with the record of genome assembly in NCBI and tabulated the assembly availability of the species in the list. The combined data shows a low percentage (2.1%) of the availability of whole genome sequence data for the taxa ranked on the Japanese Red List as well as a strong bias towards mammals and birds in Animalia and vascular plants in Plantae. Our data presentation highlights potential systematic limitations in genome sequencing (e.g., budget for sequencing large genomes of amphibians) and instructs future policies including which taxon needs more effort for genome sequencing. The resultant tables are available in the original website https://treethinkers.nig.ac.jp/redlist/ and are regularly updated.}, } @article {pmid39049113, year = {2024}, author = {Yurkov, A and Visagie, CM and Crous, PW and Hashimoto, A and Baschien, C and Begerow, D and Kemler, M and Schoutteten, N and Stadler, M and Wijayawardene, NN and Hyde, KD and Zhang, N and Boekhout, T and , and May, TW and Thines, M and Hawksworth, DL}, title = {Cultures as types and the utility of viable specimens for fungal nomenclature.}, journal = {IMA fungus}, volume = {15}, number = {1}, pages = {20}, pmid = {39049113}, issn = {2210-6340}, abstract = {The debates over the requirement of the International Code of Nomenclature for algae, fungi, and plants (ICNafp) for a viable specimen to represent the name-bearing type material for a species or infraspecific taxon have a long history. Taxonomy of fungi commonly studied as living cultures exemplified by yeasts and moulds, strongly depend on viable reference material. The availability of viable cultures is also particularly useful for several groups of filamentous and dimorphic fungi. While the preservation of metabolically inactive cultures is permitted and recommended by the ICNafp, there is room for improvement. Below, we review the history and current status of cultures as the name-bearing type material under the Code. We also present a roadmap with tasks to be achieved in order to establish a stable nomenclatural system that properly manages taxa typified by viable specimens. Furthermore, we propose setting up rules and defining the nomenclatural status of ex-type cultures under Chapter F, the section of the ICNafp that includes provisions specific to names of fungi.}, } @article {pmid39048683, year = {2024}, author = {Gauci, V and Pangala, SR and Shenkin, A and Barba, J and Bastviken, D and Figueiredo, V and Gomez, C and Enrich-Prast, A and Sayer, E and Stauffer, T and Welch, B and Elias, D and McNamara, N and Allen, M and Malhi, Y}, title = {Global atmospheric methane uptake by upland tree woody surfaces.}, journal = {Nature}, volume = {631}, number = {8022}, pages = {796-800}, pmid = {39048683}, issn = {1476-4687}, mesh = {*Atmosphere/chemistry ; *Forests ; *Methane/metabolism/analysis ; Taiga ; *Trees/chemistry/metabolism/microbiology ; Tropical Climate ; *Wood/chemistry/metabolism/microbiology ; Greenhouse Gases/analysis/metabolism ; Carbon Isotopes ; Forestry ; Global Warming/prevention & control/statistics & numerical data ; Greenhouse Effect/prevention & control/statistics & numerical data ; }, abstract = {Methane is an important greenhouse gas[1], but the role of trees in the methane budget remains uncertain[2]. Although it has been shown that wetland and some upland trees can emit soil-derived methane at the stem base[3,4], it has also been suggested that upland trees can serve as a net sink for atmospheric methane[5,6]. Here we examine in situ woody surface methane exchange of upland tropical, temperate and boreal forest trees. We find that methane uptake on woody surfaces, in particular at and above about 2 m above the forest floor, can dominate the net ecosystem contribution of trees, resulting in a net tree methane sink. Stable carbon isotope measurement of methane in woody surface chamber air and process-level investigations on extracted wood cores are consistent with methanotrophy, suggesting a microbially mediated drawdown of methane on and in tree woody surfaces and tissues. By applying terrestrial laser scanning-derived allometry to quantify global forest tree woody surface area, a preliminary first estimate suggests that trees may contribute 24.6-49.9 Tg of atmospheric methane uptake globally. Our findings indicate that the climate benefits of tropical and temperate forest protection and reforestation may be greater than previously assumed.}, } @article {pmid39048062, year = {2024}, author = {Kondak, S and Kondak, D and Kabadayi, O and Erdei, L and Rónavári, A and Kónya, Z and Galbács, G and Kolbert, Z}, title = {Current insights into the green synthesis, in planta characterization and phytoeffects of nickel nanoparticles and their agricultural implications.}, journal = {Environmental research}, volume = {260}, number = {}, pages = {119665}, doi = {10.1016/j.envres.2024.119665}, pmid = {39048062}, issn = {1096-0953}, mesh = {*Nickel/toxicity ; *Metal Nanoparticles/toxicity ; Plants/drug effects ; Agriculture ; Green Chemistry Technology ; }, abstract = {The intensifying production and release into the environment as well as the increasing potential in agricultural applications make the relationship between plants and nickel nanoparticles (Ni NPs) a relevant and timely topic. The aim of this review is to give an overview and discuss the latest findings about the relationship of Ni NPs and plants. Ni NPs can be synthesized using phytochemicals derived from plant parts in an environmentally friendly manner. There are several ways for these nanoparticles to enter plant cells and tissues. This can be demonstrated through various imaging and chemical mapping approaches (e.g., transmission electron microscopy, X-ray fluorescence spectroscopy etc.). NiO NPs affect plants at multiple levels, including subcellular, cellular, tissue, organ, and whole-plant levels. However, the effects of Ni NPs on plants' ecological partners (e.g., rhizobiome, pollinators) remain largely unknown despite their ecotoxicological significance. The main cause of the Ni NPs-triggered damages is the reactive oxygen species imbalance as a consequence of the modulation of antioxidants. In non-tolerant plants, the toxicity of NiO NPs can be mitigated by exogenous treatments such as the application of silicon, salicylic acid, or jasmonic acid, which induce defense mechanisms whereas Ni-hypertolerant plant species possess endogenous defense systems, such as cell wall modifications and nitrosative signaling against NiO NP stress. Research highlights the role of Ni NPs in managing fungal diseases, showcasing their antifungal properties against specific pathogens. Due to the essentiality of Ni, the application of Ni NPs as nanofertilizers might be promising and has recently started to come into view.}, } @article {pmid39047578, year = {2024}, author = {Maxion, A and Gaebler, AJ and Röhrig, R and Mathiak, K and Zweerings, J and Kutafina, E}, title = {Spectral changes in electroencephalography linked to neuroactive medications: A computational pipeline for data mining and analysis.}, journal = {Computer methods and programs in biomedicine}, volume = {255}, number = {}, pages = {108319}, doi = {10.1016/j.cmpb.2024.108319}, pmid = {39047578}, issn = {1872-7565}, mesh = {Humans ; *Electroencephalography/methods ; *Data Mining/methods ; Carbamazepine/therapeutic use/pharmacology ; Risperidone ; Antipsychotic Agents/pharmacology ; Anticonvulsants/pharmacology/therapeutic use ; Brain/drug effects ; }, abstract = {BACKGROUND AND OBJECTIVES: The increasing amount of open-access medical data provides new opportunities to gain clinically relevant information without recruiting new patients. We developed an open-source computational pipeline, that utilizes the publicly available electroencephalographic (EEG) data of the Temple University Hospital to identify EEG profiles associated with the usage of neuroactive medications. It facilitates access to the data and ensures consistency in data processing and analysis, thus reducing the risk of errors and creating comparable and reproducible results. Using this pipeline, we analyze the influence of common neuroactive medications on brain activity.

METHODS: The pipeline is constructed using easily controlled modules. The user defines the medications of interest and comparison groups. The data is downloaded and preprocessed, spectral features are extracted, and statistical group comparison with visualization through a topographic EEG map is performed. The pipeline is adjustable to answer a variety of research questions. Here, the effects of carbamazepine and risperidone were statistically compared with control data and with other medications from the same classes (anticonvulsants and antipsychotics).

RESULTS: The comparison between carbamazepine and the control group showed an increase in absolute and relative power for delta and theta, and a decrease in relative power for alpha, beta, and gamma. Compared to antiseizure medications, carbamazepine showed an increase in alpha and theta for absolute powers, and for relative powers an increase in alpha and theta, and a decrease in gamma and delta. Risperidone compared with the control group showed a decrease in absolute and relative power for alpha and beta and an increase in theta for relative power. Compared to antipsychotic medications, risperidone showed a decrease in delta for absolute powers. These results show good agreement with state-of-the-art research. The database allows to create large groups for many different medications. Additionally, it provides a collection of records labeled as "normal" after expert assessment, which is convenient for the creation of control groups.

CONCLUSIONS: The pipeline allows fast testing of different hypotheses regarding links between medications and EEG spectrum through ecological usage of readily available data. It can be utilized to make informed decisions about the design of new clinical studies.}, } @article {pmid39045996, year = {2024}, author = {Lima, AGCF and Ribeiro, CJN and Lima, SVMA and Barbosa, YM and Oliveira, IM and Araújo, KCGM}, title = {Space-time analysis of work-related musculoskeletal disorders in Brazil: an ecological study.}, journal = {Cadernos de saude publica}, volume = {40}, number = {7}, pages = {e00141823}, pmid = {39045996}, issn = {1678-4464}, mesh = {Humans ; Brazil/epidemiology ; *Musculoskeletal Diseases/epidemiology ; *Occupational Diseases/epidemiology ; *Spatio-Temporal Analysis ; Incidence ; Male ; Female ; Bayes Theorem ; Risk Factors ; Adult ; }, abstract = {This study aimed to analyze the incidence of work-related musculoskeletal disorders (WMSD) in Brazil from 2007 to 2019, examining the spatial, temporal, and spatiotemporal patterns of their occurrence. An ecological time series study was conducted using spatial analysis techniques. WMSD morbidity data from 2007 to 2019 were collected from the Brazilian Information System for Notificable Diseases of the Brazilian Health Informatics Department. Incidence rates were standardized and smoothed using the local empirical Bayes' theorem. Time trends were analyzed by segmented linear regression. Spatial analysis was performed using Moran's univariate global (I) and local (LISA) indexes. The spatiotemporal scan statistic was used to identify high-risk spatiotemporal clusters for WMSD. A total of 93,387 cases of WMSD were recorded in Brazil. Temporal trends showed an increase in all regions except the Northeast, which remained stable. The incidence of WMSD showed a spatial dependence, with spatial and space-time clusters identified, especially in the Southeast region, overlapping the largest economic-industrial center of the country. The spatiotemporal clustering observed in one region suggests the highest level of industrial and economic development. Our findings highlight the need to implement intersectoral surveillance policies, inspect working conditions, and invest in the prevention and promotion of workers' health.}, } @article {pmid39045504, year = {2024}, author = {Märtz, J and Tallian, A and Wikenros, C and Heeres, RW}, title = {"ClusterApp": A Shiny R application to guide cluster studies based on GPS data.}, journal = {Ecology and evolution}, volume = {14}, number = {7}, pages = {e11695}, pmid = {39045504}, issn = {2045-7758}, abstract = {The rapid evolution of GPS devices, and therefore, collection of GPS data can be used to investigate a wide variety of topics in wildlife research. The combination of remotely collected GPS data with on-the-ground field investigations is a powerful tool for exploring behavioral ecology. "GPS cluster studies" are aimed at pinpointing and investigating identified clusters in the field. Activity clusters can be based on various parameters (e.g., distance between GPS locations and the number of locations needed to establish a cluster), which are closely related to the set research questions. Variation in methods across years within the same study may result in data collection biases. Therefore, a streamlined method to parametrize, generate interactive maps, and extract activity cluster data using a predefined approach will limit biases, and make field work and data management straightforward for field technicians. We developed the "ClusterApp" Shiny application in the R software to facilitate a step-by-step guide to execute cluster analyses and data management of cluster studies on any species using GPS data. We illustrate the use of the "ClusterApp" with two location datasets constructed by data collected on brown bears (Ursus arctos) and gray wolves (Canis lupus).}, } @article {pmid39032255, year = {2024}, author = {Hossain, M and Wiegand, B and Reza, A and Chaudhuri, H and Mukhopadhyay, A and Yadav, A and Patra, PK}, title = {A machine learning approach to investigate the impact of land use land cover (LULC) changes on groundwater quality, health risks and ecological risks through GIS and response surface methodology (RSM).}, journal = {Journal of environmental management}, volume = {366}, number = {}, pages = {121911}, doi = {10.1016/j.jenvman.2024.121911}, pmid = {39032255}, issn = {1095-8630}, mesh = {*Groundwater/analysis ; *Machine Learning ; *Water Quality ; *Geographic Information Systems ; India ; Environmental Monitoring/methods ; Bayes Theorem ; Humans ; Agriculture ; }, abstract = {Groundwater resources are enormously affected by land use land cover (LULC) dynamics caused by increasing urbanisation, agricultural and household discharge as a result of global population growth. This study investigates the impact of decadal LULC changes in groundwater quality, human and ecological health from 2009 to 2021 in a diverse landscape, West Bengal, India. Using groundwater quality data from 479 wells in 2009 and 734 well in 2021, a recently proposed Water Pollution Index (WPI) was computed, and its geospatial distribution by a machine learning-based 'Empirical Bayesian Kriging' (EBK) tool manifested a decline in water quality since the number of excellent water category decreased from 30.5% to 28% and polluted water increased from 44% to 45%. ANOVA and Friedman tests revealed statistically significant differences (p < 0.0001) in year-wise water quality parameters as well as group comparisons for both years. Landsat 7 and 8 satellite images were used to classify the LULC types applying machine learning tools for both years, and were coupled with response surface methodology (RSM) for the first time, which revealed that the alteration of groundwater quality were attributed to LULC changes, e.g. WPI showed a positive correlation with built-up areas, village-vegetation cover, agricultural lands, and a negative correlation with surface water, barren lands, and forest cover. Expansion in built-up areas by 0.7%, and village-vegetation orchards by 2.3%, accompanied by a reduction in surface water coverage by 0.6%, and 2.4% in croplands caused a 1.5% drop in excellent water and 1% increase in polluted water category. However, ecological risks through the ecological risk index (ERI) exhibited a lower risk in 2021 attributed to reduced high-risk potential zones. This study highlights the potentiality in linking LULC and water quality changes using some advanced statistical tools like GIS and RSM for better management of water quality and landscape ecology.}, } @article {pmid39032150, year = {2024}, author = {Kim, J and Foo, JC and Murata, T and Togo, F}, title = {Reduced heart rate variability is related to fluctuations in psychological stress levels in daily life.}, journal = {Stress and health : journal of the International Society for the Investigation of Stress}, volume = {40}, number = {5}, pages = {e3447}, doi = {10.1002/smi.3447}, pmid = {39032150}, issn = {1532-2998}, support = {19K24283//Japan Society for the Promotion of Science/ ; 21K17681//Japan Society for the Promotion of Science/ ; 031L0190A//Bundesministerium für Bildung und Forschung/ ; }, mesh = {Humans ; *Heart Rate/physiology ; *Stress, Psychological/physiopathology/psychology ; Male ; Female ; Adult ; *Ecological Momentary Assessment ; Young Adult ; Affect/physiology ; Exercise/psychology/physiology ; }, abstract = {Laboratory-based studies have shown that psychological stress caused by response to various stressors triggers acute changes in the cardiovascular system. A better understanding is needed of the emerging evidence on temporal associations between psychological stress and cardiovascular responses in natural settings. This study examined the association of psychological stress and heart rate variability (HRV) in daily life, at high resolution over 2 weeks, taking the effect of physical activity into account. Participants (n = 34) completed ecological momentary assessments (EMA) 6 times per day, reporting levels of perceived stress, low-arousal negative affect (LNA), and high-arousal negative affect. Chest-mounted heart-rate monitors were worn to assess HRV. Multilevel models were used to examine the association between psychological stress levels and preceding/subsequent HRV. Reduced time domain HRV measures (mean and standard deviation of R-wave to R-wave intervals) during the prior hour predicted higher levels of perceived stress. Frequency domain HRV measures higher low to high frequency (LF/HF) and lower HF to total power (HF nu) ratios during the preceding 10 min predicted higher perceived stress levels, suggesting the dominance of sympathetic nervous system activity. EMA reports of higher perceived stress levels were associated with reduced time domain HRV measures during the following 10 min. On the other hand, higher LNA were related to increased HRV measures, such as lower LF/HF and higher HF nu during the following hour. The dynamic associations observed may have therapeutic implications for 'just-in-time' interventions in the management of daily stress and cardiovascular health.}, } @article {pmid39031697, year = {2024}, author = {Zembere, K and Jones, CM and Mthawanji, R and Nkolokosa, C and Kamwezi, R and Kalonde, PK and Stanton, MC}, title = {Small dams drive Anopheles abundance during the dry season in a high malaria burden area of Malawi.}, journal = {Medical and veterinary entomology}, volume = {38}, number = {4}, pages = {375-392}, doi = {10.1111/mve.12733}, pmid = {39031697}, issn = {1365-2915}, support = {215184/Z/19/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Animals ; *Anopheles/physiology ; Malawi ; *Seasons ; *Mosquito Vectors/physiology ; *Malaria/transmission ; *Population Density ; Larva/physiology/growth & development ; Female ; }, abstract = {This study explores the influence of small dams on the exposure to malaria vectors during the dry season in Kasungu district, Malawi, an area recently identified as high priority for malaria interventions by the National Malaria Control Programme. Small dam impoundments provide communities with a continuous supply of water for domestic and agricultural activities across sub-Saharan Africa and are considered vital to food security and climate change resilience. However, these permanent water bodies also create ideal breeding sites for mosquitoes in typically arid landscapes. The study focuses on a specific dam impoundment and its vicinity, aiming to assess its spatial and temporal influence on indoor vector densities. From May to August 2021, CDC light traps were used to measure indoor mosquito densities for two consecutive nights per month in three communities located at increasing distances from the dam (0, ~1 and ~2 km). Simultaneously, drone imagery was captured for each community, enabling the identification of additional standing water within approximately 400 m of selected households. Larval sampling was carried out within the impoundment periphery and in additional water bodies identified in the drone imagery. Generalised linear mixed models (GLMMs) were employed to analyse the indoor Anopheles abundance data, estimating the effects of household structure (open/closed eaves), month, temperature and water proximity on malaria vector exposure. Throughout 685 trapping nights, a total of 1256 mosquitoes were captured, with 33% (412) being female Anopheles. Among these, 91% were morphologically identified as Anopheles funestus s.l., and 5% as Anopheles gambiae s.l. Catches progressively decline in each consecutive trapping month as the environment became drier. This decline was much slower in Malangano, the community next to the dam, with abundance being notably higher in June and July. Further, the majority of An. gambiae s.l. were caught in May, with none identified in July and August. Anopheles larvae were found both in the impoundment and other smaller water bodies such as irrigation wells in each survey month; however, the presence of these smaller water bodies did not have a significant impact on adult female mosquito catches in the GLMM. The study concludes that proximity to the dam impoundment was the primary driver of differences between survey communities with the abundance in Chikhombwe (~1 km away) and Chiponde (~2 km away) being 0.35 (95% confidence interval [CI], 0.19-0.66) and 0.28 (95% CI, 0.16-0.47) lower than Malangano, respectively, after adjusting for other factors. These findings underscore the importance of targeted interventions, such as larval source management or housing improvements, near small dams to mitigate malaria transmission risks during the dry season. Further research is needed to develop cost-effective strategies for vector control within and around these impoundments.}, } @article {pmid39029911, year = {2024}, author = {Tyagi, S and Katara, P}, title = {Metatranscriptomics: A Tool for Clinical Metagenomics.}, journal = {Omics : a journal of integrative biology}, volume = {28}, number = {8}, pages = {394-407}, doi = {10.1089/omi.2024.0130}, pmid = {39029911}, issn = {1557-8100}, mesh = {*Metagenomics/methods ; *Microbiota/genetics ; Humans ; *Computational Biology/methods ; *Transcriptome/genetics ; Gene Expression Profiling/methods ; RNA, Ribosomal, 16S/genetics ; Metagenome/genetics ; }, abstract = {In the field of bioinformatics, amplicon sequencing of 16S rRNA genes has long been used to investigate community membership and taxonomic abundance in microbiome studies. As we can observe, shotgun metagenomics has become the dominant method in this field. This is largely owing to advancements in sequencing technology, which now allow for random sequencing of the entire genetic content of a microbiome. Furthermore, this method allows profiling both genes and the microbiome's membership. Although these methods have provided extensive insights into various microbiomes, they solely assess the existence of organisms or genes, without determining their active role within the microbiome. Microbiome scholarship now includes metatranscriptomics to decipher how a community of microorganisms responds to changing environmental conditions over a period of time. Metagenomic studies identify the microbes that make up a community but metatranscriptomics explores the diversity of active genes within that community, understanding their expression profile and observing how these genes respond to changes in environmental conditions. This expert review article offers a critical examination of the computational metatranscriptomics tools for studying the transcriptomes of microbial communities. First, we unpack the reasons behind the need for community transcriptomics. Second, we explore the prospects and challenges of metatranscriptomic workflows, starting with isolation and sequencing of the RNA community, then moving on to bioinformatics approaches for quantifying RNA features, and statistical techniques for detecting differential expression in a community. Finally, we discuss strengths and shortcomings in relation to other microbiome analysis approaches, pipelines, use cases and limitations, and contextualize metatranscriptomics as a tool for clinical metagenomics.}, } @article {pmid39027808, year = {2024}, author = {Falk, S and Poole, O and , and , and , and , and , and , and , }, title = {The genome sequence of a hoverfly, Cheilosia impressa (Loew, 1840).}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {74}, pmid = {39027808}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual male Cheilosia impressa (hoverfly; Arthropoda; Insecta; Diptera; Syrphidae). The genome sequence is 395.0 megabases in span. Most of the assembly is scaffolded into 6 chromosomal pseudomolecules, including the X sex chromosome. The mitochondrial genome has also been assembled and is 16.87 kilobases in length.}, } @article {pmid39026607, year = {2023}, author = {Boyes, D and Holland, PWH and , and , and , and , and , and , }, title = {The genome sequence of the Brindled Beauty, Lycia hirtaria (Clerck, 1759).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {303}, pmid = {39026607}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual male Lycia hirtaria (the Brindled Beauty; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 552.0 megabases in span. Most of the assembly is scaffolded into 14 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.58 kilobases in length.}, } @article {pmid39026606, year = {2023}, author = {Boyes, D and Crowley, LM and Boyes, C and , and , and , and , and , and , }, title = {The genome sequence of the Little Grey, Eudonia lacustrata (Panzer, 1804).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {302}, pmid = {39026606}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual male Eudonia lacustrata (the Little Grey; Arthropoda; Insecta; Lepidoptera; Crambidae). The genome sequence is 699.5 megabases in span. Most of the assembly is scaffolded into 30 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.29 kilobases in length. Gene annotation of this assembly on Ensembl identified 21,652 protein coding genes.}, } @article {pmid39026203, year = {2024}, author = {Piacenza, F and Di Rosa, M and Soraci, L and Montesanto, A and Corsonello, A and Cherubini, A and Fabbietti, P and Provinciali, M and Lisa, R and Bonfigli, AR and Filicetti, E and Greco, GI and Muglia, L and Lattanzio, F and Volpentesta, M and Biscetti, L}, title = {Interactions between patterns of multimorbidity and functional status among hospitalized older patients: a novel approach using cluster analysis and association rule mining.}, journal = {Journal of translational medicine}, volume = {22}, number = {1}, pages = {669}, pmid = {39026203}, issn = {1479-5876}, support = {RF-2013-02358848//Ministero della Salute/ ; }, mesh = {Humans ; Male ; Female ; *Multimorbidity ; Aged ; Cluster Analysis ; *Hospitalization ; Aged, 80 and over ; *Activities of Daily Living ; Functional Status ; Data Mining ; Retrospective Studies ; }, abstract = {BACKGROUND: Multimorbidity (MM) is generally defined as the presence of 2 or more chronic diseases in the same patient and seems to be frequently associated with frailty and poor quality of life. However, the complex interplay between MM and functional status in hospitalized older patients has not been fully elucidated so far. Here, we implemented a 2-step approach, combining cluster analysis and association rule mining to explore how patterns of MM and disease associations change as a function of disability.

METHODS: This retrospective cohort study included 3366 hospitalized older patients discharged from acute care units of Ancona and Cosenza sites of Italian National Institute on Aging (INRCA-IRCCS) between 2011 and 2017. Cluster analysis and association rule mining (ARM) were used to explore patterns of MM and disease associations in the whole population and after stratifying by dependency in activities of daily living (ADL) at discharge. Sensitivity analyses in men and women were conducted to test for robustness of study findings.

RESULTS: Out of 3366 included patients, 78% were multimorbid. According to functional status, 22.2% of patients had no disability in ADL (functionally independent group), 22.7% had 1 ADL dependency (mildly dependent group), and 57.4% 2 or more ADL impaired (moderately-severely dependent group). Two main MM clusters were identified in the whole general population and in single ADL groups. ARM revealed interesting within-cluster disease associations, characterized by high lift and confidence. Specifically, in the functionally independent group, the most significant ones involved atrial fibrillation (AF)-anemia and chronic kidney disease (CKD) (lift = 2.32), followed by coronary artery disease (CAD)-AF and heart failure (HF) (lift = 2.29); in patients with moderate-severe ADL disability, the most significant ARM involved CAD-HF and AF (lift = 1.97), thyroid dysfunction and AF (lift = 1.75), cerebrovascular disease (CVD)-CAD and AF (lift = 1.55), and hypertension-anemia and CKD (lift = 1.43).

CONCLUSIONS: Hospitalized older patients have high rates of MM and functional impairment. Combining cluster analysis to ARM may assist physicians in discovering unexpected disease associations in patients with different ADL status. This could be relevant in the view of individuating personalized diagnostic and therapeutic approaches, according to the modern principles of precision medicine.}, } @article {pmid39024004, year = {2024}, author = {Hernandez, R and Hoogendoorn, C and Gonzalez, JS and Pyatak, EA and Crespo-Ramos, G and Schneider, S}, title = {Reliability and Validity of Ecological Momentary Assessment Response Time-Based Measures of Emotional Clarity: Secondary Data Analysis.}, journal = {JMIR mental health}, volume = {11}, number = {}, pages = {e58352}, pmid = {39024004}, issn = {2368-7959}, support = {R01 DK121298/DK/NIDDK NIH HHS/United States ; P30 DK111022/DK/NIDDK NIH HHS/United States ; UL1 TR001855/TR/NCATS NIH HHS/United States ; UL1 TR000130/TR/NCATS NIH HHS/United States ; R01 AG068190/AG/NIA NIH HHS/United States ; U2C AG060408/AG/NIA NIH HHS/United States ; }, mesh = {Humans ; *Ecological Momentary Assessment ; Female ; Male ; Reproducibility of Results ; Adult ; *Emotions ; Middle Aged ; Diabetes Mellitus, Type 1/psychology ; Reaction Time/physiology ; Emotional Regulation/physiology ; Data Analysis ; Personal Satisfaction ; Surveys and Questionnaires ; Secondary Data Analysis ; }, abstract = {BACKGROUND: Emotional clarity has often been assessed with self-report measures, but efforts have also been made to measure it passively, which has advantages such as avoiding potential inaccuracy in responses stemming from social desirability bias or poor insight into emotional clarity. Response times (RTs) to emotion items administered in ecological momentary assessments (EMAs) may be an indirect indicator of emotional clarity. Another proposed indicator is the drift rate parameter, which assumes that, aside from how fast a person responds to emotion items, the measurement of emotional clarity also requires the consideration of how careful participants were in providing responses.

OBJECTIVE: This paper aims to examine the reliability and validity of RTs and drift rate parameters from EMA emotion items as indicators of individual differences in emotional clarity.

METHODS: Secondary data analysis was conducted on data from 196 adults with type 1 diabetes who completed a 2-week EMA study involving the completion of 5 to 6 surveys daily. If lower RTs and higher drift rates (from EMA emotion items) were indicators of emotional clarity, we hypothesized that greater levels (ie, higher clarity) should be associated with greater life satisfaction; lower levels of neuroticism, depression, anxiety, and diabetes distress; and fewer difficulties with emotion regulation. Because prior literature suggested emotional clarity could be valence specific, EMA items for negative affect (NA) and positive affect were examined separately.

RESULTS: Reliability of the proposed indicators of emotional clarity was acceptable with a small number of EMA prompts (ie, 4 to 7 prompts in total or 1 to 2 days of EMA surveys). Consistent with expectations, the average drift rate of NA items across multiple EMAs had expected associations with other measures, such as correlations of r=-0.27 (P<.001) with depression symptoms, r=-0.27 (P=.001) with anxiety symptoms, r=-0.15 (P=.03) with emotion regulation difficulties, and r=0.63 (P<.001) with RTs to NA items. People with a higher NA drift rate responded faster to NA emotion items, had greater subjective well-being (eg, fewer depression symptoms), and had fewer difficulties with overall emotion regulation, which are all aligned with the expectation for an emotional clarity measure. Contrary to expectations, the validities of average RTs to NA items, the drift rate of positive affect items, and RTs to positive affect items were not strongly supported by our results.

CONCLUSIONS: Study findings provided initial support for the validity of NA drift rate as an indicator of emotional clarity but not for that of other RT-based clarity measures. Evidence was preliminary because the sample size was not sufficient to detect small but potentially meaningful correlations, as the sample size of the diabetes EMA study was chosen for other more primary research questions. Further research on passive emotional clarity measures is needed.}, } @article {pmid39023004, year = {2024}, author = {Rillig, MC and Li, C and Rodríguez Del Río, Á and Zhu, YG and Jin, L}, title = {Elevated levels of antibiotic resistance genes as a factor of human-caused global environmental change.}, journal = {Global change biology}, volume = {30}, number = {7}, pages = {e17419}, doi = {10.1111/gcb.17419}, pmid = {39023004}, issn = {1365-2486}, support = {C5063-22G//Research Grants Council of Hong Kong/ ; 2021-DST-004//Ningbo S&T/ ; P0044024//Hong Kong Polytechnic University/ ; P0040336//Hong Kong Polytechnic University/ ; //Alexander-von-Humboldt Foundation/ ; }, mesh = {Humans ; *Drug Resistance, Microbial/genetics ; Anti-Bacterial Agents/pharmacology ; Climate Change ; Ecosystem ; Human Activities ; }, abstract = {Antibiotic resistance genes (ARGs) have moved into focus as a critically important response variable in global change biology, given the increasing environmental and human health threat posed by these genes. However, we propose that elevated levels of ARGs should also be considered a factor of global change, not just a response. We provide evidence that elevated levels of ARGs are a global change factor, since this phenomenon is linked to human activity, occurs globally, and affects biota. We explain why ARGs could be considered the global change factor, rather than the organisms containing them; and we highlight the difference between ARGs and the presence of antibiotics, which are not necessarily linked since elevated levels of ARGs are caused by multiple factors. Importantly, shifting the perspective to elevated levels of ARGs as a factor of global change opens new avenues of research, where ARGs can be the experimental treatment. This includes asking questions about how elevated ARG levels interact with other global change factors, or how ARGs influence ecosystem processes, biodiversity or trophic relationships. Global change biology stands to profit from this new framing in terms of capturing more completely the real extent of human impacts on this planet.}, } @article {pmid39018100, year = {2024}, author = {Corponi, F and Li, BM and Anmella, G and Valenzuela-Pascual, C and Mas, A and Pacchiarotti, I and Valentí, M and Grande, I and Benabarre, A and Garriga, M and Vieta, E and Young, AH and Lawrie, SM and Whalley, HC and Hidalgo-Mazzei, D and Vergari, A}, title = {Wearable Data From Subjects Playing Super Mario, Taking University Exams, or Performing Physical Exercise Help Detect Acute Mood Disorder Episodes via Self-Supervised Learning: Prospective, Exploratory, Observational Study.}, journal = {JMIR mHealth and uHealth}, volume = {12}, number = {}, pages = {e55094}, pmid = {39018100}, issn = {2291-5222}, mesh = {Humans ; *Supervised Machine Learning ; Prospective Studies ; *Wearable Electronic Devices/statistics & numerical data/standards ; Male ; Female ; *Mood Disorders/diagnosis/psychology ; Adult ; Exercise/psychology/physiology ; Universities/statistics & numerical data/organization & administration ; }, abstract = {BACKGROUND: Personal sensing, leveraging data passively and near-continuously collected with wearables from patients in their ecological environment, is a promising paradigm to monitor mood disorders (MDs), a major determinant of the worldwide disease burden. However, collecting and annotating wearable data is resource intensive. Studies of this kind can thus typically afford to recruit only a few dozen patients. This constitutes one of the major obstacles to applying modern supervised machine learning techniques to MD detection.

OBJECTIVE: In this paper, we overcame this data bottleneck and advanced the detection of acute MD episodes from wearables' data on the back of recent advances in self-supervised learning (SSL). This approach leverages unlabeled data to learn representations during pretraining, subsequently exploited for a supervised task.

METHODS: We collected open access data sets recording with the Empatica E4 wristband spanning different, unrelated to MD monitoring, personal sensing tasks-from emotion recognition in Super Mario players to stress detection in undergraduates-and devised a preprocessing pipeline performing on-/off-body detection, sleep/wake detection, segmentation, and (optionally) feature extraction. With 161 E4-recorded subjects, we introduced E4SelfLearning, the largest-to-date open access collection, and its preprocessing pipeline. We developed a novel E4-tailored transformer (E4mer) architecture, serving as the blueprint for both SSL and fully supervised learning; we assessed whether and under which conditions self-supervised pretraining led to an improvement over fully supervised baselines (ie, the fully supervised E4mer and pre-deep learning algorithms) in detecting acute MD episodes from recording segments taken in 64 (n=32, 50%, acute, n=32, 50%, stable) patients.

RESULTS: SSL significantly outperformed fully supervised pipelines using either our novel E4mer or extreme gradient boosting (XGBoost): n=3353 (81.23%) against n=3110 (75.35%; E4mer) and n=2973 (72.02%; XGBoost) correctly classified recording segments from a total of 4128 segments. SSL performance was strongly associated with the specific surrogate task used for pretraining, as well as with unlabeled data availability.

CONCLUSIONS: We showed that SSL, a paradigm where a model is pretrained on unlabeled data with no need for human annotations before deployment on the supervised target task of interest, helps overcome the annotation bottleneck; the choice of the pretraining surrogate task and the size of unlabeled data for pretraining are key determinants of SSL success. We introduced E4mer, which can be used for SSL, and shared the E4SelfLearning collection, along with its preprocessing pipeline, which can foster and expedite future research into SSL for personal sensing.}, } @article {pmid39015757, year = {2023}, author = {Boyes, D and Boyes, C and , and , and , and , and , and , }, title = {The genome sequence of the Wainscot Smudge, Ypsolopha scabrella (Linnaeus, 1761).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {341}, pmid = {39015757}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual male Ypsolopha scabrella (the Wainscot Smudge; Arthropoda; Insecta; Lepidoptera; Ypsolophidae). The genome sequence is 853.6 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 16.7 kilobases in length. Gene annotation of this assembly on Ensembl identified 20,594 protein coding genes.}, } @article {pmid39015615, year = {2024}, author = {Boyes, D and Lewis, OT and , and , and , and , and , and , and , }, title = {The genome sequence of the Mottled Pug, Eupithecia exiguata (Hübner, 1813).}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {65}, pmid = {39015615}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual male Eupithecia exiguata (the Mottled Pug; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 372.9 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 16.39 kilobases in length. Gene annotation of this assembly on Ensembl identified 11,194 protein coding genes.}, } @article {pmid39015613, year = {2024}, author = {Obbard, DJ and , and , and , and , and , and , }, title = {The genome sequence of a drosophilid fruit fly, Drosophila histrio (Meigen, 1830).}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {56}, pmid = {39015613}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual female Drosophila histrio (the drosophilid fruit fly; Arthropoda; Insecta; Diptera; Drosophilidae). The genome sequence is 189.2 megabases in span. Most of the assembly is scaffolded into 5 chromosomal pseudomolecules, including the X sex chromosome. The mitochondrial genome has also been assembled and is 16.02 kilobases in length.}, } @article {pmid39015611, year = {2024}, author = {Boyes, D and Boyes, C and , and , and , and , and , and , and , }, title = {The genome sequence of the Dotted Grey Groundling, Athrips mouffetella (Linnaeus, 1758).}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {42}, pmid = {39015611}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual female Athrips mouffetella (the Dotted Grey Groundling; Arthropoda; Insecta; Lepidoptera; Gelechiidae). The genome sequence is 869.7 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z and W sex chromosomes. The mitochondrial genome has also been assembled and is 15.23 kilobases in length. Gene annotation of this assembly on Ensembl identified 22,889 protein coding genes.}, } @article {pmid39014019, year = {2024}, author = {Cavaliere, M and Yang, G and De Dreu, CKW and Gross, J}, title = {Cooperation and social organization depend on weighing private and public reputations.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {16443}, pmid = {39014019}, issn = {2045-2322}, mesh = {Humans ; *Cooperative Behavior ; Social Networking ; Game Theory ; Interpersonal Relations ; }, abstract = {To avoid exploitation by defectors, people can use past experiences with others when deciding to cooperate or not ('private information'). Alternatively, people can derive others' reputation from 'public' information provided by individuals within the social network. However, public information may be aligned or misaligned with one's own private experiences and different individuals, such as 'friends' and 'enemies', may have different opinions about the reputation of others. Using evolutionary agent-based simulations, we examine how cooperation and social organization is shaped when agents (1) prioritize private or public information about others' reputation, and (2) integrate others' opinions using a friend-focused or a friend-and-enemy focused heuristic (relying on reputation information from only friends or also enemies, respectively). When agents prioritize public information and rely on friend-and-enemy heuristics, we observe polarization cycles marked by high cooperation, invasion by defectors, and subsequent population fragmentation. Prioritizing private information diminishes polarization and defector invasions, but also results in limited cooperation. Only when using friend-focused heuristics and following past experiences or the recommendation of friends create prosperous and stable populations based on cooperation. These results show how combining one's own experiences and the opinions of friends can lead to stable and large-scale cooperation and highlight the important role of following the advice of friends in the evolution of group cooperation.}, } @article {pmid39008135, year = {2024}, author = {Urbano, F and Viterbi, R and Pedrotti, L and Vettorazzo, E and Movalli, C and Corlatti, L}, title = {Correction to: Enhancing biodiversity conservation and monitoring in protected areas through efficient data management.}, journal = {Environmental monitoring and assessment}, volume = {196}, number = {8}, pages = {733}, doi = {10.1007/s10661-024-12886-7}, pmid = {39008135}, issn = {1573-2959}, } @article {pmid39007251, year = {2024}, author = {Pili, AN and Leroy, B and Measey, JG and Farquhar, JE and Toomes, A and Cassey, P and Chekunov, S and Grenié, M and van Winkel, D and Maria, L and Diesmos, MLL and Diesmos, AC and Zurell, D and Courchamp, F and Chapple, DG}, title = {Forecasting potential invaders to prevent future biological invasions worldwide.}, journal = {Global change biology}, volume = {30}, number = {7}, pages = {e17399}, doi = {10.1111/gcb.17399}, pmid = {39007251}, issn = {1365-2486}, support = {DP210103050//Australian Research Council/ ; FT200100108//Australian Research Council/ ; IL230100175//Australian Research Council/ ; //Monash University Faculty of Science's Dean's Postgraduate Research Scholarship and Dean's International Postgraduate Research Scholarship, and by Monash University Graduate Research Office's Graduate Research Completion Award and Post-Graduate Publication Award/ ; BIFA3_026//the Philippine Department of Environment and Natural Resources FORIS project and the Global Biodiversity Information Facility Biodiversity Fund for Asia Project/ ; }, mesh = {*Introduced Species ; Animals ; *Forecasting ; *Reptiles/physiology ; *Amphibians/physiology ; Risk Assessment/methods ; Models, Theoretical ; Models, Biological ; }, abstract = {The ever-increasing and expanding globalisation of trade and transport underpins the escalating global problem of biological invasions. Developing biosecurity infrastructures is crucial to anticipate and prevent the transport and introduction of invasive alien species. Still, robust and defensible forecasts of potential invaders are rare, especially for species without known invasion history. Here, we aim to support decision-making by developing a quantitative invasion risk assessment tool based on invasion syndromes (i.e., generalising typical attributes of invasive alien species). We implemented a workflow based on 'Multiple Imputation with Chain Equation' to estimate invasion syndromes from imputed datasets of species' life-history and ecological traits and macroecological patterns. Importantly, our models disentangle the factors explaining (i) transport and introduction and (ii) establishment. We showcase our tool by modelling the invasion syndromes of 466 amphibians and reptile species with invasion history. Then, we project these models to amphibians and reptiles worldwide (16,236 species [c.76% global coverage]) to identify species with a risk of being unintentionally transported and introduced, and risk of establishing alien populations. Our invasion syndrome models showed high predictive accuracy with a good balance between specificity and generality. Unintentionally transported and introduced species tend to be common and thrive well in human-disturbed habitats. In contrast, those with established alien populations tend to be large-sized, are habitat generalists, thrive well in human-disturbed habitats, and have large native geographic ranges. We forecast that 160 amphibians and reptiles without known invasion history could be unintentionally transported and introduced in the future. Among them, 57 species have a high risk of establishing alien populations. Our reliable, reproducible, transferable, statistically robust and scientifically defensible quantitative invasion risk assessment tool is a significant new addition to the suite of decision-support tools needed for developing a future-proof preventative biosecurity globally.}, } @article {pmid39004905, year = {2024}, author = {Herraiz, C and Triguero-Ocaña, R and Laguna, E and Jiménez-Ruiz, S and Peralbo-Moreno, A and Martínez-López, B and García-Bocanegra, I and Risalde, MÁ and Vicente, J and Acevedo, P}, title = {Movement-driven modelling reveals new patterns in disease transmission networks.}, journal = {The Journal of animal ecology}, volume = {93}, number = {9}, pages = {1275-1287}, doi = {10.1111/1365-2656.14142}, pmid = {39004905}, issn = {1365-2656}, support = {PID2019-111699RB-I00//Ministerio de Ciencia e Innovación/ ; AGL2013-48523-C3-1-R//Ministerio de Economía y Competitividad/ ; AGL2016-76358-R//Ministerio de Economía y Competitividad/ ; //European Social Fund/ ; //Government of Castilla-La Mancha/ ; //University of Castilla-La Mancha/ ; }, mesh = {Animals ; Cattle ; Swine ; *Models, Biological ; Spain ; Geographic Information Systems ; Tuberculosis, Bovine/transmission/microbiology ; Swine Diseases/transmission/microbiology ; Movement ; }, abstract = {Interspecific interactions are highly relevant in the potential transmission of shared pathogens in multi-host systems. In recent decades, several technologies have been developed to study pathogen transmission, such as proximity loggers, GPS tracking devices and/or camera traps. Despite the diversity of methods aimed at detecting contacts, the analysis of transmission risk is often reduced to contact rates and the probability of transmission given the contact. However, the latter process is continuous over time and unique for each contact, and is influenced by the characteristics of the contact and the pathogen's relationship with both the host and the environment. Our objective was to assess whether a more comprehensive approach, using a movement-based model which assigns a unique transmission risk to each contact by decomposing transmission into contact formation, contact duration and host characteristics, could reveal disease transmission dynamics that are not detected with more traditional approaches. The model was built from GPS-collar data from two management systems in Spain where animal tuberculosis (TB) circulates: a national park with extensively reared endemic cattle, and an area with extensive free-range pigs and cattle farms. In addition, we evaluated the effect of the GPS device fix rate on the performance of the model. Different transmission dynamics were identified between both management systems. Considering the specific conditions under which each contact occurs (i.e. whether the contact is direct or indirect, its duration, the hosts characteristics, the environmental conditions, etc.) resulted in the identification of different transmission dynamics compared to using only contact rates. We found that fix intervals greater than 30 min in the GPS tracking data resulted in missed interactions, and intervals greater than 2 h may be insufficient for epidemiological purposes. Our study shows that neglecting the conditions under which each contact occurs may result in a misidentification of the real role of each species in disease transmission. This study describes a clear and repeatable framework to study pathogen transmission from GPS data and provides further insights to understand how TB is maintained in multi-host systems in Mediterranean environments.}, } @article {pmid39004875, year = {2024}, author = {Taylor, A and Sigona, A and Kelly, M}, title = {Centering Amah Mutsun voices in the analysis of a culturally important, fire-managed coastal grassland.}, journal = {Ecological applications : a publication of the Ecological Society of America}, volume = {34}, number = {6}, pages = {e3014}, doi = {10.1002/eap.3014}, pmid = {39004875}, issn = {1051-0761}, support = {//Critical Mission Studies Grant program of the University of California/ ; //Joseph A. Myers Center for Research on Native American Issues, UC Berkeley/ ; //California Native Plant Society (both statewide and from the Santa Clara Valley chapter)/ ; //UC Berkeley Chapter of Sigma Xi/ ; //California Native Grasslands Association/ ; //Department of Environmental Science, Policy, and Management at UC Berkeley/ ; //University of California Graduate Division Fellowship/ ; //Phi Beta Kappa Fellowship, UC Berkeley/ ; //Inter-institutional Network for Food, Agriculture and Sustainability and Intertribal Agriculture Council Tribal Fellowship/ ; //UC Berkeley Graduate Fellowship in Climate Equity/ ; //Ford Foundation Predoctoral Fellowship Program/ ; //Wilderness Society Scholarship/ ; //UC Berkeley Chancellor's Fellowship/ ; }, mesh = {*Grassland ; California ; *Fires ; *Conservation of Natural Resources ; Humans ; Wildfires ; Indigenous Peoples ; }, abstract = {Indigenous communities throughout California, USA, are increasingly advocating for and practicing cultural fire stewardship, leading to a host of social, cultural, and ecological benefits. Simultaneously, state agencies are recognizing the importance of controlled burning and cultural fire as a means of reducing the risk of severe wildfire while benefiting fire-adapted ecosystems. However, much of the current research on the impacts of controlled burning ignores the cultural importance of these ecosystems, and risks further marginalizing Indigenous knowledge systems. Our work adds a critical Indigenous perspective to the study of controlled burning in California's unique coastal grasslands, one of the most biodiverse and endangered ecosystems in the country. In this study, we partnered with the Amah Mutsun Tribal Band to investigate how the abundance and occurrence of shrubs, cultural plants, and invasive plants differed among three adjacent coastal grasslands with varying fire histories. These three sites are emblematic of the state's diverging approaches to grassland management: fire suppression, fire suppression followed by wildfire, and an exceedingly rare example of a grassland that has been repeatedly burned approximately every 2 years for more than 30 years. We found that Danthonia californica was significantly more abundant on the burned sites, whereas all included shrub species (Baccharis pilularis, Frangula californica, and Rubus ursinus) were significantly more abundant on the site with no recorded fire, results that have important implications for future cultural revitalization efforts and the loss of coastal grasslands to shrub encroachment. In addition to conducting a culturally relevant vegetation survey, we used Sentinel-2 satellite imagery to compare the relative severities of the two most recent fire events within the study area. Critically, we used interviews with Amah Mutsun tribal members to contextualize the results of our vegetation survey and remote sensing analysis, and to investigate how cultural burning contrasts from typical Western fire management approaches in this region. Our study is a novel example of how interviews, field data, and satellite imagery can be combined to gain a deeper ecological and cultural understanding of fire in California's endangered coastal grasslands.}, } @article {pmid39004446, year = {2024}, author = {Fummey, E and Navarro, P and Plazzer, JP and Frayling, IM and Knott, S and Tenesa, A}, title = {Estimating cancer risk in carriers of Lynch syndrome variants in UK Biobank.}, journal = {Journal of medical genetics}, volume = {61}, number = {9}, pages = {861-869}, pmid = {39004446}, issn = {1468-6244}, mesh = {Humans ; *Colorectal Neoplasms, Hereditary Nonpolyposis/genetics/epidemiology ; Female ; United Kingdom/epidemiology ; *Biological Specimen Banks ; Middle Aged ; *DNA Mismatch Repair/genetics ; *Genetic Predisposition to Disease ; Aged ; Heterozygote ; Exome Sequencing ; Incidence ; Adult ; Breast Neoplasms/genetics/epidemiology ; Endometrial Neoplasms/genetics/epidemiology ; DNA-Binding Proteins/genetics ; MutL Protein Homolog 1/genetics ; UK Biobank ; MutS Homolog 2 Protein ; }, abstract = {UNLABELLED: BackgroundLynch syndrome (LS) is an inherited cancer predisposition syndrome caused by genetic variants affecting DNA mismatch repair (MMR) genes MLH1, MSH2, MSH6 and PMS2 Cancer risk in LS is estimated from cohorts of individuals ascertained by individual or family history of cancer, which may upwardly bias estimates.

METHODS: 830 carriers of pathogenic or likely pathogenic (path_MMR) MMR gene variants classified by InSiGHT were identified in 454 756 UK Biobank (UKB) participants using whole-exome sequence. Nelson-Aalen survival analysis was used to estimate cumulative incidence of colorectal, endometrial and breast cancer (BC).

RESULTS: Cumulative incidence of colorectal and endometrial cancer (EC) by age 70 years was elevated in path_MMR carriers compared with non-carriers (colorectal: 11.8% (95% confidence interval (CI): 9.5% to 14.6%) vs 1.7% (95% CI: 1.6% to 1.7%), endometrial: 13.4% (95% CI: 10.2% to 17.6%) vs 1.0% (95% CI: 0.9% to 1.0%)), but the magnitude of this increase differed between genes. Cumulative BC incidence by age 70 years was not elevated in path_MMR carriers compared with non-carriers (8.9% (95% CI: 6.3% to 12.4%) vs 7.5% (95% CI: 7.4% to 7.6%)). Cumulative cancer incidence estimates in UKB were similar to estimates from the Prospective Lynch Syndrome Database for all genes and cancers, except there was no evidence for elevated EC risk in carriers of pathogenic PMS2 variants in UKB.

CONCLUSION: These results support offering incidentally identified carriers of any path_MMR surveillance to manage colorectal cancer risk. Incidentally identified carriers of pathogenic variants in MLH1, MSH2 and MSH6 would also benefit from interventions to reduce EC risk. The results suggest that BC is not an LS-related cancer.}, } @article {pmid39004058, year = {2024}, author = {Guo, J and Jin, Y and Liu, S and Li, T and Ji, D and Hou, C and Tang, H}, title = {Investigation of the causes and mechanisms of hypoxia in the central Bohai Sea in the summer of 2022.}, journal = {Marine pollution bulletin}, volume = {206}, number = {}, pages = {116710}, doi = {10.1016/j.marpolbul.2024.116710}, pmid = {39004058}, issn = {1879-3363}, mesh = {*Seasons ; China ; *Eutrophication ; *Environmental Monitoring ; *Oceans and Seas ; Seawater/chemistry ; Animals ; Temperature ; }, abstract = {The deep-water area in the central Bohai Sea (BS) serves as a spawning ground and nursery for fish, shrimp, and crabs. Frequent hypoxia will affect the ecological environment in the central BS. Data from an on-site investigation of the central BS in the spring and summer of 2022 were used to analyze the relevant factors generating the occurrence of hypoxia in the central BS through the eutrophication index E, apparent oxygen consumption (AOU), and Spearman correlation. The hypoxia area was largely distributed in the study area's deep water section, and stratification was the main cause of hypoxia at the bottom. Organic matter mineralization, degradation, and biological respiration further exacerbated the hypoxia. In the summer of 2022, temperature stratification was the dominant factor influencing hypoxia.}, } @article {pmid39001963, year = {2024}, author = {Lu, Y and Xiao, X and Liang, Y and Li, J and Guo, C and Xu, L and Liu, Q and Xiao, Y and Zhou, S}, title = {Distribution and transformation of potentially toxic elements in cracks under coal mining disturbance in farmland.}, journal = {Environmental geochemistry and health}, volume = {46}, number = {9}, pages = {312}, pmid = {39001963}, issn = {1573-2983}, support = {52130402//State Key Program of National Natural Science Foundation of China/ ; }, mesh = {*Soil Pollutants/analysis/toxicity ; *Coal Mining ; *Environmental Monitoring ; *Metals, Heavy/analysis/toxicity ; Soil/chemistry ; Farms ; Risk Assessment ; }, abstract = {The ground cracks resulting from coal mining activities induce alterations in the physical and chemical characteristics of soil. However, limited knowledge exists regarding the impact of subsidence caused by coal mining on the distribution of potentially toxic elements (PTEs) fractions in farmland soil. In this study, we collected 19 soil profiles at varying depths from the soil surface and at horizontal distances of 0, 1, 2, and 5 m from the vertical crack. Using BCR extraction fractionation, we determined the geochemical fractions and total concentrations of Chromium (Cr), nickel (Ni), copper (Cu), zinc (Zn), arsenic (As), cadmium (Cd) and lead (Pb) to investigate their ecological risk, spatial fraction distribution, and main influencing factors. Results showed that the E r i values of Cd appearing in 68.7% of the samples were higher than 40 and less than 80, presented a moderate ecological risk. Chromium (Cr), nickel (Ni), copper (Cu), zinc (Zn), arsenic (As), and lead (Pb) were mainly bound to residual fractions (> 60%) with lower mobility and Cd was dominated by F1 (acid-soluble fractions, 50%) and F2 (reducible fractions, 29%) in surface soil (0-20 cm). The geochemical fractionation revealed that the mobile fractions (F1-acid-soluble and F2-reducible) of PTEs were primarily located near the crack, influenced by available potassium. In contrast, the less mobile fractions (F3-oxidizable and F4-residual) exhibited higher concentrations at distances of 2 and 5 m from the crack, except for arsenic, influenced by the presence of clay particles and available phosphorus.}, } @article {pmid39001714, year = {2024}, author = {Williams, TA and Davin, AA and Szánthó, LL and Stamatakis, A and Wahl, NA and Woodcroft, BJ and Soo, RM and Eme, L and Sheridan, PO and Gubry-Rangin, C and Spang, A and Hugenholtz, P and Szöllősi, GJ}, title = {Phylogenetic reconciliation: making the most of genomes to understand microbial ecology and evolution.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {39001714}, issn = {1751-7370}, support = {GBMF9741//Gordon and Betty Moore Foundation/ ; 714774//European Union's Horizon 2020 Research and Innovation Programme/ ; /ERC_/European Research Council/International ; 947317//European Union's Horizon 2020 Research and Innovation Programme/ ; 735929LPI//Simons Foundation/ ; FL150100038//Australian Research Council Laureate Fellowship/ ; 812811//Simons Foundation/ ; 101087081//European Union's Horizon Europe ERA Chair Program/ ; URF150571//Royal Society University Research Fellowship/ ; }, mesh = {*Phylogeny ; *Archaea/genetics/classification ; Bacteria/genetics/classification ; Evolution, Molecular ; Genome, Bacterial ; Symbiosis ; Ecology ; }, abstract = {In recent years, phylogenetic reconciliation has emerged as a promising approach for studying microbial ecology and evolution. The core idea is to model how gene trees evolve along a species tree and to explain differences between them via evolutionary events including gene duplications, transfers, and losses. Here, we describe how phylogenetic reconciliation provides a natural framework for studying genome evolution and highlight recent applications including ancestral gene content inference, the rooting of species trees, and the insights into metabolic evolution and ecological transitions they yield. Reconciliation analyses have elucidated the evolution of diverse microbial lineages, from Chlamydiae to Asgard archaea, shedding light on ecological adaptation, host-microbe interactions, and symbiotic relationships. However, there are many opportunities for broader application of the approach in microbiology. Continuing improvements to make reconciliation models more realistic and scalable, and integration of ecological metadata such as habitat, pH, temperature, and oxygen use offer enormous potential for understanding the rich tapestry of microbial life.}, } @article {pmid39000743, year = {2024}, author = {Macchia, A and Marinelli, L and Barbaccia, FI and de Caro, T and Hansen, A and Schuberthan, LM and Izzo, FC and Pintus, V and Testa Chiari, K and La Russa, MF}, title = {Mattel's ©Barbie: Preventing Plasticizers Leakage in PVC Artworks and Design Objects through Film-Forming Solutions.}, journal = {Polymers}, volume = {16}, number = {13}, pages = {}, pmid = {39000743}, issn = {2073-4360}, abstract = {The main conservation problem of p-PVC artworks is phthalate-based plasticizer migration. Phthalate migration from the bulk to the surface of the materials leads to the formation of a glossy and oily film on the outer layers, ultimately reducing the flexibility of the material. This study aimed to develop a removable coating for the preservation of contemporary artworks and design objects made of plasticized polyvinyl chloride (p-PVC). Several coatings incorporating chitosan, collagen, and cellulose ethers were assessed as potential barriers to inhibiting plasticizer migration. Analytical techniques including optical microscopy (OM), ultraviolet/visible/near-infrared spectroscopy (UV/Vis/NIR), Fourier transform infrared spectroscopy with attenuated total reflection (FTIR-ATR), and scanning electron microscopy (SEM) were utilized to evaluate the optical and chemical stability of selected coating formulations applied to laboratory p-PVC sheet specimens. Subsequently, formulations were tested on a real tangible example of a design object, ©Barbie doll, characterized by the prevalent issue of plasticizer migration. Furthermore, the results obtained with the tested formulations were evaluated by a group of conservators using a tailored survey. Finally, a suitable coating formulation capable of safeguarding plastic substrates was suggested.}, } @article {pmid39000053, year = {2024}, author = {Wang, XY and Ren, CX and Fan, QW and Xu, YP and Wang, LW and Mao, ZL and Cai, XZ}, title = {Integrated Assays of Genome-Wide Association Study, Multi-Omics Co-Localization, and Machine Learning Associated Calcium Signaling Genes with Oilseed Rape Resistance to Sclerotinia sclerotiorum.}, journal = {International journal of molecular sciences}, volume = {25}, number = {13}, pages = {}, pmid = {39000053}, issn = {1422-0067}, support = {2021C02064//Zhejiang Science and Technology Major Program on Agricultural New Variety Breeding/ ; LZ18C140002//Zhejiang Provincial Natural Science Foundation of China/ ; 324CXTD430//Hainan Provincial Natural Science Foundation of China/ ; }, mesh = {*Ascomycota/pathogenicity ; *Machine Learning ; *Disease Resistance/genetics ; *Genome-Wide Association Study ; *Plant Diseases/microbiology/genetics ; *Brassica napus/genetics/microbiology/immunology ; *Calcium Signaling/genetics ; Polymorphism, Single Nucleotide ; Quantitative Trait Loci ; Genomics/methods ; Multiomics ; }, abstract = {Sclerotinia sclerotiorum (Ss) is one of the most devastating fungal pathogens, causing huge yield loss in multiple economically important crops including oilseed rape. Plant resistance to Ss pertains to quantitative disease resistance (QDR) controlled by multiple minor genes. Genome-wide identification of genes involved in QDR to Ss is yet to be conducted. In this study, we integrated several assays including genome-wide association study (GWAS), multi-omics co-localization, and machine learning prediction to identify, on a genome-wide scale, genes involved in the oilseed rape QDR to Ss. Employing GWAS and multi-omics co-localization, we identified seven resistance-associated loci (RALs) associated with oilseed rape resistance to Ss. Furthermore, we developed a machine learning algorithm and named it Integrative Multi-Omics Analysis and Machine Learning for Target Gene Prediction (iMAP), which integrates multi-omics data to rapidly predict disease resistance-related genes within a broad chromosomal region. Through iMAP based on the identified RALs, we revealed multiple calcium signaling genes related to the QDR to Ss. Population-level analysis of selective sweeps and haplotypes of variants confirmed the positive selection of the predicted calcium signaling genes during evolution. Overall, this study has developed an algorithm that integrates multi-omics data and machine learning methods, providing a powerful tool for predicting target genes associated with specific traits. Furthermore, it makes a basis for further understanding the role and mechanisms of calcium signaling genes in the QDR to Ss.}, } @article {pmid38997687, year = {2024}, author = {Prakofjewa, J and Sartori, M and Šarka, P and Kalle, R and Pieroni, A and Sõukand, R}, title = {Knowledge in motion: temporal dynamics of wild food plant use in the Polish-Lithuanian-Belarusian border region.}, journal = {Journal of ethnobiology and ethnomedicine}, volume = {20}, number = {1}, pages = {65}, pmid = {38997687}, issn = {1746-4269}, support = {grant agreement No 714874//European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme/ ; grant agreement No 714874//European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme/ ; grant agreement No 714874//European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme/ ; grant agreement No 714874//European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme/ ; grant agreement No 714874//European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme/ ; grant agreement No 714874//European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme/ ; }, mesh = {Lithuania ; Poland ; *Plants, Edible/classification ; Republic of Belarus ; Humans ; Knowledge ; Ethnobotany ; }, abstract = {BACKGROUND: Understanding how Local Ecological Knowledge (LEK) evolves over time is crucial for fostering social and environmental responsibility. This study aims to develop a conceptual model of plant knowledge circulation, providing insights into the temporal dynamics of LEK in the Polish-Lithuanian-Belarusian border region. It explores the key patterns and driving forces behind changes in the use of wild plants for food.

METHODS: Field research was conducted in 60 rural settlements across Podlasie Voivodeship (Poland), Vilnius Region (Lithuania), and Hrodna Region (Belarus). This included 200 semi-structured interviews and participant observation among two local communities, Lithuanians and Poles. To assess the temporal dynamics of wild food use, we performed a cross-ethnic, cross-border analysis over time, dividing the data into three major temporal dimensions: past, continuous, and recently acquired uses.

RESULTS: Of the 72 wild plant taxa reported by Poles or Lithuanians in the Polish-Lithuanian-Belarusian borderland, 47 were continuously used for food, 58 were utilised in the past, and 41 were recently acquired. Cross-country trends were similar, with Poland showing more past uses. Diachronic comparisons between Poles and Lithuanians in each studied country revealed no significant differences. Recently acquired taxa overlapped considerably with those used continuously and in the past. The most diversely utilised taxa showed the greatest overlaps. By observing the movement of specific plant taxa within various time dimensions, we distinguished overlapping flow variations: retention (3 taxa), decay (11), invention (8), stagnation (17), revitalisation (6), re-invention (3), and knowledge in motion (24). Shifts in the use of wild food plants were influenced by changes in environmental conditions, governmental policies, cultural practices, and economic factors.

CONCLUSION: The findings of this study have important implications for improving methods of tracking changes in LEK and enhancing our understanding of the relationship between people and nature. Our results underscore the importance of considering knowledge circulation over time in different directions. Recognising the various stages of knowledge circulation might help in pursuing sustainable solutions that balance the needs of human communities with environmental protection.}, } @article {pmid38995977, year = {2024}, author = {Rosenblatt, E and Cook, JD and DiRenzo, GV and Grant, EHC and Arce, F and Pepin, KM and Rudolph, FJ and Runge, MC and Shriner, S and Walsh, DP and Mosher, BA}, title = {Epidemiological modeling of SARS-CoV-2 in white-tailed deer (Odocoileus virginianus) reveals conditions for introduction and widespread transmission.}, journal = {PLoS computational biology}, volume = {20}, number = {7}, pages = {e1012263}, pmid = {38995977}, issn = {1553-7358}, mesh = {Animals ; *Deer/virology ; *COVID-19/transmission/epidemiology/veterinary/virology ; *SARS-CoV-2 ; Humans ; Epidemiological Models ; Animals, Wild/virology ; Computational Biology ; Disease Outbreaks/veterinary/statistics & numerical data ; Zoonoses/transmission/epidemiology/virology ; }, abstract = {Emerging infectious diseases with zoonotic potential often have complex socioecological dynamics and limited ecological data, requiring integration of epidemiological modeling with surveillance. Although our understanding of SARS-CoV-2 has advanced considerably since its detection in late 2019, the factors influencing its introduction and transmission in wildlife hosts, particularly white-tailed deer (Odocoileus virginianus), remain poorly understood. We use a Susceptible-Infected-Recovered-Susceptible epidemiological model to investigate the spillover risk and transmission dynamics of SARS-CoV-2 in wild and captive white-tailed deer populations across various simulated scenarios. We found that captive scenarios pose a higher risk of SARS-CoV-2 introduction from humans into deer herds and subsequent transmission among deer, compared to wild herds. However, even in wild herds, the transmission risk is often substantial enough to sustain infections. Furthermore, we demonstrate that the strength of introduction from humans influences outbreak characteristics only to a certain extent. Transmission among deer was frequently sufficient for widespread outbreaks in deer populations, regardless of the initial level of introduction. We also explore the potential for fence line interactions between captive and wild deer to elevate outbreak metrics in wild herds that have the lowest risk of introduction and sustained transmission. Our results indicate that SARS-CoV-2 could be introduced and maintained in deer herds across a range of circumstances based on testing a range of introduction and transmission risks in various captive and wild scenarios. Our approach and findings will aid One Health strategies that mitigate persistent SARS-CoV-2 outbreaks in white-tailed deer populations and potential spillback to humans.}, } @article {pmid38994633, year = {2024}, author = {Gómez-García, A and Prinz, AK and Jiménez, DAA and Zamora, WJ and Barazorda-Ccahuana, HL and Chávez-Fumagalli, MÁ and Valli, M and Andricopulo, AD and da S Bolzani, V and Olmedo, DA and Solís, PN and Núñez, MJ and Rodríguez Pérez, JR and Sánchez, HAV and Cortés Hernández, HF and Mosquera Martinez, OM and Koch, O and Medina-Franco, JL}, title = {Updating and profiling the natural product-likeness of Latin American compound libraries.}, journal = {Molecular informatics}, volume = {43}, number = {7}, pages = {e202400052}, doi = {10.1002/minf.202400052}, pmid = {38994633}, issn = {1868-1751}, mesh = {*Biological Products/chemistry/pharmacology ; Latin America ; Small Molecule Libraries/pharmacology/chemistry ; Drug Discovery ; Cheminformatics ; Databases, Chemical ; }, abstract = {Compound databases of natural products play a crucial role in drug discovery and development projects and have implications in other areas, such as food chemical research, ecology and metabolomics. Recently, we put together the first version of the Latin American Natural Product database (LANaPDB) as a collective effort of researchers from six countries to ensemble a public and representative library of natural products in a geographical region with a large biodiversity. The present work aims to conduct a comparative and extensive profiling of the natural product-likeness of an updated version of LANaPDB and the individual ten compound databases that form part of LANaPDB. The natural product-likeness profile of the Latin American compound databases is contrasted with the profile of other major natural product databases in the public domain and a set of small-molecule drugs approved for clinical use. As part of the extensive characterization, we employed several chemoinformatics metrics of natural product likeness. The results of this study will capture the attention of the global community engaged in natural product databases, not only in Latin America but across the world.}, } @article {pmid38992177, year = {2024}, author = {Alvarez-Mora, I and Arturi, K and Béen, F and Buchinger, S and El Mais, AER and Gallampois, C and Hahn, M and Hollender, J and Houtman, C and Johann, S and Krauss, M and Lamoree, M and Margalef, M and Massei, R and Brack, W and Muz, M}, title = {Progress, applications, and challenges in high-throughput effect-directed analysis for toxicity driver identification - is it time for HT-EDA?.}, journal = {Analytical and bioanalytical chemistry}, volume = {}, number = {}, pages = {}, pmid = {38992177}, issn = {1618-2650}, abstract = {The rapid increase in the production and global use of chemicals and their mixtures has raised concerns about their potential impact on human and environmental health. With advances in analytical techniques, in particular, high-resolution mass spectrometry (HRMS), thousands of compounds and transformation products with potential adverse effects can now be detected in environmental samples. However, identifying and prioritizing the toxicity drivers among these compounds remain a significant challenge. Effect-directed analysis (EDA) emerged as an important tool to address this challenge, combining biotesting, sample fractionation, and chemical analysis to unravel toxicity drivers in complex mixtures. Traditional EDA workflows are labor-intensive and time-consuming, hindering large-scale applications. The concept of high-throughput (HT) EDA has recently gained traction as a means of accelerating these workflows. Key features of HT-EDA include the combination of microfractionation and downscaled bioassays, automation of sample preparation and biotesting, and efficient data processing workflows supported by novel computational tools. In addition to microplate-based fractionation, high-performance thin-layer chromatography (HPTLC) offers an interesting alternative to HPLC in HT-EDA. This review provides an updated perspective on the state-of-the-art in HT-EDA, and novel methods/tools that can be incorporated into HT-EDA workflows. It also discusses recent studies on HT-EDA, HT bioassays, and computational prioritization tools, along with considerations regarding HPTLC. By identifying current gaps in HT-EDA and proposing new approaches to overcome them, this review aims to bring HT-EDA a step closer to monitoring applications.}, } @article {pmid38989474, year = {2024}, author = {Li, R and Li, J and Lemer, S and Lopez, JV and Oatley, G and Clayton-Lucey, IA and Sinclair, E and Aunin, E and Gettle, N and Santos, C and Paulini, M and Niu, H and McKenna, V and O'Brien, R and , and , and , and , and , }, title = {The genome sequence of a heart cockle, Fragum fragum (Linnaeus, 1758).}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {129}, pmid = {38989474}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual specimen of Fragum fragum (a heart cockle; Mollusca; Bivalvia; Veneroida; Cardiidae). The genome sequence is 1,153.1 megabases in span. Most of the assembly is scaffolded into 19 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 22.36 kilobases in length. Gene annotation of this assembly on Ensembl identified 17,262 protein coding genes.}, } @article {pmid38986397, year = {2024}, author = {Hung, CC and Hsieh, HH and Chou, WC and Liu, EC and Chow, CH and Chang, Y and Lee, TM and Santschi, PH and Ranatunga, RRMKP and Bacosa, HP and Shih, YY}, title = {Assessing CO2 sources and sinks in and around Taiwan: Implication for achieving regional carbon neutrality by 2050.}, journal = {Marine pollution bulletin}, volume = {206}, number = {}, pages = {116664}, doi = {10.1016/j.marpolbul.2024.116664}, pmid = {38986397}, issn = {1879-3363}, mesh = {Taiwan ; *Carbon Dioxide/analysis ; *Carbon Sequestration ; Environmental Monitoring/methods ; Carbon/analysis ; Oceans and Seas ; Forests ; }, abstract = {Taiwan has pledged to achieve net-zero carbon emissions by 2050, but the current extent of carbon sinks in Taiwan remains unclear. Therefore, this study aims to first review the existing nature-based carbon sinks on land and in the oceans around Taiwan. Subsequently, we suggest potential strategies to reduce CO2 emissions and propose carbon dioxide removal methods (CDRs). The natural carbon sinks by forests, sediments, and oceans in and around Taiwan are approximately 21.5, 42.1, and 96.8 Mt-CO2 y[-1], respectively, which is significantly less than Taiwan's CO2 emissions (280 Mt-CO2 y[-1]). Taiwan must consider decarbonization strategies like using electric vehicles, renewable energy, and hydrogen energy by formulating enabling policies. Besides more precisely assessing both terrestrial and marine carbon sinks, Taiwan should develop novel CDRs such as bioenergy with carbon capture and storage, afforestation, reforestation, biochar, seaweed cultivation, and ocean alkalinity enhancement, to reach carbon neutrality by 2050.}, } @article {pmid38985613, year = {2024}, author = {Filice, M and Crocco, MC and Agostino, RG and Barberi, RC and Amelio, D and Imbrogno, S and Formoso, V and Cerra, MC}, title = {An X-ray computed μ-tomography analysis for the characterization of 3D-heart shape in a model of cardiac plasticity.}, journal = {Vascular pharmacology}, volume = {155}, number = {}, pages = {107310}, doi = {10.1016/j.vph.2024.107310}, pmid = {38985613}, issn = {1879-3649}, mesh = {Animals ; *Imaging, Three-Dimensional ; *X-Ray Microtomography ; Heart/diagnostic imaging ; Radiographic Image Interpretation, Computer-Assisted ; }, } @article {pmid38982382, year = {2024}, author = {Blazanin, M}, title = {gcplyr: an R package for microbial growth curve data analysis.}, journal = {BMC bioinformatics}, volume = {25}, number = {1}, pages = {232}, pmid = {38982382}, issn = {1471-2105}, mesh = {*Software ; Computational Biology/methods ; Data Analysis ; }, abstract = {BACKGROUND: Characterization of microbial growth is of both fundamental and applied interest. Modern platforms can automate collection of high-throughput microbial growth curves, necessitating the development of computational tools to handle and analyze these data to produce insights.

RESULTS: To address this need, here I present a newly-developed R package: gcplyr. gcplyr can flexibly import growth curve data in common tabular formats, and reshapes it under a tidy framework that is flexible and extendable, enabling users to design custom analyses or plot data with popular visualization packages. gcplyr can also incorporate metadata and generate or import experimental designs to merge with data. Finally, gcplyr carries out model-free (non-parametric) analyses. These analyses do not require mathematical assumptions about microbial growth dynamics, and gcplyr is able to extract a broad range of important traits, including growth rate, doubling time, lag time, maximum density and carrying capacity, diauxie, area under the curve, extinction time, and more.

CONCLUSIONS: gcplyr makes scripted analyses of growth curve data in R straightforward, streamlines common data wrangling and analysis steps, and easily integrates with common visualization and statistical analyses.}, } @article {pmid38979877, year = {2024}, author = {Overgaard, CK and Jamy, M and Radutoiu, S and Burki, F and Dueholm, MKD}, title = {Benchmarking long-read sequencing strategies for obtaining ASV-resolved rRNA operons from environmental microeukaryotes.}, journal = {Molecular ecology resources}, volume = {24}, number = {7}, pages = {e13991}, doi = {10.1111/1755-0998.13991}, pmid = {38979877}, issn = {1755-0998}, support = {9041-00236B//Danmarks Frie Forskningsfond/ ; 2021-04055//Vetenskapsrådet/ ; 101044505/ERC_/European Research Council/International ; }, mesh = {*Eukaryota/genetics/classification ; *Computational Biology/methods ; *Benchmarking ; *High-Throughput Nucleotide Sequencing/methods ; *rRNA Operon/genetics ; RNA, Ribosomal, 18S/genetics ; Sequence Analysis, DNA/methods ; Phylogeny ; }, abstract = {The use of short-read metabarcoding for classifying microeukaryotes is challenged by the lack of comprehensive 18S rRNA reference databases. While recent advances in high-throughput long-read sequencing provide the potential to greatly increase the phylogenetic coverage of these databases, the performance of different sequencing technologies and subsequent bioinformatics processing remain to be evaluated, primarily because of the absence of well-defined eukaryotic mock communities. To address this challenge, we created a eukaryotic rRNA operon clone-library and turned it into a precisely defined synthetic eukaryotic mock community. This mock community was then used to evaluate the performance of three long-read sequencing strategies (PacBio circular consensus sequencing and two Nanopore approaches using unique molecular identifiers) and three tools for resolving amplicons sequence variants (ASVs) (USEARCH, VSEARCH, and DADA2). We investigated the sensitivity of the sequencing techniques based on the number of detected mock taxa, and the accuracy of the different ASV-calling tools with a specific focus on the presence of chimera among the final rRNA operon ASVs. Based on our findings, we provide recommendations and best practice protocols for how to cost-effectively obtain essentially error-free rRNA operons in high-throughput. An agricultural soil sample was used to demonstrate that the sequencing and bioinformatic results from the mock community also translates to highly diverse natural samples, which enables us to identify previously undescribed microeukaryotic lineages.}, } @article {pmid38977855, year = {2024}, author = {Sharaf, A and Nesengani, LT and Hayah, I and Kuja, JO and Mdyogolo, S and Omotoriogun, TC and Odogwu, BA and Beedessee, G and Smith, RM and Barakat, A and Moila, AM and El Hamouchi, A and Benkahla, A and Boukteb, A and Elmouhtadi, A and Mafwila, AL and Abushady, AM and Elsherif, AK and Ahmed, B and Wairuri, C and Ndiribe, CC and Ebuzome, C and Kinnear, CJ and Ndlovu, DF and Iraqi, D and El Fahime, E and Assefa, E and Ouardi, F and Belharfi, FZ and Tmimi, FZ and Markey, FB and Radouani, F and Zeukeng, F and Mvumbi, GL and Ganesan, H and Hanachi, M and Nigussie, H and Charoute, H and Benamri, I and Mkedder, I and Haddadi, I and Meftah-Kadmiri, I and Mubiru, JF and Domelevo Entfellner, JK and Rokani, JB and Ogwang, J and Daiga, JB and Omumbo, J and Ideozu, JE and Errafii, K and Labuschagne, K and Komi, KK and Tonfack, LB and Hadjeras, L and Ramantswana, M and Chaisi, M and Botes, MW and Kilian, M and Kvas, M and Melloul, M and Chaouch, M and Khyatti, M and Abdo, M and Phasha-Muchemenye, M and Hijri, M and Mediouni, MR and Hassan, MA and Piro, M and Mwale, M and Maaloum, M and Mavhunga, M and Olivier, NA and Aminou, O and Arbani, O and Souiai, O and Djocgoue, PF and Mentag, R and Zipfel, RD and Tata, RB and Megnekou, R and Muzemil, S and Paez, S and Salifu, SP and Kagame, SP and Selka, S and Edwards, S and Gaouar, SBS and Reda, SRA and Fellahi, S and Khayi, S and Ayed, S and Madisha, T and Sahil, T and Udensi, OU and Ras, V and Ezebuiro, V and Duru, VC and David, X and Geberemichael, Y and Tchiechoua, YH and Mungloo-Dilmohamud, Z and Chen, Z and Happi, C and Kariuki, T and Ziyomo, C and Djikeng, A and Badaoui, B and Mapholi, N and Muigai, A and Osuji, JO and Ebenezer, TE}, title = {Establishing African genomics and bioinformatics programs through annual regional workshops.}, journal = {Nature genetics}, volume = {56}, number = {8}, pages = {1556-1565}, pmid = {38977855}, issn = {1546-1718}, mesh = {*Genomics/education ; *Computational Biology/methods/education ; Africa ; Humans ; Biodiversity ; }, abstract = {The African BioGenome Project (AfricaBP) Open Institute for Genomics and Bioinformatics aims to overcome barriers to capacity building through its distributed African regional workshops and prioritizes the exchange of grassroots knowledge and innovation in biodiversity genomics and bioinformatics. In 2023, we implemented 28 workshops on biodiversity genomics and bioinformatics, covering 11 African countries across the 5 African geographical regions. These regional workshops trained 408 African scientists in hands-on molecular biology, genomics and bioinformatics techniques as well as the ethical, legal and social issues associated with acquiring genetic resources. Here, we discuss the implementation of transformative strategies, such as expanding the regional workshop model of AfricaBP to involve multiple countries, institutions and partners, including the proposed creation of an African digital database with sequence information relating to both biodiversity and agriculture. This will ultimately help create a critical mass of skilled genomics and bioinformatics scientists across Africa.}, } @article {pmid38976642, year = {2024}, author = {Pisarenco, VA and Vizueta, J and Rozas, J}, title = {GALEON: a comprehensive bioinformatic tool to analyse and visualize gene clusters in complete genomes.}, journal = {Bioinformatics (Oxford, England)}, volume = {40}, number = {7}, pages = {}, pmid = {38976642}, issn = {1367-4811}, support = {MCIN/AEI/10.13039/501100011033//Ministerio de Ciencia e Innovación of Spain/ ; }, mesh = {*Multigene Family ; *Software ; *Computational Biology/methods ; Genome ; Genomics/methods ; Evolution, Molecular ; Humans ; }, abstract = {MOTIVATION: Gene clusters, defined as a set of genes encoding functionally related proteins, are abundant in eukaryotic genomes. Despite the increasing availability of chromosome-level genomes, the comprehensive analysis of gene family evolution remains largely unexplored, particularly for large and highly dynamic gene families or those including very recent family members. These challenges stem from limitations in genome assembly contiguity, particularly in repetitive regions such as large gene clusters. Recent advancements in sequencing technology, such as long reads and chromatin contact mapping, hold promise in addressing these challenges.

RESULTS: To facilitate the identification, analysis, and visualization of physically clustered gene family members within chromosome-level genomes, we introduce GALEON, a user-friendly bioinformatic tool. GALEON identifies gene clusters by studying the spatial distribution of pairwise physical distances among gene family members along with the genome-wide gene density. The pipeline also enables the simultaneous analysis and comparison of two gene families and allows the exploration of the relationship between physical and evolutionary distances. This tool offers a novel approach for studying the origin and evolution of gene families.

GALEON is freely available from https://www.ub.edu/softevol/galeon and https://github.com/molevol-ub/galeon.}, } @article {pmid38974014, year = {2024}, author = {Cassee, FR and Bleeker, EAJ and Durand, C and Exner, T and Falk, A and Friedrichs, S and Heunisch, E and Himly, M and Hofer, S and Hofstätter, N and Hristozov, D and Nymark, P and Pohl, A and Soeteman-Hernández, LG and Suarez-Merino, B and Valsami-Jones, E and Groenewold, M}, title = {Roadmap towards safe and sustainable advanced and innovative materials. (Outlook for 2024-2030).}, journal = {Computational and structural biotechnology journal}, volume = {25}, number = {}, pages = {105-126}, pmid = {38974014}, issn = {2001-0370}, abstract = {The adoption of innovative advanced materials holds vast potential, contingent upon addressing safety and sustainability concerns. The European Commission advocates the integration of Safe and Sustainable by Design (SSbD) principles early in the innovation process to streamline market introduction and mitigate costs. Within this framework, encompassing ecological, social, and economic factors is paramount. The NanoSafety Cluster (NSC) delineates key safety and sustainability areas, pinpointing unresolved issues and research gaps to steer the development of safe(r) materials. Leveraging FAIR data management and integration, alongside the alignment of regulatory aspects, fosters informed decision-making and innovation. Integrating circularity and sustainability mandates clear guidance, ensuring responsible innovation at every stage. Collaboration among stakeholders, anticipation of regulatory demands, and a commitment to sustainability are pivotal for translating SSbD into tangible advancements. Harmonizing standards and test guidelines, along with regulatory preparedness through an exchange platform, is imperative for governance and market readiness. By adhering to these principles, the effective and sustainable deployment of innovative materials can be realized, propelling positive transformation and societal acceptance.}, } @article {pmid38973368, year = {2024}, author = {Martínez, L and Zattara, EE and Arbetman, MP and Morales, CL and Masonbrink, RE and Severin, AJ and Aizen, MA and Toth, AL}, title = {Chromosome-Level Assembly and Annotation of the Genome of the Endangered Giant Patagonian Bumble Bee Bombus dahlbomii.}, journal = {Genome biology and evolution}, volume = {16}, number = {7}, pages = {}, doi = {10.1093/gbe/evae146}, pmid = {38973368}, issn = {1759-6653}, support = {//Fulbright Science and Technology Award, Argentina Commission/ ; //Iowa State University Faculty Professional Development Leave/ ; NGS-57001R-19//National Geographic Society/ ; }, mesh = {Animals ; Bees/genetics ; *Endangered Species ; *Molecular Sequence Annotation ; *Genome, Insect ; Male ; Chromosomes, Insect/genetics ; }, abstract = {This article describes a genome assembly and annotation for Bombus dahlbomii, the giant Patagonian bumble bee. DNA from a single, haploid male collected in Argentina was used for PacBio (HiFi) sequencing, and Hi-C technology was then used to map chromatin contacts. Using Juicer and manual curation, the genome was scaffolded into 18 main pseudomolecules, representing a high-quality, near chromosome-level assembly. The sequenced genome size is estimated at 265 Mb. The genome was annotated based on RNA sequencing data of another male from Argentina, and BRAKER3 produced 15,767 annotated genes. The genome and annotation show high completeness, with >95% BUSCO scores for both the genome and annotated genes (based on conserved genes from Hymenoptera). This genome provides a valuable resource for studying the biology of this iconic and endangered species, as well as for understanding the impacts of its decline and designing strategies for its preservation.}, } @article {pmid38972117, year = {2024}, author = {Hyman, S and Zhang, J and Lim, YH and Jovanovic Andersen, Z and Cole-Hunter, T and Li, Y and Møller, P and Daras, K and Williams, R and Thomas, ML and Labib, SM and Topping, D}, title = {Residential greenspace and COVID-19 Severity: A cohort study of 313,657 individuals in Greater Manchester, United Kingdom.}, journal = {Environment international}, volume = {190}, number = {}, pages = {108843}, doi = {10.1016/j.envint.2024.108843}, pmid = {38972117}, issn = {1873-6750}, mesh = {*COVID-19/epidemiology/mortality ; Humans ; Male ; Female ; Middle Aged ; Aged ; United Kingdom/epidemiology ; Retrospective Studies ; *Air Pollution/statistics & numerical data ; *Hospitalization/statistics & numerical data ; SARS-CoV-2 ; Adult ; Cohort Studies ; Severity of Illness Index ; Aged, 80 and over ; }, abstract = {BACKGROUND: Greenspaces contribute positively to mental and physical well-being, promote social cohesion, and alleviate environmental stressors, such as air pollution. Ecological studies suggest that greenspace may affect incidence and severity of Coronavirus Disease 2019 (COVID-19).

OBJECTIVE: This study examines the association between residential greenspace and COVID-19 related hospitalization and death.

METHOD: In this retrospective cohort based on patient records from the Greater Manchester Care Records, all first COVID-19 cases diagnosed between March 1, 2020, and May 31, 2022 were followed until COVID-19 related hospitalization or death within 28 days. Residential greenspace availability was assessed using the Normalized Difference Vegetation Index per lower super output area in Greater Manchester. The association of greenspace with COVID-19 hospitalization and mortality were estimated using multivariate logistic regression models after adjusting for potential individual, temporal, and spatial confounders. We explored potential effect modifications of the associations with greenspace and COVID-19 severity by age, sex, body mass index, smoking, deprivation, and certain comorbidities. Combined effects of greenspace and air pollution (NO2 and PM2.5) were investigated by mutually adjusting pairs with correlation coefficients ≤ 0·7.

RESULTS: Significant negative associations were observed between greenspace availability and COVID-19 hospitalization and mortality with odds ratios [OR] (95 % Confidence Intervals [CI]) of 0·96 (0·94-0·97) and 0·84 (0·80-0·88) (per interquartile range [IQR]), respectively. These were significantly modified by deprivation (P-value for interaction < 0.05), showing that those most deprived obtained largest benefits from greenspace. Inclusion of NO2 and PM2.5 diminished associations to null for COVID-19 hospitalization, but only reduced them slightly for mortality, where inverse associations remained.

CONCLUSION: In the Greater Manchester area, residential greenspace is associated with reduced risk of hospitalization or death in individuals with COVID-19, with deprived groups obtaining the greatest benefits. Associations were strongest for COVID-19 mortality, which were robust to inclusion of air pollutants in the models.}, } @article {pmid38972039, year = {2024}, author = {Nurkolis, F and Wiyarta, E and Taslim, NA and Kurniawan, R and Thibault, R and Fernandez, ML and Yang, Y and Han, J and Tsopmo, A and Mayulu, N and Tjandrawinata, RR and Tallei, TE and Hardinsyah, H}, title = {Unraveling diabetes complexity through natural products, miRNAs modulation, and future paradigms in precision medicine and global health.}, journal = {Clinical nutrition ESPEN}, volume = {63}, number = {}, pages = {283-293}, doi = {10.1016/j.clnesp.2024.06.043}, pmid = {38972039}, issn = {2405-4577}, mesh = {Humans ; *Precision Medicine ; *MicroRNAs/genetics ; *Diabetes Mellitus/therapy/genetics ; *Biological Products/therapeutic use ; *Global Health ; Metabolomics ; Computational Biology ; Biomarkers/blood ; Genomics ; }, abstract = {BACKGROUND AND AIMS: The challenge posed by diabetes necessitates a paradigm shift from conventional diagnostic approaches focusing on glucose and lipid levels to the transformative realm of precision medicine. This approach, leveraging advancements in genomics and proteomics, acknowledges the individualistic genetic variations, dietary preferences, and environmental exposures in diabetes management. The study comprehensively analyzes the evolving diabetes landscape, emphasizing the pivotal role of genomics, proteomics, microRNAs (miRNAs), metabolomics, and bioinformatics.

RESULTS: Precision medicine revolutionizes diabetes research and treatment by diverging from traditional diagnostic methods, recognizing the heterogeneous nature of the condition. MiRNAs, crucial post-transcriptional gene regulators, emerge as promising therapeutic targets, influencing key facets such as insulin signaling and glucose homeostasis. Metabolomics, an integral component of omics sciences, contributes significantly to diabetes research, elucidating metabolic disruptions, and offering potential biomarkers for early diagnosis and personalized therapies. Bioinformatics unveils dynamic connections between natural substances, miRNAs, and cellular pathways, aiding in the exploration of the intricate molecular terrain in diabetes. The study underscores the imperative for experimental validation in natural product-based diabetes therapy, emphasizing the need for in vitro and in vivo studies leading to clinical trials for assessing effectiveness, safety, and tolerability in real-world applications. Global cooperation and ethical considerations play a pivotal role in addressing diabetes challenges worldwide, necessitating a multifaceted approach that integrates traditional knowledge, cultural competence, and environmental awareness.

CONCLUSIONS: The key components of diabetes treatment, including precision medicine, metabolomics, bioinformatics, and experimental validation, converge in future strategies, embodying a holistic paradigm for diabetes care anchored in cutting-edge research and global healthcare accessibility.}, } @article {pmid38971026, year = {2024}, author = {Ou, X and Chen, J and Li, B and Yang, Y and Liu, X and Xu, Z and Xiang, X and Wang, Q}, title = {Multiomics reveals the ameliorating effect and underlying mechanism of aqueous extracts of polygonatum sibiricum rhizome on obesity and liver fat accumulation in high-fat diet-fed mice.}, journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology}, volume = {132}, number = {}, pages = {155843}, doi = {10.1016/j.phymed.2024.155843}, pmid = {38971026}, issn = {1618-095X}, mesh = {Animals ; Male ; Mice ; Akkermansia ; Diet, High-Fat/adverse effects ; Gastrointestinal Microbiome/drug effects ; Lipid Metabolism/drug effects ; *Liver/drug effects/metabolism ; Mice, Inbred C57BL ; Multiomics ; *Non-alcoholic Fatty Liver Disease/drug therapy ; *Obesity/drug therapy/etiology ; Orlistat/pharmacology ; *Plant Extracts/pharmacology ; *Polygonatum/chemistry ; Rhizome/chemistry ; Disease Models, Animal ; }, abstract = {BACKGROUND: Polygonatum sibiricum polysaccharides protect against obesity and NAFLD. However, the potential effects of PS rhizome aqueous extracts (PSRwe) on adiposity and hepatic lipid accumulation remains unexplored.

PURPOSE: Elucidating the impact and underlying mechanism of PSRwe on HFD-induced obesity and liver fat depostition.

STUDY DESIGN: 56 male mice, aged eight weeks, were divided into seven groups: Positive, four doses of PSRwe, Model, and Control. HFD was fed for eight weeks, followed by alternate-day gavage of orlistat and PSRwe for an additional eight-week period. Integrative analysis encompassing multiomics, physiological and histopathological, and biochemical indexes was employed.

METHODS: Body weight (BW); liver, fat and Lee's indexes; TC, TG, LDL-C, HDL-C, AST, ALT, FFA, leptin, and adiponectin in the liver and blood; TNFα, IL-6, and LPS in the colon, plasma, and liver; H&E, PAS and oil red O staining on adipose and liver samples were examined. OGTT and ITT were conducted The gut microbiome, microbial metabolome, colonic and liver transcriptome, plasma and liver metabolites were investigated.

RESULTS: PSRwe at the dosage of 7.5 mg/kg demonstrated significant and consistent reduction in BW and hepatic fat deposition than orlistat. PSRwe significantly decreased TC, TG, LDL-C, LEP, FFA levels in blood and liver. PSRwe significantly enhanced the relative abundance of probiotics including Akkermansia muciniphila, Bifidobacterium pseudolongum, Lactobacillus reuteri, and metabolic pathways including glycolysis and fatty acids β-oxidation. The 70 up-regulated microbial metabolites in PSRwe-treated mice mainly involved in nucleotides and amino acids metabolism, while 40 decreased metabolites primarily associated with lipid metabolism. The up-regulated colonic differentially expressed genes (DEGs) participate in JAK-STAT/PI3K-Akt/FoxO signaling pathway, serotonergic/cholinergic/glutamatergic synapses, while the down-regulated DEGs predominantly focused on fat absorption and transport. The up-regulated liver DEGs mainly concentrated on fatty acid oxidation and metabolism. Liver metabolisms revealed 131 differential metabolites, among which carnitine and oxidized lipids significantly increased in PSRwe-treated mice. In plasma, the 58 up-regulated metabolites mainly participate in co-factors/vitamins metabolism while 154 down-regulated ones in fatty acids biosynthesis. Comprehensive multiomics association analysis revealed significant associations between gut microbiota and colonic/liver gene expression, and suggested exogenous and endogenous betaine may be active compound in alleviating HFD-induced symptoms.

CONCLUSION: PSRwe effectively mitigate HFD-induced obesity and hepatic steatosis by increasing beneficial bacteria, reducing colonic fat digestion/absorption, increasing hepatic lipid metabolism, and elevating betaine levels.}, } @article {pmid38970356, year = {2024}, author = {Chan, KO}, title = {Next-generation bioinformatics: An ultrafast and user-friendly tool for phylogenomic data exploration.}, journal = {Molecular ecology resources}, volume = {24}, number = {7}, pages = {e13993}, doi = {10.1111/1755-0998.13993}, pmid = {38970356}, issn = {1755-0998}, mesh = {*Computational Biology/methods ; *Software ; *Phylogeny ; Genomics/methods ; User-Computer Interface ; }, abstract = {With increasingly large genomic datasets, even routine bioinformatic tasks can be arduous, computationally demanding, and time-consuming. Additionally, most bioinformatic programs do not have a graphical user interface (GUI) and thus, require users to be minimally competent in command-line. These impediments present significant economic and technological barriers for practitioners who do not have access to advanced computational resources and support. In this issue of Molecular Ecology Resources, Handika and Esselstyn (2024) developed an ultrafast and memory-efficient bioinformatic tool, SEGUL, that performs common manipulations and calculations of summary statistics on phylogenomic datasets. SEGUL has two main features that distinguish it from other bioinformatic programs: (1) it is based on the recently emergent, high-performance programming language Rust, and (2) it has a GUI written using Flutter, a cross-platform programming framework that also supports mobile operating systems (mobile iOS, iPadOS and Android). By leveraging and combining the power of Rust and Flutter, SEGUL achieves significantly faster computation times and lower memory usage across different platforms and CPU architectures compared to similar programs. The unique and innovative features of SEGUL pave the way for a new era of bioinformatics that can be more energy-efficient, inclusive, and available to a broader swathe of users.}, } @article {pmid38968897, year = {2024}, author = {Zhu, Y and Chen, F and Jiang, F and Hua, Z and Luo, Z and Ma, J}, title = {Enhanced remediation of PFAS-metal co-contaminated soil by ceramsite supported Fe3O4-MoS2 heterojunction as a high-performance piezocatalyst.}, journal = {Journal of environmental management}, volume = {365}, number = {}, pages = {121716}, doi = {10.1016/j.jenvman.2024.121716}, pmid = {38968897}, issn = {1095-8630}, mesh = {*Soil Pollutants/chemistry/metabolism ; *Soil/chemistry ; *Metals, Heavy/chemistry ; Environmental Restoration and Remediation/methods ; Biodegradation, Environmental ; }, abstract = {In this study, a novel piezoremediation system was developed to remediate an actual soil co-polluted by high contents of per- and polyfluoroalkyl substances (PFAS, 5725 μg/kg soil) and heavy metals (6455 mg/kg soil). Two piezocatalysts, MoS2/ceramsite (MC) and Fe3O4-MoS2/ceramsite (FMC), were synthesized using a facile hydrothermal-coprecipitation method. These two materials were employed to treat the co-contaminated soil in soil slurry environment under sonication. FMC exhibited significantly higher piezoremediation performance than MC, wherein 91.6% of PFAS, 97.8% of Cr[6+] ions and 81% of total metals (Cr, Cu, Zn and Ni) were removed from the soil after 50 min of the FMC piezoremediation process. FMC also exhibited the advantages of easy separation from the slurry phase and excellent reusability. In comparison with MC, the Fe3O4-MoS2 heterojunction in FMC can stabilize MoS2 particles on the surface of ceramsite granules, promote the separation of electron/hole pairs, accelerate charge transfer, therefore enhancing piezocatalytic performance. The electron spin resonance analysis and free radical quenching tests show that [•]OH was the dominant oxidative radical responsible for PFAS degradation. The count of bacteria and the bacterial community structure in the treated soil can be basically restored to the initial states after 30 days of incubation under nutrient stimulation. Overall, this study not only provides a deep insight on soil remediation process, but also offers an efficient and reliable technique for simultaneous decontamination of organic and metal pollutants in soil.}, } @article {pmid38968305, year = {2024}, author = {Fu, X and Withers, J and Miyamae, JA and Moore, TY}, title = {ArborSim: Articulated, branching, OpenSim routing for constructing models of multi-jointed appendages with complex muscle-tendon architecture.}, journal = {PLoS computational biology}, volume = {20}, number = {7}, pages = {e1012243}, pmid = {38968305}, issn = {1553-7358}, mesh = {*Tendons/physiology/anatomy & histology ; Humans ; Biomechanical Phenomena ; *Software ; *Joints/physiology/anatomy & histology ; *Muscle, Skeletal/physiology/anatomy & histology ; Models, Biological ; Computational Biology ; Computer Simulation ; Animals ; }, abstract = {Computational models of musculoskeletal systems are essential tools for understanding how muscles, tendons, bones, and actuation signals generate motion. In particular, the OpenSim family of models has facilitated a wide range of studies on diverse human motions, clinical studies of gait, and even non-human locomotion. However, biological structures with many joints, such as fingers, necks, tails, and spines, have been a longstanding challenge to the OpenSim modeling community, especially because these structures comprise numerous bones and are frequently actuated by extrinsic muscles that span multiple joints-often more than three-and act through a complex network of branching tendons. Existing model building software, typically optimized for limb structures, makes it difficult to build OpenSim models that accurately reflect these intricacies. Here, we introduce ArborSim, customized software that efficiently creates musculoskeletal models of highly jointed structures and can build branched muscle-tendon architectures. We used ArborSim to construct toy models of articulated structures to determine which morphological features make a structure most sensitive to branching. By comparing the joint kinematics of models constructed with branched and parallel muscle-tendon units, we found that among various parameters-the number of tendon branches, the number of joints between branches, and the ratio of muscle fiber length to muscle tendon unit length-the number of tendon branches and the number of joints between branches are most sensitive to branching modeling method. Notably, the differences between these models showed no predictable pattern with increased complexity. As the proportion of muscle increased, the kinematic differences between branched and parallel models units also increased. Our findings suggest that stress and strain interactions between distal tendon branches and proximal tendon and muscle greatly affect the overall kinematics of a musculoskeletal system. By incorporating complex muscle-tendon branching into OpenSim models using ArborSim, we can gain deeper insight into the interactions between the axial and appendicular skeleton, model the evolution and function of diverse animal tails, and understand the mechanics of more complex motions and tasks.}, } @article {pmid38968199, year = {2024}, author = {Stratton, CA and Thompson, Y and Zio, K and Morrison, WR and Murrell, EG}, title = {uafR: An R package that automates mass spectrometry data processing.}, journal = {PloS one}, volume = {19}, number = {7}, pages = {e0306202}, pmid = {38968199}, issn = {1932-6203}, mesh = {*Gas Chromatography-Mass Spectrometry/methods ; *Algorithms ; *Software ; Cheminformatics/methods ; }, abstract = {Chemical information has become increasingly ubiquitous and has outstripped the pace of analysis and interpretation. We have developed an R package, uafR, that automates a grueling retrieval process for gas -chromatography coupled mass spectrometry (GC -MS) data and allows anyone interested in chemical comparisons to quickly perform advanced structural similarity matches. Our streamlined cheminformatics workflows allow anyone with basic experience in R to pull out component areas for tentative compound identifications using the best published understanding of molecules across samples (pubchem.gov). Interpretations can now be done at a fraction of the time, cost, and effort it would typically take using a standard chemical ecology data analysis pipeline. The package was tested in two experimental contexts: (1) A dataset of purified internal standards, which showed our algorithms correctly identified the known compounds with R2 values ranging from 0.827-0.999 along concentrations ranging from 1 × 10-5 to 1 × 103 ng/μl, (2) A large, previously published dataset, where the number and types of compounds identified were comparable (or identical) to those identified with the traditional manual peak annotation process, and NMDS analysis of the compounds produced the same pattern of significance as in the original study. Both the speed and accuracy of GC -MS data processing are drastically improved with uafR because it allows users to fluidly interact with their experiment following tentative library identifications [i.e. after the m/z spectra have been matched against an installed chemical fragmentation database (e.g. NIST)]. Use of uafR will allow larger datasets to be collected and systematically interpreted quickly. Furthermore, the functions of uafR could allow backlogs of previously collected and annotated data to be processed by new personnel or students as they are being trained. This is critical as we enter the era of exposomics, metabolomics, volatilomes, and landscape level, high-throughput chemotyping. This package was developed to advance collective understanding of chemical data and is applicable to any research that benefits from GC -MS analysis. It can be downloaded for free along with sample datasets from Github at github.org/castratton/uafR or installed directly from R or RStudio using the developer tools: 'devtools::install_github("castratton/uafR")'.}, } @article {pmid38967613, year = {2024}, author = {Hanners, A and Melnyk, B and Bedell, T and Conroy, S and Volek, J and Brock, G and Kelley, M}, title = {A pilot study of Keto Prescribed+: A healthy thinking and eating educational program for African American women.}, journal = {Journal of the American Association of Nurse Practitioners}, volume = {36}, number = {7}, pages = {377-384}, pmid = {38967613}, issn = {2327-6924}, support = {L30 HL159699/HL/NHLBI NIH HHS/United States ; UL1TR002733//Center for Clinical and Translational Science, Ohio State University/ ; TL1TR002735//Center for Clinical and Translational Science, Ohio State University/ ; }, mesh = {Adult ; Female ; Humans ; Middle Aged ; *Black or African American/psychology/statistics & numerical data ; Pilot Projects ; Patient Education as Topic ; *Health Promotion ; Healthy Lifestyle ; }, abstract = {African American (AA) women have the highest prevalence of obesity in addition to health disparities in preventable diet-related diseases (i.e., diabetes, hypertension), which places them at increased risk for cardiovascular disease. The purpose of this pilot study was to assess the feasibility, acceptability, and preliminary effectiveness of the Keto Prescribed+ (KetoRx+) program on associated physical and psychosocial outcomes among this population. The KetoRx+ program is a healthy eating and thinking educational intervention. The program combined online and in-person community group sessions over 8 weeks. The Keto Prescribed+ was found to be feasible and acceptable with comments on ways to increase acceptability from participants completing program (n = 10). Physical outcomes changed showed an average decrease in weight of 10lbs (SD = 5), baseline average 226lbs. Waist-to-hip ratio and systolic blood pressure also trended down. Psychosocial outcomes showed improvement trends. The KetoRx+ program is feasible and acceptable for overweight or obese AA women. Preliminary efficacy was established for most physical and psychosocial outcomes. However, more research is needed to identify specific program components contributing to healthy lifestyle behavior change and to establish program efficacy and effectiveness. Culturally adapted community-based biopsychosocial interventions using ketogenic nutrition therapy may help improve cardiovascular health of adult AA women.}, } @article {pmid38966305, year = {2024}, author = {Crowley, LM and Roy, HE and Brown, PMJ and , and , and , and , and , and , and , }, title = {The genome sequence of the ten-spot ladybird, Adalia decempunctata (Linnaeus, 1758).}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {106}, pmid = {38966305}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual male Adalia decempunctata (the ten-spot ladybird; Arthropoda; Insecta; Coleoptera; Coccinellidae). The genome sequence is 489.4 megabases in span. Most of the assembly is scaffolded into 12 chromosomal pseudomolecules, including the X and Y sex chromosomes. The mitochondrial genome has also been assembled and is 19.68 kilobases in length.}, } @article {pmid38964062, year = {2024}, author = {Jeon, Y and Kwon, YS and Noh, YJ and Lee, SM and Song, JW and Kim, JH and Seo, JS}, title = {Unraveling the mechanisms of benzo[a]pyrene degradation by Pigmentiphaga kullae strain KIT-003 using a multi-omics approach.}, journal = {Ecotoxicology and environmental safety}, volume = {281}, number = {}, pages = {116665}, doi = {10.1016/j.ecoenv.2024.116665}, pmid = {38964062}, issn = {1090-2414}, mesh = {*Benzo(a)pyrene/metabolism/toxicity ; *Biodegradation, Environmental ; Republic of Korea ; Proteomics ; Water Pollutants, Chemical/metabolism/toxicity ; Gas Chromatography-Mass Spectrometry ; Catechols/metabolism ; Rivers/chemistry/microbiology ; Multiomics ; }, abstract = {Polycyclic aromatic hydrocarbons (PAHs), notably benzo[a]pyrene (BaP), are environmental contaminants with multiple adverse ecological implications. Numerous studies have suggested the use of BaP biodegradation using various bacterial strains to remove BaP from the environment. This study investigates the BaP biodegradation capability of Pigmentiphaga kullae strain KIT-003, isolated from the Nak-dong River (South Korea) under specific environmental conditions. The optimum conditions of biodegradation were found to be pH 7.0, 35°C, and a salinity of 0 %. GC-MS analysis suggested alternative pathways by which KIT-003 produced catechol from BaP through several intermediate metabolites, including 4-formylchrysene-5-carboxylic acid, 5,6-dihydro-5,6-dihydroxychrysene-5-carboxylic acid (isomer: 3,4-dihydro-3,4-dihydroxychrysene-4-carboxylic acid), naphthalene-1,2-dicarboxylic acid, and 2-hydroxy-1-naphthoic acid. Proteomic profiles indicated upregulation of enzymes associated with aromatic compound degradation, such as nahAc and nahB, and of those integral to the tricarboxylic acid cycle, reflecting the strain's adaptability to and degradation of BaP. Lipidomic analysis of KIT-003 demonstrated that BaP exposure induced an accumulation of glycerolipids such as diacylglycerol and triacylglycerol, indicating their crucial role in bacterial adaptation mechanisms under BaP stress. This study provides significant scientific knowledge regarding the intricate mechanisms involved in BaP degradation by microorganisms.}, } @article {pmid38961615, year = {2024}, author = {Papageorgiou, D and Cherono, W and Gall, G and Nyaguthii, B and Farine, DR}, title = {Testing the information centre hypothesis in a multilevel society.}, journal = {The Journal of animal ecology}, volume = {93}, number = {8}, pages = {1147-1159}, doi = {10.1111/1365-2656.14131}, pmid = {38961615}, issn = {1365-2656}, support = {//Max Planck Society/ ; //Wissenschaftskolleg zu Berlin/ ; 422037984//Deutsche Forschungsgemeinschaft/ ; //Deutscher Akademischer Austauschdienst/ ; WW-175ER-17//National Geographic Society/ ; PCEFP3_187058/SNSF_/Swiss National Science Foundation/Switzerland ; 850859/ERC_/European Research Council/International ; }, mesh = {Animals ; *Social Behavior ; *Galliformes/physiology ; Geographic Information Systems ; Female ; Male ; }, abstract = {In various animal species conspecifics aggregate at sleeping sites. Such aggregations can act as information centres where individuals acquire up-to-date knowledge about their environment. In some species, communal sleeping sites comprise individuals from multiple groups, where each group maintains stable membership over time. We used GPS tracking to simultaneously record group movement in a population of wild vulturine guineafowl (Acryllium vulturinum) to investigate whether communal sleeping sites can facilitate the transfer of information among individuals across distinct groups. These birds live in large and stable groups that move both together and apart, often forming communal roosts containing up to five groups. We first test whether roosts provide the opportunity for individuals to acquire information from members of other groups by examining the spatial organization at roosts. The GPS data reveal that groups intermix, thereby providing an opportunity for individuals to acquire out-group information. We next conduct a field experiment to test whether naïve groups can locate novel food patches when co-roosting with knowledgeable groups. We find that co-roosting substantially increases the chances for the members of a naïve group to discover a patch known to individuals from other groups at the shared roost. Further, we find that the discovery of food patches by naïve groups subsequently shapes their space use and inter-group associations. We also draw on our long-term tracking to provide examples that demonstrate natural cases where communal roosting has preceded large-scale multi-group collective movements that extend into areas beyond the groups' normal ranges. Our findings support the extension of the information centre hypothesis to communal sleeping sites that consist of distinct social groups.}, } @article {pmid38960861, year = {2024}, author = {Dolenz, S and van der Valk, T and Jin, C and Oppenheimer, J and Sharif, MB and Orlando, L and Shapiro, B and Dalén, L and Heintzman, PD}, title = {Unravelling reference bias in ancient DNA datasets.}, journal = {Bioinformatics (Oxford, England)}, volume = {40}, number = {7}, pages = {}, pmid = {38960861}, issn = {1367-4811}, support = {2021.0048//Knut and Alice Wallenberg Foundation/ ; }, mesh = {*DNA, Ancient/analysis ; Humans ; *Sequence Analysis, DNA/methods ; Software ; Animals ; Sequence Alignment/methods ; Computational Biology/methods ; Algorithms ; }, abstract = {MOTIVATION: The alignment of sequencing reads is a critical step in the characterization of ancient genomes. However, reference bias and spurious mappings pose a significant challenge, particularly as cutting-edge wet lab methods generate datasets that push the boundaries of alignment tools. Reference bias occurs when reference alleles are favoured over alternative alleles during mapping, whereas spurious mappings stem from either contamination or when endogenous reads fail to align to their correct position. Previous work has shown that these phenomena are correlated with read length but a more thorough investigation of reference bias and spurious mappings for ancient DNA has been lacking. Here, we use a range of empirical and simulated palaeogenomic datasets to investigate the impacts of mapping tools, quality thresholds, and reference genome on mismatch rates across read lengths.

RESULTS: For these analyses, we introduce AMBER, a new bioinformatics tool for assessing the quality of ancient DNA mapping directly from BAM-files and informing on reference bias, read length cut-offs and reference selection. AMBER rapidly and simultaneously computes the sequence read mapping bias in the form of the mismatch rates per read length, cytosine deamination profiles at both CpG and non-CpG sites, fragment length distributions, and genomic breadth and depth of coverage. Using AMBER, we find that mapping algorithms and quality threshold choices dictate reference bias and rates of spurious alignment at different read lengths in a predictable manner, suggesting that optimized mapping parameters for each read length will be a key step in alleviating reference bias and spurious mappings.

AMBER is available for noncommercial use on GitHub (https://github.com/tvandervalk/AMBER.git). Scripts used to generate and analyse simulated datasets are available on Github (https://github.com/sdolenz/refbias_scripts).}, } @article {pmid38959816, year = {2024}, author = {Zhang, Y and Li, D and Li, X and Zhou, X and Newman, G}, title = {The integration of geographic methods and ecological momentary assessment in public health research: A systematic review of methods and applications.}, journal = {Social science & medicine (1982)}, volume = {354}, number = {}, pages = {117075}, pmid = {38959816}, issn = {1873-5347}, support = {R01 MD016587/MD/NIMHD NIH HHS/United States ; }, mesh = {Humans ; *Ecological Momentary Assessment ; *Geographic Information Systems ; *Public Health/methods ; }, abstract = {With the widespread prevalence of mobile devices, ecological momentary assessment (EMA) can be combined with geospatial data acquired through geographic techniques like global positioning system (GPS) and geographic information system. This technique enables the consideration of individuals' health and behavior outcomes of momentary exposures in spatial contexts, mostly referred to as "geographic ecological momentary assessment" or "geographically explicit EMA" (GEMA). However, the definition, scope, methods, and applications of GEMA remain unclear and unconsolidated. To fill this research gap, we conducted a systematic review to synthesize the methodological insights, identify common research interests and applications, and furnish recommendations for future GEMA studies. We followed the Preferred Reporting Items for Systematic Reviews and Meta-Analysis guidelines to systematically search peer-reviewed studies from six electronic databases in 2022. Screening and eligibility were conducted following inclusion criteria. The risk of bias assessment was performed, and narrative synthesis was presented for all studies. From the initial search of 957 publications, we identified 47 articles included in the review. In public health, GEMA was utilized to measure various outcomes, such as psychological health, physical and physiological health, substance use, social behavior, and physical activity. GEMA serves multiple research purposes: 1) enabling location-based EMA sampling, 2) quantifying participants' mobility patterns, 3) deriving exposure variables, 4) describing spatial patterns of outcome variables, and 5) performing data linkage or triangulation. GEMA has advanced traditional EMA sampling strategies and enabled location-based sampling by detecting location changes and specified geofences. Furthermore, advances in mobile technology have prompted considerations of additional sensor-based data in GEMA. Our results highlight the efficacy and feasibility of GEMA in public health research. Finally, we discuss sampling strategy, data privacy and confidentiality, measurement validity, mobile applications and technologies, and GPS accuracy and missing data in the context of current and future public health research that uses GEMA.}, } @article {pmid38956468, year = {2024}, author = {Li, X and Cao, T and Liu, H and Fu, L and Wang, Q}, title = {Identification and expression analysis of Sox family genes in echinoderms.}, journal = {BMC genomics}, volume = {25}, number = {1}, pages = {655}, pmid = {38956468}, issn = {1471-2164}, support = {ZR2021QD158//Natural Science Foundation of Shandong Province, China/ ; ZR2021MC151//Natural Science Foundation of Shandong Province, China/ ; 2023XBZD003//Scientific Research Project of Yantai Vocational College/ ; }, mesh = {Animals ; *SOX Transcription Factors/genetics/metabolism ; *Phylogeny ; *Echinodermata/genetics ; *Multigene Family ; Gene Expression Profiling ; Evolution, Molecular ; Gene Expression Regulation, Developmental ; Computational Biology/methods ; }, abstract = {The Sox gene family, a collection of transcription factors widely distributed throughout the animal kingdom, plays a crucial role in numerous developmental processes. Echinoderms occupy a pivotal position in many research fields, such as neuroscience, sex determination and differentiation, and embryonic development. However, to date, no comprehensive study has been conducted to characterize and analyze Sox genes in echinoderms. In the present study, the evolution and expression of Sox family genes across 11 echinoderms were analyzed using bioinformatics methods. The results revealed a total of 70 Sox genes, with counts ranging from 5 to 8 across different echinoderms. Phylogenetic analysis revealed that the identified Sox genes could be categorized into seven distinct classes: the SoxB1 class, SoxB2 class, SoxC class, SoxD class, SoxE class, SoxF class and SoxH class. Notably, the SoxB1, SoxB2, and SoxF genes were ubiquitously present in all the echinoderms studied, which suggests that these genes may be conserved in echinoderms. The spatiotemporal expression patterns observed for Sox genes in the three echinoderms indicated that various Sox members perform distinct functional roles. Notably, SoxB1 is likely involved in echinoderm ovary development, while SoxH may play a crucial role in testis development in starfish and sea cucumber. In general, the present investigation provides a molecular foundation for exploring the Sox gene in echinoderms, providing a valuable resource for future phylogenetic and genomic studies.}, } @article {pmid38955825, year = {2024}, author = {Pan, H and Wattiez, R and Gillan, D}, title = {Soil Metaproteomics for Microbial Community Profiling: Methodologies and Challenges.}, journal = {Current microbiology}, volume = {81}, number = {8}, pages = {257}, pmid = {38955825}, issn = {1432-0991}, support = {No.2023-BSBA-024//Joint Funds of the Natural Science Foundation of Liaoning Province of China/ ; }, mesh = {*Soil Microbiology ; *Proteomics/methods ; *Metagenomics/methods ; *Bacteria/genetics/classification/metabolism/isolation & purification ; *Microbiota ; Fungi/classification/genetics/metabolism/isolation & purification ; Soil/chemistry ; Computational Biology/methods ; }, abstract = {Soil represents a complex and dynamic ecosystem, hosting a myriad of microorganisms that coexist and play vital roles in nutrient cycling and organic matter transformation. Among these microorganisms, bacteria and fungi are key members of the microbial community, profoundly influencing the fate of nitrogen, sulfur, and carbon in terrestrial environments. Understanding the intricacies of soil ecosystems and the biological processes orchestrated by microbial communities necessitates a deep dive into their composition and metabolic activities. The advent of next-generation sequencing and 'omics' techniques, such as metagenomics and metaproteomics, has revolutionized our understanding of microbial ecology and the functional dynamics of soil microbial communities. Metagenomics enables the identification of microbial community composition in soil, while metaproteomics sheds light on the current biological functions performed by these communities. However, metaproteomics presents several challenges, both technical and computational. Factors such as the presence of humic acids and variations in extraction methods can influence protein yield, while the absence of high-resolution mass spectrometry and comprehensive protein databases limits the depth of protein identification. Notwithstanding these limitations, metaproteomics remains a potent tool for unraveling the intricate biological processes and functions of soil microbial communities. In this review, we delve into the methodologies and challenges of metaproteomics in soil research, covering aspects such as protein extraction, identification, and bioinformatics analysis. Furthermore, we explore the applications of metaproteomics in soil bioremediation, highlighting its potential in addressing environmental challenges.}, } @article {pmid38954338, year = {2024}, author = {Yao, Z and Zhou, X and Jin, T and Wang, L and Liu, N and Wu, L}, title = {Remediation of phenanthrene contaminated soil by persulphate coupled with Pseudomonas aeruginosa GZ7 based on oxidation prediction model.}, journal = {Environmental science and pollution research international}, volume = {31}, number = {31}, pages = {44415-44430}, pmid = {38954338}, issn = {1614-7499}, support = {52270171//Innovative Research Group Project of the National Natural Science Foundation of China/ ; 51974314//Innovative Research Group Project of the National Natural Science Foundation of China/ ; }, mesh = {*Phenanthrenes/metabolism ; *Pseudomonas aeruginosa ; *Soil Pollutants ; *Oxidation-Reduction ; *Soil/chemistry ; Soil Microbiology ; Environmental Restoration and Remediation/methods ; Biodegradation, Environmental ; Polycyclic Aromatic Hydrocarbons ; Sulfates/chemistry ; }, abstract = {Chemical oxidation coupled with microbial remediation has attracted widespread attention for the removal of polycyclic aromatic hydrocarbons (PAHs). Among them, the precise evaluation of the feasible oxidant concentration of PAH-contaminated soil is the key to achieving the goal of soil functional ecological remediation. In this study, phenanthrene (PHE) was used as the target pollutant, and Fe[2+]-activated persulphate (PS) was used to remediate four types of soils. Linear regression analysis identified the following important factors influencing remediation: PS dosage and soil PHE content for PHE degradation, Fe[2+] dosage, hydrolysable nitrogen (HN), and available phosphorus for PS decomposition. A comprehensive model of "soil characteristics-oxidation conditions-remediation effect" with a high predictive accuracy was constructed. Based on model identification, Pseudomonas aeruginosa GZ7, which had high PAHs degrading ability after domestication, was further applied to coupling repair remediation. The results showed that the optimal PS dose was 0.75% (w/w). The response relationship between soil physical, chemical, and biological indicators at the intermediate interface and oxidation conditions was analysed. Coupled remediation effects were clarified using microbial diversity sequencing. The introduction of Pseudomonas aeruginosa GZ7 stimulated the relative abundance of Cohnella, Enterobacter, Paenibacillus, and Bacillus, which can promote material metabolism and energy transformation during remediation.}, } @article {pmid38954067, year = {2024}, author = {Bazkiaee, PA and Kamkar, B and Amiri, E and Kazemi, H and Rezaei, M and Araji, HA}, title = {Multi-criteria GIS-based land suitability analysis for rice cultivation: a case study in Guilan Province, Iran.}, journal = {Environmental monitoring and assessment}, volume = {196}, number = {7}, pages = {680}, pmid = {38954067}, issn = {1573-2959}, mesh = {*Oryza/growth & development ; Iran ; *Geographic Information Systems ; *Environmental Monitoring/methods ; *Agriculture/methods ; *Soil/chemistry ; Conservation of Natural Resources ; Climate ; }, abstract = {Ensuring food security and sustainable resource management has become a paramount global concern, prompting significant attention to land suitability analysis for enhancing agricultural production. In this study, an AHP-weighted overlay method was employed to delineate rice cultivation suitability in Guilan province, Iran, a central hub for rice production. Sixteen climatic, topographic, and soil variables were integrated, and individual maps were reclassified to align with the specific requisites for rice production. The results revealed three suitability classes: including 'very suitable,' 'suitable,' and 'moderately suitable', covering 91%, 6%, and 3% of the land, respectively. Soil attributes, particularly organic matter, significantly influenced suitability (weight value of 0.745), with topographic and soil factors outweighing climate in assessment. While salinity is generally absent, organic matter deficiency affects 44% of the land. Phosphorus imbalances are prevalent, with potassium toxicity observed in 10%. Microelement deficiencies, especially in iron and zinc, are noted. Additionally, the results indicated that topographic and soil attributes played a more significant role than climate-related factors in assessing land suitability for rice cultivation within the study area. This research provides a comprehensive spatial analysis of all variables in the study region, shedding light on the complexities of land suitability for rice cultivation. These findings contribute to the understanding of agricultural sustainability and resource management strategies in the context of food security.}, } @article {pmid38951915, year = {2024}, author = {Koci, O and Russell, RK and Shaikh, MG and Edwards, C and Gerasimidis, K and Ijaz, UZ}, title = {CViewer: a Java-based statistical framework for integration of shotgun metagenomics with other omics datasets.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {117}, pmid = {38951915}, issn = {2049-2618}, support = {NE/L011956/1//NERC Environmental Bioinformatics Centre/ ; BB/T010657/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; EP/V030515/1//Engineering and Physical Sciences Research Council/ ; }, mesh = {*Metagenomics/methods ; Humans ; *Software ; Microbiota/genetics ; Gastrointestinal Microbiome/genetics ; Computational Biology/methods ; Metagenome ; Crohn Disease/microbiology/genetics ; }, abstract = {BACKGROUND: Shotgun metagenomics for microbial community survey recovers enormous amount of information for microbial genomes that include their abundances, taxonomic, and phylogenetic information, as well as their genomic makeup, the latter of which then helps retrieve their function based on annotated gene products, mRNA, protein, and metabolites. Within the context of a specific hypothesis, additional modalities are often included, to give host-microbiome interaction. For example, in human-associated microbiome projects, it has become increasingly common to include host immunology through flow cytometry. Whilst there are plenty of software approaches available, some that utilize marker-based and assembly-based approaches, for downstream statistical analyses, there is still a dearth of statistical tools that help consolidate all such information in a single platform. By virtue of stringent computational requirements, the statistical workflow is often passive with limited visual exploration.

RESULTS: In this study, we have developed a Java-based statistical framework (https://github.com/KociOrges/cviewer) to explore shotgun metagenomics data, which integrates seamlessly with conventional pipelines and offers exploratory as well as hypothesis-driven analyses. The end product is a highly interactive toolkit with a multiple document interface, which makes it easier for a person without specialized knowledge to perform analysis of multiomics datasets and unravel biologically relevant patterns. We have designed algorithms based on frequently used numerical ecology and machine learning principles, with value-driven from integrated omics tools which not only find correlations amongst different datasets but also provide discrimination based on case-control relationships.

CONCLUSIONS: CViewer was used to analyse two distinct metagenomic datasets with varying complexities. These include a dietary intervention study to understand Crohn's disease changes during a dietary treatment to include remission, as well as a gut microbiome profile for an obesity dataset comparing subjects who suffer from obesity of different aetiologies and against controls who were lean. Complete analyses of both studies in CViewer then provide very powerful mechanistic insights that corroborate with the published literature and demonstrate its full potential. Video Abstract.}, } @article {pmid38949108, year = {2024}, author = {Bahl, A and Halappanavar, S and Wohlleben, W and Nymark, P and Kohonen, P and Wallin, H and Vogel, U and Haase, A}, title = {Bioinformatics and machine learning to support nanomaterial grouping.}, journal = {Nanotoxicology}, volume = {18}, number = {4}, pages = {373-400}, doi = {10.1080/17435390.2024.2368005}, pmid = {38949108}, issn = {1743-5404}, mesh = {*Machine Learning ; *Nanostructures/chemistry/toxicity ; *Computational Biology/methods ; Humans ; Risk Assessment ; Animals ; }, abstract = {Nanomaterials (NMs) offer plenty of novel functionalities. Moreover, their physicochemical properties can be fine-tuned to meet the needs of specific applications, leading to virtually unlimited numbers of NM variants. Hence, efficient hazard and risk assessment strategies building on New Approach Methodologies (NAMs) become indispensable. Indeed, the design, the development and implementation of NAMs has been a major topic in a substantial number of research projects. One of the promising strategies that can help to deal with the high number of NMs variants is grouping and read-across. Based on demonstrated structural and physicochemical similarity, NMs can be grouped and assessed together. Within an established NM group, read-across may be performed to fill in data gaps for data-poor variants using existing data for NMs within the group. Establishing a group requires a sound justification, usually based on a grouping hypothesis that links specific physicochemical properties to well-defined hazard endpoints. However, for NMs these interrelationships are only beginning to be understood. The aim of this review is to demonstrate the power of bioinformatics with a specific focus on Machine Learning (ML) approaches to unravel the NM Modes-of-Action (MoA) and identify the properties that are relevant to specific hazards, in support of grouping strategies. This review emphasizes the following messages: 1) ML supports identification of the most relevant properties contributing to specific hazards; 2) ML supports analysis of large omics datasets and identification of MoA patterns in support of hypothesis formulation in grouping approaches; 3) omics approaches are useful for shifting away from consideration of single endpoints towards a more mechanistic understanding across multiple endpoints gained from one experiment; and 4) approaches from other fields of Artificial Intelligence (AI) like Natural Language Processing or image analysis may support automated extraction and interlinkage of information related to NM toxicity. Here, existing ML models for predicting NM toxicity and for analyzing omics data in support of NM grouping are reviewed. Various challenges related to building robust models in the field of nanotoxicology exist and are also discussed.}, } @article {pmid38947430, year = {2024}, author = {Li, S and Mao, Y and Yang, J and Li, Y and Dong, J and Wang, Z and Jiang, L and He, S}, title = {Efficient integration of covalent triazine frameworks (CTFs) for augmented photocatalytic efficacy: A review of synthesis, strategies, and applications.}, journal = {Heliyon}, volume = {10}, number = {11}, pages = {e32202}, pmid = {38947430}, issn = {2405-8440}, abstract = {Heterogeneous photocatalysis emerges as an exceptionally appealing technological avenue for the direct capture, conversion, and storage of renewable solar energy, facilitating the generation of sustainable and ecologically benign solar fuels and a spectrum of other pertinent applications. Heterogeneous nanocomposites, incorporating Covalent Triazine Frameworks (CTFs), exhibit a wide-ranging spectrum of light absorption, well-suited electronic band structures, rapid charge carrier mobility, ample resource availability, commendable chemical robustness, and straightforward synthetic routes. These attributes collectively position them as highly promising photocatalysts with applicability in diverse fields, including but not limited to the production of photocatalytic solar fuels and the decomposition of environmental contaminants. As the field of photocatalysis through the hybridization of CTFs undergoes rapid expansion, there is a pressing and substantive need for a systematic retrospective analysis and forward-looking evaluation to elucidate pathways for enhancing performance. This comprehensive review commences by directing attention to diverse synthetic methodologies for the creation of composite materials. And then it delves into a thorough exploration of strategies geared towards augmenting performance, encompassing the introduction of electron donor-acceptor (D-A) units, heteroatom doping, defect Engineering, architecture of Heterojunction and optimization of morphology. Following this, it systematically elucidates applications primarily centered around the efficient generation of photocatalytic hydrogen, reduction of carbon dioxide through photocatalysis, and the degradation of organic pollutants. Ultimately, the discourse turns towards unresolved challenges and the prospects for further advancement, offering valuable guidance for the potent harnessing of CTFs in high-efficiency photocatalytic processes.}, } @article {pmid38945180, year = {2024}, author = {Pearl, RL and Donze, LF and Rosas, LG and Agurs-Collins, T and Baskin, ML and Breland, JY and Byker Shanks, C and Cooksey Stowers, K and Johnson, S and Lee, BY and Martin, MY and Mujuru, P and Odoms-Young, A and Panza, E and Pronk, NP and Calicutt, K and Nadglowski, J and Nece, PM and Tedder, M and Chow, LS and Krishnamurti, H and Jay, M and Xi, D and Jastreboff, AM and Stanford, FC}, title = {Ending Weight Stigma to Advance Health Equity.}, journal = {American journal of preventive medicine}, volume = {67}, number = {5}, pages = {785-791}, doi = {10.1016/j.amepre.2024.06.021}, pmid = {38945180}, issn = {1873-2607}, support = {K23 MD015092/MD/NIMHD NIH HHS/United States ; U24 DK132733/DK/NIDDK NIH HHS/United States ; UE5 DK137285/DK/NIDDK NIH HHS/United States ; UM1 TR004921/TR/NCATS NIH HHS/United States ; UL1 TR003142/TR/NCATS NIH HHS/United States ; }, } @article {pmid38941024, year = {2024}, author = {Holstein, T and Muth, T}, title = {Bioinformatic Workflows for Metaproteomics.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2820}, number = {}, pages = {187-213}, pmid = {38941024}, issn = {1940-6029}, mesh = {*Proteomics/methods ; *Computational Biology/methods ; *Workflow ; *Software ; *Microbiota/genetics ; Humans ; Databases, Protein ; Metagenomics/methods ; }, abstract = {The strong influence of microbiomes on areas such as ecology and human health has become widely recognized in the past years. Accordingly, various techniques for the investigation of the composition and function of microbial community samples have been developed. Metaproteomics, the comprehensive analysis of the proteins from microbial communities, allows for the investigation of not only the taxonomy but also the functional and quantitative composition of microbiome samples. Due to the complexity of the investigated communities, methods developed for single organism proteomics cannot be readily applied to metaproteomic samples. For this purpose, methods specifically tailored to metaproteomics are required. In this work, a detailed overview of current bioinformatic solutions and protocols in metaproteomics is given. After an introduction to the proteomic database search, the metaproteomic post-processing steps are explained in detail. Ten specific bioinformatic software solutions are focused on, covering various steps including database-driven identification and quantification as well as taxonomic and functional assignment.}, } @article {pmid38938637, year = {2024}, author = {Yang, J and Deng, H and Zhang, Y and Zhou, Y and Miao, T}, title = {Application of amodal segmentation for shape reconstruction and occlusion recovery in occluded tomatoes.}, journal = {Frontiers in plant science}, volume = {15}, number = {}, pages = {1376138}, pmid = {38938637}, issn = {1664-462X}, abstract = {Common object detection and image segmentation methods are unable to accurately estimate the shape of the occluded fruit. Monitoring the growth status of shaded crops in a specific environment is challenging, and certain studies related to crop harvesting and pest detection are constrained by the natural shadow conditions. Amodal segmentation can focus on the occluded part of the fruit and complete the overall shape of the fruit. We proposed a Transformer-based amodal segmentation algorithm to infer the amodal shape of occluded tomatoes. Considering the high cost of amodal annotation, we only needed modal dataset to train the model. The dataset was taken from two greenhouses on the farm and contains rich occlusion information. We introduced boundary estimation in the hourglass structured network to provide a priori information about the completion of the amodal shapes, and reconstructed the occluded objects using a GAN network (with discriminator) and GAN loss. The model in this study showed accuracy, with average pairwise accuracy of 96.07%, mean intersection-over-union (mIoU) of 94.13% and invisible mIoU of 57.79%. We also examined the quality of pseudo-amodal annotations generated by our proposed model using Mask R-CNN. Its average precision (AP) and average precision with intersection over union (IoU) 0.5 (AP50) reached 63.91%,86.91% respectively. This method accurately and rationally achieves the shape of occluded tomatoes, saving the cost of manual annotation, and is able to deal with the boundary information of occlusion while decoupling the relationship of occluded objects from each other. Future work considers how to complete the amodal segmentation task without overly relying on the occlusion order and the quality of the modal mask, thus promising applications to provide technical support for the advancement of ecological monitoring techniques and ecological cultivation.}, } @article {pmid38937989, year = {2024}, author = {Wu, H and Mu, C and Li, X and Fan, W and Shen, L and Zhu, W}, title = {Breed-Driven Microbiome Heterogeneity Regulates Intestinal Stem Cell Proliferation via Lactobacillus-Lactate-GPR81 Signaling.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {11}, number = {33}, pages = {e2400058}, pmid = {38937989}, issn = {2198-3844}, support = {32030104//National Natural Science Foundation of China/ ; 2022YFD1300402//National Key Research and Development Program of China/ ; }, mesh = {Animals ; *Cell Proliferation/physiology ; *Stem Cells/metabolism/cytology ; *Lactobacillus/metabolism/genetics ; *Receptors, G-Protein-Coupled/metabolism/genetics ; *Gastrointestinal Microbiome/physiology/genetics ; Swine ; *Lactic Acid/metabolism ; Signal Transduction/physiology ; Wnt Signaling Pathway/physiology/genetics ; Jejunum/microbiology/metabolism/cytology ; Obesity/metabolism/microbiology ; Intestinal Mucosa/metabolism/microbiology/cytology ; }, abstract = {Genetically lean and obese individuals have distinct intestinal microbiota and function. However, the underlying mechanisms of the microbiome heterogeneity and its regulation on epithelial function such as intestinal stem cell (ISC) fate remain unclear. Employing pigs of genetically distinct breeds (obese Meishan and lean Yorkshire), this study reveals transcriptome-wide variations in microbial ecology of the jejunum, characterized by enrichment of active Lactobacillus species, notably the predominant Lactobacillus amylovorus (L. amylovorus), and lactate metabolism network in obese breeds. The L. amylovorus-dominant heterogeneity is paralleled with epithelial functionality difference as reflected by highly expressed GPR81, more proliferative ISCs and activated Wnt/β-catenin signaling. Experiments using in-house developed porcine jejunal organoids prove that live L. amylovorus and its metabolite lactate promote intestinal organoid growth. Mechanistically, L. amylovorus and lactate activate Wnt/β-catenin signaling in a GPR81-dependent manner to promote ISC-mediated epithelial proliferation. However, heat-killed L. amylovorus fail to cause these changes. These findings uncover a previously underrepresented role of L. amylovorus in regulating jejunal stem cells via Lactobacillus-lactate-GPR81 axis, a key mechanism bridging breed-driven intestinal microbiome heterogeneity with ISC fate. Thus, results from this study provide new insights into the role of gut microbiome and stem cell interactions in maintaining intestinal homeostasis.}, } @article {pmid38936731, year = {2024}, author = {Li, Y and Hou, K and Chang, Y and Yuan, B and Li, X}, title = {A methodological study on the identification of ecological security change processes and zoning control strategies -- Based on the perspective of sustainable development.}, journal = {The Science of the total environment}, volume = {946}, number = {}, pages = {174190}, doi = {10.1016/j.scitotenv.2024.174190}, pmid = {38936731}, issn = {1879-1026}, abstract = {Ecological security (ES) is a crucial indicator for assessing the sustainable development of a region. Currently, most studies on ES primarily focus on process analysis, and the integration of environmental variability into the development of tailored control strategies for regions with varying ecological quality is overlooked. Therefore, in this study, we identified regional ES change processes, employed an optimized system to calculate the ecological security index (ESI), and identified ecological corridors (ECs) through the Minimum Constrained Resource (MCR) model to determine zoning strategies for typical arid regions, using the Ningxia region in the Yellow River Basin of China as an example. The findings showed that (1) from 2006 to 2020, the ESI values of most regions were between 0.2 and 0.4, with small but consistent increases in the ESI values over the years. (2) The proportion of regions with high ES ratings increased by 9.08 % across all districts and counties, and the center of gravity of ES shifted in a north-south and east-west direction. (3) The ESI exhibited a strong positive spatial correlation, characterized by spatial diffusion and spillover effects in most regions. (4) The ECs were predominantly distributed in a north-south direction, involving a total of 20 districts and counties. Based on the principles of sustainable development, we developed a model for the dynamic identification and zoning control of regional ES, aiming to provide a practical framework for effective ecological restoration and protection measures. Additionally, the strategies and methodologies presented in this study serve as important references for similar regions worldwide to facilitate the zoning control of ES, highlighting the broader significance and applicability of the study.}, } @article {pmid38936185, year = {2024}, author = {Hu, CJ and Lv, YQ and Xian, WD and Jiao, JY and Lian, ZH and Tan, S and Li, MM and Luo, ZH and Liu, ZT and Lv, AP and Liu, L and Ali, M and Liu, WQ and Li, WJ}, title = {Multi-omics insights into the function and evolution of sodium benzoate biodegradation pathway in Benzoatithermus flavus gen. nov., sp. nov. from hot spring.}, journal = {Journal of hazardous materials}, volume = {476}, number = {}, pages = {135017}, doi = {10.1016/j.jhazmat.2024.135017}, pmid = {38936185}, issn = {1873-3336}, mesh = {*Sodium Benzoate/metabolism ; *Biodegradation, Environmental ; *Hot Springs/microbiology ; *Phylogeny ; Water Pollutants, Chemical/metabolism ; Multiomics ; }, abstract = {Biodegradation stands as an eco-friendly and effective approach for organic contaminant remediation. However, research on microorganisms degrading sodium benzoate contaminants in extreme environments remains limited. In this study, we report to display the isolation of a novel hot spring enriched cultures with sodium benzoate (400 mg/L) as the sole carbon source. The results revealed that the phylum Pseudomonadota was the potential sodium benzoate degrader and a novel genus within the family Geminicoccaceae of this phylum. The isolated strain was named Benzoatithermus flavus SYSU G07066[T] and was isolated from HNT-2 hot spring samples. Genomic analysis revealed that SYSU G07066[T] carried benABC genes and physiological experiments indicated the ability to utilize sodium benzoate as a sole carbon source for growth, which was further confirmed by transcriptomic data with expression of benABC. Phylogenetic analysis suggested that Horizontal Gene Transfer (HGT) plays a significant role in acquiring sodium benzoate degradation capability among prokaryotes, and SYSU G07066[T] might have acquired benABC genes through HGT from the family Acetobacteraceae. The discovery of the first microorganism with sodium benzoate degradation function from a hot spring enhances our understanding of the diverse functions within the family Geminicoccaceae. This study unearths the first novel genus capable of efficiently degrading sodium benzoate and its evolution history at high temperatures, holding promising industrial applications, and provides a new perspective for further exploring the application potential of hot spring "microbial dark matter".}, } @article {pmid38935782, year = {2024}, author = {Louvet, A and Mantoux, C and Machon, N}, title = {Assessing the extinction risk of the spontaneous flora in urban tree bases.}, journal = {PLoS computational biology}, volume = {20}, number = {6}, pages = {e1012191}, pmid = {38935782}, issn = {1553-7358}, mesh = {*Extinction, Biological ; *Trees ; *Bayes Theorem ; *Cities ; *Ecosystem ; Computational Biology ; Markov Chains ; Models, Biological ; Paris ; }, abstract = {As the spatial arrangement of trees planted along streets in cities makes their bases potential ecological corridors for the flora, urban tree bases may be a key contributor to the overall connectivity of the urban ecosystem. However, these tree bases are also a highly fragmented environment in which extinctions are frequent. The goal of this study was to assess the plant species' ability to survive and spread through urban tree bases. To do so, we developed a Bayesian framework to assess the extinction risk of a plant metapopulation using presence/absence data, assuming that the occupancy dynamics was described by a Hidden Markov Model. The novelty of our approach is to take into account the combined effect of low-distance dispersal and the potential presence of a seed bank on the extinction risk. We introduced a metric of the extinction risk and examined its performance over a wide range of metapopulation parameters. We applied our framework to yearly floristic inventories carried out in 1324 tree bases in Paris, France. While local extinction risks were generally high, extinction risks at the street scale varied greatly from one species to another. We identified 10 plant species that could survive and spread through urban tree bases, and three plant traits correlated with the extinction risk at the metapopulation scale: the maximal height, and the beginning and end of the flowering period. Our results suggest that some plant species can use urban tree bases as ecological corridors despite high local extinction risks by forming a seed bank. We also identified other plant traits correlated with the ability to survive in tree bases, related to the action of gardeners. Moreover, our findings demonstrate that our Bayesian estimation framework based on percolation theory has the potential to be extended to more general metapopulations.}, } @article {pmid38932245, year = {2024}, author = {Conradie, T and Caparros-Martin, JA and Egan, S and Kicic, A and Koks, S and Stick, SM and Agudelo-Romero, P}, title = {Exploring the Complexity of the Human Respiratory Virome through an In Silico Analysis of Shotgun Metagenomic Data Retrieved from Public Repositories.}, journal = {Viruses}, volume = {16}, number = {6}, pages = {}, pmid = {38932245}, issn = {1999-4915}, support = {NHMRC115648//National Health and Medical Research Council/ ; Synergy grant APP118364//National Health and Medical Research Council/ ; Theme Collaboration Award 2023//Telethon Kids Institute/ ; N/A//Google cloud education program/ ; Investigator grant 2021/GR000216//National Health and Medical Research Council/ ; }, mesh = {Humans ; *Metagenomics/methods ; *Virome ; *Genome, Viral ; *Respiratory System/virology ; *Viruses/genetics/classification/isolation & purification ; Metagenome ; Computer Simulation ; Phylogeny ; Computational Biology/methods ; Microbiota ; Bacteriophages/genetics/classification/isolation & purification ; }, abstract = {BACKGROUND: Respiratory viruses significantly impact global morbidity and mortality, causing more disease in humans than any other infectious agent. Beyond pathogens, various viruses and bacteria colonize the respiratory tract without causing disease, potentially influencing respiratory diseases' pathogenesis. Nevertheless, our understanding of respiratory microbiota is limited by technical constraints, predominantly focusing on bacteria and neglecting crucial populations like viruses. Despite recent efforts to improve our understanding of viral diversity in the human body, our knowledge of viral diversity associated with the human respiratory tract remains limited.

METHODS: Following a comprehensive search in bibliographic and sequencing data repositories using keyword terms, we retrieved shotgun metagenomic data from public repositories (n = 85). After manual curation, sequencing data files from 43 studies were analyzed using EVEREST (pipEline for Viral assEmbly and chaRactEriSaTion). Complete and high-quality contigs were further assessed for genomic and taxonomic characterization.

RESULTS: Viral contigs were obtained from 194 out of the 868 FASTQ files processed through EVEREST. Of the 1842 contigs that were quality assessed, 8% (n = 146) were classified as complete/high-quality genomes. Most of the identified viral contigs were taxonomically classified as bacteriophages, with taxonomic resolution ranging from the superkingdom level down to the species level. Captured contigs were spread across 25 putative families and varied between RNA and DNA viruses, including previously uncharacterized viral genomes. Of note, airway samples also contained virus(es) characteristic of the human gastrointestinal tract, which have not been previously described as part of the lung virome. Additionally, by performing a meta-analysis of the integrated datasets, ecological trends within viral populations linked to human disease states and their biogeographical distribution along the respiratory tract were observed.

CONCLUSION: By leveraging publicly available repositories of shotgun metagenomic data, the present study provides new insights into viral genomes associated with specimens from the human respiratory tract across different disease spectra. Further studies are required to validate our findings and evaluate the potential impact of these viral communities on respiratory tract physiology.}, } @article {pmid38926582, year = {2024}, author = {Tian, SY and Yasuhara, M and Condamine, FL and Huang, HM and Fernando, AGS and Aguilar, YM and Pandita, H and Irizuki, T and Iwatani, H and Shin, CP and Renema, W and Kase, T}, title = {Cenozoic history of the tropical marine biodiversity hotspot.}, journal = {Nature}, volume = {632}, number = {8024}, pages = {343-349}, pmid = {38926582}, issn = {1476-4687}, mesh = {Animals ; *Aquatic Organisms/classification/isolation & purification ; *Biodiversity ; Climate Change ; Datasets as Topic ; Extinction, Biological ; *Fossils ; Genetic Speciation ; History, Ancient ; Time Factors ; *Tropical Climate ; Pacific Ocean ; Coral Reefs ; }, abstract = {The region with the highest marine biodiversity on our planet is known as the Coral Triangle or Indo-Australian Archipelago (IAA)[1,2]. Its enormous biodiversity has long attracted the interest of biologists; however, the detailed evolutionary history of the IAA biodiversity hotspot remains poorly understood[3]. Here we present a high-resolution reconstruction of the Cenozoic diversity history of the IAA by inferring speciation-extinction dynamics using a comprehensive fossil dataset. We found that the IAA has exhibited a unidirectional diversification trend since about 25 million years ago, following a roughly logistic increase until a diversity plateau beginning about 2.6 million years ago. The growth of diversity was primarily controlled by diversity dependency and habitat size, and also facilitated by the alleviation of thermal stress after 13.9 million years ago. Distinct net diversification peaks were recorded at about 25, 20, 16, 12 and 5 million years ago, which were probably related to major tectonic events in addition to climate transitions. Key biogeographic processes had far-reaching effects on the IAA diversity as shown by the long-term waning of the Tethyan descendants versus the waxing of cosmopolitan and IAA taxa. Finally, it seems that the absence of major extinctions and the Cenozoic cooling have been essential in making the IAA the richest marine biodiversity hotspot on Earth.}, } @article {pmid38924481, year = {2024}, author = {Ramos, SR and Reynolds, H and Johnson, C and Melkus, G and Kershaw, T and Thayer, JF and Vorderstrasse, A}, title = {Perceptions of HIV-Related Comorbidities and Usability of a Virtual Environment for Cardiovascular Disease Prevention Education in Sexual Minority Men With HIV: Formative Phases of a Pilot Randomized Controlled Trial.}, journal = {Journal of medical Internet research}, volume = {26}, number = {}, pages = {e57351}, pmid = {38924481}, issn = {1438-8871}, mesh = {Humans ; Male ; *Cardiovascular Diseases/prevention & control ; *HIV Infections/prevention & control/psychology ; Pilot Projects ; *Sexual and Gender Minorities/psychology/statistics & numerical data ; Adult ; Middle Aged ; Comorbidity ; Virtual Reality ; User-Computer Interface ; }, abstract = {BACKGROUND: Sexual minority men with HIV are at an increased risk of cardiovascular disease (CVD) and have been underrepresented in behavioral research and clinical trials.

OBJECTIVE: This study aims to explore perceptions of HIV-related comorbidities and assess the interest in and usability of a virtual environment for CVD prevention education in Black and Latinx sexual minority men with HIV.

METHODS: This is a 3-phase pilot behavioral randomized controlled trial. We report on formative phases 1 and 2 that informed virtual environment content and features using qualitative interviews, usability testing, and beta testing with a total of 25 individuals. In phase 1, a total of 15 participants completed interviews exploring HIV-related illnesses of concern that would be used to tailor the virtual environment. In phase 2, usability testing and beta testing were conducted with 10 participants to assess interest, features, and content.

RESULTS: In phase 1, we found that CVD risk factors included high blood pressure, myocardial infarction, stroke, and diabetes. Cancer (prostate, colon, and others) was a common concern, as were mental health conditions. In phase 2, all participants completed the 12-item usability checklist with favorable feedback within 30 to 60 minutes. Beta-testing interviews suggested (1) mixed perceptions of health and HIV, (2) high risk for comorbid conditions, (3) virtual environment features were promising, and (4) the need for diverse avatar representations.

CONCLUSIONS: We identified several comorbid conditions of concern, and findings carry significant implications for mitigating barriers to preventive health screenings, given the shared risk factors between HIV and related comorbidities. Highly rated aspects of the virtual environment were anonymity; meeting others with HIV who identify as gay or bisexual; validating lesbian, gay, bisexual, transgender, queer, and others (LGBTQ+) images and content; and accessibility to CVD prevention education. Critical end-user feedback from beta testing suggested more options for avatar customization in skin, hair, and body representation. Our next phase will test the virtual environment as a new approach to advancing cardiovascular health equity in ethnic and racial sexual minority men with HIV.

TRIAL REGISTRATION: ClinicalTrials.gov NCT04061915; https://clinicaltrials.gov/study/NCT05242952.

RR2-10.2196/38348.}, } @article {pmid38920364, year = {2024}, author = {Mau, RL and Hayer, M and Purcell, AM and Geisen, S and Hungate, BA and Schwartz, E}, title = {Measurements of soil protist richness and community composition are influenced by primer pair, annealing temperature, and bioinformatics choices.}, journal = {Applied and environmental microbiology}, volume = {90}, number = {7}, pages = {e0080024}, pmid = {38920364}, issn = {1098-5336}, support = {DE-AC52-07NA27344//U.S. Department of Energy (DOE)/ ; DE-SC0020172//U.S. Department of Energy (DOE)/ ; DE-SC0023126//U.S. Department of Energy (DOE)/ ; }, mesh = {*RNA, Ribosomal, 18S/genetics ; *Computational Biology/methods ; *Eukaryota/genetics/classification ; *DNA Primers/genetics ; *Soil Microbiology ; Biodiversity ; Temperature ; Soil/parasitology/chemistry ; Polymerase Chain Reaction ; }, abstract = {Protists are a diverse and understudied group of microbial eukaryotic organisms especially in terrestrial environments. Advances in molecular methods are increasing our understanding of the distribution and functions of these creatures; however, there is a vast array of choices researchers make including barcoding genes, primer pairs, PCR settings, and bioinformatic options that can impact the outcome of protist community surveys. Here, we tested four commonly used primer pairs targeting the V4 and V9 regions of the 18S rRNA gene using different PCR annealing temperatures and processed the sequences with different bioinformatic parameters in 10 diverse soils to evaluate how primer pair, amplification parameters, and bioinformatic choices influence the composition and richness of protist and non-protist taxa using Illumina sequencing. Our results showed that annealing temperature influenced sequencing depth and protist taxon richness for most primer pairs, and that merging forward and reverse sequencing reads for the V4 primer pairs dramatically reduced the number of sequences and taxon richness of protists. The data sets of primers that targeted the same 18S rRNA gene region (e.g., V4 or V9) had similar protist community compositions; however, data sets from primers targeting the V4 18S rRNA gene region detected a greater number of protist taxa compared to those prepared with primers targeting the V9 18S rRNA region. There was limited overlap of protist taxa between data sets targeting the two different gene regions (80/549 taxa). Together, we show that laboratory and bioinformatic choices can substantially affect the results and conclusions about protist diversity and community composition using metabarcoding.IMPORTANCEEcosystem functioning is driven by the activity and interactions of the microbial community, in both aquatic and terrestrial environments. Protists are a group of highly diverse, mostly unicellular microbes whose identity and roles in terrestrial ecosystem ecology have been largely ignored until recently. This study highlights the importance of choices researchers make, such as primer pair, on the results and conclusions about protist diversity and community composition in soils. In order to better understand the roles protist taxa play in terrestrial ecosystems, biases in methodological and analytical choices should be understood and acknowledged.}, } @article {pmid38917931, year = {2024}, author = {Wang, H and Li, Y and Huang, G and Ma, Y and Zhang, Q and Li, Y}, title = {Analyzing variation of water inflow to inland lakes under climate change: Integrating deep learning and time series data mining.}, journal = {Environmental research}, volume = {259}, number = {}, pages = {119478}, doi = {10.1016/j.envres.2024.119478}, pmid = {38917931}, issn = {1096-0953}, mesh = {*Lakes/chemistry ; *Climate Change ; *Deep Learning ; Data Mining ; Environmental Monitoring/methods ; }, abstract = {The alarming depletion of global inland lakes in recent decades makes it essential to predict water inflow from rivers to lakes (WIRL) trend and unveil the dominant influencing driver, particularly in the context of climate change. The raw time series data contains multiple components (i.e., long-term trend, seasonal periodicity, and random noise), which makes it challenging for traditional machine/deep learning techniques to effectively capture long-term trend information. In this study, a novel FactorConvSTLnet (FCS) method is developed through integrating STL decomposition, convolutional neural networks (CNN), and factorial analysis into a general framework. FCS is more robust in long-term WIRL trend prediction through separating trend information as a modeling predictor, as well as unveiling predominant drivers. FCS is applied to typical inland lakes (the Aral Sea and the Lake Balkhash) in Central Asia, and results indicate that FCS (Nash-Sutcliffe efficiency = 0.88, root mean squared error = 67m[3]/s, mean relative error = 10%) outperforms the traditional CNN. Some main findings are: (i) during 1960-1990, reservoir water storage (WSR) was the dominant driver for the two lakes, respectively contributing to 71% and 49%; during 1991-2014 and 2015-2099, evaporation (EVAP) would be the dominant driver, with the contribution of 30% and 47%; (ii) climate change would shift the dominant driver from human activities to natural factors, where EVAP and surface snow amount (SNW) have an increasing influence on WIRL; (iii) compared to SSP1-2.6, the SNW contribution would decrease by 26% under SSP5-8.5, while the EVAP contribution would increase by 9%. The findings reveal the main drivers of shrinkage of the inland lakes and provide the scientific basis for promoting regional ecological sustainability.}, } @article {pmid38917628, year = {2024}, author = {Li, Q and Ma, Q and Zhou, Y and Jiang, X and Parales, RE and Zhao, S and Zhuang, Y and Ruan, Z}, title = {Isolation, identification, and degradation mechanism by multi-omics of mesotrione-degrading Amycolatopsis nivea La24.}, journal = {Journal of hazardous materials}, volume = {476}, number = {}, pages = {134951}, doi = {10.1016/j.jhazmat.2024.134951}, pmid = {38917628}, issn = {1873-3336}, mesh = {*Herbicides/metabolism/chemistry ; *Cyclohexanones/metabolism ; *Biodegradation, Environmental ; *Amycolatopsis/metabolism/genetics ; Metabolomics ; Sulfonylurea Compounds/metabolism ; Soil Pollutants/metabolism ; Multiomics ; }, abstract = {Mesotrione is a herbicide used in agricultural production; however, its stability and long-term residues pose ecological risks to soil health and subsequent crops. In this research, the strain Amycolatopsis nivea La24 was identified as capable of completely degrading 50 mg∙L[-1] mesotrione within 48 h. It exhibited a broad adaptability to various environment and could degrade three sulfonylurea herbicides (nicosulfuron, chlorimuron-methyl, and cinosulfuron). Non-target metabonomic and mass spectrometry demonstrated that La24 strain broke down the mesotrione parent molecule by targeting the β-diketone bond and nitro group, resulting in the production of five possible degradation products. The differentially expressed genes were significantly enriched in fatty acid degradation, amino acid metabolism, and other pathways, and the differentially metabolites in glutathione metabolism, arginine/proline metabolism, cysteine/methionine metabolism, and other pathways. Additionally, it was confirmed by heterologous expression that nitroreductase was directly involved in the mesotrione degradation, and NDMA-dependent methanol dehydrogenase would increase the resistance to mesotrione. Finally, the intracellular response of La24 during mesotrione degradation was proposed. This work provides insight for a comprehensive understanding of the mesotrione biodegradation mechanism, significantly expands the resources for pollutant degradation, and offers the potential for a more sustainable solution to address herbicide pollution in soil.}, } @article {pmid38917233, year = {2024}, author = {Costa, IB and Pimenta, IDSF and Aiquoc, KM and Oliveira, ÂGRDC}, title = {Congenital syphilis, syphilis in pregnancy and prenatal care in Brazil: An ecological study.}, journal = {PloS one}, volume = {19}, number = {6}, pages = {e0306120}, pmid = {38917233}, issn = {1932-6203}, mesh = {Humans ; Pregnancy ; Female ; Brazil/epidemiology ; *Syphilis, Congenital/epidemiology ; *Prenatal Care ; *Pregnancy Complications, Infectious/epidemiology ; Incidence ; Adult ; Socioeconomic Factors ; Syphilis/epidemiology/diagnosis ; Adolescent ; Young Adult ; }, abstract = {The aim of this research was to evaluate the incidence of congenital syphilis and the ratio between congenital syphilis and syphilis in pregnant women in Brazil according to socioeconomic indicators (inadequate water supply and sanitation; illiteracy at 15 years of age or older; household income per capita; proportion of poor people; Gini index; human development index; and average health expenditure per inhabitant by the health system) and prenatal quality-of-care indicators. We conducted an ecological study using a sample composed of 257 municipalities, each with ≥ 100,000 inhabitants. Data was collected from four public databases: the Brazilian Institute of Geography and Statistics, comprising socioeconomical data from the 2010 census; and the data of 2019 available in the databases of the Department of Informatics of the Brazilian Health System, Information and Management of Primary Care, and the Electronic Citizen Information System. Descriptive analysis of dependent and independent variables and bivariate analysis by Negative Binomial regression were carried out. The mean incidence of congenital syphilis was 38% higher in municipalities with a Human Development Index up to 0.785 (ratio of means [RM] = 1.38; p = 0.049) and 57% higher among populations where less than 50% of primary healthcare services provided a rapid test for syphilis (RM = 1.57; p < 0.001). The ratio between congenital syphilis and syphilis in pregnant women was 29% higher in municipalities with a low household income per capita (RM = 1.29; p < 0.001) and 28% higher in locations where less than 50% of the primary healthcare services provided a rapid test for syphilis (RM = 1.28; p < 0.001). There was no statistical significance of the quality of prenatal care compared to the outcomes. This result underscores the challenges in detecting syphilis infections among pregnant women during prenatal care, consequently increasing the risk of vertical transmission of the disease to the fetus. Traits of inequality in the occurrence of congenital syphilis also draw attention to strategies to reduce health inequities and improve prenatal care.}, } @article {pmid38916705, year = {2024}, author = {Yu, J and Chen, S}, title = {The Use of Big Data Analysis in Digital Empowerment of Sustainable Technological Innovation Management of Ecological Enterprises.}, journal = {Environmental science and pollution research international}, volume = {31}, number = {31}, pages = {43956-43966}, pmid = {38916705}, issn = {1614-7499}, mesh = {*Big Data ; China ; Inventions ; Ecology ; Empowerment ; Environmental Monitoring/methods ; Conservation of Natural Resources ; }, abstract = {With the social economy's rapid progress and the popularization of environmental awareness, ecological enterprises have gradually become a crucial trend in the development of modern enterprises. This work intends to promote the development of ecological enterprises to a higher level. This work first analyzes the management mode of ecological enterprises in the context of big data in China. Then, it establishes various indicators to analyze the role of sustainable technological innovation in enterprise development and the impact of digital empowerment on enterprise development. Finally, this work takes China's manufacturing industry and ecological enterprises in Hubei Province as examples to summarize the digital empowerment of sustainable technological innovation management of ecological enterprises under the background of big data. The final result indicates that sustainable technological innovation significantly reduces ecological enterprises' resource consumption and waste emissions. Additionally, it has a significant positive effect on improving enterprise output value and economic benefits. The digital empowerment of enterprises has a significant driving effect on sustainable technological innovation, with a digital driving coefficient of 26. This work provides a feasible scheme for the specific application of big data analysis in the technology innovation management of ecological enterprises, including market demand analysis, environmental monitoring and governance, technology assessment and risk management. This work expounds the role of big data analysis technology in improving decision-making efficiency, optimizing resource allocation and enhancing the competitiveness of enterprises in the digital empowerment of ecological enterprises.}, } @article {pmid38915508, year = {2024}, author = {Shukla, HG and Chakraborty, M and Emerson, JJ}, title = {Genetic variation in recalcitrant repetitive regions of the Drosophila melanogaster genome.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {38915508}, issn = {2692-8205}, support = {S10 OD021718/OD/NIH HHS/United States ; R35 GM153327/GM/NIGMS NIH HHS/United States ; P30 AR075047/AR/NIAMS NIH HHS/United States ; R01 GM123303/GM/NIGMS NIH HHS/United States ; S10 OD010794/OD/NIH HHS/United States ; P30 CA062203/CA/NCI NIH HHS/United States ; R00 GM129411/GM/NIGMS NIH HHS/United States ; }, abstract = {Many essential functions of organisms are encoded in highly repetitive genomic regions, including histones involved in DNA packaging, centromeres that are core components of chromosome segregation, ribosomal RNA comprising the protein translation machinery, telomeres that ensure chromosome integrity, piRNA clusters encoding host defenses against selfish elements, and virtually the entire Y chromosome. These regions, formed by highly similar tandem arrays, pose significant challenges for experimental and informatic study, impeding sequence-level descriptions essential for understanding genetic variation. Here, we report the assembly and variation analysis of such repetitive regions in Drosophila melanogaster, offering significant improvements to the existing community reference assembly. Our work successfully recovers previously elusive segments, including complete reconstructions of the histone locus and the pericentric heterochromatin of the X chromosome, spanning the Stellate locus to the distal flank of the rDNA cluster. To infer structural changes in these regions where alignments are often not practicable, we introduce landmark anchors based on unique variants that are putatively orthologous. These regions display considerable structural variation between different D. melanogaster strains, exhibiting differences in copy number and organization of homologous repeat units between haplotypes. In the histone cluster, although we observe minimal genetic exchange indicative of crossing over, the variation patterns suggest mechanisms such as unequal sister chromatid exchange. We also examine the prevalence and scale of concerted evolution in the histone and Stellate clusters and discuss the mechanisms underlying these observed patterns.}, } @article {pmid38915006, year = {2024}, author = {Reininghaus, U and Schwannauer, M and Barne, I and Beames, JR and Bonnier, RA and Brenner, M and Breznoščáková, D and Dančík, D and De Allegri, M and Di Folco, S and Durstewitz, D and Gugel, J and Hajdúk, M and Heretik, A and Izáková, Ľ and Katreniakova, Z and Kiekens, G and Koppe, G and Kurilla, A and Marelli, L and Nagyova, I and Nguyen, H and Pečeňák, J and Schulte-Strathaus, JCC and Sotomayor-Enriquez, K and Uyttebroek, L and Weermeijer, J and Wolters, M and Wensing, M and Boehnke, JR and Myin-Germeys, I and Schick, A}, title = {Strategies, processes, outcomes, and costs of implementing experience sampling-based monitoring in routine mental health care in four European countries: study protocol for the IMMERSE effectiveness-implementation study.}, journal = {BMC psychiatry}, volume = {24}, number = {1}, pages = {465}, pmid = {38915006}, issn = {1471-244X}, support = {945263//Horizon 2020/ ; 945263//Horizon 2020/ ; 945263//Horizon 2020/ ; 945263//Horizon 2020/ ; 945263//Horizon 2020/ ; 945263//Horizon 2020/ ; 945263//Horizon 2020/ ; 945263//Horizon 2020/ ; 945263//Horizon 2020/ ; 945263//Horizon 2020/ ; 945263//Horizon 2020/ ; 389624707//DFG/ ; 101063326//Marie Skłodowska-Curie fellowship/ ; 1204924N//Research Foundation Flanders/ ; APVV-22-0587//Agentúra na Podporu Výskumu a Vývoja/ ; }, mesh = {Humans ; Belgium ; Cost-Benefit Analysis/methods ; Ecological Momentary Assessment ; Europe ; Germany ; Mental Disorders/therapy/economics ; *Mental Health Services/economics ; Slovakia ; *Randomized Controlled Trials as Topic ; *Multicenter Studies as Topic ; }, abstract = {BACKGROUND: Recent years have seen a growing interest in the use of digital tools for delivering person-centred mental health care. Experience Sampling Methodology (ESM), a structured diary technique for capturing moment-to-moment variation in experience and behaviour in service users' daily life, reflects a particularly promising avenue for implementing a person-centred approach. While there is evidence on the effectiveness of ESM-based monitoring, uptake in routine mental health care remains limited. The overarching aim of this hybrid effectiveness-implementation study is to investigate, in detail, reach, effectiveness, adoption, implementation, and maintenance as well as contextual factors, processes, and costs of implementing ESM-based monitoring, reporting, and feedback into routine mental health care in four European countries (i.e., Belgium, Germany, Scotland, Slovakia).

METHODS: In this hybrid effectiveness-implementation study, a parallel-group, assessor-blind, multi-centre cluster randomized controlled trial (cRCT) will be conducted, combined with a process and economic evaluation. In the cRCT, 24 clinical units (as the cluster and unit of randomization) at eight sites in four European countries will be randomly allocated using an unbalanced 2:1 ratio to one of two conditions: (a) the experimental condition, in which participants receive a Digital Mobile Mental Health intervention (DMMH) and other implementation strategies in addition to treatment as usual (TAU) or (b) the control condition, in which service users are provided with TAU. Outcome data in service users and clinicians will be collected at four time points: at baseline (t0), 2-month post-baseline (t1), 6-month post-baseline (t2), and 12-month post-baseline (t3). The primary outcome will be patient-reported service engagement assessed with the service attachment questionnaire at 2-month post-baseline. The process and economic evaluation will provide in-depth insights into in-vivo context-mechanism-outcome configurations and economic costs of the DMMH and other implementation strategies in routine care, respectively.

DISCUSSION: If this trial provides evidence on reach, effectiveness, adoption, implementation and maintenance of implementing ESM-based monitoring, reporting, and feedback, it will form the basis for establishing its public health impact and has significant potential to bridge the research-to-practice gap and contribute to swifter ecological translation of digital innovations to real-world delivery in routine mental health care.

TRIAL REGISTRATION: ISRCTN15109760 (ISRCTN registry, date: 03/08/2022).}, } @article {pmid38914930, year = {2024}, author = {Jiang, G and Zheng, JY and Ren, SN and Yin, W and Xia, X and Li, Y and Wang, HL}, title = {A comprehensive workflow for optimizing RNA-seq data analysis.}, journal = {BMC genomics}, volume = {25}, number = {1}, pages = {631}, pmid = {38914930}, issn = {1471-2164}, mesh = {*Workflow ; *RNA-Seq/methods ; *Software ; Fungi/genetics ; Computational Biology/methods ; Sequence Analysis, RNA/methods ; Alternative Splicing ; }, abstract = {BACKGROUND: Current RNA-seq analysis software for RNA-seq data tends to use similar parameters across different species without considering species-specific differences. However, the suitability and accuracy of these tools may vary when analyzing data from different species, such as humans, animals, plants, fungi, and bacteria. For most laboratory researchers lacking a background in information science, determining how to construct an analysis workflow that meets their specific needs from the array of complex analytical tools available poses a significant challenge.

RESULTS: By utilizing RNA-seq data from plants, animals, and fungi, it was observed that different analytical tools demonstrate some variations in performance when applied to different species. A comprehensive experiment was conducted specifically for analyzing plant pathogenic fungal data, focusing on differential gene analysis as the ultimate goal. In this study, 288 pipelines using different tools were applied to analyze five fungal RNA-seq datasets, and the performance of their results was evaluated based on simulation. This led to the establishment of a relatively universal and superior fungal RNA-seq analysis pipeline that can serve as a reference, and certain standards for selecting analysis tools were derived for reference. Additionally, we compared various tools for alternative splicing analysis. The results based on simulated data indicated that rMATS remained the optimal choice, although consideration could be given to supplementing with tools such as SpliceWiz.

CONCLUSION: The experimental results demonstrate that, in comparison to the default software parameter configurations, the analysis combination results after tuning can provide more accurate biological insights. It is beneficial to carefully select suitable analysis software based on the data, rather than indiscriminately choosing tools, in order to achieve high-quality analysis results more efficiently.}, } @article {pmid38911902, year = {2024}, author = {Boyes, D and Holland, PWH and , and , and , and , and , and , and , }, title = {The genome sequence of the White-point, Mythimna albipuncta (Denis & Schiffermüller, 1775).}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {62}, pmid = {38911902}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual male Mythimna albipuncta (the White-point; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 698.6 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.38 kilobases in length. Gene annotation of this assembly on Ensembl identified 13,679 protein coding genes.}, } @article {pmid38909735, year = {2024}, author = {Su, F and Huo, D and Yang, H and Sun, L}, title = {CircRNA8388 functions as the sponge for miR-2392 during intestinal regeneration in sea cucumber Apostichopus japonicus.}, journal = {International journal of biological macromolecules}, volume = {274}, number = {Pt 2}, pages = {133302}, doi = {10.1016/j.ijbiomac.2024.133302}, pmid = {38909735}, issn = {1879-0003}, mesh = {Animals ; Gene Expression Profiling ; Gene Expression Regulation ; Gene Ontology ; *Intestines ; *MicroRNAs/genetics ; *Regeneration/genetics ; *RNA, Circular/genetics ; *Stichopus/genetics ; }, abstract = {The sea cucumber Apostichopus japonicus can expel internal organs under stress and regenerate them subsequently. However, growth is delayed during regeneration, significantly impacting the industry. Circular RNAs (circRNAs) are single-stranded circular RNA molecules produced through alternative splicing of mRNA precursors. They play crucial roles in regulating gene expression via the ceRNA mechanism. In this study, circRNA profiles of control and regenerated intestines were constructed. A total of 15,874 circRNAs were identified, with a length of 300-350 nucleotides (nt) being the most abundant. Sanger sequencing confirmed the circular structure of circRNA398. Compared with the normal intestine, 50 and 83 differentially expressed circRNAs (DE-circRNAs) were identified in the regenerated intestine at 1 and 3 days post evisceration (dpe), respectively. Gene ontology (GO) terms for signal transduction and development regulation were most significantly enriched in 1dpeVScon and 3dpeVScon treatments, respectively. The dual-luciferase assay revealed that circRNA8388 functions as a sponge for miR-2392, participating in the remodeling of the extracellular matrix (ECM). In conclusion, these findings will contribute to the enhancement of the non-coding RNA database for echinoderms and lay the groundwork for future investigations into circRNA regulation during intestinal regeneration.}, } @article {pmid38908558, year = {2024}, author = {Yang, Y and Li, Z and Wen, J}, title = {Long term impact of Wenchuan earthquake on population mental and behavioral disorders in heavily-stricken areas: An ecological study based on big data.}, journal = {Journal of affective disorders}, volume = {361}, number = {}, pages = {589-595}, doi = {10.1016/j.jad.2024.06.070}, pmid = {38908558}, issn = {1573-2517}, mesh = {Humans ; *Earthquakes ; China/epidemiology ; Male ; Female ; Middle Aged ; Adult ; *Mental Disorders/epidemiology ; *Disasters/statistics & numerical data ; *Survivors/psychology/statistics & numerical data ; Prevalence ; Adolescent ; Aged ; *Big Data ; Young Adult ; Risk Factors ; Child ; Urbanization ; }, abstract = {BACKGROUND: This study aimed to explore and evaluate the development trends and differential changes in the prevalence of mental and behavioral disorders among the earthquake survivors in exposure groups (highly hard-hit areas) and control groups (general disaster areas) from 2015 to 2019, as well as to investigate the potential influencing factors.

METHODS: Data was obtained from the Sichuan Health Information System and the Sichuan Health Yearbook, the prevalence of the exposure group and the control group were calculated, the difference between the two groups was evaluated using the prevalence rate ratio, and a fixed effect model was developed to investigate the potential influencing factors of the prevalence.

RESULTS: The prevalence by gender and age in the exposure group was always greater than those in the control group (RR>1), although the disparity between the two proceeded to diminish with time. The urbanization rate (β = 0.0448, P < 0.05) and disaster area levels (β = 0.0104, P < 0.05) were risk factors for the prevalence of mental and behavioral disorders.

LIMITATIONS: The study only collected data at the group level following the Wenchuan earthquake. Consequently, the findings are only applicable at the group level. Furthermore, diagnostic criteria for various types of mental and behavioral disorders diseases were not provided.

CONCLUSIONS: The earthquake has a significant long-term impact on mental health. It is necessary to continuously monitor the mental health of Wenchuan earthquake survivors and take appropriate post-disaster intervention measures.}, } @article {pmid38907904, year = {2024}, author = {Roved, J}, title = {MHCtools 1.5: Analysis of MHC Sequencing Data in R.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2809}, number = {}, pages = {275-295}, pmid = {38907904}, issn = {1940-6029}, mesh = {*Major Histocompatibility Complex/genetics ; Humans ; *High-Throughput Nucleotide Sequencing/methods ; *Software ; Animals ; *Haplotypes/genetics ; Computational Biology/methods ; Sequence Analysis, DNA/methods ; Genetic Variation ; Genotyping Techniques/methods ; Genotype ; }, abstract = {The genes of the major histocompatibility complex (MHC) play a vital role in the vertebrate immune system and have attracted considerable interest in evolutionary biology. While the MHC has been characterized in detail in humans (human leukocyte antigen, HLA) and in model organisms such as the mouse, studies in non-model organisms often lack prior knowledge about structure, genetic variability, and evolutionary properties of this locus. MHC genotyping in non-model species commonly relies on PCR-based amplicon sequencing, and while several published protocols facilitate generation of MHC sequence data, there is a lack of transparent and standardized tools for downstream data analysis.Here, I present the R package MHCtools version 1.5, which contains 15 tools that (i) assist accurate MHC genotyping from high-throughput amplicon sequencing data, and provide standardized methods to analyze (ii) MHC diversity, (iii) MHC supertypes, and (iv) MHC haplotypes.I hope that MHCtools will be helpful in future studies of the MHC in non-model species and that it may help to advance our understanding of the important roles of the MHC in ecology and evolution.}, } @article {pmid38904377, year = {2024}, author = {Berasategui, A and Salem, H and Moller, AG and Christopher, Y and Vidaurre Montoya, Q and Conn, C and Read, TD and Rodrigues, A and Ziemert, N and Gerardo, N}, title = {Genomic insights into the evolution of secondary metabolism of Escovopsis and its allies, specialized fungal symbionts of fungus-farming ants.}, journal = {mSystems}, volume = {9}, number = {7}, pages = {e0057624}, pmid = {38904377}, issn = {2379-5077}, support = {BE6922/1-1//Deutsche Forschungsgemeinschaft (DFG)/ ; EXC 2124 - 390838134//Deutsche Forschungsgemeinschaft (DFG)/ ; 1711545//National Science Foundation (NSF)/ ; 1754595//National Science Foundation (NSF)/ ; 1927411//National Science Foundation (NSF)/ ; 2021/04706-1//Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)/ ; 2019/03746-0//Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)/ ; }, mesh = {*Symbiosis ; *Ants/microbiology ; Animals ; *Secondary Metabolism/genetics ; *Phylogeny ; *Genome, Fungal ; *Hypocreales/genetics/metabolism ; Evolution, Molecular ; Genomics ; Biosynthetic Pathways/genetics ; }, abstract = {The metabolic intimacy of symbiosis often demands the work of specialists. Natural products and defensive secondary metabolites can drive specificity by ensuring infection and propagation across host generations. But in contrast to bacteria, little is known about the diversity and distribution of natural product biosynthetic pathways among fungi and how they evolve to facilitate symbiosis and adaptation to their host environment. In this study, we define the secondary metabolism of Escovopsis and closely related genera, symbionts in the gardens of fungus-farming ants. We ask how the gain and loss of various biosynthetic pathways correspond to divergent lifestyles. Long-read sequencing allowed us to define the chromosomal features of representative Escovopsis strains, revealing highly reduced genomes composed of seven to eight chromosomes. The genomes are highly syntenic with macrosynteny decreasing with increasing phylogenetic distance, while maintaining a high degree of mesosynteny. An ancestral state reconstruction analysis of biosynthetic pathways revealed that, while many secondary metabolites are shared with non-ant-associated Sordariomycetes, 56 pathways are unique to the symbiotic genera. Reflecting adaptation to diverging ant agricultural systems, we observe that the stepwise acquisition of these pathways mirrors the ecological radiations of attine ants and the dynamic recruitment and replacement of their fungal cultivars. As different clades encode characteristic combinations of biosynthetic gene clusters, these delineating profiles provide important insights into the possible mechanisms underlying specificity between these symbionts and their fungal hosts. Collectively, our findings shed light on the evolutionary dynamic nature of secondary metabolism in Escovopsis and its allies, reflecting adaptation of the symbionts to an ancient agricultural system.IMPORTANCEMicrobial symbionts interact with their hosts and competitors through a remarkable array of secondary metabolites and natural products. Here, we highlight the highly streamlined genomic features of attine-associated fungal symbionts. The genomes of Escovopsis species, as well as species from other symbiont genera, many of which are common with the gardens of fungus-growing ants, are defined by seven chromosomes. Despite a high degree of metabolic conservation, we observe some variation in the symbionts' potential to produce secondary metabolites. As the phylogenetic distribution of the encoding biosynthetic gene clusters coincides with attine transitions in agricultural systems, we highlight the likely role of these metabolites in mediating adaptation by a group of highly specialized symbionts.}, } @article {pmid38902323, year = {2024}, author = {Horváth, G and Sos, T and Bóné, G and Lőrincz, CE and Pap, PL and Herczeg, G}, title = {Integrating behavioural thermoregulatory strategy into the animal personality framework using the common lizard, Zootoca vivipara as a model.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {14200}, pmid = {38902323}, issn = {2045-2322}, support = {PD 132041//Nemzeti Kutatási, Fejlesztési és Innovaciós Alap/ ; }, mesh = {Animals ; *Lizards/physiology ; *Body Temperature Regulation/physiology ; *Behavior, Animal/physiology ; Personality/physiology ; Male ; Female ; }, abstract = {The study of consistent between-individual behavioural variation in single (animal personality) and across two or more behavioural traits (behavioural syndrome) is a central topic of behavioural ecology. Besides behavioural type (individual mean behaviour), behavioural predictability (environment-independent within-individual behavioural variation) is now also seen as an important component of individual behavioural strategy. Research focus is still on the 'Big Five' traits (activity, exploration, risk-taking, sociability and aggression), but another prime candidate to integrate to the personality framework is behavioural thermoregulation in small-bodied poikilotherms. Here, we found animal personality in thermoregulatory strategy (selected body temperature, voluntary thermal maximum, setpoint range) and 'classic' behavioural traits (activity, sheltering, risk-taking) in common lizards (Zootoca vivipara). Individual state did not explain the between-individual variation. There was a positive behavioural type-behavioural predictability correlation in selected body temperature. Besides an activity-risk-taking syndrome, we also found a risk-taking-selected body temperature syndrome. Our results suggest that animal personality and behavioural syndrome are present in common lizards, both including thermoregulatory and 'classic' behavioural traits, and selecting high body temperature with high predictability is part of the risk-prone behavioural strategy. We propose that thermoregulatory behaviour should be considered with equal weight to the 'classic' traits in animal personality studies of poikilotherms employing active behavioural thermoregulation.}, } @article {pmid38899724, year = {2024}, author = {Parra, J and Jarmusch, SA and Duncan, KR}, title = {Multi-omics analysis of antagonistic interactions among free-living Pseudonocardia from diverse ecosystems.}, journal = {Environmental microbiology}, volume = {26}, number = {6}, pages = {e16635}, doi = {10.1111/1462-2920.16635}, pmid = {38899724}, issn = {1462-2920}, support = {2-1-4-17-1-037//Ministerio de Ciencia Tecnología y Telecomunicaciones, Costa Rica/ ; NNF19OC0055625//Novo Nordisk Fonden/ ; DNRF137//Danmarks Grundforskningsfond/ ; }, mesh = {Antibiosis ; *Ecosystem ; Genomics ; Geologic Sediments/microbiology ; *Metabolomics ; Multigene Family ; Multiomics ; *Phylogeny ; *Pseudonocardia/genetics ; }, abstract = {Actinomycetes are a phylogenetically diverse bacterial group which are widely distributed across terrestrial and aquatic ecosystems. Within this order, the genus Pseudonocardia and their specialised metabolites have been the focus of previous ecological studies due to their antagonistic interactions with other microorganisms and their mutualistic interactions with insects. However, the chemical ecology of free-living Pseudonocardia remains understudied. This study applies a multi-omics approach to investigate the chemical ecology of free-living actinomycetes from the genus Pseudonocardia. In a comparative genomics analysis, it was observed that the biosynthetic gene cluster family distribution was influenced mainly by phylogenetic distance rather than the geographic or ecological origin of strains. This finding was also observed in the mass spectrometry-based metabolomic profiles of nine Pseudonocardia species isolated from marine sediments and two terrestrial species. Antagonist interactions between these 11 species were examined, and matrix-assisted laser desorption/ionisation-mass spectrometry imaging was used to examine in situ chemical interactions between the Southern Ocean strains and their phylogenetically close relatives. Overall, it was demonstrated that phylogeny was the main predictor of antagonistic interactions among free-living Pseudonocardia. Moreover, two features at m/z 441.15 and m/z 332.20 were identified as metabolites related to these interspecies interactions.}, } @article {pmid38897481, year = {2024}, author = {Kepp, KP and Aavitsland, P and Ballin, M and Balloux, F and Baral, S and Bardosh, K and Bauchner, H and Bendavid, E and Bhopal, R and Blumstein, DT and Boffetta, P and Bourgeois, F and Brufsky, A and Collignon, PJ and Cripps, S and Cristea, IA and Curtis, N and Djulbegovic, B and Faude, O and Flacco, ME and Guyatt, GH and Hajishengallis, G and Hemkens, LG and Hoffmann, T and Joffe, AR and Klassen, TP and Koletsi, D and Kontoyiannis, DP and Kuhl, E and La Vecchia, C and Lallukka, T and Lambris, J and Levitt, M and Makridakis, S and Maltezou, HC and Manzoli, L and Marusic, A and Mavragani, C and Moher, D and Mol, BW and Muka, T and Naudet, F and Noble, PW and Nordström, A and Nordström, P and Pandis, N and Papatheodorou, S and Patel, CJ and Petersen, I and Pilz, S and Plesnila, N and Ponsonby, AL and Rivas, MA and Saltelli, A and Schabus, M and Schippers, MC and Schünemann, H and Solmi, M and Stang, A and Streeck, H and Sturmberg, JP and Thabane, L and Thombs, BD and Tsakris, A and Wood, SN and Ioannidis, JPA}, title = {Panel stacking is a threat to consensus statement validity.}, journal = {Journal of clinical epidemiology}, volume = {173}, number = {}, pages = {111428}, doi = {10.1016/j.jclinepi.2024.111428}, pmid = {38897481}, issn = {1878-5921}, mesh = {Humans ; *COVID-19/prevention & control ; *Delphi Technique ; *Consensus ; SARS-CoV-2 ; Conflict of Interest ; Reproducibility of Results ; Pandemics ; }, abstract = {Consensus statements can be very influential in medicine and public health. Some of these statements use systematic evidence synthesis but others fail on this front. Many consensus statements use panels of experts to deduce perceived consensus through Delphi processes. We argue that stacking of panel members toward one particular position or narrative is a major threat, especially in absence of systematic evidence review. Stacking may involve financial conflicts of interest, but nonfinancial conflicts of strong advocacy can also cause major bias. Given their emerging importance, we describe here how such consensus statements may be misleading, by analyzing in depth a recent high-impact Delphi consensus statement on COVID-19 recommendations as a case example. We demonstrate that many of the selected panel members and at least 35% of the core panel members had advocated toward COVID-19 elimination (Zero-COVID) during the pandemic and were leading members of aggressive advocacy groups. These advocacy conflicts were not declared in the Delphi consensus publication, with rare exceptions. Therefore, we propose that consensus statements should always require rigorous evidence synthesis and maximal transparency on potential biases toward advocacy or lobbyist groups to be valid. While advocacy can have many important functions, its biased impact on consensus panels should be carefully avoided.}, } @article {pmid38896539, year = {2024}, author = {Sänger, M and De Mecquenem, N and Lewińska, KE and Bountris, V and Lehmann, F and Leser, U and Kosch, T}, title = {A qualitative assessment of using ChatGPT as large language model for scientific workflow development.}, journal = {GigaScience}, volume = {13}, number = {}, pages = {}, pmid = {38896539}, issn = {2047-217X}, support = {//German Research Foundation/ ; }, mesh = {*Workflow ; Programming Languages ; Software ; Computational Biology/methods ; Humans ; }, abstract = {BACKGROUND: Scientific workflow systems are increasingly popular for expressing and executing complex data analysis pipelines over large datasets, as they offer reproducibility, dependability, and scalability of analyses by automatic parallelization on large compute clusters. However, implementing workflows is difficult due to the involvement of many black-box tools and the deep infrastructure stack necessary for their execution. Simultaneously, user-supporting tools are rare, and the number of available examples is much lower than in classical programming languages.

RESULTS: To address these challenges, we investigate the efficiency of large language models (LLMs), specifically ChatGPT, to support users when dealing with scientific workflows. We performed 3 user studies in 2 scientific domains to evaluate ChatGPT for comprehending, adapting, and extending workflows. Our results indicate that LLMs efficiently interpret workflows but achieve lower performance for exchanging components or purposeful workflow extensions. We characterize their limitations in these challenging scenarios and suggest future research directions.

CONCLUSIONS: Our results show a high accuracy for comprehending and explaining scientific workflows while achieving a reduced performance for modifying and extending workflow descriptions. These findings clearly illustrate the need for further research in this area.}, } @article {pmid38892087, year = {2024}, author = {Suárez, I and Collado, IG and Garrido, C}, title = {Revealing Hidden Genes in Botrytis cinerea: New Insights into Genes Involved in the Biosynthesis of Secondary Metabolites.}, journal = {International journal of molecular sciences}, volume = {25}, number = {11}, pages = {}, pmid = {38892087}, issn = {1422-0067}, support = {PID-2021-1228990-B-C21 and PID-2021-1228990-B-C22//MCIN/AEI/ 10.13039/501100011033 and ERDF A way of making Europe/ ; }, mesh = {*Botrytis/genetics/pathogenicity ; *Secondary Metabolism/genetics ; *Peptide Synthases/genetics/metabolism ; *Polyketide Synthases/genetics/metabolism ; Fungal Proteins/genetics/metabolism ; Computational Biology/methods ; Multigene Family ; Genes, Fungal ; }, abstract = {Utilizing bioinformatics tools, this study expands our understanding of secondary metabolism in Botrytis cinerea, identifying novel genes within polyketide synthase (PKS), non-ribosomal peptide synthetase (NRPS), sesquiterpene cyclase (STC), diterpene cyclase (DTC), and dimethylallyltryptophan synthase (DMATS) families. These findings enrich the genetic framework associated with B. cinerea's pathogenicity and ecological adaptation, offering insights into uncharted metabolic pathways. Significantly, the discovery of previously unannotated genes provides new molecular targets for developing targeted antifungal strategies, promising to enhance crop protection and advance our understanding of fungal biochemistry. This research not only broadens the scope of known secondary metabolites but also opens avenues for future exploration into B. cinerea's biosynthetic capabilities, potentially leading to novel antifungal compounds. Our work underscores the importance of integrating bioinformatics and genomics for fungal research, paving the way for sustainable agricultural practices by pinpointing precise molecular interventions against B. cinerea. This study sets a foundation for further investigations into the fungus's secondary metabolism, with implications for biotechnology and crop disease management.}, } @article {pmid38888768, year = {2024}, author = {Sanderson, H and White, AP}, title = {Methods for Genomic Epidemiology of Bacterial Pathogens: Example Salmonella.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2813}, number = {}, pages = {19-37}, pmid = {38888768}, issn = {1940-6029}, mesh = {*Salmonella/genetics ; Humans ; *Genomics/methods ; *Salmonella Infections/microbiology/epidemiology ; *Phylogeny ; *Genome, Bacterial ; *Molecular Epidemiology/methods ; Virulence Factors/genetics ; Disease Outbreaks ; Drug Resistance, Bacterial/genetics ; Interspersed Repetitive Sequences/genetics ; }, abstract = {Genomics has revolutionized how we characterize and monitor infectious diseases for public health. The surveillance and characterization of Salmonella has improved drastically within the past decade. In this chapter, we discuss the prerequisites for good bacterial genomics studies and make note of advantages and disadvantages of this research approach. We discuss methods for outbreak detection and the evolutionary and epidemiological characterization of Salmonella spp. We provide an outline for determining the sequence type and serotype of isolates, building a core genome phylogenetic tree, and detecting antimicrobial resistance genes, virulence factors, and mobile genetic elements. These methods can be used to study other pathogenic bacterial species.}, } @article {pmid38882711, year = {2023}, author = {Waterhouse, RM and Adam-Blondon, AF and Balech, B and Barta, E and Ying Shi Chua, P and Di Cola, V and Heil, KF and Hughes, GM and Jermiin, LS and Kalaš, M and Lanfear, J and Pafilis, E and Palagi, PM and Papageorgiou, AC and Paupério, J and Psomopoulos, F and Raes, N and Burgin, J and Gabaldón, T}, title = {The ELIXIR Biodiversity Community: Understanding short- and long-term changes in biodiversity.}, journal = {F1000Research}, volume = {12}, number = {}, pages = {}, pmid = {38882711}, issn = {2046-1402}, mesh = {Humans ; *Biodiversity ; Conservation of Natural Resources ; }, abstract = {Biodiversity loss is now recognised as one of the major challenges for humankind to address over the next few decades. Unless major actions are taken, the sixth mass extinction will lead to catastrophic effects on the Earth's biosphere and human health and well-being. ELIXIR can help address the technical challenges of biodiversity science, through leveraging its suite of services and expertise to enable data management and analysis activities that enhance our understanding of life on Earth and facilitate biodiversity preservation and restoration. This white paper, prepared by the ELIXIR Biodiversity Community, summarises the current status and responses, and presents a set of plans, both technical and community-oriented, that should both enhance how ELIXIR Services are applied in the biodiversity field and how ELIXIR builds connections across the many other infrastructures active in this area. We discuss the areas of highest priority, how they can be implemented in cooperation with the ELIXIR Platforms, and their connections to existing ELIXIR Communities and international consortia. The article provides a preliminary blueprint for a Biodiversity Community in ELIXIR and is an appeal to identify and involve new stakeholders.}, } @article {pmid38882082, year = {2024}, author = {Fei, J and Jiang, X and Yang, H and Fan, K and Che, Y and Sun, B and Guo, T}, title = {Research and Development of a Big Data Application Platform for Intelligent Blast Furnace Intensive Management and Control.}, journal = {ACS omega}, volume = {9}, number = {23}, pages = {24674-24684}, pmid = {38882082}, issn = {2470-1343}, abstract = {The blast furnaces of Anshan Iron and Steel have completed large-scale modernization, and a large amount of information technology has been popularized and applied to the process of blast furnaces. This paper takes the Anshan Iron and Steel blast furnace group as the research background. Based on big data and industrial Internet technology, combining the smelting process mechanism of blast furnace production and using artificial intelligence, cloud analysis, and other technologies, the data management platform was used to effectively integrate the data of each process of the blast furnace and design the data asset catalogue. The big data application platform for the intensive control of the blast furnace was established. The data were in multidimensional in-depth mining, and the intelligent application model of the blast furnace was established. The visual intelligent monitoring of the safe production and operation of the blast furnace was realized, and the production operation of the blast furnace was guided. The overall information and intelligent level of production operation and management of the blast furnace have been improved.}, } @article {pmid38880940, year = {2024}, author = {Medo, A and Ohte, N and Doi, H and Kamdee, K and Koba, K and Arai, N and Mitsunaga, Y and Kume, M and Kojima, D and Nose, T and Yokoyama, A and Viputhanumas, T and Mitamura, H}, title = {Trophic niche partitioning and intraspecific variation in food resource use in the genus Pangasianodon in a reservoir revealed by stable isotope analysis of multiple tissues.}, journal = {Journal of fish biology}, volume = {105}, number = {3}, pages = {814-824}, doi = {10.1111/jfb.15842}, pmid = {38880940}, issn = {1095-8649}, support = {16H05792//Japan Society for the Promotion of Science/ ; 22J13642//Japan Society for the Promotion of Science/ ; 202180216//Japan Society for the Promotion of Science/ ; //Shikata Memorial Trust for Nature Conservation/ ; 25610919060008//Thailand Institute of Nuclear Technology/ ; }, mesh = {Animals ; *Nitrogen Isotopes/analysis ; *Carbon Isotopes/analysis ; *Diet/veterinary ; Food Chain ; Thailand ; Liver/chemistry ; Ecosystem ; Catfishes ; }, abstract = {Understanding the mechanism by which non-native fish species integrate into native communities is crucial for evaluating the possibility of their establishment success. The genus Pangasianodon, comprising Pangasianodon gigas and Pangasianodon hypophthalmus, has been introduced into reservoirs, which are non-native habitats, for fishery stock enhancement. P. gigas and P. hypophthalmus often successfully establish and co-occur in several Thai reservoirs, but there is little information on differences in food resource use between the two species. To investigate the trophic niche width of P. gigas and P. hypophthalmus in a Thai reservoir, we conducted stable carbon and nitrogen ratio (δ[13]C and δ[15]N) analyses. We examined the degree of individual specialization in both species using the δ[13]C and δ[15]N values of muscle and liver tissues, which provides long- and short-term diet information. The isotopic niches did not overlap between P. gigas and P. hypophthalmus. The δ[15]N value of P. gigas was significantly higher than that of P. hypophthalmus, whereas the δ[13]C value did not significantly differ between the two species. The isotopic niche sizes were larger in P. hypophthalmus than in P. gigas. Individual specialization was observed in P. hypophthalmus but not in P. gigas, indicating that intraspecific variation in food resource use was larger in P. hypophthalmus compared to P. gigas. These findings suggest that trophic niche partitioning was one of the factors facilitating the establishment success of P. gigas and P. hypophthalmus in a reservoir, but the establishment process may differ between the two species.}, } @article {pmid38873190, year = {2023}, author = {Boyes, D and Hammond, J and , and , and , and , and , and , }, title = {The genome sequence of the Notch-wing Button, Acleris emargana (Fabricius, 1775).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {376}, pmid = {38873190}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual male Acleris emargana (the Notch-wing Button; Arthropoda; Insecta; Lepidoptera; Tortricidae). The genome sequence is 691.4 megabases in span. Most of the assembly is scaffolded into 30 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 16.34 kilobases in length. Gene annotation of this assembly on Ensembl identified 21,886 protein coding genes.}, } @article {pmid38870844, year = {2024}, author = {Rocha, LP and Machado, ÍE and Fogal, AS and Malta, DC and Velasquez-Melendez, G and Felisbino-Mendes, MS}, title = {Burden of disease and direct costs to the health system attributable to high body mass index in Brazil.}, journal = {Public health}, volume = {233}, number = {}, pages = {121-129}, doi = {10.1016/j.puhe.2024.05.013}, pmid = {38870844}, issn = {1476-5616}, mesh = {Humans ; Brazil/epidemiology ; *Body Mass Index ; Cross-Sectional Studies ; Male ; *Cost of Illness ; Female ; Middle Aged ; Adult ; *Health Care Costs/statistics & numerical data ; Hospitalization/statistics & numerical data/economics ; National Health Programs/economics/statistics & numerical data ; Obesity/epidemiology/economics ; Aged ; Disability-Adjusted Life Years ; }, abstract = {OBJECTIVES: Excess weight, measured by a high body mass index (BMI), is associated with the onset of many diseases, which can, in turn, lead to disability and premature death, subsequently placing a significant burden on healthcare services. This study analysed the burden of disease and the direct costs to the Brazilian Unified Health System (Sistema Único de Saúde [SUS]) attributable to high BMI in the Brazilian population.

STUDY DESIGN: Ecological study.

METHODS: This ecological study had two components: (1) a time-series assessment to analyse the burden of diseases attributable to high BMI from 1990 to 2019 in Brazil; and (2) a cross-sectional design to estimate the direct costs of SUS hospitalisations and outpatient procedures attributable to high BMI in 2019. Estimates from the Global Burden of Disease study and the costs of hospital admissions and outpatient procedures from the Department of Informatics of the Brazilian Unified Health System were used. Deaths, years of life lost to premature death (YLLs), years lived with disability (YLDs), and years of life lost adjusted for disability (DALYs) were analysed. The direct health cost was obtained in Brazilian Real (R$) and converted in international Dollars (INT$).

RESULTS: The current study found a reduction in the number of DALYs, YLLs, and deaths per 100,000 population of cardiovascular disease (CVD) attributable to high BMI and an increase in YLD due to diabetes and cardiovascular disease attributable to high BMI from 1990 to 2019. In 2019, high BMI resulted in 2404 DALYs, 658 YLDs, 1746 YLLs, and 76 deaths per 100,000 inhabitants. In the same year, INT$377.30 million was spent on hospitalisations and high- and medium-complexity procedures to control non-communicable diseases attributable to high BMI. The states in the South and Southeast regions of Brazil presented the highest total cost per 10,000 inhabitants. CVDs and chronic kidney disease showed the highest costs per hospital admission, whereas neoplasms and CVDs presented the highest costs for outpatient procedures.

CONCLUSIONS: High BMI causes significant disease burden and financial costs. The highest expenses observed were not in locations with the highest burden of disease attributable to high BMI. These findings highlight the need to improve current public policies and apply cost-effective intervention packages, focussing on equity and the promotion of healthier lifestyles to reduce overweight/obesity, especially in localities with low socioeconomic status.}, } @article {pmid38870774, year = {2024}, author = {Bucci, S and Berry, N and Ainsworth, J and Berry, K and Edge, D and Eisner, E and Emsley, R and Forbes, G and Hassan, L and Lewis, S and Machin, M and Haddock, G}, title = {Effects of Actissist, a digital health intervention for early psychosis: A randomized clinical trial.}, journal = {Psychiatry research}, volume = {339}, number = {}, pages = {116025}, doi = {10.1016/j.psychres.2024.116025}, pmid = {38870774}, issn = {1872-7123}, mesh = {Humans ; Female ; Male ; Adult ; *Psychotic Disorders/therapy ; *Schizophrenia/therapy ; *Mobile Applications ; *Cognitive Behavioral Therapy/methods ; *Telemedicine ; Young Adult ; Middle Aged ; Outcome Assessment, Health Care ; Treatment Outcome ; Digital Health ; }, abstract = {Schizophrenia affects 24 million people worldwide. Digital health interventions drawing on psychological principles have been developed, but their effectiveness remains unclear. This parallel, assessor-blinded, randomized clinical trial aimed to investigate whether a cognitive behaviour therapy-informed digital health intervention (Actissist app) confers added benefit on psychotic symptoms over and above remote symptom monitoring (ClinTouch app). Participants recruited from UK community health services were randomized 1:1 to receive either Actissist plus treatment as usual (TAU) or ClinTouch plus TAU. Eligible participants were adults with schizophrenia-spectrum psychosis within five years of first episode onset meeting a criterion level of positive symptoms severity. The primary outcome was Positive and Negative Syndrome Scale (PANSS) symptoms total score at 12 weeks post-randomization. Intention-to-treat analysis included 172 participants, with 149 participants (86.6 %) providing primary outcome data. Actissist plus TAU was not associated with greater reduction than an active control remote symptom monitoring app (ClinTouch) in PANSS total score at post-randomization. There were no significant effects between groups across secondary measures. There were no serious adverse reactions. Both groups improved on the primary psychotic symptoms measure at primary end-point and on secondary measures over time. The Actissist app is safe but not superior to digital symptom monitoring.}, } @article {pmid38868628, year = {2023}, author = {Obbard, DJ and , and , and , and , }, title = {The genome sequence of a drosophilid fruit fly, Hirtodrosophila cameraria (Haliday, 1833).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {361}, pmid = {38868628}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual female Hirtodrosophila cameraria (a drosophilid fruit fly; Arthropoda; Insecta; Diptera; Drosophilidae). The genome sequence is 214.5 megabases in span. Most of the assembly is scaffolded into 4 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 15.94 kilobases in length.}, } @article {pmid38867756, year = {2024}, author = {Boyes, D and Lewis, OT and , and , and , and , and , and , and , }, title = {The genome sequence of the Marbled White Spot, Protodeltote pygarga (Hufnagel, 1766).}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {7}, pmid = {38867756}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual male Protodeltote pygarga (the Marbled White Spot; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 421.1 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.48 kilobases in length. Gene annotation of this assembly on Ensembl identified 17,784 protein coding genes.}, } @article {pmid38867206, year = {2024}, author = {Anjos, C and Duarte, D and Fatsini, E and Matias, D and Cabrita, E}, title = {Comparative transcriptome analysis reveals molecular damage associated with cryopreservation in Crassostrea angulata D-larvae rather than to cryoprotectant exposure.}, journal = {BMC genomics}, volume = {25}, number = {1}, pages = {591}, pmid = {38867206}, issn = {1471-2164}, support = {SFRH/BD/130910/2017//Fundação para a Ciência e a Tecnologia/ ; CCMAR/Multi/04326/2022//Fundação para a Ciência e a Tecnologia/ ; 0139_VENUS_5_E//Interreg POCTEP/ ; JRA2-H2020-INFRAIA-2016-2017//European Commission/ ; EBB-EAPA_501/2016//Interreg Atlantic Area/ ; }, mesh = {Animals ; *Cryopreservation ; *Crassostrea/genetics/growth & development ; *Cryoprotective Agents/pharmacology/toxicity ; *Larva/genetics/drug effects/growth & development ; *Gene Expression Profiling ; Transcriptome ; Gene Ontology ; }, abstract = {BACKGROUND: The Portuguese oyster Crassostrea angulata, a bivalve of significant economic and ecological importance, has faced a decline in both production and natural populations due to pathologies, climate change, and anthropogenic factors. To safeguard its genetic diversity and improve reproductive management, cryopreservation emerges as a valuable strategy. However, the cryopreservation methodologies lead to some damage in structures and functions of the cells and tissues that can affect post-thaw quality. Transcriptomics may help to understand the molecular consequences related to cryopreservation steps and therefore to identify different freezability biomarkers. This study investigates the molecular damage induced by cryopreservation in C. angulata D-larvae, focusing on two critical steps: exposure to cryoprotectant solution and the freezing/thawing process.

RESULTS: Expression analysis revealed 3 differentially expressed genes between larvae exposed to cryoprotectant solution and fresh larvae and 611 differentially expressed genes in cryopreserved larvae against fresh larvae. The most significantly enriched gene ontology terms were "carbohydrate metabolic process", "integral component of membrane" and "chitin binding" for biological processes, cellular components and molecular functions, respectively. Kyoto Encyclopedia of Genes and Genomes enrichment analysis identified the "neuroactive ligand receptor interaction", "endocytosis" and "spliceosome" as the most enriched pathways. RNA sequencing results were validate by quantitative RT-PCR, once both techniques presented the same gene expression tendency and a group of 11 genes were considered important molecular biomarkers to be used in further studies for the evaluation of cryodamage.

CONCLUSIONS: The current work provided valuable insights into the molecular repercussions of cryopreservation on D-larvae of Crassostrea angulata, revealing that the freezing process had a more pronounced impact on larval quality compared to any potential cryoprotectant-induced toxicity. Additionally, was identify 11 genes serving as biomarkers of freezability for D-larvae quality assessment. This research contributes to the development of more effective cryopreservation protocols and detection methods for cryodamage in this species.}, } @article {pmid38865434, year = {2024}, author = {Iverson, AR and Humple, DL and Cormier, RL and Hahn, TP and Block, TA and Shizuka, D and Lyon, BE and Chaine, AS and Hudson, EJ and Hull, EM}, title = {Winter GPS tagging reveals home ranges during the breeding season for a boreal-nesting migrant songbird, the Golden-crowned Sparrow.}, journal = {PloS one}, volume = {19}, number = {6}, pages = {e0305369}, pmid = {38865434}, issn = {1932-6203}, mesh = {Animals ; *Seasons ; *Geographic Information Systems ; *Animal Migration/physiology ; *Sparrows/physiology ; *Homing Behavior/physiology ; Breeding ; Ecosystem ; British Columbia ; Alaska ; Nesting Behavior/physiology ; }, abstract = {Determining space use for species is fundamental to understanding their ecology, and tracking animals can reveal insights into their spatial ecology on home ranges and territories. Recent technological advances have led to GPS-tracking devices light enough for birds as small as ~30 g, creating novel opportunities to remotely monitor fine-scale movements and space use for these smaller species. We tested whether miniaturized GPS tags can allow us to understand space use of migratory birds away from their capture sites and sought to understand both pre-breeding space use as well as territory and habitat use on the breeding grounds. We used GPS tags to characterize home ranges on the breeding grounds for a migratory songbird with limited available breeding information, the Golden-crowned Sparrow (Zonotrichia atricapilla). Using GPS points from 23 individuals across 26 tags (three birds tagged twice), we found home ranges in Alaska and British Columbia were on average 44.1 ha (95% kernel density estimate). In addition, estimates of territory sizes based on field observations (mean 2.1 ha, 95% minimum convex polygon [MCP]) were three times smaller than 95% MCPs created using GPS tags (mean 6.5 ha). Home ranges included a variety of land cover classes, with shrubland particularly dominant (64-100% of home range cover for all but one bird). Three birds tracked twice returned to the same breeding area each year, supporting high breeding site fidelity for this species. We found reverse spring migration for five birds that flew up to 154 km past breeding destinations before returning. GPS-tracking technology allowed for critical ecological insights into this migratory species that breeds in very remote locations.}, } @article {pmid38865431, year = {2024}, author = {Tedersoo, L and Hosseyni Moghaddam, MS and Mikryukov, V and Hakimzadeh, A and Bahram, M and Nilsson, RH and Yatsiuk, I and Geisen, S and Schwelm, A and Piwosz, K and Prous, M and Sildever, S and Chmolowska, D and Rueckert, S and Skaloud, P and Laas, P and Tines, M and Jung, JH and Choi, JH and Alkahtani, S and Anslan, S}, title = {EUKARYOME: the rRNA gene reference database for identification of all eukaryotes.}, journal = {Database : the journal of biological databases and curation}, volume = {2024}, number = {}, pages = {}, pmid = {38865431}, issn = {1758-0463}, support = {Distinguished Scientist Fellowship Programme//King Saud University/ ; MOBERC66 MOBTP198//European Regional Development Fund/ ; //LOEWE Zentrum AdRIA/ ; Distinguished Scientist Fellowship Programme//King Saud University/ ; MOBERC66 MOBTP198//European Regional Development Fund/ ; //LOEWE Zentrum AdRIA/ ; }, mesh = {*Eukaryota/genetics ; RNA, Ribosomal, 18S/genetics ; Databases, Genetic ; Databases, Nucleic Acid ; Animals ; Genes, rRNA/genetics ; Phylogeny ; }, abstract = {Molecular identification of micro- and macroorganisms based on nuclear markers has revolutionized our understanding of their taxonomy, phylogeny and ecology. Today, research on the diversity of eukaryotes in global ecosystems heavily relies on nuclear ribosomal RNA (rRNA) markers. Here, we present the research community-curated reference database EUKARYOME for nuclear ribosomal 18S rRNA, internal transcribed spacer (ITS) and 28S rRNA markers for all eukaryotes, including metazoans (animals), protists, fungi and plants. It is particularly useful for the identification of arbuscular mycorrhizal fungi as it bridges the four commonly used molecular markers-ITS1, ITS2, 18S V4-V5 and 28S D1-D2 subregions. The key benefits of this database over other annotated reference sequence databases are that it is not restricted to certain taxonomic groups and it includes all rRNA markers. EUKARYOME also offers a number of reference long-read sequences that are derived from (meta)genomic and (meta)barcoding-a unique feature that can be used for taxonomic identification and chimera control of third-generation, long-read, high-throughput sequencing data. Taxonomic assignments of rRNA genes in the database are verified based on phylogenetic approaches. The reference datasets are available in multiple formats from the project homepage, http://www.eukaryome.org.}, } @article {pmid38863181, year = {2024}, author = {Wong, RE and Berner, LT and Sullivan, PF and Potter, CS and Dial, RJ}, title = {Pixel walking along the boreal forest-Arctic tundra ecotone: Large scale ground-truthing of satellite-derived greenness (NDVI).}, journal = {Global change biology}, volume = {30}, number = {6}, pages = {e17374}, doi = {10.1111/gcb.17374}, pmid = {38863181}, issn = {1365-2486}, support = {80NSSC22K1247/NASA/NASA/United States ; 80NSSC20M0070//Alaska Space Grant Program/ ; DEB-2133494//National Science Foundation/ ; OPP-1748773//National Science Foundation/ ; OPP-1748849//National Science Foundation/ ; 80NSSC19M0062//Alaska NASA EPSCoR/ ; }, mesh = {Alaska ; Arctic Regions ; *Satellite Imagery ; *Tundra ; Remote Sensing Technology/methods ; Taiga ; Environmental Monitoring/methods ; }, abstract = {In this Technical Advance, we describe a novel method to improve ecological interpretation of remotely sensed vegetation greenness measurements that involved sampling 24,395 Landsat pixels (30 m) across 639 km of Alaska's central Brooks Range. The method goes well beyond the spatial scale of traditional plot-based sampling and thereby more thoroughly relates ground-based observations to satellite measurements. Our example dataset illustrates that, along the boreal-Arctic boundary, vegetation with the greatest Landsat Normalized Difference Vegetation Index (NDVI) is taller than 1 m, woody, and deciduous; whereas vegetation with lower NDVI tends to be shorter, evergreen, or non-woody. The field methods and associated analyses advance efforts to inform satellite data with ground-based vegetation observations using field samples collected at spatial scales that closely match the resolution of remotely sensed imagery.}, } @article {pmid38862613, year = {2024}, author = {Venu, V and Roth, C and Adikari, SH and Small, EM and Starkenburg, SR and Sanbonmatsu, KY and Steadman, CR}, title = {Multi-omics analysis reveals the dynamic interplay between Vero host chromatin structure and function during vaccinia virus infection.}, journal = {Communications biology}, volume = {7}, number = {1}, pages = {721}, pmid = {38862613}, issn = {2399-3642}, support = {20210134ER//DOE | LDRD | Los Alamos National Laboratory (Los Alamos Lab)/ ; }, mesh = {*Chromatin/metabolism/genetics ; Animals ; *Vaccinia virus/genetics/physiology ; Chlorocebus aethiops ; Vero Cells ; Vaccinia/virology/immunology ; Host-Pathogen Interactions/genetics ; Multiomics ; }, abstract = {The genome folds into complex configurations and structures thought to profoundly impact its function. The intricacies of this dynamic structure-function relationship are not well understood particularly in the context of viral infection. To unravel this interplay, here we provide a comprehensive investigation of simultaneous host chromatin structural (via Hi-C and ATAC-seq) and functional changes (via RNA-seq) in response to vaccinia virus infection. Over time, infection significantly impacts global and local chromatin structure by increasing long-range intra-chromosomal interactions and B compartmentalization and by decreasing chromatin accessibility and inter-chromosomal interactions. Local accessibility changes are independent of broad-scale chromatin compartment exchange (~12% of the genome), underscoring potential independent mechanisms for global and local chromatin reorganization. While infection structurally condenses the host genome, there is nearly equal bidirectional differential gene expression. Despite global weakening of intra-TAD interactions, functional changes including downregulated immunity genes are associated with alterations in local accessibility and loop domain restructuring. Therefore, chromatin accessibility and local structure profiling provide impactful predictions for host responses and may improve development of efficacious anti-viral counter measures including the optimization of vaccine design.}, } @article {pmid38862357, year = {2024}, author = {Knight, E and Rhinehart, T and de Zwaan, DR and Weldy, MJ and Cartwright, M and Hawley, SH and Larkin, JL and Lesmeister, D and Bayne, E and Kitzes, J}, title = {Individual identification in acoustic recordings.}, journal = {Trends in ecology & evolution}, volume = {39}, number = {10}, pages = {947-960}, doi = {10.1016/j.tree.2024.05.007}, pmid = {38862357}, issn = {1872-8383}, mesh = {*Acoustics ; Animals ; Vocalization, Animal ; }, abstract = {Recent advances in bioacoustics combined with acoustic individual identification (AIID) could open frontiers for ecological and evolutionary research because traditional methods of identifying individuals are invasive, expensive, labor-intensive, and potentially biased. Despite overwhelming evidence that most taxa have individual acoustic signatures, the application of AIID remains challenging and uncommon. Furthermore, the methods most commonly used for AIID are not compatible with many potential AIID applications. Deep learning in adjacent disciplines suggests opportunities to advance AIID, but such progress is limited by training data. We suggest that broadscale implementation of AIID is achievable, but researchers should prioritize methods that maximize the potential applications of AIID, and develop case studies with easy taxa at smaller spatiotemporal scales before progressing to more difficult scenarios.}, } @article {pmid38860489, year = {2024}, author = {Toga, K and Sakamoto, T and Kanda, M and Tamura, K and Okuhara, K and Tabunoki, H and Bono, H}, title = {Long-read genome assembly of the Japanese parasitic wasp Copidosoma floridanum (Hymenoptera: Encyrtidae).}, journal = {G3 (Bethesda, Md.)}, volume = {14}, number = {8}, pages = {}, pmid = {38860489}, issn = {2160-1836}, support = {JPMJPF2010//Center of Innovation for Bio-Digital Transformation/ ; 23K17418//JSPS KAKENHI/ ; }, mesh = {Animals ; Genome, Insect ; Genomics/methods ; Japan ; *Molecular Sequence Annotation ; *Wasps/genetics ; }, abstract = {Copidosoma floridanum is a cosmopolitan species and an egg-larval parasitoid of the Plusiine moth. C. floridanum has a unique development mode called polyembryony, in which over two thousand genetically identical embryos are produced from a single egg. Some embryos develop into sterile soldier larvae precociously, and their emergence period and aggressive behavior differ between the US and Japanese C. floridanum strains. Genome sequencing expects to contribute to our understanding of the molecular bases underlying the progression of polyembryony. However, only the genome sequence of the US strain generated by the short-read assembly has been reported. In the present study, we determined the genome sequence of the Japanese strain using Pacific Biosciences high-fidelity reads and generating a highly contiguous assembly (552.7 Mb, N50: 17.9 Mb). Gene prediction and annotation identified 13,886 transcripts derived from 10,786 gene models. We searched the genomic differences between US and Japanese strains. Among gene models predicted in this study, 100 gene loci in the Japanese strain had extremely different gene structures from those in the US strain. This was accomplished through functional annotation (GGSEARCH) and long-read sequencing. Genomic differences between strains were also reflected in amino acid sequences of vasa that play a central role in caste determination in this species. The genome assemblies constructed in this study will facilitate the genomic comparisons between Japanese and US strains, leading to our understanding of detailed genomic regions responsible for the ecological and physiological characteristics of C. floridanum.}, } @article {pmid38856681, year = {2024}, author = {Dasgupta, S}, title = {Thinking Beyond Disease Silos: Dysregulated Genes Common in Tuberculosis and Lung Cancer as Identified by Systems Biology and Machine Learning.}, journal = {Omics : a journal of integrative biology}, volume = {28}, number = {7}, pages = {347-356}, doi = {10.1089/omi.2024.0116}, pmid = {38856681}, issn = {1557-8100}, mesh = {Humans ; *Machine Learning ; *Lung Neoplasms/genetics ; *Tuberculosis/genetics ; *Systems Biology/methods ; Computational Biology/methods ; Gene Expression Profiling/methods ; Gene Regulatory Networks ; }, abstract = {The traditional way of thinking about human diseases across clinical and narrow phenomics silos often masks the underlying shared molecular substrates across human diseases. One Health and planetary health fields particularly address such complexities and invite us to think across the conventional disease nosologies. For example, tuberculosis (TB) and lung cancer (LC) are major pulmonary diseases with significant planetary health implications. Despite distinct etiologies, they can coexist in a given community or patient. This is both a challenge and an opportunity for preventive medicine, diagnostics, and therapeutics innovation. This study reports a bioinformatics analysis of publicly available gene expression data, identifying overlapping dysregulated genes, downstream regulators, and pathways in TB and LC. Analysis of NCBI-GEO datasets (GSE83456 and GSE103888) unveiled differential expression of CEACAM6, MUC1, ADM, DYSF, PLOD2, and GAS6 genes in both diseases, with pathway analysis indicating association with lysine degradation pathway. Random forest, a machine-learning-based classification, achieved accuracies of 84% for distinguishing TB from controls and 83% for discriminating LC from controls using these specific genes. Additionally, potential drug targets were identified, with molecular docking confirming the binding affinity of warfarin to GAS6. Taken together, the present study speaks of the pressing need to rethink clinical diagnostic categories of human diseases and that TB and LC might potentially share molecular substrates. Going forward, planetary health and One Health scholarship are poised to cultivate new ways of thinking about diseases not only across medicine and ecology but also across traditional diagnostic conventions.}, } @article {pmid38855721, year = {2023}, author = {Boyes, D and Broad, GR and Holland, PWH and , and , and , and , and , and , and , }, title = {The genome sequence of the Cloaked Minor, Mesoligia furuncula (Denis & Schiffermüller, 1775).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {251}, pmid = {38855721}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual female Mesoligia furuncula (the Cloaked Minor; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 889.6 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.3 kilobases in length. Gene annotation of this assembly on Ensembl identified 21,903 protein coding genes.}, } @article {pmid38854694, year = {2024}, author = {Christenhusz, MJM and Pannell, JR and Twyford, AD and , and , and , and , and , and , and , }, title = {The genome sequence of the Annual Mercury, Mercurialis annua L., 1753 (Euphorbiaceae).}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {102}, pmid = {38854694}, issn = {2398-502X}, abstract = {We present a genome assembly from a diploid female Mercurialis annua (the Annual Mercury; Tracheophyta; Magnoliopsida; Malpighiales; Euphorbiaceae). The genome sequence is 453.2 megabases in span. Most of the assembly is scaffolded into 8 chromosomal pseudomolecules, including the X chromosome. The organelle genomes have also been assembled, and the mitochondrial genome is 435.28 kilobases in length, while the plastid genome is 169.65 kilobases in length.}, } @article {pmid38853065, year = {2024}, author = {O'Connor, JB and Mottlowitz, M and Wagner, BD and Harris, JK and Laguna, TA}, title = {Metabolomics analysis of bronchoalveolar lavage fluid predicts unique features of the lower airway in pediatric cystic fibrosis.}, journal = {Journal of cystic fibrosis : official journal of the European Cystic Fibrosis Society}, volume = {23}, number = {6}, pages = {1087-1094}, doi = {10.1016/j.jcf.2024.04.017}, pmid = {38853065}, issn = {1873-5010}, mesh = {Humans ; *Cystic Fibrosis/microbiology/metabolism/physiopathology ; *Bronchoalveolar Lavage Fluid/chemistry/microbiology ; Child ; Female ; Male ; *Metabolomics/methods ; Microbiota ; Adolescent ; Bronchoscopy/methods ; RNA, Ribosomal, 16S/analysis ; Respiratory Function Tests/methods ; }, abstract = {BACKGROUND: Progressive, obstructive lung disease resulting from chronic infection and inflammation is the leading cause of morbidity and mortality in persons with cystic fibrosis (PWCF). Metabolomics and next -generation sequencing (NGS) of airway secretions can allow for better understanding of cystic fibrosis (CF) pathophysiology. In this study, global metabolomic profiling on bronchoalveolar lavage fluid (BALF) obtained from pediatric PWCF and disease controls (DCs) was performed and compared to lower airway microbiota, inflammation, and lung function.

METHODS: BALF was collected from children undergoing flexible bronchoscopies for clinical indications. Metabolomic profiling was performed using a platform developed by Metabolon Inc. Total bacterial load (TBL) was measured using quantitative polymerase chain reaction (qPCR), and bacterial communities were characterized using 16S ribosomal RNA (rRNA) sequencing. Random Forest Analysis (RFA), principal component analysis (PCA), and hierarchical clustering analysis (HCA) were performed.

RESULTS: One hundred ninety-five BALF samples were analyzed, 142 (73 %) from PWCF. Most metabolites (425/665) and summed categories (7/9) were significantly increased in PWCF. PCA of the metabolomic data revealed CF BALF exhibited more dispersed clustering compared to DC BALF. Higher metabolite concentrations correlated with increased inflammation, increased abundance of Staphylococcus, and decreased lung function.

CONCLUSIONS: The lower airway metabolome of PWCF was defined by a complex expansion of metabolomic activity. These findings could be attributed to heightened inflammation in PWCF and aspects of the CF airway polymicrobial ecology. CF-specific metabolomic features are associated with the unique underlying biology of the CF airway.}, } @article {pmid38852834, year = {2024}, author = {Goodus, MT and Alfredo, AN and Carson, KE and Dey, P and Pukos, N and Schwab, JM and Popovich, PG and Gao, J and Mo, X and Bruno, RS and McTigue, DM}, title = {Spinal cord injury-induced metabolic impairment and steatohepatitis develops in non-obese rats and is exacerbated by premorbid obesity.}, journal = {Experimental neurology}, volume = {379}, number = {}, pages = {114847}, doi = {10.1016/j.expneurol.2024.114847}, pmid = {38852834}, issn = {1090-2430}, mesh = {Animals ; *Spinal Cord Injuries/complications/metabolism/pathology ; Rats ; *Obesity/complications/metabolism/pathology ; Male ; Fatty Liver/metabolism/pathology/etiology ; Rats, Sprague-Dawley ; Metabolic Syndrome/metabolism/complications/pathology ; Disease Models, Animal ; Insulin Resistance/physiology ; }, abstract = {Impaired sensorimotor functions are prominent complications of spinal cord injury (SCI). A clinically important but less obvious consequence is development of metabolic syndrome (MetS), including increased adiposity, hyperglycemia/insulin resistance, and hyperlipidemia. MetS predisposes SCI individuals to earlier and more severe diabetes and cardiovascular disease compared to the general population, which trigger life-threatening complications (e.g., stroke, myocardial infarcts). Although each comorbidity is known to be a risk factor for diabetes and other health problems in obese individuals, their relative contribution or perceived importance in propagating systemic pathology after SCI has received less attention. This could be explained by an incomplete understanding of MetS promoted by SCI compared with that from the canonical trigger diet-induced obesity (DIO). Thus, here we compared metabolic-related outcomes after SCI in lean rats to those of uninjured rats with DIO. Surprisingly, SCI-induced MetS features were equal to or greater than those in obese uninjured rats, including insulin resistance, endotoxemia, hyperlipidemia, liver inflammation and steatosis. Considering the endemic nature of obesity, we also evaluated the effect of premorbid obesity in rats receiving SCI; the combination of DIO + SCI exacerbated MetS and liver pathology compared to either alone, suggesting that obese individuals that sustain a SCI are especially vulnerable to metabolic dysfunction. Notably, premorbid obesity also exacerbated intraspinal lesion pathology and worsened locomotor recovery after SCI. Overall, these results highlight that normal metabolic function requires intact spinal circuitry and that SCI is not just a sensory-motor disorder, but also has significant metabolic consequences.}, } @article {pmid38850116, year = {2024}, author = {Yi, X and Kemppainen, P and Merilä, J}, title = {SLRfinder: A method to detect candidate sex-linked regions with linkage disequilibrium clustering.}, journal = {Molecular ecology resources}, volume = {24}, number = {6}, pages = {e13985}, doi = {10.1111/1755-0998.13985}, pmid = {38850116}, issn = {1755-0998}, support = {N_HKU763/21//National Natural Science Foundation of China/Research Grants Council (RGC) Joint Research Scheme/ ; }, mesh = {*Linkage Disequilibrium ; *Sex Chromosomes/genetics ; Computational Biology/methods ; Animals ; Male ; Female ; Cluster Analysis ; }, abstract = {Despite their critical roles in genetic sex determination, sex chromosomes remain unknown in many non-model organisms, especially those having recently evolved sex-linked regions (SLRs). These evolutionarily young and labile sex chromosomes are important for understanding early sex chromosome evolution but are difficult to identify due to the lack of Y/W degeneration and SLRs limited to small genomic regions. Here, we present SLRfinder, a method to identify candidate SLRs using linkage disequilibrium (LD) clustering, heterozygosity and genetic divergence. SLRfinder does not rely on specific sequencing methods or a specific type of reference genome (e.g., from the homomorphic sex). In addition, the input of SLRfinder does not require phenotypic sexes, which may be unknown from population sampling, but sex information can be incorporated and is necessary to validate candidate SLRs. We tested SLRfinder using various published datasets and compared it to the local principal component analysis (PCA) method and the depth-based method Sex Assignment Through Coverage (SATC). As expected, the local PCA method could not be used to identify unknown SLRs. SATC works better on conserved sex chromosomes, whereas SLRfinder outperforms SATC in analysing labile sex chromosomes, especially when SLRs harbour inversions. Power analyses showed that SLRfinder worked better when sampling more populations that share the same SLR. If analysing one population, a relatively larger sample size (around 50) is needed for sufficient statistical power to detect significant SLR candidates, although true SLRs are likely always top-ranked. SLRfinder provides a novel and complementary approach for identifying SLRs and uncovering additional sex chromosome diversity in nature.}, } @article {pmid38845010, year = {2024}, author = {Wang, S and Lee, HC and Lee, S}, title = {Predicting herb-disease associations using network-based measures in human protein interactome.}, journal = {BMC complementary medicine and therapies}, volume = {24}, number = {Suppl 2}, pages = {218}, pmid = {38845010}, issn = {2662-7671}, support = {GIST Research Institute IIBR//Gwangju Institute of Science and Technology/ ; GIST Research Institute (GRI) GIST-MIT research Collaboration//Gwangju Institute of Science and Technology/ ; 2021M3A9G8022959//Ministry of Science and ICT, South Korea/ ; 2021R1C1C1006336//Ministry of Science and ICT, South Korea/ ; HR22C141105//Ministry of Health and Welfare/ ; }, mesh = {Humans ; *Protein Interaction Maps ; Computer Simulation ; Computational Biology/methods ; }, abstract = {BACKGROUND: Natural herbs are frequently used to treat diseases or to relieve symptoms in many countries. Moreover, as their safety has been proven for a long time, they are considered as main sources of new drug development. However, in many cases, the herbs are still prescribed relying on ancient records and/or traditional practices without scientific evidences. More importantly, the medicinal efficacy of the herbs has to be evaluated in the perspective of MCMT (multi-compound multi-target) effects, but most efforts focus on identifying and analyzing a single compound experimentally. To overcome these hurdles, computational approaches which are based on the scientific evidences and are able to handle the MCMT effects are needed to predict the herb-disease associations.

RESULTS: In this study, we proposed a network-based in silico method to predict the herb-disease associations. To this end, we devised a new network-based measure, WACP (weighted average closest path length), which not only quantifies proximity between herb-related genes and disease-related genes but also considers compound compositions of each herb. As a result, we confirmed that our method successfully predicts the herb-disease associations in the human protein interactome (AUROC = 0.777). In addition, we observed that our method is superior than the other simple network-based proximity measures (e.g. average shortest and closest path length). Additionally, we analyzed the associations between Brassica oleracea var. italica and its known associated diseases more specifically as case studies. Finally, based on the prediction results of the WACP, we suggested novel herb-disease pairs which are expected to have potential relations and their literature evidences.

CONCLUSIONS: This method could be a promising solution to modernize the use of the natural herbs by providing the scientific evidences about the molecular associations between the herb-related genes targeted by multiple compounds and the disease-related genes in the human protein interactome.}, } @article {pmid38844398, year = {2024}, author = {Xiao, Z and Robertson, S and Long, E and Flaig, R and Kirby, L and Romaniuk, L and Murray, A and Whalley, H}, title = {Loneliness in the Digital World: protocol for a co-produced ecological momentary assessment study in adolescents.}, journal = {BMJ open}, volume = {14}, number = {6}, pages = {e087374}, pmid = {38844398}, issn = {2044-6055}, support = {/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Humans ; *Loneliness/psychology ; Adolescent ; *Ecological Momentary Assessment ; *Mental Health ; Female ; Child ; Male ; Social Interaction ; Surveys and Questionnaires ; Research Design ; Depression ; Scotland ; Anxiety ; }, abstract = {INTRODUCTION: Loneliness has been identified as an important public health issue, peaking during adolescence. Previous research has suggested that social interaction is a key factor in loneliness, and positive social interaction can act as a protective factor against loneliness. However, it is unclear whether there are differing impacts of in-person and online social interaction on adolescents' loneliness and mental health. Ecological Momentary Assessment (EMA) designs are ideally suited for better understanding these associations.

METHOD AND ANALYSIS: In the 'Loneliness in the Digital World' study, we will use a co-developed EMA design to capture daily social interactions, loneliness and mental health such as positive and negative emotions, depression and anxiety in approximately 200 adolescents aged 12-15 years. We will combine this with comprehensive information gathered from online surveys. Analysing the data using techniques such as dynamic structural equation modelling, we will examine, among other research questions, the associations between online and in-person social interaction and feelings of loneliness. The results can help inform interventions to support adolescents with high levels of loneliness and poor mental health.

ETHICS AND DISSEMINATION: We received the ethics approval for the data collection from The Academic and Clinical Central Office for Research and Development, followed by the College of Medicine and Veterinary Medicine Ethics panel at University of Edinburgh, and finally reviewed by East of Scotland Research Ethics Service. The results will be disseminated through journal publications, conferences and seminar presentations and to relevant stakeholders such as teachers.}, } @article {pmid38841890, year = {2024}, author = {Pedersen, MB and Beedholm, K and Hubancheva, A and Koseva, K and Uebel, AS and Hochradel, K and Madsen, PT and Stidsholt, L}, title = {Clutter resilience via auditory stream segregation in echolocating greater mouse-eared bats.}, journal = {The Journal of experimental biology}, volume = {227}, number = {12}, pages = {}, doi = {10.1242/jeb.246889}, pmid = {38841890}, issn = {1477-9145}, support = {//Frands Christian Frantsen Foundation/ ; FP2 0135-00343B//Natur og Univers, Det Frie Forskningsråd/ ; AU337272//Fonden Frands Christian Frantsens Legat/ ; 41386//Villum Fonden/ ; CF16-0405//Carlsbergfondet/ ; }, mesh = {Animals ; *Chiroptera/physiology ; *Echolocation/physiology ; Male ; Female ; Vocalization, Animal/physiology ; }, abstract = {Bats use echolocation to navigate and hunt in darkness, and must in that process segregate target echoes from unwanted clutter echoes. Bats may do this by approaching a target at steep angles relative to the plane of the background, utilizing their directional transmission and receiving systems to minimize clutter from background objects, but it remains unknown how bats negotiate clutter that cannot be spatially avoided. Here, we tested the hypothesis that when movement no longer offers spatial release, echolocating bats mitigate clutter by calling at lower source levels and longer call intervals to ease auditory streaming. We trained five greater mouse-eared bats (Myotis myotis) to land on a spherical loudspeaker with two microphones attached. We used a phantom-echo setup, where the loudspeaker/target transmitted phantom clutter echoes by playing back the bats' own calls at time delays of 1, 3 and 5 ms with a virtual target strength 7 dB higher than the physical target. We show that the bats successfully landed on the target, irrespective of the clutter echo delays. Rather than decreasing their source levels, the bats used similar source level distributions in clutter and control trials. Similarly, the bats did not increase their call intervals, but instead used the same distribution of call intervals across control and clutter trials. These observations reject our hypothesis, leading us to conclude that bats display great resilience to clutter via short auditory integration times and acute auditory stream segregation rather than via biosonar adjustments.}, } @article {pmid38840517, year = {2024}, author = {Walker, XJ and Hart, S and Hansen, WD and Jean, M and Brown, CD and Stuart Chapin, F and Hewitt, R and Hollingsworth, TN and Mack, MC and Johnstone, JF}, title = {Factors limiting the potential range expansion of lodgepole pine in Interior Alaska.}, journal = {Ecological applications : a publication of the Ecological Society of America}, volume = {34}, number = {5}, pages = {e2983}, doi = {10.1002/eap.2983}, pmid = {38840517}, issn = {1051-0761}, support = {05-1-2-06//Joint Fire Science Program/ ; //Natural Sciences and Engineering Research Council of Canada/ ; PNW01-JV11261952-23//U.S. Fish and Wildlife Service/ ; RC-2109//Strategic Environmental Research and Development Program/ ; RC-2754//Strategic Environmental Research and Development Program/ ; DEB-0620579//National Science Foundation/ ; DEB-1636476//National Science Foundation/ ; DEB-2224776//National Science Foundation/ ; USFS-PNW01-JV11261952-23//National Science Foundation/ ; RJVA-PNW-20-JV-11261932-018//National Science Foundation/ ; OPP-2116862//National Science Foundation/ ; NNX15AT71A/NASA/NASA/United States ; }, mesh = {*Pinus/physiology ; Alaska ; Climate Change ; Models, Biological ; Seedlings ; Demography ; Animals ; Ecosystem ; }, abstract = {Understanding the factors influencing species range limits is increasingly crucial in anticipating migrations due to human-caused climate change. In the boreal biome, ongoing climate change and the associated increases in the rate, size, and severity of disturbances may alter the distributions of boreal tree species. Notably, Interior Alaska lacks native pine, a biogeographical anomaly that carries implications for ecosystem structure and function. The current range of lodgepole pine (Pinus contorta var. latifolia) in the adjacent Yukon Territory may expand into Interior Alaska, particularly with human assistance. Evaluating the potential for pine expansion in Alaska requires testing constraints on range limits such as dispersal limitations, environmental tolerance limits, and positive or negative biotic interactions. In this study, we used field experiments with pine seeds and transplanted seedlings, complemented by model simulations, to assess the abiotic and biotic factors influencing lodgepole pine seedling establishment and growth after fire in Interior Alaska. We found that pine could successfully recruit, survive, grow, and reproduce across our broadly distributed network of experimental sites. Our results show that both mammalian herbivory and competition from native tree species are unlikely to constrain pine growth and that environmental conditions commonly found in Interior Alaska fall well within the tolerance limits for pine. If dispersal constraints are released, lodgepole pine could have a geographically expansive range in Alaska, and once established, its growth is sufficient to support pine-dominated stands. Given the impacts of lodgepole pine on ecosystem processes such as increases in timber production, carbon sequestration, landscape flammability, and reduced forage quality, natural or human-assisted migration of this species is likely to substantially alter responses of Alaskan forest ecosystems to climate change.}, } @article {pmid38839953, year = {2024}, author = {Senior, RA and Bagwyn, R and Leng, D and Killion, AK and Jetz, W and Wilcove, DS}, title = {Global shortfalls in documented actions to conserve biodiversity.}, journal = {Nature}, volume = {630}, number = {8016}, pages = {387-391}, pmid = {38839953}, issn = {1476-4687}, mesh = {Animals ; *Biodiversity ; *Conservation of Natural Resources/methods/statistics & numerical data ; Databases, Factual ; *Endangered Species/statistics & numerical data ; Extinction, Biological ; *Internationality ; Introduced Species/statistics & numerical data ; }, abstract = {Threatened species are by definition species that are in need of assistance. In the absence of suitable conservation interventions, they are likely to disappear soon[1]. There is limited understanding of how and where conservation interventions are applied globally, or how well they work[2,3]. Here, using information from the International Union for Conservation of Nature Red List and other global databases, we find that for species at risk from three of the biggest drivers of biodiversity loss-habitat loss, overexploitation for international trade and invasive species[4]-many appear to lack the appropriate types of conservation interventions. Indeed, although there has been substantial recent expansion of the protected area network, we still find that 91% of threatened species have insufficient representation of their habitats within protected areas. Conservation interventions are not implemented uniformly across different taxa and regions and, even when present, have infrequently led to substantial improvements in the status of species. For 58% of the world's threatened terrestrial species, we find conservation interventions to be notably insufficient or absent. We cannot determine whether such species are truly neglected, or whether efforts to recover them are not included in major conservation databases. If they are indeed neglected, the outlook for many of the world's threatened species is grim without more and better targeted action.}, } @article {pmid38838462, year = {2024}, author = {Runge, MC and Shea, K and Howerton, E and Yan, K and Hochheiser, H and Rosenstrom, E and Probert, WJM and Borchering, R and Marathe, MV and Lewis, B and Venkatramanan, S and Truelove, S and Lessler, J and Viboud, C}, title = {Scenario design for infectious disease projections: Integrating concepts from decision analysis and experimental design.}, journal = {Epidemics}, volume = {47}, number = {}, pages = {100775}, doi = {10.1016/j.epidem.2024.100775}, pmid = {38838462}, issn = {1878-0067}, support = {U24 GM132013/GM/NIGMS NIH HHS/United States ; }, mesh = {Humans ; *COVID-19/epidemiology/prevention & control/transmission ; *Decision Support Techniques ; Forecasting ; SARS-CoV-2 ; Communicable Diseases/epidemiology ; Pandemics/prevention & control ; Decision Making ; Research Design ; }, abstract = {Across many fields, scenario modeling has become an important tool for exploring long-term projections and how they might depend on potential interventions and critical uncertainties, with relevance to both decision makers and scientists. In the past decade, and especially during the COVID-19 pandemic, the field of epidemiology has seen substantial growth in the use of scenario projections. Multiple scenarios are often projected at the same time, allowing important comparisons that can guide the choice of intervention, the prioritization of research topics, or public communication. The design of the scenarios is central to their ability to inform important questions. In this paper, we draw on the fields of decision analysis and statistical design of experiments to propose a framework for scenario design in epidemiology, with relevance also to other fields. We identify six different fundamental purposes for scenario designs (decision making, sensitivity analysis, situational awareness, horizon scanning, forecasting, and value of information) and discuss how those purposes guide the structure of scenarios. We discuss other aspects of the content and process of scenario design, broadly for all settings and specifically for multi-model ensemble projections. As an illustrative case study, we examine the first 17 rounds of scenarios from the U.S. COVID-19 Scenario Modeling Hub, then reflect on future advancements that could improve the design of scenarios in epidemiological settings.}, } @article {pmid38837409, year = {2024}, author = {Rico-Jiménez, M and Udaondo, Z and Krell, T and Matilla, MA}, title = {Auxin-mediated regulation of susceptibility to toxic metabolites, c-di-GMP levels, and phage infection in the rhizobacterium Serratia plymuthica.}, journal = {mSystems}, volume = {9}, number = {7}, pages = {e0016524}, pmid = {38837409}, issn = {2379-5077}, support = {PID2020-112612GB-I00//Spanish Ministry for Science and Innovation/ ; PID2019-103972GA-I00//Spanish Ministry for Science and Innovation/ ; 2023AEP002//Consejo Superior de Investigaciones Científicas (CSIC)/ ; P18-FR-1621//Junta de Andalucia/ ; }, mesh = {*Indoleacetic Acids/metabolism ; *Serratia/metabolism/genetics/drug effects/pathogenicity ; *Cyclic GMP/metabolism/analogs & derivatives ; Gene Expression Regulation, Bacterial/drug effects ; Bacteriophages ; Signal Transduction/drug effects ; Biofilms/drug effects/growth & development ; Bacterial Proteins/metabolism/genetics ; Plant Growth Regulators/metabolism ; Transcriptome/drug effects ; }, abstract = {UNLABELLED: The communication between plants and their microbiota is highly dynamic and involves a complex network of signal molecules. Among them, the auxin indole-3-acetic acid (IAA) is a critical phytohormone that not only regulates plant growth and development, but is emerging as an important inter- and intra-kingdom signal that modulates many bacterial processes that are important during interaction with their plant hosts. However, the corresponding signaling cascades remain largely unknown. Here, we advance our understanding of the largely unknown mechanisms by which IAA carries out its regulatory functions in plant-associated bacteria. We showed that IAA caused important changes in the global transcriptome of the rhizobacterium Serratia plymuthica and multidisciplinary approaches revealed that IAA sensing interferes with the signaling mediated by other pivotal plant-derived signals such as amino acids and 4-hydroxybenzoic acid. Exposure to IAA caused large alterations in the transcript levels of genes involved in amino acid metabolism, resulting in significant metabolic alterations. IAA treatment also increased resistance to toxic aromatic compounds through the induction of the AaeXAB pump, which also confers resistance to IAA. Furthermore, IAA promoted motility and severely inhibited biofilm formation; phenotypes that were associated with decreased c-di-GMP levels and capsule production. IAA increased capsule gene expression and enhanced bacterial sensitivity to a capsule-dependent phage. Additionally, IAA induced the expression of several genes involved in antibiotic resistance and led to changes in the susceptibility and responses to antibiotics with different mechanisms of action. Collectively, our study illustrates the complexity of IAA-mediated signaling in plant-associated bacteria.

IMPORTANCE: Signal sensing plays an important role in bacterial adaptation to ecological niches and hosts. This communication appears to be particularly important in plant-associated bacteria since they possess a large number of signal transduction systems that respond to a wide diversity of chemical, physical, and biological stimuli. IAA is emerging as a key inter- and intra-kingdom signal molecule that regulates a variety of bacterial processes. However, despite the extensive knowledge of the IAA-mediated regulatory mechanisms in plants, IAA signaling in bacteria remains largely unknown. Here, we provide insight into the diversity of mechanisms by which IAA regulates primary and secondary metabolism, biofilm formation, motility, antibiotic susceptibility, and phage sensitivity in a biocontrol rhizobacterium. This work has important implications for our understanding of bacterial ecology in plant environments and for the biotechnological and clinical applications of IAA, as well as related molecules.}, } @article {pmid38831386, year = {2024}, author = {Duo, H and Li, Y and Lan, Y and Tao, J and Yang, Q and Xiao, Y and Sun, J and Li, L and Nie, X and Zhang, X and Liang, G and Liu, M and Hao, Y and Li, B}, title = {Systematic evaluation with practical guidelines for single-cell and spatially resolved transcriptomics data simulation under multiple scenarios.}, journal = {Genome biology}, volume = {25}, number = {1}, pages = {145}, pmid = {38831386}, issn = {1474-760X}, support = {KJQN202100538//Science and Technology Research Program of Chongqing Municipal Education Commission/ ; 62101087//National Natural Science Foundation of China/ ; 2021MD703942//China Postdoctoral Science Foundation/ ; YKC23027//Graduate Research Innovation Project of Chongqing Normal University/ ; YNPRAEC-2023004//Open Fund of Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology/ ; }, mesh = {*Single-Cell Analysis/methods ; *Gene Expression Profiling/methods ; Humans ; Software ; Computer Simulation ; Transcriptome ; Computational Biology/methods ; Sequence Analysis, RNA/methods ; RNA-Seq/methods/standards ; }, abstract = {BACKGROUND: Single-cell RNA sequencing (scRNA-seq) and spatially resolved transcriptomics (SRT) have led to groundbreaking advancements in life sciences. To develop bioinformatics tools for scRNA-seq and SRT data and perform unbiased benchmarks, data simulation has been widely adopted by providing explicit ground truth and generating customized datasets. However, the performance of simulation methods under multiple scenarios has not been comprehensively assessed, making it challenging to choose suitable methods without practical guidelines.

RESULTS: We systematically evaluated 49 simulation methods developed for scRNA-seq and/or SRT data in terms of accuracy, functionality, scalability, and usability using 152 reference datasets derived from 24 platforms. SRTsim, scDesign3, ZINB-WaVE, and scDesign2 have the best accuracy performance across various platforms. Unexpectedly, some methods tailored to scRNA-seq data have potential compatibility for simulating SRT data. Lun, SPARSim, and scDesign3-tree outperform other methods under corresponding simulation scenarios. Phenopath, Lun, Simple, and MFA yield high scalability scores but they cannot generate realistic simulated data. Users should consider the trade-offs between method accuracy and scalability (or functionality) when making decisions. Additionally, execution errors are mainly caused by failed parameter estimations and appearance of missing or infinite values in calculations. We provide practical guidelines for method selection, a standard pipeline Simpipe (https://github.com/duohongrui/simpipe ; https://doi.org/10.5281/zenodo.11178409), and an online tool Simsite (https://www.ciblab.net/software/simshiny/) for data simulation.

CONCLUSIONS: No method performs best on all criteria, thus a good-yet-not-the-best method is recommended if it solves problems effectively and reasonably. Our comprehensive work provides crucial insights for developers on modeling gene expression data and fosters the simulation process for users.}, } @article {pmid38826163, year = {2024}, author = {Onyango, B and Copeland, R and Mbogholi, J and Wamalwa, M and Kibet, C and Tonnang, HEZ and Senagi, K}, title = {WiPFIM: A digital platform for interlinking biocollections of wild plants, fruits, associated insects, and their molecular barcodes.}, journal = {Ecology and evolution}, volume = {14}, number = {6}, pages = {e11457}, pmid = {38826163}, issn = {2045-7758}, abstract = {The current knowledge on insects feeding on fruits is limited, and some of the scarce existing data on the fruit-associated insects are secluded within the host institutions. Consequently, their value is not fully realized. Moreover, in countries like Kenya, the integration of biocollections data within a digital framework has not been fully exploited. To address these gaps, this article presents a description of the development of a web-based platform for data sharing and integrating biodiversity historical data of wild plants, fruits, associated insects, and their molecular barcodes (WiPFIM) while leveraging data science technologies. The barcodes corresponding to the biocollections data were retrieved from BOLD database. The platform is an online resource about fruit-insect interactions that can be of interest to a worldwide community of users and can be useful in building innovative tools. The platform is accessible online at https://test-dmmg.icipe.org/wpfhi.}, } @article {pmid38825206, year = {2024}, author = {Wei, Q and Xue, L and Liao, S and Liu, Y}, title = {Ecohydrological indicators and environmental flow assessment in the middle and lower reaches of the Huai River, China.}, journal = {The Science of the total environment}, volume = {940}, number = {}, pages = {173639}, doi = {10.1016/j.scitotenv.2024.173639}, pmid = {38825206}, issn = {1879-1026}, abstract = {The vitality of river ecosystems is vital for the sustainable development of river basins, with the assessment of environmental flow (EF) playing a pivotal role in eco-informatics. This study delves into the middle and lower reaches (MLR) of the Huai River basin (HRB) in China, utilizing hydrological data spanning from 1950 to 2020. Its principal objective lies in the selection of ecohydrological indicators to refine the estimation of EF in the HRB. Employing principal component analysis (PCA), ecologically relevant hydrological indicators (ERHIs) were discerned and scrutinized for their hydrological characteristics. The analysis extended to evaluating hydrological shifts at different stations using ERHIs, determining suitable EF in the MLR, and delineating the trajectories of appropriate intra-annual flows in different hydrological years through HEC-RPT. Based on a variety of mutation test methods, the change point of runoff sequence was determined in 1991. The PCA analysis identified eight ERHIs, reflecting hydrological changes of 49.79 % and 56.26 % at Bengbu and Sanhezha, respectively, which indicate a moderate alteration. Based on ERHIs, the other stations in the HRB exhibited hydrological alterations ranging from 33 % to 47 %, notably highlighting substantial changes in maximal 30d flow and flow fall rate. The optimal flood pulse discharge in the middle reaches is 4150 m[3]/s, 3140 m[3]/s and 2150 m[3]/s in wet, dry and dry years, respectively. Downstream, flood pulse flow in wet, normal and dry years should exceed 4070 m[3]/s, 3110 m[3]/s and 1980 m[3]/s, respectively. The research contributes significantly to the management of rivers and the sustainable conservation of the ecological milieu.}, } @article {pmid38824636, year = {2024}, author = {Xie, PZ and Fan, YX and Chapman, C and Ma, C and Wu, CF and Hu, P and Hu, LL and Fan, PF}, title = {Determinants of macaques' space use: A test for the ecological constraints model using GPS collars.}, journal = {American journal of primatology}, volume = {86}, number = {8}, pages = {e23636}, doi = {10.1002/ajp.23636}, pmid = {38824636}, issn = {1098-2345}, support = {33000-42090019//Forestry Administration of Guangdong Province/ ; Basic Research 20180285//Shenzhen Science and Technology Innovation Committee/ ; 23lgzy002//Fundamental Research Funds for the Central Universities, Sun Yat-sun University/ ; }, mesh = {Animals ; *Macaca mulatta/physiology ; *Geographic Information Systems ; *Homing Behavior ; China ; Male ; Female ; Ecosystem ; Temperature ; Seasons ; Islands ; }, abstract = {As a central topic in Behavioral Ecology, animal space use involves dynamic responses to social and ecological factors. We collared 22 rhesus macaques (Macaca mulatta) from six groups on Neilingding Island, China, and collected 80,625 hourly fixes over a year. Using this high-resolution location data set, we quantified the macaques' space use at the individual level and tested the ecological constraints model while considering various environmental and human interfering factors. As predicted by the ecological constraints model, macaques in larger groups had longer daily path lengths (DPLs) and larger home ranges. We found an inverted U-shape relationship between mean daily temperatures and DPLs, indicating that macaques traveled farther on mild temperature days, while they decreased DPLs when temperatures were too high or too low. Anthropogenic food subsidies were positively correlated to DPLs, while the effect of rainfall was negative. Macaques decreased their DPLs and core areas when more flowers and less leaves were available, suggesting that macaques shifted their space use patterns to adapt to the seasonal differences in food resources. By applying GPS collars on a large number of individuals living on a small island, we gained valuable insights into within-group exploitation competition in wild rhesus macaques.}, } @article {pmid38823656, year = {2024}, author = {Sundar Panja, A}, title = {The systematic codon usage bias has an important effect on genetic adaption in native species.}, journal = {Gene}, volume = {926}, number = {}, pages = {148627}, doi = {10.1016/j.gene.2024.148627}, pmid = {38823656}, issn = {1879-0038}, mesh = {*Codon Usage ; *Selection, Genetic ; *Evolution, Molecular ; Endangered Species ; Mutation ; Animals ; Codon/genetics ; Adaptation, Physiological/genetics ; Extremophiles/genetics ; }, abstract = {Random mutations increase genetic variety and natural selection enhances adaption over generations. Codon usage biases (CUB) provide clues about the genome adaptation mechanisms of native species and extremophile species. Significant numbers of gene (CDS) of nine classes of endangered, native species, including extremophiles and mesophiles were utilised to compute CUB. Codon usage patterns differ among the lineages of endangered and extremophiles with native species. Polymorphic usage of nucleotides with codon burial suggests parallelism of native species within relatively confined taxonomic groups. Utilizing the deviation pattern of CUB of endangered and native species, I present a calculation parameter to estimate the extinction risk of endangered species. Species diversity and extinction risk are both positively associated with the propensity of random mutation in CDS (Coding DNA sequence). Codon bias tenet profoundly selected and it governs to adaptive evolution of native species.}, } @article {pmid38823290, year = {2024}, author = {Lopez-Labrador, FX and Huber, M and Sidorov, IA and Brown, JR and Cuypers, L and Laenen, L and Vanmechelen, B and Maes, P and Fischer, N and Pichler, I and Storey, N and Atkinson, L and Schmutz, S and Kufner, V and van Boheemen, S and Mulders, CE and Grundhoff, A and Blümke, P and Robitaille, A and Cinek, O and Hubáčková, K and Mourik, K and Boers, SA and Stauber, L and Salmona, M and Cappy, P and Ramette, A and Franze', A and LeGoff, J and Claas, ECJ and Rodriguez, C and de Vries, JJC and , }, title = {Multicenter benchmarking of short and long read wet lab protocols for clinical viral metagenomics.}, journal = {Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology}, volume = {173}, number = {}, pages = {105695}, doi = {10.1016/j.jcv.2024.105695}, pmid = {38823290}, issn = {1873-5967}, mesh = {*Metagenomics/methods/standards ; Humans ; *Benchmarking ; *Viruses/genetics/classification/isolation & purification ; *Sensitivity and Specificity ; High-Throughput Nucleotide Sequencing/methods/standards ; Virus Diseases/diagnosis/virology ; Computational Biology/methods ; }, abstract = {Metagenomics is gradually being implemented for diagnosing infectious diseases. However, in-depth protocol comparisons for viral detection have been limited to individual sets of experimental workflows and laboratories. In this study, we present a benchmark of metagenomics protocols used in clinical diagnostic laboratories initiated by the European Society for Clinical Virology (ESCV) Network on NGS (ENNGS). A mock viral reference panel was designed to mimic low biomass clinical specimens. The panel was used to assess the performance of twelve metagenomic wet lab protocols currently in use in the diagnostic laboratories of participating ENNGS member institutions. Both Illumina and Nanopore, shotgun and targeted capture probe protocols were included. Performance metrics sensitivity, specificity, and quantitative potential were assessed using a central bioinformatics pipeline. Overall, viral pathogens with loads down to 10[4] copies/ml (corresponding to CT values of 31 in our PCR assays) were detected by all the evaluated metagenomic wet lab protocols. In contrast, lower abundant mixed viruses of CT values of 35 and higher were detected only by a minority of the protocols. Considering the reference panel as the gold standard, optimal thresholds to define a positive result were determined per protocol, based on the horizontal genome coverage. Implementing these thresholds, sensitivity and specificity of the protocols ranged from 67 to 100 % and 87 to 100 %, respectively. A variety of metagenomic protocols are currently in use in clinical diagnostic laboratories. Detection of low abundant viral pathogens and mixed infections remains a challenge, implying the need for standardization of metagenomic analysis for use in clinical settings.}, } @article {pmid38822995, year = {2024}, author = {Meier, TA and Refahi, MS and Hearne, G and Restifo, DS and Munoz-Acuna, R and Rosen, GL and Woloszynek, S}, title = {The Role and Applications of Artificial Intelligence in the Treatment of Chronic Pain.}, journal = {Current pain and headache reports}, volume = {28}, number = {8}, pages = {769-784}, pmid = {38822995}, issn = {1534-3081}, mesh = {Humans ; *Chronic Pain/therapy ; *Artificial Intelligence ; Pain Management/methods ; Precision Medicine/methods ; }, abstract = {PURPOSE OF REVIEW: This review aims to explore the interface between artificial intelligence (AI) and chronic pain, seeking to identify areas of focus for enhancing current treatments and yielding novel therapies.

RECENT FINDINGS: In the United States, the prevalence of chronic pain is estimated to be upwards of 40%. Its impact extends to increased healthcare costs, reduced economic productivity, and strain on healthcare resources. Addressing this condition is particularly challenging due to its complexity and the significant variability in how patients respond to treatment. Current options often struggle to provide long-term relief, with their benefits rarely outweighing the risks, such as dependency or other side effects. Currently, AI has impacted four key areas of chronic pain treatment and research: (1) predicting outcomes based on clinical information; (2) extracting features from text, specifically clinical notes; (3) modeling 'omic data to identify meaningful patient subgroups with potential for personalized treatments and improved understanding of disease processes; and (4) disentangling complex neuronal signals responsible for pain, which current therapies attempt to modulate. As AI advances, leveraging state-of-the-art architectures will be essential for improving chronic pain treatment. Current efforts aim to extract meaningful representations from complex data, paving the way for personalized medicine. The identification of unique patient subgroups should reveal targets for tailored chronic pain treatments. Moreover, enhancing current treatment approaches is achievable by gaining a more profound understanding of patient physiology and responses. This can be realized by leveraging AI on the increasing volume of data linked to chronic pain.}, } @article {pmid38822898, year = {2024}, author = {Asefa, A and Reuber, VM and Miehe, G and Wraase, L and Wube, T and Farwig, N and Schabo, DG}, title = {Giant root-rat engineering and livestock grazing activities regulate plant functional trait diversity of an Afroalpine vegetation community in the Bale Mountains, Ethiopia.}, journal = {Oecologia}, volume = {205}, number = {2}, pages = {281-293}, pmid = {38822898}, issn = {1432-1939}, support = {NA 783/12-2, FA-925/14-1 und SCHA-2085/3-1, MI271/33-2]//German Research Council (DFG) within the Research Unit 2358 ("The Mountain Exile Hypothesis")/ ; }, mesh = {Ethiopia ; Animals ; *Livestock ; *Ecosystem ; Rodentia/physiology ; }, abstract = {Disturbances from rodent engineering and human activities profoundly impact ecosystem structure and functioning. Whilst we know that disturbances modulate plant communities, comprehending the mechanisms through which rodent and human disturbances influence the functional trait diversity and trait composition of plant communities is important to allow projecting future changes and to enable informed decisions in response to changing intensity of the disturbances. Here, we evaluated the changes in functional trait diversity and composition of Afroalpine plant communities in the Bale Mountains of Ethiopia along gradients of engineering disturbances of a subterranean endemic rodent, the giant root-rat (Tachyoryctes macrocephalus Rüppell 1842) and human activities (settlement establishment and livestock grazing). We conducted RLQ (co-inertia analysis) and fourth-corner analyses to test for trait-disturbance (rodent engineering/human activities) covariation. Overall, our results show an increase in plant functional trait diversity with increasing root-rat engineering and increasing human activities. We found disturbance specific association with traits. Specifically, we found strong positive association of larger seed mass with increasing root-rat fresh burrow density, rhizomatous vegetative propagation negatively associated with increasing root-rat old burrow, and stolonifereous vegetative propagation positively associated with presence of root-rat mima mound. Moreover, both leaf size and leaf nitrogen content were positively associated with livestock dung abundance but negatively with distance from settlement. Overall, our results suggest that disturbances by rodents filter plant traits related to survival and reproduction strategies, whereas human activities such as livestock grazing act as filters for traits related to leaf economics spectrum along acquisitive resource-use strategy.}, } @article {pmid38822152, year = {2024}, author = {Li, X and Bai, Y and Xu, C and Liu, S and Yu, H and Kong, L and Du, S and Li, Q}, title = {OysterDB: A Genome Database for Ostreidae.}, journal = {Marine biotechnology (New York, N.Y.)}, volume = {26}, number = {4}, pages = {827-834}, pmid = {38822152}, issn = {1436-2236}, support = {2022LZGCQY010, 2021ZLGX03 and 2021TSGC1240//Shandong Province Agriculture Research System Project/ ; CARS-49//China Agriculture Research System Project/ ; }, mesh = {Animals ; *Databases, Genetic ; *Ostreidae/genetics ; *Genome ; Molecular Sequence Annotation ; Computational Biology ; Genomics ; }, abstract = {The molluscan family Ostreidae, commonly known as oysters, is an important molluscan group due to its economic and ecological importance. In recent years, an abundance of genomic data of Ostreidae species has been generated and available in public domain. However, there is still a lack of a high-efficiency database platform to store and distribute these data with comprehensive tools. In this study, we developed an oyster genome database (OysterDB) to consolidate oyster genomic data. This database includes eight oyster genomes and 208,923 protein-coding gene annotations. Bioinformatic tools, such as BLAST and JBrowse, are integrated into the database to provide a user-friendly platform for homologous sequence searching, visualization of genomes, and screen for candidate gene information. Moreover, OysterDB will be continuously updated with ever-growing oyster genomic resources and facilitate future studies for comparative and functional genomic analysis of oysters (http://oysterdb.com.cn/).}, } @article {pmid38820292, year = {2023}, author = {Damian-Serrano, A and Sutherland, KR}, title = {A Developmental Ontology for the Colonial Architecture of Salps.}, journal = {The Biological bulletin}, volume = {245}, number = {1}, pages = {9-18}, doi = {10.1086/730459}, pmid = {38820292}, issn = {1939-8697}, mesh = {Animals ; *Urochordata/growth & development/physiology/anatomy & histology ; Life Cycle Stages/physiology ; Biological Ontologies ; }, abstract = {AbstractColonial animals are composed of clonal individuals that remain physically connected and physiologically integrated. Salps are tunicates with a dual life cycle, including an asexual solitary stage that buds sexual colonies composed of jet-propelling zooids that efficiently swim together as a single unit by multijet propulsion. Colonies from different species develop distinct architectures characterized by their zooid arrangement patterns, but this diversity has received little attention. Thus, these architectures have never been formally defined using a framework of variables and axes that would allow comparative analyses. We set out to define an ontology of the salp colony architecture morphospace and describe the developmental pathways that build the different architectures. To inform these definitions, we collected and photographed live specimens of adult and developing colonies through offshore scuba diving. Since all salp colonies begin their development as a transversal double chain, we characterized each adult colonial architecture as a series of developmental transitions, such as rotations and translations of zooids, relative to their orientation at this early shared stage. We hypothesize that all adult architectures are either final or intermediate stages within three developmental pathways toward bipinnate, cluster, or helical forms. This framework will enable comparative studies on the biomechanical implications, ecological functions, evolutionary history, and engineering applications of the diversity of salp colony architectures.}, } @article {pmid38819974, year = {2024}, author = {Tang, Z and Tang, S and Wang, H and Li, R and Zhang, X and Zhang, W and Yuan, X and Zang, Y and Li, Y and Zhou, T and Li, Y}, title = {S2VQ-VAE: Semi-Supervised Vector Quantised-Variational AutoEncoder for Automatic Evaluation of Trail Making Test.}, journal = {IEEE journal of biomedical and health informatics}, volume = {28}, number = {8}, pages = {4456-4470}, doi = {10.1109/JBHI.2024.3407881}, pmid = {38819974}, issn = {2168-2208}, mesh = {Humans ; *Cognitive Dysfunction/diagnosis ; Aged ; Male ; Female ; *Trail Making Test ; Supervised Machine Learning ; Aged, 80 and over ; Algorithms ; Deep Learning ; Diagnosis, Computer-Assisted/methods ; Signal Processing, Computer-Assisted ; }, abstract = {BACKGROUND: Computer-aided detection of cognitive impairment garnered increasing attention, offering older adults in the community access to more objective, ecologically valid, and convenient cognitive assessments using multimodal sensing technology on digital devices.

METHODOLOGY: In this study, we aimed to develop an automated method for screening cognitive impairment, building on paper- and electronic TMTs. We proposed a novel deep representation learning approach named Semi-Supervised Vector Quantised-Variational AutoEncoder (S2VQ-VAE). Within S2VQ-VAE, we incorporated intra- and inter-class correlation losses to disentangle class-related factors. These factors were then combined with various real-time obtainable features (including demographic, time-related, pressure-related, and jerk-related features) to create a robust feature engineering block. Finally, we identified the light gradient boosting machine as the optimal classifier. The experiments were conducted on a dataset collected from older adults in the community.

RESULTS: The experimental results showed that the proposed multi-type feature fusion method outperformed the conventional method used in paper-based TMTs and the existing VAE-based feature extraction in terms of screening performance.

CONCLUSIONS: In conclusion, the proposed deep representation learning method significantly enhances the cognitive diagnosis capabilities of behavior-based TMTs and streamlines large-scale community-based cognitive impairment screening while reducing the workload of professional healthcare staff.}, } @article {pmid38819559, year = {2024}, author = {Sanchez, FB and Sato Guima, SE and Setubal, JC}, title = {How to Obtain and Compare Metagenome-Assembled Genomes.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2802}, number = {}, pages = {135-163}, pmid = {38819559}, issn = {1940-6029}, mesh = {*Metagenome/genetics ; *Metagenomics/methods ; Software ; Computational Biology/methods ; Databases, Genetic ; Sequence Analysis, DNA/methods ; Genome, Bacterial ; }, abstract = {Metagenome-assembled genomes, or MAGs, are genomes retrieved from metagenome datasets. In the vast majority of cases, MAGs are genomes from prokaryotic species that have not been isolated or cultivated in the lab. They, therefore, provide us with information on these species that are impossible to obtain otherwise, at least until new cultivation methods are devised. Thanks to improvements and cost reductions of DNA sequencing technologies and growing interest in microbial ecology, the rise in number of MAGs in genome repositories has been exponential. This chapter covers the basics of MAG retrieval and processing and provides a practical step-by-step guide using a real dataset and state-of-the-art tools for MAG analysis and comparison.}, } @article {pmid38818975, year = {2024}, author = {Shi, H and Zhu, Y and Wu, X and Jiang, T and Li, X and Liu, J and Di, Y and Chen, F and Gao, J and Xu, X and Xiao, N and Feng, X and Zhang, P and Wu, Y and La, Q and Li, A and Chen, P and Li, X}, title = {CropMetabolome: a comprehensive metabolome database for major crops cross eight categories.}, journal = {The Plant journal : for cell and molecular biology}, volume = {119}, number = {3}, pages = {1613-1626}, doi = {10.1111/tpj.16858}, pmid = {38818975}, issn = {1365-313X}, support = {2023ZD04073//National Key R&D Program of China/ ; XDA24010400//Strategic Priority Research Program of Chinese Academy of Sciences/ ; BE2023336//Key R&D Program of Jiangsu Province Modern Agriculture/ ; 32270719//National Natural Science Foundation of China/ ; 31900470//National Natural Science Foundation of China/ ; 32200093//National Natural Science Foundation of China/ ; CARS-11//Earmarked Fund for China Agriculture Research System/ ; 2022M713144//China Postdoctoral Science Foundation/ ; }, mesh = {*Crops, Agricultural/metabolism/genetics ; *Metabolome ; *Metabolomics/methods ; *Databases, Factual ; Flavonoids/metabolism ; Mass Spectrometry ; }, abstract = {Chemical compositions of crops are of great agronomical importance, as crops serve as resources for nutrition, energy, and medicines for human and livestock. For crop metabolomics research, the lack of crop reference metabolome and high-quality reference compound mass spectra, as well as utilities for metabolic profiling, has hindered the discovery and functional study of phytochemicals in crops. To meet these challenging needs, we have developed the Crop Metabolome database (abbreviated as CropMetabolome) that is dedicated to the construction of crop reference metabolome, repository, and dissemination of crop metabolomic data, and profiling and analytic tools for metabolomics research. CropMetabolome contains a metabolomics database for more than 50 crops (belonging to eight categories) that integrated self-generated raw mass spectral data and public-source datasets. The reference metabolome for 59 crop species was constructed, which have functions that parallel those of reference genome in genomic studies. CropMetabolome also contains 'Standard compound mass spectral library', 'Flavonoids library', 'Pesticide library', and a set of related analytical tools that enable metabolic profiling based on a reference metabolome (CropRefMetaBlast), annotation and identification of new metabolites (CompoundLibBlast), deducing the structure of novel flavonoid derivatives (FlavoDiscover), and detecting possible residual pesticides in crop samples (PesticiDiscover). In addition, CropMetabolome is a repository to share and disseminate metabolomics data and a platform to promote collaborations to develop reference metabolome for more crop species. CropMetabolome is a comprehensive platform that offers important functions in crop metabolomics research and contributes to improve crop breeding, nutrition, and safety. CropMetabolome is freely available at https://www.cropmetabolome.com/.}, } @article {pmid38816346, year = {2024}, author = {Locke, MA and Witthaus, LM and Lizotte, RE and Heintzman, LJ and Moore, MT and O'Reilly, A and Wells, RR and Langendoen, EJ and Bingner, RL and Gholson, DM and Taylor, JM and Johnson, FE}, title = {The LTAR Cropland Common Experiment in the Lower Mississippi River Basin.}, journal = {Journal of environmental quality}, volume = {53}, number = {6}, pages = {957-967}, doi = {10.1002/jeq2.20577}, pmid = {38816346}, issn = {1537-2537}, mesh = {*Rivers ; *Agriculture/methods ; *Crops, Agricultural ; Conservation of Natural Resources/methods ; }, abstract = {The Lower Mississippi River Basin Long-Term Agroecosystem Research Site (LMRB-LTAR) encompasses six states from Missouri to the Gulf of Mexico and is coordinated by the USDA-ARS National Sedimentation Laboratory, Oxford, MS. The overarching goal of LTAR is to assess regionally diverse and geographically scalable farming practices for enhanced sustainability of agroecosystem goods and services under changing environment and resource-use conditions. The LMRB-LTAR overall goal is to assess sustainable row crop agricultural production systems that integrate regional environmental and socioeconomic needs. Primary row crops in the region include soybeans, corn, cotton, rice, and sugarcane with crop rotations influenced by commodity crop price and other factors. The field-scale common experiment (CE) includes four row crop farms (26-101 ha) established in 2021 and 2023. Three fields are managed with alternative practices, including reduced tillage, cover crops, and automated prescription irrigation, and three fields are managed with prevailing farming practices, consisting of conventional tillage, no cover crop, and nonprescription irrigation. Treatment effects on crop productivity, soil quality, water use efficiency, water quality, and carbon storage are assessed. Research from the LMRB CE will deliver outcomes linked to overarching LTAR network goals, including innovative agricultural systems, strengthened partnerships, data management technologies, and precision environmental tools.}, } @article {pmid38814981, year = {2024}, author = {Mullon, C and Peña, J and Lehmann, L}, title = {The evolution of environmentally mediated social interactions and posthumous spite under isolation by distance.}, journal = {PLoS computational biology}, volume = {20}, number = {5}, pages = {e1012071}, pmid = {38814981}, issn = {1553-7358}, mesh = {*Biological Evolution ; *Social Interaction ; Computational Biology ; Phenotype ; Animals ; Environment ; Humans ; }, abstract = {Many social interactions happen indirectly via modifications of the environment, e.g. through the secretion of functional compounds or the depletion of renewable resources. Here, we derive the selection gradient on a quantitative trait affecting dynamical environmental variables that feed back on reproduction and survival in a finite patch-structured population subject to isolation by distance. Our analysis shows that the selection gradient depends on how a focal individual influences the fitness of all future individuals in the population through modifications of the environmental variables they experience, weighted by the neutral relatedness between recipients and the focal. The evolutionarily relevant trait-driven environmental modifications are formalized as the extended phenotypic effects of an individual, quantifying how a trait change in an individual in the present affects the environmental variables in all patches at all future times. When the trait affects reproduction and survival through a payoff function, the selection gradient can be expressed in terms of extended phenotypic effects weighted by scaled relatedness. We show how to compute extended phenotypic effects, relatedness, and scaled relatedness using Fourier analysis, which allow us to investigate a broad class of environmentally mediated social interactions in a tractable way. We use our approach to study the evolution of a trait controlling the costly production of some lasting commons (e.g. a common-pool resource or a toxic compound) that can diffuse in space and persist in time. We show that indiscriminate posthumous spite readily evolves in this scenario. More generally, whether selection favours environmentally mediated altruism or spite is determined by the spatial correlation between an individual's lineage and the commons originating from its patch. The sign of this correlation depends on interactions between dispersal patterns and the commons' renewal dynamics. More broadly, we suggest that selection can favour a wide range of social behaviours when these have carry-over effects in space and time.}, } @article {pmid38814957, year = {2024}, author = {Schoenecker, KA and King, SRB and Hennig, JD and Cole, MJ and Scasta, JD and Beck, JL}, title = {Effects of telemetry collars on two free-roaming feral equid species.}, journal = {PloS one}, volume = {19}, number = {5}, pages = {e0303312}, pmid = {38814957}, issn = {1932-6203}, mesh = {Animals ; *Telemetry ; *Equidae/physiology ; *Geographic Information Systems ; Horses ; Female ; Male ; }, abstract = {There are two species of free-roaming feral equids in North America: horses (Equus caballus) and donkeys or "burros" (E. asinus). Both species were introduced as domestic animals to North America in the early 1500s and currently inhabit rangelands across the western United States, Canada, and all continents except Antarctica. Despite their global distribution, little is known about their fine scale spatial ecology. Contemporary research tools to assess space use include global positioning system (GPS) tracking collars, but older models were problematic due to stiff collar belting causing poor fit. We tested modern designs of GPS collars on n = 105 horses and n = 60 burros for 4 years in five populations (3 horse, 2 burro) across the western United States, to assess whether collars posed welfare risks to horses or burros. We found no difference in survival of collared versus uncollared mares and jennies, and no difference in survival of their foals. In 4036 of 4307 observations for horses (93.7%) and 2115 of 2258 observations for burros (93.6%), collars were observed symmetrical, maintaining proper fit on the neck. Fur effects from collars (sweaty neck, indented fur, broken fur) were seen in 3% of horse observations and 25% of burro observations. Superficial effects (chafes and marks on skin surface) were seen in 2% of horse observations and 11% of burro observations; no severe effects from collars were seen. Body condition was not affected by collars; mean body condition of collared horses was 4.70 ± 0.54 (mean ± s.d) and 4.71 ± 0.65 for collared burros. Behavior results indicated minimal effects; collared horses stood slightly more than uncollared, and collared burros stood and foraged more in one population, but not in the other. For 6.3% of observations of horses and 6.4% of observations of burros, we found an effect of time wearing a collar on the cumulative sum of fur effects which increased over time (burros: rs = 0.87, P = <0.0001; horses: rs = 0.31, P = 0.002). Burros also showed an increase over time in the number of superficial effects, but horses did not. Collars occasionally moved into the wrong position, shifting forward over the ears; we observed this on 19 horses and 1 burro. Of those, most collars went over the ears in summer (n = 12). All collars were equipped with a remote release mechanism as well as a timed-release mechanism for redundancy, thus removed when observed in wrong position to avoid rubbing or discomfort. Our finding of no consequential physical effects in 98% of horse observations, and 89% of burro observations suggests the consequences of collars on free-roaming equid welfare and survival is biologically insignificant, although collars should be monitored regularly and continue to be equipped with a remote release mechanism to remove a collar if needed. With frequent welfare-driven, visual monitoring, collaring of free-roaming equids can be a safe and useful tool to increase our understanding of their spatial ecology, demography, habitat use, behavior, and interactions with other wildlife.}, } @article {pmid38813661, year = {2024}, author = {Cong, Y and Endo, T}, title = {A Quadruple Revolution: Deciphering Biological Complexity with Artificial Intelligence, Multiomics, Precision Medicine, and Planetary Health.}, journal = {Omics : a journal of integrative biology}, volume = {28}, number = {6}, pages = {257-260}, doi = {10.1089/omi.2024.0110}, pmid = {38813661}, issn = {1557-8100}, mesh = {*Precision Medicine/methods/trends ; *Artificial Intelligence ; Humans ; Systems Biology/methods ; Genomics/methods ; Machine Learning ; Multiomics ; }, abstract = {A quiet quadruple revolution has been in the making in systems science with convergence of (1) artificial intelligence, machine learning, and other digital technologies; (2) multiomics big data integration; (3) growing interest in the "variability science" of precision/personalized medicine that aims to account for patient-to-patient and between-population differences in disease susceptibilities and responses to health interventions such as drugs, nutrition, vaccines, and radiation; and (4) planetary health scholarship that both scales up and integrates biological, clinical, and ecological contexts of health and disease. Against this overarching background, this article presents and highlights some of the salient challenges and prospects of multiomics research, emphasizing the attendant pivotal role of systems medicine and systems biology. In addition, we emphasize the rapidly growing importance of planetary health research for systems medicine, particularly amid climate emergency, ecological degradation, and loss of planetary biodiversity. Looking ahead, we anticipate that the integration and utilization of multiomics big data and artificial intelligence will drive further progress in systems medicine and systems biology, heralding a promising future for both human and planetary health.}, } @article {pmid38813550, year = {2023}, author = {Boyes, D and , and , and , and , and , and , }, title = {The genome sequence of the Six-belted Clearwing, Bembecia ichneumoniformis (Denis & Schiffermüller, 1775).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {515}, pmid = {38813550}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual male Bembecia ichneumoniformis (the Six-belted Clearwing; Arthropoda; Insecta; Lepidoptera; Sesiidae). The genome sequence is 511.4 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.32 kilobases in length. Gene annotation of this assembly on Ensembl identified 12,114 protein coding genes.}, } @article {pmid38813548, year = {2023}, author = {Boyes, D and Holland, PWH and , and , and , and , and , and , }, title = {The genome sequence of the July Highflyer, Hydriomena furcata (Thunberg, 1784).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {496}, pmid = {38813548}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual male Hydriomena furcata (the July Highflyer; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 423.3 megabases in span. Most of the assembly is scaffolded into 28 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.89 kilobases in length. Gene annotation of this assembly on Ensembl identified 17,324 protein coding genes.}, } @article {pmid38813465, year = {2024}, author = {Falk, S and Poole, O and , and , and , and , and , and , and , }, title = {The genome sequence of the parsley Cheilosia, Cheilosia pagana (Meigen, 1822).}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {54}, pmid = {38813465}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual female Cheilosia pagana (the parsley Cheilosia; Arthropoda; Insecta; Diptera; Syrphidae). The genome sequence is 354.1 megabases in span. Most of the assembly is scaffolded into 6 chromosomal pseudomolecules, including the X sex chromosome. The mitochondrial genome has also been assembled and is 16.76 kilobases in length.}, } @article {pmid38808804, year = {2024}, author = {Freitas, GA and Marcon, GEB and Welch, JR and Silva, CMFPD}, title = {Analysis of the completeness and consistency of records of violence against indigenous women in the health macro-region of Dourados, Mato Grosso do Sul state, Brazil, 2009-2020.}, journal = {Epidemiologia e servicos de saude : revista do Sistema Unico de Saude do Brasil}, volume = {33}, number = {}, pages = {e20231075}, pmid = {38808804}, issn = {2237-9622}, mesh = {Adult ; Indians, South American/statistics & numerical data ; Information Systems ; Time Factors ; Female ; South American People ; Humans ; Brazil ; Communication ; Indigenous Peoples/statistics & numerical data ; *Violence/statistics & numerical data ; Educational Status ; Gender-Based Violence/statistics & numerical data ; }, abstract = {OBJECTIVE: To analyze the temporal trend of completeness and consistency of data on notifications of violence against indigenous women in the health macro-region of Dourados, state of Mato Grosso do Sul, Brazil, between 2009 and 2020.

METHODS: An ecological time series study was conducted using data from the Notifiable Health Conditions Information System; Prais-Winsten regression was used to analyze the trend of data completeness and consistency, as well as the proportion of completed and coherent fields.

RESULTS: A total of 2,630 cases were reported; completeness was found to be very poor in the variable "occupation" (48.9%) and poor in the variables "schooling" (68.3%) and "time of occurrence" (67.9%); in the analysis of temporal trends, only the variable "occupation" showed a decreasing trend (p = 0.045).

CONCLUSION: The data analyzed demonstrated the need for improvement in the completeness of the variables "schooling", "occupation" and "time of occurrence" of the violent act.

MAIN RESULTS: There was a progressive increase in notifications over the years. Most of the variables showed regular or excellent completeness and consistency. In the analysis of temporal trend, only the "occupation" variable showed a decreasing trend.

IMPLICATIONS FOR SERVICES: Care for victims of violence is part of the daily routine of health services, and it is essential for health professionals to provide adequate compulsory notification for a comprehensive understanding of the victims' profile, thus assisting in addressing this issue.

PERSPECTIVES: Further studies are needed to understand the factors associated with violence against indigenous women, which could help the development of health promotion actions and violence prevention strategies targeting these women.}, } @article {pmid38808214, year = {2024}, author = {Kyalo, H and Tonnang, HEZ and Egonyu, JP and Olukuru, J and Tanga, CM and Senagi, K}, title = {A convolutional neural network with image and numerical data to improve farming of edible crickets as a source of food-A decision support system.}, journal = {Frontiers in artificial intelligence}, volume = {7}, number = {}, pages = {1403593}, pmid = {38808214}, issn = {2624-8212}, abstract = {Crickets (Gryllus bimaculatus) produce sounds as a natural means to communicate and convey various behaviors and activities, including mating, feeding, aggression, distress, and more. These vocalizations are intricately linked to prevailing environmental conditions such as temperature and humidity. By accurately monitoring, identifying, and appropriately addressing these behaviors and activities, the farming and production of crickets can be enhanced. This research implemented a decision support system that leverages machine learning (ML) algorithms to decode and classify cricket songs, along with their associated key weather variables (temperature and humidity). Videos capturing cricket behavior and weather variables were recorded. From these videos, sound signals were extracted and classified such as calling, aggression, and courtship. Numerical and image features were extracted from the sound signals and combined with the weather variables. The extracted numerical features, i.e., Mel-Frequency Cepstral Coefficients (MFCC), Linear Frequency Cepstral Coefficients, and chroma, were used to train shallow (support vector machine, k-nearest neighbors, and random forest (RF)) ML algorithms. While image features, i.e., spectrograms, were used to train different state-of-the-art deep ML models, i,e., convolutional neural network architectures (ResNet152V2, VGG16, and EfficientNetB4). In the deep ML category, ResNet152V2 had the best accuracy of 99.42%. The RF algorithm had the best accuracy of 95.63% in the shallow ML category when trained with a combination of MFCC+chroma and after feature selection. In descending order of importance, the top 6 ranked features in the RF algorithm were, namely humidity, temperature, C#, mfcc11, mfcc10, and D. From the selected features, it is notable that temperature and humidity are necessary for growth and metabolic activities in insects. Moreover, the songs produced by certain cricket species naturally align to musical tones such as C# and D as ranked by the algorithm. Using this knowledge, a decision support system was built to guide farmers about the optimal temperature and humidity ranges and interpret the songs (calling, aggression, and courtship) in relation to weather variables. With this information, farmers can put in place suitable measures such as temperature regulation, humidity control, addressing aggressors, and other relevant interventions to minimize or eliminate losses and enhance cricket production.}, } @article {pmid38807051, year = {2024}, author = {Xie, J and Lan, Y and Zou, C and He, J and Huang, Q and Zeng, J and Pan, M and Mei, Y and Luo, J and Zou, D}, title = {Single-nucleus analysis reveals microenvironment-specific neuron and glial cell enrichment in Alzheimer's disease.}, journal = {BMC genomics}, volume = {25}, number = {1}, pages = {526}, pmid = {38807051}, issn = {1471-2164}, support = {YCSW2023244//the Innovation Project of Guangxi Graduate Education/ ; 2024GXNSFBA010054//the Joint Project on Regional High-Incidence Diseases Research of Guangxi Natural Science Foundation/ ; 2024GXNSFDA010001//the Joint Project on Regional High-Incidence Diseases Research of Guangxi Natural Science Foundation/ ; }, mesh = {*Alzheimer Disease/genetics/pathology/metabolism ; Humans ; *Neuroglia/metabolism/pathology ; *Neurons/metabolism ; *Single-Cell Analysis ; Cellular Microenvironment/genetics ; Computational Biology/methods ; }, abstract = {BACKGROUND: Alzheimer's disease (AD) is a complicated neurodegenerative disease. Neuron-glial cell interactions are an important but not fully understood process in the progression of AD. We used bioinformatic methods to analyze single-nucleus RNA sequencing (snRNA-seq) data to investigate the cellular and molecular biological processes of AD.

METHOD: snRNA-seq data were downloaded from Gene Expression Omnibus (GEO) datasets and reprocessed to identify 240,804 single nuclei from healthy controls and patients with AD. The cellular composition of AD was further explored using Uniform Manifold Approximation and Projection (UMAP). Enrichment analysis for the functions of the DEGs was conducted and cell development trajectory analyses were used to reveal underlying cell fate decisions. iTALK was performed to identify ligand-receptor pairs among various cell types in the pathological ecological microenvironment of AD.

RESULTS: Six cell types and multiple subclusters were identified based on the snRNA-seq data. A subcluster of neuron and glial cells co-expressing lncRNA-SNHG14, myocardin-related transcription factor A (MRTFA), and MRTFB was found to be more abundant in the AD group. This subcluster was enriched in mitogen-activated protein kinase (MAPK)-, immune-, and apoptosis-related pathways. Through molecular docking, we found that lncRNA-SNHG14 may bind MRTFA and MRTFB, resulting in an interaction between neurons and glial cells.

CONCLUSIONS: The findings of this study describe a regulatory relationship between lncRNA-SNHG14, MRTFA, and MRTFB in the six main cell types of AD. This relationship may contribute to microenvironment remodeling in AD and provide a theoretical basis for a more in-depth analysis of AD.}, } @article {pmid38805961, year = {2024}, author = {Edwin, IE and Chukwuka, O and Ochege, FU and Ling, Q and Chen, B and Nzabarinda, V and Ajaero, C and Hamdi, R and Luo, G}, title = {Quantifying land change dynamics, resilience and feedback: A comparative analysis of the lake Chad basin in Africa and Aral Sea basin in Central Asia.}, journal = {Journal of environmental management}, volume = {361}, number = {}, pages = {121218}, doi = {10.1016/j.jenvman.2024.121218}, pmid = {38805961}, issn = {1095-8630}, mesh = {*Lakes ; *Climate Change ; Africa ; Geographic Information Systems ; Conservation of Natural Resources ; Asia ; }, abstract = {The intricate interaction of natural and anthropogenic factors drives changes in land and water in response to societal demands and climate change. However, there has been insufficient information on the feedback effects in dryland hotspots altered by land change dynamics. This research compared two transboundary inland lakes, the Lake Chad basin (LCB) in Africa and the Aral Sea basin (ASB) in Central Asia, using remote sensing and geographic information system techniques to analyze and quantify present and future land cover dynamics, resilience, and their feedback effects. The study integrated Cellular Automata, Markov Chain, and Multilayer Perceptron models to predict LULC changes up to 2030. Descriptive statistics, ordinary least squares regression, hotspot Gi-Bin, trend analysis, and advanced geostatistical methods were utilized to identify relationships, patterns, magnitudes, and directions of observed changes in the feedback effects. From 2000 to 2030, the analysis unveils intriguing trends, including an increase in cropland from 48% to 51% and a decrease in shrubland from 18% to 15% in the LCB. The grassland increased from 21% to 22%, and the settlement expanded from 0.10 to 0.60% in the ASB. Water bodies remained stable at 1.60 % in LCB, while in ASB, it declined from 3% to 2%. These changes were significantly influenced by population, elevation, and temperature in both basins, with irrigation also playing a significant role in the ASB and slope in LCB. The study further revealed discernible shifts in normalized difference vegetation index, temperature, and precipitation linked to specific land cover conversions, suggesting alterations in surface properties and vegetation health. This study underscores the complex interplay between land cover dynamics, resilience, climate variability, and feedback mechanisms in LCB and ASB.}, } @article {pmid38805695, year = {2024}, author = {McElroy, KE and Masonbrink, R and Chudalayandi, S and Severin, AJ and Serb, JM}, title = {A chromosome-level genome assembly of the disco clam, Ctenoides ales.}, journal = {G3 (Bethesda, Md.)}, volume = {14}, number = {9}, pages = {}, pmid = {38805695}, issn = {2160-1836}, support = {DEB 1754331//National Science Foundation/ ; 1726447//NSF/ ; }, mesh = {Animals ; *Bivalvia/genetics ; *Genome ; *Molecular Sequence Annotation ; Chromosomes/genetics ; Genomics/methods ; Phylogeny ; }, abstract = {The bivalve subclass Pteriomorphia, which includes the economically important scallops, oysters, mussels, and ark clams, exhibits extreme ecological, morphological, and behavioral diversity. Among this diversity are five morphologically distinct eye types, making Pteriomorphia an excellent setting to explore the molecular basis for the evolution of novel traits. Of pteriomorphian bivalves, Limida is the only order lacking genomic resources, greatly limiting the potential phylogenomic analyses related to eyes and phototransduction. Here, we present a limid genome assembly, the disco clam, Ctenoides ales (C. ales), which is characterized by invaginated eyes, exceptionally long tentacles, and a flashing light display. This genome assembly was constructed with PacBio long reads and Dovetail Omni-CTM proximity-ligation sequencing. The final assembly is ∼2.3Gb and over 99% of the total length is contained in 18 pseudomolecule scaffolds. We annotated 41,064 protein coding genes and reported a BUSCO completeness of 91.9% for metazoa_obd10. Additionally, we report a complete and annotated mitochondrial genome, which also had been lacking from Limida. The ∼20Kb mitogenome has 12 protein coding genes, 22 tRNAs, 2 rRNA genes, and a 1,589 bp duplicated sequence containing the origin of replication. The C. ales nuclear genome size is substantially larger than other pteriomorphian genomes, mainly accounted for by transposable element sequences. We inventoried the genome for opsins, the signaling proteins that initiate phototransduction, and found that, unlike its closest eyed-relatives, the scallops, C. ales lacks duplication of the rhabdomeric Gq-protein-coupled opsin that is typically used for invertebrate vision. In fact, C. ales has uncharacteristically few opsins relative to the other pteriomorphian families, all of which have unique expansions of xenopsins, a recently discovered opsin subfamily. This chromosome-level assembly, along with the mitogenome, is a valuable resource for comparative genomics and phylogenetics in bivalves and particularly for the understudied but charismatic limids.}, } @article {pmid38805543, year = {2024}, author = {Lansch-Justen, L and El Karoui, M and Alexander, HK}, title = {Estimating mutation rates under heterogeneous stress responses.}, journal = {PLoS computational biology}, volume = {20}, number = {5}, pages = {e1012146}, pmid = {38805543}, issn = {1553-7358}, support = {/WT_/Wellcome Trust/United Kingdom ; }, mesh = {*Mutation Rate ; *Escherichia coli/genetics ; *Stress, Physiological/genetics ; *Models, Genetic ; SOS Response, Genetics/genetics ; Computer Simulation ; Computational Biology/methods ; Mutation ; }, abstract = {Exposure to environmental stressors, including certain antibiotics, induces stress responses in bacteria. Some of these responses increase mutagenesis and thus potentially accelerate resistance evolution. Many studies report increased mutation rates under stress, often using the standard experimental approach of fluctuation assays. However, single-cell studies have revealed that many stress responses are heterogeneously expressed in bacterial populations, which existing estimation methods have not yet addressed. We develop a population dynamic model that considers heterogeneous stress responses (subpopulations of cells with the response off or on) that impact both mutation rate and cell division rate, inspired by the DNA-damage response in Escherichia coli (SOS response). We derive the mutant count distribution arising in fluctuation assays under this model and then implement maximum likelihood estimation of the mutation-rate increase specifically associated with the expression of the stress response. Using simulated mutant count data, we show that our inference method allows for accurate and precise estimation of the mutation-rate increase, provided that this increase is sufficiently large and the induction of the response also reduces the division rate. Moreover, we find that in many cases, either heterogeneity in stress responses or mutant fitness costs could explain similar patterns in fluctuation assay data, suggesting that separate experiments would be required to identify the true underlying process. In cases where stress responses and mutation rates are heterogeneous, current methods still correctly infer the effective increase in population mean mutation rate, but we provide a novel method to infer distinct stress-induced mutation rates, which could be important for parameterising evolutionary models.}, } @article {pmid38805169, year = {2024}, author = {Peng, X and Yang, Y and Zhong, R and Yang, Y and Yan, F and Liang, N and Yuan, S}, title = {Zinc and Inflammatory Bowel Disease: From Clinical Study to Animal Experiment.}, journal = {Biological trace element research}, volume = {}, number = {}, pages = {}, doi = {10.1007/s12011-024-04193-6}, pmid = {38805169}, issn = {1559-0720}, support = {2081921001//Chengdu University/ ; CDUCX2024759//Training Program for Innovation and Entrepreneurship of Chengdu University/ ; 32370557//National Natural Science Foundation of China/ ; NCKL202201//Nanchong Key Laboratory of Wildlife Nutrition Ecology and Disease Control/ ; }, abstract = {Inflammatory bowel disease (IBD) is a chronic inflammatory disease of the gastrointestinal tract (GI) with a high incidence rate globally, and IBD patients are often accompanied by zinc deficiency. This review aims to summarize the potential therapeutic value of zinc supplementation in IBD clinical patients and animal models. Zinc supplementation can relieve the severity of IBD especially in patients with zinc deficiency. The clinical severity of IBD were mainly evaluated through some scoring methods involving clinical performance, endoscopic observation, blood biochemistry, and pathologic biopsy. Through conducting animal experiments, it has been found that zinc plays an important role in alleviating clinical symptoms and improving pathological lesions. In both clinical observation and animal experiment of IBD, the therapeutic mechanisms of zinc interventions have been found to be related to immunomodulation, intestinal epithelial repair, and gut microbiota's balance. Furthermore, the antioxidant activity of zinc was clarified in animal experiment. Appropriate zinc supplementation is beneficial for IBD therapy, and the present evidence highlights that alleviating zinc-deficient status can effectively improve the severity of clinical symptoms in IBD patients and animal models.}, } @article {pmid38803273, year = {2024}, author = {Wang, Y and Yang, Y and Liu, Y and Liu, C and Xu, M and Fang, M and Mu, X}, title = {CoSFISH: a comprehensive reference database of COI and 18S rRNA barcodes for fish.}, journal = {Database : the journal of biological databases and curation}, volume = {2024}, number = {}, pages = {}, pmid = {38803273}, issn = {1758-0463}, support = {2022SBH00001//Guangdong Rural Revitalization Strategy Special Provincial Organization/ ; 2023KJ134 2023KJ150//Modern Agriculture Industry Technology Innovation Team/ ; CAMC-2018F//China-ASEAN Maritime Cooperation Fund/ ; FGRC18537//National Freshwater Genetic Resource Center/ ; 2022SBH00001//Guangdong Rural Revitalization Strategy Special Provincial Organization/ ; 2023KJ134 2023KJ150//Modern Agriculture Industry Technology Innovation Team/ ; CAMC-2018F//China-ASEAN Maritime Cooperation Fund/ ; FGRC18537//National Freshwater Genetic Resource Center/ ; }, mesh = {Animals ; *Fishes/genetics/classification ; *RNA, Ribosomal, 18S/genetics ; *Electron Transport Complex IV/genetics ; *DNA Barcoding, Taxonomic/methods ; Databases, Genetic ; Phylogeny ; Databases, Nucleic Acid ; }, abstract = {Fish, being a crucial component of aquatic ecosystems, holds significant importance from both economic and ecological perspectives. However, the identification of fish at the species level remains challenging, and there is a lack of a taxonomically complete and comprehensive reference sequence database for fish. Therefore, we developed CoSFISH, an online fish database. Currently, the database contains 21 535 cytochrome oxidase I sequences and 1074 18S rRNA sequences of 21 589 species, belonging to 8 classes and 90 orders. We additionally incorporate online analysis tools to aid users in comparing, aligning and analyzing sequences, as well as designing primers. Users can upload their own data for analysis, in addition to using the data stored in the database directly. CoSFISH offers an extensive fish database and incorporates online analysis tools, making it a valuable resource for the study of fish diversity, phylogenetics and biological evolution. Database URL: http://210.22.121.250:8888/CoSFISH/home/indexPage.}, } @article {pmid38803140, year = {2024}, author = {Jacobson, OT and Barrett, BJ and Perry, SE and Finerty, GE and Tiedeman, KM and Crofoot, MC}, title = {A new approach to geostatistical synthesis of historical records reveals capuchin spatial responses to climate and demographic change.}, journal = {Ecology letters}, volume = {27}, number = {5}, pages = {e14443}, doi = {10.1111/ele.14443}, pmid = {38803140}, issn = {1461-0248}, support = {//Wenner-Gren Foundation/ ; //American Society of Primatologists/ ; //Alexander von Humboldt-Stiftung/ ; //Max-Planck-Gesellschaft/ ; //Department of Anthropology, University of California, Los Angeles/ ; 20113909//National Geographic Society/ ; 45176R-18//National Geographic Society/ ; 7968-06//National Geographic Society/ ; 8671-09//National Geographic Society/ ; 9795-15//National Geographic Society/ ; 9633991//National Science Foundation/ ; BCS-0613226//National Science Foundation/ ; BCS-1638428//National Science Foundation/ ; BCS-848360//National Science Foundation/ ; DDIG 1232371//National Science Foundation/ ; SE9870429//National Science Foundation/ ; //Achievement Rewards for College Scientists Foundation/ ; //Leakey Foundation/ ; 1650042//National Science Foundation Graduate Research Fellowship Program/ ; Grant 0208/TWCF/TWCF/United States ; }, mesh = {Animals ; Costa Rica ; *Climate Change ; *Cebus/physiology ; Homing Behavior ; Geographic Information Systems ; Population Dynamics ; Demography ; }, abstract = {Recent proliferation of GPS technology has transformed animal movement research. Yet, time-series data from this recent technology rarely span beyond a decade, constraining longitudinal research. Long-term field sites hold valuable historic animal location records, including hand-drawn maps and semantic descriptions. Here, we introduce a generalised workflow for converting such records into reliable location data to estimate home ranges, using 30 years of sleep-site data from 11 white-faced capuchin (Cebus imitator) groups in Costa Rica. Our findings illustrate that historic sleep locations can reliably recover home range size and geometry. We showcase the opportunity our approach presents to resolve open questions that can only be addressed with very long-term data, examining how home ranges are affected by climate cycles and demographic change. We urge researchers to translate historical records into usable movement data before this knowledge is lost; it is essential to understanding how animals are responding to our changing world.}, } @article {pmid38802965, year = {2024}, author = {Hosseinzadeh-Shanjani, Z and Khodayari-Zarnaq, R and Khosravi, MF and Arab-Zozani, M and Alizadeh, G}, title = {Factors affecting major depression in Iran: a mixed-method study.}, journal = {Journal of health, population, and nutrition}, volume = {43}, number = {1}, pages = {73}, pmid = {38802965}, issn = {2072-1315}, mesh = {Humans ; Iran/epidemiology ; *Depressive Disorder, Major/epidemiology ; Risk Factors ; Health Policy ; Socioeconomic Factors ; Economic Recession ; Politics ; Female ; Male ; }, abstract = {Depression is a major cause of disability and, if left untreated, can increase the risk of suicide. Evidence on the determinants of depression is incomplete, making it challenging to interpret results across studies. This study aims to identify the social, economic, environmental, political, and technological factors influencing the great recession in Iran. The study was conducted in two parts. The first step involved a literature review to identify the factors, using PubMed, Scopus, and Web of Science for the search. The reference lists of all identified articles were reviewed to find relevant studies, and the extracted information was summarized and reported descriptively. The second steps involved compiling and consulting 14 experts from different fields, using a framework analysis method. Twenty-four articles were used as primary sources of information, and a total of 28 factors were found to exist. After removing duplicates and related factors, 19 of these were subsequently declared as factors, resulting in a total of 36 determinants being identified. Most of these factors belong to the social category. The health policies implemented have a significant impact on disease risk factors and ultimately their occurrence. Political decisions and policy-making processes play a crucial role in all areas, particularly in addressing disease risk factors. Severe depression can disrupt all aspects of the healthcare system, underscoring the importance of access to care. Policies concerning physical education, transportation, nutrition, employment, green spaces, recreational facilities, and tobacco are vital in this context. The influence of health policies on disease risk factors and disease occurrence is profound. Severe depression can have far-reaching effects on the healthcare system, emphasizing the critical need for access to care. The formulation of policies to combat depression must be thoroughly evaluated in terms of economic, political, social, technological, and environmental factors. The findings suggest that addressing social inequalities and emphasizing the role of political action, as highlighted by the social determinants of health, should be top priorities in addressing depression. Efforts to prevent depression should incorporate ecological approaches that consider the impact of the socioeconomic environment on depressive symptoms.}, } @article {pmid38802223, year = {2024}, author = {Lv, H and Lu, Z and Fu, G and Lv, S and Jiang, J and Xie, Y and Luo, X and Zeng, J and Xue, S}, title = {Pollution characteristics and quantitative source apportionment of heavy metals within a zinc smelting site by GIS-based PMF and APCS-MLR models.}, journal = {Journal of environmental sciences (China)}, volume = {144}, number = {}, pages = {100-112}, doi = {10.1016/j.jes.2023.09.033}, pmid = {38802223}, issn = {1001-0742}, mesh = {*Metals, Heavy/analysis ; *Zinc/analysis ; *Environmental Monitoring/methods ; *Soil Pollutants/analysis ; *Metallurgy ; Geographic Information Systems ; Models, Chemical ; }, abstract = {The abandoned smelters present a substantial pollution threat to the nearby soil and groundwater. In this study, 63 surface soil samples were collected from a zinc smelter to quantitatively describe the pollution characteristics, ecological risks, and source apportionment of heavy metal(loid)s (HMs). The results revealed that the average contents of Zn, Cd, Pb, As, and Hg were 0.4, 12.2, 3.3, 5.3, and 12.7 times higher than the risk screening values of the construction sites, respectively. Notably, the smelter was accumulated heavily with Cd and Hg, and the contribution of Cd (0.38) and Hg (0.53) to ecological risk was 91.58%. ZZ3 and ZZ7 were the most polluted workshops, accounting for 25.7% and 35.0% of the pollution load and ecological risk, respectively. The influence of soil parent materials on pollution was minor compared to various workshops within the smelter. Combined with PMF, APCS-MLR and GIS analysis, four sources of HMs were identified: P1(25.5%) and A3(18.4%) were atmospheric deposition from the electric defogging workshop and surface runoff from the smelter; P2(32.7%) and A2(20.9%) were surface runoff of As-Pb foul acid; P3(14.5%) and A4(49.8%) were atmospheric deposition from the leach slag drying workshop; P4(27.3%) and A1(10.8%) were the smelting process of zinc products. This paper described the distribution characteristics and specific sources of HMs in different process workshops, providing a new perspective for the precise remediation of the smelter by determining the priority control factors.}, } @article {pmid38800997, year = {2025}, author = {Madrigal, G and Minhas, BF and Catchen, J}, title = {Klumpy: A tool to evaluate the integrity of long-read genome assemblies and illusive sequence motifs.}, journal = {Molecular ecology resources}, volume = {25}, number = {1}, pages = {e13982}, pmid = {38800997}, issn = {1755-0998}, support = {1645087//Division of Antarctic Sciences/ ; }, mesh = {Animals ; Bees/genetics ; *Computational Biology/methods ; Sequence Analysis, DNA/methods ; Antifreeze Proteins/genetics/chemistry ; High-Throughput Nucleotide Sequencing/methods ; Genome/genetics ; Genomics/methods ; Software ; Fishes/genetics ; }, abstract = {The improvement and decreasing costs of third-generation sequencing technologies has widened the scope of biological questions researchers can address with de novo genome assemblies. With the increasing number of reference genomes, validating their integrity with minimal overhead is vital for establishing confident results in their applications. Here, we present Klumpy, a tool for detecting and visualizing both misassembled regions in a genome assembly and genetic elements (e.g. genes) of interest in a set of sequences. By leveraging the initial raw reads in combination with their respective genome assembly, we illustrate Klumpy's utility by investigating antifreeze glycoprotein (afgp) loci across two icefishes, by searching for a reported absent gene in the northern snakehead fish, and by scanning the reference genomes of a mudskipper and bumblebee for misassembled regions. In the two former cases, we were able to provide support for the noncanonical placement of an afgp locus in the icefishes and locate the missing snakehead gene. Furthermore, our genome scans were able identify an unmappable locus in the mudskipper reference genome and identify a putative repetitive element shared among several species of bees.}, } @article {pmid38800521, year = {2024}, author = {Obbard, DJ and , and , and , and , and , and , }, title = {The genome sequence of the drosophilid fruit fly, Drosophila phalerata (Meigen, 1830).}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {63}, pmid = {38800521}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual male Drosophila phalerata (drosophilid fruit fly, Arthropoda; Insecta; Diptera; Drosophilidae). The genome sequence is 223.9 megabases in span. Most of the assembly is scaffolded into 7 chromosomal pseudomolecules, including the X and Y sex chromosomes. The mitochondrial genome has also been assembled and is 16.14 kilobases in length. Gene annotation of this assembly on Ensembl identified 18,973 protein coding genes.}, } @article {pmid38800516, year = {2024}, author = {Li, R and Li, J and Lopez, JV and Oatley, G and Clayton-Lucey, IA and Sinclair, E and Aunin, E and Gettle, N and Santos, C and Paulini, M and Niu, H and McKenna, V and O'Brien, R and , and , and , and , and , }, title = {The genome sequence of the giant clam, Tridacna gigas (Linnaeus, 1758).}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {145}, pmid = {38800516}, issn = {2398-502X}, abstract = {We present a chromosomal-level genome assembly from an individual Tridacna gigas (the giant clam; Mollusca; Bivalvia; Veneroida; Cardiidae). The genome sequence is 1,175.9 megabases in span. Most of the assembly is scaffolded into 17 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 25.34 kilobases in length. Gene annotation of this assembly on Ensembl identified 18,177 protein coding genes.}, } @article {pmid38798998, year = {2023}, author = {Obbard, DJ and , and , and , and , }, title = {The genome sequence of a drosophilid fruit fly, Drosophila funebris (Fabricius, 1789).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {437}, pmid = {38798998}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual male Drosophila funebris (drosophilid fruit fly; Arthropoda; Insecta; Diptera; Drosophilidae). The genome sequence is 181.1 megabases in span. Most of the assembly is scaffolded into 7 chromosomal pseudomolecules, including the X and Y sex chromosomes. The mitochondrial genome has also been assembled and is 16.15 kilobases in length.}, } @article {pmid38798994, year = {2023}, author = {Hawkes, WLS and Wotton, KR and , and , and , and , and , and , }, title = {The genome sequence of the Common Spotted Hoverfly, Eupeodes luniger (Meigen, 1822).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {472}, pmid = {38798994}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual female Eupeodes luniger (the Common Spotted Hoverfly; Arthropoda; Insecta; Diptera; Syrphidae). The genome sequence is 616.9 megabases in span. Most of the assembly is scaffolded into 4 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 17.45 kilobases in length.}, } @article {pmid38798992, year = {2023}, author = {Hawkes, WLS and Wotton, KR and , and , and , and , and , and , }, title = {The genome sequence of the slender grass hoverfly, Melanostoma scalare (Fabricius, 1794).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {489}, pmid = {38798992}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual male Melanostoma scalare (the slender grass hoverfly; Arthropoda; Insecta; Diptera; Syrphidae). The genome sequence is 738.2 megabases in span. Most of the assembly is scaffolded into 5 chromosomal pseudomolecules, including the X and Y sex chromosomes. The mitochondrial genome has also been assembled and is 16.08 kilobases in length.}, } @article {pmid38796535, year = {2024}, author = {Wenk, EH and Sauquet, H and Gallagher, RV and Brownlee, R and Boettiger, C and Coleman, D and Yang, S and Auld, T and Barrett, R and Brodribb, T and Choat, B and Dun, L and Ellsworth, D and Gosper, C and Guja, L and Jordan, GJ and Le Breton, T and Leigh, A and Lu-Irving, P and Medlyn, B and Nolan, R and Ooi, M and Sommerville, KD and Vesk, P and White, M and Wright, IJ and Falster, DS}, title = {The AusTraits plant dictionary.}, journal = {Scientific data}, volume = {11}, number = {1}, pages = {537}, pmid = {38796535}, issn = {2052-4463}, mesh = {*Plants ; Databases, Factual ; Dictionaries as Topic ; }, abstract = {Traits with intuitive names, a clear scope and explicit description are essential for all trait databases. The lack of unified, comprehensive, and machine-readable plant trait definitions limits the utility of trait databases, including reanalysis of data from a single database, or analyses that integrate data across multiple databases. Both can only occur if researchers are confident the trait concepts are consistent within and across sources. Here we describe the AusTraits Plant Dictionary (APD), a new data source of terms that extends the trait definitions included in a recent trait database, AusTraits. The development process of the APD included three steps: review and formalisation of the scope of each trait and the accompanying trait description; addition of trait metadata; and publication in both human and machine-readable forms. Trait definitions include keywords, references, and links to related trait concepts in other databases, enabling integration of AusTraits with other sources. The APD will both improve the usability of AusTraits and foster the integration of trait data across global and regional plant trait databases.}, } @article {pmid38796014, year = {2024}, author = {Graham, CC}, title = {The role of Geographic Information Systems in mitigating plastics pollution in the Global South-A spatial analysis of recycling facilities in Costa Rica.}, journal = {The Science of the total environment}, volume = {937}, number = {}, pages = {173396}, doi = {10.1016/j.scitotenv.2024.173396}, pmid = {38796014}, issn = {1879-1026}, mesh = {Costa Rica ; *Plastics/analysis ; *Geographic Information Systems ; *Recycling ; *Environmental Pollution/statistics & numerical data ; Spatial Analysis ; Conservation of Natural Resources/methods ; Environmental Monitoring ; }, abstract = {Costa Rica is at the forefront of environmental conservation in Central America, with its focus on sustainability and green practices. Building on this foundation, the country joins a cohort of middle-income developing countries that have set forth ambitious goals to eliminate plastic pollution and become plastics-free. Recycling remains one of the most effective ways of removing plastic waste from the environment. Although GIS has been utilized in environmental research, its use is still expanding in developing countries of the Global South. These countries are experiencing unprecedented adverse climate and ecological impacts while also pursuing fundamental socioeconomic growth. The application of more cost-effective and strategic technological solutions, as well as data-driven decision-making, could fast-track the achievement of their urgent environmental goals. Using Geographic Information Systems (GIS) analysis, this study applies hot spot, location-allocation, and time-distance measures to examine Costa Rica's capacity to recycle plastic waste. Focusing specifically on availability and the public's access to recycling facilities, this article offers insights into the resource constraints and evolution of plastics governance in developing countries with environmentally-focused priorities. The findings of this study suggest that while Costa Rica is implementing progressive plastics regulatory policies, the ability to achieve plastics-free status is hampered by shortfalls in the number and distribution of recycling facilities and the public's access to recycling services. Expanding recycling infrastructure, including transportation, and adopting a less canton-centric waste administration system could contribute to resolving these challenges. This study contributes to discourses on global plastics governance and environmental change management in the Global South.}, } @article {pmid38795997, year = {2024}, author = {Lu, J and Peng, Q and Song, Y and Lyu, L and Chen, D and Huang, P and Peng, F and Liu, Y}, title = {Characteristics and effects of global sloping land urbanization from 2000 to 2020.}, journal = {The Science of the total environment}, volume = {937}, number = {}, pages = {173348}, doi = {10.1016/j.scitotenv.2024.173348}, pmid = {38795997}, issn = {1879-1026}, abstract = {Cities usually expand on flat land. However, in recent decades, the increasing scarcity of available flat land has compelled many cities to expand to sloping land (sloping land urbanization, SLU), and the understanding for global SLU is still unclear. This study, based on the currently available high-precision global Digital Elevation Model (FABDEM) and global land cover dataset (GlobeLand30), investigated the characteristics and impacts of SLU in 26,402 urban residential areas worldwide from 2000 to 2020. Results show that the total area of SLU globally is 16,383 km[2], accounting for 9.54 % of the overall urban expansion. This phenomenon is widespread globally and relatively concentrated in a few countries, with 42.78 %, 24.35 %, and 21.83 % of the area coming from cultivated land, forest, and grassland respectively. Global SLU has accommodated 34.78 million urban population, and indirectly protected 8922 km[2] of flat cultivated land, while causing a net loss of 4373 km[2] of green ecological land. Deliberately balancing the dual effects of SLU is crucial for advancing sustainable global urbanization.}, } @article {pmid38791265, year = {2024}, author = {Bartas, M and Brázda, V and Pečinka, P}, title = {Special Issue "Bioinformatics of Unusual DNA and RNA Structures".}, journal = {International journal of molecular sciences}, volume = {25}, number = {10}, pages = {}, pmid = {38791265}, issn = {1422-0067}, support = {CZ.10.03.01/00/22_003/0000003//Operational Programme Just Transition, European Union/ ; }, mesh = {*RNA/chemistry/metabolism ; *DNA/chemistry/metabolism ; *Computational Biology/methods ; *Nucleic Acid Conformation ; Humans ; }, abstract = {Nucleic acids are not only static carriers of genetic information but also play vital roles in controlling cellular lifecycles through their fascinating structural diversity [...].}, } @article {pmid38789640, year = {2024}, author = {Leigh, DM and Vandergast, AG and Hunter, ME and Crandall, ED and Funk, WC and Garroway, CJ and Hoban, S and Oyler-McCance, SJ and Rellstab, C and Segelbacher, G and Schmidt, C and Vázquez-Domínguez, E and Paz-Vinas, I}, title = {Best practices for genetic and genomic data archiving.}, journal = {Nature ecology & evolution}, volume = {8}, number = {7}, pages = {1224-1232}, pmid = {38789640}, issn = {2397-334X}, support = {31BD30_193900//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; }, mesh = {*Genomics ; Databases, Genetic ; Data Management ; Metadata ; }, abstract = {Genetic and genomic data are collected for a vast array of scientific and applied purposes. Despite mandates for public archiving, data are typically used only by the generating authors. The reuse of genetic and genomic datasets remains uncommon because it is difficult, if not impossible, due to non-standard archiving practices and lack of contextual metadata. But as the new field of macrogenetics is demonstrating, if genetic data and their metadata were more accessible and FAIR (findable, accessible, interoperable and reusable) compliant, they could be reused for many additional purposes. We discuss the main challenges with existing genetic and genomic data archives, and suggest best practices for archiving genetic and genomic data. Recognizing that this is a longstanding issue due to little formal data management training within the fields of ecology and evolution, we highlight steps that research institutions and publishers could take to improve data archiving.}, } @article {pmid38787862, year = {2024}, author = {Wang, L and Cui, H}, title = {Identification and classification of urban employment centers based on big data: A case study of Beijing.}, journal = {PloS one}, volume = {19}, number = {5}, pages = {e0299726}, pmid = {38787862}, issn = {1932-6203}, mesh = {Beijing ; Humans ; *Employment/statistics & numerical data ; *Transportation/statistics & numerical data ; Big Data ; Workplace ; Urban Population ; }, abstract = {The layout, scale and spatial form of urban employment centers are important guidelines for the rational layout of public service facilities such as urban transportation, medical care, and education. In this paper, we use Internet cell phone positioning data to identify the workplace and residence of users in the Beijing city area and obtain commuting data of the employed to measure the employment center system in Beijing. Firstly, the employment density distribution is generated using the data of the working places of the employed persons, and the employment centers are identified based on the employment density of Beijing. Then, we use the business registration data of employment centers to measure the industrial diversity within the employment centers by using the ecological Shannon Wiener Diversity Index, and combine the commuting links between employment centers and places of residence to measure the energy level of each employment center, analyze the hinterland and sphere of influence of each center, and finally using the industrial diversity index of employment centers and the average commuting time of employed persons, combined with the K-Means clustering algorithm, to classify the employment centers in Beijing. The employment center identification and classification method based on big data constructed in this study can help solve the limitations of the previous employment center system research in terms of center identification and commuting linkage measurement due to large spatial units and lack of commuting data to a certain extent. The study can provide reference for the regular understanding and technical analysis of employment centers and provide help for the employment multi-center system in Beijing in terms of quantifying the employment spatial structure, guiding the construction of multi-center system, and adjusting the land use rules.}, } @article {pmid38785034, year = {2024}, author = {McEachran, MC and Harvey, JA and Mummah, RO and Bletz, MC and Teitelbaum, CS and Rosenblatt, E and Rudolph, FJ and Arce, F and Yin, S and Prosser, DJ and Mosher, BA and Mullinax, JM and DiRenzo, GV and Couret, J and Runge, MC and Grant, EHC and Cook, JD}, title = {Reframing wildlife disease management problems with decision analysis.}, journal = {Conservation biology : the journal of the Society for Conservation Biology}, volume = {38}, number = {4}, pages = {e14284}, doi = {10.1111/cobi.14284}, pmid = {38785034}, issn = {1523-1739}, support = {//National Science Foundation/ ; 2200310//PIPP Phase 1: International Center for Avian Influenza Pandemic Prediction and Prevention/ ; P.L. 116-136//Coronavirus Aid, Relief, and Economic Security Act/ ; }, mesh = {Animals ; *Animals, Wild ; *Decision Support Techniques ; *Conservation of Natural Resources/methods ; *Decision Making ; COVID-19/epidemiology ; SARS-CoV-2 ; Uncertainty ; }, abstract = {Contemporary wildlife disease management is complex because managers need to respond to a wide range of stakeholders, multiple uncertainties, and difficult trade-offs that characterize the interconnected challenges of today. Despite general acknowledgment of these complexities, managing wildlife disease tends to be framed as a scientific problem, in which the major challenge is lack of knowledge. The complex and multifactorial process of decision-making is collapsed into a scientific endeavor to reduce uncertainty. As a result, contemporary decision-making may be oversimplified, rely on simple heuristics, and fail to account for the broader legal, social, and economic context in which the decisions are made. Concurrently, scientific research on wildlife disease may be distant from this decision context, resulting in information that may not be directly relevant to the pertinent management questions. We propose reframing wildlife disease management challenges as decision problems and addressing them with decision analytical tools to divide the complex problems into more cognitively manageable elements. In particular, structured decision-making has the potential to improve the quality, rigor, and transparency of decisions about wildlife disease in a variety of systems. Examples of management of severe acute respiratory syndrome coronavirus 2, white-nose syndrome, avian influenza, and chytridiomycosis illustrate the most common impediments to decision-making, including competing objectives, risks, prediction uncertainty, and limited resources.}, } @article {pmid38784435, year = {2024}, author = {Boyes, D and Crowley, LM and Holland, PWH and , and , and , and , and , and , and , }, title = {The genome sequence of the Summer Chafer, Amphimallon solstitiale (Linnaeus, 1758).}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {138}, pmid = {38784435}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual male Amphimallon solstitiale (the Summer Chafer; Arthropoda; Insecta; Coleoptera; Scarabaeidae). The genome sequence is 1,584.1 megabases in span. Most of the assembly is scaffolded into 11 chromosomal pseudomolecules, including the X and Y sex chromosomes. The mitochondrial genome has also been assembled and is 19.29 kilobases in length.}, } @article {pmid38781445, year = {2024}, author = {Vuruputoor, VS and Starovoitov, A and Cai, Y and Liu, Y and Rahmatpour, N and Hedderson, TA and Wilding, N and Wegrzyn, JL and Goffinet, B}, title = {Crossroads of assembling a moss genome: navigating contaminants and horizontal gene transfer in the moss Physcomitrellopsis africana.}, journal = {G3 (Bethesda, Md.)}, volume = {14}, number = {7}, pages = {}, pmid = {38781445}, issn = {2160-1836}, support = {DEB-0919284//US National Science Foundation/ ; }, mesh = {*Gene Transfer, Horizontal ; *Bryopsida/genetics ; *Genome, Plant ; *Phylogeny ; Genomics/methods ; Molecular Sequence Annotation ; }, abstract = {The first chromosome-scale reference genome of the rare narrow-endemic African moss Physcomitrellopsis africana (P. africana) is presented here. Assembled from 73 × Oxford Nanopore Technologies (ONT) long reads and 163 × Beijing Genomics Institute (BGI)-seq short reads, the 414 Mb reference comprises 26 chromosomes and 22,925 protein-coding genes [Benchmarking Universal Single-Copy Ortholog (BUSCO) scores: C:94.8% (D:13.9%)]. This genome holds 2 genes that withstood rigorous filtration of microbial contaminants, have no homolog in other land plants, and are thus interpreted as resulting from 2 unique horizontal gene transfers (HGTs) from microbes. Further, P. africana shares 176 of the 273 published HGT candidates identified in Physcomitrium patens (P. patens), but lacks 98 of these, highlighting that perhaps as many as 91 genes were acquired in P. patens in the last 40 million years following its divergence from its common ancestor with P. africana. These observations suggest rather continuous gene gains via HGT followed by potential losses during the diversification of the Funariaceae. Our findings showcase both dynamic flux in plant HGTs over evolutionarily "short" timescales, alongside enduring impacts of successful integrations, like those still functionally maintained in extant P. africana. Furthermore, this study describes the informatic processes employed to distinguish contaminants from candidate HGT events.}, } @article {pmid38781323, year = {2024}, author = {Edwards, SV and Cloutier, A and Cockburn, G and Driver, R and Grayson, P and Katoh, K and Baldwin, MW and Sackton, TB and Baker, AJ}, title = {A nuclear genome assembly of an extinct flightless bird, the little bush moa.}, journal = {Science advances}, volume = {10}, number = {21}, pages = {eadj6823}, doi = {10.1126/sciadv.adj6823}, pmid = {38781323}, issn = {2375-2548}, mesh = {Animals ; *Birds/genetics ; *Genome ; *Extinction, Biological ; Cell Nucleus/genetics ; Phylogeny ; Fossils ; Genome, Mitochondrial ; Flight, Animal ; New Zealand ; Male ; DNA Transposable Elements/genetics ; Genomics/methods ; }, abstract = {We present a draft genome of the little bush moa (Anomalopteryx didiformis)-one of approximately nine species of extinct flightless birds from Aotearoa, New Zealand-using ancient DNA recovered from a fossil bone from the South Island. We recover a complete mitochondrial genome at 249.9× depth of coverage and almost 900 megabases of a male moa nuclear genome at ~4 to 5× coverage, with sequence contiguity sufficient to identify more than 85% of avian universal single-copy orthologs. We describe a diverse landscape of transposable elements and satellite repeats, estimate a long-term effective population size of ~240,000, identify a diverse suite of olfactory receptor genes and an opsin repertoire with sensitivity in the ultraviolet range, show that the wingless moa phenotype is likely not attributable to gene loss or pseudogenization, and identify potential function-altering coding sequence variants in moa that could be synthesized for future functional assays. This genomic resource should support further studies of avian evolution and morphological divergence.}, } @article {pmid38779566, year = {2024}, author = {Scanu, M and Toto, F and Petito, V and Masi, L and Fidaleo, M and Puca, P and Baldelli, V and Reddel, S and Vernocchi, P and Pani, G and Putignani, L and Scaldaferri, F and Del Chierico, F}, title = {An integrative multi-omic analysis defines gut microbiota, mycobiota, and metabolic fingerprints in ulcerative colitis patients.}, journal = {Frontiers in cellular and infection microbiology}, volume = {14}, number = {}, pages = {1366192}, pmid = {38779566}, issn = {2235-2988}, mesh = {Humans ; *Colitis, Ulcerative/microbiology/metabolism ; *Gastrointestinal Microbiome ; Male ; Adult ; Female ; *Bacteria/classification/isolation & purification/metabolism/genetics ; Middle Aged ; *Metabolomics/methods ; *RNA, Ribosomal, 16S/genetics ; *Gas Chromatography-Mass Spectrometry ; *Feces/microbiology ; *Fungi/classification/isolation & purification/metabolism ; Dysbiosis/microbiology ; Metabolome ; Aged ; Young Adult ; Solid Phase Microextraction ; Mycobiome ; Multiomics ; }, abstract = {BACKGROUND: Ulcerative colitis (UC) is a multifactorial chronic inflammatory bowel disease (IBD) that affects the large intestine with superficial mucosal inflammation. A dysbiotic gut microbial profile has been associated with UC. Our study aimed to characterize the UC gut bacterial, fungal, and metabolic fingerprints by omic approaches.

METHODS: The 16S rRNA- and ITS2-based metataxonomics and gas chromatography-mass spectrometry/solid phase microextraction (GC-MS/SPME) metabolomic analysis were performed on stool samples of 53 UC patients and 37 healthy subjects (CTRL). Univariate and multivariate approaches were applied to separated and integrated omic data, to define microbiota, mycobiota, and metabolic signatures in UC. The interaction between gut bacteria and fungi was investigated by network analysis.

RESULTS: In the UC cohort, we reported the increase of Streptococcus, Bifidobacterium, Enterobacteriaceae, TM7-3, Granulicatella, Peptostreptococcus, Lactobacillus, Veillonella, Enterococcus, Peptoniphilus, Gemellaceae, and phenylethyl alcohol; and we also reported the decrease of Akkermansia; Ruminococcaceae; Ruminococcus; Gemmiger; Methanobrevibacter; Oscillospira; Coprococus; Christensenellaceae; Clavispora; Vishniacozyma; Quambalaria; hexadecane; cyclopentadecane; 5-hepten-2-ol, 6 methyl; 3-carene; caryophyllene; p-Cresol; 2-butenal; indole, 3-methyl-; 6-methyl-3,5-heptadiene-2-one; 5-octadecene; and 5-hepten-2-one, 6 methyl. The integration of the multi-omic data confirmed the presence of a distinctive bacterial, fungal, and metabolic fingerprint in UC gut microbiota. Moreover, the network analysis highlighted bacterial and fungal synergistic and/or divergent interkingdom interactions.

CONCLUSION: In this study, we identified intestinal bacterial, fungal, and metabolic UC-associated biomarkers. Furthermore, evidence on the relationships between bacterial and fungal ecosystems provides a comprehensive perspective on intestinal dysbiosis and ecological interactions between microorganisms in the framework of UC.}, } @article {pmid38779149, year = {2024}, author = {Boyes, D and Mulhair, PO and , and , and , and , and , and , and , }, title = {The genome sequence of the Water Veneer, Acentria ephemerella (Denis & Schiffermüller, 1775).}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {134}, pmid = {38779149}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual male Acentria ephemerella (the Water Veneer; Arthropoda; Insecta; Lepidoptera; Crambidae). The genome sequence is 340.8 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.35 kilobases in length. Gene annotation of this assembly on Ensembl identified 17,748 protein coding genes.}, } @article {pmid38779060, year = {2023}, author = {Boyes, D and Mulhair, PO and , and , and , and , and , and , }, title = {The genome sequence of the Scarce Umber, Agriopis aurantiaria (Hübner, 1799).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {463}, pmid = {38779060}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual male Agriopis aurantiaria (the Scarce Umber; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 485.4 megabases in span. The whole assembly is scaffolded into 30 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.44 kilobases in length. Gene annotation of this assembly on Ensembl identified 16,963 protein coding genes.}, } @article {pmid38779056, year = {2023}, author = {Boyes, D and Holland, PWH and , and , and , and , and , and , }, title = {The genome sequence of the Pinion-streaked Snout, Schrankia costaestrigalis (Stephens, 1834).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {203}, pmid = {38779056}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual male Schrankia costaestrigalis (the Pinion-streaked Snout; Arthropoda; Insecta; Lepidoptera; Erebidae). The genome sequence is 572.0 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 16.1 kilobases in length. Gene annotation of this assembly on Ensembl identified 19,453 protein coding genes.}, } @article {pmid38779055, year = {2023}, author = {Boyes, D and , and , and , and , and , and , }, title = {The genome sequence of the Diamondback Moth, Plutella xylostella (Linnaeus, 1758).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {404}, pmid = {38779055}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual male Plutella xylostella (the Diamondback Moth; Arthropoda; Insecta; Lepidoptera; Plutellidae). The genome sequence is 323.3 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 35.12 kilobases in length. Gene annotation of this assembly on Ensembl identified 17,190 protein coding genes.}, } @article {pmid38779054, year = {2023}, author = {Boyes, D and Boyes, C and , and , and , and , and , and , }, title = {The genome sequence of the Coxcomb Prominent, Ptilodon capucinus (Linnaeus, 1758).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {242}, pmid = {38779054}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual male Ptilodon capucinus (the Coxcomb Prominent; Arthropoda; Insecta; Lepidoptera; Notodontidae). The genome sequence is 348.7 megabases in span. The assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.38 kilobases in length. Gene annotation of this assembly on Ensembl identified 16,968 protein coding genes.}, } @article {pmid38779050, year = {2023}, author = {Boyes, D and Hammond, J and , and , and , and , and , and , }, title = {The genome sequence of the Grey Poplar Bell, Epinotia nisella (Clerck, 1759).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {281}, pmid = {38779050}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual male Epinotia nisella (the Grey Poplar Bell; Arthropoda; Insecta; Lepidoptera; Tortricidae). The genome sequence is 585.0 megabases in span. Most of the assembly is scaffolded into 28 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.44 kilobases in length. Gene annotation of this assembly on Ensembl identified 18,952 protein coding genes.}, } @article {pmid38779048, year = {2023}, author = {Boyes, D and Mulley, JF and , and , and , and , and , and , }, title = {The genome sequence of the Six-striped Rustic, Xestia sexstrigata (Haworth, 1809).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {399}, pmid = {38779048}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual female Xestia sexstrigata (the Six-striped Rustic; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 638.3 megabases in span. Most of the assembly is scaffolded into 32 chromosomal pseudomolecules, including the W and Z sex chromosomes. The mitochondrial genome has also been assembled and is 15.36 kilobases in length. Gene annotation of this assembly on Ensembl identified 15,104 protein coding genes.}, } @article {pmid38779046, year = {2023}, author = {Boyes, D and Holland, PWH and , and , and , and , and , and , }, title = {The genome sequence of the Red-green Carpet, Chloroclysta siterata (Hufnagel, 1767).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {206}, pmid = {38779046}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual male Chloroclysta siterata (the Red-green Carpet; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 437.9 megabases in span. Most of the assembly is scaffolded into 21 chromosomal pseudomolecules including the Z sex chromosome. The mitochondrial genome has also been assembled and is 16.7 kilobases in length. Gene annotation of this assembly on Ensembl identified 11,814 protein coding genes.}, } @article {pmid38778011, year = {2024}, author = {Mercuri, AM and Clò, E and Zappa, J and Bosi, G and Furia, E and Ricucci, C and Di Lena, M and Camerini, F and Florenzano, A}, title = {BRAIN - Holocene archaeo-data for assessing plant-cultural diversity in Italy and other Mediterranean regions.}, journal = {Scientific data}, volume = {11}, number = {1}, pages = {520}, pmid = {38778011}, issn = {2052-4463}, mesh = {*Archaeology ; Botany/history ; Italy ; Mediterranean Region ; *Plants ; *Pollen ; Databases as Topic ; }, abstract = {In the field of botany applied to archaeological and palaeoecological studies, the multi- and inter-disciplinary nature of this research produces a lack of data sharing and scattered articles in the specialty literature or in national and international journals. The vast production of archaeobotany and palynology data makes it necessary to develop a tool for the availability, accessibility, and dissemination of existing research. Many databases exist on palaeoecology, archaeobotany or pollen data. There are no collections focused on archaeological sites and human-induced environments and centred on Southern Europe and the Mediterranean. BRAIN - Botanical Records of Archaeobotany Italian Network is the first database listing sites from which all types of plant records are available in Italy and nearby Mediterranean regions. BRAIN represents the largest integrated collection of archaeo/palaeo-botanical data and a range of descriptive information that makes data recovery FAIR ready. This unique network hosts data on the availability of anthropogenic pollen, palynomorphs and plant macroremains in the same database, and experts of different research fields may contribute to it.}, } @article {pmid38777192, year = {2024}, author = {Aggarwal, R and Peters, G}, title = {Freshwater ecotoxicity characterization factors for PMT/vPvM substances.}, journal = {Chemosphere}, volume = {360}, number = {}, pages = {142391}, doi = {10.1016/j.chemosphere.2024.142391}, pmid = {38777192}, issn = {1879-1298}, mesh = {*Water Pollutants, Chemical/toxicity ; *Ecotoxicology ; *Fresh Water/chemistry ; Environmental Monitoring/methods ; Risk Assessment ; Germany ; Databases, Factual ; }, abstract = {This study addresses the gap in freshwater ecotoxicological characterization factors (CFs) for Persistent, Mobile, and Toxic (PMT) and Very Persistent and Very Mobile (vPvM) substances. These CFs are vital for integrating the ecotoxicity impacts of these chemicals into life cycle assessments. Our goals are twofold: first, to calculate experimental freshwater CFs for PMT/vPvM substances listed by the German Environment Agency (UBA); second, to compare these CFs with those from the USEtox database. The expanded UBA list includes 343 PMT/vPvM substances, each representing a unique chemical structure, and linked to 474 REACH-registered substances. This study successfully computed CFs for 244 substances, with 107 overlapping the USEtox database and 137 being new. However, ecotoxicity data limitations prevented CF determination for 97 substances. This research enhances our understanding of freshwater CFs for PMT/vPvM substances, covering 72% of UBA's 343 PMT/vPvM substances. Data scarcity remains a significant challenge, which invariably impedes CF calculations. Notably, the disparities observed between CF values in the USEtox database and those derived in this research largely stem from variations in ecotoxicity data. Consequently, this research underscores the dynamic nature of CFs for substances, emphasizing the need for regular updates to ensure their accuracy and relevance.}, } @article {pmid38776304, year = {2024}, author = {Karlgren, K and Andersson Franko, M and Kilström, D}, title = {'Experiencing one thing and saying another'-Ecological Momentary Assessment (EMA) of nursing students' competence and challenge during clinical placements compared with retrospective interviews.}, journal = {PloS one}, volume = {19}, number = {5}, pages = {e0302866}, pmid = {38776304}, issn = {1932-6203}, mesh = {Humans ; *Students, Nursing/psychology ; Female ; Retrospective Studies ; *Clinical Competence ; Male ; *Ecological Momentary Assessment ; Adult ; Young Adult ; Interviews as Topic ; Smartphone ; }, abstract = {UNLABELLED: Clinical placements are essential to nursing education and understanding students' challenges in the clinical context is important for educators. Nevertheless, few studies have investigated students' experiences in the clinical context itself but rely on methods which ask participants to generalize their clinical experiences retrospectively.

OBJECTIVES: This study aimed to explore nursing students' experiences of clinical activities during and after clinical placements with a focus on feelings of competence and challenge. A particular interest was on comparing momentary assessments in the clinical context with retrospective interview data.

METHODS: Smartphones were used for ecological momentary assessment of students' experiences of clinical activities during five-week placements at 21 nursing homes. Both quantitative and qualitative data were collected. Interviews were conducted after the placements.

RESULTS: 575 responses were obtained showing final-year nursing students rated their competence significantly higher and challenge significantly lower than first-year students. An analysis of the quantitative data using the four-channel flow model showed that first-year students' activities were to a significantly higher extent associated with flow and anxiety, compared to those of final-year students. Conversely, the final-year students' activities were to a significantly higher extent associated with boredom than those of first-year students. The analysis of the students' reflections resulted in five themes: Specific activities are challenging, Lack of challenge, Learning and developing, Reflects critically on competence, and Arrangement of the clinical placement.

DISCUSSION: Final-year nursing students were significantly less challenged during the placements compared to first-year students. There was overlap in how students described their clinical experiences during and after placements, but there were also striking differences. The first-year students were overwhelmed by the challenges during the placements but viewed these experiences as valuable learning experiences afterwards. The final-year students also described several challenging clinical activities during the placements but none of these challenges were brought up afterwards in the interviews and instead a lack of challenge was emphasized. Momentary assessment thus enabled capturing data about clinical activities which may be overlooked by retrospective methods.}, } @article {pmid38776282, year = {2024}, author = {MacPhail, VJ and Hatfield, R and Colla, SR}, title = {Bumble Bee Watch community science program increases scientific understanding of an important pollinator group across Canada and the USA.}, journal = {PloS one}, volume = {19}, number = {5}, pages = {e0303335}, pmid = {38776282}, issn = {1932-6203}, mesh = {Animals ; Bees/physiology ; United States ; *Pollination ; Canada ; Databases, Factual ; }, abstract = {In a time of increasing threats to bumble bees (Hymenoptera: Apidae: Bombus), it is important to understand their ecology and distribution. As experts are limited in resources to conduct field surveys, there is potential for community scientists to help. The Bumble Bee Watch (BBW) community science program involves volunteers taking photos of bumble bees in Canada and the USA and submitting them, along with geographic and optional plant information, to a website or through an app. Taxon experts then verify the bee species identification. The Bumble Bees of North America database (BBNA) stores data (no photographs) collected and identified by more traditional scientific methods over the same range. Here we compared BBW data to BBNA data over all years and just 2010-2020 to understand the scientific contribution of community scientists to the state of the knowledge about native bumble bees. We found that BBW had similar geographic and species coverage as BBNA. It had records from all 63 provinces, states, and territories where bumble bees occur (including four more than BBNA in 2010-2020), and represented 41 of the 48 species in BBNA (with ten more species than BBNA in 2010-2020). While BBW contributed only 8.50% of records overall, it contributed 25.06% of all records over 2010-2020. BBW confirmed the persistence of species and identified new locations of species, both inside and outside of the previously known extent of occurrences. BBW also contributed a wealth of ecological information, such as unique plant genera and species data for almost all the bee species. Thus, while BBW had fewer bee records than the BBNA database overall, it helped to fill in data gaps and provided novel information, complementing the traditional methods. This community science program is valuable in helping to inform conservation management for bumble bee species.}, } @article {pmid38775247, year = {2024}, author = {Oliveira, S and Marchi, N and Excoffier, L}, title = {Assessing the limits of local ancestry inference from small reference panels.}, journal = {Molecular ecology resources}, volume = {24}, number = {6}, pages = {e13981}, doi = {10.1111/1755-0998.13981}, pmid = {38775247}, issn = {1755-0998}, support = {310030_188883//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; }, mesh = {*Genetics, Population/methods ; Humans ; Computational Biology/methods ; }, abstract = {Admixture is a common biological phenomenon among populations of the same or different species. Identifying admixed tracts within individual genomes can provide valuable information to date admixture events, reconstruct ancestry-specific demographic histories, or detect adaptive introgression, genetic incompatibilities, as well as regions of the genomes affected by (associative-) overdominance. Although many local ancestry inference (LAI) methods have been developed in the last decade, their performance was accessed using large reference panels, which are rarely available for non-model organisms or ancient samples. Moreover, the demographic conditions for which LAI becomes unreliable have not been explicitly outlined. Here, we identify the demographic conditions for which local ancestries can be best estimated using very small reference panels. Furthermore, we compare the performance of two LAI methods (RFMix and MOSAIC) with the performance of a newly developed approach (simpLAI) that can be used even when reference populations consist of single individuals. Based on simulations of various demographic models, we also determine the limits of these LAI tools and propose post-painting filtering steps to reduce false-positive rates and improve the precision and accuracy of the inferred admixed tracts. Besides providing a guide for using LAI, our work shows that reasonable inferences can be obtained from a single diploid genome per reference under demographic conditions that are not uncommon among past human groups and non-model organisms.}, } @article {pmid38775206, year = {2024}, author = {Veglia, AJ and Rivera-Vicéns, RE and Grupstra, CGB and Howe-Kerr, LI and Correa, AMS}, title = {vAMPirus: A versatile amplicon processing and analysis program for studying viruses.}, journal = {Molecular ecology resources}, volume = {24}, number = {6}, pages = {e13978}, doi = {10.1111/1755-0998.13978}, pmid = {38775206}, issn = {1755-0998}, support = {OCE 22-24354//Directorate for Biological Sciences/ ; OCE-2145472//Directorate for Biological Sciences/ ; //Wagoner Foreign Study Award/ ; //Kirk W. Dotson Endowed Graduate Fellowship in Ecology and Evolutionary Biology/ ; //Lewis and Clark Grants for Exploration/ ; 100009646//Gulf Research Program of the National Academies of Sciences/ ; }, mesh = {*Software ; Computational Biology/methods ; DNA Viruses/genetics/classification ; Viruses/genetics/classification/isolation & purification ; RNA Viruses/genetics/classification/isolation & purification ; Phylogeny ; }, abstract = {Amplicon sequencing is an effective and increasingly applied method for studying viral communities in the environment. Here, we present vAMPirus, a user-friendly, comprehensive, and versatile DNA and RNA virus amplicon sequence analysis program, designed to support investigators in exploring virus amplicon sequencing data and running informed, reproducible analyses. vAMPirus intakes raw virus amplicon libraries and, by default, performs nucleotide- and amino acid-based analyses to produce results such as sequence abundance information, taxonomic classifications, phylogenies and community diversity metrics. The vAMPirus analytical framework leverages 16 different opensource tools and provides optional approaches that can increase the ratio of biological signal-to-noise and thereby reveal patterns that would have otherwise been masked. Here, we validate the vAMPirus analytical framework and illustrate its implementation as a general virus amplicon sequencing workflow by recapitulating findings from two previously published double-stranded DNA virus datasets. As a case study, we also apply the program to explore the diversity and distribution of a coral reef-associated RNA virus. vAMPirus is streamlined within Nextflow, offering straightforward scalability, standardization and communication of virus lineage-specific analyses. The vAMPirus framework is designed to be adaptable; community-driven analytical standards will continue to be incorporated as the field advances. vAMPirus supports researchers in revealing patterns of virus diversity and population dynamics in nature, while promoting study reproducibility and comparability.}, } @article {pmid38774958, year = {2024}, author = {Huson, D and Xavier, JC and Steel, M}, title = {Self-generating autocatalytic networks: structural results, algorithms and their relevance to early biochemistry.}, journal = {Journal of the Royal Society, Interface}, volume = {21}, number = {214}, pages = {20230732}, pmid = {38774958}, issn = {1742-5662}, mesh = {*Algorithms ; Catalysis ; Models, Biological ; Biochemistry ; Origin of Life ; }, abstract = {The concept of an autocatalytic network of reactions that can form and persist, starting from just an available food source, has been formalized by the notion of a reflexively autocatalytic and food-generated (RAF) set. The theory and algorithmic results concerning RAFs have been applied to a range of settings, from metabolic questions arising at the origin of life, to ecological networks, and cognitive models in cultural evolution. In this article, we present new structural and algorithmic results concerning RAF sets, by studying more complex modes of catalysis that allow certain reactions to require multiple catalysts (or to not require catalysis at all), and discuss the differing ways catalysis has been viewed in the literature. We also focus on the structure and analysis of minimal RAFs and derive structural results and polynomial-time algorithms. We then apply these new methods to a large metabolic network to gain insights into possible biochemical scenarios near the origin of life.}, } @article {pmid38772433, year = {2024}, author = {Chagas, ÉCDS and Ferreira, FADS and Mwangi, VI and Terrazas, WCM and Becker, JN and Simões, RC and Pacífico, EMSS and Silva, ASD and Marques, CDS and Chagas, ECDS and Machado, MB and Figueira, EAG and Castro, DB and Ramos, TCA and Oliveira, JH}, title = {Spatio-temporal analysis of American Tegumentary Leishmaniasis incidences in the Brazilian state of Amazonas: 2011 to 2022.}, journal = {Acta tropica}, volume = {256}, number = {}, pages = {107266}, doi = {10.1016/j.actatropica.2024.107266}, pmid = {38772433}, issn = {1873-6254}, mesh = {Brazil/epidemiology ; Humans ; Incidence ; *Leishmaniasis, Cutaneous/epidemiology ; *Spatio-Temporal Analysis ; *Seasons ; Climate ; Female ; Male ; Adult ; Adolescent ; Young Adult ; Child ; }, abstract = {This study aimed to conduct a spatio-temporal analysis of tegumentary leishmaniasis occurrences in the Amazonas state, Brazil. An ecological study encompassing time series and spatial analysis was performed, exploring the geographic distribution and temporal trends of American Tegumentary Leishmaniasis (ATL) in Amazonas between 2011 and 2022. Secondary data extracted from the Department of Informatics of the Unified Health System (DATASUS) were utilized for this analysis. The study evaluated the relationship between disease cases and environmental/climatic variables (deforestation, temperature, precipitation, and relative humidity). Over the study period, 19,730 cases of tegumentary leishmaniasis were recorded, averaging an incidence of 41.4/100,000 inhabitants across the 62 municipalities of Amazonas state. Disease intensity varied with seasons. Generally, Amazonas state displayed a declining trend in ATL cases. However, certain municipalities, notably Rio Preto da Eva and Presidente Figueiredo, exhibited high incidence rates, while Canutama, Envira, Eirunepé, and Pauini municipalities demand closer attention due to their demonstrated increasing temporal trend of ATL cases. The analysis indicated a correlation between the number of ATL cases reported and relative humidity as well as precipitation. These findings underscore the significance of tegumentary leishmaniasis as a public health issue in the region and emphasize the necessity for public initiatives aimed at preventing this endemic illness.}, } @article {pmid38771704, year = {2024}, author = {Warren, WC and Rice, ES and X, M and Roback, E and Keene, A and Martin, F and Ogeh, D and Haggerty, L and Carroll, RA and McGaugh, S and Rohner, N}, title = {Astyanax mexicanus surface and cavefish chromosome-scale assemblies for trait variation discovery.}, journal = {G3 (Bethesda, Md.)}, volume = {14}, number = {8}, pages = {}, pmid = {38771704}, issn = {2160-1836}, support = {//University of Missouri/ ; 1923372//National Science Foundation/ ; WT222155/Z/20/Z/WT_/Wellcome Trust/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; R24 OD011198/OD/NIH HHS/United States ; 1R01GM127872-01/GF/NIH HHS/United States ; }, mesh = {Animals ; *Characidae/genetics ; *Chromosomes/genetics ; *Caves ; Phylogeny ; Genome ; Genomics/methods ; Genetic Variation ; Quantitative Trait Loci ; Synteny ; Phenotype ; }, abstract = {The ability of organisms to adapt to sudden extreme environmental changes produces some of the most drastic examples of rapid phenotypic evolution. The Mexican Tetra, Astyanax mexicanus, is abundant in the surface waters of northeastern Mexico, but repeated colonizations of cave environments have resulted in the independent evolution of troglomorphic phenotypes in several populations. Here, we present three chromosome-scale assemblies of this species, for one surface and two cave populations, enabling the first whole-genome comparisons between independently evolved cave populations to evaluate the genetic basis for the evolution of adaptation to the cave environment. Our assemblies represent the highest quality of sequence completeness with predicted protein-coding and noncoding gene metrics far surpassing prior resources and, to our knowledge, all long-read assembled teleost genomes, including zebrafish. Whole-genome synteny alignments show highly conserved gene order among cave forms in contrast to a higher number of chromosomal rearrangements when compared with other phylogenetically close or distant teleost species. By phylogenetically assessing gene orthology across distant branches of amniotes, we discover gene orthogroups unique to A. mexicanus. When compared with a representative surface fish genome, we find a rich amount of structural sequence diversity, defined here as the number and size of insertions and deletions as well as expanding and contracting repeats across cave forms. These new more complete genomic resources ensure higher trait resolution for comparative, functional, developmental, and genetic studies of drastic trait differences within a species.}, } @article {pmid38770718, year = {2024}, author = {Schwarzerova, J and Hurta, M and Barton, V and Lexa, M and Walther, D and Provaznik, V and Weckwerth, W}, title = {A perspective on genetic and polygenic risk scores-advances and limitations and overview of associated tools.}, journal = {Briefings in bioinformatics}, volume = {25}, number = {3}, pages = {}, pmid = {38770718}, issn = {1477-4054}, support = {FEKT/FIT-J-23-8274//Brno University of Technology intra-university junior project/ ; }, mesh = {Humans ; *Multifactorial Inheritance ; *Genetic Predisposition to Disease ; *Software ; Computational Biology/methods ; Genome-Wide Association Study/methods ; Risk Factors ; Risk Assessment/methods ; Genetic Risk Score ; }, abstract = {Polygenetic Risk Scores are used to evaluate an individual's vulnerability to developing specific diseases or conditions based on their genetic composition, by taking into account numerous genetic variations. This article provides an overview of the concept of Polygenic Risk Scores (PRS). We elucidate the historical advancements of PRS, their advantages and shortcomings in comparison with other predictive methods, and discuss their conceptual limitations in light of the complexity of biological systems. Furthermore, we provide a survey of published tools for computing PRS and associated resources. The various tools and software packages are categorized based on their technical utility for users or prospective developers. Understanding the array of available tools and their limitations is crucial for accurately assessing and predicting disease risks, facilitating early interventions, and guiding personalized healthcare decisions. Additionally, we also identify potential new avenues for future bioinformatic analyzes and advancements related to PRS.}, } @article {pmid38767676, year = {2024}, author = {Geng, A and Zhang, C and Wang, J and Zhang, X and Qiu, W and Wang, L and Xi, J and Yang, B}, title = {Current advances of chlorinated organics degradation by bioelectrochemical systems: a review.}, journal = {World journal of microbiology & biotechnology}, volume = {40}, number = {7}, pages = {208}, pmid = {38767676}, issn = {1573-0972}, support = {2022YFC3702000//National Key Research and Development Program of China/ ; BE2020773//Social Development Project/ ; 23KJA610008//the Natural Science Foundation of Jiangsu Higher Education Institutions of China/ ; }, mesh = {*Biodegradation, Environmental ; *Electrochemical Techniques ; Wastewater/chemistry ; Hydrocarbons, Chlorinated/metabolism ; Water Pollutants, Chemical/metabolism ; Groundwater/chemistry ; Organic Chemicals/metabolism ; }, abstract = {Chlorinated organic compounds (COCs) are typical refractory organic compounds, having high biological toxicity. These compounds are a type of pervasive pollutants that can be present in polluted soil, air, and various types of waterways, such as groundwater, rivers, and lakes, posing a significant threat to the ecological environment and human health. Bioelectrochemical systems (BESs) are an effective strategy for the degradation of bio-refractory compounds. BESs improve the waste treatment efficiency through the application of weak electrical stimulation. This review discusses the processes of BESs configurations and degradation performances in different environmental media including wastewater, soil, waste gas and groundwater. In addition, the degradation mechanisms and performance-enhancing additives are summarized. The future challenges and perspectives on the development of BES for COCs removal are briefly discussed.}, } @article {pmid38767452, year = {2024}, author = {Rashidi, A and Ebadi, M and Rehman, TU and Elhusseini, H and Kazadi, D and Halaweish, H and Khan, MH and Hoeschen, A and Cao, Q and Luo, X and Kabage, AJ and Lopez, S and Ramamoorthy, S and Holtan, SG and Weisdorf, DJ and Khoruts, A and Staley, C}, title = {Multi-omics Analysis of a Fecal Microbiota Transplantation Trial Identifies Novel Aspects of Acute GVHD Pathogenesis.}, journal = {Cancer research communications}, volume = {4}, number = {6}, pages = {1454-1466}, pmid = {38767452}, issn = {2767-9764}, support = {KL2 TR002492/TR/NCATS NIH HHS/United States ; UL1 TR002494/TR/NCATS NIH HHS/United States ; KL2TR002492//Foundation for the National Institutes of Health (FNIH)/ ; UL1TR002494//Foundation for the National Institutes of Health (FNIH)/ ; P30CA07759//HHS | NIH | National Cancer Institute (NCI)/ ; Chainbreaker grant//UMN | Clinical and Translational Science Institute, University of Minnesota (CTSI)/ ; n/a//Achieving Cures Together/ ; }, mesh = {Humans ; *Graft vs Host Disease/microbiology/immunology ; *Fecal Microbiota Transplantation ; *Gastrointestinal Microbiome ; Male ; Female ; Middle Aged ; *Hematopoietic Stem Cell Transplantation/methods/adverse effects ; Adult ; Leukemia, Myeloid, Acute/therapy/microbiology/immunology ; Transplantation, Homologous/methods/adverse effects ; Faecalibacterium ; Aged ; Acute Disease ; Feces/microbiology ; Metabolome ; Multiomics ; }, abstract = {UNLABELLED: Acute GVHD (aGVHD) is a major complication of allogeneic hematopoietic cell transplantation (alloHCT) associated with gut microbiota disruptions. However, whether therapeutic microbiota modulation prevents aGVHD is unknown. We conducted a randomized, placebo-controlled trial of third-party fecal microbiota transplantation (FMT) administered at the peak of microbiota injury in 100 patients with acute myeloid leukemia receiving induction chemotherapy and alloHCT recipients. Despite improvements in microbiome diversity, expansion of commensals, and shrinkage of potential pathogens, aGVHD occurred more frequently after FMT than placebo. Although this unexpected finding could be explained by clinical differences between the two arms, we asked whether a microbiota explanation might be also present. To this end, we performed multi-omics analysis of preintervention and postintervention gut microbiome and serum metabolome. We found that postintervention expansion of Faecalibacterium, a commensal genus with gut-protective and anti-inflammatory properties under homeostatic conditions, predicted a higher risk for aGVHD. Faecalibacterium expansion occurred predominantly after FMT and was due to engraftment of unique donor taxa, suggesting that donor Faecalibacterium-derived antigens might have stimulated allogeneic immune cells. Faecalibacterium and ursodeoxycholic acid (an anti-inflammatory secondary bile acid) were negatively correlated, offering an alternative mechanistic explanation. In conclusion, we demonstrate context dependence of microbiota effects where a normally beneficial bacteria may become detrimental in disease. While FMT is a broad, community-level intervention, it may need precision engineering in ecologically complex settings where multiple perturbations (e.g., antibiotics, intestinal damage, alloimmunity) are concurrently in effect.

SIGNIFICANCE: Post-FMT expansion of Faecalibacterium, associated with donor microbiota engraftment, predicted a higher risk for aGVHD in alloHCT recipients. Although Faecalibacterium is a commensal genus with gut-protective and anti-inflammatory properties under homeostatic conditions, our findings suggest that it may become pathogenic in the setting of FMT after alloHCT. Our results support a future trial with precision engineering of the FMT product used as GVHD prophylaxis after alloHCT.}, } @article {pmid38764972, year = {2023}, author = {Boyes, D and Holland, PWH and , and , and , and , and , and , }, title = {The genome sequence of the Common Emerald, Hemithea aestivaria (Hübner, 1789).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {243}, pmid = {38764972}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual male Hemithea aestivaria (the Common Emerald; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 501.7 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 17.05 kilobases in length. Gene annotation of this assembly on Ensembl identified 18,477 protein coding genes.}, } @article {pmid38764970, year = {2023}, author = {Boyes, D and Lewis, OT and , and , and , and , and , and , }, title = {The genome sequence of the Pebble Hook-tip, Drepana falcataria (Linnaeus, 1758).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {207}, pmid = {38764970}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual male Drepana falcataria (the Pebble Hook-tip; Arthropoda; Insecta; Lepidoptera; Drepanidae). The genome sequence is 326.7 megabases in span. The whole assembly is scaffolded into 31 chromosomal pseudomolecules, including the assembled Z sex chromosome. The mitochondrial genome has also been assembled and is 15.4 kilobases in length.}, } @article {pmid38764134, year = {2024}, author = {Wang, J and Li, Y and Rahman, MM and Li, B and Yan, Z and Song, G and Zhao, Y and Wu, J and Chu, C}, title = {Unraveling the drivers and impacts of leaf phenological diversity in a subtropical forest: A fine-scale analysis using PlanetScope CubeSats.}, journal = {The New phytologist}, volume = {243}, number = {2}, pages = {607-619}, doi = {10.1111/nph.19850}, pmid = {38764134}, issn = {1469-8137}, support = {20220816162849005//Shenzhen Science and Technology Program/ ; 32301350//National Natural Science Foundation of China/ ; 31925027//National Natural Science Foundation of China/ ; 31922090//National Natural Science Foundation of China/ ; 32271595//National Natural Science Foundation of China/ ; 17305321//Hong Kong Research Grant Council General Research Fund/ ; //HKU Seed Funding for Strategic Interdisciplinary Research Scheme, the Hung Ying Physical Science Research Fund 2021-22/ ; //Innovation and Technology Fund (funding support to State Key Laboratories in Hong Kong of Agrobiotechnology) of the HKSAR, China/ ; LVEC-2023rc01//Key Talent Project of the State Key Laboratory of Vegetation and Environmental Change/ ; }, mesh = {*Plant Leaves/physiology ; *Forests ; *Biodiversity ; *Tropical Climate ; Biomass ; Soil ; China ; }, abstract = {Leaf phenology variations within plant communities shape community assemblages and influence ecosystem properties and services. However, questions remain regarding quantification, drivers, and productivity impacts of intra-site leaf phenological diversity. With a 50-ha subtropical forest plot in China's Heishiding Provincial Nature Reserve (part of the global ForestGEO network) as a testbed, we gathered a unique dataset combining ground-derived abiotic (topography, soil) and biotic (taxonomic diversity, functional diversity, functional traits) factors. We investigated drivers underlying leaf phenological diversity extracted from high-resolution PlanetScope data, and its influence on aboveground biomass (AGB) using structural equation modeling (SEM). Our results reveal considerable fine-scale leaf phenological diversity across the subtropical forest landscape. This diversity is directly and indirectly influenced by abiotic and biotic factors (e.g. slope, soil, traits, taxonomic diversity; r[2] = 0.43). While a notable bivariate relationship between AGB and leaf phenological diversity was identified (r = -0.24, P < 0.05), this relationship did not hold in SEM analysis after considering interactions with other biotic and abiotic factors (P > 0.05). These findings unveil the underlying mechanism regulating intra-site leaf phenological diversity. While leaf phenology is known to be associated with ecosystem properties, our findings confirm that AGB is primarily influenced by functional trait composition and taxonomic diversity rather than leaf phenological diversity.}, } @article {pmid38764024, year = {2024}, author = {Trujillano, F and Jimenez, G and Manrique, E and Kahamba, NF and Okumu, F and Apollinaire, N and Carrasco-Escobar, G and Barrett, B and Fornace, K}, title = {Using image segmentation models to analyse high-resolution earth observation data: new tools to monitor disease risks in changing environments.}, journal = {International journal of health geographics}, volume = {23}, number = {1}, pages = {13}, pmid = {38764024}, issn = {1476-072X}, support = {/WT_/Wellcome Trust/United Kingdom ; 221963/Z/20/Z//Wellcome Trust and Royal Society/ ; BB/X511110/1//BBSRC and EPSRC Impact Accelerator Accounts/ ; }, mesh = {Humans ; Animals ; *Climate Change ; Malaria/epidemiology ; Mosquito Vectors ; Remote Sensing Technology/methods ; Geographic Information Systems ; Image Processing, Computer-Assisted/methods ; }, abstract = {BACKGROUND: In the near future, the incidence of mosquito-borne diseases may expand to new sites due to changes in temperature and rainfall patterns caused by climate change. Therefore, there is a need to use recent technological advances to improve vector surveillance methodologies. Unoccupied Aerial Vehicles (UAVs), often called drones, have been used to collect high-resolution imagery to map detailed information on mosquito habitats and direct control measures to specific areas. Supervised classification approaches have been largely used to automatically detect vector habitats. However, manual data labelling for model training limits their use for rapid responses. Open-source foundation models such as the Meta AI Segment Anything Model (SAM) can facilitate the manual digitalization of high-resolution images. This pre-trained model can assist in extracting features of interest in a diverse range of images. Here, we evaluated the performance of SAM through the Samgeo package, a Python-based wrapper for geospatial data, as it has not been applied to analyse remote sensing images for epidemiological studies.

RESULTS: We tested the identification of two land cover classes of interest: water bodies and human settlements, using different UAV acquired imagery across five malaria-endemic areas in Africa, South America, and Southeast Asia. We employed manually placed point prompts and text prompts associated with specific classes of interest to guide the image segmentation and assessed the performance in the different geographic contexts. An average Dice coefficient value of 0.67 was obtained for buildings segmentation and 0.73 for water bodies using point prompts. Regarding the use of text prompts, the highest Dice coefficient value reached 0.72 for buildings and 0.70 for water bodies. Nevertheless, the performance was closely dependent on each object, landscape characteristics and selected words, resulting in varying performance.

CONCLUSIONS: Recent models such as SAM can potentially assist manual digitalization of imagery by vector control programs, quickly identifying key features when surveying an area of interest. However, accurate segmentation still requires user-provided manual prompts and corrections to obtain precise segmentation. Further evaluations are necessary, especially for applications in rural areas.}, } @article {pmid38762947, year = {2024}, author = {Liu, D and Zhou, M and Tan, H and Xiong, G and Wang, L and Shi, L and Li, C and Wu, W and Qiao, Y}, title = {Metabolomics, volatolomics, and bioinformatics analyses of the effects of ultra-high pressure pretreatment on taste and flavour parameters of cured Culter alburnus.}, journal = {Food chemistry}, volume = {453}, number = {}, pages = {139649}, doi = {10.1016/j.foodchem.2024.139649}, pmid = {38762947}, issn = {1873-7072}, mesh = {Animals ; *Taste ; *Flavoring Agents/chemistry/metabolism ; *Metabolomics ; *Computational Biology ; Fish Products/analysis/microbiology ; Pressure ; Cyprinidae/metabolism/microbiology ; Volatile Organic Compounds/chemistry/metabolism/analysis ; Bacteria/metabolism/genetics/classification/isolation & purification ; Humans ; Food Handling ; Amino Acids/metabolism/analysis ; }, abstract = {The effects of ultra-high pressure (UHP) pretreatment (50-250 MPa) on the fish curing were studied. UHP increased the overall volatile compound concentration of cured fish. Among 50-250 MPa five treatment groups, 150 MPa UHP group exhibited the highest total free amino acid content (294.34 mg/100 g) with that of the control group being 92.39 mg/100 g. The activity of cathepsin L was increased under 50-200 MPa UHP treatment (62.28-58.15 U/L), compared with that in the control group (53.80 U/L). UHP treatment resulted in a significant increase in small molecule compounds, especially the amino acid dipeptides and ATP metabolic products. Under UHP treatments, the bacterial phyla Actinobacteriota (1.04-5.25 %), Bacteroidota (0.20-4.47 %), and Deinococcota (0.00-0.05 %) exhibited an increased abundance, and they promoted taste and flavor formation. Our results indicated that UHP is a promising pretreatment method to improve taste and flavour in cured fish by affecting the microorganisms, cathepsin, and proteins.}, } @article {pmid38760814, year = {2024}, author = {Sakai, K and Igarashi, Y and Tounai, S and Shirai, C and Tsurugi, Y and Kakuno, F and Komasa, Y and Fujimura, M and Uruha, M and Mori, K and Tateishi, S}, title = {Key issues in Japan's public health centers to prepare for future pandemics: a text mining study using a topic model.}, journal = {BMC health services research}, volume = {24}, number = {1}, pages = {636}, pmid = {38760814}, issn = {1472-6963}, mesh = {Humans ; Japan ; *COVID-19/epidemiology ; Cross-Sectional Studies ; *Pandemics ; Surveys and Questionnaires ; Data Mining/methods ; Public Health ; SARS-CoV-2 ; Male ; }, abstract = {BACKGROUND: In Japan, over 450 public health centers played a central role in the operation of the local public health system in response to the COVID-19 pandemic. This study aimed to identify key issues for improving the system for public health centers for future pandemics.

METHODS: We conducted a cross-sectional study using an online questionnaire. The respondents were first line workers in public health centers or local governments during the pandemic. We solicited open-ended responses concerning improvements needed for future pandemics. Issues were identified from these descriptions using morphological analysis and a topic model with KHcoder3.0. The number of topics was estimated using Perplexity as a measure, and Latent Dirichlet Allocation for meaning identification.

RESULTS: We received open-ended responses from 784 (48.6%) of the 1,612 survey respondents, which included 111 physicians, 330 nurses, and 172 administrative staff. Morphological analysis processed these descriptions into 36,632 words. The topic model summarized them into eight issues: 1) establishment of a crisis management system, 2) division of functions among public health centers, prefectures, and medical institutions, 3) clear role distribution in public health center staff, 4) training of specialists, 5) information sharing system (information about infectious diseases and government policies), 6) response to excessive workload (support from other local governments, cooperation within public health centers, and outsourcing), 7) streamlining operations, and 8) balance with regular duties.

CONCLUSIONS: This study identified key issues that need to be addressed to prepare Japan's public health centers for future pandemics. These findings are vital for discussions aimed at strengthening the public health system based on experiences from the COVID-19 pandemic.}, } @article {pmid38758962, year = {2024}, author = {Massey, A and Boennec, C and Restrepo-Ortiz, CX and Blanchet, C and Alizon, S and Sofonea, MT}, title = {Real-time forecasting of COVID-19-related hospital strain in France using a non-Markovian mechanistic model.}, journal = {PLoS computational biology}, volume = {20}, number = {5}, pages = {e1012124}, pmid = {38758962}, issn = {1553-7358}, mesh = {*COVID-19/epidemiology ; Humans ; France/epidemiology ; *Forecasting/methods ; *SARS-CoV-2 ; Computational Biology/methods ; Retrospective Studies ; Models, Statistical ; Pandemics/statistics & numerical data ; Hospitals/statistics & numerical data ; Hospitalization/statistics & numerical data ; Bed Occupancy/statistics & numerical data ; }, abstract = {Projects such as the European Covid-19 Forecast Hub publish forecasts on the national level for new deaths, new cases, and hospital admissions, but not direct measurements of hospital strain like critical care bed occupancy at the sub-national level, which is of particular interest to health professionals for planning purposes. We present a sub-national French framework for forecasting hospital strain based on a non-Markovian compartmental model, its associated online visualisation tool and a retrospective evaluation of the real-time forecasts it provided from January to December 2021 by comparing to three baselines derived from standard statistical forecasting methods (a naive model, auto-regression, and an ensemble of exponential smoothing and ARIMA). In terms of median absolute error for forecasting critical care unit occupancy at the two-week horizon, our model only outperformed the naive baseline for 4 out of 14 geographical units and underperformed compared to the ensemble baseline for 5 of them at the 90% confidence level (n = 38). However, for the same level at the 4 week horizon, our model was never statistically outperformed for any unit despite outperforming the baselines 10 times spanning 7 out of 14 geographical units. This implies modest forecasting utility for longer horizons which may justify the application of non-Markovian compartmental models in the context of hospital-strain surveillance for future pandemics.}, } @article {pmid38752675, year = {2024}, author = {Schaupp, CM and Byrne, G and Chan, M and Haggard, DE and Hazemi, M and Jankowski, MD and LaLone, CA and LaTier, A and Mattingly, KZ and Olker, JH and Renner, J and Sharma, B and Villeneuve, DL}, title = {An automated computational data pipeline to rapidly acquire, score, and rank toxicological data for ecological hazard assessment.}, journal = {Integrated environmental assessment and management}, volume = {20}, number = {6}, pages = {2203-2217}, doi = {10.1002/ieam.4945}, pmid = {38752675}, issn = {1551-3793}, support = {//USEPA Office of Research and Development, Chemical Safety for Sustainability National Research Program/ ; }, mesh = {Risk Assessment/methods ; *Environmental Monitoring/methods ; Animals ; Endangered Species ; Water Pollutants, Chemical/toxicity/analysis ; Ecotoxicology/methods ; United States ; Quantitative Structure-Activity Relationship ; }, abstract = {Biological Evaluations support Endangered Species Act (ESA) consultation with the US Fish and Wildlife Service and National Marine Fisheries Service by federal action agencies, such as the USEPA, regarding impacts of federal activities on threatened or endangered species. However, they are often time-consuming and challenging to conduct. The identification of pollutant benchmarks or guidance to protect taxa for states and tribes when USEPA has not yet developed criteria recommendations is also of importance to ensure a streamlined approach to Clean Water Act program implementation. Due to substantial workloads, tight regulatory timelines, and the often-protracted length of ESA consultations, there is a need to streamline the development of biological evaluation toxicity assessments for determining the impact of chemical pollutants on ESA-listed species. Moreover, there is limited availability of species-specific toxicity data for many contaminants, further complicating the consultation process. New approach methodologies are being increasingly used in toxicology and chemical safety assessment to rapidly and cost-effectively provide data that can fill gaps in hazard and/or exposure characterization. Here, we present the development of an automated computational pipeline-RASRTox (Rapidly Acquire, Score, and Rank Toxicological data)-to rapidly extract and categorize ecological toxicity benchmark values from curated data sources (ECOTOX, ToxCast) and well-established quantitative structure-activity relationships (TEST, ECOSAR). As a proof of concept, points-of-departure (PODs) generated in RASRTox for 13 chemicals were compared against benchmark values derived using traditional methods-toxicity reference values (TRVs) and water quality criteria (WQC). The RASRTox PODs were generally within an order of magnitude of corresponding TRVs, though less concordant compared with WQC. The greatest utility of RASRTox, however, lies in its ability to quickly and systematically identify critical studies that may serve as a basis for screening value derivation by toxicologists as part of an ecological hazard assessment. As such, the strategy described in this case study can potentially be adapted for other risk assessment contexts and stakeholder needs. Integr Environ Assess Manag 2024;20:2203-2217. © 2024 Society of Environmental Toxicology & Chemistry (SETAC). This article has been contributed to by U.S. Government employees and their work is in the public domain in the USA.}, } @article {pmid38746391, year = {2024}, author = {Acheampong, DA and Jenjaroenpun, P and Wongsurawat, T and Krulilung, A and Pomyen, Y and Kandel, S and Kunadirek, P and Chuaypen, N and Kusonmano, K and Nookaew, I}, title = {CAIM: Coverage-based Analysis for Identification of Microbiome.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {38746391}, issn = {2692-8205}, support = {P20 GM125503/GM/NIGMS NIH HHS/United States ; R01 CA143130/CA/NCI NIH HHS/United States ; }, abstract = {Accurate taxonomic profiling of microbial taxa in a metagenomic sample is vital to gain insights into microbial ecology. Recent advancements in sequencing technologies have contributed tremendously toward understanding these microbes at species resolution through a whole shotgun metagenomic (WMS) approach. In this study, we developed a new bioinformatics tool, CAIM, for accurate taxonomic classification and quantification within both long- and short-read metagenomic samples using an alignment-based method. CAIM depends on two different containment techniques to identify species in metagenomic samples using their genome coverage information to filter out false positives rather than the traditional approach of relative abundance. In addition, we propose a nucleotide-count based abundance estimation, which yield lesser root mean square error than the traditional read-count approach. We evaluated the performance of CAIM on 28 metagenomic mock communities and 2 synthetic datasets by comparing it with other top-performing tools. CAIM maintained a consitently good performance across datasets in identifying microbial taxa and in estimating relative abundances than other tools. CAIM was then applied to a real dataset sequenced on both Nanopore (with and without amplification) and Illumina sequencing platforms and found high similality of taxonomic profiles between the sequencing platforms. Lastly, CAIM was applied to fecal shotgun metagenomic datasets of 232 colorectal cancer patients and 229 controls obtained from 4 different countries and primary 44 liver cancer patients and 76 controls. The predictive performance of models using the genome-coverage cutoff was better than those using the relative-abundance cutoffs in discriminating colorectal cancer and primary liver cancer patients from healthy controls with a highly confident species markers.}, } @article {pmid38741754, year = {2024}, author = {Klatt, S and Otte, FW and Beavan, A and Schumacher, T and Millar, SK}, title = {How did you perform? Investigating football players' perception of self-regulated passing performances under auditory noise environments.}, journal = {Frontiers in psychology}, volume = {15}, number = {}, pages = {1390487}, pmid = {38741754}, issn = {1664-1078}, abstract = {INTRODUCTION: This paper deals with the question on how sport performances may be influenced by internal, emotional processes, which stem from outside feedback.

METHODS: In terms of methods, players' subjective performance ratings for four experimental auditory cue conditions were examined; these included both 'positive' and 'negative' stadium noise, 'no (auditory) conditions,' and a control/'baseline' condition. This resulted in a qualitative-analytic data set that was obtained succeeding each auditory cue condition using a unique football training machine (i.e., known as 'Footbonaut'). Without having received any coaching/performance feedback, players were asked to rate and individually comment on their perceived performance ratings for each experimental auditory condition.

RESULTS: Findings indicate stronger and more significant correlations between auditory conditions and subjective ratings compared to the non-auditory condition and its subjective rating. Furthermore, data provides initial insight into players' emotional experiences during each of the practice conditions.

DISCUSSION: These noteworthy findings on players' abilities to accurately judge their performances based on selfmonitoring and intrinsic feedback are discussed from an Ecological Dynamics perspective, linked to a Nonlinear Pedagogy for coaching. Here, representative and affective learning designs for skill learning and performance preparation are presented. Finally, a hypothetical catalyst effect of auditory stadium noise on subjective performance rating is proposed.}, } @article {pmid38741150, year = {2024}, author = {Sõukand, R}, title = {Dark local knowledge: the yet-to-be scientifically discovered and locally acknowledged aspects of local knowledge systems.}, journal = {Journal of ethnobiology and ethnomedicine}, volume = {20}, number = {1}, pages = {50}, pmid = {38741150}, issn = {1746-4269}, mesh = {*Knowledge ; Humans ; Science ; }, abstract = {This essay brings forward the idea that there is more than meets the eye in local knowledge systems than what science can show us now. To comprehend this, we need to make a conceptual jump and look for the "dark matter" (the notion borrowed from astronomy that refers to a hypothetical form of matter that does not interact with light or electromagnetic fields) that can potentially sustain local knowledge. Considering that it is a complex of knowledge, practices, and beliefs contained in TEK, knowledge in LEK does not correspond to the notion of knowledge in science. Therefore, in order to map LEK-science interactions, we will refer to the concept of peoples' knowledge of LEK as acknowledgement and the scientific recognition and awareness of information, facts, and principles as knowledge. Applying this to a Johari Window, we can observe four categories of LEK in a known-unknown/acknowledged-unacknowledged matrix. We can refer to unknown and unacknowledged as dark local knowledge. Indeed, local knowledge systems contain many aspects that modern science cannot yet explain, as a major part of its components are not even considered in scholarly research. Dark local knowledge can potentially provide us with the invaluable touch of experience of countless generations, opening different ways of seeing reality.}, } @article {pmid38739654, year = {2024}, author = {Bloxham, B and Lee, H and Gore, J}, title = {Biodiversity is enhanced by sequential resource utilization and environmental fluctuations via emergent temporal niches.}, journal = {PLoS computational biology}, volume = {20}, number = {5}, pages = {e1012049}, pmid = {38739654}, issn = {1553-7358}, mesh = {*Biodiversity ; *Models, Biological ; *Ecosystem ; Computational Biology ; Animals ; }, abstract = {How natural communities maintain their remarkable biodiversity and which species survive in complex communities are central questions in ecology. Resource competition models successfully explain many phenomena but typically predict only as many species as resources can coexist. Here, we demonstrate that sequential resource utilization, or diauxie, with periodic growth cycles can support many more species than resources. We explore how communities modify their own environments by sequentially depleting resources to form sequences of temporal niches, or intermediately depleted environments. Biodiversity is enhanced when community-driven or environmental fluctuations modulate the resource depletion order and produce different temporal niches on each growth cycle. Community-driven fluctuations under constant environmental conditions are rare, but exploring them illuminates the temporal niche structure that emerges from sequential resource utilization. With environmental fluctuations, we find most communities have more stably coexisting species than resources with survivors accurately predicted by the same temporal niche structure and each following a distinct optimal strategy. Our results thus present a new niche-based approach to understanding highly diverse fluctuating communities.}, } @article {pmid38729378, year = {2024}, author = {Yu, H and Yin, D and Yang, B and Yang, Y and Chen, F}, title = {Challenges for sustainable development goal of land degradation neutrality in drylands: Evidence from the Northern Slope of the Tianshan Mountains, China.}, journal = {The Science of the total environment}, volume = {932}, number = {}, pages = {173094}, doi = {10.1016/j.scitotenv.2024.173094}, pmid = {38729378}, issn = {1879-1026}, abstract = {The SDG 15.3.1 target of Land Degradation Neutrality (LDN) only has 15 years from conception (in 2015) to realization (in 2030). Therefore, investigating the effectiveness and challenges of LDN has become a priority, especially in drylands, where fragile ecosystems intersect with multiple disturbances. In this study, solutions are proposed and validated based on the challenges of LDN. We chose the Northern Slope of the Tianshan Mountains as a case study and set baselines in 2005 and 2010. The region and degree of land change (including degraded, stable, and improved) were depicted at the pixel scale (100 × 100 m), and LDN realization was assessed at the regional scale (including administrative districts and 5000 × 5000 m grids). The results showed a significant disparity between the two baselines. The number of areas that realized the LDN target was rare, regardless of the scale of the administrative districts or grids. Chord plots, Spearman's correlation, and curve estimation were employed to reveal the relationship between LDN and seven natural or socioeconomic factors. We found that substantial degradation was closely related to the expansion of unused, urban, and mining land and reduction in water, glaciers, and forests. Further evidence suggests that agricultural development both positively and negatively affects LDN, whereas urbanization and mining activities are undesirable for LDN. Notably, the adverse effects of glacier melting require additional attention. Therefore, we consider the easy-to-achieve and hard-to-achieve baselines as the mandatory and desirable targets of LDN, respectively, and focus further efforts in three aspects: preventing agricultural exploitation from occupying ecological resources, defining reasonable zones for urbanization and mining, and reducing greenhouse gas emissions to mitigate warming. Overall, this study is expected to be a beneficial addition to existing LDN theoretical systems and serve as a case validation of the challenges of LDN in drylands.}, } @article {pmid38729197, year = {2024}, author = {Caini, S and Meijer, A and Nunes, MC and Henaff, L and Zounon, M and Boudewijns, B and Del Riccio, M and Paget, J}, title = {Probable extinction of influenza B/Yamagata and its public health implications: a systematic literature review and assessment of global surveillance databases.}, journal = {The Lancet. Microbe}, volume = {5}, number = {8}, pages = {100851}, doi = {10.1016/S2666-5247(24)00066-1}, pmid = {38729197}, issn = {2666-5247}, mesh = {Humans ; *Influenza, Human/epidemiology/virology ; *Influenza B virus/genetics/isolation & purification ; *Public Health ; Global Health ; COVID-19/epidemiology/prevention & control ; Databases, Factual ; SARS-CoV-2 ; Pandemics ; }, abstract = {Early after the start of the COVID-19 pandemic, the detection of influenza B/Yamagata cases decreased globally. Given the potential public health implications of this decline, in this Review, we systematically analysed data on influenza B/Yamagata virus circulation (for 2020-23) from multiple complementary sources of information. We identified relevant articles published in PubMed and Embase, and data from the FluNet, Global Initiative on Sharing All Influenza Data, and GenBank databases, webpages of respiratory virus surveillance systems from countries worldwide, and the Global Influenza Hospital Surveillance Network. A progressive decline of influenza B/Yamagata detections was reported across all sources, in absolute terms (total number of cases), as positivity rate, and as a proportion of influenza B detections. Sporadically reported influenza B/Yamagata cases since March, 2020 were mostly vaccine-derived, attributed to data entry errors, or have yet to be definitively confirmed. The likelihood of extinction necessitates a rapid response in terms of reassessing the composition of influenza vaccines, enhanced surveillance for B/Yamagata, and a possible change in the biosafety level when handling B/Yamagata viruses in laboratories.}, } @article {pmid38724591, year = {2024}, author = {Bhandari, N and Bald, L and Wraase, L and Zeuss, D}, title = {Multispectral analysis-ready satellite data for three East African mountain ecosystems.}, journal = {Scientific data}, volume = {11}, number = {1}, pages = {473}, pmid = {38724591}, issn = {2052-4463}, support = {5064//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 2358//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; }, mesh = {Climate Change ; *Ecosystem ; Environmental Monitoring/methods ; Ethiopia ; Remote Sensing Technology ; *Satellite Imagery ; Tanzania ; }, abstract = {The East African mountain ecosystems are facing increasing threats due to global change, putting their unique socio-ecological systems at risk. To monitor and understand these changes, researchers and stakeholders require accessible analysis-ready remote sensing data. Although satellite data is available for many applications, it often lacks accurate geometric orientation and has extensive cloud cover. This can generate misleading results and make it unreliable for time-series analysis. Therefore, it needs comprehensive processing before usage, which encompasses multi-step operations, requiring large computational and storage capacities, as well as expert knowledge. Here, we provide high-quality, atmospherically corrected, and cloud-free analysis-ready Sentinel-2 imagery for the Bale Mountains (Ethiopia), Mounts Kilimanjaro and Meru (Tanzania) ecosystems in East Africa. Our dataset ranges from 2017 to 2021 and is provided as monthly and annual aggregated products together with 24 spectral indices. Our dataset enables researchers and stakeholders to conduct immediate and impactful analyses. These applications can include vegetation mapping, wildlife habitat assessment, land cover change detection, ecosystem monitoring, and climate change research.}, } @article {pmid38724027, year = {2024}, author = {Dar, FA and Hamid, M and Malik, RA and Wani, SA and Singh, CP and Shah, MA and Khuroo, AA}, title = {ToTE: A global database on trees of the treeline ecotone.}, journal = {Ecology}, volume = {105}, number = {6}, pages = {e4309}, doi = {10.1002/ecy.4309}, pmid = {38724027}, issn = {1939-9170}, support = {923/CSIR-UGC NET JUNE 2019//University Grants Commission/ ; SR/FST/LS-II/2017/103(C)//Department of Science & Technology, Govt. of India, New Delhi/ ; SAC/EPSA/ALPINE/SHRESTI/10/2019//Space Applications Centre (SAC) ISRO, Ahmedabad/ ; }, mesh = {*Trees ; *Databases, Factual ; Biodiversity ; Forests ; Ecosystem ; }, abstract = {Globally, treelines form a transition zone between tree-dominated forest downslope and treeless alpine vegetation upslope. Treelines represent the highest boundary of "tree" life form in high-elevation mountains and at high latitudes. Recently, treelines have been shifting upslope in response to climate warming, so it has become important to understand global tree diversity and treeline distributions. However, to the best of our knowledge, no global database on tree flora of treelines exists, which limits our capacity to undertake macroecological analyses. Here, for the first time, we present a global data set on the trees of the treeline ecotone, supported by an online ToTE database. We synthesized the database from 1202 studies published over the last 60 years (1962 to 2022) following the Preferred Reporting Items in Systematic Reviews and Meta-Analysis (PRISMA) protocol. We classified the tree species in the database into three categories: treeline tree (TL) species, near to treeline (NTL) tree species, and tree species with an upper montane range limit (TUMR). The ToTE Version-1 presents a total of 208 tree taxa, including 189 species, five subspecies, and 14 varieties, belonging to 54 genera and 26 families distributed across 34 mountain regions worldwide that either grow exactly at the treeline or have a range limit below the treeline. Of the total taxa, 155, 14, and 39 belong to TL, NTL, and TUMR, respectively. Genera such as Abies, Picea, Pinus, Larix, and Juniperus are more represented in the treeline tree category. On the other hand, Acer, Prunus, Populus, and Quercus have more representatives in the near to treeline category, whereas Erica, Nothofagus, and Polylepis contribute more tree species with an upper montane range limit. Furthermore, families such as Rosaceae and Pinaceae include trees that occur both at the treeline and with an upper montane range limit, whereas Sapindaceae includes trees that occur exclusively near to treeline. Our database also includes information on the global distribution patterns of treeline tree species richness across mountains and biomes. The mountains with the highest number of tree species are the Andes (39) followed by the Himalaya (37). Close to 67% of tree species show restricted distributions in different mountains, with the highest endemism in the Andes and the Himalaya. In terms of tree species distribution, Pinus sylvestris was widespread, with a distribution across nine mountain regions, followed by Picea glauca and Fagus sylvatica, both distributed across five mountain regions. In terms of species' distribution across biomes, the temperate biome harbors the highest treeline tree species richness (152 species), which may reflect the fact that the majority of studies are available from the temperate regions of the world. The remaining 56 species are distributed within five other biomes, with the least in dry tropical and subarctic (four species each). Furthermore, currently 40 treeline tree species fall under different International Union for Conservation of Nature threat categories. We anticipate that our database will help advance research on macroecological, biogeographic, evolutionary, climate-change, and conservation aspects of the treeline on a global scale. The data are released under a Creative Commons Attribution 4.0 international license. Please cite this data paper when the data are reused.}, } @article {pmid38723067, year = {2024}, author = {Holstad, A and Voje, KL and Opedal, ØH and Bolstad, GH and Bourg, S and Hansen, TF and Pélabon, C}, title = {Evolvability predicts macroevolution under fluctuating selection.}, journal = {Science (New York, N.Y.)}, volume = {384}, number = {6696}, pages = {688-693}, doi = {10.1126/science.adi8722}, pmid = {38723067}, issn = {1095-9203}, mesh = {Animals ; *Biological Evolution ; *Fossils ; Genetic Variation ; *Selection, Genetic ; Datasets as Topic ; }, abstract = {Heritable variation is a prerequisite for evolutionary change, but the relevance of genetic constraints on macroevolutionary timescales is debated. By using two datasets on fossil and contemporary taxa, we show that evolutionary divergence among populations, and to a lesser extent among species, increases with microevolutionary evolvability. We evaluate and reject several hypotheses to explain this relationship and propose that an effect of evolvability on population and species divergence can be explained by the influence of genetic constraints on the ability of populations to track rapid, stationary environmental fluctuations.}, } @article {pmid38721834, year = {2024}, author = {Freedman, AH and Sackton, TB}, title = {Rethinking eco-evo studies of gene expression for non-model organisms in the genomic era.}, journal = {Molecular ecology}, volume = {}, number = {}, pages = {e17378}, doi = {10.1111/mec.17378}, pmid = {38721834}, issn = {1365-294X}, abstract = {Recent advances in genomic technology, including the rapid development of long-read sequencing technology and single-cell RNA-sequencing methods, are poised to significantly expand the kinds of studies that are feasible in ecological genomics. In this perspective, we review these new technologies and discuss their potential impact on gene expression studies in non-model organisms. Although traditional RNA-sequencing methods have been an extraordinarily powerful tool to apply functional genomics in an ecological context, bulk RNA-seq approaches often rely on de novo transcriptome assembly, and cannot capture expression changes in rare cell populations or distinguish shifts in cell type abundance. Advancements in genome assembly technology, particularly long-read sequencing, and improvements in the scalability of single-cell RNA-sequencing (scRNA-seq) offer unprecedented resolution in understanding cellular heterogeneity and gene regulation. We discuss the potential of these technologies to enable disentangling differential gene regulation from cell type composition differences and uncovering subtle expression patterns masked by bulk RNA-seq. The integration of these approaches provides a more nuanced understanding of the ecological and evolutionary dynamics of gene expression, paving the way for refined models and deeper insights into the generation of biodiversity.}, } @article {pmid38721398, year = {2024}, author = {Ross, KE and Bastian, FB and Buys, M and Cook, CE and D'Eustachio, P and Harrison, M and Hermjakob, H and Li, D and Lord, P and Natale, DA and Peters, B and Sternberg, PW and Su, AI and Thakur, M and Thomas, PD and Bateman, A and , }, title = {Perspectives on tracking data reuse across biodata resources.}, journal = {Bioinformatics advances}, volume = {4}, number = {1}, pages = {vbae057}, pmid = {38721398}, issn = {2635-0041}, support = {R35 GM141873/GM/NIGMS NIH HHS/United States ; }, abstract = {MOTIVATION: Data reuse is a common and vital practice in molecular biology and enables the knowledge gathered over recent decades to drive discovery and innovation in the life sciences. Much of this knowledge has been collated into molecular biology databases, such as UniProtKB, and these resources derive enormous value from sharing data among themselves. However, quantifying and documenting this kind of data reuse remains a challenge.

RESULTS: The article reports on a one-day virtual workshop hosted by the UniProt Consortium in March 2023, attended by representatives from biodata resources, experts in data management, and NIH program managers. Workshop discussions focused on strategies for tracking data reuse, best practices for reusing data, and the challenges associated with data reuse and tracking. Surveys and discussions showed that data reuse is widespread, but critical information for reproducibility is sometimes lacking. Challenges include costs of tracking data reuse, tensions between tracking data and open sharing, restrictive licenses, and difficulties in tracking commercial data use. Recommendations that emerged from the discussion include: development of standardized formats for documenting data reuse, education about the obstacles posed by restrictive licenses, and continued recognition by funding agencies that data management is a critical activity that requires dedicated resources.

Summaries of survey results are available at: https://docs.google.com/forms/d/1j-VU2ifEKb9C-sW6l3ATB79dgHdRk5v_lESv2hawnso/viewanalytics (survey of data providers) and https://docs.google.com/forms/d/18WbJFutUd7qiZoEzbOytFYXSfWFT61hVce0vjvIwIjk/viewanalytics (survey of users).}, } @article {pmid38720068, year = {2024}, author = {Mahon, MB and Sack, A and Aleuy, OA and Barbera, C and Brown, E and Buelow, H and Civitello, DJ and Cohen, JM and de Wit, LA and Forstchen, M and Halliday, FW and Heffernan, P and Knutie, SA and Korotasz, A and Larson, JG and Rumschlag, SL and Selland, E and Shepack, A and Vincent, N and Rohr, JR}, title = {A meta-analysis on global change drivers and the risk of infectious disease.}, journal = {Nature}, volume = {629}, number = {8013}, pages = {830-836}, pmid = {38720068}, issn = {1476-4687}, mesh = {Animals ; Humans ; Anthropogenic Effects ; *Biodiversity ; *Climate Change/statistics & numerical data ; *Communicable Diseases/epidemiology/etiology ; Conservation of Natural Resources/trends ; Datasets as Topic ; *Environmental Pollution/adverse effects ; Forestry ; Forests ; *Introduced Species/statistics & numerical data ; Plant Diseases/etiology ; Risk Assessment ; Urbanization ; }, abstract = {Anthropogenic change is contributing to the rise in emerging infectious diseases, which are significantly correlated with socioeconomic, environmental and ecological factors[1]. Studies have shown that infectious disease risk is modified by changes to biodiversity[2-6], climate change[7-11], chemical pollution[12-14], landscape transformations[15-20] and species introductions[21]. However, it remains unclear which global change drivers most increase disease and under what contexts. Here we amassed a dataset from the literature that contains 2,938 observations of infectious disease responses to global change drivers across 1,497 host-parasite combinations, including plant, animal and human hosts. We found that biodiversity loss, chemical pollution, climate change and introduced species are associated with increases in disease-related end points or harm, whereas urbanization is associated with decreases in disease end points. Natural biodiversity gradients, deforestation and forest fragmentation are comparatively unimportant or idiosyncratic as drivers of disease. Overall, these results are consistent across human and non-human diseases. Nevertheless, context-dependent effects of the global change drivers on disease were found to be common. The findings uncovered by this meta-analysis should help target disease management and surveillance efforts towards global change drivers that increase disease. Specifically, reducing greenhouse gas emissions, managing ecosystem health, and preventing biological invasions and biodiversity loss could help to reduce the burden of plant, animal and human diseases, especially when coupled with improvements to social and economic determinants of health.}, } @article {pmid38718196, year = {2024}, author = {Leroux, A and Crainiceanu, C and Zeger, S and Taub, M and Ansari, B and Wager, TD and Bayman, E and Coffey, C and Langefeld, C and McCarthy, R and Tsodikov, A and Brummet, C and Clauw, DJ and Edwards, RR and Lindquist, MA and , }, title = {Statistical modeling of acute and chronic pain patient-reported outcomes obtained from ecological momentary assessment.}, journal = {Pain}, volume = {165}, number = {9}, pages = {1955-1965}, doi = {10.1097/j.pain.0000000000003214}, pmid = {38718196}, issn = {1872-6623}, support = {U54 DA049113/DA/NIDA NIH HHS/United States ; }, mesh = {Humans ; *Chronic Pain/diagnosis ; *Patient Reported Outcome Measures ; *Ecological Momentary Assessment ; *Models, Statistical ; *Pain Measurement/methods ; *Acute Pain/diagnosis ; Male ; Female ; }, abstract = {Ecological momentary assessment (EMA) allows for the collection of participant-reported outcomes (PROs), including pain, in the normal environment at high resolution and with reduced recall bias. Ecological momentary assessment is an important component in studies of pain, providing detailed information about the frequency, intensity, and degree of interference of individuals' pain. However, there is no universally agreed on standard for summarizing pain measures from repeated PRO assessment using EMA into a single, clinically meaningful measure of pain. Here, we quantify the accuracy of summaries (eg, mean and median) of pain outcomes obtained from EMA and the effect of thresholding these summaries to obtain binary clinical end points of chronic pain status (yes/no). Data applications and simulations indicate that binarizing empirical estimators (eg, sample mean, random intercept linear mixed model) can perform well. However, linear mixed-effect modeling estimators that account for the nonlinear relationship between average and variability of pain scores perform better for quantifying the true average pain and reduce estimation error by up to 50%, with larger improvements for individuals with more variable pain scores. We also show that binarizing pain scores (eg, <3 and ≥3) can lead to a substantial loss of statistical power (40%-50%). Thus, when examining pain outcomes using EMA, the use of linear mixed models using the entire scale (0-10) is superior to splitting the outcomes into 2 groups (<3 and ≥3) providing greater statistical power and sensitivity.}, } @article {pmid38717702, year = {2024}, author = {Zhou, Q and Song, Y and Zhang, Y and Ping, Z and Zheng, Y and Chen, H and Liu, P and Hong, P and Zheng, Z}, title = {Land use transition and its effect on ecosystem service value with introducing "three wastes" factor in the industrial county, China.}, journal = {Environmental science and pollution research international}, volume = {31}, number = {24}, pages = {34962-34980}, pmid = {38717702}, issn = {1614-7499}, support = {ZR2023MD033//Natural Science Foundation of Shandong Province/ ; LJNY202103//Key Technology Research and Development Program of Shandong Province/ ; }, mesh = {China ; *Ecosystem ; Conservation of Natural Resources ; Urbanization ; Forests ; Environmental Monitoring ; }, abstract = {Land use transition and its impact on ecosystem service value (ESV) are the foundation for optimizing the layout of territorial space and ecological civilization construction. With the acceleration of industrialization and urbanization, the area of construction land expands in China. To accurately estimate the ESV in industrial counties, the impact of construction land on the ecological environment should be fully considered. This paper took Gangcheng District, Jinan City, a steel base in the Shandong Province of China as an example, then the value coefficients of "three wastes" factors (waste gas, wastewater, and waste) were introduced, and an improved calculation method of ESV was put forward for industrial counties in combination with remote sensing and land use data. Finally, the land use transition and its ESV effect in typical industrial counties were analyzed using geo-informatic Tupu and grid method. The results showed that the most important land use transitions were from grassland and forestland to cultivated land, from cultivated land and forestland to construction land in 1990-2010, and from cultivated land transformed to forestland in 2010-2021. The types of land use transition were mainly repetitive and continuous. The ESV first decreased and then increased, with a slight overall decline for more than 30 years, showing a spatial distribution characteristic of "low in the south-central and high around." Land use transition had the impact on ESV with the negative contribution rate of 68.28% in 1990-2000 and 73.16% in 2000-2010, mainly caused by the transition from forestland and grassland to cultivated land and construction land, and the positive contribution rate of 81.72% in 2010-2021, mainly caused by the transition from cultivated land to forestland. Compared with the ESV calculation method without introducing the "three wastes" factor and Xie Gaodi's method, the improved method in this paper considered the inevitable impact of construction land on ESV in industrial counties and made the ESV calculated more accurate according to the regional nature. This paper cannot only enrich the theories and technical methods of land use transition and its effects, and provide a case reference for similar industrial counties, but also provide data and decision-making support for the spatial layout and ecological protection in the study area.}, } @article {pmid38716048, year = {2023}, author = {Boyes, D and Hammond, J and , and , and , and , and , and , }, title = {The genome sequence of the Ruddy Flat-body, Agonopterix subpropinquella (Stainton, 1849).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {487}, pmid = {38716048}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual male Agonopterix subpropinquella (the Ruddy Flat-body; Arthropoda; Insecta; Lepidoptera; Depressariidae). The genome sequence is 667.9 megabases in span. Most of the assembly is scaffolded into 28 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 16.5 kilobases in length. Gene annotation of this assembly on Ensembl identified 18,796 protein coding genes.}, } @article {pmid38714914, year = {2024}, author = {Zhang, L and Zhang, Y and Liu, Y and Miao, W and Ai, J and Li, J and Peng, S and Li, S and Ye, L and Zeng, R and Shi, X and Ma, J and Lin, Y and Kuang, W and Cui, R}, title = {Multi-omics analysis revealed that the protein kinase MoKin1 affected the cellular response to endoplasmic reticulum stress in the rice blast fungus, Magnaporthe oryzae.}, journal = {BMC genomics}, volume = {25}, number = {1}, pages = {449}, pmid = {38714914}, issn = {1471-2164}, mesh = {*Endoplasmic Reticulum Stress ; *Oryza/microbiology/genetics ; *Fungal Proteins/metabolism/genetics ; *Proteomics ; Plant Diseases/microbiology ; Gene Expression Regulation, Fungal ; Protein Kinases/metabolism/genetics ; Mutation ; Multiomics ; Ascomycota ; }, abstract = {BACKGROUND: Previous studies have shown that protein kinase MoKin1 played an important role in the growth, conidiation, germination and pathogenicity in rice blast fungus, Magnaporthe oryzae. ΔMokin1 mutant showed significant phenotypic defects and significantly reduced pathogenicity. However, the internal mechanism of how MoKin1 affected the development of physiology and biochemistry remained unclear in M. oryzae.

RESULT: This study adopted a multi-omics approach to comprehensively analyze MoKin1 function, and the results showed that MoKin1 affected the cellular response to endoplasmic reticulum stress (ER stress). Proteomic analysis revealed that the downregulated proteins in ΔMokin1 mutant were enriched mainly in the response to ER stress triggered by the unfolded protein. Loss of MoKin1 prevented the ER stress signal from reaching the nucleus. Therefore, the phosphorylation of various proteins regulating the transcription of ER stress-related genes and mRNA translation was significantly downregulated. The insensitivity to ER stress led to metabolic disorders, resulting in a significant shortage of carbohydrates and a low energy supply, which also resulted in severe phenotypic defects in ΔMokin1 mutant. Analysis of MoKin1-interacting proteins indicated that MoKin1 really took participate in the response to ER stress.

CONCLUSION: Our results showed the important role of protein kinase MoKin1 in regulating cellular response to ER stress, providing a new research direction to reveal the mechanism of MoKin1 affecting pathogenic formation, and to provide theoretical support for the new biological target sites searching and bio-pesticides developing.}, } @article {pmid38714759, year = {2024}, author = {Lee, KS and Landry, Z and Athar, A and Alcolombri, U and Pramoj Na Ayutthaya, P and Berry, D and de Bettignies, P and Cheng, JX and Csucs, G and Cui, L and Deckert, V and Dieing, T and Dionne, J and Doskocil, O and D'Souza, G and García-Timermans, C and Gierlinger, N and Goda, K and Hatzenpichler, R and Henshaw, RJ and Huang, WE and Iermak, I and Ivleva, NP and Kneipp, J and Kubryk, P and Küsel, K and Lee, TK and Lee, SS and Ma, B and Martínez-Pérez, C and Matousek, P and Meckenstock, RU and Min, W and Mojzeš, P and Müller, O and Kumar, N and Nielsen, PH and Notingher, I and Palatinszky, M and Pereira, FC and Pezzotti, G and Pilat, Z and Plesinger, F and Popp, J and Probst, AJ and Riva, A and Saleh, AAE and Samek, O and Sapers, HM and Schubert, OT and Stubbusch, AKM and Tadesse, LF and Taylor, GT and Wagner, M and Wang, J and Yin, H and Yue, Y and Zenobi, R and Zini, J and Sarkans, U and Stocker, R}, title = {MicrobioRaman: an open-access web repository for microbiological Raman spectroscopy data.}, journal = {Nature microbiology}, volume = {9}, number = {5}, pages = {1152-1156}, pmid = {38714759}, issn = {2058-5276}, support = {GBMF9197//Gordon and Betty Moore Foundation (Gordon E. and Betty I. Moore Foundation)/ ; 542395//Simons Foundation/ ; }, mesh = {*Spectrum Analysis, Raman/methods ; *Internet ; Humans ; Databases, Factual ; }, } @article {pmid38714055, year = {2024}, author = {Li, Z and Wang, J and Yue, H and Rehman, A and Yousaf, M and Du, M and Zhang, X}, title = {Applying metabolic modeling and multi-omics to elucidate the biotransformation mechanisms of marine algal toxin domoic acid (DA) in sediments.}, journal = {Journal of hazardous materials}, volume = {472}, number = {}, pages = {134541}, doi = {10.1016/j.jhazmat.2024.134541}, pmid = {38714055}, issn = {1873-3336}, mesh = {*Kainic Acid/analogs & derivatives/metabolism ; *Geologic Sediments/microbiology ; *Biotransformation ; *Marine Toxins/metabolism ; Microbiota ; Metabolome ; Biodegradation, Environmental ; Metagenome ; Water Pollutants, Chemical/metabolism ; Multiomics ; }, abstract = {Domoic acid (DA)-producing algal blooms are a global marine environmental issue. However, there has been no previous research addressing the question regarding the fate of DA in marine benthic environments. In this work, we investigated the DA fate in the water-sediment microcosm via the integrative analysis of a top-down metabolic model, metagenome, and metabolome. Results demonstrated that biodegradation is the leading mechanism for the nonconservative attenuation of DA. Specifically, DA degradation was prominently completed by the sediment aerobic community, with a degradation rate of 0.0681 ± 0.00954 d[-1]. The DA degradation pathway included hydration, dehydrogenation, hydrolysis, decarboxylation, automatic ring opening of hydration, and β oxidation reactions. Moreover, the reverse ecological analysis demonstrated that the microbial community transitioned from nutrient competition to metabolic cross-feeding during DA degradation, further enhancing the cooperation between DA degraders and other taxa. Finally, we reconstructed the metabolic process of microbial communities during DA degradation and confirmed that the metabolism of amino acid and organic acid drove the degradation of DA. Overall, our work not only elucidated the fate of DA in marine environments but also provided crucial insights for applying metabolic models and multi-omics to investigate the biotransformation of other contaminants.}, } @article {pmid38713735, year = {2024}, author = {Oszoli, I and Zachar, I}, title = {Group-selection via aggregative propagule-formation enables cooperative multicellularity in an individual based, spatial model.}, journal = {PLoS computational biology}, volume = {20}, number = {5}, pages = {e1012107}, pmid = {38713735}, issn = {1553-7358}, mesh = {*Models, Biological ; *Biological Evolution ; Computational Biology ; Ecosystem ; Animals ; Predatory Behavior/physiology ; Selection, Genetic ; Computer Simulation ; }, abstract = {The emergence of multicellularity is one of the major transitions in evolution that happened multiple times independently. During aggregative multicellularity, genetically potentially unrelated lineages cooperate to form transient multicellular groups. Unlike clonal multicellularity, aggregative multicellular organisms do not rely on kin selection instead other mechanisms maintain cooperation against cheater phenotypes that benefit from cooperators but do not contribute to groups. Spatiality with limited diffusion can facilitate group selection, as interactions among individuals are restricted to local neighbourhoods only. Selection for larger size (e.g. avoiding predation) may facilitate the emergence of aggregation, though it is unknown, whether and how much role such selection played during the evolution of aggregative multicellularity. We have investigated the effect of spatiality and the necessity of predation on the stability of aggregative multicellularity via individual-based modelling on the ecological timescale. We have examined whether aggregation facilitates the survival of cooperators in a temporally heterogeneous environment against cheaters, where only a subset of the population is allowed to periodically colonize a new, resource-rich habitat. Cooperators constitutively produce adhesive molecules to promote aggregation and propagule-formation while cheaters spare this expense to grow faster but cannot aggregate on their own, hence depending on cooperators for long-term survival. We have compared different population-level reproduction modes with and without individual selection (predation) to evaluate the different hypotheses. In a temporally homogeneous environment without propagule-based colonization, cheaters always win. Predation can benefit cooperators, but it is not enough to maintain the necessary cooperator amount in successive dispersals, either randomly or by fragmentation. Aggregation-based propagation however can ensure the adequate ratio of cooperators-to-cheaters in the propagule and is sufficient to do so even without predation. Spatiality combined with temporal heterogeneity helps cooperators via group selection, thus facilitating aggregative multicellularity. External stress selecting for larger size (e.g. predation) may facilitate aggregation, however, according to our results, it is neither necessary nor sufficient for aggregative multicellularity to be maintained when there is effective group-selection.}, } @article {pmid38711355, year = {2024}, author = {Tsutsui, K and Tanaka, R and Takeda, K and Fujii, K}, title = {Collaborative hunting in artificial agents with deep reinforcement learning.}, journal = {eLife}, volume = {13}, number = {}, pages = {}, pmid = {38711355}, issn = {2050-084X}, support = {20H04075//Japan Society for the Promotion of Science/ ; 21H04892//Japan Society for the Promotion of Science/ ; 21H05300//Japan Society for the Promotion of Science/ ; 22K17673//Japan Society for the Promotion of Science/ ; JPMJPR20CA//Japan Science and Technology Agency/ ; }, mesh = {Animals ; *Deep Learning ; *Predatory Behavior ; *Reinforcement, Psychology ; Cooperative Behavior ; Humans ; Computer Simulation ; Decision Making ; }, abstract = {Collaborative hunting, in which predators play different and complementary roles to capture prey, has been traditionally believed to be an advanced hunting strategy requiring large brains that involve high-level cognition. However, recent findings that collaborative hunting has also been documented in smaller-brained vertebrates have placed this previous belief under strain. Here, using computational multi-agent simulations based on deep reinforcement learning, we demonstrate that decisions underlying collaborative hunts do not necessarily rely on sophisticated cognitive processes. We found that apparently elaborate coordination can be achieved through a relatively simple decision process of mapping between states and actions related to distance-dependent internal representations formed by prior experience. Furthermore, we confirmed that this decision rule of predators is robust against unknown prey controlled by humans. Our computational ecological results emphasize that collaborative hunting can emerge in various intra- and inter-specific interactions in nature, and provide insights into the evolution of sociality.}, } @article {pmid38709778, year = {2024}, author = {Xu, N and Zeng, P and Guo, Y and Siddique, MA and Li, J and Ren, X and Tang, F and Zhang, R}, title = {The spatiotemporal evolution of rural landscape patterns in Chinese metropolises under rapid urbanization.}, journal = {PloS one}, volume = {19}, number = {5}, pages = {e0301754}, pmid = {38709778}, issn = {1932-6203}, mesh = {China ; Cities ; Conservation of Natural Resources ; Ecosystem ; Geographic Information Systems ; Rural Population ; Spatio-Temporal Analysis ; *Urbanization ; }, abstract = {Understanding the evolution of rural landscapes in metropolises during rapid urbanization is crucial for formulating policies to protect the rural ecological environment. In this study, remote sensing and geographical information system data, as well as applied landscape index analysis, are used to examine the spatiotemporal evolution of rural landscape patterns in the Beijing-Tianjin region of China, which has experienced rapid urbanization. The relationships between land use/land cover changes and changes in rural landscape patterns are explored. The results revealed significant spatial differences in the rural landscapes in the Beijing-Tianjin region; farmland and forestland were the main types of landscapes, creating a "mountain-field-sea" natural landscape pattern. The conversion of rural landscapes in the Beijing-Tianjin region involved mainly the conversion of farmland to urban areas, with few exchanges between other landscape types. The urban areas in the Beijing-Tianjin region increased by 3% per decade; farmland decreased at the same rate. Additionally, the rural landscape patterns in the Beijing-Tianjin region were dominated by fragmentation, dispersion, and heterogeneity and moved from complex to regular. Water bodies displayed the most fragmented natural landscape; their number of patches increased by 36%, though their network characteristics were maintained. Forestland was the most concentrated natural landscape. In this study, theoretical support and a scientific reference for the optimization of rural landscape patterns and the improvement in rural living environments in rapidly urbanizing areas are provided.}, } @article {pmid38708866, year = {2024}, author = {Villarreal-Rosas, J and Brown, CJ and Andradi-Brown, DA and Domínguez, R and Jacobo, P and Martínez, A and Mascote, C and Najera, E and Paiz, Y and Vázquez Moran, VH and Villarreal, J and Adame, MF}, title = {Integrating socioeconomic and ecological data into restoration practice.}, journal = {Conservation biology : the journal of the Society for Conservation Biology}, volume = {38}, number = {4}, pages = {e14286}, doi = {10.1111/cobi.14286}, pmid = {38708866}, issn = {1523-1739}, support = {//Advance Queensland Industry Research Fellowship/ ; //Jeremy and Hannelore Grantham Environmental Trust/ ; FT210100792//Australian Research Council/ ; }, mesh = {*Conservation of Natural Resources/methods/economics ; Mexico ; *Socioeconomic Factors ; Environmental Restoration and Remediation/economics ; Ecosystem ; Decision Support Techniques ; }, abstract = {Driven by the United Nations Decade on Restoration and international funding initiatives, such as the Mangrove Breakthrough, investment in mangrove restoration is expected to increase. Yet, mangrove restoration efforts frequently fail, usually because of ad hoc site-selection processes that do not consider mangrove ecology and the socioeconomic context. Using decision analysis, we developed an approach that accounts for socioeconomic and ecological data to identify sites with the highest likelihood of mangrove restoration success. We applied our approach in the Biosphere Reserve Marismas Nacionales Nayarit, Mexico, an area that recently received funding for implementing mangrove restoration actions. We identified 468 potential restoration sites, assessed their restorability potential based on socioeconomic and ecological metrics, and ranked sites for implementation with spatial optimization. The metrics we used included favorable conditions for propagules to establish and survive under sea-level rise, provision of ecosystem services, and community dynamics. Sites that were selected based on socioeconomic or ecological metrics alone had lower likelihood of mangrove restoration success than sites that were selected based on integrated socioeconomic and ecological metrics. For example, selecting sites based on only socioeconomic metrics captured 16% of the maximum attainable value of functioning mangroves able to provide propagules to potential restoration sites, whereas selecting sites based on ecological and socioeconomic metrics captured 46% of functioning mangroves. Our approach was developed as part of a collaboration between nongovernmental organizations, local government, and academics under rapid delivery time lines given preexisting mangrove restoration implementation commitments. The systematic decision process we used integrated socioeconomic and ecological considerations even under short delivery deadlines, and our approach can be adapted to help mangrove restoration site-selection decisions elsewhere.}, } @article {pmid38707490, year = {2023}, author = {Boyes, D and Phillips, D and , and , and , and , and , and , }, title = {The genome sequence of the Early Thorn, Selenia dentaria (Fabricius, 1775).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {485}, pmid = {38707490}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual male Selenia dentaria (the Early Thorn; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 1,030.8 megabases in span. Most of the assembly is scaffolded into 30 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.41 kilobases in length. Gene annotation of this assembly on Ensembl identified 21,390 protein coding genes.}, } @article {pmid38705187, year = {2024}, author = {Meier, R and Hartop, E and Pylatiuk, C and Srivathsan, A}, title = {Towards holistic insect monitoring: species discovery, description, identification and traits for all insects.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {379}, number = {1904}, pages = {20230120}, pmid = {38705187}, issn = {1471-2970}, mesh = {*Insecta/physiology/classification/genetics ; Animals ; *DNA Barcoding, Taxonomic/methods ; Biodiversity ; }, abstract = {Holistic insect monitoring needs scalable techniques to overcome taxon biases, determine species abundances, and gather functional traits for all species. This requires that we address taxonomic impediments and the paucity of data on abundance, biomass and functional traits. We here outline how these data deficiencies could be addressed at scale. The workflow starts with large-scale barcoding (megabarcoding) of all specimens from mass samples obtained at biomonitoring sites. The barcodes are then used to group the specimens into molecular operational taxonomic units that are subsequently tested/validated as species with a second data source (e.g. morphology). New species are described using barcodes, images and short diagnoses, and abundance data are collected for both new and described species. The specimen images used for species discovery then become the raw material for training artificial intelligence identification algorithms and collecting trait data such as body size, biomass and feeding modes. Additional trait data can be obtained from vouchers by using genomic tools developed by molecular ecologists. Applying this pipeline to a few samples per site will lead to greatly improved insect monitoring regardless of whether the species composition of a sample is determined with images, metabarcoding or megabarcoding. This article is part of the theme issue 'Towards a toolkit for global insect biodiversity monitoring'.}, } @article {pmid38704010, year = {2024}, author = {Song, X and Li, C and Qiu, Z and Wang, C and Zeng, Q}, title = {Ecotoxicological effects of polyethylene microplastics and lead (Pb) on the biomass, activity, and community diversity of soil microbes.}, journal = {Environmental research}, volume = {252}, number = {Pt 3}, pages = {119012}, doi = {10.1016/j.envres.2024.119012}, pmid = {38704010}, issn = {1096-0953}, mesh = {*Soil Microbiology ; *Lead/toxicity ; *Soil Pollutants/toxicity ; *Microplastics/toxicity ; *Biomass ; *Polyethylene/toxicity ; Soil/chemistry ; Ecotoxicology ; }, abstract = {Microplastics and heavy metals are ubiquitous and persistent contaminants that are widely distributed worldwide, yet little is known about the effects of their interaction on soil ecosystems. A soil incubation experiment was conducted to investigate the individual and combined effects of polyethylene microplastics (PE-MPs) and lead (Pb) on soil enzymatic activities, microbial biomass, respiration rate, and community diversity. The results indicate that the presence of PE-MPs notably reduced soil pH and elevated soil Pb bioavailability, potentially exacerbated the combined toxicity on the biogeochemical cycles of soil nutrients, microbial biomass carbon and nitrogen, and the activities of soil urease, sucrase, and alkaline phosphatase. Soil CO2 emissions increased by 7.9% with PE-MPs alone, decreased by 46.3% with single Pb, and reduced by 69.4% with PE-MPs and Pb co-exposure, compared to uncontaminated soils. Specifically, the presence of PE-MPs and Pb, individually and in combination, facilitated the soil metabolic quotient, leading to reduced microbial metabolic efficiency. Moreover, the addition of Pb and PE-MPs modified the composition of the microbial community, leading to the enrichment of specific taxa. Tax4Fun analysis showed the effects of Pb, PE-MPs and their combination on the biogeochemical processes and ecological functions of microbes were mainly by altering amino acid metabolism, carbohydrate metabolism, membrane transport, and signal transduction. These findings offer valuable insights into the ecotoxicological effects of combined PE-MPs and Pb on soil microbial dynamics, reveals key assembly mechanisms and environmental drivers, and highlights the potential threat of MPs and heavy metals to the multifunctionality of soil ecosystems.}, } @article {pmid38703986, year = {2024}, author = {Li, JY and Yao, S and Mo, Z and Miao, Y and Chen, Y and He, W and Jin, L and Tang, W}, title = {Submerged plant-biochar composite system exhibits effective control over residual organic pollutants in the benthic organisms of aquaculture ponds.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {351}, number = {}, pages = {124078}, doi = {10.1016/j.envpol.2024.124078}, pmid = {38703986}, issn = {1873-6424}, mesh = {*Aquaculture ; *Water Pollutants, Chemical/analysis/metabolism ; *Charcoal/chemistry ; *Ponds/chemistry ; *Geologic Sediments/chemistry ; Corbicula ; Biodegradation, Environmental ; Hydrocharitaceae/metabolism ; Animals ; }, abstract = {As of now, submerged plants and biochar have demonstrated significant benefits in aquaculture pond sediment remediation. However, there is limited research on the synergistic effects of biochar and submerged plants in mitigating hydrophobic organic contaminant (HOC) accumulation in aquaculture benthic organisms and in controlling the nutrient (nitrogen and phosphorus) levels in aquaculture water. This study assesses a submerged plant-biochar system's efficacy in removing HOCs from simulated freshwater aquaculture ponds. Vallisneria natans was planted in sediment with varying levels of wheat straw biochar, while Corbicula fluminea served as the targeted benthic organism. The bioaccumulation experiment identified the optimal biochar ratio for the Vallisneria natans-biochar system in controlling HOCs in aquaculture products. Analyses included final accumulation concentrations in benthic organisms, changes in freely-dissolved concentrations in aquaculture sediment, and a mass balance calculation to explore key factors in their removal from the system. Results indicated that the Vallisneria natans-1.5% biochar composite system achieved optimal control of HOCs in sediment and aquaculture products. Biochar addition to the sediment in the composite system demonstrated a "promotion with low addition, inhibition with high addition" effect on Vallisneria natans growth. Notably, the addition of 1.5% biochar (VN1.5 group) significantly promoted the growth of Vallisneria natans leaves and roots. Comparing the final pollutant proportions in different environmental media, concentrations in water (0.20%-1.8%), clam accumulation (0.032%-0.11%), and plant absorption (0.10%-0.44%) constituted a minimal portion of the overall pollutant load in the system. The majority of pollutants (24%-65%) were degraded in the aquaculture environment, with microbial degradation likely playing a predominant role. Bacterial phyla, particularly Proteobacteria and Firmicutes, were identified as potential direct contributors to pollutant degradation in the Vallisneria natans-biochar system.}, } @article {pmid38696025, year = {2024}, author = {Xiao, Y and Luan, H and Lu, S and Xing, M and Guo, C and Qian, R and Xiao, X}, title = {Correction: Toxic effects of atmospheric deposition in mining areas on wheat seedlings.}, journal = {Environmental geochemistry and health}, volume = {46}, number = {6}, pages = {199}, doi = {10.1007/s10653-024-01986-5}, pmid = {38696025}, issn = {1573-2983}, } @article {pmid38689759, year = {2024}, author = {Falk, S and Poole, O and , and , and , and , and , and , and , }, title = {The genome sequence of a conopid fly, Myopa testacea (Linnaeus, 1767).}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {99}, pmid = {38689759}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual male Myopa testacea (conopid fly; Arthropoda; Insecta; Diptera; Conopidae). The genome sequence is 243.3 megabases in span. Most of the assembly is scaffolded into 5 chromosomal pseudomolecules, including the X and Y sex chromosomes. The mitochondrial genome has also been assembled and is 17.61 kilobases in length. Gene annotation of this assembly on Ensembl identified 25,472 protein coding genes.}, } @article {pmid38688803, year = {2024}, author = {Binion, KE and Perreira, KM and Villa Torres, L and White, JT and Hernandez, GC and Kaefer, M and Misseri, R and Ross, S and Chan, KH}, title = {A multi-site cultural and linguistic adaptation of a hypospadias decision aid for Latinx communities.}, journal = {Journal of pediatric urology}, volume = {20}, number = {4}, pages = {674.e1-674.e9}, pmid = {38688803}, issn = {1873-4898}, support = {UL1 TR002489/TR/NCATS NIH HHS/United States ; UM1 TR004406/TR/NCATS NIH HHS/United States ; }, mesh = {Humans ; Male ; *Hispanic or Latino/psychology ; *Hypospadias/ethnology/surgery/psychology ; *Decision Support Techniques ; Focus Groups ; Parents/psychology ; Child, Preschool ; Female ; Language ; Linguistics ; Cultural Characteristics ; }, abstract = {INTRODUCTION: Latinx, Spanish-speaking (LSS) patients are more likely to experience decisional conflict and regret about healthcare decisions than non-Hispanic, white, English-speaking patients.

OBJECTIVE: To adapt the Hypospadias Hub (Hub), a rigorously developed and tested web-based decision aid (DA), for LSS parents.

METHODS: Guided by the Ecological Validity Model (EVM), a heuristic framework was followed to culturally adapt the Hub (see Extended Summary Figure). In stage 1, recommendations were obtained from a focus group with members of the institution's Latinx Community Review Board (Latinx CRB) and semi-structured interviews with pediatricians with Latinx-focused practices. In stage 2, preliminary cultural modifications were made, the Hub was translated into Spanish, and a second focus group with the Latinx CRB was convened to review the revised Hub. In stage 3, semi-structured interviews with LSS parents of healthy boys (i.e., without hypospadias) ≤ 5 years old were conducted to identify any cultural adaptations and/or usability issues regarding the revised Hub. In stage 4, based on parents' feedback, final revisions to the Hub were made. The focus groups and parent interviews were conducted in Spanish; then, the recordings were professionally transcribed in Spanish and translated into English. Interviews with pediatricians were conducted in English; then, the recordings were professionally transcribed. Three coders conducted a qualitative content analysis to identify areas for revision. Changes were applied iteratively.

RESULTS: Participants included 3 Latinx CRB members (2 women, 1 did not disclose gender; mean age = 48.3, SD = 21.2), 3 non-Latinx pediatricians (2 women, 1 man; mean age = 49.6, SD = 9.1), and 5 Latinx mothers (mean age = 34.0, SD = 1.26). Participants recommended: 1) featuring video testimonials from Latinx families or including Spanish voice-overs/subtitles; 2) diversifying racial/ethnic/geographic representation and including extended families in photographs/illustrations; 3) adding information about health insurance coverage and circumcision, 4) reassuring parents that the condition is not their fault, 5) considering cultural values (e.g., reliance on expert advice), and 6) clarifying medical terminology. Feedback related to seven EVM dimensions: concepts, content, context, goals, language, metaphors, and methods.

DISCUSSION: Participants perceived the Hub to be informative in guiding parents' treatment decisions. Revisions were reasonable and acceptable for a linguistic and cultural adaptation for LSS parents.

CONCLUSIONS: We identified and implemented preliminary cultural modifications to the Hub and applied user-centered design methods to test and revise the website. The product is a culturally appropriate DA for LSS parents. Next, English and Spanish-versions of the Hub will be tested in a randomized controlled trial.}, } @article {pmid38688387, year = {2024}, author = {Hu, YL and Liu, Y and Fu, W and Yang, H}, title = {Efficiency and mechanism of enhanced norfloxacin removal using amorphous TiO2-modified biochar.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {351}, number = {}, pages = {124027}, doi = {10.1016/j.envpol.2024.124027}, pmid = {38688387}, issn = {1873-6424}, mesh = {*Charcoal/chemistry ; *Titanium/chemistry ; *Norfloxacin/chemistry ; Adsorption ; *Water Pollutants, Chemical/chemistry ; Anti-Bacterial Agents/chemistry ; Wastewater/chemistry ; Waste Disposal, Fluid/methods ; }, abstract = {Inadequate treatment of antibiotic-contaminated wastewater, including compounds such as norfloxacin (NOR), poses a substantial treat to both ecological safety and human well-being. An innovative approach was devised to address NOR pollution using amorphous TiO2 modified biochar (A-TiO2/BC) prepared via sol-gel impregnation. The resultant had a commendably specific surface area of 131.8 m[2]/g[-1], which was 1.91 times more than the original surface area of unmodified BC. A-TiO2/BC also exhibited abundant hydroxyl and oxygen-containing functional groups, thereby provided adequately active sites for NOR adsorption. R[2] values obtained from NOR isotherm adsorption models descended in order of Freundlich < Temkin < Sips < Langmuir, which indicated that the NOR removal by A-TiO2/BC mainly complied with monolayer adsorption accompanied by heterogeneous surface adsorption. Under weakly acidic conditions, NOR adsorption benefits from the synergistic physicochemical interactions of A-TiO2 and BC. Notably, A-TiO2/BC demonstrated an impressive NOR adsorption capacity of up to 78.14 mg g[-1], with a dosage of 20 mg L[-1] at 25 °C under pH 6. Such A-TiO2 modified biochar thus presents a promising alternative for NOR removal.}, } @article {pmid38688113, year = {2024}, author = {Ghani, MI and Yi, B and Rehmani, MS and Wei, X and Siddiqui, JA and Fan, R and Liu, Y and El-Sheikh, MA and Chen, X and Ahmad, P}, title = {Potential of melatonin and Trichoderma harzianum inoculation in ameliorating salt toxicity in watermelon: Insights into antioxidant system, leaf ultrastructure, and gene regulation.}, journal = {Plant physiology and biochemistry : PPB}, volume = {211}, number = {}, pages = {108639}, doi = {10.1016/j.plaphy.2024.108639}, pmid = {38688113}, issn = {1873-2690}, mesh = {*Citrullus/microbiology/drug effects/metabolism ; *Melatonin/pharmacology ; *Antioxidants/metabolism ; *Plant Leaves/drug effects/metabolism ; *Gene Expression Regulation, Plant/drug effects ; Salt Stress ; Hypocreales ; Photosynthesis/drug effects ; Oxidative Stress/drug effects ; }, abstract = {Melatonin (MT) is an extensively studied biomolecule with dual functions, serving as an antioxidant and a signaling molecule. Trichoderma Harzianum (TH) is widely recognized for its effectiveness as a biocontrol agent against many plant pathogens. However, the interplay between seed priming and MT (150 μm) in response to NaCl (100 mM) and its interaction with TH have rarely been investigated. This study aimed to evaluate the potential of MT and TH, alone and in combination, to mitigate salt stress (SS) in watermelon plants. The findings of this study revealed a significant decline in the morphological, physiological, and biochemical indices of watermelon seedlings exposed to SS. However, MT and TH treatments reduced the negative impact of salt stress. The combined application of MT and TH exerted a remarkable positive effect by increasing the growth, photosynthetic and gas exchange parameters, chlorophyll fluorescence indices, and ion balance (decreasing Na[+] and enhancing K[+]). MT and TH effectively alleviated oxidative injury by inhibiting hydrogen peroxide formation in saline and non-saline environments, as established by reduced lipid peroxidation and electrolyte leakage. Moreover, oxidative injury induced by SS on the cells was significantly mitigated by regulation of the antioxidant system, AsA-GSH-related enzymes, the glyoxalase system, augmentation of osmolytes, and activation of several genes involved in the defense system. Additionally, the reduction in oxidative damage was examined by chloroplast integrity via transmission electron microscopy (TEM). Overall, the results of this study provide a promising contribution of MT and TH in safeguarding the watermelon crop from oxidative damage induced by salt stress.}, } @article {pmid38686023, year = {2024}, author = {Boyes, D and Blaxter, ML and , and , and , and , and , and , }, title = {The genome sequence of the Tipped Oak Case-bearer, Coleophora flavipennella (Duponchel 1843).}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {3}, pmid = {38686023}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual female Coleophora flavipennella (the Tipped Oak Case-bearer; Arthropoda; Insecta; Lepidoptera; Coleophoridae). The genome sequence is 989.3 megabases in span. Most of the assembly is scaffolded into 57 chromosomal pseudomolecules, including the W and Z sex chromosomes. The mitochondrial genome has also been assembled and is 15.77 kilobases in length.}, } @article {pmid38684755, year = {2024}, author = {Yang, P and Huang, G and Li, Y and Yu, L and Yin, Z and Li, Q}, title = {Identification of PANoptosis-related biomarkers and analysis of prognostic values in head and neck squamous cell carcinoma.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {9824}, pmid = {38684755}, issn = {2045-2322}, mesh = {Humans ; *Squamous Cell Carcinoma of Head and Neck/genetics/pathology/metabolism/mortality ; *Biomarkers, Tumor/metabolism/genetics ; Prognosis ; *Head and Neck Neoplasms/genetics/pathology/metabolism ; *Gene Expression Regulation, Neoplastic ; Female ; Male ; Computational Biology/methods ; Gene Expression Profiling ; Fas-Associated Death Domain Protein/metabolism/genetics ; Lymphatic Metastasis ; }, abstract = {PANoptosis plays a crucial role in cancer initiation and progression. However, the roles of PANoptosis-related genes (PARGs) in the prognosis and immune landscape of head and neck squamous cell carcinoma (HNSCC) remain unclear. Integrated bioinformatics analyses based on the data of HNSCC patients in the TCGA database were conducted. We extracted 48 PARGs expression profile and then conducted differentially expressed analysis, following building a Cox model to predict the survival of HNSCC patients. Subsequently, the relationships between the risk score, immune landscape, chemo-, and immune-therapy responses were analyzed, respectively. Moreover, we investigated the prognostic value, and further predicted the pathways influenced by PARGs. Finally, we identified the biological function of crucial PARGs. A total of 18 differentially expressed PARGs were identified in HNSCC, and a Cox model including CASP8, FADD, NLRP1, TNF, and ZBP1 was constructed, which showed that the risk score was associated with the prognosis as well as immune infiltration of HNSCC patients, and the risk score could be regarded as an independent biomarker. Additionally, patients with high-risk score might be an indicator of lymph node metastasis and advanced clinical stage. High-risk scores also contributed to the chemotherapy resistance and immune escape of HNSCC patients. In addition, FADD and ZBP1 played a crucial role in various cancer-related pathways, such as the MAPK, WNT, and MTOR signaling pathways. On the other hand, we suggested that FADD facilitated the progression and 5-fluorouracil (5-FU) resistance of HNSCC cells. A signature based on PANoptosis showed great predictive power for lymph node metastasis and advanced stage, suggesting that the risk score might be an independent prognostic biomarker for HNSCC. Meanwhile, FADD, identified as a prognostic biomarker, may represent an effective therapeutic target for HNSCC.}, } @article {pmid38684726, year = {2024}, author = {Poquérusse, J and Brown, CL and Gaillard, C and Doughty, C and Dalén, L and Gallagher, AJ and Wooller, M and Zimov, N and Church, GM and Lamm, B and Hysolli, E}, title = {Assessing contemporary Arctic habitat availability for a woolly mammoth proxy.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {9804}, pmid = {38684726}, issn = {2045-2322}, mesh = {Arctic Regions ; *Ecosystem ; Animals ; *Mammoths ; *Biomass ; Alaska ; Carbon/analysis/metabolism ; }, abstract = {Interest continues to grow in Arctic megafaunal ecological engineering, but, since the mass extinction of megafauna ~ 12-15 ka, key physiographic variables and available forage continue to change. Here we sought to assess the extent to which contemporary Arctic ecosystems are conducive to the rewilding of megaherbivores, using a woolly mammoth (M. primigenius) proxy as a model species. We first perform a literature review on woolly mammoth dietary habits. We then leverage Oak Ridge National Laboratories Distributive Active Archive Center Global Aboveground and Belowground Biomass Carbon Density Maps to generate aboveground biomass carbon density estimates in plant functional types consumed by the woolly mammoth at 300 m resolution on Alaska's North Slope. We supplement these analyses with a NASA Arctic Boreal Vulnerability Experiment dataset to downgrade overall biomass estimates to digestible levels. We further downgrade available forage by using a conversion factor representing the relationship between total biomass and net primary productivity (NPP) for arctic vegetation types. Integrating these estimates with the forage needs of woolly mammoths, we conservatively estimate Alaska's North Slope could support densities of 0.0-0.38 woolly mammoth km[-2] (mean 0.13) across a variety of habitats. These results may inform innovative rewilding strategies.}, } @article {pmid38683839, year = {2024}, author = {Ma, R and Li, C and Gao, A and Jiang, N and Li, J and Hu, W and Feng, X}, title = {Tick species diversity and potential distribution alternation of dominant ticks under different climate scenarios in Xinjiang, China.}, journal = {PLoS neglected tropical diseases}, volume = {18}, number = {4}, pages = {e0012108}, pmid = {38683839}, issn = {1935-2735}, mesh = {*Ticks/classification ; *Tick-Borne Diseases/epidemiology/parasitology ; China/epidemiology ; *Datasets as Topic ; Biodiversity ; Animal Distribution ; Humans ; Animals ; Climate Change ; }, abstract = {Ticks are a hematophagous parasite and a vector of pathogens for numerous human and animal diseases of significant importance. The expansion of tick distribution and the increased risk of tick-borne diseases due to global climate change necessitates further study of the spatial distribution trend of ticks and their potential influencing factors. This study constructed a dataset of tick species distribution in Xinjiang for 60 years based on literature database retrieval and historical data collection (January 1963-January 2023). The distribution data were extracted, corrected, and deduplicated. The dominant tick species were selected for analysis using the MaxEnt model to assess their potential distribution in different periods under the current and BCC-CSM2.MR mode scenarios. The results indicated that there are eight genera and 48 species of ticks in 108 cities and counties of Xinjiang, with Hyalomma asiaticum, Rhipicephalus turanicus, Dermacentor marginatus, and Haemaphysalis punctatus being the top four dominant species. The MaxEnt model analysis revealed that the suitability areas of the four dominant ticks were mainly distributed in the north of Xinjiang, in areas such as Altay and Tacheng Prefecture. Over the next four periods, the medium and high suitable areas within the potential distribution range of the four tick species will expand towards the northwest. Additionally, new suitability areas will emerge in Altay, Changji Hui Autonomous Prefecture, and other local areas. The 60-year tick dataset in this study provides a map of preliminary tick distribution in Xinjiang, with a diverse array of tick species and distribution patterns throughout the area. In addition, the MaxEnt model revealed the spatial change characteristics and future distribution trend of ticks in Xinjiang, which can provide an instrumental data reference for tick monitoring and tick-borne disease risk prediction not only in the region but also in other countries participating in the Belt and Road Initiative.}, } @article {pmid38683244, year = {2024}, author = {Bai, Y and Song, K and Gao, M and Ma, J and Zhou, Y and Liu, H and Zeng, H and Wang, J and Zheng, X}, title = {Using multi-omics to explore the effect of Bacillus velezensis SAAS-63 on resisting nutrient stress in lettuce.}, journal = {Applied microbiology and biotechnology}, volume = {108}, number = {1}, pages = {313}, pmid = {38683244}, issn = {1432-0614}, mesh = {*Bacillus/metabolism/genetics ; *Lactuca/microbiology/growth & development ; *Rhizosphere ; *Soil Microbiology ; *Nutrients/metabolism ; *Stress, Physiological ; Plant Roots/microbiology ; Microbiota ; Multiomics ; }, abstract = {To avoid the unreasonable use of chemical fertilizer, an environmentally friendly means of improving soil fertility is required. This study explored the role of the plant growth-promoting rhizosphere bacteria (PGPR) strain Bacillus velezensis SAAS-63 in improving nutrient stress in lettuce. Compared with no inoculation, B. velezensis SAAS-63 inoculants exhibited significantly increased fresh weight, root length, and shoot height under nutrient deficiency, as well as improved antioxidant activities and proline contents. The exogenous addition of B. velezensis SAAS-63 also significantly increased the accumulation of macroelements and micronutrients in lettuce. To elucidate the resistance mechanisms induced by B. velezensis SAAS-63 under nutrient stress, high-throughput sequencing and multi-omics analysis were performed. Inoculation with B. velezensis SAAS-63 altered the microbial community of the rhizosphere and increased the relative abundances of Streptomyces, Actinoallomurus, Verrucomicrobia, and Chloroflexi. It is worth noting that the inoculant SAAS-63 can affect plant rhizosphere metabolism. The inoculant changed the metabolic flow of phenylpropanoid metabolic pathway under nutrient deficiency and promoted phenylalanine to participate more in the synthesis of lignin precursors and coumarin substances by inhibiting the synthesis of flavone and isoflavone, thus improving plant resistance. This study showed that the addition of inoculant SAAS-63 could help plants recruit microorganisms to decompose and utilize trehalose and re-established the carbon metabolism of the plant rhizosphere. Additionally, microbes were found to be closely related to the accumulation of metabolites based on correlation analysis. The results indicated that the addition of PGPRs has an important role in regulating soil rhizosphere microbes and metabolism, providing valuable information for understanding how PGPRs affect complex biological processes and enhance plant adaptation to nutrient deficiency. KEY POINTS: • Inoculation with SAAS-63 significantly promoted plant growth under nutrient-deficient conditions • Inoculation with SAAS-63 affected rhizosphere microbial diversity and community structure • Inoculation with SAAS-63 affected plant rhizosphere metabolism and induced plants to synthesize substances that resist stress.}, } @article {pmid38680650, year = {2023}, author = {Boyes, D and Hammond, J and , and , and , and , and , and , }, title = {The genome sequence of the Crescent Bell, Epinotia bilunana (Haworth, 1811).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {163}, pmid = {38680650}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual male Epinotia bilunana (the Crescent Bell; Arthropoda; Insecta; Lepidoptera; Tortricidae). The genome sequence is 659.0 megabases in span. Most of the assembly is scaffolded into 28 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.4 kilobases in length.}, } @article {pmid38677227, year = {2024}, author = {Alves, RA and Santos, MMD and Rudke, AP and Francisquetti Venturin, PR and Martins, JA}, title = {Site selection for nature-based solutions for stormwater management in urban areas: An approach combining GIS and multi-criteria analysis.}, journal = {Journal of environmental management}, volume = {359}, number = {}, pages = {120999}, doi = {10.1016/j.jenvman.2024.120999}, pmid = {38677227}, issn = {1095-8630}, mesh = {*Geographic Information Systems ; Brazil ; *Conservation of Natural Resources/methods ; *Rain ; Ecosystem ; Sustainable Development ; }, abstract = {In recent years, particularly following the definition of the UN Sustainable Development Goals (SDGs) for 2030, Nature-Based Solutions (NBS) have gained considerable attention, capturing the interest of both the scientific community and policymakers committed to addressing urban environmental issues. However, the need for studies to guide decision-makers in identifying suitable locations for NBS implementation within urban stormwater management is evident. To address this gap, the present study employs a methodological approach grounded in multi-criteria analysis integrated with Geographic Information Systems (GIS) to identify areas with potential for NBS implementation. In this process, ten NBS were proposed and tested in the drainage area of a shallow tropical urban lake in Londrina, southern Brazil. Additionally, the study investigates areas hosting lower-income populations, a relevant aspect for public managers given the diverse economic subsidies required to implement NBS. Furthermore, the study incorporates a preliminary analysis that evaluates the potential ecosystem benefits to determine the most suitable NBS for a specific site. The result shows that all the ten analyzed NBS were deemed suitable for the study area. Rain barrels had the highest percentage coverage in the study area (37.1%), followed by tree pits (27.9%), and rain gardens (25.4%). Despite having the highest distribution in the basin area, rain barrels exhibited only moderate ecosystem benefits, prompting the prioritization of other NBS with more significant ecological advantages in the final integrated map. In summary, the methodology proposed showed to be a robust approach to selecting optimal solutions in densely populated urban areas.}, } @article {pmid38672746, year = {2024}, author = {Bakacsy, L and Kardos, LV and Szepesi, Á and Nagy, KN and Vasas, A and Feigl, G}, title = {Investigation of the Allelopathic Effect of Two Invasive Plant Species in Rhizotron System.}, journal = {Life (Basel, Switzerland)}, volume = {14}, number = {4}, pages = {}, pmid = {38672746}, issn = {2075-1729}, support = {FK129061//National Research, Development and Innovation Office (Hungary)/ ; }, abstract = {A key question in plant invasion biology is why invasive plants are more competitive in their introduced habitat than in their native habitat. Studies show that invasive species exhibit allelopathy, influencing other plants by releasing chemicals. Research on allelopathy uses in vitro tests, investigating effects on seed germination and seedling development. Although soil plays a role in modifying allelopathic effects, observations with soil are rare and almost nothing is known about the root development of test plants developing in soil and the effects of allelopathic compounds on root architecture. Our study evaluates the allelopathic effects of false indigo-bush (Amorpha fruticosa L.) and common milkweed (Asclepias syriaca L.) on oilseed rape growth as a model plant. The rhizotron system was used to study the effect of morphology and root architecture. Leaf-soil mixtures at 0.5%, 1%, and 5% concentrations were used. Shoot and root development was strongly inhibited at 5%. But there was no difference between the allelopathy of the two species, and the application of lower concentrations did not show any effect, demonstrating that soil has a significant modifying effect on their allelopathy. Our results highlight that the development of roots growing in the soil is also worth investigating in connection with allelopathy, which can strengthen the ecological importance of allelochemicals during successful invasions.}, } @article {pmid38670119, year = {2024}, author = {Atağ, G and Kaptan, D and Yüncü, E and Başak Vural, K and Mereu, P and Pirastru, M and Barbato, M and Leoni, GG and Güler, MN and Er, T and Eker, E and Yazıcı, TD and Kılıç, MS and Altınışık, NE and Çelik, EA and Morell Miranda, P and Dehasque, M and Floridia, V and Götherström, A and Bilgin, CC and Togan, İ and Günther, T and Özer, F and Hadjisterkotis, E and Somel, M}, title = {Population Genomic History of the Endangered Anatolian and Cyprian Mouflons in Relation to Worldwide Wild, Feral, and Domestic Sheep Lineages.}, journal = {Genome biology and evolution}, volume = {16}, number = {5}, pages = {}, pmid = {38670119}, issn = {1759-6653}, support = {/ERC_/European Research Council/International ; 772390//European Union's Horizon 2020 research and innovation programme/ ; //Scientific and Technological Research Council of Turkey/ ; //National Scholarship Programme/ ; //Swedish Research Council Vetenskapsrådet/ ; //Carl Tryggers Stiftelse för Vetenskaplig Forskning/ ; 772390/ERC_/European Research Council/International ; }, mesh = {Animals ; *Endangered Species ; Sheep/genetics ; *Sheep, Domestic/genetics ; Genome ; Genetic Variation ; }, abstract = {Once widespread in their homelands, the Anatolian mouflon (Ovis gmelini anatolica) and the Cyprian mouflon (Ovis gmelini ophion) were driven to near extinction during the 20th century and are currently listed as endangered populations by the International Union for Conservation of Nature. While the exact origins of these lineages remain unclear, they have been suggested to be close relatives of domestic sheep or remnants of proto-domestic sheep. Here, we study whole genome sequences of n = 5 Anatolian mouflons and n = 10 Cyprian mouflons in terms of population history and diversity, comparing them with eight other extant sheep lineages. We find reciprocal genetic affinity between Anatolian and Cyprian mouflons and domestic sheep, higher than all other studied wild sheep genomes, including the Iranian mouflon (O. gmelini). Studying diversity indices, we detect a considerable load of short runs of homozygosity blocks (<2 Mb) in both Anatolian and Cyprian mouflons, reflecting small effective population size (Ne). Meanwhile, Ne and mutation load estimates are lower in Cyprian compared with Anatolian mouflons, suggesting the purging of recessive deleterious variants in Cyprian sheep under a small long-term Ne, possibly attributable to founder effects, island isolation, introgression from domestic lineages, or differences in their bottleneck dynamics. Expanding our analyses to worldwide wild and feral Ovis genomes, we observe varying viability metrics among different lineages and a limited consistency between viability metrics and International Union for Conservation of Nature conservation status. Factors such as recent inbreeding, introgression, and unique population dynamics may have contributed to the observed disparities.}, } @article {pmid38668970, year = {2024}, author = {Muthye, V and Lavrov, DV}, title = {Characterization of the Mitochondrial Proteome in the Ctenophore Mnemiopsis leidyi Using MitoPredictor.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2757}, number = {}, pages = {239-257}, pmid = {38668970}, issn = {1940-6029}, mesh = {Animals ; *Ctenophora/metabolism/genetics ; *Proteome ; *Mitochondrial Proteins/metabolism/genetics ; Computational Biology/methods ; Mitochondria/metabolism ; Proteomics/methods ; Software ; }, abstract = {Mitochondrial proteomes have been experimentally characterized for only a handful of animal species. However, the increasing availability of genomic and transcriptomic data allows one to infer mitochondrial proteins using computational tools. MitoPredictor is a novel random forest classifier, which utilizes orthology search, mitochondrial targeting signal (MTS) identification, and protein domain content to infer mitochondrial proteins in animals. MitoPredictor's output also includes an easy-to-use R Shiny applet for the visualization and analysis of the results. In this article, we provide a guide for predicting and analyzing the mitochondrial proteome of the ctenophore Mnemiopsis leidyi using MitoPredictor.}, } @article {pmid38668514, year = {2024}, author = {Li, Q and Yao, S and Wen, H and Li, W and Jin, L and Huang, X}, title = {Improving Lead Phytoremediation Using Endophytic Bacteria Isolated from the Pioneer Plant Ageratina adenophora (Spreng.) from a Mining Area.}, journal = {Toxics}, volume = {12}, number = {4}, pages = {}, pmid = {38668514}, issn = {2305-6304}, support = {2020KY15017//Project for Enhancing Young and Middle-aged Teacher's Research Basis Ability in Colleges of Guangxi/ ; }, abstract = {This study aimed to isolate and characterise endophytic bacteria from the pioneer plant Ageratina adenophora in a mining area. Seven strains of metal-resistant endophytic bacteria that belong to five genera were isolated from the roots of A. adenophora. These strains exhibited various plant growth-promoting (PGP) capabilities. Sphingomonas sp. ZYG-4, which exhibited the ability to secrete indoleacetic acid (IAA; 53.2 ± 8.3 mg·L[-1]), solubilize insoluble inorganic phosphates (Phosphate solubilization; 11.2 ± 2.9 mg·L[-1]), and regulate root ethylene levels (1-aminocyclopropane-1-carboxylic acid deaminase activity; 2.87 ± 0.19 µM α-KB·mg[-1]·h[-1]), had the highest PGP potential. Therefore, Sphingomonas sp. ZYG-4 was used in a pot experiment to study its effect on the biomass and Pb uptake of both host (Ageratina adenophora) and non-host (Dysphania ambrosioides) plants. Compared to the uninoculated control, Sphingomonas sp. ZYG-4 inoculation increased the biomass of shoots and roots by 59.4% and 144.4% for A. adenophora and by 56.2% and 57.1% for D. ambrosioides, respectively. In addition, Sphingomonas sp. ZYG-4 inoculation enhanced Pb accumulation in the shoot and root by 268.9% and 1187.3% for A. adenophora, and by 163.1% and 343.8% for D. ambrosioides, respectively, compared to plants without bacterial inoculation. Our research indicates that endophytic bacteria are promising candidates for enhancing plant growth and facilitating microbe-assisted phytoremediation in heavy metal-contaminated soil.}, } @article {pmid38668506, year = {2024}, author = {Li, S and Yang, J and Zheng, K and He, S and Liu, Z and Song, S and Zeng, T}, title = {Effective Activation of Peroxymonosulfate by Oxygen Vacancy Induced Musa Basjoo Biochar to Degrade Sulfamethoxazole: Efficiency and Mechanism.}, journal = {Toxics}, volume = {12}, number = {4}, pages = {}, pmid = {38668506}, issn = {2305-6304}, support = {2023M743772//China Postdoctoral Science Foundation/ ; 22276172//National Natural Science Foundation of China/ ; 22076168//National Natural Science Foundation of China/ ; LR21E080001//Zhejiang Provincial Natural Science Foundation of China/ ; RF-B2022005//Fundamental Research Funds for the Provincial Universities of Zhejiang/ ; 2023C03132//"Leading Goose" R&D Program of Zhejiang/ ; }, abstract = {Biochar materials have garnered attention as potential catalysts for peroxymonosulfate (PMS) activation due to their cost-effectiveness, notable specific surface area, and advantageous structural properties. In this study, a suite of plantain-derived biochar (MBB-400, MBB-600, and MBB-800), possessing a well-defined pore structure and a substantial number of uniformly distributed active sites (oxygen vacancy, OVs), was synthesized through a facile calcination process at varying temperatures (400, 600, and 800 °C). These materials were designed for the activation of PMS in the degradation of sulfamethoxazole (SMX). Experimental investigations revealed that OVs not only functioned as enriched sites for pollutants, enhancing the opportunities for free radicals ([•]OH/SO4[•-]) and surface-bound radicals (SBRs) to attack pollutants, but also served as channels for intramolecular charge transfer leaps. This role contributed to a reduction in interfacial charge transfer resistance, expediting electron transfer rates with PMS, thereby accelerating the decomposition of pollutants. Capitalizing on these merits, the MBB-800/PMS system displayed a 61-fold enhancement in the conversion rate for SMX degradation compared to inactivated MBB/PMS system. Furthermore, the MBB-800 exhibited less cytotoxicity towards rat pheochromocytoma (PC12) cells. Hence, the straightforward calcination synthesis of MBB-800 emerges as a promising biochar catalyst with vast potential for sustainable and efficient wastewater treatment and environmental remediation.}, } @article {pmid38666081, year = {2024}, author = {Omar, KM and Kitundu, GL and Jimoh, AO and Namikelwa, DN and Lisso, FM and Babajide, AA and Olufemi, SE and Awe, OI}, title = {Investigating antimicrobial resistance genes in Kenya, Uganda and Tanzania cattle using metagenomics.}, journal = {PeerJ}, volume = {12}, number = {}, pages = {e17181}, pmid = {38666081}, issn = {2167-8359}, mesh = {Animals ; Cattle ; *Metagenomics ; Kenya/epidemiology ; Uganda/epidemiology ; Tanzania ; *Drug Resistance, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology/therapeutic use ; Genes, Bacterial/genetics ; }, abstract = {Antimicrobial resistance (AMR) is a growing problem in African cattle production systems, posing a threat to human and animal health and the associated economic value chain. However, there is a poor understanding of the resistomes in small-holder cattle breeds in East African countries. This study aims to examine the distribution of antimicrobial resistance genes (ARGs) in Kenya, Tanzania, and Uganda cattle using a metagenomics approach. We used the SqueezeMeta-Abricate (assembly-based) pipeline to detect ARGs and benchmarked this approach using the Centifuge-AMRplusplus (read-based) pipeline to evaluate its efficiency. Our findings reveal a significant number of ARGs of critical medical and economic importance in all three countries, including resistance to drugs of last resort such as carbapenems, suggesting the presence of highly virulent and antibiotic-resistant bacterial pathogens (ESKAPE) circulating in East Africa. Shared ARGs such as aph(6)-id (aminoglycoside phosphotransferase), tet (tetracycline resistance gene), sul2 (sulfonamide resistance gene) and cfxA_gen (betalactamase gene) were detected. Assembly-based methods revealed fewer ARGs compared to read-based methods, indicating the sensitivity and specificity of read-based methods in resistome characterization. Our findings call for further surveillance to estimate the intensity of the antibiotic resistance problem and wider resistome classification. Effective management of livestock and antibiotic consumption is crucial in minimizing antimicrobial resistance and maximizing productivity, making these findings relevant to stakeholders, agriculturists, and veterinarians in East Africa and Africa at large.}, } @article {pmid38662943, year = {2024}, author = {Lu, XY and Wu, HP and Ma, H and Li, H and Li, J and Liu, YT and Pan, ZY and Xie, Y and Wang, L and Ren, B and Liu, GK}, title = {Deep Learning-Assisted Spectrum-Structure Correlation: State-of-the-Art and Perspectives.}, journal = {Analytical chemistry}, volume = {96}, number = {20}, pages = {7959-7975}, doi = {10.1021/acs.analchem.4c01639}, pmid = {38662943}, issn = {1520-6882}, abstract = {Spectrum-structure correlation is playing an increasingly crucial role in spectral analysis and has undergone significant development in recent decades. With the advancement of spectrometers, the high-throughput detection triggers the explosive growth of spectral data, and the research extension from small molecules to biomolecules accompanies massive chemical space. Facing the evolving landscape of spectrum-structure correlation, conventional chemometrics becomes ill-equipped, and deep learning assisted chemometrics rapidly emerges as a flourishing approach with superior ability of extracting latent features and making precise predictions. In this review, the molecular and spectral representations and fundamental knowledge of deep learning are first introduced. We then summarize the development of how deep learning assist to establish the correlation between spectrum and molecular structure in the recent 5 years, by empowering spectral prediction (i.e., forward structure-spectrum correlation) and further enabling library matching and de novo molecular generation (i.e., inverse spectrum-structure correlation). Finally, we highlight the most important open issues persisted with corresponding potential solutions. With the fast development of deep learning, it is expected to see ultimate solution of establishing spectrum-structure correlation soon, which would trigger substantial development of various disciplines.}, } @article {pmid38658779, year = {2024}, author = {Andrianova, MA and Seplyarskiy, VB and Terradas, M and Sánchez-Heras, AB and Mur, P and Soto, JL and Aiza, G and Borràs, E and Kondrashov, FA and Kondrashov, AS and Bazykin, GA and Valle, L}, title = {Discovery of recessive effect of human polymerase δ proofreading deficiency through mutational analysis of POLD1-mutated normal and cancer cells.}, journal = {European journal of human genetics : EJHG}, volume = {32}, number = {7}, pages = {837-845}, pmid = {38658779}, issn = {1476-5438}, support = {PID2020-112595RB-I00//Ministry of Economy and Competitiveness | Agencia Estatal de Investigación (Spanish Agencia Estatal de Investigación)/ ; AGAUR 2017SGR1282; CERCA Program//Government of Catalonia | Departament de Salut, Generalitat de Catalunya/ ; ISCIII-AES-2017 PI17/01082//Ministry of Economy and Competitiveness | Instituto de Salud Carlos III (Institute of Health Carlos III)/ ; I5127-B//Austrian Science Fund (Fonds zur Förderung der Wissenschaftlichen Forschung)/ ; 429960716//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; ERC Consolidator (771209)//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; }, mesh = {Humans ; *DNA Polymerase III/genetics/metabolism ; Female ; Male ; Pedigree ; Heterozygote ; Genes, Recessive ; Neoplasms/genetics/pathology ; Mutation ; Germ-Line Mutation ; Adult ; }, abstract = {Constitutional heterozygous pathogenic variants in the exonuclease domain of POLE and POLD1, which affect the proofreading activity of the corresponding polymerases, cause a cancer predisposition syndrome characterized by increased risk of gastrointestinal polyposis, colorectal cancer, endometrial cancer and other tumor types. The generally accepted explanation for the connection between the disruption of the proofreading activity of polymerases epsilon and delta and cancer development is through an increase in the somatic mutation rate. Here we studied an extended family with multiple members heterozygous for the pathogenic POLD1 variant c.1421T>C p.(Leu474Pro), which segregates with the polyposis and cancer phenotypes. Through the analysis of mutational patterns of patient-derived fibroblasts colonies and de novo mutations obtained by parent-offspring comparisons, we concluded that heterozygous POLD1 L474P just subtly increases the somatic and germline mutation burden. In contrast, tumors developed in individuals with a heterozygous mutation in the exonuclease domain of POLD1, including L474P, have an extremely high mutation rate (>100 mut/Mb) associated with signature SBS10d. We solved this contradiction through the observation that tumorigenesis involves somatic inactivation of the wildtype POLD1 allele. These results imply that exonuclease deficiency of polymerase delta has a recessive effect on mutation rate.}, } @article {pmid38656485, year = {2024}, author = {Jiménez-Madrigal, JP and Till, BJ and Gatica-Arias, A}, title = {Genetic Diversity Assessment in Plants from Reduced Representation Sequencing Data.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2787}, number = {}, pages = {107-122}, pmid = {38656485}, issn = {1940-6029}, mesh = {*Genetic Variation ; *Plants/genetics ; *Genome, Plant ; Software ; Sequence Analysis, DNA/methods ; High-Throughput Nucleotide Sequencing/methods ; Computational Biology/methods ; Genomics/methods ; }, abstract = {Genetic diversity refers to the variety of genetic traits within a population or a species. It is an essential aspect of both plant ecology and plant breeding because it contributes to the adaptability, survival, and resilience of populations in changing environments. This chapter outlines a pipeline for estimating genetic diversity statistics from reduced representation or whole genome sequencing data. The pipeline involves obtaining DNA sequence reads, mapping the corresponding reads to a reference genome, calling variants from the alignments, and generating an unbiased estimation of nucleotide diversity and divergence between populations. The pipeline is suitable for single-end Illumina reads and can be adjusted for paired-end reads. The resulting pipeline provides a comprehensive approach for aligning and analyzing sequencing data to estimate genetic diversity.}, } @article {pmid38655208, year = {2023}, author = {Wu, SH and Ko, JC and Lin, RS and Chang-Yang, CH and Chang, HW}, title = {Evaluating community-wide temporal sampling in passive acoustic monitoring: A comprehensive study of avian vocal patterns in subtropical montane forests.}, journal = {F1000Research}, volume = {12}, number = {}, pages = {1299}, pmid = {38655208}, issn = {2046-1402}, mesh = {Animals ; *Vocalization, Animal/physiology ; *Acoustics ; *Birds/physiology ; *Forests ; Environmental Monitoring/methods ; }, abstract = {BACKGROUND: From passive acoustic monitoring (PAM) recordings, the vocal activity rate (VAR), vocalizations per unit of time, can be calculated and is essential for assessing bird population abundance. However, VAR is subject to influences from a range of factors, including species and environmental conditions. Identifying the optimal sampling design to obtain representative acoustic data for VAR estimation is crucial for research objectives. PAM commonly uses temporal sampling strategies to decrease the volume of recordings and the resources needed for audio data management. Yet, the comprehensive impact of this sampling approach on VAR estimation remains insufficiently explored.

METHODS: In this study, we used vocalizations extracted from recordings of 12 bird species, taken at 14 PAM stations situated in subtropical montane forests over a four-month period, to assess the impact of temporal sampling on VAR across three distinct scales: short-term periodic, diel, and hourly. For short-term periodic sampling analysis, we employed hierarchical clustering analysis (HCA) and the coefficient of variation (CV). Generalized additive models (GAMs) were utilized for diel sampling analysis, and we determined the average difference in VAR values per minute for the hourly sampling analysis.

RESULTS: We identified significant day and species-specific VAR fluctuations. The survey season was divided into five segments; the earliest two showed high variability and are best avoided for surveys. Data from days with heavy rain and strong winds showed reduced VAR values and should be excluded from analysis. Continuous recordings spanning at least seven days, extending to 14 days is optimal for minimizing sampling variance. Morning chorus recordings effectively capture the majority of bird vocalizations, and hourly sampling with frequent, shorter intervals aligns closely with continuous recording outcomes.

CONCLUSIONS: While our findings are context-specific, they highlight the significance of strategic sampling in avian monitoring, optimizing resource utilization and enhancing the breadth of monitoring efforts.}, } @article {pmid38654647, year = {2024}, author = {Spake, L and Hassan, A and Schaffnit, SB and Alam, N and Amoah, AS and Badjie, J and Cerami, C and Crampin, A and Dube, A and Kaye, MP and Kotch, R and Liew, F and McLean, E and Munthali-Mkandawire, S and Mwalwanda, L and Petersen, AC and Prentice, AM and Zohora, FT and Watts, J and Sear, R and Shenk, MK and Sosis, R and Shaver, JH}, title = {A practical guide to cross-cultural and multi-sited data collection in the biological and behavioural sciences.}, journal = {Proceedings. Biological sciences}, volume = {291}, number = {2021}, pages = {20231422}, pmid = {38654647}, issn = {1471-2954}, mesh = {Humans ; *Behavioral Sciences ; *Data Collection/methods ; Cross-Cultural Comparison ; Research Design ; Ecology/methods ; }, abstract = {Researchers in the biological and behavioural sciences are increasingly conducting collaborative, multi-sited projects to address how phenomena vary across ecologies. These types of projects, however, pose additional workflow challenges beyond those typically encountered in single-sited projects. Through specific attention to cross-cultural research projects, we highlight four key aspects of multi-sited projects that must be considered during the design phase to ensure success: (1) project and team management; (2) protocol and instrument development; (3) data management and documentation; and (4) equitable and collaborative practices. Our recommendations are supported by examples from our experiences collaborating on the Evolutionary Demography of Religion project, a mixed-methods project collecting data across five countries in collaboration with research partners in each host country. To existing discourse, we contribute new recommendations around team and project management, introduce practical recommendations for exploring the validity of instruments through qualitative techniques during piloting, highlight the importance of good documentation at all steps of the project, and demonstrate how data management workflows can be strengthened through open science practices. While this project was rooted in cross-cultural human behavioural ecology and evolutionary anthropology, lessons learned from this project are applicable to multi-sited research across the biological and behavioural sciences.}, } @article {pmid38649162, year = {2024}, author = {Niimura, Y and Biswa, BB and Kishida, T and Toyoda, A and Fujiwara, K and Ito, M and Touhara, K and Inoue-Murayama, M and Jenkins, SH and Adenyo, C and Kayang, BB and Koide, T}, title = {Synchronized Expansion and Contraction of Olfactory, Vomeronasal, and Taste Receptor Gene Families in Hystricomorph Rodents.}, journal = {Molecular biology and evolution}, volume = {41}, number = {4}, pages = {}, pmid = {38649162}, issn = {1537-1719}, support = {18K06359//JSPS KAKENHI/ ; JPMJAS2017//JST aXis/ ; 1B2020//National Institute of Genetics, NIG-Joint/ ; }, mesh = {Animals ; *Evolution, Molecular ; *Multigene Family ; *Phylogeny ; Receptors, G-Protein-Coupled/genetics ; *Receptors, Odorant/genetics ; Receptors, Pheromone/genetics/metabolism ; *Rodentia/genetics ; Smell/genetics ; Taste/genetics ; *Vomeronasal Organ/metabolism ; }, abstract = {Chemical senses, including olfaction, pheromones, and taste, are crucial for the survival of most animals. There has long been a debate about whether different types of senses might influence each other. For instance, primates with a strong sense of vision are thought to have weakened olfactory abilities, although the oversimplified trade-off theory is now being questioned. It is uncertain whether such interactions between different chemical senses occur during evolution. To address this question, we examined four receptor gene families related to olfaction, pheromones, and taste: olfactory receptor (OR), vomeronasal receptor type 1 and type 2 (V1R and V2R), and bitter taste receptor (T2R) genes in Hystricomorpha, which is morphologically and ecologically the most diverse group of rodents. We also sequenced and assembled the genome of the grasscutter, Thryonomys swinderianus. By examining 16 available genome assemblies alongside the grasscutter genome, we identified orthologous gene groups among hystricomorph rodents for these gene families to separate the gene gain and loss events in each phylogenetic branch of the Hystricomorpha evolutionary tree. Our analysis revealed that the expansion or contraction of the four gene families occurred synchronously, indicating that when one chemical sense develops or deteriorates, the others follow suit. The results also showed that V1R/V2R genes underwent the fastest evolution, followed by OR genes, and T2R genes were the most evolutionarily stable. This variation likely reflects the difference in ligands of V1R/V2Rs, ORs, and T2Rs: species-specific pheromones, environment-based scents, and toxic substances common to many animals, respectively.}, } @article {pmid38648741, year = {2024}, author = {Crauwels, C and Heidig, SL and Díaz, A and Vranken, WF}, title = {Large-scale structure-informed multiple sequence alignment of proteins with SIMSApiper.}, journal = {Bioinformatics (Oxford, England)}, volume = {40}, number = {5}, pages = {}, pmid = {38648741}, issn = {1367-4811}, support = {1SE5923N//Research Foundation Flanders/ ; }, mesh = {*Software ; *Proteins/chemistry ; *Sequence Alignment/methods ; *Sequence Analysis, Protein/methods ; Algorithms ; Amino Acid Sequence ; Computational Biology/methods ; Databases, Protein ; }, abstract = {SUMMARY: SIMSApiper is a Nextflow pipeline that creates reliable, structure-informed MSAs of thousands of protein sequences faster than standard structure-based alignment methods. Structural information can be provided by the user or collected by the pipeline from online resources. Parallelization with sequence identity-based subsets can be activated to significantly speed up the alignment process. Finally, the number of gaps in the final alignment can be reduced by leveraging the position of conserved secondary structure elements.

The pipeline is implemented using Nextflow, Python3, and Bash. It is publicly available on github.com/Bio2Byte/simsapiper.}, } @article {pmid38648214, year = {2024}, author = {Lauber, C and Zhang, X and Vaas, J and Klingler, F and Mutz, P and Dubin, A and Pietschmann, T and Roth, O and Neuman, BW and Gorbalenya, AE and Bartenschlager, R and Seitz, S}, title = {Deep mining of the Sequence Read Archive reveals major genetic innovations in coronaviruses and other nidoviruses of aquatic vertebrates.}, journal = {PLoS pathogens}, volume = {20}, number = {4}, pages = {e1012163}, pmid = {38648214}, issn = {1553-7374}, mesh = {Animals ; *Nidovirales/genetics ; *Genome, Viral ; *Coronavirus/genetics/classification ; *Phylogeny ; Vertebrates/virology/genetics ; Fishes/virology ; Evolution, Molecular ; Data Mining ; Nidovirales Infections/virology/genetics ; }, abstract = {Virus discovery by genomics and metagenomics empowered studies of viromes, facilitated characterization of pathogen epidemiology, and redefined our understanding of the natural genetic diversity of viruses with profound functional and structural implications. Here we employed a data-driven virus discovery approach that directly queries unprocessed sequencing data in a highly parallelized way and involves a targeted viral genome assembly strategy in a wide range of sequence similarity. By screening more than 269,000 datasets of numerous authors from the Sequence Read Archive and using two metrics that quantitatively assess assembly quality, we discovered 40 nidoviruses from six virus families whose members infect vertebrate hosts. They form 13 and 32 putative viral subfamilies and genera, respectively, and include 11 coronaviruses with bisegmented genomes from fishes and amphibians, a giant 36.1 kilobase coronavirus genome with a duplicated spike glycoprotein (S) gene, 11 tobaniviruses and 17 additional corona-, arteri-, cremega-, nanhypo- and nangoshaviruses. Genome segmentation emerged in a single evolutionary event in the monophyletic lineage encompassing the subfamily Pitovirinae. We recovered the bisegmented genome sequences of two coronaviruses from RNA samples of 69 infected fishes and validated the presence of poly(A) tails at both segments using 3'RACE PCR and subsequent Sanger sequencing. We report a genetic linkage between accessory and structural proteins whose phylogenetic relationships and evolutionary distances are incongruent with the phylogeny of replicase proteins. We rationalize these observations in a model of inter-family S recombination involving at least five ancestral corona- and tobaniviruses of aquatic hosts. In support of this model, we describe an individual fish co-infected with members from the families Coronaviridae and Tobaniviridae. Our results expand the scale of the known extraordinary evolutionary plasticity in nidoviral genome architecture and call for revisiting fundamentals of genome expression, virus particle biology, host range and ecology of vertebrate nidoviruses.}, } @article {pmid38646766, year = {2024}, author = {Hu, JY and Liu, LY and Dai, QL and Yang, B and Zhou, WJ}, title = {Evaluation of ecotourism suitability based on AHP-GIS: Taking Xiaoxiangling area of the Giant Panda National Park and the surrounding communities as an example.}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {35}, number = {3}, pages = {780-788}, doi = {10.13287/j.1001-9332.202403.020}, pmid = {38646766}, issn = {1001-9332}, mesh = {Animals ; *Conservation of Natural Resources ; China ; *Parks, Recreational ; *Ecosystem ; *Ursidae ; *Geographic Information Systems ; Recreation ; }, abstract = {The primary goal of national parks is to protect ecological environment, but also with the functions of scientific research, education, and recreation. Aiming for the realization of universal sharing, we used the analytic hierarchy process (AHP) to construct an ecotourism suitability evaluation system by selecting four factors, including landscape resources, ecological environment carrying capacity, recreation utilization capacity and social condition, taking Xiaoxiangling area of Giant Panda National Park and the surrounding communities as an example. We evaluated the ecotourism suitability based on GIS, and conducted a questionnaire survey of tourists, to propose suggestions on the functional zoning in terms of ecotourism suitability and subjective choice preferences of tourists. The results showed that the ecotourism suitability of the evaluation area could be classified into five levels. The most suitable areas were located nearby the natural landscape resources and far away from the core conservation area, and the least suitable areas distributed at the edge of the core conservation area. According to the results of suitability analysis, the evaluation area was divided into suitable development area, moderate development area, and restricted development area. Combined with the tourist preferences, we divided the recreational activities in the evaluation area into seven activities, namely, ecotourism, eco-camping, science education, leisure vacation, agricultural and animal husbandry culture experience, eco-education, and mountain adventure. These findings could help provide suitable services for different tourists and offer reference for the ecotourism developmental planning of the Xiaoxiangling area of the Giant Panda National Park.}, } @article {pmid38646687, year = {2024}, author = {Filatov, DA}, title = {ProSeq4: A user-friendly multiplatform program for preparation and analysis of large-scale DNA polymorphism datasets.}, journal = {Molecular ecology resources}, volume = {24}, number = {5}, pages = {e13962}, pmid = {38646687}, issn = {1755-0998}, support = {BB/P009808/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {*Software ; *Polymorphism, Genetic ; *Computational Biology/methods ; Sequence Analysis, DNA/methods ; }, abstract = {Preparation of DNA polymorphism datasets for analysis is an important step in evolutionary genetic and molecular ecology studies. Ever-growing dataset sizes make this step time consuming, but few convenient software tools are available to facilitate processing of large-scale datasets including thousands of sequence alignments. Here I report "processor of sequences v4" (proSeq4)-a user-friendly multiplatform software for preparation and evolutionary genetic analyses of genome- or transcriptome-scale sequence polymorphism datasets. The program has an easy-to-use graphic user interface and is designed to process and analyse many thousands of datasets. It supports over two dozen file formats, includes a flexible sequence editor and various tools for data visualization, quality control and most commonly used evolutionary genetic analyses, such as NJ-phylogeny reconstruction, DNA polymorphism analyses and coalescent simulations. Command line tools (e.g. vcf2fasta) are also provided for easier integration into bioinformatic pipelines. Apart of molecular ecology and evolution research, proSeq4 may be useful for teaching, e.g. for visual illustration of different shapes of phylogenies generated with coalescent simulations in different scenarios. ProSeq4 source code and binaries for Windows, MacOS and Ubuntu are available from https://sourceforge.net/projects/proseq/.}, } @article {pmid38644930, year = {2023}, author = {Boyes, D and Boyes, C and , and , and , and , and , and , }, title = {The genome sequence of the Scalloped Oak, Crocallis elinguaria (Linneas, 1758).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {426}, pmid = {38644930}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual female Crocallis elinguaria (the Scalloped Oak; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 430.4 megabases in span. Most of the assembly is scaffolded into 17 chromosomal pseudomolecules, including the Z and W sex chromosomes. The mitochondrial genome has also been assembled and is 16.86 kilobases in length. Gene annotation of this assembly on Ensembl identified 17,741 protein coding genes.}, } @article {pmid38644519, year = {2024}, author = {Chen, J and Lin, JJ and Wang, W and Huang, H and Pan, Z and Ye, G and Dong, S and Lin, Y and Lin, C and Huang, Q}, title = {EV-COMM: A database of interspecies and intercellular interactions mediated by extracellular vesicles.}, journal = {Journal of extracellular vesicles}, volume = {13}, number = {4}, pages = {e12442}, pmid = {38644519}, issn = {2001-3078}, support = {2021J06037//Fujian Provincial Department of Science and Technology/ ; 2022T3063//Fujian Provincial Department of Science and Technology/ ; 32161143016//National Natural Science Foundation of China/ ; 42177362//National Natural Science Foundation of China/ ; 42250410328//National Natural Science Foundation of China/ ; CAS-WX2021SF-0302//Chinese Academy of Sciences/ ; NO. NBSDC-DB-21//National Basic Science Data Center "Environment Health DataBase"/ ; }, mesh = {Animals ; Humans ; *Cell Communication ; Databases, Factual ; *Extracellular Vesicles/metabolism ; MicroRNAs/metabolism/genetics ; }, abstract = {Intra- and inter-organismal interactions play a crucial role in the maintenance and function of individuals, as well as communities. Extracellular vesicles (EVs) have been identified as effective mediators for the communication both within and between species. They can carry and transport molecular cargoes to transmit biological messages. Several databases (ExoBCD, ExoCarta, EVpedia, EV-TRACK, Vesiclepedia) complied the cargoes information including DNA, RNA, protein, lipid and metabolite associated with EVs. Databases that refer to the complete records on both donor and recipient information are warranted to facilitate the understanding of the interaction across cells and species. In this study, we developed a database that compiled the records equipped with a structured process of EV-mediated interaction. The sources of donor and recipient were classified by cell type, tissues/organs and species, thus providing an extended knowledge of cell-cell, species-species interaction. The isolation and identification methods were presented for assessing the quality of EVs. Information on functional cargoes was included, where microRNA was linked to a prediction server to broaden its potential effects. Physiological and pathological context was marked to show the environment where EVs functioned. At present, a total of 1481 data records in our database, including 971 cell-cell interactions belonging to more than 40 different tissues/organs, and 510 cross-species records. The database provides a web interface to browse, search, visualize and download the interaction records. Users can search for interactions by selecting the context of interest or specific cells/species types, as well as functional cargoes. To the best of our knowledge, the database is the first comprehensive database focusing on interactions between donor and recipient cells or species mediated by EVs, serving as a convenient tool to explore and validate interactions. The Database, shorten as EV-COMM (EV mediated communication) is freely available at http://sdc.iue.ac.cn/evs/list/ and will be continuously updated.}, } @article {pmid38643978, year = {2024}, author = {Rosbakh, S and Carta, A and Fernández-Pascual, E and Phartyal, SS and Dayrell, RLC and Mattana, E and Saatkamp, A and Vandelook, F and Baskin, JM and Baskin, CC}, title = {Large dataset analyses advance knowledge of seed ecology and evolutionary biology.}, journal = {The New phytologist}, volume = {242}, number = {6}, pages = {2399-2400}, doi = {10.1111/nph.19752}, pmid = {38643978}, issn = {1469-8137}, support = {//Novo Nordisk Foundation/ ; }, mesh = {*Biological Evolution ; *Seeds/physiology/genetics ; *Ecology ; Datasets as Topic ; }, } @article {pmid38643126, year = {2024}, author = {Xiao, W and Chen, YL and Du, LY and Wu, J and Wang, Z and Mao, B and Wen, FQ and Gibson, PG and McDonald, VM and Yu, H and Fu, JJ}, title = {Bacterial interactome disturbance in chronic obstructive pulmonary disease clinical stability and exacerbations.}, journal = {Respiratory research}, volume = {25}, number = {1}, pages = {173}, pmid = {38643126}, issn = {1465-993X}, support = {No.82100046//National Natural Science Foundation of China/ ; No.81870014//National Natural Science Foundation of China/ ; 2023NSFSC1460//Sichuan Science and Technology Program of China/ ; 2020YFS0145//Sichuan Science and Technology Program of China/ ; }, mesh = {Humans ; *Dysbiosis ; *Pulmonary Disease, Chronic Obstructive/drug therapy ; Lung ; Haemophilus ; Sputum/microbiology ; Disease Progression ; }, abstract = {RATIONALE: Our understanding of airway dysbiosis in chronic obstructive pulmonary disease (COPD) remains incomplete, which may be improved by unraveling the complexity in microbial interactome.

OBJECTIVES: To characterize reproducible features of airway bacterial interactome in COPD at clinical stability and during exacerbation, and evaluate their associations with disease phenotypes.

METHODS: We performed weighted ensemble-based co-occurrence network analysis of 1742 sputum microbiomes from published and new microbiome datasets, comprising two case-control studies of stable COPD versus healthy control, two studies of COPD stability versus exacerbation, and one study with exacerbation-recovery time series data.

RESULTS: Patients with COPD had reproducibly lower degree of negative bacterial interactions, i.e. total number of negative interactions as a proportion of total interactions, in their airway microbiome compared with healthy controls. Evaluation of the Haemophilus interactome showed that the antagonistic interaction networks of this established pathogen rather than its abundance consistently changed in COPD. Interactome dynamic analysis revealed reproducibly reduced antagonistic interactions but not diversity loss during COPD exacerbation, which recovered after treatment. In phenotypic analysis, unsupervised network clustering showed that loss of antagonistic interactions was associated with worse clinical symptoms (dyspnea), poorer lung function, exaggerated neutrophilic inflammation, and higher exacerbation risk. Furthermore, the frequent exacerbators (≥ 2 exacerbations per year) had significantly reduced antagonistic bacterial interactions while exhibiting subtle compositional changes in their airway microbiota.

CONCLUSIONS: Bacterial interactome disturbance characterized by reduced antagonistic interactions, rather than change in pathogen abundance or diversity, is a reproducible feature of airway dysbiosis in COPD clinical stability and exacerbations, which suggests that we may target interactome rather than pathogen alone for disease treatment.}, } @article {pmid38632407, year = {2024}, author = {Maes, SL and Dietrich, J and Midolo, G and Schwieger, S and Kummu, M and Vandvik, V and Aerts, R and Althuizen, IHJ and Biasi, C and Björk, RG and Böhner, H and Carbognani, M and Chiari, G and Christiansen, CT and Clemmensen, KE and Cooper, EJ and Cornelissen, JHC and Elberling, B and Faubert, P and Fetcher, N and Forte, TGW and Gaudard, J and Gavazov, K and Guan, Z and Guðmundsson, J and Gya, R and Hallin, S and Hansen, BB and Haugum, SV and He, JS and Hicks Pries, C and Hovenden, MJ and Jalava, M and Jónsdóttir, IS and Juhanson, J and Jung, JY and Kaarlejärvi, E and Kwon, MJ and Lamprecht, RE and Le Moullec, M and Lee, H and Marushchak, ME and Michelsen, A and Munir, TM and Myrsky, EM and Nielsen, CS and Nyberg, M and Olofsson, J and Óskarsson, H and Parker, TC and Pedersen, EP and Petit Bon, M and Petraglia, A and Raundrup, K and Ravn, NMR and Rinnan, R and Rodenhizer, H and Ryde, I and Schmidt, NM and Schuur, EAG and Sjögersten, S and Stark, S and Strack, M and Tang, J and Tolvanen, A and Töpper, JP and Väisänen, MK and van Logtestijn, RSP and Voigt, C and Walz, J and Weedon, JT and Yang, Y and Ylänne, H and Björkman, MP and Sarneel, JM and Dorrepaal, E}, title = {Environmental drivers of increased ecosystem respiration in a warming tundra.}, journal = {Nature}, volume = {629}, number = {8010}, pages = {105-113}, pmid = {38632407}, issn = {1476-4687}, mesh = {Arctic Regions ; Carbon/metabolism/analysis ; Carbon Cycle ; Datasets as Topic ; *Ecosystem ; *Global Warming ; Hydrogen-Ion Concentration ; Nitrogen/metabolism/analysis ; Plants/metabolism ; Seasons ; Soil/chemistry ; Soil Microbiology ; Temperature ; *Tundra ; Time Factors ; *Cell Respiration ; }, abstract = {Arctic and alpine tundra ecosystems are large reservoirs of organic carbon[1,2]. Climate warming may stimulate ecosystem respiration and release carbon into the atmosphere[3,4]. The magnitude and persistency of this stimulation and the environmental mechanisms that drive its variation remain uncertain[5-7]. This hampers the accuracy of global land carbon-climate feedback projections[7,8]. Here we synthesize 136 datasets from 56 open-top chamber in situ warming experiments located at 28 arctic and alpine tundra sites which have been running for less than 1 year up to 25 years. We show that a mean rise of 1.4 °C [confidence interval (CI) 0.9-2.0 °C] in air and 0.4 °C [CI 0.2-0.7 °C] in soil temperature results in an increase in growing season ecosystem respiration by 30% [CI 22-38%] (n = 136). Our findings indicate that the stimulation of ecosystem respiration was due to increases in both plant-related and microbial respiration (n = 9) and continued for at least 25 years (n = 136). The magnitude of the warming effects on respiration was driven by variation in warming-induced changes in local soil conditions, that is, changes in total nitrogen concentration and pH and by context-dependent spatial variation in these conditions, in particular total nitrogen concentration and the carbon:nitrogen ratio. Tundra sites with stronger nitrogen limitations and sites in which warming had stimulated plant and microbial nutrient turnover seemed particularly sensitive in their respiration response to warming. The results highlight the importance of local soil conditions and warming-induced changes therein for future climatic impacts on respiration.}, } @article {pmid38632405, year = {2024}, author = {Swain, A and Woodhouse, A and Fagan, WF and Fraass, AJ and Lowery, CM}, title = {Biogeographic response of marine plankton to Cenozoic environmental changes.}, journal = {Nature}, volume = {629}, number = {8012}, pages = {616-623}, pmid = {38632405}, issn = {1476-4687}, mesh = {Animals ; *Aquatic Organisms/physiology/classification ; Biodiversity ; Biological Evolution ; *Climate Change/history ; Datasets as Topic ; Extinction, Biological ; *Foraminifera/classification/physiology ; History, Ancient ; *Phylogeography ; *Plankton/classification/physiology ; Spatio-Temporal Analysis ; }, abstract = {In palaeontological studies, groups with consistent ecological and morphological traits across a clade's history (functional groups)[1] afford different perspectives on biodiversity dynamics than do species and genera[2,3], which are evolutionarily ephemeral. Here we analyse Triton, a global dataset of Cenozoic macroperforate planktonic foraminiferal occurrences[4], to contextualize changes in latitudinal equitability gradients[1], functional diversity, palaeolatitudinal specialization and community equitability. We identify: global morphological communities becoming less specialized preceding the richness increase after the Cretaceous-Palaeogene extinction; ecological specialization during the Early Eocene Climatic Optimum, suggesting inhibitive equatorial temperatures during the peak of the Cenozoic hothouse; increased specialization due to circulation changes across the Eocene-Oligocene transition, preceding the loss of morphological diversity; changes in morphological specialization and richness about 19 million years ago, coeval with pelagic shark extinctions[5]; delayed onset of changing functional group richness and specialization between hemispheres during the mid-Miocene plankton diversification. The detailed nature of the Triton dataset permits a unique spatiotemporal view of Cenozoic pelagic macroevolution, in which global biogeographic responses of functional communities and richness are decoupled during Cenozoic climate events. The global response of functional groups to similar abiotic selection pressures may depend on the background climatic state (greenhouse or icehouse) to which a group is adapted.}, } @article {pmid38632210, year = {2024}, author = {Griesberger, P and Kunz, F and Hackländer, K and Mattsson, B}, title = {Building a decision-support tool to inform sustainability approaches under complexity: Case study on managing wild ruminants.}, journal = {Ambio}, volume = {53}, number = {9}, pages = {1307-1322}, pmid = {38632210}, issn = {1654-7209}, mesh = {Animals ; *Conservation of Natural Resources/methods ; *Animals, Wild ; *Decision Support Techniques ; *Bayes Theorem ; *Ruminants ; Austria ; Decision Making ; }, abstract = {In wildlife management, differing perspectives among stakeholders generate conflicts about how to achieve disparate sustainability goals that include ecological, economic, and sociocultural dimensions. To mitigate such conflicts, decisions regarding wildlife management must be taken thoughtfully. To our knowledge, there exists no integrative modeling framework to inform these decisions, considering all dimensions of sustainability. We constructed a decision-support tool based on stakeholder workshops and a Bayesian decision network to inform management of wild ruminants in the federal state of Lower Austria. We use collaborative decision analysis to compare resource allocations while accounting for trade-offs among dimensions of sustainability. The tool is designed for application by non-technical users across diverse decision-making contexts with particular sets of wildlife management actions, objectives, and uncertainties. Our tool represents an important step toward developing and evaluating a transparent and replicable approach for mitigating wildlife-based conflicts in Europe and beyond.}, } @article {pmid38630866, year = {2024}, author = {Ma, L and Hu, Z and Shen, W and Zhang, Y and Wang, G and Chang, B and Lu, J and Cui, Y and Xu, H and Feng, Y and Jin, B and Zhang, X and Wang, L and Lin, J}, title = {Three-dimensional reconstruction and multiomics analysis reveal a unique pattern of embryogenesis in Ginkgo biloba.}, journal = {Plant physiology}, volume = {196}, number = {1}, pages = {95-111}, doi = {10.1093/plphys/kiae219}, pmid = {38630866}, issn = {1532-2548}, support = {5232016//Beijing Municipal Natural Science Foundation/ ; 32000558//National Natural Science Foundation of China/ ; BLX202116//Fundamental Research Funds for the Central Universities/ ; B13007//Program of Introducing Talents of Discipline to Universities/ ; }, mesh = {*Ginkgo biloba/genetics/embryology ; *Seeds/genetics/growth & development ; Imaging, Three-Dimensional/methods ; Gene Expression Regulation, Plant ; Plant Proteins/metabolism/genetics ; X-Ray Microtomography ; Cotyledon/genetics ; Multiomics ; }, abstract = {Ginkgo (Ginkgo biloba L.) is one of the earliest extant species in seed plant phylogeny. Embryo development patterns can provide fundamental evidence for the origin, evolution, and adaptation of seeds. However, the architectural and morphological dynamics during embryogenesis in G. biloba remain elusive. Herein, we obtained over 2,200 visual slices from 3 stages of embryo development using micro-computed tomography imaging with improved staining methods. Based on 3-dimensional (3D) spatiotemporal pattern analysis, we found that a shoot apical meristem with 7 highly differentiated leaf primordia, including apical and axillary leaf buds, is present in mature Ginkgo embryos. 3D rendering from the front, top, and side views showed 2 separate transport systems of tracheids located in the hypocotyl and cotyledon, representing a unique pattern of embryogenesis. Furthermore, the morphological dynamic analysis of secretory cavities indicated their strong association with cotyledons during development. In addition, we identified genes GbLBD25a (lateral organ boundaries domain 25a), GbCESA2a (cellulose synthase 2a), GbMYB74c (myeloblastosis 74c), GbPIN2 (PIN-FORMED 2) associated with vascular development regulation, and GbWRKY1 (WRKYGOK 1), GbbHLH12a (basic helix-loop-helix 12a), and GbJAZ4 (jasmonate zim-domain 4) potentially involved in the formation of secretory cavities. Moreover, we found that flavonoid accumulation in mature embryos could enhance postgerminative growth and seedling establishment in harsh environments. Our 3D spatial reconstruction technique combined with multiomics analysis opens avenues for investigating developmental architecture and molecular mechanisms during embryogenesis and lays the foundation for evolutionary studies of embryo development and maturation.}, } @article {pmid38629556, year = {2024}, author = {Dai, WT and Zhang, H and Wu, X and Zhong, M and Duan, GL and Dong, JH and Zhang, PP and Fan, HM}, title = {[Pollution Characteristics and Source Analysis of Soil Heavy Metal in Coal Mine Area near the Yellow River in Shandong].}, journal = {Huan jing ke xue= Huanjing kexue}, volume = {45}, number = {5}, pages = {2952-2961}, doi = {10.13227/j.hjkx.202306029}, pmid = {38629556}, issn = {0250-3301}, abstract = {To explore the pollution characteristics and source of soil heavy metal in a coal mine area near the Yellow River in Shandong, the geo-accumulation index method and improved Nemerow pollution index method were used to evaluate the pollution characteristics of soil heavy metal. The absolute principal component-multiple linear regression model (APCS-MLR) was used to quantitatively analyze the source of soil heavy metal, and the spatial distribution of Hg and Cd were analyzed using the Kriging spatial difference method in ArcGIS. The result accuracy of the APCS-MLR model was further verified. The results showed that:The measured contents of soil heavy metal Cu, Zn, Pb, Cr, Cd, Ni, As, and Hg all exceeded the normal site, among which, Hg and Cd exceeded the background values of soil elements in Shandong. The coefficient of variation (CV) of Hg was higher than 0.500, indicating significant spatial heterogeneity. Moreover, the correlation between Hg and other heavy metals was generally low, and the possibility of the same pollution source was small. The results of the geo-accumulation index and improved Nemerow pollution index showed that the overall soil heavy metal pollution was at a moderate level, among which the Hg pollution level was the highest, and its maximum value was at a slanted-heavy pollution level; Cu, Cd, and As in soil caused local pollution, which were at a slanted-light pollution level. Soil heavy metal pollution was closely related to mining activities, rehabilitation, and engineering construction in the coal mine area. The two major pollution sources of soil heavy metal in the research area were the compound source of the parent material and industrial and mining transportation sources (known source 1) and the compound source of atmospheric sedimentation and coal production (known source 2), the contribution rates of which were 76.705% and 16.171%, respectively. The results of the APCS-MLR model were shown to be reliable by analyzing the content distribution of Hg and Cd using the Kriging space difference mode. This research can provide scientific basis for the precise control and improvement of soil heavy metal pollution, ensuring the safety of food and agricultural products and improving the quality of the ecological environment in the coal mine area in the Shandong section of the Yellow River Basin.}, } @article {pmid38629131, year = {2024}, author = {Reginato, M and Ordónez-Parra, CA and Messeder, JVS and Brito, VLG and Dellinger, A and Kriebel, R and Marra, C and Melo, L and Cornelissen, T and Fuzessy, L and Sperotto, P and Calderón-Hernández, M and Guerra, TJ and Kopper, C and Mancipe-Murillo, C and Pizo, MA and Posada-Herrera, JM and Hasui, É and Silva, WR and Silveira, FAO}, title = {MelastomaTRAITs 1.0: A database of functional traits in Melastomataceae, a large pantropical angiosperm family.}, journal = {Ecology}, volume = {105}, number = {6}, pages = {e4308}, doi = {10.1002/ecy.4308}, pmid = {38629131}, issn = {1939-9170}, support = {//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; FWF P-30669 T-1186//Austrian Science Fund/ ; //Fundação de Amparo à Pesquisa do Estado de Minas Gerais/ ; //Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; //Fulbright Association/ ; }, mesh = {*Databases, Factual ; Ecosystem ; *Melastomataceae/physiology/genetics ; }, abstract = {The recent availability of open-access repositories of functional traits has revolutionized trait-based approaches in ecology and evolution. Nevertheless, the underrepresentation of tropical regions and lineages remains a pervasive bias in plant functional trait databases, which constrains large-scale assessments of plant ecology, evolution, and biogeography. Here, we present MelastomaTRAITs 1.0, a comprehensive and updatable database of functional traits for the pantropical Melastomataceae, the ninth-largest angiosperm family with 177 genera and more than 5800 species. Melastomataceae encompass species with a wide diversity of growth forms (herbs, shrubs, trees, epiphytes, and woody climbers), habitats (including tropical forests, savannas, grasslands, and wetlands from sea level to montane areas above the treeline), ecological strategies (from pioneer, edge-adapted and invasive species to shade-tolerant understory species), geographic distribution (from microendemic to continental-wide distribution), reproductive, pollination, and seed dispersal systems. MelastomaTRAITs builds on 581 references, such as taxonomic monographs, ecological research, and unpublished data, and includes four whole-plant traits, six leaf traits, 11 flower traits, 18 fruit traits, and 27 seed traits for 2520 species distributed in 144 genera across all 21 tribes. Most data come from the Neotropics where the family is most species-rich. Miconieae (the largest tribe) contains the highest number of trait records (49.6%) and species (41.1%) records. The trait types with the most information in the database were whole-plant traits, flowers, and leaf traits. With the breadth of functional traits recorded, our database helps to fill a gap in information for tropical plants and will significantly improve our capacity for large-scale trait-based syntheses across levels of organization, plant-animal interactions, regeneration ecology, and thereby support conservation and restoration programs. There are no copyright restrictions on the dataset; please cite this data paper when reusing the data.}, } @article {pmid38627476, year = {2024}, author = {Ridley, RS and Conrad, RE and Lindner, BG and Woo, S and Konstantinidis, KT}, title = {Potential routes of plastics biotransformation involving novel plastizymes revealed by global multi-omic analysis of plastic associated microbes.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {8798}, pmid = {38627476}, issn = {2045-2322}, support = {2136146//National Science Foundation/ ; }, mesh = {Humans ; *Multiomics ; *Plastics ; Polymers ; Biotransformation ; Biodegradation, Environmental ; }, abstract = {Despite increasing efforts across various disciplines, the fate, transport, and impact of synthetic plastics on the environment and public health remain poorly understood. To better elucidate the microbial ecology of plastic waste and its potential for biotransformation, we conducted a large-scale analysis of all publicly available meta-omic studies investigating plastics (n = 27) in the environment. Notably, we observed low prevalence of known plastic degraders throughout most environments, except for substantial enrichment in riverine systems. This indicates rivers may be a highly promising environment for discovery of novel plastic bioremediation products. Ocean samples associated with degrading plastics showed clear differentiation from non-degrading polymers, showing enrichment of novel putative biodegrading taxa in the degraded samples. Regarding plastisphere pathogenicity, we observed significant enrichment of antimicrobial resistance genes on plastics but not of virulence factors. Additionally, we report a co-occurrence network analysis of 10 + million proteins associated with the plastisphere. This analysis revealed a localized sub-region enriched with known and putative plastizymes-these may be useful for deeper investigation of nature's ability to biodegrade man-made plastics. Finally, the combined data from our meta-analysis was used to construct a publicly available database, the Plastics Meta-omic Database (PMDB)-accessible at plasticmdb.org. These data should aid in the integrated exploration of the microbial plastisphere and facilitate research efforts investigating the fate and bioremediation potential of environmental plastic waste.}, } @article {pmid38627422, year = {2024}, author = {Hammoud, R and Tognin, S and Smythe, M and Gibbons, J and Davidson, N and Bakolis, I and Mechelli, A}, title = {Smartphone-based ecological momentary assessment reveals an incremental association between natural diversity and mental wellbeing.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {7051}, pmid = {38627422}, issn = {2045-2322}, support = {/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Humans ; *Smartphone ; *Ecological Momentary Assessment ; Mental Health ; Trees ; Biodiversity ; }, abstract = {Using smartphone-based ecological momentary assessment, this study investigated an association between natural diversity on mental wellbeing. A sample of 1,998 participants completed 41,448 assessments between April 2018 and September 2023. Environments which included a larger range of natural features, such as trees, plants and birdlife (high natural diversity) were associated with greater mental wellbeing than environments including a smaller range of natural features (low natural diversity). There was evidence of a mediating effect of natural diversity on the association between natural environments and mental wellbeing. These results highlight the importance of policies and practices that support richness of biodiversity for public mental health.}, } @article {pmid38625737, year = {2024}, author = {Jonathan, J and Barakabitze, AA and Fast, CD and Cox, C}, title = {Machine Learning for Prediction of Tuberculosis Detection: Case Study of Trained African Giant Pouched Rats.}, journal = {Online journal of public health informatics}, volume = {16}, number = {}, pages = {e50771}, pmid = {38625737}, issn = {1947-2579}, abstract = {BACKGROUND: Technological advancement has led to the growth and rapid increase of tuberculosis (TB) medical data generated from different health care areas, including diagnosis. Prioritizing better adoption and acceptance of innovative diagnostic technology to reduce the spread of TB significantly benefits developing countries. Trained TB-detection rats are used in Tanzania and Ethiopia for operational research to complement other TB diagnostic tools. This technology has increased new TB case detection owing to its speed, cost-effectiveness, and sensitivity.

OBJECTIVE: During the TB detection process, rats produce vast amounts of data, providing an opportunity to identify interesting patterns that influence TB detection performance. This study aimed to develop models that predict if the rat will hit (indicate the presence of TB within) the sample or not using machine learning (ML) techniques. The goal was to improve the diagnostic accuracy and performance of TB detection involving rats.

METHODS: APOPO (Anti-Persoonsmijnen Ontmijnende Product Ontwikkeling) Center in Morogoro provided data for this study from 2012 to 2019, and 366,441 observations were used to build predictive models using ML techniques, including decision tree, random forest, naïve Bayes, support vector machine, and k-nearest neighbor, by incorporating a variety of variables, such as the diagnostic results from partner health clinics using methods endorsed by the World Health Organization (WHO).

RESULTS: The support vector machine technique yielded the highest accuracy of 83.39% for prediction compared to other ML techniques used. Furthermore, this study found that the inclusion of variables related to whether the sample contained TB or not increased the performance accuracy of the predictive model.

CONCLUSIONS: The inclusion of variables related to the diagnostic results of TB samples may improve the detection performance of the trained rats. The study results may be of importance to TB-detection rat trainers and TB decision-makers as the results may prompt them to take action to maintain the usefulness of the technology and increase the TB detection performance of trained rats.}, } @article {pmid38622188, year = {2024}, author = {Liu, X and Chen, J and Tang, BH and He, L and Xu, Y and Yang, C}, title = {Eco-environmental changes due to human activities in the Erhai Lake Basin from 1990 to 2020.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {8646}, pmid = {38622188}, issn = {2045-2322}, support = {42301454//National Natural Science Foundation of China/ ; 42230109//National Natural Science Foundation of China/ ; 42201319//National Natural Science Foundation of China/ ; }, mesh = {Humans ; *Lakes ; *Sustainable Development ; Human Activities ; China ; Environmental Monitoring/methods ; }, abstract = {Human activities have increased with urbanisation in the Erhai Lake Basin, considerably impacting its eco-environmental quality (EEQ). This study aims to reveal the evolution and driving forces of the EEQ using water benefit-based ecological index (WBEI) in response to human activities and policy variations in the Erhai Lake Basin from 1990 to 2020. Results show that (1) the EEQ exhibited a pattern of initial degradation, subsequent improvement, further degradation and a rebound from 1990 to 2020, and the areas with poor and fair EEQ levels mainly concentrated around the Erhai Lake Basin with a high level of urbanisation and relatively flat terrain; (2) the EEQ levels were not optimistic in 1990, 1995 and 2015, and areas with poor and fair EEQ levels accounted for 43.41%, 47.01% and 40.05% of the total area, respectively; and (3) an overall improvement in the EEQ was observed in 1995-2000, 2000-2005, 2005-2009 and 2015-2020, and the improvement was most significant in 1995-2000, covering an area of 823.95 km[2] and accounting for 31.79% of the total area. Results also confirmed that the EEQ changes in the Erhai Lake Basin were primarily influenced by human activities and policy variations. Moreover, these results can provide a scientific basis for the formulation and planning of sustainable development policy in the Erhai Lake Basin.}, } @article {pmid38621404, year = {2024}, author = {Turtle, L and Elliot, S and Drake, TM and Thorpe, M and Khoury, EG and Greenhalf, W and Hardwick, HE and Leeming, G and Law, A and Oosthuyzen, W and Pius, R and Shaw, CA and Baillie, JK and Openshaw, PJM and Docherty, AB and Semple, MG and Harrison, EM and Palmieri, C and , }, title = {Changes in hospital mortality in patients with cancer during the COVID-19 pandemic (ISARIC-CCP-UK): a prospective, multicentre cohort study.}, journal = {The Lancet. Oncology}, volume = {25}, number = {5}, pages = {636-648}, doi = {10.1016/S1470-2045(24)00107-4}, pmid = {38621404}, issn = {1474-5488}, mesh = {Humans ; *COVID-19/mortality/epidemiology ; *Neoplasms/mortality/therapy ; Male ; Female ; Prospective Studies ; Aged ; Middle Aged ; *Hospital Mortality ; United Kingdom/epidemiology ; *SARS-CoV-2 ; Adult ; Aged, 80 and over ; Pandemics ; }, abstract = {BACKGROUND: Patients with cancer are at greater risk of dying from COVID-19 than many other patient groups. However, how this risk evolved during the pandemic remains unclear. We aimed to determine, on the basis of the UK national pandemic protocol, how factors influencing hospital mortality from COVID-19 could differentially affect patients undergoing cancer treatment. We also examined changes in hospital mortality and escalation of care in patients on cancer treatment during the first 2 years of the COVID-19 pandemic in the UK.

METHODS: We conducted a prospective cohort study of patients aged older than 19 years and admitted to 306 health-care facilities in the UK with confirmed SARS-CoV-2 infection, who were enrolled in the International Severe Acute Respiratory and emerging Infections Consortium (ISARIC) WHO Clinical Characterisation Protocol (CCP) across the UK from April 23, 2020, to Feb 28, 2022; this analysis included all patients in the complete dataset when the study closed. The primary outcome was 30-day in-hospital mortality, comparing patients on cancer treatment and those without cancer. The study was approved by the South Central-Oxford C Research Ethics Committee in England (Ref: 13/SC/0149) and the Scotland A Research Ethics Committee (Ref 20/SS/0028), and is registered on the ISRCTN Registry (ISRCTN66726260).

FINDINGS: 177 871 eligible adult patients either with no history of cancer (n=171 303) or on cancer treatment (n=6568) were enrolled; 93 205 (52·4%) were male, 84 418 (47·5%) were female, and in 248 (13·9%) sex or gender details were not specified or data were missing. Patients were followed up for a median of 13 (IQR 6-21) days. Of the 6568 patients receiving cancer treatment, 2080 (31·7%) died at 30 days, compared with 30 901 (18·0%) of 171 303 patients without cancer. Patients aged younger than 50 years on cancer treatment had the highest age-adjusted relative risk (hazard ratio [HR] 5·2 [95% CI 4·0-6·6], p<0·0001; vs 50-69 years 2·4 [2·2-2·6], p<0·0001; 70-79 years 1·8 [1·6-2·0], p<0·0001; and >80 years 1·5 [1·3-1·6], p<0·0001) but a lower absolute risk (51 [6·7%] of 763 patients <50 years died compared with 459 [30·2%] of 1522 patients aged >80 years). In-hospital mortality decreased for all patients during the pandemic but was higher for patients on cancer treatment than for those without cancer throughout the study period.

INTERPRETATION: People with cancer have a higher risk of mortality from COVID-19 than those without cancer. Patients younger than 50 years with cancer treatment have the highest relative risk of death. Continued action is needed to mitigate the poor outcomes in patients with cancer, such as through optimising vaccination, long-acting passive immunisation, and early access to therapeutics. These findings underscore the importance of the ISARIC-WHO pandemic preparedness initiative.

FUNDING: National Institute for Health Research and the Medical Research Council.}, } @article {pmid38618197, year = {2023}, author = {Short, S and Green Etxabe, A and Robinson, A and Spurgeon, D and Kille, P and , and , and , and , }, title = {The genome sequence of the red compost earthworm, Lumbricus rubellus (Hoffmeister, 1843).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {354}, pmid = {38618197}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual Lumbricus rubellus (the red compost earthworm; Annelida; Clitellata; Haplotaxida; Lumbricidae). The genome sequence is 787.5 megabases in span. Most of the assembly is scaffolded into 18 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 15.81 kilobases in length. Gene annotation of this assembly on Ensembl identified 33,426 protein coding genes.}, } @article {pmid38617028, year = {2024}, author = {Liu, J and He, C and Si, Y and Li, B and Wu, Q and Ni, J and Zhao, Y and Hu, Q and Du, S and Lu, Z and Jin, J and Xu, C}, title = {Toward Better and Healthier Air Quality: Global PM2.5 and O3 Pollution Status and Risk Assessment Based on the New WHO Air Quality Guidelines for 2021.}, journal = {Global challenges (Hoboken, NJ)}, volume = {8}, number = {4}, pages = {2300258}, pmid = {38617028}, issn = {2056-6646}, abstract = {To reduce the high burden of disease caused by air pollution, the World Health Organization (WHO) released new Air Quality Guidelines (AQG) on September 22, 2021. In this study, the daily fine particulate matter (PM2.5) and surface ozone (O3) data of 618 cities around the world is collected from 2019 to 2022. Based on the new AQG, the number of attainment days for daily average concentrations of PM2.5 (≤ 15 µg m[-3]) and O3 (≤ 100 µg m[-3]) is approximately 10% and 90%, respectively. China and India exhibit a decreasing trend in the number of highly polluted days (> 75 µg m[-3]) for PM. Every year over 68% and 27% of cities in the world are exposed to harmful PM2.5 (> 35 µg m[-3]) and O3 (> 100 µg m[-3]) pollution, respectively. Combined with the United Nations Sustainable Development Goals (SDGs), it is found that more than 35% of the world's cities face PM2.5-O3 compound pollution. Furthermore, the exposure risks in these cities (China, India, etc.) are mainly categorized as "High Risk", "Risk", and "Stabilization". In contrast, economically developed cities are mainly categorized as "High Safety", "Safety", and "Deep Stabilization." These findings indicate that global implementation of the WHO's new AQG will minimize the inequitable exposure risk from air pollution.}, } @article {pmid38616489, year = {2024}, author = {Bleker, C and Ramšak, Ž and Bittner, A and Podpečan, V and Zagorščak, M and Wurzinger, B and Baebler, Š and Petek, M and Križnik, M and van Dieren, A and Gruber, J and Afjehi-Sadat, L and Weckwerth, W and Županič, A and Teige, M and Vothknecht, UC and Gruden, K}, title = {Stress Knowledge Map: A knowledge graph resource for systems biology analysis of plant stress responses.}, journal = {Plant communications}, volume = {5}, number = {6}, pages = {100920}, pmid = {38616489}, issn = {2590-3462}, mesh = {*Systems Biology ; *Stress, Physiological ; *Plants/genetics/metabolism ; Plant Physiological Phenomena/genetics ; Signal Transduction/genetics ; Databases, Factual ; }, abstract = {Stress Knowledge Map (SKM; https://skm.nib.si) is a publicly available resource containing two complementary knowledge graphs that describe the current knowledge of biochemical, signaling, and regulatory molecular interactions in plants: a highly curated model of plant stress signaling (PSS; 543 reactions) and a large comprehensive knowledge network (488 390 interactions). Both were constructed by domain experts through systematic curation of diverse literature and database resources. SKM provides a single entry point for investigations of plant stress response and related growth trade-offs, as well as interactive explorations of current knowledge. PSS is also formulated as a qualitative and quantitative model for systems biology and thus represents a starting point for a plant digital twin. Here, we describe the features of SKM and show, through two case studies, how it can be used for complex analyses, including systematic hypothesis generation and design of validation experiments, or to gain new insights into experimental observations in plant biology.}, } @article {pmid38616247, year = {2024}, author = {Kibet, CK and Entfellner, JD and Jjingo, D and de Villiers, EP and de Villiers, S and Wambui, K and Kinyanjui, S and Masiga, D}, title = {Designing and delivering bioinformatics project-based learning in East Africa.}, journal = {BMC bioinformatics}, volume = {25}, number = {1}, pages = {150}, pmid = {38616247}, issn = {1471-2105}, support = {U2R TW010677/TW/FIC NIH HHS/United States ; U2RTW010677/TW/FIC NIH HHS/United States ; }, mesh = {Humans ; *Learning ; Africa, Eastern ; *COVID-19/epidemiology ; Computational Biology ; Pandemics ; }, abstract = {BACKGROUND: The Eastern Africa Network for Bioinformatics Training (EANBiT) has matured through continuous evaluation, feedback, and codesign. We highlight how the program has evolved to meet challenges and achieve its goals and how experiential learning through mini projects enhances the acquisition of skills and collaboration. We continued to learn and grow through honest feedback and evaluation of the program, trainers, and modules, enabling us to provide robust training even during the Coronavirus disease 2019 (COVID-19) pandemic, when we had to redesign the program due to restricted travel and in person group meetings.

RESULTS: In response to the pandemic, we developed a program to maintain "residential" training experiences and benefits remotely. We had to answer the following questions: What must change to still achieve the RT goals? What optimal platforms should be used? How would we manage connectivity and data challenges? How could we avoid online fatigue? Going virtual presented an opportunity to reflect on the essence and uniqueness of the program and its ability to meet the objective of strengthening bioinformatics skills among the cohorts of students using different delivery approaches. It allowed an increase in the number of participants. Evaluating each program component is critical for improvement, primarily when feedback feeds into the program's continuous amendment. Initially, the participants noted that there were too many modules, insufficient time, and a lack of hands-on training as a result of too much focus on theory. In the subsequent iterations, we reduced the number of modules from 27 to five, created a harmonized repository for the materials on GitHub, and introduced project-based learning through the mini projects.

CONCLUSION: We demonstrate that implementing a program design through detailed monitoring and evaluation leads to success, especially when participants who are the best fit for the program are selected on an appropriate level of skills, motivation, and commitment.}, } @article {pmid38614075, year = {2024}, author = {Breeyear, JH and Mautz, BS and Keaton, JM and Hellwege, JN and Torstenson, ES and Liang, J and Bray, MJ and Giri, A and Warren, HR and Munroe, PB and Velez Edwards, DR and Zhu, X and Li, C and Edwards, TL}, title = {A new test for trait mean and variance detects unreported loci for blood-pressure variation.}, journal = {American journal of human genetics}, volume = {111}, number = {5}, pages = {954-965}, pmid = {38614075}, issn = {1537-6605}, support = {U01 HG006378/HG/NHGRI NIH HHS/United States ; U19 HL065962/HL/NHLBI NIH HHS/United States ; S10 RR025141/RR/NCRR NIH HHS/United States ; R01 HG004517/HG/NHGRI NIH HHS/United States ; TL1 TR002244/TR/NCATS NIH HHS/United States ; U01 HG008672/HG/NHGRI NIH HHS/United States ; U01 HG008684/HG/NHGRI NIH HHS/United States ; U01 HG008679/HG/NHGRI NIH HHS/United States ; RC2 GM092618/GM/NIGMS NIH HHS/United States ; P50 GM115305/GM/NIGMS NIH HHS/United States ; U01 HG006379/HG/NHGRI NIH HHS/United States ; U01 HG008664/HG/NHGRI NIH HHS/United States ; U01 HG008701/HG/NHGRI NIH HHS/United States ; U01 HG008676/HG/NHGRI NIH HHS/United States ; UL1 TR000445/TR/NCATS NIH HHS/United States ; F31 EY033663/EY/NEI NIH HHS/United States ; K12 HD043483/HD/NICHD NIH HHS/United States ; R01 HD074711/HD/NICHD NIH HHS/United States ; U01 HG008657/HG/NHGRI NIH HHS/United States ; U19 HL065962/HL/NHLBI NIH HHS/United States ; R01 HG004517/HG/NHGRI NIH HHS/United States ; U01 HG008666/HG/NHGRI NIH HHS/United States ; R01 HD074711/HD/NICHD NIH HHS/United States ; U01 HG004798/HG/NHGRI NIH HHS/United States ; K12 HD043483/HD/NICHD NIH HHS/United States ; U01 HG008680/HG/NHGRI NIH HHS/United States ; U01 HG006378/HG/NHGRI NIH HHS/United States ; UL1 RR024975/RR/NCRR NIH HHS/United States ; R01 AI093234/AI/NIAID NIH HHS/United States ; U01 HG008673/HG/NHGRI NIH HHS/United States ; R01 NS032830/NS/NINDS NIH HHS/United States ; U01 HG004798/HG/NHGRI NIH HHS/United States ; R21 HL121429/HL/NHLBI NIH HHS/United States ; R21 HL121429/HL/NHLBI NIH HHS/United States ; R01 NS032830/NS/NINDS NIH HHS/United States ; UL1 TR002243/TR/NCATS NIH HHS/United States ; U01 HG008685/HG/NHGRI NIH HHS/United States ; RC2 GM092618/GM/NIGMS NIH HHS/United States ; F31 EY033663/EY/NEI NIH HHS/United States ; }, mesh = {Humans ; *Blood Pressure/genetics ; *Quantitative Trait Loci ; *Genome-Wide Association Study ; Polymorphism, Single Nucleotide ; Models, Genetic ; Genotype ; Genetic Variation ; Computer Simulation ; Phenotype ; }, abstract = {Variability in quantitative traits has clinical, ecological, and evolutionary significance. Most genetic variants identified for complex quantitative traits have only a detectable effect on the mean of trait. We have developed the mean-variance test (MVtest) to simultaneously model the mean and log-variance of a quantitative trait as functions of genotypes and covariates by using estimating equations. The advantages of MVtest include the facts that it can detect effect modification, that multiple testing can follow conventional thresholds, that it is robust to non-normal outcomes, and that association statistics can be meta-analyzed. In simulations, we show control of type I error of MVtest over several alternatives. We identified 51 and 37 previously unreported associations for effects on blood-pressure variance and mean, respectively, in the UK Biobank. Transcriptome-wide association studies revealed 633 significant unique gene associations with blood-pressure mean variance. MVtest is broadly applicable to studies of complex quantitative traits and provides an important opportunity to detect novel loci.}, } @article {pmid38613584, year = {2024}, author = {Kredics, L and Büchner, R and Balázs, D and Allaga, H and Kedves, O and Racić, G and Varga, A and Nagy, VD and Vágvölgyi, C and Sipos, G}, title = {Recent advances in the use of Trichoderma-containing multicomponent microbial inoculants for pathogen control and plant growth promotion.}, journal = {World journal of microbiology & biotechnology}, volume = {40}, number = {5}, pages = {162}, pmid = {38613584}, issn = {1573-0972}, mesh = {Humans ; *Agricultural Inoculants ; *Trichoderma ; Fertilizers ; *Pesticides ; Soil ; }, abstract = {Chemical pesticides and fertilizers are used in agricultural production worldwide to prevent damage from plant pathogenic microorganisms, insects, and nematodes, to minimize crop losses and to preserve crop quality. However, the use of chemical pesticides and fertilizers can severely pollute soil, water, and air, posing risks to the environment and human health. Consequently, developing new, alternative, environment-friendly microbial soil treatment interventions for plant protection and crop yield increase has become indispensable. Members of the filamentous fungal genus Trichoderma (Ascomycota, Sordariomycetes, Hypocreales) have long been known as efficient antagonists of plant pathogenic microorganisms based on various beneficial traits and abilities of these fungi. This minireview aims to discuss the advances in the field of Trichoderma-containing multicomponent microbiological inoculants based on recent experimental updates. Trichoderma strains can be combined with each other, with other fungi and/or with beneficial bacteria. The development and field performance of such inoculants will be addressed, focusing on the complementarity, synergy, and compatibility of their microbial components.}, } @article {pmid38613177, year = {2024}, author = {Wan, JSH and Bonser, SP and Pang, CK and Fazlioglu, F and Rutherford, S}, title = {Adaptive responses to living in stressful habitats: Do invasive and native plant populations use different strategies?.}, journal = {Ecology letters}, volume = {27}, number = {4}, pages = {e14419}, doi = {10.1111/ele.14419}, pmid = {38613177}, issn = {1461-0248}, mesh = {Reproduction ; *Plant Physiological Phenomena ; *Stress, Physiological ; }, abstract = {Plants inhabit stressful environments characterized by a variety of stressors, including mine sites, mountains, deserts, and high latitudes. Populations from stressful and reference (non-stressful) sites often have performance differences. However, while invasive and native species may respond differently to stressful environments, there is limited understanding of the patterns in reaction norms of populations from these sites. Here, we use phylogenetically controlled meta-analysis to assess the performance of populations under stress and non-stress conditions. We ask whether stress populations of natives and invasives differ in the magnitude of lowered performance under non-stress conditions and if they vary in the degree of performance advantage under stress. We also assessed whether these distinctions differ with stress intensity. Our findings revealed that natives not only have greater adaptive advantages but also more performance reductions than invasives. Populations from very stressful sites had more efficient adaptations, and performance costs increased with stress intensity in natives only. Overall, the results support the notion that adaptation is frequently costless. Reproductive output was most closely associated with adaptive costs and benefits. Our study characterized the adaptive strategies used by invasive and native plants under stressful conditions, thereby providing important insights into the limitations of adaptation to extreme sites.}, } @article {pmid38613081, year = {2024}, author = {Jeong, S and Choi, YJ}, title = {Association between Socioecological Status, Nutrient Intake, and Cancer Screening Behaviors in Adults Aged 40 and Over: Insights from the Eighth Korea National Health and Nutrition Examination Survey (KNHANES, 2019).}, journal = {Nutrients}, volume = {16}, number = {7}, pages = {}, pmid = {38613081}, issn = {2072-6643}, mesh = {Adult ; Humans ; Middle Aged ; *Early Detection of Cancer ; Nutrition Surveys ; Eating ; Energy Intake ; Republic of Korea ; *Neoplasms ; }, abstract = {Cancer screening is pivotal for early detection and improved survival rates. While socio-ecological factors are known to influence screening uptake, the role of lifestyle, dietary habits, and general health in shaping these decisions remains underexplored. Utilizing the 2019 Korea National Health and Nutrition Examination Survey (KNHANES), this study examined the myriad of factors impacting cancer screening utilization. Data from 274,872 adults aged 40 years or older were scrutinized, highlighting demographics, income, lifestyle behaviors, health-related variables, nutrient intake, and dietary quality. A combination of descriptive statistics and logistic regression helped us ascertain influential determinants. Higher educational attainment and income quartiles were positively correlated with cancer screening rates. Regular walkers, those engaged in moderate physical activity, and individuals with a previous cancer diagnosis were more likely to get screened. High-risk drinkers and smokers were less inclined towards screening. Dietary habits also influenced screening decisions. Notably, participants with healthier eating behaviors, indicated by factors such as regular breakfasts and fewer meals out, were more likely to undergo screening. Additionally, nutrient intake analysis revealed that those who had undergone screening consumed greater quantities of most nutrients, bar a few exceptions. For individuals aged 50-64, nutritional assessment indicators highlighted a higher mean adequacy ratio (MAR) and index of nutritional quality (INQ) value among those who participated in screening, suggesting better nutritional quality. This study elucidates the complex socio-ecological and nutritional landscape influencing cancer screening decisions. The results underscore the importance of a holistic approach, emphasizing lifestyle, dietary habits, and socio-economic considerations. It provides a roadmap for policymakers to craft more inclusive screening programs, ensuring equal access and promoting early detection.}, } @article {pmid38612552, year = {2024}, author = {Jankovic, M and Knezevic, T and Tomic, A and Milicevic, O and Jovanovic, T and Djunic, I and Mihaljevic, B and Knezevic, A and Todorovic-Balint, M}, title = {Human Cytomegalovirus Oncoprotection across Diverse Populations, Tumor Histologies, and Age Groups: The Relevance for Prospective Vaccinal Therapy.}, journal = {International journal of molecular sciences}, volume = {25}, number = {7}, pages = {}, pmid = {38612552}, issn = {1422-0067}, support = {200110/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Humans ; Cytomegalovirus ; Prospective Studies ; Seroepidemiologic Studies ; *Neoplasms/epidemiology ; *Cytomegalovirus Infections/epidemiology ; }, abstract = {The oncogenicity of the human cytomegalovirus (CMV) is currently being widely debated. Most recently, mounting clinical evidence suggests an anti-cancer effect via CMV-induced T cell-mediated tumor destruction. However, the data were mostly obtained from single-center studies and in vitro experiments. Broad geographic coverage is required to offer a global perspective. Our study examined the correlation between country-specific CMV seroprevalence (across 73 countries) and the age-standardized incidence rate (of 34 invasive tumors). The populations studied were stratified according to decadal age periods as the immunologic effects of CMV seropositivity may depend upon age at initial infection. The International Agency for Research on Cancer of the World Health Organization (IARC WHO) database was used. The multivariate linear regression analysis revealed a worldwide inverse correlation between CMV seroprevalence and the incidences of 62.8% tumors. Notably, this inverse link persists for all cancers combined (Spearman's ρ = -0.732, p < 0.001; β = -0.482, p < 0.001, adjusted R[2] = 0.737). An antithetical and significant correlation was also observed in particular age groups for the vast majority of tumors. Our results corroborate the conclusions of previous studies and indicate that this oncopreventive phenomenon holds true on a global scale. It applies to a wide spectrum of cancer histologies, additionally supporting the idea of a common underlying mechanism-CMV-stimulated T cell tumor targeting. Although these results further advance the notion of CMV-based therapies, in-depth investigation of host-virus interactions is still warranted.}, } @article {pmid38611576, year = {2024}, author = {Sulaiman, N and Salehi, F and Prakofjewa, J and Cavalleri, SAE and Ahmed, HM and Mattalia, G and Rastegar, A and Maghsudi, M and Amin, HM and Rasti, A and Hosseini, SH and Ghorbani, A and Pieroni, A and Sõukand, R}, title = {Cultural vs. State Borders: Plant Foraging by Hawraman and Mukriyan Kurds in Western Iran.}, journal = {Plants (Basel, Switzerland)}, volume = {13}, number = {7}, pages = {}, pmid = {38611576}, issn = {2223-7747}, abstract = {Plant foraging is a millennia-old activity still practiced by many people in the Middle East, particularly in the Fertile Crescent region, where several socioeconomic, ecological, and cultural factors shape this practice. This study seeks to understand the drivers of plant foraging in this complex region characterized by highly diverse linguistic, religious, and cultural groups. Our study aims to document the wild plants used by Kurds in Western Iran, identify similarities and differences among Hawraman and Mukriyan Kurdish groups in Iran, and compare our findings with a previous study on the Hawramani in Iraq. Forty-three semi-structured in-depth interviews were conducted in Kurdish villages of Western Iran. The results revealed the use of 44 wild food plant taxa, their preparation, and culinary uses. Among the reported taxa, 28 plant taxa were used by Mukriyani, and 33 by Hawramani. The study revealed a significant difference between the Hawraman and Mukriyan regions in Iran, whereas there is a high similarity between Hawramani Kurds in Iran and Iraq. We found that the invisible cultural border carries more weight than political divisions, and this calls for a paradigm shift in how we perceive and map the distribution of ethnobotanical knowledge.}, } @article {pmid38609485, year = {2024}, author = {Kazlou, A and Bornukova, K and Wickham, A and Slaykovskiy, V and Peven, K and Klepchukova, A and Ponzo, S and Garfinkel, S}, title = {Effects of stress on pain in females using a mobile health app in the Russia-Ukraine conflict.}, journal = {Npj mental health research}, volume = {3}, number = {1}, pages = {2}, pmid = {38609485}, issn = {2731-4251}, support = {MR/V037676/1//MRC/NIHR/ ; }, abstract = {The chronic and acute effects of stress can have divergent effects on health; long-term effects are associated with detrimental physical and mental health sequelae, while acute effects may be advantageous in the short-term. Stress-induced analgesia, the attenuation of pain perception due to stress, is a well-known phenomenon that has yet to be systematically investigated under ecological conditions. Using Flo, a women's health and wellbeing app and menstrual cycle tracker, with a world-wide monthly active usership of more than 57 million, women in Ukraine were monitored for their reporting of stress, pain and affective symptoms before, and immediately after, the onset of the Russian-Ukrainian conflict. To avoid potential selection (attrition) or collider bias, we rely on a sample of 87,315 users who were actively logging multiple symptoms before and after the start of the war. We found an inverse relationship between stress and pain, whereby higher reports of stress predicted lower rates of pain. Stress did not influence any other physiological symptoms with a similar magnitude, nor did any other symptom have a similar effect on pain. This relationship generally decreased in magnitude in countries neighbouring and surrounding Ukraine, with Ukraine serving as the epicentre. These findings help characterise the relationship between stress and health in a real-world setting.}, } @article {pmid38605417, year = {2024}, author = {Roder, T and Pimentel, G and Fuchsmann, P and Stern, MT and von Ah, U and Vergères, G and Peischl, S and Brynildsrud, O and Bruggmann, R and Bär, C}, title = {Scoary2: rapid association of phenotypic multi-omics data with microbial pan-genomes.}, journal = {Genome biology}, volume = {25}, number = {1}, pages = {93}, pmid = {38605417}, issn = {1474-760X}, support = {GRS-070/17//Gebert Rüf Stiftung/ ; }, mesh = {*Genome-Wide Association Study ; *Multiomics ; Phenotype ; Genes, Bacterial ; Genomics ; }, abstract = {Unraveling bacterial gene function drives progress in various areas, such as food production, pharmacology, and ecology. While omics technologies capture high-dimensional phenotypic data, linking them to genomic data is challenging, leaving 40-60% of bacterial genes undescribed. To address this bottleneck, we introduce Scoary2, an ultra-fast microbial genome-wide association studies (mGWAS) software. With its data exploration app and improved performance, Scoary2 is the first tool to enable the study of large phenotypic datasets using mGWAS. As proof of concept, we explore the metabolome of yogurts, each produced with a different Propionibacterium reichii strain and discover two genes affecting carnitine metabolism.}, } @article {pmid38604487, year = {2024}, author = {Zhang, Y and Huang, C and Zhao, J and Hu, L and Yang, L and Zhang, Y and Sang, W}, title = {Insights into tolerance mechanisms of earthworms (Eisenia fetida) in copper-contaminated soils by integrating multi-omics analyses.}, journal = {Environmental research}, volume = {252}, number = {Pt 2}, pages = {118910}, doi = {10.1016/j.envres.2024.118910}, pmid = {38604487}, issn = {1096-0953}, mesh = {*Oligochaeta/metabolism/drug effects ; Animals ; *Soil Pollutants/toxicity/metabolism ; *Copper/toxicity/metabolism ; Gastrointestinal Microbiome/drug effects ; Metabolomics ; Oxidative Stress/drug effects ; Multiomics ; }, abstract = {Earthworms can resist high levels of soil copper (Cu) contamination and play an essential role in absorbing them effectively. However, the molecular mechanisms underlying Cu tolerance in earthworms are poorly understood. To address this research gap, we studied alterations of Eisenia fetida in antioxidant enzymes, gut microbiota, metabolites, and genes under varying levels of Cu exposure soils (0, 67.58, 168.96, 337.92 mg/kg). Our results revealed a reduction in antioxidant enzyme activities across all treatment groups, indicating an adaptive response to alleviate Cu-induced oxidative stress. Analysis of gut microbiota revealed a significant increase in the abundance of bacteria associated with nutrient uptake and Cu[2+] excretion under Cu stress. Furthermore, metabolomic analysis discovered an increase in certain metabolites associated with energy metabolism, such as pyruvic acid, L-malic acid, and fumaric acid, as Cu concentration escalated. These results suggested that enhanced energy supply contributes to the elevated tolerance of E. fetida towards Cu. Additionally, transcriptome analysis not only identified crucial detoxification genes (Hsp70, CTSL, GST, CHAC, and GCLC), but also confirmed the critical role of glutathione metabolism as a key pathway in E. fetida Cu detoxification processes. These findings provide a new perspective on the molecular mechanisms of Cu tolerance in earthworms.}, } @article {pmid38602562, year = {2024}, author = {Nurkassimova, M and Omarova, N and Zinicovscaia, I and Yushin, N and Chaligava, O}, title = {Mosses as bioindicators of air pollution with potentially toxic elements in the Burabay State National Natural Park, Kazakhstan.}, journal = {Environmental monitoring and assessment}, volume = {196}, number = {5}, pages = {442}, pmid = {38602562}, issn = {1573-2959}, mesh = {Humans ; Environmental Biomarkers ; Parks, Recreational ; Kazakhstan ; Environmental Monitoring ; *Air Pollution ; *Bryophyta ; }, abstract = {The Burabay State National Natural Park is a national park of the great natural and historical values located in the north of Kazakhstan, which has been exposed in recent years to significant anthropogenic impact. The moss biomonitoring was performed in the Borovoye resort community, an important tourist destination in the national park, to identify the level of air pollution. Mosses collected at 29 locations were subjected to neutron activation analysis to determine 36 elements and additionally to ICP-OES to detect the level of Cu and Pb. Factor analysis was applied to check if there are any associations between identified elements and to link them with possible emission sources. According to contamination factor and pollution load indices the investigated area belongs to three classes of pollution: unpolluted, suspected and moderate. Potential ecological risk index calculated for selected elements revealed harmless risk to human health. The level of element obtained in Burabay State National Natural Park was compared with the data available for other national parks.}, } @article {pmid38598963, year = {2024}, author = {Shen, C and Feng, G and Zhao, F and Huang, X and Li, X}, title = {The multi-omics analysis in the hepatopancreas of Eriocheir sinensis provides novel insights into the response mechanism of heat stress.}, journal = {Comparative biochemistry and physiology. Part D, Genomics & proteomics}, volume = {50}, number = {}, pages = {101232}, doi = {10.1016/j.cbd.2024.101232}, pmid = {38598963}, issn = {1878-0407}, mesh = {Animals ; *Hepatopancreas/metabolism ; *Brachyura/physiology/genetics/metabolism ; *Heat-Shock Response ; *Arthropod Proteins/genetics/metabolism ; *Proteomics ; Transcriptome ; Energy Metabolism ; Heat-Shock Proteins/genetics/metabolism ; Proteome ; Multiomics ; }, abstract = {Under global warming, heat stress can induce the excessive production of reactive oxygen species, causing irreversible damage to aquatic animals. It is essential to predict potentially harmful impacts on aquatic organisms under heat stress. Eriocheir sinensis, a typical crustacean crab, is widely distributed in China, American and Europe. Parent E. sinensis need migrate to the estuaries to reproduce in winter, and temperature is a key environmental factor. Herein, we performed a comprehensive transcriptomic and proteomic analysis in the hepatopancreas of E. sinensis under heat stress (20 °C and 30 °C), focusing on heat shock protein family, antioxidant system, energy metabolism and immune defense. The results revealed that parent E. sinensis generated adaptative responses to maintain physiological function under 20 °C stress via the transcriptional up-regulation of energy metabolism enzymes, mRNA synthesis and heat shock proteins. The transcriptional inhibition of key enzymes related to energy metabolism implied that 30 °C stress may lead to the dysfunction of energy metabolism in parent E. sinensis. Meanwhile, parent E. sinensis also enhanced the expression of ferritin and phospholipase D at translational level, and the glutathione s-transferase and heat shock protein 70 at both transcriptional and translational levels, speculating that parent E. sinensis can strengthen antioxidant and immune capacity to resist oxidative stress under 30 °C stress. This study elucidated the potential molecular mechanism in response to heat stress of parent E. sinensis hepatopancreas. The preliminary selection of heat tolerance genes or proteins in E. sinensis can provide a reference for the population prediction and the study of evolutionary mechanism under heat stress in crabs.}, } @article {pmid38598334, year = {2024}, author = {Wei, X and Tsai, MS and Liang, L and Jiang, L and Hung, CJ and Jelliffe-Pawlowski, L and Rand, L and Snyder, M and Jiang, C}, title = {Vaginal microbiomes show ethnic evolutionary dynamics and positive selection of Lactobacillus adhesins driven by a long-term niche-specific process.}, journal = {Cell reports}, volume = {43}, number = {4}, pages = {114078}, doi = {10.1016/j.celrep.2024.114078}, pmid = {38598334}, issn = {2211-1247}, mesh = {Humans ; *Vagina/microbiology ; Female ; *Microbiota/genetics ; *Lactobacillus/genetics ; Adhesins, Bacterial/genetics ; Ethnicity/genetics ; Adult ; Evolution, Molecular ; Pregnancy ; Selection, Genetic ; Biological Evolution ; }, abstract = {The vaginal microbiome's composition varies among ethnicities. However, the evolutionary landscape of the vaginal microbiome in the multi-ethnic context remains understudied. We perform a systematic evolutionary analysis of 351 vaginal microbiome samples from 35 multi-ethnic pregnant women, in addition to two validation cohorts, totaling 462 samples from 90 women. Microbiome alpha diversity and community state dynamics show strong ethnic signatures. Lactobacillaceae have a higher ratio of non-synonymous to synonymous polymorphism and lower nucleotide diversity than non-Lactobacillaceae in all ethnicities, with a large repertoire of positively selected genes, including the mucin-binding and cell wall anchor genes. These evolutionary dynamics are driven by the long-term evolutionary process unique to the human vaginal niche. Finally, we propose an evolutionary model reflecting the environmental niches of microbes. Our study reveals the extensive ethnic signatures in vaginal microbial ecology and evolution, highlighting the importance of studying the host-microbiome ecosystem from an evolutionary perspective.}, } @article {pmid38597343, year = {2024}, author = {Schwartz, LC and González, VL and Strong, EE and Truebano, M and Hilbish, TJ}, title = {Transgressive gene expression and expression plasticity under thermal stress in a stable hybrid zone.}, journal = {Molecular ecology}, volume = {33}, number = {9}, pages = {e17333}, doi = {10.1111/mec.17333}, pmid = {38597343}, issn = {1365-294X}, support = {//National Museum of Natural History/ ; //University of South Carolina/ ; }, mesh = {Animals ; *Hybridization, Genetic ; Temperature ; Climate Change ; Stress, Physiological/genetics ; Gene Expression/genetics ; Phenotype ; Mytilus/genetics ; Transcriptome ; }, abstract = {Interspecific hybridization can lead to myriad outcomes, including transgressive phenotypes in which the hybrids are more fit than either parent species. Such hybrids may display important traits in the context of climate change, able to respond to novel environmental conditions not previously experienced by the parent populations. While this has been evaluated in an agricultural context, the role of transgressive hybrids under changing conditions in the wild remains largely unexplored; this is especially true regarding transgressive gene expression. Using the blue mussel species complex (genus Mytilus) as a model system, we investigated the effects of hybridization on temperature induced gene expression plasticity by comparing expression profiles in parental species and their hybrids following a 2-week thermal challenge. Hybrid expression plasticity was most often like one parent or the other (50%). However, a large fraction of genes (26%) showed transgressive expression plasticity (i.e. the change in gene expression was either greater or lesser than that of both parent species), while only 2% were intermediately plastic in hybrids. Despite their close phylogenetic relationship, there was limited overlap in the differentially expressed genes responding to temperature, indicating interspecific differences in the responses to high temperature in which responses from hybrids are distinct from both parent species. We also identified differentially expressed long non-coding RNAs (lncRNAs), which we suggest may contribute to species-specific differences in thermal tolerance. Our findings provide important insight into the impact of hybridization on gene expression under warming. We propose transgressive hybrids may play an important role in population persistence under future warming conditions.}, } @article {pmid38594342, year = {2024}, author = {Brodie, JF and Mohd-Azlan, J and Chen, C and Wearn, OR and Deith, MCM and Ball, JGC and Slade, EM and Burslem, DFRP and Teoh, SW and Williams, PJ and Nguyen, A and Moore, JH and Goetz, SJ and Burns, P and Jantz, P and Hakkenberg, CR and Kaszta, ZM and Cushman, S and Coomes, D and Helmy, OE and Reynolds, G and Rodríguez, JP and Jetz, W and Luskin, MS}, title = {Author Correction: Landscape-scale benefits of protected areas for tropical biodiversity.}, journal = {Nature}, volume = {628}, number = {8009}, pages = {E5}, doi = {10.1038/s41586-024-07333-z}, pmid = {38594342}, issn = {1476-4687}, } @article {pmid38594221, year = {2024}, author = {Mujica, MI and Silva-Flores, P and Bueno, CG and Duchicela, J}, title = {Integrating perspectives in developing mycorrhizal trait databases: a call for inclusive and collaborative continental efforts.}, journal = {The New phytologist}, volume = {242}, number = {4}, pages = {1436-1440}, doi = {10.1111/nph.19754}, pmid = {38594221}, issn = {1469-8137}, support = {Ramón y Cajal fellowship #RYC2021-032533-I//Ministerio de Ciencia e Innovación/ ; 11230870//Fondo Nacional de Desarrollo Científico y Tecnológico/ ; 3200774//Fondo Nacional de Desarrollo Científico y Tecnológico/ ; }, mesh = {Biodiversity ; Databases, Factual ; *Mycorrhizae/physiology ; Quantitative Trait, Heritable ; *Symbiosis ; }, abstract = {Global assessments of mycorrhizal symbiosis present large sampling gaps in rich biodiversity regions. Filling these gaps is necessary to build large-scale, unbiased mycorrhizal databases to obtain reliable analyses and prevent misleading generalizations. Underrepresented regions in mycorrhizal research are mainly in Africa, Asia, and South America. Despite the high biodiversity and endemism in these regions, many groups of organisms remain understudied, especially mycorrhizal fungi. In this Viewpoint, we emphasize the importance of inclusive and collaborative continental efforts in integrating perspectives for comprehensive trait database development and propose a conceptual framework that can help build large mycorrhizal databases in underrepresented regions. Based on the four Vs of big data (volume, variety, veracity, and velocity), we identify the main challenges of constructing a large mycorrhizal dataset and propose solutions for each challenge. We share our collaborative methodology, which involves employing open calls and working groups to engage all mycorrhizal researchers in the region to build a South American Mycorrhizal Database. By fostering interdisciplinary collaborations and embracing a continental-scale approach, we can create robust mycorrhizal trait databases that provide valuable insights into the evolution, ecology, and functioning of mycorrhizal associations, reducing the geographical biases that are so common in large-scale ecological studies.}, } @article {pmid38589621, year = {2024}, author = {Liew, F and Efstathiou, C and Fontanella, S and Richardson, M and Saunders, R and Swieboda, D and Sidhu, JK and Ascough, S and Moore, SC and Mohamed, N and Nunag, J and King, C and Leavy, OC and Elneima, O and McAuley, HJC and Shikotra, A and Singapuri, A and Sereno, M and Harris, VC and Houchen-Wolloff, L and Greening, NJ and Lone, NI and Thorpe, M and Thompson, AAR and Rowland-Jones, SL and Docherty, AB and Chalmers, JD and Ho, LP and Horsley, A and Raman, B and Poinasamy, K and Marks, M and Kon, OM and Howard, LS and Wootton, DG and Quint, JK and de Silva, TI and Ho, A and Chiu, C and Harrison, EM and Greenhalf, W and Baillie, JK and Semple, MG and Turtle, L and Evans, RA and Wain, LV and Brightling, C and Thwaites, RS and Openshaw, PJM and , and , }, title = {Large-scale phenotyping of patients with long COVID post-hospitalization reveals mechanistic subtypes of disease.}, journal = {Nature immunology}, volume = {25}, number = {4}, pages = {607-621}, pmid = {38589621}, issn = {1529-2916}, support = {/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Humans ; Post-Acute COVID-19 Syndrome ; *COVID-19 ; *Biomedical Research ; Hospitalization ; Immunoglobulin G ; }, abstract = {One in ten severe acute respiratory syndrome coronavirus 2 infections result in prolonged symptoms termed long coronavirus disease (COVID), yet disease phenotypes and mechanisms are poorly understood[1]. Here we profiled 368 plasma proteins in 657 participants ≥3 months following hospitalization. Of these, 426 had at least one long COVID symptom and 233 had fully recovered. Elevated markers of myeloid inflammation and complement activation were associated with long COVID. IL-1R2, MATN2 and COLEC12 were associated with cardiorespiratory symptoms, fatigue and anxiety/depression; MATN2, CSF3 and C1QA were elevated in gastrointestinal symptoms and C1QA was elevated in cognitive impairment. Additional markers of alterations in nerve tissue repair (SPON-1 and NFASC) were elevated in those with cognitive impairment and SCG3, suggestive of brain-gut axis disturbance, was elevated in gastrointestinal symptoms. Severe acute respiratory syndrome coronavirus 2-specific immunoglobulin G (IgG) was persistently elevated in some individuals with long COVID, but virus was not detected in sputum. Analysis of inflammatory markers in nasal fluids showed no association with symptoms. Our study aimed to understand inflammatory processes that underlie long COVID and was not designed for biomarker discovery. Our findings suggest that specific inflammatory pathways related to tissue damage are implicated in subtypes of long COVID, which might be targeted in future therapeutic trials.}, } @article {pmid38587202, year = {2024}, author = {Montfort, J and Hervas-Sotomayor, F and Le Cam, A and Murat, F}, title = {FEVER: an interactive web-based resource for evolutionary transcriptomics across fishes.}, journal = {Nucleic acids research}, volume = {52}, number = {W1}, pages = {W65-W69}, pmid = {38587202}, issn = {1362-4962}, support = {ANR-23-CE13-0008//ANR/ ; }, mesh = {Animals ; *Fishes/genetics ; *Evolution, Molecular ; *Transcriptome/genetics ; *Internet ; Gene Expression Profiling/methods ; Databases, Genetic ; Phylogeny ; Genomics/methods ; Software ; Genome/genetics ; }, abstract = {Teleost fish represent one of the largest and most diverse clades of vertebrates, which makes them great models in various research areas such as ecology and evolution. Recent sequencing endeavors provided high-quality genomes for species covering the main fish evolutionary lineages, opening up large-scale comparative genomics studies. However, transcriptomic data across fish species and organs are heterogenous and have not been integrated with newly sequenced genomes making gene expression quantification and comparative analyses particularly challenging. Thus, resources integrating genomic and transcriptomic data across fish species and organs are still lacking. Here, we present FEVER, a web-based resource allowing evolutionary transcriptomics across species and tissues. First, based on query genes FEVER reconstructs gene trees providing orthologous and paralogous relationships as well as their evolutionary dynamics across 13 species covering the major fish lineages, and 4 model species as evolutionary outgroups. Second, it provides unbiased gene expression across 11 tissues using up-to-date fish genomes. Finally, genomic and transcriptomic data are combined together allowing the exploration of gene expression evolution following speciation and duplication events. FEVER is freely accessible at https://fever.sk8.inrae.fr/.}, } @article {pmid38584951, year = {2024}, author = {Badiyal, A and Mahajan, R and Rana, RS and Sood, R and Walia, A and Rana, T and Manhas, S and Jayswal, DK}, title = {Synergizing biotechnology and natural farming: pioneering agricultural sustainability through innovative interventions.}, journal = {Frontiers in plant science}, volume = {15}, number = {}, pages = {1280846}, pmid = {38584951}, issn = {1664-462X}, abstract = {The world has undergone a remarkable transformation from the era of famines to an age of global food production that caters to an exponentially growing population. This transformation has been made possible by significant agricultural revolutions, marked by the intensification of agriculture through the infusion of mechanical, industrial, and economic inputs. However, this rapid advancement in agriculture has also brought about the proliferation of agricultural inputs such as pesticides, fertilizers, and irrigation, which have given rise to long-term environmental crises. Over the past two decades, we have witnessed a concerning plateau in crop production, the loss of arable land, and dramatic shifts in climatic conditions. These challenges have underscored the urgent need to protect our global commons, particularly the environment, through a participatory approach that involves countries worldwide, regardless of their developmental status. To achieve the goal of sustainability in agriculture, it is imperative to adopt multidisciplinary approaches that integrate fields such as biology, engineering, chemistry, economics, and community development. One noteworthy initiative in this regard is Zero Budget Natural Farming, which highlights the significance of leveraging the synergistic effects of both plant and animal products to enhance crop establishment, build soil fertility, and promote the proliferation of beneficial microorganisms. The ultimate aim is to create self-sustainable agro-ecosystems. This review advocates for the incorporation of biotechnological tools in natural farming to expedite the dynamism of such systems in an eco-friendly manner. By harnessing the power of biotechnology, we can increase the productivity of agro-ecology and generate abundant supplies of food, feed, fiber, and nutraceuticals to meet the needs of our ever-expanding global population.}, } @article {pmid38583934, year = {2024}, author = {Swanson, SA and Miller, M}, title = {Toward a clearer understanding of what works to reduce gun violence: the role of falsification strategies.}, journal = {American journal of epidemiology}, volume = {193}, number = {8}, pages = {1061-1065}, doi = {10.1093/aje/kwae036}, pmid = {38583934}, issn = {1476-6256}, mesh = {Humans ; *Gun Violence/prevention & control/statistics & numerical data ; United States ; *Firearms/legislation & jurisprudence ; Data Interpretation, Statistical ; Homicide/prevention & control/statistics & numerical data ; Wounds, Gunshot/prevention & control/epidemiology ; }, abstract = {Strong epidemiologic evidence from ecological and individual-level studies in the United States supports the claim that access to firearms substantially increases the risk of dying by suicide, homicide, and firearm accidents. Less certain is how well particular interventions work to prevent these deaths and other firearm-related harms. Given the limits of existing data to study firearm violence and the infeasibility of conducting randomized trials of firearm access, it is important to do the best we can with the data we already have. We argue that falsification strategies are a critical-yet underutilized-component of any such analytical approach. The falsification strategies we focus on are versions of "negative controls" analyses in which we expect that an analysis should yield a null causal effect, and thus where not obtaining a null effect estimate raises questions about the assumptions underlying causal interpretation of a study's findings. We illustrate the saliency of this issue today with examples drawn from studies published in leading peer-reviewed journals within the last 5 years. Collecting rich, high-quality data always takes time, urgent as the need may be. On the other hand, doing better with the data we already have can start right now.}, } @article {pmid38581683, year = {2024}, author = {Loos, D and Filho, APDC and Dutilh, BE and Barber, AE and Panagiotou, G}, title = {A global survey of host, aquatic, and soil microbiomes reveals shared abundance and genomic features between bacterial and fungal generalists.}, journal = {Cell reports}, volume = {43}, number = {4}, pages = {114046}, doi = {10.1016/j.celrep.2024.114046}, pmid = {38581683}, issn = {2211-1247}, mesh = {*Soil Microbiology ; *Fungi/genetics/classification ; *Microbiota/genetics ; *Bacteria/genetics/classification ; Humans ; Biodiversity ; Genomics/methods ; Phylogeny ; }, abstract = {Environmental change, coupled with alteration in human lifestyles, is profoundly impacting the microbial communities critical to the health of the Earth and its inhabitants. To identify bacteria and fungi that are resistant and susceptible to habitat change, we analyze thousands of genera detected in 1,580 host, soil, and aquatic samples. This large-scale analysis identifies 48 bacterial and 4 fungal genera that are abundant across the three biomes, demonstrating fitness in diverse environmental conditions. Samples containing these generalists have significantly higher alpha diversity. These generalists play a significant role in shaping cross-kingdom community structure, boasting larger genomes with more secondary metabolism and antimicrobial resistance genes. Conversely, 30 bacterial and 19 fungal genera are only found in a single habitat, suggesting a limited ability to adapt to different and changing environments. These findings contribute to our understanding of microbial niche breadth and its consequences for global biodiversity loss.}, } @article {pmid38581418, year = {2024}, author = {Chen, Z and Ain, NU and Zhao, Q and Zhang, X}, title = {From tradition to innovation: conventional and deep learning frameworks in genome annotation.}, journal = {Briefings in bioinformatics}, volume = {25}, number = {3}, pages = {}, pmid = {38581418}, issn = {1477-4054}, support = {2021YFF1000900//National Key Research and Development Program of China/ ; RCYX20210706092103024//Shenzhen Science and Technology Program/ ; 32222019//National Natural Science Foundation of China/ ; }, mesh = {Humans ; *Deep Learning ; Genome ; Algorithms ; Software ; Computational Biology/methods ; Molecular Sequence Annotation ; }, abstract = {Following the milestone success of the Human Genome Project, the 'Encyclopedia of DNA Elements (ENCODE)' initiative was launched in 2003 to unearth information about the numerous functional elements within the genome. This endeavor coincided with the emergence of numerous novel technologies, accompanied by the provision of vast amounts of whole-genome sequences, high-throughput data such as ChIP-Seq and RNA-Seq. Extracting biologically meaningful information from this massive dataset has become a critical aspect of many recent studies, particularly in annotating and predicting the functions of unknown genes. The core idea behind genome annotation is to identify genes and various functional elements within the genome sequence and infer their biological functions. Traditional wet-lab experimental methods still rely on extensive efforts for functional verification. However, early bioinformatics algorithms and software primarily employed shallow learning techniques; thus, the ability to characterize data and features learning was limited. With the widespread adoption of RNA-Seq technology, scientists from the biological community began to harness the potential of machine learning and deep learning approaches for gene structure prediction and functional annotation. In this context, we reviewed both conventional methods and contemporary deep learning frameworks, and highlighted novel perspectives on the challenges arising during annotation underscoring the dynamic nature of this evolving scientific landscape.}, } @article {pmid38578160, year = {2024}, author = {Zhang, T and Peng, W and Xiao, H and Cao, S and Chen, Z and Su, X and Luo, Y and Liu, Z and Peng, Y and Yang, X and Jiang, GF and Xu, X and Ma, Z and Zhou, Y}, title = {Population genomics highlights structural variations in local adaptation to saline coastal environments in woolly grape.}, journal = {Journal of integrative plant biology}, volume = {66}, number = {7}, pages = {1408-1426}, doi = {10.1111/jipb.13653}, pmid = {38578160}, issn = {1744-7909}, support = {20210020//Guangxi University, Bama Institute of Integration of Industry and Education, postgraduate joint training project/ ; 20210039//Guangxi University, Bama Institute of Integration of Industry and Education, postgraduate joint training project/ ; 2023YFF1000100//the National Key Research and Development Program of China/ ; 2023YFD2200700//the National Key Research and Development Program of China/ ; 32300191//National Natural Science Foundation of China/ ; 32372662//National Natural Science Foundation of China/ ; No.20210020;No.20210039//Guangxi University, Bama Institute of Integration of Industry and Education, postgraduate joint training project/ ; 2023YFF1000100;2023YFD2200700;//the National Key Research and Development Program of China/ ; No.32300191;No.32372662//National Natural Science Foundation of China/ ; }, mesh = {*Vitis/genetics ; Adaptation, Physiological/genetics ; Genome, Plant/genetics ; Genetics, Population ; Polymorphism, Single Nucleotide/genetics ; Salt Tolerance/genetics ; Genomic Structural Variation/genetics ; Genomics ; Genes, Plant ; }, abstract = {Structural variations (SVs) are a feature of plant genomes that has been largely unexplored despite their significant impact on plant phenotypic traits and local adaptation to abiotic and biotic stress. In this study, we employed woolly grape (Vitis retordii), a species native to the tropical and subtropical regions of East Asia with both coastal and inland habitats, as a valuable model for examining the impact of SVs on local adaptation. We assembled a haplotype-resolved chromosomal reference genome for woolly grape, and conducted population genetic analyses based on whole-genome sequencing (WGS) data from coastal and inland populations. The demographic analyses revealed recent bottlenecks in all populations and asymmetric gene flow from the inland to the coastal population. In total, 1,035 genes associated with plant adaptive regulation for salt stress, radiation, and environmental adaptation were detected underlying local selection by SVs and SNPs in the coastal population, of which 37.29% and 65.26% were detected by SVs and SNPs, respectively. Candidate genes such as FSD2, RGA1, and AAP8 associated with salt tolerance were found to be highly differentiated and selected during the process of local adaptation to coastal habitats in SV regions. Our study highlights the importance of SVs in local adaptation; candidate genes related to salt stress and climatic adaptation to tropical and subtropical environments are important genomic resources for future breeding programs of grapevine and its rootstocks.}, } @article {pmid38577785, year = {2024}, author = {Baril, T and Galbraith, J and Hayward, A}, title = {Earl Grey: A Fully Automated User-Friendly Transposable Element Annotation and Analysis Pipeline.}, journal = {Molecular biology and evolution}, volume = {41}, number = {4}, pages = {}, pmid = {38577785}, issn = {1537-1719}, support = {/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; *DNA Transposable Elements/genetics ; Molecular Sequence Annotation ; *Drosophila melanogaster/genetics ; Genomics/methods ; Computational Biology ; }, abstract = {Transposable elements (TEs) are major components of eukaryotic genomes and are implicated in a range of evolutionary processes. Yet, TE annotation and characterization remain challenging, particularly for nonspecialists, since existing pipelines are typically complicated to install, run, and extract data from. Current methods of automated TE annotation are also subject to issues that reduce overall quality, particularly (i) fragmented and overlapping TE annotations, leading to erroneous estimates of TE count and coverage, and (ii) repeat models represented by short sections of total TE length, with poor capture of 5' and 3' ends. To address these issues, we present Earl Grey, a fully automated TE annotation pipeline designed for user-friendly curation and annotation of TEs in eukaryotic genome assemblies. Using nine simulated genomes and an annotation of Drosophila melanogaster, we show that Earl Grey outperforms current widely used TE annotation methodologies in ameliorating the issues mentioned above while scoring highly in benchmarking for TE annotation and classification and being robust across genomic contexts. Earl Grey provides a comprehensive and fully automated TE annotation toolkit that provides researchers with paper-ready summary figures and outputs in standard formats compatible with other bioinformatics tools. Earl Grey has a modular format, with great scope for the inclusion of additional modules focused on further quality control and tailored analyses in future releases.}, } @article {pmid38569653, year = {2024}, author = {Augustijn, HE and Roseboom, AM and Medema, MH and van Wezel, GP}, title = {Harnessing regulatory networks in Actinobacteria for natural product discovery.}, journal = {Journal of industrial microbiology & biotechnology}, volume = {51}, number = {}, pages = {}, pmid = {38569653}, issn = {1476-5535}, support = {948770/ERC_/European Research Council/International ; }, mesh = {*Actinobacteria/metabolism/genetics ; *Biological Products/metabolism ; Biosynthetic Pathways ; Computational Biology/methods ; *Drug Discovery ; Gene Expression Regulation, Bacterial ; *Gene Regulatory Networks ; Multigene Family ; Transcription Factors/metabolism/genetics ; }, abstract = {UNLABELLED: Microbes typically live in complex habitats where they need to rapidly adapt to continuously changing growth conditions. To do so, they produce an astonishing array of natural products with diverse structures and functions. Actinobacteria stand out for their prolific production of bioactive molecules, including antibiotics, anticancer agents, antifungals, and immunosuppressants. Attention has been directed especially towards the identification of the compounds they produce and the mining of the large diversity of biosynthetic gene clusters (BGCs) in their genomes. However, the current return on investment in random screening for bioactive compounds is low, while it is hard to predict which of the millions of BGCs should be prioritized. Moreover, many of the BGCs for yet undiscovered natural products are silent or cryptic under laboratory growth conditions. To identify ways to prioritize and activate these BGCs, knowledge regarding the way their expression is controlled is crucial. Intricate regulatory networks control global gene expression in Actinobacteria, governed by a staggering number of up to 1000 transcription factors per strain. This review highlights recent advances in experimental and computational methods for characterizing and predicting transcription factor binding sites and their applications to guide natural product discovery. We propose that regulation-guided genome mining approaches will open new avenues toward eliciting the expression of BGCs, as well as prioritizing subsets of BGCs for expression using synthetic biology approaches.

ONE-SENTENCE SUMMARY: This review provides insights into advances in experimental and computational methods aimed at predicting transcription factor binding sites and their applications to guide natural product discovery.}, } @article {pmid38560995, year = {2024}, author = {Stiller, J and Feng, S and Chowdhury, AA and Rivas-González, I and Duchêne, DA and Fang, Q and Deng, Y and Kozlov, A and Stamatakis, A and Claramunt, S and Nguyen, JMT and Ho, SYW and Faircloth, BC and Haag, J and Houde, P and Cracraft, J and Balaban, M and Mai, U and Chen, G and Gao, R and Zhou, C and Xie, Y and Huang, Z and Cao, Z and Yan, Z and Ogilvie, HA and Nakhleh, L and Lindow, B and Morel, B and Fjeldså, J and Hosner, PA and da Fonseca, RR and Petersen, B and Tobias, JA and Székely, T and Kennedy, JD and Reeve, AH and Liker, A and Stervander, M and Antunes, A and Tietze, DT and Bertelsen, MF and Lei, F and Rahbek, C and Graves, GR and Schierup, MH and Warnow, T and Braun, EL and Gilbert, MTP and Jarvis, ED and Mirarab, S and Zhang, G}, title = {Complexity of avian evolution revealed by family-level genomes.}, journal = {Nature}, volume = {629}, number = {8013}, pages = {851-860}, pmid = {38560995}, issn = {1476-4687}, mesh = {Animals ; *Birds/genetics/classification/anatomy & histology ; Brain/anatomy & histology ; *Evolution, Molecular ; Extinction, Biological ; *Genome/genetics ; Genomics ; *Phylogeny ; Population Density ; Male ; Female ; }, abstract = {Despite tremendous efforts in the past decades, relationships among main avian lineages remain heavily debated without a clear resolution. Discrepancies have been attributed to diversity of species sampled, phylogenetic method and the choice of genomic regions[1-3]. Here we address these issues by analysing the genomes of 363 bird species[4] (218 taxonomic families, 92% of total). Using intergenic regions and coalescent methods, we present a well-supported tree but also a marked degree of discordance. The tree confirms that Neoaves experienced rapid radiation at or near the Cretaceous-Palaeogene boundary. Sufficient loci rather than extensive taxon sampling were more effective in resolving difficult nodes. Remaining recalcitrant nodes involve species that are a challenge to model due to either extreme DNA composition, variable substitution rates, incomplete lineage sorting or complex evolutionary events such as ancient hybridization. Assessment of the effects of different genomic partitions showed high heterogeneity across the genome. We discovered sharp increases in effective population size, substitution rates and relative brain size following the Cretaceous-Palaeogene extinction event, supporting the hypothesis that emerging ecological opportunities catalysed the diversification of modern birds. The resulting phylogenetic estimate offers fresh insights into the rapid radiation of modern birds and provides a taxon-rich backbone tree for future comparative studies.}, } @article {pmid38560613, year = {2024}, author = {Boyes, D and Gibbs, M and , and , and , and , and , and , }, title = {The genome sequence of the Brown Oak Tortrix, Archips crataeganus (Hübner, 1796).}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {9}, pmid = {38560613}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual female Archips crataeganus (the Brown Oak Tortrix; Arthropoda; Insecta; Lepidoptera; Tortricidae). The genome sequence is 626.9 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z and W sex chromosomes. The mitochondrial genome has also been assembled and is 16.64 kilobases in length. Gene annotation of this assembly on Ensembl identified 19,596 protein coding genes.}, } @article {pmid38554963, year = {2024}, author = {Li, W and Feng, Q and Li, Z and Jin, T and Zhang, Y and Southam, G}, title = {Inhibition of iron oxidation in Acidithiobacillus ferrooxidans by low-molecular-weight organic acids: Evaluation of performance and elucidation of mechanisms.}, journal = {The Science of the total environment}, volume = {927}, number = {}, pages = {171919}, doi = {10.1016/j.scitotenv.2024.171919}, pmid = {38554963}, issn = {1879-1026}, mesh = {*Acidithiobacillus/metabolism/drug effects ; *Iron/metabolism ; *Oxidation-Reduction ; Mining ; Formates/metabolism ; Acetic Acid/metabolism ; *Propionates ; }, abstract = {The catalytic role of Acidithiobacillus ferrooxidans (A. ferrooxidans) in iron biooxidation is pivotal in the formation of Acid Mine Drainage (AMD), which poses a significant threat to the environment. To control AMD generation, treatments with low-molecular-weight organic acids are being studied, yet their exact mechanisms are unclear. In this study, AMD materials, organic acids, and molecular methods were employed to gain a deeper understanding of the inhibitory effects of low-molecular-weight organic acids on the biooxidation of iron by A. ferrooxidans. The inhibition experiments of A. ferrooxidans on the oxidation of Fe[2+] showed that to attain a 90 % inhibition efficacy within 72 h, the minimum concentrations required for formic acid, acetic acid, propionic acid, and lactic acid are 0.5, 6, 4, and 10 mmol/L, respectively. Bacterial imaging illustrated the detrimental effects of these organic acids on the cell envelope structure. This includes severe damage to the outer membrane, particularly from formic and acetic acids, which also caused cell wall damage. Coupled with alterations in the types and quantities of protein, carbohydrate, and nucleic acid content in extracellular polymeric substances (EPS), indicate the mechanisms underlying these inhibitory treatments. Transcriptomic analysis revealed interference of these organic acids with crucial metabolic pathways, particularly those related to energy metabolism. These findings establish a comprehensive theoretical basis for understanding the inhibition of A. ferrooxidans' biooxidation by low-molecular-weight organic acids, offering a novel opportunity to effectively mitigate the generation of AMD at its source.}, } @article {pmid38554685, year = {2024}, author = {Sfriso, AA and Juhmani, AS and Tomio, Y and Sfriso, A and Rizzolio, F and Adeel, M and Wahsha, M and Munari, C and Mistri, M}, title = {Microplastic accumulation and ecological impacts on benthic invertebrates: Insights from a microcosm experiment.}, journal = {Marine pollution bulletin}, volume = {202}, number = {}, pages = {116231}, doi = {10.1016/j.marpolbul.2024.116231}, pmid = {38554685}, issn = {1879-3363}, mesh = {Animals ; *Water Pollutants, Chemical/analysis ; *Invertebrates ; *Environmental Monitoring ; *Microplastics ; Aquatic Organisms ; Ecosystem ; }, abstract = {Microplastic (MP) pollution poses a global concern, especially for benthic invertebrates. This one-month study investigated the accumulation of small MP polymers (polypropylene and polyester resin, 3-500 μm, 250 μg L[-1]) in benthic invertebrates and on one alga species. Results revealed species-specific preferences for MP size and type, driven by ingestion, adhesion, or avoidance behaviours. Polyester resin accumulated in Mytilus galloprovincialis, Chamelea gallina, Hexaplex trunculus, and Paranemonia cinerea, while polypropylene accumulated on Ulva rigida. Over time, MP accumulation decreased in count but not size, averaging 6.2 ± 5.0 particles per individual after a month. MP were mainly found inside of the organisms, especially in the gut, gills, and gonads and externally adherent MP ranged from 11 to 35 % of the total. Biochemical energy assessments after two weeks of MP exposure indicated energy gains for water column species but energy loss for sediment-associated species, highlighting the susceptibility of infaunal benthic communities to MP contamination.}, } @article {pmid38552719, year = {2024}, author = {Martin, NG and Defres, S and Willis, L and Beckley, R and Hardwick, H and Coxon, A and Kadambari, S and Yu, LM and Liu, X and Galal, U and Conlin, K and Griffiths, MJ and Kneen, R and Nadel, S and Heath, PT and Kelly, DE and Solomon, T and Sadarangani, M and Pollard, AJ and , }, title = {Paediatric meningitis in the conjugate vaccine era and a novel clinical decision model to predict bacterial aetiology.}, journal = {The Journal of infection}, volume = {88}, number = {5}, pages = {106145}, doi = {10.1016/j.jinf.2024.106145}, pmid = {38552719}, issn = {1532-2742}, mesh = {Humans ; Child ; Infant ; *Meningitis, Bacterial/diagnosis/cerebrospinal fluid/microbiology ; Child, Preschool ; Adolescent ; Female ; Male ; Prospective Studies ; *Vaccines, Conjugate ; *Meningitis, Viral/diagnosis/cerebrospinal fluid ; Clinical Decision Rules ; United Kingdom/epidemiology ; Neisseria meningitidis/isolation & purification ; Streptococcus pneumoniae/isolation & purification ; Decision Support Techniques ; }, abstract = {OBJECTIVES: The aims of this study were to assess aetiology and clinical characteristics in childhood meningitis, and develop clinical decision rules to distinguish bacterial meningitis from other similar clinical syndromes.

METHODS: Children aged <16 years hospitalised with suspected meningitis/encephalitis were included, and prospectively recruited at 31 UK hospitals. Meningitis was defined as identification of bacteria/viruses from cerebrospinal fluid (CSF) and/or a raised CSF white blood cell count. New clinical decision rules were developed to distinguish bacterial from viral meningitis and those of alternative aetiology.

RESULTS: The cohort included 3002 children (median age 2·4 months); 1101/3002 (36·7%) had meningitis, including 180 bacterial, 423 viral and 280 with no pathogen identified. Enterovirus was the most common pathogen in those aged <6 months and 10-16 years, with Neisseria meningitidis and/or Streptococcus pneumoniae commonest at age 6 months to 9 years. The Bacterial Meningitis Score had a negative predictive value of 95·3%. We developed two clinical decision rules, that could be used either before (sensitivity 82%, specificity 71%) or after lumbar puncture (sensitivity 84%, specificity 93%), to determine risk of bacterial meningitis.

CONCLUSIONS: Bacterial meningitis comprised 6% of children with suspected meningitis/encephalitis. Our clinical decision rules provide potential novel approaches to assist with identifying children with bacterial meningitis.

FUNDING: This study was funded by the Meningitis Research Foundation, Pfizer and the NIHR Programme Grants for Applied Research.}, } @article {pmid38552245, year = {2024}, author = {Han, B and Tian, D and Li, X and Liu, S and Tian, F and Liu, D and Wang, S and Zhao, K}, title = {Multiomics Analyses Provide New Insight into Genetic Variation of Reproductive Adaptability in Tibetan Sheep.}, journal = {Molecular biology and evolution}, volume = {41}, number = {3}, pages = {}, pmid = {38552245}, issn = {1537-1719}, support = {No. 2022-ZJ-901//Natural Science Foundation of Qinghai Province/ ; }, mesh = {Humans ; Female ; Sheep/genetics ; Animals ; Tibet ; *Genome-Wide Association Study ; *Multiomics ; Proteomics ; Reproduction ; Mutation ; }, abstract = {Domestication and artificial selection during production-oriented breeding have greatly shaped the level of genomic variability in sheep. However, the genetic variation associated with increased reproduction remains elusive. Here, two groups of samples from consecutively monotocous and polytocous sheep were collected for genome-wide association, transcriptomic, proteomic, and metabolomic analyses to explore the genetic variation in fecundity in Tibetan sheep. Genome-wide association study revealed strong associations between BMPR1B (p.Q249R) and litter size, as well as between PAPPA and lambing interval; these findings were validated in 1,130 individuals. Furthermore, we constructed the first single-cell atlas of Tibetan sheep ovary tissues and identified a specific mural granulosa cell subtype with PAPPA-specific expression and differential expression of BMPR1B between the two groups. Bulk RNA-seq indicated that BMPR1B and PAPPA expressions were similar between the two groups of sheep. 3D protein structure prediction and coimmunoprecipitation analysis indicated that mutation and mutually exclusive exons of BMPR1B are the main mechanisms for prolific Tibetan sheep. We propose that PAPPA is a key gene for stimulating ovarian follicular growth and development, and steroidogenesis. Our work reveals the genetic variation in reproductive performance in Tibetan sheep, providing insights and valuable genetic resources for the discovery of genes and regulatory mechanisms that improve reproductive success.}, } @article {pmid38552150, year = {2024}, author = {Howard-Varona, C and Lindback, MM and Fudyma, JD and Krongauz, A and Solonenko, NE and Zayed, AA and Andreopoulos, WB and Olson, HM and Kim, YM and Kyle, JE and Glavina Del Rio, T and Adkins, JN and Tfaily, MM and Paul, S and Sullivan, MB and Duhaime, MB}, title = {Environment-specific virocell metabolic reprogramming.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {38552150}, issn = {1751-7370}, support = {2149505//NSF Advances in Biological Informatics/ ; DE-AC05-76RL0-1830//U.S. Department of Energy/ ; //Joint Genome Institute/ ; //U.S. Department of Energy/ ; 1536989//National Science Foundation/ ; //University of Michigan/ ; 034//C-CoMP/ ; //Department of Energy/ ; T32 AI112542/AI/NIAID NIH HHS/United States ; 2055455//NSF Polar Programs/ ; 1-T32-AI-112542//National Institutes of Health (NIH)/National Institute of Allergy and Infectious Diseases (NIAID)/ ; //Facilities Integrating Collaborations for User Science/ ; 3790//Gordon and Betty Moore Foundation/ ; //EMSL/ ; //Office of Science/ ; DGE1256260//NSF Graduate Research Fellowship/ ; DE-AC02-05CH11231//Biological and Environmental Research/ ; C-CoMP NSF-STC 2019589//NSF Center for Chemical Currencies of a Microbial Planet/ ; //Environmental Molecular Sciences Laboratory/ ; DE-SC0020173//Office of Biological and Environmental Research/ ; }, mesh = {*Bacteriophages/genetics/physiology ; Proteomics ; Phosphates/metabolism ; Metabolomics ; Systems Biology ; Transcriptome ; Metabolic Reprogramming ; }, abstract = {Viruses impact microbial systems through killing hosts, horizontal gene transfer, and altering cellular metabolism, consequently impacting nutrient cycles. A virus-infected cell, a "virocell," is distinct from its uninfected sister cell as the virus commandeers cellular machinery to produce viruses rather than replicate cells. Problematically, virocell responses to the nutrient-limited conditions that abound in nature are poorly understood. Here we used a systems biology approach to investigate virocell metabolic reprogramming under nutrient limitation. Using transcriptomics, proteomics, lipidomics, and endo- and exo-metabolomics, we assessed how low phosphate (low-P) conditions impacted virocells of a marine Pseudoalteromonas host when independently infected by two unrelated phages (HP1 and HS2). With the combined stresses of infection and nutrient limitation, a set of nested responses were observed. First, low-P imposed common cellular responses on all cells (virocells and uninfected cells), including activating the canonical P-stress response, and decreasing transcription, translation, and extracellular organic matter consumption. Second, low-P imposed infection-specific responses (for both virocells), including enhancing nitrogen assimilation and fatty acid degradation, and decreasing extracellular lipid relative abundance. Third, low-P suggested virocell-specific strategies. Specifically, HS2-virocells regulated gene expression by increasing transcription and ribosomal protein production, whereas HP1-virocells accumulated host proteins, decreased extracellular peptide relative abundance, and invested in broader energy and resource acquisition. These results suggest that although environmental conditions shape metabolism in common ways regardless of infection, virocell-specific strategies exist to support viral replication during nutrient limitation, and a framework now exists for identifying metabolic strategies of nutrient-limited virocells in nature.}, } @article {pmid38551211, year = {2024}, author = {Groote-Woortmann, W and Korbel, K and Hose, GC}, title = {STYGOTOX: A Quality-Assessed Database of (Eco)Toxicological Data on Stygofauna and Other Aquatic Subterranean Organisms.}, journal = {Environmental toxicology and chemistry}, volume = {43}, number = {12}, pages = {2492-2500}, pmid = {38551211}, issn = {1552-8618}, support = {LP190100927//Australian Research Council/ ; }, mesh = {Animals ; *Water Pollutants, Chemical/toxicity ; *Aquatic Organisms/drug effects ; *Databases, Factual ; Environmental Monitoring ; Risk Assessment ; }, abstract = {We have compiled the toxicity data on stygofauna and other aquatic subterranean organisms in one (eco)toxicological database. A total of 46 studies were found, containing 472 toxic endpoints covering 43 different stressors. These compounds were tested on subterranean organisms from four phyla, 12 orders, 24 genera, and 55 species. The studies included were published between 1976 and December 2023 using fauna collected in 13 different countries. The suitability of the studies was assessed to indicate the completeness of reporting and their suitability for use in hazard and risk assessment. This compilation provides a valuable source of data for future development of toxicity testing protocols for groundwater organisms, and to support decision-making, ecological risk assessments and the derivation of water quality criteria for the protection of groundwater ecosystems. Environ Toxicol Chem 2024;43:2492-2500. © 2024 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals LLC on behalf of SETAC.}, } @article {pmid38547306, year = {2024}, author = {Milić, D and Rat, M and Bokić, B and Mudri-Stojnić, S and Milošević, N and Sukur, N and Jakovetić, D and Radak, B and Tot, T and Vujanović, D and Anačkov, G and Radišić, D}, title = {Exploring the effects of habitat management on grassland biodiversity: A case study from northern Serbia.}, journal = {PloS one}, volume = {19}, number = {3}, pages = {e0301391}, pmid = {38547306}, issn = {1932-6203}, mesh = {Animals ; *Grassland ; Serbia ; *Ecosystem ; Biodiversity ; Agriculture ; Insecta ; Plants ; Birds/physiology ; }, abstract = {Grasslands represent a biodiversity hotspot in the European agricultural landscape, their restoration is necessary and offers a great opportunity to mitigate or halt harmful processes. These measures require a comprehensive knowledge of historical landscape changes, but also adequate management strategies. The required data was gathered from the sand grasslands of northern Serbia, as this habitat is of high conservation priority. This area also has a long history of different habitat management approaches (grazing and mowing versus unmanaged), which has been documented over of the last two decades. This dataset enabled us to quantify the effects of different measures across multiple taxa (plants, insect pollinators, and birds). We linked the gathered data on plants, pollinators, and birds with habitat management measures. Our results show that, at the taxon level, the adopted management strategies were beneficial for species richness, abundance, and composition, as the highest diversity of plant, insect pollinator, and bird species was found in managed areas. Thus, an innovative modelling approach was adopted in this work to identify and explain the effects of management practices on changes in habitat communities. The findings yielded can be used in the decision making as well as development of new management programmes. We thus posit that, when restoring and establishing particular communities, priority needs to be given to species with a broad ecological response. We recommend using the decision tree as a suitable machine learning model for this purpose.}, } @article {pmid38540697, year = {2024}, author = {Giordano, D and Bonora, S and D'Orsi, I and D'Alelio, D and Facchiano, A}, title = {Structural and Functional Characterization of Lipoxygenases from Diatoms by Bioinformatics and Modelling Studies.}, journal = {Biomolecules}, volume = {14}, number = {3}, pages = {}, pmid = {38540697}, issn = {2218-273X}, mesh = {*Lipoxygenases/chemistry/genetics ; *Diatoms/genetics ; Oxylipins ; Phylogeny ; Molecular Docking Simulation ; Ecosystem ; Computational Biology ; }, abstract = {Lipoxygenases make several biological functions in cells, based on the products of the catalyzed reactions. In diatoms, microalgae ubiquitous in aquatic ecosystems, lipoxygenases have been noted for the oxygenation of fatty acids with the production of oxylipins, which are involved in many physiological and pathological processes in marine organisms. The interest in diatoms' lipoxygenases and oxylipins has increased due to their possible biotechnological applications, ranging from ecology to medicine. We investigated using bioinformatics and molecular docking tools the lipoxygenases of diatoms and the possible interaction with substrates. A large-scale analysis of sequence resources allowed us to retrieve 45 sequences of lipoxygenases from diatoms. We compared and analyzed the sequences by multiple alignments and phylogenetic trees, suggesting the possible clustering in phylogenetic groups. Then, we modelled the 3D structure of representative enzymes from the different groups and investigated in detail the structural and functional properties by docking simulations with possible substrates. The results allowed us to propose a classification of the lipoxygenases from diatoms based on their sequence features, which may be reflected in specific structural differences and possible substrate specificity.}, } @article {pmid38540627, year = {2024}, author = {Santric-Milicevic, M and Pavlekic, K and Bukumiric, Z and Stevanovic, A and Nikolic, D and Matejic, B and Matanovic, D and Backovic, D and Tulic, G and Lukic, R and Zivanovic, D and Radosavljevic, S and Milovanovic, V and Zdujic, M and Stankovic, S and Asanin, M and Zdravkovic, M and Tomasevic, R}, title = {Nurses' Perception of Tension, Stress, and Pressure before and during the COVID-19 Pandemic: A Multicenter Serbian Study.}, journal = {Healthcare (Basel, Switzerland)}, volume = {12}, number = {6}, pages = {}, pmid = {38540627}, issn = {2227-9032}, abstract = {The mental health of healthcare workers, especially the nursing staff in intensive care units, is crucial for the optimal functioning of healthcare systems during medical emergencies. This study implements a cross-sectional design to investigate the associations between nurses' personal characteristics, workplace challenges, and job satisfaction with the increased perception of tension, stress, and pressure at the workplace (TSPW) before and during the COVID-19 pandemic. In 2021, we surveyed 4210 nurses from 19 intensive healthcare facilities in the capital of Serbia, Belgrade, and, at that time, collected data about their perceived TSPW before and during the COVID-19 pandemic. Our study identified six predictors of the increase in TSPW, as perceived by nurses: their work in COVID-19 infectious zones (OR = 1.446), exhaustion due to work under protective equipment (OR = 1.413), uncertainty and fear of infection (OR = 1.481), a high degree of superiors' appreciation and respect (OR = 1.147), a high degree of patients' attitudes (OR = 1.111), and a low degree of work autonomy (OR = 0.889). The study's findings suggest that a solution to this issue is necessary to ensure that nurses are safe and able to alleviate the physical and mental strain that comes with prolonged use of protective equipment. Nurses on the frontline of the pandemic require better health protection, better conditions, and respect for their role. Strategies to promote mental health would help reduce nurses' stress and increase job satisfaction.}, } @article {pmid38538788, year = {2024}, author = {Johnson, TF and Beckerman, AP and Childs, DZ and Webb, TJ and Evans, KL and Griffiths, CA and Capdevila, P and Clements, CF and Besson, M and Gregory, RD and Thomas, GH and Delmas, E and Freckleton, RP}, title = {Revealing uncertainty in the status of biodiversity change.}, journal = {Nature}, volume = {628}, number = {8009}, pages = {788-794}, pmid = {38538788}, issn = {1476-4687}, mesh = {Animals ; *Biodiversity ; Conservation of Natural Resources/methods/trends ; Datasets as Topic ; Phylogeny ; Spatio-Temporal Analysis ; Time Factors ; *Uncertainty ; }, abstract = {Biodiversity faces unprecedented threats from rapid global change[1]. Signals of biodiversity change come from time-series abundance datasets for thousands of species over large geographic and temporal scales. Analyses of these biodiversity datasets have pointed to varied trends in abundance, including increases and decreases. However, these analyses have not fully accounted for spatial, temporal and phylogenetic structures in the data. Here, using a new statistical framework, we show across ten high-profile biodiversity datasets[2-11] that increases and decreases under existing approaches vanish once spatial, temporal and phylogenetic structures are accounted for. This is a consequence of existing approaches severely underestimating trend uncertainty and sometimes misestimating the trend direction. Under our revised average abundance trends that appropriately recognize uncertainty, we failed to observe a single increasing or decreasing trend at 95% credible intervals in our ten datasets. This emphasizes how little is known about biodiversity change across vast spatial and taxonomic scales. Despite this uncertainty at vast scales, we reveal improved local-scale prediction accuracy by accounting for spatial, temporal and phylogenetic structures. Improved prediction offers hope of estimating biodiversity change at policy-relevant scales, guiding adaptive conservation responses.}, } @article {pmid38532952, year = {2024}, author = {Feutz, E and Biswas, PK and Ndeketa, L and Ogwel, B and Onwuchekwa, U and Sarwar, G and Sultana, S and Peñataro Yori, P and Acebedo, A and Ahmed, N and Ahmed, I and Atlas, HE and Awuor, AO and Bhuiyan, MAI and Conteh, B and Diawara, O and Elwood, S and Fane, M and Hossen, MI and Ireen, M and Jallow, AF and Karim, M and Kosek, MN and Kotloff, KL and Lefu, C and Liu, J and Maguire, R and Qamar, FN and Ndalama, M and Ochieng, JB and Okonji, C and Paredes, LFZ and Pavlinac, PB and Perez, K and Qureshi, S and Schiaffino, F and Traore, M and Tickell, KD and Wachepa, R and Witte, D and Cornick, J and Jahangir Hossain, M and Khanam, F and Olortegui, MP and Omore, R and Sow, SO and Yousafzai, MT and Galagan, SR}, title = {Data Management in Multicountry Consortium Studies: The Enterics For Global Health (EFGH) Shigella Surveillance Study Example.}, journal = {Open forum infectious diseases}, volume = {11}, number = {Suppl 1}, pages = {S48-S57}, pmid = {38532952}, issn = {2328-8957}, support = {D43 TW010913/TW/FIC NIH HHS/United States ; K43 TW012298/TW/FIC NIH HHS/United States ; UL1 TR002319/TR/NCATS NIH HHS/United States ; }, abstract = {BACKGROUND: Rigorous data management systems and planning are essential to successful research projects, especially for large, multicountry consortium studies involving partnerships across multiple institutions. Here we describe the development and implementation of data management systems and procedures for the Enterics For Global Health (EFGH) Shigella surveillance study-a 7-country diarrhea surveillance study that will conduct facility-based surveillance concurrent with population-based enumeration and a health care utilization survey to estimate the incidence of Shigella--associated diarrhea in children 6 to 35 months old.

METHODS: The goals of EFGH data management are to utilize the knowledge and experience of consortium members to collect high-quality data and ensure equity in access and decision-making. During the planning phase before study initiation, a working group of representatives from each EFGH country site, the coordination team, and other partners met regularly to develop the data management systems for the study.

RESULTS: This resulted in the Data Management Plan, which included selecting REDCap and SurveyCTO as the primary database systems. Consequently, we laid out procedures for data processing and storage, study monitoring and reporting, data quality control and assurance activities, and data access. The data management system and associated real-time visualizations allow for rapid data cleaning activities and progress monitoring and will enable quicker time to analysis.

CONCLUSIONS: Experiences from this study will contribute toward enriching the sparse landscape of data management methods publications and serve as a case study for future studies seeking to collect and manage data consistently and rigorously while maintaining equitable access to and control of data.}, } @article {pmid38531865, year = {2024}, author = {Corponi, F and Li, BM and Anmella, G and Mas, A and Pacchiarotti, I and Valentí, M and Grande, I and Benabarre, A and Garriga, M and Vieta, E and Lawrie, SM and Whalley, HC and Hidalgo-Mazzei, D and Vergari, A}, title = {Automated mood disorder symptoms monitoring from multivariate time-series sensory data: getting the full picture beyond a single number.}, journal = {Translational psychiatry}, volume = {14}, number = {1}, pages = {161}, pmid = {38531865}, issn = {2158-3188}, mesh = {Humans ; *Mood Disorders/diagnosis ; *Affect ; Machine Learning ; Sleep ; }, abstract = {Mood disorders (MDs) are among the leading causes of disease burden worldwide. Limited specialized care availability remains a major bottleneck thus hindering pre-emptive interventions. MDs manifest with changes in mood, sleep, and motor activity, observable in ecological physiological recordings thanks to recent advances in wearable technology. Therefore, near-continuous and passive collection of physiological data from wearables in daily life, analyzable with machine learning (ML), could mitigate this problem, bringing MDs monitoring outside the clinician's office. Previous works predict a single label, either the disease state or a psychometric scale total score. However, clinical practice suggests that the same label may underlie different symptom profiles, requiring specific treatments. Here we bridge this gap by proposing a new task: inferring all items in HDRS and YMRS, the two most widely used standardized scales for assessing MDs symptoms, using physiological data from wearables. To that end, we develop a deep learning pipeline to score the symptoms of a large cohort of MD patients and show that agreement between predictions and assessments by an expert clinician is clinically significant (quadratic Cohen's κ and macro-average F1 score both of 0.609). While doing so, we investigate several solutions to the ML challenges associated with this task, including multi-task learning, class imbalance, ordinal target variables, and subject-invariant representations. Lastly, we illustrate the importance of testing on out-of-distribution samples.}, } @article {pmid38531495, year = {2024}, author = {Yuan, Q and Yao, LF and Tang, JW and Ma, ZW and Mou, JY and Wen, XR and Usman, M and Wu, X and Wang, L}, title = {Rapid discrimination and ratio quantification of mixed antibiotics in aqueous solution through integrative analysis of SERS spectra via CNN combined with NN-EN model.}, journal = {Journal of advanced research}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jare.2024.03.016}, pmid = {38531495}, issn = {2090-1224}, abstract = {INTRODUCTION: Abusing antibiotic residues in the natural environment has become a severe public health and ecological environmental problem. The side effects of its biochemical and physiological consequences are severe. To avoid antibiotic contamination in water, implementing universal and rapid antibiotic residue detection technology is critical to maintaining antibiotic safety in aquatic environments. Surface-enhanced Raman spectroscopy (SERS) provides a powerful tool for identifying small molecular components with high sensitivity and selectivity. However, it remains a challenge to identify pure antibiotics from SERS spectra due to coexisting components in the mixture.

OBJECTIVES: In this study, an intelligent analysis model for the SERS spectrum based on a deep learning algorithm was proposed for rapid identification of the antibiotic components in the mixture and quantitative determination of the ratios of these components.

METHODS: We established a water environment system containing three antibiotic residues of ciprofloxacin, doxycycline, and levofloxacin. To facilitate qualitative and quantitative analysis of the SERS spectra antibiotic mixture datasets, we developed a computational framework integrating a convolutional neural network (CNN) and a non-negative elastic network (NN-EN) method.

RESULTS: The experimental results demonstrate that the CNN model has a recognition accuracy of 98.68%, and the interpretation analysis of Shapley Additive exPlanations (SHAP) shows that our model can specifically focus on the characteristic peak distribution. In contrast, the NN-EN model can accurately quantify each component's ratio in the mixture.

CONCLUSION: Integrating the SERS technique assisted by the CNN combined with the NN-EN model exhibits great potential for rapid identification and high-precision quantification of antibiotic residues in aquatic environments.}, } @article {pmid38531460, year = {2024}, author = {Enjavinejad, SM and Zahedifar, M and Moosavi, AA and Khosravani, P}, title = {Integrated application of multiple indicators and geographic information system-based approaches for comprehensive assessment of environmental impacts of toxic metals-contaminated agricultural soils and vegetables.}, journal = {The Science of the total environment}, volume = {926}, number = {}, pages = {171747}, doi = {10.1016/j.scitotenv.2024.171747}, pmid = {38531460}, issn = {1879-1026}, mesh = {Adult ; Child ; Humans ; Vegetables ; Geographic Information Systems ; Environmental Monitoring ; Cadmium/analysis ; Copper/analysis ; Lead/analysis ; Risk Assessment ; *Metals, Heavy/analysis ; Soil/chemistry ; Carcinogens/analysis ; Receptors, Antigen, T-Cell ; *Soil Pollutants/analysis ; China ; }, abstract = {Conventional monitoring and mapping approaches are laborious, expensive, and time-consuming because they need a large number of data and consequently extensive sampling and experimental operations. Therefore, due to the growing concern about the potential of contamination of soils and agricultural products with heavy metals (HMs), a field experiment was conducted on 77 farm lands in an area of 2300 ha in the southeast of Shiraz (Iran) to investigate the source of metal contamination in the soils and vegetables and to model spatial distribution of HMs (iron, Fe; manganese, Mn; copper, Cu; zinc, Zn; cadmium, Cd; nickel, Ni, and lead, Pb) over the region using geographic information system (GIS) and geostatistical (Ordinary Kriging, OK) approaches and compare the results with deterministic approaches (Inverse Distance Weighting, IDW with different weighting power). Furthermore, some ecological and health risks indices including Pollution index (PI), Nemerow integrated pollution index (NIPI), pollution load index (PLI), degree of contamination (Cdeg), modified contamination degree (mCd), PIaverage and PIvector for soil quality, multi-element contamination (MEC), the probability of toxicity (MERMQ), the potential ecological index (RI), total hazard index (THI) and total carcinogenic risk index (TCR) based on ingestion, inhalation, and dermal exposure pathways for adults and children respectively for analyzing the noncarcinogenic and carcinogenic risks were calculated. Experimental semivariogram of the mentioned HMs were calculated and theoretical models (i.e., exponential, spherical, Gaussian, and linear models) were fitted in order to model their spatial structures and to investigate the most representative models. Moreover, principal component analysis (PCA) and cluster analysis (CA) were used to identify sources of HMs in the soils. Results showed that IDW method was more efficient than the OK approach to estimate the properties and HMs contents in the soils and plants. The estimated daily intake of metals (DIM) values of Pb and Ni exceeded their safe limits. In addition, Cd was the main element responsible for ecological risk. The PIave and PIvector indices showed that soil quality in the study area is not suitable. According to mCd values, the soils classified as ultra-high contaminated for Cu and Cd, extremely high for Zn and Pb, very high, high, and very low degree of contamination for Ni, Mn, and Fe, respectively. 36, 60, and 4 % of the sampling sites had high, medium, and low risk levels with 49, 21, and 9 % probability of toxicity, respectively. The maximum health risk index (HRI) value of 20.42 with extremely high risk for children was obtained for Ni and the HI for adults and children were 0.22 and 1.55, respectively. The THI values of Pb and Cd were the highest compared to the other HMs studied, revealing a possible non-cancer risk in children associated with exposure to these metals. The routes of exposure with the greatest influence on the THI and TCR indices were in the order of ingestion > inhalation > dermal. Therefore, ingestion, as the main route of exposure, is the route of greatest contribution to health risks. PCA analysis revealed that Fe, Mn, Cu, and Ni may originate from natural sources, while Fe was appeared to be controlled by fertilizer, and Cu primarily coming from pesticide, while Cd and Pb were mainly associated with the anthropogenic contamination, atmospheric depositions, and terrific in the urban soils. While, Zn mainly originated from fertilization. Findings are vital for developing remediation approaches for controlling the contaminants distribution as well as for monitoring and mapping the quality and health of soil resources.}, } @article {pmid38528816, year = {2024}, author = {Del Bianco, T and Haartsen, R and Mason, L and Leno, VC and Springer, C and Potter, M and Mackay, W and Smit, P and Plessis, CD and Brink, L and Johnson, MH and Murphy, D and Loth, E and Odendaal, H and Jones, EJH}, title = {The importance of decomposing periodic and aperiodic EEG signals for assessment of brain function in a global context.}, journal = {Developmental psychobiology}, volume = {66}, number = {4}, pages = {e22484}, doi = {10.1002/dev.22484}, pmid = {38528816}, issn = {1098-2302}, support = {777394//EU/EFPIA/SFARI/Autistica/AUTISM SPEAKS Innovative Medicines Initiative 2 Joint Undertaking (AIMS-2-TRIALS)/ ; 115300//Innovative Medicines Initiative 1 Joint Undertaking (AIMS-2-TRIALS)/ ; MR/K021389/1//the Medical Research Council for the projects "The Development of Social Attention and Perception Abilities in Typical and At-risk Infants"/ ; MR/T003057/1//"Human neurocognitive development: Early-stage processing, modifiers, and outcomes"/ ; 213608/Z/18/Z//Sir Henry Wellcome Postdoctoral Fellowship/ ; MR/S036423/1//UK Research and Innovation/ ; }, mesh = {Child ; Humans ; Female ; *Electroencephalography ; *Brain ; Brain Mapping ; Cognition ; }, abstract = {Measures of early neuro-cognitive development that are suitable for use in low-resource settings are needed to enable studies of the effects of early adversity on the developing brain in a global context. These measures should have high acquisition rates and good face and construct validity. Here, we investigated the feasibility of a naturalistic electroencephalography (EEG) paradigm in a low-resource context during childhood. Additionally, we examined the sensitivity of periodic and aperiodic EEG metrics to social and non-social stimuli. We recorded simultaneous 20-channel EEG and eye-tracking in 72 children aged 4-12 years (45 females) while they watched videos of women singing nursery rhymes and moving toys, selected to represent familiar childhood experiences. These measures were part of a feasibility study that assessed the feasibility and acceptability of a follow-up data collection of the South African Safe Passage Study, which tracks environmental adversity and brain and cognitive development from before birth up until childhood. We examined whether data quantity and quality varied with child characteristics and the sensitivity of varying EEG metrics (canonical band power in the theta and alpha band and periodic and aperiodic features of the power spectra). We found that children who completed the EEG and eye-tracking assessment were, in general, representative of the full cohort. Data quantity was higher in children with greater visual attention to the stimuli. Out of the tested EEG metrics, periodic measures in the theta frequency range were most sensitive to condition differences, compared to alpha range measures and canonical and aperiodic EEG measures. Our results show that measuring EEG during ecologically valid social and non-social stimuli is feasible in low-resource settings, is feasible for most children, and produces robust indices of social brain function. This work provides preliminary support for testing longitudinal links between social brain function, environmental factors, and emerging behaviors.}, } @article {pmid38527064, year = {2024}, author = {Barrett, C and Chiphwanya, J and Mkwanda, S and Matipula, DE and Ndhlovu, P and Chaponda, L and Turner, JD and Giorgi, E and Betts, H and Martindale, S and Taylor, MJ and Read, JM and Kelly-Hope, LA}, title = {The national distribution of lymphatic filariasis cases in Malawi using patient mapping and geostatistical modelling.}, journal = {PLoS neglected tropical diseases}, volume = {18}, number = {3}, pages = {e0012056}, pmid = {38527064}, issn = {1935-2735}, mesh = {Humans ; *Elephantiasis, Filarial/epidemiology ; Malawi/epidemiology ; Prevalence ; Data Management ; Surveys and Questionnaires ; }, abstract = {BACKGROUND: In 2020 the World Health Organization (WHO) declared that Malawi had successfully eliminated lymphatic filariasis (LF) as a public health problem. Understanding clinical case distributions at a national and sub-national level is important, so essential care packages can be provided to individuals living with LF symptoms. This study aimed to develop a national database and map of LF clinical cases across Malawi using geostatistical modelling approaches, programme-identified clinical cases, antigenaemia prevalence and climate information.

METHODOLOGY: LF clinical cases identified through programme house-to-house surveys across 90 sub-district administrative boundaries (Traditional Authority (TA)) and antigenaemia prevalence from 57 sampled villages in Malawi were used in a two-step geostatistical modelling process to predict LF clinical cases across all TAs of the country. First, we modelled antigenaemia prevalence in relation to climate covariates to predict nationwide antigenaemia prevalence. Second, we modelled clinical cases for unmapped TAs based on our antigenaemia prevalence spatial estimates.

PRINCIPLE FINDINGS: The models estimated 20,938 (95% CrI 18,091 to 24,071) clinical cases in unmapped TAs (70.3%) in addition to the 8,856 (29.7%), programme-identified cases in mapped TAs. In total, the overall national number of LF clinical cases was estimated to be 29,794 (95% CrI 26,957 to 32,927). The antigenaemia prevalence and clinical case mapping and modelling found the highest burden of disease in Chikwawa and Nsanje districts in the Southern Region and Karonga district in the Northern Region of the country.

CONCLUSIONS: The models presented in this study have facilitated the development of the first national LF clinical case database and map in Malawi, the first endemic country in sub-Saharan Africa. It highlights the value of using existing LF antigenaemia prevalence and clinical case data together with modelling approaches to produce estimates that may be used for the WHO dossier requirements, to help target limited resources and implement long-term health strategies.}, } @article {pmid38523092, year = {2024}, author = {Ouyang, YY and Su, ZW and Li, CH and Zeng, AC and Guo, FT}, title = {Forest fire risk zoning based on fuzzy logic and analytical network process.}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {35}, number = {2}, pages = {354-362}, doi = {10.13287/j.1001-9332.202402.024}, pmid = {38523092}, issn = {1001-9332}, mesh = {Humans ; Fires/prevention & control ; Forests ; *Fuzzy Logic ; Geographic Information Systems ; Trees ; *Wildfires/statistics & numerical data ; }, abstract = {Forest fires have a significant impact on human life, property safety, and ecological environment. Deve-loping high-quality forest fire risk maps is beneficial for preventing forest fires, guiding resource allocation for firefighting, assisting in fire suppression efforts, and supporting decision-making. With a multi-criteria decision analysis (MCDA) method based on geographic information systems (GIS) and literature review, we assessed the main factors influencing the occurrences of forest fires in Youxi County, Fujian Province. We analyzed the importance of each fire risk factor using the analytic network process (ANP) and assigned weights, and evaluated the sub-standard weights using fuzzy logic assessment. Using ArcGIS aggregation functions, we generated a forest fire risk map and validated it with satellite fire points. The results showed that the areas classified as level 4 or higher fire risk accounted for a considerable proportion in Youxi County, and that the central and northern regions were at higher risk. The overall fire risk situation in the county was severe. The fuzzy ANP model demonstrated a high accuracy of 85.8%. The introduction of this novel MCDA method could effectively improve the accuracy of forest fire risk mapping at a small scale, providing a basis for early fire warning and the planning and allocation of firefighting resources.}, } @article {pmid38521905, year = {2024}, author = {Wu, J and Lv, Y and Hao, P and Zhang, Z and Zheng, Y and Chen, E and Fan, Y}, title = {Immunological profile of lactylation-related genes in Crohn's disease: a comprehensive analysis based on bulk and single-cell RNA sequencing data.}, journal = {Journal of translational medicine}, volume = {22}, number = {1}, pages = {300}, pmid = {38521905}, issn = {1479-5876}, support = {82300630//National Natural Science Foundation of China/ ; 2022GGB011//Project of Young and Middle-aged Backbone Talents Cultivation/ ; 2021J011329//Fujian Provincial Natural Science Foundation/ ; 2021QNB017//Health Science Foundation of Fujian Youth Program/ ; }, mesh = {Humans ; *Crohn Disease/genetics ; Databases, Factual ; Lactic Acid ; Sequence Analysis, RNA ; }, abstract = {BACKGROUND: Crohn's disease (CD) is a disease characterized by intestinal immune dysfunction, often accompanied by metabolic abnormalities. Disturbances in lactate metabolism have been found in the intestine of patients with CD, but studies on the role of lactate and related Lactylation in the pathogenesis of CD are still unknown.

METHODS: We identified the core genes associated with Lactylation by downloading and merging three CD-related datasets (GSE16879, GSE75214, and GSE112366) from the GEO database, and analyzed the functions associated with the hub genes and the correlation between their expression levels and immune infiltration through comprehensive analysis. We explored the Lactylation levels of different immune cells using single-cell data and further analyzed the differences in Lactylation levels between inflammatory and non-inflammatory sites.

RESULTS: We identified six Lactylation-related hub genes that are highly associated with CD. Further analysis revealed that these six hub genes were highly correlated with the level of immune cell infiltration. To further clarify the effect of Lactylation on immune cells, we analyzed single-cell sequencing data of immune cells from inflammatory and non-inflammatory sites in CD patients and found that there were significant differences in the levels of Lactylation between different types of immune cells, and that the levels of Lactylation were significantly higher in immune cells from inflammatory sites.

CONCLUSIONS: These results suggest that Lactylation-related genes and their functions are closely associated with changes in inflammatory cells in CD patients.}, } @article {pmid38514998, year = {2024}, author = {Alari, A and Ranzani, O and Olmos, S and Milà, C and Rico, A and Ballester, J and Basagaña, X and Dadvand, P and Duarte-Salles, T and Nieuwenhuijsen, M and Vivanco-Hidalgo, RM and Tonne, C}, title = {Short-term exposure to air pollution and hospital admission after COVID-19 in Catalonia: the COVAIR-CAT study.}, journal = {International journal of epidemiology}, volume = {53}, number = {2}, pages = {}, doi = {10.1093/ije/dyae041}, pmid = {38514998}, issn = {1464-3685}, support = {//Health Effects Institute/ ; }, mesh = {Humans ; Spain/epidemiology ; Cohort Studies ; Nitrogen Dioxide/adverse effects/analysis ; COVID-19 Testing ; *COVID-19/epidemiology ; *Air Pollution/adverse effects/analysis ; *Air Pollutants/adverse effects/analysis ; Particulate Matter/adverse effects/analysis ; *Ozone/adverse effects/analysis ; Hospitalization ; Hospitals ; Environmental Exposure/adverse effects/analysis ; }, abstract = {BACKGROUND: A growing body of evidence has reported positive associations between long-term exposure to air pollution and poor COVID-19 outcomes. Inconsistent findings have been reported for short-term air pollution, mostly from ecological study designs. Using individual-level data, we studied the association between short-term variation in air pollutants [nitrogen dioxide (NO2), particulate matter with a diameter of <2.5 µm (PM2.5) and a diameter of <10 µm (PM10) and ozone (O3)] and hospital admission among individuals diagnosed with COVID-19.

METHODS: The COVAIR-CAT (Air pollution in relation to COVID-19 morbidity and mortality: a large population-based cohort study in Catalonia, Spain) cohort is a large population-based cohort in Catalonia, Spain including 240 902 individuals diagnosed with COVID-19 in the primary care system from 1 March until 31 December 2020. Our outcome was hospitalization within 30 days of COVID-19 diagnosis. We used individual residential address to assign daily air-pollution exposure, estimated using machine-learning methods for spatiotemporal prediction. For each pandemic wave, we fitted Cox proportional-hazards models accounting for non-linear-distributed lagged exposure over the previous 7 days.

RESULTS: Results differed considerably by pandemic wave. During the second wave, an interquartile-range increase in cumulative weekly exposure to air pollution (lag0_7) was associated with a 12% increase (95% CI: 4% to 20%) in COVID-19 hospitalizations for NO2, 8% (95% CI: 1% to 16%) for PM2.5 and 9% (95% CI: 3% to 15%) for PM10. We observed consistent positive associations for same-day (lag0) exposure, whereas lag-specific associations beyond lag0 were generally not statistically significant.

CONCLUSIONS: Our study suggests positive associations between NO2, PM2.5 and PM10 and hospitalization risk among individuals diagnosed with COVID-19 during the second wave. Cumulative hazard ratios were largely driven by exposure on the same day as hospitalization.}, } @article {pmid38514747, year = {2024}, author = {Chanda, MM and Purse, BV and Hemadri, D and Patil, SS and Yogisharadhya, R and Prajapati, A and Shivachandra, SB}, title = {Spatial and temporal analysis of haemorrhagic septicaemia outbreaks in India over three decades (1987-2016).}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {6773}, pmid = {38514747}, issn = {2045-2322}, mesh = {Animals ; Cattle ; *Hemorrhagic Septicemia/epidemiology/veterinary/microbiology ; *Pasteurella multocida ; Buffaloes/microbiology ; Disease Outbreaks ; India/epidemiology ; *Cattle Diseases/microbiology ; }, abstract = {Haemorrhagic septicaemia (HS) is an economically important disease affecting cattle and buffaloes and the livelihoods of small-holder farmers that depend upon them. The disease is caused by Gram-negative bacterium, Pasteurella multocida, and is considered to be endemic in many states of India with more than 25,000 outbreaks in the past three decades. Currently, there is no national policy for control of HS in India. In this study, we analysed thirty year (1987-2016) monthly data on HS outbreaks using different statistical and mathematical methods to identify spatial variability and temporal patterns (seasonality, periodicity). There was zonal variation in the trend and seasonality of HS outbreaks. Overall, South zone reported maximum proportion of the outbreaks (70.2%), followed by East zone (7.2%), Central zone (6.4%), North zone (5.6%), West zone (5.5%) and North-East zone (4.9%). Annual state level analysis indicated that the reporting of HS outbreaks started at different years independently and there was no apparent transmission between the states. The results of the current study are useful for the policy makers to design national control programme on HS in India and implement state specific strategies. Further, our study and strategies could aid in implementation of similar approaches in HS endemic tropical countries around the world.}, } @article {pmid38514421, year = {2024}, author = {Morel, B and Williams, TA and Stamatakis, A and Szöllősi, GJ}, title = {AleRax: a tool for gene and species tree co-estimation and reconciliation under a probabilistic model of gene duplication, transfer, and loss.}, journal = {Bioinformatics (Oxford, England)}, volume = {40}, number = {4}, pages = {}, pmid = {38514421}, issn = {1367-4811}, support = {//Klaus Tschira Foundation/ ; /ERC_/European Research Council/International ; }, mesh = {Phylogeny ; *Gene Duplication ; *Algorithms ; Software ; Models, Statistical ; Evolution, Molecular ; }, abstract = {MOTIVATION: Genomes are a rich source of information on the pattern and process of evolution across biological scales. How best to make use of that information is an active area of research in phylogenetics. Ideally, phylogenetic methods should not only model substitutions along gene trees, which explain differences between homologous gene sequences, but also the processes that generate the gene trees themselves along a shared species tree. To conduct accurate inferences, one needs to account for uncertainty at both levels, that is, in gene trees estimated from inherently short sequences and in their diverse evolutionary histories along a shared species tree.

RESULTS: We present AleRax, a software that can infer reconciled gene trees together with a shared species tree using a simple, yet powerful, probabilistic model of gene duplication, transfer, and loss. A key feature of AleRax is its ability to account for uncertainty in the gene tree and its reconciliation by using an efficient approximation to calculate the joint phylogenetic-reconciliation likelihood and sample reconciled gene trees accordingly. Simulations and analyses of empirical data show that AleRax is one order of magnitude faster than competing gene tree inference tools while attaining the same accuracy. It is consistently more robust than species tree inference methods such as SpeciesRax and ASTRAL-Pro 2 under gene tree uncertainty. Finally, AleRax can process multiple gene families in parallel thereby allowing users to compare competing phylogenetic hypotheses and estimate model parameters, such as duplication, transfer, and loss probabilities for genome-scale datasets with hundreds of taxa.

GNU GPL at https://github.com/BenoitMorel/AleRax and data are made available at https://cme.h-its.org/exelixis/material/alerax_data.tar.gz.}, } @article {pmid38512945, year = {2024}, author = {Scalabrin, E and Radaelli, M and Capodaglio, G and Pierobon, M and Del Vecchio, S and Buffa, G}, title = {Hemp cultivation opportunities for marginal lands development.}, journal = {PloS one}, volume = {19}, number = {3}, pages = {e0299981}, pmid = {38512945}, issn = {1932-6203}, mesh = {*Cannabis ; Flowers ; Inflorescence ; Dietary Supplements ; Plant Leaves ; }, abstract = {Agricultural diversification and high-quality products deriving from sustainable crops such as hemp can represent a solution to revitalize marginal areas and reverse land abandonment. This study aimed at comparing four different hemp cultivars (Carmagnola Selezionata, "CS"; Futura 75, "FUT"; Felina 32, "FEL"; Secuieni Jubileu, "JUB") to provide information to select the best suited cultivar for cultivation in mountain marginal areas and for specific end-use applications. Hemp cultivars were cultivated in a single experimental field to compare their ecological and agronomic behavior (duration of life cycle phases, plant size and biomass allocation, and plant resource-use strategies). Through metabolomic analysis of both vegetative and reproductive parts of the plants we tested the presence of substances of nutraceutical interest and traced seed nutritional profile. The four cultivars had different ecological and agronomic behavior, and nutritional profile. We found several compounds with potential pharmaceutical and nutraceutical values in all parts of the plant (leaves, inflorescences, and stems). JUB resulted the most suitable for seed production while CS showed the highest content of bioactive compounds in flowers and leaves. FUT, showed the best suitability for multi-purpose cultivation, while FEL seemed to be not appropriate for the cultivation in mountain area. The multi-disciplinary approach we adopted was effective in distinguish across hemp cultivars and provided information to farmers for the selection of the best hemp cultivar to select. Hemp had a high potential for cultivation in marginal lands, demonstrating to be an economic resource due to its multi-purpose use and to the possibility to generate high-added values products. Our results could serve as a stimulus for the reintroduction of this culture in the study area and in other similar environments.}, } @article {pmid38509110, year = {2024}, author = {Berner, LT and Orndahl, KM and Rose, M and Tamstorf, M and Arndal, MF and Alexander, HD and Humphreys, ER and Loranty, MM and Ludwig, SM and Nyman, J and Juutinen, S and Aurela, M and Happonen, K and Mikola, J and Mack, MC and Vankoughnett, MR and Iversen, CM and Salmon, VG and Yang, D and Kumar, J and Grogan, P and Danby, RK and Scott, NA and Olofsson, J and Siewert, MB and Deschamps, L and Lévesque, E and Maire, V and Morneault, A and Gauthier, G and Gignac, C and Boudreau, S and Gaspard, A and Kholodov, A and Bret-Harte, MS and Greaves, HE and Walker, D and Gregory, FM and Michelsen, A and Kumpula, T and Villoslada, M and Ylänne, H and Luoto, M and Virtanen, T and Forbes, BC and Hölzel, N and Epstein, H and Heim, RJ and Bunn, A and Holmes, RM and Hung, JKY and Natali, SM and Virkkala, AM and Goetz, SJ}, title = {The Arctic Plant Aboveground Biomass Synthesis Dataset.}, journal = {Scientific data}, volume = {11}, number = {1}, pages = {305}, pmid = {38509110}, issn = {2052-4463}, support = {80NSSC21K1364//National Aeronautics and Space Administration (NASA)/ ; 80NSSC22K1247//National Aeronautics and Space Administration (NASA)/ ; 80NSSC22K1247//National Aeronautics and Space Administration (NASA)/ ; NNX12AK83G//National Aeronautics and Space Administration (NASA)/ ; NNX15AP04H//National Aeronautics and Space Administration (NASA)/ ; 2127273//National Science Foundation (NSF)/ ; 1417745//National Science Foundation (NSF)/ ; 1636476//National Science Foundation (NSF)/ ; 2224776//National Science Foundation (NSF)/ ; 2127273//National Science Foundation (NSF)/ ; 330319//Academy of Finland (Suomen Akatemia)/ ; 330319//Academy of Finland (Suomen Akatemia)/ ; 330845//Academy of Finland (Suomen Akatemia)/ ; 1342890//Academy of Finland (Suomen Akatemia)/ ; 256991//Academy of Finland (Suomen Akatemia)/ ; 2021-05767//Vetenskapsrådet (Swedish Research Council)/ ; FRQNT-2018-PR-208107//Fonds de Recherche du Québec - Nature et Technologies (Quebec Fund for Research in Nature and Technology)/ ; FRQNT-2018-PR-208107//Fonds de Recherche du Québec - Nature et Technologies (Quebec Fund for Research in Nature and Technology)/ ; }, mesh = {Arctic Regions ; Biomass ; *Ecosystem ; *Trees ; *Plants ; }, abstract = {Plant biomass is a fundamental ecosystem attribute that is sensitive to rapid climatic changes occurring in the Arctic. Nevertheless, measuring plant biomass in the Arctic is logistically challenging and resource intensive. Lack of accessible field data hinders efforts to understand the amount, composition, distribution, and changes in plant biomass in these northern ecosystems. Here, we present The Arctic plant aboveground biomass synthesis dataset, which includes field measurements of lichen, bryophyte, herb, shrub, and/or tree aboveground biomass (g m[-2]) on 2,327 sample plots from 636 field sites in seven countries. We created the synthesis dataset by assembling and harmonizing 32 individual datasets. Aboveground biomass was primarily quantified by harvesting sample plots during mid- to late-summer, though tree and often tall shrub biomass were quantified using surveys and allometric models. Each biomass measurement is associated with metadata including sample date, location, method, data source, and other information. This unique dataset can be leveraged to monitor, map, and model plant biomass across the rapidly warming Arctic.}, } @article {pmid38507308, year = {2024}, author = {Sánchez Reyes, LL and McTavish, EJ and O'Meara, B}, title = {DateLife: Leveraging Databases and Analytical Tools to Reveal the Dated Tree of Life.}, journal = {Systematic biology}, volume = {73}, number = {2}, pages = {470-485}, pmid = {38507308}, issn = {1076-836X}, support = {ABI-1458603//National Science Foundation/ ; DBI-0905606//National Evolutionary Synthesis Center/ ; ABI-1759846//Open Tree of Life project/ ; ABI-1458572//Phylotastic project/ ; }, mesh = {*Phylogeny ; *Classification/methods ; *Software ; Databases, Factual ; }, abstract = {Chronograms-phylogenies with branch lengths proportional to time-represent key data on timing of evolutionary events, allowing us to study natural processes in many areas of biological research. Chronograms also provide valuable information that can be used for education, science communication, and conservation policy decisions. Yet, achieving a high-quality reconstruction of a chronogram is a difficult and resource-consuming task. Here we present DateLife, a phylogenetic software implemented as an R package and an R Shiny web application available at www.datelife.org, that provides services for efficient and easy discovery, summary, reuse, and reanalysis of node age data mined from a curated database of expert, peer-reviewed, and openly available chronograms. The main DateLife workflow starts with one or more scientific taxon names provided by a user. Names are processed and standardized to a unified taxonomy, allowing DateLife to run a name match across its local chronogram database that is curated from Open Tree of Life's phylogenetic repository, and extract all chronograms that contain at least two queried taxon names, along with their metadata. Finally, node ages from matching chronograms are mapped using the congruification algorithm to corresponding nodes on a tree topology, either extracted from Open Tree of Life's synthetic phylogeny or one provided by the user. Congruified node ages are used as secondary calibrations to date the chosen topology, with or without initial branch lengths, using different phylogenetic dating methods such as BLADJ, treePL, PATHd8, and MrBayes. We performed a cross-validation test to compare node ages resulting from a DateLife analysis (i.e, phylogenetic dating using secondary calibrations) to those from the original chronograms (i.e, obtained with primary calibrations), and found that DateLife's node age estimates are consistent with the age estimates from the original chronograms, with the largest variation in ages occurring around topologically deeper nodes. Because the results from any software for scientific analysis can only be as good as the data used as input, we highlight the importance of considering the results of a DateLife analysis in the context of the input chronograms. DateLife can help to increase awareness of the existing disparities among alternative hypotheses of dates for the same diversification events, and to support exploration of the effect of alternative chronogram hypotheses on downstream analyses, providing a framework for a more informed interpretation of evolutionary results.}, } @article {pmid38506735, year = {2024}, author = {Stefanovic, M and Takano, K and Wittekind, CE and Ehring, T}, title = {Dynamic symptom associations in posttraumatic stress disorder: a network approach.}, journal = {European journal of psychotraumatology}, volume = {15}, number = {1}, pages = {2317675}, pmid = {38506735}, issn = {2000-8066}, mesh = {Humans ; *Stress Disorders, Post-Traumatic/diagnosis ; Anxiety ; Checklist ; Diagnostic and Statistical Manual of Mental Disorders ; Ecological Momentary Assessment ; }, abstract = {Background and objective: The current study aimed to investigate the within-day symptom dynamics in PTSD patients, specifically focusing on symptoms that most predict changes in other symptoms. The study included a baseline diagnostic assessment, followed by an assessment using the experience sampling method (ESM) via a smartphone.Method: Participants answered questions related to their PTSD symptoms four times per day for 15 consecutive days (compliance rate 75%). The clinical sample consisted of 48 treatment-seeking individuals: 44 with PTSD as a primary diagnosis, and four patients with subsyndromal PTSD, all of whom had not yet begun trauma-focused treatment. The ESM assessment included the 20 items from the PTSD Checklist for DSM-5, five items from the International Trauma Questionnaire (ITQ) assessing disturbances in relationships and functional impairment, and two items from the Clinician-Administered PTSD Scale for DSM-5 assessing symptoms of depersonalization and derealization.Results: Temporal networks (prospective associations between symptoms) showed that changes in hypervigilance predicted changes in the greatest number of symptoms at the next time point. Furthermore, hypervigilance showed temporal connections with at least one additional symptom from each of the DSM-5 PTSD symptom clusters.Conclusions: Results show that the contemporaneous network (representing the relationship between given symptoms within the same assessment occasion) and the temporal network (representing prospective associations between symptoms) differ and that it is important to estimate both. Some findings from earlier research are replicated, but heterogeneity across studies remains. Future studies should include potential moderators.}, } @article {pmid38505831, year = {2023}, author = {Clifton-Brown, J and Hastings, A and von Cossel, M and Murphy-Bokern, D and McCalmont, J and Whitaker, J and Alexopoulou, E and Amaducci, S and Andronic, L and Ashman, C and Awty-Carroll, D and Bhatia, R and Breuer, L and Cosentino, S and Cracroft-Eley, W and Donnison, I and Elbersen, B and Ferrarini, A and Ford, J and Greef, J and Ingram, J and Lewandowski, I and Magenau, E and Mos, M and Petrick, M and Pogrzeba, M and Robson, P and Rowe, RL and Sandu, A and Schwarz, KU and Scordia, D and Scurlock, J and Shepherd, A and Thornton, J and Trindade, LM and Vetter, S and Wagner, M and Wu, PC and Yamada, T and Kiesel, A}, title = {Perennial biomass cropping and use: Shaping the policy ecosystem in European countries.}, journal = {Global change biology. Bioenergy}, volume = {15}, number = {5}, pages = {538-558}, pmid = {38505831}, issn = {1757-1693}, abstract = {Demand for sustainably produced biomass is expected to increase with the need to provide renewable commodities, improve resource security and reduce greenhouse gas emissions in line with COP26 commitments. Studies have demonstrated additional environmental benefits of using perennial biomass crops (PBCs), when produced appropriately, as a feedstock for the growing bioeconomy, including utilisation for bioenergy (with or without carbon capture and storage). PBCs can potentially contribute to Common Agricultural Policy (CAP) (2023-27) objectives provided they are carefully integrated into farming systems and landscapes. Despite significant research and development (R&D) investment over decades in herbaceous and coppiced woody PBCs, deployment has largely stagnated due to social, economic and policy uncertainties. This paper identifies the challenges in creating policies that are acceptable to all actors. Development will need to be informed by measurement, reporting and verification (MRV) of greenhouse gas emissions reductions and other environmental, economic and social metrics. It discusses interlinked issues that must be considered in the expansion of PBC production: (i) available land; (ii) yield potential; (iii) integration into farming systems; (iv) R&D requirements; (v) utilisation options; and (vi) market systems and the socio-economic environment. It makes policy recommendations that would enable greater PBC deployment: (1) incentivise farmers and land managers through specific policy measures, including carbon pricing, to allocate their less productive and less profitable land for uses which deliver demonstrable greenhouse gas reductions; (2) enable greenhouse gas mitigation markets to develop and offer secure contracts for commercial developers of verifiable low-carbon bioenergy and bioproducts; (3) support innovation in biomass utilisation value chains; and (4) continue long-term, strategic R&D and education for positive environmental, economic and social sustainability impacts.}, } @article {pmid38493394, year = {2024}, author = {Ketterer, T and Sieke, E and Min, J and Quidgley-Martin, M and Barral, RL and Akers, A and Adams, A and Miller, E and Miller, MK and Mollen, C}, title = {Contraception Initiation in the Emergency Department: Adolescent Perspectives.}, journal = {The Journal of adolescent health : official publication of the Society for Adolescent Medicine}, volume = {75}, number = {1}, pages = {147-154}, pmid = {38493394}, issn = {1879-1972}, support = {K23 HD109464/HD/NICHD NIH HHS/United States ; R21 HD095096/HD/NICHD NIH HHS/United States ; }, mesh = {Humans ; Adolescent ; Female ; *Emergency Service, Hospital ; Pregnancy ; *Pregnancy in Adolescence/prevention & control ; *Contraception Behavior/psychology ; Health Knowledge, Attitudes, Practice ; Qualitative Research ; Prospective Studies ; Adolescent Behavior/psychology ; Interviews as Topic ; Contraception/psychology ; Counseling ; }, abstract = {PURPOSE: The purpose of this study was to identify factors affecting contraceptive intention and behavior among adolescent females in the pediatric Emergency Department.

METHODS: We conducted a qualitative interview study nested within a larger prospective cohort study examining adolescent contraceptive counseling for females ages 15-18 years at-risk of unintended pregnancy presenting to the pediatric Emergency Department. Interviews were conducted in a subset of participants. The ecologically expanded Theory of Planned Behavior, expert opinion, and literature review informed the interview guide. Interviews were recorded, transcribed, coded and monitored for thematic saturation.

RESULTS: Twenty-eight interviews were analyzed. Mean age was 17.1 years. Themes were mapped to ecologically expanded Theory of Planned Behavior constructs. Within health system influences, prior contraceptive experiences and patient-clinician interactions were described. Within community influences, contraceptive education, knowledge and misinformation, teen pregnancy norms, and social media impacts were described. Within attitudes influences, side-effect and safety concerns, contraceptive motivations and teen pregnancy beliefs were described. Within subjective norm influences, peer and family impacts were described. Within perceived behavioral control, Emergency Department (ED) counseling intervention impacts were described.

DISCUSSION: We identified factors affecting contraceptive initiation/behavior among an ED adolescent population that otherwise may not have received contraceptive education in similar detail as provided by study clinicians. Adolescents' prior contraceptive and clinician interactions, limited access to contraceptive education, knowledge and misinformation, and side-effect and safety concerns affected initiation. Peer/family sharing and social media were leading contraceptive information sources. Future studies should incorporate insights into adolescent ED intervention design to make optimal use of resources while maximizing potential benefit.}, } @article {pmid38493360, year = {2024}, author = {Wen, F and Liu, R and Garcia Y Garcia, A and Ye, H and Lu, L and Qimuge, E and Sun, Z and Nie, C and Han, X and Zhang, Y}, title = {Study on the prediction method of grasshopper occurrence risk in Inner Mongolia based on the maximum entropy model during the growing period.}, journal = {Journal of economic entomology}, volume = {117}, number = {3}, pages = {843-857}, doi = {10.1093/jee/toae036}, pmid = {38493360}, issn = {1938-291X}, support = {CBAS2022 DF001//Director of the International Research Center for Big Data for Sustainable SDG/ ; 420QN293//Hainan Provincial Natural Science Foundation of China/ ; 2021119//Youth Innovation Promotion Association CAS/ ; 2020 KTYWLZX08//Future Star Talent Program of Aerospace Information Research Institute, Chinese Academy of Sciences/ ; }, mesh = {*Grasshoppers/growth & development/physiology ; Animals ; Entropy ; *Models, Statistical ; Animal Husbandry ; Herbivory ; Population Dynamics ; Animal Migration ; Ecosystem ; Agriculture ; Ecological Momentary Assessment ; Geographic Information Systems ; Surveys and Questionnaires ; Remote Sensing Technology ; }, abstract = {Grasshoppers represent a significant biological challenge in Inner Mongolia's grasslands, severely affecting the region's animal husbandry. Thus, dynamic monitoring of grasshopper infestation risk is crucial for sustainable livestock farming. This study employed the Maxent model, along with remote sensing data, to forecast Oedaleus decorus asiaticus occurrence during the growing season, using grasshopper suitability habitats as a base. The Maxent model's predictive accuracy was high, with an AUC of 0.966. The most influential environmental variables for grasshopper distribution were suitable habitat data (34.27%), the temperature-vegetation dryness index during the spawning period (18.81%), and various other meteorological and vegetation factors. The risk index model was applied to calculate the grasshopper distribution across different risk levels for the years 2019-2022. The data indicated that the level 1 risk area primarily spans central, eastern, and southwestern Inner Mongolia. By examining the variable weights, the primary drivers of risk level fluctuation from 2019 to 2022 were identified as accumulated precipitation and land surface temperature anomalies during the overwintering period. This study offers valuable insights for future O. decorus asiaticus monitoring in Inner Mongolia.}, } @article {pmid38486028, year = {2024}, author = {Arslan, D and Akdağ, B and Yaşar, Ç and Olivier, A and Benedetti, Y and Morelli, F and Çiçek, K}, title = {An extensive database on the traits and occurrences of amphibian species in Turkey.}, journal = {Scientific data}, volume = {11}, number = {1}, pages = {292}, pmid = {38486028}, issn = {2052-4463}, mesh = {Animals ; *Amphibians ; Biodiversity ; *Ecosystem ; Turkey ; Databases, Factual ; }, abstract = {Amphibians are the most endangered taxa among vertebrates, and they face many threats during their complex life cycles. The species' life history traits and occurrence database help understand species responses against ecological factors. Consequently, the species-level-trait database has gained more prominence in recent years as a useful tool for understanding the dimensions of communities, assembly processes of communities, and conserving biodiversity at the ecosystem level against environmental changes. However, in Turkey, there are deficiencies in the knowledge of the ecological traits of amphibians compared to other vertebrate taxa, as most studies have focused on their distribution or taxonomic status. Consequently, there is a need to create such a database for future research on all known extant amphibians in Turkey. We compiled a species-level data set of species traits and occurrences for all amphibians in Turkey using 436 literature sources. We completed 36 trait categories with 5611 occurrence data for 37 amphibian species in Turkey. This study provides an open, useful, and comprehensive database for macroecological and conservation studies on amphibians in Turkey.}, } @article {pmid38483685, year = {2024}, author = {Guo, Y and Li, X and Li, Q and Hu, Z}, title = {Environmental impact assessment of acidic coal gangue leaching solution on groundwater: a coal gangue pile in Shanxi, China.}, journal = {Environmental geochemistry and health}, volume = {46}, number = {4}, pages = {120}, pmid = {38483685}, issn = {1573-2983}, mesh = {Coal/analysis ; Environmental Pollution ; Soil ; *Environmental Pollutants ; Ions ; China ; *Soil Pollutants/analysis ; *Coal Mining ; }, abstract = {With the continual advancement of coal resource development, the comprehensive utilization of coal gangue as a by-product encounters certain constraints. A substantial amount of untreated coal gangue is openly stored, particularly acidic gangue exposed to rainfall. The leaching effect of acidic solutions, containing heavy metal ions and other pollutants, results in environmental challenges such as local soil or groundwater pollution, presenting a significant concern in the current ecological landscape of mining areas. Investigating the migration patterns of pollutants in the soil-groundwater system and elucidating the characteristics of polluted solute migration are imperative. To understand the migration dynamics of pollutants and unveil the features of solute migration, this study focuses on a coal gangue dump in a mining area in Shanxi. Utilizing indoor leaching experiments and soil column migration experiments, a two-dimensional soil-groundwater model is established using the finite element method of COMSOL. This model quantitatively delineates the migration patterns of key pollutant components leached from coal gangue into the groundwater. The findings reveal that sulfate ions can migrate and infiltrate groundwater within a mere 7 years in the vadose zone of aeration. Moreover, the average concentration of iron ions in groundwater can reach approximately 58.3 mg/L. Convection, hydrodynamic dispersion, and adsorption emerge as the primary factors influencing pollution transport. Understanding the leaching patterns and environmental impacts of major pollutants in acidic coal gangue is crucial for predicting soil-groundwater pollution and implementing effective protective measures.}, } @article {pmid38483497, year = {2024}, author = {Yang, R and Feng, J and Tang, J and Sun, Y}, title = {Risk assessment and classification prediction for water environment treatment PPP projects.}, journal = {Water science and technology : a journal of the International Association on Water Pollution Research}, volume = {89}, number = {5}, pages = {1264-1281}, doi = {10.2166/wst.2024.052}, pmid = {38483497}, issn = {0273-1223}, mesh = {*Environment ; Risk Assessment ; *Risk Management ; }, abstract = {Water treatment public-private partnership (PPP) projects are pivotal for sustainable water management but are often challenged by complex risk factors. Efficient risk management in these projects is crucial, yet traditional methodologies often fall short of addressing the dynamic and intricate nature of these risks. Addressing this gap, this comprehensive study introduces an advanced risk classification prediction model tailored for water treatment PPP projects, aimed at enhancing risk management capabilities. The proposed model encompasses an intricate evaluation of crucial risk areas: the natural and ecological environments, socio-economic factors, and engineering entities. It delves into the complex relationships between these risk elements and the overall risk profile of projects. Grounded in a sophisticated ensemble learning framework employing stacking, our model is further refined through a weighted voting mechanism, significantly elevating its predictive accuracy. Rigorous validation using data from the Jiujiang City water environment system project Phase I confirms the model's superiority over standard machine learning models. The development of this model marks a significant stride in risk classification for water treatment PPP projects, offering a powerful tool for enhancing risk management practices. Beyond accurately predicting project risks, this model also aids in developing effective government risk management strategies.}, } @article {pmid38483377, year = {2024}, author = {Browning, CR and Pinchak, NP and Calder, CA and Boettner, B}, title = {Racial Differences in Activity Space Exposures and Everyday Perceptions of Safety Among Urban Youth.}, journal = {The Journal of adolescent health : official publication of the Society for Adolescent Medicine}, volume = {74}, number = {6}, pages = {1156-1163}, pmid = {38483377}, issn = {1879-1972}, support = {P2C HD042849/HD/NICHD NIH HHS/United States ; P2C HD058484/HD/NICHD NIH HHS/United States ; R01 DA032371/DA/NIDA NIH HHS/United States ; R01 HD088545/HD/NICHD NIH HHS/United States ; }, mesh = {Adolescent ; Child ; Female ; Humans ; Male ; *Black or African American/psychology ; Geographic Information Systems ; Ohio ; Perception ; *Residence Characteristics ; *Safety ; *Urban Population ; Violence/ethnology ; *White ; }, abstract = {PURPOSE: The everyday experience of safety promotes health and successful development during adolescence. To date, few studies have examined racial variation in the spatial determinants of in-the-moment perceived safety.

METHODS: Drawing on data from the Columbus, Ohio-based Adolescent Health and Development in Context study (N = 1,405), we consider the influence of intraindividual variability in Global Positioning System-based exposure to both high-proportion White urban neighborhoods and neighborhood violence for the everyday location-based safety perceptions of Black and White youth (ages 11-17) as captured by ecological momentary assessment.

RESULTS: Exposure to higher area-level violence reduces youths' safety perceptions. Momentary exposure to residentially White-dominated neighborhoods also reduces perceived safety, but only for Black youth who spend more time, on average, in White areas. In contrast, we observe some limited evidence that White youth perceive greater safety when in White neighborhoods if they spend more time in white neighborhoods on average.

DISCUSSION: These findings point to the need for greater attention to in situ experiences in understanding the origins of racial disparities in health and wellbeing. For Black youth, a restricted focus on the consequences of residing in Black segregated neighborhoods may obscure potentially health consequential exposures beyond these areas.}, } @article {pmid38482998, year = {2024}, author = {Furuya, S and Zheng, F and Lu, Q and Fletcher, JM}, title = {Separating Scarring Effect and Selection of Early-Life Exposures With Genetic Data.}, journal = {Demography}, volume = {61}, number = {2}, pages = {363-392}, doi = {10.1215/00703370-11239766}, pmid = {38482998}, issn = {1533-7790}, mesh = {Humans ; Infant ; Educational Status ; *Environmental Exposure ; Infant Mortality ; Life Change Events ; Prenatal Exposure Delayed Effects ; Gene-Environment Interaction ; }, abstract = {Causal life course research examining consequences of early-life exposures has largely relied on associations between early-life environments and later-life outcomes using exogenous environmental shocks. Nonetheless, even with (quasi-)randomized early-life exposures, these associations may reflect not only causation ("scarring") but also selection (i.e., which members are included in data assessing later life). Investigating this selection and its impacts on estimated effects of early-life conditions has, however, often been ignored because of a lack of pre-exposure data. This study proposes an approach for assessing and correcting selection, separately from scarring, using genetic measurements. Because genetic measurements are determined at the time of conception, any associations with early-life exposures should be interpreted as selection. Using data from the UK Biobank, we find that in utero exposure to a higher area-level infant mortality rate is associated with genetic predispositions correlated with better educational attainment and health. These findings point to the direction and magnitude of selection from this exposure. Corrections for this selection in examinations of effects of exposure on later educational attainment suggest underestimates of 26-74%; effects on other life course outcomes also vary across selection correction methods.}, } @article {pmid38479865, year = {2024}, author = {Kekalih, A and Adi, NP and Soemarko, DS}, title = {Preparation and Challenges in Developing a Big Data Analysis Framework in Occupational Medicine in Indonesia.}, journal = {Journal of UOEH}, volume = {46}, number = {1}, pages = {113-118}, doi = {10.7888/juoeh.46.113}, pmid = {38479865}, issn = {0387-821X}, mesh = {Humans ; *Artificial Intelligence ; *Occupational Medicine ; Big Data ; Indonesia ; Pandemics ; }, abstract = {This mini review explores the transformative potential of big data analysis and artificial intelligence (AI) in reforming occupational medicine in Indonesia. Emphasizing the preconditions, case studies, and benefits, it underscores the role of big data in enhancing worker well-being. The review highlights the importance of informative health big data, especially in high-risk industries, with examples of case studies of AI implementation in occupational medicine during the COVID-19 pandemic and other relevant scenarios. While acknowledging the challenges of AI implementation, the essay identifies the role of academic and professional organizations as pioneers in big data utilization. Six potential benefits that are identified, including improved patient care and efficient resource allocation, demonstrate the transformative impact of big data analysis. The proposed pathway of preparation underscores the need for awareness, skill enhancement, and collaboration, addressing challenges in data management and stakeholder engagement. The conclusion emphasizes continuous assessment, feasibility studies, and commitment as essential steps in advancing occupational medicine through big data analysis.}, } @article {pmid38476212, year = {2024}, author = {Kearsley, E and Verbeeck, H and Stoffelen, P and Janssens, SB and Yakusu, EK and Kosmala, M and De Mil, T and Bauters, M and Kitima, ER and Ndiapo, JM and Chuda, AL and Richardson, AD and Wingate, L and Ilondea, BA and Beeckman, H and van den Bulcke, J and Boeckx, P and Hufkens, K}, title = {Historical tree phenology data reveal the seasonal rhythms of the Congo Basin rainforest.}, journal = {Plant-environment interactions (Hoboken, N.J.)}, volume = {5}, number = {2}, pages = {e10136}, pmid = {38476212}, issn = {2575-6265}, abstract = {Tropical forest phenology directly affects regional carbon cycles, but the relation between species-specific and whole-canopy phenology remains largely uncharacterized. We present a unique analysis of historical tropical tree phenology collected in the central Congo Basin, before large-scale impacts of human-induced climate change. Ground-based long-term (1937-1956) phenological observations of 140 tropical tree species are recovered, species-specific phenological patterns analyzed and related to historical meteorological records, and scaled to characterize stand-level canopy dynamics. High phenological variability within and across species and in climate-phenology relationships is observed. The onset of leaf phenophases in deciduous species was triggered by drought and light availability for a subset of species and showed a species-specific decoupling in time along a bi-modal seasonality. The majority of the species remain evergreen, although central African forests experience relatively low rainfall. Annually a maximum of 1.5% of the canopy is in leaf senescence or leaf turnover, with overall phenological variability dominated by a few deciduous species, while substantial variability is attributed to asynchronous events of large and/or abundant trees. Our results underscore the importance of accounting for constituent signals in canopy-wide scaling and the interpretation of remotely sensed phenology signals.}, } @article {pmid38474911, year = {2024}, author = {Omega, RL and Ishigaki, Y and Permana, S and Matsumoto, Y and Yamamoto, K and Shozugawa, K and Hori, M}, title = {Low-Cost Sensor Deployment on a Public Minibus in Fukushima Prefecture.}, journal = {Sensors (Basel, Switzerland)}, volume = {24}, number = {5}, pages = {}, pmid = {38474911}, issn = {1424-8220}, support = {20KK0231//JSPS KAKENHI/ ; }, mesh = {*Radiation Monitoring ; *Fukushima Nuclear Accident ; Motor Vehicles ; Geographic Information Systems ; Electrocardiography ; Japan ; Radiation Dosage ; }, abstract = {This study analyzed radiation dose data to observe the annual decline in ambient radiation doses and assess the factors contributing to fluctuations in reconstructed areas of the Fukushima prefecture. Utilizing a novel mobile monitoring system installed on a community minibus, the study employed a cost-effective sensor, namely, Pocket Geiger which was integrated with a microcontroller and telecommunication system for data transfer, access, visualization, and accumulation. The study area included the region between Okuma and Tomioka towns. The ambient dose rate recorded along the minibus route was depicted on a map, averaged within a 1 × 1 km mesh created with the Quantum Geographic Information System. To ensure accuracy, the shielding factor of the minibus material is determined to adjust the dose readings. A significant decrease (p < 0.001) in the radiation dose ranges from 2022 to 2023 was observed. The land use classification by the Advanced Land Observation Satellite revealed an ecological half-life ranging from 2.41 years to 1 year, suggesting a rapid radiation decay across all land types. This underscores the close connection between radiation attenuation and environmental factors, as well as decontamination efforts across diverse land categories.}, } @article {pmid38474163, year = {2024}, author = {Kozicki, M and Sąsiadek-Andrzejczak, E and Wach, R and Maras, P}, title = {Flexible Cotton Fabric-Based Ionizing Radiation Dosimeter for 2D Dose Distribution Measurements over a Wide Dose Range at High Dose Rates.}, journal = {International journal of molecular sciences}, volume = {25}, number = {5}, pages = {}, pmid = {38474163}, issn = {1422-0067}, mesh = {*Radiation Dosimeters ; *Radiation, Ionizing ; Cellulose ; Radiometry/methods ; }, abstract = {This work presents an ecological, flexible 2D radiochromic dosimeter for measuring ionizing radiation in the kilogray dose range. Cotton woven fabric made of cellulose was volume-modified with nitrotetrazolium blue chloride as a radiation-sensitive compound. Its features include a color change during exposure from yellowish to purple-brown and flexibility that allows it to adapt to various shapes. It was found that (i) the dose response is up to ~80 kGy, (ii) it is independent of the dose rate for 1.1-73.1 kGy/min, (iii) it can be measured in 2D using a flatbed scanner, (iv) the acquired images can be filtered using a mean filter, which improves its dose resolution, (v) the dose resolution is -0.07 to -0.4 kGy for ~0.6 to ~75.7 kGy for filtered images, and (vi) two linear dose subranges can be distinguished: ~0.6 to ~7.6 kGy and ~9.9 to ~62.0 kGy. The dosimeter combined with flatbed scanner reading and data processing using dedicated software packages constitutes a comprehensive system for measuring dose distributions for objects with complex shapes.}, } @article {pmid38473771, year = {2024}, author = {Li, Z and Fan, H and Yang, L and Wang, S and Hong, D and Cui, W and Wang, T and Wei, C and Sun, Y and Wang, K and Liu, Y}, title = {Multi-Omics Analysis of the Effects of Soil Amendment on Rapeseed (Brassica napus L.) Photosynthesis under Drip Irrigation with Brackish Water.}, journal = {International journal of molecular sciences}, volume = {25}, number = {5}, pages = {}, pmid = {38473771}, issn = {1422-0067}, support = {2022B02021-3-1//The research was funded by the Major Science and Technology Project and Key Research and Development of Autonomous region, Xinjiang, China/ ; (Title: Research and demonstration on the key technologies of soil improvement and ecological prevention and control in the desert desert belt of Southern Xinjiang)//The Central Government Guides Local Science and Technology Development Fund Projects/ ; CXFZ202207//Shihezi University Innovative Development Special Projectand, China/ ; }, mesh = {*Brassica napus ; Antioxidants ; Multiomics ; *Brassica rapa ; Photosynthesis ; Crops, Agricultural ; Water ; }, abstract = {Drip irrigation with brackish water increases the risk of soil salinization while alleviating water shortage in arid areas. In order to alleviate soil salinity stress on crops, polymer soil amendments are increasingly used. But the regulation mechanism of a polymer soil amendment composed of polyacrylamide polyvinyl alcohol, and manganese sulfate (PPM) on rapeseed photosynthesis under drip irrigation with different types of brackish water is still unclear. In this field study, PPM was applied to study the responses of the rapeseed (Brassica napus L.) phenotype, photosynthetic physiology, transcriptomics, and metabolomics at the peak flowering stage under drip irrigation with water containing 6 g·L[-1] NaCl (S) and Na2CO3 (A). The results showed that the inhibitory effect of the A treatment on rapeseed photosynthesis was greater than that of the S treatment, which was reflected in the higher Na[+] content (73.30%) and lower photosynthetic-fluorescence parameters (6.30-61.54%) and antioxidant enzyme activity (53.13-77.10%) of the A-treated plants. The application of PPM increased the biomass (63.03-75.91%), photosynthetic parameters (10.55-34.06%), chlorophyll fluorescence parameters (33.83-62.52%), leaf pigment content (10.30-187.73%), and antioxidant enzyme activity (28.37-198.57%) under S and A treatments. However, the difference is that under the S treatment, PPM regulated the sulfur metabolism, carbon fixation and carbon metabolism pathways in rapeseed leaves. And it also regulated the photosynthesis-, oxidative phosphorylation-, and TCA cycle-related metabolic pathways in rapeseed leaves under A treatment. This study will provide new insights for the application of polymer materials to tackle the salinity stress on crops caused by drip irrigation with brackish water, and solve the difficulty in brackish water utilization.}, } @article {pmid38467837, year = {2024}, author = {Bhosle, A and Bae, S and Zhang, Y and Chun, E and Avila-Pacheco, J and Geistlinger, L and Pishchany, G and Glickman, JN and Michaud, M and Waldron, L and Clish, CB and Xavier, RJ and Vlamakis, H and Franzosa, EA and Garrett, WS and Huttenhower, C}, title = {Integrated annotation prioritizes metabolites with bioactivity in inflammatory bowel disease.}, journal = {Molecular systems biology}, volume = {20}, number = {4}, pages = {338-361}, pmid = {38467837}, issn = {1744-4292}, support = {P30 DK040561/DK/NIDDK NIH HHS/United States ; P30 DK043351/DK/NIDDK NIH HHS/United States ; R01 CA230551/CA/NCI NIH HHS/United States ; R24 DK110499/DK/NIDDK NIH HHS/United States ; }, mesh = {Humans ; Animals ; Mice ; *Inflammatory Bowel Diseases/drug therapy/metabolism ; *Colitis ; Metabolome ; Bile Acids and Salts ; }, abstract = {Microbial biochemistry is central to the pathophysiology of inflammatory bowel diseases (IBD). Improved knowledge of microbial metabolites and their immunomodulatory roles is thus necessary for diagnosis and management. Here, we systematically analyzed the chemical, ecological, and epidemiological properties of ~82k metabolic features in 546 Integrative Human Microbiome Project (iHMP/HMP2) metabolomes, using a newly developed methodology for bioactive compound prioritization from microbial communities. This suggested >1000 metabolic features as potentially bioactive in IBD and associated ~43% of prevalent, unannotated features with at least one well-characterized metabolite, thereby providing initial information for further characterization of a significant portion of the fecal metabolome. Prioritized features included known IBD-linked chemical families such as bile acids and short-chain fatty acids, and less-explored bilirubin, polyamine, and vitamin derivatives, and other microbial products. One of these, nicotinamide riboside, reduced colitis scores in DSS-treated mice. The method, MACARRoN, is generalizable with the potential to improve microbial community characterization and provide therapeutic candidates.}, } @article {pmid38465958, year = {2024}, author = {Rivero-Marcos, M and Lasa, B and Neves, T and Zamarreño, ÁM and García-Mina, JM and García-Olaverri, C and Aparicio-Tejo, PM and Cruz, C and Ariz, I}, title = {Plant ammonium sensitivity is associated with external pH adaptation, repertoire of nitrogen transporters, and nitrogen requirement.}, journal = {Journal of experimental botany}, volume = {75}, number = {11}, pages = {3557-3578}, pmid = {38465958}, issn = {1460-2431}, support = {RYC2021-032345-I//European Union Next Generation EU/PRTR/ ; }, mesh = {*Nitrogen/metabolism ; Hydrogen-Ion Concentration ; *Ammonium Compounds/metabolism ; Nitrates/metabolism ; Plant Proteins/metabolism/genetics ; Plants/metabolism ; Adaptation, Physiological ; }, abstract = {Modern crops exhibit diverse sensitivities to ammonium as the primary nitrogen source, influenced by environmental factors such as external pH and nutrient availability. Despite its significance, there is currently no systematic classification of plant species based on their ammonium sensitivity. We conducted a meta-analysis of 50 plant species and present a new classification method based on the comparison of fresh biomass obtained under ammonium and nitrate nutrition. The classification uses the natural logarithm of the biomass ratio as the size effect indicator of ammonium sensitivity. This numerical parameter is associated with critical factors for nitrogen demand and form preference, such as Ellenberg indicators and the repertoire of nitrogen transporters for ammonium and nitrate uptake. Finally, a comparative analysis of the developmental and metabolic responses, including hormonal balance, is conducted in two species with divergent ammonium sensitivity values in the classification. Results indicate that nitrate has a key role in counteracting ammonium toxicity in species with a higher abundance of genes encoding NRT2-type proteins and fewer of those encoding the AMT2-type proteins. Additionally, the study demonstrates the reliability of the phytohormone balance and methylglyoxal content as indicators for anticipating ammonium toxicity.}, } @article {pmid38461307, year = {2024}, author = {Zhang, L and Li, H and Shi, M and Ren, K and Zhang, W and Cheng, Y and Wang, Y and Xia, XQ}, title = {FishSNP: a high quality cross-species SNP database of fishes.}, journal = {Scientific data}, volume = {11}, number = {1}, pages = {286}, pmid = {38461307}, issn = {2052-4463}, mesh = {Animals ; *Fishes/genetics ; Genome ; *Genomics ; *Polymorphism, Single Nucleotide ; Reproducibility of Results ; *Databases, Genetic ; }, abstract = {The progress of aquaculture heavily depends on the efficient utilization of diverse genetic resources to enhance production efficiency and maximize profitability. Single nucleotide polymorphisms (SNPs) have been widely used in the study of aquaculture genomics, genetics, and breeding research since they are the most prevalent molecular markers on the genome. Currently, a large number of SNP markers from cultured fish species are scattered in individual studies, making querying complicated and data reuse problematic. We compiled relevant SNP data from literature and public databases to create a fish SNP database, FishSNP (http://bioinfo.ihb.ac.cn/fishsnp), and also used a unified analysis pipeline to process raw data that the author of the literature did not perform SNP calling on to obtain SNPs with high reliability. This database presently contains 45,690,243 (45 million) nonredundant SNP data for 13 fish species, with 30,288,958 (30 million) of those being high-quality SNPs. The main function of FishSNP is to search, browse, annotate and download SNPs, which provide researchers various and comprehensive associated information.}, } @article {pmid38452667, year = {2024}, author = {Chen, X and Zhu, Y and Zheng, W and Yan, S and Li, Y and Xie, S}, title = {Elucidating doxycycline biotransformation mechanism by Chryseobacterium sp. WX1: Multi-omics insights.}, journal = {Journal of hazardous materials}, volume = {469}, number = {}, pages = {133975}, doi = {10.1016/j.jhazmat.2024.133975}, pmid = {38452667}, issn = {1873-3336}, mesh = {*Doxycycline ; *Chryseobacterium/genetics ; Multiomics ; Proteomics ; Biotransformation ; }, abstract = {Doxycycline (DOX) represents a second-generation tetracycline antibiotic that persists as a challenging-to-degrade contaminant in environmental compartments. Despite its ubiquity, scant literature exists on bacteria proficient in DOX degradation. This study marked a substantial advancement in this field by isolating Chryseobacterium sp. WX1 from an activated sludge enrichment culture, showcasing its unprecedented ability to completely degrade 50 mg/L of DOX within 44 h. Throughout the degradation process, seven biotransformation products were identified, revealing a complex pathway that began with the hydroxylation of DOX, followed by a series of transformations. Employing an integrated multi-omics approach alongside in vitro heterologous expression assays, our study distinctly identified the tetX gene as a critical facilitator of DOX hydroxylation. Proteomic analyses further pinpointed the enzymes postulated to mediate the downstream modifications of DOX hydroxylation derivatives. The elucidated degradation pathway encompassed several key biological processes, such as the microbial transmembrane transport of DOX and its intermediates, the orchestration of enzyme synthesis for transformation, energy metabolism, and other gene-regulated biological directives. This study provides the first insight into the adaptive biotransformation strategies of Chryseobacterium under DOX-induced stress, highlighting the potential applications of this strain to augment DOX removal in wastewater treatment systems containing high concentrations of DOX.}, } @article {pmid38451645, year = {2024}, author = {Souza, IM and Araújo, EM and Silva Filho, AMD}, title = {Incomplete recording of race/colour in health information systems in Brazil: time trend, 2009-2018.}, journal = {Ciencia & saude coletiva}, volume = {29}, number = {3}, pages = {e05092023}, doi = {10.1590/1413-81232024293.05092023}, pmid = {38451645}, issn = {1678-4561}, mesh = {Humans ; Black People ; Brazil/epidemiology ; *Health Information Systems ; *Hospital Information Systems ; Racial Groups ; Ethnicity ; }, abstract = {This ecological study of time trends and multiple groups evaluated incompleteness in the race/colour field of Brazilian health information system records and the related time trend, 2009-2018, for the diseases and disorders most prevalent in the black population. The Romero and Cunha (2006) classification was applied in order to examine incompleteness using secondary data from Brazil's National Notifiable Diseases System, Hospital Information System and Mortality Information System, by administrative regions of Brazil, while percentage underreporting and time trend were calculated using simple linear regression models with Prais-Winsten correction (p-value<0.05). All records scored poorly except those for mortality from external causes (excellent), tuberculosis (good) and infant mortality (fair). An overall downward trend was observed in percentage incompleteness. Analysis by region found highest mean incompleteness in the North (30.5%), Northeast (33.3%) and Midwest (33.0%) regions. The Southeast and Northeast regions showed the strongest downward trends. The findings intended to increase visibility on the implications of the race/color field for health equity.}, } @article {pmid38448699, year = {2024}, author = {Tao, F and Houlton, BZ and Frey, SD and Lehmann, J and Manzoni, S and Huang, Y and Jiang, L and Mishra, U and Hungate, BA and Schmidt, MWI and Reichstein, M and Carvalhais, N and Ciais, P and Wang, YP and Ahrens, B and Hugelius, G and Hocking, TD and Lu, X and Shi, Z and Viatkin, K and Vargas, R and Yigini, Y and Omuto, C and Malik, AA and Peralta, G and Cuevas-Corona, R and Di Paolo, LE and Luotto, I and Liao, C and Liang, YS and Saynes, VS and Huang, X and Luo, Y}, title = {Reply to: Model uncertainty obscures major driver of soil carbon.}, journal = {Nature}, volume = {627}, number = {8002}, pages = {E4-E6}, pmid = {38448699}, issn = {1476-4687}, mesh = {*Uncertainty ; }, } @article {pmid38447714, year = {2024}, author = {Liu, Y and You, S and Ding, L and Yuan, F and Sun, Y}, title = {Hepatotoxic effects of chronic exposure to environmentally relevant concentrations of Di-(2-ethylhexyl) phthalate (DEHP) on crucian carp: Insights from multi-omics analyses.}, journal = {The Science of the total environment}, volume = {923}, number = {}, pages = {171447}, doi = {10.1016/j.scitotenv.2024.171447}, pmid = {38447714}, issn = {1879-1026}, mesh = {Animals ; *Diethylhexyl Phthalate/metabolism ; Ecosystem ; *Carps/metabolism ; Multiomics ; *Phthalic Acids/toxicity/analysis ; }, abstract = {Di-(2-ethylhexyl) phthalate (DEHP) is an extensively used phthalate esters (PAEs) that raise growing ecotoxicological concerns due to detrimental effects on living organisms and ecosystems. This study performed hepatotoxic investigations on crucian carp under chronic low-dosage (CLD) exposure to DEHP at environmentally relevant concentrations (20-500 μg/L). The results demonstrated that the CLD exposure induced irreversible damage to the liver tissue. Multi-omics (transcriptomics and metabolomics) analyses revealed the predominant toxicological mechanisms underlying DEHP-induced hepatotoxicity by inhibiting energy production pathways and the up-regulation of the purine metabolism. Disruption of metabolic pathways led to excessive reactive oxygen species (ROS) production and subsequent oxidative stress. The adverse metabolic effects were exacerbated by an interplay between oxidative stress and endoplasmic reticulum stress. This study not only provides new mechanistic insights into the ecotoxicological effects of DEHP under chronic low-dosage exposure, but also suggests a potential strategy for further ecological risk assessment of PAEs.}, } @article {pmid38447388, year = {2024}, author = {van der Feltz-Cornelis, C and Turk, F and Sweetman, J and Khunti, K and Gabbay, M and Shepherd, J and Montgomery, H and Strain, WD and Lip, GYH and Wootton, D and Watkins, CL and Cuthbertson, DJ and Williams, N and Banerjee, A}, title = {Prevalence of mental health conditions and brain fog in people with long COVID: A systematic review and meta-analysis.}, journal = {General hospital psychiatry}, volume = {88}, number = {}, pages = {10-22}, doi = {10.1016/j.genhosppsych.2024.02.009}, pmid = {38447388}, issn = {1873-7714}, mesh = {Humans ; *COVID-19/epidemiology ; Prevalence ; *Post-Acute COVID-19 Syndrome ; Cognitive Dysfunction/epidemiology/etiology ; Mental Disorders/epidemiology ; }, abstract = {OBJECTIVE: Long COVID can include impaired cognition ('brain fog'; a term encompassing multiple symptoms) and mental health conditions. We performed a systematic review and meta-analysis to estimate their prevalence and to explore relevant factors associated with the incidence of impaired cognition and mental health conditions.

METHODS: Searches were conducted in Medline and PsycINFO to cover the start of the pandemic until August 2023. Included studies reported prevalence of mental health conditions and brain fog in adults with long COVID after clinically-diagnosed or PCR-confirmed SARS-CoV-2 infection.

FINDINGS: 17 studies were included, reporting 41,249 long COVID patients. Across all timepoints (3-24 months), the combined prevalence of mental health conditions and brain fog was 20·4% (95% CI 11·1%-34·4%), being lower among those previously hospitalised than in community-managed patients(19·5 vs 29·7% respectively; p = 0·047). The odds of mental health conditions and brain fog increased over time and when validated instruments were used. Odds of brain fog significantly decreased with increasing vaccination rates (p = ·000).

CONCLUSIONS: Given the increasing prevalence of mental health conditions and brain fog over time, preventive interventions and treatments are needed. Research is needed to explore underlying mechanisms that could inform further research in development of effective treatments. The reduced risk of brain fog associated with vaccination emphasizes the need for ongoing vaccination programs.}, } @article {pmid38445504, year = {2024}, author = {Kudamba, A and Kasolo, JN and Bbosa, GS and Lugaajju, A and Wabinga, H and Kafeero, HM and Ssenku, JE and Alemu, SO and Walusansa, A and Niyonzima, N and Muwonge, H}, title = {Review of Herbal Medicinal Plants Used in the Management of Cancers in the East Africa Region from 2019 to 2023.}, journal = {Integrative cancer therapies}, volume = {23}, number = {}, pages = {15347354241235583}, pmid = {38445504}, issn = {1552-695X}, mesh = {Male ; Humans ; *Plants, Medicinal ; Africa, Eastern ; *Prostatic Neoplasms ; *Apocynaceae ; Databases, Factual ; }, abstract = {BACKGROUND: In the East African region, herbal plants are essential in the treatment and control of cancer. Given the diverse ecological and cultural makeup of the regional states, it is likely that different ethnic groups will use the same or different plants for the same or different diseases. However, since 2019, this has not been compiled into a single study.

PURPOSE: The study aimed to compile and record the medicinal plants utilized in East Africa from April 2019 to June 2023 to treat various cancer types.

MATERIALS AND METHODS: The study examined 13 original studies that included ethnobotanical research conducted in East Africa. They were retrieved from several internet databases, including Google Scholar, Scopus, PubMed/Medline, Science Direct, and Research for Life. The study retrieved databases on plant families and species, plant parts used, preparation methods and routes of administration, and the country where the ethnobotanical field surveys were conducted. Graphs were produced using the GraphPad Prism 8.125 program (GraphPad Software, Inc., San Diego, CA). Tables and figures were used to present the data, which had been condensed into percentages and frequencies.

RESULTS: A total of 105 different plant species from 45 different plant families were identified, including Asteraceae (14), Euphorbiaceae (12), Musaceae (8), and Apocynaceae (7). Uganda registered the highest proportion (46% of the medicinal plants used). The most commonly mentioned medicinal plant species in cancer management was Prunus africana. Herbs (32%), trees and shrubs (28%), and leaves (45%) constituted the majority of herbal remedies. Most herbal remedies were prepared by boiling (decoction) and taken orally (57%).

CONCLUSION: East Africa is home to a wide variety of medicinal plant species that local populations and herbalists, or TMP, frequently use in the treatment of various types of cancer. The most frequently used families are Asteraceae and Euphorbiaceae, with the majority of species being found in Uganda. The most frequently utilized plant species is Prunus africana. Studies on the effectiveness of Prunus africana against other malignancies besides prostate cancer are required.}, } @article {pmid38444395, year = {2024}, author = {Liu, Y and Li, L and Feng, J and Wan, B and Tu, Q and Cai, W and Jin, F and Tang, G and Rodrigues, LR and Zhang, X and Yin, J and Zhang, Y}, title = {Modulation of chronic obstructive pulmonary disease progression by antioxidant metabolites from Pediococcus pentosaceus: enhancing gut probiotics abundance and the tryptophan-melatonin pathway.}, journal = {Gut microbes}, volume = {16}, number = {1}, pages = {2320283}, pmid = {38444395}, issn = {1949-0984}, mesh = {Animals ; Mice ; Antioxidants ; Pediococcus pentosaceus ; *Melatonin/pharmacology ; Tryptophan ; *Gastrointestinal Microbiome ; *Probiotics ; *Pulmonary Disease, Chronic Obstructive ; }, abstract = {Chronic obstructive pulmonary disease (COPD), a condition primarily linked to oxidative stress, poses significant health burdens worldwide. Recent evidence has shed light on the association between the dysbiosis of gut microbiota and COPD, and their metabolites have emerged as potential modulators of disease progression through the intricate gut-lung axis. Here, we demonstrate the efficacy of oral administration of the probiotic Pediococcus pentosaceus SMM914 (SMM914) in delaying the progression of COPD by attenuating pulmonary oxidative stress. Specially, SMM914 induces a notable shift in the gut microbiota toward a community structure characterized by an augmented abundance of probiotics producing short-chain fatty acids and antioxidant metabolisms. Concurrently, SMM914 synthesizes L-tryptophanamide, 5-hydroxy-L-tryptophan, and 3-sulfino-L-alanine, thereby enhancing the tryptophan-melatonin pathway and elevating 6-hydroxymelatonin and hypotaurine in the lung environment. This modulation amplifies the secretion of endogenous anti-inflammatory factors, diminishes macrophage polarization toward the M1 phenotype, and ultimately mitigates the oxidative stress in mice with COPD. The demonstrated efficacy of the probiotic intervention, specifically with SMM914, not only highlights the modulation of intestine microbiota but also emphasizes the consequential impact on the intricate interplay between the gastrointestinal system and respiratory health.}, } @article {pmid38443441, year = {2024}, author = {Zhang, Z and Xu, H and Zhu, G}, title = {Incorporating high-frequency information into edge convolution for link prediction in complex networks.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {5437}, pmid = {38443441}, issn = {2045-2322}, support = {1908085QF283//Natural Science Foundation of Anhui Province/ ; 2019jb08//Doctoral Startup Research Fund of Suzhou University/ ; 2021bsk016//Doctoral Startup Research Fund of Suzhou University/ ; GXXT-2022-047//University Synergy Innovation Program of Anhui Province/ ; 2021XJPT50, 2022xhx004, 2022xhx099//Scientific Research Projects Funded by Suzhou University/ ; AE202201//Open Research Fund of National Engineering Research Center for Agro-Ecological Big Data Analysis & Application, Anhui University/ ; }, abstract = {Link prediction in complex networks aims to mine hidden or to-be-generated links between network nodes, which plays a significant role in fields such as the cold start of recommendation systems, knowledge graph completion and biomedical experiments. The existing link prediction models based on graph neural networks, such as graph convolution neural networks, often only learn the low-frequency information reflecting the common characteristics of nodes while ignoring the high-frequency information reflecting the differences between nodes when learning node representation, which makes the corresponding link prediction models show over smoothness and poor performance. Focusing on links in complex networks, this paper proposes an edge convolutional graph neural network EdgeConvHiF that fuses high-frequency node information to achieve the representation learning of links so that link prediction can be realized by implementing the classification of links. EdgeConvHiF can also be employed as a baseline, and extensive experiments on real-world benchmarks validate that EdgeConvHiF not only has high stability but also has more advantages than the existing representative baselines.}, } @article {pmid38443432, year = {2024}, author = {Ge, X and Peng, L and Deng, Z and Du, J and Sun, C and Wang, B}, title = {Chromosome-scale genome assemblies of Himalopsyche anomala and Eubasilissa splendida (Insecta: Trichoptera).}, journal = {Scientific data}, volume = {11}, number = {1}, pages = {267}, pmid = {38443432}, issn = {2052-4463}, support = {32271631//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {Animals ; Comparative Genomic Hybridization ; Ecology ; *Insecta/genetics ; *Genome, Insect ; *Databases, Genetic ; }, abstract = {Trichoptera is one of the most evolutionarily successful aquatic insect lineages and is highly valued value in adaptive evolution research. This study presents the chromosome-level genome assemblies of Himalopsyche anomala and Eubasilissa splendida achieved using PacBio, Illumina, and Hi-C sequencing. For H. anomala and E. splendida, assembly sizes were 663.43 and 859.28 Mb, with scaffold N50 lengths of 28.44 and 31.17 Mb, respectively. In H. anomala and E. splendida, we anchored 24 and 29 pseudochromosomes, and identified 11,469 and 10,554 protein-coding genes, respectively. The high-quality genomes of H. anomala and E. splendida provide critical genomic resources for understanding the evolution and ecology of Trichoptera and performing comparative genomics analyses.}, } @article {pmid38443357, year = {2024}, author = {Zhou, H and Zhang, X and Liu, H and Ma, J and Hao, F and Ye, H and Wang, Y and Zhang, S and Yue, M and Zhao, P}, title = {Chromosome-level genome assembly of Platycarya strobilacea.}, journal = {Scientific data}, volume = {11}, number = {1}, pages = {269}, pmid = {38443357}, issn = {2052-4463}, support = {32370386, 32070372, and 32200295//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {Asia, Eastern ; Biological Evolution ; Chromosomes ; *Juglandaceae/genetics ; Phylogeny ; *Genome, Plant ; *Databases, Genetic ; }, abstract = {Platycarya strobilacea belongs to the walnut family (Juglandaceae), is commonly known as species endemic to East Asia, and is an ecologically important, wind pollinated, woody deciduous tree. To facilitate this ancient tree for the ecological value and conservation of this ancient tree, we report a new high-quality genome assembly of P. strobilacea. The genome size was 677.30 Mb, with a scaffold N50 size of 45,791,698 bp, and 98.43% of the assembly was anchored to 15 chromosomes. We annotated 32,246 protein-coding genes in the genome, of which 96.30% were functionally annotated in six databases. This new high-quality assembly of P. strobilacea provide valuable resource for the phylogenetic and evolutionary analysis of the walnut family and angiosperm.}, } @article {pmid38442095, year = {2024}, author = {Tamosiunaite, M and Tetzlaff, C and Wörgötter, F}, title = {Unsupervised learning of perceptual feature combinations.}, journal = {PLoS computational biology}, volume = {20}, number = {3}, pages = {e1011926}, pmid = {38442095}, issn = {1553-7358}, mesh = {Animals ; *Unsupervised Machine Learning ; *Models, Neurological ; Neurons/physiology ; }, abstract = {In many situations it is behaviorally relevant for an animal to respond to co-occurrences of perceptual, possibly polymodal features, while these features alone may have no importance. Thus, it is crucial for animals to learn such feature combinations in spite of the fact that they may occur with variable intensity and occurrence frequency. Here, we present a novel unsupervised learning mechanism that is largely independent of these contingencies and allows neurons in a network to achieve specificity for different feature combinations. This is achieved by a novel correlation-based (Hebbian) learning rule, which allows for linear weight growth and which is combined with a mechanism for gradually reducing the learning rate as soon as the neuron's response becomes feature combination specific. In a set of control experiments, we show that other existing advanced learning rules cannot satisfactorily form ordered multi-feature representations. In addition, we show that networks, which use this type of learning always stabilize and converge to subsets of neurons with different feature-combination specificity. Neurons with this property may, thus, serve as an initial stage for the processing of ecologically relevant real world situations for an animal.}, } @article {pmid38441325, year = {2024}, author = {Davies, H and Blackwell, E and Fins, IS and Noble, PJM and Pinchbeck, G and Pirmohamed, M and Killick, DR}, title = {Recording of suspected adverse drug reaction reporting in veterinary free-text clinical narratives.}, journal = {The Journal of small animal practice}, volume = {65}, number = {6}, pages = {361-367}, doi = {10.1111/jsap.13721}, pmid = {38441325}, issn = {1748-5827}, support = {VM0541//Veterinary Medicines Directorate/ ; SRP 02.21//British Small Animal Veterinary Association/ ; 204822/z/16/z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {*Adverse Drug Reaction Reporting Systems/statistics & numerical data ; Animals ; *Drug-Related Side Effects and Adverse Reactions/veterinary ; Data Mining ; Veterinary Drugs/adverse effects ; Electronic Health Records ; Veterinary Medicine ; Pharmacovigilance ; }, abstract = {OBJECTIVES: To use text mining approaches to identify instances of suspected adverse drug reactions recorded in first opinion veterinary free-text clinical narratives, and to evaluate whether these were also reported to either the Veterinary Medicines Directorate or the relevant Marketing Authorisation holder in order to derive an estimate of the suspected adverse drug reaction (sADR) minimum under-reporting rate. To characterise sADR reports and explore whether particular features are associated with report submission.

MATERIALS AND METHODS: Two regular expressions were developed to identify mentions of "adverse drug reactions" and "side effects" in the free-text clinical narratives of electronic health records contained within the Small Animal Veterinary Surveillance Network database. Consultations containing a match for the developed regular expressions were manually reviewed for inclusion and further classified to determine the suspected product, seriousness and expectedness of the event, and an indication of whether the event had been reported. The associations between event characteristics and reporting were explored using Fisher's exact tests.

RESULTS: A total of 10,565 records were manually reviewed from which 827 sADRs were identified. Approximately 90% of these sADRs were not recorded as reported. Suspected adverse drug reactions that were not considered "expected" were recorded as reported more frequently than "expected" sADRs. However, clinical severity did not appear to impact on whether there was a record of reporting.

CLINICAL SIGNIFICANCE: This is the first estimate of under reporting sADRs based on real world evidence from veterinary clinical records. The under-reporting rate implied by this study highlights that further interventions are required to improve reporting rate within the veterinary profession in order to support pharmacovigilance activities and improve drug safety.}, } @article {pmid38438998, year = {2024}, author = {Wu, LF and Zhu, WG and Yu, EP and Cao, HL and Wang, ZF}, title = {Draft genome of Brasenia schreberi, a worldwide distributed and endangered aquatic plant.}, journal = {BMC genomic data}, volume = {25}, number = {1}, pages = {24}, pmid = {38438998}, issn = {2730-6844}, mesh = {*Seeds ; *Plant Weeds ; Allelopathy ; China ; Databases, Factual ; }, abstract = {OBJECTIVES: Brasenia is a monotypic genus in the family of Cabombaceae. The only species, B. schreberi, is a macrophyte distributed worldwide. Because it requires good water quality, it is endangered in China and other countries due to the deterioration of aquatic habitats. The young leaves and stems of B. schreberi are covered by thick mucilage, which has high medical value. As an allelopathic aquatic plant, it can also be used in the management of aquatic weeds. Here, we present its assembled and annotated genome to help shed light on medial and allelopathic substrates and facilitate their conservation.

DATA DESCRIPTION: Genomic DNA and RNA extracted from B. schreberi leaf tissues were used for whole genome and RNA sequencing using a Nanopore and/or MGI sequencer. The assembly was 1,055,148,839 bp in length, with 92 contigs and an N50 of 22,379,495 bp. The repetitive elements in the assembly were 555,442,205 bp. A completeness assessment of the assembly with BUSCO and compleasm indicated 88.4 and 90.9% completeness in the Eudicots database and 95.4 and 96.6% completeness in the Embryphyta database. Gene annotation revealed 67,747 genes that coded for 73,344 proteins.}, } @article {pmid38436579, year = {2024}, author = {Qian, J and Qian, L and Pu, N and Bi, Y and Wilhelms, A and Norra, S}, title = {An Intelligent Early Warning System for Harmful Algal Blooms: Harnessing the Power of Big Data and Deep Learning.}, journal = {Environmental science & technology}, volume = {58}, number = {35}, pages = {15607-15618}, doi = {10.1021/acs.est.3c03906}, pmid = {38436579}, issn = {1520-5851}, mesh = {*Deep Learning ; *Harmful Algal Bloom ; *Big Data ; *Environmental Monitoring/methods ; Lakes ; }, abstract = {Harmful algal blooms (HABs) pose a significant ecological threat and economic detriment to freshwater environments. In order to develop an intelligent early warning system for HABs, big data and deep learning models were harnessed in this study. Data collection was achieved utilizing the vertical aquatic monitoring system (VAMS). Subsequently, the analysis and stratification of the vertical aquatic layer were conducted employing the "DeepDPM-Spectral Clustering" method. This approach drastically reduced the number of predictive models and enhanced the adaptability of the system. The Bloomformer-2 model was developed to conduct both single-step and multistep predictions of Chl-a, integrating the " Alert Level Framework" issued by the World Health Organization to accomplish early warning for HABs. The case study conducted in Taihu Lake revealed that during the winter of 2018, the water column could be partitioned into four clusters (Groups W1-W4), while in the summer of 2019, the water column could be partitioned into five clusters (Groups S1-S5). Moreover, in a subsequent predictive task, Bloomformer-2 exhibited superiority in performance across all clusters for both the winter of 2018 and the summer of 2019 (MAE: 0.175-0.394, MSE: 0.042-0.305, and MAPE: 0.228-2.279 for single-step prediction; MAE: 0.184-0.505, MSE: 0.101-0.378, and MAPE: 0.243-4.011 for multistep prediction). The prediction for the 3 days indicated that Group W1 was in a Level I alert state at all times. Conversely, Group S1 was mainly under an Level I alert, with seven specific time points escalating to a Level II alert. Furthermore, the end-to-end architecture of this system, coupled with the automation of its various processes, minimized human intervention, endowing it with intelligent characteristics. This research highlights the transformative potential of integrating big data and artificial intelligence in environmental management and emphasizes the importance of model interpretability in machine learning applications.}, } @article {pmid38436026, year = {2024}, author = {Specker, F and Paz, A and Crowther, TW and Maynard, DS}, title = {Treemendous: an R package for integrating taxonomic information across backbones.}, journal = {PeerJ}, volume = {12}, number = {}, pages = {e16896}, pmid = {38436026}, issn = {2167-8359}, mesh = {*Biodiversity ; Databases, Factual ; *Ecology ; Forests ; Software ; Trees ; }, abstract = {Standardizing and translating species names from different databases is key to the successful integration of data sources in biodiversity research. There are numerous taxonomic name-resolution applications that implement increasingly powerful name-cleaning and matching approaches, allowing the user to resolve species relative to multiple backbones simultaneously. Yet there remains no principled approach for combining information across these underlying taxonomic backbones, complicating efforts to combine and merge species lists with inconsistent and conflicting taxonomic information. Here, we present Treemendous, an open-source software package for the R programming environment that integrates taxonomic relationships across four publicly available backbones to improve the name resolution of tree species. By mapping relationships across the backbones, this package can be used to resolve datasets with conflicting and inconsistent taxonomic origins, while ensuring the resulting species are accepted and consistent with a single reference backbone. The user can chain together different functionalities ranging from simple matching to a single backbone, to graph-based iterative matching using synonym-accepted relations across all backbones in the database. In addition, the package allows users to 'translate' one tree species list into another, streamlining the assimilation of new data into preexisting datasets or models. The package provides a flexible workflow depending on the use case, and can either be used as a stand-alone name-resolution package or in conjunction with existing packages as a final step in the name-resolution pipeline. The Treemendous package is fast and easy to use, allowing users to quickly merge different data sources by standardizing their species names according to the regularly updated database. By combining taxonomic information across multiple backbones, the package increases matching rates and minimizes data loss, allowing for more efficient translation of tree species datasets to aid research into forest biodiversity and tree ecology.}, } @article {pmid38434748, year = {2023}, author = {Boyes, D and Hammond, J and , and , and , and , and , and , }, title = {The genome sequence of the Diamond-back Marble, Eudemis profundana (Denis & Schiffermüller, 1775).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {184}, pmid = {38434748}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual male Eudemis profundana (the Diamond-back Marble; Arthropoda; Insecta; Lepidoptera; Tortricidae). The genome sequence is 691.3 megabases in span. Most of the assembly is scaffolded into 28 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 16.5 kilobases in length.}, } @article {pmid38434745, year = {2023}, author = {Boyes, D and Lees, DC and Hammond, J and , and , and , and , and , and , and , }, title = {The genome sequence of the Ashy Button, Acleris sparsana (Denis & Schiffermüller, 1775).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {241}, pmid = {38434745}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual male Acleris sparsana (the Ashy Button; Arthropoda; Insecta; Lepidoptera; Tortricidae). The genome sequence is 589.5 megabases in span. Most of the assembly is scaffolded into 30 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 16.4 kilobases in length. Gene annotation of this assembly on Ensembl identified 22,123 protein coding genes.}, } @article {pmid38434742, year = {2023}, author = {Boyes, D and Boyes, C and , and , and , and , and , and , }, title = {The genome sequence of the Minor Shoulder-knot, Brachylomia viminalis (Fabricius, 1777).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {245}, pmid = {38434742}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual male Brachylomia viminalis (the Minor Shoulder-knot; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 782.2 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 16.15 kilobases in length. Gene annotation of this assembly on Ensembl identified 20,191 protein coding genes.}, } @article {pmid38434736, year = {2023}, author = {Boyes, D and Lewis, OT and , and , and , and , and , and , }, title = {The genome sequence of the Orange Footman, Eilema sororcula (Hufnagel, 1766).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {282}, pmid = {38434736}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual male Eilema sororcula (the Orange Footman; Arthropoda; Insecta; Lepidoptera; Erebidae). The genome sequence is 729.4 megabases in span. Most of the assembly is scaffolded into 30 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.46 kilobases in length. Gene annotation of this assembly on Ensembl identified 21,093 protein coding genes.}, } @article {pmid38434623, year = {2023}, author = {Thiébaut, A and Altenhoff, AM and Campli, G and Glover, N and Dessimoz, C and Waterhouse, RM}, title = {DrosOMA: the Drosophila Orthologous Matrix browser.}, journal = {F1000Research}, volume = {12}, number = {}, pages = {936}, pmid = {38434623}, issn = {2046-1402}, mesh = {Animals ; *Drosophila/genetics ; Comparative Genomic Hybridization ; Databases, Factual ; *Evolution, Molecular ; Genomics ; }, abstract = {BACKGROUND: Comparative genomic analyses to delineate gene evolutionary histories inform the understanding of organismal biology by characterising gene and gene family origins, trajectories, and dynamics, as well as enabling the tracing of speciation, duplication, and loss events, and facilitating the transfer of gene functional information across species. Genomic data are available for an increasing number of species from the genus Drosophila, however, a dedicated resource exploiting these data to provide the research community with browsable results from genus-wide orthology delineation has been lacking.

METHODS: Using the OMA Orthologous Matrix orthology inference approach and browser deployment framework, we catalogued orthologues across a selected set of Drosophila species with high-quality annotated genomes. We developed and deployed a dedicated instance of the OMA browser to facilitate intuitive exploration, visualisation, and downloading of the genus-wide orthology delineation results.

RESULTS: DrosOMA - the Drosophila Orthologous Matrix browser, accessible from https://drosoma.dcsr.unil.ch/ - presents the results of orthology delineation for 36 drosophilids from across the genus and four outgroup dipterans. It enables querying and browsing of the orthology data through a feature-rich web interface, with gene-view, orthologous group-view, and genome-view pages, including comprehensive gene name and identifier cross-references together with available functional annotations and protein domain architectures, as well as tools to visualise local and global synteny conservation.

CONCLUSIONS: The DrosOMA browser demonstrates the deployability of the OMA browser framework for building user-friendly orthology databases with dense sampling of a selected taxonomic group. It provides the Drosophila research community with a tailored resource of browsable results from genus-wide orthology delineation.}, } @article {pmid38433952, year = {2024}, author = {Mallinson, DC and Elwert, F and Ehrenthal, DB}, title = {Spillover effects of gestational age on sibling's literacy.}, journal = {Early child development and care}, volume = {194}, number = {2}, pages = {244-259}, pmid = {38433952}, issn = {0300-4430}, support = {R01 HD102125/HD/NICHD NIH HHS/United States ; T32 HD007014/HD/NICHD NIH HHS/United States ; }, abstract = {Adverse health events within families can harm children's development, including their early literacy. Using data from a longitudinal Wisconsin birth cohort, we estimated the spillover effect of younger siblings' gestational ages on older siblings' kindergarten-level literacy. We sampled 20,014 sibling pairs born during 2007-2010 who took Phonological Awareness Literacy Screening-Kindergarten tests during 2012-2016. Exposures were gestational age (completed weeks), preterm birth (gestational age <37 weeks), and very preterm birth (gestational age <32 weeks). We used gain-score regression-a fixed effects strategy-to estimate spillover effect. A one-week increase in younger siblings' gestational age improved the older siblings' test score by 0.011 SD (95% confidence interval: 0.001, 0.021 SD). The estimated spillover effect was larger among siblings whose mothers reported having a high school diploma/equivalent only (0.024 SD; 95% CI: 0.004, 0.044 SD). The finding underscores the networked effects of one individual's early-life health shocks on their family members.}, } @article {pmid38432384, year = {2024}, author = {Baima Ferreira Freitas, I and Duarte-Neto, PJ and Sorigotto, LR and Cardoso Yoshii, MP and de Palma Lopes, LF and de Almeida Pereira, MM and Girotto, L and Badolato Athayde, D and Veloso Goulart, B and Montagner, CC and Schiesari, LC and Martinelli, LA and Gaeta Espíndola, EL}, title = {Effects of pasture intensification and sugarcane cultivation on non-target species: A realistic evaluation in pesticide-contaminated mesocosms.}, journal = {The Science of the total environment}, volume = {922}, number = {}, pages = {171425}, doi = {10.1016/j.scitotenv.2024.171425}, pmid = {38432384}, issn = {1879-1026}, mesh = {Female ; Animals ; Cattle ; *Pesticides/toxicity ; *Saccharum ; Environmental Biomarkers ; Soil ; Water/chemistry ; 2,4-Dichlorophenoxyacetic Acid/toxicity ; *Water Pollutants, Chemical/toxicity ; }, abstract = {Conventional soil management in agricultural areas may expose non-target organisms living nearby to several types of contaminants. In this study, the effects of soil management in extensive pasture (EP), intensive pasture (IP), and sugarcane crops (C) were evaluated in a realistic-field-scale study. Thirteen aquatic mesocosms embedded in EP, IP, and C treatments were monitored over 392 days. The recommended management for each of the areas was simulated, such as tillage, fertilizer, pesticides (i.e. 2,4-D, fipronil) and vinasse application, and cattle pasture. To access the potential toxic effects that the different steps of soil management in these areas may cause, the cladoceran Ceriophania silvestrii was used as aquatic bioindicator, the dicot Eruca sativa as phytotoxicity bioindicator in water, and the dipteran Chironomus sancticaroli as sediment bioindicator. Generalized linear mixed models were used to identify differences between the treatments. Low concentrations of 2,4-D (<97 μg L[-1]) and fipronil (<0.21 μg L[-1]) in water were able to alter fecundity, female survival, and the intrinsic rate of population increase of C. silvestrii in IP and C treatments. Similarly, the dicot E. sativa had germination, shoot and root growth affected mainly by 2,4-D concentrations in the water. For C. sancticarolli, larval development was affected by the presence of fipronil (<402.6 ng g[-1]). The acidic pH (below 5) reduced the fecundity and female survival of C. silvestrii and affected the germination and growth of E. sativa. Fecundity and female survival of C. silvestrii decrease in the presence of phosphorus-containing elements. The outcomes of this study may improve our understanding of the consequences of exposure of freshwater biota to complex stressors in an environment that is rapidly and constantly changing.}, } @article {pmid38430051, year = {2024}, author = {Rillig, MC and Mansour, I and Hempel, S and Bi, M and König-Ries, B and Kasirzadeh, A}, title = {How widespread use of generative AI for images and video can affect the environment and the science of ecology.}, journal = {Ecology letters}, volume = {27}, number = {3}, pages = {e14397}, doi = {10.1111/ele.14397}, pmid = {38430051}, issn = {1461-0248}, mesh = {*Artificial Intelligence ; *Biodiversity ; }, abstract = {Generative artificial intelligence (AI) models will have broad impacts on society including the scientific enterprise; ecology and environmental science will be no exception. Here, we discuss the potential opportunities and risks of advanced generative AI for visual material (images and video) for the science of ecology and the environment itself. There are clearly opportunities for positive impacts, related to improved communication, for example; we also see possibilities for ecological research to benefit from generative AI (e.g., image gap filling, biodiversity surveys, and improved citizen science). However, there are also risks, threatening to undermine the credibility of our science, mostly related to actions of bad actors, for example in terms of spreading fake information or committing fraud. Risks need to be mitigated at the level of government regulatory measures, but we also highlight what can be done right now, including discussing issues with the next generation of ecologists and transforming towards radically open science workflows.}, } @article {pmid38429902, year = {2024}, author = {Chen, C and He, Y and Ni, Y and Tang, Z and Zhang, W}, title = {Identification of crosstalk genes relating to ECM-receptor interaction genes in MASH and DN using bioinformatics and machine learning.}, journal = {Journal of cellular and molecular medicine}, volume = {28}, number = {6}, pages = {e18156}, pmid = {38429902}, issn = {1582-4934}, support = {81771152//National Nature Science Foundation of China/ ; }, mesh = {Humans ; *Interleukin-17 ; *Diabetic Nephropathies ; Phosphatidylinositol 3-Kinases ; Computational Biology ; Machine Learning ; }, abstract = {This study aimed to identify genes shared by metabolic dysfunction-associated fatty liver disease (MASH) and diabetic nephropathy (DN) and the effect of extracellular matrix (ECM) receptor interaction genes on them. Datasets with MASH and DN were downloaded from the Gene Expression Omnibus (GEO) database. Pearson's coefficients assessed the correlation between ECM-receptor interaction genes and cross talk genes. The coexpression network of co-expression pairs (CP) genes was integrated with its protein-protein interaction (PPI) network, and machine learning was employed to identify essential disease-representing genes. Finally, immuno-penetration analysis was performed on the MASH and DN gene datasets using the CIBERSORT algorithm to evaluate the plausibility of these genes in diseases. We found 19 key CP genes. Fos proto-oncogene (FOS), belonging to the IL-17 signalling pathway, showed greater centrality PPI network; Hyaluronan Mediated Motility Receptor (HMMR), belonging to ECM-receptor interaction genes, showed most critical in the co-expression network map of 19 CP genes; Forkhead Box C1 (FOXC1), like FOS, showed a high ability to predict disease in XGBoost analysis. Further immune infiltration showed a clear positive correlation between FOS/FOXC1 and mast cells that secrete IL-17 during inflammation. Combining the results of previous studies, we suggest a FOS/FOXC1/HMMR regulatory axis in MASH and DN may be associated with mast cells in the acting IL-17 signalling pathway. Extracellular HMMR may regulate the IL-17 pathway represented by FOS through the Mitogen-Activated Protein Kinase 1 (ERK) or PI3K-Akt-mTOR pathway. HMMR may serve as a signalling carrier between MASH and DN and could be targeted for therapeutic development.}, } @article {pmid38426108, year = {2024}, author = {Huo, J and Li, X and Hu, X and Lv, A}, title = {Multi-omics analysis of miRNA-mediated intestinal microflora changes in crucian carp Carassius auratus infected with Rahnella aquatilis.}, journal = {Frontiers in immunology}, volume = {15}, number = {}, pages = {1335602}, pmid = {38426108}, issn = {1664-3224}, mesh = {Animals ; Goldfish/genetics ; *Carps/genetics ; *Rahnella/genetics ; NF-kappa B ; Multiomics ; *Gastrointestinal Microbiome ; Tumor Necrosis Factor-alpha ; Inflammation ; *Enteritis ; Transforming Growth Factor beta ; *MicroRNAs/genetics ; }, abstract = {Infection by an emerging bacterial pathogen Rahnella aquatilis caused enteritis and septicemia in fish. However, the molecular pathogenesis of enteritis induced by R. aquatilis infection and its interacting mechanism of the intestinal microflora associated with microRNA (miRNA) immune regulation in crucian carp Carassius auratus are still unclear. In this study, C. auratus intraperitoneally injected with R. aquatilis KCL-5 was used as an experimental animal model, and the intestinal pathological changes, microflora, and differentially expressed miRNAs (DEMs) were investigated by multi-omics analysis. The significant changes in histopathological features, apoptotic cells, and enzyme activities (e.g., lysozyme (LYS), alkaline phosphatase (AKP), alanine aminotransferase (ALT), aspartate transaminase (AST), and glutathione peroxidase (GSH-Px)) in the intestine were examined after infection. Diversity and composition analysis of the intestinal microflora clearly demonstrated four dominant bacteria: Proteobacteria, Fusobacteria, Bacteroidetes, and Firmicutes. A total of 87 DEMs were significantly screened, and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses revealed that the potential target genes were mainly involved in the regulation of lipid, glutathione, cytosine, and purine metabolism, which participated in the local immune response through the intestinal immune network for IgA production, lysosome, and Toll-like receptor (TLR) pathways. Moreover, the expression levels of 11 target genes (e.g., TLR3, MyD88, NF-κB, TGF-β, TNF-α, MHC II, IL-22, LysC, F2, F5, and C3) related to inflammation and immunity were verified by qRT-PCR detection. The correlation analysis indicated that the abundance of intestinal Firmicutes and Proteobacteria was significantly associated with the high local expression of miR-203/NF-κB, miR-129/TNF-α, and miR-205/TGF-β. These findings will help to elucidate the molecular regulation mechanism of the intestinal microflora, inflammation, and immune response-mediated miRNA-target gene axis in cyprinid fish.}, } @article {pmid38423780, year = {2024}, author = {Hitchings, L and Fleet, B and Smith, DT and Read, JM and Melville, C and Sedda, L}, title = {Determining the distance patterns in the movements of future doctors in UK between 2002 and 2015: a retrospective cohort study.}, journal = {BMJ open}, volume = {14}, number = {3}, pages = {e077635}, pmid = {38423780}, issn = {2044-6055}, mesh = {Humans ; Retrospective Studies ; *Career Choice ; Gender Identity ; Social Class ; *Students, Medical ; Schools, Medical ; United Kingdom ; }, abstract = {OBJECTIVE: To determine and identify distance patterns in the movements of medical students and junior doctors between their training locations.

DESIGN: A retrospective cohort study of UK medical students from 2002 to 2015 (UKMED data).

SETTING: All UK medical schools, foundations and specialty training organisation.

PARTICIPANTS: All UK medical students from 2002 to 2015, for a total of 97 932 participants.

OUTCOME MEASURES: Individual movements and number of movements by county of students from family home to medical school training, from medical school to foundation training and from foundation to specialty training.

METHODS: Leslie matrix, principal components analysis, Gini coefficient, χ[2] test, generalised linear models and variable selection methods were employed to explore the different facets of students' and junior doctors' movements from the family home to medical school and for the full pathway (from family home to specialty training).

RESULTS: The majority of the movements between the different stages of the full pathway were restricted to a distance of up to 50 km; although the proportion of movements changed from year-to-year, with longer movements during 2007-2008. At the individual level, ethnicity, socioeconomic class of the parent(s) and the deprivation score of the family home region were found to be the most important factors associated with the length of the movements from the family home to medical school. Similar results were found when movements were aggregated at the county level, with the addition of factors such as gender and qualification at entry (to medical school) being statistically associated with the number of new entrant students moving between counties.

CONCLUSION: Our findings show that while future doctors do not move far from their family home or training location, this pattern is not homogeneous over time. Distances are influenced by demographics, socioeconomic status and deprivation. These results may contribute in designing interventions aimed at solving the chronic problems of maldistribution and underdoctoring in the UK.}, } @article {pmid38422100, year = {2024}, author = {Barrenechea Angeles, I and Nguyen, NL and Greco, M and Tan, KS and Pawlowski, J}, title = {Assigning the unassigned: A signature-based classification of rDNA metabarcodes reveals new deep-sea diversity.}, journal = {PloS one}, volume = {19}, number = {2}, pages = {e0298440}, pmid = {38422100}, issn = {1932-6203}, mesh = {Phylogeny ; *DNA, Environmental ; DNA, Ribosomal ; Databases, Factual ; *Foraminifera/genetics ; Water ; }, abstract = {Environmental DNA metabarcoding reveals a vast genetic diversity of marine eukaryotes. Yet, most of the metabarcoding data remain unassigned due to the paucity of reference databases. This is particularly true for the deep-sea meiofauna and eukaryotic microbiota, whose hidden diversity is largely unexplored. Here, we tackle this issue by using unique DNA signatures to classify unknown metabarcodes assigned to deep-sea foraminifera. We analyzed metabarcoding data obtained from 311 deep-sea sediment samples collected in the Clarion-Clipperton Fracture Zone, an area of potential polymetallic nodule exploitation in the Eastern Pacific Ocean. Using the signatures designed in the 37F hypervariable region of the 18S rRNA gene, we were able to classify 802 unassigned metabarcodes into 61 novel lineages, which have been placed in 27 phylogenetic clades. The comparison of new lineages with other foraminiferal datasets shows that most novel lineages are widely distributed in the deep sea. Five lineages are also present in the shallow-water datasets; however, phylogenetic analysis of these lineages separates deep-sea and shallow-water metabarcodes except in one case. While the signature-based classification does not solve the problem of gaps in reference databases, this taxonomy-free approach provides insight into the distribution and ecology of deep-sea species represented by unassigned metabarcodes, which could be useful in future applications of metabarcoding for environmental monitoring.}, } @article {pmid38418873, year = {2024}, author = {Delavaux, CS and Crowther, TW and Bever, JD and Weigelt, P and Gora, EM}, title = {Mutualisms weaken the latitudinal diversity gradient among oceanic islands.}, journal = {Nature}, volume = {627}, number = {8003}, pages = {335-339}, pmid = {38418873}, issn = {1476-4687}, mesh = {Animals ; *Biodiversity ; Datasets as Topic ; *Geographic Mapping ; *Islands ; Mycorrhizae/physiology ; *Plants/microbiology ; Pollination ; *Symbiosis ; Tropical Climate ; Oceans and Seas ; Phylogeography ; }, abstract = {The latitudinal diversity gradient (LDG) dominates global patterns of diversity[1,2], but the factors that underlie the LDG remain elusive. Here we use a unique global dataset[3] to show that vascular plants on oceanic islands exhibit a weakened LDG and explore potential mechanisms for this effect. Our results show that traditional physical drivers of island biogeography[4]-namely area and isolation-contribute to the difference between island and mainland diversity at a given latitude (that is, the island species deficit), as smaller and more distant islands experience reduced colonization. However, plant species with mutualists are underrepresented on islands, and we find that this plant mutualism filter explains more variation in the island species deficit than abiotic factors. In particular, plant species that require animal pollinators or microbial mutualists such as arbuscular mycorrhizal fungi contribute disproportionately to the island species deficit near the Equator, with contributions decreasing with distance from the Equator. Plant mutualist filters on species richness are particularly strong at low absolute latitudes where mainland richness is highest, weakening the LDG of oceanic islands. These results provide empirical evidence that mutualisms, habitat heterogeneity and dispersal are key to the maintenance of high tropical plant diversity and mediate the biogeographic patterns of plant diversity on Earth.}, } @article {pmid38416313, year = {2024}, author = {Vigna-Taglianti, FD and Martorana, M and Viola, E and Renna, M and Vadrucci, S and Sciutto, A and Andrà, C and Mehanović, E and Ginechesi, M and Vullo, C and Ceccano, A and Casella, P and Faggiano, F and , }, title = {Evaluation of Effectiveness of the Unplugged Program on Gambling Behaviours among Adolescents: Study Protocol of the Experimental Controlled Study "GAPUnplugged".}, journal = {Journal of prevention (2022)}, volume = {45}, number = {3}, pages = {405-429}, pmid = {38416313}, issn = {2731-5541}, support = {0005406//ASLRoma1/ ; }, mesh = {Humans ; *Gambling/prevention & control/psychology ; Adolescent ; Female ; Male ; Surveys and Questionnaires ; Adolescent Behavior/psychology ; Program Evaluation ; Risk-Taking ; Students/psychology ; Italy ; }, abstract = {Gambling risk behaviour is an emerging problem among adolescents. "Unplugged" is an effective Social Influence curriculum for preventing substance use among students. This study aims to develop and test a new component focused on gambling added to the Unplugged program. Schools of Piedmont region and Rome city were invited to participate in the study. A self-completed anonymous questionnaire including questions on socio-demographic characteristics, addictive behaviours, beliefs, attitudes and risk perceptions about gambling, normative perceptions, parental practices, school climate, refusal skills, impulsiveness, self-esteem, antisocial behaviours and sensation seeking was prepared for baseline and follow-up surveys. The protocol of the study was submitted and approved by the Novara Ethical Committee and registered in ClinicalTrials.gov (NCT05630157, Protocol ID: 080.742, 11/17/2022). Twenty-nine schools accepted to participate in the study. Sixty-three classes (1325 students) satisfied the eligibility criteria for intervention and were allocated to the intervention arm, and the other 61 (1269 students) were allocated to the control arm. Because of drop-out, absentees, refusals, and invalid questionnaires, data on 1874 students (998 in the intervention and 876 in the control arm), were available for the analysis at baseline. Data management of follow-up questionnaires is in progress. Results of the present study will be useful to clarify the effectiveness of prevention interventions in reducing gambling behaviours among adolescents. Moreover, this will be the first experience of evaluating a new component focused on a different risk behaviour, added to a curriculum previously shown as effective on other risk behaviours.}, } @article {pmid38415798, year = {2024}, author = {Jager, T}, title = {Identifying and Predicting Delayed Mortality with Toxicokinetic-Toxicodynamic Models.}, journal = {Environmental toxicology and chemistry}, volume = {43}, number = {5}, pages = {1030-1035}, doi = {10.1002/etc.5833}, pmid = {38415798}, issn = {1552-8618}, mesh = {Animals ; Humans ; Daphnia magna/drug effects ; Datasets as Topic ; Death ; *Ecotoxicology/methods ; Fluoroquinolones/toxicity ; *Mortality ; Pesticides/toxicity ; *Pharmacokinetics ; Risk Assessment ; Stochastic Processes ; Time Factors ; *Toxicity Tests, Acute/methods/standards ; }, abstract = {The prevalence of standardized toxicity testing in ecotoxicology has largely obscured the notion that toxicity is a function of time as well. The necessity of considering time is vividly demonstrated by observations of delayed mortality, that is, deaths continue to occur even when animals are no longer exposed to a toxicant. In this contribution, I explore to what extent toxicokinetic-toxicodynamic (TKTD) models from the framework of the General Unified Threshold model for Survival (GUTS) can capture delayed mortality, and to what extent this phenomenon can be predicted from short-term standard tests. I use a previously published data set for fluoroquinolones in Daphnia magna that shows strongly delayed mortality (using immobilization as a proxy for death). The model analysis shows that the GUTS stochastic death models can capture delayed mortality in the complete data set with a long recovery phase, but that the delayed effects would not have been predicted from a 2-day standard test. The study underlines the limited information content of standard acute test designs. Toxicokinetic-toxicodynamic modeling offers a handle on the time aspects of toxicity but cannot always be relied on to provide accurate extrapolations based on severely limited standard tests. The phenomenon of delayed toxicity requires more structured study to clarify its prevalence and impact; I discuss several avenues for further investigation. Environ Toxicol Chem 2024;43:1030-1035. © 2024 SETAC.}, } @article {pmid38413777, year = {2024}, author = {Lemane, T and Lezzoche, N and Lecubin, J and Pelletier, E and Lescot, M and Chikhi, R and Peterlongo, P}, title = {Indexing and real-time user-friendly queries in terabyte-sized complex genomic datasets with kmindex and ORA.}, journal = {Nature computational science}, volume = {4}, number = {2}, pages = {104-109}, pmid = {38413777}, issn = {2662-8457}, support = {ANR-19-CE45-0008//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-19-CE45-0008//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-19-CE45-0008//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-19-CE45-0008//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-22-CE45-0007//Agence Nationale de la Recherche (French National Research Agency)/ ; PIA/ANR16-CONV-0005//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-19-P3IA-0001//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-19-CE45-0008//Agence Nationale de la Recherche (French National Research Agency)/ ; 956229//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 Marie Skłodowska-Curie Actions (H2020 Excellent Science - Marie Skłodowska-Curie Actions)/ ; 872539//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 Marie Skłodowska-Curie Actions (H2020 Excellent Science - Marie Skłodowska-Curie Actions)/ ; }, mesh = {*Genomics ; Oceans and Seas ; *Seawater ; Metagenome/genetics ; Databases, Nucleic Acid ; }, abstract = {Public sequencing databases contain vast amounts of biological information, yet they are largely underutilized as it is challenging to efficiently search them for any sequence(s) of interest. We present kmindex, an approach that can index thousands of metagenomes and perform sequence searches in a fraction of a second. The index construction is an order of magnitude faster than previous methods, while search times are two orders of magnitude faster. With negligible false positive rates below 0.01%, kmindex outperforms the precision of existing approaches by four orders of magnitude. Here we demonstrate the scalability of kmindex by successfully indexing 1,393 marine seawater metagenome samples from the Tara Oceans project. Additionally, we introduce the publicly accessible web server Ocean Read Atlas, which enables real-time queries on the Tara Oceans dataset.}, } @article {pmid38413616, year = {2024}, author = {Xu, W and Pan, Z and Wu, Y and An, XL and Wang, W and Adamovich, B and Zhu, YG and Su, JQ and Huang, Q}, title = {A database on the abundance of environmental antibiotic resistance genes.}, journal = {Scientific data}, volume = {11}, number = {1}, pages = {250}, pmid = {38413616}, issn = {2052-4463}, support = {32161143016//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42177362//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42250410328//National Natural Science Foundation of China (National Science Foundation of China)/ ; GPNI GR no. 20212317//Belarusian Republican Foundation for Fundamental Research (BRFFR)/ ; }, mesh = {*Anti-Bacterial Agents/pharmacology ; China ; *Drug Resistance, Microbial/genetics ; Genes, Bacterial ; *Microbiota ; *Databases, Genetic ; }, abstract = {Antimicrobial resistance (AMR) poses a severe threat to global health. The wide distribution of environmental antibiotic resistance genes (ARGs), which can be transferred between microbiota, especially clinical pathogens and human commensals, contributed significantly to AMR. However, few databases on the spatiotemporal distribution, abundance, and health risk of ARGs from multiple environments have been developed, especially on the absolute level. In this study, we compiled the ARG occurrence data generated by a high-throughput quantitative PCR platform from 1,403 samples in 653 sampling sites across 18 provinces in China. The database possessed 291,870 records from five types of habitats on the abundance of 290 ARGs, as well as 8,057 records on the abundance of 30 mobile genetic elements (MGEs) from 2013 to 2020. These ARGs conferred resistance to major common types of antibiotics (a total of 15 types) and represented five major resistance mechanisms, as well as four risk ranks. The database can provide information for studies on the dynamics of ARGs and is useful for the health risk assessment of AMR.}, } @article {pmid38407293, year = {2024}, author = {Dai, Y and Chen, H and Yu, J and Cai, J and Lu, B and Dai, M and Zhu, L}, title = {Global and regional trends in the incidence and prevalence of uterine fibroids and attributable risk factors at the national level from 2010 to 2019: A worldwide database study.}, journal = {Chinese medical journal}, volume = {137}, number = {21}, pages = {2583-2589}, pmid = {38407293}, issn = {2542-5641}, mesh = {Humans ; Female ; *Leiomyoma/epidemiology ; Incidence ; Risk Factors ; Prevalence ; Adult ; Middle Aged ; Uterine Neoplasms/epidemiology ; Disability-Adjusted Life Years ; Databases, Factual ; }, abstract = {BACKGROUND: Uterine fibroids (UFs), the most common tumors in women worldwide, may reduce quality of life and daily activities and even lead to adverse fertility and general health events in patients, causing significant societal health and financial burdens. The objective of this study was to evaluate the global burden through epidemiological trends and examine the potential risk factors for UFs at the national level.

METHODS: Data on the incidence, prevalence, disability-adjusted life years (DALYs), age-standardized incidence rates (ASIRs), age-standardized prevalence rates (ASPRs), and age-standardized DALY rates for UFs were collected, and the associations with the Human Development Index (HDI) and fertility were evaluated. The age trends in the average annual percent change (AAPC) of the incidence and prevalence rates of UFs were evaluated by joinpoint regression analysis. The associations between lifestyle, metabolic, and socioeconomic factors and the ASIRs of UFs were examined using multivariable linear regression analysis.

RESULTS: The worldwide incidence and prevalence of UFs have been increasing in the past decade, with AAPCs of 0.27% in the incidence rate and 0.078% in the prevalence rate. During 2010-2019, significant increasing trends in UF ASIR were observed in 52 of 88 countries. The age-specific incidence and prevalence of UFs in most age groups showed increasing trends except for 45-54-year-old women which showed no significant trend. Ecological analysis demonstrated no relationship between the incidence of UFs and the HDI but an inverse association with fertility. The incidence of UFs was positively correlated with alcohol intake, hypertension, overweight, and obesity and negatively correlated with smoking.

CONCLUSION: With the increasing incidence and prevalence worldwide, effective targeted prevention and control of relevant risk factors at the national level should be encouraged to reduce the disease burden of UFs.}, } @article {pmid38405013, year = {2024}, author = {Boyes, D and Sims, I and Lees, DC and Eagles, M and , and , and , and , and , and , and , and , }, title = {The genome sequence of the Chequered Fruit-tree Tortrix, Pandemis corylana (Fabricius, 1794).}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {6}, pmid = {38405013}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual male Pandemis corylana (the Chequered Fruit-tree Tortrix; Arthropoda; Insecta; Lepidoptera; Tortricidae). The genome sequence is 441.6 megabases in span. Most of the assembly is scaffolded into 30 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.53 kilobases in length. Gene annotation of this assembly on Ensembl identified 19,608 protein coding genes.}, } @article {pmid38404638, year = {2023}, author = {Boyes, D and Eagles, M and , and , and , and , and , and , }, title = {The genome sequence of the Light Emerald, Campaea margaritaria (Linnaeus, 1761).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {476}, pmid = {38404638}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual male Campaea margaritaria (the Light Emerald; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 335.2 megabases in span. The whole assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 16.9 kilobases in length. Gene annotation of this assembly on Ensembl identified 16,403 protein coding genes.}, } @article {pmid38404637, year = {2023}, author = {Boyes, D and Holland, PWH and , and , and , and , and , and , }, title = {The genome sequence of the Phoenix, Eulithis prunata (Linnaeus, 1758).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {185}, pmid = {38404637}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual male Eulithis prunata (the Phoenix; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 263.1 megabases in span. Most of the assembly is scaffolded into 30 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.9 kilobases in length. Gene annotation of this assembly on Ensembl identified 16,023 protein coding genes.}, } @article {pmid38404636, year = {2023}, author = {Boyes, D and Eagles, M and , and , and , and , and , and , }, title = {The genome sequence of the Flame Shoulder, Ochropleura plecta (Linnaeus, 1761).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {506}, pmid = {38404636}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual female Ochropleura plecta (the Flame Shoulder; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 643.9 megabases in span. Most of the assembly is scaffolded into 32 chromosomal pseudomolecules, including the W and Z sex chromosomes. The mitochondrial genome has also been assembled and is 15.34 kilobases in length. Gene annotation of this assembly on Ensembl identified 19,016 protein coding genes.}, } @article {pmid38404635, year = {2023}, author = {Hayward, A and Lohse, K and Vila, R and Laetsch, DR and Hedlund, JSU and , and , and , and , }, title = {The genome sequence of the Brown Argus, Aricia agestis (Denis & Schiffermüller, 1775).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {336}, pmid = {38404635}, issn = {2398-502X}, abstract = {We present genome assemblies from two male Aricia agestis specimens (the Brown Argus; Arthropoda; Insecta; Lepidoptera; Lycaenidae). The genome sequences are 435.3 and 437.4 megabases in span. Each assembly is scaffolded into 23 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genomes were assembled and are 15.47 and 15.45 kilobases in length. Gene annotation of these assemblies on Ensembl identified 12,688 and 12,654 protein coding genes.}, } @article {pmid38402992, year = {2024}, author = {Zhu, Y and Wang, L and Ma, J and Hua, Z and Yang, Y and Chen, F}, title = {Assessment of carbon sequestration potential of mining areas under ecological restoration in China.}, journal = {The Science of the total environment}, volume = {921}, number = {}, pages = {171179}, doi = {10.1016/j.scitotenv.2024.171179}, pmid = {38402992}, issn = {1879-1026}, abstract = {Mining activities aggravate the ecological degradation and emission of greenhouse gases throughout the world, thereby affecting the global climate and posing a serious threat to the ecological safety. Vegetation restoration is considered to be an effective and sustainable strategy to improve the post-mining soil quality and functions. However, we still have a limited knowledge of the impact of vegetation restoration on carbon sequestration potential in mining areas. In this pursuit, the present study was envisaged to integrate the findings from studies on soil organic carbon (SOC) sequestration in mining areas under vegetation restoration with field monitoring data. The carbon sequestration potential under vegetation restoration in China's mining areas was estimated by using a machine learning model. The results showed that (1) Vegetation restoration exhibited a consistently positive impact on the changes in the SOC reserves. The carbon sequestration potential was the highest in mixed forests, followed by broad-leaved forests, coniferous forests, grassland, shrubland, and farmland; (2) The number of years of vegetation restoration and mean annual precipitation were found to be the important moderating variables affecting the SOC reserves in reclaimed soils in mining areas; (3) There were significant differences in the SOC sequestration potential under different vegetation restoration scenarios in mining areas in China. The SOC sequestration potential reached up to 9.86 million t C a[-1], when the soil was restored to the initial state. Based on the meta-analysis, the maximal attainable SOC sequestration potential was found to be 4.26 million t C a[-1]. The SOC sequestration potential reached the highest level of 12.86 million t C a[-1], when the optimal vegetation type in a given climate was restored. The results indicated the importance of vegetation restoration for improving the soil sequestration potential in mining areas. The time lag in carbon sequestration potential for different vegetation types in mining areas was also revealed. Our findings can assist the development of ecological restoration regimens in mining areas to mitigate the global climate change.}, } @article {pmid38402941, year = {2024}, author = {Ulanova, A and Mansfeldt, C}, title = {EcoGenoRisk: Developing a computational ecological risk assessment tool for synthetic biology.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {346}, number = {}, pages = {123647}, doi = {10.1016/j.envpol.2024.123647}, pmid = {38402941}, issn = {1873-6424}, mesh = {*Synthetic Biology ; *Software ; Risk Assessment ; Computational Biology ; Genome, Bacterial ; }, abstract = {The expanding field of synthetic biology (synbio) supports new opportunities in the design of targeted bioproducts or modified microorganisms. However, this rapid development of synbio products raises concerns surrounding the potential risks of modified microorganisms contaminating unintended environments. These potential invasion risks require new bioinformatic tools to inform the design phase. EcoGenoRisk is a newly constructed computational risk assessment tool for invasiveness that aims to predict where synbio microorganisms may establish a population by screening for habitats of genetically similar microorganisms. The first module of the tool identifies genetically similar microorganisms and potential ecological relationships such as competition, mutualism, and inhibition. In total, 520 archaeal and 32,828 bacterial complete assembly genomes were analyzed to test the specificity and accuracy of the tool as well as to characterize the enzymatic profiles of different taxonomic lineages. Additionally, ecological relationships were analyzed to determine which would result in the greatest potential overlap between shared functional profiles. Notably, competition displayed the significantly highest overlap of shared functions between compared genomes. Overall, EcoGenoRisk is a flexible software pipeline that assists environmental risk assessors to query large databases of known microorganisms and prioritize follow-up bench scale studies.}, } @article {pmid38402789, year = {2024}, author = {Gonyo, SB and Burkart, H and Regan, S}, title = {Leveraging big data for outdoor recreation management: A case study from the York river in Virginia.}, journal = {Journal of environmental management}, volume = {354}, number = {}, pages = {120482}, doi = {10.1016/j.jenvman.2024.120482}, pmid = {38402789}, issn = {1095-8630}, mesh = {Child ; Humans ; Child, Preschool ; Middle Aged ; *Recreation ; Virginia ; *Rivers ; Big Data ; Quality of Life ; }, abstract = {Outdoor recreation is important for improving quality of life, well-being, and local economies, but quantifying its value without direct monetary transactions can be challenging. This study explores combining non-market valuation techniques with emerging big data sources to estimate the value of recreation for the York River and surrounding parks in Virginia. By applying the travel cost method to anonymous human mobility data, we gain deeper insights into the significance of recreational experiences for visitors and the local economy. Results of a zero-inflated Negative Binomial model show a mean consumer surplus value of $26.91 per trip, totaling $15.5 million across nearly 600,000 trips observed in 2022. Further, weekends, holidays, and the summer and fall months are found to be peak visitation times, whereas those with young children and who are Hispanic or over 64 years old are less likely to visit. These findings shed light on various factors influencing visitation patterns and recreation values, including temporal effects and socio-demographics, revealing disparities that warrant targeted efforts for inclusivity and accessibility. Policymakers can use these insights to make informed and sustainable choices in outdoor recreation management, fostering the preservation of natural resources for the benefit of both visitors and the environment.}, } @article {pmid38398847, year = {2024}, author = {Navratilova, HF and Lanham-New, S and Whetton, AD and Geifman, N}, title = {Associations of Diet with Health Outcomes in the UK Biobank: A Systematic Review.}, journal = {Nutrients}, volume = {16}, number = {4}, pages = {}, pmid = {38398847}, issn = {2072-6643}, mesh = {Female ; Humans ; Male ; Middle Aged ; *Cardiovascular Diseases/epidemiology/etiology ; Colorectal Neoplasms/epidemiology/etiology/prevention & control ; *Diabetes Mellitus, Type 2/epidemiology/etiology ; *Diet/statistics & numerical data/adverse effects ; Diet, Healthy/statistics & numerical data ; Neoplasms/epidemiology/etiology ; Risk Factors ; UK Biobank/statistics & numerical data ; United Kingdom/epidemiology ; }, abstract = {The UK Biobank is a cohort study that collects data on diet, lifestyle, biomarkers, and health to examine diet-disease associations. Based on the UK Biobank, we reviewed 36 studies on diet and three health conditions: type 2 diabetes (T2DM), cardiovascular disease (CVD), and cancer. Most studies used one-time dietary data instead of repeated 24 h recalls, which may lead to measurement errors and bias in estimating diet-disease associations. We also found that most studies focused on single food groups or macronutrients, while few studies adopted a dietary pattern approach. Several studies consistently showed that eating more red and processed meat led to a higher risk of lung and colorectal cancer. The results suggest that high adherence to "healthy" dietary patterns (consuming various food types, with at least three servings/day of whole grain, fruits, and vegetables, and meat and processed meat less than twice a week) slightly lowers the risk of T2DM, CVD, and colorectal cancer. Future research should use multi-omics data and machine learning models to account for the complexity and interactions of dietary components and their effects on disease risk.}, } @article {pmid38396178, year = {2024}, author = {Wang, F and Sun, N and Zhang, C and Fan, C and Xiong, J and Wei, X and Hao, W}, title = {Experimental study on mine water purification mechanism for broken coal and rock masses in the underground reservoir of ecologically vulnerable mining area.}, journal = {Environmental science and pollution research international}, volume = {31}, number = {14}, pages = {21442-21457}, pmid = {38396178}, issn = {1614-7499}, support = {52104155//National Natural Science Foundation of China/ ; 51974297//National Natural Science Foundation of China/ ; }, mesh = {*Coal ; *Mining ; Water Quality ; Minerals ; }, abstract = {Water-rock interaction mechanism and water purification capacity of broken coal and rock masses are very important for the efficient operation of the underground reservoir. In this paper, a water purification simulation device for an underground mine reservoir was designed. The experimental study on the dynamic interaction between broken coal and rock masses and mine water was carried out. The water purification mechanism is analyzed from the changes in rock mineral composition and mine water quality before and after the test. The results show that after the broken coal and rock mass purification, the water turbidity and the concentration of chlorides and suspended solids decreased obviously. The water purification capacities of mudstone and sandstone are stronger than that of coal samples. After 60 days of reaction between the working face sewage and the broken samples (mudstone, sandstone, and coal), the turbidity, chromaticity, and residual chlorine decreased by > 90%, 90%, and 60%, respectively; and COD decreased by 35.29%, 30.59%, and 28.99%, respectively. While the TDS and the total hardness increased by about 40%, 30%, and 10% for the mudstone, sandstone, and coal, respectively. It shows that coal also has the worst degradation performance. The water purification effect of broken coal and rock masses has a significant time effect. The early stage of water-rock interaction is dominated by mineral dissolution, and the middle stage is dominated by precipitation and adsorption. The pH value of the solution has a certain influence on the ion change. In the later stage, the water-rock interaction is weak in a dynamic equilibrium state, and the change in the mine water quality index is not obvious. Considering the influence of rock lithology on water quality and the law of water-rock interaction time, the construction site selection and water storage time optimization of underground reservoirs in Jinjie Coal Mine were carried out, respectively.}, } @article {pmid38396055, year = {2024}, author = {Gauzens, B and Kalinkat, G and Antunes, AC and Boy, T and O'Gorman, EJ and Jacob, U and Jochum, M and Kortsch, S and Rosenbaum, B and Figueiredo, L and Brose, U}, title = {Quantitative description of six fish species' gut contents and prey abundances in the Baltic Sea (1968-1978).}, journal = {Scientific data}, volume = {11}, number = {1}, pages = {236}, pmid = {38396055}, issn = {2052-4463}, support = {DFG-FZT 118, 202548816//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; DFG-FZT 118, 202548816//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; DFG-FZT 118, 202548816//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; DFG-FZT 118, 202548816//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; DFG-FZT 118, 202548816//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; DFG-FZT 118, 202548816//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; DAAD, 57070483//Deutscher Akademischer Austauschdienst (German Academic Exchange Service)/ ; }, mesh = {Animals ; Baltic States ; *Fishes ; *Gastrointestinal Contents ; Oceans and Seas ; }, abstract = {The dataset presents a compilation of stomach contents from six demersal fish species from two functional groups inhabiting the Baltic Sea. It includes detailed information on prey identities, body masses, and biomasses recovered from both the fish's digestive systems and their surrounding environment. Environmental parameters, such as salinity and temperature levels, have been integrated to enrich this dataset. The juxtaposition of information on prey found in stomachs and in the environment provides an opportunity to quantify trophic interactions across different environmental contexts and investigate how fish foraging behaviour adapts to changes in their environment, such as an increase in temperature. The compilation of body mass and taxonomic information for all species allows approaching these new questions using either a taxonomic (based on species identity) or functional trait (based on body mass) approach.}, } @article {pmid38395906, year = {2024}, author = {Ou, AH and Rosenthal, SB and Adli, M and Akiyama, K and Akula, N and Alda, M and Amare, AT and Ardau, R and Arias, B and Aubry, JM and Backlund, L and Bauer, M and Baune, BT and Bellivier, F and Benabarre, A and Bengesser, S and Bhattacharjee, AK and Biernacka, JM and Cervantes, P and Chen, GB and Chen, HC and Chillotti, C and Cichon, S and Clark, SR and Colom, F and Cousins, DA and Cruceanu, C and Czerski, PM and Dantas, CR and Dayer, A and Del Zompo, M and Degenhardt, F and DePaulo, JR and Étain, B and Falkai, P and Fellendorf, FT and Ferensztajn-Rochowiak, E and Forstner, AJ and Frisén, L and Frye, MA and Fullerton, JM and Gard, S and Garnham, JS and Goes, FS and Grigoroiu-Serbanescu, M and Grof, P and Gruber, O and Hashimoto, R and Hauser, J and Heilbronner, U and Herms, S and Hoffmann, P and Hofmann, A and Hou, L and Jamain, S and Jiménez, E and Kahn, JP and Kassem, L and Kato, T and Kittel-Schneider, S and König, B and Kuo, PH and Kusumi, I and Lackner, N and Laje, G and Landén, M and Lavebratt, C and Leboyer, M and Leckband, SG and Jaramillo, CAL and MacQueen, G and Maj, M and Manchia, M and Marie-Claire, C and Martinsson, L and Mattheisen, M and McCarthy, MJ and McElroy, SL and McMahon, FJ and Mitchell, PB and Mitjans, M and Mondimore, FM and Monteleone, P and Nievergelt, CM and Nöthen, MM and Novák, T and Ösby, U and Ozaki, N and Papiol, S and Perlis, RH and Pisanu, C and Potash, JB and Pfennig, A and Reich-Erkelenz, D and Reif, A and Reininghaus, EZ and Rietschel, M and Rouleau, GA and Rybakowski, JK and Schalling, M and Schofield, PR and Schubert, KO and Schulze, TG and Schweizer, BW and Seemüller, F and Severino, G and Shekhtman, T and Shilling, PD and Shimoda, K and Simhandl, C and Slaney, CM and Squassina, A and Stamm, T and Stopkova, P and Tighe, SK and Tortorella, A and Turecki, G and Vieta, E and Volkert, J and Witt, S and Wray, NR and Wright, A and Young, LT and Zandi, PP and Kelsoe, JR}, title = {Lithium response in bipolar disorder is associated with focal adhesion and PI3K-Akt networks: a multi-omics replication study.}, journal = {Translational psychiatry}, volume = {14}, number = {1}, pages = {109}, pmid = {38395906}, issn = {2158-3188}, support = {R01 MH059556/MH/NIMH NIH HHS/United States ; Z01 MH002810/ImNIH/Intramural NIH HHS/United States ; R01 MH059535/MH/NIMH NIH HHS/United States ; R01 MH059567/MH/NIMH NIH HHS/United States ; R01 MH059545/MH/NIMH NIH HHS/United States ; P01 CA089392/CA/NCI NIH HHS/United States ; R01 MH059548/MH/NIMH NIH HHS/United States ; R01 MH059534/MH/NIMH NIH HHS/United States ; R01 MH059533/MH/NIMH NIH HHS/United States ; U01 MH092758/MH/NIMH NIH HHS/United States ; K02 DA021237/DA/NIDA NIH HHS/United States ; MR/L006642/1/MRC_/Medical Research Council/United Kingdom ; R01 MH059553/MH/NIMH NIH HHS/United States ; R01 MH060068/MH/NIMH NIH HHS/United States ; }, mesh = {Humans ; *Lithium/pharmacology/therapeutic use ; *Bipolar Disorder/drug therapy/genetics ; Proto-Oncogene Proteins c-akt/genetics ; Phosphatidylinositol 3-Kinases/genetics ; Genome-Wide Association Study ; Multiomics ; Focal Adhesions ; }, abstract = {Lithium is the gold standard treatment for bipolar disorder (BD). However, its mechanism of action is incompletely understood, and prediction of treatment outcomes is limited. In our previous multi-omics study of the Pharmacogenomics of Bipolar Disorder (PGBD) sample combining transcriptomic and genomic data, we found that focal adhesion, the extracellular matrix (ECM), and PI3K-Akt signaling networks were associated with response to lithium. In this study, we replicated the results of our previous study using network propagation methods in a genome-wide association study of an independent sample of 2039 patients from the International Consortium on Lithium Genetics (ConLiGen) study. We identified functional enrichment in focal adhesion and PI3K-Akt pathways, but we did not find an association with the ECM pathway. Our results suggest that deficits in the neuronal growth cone and PI3K-Akt signaling, but not in ECM proteins, may influence response to lithium in BD.}, } @article {pmid38395161, year = {2024}, author = {Brunelli, A and Cazzagon, V and Faraggiana, E and Bettiol, C and Picone, M and Marcomini, A and Badetti, E}, title = {An overview on dispersion procedures and testing methods for the ecotoxicity testing of nanomaterials in the marine environment.}, journal = {The Science of the total environment}, volume = {921}, number = {}, pages = {171132}, doi = {10.1016/j.scitotenv.2024.171132}, pmid = {38395161}, issn = {1879-1026}, mesh = {*Nanostructures/toxicity/chemistry ; Oxides/chemistry ; Research Design ; Ecotoxicology ; }, abstract = {Considerable efforts have been devoted to develop or adapt existing guidelines and protocols, to obtain robust and reproducible results from (eco)toxicological assays on engineered nanomaterials (NMs). However, while many studies investigated adverse effects of NMs on freshwater species, less attention was posed to the marine environment, a major sink for these contaminants. This review discusses the procedures used to assess the ecotoxicity of NMs in the marine environment, focusing on the use of protocols and methods for preparing NMs dispersions and on the NMs physicochemical characterization in exposure media. To this purpose, a critical analysis of the literature since 2010 was carried out, based on the publication of the first NMs dispersion protocols. Among the 89 selected studies, only <5 % followed a standardized dispersion protocol combined with NMs characterization in ecotoxicological media, while more than half used a non-standardized dispersion method but performed NMs characterization. In the remaining studies, only partial or no information on dispersion procedures or on physicochemical characterization was provided. This literature review also highlighted that metal oxides NMs were the most studied (42 %), but with an increasing interest in last years towards nanoplastics (14 %) and multicomponent nanomaterials (MCNMs, 7 %), in line with the growing attention on these emerging contaminants. For all these NMs, primary producers as algae and bacteria were the most studied groups of marine species, in addition to mollusca, while organisms at higher trophic levels were less represented, likely due to challenges in evaluating adverse effects on more complex organisms. Thus, despite the wide use of NMs in different applications, standard dispersion protocols are not often used for ecotoxicity testing with marine species. However, the efforts to characterize NMs in ecotoxicological media recognize the importance of following conditions that are as standardized as possible to support the ecological hazard assessment of NMs.}, } @article {pmid38390626, year = {2024}, author = {Kumar, A and Ojha, PK and Roy, K}, title = {First report on pesticide sub-chronic and chronic toxicities against dogs using QSAR and chemical read-across.}, journal = {SAR and QSAR in environmental research}, volume = {35}, number = {3}, pages = {241-263}, doi = {10.1080/1062936X.2024.2320143}, pmid = {38390626}, issn = {1029-046X}, mesh = {Dogs ; Animals ; *Pesticides/toxicity ; Quantitative Structure-Activity Relationship ; Reproducibility of Results ; Databases, Factual ; }, abstract = {Excessive use of chemicals is the outcome of the industrialization of agricultural sectors which leads to disturbance of ecological balance. Various agrochemicals are widely used in agricultural fields, urban green areas, and to protect from various pest-associated diseases. Due to their long-term health and environmental hazards, chronic toxicity assessment is crucial. Since in vivo and in vitro toxicity assessments are costly, lengthy, and require a large number of animal experiments, in silico toxicity approaches are better alternatives to save time, cost, and animal experimentation. We have developed the first regression-based 2D-QSAR models using different sub-chronic and chronic toxicity data of pesticides against dogs employing 2D descriptors. From the statistical results (ntrain=53-62, r2 = 0.614 to 0.754, QLOO2 = 0.501 to 0.703 and QF12 = 0.531 to 0.718, QF22=0.523-0.713), it was concluded that the models are robust, reliable, interpretable, and predictive. Similarity-based read-across algorithm was also used to improve the predictivity (QF12=0.595-0.813,QF22=0.573-0.809) of the models. 5132 chemicals obtained from the CPDat and 1694 pesticides obtained from the PPDB database were also screened using the developed models, and their predictivity and reliability were checked. Thus, these models will be helpful for eco-toxicological data-gap filling, toxicity prediction of untested pesticides, and development of novel, safer & eco-friendly pesticides.}, } @article {pmid38389111, year = {2024}, author = {Messer, LF and Lee, CE and Wattiez, R and Matallana-Surget, S}, title = {Novel functional insights into the microbiome inhabiting marine plastic debris: critical considerations to counteract the challenges of thin biofilms using multi-omics and comparative metaproteomics.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {36}, pmid = {38389111}, issn = {2049-2618}, support = {NE/V009621/1//Natural Environment Research Council/ ; NE/V009621/1//Natural Environment Research Council/ ; NE/V009621/1//Natural Environment Research Council/ ; NE/S007342/1//NERC Scottish Universities Partnership for Environmental Research (SUPER) Doctoral Training Partnership/ ; }, mesh = {*Plastics ; Bacteria/genetics ; Multiomics ; Biofilms ; Biodegradation, Environmental ; *Microbiota/genetics ; }, abstract = {BACKGROUND: Microbial functioning on marine plastic surfaces has been poorly documented, especially within cold climates where temperature likely impacts microbial activity and the presence of hydrocarbonoclastic microorganisms. To date, only two studies have used metaproteomics to unravel microbial genotype-phenotype linkages in the marine 'plastisphere', and these have revealed the dominance of photosynthetic microorganisms within warm climates. Advancing the functional representation of the marine plastisphere is vital for the development of specific databases cataloging the functional diversity of the associated microorganisms and their peptide and protein sequences, to fuel biotechnological discoveries. Here, we provide a comprehensive assessment for plastisphere metaproteomics, using multi-omics and data mining on thin plastic biofilms to provide unique insights into plastisphere metabolism. Our robust experimental design assessed DNA/protein co-extraction and cell lysis strategies, proteomics workflows, and diverse protein search databases, to resolve the active plastisphere taxa and their expressed functions from an understudied cold environment.

RESULTS: For the first time, we demonstrate the predominance and activity of hydrocarbonoclastic genera (Psychrobacter, Flavobacterium, Pseudomonas) within a primarily heterotrophic plastisphere. Correspondingly, oxidative phosphorylation, the citrate cycle, and carbohydrate metabolism were the dominant pathways expressed. Quorum sensing and toxin-associated proteins of Streptomyces were indicative of inter-community interactions. Stress response proteins expressed by Psychrobacter, Planococcus, and Pseudoalteromonas and proteins mediating xenobiotics degradation in Psychrobacter and Pseudoalteromonas suggested phenotypic adaptations to the toxic chemical microenvironment of the plastisphere. Interestingly, a targeted search strategy identified plastic biodegradation enzymes, including polyamidase, hydrolase, and depolymerase, expressed by rare taxa. The expression of virulence factors and mechanisms of antimicrobial resistance suggested pathogenic genera were active, despite representing a minor component of the plastisphere community.

CONCLUSION: Our study addresses a critical gap in understanding the functioning of the marine plastisphere, contributing new insights into the function and ecology of an emerging and important microbial niche. Our comprehensive multi-omics and comparative metaproteomics experimental design enhances biological interpretations to provide new perspectives on microorganisms of potential biotechnological significance beyond biodegradation and to improve the assessment of the risks associated with microorganisms colonizing marine plastic pollution. Video Abstract.}, } @article {pmid38386279, year = {2024}, author = {Ambrosini, E and Giangregorio, C and Lomurno, E and Moccia, S and Milis, M and Loizou, C and Azzolino, D and Cesari, M and Cid Gala, M and Galán de Isla, C and Gomez-Raja, J and Borghese, NA and Matteucci, M and Ferrante, S}, title = {Automatic Spontaneous Speech Analysis for the Detection of Cognitive Functional Decline in Older Adults: Multilanguage Cross-Sectional Study.}, journal = {JMIR aging}, volume = {7}, number = {}, pages = {e50537}, pmid = {38386279}, issn = {2561-7605}, support = {001/WHO_/World Health Organization/International ; }, mesh = {Humans ; Aged ; Female ; Male ; *Cognitive Dysfunction/diagnosis ; Cross-Sectional Studies ; Italy/epidemiology ; Aged, 80 and over ; *Speech/physiology ; Spain/epidemiology ; Mental Status and Dementia Tests ; Machine Learning ; Algorithms ; }, abstract = {BACKGROUND: The rise in life expectancy is associated with an increase in long-term and gradual cognitive decline. Treatment effectiveness is enhanced at the early stage of the disease. Therefore, there is a need to find low-cost and ecological solutions for mass screening of community-dwelling older adults.

OBJECTIVE: This work aims to exploit automatic analysis of free speech to identify signs of cognitive function decline.

METHODS: A sample of 266 participants older than 65 years were recruited in Italy and Spain and were divided into 3 groups according to their Mini-Mental Status Examination (MMSE) scores. People were asked to tell a story and describe a picture, and voice recordings were used to extract high-level features on different time scales automatically. Based on these features, machine learning algorithms were trained to solve binary and multiclass classification problems by using both mono- and cross-lingual approaches. The algorithms were enriched using Shapley Additive Explanations for model explainability.

RESULTS: In the Italian data set, healthy participants (MMSE score≥27) were automatically discriminated from participants with mildly impaired cognitive function (20≤MMSE score≤26) and from those with moderate to severe impairment of cognitive function (11≤MMSE score≤19) with accuracy of 80% and 86%, respectively. Slightly lower performance was achieved in the Spanish and multilanguage data sets.

CONCLUSIONS: This work proposes a transparent and unobtrusive assessment method, which might be included in a mobile app for large-scale monitoring of cognitive functionality in older adults. Voice is confirmed to be an important biomarker of cognitive decline due to its noninvasive and easily accessible nature.}, } @article {pmid38385125, year = {2023}, author = {Boyes, D and Turnbull, L and , and , and , and , and , and , }, title = {The genome sequence of the Hornet Moth, Sesia apiformis (Clerck, 1759).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {499}, pmid = {38385125}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual male Sesia apiformis (the Hornet Moth; Arthropoda; Insecta; Lepidoptera; Sesiidae). The genome sequence is 546.8 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.4 kilobases in length. Gene annotation of this assembly on Ensembl identified 16,358 protein coding genes.}, } @article {pmid38385124, year = {2023}, author = {Boyes, D and Broad, GR and , and , and , and , and , and , and Holland, PWH and , }, title = {The genome sequence of the Shuttle-shaped Dart, Agrotis puta (Hübner, 1803).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {84}, pmid = {38385124}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual male Agrotis puta (the Shuttle-shaped Dart; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 522 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the assembled Z chromosome. The mitochondrial genome has also been assembled and is 15.4 kilobases in length. Gene annotation of this assembly on Ensembl has identified 15,136 protein coding genes.}, } @article {pmid38383691, year = {2024}, author = {Yu, D and Zhang, Y and Dang, H and Zhang, Q}, title = {Multiomics analyses reveal the mechanisms of the responses of subalpine treeline trees to phenology and winter low-temperature stress.}, journal = {Physiologia plantarum}, volume = {176}, number = {1}, pages = {e14218}, doi = {10.1111/ppl.14218}, pmid = {38383691}, issn = {1399-3054}, support = {31971491//National Natural Science Foundation of China/ ; 32201371//National Natural Science Foundation of China/ ; }, mesh = {*Trees/genetics ; Temperature ; *Multiomics ; Cold Temperature ; Seasons ; }, abstract = {Withstanding extreme cold stress is a prerequisite for alpine treeline trees to persist and survive. However, the underlying mechanism by which treeline trees sense phenological changes and survive hard winters has not been fully elucidated. Here, we investigated the physiology, transcriptome, and metabolome of the subalpine treeline species Larix chinensis to identify the molecular mechanism of phenological and cold resistance. Calcium and antioxidant enzyme activities (e.g., superoxide dismutase and glutathione peroxidase) are essential for coping with winter cold stress in L. chinensis. Transcriptome analysis revealed that circadian rhythm and phytohormone signalling transduction played important roles in regulating L. chinensis phenological changes and cold stress responses. The variations in the transcriptome identified were accompanied by the specific accumulation of flavones, flavonols, and monosaccharides. The flavonoid biosynthesis and phenylpropanoid biosynthesis pathways played important roles in the adaptation of L. chinensis to the extreme winter environment, and flavone and flavonol biosynthesis was an important pathway involved in bud burst. In addition, temperature and photoperiod had synergistic influences on the formation and release of bud dormancy. Thus, our findings provided new insights into the mechanism of subalpine treeline formation.}, } @article {pmid38379958, year = {2024}, author = {Tran, T and Xie, S}, title = {Mitigating Wildlife Spillover in the Clinical Setting: How Physicians and Veterinarians Can Help Prevent Future Disease Outbreaks.}, journal = {AJPM focus}, volume = {3}, number = {2}, pages = {100193}, pmid = {38379958}, issn = {2773-0654}, abstract = {INTRODUCTION: The transmission of pathogens from wildlife to humans is a major global health threat that has been highlighted by the proposed origins of the COVID-19 pandemic. Numerous barriers impede pathogen spillover events from ensuing widespread human transmission, but human activity has accelerated the frequency of spillovers and subsequent disease outbreaks, in part through a booming wildlife trade whose impacts on health are not well understood.

METHODS: A literature review was conducted to examine the risk that the wildlife trade poses to public health and the degree to which these risks are recognized and addressed in clinical practice and medical and veterinary education.

RESULTS: The illicit aspects of the wildlife trade challenge efforts to understand its impacts on health. The U.S. and Europe play a leading role in the global wildlife trade that often goes unacknowledged. In particular, the consumption of wild meat and ownership of exotic pets poses public health risks. The potential role of clinicians is underutilized, both in the clinical setting and in clinical education.

DISCUSSION: Physicians and veterinarians have the unique opportunity to utilize their clinical roles to address these knowledge gaps and mitigate future outbreaks. We outline a multifaceted approach that includes increasing clinical knowledge about the ecology of zoonotic diseases, leveraging opportunities for mitigation during patient/client-clinician interactions, and incorporating One Health core competencies into medical and veterinary school curricula.}, } @article {pmid38379504, year = {2024}, author = {Castro-Alvarez, S and Sinharay, S and Bringmann, LF and Meijer, RR and Tendeiro, JN}, title = {Assessment of fit of the time-varying dynamic partial credit model using the posterior predictive model checking method.}, journal = {The British journal of mathematical and statistical psychology}, volume = {77}, number = {3}, pages = {532-552}, doi = {10.1111/bmsp.12339}, pmid = {38379504}, issn = {2044-8317}, mesh = {Humans ; *Psychometrics/methods/statistics & numerical data ; *Models, Statistical ; *Computer Simulation ; Longitudinal Studies ; Time Factors ; Bayes Theorem ; Data Interpretation, Statistical ; Regression Analysis ; }, abstract = {Several new models based on item response theory have recently been suggested to analyse intensive longitudinal data. One of these new models is the time-varying dynamic partial credit model (TV-DPCM; Castro-Alvarez et al., Multivariate Behavioral Research, 2023, 1), which is a combination of the partial credit model and the time-varying autoregressive model. The model allows the study of the psychometric properties of the items and the modelling of nonlinear trends at the latent state level. However, there is a severe lack of tools to assess the fit of the TV-DPCM. In this paper, we propose and develop several test statistics and discrepancy measures based on the posterior predictive model checking (PPMC) method (PPMC; Rubin, The Annals of Statistics, 1984, 12, 1151) to assess the fit of the TV-DPCM. Simulated and empirical data are used to study the performance of and illustrate the effectiveness of the PPMC method.}, } @article {pmid38376945, year = {2024}, author = {Townley, B and Akin, D and Dimaguila, GL and Sawires, R and Sepulveda Kattan, G and King, S and Bines, J and Wood, N and Lambert, S and Buttery, J}, title = {Exploring the Infectious Contribution to Intussusception Causality Using the Effects of COVID-19 Lockdowns in Australia: An Ecological Study.}, journal = {Clinical infectious diseases : an official publication of the Infectious Diseases Society of America}, volume = {79}, number = {1}, pages = {255-262}, doi = {10.1093/cid/ciae084}, pmid = {38376945}, issn = {1537-6591}, support = {//Murdoch Children's/ ; //Research Institute/ ; //Child Health Analytics and Informatics Research/ ; }, mesh = {Humans ; *COVID-19/epidemiology/prevention & control ; *Intussusception/epidemiology/etiology ; Infant ; Retrospective Studies ; Child, Preschool ; Child ; Male ; Female ; Australia/epidemiology ; Adolescent ; *SARS-CoV-2 ; Infant, Newborn ; Adult ; Hospitalization/statistics & numerical data ; Middle Aged ; Young Adult ; Aged ; New South Wales/epidemiology ; Queensland/epidemiology ; Victoria/epidemiology ; }, abstract = {BACKGROUND: Intussusception is the primary cause of acute bowel obstruction in infants. The majority of cases <2 years of age are classed as idiopathic, with viral infection implicated as one of the causes. Coronavirus disease 2019 (COVID-19) public health measures led to significant decreases in communicable disease prevalence. During these times, reductions in intussusception frequency were greater than would be expected with our previous understanding of its infectious etiology.

METHODS: We conducted a retrospective, multistate, ecological study over a 12-year period. Monthly case numbers of "intussusception"-coded admissions (code K56.1; International Classification of Diseases and Related Health Problems, Tenth Revision, Australian Modification) were acquired from state-wide admissions data sets from New South Wales, Victoria, and Queensland, representing 77.62% of the eligible Australian population. These counts within differing jurisdictional lockdowns were compared with non-lockdown periods in order to investigate a correlation between intussusception frequency and lockdown periods.

RESULTS: We found a negative association between intussusception frequency and lockdown periods in both eligible states. The largest reductions were seen in the <2-year age groups, with Victoria experiencing a 62.7% reduction (rate ratio, 0.37; P < .001) and New South Wales a 40.1% reduction (0.599; P = .006) during lockdown times. Controls for variations in lockdown restrictions between both regional and metropolitan areas also showed expected decreases.

CONCLUSIONS: Our ecological study demonstrates significant decreases in the frequency of pediatric intussusception admissions during the COVID-19 lockdown periods. The unexpected magnitude of the reductions suggests that the true proportion of infectious disease-caused idiopathic intussusception is greatly underestimated.}, } @article {pmid38376180, year = {2024}, author = {Schaan, AP and Vidal, A and Zhang, A-N and Poyet, M and Alm, EJ and Groussin, M and Ribeiro-Dos-Santos, Â}, title = {Temporal dynamics of gut microbiomes in non-industrialized urban Amazonia.}, journal = {mSystems}, volume = {9}, number = {3}, pages = {e0070723}, pmid = {38376180}, issn = {2379-5077}, support = {88882.160155/2017-01//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)/ ; 304413/2015-1//Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Brazil ; *Microbiota ; Bacteria ; Urbanization ; }, abstract = {Increasing levels of industrialization have been associated with changes in gut microbiome structure and loss of features thought to be crucial for maintaining gut ecological balance. The stability of gut microbial communities over time within individuals seems to be largely affected by these changes but has been overlooked among transitioning populations from low- to middle-income countries. Here, we used metagenomic sequencing to characterize the temporal dynamics in gut microbiomes of 24 individuals living an urban non-industrialized lifestyle in the Brazilian Amazon. We further contextualized our data with 165 matching longitudinal samples from an urban industrialized and a rural non-industrialized population. We show that gut microbiome composition and diversity have greater variability over time among non-industrialized individuals when compared to industrialized counterparts and that taxa may present diverse temporal dynamics across human populations. Enterotype classifications show that community types are generally stable over time despite shifts in microbiome structure. Furthermore, by tracking genomes over time, we show that levels of bacterial population replacements are more frequent among Amazonian individuals and that non-synonymous variants accumulate in genes associated with degradation of host dietary polysaccharides. Taken together, our results suggest that the stability of gut microbiomes is influenced by levels of industrialization and that tracking microbial population dynamics is important to understand how the microbiome will adapt to these transitions.IMPORTANCEThe transition from a rural or non-industrialized lifestyle to urbanization and industrialization has been linked to changes in the structure and function of the human gut microbiome. Understanding how the gut microbiomes changes over time is crucial to define healthy states and to grasp how the gut microbiome interacts with the host environment. Here, we investigate the temporal dynamics of gut microbiomes from an urban and non-industrialized population in the Amazon, as well as metagenomic data sets from urban United States and rural Tanzania. We showed that healthy non-industrialized microbiomes experience greater compositional shifts over time compared to industrialized individuals. Furthermore, bacterial strain populations are more frequently replaced in non-industrialized microbiomes, and most non-synonymous mutations accumulate in genes associated with the degradation of host dietary components. This indicates that microbiome stability is affected by transitions to industrialization, and that strain tracking can elucidate the ecological dynamics behind such transitions.}, } @article {pmid38376167, year = {2024}, author = {Hegarty, B and Riddell V, J and Bastien, E and Langenfeld, K and Lindback, M and Saini, JS and Wing, A and Zhang, J and Duhaime, M}, title = {Benchmarking informatics approaches for virus discovery: caution is needed when combining in silico identification methods.}, journal = {mSystems}, volume = {9}, number = {3}, pages = {e0110523}, pmid = {38376167}, issn = {2379-5077}, support = {DGE1256260, 2055455, DGE134012//National Science Foundation (NSF)/ ; NA17OAR4320152//DOC | National Oceanic and Atmospheric Administration (NOAA)/ ; Blue Sky Initiative//College of Engineering, University of Michigan/ ; }, mesh = {*Benchmarking ; Ecosystem ; *Viruses ; Metagenomics/methods ; Databases, Nucleic Acid ; }, abstract = {UNLABELLED: Understanding the ecological impacts of viruses on natural and engineered ecosystems relies on the accurate identification of viral sequences from community sequencing data. To maximize viral recovery from metagenomes, researchers frequently combine viral identification tools. However, the effectiveness of this strategy is unknown. Here, we benchmarked combinations of six widely used informatics tools for viral identification and analysis (VirSorter, VirSorter2, VIBRANT, DeepVirFinder, CheckV, and Kaiju), called "rulesets." Rulesets were tested against mock metagenomes composed of taxonomically diverse sequence types and diverse aquatic metagenomes to assess the effects of the degree of viral enrichment and habitat on tool performance. We found that six rulesets achieved equivalent accuracy [Matthews Correlation Coefficient (MCC) = 0.77, Padj ≥ 0.05]. Each contained VirSorter2, and five used our "tuning removal" rule designed to remove non-viral contamination. While DeepVirFinder, VIBRANT, and VirSorter were each found once in these high-accuracy rulesets, they were not found in combination with each other: combining tools does not lead to optimal performance. Our validation suggests that the MCC plateau at 0.77 is partly caused by inaccurate labeling within reference sequence databases. In aquatic metagenomes, our highest MCC ruleset identified more viral sequences in virus-enriched (44%-46%) than in cellular metagenomes (7%-19%). While improved algorithms may lead to more accurate viral identification tools, this should be done in tandem with careful curation of sequence databases. We recommend using the VirSorter2 ruleset and our empirically derived tuning removal rule. Our analysis provides insight into methods for in silico viral identification and will enable more robust viral identification from metagenomic data sets.

IMPORTANCE: The identification of viruses from environmental metagenomes using informatics tools has offered critical insights in microbial ecology. However, it remains difficult for researchers to know which tools optimize viral recovery for their specific study. In an attempt to recover more viruses, studies are increasingly combining the outputs from multiple tools without validating this approach. After benchmarking combinations of six viral identification tools against mock metagenomes and environmental samples, we found that these tools should only be combined cautiously. Two to four tool combinations maximized viral recovery and minimized non-viral contamination compared with either the single-tool or the five- to six-tool ones. By providing a rigorous overview of the behavior of in silico viral identification strategies and a pipeline to replicate our process, our findings guide the use of existing viral identification tools and offer a blueprint for feature engineering of new tools that will lead to higher-confidence viral discovery in microbiome studies.}, } @article {pmid38371853, year = {2024}, author = {Meyer, F and Sandbakk, Ø and Millet, GP}, title = {Editorial: Sport performance analysis: from the laboratory to the field.}, journal = {Frontiers in sports and active living}, volume = {6}, number = {}, pages = {1372080}, pmid = {38371853}, issn = {2624-9367}, } @article {pmid38368650, year = {2024}, author = {Shchepin, ON and López Villalba, Á and Inoue, M and Prikhodko, IS and Erastova, DA and Okun, MV and Woyzichovski, J and Yajima, Y and Gmoshinskiy, VI and Moreno, G and Novozhilov, YK and Schnittler, M}, title = {DNA barcodes reliably differentiate between nivicolous species of Diderma (Myxomycetes, Amoebozoa) and reveal regional differences within Eurasia.}, journal = {Protist}, volume = {175}, number = {2}, pages = {126023}, doi = {10.1016/j.protis.2024.126023}, pmid = {38368650}, issn = {1618-0941}, mesh = {*Myxomycetes ; DNA Barcoding, Taxonomic/methods ; Bayes Theorem ; Phylogeny ; DNA, Ribosomal/genetics ; }, abstract = {The nivicolous species of the genus Diderma are challenging to identify, and there are several competing views on their delimitation. We analyzed 102 accessions of nivicolous Diderma spp. that were sequenced for two or three unlinked genes to determine which of the current taxonomic treatments is better supported by molecular species delimitation methods. The results of a haplotype web analysis, Bayesian species delimitation under a multispecies coalescent model, and phylogenetic analyses on concatenated alignments support a splitting approach that distinguishes six taxa: Diderma alpinum, D. europaeum, D. kamchaticum, D. meyerae, D. microcarpum and D. niveum. The first two approaches also support the separation of Diderma alpinum into two species with allopatric distribution. An extended dataset of 800 specimens (mainly from Europe) that were barcoded with 18S rDNA revealed only barcode variants similar to those in the species characterized by the first data set, and showed an uneven distribution of these species in the Northern Hemisphere: Diderma microcarpum and D. alpinum were the only species found in all seven intensively sampled mountain regions. Partial 18S rDNA sequences serving as DNA barcodes provided clear signatures that allowed for unambiguous identification of the nivicolous Diderma spp., including two putative species in D. alpinum.}, } @article {pmid38366261, year = {2024}, author = {Jensen, PM and Danielsen, F and Jacobsen, SK and Vikstrøm, T}, title = {Fair concordance between Google Trends and Danish ornithologists in the assessment of temporal trends in Danish bird populations highlights the informational value of big data.}, journal = {Environmental monitoring and assessment}, volume = {196}, number = {3}, pages = {276}, pmid = {38366261}, issn = {1573-2959}, support = {869673//CAPARDUS/ ; 862731//FRAMEwork/ ; 101058509//ECS/ ; 101096887//BestLife2030/ ; 5228-00001B//UArctic/ ; }, mesh = {Animals ; Humans ; *Ecosystem ; *Search Engine ; Big Data ; Environmental Monitoring ; Birds ; Denmark ; }, abstract = {The ongoing depletion of natural systems and associated biodiversity decline is of growing international concern. Climate change is expected to exacerbate anthropogenic impacts on wild populations. The scale of impact on ecosystems and ecosystem services will be determined by the impact on a multitude of species and functional groups, which due to their biology and numbers are difficult to monitor. The IPCC has argued that surveillance or monitoring is critical and proposed that monitoring systems should be developed, which not only track developments but also function as "early warning systems." Human populations are already generating large continuous datasets on multiple taxonomic groups through internet searches. These time series could in principle add substantially to current monitoring if they reflect true changes in the natural world. We here examined whether information on internet search frequencies delivered by the Danish population and captured by Google Trends (GT) appropriately informs on population trends in 106 common Danish bird species. We compared the internet search activity with independent equivalent population trend assessments from the Danish Ornithological Society (BirdLife Denmark/DOF). We find a fair concordance between the GT trends and the assessments by DOF. A substantial agreement can be obtained by omitting species without clear temporal trends. Our findings suggest that population trend proxies from internet search frequencies can be used to supplement existing wildlife population monitoring and to ask questions about an array of ecological phenomena, which potentially can be integrated into an early warning system for biodiversity under climate change.}, } @article {pmid38365244, year = {2024}, author = {Yu, XA and McLean, C and Hehemann, JH and Angeles-Albores, D and Wu, F and Muszyński, A and Corzett, CH and Azadi, P and Kujawinski, EB and Alm, EJ and Polz, MF}, title = {Low-level resource partitioning supports coexistence among functionally redundant bacteria during successional dynamics.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {38365244}, issn = {1751-7370}, support = {DE-SC0008743//United States Department of Energy/ ; DE-SC0015662//United States Department of Energy/ ; }, mesh = {Bacteria/genetics ; *Seaweed ; *Microbiota ; }, abstract = {Members of microbial communities can substantially overlap in substrate use. However, what enables functionally redundant microorganisms to coassemble or even stably coexist remains poorly understood. Here, we show that during unstable successional dynamics on complex, natural organic matter, functionally redundant bacteria can coexist by partitioning low-concentration substrates even though they compete for one simple, dominant substrate. We allowed ocean microbial communities to self-assemble on leachates of the brown seaweed Fucus vesiculosus and then analyzed the competition among 10 taxonomically diverse isolates representing two distinct stages of the succession. All, but two isolates, exhibited an average of 90% ± 6% pairwise overlap in resource use, and functional redundancy of isolates from the same assembly stage was higher than that from between assembly stages, leading us to construct a simpler four-isolate community with two isolates from each of the early and late stages. We found that, although the short-term dynamics of the four-isolate communities in F. vesiculosus leachate was dependent on initial isolate ratios, in the long term, the four isolates stably coexist in F. vesiculosus leachate, albeit with some strains at low abundance. We therefore explored the potential for nonredundant substrate use by genomic content analysis and RNA expression patterns. This analysis revealed that the four isolates mainly differed in peripheral metabolic pathways, such as the ability to degrade pyrimidine, leucine, and tyrosine, as well as aromatic substrates. These results highlight the importance of fine-scale differences in metabolic strategies for supporting the frequently observed coexistence of large numbers of rare organisms in natural microbiomes.}, } @article {pmid38365075, year = {2024}, author = {Lyu, Y and Gao, Y and Pang, X and Sun, S and Luo, P and Cai, D and Qin, K and Wu, Z and Wang, B}, title = {Elucidating contributions of volatile organic compounds to ozone formation using random forest during COVID-19 pandemic: A case study in China.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {346}, number = {}, pages = {123532}, doi = {10.1016/j.envpol.2024.123532}, pmid = {38365075}, issn = {1873-6424}, mesh = {Humans ; *Air Pollutants/analysis ; *Volatile Organic Compounds/analysis ; Pandemics ; *Ozone/analysis ; Random Forest ; Nitrogen Dioxide ; *COVID-19 ; Toluene ; Alkenes ; China ; Environmental Monitoring ; *Xylenes ; }, abstract = {Ozone has been reported to increase despite nitrogen oxides reductions during the COVID-19 pandemic, and ozone formation needs to be revisited using volatile organic compounds (VOCs), which are rarely measured during the pandemic. Here, a total of 98 VOCs species were monitored in an economy-active city in China from January 2021 to August 2022 to assess contributions to ozone formation during the pandemic. Total VOCs concentrations were 35.55 ± 21.47 ppb during the entire period, among which alkanes account for the largest fraction (13.78 ppb, 38.0%), followed by aromatics (6.16 ppb, 16.8%) and oxygenated VOCs (OVOCs, 5.69 ppb, 15.7%). Most VOCs groups (e.g., alkenes, OVOCs) and individual species (e.g., isoprene, methyl vinyl ketone) display obvious seasonal and diurnal variations, which are related to their sources and reactivities. No weekend effects of VOCs suggest limited influences from traffic emissions during pandemic. Aromatics and alkenes are the major contributors (39% and 33%) to ozone formation potential, largely driven by o/m/p-xylene (21%), ethylene (15%), toluene (9%). Secondary organic aerosol formation potential is dominated by toluene (>50%) despite its low proportion (5%). Further inclusion of VOCs and meteorology in the Random Forest model shows good ozone prediction performance (R[2] = 0.77-0.86, RMSE = 11.95-19.91 μg/m[3], MAE = 8.89-14.58 μg/m[3]). VOCs and NO2 contribute >50% of total importance with the largest difference in importance ratio of VOCs/NO2 in the summer and winter, implying ozone formation regime may vary. No seasonal variations in importance of meteorology are observed, while importance of other variables (e.g., PM2.5) is highest in the summer. This work identifies critical VOCs groups and species for ozone formation during the pandemic, and demonstrates the feasibility of machine learning algorithms in elucidation of ozone formation mechanisms.}, } @article {pmid38360168, year = {2024}, author = {Ko, CY and Lee, YC and Wang, YC and Hsu, HH and Chow, CH and Chen, RG and Liu, TH and Chen, CS and Chiu, TS and Chiang, DH and Wu, RF and Tseng, WL}, title = {Modulations of ocean-atmosphere interactions on squid abundance over Southwest Atlantic.}, journal = {Environmental research}, volume = {250}, number = {}, pages = {118444}, doi = {10.1016/j.envres.2024.118444}, pmid = {38360168}, issn = {1096-0953}, mesh = {*Decapodiformes/physiology ; Animals ; Atlantic Ocean ; *Atmosphere ; Temperature ; Seasons ; Climate Change ; }, abstract = {Anthropogenic shifts in seas are reshaping fishing trends, with significant implications for aquatic food sources throughout this century. Examining a 21-year abundance dataset of Argentine shortfin squids Illex argentinus paired with a regional oceanic analysis, we noted strong correlations between squid annual abundance and sea surface temperature (SST) in January and February and eddy kinetic energy (EKE) from March to May in the Southwest Atlantic. A deeper analysis revealed combined ocean-atmosphere interactions, pinpointed as the primary mode in a rotated empirical orthogonal function analysis of SST. This pattern produced colder SST and amplified EKE in the surrounding seas, factors crucial for the unique life stages of squids. Future projections from the CMIP6 archive indicated that this ocean-atmosphere pattern, referred to as the Atlantic symmetric pattern, would persist in its cold SST phase, promoting increased squid abundance. However, rising SSTs due to global warming might counteract the abundance gains. Our findings uncover a previously unrecognized link between squids and specific environmental conditions governed by broader ocean-atmosphere interactions in the Southwest Atlantic. Integrating these insights with seasonal and decadal projections can offer invaluable information to stakeholders in squid fisheries and marine conservation under a changing climate.}, } @article {pmid38358627, year = {2024}, author = {Akar, AU and Sisman, S and Ulku, H and Yel, E and Yalpir, S}, title = {Evaluating lake water quality with a GIS-based MCDA integrated approach: a case in Konya/Karapınar.}, journal = {Environmental science and pollution research international}, volume = {31}, number = {13}, pages = {19478-19499}, pmid = {38358627}, issn = {1614-7499}, mesh = {Humans ; *Water Quality ; *Geographic Information Systems ; Lakes ; Environmental Monitoring/methods ; Decision Support Techniques ; }, abstract = {Considering water quality is an essential requirement in terms of environmental planning and management. To protect and manage water resources effectively, it is necessary to develop an analytical decision-support system. In this study, a systematic approach was suggested to evaluate the lake water quality. The methodology includes the prediction of the values in different locations of the lakes from experimental data through inverse distance weighting (IDW) method, creation of maps by using Geographic Information System (GIS) integrated with analytic hierarchy process (AHP) from multi-criteria decision analysis (MCDA), reclassification into five class, combining the time-related spatial data into a single map to predict the whole lake water quality from the data of sampling points, and finally overlapping the final maps with topography/geology and land use. The proposed approach was verified and presented as case study for Meke and Acigol Lakes in Konya/Turkey which were affected by human and natural factors although they have ecological, hydromorphological, and socio-economic importance. In the proposed approach, categorizing water quality parameters as "hardness and minerals," "substrates and nutrients," "solids content," "metals," and "oil-grease" groups was helpful for AHP with the determined group weights of 0.484, 0.310, 0.029, and 0.046, respectively. Assigning weights within each group and then assigning weights between groups resulted in creating accurate final map. The proposed approach is flexible and applicable to any lake water quality data; even with a limited number of data, the whole lake water quality maps could be created for assessment.}, } @article {pmid38358505, year = {2024}, author = {Zhang, J and Wu, Z and Dong, B and Ge, S and He, S}, title = {Effective degradation of quinoline by catalytic ozonation with MnCexOy catalysts: performance and mechanism.}, journal = {Water science and technology : a journal of the International Association on Water Pollution Research}, volume = {89}, number = {3}, pages = {823-837}, doi = {10.2166/wst.2024.027}, pmid = {38358505}, issn = {0273-1223}, mesh = {Humans ; Manganese Compounds ; Oxides ; Catalysis ; *Quinolines ; *Cocaine ; *Coke ; Oxygen ; *Ozone ; }, abstract = {Quinoline inevitably remains in the effluent of coking wastewater treatment plants due to its bio-refractory nature, which might cause unfavorable effects on human and ecological environments. In this study, MnCexOy was consciously synthesized by α-MnO2 doped with Ce[3+] (Ce:Mn = 1:10) and employed as the ozonation catalyst for quinoline degradation. After that, the removal efficiency and mechanism of quinoline were systematically analyzed by characterizing the physicochemical properties of MnCexOy, investigating free radicals and monitoring the solution pH. Results indicated that the removal rate of quinoline was greatly improved by the prepared MnCexOy catalyst. Specifically, the removal efficiencies of quinoline could be 93.73, 62.57 and 43.76%, corresponding to MnCexOy, α-MnO2 and single ozonation systems, respectively. The radical scavenging tests demonstrated that [•]OH and [•]O2[-] were the dominant reactive oxygen species in the MnCexOy ozonation system. Meanwhile, the contribution levels of [•]OH and [•]O2[-] to quinoline degradation were about 42 and 35%, respectively. The abundant surface hydroxyl groups and oxygen vacancies of the MnCexOy catalyst were two important factors for decomposing molecular O3 into more [•]OH and [•]O2[-]. This study could provide scientific support for the application of the MnCexOy/O3 system in degrading quinoline in bio-treated coking wastewater.}, } @article {pmid38357349, year = {2024}, author = {Moore, LR and Caspi, R and Campbell, DA and Casey, JR and Crevecoeur, S and Lea-Smith, DJ and Long, B and Omar, NM and Paley, SM and Schmelling, NM and Torrado, A and Zehr, JP and Karp, PD}, title = {CyanoCyc cyanobacterial web portal.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1340413}, pmid = {38357349}, issn = {1664-302X}, abstract = {CyanoCyc is a web portal that integrates an exceptionally rich database collection of information about cyanobacterial genomes with an extensive suite of bioinformatics tools. It was developed to address the needs of the cyanobacterial research and biotechnology communities. The 277 annotated cyanobacterial genomes currently in CyanoCyc are supplemented with computational inferences including predicted metabolic pathways, operons, protein complexes, and orthologs; and with data imported from external databases, such as protein features and Gene Ontology (GO) terms imported from UniProt. Five of the genome databases have undergone manual curation with input from more than a dozen cyanobacteria experts to correct errors and integrate information from more than 1,765 published articles. CyanoCyc has bioinformatics tools that encompass genome, metabolic pathway and regulatory informatics; omics data analysis; and comparative analyses, including visualizations of multiple genomes aligned at orthologous genes, and comparisons of metabolic networks for multiple organisms. CyanoCyc is a high-quality, reliable knowledgebase that accelerates scientists' work by enabling users to quickly find accurate information using its powerful set of search tools, to understand gene function through expert mini-reviews with citations, to acquire information quickly using its interactive visualization tools, and to inform better decision-making for fundamental and applied research.}, } @article {pmid38356288, year = {2024}, author = {Speyer, LG and Murray, AL and Kievit, R}, title = {Investigating Moderation Effects at the Within-Person Level Using Intensive Longitudinal Data: A Two-Level Dynamic Structural Equation Modelling Approach in Mplus.}, journal = {Multivariate behavioral research}, volume = {59}, number = {3}, pages = {620-637}, doi = {10.1080/00273171.2023.2288575}, pmid = {38356288}, issn = {1532-7906}, mesh = {Humans ; Longitudinal Studies ; *Latent Class Analysis ; Depression/psychology ; Social Media/statistics & numerical data ; Software ; Loneliness/psychology ; Models, Statistical ; Female ; Male ; Data Interpretation, Statistical ; }, abstract = {Recent technological advances have provided new opportunities for the collection of intensive longitudinal data. Using methods such as dynamic structural equation modeling, these data can provide new insights into moment-to-moment dynamics of psychological and behavioral processes. In intensive longitudinal data (t > 20), researchers often have theories that imply that factors that change from moment to moment within individuals act as moderators. For instance, a person's level of sleep deprivation may affect how much an external stressor affects mood. Here, we describe how researchers can implement, test, and interpret dynamically changing within-person moderation effects using two-level dynamic structural equation modeling as implemented in the structural equation modeling software Mplus. We illustrate the analysis of within-person moderation effects using an empirical example investigating whether changes in spending time online using social media affect the moment-to-moment effect of loneliness on depressive symptoms, and highlight avenues for future methodological development. We provide annotated Mplus code, enabling researchers to better isolate, estimate, and interpret the complexities of within-person interaction effects.}, } @article {pmid38355478, year = {2024}, author = {Zhang, M and Qiao, L and Sun, P and Jiang, H and Shi, Y and Zhang, W and Mei, Y and Yu, M and Wang, H}, title = {Spatiotemporal pattern of leprosy in southwest China from 2010 to 2020: an ecological study.}, journal = {BMC public health}, volume = {24}, number = {1}, pages = {465}, pmid = {38355478}, issn = {1471-2458}, support = {2019YFE0113300//The National Key R&D Program of China/ ; 81972950, 82173431, 82103748//National Natural Science Foundation of China/ ; ZDXYS202204//Jiangsu Provincial Medical Key Laboratory, Jiangsu Province Capability Improvement Project through Science, Technology and Education/ ; 2019060001//The Nanjing Incubation Program for National Clinical Research Center/ ; 2022-I2M-C&T-B-094//Chinese Academy of Medical Sciences Innovation Fund for Medical Science/ ; }, mesh = {Humans ; China/epidemiology ; *Leprosy/epidemiology ; Spatial Analysis ; Cluster Analysis ; Databases, Factual ; Spatio-Temporal Analysis ; }, abstract = {BACKGROUND: Despite many efforts to control leprosy worldwide, it is still a significant public health problem in low- and middle-income regions. It has been endemic in China for thousands of years, and southwest China has the highest leprosy burden in the country.

METHODS: This observational study was conducted with all newly detected leprosy cases in southwest China from 2010 to 2020. Data were extracted from the Leprosy Management Information System (LEPMIS) database in China. The Joinpoint model was used to determine the time trends in the study area. Spatial autocorrelation statistics was performed to understand spatial distribution of leprosy cases. Spatial scan statistics was applied to identify significant clusters with high rate.

RESULTS: A total of 4801 newly detected leprosy cases were reported in southwest China over 11 years. The temporal trends declined stably. The new case detection rate (NCDR) dropped from 4.38/1,000,000 population in 2010 to 1.25/1,000,000 population in 2020, with an average decrease of 12.24% (95% CI: -14.0 to - 10.5; P < 0.001). Results of global spatial autocorrelation showed that leprosy cases presented clustering distribution in the study area. Most likely clusters were identified during the study period and were frequently located at Yunnan or the border areas between Yunnan and Guizhou Provinces. Secondary clusters were always located in the western counties, the border areas between Yunnan and Sichuan Provinces.

CONCLUSIONS: Geographic regions characterized by clusters with high rates were considered as leprosy high-risk areas. The findings of this study could be used to design leprosy control measures and provide indications to strengthen the surveillance of high-risk areas. These areas should be prioritized in the allocation of resources.}, } @article {pmid38355366, year = {2024}, author = {Jones, CB and Stock, K and Perkins, SE}, title = {AI-based discovery of habitats from museum collections.}, journal = {Trends in ecology & evolution}, volume = {39}, number = {4}, pages = {323-327}, doi = {10.1016/j.tree.2024.01.006}, pmid = {38355366}, issn = {1872-8383}, mesh = {*Museums ; *Artificial Intelligence ; Ecosystem ; Biological Evolution ; }, abstract = {Museum collection records are a source of historic data for species occurrence, but little attention is paid to the associated descriptions of habitat at the sample locations. We propose that artificial intelligence methods have potential to use these descriptions for reconstructing past habitat, to address ecological and evolutionary questions.}, } @article {pmid38353941, year = {2024}, author = {Iyamu, I and McKee, G and Haag, D and Gilbert, M}, title = {Defining the role of digital public health in the evolving digital health landscape: policy and practice implications in Canada.}, journal = {Health promotion and chronic disease prevention in Canada : research, policy and practice}, volume = {44}, number = {2}, pages = {66-69}, pmid = {38353941}, issn = {2368-738X}, mesh = {Humans ; *Digital Health ; *Public Health ; Canada ; Policy ; }, } @article {pmid38350096, year = {2024}, author = {Krys, K and Kostoula, O and van Tilburg, WAP and Mosca, O and Lee, JH and Maricchiolo, F and Kosiarczyk, A and Kocimska-Bortnowska, A and Torres, C and Hitokoto, H and Liew, K and Bond, MH and Lun, VM and Vignoles, VL and Zelenski, JM and Haas, BW and Park, J and Vauclair, CM and Kwiatkowska, A and Roczniewska, M and Witoszek, N and Işık, İ and Kosakowska-Berezecka, N and Domínguez-Espinosa, A and Yeung, JC and Górski, M and Adamovic, M and Albert, I and Pavlopoulos, V and Fülöp, M and Sirlopu, D and Okvitawanli, A and Boer, D and Teyssier, J and Malyonova, A and Gavreliuc, A and Serdarevich, U and Akotia, CS and Appoh, L and Mira, DMA and Baltin, A and Denoux, P and Esteves, CS and Gamsakhurdia, V and Garðarsdóttir, RB and Igbokwe, DO and Igou, ER and Kascakova, N and Klůzová Kracˇmárová, L and Kronberger, N and Barrientos, PE and Mohoricć, T and Murdock, E and Mustaffa, NF and Nader, M and Nadi, A and van Osch, Y and Pavlović, Z and Polácˇková Šolcová, I and Rizwan, M and Romashov, V and Røysamb, E and Sargautyte, R and Schwarz, B and Selecká, L and Selim, HA and Stogianni, M and Sun, CR and Wojtczuk-Turek, A and Xing, C and Uchida, Y}, title = {Happiness Maximization Is a WEIRD Way of Living.}, journal = {Perspectives on psychological science : a journal of the Association for Psychological Science}, volume = {}, number = {}, pages = {17456916231208367}, doi = {10.1177/17456916231208367}, pmid = {38350096}, issn = {1745-6924}, abstract = {Psychological science tends to treat subjective well-being and happiness synonymously. We start from the assumption that subjective well-being is more than being happy to ask the fundamental question: What is the ideal level of happiness? From a cross-cultural perspective, we propose that the idealization of attaining maximum levels of happiness may be especially characteristic of Western, educated, industrial, rich, and democratic (WEIRD) societies but less so for others. Searching for an explanation for why "happiness maximization" might have emerged in these societies, we turn to studies linking cultures to their eco-environmental habitat. We discuss the premise that WEIRD cultures emerged in an exceptionally benign ecological habitat (i.e., faced relatively light existential pressures compared with other regions). We review the influence of the Gulf Stream on the Northwestern European climate as a source of these comparatively benign geographical conditions. We propose that the ecological conditions in which WEIRD societies emerged afforded them a basis to endorse happiness as a value and to idealize attaining its maximum level. To provide a nomological network for happiness maximization, we also studied some of its potential side effects, namely alcohol and drug consumption and abuse and the prevalence of mania. To evaluate our hypothesis, we reanalyze data from two large-scale studies on ideal levels of personal life satisfaction-the most common operationalization of happiness in psychology-involving respondents from 61 countries. We conclude that societies whose members seek to maximize happiness tend to be characterized as WEIRD, and generalizing this across societies can prove problematic if adopted at the ideological and policy level.}, } @article {pmid38344693, year = {2023}, author = {Boyes, D and Gibbs, M and , and , and , and , and , and , }, title = {The genome sequence of the Variegated Golden Tortrix, Archips xylosteana (Linnaeus, 1758).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {538}, pmid = {38344693}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual female Archips xylosteana (the Variegated Golden Tortrix; Arthropoda; Insecta; Lepidoptera; Tortricidae). The genome sequence is 650.6 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the W and Z sex chromosomes. The mitochondrial genome has also been assembled and is 16.39 kilobases in length. Gene annotation of this assembly on Ensembl identified 19,861 protein coding genes.}, } @article {pmid38343945, year = {2024}, author = {Kwon, H and Jin, BR and Kim, HJ and Kwon, J and Park, K and Kim, C and Kim, JG and Hwang, BY and Kwon, SL and Kim, JJ and Shim, SH and Guo, Y and An, HJ and Lee, D}, title = {New Pimarane Diterpenoids Isolated from EtOAc-Extract of Apiospora arundinis Culture Medium Show Antibenign Prostatic Hyperplasia Potential.}, journal = {ACS omega}, volume = {9}, number = {5}, pages = {5616-5623}, pmid = {38343945}, issn = {2470-1343}, abstract = {Three new pimarane diterpenoids, libertellenones U-W (1-3), together with libertellenone C (4) and myrocin A (5) were isolated from an EtOAc-extract of Apiospora arundinis culture medium. The chemical structures of the new compounds were elucidated using MS, NMR, and CD spectroscopic data. Benign prostatic hyperplasia (BPH), the abnormal and pathological proliferation of epithelial and stromal cells in prostatic tissues, is a common disease in middle-aged and elderly men. In this study, the anti-BPH effects of myrocin A (5) were evaluated using BPH-1 and WPMY-1 cells. Treatment with myrocin A (5) exerted antiproliferative effects in BPH-1 and dihydrotestosterone (DHT)-stimulated WPMY-1 cells. In BPH, treatment with myrocin A (5) significantly suppressed the mRNA levels of androgen receptor (AR) and its downstream targets nuclear receptor coactivator 1 (NCOA1), proliferating cell nuclear antigen (PCNA) and kallikrein-related peptidase 3 (KLK3). Additionally, DHT-stimulated WPMY-1 cells demonstrated an upregulated mRNA levels of AR, NCOA1, PCNA, and KLK3. However, treatment with myrocin A (5) resulted in suppression of the mRNA levels. Moreover, myrocin A (5) docked computationally into the binding site of the androgen receptor (-5.5 kcal/mol).}, } @article {pmid38342840, year = {2024}, author = {Xiao, Y and Luan, H and Lu, S and Xing, M and Guo, C and Qian, R and Xiao, X}, title = {Toxic effects of atmospheric deposition in mining areas on wheat seedlings.}, journal = {Environmental geochemistry and health}, volume = {46}, number = {2}, pages = {69}, pmid = {38342840}, issn = {1573-2983}, support = {52130402//the Key Program of the National Natural Science Foundation of China/ ; DYGX-2023-035//2023 China University of Mining and Technology Large Instrument and Equipment Open Sharing Fund Project/ ; }, mesh = {Triticum ; Seedlings ; Soil ; Cadmium ; Lead ; *Soil Pollutants/toxicity/analysis ; *Metals, Heavy/analysis ; Coal ; Environmental Monitoring/methods ; China ; Risk Assessment ; }, abstract = {Storage and transportation of coal, as well as operation of coal-fired power plants, produce amounts of metallic exhaust that may lead to different atmospheric environment in the overlapped areas of farmland and coal resource (OAFCR) environment. To investigate the effects of different atmospheric environment in the OAFCR region (north of Xuzhou) on wheat seedlings (AK-58), a box experiment was conducted and compared to an area far from the OAFCR (south of Xuzhou). The study revealed that (1) compared to the southern suburb of Xuzhou, the fresh and dry weight, activities of photosynthetic enzymes and POD of wheat seedlings in the OAFCR reduced obviously. (2) Significantly higher levels of Cr, Cd, Pb, Zn, and Cu were found in the shoots and roots of wheat seedlings in the OAFCR, with lower transfer factor for heavy metals (except Cd and As) in comparison to those in the southern suburb. And the bioconcentration factors of heavy metals (except As) in wheat seedlings in the OAFCR were significantly higher. (3) Nearly 90% of heavy metals (Pb, Cu, Cd, Zn, and Cr) absorbed by wheat were stored in cell walls and soluble fractions, with significantly higher contents of Cu and Cr in wheat seedlings' cell walls and higher contents of Pb, Zn, and Cd in soluble components found in the OAFCR. Our results showed that atmospheric deposition in the mining area has a certain toxic effect on wheat seedlings, and this study provides a theoretical basis for OAFCR crop toxicity management.}, } @article {pmid38342219, year = {2024}, author = {Lausch, A and Selsam, P and Pause, M and Bumberger, J}, title = {Monitoring vegetation- and geodiversity with remote sensing and traits.}, journal = {Philosophical transactions. Series A, Mathematical, physical, and engineering sciences}, volume = {382}, number = {2269}, pages = {20230058}, pmid = {38342219}, issn = {1471-2962}, mesh = {*Ecosystem ; *Remote Sensing Technology ; Phylogeny ; Biodiversity ; Phenotype ; }, abstract = {Geodiversity has shaped and structured the Earth's surface at all spatio-temporal scales, not only through long-term processes but also through medium- and short-term processes. Geodiversity is, therefore, a key control and regulating variable in the overall development of landscapes and biodiversity. However, climate change and land use intensity are leading to major changes and disturbances in bio- and geodiversity. For sustainable ecosystem management, temporal, economically viable and standardized monitoring is needed to monitor and model the effects and changes in vegetation- and geodiversity. RS approaches have been used for this purpose for decades. However, to understand in detail how RS approaches capture vegetation- and geodiversity, the aim of this paper is to describe how five features of vegetation- and geodiversity are captured using RS technologies, namely: (i) trait diversity, (ii) phylogenetic/genese diversity, (iii) structural diversity, (iv) taxonomic diversity and (v) functional diversity. Trait diversity is essential for establishing the other four. Traits provide a crucial interface between in situ, close-range, aerial and space-based RS monitoring approaches. The trait approach allows complex data of different types and formats to be linked using the latest semantic data integration techniques, which will enable ecosystem integrity monitoring and modelling in the future. This article is part of the Theo Murphy meeting issue 'Geodiversity for science and society'.}, } @article {pmid38339498, year = {2024}, author = {Li, J and Xing, Q and Li, X and Arif, M and Li, J}, title = {Monitoring Off-Shore Fishing in the Northern Indian Ocean Based on Satellite Automatic Identification System and Remote Sensing Data.}, journal = {Sensors (Basel, Switzerland)}, volume = {24}, number = {3}, pages = {}, pmid = {38339498}, issn = {1424-8220}, support = {CAS-WX2021SF-0408//Informatization Plan of Chinese Academy of Sciences/ ; XDA19060501//International Partnership Program of Chinese Academy of Sciences, the Strategic Priority Research Program of the Chinese Academy of Sciences (Class A)/ ; }, abstract = {Satellite-derived Sea Surface Temperature (SST) and sea-surface Chlorophyll a concentration (Chl-a), along with Automatic Identification System (AIS) data of fishing vessels, were used in the examination of the correlation between fishing operations and oceanographic factors within the northern Indian Ocean from March 2020 to February 2023. Frequency analysis and the empirical cumulative distribution function (ECDF) were used to calculate the optimum ranges of two oceanographic factors for fishing operations. The results revealed a substantial influence of the northeast and southwest monsoons significantly impacting fishing operations in the northern Indian Ocean, with extensive and active operations during the period from October to March and a notable reduction from April to September. Spatially, fishing vessels were mainly concentrated between 20° N and 6° S, extending from west of 90° E to the eastern coast of Africa. Observable seasonal variations in the distribution of fishing vessels were observed in the central and southeastern Arabian Sea, along with its adjacent high sea of the Indian Ocean. Concerning the marine environment, it was observed that during the northeast monsoon, the suitable SST contributed to high CPUEs in fishing operation areas. Fishing vessels were widely distributed in the areas with both mid-range and low-range Chl-a concentrations, with a small part distributed in high-concentration areas. Moreover, the monthly numbers of fishing vessels showed seasonal fluctuations between March 2020 and February 2023, displaying a periodic pattern with an overall increasing trend. The total number of fishing vessels decreased due to the impact of the COVID-19 pandemic in 2020, but this was followed by a gradual recovery in the subsequent two years. For fishing operations in the northern Indian Ocean, the optimum ranges for SST and Chl-a concentration were 27.96 to 29.47 °C and 0.03 to 1.81 mg/m[3], respectively. The preliminary findings of this study revealed the spatial-temporal distribution characteristics of fishing vessels in the northern Indian Ocean and the suitable ranges of SST and Chl-a concentration for fishing operations. These results can serve as theoretical references for the production and resource management of off-shore fishing operations in the northern Indian Ocean.}, } @article {pmid38337048, year = {2024}, author = {Trepel, J and le Roux, E and Abraham, AJ and Buitenwerf, R and Kamp, J and Kristensen, JA and Tietje, M and Lundgren, EJ and Svenning, JC}, title = {Meta-analysis shows that wild large herbivores shape ecosystem properties and promote spatial heterogeneity.}, journal = {Nature ecology & evolution}, volume = {8}, number = {4}, pages = {705-716}, pmid = {38337048}, issn = {2397-334X}, support = {1131-00006B//Det Frie Forskningsråd (Danish Council for Independent Research)/ ; 0135-00225B//Det Frie Forskningsråd (Danish Council for Independent Research)/ ; 101062339//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; CF20-0238//Carlsbergfondet (Carlsberg Foundation)/ ; DNRF173//Danmarks Grundforskningsfond (Danish National Research Foundation)/ ; 16549//Villum Fonden (Villum Foundation)/ ; }, mesh = {Animals ; *Ecosystem ; *Herbivory ; Biodiversity ; Soil ; Biological Evolution ; }, abstract = {Megafauna (animals ≥45 kg) have probably shaped the Earth's terrestrial ecosystems for millions of years with pronounced impacts on biogeochemistry, vegetation, ecological communities and evolutionary processes. However, a quantitative global synthesis on the generality of megafauna effects on ecosystems is lacking. Here we conducted a meta-analysis of 297 studies and 5,990 individual observations across six continents to determine how wild herbivorous megafauna influence ecosystem structure, ecological processes and spatial heterogeneity, and whether these impacts depend on body size and environmental factors. Despite large variability in megafauna effects, we show that megafauna significantly alter soil nutrient availability, promote open vegetation structure and reduce the abundance of smaller animals. Other responses (14 out of 26), including, for example, soil carbon, were not significantly affected. Further, megafauna significantly increase ecosystem heterogeneity by affecting spatial heterogeneity in vegetation structure and the abundance and diversity of smaller animals. Given that spatial heterogeneity is considered an important driver of biodiversity across taxonomic groups and scales, these results support the hypothesis that megafauna may promote biodiversity at large scales. Megafauna declined precipitously in diversity and abundance since the late Pleistocene, and our results indicate that their restoration would substantially influence Earth's terrestrial ecosystems.}, } @article {pmid38333733, year = {2023}, author = {Boyes, D and Boyes, C and , and , and , and , and , and , }, title = {The genome sequence of the Ingrailed Clay, Diarsia mendica (Fabricius, 1775).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {448}, pmid = {38333733}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual male Diarsia mendica (the Ingrailed Clay; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 727.9 megabases in span. Most of the assembly is scaffolded into 32 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.37 kilobases in length. Gene annotation of this assembly on Ensembl identified 14,077 protein coding genes.}, } @article {pmid38332565, year = {2024}, author = {Hou, Z and Qiang, W and Wang, X and Chen, X and Hu, X and Han, X and Shen, W and Zhang, B and Xing, P and Shi, W and Dai, J and Huang, X and Zhao, G}, title = {"Cell Disk" DNA Storage System Capable of Random Reading and Rewriting.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {11}, number = {15}, pages = {e2305921}, pmid = {38332565}, issn = {2198-3844}, support = {2021YFF1201700//National Key Research and Development Program of China/ ; 2018YFA0900100//National Key Research and Development Program of China/ ; 31971340//National Natural Science Foundation of China/ ; 31800080//National Natural Science Foundation of China/ ; 32030004//National Natural Science Foundation of China/ ; 32150025//National Natural Science Foundation of China/ ; XDB0480000//Strategic Priority Research Program of the Chinese Academy of Sciences/ ; 2021M692645//China Postdoctoral Science Foundation/ ; 172644KYSB20180022//Bureau of International Co-operation, Chinese Academy of Sciences/ ; KQTD20180413181837372//Shenzhen Science and Technology Innovation Program/ ; RCYX20221008092950122//Shenzhen Science and Technology Innovation Program/ ; //Shenzhen Outstanding Talents Training Fund/ ; }, mesh = {*Reading ; Reproducibility of Results ; *Saccharomyces cerevisiae/genetics ; DNA/genetics ; Information Storage and Retrieval ; }, abstract = {DNA has emerged as an appealing material for information storage due to its great storage density and durability. Random reading and rewriting are essential tasks for practical large-scale data storage. However, they are currently difficult to implement simultaneously in a single DNA-based storage system, strongly limiting their practicability. Here, a "Cell Disk" storage system is presented, achieving high-density in vivo DNA data storage that enables both random reading and rewriting. In this system, each yeast cell is used as a chamber to store information, similar to a "disk block" but with the ability to self-replicate. Specifically, each genome of yeast cell has a customized CRISPR/Cas9-based "lock-and-key" module inserted, which allows selective retrieval, erasure, or rewriting of the targeted cell "block" from a pool of cells ("disk"). Additionally, a codec algorithm with lossless compression ability is developed to improve the information density of each cell "block". As a proof of concept, target-specific reading and rewriting of the compressed data from a mimic cell "disk" comprising up to 10[5] "blocks" are demonstrated and achieve high specificity and reliability. The "Cell Disk" system described here concurrently supports random reading and rewriting, and it should have great scalability for practical data storage use.}, } @article {pmid38331396, year = {2024}, author = {Li, C and Li, X and Bank, MS and Dong, T and Fang, JK and Leusch, FDL and Rillig, MC and Wang, J and Wang, L and Xia, Y and Xu, EG and Yang, Y and Zhang, C and Zhu, D and Liu, J and Jin, L}, title = {The "Microplastome" - A Holistic Perspective to Capture the Real-World Ecology of Microplastics.}, journal = {Environmental science & technology}, volume = {58}, number = {9}, pages = {4060-4069}, pmid = {38331396}, issn = {1520-5851}, mesh = {*Microplastics ; Plastics/toxicity ; Ecosystem ; Prospective Studies ; Environmental Monitoring ; *Water Pollutants, Chemical/toxicity ; }, abstract = {Microplastic pollution, an emerging pollution issue, has become a significant environmental concern globally due to its ubiquitous, persistent, complex, toxic, and ever-increasing nature. As a multifaceted and diverse suite of small plastic particles with different physicochemical properties and associated matters such as absorbed chemicals and microbes, future research on microplastics will need to comprehensively consider their multidimensional attributes. Here, we introduce a novel, conceptual framework of the "microplastome", defined as the entirety of various plastic particles (<5 mm), and their associated matters such as chemicals and microbes, found within a sample and its overall environmental and toxicological impacts. As a novel concept, this paper aims to emphasize and call for a collective quantification and characterization of microplastics and for a more holistic understanding regarding the differences, connections, and effects of microplastics in different biotic and abiotic ecosystem compartments. Deriving from this lens, we present our insights and prospective trajectories for characterization, risk assessment, and source apportionment of microplastics. We hope this new paradigm can guide and propel microplastic research toward a more holistic era and contribute to an informed strategy for combating this globally important environmental pollution issue.}, } @article {pmid38330650, year = {2024}, author = {Li, X and Cheng, X and Wu, J and Cai, Z and Wang, Z and Zhou, J}, title = {Multi-omics reveals different impact patterns of conventional and biodegradable microplastics on the crop rhizosphere in a biofertilizer environment.}, journal = {Journal of hazardous materials}, volume = {467}, number = {}, pages = {133709}, doi = {10.1016/j.jhazmat.2024.133709}, pmid = {38330650}, issn = {1873-3336}, mesh = {*Microplastics ; *Multiomics ; Plastics ; Rhizosphere ; Polyethylene ; Crops, Agricultural ; Polyesters ; }, abstract = {Microplastics (MPs) from the incomplete degradation of agricultural mulch can stress the effectiveness of biofertilizers and ultimately affect the rhizosphere environment of crops. Yet, the involved mechanisms are poorly known and robust empirical data is generally lacking. Here, conventional polyethylene (PE) MPs and poly(butylene adipate-co-butylene terephthalate) (PBAT) / poly(lactic acid) (PLA) biodegradable MPs (PBAT-PLA BioMPs) were investigated to assess their potential impact on the rhizosphere environment of Brassica parachinensis in the presence of Bacillus amyloliquefaciens biofertilizer. The results revealed that both MPs caused different levels of inhibited crop both above- and belowground crop biomass (up to 50.11% and 57.09%, respectively), as well as a significant decrease in plant height (up to 48.63% and 25.95%, respectively), along with an imbalance of microbial communities. Transcriptomic analyses showed that PE MPs mainly affected root's vitamin metabolism, whereas PBAT-PLA BioMPs mainly interfered with the lipid's enrichment. Metabolomic analyses further indicated that PE MPs interfered with amino acid synthesis that involved in crops' oxidative stress, and that PBAT-PLA BioMPs mainly affected the pathways associated with root growth. Additionally, PBAT-PLA BioMPs had a bigger ecological negative impact than did PE MPs, as evidenced by more pronounced alterations in root antioxidant abilities, a higher count of identified differential metabolites, more robust interrelationships among rhizosphere parameters, and a more intricate pattern of impacts on rhizosphere metrics. This study highlights the MPs' impact on crop rhizosphere in a biofertilizer environment from a rhizosphere multi-omics perspective, and has theoretical implications for scientific application of biofertilizers.}, } @article {pmid38322859, year = {2024}, author = {Mahmoudzadeh, H and Abedini, A and Aram, F and Mosavi, A}, title = {Evaluating urban environmental quality using multi criteria decision making.}, journal = {Heliyon}, volume = {10}, number = {3}, pages = {e24921}, pmid = {38322859}, issn = {2405-8440}, abstract = {In the urban environment, the quality refers to the capacity that provides and fulfills the material and spiritual needs of inhabitants. In order to improve the quality of urban life and standard of living for their citizens, planners and managers strive to raise Urban Environmental Quality. The objective of this study is to evaluate the quality of urban environment through the spatial analysis of a multi-criteria decision making (MCDM) method utilizing CRITIC. This research is conducted in district 4 and district 2 of the Tabriz Metropolis Municipality. In order to determine the quality of an urban environment, air pollution, vegetation coverage, land surface temperature, production of waste, population density, noise pollution, health care per capita, green spaces per capita, recreational spaces per capita, and distance from fault lines are used. After evaluating and producing environmental quality maps in two separate districts, 10 indicators were tested for significance and a comparative evaluation of two districts was conducted in order to determine which district was in better condition based on a statistical analysis of the T-test results. In accordance with the CRITIC method, there are significant differences between averages of waste production, population density, noise pollution, distance from fault lines, Land Surface Temperature, Normalized difference vegetation index, and distance from fault lines between the two districts. It appears that recreational space, air pollution, health care per capita, and green space per capita are not meaningfully different on averages. The preparation of environmental quality maps reveals the importance of meaningful indicators at the neighborhood level in two urban districts. In both districts by strengthening the continuity of the landscape through the development of ecological corridors and an increase in per capita can contribute to the improvement of the quality of the urban environment.}, } @article {pmid38322797, year = {2023}, author = {Faria, AL and Almeida, Y and Branco, D and Câmara, J and Cameirão, M and Ferreira, L and Moreira, A and Paulino, T and Rodrigues, P and Spinola, M and Vilar, M and Bermúdez I Badia, S and Simões, M and Fermé, E}, title = {NeuroAIreh@b: an artificial intelligence-based methodology for personalized and adaptive neurorehabilitation.}, journal = {Frontiers in neurology}, volume = {14}, number = {}, pages = {1258323}, pmid = {38322797}, issn = {1664-2295}, abstract = {Cognitive impairments are a prevalent consequence of acquired brain injury, dementia, and age-related cognitive decline, hampering individuals' daily functioning and independence, with significant societal and economic implications. While neurorehabilitation represents a promising avenue for addressing these deficits, traditional rehabilitation approaches face notable limitations. First, they lack adaptability, offering one-size-fits-all solutions that may not effectively meet each patient's unique needs. Furthermore, the resource-intensive nature of these interventions, often confined to clinical settings, poses barriers to widespread, cost-effective, and sustained implementation, resulting in suboptimal outcomes in terms of intervention adaptability, intensity, and duration. In response to these challenges, this paper introduces NeuroAIreh@b, an innovative cognitive profiling and training methodology that uses an AI-driven framework to optimize neurorehabilitation prescription. NeuroAIreh@b effectively bridges the gap between neuropsychological assessment and computational modeling, thereby affording highly personalized and adaptive neurorehabilitation sessions. This approach also leverages virtual reality-based simulations of daily living activities to enhance ecological validity and efficacy. The feasibility of NeuroAIreh@b has already been demonstrated through a clinical study with stroke patients employing a tablet-based intervention. The NeuroAIreh@b methodology holds the potential for efficacy studies in large randomized controlled trials in the future.}, } @article {pmid38316926, year = {2024}, author = {Zuffa, S and Schmid, R and Bauermeister, A and P Gomes, PW and Caraballo-Rodriguez, AM and El Abiead, Y and Aron, AT and Gentry, EC and Zemlin, J and Meehan, MJ and Avalon, NE and Cichewicz, RH and Buzun, E and Terrazas, MC and Hsu, CY and Oles, R and Ayala, AV and Zhao, J and Chu, H and Kuijpers, MCM and Jackrel, SL and Tugizimana, F and Nephali, LP and Dubery, IA and Madala, NE and Moreira, EA and Costa-Lotufo, LV and Lopes, NP and Rezende-Teixeira, P and Jimenez, PC and Rimal, B and Patterson, AD and Traxler, MF and Pessotti, RC and Alvarado-Villalobos, D and Tamayo-Castillo, G and Chaverri, P and Escudero-Leyva, E and Quiros-Guerrero, LM and Bory, AJ and Joubert, J and Rutz, A and Wolfender, JL and Allard, PM and Sichert, A and Pontrelli, S and Pullman, BS and Bandeira, N and Gerwick, WH and Gindro, K and Massana-Codina, J and Wagner, BC and Forchhammer, K and Petras, D and Aiosa, N and Garg, N and Liebeke, M and Bourceau, P and Kang, KB and Gadhavi, H and de Carvalho, LPS and Silva Dos Santos, M and Pérez-Lorente, AI and Molina-Santiago, C and Romero, D and Franke, R and Brönstrup, M and Vera Ponce de León, A and Pope, PB and La Rosa, SL and La Barbera, G and Roager, HM and Laursen, MF and Hammerle, F and Siewert, B and Peintner, U and Licona-Cassani, C and Rodriguez-Orduña, L and Rampler, E and Hildebrand, F and Koellensperger, G and Schoeny, H and Hohenwallner, K and Panzenboeck, L and Gregor, R and O'Neill, EC and Roxborough, ET and Odoi, J and Bale, NJ and Ding, S and Sinninghe Damsté, JS and Guan, XL and Cui, JJ and Ju, KS and Silva, DB and Silva, FMR and da Silva, GF and Koolen, HHF and Grundmann, C and Clement, JA and Mohimani, H and Broders, K and McPhail, KL and Ober-Singleton, SE and Rath, CM and McDonald, D and Knight, R and Wang, M and Dorrestein, PC}, title = {microbeMASST: a taxonomically informed mass spectrometry search tool for microbial metabolomics data.}, journal = {Nature microbiology}, volume = {9}, number = {2}, pages = {336-345}, pmid = {38316926}, issn = {2058-5276}, support = {R01 GM107550/GM/NIGMS NIH HHS/United States ; U01 DK119702/DK/NIDDK NIH HHS/United States ; R01 AI167860/AI/NIAID NIH HHS/United States ; R01 LM013115/LM/NLM NIH HHS/United States ; R35 GM142938/GM/NIGMS NIH HHS/United States ; T32 DK007202/DK/NIDDK NIH HHS/United States ; R01 GM132649/GM/NIGMS NIH HHS/United States ; DP2 GM137413/GM/NIGMS NIH HHS/United States ; R01 GM137135/GM/NIGMS NIH HHS/United States ; S10 OD021750/OD/NIH HHS/United States ; F32 AT011475/AT/NCCIH NIH HHS/United States ; U24 DK133658/DK/NIDDK NIH HHS/United States ; T32 AR064194/AR/NIAMS NIH HHS/United States ; DP1 AT010885/AT/NCCIH NIH HHS/United States ; U19 AG063744/AG/NIA NIH HHS/United States ; P 31915/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Humans ; *Tandem Mass Spectrometry ; *Metabolomics/methods ; Databases, Factual ; }, abstract = {microbeMASST, a taxonomically informed mass spectrometry (MS) search tool, tackles limited microbial metabolite annotation in untargeted metabolomics experiments. Leveraging a curated database of >60,000 microbial monocultures, users can search known and unknown MS/MS spectra and link them to their respective microbial producers via MS/MS fragmentation patterns. Identification of microbe-derived metabolites and relative producers without a priori knowledge will vastly enhance the understanding of microorganisms' role in ecology and human health.}, } @article {pmid38296495, year = {2024}, author = {Haga, Y and Manabe, S and Tsujino, H and Asahara, H and Higashisaka, K and Tsutsumi, Y}, title = {[Mechanisms of Cell Toxicity Caused by Degraded Microplastics].}, journal = {Yakugaku zasshi : Journal of the Pharmaceutical Society of Japan}, volume = {144}, number = {2}, pages = {177-181}, doi = {10.1248/yakushi.23-00152-3}, pmid = {38296495}, issn = {1347-5231}, mesh = {Animals ; Humans ; *Microplastics/toxicity ; Plastics/toxicity ; Ultraviolet Rays ; *Water Pollutants, Chemical/toxicity/analysis ; Fishes ; }, abstract = {Microplastics (MPs), defined as plastic particles less than 5 mm in size, are ubiquitous in the environment. The accumulation of MPs in various environmental compartments, such as the ocean, soil, and air, has raised considerable concerns regarding their impact on ecological systems, including marine life and human health. Notably, MPs have been detected in marine organisms such as shellfish and fish, and have even been found in the human body, including in the blood and placenta. Moreover, considering that MPs have been detected in drinking water, human exposure to these particles in daily life is inevitable. To assess the risk posed by MPs to human health, it is essential to consider their physiological and chemical properties, including size, shape, surface modification, and material composition. However, current risk analyses focus primarily on spherical MPs with smooth surfaces, which differ substantially from most of the MPs detected in the environment. Environmental factors, such as ocean waves and ultraviolet radiation, alter the properties of MPs, including size, shape, and surface characteristics. In this review, we summarize current research on MPs, with a particular emphasis on the effects of MP degradation on human health. Furthermore, we generated MPs with surface degradation and evaluated their impact on cell toxicity, along with the underlying biological mechanisms.}, } @article {pmid38315121, year = {2024}, author = {Han, K and Li, J and Yang, D and Zhuang, Q and Zeng, H and Rong, C and Yue, J and Li, N and Gu, C and Chen, L and Chen, C}, title = {Detecting horizontal gene transfer with metagenomics co-barcoding sequencing.}, journal = {Microbiology spectrum}, volume = {12}, number = {3}, pages = {e0360223}, pmid = {38315121}, issn = {2165-0497}, support = {2021YFF0703805//MOST | National Key Research and Development Program of China (NKPs)/ ; 82102447//MOST | National Natural Science Foundation of China (NSFC)/ ; DFL20191801//Beijing Hospital Authority/ ; Z201100005520040//Beijing Municipal Science and Technology Commission, Adminitrative Commission of Zhongguancun Science Park/ ; QML20230701//Beijing Hospitals Authority Youth Programme/ ; }, mesh = {Animals ; Humans ; Mice ; *Gene Transfer, Horizontal ; *Metagenomics/methods ; Computational Biology/methods ; Metagenome ; Bacteria/genetics ; DNA ; }, abstract = {Horizontal gene transfer (HGT) is the process through which genetic information is transferred between different genomes and that played a crucial role in bacterial evolution. HGT can enable bacteria to rapidly acquire antibiotic resistance and bacteria that have acquired resistance is spreading within the microbiome. Conventional methods of characterizing HGT patterns include short-read metagenomic sequencing (short-reads mNGS), long-read sequencing, and single-cell sequencing. These approaches present several limitations, such as short-read fragments, high amounts of input DNA, and sequencing costs, respectively. Here, we attempt to circumvent present limitations to detect HGT by developing a metagenomics co-barcode sequencing workflow (MECOS) and applying it to the human and mouse gut microbiomes. In addition to that, we have over 10-fold increased contig length compared to short-reads mNGS; we also obtained exceeding 30 million paired reads with co-barcode information. Applying the novel bioinformatic pipeline, we integrated this co-barcoding information and the context information from long reads, and observed over 50-fold HGT events after we corrected the potential wrong HGT events. Specifically, we detected approximately 3,000 HGT blocks in individual samples, encompassing ~6,000 genes and ~100 taxonomic groups, including loci conferring tetracycline resistance through ribosomal protection. MECOS provides a valuable tool for investigating HGT and advance our understanding on the evolution of natural microbial communities within hosts.IMPORTANCEIn this study, to better identify horizontal gene transfer (HGT) in individual samples, we introduce a new co-barcoding sequencing system called metagenomics co-barcoding sequencing (MECOS), which has three significant improvements: (i) long DNA fragment extraction, (ii) a special transposome insertion, (iii) hybridization of DNA to barcode beads, and (4) an integrated bioinformatic pipeline. Using our approach, we have over 10-fold increased contig length compared to short-reads mNGS, and observed over 50-fold HGT events after we corrected the potential wrong HGT events. Our results indicate the presence of approximately 3,000 HGT blocks, involving roughly 6,000 genes and 100 taxonomic groups in individual samples. Notably, these HGT events are predominantly enriched in genes that confer tetracycline resistance via ribosomal protection. MECOS is a useful tool for investigating HGT and the evolution of natural microbial communities within hosts, thereby advancing our understanding of microbial ecology and evolution.}, } @article {pmid38315112, year = {2024}, author = {Chandel, AS}, title = {Geo-spatial technology based on a multi-criteria evaluation technique used to find potential landfill sites in the town of Bule Hora in southern Ethiopia.}, journal = {Journal of the Air & Waste Management Association (1995)}, volume = {74}, number = {4}, pages = {207-239}, doi = {10.1080/10962247.2024.2312889}, pmid = {38315112}, issn = {2162-2906}, mesh = {Humans ; *Solid Waste ; Ethiopia ; Prospective Studies ; Quality of Life ; Geographic Information Systems ; Decision Support Techniques ; *Refuse Disposal/methods ; Waste Disposal Facilities ; Technology ; }, abstract = {Solid waste has surfaced as an eminent and critical concern of environmental and social significance on a global scale, and Ethiopia, a developing country with limited income, has also encountered unfavorable outcomes due to substandard waste management practices. When pinpointing a fitting landfill location in the town of Bule Hora, various ecological, economic, and societal aspects must be considered; these may result in discord and exacerbate a multifaceted and lengthy process. Hence, this research aims to identify prospective landfill sites within the town and utilize geospatial methods, such as Multi-Criteria Evaluation and Analytic Hierarchy Process, to accomplish its objectives. The utilization of geospatial technology and multi-criteria evaluation provides an efficient manner to simultaneously address all bottlenecks involved in the selection of an appropriate landfill location. Geospatial technology evaluates and manages environmental constraints, whereas multi-criteria assessment categorizes choices based on their desirability. Furthermore, by employing a restriction map adhering to established standards, seven landfill sites have successfully been identified within the town. The Land Suitability Index assesses site suitability based on ecological factors, while the Total Hauling Distance evaluates sites within an economic framework. AHP determines weightings through 25.4 pairwise comparisons, resulting in a consistency ratio of 1.95%. The cartographic analysis is conducted using ESRI ArcGIS version 10.8 software. The findings of this study reveal that 98.69% of the area under study is subject to restrictions. The study recommends the implementation of geospatial methods for identifying suitable landfill sites, which would aid in the decision-making process and prevent hasty decisions from triggering environmental degradation. Proper waste disposal would augment the quality of life for residents by diminishing health hazards. The study endeavors to serve as a reference for other developing countries in selecting appropriate landfill sites.Implications: The town of Bule Hora also faces the problem of waste disposal; there is no scientifically selected suitable landfill. Residents of the town of Bule Hora practice waste disposal in open fields, near settlements, water bodies, roads, agricultural land, and other places. The main sources of solid waste in the town are homes, shops, hotels, restaurants, open markets, hospitals, educational institutions, private clinics, etc. Water pollution can potentially lead to the spread of waterborne diseases. According to reports from the Bule Horas Health Department, many people are affected by water-related diseases every year. These open landfill systems with no regard for settlement, topography, geology, surface, or groundwater conditions are the consequences of these unsuitable habitats and health problems. To reduce these problems, this study plays an important role in determining the suitability of landfills for the town and proposing alternative measures that can minimize negative environmental impacts from waste. This study aims to apply geospatial-based technology to a multi-criteria assessment technique to select perfectly suitable landfill sites that are environmentally friendly, economically cost-effective, and socially responsible; examine the town's current waste management system; calculate the selected parameter weights for feature ranking; and delineate solid waste landfills.}, } @article {pmid38312217, year = {2024}, author = {Ogawa, T and Tsuzuki, S and Ohbe, H and Matsui, H and Fushimi, K and Yasunaga, H and Kutsuna, S}, title = {Analysis of Differences in Characteristics of High-Risk Endemic Areas for Contracting Japanese Spotted Fever, Tsutsugamushi Disease, and Severe Fever With Thrombocytopenia Syndrome.}, journal = {Open forum infectious diseases}, volume = {11}, number = {2}, pages = {ofae025}, pmid = {38312217}, issn = {2328-8957}, abstract = {BACKGROUND: Tick-borne infections, including tsutsugamushi disease, Japanese spotted fever, and severe fever with thrombocytopenia syndrome (SFTS), are prevalent in East Asia with varying geographic distribution and seasonality. This study aimed to investigate the differences in the characteristics among endemic areas for contracting each infection.

METHODS: We conducted an ecologic study in Japan, using data from a nationwide inpatient database and publicly available geospatial data. We identified 4493 patients who were hospitalized for tick-borne infections between July 2010 and March 2021. Mixed-effects modified Poisson regression analysis was used to identify factors associated with a higher risk of contracting each tick-borne disease (Tsutsugamushi, Japanese spotted fever, and SFTS).

RESULTS: Mixed-effects modified Poisson regression analysis revealed that environmental factors, such as temperature, sunlight duration, elevation, precipitation, and vegetation, were associated with the risk of contracting these diseases. Tsutsugamushi disease was positively associated with higher temperatures, farms, and forests, whereas Japanese spotted fever and SFTS were positively associated with higher solar radiation and forests.

CONCLUSIONS: Our findings from this ecologic study indicate that different environmental factors play a significant role in the risk of transmission of tick-borne infections. Understanding the differences can aid in identifying high-risk areas and developing public health strategies for infection prevention. Further research is needed to address causal relationships.}, } @article {pmid38311099, year = {2024}, author = {Stanic, B and Sukur, N and Milošević, N and Markovic Filipovic, J and Pogrmic-Majkic, K and Andric, N}, title = {Differential eigengene network analysis reveals benzo[a]pyrene and 2,3,7,8-tetrachlorodibenzo-p-dioxin consensus regulatory network in human liver cell line HepG2.}, journal = {Toxicology}, volume = {502}, number = {}, pages = {153737}, doi = {10.1016/j.tox.2024.153737}, pmid = {38311099}, issn = {1879-3185}, mesh = {Humans ; *Benzo(a)pyrene/toxicity ; *Polychlorinated Dibenzodioxins/toxicity ; Consensus ; Liver/metabolism ; Cell Line, Tumor ; Receptors, Aryl Hydrocarbon/genetics/metabolism ; }, abstract = {Aryl hydrocarbon receptor (AHR) is one of the main mediators of the toxic effects of benzo[a]pyrene (BaP) and 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD). However, a vast number of BaP- and TCDD-affected genes may suggest a more complex transcriptional regulatory network driving common adverse effects of these two chemicals. Unlike TCDD, BaP is rapidly metabolized in the liver, yielding products with a questionable ability to bind and activate AHR. In this study, we used transcriptomics data from the BaP- and TCCD-exposed human liver cell line HepG2, and performed differential eigengene network analysis to understand the correlation among genes and to untangle the common regulatory mechanism in the action of BaP and TCDD. The genes were grouped into 11 meta-modules with an overall preservation of 0.72 and were also segregated into three consensus time clusters: 12, 24, and 48 h. The analysis showed that the consensus genes in each time cluster were either directly regulated by the AHR or the AHR-TF interactions. Some TFs form a direct physical interaction with AHR such as ESR1, FOXA1, and E2F1, whereas others, including CTCF, RXRA, FOXO1, CEBPA, CEBPB, and TP53 show an indirect interaction with AHR. The analysis of biological processes (BPs) identified unique and common BPs in BaP and TCDD samples, with DNA damage response detected in all three time points. In summary, we identified a consensus transcriptional regulatory network common for BaP and TCDD consisting of direct AHR targets and AHR-TF targets. This analysis sheds new light on the common mechanism of action of a genotoxic (BaP) and non-genotoxic (TCDD) chemical in liver cells.}, } @article {pmid38308167, year = {2024}, author = {Wang, Y and Chen, Y and Lu, S and Guo, X}, title = {Development and trends of constructed wetland substrates over the past 30 years: a literature visualization analysis based on CiteSpace.}, journal = {Environmental science and pollution research international}, volume = {31}, number = {10}, pages = {14537-14552}, pmid = {38308167}, issn = {1614-7499}, mesh = {Humans ; *Wetlands ; Cluster Analysis ; Databases, Factual ; *Environmental Pollutants ; Sewage ; }, abstract = {Constructed wetland substrates (CWSs) have received considerable attention owing to their importance in adsorbing and degrading pollutants, providing growth attachment points for microorganisms, and supporting wetland plants. There are differences in the configurations and functions of constructed wetlands (CWs) for treating different water bodies and sewage, resulting in a wide variety of substrates. Research on the application and mechanism of CWSs is not sufficiently systematic. Therefore, the current research advancements and hotspots must be identified. Hence, we used CiteSpace to analyze 1955 English publications from the core collection database of the Web of Science to assess the current state of the CWS research field. Based on the cooperative network analysis, the roles of various countries, institutions, and authors in research on CWSs were reviewed. Keyword co-occurrence and cluster analyses were used to discuss the transformation of CWSs from removing traditional pollutants to emerging pollutants and the transition from incorporating natural substrates to artificial substrates. Finally, we underscored the need for more emphasis to be placed on the collocation and application of the CWSs at different latitudes. Furthermore, the substrate micro-interface process and its effects on the interaction patterns of pollutants and microorganisms should be thoroughly investigated to provide theoretical guidance for the development of wetland applications and mechanisms.}, } @article {pmid38307178, year = {2024}, author = {Fu, Y and He, Y and Chen, W and Xiao, W and Ren, H and Shi, Y and Hu, Z}, title = {Dynamics of carbon storage driven by land use/land cover transformation in coal mining areas with a high groundwater table: A case study of Yanzhou Coal Mine, China.}, journal = {Environmental research}, volume = {247}, number = {}, pages = {118392}, doi = {10.1016/j.envres.2024.118392}, pmid = {38307178}, issn = {1096-0953}, mesh = {Humans ; *Coal Mining ; Carbon ; China ; *Groundwater ; Coal ; Ecosystem ; Conservation of Natural Resources ; }, abstract = {Intensive anthropogenic activities have led to drastic changes in land use/land cover (LULC) and impacted the carbon storage in high-groundwater coal basins. In this paper, we conduct a case study on the Yanzhou Coalfield in Shandong Province of China. We further classify waterbodies by using the Google Earth Engine (GEE) to better investigate the process of LULC transformation and the forces driving it in four periods from 1985 to 2020 (i.e., 1985-1995, 1995-2005, 2005-2015, and 2015-2020). We modeled the spatiotemporal dynamics of carbon storage by using InVEST based on the transformation in LULC and its drivers, including mining (M), reclamation (R), urbanization and village relocation (U), and ecological restoration (E). The results indicate that carbon storage had depleted by 19.69 % (321099.06 Mg) owing to intensive transformations in LULC. The area of cropland shrank with the expansion of built-up land and waterbodies, and 56.31 % of the study area underwent transitions in land use in the study period. U was the primary driver of carbon loss while E was the leading driver of carbon gain. While the direct impact of M on carbon loss accounted for only 5.23 % of the total, it affected urbanization and led to village relocation. R led to the recovery of cropland and the reclamation of water for aquaculture, which in turn improved the efficiency of land use. However, it contributed only 2.09 % to the total increase in carbon storage. Numerous complicated and intertwined processes (211) drove the changes in carbon storage in the study area. The work here provides valuable information for decision-makers as well as people involved in reclamation and ecological restoration to better understand the link between carbon storage and the forces influencing it. The results can be used to integrate the goals of carbon sequestration into measures for land management.}, } @article {pmid38305922, year = {2024}, author = {Eshetu, SB and Kipkulei, HK and Koepke, J and Kächele, H and Sieber, S and Löhr, K}, title = {Impact of forest landscape restoration in combating soil erosion in the Lake Abaya catchment, Southern Ethiopia.}, journal = {Environmental monitoring and assessment}, volume = {196}, number = {3}, pages = {228}, pmid = {38305922}, issn = {1573-2959}, mesh = {*Soil Erosion ; *Ecosystem ; Ethiopia ; Lakes ; Environmental Monitoring/methods ; Conservation of Natural Resources ; Soil ; Geographic Information Systems ; Forests ; }, abstract = {As an effect of forest degradation, soil erosion is among Ethiopia's most pressing environmental challenges and a major threat to food security where it could potentially compromise the ecosystem functions and services. As the effects of soil erosion intensify, the landscape's capacity to support ecosystem functions and services is compromised. Exploring the ecological implications of soil erosion is crucial. This study investigated the soil loss and land degradation in the Lake Abaya catchment to explore forest landscape restoration (FLR) implementation as a possible countermeasure to the effects. The study used a geographic information system (GIS)-based approach of the Revised Universal Soil Loss Equation (RUSLE) to determine the potential annual soil loss and develop an erosion risk map. Results show that 13% of the catchment, which accounts for approximately 110,000 ha, is under high erosion risk of exceeding the average annual tolerable soil loss of 10 t/ha/year. Allocation of land on steep slopes to crop production is the major reason for the calculated high erosion risk in the catchment. A scenario-based analysis was implemented following the slope-based land-use allocation proposal indicated in the Rural Land Use Proclamation 456/2005 of Ethiopia. The scenario analysis resulted in a reversal erosion effect whereby an estimated 3000 t/ha/year of soil loss in the catchment. Thus, FLR activities hold great potential for minimizing soil loss and contributing to supporting functioning and providing ecosystem services. Tree-based agroforestry systems are among the key FLR measures championed in highly degraded landscapes in Ethiopia. This study helps policymakers and FLR implementors identify erosion risk areas for future FLR activities. Thereby, it contributes to achieving the country's restoration commitment.}, } @article {pmid38305133, year = {2024}, author = {Ramakodi, MP}, title = {Merging and concatenation of sequencing reads: a bioinformatics workflow for the comprehensive profiling of microbiome from amplicon data.}, journal = {FEMS microbiology letters}, volume = {371}, number = {}, pages = {}, doi = {10.1093/femsle/fnae009}, pmid = {38305133}, issn = {1574-6968}, mesh = {RNA, Ribosomal, 18S/genetics ; Workflow ; *Microbiota/genetics ; Bacteria/genetics ; High-Throughput Nucleotide Sequencing/methods ; Computational Biology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {A comprehensive profiling of microbial diversity is essential to understand the ecosystem functions. Universal primer sets such as the 515Y/926R could amplify a part of 16S and 18S rRNA and infer the diversity of prokaryotes and eukaryotes. However, the analyses of mixed sequencing data pose a bioinformatics challenge; the 16S and 18S rRNA sequences need to be separated first and analysed individually/independently due to variations in the amplicon length. This study describes an alternative strategy, a merging and concatenation workflow, to analyse the mixed amplicon data without separating the 16S and 18S rRNA sequences. The workflow was tested with 24 mock community (MC) samples, and the analyses resolved the composition of prokaryotes and eukaryotes adequately. In addition, there was a strong correlation (cor = 0.950; P-value = 4.754e-10) between the observed and expected abundances in the MC samples, which suggests that the computational approach could infer the microbial proportions accurately. Further, 18 samples collected from the Sundarbans mangrove region were analysed as a case study. The analyses identified Proteobacteria, Bacteroidota, Actinobacteriota, Cyanobacteria, and Crenarchaeota as dominant bacterial phyla and eukaryotic divisions such as Metazoa, Gyrista, Cryptophyta, Chlorophyta, and Dinoflagellata were found to be dominant in the samples. Thus, the results support the applicability of the method in environmental microbiome research. The merging and concatenation workflow presented here requires considerably less computational resources and uses widely/commonly used bioinformatics packages, saving researchers analyses time (for equivalent sample numbers, compared to the conventional approach) required to infer the diversity of major microbial domains from mixed amplicon data at comparable accuracy.}, } @article {pmid38302634, year = {2024}, author = {Rajan, SC and M, V and Mitra, A and N P, S and K, A and Pillai, MS and R, J}, title = {Threshold of anthropogenic sound levels within protected landscapes in Kerala, India, for avian habitat quality and conservation.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {2701}, pmid = {38302634}, issn = {2045-2322}, mesh = {Animals ; Acoustics ; *Birds ; Conservation of Natural Resources/methods ; *Ecosystem ; India ; *Anthropogenic Effects ; *Sound ; }, abstract = {Anthrophony is an important determinant of habitat quality in the Anthropocene. Acoustic adaptation of birds at lower levels of anthrophony is known. However, threshold anthrophony, beyond which biophony starts decreasing, is less explored. Here, we present empirical results of the relationship between anthrophony and biophony in four terrestrial soundscapes. The constancy of the predicted threshold vector normalised anthropogenic power spectral density (~ 0.40 Watts/Hz) at all the study sites is intriguing. We propose the threshold value of anthropogenic power spectral density as an indicator of the avian acoustic tolerance level in the study sites. The findings pave the way to determine permissible sound levels within protected landscapes and directly contribute to conservation planning.}, } @article {pmid38301473, year = {2024}, author = {Huang, Y and Qin, R and Wei, H and Chai, N and Yang, Y and Li, Y and Wan, P and Li, Y and Zhao, W and Lawawirojwong, S and Suepa, T and Zhang, F}, title = {Plastic film mulching application improves potato yields, reduces ammonia emissions, but boosts the greenhouse gas emissions in China.}, journal = {Journal of environmental management}, volume = {353}, number = {}, pages = {120241}, doi = {10.1016/j.jenvman.2024.120241}, pmid = {38301473}, issn = {1095-8630}, mesh = {*Greenhouse Gases/analysis ; *Solanum tuberosum ; Ammonia ; Carbon Dioxide/analysis ; Agriculture ; Soil ; China ; Methane/analysis ; Nitrous Oxide/analysis ; Fertilizers/analysis ; }, abstract = {With global population growth and climate change, food security and global warming have emerged as two major challenges to agricultural development. Plastic film mulching (PM) has long been used to improve yields in rain-fed agricultural systems, but few studies have focused on soil gas emissions from mulched rainfed potatoes on a long-term and regional scale. This study integrated field data with the Denitrification-Decomposition (DNDC) model to evaluate the impacts of PM on potato yields, greenhouse gas (GHG) and ammonia (NH3) emissions in rainfed agricultural systems in China. We found that PM increased potato yield by 39.7 % (1505 kg ha[-1]), carbon dioxide (CO2) emissions by 15.4 % (123 kg CO2 eq ha[-1]), nitrous oxide (N2O) emissions by 47.8 % (1016 kg CO2 eq ha[-1]), and global warming potential (GWP) by 38.9 % (1030 kg CO2 eq ha[-1]), while NH3 volatilization decreased by 33.9 % (8.4 kg NH3 ha[-1]), and methane (CH4) emissions were little changed compared to CK. Specifically, the yield after PM significantly increased in South China (SC), North China (NC), and Northwest China (NWC), with increases of 66.1 % (2429 kg ha[-1]), 44.1 % (1173 kg ha[-1]), and 43.6 % (956 kg ha[-1]) compared to CK, respectively. The increase in GWP and greenhouse gas emission intensity (GHGI) under PM was more pronounced in the Northeast China (NEC) and NWC regions, with respective increases of 57.1 % and 60.2 % in GWP, 16.9 % and 10.3 % in GHGI. While in the Middle and Lower reaches of the Yangtze River (MLYR) and SC, PM decreased GHGI with 10.2 % and 31.1 %, respectively. PM significantly reduced NH3 emissions in all regions and these reductions were most significant in Southwest China (SWC), SCand MLYR, which were 41 %, 38.0 %, and 38.0 % lower than CK, respectively. In addition, climatic and edaphic variables were the main contributors to GHG and NH3 emissions. In conclusion, it is appropriate to promote the use of PM in the MLYR and SC regions, because of the ability to increase yields while reducing environmental impacts (lower GHGI and NH3 emissions). The findings provide a theoretical basis for sustainable agricultural production of PM potatoes.}, } @article {pmid38297840, year = {2024}, author = {Tian, C and Li, J and Wu, Y and Wang, G and Zhang, Y and Zhang, X and Sun, Y and Wang, Y}, title = {An integrative database and its application for plant synthetic biology research.}, journal = {Plant communications}, volume = {5}, number = {5}, pages = {100827}, pmid = {38297840}, issn = {2590-3462}, mesh = {*Synthetic Biology/methods ; Plants/genetics ; Databases, Genetic ; Nicotiana/genetics ; Computational Biology/methods ; }, abstract = {Plant synthetic biology research requires diverse bioparts that facilitate the redesign and construction of new-to-nature biological devices or systems in plants. Limited by few well-characterized bioparts for plant chassis, the development of plant synthetic biology lags behind that of its microbial counterpart. Here, we constructed a web-based Plant Synthetic BioDatabase (PSBD), which currently categorizes 1677 catalytic bioparts and 384 regulatory elements and provides information on 309 species and 850 chemicals. Online bioinformatics tools including local BLAST, chem similarity, phylogenetic analysis, and visual strength are provided to assist with the rational design of genetic circuits for manipulation of gene expression in planta. We demonstrated the utility of the PSBD by functionally characterizing taxadiene synthase 2 and its quantitative regulation in tobacco leaves. More powerful synthetic devices were then assembled to amplify the transcriptional signals, enabling enhanced expression of flavivirus non-structure 1 proteins in plants. The PSBD is expected to be an integrative and user-centered platform that provides a one-stop service for diverse applications in plant synthetic biology research.}, } @article {pmid38297125, year = {2024}, author = {Xu, P and Li, G and Zheng, Y and Fung, JCH and Chen, A and Zeng, Z and Shen, H and Hu, M and Mao, J and Zheng, Y and Cui, X and Guo, Z and Chen, Y and Feng, L and He, S and Zhang, X and Lau, AKH and Tao, S and Houlton, BZ}, title = {Fertilizer management for global ammonia emission reduction.}, journal = {Nature}, volume = {626}, number = {8000}, pages = {792-798}, pmid = {38297125}, issn = {1476-4687}, mesh = {*Ammonia/analysis/metabolism ; *Crop Production/methods/statistics & numerical data/trends ; Datasets as Topic ; Ecosystem ; *Fertilizers/adverse effects/analysis/statistics & numerical data ; Machine Learning ; Nitrogen/analysis/metabolism ; Oryza/metabolism ; Soil/chemistry ; Triticum/metabolism ; Zea mays/metabolism ; Climate Change/statistics & numerical data ; }, abstract = {Crop production is a large source of atmospheric ammonia (NH3), which poses risks to air quality, human health and ecosystems[1-5]. However, estimating global NH3 emissions from croplands is subject to uncertainties because of data limitations, thereby limiting the accurate identification of mitigation options and efficacy[4,5]. Here we develop a machine learning model for generating crop-specific and spatially explicit NH3 emission factors globally (5-arcmin resolution) based on a compiled dataset of field observations. We show that global NH3 emissions from rice, wheat and maize fields in 2018 were 4.3 ± 1.0 Tg N yr[-1], lower than previous estimates that did not fully consider fertilizer management practices[6-9]. Furthermore, spatially optimizing fertilizer management, as guided by the machine learning model, has the potential to reduce the NH3 emissions by about 38% (1.6 ± 0.4 Tg N yr[-1]) without altering total fertilizer nitrogen inputs. Specifically, we estimate potential NH3 emissions reductions of 47% (44-56%) for rice, 27% (24-28%) for maize and 26% (20-28%) for wheat cultivation, respectively. Under future climate change scenarios, we estimate that NH3 emissions could increase by 4.0 ± 2.7% under SSP1-2.6 and 5.5 ± 5.7% under SSP5-8.5 by 2030-2060. However, targeted fertilizer management has the potential to mitigate these increases.}, } @article {pmid38294243, year = {2024}, author = {Omondi, VO and Bosire, GO and Onyari, JM and Kibet, C and Mwasya, S and Onyonyi, VN and Getahun, MN}, title = {Multi-omics analyses reveal rumen microbes and secondary metabolites that are unique to livestock species.}, journal = {mSystems}, volume = {9}, number = {2}, pages = {e0122823}, pmid = {38294243}, issn = {2379-5077}, support = {B1126A-185//Max Planck Institute for Chemical Ecology/ ; B1126A-185//International Centre of Insect Physiology and Ecology (ICIPE)/ ; }, mesh = {Cattle ; Humans ; Sheep ; Animals ; *Livestock/microbiology ; Rumen/metabolism ; Camelus ; Multiomics ; Ruminants/microbiology ; *Microbiota/genetics ; Goats/physiology ; Animal Feed/analysis ; }, abstract = {Ruminant livestock, including cattle, sheep, goats, and camels, possess a distinctive digestive system with complex microbiota communities critical for feed conversion and secondary metabolite production, including greenhouse gases. Yet, there is limited knowledge regarding the diversity of rumen microbes and metabolites benefiting livestock physiology, productivity, climate impact, and defense mechanisms across ruminant species. In this study, we utilized metataxonomics and metabolomics data from four evolutionarily distinct livestock species, which had fed on diverse plant materials like grass, shrubs, and acacia trees, to uncover the unique signature microbes and secondary metabolites. We established the presence of a distinctive anaerobic fungus called Oontomyces in camels, while cattle exhibited a higher prevalence of unique microbes like Psychrobacter, Anaeromyces, Cyllamyces, and Orpinomyces. Goats hosted Cleistothelebolus, and Liebetanzomyces was unique to sheep. Furthermore, we identified a set of conserved core microbes, including Prevotella, Rickenellaceae, Cladosporium, and Pecoramyces, present in all the ruminants, irrespective of host genetics and dietary composition. This underscores their indispensable role in maintaining crucial physiological functions. Regarding secondary metabolites, camel's rumen is rich in organic acids, goat's rumen is rich in alcohols and hydrocarbons, sheep's rumen is rich in indoles, and cattle's rumen is rich in sesquiterpenes. Additionally, linalool propionate and terpinolene were uniquely found in sheep rumen, while valencene was exclusive to cattle. This may suggest the existence of species-specific microbes and metabolites that require host rumen-microbes' environment balance. These results have implications for manipulating the rumen environment to target specific microbes and secondary metabolite networks, thereby enhancing livestock productivity, resilience, reducing susceptibility to vectors, and environmentally preferred livestock husbandry.IMPORTANCERumen fermentation, which depends on feed components and rumen microbes, plays a crucial role in feed conversion and the production of various metabolites important for the physiological functions, health, and environmental smartness of ruminant livestock, in addition to providing food for humans. However, given the complexity and variation of the rumen ecosystem and feed of these various livestock species, combined with inter-individual differences between gut microbial communities, how they influence the rumen secondary metabolites remains elusive. Using metagenomics and metabolomics approaches, we show that each livestock species has a signature microbe(s) and secondary metabolites. These findings may contribute toward understanding the rumen ecosystem, microbiome and metabolite networks, which may provide a gateway to manipulating rumen ecosystem pathways toward making livestock production efficient, sustainable, and environmentally friendly.}, } @article {pmid38292065, year = {2023}, author = {Macgregor, CJ and Saccheri, IJ and , and , and , and , }, title = {The genome sequence of the Rock Grayling, Hipparchia semele (Linnaeus, 1758).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {495}, pmid = {38292065}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual female Hipparchia semele (the Rock Grayling; Arthropoda; Insecta; Lepidoptera; Nymphalidae). The genome sequence is 403.4 megabases in span. Most of the assembly is scaffolded into 30 chromosomal pseudomolecules, including the W and Z sex chromosomes. The mitochondrial genome has also been assembled and is 15.22 kilobases in length. Gene annotation of this assembly on Ensembl identified 17,540 protein coding genes.}, } @article {pmid38285940, year = {2024}, author = {Long, C and Deng, J and Nguyen, J and Liu, YY and Alm, EJ and Solé, R and Saavedra, S}, title = {Structured community transitions explain the switching capacity of microbial systems.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {121}, number = {6}, pages = {e2312521121}, pmid = {38285940}, issn = {1091-6490}, support = {R01 AI141529/AI/NIAID NIH HHS/United States ; }, mesh = {*Microbiota ; *Environment ; *Ecology ; }, abstract = {Microbial systems appear to exhibit a relatively high switching capacity of moving back and forth among few dominant communities (taxon memberships). While this switching behavior has been mainly attributed to random environmental factors, it remains unclear the extent to which internal community dynamics affect the switching capacity of microbial systems. Here, we integrate ecological theory and empirical data to demonstrate that structured community transitions increase the dependency of future communities on the current taxon membership, enhancing the switching capacity of microbial systems. Following a structuralist approach, we propose that each community is feasible within a unique domain in environmental parameter space. Then, structured transitions between any two communities can happen with probability proportional to the size of their feasibility domains and inversely proportional to their distance in environmental parameter space-which can be treated as a special case of the gravity model. We detect two broad classes of systems with structured transitions: one class where switching capacity is high across a wide range of community sizes and another class where switching capacity is high only inside a narrow size range. We corroborate our theory using temporal data of gut and oral microbiota (belonging to class 1) as well as vaginal and ocean microbiota (belonging to class 2). These results reveal that the topology of feasibility domains in environmental parameter space is a relevant property to understand the changing behavior of microbial systems. This knowledge can be potentially used to understand the relevant community size at which internal dynamics can be operating in microbial systems.}, } @article {pmid38284174, year = {2024}, author = {Challa, A and Maras, JS and Nagpal, S and Tripathi, G and Taneja, B and Kachhawa, G and Sood, S and Dhawan, B and Acharya, P and Upadhyay, AD and Yadav, M and Sharma, R and Bajpai, M and Gupta, S}, title = {Multi-omics analysis identifies potential microbial and metabolite diagnostic biomarkers of bacterial vaginosis.}, journal = {Journal of the European Academy of Dermatology and Venereology : JEADV}, volume = {38}, number = {6}, pages = {1152-1165}, doi = {10.1111/jdv.19805}, pmid = {38284174}, issn = {1468-3083}, support = {8-06/AC-06/2018-RS//All India Institute of Medical Sciences/ ; }, mesh = {Humans ; Female ; *Vaginosis, Bacterial/diagnosis/microbiology ; *Biomarkers/metabolism ; Adult ; *Machine Learning ; *Microbiota ; Metabolomics/methods ; Young Adult ; Vagina/microbiology ; Metabolome ; RNA, Ribosomal, 16S/genetics ; Multiomics ; }, abstract = {BACKGROUND: Bacterial vaginosis (BV) is a common clinical manifestation of a perturbed vaginal ecology associated with adverse sexual and reproductive health outcomes if left untreated. The existing diagnostic modalities are either cumbersome or require skilled expertise, warranting alternate tests. Application of machine-learning tools to heterogeneous and high-dimensional multi-omics datasets finds promising potential in data integration and may aid biomarker discovery.

OBJECTIVES: The present study aimed to evaluate the potential of the microbiome and metabolome-derived biomarkers in BV diagnosis. Interpretable machine-learning algorithms were used to evaluate the utility of an integrated-omics-derived classification model.

METHODS: Vaginal samples obtained from reproductive-age group women with (n = 40) and without BV (n = 40) were subjected to 16S rRNA amplicon sequencing and LC-MS-based metabolomics. The vaginal microbiome and metabolome were characterized, and machine-learning analysis was performed to build a classification model using biomarkers with the highest diagnostic accuracy.

RESULTS: Microbiome-based diagnostic model exhibited a ROC-AUC (10-fold CV) of 0.84 ± 0.21 and accuracy of 0.79 ± 0.18, and important features were Aerococcus spp., Mycoplasma hominis, Sneathia spp., Lactobacillus spp., Prevotella spp., Gardnerella spp. and Fannyhessea vaginae. The metabolome-derived model displayed superior performance with a ROC-AUC of 0.97 ± 0.07 and an accuracy of 0.92 ± 0.08. Beta-leucine, methylimidazole acetaldehyde, dimethylethanolamine, L-arginine and beta cortol were among key predictive metabolites for BV. A predictive model combining both microbial and metabolite features exhibited a high ROC-AUC of 0.97 ± 0.07 and accuracy of 0.94 ± 0.08 with diagnostic performance only slightly superior to the metabolite-based model.

CONCLUSION: Application of machine-learning tools to multi-omics datasets aid biomarker discovery with high predictive performance. Metabolome-derived classification models were observed to have superior diagnostic performance in predicting BV than microbiome-based biomarkers.}, } @article {pmid38283543, year = {2024}, author = {Wang, H and Chen, Z and Li, Z and He, X and Subramanian, SV}, title = {How economic development affects healthcare access for people with disabilities: A multilevel study in China.}, journal = {SSM - population health}, volume = {25}, number = {}, pages = {101594}, pmid = {38283543}, issn = {2352-8273}, abstract = {Meeting the healthcare needs of people with disabilities is an important challenge in achieving the central promise of "leave no one behind" during the Sustainable Development Goals era. In this study, we describe the accessibility of healthcare for people living with disabilities, as well as the potential influences of individuals' socioeconomic status and regional economic development. Our data covered 324 prefectural cities in China in 2019 and captured the access to healthcare services for people with disabilities. First, we used linear probability regression models to investigate the association between individual socioeconomic status, including residence, poverty status, education, and healthcare access. Second, we conducted an ecological analysis to test the association between prefectural economic indicators, including GDP (gross domestic product) per capita, urbanization ratio, average years of education, Engel's coefficient, and the overall prevalence of access to healthcare for people with disabilities within prefectures. Third, we used multilevel regression models to explore the association between the individual's socio-economic status, prefectural economic indicators, and access to healthcare at the individual level for people with disabilities. The results showed, first, that higher individual socioeconomic status (urban residence or higher educational level) was associated with better access to healthcare for people with disabilities. Second, regional economic indicators were positively associated with access to healthcare at the aggregate and individual levels. This study suggests that local governments, particularly in low- and middle-income countries, should promote economic development and conduct poverty alleviation policies to improve healthcare access for disadvantaged groups.}, } @article {pmid38279205, year = {2024}, author = {Reuber, VM and Westbury, MV and Rey-Iglesia, A and Asefa, A and Farwig, N and Miehe, G and Opgenoorth, L and Šumbera, R and Wraase, L and Wube, T and Lorenzen, ED and Schabo, DG}, title = {Topographic barriers drive the pronounced genetic subdivision of a range-limited fossorial rodent.}, journal = {Molecular ecology}, volume = {33}, number = {5}, pages = {e17271}, doi = {10.1111/mec.17271}, pmid = {38279205}, issn = {1365-294X}, support = {FOR 2358//Deutsche Forschungsgemeinschaft/ ; }, mesh = {Animals ; *Ecosystem ; *Rodentia/genetics ; Ethiopia ; Gene Flow ; Microsatellite Repeats ; Genetic Variation/genetics ; Genetics, Population ; }, abstract = {Due to their limited dispersal ability, fossorial species with predominantly belowground activity usually show increased levels of population subdivision across relatively small spatial scales. This may be exacerbated in harsh mountain ecosystems, where landscape geomorphology limits species' dispersal ability and leads to small effective population sizes, making species relatively vulnerable to environmental change. To better understand the environmental drivers of species' population subdivision in remote mountain ecosystems, particularly in understudied high-elevation systems in Africa, we studied the giant root-rat (Tachyoryctes macrocephalus), a fossorial rodent confined to the afro-alpine ecosystem of the Bale Mountains in Ethiopia. Using mitochondrial and low-coverage nuclear genomes, we investigated 77 giant root-rat individuals sampled from nine localities across its entire ~1000 km[2] range. Our data revealed a distinct division into a northern and southern group, with no signs of gene flow, and higher nuclear genetic diversity in the south. Landscape genetic analyses of the mitochondrial and nuclear genomes indicated that population subdivision was driven by slope and elevation differences of up to 500 m across escarpments separating the north and south, potentially reinforced by glaciation of the south during the Late Pleistocene (~42,000-16,000 years ago). Despite this landscape-scale subdivision between the north and south, weak geographic structuring of sampling localities within regions indicated gene flow across distances of at least 16 km at the local scale, suggesting high, aboveground mobility for relatively long distances. Our study highlights that despite the potential for local-scale gene flow in fossorial species, topographic barriers can result in pronounced genetic subdivision. These factors can reduce genetic variability, which should be considered when developing conservation strategies.}, } @article {pmid38278971, year = {2024}, author = {Larivière, D and Abueg, L and Brajuka, N and Gallardo-Alba, C and Grüning, B and Ko, BJ and Ostrovsky, A and Palmada-Flores, M and Pickett, BD and Rabbani, K and Antunes, A and Balacco, JR and Chaisson, MJP and Cheng, H and Collins, J and Couture, M and Denisova, A and Fedrigo, O and Gallo, GR and Giani, AM and Gooder, GM and Horan, K and Jain, N and Johnson, C and Kim, H and Lee, C and Marques-Bonet, T and O'Toole, B and Rhie, A and Secomandi, S and Sozzoni, M and Tilley, T and Uliano-Silva, M and van den Beek, M and Williams, RW and Waterhouse, RM and Phillippy, AM and Jarvis, ED and Schatz, MC and Nekrutenko, A and Formenti, G}, title = {Scalable, accessible and reproducible reference genome assembly and evaluation in Galaxy.}, journal = {Nature biotechnology}, volume = {42}, number = {3}, pages = {367-370}, pmid = {38278971}, issn = {1546-1696}, support = {U24 HG010263/HG/NHGRI NIH HHS/United States ; U24 CA231877/CA/NCI NIH HHS/United States ; U41 HG006620/HG/NHGRI NIH HHS/United States ; U01 CA253481/CA/NCI NIH HHS/United States ; U24 HG006620/HG/NHGRI NIH HHS/United States ; }, mesh = {*Computational Biology ; *Software ; }, } @article {pmid38278172, year = {2024}, author = {, }, title = {Effects of education on adult mortality: a global systematic review and meta-analysis.}, journal = {The Lancet. Public health}, volume = {9}, number = {3}, pages = {e155-e165}, pmid = {38278172}, issn = {2468-2667}, mesh = {Adult ; Humans ; Databases, Factual ; Educational Status ; *Life Expectancy ; Norway ; *Mortality ; }, abstract = {BACKGROUND: The positive effect of education on reducing all-cause adult mortality is known; however, the relative magnitude of this effect has not been systematically quantified. The aim of our study was to estimate the reduction in all-cause adult mortality associated with each year of schooling at a global level.

METHODS: In this systematic review and meta-analysis, we assessed the effect of education on all-cause adult mortality. We searched PubMed, Web of Science, Scopus, Embase, Global Health (CAB), EconLit, and Sociology Source Ultimate databases from Jan 1, 1980, to May 31, 2023. Reviewers (LD, TM, HDV, CW, IG, AG, CD, DS, KB, KE, and AA) assessed each record for individual-level data on educational attainment and mortality. Data were extracted by a single reviewer into a standard template from the Global Burden of Diseases, Injuries, and Risk Factors Study. We excluded studies that relied on case-crossover or ecological study designs to reduce the risk of bias from unlinked data and studies that did not report key measures of interest (all-cause adult mortality). Mixed-effects meta-regression models were implemented to address heterogeneity in referent and exposure measures among studies and to adjust for study-level covariates. This study was registered with PROSPERO (CRD42020183923).

FINDINGS: 17 094 unique records were identified, 603 of which were eligible for analysis and included data from 70 locations in 59 countries, producing a final dataset of 10 355 observations. Education showed a dose-response relationship with all-cause adult mortality, with an average reduction in mortality risk of 1·9% (95% uncertainty interval 1·8-2·0) per additional year of education. The effect was greater in younger age groups than in older age groups, with an average reduction in mortality risk of 2·9% (2·8-3·0) associated with each additional year of education for adults aged 18-49 years, compared with a 0·8% (0·6-1·0) reduction for adults older than 70 years. We found no differential effect of education on all-cause mortality by sex or Socio-demographic Index level. We identified publication bias (p<0·0001) and identified and reported estimates of between-study heterogeneity.

INTERPRETATION: To our knowledge, this is the first systematic review and meta-analysis to quantify the importance of years of schooling in reducing adult mortality, the benefits of which extend into older age and are substantial across sexes and economic contexts. This work provides compelling evidence of the importance of education in improving life expectancy and supports calls for increased investment in education as a crucial pathway for reducing global inequities in mortality.

FUNDING: Research Council of Norway and the Bill & Melinda Gates Foundation.}, } @article {pmid38277106, year = {2024}, author = {Shen, Z and Shi, H and Jiang, Y and Sun, Z}, title = {Diurnal variation in the urban thermal environment and its relationship to human activities in China: a Tencent location-based service geographic big data perspective.}, journal = {Environmental science and pollution research international}, volume = {31}, number = {9}, pages = {14218-14228}, pmid = {38277106}, issn = {1614-7499}, mesh = {Humans ; *Hot Temperature ; Cities ; *Big Data ; Environmental Monitoring/methods ; Temperature ; China ; }, abstract = {The main factor of the formation and deterioration in China's urban thermal environment is human activity, which is difficult to describe and measure. A new perspective on the effect of human activity on the urban thermal environment can be obtained by examining the interaction between location-based service (LBS) data and the urban thermal environment in China. However, relevant research is still limited. In this study, we used Tencent LBS data, Terra/Aqua MODIS land surface temperature (LST) data, and land use data to investigate the relationship between LBS and the urban thermal environment, specifically the LST and surface urban heat island intensity (SUHII) across China and its provinces. Our results showed that (1) in summer, the heat island effect was an issue in 94% of the urban areas in China, which was worse during the day. The high- and low-value periods of LBS data on a given day coincided with the acquisition times of MODIS LST products during the day and at night, respectively. (2) During both the day and at night, there was a significant connection between LBS data and the urban thermal environment in China. The highest correlation coefficient (r) between LBS data and the LST could reach 0.55 (p < 0.01) at the provincial level, and the highest correlation coefficient (r) between LBS data and the SUHII could reach 0.78 (p < 0.01) at the provincial level. (3) The urban thermal environment diurnal difference and LBS data exhibited a significant relationship. The ΔLBS diurnal differences were significantly positively related to the SUHII diurnal differences in China. The overall study findings revealed that LBS data constitute an important parameter to represent the human activity intensity when investigating the formation of the urban thermal environment in China.}, } @article {pmid38274410, year = {2023}, author = {Boyes, D and Mulley, JF and , and , and , and , and , and , }, title = {The genome sequence of the Common Pug, Eupithecia vulgata (Haworth, 1809).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {129}, pmid = {38274410}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual male Eupithecia vulgata (the Common Pug; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 454.7 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the assembled Z sex chromosome. The mitochondrial genome has also been assembled and is 17.1 kilobases in length.}, } @article {pmid38273575, year = {2024}, author = {Augustine, SP and Bailey-Marren, I and Charton, KT and Kiel, NG and Peyton, MS}, title = {Improper data practices erode the quality of global ecological databases and impede the progress of ecological research.}, journal = {Global change biology}, volume = {30}, number = {1}, pages = {e17116}, doi = {10.1111/gcb.17116}, pmid = {38273575}, issn = {1365-2486}, mesh = {*Plant Leaves ; *Plants ; Big Data ; Databases, Factual ; Phenotype ; }, abstract = {The scientific community has entered an era of big data. However, with big data comes big responsibilities, and best practices for how data are contributed to databases have not kept pace with the collection, aggregation, and analysis of big data. Here, we rigorously assess the quantity of data for specific leaf area (SLA) available within the largest and most frequently used global plant trait database, the TRY Plant Trait Database, exploring how much of the data were applicable (i.e., original, representative, logical, and comparable) and traceable (i.e., published, cited, and consistent). Over three-quarters of the SLA data in TRY either lacked applicability or traceability, leaving only 22.9% of the original data usable compared with the 64.9% typically deemed usable by standard data cleaning protocols. The remaining usable data differed markedly from the original for many species, which led to altered interpretation of ecological analyses. Though the data we consider here make up only 4.5% of SLA data within TRY, similar issues of applicability and traceability likely apply to SLA data for other species as well as other commonly measured, uploaded, and downloaded plant traits. We end with suggested steps forward for global ecological databases, including suggestions for both uploaders to and curators of databases with the hope that, through addressing the issues raised here, we can increase data quality and integrity within the ecological community.}, } @article {pmid38273562, year = {2024}, author = {Ross, SRP and Friedman, NR and Dudley, KL and Yoshida, T and Yoshimura, M and Economo, EP and Armitage, DW and Donohue, I}, title = {Divergent ecological responses to typhoon disturbance revealed via landscape-scale acoustic monitoring.}, journal = {Global change biology}, volume = {30}, number = {1}, pages = {e17067}, doi = {10.1111/gcb.17067}, pmid = {38273562}, issn = {1365-2486}, support = {//Canon Foundation in Europe/ ; GOIPG/2018/3023//Irish Research Council/ ; //Okinawa Institute of Science and Technology Graduate University/ ; }, mesh = {Animals ; *Cyclonic Storms ; Ecosystem ; Climate Change ; Birds/physiology ; Acoustics ; }, abstract = {Climate change is increasing the frequency, intensity, and duration of extreme weather events across the globe. Understanding the capacity for ecological communities to withstand and recover from such events is critical. Typhoons are extreme weather events that are expected to broadly homogenize ecological dynamics through structural damage to vegetation and longer-term effects of salinization. Given their unpredictable nature, monitoring ecological responses to typhoons is challenging, particularly for mobile animals such as birds. Here, we report spatially variable ecological responses to typhoons across terrestrial landscapes. Using a high temporal resolution passive acoustic monitoring network across 24 sites on the subtropical island of Okinawa, Japan, we found that typhoons elicit divergent ecological responses among Okinawa's diverse terrestrial habitats, as indicated by increased spatial variability of biological sound production (biophony) and individual species detections. This suggests that soniferous communities are capable of a diversity of different responses to typhoons. That is, spatial insurance effects among local ecological communities provide resilience to typhoons at the landscape scale. Even though site-level typhoon impacts on soundscapes and bird detections were not particularly strong, monitoring at scale with high temporal resolution across a broad spatial extent nevertheless enabled detection of spatial heterogeneity in typhoon responses. Further, species-level responses mirrored those of acoustic indices, underscoring the utility of such indices for revealing insight into fundamental questions concerning disturbance and stability. Our findings demonstrate the significant potential of landscape-scale acoustic sensor networks to capture the understudied ecological impacts of unpredictable extreme weather events.}, } @article {pmid38273542, year = {2024}, author = {Zeuss, D and Bald, L and Gottwald, J and Becker, M and Bellafkir, H and Bendix, J and Bengel, P and Beumer, LT and Brandl, R and Brändle, M and Dahlke, S and Farwig, N and Freisleben, B and Friess, N and Heidrich, L and Heuer, S and Höchst, J and Holzmann, H and Lampe, P and Leberecht, M and Lindner, K and Masello, JF and Mielke Möglich, J and Mühling, M and Müller, T and Noskov, A and Opgenoorth, L and Peter, C and Quillfeldt, P and Rösner, S and Royauté, R and Mestre-Runge, C and Schabo, D and Schneider, D and Seeger, B and Shayle, E and Steinmetz, R and Tafo, P and Vogelbacher, M and Wöllauer, S and Younis, S and Zobel, J and Nauss, T}, title = {Nature 4.0: A networked sensor system for integrated biodiversity monitoring.}, journal = {Global change biology}, volume = {30}, number = {1}, pages = {e17056}, doi = {10.1111/gcb.17056}, pmid = {38273542}, issn = {1365-2486}, support = {519/03/04.001 - (0006)//Hessian state research programme for the development of scientific-economic excellence (LOEWE, Germany)/ ; }, mesh = {Animals ; *Ecosystem ; *Conservation of Natural Resources ; Biodiversity ; Plants ; }, abstract = {Ecosystem functions and services are severely threatened by unprecedented global loss in biodiversity. To counteract these trends, it is essential to develop systems to monitor changes in biodiversity for planning, evaluating, and implementing conservation and mitigation actions. However, the implementation of monitoring systems suffers from a trade-off between grain (i.e., the level of detail), extent (i.e., the number of study sites), and temporal repetition. Here, we present an applied and realized networked sensor system for integrated biodiversity monitoring in the Nature 4.0 project as a solution to these challenges, which considers plants and animals not only as targets of investigation, but also as parts of the modular sensor network by carrying sensors. Our networked sensor system consists of three main closely interlinked components with a modular structure: sensors, data transmission, and data storage, which are integrated into pipelines for automated biodiversity monitoring. We present our own real-world examples of applications, share our experiences in operating them, and provide our collected open data. Our flexible, low-cost, and open-source solutions can be applied for monitoring individual and multiple terrestrial plants and animals as well as their interactions. Ultimately, our system can also be applied to area-wide ecosystem mapping tasks, thereby providing an exemplary cost-efficient and powerful solution for biodiversity monitoring. Building upon our experiences in the Nature 4.0 project, we identified ten key challenges that need to be addressed to better understand and counteract the ongoing loss of biodiversity using networked sensor systems. To tackle these challenges, interdisciplinary collaboration, additional research, and practical solutions are necessary to enhance the capability and applicability of networked sensor systems for researchers and practitioners, ultimately further helping to ensure the sustainable management of ecosystems and the provision of ecosystem services.}, } @article {pmid38273499, year = {2024}, author = {Liang, C and Zhang, M and Wang, Z and Xiang, X and Gong, H and Wang, K and Liu, H}, title = {The strengthened impact of water availability at interannual and decadal time scales on vegetation GPP.}, journal = {Global change biology}, volume = {30}, number = {1}, pages = {e17138}, doi = {10.1111/gcb.17138}, pmid = {38273499}, issn = {1365-2486}, support = {164320H116//Priority Academic Program Development of Jiangsu Higher Education Institutions/ ; CAS-WX2021SF-0305//Special application demonstration project of network security and informatization of Chinese Academy of Sciences/ ; 41971382//National Natural Science Foundation of China/ ; 32271663//National Natural Science Foundation of China/ ; 41930652//National Natural Science Foundation of China/ ; U19A2051//National Natural Science Foundation of China/ ; U20A2048//National Natural Science Foundation of China/ ; KYCX22_1593//Postgraduate Research amp; Practice Innovation Program of Jiangsu Province/ ; KYCX23_1712//Postgraduate Research amp; Practice Innovation Program of Jiangsu Province/ ; }, mesh = {*Ecosystem ; *Water ; Forests ; Carbon Cycle ; Climate Change ; }, abstract = {Water availability (WA) is a key factor influencing the carbon cycle of terrestrial ecosystems under climate warming, but its effects on gross primary production (EWA-GPP) at multiple time scales are poorly understood. We used ensemble empirical mode decomposition (EEMD) and partial correlation analysis to assess the WA-GPP relationship (RWA-GPP) at different time scales, and geographically weighted regression (GWR) to analyze their temporal dynamics from 1982 to 2018 with multiple GPP datasets, including near-infrared radiance of vegetation GPP, FLUXCOM GPP, and eddy covariance-light-use efficiency GPP. We found that the 3- and 7-year time scales dominated global WA variability (61.18% and 11.95%), followed by the 17- and 40-year time scales (7.28% and 8.23%). The long-term trend also influenced 10.83% of the regions, mainly in humid areas. We found consistent spatiotemporal patterns of the EWA-GPP and RWA-GPP with different source products: In high-latitude regions, RWA-GPP changed from negative to positive as the time scale increased, while the opposite occurred in mid-low latitudes. Forests had weak RWA-GPP at all time scales, shrublands showed negative RWA-GPP at long time scales, and grassland (GL) showed a positive RWA-GPP at short time scales. Globally, the EWA-GPP , whether positive or negative, enhanced significantly at 3-, 7-, and 17-year time scales. For arid and humid zones, the semi-arid and sub-humid zones experienced a faster increase in the positive EWA-GPP , whereas the humid zones experienced a faster increase in the negative EWA-GPP . At the ecosystem types, the positive EWA-GPP at a 3-year time scale increased faster in GL, deciduous broadleaf forest, and savanna (SA), whereas the negative EWA-GPP at other time scales increased faster in evergreen needleleaf forest, woody savannas, and SA. Our study reveals the complex and dynamic EWA-GPP at multiple time scales, which provides a new perspective for understanding the responses of terrestrial ecosystems to climate change.}, } @article {pmid38272936, year = {2024}, author = {Gnacek, M and Quintero, L and Mavridou, I and Balaguer-Ballester, E and Kostoulas, T and Nduka, C and Seiss, E}, title = {AVDOS-VR: Affective Video Database with Physiological Signals and Continuous Ratings Collected Remotely in VR.}, journal = {Scientific data}, volume = {11}, number = {1}, pages = {132}, pmid = {38272936}, issn = {2052-4463}, support = {EP/L016540/1//RCUK | Engineering and Physical Sciences Research Council (EPSRC)/ ; }, abstract = {Investigating emotions relies on pre-validated stimuli to evaluate induced responses through subjective self-ratings and physiological changes. The creation of precise affect models necessitates extensive datasets. While datasets related to pictures, words, and sounds are abundant, those associated with videos are comparatively scarce. To overcome this challenge, we present the first virtual reality (VR) database with continuous self-ratings and physiological measures, including facial EMG. Videos were rated online using a head-mounted VR device (HMD) with attached emteqPRO mask and a cinema VR environment in remote home and laboratory settings with minimal setup requirements. This led to an affective video database with continuous valence and arousal self-rating measures and physiological responses (PPG, facial-EMG (7x), IMU). The AVDOS-VR database includes data from 37 participants who watched 30 randomly ordered videos (10 positive, neutral, and negative). Each 30-second video was assessed with two-minute relaxation between categories. Validation results suggest that remote data collection is ecologically valid, providing an effective strategy for future affective study designs. All data can be accessed via: www.gnacek.com/affective-video-database-online-study .}, } @article {pmid38272335, year = {2024}, author = {Chen, Y and Shi, Y and Liang, C and Min, Z and Deng, Q and Yu, R and Zhang, J and Chang, K and Chen, L and Yan, K and Wang, C and Tan, Y and Wang, X and Chen, J and Hua, Q}, title = {MicrobeTCM: A comprehensive platform for the interactions of microbiota and traditional Chinese medicine.}, journal = {Pharmacological research}, volume = {201}, number = {}, pages = {107080}, doi = {10.1016/j.phrs.2024.107080}, pmid = {38272335}, issn = {1096-1186}, mesh = {*Medicine, Chinese Traditional ; Medicine, Traditional ; *Microbiota ; Computational Biology ; Databases, Factual ; }, abstract = {Thanks to the advancements in bioinformatics, drugs, and other interventions that modulate microbes to treat diseases have been emerging continuously. In recent years, an increasing number of databases related to traditional Chinese medicine (TCM) or gut microbes have been established. However, a database combining the two has not yet been developed. To accelerate TCM research and address the traditional medicine and micro ecological system connection between short board, we have developed the most comprehensive micro-ecological database of TCM. This initiative includes the standardization of the following advantages: (1) A repeatable process achieved through the standardization of a retrieval strategy to identify literature. This involved identifying 419 experiment articles from PubMed and six authoritative databases; (2) High-quality data integration achieved through double-entry extraction of literature, mitigating uncertainties associated with natural language extraction; (3) Implementation of a similar strategy aiding in the prediction of mechanisms of action. Leveraging drug similarity, target entity similarity, and known drug-target entity association, our platform enables the prediction of the effects of a new herb or acupoint formulas using the existing data. In total, MicrobeTCM includes 171 diseases, 725 microbes, 1468 herb-formulas, 1032 herbs, 15780 chemical compositions, 35 acupoint-formulas, and 77 acupoints. For further exploration, please visit https://www.microbetcm.com.}, } @article {pmid38271874, year = {2024}, author = {Ren, XY and Zheng, YL and Liu, ZL and Duan, GL and Zhu, D and Ding, LJ}, title = {Exploring ecological effects of arsenic and cadmium combined exposure on cropland soil: from multilevel organisms to soil functioning by multi-omics coupled with high-throughput quantitative PCR.}, journal = {Journal of hazardous materials}, volume = {466}, number = {}, pages = {133567}, doi = {10.1016/j.jhazmat.2024.133567}, pmid = {38271874}, issn = {1873-3336}, mesh = {Cadmium/metabolism ; *Arsenic/toxicity/analysis ; Soil ; Multiomics ; *Microbiota/genetics ; *Environmental Pollutants/analysis ; Crops, Agricultural/metabolism ; Polymerase Chain Reaction ; *Soil Pollutants/metabolism ; }, abstract = {Arsenic (As) and cadmium (Cd) pose potential ecological threats to cropland soils; however, few studies have investigated their combined effects on multilevel organisms and soil functioning. Here, we used collembolans and soil microbiota as test organisms to examine their responses to soil As and Cd co-contamination at the gene, individual, and community levels, respectively, and further uncovered ecological relationships between pollutants, multilevel organisms, and soil functioning. At the gene level, collembolan transcriptome revealed that elevated As concentrations stimulated As-detoxifying genes AS3MT and GST, whereas the concurrent Cd restrained GST gene expression. At the individual level, collembolan reproduction was sensitive to pollutants while collembolan survival wasn't. At the community level, significant but inconsistent correlations were observed between the biodiversity of different soil keystone microbial clusters and soil As levels. Moreover, soil functioning related to nutrient (e.g., carbon, nitrogen, phosphorus, and sulfur) cycles was inhibited under As and Cd co-exposure only through the mediation of plant pathogens. Overall, these findings suggested multilevel bioindicators (i.e., AS3MT gene expression in collembolans, collembolan reproduction, and biodiversity of soil keystone microbial clusters) in cropland soils co-contaminated with As and Cd, thus improving the understanding of the ecotoxicological impact of heavy metal co-contamination on soil ecosystems.}, } @article {pmid38271521, year = {2024}, author = {Couce, A and Limdi, A and Magnan, M and Owen, SV and Herren, CM and Lenski, RE and Tenaillon, O and Baym, M}, title = {Changing fitness effects of mutations through long-term bacterial evolution.}, journal = {Science (New York, N.Y.)}, volume = {383}, number = {6681}, pages = {eadd1417}, doi = {10.1126/science.add1417}, pmid = {38271521}, issn = {1095-9203}, support = {R35 GM133700/GM/NIGMS NIH HHS/United States ; }, mesh = {Adaptation, Physiological/genetics ; *Escherichia coli/genetics ; *Evolution, Molecular ; *Genetic Fitness ; Mutagenesis, Insertional ; Mutation ; Selection, Genetic ; }, abstract = {The distribution of fitness effects of new mutations shapes evolution, but it is challenging to observe how it changes as organisms adapt. Using Escherichia coli lineages spanning 50,000 generations of evolution, we quantify the fitness effects of insertion mutations in every gene. Macroscopically, the fraction of deleterious mutations changed little over time whereas the beneficial tail declined sharply, approaching an exponential distribution. Microscopically, changes in individual gene essentiality and deleterious effects often occurred in parallel; altered essentiality is only partly explained by structural variation. The identity and effect sizes of beneficial mutations changed rapidly over time, but many targets of selection remained predictable because of the importance of loss-of-function mutations. Taken together, these results reveal the dynamic-but statistically predictable-nature of mutational fitness effects.}, } @article {pmid38269820, year = {2024}, author = {Andison, M}, title = {Digital Health Safety Matters: A Promising Practice Study into the Adoption of Patient Safety Guidelines in Australia.}, journal = {Studies in health technology and informatics}, volume = {310}, number = {}, pages = {334-338}, doi = {10.3233/SHTI230982}, pmid = {38269820}, issn = {1879-8365}, mesh = {Humans ; *Digital Health ; *Patient Safety ; Australia ; Artifacts ; Data Mining ; }, abstract = {A foundation for digitally enabling healthier living is the safe development and use of technology. The practice of digital health safety has emerged from patient harm attributed to failing technologies. The study aimed to investigate how to adopt and implement digital health safety guidelines at scale. Data was collected through an online survey, semi-structured interviews, focus groups, document review, and data mining of artefacts. The findings of this study capture the emerging practice from Australia in a way that offers insights into the problem of practice, patient safety practice, safety culture, and socio-technical factors. The research findings contribute to better understanding of the complexities of balancing digital innovation with patient safety. The four recommendations from the study and the provision of a logic model will support the audience to implement actions toward a safer digital health ecology.}, } @article {pmid38268612, year = {2023}, author = {Boyes, D and Holland, PWH and , and , and , and , and , and , }, title = {The genome sequence of the Muslin moth, Diaphora mendica (Clerck, 1759).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {257}, pmid = {38268612}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual male Diaphora mendica (the Muslin moth; Arthropoda; Insecta; Lepidoptera; Erebidae). The genome sequence is 748.7 megabases in span. Most of the assembly is scaffolded into 26 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.41 kilobases in length.}, } @article {pmid38263406, year = {2024}, author = {Ismaeel, A and Tai, APK and Santos, EG and Maraia, H and Aalto, I and Altman, J and Doležal, J and Lembrechts, JJ and Camargo, JL and Aalto, J and Sam, K and Avelino do Nascimento, LC and Kopecký, M and Svátek, M and Nunes, MH and Matula, R and Plichta, R and Abera, T and Maeda, EE}, title = {Patterns of tropical forest understory temperatures.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {549}, pmid = {38263406}, issn = {2041-1723}, support = {319905//Academy of Finland (Suomen Akatemia)/ ; 345472//Academy of Finland (Suomen Akatemia)/ ; }, mesh = {*Ecosystem ; Temperature ; *Forests ; Climate Change ; Computer Systems ; }, abstract = {Temperature is a fundamental driver of species distribution and ecosystem functioning. Yet, our knowledge of the microclimatic conditions experienced by organisms inside tropical forests remains limited. This is because ecological studies often rely on coarse-gridded temperature estimates representing the conditions at 2 m height in an open-air environment (i.e., macroclimate). In this study, we present a high-resolution pantropical estimate of near-ground (15 cm above the surface) temperatures inside forests. We quantify diurnal and seasonal variability, thus revealing both spatial and temporal microclimate patterns. We find that on average, understory near-ground temperatures are 1.6 °C cooler than the open-air temperatures. The diurnal temperature range is on average 1.7 °C lower inside the forests, in comparison to open-air conditions. More importantly, we demonstrate a substantial spatial variability in the microclimate characteristics of tropical forests. This variability is regulated by a combination of large-scale climate conditions, vegetation structure and topography, and hence could not be captured by existing macroclimate grids. Our results thus contribute to quantifying the actual thermal ranges experienced by organisms inside tropical forests and provide new insights into how these limits may be affected by climate change and ecosystem disturbances.}, } @article {pmid38262510, year = {2024}, author = {Sajjad, W and Ilahi, N and Haq, A and Shang, Z and Nabi, G and Rafiq, M and Bahadur, A and Banerjee, A and Kang, S}, title = {Bacteria populating freshly appeared supraglacial lake possess metals and antibiotic-resistant genes.}, journal = {Environmental research}, volume = {247}, number = {}, pages = {118288}, doi = {10.1016/j.envres.2024.118288}, pmid = {38262510}, issn = {1096-0953}, mesh = {*Anti-Bacterial Agents/pharmacology ; *Bacteria/genetics ; Genes, Bacterial ; Drug Resistance, Microbial/genetics ; Lakes/microbiology ; Metals ; }, abstract = {Antibiotic resistance (AR) has been extensively studied in natural habitats and clinical applications. AR is mainly reported with the use and misuse of antibiotics; however, little is known about its presence in antibiotic-free remote supraglacial lake environments. This study evaluated bacterial strains isolated from supraglacial lake debris and meltwater in Dook Pal Glacier, northern Pakistan, for antibiotic-resistant genes (ARGs) and metal-tolerant genes (MTGs) using conventional PCR. Several distinct ARGs were reported in the bacterial strains isolated from lake debris (92.5%) and meltwater (100%). In lake debris, 57.5% of isolates harbored the blaTEM gene, whereas 58.3% of isolates in meltwater possessed blaTEM and qnrA each. Among the ARGs, qnrA was dominant in debris isolates (19%), whereas in meltwater isolates, qnrA (15.2%) and blaTEM (15.2%) were dominant. ARGs were widely distributed among the bacterial isolates and different bacteria shared similar types of ARGs. Relatively greater number of ARGs were reported in Gram-negative bacterial strains. In addition, 92.5% of bacterial isolates from lake debris and 83.3% of isolates from meltwater harbored MTGs. Gene copA was dominant in meltwater isolates (50%), whereas czcA was greater in debris bacterial isolates (45%). Among the MTGs, czcA (18.75%) was dominant in debris strains, whereas copA (26.0%) was greater in meltwater isolates. This presents the co-occurrence and co-selection of MTGs and ARGs in a freshly appeared supraglacial lake. The same ARGs and MTGs were present in different bacteria, exhibiting horizontal gene transfer (HGT). Both positive and negative correlations were determined between ARGs and MTGs. The research provides insights into the existence of MTGs and ARGs in bacterial strains isolated from remote supraglacial lake environments, signifying the need for a more detailed study of bacteria harboring ARGs and MTGs in supraglacial lakes.}, } @article {pmid38259099, year = {2024}, author = {Caesar, L and Rice, DW and McAfee, A and Underwood, R and Ganote, C and Tarpy, DR and Foster, LJ and Newton, ILG}, title = {Metagenomic analysis of the honey bee queen microbiome reveals low bacterial diversity and Caudoviricetes phages.}, journal = {mSystems}, volume = {9}, number = {2}, pages = {e0118223}, pmid = {38259099}, issn = {2379-5077}, support = {2005306//National Science Foundation (NSF)/ ; 2022049//National Science Foundation (NSF)/ ; //L'Oreal USA (L'Oréal)/ ; //Project Apis m. (PAm)/ ; 2017-51300-26814//U.S. Department of Agriculture (USDA)/ ; }, mesh = {Bees ; Female ; Animals ; *Bacteriophages/genetics ; *Microbiota/genetics ; Reproduction ; Metagenome ; }, abstract = {In eusocial insects, the health of the queens-the colony founders and sole reproductive females-is a primary determinant for colony success. Queen failure in the honey bee Apis mellifera, for example, is a major concern of beekeepers who annually suffer colony losses, necessitating a greater knowledge of queen health. Several studies on the microbiome of honey bees have characterized its diversity and shown its importance for the health of worker bees, the female non-reproductive caste. However, the microbiome of workers differs from that of queens, which, in comparison, is still poorly studied. Thus, direct investigations of the queen microbiome are required to understand colony-level microbiome assembly, functional roles, and evolution. Here, we used metagenomics to comprehensively characterize the honey bee queen microbiome. Comparing samples from different geographic locations and breeder sources, we show that the microbiome of queens is mostly shaped by the environment experienced since early life and is predicted to play roles in the breakdown of the diet and protection from pathogens and xenobiotics. We also reveal that the microbiome of queens comprises only four candidate core bacterial species, Apilactobacillus kunkeei, Lactobacillus apis, Bombella apis, and Commensalibacter sp. Interestingly, in addition to bacteria, we show that bacteriophages infect the queen microbiome, for which Lactobacillaceae are predicted to be the main reservoirs. Together, our results provide the basis to understand the honey bee colony microbiome assemblage, can guide improvements in queen-rearing processes, and highlight the importance of considering bacteriophages for queen microbiome health and microbiome homeostasis in eusocial insects.IMPORTANCEThe queen caste plays a central role in colony success in eusocial insects, as queens lay eggs and regulate colony behavior and development. Queen failure can cause colonies to collapse, which is one of the major concerns of beekeepers. Thus, understanding the biology behind the queen's health is a pressing issue. Previous studies have shown that the bee microbiome plays an important role in worker bee health, but little is known about the queen microbiome and its function in vivo. Here, we characterized the queen microbiome, identifying for the first time the present species and their putative functions. We show that the queen microbiome has predicted nutritional and protective roles in queen association and comprises only four consistently present bacterial species. Additionally, we bring to attention the spread of phages in the queen microbiome, which increased in abundance in failing queens and may impact the fate of the colony.}, } @article {pmid38259095, year = {2024}, author = {Wang, C and Ma, A and Li, Y and McNutt, ME and Zhang, S and Zhu, J and Hoyd, R and Wheeler, CE and Robinson, LA and Chan, CHF and Zakharia, Y and Dodd, RD and Ulrich, CM and Hardikar, S and Churchman, ML and Tarhini, AA and Singer, EA and Ikeguchi, AP and McCarter, MD and Denko, N and Tinoco, G and Husain, M and Jin, N and Osman, AEG and Eljilany, I and Tan, AC and Coleman, SS and Denko, L and Riedlinger, G and Schneider, BP and Spakowicz, D and Ma, Q and , }, title = {A Bioinformatics Tool for Identifying Intratumoral Microbes from the ORIEN Dataset.}, journal = {Cancer research communications}, volume = {4}, number = {2}, pages = {293-302}, pmid = {38259095}, issn = {2767-9764}, support = {UL1 TR000090/TR/NCATS NIH HHS/United States ; U01 CA206110/CA/NCI NIH HHS/United States ; P30 CA016058/CA/NCI NIH HHS/United States ; AS1695/AS/Autism Speaks/United States ; P30 CA042014/CA/NCI NIH HHS/United States ; }, mesh = {Humans ; Phylogeny ; *Microbiota/genetics ; Computational Biology ; High-Throughput Nucleotide Sequencing ; }, abstract = {UNLABELLED: Evidence supports significant interactions among microbes, immune cells, and tumor cells in at least 10%-20% of human cancers, emphasizing the importance of further investigating these complex relationships. However, the implications and significance of tumor-related microbes remain largely unknown. Studies have demonstrated the critical roles of host microbes in cancer prevention and treatment responses. Understanding interactions between host microbes and cancer can drive cancer diagnosis and microbial therapeutics (bugs as drugs). Computational identification of cancer-specific microbes and their associations is still challenging due to the high dimensionality and high sparsity of intratumoral microbiome data, which requires large datasets containing sufficient event observations to identify relationships, and the interactions within microbial communities, the heterogeneity in microbial composition, and other confounding effects that can lead to spurious associations. To solve these issues, we present a bioinformatics tool, microbial graph attention (MEGA), to identify the microbes most strongly associated with 12 cancer types. We demonstrate its utility on a dataset from a consortium of nine cancer centers in the Oncology Research Information Exchange Network. This package has three unique features: species-sample relations are represented in a heterogeneous graph and learned by a graph attention network; it incorporates metabolic and phylogenetic information to reflect intricate relationships within microbial communities; and it provides multiple functionalities for association interpretations and visualizations. We analyzed 2,704 tumor RNA sequencing samples and MEGA interpreted the tissue-resident microbial signatures of each of 12 cancer types. MEGA can effectively identify cancer-associated microbial signatures and refine their interactions with tumors.

SIGNIFICANCE: Studying the tumor microbiome in high-throughput sequencing data is challenging because of the extremely sparse data matrices, heterogeneity, and high likelihood of contamination. We present a new deep learning tool, MEGA, to refine the organisms that interact with tumors.}, } @article {pmid38258939, year = {2024}, author = {Mori, K and Odagami, K and Inagaki, M and Moriya, K and Fujiwara, H and Eguchi, H}, title = {Work engagement among older workers: a systematic review.}, journal = {Journal of occupational health}, volume = {66}, number = {1}, pages = {}, doi = {10.1093/joccuh/uiad008}, pmid = {38258939}, issn = {1348-9585}, mesh = {Humans ; Adult ; Middle Aged ; *Work Engagement ; *Aging ; Databases, Factual ; Employment ; Europe ; Observational Studies as Topic ; }, abstract = {OBJECTIVES: Given current labor force conditions, including population aging, keeping older workers engaged in work and motivated is important. Aging may alter the effects that psychological and environmental factors have on work engagement. We conducted a systematic review to understand the features of work engagement among older workers.

METHODS: A systematic search was conducted in July 2022 using 4 databases. The review included relevant articles that focused on participants aged 40 years and older.

RESULTS: Fifty articles were selected for our review, which were grouped into 5 categories: (1) studies examining the relationship between chronological age and work engagement, (2) studies investigating the moderating effects of age on the relationship between job-related psychological factors and work environment factors and work engagement, (3) studies comparing the relationship of job-related psychological factors and work environment factors with work engagement across different age groups, (4) studies exploring the relationship between work engagement and retirement intentions or continued employment beyond retirement age, and (5) other studies discussing work engagement in the context of older workers. Most articles focused on workers in Europe and the United States and used observational study designs.

CONCLUSIONS: Work engagement increases with age, and is mainly mediated by increased emotional regulation. In addition, age moderates the relationships between various job-related psychological and work-environmental factors and work engagement. Work engagement is associated with working beyond retirement age. Organizations should understand the characteristics of work engagement among older workers and make age-conscious efforts to support them in adapting to social changes.}, } @article {pmid38258936, year = {2024}, author = {Tani, N and Fujihara, H and Ishii, K and Kamakura, Y and Tsunemi, M and Yamaguchi, C and Eguchi, H and Imamura, K and Kanamori, S and Kojimahara, N and Ebara, T}, title = {What digital health technology types are used in mental health prevention and intervention? Review of systematic reviews for systematization of technologies.}, journal = {Journal of occupational health}, volume = {66}, number = {1}, pages = {}, pmid = {38258936}, issn = {1348-9585}, support = {JP22rea522006//Japan Agency for Medical Research and Development (AMED)/ ; }, mesh = {Humans ; *Digital Health ; *Mental Health ; Systematic Reviews as Topic ; Technology ; Avatar ; }, abstract = {Digital health technology has been widely applied to mental health interventions worldwide. Using digital phenotyping to identify an individual's mental health status has become particularly important. However, many technologies other than digital phenotyping are expected to become more prevalent in the future. The systematization of these technologies is necessary to accurately identify trends in mental health interventions. However, no consensus on the technical classification of digital health technologies for mental health interventions has emerged. Thus, we conducted a review of systematic review articles on the application of digital health technologies in mental health while attempting to systematize the technology using the Delphi method. To identify technologies used in digital phenotyping and other digital technologies, we included 4 systematic review articles that met the inclusion criteria, and an additional 8 review articles, using a snowballing approach, were incorporated into the comprehensive review. Based on the review results, experts from various disciplines participated in the Delphi process and agreed on the following 11 technical categories for mental health interventions: heart rate estimation, exercise or physical activity, sleep estimation, contactless heart rate/pulse wave estimation, voice and emotion analysis, self-care/cognitive behavioral therapy/mindfulness, dietary management, psychological safety, communication robots, avatar/metaverse devices, and brain wave devices. The categories we defined intentionally included technologies that are expected to become widely used in the future. Therefore, we believe these 11 categories are socially implementable and useful for mental health interventions.}, } @article {pmid38258809, year = {2024}, author = {Viera, A and Ondrusek, A and Tengatenga, C and McBurney, E and Lauckner, J and Tran, E and Muilenburg, J and Kershaw, T and Lauckner, C}, title = {A Qualitative Exploration of Attitudes Toward Global Positioning System Tracking and Ecological Momentary Assessment Among Individuals in Substance Use Treatment.}, journal = {Substance use & addiction journal}, volume = {45}, number = {2}, pages = {260-267}, doi = {10.1177/29767342231218514}, pmid = {38258809}, issn = {2976-7350}, mesh = {Humans ; *Ecological Momentary Assessment ; Geographic Information Systems ; *Substance-Related Disorders ; Craving ; Georgia ; }, abstract = {BACKGROUND: The use of tracking technology in substance use research can uncover the role of contextual factors, such as social networks and environmental cues, in triggering cravings and precipitating return to use. Few studies have explored the opinions of individuals in substance use treatment related to tracking technology.

METHODS: We conducted 30 semi-structured interviews with individuals in substance use treatment facilities in Connecticut and Georgia. Interviews were not limited to individuals with any specific substance use disorder. Interviewers described a hypothetical study involving ecological momentary assessment and global positioning system tracking to examine place-based predictors of substance use. Participants were invited to share reactions to this description. We used thematic analysis to identify themes in participant perceptions of this hypothetical research study.

RESULTS: Most participants shared positive opinions about study participation and expressed little to no concern about the tracking components. Participant concerns focused on the security of their information and the potential burden of responding to study questions. Participants largely understood the importance of study participation for promoting greater understanding of substance use and identified potential therapeutic effects of study participation on their own recovery.

CONCLUSIONS: Individuals in substance use treatment expressed little concern with research studies or interventions incorporating mobile-tracking elements. Future studies should explore the responsible use of tracking elements in recovery support interventions.}, } @article {pmid38257567, year = {2024}, author = {Kraft, R and Reichert, M and Pryss, R}, title = {Mobile Crowdsensing in Ecological Momentary Assessment mHealth Studies: A Systematic Review and Analysis.}, journal = {Sensors (Basel, Switzerland)}, volume = {24}, number = {2}, pages = {}, pmid = {38257567}, issn = {1424-8220}, mesh = {Humans ; *Ecological Momentary Assessment ; Computers, Handheld ; Data Collection ; Databases, Factual ; *Telemedicine ; }, abstract = {As mobile devices have become a central part of our daily lives, they are also becoming increasingly important in research. In the medical context, for example, smartphones are used to collect ecologically valid and longitudinal data using Ecological Momentary Assessment (EMA), which is mostly implemented through questionnaires delivered via smart notifications. This type of data collection is intended to capture a patient's condition on a moment-to-moment and longer-term basis. To collect more objective and contextual data and to understand patients even better, researchers can not only use patients' input via EMA, but also use sensors as part of the Mobile Crowdsensing (MCS) approach. In this paper, we examine how researchers have embraced the topic of MCS in the context of EMA through a systematic literature review. This PRISMA-guided review is based on the databases PubMed, Web of Science, and EBSCOhost. It is shown through the results that both EMA research in general and the use of sensors in EMA research are steadily increasing. In addition, most of the studies reviewed used mobile apps to deliver EMA to participants, used a fixed-time prompting strategy, and used signal-contingent or interval-contingent self-assessment as sampling/assessment strategies. The most commonly used sensors in EMA studies are the accelerometer and GPS. In most studies, these sensors are used for simple data collection, but sensor data are also commonly used to verify study participant responses and, less commonly, to trigger EMA prompts. Security and privacy aspects are addressed in only a subset of mHealth EMA publications. Moreover, we found that EMA adherence was negatively correlated with the total number of prompts and was higher in studies using a microinteraction-based EMA (μEMA) approach as well as in studies utilizing sensors. Overall, we envision that the potential of the technological capabilities of smartphones and sensors could be better exploited in future, more automated approaches.}, } @article {pmid38256741, year = {2024}, author = {Hanazaki, N}, title = {Brazilian Environment and Plants as Seen by Japanese Eyes Two Hundred and Twenty Years Ago.}, journal = {Plants (Basel, Switzerland)}, volume = {13}, number = {2}, pages = {}, pmid = {38256741}, issn = {2223-7747}, support = {305789/2022-1//National Council for Scientific and Technological Development/ ; }, abstract = {In 2023, the Japanese migration to Brazil completed 115 years. However, the first time Japanese people arrived in Brazil and left a testimony of their experience was about two centuries ago. Their reports were registered in a historical document, handwritten during the Edo period when Japan was adopting a closed-door policy. The episode of their visit to Brazil is only a small part of the odyssey of these four Japanese sailors who departed from Ishinomiya to Tokyo at the end of the 18th century, but unexpectedly traveled around the globe. After a storm, they were adrift for six months until shipwrecking on the Aleutian Islands; from the Russian Aleutian Islands, they crossed the whole of Russia and boarded, in Saint Petersburg, on the first Russian expedition to circumnavigate the world. Their only stop in South America was at Santa Catarina Island, southern Brazil, and this is the first analysis of this episode from an ethnobiological perspective. Their reports described both the forest environment and the plants they observed and included at least 23 taxa of plants, mostly cultivated. These descriptions of plants and the environment are in contrast with other reports from the same period and to the current environment found in Santa Catarina Island, inspiring reflections on the construction of Brazil's image in Japan before the 20th century.}, } @article {pmid38256002, year = {2024}, author = {Han, S and Han, X and Qi, C and Guo, F and Yin, J and Liu, Y and Zhu, Y}, title = {Genome-Wide Identification of DUF668 Gene Family and Expression Analysis under F. solani, Chilling, and Waterlogging Stresses in Zingiber officinale.}, journal = {International journal of molecular sciences}, volume = {25}, number = {2}, pages = {}, pmid = {38256002}, issn = {1422-0067}, support = {CARS-24-G-17//Fengling Guo/ ; }, mesh = {*Zingiber officinale/genetics ; Amino Acid Sequence ; Cold-Shock Response/genetics ; Computational Biology ; *Fusariosis ; *MicroRNAs/genetics ; }, abstract = {The domains of unknown function (DUF) superfamilies contain proteins with conserved amino acid sequences without known functions. Among them, DUF668 was indicated widely involving the stress response of plants. However, understanding ZoDUF668 is still lacking. Here, 12 ZoDUF668 genes were identified in ginger by the bioinformatics method and unevenly distributed on six chromosomes. Conserved domain analysis showed that members of the same subfamily had similar conserved motifs and gene structures. The promoter region of ZoDUF668s contained the light, plant hormone and stress-responsive elements. The prediction of miRNA targeting relationship showed that nine ginger miRNAs targeted four ZoDUF668 genes through cleavage. The expression patterns of 12 ZoDUF668 genes under biotic and abiotic stress were analyzed using RT-qPCR. The results showed that the expression of seven ZoDUF668 genes was significantly downregulated under Fusarium solani infection, six ZoDUF668 genes were upregulated under cold stress, and five ZoDUF668 genes were upregulated under waterlogging stress. These results indicate that the ZoDUF668 gene has different expression patterns under different stress conditions. This study provides excellent candidate genes and provides a reference for stress-resistance research in ginger.}, } @article {pmid38254931, year = {2023}, author = {Yang, D and Zhang, X and Cao, M and Yin, L and Gao, A and An, K and Gao, S and Guo, S and Yin, H}, title = {Genome-Wide Identification, Expression and Interaction Analyses of PP2C Family Genes in Chenopodium quinoa.}, journal = {Genes}, volume = {15}, number = {1}, pages = {}, pmid = {38254931}, issn = {2073-4425}, support = {2022SZX17//Science & Technology Specific Projects in Agricultural High-tech Industrial Demonstration Area of the Yellow River Delta/ ; 2019BHLC001//the "Bohai Sea Granary" Science and Technology Demonstration Project of Shandong Provincial/ ; }, mesh = {Humans ; *Chenopodium quinoa/genetics ; Genome-Wide Association Study ; Phylogeny ; Biological Evolution ; Data Interpretation, Statistical ; Phosphoric Monoester Hydrolases ; }, abstract = {Plant protein phosphatase 2Cs (PP2Cs) function as inhibitors in protein kinase cascades involved in various processes and are crucial participants in both plant development and signaling pathways activated by abiotic stress. In this study, a genome-wide study was conducted on the CqPP2C gene family. A total of putative 117 CqPP2C genes were identified. Comprehensive analyses of physicochemical properties, chromosome localization and subcellular localization were conducted. According to phylogenetic analysis, CqPP2Cs were divided into 13 subfamilies. CqPP2Cs in the same subfamily had similar gene structures, and conserved motifs and all the CqPP2C proteins had the type 2C phosphatase domains. The expansion of CqPP2Cs through gene duplication was primarily driven by segmental duplication, and all duplicated CqPP2Cs underwent evolutionary changes guided by purifying selection. The expression of CqPP2Cs in various tissues under different abiotic stresses was analyzed using RNA-seq data. The findings indicated that CqPP2C genes played a role in regulating both the developmental processes and stress responses of quinoa. Real-time quantitative reverse transcription PCR (qRT-PCR) analysis of six CqPP2C genes in subfamily A revealed that they were up-regulated or down-regulated under salt and drought treatments. Furthermore, the results of yeast two-hybrid assays revealed that subfamily A CqPP2Cs interacted not only with subclass III CqSnRK2s but also with subclass II CqSnRK2s. Subfamily A CqPP2Cs could interact with CqSnRK2s in different combinations and intensities in a variety of biological processes and biological threats. Overall, our results will be useful for understanding the functions of CqPP2C in regulating ABA signals and responding to abiotic stress.}, } @article {pmid38251877, year = {2024}, author = {Schloss, PD}, title = {Rarefaction is currently the best approach to control for uneven sequencing effort in amplicon sequence analyses.}, journal = {mSphere}, volume = {9}, number = {2}, pages = {e0035423}, pmid = {38251877}, issn = {2379-5042}, support = {R01 CA215574/CA/NCI NIH HHS/United States ; U01 CA264071/CA/NCI NIH HHS/United States ; U01 AI124255/AI/NIAID NIH HHS/United States ; P30 DK034933/DK/NIDDK NIH HHS/United States ; }, mesh = {RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; High-Throughput Nucleotide Sequencing/methods ; Sequence Analysis, DNA/methods ; Computational Biology/methods ; }, abstract = {UNLABELLED: Considering it is common to find as much as 100-fold variation in the number of 16S rRNA gene sequences across samples in a study, researchers need to control for the effect of uneven sequencing effort. How to do this has become a contentious question. Some have argued that rarefying or rarefaction is "inadmissible" because it omits valid data. A number of alternative approaches have been developed to normalize and rescale the data that purport to be invariant to the number of observations. I generated community distributions based on 12 published data sets where I was able to assess the ability of multiple methods to control for uneven sequencing effort. Rarefaction was the only method that could control for variation in uneven sequencing effort when measuring commonly used alpha and beta diversity metrics. Next, I compared the false detection rate and power to detect true differences between simulated communities with a known effect size using various alpha and beta diversity metrics. Although all methods of controlling for uneven sequencing effort had an acceptable false detection rate when samples were randomly assigned to two treatment groups, rarefaction was consistently able to control for differences in sequencing effort when sequencing depth was confounded with treatment group. Finally, the statistical power to detect differences in alpha and beta diversity metrics was consistently the highest when using rarefaction. These simulations underscore the importance of using rarefaction to normalize the number of sequences across samples in amplicon sequencing analyses.

IMPORTANCE: Sequencing 16S rRNA gene fragments has become a fundamental tool for understanding the diversity of microbial communities and the factors that affect their diversity. Due to technical challenges, it is common to observe wide variation in the number of sequences that are collected from different samples within the same study. However, the diversity metrics used by microbial ecologists are sensitive to differences in sequencing effort. Therefore, tools are needed to control for the uneven levels of sequencing. This simulation-based analysis shows that despite a longstanding controversy, rarefaction is the most robust approach to control for uneven sequencing effort. The controversy started because of confusion over the definition of rarefaction and violation of assumptions that are made by methods that have been borrowed from other fields. Microbial ecologists should use rarefaction.}, } @article {pmid38250723, year = {2024}, author = {Abdullah, NI and Elias, NA and Ohte, N and Vincenot, C}, title = {Resource partitioning among bat species in Peninsular Malaysia rice fields.}, journal = {PeerJ}, volume = {12}, number = {}, pages = {e16657}, pmid = {38250723}, issn = {2167-8359}, mesh = {Humans ; Pregnancy ; Animals ; Female ; Male ; *Oryza ; *Chiroptera ; Lactation ; Malaysia ; *Coleoptera ; *Lepidoptera ; }, abstract = {Resource partitioning among tropical bats in agricultural areas of Peninsular Malaysia remains unclear. This study was conducted to evaluate resource partitioning among bats by examining their fecal samples. The main bat species sampled included: Rhinolophus coelophyllus, Rhinolophus malayanus, Rhinolophus pusillus, Rhinolophus refulgens, Taphozous melanopogon and Hipposideros larvatus. Two harp traps were set at different elevations on a hilltop (Gunung Keriang) and two high nets were used in neighboring rice fields at three sites, for three consecutive nights per sampling from April 2021 to February 2022. A total of 301 bats and 1,505 pellets were analyzed using a conventional approach which examined the fecal sample under the microscope. All of the bat species within the study had insects from the order Coleoptera, Lepidoptera, Diptera and Hemiptera in their diet. Larger bats exhibited a greater variety of prey consumption. Male individuals were observed to be generalists while female individuals were specialists, particularly during pregnancy and lactating reproductive stages. Bat species and insect order had a significant impact on the percentage fragment frequency of the insects consumed. Rhinolophus coelophyllus specialized in feeding on Coleoptera and Diptera, H. larvatus fed on Coleoptera, R. malayanus fed on Hemiptera, R. pusillus and T. melanopogon fed on Lepidoptera. Future molecular analysis can be carried out to further identify the insect pests consumed by these bats up to species level. These findings enhance our understanding of bats' ecological roles in agricultural landscapes and contribute to conservation and pest management strategies.}, } @article {pmid38249959, year = {2023}, author = {Blaxter, ML and Spurgeon, D and Kille, P and , and , and , and , }, title = {The genome sequence of the common earthworm, Lumbricus terrestris (Linnaeus, 1758).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {500}, pmid = {38249959}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual Lumbricus terrestris (the common earthworm; Annelida; Clitellata; Haplotaxida; Lumbricidae). The genome sequence is 1,056.5 megabases in span. Most of the assembly is scaffolded into 18 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 15.93 kilobases in length.}, } @article {pmid38249957, year = {2023}, author = {Boyes, D and Eagles, M and Holland, PWH and , and , and , and , and , }, title = {The genome sequence of the Willow Beauty, Peribatodes rhomboidaria (Denis & Schiffermüller, 1775).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {233}, pmid = {38249957}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual male Peribatodes rhomboidaria (the Willow Beauty; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 499.7 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.7 kilobases in length. Gene annotation of this assembly on Ensembl identified 18,486 protein coding genes.}, } @article {pmid38248287, year = {2024}, author = {Sokołowska, B}, title = {Being in Virtual Reality and Its Influence on Brain Health-An Overview of Benefits, Limitations and Prospects.}, journal = {Brain sciences}, volume = {14}, number = {1}, pages = {}, pmid = {38248287}, issn = {2076-3425}, abstract = {BACKGROUND: Dynamic technological development and its enormous impact on modern societies are posing new challenges for 21st-century neuroscience. A special place is occupied by technologies based on virtual reality (VR). VR tools have already played a significant role in both basic and clinical neuroscience due to their high accuracy, sensitivity and specificity and, above all, high ecological value.

OBJECTIVE: Being in a digital world affects the functioning of the body as a whole and its individual systems. The data obtained so far, both from experimental and modeling studies, as well as (clinical) observations, indicate their great and promising potential, but apart from the benefits, there are also losses and negative consequences for users.

METHODS: This review was conducted according to the PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) framework across electronic databases (such as Web of Science Core Collection; PubMed; and Scopus, Taylor & Francis Online and Wiley Online Library) to identify beneficial effects and applications, as well as adverse impacts, especially on brain health in human neuroscience.

RESULTS: More than half of these articles were published within the last five years and represent state-of-the-art approaches and results (e.g., 54.7% in Web of Sciences and 63.4% in PubMed), with review papers accounting for approximately 16%. The results show that in addition to proposed novel devices and systems, various methods or procedures for testing, validation and standardization are presented (about 1% of articles). Also included are virtual developers and experts, (bio)(neuro)informatics specialists, neuroscientists and medical professionals.

CONCLUSIONS: VR environments allow for expanding the field of research on perception and cognitive and motor imagery, both in healthy and patient populations. In this context, research on neuroplasticity phenomena, including mirror neuron networks and the effects of applied virtual (mirror) tasks and training, is of interest in virtual prevention and neurogeriatrics, especially in neurotherapy and neurorehabilitation in basic/clinical and digital neuroscience.}, } @article {pmid38247366, year = {2024}, author = {Erickson, BA and Griffith, JW and Wensheng, G and Mengying, Y and Herman, T and Bradley, CS and Quentin Clemens, J and Farrar, JT and Gupta, P and Kreder, KJ and Henry Lai, H and Naliboff, BD and Newman, DK and Rodriguez, LV and Spitznagle, T and Sutcliffe, S and Sutherland, SE and Taple, BJ and Richard Landis, J}, title = {Ecological momentary assessment of pelvic pain and urinary urgency variability in urologic chronic pelvic pain syndrome and their association with illness impact and quality of life: Findings from the multidisciplinary approach to the study of chronic pelvic pain symptom patterns study.}, journal = {Neurourology and urodynamics}, volume = {43}, number = {4}, pages = {893-901}, pmid = {38247366}, issn = {1520-6777}, support = {U01 DK082345/DK/NIDDK NIH HHS/United States ; U01 DK082315/DK/NIDDK NIH HHS/United States ; U01 DK082344/DK/NIDDK NIH HHS/United States ; U01 DK082333/DK/NIDDK NIH HHS/United States ; R01 DK117208/DK/NIDDK NIH HHS/United States ; U24 DK082333/DK/NIDDK NIH HHS/United States ; U01 DK082325/DK/NIDDK NIH HHS/United States ; U01 DK082342/DK/NIDDK NIH HHS/United States ; }, mesh = {Humans ; Female ; Male ; *Quality of Life ; Ecological Momentary Assessment ; *Chronic Pain/diagnosis ; Pelvic Pain/diagnosis ; Pain Measurement ; }, abstract = {PURPOSE: This study tested the hypothesis that ecological momentary assessment (EMA) of pelvic pain (PP) and urinary urgency (UU) would reveal unique Urologic Chronic Pelvic Pain Syndrome (UCPPS) phenotypes that would be associated with disease specific quality of life (QOL) and illness impact metrics (IIM).

MATERIALS AND METHODS: A previously validated smart phone app (M-app) was provided to willing Multidisciplinary Approach to the Study of Chronic Pelvic Pain (MAPP) participants. M-app notifications were sent 4-times daily for 14 days inquiring about PP and UU severity. A clustering algorithm that accounted for variance placed participants into PP and UU variability? clusters. Associations between clusters and QOL and IIM were then determined.

RESULTS: A total of 204 participants enrolled in the M-app study (64% female). M-app compliance was high (median 63% of surveys). Cluster analysis revealed k = 3 (high, low, none) PP clusters and k = 2 (high, low) UU clusters. When adjusting for baseline pain severity, high PP variability, but not UU variability, was strongly associated with QOL and IIM; specifically worse mood, worse sleep and higher anxiety. UU and PP clusters were associated with each other (p < 0.0001), but a large percentage (33%) of patients with high PP variability had low UU variability.

CONCLUSIONS: PP variability is an independent predictor of worse QOL and more severe IIM in UCPPS participants after controlling for baseline pain severity and UU. These findings suggest alternative pain indices, such as pain variability and unpredictability, may be useful adjuncts to traditional measures of worst and average pain when assessing UCPPS treatment responses.}, } @article {pmid38246154, year = {2024}, author = {McConnell, RJ and Kamysh, O and O'Kane, PL and Greenebaum, E and Rozhko, AV and Yauseyenka, VV and Minenko, VF and Drozdovitch, V and Yarets, Y and Kukhta, T and Mabuchi, K and Little, MP and Cahoon, EK and Zablotska, LB}, title = {Radiation Dose Does Not Affect the Predictive Value of Thyroid Biopsy for Diagnosing Papillary Thyroid Cancer in a Belarusian Cohort Exposed to Chernobyl Fallout.}, journal = {Acta cytologica}, volume = {68}, number = {1}, pages = {34-44}, pmid = {38246154}, issn = {1938-2650}, support = {N01CP21178/CP/NCI NIH HHS/United States ; ZIA CP010132/ImNIH/Intramural NIH HHS/United States ; }, mesh = {Adolescent ; Child ; Humans ; Biopsy ; *Carcinoma, Papillary/pathology ; *Chernobyl Nuclear Accident ; *Eastern European People ; Radiation Dosage ; Thyroid Cancer, Papillary/diagnosis ; *Thyroid Neoplasms/diagnosis/epidemiology/pathology ; Adult ; }, abstract = {INTRODUCTION: The Chernobyl nuclear accident exposed residents of contaminated territories to substantial quantities of radioiodines and was followed by an increase in thyroid cancer, primarily papillary thyroid cancer (PTC), among exposed children and adolescents. Although thyroid biopsy is an essential component of screening programs following accidental exposure to radioiodines, it is unknown whether the predictive value of biopsy is affected by different levels of environmental exposure.

METHODS: A cohort of 11,732 Belarusians aged ≤18 years at the time of the Chernobyl accident with individual thyroid radiation dose estimates was screened at least once 11-22 years later. Paired cytologic conclusions and histopathologic diagnoses were possible for 258 thyroid nodules from 238 cohort members. Cytologic conclusions were divided into five reporting categories, with all follicular lesion aspirates combined into a single indeterminate category. Standard performance indicators, risk of malignancy (ROM), and odds ratios for a correct cytologic conclusion were calculated, both overall and according to quintile of thyroid radiation dose.

RESULTS: The arithmetic mean thyroid dose estimate for the study group was 1.73 Gy (range: 0.00-23.64 Gy). The final histopathologic diagnosis was cancer for 136 of 258 biopsies (52.7%; 135 papillary and 1 follicular). The overall ROM was 96.7% for cytologies definite for PTC, 83.7% for suspicious for PTC, 33.0% for indeterminate, 8.1% for benign, and 31.0% for non-diagnostic. The ROM showed little change according to level of radiation exposure. Overall, there was no association between thyroid radiation dose and the odds ratio for a correct cytologic conclusion (p = 0.24). When analyzed according to dose quintile, the odds ratio for a correct conclusion increased two-fold at 0.10-0.29 Gy compared to a dose of 0.00-0.09 Gy and decreased at doses of 0.3-24 Gy (p value for linear trend = 0.99).

CONCLUSIONS: At radiation doses received by a cohort of young Belarusians exposed to radioiodines by the Chernobyl accident, the predictive value of thyroid biopsy for diagnosing PTC was not significantly affected by level of radiation exposure.}, } @article {pmid38246125, year = {2024}, author = {Mahony, J}, title = {Biological and bioinformatic tools for the discovery of unknown phage-host combinations.}, journal = {Current opinion in microbiology}, volume = {77}, number = {}, pages = {102426}, doi = {10.1016/j.mib.2024.102426}, pmid = {38246125}, issn = {1879-0364}, mesh = {*Bacteriophages/genetics ; Artificial Intelligence ; Computational Biology ; *Microbiota ; Metagenomics ; }, abstract = {The field of microbial ecology has been transformed by metagenomics in recent decades and has culminated in vast datasets that facilitate the bioinformatic dissection of complex microbial communities. Recently, attention has turned from defining the microbiota composition to the interactions and relationships that occur between members of the microbiota. Within complex microbiota, the identification of bacteriophage-host combinations has been a major challenge. Recent developments in artificial intelligence tools to predict protein structure and function as well as the relationships between bacteria and their infecting bacteriophages allow a strategic approach to identifying and validating phage-host relationships. However, biological validation of these predictions remains essential and will serve to improve the existing predictive tools. In this review, I provide an overview of the most recent developments in both bioinformatic and experimental approaches to predicting and experimentally validating unknown phage-host combinations.}, } @article {pmid38245889, year = {2024}, author = {Schlapbach, LJ and Watson, RS and Sorce, LR and Argent, AC and Menon, K and Hall, MW and Akech, S and Albers, DJ and Alpern, ER and Balamuth, F and Bembea, M and Biban, P and Carrol, ED and Chiotos, K and Chisti, MJ and DeWitt, PE and Evans, I and Flauzino de Oliveira, C and Horvat, CM and Inwald, D and Ishimine, P and Jaramillo-Bustamante, JC and Levin, M and Lodha, R and Martin, B and Nadel, S and Nakagawa, S and Peters, MJ and Randolph, AG and Ranjit, S and Rebull, MN and Russell, S and Scott, HF and de Souza, DC and Tissieres, P and Weiss, SL and Wiens, MO and Wynn, JL and Kissoon, N and Zimmerman, JJ and Sanchez-Pinto, LN and Bennett, TD and , }, title = {International Consensus Criteria for Pediatric Sepsis and Septic Shock.}, journal = {JAMA}, volume = {331}, number = {8}, pages = {665-674}, pmid = {38245889}, issn = {1538-3598}, support = {/WT_/Wellcome Trust/United Kingdom ; R01 HD105939/HD/NICHD NIH HHS/United States ; }, mesh = {Humans ; Child ; *Shock, Septic/mortality ; Multiple Organ Failure/diagnosis/etiology ; Consensus ; *Sepsis/mortality ; Systemic Inflammatory Response Syndrome/diagnosis ; Organ Dysfunction Scores ; }, abstract = {IMPORTANCE: Sepsis is a leading cause of death among children worldwide. Current pediatric-specific criteria for sepsis were published in 2005 based on expert opinion. In 2016, the Third International Consensus Definitions for Sepsis and Septic Shock (Sepsis-3) defined sepsis as life-threatening organ dysfunction caused by a dysregulated host response to infection, but it excluded children.

OBJECTIVE: To update and evaluate criteria for sepsis and septic shock in children.

EVIDENCE REVIEW: The Society of Critical Care Medicine (SCCM) convened a task force of 35 pediatric experts in critical care, emergency medicine, infectious diseases, general pediatrics, nursing, public health, and neonatology from 6 continents. Using evidence from an international survey, systematic review and meta-analysis, and a new organ dysfunction score developed based on more than 3 million electronic health record encounters from 10 sites on 4 continents, a modified Delphi consensus process was employed to develop criteria.

FINDINGS: Based on survey data, most pediatric clinicians used sepsis to refer to infection with life-threatening organ dysfunction, which differed from prior pediatric sepsis criteria that used systemic inflammatory response syndrome (SIRS) criteria, which have poor predictive properties, and included the redundant term, severe sepsis. The SCCM task force recommends that sepsis in children be identified by a Phoenix Sepsis Score of at least 2 points in children with suspected infection, which indicates potentially life-threatening dysfunction of the respiratory, cardiovascular, coagulation, and/or neurological systems. Children with a Phoenix Sepsis Score of at least 2 points had in-hospital mortality of 7.1% in higher-resource settings and 28.5% in lower-resource settings, more than 8 times that of children with suspected infection not meeting these criteria. Mortality was higher in children who had organ dysfunction in at least 1 of 4-respiratory, cardiovascular, coagulation, and/or neurological-organ systems that was not the primary site of infection. Septic shock was defined as children with sepsis who had cardiovascular dysfunction, indicated by at least 1 cardiovascular point in the Phoenix Sepsis Score, which included severe hypotension for age, blood lactate exceeding 5 mmol/L, or need for vasoactive medication. Children with septic shock had an in-hospital mortality rate of 10.8% and 33.5% in higher- and lower-resource settings, respectively.

CONCLUSIONS AND RELEVANCE: The Phoenix sepsis criteria for sepsis and septic shock in children were derived and validated by the international SCCM Pediatric Sepsis Definition Task Force using a large international database and survey, systematic review and meta-analysis, and modified Delphi consensus approach. A Phoenix Sepsis Score of at least 2 identified potentially life-threatening organ dysfunction in children younger than 18 years with infection, and its use has the potential to improve clinical care, epidemiological assessment, and research in pediatric sepsis and septic shock around the world.}, } @article {pmid38244396, year = {2024}, author = {Sakamoto, Y and Miyoshi, K}, title = {A confidence framing effect: Flexible use of evidence in metacognitive monitoring.}, journal = {Consciousness and cognition}, volume = {118}, number = {}, pages = {103636}, doi = {10.1016/j.concog.2024.103636}, pmid = {38244396}, issn = {1090-2376}, mesh = {Humans ; *Decision Making ; Choice Behavior ; *Metacognition ; }, abstract = {Human behavior is flexibly regulated by specific goals of cognitive tasks. One notable example is goal-directed modulation of metacognitive behavior, where logically equivalent decision-making problems can yield different patterns of introspective confidence depending on the frame in which they are presented. While this observation highlights the important heuristic nature of metacognitive monitoring, computational mechanisms underlying this phenomenon remain elusive. We confirmed the confidence framing effect in two-alternative dot-number discrimination and in previously published preference-choice data, demonstrating distinctive confidence patterns between "choose more" or "choose less" frames. Formal model comparisons revealed a simple confidence heuristic behind this phenomenon, which assigns greater weight to chosen than unchosen stimulus evidence. This computation appears to be based on internal evidence constituted under specific task demands rather than physical stimulus intensity itself, a view justified in terms of ecological rationality. These results shed light on the adaptive nature of human decision-making and metacognitive monitoring.}, } @article {pmid38243062, year = {2024}, author = {Kwon, H and Ann, HW and Park, S and Kwon, J and Park, K and Ryu, SM and Guo, Y and Kim, JJ and Yim, JH and Kim, IC and Shim, SH and Lee, S and Lee, D}, title = {Mass spectrometry-guided isolation of thiodiketopiperazines from an EtOAc-extract of Setosphaeria rostrata culture medium and their anti-skin aging effects on TNF-α-induced human dermal fibroblasts.}, journal = {The Journal of antibiotics}, volume = {77}, number = {4}, pages = {257-263}, pmid = {38243062}, issn = {1881-1469}, support = {PE23150//Korea Polar Research Institute (KOPRI)/ ; NRF-2022R1A4A3022401//National Research Foundation of Korea (NRF)/ ; NRF-2019R1A2C1006226//National Research Foundation of Korea (NRF)/ ; }, mesh = {Humans ; *Tumor Necrosis Factor-alpha ; *Matrix Metalloproteinase 1/pharmacology ; Reactive Oxygen Species ; Fibroblasts ; *Ascomycota ; }, abstract = {Using mass spectrometry (MS)-guided isolation methods, a new thiodiketopiperazine derivative (1) and exserohilone (2) were isolated from an EtOAc-extract of Setosphaeria rostrata culture medium. The chemical structure of the new compound was elucidated by MS and NMR spectroscopy, and the absolute configurations were established by the quantum mechanical calculations of electronic circular dichroism. All isolated compounds were examined for their effects on reactive oxygen species (ROS) production, matrix metalloproteinase 1 (MMP-1) secretion, and procollagen type I α1 secretion in tumor necrosis factor (TNF)-α-induced human dermal fibroblasts. Compound 1 and exserohilone (2) exhibited the inhibition of TNF-α-induced ROS generation and MMP-1 secretion. Additionally, compound 1 and exserohilone (2) increased the procollagen type I α1 secretion. Compound 1 docked computationally into the active site of MMP-1 (-6.0 kcal/mol).}, } @article {pmid38242303, year = {2024}, author = {Rojo, J and Cervigón, P and Ferencova, Z and Cascón, Á and Galán Díaz, J and Romero-Morte, J and Sabariego, S and Torres, M and Gutiérrez-Bustillo, AM}, title = {Assessment of environmental risk areas based on airborne pollen patterns as a response to land use and land cover distribution.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {344}, number = {}, pages = {123385}, doi = {10.1016/j.envpol.2024.123385}, pmid = {38242303}, issn = {1873-6424}, mesh = {Cluster Analysis ; Databases, Factual ; *Pollen ; Public Health ; *Respiratory Tract Diseases ; }, abstract = {Allergic respiratory diseases are considered to be among the most important public health concerns, and pollen is the main cause of allergic respiratory diseases worldwide. However, the biological component of air quality is largely underestimated, and there is an important gap in the legislation in this area. The aims of this study were to characterise the occurrence and incidence of pollen exposure in relation to potential pollen sources and to delineate the main areas of aerobiological risk in the Madrid Autonomous Region based on homogeneous patterns of pollen exposure. This study uses the historical aerobiological database of the Madrid Region Palynological Network (central Spain) from ten pollen stations from 1994 to 2022, and the land-use information from the Corine Land Cover. Multiple clustering approaches were followed to group the sampling stations and subsequently all the 1 × 1km pixels for the Madrid Autonomous Region. The clustering dendrogram for land-use distribution was compared to the dendrogram for historical airborne pollen data. The two dendrograms showed a good alignment with a very high correlation (0.95) and very low entanglement (0.15), which indicates a close correspondence between the distribution of the potential pollen sources and the airborne pollen dynamics. Based on this knowledge, the Madrid Autonomous Region was divided into six aerobiological risk areas following a clear anthropogenic gradient in terms of the potential pollen sources that determine pollen exposure in the Madrid Region. Spatial regionalisation is a common practice in environmental risk assessment to improve the application of management plans and optimise the air quality monitoring networks. The risk areas proposed by scientific criteria in the Madrid Autonomous Region can be adjusted to other operational criteria following a framework equivalent to other air quality networks.}, } @article {pmid38236268, year = {2024}, author = {Rogoza, R and Krammer, G and Jauk, E and Flakus, M and Baran, L and Di Sarno, M and Di Pierro, R and Zajenkowski, M and Dufner, M and Fatfouta, R}, title = {The peaks and valleys of narcissism: The factor structure of narcissistic states and their relations to trait measures.}, journal = {Psychological assessment}, volume = {36}, number = {2}, pages = {147-161}, doi = {10.1037/pas0001295}, pmid = {38236268}, issn = {1939-134X}, support = {//National Science Centre/ ; //Austrian Science Fund (FWF)/ ; }, mesh = {Humans ; *Narcissism ; Databases, Factual ; *Ecological Momentary Assessment ; Phenotype ; }, abstract = {Although interindividual differences in narcissism are well studied, little is known about assessing narcissism at the within-person level. To fill this research gap, we investigated whether the narcissism construct is represented in the same way at the between- and within-person levels. We analyzed four established narcissism measures across multiple studies. In each of the studies, participants completed narcissism measures in ecological momentary assessment or daily diary studies. Equivalent construct representation across between- and within-person narcissism (i.e., cross-level measurement invariance) was found. State narcissism measures showed convergent validities for the trait narcissism scales. Moreover, we also found that antagonistic narcissism was most strongly related to within-person variability in narcissism. Our investigation sheds new light on the structure and assessment of narcissism on the within-person level by providing a comprehensive examination of its measurement. (PsycInfo Database Record (c) 2024 APA, all rights reserved).}, } @article {pmid38235411, year = {2024}, author = {Coury, SM and López, V and Bajwa, Z and Garcia, JM and Teresi, GI and Kuhlman, KR and Li, Y and Cole, S and Miklowitz, DJ and Pappas, I and Ho, TC}, title = {Protocol for teen inflammation glutamate emotion research (TIGER): Toward predictors of treatment response and clinical course in depressed adolescents.}, journal = {Brain, behavior, & immunity - health}, volume = {35}, number = {}, pages = {100718}, pmid = {38235411}, issn = {2666-3546}, support = {K01 MH117442/MH/NIMH NIH HHS/United States ; P30 AG066530/AG/NIA NIH HHS/United States ; R01 MH127176/MH/NIMH NIH HHS/United States ; }, abstract = {Adolescent-onset depression is a prevalent and debilitating condition commonly associated with treatment refractory depression and non-response to first-line antidepressants. There are, however, no objective tests to determine who may or may not respond to antidepressants. As depressed adolescents are especially vulnerable to the lifelong consequences of ineffectively-treated depression, it is critical to identify neurobiological predictors of treatment non-response in this population. Here, we describe the scientific rationale and protocol for the Teen Inflammation Glutamate Emotion Research (TIGER) study, a prospective 18-month investigation of 160 depressed adolescents who will be assessed before and after treatment with selective serotonin reuptake inhibitors. TIGER will be using ultra-high field imaging to test the effects of acute stress and antidepressant treatment on inflammatory and glutamatergic processes hypothesized to underlie depression maintenance. Results from this work will motivate future studies testing alternative therapeutics for depressed adolescents at risk for treatment resistant depression. ClinicalTrials.gov Identifier: NCT05329441.}, } @article {pmid38232851, year = {2024}, author = {Liu, YE and Luo, XJ and Huang, CC and Lu, Q and Wang, S and Mai, BX}, title = {Insights into the occurrence, spatial distribution, and ecological implications of organophosphate triesters in surface sediments from polluted urban rivers across China.}, journal = {The Science of the total environment}, volume = {915}, number = {}, pages = {170108}, doi = {10.1016/j.scitotenv.2024.170108}, pmid = {38232851}, issn = {1879-1026}, abstract = {Organophosphate triesters (tri-OPEs) are a kind of widespread contaminants in the world, particularly in China, which is a major producer and user of tri-OPEs. However, tri-OPE pollution in urban river sediments in China remains unclear. In current work, we carried out the first nationwide investigation to comprehensively monitor 10 conventional and five emerging tri-OPEs in sediments of 173 black-odorous urban rivers throughout China. Concentrations of 10 conventional and five emerging tri-OPEs were 3.8-1240 ng/g dw (mean: 253 ng/g dw) and 0.21-1107 ng/g dw (68 ng/g dw), respectively, and significantly differed among the cities sampled but generally decreased from Northeast and East China to Central and West China. These spatial patterns suggest that tri-OPE pollution was mainly from local sources and was controlled by the industrial and economic development levels in these four areas, as indicated by the significant correlations between tri-OPE concentrations and gross domestic production, gross industrial output, and daily wastewater treatment capacity. Although the tri-OPE composition varied spatially at different sites, which indicated different tri-OPE input patterns, it was commonly dominated by tris(2-chloroethyl) phosphate, tris(2-ethylhexyl) phosphate, and tris(1-chloro-2-propyl) phosphate (conventional tri-OPEs) and bisphenol A-bis(diphenyl phosphate) and isodecyl diphenyl phosphate (emerging tri-OPEs). A risk assessment indicated that tri-OPEs in most sampling sediments had a low to moderate risk to aquatic organisms.}, } @article {pmid38231860, year = {2024}, author = {Grones, C and Eekhout, T and Shi, D and Neumann, M and Berg, LS and Ke, Y and Shahan, R and Cox, KL and Gomez-Cano, F and Nelissen, H and Lohmann, JU and Giacomello, S and Martin, OC and Cole, B and Wang, JW and Kaufmann, K and Raissig, MT and Palfalvi, G and Greb, T and Libault, M and De Rybel, B}, title = {Best practices for the execution, analysis, and data storage of plant single-cell/nucleus transcriptomics.}, journal = {The Plant cell}, volume = {36}, number = {4}, pages = {812-828}, pmid = {38231860}, issn = {1532-298X}, support = {F32 GM136030/GM/NIGMS NIH HHS/United States ; /ERC_/European Research Council/International ; }, mesh = {Reproducibility of Results ; *Gene Expression Profiling ; *Plants/genetics ; Stress, Physiological/genetics ; Information Storage and Retrieval ; }, abstract = {Single-cell and single-nucleus RNA-sequencing technologies capture the expression of plant genes at an unprecedented resolution. Therefore, these technologies are gaining traction in plant molecular and developmental biology for elucidating the transcriptional changes across cell types in a specific tissue or organ, upon treatments, in response to biotic and abiotic stresses, or between genotypes. Despite the rapidly accelerating use of these technologies, collective and standardized experimental and analytical procedures to support the acquisition of high-quality data sets are still missing. In this commentary, we discuss common challenges associated with the use of single-cell transcriptomics in plants and propose general guidelines to improve reproducibility, quality, comparability, and interpretation and to make the data readily available to the community in this fast-developing field of research.}, } @article {pmid38229583, year = {2024}, author = {Devine, K and Russell, CD and Blanco, GR and Walker, BR and Homer, NZM and Denham, SG and Simpson, JP and Leavy, OC and Elneima, O and McAuley, HJC and Shikotra, A and Singapuri, A and Sereno, M and Saunders, RM and Harris, VC and Houchen-Wolloff, L and Greening, NJ and Lone, NI and Thorpe, M and Greenhalf, W and Chalmers, JD and Ho, LP and Horsley, A and Marks, M and Raman, B and Moore, SC and Dunning, J and Semple, MG and Andrew, R and Wain, LV and Evans, RA and Brightling, CE and Kenneth Baillie, J and Reynolds, RM and , }, title = {Plasma steroid concentrations reflect acute disease severity and normalise during recovery in people hospitalised with COVID-19.}, journal = {Clinical endocrinology}, volume = {100}, number = {4}, pages = {317-327}, doi = {10.1111/cen.15012}, pmid = {38229583}, issn = {1365-2265}, support = {MC_PC_19059/MRC_/Medical Research Council/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; }, mesh = {Humans ; Male ; Female ; *COVID-19 ; Hydrocortisone ; Acute Disease ; Aftercare ; Patient Discharge ; Glucocorticoids/therapeutic use ; Steroids/therapeutic use ; Patient Acuity ; Testosterone ; }, abstract = {OBJECTIVE: Endocrine systems are disrupted in acute illness, and symptoms reported following coronavirus disease 2019 (COVID-19) are similar to those found with clinical hormone deficiencies. We hypothesised that people with severe acute COVID-19 and with post-COVID symptoms have glucocorticoid and sex hormone deficiencies.

DESIGN/PATIENTS: Samples were obtained for analysis from two UK multicentre cohorts during hospitalisation with COVID-19 (International Severe Acute Respiratory Infection Consortium/World Health Organisation [WHO] Clinical Characterization Protocol for Severe Emerging Infections in the UK study), and at follow-up 5 months after hospitalisation (Post-hospitalisation COVID-19 study).

MEASUREMENTS: Plasma steroids were quantified by liquid chromatography-mass spectrometry. Steroid concentrations were compared against disease severity (WHO ordinal scale) and validated symptom scores. Data are presented as geometric mean (SD).

RESULTS: In the acute cohort (n = 239, 66.5% male), plasma cortisol concentration increased with disease severity (cortisol 753.3 [1.6] vs. 429.2 [1.7] nmol/L in fatal vs. least severe, p < .001). In males, testosterone concentrations decreased with severity (testosterone 1.2 [2.2] vs. 6.9 [1.9] nmol/L in fatal vs. least severe, p < .001). In the follow-up cohort (n = 198, 62.1% male, 68.9% ongoing symptoms, 165 [121-192] days postdischarge), plasma cortisol concentrations (275.6 [1.5] nmol/L) did not differ with in-hospital severity, perception of recovery, or patient-reported symptoms. Male testosterone concentrations (12.6 [1.5] nmol/L) were not related to in-hospital severity, perception of recovery or symptom scores.

CONCLUSIONS: Circulating glucocorticoids in patients hospitalised with COVID-19 reflect acute illness, with a marked rise in cortisol and fall in male testosterone. These findings are not observed 5 months from discharge. The lack of association between hormone concentrations and common post-COVID symptoms suggests steroid insufficiency does not play a causal role in this condition.}, } @article {pmid38229470, year = {2024}, author = {Wondimagegnehu, A and Assefa, M and Teferra, S and Kantelhardt, EJ and Zebrack, B and Addissie, A}, title = {A Qualitative Study on Psychosocial Challenges of Patients With Cancer in Ethiopia Using the Social-Ecological Model.}, journal = {Qualitative health research}, volume = {34}, number = {8-9}, pages = {828-841}, doi = {10.1177/10497323231219409}, pmid = {38229470}, issn = {1049-7323}, mesh = {Humans ; Ethiopia ; *Neoplasms/psychology/therapy ; *Qualitative Research ; Female ; Male ; Adult ; *Social Support ; Middle Aged ; *Focus Groups ; Interviews as Topic ; Young Adult ; Family/psychology ; Aged ; Stress, Psychological/psychology ; Depression/psychology/therapy ; }, abstract = {Cancer diagnosis and treatment can be physically arduous, disrupting patients' social and work lives. Understanding the extent of these problems is key to addressing patients' needs, but specific psychosocial challenges have not yet been well studied in resource-limited settings. A qualitative study was conducted in the capital and two regions of Ethiopia with the aim of exploring psychosocial challenges among cancer patients. A total of 14 in-depth interviews (IDIs) and 16 focus group discussions (FGDs) were done with cancer patients, health professionals, community representatives, and religious leaders. Four separate interview guides were used to facilitate the interviews and discussions. All transcribed documents, field notes, and reflexive memos were entered into NVivo 12 software, and deductive thematic analysis using the social-ecological model was applied to summarize the main findings. At an individual level, emotional distress, suicidal risk, denial, and refusal of treatment were identified immediately after diagnosis while hopelessness, feeling depressed, and fear of death were commonly reported psychosocial challenges during the course of treatment. Involvement of family members in major treatment decisions was recognized at an interpersonal level. Our result also revealed that cancer patients had strong social support from family members and close friends. In the community, traditional medicine and religious rituals were considered an alternative treatment for cancer. The findings indicate that counselling and psychoeducation are crucial for cancer patients, family members, and close friends. Awareness creation programmes should be delivered through collaboration with religious leaders and traditional healers.}, } @article {pmid38225503, year = {2024}, author = {Gubó, E and Plutzer, J and Molnár, T and Pordán-Háber, D and Szabó, L and Szalai, Z and Gubó, R and Szakál, P and Szakál, T and Környei, L and Bede-Fazekas, Á and Kalocsai, R}, title = {Correction to: A 4‑year study of bovine reproductive hormones that are induced by pharmaceuticals and appear as steroid estrogenic pollutants in the resulting slurry, using in vitro and instrumental analytical methods.}, journal = {Environmental science and pollution research international}, volume = {31}, number = {6}, pages = {9868}, doi = {10.1007/s11356-024-31992-0}, pmid = {38225503}, issn = {1614-7499}, } @article {pmid38218164, year = {2024}, author = {Pérez, G and O'Leary, BC and Allegri, E and Casal, G and Cornet, CC and de Juan, S and Failler, P and Fredriksen, S and Fonseca, C and Furlan, E and Gil, A and Hawkins, JP and Maréchal, JP and McCarthy, T and Roberts, CM and Trégarot, E and van der Geest, M and Simide, R}, title = {A conceptual framework to help choose appropriate blue nature-based solutions.}, journal = {Journal of environmental management}, volume = {352}, number = {}, pages = {119936}, doi = {10.1016/j.jenvman.2023.119936}, pmid = {38218164}, issn = {1095-8630}, mesh = {Humans ; *Ecosystem ; *Biodiversity ; Climate Change ; }, abstract = {Biodiversity loss and climate change have severely impacted ecosystems and livelihoods worldwide, compromising access to food and water, increasing disaster risk, and affecting human health globally. Nature-based Solutions (NbS) have gained interest in addressing these global societal challenges. Although much effort has been directed to NbS in urban and terrestrial environments, the implementation of NbS in marine and coastal environments (blue NbS) lags. The lack of a framework to guide decision-makers and practitioners through the initial planning stages appears to be one of the main obstacles to the slow implementation of blue NbS. To address this, we propose an integrated conceptual framework, built from expert knowledge, to inform the selection of the most appropriate blue NbS based on desired intervention objectives and social-ecological context. Our conceptual framework follows a four incremental steps structure: Step 1 aims to identify the societal challenge(s) to address; Step 2 highlights ecosystem services and the underlying biodiversity and ecological functions that could contribute to confronting the societal challenge(s); Step 3 identify the specific environmental context the intervention needs to be set within (e.g. the spatial scale the intervention will operate within, the ecosystem's vulnerability to stressors, and its ecological condition); and Step 4 provides a selection of potential blue NbS interventions that would help address the targeted societal challenge(s) considering the context defined through Step 3. Designed to maintain, enhance, recover, rehabilitate, or create ecosystem services by supporting biodiversity, the blue NbS intervention portfolio includes marine protection (i.e., fully, highly, lightly, and minimally protected areas), restorative activities (i.e., active, passive, and partial restoration; rehabilitation of ecological function and ecosystem creation), and other management measures (i.e., implementation and enforcement of regulation). Ultimately, our conceptual framework guides decision-makers toward a versatile portfolio of interventions that cater to the specific needs of each ecosystem rather than imposing a rigid, one-size-fits-all model. In the future, this framework needs to integrate socio-economic considerations more comprehensively and be kept up-to-date by including the latest scientific information.}, } @article {pmid38215805, year = {2024}, author = {Lacson, R and Pianykh, O and Hartmann, S and Johnston, H and Daye, D and Flores, E and Kapoor, N and Khorasani, R}, title = {Factors Associated With Timeliness and Equity of Access to Outpatient MRI Examinations.}, journal = {Journal of the American College of Radiology : JACR}, volume = {21}, number = {7}, pages = {1049-1057}, doi = {10.1016/j.jacr.2023.12.028}, pmid = {38215805}, issn = {1558-349X}, mesh = {Humans ; Female ; Male ; *Magnetic Resonance Imaging ; *Health Services Accessibility ; Middle Aged ; Adult ; Time Factors ; Aged ; Ambulatory Care/statistics & numerical data ; Outpatients ; }, abstract = {OBJECTIVE: The role of MRI in guiding patients' diagnosis and treatment is increasing. Therefore, timely MRI performance prevents delays that can impact patient care. We assessed the timeliness of performing outpatient MRIs using the socio-ecological model approach and evaluated multilevel factors associated with delays.

METHODS: This institutional review board-approved study included outpatient MRI examinations ordered between October 1, 2021, and December 31, 2022, for performance at a large quaternary care health system. Mean order-to-performed (OtoP) interval (in days) and prolonged OtoP interval (defined as >10 days) for MRI orders with an expected date of 1 day to examination performance were measured. Logistic regression was used to assess patient-level (demographic and social determinants of health), radiology practice-level, and community-level factors associated with prolonged OtoP interval.

RESULTS: There were 126,079 MRI examination orders with expected performance within 1 day placed during the study period (56% of all MRI orders placed). After excluding duplicates, there were 97,160 orders for unique patients. Of the MRI orders, 48% had a prolonged OtoP interval, and mean OtoP interval was 18.5 days. Factors significantly associated with delay in MRI performance included public insurance (odds ratio [OR] = 1.11, P < .001), female gender (OR = 1.11, P < .001), radiology subspecialty (ie, cardiac, OR = 1.71, P < .001), and patients from areas that are most deprived (ie, highest Area Deprivation Index quintile, OR = 1.70, P < .001).

DISCUSSION: Nearly half of outpatient MRI orders were delayed, performed >10 days from the expected date selected by the ordering provider. Addressing multilevel factors associated with such delays may help enhance timeliness and equity of access to MRI examinations, potentially reducing diagnostic errors and treatment delays.}, } @article {pmid38215053, year = {2024}, author = {Ho, PC and Yu, WH and Tee, BL and Lee, WP and Li, C and Gu, Y and Yokoyama, JS and Reyes-Dumeyer, D and Choi, YB and Yang, HS and Vardarajan, BN and Tzuang, M and Lieu, K and Lu, A and Faber, KM and Potter, ZD and Revta, C and Kirsch, M and McCallum, J and Mei, D and Booth, B and Cantwell, LB and Chen, F and Chou, S and Clark, D and Deng, M and Hong, TH and Hwang, LJ and Jiang, L and Joo, Y and Kang, Y and Kim, ES and Kim, H and Kim, K and Kuzma, AB and Lam, E and Lanata, SC and Lee, K and Li, D and Li, M and Li, X and Liu, CL and Liu, C and Liu, L and Lupo, JL and Nguyen, K and Pfleuger, SE and Qian, J and Qian, W and Ramirez, V and Russ, KA and Seo, EH and Song, YE and Tartaglia, MC and Tian, L and Torres, M and Vo, N and Wong, EC and Xie, Y and Yau, EB and Yi, I and Yu, V and Zeng, X and St George-Hyslop, P and Au, R and Schellenberg, GD and Dage, JL and Varma, R and Hsiung, GR and Rosen, H and Henderson, VW and Foroud, T and Kukull, WA and Peavy, GM and Lee, H and Feldman, HH and Mayeux, R and Chui, H and Jun, GR and Ta Park, VM and Chow, TW and Wang, LS}, title = {Asian Cohort for Alzheimer's Disease (ACAD) pilot study on genetic and non-genetic risk factors for Alzheimer's disease among Asian Americans and Canadians.}, journal = {Alzheimer's & dementia : the journal of the Alzheimer's Association}, volume = {20}, number = {3}, pages = {2058-2071}, pmid = {38215053}, issn = {1552-5279}, support = {R01 AG080469/AG/NIA NIH HHS/United States ; U24 AG021886/AG/NIA NIH HHS/United States ; U19AG068753/AG/NIA NIH HHS/United States ; K23AG062750/AG/NIA NIH HHS/United States ; UH2 AG083258/AG/NIA NIH HHS/United States ; U19 AG068753/AG/NIA NIH HHS/United States ; R21 AG068757/AG/NIA NIH HHS/United States ; P30AG062422/AG/NIA NIH HHS/United States ; K24 AG045333/AG/NIA NIH HHS/United States ; R56 AG069130/AG/NIA NIH HHS/United States ; R24 AG063718/AG/NIA NIH HHS/United States ; R01 AG062588/AG/NIA NIH HHS/United States ; U19 AG079774/AG/NIA NIH HHS/United States ; ALZ-NAN-22-928181/ALZ/Alzheimer's Association/United States ; R01AG080469/AG/NIA NIH HHS/United States ; P30 AG062422/AG/NIA NIH HHS/United States ; R01 AG083840/AG/NIA NIH HHS/United States ; P01 AG019724/AG/NIA NIH HHS/United States ; P30 AG066462/AG/NIA NIH HHS/United States ; R24AG063718/AG/NIA NIH HHS/United States ; UH2AG083258/AG/NIA NIH HHS/United States ; P30 AG066530/AG/NIA NIH HHS/United States ; R01 AG083926/AG/NIA NIH HHS/United States ; AACSFD-22-972143/ALZ/Alzheimer's Association/United States ; R61 AG083582/AG/NIA NIH HHS/United States ; U19AG079774/AG/NIA NIH HHS/United States ; R01AG083926/AG/NIA NIH HHS/United States ; K23 AG062750/AG/NIA NIH HHS/United States ; U10EY017337/EY/NEI NIH HHS/United States ; R01AG083840/AG/NIA NIH HHS/United States ; R21AG077649/AG/NIA NIH HHS/United States ; R21 AG077649/AG/NIA NIH HHS/United States ; R21AG068757/AG/NIA NIH HHS/United States ; R61AG083582/AG/NIA NIH HHS/United States ; U10 EY017337/EY/NEI NIH HHS/United States ; U24AG021886/AG/NIA NIH HHS/United States ; }, mesh = {Humans ; *Alzheimer Disease/genetics ; Pilot Projects ; Asian/genetics ; Canada ; Risk Factors ; *North American People ; }, abstract = {INTRODUCTION: Clinical research in Alzheimer's disease (AD) lacks cohort diversity despite being a global health crisis. The Asian Cohort for Alzheimer's Disease (ACAD) was formed to address underrepresentation of Asians in research, and limited understanding of how genetics and non-genetic/lifestyle factors impact this multi-ethnic population.

METHODS: The ACAD started fully recruiting in October 2021 with one central coordination site, eight recruitment sites, and two analysis sites. We developed a comprehensive study protocol for outreach and recruitment, an extensive data collection packet, and a centralized data management system, in English, Chinese, Korean, and Vietnamese.

RESULTS: ACAD has recruited 606 participants with an additional 900 expressing interest in enrollment since program inception.

DISCUSSION: ACAD's traction indicates the feasibility of recruiting Asians for clinical research to enhance understanding of AD risk factors. ACAD will recruit > 5000 participants to identify genetic and non-genetic/lifestyle AD risk factors, establish blood biomarker levels for AD diagnosis, and facilitate clinical trial readiness.

HIGHLIGHTS: The Asian Cohort for Alzheimer's Disease (ACAD) promotes awareness of under-investment in clinical research for Asians. We are recruiting Asian Americans and Canadians for novel insights into Alzheimer's disease. We describe culturally appropriate recruitment strategies and data collection protocol. ACAD addresses challenges of recruitment from heterogeneous Asian subcommunities. We aim to implement a successful recruitment program that enrolls across three Asian subcommunities.}, } @article {pmid38212658, year = {2024}, author = {Ning, D and Wang, Y and Fan, Y and Wang, J and Van Nostrand, JD and Wu, L and Zhang, P and Curtis, DJ and Tian, R and Lui, L and Hazen, TC and Alm, EJ and Fields, MW and Poole, F and Adams, MWW and Chakraborty, R and Stahl, DA and Adams, PD and Arkin, AP and He, Z and Zhou, J}, title = {Environmental stress mediates groundwater microbial community assembly.}, journal = {Nature microbiology}, volume = {9}, number = {2}, pages = {490-501}, pmid = {38212658}, issn = {2058-5276}, support = {DE-AC02-05CH11231//DOE | SC | Biological and Environmental Research (BER)/ ; EF-2025558//National Science Foundation (NSF)/ ; DEB-2129235//National Science Foundation (NSF)/ ; }, mesh = {Phylogeny ; *Microbiota ; *Groundwater ; Stochastic Processes ; }, abstract = {Community assembly describes how different ecological processes shape microbial community composition and structure. How environmental factors impact community assembly remains elusive. Here we sampled microbial communities and >200 biogeochemical variables in groundwater at the Oak Ridge Field Research Center, a former nuclear waste disposal site, and developed a theoretical framework to conceptualize the relationships between community assembly processes and environmental stresses. We found that stochastic assembly processes were critical (>60% on average) in shaping community structure, but their relative importance decreased as stress increased. Dispersal limitation and 'drift' related to random birth and death had negative correlations with stresses, whereas the selection processes leading to dissimilar communities increased with stresses, primarily related to pH, cobalt and molybdenum. Assembly mechanisms also varied greatly among different phylogenetic groups. Our findings highlight the importance of microbial dispersal limitation and environmental heterogeneity in ecosystem restoration and management.}, } @article {pmid38204360, year = {2024}, author = {Kiran, A and Hanachi, M and Alsayed, N and Fassatoui, M and Oduaran, OH and Allali, I and Maslamoney, S and Meintjes, A and Zass, L and Rocha, JD and Kefi, R and Benkahla, A and Ghedira, K and Panji, S and Mulder, N and Fadlelmola, FM and Souiai, O}, title = {The African Human Microbiome Portal: a public web portal of curated metagenomic metadata.}, journal = {Database : the journal of biological databases and curation}, volume = {2024}, number = {}, pages = {}, pmid = {38204360}, issn = {1758-0463}, support = {U24 HG006941/HG/NHGRI NIH HHS/United States ; }, mesh = {Humans ; *Metadata ; Metagenome ; Databases, Factual ; Metagenomics ; *Microbiota/genetics ; }, abstract = {There is growing evidence that comprehensive and harmonized metadata are fundamental for effective public data reusability. However, it is often challenging to extract accurate metadata from public repositories. Of particular concern is the metagenomic data related to African individuals, which often omit important information about the particular features of these populations. As part of a collaborative consortium, H3ABioNet, we created a web portal, namely the African Human Microbiome Portal (AHMP), exclusively dedicated to metadata related to African human microbiome samples. Metadata were collected from various public repositories prior to cleaning, curation and harmonization according to a pre-established guideline and using ontology terms. These metadata sets can be accessed at https://microbiome.h3abionet.org/. This web portal is open access and offers an interactive visualization of 14 889 records from 70 bioprojects associated with 72 peer reviewed research articles. It also offers the ability to download harmonized metadata according to the user's applied filters. The AHMP thereby supports metadata search and retrieve operations, facilitating, thus, access to relevant studies linked to the African Human microbiome. Database URL: https://microbiome.h3abionet.org/.}, } @article {pmid38203410, year = {2023}, author = {Di Martino, J and Arcieri, M and Madeddu, F and Pieroni, M and Carotenuto, G and Bottoni, P and Botta, L and Castrignanò, T and Gabellone, S and Saladino, R}, title = {Molecular Dynamics Investigations of Human DNA-Topoisomerase I Interacting with Novel Dewar Valence Photo-Adducts: Insights into Inhibitory Activity.}, journal = {International journal of molecular sciences}, volume = {25}, number = {1}, pages = {}, pmid = {38203410}, issn = {1422-0067}, mesh = {Humans ; *Molecular Dynamics Simulation ; *DNA Topoisomerases, Type I ; Biomimetics ; DNA Adducts ; Data Interpretation, Statistical ; Pyrimidine Dimers ; }, abstract = {Chronic exposure to ultraviolet (UV) radiation is known to induce the formation of DNA photo-adducts, including cyclobutane pyrimidine dimers (CPDs) and Dewar valence derivatives (DVs). While CPDs usually occur at higher frequency than DVs, recent studies have shown that the latter display superior selectivity and significant stability in interaction with the human DNA/topoisomerase 1 complex (TOP1). With the aim to deeply investigate the mechanism of interaction of DVs with TOP1, we report here four all-atom molecular dynamic simulations spanning one microsecond. These simulations are focused on the stability and conformational changes of two DNA/TOP1-DV complexes in solution, the data being compared with the biomimetic thymine dimer counterparts. Results from root-mean-square deviation (RMSD) and root-mean-square fluctuation (RMSF) analyses unequivocally confirmed increased stability of the DNA/TOP1-DV complexes throughout the simulation duration. Detailed interaction analyses, uncovering the presence of salt bridges, hydrogen bonds, water-mediated interactions, and hydrophobic interactions, as well as pinpointing the non-covalent interactions within the complexes, enabled the identification of specific TOP1 residues involved in the interactions over time and suggested a potential TOP1 inhibition mechanism in action.}, } @article {pmid38196369, year = {2024}, author = {Hauber, ME and Nagy, J and Sheard, C and Antonson, ND and Street, SE and Healy, SD and Lala, KN and Mainwaring, MC}, title = {Nest architecture influences host use by avian brood parasites and is shaped by coevolutionary dynamics.}, journal = {Proceedings. Biological sciences}, volume = {291}, number = {2014}, pages = {20231734}, pmid = {38196369}, issn = {1471-2954}, mesh = {Animals ; Biological Evolution ; *Birds ; Databases, Factual ; Host Specificity ; *Nesting Behavior ; }, abstract = {Brood (social) parasites and their hosts exhibit a wide range of adaptations and counter-adaptations as part of their ongoing coevolutionary arms races. Obligate avian brood parasites are expected to use potential host species with more easily accessible nests, while potential hosts are expected to evade parasitism by building more concealed nests that are difficult for parasites to enter and in which to lay eggs. We used phylogenetically informed comparative analyses, a global database of the world's brood parasites, their host species, and the design of avian host and non-host nests (approx. 6200 bird species) to examine first, whether parasites preferentially target host species that build open nests and, second, whether host species that build enclosed nests are more likely to be targeted by specialist parasites. We found that species building more accessible nests are more likely to serve as hosts, while host species with some of the more inaccessible nests are targeted by more specialist brood parasites. Furthermore, evolutionary-transition analyses demonstrate that host species building enclosed nests frequently evolve to become non-hosts. We conclude that nest architecture and the accessibility of nests for parasitism represent a critical stage of the ongoing coevolutionary arms race between avian brood parasites and their hosts.}, } @article {pmid38195441, year = {2024}, author = {Rádai, Z and Váradi, A and Takács, P and Nagy, NA and Schmitt, N and Prépost, E and Kardos, G and Laczkó, L}, title = {An overlooked phenomenon: complex interactions of potential error sources on the quality of bacterial de novo genome assemblies.}, journal = {BMC genomics}, volume = {25}, number = {1}, pages = {45}, pmid = {38195441}, issn = {1471-2164}, support = {GINOP-2.3.4-15-2020-00008//European Regional Development Fund/ ; GINOP-2.3.4-15-2020-00008//European Regional Development Fund/ ; GINOP-2.3.4-15-2020-00008//European Regional Development Fund/ ; GINOP-2.3.4-15-2020-00008//European Regional Development Fund/ ; GINOP-2.3.4-15-2020-00008//European Regional Development Fund/ ; GINOP-2.3.4-15-2020-00008//European Regional Development Fund/ ; GINOP-2.3.4-15-2020-00008//European Regional Development Fund/ ; }, mesh = {*Research Design ; *Genome, Bacterial ; Benchmarking ; High-Throughput Nucleotide Sequencing ; }, abstract = {BACKGROUND: Parameters adversely affecting the contiguity and accuracy of the assemblies from Illumina next-generation sequencing (NGS) are well described. However, past studies generally focused on their additive effects, overlooking their potential interactions possibly exacerbating one another's effects in a multiplicative manner. To investigate whether or not they act interactively on de novo genome assembly quality, we simulated sequencing data for 13 bacterial reference genomes, with varying levels of error rate, sequencing depth, PCR and optical duplicate ratios.

RESULTS: We assessed the quality of assemblies from the simulated sequencing data with a number of contiguity and accuracy metrics, which we used to quantify both additive and multiplicative effects of the four parameters. We found that the tested parameters are engaged in complex interactions, exerting multiplicative, rather than additive, effects on assembly quality. Also, the ratio of non-repeated regions and GC% of the original genomes can shape how the four parameters affect assembly quality.

CONCLUSIONS: We provide a framework for consideration in future studies using de novo genome assembly of bacterial genomes, e.g. in choosing the optimal sequencing depth, balancing between its positive effect on contiguity and negative effect on accuracy due to its interaction with error rate. Furthermore, the properties of the genomes to be sequenced also should be taken into account, as they might influence the effects of error sources themselves.}, } @article {pmid38194414, year = {2024}, author = {Terpstra, S and Marquitti, FMD and Vasconcelos, VV}, title = {Adaptive foraging of pollinators fosters gradual tipping under resource competition and rapid environmental change.}, journal = {PLoS computational biology}, volume = {20}, number = {1}, pages = {e1011762}, pmid = {38194414}, issn = {1553-7358}, mesh = {Humans ; *Pollination/physiology ; *Models, Biological ; Models, Theoretical ; Plants ; Food Chain ; }, abstract = {Plant and pollinator communities are vital for transnational food chains. Like many natural systems, they are affected by global change: rapidly deteriorating conditions threaten their numbers. Previous theoretical studies identified the potential for community-wide collapse above critical levels of environmental stressors-so-called bifurcation-induced tipping points. Fortunately, even as conditions deteriorate, individuals have some adaptive capacity, potentially increasing the boundary for a safe operating space where changes in ecological processes are reversible. Our study considers this adaptive capacity of pollinators to resource availability and identifies a new threat to disturbed pollinator communities. We model the adaptive foraging of pollinators in changing environments. Pollinator's adaptive foraging alters the dynamical responses of species, to the advantage of some-typically generalists-and the disadvantage of others, with systematic non-linear and non-monotonic effects on the abundance of particular species. We show that, in addition to the extent of environmental stress, the pace of change of environmental stress can also lead to the early collapse of both adaptive and nonadaptive pollinator communities. Specifically, perturbed communities exhibit rate-induced tipping points at stress levels within the safe boundary defined for constant stressors. With adaptive foraging, tipping is a more asynchronous collapse of species compared to nonadaptive pollinator communities, meaning that not all pollinator species reach a tipping event simultaneously. These results suggest that it is essential to consider the adaptive capacity of pollinator communities for monitoring and conservation. Both the extent and the rate of stress change relative to the ability of communities to recover are critical environmental boundaries.}, } @article {pmid38188173, year = {2024}, author = {Lizardo, V and García Trejo, EA and Morrone, JJ}, title = {Niche conservatism and convergence in birds of three cenocrons in the Mexican Transition Zone.}, journal = {PeerJ}, volume = {12}, number = {}, pages = {e16664}, pmid = {38188173}, issn = {2167-8359}, mesh = {Animals ; Phylogeny ; *Biological Evolution ; *Biota ; Birds ; }, abstract = {BACKGROUND: The niche conservatism hypothesis postulates that physiological and phylogenetic factors constrain species distributions, creating richness hotspots with older lineages in ancestral climatic conditions. Conversely, niche convergence occurs when species successfully disperse to novel environments, diversifying and resulting in areas with high phylogenetic clustering and endemism, low diversity, and lower clade age. The Mexican Transition Zone exhibits both patterns as its biotic assembly resulted from successive dispersal events of different biotic elements called cenocrons. We test the hypothesis that biogeographic transitionallity in the area is a product of niche conservatism in the Nearctic and Typical Neotropical cenocrons and niche convergence in the Mountain Mesoamerican cenocron.

METHODS: We split the avifauna into three species sets representing cenocrons (sets of taxa that share the same biogeographic history, constituting an identifiable subset within a biota by their common biotic origin and evolutionary history). Then, we correlated richness, endemism, phylogenetic diversity, number of nodes, and crowning age with environmental and topographic variables. These correlations were then compared with the predictions of niche conservatism versus niche convergence. We also detected areas of higher species density in environmental space and interpreted them as an environmental transition zone where birds' niches converge.

RESULTS: Our findings support the expected predictions on how niches evolved. Nearctic and Typical Neotropical species behaved as predicted by niche conservatism, whereas Mountain Mesoamerican species and the total of species correlations indicated niche convergence. We also detected distinct ecological and evolutionary characteristics of the cenocrons on a macroecological scale and the environmental conditions where the three cenocrons overlap in the Mesoamerican region.}, } @article {pmid38184954, year = {2024}, author = {Loo, SL and Howerton, E and Contamin, L and Smith, CP and Borchering, RK and Mullany, LC and Bents, S and Carcelen, E and Jung, SM and Bogich, T and van Panhuis, WG and Kerr, J and Espino, J and Yan, K and Hochheiser, H and Runge, MC and Shea, K and Lessler, J and Viboud, C and Truelove, S}, title = {The US COVID-19 and Influenza Scenario Modeling Hubs: Delivering long-term projections to guide policy.}, journal = {Epidemics}, volume = {46}, number = {}, pages = {100738}, doi = {10.1016/j.epidem.2023.100738}, pmid = {38184954}, issn = {1878-0067}, support = {U24 GM132013/GM/NIGMS NIH HHS/United States ; }, mesh = {Humans ; *COVID-19/epidemiology ; *Influenza, Human/epidemiology ; Pandemics ; Policy ; Public Health ; }, abstract = {Between December 2020 and April 2023, the COVID-19 Scenario Modeling Hub (SMH) generated operational multi-month projections of COVID-19 burden in the US to guide pandemic planning and decision-making in the context of high uncertainty. This effort was born out of an attempt to coordinate, synthesize and effectively use the unprecedented amount of predictive modeling that emerged throughout the COVID-19 pandemic. Here we describe the history of this massive collective research effort, the process of convening and maintaining an open modeling hub active over multiple years, and attempt to provide a blueprint for future efforts. We detail the process of generating 17 rounds of scenarios and projections at different stages of the COVID-19 pandemic, and disseminating results to the public health community and lay public. We also highlight how SMH was expanded to generate influenza projections during the 2022-23 season. We identify key impacts of SMH results on public health and draw lessons to improve future collaborative modeling efforts, research on scenario projections, and the interface between models and policy.}, } @article {pmid38182924, year = {2024}, author = {Brodie, JF and Mohd-Azlan, J and Chen, C and Wearn, OR and Deith, MCM and Ball, JGC and Slade, EM and Burslem, DFRP and Teoh, SW and Williams, PJ and Nguyen, A and Moore, JH and Goetz, SJ and Burns, P and Jantz, P and Hakkenberg, CR and Kaszta, ZM and Cushman, S and Coomes, D and Helmy, OE and Reynolds, G and Rodríguez, JP and Jetz, W and Luskin, MS}, title = {Publisher Correction: Landscape-scale benefits of protected areas for tropical biodiversity.}, journal = {Nature}, volume = {625}, number = {7996}, pages = {E28}, doi = {10.1038/s41586-023-07007-2}, pmid = {38182924}, issn = {1476-4687}, } @article {pmid38182741, year = {2024}, author = {Ryu, H and Kinoshita, K and Joo, S and Choi, YS and Kim, SS}, title = {Increased urinary creatinine during hibernation and day roosting in the Eastern bent-winged bat (Miniopterus fuliginosus) in Korea.}, journal = {Communications biology}, volume = {7}, number = {1}, pages = {42}, pmid = {38182741}, issn = {2399-3642}, mesh = {Animals ; *Hibernation ; *Chiroptera ; Creatinine ; *Torpor ; Republic of Korea ; }, abstract = {Torpor and arousal cycles, both daily and seasonal (e.g. hibernation), are crucial for small mammals, including bats, to maintain the energy and water balance. The alternation between torpor and arousal leads to metabolic changes, leaving traceable evidence of metabolic wastes in urine. In this study we investigated urinary creatinine and acetoacetate (a ketone body) in the Eastern bent-wing bat (Miniopterus fuliginosus) in Mungyeong, South Korea. We found an increase in urinary creatinine during torpor in summer, indicating changes in renal water reabsorption rates during the active season. Although we could not confirm ketonuria in hibernating bats due to a methodological limitation caused by the small amount of urine, we verified an increase in urinary creatinine concentration during hibernation. This finding suggests that managing water stress resulting from evaporative water loss is one of key reasons for arousal during hibernation in Eastern bent-wing bats.}, } @article {pmid38175682, year = {2024}, author = {Henry, LM and Hansen, E and Chimoff, J and Pokstis, K and Kiderman, M and Naim, R and Kossowsky, J and Byrne, ME and Lopez-Guzman, S and Kircanski, K and Pine, DS and Brotman, MA}, title = {Selecting an Ecological Momentary Assessment Platform: Tutorial for Researchers.}, journal = {Journal of medical Internet research}, volume = {26}, number = {}, pages = {e51125}, pmid = {38175682}, issn = {1438-8871}, support = {K01 DA057374/DA/NIDA NIH HHS/United States ; ZIA MH002969/ImNIH/Intramural NIH HHS/United States ; }, mesh = {Adolescent ; Child ; Humans ; *Ecological Momentary Assessment ; Data Management ; Digital Technology ; Laboratories ; *Medicine ; }, abstract = {BACKGROUND: Although ecological momentary assessment (EMA) has been applied in psychological research for decades, delivery methods have evolved with the proliferation of digital technology. Technological advances have engendered opportunities for enhanced accessibility, convenience, measurement precision, and integration with wearable sensors. Notwithstanding, researchers must navigate novel complexities in EMA research design and implementation.

OBJECTIVE: In this paper, we aimed to provide guidance on platform selection for clinical scientists launching EMA studies.

METHODS: Our team includes diverse specialties in child and adolescent behavioral and mental health with varying expertise on EMA platforms (eg, users and developers). We (2 research sites) evaluated EMA platforms with the goal of identifying the platform or platforms with the best fit for our research. We created a list of extant EMA platforms; conducted a web-based review; considered institutional security, privacy, and data management requirements; met with developers; and evaluated each of the candidate EMA platforms for 1 week.

RESULTS: We selected 2 different EMA platforms, rather than a single platform, for use at our 2 research sites. Our results underscore the importance of platform selection driven by individualized and prioritized laboratory needs; there is no single, ideal platform for EMA researchers. In addition, our project generated 11 considerations for researchers in selecting an EMA platform: (1) location; (2) developer involvement; (3) sample characteristics; (4) onboarding; (5) survey design features; (6) sampling scheme and scheduling; (7) viewing results; (8) dashboards; (9) security, privacy, and data management; (10) pricing and cost structure; and (11) future directions. Furthermore, our project yielded a suggested timeline for the EMA platform selection process.

CONCLUSIONS: This study will guide scientists initiating studies using EMA, an in vivo, real-time research tool with tremendous promise for facilitating advances in psychological assessment and intervention.}, } @article {pmid38173562, year = {2023}, author = {Boyes, D and Boyes, C and , and , and , and , and , and , }, title = {The genome sequence of the Pine Hawkmoth, Sphinx pinastri (Linneaus 1758).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {312}, pmid = {38173562}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual male Sphinx pinastri (the Pine Hawkmoth; Arthropoda; Insecta; Lepidoptera; Sphingidae). The genome sequence is 509.2 megabases in span. Most of the assembly is scaffolded into 28 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.3 kilobases in length.}, } @article {pmid38172362, year = {2024}, author = {Paolo, FS and Kroodsma, D and Raynor, J and Hochberg, T and Davis, P and Cleary, J and Marsaglia, L and Orofino, S and Thomas, C and Halpin, P}, title = {Satellite mapping reveals extensive industrial activity at sea.}, journal = {Nature}, volume = {625}, number = {7993}, pages = {85-91}, pmid = {38172362}, issn = {1476-4687}, mesh = {Humans ; COVID-19/epidemiology ; Deep Learning ; Energy-Generating Resources/statistics & numerical data ; Food Supply/statistics & numerical data ; Geographic Information Systems ; Geographic Mapping ; *Human Activities/economics/statistics & numerical data ; Hunting/statistics & numerical data ; *Industry/economics/statistics & numerical data ; *Oceans and Seas ; *Satellite Imagery ; Ships/statistics & numerical data ; Wind ; }, abstract = {The world's population increasingly relies on the ocean for food, energy production and global trade[1-3], yet human activities at sea are not well quantified[4,5]. We combine satellite imagery, vessel GPS data and deep-learning models to map industrial vessel activities and offshore energy infrastructure across the world's coastal waters from 2017 to 2021. We find that 72-76% of the world's industrial fishing vessels are not publicly tracked, with much of that fishing taking place around South Asia, Southeast Asia and Africa. We also find that 21-30% of transport and energy vessel activity is missing from public tracking systems. Globally, fishing decreased by 12 ± 1% at the onset of the COVID-19 pandemic in 2020 and had not recovered to pre-pandemic levels by 2021. By contrast, transport and energy vessel activities were relatively unaffected during the same period. Offshore wind is growing rapidly, with most wind turbines confined to small areas of the ocean but surpassing the number of oil structures in 2021. Our map of ocean industrialization reveals changes in some of the most extensive and economically important human activities at sea.}, } @article {pmid38172330, year = {2024}, author = {Gong, Y and Zha, J and Guo, Q and Guo, G}, title = {A new indicator for estimating the degree of mining-induced land subsidence: the overburden's average GSI value.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {332}, pmid = {38172330}, issn = {2045-2322}, support = {2023YFC3804200//National Key Research and Development Program of China/ ; 2023YFC3804200//National Key Research and Development Program of China/ ; 2023YFC3804200//National Key Research and Development Program of China/ ; U21A20109, 4227040173, 52274164, 42174048//National Natural Science Foundation of China/ ; U21A20109, 4227040173, 52274164, 42174048//National Natural Science Foundation of China/ ; U21A20109, 4227040173, 52274164, 42174048//National Natural Science Foundation of China/ ; }, abstract = {Underground coal mining leads to land subsidence, which, in turn, results in damage to buildings and infrastructure, disturbs the original ecological environment, and hinders the sustainable development of coal mining cities. A reasonable estimation of land subsidence, on the other hand, is the foundation for building protection, land reclamation, and ecological environment reconstruction. However, when we applied the existing land subsidence estimation theory to the deep mining areas of the Ordos coalfield in western China, there was a significant deviation between the estimations and the measurements. To explain such unusual case, we propose using the overburden's average GSI (Geological Strength Index) value instead of the compressive strength (UCS) of rock specimens for a better representation of the overburden's overall properties. By using on-site subsidence monitoring results and historical data, we provided evidence which supports that the overburden's average GSI value has a much greater impact on subsidence rates than the UCS. Subsequently, we investigated the relationship between three typical overburden's GSI values and the subsidence rates via a calibrated numerical model, revealing the variation patterns of maximum surface subsidence when the overburden's average GSI value is set at 30, 50, and 75, respectively. Finally, on the basis of the measured and simulated results, we discussed a non-conventional strip mining method for mining subsidence control in the deep mining areas of the Ordos coalfield in western China, and explained why it is possible and what are the significant advantages behind. The proposed methods, findings, and suggestions in this paper are therefore quite helpful for researchers and engineers who wish to estimate and control the mining-induced land subsidence, as well as for those who are particularly interested in the study of environment science related to land subsidence.}, } @article {pmid38172116, year = {2024}, author = {Külling, N and Adde, A and Fopp, F and Schweiger, AK and Broennimann, O and Rey, PL and Giuliani, G and Goicolea, T and Petitpierre, B and Zimmermann, NE and Pellissier, L and Altermatt, F and Lehmann, A and Guisan, A}, title = {SWECO25: a cross-thematic raster database for ecological research in Switzerland.}, journal = {Scientific data}, volume = {11}, number = {1}, pages = {21}, pmid = {38172116}, issn = {2052-4463}, abstract = {Standard and easily accessible cross-thematic spatial databases are key resources in ecological research. In Switzerland, as in many other countries, available data are scattered across computer servers of research institutions and are rarely provided in standard formats (e.g., different extents or projections systems, inconsistent naming conventions). Consequently, their joint use can require heavy data management and geomatic operations. Here, we introduce SWECO25, a Swiss-wide raster database at 25-meter resolution gathering 5,265 layers. The 10 environmental categories included in SWECO25 are: geologic, topographic, bioclimatic, hydrologic, edaphic, land use and cover, population, transportation, vegetation, and remote sensing. SWECO25 layers were standardized to a common grid sharing the same resolution, extent, and geographic coordinate system. SWECO25 includes the standardized source data and newly calculated layers, such as those obtained by computing focal or distance statistics. SWECO25 layers were validated by a data integrity check, and we verified that the standardization procedure had a negligible effect on the output values. SWECO25 is available on Zenodo and is intended to be updated and extended regularly.}, } @article {pmid38167330, year = {2024}, author = {Li, M and Liang, H and Yang, H and Ding, Q and Xia, R and Chen, J and Zhou, W and Yang, Y and Zhang, Z and Yao, Y and Ran, C and Zhou, Z}, title = {Deciphering the gut microbiome of grass carp through multi-omics approach.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {2}, pmid = {38167330}, issn = {2049-2618}, support = {31925038//National Natural Science Foundation of China/ ; 31925038//National Natural Science Foundation of China/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; *Carps ; Multiomics ; *Microbiota ; Proteobacteria/genetics ; Fusobacteria/genetics ; Bacteroidetes/genetics ; Firmicutes/genetics ; Fusobacterium/genetics ; RNA, Ribosomal, 16S/genetics ; Mammals/genetics ; }, abstract = {BACKGROUND: Aquaculture plays an important role in global protein supplies and food security. The ban on antibiotics as feed additive proposes urgent need to develop alternatives. Gut microbiota plays important roles in the metabolism and immunity of fish and has the potential to give rise to novel solutions for challenges confronted by fish culture. However, our understanding of fish gut microbiome is still lacking.

RESULTS: We identified 575,856 non-redundant genes by metagenomic sequencing of the intestinal content samples of grass carp. Taxonomic and functional annotation of the gene catalogue revealed specificity of the gut microbiome of grass carp compared with mammals. Co-occurrence analysis indicated exclusive relations between the genera belonging to Proteobacteria and Fusobacteria/Firmicutes/Bacteroidetes, suggesting two independent ecological groups of the microbiota. The association pattern of Proteobacteria with the gene expression modules of fish gut and the liver was consistently opposite to that of Fusobacteria, Firmicutes, and Bacteroidetes, implying differential functionality of Proteobacteria and Fusobacteria/Firmicutes/Bacteroidetes. Therefore, the two ecological groups were considered as two functional groups, i.e., Functional Group 1: Proteobacteria and Functional Group 2: Fusobacteria/Firmicutes/Bacteroidetes. Further analysis revealed that the two functional groups differ in genetic capacity for carbohydrate utilization, virulence factors, and antibiotic resistance. Finally, we proposed that the ratio of "Functional Group 2/Functional Group 1" can be used as a biomarker that efficiently reflects the structural and functional characteristics of the microbiota of grass carp.

CONCLUSIONS: The gene catalogue is an important resource for investigating the gut microbiome of grass carp. Multi-omics analysis provides insights into functional implications of the main phyla that comprise the fish microbiota and shed lights on targets for microbiota regulation. Video Abstract.}, } @article {pmid38166118, year = {2024}, author = {Muraleedharan, V and Rajan, SC and R, J}, title = {Geometric entropy of plant leaves: A measure of morphological complexity.}, journal = {PloS one}, volume = {19}, number = {1}, pages = {e0293596}, pmid = {38166118}, issn = {1932-6203}, mesh = {Entropy ; *Plants ; *Biological Evolution ; Physical Phenomena ; Plant Leaves/anatomy & histology ; }, abstract = {Shape is an objective characteristic of an object. A boundary separates a physical object from its surroundings. It defines the shape and regulates energy flux into and from an object. Visual perception of a definite shape (geometry) of physical objects is an abstraction. While the perceived geometry at an object's sharp interface (macro) creates a Euclidian illusion of actual shape, the notion of diffuse interfaces (micro) allows an understanding of the realistic form of objects. Here, we formulate a dimensionless geometric entropy of plant leaves (SL) by a 2-D description of a phase-field function. We applied this method to 112 tropical plant leaf images. SL was estimated from the leaf perimeter (P) and leaf area (A). It correlates positively with a fractal dimensional measure of leaf complexity, viz., segmental fractal complexity. Leaves with a higher P: A ratio have higher SL and possess complex morphology. The univariate cluster analysis of SL reveals the taxonomic relationship among the leaf shapes at the genus level. An increase in SL of plant leaves could be an evolutionary strategy. The results of morphological complexity presented in this paper will trigger discussion on the causal links between leaf adaptive stability/efficiency and complexity. We present SL as a derived plant trait to describe plant leaf complexity and adaptive stability. Integrating SL into other leaf physiological measures will help to understand the dynamics of energy flow between plants and their environment.}, } @article {pmid38160970, year = {2024}, author = {Thenmozhi, M and Sujatha, M and Kavitha, M and Senthilraja, S and Babu, M and Priya, V}, title = {Assessment of cyclone risk and case study of Gaja cyclone using GIS techniques and machine learning algorithms in coastal zone of Tamil Nadu, India.}, journal = {Environmental research}, volume = {246}, number = {}, pages = {118089}, doi = {10.1016/j.envres.2023.118089}, pmid = {38160970}, issn = {1096-0953}, mesh = {*Cyclonic Storms ; India ; Geographic Information Systems ; *Disasters ; Algorithms ; }, abstract = {Cyclones can cause devastating impacts, including strong winds, heavy rainfall, storm surges, and flooding. The aftermath includes infrastructure damage, loss of life, displacement of communities, and ecological disruptions. Timely response and recovery efforts are crucial to minimize the socio-economic and environmental consequences of cyclones. To accelerate the time-consuming risk assessment process, particularly in geographically diverse regions, a blend of multi-criteria decision-making and machine learning models was utilized. This novel approach swiftly assessed cyclone risk and the impact of the Gaja cyclone in Nagapattinam, India. The method involved assigning weights to distinct criteria, unveiling notable vulnerability aspects like elevation, slope, proximity to the coast, distance from cyclone tracts, Lu/Lc, population density, proximity to cyclone shelters, household density, accessibility to healthcare facilities, NDVI, and levels of awareness. Daddavari, Ettugudi, Kodikarai, Vedharanyam, Velankanni, and Thirupoondi face high/extreme cyclone risk. Nagore, Nagapattinam, Pillai, Enangudi, and Sannanllur have low/no threat. To further enhance the precision of the study, machine learning algorithms like SVM, SAM, and MLC were deployed. These models were instrumental in generating pre- and post-cyclone land use maps. The influence of Gaja cyclones effects shows decreasing of agriculture land from 34% to 30%, aquaculture increase 1%, barren land decrease from 8% to 6%, Built-up land decrease from 15% to 13%, land with scrub and salt pan also decrease from 21% to 17% and 10%-8%. Mostly effect of Gaja cyclone is dramatic increase of water body from 8% to 21%. Conducting cyclone risk zone analysis and pre/post-cyclone Land Use Land Cover (LULC) detection in Nagapattinam offers valuable insights for disaster preparedness, infrastructure planning, and climate resilience. This study can enhance understanding of vulnerability and aid in formulating strategies to mitigate cyclone impacts, ensuring sustainable development in the region.}, } @article {pmid38160816, year = {2024}, author = {Jevšenak, J and Klisz, M and Mašek, J and Čada, V and Janda, P and Svoboda, M and Vostarek, O and Treml, V and van der Maaten, E and Popa, A and Popa, I and van der Maaten-Theunissen, M and Zlatanov, T and Scharnweber, T and Ahlgrimm, S and Stolz, J and Sochová, I and Roibu, CC and Pretzsch, H and Schmied, G and Uhl, E and Kaczka, R and Wrzesiński, P and Šenfeldr, M and Jakubowski, M and Tumajer, J and Wilmking, M and Obojes, N and Rybníček, M and Lévesque, M and Potapov, A and Basu, S and Stojanović, M and Stjepanović, S and Vitas, A and Arnič, D and Metslaid, S and Neycken, A and Prislan, P and Hartl, C and Ziche, D and Horáček, P and Krejza, J and Mikhailov, S and Světlík, J and Kalisty, A and Kolář, T and Lavnyy, V and Hordo, M and Oberhuber, W and Levanič, T and Mészáros, I and Schneider, L and Lehejček, J and Shetti, R and Bošeľa, M and Copini, P and Koprowski, M and Sass-Klaassen, U and Izmir, ŞC and Bakys, R and Entner, H and Esper, J and Janecka, K and Martinez Del Castillo, E and Verbylaite, R and Árvai, M and de Sauvage, JC and Čufar, K and Finner, M and Hilmers, T and Kern, Z and Novak, K and Ponjarac, R and Puchałka, R and Schuldt, B and Škrk Dolar, N and Tanovski, V and Zang, C and Žmegač, A and Kuithan, C and Metslaid, M and Thurm, E and Hafner, P and Krajnc, L and Bernabei, M and Bojić, S and Brus, R and Burger, A and D'Andrea, E and Đorem, T and Gławęda, M and Gričar, J and Gutalj, M and Horváth, E and Kostić, S and Matović, B and Merela, M and Miletić, B and Morgós, A and Paluch, R and Pilch, K and Rezaie, N and Rieder, J and Schwab, N and Sewerniak, P and Stojanović, D and Ullmann, T and Waszak, N and Zin, E and Skudnik, M and Oštir, K and Rammig, A and Buras, A}, title = {Incorporating high-resolution climate, remote sensing and topographic data to map annual forest growth in central and eastern Europe.}, journal = {The Science of the total environment}, volume = {913}, number = {}, pages = {169692}, doi = {10.1016/j.scitotenv.2023.169692}, pmid = {38160816}, issn = {1879-1026}, mesh = {*Ecosystem ; *Remote Sensing Technology ; Forests ; Trees ; Climate Change ; Europe, Eastern ; Europe ; }, abstract = {To enhance our understanding of forest carbon sequestration, climate change mitigation and drought impact on forest ecosystems, the availability of high-resolution annual forest growth maps based on tree-ring width (TRW) would provide a significant advancement to the field. Site-specific characteristics, which can be approximated by high-resolution Earth observation by satellites (EOS), emerge as crucial drivers of forest growth, influencing how climate translates into tree growth. EOS provides information on surface reflectance related to forest characteristics and thus can potentially improve the accuracy of forest growth models based on TRW. Through the modelling of TRW using EOS, climate and topography data, we showed that species-specific models can explain up to 52 % of model variance (Quercus petraea), while combining different species results in relatively poor model performance (R[2] = 13 %). The integration of EOS into models based solely on climate and elevation data improved the explained variance by 6 % on average. Leveraging these insights, we successfully generated a map of annual TRW for the year 2021. We employed the area of applicability (AOA) approach to delineate the range in which our models are deemed valid. The calculated AOA for the established forest-type models was 73 % of the study region, indicating robust spatial applicability. Notably, unreliable predictions predominantly occurred in the climate margins of our dataset. In conclusion, our large-scale assessment underscores the efficacy of combining climate, EOS and topographic data to develop robust models for mapping annual TRW. This research not only fills a critical void in the current understanding of forest growth dynamics but also highlights the potential of integrated data sources for comprehensive ecosystem assessments.}, } @article {pmid38159778, year = {2024}, author = {Kelly, MG and Mann, DG and Taylor, JD and Juggins, S and Walsh, K and Pitt, JA and Read, DS}, title = {Maximising environmental pressure-response relationship signals from diatom-based metabarcoding in rivers.}, journal = {The Science of the total environment}, volume = {914}, number = {}, pages = {169445}, doi = {10.1016/j.scitotenv.2023.169445}, pmid = {38159778}, issn = {1879-1026}, mesh = {*Rivers ; *Diatoms ; Fresh Water ; Biodiversity ; Databases, Factual ; Environmental Monitoring ; Ecosystem ; }, abstract = {DNA metabarcoding has been performed on a large number of river phytobenthos samples collected from the UK, using rbcL primers optimised for diatoms. Within this dataset the composition of non-diatom sequence reads was studied and the effect of including these in models for evaluating the nutrient gradient was assessed. Whilst many non-diatom taxonomic groups were detected, few contained the full diversity expected in riverine environments. This may be due to the performance of the current primers in characterising the wider phytobenthic community and influenced by the sampling method employed, as both were developed specifically for diatoms. Nevertheless, the study identified considerable diversity in some groups, e.g. Eustigmatophyceae and a wider distribution than previously thought for freshwater Phaeophyceae. These results offer a strong case for the benefits of metabarcoding for expanding knowledge of aquatic biodiversity in the UK and elsewhere. Many of the ASVs associated with non-diatoms showed significant pressure responses; however, models that included non-diatoms had similar predictive strength to those based on diatoms alone. Whilst limitations of the primers for assessing non-diatoms may play a role in explaining these results, the diatoms provide a strong signal along the nutrient gradient and other algae, therefore, add little unique information. We recommend that future developments should use ASVs to calculate metrics, with links to reference databases made as a final step to generate lists of taxa to support interpretation. Any further exploration of the potential of non-diatoms would benefit from access to a well-curated reference database, similar to diat.barcode. Such a database does not yet exist, and we caution against the indiscriminate use of NCBI GenBank as a taxonomic resource as many rbcL sequences deposited have not been curated.}, } @article {pmid38155557, year = {2024}, author = {Forbes, VE and Accolla, C and Banitz, T and Crouse, K and Galic, N and Grimm, V and Raimondo, S and Schmolke, A and Vaugeois, M}, title = {Mechanistic population models for ecological risk assessment and decision support: The importance of good conceptual model diagrams.}, journal = {Integrated environmental assessment and management}, volume = {20}, number = {5}, pages = {1566-1574}, doi = {10.1002/ieam.4886}, pmid = {38155557}, issn = {1551-3793}, support = {//Helmholtz/ ; 2018-06139//Svenska Forskningsrådet Formas/ ; }, mesh = {Risk Assessment/methods ; *Ecology ; *Decision Support Techniques ; Models, Theoretical ; Environmental Monitoring/methods ; }, abstract = {The use of mechanistic population models as research and decision-support tools in ecology and ecological risk assessment (ERA) is increasing. This growth has been facilitated by advances in technology, allowing the simulation of more complex systems, as well as by standardized approaches for model development, documentation, and evaluation. Mechanistic population models are particularly useful for simulating complex systems, but the required model complexity can make them challenging to communicate. Conceptual diagrams that summarize key model elements, as well as elements that were considered but not included, can facilitate communication and understanding of models and increase their acceptance as decision-support tools. Currently, however, there are no consistent standards for creating or presenting conceptual model diagrams (CMDs), and both terminology and content vary widely. Here, we argue that greater consistency in CMD development and presentation is an important component of good modeling practice, and we provide recommendations, examples, and a free web app (pop-cmd.com) for achieving this for population models used for decision support in ERAs. Integr Environ Assess Manag 2024;20:1566-1574. © 2023 SETAC.}, } @article {pmid38149298, year = {2023}, author = {Fins, IS and Singleton, DA and Radford, AD and Sánchez-Vizcaíno, F and Pinchbeck, GL}, title = {A mixed-methods approach utilising electronic health records to examine antimicrobial prescription surrounding gastrointestinal clinical presentations in dogs and cats.}, journal = {Frontiers in veterinary science}, volume = {10}, number = {}, pages = {1166114}, pmid = {38149298}, issn = {2297-1769}, abstract = {INTRODUCTION: Systemically-administered antimicrobials are often prescribed in canine and feline gastrointestinal clinical presentations. Responsible use of antimicrobials, particularly those considered Highest Priority Critically Important Antimicrobials (HPCIAs) is vital to tackle antimicrobial resistance. Although practice-level prescription guidance is available, further strategies based on a greater understanding of antimicrobial prescription at the population-level are needed. Here, we used a mixed-methods approach, harnessing veterinary electronic health records (EHRs) to characterise the use of antimicrobials in canine and feline gastrointestinal presentations, and to explore justification and reasoning around antimicrobial prescribing, particularly of HPCIAs.

METHODS: This observational study used 23,337 EHRs complemented with veterinary practitioner-completed questionnaires, from canine and feline gastrointestinal consultations from 225 volunteer UK veterinary practices between April 2014 and September 2018.

RESULTS: A total of 83.4% (95% confidence interval (CI) 82.6-84.3) gastrointestinal presentations were reported as mild, with non-haemorrhagic diarrhoea and vomiting the most frequently reported clinical signs. Systemically-administered antimicrobials occurred in 28.6% of canine (95% CI 26.9-30.3) and 22.4% of feline (95% CI 20.4-24.4) gastrointestinal consultations, with HPCIA prescription occurring more frequently in cats. Results of multivariable analysis showed the presence of non-haemorrhagic diarrhoea (canine Odds Ratio (OR) 2.1, 95% CI 1.9-2.3; feline OR 1.8, 95% CI 1.5-2.1), haemorrhagic diarrhoea (canine OR 4.2, 95% CI 3.8-4.7; feline OR 3.1, 95% CI 2.4-3.8), and moderate/severe presentations (canine OR 1.9, 95% CI 1.7-2.8; feline OR 2.0, 95% CI 1.7-2.5) were positively associated with receiving a systemically-administered antimicrobial. Thematic analysis of clinical narrative content of 516 gastrointestinal consultations where HPCIAs were prescribed allowed the identification of ten factors underpinning reasoning or decision-making for HPCIA prescription: perceived animal/owner compliance; owner's expectations; perceived risk of infection; clinical signs; recent clinical history; perceived positive previous response to antimicrobial therapy; geriatric patients and euthanasia; concomitant conditions; diagnostic testing and the behavioral trend to trial antimicrobial therapy empirically in gastrointestinal cases. No explicit justification for HPCIA prescription was recorded in 77% of cases.

DISCUSSION: Improving recorded justification represents a clear target for stewardship programmes. By utilising a complementary mixed-methods approach to EHRs, this study unlocks previously untapped data recorded within EHRs. These results can help inform targeted interventions, contributing towards enhanced antimicrobial stewardship.}, } @article {pmid38149262, year = {2023}, author = {Wang, Y and Shojaie, A and Randolph, T and Knight, P and Ma, J}, title = {GENERALIZED MATRIX DECOMPOSITION REGRESSION: ESTIMATION AND INFERENCE FOR TWO-WAY STRUCTURED DATA.}, journal = {The annals of applied statistics}, volume = {17}, number = {4}, pages = {2944-2969}, pmid = {38149262}, issn = {1932-6157}, support = {R01 GM129512/GM/NIGMS NIH HHS/United States ; U19 CA203654/CA/NCI NIH HHS/United States ; T32 GM135117/GM/NIGMS NIH HHS/United States ; R01 GM145772/GM/NIGMS NIH HHS/United States ; P50 CA228944/CA/NCI NIH HHS/United States ; R01 HL155417/HL/NHLBI NIH HHS/United States ; R01 GM133848/GM/NIGMS NIH HHS/United States ; }, abstract = {Motivated by emerging applications in ecology, microbiology, and neuroscience, this paper studies high-dimensional regression with two-way structured data. To estimate the high-dimensional coefficient vector, we propose the generalized matrix decomposition regression (GMDR) to efficiently leverage auxiliary information on row and column structures. GMDR extends the principal component regression (PCR) to two-way structured data, but unlike PCR, GMDR selects the components that are most predictive of the outcome, leading to more accurate prediction. For inference on regression coefficients of individual variables, we propose the generalized matrix decomposition inference (GMDI), a general high-dimensional inferential framework for a large family of estimators that include the proposed GMDR estimator. GMDI provides more flexibility for incorporating relevant auxiliary row and column structures. As a result, GMDI does not require the true regression coefficients to be sparse, but constrains the coordinate system representing the regression coefficients according to the column structure. GMDI also allows dependent and heteroscedastic observations. We study the theoretical properties of GMDI in terms of both the type-I error rate and power and demonstrate the effectiveness of GMDR and GMDI in simulation studies and an application to human microbiome data.}, } @article {pmid38147867, year = {2023}, author = {He, Z and Pfaff, E and Guo, SJ and Guo, Y and Wu, Y and Tao, C and Stiglic, G and Bian, J}, title = {Enriching Real-world Data with Social Determinants of Health for Health Outcomes and Health Equity: Successes, Challenges, and Opportunities.}, journal = {Yearbook of medical informatics}, volume = {32}, number = {1}, pages = {253-263}, pmid = {38147867}, issn = {2364-0502}, support = {U2C ES026555/ES/NIEHS NIH HHS/United States ; R21 LM013911/LM/NLM NIH HHS/United States ; R21 ES032762/ES/NIEHS NIH HHS/United States ; R01 AG080624/AG/NIA NIH HHS/United States ; R21 CA245858/CA/NCI NIH HHS/United States ; UL1 TR001427/TR/NCATS NIH HHS/United States ; R01 DK133465/DK/NIDDK NIH HHS/United States ; R01 CA246418/CA/NCI NIH HHS/United States ; U18DP006512/ACL/ACL HHS/United States ; P01 AA029547/AA/NIAAA NIH HHS/United States ; UL1 TR002489/TR/NCATS NIH HHS/United States ; }, mesh = {Humans ; *Health Equity ; Social Determinants of Health ; Electronic Health Records ; *Population Health ; Outcome Assessment, Health Care ; }, abstract = {OBJECTIVE: To summarize the recent methods and applications that leverage real-world data such as electronic health records (EHRs) with social determinants of health (SDoH) for public and population health and health equity and identify successes, challenges, and possible solutions.

METHODS: In this opinion review, grounded on a social-ecological-model-based conceptual framework, we surveyed data sources and recent informatics approaches that enable leveraging SDoH along with real-world data to support public health and clinical health applications including helping design public health intervention, enhancing risk stratification, and enabling the prediction of unmet social needs.

RESULTS: Besides summarizing data sources, we identified gaps in capturing SDoH data in existing EHR systems and opportunities to leverage informatics approaches to collect SDoH information either from structured and unstructured EHR data or through linking with public surveys and environmental data. We also surveyed recently developed ontologies for standardizing SDoH information and approaches that incorporate SDoH for disease risk stratification, public health crisis prediction, and development of tailored interventions.

CONCLUSIONS: To enable effective public health and clinical applications using real-world data with SDoH, it is necessary to develop both non-technical solutions involving incentives, policies, and training as well as technical solutions such as novel social risk management tools that are integrated into clinical workflow. Ultimately, SDoH-powered social risk management, disease risk prediction, and development of SDoH tailored interventions for disease prevention and management have the potential to improve population health, reduce disparities, and improve health equity.}, } @article {pmid38147769, year = {2024}, author = {Wang, M and Ji, L and Xie, Y and Huang, G}, title = {Regional bioethanol supply chain optimization with the integration of GIS-MCDM method and quantile-based scenario analysis.}, journal = {Journal of environmental management}, volume = {351}, number = {}, pages = {119883}, doi = {10.1016/j.jenvman.2023.119883}, pmid = {38147769}, issn = {1095-8630}, mesh = {*Geographic Information Systems ; Biomass ; Uncertainty ; *Agriculture ; China ; }, abstract = {This study presents a novel decision-support framework for the bioethanol supply chain network planning and management under uncertainties. Under the holistic framework, the most suitable sites for biorefineries are first screened out by adopting a GIS-based multi-criteria decision-making approach. Then, a mixed-integer linear programming model combined with quantile-based scenario analysis is developed to determine the strategic planning (i.e. locations and size of biorefineries) and tactical management (i.e. biomass purchasing, feedstock transportation, bioethanol production, and product delivery) under uncertainties. The model can effectively search for reliable solutions under uncertainties and achieve tradeoff solutions with the consideration of decision makers' risk tolerance. The proposed framework is demonstrated through a case study in China. It is suggested to build seven biorefineries with a capacity of 100 million liters in Zhumadian city. Utilizing 41% of local agricultural residues could satisfy the bioethanol requirement in the transportation sector under the E20 policy. However, the estimated production cost of bioethanol in Zhumadian is very high, about 1.11 $/L, which makes it lose cost advantage in the fuel market. Thus, currently, effective subsidies, mandatory energy substitution policies, along other environmental regulatory measures are desired to promote the bioethanol industry development.}, } @article {pmid38147054, year = {2024}, author = {Cusack, CE and Vanzhula, IA and Sandoval-Araujo, LE and Pennesi, JL and Kelley, SW and Levinson, CA}, title = {Are central eating disorder network symptoms sensitive to item selection and sample? Implications for conceptualization of eating disorder psychopathology from a network perspective.}, journal = {Journal of psychopathology and clinical science}, volume = {133}, number = {1}, pages = {48-60}, pmid = {38147054}, issn = {2769-755X}, support = {R15 MH121445/MH/NIMH NIH HHS/United States ; }, mesh = {Humans ; *Concept Formation ; *Feeding and Eating Disorders/diagnosis ; Databases, Factual ; Ecological Momentary Assessment ; Fear ; }, abstract = {Item selection is a critical decision in modeling psychological networks. The current preregistered two-study research used random selections of 1,000 symptom networks to examine which eating disorder (ED) and co-occurring symptoms are most central in longitudinal networks among individuals with EDs (N = 71, total observations = 6,060) and tested whether centrality changed based on which items were included in the network. Participants completed 2 weeks of ecological momentary assessment (five surveys/day). In Study 1, we obtained initial strength centrality values by estimating an a priori network using eight items with the highest means. We then estimated 1,000 networks and their centrality from a random selection of unique eight-item symptom combinations. We compared the strength centrality from the a priori network to the distribution of strength centrality estimates from the random-item networks. In Study 2, we repeated this procedure in an independent longitudinal dataset (N = 41, total observations = 4,575) to determine if our results generalized across samples. Shame, guilt, worry, and fear of losing control were consistently central across networks, regardless of items included in the network or sample. Results suggest that these symptoms may be important to the structure of ED psychopathology and have implications for how we understand the structure of ED psychopathology. Existing methods for item inclusion in psychological networks may distort the structure of ED symptom networks by either under- or overestimating strength centrality, or by omitting consistently central symptoms that are nontraditional ED symptoms. Future research should consider including these symptoms in models of ED psychopathology. (PsycInfo Database Record (c) 2023 APA, all rights reserved).}, } @article {pmid38144190, year = {2023}, author = {Graves, SJ and Marconi, S and Stewart, D and Harmon, I and Weinstein, B and Kanazawa, Y and Scholl, VM and Joseph, MB and McGlinchy, J and Browne, L and Sullivan, MK and Estrada-Villegas, S and Wang, DZ and Singh, A and Bohlman, S and Zare, A and White, EP}, title = {Data science competition for cross-site individual tree species identification from airborne remote sensing data.}, journal = {PeerJ}, volume = {11}, number = {}, pages = {e16578}, pmid = {38144190}, issn = {2167-8359}, mesh = {Humans ; *Remote Sensing Technology ; *Data Science ; Neural Networks, Computer ; Ecosystem ; }, abstract = {Data on individual tree crowns from remote sensing have the potential to advance forest ecology by providing information about forest composition and structure with a continuous spatial coverage over large spatial extents. Classifying individual trees to their taxonomic species over large regions from remote sensing data is challenging. Methods to classify individual species are often accurate for common species, but perform poorly for less common species and when applied to new sites. We ran a data science competition to help identify effective methods for the task of classification of individual crowns to species identity. The competition included data from three sites to assess each methods' ability to generalize patterns across two sites simultaneously and apply methods to an untrained site. Three different metrics were used to assess and compare model performance. Six teams participated, representing four countries and nine individuals. The highest performing method from a previous competition in 2017 was applied and used as a baseline to understand advancements and changes in successful methods. The best species classification method was based on a two-stage fully connected neural network that significantly outperformed the baseline random forest and gradient boosting ensemble methods. All methods generalized well by showing relatively strong performance on the trained sites (accuracy = 0.46-0.55, macro F1 = 0.09-0.32, cross entropy loss = 2.4-9.2), but generally failed to transfer effectively to the untrained site (accuracy = 0.07-0.32, macro F1 = 0.02-0.18, cross entropy loss = 2.8-16.3). Classification performance was influenced by the number of samples with species labels available for training, with most methods predicting common species at the training sites well (maximum F1 score of 0.86) relative to the uncommon species where none were predicted. Classification errors were most common between species in the same genus and different species that occur in the same habitat. Most methods performed better than the baseline in detecting if a species was not in the training data by predicting an untrained mixed-species class, especially in the untrained site. This work has highlighted that data science competitions can encourage advancement of methods, particularly by bringing in new people from outside the focal discipline, and by providing an open dataset and evaluation criteria from which participants can learn.}, } @article {pmid38140503, year = {2023}, author = {Tunklová, B and Šerá, B and Šrámková, P and Ďurčányová, S and Šerý, M and Kováčik, D and Zahoranová, A and Hnilička, F}, title = {Growth Stimulation of Durum Wheat and Common Buckwheat by Non-Thermal Atmospheric Pressure Plasma.}, journal = {Plants (Basel, Switzerland)}, volume = {12}, number = {24}, pages = {}, pmid = {38140503}, issn = {2223-7747}, support = {APVV-21-147//Slovak Research and Development Agency/ ; }, abstract = {The grains of durum wheat (Triticum durum Desf.) and achenes of common buckwheat (Fagopyrum esculentum Moench) were tested after treatment with two sources of non-thermal atmospheric pressure plasma (DCSBD, MSDBD) with different treatment times (0, 3, 5, 10, 20, 30, and 40 s). The effect of these treatments was monitored with regard to the seed surface diagnostics (water contact angle-WCA, chemical changes by Fourier transform infrared spectroscopy-FTIR); twenty parameters associated with germination and initial seed growth were monitored. A study of the wettability confirmed a decrease in WCA values indicating an increase in surface energy and hydrophilicity depending on the type of seed, plasma source, and treatment time. Surface analysis by attenuated total reflectance FTIR (ATR-FTIR) showed no obvious changes in the chemical bonds on the surface of the plasma-treated seeds, which confirms the non-destructive effect of the plasma on the chemical composition of the seed shell. A multivariate analysis of the data showed many positive trends (not statistically significant) in germination and initial growth parameters. The repeated results for germination rate and root/shoot dry matter ratio indicate the tendency of plants to invest in underground organs. Durum wheat required longer treatment times with non-thermal plasma (10 s, 20 s) for germination and early growth, whereas buckwheat required shorter times (5 s, 10 s). The responses of durum wheat grains to the two non-thermal plasma sources used were equal. In contrast, the responses of buckwheat achenes were more favorable to MSDBD treatment than to DCSBD.}, } @article {pmid38138669, year = {2023}, author = {Abramovskis, V and Drunka, R and Csáki, Š and Lukáč, F and Veverka, J and Illkova, K and Gavrilovs, P and Shishkin, A}, title = {Preparation and Characteristics of High-Performance, Low-Density Metallo-Ceramics Composite.}, journal = {Materials (Basel, Switzerland)}, volume = {16}, number = {24}, pages = {}, pmid = {38138669}, issn = {1996-1944}, support = {VPP-AIPP-2021/1-0015//Latvian research council/ ; ZM-2023/10//B57 RTU internal scientific research, ZM-2023/10/ ; }, abstract = {By applying the physical vapour deposition method, hollow ceramic microspheres were coated with titanium, and subsequently, they were sintered using the spark plasma sintering technique to create a porous ceramic material that is lightweight and devoid of a matrix. The sintering process was carried out at temperatures ranging from 1050 to 1200 °C, with a holding time of 2 min. The samples were subjected to conventional thermal analyses (differential scanning calorimetry, thermogravimetry, dilatometry), oxidation resistance tests, and thermal diffusivity measurements. Phase analysis of the samples was performed using the XRD and the microstructure of the prepared specimens was examined using electron microscopy. The titanium coating on the microspheres increased the compressive strength and density of the resulting ceramic material as the sintering temperature increased. The morphology of the samples was carefully examined, and phase transitions were also identified during the analysis of the samples.}, } @article {pmid38138064, year = {2023}, author = {Bedard, DL and Van Slyke, G and Nübel, U and Bateson, MM and Brumfield, S and An, YJ and Becraft, ED and Wood, JM and Thiel, V and Ward, DM}, title = {Geographic and Ecological Diversity of Green Sulfur Bacteria in Hot Spring Mat Communities.}, journal = {Microorganisms}, volume = {11}, number = {12}, pages = {}, pmid = {38138064}, issn = {2076-2607}, support = {CAN-97-01-055-004/NASA/NASA/United States ; NCC2-1073/NASA/NASA/United States ; NAG5-8824/NASA/NASA/United States ; NNX16AJ62G/NASA/NASA/United States ; }, abstract = {Three strains of thermophilic green sulfur bacteria (GSB) are known; all are from microbial mats in hot springs in Rotorua, New Zealand (NZ) and belong to the species Chlorobaculum tepidum. Here, we describe diverse populations of GSB inhabiting Travel Lodge Spring (TLS) (NZ) and hot springs ranging from 36.1 °C to 51.1 °C in the Republic of the Philippines (PHL) and Yellowstone National Park (YNP), Wyoming, USA. Using targeted amplification and restriction fragment length polymorphism analysis, GSB 16S rRNA sequences were detected in mats in TLS, one PHL site, and three regions of YNP. GSB enrichments from YNP and PHL mats contained small, green, nonmotile rods possessing chlorosomes, chlorobactene, and bacteriochlorophyll c. Partial 16S rRNA gene sequences from YNP, NZ, and PHL mats and enrichments from YNP and PHL samples formed distinct phylogenetic clades, suggesting geographic isolation, and were associated with samples differing in temperature and pH, suggesting adaptations to these parameters. Sequences from enrichments and corresponding mats formed clades that were sometimes distinct, increasing the diversity detected. Sequence differences, monophyly, distribution patterns, and evolutionary simulation modeling support our discovery of at least four new putative moderately thermophilic Chlorobaculum species that grew rapidly at 40 °C to 44 °C.}, } @article {pmid38129780, year = {2023}, author = {Duan, L and Wang, F and Shen, H and Xie, S and Chen, X and Xie, Q and Li, R and Cao, A and Li, H}, title = {Identification, evolution, and expression of GDSL-type Esterase/Lipase (GELP) gene family in three cotton species: a bioinformatic analysis.}, journal = {BMC genomics}, volume = {24}, number = {1}, pages = {795}, pmid = {38129780}, issn = {1471-2164}, support = {31960413//National Natural Science Foundation of China/ ; 2016AC017, 2020BC002//Science and Technology Project of Bingtuan/ ; }, mesh = {*Esterases/genetics/metabolism ; *Lipase/genetics/metabolism ; Gossypium/metabolism ; Genome, Plant ; Gene Duplication ; Computational Biology ; Gene Expression Regulation, Plant ; Phylogeny ; Plant Proteins/genetics/metabolism ; }, abstract = {BACKGROUND: GDSL esterase/lipases (GELPs) play important roles in plant growth, development, and response to biotic and abiotic stresses. Presently, an extensive and in-depth analysis of GELP family genes in cotton is still not clear enough, which greatly limits the further understanding of cotton GELP function and regulatory mechanism.

RESULTS: A total of 389 GELP family genes were identified in three cotton species of Gossypium hirsutum (193), G. arboreum (97), and G. raimondii (99). These GELPs could be classified into three groups and eight subgroups, with the GELPs in same group to have similar gene structures and conserved motifs. Evolutionary event analysis showed that the GELP family genes tend to be diversified at the spatial dimension and certain conservative at the time dimension, with a trend of potential continuous expansion in the future. The orthologous or paralogous GELPs among different genomes/subgenomes indicated the inheritance from genome-wide duplication during polyploidization, and the paralogous GELPs were derived from chromosomal segment duplication or tandem replication. GELP genes in the A/D subgenome underwent at least three large-scale replication events in the evolutionary process during the period of 0.6-3.2 MYA, with two large-scale evolutionary events between 0.6-1.8 MYA that were associated with tetraploidization, and the large-scale duplication between 2.6-9.1 MYA that occurred during diploidization. The cotton GELPs indicated diverse expression patterns in tissue development, ovule and fiber growth, and in response to biotic and abiotic stresses, combining the existing cis-elements in the promoter regions, suggesting the GELPs involvements of functions to be diversification and of the mechanisms to be a hormone-mediated manner.

CONCLUSIONS: Our results provide a systematic and comprehensive understanding the function and regulatory mechanism of cotton GELP family, and offer an effective reference for in-depth genetic improvement utilization of cotton GELPs.}, } @article {pmid38128801, year = {2024}, author = {Wang, G and Jiang, G and Peng, R and Wang, Y and Li, J and Sima, Y and Xu, S}, title = {Multi-omics integrative analysis revealed characteristic changes in blood cell immunity and amino acid metabolism in a silkworm model of hyperproteinemia.}, journal = {International journal of biological macromolecules}, volume = {258}, number = {Pt 1}, pages = {128809}, doi = {10.1016/j.ijbiomac.2023.128809}, pmid = {38128801}, issn = {1879-0003}, mesh = {Humans ; Animals ; Histones/metabolism ; *Bombyx/metabolism ; Lysine/metabolism ; Multiomics ; Chromatin ; Blood Proteins/metabolism ; Blood Cells/metabolism ; *Metabolic Diseases ; Acetylation ; }, abstract = {Hyperproteinemia is a serious metabolic disease of both humans and animals characterized by an abnormally high plasma protein concentration (HPPC). Although hyperproteinemia can cause an imbalance in blood cell homeostasis, the functional changes to blood cells remain unclear. Here, a HPPC silkworm model was used to assess changes to the chromatin accessibility and transcript levels of genes related to blood cell metabolism and immune function. The results showed that HPPC enhanced phagocytosis of blood cells, increased chromatin accessibility and transcript levels of genes involved in cell phagocytosis, proliferation, stress, and programmed death, while genes associated with aromatic amino acid metabolism, and antibacterial peptide synthesis were inhibited in blood cells. Further analysis of the chromatin accessibility of the promoter region found that the high chromatin accessibility of genes sensitive to HPPC, was related to histone modifications, including tri-methylation of lysine residue 4 of histone H3 and acetylation of lysine residue 27 of histone H3. Changes to the chromatin accessibility and transcript levels of genes related to immune function and amino acid metabolism in the blood cells of the HPPC silkworm model provided useful references for future studies of the mechanisms underlying epigenomic regulation mediated by hyperproteinemia.}, } @article {pmid38125713, year = {2023}, author = {Tamburro, G and Fiedler, P and De Fano, A and Raeisi, K and Khazaei, M and Vaquero, L and Bruña, R and Oppermann, H and Bertollo, M and Filho, E and Zappasodi, F and Comani, S}, title = {An ecological study protocol for the multimodal investigation of the neurophysiological underpinnings of dyadic joint action.}, journal = {Frontiers in human neuroscience}, volume = {17}, number = {}, pages = {1305331}, pmid = {38125713}, issn = {1662-5161}, abstract = {A novel multimodal experimental setup and dyadic study protocol were designed to investigate the neurophysiological underpinnings of joint action through the synchronous acquisition of EEG, ECG, EMG, respiration and kinematic data from two individuals engaged in ecologic and naturalistic cooperative and competitive joint actions involving face-to-face real-time and real-space coordinated full body movements. Such studies are still missing because of difficulties encountered in recording reliable neurophysiological signals during gross body movements, in synchronizing multiple devices, and in defining suitable study protocols. The multimodal experimental setup includes the synchronous recording of EEG, ECG, EMG, respiration and kinematic signals of both individuals via two EEG amplifiers and a motion capture system that are synchronized via a single-board microcomputer and custom Python scripts. EEG is recorded using new dry sports electrode caps. The novel study protocol is designed to best exploit the multimodal data acquisitions. Table tennis is the dyadic motor task: it allows naturalistic and face-to-face interpersonal interactions, free in-time and in-space full body movement coordination, cooperative and competitive joint actions, and two task difficulty levels to mimic changing external conditions. Recording conditions-including minimum table tennis rally duration, sampling rate of kinematic data, total duration of neurophysiological recordings-were defined according to the requirements of a multilevel analytical approach including a neural level (hyperbrain functional connectivity, Graph Theoretical measures and Microstate analysis), a cognitive-behavioral level (integrated analysis of neural and kinematic data), and a social level (extending Network Physiology to neurophysiological data recorded from two interacting individuals). Four practical tests for table tennis skills were defined to select the study population, permitting to skill-match the dyad members and to form two groups of higher and lower skilled dyads to explore the influence of skill level on joint action performance. Psychometric instruments are included to assess personality traits and support interpretation of results. Studying joint action with our proposed protocol can advance the understanding of the neurophysiological mechanisms sustaining daily life joint actions and could help defining systems to predict cooperative or competitive behaviors before being overtly expressed, particularly useful in real-life contexts where social behavior is a main feature.}, } @article {pmid38116500, year = {2023}, author = {Ji, JS and Xia, Y and Liu, L and Zhou, W and Chen, R and Dong, G and Hu, Q and Jiang, J and Kan, H and Li, T and Li, Y and Liu, Q and Liu, Y and Long, Y and Lv, Y and Ma, J and Ma, Y and Pelin, K and Shi, X and Tong, S and Xie, Y and Xu, L and Yuan, C and Zeng, H and Zhao, B and Zheng, G and Liang, W and Chan, M and Huang, C}, title = {China's public health initiatives for climate change adaptation.}, journal = {The Lancet regional health. Western Pacific}, volume = {40}, number = {}, pages = {100965}, pmid = {38116500}, issn = {2666-6065}, abstract = {China's health gains over the past decades face potential reversals if climate change adaptation is not prioritized. China's temperature rise surpasses the global average due to urban heat islands and ecological changes, and demands urgent actions to safeguard public health. Effective adaptation need to consider China's urbanization trends, underlying non-communicable diseases, an aging population, and future pandemic threats. Climate change adaptation initiatives and strategies include urban green space, healthy indoor environments, spatial planning for cities, advance location-specific early warning systems for extreme weather events, and a holistic approach for linking carbon neutrality to health co-benefits. Innovation and technology uptake is a crucial opportunity. China's successful climate adaptation can foster international collaboration regionally and beyond.}, } @article {pmid38114459, year = {2023}, author = {Novella-Fernandez, R and Brandl, R and Pinkert, S and Zeuss, D and Hof, C}, title = {Seasonal variation in dragonfly assemblage colouration suggests a link between thermal melanism and phenology.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {8427}, pmid = {38114459}, issn = {2041-1723}, mesh = {Animals ; Seasons ; *Odonata ; Climate ; Temperature ; Insecta ; Climate Change ; }, abstract = {Phenology, the seasonal timing of life events, is an essential component of diversity patterns. However, the mechanisms involved are complex and understudied. Body colour may be an important factor, because dark-bodied species absorb more solar radiation, which is predicted by the Thermal Melanism Hypothesis to enable them to thermoregulate successfully in cooler temperatures. Here we show that colour lightness of dragonfly assemblages varies in response to seasonal changes in solar radiation, with darker early- and late-season assemblages and lighter mid-season assemblages. This finding suggests a link between colour-based thermoregulation and insect phenology. We also show that the phenological pattern of dragonfly colour lightness advanced over the last decades. We suggest that changing seasonal temperature patterns due to global warming together with the static nature of solar radiation may drive dragonfly flight periods to suboptimal seasonal conditions. Our findings open a research avenue for a more mechanistic understanding of phenology and spatio-phenological impacts of climate warming on insects.}, } @article {pmid38114230, year = {2023}, author = {Wu, TF and Deng, J and Wang, X and Liu, HQ and Teng, YX and Ma, ZG and Wu, MH and Huang, WZ and Cao, H and Zhang, Y}, title = {[Textual research on Bungarus Parvus].}, journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica}, volume = {48}, number = {22}, pages = {6234-6248}, doi = {10.19540/j.cnki.cjcmm.20230708.101}, pmid = {38114230}, issn = {1001-5302}, mesh = {Animals ; *Bungarus ; Snakes ; China ; Medicine, Chinese Traditional ; *Drugs, Chinese Herbal ; }, abstract = {Bungarus Parvus, a precious animal Chinese medicinal material used in clinical practice, is believed to be first recorded in Ying Pian Xin Can published in 1936. This study was carried out to analyze the names, geographical distribution, morphological characteristics, ecological habits, poisonousness, and medicinal parts by consulting ancient Chinese medical books and local chronicles, Chinese Pharmacopeia, different processing standards of trditional Chinese medicine(TCM) decoction pieces, and modern literatures. The results showed that the earliest medicinal record of Bungarus Parvus was traced to 1894. In 1930, this medicinal material was used in the formulation of Annao Pills. The original animal, Bungarus multicinctus, was recorded by the name of "Bojijia" in 1521. The morphological characteristics, ecological habits, and poisonousness of the original animal are the same in ancient and modern records. The geographical distribution is similar between the ancient records and modern documents such as China Medicinal Animal Fauna. The dried body of young B. multicinctus is used as Bungarus Parvus, which lack detailed references. As a matter of fact, it is still inconclusive whether there are differences between young snakes and adult snakes in terms of active ingredients, pharmacological effects, and clinical applications. This study clarified the medicinal history and present situation of Bungarus Parvus. On the basis of the results, it is suggested that systematic comparison on young and adult B. multicinctus should be carried out to provide references for revising the medicinal parts of B. multicinctus.}, } @article {pmid38113992, year = {2024}, author = {Hussain, A and Maitra, J and Saifi, A and Ahmed, S and Ahmed, J and Shrestha, NK and Qureshi, F and Kamyab, H and Chelliapan, S and Yusuf, M}, title = {A sustainable approach for fluoride treatment using coconut fiber cellulose as an adsorbent.}, journal = {Environmental research}, volume = {244}, number = {}, pages = {117952}, doi = {10.1016/j.envres.2023.117952}, pmid = {38113992}, issn = {1096-0953}, mesh = {Fluorides ; Cellulose ; *Drinking Water ; Cocos ; Fluoride Treatment ; Kinetics ; *Water Pollutants, Chemical/analysis ; *Water Purification/methods ; Hydrogen-Ion Concentration ; Adsorption ; }, abstract = {In developing countries like India, an economically viable and ecologically approachable strategy is required to safeguard the drinking water. Excessive fluoride intake through drinking water can lead to dental fluorosis, skeletal fluorosis, or both. The present study has been under with an objective to investigate the feasibility of using cellulose derived from coconut fiber as an adsorbent under varying pH conditions for fluoride elimination from water. The assessment of equilibrium concentration of metal ions using adsorption isotherms is an integral part of the study. This present finding indicates the considerable effect of variation of adsorbent dosages on the fluoride removal efficiency under constant temperature conditions of 25 ± 2 °C with a contact period of 24 h. It is pertinent to mention that maximum adsorption of 88% has been observed with a pH value of 6 with 6 h time duration with fluoride dosage of 50 mg/L. The equilibrium concentration dwindled to 0.4 mg/L at fluoride concentration of 20 mg/L. The Langmuir model designates the adsorption capacity value of 2.15 mg/L with initial fluoride concentration of 0.21 mg/g with R[2] value of 0.660. Similarly, the adsorption capacity using Freundlich isotherms is found to be 0.58 L/g and 0.59 L/g with fluoride concentration of 1.84 mg/L and 2.15 mg/L respectively. The results from the present study confirm that coconut fiber possesses appropriate sorption capabilities of fluoride ion but is a pH dependent phenomenon. The outcomes of the study indicate the possible use of cellulose extracted from waste coconut fiber as a low-cost fluoride adsorbent. The present study can be well implemented on real scale systems as it will be beneficial economically as well as environmentally.}, } @article {pmid38111463, year = {2024}, author = {Li, C and Gillings, MR and Zhang, C and Chen, Q and Zhu, D and Wang, J and Zhao, K and Xu, Q and Leung, PH and Li, X and Liu, J and Jin, L}, title = {Ecology and risks of the global plastisphere as a newly expanding microbial habitat.}, journal = {Innovation (Cambridge (Mass.))}, volume = {5}, number = {1}, pages = {100543}, pmid = {38111463}, issn = {2666-6758}, abstract = {Plastic offers a new niche for microorganisms, the plastisphere. The ever-increasing emission of plastic waste makes it critical to understand the microbial ecology of the plastisphere and associated effects. Here, we present a global fingerprint of the plastisphere, analyzing samples collected from freshwater, seawater, and terrestrial ecosystems. The plastisphere assembles a distinct microbial community that has a clearly higher heterogeneity and a more deterministically dominated assembly compared to natural habitats. New coexistence patterns-loose and fragile networks with mostly specialist linkages among microorganisms that are rarely found in natural habitats-are seen in the plastisphere. Plastisphere microbiomes generally have a great potential to metabolize organic compounds, which could accelerate carbon turnover. Microorganisms involved in the nitrogen cycle are also altered in the plastisphere, especially in freshwater plastispheres, where a high abundance of denitrifiers may increase the release of nitrite (aquatic toxicant) and nitrous oxide (greenhouse gas). Enrichment of animal, plant, and human pathogens means that the plastisphere could become an increasingly mobile reservoir of harmful microorganisms. Our findings highlight that if the trajectory of plastic emissions is not reversed, the expanding plastisphere could pose critical planetary health challenges.}, } @article {pmid38111050, year = {2023}, author = {Cochetel, N and Minio, A and Guarracino, A and Garcia, JF and Figueroa-Balderas, R and Massonnet, M and Kasuga, T and Londo, JP and Garrison, E and Gaut, BS and Cantu, D}, title = {A super-pangenome of the North American wild grape species.}, journal = {Genome biology}, volume = {24}, number = {1}, pages = {290}, pmid = {38111050}, issn = {1474-760X}, support = {1741627//National Science Foundation/ ; }, mesh = {*Genome, Plant ; *Vitis/genetics ; Plant Breeding ; Genomics ; North America ; }, abstract = {BACKGROUND: Capturing the genetic diversity of wild relatives is crucial for improving crops because wild species are valuable sources of agronomic traits that are essential to enhance the sustainability and adaptability of domesticated cultivars. Genetic diversity across a genus can be captured in super-pangenomes, which provide a framework for interpreting genomic variations.

RESULTS: Here we report the sequencing, assembly, and annotation of nine wild North American grape genomes, which are phased and scaffolded at chromosome scale. We generate a reference-unbiased super-pangenome using pairwise whole-genome alignment methods, revealing the extent of the genomic diversity among wild grape species from sequence to gene level. The pangenome graph captures genomic variation between haplotypes within a species and across the different species, and it accurately assesses the similarity of hybrids to their parents. The species selected to build the pangenome are a great representation of the genus, as illustrated by capturing known allelic variants in the sex-determining region and for Pierce's disease resistance loci. Using pangenome-wide association analysis, we demonstrate the utility of the super-pangenome by effectively mapping short reads from genus-wide samples and identifying loci associated with salt tolerance in natural populations of grapes.

CONCLUSIONS: This study highlights how a reference-unbiased super-pangenome can reveal the genetic basis of adaptive traits from wild relatives and accelerate crop breeding research.}, } @article {pmid38110096, year = {2024}, author = {Chatterjee, D and Singh, PK and Singh, D and Singh, VP}, title = {A novel partitioning of gross primary production and water use efficiency for sustaining water and food security using Budyko hypothesis.}, journal = {The Science of the total environment}, volume = {912}, number = {}, pages = {169283}, doi = {10.1016/j.scitotenv.2023.169283}, pmid = {38110096}, issn = {1879-1026}, mesh = {*Water ; *Hydrology ; Agriculture ; Rivers ; Food Security ; }, abstract = {This study coupled the green water and blue water accounting with the existing standard Budyko framework and Fu's 1-parameter Budyko framework to diagnose the basin hydrological behavior. Both Budyko frameworks were employed to determine green water consumption (ETGreen) and blue water consumption (ETBlue) which, in turn, were used to map the blue water index (BWI) hotspots and green water index (GWI) bright spots. The relative contributions of green water and blue water were quantified for sustaining water and food security. A new methodology is proposed using BWI and GWI for partitioning the Gross Primary Production (GPP) and Water Use Efficiency (WUE) into GPPBlue, GPPGreen and WUEBlue and WUEGreen. The methodology was applied to five sub-basins of the Central Godavari River Basin (CGRB): Purna, Dhalegaon, GR Bridge, Yeli and Delta. Results showed that all five basins exhibited larger deviations from the theoretical Budyko curve of Fu's 1-parameter Budyko framework than did the standard Budyko framework and the Dhalegaon basin showed the largest deviations. The partitioning of GPP and WUE by the proposed methodology showed that the proportion of GPPGreen to the total GPP was much higher than that of the GPPBlue. Similarly, the proportion of WUEGreen to WUE was more than that of WUEBlue. The mapping of GPPBlue and GPPGreen, and WUEBlue and WUEGreen showed that the Delta and Yeli basins had the highest values of both GPPGreen & GPPBlue and WUEBlue and WUEGreen (bright spot basins) and the Dhalegaon and parts of GR Bridge basin had the lowest values (hot spot basins). The proposed partitioning of GPP and WUE will help identify the relative contributions of green water and blue water (for managing agricultural waters) and formulate agronomical and engineering practices for stakeholders and policy makers for increasing the overall WUE and GPP to sustain water and food security.}, } @article {pmid38108929, year = {2024}, author = {Liu, M and Wang, L and Yu, Q and Song, J and Zhu, L and Jia, KH and Qin, X}, title = {The response of LncRNAs associated with photosynthesis-and pigment synthesis-related genes to green light in Chlamydomonas reinhardtii.}, journal = {Photosynthesis research}, volume = {161}, number = {1-2}, pages = {65-78}, pmid = {38108929}, issn = {1573-5079}, mesh = {*Chlamydomonas reinhardtii/genetics/metabolism/radiation effects ; Gene Expression Profiling ; Gene Expression Regulation, Plant ; Gene Ontology ; Gene Regulatory Networks ; *Green Light ; *Photosynthesis/genetics ; Pigments, Biological/metabolism ; *RNA, Long Noncoding/genetics/metabolism ; Transcriptome ; }, abstract = {The quality of light is an important abiotic factor that affects the growth and development of green plants. Ultraviolet, red, blue, and far-red light all have demonstrated roles in regulating green plant growth and development, as well as light morphogenesis. However, the mechanism underlying photosynthetic organism responses to green light throughout the life of them are not clear. In this study, we exposed the unicellular green alga Chlamydomonas reinhardtii to green light and analyzed the dynamics of transcriptome changes. Based on the whole transcriptome data from C. reinhardtii, a total of 9974 differentially expressed genes (DEGs) were identified under green light. The Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses indicated that these DEGs were mainly related to "carboxylic acid metabolic process," "enzyme activity," "carbon metabolism," and "photosynthesis and other processes." At the same time, 253 differentially expressed long non-coding RNAs (DELs) were characterized as green light responsive. We also made a detailed analysis of the responses of photosynthesis- and pigment synthesis-related genes in C. reinhardtii to green light and found that these genes exhibited obvious dynamic expression. Lastly, we constructed a co-expression regulatory network, comprising 49 long non-coding RNAs (lncRNAs) and 20 photosynthesis and pigment related genes, of which 9 mRNAs were also the predicted trans/cis-targets of 8 lncRNAs, these results suggested that lncRNAs may affect the expression of mRNAs related to photosynthesis and pigment synthesis. Our findings give a preliminary explanation of the response mechanism of C. reinhardtii to green light at the transcriptional level.}, } @article {pmid38105177, year = {2023}, author = {Aziz, MA and Hassan, M and Ullah, A and Ullah, Z and Sõukand, R and Pieroni, A}, title = {Keeping their own and integrating the other: medicinal plant use among Ormurs and Pathans in South Waziristan, Pakistan.}, journal = {Journal of ethnobiology and ethnomedicine}, volume = {19}, number = {1}, pages = {62}, pmid = {38105177}, issn = {1746-4269}, mesh = {Phytotherapy ; *Plants, Medicinal ; South Asian People ; Medicine, Traditional/methods ; Ethnobotany ; Humans ; Pakistan ; }, abstract = {BACKGROUND: In multicultural societies, traditional knowledge among minorities faces several challenges. Minority groups often face difficult situations living in specific peripheral geographies and striving to retain their biocultural heritage, including medicinal plant knowledge and practices. Folk medicinal plant knowledge is a dynamic eco-cultural complex influenced by various environmental, socio-cultural, and political factors. Examining medicinal plant knowledge among minorities has been an increasingly popular topic in cross-cultural ethnobiology. It also helps understand the dynamics of local/traditional ecological knowledge (LEK/TEK) change within a given community. The current study was designed to investigate the status of medicinal plant knowledge among two linguistic groups, i.e. Ormurs and Pathans, living in a remote valley of West Pakistan.

METHODS: We recruited 70 male study participants from the studied groups for semi-structured interviews to record the medicinal plant use of their communities. Data were compared among the two studied communities using the stacked charts employing the presence or absence of data with Past 4.03 and Venn diagrams. Use reports (URs) were counted for each recorded taxon.

RESULTS AND DISCUSSION: A total of seventy-four medicinal plants were quoted as used as ethnomedicines by the researched communities. Most of the reported plants were used to treat digestive and liver problems. The cross-cultural comparison revealed a considerable homogeneity of medicinal plant knowledge (the two groups commonly used more than seventy plants); however, comparing uses recorded for the widely utilised medicinal plants showed numerous idiosyncratic uses among Ormurs but very few among Pathans. Ormurs reported a higher number of cultivated, wild, and imported plant uses than did Pathans. These results indicate that, compared to Pathans, the Ormur linguistic minority retain more folk medicinal plant knowledge, which may be explained by the fact that they have incorporated different folk remedies: their "own knowledge" plus that of Pathans, with whom they have lived together for centuries. Moreover, the local plant nomenclature among Ormurs was highly affected by the plant nomenclature of Pathans.

CONCLUSION: The current study revealed that living together for a few centuries has not implied sharing plant knowledge (as the Pathans do not seem to have learnt from the Ormurs) or, in other words, that plant knowledge exchanges have been unidirectional. The findings show that the Pashto dominant culture may have possibly put pressure on the minority groups and affected local plant-centred cultural practices, as we see in the case of local plant nomenclature hybridisation among Omuri speakers. Hence, it is imperative to employ diverse educational strategies to revitalise the decline of medicinal plant knowledge in the studied communities, especially among Ormurs, who need more attention as they face more challenges than the other group. Locally based strategies should be devised to restore the fading connection with nature, which will be advantageous for revitalising plant knowledge.}, } @article {pmid38105079, year = {2024}, author = {Liu, C and How, ZT and Ju, Y and Feng, L and Ren, X and Gamal El-Din, M}, title = {Experimental and theoretical insight into carbamazepine degradation by chlorine-based advanced oxidation processes: Efficiency, energy consumption, mechanism and DBPs formation.}, journal = {Journal of environmental sciences (China)}, volume = {139}, number = {}, pages = {72-83}, doi = {10.1016/j.jes.2023.05.012}, pmid = {38105079}, issn = {1001-0742}, mesh = {Chlorine ; Disinfection ; *Water Purification ; *Water Pollutants, Chemical/analysis ; Carbamazepine ; Oxidation-Reduction ; Halogenation ; Chlorides ; Ultraviolet Rays ; }, abstract = {Chlorine has been widely used in different advanced oxidation processes (AOPs) for micropollutants removal. In this study, different chlorine-based AOPs, namely medium pressure (MP) UV/chlorine, low pressure (LP) UV/chlorine, and in-situ chlorination, were compared for carbamazepine (CBZ) removal efficiency, energy consumption, and disinfection by-products (DBPs) formation. All three processes could achieve nearly 100% CBZ removal, while the reaction time needed by in-situ chlorination was double the time required by UV/chlorine processes. The energy consumed per magnitude of CBZ removed (EE/O) of MP UV/chlorine was 13 times higher than that of LP UV/chlorine, and relative to that of in-situ chlorination process. Accordingly, MP and LP UV/chlorine processes generated one to two orders of magnitude more hydroxyl radicals ([•]OH) and reactive chlorine species (RCS) than in-situ chlorination. Besides, RCS were the dominant reactive species, contributing to 78.3%, 75.6%, and 71.6% of CBZ removal in MP, LP UV/chlorine, and in-situ chlorination, respectively. According to the Gibbs free energy barriers between CBZ and RCS/[•]OH calculated based on density functional theory (DFT), RCS had more reaction routes with CBZ and showed lower energy barrier in the main CBZ degradation pathways like epoxidation and formation of iminostilbene. When applied to secondary wastewater effluent, UV/chlorine and in-situ chlorination produced overall DBPs ranging from 104.77 to 135.41 µg/L. However, the production of chlorate during UV/chlorine processes was 15 times higher than that during in-situ chlorination.}, } @article {pmid38104847, year = {2024}, author = {Khatri-Chhetri, U and Banerjee, S and Thompson, KA and Quideau, SA and Boyce, MS and Bork, EW and Carlyle, CN}, title = {Cattle grazing management affects soil microbial diversity and community network complexity in the Northern Great Plains.}, journal = {The Science of the total environment}, volume = {912}, number = {}, pages = {169353}, doi = {10.1016/j.scitotenv.2023.169353}, pmid = {38104847}, issn = {1879-1026}, mesh = {Animals ; Cattle ; Humans ; *Ecosystem ; Soil ; Grassland ; Soil Microbiology ; Community Networks ; Canada ; *Microbiota ; Bacteria ; }, abstract = {Soil microbial communities play a vital role in the biogeochemical cycling and ecological functioning of grassland, but may be affected by common land uses such as cattle grazing. Changes in microbial diversity and network complexity can affect key ecosystem functions such as nutrient cycling. However, it is not well known how microbial diversity and network complexity respond to grazing in the Northern Great Plains. Consequently, it is important to understand whether variation in grazing management alters the diversity and complexity of grassland microbial communities. We compared the effect of intensive adaptive multi-paddock (AMP) grazing and conventional grazing practices on soil microbial communities using 16S/ITS amplicon sequencing. Samples were collected from grasslands in 13 AMP ranches and 13 neighboring, conventional ranches located across the Canadian prairies. We found that AMP grazing increased fungal diversity and evenness, and led to more complex microbial associations. Acidobacteria, Actinobacteria, Gemmatimonadetes, and Bacteroidetes were keystone taxa associated with AMP grazing, while Actinobacteria, Acidobacteria, Proteobacteria, and Armatimonadetes were keystone taxa under conventional grazing. Besides overall grazing treatment effects, specific grazing metrics like cattle stocking rate and rest-to-grazing ratio affected microbial richness and diversity. Bacterial and fungal richness increased with elevated stocking rate, and fungal richness and diversity increased directly with the rest-to-grazing ratio. These results suggest that AMP grazing may improve ecosystem by enhancing fungal diversity and increasing microbial network complexity and connectivity.}, } @article {pmid38102035, year = {2024}, author = {Del Campo, J and Carlos-Oliveira, M and Čepička, I and Hehenberger, E and Horák, A and Karnkowska, A and Kolisko, M and Lara, E and Lukeš, J and Pánek, T and Piwosz, K and Richter, DJ and Škaloud, P and Sutak, R and Tachezy, J and Hampl, V}, title = {The protist cultural renaissance.}, journal = {Trends in microbiology}, volume = {32}, number = {2}, pages = {128-131}, doi = {10.1016/j.tim.2023.11.010}, pmid = {38102035}, issn = {1878-4380}, mesh = {*Eukaryota/genetics ; Multiomics ; }, abstract = {Protists are key players in the biosphere. Here, we provide a perspective on integrating protist culturing with omics approaches, imaging, and high-throughput single-cell manipulation strategies, concluding with actions required for a successful return of the golden age of protist culturing.}, } @article {pmid38100404, year = {2023}, author = {Biswas, A and Kumari, A and Gaikwad, DS and Pandey, DK}, title = {Revolutionizing Biological Science: The Synergy of Genomics in Health, Bioinformatics, Agriculture, and Artificial Intelligence.}, journal = {Omics : a journal of integrative biology}, volume = {27}, number = {12}, pages = {550-569}, doi = {10.1089/omi.2023.0197}, pmid = {38100404}, issn = {1557-8100}, mesh = {Animals ; Humans ; *Artificial Intelligence ; *Ecosystem ; Genomics ; Computational Biology ; Agriculture ; }, abstract = {With climate emergency, COVID-19, and the rise of planetary health scholarship, the binary of human and ecosystem health has been deeply challenged. The interdependence of human and nonhuman animal health is increasingly acknowledged and paving the way for new frontiers in integrative biology. The convergence of genomics in health, bioinformatics, agriculture, and artificial intelligence (AI) has ushered in a new era of possibilities and applications. However, the sheer volume of genomic/multiomics big data generated also presents formidable sociotechnical challenges in extracting meaningful biological, planetary health and ecological insights. Over the past few years, AI-guided bioinformatics has emerged as a powerful tool for managing, analyzing, and interpreting complex biological datasets. The advances in AI, particularly in machine learning and deep learning, have been transforming the fields of genomics, planetary health, and agriculture. This article aims to unpack and explore the formidable range of possibilities and challenges that result from such transdisciplinary integration, and emphasizes its radically transformative potential for human and ecosystem health. The integration of these disciplines is also driving significant advancements in precision medicine and personalized health care. This presents an unprecedented opportunity to deepen our understanding of complex biological systems and advance the well-being of all life in planetary ecosystems. Notwithstanding in mind its sociotechnical, ethical, and critical policy challenges, the integration of genomics, multiomics, planetary health, and agriculture with AI-guided bioinformatics opens up vast opportunities for transnational collaborative efforts, data sharing, analysis, valorization, and interdisciplinary innovations in life sciences and integrative biology.}, } @article {pmid38095449, year = {2024}, author = {Arehart, CH and Sterrett, JD and Garris, RL and Quispe-Pilco, RE and Gignoux, CR and Evans, LM and Stanislawski, MA}, title = {Poly-omic risk scores predict inflammatory bowel disease diagnosis.}, journal = {mSystems}, volume = {9}, number = {1}, pages = {e0067723}, pmid = {38095449}, issn = {2379-5077}, support = {K01 HL157658/HL/NHLBI NIH HHS/United States ; P30 DK048520/DK/NIDDK NIH HHS/United States ; T32 MH016880/MH/NIMH NIH HHS/United States ; }, mesh = {Humans ; *Inflammatory Bowel Diseases/diagnosis ; Metagenomics/methods ; Phenotype ; *Microbiota ; Risk Factors ; }, abstract = {Inflammatory bowel disease (IBD) is characterized by complex etiology and a disrupted colonic ecosystem. We provide a framework for the analysis of multi-omic data, which we apply to study the gut ecosystem in IBD. Specifically, we train and validate models using data on the metagenome, metatranscriptome, virome, and metabolome from the Human Microbiome Project 2 IBD multi-omic database, with 1,785 repeated samples from 130 individuals (103 cases and 27 controls). After splitting the participants into training and testing groups, we used mixed-effects least absolute shrinkage and selection operator regression to select features for each omic. These features, with demographic covariates, were used to generate separate single-omic prediction scores. All four single-omic scores were then combined into a final regression to assess the relative importance of the individual omics and the predictive benefits when considered together. We identified several species, pathways, and metabolites known to be associated with IBD risk, and we explored the connections between data sets. Individually, metabolomic and viromic scores were more predictive than metagenomics or metatranscriptomics, and when all four scores were combined, we predicted disease diagnosis with a Nagelkerke's R[2] of 0.46 and an area under the curve of 0.80 (95% confidence interval: 0.63, 0.98). Our work supports that some single-omic models for complex traits are more predictive than others, that incorporating multiple omic data sets may improve prediction, and that each omic data type provides a combination of unique and redundant information. This modeling framework can be extended to other complex traits and multi-omic data sets.IMPORTANCEComplex traits are characterized by many biological and environmental factors, such that multi-omic data sets are well-positioned to help us understand their underlying etiologies. We applied a prediction framework across multiple omics (metagenomics, metatranscriptomics, metabolomics, and viromics) from the gut ecosystem to predict inflammatory bowel disease (IBD) diagnosis. The predicted scores from our models highlighted key features and allowed us to compare the relative utility of each omic data set in single-omic versus multi-omic models. Our results emphasized the importance of metabolomics and viromics over metagenomics and metatranscriptomics for predicting IBD status. The greater predictive capability of metabolomics and viromics is likely because these omics serve as markers of lifestyle factors such as diet. This study provides a modeling framework for multi-omic data, and our results show the utility of combining multiple omic data types to disentangle complex disease etiologies and biological signatures.}, } @article {pmid38093346, year = {2023}, author = {Masroni, MSB and Lee, KW and Lee, VKM and Ng, SB and Law, CT and Poon, KS and Lee, BT and Liu, Z and Tan, YP and Chng, WL and Tucker, S and Ngo, LS and Yip, GWC and Nga, ME and Hue, SSS and Putti, TC and Bay, BH and Lin, Q and Zhou, L and Hartman, M and Loh, TP and Lakshmanan, M and Lee, SY and Tergaonkar, V and Chua, H and Lee, AVH and Yeo, EYM and Li, MH and Chang, CF and Kee, Z and Tan, KM and Tan, SY and Koay, ES and Archetti, M and Leong, SM}, title = {Dynamic altruistic cooperation within breast tumors.}, journal = {Molecular cancer}, volume = {22}, number = {1}, pages = {206}, pmid = {38093346}, issn = {1476-4598}, support = {NUS Postgraduate Research Scholarships//National University of Singapore/ ; NUS Postgraduate Research Scholarships//National University of Singapore/ ; Department of Pathology Startup Grants//National University of Singapore/ ; Department of Pathology Startup Grants//National University of Singapore/ ; T1- NUHS Joint Grant Call FY17 - 2nd call-10//Ministry of Education - Singapore/ ; NMRC-NIG NMRC/CNIG/1119/2014//National Medical Research Council/ ; A*STAR-SERC Public Service Fund 1121202021//Agency for Science, Technology and Research/ ; NUHS Bridging fund//National University Health System/ ; }, mesh = {Humans ; Female ; Altruism ; Phosphatidylinositol 3-Kinases ; *MicroRNAs/genetics ; *Breast Neoplasms/genetics ; }, abstract = {BACKGROUND: Social behaviors such as altruism, where one self-sacrifices for collective benefits, critically influence an organism's survival and responses to the environment. Such behaviors are widely exemplified in nature but have been underexplored in cancer cells which are conventionally seen as selfish competitive players. This multidisciplinary study explores altruism and its mechanism in breast cancer cells and its contribution to chemoresistance.

METHODS: MicroRNA profiling was performed on circulating tumor cells collected from the blood of treated breast cancer patients. Cancer cell lines ectopically expressing candidate miRNA were used in co-culture experiments and treated with docetaxel. Ecological parameters like relative survival and relative fitness were assessed using flow cytometry. Functional studies and characterization performed in vitro and in vivo include proliferation, iTRAQ-mass spectrometry, RNA sequencing, inhibition by small molecules and antibodies, siRNA knockdown, CRISPR/dCas9 inhibition and fluorescence imaging of promoter reporter-expressing cells. Mathematical modeling based on evolutionary game theory was performed to simulate spatial organization of cancer cells.

RESULTS: Opposing cancer processes underlie altruism: an oncogenic process involving secretion of IGFBP2 and CCL28 by the altruists to induce survival benefits in neighboring cells under taxane exposure, and a self-sacrificial tumor suppressive process impeding proliferation of altruists via cell cycle arrest. Both processes are regulated concurrently in the altruists by miR-125b, via differential NF-κB signaling specifically through IKKβ. Altruistic cells persist in the tumor despite their self-sacrifice, as they can regenerate epigenetically from non-altruists via a KLF2/PCAF-mediated mechanism. The altruists maintain a sparse spatial organization by inhibiting surrounding cells from adopting the altruistic fate via a lateral inhibition mechanism involving a GAB1-PI3K-AKT-miR-125b signaling circuit.

CONCLUSIONS: Our data reveal molecular mechanisms underlying manifestation, persistence and spatial spread of cancer cell altruism. A minor population behave altruistically at a cost to itself producing a collective benefit for the tumor, suggesting tumors to be dynamic social systems governed by the same rules of cooperation in social organisms. Understanding cancer cell altruism may lead to more holistic models of tumor evolution and drug response, as well as therapeutic paradigms that account for social interactions. Cancer cells constitute tractable experimental models for fields beyond oncology, like evolutionary ecology and game theory.}, } @article {pmid38093003, year = {2023}, author = {Reis, ALM and Rapadas, M and Hammond, JM and Gamaarachchi, H and Stevanovski, I and Ayuputeri Kumaheri, M and Chintalaphani, SR and Dissanayake, DSB and Siggs, OM and Hewitt, AW and Llamas, B and Brown, A and Baynam, G and Mann, GJ and McMorran, BJ and Easteal, S and Hermes, A and Jenkins, MR and , and Patel, HR and Deveson, IW}, title = {The landscape of genomic structural variation in Indigenous Australians.}, journal = {Nature}, volume = {624}, number = {7992}, pages = {602-610}, pmid = {38093003}, issn = {1476-4687}, mesh = {Microsatellite Repeats/genetics ; *Australian Aboriginal and Torres Strait Islander Peoples/genetics ; DNA Copy Number Variations/genetics ; *Genomic Structural Variation/genetics ; *Genome, Human/genetics ; Datasets as Topic ; Genetics, Medical ; Australia/ethnology ; Interspersed Repetitive Sequences/genetics ; Australasian People ; Genetic Loci/genetics ; Alleles ; INDEL Mutation/genetics ; Humans ; Genomics ; }, abstract = {Indigenous Australians harbour rich and unique genomic diversity. However, Aboriginal and Torres Strait Islander ancestries are historically under-represented in genomics research and almost completely missing from reference datasets[1-3]. Addressing this representation gap is critical, both to advance our understanding of global human genomic diversity and as a prerequisite for ensuring equitable outcomes in genomic medicine. Here we apply population-scale whole-genome long-read sequencing[4] to profile genomic structural variation across four remote Indigenous communities. We uncover an abundance of large insertion-deletion variants (20-49 bp; n = 136,797), structural variants (50 b-50 kb; n = 159,912) and regions of variable copy number (>50 kb; n = 156). The majority of variants are composed of tandem repeat or interspersed mobile element sequences (up to 90%) and have not been previously annotated (up to 62%). A large fraction of structural variants appear to be exclusive to Indigenous Australians (12% lower-bound estimate) and most of these are found in only a single community, underscoring the need for broad and deep sampling to achieve a comprehensive catalogue of genomic structural variation across the Australian continent. Finally, we explore short tandem repeats throughout the genome to characterize allelic diversity at 50 known disease loci[5], uncover hundreds of novel repeat expansion sites within protein-coding genes, and identify unique patterns of diversity and constraint among short tandem repeat sequences. Our study sheds new light on the dimensions and dynamics of genomic structural variation within and beyond Australia.}, } @article {pmid38085368, year = {2023}, author = {Ilyas, MZ and Sa, KJ and Ali, MW and Lee, JK}, title = {Toxic effects of lead on plants: integrating multi-omics with bioinformatics to develop Pb-tolerant crops.}, journal = {Planta}, volume = {259}, number = {1}, pages = {18}, pmid = {38085368}, issn = {1432-2048}, mesh = {*Lead/toxicity ; Multiomics ; *Soil Pollutants/metabolism ; Crops, Agricultural/genetics/metabolism ; Computational Biology ; }, abstract = {Lead disrupts plant metabolic homeostasis and key structural elements. Utilizing modern biotechnology tools, it's feasible to develop Pb-tolerant varieties by discovering biological players regulating plant metabolic pathways under stress. Lead (Pb) has been used for a variety of purposes since antiquity despite its toxic nature. After arsenic, lead is the most hazardous heavy metal without any known beneficial role in the biological system. It is a crucial inorganic pollutant that affects plant biochemical and morpho-physiological attributes. Lead toxicity harms plants throughout their life cycle and the extent of damage depends on the concentration and duration of exposure. Higher levels of lead exposure disrupt numerous key metabolic activities of plants including oxygen-evolving complex, organelles integrity, photosystem II connectivity, and electron transport chain. This review summarizes the detrimental effects of lead toxicity on seed germination, crop growth, and yield, oxidative and ultra-structural alterations, as well as nutrient absorption, transport, and assimilation. Further, it discusses the Pb-induced toxic modulation of stomatal conductance, photosynthesis, respiration, metabolic-enzymatic activity, osmolytes accumulation, and antioxidant activity. It is a comprehensive review that reports on omics-based studies along with morpho-physiological and biochemical modifications caused by lead stress. With advances in DNA sequencing technologies, genomics and transcriptomics are gradually becoming popular for studying Pb stress effects in plants. Proteomics and metabolomics are still underrated and there is a scarcity of published data, and this review highlights both their technical and research gaps. Besides, there is also a discussion on how the integration of omics with bioinformatics and the use of the latest biotechnological tools can aid in developing Pb-tolerant crops. The review concludes with core challenges and research directions that need to be addressed soon.}, } @article {pmid38085351, year = {2024}, author = {Paul, T and Aggarwal, A and Behera, SK and Meher, SK and Gupta, S and Baskaran, D and Rene, ER and Pakshirajan, K and Pugazhenthi, G}, title = {Neuro-fuzzy modelling of a continuous stirred tank bioreactor with ceramic membrane technology for treating petroleum refinery effluent: a case study from Assam, India.}, journal = {Bioprocess and biosystems engineering}, volume = {47}, number = {1}, pages = {91-103}, pmid = {38085351}, issn = {1615-7605}, mesh = {*Artificial Intelligence ; Waste Disposal, Fluid/methods ; *Petroleum ; Bayes Theorem ; Bioreactors ; Ceramics ; Lipids ; }, abstract = {A continuous stirred tank bioreactor (CSTB) with cell recycling combined with ceramic membrane technology and inoculated with Rhodococcus opacus PD630 was employed to treat petroleum refinery wastewater for simultaneous chemical oxygen demand (COD) removal and lipid production from the retentate obtained during wastewater treatment. In the present study, the COD removal efficiency (CODRE) (%) and lipid concentration (g/L) were predicted using two artificial intelligence models, i.e., an artificial neural network (ANN) and a neuro-fuzzy neural network (NF-NN) with a network topology of 6-25-2 being the best for NF-NN. The results revealed the superiority of NF-NN over ANN in terms of determination coefficient (R[2]), root mean square error (RMSE), and mean absolute percentage error (MAPE). Three learning algorithms were tested with NF-NN; among them, the Bayesian regularization backpropagation (BR-BP) outperformed others. The sensitivity analysis revealed that, if solid retention time and biomass concentrations were maintained between 35 and 75 h and 3.0 g/L and 3.5 g/L, respectively, high CODRE (93%) and lipid concentration (2.8 g/L) could be obtained consistently.}, } @article {pmid38084497, year = {2024}, author = {Dalla Costa, G and Nos, C and Zabalza, A and Buron, M and Magyari, M and Sellebjerg, F and Guerrero, AI and Roselli, L and La Porta, ML and Martinis, M and Bailon, R and Kontaxis, S and Laporta, E and Garcia, E and Pokorny, FB and Schuller, BW and Folarin, A and Stewart, C and Leocani, L and Vairavan, S and Cummins, N and Dobson, R and Hotopf, M and Narayan, V and Montalban, X and Sorensen, PS and Comi, G}, title = {A wearable device perspective on the standard definitions of disability progression in multiple sclerosis.}, journal = {Multiple sclerosis (Houndmills, Basingstoke, England)}, volume = {30}, number = {1}, pages = {103-112}, doi = {10.1177/13524585231214362}, pmid = {38084497}, issn = {1477-0970}, mesh = {Female ; Humans ; Male ; Middle Aged ; Disability Evaluation ; *Disabled Persons ; *Multiple Sclerosis/diagnosis ; Walk Test ; Walking/physiology ; *Wearable Electronic Devices ; Adult ; }, abstract = {INTRODUCTION: Multiple sclerosis (MS) is a leading cause of disability among young adults, but standard clinical scales may not accurately detect subtle changes in disability occurring between visits. This study aims to explore whether wearable device data provides more granular and objective measures of disability progression in MS.

METHODS: Remote Assessment of Disease and Relapse in Central Nervous System Disorders (RADAR-CNS) is a longitudinal multicenter observational study in which 400 MS patients have been recruited since June 2018 and prospectively followed up for 24 months. Monitoring of patients included standard clinical visits with assessment of disability through use of the Expanded Disability Status Scale (EDSS), 6-minute walking test (6MWT) and timed 25-foot walk (T25FW), as well as remote monitoring through the use of a Fitbit.

RESULTS: Among the 306 patients who completed the study (mean age, 45.6 years; females 67%), confirmed disability progression defined by the EDSS was observed in 74 patients, who had approximately 1392 fewer daily steps than patients without disability progression. However, the decrease in the number of steps experienced over time by patients with EDSS progression and stable patients was not significantly different. Similar results were obtained with disability progression defined by the 6MWT and the T25FW.

CONCLUSION: The use of continuous activity monitoring holds great promise as a sensitive and ecologically valid measure of disability progression in MS.}, } @article {pmid38079567, year = {2023}, author = {Deng, CH and Naithani, S and Kumari, S and Cobo-Simón, I and Quezada-Rodríguez, EH and Skrabisova, M and Gladman, N and Correll, MJ and Sikiru, AB and Afuwape, OO and Marrano, A and Rebollo, I and Zhang, W and Jung, S}, title = {Genotype and phenotype data standardization, utilization and integration in the big data era for agricultural sciences.}, journal = {Database : the journal of biological databases and curation}, volume = {2023}, number = {}, pages = {}, pmid = {38079567}, issn = {1758-0463}, support = {//National Science Foundation (NSF)/ ; 2126334//Research Coordination Network (RCN)/ ; //National Science Foundation (NSF)/ ; 2126334//Research Coordination Network (RCN)/ ; }, mesh = {*Big Data ; *Databases, Genetic ; Genotype ; Phenotype ; Plant Breeding ; }, abstract = {Large-scale genotype and phenotype data have been increasingly generated to identify genetic markers, understand gene function and evolution and facilitate genomic selection. These datasets hold immense value for both current and future studies, as they are vital for crop breeding, yield improvement and overall agricultural sustainability. However, integrating these datasets from heterogeneous sources presents significant challenges and hinders their effective utilization. We established the Genotype-Phenotype Working Group in November 2021 as a part of the AgBioData Consortium (https://www.agbiodata.org) to review current data types and resources that support archiving, analysis and visualization of genotype and phenotype data to understand the needs and challenges of the plant genomic research community. For 2021-22, we identified different types of datasets and examined metadata annotations related to experimental design/methods/sample collection, etc. Furthermore, we thoroughly reviewed publicly funded repositories for raw and processed data as well as secondary databases and knowledgebases that enable the integration of heterogeneous data in the context of the genome browser, pathway networks and tissue-specific gene expression. Based on our survey, we recommend a need for (i) additional infrastructural support for archiving many new data types, (ii) development of community standards for data annotation and formatting, (iii) resources for biocuration and (iv) analysis and visualization tools to connect genotype data with phenotype data to enhance knowledge synthesis and to foster translational research. Although this paper only covers the data and resources relevant to the plant research community, we expect that similar issues and needs are shared by researchers working on animals. Database URL: https://www.agbiodata.org.}, } @article {pmid38078767, year = {2024}, author = {Smith, AB and Specker, JT and Hewlett, KK and Scoggins, TR and Knight, M and Lustig, AM and Li, Y and Evans, KM and Guo, Y and She, Q and Christopher, MW and Garrett, TJ and Moustafa, AM and Van Tyne, D and Prentice, BM and Zackular, JP}, title = {Liberation of host heme by Clostridioides difficile-mediated damage enhances Enterococcus faecalis fitness during infection.}, journal = {mBio}, volume = {15}, number = {1}, pages = {e0165623}, pmid = {38078767}, issn = {2150-7511}, support = {K22 AI137220/AI/NIAID NIH HHS/United States ; R21 AI164018/AI/NIAID NIH HHS/United States ; U19 AI174998/AI/NIAID NIH HHS/United States ; R03 AI168491/AI/NIAID NIH HHS/United States ; L40 AI147162/AI/NIAID NIH HHS/United States ; R35 GM138369/GM/NIGMS NIH HHS/United States ; }, mesh = {Humans ; *Clostridioides difficile ; Enterococcus faecalis ; *Clostridium Infections/microbiology ; Bacteria ; *Gastrointestinal Microbiome ; }, abstract = {Clostridioides difficile and Enterococcus faecalis are two pathogens of great public health importance. Both bacteria colonize the human gastrointestinal tract where they are known to interact in ways that worsen disease outcomes. We show that the damage associated with C. difficile infection (CDI) releases nutrients that benefit E. faecalis. One particular nutrient, heme, allows E. faecalis to use oxygen to generate energy and grow better in the gut. Understanding the mechanisms of these interspecies interactions could inform therapeutic strategies for CDI.}, } @article {pmid38078294, year = {2023}, author = {Groom, Q and Dillen, M and Addink, W and Ariño, AHH and Bölling, C and Bonnet, P and Cecchi, L and Ellwood, ER and Figueira, R and Gagnier, PY and Grace, OM and Güntsch, A and Hardy, H and Huybrechts, P and Hyam, R and Joly, AAJ and Kommineni, VK and Larridon, I and Livermore, L and Lopes, RJ and Meeus, S and Miller, JA and Milleville, K and Panda, R and Pignal, M and Poelen, J and Ristevski, B and Robertson, T and Rufino, AC and Santos, J and Schermer, M and Scott, B and Seltmann, KC and Teixeira, H and Trekels, M and Gaikwad, J}, title = {Envisaging a global infrastructure to exploit the potential of digitised collections.}, journal = {Biodiversity data journal}, volume = {11}, number = {}, pages = {e109439}, pmid = {38078294}, issn = {1314-2828}, abstract = {Tens of millions of images from biological collections have become available online over the last two decades. In parallel, there has been a dramatic increase in the capabilities of image analysis technologies, especially those involving machine learning and computer vision. While image analysis has become mainstream in consumer applications, it is still used only on an artisanal basis in the biological collections community, largely because the image corpora are dispersed. Yet, there is massive untapped potential for novel applications and research if images of collection objects could be made accessible in a single corpus. In this paper, we make the case for infrastructure that could support image analysis of collection objects. We show that such infrastructure is entirely feasible and well worth investing in.}, } @article {pmid38075858, year = {2023}, author = {Marcos-Zambrano, LJ and López-Molina, VM and Bakir-Gungor, B and Frohme, M and Karaduzovic-Hadziabdic, K and Klammsteiner, T and Ibrahimi, E and Lahti, L and Loncar-Turukalo, T and Dhamo, X and Simeon, A and Nechyporenko, A and Pio, G and Przymus, P and Sampri, A and Trajkovik, V and Lacruz-Pleguezuelos, B and Aasmets, O and Araujo, R and Anagnostopoulos, I and Aydemir, Ö and Berland, M and Calle, ML and Ceci, M and Duman, H and Gündoğdu, A and Havulinna, AS and Kaka Bra, KHN and Kalluci, E and Karav, S and Lode, D and Lopes, MB and May, P and Nap, B and Nedyalkova, M and Paciência, I and Pasic, L and Pujolassos, M and Shigdel, R and Susín, A and Thiele, I and Truică, CO and Wilmes, P and Yilmaz, E and Yousef, M and Claesson, MJ and Truu, J and Carrillo de Santa Pau, E}, title = {A toolbox of machine learning software to support microbiome analysis.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1250806}, pmid = {38075858}, issn = {1664-302X}, abstract = {The human microbiome has become an area of intense research due to its potential impact on human health. However, the analysis and interpretation of this data have proven to be challenging due to its complexity and high dimensionality. Machine learning (ML) algorithms can process vast amounts of data to uncover informative patterns and relationships within the data, even with limited prior knowledge. Therefore, there has been a rapid growth in the development of software specifically designed for the analysis and interpretation of microbiome data using ML techniques. These software incorporate a wide range of ML algorithms for clustering, classification, regression, or feature selection, to identify microbial patterns and relationships within the data and generate predictive models. This rapid development with a constant need for new developments and integration of new features require efforts into compile, catalog and classify these tools to create infrastructures and services with easy, transparent, and trustable standards. Here we review the state-of-the-art for ML tools applied in human microbiome studies, performed as part of the COST Action ML4Microbiome activities. This scoping review focuses on ML based software and framework resources currently available for the analysis of microbiome data in humans. The aim is to support microbiologists and biomedical scientists to go deeper into specialized resources that integrate ML techniques and facilitate future benchmarking to create standards for the analysis of microbiome data. The software resources are organized based on the type of analysis they were developed for and the ML techniques they implement. A description of each software with examples of usage is provided including comments about pitfalls and lacks in the usage of software based on ML methods in relation to microbiome data that need to be considered by developers and users. This review represents an extensive compilation to date, offering valuable insights and guidance for researchers interested in leveraging ML approaches for microbiome analysis.}, } @article {pmid38069903, year = {2024}, author = {Mirchandani, CD and Shultz, AJ and Thomas, GWC and Smith, SJ and Baylis, M and Arnold, B and Corbett-Detig, R and Enbody, E and Sackton, TB}, title = {A Fast, Reproducible, High-throughput Variant Calling Workflow for Population Genomics.}, journal = {Molecular biology and evolution}, volume = {41}, number = {1}, pages = {}, pmid = {38069903}, issn = {1537-1719}, mesh = {Animals ; *Software ; *Metagenomics ; Workflow ; Genomics ; Sequence Analysis, DNA ; High-Throughput Nucleotide Sequencing ; }, abstract = {The increasing availability of genomic resequencing data sets and high-quality reference genomes across the tree of life present exciting opportunities for comparative population genomic studies. However, substantial challenges prevent the simple reuse of data across different studies and species, arising from variability in variant calling pipelines, data quality, and the need for computationally intensive reanalysis. Here, we present snpArcher, a flexible and highly efficient workflow designed for the analysis of genomic resequencing data in nonmodel organisms. snpArcher provides a standardized variant calling pipeline and includes modules for variant quality control, data visualization, variant filtering, and other downstream analyses. Implemented in Snakemake, snpArcher is user-friendly, reproducible, and designed to be compatible with high-performance computing clusters and cloud environments. To demonstrate the flexibility of this pipeline, we applied snpArcher to 26 public resequencing data sets from nonmammalian vertebrates. These variant data sets are hosted publicly to enable future comparative population genomic analyses. With its extensibility and the availability of public data sets, snpArcher will contribute to a broader understanding of genetic variation across species by facilitating the rapid use and reuse of large genomic data sets.}, } @article {pmid38069227, year = {2023}, author = {Wang, Z and Yadav, V and Chen, X and Zhang, S and Yuan, X and Li, H and Ma, J and Zhang, Y and Yang, J and Zhang, X and Wei, C}, title = {Multi-Omics Analysis Reveals Intricate Gene Networks Involved in Female Development in Melon.}, journal = {International journal of molecular sciences}, volume = {24}, number = {23}, pages = {}, pmid = {38069227}, issn = {1422-0067}, support = {No. 2023-JC-YB-199//National Natural Science Foundation of Shaanxi Province, China/ ; 2452022116//Northwest A&F University/ ; Ylzy-sc-01//Key Research and Development Project of Yangling Seed Industry Innovation Center/ ; NGSB-2021-7//High-quality Development and Ecological Protection Science and Technology Innovation Project of Ningxia Academy of Agriculture and Forestry Sciences/ ; }, mesh = {*Cucurbitaceae ; Gene Regulatory Networks ; Multiomics ; Ethylenes/metabolism ; Indoleacetic Acids ; Gene Expression Regulation, Plant ; Fruit/metabolism ; }, abstract = {Sexual differentiation is an important developmental phenomenon in cucurbits that directly affects fruit yield. The natural existence of multiple flower types in melon offers an inclusive structure for studying the molecular basis of sexual differentiation. The current study aimed to identify and characterize the molecular network involved in sex determination and female development in melon. Male and female pools separated by the F2 segregated generation were used for sequencing. The comparative multi-omics data revealed 551 DAPs and 594 DEGs involved in multiple pathways of melon growth and development, and based on functional annotation and enrichment analysis, we summarized four biological process modules, including ethylene biosynthesis, flower organ development, plant hormone signaling, and ubiquitinated protein metabolism, that are related to female development. Furthermore, the detailed analysis of the female developmental regulatory pathway model of ethylene biosynthesis, signal transduction, and target gene regulation identified some important candidates that might have a crucial role in female development. Two CMTs ((cytosine-5)-methyltransferase), one AdoHS (adenosylhomocysteinase), four ACSs (1-aminocyclopropane-1-carboxylic acid synthase), three ACOs (ACC oxidase), two ARFs (auxin response factor), four ARPs (auxin-responsive protein), and six ERFs (Ethylene responsive factor) were identified based on various female developmental regulatory models. Our data offer new and valuable insights into female development and hold the potential to offer a deeper comprehension of sex differentiation mechanisms in melon.}, } @article {pmid38061019, year = {2024}, author = {Ganasegeran, K and Abdul Manaf, MR and Safian, N and Waller, LA and Abdul Maulud, KN and Mustapha, FI}, title = {GIS-Based Assessments of Neighborhood Food Environments and Chronic Conditions: An Overview of Methodologies.}, journal = {Annual review of public health}, volume = {45}, number = {1}, pages = {109-132}, doi = {10.1146/annurev-publhealth-101322-031206}, pmid = {38061019}, issn = {1545-2093}, mesh = {Humans ; *Geographic Information Systems ; *Residence Characteristics/statistics & numerical data ; Chronic Disease/epidemiology ; Food Supply/statistics & numerical data ; Spatial Analysis ; }, abstract = {The industrial revolution and urbanization fundamentally restructured populations' living circumstances, often with poor impacts on health. As an example, unhealthy food establishments may concentrate in some neighborhoods and, mediated by social and commercial drivers, increase local health risks. To understand the connections between neighborhood food environments and public health, researchers often use geographic information systems (GIS) and spatial statistics to analyze place-based evidence, but such tools require careful application and interpretation. In this article, we summarize the factors shaping neighborhood health in relation to local food environments and outline the use of GIS methodologies to assess associations between the two. We provide an overview of available data sources, analytical approaches, and their strengths and weaknesses. We postulate next steps in GIS integration with forecasting, prediction, and simulation measures to frame implications for local health policies.}, } @article {pmid38060123, year = {2024}, author = {Brusati, A and Agostinetto, G and Bruno, A and Casiraghi, M and Pescini, D and Sandionigi, A and Balech, B}, title = {Exploration and Retrieval of Virus-Related Molecular Data Using ExTaxsI: The Monkeypox Use Case.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2732}, number = {}, pages = {145-154}, pmid = {38060123}, issn = {1940-6029}, mesh = {Humans ; *Mpox (monkeypox) ; Biodiversity ; Databases, Factual ; Bacteria ; *Viruses/genetics ; }, abstract = {Retrieval and visualization of biological data are essential for understanding complex systems. With the increasing volume of data generated from high-throughput sequencing technologies, effective and optimized data visualization tools have become indispensable. This is particularly relevant in the COVID-19 postpandemic period, where understanding the diversity and interactions of microbial communities (i.e., viral and bacterial) constitutes an important asset to develop and plan suitable interventions.In this chapter, we show the usage and the potentials of ExTaxsI (Exploring Taxonomy Information) tool to retrieve viral biodiversity data stored in National Center for Biotechnology Information (NCBI) databases and create the related visualization. In addition, by integrating different functions and modules, the tool generates relevant types of visualization plots to facilitate the exploration of microbial biodiversity communities useful to deep dive into ecological and taxonomic relationships among different species and identify potential significant targets.Using the Monkeypox virus as a case study, this work points out significant perspectives on biological data visualization, which can be used to gain insights into the ecology, evolution, and pathogenesis of viruses. Accordingly, we show the potentiality of ExTaxsI to organize and describe the available/downloaded data in an easy, simple, and interpretable way allowing the user to interact dynamically with the visualization plots through specific filters, zoom, and explore functions.}, } @article {pmid38059267, year = {2023}, author = {Massey, R and Rogers, BM and Berner, LT and Cooperdock, S and Mack, MC and Walker, XJ and Goetz, SJ}, title = {Forest composition change and biophysical climate feedbacks across boreal North America.}, journal = {Nature climate change}, volume = {13}, number = {12}, pages = {1368-1375}, pmid = {38059267}, issn = {1758-678X}, abstract = {Deciduous tree cover is expected to increase in North American boreal forests with climate warming and wildfire. This shift in composition has the potential to generate biophysical cooling via increased land surface albedo. Here we use Landsat-derived maps of continuous tree canopy cover and deciduous fractional composition to assess albedo change over recent decades. We find, on average, a small net decrease in deciduous fraction from 2000 to 2015 across boreal North America and from 1992 to 2015 across Canada, despite extensive fire disturbance that locally increased deciduous vegetation. We further find near-neutral net biophysical change in radiative forcing associated with albedo when aggregated across the domain. Thus, while there have been widespread changes in forest composition over the past several decades, the net changes in composition and associated post-fire radiative forcing have not induced systematic negative feedbacks to climate warming over the spatial and temporal scope of our study.}, } @article {pmid38058223, year = {2024}, author = {Fins, IS and Davies, H and Farrell, S and Torres, JR and Pinchbeck, G and Radford, AD and Noble, PJ}, title = {Evaluating ChatGPT text mining of clinical records for companion animal obesity monitoring.}, journal = {The Veterinary record}, volume = {194}, number = {3}, pages = {e3669}, pmid = {38058223}, issn = {2042-7670}, support = {/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; *Pets ; *Data Mining ; Language ; Narration ; Obesity/veterinary ; }, abstract = {BACKGROUND: Veterinary clinical narratives remain a largely untapped resource for addressing complex diseases. Here we compare the ability of a large language model (ChatGPT) and a previously developed regular expression (RegexT) to identify overweight body condition scores (BCS) in veterinary narratives pertaining to companion animals.

METHODS: BCS values were extracted from 4415 anonymised clinical narratives using either RegexT or by appending the narrative to a prompt sent to ChatGPT, prompting the model to return the BCS information. Data were manually reviewed for comparison.

RESULTS: The precision of RegexT was higher (100%, 95% confidence interval [CI] 94.81%-100%) than that of ChatGPT (89.3%, 95% CI 82.75%-93.64%). However, the recall of ChatGPT (100%, 95% CI 96.18%-100%) was considerably higher than that of RegexT (72.6%, 95% CI 63.92%-79.94%).

LIMITATIONS: Prior anonymisation and subtle prompt engineering are needed to improve ChatGPT output.

CONCLUSIONS: Large language models create diverse opportunities and, while complex, present an intuitive interface to information. However, they require careful implementation to avoid unpredictable errors.}, } @article {pmid38055593, year = {2023}, author = {Silva, ABDS and Costa, LS and Frias, PG and Araújo, ACM and Bonfim, CVD}, title = {Temporal analysis of mortality from preventable causes in the first 24 hours of life, 2000-2021.}, journal = {Revista latino-americana de enfermagem}, volume = {31}, number = {}, pages = {e4079}, pmid = {38055593}, issn = {1518-8345}, mesh = {Humans ; Cause of Death ; *Information Systems ; Brazil ; *Mortality ; }, abstract = {OBJECTIVE: to analyze the temporal pattern and estimate mortality rates in the first 24 hours of life and from preventable causes in the state of Pernambuco from 2000 to 2021.

METHOD: an ecological study, using the quarter as the unit of analysis. The data source was made up of the Mortality Information System and the Live Birth Information System. The time series modeling was conducted according to the Autoregressive Integrated Moving Average Model.

RESULTS: 14,462 deaths were recorded in the first 24 hours of life, 11,110 (76.8%) of which being preventable. It is observed from the forecasts that the mortality rate in the first 24 hours of life ranged from 3.3 to 2.4 per 1,000 live births, and the mortality rate from preventable causes ranged from 2.3 to 1.8 per 1,000 live births.

CONCLUSION: the prediction suggested progress in reducing mortality in the first 24 hours of life in the state and from preventable causes. The ARIMA models presented satisfactory estimates for mortality rates and preventable causes in the first 24 hours of life.}, } @article {pmid38053578, year = {2023}, author = {Esterhuizen, M and Park, CB and Kim, YJ and Kim, TY and Yoon, H and Andres, F and Rodriguez-Rodriguez, R and Tanabe, S}, title = {A perspective on the role of physiological stresses in cancer, diabetes and cognitive disease as environmental diseases.}, journal = {Frontiers in molecular biosciences}, volume = {10}, number = {}, pages = {1274221}, pmid = {38053578}, issn = {2296-889X}, abstract = {With rapid industrialization, urbanization, and climate change, the impact of environmental factors on human health is becoming increasingly evident and understanding the complex mechanisms involved is vital from a healthcare perspective. Nevertheless, the relationship between physiological stress resulting from environmental stressors and environmental disease is complex and not well understood. Chronic exposure to environmental stressors, such as air and water contaminants, pesticides, and toxic metals, has been recognized as a potent elicitor of physiological responses ranging from systemic inflammation to immune system dysregulation causing or progressing environmental diseases. Conversely, physiological stress can exacerbate susceptibility to environmental diseases. Stress-induced alterations in immune function and hormonal balance may impair the ability to detoxify harmful substances and combat pathogens. Additionally, prolonged stress can impact lifestyle choices, leading to harmful behaviors. Understanding the link between physiological stress and environmental disease requires a systematic, multidisciplinary approach. Addressing this complex relationship necessitates the establishment of a global research network. This perspective discusses the intricate interplay between physiological stress and environmental disease, focusing on common environmental diseases, cancer, diabetes, and cognitive degeneration. Furthermore, we highlight the intricate and reciprocal nature of the connection between physiological stress and these environmental diseases giving a perspective on the current state of knowledge as well as identifying where further information is necessary. Recognizing the role of physiological stress in environmental health outcomes will aid in the development of comprehensive strategies to safeguard public health and promote ecological balance.}, } @article {pmid38052982, year = {2024}, author = {Choudhary, P and Monasso, GS and Karhunen, V and Ronkainen, J and Mancano, G and Howe, CG and Niu, Z and Zeng, X and Guan, W and Dou, J and Feinberg, JI and Mordaunt, C and Pesce, G and Baïz, N and Alfano, R and Martens, DS and Wang, C and Isaevska, E and Keikkala, E and Mustaniemi, S and Thio, CHL and Fraszczyk, E and Tobi, EW and Starling, AP and Cosin-Tomas, M and Urquiza, J and Röder, S and Hoang, TT and Page, C and Jima, DD and House, JS and Maguire, RL and Ott, R and Pawlow, X and Sirignano, L and Zillich, L and Malmberg, A and Rauschert, S and Melton, P and Gong, T and Karlsson, R and Fore, R and Perng, W and Laubach, ZM and Czamara, D and Sharp, G and Breton, CV and Schisterman, E and Yeung, E and Mumford, SL and Fallin, MD and LaSalle, JM and Schmidt, RJ and Bakulski, KM and Annesi-Maesano, I and Heude, B and Nawrot, TS and Plusquin, M and Ghantous, A and Herceg, Z and Nisticò, L and Vafeiadi, M and Kogevinas, M and Vääräsmäki, M and Kajantie, E and Snieder, H and Corpeleijn, E and Steegers-Theunissen, RPM and Yang, IV and Dabelea, D and Fossati, S and Zenclussen, AC and Herberth, G and Magnus, M and Håberg, SE and London, SJ and Munthe-Kaas, MC and Murphy, SK and Hoyo, C and Ziegler, AG and Hummel, S and Witt, SH and Streit, F and Frank, J and Räikkönen, K and Lahti, J and Huang, RC and Almqvist, C and Hivert, MF and Jaddoe, VWV and Järvelin, MR and Kantomaa, M and Felix, JF and Sebert, S}, title = {Maternal educational attainment in pregnancy and epigenome-wide DNA methylation changes in the offspring from birth until adolescence.}, journal = {Molecular psychiatry}, volume = {29}, number = {2}, pages = {348-358}, pmid = {38052982}, issn = {1476-5578}, support = {P30 ES025128/ES/NIEHS NIH HHS/United States ; R00 ES030400/ES/NIEHS NIH HHS/United States ; MC_PC_19009/MRC_/Medical Research Council/United Kingdom ; U24 ES028533/ES/NIEHS NIH HHS/United States ; MC_PC_15018/MRC_/Medical Research Council/United Kingdom ; 873749//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; 733206//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; R24 ES028531/ES/NIEHS NIH HHS/United States ; G9815508/MRC_/Medical Research Council/United Kingdom ; 848158//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; 001/WHO_/World Health Organization/International ; R01 ES025531/ES/NIEHS NIH HHS/United States ; }, mesh = {Humans ; *DNA Methylation/genetics ; Female ; Pregnancy ; Adolescent ; *Epigenome/genetics ; Child ; *Educational Status ; Male ; *Genome-Wide Association Study/methods ; *Epigenesis, Genetic/genetics ; Prenatal Exposure Delayed Effects/genetics ; Child, Preschool ; Infant ; Mothers ; Infant, Newborn ; Adult ; Academic Success ; }, abstract = {Maternal educational attainment (MEA) shapes offspring health through multiple potential pathways. Differential DNA methylation may provide a mechanistic understanding of these long-term associations. We aimed to quantify the associations of MEA with offspring DNA methylation levels at birth, in childhood and in adolescence. Using 37 studies from high-income countries, we performed meta-analysis of epigenome-wide association studies (EWAS) to quantify the associations of completed years of MEA at the time of pregnancy with offspring DNA methylation levels at birth (n = 9 881), in childhood (n = 2 017), and adolescence (n = 2 740), adjusting for relevant covariates. MEA was found to be associated with DNA methylation at 473 cytosine-phosphate-guanine sites at birth, one in childhood, and four in adolescence. We observed enrichment for findings from previous EWAS on maternal folate, vitamin-B12 concentrations, maternal smoking, and pre-pregnancy BMI. The associations were directionally consistent with MEA being inversely associated with behaviours including smoking and BMI. Our findings form a bridge between socio-economic factors and biology and highlight potential pathways underlying effects of maternal education. The results broaden our understanding of bio-social associations linked to differential DNA methylation in multiple early stages of life. The data generated also offers an important resource to help a more precise understanding of the social determinants of health.}, } @article {pmid38052241, year = {2023}, author = {Cribb, AT and Formoso, KK and Woolley, CH and Beech, J and Brophy, S and Byrne, P and Cassady, VC and Godbold, AL and Larina, E and Maxeiner, PP and Wu, YH and Corsetti, FA and Bottjer, DJ}, title = {Contrasting terrestrial and marine ecospace dynamics after the end-Triassic mass extinction event.}, journal = {Proceedings. Biological sciences}, volume = {290}, number = {2012}, pages = {20232232}, pmid = {38052241}, issn = {1471-2954}, mesh = {*Ecosystem ; *Extinction, Biological ; Fossils ; Databases, Factual ; Biodiversity ; }, abstract = {Mass extinctions have fundamentally altered the structure of the biosphere throughout Earth's history. The ecological severity of mass extinctions is well studied in marine ecosystems by categorizing marine taxa into functional groups based on 'ecospace' approaches, but the ecological response of terrestrial ecosystems to mass extinctions is less well understood due to the lack of a comparable methodology. Here, we present a new terrestrial ecospace framework that categorizes fauna into functional groups as defined by tiering, motility and feeding traits. We applied the new terrestrial and traditional marine ecospace analyses to data from the Paleobiology Database across the end-Triassic mass extinction-a time of catastrophic global warming-to compare changes between the marine and terrestrial biospheres. We found that terrestrial functional groups experienced higher extinction severity, that taxonomic and functional richness are more tightly coupled in the terrestrial, and that the terrestrial realm continued to experience high ecological dissimilarity in the wake of the extinction. Although signals of extinction severity and ecological turnover are sensitive to the quality of the terrestrial fossil record, our findings suggest greater ecological pressure from the end-Triassic mass extinction on terrestrial ecosystems than marine ecosystems, contributing to more prolonged terrestrial ecological flux.}, } @article {pmid38051947, year = {2023}, author = {Wroblewski, TH and Witt, KE and Lee, SB and Malhi, RS and Peede, D and Huerta-Sánchez, E and Villanea, FA and Claw, KG}, title = {Pharmacogenetic Variation in Neanderthals and Denisovans and Implications for Human Health and Response to Medications.}, journal = {Genome biology and evolution}, volume = {15}, number = {12}, pages = {}, pmid = {38051947}, issn = {1759-6653}, support = {1R35GM128946-01/NH/NIH HHS/United States ; R35 HG011319/HG/NHGRI NIH HHS/United States ; R35 GM128946/GM/NIGMS NIH HHS/United States ; R35HG011319/HG/NHGRI NIH HHS/United States ; T32 GM128596/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Humans ; *Neanderthals/genetics ; Pharmacogenetics ; Genome, Human ; *Hominidae/genetics ; Biological Evolution ; }, abstract = {Modern humans carry both Neanderthal and Denisovan (archaic) genome elements that are part of the human gene pool and affect the life and health of living individuals. The impact of archaic DNA may be particularly evident in pharmacogenes-genes responsible for the processing of exogenous substances such as food, pollutants, and medications-as these can relate to changing environmental effects, and beneficial variants may have been retained as modern humans encountered new environments. However, the health implications and contribution of archaic ancestry in pharmacogenes of modern humans remain understudied. Here, we explore 11 key cytochrome P450 genes (CYP450) involved in 75% of all drug metabolizing reactions in three Neanderthal and one Denisovan individuals and examine archaic introgression in modern human populations. We infer the metabolizing efficiency of these 11 CYP450 genes in archaic individuals and find important predicted phenotypic differences relative to modern human variants. We identify several single nucleotide variants shared between archaic and modern humans in each gene, including some potentially function-altering mutations in archaic CYP450 genes, which may result in altered metabolism in living people carrying these variants. We also identified several variants in the archaic CYP450 genes that are novel and unique to archaic humans as well as one gene, CYP2B6, that shows evidence for a gene duplication found only in Neanderthals and modern Africans. Finally, we highlight CYP2A6, CYP2C9, and CYP2J2, genes which show evidence for archaic introgression into modern humans and posit evolutionary hypotheses that explain their allele frequencies in modern populations.}, } @article {pmid38051448, year = {2023}, author = {Urbano, F and Viterbi, R and Pedrotti, L and Vettorazzo, E and Movalli, C and Corlatti, L}, title = {Enhancing biodiversity conservation and monitoring in protected areas through efficient data management.}, journal = {Environmental monitoring and assessment}, volume = {196}, number = {1}, pages = {12}, pmid = {38051448}, issn = {1573-2959}, mesh = {Humans ; *Ecosystem ; *Conservation of Natural Resources/methods ; Data Management ; Environmental Monitoring ; Biodiversity ; }, abstract = {A scientifically informed approach to decision-making is key to ensuring the sustainable management of ecosystems, especially in the light of increasing human pressure on habitats and species. Protected areas, with their long-term institutional mandate for biodiversity conservation, play an important role as data providers, for example, through the long-term monitoring of natural resources. However, poor data management often limits the use and reuse of this wealth of information. In this paper, we share lessons learned in managing long-term data from the Italian Alpine national parks. Our analysis and examples focus on specific issues faced by managers of protected areas, which partially differ from those faced by academic researchers, predominantly owing to different mission, governance, and temporal perspectives. Rigorous data quality control, the use of appropriate data management tools, and acquisition of the necessary skills remain the main obstacles. Common protocols for data collection offer great opportunities for the future, and complete recovery and documentation of time series is an urgent priority. Notably, before data can be shared, protected areas should improve their data management systems, a task that can be achieved only with adequate resources and a long-term vision. We suggest strategies that protected areas, funding agencies, and the scientific community can embrace to address these problems. The added value of our work lies in promoting engagement with managers of protected areas and in reporting and analysing their concrete requirements and problems, thereby contributing to the ongoing discussion on data management and sharing through a bottom-up approach.}, } @article {pmid38046930, year = {2023}, author = {Tschernosterová, K and Trávníčková, E and Grattarola, F and Rosse, C and Keil, P}, title = {SPARSE 1.0: a template for databases of species inventories, with an open example of Czech birds.}, journal = {Biodiversity data journal}, volume = {11}, number = {}, pages = {e108731}, pmid = {38046930}, issn = {1314-2828}, abstract = {Here, we introduce SPARSE (acronym for "SPecies AcRoss ScalEs"), a simple and portable template for databases that can store data on species composition derived from ecological inventories, surveys and checklists, with emphasis on metadata describing sampling effort and methods. SPARSE can accommodate resurveys and time series and data from different spatial scales, as well as complex sampling designs. SPARSE focuses on inventories that report multiple species for a given site, together with sampling methods and effort, which can be used in statistical models of true probability of occurrence of species. SPARSE is spatially explicit and can accommodate nested spatial structures from multiple spatial scales, including sampling designs where multiple sites within a larger area have been surveyed and the larger area can again be nested in an even larger region. Each site in SPARSE is represented either by a point, line (for transects) or polygon, stored in an ESRI shapefile. SPARSE implements a new combination of our own field definitions with Darwin Core biodiversity data standard and its Humboldt core extension. The use of Humboldt core also makes SPARSE suitable for biodiversity data with temporal replication. We provide an example use of the SPARSE framework by digitising data on birds from the Czech Republic, from 348 sites and 524 sampling events, with 15,969 unique species-per-event observations of presence, abundance or population density. To facilitate use without the need for a high-level database expertise, the Czech bird example is implemented as MS Access .accdb file, but can be ported to other database engines. The example of Czech birds complements other bird datasets from the Czech Republic, specifically the four gridded national atlases and the breeding bird survey which cover a similar temporal extent, but different locations and spatial scales.}, } @article {pmid38046192, year = {2023}, author = {Boyes, D and Sims, I and Lees, D and Holland, PWH and , and , and , and , and , and , }, title = {The genome sequence of the Black-tipped Ermine, Yponomeuta plumbella (Denis & Schiffermüller, 1775).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {246}, pmid = {38046192}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual male Yponomeuta plumbella (the Black-tipped Ermine; Arthropoda; Insecta; Lepidoptera; Yponomeutidae). The genome sequence is 636.6 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 16.5 kilobases in length.}, } @article {pmid38046063, year = {2023}, author = {Suresh, KP and Barman, NN and Bari, T and Jagadish, D and Sushma, B and Darshan, HV and Patil, SS and Bora, M and Deka, A}, title = {Application of machine learning models for risk estimation and risk prediction of classical swine fever in Assam, India.}, journal = {Virusdisease}, volume = {34}, number = {4}, pages = {514-525}, pmid = {38046063}, issn = {2347-3584}, abstract = {UNLABELLED: The present study is aimed to develop an early warning system of Classical swine fever (CSF) disease by applying machine learning models and to study the climate-disease relationship with respect to the spatial occurrence and outbreaks of the disease in the north-eastern state of Assam, India. The disease incidence data from the year 2005 to 2021 was used. The linear discriminant analysis (LDA) revealed that significant environmental and remote sensing risk factors like air temperature, enhanced vegetation index, land surface temperature, potential evaporation rate and wind speed were significantly contributing to CSF incidences in Assam. Furthermore, the climate-based disease modelling was applied to relevant ecological and environmental risk factors determined using LDA and risk maps were generated. The western and eastern regions of the state were predicted to be at high risk of CSF with presence of significant hotspots. For the districts that are significantly clustered, the Basic reproduction number (R0) was calculated after the predicted results were superimposed onto the risk maps. The R0 value ranged from 1.04 to 2.07, implying that the eastern and western regions of Assam are more susceptible to CSF. Machine learning models were implemented using R statistical software version 3.1.3. The random forest, classification tree analysis and gradient boosting machine were found to be the best-fitted models for the study group. The models' performance was measured using the Receiving Operating Characteristic (ROC) curve, Cohen's Kappa, True Skill Statistics, Area Under ROC Curve, ACCURACY, ERROR RATE, F1 SCORE, and Logistic Loss. As a part of the suggested study, these models will help us to understand the disease transmission dynamics, risk factors and spatio-temporal pattern of spread and evaluate the efficacy of control measures to battle the economic losses caused by CSF outbreaks.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13337-023-00847-6.}, } @article {pmid38045543, year = {2023}, author = {Lin, B and Shi, W and Lu, Q and Shito, TT and Yu, H and Dong, B}, title = {Establishment of a developmental atlas and transgenetic tools in the ascidian Styela clava.}, journal = {Marine life science & technology}, volume = {5}, number = {4}, pages = {435-454}, pmid = {38045543}, issn = {2662-1746}, abstract = {UNLABELLED: The ascidian Styela clava is an ecologically important species that is distributed along coastal regions worldwide. It has a long history as a model animal for evolutionary and developmental biology research owing to its phylogenetic position between vertebrates and invertebrates, and its classical mosaic expression patterns. However, the standard developmental atlas and protocols and tools for molecular manipulation of this organism are inadequate. In this study, we established a standard developmental table and provided a web-based digital image resource for S. clava embryogenesis at each developmental stage from fertilized eggs to hatching larvae by utilizing confocal laser microscopy and 3D reconstruction images. It takes around 10 h for fertilized eggs to develop into swimming larvae and 20-30 min to complete the tail regression processes at the metamorphic stage. We observed that the notochord cells in S. clava embryos did not produce an extracellular lumen like Ciona robusta, but showed polarized elongation behaviors, providing us an ideal comparative model to study tissue morphogenesis. In addition, we established a chemical-washing procedure to remove the chorion easily from the fertilized eggs. Based on the dechorionation technique, we further realized transgenic manipulation by electroporation and successfully applied tissue-specific fluorescent labeling in S. clava embryos. Our work provides a standard imaging atlas and powerful genetic tools for investigating embryogenesis and evolution using S. clava as a model organism.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s42995-023-00200-2.}, } @article {pmid39268176, year = {2023}, author = {Boyes, D and Holland, PWH and , and , and , and , and , and , }, title = {The genome sequence of the White Satin, Leucoma salicis (Linnaeus, 1758).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {323}, pmid = {39268176}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual male Leucoma salicis (the White Satin; Arthropoda; Insecta; Lepidoptera; Erebidae). The genome sequence is 733.2 megabases in span. Most of the assembly is scaffolded into 30 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.73 kilobases in length. Gene annotation of this assembly on Ensembl identified 20,222 protein coding genes.}, } @article {pmid39114813, year = {2023}, author = {Boyes, D and Hammond, J and , and , and , and , and , and , }, title = {The genome sequence of the Thicket Knot-horn, Acrobasis suavella (Zincken, 1818).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {252}, pmid = {39114813}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual male Acrobasis suavella (the Thicket Knot-horn; Arthropoda; Insecta; Lepidoptera; Pyralidae). The genome sequence is 647.3 megabases in span. Most of the assembly is scaffolded into 30 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.31 kilobases in length. Gene annotation of this assembly on Ensembl identified 19,101 protein coding genes.}, } @article {pmid39430045, year = {2023}, author = {Boyes, D and Holland, PWH and , and , and , and , and , and , }, title = {The genome sequence of the Olive Pearl, Udea olivalis (Denis & Schiffermüller, 1775).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {238}, pmid = {39430045}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual male Udea olivalis (the Olive Pearl; Arthropoda; Insecta; Lepidoptera; Crambidae). The genome sequence is 624.4 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.3 kilobases in length.}, } @article {pmid39242656, year = {2023}, author = {Hui, C and Pyšek, P and Richardson, DM}, title = {Disentangling the relationships among abundance, invasiveness and invasibility in trait space.}, journal = {npj biodiversity}, volume = {2}, number = {1}, pages = {13}, pmid = {39242656}, issn = {2731-4243}, support = {89967//National Research Foundation/ ; NE/V007548/1//Natural Environment Research Council/ ; DP200101680//Australian Research Council/ ; 101059592//HORIZON EUROPE European Research Council/ ; EXPRO 19-28807X//Czech Science Foundation/ ; RVO 67985939//Czech Academy of Sciences/ ; RVO 67985939//Czech Academy of Sciences/ ; CZ.02.2.69/0.0/0.0/18_053/0017850//Ministry of Education, Youth, and Sports of the Czech Republic/ ; }, abstract = {Identifying conditions and traits that allow an introduced species to grow and spread, from being initially rare to becoming abundant (defined as invasiveness), is the crux of invasion ecology. Invasiveness and abundance are related but not the same, and we need to differentiate these concepts. Predicting both species abundance and invasiveness and their relationship in an invaded community is highly contextual, being contingent on the community trait profile and its invasibility. We operationalised a three-pronged invasion framework that considers traits, environmental context, and propagule pressure. Specifically, we measure the invasiveness of an alien species by combining three components (performance reflecting environmental suitability, product of species richness and the covariance between interaction strength and species abundance, and community-level interaction pressure); the expected population growth rate of alien species simply reflects the total effect of propagule pressure and the product of their population size and invasiveness. The invasibility of a community reflects the size of opportunity niches (the integral of positive invasiveness in the trait space) under the given abiotic conditions of the environment. Both species abundance and the surface of invasiveness over the trait space can be dynamic and variable. Whether an introduced species with functional traits similar to those of an abundant species in the community exhibits high or low invasiveness depends largely on the kernel functions of performance and interaction strength with respect to traits and environmental conditions. Knowledge of the covariance between interaction strength and species abundance and these kernel functions, thus, holds the key to accurate prediction of invasion dynamics.}, } @article {pmid38903245, year = {2023}, author = {Boyes, D and Goate, Z and , and , and , and , and , and , }, title = {The genome sequence of the White-backed Marble, Hedya salicella (Linnaeus, 1758).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {219}, pmid = {38903245}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual male Hedya salicella (the White-backed Marble; Arthropoda; Insecta; Lepidoptera; Tortricidae). The genome sequence is 742.3 megabases in span. Most of the assembly is scaffolded into 25 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 16.3 kilobases in length. Gene annotation of this assembly on Ensembl identified 11,961 protein coding genes.}, } @article {pmid39262678, year = {2023}, author = {Boyes, D and Holland, PWH and , and , and , and , and , and , }, title = {The genome sequence of the Brindled Flat-body, Agonopterix arenella (Denis & Schiffermüller, 1775).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {214}, pmid = {39262678}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual male Agonopterix arenella (the Brindled Flat-body; Arthropoda; Insecta; Lepidoptera; Depressariidae). The genome sequence is 545.8 megabases in span. Most of the assembly is scaffolded into 30 chromosomal pseudomolecules, including the assembled Z sex chromosome. The mitochondrial genome has also been assembled and is 15.3 kilobases in length.}, } @article {pmid39502585, year = {2023}, author = {Boyes, D and Lewis, OT and , and , and , and , and , and , }, title = {The genome sequence of the Small Phoenix, Ecliptopera silaceata (Denis & Schiffermüller, 1775).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {209}, pmid = {39502585}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual male Ecliptopera silaceata (the Small Phoenix; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 316.5 megabases in span. Most of the assembly is scaffolded into 29 chromosomal pseudomolecules, including the assembled Z sex chromosome. The mitochondrial genome has also been assembled and is 17.5 kilobases in length. Gene annotation of this assembly on Ensembl identified 16,770 protein coding genes.}, } @article {pmid39211527, year = {2023}, author = {Boyes, D and Holland, PWH and , and , and , and , and , and , }, title = {The genome sequence of the Small Square-spot, Diarsia rubi (Vieweg, 1790).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {210}, pmid = {39211527}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual female Diarsia rubi (the Small Square-spot; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 624.9 megabases in span. Most of the assembly is scaffolded into 32 chromosomal pseudomolecules, including the Z and W sex chromosomes. The mitochondrial genome has also been assembled and is 15.3 kilobases in length. Gene annotation of this assembly on Ensembl identified 19,173 protein coding genes.}, } @article {pmid38817338, year = {2022}, author = {Cocker, D and Sammarro, M and Chidziwisano, K and Elviss, N and Jacob, ST and Kajumbula, H and Mugisha, L and Musoke, D and Musicha, P and Roberts, AP and Rowlingson, B and Singer, AC and Byrne, RL and Edwards, T and Lester, R and Wilson, CN and Hollihead, B and Thomson, NR and Jewell, CP and Morse, T and Feasey, NA}, title = {Drivers of Resistance in Uganda and Malawi (DRUM): a protocol for the evaluation of One-Health drivers of Extended Spectrum Beta Lactamase (ESBL) resistance in Low-Middle Income Countries (LMICs).}, journal = {Wellcome open research}, volume = {7}, number = {}, pages = {55}, pmid = {38817338}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; MR/R015074/1/MRC_/Medical Research Council/United Kingdom ; MR/S004793/1/MRC_/Medical Research Council/United Kingdom ; }, abstract = {In sub-Saharan Africa (sSA), there is high morbidity and mortality from severe bacterial infection and this is compounded by antimicrobial resistance, in particular, resistance to 3rd-generation cephalosporins. This resistance is typically mediated by extended-spectrum beta lactamases (ESBLs). To interrupt ESBL transmission it will be important to investigate how human behaviour, water, sanitation, and hygiene (WASH) practices, environmental contamination, and antibiotic usage in both urban and rural settings interact to contribute to transmission of ESBL E. coli and ESBL K. pneumoniae between humans, animals, and the environment. Here we present the protocol for the Drivers of Resistance in Uganda and Malawi (DRUM) Consortium, in which we will collect demographic, geospatial, clinical, animal husbandry and WASH data from a total of 400 households in Uganda and Malawi. Longitudinal human, animal and environmental sampling at each household will be used to isolate ESBL E. coli and ESBL K. pneumoniae. This will be complimented by a Risks, Attitudes, Norms, Abilities and Self-Regulation (RANAS) survey and structured observations to understand the contextual and psychosocial drivers of regional WASH practices. Bacterial isolates and plate sweeps will be further characterised using a mixture of short-,long-read and metagenomic whole-genome sequencing. These datasets will be integrated into agent-based models to describe the transmission of EBSL resistance in Uganda and Malawi and allow us to inform the design of interventions for interrupting transmission of ESBL-bacteria.}, } @article {pmid38779052, year = {2023}, author = {Lohse, K and Hayward, A and Laetsch, DR and Marques, V and Vila, R and Tyler-Smith, C and , and , and , and , }, title = {The genome sequence of the Mazarine Blue, Cyaniris semiargus (Rottemburg, 1775).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {181}, pmid = {38779052}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual male Cyaniris semiargus (the Mazarine Blue; Arthropoda; Insecta; Lepidoptera; Lycaenidae). The genome sequence is 441.5 megabases in span. Most of the assembly is scaffolded into 24 chromosomal pseudomolecules, including the assembled Z sex chromosome. The mitochondrial genome has also been assembled and is 15.4 kilobases in length. Gene annotation of this assembly on Ensembl identified 16,408 protein coding genes.}, } @article {pmid38798993, year = {2023}, author = {Boyes, D and Lewis, OT and , and , and , and , and , and , }, title = {The genome sequence of the Lilac Beauty, Apeira syringaria (Linnaeus, 1758).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {159}, pmid = {38798993}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual female Apeira syringaria (the Lilac Beauty; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 544.4 megabases in span. Most of the assembly is scaffolded into 30 chromosomal pseudomolecules, including the assembled Z sex chromosome. The mitochondrial genome has also been assembled and is 15.5 kilobases in length. Gene annotation of this assembly on Ensembl identified 18,426 protein coding genes.}, } @article {pmid38770266, year = {2023}, author = {Vila, R and Lohse, K and Hayward, A and Laetsch, DR and Wright, C and , and , and , and , }, title = {The genome sequence of the Chalkhill Blue, Lysandra coridon (Poda, 1761).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {162}, pmid = {38770266}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual male Lysandra coridon (the Chalkhill Blue; Arthropoda; Insecta; Lepidoptera; Lycaenidae). The genome sequence is 541 megabases in span. Most of the assembly is scaffolded into 90 chromosomal pseudomolecules, including the assembled Z sex chromosome. The mitochondrial genome has also been assembled and is 15.4 kilobases in length. Gene annotation of this assembly on Ensembl identified 13,334 protein coding genes.}, } @article {pmid38764974, year = {2023}, author = {Boyes, D and Hammond, J and , and , and , and , and , and , }, title = {The genome sequence of the Sycamore Piercer, Pammene aurita (Razowski, 1991).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {160}, pmid = {38764974}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual male Pammene aurita (the Sycamore Piercer; Arthropoda; Insecta; Lepidoptera; Tortricidae). The genome sequence is 1,041.8 megabases in span. Most of the assembly is scaffolded into 28 chromosomal pseudomolecules, including the assembled Z sex chromosome. The mitochondrial genome has also been assembled and is 16.7 kilobases in length.}, } @article {pmid39219859, year = {2023}, author = {Boyes, D and Lewis, OT and , and , and , and , and , and , }, title = {The genome sequence of the Ruby Tiger, Phragmatobia fuliginosa (Linnaeus, 1758).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {124}, pmid = {39219859}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual male Phragmatobia fuliginosa (the Ruby Tiger; Arthropoda; Insecta; Lepidoptera; Erebidae). The genome sequence is 629.4 megabases in span. Most of the assembly is scaffolded into 28 chromosomal pseudomolecules, including the assembled Z sex chromosome. The mitochondrial genome has also been assembled and is 15.4 kilobases in length. Gene annotation of this assembly on Ensembl identified 13,338 protein coding genes.}, } @article {pmid38707488, year = {2023}, author = {Boyes, D and , and , and , and , and , and Boyes, C and , }, title = {The genome sequence of the Fulvous Clothes Moth, Tinea semifulvella (Haworth, 1828).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {104}, pmid = {38707488}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual male Tinea semifulvella (the Fulvous Clothes Moth; Arthropoda; Insecta; Lepidoptera; Tineidae). The genome sequence is 596.6 megabases in span. The whole assembly is scaffolded into 45 chromosomal pseudomolecules, with the Z sex chromosome assembled. The mitochondrial genome has also been assembled and is 16.8 kilobases in length. Gene annotation of this assembly on Ensembl has identified 11,516 protein coding genes.}, } @article {pmid39129913, year = {2023}, author = {Boyes, D and , and , and , and , and , and Mulley, JF and , }, title = {The genome sequence of the Dark Arches Apamea monoglypha (Hufnagel, 1766).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {63}, pmid = {39129913}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual male Apamea monoglypha (the Dark Arches, Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 576 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the assembled Z sex chromosome. The mitochondrial genome has also been assembled and is 16.5 kilobases in length. Gene annotation of this assembly on Ensembl has identified 17,963 protein coding genes.}, } @article {pmid39148947, year = {2023}, author = {Boyes, D and , and , and , and , and , and Holland, PWH and , }, title = {The genome sequence of the Green-brindled Crescent, Allophyes oxyacanthae (Linnaeus, 1758).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {53}, pmid = {39148947}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual male Allophyes oxyacanthae (the Green-brindled Crescent; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 458 megabases in span. The whole assembly is scaffolded into 31 chromosomal pseudomolecules, including the assembled Z sex chromosome. The mitochondrial genome has also been assembled and is 15.3 kilobases in length. Gene annotation of this assembly on Ensembl has identified 17,301 protein coding genes.}, } @article {pmid38868331, year = {2023}, author = {Li, C and Jin, L and Zhang, C and Li, S and Zhou, T and Hua, Z and Wang, L and Ji, S and Wang, Y and Gan, Y and Liu, J}, title = {Destabilized microbial networks with distinct performances of abundant and rare biospheres in maintaining networks under increasing salinity stress.}, journal = {iMeta}, volume = {2}, number = {1}, pages = {e79}, pmid = {38868331}, issn = {2770-596X}, abstract = {Global changes such as seawater intrusion and freshwater resource salinization increase environmental stress imposed on the aquatic microbiome. A strong predictive understanding of the responses of the aquatic microbiome to environmental stress will help in coping with the "gray rhino" events in the environment, thereby contributing to an ecologically sustainable future. Considering that microbial ecological networks are tied to the stability of ecosystem functioning and that abundant and rare biospheres with different biogeographic patterns are important drivers of ecosystem functioning, the roles of abundant and rare biospheres in maintaining ecological networks need to be clarified. Here we showed that, with the increasing salinity stress induced by the freshwater-to-seawater transition, the microbial diversity reduced significantly and the taxonomic structure experienced a strong succession. The complexity and stability of microbial ecological networks were diminished by the increasing stress. The composition of the microorganisms supporting the networks underwent sharp turnovers during the freshwater-to-seawater transition, with the abundant biosphere behaving more robustly than the rare biosphere. Notably, the abundant biosphere played a much more important role than the rare biosphere in stabilizing ecological networks under low-stress environments, but the difference between their relative importance narrowed significantly with the increasing stress, suggesting that the environmental stress weakened the "Matthew effect" in the microbial world. With in-depth insights into the aquatic microbial ecology under stress, our findings highlight the importance of adjusting conservation strategies for the abundant and rare biospheres to maintain ecosystem functions and services in response to rising environmental stress.}, } @article {pmid39328383, year = {2023}, author = {Catalàn, N and Campo, RD and Talluto, L and Mendoza-Lera, C and Grandi, G and Bernal, S and Schiller, DV and Singer, G and Bertuzzo, E}, title = {Pulse, Shunt and Storage: Hydrological Contraction Shapes Processing and Export of Particulate Organic Matter in River Networks.}, journal = {Ecosystems (New York, N.Y.)}, volume = {26}, number = {4}, pages = {873-892}, pmid = {39328383}, issn = {1432-9840}, abstract = {UNLABELLED: Streams and rivers act as landscape-scale bioreactors processing large quantities of terrestrial particulate organic matter (POM). This function is linked to their flow regime, which governs residence times, shapes organic matter reactivity and controls the amount of carbon (C) exported to the atmosphere and coastal oceans. Climate change impacts flow regimes by increasing both flash floods and droughts. Here, we used a modelling approach to explore the consequences of lateral hydrological contraction, that is, the reduction of the wet portion of the streambed, for POM decomposition and transport at the river network scale. Our model integrates seasonal leaf litter input as generator of POM, transient storage of POM on wet and dry streambed portions with associated decomposition and ensuing changes in reactivity, and transport dynamics through a dendritic river network. Simulations showed that the amount of POM exported from the river network and its average reactivity increased with lateral hydrological contraction, due to the combination of (1) low processing of POM while stored on dry streambeds, and (2) large shunting during flashy events. The sensitivity analysis further supported that high lateral hydrological contraction leads to higher export of higher reactivity POM, regardless of transport coefficient values, average reactivity of fresh leaf litter and differences between POM reactivity under wet and dry conditions. Our study incorporates storage in dry streambed areas into the pulse-shunt concept (Raymond and others in Ecology 97(1):5-16, 2016. 10.1890/14-1684.1), providing a mechanistic framework and testable predictions about leaf litter storage, transport and decomposition in fluvial networks.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s10021-022-00802-4.}, } @article {pmid38799509, year = {2022}, author = {Boyes, D and , and , and , and , and , and Parkerson, L and , }, title = {The genome sequence of the common grass-veneer, Agriphila tristella (Denis & Schiffermüller, 1775).}, journal = {Wellcome open research}, volume = {7}, number = {}, pages = {304}, pmid = {38799509}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual male Agriphila tristella (the common grass-veneer; Arthropoda; Insecta; Lepidoptera; Crambidae). The genome sequence is 802 megabases in span. Most of the assembly (99.83%) is scaffolded into 23 chromosomal pseudomolecules with the Z sex chromosome assembled. The mitochondrial genome was also assembled and is 15.3 kilobases in length.}, } @article {pmid38867895, year = {2022}, author = {Wu, D and Liu, L and Jiao, N and Zhang, Y and Yang, L and Tian, C and Lan, P and Zhu, L and Loomba, R and Zhu, R}, title = {Targeting keystone species helps restore the dysbiosis of butyrate-producing bacteria in nonalcoholic fatty liver disease.}, journal = {iMeta}, volume = {1}, number = {4}, pages = {e61}, pmid = {38867895}, issn = {2770-596X}, support = {P42 ES010337/ES/NIEHS NIH HHS/United States ; R01 DK106419/DK/NIDDK NIH HHS/United States ; UL1 TR001442/TR/NCATS NIH HHS/United States ; }, abstract = {The dysbiosis of the gut microbiome is one of the pathogenic factors of nonalcoholic fatty liver disease (NAFLD) and also affects the treatment and intervention of NAFLD. Among gut microbiomes, keystone species that regulate the integrity and stability of an ecological community have become the potential intervention targets for NAFLD. Here, we collected stool samples from 22 patients with nonalcoholic steatohepatitis (NASH), 25 obese patients, and 16 healthy individuals from New York for 16S rRNA gene sequencing. An algorithm was implemented to identify keystone species based on causal inference theories and dynamic intervention simulation. External validation was performed in an independent cohort from California. Eight keystone species in the gut of NAFLD, represented by Porphyromonas loveana, Alistipes indistinctus, and Dialister pneumosintes, were identified, which could efficiently restore the microbial composition of the NAFLD toward a normal gut microbiome with 92.3% recovery. These keystone species regulate intestinal amino acid metabolism and acid-base environment to promote the growth of the butyrate-producing Lachnospiraceae and Ruminococcaceae species that are significantly reduced in NAFLD patients. Our findings demonstrate the importance of keystone species in restoring the microbial composition toward a normal gut microbiome, suggesting a novel potential microbial treatment for NAFLD.}, } @article {pmid39144291, year = {2022}, author = {Fitzhugh, B and Brown, WA and Misarti, N and Takase, K and Tremayne, AH}, title = {Human Paleodemography and Paleoecology of the North Pacific Rim from the Mid to Late Holocene.}, journal = {Quaternary research}, volume = {108}, number = {PESAS}, pages = {123-149}, pmid = {39144291}, issn = {0033-5894}, support = {P2C HD042828/HD/NICHD NIH HHS/United States ; }, abstract = {Using 14 proxy human population time series from around the North Pacific (Alaska, Hokkaido and the Kuril Islands), we evaluate the possibility that the North Pacific climate and marine ecosystem includes a millennial-scale regime shift cycle affecting subsistence and migration. We develop both visual and statistical methods for addressing questions about relative population growth and movement in the past. We introduce and explore the use of a Time Iterative Moran I (TIMI) spatial autocorrelation method to compare time series trends quantitatively - a method that could prove useful in other paleoecological analyses. Results reveal considerable population dynamism around the North Pacific in the last 5000 years and strengthen a previously reported inverse correlation between Northeast and Northwest Pacific proxy population indices. Visual and TIMI analyses suggest multiple, overlapping explanations for the variability, including the potential that oscillating ecological regime shifts affect the North Pacific basin. These results provide an opening for coordinated research to unpack the interrelated social, cultural and environmental dynamics around the subarctic and arctic North Pacific at different spatial and temporal scales by international teams of archaeologists, historians, paleoecologists, paleoceanographers, paleoclimatologists, modelers and data management specialists.}, } @article {pmid38235459, year = {2022}, author = {De Castro Martins, C and Chaminade, T and Cavazza, M}, title = {Causal Analysis of Activity in Social Brain Areas During Human-Agent Conversation.}, journal = {Frontiers in neuroergonomics}, volume = {3}, number = {}, pages = {843005}, pmid = {38235459}, issn = {2673-6195}, abstract = {This article investigates the differences in cognitive and neural mechanisms between human-human and human-virtual agent interaction using a dataset recorded in an ecologically realistic environment. We use Convergent Cross Mapping (CCM) to investigate functional connectivity between pairs of regions involved in the framework of social cognitive neuroscience, namely the fusiform gyrus, superior temporal sulcus (STS), temporoparietal junction (TPJ), and the dorsolateral prefrontal cortex (DLPFC)-taken as prefrontal asymmetry. Our approach is a compromise between investigating local activation in specific regions and investigating connectivity networks that may form part of larger networks. In addition to concording with previous studies, our results suggest that the right TPJ is one of the most reliable areas for assessing processes occurring during human-virtual agent interactions, both in a static and dynamic sense.}, } @article {pmid38799510, year = {2022}, author = {Boyes, D and Holland, PWH and , and , and , and , and , and , }, title = {The genome sequence of the silver Y moth, Autographa gamma (Linnaeus, 1758).}, journal = {Wellcome open research}, volume = {7}, number = {}, pages = {100}, pmid = {38799510}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual female Autographa gamma (the silver Y; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 373 megabases in span. The majority of the assembly (99.65%) is scaffolded into 32 chromosomal pseudomolecules, with the W and Z sex chromosomes assembled. The mitochondrial genome was also assembled and is 15.2 kilobases in length.}, } @article {pmid39175988, year = {2021}, author = {Boyes, D and Holland, PWH and , and , and , and , and , and , }, title = {The genome sequence of the bramble shoot moth, Notocelia uddmanniana (Linnaeus, 1758).}, journal = {Wellcome open research}, volume = {6}, number = {}, pages = {348}, pmid = {39175988}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual male Notocelia uddmanniana (the bramble shoot moth; Arthropoda; Insecta; Lepidoptera; Tortricidae). The genome sequence is 794 megabases in span. The majority of the assembly, 99.96%, is scaffolded into 28 chromosomal pseudomolecules, with the Z sex chromosome assembled.}, } @article {pmid38912275, year = {2021}, author = {Boyes, D and Holland, PWH and , and , and , and , and , and , }, title = {The genome sequence of the iron prominent, Notodonta dromedarius (Linnaeus, 1767).}, journal = {Wellcome open research}, volume = {6}, number = {}, pages = {341}, pmid = {38912275}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual male Notodonta dromedarius (iron prominent; Arthropoda; Insecta; Lepidoptera; Notodontidae). The genome sequence is 342 megabases in span. The majority of the assembly, 99.35%, is scaffolded into 31 chromosomal pseudomolecules, with the Z sex chromosome assembled.}, } @article {pmid39449730, year = {2021}, author = {Boyes, D and Crowley, LM and Holland, PWH and , and , and , and , and , and , }, title = {The genome sequence of Svensson's copper underwing, Amphipyra berbera Rungs, 1949.}, journal = {Wellcome open research}, volume = {6}, number = {}, pages = {314}, pmid = {39449730}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual male Amphipyra berbera (Svensson's copper underwing; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 582 megabases in span. The majority (99.97%) of the assembly is scaffolded into 31 chromosomal pseudomolecules, with the Z sex chromosome assembled.}, } @article {pmid38044542, year = {2024}, author = {Cains, MG and Desrousseaux, AOS and Boxall, ABA and Molander, S and Molina-Navarro, E and Sussams, J and Critto, A and Stahl, RG and Rother, HA}, title = {Environmental management cycles for chemicals and climate change, EMC[4] : A new conceptual framework contextualizing climate and chemical risk assessment and management.}, journal = {Integrated environmental assessment and management}, volume = {20}, number = {2}, pages = {433-453}, doi = {10.1002/ieam.4872}, pmid = {38044542}, issn = {1551-3793}, mesh = {Humans ; *Climate Change ; *Conservation of Natural Resources ; Risk Assessment ; Risk Management ; Ecotoxicology ; }, abstract = {The environmental management cycles for chemicals and climate change (EMC[4]) is a suggested conceptual framework for integrating climate change aspects into chemical risk management. The interaction of climate change and chemical risk brings together complex systems that are imperfectly understood by science. Making management decisions in this context is therefore difficult and often exacerbated by a lack of data. The consequences of poor decision-making can be significant for both environmental and human health. This article reflects on the ways in which existing chemicals management systems consider climate change and proposes the EMC[4] conceptual framework, which is a tool for decision-makers operating at different spatial scales. Also presented are key questions raised by the tool to help the decision-maker identify chemical risks from climate change, management options, and, importantly, the different types of actors that are instrumental in managing that risk. Case studies showing decision-making at different spatial scales are also presented highlighting the conceptual framework's applicability to multiple scales. The United Nations Environment Programme's development of an intergovernmental Science Policy Panel on Chemicals and Waste has presented an opportunity to promote and generate research highlighting the impacts of chemicals and climate change interlinkages. Integr Environ Assess Manag 2024;20:433-453. © 2023 The Authors. Integrated Environmental Assessment and Management published by Wiley Periodicals LLC on behalf of Society of Environmental Toxicology & Chemistry (SETAC).}, } @article {pmid38043132, year = {2024}, author = {Golden, E and Allen, D and Amberg, A and Anger, LT and Baker, E and Baran, SW and Bringezu, F and Clark, M and Duchateau-Nguyen, G and Escher, SE and Giri, V and Grevot, A and Hartung, T and Li, D and Lotfi, L and Muster, W and Snyder, K and Wange, R and Steger-Hartmann, T}, title = {Toward implementing virtual control groups in nonclinical safety studies.}, journal = {ALTEX}, volume = {41}, number = {2}, pages = {282-301}, doi = {10.14573/altex.2310041}, pmid = {38043132}, issn = {1868-8551}, mesh = {Animals ; Control Groups ; Pharmaceutical Preparations ; *Research ; }, abstract = {Historical data from control groups in animal toxicity studies are currently mainly used for comparative purposes to assess validity and robustness of study results. Due to the highly controlled environment in which the studies are performed and the homogeneity of the animal collectives it has been proposed to use the historical data to build so-called virtual control groups, which could partly or entirely replace the concurrent control group. This would constitute a substantial contribution to the reduction of animal use in safety studies. Before the concept can be implemented, the prerequisites regarding data collection, curation, and statistical evaluation together with a validation strategy need to be identified to avoid any impairment of the study outcome and subsequent consequences for human risk assessment. To further assess and develop the concept of virtual control groups, the transatlantic think tank for toxicology (t4) sponsored a workshop with stakeholders from the phar­maceutical and chemical industry, academia, FDA, contract research organizations (CROs), and non-governmental organizations in Washington, which took place in March 2023. This report sum­marizes the current efforts of a European initiative to share, collect, and curate animal control data in a centralized database and the first approaches to identify optimal matching criteria between virtual controls and the treatment arms of a study as well as first reflections about strategies for a qualifi­cation procedure and potential pitfalls of the concept.}, } @article {pmid38042774, year = {2023}, author = {Mendoza, JN and Hanazaki, N and Prūse, B and Martini, A and Bittner, MV and Kochalski, S and Macusi, E and Ciriaco, A and Mattalia, G and Sõukand, R}, title = {Ethnobotanical contributions to global fishing communities: a review.}, journal = {Journal of ethnobiology and ethnomedicine}, volume = {19}, number = {1}, pages = {57}, pmid = {38042774}, issn = {1746-4269}, mesh = {Humans ; *Ecosystem ; *Conservation of Natural Resources/methods ; Hunting ; Ethnobotany ; Fisheries ; }, abstract = {BACKGROUND: Ethnobotanical knowledge about the role of plants in fisheries provides valuable ecological information vital for sustainable management of local resources; however, it is diluted and understudied globally. This literature review aims to map the knowledge of plant use within traditional fishing communities.

METHODS: Through the PRISMA method, we identified and selected 34 articles reporting the use of plants in fisheries, and including 344 taxa of plants and algae. Uses of plants and algae were grouped into different categories.

RESULTS: In the novel categorization of fishery-related uses we proposed, the most mentioned were for fishing and building/repair of fishing artifacts and habitat-related uses, while the records of plants related to fiber uses, providing aid in fishing management and species causing problems, were among the least mentioned. Semi-structured interview is most commonly used with local resource users, especially fishery experts, in exploring perceptions on plant use within traditional fishing communities. Diversity was high in all the recorded families, but most were reported locally.

CONCLUSION: Ethnobotanical studies with fishers are not common in the documented literature but they provide a large number of use reports. On the basis this review, in most of the world, the information is of a casual and sporadic nature. Fishers can provide information on aquatic plants and algae that create problems and aid in fishing management, which are crucial in understanding the ecosystem of a region experiencing environmental challenges. This knowledge is greatly understudied globally and undergoing a rapid decline, as highlighted in several of the reviewed articles. Thus, further systematic research on fishery-related uses of plants by fisherfolk is needed considering its potential contribution to the sustainable management of fishery resources.}, } @article {pmid38042196, year = {2024}, author = {Zhang, Y and Cai, L and Chen, L and Zhang, H and Li, G and Wang, G and Cui, J and Filatova, I and Liu, Y}, title = {Effect of micro-nano bubbles on the remediation of saline-alkali soil with microbial agent.}, journal = {The Science of the total environment}, volume = {912}, number = {}, pages = {168940}, doi = {10.1016/j.scitotenv.2023.168940}, pmid = {38042196}, issn = {1879-1026}, mesh = {*Alkalies ; *Soil/chemistry ; Plants ; Environmental Pollution ; *Benzenesulfonates ; }, abstract = {The widespread distribution of saline-alkali soil around the world affects the health of ecological systems and the development of the national economy by limiting the growth of plants. However, the commonly used remediation technologies have the drawbacks of low efficiency, high cost, and secondary pollution. This study investigated the feasibility and efficacy of novel combined micro-nanobubbles (MNBs) and microbial agent (MA) technology for the remediation of saline-alkali soil. The results demonstrated that the combined MA-MNBs method greatly renovated the properties of saline-alkali soil compared with the technologies of single utilization of MA or MNBs process in the laboratory. The method resulted in a reduction of soil electrical conductivity and pH levels, an improvement in soil fertility, and the formation of soil aggregates. Moreover, the method significantly impacted the growth of plants, particularly in plant length, dry weight, and rhizome elongation. Further high-throughput sequencing and gene expression analysis revealed that the MA-MNBs method enhanced the abundance of soil microbial community compared with single MA and MNBs treatment. Gene enrichment analysis revealed that the MA-MNBs method could compensate for the shortcomings of single MA treatment and enhance the expression of energy metabolism and salt stress-related genes attributed to MNBs treatment, thereby significantly improving the growth and development of plants. Consistently, 6115 kg/ha of rice was yielded in the field for the saline-alkali soils using this MA-MNBs method, with zero crops before remediation. This study provided a novel, efficient, and green strategy for the remediation of saline-alkali soil without adding any chemicals.}, } @article {pmid38042080, year = {2024}, author = {Xiao, L and Leng, M and Greenwood, P and Zhao, R and Xie, Z and You, Z and Liu, J}, title = {Temporal and vertical dynamics of carbon accumulation potential under grazing-excluded grasslands in China: The role of soil bulk density.}, journal = {Journal of environmental management}, volume = {351}, number = {}, pages = {119696}, doi = {10.1016/j.jenvman.2023.119696}, pmid = {38042080}, issn = {1095-8630}, mesh = {*Soil ; *Carbon/analysis ; Grassland ; Biomass ; China ; Carbon Sequestration ; }, abstract = {Despite the progress made in understanding relevant carbon dynamics under grazing exclusion, previous studies have underestimated the role of soil bulk density (BD), and its implications for potential accumulation of soil organic carbon (SOC), especially at regional scale over long term. In this study, we first constructed a database covering a vast majority of the grasslands in northwestern China based on 131 published literatures. A synthesis was then conducted by analyzing the experimental data to comprehensively investigate the mechanisms of vegetation recovery, carbon-nitrogen coupling, and the importance of changed soil BD in evaluating SOC sequestration potential. The results showed that although the recovery of vegetation height and cover were both critical for improving vegetation biomass, vegetation height required a longer recovery period. While the SOC accumulation was found to be greater in surface layers than deeper ones, it exhibited a reduced capacity for carbon sequestration and an increased risk of SOC loss. Grazing exclusion significantly reduced soil BD across different soil profiles, with the rate of change influenced by soil depth, time, geographical and climatic conditions. The potential for SOC accumulation in the top 30 cm of soil based on data of 2003-2022 was 0.78 Mg ha[-1] yr[-1] without considering BD effects, which was significantly underestimated compared to that of 1.16 Mg ha[-1] yr[-1] when BD changes were considered properly. This suggests that the efficiency of grazing exclusion in carbon sequestration and climate mitigation may have been previously underreported. Furthermore, mean annual precipitation represented the most relevant environmental factor that positively correlated to SOC accumulation, and a wetter climate may offer greater potential for carbon accumulation. Overall, this study implies grazing exclusion may play an even more critical role in carbon sequestration and climate change mitigation over long-term than previously recognized, which provides essential scientific evidence for implementing stepwise ecological restoration in grasslands.}, } @article {pmid38042076, year = {2024}, author = {Parent, JR and Gold, AJ and Vogler, E and Lowder, KA}, title = {Guiding decisions on the future of dams: A GIS database characterizing ecological and social considerations of Dam decisions.}, journal = {Journal of environmental management}, volume = {351}, number = {}, pages = {119683}, doi = {10.1016/j.jenvman.2023.119683}, pmid = {38042076}, issn = {1095-8630}, mesh = {Animals ; *Conservation of Natural Resources ; *Geographic Information Systems ; New England ; Rivers ; Fishes ; Ecosystem ; }, abstract = {In the United States and elsewhere, there are a growing number of dams which have exceeded their design life and will need to be repaired or removed in the coming decades. Most of these dams no longer serve their original purpose and removal can provide ecological benefits and eliminate future maintenance costs and hazards. However, many decision-makers have been ill-prepared by community resistance to proposals to remove dams. Given the number of dam removal initiatives that have failed or been delayed due to community resistance, both ecological and social attributes of dams need to be better mapped and conveyed in understandable ways. The goal of this study was to support future decisions regarding dams by 1) developing a set of metrics to assess the social and ecological dimensions of dams, and 2) using these metrics to develop a GIS database, for the 1000+ dams in the Narragansett Bay/Rhode Island area of southern New England. The database characterizes the ecological benefits of dam removal or modification, in terms of fish passage, and the social dimensions that may need to be considered when engaging a community in discussions about the future of a dam. Our emphasis was on small-head dams (i.e. <5 m tall) which comprise most dams in the study area. We created social value metrics that used GIS data to assess dams and their impoundments for potential benefits to waterfront properties, history, sense-of-place, and recreation. We modeled our ecological metrics and ranking system after the Nature Conservancy's Northeast Aquatic Connectivity study which considered factors relating to river connectivity and watershed quality. We evaluated our social and ecological metrics using case studies of dams in the study area that had been previously removed or modified. We assumed that both sets of dams were ecologically important, but the modified dams had higher social value that prohibited their removal. Dams that had been removed or modified were both ranked as high priority in terms of value for fish passage, particularly for diadromous fish. Dams that were modified to include fish passage had substantially larger impoundments, more waterfront properties, and more features associated with recreational or cultural value (e.g. boating opportunity, visibility, etc.). Our social metrics were consistent with expectations based on the limited case studies (7 removals, 19 modifications) available in the study area. We made the dam assessment metrics readily accessible to stakeholders through an interactive ArcGIS Online web map.}, } @article {pmid38037645, year = {2022}, author = {Lees, D and Boyes, D and , and , and , and , and , and , and , }, title = {The genome sequence of the early grey, Xylocampa areola (Esper, 1789).}, journal = {Wellcome open research}, volume = {7}, number = {}, pages = {312}, pmid = {38037645}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual Xylocampa areola (the early grey; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 565 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the assembled Z sex chromosome. The mitochondrial genome has also been assembled and is 15.5 kilobases in length. Gene annotation of this assembly on Ensembl identified 18,869 protein coding genes.}, } @article {pmid38037560, year = {2023}, author = {Boyes, D and , and , and , and , and Hammond, J and , }, title = {The genome sequence of the Gold Triangle, Hypsopygia costalis (Fabricius, 1775).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {15}, pmid = {38037560}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual male Hypsopygia costalis (the Gold Triangle; Arthropoda; Insecta; Lepidoptera; Pyralidae). The genome sequence is 818 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules with the Z sex chromosome assembled. The mitochondrial genome has also been assembled and is 15.3 kilobases in length. Gene annotation of this assembly on Ensembl identified 19,248 protein coding genes.}, } @article {pmid38037477, year = {2023}, author = {Turk, F and Sweetman, J and Allsopp, G and Crooks, M and Cuthbertson, DJ and Gabbay, M and Hishmeh, L and Lip, GYH and Strain, WD and Williams, N and Wootton, D and Banerjee, A and van der Feltz-Cornelis, C and , }, title = {Pathways to care for Long COVID and for long-term conditions from patients' and clinicians' perspective.}, journal = {Journal of evidence-based medicine}, volume = {16}, number = {4}, pages = {435-437}, doi = {10.1111/jebm.12563}, pmid = {38037477}, issn = {1756-5391}, support = {COV-LT2-0043//National Institute for Health and Care Research/ ; }, mesh = {Humans ; *Post-Acute COVID-19 Syndrome ; *COVID-19 ; Attitude of Health Personnel ; }, } @article {pmid38036774, year = {2023}, author = {Belho, K and Rawat, MS and Rawat, PK}, title = {GIS modeling to investigate environmental change and degradation in Kohima district, North East Hill (NEH) region of India.}, journal = {Environmental monitoring and assessment}, volume = {195}, number = {12}, pages = {1553}, pmid = {38036774}, issn = {1573-2959}, support = {202021-NFST-NAG-00170//Ministry of Tribal Affairs/ ; }, mesh = {*Geographic Information Systems ; *Environmental Monitoring/methods ; Forests ; India ; Water ; }, abstract = {As a part of the Himalayan mountains, the North East Hill (NEH) region of India is geophysically dynamic and seismotectonically active since its formation about 55 million years ago with a head-on collision of the Indian plate and the Eurasian plate. The region still has been underthrusting at a rate of 4.5-5 cm/year causing the reshaping and changing of its geophysical characteristics (geology, geomorphology, relief, slope gradient, drainage system, etc.), whereas anthropogenic activities, particularly shifting cultivation and technological intervention, have caused changes or degradation of the ecological environment (air, land, water, vegetation, crop pattern, climate, wildlife, etc.). Addressing this burning geoecological problem, a geospatial technology-based case study from the Kohima district of Nagaland in the North East Hill region of India is presented here. Through the development and integration of multiple GIS modules, this reconnaissance study suggests that continuous seismic activities (about 27 seismic events/year) along tectonic faults, thrusts, and lithological shear zones have been reshaping and changing the geophysical environment, whereas the ecological environment has been changing or degrading due to decreasing natural landscape and habitats (forest area, water bodies, and shrubs) at an annual rate of 5.91 km[2] (0.60%), increasing built-up area, agricultural land, and wasteland at an annual rate of 2.73 km[2] (0.28%), 2.69 km[2] (0.27%), and 0.49 km[2] (0.05%) respectively. Results also suggest that environmental degradation results in accelerated trends of climate change (rising temperature at the rate of 0.13 °C/year, decreasing annual rainy days at the rate of 2 days/year, decreasing annual rainfall at the rate of 9.55 cm/year, mounting climatic zones at the rate of 175 m/year) and its adverse impacts (increasing extreme rainfall events at the rate of 3 events/year and causing cloud burst, erosion, landslides, and floods) in the region.}, } @article {pmid38031900, year = {2024}, author = {Mori, Y and Okawara, M and Shibao, K and Kohi, S and Tamura, T and Sato, N and Fujino, Y and Fushimi, K and Matsuda, S and Hirata, K}, title = {Short-term outcomes of pancreatoduodenectomy in older individuals over a 9-year period using real-world data: A multilevel analysis based on a nationwide administrative database in Japan.}, journal = {Journal of hepato-biliary-pancreatic sciences}, volume = {31}, number = {4}, pages = {262-272}, doi = {10.1002/jhbp.1396}, pmid = {38031900}, issn = {1868-6982}, support = {20AA2005//Ministry of Health, Labour and Welfare/ ; }, mesh = {Humans ; *Pancreaticoduodenectomy/mortality ; Japan/epidemiology ; Aged ; Male ; Female ; Aged, 80 and over ; *Hospital Mortality ; *Databases, Factual ; *Length of Stay/statistics & numerical data ; Postoperative Complications/epidemiology ; Age Factors ; Multilevel Analysis ; Middle Aged ; Retrospective Studies ; Treatment Outcome ; }, abstract = {BACKGROUND: We aimed to evaluate the short-term outcomes of pancreatoduodenectomy (PD) in older individuals.

METHODS: Data from the Japanese Diagnosis Procedure Combination database on 62 275 patients who underwent PD from 1 April 2012 to 31 March 2020 were analyzed. Patients were divided into five age groups: <70, 70-74, 75-79, 80-84, and ≥85 years. The associations between postoperative outcomes and age were investigated using multilevel analysis. The mean differences in length of hospital stay and cost were also compared.

RESULTS: The rate of PD in older individuals increased annually. Compared with the youngest age group (< 70 years), the incidence rate ratios for in-hospital mortality were 1.52 (95% confidence interval [CI]: 1.30-1.76), 2.07 (1.82-2.37), 2.29 (1.94-2.71), and 2.92 (2.20-3.87) in the 70-74, 75-79, 80-84, and ≥ 85-year-old age groups, respectively (all p < .001). Postoperative complications, length of postoperative hospital stay, and cost increased significantly with increasing age.

CONCLUSIONS: These real-world data emphasize the higher levels of morbidity, mortality, and cost in older patients. Careful attention should be paid when considering the indication for PD in older individuals.}, } @article {pmid38029580, year = {2024}, author = {Díaz Alarcón, JA and Fonseca Alfonso, PM and Vergara Gómez, I and Díaz Lagos, M and Videira-Quintela, D and Montalvo, G}, title = {Assessment of potentially hazardous elements in soils of the Boyacá industrial corridor (Colombia) using GIS, multivariate statistical analysis, and geochemical indexes.}, journal = {Ecotoxicology and environmental safety}, volume = {269}, number = {}, pages = {115725}, doi = {10.1016/j.ecoenv.2023.115725}, pmid = {38029580}, issn = {1090-2414}, mesh = {Soil ; *Metals, Heavy/analysis ; Geographic Information Systems ; Colombia ; Cadmium/analysis ; Lead/analysis ; *Soil Pollutants/analysis ; Environmental Monitoring/methods ; *Mercury/analysis ; Risk Assessment ; China ; }, abstract = {In the industrial corridor of Boyacá, Colombia, population growth is accompanied by anthropogenic activities such as industrial operations, vehicle exhaust fumes, mining, smelting, atmospheric deposition, and excessive use of chemical products to promote crop growth. These activities are known to have a significant impact on urban and rural soils, contributing significantly to elevated concentrations of potentially hazardous elements in the environment. This industrial corridor is an area of economic and social development that needs to provide reference information that will allow us to know the state of soil quality to preserve and manage the public and geoenvironmental health of this region. Anthropogenic activities have contributed to the accumulation of potentially hazardous elements in the environment, affecting various levels of life and creating risks with economic and social implications. However, igneous activity or detrital deposition also enriches soils and creates geochemical anomalies in specific locations. In these cases, the identification of potentially hazardous elements involves the determination of likely sources of contamination and their relationship to the geological setting. In this study, the concentrations of As, Cd, Pb, Mn, Fe, Zn, Hg, Cu and Ni were determined in eighty-one soil samples from the Boyacá industrial corridor (Colombia). The sequential trend of the concentrations of potentially hazardous elements was as follows: Fe > Mn > Zn > Ni > Cu> Pb > As > Cd > Hg. Furthermore, the application of spatial analysis criteria in GIS software with multivariate statistical tools and geochemical indices allowed the identification of anthropogenic and geogenic sources. Most of the potentially hazardous elements were found in soils exposed to industrial and agricultural activities, except for iron. This element showed low variability in all samples, regardless of the geological formations. Due to the lack of reference values for potentially hazardous elements in Colombia, the concentrations were compared with the environmental standards of the Environmental Protection Agency (EPA) and the Ecuadorian Ministry of Environment, Water and Ecological Transition (MAE). The results demonstrate the complexity of the soil and represent the first exploratory study of potentially hazardous elements in this industrial corridor. These results are the starting point for the establishment of geochemical background lines in Colombia and for inspection policies for areas where productive activities converge.}, } @article {pmid38023870, year = {2023}, author = {Engloner, AI and Németh, K and Kós, PB and Meglécz, E and Bereczki, J}, title = {Genetic diversity of the submerged macrophyte Ceratophyllum demersum depends on habitat hydrology and habitat fragmentation.}, journal = {Frontiers in plant science}, volume = {14}, number = {}, pages = {1277916}, pmid = {38023870}, issn = {1664-462X}, abstract = {The adaptability of plant populations to a changing environment depends on their genetic diversity, which in turn is influenced by the degree of sexual reproduction and gene flow from distant areas. Aquatic macrophytes can reproduce both sexually and asexually, and their reproductive fragments are spread in various ways (e.g. by water). Although these plants are obviously exposed to hydrological changes, the degree of vulnerability may depend on the types of their reproduction and distribution, as well as the hydrological differences of habitats. The aim of this study was to investigate the genetic diversity of the cosmopolitan macrophyte Ceratophyllum demersum in hydrologically different aquatic habitats, i.e. rivers and backwaters separated from the main river bed to a different extent. For this purpose, the first microsatellite primer set was developed for this species. Using 10 developed primer pairs, a high level of genetic variation was explored in C. demersum populations. Overall, more than 80% of the loci were found to be polymorphic, a total of 46 different multilocus genotypes and 18 private alleles were detected in the 63 individuals examined. The results demonstrated that microsatellite polymorphism in this species depends on habitat hydrology. The greatest genetic variability was revealed in populations of rivers, where flowing water provides constant longitudinal connections with distant habitats. The populations of the hydrologically isolated backwaters showed the lowest microsatellite polymorphism, while plants from an oxbow occasionally flooded by the main river had medium genetic diversity. The results highlight that in contrast to species that spread independently of water flow or among hydrologically isolated water bodies, macrophytes with exclusive or dominant hydrochory may be most severely affected by habitat fragmentation, for example due to climate change.}, } @article {pmid38020677, year = {2023}, author = {Horvatić, S and Parmentier, E and Malavasi, S and Amorim, MPC and Fonseca, PJ and Zanella, D}, title = {Endemic fish calling: Acoustics and reproductive behaviour of the Neretva dwarf goby Orsinigobius croaticus.}, journal = {Ecology and evolution}, volume = {13}, number = {11}, pages = {e10673}, pmid = {38020677}, issn = {2045-7758}, abstract = {The Neretva dwarf goby Orsinigobius croaticus (Gobiiformes, Gobionellidae) is an endemic fish native to the freshwaters of the Adriatic Basin in Croatia and Bosnia and Herzegovina, a Mediterranean Biodiversity Hotspot. Due to its limited distribution range, specific karst habitat and endangered status, laboratory studies on reproductive biology are scarce but crucial. Herein, we investigated the sound production and acoustic behaviour of the endangered O. croaticus during reproductive intersexual laboratory encounters, utilising an interdisciplinary approach. We also performed dissections and micro-computed tomography (μCT) scanning of the pectoral girdle to explore its potential involvement in sound production. Finally, comparative acoustic analysis was conducted on sounds produced by previously recorded soniferous sand gobies to investigate whether acoustic features are species-specific. The endemic O. croaticus is a soniferous species. Males of this species emit pulsatile sounds composed of a variable number of short (~15 ms) consecutive pulses when interacting with females, usually during the pre-spawning phase in the nest, but also during courtship outside the nest. Pulsatile sounds were low-frequency and short pulse trains (~140 Hz, <1000 ms). Male visual behaviour rate was higher when co-occurring with sounds and females entered the male's nest significantly more frequently when sounds were present. Characteristic body movements accompanied male sound production, such as head thrust and fin spreading. Furthermore, μCT scans and dissections suggest that O. croaticus shares certain anatomical similarities of the pectoral girdle (i.e. osseous elements and arrangement of levator pectoralis muscles) to previously studied sand gobies that could be involved in sound production. Multivariate comparisons, using sounds produced by eight soniferous European sand gobies, effectively distinguished soniferous (and sympatric) species based on their acoustic properties. However, the discrimination success decreased when temperature-dependent features (sound duration and pulse repetition rate) were excluded from the analysis. Therefore, we suggest both spectral and temporal features are important for the acoustic differentiation of sand gobies.}, } @article {pmid38019786, year = {2023}, author = {Lu, Z and Zhong, H and Tang, L and Luo, J and Zhou, W and Liu, L}, title = {Predicting lncRNA-disease associations based on heterogeneous graph convolutional generative adversarial network.}, journal = {PLoS computational biology}, volume = {19}, number = {11}, pages = {e1011634}, pmid = {38019786}, issn = {1553-7358}, mesh = {Humans ; *RNA, Long Noncoding/genetics ; Computational Biology/methods ; *Neoplasms/genetics ; *MicroRNAs ; Neural Networks, Computer ; Algorithms ; }, abstract = {There is a growing body of evidence indicating the crucial roles that long non-coding RNAs (lncRNAs) play in the development and progression of various diseases, including cancers, cardiovascular diseases, and neurological disorders. However, accurately predicting potential lncRNA-disease associations remains a challenge, as existing methods have limitations in extracting heterogeneous association information and handling sparse and unbalanced data. To address these issues, we propose a novel computational method, called HGC-GAN, which combines heterogeneous graph convolutional neural networks (GCN) and generative adversarial networks (GAN) to predict potential lncRNA-disease associations. Specifically, we construct a lncRNA-miRNA-disease heterogeneous network by integrating multiple association data and sequence information. The GCN-based generator is then employed to aggregate neighbor information of nodes and obtain node embeddings, which are used to predict lncRNA-disease associations. Meanwhile, the GAN-based discriminator is trained to distinguish between real and fake lncRNA-disease associations generated by the generator, enabling the generator to improve its ability to generate accurate lncRNA-disease associations gradually. Our experimental results demonstrate that HGC-GAN performs better in predicting potential lncRNA-disease associations, with AUC and AUPR values of 0.9591 and 0.9606, respectively, under 10-fold cross-validation. Moreover, our case study further confirms the effectiveness of HGC-GAN in predicting potential lncRNA-disease associations, even for novel lncRNAs without any known lncRNA-disease associations. Overall, our proposed method HGC-GAN provides a promising approach to predict potential lncRNA-disease associations and may have important implications for disease diagnosis, treatment, and drug development.}, } @article {pmid38018647, year = {2023}, author = {Gouvêa, ECDP and Ribeiro, AM and Aquino, EC and Stopa, SR}, title = {Mortality trend due to chronic kidney disease in Brazil: an ecological study.}, journal = {Epidemiologia e servicos de saude : revista do Sistema Unico de Saude do Brasil}, volume = {32}, number = {3}, pages = {e2023313}, pmid = {38018647}, issn = {2237-9622}, mesh = {Female ; Humans ; Male ; Brazil/epidemiology ; Information Systems ; *Renal Insufficiency, Chronic/mortality ; *Mortality/trends ; }, abstract = {OBJECTIVE: To analyze chronic kidney disease mortality in Brazil according to sex, age group and region of residence, from 2009 to 2020.

METHODS: This was a time series study having deaths as its unit of analysis, based on Mortality Information System data. The mortality rate was standardized using the direct method and the temporal trend was analyzed using the Prais-Winsten method.

RESULTS: There was a rising trend in chronic kidney disease mortality, ranging from 2.82, in 2009, to 3.24 in 2020 (average annual increase 1.29%; 95%CI 0.73;1.85), with a greater increase in males (1.14% per year; 95%CI 0.52;1.76), those aged 75 years and over (2.23% per year; 95%CI 1.87; 2.60) and in the Northern Region (3.86% per year; 95%CI 1.86;5.90) and Northeast Region (3.36% per year; 95%CI 2.24;4.50).

CONCLUSION: Chronic kidney disease mortality showed a rising trend in the period, with sociodemographic disparities.

MAIN RESULTS: A rising mortality trend was found for both sexes, with a greater increase in males, those aged over 75 years and in the North and Northeast regions of Brazil; mortality was highest in the Midwest region throughout the entire period.

IMPLICATIONS FOR SERVICES: The results point to the need to implement public policies with guidelines for addressing chronic kidney disease, focused on strengthening Primary Health Care (PHC).

PERSPECTIVES: Expanding access to health services, health education and integration between PHC, health surveillance and specialized care are strategies that would possibly prove to be efficient in managing this chronic health condition.}, } @article {pmid38017684, year = {2023}, author = {Yin, FF and Shi, X and Guo, HF and Shen, YR}, title = {Performance evaluation of rural water environment governance based on AHP: a case study of the Beitang River Basin.}, journal = {Water science and technology : a journal of the International Association on Water Pollution Research}, volume = {88}, number = {10}, pages = {2661-2676}, doi = {10.2166/wst.2023.354}, pmid = {38017684}, issn = {0273-1223}, mesh = {*Rivers ; *Analytic Hierarchy Process ; Water Quality ; Conservation of Natural Resources ; China ; }, abstract = {Rural water environment governance in China still lacks a systematic and comprehensive assessment protocol to help analyze and improve such governance performance. The Analytic Hierarchy Process (AHP) method was employed in this study to build a governance assessment system that integrates ecological conditions, water pollution control, and public satisfaction. To cover these topics, the assessment system is composed of an indicator layer that is customized to rural water environment governance in China. The Beitang River, located in the rural region of Hangzhou, Zhejiang, China, was presented as a case study. Field investigation provided raw data for this assessment. A questionnaire survey was conducted to interview local residents on the governance performance. An additional survey with executives who played major roles in the governance was performed to reconstruct a water environment assessment on the Beitang River prior to the governance, in order to highlight the effects of the governance through contrast. The results showed consistency in the questionnaire survey and the assessment system. The AHP assessment system was able to reflect the improvement in the water quality, river ecology, and residential welfare after the governance, and suggested limits and future directions in the following upgrade programs for the river basin.}, } @article {pmid38017319, year = {2023}, author = {Lawler, T and Warren Andersen, S and Trentham-Dietz, A and Sethi, AK and Tevaarwerk, AJ and Malecki, KMC and Litzelman, K and Pophali, PA and Gangnon, RE and Hampton, JM and Kwekkeboom, K and LoConte, NK}, title = {Change in alcohol consumption during the Covid-19 pandemic and associations with mental health and financial hardship: results from a survey of Wisconsin patients with cancer.}, journal = {Journal of cancer survivorship : research and practice}, volume = {}, number = {}, pages = {}, pmid = {38017319}, issn = {1932-2267}, support = {P30 CA014520/CA/NCI NIH HHS/United States ; UL1 TR002373/TR/NCATS NIH HHS/United States ; P30CA014520/CA/NCI NIH HHS/United States ; UL1TR002373/NH/NIH HHS/United States ; }, abstract = {PURPOSE: Alcohol consumption increases health risks for patients with cancer. The Covid-19 pandemic may have affected drinking habits for these individuals. We surveyed patients with cancer to examine whether changes in drinking habits were related to mental health or financial effects of the pandemic.

METHODS: From October 2020 to April 2021, adult patients (age 18-80 years at diagnosis) treated for cancer in southcentral Wisconsin were invited to complete a survey. Age-adjusted percentages for history of anxiety or depression, emotional distress, and financial impacts of Covid-19 overall and by change in alcohol consumption (non-drinker, stable, decreased, or increased) were obtained via logistic regression.

RESULTS: In total, 1,875 patients were included in the analysis (median age 64, range 19-87 years), including 9% who increased and 23% who decreased drinking. Compared to stable drinkers (32% of sample), a higher proportion of participants who increased drinking alcohol also reported anxiety or depression (45% vs. 26%), moderate to severe emotional distress (61% vs. 37%) and viewing Covid-19 as a threat to their community (67% vs. 55%). Decreased (vs. stable) drinking was associated with higher prevalence of depression or anxiety diagnosis, emotional distress, and negative financial impacts of the pandemic. Compared to non-drinkers (36% of sample), participants who increased drinking were more likely to report emotional distress (61% vs. 48%).

CONCLUSIONS: Patients with cancer from Wisconsin who changed their alcohol consumption during the Covid-19 pandemic were more likely to report poor mental health including anxiety, depression, and emotional distress than persons whose alcohol consumption was stable.

Clinicians working with cancer survivors should be aware of the link between poor mental health and increased alcohol consumption and be prepared to offer guidance or referrals to counseling, as needed.}, } @article {pmid38017016, year = {2023}, author = {Adhurya, S and Lee, DY and Lee, DS and Park, YS}, title = {Functional trait dataset of benthic macroinvertebrates in South Korean streams.}, journal = {Scientific data}, volume = {10}, number = {1}, pages = {838}, pmid = {38017016}, issn = {2052-4463}, support = {NRF-2019R1A2C1087099//National Research Foundation of Korea (NRF)/ ; 2020003050003//MOE | Korea Environmental Industry and Technology Institute (KEITI)/ ; }, mesh = {Animals ; Biodiversity ; *Ecosystem ; Environmental Monitoring ; *Invertebrates ; Rivers ; Republic of Korea ; }, abstract = {Functional traits are the result of evolution and adaptation, providing important ecological insights into how organisms interact with their environment. Benthic macroinvertebrates, in particular, have garnered attention as biomonitoring indicators for freshwater ecosystems. This study presents a functional trait dataset for benthic macroinvertebrates, comprising 447 taxa (393 at genus level, 53 at family level and one at class level) from five phyla (Annelida, Arthropoda, Mollusca, Nematomorpha, and Platyhelmenthes), categorized into nine traits related to life history, morphology, and habit. To account for variation in available trait information, we assigned confidence levels to each taxon and functional trait based on the level of evidence using fuzzy coding. Our dataset provides an important resource for understanding the ecology of benthic macroinvertebrates in South Korea, serving as a valuable baseline dataset for studying their biodiversity, conservation, and biomonitoring in freshwater ecosystems.}, } @article {pmid38014157, year = {2023}, author = {Warren, WC and Rice, ES and Maggs, X and Roback, E and Keene, A and Martin, F and Ogeh, D and Haggerty, L and Carroll, RA and McGaugh, S and Rohner, N}, title = {Astyanax mexicanus surface and cavefish chromosome-scale assemblies for trait variation discovery.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {38014157}, issn = {2692-8205}, support = {/WT_/Wellcome Trust/United Kingdom ; R01 GM127872/GM/NIGMS NIH HHS/United States ; R24 OD011198/OD/NIH HHS/United States ; }, abstract = {The ability of organisms to adapt to sudden extreme environmental changes produces some of the most drastic examples of rapid phenotypic evolution. The Mexican Tetra, Astyanax mexicanus, is abundant in the surface waters of northeastern Mexico, but repeated colonizations of cave environments have resulted in the independent evolution of troglomorphic phenotypes in several populations. Here, we present three chromosome-scale assemblies of this species, for one surface and two cave populations, enabling the first whole-genome comparisons between independently evolved cave populations to evaluate the genetic basis for the evolution of adaptation to the cave environment. Our assemblies represent the highest quality of sequence completeness with predicted protein-coding and non-coding gene metrics far surpassing prior resources and, to our knowledge, all long-read assembled teleost genomes, including zebrafish. Whole genome synteny alignments show highly conserved gene order among cave forms in contrast to a higher number of chromosomal rearrangements when compared to other phylogenetically close or distant teleost species. By phylogenetically assessing gene orthology across distant branches of amniotes, we discover gene orthogroups unique to A. mexicanus. When compared to a representative surface fish genome, we find a rich amount of structural sequence diversity, defined here as the number and size of insertions and deletions as well as expanding and contracting repeats across cave forms. These new more complete genomic resources ensure higher trait resolution for comparative, functional, developmental, and genetic studies of drastic trait differences within a species.}, } @article {pmid38013951, year = {2022}, author = {Wang, Z and Yang, W and Ryan, K and Garai, S and Auerbach, BM and Shen, L}, title = {Using Optimal Transport to Improve Spherical Harmonic Quantification of Complex Biological Shapes.}, journal = {Proceedings. IEEE International Conference on Bioinformatics and Biomedicine}, volume = {2022}, number = {}, pages = {1255-1261}, pmid = {38013951}, issn = {2156-1125}, support = {RF1 AG068191/AG/NIA NIH HHS/United States ; U01 AG068057/AG/NIA NIH HHS/United States ; }, abstract = {The knowledge of the anatomical shape of both gross and microscopic structures is the key to understanding the effects of disease processes on cellular structure. Geometric morphometric methods, such as Procrustes superimposition, and Spherical Harmonics (SPHARM), have been used to capture the biological shape variation and group differences in morphology. Previous SPHARM-MAT techniques use the CALD algorithm to parameterize the mesh surface. It starts from initial mapping and performs local and global smoothing methods alternately to control the area and length distortions simultaneously. However, this parameterization may not be sufficient in complex morphological cases. To bridge this gap, we propose SPHARM-OT, an enhanced SPHARM surface modeling method using optimal transport (OT) for spherical parameterization. First, the genus 0 3D objects are conformally mapped onto a sphere. Then the optimal transport theory via spherical power diagram is introduced to minimize the area distortion. This new algorithm can effectively reduce the area distortion and lead to a better reconstruction result. We demonstrate the effectiveness of the method by applying it to the human sphenoidal paranasal sinuses.}, } @article {pmid38011826, year = {2024}, author = {Wilson, J and Sokhansanj, BA and Chong, WC and Chandraghatgi, R and Rosen, GL and Ji, HF}, title = {Fragment databases from screened ligands for drug discovery (FDSL-DD).}, journal = {Journal of molecular graphics & modelling}, volume = {127}, number = {}, pages = {108669}, doi = {10.1016/j.jmgm.2023.108669}, pmid = {38011826}, issn = {1873-4243}, mesh = {Ligands ; *Drug Discovery/methods ; *Drug Design ; High-Throughput Screening Assays ; Databases, Factual ; }, abstract = {Fragment-based drug design (FBDD) is one major drug discovery method employed in computer-aided drug discovery. Due to its inherent limitations, this process experiences long processing times and limited success rates. Here we present a new Fragment Databases from Screened Ligands Drug Design method (FDSL-DD) that intelligently incorporates information about fragment characteristics into a fragment-based design approach to the drug development process. The initial step of the FDSL-DD is the creation of a fragment database from a library of docked, drug-like ligands for a specific target, which deviates from the traditional in silico FBDD strategy, incorporating structure-based design screening techniques to combine the advantages of both approaches. Three different protein targets have been tested in this study to demonstrate the potential of the created fragment library and FDSL-DD. Utilizing the FDSL-DD led to an increase in binding affinity for each protein target. The most substantial increase was exhibited by the ligand designed for TIPE2, with a 3.6 kcalmol[-1] difference between the top ligand from the FDSL-DD and top ligand from the high throughput virtual screening (HTVS). Using drug-like ligands in the initial HTVS allows for a greater search of chemical space, with higher efficiency in fragments selection, less grid boxes, and potentially identifying more interactions.}, } @article {pmid38010780, year = {2024}, author = {Jovanović, V and Rudnev, M and Abdelrahman, M and Abdul Kadir, NB and Adebayo, DF and Akaliyski, P and Alaseel, R and Alkamali, YA and Alonso Palacio, LM and Amin, A and Andres, A and Ansari-Moghaddam, A and Aruta, JJB and Avanesyan, HM and Ayub, N and Bacikova-Sleskova, M and Baikanova, R and Bakkar, B and Bartoluci, S and Benitez, D and Bodnar, I and Bolatov, A and Borchet, J and Bosnar, K and Broche-Pérez, Y and Buzea, C and Cassibba, R and Del Pilar Grazioso, M and Dhakal, S and Dimitrova, R and Dominguez, A and Duong, CD and Dutra Thome, L and Estavela, AJ and Fayankinnu, EA and Ferenczi, N and Fernández-Morales, R and Friehs, MT and Gaete, J and Gharz Edine, W and Gindi, S and Giordani, RCF and Gjoneska, B and Godoy, JC and Hancheva, CD and Hapunda, G and Hihara, S and Islam, MS and Janovská, A and Javakhishvili, N and Kabir, RS and Kabunga, A and Karakulak, A and Karl, JA and Katović, D and Kauyzbay, Z and Kaźmierczak, M and Khanna, R and Khosla, M and Kisaakye, P and Klicperova-Baker, M and Kokera, R and Kozina, A and Krauss, SE and Landabur, R and Lefringhausen, K and Lewandowska-Walter, A and Liang, YH and Lizarzaburu-Aguinaga, D and López Steinmetz, LC and Makashvili, A and Malik, S and Manrique-Millones, D and Martín-Carbonell, M and Mattar Yunes, MA and McGrath, B and Mechili, EA and Mejía Alvarez, M and Mhizha, S and Michałek-Kwiecień, J and Mishra, SK and Mohammadi, M and Mohsen, F and Moreta-Herrera, R and Muradyan, MD and Musso, P and Naterer, A and Nemat, A and Neto, F and Neto, J and Okati-Aliabad, H and Orellana, CI and Orellana, L and Park, J and Pavlova, I and Peralta, EA and Petrytsa, P and Pilkauskaite Valickiene, R and Et Al, }, title = {The Coronavirus Anxiety Scale: Cross-national measurement invariance and convergent validity evidence.}, journal = {Psychological assessment}, volume = {36}, number = {1}, pages = {14-29}, doi = {10.1037/pas0001270}, pmid = {38010780}, issn = {1939-134X}, support = {//Cooperative University of Colombia/ ; //Agencia Nacional de Investigación y Desarrollo; Millennium Science Initiative Program/ ; //GESIS-Leibniz Institute for the Social Sciences/ ; //Ministry of Education, Youth, and Sports; European Union-Next Generation European Union/ ; //RA Science Committee/ ; //American Psychological Association; Division 48/ ; //Foundation for Polish Science/ ; //Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; }, mesh = {Humans ; Reproducibility of Results ; Psychometrics/methods ; *Anxiety/diagnosis ; *COVID-19/diagnosis ; Fear ; }, abstract = {Coronavirus Anxiety Scale (CAS) is a widely used measure that captures somatic symptoms of coronavirus-related anxiety. In a large-scale collaboration spanning 60 countries (Ntotal = 21,513), we examined the CAS's measurement invariance and assessed the convergent validity of CAS scores in relation to the fear of COVID-19 (FCV-19S) and the satisfaction with life (SWLS-3) scales. We utilized both conventional exact invariance tests and alignment procedures, with results revealing that the single-factor model fit the data well in almost all countries. Partial scalar invariance was supported in a subset of 56 countries. To ensure the robustness of results, given the unbalanced samples, we employed resampling techniques both with and without replacement and found the results were more stable in larger samples. The alignment procedure demonstrated a high degree of measurement invariance with 9% of the parameters exhibiting noninvariance. We also conducted simulations of alignment using the parameters estimated in the current model. Findings demonstrated reliability of the means but indicated challenges in estimating the latent variances. Strong positive correlations between CAS and FCV-19S estimated with all three different approaches were found in most countries. Correlations of CAS and SWLS-3 were weak and negative but significantly differed from zero in several countries. Overall, the study provided support for the measurement invariance of the CAS and offered evidence of its convergent validity while also highlighting issues with variance estimation. (PsycInfo Database Record (c) 2024 APA, all rights reserved).}, } @article {pmid38007505, year = {2023}, author = {Wang, Z and Jia, Y and Li, P and Tang, Z and Guo, Y and Wen, L and Yu, H and Cui, F and Hu, F}, title = {Study on environmental factors affecting the quality of codonopsis radix based on MaxEnt model and all-in-one functional factor.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {20726}, pmid = {38007505}, issn = {2045-2322}, support = {81972018//National Natural Science Foundation of China/ ; 21ZD4FA013//Major science and technology project of Gansu Province/ ; 20CX4FK014//People's Livelihood Special Project from Technical Innovation Guide Plan of Gansu Province/ ; [2022] Gan-71//Key Talent Project of Organization Department of Gansu Provincial Party Committee/ ; 22ZY1QA012//Central Government Guiding Local Science and Technology Development Fund Project/ ; 22CX8GA009//Special Project of Science and Technology Commissioner of Gansu Province/ ; 2017-RC-115, 2020-RC-41//Talent Innovation and Entrepreneurship Project of Lanzhou/ ; }, mesh = {*Codonopsis/chemistry ; Geographic Information Systems ; Plant Roots/chemistry ; Altitude ; }, abstract = {Owing to the increasing market demand of Codonopsis Radix, the cropper blindly cultivates to expand planting area for economic benefits, which seriously affects the quality of Codonopsis Radix. Therefore, this study synthesized 207 batches of Codonopsis Radix and 115 ecological factors, and analyzed the suitable planting areas of Codonopsis pilosula under current and future climate change based on Geographic Information System (GIS) and MaxEnt model. Secondly, we evaluated the quality of Codonopsis Radix based on the all-in-one functional factor including chromatographic fingerprint, the index components, the effective compounds groups, the nutritional components, and the nutritional elements, and the quality regionalization of Codonopsis Radix was analyzed. Finally, the ecological factors affecting the accumulation of effective components of Codonopsis Radix were analyzed. This study found for the first time that the highly suitable area of Codonopsis pilosula was mainly distributed in the Weihe River system and the Bailongjiang River system in Gansu Province. There were differences in the quality of Codonopsis Radix from different ecologically suitable areas based on the all-in-one functional factors, and the comprehensive high-quality area of Codonopsis Radix was mainly distributed in Longnan and Longxi district of Gansu Province. The precipitation, temperature and altitude play a key role in the accumulation of chemical components in the 10 ecological factors affecting the distribution of Codonopsis pilosula. Under future climatic conditions, the highly suitable area of Codonopsis pilosula is decreased.}, } @article {pmid38005973, year = {2023}, author = {Klee, B and Diexer, S and Sarajan, MH and Glaser, N and Binder, M and Frese, T and Girndt, M and Sedding, D and Hoell, JI and Moor, I and Gekle, M and Mikolajczyk, R and Gottschick, C}, title = {Regional Differences in Uptake of Vaccination against COVID-19 and Influenza in Germany: Results from the DigiHero Cohort.}, journal = {Vaccines}, volume = {11}, number = {11}, pages = {}, pmid = {38005973}, issn = {2076-393X}, abstract = {During the COVID-19 pandemic in Germany, vaccination uptake exhibited considerable regional disparities. To assess the factors contributing to this variation, we examined the association of sociodemographic variables with COVID-19, COVID-19 booster, and influenza vaccination status within a cohort of 37,078 participants from 13 German federal states in the digital health cohort study commonly known as DigiHero. Our findings revealed variations in vaccination rates based on sociodemographic factors. However, these factors had limited explanatory power regarding regional differences in vaccine uptake. In contrast, we found substantial correlations between regional support of specific parties during the last local elections and the vaccination uptake at the level of each administrative district. In conclusion, sociodemographic factors alone did not suffice to explain the regional disparities in vaccine uptake. Political stances can play a major role, although the current investigation did not assess individual political orientations but rather used only an ecological approach.}, } @article {pmid38005880, year = {2023}, author = {Barnes, M and Price, DC}, title = {Endogenous Viral Elements in Ixodid Tick Genomes.}, journal = {Viruses}, volume = {15}, number = {11}, pages = {}, pmid = {38005880}, issn = {1999-4915}, support = {Capacity Project NE1943: "Biology, Ecology & Management of Emerging Disease Vectors"//United States Department of Agriculture/ ; }, mesh = {Animals ; Humans ; *Ixodidae/genetics ; *Arthropods ; *Ixodes ; *RNA Viruses ; *Viruses ; }, abstract = {The documentation of endogenous viral elements (EVEs; virus-derived genetic material integrated into the genome of a nonviral host) has offered insights into how arthropods respond to viral infection via RNA interference pathways. Small non-coding RNAs derived from EVE loci serve to direct RNAi pathways in limiting replication and infection from cognate viruses, thus benefiting the host's fitness and, potentially, vectorial capacity. Here we use informatic approaches to analyze nine available genome sequences of hard ticks (Acari: Ixodidae; Rhipicephalus sanguineus, R. microplus, R. annulatus, Ixodes ricinus, I. persulcatus, I. scapularis, Hyalomma asiaticum, Haemaphysalis longicornis, and Dermacentor silvarum) to identify endogenous viral elements and to illustrate the shared ancestry of all elements identified. Our results highlight a broad diversity of viral taxa as having given rise to 1234 identified EVEs in ticks, with Mononegavirales (specifically Rhabdoviridae) well-represented in this subset of hard ticks. Further investigation revealed extensive adintovirus integrations in several Ixodes species, the prevalence of Bunyavirales EVEs (notably not observed in mosquitoes), and the presence of several elements similar to known emerging human and veterinary pathogens. These results will inform subsequent work on current and past associations with tick species with regard to the viruses from which their "viral fossils" are derived and may serve as a reference for quality control of various tick-omics data that may suffer from misidentification of EVEs as viral genetic material.}, } @article {pmid38004638, year = {2023}, author = {Zhu, Q and Ruan, M and Hu, Z and Miao, K and Ye, C}, title = {The Relationship between Acid Production and the Microbial Community of Newly Produced Coal Gangue in the Early Oxidation Stage.}, journal = {Microorganisms}, volume = {11}, number = {11}, pages = {}, pmid = {38004638}, issn = {2076-2607}, support = {grant number 2019YFC1805003//National Key Research and Development Program/ ; }, abstract = {Coal gangue is a solid waste formed during coal production, and the acid mine drainage it generates during open-pit storage severely pollutes the ecological environment of mining areas. Microorganisms play a crucial catalytic role in acidification, and their species and gene functions change during the oxidation process of coal gangue. In this study, the changes in microbial community structure were investigated during the initial acidification process for newly produced gangue exposed to moisture by monitoring the changes in pH, EC, sulfate ion concentration, and the iron oxidation rate of gangue leaching solutions. Moreover, the composition and functional abundance of microbial communities on the surface of the gangue were analyzed with rainfall simulation experiments and 16S rRNA sequencing. The study yielded the following findings: (1) The critical period for newly produced gangue oxidation spanned from 0~15 d after its exposure to water; the pH of leaching solutions decreased from 4.65 to 4.09 during this time, and the concentration and oxidation rate of iron in the leaching solutions remained at low levels, indicating that iron oxidation was not the main driver for acidification during this stage. (2) When the gangue was kept dry, Burkholderia spp. dominated the gangue microbial community. When the gangue was exposed to moisture, the rate of acidification accelerated, and Pseudomonas replaced Burkholderia as the dominant genus in the community. (3) In terms of gene function, the microbial community of the acidified gangue had stronger nitrogen cycling functions, and an increase in the abundance of microorganisms related to the sulfur cycle occurred after day 15 of the experiment. The microbial community in the acidified gangue had more stress resistance than the community of the newly formed gangue, but its potential to decompose environmental pollutants decreased.}, } @article {pmid38001289, year = {2023}, author = {Zhou, L and Wang, Y and Li, D and Zhang, J and Zhu, X}, title = {Efficient degradation of phenanthrene by biochar-supported nano zero-valent iron activated persulfate: performance evaluation and mechanism insights.}, journal = {Environmental science and pollution research international}, volume = {30}, number = {60}, pages = {125731-125740}, pmid = {38001289}, issn = {1614-7499}, mesh = {Iron/chemistry ; *Water Pollutants, Chemical/analysis ; Charcoal/chemistry ; *Phenanthrenes ; }, abstract = {Biochar-supported nano zero-valent iron (BC@nZVI) is a novel and efficient non-homogeneous activator for persulfate (PS). This study aimed to identify the primary pathways, the degradation mechanism and the performance of phenanthrene (PHE) with PS activated by BC@nZVI (BC@nZVI/PS). BC@nZVI as an activator for PS was prepared by liquid phase reduction method. BC@nZVI was characterized using scanning electron microscopy, transmission electron microscopy, X-ray diffractometer and Fourier transform infrared spectroscopy. The effects of the iron-carbon mass ratio and BC@nZVI dosage were investigated, and a pseudo-first-order kinetic model was used to evaluate the PHE degradation. The results showed that BC supported nZVI and inhibited the agglomeration of nZVI, improving PS's activation efficiency. The optimal iron-carbon mass ratio was determined to be 1:4, accompanied by a dosage of 0.6 g/L of BC@nZVI. During PS activation, nZVI was transformed to Fe[2+] and Fe[3+], with the majority being Fe[3+]. The reducibility of nZVI in BC@nZVI enabled the reduction of Fe[3+] to Fe[2+] to activate PS. Radical quenching and electron paramagnetic resonance (EPR) revealed that the oxidative radicals in the BC@nZVI/PS system were mainly SO4[-]· and ·OH, where SO4[-]· was the primary free radical under acidic and neutral conditions and ·OH in alkaline conditions. Additionally, BC@nZVI adsorption had a limited role in PHE removal. This study can provide mechanism insights of PHE degradation in water with BC@nZVI activation of the Na2S2O8 system.}, } @article {pmid37999540, year = {2023}, author = {Tan, M and Dong, J and Qu, J and Hao, M}, title = {The Patterns of Migration of Potentially Toxic Elements from Coal Mining Subsidence Areas and Associated Soils to Waterlogged Areas.}, journal = {Toxics}, volume = {11}, number = {11}, pages = {}, pmid = {37999540}, issn = {2305-6304}, support = {52204190//National Natural Science Foundation of China/ ; 42271368//National Natural Science Foundation of China/ ; 2021YCPY0113//Fundamental Research Funds for the Central Universities/ ; 2019ZD03//Xuzhou Ecological Civilization Construction research project/ ; }, abstract = {It is crucial for effectively controlling potentially toxic element (PTE) pollution to understand the pollution situation, ecological risks, health risks, and migration patterns of PTEs. However, currently, no research has been conducted on the migration patterns of soil PTEs from coal mining subsidence areas to waterlogged areas under different restoration modes. In this study, a total of 15 sediment samples and 60 soil samples were collected from landscaped wetlands, aquaculture wetland, fish-photovoltaic complementary wetland, photovoltaic wetland, and waterlogged areas with untreated coal mining subsidence. The PTE pollution status, ecological risks, health risks, migration patterns, and the important factors influencing the migration were analyzed. The results indicated that the comprehensive pollution level of PTEs in waterlogged areas with coal mining subsidence can be reduced by developing them into landscaped wetlands, aquaculture wetlands, fish-photovoltaic complementary wetlands, and photovoltaic wetlands. Additionally, the closer to the waterlogged area, the higher the Cu content in the subsidence area soil is, reaching its peak in the waterlogged area. The Cd was influenced positively by SOC and pH. The research results were of great significance for formulating reclamation plans for waterlogged areas and controlling PTE pollution.}, } @article {pmid37996937, year = {2023}, author = {Dougan, KE and Deng, ZL and Wöhlbrand, L and Reuse, C and Bunk, B and Chen, Y and Hartlich, J and Hiller, K and John, U and Kalvelage, J and Mansky, J and Neumann-Schaal, M and Overmann, J and Petersen, J and Sanchez-Garcia, S and Schmidt-Hohagen, K and Shah, S and Spröer, C and Sztajer, H and Wang, H and Bhattacharya, D and Rabus, R and Jahn, D and Chan, CX and Wagner-Döbler, I}, title = {Multi-omics analysis reveals the molecular response to heat stress in a "red tide" dinoflagellate.}, journal = {Genome biology}, volume = {24}, number = {1}, pages = {265}, pmid = {37996937}, issn = {1474-760X}, support = {Transregio SFB TRR-52 Roseobacter//Deutsche Forschungsgemeinschaft/ ; Transregio SFB TRR-52 Roseobacter//Deutsche Forschungsgemeinschaft/ ; Transregio SFB TRR-52 Roseobacter//Deutsche Forschungsgemeinschaft/ ; Transregio SFB TRR-52 Roseobacter//Deutsche Forschungsgemeinschaft/ ; Transregio SFB TRR-52 Roseobacter//Deutsche Forschungsgemeinschaft/ ; DP190102474//Australian Research Council/ ; DP190102474//Australian Research Council/ ; Thomas Davies Research Grant for Marine//Australian Academy of Science/ ; Soil//Australian Academy of Science/ ; Plant Biology//Australian Academy of Science/ ; }, mesh = {Humans ; *Harmful Algal Bloom ; *Dinoflagellida/genetics ; Multiomics ; Genomics ; Heat-Shock Response ; }, abstract = {BACKGROUND: "Red tides" are harmful algal blooms caused by dinoflagellate microalgae that accumulate toxins lethal to other organisms, including humans via consumption of contaminated seafood. These algal blooms are driven by a combination of environmental factors including nutrient enrichment, particularly in warm waters, and are increasingly frequent. The molecular, regulatory, and evolutionary mechanisms that underlie the heat stress response in these harmful bloom-forming algal species remain little understood, due in part to the limited genomic resources from dinoflagellates, complicated by the large sizes of genomes, exhibiting features atypical of eukaryotes.

RESULTS: We present the de novo assembled genome (~ 4.75 Gbp with 85,849 protein-coding genes), transcriptome, proteome, and metabolome from Prorocentrum cordatum, a globally abundant, bloom-forming dinoflagellate. Using axenic algal cultures, we study the molecular mechanisms that underpin the algal response to heat stress, which is relevant to current ocean warming trends. We present the first evidence of a complementary interplay between RNA editing and exon usage that regulates the expression and functional diversity of biomolecules, reflected by reduction in photosynthesis, central metabolism, and protein synthesis. These results reveal genomic signatures and post-transcriptional regulation for the first time in a pelagic dinoflagellate.

CONCLUSIONS: Our multi-omics analyses uncover the molecular response to heat stress in an important bloom-forming algal species, which is driven by complex gene structures in a large, high-G+C genome, combined with multi-level transcriptional regulation. The dynamics and interplay of molecular regulatory mechanisms may explain in part how dinoflagellates diversified to become some of the most ecologically successful organisms on Earth.}, } @article {pmid37994954, year = {2023}, author = {Aksoy, H}, title = {Determination of landslide susceptibility with Analytic Hierarchy Process (AHP) and the role of forest ecosystem services on landslide susceptibility.}, journal = {Environmental monitoring and assessment}, volume = {195}, number = {12}, pages = {1525}, pmid = {37994954}, issn = {1573-2959}, mesh = {*Ecosystem ; *Landslides ; Analytic Hierarchy Process ; Environmental Monitoring/methods ; Geographic Information Systems ; Forests ; }, abstract = {The analysis of landslide susceptibility is a crucial tool in the mitigation and management of ecological and economic hazards. The number of studies examining how the form and durability of forest areas affect landslide susceptibility is very limited. This study was conducted in the Marmara region of northwestern Türkiye, where forested areas and industrial zones are intertwined and dense. The landslide susceptibility map was produced by Analytic Hierarchy Process (AHP) method. In the context of AHP, a total of 12 different variables were employed, namely lithology, slope, curvatures, precipitations, aspect, distance to fault lines, distance to streams, distance to roads, land use, soil, elevation, and Normalized Difference Vegetation Index (NDVI). The performance analysis of the landslide susceptibility map was conducted using the Receiver Operating Characteristics (ROC) curve method. The AUC value was computed (0.809) for the landslide susceptibility map generated by using the AHP technique. Forest type maps were used to analyze the impact of forests on landslide susceptibility. In terms of forest structure, 4 main criteria were determined: stand structure, development stage, crown closure, and stand age. Each criterion was analyzed with Geographic Information Systems (GIS) by overlaying it with the landslide susceptibility map of the study area. The results showed that the risk of landslides was lowest in forests with more than one tree species, mature, development stage and of (e) > 52 cm, and crown closure of 41%-70% (2).}, } @article {pmid37994909, year = {2023}, author = {Jiahui, G and Feilong, M and Nastase, SA and Haxby, JV and Gobbini, MI}, title = {Cross-movie prediction of individualized functional topography.}, journal = {eLife}, volume = {12}, number = {}, pages = {}, pmid = {37994909}, issn = {2050-084X}, support = {R01 MH127199/MH/NIMH NIH HHS/United States ; MH127199/MH/NIMH NIH HHS/United States ; }, mesh = {Humans ; *Motion Pictures ; *Academies and Institutes ; Brain ; Cognition ; Databases, Factual ; }, abstract = {Participant-specific, functionally defined brain areas are usually mapped with functional localizers and estimated by making contrasts between responses to single categories of input. Naturalistic stimuli engage multiple brain systems in parallel, provide more ecologically plausible estimates of real-world statistics, and are friendly to special populations. The current study shows that cortical functional topographies in individual participants can be estimated with high fidelity from naturalistic stimuli. Importantly, we demonstrate that robust, individualized estimates can be obtained even when participants watched different movies, were scanned with different parameters/scanners, and were sampled from different institutes across the world. Our results create a foundation for future studies that allow researchers to estimate a broad range of functional topographies based on naturalistic movies and a normative database, making it possible to integrate high-level cognitive functions across datasets from laboratories worldwide.}, } @article {pmid37994038, year = {2024}, author = {Nahas, C and Gandit, M and Quillion-Dupré, L and Monfort, E}, title = {How to engage patients in computerized cognitive training: a cognitive rehabilitation expert's perspective.}, journal = {Disability and rehabilitation. Assistive technology}, volume = {19}, number = {6}, pages = {2306-2318}, doi = {10.1080/17483107.2023.2284879}, pmid = {37994038}, issn = {1748-3115}, mesh = {Adult ; Female ; Humans ; Male ; Middle Aged ; *Cognitive Training/methods ; Interviews as Topic ; Patient Participation ; Qualitative Research ; *Software ; Therapy, Computer-Assisted ; }, abstract = {PURPOSE: The relationship between a patient and their therapist plays a crucial role in patient engagement. While Computerized Cognitive Training (CCT) may assist in preserving cognitive skills in cases of aging, dementia or acquired brain injuries, its effectiveness has not been definitively proven. Improving user engagement, acceptance, and software usability could aid in addressing this issue. The present study aims to identify potential obstacles and facilitators by examining the perspectives of rehabilitation professionals on the current usage of CCT software.

METHODS: Semi-structured interviews were conducted with 16 rehabilitation professionals, familiar with a CCT software. The data were transcribed and followed by an independent iterative thematic analysis.

RESULTS: Two major themes were identified: (1) facilitating factors and (2) difficulties related to use. The main obstacles were difficulties related to the computerized nature of the exercises, technology use, understanding the software and general learning difficulties. The main facilitators were the ecological and novel nature of the exercises, and the adaptability of the difficulty levels.

CONCLUSION: The complexity of the CCT presents challenges for its usage by rehabilitation professionals, which in turn can impede patient utilization as well. To address this issue and promote sustainable use of the software, providing instruction delivery to facilitate learning and understanding of the CCT is essential. Additionally, creating a standardized foundation that therapists can refer to for guidance may also aid in optimizing the software's usage. It is recommended to utilize a model for CCT acceptability and acceptance in developing these solutions to enhance patient engagement.}, } @article {pmid37985899, year = {2023}, author = {Gonzalez, A and Vihervaara, P and Balvanera, P and Bates, AE and Bayraktarov, E and Bellingham, PJ and Bruder, A and Campbell, J and Catchen, MD and Cavender-Bares, J and Chase, J and Coops, N and Costello, MJ and Czúcz, B and Delavaud, A and Dornelas, M and Dubois, G and Duffy, EJ and Eggermont, H and Fernandez, M and Fernandez, N and Ferrier, S and Geller, GN and Gill, M and Gravel, D and Guerra, CA and Guralnick, R and Harfoot, M and Hirsch, T and Hoban, S and Hughes, AC and Hugo, W and Hunter, ME and Isbell, F and Jetz, W and Juergens, N and Kissling, WD and Krug, CB and Kullberg, P and Le Bras, Y and Leung, B and Londoño-Murcia, MC and Lord, JM and Loreau, M and Luers, A and Ma, K and MacDonald, AJ and Maes, J and McGeoch, M and Mihoub, JB and Millette, KL and Molnar, Z and Montes, E and Mori, AS and Muller-Karger, FE and Muraoka, H and Nakaoka, M and Navarro, L and Newbold, T and Niamir, A and Obura, D and O'Connor, M and Paganini, M and Pelletier, D and Pereira, H and Poisot, T and Pollock, LJ and Purvis, A and Radulovici, A and Rocchini, D and Roeoesli, C and Schaepman, M and Schaepman-Strub, G and Schmeller, DS and Schmiedel, U and Schneider, FD and Shakya, MM and Skidmore, A and Skowno, AL and Takeuchi, Y and Tuanmu, MN and Turak, E and Turner, W and Urban, MC and Urbina-Cardona, N and Valbuena, R and Van de Putte, A and van Havre, B and Wingate, VR and Wright, E and Torrelio, CZ}, title = {Author Correction: A global biodiversity observing system to unite monitoring and guide action.}, journal = {Nature ecology & evolution}, volume = {7}, number = {12}, pages = {2173}, doi = {10.1038/s41559-023-02263-x}, pmid = {37985899}, issn = {2397-334X}, } @article {pmid37985664, year = {2023}, author = {Howerton, E and Contamin, L and Mullany, LC and Qin, M and Reich, NG and Bents, S and Borchering, RK and Jung, SM and Loo, SL and Smith, CP and Levander, J and Kerr, J and Espino, J and van Panhuis, WG and Hochheiser, H and Galanti, M and Yamana, T and Pei, S and Shaman, J and Rainwater-Lovett, K and Kinsey, M and Tallaksen, K and Wilson, S and Shin, L and Lemaitre, JC and Kaminsky, J and Hulse, JD and Lee, EC and McKee, CD and Hill, A and Karlen, D and Chinazzi, M and Davis, JT and Mu, K and Xiong, X and Pastore Y Piontti, A and Vespignani, A and Rosenstrom, ET and Ivy, JS and Mayorga, ME and Swann, JL and España, G and Cavany, S and Moore, S and Perkins, A and Hladish, T and Pillai, A and Ben Toh, K and Longini, I and Chen, S and Paul, R and Janies, D and Thill, JC and Bouchnita, A and Bi, K and Lachmann, M and Fox, SJ and Meyers, LA and Srivastava, A and Porebski, P and Venkatramanan, S and Adiga, A and Lewis, B and Klahn, B and Outten, J and Hurt, B and Chen, J and Mortveit, H and Wilson, A and Marathe, M and Hoops, S and Bhattacharya, P and Machi, D and Cadwell, BL and Healy, JM and Slayton, RB and Johansson, MA and Biggerstaff, M and Truelove, S and Runge, MC and Shea, K and Viboud, C and Lessler, J}, title = {Evaluation of the US COVID-19 Scenario Modeling Hub for informing pandemic response under uncertainty.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {7260}, pmid = {37985664}, issn = {2041-1723}, support = {U01IP001137/ACL/ACL HHS/United States ; R01 GM140564/GM/NIGMS NIH HHS/United States ; UL1 TR002489/TR/NCATS NIH HHS/United States ; U01 IP001137/IP/NCIRD CDC HHS/United States ; NU38OT000297/CC/CDC HHS/United States ; U01IP001136/ACL/ACL HHS/United States ; R01 AI151176/AI/NIAID NIH HHS/United States ; UM1 TR004406/TR/NCATS NIH HHS/United States ; U24 GM132013/GM/NIGMS NIH HHS/United States ; R35 GM119582/GM/NIGMS NIH HHS/United States ; R01 GM109718/GM/NIGMS NIH HHS/United States ; U01 IP001136/IP/NCIRD CDC HHS/United States ; R21 AI164391/AI/NIAID NIH HHS/United States ; U01 IP001122/IP/NCIRD CDC HHS/United States ; R01 AI102939/AI/NIAID NIH HHS/United States ; }, mesh = {Humans ; *COVID-19/epidemiology ; Pandemics/prevention & control ; SARS-CoV-2 ; Uncertainty ; }, abstract = {Our ability to forecast epidemics far into the future is constrained by the many complexities of disease systems. Realistic longer-term projections may, however, be possible under well-defined scenarios that specify the future state of critical epidemic drivers. Since December 2020, the U.S. COVID-19 Scenario Modeling Hub (SMH) has convened multiple modeling teams to make months ahead projections of SARS-CoV-2 burden, totaling nearly 1.8 million national and state-level projections. Here, we find SMH performance varied widely as a function of both scenario validity and model calibration. We show scenarios remained close to reality for 22 weeks on average before the arrival of unanticipated SARS-CoV-2 variants invalidated key assumptions. An ensemble of participating models that preserved variation between models (using the linear opinion pool method) was consistently more reliable than any single model in periods of valid scenario assumptions, while projection interval coverage was near target levels. SMH projections were used to guide pandemic response, illustrating the value of collaborative hubs for longer-term scenario projections.}, } @article {pmid37981161, year = {2024}, author = {Sajjad, W and Ilahi, N and Kang, S and Bahadur, A and Banerjee, A and Zada, S and Ali, B and Rafiq, M and Zheng, G}, title = {Microbial diversity and community structure dynamics in acid mine drainage: Acidic fire with dissolved heavy metals.}, journal = {The Science of the total environment}, volume = {909}, number = {}, pages = {168635}, doi = {10.1016/j.scitotenv.2023.168635}, pmid = {37981161}, issn = {1879-1026}, mesh = {*Ecosystem ; Phylogeny ; *Metals, Heavy/analysis ; Environmental Pollution ; Archaea ; }, abstract = {Acid mine drainage (AMD) is one of the leading causes of environmental pollution and is linked to public health and ecological consequences. Microbes-mineral interaction generates AMD, but microorganisms can also remedy AMD pollution. Exploring the microbial response to AMD effluents may reveal survival strategies in extreme ecosystems. Three distinct sites across a mine (inside the mine, the entrance of the mine, and outside) were selected to study their heavy metal concentrations due to significant variations in pH and physicochemical characteristics, and high-throughput sequencing was carried out to investigate the microbial diversity. The metal and ion concentrations followed the order SO4[2-], Fe, Cu, Zn, Mg, Pb, Co, Cr, and Ni from highest to lowest, respectively. Maximum sequences were allocated to Proteobacteria and Firmicutes. Among archaea, the abundance of Thaumarchaeota and Euryarchaeota was higher outside of mine. Most of the genera (23.12 %) were unclassified and unknown. The average OTUs (operational taxonomic units) were significantly higher outside the mine; however, diversity indices were not significantly different across the mine sites. Hierarchical clustering of selective genera and nMDS ordination of OTUs displayed greater segregation resolution inside and outside of mine, whereas the entrance samples clustered with greater similarity. Heterogeneous selection might be the main driver of community composition outside the mine, whereas stochastic processes became prominent inside the mine. However, the ANOSIM test shows a relatively even distribution of community composition within and between the groups. Microbial phyla showed both positive and negative correlations with physicochemical factors. A greater number of biomarkers were reported outside of the mine. Predictive functional investigation revealed the existence of putative degradative, metabolic, and biosynthetic pathways. This study presents a rare dataset in our understanding of microbial diversity and distribution as shaped by the ecological gradient and potential novelty in phylogenetic/taxonomic diversity in AMD, with potential biotechnological applications.}, } @article {pmid37980986, year = {2024}, author = {Iqbal, A and Maqsood Ur Rehman, M and Sajjad, W and Degen, AA and Rafiq, M and Jiahuan, N and Khan, S and Shang, Z}, title = {Patterns of bacterial communities in the rhizosphere and rhizoplane of alpine wet meadows.}, journal = {Environmental research}, volume = {241}, number = {}, pages = {117672}, doi = {10.1016/j.envres.2023.117672}, pmid = {37980986}, issn = {1096-0953}, mesh = {Humans ; *Rhizosphere ; *Ecosystem ; Carbon ; Grassland ; Soil/chemistry ; Soil Microbiology ; Bacteria/genetics ; Plants ; Nitrogen ; }, abstract = {Wet meadows, a type of wetland, are vulnerable to climate change and human activity, impacting soil properties and microorganisms that are crucial to the ecosystem processes of wet meadows. To decipher the ecological mechanisms and processes involved in wet meadows, it is necessary to examine the bacterial communities associated with plant roots. To gain valuable insight into the microbial dynamics of alpine wet meadows, we used Illumina MiSeq sequencing to investigate how environmental factors shape the bacterial communities thriving in the rhizosphere and rhizoplane of three plant species: Cremanthodium ellisii, Caltha scaposa, and Cremanthodium lineare. The most abundant bacterial phyla in rhizosphere and rhizoplane were Proteobacteria > Firmicutes > Actinobacteria, while Macrococcus, Lactococcus, and Exiguobacterium were the most abundant bacterial genera between rhizosphere and rhizoplane. The mantel test, network, and structure equation models revealed that bacterial communities of rhizosphere were shaped by total nitrogen (TN), soil water content (SWC), soil organic carbon (SOC), microbial biomass carbon (MBC), microbial biomass nitrogen (MBN), pH, however, rhizoplane bacterial communities exhibited varying results. The bacterial communities exhibited significant heterogeneity, with stochastic process predominating in both the rhizosphere and rhizoplane. PICRUSt2 and FAPROTAX analysis revealed substantial differences in key biogeochemical cycles and metabolic functional predictions. It was concluded that root compartments significantly influenced the bacterial communities, although plant species and elevation asserted varying effects. This study portrays how physicochemical properties, plant species, and elevations can shift the overall structure and functional repertoire of bacterial communities in alpine wet meadows.}, } @article {pmid37979845, year = {2024}, author = {Henke, AN and Chilukuri, S and Langan, LM and Brooks, BW}, title = {Reporting and reproducibility: Proteomics of fish models in environmental toxicology and ecotoxicology.}, journal = {The Science of the total environment}, volume = {912}, number = {}, pages = {168455}, doi = {10.1016/j.scitotenv.2023.168455}, pmid = {37979845}, issn = {1879-1026}, mesh = {Animals ; *Ecotoxicology/methods ; *Proteomics/methods ; Reproducibility of Results ; Fishes ; Computational Biology ; }, abstract = {Environmental toxicology and ecotoxicology research efforts are employing proteomics with fish models as New Approach Methodologies, along with in silico, in vitro and other omics techniques to elucidate hazards of toxicants and toxins. We performed a critical review of toxicology studies with fish models using proteomics and reported fundamental parameters across experimental design, sample preparation, mass spectrometry, and bioinformatics of fish, which represent alternative vertebrate models in environmental toxicology, and routinely studied animals in ecotoxicology. We observed inconsistencies in reporting and methodologies among experimental designs, sample preparations, data acquisitions and bioinformatics, which can affect reproducibility of experimental results. We identified a distinct need to develop reporting guidelines for proteomics use in environmental toxicology and ecotoxicology, increased QA/QC throughout studies, and method optimization with an emphasis on reducing inconsistencies among studies. Several recommendations are offered as logical steps to advance development and application of this emerging research area to understand chemical hazards to public health and the environment.}, } @article {pmid37978186, year = {2023}, author = {Clark, MS and Hoffman, JI and Peck, LS and Bargelloni, L and Gande, D and Havermans, C and Meyer, B and Patarnello, T and Phillips, T and Stoof-Leichsenring, KR and Vendrami, DLJ and Beck, A and Collins, G and Friedrich, MW and Halanych, KM and Masello, JF and Nagel, R and Norén, K and Printzen, C and Ruiz, MB and Wohlrab, S and Becker, B and Dumack, K and Ghaderiardakani, F and Glaser, K and Heesch, S and Held, C and John, U and Karsten, U and Kempf, S and Lucassen, M and Paijmans, A and Schimani, K and Wallberg, A and Wunder, LC and Mock, T}, title = {Multi-omics for studying and understanding polar life.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {7451}, pmid = {37978186}, issn = {2041-1723}, mesh = {*Ecosystem ; *Multiomics ; Biodiversity ; Forecasting ; }, abstract = {Polar ecosystems are experiencing amongst the most rapid rates of regional warming on Earth. Here, we discuss 'omics' approaches to investigate polar biodiversity, including the current state of the art, future perspectives and recommendations. We propose a community road map to generate and more fully exploit multi-omics data from polar organisms. These data are needed for the comprehensive evaluation of polar biodiversity and to reveal how life evolved and adapted to permanently cold environments with extreme seasonality. We argue that concerted action is required to mitigate the impact of warming on polar ecosystems via conservation efforts, to sustainably manage these unique habitats and their ecosystem services, and for the sustainable bioprospecting of novel genes and compounds for societal gain.}, } @article {pmid37977539, year = {2024}, author = {Chen, F and Mao, P and Wang, M and Li, Y and Li, Y and Xia, K and Chen, J and Mo, H and Wang, F and Li, Z and Zhuang, P}, title = {Benefit evaluation of in-situ Cd immobilization with naturally occurring minerals using an analytical hierarchy process.}, journal = {Chemosphere}, volume = {347}, number = {}, pages = {140720}, doi = {10.1016/j.chemosphere.2023.140720}, pmid = {37977539}, issn = {1879-1298}, mesh = {Cadmium/analysis ; Analytic Hierarchy Process ; Calcium Carbonate ; *Metals, Heavy/analysis ; Soil ; *Oryza ; *Soil Pollutants/analysis ; }, abstract = {Immobilization has a wide range of applications in heavy metal-contaminated soil remediation, and immobilization agents serve as the key to the successful application of this technology. In this study, we designed a comprehensive and efficient scoring system based on an analytic hierarchy process (AHP) to evaluate the feasibility and effectiveness of three immobilization agents (wollastonite, dolomite, and calcite) in remediating Cd-polluted soil. The scoring system comprised four criteria and 11 indicators, and the results showed that all three immobilization agents significantly reduced the accumulation of Cd in rice. The Cd reduction rates of early rice with a single application of wollastonite, dolomite, and calcite were 67.6%, 46.9%, and 83.8%, respectively. Single or combined application of dolomite and calcite decreased the available Cd concentration in early rice soil, and the application of calcite resulted in an excellent rating of both early and late rice, demonstrating its highest immobilization and stability performance. Therefore, the immobilization efficiency of the three materials in descending order followed calcite > dolomite + thioglycols > wollastonite. In summary, this comprehensive evaluation system offers new insight into assessing the efficiency of soil remediation, serving as a valuable reference for selecting immobilization agents and making decisions regarding remediation plans for heavy metal-contaminated soil.}, } @article {pmid37976789, year = {2024}, author = {Karimian, H and Zou, W and Chen, Y and Xia, J and Wang, Z}, title = {Corrigendum to 'Landscape ecological risk assessment and driving factor analysis in Dongjiang river watershed' [Chemosphere 307 (2022)135835].}, journal = {Chemosphere}, volume = {346}, number = {}, pages = {140599}, doi = {10.1016/j.chemosphere.2023.140599}, pmid = {37976789}, issn = {1879-1298}, } @article {pmid37971111, year = {2023}, author = {Stahnke, DN and Nied, C and Oliveira, MLG and Costa, JSDD}, title = {Trends in hospital admissions and mortality from diabetes mellitus in Rio Grande do Sul: historical series 2000-2020.}, journal = {Revista gaucha de enfermagem}, volume = {44}, number = {}, pages = {e20230103}, doi = {10.1590/1983-1447.2023.20230103.en}, pmid = {37971111}, issn = {1983-1447}, mesh = {Humans ; Brazil/epidemiology ; *Information Systems ; Hospitalization ; *Diabetes Mellitus/epidemiology ; Hospitals ; }, abstract = {OBJECTIVE: To analyze the trends of hospital admissions and deaths from diabetes mellitus in the 18 host municipalities of the 19 regional health coordination offices and in Rio Grande do Sul, 2000-2020.

METHOD: Ecological study with secondary data collected in the Hospital Information System, the Mortality Information System, and the Brazilian Institute of Geography and Statistics, from 2000-2020. Coefficients were standardized using the direct method and Prais-Winsten regression analysis.

RESULTS: A downward trend wasfound in the coefficients of hospitalizations for diabetes mellitus in most cities and states. In 2020, for both areas, hospitalizations for diabetes mellitus were below the average of the period. The mortality trend remained stationary in almost all municipalities and in the state.

CONCLUSION: There was evidence of a decrease in hospitalizations and stationary mortality by DM in most municipalities analyzed, possibly due to the policies and actions implemented in the period, despite the aging of the population.}, } @article {pmid37968269, year = {2023}, author = {Swets, MC and Kerr, S and Scott-Brown, J and Brown, AB and Gupta, R and Millar, JE and Spata, E and McCurrach, F and Bretherick, AD and Docherty, A and Harrison, D and Rowan, K and Young, N and , and Groeneveld, GH and Dunning, J and Nguyen-Van-Tam, JS and Openshaw, P and Horby, PW and Harrison, E and Staplin, N and Semple, MG and Lone, N and Baillie, JK}, title = {Evaluation of pragmatic oxygenation measurement as a proxy for Covid-19 severity.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {7374}, pmid = {37968269}, issn = {2041-1723}, support = {/WT_/Wellcome Trust/United Kingdom ; MC_PC_19025/MRC_/Medical Research Council/United Kingdom ; MC_PC_20004/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Humans ; Reproducibility of Results ; *COVID-19/diagnosis ; Lung ; Sample Size ; }, abstract = {Choosing optimal outcome measures maximizes statistical power, accelerates discovery and improves reliability in early-phase trials. We devised and evaluated a modification to a pragmatic measure of oxygenation function, the [Formula: see text] ratio. Because of the ceiling effect in oxyhaemoglobin saturation, [Formula: see text] ratio ceases to reflect pulmonary oxygenation function at high [Formula: see text] values. We found that the correlation of [Formula: see text] with the reference standard ([Formula: see text]/[Formula: see text] ratio) improves substantially when excluding [Formula: see text] and refer to this measure as [Formula: see text]. Using observational data from 39,765 hospitalised COVID-19 patients, we demonstrate that [Formula: see text] is predictive of mortality, and compare the sample sizes required for trials using four different outcome measures. We show that a significant difference in outcome could be detected with the smallest sample size using [Formula: see text]. We demonstrate that [Formula: see text] is an effective intermediate outcome measure in COVID-19. It is a non-invasive measurement, representative of disease severity and provides greater statistical power.}, } @article {pmid37967264, year = {2023}, author = {Yuan, Y and Li, X and Li, L and Jiang, FJ and Tang, X and Zhang, F and Goncalves, J and Voss, HU and Ding, H and Kurths, J}, title = {Machine discovery of partial differential equations from spatiotemporal data: A sparse Bayesian learning framework.}, journal = {Chaos (Woodbury, N.Y.)}, volume = {33}, number = {11}, pages = {}, doi = {10.1063/5.0160900}, pmid = {37967264}, issn = {1089-7682}, abstract = {This study presents a general framework, namely, Sparse Spatiotemporal System Discovery (S3d), for discovering dynamical models given by Partial Differential Equations (PDEs) from spatiotemporal data. S3d is built on the recent development of sparse Bayesian learning, which enforces sparsity in the estimated PDEs. This approach enables a balance between model complexity and fitting error with theoretical guarantees. The proposed framework integrates Bayesian inference and a sparse priori distribution with the sparse regression method. It also introduces a principled iterative re-weighted algorithm to select dominant features in PDEs and solve for the sparse coefficients. We have demonstrated the discovery of the complex Ginzburg-Landau equation from a traveling-wave convection experiment, as well as several other PDEs, including the important cases of Navier-Stokes and sine-Gordon equations, from simulated data.}, } @article {pmid37967119, year = {2023}, author = {Xue, J and Zhu, J and Hu, L and Yang, J and Lv, Y and Zhao, F and Liu, Y and Zhang, T and Cai, Y and Fang, M}, title = {EISA-EXPOSOME: One Highly Sensitive and Autonomous Exposomic Platform with Enhanced in-Source Fragmentation/Annotation.}, journal = {Analytical chemistry}, volume = {95}, number = {47}, pages = {17228-17237}, doi = {10.1021/acs.analchem.3c02697}, pmid = {37967119}, issn = {1520-6882}, mesh = {Tandem Mass Spectrometry/methods ; *Exposome ; *Pesticides/analysis ; Metabolomics/methods ; Ions ; Dust ; }, abstract = {Lacking a highly sensitive exposome screening technique is one of the biggest challenges in moving exposomic research forward. Enhanced in-source fragmentation/annotation (EISA) has been developed to facilitate molecular identification in untargeted metabolomics and proteomics. In this work, with a mixture of 50 pesticides at three concentration levels (20, 4, and 0.8 ppb), we investigated the analytical performance of the EISA technique over the well-accepted targeted MS/MS mode (TMM) in the detection and identification of chemicals at low levels using a quadrupole time-of-flight (qTOF) instrument. Compared with the TMM method, the EISA technique can recognize additional 1, 20, and 23 chemicals, respectively, at the three concentration levels (20, 4, and 0.8 ppb, respectively) investigated. At the 0.8 ppb level, intensities of precursor ions and fragments observed using the EISA technique are 30-1,154 and 3-80 times higher, respectively, than those observed at the TMM mode. A higher matched fragment ratio (MFR) between the EISA technique and the TMM method was recognized for most chemicals. We further developed a chemical annotation informatics algorithm, EISA-EXPOSOME, which can automatically search each precursor ion (m/z) in the MS/MS library against the EISA MS1 spectra. This algorithm then calculated a weighted score to rank the candidate features by comparing the experimental fragment spectra to those in the library. The peak intensity, zigzag index, and retention time prediction model as well as the peak correlation coefficient were further adopted in the algorithm to filter false positives. The performance of EISA-EXPOSOME was demonstrated using a pooled dust extract with a pesticide mixture (n = 200) spiked at 5 ppb. One urine sample spiked with a contaminant mixture (n = 50) at the 5 ppb level was also used for the validation of the pipeline. Proof-of-principal application of EISA-EXPOSOME in the real sample was further evaluated on the pooled dust sample with a modified T3DB database (n = 1650). Our results show that the EISA-EXPOSOME algorithm can remarkably improve the detection and annotation coverage at trace levels beyond the traditional approach as well as facilitate the high throughput screening of suspected chemicals.}, } @article {pmid37967108, year = {2023}, author = {Zhao, H and Zheng, J and Ma, S and Zhao, L and Xu, P and Li, J}, title = {Spatial distribution and influencing factors analysis of national key rural tourism villages in the Yangtze River Delta region based on geographically weighted regression.}, journal = {PloS one}, volume = {18}, number = {11}, pages = {e0291614}, pmid = {37967108}, issn = {1932-6203}, mesh = {Humans ; China ; *Spatial Regression ; *Tourism ; Spatial Analysis ; Cities ; }, abstract = {National key rural tourism villages (NKRTVs) can lead to the high-quality development of rural tourism, and their spatial distribution is influenced by a variety of factors. However, existing studies have neglected the fact that influencing factors can have different directions and effects in different geographic spaces. This study investigates 156 NKRTVs in the Yangtze River Delta region of China as the research object and employs ArcGIS spatial analysis technology to examine their spatial distribution characteristics. Additionally, two new indicators of land and culture are introduced to enhance the index system of influencing factors. A geographically weighted regression model is utilized to identify the spatial heterogeneity of various factors that affect the spatial distribution of NKRTVs. The results of this study indicate the following: (1) The spatial distribution of NKRTVs in the Yangtze River Delta region is characterized by "small clustering and large dispersion." The spatial distribution exhibits strong spatial correlation, with Shanghai serving as the primary spatial clustering core and Huangshan city forming a secondary spatial clustering subcore. The distribution of NKRTVs is relatively scattered in other areas, with obvious differences in the spatial distribution of cold and hot spots. (2) The results of the geographically weighted regression model show that with the change in spatial location, the influence effect of each influencing factor on the spatial distribution of NKRTVs has obvious spatial differences. Based on the spatial heterogeneity of the influencing factors, this study proposes targeted suggestions for the development of rural tourism in different regions.}, } @article {pmid37967091, year = {2023}, author = {Radovic, I and Krdzic, I and Jovanovic, A and Vukasinovic, D and Soldatovic, I and Petrovic, M and Tomic, A and Jesic-Petrovic, T and Matejic, A and Salovic, B and Jelena, IZ}, title = {Transcultural adaptation and validation of the Serbian version of Functional Assessment of Chronic Illness Therapy-Treatment Satisfaction-Patient Satisfaction (FACIT-TS-PS) questionnaire.}, journal = {PloS one}, volume = {18}, number = {11}, pages = {e0294339}, pmid = {37967091}, issn = {1932-6203}, mesh = {Humans ; *Patient Satisfaction ; Reproducibility of Results ; Serbia ; Quality of Life ; Language ; Surveys and Questionnaires ; *Neoplasms/therapy ; Chronic Disease ; Personal Satisfaction ; Psychometrics/methods ; }, abstract = {OBJECTIVE: Transcultural adaptation and validation of FACIT-TS-PS questionnaire to Serbian language.

METHODS: Standard forward and backward translation from English to Serbian language was performed. Pilot testing of FACIT-TS-PS was conducted on 12 patients with a confirmed diagnosis of malignant tumor. The study included 154 patients with malignant disease. The Questionnaire of Patient Satisfaction was used as a validated tool to evaluate concurrent validity of FACIT-TS-PS questionnaire. Reproducibility was tested on 30 subjects who answered the questionnaire for the second time two weeks later.

RESULTS: Three FACIT-TS-PS subscales (Physician Communication, Treatment Staff Communication and Nurse Communication) demonstrated satisfactory construct validity using Cronbach's alpha, the remaining two subscales (Technical Competence and Confidence & Trust) showed high ceiling effect. Treatment Staff Communication subscale showed large floor effect. Concurrent validity was demonstrated by correlation with the two dimensions of the Questionnaire of Patient Satisfaction. Satisfactory reproducibility was demonstrated on 30 patients who filled the questionnaire for the second time two weeks after initial interview.

CONCLUSION: The Serbian version of FACIT-TS-PS with the omission of Treatment Staff Communication subscale could be used as a valid instrument to assess patient and treatment satisfaction in chronically ill patients in the Serbian population. Omission of Treatment Staff Communication subscale is necessary because it contains questions not relevant for patients in Serbian healthcare system.}, } @article {pmid37966364, year = {2023}, author = {Hutt Vater, C and Biederman, J and DiSalvo, M and O'Connor, H and Parker, H and Woodworth, KY and Wozniak, J and Faraone, SV}, title = {Growth Trajectories in Stimulant Treated Children and Adolescents: A Qualitative Review of the Literature from Comprehensive Datasets and Registries.}, journal = {Journal of child and adolescent psychopharmacology}, volume = {33}, number = {9}, pages = {344-355}, pmid = {37966364}, issn = {1557-8992}, support = {U01 AR076092/AR/NIAMS NIH HHS/United States ; R21 MH126494/MH/NIMH NIH HHS/United States ; R01 MH116037/MH/NIMH NIH HHS/United States ; R01 NS128535/NS/NINDS NIH HHS/United States ; }, mesh = {Adult ; Adolescent ; Humans ; Child ; *Central Nervous System Stimulants/adverse effects ; Registries ; Body Mass Index ; Databases, Factual ; *Drug-Related Side Effects and Adverse Reactions ; }, abstract = {Objective: Attention-deficit/hyperactivity disorder (ADHD) treatment with stimulant products has been shown to be safe and effective; however, there are remaining concerns about their possible adverse effects on growth trajectories. We conducted a systematic review of the extant literature derived from ecologically valid databases and registries to assess the body of knowledge about the effects of stimulants on growth trajectories in naturalistic samples. Methods: Using PubMed and PsycINFO, we searched for articles published before February 8, 2023 that focused on growth findings associated with stimulant treatment in pediatric ADHD from comprehensive datasets derived from naturalistic population studies. Results: Of the 1070 articles initially identified, 12 met all inclusion criteria. Sample sizes ranged from 157 to 163,820 youths. Seven of 10 articles examining height found significant decreases in height associated with chronic stimulant treatment that normalized over time in 2 studies. Three articles found no significant association between stimulant treatment and height. No clear associations were identified between cumulative duration and dose of stimulant treatment and adult height. All articles examining weight and six of eight articles examining body mass index (BMI) found significant initial decreases that tended to normalize then increase over time. Longer duration of stimulant medication use was predominantly associated with significant weight and BMI reductions. The effects of stimulant dose on weight and BMI were mostly weak and clinically insignificant. Most studies found no significant association between age at start of stimulant treatment and change in height, weight, or BMI. Most studies did not find significant sex effects in relation to growth parameters. Conclusions: This review of ecologically informative samples revealed that the effects of stimulant treatment on growth trajectories are mainly small and transient. These effects seem to be clinically insignificant for most youth with ADHD who receive stimulant treatment from childhood onto adolescence and adulthood.}, } @article {pmid37966259, year = {2024}, author = {Schiebelhut, LM and Guillaume, AS and Kuhn, A and Schweizer, RM and Armstrong, EE and Beaumont, MA and Byrne, M and Cosart, T and Hand, BK and Howard, L and Mussmann, SM and Narum, SR and Rasteiro, R and Rivera-Colón, AG and Saarman, N and Sethuraman, A and Taylor, HR and Thomas, GWC and Wellenreuther, M and Luikart, G}, title = {Genomics and conservation: Guidance from training to analyses and applications.}, journal = {Molecular ecology resources}, volume = {24}, number = {2}, pages = {e13893}, doi = {10.1111/1755-0998.13893}, pmid = {37966259}, issn = {1755-0998}, support = {80NSSC19K0185/NASA/NASA/United States ; 80NSSC19K0185/NASA/NASA/United States ; }, mesh = {Humans ; *Conservation of Natural Resources/methods ; *Genomics ; Biodiversity ; Genome ; }, abstract = {Environmental change is intensifying the biodiversity crisis and threatening species across the tree of life. Conservation genomics can help inform conservation actions and slow biodiversity loss. However, more training, appropriate use of novel genomic methods and communication with managers are needed. Here, we review practical guidance to improve applied conservation genomics. We share insights aimed at ensuring effectiveness of conservation actions around three themes: (1) improving pedagogy and training in conservation genomics including for online global audiences, (2) conducting rigorous population genomic analyses properly considering theory, marker types and data interpretation and (3) facilitating communication and collaboration between managers and researchers. We aim to update students and professionals and expand their conservation toolkit with genomic principles and recent approaches for conserving and managing biodiversity. The biodiversity crisis is a global problem and, as such, requires international involvement, training, collaboration and frequent reviews of the literature and workshops as we do here.}, } @article {pmid37966155, year = {2024}, author = {Amendola, S and Hengartner, MP}, title = {Antidepressants use in Italy: an ecological study of national and regional trends and associated factors.}, journal = {International clinical psychopharmacology}, volume = {39}, number = {2}, pages = {93-105}, doi = {10.1097/YIC.0000000000000522}, pmid = {37966155}, issn = {1473-5857}, mesh = {Humans ; Italy/epidemiology ; *Antidepressive Agents/therapeutic use ; *Patient Discharge ; Mood Disorders/drug therapy ; Data Management ; }, abstract = {The present study aimed to (1) provide an update on trends in AD consumption both at the national and regional unit of analysis for the period 2000-2020 in Italy and (2) analyze sociodemographic and healthcare system-related factors associated with AD prescribing at the regional-population level between 2000 and 2019. Data were extracted from reports of the Italian Medicines Agency and databases of the Italian National Institute of Statistics. Linear regression and mixed models were applied to analyze trends in AD use (DDD/1000/day) and ecological factors associated with AD prescribing. Between 2000 and 2010 AD prescription rates constantly increased. Thereafter they stabilized until 2017 when a positive trend began again. There was a positive ecological association between AD prescribing and rates of hospital discharge due to affective disorders, antibiotics prescribing, public non-drug healthcare spending per capita, and Northern regions compared to Southern regions. AD consumption increased massively during the 2000s, flattened during the 2010s but thereafter increased again until 2020. The ecological correlation between healthcare provision/spending and AD consumption suggests that health-economic factors may play an important role.}, } @article {pmid37965283, year = {2023}, author = {Boyes, D and , and , and , and , and , and Holland, PWH and , }, title = {The genome sequence of the Leopard Moth, Zeuzera pyrina (Linnaeus, 1761).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {94}, pmid = {37965283}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual male Zeuzera pyrina (the Leopard Moth, Arthropoda; Insecta; Lepidoptera; Cossidae). The genome sequence is 687 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the assembled Z sex chromosome. The mitochondrial genome has also been assembled and is 15.3 kilobases in length. Gene annotation of this assembly on Ensembl identified 22,738 protein coding genes.}, } @article {pmid37964699, year = {2024}, author = {Knoch, D and Meyer, RC and Heuermann, MC and Riewe, D and Peleke, FF and Szymański, J and Abbadi, A and Snowdon, RJ and Altmann, T}, title = {Integrated multi-omics analyses and genome-wide association studies reveal prime candidate genes of metabolic and vegetative growth variation in canola.}, journal = {The Plant journal : for cell and molecular biology}, volume = {117}, number = {3}, pages = {713-728}, doi = {10.1111/tpj.16524}, pmid = {37964699}, issn = {1365-313X}, support = {234585441//Deutsche Forschungsgemeinschaft/ ; 491250510//Deutsche Forschungsgemeinschaft/ ; }, mesh = {*Genome-Wide Association Study ; *Multiomics ; Quantitative Trait Loci/genetics ; Genomics ; Phenotype ; }, abstract = {Genome-wide association studies (GWAS) identified thousands of genetic loci associated with complex plant traits, including many traits of agronomical importance. However, functional interpretation of GWAS results remains challenging because of large candidate regions due to linkage disequilibrium. High-throughput omics technologies, such as genomics, transcriptomics, proteomics and metabolomics open new avenues for integrative systems biological analyses and help to nominate systems information supported (prime) candidate genes. In the present study, we capitalise on a diverse canola population with 477 spring-type lines which was previously analysed by high-throughput phenotyping of growth-related traits and by RNA sequencing and metabolite profiling for multi-omics-based hybrid performance prediction. We deepened the phenotypic data analysis, now providing 123 time-resolved image-based traits, to gain insight into the complex relations during early vegetative growth and reanalysed the transcriptome data based on the latest Darmor-bzh v10 genome assembly. Genome-wide association testing revealed 61 298 robust quantitative trait loci (QTL) including 187 metabolite QTL, 56814 expression QTL and 4297 phenotypic QTL, many clustered in pronounced hotspots. Combining information about QTL colocalisation across omics layers and correlations between omics features allowed us to discover prime candidate genes for metabolic and vegetative growth variation. Prioritised candidate genes for early biomass accumulation include A06p05760.1_BnaDAR (PIAL1), A10p16280.1_BnaDAR, C07p48260.1_BnaDAR (PRL1) and C07p48510.1_BnaDAR (CLPR4). Moreover, we observed unequal effects of the Brassica A and C subgenomes on early biomass production.}, } @article {pmid37962866, year = {2023}, author = {Zang, Z and Zhang, Y and Zuo, C and Chen, J and He, B and Luo, N and Zou, J and Zhao, W and Shi, W and Yan, X}, title = {Exploring Global Land Coarse-Mode Aerosol Changes from 2001-2021 Using a New Spatiotemporal Coaction Deep-Learning Model.}, journal = {Environmental science & technology}, volume = {57}, number = {48}, pages = {19881-19890}, doi = {10.1021/acs.est.3c07982}, pmid = {37962866}, issn = {1520-5851}, mesh = {*Air Pollutants/analysis ; *Deep Learning ; Environmental Monitoring/methods ; Dust/analysis ; Aerosols/analysis ; }, abstract = {Coarse-mode aerosol optical depths (cAODs) are critical for understanding the impact of coarse particle sizes, especially dust aerosols, on climate. Currently, the limited data length and high uncertainty of satellite products diminish the applicability of cAOD for climate research. Here, we propose a spatiotemporal coaction deep-learning model (SCAM) for the retrieval of global land cAOD (500 nm) from 2001-2021. In contrast to conventional deep-learning models, the SCAM considers the impacts of spatiotemporal feature interactions and can simultaneously describe linear and nonlinear relationships for retrievals. Based on these unique characteristics, the SCAM considerably improved global daily cAOD accuracies and coverages (R = 0.82, root-mean-square error [RMSE] = 0.04). Compared to official products from the multiangle imaging spectroradiometer (MISR), the moderate resolution imaging spectroradiometer (MODIS), and the polarization and directionality of Earth's reflectances (POLDER) instrument, as well as the physical-deep learning (Phy-DL) derived cAOD, the SCAM cAOD improved the monthly R from 0.44 to 0.88 and more accurately captured over the desert regions. Based on the SCAM cAOD, daily dust cases decreased over the Sahara, Thar Desert, Gobi Desert, and Middle East during 2001-2021 (>3 × 10[-3]/year). The SCAM-retrieved cAOD can contribute considerably to resolving the climate change uncertainty related to coarse-mode aerosols. Our proposed method is highly valuable for reducing uncertainties regarding coarse aerosols and climate interactions.}, } @article {pmid37961949, year = {2024}, author = {O'Brien, MJ and Valverde, S and Duran-Nebreda, S and Vidiella, B and Bentley, RA}, title = {Punctuated equilibrium at 50: Anything there for evolutionary anthropology? Yes; definitely.}, journal = {Evolutionary anthropology}, volume = {33}, number = {1}, pages = {e22009}, doi = {10.1002/evan.22009}, pmid = {37961949}, issn = {1520-6505}, support = {2019 BP 00206//Beatriu de Pinós postdoctoral programme in the Office of the General Secretary of Research and Universities and the Ministry of Research and Univertisites/ ; 801370//Marie Sklodowska-Curie COFUND/ ; //2020-2021 Biodiversa and Water JPI/ ; 101003777//BiodivRestore ERA-NET Cofund/ ; //Innovation Fund Denmark (IFD)/ ; //Agence Nationale de la Recherche (ANR)/ ; //Fundação para a Ciência e a Tecnologia (FCT)/ ; //Swedish Environmental Protection Agency (SEPA)/ ; PCI2022-132936//MCIN/AEI/10.13039/501100011033/ ; //European Union NextGenerationEU/PRTR/ ; PID2020-117822GB-I00/AEI/10.13039/501100011033//Spanish Ministry of Science and Innovation through the State Research Agency (AEI)/ ; }, mesh = {Humans ; *Biological Evolution ; *Fossils ; Cultural Diversity ; Databases, Factual ; }, abstract = {The theory of punctuated equilibrium (PE) was developed a little over 50 years ago to explain long-term, large-scale appearance and disappearance of species in the fossil record. A theory designed specifically for that purpose cannot be expected, out of the box, to be directly applicable to biocultural evolution, but in revised form, PE offers a promising approach to incorporating not only a wealth of recent empirical research on genetic, linguistic, and technological evolution but also large databases that document human biological and cultural diversity across time and space. Here we isolate the fundamental components of PE and propose which pieces, when reassembled or renamed, can be highly useful in evolutionary anthropology, especially as humanity faces abrupt ecological challenges on an increasingly larger scale.}, } @article {pmid37960453, year = {2023}, author = {Abbas, Q and Ahmad, G and Alyas, T and Alghamdi, T and Alsaawy, Y and Alzahrani, A}, title = {Revolutionizing Urban Mobility: IoT-Enhanced Autonomous Parking Solutions with Transfer Learning for Smart Cities.}, journal = {Sensors (Basel, Switzerland)}, volume = {23}, number = {21}, pages = {}, pmid = {37960453}, issn = {1424-8220}, abstract = {Smart cities have emerged as a specialized domain encompassing various technologies, transitioning from civil engineering to technology-driven solutions. The accelerated development of technologies, such as the Internet of Things (IoT), software-defined networks (SDN), 5G, artificial intelligence, cognitive science, and analytics, has played a crucial role in providing solutions for smart cities. Smart cities heavily rely on devices, ad hoc networks, and cloud computing to integrate and streamline various activities towards common goals. However, the complexity arising from multiple cloud service providers offering myriad services necessitates a stable and coherent platform for sustainable operations. The Smart City Operational Platform Ecology (SCOPE) model has been developed to address the growing demands, and incorporates machine learning, cognitive correlates, ecosystem management, and security. SCOPE provides an ecosystem that establishes a balance for achieving sustainability and progress. In the context of smart cities, Internet of Things (IoT) devices play a significant role in enabling automation and data capture. This research paper focuses on a specific module of SCOPE, which deals with data processing and learning mechanisms for object identification in smart cities. Specifically, it presents a car parking system that utilizes smart identification techniques to identify vacant slots. The learning controller in SCOPE employs a two-tier approach, and utilizes two different models, namely Alex Net and YOLO, to ensure procedural stability and improvement.}, } @article {pmid37954922, year = {2023}, author = {Boyes, D and , and , and , and , and , and Holland, PWH and , }, title = {The genome sequence of the Miller, Acronicta leporina (Linnaeus, 1758).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {49}, pmid = {37954922}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual female Acronicta leporina (the Miller; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 466 megabases in span. Most of the assembly is scaffolded into 32 chromosomal pseudomolecules, including the W and Z sex chromosomes. The mitochondrial genome has also been assembled and is 15.4 kilobases in length.}, } @article {pmid37953792, year = {2023}, author = {Furtado, DP and Vieira, EA and Nascimento, WF and Inagaki, KY and Bleuel, J and Alves, MAZ and Longo, GO and Oliveira, LS}, title = {#DeOlhoNosCorais: a polygonal annotated dataset to optimize coral monitoring.}, journal = {PeerJ}, volume = {11}, number = {}, pages = {e16219}, pmid = {37953792}, issn = {2167-8359}, mesh = {Humans ; Animals ; *Anthozoa/physiology ; Coral Reefs ; Ecosystem ; Crustacea ; Fishes ; }, abstract = {Corals are colonial animals within the Phylum Cnidaria that form coral reefs, playing a significant role in marine environments by providing habitat for fish, mollusks, crustaceans, sponges, algae, and other organisms. Global climate changes are causing more intense and frequent thermal stress events, leading to corals losing their color due to the disruption of a symbiotic relationship with photosynthetic endosymbionts. Given the importance of corals to the marine environment, monitoring coral reefs is critical to understanding their response to anthropogenic impacts. Most coral monitoring activities involve underwater photographs, which can be costly to generate on large spatial scales and require processing and analysis that may be time-consuming. The Marine Ecology Laboratory (LECOM) at the Federal University of Rio Grande do Norte (UFRN) developed the project "#DeOlhoNosCorais" which encourages users to post photos of coral reefs on their social media (Instagram) using this hashtag, enabling people without previous scientific training to contribute to coral monitoring. The laboratory team identifies the species and gathers information on coral health along the Brazilian coast by analyzing each picture posted on social media. To optimize this process, we conducted baseline experiments for image classification and semantic segmentation. We analyzed the classification results of three different machine learning models using the Local Interpretable Model-agnostic Explanations (LIME) algorithm. The best results were achieved by combining EfficientNet for feature extraction and Logistic Regression for classification. Regarding semantic segmentation, the U-Net Pix2Pix model produced a pixel-level accuracy of 86%. Our results indicate that this tool can enhance image selection for coral monitoring purposes and open several perspectives for improving classification performance. Furthermore, our findings can be expanded by incorporating other datasets to create a tool that streamlines the time and cost associated with analyzing coral reef images across various regions.}, } @article {pmid37953409, year = {2024}, author = {Abarenkov, K and Nilsson, RH and Larsson, KH and Taylor, AFS and May, TW and Frøslev, TG and Pawlowska, J and Lindahl, B and Põldmaa, K and Truong, C and Vu, D and Hosoya, T and Niskanen, T and Piirmann, T and Ivanov, F and Zirk, A and Peterson, M and Cheeke, TE and Ishigami, Y and Jansson, AT and Jeppesen, TS and Kristiansson, E and Mikryukov, V and Miller, JT and Oono, R and Ossandon, FJ and Paupério, J and Saar, I and Schigel, D and Suija, A and Tedersoo, L and Kõljalg, U}, title = {The UNITE database for molecular identification and taxonomic communication of fungi and other eukaryotes: sequences, taxa and classifications reconsidered.}, journal = {Nucleic acids research}, volume = {52}, number = {D1}, pages = {D791-D797}, pmid = {37953409}, issn = {1362-4962}, support = {PRG1170//Estonian Research Council/ ; 101059492//Horizon 2020/ ; //Estonian Research Infrastructure/ ; //UNITE Community/ ; }, mesh = {DNA, Ribosomal Spacer ; *Fungi/genetics ; *Databases, Nucleic Acid ; Biodiversity ; DNA, Fungal ; Phylogeny ; }, abstract = {UNITE (https://unite.ut.ee) is a web-based database and sequence management environment for molecular identification of eukaryotes. It targets the nuclear ribosomal internal transcribed spacer (ITS) region and offers nearly 10 million such sequences for reference. These are clustered into ∼2.4M species hypotheses (SHs), each assigned a unique digital object identifier (DOI) to promote unambiguous referencing across studies. UNITE users have contributed over 600 000 third-party sequence annotations, which are shared with a range of databases and other community resources. Recent improvements facilitate the detection of cross-kingdom biological associations and the integration of undescribed groups of organisms into everyday biological pursuits. Serving as a digital twin for eukaryotic biodiversity and communities worldwide, the latest release of UNITE offers improved avenues for biodiversity discovery, precise taxonomic communication and integration of biological knowledge across platforms.}, } @article {pmid37953341, year = {2024}, author = {Shi, H and Wu, X and Zhu, Y and Jiang, T and Wang, Z and Li, X and Liu, J and Zhang, Y and Chen, F and Gao, J and Xu, X and Zhang, G and Xiao, N and Feng, X and Zhang, P and Wu, Y and Li, A and Chen, P and Li, X}, title = {RefMetaPlant: a reference metabolome database for plants across five major phyla.}, journal = {Nucleic acids research}, volume = {52}, number = {D1}, pages = {D1614-D1628}, pmid = {37953341}, issn = {1362-4962}, support = {XDA24010400//Strategic Priority Research Program of Chinese Academy of Sciences/ ; 32270719//National Natural Science Foundation of China/ ; CARS-11//Earmarked Fund for China Agriculture Research System/ ; BK20220307//Natural Science Foundation of Jiangsu Province/ ; 2021387//Shanghai Post-doctoral Excellence Program/ ; SJ(22)107//Special funds for scientific research and development of Institute of Agricultural Sciences for Lixiahe Region in Jiangsu/ ; }, mesh = {Chromatography, Liquid ; *Databases, Factual ; *Metabolome/genetics ; Metabolomics/methods ; Plants/metabolism ; Tandem Mass Spectrometry ; }, abstract = {Plants are unique with tremendous chemical diversity and metabolic complexity, which is highlighted by estimates that green plants collectively produce metabolites numbering in the millions. Plant metabolites play crucial roles in all aspects of plant biology, like growth, development, stress responses, etc. However, the lack of a reference metabolome for plants, and paucity of high-quality standard compound spectral libraries and related analytical tools, have hindered the discovery and functional study of phytochemicals in plants. Here, by leveraging an advanced LC-MS platform, we generated untargeted mass spectral data from >150 plant species collected across the five major phyla. Using a self-developed computation protocol, we constructed reference metabolome for 153 plant species. A 'Reference Metabolome Database for Plants' (RefMetaPlant) was built to encompass the reference metabolome, integrated standard compound mass spectral libraries for annotation, and related query and analytical tools like 'LC-MS/MS Query', 'RefMetaBlast' and 'CompoundLibBlast' for searches and profiling of plant metabolome and metabolite identification. Analogous to a reference genome in genomic research, RefMetaPlant provides a powerful platform to support plant genome-scale metabolite analysis to promote knowledge/data sharing and collaboration in the field of metabolomics. RefMetaPlant is freely available at https://www.biosino.org/RefMetaDB/.}, } @article {pmid37952420, year = {2024}, author = {Hao, W and Shan, YF and Kimura, T and Ukawa, S and Ohira, H and Okabayashi, S and Wakai, K and Ando, M and Tamakoshi, A}, title = {Dual decline in subjective gait speed and domain-specific cognition is associated with higher risk of incident dementia in older Japanese adults: A 15-year age-specific cohort study.}, journal = {Archives of gerontology and geriatrics}, volume = {117}, number = {}, pages = {105254}, doi = {10.1016/j.archger.2023.105254}, pmid = {37952420}, issn = {1872-6976}, mesh = {Male ; Humans ; Aged ; Aged, 80 and over ; Walking Speed ; Cohort Studies ; East Asian People ; Gait ; Cognition ; *Dementia/epidemiology ; Age Factors ; *Cognitive Dysfunction ; }, abstract = {OBJECTIVES: Dual decline in gait speed and cognition has been found to have higher dementia risk than no decline or pure decline. However, evidence from the Asian population is lacking. Therefore, we aimed to investigate the association of dual decline from age 65 to 70 years with late-life dementia in older Japanese adults with different personal characteristics.

METHODS: Data were collected from an age-specific cohort study conducted in 482 Japanese 65-year-old adults. We investigated participant demographics, medical histories, lifestyles, subjective gait speed, and cognition at both 64/65 and 70/71 years old, and confirmed dementia until age of 85 years. Cox proportion hazard models were used to estimate the risk of dementia, with adjustments for covariates, and death was treated as a competing risk.

RESULTS: After a mean follow-up period of 12.5-years, 111 participants developed dementia. Older adults with dual decline are more likely to have hyperlipidemia, diabetes, and smoking habits. And we found that dual decline in gait speed and domain-specific cognition was associated with a higher risk of dementia compared with no decline in most cognitive tests, with the highest risk observed for gait speed combined with memory (sub-distribution hazard ratio:3.89, 95 %, confidence intervals: [1.68-9.01]). However, significant differences only existed in men after stratification by sex.

CONCLUSIONS: A dual decline in subjective gait speed and cognition may serve as a robust predictor of dementia over a decade prior to its onset, particularly in men. These findings highlighted the importance of screening for dual decline at an early age.}, } @article {pmid37951122, year = {2023}, author = {Waqas, M and Wong, MS and Stocchino, A and Abbas, S and Hafeez, S and Zhu, R}, title = {Marine plastic pollution detection and identification by using remote sensing-meta analysis.}, journal = {Marine pollution bulletin}, volume = {197}, number = {}, pages = {115746}, doi = {10.1016/j.marpolbul.2023.115746}, pmid = {37951122}, issn = {1879-3363}, mesh = {*Ecosystem ; *Remote Sensing Technology ; Environmental Monitoring/methods ; Plastics/analysis ; Oceans and Seas ; Waste Products/analysis ; }, abstract = {The persistent plastic litter, originating from different sources and transported from rivers to oceans, has posed serious biological, ecological, and chemical effects on the marine ecosystem, and is considered a global issue. In the past decade, many studies have identified, monitored, and tracked marine plastic debris in coastal and open ocean areas using remote sensing technologies. Compared to traditional surveying methods, high-resolution (spatial and temporal) multispectral or hyperspectral remote sensing data have been substantially used to monitor floating marine macro litter (FMML). In this systematic review, we present an overview of remote sensing data and techniques for detecting FMML, as well as their challenges and opportunities. We reviewed the studies based on different sensors and platforms, spatial and spectral resolution, ground sampling data, plastic detection methods, and accuracy obtained in detecting marine litter. In addition, this study elaborates the usefulness of high-resolution remote sensing data in Visible (VIS), Near-infrared (NIR), and Short-Wave InfraRed (SWIR) range, along with spectral signatures of plastic, in-situ samples, and spectral indices for automatic detection of FMML. Moreover, the Thermal Infrared (TIR), Synthetic aperture radar (SAR), and Light Detection and Ranging (LiDAR) data were introduced and these were demonstrated that could be used as a supplement dataset for the identification and quantification of FMML.}, } @article {pmid37950741, year = {2024}, author = {Kimotho, RN and Maina, S}, title = {Unraveling plant-microbe interactions: can integrated omics approaches offer concrete answers?.}, journal = {Journal of experimental botany}, volume = {75}, number = {5}, pages = {1289-1313}, pmid = {37950741}, issn = {1460-2431}, support = {//Chinese Government Scholarship/ ; //University of Chinese Academy of Sciences/ ; }, mesh = {*Multiomics ; *Microbiota ; Plants/genetics ; Symbiosis ; }, abstract = {Advances in high throughput omics techniques provide avenues to decipher plant microbiomes. However, there is limited information on how integrated informatics can help provide deeper insights into plant-microbe interactions in a concerted way. Integrating multi-omics datasets can transform our understanding of the plant microbiome from unspecified genetic influences on interacting species to specific gene-by-gene interactions. Here, we highlight recent progress and emerging strategies in crop microbiome omics research and review key aspects of how the integration of host and microbial omics-based datasets can be used to provide a comprehensive outline of complex crop-microbe interactions. We describe how these technological advances have helped unravel crucial plant and microbial genes and pathways that control beneficial, pathogenic, and commensal plant-microbe interactions. We identify crucial knowledge gaps and synthesize current limitations in our understanding of crop microbiome omics approaches. We highlight recent studies in which multi-omics-based approaches have led to improved models of crop microbial community structure and function. Finally, we recommend holistic approaches in integrating host and microbial omics datasets to achieve precision and efficiency in data analysis, which is crucial for biotic and abiotic stress control and in understanding the contribution of the microbiota in shaping plant fitness.}, } @article {pmid37947402, year = {2023}, author = {Alexander, H and Hu, SK and Krinos, AI and Pachiadaki, M and Tully, BJ and Neely, CJ and Reiter, T}, title = {Eukaryotic genomes from a global metagenomic data set illuminate trophic modes and biogeography of ocean plankton.}, journal = {mBio}, volume = {14}, number = {6}, pages = {e0167623}, pmid = {37947402}, issn = {2150-7511}, support = {OCE-1948025//National Science Foundation (NSF)/ ; OCE-0939564, OCE-194777, OCE-2327203//National Science Foundation (NSF)/ ; 931886//Simons Foundation (SF)/ ; DE-SC0020347//U.S. Department of Energy (DOE)/ ; OCE-1924492//National Science Foundation (NSF)/ ; OCE-0939654//National Science Foundation (NSF)/ ; }, mesh = {*Metagenomics/methods ; *Plankton/genetics/classification ; *Eukaryota/genetics/classification ; *Oceans and Seas ; *Metagenome ; Biodiversity ; Computational Biology/methods ; Phylogeny ; Seawater/microbiology ; Phylogeography ; }, abstract = {Single-celled eukaryotes play ecologically significant roles in the marine environment, yet fundamental questions about their biodiversity, ecological function, and interactions remain. Environmental sequencing enables researchers to document naturally occurring protistan communities, without culturing bias, yet metagenomic and metatranscriptomic sequencing approaches cannot separate individual species from communities. To more completely capture the genomic content of mixed protistan populations, we can create bins of sequences that represent the same organism (metagenome-assembled genomes [MAGs]). We developed the EukHeist pipeline, which automates the binning of population-level eukaryotic and prokaryotic genomes from metagenomic reads. We show exciting insight into what protistan communities are present and their trophic roles in the ocean. Scalable computational tools, like EukHeist, may accelerate the identification of meaningful genetic signatures from large data sets and complement researchers' efforts to leverage MAG databases for addressing ecological questions, resolving evolutionary relationships, and discovering potentially novel biodiversity.}, } @article {pmid37943735, year = {2023}, author = {Skoric, D and Rakic, JG and Jovanovic, V and Backovic, D and Soldatovic, I and Zivojinovic, JI}, title = {Psychosocial school factors and mental health of first grade secondary school students-Results of the Health Behaviour in School-aged Children Survey in Serbia.}, journal = {PloS one}, volume = {18}, number = {11}, pages = {e0293179}, pmid = {37943735}, issn = {1932-6203}, mesh = {Female ; Humans ; Child ; Adolescent ; Male ; *Mental Health ; Serbia/epidemiology ; Cross-Sectional Studies ; *Schools ; Psychophysiologic Disorders ; Students/psychology ; Health Behavior ; }, abstract = {This cross-sectional study aimed to investigate the association between psychosocial school factors and life satisfaction, symptoms of depression and psychosomatic health complaints among first grade secondary school students in Serbia. We analysed data from the 2018 Health Behaviour in School-aged Children (HBSC) study in the Republic of Serbia. Analyzed psychosocial school factors included satisfaction with school, schoolwork pressure, teacher support, classmate support and being bullied at school. Life satisfaction was assessed by the 11-step Cantril's ladder (cutoff >5). Symptoms of depression were measured by the Center for Epidemiologic Studies Depression Scale (CESD-10) and psychosomatic health complaints by using the HBSC symptom checklist. Univariable and multivariable binary logistic regression was used to determine independent predictors of students' life satisfaction, symptoms of depression and psychosomatic health complaints in the school environment, while also considering their socio-demographic characteristics and perceived family and friend support. The study included 1605 students (average age 15.26 ±0.44 years), of whom 50.3% were females. Results from the binary logistic regression analyses showed that life satisfaction was positively related to school satisfaction and classmate support, and negatively to being bullied at school. Symptoms of depression were positively associated with schoolwork pressure and being bullied at school, and negatively with teacher and classmate support. All analyzed factors of the school environment were significantly related to psychosomatic health complaints, whereby schoolwork pressure and being bullied at school were positively associated, while teacher and classmate support and satisfaction with school were negatively associated. Given the established association of psychosocial school factors with mental health, there is a need for targeted measures both at school and community level with the aim of improving social support in the school environment, reducing schoolwork burden and preventing bullying at school, potentially resulting in the overall improvement of mental health of the first grade secondary school students.}, } @article {pmid37942709, year = {2023}, author = {Furuya, S and Liu, J and Sun, Z and Lu, Q and Fletcher, JM}, title = {The Big (Genetic) Sort? A Research Note on Migration Patterns and Their Genetic Imprint in the United Kingdom.}, journal = {Demography}, volume = {60}, number = {6}, pages = {1649-1664}, doi = {10.1215/00703370-11054960}, pmid = {37942709}, issn = {1533-7790}, mesh = {Humans ; United Kingdom ; *Transients and Migrants ; Educational Status ; }, abstract = {This research note reinvestigates Abdellaoui et al.'s (2019) findings that genetically selective migration may lead to persistent and accumulating socioeconomic and health inequalities between types (coal mining or non-coal mining) of places in the United Kingdom. Their migration measure classified migrants who moved to the same type of place (coal mining to coal mining or non-coal mining to non-coal mining) into "stay" categories, preventing them from distinguishing migrants from nonmigrants. We reinvestigate the question of genetically selective migration by examining migration patterns between places rather than place types and find genetic selectivity in whether people migrate and where. For example, we find evidence of positive selection: people with genetic variants correlated with better education moved from non-coal mining to coal mining places with our measure of migration. Such findings were obscured in earlier work that could not distinguish nonmigrants from migrants.}, } @article {pmid37942213, year = {2022}, author = {Boyes, D and , and , and , and , and , and Palmada-Flores, M and , }, title = {The genome sequence of the lesser treble-bar moth, Aplocera efformata (Guenée, 1857).}, journal = {Wellcome open research}, volume = {7}, number = {}, pages = {303}, pmid = {37942213}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual female Aplocera efformata (the lesser treble-bar; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 350 megabases in span. Most of the assembly (99.97%) is scaffolded into 32 chromosomal pseudomolecules, with W and Z sex chromosomes assembled. The complete mitochondrial genome was also assembled and is 15.4 kilobases in length. Gene annotation of this assembly on Ensembl has identified 11,393 protein coding genes.}, } @article {pmid37939139, year = {2023}, author = {Conte, L and Gonella, F and Giansanti, A and Kleidon, A and Romano, A}, title = {Modeling cell populations metabolism and competition under maximum power constraints.}, journal = {PLoS computational biology}, volume = {19}, number = {11}, pages = {e1011607}, pmid = {37939139}, issn = {1553-7358}, mesh = {Humans ; *Ecosystem ; *Multiple Myeloma/pathology ; Bone Marrow/metabolism ; Models, Theoretical ; Tumor Microenvironment/physiology ; }, abstract = {Ecological interactions are fundamental at the cellular scale, addressing the possibility of a description of cellular systems that uses language and principles of ecology. In this work, we use a minimal ecological approach that encompasses growth, adaptation and survival of cell populations to model cell metabolisms and competition under energetic constraints. As a proof-of-concept, we apply this general formulation to study the dynamics of the onset of a specific blood cancer-called Multiple Myeloma. We show that a minimal model describing antagonist cell populations competing for limited resources, as regulated by microenvironmental factors and internal cellular structures, reproduces patterns of Multiple Myeloma evolution, due to the uncontrolled proliferation of cancerous plasma cells within the bone marrow. The model is characterized by a class of regime shifts to more dissipative states for selectively advantaged malignant plasma cells, reflecting a breakdown of self-regulation in the bone marrow. The transition times obtained from the simulations range from years to decades consistently with clinical observations of survival times of patients. This irreversible dynamical behavior represents a possible description of the incurable nature of myelomas based on the ecological interactions between plasma cells and the microenvironment, embedded in a larger complex system. The use of ATP equivalent energy units in defining stocks and flows is a key to constructing an ecological model which reproduces the onset of myelomas as transitions between states of a system which reflects the energetics of plasma cells. This work provides a basis to construct more complex models representing myelomas, which can be compared with model ecosystems.}, } @article {pmid37939092, year = {2023}, author = {Suire, A and Kunita, I and Harel, R and Crofoot, M and Mutinda, M and Kamau, M and Hassel, JM and Murray, S and Kawamura, S and Matsumoto-Oda, A}, title = {Estimating individual exposure to predation risk in group-living baboons, Papio anubis.}, journal = {PloS one}, volume = {18}, number = {11}, pages = {e0287357}, pmid = {37939092}, issn = {1932-6203}, mesh = {Humans ; Animals ; Male ; *Papio anubis ; Papio ; *Predatory Behavior ; Geographic Information Systems ; }, abstract = {In environments with multiple predators, vulnerabilities associated with the spatial positions of group-living prey are non-uniform and depend on the hunting styles of the predators. Theoretically, coursing predators follow their prey over long distances and attack open areas, exposing individuals at the edge of the group to predation risk more than those at the center (marginal predation). In contrast, ambush predators lurk unnoticed by their prey and appear randomly anywhere in the group; therefore, isolated individuals in the group would be more vulnerable to predators. These positions of vulnerability to predation are expected to be taken by larger-bodied males. Moreover, dominant males presumably occupy the center of the safe group. However, identifying individuals at higher predation risk requires both simultaneous recording of predator location and direct observation of predation events; empirical observations leave ambiguity as to who is at risk. Instead, several theoretical methods (predation risk proxies) have been proposed to assess predation risk: (1) the size of the individual 'unlimited domain of danger' based on Voronoi tessellation, (2) the size of the 'limited domain of danger' based on predator detection distance, (3) peripheral/center position in the group (minimum convex polygon), (4) the number and direction of others in the vicinity (surroundedness), and (5) dyadic distances. We explored the age-sex distribution of individuals in at-risk positions within a wild baboon group facing predation risk from leopards, lions, and hyenas, using Global Positioning System collars. Our analysis of the location data from 26 baboons revealed that adult males were consistently isolated at the edge of the group in all predation risk proxies. Empirical evidence from previous studies indicates that adult male baboons are the most frequently preyed upon, and our results highlights the importance of spatial positioning in this.}, } @article {pmid37937916, year = {2023}, author = {Furuya, S and Liu, J and Sun, Z and Lu, Q and Fletcher, JM}, title = {Understanding Internal Migration: A Research Note Providing an Assessment of Migration Selection With Genetic Data.}, journal = {Demography}, volume = {60}, number = {6}, pages = {1631-1648}, doi = {10.1215/00703370-11053145}, pmid = {37937916}, issn = {1533-7790}, mesh = {Humans ; *Emigration and Immigration ; Cross-Sectional Studies ; Genome-Wide Association Study ; *Transients and Migrants ; Social Class ; }, abstract = {Migration is selective, resulting in inequalities between migrants and nonmigrants. However, investigating migration selection is empirically challenging because combined pre- and post-migration data are rarely available. We propose an alternative approach to assessing internal migration selection by integrating genetic data, enabling an investigation of migration selection with cross-sectional data collected post-migration. Using data from the UK Biobank, we utilized standard tools from statistical genetics to conduct a genome-wide association study (GWAS) for migration distance. We then calculated genetic correlations to compare GWAS results for migration with those for other characteristics. Given that individual genetics are determined at conception, these analyses allow a unique exploration of the association between pre-migration characteristics and migration. Results are generally consistent with the healthy migrant literature: genetics correlated with longer migration distance are associated with higher socioeconomic status and better health. We also extended the analysis to 53 traits and found novel correlations between migration and several physical health, mental health, personality, and sociodemographic traits.}, } @article {pmid37934751, year = {2024}, author = {Laporte, C and Fortin, F and Dupouy, J and Darmon, D and Pereira, B and Authier, N and Delorme, J and Chenaf, C and Maisonneuve, H and Schuers, M}, title = {The French ecology of medical care. A nationwide population-based cross sectional study.}, journal = {Family practice}, volume = {41}, number = {2}, pages = {92-98}, doi = {10.1093/fampra/cmad098}, pmid = {37934751}, issn = {1460-2229}, mesh = {Male ; Humans ; Female ; Adolescent ; Young Adult ; Adult ; Cross-Sectional Studies ; *General Practitioners ; Referral and Consultation ; Hospitalization ; Ambulatory Care ; }, abstract = {PURPOSE: Studies in the United States, Canada, Belgium, and Switzerland showed that the majority of health problems are managed within primary health care; however, the ecology of French medical care has not yet been described.

METHODS: Nationwide, population-based, cross sectional study. In 2018, we included data from 576,125 beneficiaries from the General Sample of Beneficiaries database. We analysed the reimbursement of consultations with (i) a general practitioner (GP), (ii) an outpatient doctor other than a GP, (iii) a doctor from a university or non-university hospital; and the reimbursement of (iv) hospitalization in a private establishment, (v) general hospital, and (vi) university hospital. For each criterion, we calculated the average monthly number of reimbursements reported on 1,000 beneficiaries. For categorical variables, we used the χ2 test, and to compare means we used the z test. All tests were 2-tailed with a P-value < 5% considered significant.

RESULTS: Each month, on average, 454 (out of 1,000) beneficiaries received at least 1 reimbursement, 235 consulted a GP, 74 consulted other outpatient doctors in ambulatory care and 24 in a hospital, 13 were hospitalized in a public non-university hospital and 10 in the private sector, and 5 were admitted to a university hospital. Independently of age, people consulted GPs twice as much as other specialists. The 13-25-year-old group consulted the least. Women consulted more than men. Individuals covered by complementary universal health insurance had more care.

CONCLUSIONS: Our study on reimbursement data confirmed that, like in other countries, in France the majority of health problems are managed within primary health care.}, } @article {pmid37934729, year = {2023}, author = {Vasileiou, D and Karapiperis, C and Baltsavia, I and Chasapi, A and Ahrén, D and Janssen, PJ and Iliopoulos, I and Promponas, VJ and Enright, AJ and Ouzounis, CA}, title = {CGG toolkit: Software components for computational genomics.}, journal = {PLoS computational biology}, volume = {19}, number = {11}, pages = {e1011498}, pmid = {37934729}, issn = {1553-7358}, mesh = {Reproducibility of Results ; *Genomics/methods ; *Software ; Computational Biology/methods ; Genome ; }, abstract = {Public-domain availability for bioinformatics software resources is a key requirement that ensures long-term permanence and methodological reproducibility for research and development across the life sciences. These issues are particularly critical for widely used, efficient, and well-proven methods, especially those developed in research settings that often face funding discontinuities. We re-launch a range of established software components for computational genomics, as legacy version 1.0.1, suitable for sequence matching, masking, searching, clustering and visualization for protein family discovery, annotation and functional characterization on a genome scale. These applications are made available online as open source and include MagicMatch, GeneCAST, support scripts for CoGenT-like sequence collections, GeneRAGE and DifFuse, supported by centrally administered bioinformatics infrastructure funding. The toolkit may also be conceived as a flexible genome comparison software pipeline that supports research in this domain. We illustrate basic use by examples and pictorial representations of the registered tools, which are further described with appropriate documentation files in the corresponding GitHub release.}, } @article {pmid37933857, year = {2024}, author = {Yang, S and Zong, W and Shi, L and Li, R and Ma, Z and Ma, S and Si, J and Wu, Z and Zhai, J and Ma, Y and Fan, Z and Chen, S and Huang, H and Zhang, D and Bao, Y and Li, R and Xie, J}, title = {PPGR: a comprehensive perennial plant genomes and regulation database.}, journal = {Nucleic acids research}, volume = {52}, number = {D1}, pages = {D1588-D1596}, pmid = {37933857}, issn = {1362-4962}, support = {QNTD202305//Central Universities/ ; 32371906//National Natural Science Foundation of China/ ; 2022YFD2201600//National Key R&D Program of China/ ; 2020132607//Forestry and Grassland Science and Technology Innovation Youth Top Talent Project of China/ ; XDB38030200//Chinese Academy of Sciences/ ; WX145XQ07-04//Genomics Data Center Construction of Chinese Academy of Sciences/ ; ANSO-PA-2020-07//Alliance of International Science Organizations/ ; //Open Biodiversity and Health Big Data Programme of IUBS/ ; }, mesh = {*Databases, Genetic ; *Genome, Plant ; *Genomics ; Plants/genetics ; Transcriptome ; }, abstract = {Perennial woody plants hold vital ecological significance, distinguished by their unique traits. While significant progress has been made in their genomic and functional studies, a major challenge persists: the absence of a comprehensive reference platform for collection, integration and in-depth analysis of the vast amount of data. Here, we present PPGR (Resource for Perennial Plant Genomes and Regulation; https://ngdc.cncb.ac.cn/ppgr/) to address this critical gap, by collecting, integrating, analyzing and visualizing genomic, gene regulation and functional data of perennial plants. PPGR currently includes 60 species, 847 million protein-protein/TF (transcription factor)-target interactions, 9016 transcriptome samples under various environmental conditions and genetic backgrounds. Noteworthy is the focus on genes that regulate wood production, seasonal dormancy, terpene biosynthesis and leaf senescence representing a wealth of information derived from experimental data, literature mining, public databases and genomic predictions. Furthermore, PPGR incorporates a range of multi-omics search and analysis tools to facilitate browsing and application of these extensive datasets. PPGR represents a comprehensive and high-quality resource for perennial plants, substantiated by an illustrative case study that demonstrates its capacity in unraveling gene functions and shedding light on potential regulatory processes.}, } @article {pmid37933429, year = {2023}, author = {Hofmeister, NR and Stuart, KC and Warren, WC and Werner, SJ and Bateson, M and Ball, GF and Buchanan, KL and Burt, DW and Cardilini, APA and Cassey, P and De Meyer, T and George, J and Meddle, SL and Rowland, HM and Sherman, CDH and Sherwin, WB and Vanden Berghe, W and Rollins, LA and Clayton, DF}, title = {Concurrent invasions of European starlings in Australia and North America reveal population-specific differentiation in shared genomic regions.}, journal = {Molecular ecology}, volume = {}, number = {}, pages = {}, doi = {10.1111/mec.17195}, pmid = {37933429}, issn = {1365-294X}, support = {//Newnham College, Cambridge/ ; //The Winston Churchill Memorial Trust/ ; BB/P013759/1//UK Biotechnology and Biological Sciences Research Council/ ; //University of New South Wales/ ; }, abstract = {A species' success during the invasion of new areas hinges on an interplay between the demographic processes common to invasions and the specific ecological context of the novel environment. Evolutionary genetic studies of invasive species can investigate how genetic bottlenecks and ecological conditions shape genetic variation in invasions, and our study pairs two invasive populations that are hypothesized to be from the same source population to compare how each population evolved during and after introduction. Invasive European starlings (Sturnus vulgaris) established populations in both Australia and North America in the 19th century. Here, we compare whole-genome sequences among native and independently introduced European starling populations to determine how demographic processes interact with rapid evolution to generate similar genetic patterns in these recent and replicated invasions. Demographic models indicate that both invasive populations experienced genetic bottlenecks as expected based on invasion history, and we find that specific genomic regions have differentiated even on this short evolutionary timescale. Despite genetic bottlenecks, we suggest that genetic drift alone cannot explain differentiation in at least two of these regions. The demographic boom intrinsic to many invasions as well as potential inversions may have led to high population-specific differentiation, although the patterns of genetic variation are also consistent with the hypothesis that this infamous and highly mobile invader adapted to novel selection (e.g., extrinsic factors). We use targeted sampling of replicated invasions to identify and evaluate support for multiple, interacting evolutionary mechanisms that lead to differentiation during the invasion process.}, } @article {pmid37930866, year = {2024}, author = {Camargo, AP and Call, L and Roux, S and Nayfach, S and Huntemann, M and Palaniappan, K and Ratner, A and Chu, K and Mukherjeep, S and Reddy, TBK and Chen, IA and Ivanova, NN and Eloe-Fadrosh, EA and Woyke, T and Baltrus, DA and Castañeda-Barba, S and de la Cruz, F and Funnell, BE and Hall, JPJ and Mukhopadhyay, A and Rocha, EPC and Stalder, T and Top, E and Kyrpides, NC}, title = {IMG/PR: a database of plasmids from genomes and metagenomes with rich annotations and metadata.}, journal = {Nucleic acids research}, volume = {52}, number = {D1}, pages = {D164-D173}, pmid = {37930866}, issn = {1362-4962}, support = {MR/W02666X/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Humans ; *Metagenome ; Metadata ; Software ; Databases, Genetic ; Plasmids/genetics ; *Microbiota ; }, abstract = {Plasmids are mobile genetic elements found in many clades of Archaea and Bacteria. They drive horizontal gene transfer, impacting ecological and evolutionary processes within microbial communities, and hold substantial importance in human health and biotechnology. To support plasmid research and provide scientists with data of an unprecedented diversity of plasmid sequences, we introduce the IMG/PR database, a new resource encompassing 699 973 plasmid sequences derived from genomes, metagenomes and metatranscriptomes. IMG/PR is the first database to provide data of plasmid that were systematically identified from diverse microbiome samples. IMG/PR plasmids are associated with rich metadata that includes geographical and ecosystem information, host taxonomy, similarity to other plasmids, functional annotation, presence of genes involved in conjugation and antibiotic resistance. The database offers diverse methods for exploring its extensive plasmid collection, enabling users to navigate plasmids through metadata-centric queries, plasmid comparisons and BLAST searches. The web interface for IMG/PR is accessible at https://img.jgi.doe.gov/pr. Plasmid metadata and sequences can be downloaded from https://genome.jgi.doe.gov/portal/IMG_PR.}, } @article {pmid37928210, year = {2023}, author = {Crowley, LM and Mitchell, R and , and , and , and , and , and , and Weston, ST and Wotton, KR and , }, title = {The genome sequence of the Lesser Hornet Hoverfly, Volucella inanis (Linnaeus, 1758).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {69}, pmid = {37928210}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual female Volucella inanis (the Lesser Hornet Hoverfly; Arthropoda; Insecta; Diptera; Syrphidae). The genome sequence is 961 megabases in span. Most of the assembly is scaffolded into six chromosomal pseudomolecules, including the assembled X sex chromosome. The mitochondrial genome has also been assembled and is 16.0 kilobases in length. Gene annotation of this assembly on Ensembl has identified 11,616 protein coding genes.}, } @article {pmid37926802, year = {2024}, author = {Šiljeg, A and Šiljeg, S and Milošević, R and Marić, I and Domazetović, F and Panđa, L}, title = {Multi-hazard susceptibility model based on high spatial resolution data-a case study of Sali settlement (Dugi otok, Croatia).}, journal = {Environmental science and pollution research international}, volume = {31}, number = {28}, pages = {40732-40747}, pmid = {37926802}, issn = {1614-7499}, mesh = {Croatia ; *Models, Theoretical ; Floods ; Geographic Information Systems ; Climate Change ; Wildfires ; Ecosystem ; }, abstract = {The world has been facing an increase in various natural hazards. The coastal regions are recognized as one of the most vulnerable due to high population pressure and climate change intensity. Mediterranean countries have one of the most burnable ecosystems in the world, one of the most exposed to pluvial floods, and have the highest erosion rates within the EU. Therefore, the aim of this study was to develop the first multihazard susceptibility model in Croatia for the Sali settlement (island of Dugi otok). The creation of a multi-hazard susceptibility model (MHSM) combined the application of geospatial technology (GST) with a local perception survey. The methodology consisted of two main steps: (1) creating individual hazard susceptibility models (soil erosion, wildfires, pluvial floods), and (2) overall hazard susceptibility modeling. Multicriterial GIS analyses and the Analytical Hierarchy Process were used to create individual hazard models. Criteria used (32) to create models are derived from very-high-resolution (VHR) models. Two versions of MHSM are created: 1) all criteria with equal weighting coefficients and 2) weight coefficients determined based on public perception. According to MHSM 1, most of the research (58%) area is moderately susceptible to multiple hazards. Highly and very highly susceptible areas are 27% of the drainage basin and are mostly located near roads and houses. MHSM 2 reveals similar results to MHSM 1. The public perceives that the research area is the most susceptible to wildfires. The wildfire ignition risk is ranked as moderate (3.00) with a standard deviation of 1.16. Pluvial flood risk is ranked low (2.78), with a standard deviation of 1.15. The risk of soil is most inferior (2.24) with a standard deviation of 0.91. The the most significant difference between public perception and the GIS-MCDA model of hazard susceptibility is related to soil erosion. However, the accuracy of the soil erosion model was confirmed by ROC curves based on recent traces of soil erosion in the research area. The proposed methodological framework of multi-hazard susceptibility modeling can be applied, with minor modifications, to other Mediterranean countries.}, } @article {pmid37925458, year = {2023}, author = {Srivastava, A and De Corte, D and Garcia, JAL and Swan, BK and Stepanauskas, R and Herndl, GJ and Sintes, E}, title = {Interplay between autotrophic and heterotrophic prokaryotic metabolism in the bathypelagic realm revealed by metatranscriptomic analyses.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {239}, pmid = {37925458}, issn = {2049-2618}, support = {I 486/FWF_/Austrian Science Fund FWF/Austria ; P 23234/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Heterotrophic Processes ; *Thiosulfates/metabolism ; Carbon/metabolism ; *Gammaproteobacteria/genetics ; Sulfur/metabolism ; Carbon Cycle ; }, abstract = {BACKGROUND: Heterotrophic microbes inhabiting the dark ocean largely depend on the settling of organic matter from the sunlit ocean. However, this sinking of organic materials is insufficient to cover their demand for energy and alternative sources such as chemoautotrophy have been proposed. Reduced sulfur compounds, such as thiosulfate, are a potential energy source for both auto- and heterotrophic marine prokaryotes.

METHODS: Seawater samples were collected from Labrador Sea Water (LSW, ~ 2000 m depth) in the North Atlantic and incubated in the dark at in situ temperature unamended, amended with 1 µM thiosulfate, or with 1 µM thiosulfate plus 10 µM glucose and 10 µM acetate (thiosulfate plus dissolved organic matter, DOM). Inorganic carbon fixation was measured in the different treatments and samples for metatranscriptomic analyses were collected after 1 h and 72 h of incubation.

RESULTS: Amendment of LSW with thiosulfate and thiosulfate plus DOM enhanced prokaryotic inorganic carbon fixation. The energy generated via chemoautotrophy and heterotrophy in the amended prokaryotic communities was used for the biosynthesis of glycogen and phospholipids as storage molecules. The addition of thiosulfate stimulated unclassified bacteria, sulfur-oxidizing Deltaproteobacteria (SAR324 cluster bacteria), Epsilonproteobacteria (Sulfurimonas sp.), and Gammaproteobacteria (SUP05 cluster bacteria), whereas, the amendment with thiosulfate plus DOM stimulated typically copiotrophic Gammaproteobacteria (closely related to Vibrio sp. and Pseudoalteromonas sp.).

CONCLUSIONS: The gene expression pattern of thiosulfate utilizing microbes specifically of genes involved in energy production via sulfur oxidation and coupled to CO2 fixation pathways coincided with the change in the transcriptional profile of the heterotrophic prokaryotic community (genes involved in promoting energy storage), suggesting a fine-tuned metabolic interplay between chemoautotrophic and heterotrophic microbes in the dark ocean. Video Abstract.}, } @article {pmid37914135, year = {2024}, author = {Hulme, PE and Ahmed, DA and Haubrock, PJ and Kaiser, BA and Kourantidou, M and Leroy, B and McDermott, SM}, title = {Widespread imprecision in estimates of the economic costs of invasive alien species worldwide.}, journal = {The Science of the total environment}, volume = {909}, number = {}, pages = {167997}, doi = {10.1016/j.scitotenv.2023.167997}, pmid = {37914135}, issn = {1879-1026}, mesh = {*Introduced Species ; Reproducibility of Results ; Databases, Factual ; *Research Design ; }, abstract = {Several hundred studies have attempted to estimate the monetary cost arising from the management and/or impacts of invasive alien species. However, the diversity of methods used to estimate the monetary costs of invasive alien species, the types of costs that have been reported, and the spatial scales at which they have been assessed raise important questions as to the precision of these reported monetary costs. Benford's Law has been increasingly used as a diagnostic tool to assess the accuracy and reliability of estimates reported in financial accounts but has rarely been applied to audit data on environmental costs. Therefore, the distributions of first, second- and leading double-digits of the monetary costs arising from biological invasions, as reported in the InvaCost database, were compared with the null expectations under Benford's Law. There was strong evidence that the reported monetary costs of biological invasions departed considerably from Benford's Law and the departures were of a scale equal to that found in global macroeconomic data. The rounding upwards of costs appears to be widespread. Furthermore, numerical heaping, where values cluster around specific numbers was evident with only 901 unique cost values accounting for half of the 13,553 cost estimates within the InvaCost database. Irrespective of the currency, the value of 1,000,000 was the most common cost estimate. An investigation of anomalous data entries concluded that non-peer reviewed official government reports need to provide greater detail regarding how costs are estimated. Despite the undeniably high economic cost of biological invasions worldwide, individual records of costs were often found to be imprecise and possibly inflated and this emphasises the need for greater transparency and rigour when reporting the costs of biological invasions. Identifying whether the irregularities found for the costs of biological invasions are general for other types of environmental costs should be a research priority.}, } @article {pmid37907108, year = {2024}, author = {Zhao, Y and Jia, H and Deng, H and Ge, C and Xing, W and Yu, H and Li, J}, title = {Integrated microbiota and multi-omics analysis reveal the differential responses of earthworm to conventional and biodegradable microplastics in soil under biogas slurry irrigation.}, journal = {The Science of the total environment}, volume = {907}, number = {}, pages = {168191}, doi = {10.1016/j.scitotenv.2023.168191}, pmid = {37907108}, issn = {1879-1026}, mesh = {Animals ; Soil ; *Oligochaeta ; Biofuels ; Microplastics ; Multiomics ; Plastics ; Polyethylene ; *Biodegradable Plastics ; *Microbiota ; Polyesters ; *Soil Pollutants/toxicity ; }, abstract = {As one of the promising alternatives of conventional plastic mulching film (C-PMF), biodegradable plastic mulching films (B-PMF) were employed in agronomy production to alleviate the environmental burden of C-PMF. However, information regarding the potential toxicity effects of biodegradable microplastics (MPs) in soil still in scarcity, and the available findings were found to be controversial. Additionally, little is known about the molecular toxicity effects of conventional and biodegradable MPs on terrestrial organisms. Thus, 5 % (w/w) biodegradable (polylactic acid, PLA) and conventional (polyvinylchloride, PVC; low-density polyvinylchloride, LDPE) MPs were employed to assess the toxicity effects on Eisenia fetida in agricultural soil with biogas slurry irrigation. In the present study, transcriptomic, metabolomic profiles and individual indexes were selected to reveal the toxicity mechanisms from molecular level to the individual response. Furthermore, dysbiosis of bacterial community in gut was also investigated for obtaining comprehensive knowledge on the MPs toxicity. At the end of the exposure, the number of survival earthworms after MPs exposure was significantly reduced. Compared with the initial body weight, PLA and LDPE increased the biomass of earthworms after MPs exposure, while no significant influence on the biomass was observed in PVC treatment. Microbacterium, Klebsiella and Chryseobacterium were significantly enriched in earthworm gut after PLA, PVC and LDPE exposure, respectively (p < 0.05). Transcriptomic and metabolomic analysis revealed that PLA exposure induced neurotransmission disorder and high energetic expenditure in earthworms. However, PVC and LDPE inhibited the nutrient absorption efficiency and activated the innate immunity responses of earthworms. The PLS-SEM results showed that the effects of MPs were dominated by the polymer types, and hence, significantly and directly influence the gut bacterial community of earthworms. This study provides a better understanding of the similarities and discrepancies in toxicity effects of biodegradable and conventional MPs from the perspectives of individual, gut bacterial community, transcriptome and metabolome.}, } @article {pmid37905937, year = {2023}, author = {Rihacek, M and Kosaristanova, L and Fialova, T and Kuthanova, M and Eichmeier, A and Hakalova, E and Cerny, M and Berka, M and Palkovicova, J and Dolejska, M and Svec, P and Adam, V and Zurek, L and Cihalova, K}, title = {Zinc effects on bacteria: insights from Escherichia coli by multi-omics approach.}, journal = {mSystems}, volume = {8}, number = {6}, pages = {e0073323}, pmid = {37905937}, issn = {2379-5077}, support = {CZ.02.2.69/0.0/0.0/19_073/0016670//EC | EU Social | European Social Fund (ESF)/ ; CZ.02.2.69/0.0/0.0/19_073/0016670//EC | EU Social | European Social Fund (ESF)/ ; CZ.02.2.69/0.0/0.0/19_073/0016670//EC | EU Social | European Social Fund (ESF)/ ; CZ.02.2.69/0.0/0.0/19_073/0016670//EC | EU Social | European Social Fund (ESF)/ ; CZ.02.2.69/0.0/0.0/19_073/0016670//EC | EU Social | European Social Fund (ESF)/ ; }, mesh = {Humans ; Animals ; *Zinc/pharmacology ; *Zinc Oxide/chemistry ; Escherichia coli/genetics ; Multiomics ; Proteomics ; }, abstract = {A long-term exposure of bacteria to zinc oxide and zinc oxide nanoparticles leads to major alterations in bacterial morphology and physiology. These included biochemical and physiological processes promoting the emergence of strains with multi-drug resistance and virulence traits. After the removal of zinc pressure, bacterial phenotype reversed back to the original state; however, certain changes at the genomic, transcriptomic, and proteomic level remained. Why is this important? The extensive and intensive use of supplements in animal feed effects the intestinal microbiota of livestock and this may negatively impact the health of animals and people. Therefore, it is crucial to understand and monitor the impact of feed supplements on intestinal microorganisms in order to adequately assess and prevent potential health risks.}, } @article {pmid37905717, year = {2024}, author = {Liu, L and Chen, J and Shen, M and Chen, X and Cao, R and Cao, X and Cui, X and Yang, W and Zhu, X and Li, L and Tang, Y}, title = {A remote sensing method for mapping alpine grasslines based on graph-cut.}, journal = {Global change biology}, volume = {30}, number = {1}, pages = {e17005}, doi = {10.1111/gcb.17005}, pmid = {37905717}, issn = {1365-2486}, support = {//Fundamental Research Funds for the Central Universities/ ; 2019QZKK0405//Second Tibetan Plateau Scientific Expedition and Research Program/ ; 2019QZKK0106//Second Tibetan Plateau Scientific Expedition and Research Program/ ; 20190ZKK0307//Second Tibetan Plateau Scientific Expedition and Research Program/ ; //Top-Notch Young Talents Program of China/ ; 23K18517//Japan Society for the Promotion of Science (JSPS) KAKENHI/ ; }, mesh = {*Remote Sensing Technology ; *Climate Change ; Tibet ; Grassland ; Ecosystem ; }, abstract = {Climate change has induced substantial shifts in vegetation boundaries such as alpine treelines and shrublines, with widespread ecological and climatic influences. However, spatial and temporal changes in the upper elevational limit of alpine grasslands ("alpine grasslines") are still poorly understood due to lack of field observations and remote sensing estimates. In this study, taking the Tibetan Plateau as an example, we propose a novel method for automatically identifying alpine grasslines from multi-source remote sensing data and determining their positions at 30-m spatial resolution. We first identified 2895 mountains potentially having alpine grasslines. On each mountain, we identified a narrow area around the upper elevational limit of alpine grasslands where the alpine grassline was potentially located. Then, we used linear discriminant analysis to adaptively generate from Landsat reflectance features a synthetic feature that maximized the difference between vegetated and unvegetated pixels in each of these areas. After that, we designed a graph-cut algorithm to integrate the advantages of the Otsu and Canny approaches, which was used to determine the precise position of the alpine grassline from the synthetic feature image. Validation against alpine grasslines visually interpreted from a large number of high-spatial-resolution images showed a high level of accuracy (R[2] , .99 and .98; mean absolute error, 22.6 and 36.2 m, vs. drone and PlanetScope images, respectively). Across the Tibetan Plateau, the alpine grassline elevation ranged from 4038 to 5380 m (5th-95th percentile), lower in the northeast and southeast and higher in the southwest. This study provides a method for remotely sensing alpine grasslines for the first-time at large scale and lays a foundation for investigating their responses to climate change.}, } @article {pmid37903262, year = {2023}, author = {Lien, AM and Banki, O and Barik, SK and Buckeridge, JS and Christidis, L and Cigliano, MM and Conix, S and Costello, MJ and Hobern, D and Kirk, PM and Kroh, A and Montgomery, N and Nikolaeva, S and Orrell, TM and Pyle, RL and Raz, L and Thiele, K and Thomson, SA and van Dijk, PP and Wambiji, N and Whalen, A and Zachos, FE and Zhang, ZQ and Garnett, ST}, title = {Widespread support for a global species list with a formal governance system.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {120}, number = {45}, pages = {e2306899120}, pmid = {37903262}, issn = {1091-6490}, support = {IUBS//International Union of Biological Sciences/ ; DP230102933//Australian Research Council/ ; T.0177.21//Fonds De La Recherche Scientifique - FNRS (FNRS)/ ; }, mesh = {Humans ; *Commerce ; Internationality ; *Physicians ; }, abstract = {Taxonomic data are a scientific common. Unlike nomenclature, which has strong governance institutions, there are currently no generally accepted governance institutions for the compilation of taxonomic data into an accepted global list. This gap results in challenges for conservation, ecological research, policymaking, international trade, and other areas of scientific and societal importance. Consensus on a global list and its management requires effective governance and standards, including agreed mechanisms for choosing among competing taxonomies and partial lists. However, governance frameworks are currently lacking, and a call for governance in 2017 generated critical responses. Any governance system to which compliance is voluntary requires a high level of legitimacy and credibility among those by and for whom it is created. Legitimacy and credibility, in turn, require adequate and credible consultation. Here, we report on the results of a global survey of taxonomists, scientists from other disciplines, and users of taxonomy designed to assess views and test ideas for a new system of taxonomic list governance. We found a surprisingly high degree of agreement on the need for a global list of accepted species and their names, and consistent views on what such a list should provide to users and how it should be governed. The survey suggests that consensus on a mechanism to create, manage, and govern a single widely accepted list of all the world's species is achievable. This finding was unexpected given past controversies about the merits of list governance.}, } @article {pmid37898720, year = {2023}, author = {Jin, Q and Gheeya, J and Nepal, S and Shi, N and Folefac, E and Webb, MZ and Grainger, EM and Wei, L and Prosek, JM and Focht, BC and Gong, M and Clinton, SK and Tabung, FK}, title = {Associations of dietary patterns with kidney cancer risk, kidney cancer-specific mortality and all-cause mortality among postmenopausal women.}, journal = {British journal of cancer}, volume = {129}, number = {12}, pages = {1978-1987}, pmid = {37898720}, issn = {1532-1827}, support = {T32 CA247815/CA/NCI NIH HHS/United States ; 75N92021D00002/HL/NHLBI NIH HHS/United States ; 75N92021D00005/WH/WHI NIH HHS/United States ; 75N92021D00001/HL/NHLBI NIH HHS/United States ; 75N92021D00003/WH/WHI NIH HHS/United States ; P30 CA016058/CA/NCI NIH HHS/United States ; 75N92021D00004/WH/WHI NIH HHS/United States ; }, mesh = {Humans ; Female ; Postmenopause ; Prospective Studies ; Diet/adverse effects ; *Carcinoma, Renal Cell ; *Kidney Neoplasms ; Risk Factors ; }, abstract = {BACKGROUND: The empirical dietary index for hyperinsulinemia (EDIH) and empirical dietary inflammatory pattern (EDIP) are novel measures of dietary quality associated with insulin hypersecretion or chronic inflammation, respectively, whereas the Healthy Eating Index (HEI-2015) measures adherence to the Dietary Guidelines for Americans (DGA). We evaluated associations of EDIH, EDIP and HEI-2015 on the risk of both kidney cancer development and mortality.

METHODS: We calculated the dietary scores from baseline food frequency questionnaires among 115,830 participants aged 50-79 years in the Women's Health Initiative. Multivariable-adjusted Cox regression was used to estimate hazard ratios (HR) and 95% confidence intervals (95%CI) for kidney cancer risk, kidney cancer-specific mortality and all-cause mortality, per 1-standard deviation increment in dietary pattern scores.

RESULTS: Higher EDIH was associated with greater risk of kidney cancer development [HR, 1.12; 95%CI, (1.01,1.23)], kidney cancer-specific death [1.22(0.99,1.48)], and all-cause mortality, [1.05(1.02,1.08)]. Higher HEI-2015 was associated with lower risk of kidney cancer development, [0.85(0.77, 0.94)], kidney cancer-specific death, [0.84(0.69,1.03)] and all-cause mortality, [0.97(0.95,1.00)]. However, EDIP was not significantly associated with outcomes. Associations did not differ by BMI categories.

CONCLUSIONS: Low-insulinemic dietary patterns and higher quality diets, are worthy of testing in dietary pattern intervention trials for kidney cancer prevention and improved survivorship.}, } @article {pmid37898190, year = {2024}, author = {Huang, C and Guan, K and Qi, X and Liu, YE and Lu, Q and Zeng, Y and Wang, S and Luo, X and Mai, B}, title = {Spatial distribution, conversion, and ecological risk assessment of hexabromocyclododecanes in the sediments of black-odorous urban rivers nationwide in China.}, journal = {The Science of the total environment}, volume = {907}, number = {}, pages = {168057}, doi = {10.1016/j.scitotenv.2023.168057}, pmid = {37898190}, issn = {1879-1026}, mesh = {Rivers ; Environmental Monitoring/methods ; Geologic Sediments ; *Hydrocarbons, Brominated/analysis ; China ; Risk Assessment ; *Flame Retardants/analysis ; }, abstract = {Hexabromocyclododecanes (HBCDs) have become a global pollution problem, particularly in China-a major producer and user of HBCDs. However, little is known about the HBCD pollution status in urban rivers nationwide in China. In this study, we comprehensively investigated the pollution characteristics of HBCDs in 173 sediment samples from black-odorous urban rivers across China. Total HBCD concentrations ranged from not-detected to 848 ng/g dw, showing significant differences among the various sampling cities, but generally increasing from west to east China. This distribution pattern of HBCDs was strongly associated with the local industrial output, gross domestic product, and daily wastewater treatment capacity. α-HBCD was the predominant diastereoisomer in most sediments, with an average proportion of 63.8 ± 18.8 %, followed by γ-HBCD (23.8 ± 19.5 %) and β-HBCD (12.4 ± 6.49 %), showing a significant increase of the α-HBCD proportions relative to those in HBCD commercial mixtures and an opposite trend for that of γ-HBCD. These results suggested that HBCDs might undergo isomerization from γ- to α-HBCD and biotic/abiotic degradation with preference for γ-HBCD. Of these conversions, the microbial degradation of HBCDs was further verified by the preferential transformation of (-)-α-, (+)-β-, and (-)-γ-HBCDs and the detection of HBCD-degrading bacteria, including Dehalococcoides, Bacillus, Sphingobium, and Pseudomonas. A risk assessment indicated that HBCDs pose low to moderate risks to aquatic organisms in most black-odorous urban river sediments.}, } @article {pmid37898004, year = {2023}, author = {Karakurt-Fischer, S and Johnson, DR and Fenner, K and Hafner, J}, title = {Making waves: Enhancing pollutant biodegradation via rational engineering of microbial consortia.}, journal = {Water research}, volume = {247}, number = {}, pages = {120756}, doi = {10.1016/j.watres.2023.120756}, pmid = {37898004}, issn = {1879-2448}, mesh = {Microbial Consortia ; *Environmental Pollutants/metabolism ; Biodegradation, Environmental ; Bacteria/genetics/metabolism ; Soil/chemistry ; *Soil Pollutants/metabolism ; Soil Microbiology ; }, abstract = {Biodegradation holds promise as an effective and sustainable process for the removal of synthetic chemical pollutants. Nevertheless, rational engineering of biodegradation for pollutant remediation remains an unfulfilled goal, while chemical pollution of waters and soils continues to advance. Efforts to (i) identify functional bacteria from aquatic and soil microbiomes, (ii) assemble them into biodegrading consortia, and (iii) identify maintenance and performance determinants, are challenged by large number of pollutants and the complexity in the enzymology and ecology of pollutant biodegradation. To overcome these challenges, approaches that leverage knowledge from environmental bio-chem-informatics and metabolic engineering are crucial. Here, we propose a novel high-throughput bio-chem-informatics pipeline, to link chemicals and their predicted biotransformation pathways with potential enzymes and bacterial strains. Our framework systematically selects the most promising candidates for the degradation of chemicals with unknown biotransformation pathways and associated enzymes from the vast array of aquatic and soil bacteria. We substantiated our perspective by validating the pipeline for two chemicals with known or predicted pathways and show that our predicted strains are consistent with strains known to biotransform those chemicals. Such pipelines can be integrated with metabolic network analysis built upon genome-scale models and ecological principles to rationally design fit-for-purpose bacterial communities for augmenting deficient biotransformation functions and study operational and design parameters that influence their structure and function. We believe that research in this direction can pave the way for achieving our long-term goal of enhancing pollutant biodegradation.}, } @article {pmid37897291, year = {2023}, author = {Zhang, HS and Zhong, XM and Xiong, Y and Wu, XR}, title = {[Big data analysis of coastal illegal fishing from the perspective of compensation of ecological and environmental damage].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {34}, number = {10}, pages = {2827-2834}, doi = {10.13287/j.1001-9332.202310.032}, pmid = {37897291}, issn = {1001-9332}, mesh = {Big Data ; China ; Conservation of Natural Resources/methods ; *Ecosystem ; *Hunting ; }, abstract = {Illegal fishing is one of the sources of marine ecological damage. The implementation of compensation of ecological and environmental damage in this field is poorly understood. In this study, we examined data pertaining to coastal illegal fishing cases during 2018-2022 using the big data publicly made available by China Judgement Online. The main results included: 1) there are numerous types of illegal fishing, and more efforts should focus on the nature and extent of illegal fishing, with electrofishing and trawl being suitable entry points; 2) Special attention should be paid to the variation characteristics of rakes in the range of high illegal catch weight and value. It was suggested to optimize and adjust its management mode to avoid the frequent occurrence of such illegal fishing cases of rake; 3) The varieties of assessment models increased the uncertainty of damages computation, which might be reduced by establishing strong criteria for value quantification and damage assessment; 4) There is limited scientific support for the compensation for releasing the most popular ecological restoration technique for illegal fishing. As a result, the "compensation" design for "restoration" should be implemented, while the potential for additional restoration methods should be investigated.}, } @article {pmid37895673, year = {2023}, author = {Dudek, M and Sąsiadek-Andrzejczak, E and Jaszczak-Kuligowska, M and Rokita, B and Kozicki, M}, title = {The Surface Modification of Papers Using Laser Processing towards Applications.}, journal = {Materials (Basel, Switzerland)}, volume = {16}, number = {20}, pages = {}, pmid = {37895673}, issn = {1996-1944}, abstract = {This work presents the results of paper laser processing. It begins with the selection and examination of the processing parameters, then an examination of the properties of the modified papers and examples of applications of the developed modification method. The properties of laser-modified paper were studied using reflectance spectrophotometry to examine the colour aspects of the modified papers, scanning electron microscopy (SEM) and confocal microscopy for a morphological analysis, and Raman spectroscopy to analyse the papers under the influence of laser light. The influence of laser processing on the wettability of paper and the evenness of unprinted and printed paper was also investigated. The knowledge gained on paper surface modification with laser light was used to propose several applications, such as methods of marking, tactile detection, the controlled removal of optical brightener, ink, and metallised coatings from paper packaging, highlighting the design and aesthetics of paper. The developed laser-assisted method shows a promising, ecological approach to the design of many value-added paper products.}, } @article {pmid37892395, year = {2023}, author = {Gutiérrez-Hellín, J and Del Coso, J and Espada, MC and Hernández-Beltrán, V and Ferreira, CC and Varillas-Delgado, D and Mendoza Laiz, N and Roberts, JD and Gamonales, JM}, title = {Research Trends in the Effect of Caffeine Intake on Fat Oxidation: A Bibliometric and Visual Analysis.}, journal = {Nutrients}, volume = {15}, number = {20}, pages = {}, pmid = {37892395}, issn = {2072-6643}, support = {UID04045/2020//Portuguese Foundation for Science and Technology/ ; GR21149//University of Extremadura/ ; }, mesh = {Humans ; United States ; Aged ; *Caffeine ; *Bibliometrics ; Netherlands ; Authorship ; Databases, Factual ; }, abstract = {In the last few decades, numerous studies pertaining to research groups worldwide have investigated the effects of oral caffeine intake on fat oxidation at rest, during exercise, and after exercise. However, there is no bibliometric analysis to assess the large volume of scientific output associated with this topic. A bibliometric analysis of this topic may be used by researchers to assess the current scientific interest in the application of caffeine as a nutritional strategy to augment fat oxidation, the journals with more interest in this type of publication, and to draw international collaborations between groups working in the same area. For these reasons, the purpose of this study was to assess the research activity regarding oral caffeine intake and fat oxidation rate in the last few decades by conducting a bibliometric and visual analysis. Relevant publications from 1992 to 2022 were retrieved from the Web of Science (WoS) Core Collection database. Quantitative and qualitative variables were collected, including the number of publications and citations, H-indexes, journals of citation reports, co-authorship, co-citation, and the co-occurrence of keywords. There were 182 total publications, while the number of annual publications is saw-shaped with a modest increase of 11.3% from 2000 to 2009 to 2010 to 2019. The United States was the country with the highest number of publications (24.17% of the total number of articles), followed by the Netherlands (17.03%). According to citation analyses, the average number of citations per document is 130, although there are 21 documents that have received more than 100 citations; the most cited document reached 644 citations. These citation data support the overall relevance of this topic in the fields of nutrition and dietetics and sport sciences that when combined harbored 85.71% of all articles published in the WoS. The most productive author was Westerterp-Plantenga with 16 articles (8.79% of the total number of articles). Nutrients was the journal that published the largest number of articles on this topic (6.59% of the total number of articles). Last, there is a tendency to include keywords such as "performance", "carbohydrate", and "ergogenic aid" in the newer articles, while "obesity", "thermogenic", and "tea" are the keywords more commonly included in older documents. Although research into the role of caffeine on fat oxidation has existed since the 1970s, our analysis suggests that the scientific output associated with this topic has progressively increased since 1992, demonstrating that this is a nutritional research area with a strong foundational base of scientific evidence. Based on the findings of this bibliometric analysis, future investigation may consider focusing on the effects of sex and tolerance to caffeine to widen the assessment of the effectiveness of oral caffeine intake as a nutritional strategy to augment the use of fat as a fuel, as these terms rarely appear in the studies included in this analysis. Additionally, more translational research is necessary as the studies that investigate the effect of oral caffeine intake in ecologically valid contexts (i.e., exercise training programs for individuals with excessive adiposity) are only a minor part of the studies on this topic.}, } @article {pmid37889410, year = {2023}, author = {Jalil, F and Yang, J and Rehman, SU and Khan, MM}, title = {Post-COVID-19's impact on green supply chain management and sustainable E-commerce performance: the moderating role of big data analytics.}, journal = {Environmental science and pollution research international}, volume = {30}, number = {54}, pages = {115683-115698}, pmid = {37889410}, issn = {1614-7499}, mesh = {*Commerce ; COVID-19 ; Data Science ; *Industry ; *Big Data ; Data Analysis ; *Sustainable Development ; Internet ; Pakistan ; }, abstract = {This study investigates the relationship between COVID-19 and the adoption of green supply chain management practices (GSCM) in the Pakistani e-commerce industry. It also assesses the impact of these practices on ecological sustainability across three dimensions and explores the role of big data analytics (BDA) in enhancing them after the pandemic. The research utilized partial least squares structural equation modeling to evaluate data and test hypotheses. The research sample was composed of 390 managers operating within Pakistan's e-commerce industry. The study's preliminary findings reveal that COVID-19 has positively influenced the adoption of GSCM practices, which are moderated by BDA. Implementing GSCM has a positive impact on the perceived environmental and social resilience of e-commerce enterprises, but no significant effect on their perceived economic resilience. Additionally, GSCM acts as a mediator in the relationship between the impact of COVID-19 and the perceived environmental and social resilience of e-commerce firms, but not for economic resilience. This research focuses on Pakistan's e-commerce industry and investigates how COVID-19 affects the adoption of eco-friendly supply chain practices. It measures the impact of these practices on ecological sustainability using three dimensions. The study also examines how BDA can improve the adoption of GSCM in e-commerce, offering new insights into sustainability during and post-pandemic. The results recommend that the e-commerce industry can use BDA and GSCM practices to improve e-commerce sustainable performance. This is initial research that integrates COVID-19 impact, BDA, GSCM practices, and e-commerce sustainability in a single framework that was overlooked previously.}, } @article {pmid37888680, year = {2023}, author = {Zhu, X and Ji, H and Hua, G and Zhou, L}, title = {Dynamic Release Characteristics and Kinetics of a Persulfate Sustained-Release Material.}, journal = {Toxics}, volume = {11}, number = {10}, pages = {}, pmid = {37888680}, issn = {2305-6304}, support = {2020YFC1806502//The National Key Research and Development Project of China/ ; }, abstract = {Sustained-release materials are increasingly being used in the delivery of oxidants for in situ chemical oxidation (ISCO) for groundwater remediation. Successful implementation of sustained-release materials depends on a clear understanding of the mechanism and kinetics of sustained release. In this research, a columnar sustained-release material (PS@PW) was prepared with paraffin wax and sodium persulfate (PS), and column experiments were performed to investigate the impacts of the PS@PW diameter and PS/PW mass ratio on PS release. The results demonstrated that a reduction in diameter led to an increase in both the rate and proportion of PS release, as well as a diminished lifespan of release. The release process followed the second-order kinetics, and the release rate constant was positively correlated with the PS@PW diameter. A matrix boundary diffusion model was utilized to determine the PS@PW diffusion coefficient of the PS release process, and the release lifespan of a material with a length of 500 mm and a diameter of 80 mm was predicted to be more than 280 days. In general, this research provided a better understanding of the release characteristics and kinetics of persulfate from a sustained-release system and could lead to the development of columnar PS@PW as a practical oxidant for in situ chemical oxidation of contaminated aquifers.}, } @article {pmid37885811, year = {2023}, author = {Boyes, D and Chua, P and , and , and , and , and , and , }, title = {The genome sequence of the Oak Hook-tip, Watsonalla binaria (Hufnagel, 1767).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {324}, pmid = {37885811}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual female Watsonalla binaria (the Oak Hook-tip; Arthropoda; Insecta; Lepidoptera; Drepanidae). The genome sequence is 333.0 megabases in span. Most of the assembly is scaffolded into 33 chromosomal pseudomolecules, including the W and Z sex chromosomes. The mitochondrial genome has also been assembled and is 15.24 kilobases in length. Gene annotation of this assembly on Ensembl identified 16,002 protein coding genes.}, } @article {pmid37883444, year = {2024}, author = {Kinkade, JA and Seetharam, AS and Sachdev, S and Bivens, NJ and Phinney, BS and Grigorean, G and Roberts, RM and Tuteja, G and Rosenfeld, CS}, title = {Extracellular vesicles from mouse trophoblast cells: Effects on neural progenitor cells and potential participants in the placenta-brain axis†.}, journal = {Biology of reproduction}, volume = {110}, number = {2}, pages = {310-328}, pmid = {37883444}, issn = {1529-7268}, support = {R01 ES025547/ES/NIEHS NIH HHS/United States ; R01 HD096083/HD/NICHD NIH HHS/United States ; S10 OD021801/OD/NIH HHS/United States ; R01HD096083/GF/NIH HHS/United States ; }, mesh = {Humans ; Pregnancy ; Female ; Animals ; Mice ; Serotonin/metabolism ; Placenta/metabolism ; *MicroRNAs/genetics/metabolism ; *Extracellular Vesicles/metabolism ; Brain/metabolism ; Trophoblasts/metabolism ; Stem Cells/metabolism ; }, abstract = {The fetal brain of the mouse is thought to be dependent upon the placenta as a source of serotonin (5-hydroxytryptamine; 5-HT) and other factors. How factors reach the developing brain remains uncertain but are postulated here to be part of the cargo carried by placental extracellular vesicles (EV). We have analyzed the protein, catecholamine, and small RNA content of EV from mouse trophoblast stem cells (TSC) and TSC differentiated into parietal trophoblast giant cells (pTGC), potential primary purveyors of 5-HT. Current studies examined how exposure of mouse neural progenitor cells (NPC) to EV from either TSC or pTGC affect their transcriptome profiles. The EV from trophoblast cells contained relatively high amounts of 5-HT, as well as dopamine and norepinephrine, but there were no significant differences between EV derived from pTGC and from TSC. Content of miRNA and small nucleolar (sno)RNA, however, did differ according to EV source, and snoRNA were upregulated in EV from pTGC. The primary inferred targets of the microRNA (miRNA) from both pTGC and TSC were mRNA enriched in the fetal brain. NPC readily internalized EV, leading to changes in their transcriptome profiles. Transcripts regulated were mainly ones enriched in neural tissues. The transcripts in EV-treated NPC that demonstrated a likely complementarity with miRNA in EV were mainly up- rather than downregulated, with functions linked to neuronal processes. Our results are consistent with placenta-derived EV providing direct support for fetal brain development and being an integral part of the placenta-brain axis.}, } @article {pmid37881861, year = {2024}, author = {Rick, JA and Brock, CD and Lewanski, AL and Golcher-Benavides, J and Wagner, CE}, title = {Reference Genome Choice and Filtering Thresholds Jointly Influence Phylogenomic Analyses.}, journal = {Systematic biology}, volume = {73}, number = {1}, pages = {76-101}, doi = {10.1093/sysbio/syad065}, pmid = {37881861}, issn = {1076-836X}, support = {DEB-1556963//National Science Foundation/ ; }, mesh = {*Phylogeny ; *Genome/genetics ; *Classification/methods ; Genomics/methods ; Computational Biology/methods ; }, abstract = {Molecular phylogenies are a cornerstone of modern comparative biology and are commonly employed to investigate a range of biological phenomena, such as diversification rates, patterns in trait evolution, biogeography, and community assembly. Recent work has demonstrated that significant biases may be introduced into downstream phylogenetic analyses from processing genomic data; however, it remains unclear whether there are interactions among bioinformatic parameters or biases introduced through the choice of reference genome for sequence alignment and variant calling. We address these knowledge gaps by employing a combination of simulated and empirical data sets to investigate the extent to which the choice of reference genome in upstream bioinformatic processing of genomic data influences phylogenetic inference, as well as the way that reference genome choice interacts with bioinformatic filtering choices and phylogenetic inference method. We demonstrate that more stringent minor allele filters bias inferred trees away from the true species tree topology, and that these biased trees tend to be more imbalanced and have a higher center of gravity than the true trees. We find the greatest topological accuracy when filtering sites for minor allele count (MAC) >3-4 in our 51-taxa data sets, while tree center of gravity was closest to the true value when filtering for sites with MAC >1-2. In contrast, filtering for missing data increased accuracy in the inferred topologies; however, this effect was small in comparison to the effect of minor allele filters and may be undesirable due to a subsequent mutation spectrum distortion. The bias introduced by these filters differs based on the reference genome used in short read alignment, providing further support that choosing a reference genome for alignment is an important bioinformatic decision with implications for downstream analyses. These results demonstrate that attributes of the study system and dataset (and their interaction) add important nuance for how best to assemble and filter short-read genomic data for phylogenetic inference.}, } @article {pmid37881225, year = {2023}, author = {Bald, L and Gottwald, J and Zeuss, D}, title = {spatialMaxent: Adapting species distribution modeling to spatial data.}, journal = {Ecology and evolution}, volume = {13}, number = {10}, pages = {e10635}, pmid = {37881225}, issn = {2045-7758}, abstract = {Conventional practices in species distribution modeling lack predictive power when the spatial structure of data is not taken into account. However, choosing a modeling approach that accounts for overfitting during model training can improve predictive performance on spatially separated test data, leading to more reliable models. This study introduces spatialMaxent (https://github.com/envima/spatialMaxent), a software that combines state-of-the-art spatial modeling techniques with the popular species distribution modeling software Maxent. It includes forward-variable-selection, forward-feature-selection, and regularization-multiplier tuning based on spatial cross-validation, which enables addressing overfitting during model training by considering the impact of spatial dependency in the training data. We assessed the performance of spatialMaxent using the National Center for Ecological Analysis and Synthesis dataset, which contains over 200 anonymized species across six regions worldwide. Our results show that spatialMaxent outperforms both conventional Maxent and models optimized according to literature recommendations without using a spatial tuning strategy in 80 percent of the cases. spatialMaxent is user-friendly and easily accessible to researchers, government authorities, and conservation practitioners. Therefore, it has the potential to play an important role in addressing pressing challenges of biodiversity conservation.}, } @article {pmid37881092, year = {2024}, author = {Wang, S and Ye, H and Shang, S and Li, Z and Peng, Y and Zhou, P}, title = {A Structure-based Data Set of Protein-peptide Affinities and its Nonredundant Benchmark: Potential Applications in Computational Peptidology.}, journal = {Current medicinal chemistry}, volume = {31}, number = {26}, pages = {4127-4137}, pmid = {37881092}, issn = {1875-533X}, mesh = {*Peptides/chemistry/metabolism ; *Databases, Protein ; *Proteins/chemistry/metabolism ; Protein Binding ; Molecular Docking Simulation ; Ligands ; Humans ; Protein Conformation ; }, abstract = {BACKGROUND: Peptides play crucial roles in diverse cellular functions and participate in many biological processes by interacting with a variety of proteins, which have also been exploited as a promising class of therapeutic agents to target druggable proteins over the past decades. Understanding the intrinsic association between the structure and affinity of protein-peptide interactions (PpIs) should be considerably valuable for the computational peptidology area, such as guiding protein-peptide docking calculations, developing protein-peptide affinity scoring functions, and designing peptide ligands for specific protein receptors.

OBJECTIVE: We attempted to create a data source for relating PpI structure to affinity.

METHODS: By exhaustively surveying the whole protein data bank (PDB) database as well as the ontologically enriched literature information, we manually curated a structure- based data set of protein-peptide affinities, PpI[S/A]DS, which assembled over 350 PpI complex samples with both the experimentally measured structure and affinity data. The data set was further reduced to a nonredundant benchmark consisting of 102 culled samples, PpI[S/A]BM, which only selected those of structurally reliable, functionally diverse and evolutionarily nonhomologous.

RESULTS: The collected structures were resolved at a high-resolution level with either Xray crystallography or solution NMR, while the deposited affinities were characterized by dissociation constant, i.e. Kd value, which is a direct biophysical measure of the intermolecular interaction strength between protein and peptide, ranging from subnanomolar to millimolar levels. The PpI samples in the set/benchmark were arbitrarily classified into α-helix, partial α-helix, β-sheet formed through binding, β-strand formed through selffolding, mixed, and other irregular ones, totally resulting in six classes according to the secondary structure of their peptide ligands. In addition, we also categorized these PpIs in terms of their biological function and binding behavior.

CONCLUSION: The PpI[S/A]DS set and PpI[S/A]BM benchmark can be considered a valuable data source in the computational peptidology community, aiming to relate the affinity to structure for PpIs.}, } @article {pmid37880625, year = {2023}, author = {Bernardini, I and Quagliariello, A and Peruzza, L and Martino, ME and Dalla Rovere, G and Iori, S and Asnicar, D and Ciscato, M and Fabrello, J and Corami, F and Cecchetto, M and Giubilato, E and Carrer, C and Bettiol, C and Semenzin, E and Marcomini, A and Matozzo, V and Bargelloni, L and Milan, M and Patarnello, T}, title = {Contaminants from dredged sediments alter the transcriptome of Manila clam and induce shifts in microbiota composition.}, journal = {BMC biology}, volume = {21}, number = {1}, pages = {234}, pmid = {37880625}, issn = {1741-7007}, mesh = {Animals ; Geologic Sediments/chemistry ; Transcriptome ; Dibenzofurans/metabolism ; *Water Pollutants, Chemical/toxicity/analysis/metabolism ; *Polychlorinated Dibenzodioxins/analysis/metabolism/toxicity ; *Bivalvia/genetics/chemistry/metabolism ; *Microbiota ; }, abstract = {BACKGROUND: The reuse of dredged sediments in ports and lagoons is a big issue as it should not affect the quality and the equilibrium of ecosystems. In the lagoon of Venice, sediment management is of crucial importance as sediments are often utilized to built-up structures necessary to limit erosion. However, the impact of sediment reuse on organisms inhabiting this delicate area is poorly known. The Manila clam is a filter-feeding species of high economic and ecological value for the Venice lagoon experiencing a drastic decline in the last decades. In order to define the molecular mechanisms behind sediment toxicity, we exposed clams to sediments sampled from different sites within one of the Venice lagoon navigable canals close to the industrial area. Moreover, we investigated the impacts of dredged sediments on clam's microbial communities.

RESULTS: Concentrations of the trace elements and organic chemicals showed increasing concentrations from the city of Venice to sites close to the industrial area of Porto Marghera, where PCDD/Fs and PCBs concentrations were up to 120 times higher than the southern lagoon. While bioaccumulation of organic contaminants of industrial origin reflected sediments' chemical concentrations, metal bioaccumulation was not consistent with metal concentrations measured in sediments probably due to the activation of ABC transporters. At the transcriptional level, we found a persistent activation of the mTORC1 signalling pathway, which is central in the coordination of cellular responses to chemical stress. Microbiota characterization showed the over-representation of potential opportunistic pathogens following exposure to the most contaminated sediments, leading to host immune response activation. Despite the limited acquisition of new microbial species from sediments, the latter play an important role in shaping Manila clam microbial communities.

CONCLUSIONS: Sediment management in the Venice lagoon will increase in the next years to maintain and create new canals as well as to allow the operation of the new mobile gates at the three Venice lagoon inlets. Our data reveal important transcriptional and microbial changes of Manila clams after exposure to sediments, therefore reuse of dredged sediments represents a potential risk for the conservation of this species and possibly for other organisms inhabiting the Venice lagoon.}, } @article {pmid37880359, year = {2023}, author = {Liang, D and Giam, X and Hu, S and Ma, L and Wilcove, DS}, title = {Assessing the illegal hunting of native wildlife in China.}, journal = {Nature}, volume = {623}, number = {7985}, pages = {100-105}, pmid = {37880359}, issn = {1476-4687}, mesh = {Animals ; Amphibians ; *Animals, Wild ; *Biodiversity ; Birds ; China ; Databases, Factual ; Endangered Species/economics/legislation & jurisprudence/statistics & numerical data ; *Hunting/economics/legislation & jurisprudence/statistics & numerical data ; Mammals ; Reptiles ; }, abstract = {Illegal harvesting and trading of wildlife have become major threats to global biodiversity and public health[1-3]. Although China is widely recognized as an important destination for wildlife illegally obtained abroad[4], little attention has been given to illegal hunting within its borders. Here we extracted 9,256 convictions for illegal hunting from a nationwide database of trial verdicts in China spanning January 2014 to March 2020. These convictions involved illegal hunting of 21% (n = 673) of China's amphibian, reptile, bird and mammal species, including 25% of imperilled species in these groups. Sample-based extrapolation indicates that many more species were taken illegally during this period. Larger body mass and range size (for all groups), and proximity to urban markets (for amphibians and birds) increase the probability of a species appearing in the convictions database. Convictions pertained overwhelmingly to illegal hunting for commercial purposes and involved all major habitats across China. A small number of convictions represented most of the animals taken, indicating the existence of large commercial poaching operations. Prefectures closer to urban markets show higher densities of convictions and more individual animals taken. Our results suggest that illegal hunting is a major, overlooked threat to biodiversity throughout China.}, } @article {pmid37880224, year = {2023}, author = {Sonkoly, J and Tóth, E and Balogh, N and Balogh, L and Bartha, D and Csendesné Bata, K and Bátori, Z and Békefi, N and Botta-Dukát, Z and Bölöni, J and Csecserits, A and Csiky, J and Csontos, P and Dancza, I and Deák, B and Dobolyi, ZK and E-Vojtkó, A and Gyulai, F and Hábenczyus, AA and Henn, T and Horváth, F and Höhn, M and Jakab, G and Kelemen, A and Király, G and Kis, S and Kovacsics-Vári, G and Kun, A and Lehoczky, É and Lengyel, A and Lhotsky, B and Löki, V and Lukács, BA and Matus, G and McIntosh-Buday, A and Mesterházy, A and Miglécz, T and Molnár V, A and Molnár, Z and Morschhauser, T and Papp, L and Pósa, P and Rédei, T and Schmidt, D and Szmorad, F and Takács, A and Tamás, J and Tiborcz, V and Tölgyesi, C and Tóth, K and Tóthmérész, B and Valkó, O and Virók, V and Wirth, T and Török, P}, title = {PADAPT 1.0 - the Pannonian Dataset of Plant Traits.}, journal = {Scientific data}, volume = {10}, number = {1}, pages = {742}, pmid = {37880224}, issn = {2052-4463}, support = {K 119225//Nemzeti Kutatási, Fejlesztési és Innovációs Hivatal (NKFI Office)/ ; K 137573//Nemzeti Kutatási, Fejlesztési és Innovációs Hivatal (NKFI Office)/ ; KKP 144068//Nemzeti Kutatási, Fejlesztési és Innovációs Hivatal (NKFI Office)/ ; PD 137747//Nemzeti Kutatási, Fejlesztési és Innovációs Hivatal (NKFI Office)/ ; KH 130320//Nemzeti Kutatási, Fejlesztési és Innovációs Hivatal (NKFI Office)/ ; PD 138859//Nemzeti Kutatási, Fejlesztési és Innovációs Hivatal (NKFI Office)/ ; PD 138715//Nemzeti Kutatási, Fejlesztési és Innovációs Hivatal (NKFI Office)/ ; PD 137828//Nemzeti Kutatási, Fejlesztési és Innovációs Hivatal (NKFI Office)/ ; BO/00587/23/8//Magyar Tudományos Akadémia (Hungarian Academy of Sciences)/ ; }, mesh = {Databases, Factual ; Europe ; Geography ; *Plants ; }, abstract = {The existing plant trait databases' applicability is limited for studies dealing with the flora and vegetation of the eastern and central part of Europe and for large-scale comparisons across regions, mostly because their geographical data coverage is limited and they incorporate records from several different sources, often from regions with markedly different climatic conditions. These problems motivated the compilation of a regional dataset for the flora of the Pannonian region (Eastern Central Europe). PADAPT, the Pannonian Dataset of Plant Traits relies on regional data sources and collates data on 54 traits and attributes of the plant species of the Pannonian region. The current version covers approximately 90% of the species of the region and consists of 126,337 records on 2745 taxa. By including species of the eastern part of Europe not covered by other databases, PADAPT can facilitate studying the flora and vegetation of the eastern part of the continent. Although data coverage is far from complete, PADAPT meets the longstanding need for a regional database of the Pannonian flora.}, } @article {pmid37879178, year = {2023}, author = {Li, D and Guan, X and Tang, T and Zhao, L and Tong, W and Wang, Z}, title = {The clean energy development path and sustainable development of the ecological environment driven by big data for mining projects.}, journal = {Journal of environmental management}, volume = {348}, number = {}, pages = {119426}, doi = {10.1016/j.jenvman.2023.119426}, pmid = {37879178}, issn = {1095-8630}, mesh = {*Sustainable Development ; *Carbon Dioxide ; Big Data ; Mining ; Economic Development ; Renewable Energy ; }, abstract = {Clean energy is urgently needed to realize mining projects' sustainable development (SD). This study aims to discuss the clean energy development path and the related issues of SD in the ecological environment driven by big data for mining projects. This study adopts a comprehensive research approach, including a literature review, case analysis, and model construction. Firstly, an in-depth literature review of the development status of clean energy is carried out, and the existing research results and technology applications are explored. Secondly, some typical mining projects are selected as cases to discuss the practice and effect of their clean energy application. Finally, the corresponding clean energy development path and the SD analysis model of the ecological environment are constructed based on big data technology to evaluate the feasibility and potential benefits of promoting and applying clean energy in mining projects. (1) It is observed that under different Gross Domestic Product (GDP) growth rates, the new and cumulative installed capacities of wind energy show an increasing trend. In 2022, under the low GDP growth rate, the cumulative installed capacity of global wind energy was 370.60 Gigawatt (GW), and the new installed capacity was 45 GW. With the high GDP growth rate, the cumulative and new installed capacities were 367.83 GW and 46 GW. As the economy grows, new wind energy capacity is expected to increase significantly by 2030. In 2046, 2047, and 2050, carbon dioxide (CO2) emissions reductions are projected to be 8183.35, 8539.22, and 9842.73 Million tons (Mt) (low scenario), 8750.68, 9087.16, and 10,468.75 Mt (medium scenario), and 9083.03, 9458.86, and 10,879.58 Mt (high scenario). By 2060, it is expected that CO2 emissions reduction will continue to increase. (2) The proposed clean energy development path model has achieved a good effect. Through this study, it is hoped to provide empirical support and decision-making reference for the development of mining projects in clean energy, and promote the SD of the mining industry, thus achieving a win-win situation of economic and ecological benefits. This is of great significance for protecting the ecological environment and realizing the sustainable utilization of resources.}, } @article {pmid37877166, year = {2024}, author = {Santos, CAQ and Tseng, M and Martinez, AI and Shankaran, S and Hodgson, HA and Ahmad, FS and Zhang, H and Sievert, DM and Trick, WE}, title = {Comparative antimicrobial use in coronavirus disease 2019 (COVID-19) and non-COVID-19 inpatients from 2019 to 2020: A multicenter ecological study.}, journal = {Infection control and hospital epidemiology}, volume = {45}, number = {3}, pages = {335-342}, doi = {10.1017/ice.2023.180}, pmid = {37877166}, issn = {1559-6834}, mesh = {Humans ; *COVID-19 ; SARS-CoV-2 ; Retrospective Studies ; Inpatients ; Anti-Bacterial Agents/therapeutic use ; *Cross Infection ; }, abstract = {OBJECTIVE: We sought to determine whether increased antimicrobial use (AU) at the onset of the coronavirus disease 2019 (COVID-19) pandemic was driven by greater AU in COVID-19 patients only, or whether AU also increased in non-COVID-19 patients.

DESIGN: In this retrospective observational ecological study from 2019 to 2020, we stratified inpatients by COVID-19 status and determined relative percentage differences in median monthly AU in COVID-19 patients versus non-COVID-19 patients during the COVID-19 period (March-December 2020) and the pre-COVID-19 period (March-December 2019). We also determined relative percentage differences in median monthly AU in non-COVID-19 patients during the COVID-19 period versus the pre-COVID-19 period. Statistical significance was assessed using Wilcoxon signed-rank tests.

SETTING: The study was conducted in 3 acute-care hospitals in Chicago, Illinois.

PATIENTS: Hospitalized patients.

RESULTS: Facility-wide AU for broad-spectrum antibacterial agents predominantly used for hospital-onset infections was significantly greater in COVID-19 patients versus non-COVID-19 patients during the COVID-19 period (with relative increases of 73%, 66%, and 91% for hospitals A, B, and C, respectively), and during the pre-COVID-19 period (with relative increases of 52%, 64%, and 66% for hospitals A, B, and C, respectively). In contrast, facility-wide AU for all antibacterial agents was significantly lower in non-COVID-19 patients during the COVID-19 period versus the pre-COVID-19 period (with relative decreases of 8%, 7%, and 8% in hospitals A, B, and C, respectively).

CONCLUSIONS: AU for broad-spectrum antimicrobials was greater in COVID-19 patients compared to non-COVID-19 patients at the onset of the pandemic. AU for all antibacterial agents in non-COVID-19 patients decreased in the COVID-19 period compared to the pre-COVID-19 period.}, } @article {pmid37874849, year = {2023}, author = {Mwangungulu, SP and Dorothea, D and Ngereja, ZR and Kaindoa, EW}, title = {Geospatial based model for malaria risk prediction in Kilombero valley, South-eastern, Tanzania.}, journal = {PloS one}, volume = {18}, number = {10}, pages = {e0293201}, pmid = {37874849}, issn = {1932-6203}, support = {/WT_/Wellcome Trust/United Kingdom ; 216448/Z/19/Z/WT_/Wellcome Trust/United Kingdom ; 107768/Z/15/Z/WT_/Wellcome Trust/United Kingdom ; /DH_/Department of Health/United Kingdom ; }, mesh = {Humans ; Tanzania/epidemiology ; *Malaria/epidemiology/prevention & control ; Environment ; Geographic Information Systems ; Public Health ; }, abstract = {BACKGROUND: Malaria continues to pose a major public health challenge in tropical regions. Despite significant efforts to control malaria in Tanzania, there are still residual transmission cases. Unfortunately, little is known about where these residual malaria transmission cases occur and how they spread. In Tanzania for example, the transmission is heterogeneously distributed. In order to effectively control and prevent the spread of malaria, it is essential to understand the spatial distribution and transmission patterns of the disease. This study seeks to predict areas that are at high risk of malaria transmission so that intervention measures can be developed to accelerate malaria elimination efforts.

METHODS: This study employs a geospatial based model to predict and map out malaria risk area in Kilombero Valley. Environmental factors related to malaria transmission were considered and assigned valuable weights in the Analytic Hierarchy Process (AHP), an online system using a pairwise comparison technique. The malaria hazard map was generated by a weighted overlay of the altitude, slope, curvature, aspect, rainfall distribution, and distance to streams in Geographic Information Systems (GIS). Finally, the risk map was created by overlaying components of malaria risk including hazards, elements at risk, and vulnerability.

RESULTS: The study demonstrates that the majority of the study area falls under moderate risk level (61%), followed by the low risk level (31%), while the high malaria risk area covers a small area, which occupies only 8% of the total area.

CONCLUSION: The findings of this study are crucial for developing spatially targeted interventions against malaria transmission in residual transmission settings. Predicted areas prone to malaria risk provide information that will inform decision-makers and policymakers for proper planning, monitoring, and deployment of interventions.}, } @article {pmid37872949, year = {2023}, author = {Ahmad, K and Shankar Pacha, A and Yahya Naqash, R and Kumar Peddamma, S and Yellapu, S and Hudson, S and Singh Baghel, D and Nigam, P and Mondol, S}, title = {Evolutionary insights on critically endangered Kashmir red deer or hangul (Cervus hanglu hanglu) through a mitogenomic lens.}, journal = {PeerJ}, volume = {11}, number = {}, pages = {e15746}, pmid = {37872949}, issn = {2167-8359}, mesh = {Animals ; Phylogeny ; Bayes Theorem ; *Deer/genetics ; Biological Evolution ; Phylogeography ; }, abstract = {BACKGROUND: The Kashmir red deer or Hangul (Cervus hanglu hanglu) is the only Tarim red deer species endemic to India. With a current estimated population size of fewer than 200 individuals, this critically endangered species is confined to the greater Dachigam landscape in Jammu and Kashmir. Poaching, habitat loss and fragmentation, resource competition with livestock, and small population size are the major conservation challenges for this species.

METHODS: Blood sampling was conducted from two wild Hangul individuals during radio-collaring operations at Dachigam National Park, Kashmir in 2013 and 2020, respectively. Using next-generation sequencing approach, we sequenced the 16,351 bp long mitogenome of two wild-caught Hangul individuals (1 M:1 F at ~14× and ~10× coverage, respectively) from Dachigam National Park.

RESULTS: The annotated sequences were identical with an AT-rich composition, including 13 protein-coding genes (11,354 bp), 22 tRNA genes (1,515 bp), two ribosomal genes (2,526 bp) and a non-coding control region (917 bp) in a conserved order like other red deer species. Bayesian phylogenetic reconstruction of the red deer complex revealed two major groups: the elaphoid and the wapitoid clades. Hangul formed a distinct clade with its other subspecies C. hanglu yarkandensis and is sister to the Hungarian red deer (C. elaphus hippelaphus). Divergence time analyses suggested that the Tarim deer species group separated ~1.55 Mya from their common ancestors and Hangul diverged ~0.75 Mya from closely related C. yarkandensis, corroborating with the known paleobiogeographic events related to refugia during glaciations in the Pleistocene era. This study provides baseline information on Hangul mitogenome for further research on phylogeography and other population parameters and helps in developing suitable conservation plans for this species.}, } @article {pmid37869838, year = {2023}, author = {Marceglia, S and Manzelli, V and Caruso, A and Prenassi, M and Prandin, R and Savino, C and Tacconi, D and Ferrucci, R and Conti, C and Candiani, G and Toraldo, C and Judica, E and Corbo, M and Masiero, M and Pravettoni, G}, title = {PainRE-Life: A FHIR Based Telemonitoring Ecosystem for the Management of Patients with Chronic Pain.}, journal = {Studies in health technology and informatics}, volume = {309}, number = {}, pages = {183-184}, doi = {10.3233/SHTI230773}, pmid = {37869838}, issn = {1879-8365}, mesh = {Humans ; *Chronic Pain/diagnosis/therapy ; Data Management ; *Electronic Health Records ; Italy ; }, abstract = {Chronic pain is a condition in which the use of digital health technologies, ecological momentary assessments, and digital communication tools may boost patient's engagement and coping. Here we present the results of the PainRE-Life a project, financed by the Lombardy Region (Italy), aimed to develop a dynamic and integrated technology ecosystem based on big data management and analysis to allow care continuity in patients with pain, and able to act as a decision aid for patients and caregivers.}, } @article {pmid37867198, year = {2023}, author = {Koludarov, I and Velasque, M and Senoner, T and Timm, T and Greve, C and Hamadou, AB and Gupta, DK and Lochnit, G and Heinzinger, M and Vilcinskas, A and Gloag, R and Harpur, BA and Podsiadlowski, L and Rost, B and Jackson, TNW and Dutertre, S and Stolle, E and von Reumont, BM}, title = {Prevalent bee venom genes evolved before the aculeate stinger and eusociality.}, journal = {BMC biology}, volume = {21}, number = {1}, pages = {229}, pmid = {37867198}, issn = {1741-7007}, mesh = {Bees/genetics ; Animals ; *Bee Venoms ; Gene Expression Profiling ; Transcriptome ; Genomics ; Gene Duplication ; }, abstract = {BACKGROUND: Venoms, which have evolved numerous times in animals, are ideal models of convergent trait evolution. However, detailed genomic studies of toxin-encoding genes exist for only a few animal groups. The hyper-diverse hymenopteran insects are the most speciose venomous clade, but investigation of the origin of their venom genes has been largely neglected.

RESULTS: Utilizing a combination of genomic and proteo-transcriptomic data, we investigated the origin of 11 toxin genes in 29 published and 3 new hymenopteran genomes and compiled an up-to-date list of prevalent bee venom proteins. Observed patterns indicate that bee venom genes predominantly originate through single gene co-option with gene duplication contributing to subsequent diversification.

CONCLUSIONS: Most Hymenoptera venom genes are shared by all members of the clade and only melittin and the new venom protein family anthophilin1 appear unique to the bee lineage. Most venom proteins thus predate the mega-radiation of hymenopterans and the evolution of the aculeate stinger.}, } @article {pmid37865683, year = {2023}, author = {Farrell, S and Appleton, C and Noble, PM and Al Moubayed, N}, title = {PetBERT: automated ICD-11 syndromic disease coding for outbreak detection in first opinion veterinary electronic health records.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {18015}, pmid = {37865683}, issn = {2045-2322}, mesh = {Animals ; *International Classification of Diseases ; *Electronic Health Records ; Disease Outbreaks/veterinary ; Public Health Surveillance ; }, abstract = {Effective public health surveillance requires consistent monitoring of disease signals such that researchers and decision-makers can react dynamically to changes in disease occurrence. However, whilst surveillance initiatives exist in production animal veterinary medicine, comparable frameworks for companion animals are lacking. First-opinion veterinary electronic health records (EHRs) have the potential to reveal disease signals and often represent the initial reporting of clinical syndromes in animals presenting for medical attention, highlighting their possible significance in early disease detection. Yet despite their availability, there are limitations surrounding their free text-based nature, inhibiting the ability for national-level mortality and morbidity statistics to occur. This paper presents PetBERT, a large language model trained on over 500 million words from 5.1 million EHRs across the UK. PetBERT-ICD is the additional training of PetBERT as a multi-label classifier for the automated coding of veterinary clinical EHRs with the International Classification of Disease 11 framework, achieving F1 scores exceeding 83% across 20 disease codings with minimal annotations. PetBERT-ICD effectively identifies disease outbreaks, outperforming current clinician-assigned point-of-care labelling strategies up to 3 weeks earlier. The potential for PetBERT-ICD to enhance disease surveillance in veterinary medicine represents a promising avenue for advancing animal health and improving public health outcomes.}, } @article {pmid37865347, year = {2024}, author = {Anmella, G and Mas, A and Sanabra, M and Valenzuela-Pascual, C and Valentí, M and Pacchiarotti, I and Benabarre, A and Grande, I and De Prisco, M and Oliva, V and Fico, G and Giménez-Palomo, A and Bastidas, A and Agasi, I and Young, AH and Garriga, M and Corponi, F and Li, BM and de Looff, P and Vieta, E and Hidalgo-Mazzei, D}, title = {Electrodermal activity in bipolar disorder: Differences between mood episodes and clinical remission using a wearable device in a real-world clinical setting.}, journal = {Journal of affective disorders}, volume = {345}, number = {}, pages = {43-50}, doi = {10.1016/j.jad.2023.10.125}, pmid = {37865347}, issn = {1573-2517}, mesh = {Humans ; *Bipolar Disorder/diagnosis/drug therapy ; Galvanic Skin Response ; Cyclothymic Disorder ; Affect ; Mania ; *Wearable Electronic Devices ; }, abstract = {BACKGROUND: Bipolar disorder (BD) lacks objective measures for illness activity and treatment response. Electrodermal activity (EDA) is a quantitative measure of autonomic function, which is altered in manic and depressive episodes. We aimed to explore differences in EDA (1) inter-individually: between patients with BD on acute mood episodes, euthymic states and healthy controls (HC), and (2) intra-individually: longitudinally within patients during acute mood episodes of BD and after clinical remission.

METHODS: A longitudinal observational study. EDA was recorded using a research-grade wearable in patients with BD during acute manic and depressive episodes and at clinical remission. Euthymic BD patients and HC were recorded during a single session. We compared EDA parameters derived from the tonic (mean EDA, mEDA) and phasic components (EDA peaks per minute, pmEDA, and EDA peaks mean amplitude, pmaEDA). Inter- and intra-individual comparisons were computed respectively with ANOVA and paired t-tests.

RESULTS: 49 patients with BD (15 manic, 9 depressed, and 25 euthymic), and 19 HC were included. Patients with bipolar depression showed significantly reduced mEDA (p = 0.003) and pmEDA (p = 0.001), which increased to levels similar to euthymia or HC after clinical remission (mEDA, p = 0.011; pmEDA, p < 0.001; pmaEDA, p < 0.001). Manic patients showed no differences compared to euthymic patients and HCs, but a significant reduction of tonic and phasic EDA parameters after clinical remission (mEDA, p = 0.035; pmEDA, p = 0.004).

LIMITATIONS: Limited sample size, high inter-individual variability of EDA parameters, limited comparability to previous studies and non-adjustment for medication.

CONCLUSION: EDA ecological monitoring might provide several opportunities for early detection of depressive symptoms, and might aid at assessing early response to treatments in mania and bipolar depression.}, } @article {pmid37858689, year = {2023}, author = {Sajjad, W and Ali, B and Niu, H and Ilahi, N and Rafiq, M and Bahadur, A and Banerjee, A and Kang, S}, title = {High prevalence of antibiotic-resistant and metal-tolerant cultivable bacteria in remote glacier environment.}, journal = {Environmental research}, volume = {239}, number = {Pt 2}, pages = {117444}, doi = {10.1016/j.envres.2023.117444}, pmid = {37858689}, issn = {1096-0953}, mesh = {*Genes, Bacterial ; *Ice Cover/microbiology ; Prevalence ; Angiotensin Receptor Antagonists ; Angiotensin-Converting Enzyme Inhibitors ; Bacteria ; Anti-Bacterial Agents/pharmacology/analysis ; Metals/analysis ; Gram-Negative Bacteria/genetics ; Drug Resistance, Bacterial/genetics ; }, abstract = {Studies of antibiotic-resistant bacteria (ARB) have mainly originated from anthropic-influenced environments, with limited information from pristine environments. Remote cold environments are major reservoirs of ARB and have been determined in polar regions; however, their abundance in non-polar cold habitats is underexplored. This study evaluated antibiotics and metals resistance profiles, prevalence of antibiotic resistance genes (ARGs) and metals tolerance genes (MTGs) in 38 ARB isolated from the glacier debris and meltwater from Baishui Glacier No 1, China. Molecular identification displayed Proteobacteria (39.3%) predominant in debris, while meltwater was dominated by Actinobacteria (30%) and Proteobacteria (30%). Bacterial isolates exhibited multiple antibiotic resistance index values > 0.2. Gram-negative bacteria displayed higher resistance to antibiotics and metals than Gram-positive. PCR amplification exhibited distinct ARGs in bacteria dominated by β-lactam genes blaCTX-M (21.1-71.1%), blaACC (21.1-60.5%), tetracycline-resistant gene tetA (21.1-60.5%), and sulfonamide-resistant gene sulI (18.4-52.6%). Moreover, different MTGs were reported in bacterial isolates, including mercury-resistant merA (21.1-63.2%), copper-resistant copB (18.4-57.9%), chromium-resistant chrA (15.8-44.7%) and arsenic-resistant arsB (10.5-44.7%). This highlights the co-selection and co-occurrence of MTGs and ARGs in remote glacier environments. Different bacteria shared same ARGs, signifying horizontal gene transfer between species. Strong positive correlation among ARGs and MTGs was reported. Metals tolerance range exhibited that Gram-negative and Gram-positive bacteria clustered distinctly. Gram-negative bacteria were significantly tolerant to metals. Amino acid sequences of blaACC,blaCTX-M,blaSHV,blaampC,qnrA, sulI, tetA and blaTEM revealed variations. This study presents promising ARB, harboring ARGs with variations in amino acid sequences, highlighting the need to assess the transcriptome study of glacier bacteria conferring ARGs and MTGs.}, } @article {pmid37857132, year = {2023}, author = {Hassan, L and Eisner, E and Berry, K and Emsley, R and Ainsworth, J and Lewis, S and Haddock, G and Edge, D and Bucci, S}, title = {User engagement in a randomised controlled trial for a digital health intervention for early psychosis (Actissist 2.0 trial).}, journal = {Psychiatry research}, volume = {329}, number = {}, pages = {115536}, doi = {10.1016/j.psychres.2023.115536}, pmid = {37857132}, issn = {1872-7123}, support = {MR/P026664/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Humans ; *Psychotic Disorders/therapy ; *Cognitive Behavioral Therapy ; *Mobile Applications ; Smartphone ; Patient Participation ; }, abstract = {Digital Health Interventions (DHIs) can help support people with mental health problems. Achieving satisfactory levels of patient engagement is a crucial, yet often underexplored, pre-requisite for health improvement. Actissist is a co-produced DHI delivered via a smartphone app for people with early psychosis, based on Cognitive Behaviour Therapy principles. This study describes and compares engagement patterns among participants in the two arms of the Actissist 2.0 randomised controlled trial. Engagement frequency and duration were measured among participants using the Actissist app in the intervention arm (n = 87) and the ClinTouch symptom monitoring only app used as the control condition (n = 81). Overall, 47.1 % of Actissist and 45.7 % of ClinTouch users completed at least a third of scheduled alerts while active in the study. The mean frequency (77.1 versus 60.2 total responses) and the median duration (80 versus 75 days until last response) of engagement were not significantly higher among Actissist users compared to ClinTouch users. Older age, White ethnicity, using their own smartphone device and, among Actissist users, an increased sense of therapeutic alliance were significantly associated with increased engagement. Through exploiting detailed usage data, this study identifies possible participant-level and DHI-level predictors of engagement to inform the practical implementation of future DHIs.}, } @article {pmid37855447, year = {2024}, author = {Gorijala, P and Aslam, MM and Dang, LT and Xicota, L and Fernandez, MV and Sung, YJ and Fan, KH and Feingold, E and Surace, EI and Chhatwal, JP and Hom, CL and , and , and Hartley, SL and Hassenstab, J and Perrin, RJ and Mapstone, M and Zaman, SH and Ances, BM and Kamboh, MI and Lee, JH and Cruchaga, C}, title = {Alzheimer's polygenic risk scores are associated with cognitive phenotypes in Down syndrome.}, journal = {Alzheimer's & dementia : the journal of the Alzheimer's Association}, volume = {20}, number = {2}, pages = {1038-1049}, pmid = {37855447}, issn = {1552-5279}, support = {P30 AG066444/AG/NIA NIH HHS/United States ; R01 AG064877/AG/NIA NIH HHS/United States ; RF1 AG071706/AG/NIA NIH HHS/United States ; RF1 AG053303/AG/NIA NIH HHS/United States ; RF1AG053303/NH/NIH HHS/United States ; U54 HD087011/HD/NICHD NIH HHS/United States ; RF1 AG074007/AG/NIA NIH HHS/United States ; P50 HD105353/HD/NICHD NIH HHS/United States ; U01 AG051412/AG/NIA NIH HHS/United States ; P50 AG005133/AG/NIA NIH HHS/United States ; /EB/NIBIB NIH HHS/United States ; UL1 TR002373/TR/NCATS NIH HHS/United States ; P01AG003991/NH/NIH HHS/United States ; P30 AG062715/AG/NIA NIH HHS/United States ; U19 AG032438/AG/NIA NIH HHS/United States ; U01 AG058922/AG/NIA NIH HHS/United States ; UL1 TR001857/TR/NCATS NIH HHS/United States ; R01 AG044546/AG/NIA NIH HHS/United States ; U24 AG021886/AG/NIA NIH HHS/United States ; SG-20-690363-DIAN/ALZ/Alzheimer's Association/United States ; P30 AG062421/AG/NIA NIH HHS/United States ; U01 AG024904/AG/NIA NIH HHS/United States ; P50 AG008702/AG/NIA NIH HHS/United States ; P01 AG003991/AG/NIA NIH HHS/United States ; P50 AG005681/AG/NIA NIH HHS/United States ; RF1AG074007/NH/NIH HHS/United States ; P01 AG026276/AG/NIA NIH HHS/United States ; RF1 AG058501/AG/NIA NIH HHS/United States ; P30 AG066519/AG/NIA NIH HHS/United States ; U19 AG068054/AG/NIA NIH HHS/United States ; U01 AG024904/NH/NIH HHS/United States ; R01 AG064614/AG/NIA NIH HHS/United States ; UL1 TR001414/TR/NCATS NIH HHS/United States ; RF1AG058501/NH/NIH HHS/United States ; RF1 AG044546/AG/NIA NIH HHS/United States ; U54 HD090256/HD/NICHD NIH HHS/United States ; R01AG064877/NH/NIH HHS/United States ; U01 AG051406/AG/NIA NIH HHS/United States ; UL1 TR001873/TR/NCATS NIH HHS/United States ; UL1 TR002345/TR/NCATS NIH HHS/United States ; U01AG058922/NH/NIH HHS/United States ; }, mesh = {Adult ; Humans ; *Alzheimer Disease/diagnosis ; *Down Syndrome/genetics ; Genetic Risk Score ; Apolipoproteins E/genetics ; Phenotype ; *Cognitive Dysfunction/diagnosis ; Biomarkers/cerebrospinal fluid ; Cognition ; Memory Disorders ; Amyloid beta-Peptides/cerebrospinal fluid ; }, abstract = {INTRODUCTION: This study aimed to investigate the influence of the overall Alzheimer's disease (AD) genetic architecture on Down syndrome (DS) status, cognitive measures, and cerebrospinal fluid (CSF) biomarkers.

METHODS: AD polygenic risk scores (PRS) were tested for association with DS-related traits.

RESULTS: The AD risk PRS was associated with disease status in several cohorts of sporadic late- and early-onset and familial late-onset AD, but not in familial early-onset AD or DS. On the other hand, lower DS Mental Status Examination memory scores were associated with higher PRS, independent of intellectual disability and APOE (PRS including APOE, PRSAPOE , p = 2.84 × 10[-4] ; PRS excluding APOE, PRSnonAPOE , p = 1.60 × 10[-2]). PRSAPOE exhibited significant associations with Aβ42, tTau, pTau, and Aβ42/40 ratio in DS.

DISCUSSION: These data indicate that the AD genetic architecture influences cognitive and CSF phenotypes in DS adults, supporting common pathways that influence memory decline in both traits.

HIGHLIGHTS: Examination of the polygenic risk of AD in DS presented here is the first of its kind. AD PRS influences memory aspects in DS individuals, independently of APOE genotype. These results point to an overlap between the genes and pathways that leads to AD and those that influence dementia and memory decline in the DS population. APOE ε4 is linked to DS cognitive decline, expanding cognitive insights in adults.}, } @article {pmid37853225, year = {2023}, author = {Jin, T and Li, D and Liu, Y and Li, K and Wang, L}, title = {Microbe combined with Fe[2+]-heat activated persulfate to decompose phenanthrene in red soil: comparison of acid-resistant degrading microflora and indigenous bacteria.}, journal = {Environmental science and pollution research international}, volume = {30}, number = {53}, pages = {113932-113947}, pmid = {37853225}, issn = {1614-7499}, support = {No. 51974314//National Natural Science Foundation of China/ ; No. 52270171//National Natural Science Foundation of China/ ; }, mesh = {Soil/chemistry ; Hot Temperature ; *Phenanthrenes/analysis ; Biodegradation, Environmental ; *Polycyclic Aromatic Hydrocarbons/analysis ; Bacteria/metabolism ; *Soil Pollutants/analysis ; Soil Microbiology ; }, abstract = {This work is designed to counteract the deficiency of targeted research on the PAHs polluted specific soil, especially when the chemicals extremely denatured it. Phenanthrene-contaminated red soil was treated through two-stage process: persulfate oxidation (on dosages of 3.48%, 5.21%, and 6.94%, combined with Fe[2+] and β-cyclodextrin, then heated) followed by biodegradation (indigenous bacteria vs. acid-resistant PAHs-degrading microflora (named ADM)) for 90 days. The dosage of oxidant greatly affected the removal efficiencies, which ranged from 46.78 to 85.34% under different treatment. After undergoing oxidation, the soil pH dropped below 3.0 synchronously and retained relatively strong oxidation state. The indigenous bacteria in red soil showed considerable degradation potential that will not vanish upon the sudden change of soil properties, whose average combined removal reached 95.43%, even higher than subgroups of bioaugmentation, but the population structure showed extremely simplex (Proteobacteria as superior occupied proportion of 91.77% after 90-day rehabilitation). The ADM screened from the coking wastewater was dominated by Klebsiella (75.4%) and Pseudomonas (23.6%), whose cooperation with 6.94% persulfate made the residual PHE reduced to less than 50 mg·kg[-1] in about 28 days. High-throughput sequencing analysis showed that the microbial community composition of the ADM applied-group was more abundant in the later stage of remediation. ADM inoculation has the advantages of shortening the restoration period and having a positive impact on the soil micro-ecology.}, } @article {pmid37853050, year = {2023}, author = {Qiao, Q and Shi, G and Yang, D and Wang, L and Zhang, X and Li, S and Bai, XE}, title = {Study on the destruction law of physical and shear properties of soil in mining disturbance.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {17751}, pmid = {37853050}, issn = {2045-2322}, support = {No. U2003103//the Key Project of Joint Funds of the National Natural Science Foundation of China/ ; S202210755006//2022 autonomous region level college students innovative training program project/ ; 2021B03004//the Special Program for Key Research and Development Tasks of Xinjiang Uygur Autonomous Region/ ; KC22075//special fund for promoting scientific and technological innovation in Xuzhou in 2022 (key research and development plan (modern agriculture) - general project/ ; }, abstract = {Underground mining activities can easily trigger surface subsidence and cause damage to surface soil. However, there is still a lack of studies on damaged soil, restricting ecological remediation in mining-induced subsidence regions to a certain degree. Focusing on the particular example of No. 4 Mine in Yili, Xinjiang, China, this study comprehensively combined field sampling, laboratory experiments, and data analysis to investigate the variation rules of basic physical properties and shear characteristics of soil samples. The latter had different subsidence degrees (0, 0-20, 20-40, and above 40 cm) and various depths (0- 10, 10-20, 20- 40, 40-60, and 60-80 cm). The experimental results show that: First, the natural density and dry unit weight of shallow soil in the serious-subsidence region were more significantly affected by mining-induced subsidence than the conditions in the deep layer, which also dropped with the increase in subsidence degree (with a mean drop rate of 7%). Second, serious subsidence could greatly counteract the positive effect of slight and moderate subsidence on the soil shear strength, with a drop rate of up to 30.7%. Third, compared with soil physical indices, mining-induced subsidence more easily affected shear strength indices. In particular, the soil samples taken from 0 to 10 cm depth in the slight subsidence area and 60-80 cm depth in the moderate subsidence area were most significantly affected by mining-induced subsidence, with PCA comprehensive scores of over 1.5. The present study can con-tribute to gaining in-depth knowledge of the damage characteristics of surface soil under mining-induced subsidence and provide a theoretical foundation for formulating reasonable coal mining strategies and ecological protection measures.}, } @article {pmid37852461, year = {2024}, author = {Ghiotto, G and Zampieri, G and Campanaro, S and Treu, L}, title = {Strain-resolved metagenomics approaches applied to biogas upgrading.}, journal = {Environmental research}, volume = {240}, number = {Pt 2}, pages = {117414}, doi = {10.1016/j.envres.2023.117414}, pmid = {37852461}, issn = {1096-0953}, mesh = {*Biofuels ; *Computational Biology ; Hydrogen ; Metagenomics ; Nucleotides ; }, abstract = {Genetic heterogeneity is a common trait in microbial populations, caused by de novo mutations and changes in variant frequencies over time. Microbes can thus differ genetically within the same species and acquire different phenotypes. For instance, performance and stability of anaerobic reactors are linked to the composition of the microbiome involved in the digestion process and to the environmental parameters imposing selective pressure on the metagenome, shaping its evolution. Changes at the strain level have the potential to determine variations in microbial functions, and their characterization could provide new insight into ecological and evolutionary processes driving anaerobic digestion. In this work, single nucleotide variant dynamics were studied in two time-course biogas upgrading experiments, testing alternative carbon sources and the response to exogenous hydrogen addition. A cumulative total of 76,229 and 64,289 high-confidence single nucleotide variants were discerned in the experiments related to carbon substrate availability and hydrogen addition, respectively. By combining complementary bioinformatic approaches, the study reconstructed the precise strain count-two for both hydrogenotrophic archaea-and tracked their abundance over time, while also characterizing tens of genes under strong selection. Results in the dominant archaea revealed the presence of nearly 100 variants within genes encoding enzymes involved in hydrogenotrophic methanogenesis. In the bacterial counterparts, 119 mutations were identified across 23 genes associated with the Wood-Ljungdahl pathway, suggesting a possible impact on the syntrophic acetate-oxidation process. Strain replacement events took place in both experiments, confirming the trends suggested by the variants trajectories and providing a comprehensive understanding of the biogas upgrading microbiome at the strain level. Overall, this resolution level allowed us to reveal fine-scale evolutionary mechanisms, functional dynamics, and strain-level metabolic variation that could contribute to the selection of key species actively involved in the carbon dioxide fixation process.}, } @article {pmid37851996, year = {2023}, author = {Alsamara, I and Ogilvie, L and Sudbrak, R and Brand, A}, title = {One Health Lens for Antimicrobial Resistance Research and Funding: A Systematic Review.}, journal = {Omics : a journal of integrative biology}, volume = {27}, number = {12}, pages = {570-580}, doi = {10.1089/omi.2023.0049}, pmid = {37851996}, issn = {1557-8100}, mesh = {Animals ; Humans ; *Anti-Bacterial Agents/pharmacology/therapeutic use ; Drug Resistance, Bacterial ; *One Health ; Databases, Factual ; }, abstract = {One Health (OH) offers conceptual and applied prospects to advance planetary health and integrative biology in the 21st century. For example, The World Health Organization (WHO) has declared antimicrobial resistance (AMR) one of humanity's top 10 health threats worldwide (AMR). The AMR research, as seen through the OH lens, recognizes the interdependence and the coproduction of the health of humans, nonhuman animals, and the environment (the OH triad). Moreover, research and development (R&D) is required to generate potential solutions to prevent, diagnose, and treat infections and control the spread and emergence of AMR. However, it is still unclear how well the OH approach is integrated into current AMR R&D. In this study, we present a systematic review on the OH funding landscape for cross-sectoral AMR R&D, and its alignment/gaps with the current global strategic agenda on AMR. A systematic literature review was conducted using public databases covering the period between January 2015 and May 2022. We included the studies and reviews on AMR encompassing more than one sector of the OH triad. Out of the 777 included studies, 475 (61%) encompassed the three OH sectors. A key finding of the present systematic review is that the environment was the most neglected sector in the OH triad. AMR surveillance, transmission, and interventions are the most commonly studied priority topics. In addition, both cross-sectoral AMR literature and investments have been increasing since 2017. The operational aspect of AMR is the most researched and funded area. However, certain priority topics in the strategic research and innovation agenda of the Joint Programming Initiative on AMR are underrepresented in OH AMR research, such as diagnosis and therapeutics. To the best of authors' knowledge, this is the first study that systematically reviews the cross-sectoral literature on AMR, classifies it, and aligns and contextualizes it in regard to the funding landscape of AMR. This systematic review identifies neglected areas in AMR R&D and could serve as critical information for policymaking so as to realize the objectives of the Global Action Plan on AMR. Going forward, more cross-sectoral AMR research and funding are needed. As integrative biology and omics systems science are poised to benefit from a rapprochement with the OH lens, the present article highlights the AMR research and funding landscapes.}, } @article {pmid37849397, year = {2023}, author = {Hartman, AL and Myler, PJ}, title = {Bunyavirales: Scientific Gaps and Prototype Pathogens for a Large and Diverse Group of Zoonotic Viruses.}, journal = {The Journal of infectious diseases}, volume = {228}, number = {Suppl 6}, pages = {S376-S389}, pmid = {37849397}, issn = {1537-6613}, support = {HHSN272201700059C/AI/NIAID NIH HHS/United States ; R01 NS101100/NS/NINDS NIH HHS/United States ; R21 AI163603/AI/NIAID NIH HHS/United States ; HHSN272201700059C/NH/NIH HHS/United States ; }, mesh = {Animals ; Humans ; *RNA Viruses ; }, abstract = {Research directed at select prototype pathogens is part of the approach put forth by the National Institute of Allergy and Infectious Disease (NIAID) to prepare for future pandemics caused by emerging viruses. We were tasked with identifying suitable prototypes for four virus families of the Bunyavirales order (Phenuiviridae, Peribunyaviridae, Nairoviridae, and Hantaviridae). This is a challenge due to the breadth and diversity of these viral groups. While there are many differences among the Bunyavirales, they generally have complex ecological life cycles, segmented genomes, and cause a range of human clinical outcomes from mild to severe and even death. Here, we delineate potential prototype species that encompass the breadth of clinical outcomes of a given family, have existing reverse genetics tools or animal disease models, and can be amenable to a platform approach to vaccine testing. Suggested prototype pathogens outlined here can serve as a starting point for further discussions.}, } @article {pmid37847320, year = {2023}, author = {Li, J and Yu, Q and Qian, R and Xiao, X and Liang, Y and Luo, P and Wang, H and Lu, Y and Xu, L and Liu, Q and Xiao, Y}, title = {Distribution and transformation of potentially toxic elements in crack under coal mining disturbance.}, journal = {Environmental monitoring and assessment}, volume = {195}, number = {11}, pages = {1327}, pmid = {37847320}, issn = {1573-2959}, mesh = {*Coal Mining ; *Metals, Heavy/analysis ; Environmental Monitoring/methods ; *Soil Pollutants/analysis ; Mining ; Soil/chemistry ; China ; Coal ; Risk Assessment ; }, abstract = {In China, coal provides about 56.8% of the energy. Most of China's coal mines are shaft mines, which cause the surface to collapse and crack during the mining process. The soil near the cracks changes its physicochemical properties due to the altered stress conditions. This will affect the distribution of PTEs in the soil. We collected 18 samples from a selected crack in the abandoned land. The pH, Eh, and PTE and their fractions of the samples were determined. With the test results, we understand the distribution characteristics of pH, Eh, PTEs, and their fractions at the cracks. Meanwhile, we explored the key factors that contribute to this distribution. It was determined that crack decreases surface soil pH while increasing Eh. The total amount of 7 PTEs is higher in the bottom soil of the main crack and 2 m away from the main crack. The content of reducible fractions of PTEs increases with the increase of soil Eh. The oxidizable and residual fractions of PTEs adsorbed to the clay particles migrate to and enrich the deeper layers of the main crack. This study emphasizes the effect of crack generation on the distribution of PTEs in soil. It provides insights to describe the distribution of PTE throughout the full life cycle of crack.}, } @article {pmid37844141, year = {2023}, author = {Wu, D and Xie, J and Liu, Y and Jin, L and Li, G and An, T}, title = {Metagenomic and Machine Learning Meta-Analyses Characterize Airborne Resistome Features and Their Hosts in China Megacities.}, journal = {Environmental science & technology}, volume = {57}, number = {43}, pages = {16414-16423}, doi = {10.1021/acs.est.3c02593}, pmid = {37844141}, issn = {1520-5851}, mesh = {*Genes, Bacterial ; *Metagenome ; Cities ; Anti-Bacterial Agents/pharmacology ; China ; }, abstract = {Urban ambient air contains a cocktail of antibiotic resistance genes (ARGs) emitted from various anthropogenic sites. However, what is largely unknown is whether the airborne ARGs exhibit site-specificity or their pathogenic hosts persistently exist in the air. Here, by retrieving 1.2 Tb metagenomic sequences (n = 136), we examined the airborne ARGs from hospitals, municipal wastewater treatment plants (WWTPs) and landfills, public transit centers, and urban sites located in seven of China's megacities. As validated by the multiple machine learning-based classification and optimization, ARGs' site-specificity was found to be the most apparent in hospital air, with featured resistances to clinical-used rifamycin and (glyco)peptides, whereas the more environmentally prevalent ARGs (e.g., resistance to sulfonamide and tetracycline) were identified being more specific to the nonclinical ambient air settings. Nearly all metagenome-assembled genomes (MAGs) that possessed the site-featured resistances were identified as pathogenic taxa, which occupied the upper-representative niches in all the neutrally distributed airborne microbial community (P < 0.01, m = 0.22-0.50, R[2] = 0.41-0.86). These niche-favored putative resistant pathogens highlighted the enduring antibiotic resistance hazards in the studied urban air. These findings are critical, albeit the least appreciated until our study, to gauge the airborne dimension of resistomes' features and fates in urban atmospheric environments.}, } @article {pmid37842337, year = {2021}, author = {Martens, M and Stierum, R and Schymanski, EL and Evelo, CT and Aalizadeh, R and Aladjov, H and Arturi, K and Audouze, K and Babica, P and Berka, K and Bessems, J and Blaha, L and Bolton, EE and Cases, M and Damalas, DΕ and Dave, K and Dilger, M and Exner, T and Geerke, DP and Grafström, R and Gray, A and Hancock, JM and Hollert, H and Jeliazkova, N and Jennen, D and Jourdan, F and Kahlem, P and Klanova, J and Kleinjans, J and Kondic, T and Kone, B and Lynch, I and Maran, U and Martinez Cuesta, S and Ménager, H and Neumann, S and Nymark, P and Oberacher, H and Ramirez, N and Remy, S and Rocca-Serra, P and Salek, RM and Sallach, B and Sansone, SA and Sanz, F and Sarimveis, H and Sarntivijai, S and Schulze, T and Slobodnik, J and Spjuth, O and Tedds, J and Thomaidis, N and Weber, RJM and van Westen, GJP and Wheelock, CE and Williams, AJ and Witters, H and Zdrazil, B and Županič, A and Willighagen, EL}, title = {ELIXIR and Toxicology: a community in development.}, journal = {F1000Research}, volume = {10}, number = {}, pages = {}, pmid = {37842337}, issn = {2046-1402}, support = {/WT_/Wellcome Trust/United Kingdom ; 001/WHO_/World Health Organization/International ; }, mesh = {*Biological Science Disciplines ; Europe ; Risk Assessment ; }, abstract = {Toxicology has been an active research field for many decades, with academic, industrial and government involvement. Modern omics and computational approaches are changing the field, from merely disease-specific observational models into target-specific predictive models. Traditionally, toxicology has strong links with other fields such as biology, chemistry, pharmacology and medicine. With the rise of synthetic and new engineered materials, alongside ongoing prioritisation needs in chemical risk assessment for existing chemicals, early predictive evaluations are becoming of utmost importance to both scientific and regulatory purposes. ELIXIR is an intergovernmental organisation that brings together life science resources from across Europe. To coordinate the linkage of various life science efforts around modern predictive toxicology, the establishment of a new ELIXIR Community is seen as instrumental. In the past few years, joint efforts, building on incidental overlap, have been piloted in the context of ELIXIR. For example, the EU-ToxRisk, diXa, HeCaToS, transQST, and the nanotoxicology community have worked with the ELIXIR TeSS, Bioschemas, and Compute Platforms and activities. In 2018, a core group of interested parties wrote a proposal, outlining a sketch of what this new ELIXIR Toxicology Community would look like. A recent workshop (held September 30th to October 1st, 2020) extended this into an ELIXIR Toxicology roadmap and a shortlist of limited investment-high gain collaborations to give body to this new community. This Whitepaper outlines the results of these efforts and defines our vision of the ELIXIR Toxicology Community and how it complements other ELIXIR activities.}, } @article {pmid37841229, year = {2023}, author = {Turner, TF and Bart, HL and McCormick, F and Besser, AC and Bowes, RE and Capps, KA and DeArmon, ES and Dillman, CB and Driscoll, KP and Dugger, A and Hamilton, GL and Harris, PM and Hendrickson, DA and Hoffman, J and Knouft, JH and Lepak, RF and López-Fernández, H and Montaña, CG and Newsome, SD and Pease, AA and Smith, WL and Taylor, CA and Welicky, RL}, title = {Long-term ecological research in freshwaters enabled by regional biodiversity collections, stable isotope analysis, and environmental informatics.}, journal = {Bioscience}, volume = {73}, number = {7}, pages = {479-493}, pmid = {37841229}, issn = {0006-3568}, support = {EPA999999/ImEPA/Intramural EPA/United States ; }, abstract = {Biodiversity collections are experiencing a renaissance fueled by the intersection of informatics, emerging technologies, and the extended use and interpretation of specimens and archived databases. In this article, we explore the potential for transformative research in ecology integrating biodiversity collections, stable isotope analysis (SIA), and environmental informatics. Like genomic DNA, SIA provides a common currency interpreted in the context of biogeochemical principles. Integration of SIA data across collections allows for evaluation of long-term ecological change at local to continental scales. Challenges including the analysis of sparse samples, a lack of information about baseline isotopic composition, and the effects of preservation remain, but none of these challenges is insurmountable. The proposed research framework interfaces with existing databases and observatories to provide benchmarks for retrospective studies and ecological forecasting. Collections and SIA add historical context to fundamental questions in freshwater ecological research, reference points for ecosystem monitoring, and a means of quantitative assessment for ecosystem restoration.}, } @article {pmid37840885, year = {2023}, author = {Boyes, D and Holland, PWH and , and , and , and , and , and , }, title = {The genome sequence of the Lesser Broad-bordered Yellow Underwing, Noctua janthe (Borkhausen, 1792).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {189}, pmid = {37840885}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual male Noctua janthe (the Lesser Broad-bordered Yellow Underwing; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 532.8 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.3 kilobases in length. Gene annotation of this assembly on Ensembl identified 17,653 protein coding genes.}, } @article {pmid37840882, year = {2023}, author = {Boyes, D and , and , and , and , and , and Langdon, WBV and , }, title = {The genome sequence of the Lunar Hornet, Sesia bembeciformis (Hübner 1806).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {109}, pmid = {37840882}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual male Sesia bembeciformis (the Lunar Hornet; Arthropoda; Insecta; Lepidoptera; Sesiidae). The genome sequence is 477.1 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 16.1 kilobases in length. Gene annotation of this assembly on Ensembl has identified 15,843 protein coding genes.}, } @article {pmid37838199, year = {2023}, author = {Zhao, X and Xie, Y and Sun, B and Liu, Y and Zhu, S and Li, W and Zhao, M and Liu, D}, title = {Unraveling microbial characteristics of simultaneous nitrification, denitrification and phosphorus removal in a membrane-aerated biofilm reactor.}, journal = {Environmental research}, volume = {239}, number = {Pt 1}, pages = {117402}, doi = {10.1016/j.envres.2023.117402}, pmid = {37838199}, issn = {1096-0953}, mesh = {*Phosphorus ; Denitrification ; Nitrification ; Phylogeny ; Wastewater ; Phosphates ; Biofilms ; Carbon ; Nitrogen ; *Ammonium Compounds ; Sulfur ; }, abstract = {This study describes the simultaneous removal of carbon, ammonium, and phosphate from domestic wastewater by a membrane-aerated biofilm reactor (MABR) which was operated for 360 days. During the operation, the maximum removal efficiencies of chemical oxygen demand (COD), total nitrogen (TN) and total phosphorus (TP) reached 93.1%, 83.98%, and 96.41%, respectively. Statistical analysis showed that the MABR could potentially treat wastewater with a high ammonium concentration and a relatively low C/N ratio. Dissolved oxygen and multiple pollutants, including ammonium, carbon, phosphate, and sulfate, shaped the structure of the microbial community in the MABR. High throughput sequencing uncovered the crucial microbiome in ammonium transformation in MABR. Phylogenetic analysis of the ammonia monooxygenase (amoA) genes revealed an important role for comammox Nitrospira in the nitrification process. Diverse novel phosphate-accumulating organisms (Thauera, Bacillus, and Pseudomonas) and sulfur-oxidizing bacteria (Thiobacillus, Thiothrix and Sulfurimonas) were potentially involved in denitrification in MABR. The results from this study suggested that MABR could be a feasible system for the simultaneous removal of nitrogen, carbon, phosphorus, and sulfur from sewage water.}, } @article {pmid37833155, year = {2023}, author = {Munley, JA and Kelly, LS and Park, G and Gillies, GS and Pons, EE and Kannan, KB and Bible, LE and Efron, PA and Nagpal, R and Mohr, AM}, title = {Sex-specific intestinal dysbiosis persists after multicompartmental injury.}, journal = {Surgery}, volume = {174}, number = {6}, pages = {1453-1462}, doi = {10.1016/j.surg.2023.08.023}, pmid = {37833155}, issn = {1532-7361}, support = {R01 GM105893/GM/NIGMS NIH HHS/United States ; }, mesh = {Female ; Male ; Rats ; Animals ; Rats, Sprague-Dawley ; *Dysbiosis/etiology ; RNA, Ribosomal, 16S ; *Multiple Trauma ; Computational Biology ; }, abstract = {BACKGROUND: Preclinical studies of the gut microbiome after severe traumatic injury have demonstrated severe dysbiosis in males, with sex-specific microbial differences up to 2 days after injury. However, the impact of host sex on injury-driven dysbiosis over time remains unknown. We hypothesized that sex-specific differences in intestinal microbiome diversity and composition after traumatic injury with and without stress would persist after 7 days.

METHODS: Male and proestrus female Sprague-Dawley rats (n = 8/group) were subjected to either polytrauma (lung contusion, hemorrhagic shock, cecectomy, bifemoral pseudofractures), polytrauma plus chronic restraint stress, or naïve controls. The fecal microbiome was measured on days 0, 3, and 7 using 16S rRNA sequencing and Quantitative Insights into Microbial Ecology bioinformatics analyses. Microbial alpha-diversity (Chao1 and Shannon indices) and beta-diversity were assessed. Analyses were performed in GraphPad and "R," with significance defined as P < .05.

RESULTS: Polytrauma and polytrauma plus chronic restraint stress reduced alpha-diversity (Chao1, Shannon) within 3 days postinjury, which persisted up to day 7 in both sexes; polytrauma and polytrauma plus chronic restraint stress females had significantly decreased Chao1 compared to male counterparts at day 7 (P = .02). At day 7, the microbiome composition in polytrauma females had higher proportion of Mucispirillum, whereas polytrauma plus chronic restraint stress males demonstrated elevated abundance of Ruminococcus and Akkermansia.

CONCLUSION: Multicompartmental trauma induces intestinal dysbiosis that is sex-specific with persistence of decreased diversity and unique "pathobiome" signatures in females after 1 week. These findings underline sex as an important biological variable that may influence variable host-specific responses and outcomes after severe trauma and critical illness. This underscores the need to consider precision medicine strategies to ameliorate these outcomes.}, } @article {pmid37831234, year = {2023}, author = {Li, Z and Li, X and Li, S and Yang, Y and Yan, W and Xu, H}, title = {Bibliometric analysis of electrochemical disinfection: current status and development trend from 2002 to 2022.}, journal = {Environmental science and pollution research international}, volume = {30}, number = {52}, pages = {111714-111731}, pmid = {37831234}, issn = {1614-7499}, support = {52270078//National Natural Science Foundation of China/ ; LZY21E080003//Welfare Technology Research Plan of Zhejiang Province/ ; 2021KFKT-7//Open Research Fund of the State Key Laboratory of Ecological Water Conservancy in the Arid area of Northwest China (Xi'an University of Technology)/ ; }, mesh = {*Disinfection ; *Bibliometrics ; Databases, Factual ; Electrochemical Techniques ; Electrodes ; }, abstract = {The removal of waterborne pathogens from water is critical in preventing the spread of waterborne diseases. Electrochemical methods have been extensively researched and implemented for disinfection, primarily owing to their simplicity, efficiency, and eco-friendliness. Thus, it is essential to conduct a review about the research progress and hotspots on this promising technique. In this paper, we provided a comprehensive bibliometric analysis to systematically study and analyze the current status, hotspots, and trends in electrochemical disinfection research from 2002 to 2022. This study analyzed literature related to electrochemical disinfection or electrochemical sterilization published in the Web of Science database from 2002 to 2022 using CiteSpace and Biblioshiny R language software packages. The analysis focused on the visualization and assessment of annual publication volume, discipline and journal distribution, collaborative networks, highly cited papers, and keywords to systematically understand the current status and trends of electrochemical disinfection. The results showed that between 2002 and 2022, 1171 publications related to electrochemical disinfection were published, with an exponential increase in the cumulative number of publications (y=17.518e[0.2147x], R[2]= 0.9788). The publications covered 76 disciplines with many articles published in high-impact journals. However, the research power was characterized by a large number of scattered research efforts and insufficient cooperation, indicating the need for further innovative collaboration. The citation analysis and keyword analysis suggest that future development in this field may focus on optimizing electrode materials, investigating the disinfection performance of ·OH based systems, optimizing conditions for actual wastewater treatment, and reducing energy consumption to promote practical applications.}, } @article {pmid37828216, year = {2023}, author = {Oza, A}, title = {Reproducibility trial: 246 biologists get different results from same data sets.}, journal = {Nature}, volume = {622}, number = {7984}, pages = {677-678}, doi = {10.1038/d41586-023-03177-1}, pmid = {37828216}, issn = {1476-4687}, mesh = {*Biology/methods/standards ; *Data Analysis ; *Datasets as Topic ; Ecology/methods/standards ; *Reproducibility of Results ; Research Personnel ; }, } @article {pmid37824826, year = {2024}, author = {Mabry, ME and Abrahams, RS and Al-Shehbaz, IA and Baker, WJ and Barak, S and Barker, MS and Barrett, RL and Beric, A and Bhattacharya, S and Carey, SB and Conant, GC and Conran, JG and Dassanayake, M and Edger, PP and Hall, JC and Hao, Y and Hendriks, KP and Hibberd, JM and King, GJ and Kliebenstein, DJ and Koch, MA and Leitch, IJ and Lens, F and Lysak, MA and McAlvay, AC and McKibben, MTW and Mercati, F and Moore, RC and Mummenhoff, K and Murphy, DJ and Nikolov, LA and Pisias, M and Roalson, EH and Schranz, ME and Thomas, SK and Yu, Q and Yocca, A and Pires, JC and Harkess, AE}, title = {Complementing model species with model clades.}, journal = {The Plant cell}, volume = {36}, number = {5}, pages = {1205-1226}, pmid = {37824826}, issn = {1532-298X}, support = {1923589/2019610//National Science Foundation, USA, and The United States-Israel Binational Science Foundation/ ; //The Goldinger Trust Jewish Fund/ ; BER-DE-SC0020358//US Department of Energy/ ; }, mesh = {*Phylogeny ; *Arabidopsis/genetics ; *Brassicaceae/genetics/classification ; Genomics/methods ; Genome, Plant/genetics ; }, abstract = {Model species continue to underpin groundbreaking plant science research. At the same time, the phylogenetic resolution of the land plant tree of life continues to improve. The intersection of these 2 research paths creates a unique opportunity to further extend the usefulness of model species across larger taxonomic groups. Here we promote the utility of the Arabidopsis thaliana model species, especially the ability to connect its genetic and functional resources, to species across the entire Brassicales order. We focus on the utility of using genomics and phylogenomics to bridge the evolution and diversification of several traits across the Brassicales to the resources in Arabidopsis, thereby extending scope from a model species by establishing a "model clade." These Brassicales-wide traits are discussed in the context of both the model species Arabidopsis and the family Brassicaceae. We promote the utility of such a "model clade" and make suggestions for building global networks to support future studies in the model order Brassicales.}, } @article {pmid37822564, year = {2023}, author = {Boyes, D and , and , and , and , and , and Langdon, WBV and , }, title = {The genome sequence of the Pied Smudge, Ypsolopha sequella (Clerck, 1759).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {32}, pmid = {37822564}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual Ypsolopha sequella (the Pied Smudge; Arthropoda; Insecta; Lepidoptera; Ypsolophidae). The genome sequence is 867 megabases in span. Most of the assembly is scaffolded into 30 chromosomal pseudomolecules with the Z sex chromosome assembled. The mitochondrial genome has also been assembled and is 15.3 kilobases in length. Gene annotation of this assembly on Ensembl identified 20,394 protein coding genes.}, } @article {pmid37821698, year = {2023}, author = {Pavlopoulos, GA and Baltoumas, FA and Liu, S and Selvitopi, O and Camargo, AP and Nayfach, S and Azad, A and Roux, S and Call, L and Ivanova, NN and Chen, IM and Paez-Espino, D and Karatzas, E and , and Iliopoulos, I and Konstantinidis, K and Tiedje, JM and Pett-Ridge, J and Baker, D and Visel, A and Ouzounis, CA and Ovchinnikov, S and Buluç, A and Kyrpides, NC}, title = {Unraveling the functional dark matter through global metagenomics.}, journal = {Nature}, volume = {622}, number = {7983}, pages = {594-602}, pmid = {37821698}, issn = {1476-4687}, support = {DP5 OD026389/OD/NIH HHS/United States ; P20 GM103475/GM/NIGMS NIH HHS/United States ; }, mesh = {Cluster Analysis ; *Metagenome/genetics ; *Metagenomics/methods ; *Proteins/chemistry/classification/genetics ; Databases, Protein ; Protein Conformation ; *Microbiology ; }, abstract = {Metagenomes encode an enormous diversity of proteins, reflecting a multiplicity of functions and activities[1,2]. Exploration of this vast sequence space has been limited to a comparative analysis against reference microbial genomes and protein families derived from those genomes. Here, to examine the scale of yet untapped functional diversity beyond what is currently possible through the lens of reference genomes, we develop a computational approach to generate reference-free protein families from the sequence space in metagenomes. We analyse 26,931 metagenomes and identify 1.17 billion protein sequences longer than 35 amino acids with no similarity to any sequences from 102,491 reference genomes or the Pfam database[3]. Using massively parallel graph-based clustering, we group these proteins into 106,198 novel sequence clusters with more than 100 members, doubling the number of protein families obtained from the reference genomes clustered using the same approach. We annotate these families on the basis of their taxonomic, habitat, geographical and gene neighbourhood distributions and, where sufficient sequence diversity is available, predict protein three-dimensional models, revealing novel structures. Overall, our results uncover an enormously diverse functional space, highlighting the importance of further exploring the microbial functional dark matter.}, } @article {pmid37819593, year = {2023}, author = {Baňas, M and Šofranková, L and Kurimský, J and Pavlík, M and Pikalík, M and Majláthová, V and Cimbala, R and Pipová, N and Wurfl, L and Majláth, I}, title = {Interspecific differences in the behavioral response of ticks exposed to radiofrequency electromagnetic radiation.}, journal = {Experimental & applied acarology}, volume = {91}, number = {3}, pages = {477-485}, pmid = {37819593}, issn = {1572-9702}, mesh = {Humans ; Male ; Female ; Animals ; *Dermacentor/physiology ; *Ixodes/physiology ; *Ixodidae ; Radio Waves/adverse effects ; Electromagnetic Fields ; }, abstract = {Artificial electromagnetic radiation is a new environmental factor that affects animals. Experiments with the effect of radio frequency electromagnetic radiation were focused on both vertebrates and invertebrates. Ticks showed a significant affinity to radiation. Our study is a continuation of this research and its aim was to monitor the effect of radiation on the behavior of four tick species: Ixodes ricinus, Dermacentor reticulatus, Dermacentor marginatus and Haemaphysalis inermis. In total 1,200 ticks, 300 of each species, were tested in modules allowing the choice of an exposed or shielded area. During the test, the ticks were exposed to electro-magnetic radiation of 900 MHz for 24 h. The position of the individuals was recorded and we evaluated the obtained data statistically. We observed a significant preference to the exposed area in both sexes of I. ricinus. Males of D. reticulatus and D. marginatus also showed an affinity to radiation, but not females of both species, nor females and males of H. inermis. The results of the study support the assumption that ticks perceive the electromagnetic field and the observed differences in their response have the potential to help understand the mechanism of perception.}, } @article {pmid37815079, year = {2023}, author = {Ilić Živojinović, J and Soldatović, I and Backović, D and Vukašinović, D and Babić, S and Tomanić, M and Ilić, B and Vlaisavljević, Ž}, title = {Personal Listening Device Use and Attitude to Noise in Relation to Depression and Anxiety among Medical Students.}, journal = {Noise & health}, volume = {25}, number = {118}, pages = {176-182}, pmid = {37815079}, issn = {1998-4030}, mesh = {Female ; Adolescent ; Humans ; Male ; *Students, Medical ; Cross-Sectional Studies ; Depression/epidemiology/etiology ; Anxiety/epidemiology/etiology ; Anxiety Disorders ; }, abstract = {BACKGROUND: High levels of environmental noise may lead to psychological symptoms. The present study has hypothesized that personal listening device (PLD) use and a negative attitude to noise are significantly related to anxiety and/or depression.

METHODS: This is a cross-sectional study conducted on 431 six-grade students (35% male) at the Faculty of Medicine, University of Belgrade. All students completed the questionnaires related to socio-demographic data, noise/music exposure habits, behaviors related to PLD use, tinnitus, headaches, consumption of alcohol, coffee, energy drinks and cigarettes, YANS (Youth Attitude to Noise Scale), CES-D (The Center for Epidemiologic Studies Depression), and GAD-7 (Generalised Anxiety Disorder Assessment - 7 item scale) questionnaires.

RESULTS: There were 396 (91.9%) of investigated students who used PLD, with more frequent use among girls compared to boys (95.0% and 86.8%, respectively; p = 0.002). We found no significant relationship between the frequency of PLD use and depression and anxiety. However, continuous daily PLD use longer than 1 hour was significantly and positively related to depression (p = 0.006). Students with depression had a lower total YANS score compared to those without depression, indicating a more negative attitude toward noise (p = 0.042). Students with no difficulties to concentrate in noise and with a positive attitude to daily noises had about 37% lower chance to suffer from depression and anxiety, respectively.

CONCLUSIONS: PLD use is common among medical students and may be associated with their mental health. Longer than 1 hour of continuous daily use of PLD may be positively related to depression. We also found a significant relationship between difficulties concentrating in noisy environments and depression, and between negative attitudes to daily noises and anxiety.}, } @article {pmid37808390, year = {2023}, author = {Sivell, D and Sivell, O and , and , and , and , and , and Hawkes, WL and Wotton, KR and , }, title = {The genome sequence of the Vagrant Hoverfly, Eupeodes corollae (Fabricius, 1794).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {112}, pmid = {37808390}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual female Eupeodes corollae (the Vagrant Hoverfly; Arthropoda; Insecta; Diptera; Syrphidae). The genome sequence is 648.2 megabases in span. Most of the assembly is scaffolded into four chromosomal pseudomolecules, including with the X sex chromosome. The mitochondrial genome has also been assembled and is 18.3 kilobases in length.}, } @article {pmid37807043, year = {2023}, author = {Hayes, MG and Langille, MGI and Gu, H}, title = {Cross-study analyses of microbial abundance using generalized common factor methods.}, journal = {BMC bioinformatics}, volume = {24}, number = {1}, pages = {380}, pmid = {37807043}, issn = {1471-2105}, support = {CGS-M Alexander Graham Bell Scholarship//Natural Sciences and Engineering Research Council of Canada/ ; RGPIN/05108-2017//Natural Sciences and Engineering Research Council of Canada/ ; Scotia Scholars Award//Nova Scotia Health Research Foundation/ ; }, mesh = {*Metagenome ; *Microbiota/genetics ; Metagenomics/methods ; Genomics ; Computational Biology/methods ; }, abstract = {BACKGROUND: By creating networks of biochemical pathways, communities of micro-organisms are able to modulate the properties of their environment and even the metabolic processes within their hosts. Next-generation high-throughput sequencing has led to a new frontier in microbial ecology, promising the ability to leverage the microbiome to make crucial advancements in the environmental and biomedical sciences. However, this is challenging, as genomic data are high-dimensional, sparse, and noisy. Much of this noise reflects the exact conditions under which sequencing took place, and is so significant that it limits consensus-based validation of study results.

RESULTS: We propose an ensemble approach for cross-study exploratory analyses of microbial abundance data in which we first estimate the variance-covariance matrix of the underlying abundances from each dataset on the log scale assuming Poisson sampling, and subsequently model these covariances jointly so as to find a shared low-dimensional subspace of the feature space.

CONCLUSIONS: By viewing the projection of the latent true abundances onto this common structure, the variation is pared down to that which is shared among all datasets, and is likely to reflect more generalizable biological signal than can be inferred from individual datasets. We investigate several ways of achieving this, demonstrate that they work well on simulated and real metagenomic data in terms of signal retention and interpretability, and recommend a particular implementation.}, } @article {pmid37802837, year = {2023}, author = {Zhang, HH and Meng, XX and Lin, YL and Chen, SL and Huang, LF}, title = {[Prediction of global potential growth areas for Panax ginseng based on GMPGIS system and MaxEnt model].}, journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica}, volume = {48}, number = {18}, pages = {4959-4966}, doi = {10.19540/j.cnki.cjcmm.20230514.102}, pmid = {37802837}, issn = {1001-5302}, mesh = {*Panax ; Ecosystem ; China ; Geographic Information Systems ; Temperature ; *Plants, Medicinal ; }, abstract = {The suitable habitat for the endangered and valuable medicinal herb Panax ginseng is gradually decreasing. It is crucial to investigate its suitable growing areas in China for global protection and sustainable utilization of P. ginseng. In this study, 371 distribution points of P. ginseng were collected, and 21 environmental factors were used as ecological indicators. The geographic information system for global medicinal plants(GMPGIS) system, MaxEnt model, and Thiessen polygon method were used to analyze the potential suitable areas for P. ginseng globally. The results showed that the key environmental variables affecting P. ginseng were precipitation in the hottest quarter(Bio18) and the coefficient of temperature seasonality(Bio4). The suitable habitats for P. ginseng were mostly located in the "One Belt, One Road" countries such as China, Japan, South Korea, North Korea, and Russia. The highly suitable habitats were mainly distributed along mountain ranges in southeastern Shandong, southern Shanxi and Shaanxi, northern Jiangsu, and northwestern Henan of China. Data analysis indicated that the current P. ginseng planting sites were all in high suitability zones, and the Thiessen polygon results showed that the geographic locations of P. ginseng production companies were unbalanced and urgently needed optimization. This study provides data support for P. ginseng planting site selection, scientific introduction, production layout, and long-term development planning.}, } @article {pmid37802618, year = {2023}, author = {Middleton, J and Colthart, G and Dem, F and Elkins, A and Fairhead, J and Hazell, RJ and Head, MG and Inacio, J and Jimbudo, M and Jones, CI and Laman, M and MacGregor, H and Novotny, V and Peck, M and Philip, J and Paliau, J and Pomat, W and Stockdale, JA and Sui, S and Stewart, AJ and Umari, R and Walker, SL and Cassell, JA}, title = {Health service needs and perspectives of a rainforest conserving community in Papua New Guinea's Ramu lowlands: a combined clinical and rapid anthropological assessment with parallel treatment of urgent cases.}, journal = {BMJ open}, volume = {13}, number = {10}, pages = {e075946}, pmid = {37802618}, issn = {2044-6055}, mesh = {Male ; Female ; Humans ; Adult ; Papua New Guinea ; *Rainforest ; *Health Services ; }, abstract = {OBJECTIVES: Determine community needs and perspectives as part of planning health service incorporation into Wanang Conservation Area, in support of locally driven sustainable development.

DESIGN: Clinical and rapid anthropological assessment (individual primary care assessments, key informant (KI) interviews, focus groups (FGs), ethnography) with treatment of urgent cases.

SETTING: Wanang (pop. c189), a rainforest community in Madang province, Papua New Guinea.

PARTICIPANTS: 129 villagers provided medical histories (54 females (f), 75 males (m); median 19 years, range 1 month to 73 years), 113 had clinical assessments (51f, 62m; median 18 years, range 1 month to 73 years). 26 ≥18 years participated in sex-stratified and age-stratified FGs (f<40 years; m<40 years; f>40 years; m>40 years). Five KIs were interviewed (1f, 4m). Daily ethnographic fieldnotes were recorded.

RESULTS: Of 113 examined, 11 were 'well' (a clinical impression based on declarations of no current illness, medical histories, conversation, no observed disease signs), 62 (30f, 32m) were treated urgently, 31 referred (15f, 16m), indicating considerable unmet need. FGs top-4 ranked health issues concorded with KI views, medical histories and clinical examinations. For example, ethnoclassifications of three ((A) 'malaria', (B) 'sotwin', (C) 'grile') translated to the five biomedical conditions diagnosed most ((A) malaria, 9 villagers; (B) upper respiratory infection, 25; lower respiratory infection, 10; tuberculosis, 9; (C) tinea imbricata, 15) and were highly represented in declared medical histories ((A) 75 participants, (B) 23, (C) 35). However, 29.2% of diagnoses (49/168) were limited to one or two people. Treatment approaches included plant medicines, stored pharmaceuticals, occasionally rituals. Travel to hospital/pharmacy was sometimes undertaken for severe/refractory disease. Service barriers included: no health patrols/accessible aid post, remote hospital, unfamiliarity with institutions and medicine costs. Service introduction priorities were: aid post, vaccinations, transport, perinatal/birth care and family planning.

CONCLUSIONS: This study enabled service planning and demonstrated a need sufficient to acquire funding to establish primary care. In doing so, it aided Wanang's community to develop sustainably, without sacrificing their forest home.}, } @article {pmid37798344, year = {2023}, author = {Shim, T and Kim, Z and Jung, J}, title = {A Benford's law-based framework to determine the threshold of occurrence sites for species distribution modelling from ecological monitoring databases.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {16777}, pmid = {37798344}, issn = {2045-2322}, mesh = {*Reproducibility of Results ; Databases, Factual ; }, abstract = {The use of data-based species distribution models (SDMs) has increased significantly in recent years. However, studies of determining the minimum requirements of occurrence sites from ecological monitoring datasets used in species distribution modelling remain insufficient. Therefore, this study proposed a framework to determine the threshold of minimum occurrence sites for SDMs by assessing compliance with Benford's law. The compliance test verified that the national-scale freshwater fish monitoring dataset was natural and reliable. Results derived from true skill statistics (TSS) determined the minimum number of occurrence sites for reliable species distribution modelling was 20 with a TSS value of 0.793 and an overall accuracy of 0.804. The Benford compliance test has shown to be a useful tool for swift and efficient evaluation of the reliability of species occurrence datasets, or the determination of the threshold of occurrence sites before species distribution modelling. Further studies regarding the evaluation of this method's transferability to other species and validation using SDM performance are required. Overall, the framework proposed in this study demonstrates that Benford compliance test applied to species monitoring datasets can be used to derive a universal and model-independent minimum occurrence threshold for SDMs.}, } @article {pmid37796561, year = {2023}, author = {Jordan, EJ and Shih, PC and Nelson, EJ and Carter, SJ and Schootman, M and Prather, AA and Yao, X and Peters, CD and Perry, CSE}, title = {Ecological Momentary Assessment of Midlife Adults' Daily Stress: Protocol for the Stress Reports in Variable Environments (STRIVE) App Study.}, journal = {JMIR research protocols}, volume = {12}, number = {}, pages = {e51845}, pmid = {37796561}, issn = {1929-0748}, support = {R21 AG077333/AG/NIA NIH HHS/United States ; }, abstract = {BACKGROUND: Daily stressors are associated with cognitive decline and increased risk of heart disease, depression, and other debilitating chronic illnesses in midlife adults. Daily stressors tend to occur at home or at work and are more frequent in urban versus rural settings. Conversely, spending time in natural environments such as parks or forests, or even viewing nature-themed images in a lab setting, is associated with lower levels of perceived stress and is hypothesized to be a strong stress "buffer," reducing perceived stress even after leaving the natural setting. However, many studies of daily stress have not captured environmental contexts and relied on end-of-day recall instead of in-the-moment data capture. With new technology, these limitations can be addressed to enhance knowledge of the daily stress experience.

OBJECTIVE: We propose to use our novel custom-built Stress Reports in Variable Environments (STRIVE) ecological momentary assessment mobile phone app to measure the experience of daily stress of midlife adults in free-living conditions. Using our app to capture data in real time will allow us to determine (1) where and when daily stress occurs for midlife adults, (2) whether midlife adults' daily stressors are linked to certain elements of the built and natural environment, and (3) how ecological momentary assessment measurement of daily stress is similar to and different from a modified version of the popular Daily Inventory of Stressful Events measurement tool that captures end-of-day stress reports (used in the Midlife in the United States [MIDUS] survey).

METHODS: We will enroll a total of 150 midlife adults living in greater Indianapolis, Indiana, in this study on a rolling basis for 3-week periods. As those in underrepresented minority groups and low-income areas have previously been found to experience greater levels of stress, we will use stratified sampling to ensure that half of our study sample is composed of underrepresented minorities (eg, Black, American Indian, Hispanic, or Native Pacific Islanders) and approximately one-third of our sample falls within low-, middle-, and high-income brackets.

RESULTS: This project is funded by the National Institute on Aging from December 2022 to November 2024. Participant enrollment began in August 2023 and is expected to finish in July 2024. Data will be spatiotemporally analyzed to determine where and when stress occurs for midlife adults. Pictures of stressful environments will be qualitatively analyzed to determine the common elements of stressful environments. Data collected by the STRIVE app will be compared with retrospective Daily Inventory of Stressful Events data.

CONCLUSIONS: Completing this study will expand our understanding of midlife adults' experience of stress in free-living conditions and pave the way for data-driven individual and community-based intervention designs to promote health and well-being in midlife adults.

DERR1-10.2196/51845.}, } @article {pmid37794496, year = {2023}, author = {Lühken, R and Becker, N and Dyczko, D and Sauer, FG and Kliemke, K and Schmidt-Chanasit, J and Rydzanicz, K}, title = {First record of Anopheles (Anopheles) hyrcanus (Pallas 1771) (Diptera: Culicidae) in Poland.}, journal = {Parasites & vectors}, volume = {16}, number = {1}, pages = {345}, pmid = {37794496}, issn = {1756-3305}, support = {BMBF//Bundesministerium für Bildung und Forschung/ ; BMBF//Bundesministerium für Bildung und Forschung/ ; BMBF//Bundesministerium für Bildung und Forschung/ ; }, mesh = {Animals ; *Culicidae ; *Anopheles/parasitology ; Poland ; Mosquito Vectors ; Climate ; Europe ; }, abstract = {The spatial distribution of mosquito species in the course of globalization and climate warming is highly dynamic. Different studies have demonstrated the spread and establishment of thermophilic mosquito species, potentially increasing the prevalence of 'nuisance' mosquitoes and the local transmission of pathogens. Here we report the first recorded sampling of Anopheles hyrcanus in Wrocław, southwest Poland. This is the most northern detection of this species to date in Europe. Future spread and population development of this potential vector of malaria parasites, viruses or zoonotic helminths, such as Dirofilaria spp., must be monitored carefully. Potential factors underlying the spread of this species are discussed.}, } @article {pmid37793967, year = {2023}, author = {Brehm, AM and Orrock, JL}, title = {Extensive behavioral data contained within existing ecological datasets.}, journal = {Trends in ecology & evolution}, volume = {38}, number = {12}, pages = {1129-1133}, doi = {10.1016/j.tree.2023.08.016}, pmid = {37793967}, issn = {1872-8383}, mesh = {*Ecology ; *Datasets as Topic ; }, abstract = {Long-term ecological datasets contain vast behavioral data, enabling the quantification of among-individual behavioral variation at unprecedented spatiotemporal scales. We detail how behaviors can be extracted and describe how such data can be used to test new hypotheses, inform population and community ecology, and address pressing conservation needs.}, } @article {pmid37789481, year = {2022}, author = {Cao, J and Zhang, Y and Tan, S and Yang, Q and Wang, HL and Xia, X and Luo, J and Guo, H and Zhang, Z and Li, Z}, title = {LSD 4.0: an improved database for comparative studies of leaf senescence.}, journal = {Molecular horticulture}, volume = {2}, number = {1}, pages = {24}, pmid = {37789481}, issn = {2730-9401}, support = {32170345//National Natural Science Foundation of China/ ; 31970196//National Natural Science Foundation of China/ ; XDA19050302//Strategic Priority Research Program of the Chinese Academy of Sciences/ ; XDB13040500//Strategic Priority Research Program of the Chinese Academy of Sciences/ ; 2017YFC0907502//National Key Research and Development Program of China, Startup Funding/ ; XXH13505-05//13th Five-year Informatization Plan of Chinese Academy of Sciences/ ; 153F11KYSB20160008//International Partnership Program of the Chinese Academy of Sciences/ ; 2019YFA0903904//National Key Research and Development Program of China/ ; }, } @article {pmid37789366, year = {2023}, author = {Reinar, WB and Tørresen, OK and Nederbragt, AJ and Matschiner, M and Jentoft, S and Jakobsen, KS}, title = {Teleost genomic repeat landscapes in light of diversification rates and ecology.}, journal = {Mobile DNA}, volume = {14}, number = {1}, pages = {14}, pmid = {37789366}, issn = {1759-8753}, support = {222378/WT_/Wellcome Trust/United Kingdom ; 222378/WT_/Wellcome Trust/United Kingdom ; }, abstract = {Repetitive DNA make up a considerable fraction of most eukaryotic genomes. In fish, transposable element (TE) activity has coincided with rapid species diversification. Here, we annotated the repetitive content in 100 genome assemblies, covering the major branches of the diverse lineage of teleost fish. We investigated if TE content correlates with family level net diversification rates and found support for a weak negative correlation. Further, we demonstrated that TE proportion correlates with genome size, but not to the proportion of short tandem repeats (STRs), which implies independent evolutionary paths. Marine and freshwater fish had large differences in STR content, with the most extreme propagation detected in the genomes of codfish species and Atlantic herring. Such a high density of STRs is likely to increase the mutational load, which we propose could be counterbalanced by high fecundity as seen in codfishes and herring.}, } @article {pmid37787405, year = {2024}, author = {Brooks, BW and van den Berg, S and Dreier, DA and LaLone, CA and Owen, SF and Raimondo, S and Zhang, X}, title = {Towards Precision Ecotoxicology: Leveraging Evolutionary Conservation of Pharmaceutical and Personal Care Product Targets to Understand Adverse Outcomes Across Species and Life Stages.}, journal = {Environmental toxicology and chemistry}, volume = {43}, number = {3}, pages = {526-536}, pmid = {37787405}, issn = {1552-8618}, support = {EPA999999/ImEPA/Intramural EPA/United States ; P01 ES028942/ES/NIEHS NIH HHS/United States ; 1P01ES028942/ES/NIEHS NIH HHS/United States ; }, mesh = {Humans ; Ecotoxicology ; Ecosystem ; Environmental Monitoring ; Risk Assessment ; *Cosmetics/toxicity/analysis ; Pharmaceutical Preparations ; *Water Pollutants, Chemical/analysis ; }, abstract = {Translation of environmental science to the practice aims to protect biodiversity and ecosystem services, and our future ability to do so relies on the development of a precision ecotoxicology approach wherein we leverage the genetics and informatics of species to better understand and manage the risks of global pollution. A little over a decade ago, a workshop focusing on the risks of pharmaceuticals and personal care products (PPCPs) in the environment identified a priority research question, "What can be learned about the evolutionary conservation of PPCP targets across species and life stages in the context of potential adverse outcomes and effects?" We review the activities in this area over the past decade, consider prospects of more recent developments, and identify future research needs to develop next-generation approaches for PPCPs and other global chemicals and waste challenges. Environ Toxicol Chem 2024;43:526-536. © 2023 SETAC. This article has been contributed to by U.S. Government employees and their work is in the public domain in the USA.}, } @article {pmid37781634, year = {2022}, author = {Vila, R and Lohse, K and Hayward, A and Laetsch, DR and , and , and , and Wahlberg, N and , }, title = {The genome sequence of the white admiral, Limenitis camilla (Linnaeus, 1764).}, journal = {Wellcome open research}, volume = {7}, number = {}, pages = {301}, pmid = {37781634}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual female Limenitis camilla (the white admiral; Arthropoda; Insecta; Lepidoptera; Nymphalidae). The genome sequence is 435 megabases in span. Most of the assembly (99.97%) is scaffolded into 31 chromosomal pseudomolecules, corresponding to 29 autosomes plus the W and Z sex chromosomes. The complete mitochondrial genome was also assembled and is 15.2 kilobases in length. Gene annotation of this assembly on Ensembl identified 12,489 protein coding genes.}, } @article {pmid37781318, year = {2023}, author = {Petza, D and Amorim, E and Ben Lamine, E and Colloca, F and Dominguez Crisóstomo, E and Fabbrizzi, E and Fraschetti, S and Galparsoro, I and Giakoumi, S and Kruse, M and Stelzenmüller, V and Katsanevakis, S}, title = {Assessing the potential of Other Effective area-based Conservation Measures (OECMs) for contributing to conservation targets: A global scoping review protocol.}, journal = {Open research Europe}, volume = {3}, number = {}, pages = {118}, pmid = {37781318}, issn = {2732-5121}, abstract = {This scoping review (ScR) protocol aims to establish the methodological approach for identifying and mapping the evidence regarding the actual contribution of Other Effective area-based Conservation Measures (OECMs) to spatial conservation targets. Emphasis will be placed on examining the research conducted, including the methodologies applied. OECMs, introduced by the Convention on Biological Diversity (CBD) in 2010, refer to areas outside of protected areas, such as fisheries restricted areas, archaeological sites, and military areas, that effectively conserve biodiversity in-situ over the long term. OECMs are recognized rather than designated. Many countries currently endeavor to identify, recognize and report OECMs to the CBD for formal acceptance to support the implementation of spatial conservation targets. Studies that assess the contribution of OECMs to spatial conservation targets will be considered. Potential OECMs with primary, secondary or ancillary conservation objectives established by all sectors in the terrestrial, freshwater and marine realm worldwide will be considered. Peer-reviewed and grey literature will be considered without imposing limitations based on publication year, stage, subject area and source type. Both experimental and observational studies in English, French, German, Greek, Italian, and Spanish will be reviewed. The ScR will follow the Joanna Briggs Institute (JBI) methodology. The protocol will be guided by the PRISMA-ScR (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) extension for scoping reviews. The search will encompass bibliographic databases such as Scopus, Web of Science and Google Scholar. Grey literature sources will include databases, pre-print archives and organizational websites. The Covidence platform will be utilized for data management and extraction.}, } @article {pmid37777307, year = {2023}, author = {Strobl, MAR and Gallaher, J and Robertson-Tessi, M and West, J and Anderson, ARA}, title = {Treatment of evolving cancers will require dynamic decision support.}, journal = {Annals of oncology : official journal of the European Society for Medical Oncology}, volume = {34}, number = {10}, pages = {867-884}, pmid = {37777307}, issn = {1569-8041}, support = {U01 CA232382/CA/NCI NIH HHS/United States ; U54 CA193489/CA/NCI NIH HHS/United States ; }, mesh = {Humans ; *Neoplasms/drug therapy ; *Decision Support Systems, Clinical ; Precision Medicine ; Models, Theoretical ; }, abstract = {Cancer research has traditionally focused on developing new agents, but an underexplored question is that of the dose and frequency of existing drugs. Based on the modus operandi established in the early days of chemotherapies, most drugs are administered according to predetermined schedules that seek to deliver the maximum tolerated dose and are only adjusted for toxicity. However, we believe that the complex, evolving nature of cancer requires a more dynamic and personalized approach. Chronicling the milestones of the field, we show that the impact of schedule choice crucially depends on processes driving treatment response and failure. As such, cancer heterogeneity and evolution dictate that a one-size-fits-all solution is unlikely-instead, each patient should be mapped to the strategy that best matches their current disease characteristics and treatment objectives (i.e. their 'tumorscape'). To achieve this level of personalization, we need mathematical modeling. In this perspective, we propose a five-step 'Adaptive Dosing Adjusted for Personalized Tumorscapes (ADAPT)' paradigm to integrate data and understanding across scales and derive dynamic and personalized schedules. We conclude with promising examples of model-guided schedule personalization and a call to action to address key outstanding challenges surrounding data collection, model development, and integration.}, } @article {pmid37776607, year = {2023}, author = {Brant, LCC and Pinheiro, PC and Passaglia, LG and de Souza, MFM and Malta, DC and Banerjee, A and Ribeiro, ALP and Nascimento, BR}, title = {Cardiovascular mortality in Brazil during the COVID-19 pandemic: a comparison between underlying and multiple causes of death.}, journal = {Public health}, volume = {224}, number = {}, pages = {131-139}, doi = {10.1016/j.puhe.2023.08.027}, pmid = {37776607}, issn = {1476-5616}, mesh = {Humans ; *COVID-19/mortality/epidemiology ; Brazil/epidemiology ; *Cardiovascular Diseases/mortality/epidemiology ; *Cause of Death ; Male ; Female ; Middle Aged ; Aged ; Adult ; Aged, 80 and over ; SARS-CoV-2 ; Pandemics ; }, abstract = {OBJECTIVES: The COVID-19 pandemic has differentially impacted cardiovascular disease (CVD) mortality worldwide. Causes of death misclassification may be one of the reasons. We evaluated the impact of the pandemic on CVD mortality in Brazil, comparing underlying causes (UCs) and multiple causes (MCs) of death.

STUDY DESIGN: Ecological time-series study.

METHODS: An ecological, time-series study was conducted analysing age-standardised death rates for CVD, from epidemiological week (EW) 10/2020 to 39/2021, using data from the Mortality Information System, Brazil. CVD was defined using the International Classification of Diseases (ICD-10) coding, if reported as UC or MC of death. Observed and expected data (mean for the same EW, 2017-2019) were compared. Risk ratios (RiRs) were analysed, and 95% confidence intervals (CIs) were calculated.

RESULTS: Age-standardised mortality rate for CVD as UC of death was 165.8 (95%CI: 165.4-166.3) per 100,000 inhabitants, similar to what was expected (165.6/100,000, 95%CI: 165.2-166.1, RiR = 1.00). There was increased out-of-hospital mortality (RiR = 1.18; 95%CI: 1.17-1.19) and deaths of ill-defined causes (RiR = 1.43; 95%CI: 1.42-1.44). The increase in out-of-hospital deaths was more pronounced in the North (RiR = 1.33; 95%CI 1.30-1.36) region, with a less resilient health system. Conversely, as MCs of death, there was a 10% increase in CVD mortality (observed: 243.2 [95%CI: 242.7-243.7], expected: 221.6 [95%CI: 221.1-222.1] per 100,000). An increase also occurred in the North and Central West regions (RiR = 1.16; 95%CI: 1.15-1.18), among men (RiR = 1.11; 95%CI: 1.11-1.12) and individuals aged ≥60 years (RiR = 1.11; 95%CI: 1.10-1.11).

CONCLUSIONS: During the pandemic, mortality rates for CVD as MCs of death increased in Brazil, whereas as UC mortality rates did not change. Higher out-of-hospital mortality, misclassification, and competing causes of death may explain this pattern.}, } @article {pmid37775284, year = {2023}, author = {Murray, A and Speyer, L and Thye, M and Stewart, T and Obsuth, I and Kane, J and Whyte, K and Devaney, J and Rohde, LA and Ushakova, A and Rhodes, S}, title = {Illuminating the daily life experiences of adolescents with and without ADHD: protocol for an ecological momentary assessment study.}, journal = {BMJ open}, volume = {13}, number = {9}, pages = {e077222}, pmid = {37775284}, issn = {2044-6055}, support = {/WT_/Wellcome Trust/United Kingdom ; 225364/Z/22/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Humans ; Adolescent ; *Attention Deficit Disorder with Hyperactivity/diagnosis ; Ecological Momentary Assessment ; Life Change Events ; State Medicine ; Mental Health ; }, abstract = {INTRODUCTION: Adolescents with attention-deficit/hyperactivity disorder (ADHD) are at elevated risk of a range of difficulties, among which emotion regulation, peer and co-occurring mental health problems are prominent challenges. To better support adolescents with ADHD, ecologically valid interventions that can be embedded in daily life to target the most proximal antecedents of these challenges are needed. Ecological momentary assessment (EMA) designs are ideally suited to meeting this need.

METHODS AND ANALYSES: In the mental health in the moment ADHD study, we will use an EMA design to capture the daily life experiences of approximately 120 adolescents aged 11-14 years with a clinical diagnosis of ADHD and the same number of age-matched and gender-matched peers without a diagnosis of ADHD. We will combine this with comprehensive information gathered from online surveys. Analysing the data using techniques such as dynamic structural equation modelling, we will examine, among other research questions, the role of emotion regulation and peer problems in mediating the links between characteristics of ADHD and commonly co-occurring outcomes such as anxiety, depression and conduct problems. The results can help inform interventions to support improved peer functioning and emotion regulation for adolescents with ADHD.

ETHICS AND DISSEMINATION: This study received a favourable ethical opinion through the National Health Service ethical review board and the University of Edinburgh PPLS Research Ethics panel. The results will be disseminated through journal publications, conferences and seminar presentations and to relevant stakeholders, such as those with ADHD, their families and clinicians.}, } @article {pmid37771003, year = {2023}, author = {Gautam, A and Bhowmik, D and Basu, S and Zeng, W and Lahiri, A and Huson, DH and Paul, S}, title = {Microbiome Metabolome Integration Platform (MMIP): a web-based platform for microbiome and metabolome data integration and feature identification.}, journal = {Briefings in bioinformatics}, volume = {24}, number = {6}, pages = {}, doi = {10.1093/bib/bbad325}, pmid = {37771003}, issn = {1477-4054}, mesh = {*Metabolome ; *Microbiota ; Metabolomics/methods ; Internet ; }, abstract = {A microbial community maintains its ecological dynamics via metabolite crosstalk. Hence, knowledge of the metabolome, alongside its populace, would help us understand the functionality of a community and also predict how it will change in atypical conditions. Methods that employ low-cost metagenomic sequencing data can predict the metabolic potential of a community, that is, its ability to produce or utilize specific metabolites. These, in turn, can potentially serve as markers of biochemical pathways that are associated with different communities. We developed MMIP (Microbiome Metabolome Integration Platform), a web-based analytical and predictive tool that can be used to compare the taxonomic content, diversity variation and the metabolic potential between two sets of microbial communities from targeted amplicon sequencing data. MMIP is capable of highlighting statistically significant taxonomic, enzymatic and metabolic attributes as well as learning-based features associated with one group in comparison with another. Furthermore, MMIP can predict linkages among species or groups of microbes in the community, specific enzyme profiles, compounds or metabolites associated with such a group of organisms. With MMIP, we aim to provide a user-friendly, online web server for performing key microbiome-associated analyses of targeted amplicon sequencing data, predicting metabolite signature, and using learning-based linkage analysis, without the need for initial metabolomic analysis, and thereby helping in hypothesis generation.}, } @article {pmid37767299, year = {2023}, author = {Cai, J and Pan, R and Lin, J and Liu, J and Zhang, L and Wen, X and Chen, X and Zhang, X}, title = {Improved EfficientNet for corn disease identification.}, journal = {Frontiers in plant science}, volume = {14}, number = {}, pages = {1224385}, pmid = {37767299}, issn = {1664-462X}, abstract = {INTRODUCTION: Corn is one of the world's essential crops, and the presence of corn diseases significantly affects both the yield and quality of corn. Accurate identification of corn diseases in real time is crucial to increasing crop yield and improving farmers' income. However, in real-world environments, the complexity of the background, irregularity of the disease region, large intraclass variation, and small interclass variation make it difficult for most convolutional neural network models to achieve disease recognition under such conditions. Additionally, the low accuracy of existing lightweight models forces farmers to compromise between accuracy and real-time.

METHODS: To address these challenges, we propose FCA-EfficientNet. Building upon EfficientNet, the fully-convolution-based coordinate attention module allows the network to acquire spatial information through convolutional structures. This enhances the network's ability to focus on disease regions while mitigating interference from complex backgrounds. Furthermore, the adaptive fusion module is employed to fuse image information from different scales, reducing interference from the background in disease recognition. Finally, through multiple experiments, we have determined the network structure that achieves optimal performance.

RESULTS: Compared to other widely used deep learning models, this proposed model exhibits outstanding performance in terms of accuracy, precision, recall, and F1 score. Furthermore, the model has a parameter count of 3.44M and Flops of 339.74M, which is lower than most lightweight network models. We designed and implemented a corn disease recognition application and deployed the model on an Android device with an average recognition speed of 92.88ms, which meets the user's needs.

DISCUSSION: Overall, our model can accurately identify corn diseases in realistic environments, contributing to timely and effective disease prevention and control.}, } @article {pmid37767015, year = {2022}, author = {Boyes, D and , and , and , and , and , and Couch, C and Plotkin, D and Kawahara, AY and , }, title = {The genome sequence of the peacock moth, Macaria notata (Linnaeus, 1758).}, journal = {Wellcome open research}, volume = {7}, number = {}, pages = {228}, pmid = {37767015}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual male Macaria notata (the peacock moth; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 394 megabases in span. The majority of the assembly (99.98%) is scaffolded into 29 chromosomal pseudomolecules with the Z sex chromosome assembled. The complete mitochondrial genome was also assembled and is 15.4 kilobases in length.}, } @article {pmid37766852, year = {2023}, author = {Boyes, D and Lewis, OT and , and , and , and , and , and , }, title = {The genome sequence of the Broken-barred Carpet, Electrophaes corylata (Thunberg, 1792).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {283}, pmid = {37766852}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual male Electrophaes corylata (the Broken-barred Carpet; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 347.5 megabases in span. Most of the assembly is scaffolded into 30 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 16.36 kilobases in length. Gene annotation of this assembly on Ensembl identified 16,031 protein coding genes.}, } @article {pmid37766851, year = {2023}, author = {Boyes, D and Lewis, OT and , and , and , and , and , and , }, title = {The genome sequence of the Dark Spectacle, Abrostola triplasia (Linnaeus, 1758).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {278}, pmid = {37766851}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual male Abrostola triplasia (the Dark Spectacle; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 362.7 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.34 kilobases in length. Gene annotation of this assembly on Ensembl identified 11,532 protein coding genes.}, } @article {pmid37759063, year = {2023}, author = {Ha, LT}, title = {Scrutinizing the nexus between green innovations and the sustainability of environmental system: novel insights from European database.}, journal = {Environmental science and pollution research international}, volume = {30}, number = {50}, pages = {109087-109109}, pmid = {37759063}, issn = {1614-7499}, mesh = {*Ecosystem ; *Agriculture ; Biodiversity ; Databases, Factual ; Europe ; Economic Development ; Carbon Dioxide ; }, abstract = {A study is presented in this paper that examines the effect of environmental innovation (EI) on environmental performance (EP). Six measures are used to reflect environmental innovation, including the percentage of enterprises that invest in environmental innovation, the percentage of enterprises implementing environmental innovation activities, the number of ISO 14001 certificates, patents related to environmental innovation, the total R&D personnel and researchers, and the amount of green early-stage investments. The estimation results show that EI positively impacts EP in 21 European countries using different econometric techniques during the 2011-2019 period. By using various econometric techniques (namely a panel-corrected standard errors (PCSE) model, a feasible generalized least square estimates (FGLS) model, and the two-step general method of moment (the two-step GMM), our research demonstrates how environmental innovation impacts on environmental quality. The short- and long-term effects of autoregressive distributed lag (ARDL) methods were also investigated using pooled mean groups (PMGs) to distinguish the short-run and long-run influences of EI. The relationship between EI and EP is explored by demonstrating how EI affects EP short- and long-term and comparing its influence on EP across many component measures of EI: air quality, sanitation, drinking water, heavy metals, waste management, biodiversity, habitat, ecosystem services, water resources, and agriculture. Notably, we find that the influences of EI become more pronounced in a country characterized by a well-developed institutional system. Our findings suggest policy implications to help countries invest in research and development with concerns about environmental damage mitigations more effectively. These findings are critical to suggest a way to help countries pursue ecological sustainability.}, } @article {pmid37755898, year = {2023}, author = {Bekele, D and Aragie, S and Alene, KA and Dejene, T and Warkaye, S and Mezemir, M and Abdena, D and Kebebew, T and Botore, A and Mekonen, G and Gutema, G and Dufera, B and Gemede, K and Kenate, B and Gobena, D and Alemu, B and Hailemariam, D and Muleta, D and Siu, GKH and Tafess, K}, title = {Spatiotemporal Distribution of Tuberculosis in the Oromia Region of Ethiopia: A Hotspot Analysis.}, journal = {Tropical medicine and infectious disease}, volume = {8}, number = {9}, pages = {}, pmid = {37755898}, issn = {2414-6366}, abstract = {Tuberculosis (TB) is a major public health concern in low- and middle-income countries including Ethiopia. This study aimed to assess the spatiotemporal distribution of TB and identify TB risk factors in Ethiopia's Oromia region. Descriptive and spatiotemporal analyses were conducted. Bayesian spatiotemporal modeling was used to identify covariates that accounted for variability in TB and its spatiotemporal distribution. A total of 206,278 new pulmonary TB cases were reported in the Oromia region between 2018 and 2022, with the lowest annual TB case notification (96.93 per 100,000 population) reported in 2020 (i.e., during the COVID-19 pandemic) and the highest TB case notification (106.19 per 100,000 population) reported in 2019. Substantial spatiotemporal variations in the distribution of notified TB case notifications were observed at zonal and district levels with most of the hotspot areas detected in the northern and southern parts of the region. The spatiotemporal distribution of notified TB incidence was positively associated with different ecological variables including temperature (β = 0.142; 95% credible interval (CrI): 0.070, 0.215), wind speed (β = -0.140; 95% CrI: -0.212, -0.068), health service coverage (β = 0.426; 95% CrI: 0.347, 0.505), and population density (β = 0.491; 95% CrI: 0.390, 0.594). The findings of this study indicated that preventive measures considering socio-demographic and health system factors can be targeted to high-risk areas for effective control of TB in the Oromia region. Further studies are needed to develop effective strategies for reducing the burden of TB in hotspot areas.}, } @article {pmid37754785, year = {2023}, author = {Leo, P and Onofri, S and Zucconi, L and Selbmann, L and Turchetti, B and Buzzini, P and Chander, AM and Simpson, A and Singh, N and Vellone, D and Tighe, S and Venkateswaran, K}, title = {Draft genome sequencing of Naganishia species isolated from the polar environments.}, journal = {Microbiology resource announcements}, volume = {12}, number = {10}, pages = {e0038823}, pmid = {37754785}, issn = {2576-098X}, support = {18-PPR18-0011//National Aeronautics and Space Administration (NASA)/ ; }, abstract = {The draft genomes of five Naganishia strains were sequenced using MinION and annotated using Funannotate pipeline. Phylogenetic and genomic analyses were performed to provide their genetic relationships, diversity, and potential functional capabilities. This approach will aid in understanding their potential to survive under microgravity and their resilience to extreme environments.}, } @article {pmid37754733, year = {2023}, author = {Ježová, Z and Prokop, P and Zvaríková, M and Zvarík, M}, title = {Unraveling the Significance of Draglines: Female Sexual Signalization in the Nursery-Web Spider, Pisaura mirabilis.}, journal = {Insects}, volume = {14}, number = {9}, pages = {}, pmid = {37754733}, issn = {2075-4450}, support = {20-0081//Slovak Research and Development Agency/ ; }, abstract = {Chemical signals used by animals to attract the opposite sex are well known in insects, but heavily understudied in spiders. We investigated the role of chemical signals in female draglines in a gift-giving spider, Pisaura mirabilis, using combined data from behavioral tests and high-performance liquid chromatography (HPLC). We also investigated whether the quality of sexual signalization is influenced by crucial factors, such as female spider ontogeny, nutritional status, and mating status. We found that draglines of adult (versus subadult) and hungry (versus fed) females stimulated male motivation to produce nuptial gift, and highly sexually excited males invested more silk in gift production than less sexually excited males. Unexpectedly, chemical signals of eggsac-carrying females were similarly sexually attractive to draglines of adult females not carrying eggsac. HPLC identified significant chemical differences in female draglines, but these differences did not always correspond to male behavior. The integration of behavioral and chemical approaches is required to better understand animal behavior in future research.}, } @article {pmid37753602, year = {2023}, author = {Aguiar, A and Gebremariam, MK and Romanenko, E and Önal, F and Kopainsky, B and Savona, N and Brown, A and Allender, S and Lien, N}, title = {System dynamics simulation models on overweight and obesity in children and adolescents: A systematic review.}, journal = {Obesity reviews : an official journal of the International Association for the Study of Obesity}, volume = {24 Suppl 2}, number = {}, pages = {e13632}, doi = {10.1111/obr.13632}, pmid = {37753602}, issn = {1467-789X}, mesh = {Child ; Adolescent ; Humans ; *Overweight/epidemiology ; *Pediatric Obesity/epidemiology/prevention & control ; Databases, Factual ; Pandemics ; Policy ; }, abstract = {It has increasingly been recognized that developing successful obesity prevention policies and interventions requires understanding of the complex mechanisms driving the obesity pandemic and that models could be useful tools for simulating policies. This paper reviews system dynamics simulation models of mechanisms driving childhood overweight and obesity and/or testing of preventive interventions. A systematic literature search was conducted in six databases from inception to January 2023 using terms related to overweight/obesity, children, and system dynamics. Study descriptives, mechanisms, and where to intervene (the leverage points), as well as quality assessments of the simulation models were extracted by two researchers into a predetermined template and narratively synthesized. Seventeen papers describing 15 models were included. Models describing the mechanisms ranged from only intrapersonal factors to models cutting across multiple levels of the ecological model, but mechanisms across levels were lacking. The majority of interventions tested in the simulation models were changes to existing model parameters with less emphasis on models that alter system structure. In conclusion, existing models included mechanisms driving youth obesity at multiple levels of the ecological model. This is useful for developing an integrated simulation model combining mechanisms at multiple levels and allowing for testing fundamental system changes.}, } @article {pmid37749493, year = {2023}, author = {Smith, SK and Frazel, PW and Khodadadi-Jamayran, A and Zappile, P and Marier, C and Okhovat, M and Brown, S and Long, MA and Heguy, A and Phelps, SM}, title = {De novo assembly and annotation of the singing mouse genome.}, journal = {BMC genomics}, volume = {24}, number = {1}, pages = {569}, pmid = {37749493}, issn = {1471-2164}, support = {P30 CA016087/CA/NCI NIH HHS/United States ; R01 NS113071/NS/NINDS NIH HHS/United States ; R01 NS113071/GF/NIH HHS/United States ; }, mesh = {Male ; Animals ; Mice ; *Genomics ; *Biological Evolution ; Multifactorial Inheritance ; Phenotype ; Reproduction ; }, abstract = {BACKGROUND: Developing genomic resources for a diverse range of species is an important step towards understanding the mechanisms underlying complex traits. Specifically, organisms that exhibit unique and accessible phenotypes-of-interest allow researchers to address questions that may be ill-suited to traditional model organisms. We sequenced the genome and transcriptome of Alston's singing mouse (Scotinomys teguina), an emerging model for social cognition and vocal communication. In addition to producing advertisement songs used for mate attraction and male-male competition, these rodents are diurnal, live at high-altitudes, and are obligate insectivores, providing opportunities to explore diverse physiological, ecological, and evolutionary questions.

RESULTS: Using PromethION, Illumina, and PacBio sequencing, we produced an annotated genome and transcriptome, which were validated using gene expression and functional enrichment analyses. To assess the usefulness of our assemblies, we performed single nuclei sequencing on cells of the orofacial motor cortex, a brain region implicated in song coordination, identifying 12 cell types.

CONCLUSIONS: These resources will provide the opportunity to identify the molecular basis of complex traits in singing mice as well as to contribute data that can be used for large-scale comparative analyses.}, } @article {pmid37748067, year = {2023}, author = {Stenseth, NC and Schlatte, R and Liu, X and Pielke, R and Chen, B and Bjørnstad, ON and Kusnezov, D and Gao, GF and Fraser, C and Whittington, JD and Gong, P and Guan, D and Johnsen, EB}, title = {Reply to Ekström and Ottersen: Real-time access to data during outbreaks is a key to avoid a local epidemic becoming a global pandemic.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {120}, number = {40}, pages = {e2312649120}, pmid = {37748067}, issn = {1091-6490}, mesh = {*Pandemics/prevention & control ; *Disease Outbreaks/prevention & control ; }, } @article {pmid37745602, year = {2023}, author = {Crits-Christoph, A and Levy, JI and Pekar, JE and Goldstein, SA and Singh, R and Hensel, Z and Gangavarapu, K and Rogers, MB and Moshiri, N and Garry, RF and Holmes, EC and Koopmans, MPG and Lemey, P and Popescu, S and Rambaut, A and Robertson, DL and Suchard, MA and Wertheim, JO and Rasmussen, AL and Andersen, KG and Worobey, M and Débarre, F}, title = {Genetic tracing of market wildlife and viruses at the epicenter of the COVID-19 pandemic.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {37745602}, issn = {2692-8205}, support = {U19 AI135995/AI/NIAID NIH HHS/United States ; R01 AI153044/AI/NIAID NIH HHS/United States ; T15 LM011271/LM/NLM NIH HHS/United States ; T32 AI007244/AI/NIAID NIH HHS/United States ; 75N93021C00015/AI/NIAID NIH HHS/United States ; /WT_/Wellcome Trust/United Kingdom ; U01 AI151812/AI/NIAID NIH HHS/United States ; R01 AI135992/AI/NIAID NIH HHS/United States ; }, abstract = {Zoonotic spillovers of viruses have occurred through the animal trade worldwide. The start of the COVID-19 pandemic was traced epidemiologically to the Huanan Wholesale Seafood Market, the site with the most reported wildlife vendors in the city of Wuhan, China. Here, we analyze publicly available qPCR and sequencing data from environmental samples collected in the Huanan market in early 2020. We demonstrate that the SARS-CoV-2 genetic diversity linked to this market is consistent with market emergence, and find increased SARS-CoV-2 positivity near and within a particular wildlife stall. We identify wildlife DNA in all SARS-CoV-2 positive samples from this stall. This includes species such as civets, bamboo rats, porcupines, hedgehogs, and one species, raccoon dogs, known to be capable of SARS-CoV-2 transmission. We also detect other animal viruses that infect raccoon dogs, civets, and bamboo rats. Combining metagenomic and phylogenetic approaches, we recover genotypes of market animals and compare them to those from other markets. This analysis provides the genetic basis for a short list of potential intermediate hosts of SARS-CoV-2 to prioritize for retrospective serological testing and viral sampling.}, } @article {pmid37741542, year = {2023}, author = {Chen, H and Zhang, X and Ji, C and Deng, W and Yang, G and Hao, Z and Chen, B}, title = {Physicochemical properties of environmental media can affect the adsorption of arsenic (As) by microplastics.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {338}, number = {}, pages = {122592}, doi = {10.1016/j.envpol.2023.122592}, pmid = {37741542}, issn = {1873-6424}, mesh = {Humans ; Microplastics/chemistry ; Plastics ; *Arsenic/analysis ; Adsorption ; *Soil Pollutants/analysis ; *Metals, Heavy/analysis ; Soil/chemistry ; }, abstract = {Microplastics are emerging pollutants that can adsorb heavy metals and threaten human health through food chain. Recently, there has been increasing interest in understanding the adsorption behavior of heavy metals by microplastics in farmland soil. In particular, arsenic (As), as a carcinogen, has the potential to be adsorbed by soil microplastics. However, the mechanisms and controlling factors of As adsorption by microplastics in farmland soil under natural conditions are still unknown. Here, microplastics and As were respectively added to farmland soils with different physicochemical properties from twelve provinces of China for adsorption experiment. We performed surface analysis of microplastics, quantified As accumulation through quasi-first-order kinetic equation and developed regression models to screen the factors controlling As adsorption. The results showed that the adsorption of As by soil microplastics was a chemical process accompanied by the loss of electrons from oxygen-containing functional groups. Soil cation exchange capacity (CEC) was the main factor controlling the adsorption rate, while soil organic matter (SOM), total nitrogen (TN) and CEC mainly influenced the equilibrium adsorption capacity. This is the first report on microplastic-As adsorption in natural soil, which allows deeper insights into risk assessment, prediction and control of microplastic-As pollution in agricultural soil.}, } @article {pmid37737917, year = {2023}, author = {Miletić, S and Beloica, J and Perović, V and Miljković, P and Lukić, S and Obradović, S and Čakmak, D and Belanović-Simić, S}, title = {Environmental sensitivity assessment and land degradation in southeastern Serbia: application of modified MEDALUS model.}, journal = {Environmental monitoring and assessment}, volume = {195}, number = {10}, pages = {1241}, pmid = {37737917}, issn = {1573-2959}, mesh = {*Environmental Monitoring ; Serbia ; *Benchmarking ; Databases, Factual ; Droughts ; }, abstract = {This paper aims to improve the methodology and results accuracy of MEDALUS model for assessing land degradation sensitivity through the application of different data detail levels and by introducing the application of Ellenberg indices in metrics related to vegetation drought sensitivity assessment. For that purpose, the MEDALUS model was applied at 2 levels of detail. Level I (municipality level) implied the use of available large-scale databases and level II (watershed) contains more detailed information about vegetation used in the calculation of the VQI and MQI factors (Fig. S6). The comparison was made using data based on CORINE Land Cover (2012) and forest inventory data, complemented with object-based classification. Results showed that data based on forest inventory data with the application of Ellenberg's indices and object-based classification have one class more, critical (C1 and C2) and that the percentage distribution of classes is different in both quantitative (area size of class sensitivity) and qualitative (aggregation and dispersion of sensitivity classes). The use of data from Forest Management Plans and the application of Ellenberg's indices affect the quality of the results and find its application in the model, especially if these results are used for monitoring and land area management on fine scales. Remote sensed data images (Sentinel-2B) were introduced into the methodology as a very important environmental monitoring tool and model results validation.}, } @article {pmid37736012, year = {2023}, author = {Boyes, D and , and , and , and , and , and Holland, PWH and , }, title = {The genome sequence of the Rustic Shoulder-knot, Apamea sordens (Hufnagel, 1766).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {51}, pmid = {37736012}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual male Apamea sordens (the Rustic Shoulder-knot; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 614 megabases in span. The whole assembly is scaffolded into 31 chromosomal pseudomolecules, including the assembled Z sex chromosome. The mitochondrial genome has also been assembled and is 16.3 kilobases in length.}, } @article {pmid37735266, year = {2024}, author = {Camargo, AP and Roux, S and Schulz, F and Babinski, M and Xu, Y and Hu, B and Chain, PSG and Nayfach, S and Kyrpides, NC}, title = {Identification of mobile genetic elements with geNomad.}, journal = {Nature biotechnology}, volume = {42}, number = {8}, pages = {1303-1312}, pmid = {37735266}, issn = {1546-1696}, mesh = {*Interspersed Repetitive Sequences/genetics ; *Plasmids/genetics ; Software ; Databases, Genetic ; Molecular Sequence Annotation ; Genome, Viral/genetics ; Viruses/genetics ; Neural Networks, Computer ; Computational Biology/methods ; }, abstract = {Identifying and characterizing mobile genetic elements in sequencing data is essential for understanding their diversity, ecology, biotechnological applications and impact on public health. Here we introduce geNomad, a classification and annotation framework that combines information from gene content and a deep neural network to identify sequences of plasmids and viruses. geNomad uses a dataset of more than 200,000 marker protein profiles to provide functional gene annotation and taxonomic assignment of viral genomes. Using a conditional random field model, geNomad also detects proviruses integrated into host genomes with high precision. In benchmarks, geNomad achieved high classification performance for diverse plasmids and viruses (Matthews correlation coefficient of 77.8% and 95.3%, respectively), substantially outperforming other tools. Leveraging geNomad's speed and scalability, we processed over 2.7 trillion base pairs of sequencing data, leading to the discovery of millions of viruses and plasmids that are available through the IMG/VR and IMG/PR databases. geNomad is available at https://portal.nersc.gov/genomad .}, } @article {pmid37733803, year = {2023}, author = {Engloner, AI and Vargha, M and Kós, P and Borsodi, AK}, title = {Planktonic and epilithic prokaryota community compositions in a large temperate river reflect climate change related seasonal shifts.}, journal = {PloS one}, volume = {18}, number = {9}, pages = {e0292057}, pmid = {37733803}, issn = {1932-6203}, mesh = {*Plankton/genetics ; Climate Change ; Seasons ; Rivers ; Global Warming ; *Gammaproteobacteria ; }, abstract = {In freshwaters, microbial communities are of outstanding importance both from ecological and public health perspectives, however, they are threatened by the impact of global warming. To reveal how different prokaryotic communities in a large temperate river respond to environment conditions related to climate change, the present study provides the first detailed insight into the composition and spatial and year-round temporal variations of planktonic and epilithic prokaryotic community. Microbial diversity was studied using high-throughput next generation amplicon sequencing. Sampling was carried out monthly in the midstream and the littoral zone of the Danube, upstream and downstream from a large urban area. Result demonstrated that river habitats predominantly determine the taxonomic composition of the microbiota; diverse and well-differentiated microbial communities developed in water and epilithon, with higher variance in the latter. The composition of bacterioplankton clearly followed the prolongation of the summer resulting from climate change, while the epilithon community was less responsive. Rising water temperatures was associated with increased abundances of many taxa (such as phylum Actinobacteria, class Gammaproteobacteria and orders Synechococcales, Alteromonadales, Chitinophagales, Pseudomonadales, Rhizobiales and Xanthomonadales), and the composition of the microbiota also reflected changes of several further environmental factors (such as turbidity, TOC, electric conductivity, pH and the concentration of phosphate, sulphate, nitrate, total nitrogen and the dissolved oxygen). The results indicate that shift in microbial community responding to changing environment may be of crucial importance in the decomposition of organic compounds (including pollutants and xenobiotics), the transformation and accumulation of heavy metals and the occurrence of pathogens or antimicrobial resistant organisms.}, } @article {pmid37731848, year = {2023}, author = {Ohashi, K and Osanai, T and Fujiwara, K and Tanikawa, T and Tani, Y and Takamiya, S and Sato, H and Morii, Y and Ogasawara, K}, title = {Access to mechanical thrombectomy and ischemic stroke mortality in Japan: a spatial ecological study.}, journal = {Frontiers in neurology}, volume = {14}, number = {}, pages = {1209446}, pmid = {37731848}, issn = {1664-2295}, abstract = {BACKGROUND: Advances in stroke treatment have greatly improved outcomes; however, disparities in access to treatment might increase. Achieving equitable access to stroke treatment is a health policy challenge, as rapid treatment is essential for positive outcomes. This ecological cross-sectional study aimed to determine the relationship between the disparities in spatial accessibility to mechanical thrombectomy (SAMT) and stroke mortality rates in Japan, hypothesizing that disparities in SAMT may increase the differences in stroke mortality between regions.

METHODS: We used the average number of ischemic stroke (IS) deaths between 2020 and 2021 as the response variable; and SAMT, medical resources, and socioeconomic characteristics of each municipality as explanatory variables. A conditional autoregressive model was used to examine the association between the risk of stroke mortality and SAMT. The standardized mortality ratio (SMR) was mapped to understand the nationwide disparities in stroke mortality risk.

RESULTS: The median number of IS deaths was 17.5 persons per year in the municipalities (2020 to 2021). The study also found that municipalities with low SAMT were located in the northern part of Japan. The non-spatial regression model results indicated that poor accessibility, a small proportion of bachelor's degrees or higher, and a high proportion of workers in secondary industries were related to high IS mortality. Three models were evaluated using spatial analysis; Model 1 with accessibility indicators alone, Model 2 with medical resources added to Model 1, and Model 3 with socioeconomic characteristics added to Model 2. In Models 1 and 2, the population-weighted spatial accessibility index (PWSAI) showed a significant negative relationship with stroke mortality. However, this was not evident in Model 3. Mapping using Model 3 showed that the high-risk areas were predominantly located in northern Japan, excluding Hokkaido.

CONCLUSION: Access to mechanical thrombectomy was estimated, and regional differences were observed. The relationship between accessibility and IS mortality is unknown; however, regardless of accessibility, municipalities with a high proportion of workers in secondary industries and a small proportion with bachelor's degrees or above are at risk of death from stroke.}, } @article {pmid37731597, year = {2023}, author = {Molina, MA and Melchers, WJG and Andralojc, KM and Leenders, WPJ and Huynen, MA}, title = {Longitudinal analysis on the ecological dynamics of the cervicovaginal microbiome in hrHPV infection.}, journal = {Computational and structural biotechnology journal}, volume = {21}, number = {}, pages = {4424-4431}, pmid = {37731597}, issn = {2001-0370}, abstract = {The cervicovaginal microbiome (CVM) is a dynamic continuous microenvironment that can be clustered in microbial community state types (CSTs) and is associated with women's cervical health. Lactobacillus-depleted communities particularly associate with an increased susceptibility for persistence of high-risk human papillomavirus (hrHPV) infections and progression of disease, but the long-term ecological dynamics of CSTs after hrHPV infection diagnosis remain poorly understood. To determine such dynamics, we examined the CVM of our longitudinal cohort of 141 women diagnosed with hrHPV infection at baseline with collected cervical smears at two timepoints six-months apart. Here we describe that the long-term microbiome dissimilarity has a positive correlation with microbial diversity at both visits and that women with high abundance and dominance for Lactobacillus iners at baseline exhibit more similar microbiome composition at second visit than women with Lactobacillus-depleted communities at baseline. We further show that the species Lactobacillus acidophilus and Megasphaera genomosp type 1 associate with CST changes between both visits. Lastly, we also observe that Gardnerella vaginalis is associated with the stability of Lactobacillus-depleted communities while L. iners is associated with the instability of Megasphaera genomosp type 1-dominated communities. Our data suggest dynamic patterns of cervicovaginal CSTs during hrHPV infection, which could be potentially used to develop microbiome-based therapies against infection progression towards disease.}, } @article {pmid37731336, year = {2024}, author = {Aizpurua, O and Dunn, RR and Hansen, LH and Gilbert, MTP and Alberdi, A}, title = {Field and laboratory guidelines for reliable bioinformatic and statistical analysis of bacterial shotgun metagenomic data.}, journal = {Critical reviews in biotechnology}, volume = {44}, number = {6}, pages = {1164-1182}, doi = {10.1080/07388551.2023.2254933}, pmid = {37731336}, issn = {1549-7801}, mesh = {*Metagenomics/methods ; *Computational Biology/methods ; *Bacteria/genetics/classification ; Guidelines as Topic ; Microbiota/genetics ; Humans ; Data Interpretation, Statistical ; Reproducibility of Results ; }, abstract = {Shotgun metagenomics is an increasingly cost-effective approach for profiling environmental and host-associated microbial communities. However, due to the complexity of both microbiomes and the molecular techniques required to analyze them, the reliability and representativeness of the results are contingent upon the field, laboratory, and bioinformatic procedures employed. Here, we consider 15 field and laboratory issues that critically impact downstream bioinformatic and statistical data processing, as well as result interpretation, in bacterial shotgun metagenomic studies. The issues we consider encompass intrinsic properties of samples, study design, and laboratory-processing strategies. We identify the links of field and laboratory steps with downstream analytical procedures, explain the means for detecting potential pitfalls, and propose mitigation measures to overcome or minimize their impact in metagenomic studies. We anticipate that our guidelines will assist data scientists in appropriately processing and interpreting their data, while aiding field and laboratory researchers to implement strategies for improving the quality of the generated results.}, } @article {pmid37731274, year = {2023}, author = {Kazemi, A and Racil, G and Ahmadi Hekmatikar, AH and Behnam Moghadam, M and Karami, P and Henselmans, M}, title = {Improved physical performance of elite soccer players based on GPS results after 4 days of carbohydrate loading followed by 3 days of low carbohydrate diet.}, journal = {Journal of the International Society of Sports Nutrition}, volume = {20}, number = {1}, pages = {2258837}, pmid = {37731274}, issn = {1550-2783}, mesh = {Adult ; Humans ; *Diet, Carbohydrate Loading ; Geographic Information Systems ; *Soccer ; Diet, Carbohydrate-Restricted ; Physical Functional Performance ; Carbohydrates ; }, abstract = {BACKGROUND: Carbohydrate loading is an established sports nutrition strategy for endur- 16 ance exercise performance. We tested if carbohydrate loading could improve the performance of 17 elite soccer players under ecologically valid circumstances using Global Positioning System (GPS) data.

METHODS: Twenty-two adult Iran Premier league soccer players were divided into a carbohydrate-loading group (CLG) and Control group (CG). The carbohydrate loading group restricted carbohydrate intake for three days to 1.5 g/kg/d while increasing exercise intensity. From days four to seven, exercise intensity was decreased and carbohydrate intake was considerably increased up to 7.5 g/kg/d on the day of the match, during which performance was analyzed using GPS data. The control group performed the same exercise training but maintained their habitual carbohydrate intake of 5-6 g/kg/d. The data were analyzed using a univariate ANCOVA with baseline data from a pre-intervention match as the control variable.

RESULTS: The carbohydrate loading team scored significantly higher on running distance, maximum speed and the number of top and repeated sprints; the carbohydrate loading group scored significantly lower on player load, metabolic power and running imbalance compared to the control team during their match.

CONCLUSIONS: Our findings suggest carbohydrate loading enabled elite soccer players to achieve greater running outputs with greater metabolic efficiency and lower fatigue compared to their habitual diets.}, } @article {pmid37725327, year = {2023}, author = {Liao, PJ and Lee, CH and Wang, SL and Chiou, HY and Chen, CJ and Seak, CJ and Wu, IW and Hsu, KH}, title = {Low-to-Moderate Arsenic Exposure and Urothelial Tract Cancers with a Long Latent Period of Follow-Up in an Arseniasis Area.}, journal = {Journal of epidemiology and global health}, volume = {13}, number = {4}, pages = {807-815}, pmid = {37725327}, issn = {2210-6014}, support = {110-2410-H-182-013-MY3//Ministry of Science and Technology, Taiwan/ ; EMRPD1L0401//Health Aging Research Center of Chang Gung University/ ; EMRPD1L0451//Health Aging Research Center of Chang Gung University/ ; CMRPD3L0021//Chang Gung Medical Foundation/ ; CMRPD3L0022//Chang Gung Medical Foundation/ ; CMRPD1M0281//Chang Gung Medical Foundation/ ; CMRPD1M0281, CMRPD1M0282//Chang Gung Medical Foundation/ ; WJY 2020-HR-01//Wang Jhan-Yang Charitable Trust Fund/ ; WJY 2021-HR-01//Wang Jhan-Yang Charitable Trust Fund/ ; WJY 2022-HR-01//Wang Jhan-Yang Charitable Trust Fund/ ; }, mesh = {Humans ; *Arsenic/toxicity ; Follow-Up Studies ; *Urinary Bladder Neoplasms/chemically induced/epidemiology ; *Arsenicals/adverse effects ; Water ; }, abstract = {BACKGROUND: Arsenic exposure can cause adverse health effects. The effects of long-term low-to-moderate exposure and methylations remain unclear.

OBJECTIVE: This study aims to examine the association between low-to-moderate arsenic exposure and urothelial tract cancers while considering the effects of methylation capacity.

METHODS: In this study, 5,811 participants were recruited from an arseniasis area in Taiwan for inorganic arsenic metabolite analysis. This follow-up study was conducted between August 1995 and December 2017. We identified 85 urothelial tract cancers in these participants, including 49 bladder and 36 upper urothelial tract cancer cases. A Cox proportional hazards model was employed.

RESULTS: The analyses revealed a significant association between concentrations of inorganic arsenic in water > 100 ug/L and bladder cancer occurrence, with a hazard ratio (HR) of 4.88 (95% CI 1.35-17.61). A monotonic trend was observed between concentrations of inorganic arsenic in water (from 0 to > 100 ug/L) and the incidence of urothelial tract cancer, including bladder cancer (p < 0.05) and upper urothelial tract cancers (p < 0.05). Participants with a lower primary methylation index or higher secondary methylation index had a prominent effect.

CONCLUSIONS: Rigorous regulations and active interventions should be considered for populations with susceptible characteristics.}, } @article {pmid37721104, year = {2023}, author = {Lu, YR and Fang, CC and He, SP}, title = {cnfishbase: A cyber Chinese fish database.}, journal = {Zoological research}, volume = {44}, number = {5}, pages = {950-953}, pmid = {37721104}, issn = {2095-8137}, mesh = {Animals ; *Databases, Factual ; *Fishes ; Internet ; }, } @article {pmid37718603, year = {2023}, author = {Hoyer, D and Bennett, JS and Reddish, J and Holder, S and Howard, R and Benam, M and Levine, J and Ludlow, F and Feinman, G and Turchin, P}, title = {Navigating polycrisis: long-run socio-cultural factors shape response to changing climate.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {378}, number = {1889}, pages = {20220402}, pmid = {37718603}, issn = {1471-2970}, mesh = {Humans ; *Climate Change ; Databases, Factual ; *Floods ; Head ; Social Interaction ; }, abstract = {Climate variability and natural hazards like floods and earthquakes can act as environmental shocks or socioecological stressors leading to instability and suffering throughout human history. Yet, societies experience a wide range of outcomes when facing such challenges: some suffer from social unrest, civil violence or complete collapse; others prove more resilient and maintain key social functions. We currently lack a clear, generally agreed-upon conceptual framework and evidentiary base to explore what causes these divergent outcomes. Here, we discuss efforts to develop such a framework through the Crisis Database (CrisisDB) programme. We illustrate that the impact of environmental stressors is mediated through extant cultural, political and economic structures that evolve over extended timescales (decades to centuries). These structures can generate high resilience to major shocks, facilitate positive adaptation, or, alternatively, undermine collective action and lead to unrest, violence and even societal collapse. By exposing the ways that different societies have reacted to crises over their lifetime, this framework can help identify the factors and complex social-ecological interactions that either bolster or undermine resilience to contemporary climate shocks. This article is part of the theme issue 'Climate change adaptation needs a science of culture'.}, } @article {pmid37714749, year = {2023}, author = {Reid, MC and Mittler, JE and Murphy, JT and Stansfield, SE and Goodreau, SM and Abernethy, N and Herbeck, JT}, title = {Evolution of HIV virulence in response to disease-modifying vaccines: A modeling study.}, journal = {Vaccine}, volume = {41}, number = {43}, pages = {6461-6469}, pmid = {37714749}, issn = {1873-2518}, support = {P2C HD042828/HD/NICHD NIH HHS/United States ; R01 AI108490/AI/NIAID NIH HHS/United States ; R01 GM125440/GM/NIGMS NIH HHS/United States ; }, mesh = {Male ; Humans ; Virulence ; Homosexuality, Male ; *HIV-1/genetics ; *HIV Infections/prevention & control/epidemiology ; *Sexual and Gender Minorities ; *AIDS Vaccines ; }, abstract = {Pathogens face a tradeoff with respect to virulence; while more virulent strains often have higher per-contact transmission rates, they are also more likely to kill their hosts earlier. Because virulence is a heritable trait, there is concern that a disease-modifying vaccine, which reduces the disease severity of an infected vaccinee without changing the underlying pathogen genotype, may result in the evolution of higher pathogen virulence. We explored the potential for such virulence evolution with a disease-modifying HIV-1 vaccine in an agent-based stochastic epidemic model of HIV in United States men who have sex with men (MSM). In the model, vaccinated agents received no protection against infection, but experienced lower viral loads and slower disease progression. We compared the genotypic set point viral load (SPVL), a measure of HIV virulence, in populations given vaccines that varied in the degree of SPVL reduction they induce. Sensitivity analyses were conducted under varying vaccine coverage scenarios. With continual vaccination rollout under ideal circumstances of 90 % coverage over thirty years, the genotypic SPVL of vaccinated individuals evolved to become greater than the genotypic SPVL of unvaccinated individuals. This virulence evolution in turn diminished the public health benefit of the vaccine, and in some scenarios resulted in an accelerated epidemic. These findings demonstrate the complexity of viral evolution and have important implications for the design and development of HIV vaccines.}, } @article {pmid37711328, year = {2023}, author = {Faria, AL and Latorre, J and Silva Cameirão, M and Bermúdez I Badia, S and Llorens, R}, title = {Ecologically valid virtual reality-based technologies for assessment and rehabilitation of acquired brain injury: a systematic review.}, journal = {Frontiers in psychology}, volume = {14}, number = {}, pages = {1233346}, pmid = {37711328}, issn = {1664-1078}, abstract = {PURPOSE: A systematic review was conducted to examine the state of the literature regarding using ecologically valid virtual environments and related technologies to assess and rehabilitate people with Acquired Brain Injury (ABI).

MATERIALS AND METHODS: A literature search was performed following the PRISMA guidelines using PubMed, Web of Science, ACM and IEEE databases. The focus was on assessment and intervention studies using ecologically valid virtual environments (VE). All studies were included if they involved individuals with ABI and simulated environments of the real world or Activities of Daily Living (ADL).

RESULTS: Seventy out of 363 studies were included in this review and grouped and analyzed according to the nature of its simulation, prefacing a total of 12 kitchens, 11 supermarkets, 10 shopping malls, 16 streets, 11 cities, and 10 other everyday life scenarios. These VE were mostly presented on computer screens, HMD's and laptops and patients interacted with them primarily via mouse, keyboard, and joystick. Twenty-five out of 70 studies had a non-experimental design.

CONCLUSION: Evidence about the clinical impact of ecologically valid VE is still modest, and further research with more extensive samples is needed. It is important to standardize neuropsychological and motor outcome measures to strengthen conclusions between studies.

identifier CRD42022301560, https://www.crd.york.ac.uk/prospero/display_record.php?RecordID=301560.}, } @article {pmid37709808, year = {2023}, author = {Cosentino, F and Castiello, G and Maiorano, L}, title = {A dataset on African bats' functional traits.}, journal = {Scientific data}, volume = {10}, number = {1}, pages = {623}, pmid = {37709808}, issn = {2052-4463}, support = {AR12117A5D86252A//Sapienza Università di Roma (Sapienza University of Rome)/ ; }, mesh = {Animals ; *Chiroptera ; Databases, Factual ; Machine Learning ; Nutritional Status ; }, abstract = {Trait-based approaches are becoming extremely common in ecological modeling and the availability of traits databases is increasing. However, data availability is often biased towards particular regions and taxa, with many taxa (e.g., bats) often under-represented. Here, we present the AfroBaT dataset, a compilation of trait data on 320 African bat species containing 76,914 values for 86 traits focusing on morphology, reproduction, life-history, trophic ecology, and species distributions. All data were gathered from published literature following the ecological trait-data standard procedure. Missing data for both numerical and categorical traits were imputed with a machine learning approach including species phylogeny. Trophic ecology traits showed the highest coverage in the literature (72% of the species averaged over all traits), while reproductive traits the lowest. Our data imputation improved the coverage of AfroBaT especially for reproductive traits, going from 27% to 58% of the species covered. AfroBaT has a range of potential applications in macroecology and community ecology, and the availability of open-access data on African bats will enable collaboration and data-sharing among researchers.}, } @article {pmid37707483, year = {2024}, author = {Guevara Beltran, D and Shiota, MN and Aktipis, A}, title = {Empathic concern motivates willingness to help in the absence of interdependence.}, journal = {Emotion (Washington, D.C.)}, volume = {24}, number = {3}, pages = {628-647}, doi = {10.1037/emo0001288}, pmid = {37707483}, issn = {1931-1516}, support = {//ASU; President's Office; Interdisciplinary Cooperation Initiative/ ; //Cooperation Science Network/ ; //Charles Koch Foundation/ ; //John Templeton Foundation/ ; }, mesh = {Humans ; *Empathy ; *Friends ; Motivation ; Data Management ; }, abstract = {Previous research suggests that empathic concern selectively promotes motivation to help those with whom we typically have interdependent relationships, such as friends or siblings, rather than strangers or acquaintances. In a sample of U.S. participants (collected between 2018 and 2020), our studies not only confirmed the finding that empathic concern is directed somewhat more strongly toward interdependent relationship partners, but also showed cross-sectionally (Studies 1a-1b), and when manipulating target distress experimentally (Study 2), that empathic concern predicts higher willingness to help only when people perceive low interdependence in their relationship with the target. In Study 3, we manipulated perceived interdependence with an acquaintance via shared fate, and found that empathic concern only predicted helping motivation when we reduced shared fate, but not when we increased shared fate. These results suggest that when people perceive high interdependence in their relationships, shared fate is the driving force behind their desire to help, whereas when people perceive low interdependence with someone in need, empathic concern motivates them to help. A relationship-building perspective on empathic concern provides avenues for testing additional moderators, including those related to target-specific characteristics and culture and ecology. (PsycInfo Database Record (c) 2024 APA, all rights reserved).}, } @article {pmid37705614, year = {2023}, author = {Mora-Rubio, A and Bravo-Ortíz, MA and Quiñones Arredondo, S and Saborit Torres, JM and Ruz, GA and Tabares-Soto, R}, title = {Classification of Alzheimer's disease stages from magnetic resonance images using deep learning.}, journal = {PeerJ. Computer science}, volume = {9}, number = {}, pages = {e1490}, pmid = {37705614}, issn = {2376-5992}, support = {P30 AG066444/AG/NIA NIH HHS/United States ; R01 AG043434/AG/NIA NIH HHS/United States ; U01 AG024904/AG/NIA NIH HHS/United States ; P01 AG003991/AG/NIA NIH HHS/United States ; P01 AG026276/AG/NIA NIH HHS/United States ; R01 EB009352/EB/NIBIB NIH HHS/United States ; UL1 TR000448/TR/NCATS NIH HHS/United States ; }, abstract = {Alzheimer's disease (AD) is a progressive type of dementia characterized by loss of memory and other cognitive abilities, including speech. Since AD is a progressive disease, detection in the early stages is essential for the appropriate care of the patient throughout its development, going from asymptomatic to a stage known as mild cognitive impairment (MCI), and then progressing to dementia and severe dementia; is worth mentioning that everyone suffers from cognitive impairment to some degree as we age, but the relevant task here is to identify which people are most likely to develop AD. Along with cognitive tests, evaluation of the brain morphology is the primary tool for AD diagnosis, where atrophy and loss of volume of the frontotemporal lobe are common features in patients who suffer from the disease. Regarding medical imaging techniques, magnetic resonance imaging (MRI) scans are one of the methods used by specialists to assess brain morphology. Recently, with the rise of deep learning (DL) and its successful implementation in medical imaging applications, it is of growing interest in the research community to develop computer-aided diagnosis systems that can help physicians to detect this disease, especially in the early stages where macroscopic changes are not so easily identified. This article presents a DL-based approach to classifying MRI scans in the different stages of AD, using a curated set of images from Alzheimer's Disease Neuroimaging Initiative and Open Access Series of Imaging Studies databases. Our methodology involves image pre-processing using FreeSurfer, spatial data-augmentation operations, such as rotation, flip, and random zoom during training, and state-of-the-art 3D convolutional neural networks such as EfficientNet, DenseNet, and a custom siamese network, as well as the relatively new approach of vision transformer architecture. With this approach, the best detection percentage among all four architectures was around 89% for AD vs. Control, 80% for Late MCI vs. Control, 66% for MCI vs. Control, and 67% for Early MCI vs. Control.}, } @article {pmid37701708, year = {2023}, author = {Paudel, S and Mueller, K and Ovando-Montejo, G and Tango, L and Rushforth, R and Lant, C}, title = {A dataset cataloging product-specific human appropriation of net primary production (HANPP) in US counties.}, journal = {Data in brief}, volume = {50}, number = {}, pages = {109530}, pmid = {37701708}, issn = {2352-3409}, abstract = {This paper describes the dataset associated with the paper "Product-Specific Human Appropriation of Net Primary Production (HANPP) in US Counties" (Paudel et al., 2023). This dataset comprises human appropriation of net primary production (HANPP) values for 3101 counties in the conterminous US for the years 1997, 2002, 2007, and 2012. For this dataset, HANPP is the carbon content of specific crop, timber, and livestock grazing products appropriated by humans in a county in a year. To calculate HANPP, raw agricultural data were downloaded from public databases such as USDA-National Agricultural Statistics Service Quick Stats and Cropland Data Layer, US Forest Service Timber Product Output, and NPP data from MODIS. These data were processed in Microsoft Excel using stoichiometry derived from established scientific literature. HANPP was partitioned by year, county, product, used and unused and above- and below-ground. This complete dataset is published in Mendeley Data and the methods used to compile them are included to make our research well documented, reproducible, and useful for future studies.}, } @article {pmid37700122, year = {2023}, author = {Yang, L and Wu, S and Li, G and Yuan, Y}, title = {Explore public concerns about environmental protection on Sina Weibo: evidence from text mining.}, journal = {Environmental science and pollution research international}, volume = {30}, number = {47}, pages = {104067-104085}, pmid = {37700122}, issn = {1614-7499}, mesh = {Male ; Humans ; Female ; *COVID-19 ; Conservation of Natural Resources ; Data Mining ; *Social Media ; Environmental Pollution ; China ; }, abstract = {The increasingly serious problem of ecological environmental pollution warns the importance of human environmental protection behavior. However, public attention to environmental protection plays an important role in solving environmental problems. Therefore, in order to explore the environmental concerns of Chinese residents, the trends in time and space, the relationship between online retweets, and the extraction of environmental concerns, this study analyzed the data of Sina Weibo users and their comments on related posts. At the same time, we used the text mining analysis method to analyze the social media text data, and the results are as follows. In that analysis of concern about environmental protection, women show a stronger attitude and willingness to protect the environment than men, and the public in economically developed areas is more concerned. In order to further investigate the public's environmental concerns, this study also utilized the PageRank algorithm to further study the forwarding relationships between users. The study found that celebrities and some good media organizations can attract environmental attention. Finally, we use pyLDAvis technology to visualize and analyze popular environmental themes and propose reasonable countermeasures and suggestions to enhance public environmental awareness based on the research results.}, } @article {pmid37699986, year = {2023}, author = {Sharaf, A and Ndiribe, CC and Omotoriogun, TC and Abueg, L and Badaoui, B and Badiane Markey, FJ and Beedessee, G and Diouf, D and Duru, VC and Ebuzome, C and Eziuzor, SC and Jaufeerally Fakim, Y and Formenti, G and Ghanmi, N and Guerfali, FZ and Houaga, I and Ideozu, JE and Katee, SM and Khayi, S and Kuja, JO and Kwon-Ndung, EH and Marks, RA and Moila, AM and Mungloo-Dilmohamud, Z and Muzemil, S and Nigussie, H and Osuji, JO and Ras, V and Tchiechoua, YH and Zoclanclounon, YAB and Tolley, KA and Ziyomo, C and Mapholi, N and Muigai, AWT and Djikeng, A and Ebenezer, TE}, title = {Bridging the gap in African biodiversity genomics and bioinformatics.}, journal = {Nature biotechnology}, volume = {41}, number = {9}, pages = {1348-1354}, pmid = {37699986}, issn = {1546-1696}, mesh = {*Computational Biology ; *Genomics ; }, } @article {pmid37697042, year = {2023}, author = {Mullowney, MW and Duncan, KR and Elsayed, SS and Garg, N and van der Hooft, JJJ and Martin, NI and Meijer, D and Terlouw, BR and Biermann, F and Blin, K and Durairaj, J and Gorostiola González, M and Helfrich, EJN and Huber, F and Leopold-Messer, S and Rajan, K and de Rond, T and van Santen, JA and Sorokina, M and Balunas, MJ and Beniddir, MA and van Bergeijk, DA and Carroll, LM and Clark, CM and Clevert, DA and Dejong, CA and Du, C and Ferrinho, S and Grisoni, F and Hofstetter, A and Jespers, W and Kalinina, OV and Kautsar, SA and Kim, H and Leao, TF and Masschelein, J and Rees, ER and Reher, R and Reker, D and Schwaller, P and Segler, M and Skinnider, MA and Walker, AS and Willighagen, EL and Zdrazil, B and Ziemert, N and Goss, RJM and Guyomard, P and Volkamer, A and Gerwick, WH and Kim, HU and Müller, R and van Wezel, GP and van Westen, GJP and Hirsch, AKH and Linington, RG and Robinson, SL and Medema, MH}, title = {Artificial intelligence for natural product drug discovery.}, journal = {Nature reviews. Drug discovery}, volume = {22}, number = {11}, pages = {895-916}, pmid = {37697042}, issn = {1474-1784}, support = {P30 CA014236/CA/NCI NIH HHS/United States ; P30 DK034987/DK/NIDDK NIH HHS/United States ; U24 AT010811/AT/NCCIH NIH HHS/United States ; }, mesh = {Humans ; *Artificial Intelligence ; Algorithms ; Machine Learning ; Drug Discovery ; Drug Design ; *Biological Products/pharmacology ; }, abstract = {Developments in computational omics technologies have provided new means to access the hidden diversity of natural products, unearthing new potential for drug discovery. In parallel, artificial intelligence approaches such as machine learning have led to exciting developments in the computational drug design field, facilitating biological activity prediction and de novo drug design for molecular targets of interest. Here, we describe current and future synergies between these developments to effectively identify drug candidates from the plethora of molecules produced by nature. We also discuss how to address key challenges in realizing the potential of these synergies, such as the need for high-quality datasets to train deep learning algorithms and appropriate strategies for algorithm validation.}, } @article {pmid37697020, year = {2023}, author = {Chen, L and Qin, L and Zhang, Y and Xu, H and Bu, Y and Wu, R and Liu, H and Hao, Q and Hu, H and Zhou, Y and Feng, J and Jing, Y and Han, J and Wang, X}, title = {Insights from multi-omics integration into seed germination of Taxus chinensis var mairei.}, journal = {Communications biology}, volume = {6}, number = {1}, pages = {931}, pmid = {37697020}, issn = {2399-3642}, mesh = {*Taxus/genetics ; Germination ; Multiomics ; Seeds ; Cycadopsida ; }, abstract = {The transition from deep dormancy to seed germination is essential for the life cycle of plants, but how this process occurs in the gymnosperm Chinese yew (Taxus chinensis var mairei), the natural source of the anticancer drug paclitaxel, remains unclear. Herein, we analyse the transcriptome, proteome, spatial metabolome, and spatial lipidome of the Chinese yew and present the multi-omics profiles of dormant and germinating seeds. Our results show that abscisic acid and gibberellic acid 12 homoeostasis is closely associated with gene transcription and protein translation, and the balance between these phytohormones thereby determines if seeds remain dormant or germinate. We find that an energy supply of carbohydrates from glycolysis and the TCA cycle feed into the pentose phosphate pathway during seed germination, and energy supplied from lipids are mainly derived from the lipolysis of triacylglycerols. Using mass spectrometry imaging, we demonstrate that the spatial distribution of plant hormones and phospholipids has a remarkable influence on embryo development. We also provide an atlas of the spatial distribution of paclitaxel C in Chinese yew seeds for the first time. The data from this study enable exploration of the germination mechanism of Chinese yew seeds across several omics levels.}, } @article {pmid37694423, year = {2023}, author = {Jiang, BY and Zhang, YL and Li, S and Li, JJ and Zheng, ZH and Wang, HG}, title = {Spatio-temporal dynamics and sensitive distance of nighttime light environment in Pearl River Delta Protected Areas, China.}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {34}, number = {6}, pages = {1601-1609}, doi = {10.13287/j.1001-9332.202306.020}, pmid = {37694423}, issn = {1001-9332}, mesh = {Humans ; *Rivers ; China ; *Big Data ; Light ; }, abstract = {Protected areas (PAs) are important barriers to ensure the ecological security of territory. Light pollution is a threat to PAs, which is particularly obvious in the urban agglomeration environment. We used multi-source big data (satellite remote sensing light data, land cover types and points of interest) to quantitatively analyze the temporal and spatial dynamics of nighttime light in the PAs of the Pearl River Delta (PRD) urban agglomeration from 2000 to 2018, the correlation between the night light environment within the PAs and human activity intensity outside, as well as the sensitive distance of the PAs to artificial light interference. The results showed that the total value of nighttime light data of PAs in the PRD increased from 71107 nanoW·cm[-2]·sr[-1] to 127682 nanoW·cm[-2]·sr[-1] from 2000 to 2018, the mean value per pixel increased from 15.3 nanoW·cm[-2]·sr[-1] to 23.7 nanoW·cm[-2]·sr[-1], and the lighted ratio increased from 73.3% to 86.4%, indicating that the nighttime light environment of PAs in the region were facing cumulative deterioration risks and serious challenges. The nighttime light intensity of the PAs in the core area of the PRD was much higher than that in the peripheral areas such as Zhaoqing and Huizhou, whereas the expansion degree of the PAs in the peripheral areas was higher than that in the core area. The nighttime light environment inside the PAs was positively correlated with the intensity of human activities around it. The most sensitive distance of the PAs to the artificial light interference around it was 10 km, and the interference degree tended to be stable after 30 km. We proposed that 0-10 km area outside the boundary of the PAs should be the light control core zone and 10-20 km area as the control buffer zone.}, } @article {pmid37693498, year = {2023}, author = {Thomas, GWC and Hughes, JJ and Kumon, T and Berv, JS and Nordgren, CE and Lampson, M and Levine, M and Searle, JB and Good, JM}, title = {The genomic landscape, causes, and consequences of extensive phylogenomic discordance in Old World mice and rats.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {37693498}, issn = {2692-8205}, support = {R01 HD094787/HD/NICHD NIH HHS/United States ; S10 OD016290/OD/NIH HHS/United States ; }, abstract = {A species tree is a central concept in evolutionary biology whereby a single branching phylogeny reflects relationships among species. However, the phylogenies of different genomic regions often differ from the species tree. Although tree discordance is often widespread in phylogenomic studies, we still lack a clear understanding of how variation in phylogenetic patterns is shaped by genome biology or the extent to which discordance may compromise comparative studies. We characterized patterns of phylogenomic discordance across the murine rodents (Old World mice and rats) - a large and ecologically diverse group that gave rise to the mouse and rat model systems. Combining new linked-read genome assemblies for seven murine species with eleven published rodent genomes, we first used ultra-conserved elements (UCEs) to infer a robust species tree. We then used whole genomes to examine finer-scale patterns of discordance and found that phylogenies built from proximate chromosomal regions had similar phylogenies. However, there was no relationship between tree similarity and local recombination rates in house mice, suggesting that genetic linkage influences phylogenetic patterns over deeper timescales. This signal may be independent of contemporary recombination landscapes. We also detected a strong influence of linked selection whereby purifying selection at UCEs led to less discordance, while genes experiencing positive selection showed more discordant and variable phylogenetic signals. Finally, we show that assuming a single species tree can result in high error rates when testing for positive selection under different models. Collectively, our results highlight the complex relationship between phylogenetic inference and genome biology and underscore how failure to account for this complexity can mislead comparative genomic studies.}, } @article {pmid37692385, year = {2023}, author = {Fan, R and Liu, Y and Bin, Y and Huang, J and Yi, B and Tang, X and Li, Y and Cai, Y and Yang, Z and Yang, M and Song, J and Pan, Q and Liu, Z and Ghani, MI and Hu, X and Chen, X}, title = {Identification of Colletotrichum aenigma as the new causal agent of leaf blight disease on Aucuba japonica Thunb., and screenings of effective fungicides for its sustainable management.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1222844}, pmid = {37692385}, issn = {1664-302X}, abstract = {Aucuba japonica Thunb is an evergreen woody ornamental plant with significant economic and ecological values. It also produces aucubin, showing a variety of biological activities. It is widely planted in the southwest region of China, including karst landscape areas in Guizhou Province. In January 2022, a serious leaf blight disease was observed on the leaves of A. japonica in the outdoor gardens of Guizhou University, Guiyang, Guizhou, China. The causal agent was identified as Colletotrichum aenigma through amplification and sequencing of the internal transcribed spacer (ITS) region, translation of the chitin synthase (CHS) and actin (ACT) genes, and morphological characterizations. Koch's postulates were confirmed by its pathogenicity on healthy leaves, including re-isolation and identification. To our knowledge, this is the first report of C. aenigma causing leaf blight on A. japonica worldwide. To identify pathogen characteristics that could be utilized for future disease management, the effects of temperature and light on mycelial growth, conidia production, and conidial germination, and the effects of humidity on conidial germination were studied. Optimal temperatures for mycelial growth of C. aenigma BY827 were 25-30°C, while 15°C and 35°C were favorable for conidia production. Concurrently, alternating 10-h light and 14-h dark, proved to be beneficial for mycelial growth and conidial germination. Additionally, conidial germination was enhanced at 90% humidity. In vitro screenings of ten chemical pesticides to assess their efficacy in suppressing C. aenigma representative strain BY827. Among them, difenoconazole showed the best inhibition rate, with an EC50 (concentration for 50% of maximal effect) value of 0.0148 μg/ml. Subsequently, field experiment results showed that difenoconazole had the highest control efficiency on A. japonica leaf blight (the decreasing rate of disease incidence and decreasing rate of disease index were 44.60 and 47.75%, respectively). Interestingly, we discovered that C. aenigma BY827 may develop resistance to mancozeb, which is not reported yet among Colletotrichum spp. strains. In conclusion, our study provided new insights into the causal agent of A. japonica leaf blight, and the effective fungicides evaluated provided an important basis and potential resource for the sustainable control of A. japonica leaf blight caused by C. aenigma in the field.}, } @article {pmid37688324, year = {2023}, author = {Zhao, D and Zhang, Y and Ren, H and Shi, Y and Dong, D and Li, Z and Cui, G and Shen, Y and Mou, Z and Kennelly, EJ and Huang, L and Ruan, J and Chen, S and Yu, D and Cun, Y}, title = {Multi-omics analysis reveals the evolutionary origin of diterpenoid alkaloid biosynthesis pathways in Aconitum.}, journal = {Journal of integrative plant biology}, volume = {65}, number = {10}, pages = {2320-2335}, doi = {10.1111/jipb.13565}, pmid = {37688324}, issn = {1744-7909}, support = {31960082//National Natural Science Foundation of China/ ; 32270395//National Natural Science Foundation of China/ ; and 31960096//National Natural Science Foundation of China/ ; }, mesh = {*Aconitum/genetics/metabolism ; Multiomics ; *Diterpenes/metabolism ; *Alkaloids/metabolism ; Transcriptome/genetics ; Plant Roots ; }, abstract = {Diterpenoid alkaloids (DAs) have been often utilized in clinical practice due to their analgesic and anti-inflammatory properties. Natural DAs are prevalent in the family Ranunculaceae, notably in the Aconitum genus. Nevertheless, the evolutionary origin of the biosynthesis pathway responsible for DA production remains unknown. In this study, we successfully assembled a high-quality, pseudochromosome-level genome of the DA-rich species Aconitum vilmorinianum (A. vilmorinianum) (5.76 Gb). An A. vilmorinianum-specific whole-genome duplication event was discovered using comparative genomic analysis, which may aid in the evolution of the DA biosynthesis pathway. We identified several genes involved in DA biosynthesis via integrated genomic, transcriptomic, and metabolomic analyses. These genes included enzymes encoding target ent-kaurene oxidases and aminotransferases, which facilitated the activation of diterpenes and insertion of nitrogen atoms into diterpene skeletons, thereby mediating the transformation of diterpenes into DAs. The divergence periods of these genes in A. vilmorinianum were further assessed, and it was shown that two major types of genes were involved in the establishment of the DA biosynthesis pathway. Our integrated analysis offers fresh insights into the evolutionary origin of DAs in A. vilmorinianum as well as suggestions for engineering the biosynthetic pathways to obtain desired DAs.}, } @article {pmid37685932, year = {2023}, author = {Milicevic, O and Loncar, A and Abazovic, D and Vukcevic, M and Despot, D and Djukic, T and Djukic, V and Milovanovic, A and Panic, N and Plecic, N and Banko, A}, title = {Transcriptome from Paired Samples Improves the Power of Comprehensive COVID-19 Host-Viral Characterization.}, journal = {International journal of molecular sciences}, volume = {24}, number = {17}, pages = {}, pmid = {37685932}, issn = {1422-0067}, mesh = {Humans ; *SARS-CoV-2/genetics ; Transcriptome ; *COVID-19/genetics ; Gene Expression Profiling ; Computational Biology ; }, abstract = {Previous transcriptome profiling studies showed significantly upregulated genes and altered biological pathways in acute COVID-19. However, changes in the transcriptional signatures during a defined time frame are not yet examined and described. The aims of this study included viral metagenomics and evaluation of the total expression in time-matched and tissue-matched paired COVID-19 samples with the analysis of the host splicing profile to reveal potential therapeutic targets. Prospective analysis of paired nasopharyngeal swabs (NPS) and blood (BL) samples from 18 COVID-19 patients with acute and resolved infection performed using Kallisto, Suppa2, Centrifuge, EdgeR, PantherDB, and L1000CDS2 tools. In NPS, we discovered 6 genes with changed splicing and 40 differentially expressed genes (DEG) that yielded 88 altered pathways. Blood samples yielded 15 alternatively spliced genes. Although the unpaired DEG analysis failed, pairing identified 78 genes and 242 altered pathways with meaningful clinical interpretation and new candidate drug combinations with up to 65% overlap. Metagenomics analyses showed SARS-CoV-2 dominance during and after the acute infection, with a significant reduction in NPS (0.008 vs. 0.002, p = 0.019). Even though both NPS and BL give meaningful insights into expression changes, this is the first demonstration of how the power of blood analysis is vastly maximized by pairing. The obtained results essentially showed that pairing is a determinant between a failed and a comprehensive study. Finally, the bioinformatics results prove to be a comprehensive tool for full-action insights, drug development, and infectious disease research when designed properly.}, } @article {pmid37683992, year = {2023}, author = {Sukur, N and Milošević, N and Pogrmic-Majkic, K and Stanic, B and Andric, N}, title = {Predicting chemicals' toxicity pathway of female reproductive disorders using AOP7 and deep neural networks.}, journal = {Food and chemical toxicology : an international journal published for the British Industrial Biological Research Association}, volume = {180}, number = {}, pages = {114013}, doi = {10.1016/j.fct.2023.114013}, pmid = {37683992}, issn = {1873-6351}, abstract = {Experimental evidence shows that certain chemicals, particularly endocrine disrupting chemicals, may negatively affect the female reproductive system, thereby lowering women's fertility. However, humans are constantly exposed to a number of different chemicals with limited or no experimental data regarding their effect and the mechanism of action in the female reproductive system. To predict chemical hazards to the female reproductive system, we used a previously defined adverse outcome pathway (AOP) that links activation of the peroxisome proliferator-activated receptor γ to the reproductive toxicity in adult females (AOP7) and the Convolutional Deep Neural Network models that produce meaningful predictions when trained on a significant amount of data. The models trained using CompTox assays with intended molecular and biological targets corresponding to AOP7 achieved high performance (over 90% validation accuracy). The integration of AOP7 and Deep Neural Network identified chemicals that could negatively affect female reproduction through the mechanism described in AOP7. We provide a solution to quickly analyze the data and produce machine learning models to identify potentially active chemicals in the female reproductive system. Although we focused on the female reproductive system, this approach could be valid for a number of other chemicals and AOPs if the right data exist.}, } @article {pmid37681394, year = {2023}, author = {Xie, X and Wu, TC and Cao, BL and Li, JZ and Xue, B}, title = {Virtual ecological technology: Concepts, systems, and application perspectives.}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {34}, number = {8}, pages = {2297-2304}, doi = {10.13287/j.1001-9332.202308.022}, pmid = {37681394}, issn = {1001-9332}, mesh = {Humans ; *Ecosystem ; *Air Pollution ; Environment ; Geography ; Sustainable Development ; }, abstract = {Virtual ecological technology is a new technology that builds the foundation of a digital ecological system, simulates the process of ecological evolution, and establishes a global knowledge analysis system based on a unified spatio-temporal benchmark. It is a new direction for the interdisciplinary integration and development of eco-logy, geographic information science, computer science and other subjects towards modernization, informatization, and intelligence. Research, development, and application of virtual ecological technology is of great significance for the development of ecology as a discipline, ecosystem management, and regional sustainable development. Curren-tly, research on virtual ecological technology is still in its infancy and lacks a complete and clearly defined framework, making it difficult to support systematic iterative development and scientific analysis. In this paper, starting from the main theories and objectives of modern ecology, we summarized the main contents and technical requirements of virtual ecological construction, and proposed a key technical system of virtual ecology that integrated vir-tual geography and digital twin technology. From the perspective of application scenarios, we analyzed the application capabilities of virtual ecological technology in air pollution and energy analysis. Finally, we summarized the deve-lopment potential of virtual ecological technology in the digital construction of the ecological environment, intelligent computing, and realistic expression of different levels of ecological space resources transformation under the background of new generation of information technology, both at the local computing point breakthrough and the global technology point fusion aspects. This would enrich and advance the technical capabilities that support China's ecological space resource transformation.}, } @article {pmid37680963, year = {2023}, author = {Tóth, F and Zsuga, K and Kerepeczki, É and Kovács, B and Magura, T and Körmöczi, L and Lövei, GL}, title = {Discordant spatiotemporal dynamics of functional and phylogenetic diversity of rotiferan communities exposed to aquaculture effluent.}, journal = {Ecology and evolution}, volume = {13}, number = {9}, pages = {e10503}, pmid = {37680963}, issn = {2045-7758}, abstract = {The growth of the human population brought about the global intensification of aquacultural production, and aquaculture became the fastest growing animal husbandry sector. Effluent from aquaculture is an anthropogenic environmental burden, containing organic matter, nutrients and suspended solids that affect water quality especially in the water bodies of high biodiversity and conservation value. Water quality assessment often relies on bioindicators, analysing changes in taxonomic diversity of various freshwater organismal groups. Stepping beyond taxon diversity, we used functional and phylogenetic diversities of rotifers to identify factors affecting their community organization in response to an aquaculture effluent gradient in the largest oxbow lake in the Carpathian Basin, Hungary. Sampling was carried out three times per season at five points along a 3.5 km section of the oxbow lake, including the point of effluent inflow. We used eight traits to evaluate functional diversity: body size, trophi type, feeding mode, protection type, body wall type, corona type, habitat preference and tolerance level. Functional and phylogenetic distances among the 24 species identified indicated trait conservatism. Rotiferan diversity increased with increasing distance from the point of influx in spring and summer. Among the factors affecting community organization in spring and summer, we find examples of environmental filtering, while in autumn the role of biotic interaction is more frequent. Under nutrient-rich conditions in spring and summer, organisms belonging to the same functional group were dominant, whereas under oligotrophic conditions, more diverse but less abundant groups were present. Considering functional and phylogenetic traits allowed us to identify organising forces of rotifer communities in the largest oxbow lake of the Hungarian Lowland.}, } @article {pmid37680030, year = {2023}, author = {Moran, ME and Aparecido, LMT and Koepke, DF and Cooper, HF and Doughty, CE and Gehring, CA and Throop, HL and Whitham, TG and Allan, GJ and Hultine, KR}, title = {Limits of thermal and hydrological tolerance in a foundation tree species (Populus fremontii) in the desert southwestern United States.}, journal = {The New phytologist}, volume = {240}, number = {6}, pages = {2298-2311}, doi = {10.1111/nph.19247}, pmid = {37680030}, issn = {1469-8137}, support = {DEB-1340852//National Science Foundation/ ; DEB-1340856//National Science Foundation/ ; DEB-2017895//National Science Foundation/ ; }, mesh = {*Trees/physiology ; *Populus/physiology ; Plant Leaves/physiology ; Southwestern United States ; Temperature ; }, abstract = {Populus fremontii is among the most dominant, and ecologically important riparian tree species in the western United States and can thrive in hyper-arid riparian corridors. Yet, P. fremontii forests have rapidly declined over the last decade, particularly in places where temperatures sometimes exceed 50°C. We evaluated high temperature tolerance of leaf metabolism, leaf thermoregulation, and leaf hydraulic function in eight P. fremontii populations spanning a 5.3°C mean annual temperature gradient in a well-watered common garden, and at source locations throughout the lower Colorado River Basin. Two major results emerged. First, despite having an exceptionally high Tcrit (the temperature at which Photosystem II is disrupted) relative to other tree taxa, recent heat waves exceeded Tcrit , requiring evaporative leaf cooling to maintain leaf-to-air thermal safety margins. Second, in midsummer, genotypes from the warmest locations maintained lower midday leaf temperatures, a higher midday stomatal conductance, and maintained turgor pressure at lower water potentials than genotypes from more temperate locations. Taken together, results suggest that under well-watered conditions, P. fremontii can regulate leaf temperature below Tcrit along the warm edge of its distribution. Nevertheless, reduced Colorado River flows threaten to lower water tables below levels needed for evaporative cooling during episodic heat waves.}, } @article {pmid37678709, year = {2023}, author = {Green Ii, DA}, title = {Tracking technologies: advances driving new insights into monarch migration.}, journal = {Current opinion in insect science}, volume = {60}, number = {}, pages = {101111}, doi = {10.1016/j.cois.2023.101111}, pmid = {37678709}, issn = {2214-5753}, mesh = {Humans ; Animals ; *Butterflies ; Animal Migration ; Ecology ; Seasons ; }, abstract = {Understanding the rules of how monarch butterflies complete their annual North American migration will be clarified by studying them within a movement ecology framework. Insect movement ecology is growing at a rapid pace due to the development of novel monitoring systems that allow ever-smaller animals to be tracked at higher spatiotemporal resolution for longer periods of time. New innovations in tracking hardware and associated software, including miniaturization, energy autonomy, data management, and wireless communication, are reducing the size and increasing the capability of next-generation tracking technologies, bringing the goal of tracking monarchs over their entire migration closer within reach. These tools are beginning to be leveraged to provide insight into different aspects of monarch biology and ecology, and to contribute to a growing capacity to understand insect movement ecology more broadly and its impact on human life.}, } @article {pmid37674876, year = {2023}, author = {Boyes, D and Holland, PWH and , and , and , and , and , and , }, title = {The genome sequence of the Feathered Gothic, Tholera decimalis (Poda, 1761).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {200}, pmid = {37674876}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual female Tholera decimalis (the Feathered Gothic; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 1,334.1 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.4 kilobases in length. Gene annotation of this assembly on Ensembl identified 12,771 protein coding genes.}, } @article {pmid37674686, year = {2023}, author = {Asaaga, FA and Sriram, A and Chanda, MM and Hoti, SL and Young, JC and Purse, BV}, title = {'It doesn't happen how you think, it is very complex!' Reconciling stakeholder priorities, evidence, and processes for zoonoses prioritisation in India.}, journal = {Frontiers in public health}, volume = {11}, number = {}, pages = {1228950}, pmid = {37674686}, issn = {2296-2565}, support = {MR/S012893/1/MRC_/Medical Research Council/United Kingdom ; MR/S012893/2/MRC_/Medical Research Council/United Kingdom ; MR/T029846/1/MRC_/Medical Research Council/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; }, mesh = {Animals ; Humans ; *Administrative Personnel ; *Cost of Illness ; Health Policy ; India ; Zoonoses/prevention & control ; }, abstract = {BACKGROUND: Why do some zoonotic diseases receive priority from health policy decision-makers and planners whereas others receive little attention? By leveraging Shiffman and Smith's political prioritisation framework, our paper advances a political economy of disease prioritisation focusing on four key components: the strength of the actors involved in the prioritisation, the power of the ideas they use to portray the issue, the political contexts in which they operate, and the characteristics of the issue itself (e.g., overall burdens, severity, cost-effective interventions). These components afford a nuanced characterisation of how zoonotic diseases are prioritised for intervention and highlight the associated knowledge gaps affecting prioritisation outcomes. We apply this framework to the case of zoonoses management in India, specifically to identify the factors that shape disease prioritisation decision-making and outcomes.

METHODS: We conducted 26 semi-structured interviews with national, state and district level health policymakers, disease managers and technical experts involved in disease surveillance and control in India.

RESULTS: Our results show pluralistic interpretation of risks, exemplified by a disconnect between state and district level actors on priority diseases. The main factors identified as shaping prioritisation outcomes were related to the nature of the zoonoses problem (the complexity of the zoonotic disease, insufficient awareness and lack of evidence on disease burdens and impacts) as well as political, social, cultural and institutional environments (isolated departmental priorities, limited institutional authority, opaque funding mechanisms), and challenges in organisation leadership for cross-sectoral engagement.

CONCLUSION: The findings highlight a compartmentalised regulatory system for zoonoses where political, social, cultural, and media factors can influence disease management and prioritisation. A major policy window is the institutionalisation of One Health to increase the political priority for strengthening cross-sectoral engagement to address several challenges, including the creation of effective institutions to reconcile stakeholder priorities and prioritisation processes.}, } @article {pmid37674040, year = {2023}, author = {Lu, AT and Fei, Z and Haghani, A and Robeck, TR and Zoller, JA and Li, CZ and Lowe, R and Yan, Q and Zhang, J and Vu, H and Ablaeva, J and Acosta-Rodriguez, VA and Adams, DM and Almunia, J and Aloysius, A and Ardehali, R and Arneson, A and Baker, CS and Banks, G and Belov, K and Bennett, NC and Black, P and Blumstein, DT and Bors, EK and Breeze, CE and Brooke, RT and Brown, JL and Carter, GG and Caulton, A and Cavin, JM and Chakrabarti, L and Chatzistamou, I and Chen, H and Cheng, K and Chiavellini, P and Choi, OW and Clarke, SM and Cooper, LN and Cossette, ML and Day, J and DeYoung, J and DiRocco, S and Dold, C and Ehmke, EE and Emmons, CK and Emmrich, S and Erbay, E and Erlacher-Reid, C and Faulkes, CG and Ferguson, SH and Finno, CJ and Flower, JE and Gaillard, JM and Garde, E and Gerber, L and Gladyshev, VN and Gorbunova, V and Goya, RG and Grant, MJ and Green, CB and Hales, EN and Hanson, MB and Hart, DW and Haulena, M and Herrick, K and Hogan, AN and Hogg, CJ and Hore, TA and Huang, T and Izpisua Belmonte, JC and Jasinska, AJ and Jones, G and Jourdain, E and Kashpur, O and Katcher, H and Katsumata, E and Kaza, V and Kiaris, H and Kobor, MS and Kordowitzki, P and Koski, WR and Krützen, M and Kwon, SB and Larison, B and Lee, SG and Lehmann, M and Lemaitre, JF and Levine, AJ and Li, C and Li, X and Lim, AR and Lin, DTS and Lindemann, DM and Little, TJ and Macoretta, N and Maddox, D and Matkin, CO and Mattison, JA and McClure, M and Mergl, J and Meudt, JJ and Montano, GA and Mozhui, K and Munshi-South, J and Naderi, A and Nagy, M and Narayan, P and Nathanielsz, PW and Nguyen, NB and Niehrs, C and O'Brien, JK and O'Tierney Ginn, P and Odom, DT and Ophir, AG and Osborn, S and Ostrander, EA and Parsons, KM and Paul, KC and Pellegrini, M and Peters, KJ and Pedersen, AB and Petersen, JL and Pietersen, DW and Pinho, GM and Plassais, J and Poganik, JR and Prado, NA and Reddy, P and Rey, B and Ritz, BR and Robbins, J and Rodriguez, M and Russell, J and Rydkina, E and Sailer, LL and Salmon, AB and Sanghavi, A and Schachtschneider, KM and Schmitt, D and Schmitt, T and Schomacher, L and Schook, LB and Sears, KE and Seifert, AW and Seluanov, A and Shafer, ABA and Shanmuganayagam, D and Shindyapina, AV and Simmons, M and Singh, K and Sinha, I and Slone, J and Snell, RG and Soltanmaohammadi, E and Spangler, ML and Spriggs, MC and Staggs, L and Stedman, N and Steinman, KJ and Stewart, DT and Sugrue, VJ and Szladovits, B and Takahashi, JS and Takasugi, M and Teeling, EC and Thompson, MJ and Van Bonn, B and Vernes, SC and Villar, D and Vinters, HV and Wallingford, MC and Wang, N and Wayne, RK and Wilkinson, GS and Williams, CK and Williams, RW and Yang, XW and Yao, M and Young, BG and Zhang, B and Zhang, Z and Zhao, P and Zhao, Y and Zhou, W and Zimmermann, J and Ernst, J and Raj, K and Horvath, S}, title = {Author Correction: Universal DNA methylation age across mammalian tissues.}, journal = {Nature aging}, volume = {3}, number = {11}, pages = {1462}, doi = {10.1038/s43587-023-00499-7}, pmid = {37674040}, issn = {2662-8465}, support = {P01 AG047200/AG/NIA NIH HHS/United States ; P01 AG051449/AG/NIA NIH HHS/United States ; R01 AG027237/AG/NIA NIH HHS/United States ; }, } @article {pmid37673539, year = {2023}, author = {Pinho-Gomes, AC and Roaf, E and Fuller, G and Fowler, D and Lewis, A and ApSimon, H and Noakes, C and Johnstone, P and Holgate, S}, title = {Air pollution and climate change.}, journal = {The Lancet. Planetary health}, volume = {7}, number = {9}, pages = {e727-e728}, doi = {10.1016/S2542-5196(23)00189-4}, pmid = {37673539}, issn = {2542-5196}, mesh = {*Climate Change ; *Air Pollution/adverse effects ; }, } @article {pmid37673174, year = {2024}, author = {Lei, T and Chang, Y and Yao, C and Zhang, H}, title = {A systematic evaluation of computational methods for predicting translated non-canonical ORFs from ribosome profiling data.}, journal = {Journal of genetics and genomics = Yi chuan xue bao}, volume = {51}, number = {1}, pages = {105-108}, doi = {10.1016/j.jgg.2023.08.010}, pmid = {37673174}, issn = {1673-8527}, mesh = {*Ribosome Profiling ; Open Reading Frames ; *Protein Biosynthesis ; Ribosomes/genetics/metabolism ; Computational Biology ; }, } @article {pmid37670833, year = {2023}, author = {Zhylkybekova, A and Turlayev, A and Grjibovski, AM and Koshmaganbetova, GK}, title = {Measures to support informal care for the older adults in Kazakhstan: a review of the current status.}, journal = {Frontiers in public health}, volume = {11}, number = {}, pages = {1247684}, pmid = {37670833}, issn = {2296-2565}, mesh = {Child ; Humans ; Aged ; Kazakhstan ; *Quality of Life ; *Patient Care ; Long-Term Care ; Databases, Factual ; }, abstract = {The demand for informal caregivers to support the older adults has grown worldwide in recent decades. However, informal caregivers themselves require support. This article aims to examine existing support measures for caregivers of the older adults in the Republic of Kazakhstan. Relevant articles and grey literature were identified through manual searches on Google and Google Scholar, as well as electronic searches using indexed databases like PubMed, Web of Science, and Scopus. Moreover, the reference lists of identified sources and government ministry websites were meticulously scrutinized. This review highlights the scarcity of research on caregiver support measures in Kazakhstan, supported by the lack of peer-reviewed articles on this subject. A comprehensive analysis of the literature shows that in Kazakhstan's legislative framework, "caregivers" exclusively refers to individuals providing care for a first-degree disability. The responsibility of caring for older adults parents lies with able-bodied children. However, there is a lack of registration and assessment procedures to evaluate the burden and quality of life of caregivers. As a result, the medical and social support provided to caregivers is standardized, failing to adequately address their unique needs and requirements. The analysis of current support measures for informal caregivers highlights the need to develop support mechanisms and recognize individuals providing informal care as key figures in the long-term care system.}, } @article {pmid37667004, year = {2023}, author = {Li, Y and Niu, Z and Zhu, M and Wang, Z and Xu, R and Li, M and Zheng, Z and Lu, Z and Dong, C and Hu, H and Yang, Y and Wu, Y and Wang, D and Yang, J and Zhang, J and Wan, D and Abbott, R and Liu, J and Yang, Y}, title = {Multi-omics data provide insight into the adaptation of the glasshouse plant Rheum nobile to the alpine subnival zone.}, journal = {Communications biology}, volume = {6}, number = {1}, pages = {906}, pmid = {37667004}, issn = {2399-3642}, mesh = {*Rheum/genetics ; Multiomics ; Acclimatization/genetics ; Comparative Genomic Hybridization ; Down-Regulation ; }, abstract = {Subnival glasshouse plants provide a text-book example of high-altitude adaptation with reproductive organs enclosed in specialized semi-translucent bracts, monocarpic reproduction and continuous survival under stress. Here, we present genomic, transcriptomic and metabolomic analyses for one such plant, the Noble rhubarb (Rheum nobile). Comparative genomic analyses show that an expanded number of genes and retained genes from two recent whole-genome duplication events are both relevant to subnival adaptation of this species. Most photosynthesis genes are downregulated within bracts compared to within leaves, and indeed bracts exhibit a sharp reduction in photosynthetic pigments, indicating that the bracts no longer perform photosynthesis. Contrastingly, genes related to flavonol synthesis are upregulated, providing enhanced defense against UV irradiation damage. Additionally, anatomically abnormal mesophyll combined with the downregulation of genes related to mesophyll differentiation in bracts illustrates the innovation and specification of the glass-like bracts. We further detect substantial accumulation of antifreeze proteins (e.g. AFPs, LEAs) and various metabolites (e.g. Proline, Protective sugars, procyanidins) in over-wintering roots. These findings provide new insights into subnival adaptation and the evolution of glasshouse alpine plants.}, } @article {pmid37665528, year = {2023}, author = {Omang, BO and Omeka, ME and Asinya, EA and Oko, PE and Aluma, VC}, title = {Application of GIS and feedforward back-propagated ANN models for predicting the ecological and health risk of potentially toxic elements in soils in Northwestern Nigeria.}, journal = {Environmental geochemistry and health}, volume = {45}, number = {11}, pages = {8599-8631}, pmid = {37665528}, issn = {1573-2983}, mesh = {Child ; Humans ; *Metals, Heavy/analysis ; Soil ; Ecosystem ; Environmental Monitoring/methods ; Geographic Information Systems ; Nigeria/epidemiology ; *Neoplasms ; Risk Assessment ; *Soil Pollutants/toxicity/analysis ; China ; }, abstract = {Potentially toxic elements (PTEs) occur naturally in most geologic materials. However, recent anthropogenic disturbances such as ore mining have contributed significantly to their enrichment in soils. Their occurrence in soil may portend a myriad of related risks to the environment and biota. Most traditional soil quality evaluation methods involve comparing the background values of the elements to the established guideline values, which is often time-consuming and fraught with computational errors. As a result, to conduct a comprehensive and unbiased evaluation of soil quality and its effects on the ecosystem and human health, this research combined geochemical, numerical, and GIS data for a composite health risk zonation of the entire study area. Furthermore, the multilayer perceptron artificial neural network (MLP-NN) was used to forecast the most important toxic components influencing soil quality. Geochemical, statistical, and quantitative soil pollution evaluation (pollution index and ecological risk index) showed that apart from mining, the spread and association of trace elements and oxides occur as a consequence of surface environmental conditions (e.g., leaching, weathering, and organo-metallic complexation). The hazard quotients (HQs) and hazard index (HI) of all PTEs were greater than one. This indicates that residents (particularly children) are more susceptible to risks from toxic element ingestion than dermal exposure and inhalation. Ingestion of As and Cr resulted in higher cancer risks and lifetime cancer risk levels (> 1.0E 04), with risk levels increasing toward the northeastern, western, and southeastern directions of the study area. The low modeling errors observed from the sum of square errors, relative errors, and coefficient of determination confirmed the efficiency of the MLP-NN in pollution load prediction. Based on the sensitivity analysis, Hg, Sr, Zn, Ba, As, and Zr showed the greatest influence on soil quality. Focus on remediation should therefore be placed on the removal of these elements from the soil.}, } @article {pmid37665400, year = {2023}, author = {Bayer, JM and Scully, RA and Dlabola, EK and Courtwright, JL and Hirsch, CL and Hockman-Wert, D and Miller, SW and Roper, BB and Saunders, WC and Snyder, MN}, title = {Sharing FAIR monitoring program data improves discoverability and reuse.}, journal = {Environmental monitoring and assessment}, volume = {195}, number = {10}, pages = {1141}, pmid = {37665400}, issn = {1573-2959}, mesh = {*Environmental Monitoring ; *Natural Resources ; }, abstract = {Data resulting from environmental monitoring programs are valuable assets for natural resource managers, decision-makers, and researchers. These data are often collected to inform specific reporting needs or decisions with a specific timeframe. While program-oriented data and related publications are effective for meeting program goals, sharing well-documented data and metadata allows users to research aspects outside initial program intentions. As part of an effort to integrate data from four long-term large-scale US aquatic monitoring programs, we evaluated the original datasets against the FAIR (Findable, Accessible, Interoperable, Reusable) data principles and offer recommendations and lessons learned. Differences in data governance across these programs resulted in considerable effort to access and reuse the original datasets. Requirements, guidance, and resources available to support data publishing and documentation are inconsistent across agencies and monitoring programs, resulting in various data formats and storage locations that are not easily found, accessed, or reused. Making monitoring data FAIR will reduce barriers to data discovery and reuse. Programs are continuously striving to improve data management, data products, and metadata; however, provision of related tools, consistent guidelines and standards, and more resources to do this work is needed. Given the value of these data and the significant effort required to access and reuse them, actions and steps intended on improving data documentation and accessibility are described.}, } @article {pmid37663792, year = {2023}, author = {Boyes, D and Sims, I and Holland, PWH and , and , and , and , and , and , and , }, title = {The genome sequence of the Round-winged Muslin, Thumatha senex (Hübner, 1804).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {298}, pmid = {37663792}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual female Thumatha senex (the Round-winged Muslin; Arthropoda; Insecta; Lepidoptera; Erebidae). The genome sequence is 810.3 megabases in span. Most of the assembly is scaffolded into 30 chromosomal pseudomolecules, including the W and Z sex chromosomes. The mitochondrial genome has also been assembled and is 15.5 kilobases in length.}, } @article {pmid37663789, year = {2023}, author = {Boyes, D and Holland, PWH and , and , and , and , and , and , }, title = {The genome sequence of the Light Brocade, Lacanobia w-latinum (Hufnagel, 1766).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {299}, pmid = {37663789}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual male Lacanobia w-latinum (the Light Brocade; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 903.9 megabases in span. Most of the assembly is scaffolded into 31 chromosomal, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.38 kilobases in length. Gene annotation of this assembly on Ensembl identified 21,592 protein coding genes.}, } @article {pmid37663407, year = {2023}, author = {Günther, F and Wong, D and Elison-Davies, S and Yau, C}, title = {Identifying factors associated with user retention and outcomes of a digital intervention for substance use disorder: a retrospective analysis of real-world data.}, journal = {JAMIA open}, volume = {6}, number = {3}, pages = {ooad072}, pmid = {37663407}, issn = {2574-2531}, abstract = {OBJECTIVES: Successful delivery of digital health interventions is affected by multiple real-world factors. These factors may be identified in routinely collected, ecologically valid data from these interventions. We propose ideas for exploring these data, focusing on interventions targeting complex, comorbid conditions.

MATERIALS AND METHODS: This study retrospectively explores pre-post data collected between 2016 and 2019 from users of digital cognitive behavioral therapy (CBT)-containing psychoeducation and practical exercises-for substance use disorder (SUD) at UK addiction services. To identify factors associated with heterogenous user responses to the technology, we employed multivariable and multivariate regressions and random forest models of user-reported questionnaire data.

RESULTS: The dataset contained information from 14 078 individuals of which 12 529 reported complete data at baseline and 2925 did so again after engagement with the CBT. Ninety-three percent screened positive for dependence on 1 of 43 substances at baseline, and 73% screened positive for anxiety or depression. Despite pre-post improvements independent of user sociodemographics, women reported more frequent and persistent symptoms of SUD, anxiety, and depression. Retention-minimum 2 use events recorded-was associated more with deployment environment than user characteristics. Prediction accuracy of post-engagement outcomes was acceptable (Area Under Curve [AUC]: 0.74-0.79), depending non-trivially on user characteristics.

DISCUSSION: Traditionally, performance of digital health interventions is determined in controlled trials. Our analysis showcases multivariate models with which real-world data from these interventions can be explored and sources of user heterogeneity in retention and symptom reduction uncovered.

CONCLUSION: Real-world data from digital health interventions contain information on natural user-technology interactions which could enrich results from controlled trials.}, } @article {pmid37660507, year = {2023}, author = {Isoyama, K and Matsuura, M and Hayasaka, M and Nagao, S and Nishimura, Y and Yoshioka, T and Imai, Y and Miyagi, E and Suzuki, Y and Saito, T}, title = {Nationwide trends in and regional factors associated with minimally invasive hysterectomy for benign indications in Japan.}, journal = {European journal of obstetrics, gynecology, and reproductive biology}, volume = {289}, number = {}, pages = {129-135}, doi = {10.1016/j.ejogrb.2023.08.388}, pmid = {37660507}, issn = {1872-7654}, mesh = {Female ; Humans ; Japan/epidemiology ; Retrospective Studies ; *Laparoscopy ; Databases, Factual ; Hysterectomy ; }, abstract = {OBJECTIVE: To examine the prevalence trends of minimally invasive hysterectomy for benign indications in Japan and investigate regional disparities.

STUDY DESIGN: A retrospective cohort and ecological study using "The National Database of Health Insurance Claims and Specific Health Checkups of Japan (NDB) Open Data".

SETTING: Nationwide Japan.

PATIENTS: Individuals who underwent hysterectomy for benign indications from 2014 to 2020.

INTERVENTIONS: Trend analysis of minimally invasive surgery (MIS) rates through laparoscopic hysterectomies (LH) and robotic-assisted laparoscopic hysterectomies (RA-LH) at the national and prefecture levels. Examination of regional factors contributing to the disparity in MIS implementation rates by second medical service area (SMSA).

RESULTS: The number of LH has increased from 16,016 in 2014 to 27,755 in 2020. The nationwide MIS hysterectomy rate increased from 29% in 2014 to 55% in 2020 (p less than 0.001). More than 50% of hysterectomies have been performed as MIS since 2019. There was an increasing trend in MIS rates in all age groups. All prefectures except one showed a significant upward trend (p less than 0.05) in the MIS rates, but MIS rates varied widely (23-84%). In a multivariable model, the MIS was more likely to be performed in the SMSAs in western Japan (p = 0.011), in the SMSAs where the number of laparoscopy-qualified gynecologists is 5-10 (p = 0.013), and 11 or higher (p less than 0.001).

CONCLUSIONS: This study reveals a shift towards minimally invasive surgery (MIS) in total hysterectomy procedures in Japan. However, significant disparities in the prevalence of MIS hysterectomy exist, potentially influenced by the number of laparoscopy-qualified gynecologists.}, } @article {pmid37659520, year = {2023}, author = {Schulz, G and van Beusekom, JEE and Jacob, J and Bold, S and Schöl, A and Ankele, M and Sanders, T and Dähnke, K}, title = {Low discharge intensifies nitrogen retention in rivers - A case study in the Elbe River.}, journal = {The Science of the total environment}, volume = {904}, number = {}, pages = {166740}, doi = {10.1016/j.scitotenv.2023.166740}, pmid = {37659520}, issn = {1879-1026}, mesh = {*Rivers ; *Nitrates/analysis ; Ecosystem ; Environmental Monitoring/methods ; Nitrogen/analysis ; Eutrophication ; Harmful Algal Bloom ; Water ; }, abstract = {Eutrophication due to excessive nutrient inputs is a major threat to coastal ecosystems worldwide, causing harmful algae blooms, seagrass loss and hypoxia. Decisions to combat eutrophication in the North Sea were made in the 1980s. Despite significant improvements during recent decades, high nitrogen loads and resulting eutrophication problems remain. In this study, long-term changes in nitrogen inputs to the Elbe Estuary (Germany) were characterized based on nitrogen data provided by the Elbe River Basin Community from 1985 to 2019. Additionally, surface water samples were taken at the weir separating the river from the estuary from 2011 to 2021 to characterize dissolved inorganic nitrogen concentrations and nitrate stable isotope composition. The findings suggest a close coupling of river discharge with the riverine nitrogen cycle. Nitrogen loads decreased disproportionately with decreasing discharge. This decrease is due to intensified nitrogen retention in the Elbe catchment, which can double nitrogen retention compared to average discharge conditions. Phytoplankton growth was enhanced by long residence times and high light availability at low water levels. This suggests that the recent decreases in nitrogen loads in the Elbe River were not only a result of management measures in the catchment but were also amplified by a recent long-lasting drought in the catchment. Based on projections from the Intergovernmental Panel on Climate Change, more frequent and extensive droughts are anticipated, which may lead to future seasonal shifts to nitrate limitation in the lower Elbe River.}, } @article {pmid37658362, year = {2023}, author = {Bezerra, ALL and de Almeida, PRB and Reis, RK and Ferreira, GRON and Sousa, FJD and Gir, E and Botelho, EP}, title = {Human immunodeficiency virus epidemic scenery among brazilian women: a spatial analysis study.}, journal = {BMC women's health}, volume = {23}, number = {1}, pages = {463}, pmid = {37658362}, issn = {1472-6874}, mesh = {Humans ; Female ; Adolescent ; *HIV ; Brazil/epidemiology ; Spatial Analysis ; Databases, Factual ; *HIV Infections/epidemiology ; }, abstract = {BACKGROUND: Approximately 37.7 million people worldwide are infected with human immunodeficiency virus (HIV). Although HIV detection among women, they still representing 53% of population living with the virus. Spatial analysis techniques are powerful tools for combating HIV allowing the association of the phenomenon with socioeconomic and political factors. Therefore, the main goal of this study was to spatially analyze HIV prevalence among Brazilian women from 2007 to 2020.

METHODS: ecological study was conducted using secondary databases of the Notifiable Diseases Information System (SINAN) for HIV and Acquired Immunodeficiency Syndrom (AIDS) in Brazilian women 15 years old and over. Age-adjusted HIV/AIDS incidence rates were analyzed using spatial distribution, autocorrelation, and spatiotemporal risk analysis techniques.

RESULTS: During the study period, 119,890 cases of HIV/AIDS were reported among Brazilian women. The southeastern region had a higher age-adjusted HIV/AIDS incidence than other Brazilian regions. Hotspot HIV/AIDS incidence rates decreased in all Brazil. Piauí, Paraná, and Minas Gerais were the only states with an increased number of cold spots. Previous spatiotemporal risk zones were observed in the states of São Paulo, Rio Grande do Sul, and Rio de Janeiro. Belém was a risk zone with a later spatiotemporal risk.

CONCLUSIONS: The efficiency of public policies fighting HIV has not been uniform among municipalities, although HIV/AIDS cases have decreased among Brazilian women. The social determinants of health in each municipality should be considered when local health authorities implement policies. Women empowerment should be promoted, and access to preventive, diagnostic, and treatment healthcare places should be expanded and guaranteed.}, } @article {pmid37657322, year = {2023}, author = {Jia, H and Zhao, Y and Deng, H and Yu, H and Ge, C and Li, J}, title = {Integrated microbiome and multi-omics analysis reveal the molecular mechanisms of Eisenia fetida in response to biochar-derived dissolved and particulate matters.}, journal = {Journal of hazardous materials}, volume = {460}, number = {}, pages = {132422}, doi = {10.1016/j.jhazmat.2023.132422}, pmid = {37657322}, issn = {1873-3336}, mesh = {Animals ; *Oligochaeta ; Multiomics ; *Microbiota ; Particulate Matter/toxicity ; Soil ; }, abstract = {At present, most ecotoxicological studies are still confined to focusing on the harmful effects of biochar itself on soil fauna. However, the potential ecotoxicity of different components separated from biochar to terrestrial invertebrates remains poorly understood. In this study, the dissolved matter (DM) and particulate matter (PM) were separated from biochar (BC) and then introduced into the soil-earthworm system to investigate the response mechanism of earthworms at the molecular level. The results showed that BC and DM exposure caused an increase in the abundance of Proteobacteria in the cast bacterial community, suggesting the dysbiosis of intestinal microbiota. It was also observed that the cast bacterial communities were more sensitive to DM exposure than PM exposure. Transcriptomic analysis showed that BC and DM exposure induced significant enrichment of functional pathways related to infectious and neuropathic diseases. Metabolomic profiling manifested that DM exposure caused metabolic dysfunction, antioxidant and detoxification abilities recession. Furthermore, significant differences in the responses of earthworms at transcriptomic and metabolic levels confirmed that DM exhibited greater ecotoxicity than PM. This study highlighted the significant contributions of dissolved matter to the ecotoxicity of biochar from the perspective of transcriptomic and metabolomic profiles.}, } @article {pmid37654707, year = {2023}, author = {LeBaron, V and Homdee, N and Ogunjirin, E and Patel, N and Blackhall, L and Lach, J}, title = {Describing and visualizing the patient and caregiver experience of cancer pain in the home context using ecological momentary assessments.}, journal = {Digital health}, volume = {9}, number = {}, pages = {20552076231194936}, pmid = {37654707}, issn = {2055-2076}, support = {R01 NR019639/NR/NINR NIH HHS/United States ; }, abstract = {BACKGROUND: Pain continues to be a difficult and pervasive problem for patients with cancer, and those who care for them. Remote health monitoring systems (RHMS), such as the Behavioral and Environmental Sensing and Intervention for Cancer (BESI-C), can utilize Ecological Momentary Assessments (EMAs) to provide a more holistic understanding of the patient and family experience of cancer pain within the home context.

METHODS: Participants used the BESI-C system for 2-weeks which collected data via EMAs deployed on wearable devices (smartwatches) worn by both patients with cancer and their primary family caregiver. We developed three unique EMA schemas that allowed patients and caregivers to describe patient pain events and perceived impact on quality of life from their own perspective. EMA data were analyzed to provide a descriptive summary of pain events and explore different types of data visualizations.

RESULTS: Data were collected from five (n = 5) patient-caregiver dyads (total 10 individual participants, 5 patients, 5 caregivers). A total of 283 user-initiated pain event EMAs were recorded (198 by patients; 85 by caregivers) over all 5 deployments with an average severity score of 5.4/10 for patients and 4.6/10 for caregivers' assessments of patient pain. Average self-reported overall distress and pain interference levels (1 = least distress; 4 = most distress) were higher for caregivers (x¯ 3.02, x¯2.60,respectively) compared to patients (x¯ 2.82, x¯ 2.25, respectively) while perceived burden of partner distress was higher for patients (i.e., patients perceived caregivers to be more distressed, x¯ 3.21, than caregivers perceived patients to be distressed, x¯2.55). Data visualizations were created using time wheels, bubble charts, box plots and line graphs to graphically represent EMA findings.

CONCLUSION: Collecting data via EMAs is a viable RHMS strategy to capture longitudinal cancer pain event data from patients and caregivers that can inform personalized pain management and distress-alleviating interventions.}, } @article {pmid37654007, year = {2024}, author = {Papadopoulos, NG and Akdis, CA and Akdis, M and Damialis, A and Esposito, G and Fergadiotou, I and Goroncy, C and Guitton, P and Gotua, M and Erotokritou, K and Jartti, T and Murray, C and Nenes, A and Nikoletseas, S and Finotto, S and Pandis, SN and Ramiconi, V and Simpson, A and Soudunsaari, A and Stårbröst, A and Staiano, M and Varriale, A and Xepapadaki, P and Zuberbier, T and Annesi-Maesano, I and , }, title = {Addressing adverse synergies between chemical and biological pollutants at schools-The 'SynAir-G' hypothesis.}, journal = {Allergy}, volume = {79}, number = {2}, pages = {294-301}, doi = {10.1111/all.15857}, pmid = {37654007}, issn = {1398-9995}, support = {101057271//HORIZON EUROPE Health/ ; }, mesh = {Child ; Humans ; *Air Pollution, Indoor/adverse effects ; *Environmental Pollutants ; *Air Pollutants/adverse effects/analysis ; Particulate Matter ; *Asthma/epidemiology/etiology ; Environmental Monitoring ; }, abstract = {While the number and types of indoor air pollutants is rising, much is suspected but little is known about the impact of their potentially synergistic interactions, upon human health. Gases, particulate matter, organic compounds but also allergens and viruses, fall within the 'pollutant' definition. Distinct populations, such as children and allergy and asthma sufferers are highly susceptible, while a low socioeconomic background is a further susceptibility factor; however, no specific guidance is available. We spend most of our time indoors; for children, the school environment is of paramount importance and potentially amenable to intervention. The interactions between some pollutant classes have been studied. However, a lot is missing with respect to understanding interactions between specific pollutants of different classes in terms of concentrations, timing and sequence, to improve targeting and upgrade standards. SynAir-G is a European Commission-funded project aiming to reveal and quantify synergistic interactions between different pollutants affecting health, from mechanisms to real life, focusing on the school setting. It will develop a comprehensive and responsive multipollutant monitoring system, advance environmentally friendly interventions, and disseminate the generated knowledge to relevant stakeholders in accessible and actionable formats. The aim of this article it to put forward the SynAir-G hypothesis, and describe its background and objectives.}, } @article {pmid37651934, year = {2023}, author = {Fang, R and Chen, T and Han, Z and Ji, W and Bai, Y and Zheng, Z and Su, Y and Jin, L and Xie, B and Wu, D}, title = {From air to airway: Dynamics and risk of inhalable bacteria in municipal solid waste treatment systems.}, journal = {Journal of hazardous materials}, volume = {460}, number = {}, pages = {132407}, doi = {10.1016/j.jhazmat.2023.132407}, pmid = {37651934}, issn = {1873-3336}, mesh = {Humans ; *Solid Waste ; China ; *Bacteria ; Dust ; Machine Learning ; }, abstract = {Municipal solid waste treatment (MSWT) system emits a cocktail of microorganisms that jeopardize environmental and public health. However, the dynamics and risks of airborne microbiota associated with MSWT are poorly understood. Here, we analyzed the bacterial community of inhalable air particulates (PM10, n = 71) and the potentially exposed on-site workers' throat swabs (n = 30) along with waste treatment chain in Shanghai, the largest city of China. Overall, the airborne bacteria varied largely in composition and abundance during the treatment (P < 0.05), especially in winter. Compared to the air conditions, MSWT-sources that contributed to 15 ∼ 70% of airborne bacteria more heavily influenced the PM10-laden bacterial communities (PLS-SEM, β = 0.40, P < 0.05). Moreover, our year-span analysis found PM10 as an important media spreading pathogens (10[4] ∼ 10[8] copies/day) into on-site workers. The machine-learning identified Lactobacillus and Streptococcus as pharynx-niched featured biomarker in summer and Rhodococcus and Capnocytophaga in winter (RandomForest, ntree = 500, mtry = 10, cross = 10, OOB = 0%), which closely related to their airborne counterparts (Procrustes test, P < 0.05), suggesting that MSWT a dynamic hotspot of airborne bacteria with the pronounced inhalable risks to the neighboring communities.}, } @article {pmid37650794, year = {2023}, author = {Roma, P and Giromini, L and Sellbom, M and Cardinale, A and Ferracuti, S and Mazza, C}, title = {The ecological validity of the IOP-29: A follow-up study using the MMPI-2-RF and the SIMS as criterion variables.}, journal = {Psychological assessment}, volume = {35}, number = {10}, pages = {868-879}, doi = {10.1037/pas0001273}, pmid = {37650794}, issn = {1939-134X}, mesh = {Humans ; Follow-Up Studies ; *MMPI ; Databases, Factual ; Malingering ; *Psychological Trauma ; }, abstract = {Current guidelines for conducting symptom validity assessments require that professionals administer multiple symptom validity tests (SVTs) and that the SVTs selected for their evaluations provide nonredundant information. However, not many SVTs are currently available, and most of them rely on the same, (in)frequency-based, feigning detection strategy. In this context, the Inventory of Problems (IOP-29) could be a valuable addition to the assessor's toolbox because of its brevity (29 items) and its different approach to assessing the credibility of presented symptoms. As its ecological validity has been poorly investigated, the present study used a criterion groups design to examine the classification accuracy of the IOP-29 in a data set of 174 court-ordered psychological evaluations focused on psychological injury. The validity scales of the Minnesota Multiphasic Personality Inventory-2 Restructured Form and the total score of the Structured Inventory of Malingered Symptoms were used as criterion variables. Overall, the results of this study confirm that the IOP-29 is an effective measure (1.70 ≤ d ≤ 2.67) that provides valuable information when added to the multimethod assessment of symptom validity in civil forensic contexts. (PsycInfo Database Record (c) 2023 APA, all rights reserved).}, } @article {pmid37648185, year = {2023}, author = {Tan, M and Bian, Z and Dong, J and Hao, M and Qu, J}, title = {Comparing the variation and influencing factors of CO2 emission from subsidence waterbodies under different restoration modes in coal mining area.}, journal = {Environmental research}, volume = {237}, number = {Pt 2}, pages = {116936}, doi = {10.1016/j.envres.2023.116936}, pmid = {37648185}, issn = {1096-0953}, abstract = {Subsidence waterbodies play an important role in carbon cycle in coal mining area. However, little effort has been made to explore the carbon dioxide (CO2) release characteristics and influencing factors in subsidence waterbodies, especially under different restoration modes. Here, we measured CO2 release fluxes (F(CO2)) across Anguo wetland (AW), louts pond (LP), fishpond (FP), fishery-floating photovoltaic wetland (FFPV), floating photovoltaic wetland (FPV) in coal mining subsidence area, with unrestored subsidence waterbodies (SW) and unaffected normal Dasha river (DR) as the control area. We sampled each waterbody and tested which physical, chemical, and biological characteristics of water and sediment related to variability in CO2. The results indicated that F(CO2) exhibited the following patterns: FFPV > FPV > FP > SW > DR > LP > AW. Trophic lake index (TLI) and microbial biomass carbon content (MBC) in sediment had a positive impact on F(CO2). The dominant archaea Euryarchaeota and Thaumarchaeota, and dominant bacteria Proteobacteria promoted F(CO2). This study can help more accurately quantify CO2 emissions and guide CO2 future emission reduction and subsidence waterbodies estoration.}, } @article {pmid37646945, year = {2023}, author = {Bosch, M and López-Pujol, J and Blanché, C and Simon, J}, title = {DCDB: Chromosome Database of Tribe Delphinieae (Ranunculaceae): Structure, Exploitation, and Recent Development.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2703}, number = {}, pages = {173-192}, pmid = {37646945}, issn = {1940-6029}, mesh = {*Ranunculaceae ; Phylogeny ; Cytogenetic Analysis ; Databases, Factual ; Internet ; }, abstract = {An updated (and now online) version of the former chromosome database of tribe Delphinieae (Ranunculaceae) is presented (http://www.delphinieae.online). This new version is the result of an accurate, exhaustive literature and Internet research, by adding chromosome counts and all related karyological information for the genera Aconitum L., Gymnaconitum (Stapf) Wei Wang & Z. D. Chen, Delphinium L. (including Staphisagria Spach), Consolida (DC.) S. F. Gray and Aconitella Spach, accumulated during the approximately last 25 years and that comprise worldwide published data from 1889 to 2021. The Delphinieae Chromosome Database (DCDB) (last updated 31.12.2021) contains a total number of 3435 reports belonging to 425 species (503 taxa), which represents 48.6% of the total species of the tribe (an increase of c. 213% and 32% compared with the 1097 and 2598 reports gathered in the 1999 and 2016 versions, respectively). This increase is due both to chromosome research progress and to improved information capture system. Moreover, recent taxonomic advances, synonymization, and new phylogenetic criteria have also been considered.The DCDB database provides the most complete currently available information on published chromosome numbers, ploidy-level estimates, and other karyological data of Delphinieae, and it is aimed to be useful for the building of cytotaxonomical databases and for specific research ongoing projects of systematics and evolution of Ranunculaceae. DCDB includes two levels of taxonomic resolution, published name (original and standardized form) and database accepted name (based on either Plants of the World - POWO or expert specialist criteria), as well as the geographic origin of each count (country, locality, geographic coordinates, elevation, or ecological information when reported in the original publication), associated karyological data if originally provided (studied material type, graphic information, chromosome measures and formulas, satellites, B chromosomes, other cytogenetic techniques used, etc.), voucher information and reference (with DOI and other links to access the original document). An effort to check the original sources and to search in grey literature allowed to indicate the counts that appear to be registered twice.}, } @article {pmid37646941, year = {2023}, author = {Henniges, MC and Johnston, E and Pellicer, J and Hidalgo, O and Bennett, MD and Leitch, IJ}, title = {The Plant DNA C-Values Database: A One-Stop Shop for Plant Genome Size Data.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2703}, number = {}, pages = {111-122}, pmid = {37646941}, issn = {1940-6029}, mesh = {Genome Size ; *Genome, Plant ; Cytogenetics ; DNA, Plant/genetics ; *Databases, Nucleic Acid ; }, abstract = {Genome size is a plant character with far-reaching implications, ranging from impacts on the financial and computing feasibility of sequencing and assembling genomes all the way to influencing the very ecology and evolution of species. The increasing recognition of the role of genome size in plant science has led to a rising demand for comprehensive and easily accessible sources of genome size data. The Plant DNA C-values database has established itself as a trusted and widely used central hub for users needing to access available plant genome size data, complemented with related cytogenetic (ploidy level) and karyological (chromosome number) information where available. Since its inception in 2001, the database has undergone six major updates to incorporate newly available genome size information, leading to the most recent release (Release 7.1), which comprises data for 12,273 species across all the major land plant and some algal lineages. Here we describe how to use the database efficiently, making use of its different query and filtering settings.}, } @article {pmid37645296, year = {2022}, author = {Anegg, M and Prakofjewa, J and Kalle, R and Sõukand, R}, title = {Local ecological knowledge and folk medicine in historical Estonia, Livonia, Courland and Galicia in Northeastern Europe, 1805-1905.}, journal = {Open research Europe}, volume = {2}, number = {}, pages = {30}, pmid = {37645296}, issn = {2732-5121}, abstract = {Background: Historical ethnobotanical data can provide valuable information about past human-nature relationships as well as serve as a basis for diachronic analysis. This data note aims to present a dataset which documented medicinal plant uses, mentioned in a selection of German-language sources from the 19 [th] century covering the historical regions of Estonia, Livonia, Courland, and Galicia. Methods: Data was mainly entered by systematic manual search in various ethnobotanical historical German-language works focused on the medicinal use of plants. Data about plant and non-plant constituents, their usage, the mode of administration, used plant parts, and their German and local names was extracted and collected into a database in the form of Use Reports.}, } @article {pmid37644145, year = {2023}, author = {Zhao, W and Zhang, P and Chen, D and Wang, H and Gu, B and Zhang, J}, title = {Data mining from process monitoring of typical polluting enterprise.}, journal = {Environmental monitoring and assessment}, volume = {195}, number = {9}, pages = {1109}, pmid = {37644145}, issn = {1573-2959}, support = {2022HT0009//Ecological Environment Research and Achievement Extension Project of Zhejiang Province/ ; 2022HT0009//Ecological Environment Research and Achievement Extension Project of Zhejiang Province/ ; 2022HT0009//Ecological Environment Research and Achievement Extension Project of Zhejiang Province/ ; 2022HT0009//Ecological Environment Research and Achievement Extension Project of Zhejiang Province/ ; 2022HT0009//Ecological Environment Research and Achievement Extension Project of Zhejiang Province/ ; 22gyb37//Science and Technology Plan Project of Taizhou/ ; 22gyb37//Science and Technology Plan Project of Taizhou/ ; 22gyb37//Science and Technology Plan Project of Taizhou/ ; 22gyb37//Science and Technology Plan Project of Taizhou/ ; 22gyb37//Science and Technology Plan Project of Taizhou/ ; 2021C03178//Science and Technology Program of Zhejiang Province/ ; 2021C03178//Science and Technology Program of Zhejiang Province/ ; }, mesh = {*Environmental Monitoring ; *Wastewater ; Data Mining ; China ; Electric Conductivity ; Vehicle Emissions ; }, abstract = {With the increasing volume of environmental monitoring data, extracting valuable insights from multivariate time series sensor data can facilitate comprehensive information utilization and support informed decision-making in environmental management. However, there is a dearth of comprehensive research on multivariate data analysis for process monitoring in typical polluting enterprises. In this study, an artificial neural network model based on back-propagation algorithm (BP-ANN) was developed to predict the wastewater and exhaust gas emissions using IoT data obtained from process monitoring of a typical polluting enterprise located in Taizhou, Zhejiang Province, China. The results indicate that the model constructed has a high predictive coefficient of determination (R[2]) with values of 0.8510, 0.9565, 0.9561, 0.9677, and 0.9061 for chemical oxygen demand (COD), potential of hydrogen (pH), electrical conductivity (EC), flue gas emission (FGE), and non-methane hydrocarbon concentration (NMHC) respectively. For the first time, the variable importance measure (VIM)-assisted BP-ANN was employed to investigate the internal and external correlations between wastewater and exhaust gas treatment, thereby enhancing the interpretability of mapping features in the BP-ANN model. The predicted errors for pH and FGE have been demonstrated to fall within the range of - 0.62 ~ 0.30 and - 0.21 ~ 0.15 m[3]/s, respectively, with average relative errors of 1.05% and 9.60%, which is advantageous in detecting anomalous data and forecasting pollution indicator values. Our approach successfully addresses the challenge of segregating data analysis for wastewater disposal and exhaust gas disposal in the process monitoring of polluting enterprises, while also unearthing potential variables that significantly contribute to the BP-ANN model, thereby facilitating the selection and extraction of characteristic variables.}, } @article {pmid37642912, year = {2023}, author = {Goparaju, L and Pillutla, RCP and Venkata, SBK}, title = {Assessment of forest fire emissions in Uttarakhand State, India, using Open Geospatial data and Google Earth Engine.}, journal = {Environmental science and pollution research international}, volume = {30}, number = {45}, pages = {100873-100891}, pmid = {37642912}, issn = {1614-7499}, mesh = {*Carbon Monoxide/analysis ; *Wildfires ; Nitrogen Dioxide/analysis ; Search Engine ; Gases/analysis ; Aerosols ; }, abstract = {In the recent past, forest fires have increased due to the changing climate pattern. It is necessary to analyse and quantify various gaseous emissions so as to mitigate their harmful effects on air pollution. Satellite remote sensing data provides an opportunity to study the greenhouse gases in the atmosphere. The multispectral sensor of the Tropospheric Monitoring Instrument (Sentinel-5) is capable of recording the reflectance of wavelengths vital for measuring the atmospheric concentrations of methane, formaldehyde, aerosol, carbon monoxide, etc., at a spatial resolution of 0.01°. The present study utilized the Google Earth Engine (GEE) platform to study the emissions caused by forest fires in four districts of Uttarakhand State of India, which witnessed unprecedented fires in April-May 2021. All the datasets were ingested in GEE, which has the capability to analyse large datasets without the need to download them. The pre-fire period chosen was September 2020; the fire period was February-May 2021, and the post-fire period was June 2021. The variables chosen were aerosol absorbing index (AAI), carbon monoxide (CO) and nitrogen dioxide (NO2). The climate parameter temperature (Moderate Resolution Imaging Spectroradiometer Land Surface Temperature) and precipitation (from Climate Hazards Group InfraRed Precipitation (CHIRPS) Pentad) were also studied for the period mentioned. The results indicate a different trend for emissions in each district. For AAI, maximum emissions were noted in district Nainital followed by Almora, Tehri Garhwal and Garhwal. For CO emissions, the most affected district was Almora followed by Nainital, Garhwal and Tehri Garhwal. For NO2 emissions, the most affected district was Garhwal, followed by Nainital, Tehri Garhwal and Almora. Delta Normalized Burn Ratio was computed from Sentinel data (difference of pre-fire and post-fire images) to assess the burnt area severity. The Delta Normalized Burn Ratio values observed that the district with the most burnt area is Garhwal, followed by Nainital, Almora and Tehri Garhwal. The elevated temperatures and scanty rainfall patterns regulated the intensity and duration of forest fire. Monitoring the gaseous emissions as a consequence of forest fire in the GEE platform is much easier and more convenient at a regional level. Such data is much needed for mitigation measures to be implemented in time.}, } @article {pmid37640770, year = {2023}, author = {Mudge, L and Bruno, JF}, title = {Disturbance intensification is altering the trait composition of Caribbean reefs, locking them into a low functioning state.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {14022}, pmid = {37640770}, issn = {2045-2322}, mesh = {Animals ; Caribbean Region ; *Anthozoa ; Climate Change ; *Cyclonic Storms ; Databases, Factual ; *Marijuana Abuse ; Plant Weeds ; }, abstract = {Anthropogenic climate change is intensifying natural disturbance regimes, which negatively affects some species, while benefiting others. This could alter the trait composition of ecological communities and influence resilience to disturbance. We investigated how the frequency and intensification of the regional storm regime (and likely other disturbances) is altering coral species composition and in turn resistance and recovery. We developed regional databases of coral cover and composition (3144 reef locations from 1970 to 2017) and of the path and strength of cyclonic storms in the region (including 10,058 unique storm-reef intersections). We found that total living coral cover declined steadily through 2017 (the median annual loss rate was ~ 0.25% per year). Our results also indicate that despite the observed increase in the intensity of Atlantic cyclonic storms, their effect on coral cover has decreased markedly. This could be due in part to selection for disturbance-resistant taxa in response to the intensifying disturbance regime. We found that storms accelerated the loss of threatened acroporid corals but had no measurable effect on the cover of more resilient "weedy" corals, thereby increasing their relative cover. Although resistance to disturbance has increased, recovery rates have slowed due to the dominance of small, slow-growing species. This feedback loop is locking coral communities into a low-functioning state dominated by weedy species with limited ecological or societal value.}, } @article {pmid37636281, year = {2023}, author = {Wang, F and Liu, J and Qin, G and Zhang, J and Zhou, J and Wu, J and Zhang, L and Thapa, P and Sanders, CJ and Santos, IR and Li, X and Lin, G and Weng, Q and Tang, J and Jiao, N and Ren, H}, title = {Coastal blue carbon in China as a nature-based solution toward carbon neutrality.}, journal = {Innovation (Cambridge (Mass.))}, volume = {4}, number = {5}, pages = {100481}, pmid = {37636281}, issn = {2666-6758}, abstract = {To achieve the Paris Agreement, China pledged to become "Carbon Neutral" by the 2060s. In addition to massive decarbonization, this would require significant changes in ecosystems toward negative CO2 emissions. The ability of coastal blue carbon ecosystems (BCEs), including mangrove, salt marsh, and seagrass meadows, to sequester large amounts of CO2 makes their conservation and restoration an important "nature-based solution (NbS)" for climate adaptation and mitigation. In this review, we examine how BCEs in China can contribute to climate mitigation. On the national scale, the BCEs in China store up to 118 Tg C across a total area of 1,440,377 ha, including over 75% as unvegetated tidal flats. The annual sedimental C burial of these BCEs reaches up to 2.06 Tg C year[-1], of which most occurs in salt marshes and tidal flats. The lateral C flux of mangroves and salt marshes contributes to 1.17 Tg C year[-1] along the Chinese coastline. Conservation and restoration of BCEs benefit climate change mitigation and provide other ecological services with a value of $32,000 ha[-1] year[-1]. The potential practices and technologies that can be implemented in China to improve BCE C sequestration, including their constraints and feasibility, are also outlined. Future directions are suggested to improve blue carbon estimates on aerial extent, carbon stocks, sequestration, and mitigation potential. Restoring and preserving BCEs would be a cost-effective step to achieve Carbon Neutral by 2060 in China despite various barriers that should be removed.}, } @article {pmid37635752, year = {2023}, author = {Boyes, D and Boyes, C and , and , and , and , and , and , }, title = {The genome sequence of the Powdered Quaker, Orthosia gracilis (Schiffermüller, 1775).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {290}, pmid = {37635752}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual male Orthosia gracilis (the powdered quaker; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 715.5 megabases in span. Most of the assembly is scaffolded into 14 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.43 kilobases in length.}, } @article {pmid37634178, year = {2023}, author = {Zhou, L and Ye, T and Zheng, S and Zhu, X and Chen, Z and Wu, Y}, title = {Experimental and modeling investigation of dual-source iron release in water-solid-gas interaction of abandoned coal mine drainage.}, journal = {Environmental geochemistry and health}, volume = {45}, number = {11}, pages = {8433-8449}, pmid = {37634178}, issn = {1573-2983}, support = {2022YFC3702203//the National Key R&D Program of China/ ; 2020ZDPYMS07//the Fundamental Research Funds for the Central Universities, China/ ; }, mesh = {*Water ; Environmental Monitoring/methods ; *Water Pollutants, Chemical/analysis ; Iron/analysis ; Minerals ; Coal ; Steel ; }, abstract = {After mine closure and flooding, abandoned iron-prone devices and equipment (e.g., steel bolts and ground support meshes) and iron-bearing minerals (e.g., pyrite) form a dual-source iron pollution system in mine groundwater. Dual-source iron contributes to the water-solid-gas interaction in abandoned coal mines and the release of iron at different periods after mine closure, posing environmental risks in groundwater and discharging acid mine drainage, which contains large amounts of iron. In this study, a series of hydrochemical experiments were conducted to simulate the iron release process of the dual-source system, and electrochemical experiments were carried out to reveal the reaction mechanism, characterize the dual-source iron pollution release mode and quantify the release rate ratio. PHREEQC package was used to simulate the long-term hydrogeochemistry reactions of the water-solid-gas interaction to determine the key factors and suitable conditions that inhibit dual-source iron release. The results show that the dual-source system of iron-bearing minerals (pyrite) and steel bolts promote iron release from each other. The resulting calculated annual iron release indicated that the overall iron release rate ratio is: dual-source > bolt > pyrite, indicating that mine water would remain acidic for a long time due to the continuous release of iron from the system. Numerical modeling results show that maintaining the environment temperature below 25 °C and the pH above 3.5 is an effective way to reduce the iron release rate.}, } @article {pmid37634023, year = {2023}, author = {Medo, A and Ohte, N and Kajitani, H and Nose, T and Manabe, Y and Sugawara, T and Onishi, Y and Goto, AS and Koba, K and Arai, N and Mitsunaga, Y and Kume, M and Nishizawa, H and Kojima, D and Yokoyama, A and Yamanaka, T and Viputhanumas, T and Mitamura, H}, title = {Striped catfish (Pangasianodon hypophthalmus) exploit food sources across anaerobic decomposition- and primary photosynthetic production-based food chains.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {13992}, pmid = {37634023}, issn = {2045-2322}, mesh = {*Catfishes/growth & development/physiology ; Animals ; Food Chain ; Ecosystem ; Thailand ; Geologic Sediments ; }, abstract = {Dietary information from aquatic organisms is instrumental in predicting biological interactions and understanding ecosystem functionality. In freshwater habitats, generalist fish species can access a diverse array of food sources from multiple food chains. These may include primary photosynthetic production and detritus derived from both oxic and anoxic decomposition. However, the exploitation of anoxic decomposition products by fish remains insufficiently explored. This study examines feeding habits of striped catfish (Pangasianodon hypophthalmus) at both adult and juvenile stages within a tropical reservoir, using stable carbon, nitrogen, and sulfur isotope ratios (δ[13]C, δ[15]N, and δ[34]S, respectively) and fatty acid (FA) analyses. The adult catfish exhibited higher δ[15]N values compared to primary consumers that feed on primary photosynthetic producers, which suggests ingestion of food sources originating from primary photosynthetic production-based food chains. On the other hand, juvenile catfish demonstrated lower δ[15]N values than primary consumers, correlating with low δ[34]S value and large proportions of bacterial FA but contained small proportions of polyunsaturated FA. This implies that juveniles utilize food sources from both anoxic decomposition and primary photosynthetic production-based food chains. Our results indicate that food chains based on anoxic decomposition can indeed contribute to the dietary sources of tropical fish species.}, } @article {pmid37633161, year = {2024}, author = {Shan, Y and Zhao, W and Hao, W and Kimura, T and Ukawa, S and Ohira, H and Kawamura, T and Wakai, K and Ando, M and Tamakoshi, A and Wang, C}, title = {Five-year changes of social activity and incident long-term care needs among depressed older adults: A 15-year follow up.}, journal = {Archives of gerontology and geriatrics}, volume = {116}, number = {}, pages = {105163}, doi = {10.1016/j.archger.2023.105163}, pmid = {37633161}, issn = {1872-6976}, mesh = {Humans ; Aged ; *Long-Term Care ; Follow-Up Studies ; Prospective Studies ; *Insurance, Long-Term Care ; }, abstract = {OBJECTIVES: To examine the effects of changes in individual/multiple social activities between 65 and 70 years of age on incident long-term care (LTC) needs between 70 and 80 in older adults with depressive symptoms.

METHODS: Participants were recruited from the New Integrated Suburban Seniority Investigation Project, an ongoing prospective cohort study. A total of 525 older adults with depressive symptoms were included. The validated 15-item Geriatric Depression Scale was used to assess depressive symptoms. A self-report questionnaire was used to measure social activities (social-related, learning, and personal). LTC needs was defined according to Japan's Long-term Care Insurance System. A competing risk model and a Laplace regression model were used to estimate the hazard ratios of LTC needs incidence and the 25th percentile difference in LTC-needs-free survival time and their 95% confidence intervals.

RESULTS: Out of 4314 person-years of mild LTC needs, 108 individuals developed it. Participants who increased their frequency of learning activities have a lower risk of developing mild LTC needs. Increasing the frequency could also prolong LTC-needs-free survival time by approximately 2.61 years. Out of 4535 person-years for severe LTC needs, 54 individuals developed it. Participants with a continuous regular frequency of learning activities had a lower risk of developing severe LTC needs. However, the association between this frequency and LTC-needs-free survival time for severe LTC needs was insignificant in the multivariable models.

CONCLUSIONS: Increased frequency of learning activities reduced the risk of LTC needs among older adults with depressive symptoms and prolonged their LTC-needs-free survival time.}, } @article {pmid37632753, year = {2022}, author = {Meyer, R and Davies, N and Pitz, KJ and Meyer, C and Samuel, R and Anderson, J and Appeltans, W and Barker, K and Chavez, FP and Duffy, JE and Goodwin, KD and Hudson, M and Hunter, ME and Karstensen, J and Laney, CM and Leinen, M and Mabee, P and Macklin, JA and Muller-Karger, F and Pade, N and Pearlman, J and Phillips, L and Provoost, P and Santi, I and Schigel, D and Schriml, LM and Soccodato, A and Suominen, S and Thibault, KM and Ung, V and van de Kamp, J and Wallis, E and Walls, R and Buttigieg, PL}, title = {The founding charter of the Omic Biodiversity Observation Network (Omic BON).}, journal = {GigaScience}, volume = {12}, number = {}, pages = {}, pmid = {37632753}, issn = {2047-217X}, mesh = {*Biodiversity ; *Knowledge ; }, abstract = {Omic BON is a thematic Biodiversity Observation Network under the Group on Earth Observations Biodiversity Observation Network (GEO BON), focused on coordinating the observation of biomolecules in organisms and the environment. Our founding partners include representatives from national, regional, and global observing systems; standards organizations; and data and sample management infrastructures. By coordinating observing strategies, methods, and data flows, Omic BON will facilitate the co-creation of a global omics meta-observatory to generate actionable knowledge. Here, we present key elements of Omic BON's founding charter and first activities.}, } @article {pmid37630465, year = {2023}, author = {Koga, S and Takazono, T and Kido, T and Muramatsu, K and Tokutsu, K and Tokito, T and Okuno, D and Ito, Y and Yura, H and Takeda, K and Iwanaga, N and Ishimoto, H and Sakamoto, N and Yatera, K and Izumikawa, K and Yanagihara, K and Fujino, Y and Fushimi, K and Matsuda, S and Mukae, H}, title = {Evaluation of the Effectiveness and Use of Anti-Methicillin-Resistant Staphylococcus aureus Agents for Aspiration Pneumonia in Older Patients Using a Nationwide Japanese Administrative Database.}, journal = {Microorganisms}, volume = {11}, number = {8}, pages = {}, pmid = {37630465}, issn = {2076-2607}, abstract = {Studies indicated potential harm from empirical broad-spectrum therapy. A recent study of hospitalizations for community-acquired pneumonia suggested that empirical anti-methicillin-resistant Staphylococcus aureus (MRSA) therapy was associated with an increased risk of death and other complications. However, limited evidence supports empirical anti-MRSA therapy for older patients with aspiration pneumonia. In a nationwide Japanese database, patients aged ≥65 years on admission with aspiration pneumonia were analyzed. Patients were divided based on presence of respiratory failure and further sub-categorized based on their condition within 3 days of hospital admission, either receiving a combination of anti-MRSA agents and other antibiotics, or not using MRSA agents. An inverse probability weighting method with estimated propensity scores was used. Out of 81,306 eligible patients, 55,098 had respiratory failure, and 26,208 did not. In the group with and without respiratory failure, 0.93% and 0.42% of the patients, respectively, received anti-MRSA agents. In patients with respiratory failure, in-hospital mortality (31.38% vs. 19.03%, p < 0.001), 30-day mortality, and 90-day mortality were significantly higher, and oxygen administration length was significantly longer in the anti-MRSA agent combination group. Anti-MRSA agent combination use did not improve the outcomes in older patients with aspiration pneumonia and respiratory failure, and should be carefully and comprehensively considered.}, } @article {pmid37626975, year = {2023}, author = {Irwin, G and Rogatzki, MJ and Wiltshire, HD and Williams, GKR and Gu, Y and Ash, GI and Tao, D and Baker, JS}, title = {Sports-Related Concussion Assessment: A New Physiological, Biomechanical, and Cognitive Methodology Incorporating a Randomized Controlled Trial Study Protocol.}, journal = {Biology}, volume = {12}, number = {8}, pages = {}, pmid = {37626975}, issn = {2079-7737}, support = {UL1 TR001863/TR/NCATS NIH HHS/United States ; }, abstract = {BACKGROUND: Taking part in moderate-to-vigorous exercise in contact sports on a regular basis may be linked to an increase in cerebrovascular injury and head trauma. Validated objective measures are lacking in the initial post-event diagnosis of head injury. The exercise style, duration, and intensity may also confound diagnostic indicators. As a result, we propose that the new Interdisciplinary Group in Movement & Performance from Acute & Chronic Head Trauma (IMPACT) analyze a variety of functional (biomechanical and motor control) tests as well as related biochemistry to see how they are affected by contact in sports and head injury. The study's goal will be to look into the performance and physiological changes in rugby players after a game for head trauma and injury.

METHODS: This one-of-a-kind study will use a randomized controlled trial (RCT) utilizing a sport participation group and a non-participation control group. Forty male rugby 7 s players will be recruited for the study and allocated randomly to the experimental groups. The intervention group will participate in three straight rugby matches during a local 7 s rugby event. At the pre-match baseline, demographic and anthropometric data will be collected. This will be followed by the pre-match baseline collection of biochemical, biomechanical, and cognitive-motor task data. After three consecutive matches, the same measures will be taken. During each match, a notational analysis will be undertaken to obtain contact information. All measurements will be taken again 24, 48, and 72 h after the third match.

DISCUSSION: When the number of games increases owing to weariness and/or stressful circumstances, we expect a decline in body movement, coordination, and cognitive-motor tasks. Changes in blood biochemistry are expected to correspond to changes in biomechanics and cognitive-motor processes. This research proposal will generate considerable, ecologically valid data on the occurrence of head trauma events under game conditions, as well as the influence of these events on the biological systems of the performers. This will lead to a greater understanding of how sports participants react to exercise-induced injuries. This study's scope will have far-reaching ramifications for doctors, coaches, managers, scientists, and sports regulatory bodies concerned with the health and well-being of athletic populations at all levels of competition, including all genders and ages.}, } @article {pmid37626434, year = {2023}, author = {Kelliher, JM and Robinson, AJ and Longley, R and Johnson, LYD and Hanson, BT and Morales, DP and Cailleau, G and Junier, P and Bonito, G and Chain, PSG}, title = {The endohyphal microbiome: current progress and challenges for scaling down integrative multi-omic microbiome research.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {192}, pmid = {37626434}, issn = {2049-2618}, mesh = {*Multiomics ; Data Analysis ; Eukaryota ; *Microbiota/genetics ; Prokaryotic Cells ; }, abstract = {As microbiome research has progressed, it has become clear that most, if not all, eukaryotic organisms are hosts to microbiomes composed of prokaryotes, other eukaryotes, and viruses. Fungi have only recently been considered holobionts with their own microbiomes, as filamentous fungi have been found to harbor bacteria (including cyanobacteria), mycoviruses, other fungi, and whole algal cells within their hyphae. Constituents of this complex endohyphal microbiome have been interrogated using multi-omic approaches. However, a lack of tools, techniques, and standardization for integrative multi-omics for small-scale microbiomes (e.g., intracellular microbiomes) has limited progress towards investigating and understanding the total diversity of the endohyphal microbiome and its functional impacts on fungal hosts. Understanding microbiome impacts on fungal hosts will advance explorations of how "microbiomes within microbiomes" affect broader microbial community dynamics and ecological functions. Progress to date as well as ongoing challenges of performing integrative multi-omics on the endohyphal microbiome is discussed herein. Addressing the challenges associated with the sample extraction, sample preparation, multi-omic data generation, and multi-omic data analysis and integration will help advance current knowledge of the endohyphal microbiome and provide a road map for shrinking microbiome investigations to smaller scales. Video Abstract.}, } @article {pmid37624884, year = {2023}, author = {Elser, D and Pflieger, D and Villette, C and Moegle, B and Miesch, L and Gaquerel, E}, title = {Evolutionary metabolomics of specialized metabolism diversification in the genus Nicotiana highlights N-acylnornicotine innovations.}, journal = {Science advances}, volume = {9}, number = {34}, pages = {eade8984}, pmid = {37624884}, issn = {2375-2548}, mesh = {*Nicotiana/genetics ; *Metabolomics ; Acclimatization ; Consensus ; Databases, Factual ; }, abstract = {Specialized metabolite (SM) diversification is a core process to plants' adaptation to diverse ecological niches. Here, we implemented a computational mass spectrometry-based metabolomics approach to exploring SM diversification in tissues of 20 species covering Nicotiana phylogenetics sections. To markedly increase metabolite annotation, we created a large in silico fragmentation database, comprising >1 million structures, and scripts for connecting class prediction to consensus substructures. Together, the approach provides an unprecedented cartography of SM diversity and section-specific innovations in this genus. As a case study and in combination with nuclear magnetic resonance and mass spectrometry imaging, we explored the distribution of N-acylnornicotines, alkaloids predicted to be specific to Repandae allopolyploids, and revealed their prevalence in the genus, albeit at much lower magnitude, as well as a greater structural diversity than previously thought. Together, the data integration approaches provided here should act as a resource for future research in plant SM evolution.}, } @article {pmid37621575, year = {2023}, author = {Boyes, D and , and , and , and , and , and Holland, PWH and , }, title = {The genome sequence of the Buff Ermine, Spilarctia lutea (Hufnagel, 1766).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {92}, pmid = {37621575}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual female Spilarctia lutea (the Buff Ermine; Arthropoda; Insecta; Lepidoptera; Erebidae). The genome sequence is 584.8 megabases in span. Most of the assembly is scaffolded into 32 chromosomal pseudomolecules, including the assembled Z and W sex chromosomes. The mitochondrial genome has also been assembled and is 15.4 kilobases in length. Gene annotation of this assembly on Ensembl identified 18,304 protein coding genes.}, } @article {pmid37620553, year = {2023}, author = {Gonzalez, A and Vihervaara, P and Balvanera, P and Bates, AE and Bayraktarov, E and Bellingham, PJ and Bruder, A and Campbell, J and Catchen, MD and Cavender-Bares, J and Chase, J and Coops, N and Costello, MJ and Czúcz, B and Delavaud, A and Dornelas, M and Dubois, G and Duffy, EJ and Eggermont, H and Fernandez, M and Fernandez, N and Ferrier, S and Geller, GN and Gill, M and Gravel, D and Guerra, CA and Guralnick, R and Harfoot, M and Hirsch, T and Hoban, S and Hughes, AC and Hugo, W and Hunter, ME and Isbell, F and Jetz, W and Juergens, N and Kissling, WD and Krug, CB and Kullberg, P and Le Bras, Y and Leung, B and Londoño-Murcia, MC and Lord, JM and Loreau, M and Luers, A and Ma, K and MacDonald, AJ and Maes, J and McGeoch, M and Mihoub, JB and Millette, KL and Molnar, Z and Montes, E and Mori, AS and Muller-Karger, FE and Muraoka, H and Nakaoka, M and Navarro, L and Newbold, T and Niamir, A and Obura, D and O'Connor, M and Paganini, M and Pelletier, D and Pereira, H and Poisot, T and Pollock, LJ and Purvis, A and Radulovici, A and Rocchini, D and Roeoesli, C and Schaepman, M and Schaepman-Strub, G and Schmeller, DS and Schmiedel, U and Schneider, FD and Shakya, MM and Skidmore, A and Skowno, AL and Takeuchi, Y and Tuanmu, MN and Turak, E and Turner, W and Urban, MC and Urbina-Cardona, N and Valbuena, R and Van de Putte, A and van Havre, B and Wingate, VR and Wright, E and Torrelio, CZ}, title = {A global biodiversity observing system to unite monitoring and guide action.}, journal = {Nature ecology & evolution}, volume = {7}, number = {12}, pages = {1947-1952}, pmid = {37620553}, issn = {2397-334X}, mesh = {*Biodiversity ; *Ecosystem ; }, } @article {pmid37619239, year = {2023}, author = {Qiu, S and Yang, A and Zeng, H}, title = {Flux balance analysis-based metabolic modeling of microbial secondary metabolism: Current status and outlook.}, journal = {PLoS computational biology}, volume = {19}, number = {8}, pages = {e1011391}, pmid = {37619239}, issn = {1553-7358}, mesh = {Secondary Metabolism ; Cell Cycle ; Cell Proliferation ; *Computational Biology ; *Engineering ; }, abstract = {In microorganisms, different from primary metabolism for cellular growth, secondary metabolism is for ecological interactions and stress responses and an important source of natural products widely used in various areas such as pharmaceutics and food additives. With advancements of sequencing technologies and bioinformatics tools, a large number of biosynthetic gene clusters of secondary metabolites have been discovered from microbial genomes. However, due to challenges from the difficulty of genome-scale pathway reconstruction and the limitation of conventional flux balance analysis (FBA) on secondary metabolism, the quantitative modeling of secondary metabolism is poorly established, in contrast to that of primary metabolism. This review first discusses current efforts on the reconstruction of secondary metabolic pathways in genome-scale metabolic models (GSMMs), as well as related FBA-based modeling techniques. Additionally, potential extensions of FBA are suggested to improve the prediction accuracy of secondary metabolite production. As this review posits, biosynthetic pathway reconstruction for various secondary metabolites will become automated and a modeling framework capturing secondary metabolism onset will enhance the predictive power. Expectedly, an improved FBA-based modeling workflow will facilitate quantitative study of secondary metabolism and in silico design of engineering strategies for natural product production.}, } @article {pmid37614677, year = {2023}, author = {Boyes, D and Hammond, J and , and , and , and , and , and , }, title = {The genome sequence of the White-shouldered Marble, Apotomis turbidana (Hübner, 1825).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {127}, pmid = {37614677}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual male Apotomis turbidana (the White-shouldered Marble; Arthropoda; Insecta; Lepidoptera; Tortricidae). The genome sequence is 720.5 megabases in span. Most of the assembly is scaffolded into 28 chromosomal pseudomolecules, including the assembled Z sex chromosome. The mitochondrial genome has also been assembled and is 16.8 kilobases in length. Gene annotation of this assembly on Ensembl identified 22,646 protein coding genes.}, } @article {pmid37614458, year = {2023}, author = {Gavurova, B and Kelemen, M and Polishchuk, V and Mudarri, T and Smolanka, V}, title = {A fuzzy decision support model for the evaluation and selection of healthcare projects in the framework of competition.}, journal = {Frontiers in public health}, volume = {11}, number = {}, pages = {1222125}, pmid = {37614458}, issn = {2296-2565}, mesh = {European Union ; *Policy ; *Delivery of Health Care ; Decision Support Techniques ; }, abstract = {Our research aims to support decision-making regarding the financing of healthcare projects by structural funds with policies targeting reduction of the development gap among different regions and countries of the European Union as well as the achievement of economic and social cohesion. A fuzzy decision support model for the evaluation and selection of healthcare projects should rank the project applications for the selected region, accounting for the investor's wishes in the form of a regional coefficient in order to reduce the development gap between regions. On the one hand, our proposed model evaluates project applications based on selected criteria, which may be structured, weakly structured, or unstructured. On the other hand, it also incorporates information on the level of healthcare development in the region. The obtained ranking increases the degree of validity of the decision regarding the selection of projects for financing by investors, considering the level of development of the region where the project will be implemented. At the expense of European Union (EU) structural funds, a village, city, region, or state can receive funds for modernization and development of the healthcare sector and all related processes. To minimize risks, it is necessary to implement adequate support systems for decision-making in the assessment of project applications, as well as regional policy in the region where the project will be implemented. The primary goal of this study was to develop a complex fuzzy decision support model for the evaluation and selection of projects in the field of healthcare with the aim of reducing the development gap between regions. Based on the above description, we formed the following scientific hypothesis for this research: if the project selected for financing can successfully achieve its stated goals and increase the level of development of its region, it should be evaluated positively. This evaluation can be obtained using a complex fuzzy model constructed to account for the region's level of development in terms of the availability and quality of healthcare services in the region where the project will be implemented.}, } @article {pmid37612675, year = {2023}, author = {Sentamu, DN and Kungu, J and Dione, M and Thomas, LF}, title = {Prevention of human exposure to livestock faecal waste in the household: a scoping study of interventions conducted in sub-Saharan Africa.}, journal = {BMC public health}, volume = {23}, number = {1}, pages = {1613}, pmid = {37612675}, issn = {1471-2458}, support = {/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Animals ; Humans ; *Livestock ; Databases, Factual ; Europe ; Feces ; *Hygiene ; }, abstract = {BACKGROUND: Poorly managed animal faecal waste can result in detrimental environmental and public health implications. Limiting human exposure to animal waste through Animal inclusive Water Sanitation and Hygiene (A-WASH) strategies is imperative to improve public health in livestock keeping households but has received little attention to date. A small number of A-WASH interventions have previously been identified through a systematic review by another research team, and published in 2017. To inform intervention design with the most up-to-date information, a scoping study was conducted to map the existing evidence for A-WASH in sub-Saharan Africa (SSA) emerging since the previous review.

METHODS: This review followed PRISMA guidelines to identify interventions in SSA published between January 2016 to October 2022. Databases searched included PubMed, PMC Europe, CabDirect and Web of Science. Studies were eligible for inclusion if they were written in English and documented interventions limiting human contact with animal faecal material in the SSA context. Key data extracted included: the intervention itself, its target population, cost, measure of effectiveness, quantification of effect, assessment of success, acceptability and limitations. These data were synthesized into a narrative, structured around the intervention type.

FINDINGS: Eight eligible articles were identified. Interventions to reduce human exposure to animal faecal matter were conducted in combination with 'standard' human-centric WASH practices. Identified interventions included the management of human-animal co-habitation, educational programs and the creation of child-safe spaces. No novel A-WASH interventions were identified in this review, beyond those identified by the review in 2017. Randomised Controlled Trials (RCTs) were used to evaluate six of the eight identified interventions, but as effect was evaluated through various measures, the ability to formally compare efficacy of interventions is lacking.

CONCLUSION: This study indicates that the number of A-WASH studies in SSA is increasing and the use of RCTs suggests a strong desire to create high-quality evidence within this field. There is a need for standardisation of effect measures to enable meta-analyses to be conducted to better understand intervention effectiveness. Evaluation of scalability and sustainability of interventions is still lacking in A - WASH research.}, } @article {pmid37612513, year = {2023}, author = {Delavaux, CS and Crowther, TW and Zohner, CM and Robmann, NM and Lauber, T and van den Hoogen, J and Kuebbing, S and Liang, J and de-Miguel, S and Nabuurs, GJ and Reich, PB and Abegg, M and Adou Yao, YC and Alberti, G and Almeyda Zambrano, AM and Alvarado, BV and Alvarez-Dávila, E and Alvarez-Loayza, P and Alves, LF and Ammer, C and Antón-Fernández, C and Araujo-Murakami, A and Arroyo, L and Avitabile, V and Aymard, GA and Baker, TR and Bałazy, R and Banki, O and Barroso, JG and Bastian, ML and Bastin, JF and Birigazzi, L and Birnbaum, P and Bitariho, R and Boeckx, P and Bongers, F and Bouriaud, O and Brancalion, PHS and Brandl, S and Brienen, R and Broadbent, EN and Bruelheide, H and Bussotti, F and Gatti, RC and César, RG and Cesljar, G and Chazdon, R and Chen, HYH and Chisholm, C and Cho, H and Cienciala, E and Clark, C and Clark, D and Colletta, GD and Coomes, DA and Cornejo Valverde, F and Corral-Rivas, JJ and Crim, PM and Cumming, JR and Dayanandan, S and de Gasper, AL and Decuyper, M and Derroire, G and DeVries, B and Djordjevic, I and Dolezal, J and Dourdain, A and Engone Obiang, NL and Enquist, BJ and Eyre, TJ and Fandohan, AB and Fayle, TM and Feldpausch, TR and Ferreira, LV and Fischer, M and Fletcher, C and Frizzera, L and Gamarra, JGP and Gianelle, D and Glick, HB and Harris, DJ and Hector, A and Hemp, A and Hengeveld, G and Hérault, B and Herbohn, JL and Herold, M and Hillers, A and Honorio Coronado, EN and Hui, C and Ibanez, TT and Amaral, I and Imai, N and Jagodziński, AM and Jaroszewicz, B and Johannsen, VK and Joly, CA and Jucker, T and Jung, I and Karminov, V and Kartawinata, K and Kearsley, E and Kenfack, D and Kennard, DK and Kepfer-Rojas, S and Keppel, G and Khan, ML and Killeen, TJ and Kim, HS and Kitayama, K and Köhl, M and Korjus, H and Kraxner, F and Laarmann, D and Lang, M and Lewis, SL and Lu, H and Lukina, NV and Maitner, BS and Malhi, Y and Marcon, E and Marimon, BS and Marimon-Junior, BH and Marshall, AR and Martin, EH and Martynenko, O and Meave, JA and Melo-Cruz, O and Mendoza, C and Merow, C and Mendoza, AM and Moreno, VS and Mukul, SA and Mundhenk, P and Nava-Miranda, MG and Neill, D and Neldner, VJ and Nevenic, RV and Ngugi, MR and Niklaus, PA and Oleksyn, J and Ontikov, P and Ortiz-Malavasi, E and Pan, Y and Paquette, A and Parada-Gutierrez, A and Parfenova, EI and Park, M and Parren, M and Parthasarathy, N and Peri, PL and Pfautsch, S and Phillips, OL and Picard, N and Piedade, MTTF and Piotto, D and Pitman, NCA and Polo, I and Poorter, L and Poulsen, AD and Pretzsch, H and Ramirez Arevalo, F and Restrepo-Correa, Z and Rodeghiero, M and Rolim, SG and Roopsind, A and Rovero, F and Rutishauser, E and Saikia, P and Salas-Eljatib, C and Saner, P and Schall, P and Schepaschenko, D and Scherer-Lorenzen, M and Schmid, B and Schöngart, J and Searle, EB and Seben, V and Serra-Diaz, JM and Sheil, D and Shvidenko, AZ and Silva-Espejo, JE and Silveira, M and Singh, J and Sist, P and Slik, F and Sonké, B and Souza, AF and Miscicki, S and Stereńczak, KJ and Svenning, JC and Svoboda, M and Swanepoel, B and Targhetta, N and Tchebakova, N and Ter Steege, H and Thomas, R and Tikhonova, E and Umunay, PM and Usoltsev, VA and Valencia, R and Valladares, F and van der Plas, F and Do, TV and van Nuland, ME and Vasquez, RM and Verbeeck, H and Viana, H and Vibrans, AC and Vieira, S and von Gadow, K and Wang, HF and Watson, JV and Werner, GDA and Wiser, SK and Wittmann, F and Woell, H and Wortel, V and Zagt, R and Zawiła-Niedźwiecki, T and Zhang, C and Zhao, X and Zhou, M and Zhu, ZX and Zo-Bi, IC and Maynard, DS}, title = {Native diversity buffers against severity of non-native tree invasions.}, journal = {Nature}, volume = {621}, number = {7980}, pages = {773-781}, pmid = {37612513}, issn = {1476-4687}, mesh = {*Biodiversity ; Databases, Factual ; Human Activities ; *Introduced Species/statistics & numerical data/trends ; Phylogeny ; Rain ; Temperature ; *Trees/classification/physiology ; *Environment ; }, abstract = {Determining the drivers of non-native plant invasions is critical for managing native ecosystems and limiting the spread of invasive species[1,2]. Tree invasions in particular have been relatively overlooked, even though they have the potential to transform ecosystems and economies[3,4]. Here, leveraging global tree databases[5-7], we explore how the phylogenetic and functional diversity of native tree communities, human pressure and the environment influence the establishment of non-native tree species and the subsequent invasion severity. We find that anthropogenic factors are key to predicting whether a location is invaded, but that invasion severity is underpinned by native diversity, with higher diversity predicting lower invasion severity. Temperature and precipitation emerge as strong predictors of invasion strategy, with non-native species invading successfully when they are similar to the native community in cold or dry extremes. Yet, despite the influence of these ecological forces in determining invasion strategy, we find evidence that these patterns can be obscured by human activity, with lower ecological signal in areas with higher proximity to shipping ports. Our global perspective of non-native tree invasion highlights that human drivers influence non-native tree presence, and that native phylogenetic and functional diversity have a critical role in the establishment and spread of subsequent invasions.}, } @article {pmid37612396, year = {2023}, author = {Dethier, EN and Silman, M and Leiva, JD and Alqahtani, S and Fernandez, LE and Pauca, P and Çamalan, S and Tomhave, P and Magilligan, FJ and Renshaw, CE and Lutz, DA}, title = {A global rise in alluvial mining increases sediment load in tropical rivers.}, journal = {Nature}, volume = {620}, number = {7975}, pages = {787-793}, pmid = {37612396}, issn = {1476-4687}, mesh = {Animals ; Humans ; Databases, Factual ; *Ecosystem ; Gold ; Hydrology ; *Rivers ; *Mining/statistics & numerical data/trends ; Fishes ; *Tropical Climate ; *Geologic Sediments/analysis ; }, abstract = {Increasing gold and mineral mining activity in rivers across the global tropics has degraded ecosystems and threatened human health[1,2]. Such river mineral mining involves intensive excavation and sediment processing in river corridors, altering river form and releasing excess sediment downstream[2]. Increased suspended sediment loads can reduce water clarity and cause siltation to levels that may result in disease and mortality in fish[3,4], poor water quality[5] and damage to human infrastructure[6]. Although river mining has been investigated at local scales, no global synthesis of its physical footprint and impacts on hydrologic systems exists, leaving its full environmental consequences unknown. We assemble and analyse a 37-year satellite database showing pervasive, increasing river mineral mining worldwide. We identify 396 mining districts in 49 countries, concentrated in tropical waterways that are almost universally altered by mining-derived sediment. Of 173 mining-affected rivers, 80% have suspended sediment concentrations (SSCs) more than double pre-mining levels. In 30 countries in which mining affects large (>50 m wide) rivers, 23 ± 19% of large river length is altered by mining-derived sediment, a globe-spanning effect representing 35,000 river kilometres, 6% (±1% s.e.) of all large tropical river reaches. Our findings highlight the ubiquity and intensity of mining-associated degradation in tropical river systems.}, } @article {pmid37612395, year = {2023}, author = {Brodie, JF and Mohd-Azlan, J and Chen, C and Wearn, OR and Deith, MCM and Ball, JGC and Slade, EM and Burslem, DFRP and Teoh, SW and Williams, PJ and Nguyen, A and Moore, JH and Goetz, SJ and Burns, P and Jantz, P and Hakkenberg, CR and Kaszta, ZM and Cushman, S and Coomes, D and Helmy, OE and Reynolds, G and Rodríguez, JP and Jetz, W and Luskin, MS}, title = {Landscape-scale benefits of protected areas for tropical biodiversity.}, journal = {Nature}, volume = {620}, number = {7975}, pages = {807-812}, pmid = {37612395}, issn = {1476-4687}, mesh = {Animals ; *Biodiversity ; *Conservation of Natural Resources/legislation & jurisprudence/methods/trends ; Mammals ; *Tropical Climate ; *Goals ; *United Nations ; Forestry/legislation & jurisprudence/methods/trends ; }, abstract = {The United Nations recently agreed to major expansions of global protected areas (PAs) to slow biodiversity declines[1]. However, although reserves often reduce habitat loss, their efficacy at preserving animal diversity and their influence on biodiversity in surrounding unprotected areas remain unclear[2-5]. Unregulated hunting can empty PAs of large animals[6], illegal tree felling can degrade habitat quality[7], and parks can simply displace disturbances such as logging and hunting to unprotected areas of the landscape[8] (a phenomenon called leakage). Alternatively, well-functioning PAs could enhance animal diversity within reserves as well as in nearby unprotected sites[9] (an effect called spillover). Here we test whether PAs across mega-diverse Southeast Asia contribute to vertebrate conservation inside and outside their boundaries. Reserves increased all facets of bird diversity. Large reserves were also associated with substantially enhanced mammal diversity in the adjacent unprotected landscape. Rather than PAs generating leakage that deteriorated ecological conditions elsewhere, our results are consistent with PAs inducing spillover that benefits biodiversity in surrounding areas. These findings support the United Nations goal of achieving 30% PA coverage by 2030 by demonstrating that PAs are associated with higher vertebrate diversity both inside their boundaries and in the broader landscape.}, } @article {pmid37611791, year = {2023}, author = {Sarkar, DJ and Das Sarkar, S and V, SK and Chanu, TN and Banerjee, T and Chakraborty, L and Bhor, M and Nag, SK and Samanta, S and Das, BK}, title = {Ameliorative effect of natural floating island as fish aggregating devices on heavy metals distribution in a freshwater wetland.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {336}, number = {}, pages = {122428}, doi = {10.1016/j.envpol.2023.122428}, pmid = {37611791}, issn = {1873-6424}, mesh = {Animals ; Humans ; Wetlands ; Geologic Sediments ; Environmental Monitoring ; *Metals, Heavy/analysis ; Fresh Water ; Risk Assessment ; *Water Pollutants, Chemical/analysis ; China ; }, abstract = {Growing human population and climate change are leading reasons for water quality deterioration globally; and ecologically important waterbodies including freshwater wetlands are in a vulnerable state due to increasing concentrations of pollutants like heavy metals. Given the declining health of these valuable resources, the present study was conducted to evaluate the effect of natural floating island in the form of fish aggregating devices (FADs) made of native weed mass on the distribution of heavy metals in the abiotic and bio compartments of a freshwater wetland. Lower concentrations of surface water heavy metals were observed inside the FADs with a reduction of 73.91%, 65.22% and 40.57-49.16% for Cd, Pb and other metals (viz. Co, Cr, Cu, Ni and Zn), respectively as compared to outside FAD. These led to 14.72-55.39% reduction in the heavy metal pollution indices inside the FAD surface water. The fish species inside the FADs were also found less contaminated (24.07-25.07% reduction) with lower health risk indices. The study signifies the valuable contribution of natural floating island as FADs in ameliorating the effect of heavy metals pollution emphasizing the tremendous role of the natural floating islands in sustainable maintenance of freshwater wetlands for better human health and livelihood.}, } @article {pmid37601214, year = {2023}, author = {Rocha, AFBM and Freitas-Junior, R and Soares, LR and Ferreira, GLR}, title = {Breast cancer screening and diagnosis in older adults women in Brazil: why it is time to reconsider the recommendations.}, journal = {Frontiers in public health}, volume = {11}, number = {}, pages = {1232668}, pmid = {37601214}, issn = {2296-2565}, mesh = {Aged ; Female ; Humans ; Brazil/epidemiology ; *Breast Neoplasms/diagnosis ; Databases, Factual ; *Early Detection of Cancer ; State Medicine ; Mammography ; Neoplasm Staging ; Middle Aged ; }, abstract = {INTRODUCTION: Breast cancer screening in women of 70 years of age or older remains controversial due to a lack of studies that include women of this age.

METHODS: This ecological study evaluated data from the Brazilian National Health Service (SUS) on breast cancer screening and staging in this age group compared to 50-69-year olds, for Brazil as a whole and for its geographical regions, between 2013 and 2019. A secondary database was obtained from the outpatient data system of the SUS's Informatics Department, the Brazil Oncology Panel, the Brazilian Institute of Geography and Statistics, the Supplementary Health Agency and the Online Mortality Atlas.

RESULTS: There was a marked reduction in screening in women ≥70 years of age (annual percent change [APC] -3.5; p < 0.001) compared to those of 50-69 years of age (APC-2.2; p = 0.010). There was a trend towards an increase in clinical staging, with a greater occurrence of stages III and IV in the ≥70 group (44.3%) compared to the women of 50-69 years of age (40.8%; p < 0.001).

CONCLUSION: Considering the increasing age of the Brazilian population and the heterogeneity among older adults women, screening for the over-70s within the SUS merits greater debate insofar as the implementation of public policies is concerned.}, } @article {pmid37600587, year = {2023}, author = {Saccheri, IJ and , and , and , and , }, title = {The genome sequence of the Squinting Bush Brown, Bicyclus anynana (Butler, 1879).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {280}, pmid = {37600587}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual female Bicyclus anynana (the Squinting Bush Brown; Arthropoda; Insecta; Lepidoptera; Nymphalidae). The genome sequence is 457.2 megabases in span. Most of the assembly is scaffolded into 28 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 16.1 kilobases in length.}, } @article {pmid37600586, year = {2023}, author = {Lohse, K and Hayward, A and Vila, R and , and , and , and Carvalho, APS and Kawahara, AY and , }, title = {The genome sequence of the Large Skipper, Ochlodes sylvanus, (Esper, 1777).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {75}, pmid = {37600586}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual female Ochlodes sylvanus, the Large Skipper (Arthropoda; Insecta; Lepidoptera; Hesperiidae). The genome sequence is 380 megabases in span. Most of the assembly (99.97%) is scaffolded into 30 chromosomal pseudomolecules, including the assembled W and Z sex chromosomes. The mitochondrial genome has also been assembled and is 17.1 kilobases in length. Gene annotation of this assembly on Ensembl identified 13,451 protein coding genes.}, } @article {pmid37600582, year = {2023}, author = {Lees, D and Boyes, D and , and , and , and , and , and , and , }, title = {The genome sequence of the Dotted Border, Agriopis marginaria (Fabricius, 1776).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {152}, pmid = {37600582}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual male Agriopis marginaria (the Dotted Border, Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 500.9 megabases in span. Most of the assembly is scaffolded into 29 chromosomal pseudomolecules, including the assembled Z sex chromosome. The mitochondrial genome has also been assembled and is 16.9 kilobases in length. Gene annotation of this assembly on Ensembl identified 12,443 protein coding genes.}, } @article {pmid37598535, year = {2023}, author = {Tokatlı, C and Uğurluoğlu, A and Muhammad, S}, title = {Ecotoxicological evaluation of organic contamination in the world's two significant gateways to the Black Sea using GIS techniques: Turkish Straits.}, journal = {Marine pollution bulletin}, volume = {194}, number = {Pt A}, pages = {115405}, doi = {10.1016/j.marpolbul.2023.115405}, pmid = {37598535}, issn = {1879-3363}, mesh = {Child ; Humans ; Black Sea ; *Ecosystem ; *Geographic Information Systems ; Ecotoxicology ; Lakes ; }, abstract = {This study was carried out to determine the spatial-temporal distributions of limnological parameters of Çanakkale Strait (ÇS) and İstanbul Strait (İS), Turkiye. Fluvial (n = 11) and lacustrine (n = 4) habitats water samples were collected in the dry and rainy seasons of 2022-2023. Among limnological parameters, the highest mean electrical conductivity values of 6063 μS/cm were noted in the İS basin during the rainy season and the lowest was 0.04 mg/L for nitrite in the ÇS basin. Generally, the levels of organic contaminants and ecological risk indices were as follows: rivers of İS > rivers of ÇS > Alibey Dam Lake (İS) > Atikhisar Dam Lake (ÇS). The highest non-carcinogenic health risks of 0.88 were noted for children in the ÇS basin during the dry season and the lowest of <0.01 in Atikhisar Dam Lake during the rainy season. Multivariate statistical techniques were applied to data to categorize investigated ecosystems and sources apportionment of contaminants and geospatial distribution.}, } @article {pmid37598281, year = {2023}, author = {Nazari Ashani, M and Alesheikh, AA and Neisani Samani, Z and Lotfata, A and Bayat, S and Alipour, S and Hoseini, B}, title = {Socioeconomic and environmental determinants of foot and mouth disease incidence: an ecological, cross-sectional study across Iran using spatial modeling.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {13526}, pmid = {37598281}, issn = {2045-2322}, mesh = {Animals ; Sheep ; Iran/epidemiology ; *Foot-and-Mouth Disease/epidemiology ; Cross-Sectional Studies ; Asia ; Goats ; Socioeconomic Factors ; }, abstract = {Foot-and-mouth disease (FMD) is a highly contagious animal disease caused by a ribonucleic acid (RNA) virus, with significant economic costs and uneven distribution across Asia, Africa, and South America. While spatial analysis and modeling of FMD are still in their early stages, this research aimed to identify socio-environmental determinants of FMD incidence in Iran at the provincial level by studying 135 outbreaks reported between March 21, 2017, and March 21, 2018. We obtained 46 potential socio-environmental determinants and selected four variables, including percentage of population, precipitation in January, percentage of sheep, and percentage of goats, to be used in spatial regression models to estimate variation in spatial heterogeneity. In our analysis, we employed global models, namely ordinary least squares (OLS), spatial error model (SEM), and spatial lag model (SLM), as well as local models, including geographically weighted regression (GWR) and multiscale geographically weighted regression (MGWR). The MGWR model yielded the highest adjusted [Formula: see text] of 90%, outperforming the other local and global models. Using local models to map the effects of environmental determinants (such as the percentage of sheep and precipitation) on the spatial variability of FMD incidence provides decision-makers with helpful information for targeted interventions. Our findings advocate for multiscale and multidisciplinary policies to reduce FMD incidence.}, } @article {pmid37598114, year = {2023}, author = {Tom, M and Lubinevsky, H and Kanari, M}, title = {Integrative data system for monitoring biota and natural habitats in the Israeli Eastern Mediterranean marine environment.}, journal = {Environmental monitoring and assessment}, volume = {195}, number = {9}, pages = {1068}, pmid = {37598114}, issn = {1573-2959}, mesh = {Humans ; Israel ; *Environmental Monitoring ; *Biota ; Databases, Factual ; Environmental Policy ; }, abstract = {An integrative data system for monitoring the biota of the Mediterranean waters of Israel as well as selected records from adjacent Levantine basin regions is presented here, aimed at providing data and research tools for long-term bio-geographic and ecological studies and more important, providing background data for assisting governmental regulators to establish educated habitat-oriented environmental policy. The system relies on the geographic information system (GIS) online map-based platform and contains at present the following components: biotic database of ~ 170,000 recorded sampling events; uniform habitat maps of 63 benthic habitats and 2 pelagic ones, constructed using relevant bathymetric features and biotic community compositions; bathymetric hill-shade map; depth contours; raster depth grid and human interference map. Other informative auxiliary maps are planned to be added (e.g., map of potential pockmark sites, detailed maps of tiny carbonate crust nolls and more). A number of 883 cited documents were listed by us for potential extraction of sampling efforts, most of them are available to us as PDFs and are available also to the users, excluding copyright-protected ones. Forty-three major projects were depicted in addition to a variety of small studies (e.g., university theses). Thirty-five sampling devices were documented and described, and 3187 species-level identifications were already recorded. In addition, the system provides access to description of sampling devices and pictures of species and seascapes. New data is continuously deposited to the system and the system is flexible, allowing future addition of new types of information. The system site is accessible through the link: https://experience.arcgis.com/experience/40e86605ff4d4e5096ed2c901fec2a2f .}, } @article {pmid37596254, year = {2023}, author = {Szymura, TH and Kassa, H and Swacha, G and Szymura, M and Zając, A and Kącki, Z}, title = {Spatial patterns of vascular plant species richness in Poland - a data set.}, journal = {Scientific data}, volume = {10}, number = {1}, pages = {542}, pmid = {37596254}, issn = {2052-4463}, mesh = {Checklist ; Computer Systems ; Databases, Factual ; Poland ; *Tracheophyta ; }, abstract = {Recognition of species richness spatial patterns is important for nature conservation and theoretical studies. Inventorying species richness, especially at a larger spatial extent is challenging, thus different data sources are joined and harmonized to obtain a comprehensive data set. Here we present a new data set showing vascular plant species richness in Poland based on a grid of 10 × 10 km squares. The data set was created using data from two sources: the Atlas of Distribution of Vascular Plants in Poland and the Polish Vegetation Database. Using this data set, we analysed 2,160 species with taxonomical nomenclature according to the Euro + Med PlantBase checklist in 3,283 squares covering the entire territory of Poland (ca. 312,000 km[2]). The species were divided into groups according to their status and frequency of distribution, and the statistics for each square were obtained. For purposes of analysis, sampling bias was assessed. The data set promotes theoretical analysis on species richness and reinforces the planning of nature conservations.}, } @article {pmid37593568, year = {2023}, author = {Jaron, KS and Berg, MP and Ellers, J and Hodson, CN and Ross, L and , and , and , and , and , }, title = {The genome sequence of the springtail Allacma fusca (Linnaeus, 1758).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {319}, pmid = {37593568}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual male Allacma fusca (the springtail; Arthropoda; Collembola; Symphypleona; Sminthuridae). The genome sequence is 392.8 megabases in span. Most of the assembly is scaffolded into 6 chromosomal pseudomolecules, including the X 1 and X 2 sex chromosomes. The mitochondrial genome has also been assembled and is 14.94 kilobases in length.}, } @article {pmid37593439, year = {2023}, author = {Santarius, T and Bieser, JCT and Frick, V and Höjer, M and Gossen, M and Hilty, LM and Kern, E and Pohl, J and Rohde, F and Lange, S}, title = {Digital sufficiency: conceptual considerations for ICTs on a finite planet.}, journal = {Annales des telecommunications}, volume = {78}, number = {5-6}, pages = {277-295}, pmid = {37593439}, issn = {1958-9395}, abstract = {ICT hold significant potential to increase resource and energy efficiencies and contribute to a circular economy. Yet unresolved is whether the aggregated net effect of ICT overall mitigates or aggravates environmental burdens. While the savings potentials have been explored, drivers that prevent these and possible counter measures have not been researched thoroughly. The concept digital sufficiency constitutes a basis to understand how ICT can become part of the essential environmental transformation. Digital sufficiency consists of four dimensions, each suggesting a set of strategies and policy proposals: (a) hardware sufficiency, which aims for fewer devices needing to be produced and their absolute energy demand being kept to the lowest level possible to perform the desired tasks; (b) software sufficiency, which covers ensuring that data traffic and hardware utilization during application are kept as low as possible; (c) user sufficiency, which strives for users applying digital devices frugally and using ICT in a way that promotes sustainable lifestyles; and (d) economic sufficiency, which aspires to digitalization supporting a transition to an economy characterized not by economic growth as the primary goal but by sufficient production and consumption within planetary boundaries. The policies for hardware and software sufficiency are relatively easily conceivable and executable. Policies for user and economic sufficiency are politically more difficult to implement and relate strongly to policies for environmental transformation in general. This article argues for comprehensive policies for digital sufficiency, which are indispensible if ICT are to play a beneficial role in overall environmental transformation.}, } @article {pmid37590347, year = {2023}, author = {O'Keefe, FR and Dunn, RE and Weitzel, EM and Waters, MR and Martinez, LN and Binder, WJ and Southon, JR and Cohen, JE and Meachen, JA and DeSantis, LRG and Kirby, ME and Ghezzo, E and Coltrain, JB and Fuller, BT and Farrell, AB and Takeuchi, GT and MacDonald, G and Davis, EB and Lindsey, EL}, title = {Pre-Younger Dryas megafaunal extirpation at Rancho La Brea linked to fire-driven state shift.}, journal = {Science (New York, N.Y.)}, volume = {381}, number = {6659}, pages = {eabo3594}, doi = {10.1126/science.abo3594}, pmid = {37590347}, issn = {1095-9203}, mesh = {Humans ; Archaeology ; Desiccation ; *Ecosystem ; *Fires ; *Fossils ; California ; *Extinction, Biological ; Animals ; }, abstract = {The cause, or causes, of the Pleistocene megafaunal extinctions have been difficult to establish, in part because poor spatiotemporal resolution in the fossil record hinders alignment of species disappearances with archeological and environmental data. We obtained 172 new radiocarbon dates on megafauna from Rancho La Brea in California spanning 15.6 to 10.0 thousand calendar years before present (ka). Seven species of extinct megafauna disappeared by 12.9 ka, before the onset of the Younger Dryas. Comparison with high-resolution regional datasets revealed that these disappearances coincided with an ecological state shift that followed aridification and vegetation changes during the Bølling-Allerød (14.69 to 12.89 ka). Time-series modeling implicates large-scale fires as the primary cause of the extirpations, and the catalyst of this state shift may have been mounting human impacts in a drying, warming, and increasingly fire-prone ecosystem.}, } @article {pmid37589308, year = {2022}, author = {Mendes de Farias, T and Wollbrett, J and Robinson-Rechavi, M and Bastian, F}, title = {Lessons learned to boost a bioinformatics knowledge base reusability, the Bgee experience.}, journal = {GigaScience}, volume = {12}, number = {}, pages = {}, pmid = {37589308}, issn = {2047-217X}, support = {U01 CA215010/CA/NCI NIH HHS/United States ; }, mesh = {*Biomedical Research ; Computational Biology ; Knowledge Bases ; }, abstract = {BACKGROUND: Enhancing interoperability of bioinformatics knowledge bases is a high-priority requirement to maximize data reusability and thus increase their utility such as the return on investment for biomedical research. A knowledge base may provide useful information for life scientists and other knowledge bases, but it only acquires exchange value once the knowledge base is (re)used, and without interoperability, the utility lies dormant.

RESULTS: In this article, we discuss several approaches to boost interoperability depending on the interoperable parts. The findings are driven by several real-world scenario examples that were mostly implemented by Bgee, a well-established gene expression knowledge base. To better justify the findings are transferable, for each Bgee interoperability experience, we also highlight similar implementations by major bioinformatics knowledge bases. Moreover, we discuss ten general main lessons learned. These lessons can be applied in the context of any bioinformatics knowledge base to foster data reusability.

CONCLUSIONS: This work provides pragmatic methods and transferable skills to promote reusability of bioinformatics knowledge bases by focusing on interoperability.}, } @article {pmid37587525, year = {2023}, author = {Ma, R and Li, C and Tian, H and Zhang, Y and Feng, X and Li, J and Hu, W}, title = {The current distribution of tick species in Inner Mongolia and inferring potential suitability areas for dominant tick species based on the MaxEnt model.}, journal = {Parasites & vectors}, volume = {16}, number = {1}, pages = {286}, pmid = {37587525}, issn = {1756-3305}, support = {U22A20526//Study on pathogen spectrum, temporal and spatial distribution and transmission features of the important emerging and re-emerging zoonosis in Inner Mongolia Autonomous Region/ ; }, mesh = {Humans ; Animals ; *Ixodes ; China/epidemiology ; *Ixodidae ; Databases, Factual ; Global Warming ; }, abstract = {BACKGROUND: Ticks are known to transmit a wide range of diseases, including those caused by bacteria, viruses, and protozoa. The expansion of tick habitats has been intensified in recent years due to various factors such as global warming, alterations in microclimate, and human activities. Consequently, the probability of human exposure to diseases transmitted by ticks has increased, leading to a higher degree of risk associated with such diseases.

METHODS: In this study, we conducted a comprehensive review of domestic and international literature databases to determine the current distribution of tick species in Inner Mongolia. Next, we employed the MaxEnt model to analyze vital climatic and environmental factors influencing dominant tick distribution. Subsequently, we predicted the potential suitability areas of these dominant tick species under the near current conditions and the BCC-CSM2.MR model SSP245 scenario for the future periods of 2021-2040, 2041-2060, 2061-2080, and 2081-2100.

RESULTS: Our study revealed the presence of 23 tick species from six genera in Inner Mongolia, including four dominant tick species (Dermacentor nuttalli, Ixodes persulcatus, Dermacentor silvarum, and Hyalomma asiaticum). Dermacentor nuttalli, D. silvarum, and I. persulcatus are predominantly found in regions such as Xilin Gol and Hulunbuir. Temperature seasonality (Bio4), elevation (elev), and precipitation seasonality (Bio15) were the primary variables impacting the distribution of three tick species. In contrast, H. asiaticum is mainly distributed in Alxa and Bayannur and demonstrates heightened sensitivity to precipitation and other climatic factors. Our modeling results suggested that the potential suitability areas of these tick species would experience fluctuations over the four future periods (2021-2040, 2041-2060, 2061-2080, and 2081-2100). Specifically, by 2081-2100, the centroid of suitable habitat for D. nuttalli, H. asiaticum, and I. persulcatus was predicted to shift westward, with new suitability areas emerging in regions such as Chifeng and Xilin Gol. The centroid of suitable habitat for H. asiaticum will move northeastward, and new suitability areas are likely to appear in areas such as Ordos and Bayannur.

CONCLUSIONS: This study provided a comprehensive overview of the tick species distribution patterns in Inner Mongolia. Our research has revealed a significant diversity of tick species in the region, exhibiting a wide distribution but with notable regional disparities. Our modeling results suggested that the dominant tick species' suitable habitats will significantly expand in the future compared to their existing distribution under the near current conditions. Temperature and precipitation are the primary variables influencing these shifts in distribution. These findings can provide a valuable reference for future research on tick distribution and the surveillance of tick-borne diseases in the region.}, } @article {pmid37586008, year = {2023}, author = {Garces, TS and Damasceno, LLV and Sousa, GJB and Cestari, VRF and Pereira, MLD and Moreira, TMM}, title = {Relationship between social development indicators and mortality due to Diabetes Mellitus in Brazil: a space-time analysis.}, journal = {Revista latino-americana de enfermagem}, volume = {31}, number = {}, pages = {e3971}, pmid = {37586008}, issn = {1518-8345}, mesh = {Humans ; *Diabetes Mellitus/mortality ; Social Factors ; Brazil/epidemiology ; Spatio-Temporal Analysis ; Income ; }, abstract = {OBJECTIVE: to identify the space-time pattern of mortality due to Diabetes Mellitus in Brazil, as well as its relationship with social development indicators.

METHOD: an ecological and time series nationwide study based on secondary data from the Unified Health System Informatics Department, with space-time analysis and inclusion of indicators in non-spatial and spatial regression models. The following was performed: overall mortality rate calculation; characterization of the sociodemographic and regional profiles of the death cases by means of descriptive and time analysis; and elaboration of thematic maps.

RESULTS: a total of 601,521 deaths related to Diabetes Mellitus were recorded in Brazil, representing a mean mortality rate of 29.5/100,000 inhabitants. The states of Rio Grande do Norte, Paraíba, Pernambuco, Alagoas and Sergipe, Rio de Janeiro, Paraná and Rio Grande do Sul presented high-high clusters. By using regression models, it was verified that the Gini index (β=11.7) and the Family Health Strategy coverage (β=3.9) were the indicators that most influenced mortality due to Diabetes Mellitus in Brazil.

CONCLUSION: in Brazil, mortality due to Diabetes presents an overall increasing trend, revealing itself as strongly associated with places that have worse social indicators.

HIGHLIGHTS: (1) The time-space pattern of mortality due to Diabetes presents an increasing trend. (2) The Northeast and South regions present high rates of mortality due to Diabetes. (3) Mortality due to Diabetes is associated with worse sociodemographic indicators. (4) A relationship is observed between income, access to health and mortality due to Diabetes.}, } @article {pmid37577540, year = {2023}, author = {Liu, C and Downey, RJ and Salminen, JS and Rojas, SA and Richer, N and Pliner, EM and Hwang, J and Cruz-Almeida, Y and Manini, TM and Hass, CJ and Seidler, RD and Clark, DJ and Ferris, DP}, title = {Electrical Brain Activity during Human Walking with Parametric Variations in Terrain Unevenness and Walking Speed.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {37577540}, issn = {2692-8205}, support = {R01 NS104772/NS/NINDS NIH HHS/United States ; F32 AG072808/AG/NIA NIH HHS/United States ; P30 AG028740/AG/NIA NIH HHS/United States ; U01 AG061389/AG/NIA NIH HHS/United States ; T32 AG062728/AG/NIA NIH HHS/United States ; }, abstract = {Mobile brain imaging with high-density electroencephalography (EEG) can provide insight into the cortical processes involved in complex human walking tasks. While uneven terrain is common in the natural environment and poses challenges to human balance control, there is limited understanding of the supraspinal processes involved with traversing uneven terrain. The primary objective of this study was to quantify electrocortical activity related to parametric variations in terrain unevenness for neurotypical young adults. We used high-density EEG to measure brain activity when thirty-two young adults walked on a novel custom-made uneven terrain treadmill surface with four levels of difficulty at a walking speed tailored to each participant. We identified multiple brain regions associated with uneven terrain walking. Alpha (8 - 13 Hz) and beta (13 - 30 Hz) spectral power decreased in the sensorimotor and posterior parietal areas with increasing terrain unevenness while theta (4 - 8 Hz) power increased in the mid/posterior cingulate area with terrain unevenness. We also found that within stride spectral power fluctuations increased with terrain unevenness. Our secondary goal was to investigate the effect of parametric changes in walking speed (0.25 m/s, 0.5m/s, 0.75 m/s, 1.0 m/s) to differentiate the effects of walking speed from uneven terrain. Our results revealed that electrocortical activities only changed substantially with speed within the sensorimotor area but not in other brain areas. Together, these results indicate there are distinct cortical processes contributing to the control of walking over uneven terrain versus modulation of walking speed on smooth, flat terrain. Our findings increase our understanding of cortical involvement in an ecologically valid walking task and could serve as a benchmark for identifying deficits in cortical dynamics that occur in people with mobility deficits.}, } @article {pmid37574463, year = {2023}, author = {Stapp, EK and Zipunnikov, V and Leroux, A and Cui, L and Husky, MM and Dey, D and Merikangas, KR}, title = {Specificity of affective dynamics of bipolar and major depressive disorder.}, journal = {Brain and behavior}, volume = {13}, number = {9}, pages = {e3134}, pmid = {37574463}, issn = {2162-3279}, support = {Z01 MH002804/ImNIH/Intramural NIH HHS/United States ; ZIA MH002804/ImNIH/Intramural NIH HHS/United States ; ZIA MH002804/MH/NIMH NIH HHS/United States ; }, mesh = {Humans ; *Depressive Disorder, Major/psychology ; *Bipolar Disorder/psychology ; Anxiety ; Anxiety Disorders ; }, abstract = {OBJECTIVE: Here, we examine whether the dynamics of the four dimensions of the circumplex model of affect assessed by ecological momentary assessment (EMA) differ among those with bipolar disorder (BD) and major depressive disorder (MDD).

METHODS: Participants aged 11-85 years (n = 362) reported momentary sad, anxious, active, and energetic dimensional states four times per day for 2 weeks. Individuals with lifetime mood disorder subtypes of bipolar-I, bipolar-II, and MDD derived from a semistructured clinical interview were compared to each other and to controls without a lifetime history of psychiatric disorders. Random effects from individual means, inertias, innovation (residual) variances, and cross-lags across the four affective dimensions simultaneously were derived from multivariate dynamic structural equation models.

RESULTS: All mood disorder subtypes were associated with higher levels of sad and anxious mood and lower energy than controls. Those with bipolar-I had lower average activation, and lower energy that was independent of activation, compared to MDD or controls. However, increases in activation were more likely to perpetuate in those with bipolar-I. Bipolar-II was characterized by higher lability of sad and anxious mood compared to bipolar-I and controls but not MDD. Compared to BD and controls, those with MDD exhibited cross-augmentation of sadness and anxiety, and sadness blunted energy.

CONCLUSION: Bipolar-I is more strongly characterized by activation and energy than sad and anxious mood. This distinction has potential implications for both specificity of intervention targets and differential pathways underlying these dynamic affective systems. Confirmation of the longer term stability and generalizability of these findings in future studies is necessary.}, } @article {pmid37572835, year = {2023}, author = {Chaemsaithong, P and Jenjaroenpun, P and Pongchaikul, P and Singsaneh, A and Thaipisuttikul, I and Romero, R and Wongsurawat, T}, title = {Rapid detection of bacteria and antimicrobial resistant genes in intraamniotic infection using nanopore adaptive sampling.}, journal = {American journal of obstetrics and gynecology}, volume = {229}, number = {6}, pages = {690-693.e1}, pmid = {37572835}, issn = {1097-6868}, support = {Z01 HD002400/ImNIH/Intramural NIH HHS/United States ; }, mesh = {Humans ; Female ; *Nanopores ; Bacteria ; *Chorioamnionitis/microbiology ; *Anti-Infective Agents ; Amniotic Fluid/microbiology ; }, abstract = {Nanopore adaptive sampling to diagnose intraamniotic infection}, } @article {pmid37568226, year = {2023}, author = {Leo, P and de Melo Texeira, M and Chander, AM and Singh, NK and Simpson, AC and Yurkov, A and Karouia, F and Stajich, JE and Mason, CE and Venkateswaran, K}, title = {Genomic characterization and radiation tolerance of Naganishia kalamii sp. nov. and Cystobasidium onofrii sp. nov. from Mars 2020 mission assembly facilities.}, journal = {IMA fungus}, volume = {14}, number = {1}, pages = {15}, pmid = {37568226}, issn = {2210-6340}, support = {18-PPR18-0011//NNH18ZDA001N-PPR/ ; }, abstract = {During the construction and assembly of the Mars 2020 mission components at two different NASA cleanrooms, several fungal strains were isolated. Based on their colony morphology, two strains that showed yeast-like appearance were further characterized for their phylogenetic position. The species-level classification of these two novel strains, using traditional colony and cell morphology methods combined with the phylogenetic reconstructions using multi-locus sequence analysis (MLSA) based on several gene loci (ITS, LSU, SSU, RPB1, RPB2, CYTB and TEF1), and whole genome sequencing (WGS) was carried out. This polyphasic taxonomic approach supported the conclusion that the two basidiomycetous yeasts belong to hitherto undescribed species. The strain FJI-L2-BK-P3[T], isolated from the Jet Propulsion Laboratory Spacecraft Assembly Facility, was placed in the Naganishia albida clade (Filobasidiales, Tremellomycetes), but is genetically and physiologically different from other members of the clade. Another yeast strain FKI-L6-BK-PAB1[T], isolated from the Kennedy Space Center Payload Hazardous and Servicing Facility, was placed in the genus Cystobasidium (Cystobasidiales, Cystobasidiomycetes) and is distantly related to C. benthicum. Here we propose two novel species with the type strains, Naganishia kalamii sp. nov. (FJI-L2-BK-P3[T] = NRRL 64466 = DSM 115730) and Cystobasidium onofrii sp. nov. (FKI-L6-BK-PAB1[T] = NRRL 64426 = DSM 114625). The phylogenetic analyses revealed that single gene phylogenies (ITS or LSU) were not conclusive, and MLSA and WGS-based phylogenies were more advantageous for species discrimination in the two genera. The genomic analysis predicted proteins associated with dehydration and desiccation stress-response and the presence of genes that are directly related to osmotolerance and psychrotolerance in both novel yeasts described. Cells of these two newly-described yeasts were exposed to UV-C radiation and compared with N. onofrii, an extremophilic UV-C resistant cold-adapted Alpine yeast. Both novel species were UV resistant, emphasizing the need for collecting and characterizing extremotolerant microbes, including yeasts, to improve microbial reduction techniques used in NASA planetary protection programs.}, } @article {pmid37567881, year = {2023}, author = {Koludarov, I and Senoner, T and Jackson, TNW and Dashevsky, D and Heinzinger, M and Aird, SD and Rost, B}, title = {Domain loss enabled evolution of novel functions in the snake three-finger toxin gene superfamily.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {4861}, pmid = {37567881}, issn = {2041-1723}, mesh = {Animals ; *Three Finger Toxins ; Phylogeny ; Snakes/genetics ; *Toxins, Biological/genetics ; Reptiles ; Elapid Venoms/genetics ; Evolution, Molecular ; }, abstract = {Three-finger toxins (3FTXs) are a functionally diverse family of toxins, apparently unique to venoms of caenophidian snakes. Although the ancestral function of 3FTXs is antagonism of nicotinic acetylcholine receptors, redundancy conferred by the accumulation of duplicate genes has facilitated extensive neofunctionalization, such that derived members of the family interact with a range of targets. 3FTXs are members of the LY6/UPAR family, but their non-toxin ancestor remains unknown. Combining traditional phylogenetic approaches, manual synteny analysis, and machine learning techniques (including AlphaFold2 and ProtT5), we have reconstructed a detailed evolutionary history of 3FTXs. We identify their immediate ancestor as a non-secretory LY6, unique to squamate reptiles, and propose that changes in molecular ecology resulting from loss of a membrane-anchoring domain and changes in gene expression, paved the way for the evolution of one of the most important families of snake toxins.}, } @article {pmid37567871, year = {2023}, author = {Tonin, R and Wilhelmi, S and Gültas, M and Gerdol, R and Paun, O and Trucchi, E and Schmitt, AO and Wellstein, C}, title = {Ice holes microrefugia harbor genetically and functionally distinct populations of Vaccinium vitis-idaea (Ericaceae).}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {13055}, pmid = {37567871}, issn = {2045-2322}, mesh = {Humans ; *Ericaceae ; *Vaccinium vitis-idaea/genetics ; Ice ; Seasons ; Polymorphism, Single Nucleotide ; }, abstract = {In the mountain terrain, ice holes are little depressions between rock boulders that are characterized by the exit of cold air able to cool down the rock surface even in summer. This cold air creates cold microrefugia in warmer surroundings that preserve plant species probably over thousands of years under extra-zonal climatic conditions. We hypothesized that ice hole populations of the model species Vaccinium vitis-idaea (Ericaceae) show genetic differentiation from nearby zonal subalpine populations, and high functional trait distinctiveness, in agreement with genetic patterns. We genotyped almost 30,000 single nucleotide polymorphisms using restriction site-associated DNA sequencing and measured eight functional traits indicative of individual performance and ecological strategies. Genetic results showed high differentiation among the six populations suggesting isolation. On siliceous bedrock, ice hole individuals exhibited higher levels of admixture than those from subalpine populations which could have experienced more bottlenecks during demographic fluctuations related to glacial cycles. Ice hole and subalpine calcareous populations clearly separated from siliceous populations, indicating a possible effect of bedrock in shaping genetic patterns. Trait analysis reflected the bedrock effect on populations' differentiation. The significant correlation between trait and genetic distances suggests the genetic contribution in shaping intraspecific functional differentiation. In conclusion, extra-zonal populations reveal a prominent genetic and phenotypic differentiation determined by history and ecological contingency. Therefore, microrefugia populations can contribute to the overall variability of the species and lead to intraspecific-driven responses to upcoming environmental changes.}, } @article {pmid37564020, year = {2023}, author = {Xu, P and Zhang, W and Wang, X and Zhu, Y and Liang, W and He, Y and Yu, X}, title = {Multiomics analysis reveals a link between Brassica-specific miR1885 and rapeseed tolerance to low temperature.}, journal = {Plant, cell & environment}, volume = {46}, number = {11}, pages = {3405-3419}, doi = {10.1111/pce.14690}, pmid = {37564020}, issn = {1365-3040}, support = {2016YFD0101900//National Programs for Science and Technology Development of China/ ; 2019NY-038//Science and Technology Program of Shaanxi Province/ ; 2022M72211//China Postdoctoral Science Foundation/ ; 21PJ1407600//Shanghai Pujiang Program/ ; 32170581//National Natural Science Foundation of China/ ; 31471883//National Natural Science Foundation of China/ ; 31571261//National Natural Science Foundation of China/ ; }, mesh = {*Brassica napus/genetics ; *Brassica rapa/genetics ; *Brassica/genetics ; Genome-Wide Association Study ; Multiomics ; Temperature ; *MicroRNAs/genetics ; RNA, Messenger ; Gene Expression Regulation, Plant ; }, abstract = {Brassica crops include various edible vegetable and plant oil crops, and their production is limited by low temperature beyond their tolerant capability. The key regulators of low-temperature resistance in Brassica remain largely unexplored. To identify posttranscriptional regulators of plant response to low temperature, we performed small RNA profiling, and found that 16 known miRNAs responded to cold treatment in Brassica rapa. The cold response of seven of those miRNAs were further confirmed by qRT-PCR and/or northern blot analyses. In parallel, a genome-wide association study of 220 accessions of Brassica napus identified four candidate MIRNA genes, all of which were cold-responsive, at the loci associated with low-temperature resistance. Specifically, these large-scale data analyses revealed a link between miR1885 and the plant response to low temperature in both B. rapa and B. napus. Using 5' rapid amplification of cDNA ends approach, we validated that miR1885 can cleave its putative target gene transcripts, Bn.TIR.A09 and Bn.TNL.A03, in B. napus. Furthermore, overexpression of miR1885 in Semiwinter type B. napus decreased the mRNA abundance of Bn.TIR.A09 and Bn.TNL.A03 and resulted in increased sensitivity to low temperature. Knocking down of miR1885 in Spring type B. napus led to increased mRNA abundance of its targets and improved rapeseed tolerance to low temperature. Together, our results suggested that the loci of miR1885 and its targets could be potential candidates for the molecular breeding of low temperature-tolerant Spring type Brassica crops.}, } @article {pmid37563691, year = {2023}, author = {Lotfata, A and Moosazadeh, M and Helbich, M and Hoseini, B}, title = {Socioeconomic and environmental determinants of asthma prevalence: a cross-sectional study at the U.S. County level using geographically weighted random forests.}, journal = {International journal of health geographics}, volume = {22}, number = {1}, pages = {18}, pmid = {37563691}, issn = {1476-072X}, mesh = {Adult ; Humans ; *Asthma/diagnosis/epidemiology ; Cross-Sectional Studies ; Environment ; Prevalence ; *Random Forest ; Socioeconomic Factors ; United States/epidemiology ; Artificial Intelligence ; }, abstract = {BACKGROUND: Some studies have established associations between the prevalence of new-onset asthma and asthma exacerbation and socioeconomic and environmental determinants. However, research remains limited concerning the shape of these associations, the importance of the risk factors, and how these factors vary geographically.

OBJECTIVE: We aimed (1) to examine ecological associations between asthma prevalence and multiple socio-physical determinants in the United States; and (2) to assess geographic variations in their relative importance.

METHODS: Our study design is cross sectional based on county-level data for 2020 across the United States. We obtained self-reported asthma prevalence data of adults aged 18 years or older for each county. We applied conventional and geographically weighted random forest (GWRF) to investigate the associations between asthma prevalence and socioeconomic (e.g., poverty) and environmental determinants (e.g., air pollution and green space). To enhance the interpretability of the GWRF, we (1) assessed the shape of the associations through partial dependence plots, (2) ranked the determinants according to their global importance scores, and (3) mapped the local variable importance spatially.

RESULTS: Of the 3059 counties, the average asthma prevalence was 9.9 (standard deviation ± 0.99). The GWRF outperformed the conventional random forest. We found an indication, for example, that temperature was inversely associated with asthma prevalence, while poverty showed positive associations. The partial dependence plots showed that these associations had a non-linear shape. Ranking the socio-physical environmental factors concerning their global importance showed that smoking prevalence and depression prevalence were most relevant, while green space and limited language were of minor relevance. The local variable importance measures showed striking geographical differences.

CONCLUSION: Our findings strengthen the evidence that socio-physical environments play a role in explaining asthma prevalence, but their relevance seems to vary geographically. The results are vital for implementing future asthma prevention programs that should be tailor-made for specific areas.}, } @article {pmid37563227, year = {2023}, author = {Lu, AT and Fei, Z and Haghani, A and Robeck, TR and Zoller, JA and Li, CZ and Lowe, R and Yan, Q and Zhang, J and Vu, H and Ablaeva, J and Acosta-Rodriguez, VA and Adams, DM and Almunia, J and Aloysius, A and Ardehali, R and Arneson, A and Baker, CS and Banks, G and Belov, K and Bennett, NC and Black, P and Blumstein, DT and Bors, EK and Breeze, CE and Brooke, RT and Brown, JL and Carter, GG and Caulton, A and Cavin, JM and Chakrabarti, L and Chatzistamou, I and Chen, H and Cheng, K and Chiavellini, P and Choi, OW and Clarke, SM and Cooper, LN and Cossette, ML and Day, J and DeYoung, J and DiRocco, S and Dold, C and Ehmke, EE and Emmons, CK and Emmrich, S and Erbay, E and Erlacher-Reid, C and Faulkes, CG and Ferguson, SH and Finno, CJ and Flower, JE and Gaillard, JM and Garde, E and Gerber, L and Gladyshev, VN and Gorbunova, V and Goya, RG and Grant, MJ and Green, CB and Hales, EN and Hanson, MB and Hart, DW and Haulena, M and Herrick, K and Hogan, AN and Hogg, CJ and Hore, TA and Huang, T and Izpisua Belmonte, JC and Jasinska, AJ and Jones, G and Jourdain, E and Kashpur, O and Katcher, H and Katsumata, E and Kaza, V and Kiaris, H and Kobor, MS and Kordowitzki, P and Koski, WR and Krützen, M and Kwon, SB and Larison, B and Lee, SG and Lehmann, M and Lemaitre, JF and Levine, AJ and Li, C and Li, X and Lim, AR and Lin, DTS and Lindemann, DM and Little, TJ and Macoretta, N and Maddox, D and Matkin, CO and Mattison, JA and McClure, M and Mergl, J and Meudt, JJ and Montano, GA and Mozhui, K and Munshi-South, J and Naderi, A and Nagy, M and Narayan, P and Nathanielsz, PW and Nguyen, NB and Niehrs, C and O'Brien, JK and O'Tierney Ginn, P and Odom, DT and Ophir, AG and Osborn, S and Ostrander, EA and Parsons, KM and Paul, KC and Pellegrini, M and Peters, KJ and Pedersen, AB and Petersen, JL and Pietersen, DW and Pinho, GM and Plassais, J and Poganik, JR and Prado, NA and Reddy, P and Rey, B and Ritz, BR and Robbins, J and Rodriguez, M and Russell, J and Rydkina, E and Sailer, LL and Salmon, AB and Sanghavi, A and Schachtschneider, KM and Schmitt, D and Schmitt, T and Schomacher, L and Schook, LB and Sears, KE and Seifert, AW and Seluanov, A and Shafer, ABA and Shanmuganayagam, D and Shindyapina, AV and Simmons, M and Singh, K and Sinha, I and Slone, J and Snell, RG and Soltanmaohammadi, E and Spangler, ML and Spriggs, MC and Staggs, L and Stedman, N and Steinman, KJ and Stewart, DT and Sugrue, VJ and Szladovits, B and Takahashi, JS and Takasugi, M and Teeling, EC and Thompson, MJ and Van Bonn, B and Vernes, SC and Villar, D and Vinters, HV and Wallingford, MC and Wang, N and Wayne, RK and Wilkinson, GS and Williams, CK and Williams, RW and Yang, XW and Yao, M and Young, BG and Zhang, B and Zhang, Z and Zhao, P and Zhao, Y and Zhou, W and Zimmermann, J and Ernst, J and Raj, K and Horvath, S}, title = {Universal DNA methylation age across mammalian tissues.}, journal = {Nature aging}, volume = {3}, number = {9}, pages = {1144-1166}, pmid = {37563227}, issn = {2662-8465}, support = {K00 CA234840/CA/NCI NIH HHS/United States ; R01 AG065403/AG/NIA NIH HHS/United States ; U34 AG068482/AG/NIA NIH HHS/United States ; R21 AG055841/AG/NIA NIH HHS/United States ; P30 AG013319/AG/NIA NIH HHS/United States ; MR/T021985/1/MRC_/Medical Research Council/United Kingdom ; R01 AG050797/AG/NIA NIH HHS/United States ; HHSN268201600003C/HL/NHLBI NIH HHS/United States ; HHSN268201500001I/HL/NHLBI NIH HHS/United States ; HHSN268201600004C/HL/NHLBI NIH HHS/United States ; P51 OD011133/OD/NIH HHS/United States ; U01 AG060908/AG/NIA NIH HHS/United States ; HHSN268201600002C/HL/NHLBI NIH HHS/United States ; HHSN268201500001C/HL/NHLBI NIH HHS/United States ; HHSN268201600018C/HL/NHLBI NIH HHS/United States ; P30 AG044271/AG/NIA NIH HHS/United States ; HHSN268201600001C/HL/NHLBI NIH HHS/United States ; P01 AG051449/AG/NIA NIH HHS/United States ; N01HC25195/HL/NHLBI NIH HHS/United States ; }, mesh = {Humans ; Mice ; Animals ; *DNA Methylation/genetics ; *Epigenesis, Genetic ; Aging/genetics ; Longevity/genetics ; Mammals/genetics ; }, abstract = {Aging, often considered a result of random cellular damage, can be accurately estimated using DNA methylation profiles, the foundation of pan-tissue epigenetic clocks. Here, we demonstrate the development of universal pan-mammalian clocks, using 11,754 methylation arrays from our Mammalian Methylation Consortium, which encompass 59 tissue types across 185 mammalian species. These predictive models estimate mammalian tissue age with high accuracy (r > 0.96). Age deviations correlate with human mortality risk, mouse somatotropic axis mutations and caloric restriction. We identified specific cytosines with methylation levels that change with age across numerous species. These sites, highly enriched in polycomb repressive complex 2-binding locations, are near genes implicated in mammalian development, cancer, obesity and longevity. Our findings offer new evidence suggesting that aging is evolutionarily conserved and intertwined with developmental processes across all mammals.}, } @article {pmid37561875, year = {2023}, author = {Haghani, A and Li, CZ and Robeck, TR and Zhang, J and Lu, AT and Ablaeva, J and Acosta-Rodríguez, VA and Adams, DM and Alagaili, AN and Almunia, J and Aloysius, A and Amor, NMS and Ardehali, R and Arneson, A and Baker, CS and Banks, G and Belov, K and Bennett, NC and Black, P and Blumstein, DT and Bors, EK and Breeze, CE and Brooke, RT and Brown, JL and Carter, G and Caulton, A and Cavin, JM and Chakrabarti, L and Chatzistamou, I and Chavez, AS and Chen, H and Cheng, K and Chiavellini, P and Choi, OW and Clarke, S and Cook, JA and Cooper, LN and Cossette, ML and Day, J and DeYoung, J and Dirocco, S and Dold, C and Dunnum, JL and Ehmke, EE and Emmons, CK and Emmrich, S and Erbay, E and Erlacher-Reid, C and Faulkes, CG and Fei, Z and Ferguson, SH and Finno, CJ and Flower, JE and Gaillard, JM and Garde, E and Gerber, L and Gladyshev, VN and Goya, RG and Grant, MJ and Green, CB and Hanson, MB and Hart, DW and Haulena, M and Herrick, K and Hogan, AN and Hogg, CJ and Hore, TA and Huang, T and Izpisua Belmonte, JC and Jasinska, AJ and Jones, G and Jourdain, E and Kashpur, O and Katcher, H and Katsumata, E and Kaza, V and Kiaris, H and Kobor, MS and Kordowitzki, P and Koski, WR and Krützen, M and Kwon, SB and Larison, B and Lee, SG and Lehmann, M and Lemaître, JF and Levine, AJ and Li, X and Li, C and Lim, AR and Lin, DTS and Lindemann, DM and Liphardt, SW and Little, TJ and Macoretta, N and Maddox, D and Matkin, CO and Mattison, JA and McClure, M and Mergl, J and Meudt, JJ and Montano, GA and Mozhui, K and Munshi-South, J and Murphy, WJ and Naderi, A and Nagy, M and Narayan, P and Nathanielsz, PW and Nguyen, NB and Niehrs, C and Nyamsuren, B and O'Brien, JK and Ginn, PO and Odom, DT and Ophir, AG and Osborn, S and Ostrander, EA and Parsons, KM and Paul, KC and Pedersen, AB and Pellegrini, M and Peters, KJ and Petersen, JL and Pietersen, DW and Pinho, GM and Plassais, J and Poganik, JR and Prado, NA and Reddy, P and Rey, B and Ritz, BR and Robbins, J and Rodriguez, M and Russell, J and Rydkina, E and Sailer, LL and Salmon, AB and Sanghavi, A and Schachtschneider, KM and Schmitt, D and Schmitt, T and Schomacher, L and Schook, LB and Sears, KE and Seifert, AW and Shafer, ABA and Shindyapina, AV and Simmons, M and Singh, K and Sinha, I and Slone, J and Snell, RG and Soltanmohammadi, E and Spangler, ML and Spriggs, M and Staggs, L and Stedman, N and Steinman, KJ and Stewart, DT and Sugrue, VJ and Szladovits, B and Takahashi, JS and Takasugi, M and Teeling, EC and Thompson, MJ and Van Bonn, B and Vernes, SC and Villar, D and Vinters, HV and Vu, H and Wallingford, MC and Wang, N and Wilkinson, GS and Williams, RW and Yan, Q and Yao, M and Young, BG and Zhang, B and Zhang, Z and Zhao, Y and Zhao, P and Zhou, W and Zoller, JA and Ernst, J and Seluanov, A and Gorbunova, V and Yang, XW and Raj, K and Horvath, S}, title = {DNA methylation networks underlying mammalian traits.}, journal = {Science (New York, N.Y.)}, volume = {381}, number = {6658}, pages = {eabq5693}, pmid = {37561875}, issn = {1095-9203}, support = {R01 AG065403/AG/NIA NIH HHS/United States ; R01 AG043930/AG/NIA NIH HHS/United States ; R21 AG055841/AG/NIA NIH HHS/United States ; 20412/CRUK_/Cancer Research UK/United Kingdom ; R56 AG072736/AG/NIA NIH HHS/United States ; R01 AG050797/AG/NIA NIH HHS/United States ; P30 AG044271/AG/NIA NIH HHS/United States ; R56 AG076607/AG/NIA NIH HHS/United States ; /WT_/Wellcome Trust/United Kingdom ; R21 ES024356/ES/NIEHS NIH HHS/United States ; U01 AG060908/AG/NIA NIH HHS/United States ; R01 AG045795/AG/NIA NIH HHS/United States ; P01 AG047200/AG/NIA NIH HHS/United States ; U34 AG068482/AG/NIA NIH HHS/United States ; R21 DE028271/DE/NIDCR NIH HHS/United States ; R01 AG067782/AG/NIA NIH HHS/United States ; P30 AG013319/AG/NIA NIH HHS/United States ; R21 OD022988/OD/NIH HHS/United States ; R01 AG072736/AG/NIA NIH HHS/United States ; }, mesh = {Adult ; Animals ; Humans ; *DNA Methylation ; *Epigenesis, Genetic ; Epigenome ; Genome ; *Mammals/genetics ; Phylogeny ; }, abstract = {Using DNA methylation profiles (n = 15,456) from 348 mammalian species, we constructed phyloepigenetic trees that bear marked similarities to traditional phylogenetic ones. Using unsupervised clustering across all samples, we identified 55 distinct cytosine modules, of which 30 are related to traits such as maximum life span, adult weight, age, sex, and human mortality risk. Maximum life span is associated with methylation levels in HOXL subclass homeobox genes and developmental processes and is potentially regulated by pluripotency transcription factors. The methylation state of some modules responds to perturbations such as caloric restriction, ablation of growth hormone receptors, consumption of high-fat diets, and expression of Yamanaka factors. This study reveals an intertwined evolution of the genome and epigenome that mediates the biological characteristics and traits of different mammalian species.}, } @article {pmid37558860, year = {2023}, author = {Béchade, B and Cabuslay, CS and Hu, Y and Mendonca, CM and Hassanpour, B and Lin, JY and Su, Y and Fiers, VJ and Anandarajan, D and Lu, R and Olson, CJ and Duplais, C and Rosen, GL and Moreau, CS and Aristilde, L and Wertz, JT and Russell, JA}, title = {Physiological and evolutionary contexts of a new symbiotic species from the nitrogen-recycling gut community of turtle ants.}, journal = {The ISME journal}, volume = {17}, number = {10}, pages = {1751-1764}, pmid = {37558860}, issn = {1751-7370}, mesh = {Animals ; *Nitrogen ; *Ants/physiology ; Phylogeny ; Symbiosis/genetics ; Urea ; }, abstract = {While genome sequencing has expanded our knowledge of symbiosis, role assignment within multi-species microbiomes remains challenging due to genomic redundancy and the uncertainties of in vivo impacts. We address such questions, here, for a specialized nitrogen (N) recycling microbiome of turtle ants, describing a new genus and species of gut symbiont-Ischyrobacter davidsoniae (Betaproteobacteria: Burkholderiales: Alcaligenaceae)-and its in vivo physiological context. A re-analysis of amplicon sequencing data, with precisely assigned Ischyrobacter reads, revealed a seemingly ubiquitous distribution across the turtle ant genus Cephalotes, suggesting ≥50 million years since domestication. Through new genome sequencing, we also show that divergent I. davidsoniae lineages are conserved in their uricolytic and urea-generating capacities. With phylogenetically refined definitions of Ischyrobacter and separately domesticated Burkholderiales symbionts, our FISH microscopy revealed a distinct niche for I. davidsoniae, with dense populations at the anterior ileum. Being positioned at the site of host N-waste delivery, in vivo metatranscriptomics and metabolomics further implicate I. davidsoniae within a symbiont-autonomous N-recycling pathway. While encoding much of this pathway, I. davidsoniae expressed only a subset of the requisite steps in mature adult workers, including the penultimate step deriving urea from allantoate. The remaining steps were expressed by other specialized gut symbionts. Collectively, this assemblage converts inosine, made from midgut symbionts, into urea and ammonia in the hindgut. With urea supporting host amino acid budgets and cuticle synthesis, and with the ancient nature of other active N-recyclers discovered here, I. davidsoniae emerges as a central player in a conserved and impactful, multipartite symbiosis.}, } @article {pmid37556975, year = {2023}, author = {Song, L and Chen, Y and Liu, S and Xu, M and Cui, J}, title = {SLWE-Net: An improved lightweight U-Net for Sargassum extraction from GOCI images.}, journal = {Marine pollution bulletin}, volume = {194}, number = {Pt B}, pages = {115349}, doi = {10.1016/j.marpolbul.2023.115349}, pmid = {37556975}, issn = {1879-3363}, mesh = {*Sargassum ; China ; Environment ; }, abstract = {The Sargassum bloom has severely impacted the ecological environment of the East China Sea and the Yellow Sea, causing significant economic losses. In recent years, deep learning has seen extensive development due to its outstanding feature extraction capabilities. However, the deep learning process typically involves a large number of parameters and computations. To address this issue, this paper proposes a lightweight deep learning network based on the U-Net framework, called SLWE-NET, which uses lightweight modules to replace the feature extraction modules in U-Net. In this experiment, SLWE-Net performed the best in both extraction accuracy and model lightweight. Compared to the formal U-Net, the number of parameters decreased by 65.83 %, the model size reduced from 94.97 MB to 32.51 MB, and the mIoU increased to 93.81 %. Therefore, the method proposed in this paper is beneficial for Sargassum extraction and provides a basis for operational monitoring.}, } @article {pmid37556709, year = {2023}, author = {Pavinati, G and Lima, LV and Palmieri, IGS and Magnabosco, GT}, title = {Distribution and spatial autocorrelation of viral hepatitis B and C in Paraná, Brazil: an ecological study, 2011-2019.}, journal = {Epidemiologia e servicos de saude : revista do Sistema Unico de Saude do Brasil}, volume = {32}, number = {2}, pages = {e2022888}, pmid = {37556709}, issn = {2237-9622}, mesh = {Humans ; Brazil/epidemiology ; *Hepatitis B/epidemiology ; Spatial Analysis ; *Hepatitis C/epidemiology ; Information Systems ; }, abstract = {OBJECTIVE: to analyze the distribution and spatial autocorrelation of hepatitis B and C detection rates in the state of Paraná, Brazil.

METHODS: this was an ecological study of hepatitis B and C notifications held on the Notifiable Health Conditions Information System, between 2011 and 2019. Percentage change in detection rates between the first and last three-year periods was estimated. Spatial autocorrelation was analyzed using Moran's index.

RESULTS: there were 16,699 notifications of hepatitis B, with a greater reduction in detection in the North (-30.0%) and Northwest (-25.9%) macro-regions. There were clusters of high occurrence in the Foz do Iguaçu, Francisco Beltrão and Cascavel regions between 2011 and 2019. There were 10,920 notifications of hepatitis C, with a greater reduction in detection in the Northwest macro-region (-18.9%) and an increase in the West (51.1%). The Paranaguá region recorded a high detection cluster between 2011 and 2016.

CONCLUSION: hepatitis B and C showed heterogeneous distribution between health regions.}, } @article {pmid37554800, year = {2023}, author = {Motuziuk, O and Nozdrenko, D and Prylutska, S and Vareniuk, I and Bogutska, K and Braniuk, S and Korotkyi, O and Prylutskyy, Y and Ritter, U and Piosik, J}, title = {The effect of C60 fullerene on the mechanokinetics of muscle gastrocnemius contraction in chronically alcoholized rats.}, journal = {Heliyon}, volume = {9}, number = {8}, pages = {e18745}, pmid = {37554800}, issn = {2405-8440}, abstract = {The C60 fullerene effect (oral administration at a dose of 1 mg kg[-1]) on the selected biomechanical parameters of muscle gastrocnemius contraction, biochemical indicators of blood and muscle tissue as well as histological changes in rat muscle tissue after chronic alcoholization for 3, 6 and 9 months was studied in detail. Water-soluble C60 fullerenes were shown to reduce the pathological processes development in the muscle apparatus by an average of (35-40)%. In particular, they reduced the time occurrence of fatigue processes in muscle during the long-term development of alcoholic myopathy and inhibited oxidative processes in muscle, thereby preventing its degradation. These findings open up the possibility of using C60 fullerenes as potent antioxidants for the correction of the pathological conditions of the muscle system arising from alcohol intoxication.}, } @article {pmid37554074, year = {2023}, author = {Mpinga, K and Rukundo, T and Mwale, O and Kamwiyo, M and Thengo, L and Ruderman, T and Matanje, B and Munyaneza, F and Connolly, E and Kulisewa, K and Udedi, M and Kachimanga, C and Dullie, L and McBain, R}, title = {Depressive disorder at the household level: prevalence and correlates of depressive symptoms among household members.}, journal = {Global health action}, volume = {16}, number = {1}, pages = {2241808}, pmid = {37554074}, issn = {1654-9880}, support = {R01 MH117760/MH/NIMH NIH HHS/United States ; }, mesh = {Humans ; Male ; Female ; Adult ; *Depressive Disorder, Major/epidemiology ; *Depression/epidemiology ; Prevalence ; Family Characteristics ; Social Determinants of Health ; Social Environment ; Adolescent ; Middle Aged ; Aged ; Aged, 80 and over ; }, abstract = {BACKGROUND: Globally, an estimated five percent of adults have major depressive disorder. However, little is known about the relationship between these individuals' depressive symptoms and their household members' mental health and well-being.

OBJECTIVES: We aimed to investigate the prevalence and predictors of depressive symptoms among adult household members of patients living with major depressive disorder in Neno District, Malawi.

METHODS: As part of a cluster randomized controlled trial providing depression care to adults with major depressive disorder, we conducted surveys with patients' household members (n = 236) and inquired about their overall health, depressive symptoms, disability, and social support. We calculated prevalence rates of depressive disorder and conducted multivariable linear regression and multivariable logistic regression analyses to assess correlates of depressive symptom severity and predictors of having depressive disorder (PHQ-9), respectively, among household members.

RESULTS: We observed that roughly one in five household members (19%) screened positive for a depressive disorder (PHQ-9 > 9). More than half of household members endorsed six or more of the nine symptoms, with 68% reporting feeling 'down, depressed, or hopeless' in the prior two weeks. Elevated depression symptom severity was associated with greater disability (β = 0.17, p < 0.001), less social support (β = -0.04, p = 0.016), and lower self-reported overall health (β = 0.54, p = 0.001). Having depressive disorder was also associated with greater disability (adjusted Odds Ratio [aOR] = 1.12, p = 0.001) and less social support (aOR = 0.97, p = 0.024).

CONCLUSIONS: In the Malawian context, we find that depressive disorder and depression symptoms are shared attributes among household members. This has implications for both screening and treatment, and it suggests that mental health should be approached from the vantage point of the broader social ecology of the household and family unit.

TRIAL REGISTRATION: ClinicalTrials.gov (NCT04777006) - March 2, 2021.}, } @article {pmid37552473, year = {2023}, author = {Jiang, Z and Liu, S and Zhang, D and Sha, Z}, title = {The Diversity and Metabolism of Culturable Nitrate-Reducing Bacteria from the Photic Zone of the Western North Pacific Ocean.}, journal = {Microbial ecology}, volume = {86}, number = {4}, pages = {2781-2789}, pmid = {37552473}, issn = {1432-184X}, mesh = {*Nitrates ; Pacific Ocean ; Chlorophyll A ; *Thiosulfates ; Seawater/microbiology ; Sulfur/metabolism ; Nitrogen/metabolism ; Carbon ; Chitin ; Phylogeny ; }, abstract = {To better understand bacterial communities and metabolism under nitrogen deficiency, 154 seawater samples were obtained from 5 to 200 m at 22 stations in the photic zone of the Western North Pacific Ocean. Total 634 nitrate-utilizing bacteria were isolated using selective media and culture-dependent methods, and 295 of them were positive for nitrate reduction. These nitrate-reducing bacteria belonged to 19 genera and 29 species and among them, Qipengyuania flava, Roseibium aggregatum, Erythrobacter aureus, Vibrio campbellii, and Stappia indica were identified from all tested seawater layers of the photic zone and at almost all stations. Twenty-nine nitrate-reducing strains representing different species were selected for further the study of nitrogen, sulfur, and carbon metabolism. All 29 nitrate-reducing isolates contained genes encoding dissimilatory nitrate reduction or assimilatory nitrate reduction. Six nitrate-reducing isolates can oxidize thiosulfate based on genomic analysis and activity testing, indicating that nitrate-reducing thiosulfate-oxidizing bacteria exist in the photic zone. Five nitrate-reducing isolates obtained near the chlorophyll a-maximum layer contained a dimethylsulfoniopropionate synthesis gene and three of them contained both dimethylsulfoniopropionate synthesis and cleavage genes. This suggests that nitrate-reducing isolates may participate in dimethylsulfoniopropionate synthesis and catabolism in photic seawater. The presence of multiple genes for chitin degradation and extracellular peptidases may indicate that almost all nitrate-reducing isolates (28/29) can use chitin and proteinaceous compounds as important sources of carbon and nitrogen. Collectively, these results reveal culturable nitrate-reducing bacterial diversity and have implications for understanding the role of such strains in the ecology and biogeochemical cycles of nitrogen, sulfur, and carbon in the oligotrophic marine photic zone.}, } @article {pmid37550506, year = {2023}, author = {Sahu, N and Indic, B and Wong-Bajracharya, J and Merényi, Z and Ke, HM and Ahrendt, S and Monk, TL and Kocsubé, S and Drula, E and Lipzen, A and Bálint, B and Henrissat, B and Andreopoulos, B and Martin, FM and Bugge Harder, C and Rigling, D and Ford, KL and Foster, GD and Pangilinan, J and Papanicolaou, A and Barry, K and LaButti, K and Virágh, M and Koriabine, M and Yan, M and Riley, R and Champramary, S and Plett, KL and Grigoriev, IV and Tsai, IJ and Slot, J and Sipos, G and Plett, J and Nagy, LG}, title = {Vertical and horizontal gene transfer shaped plant colonization and biomass degradation in the fungal genus Armillaria.}, journal = {Nature microbiology}, volume = {8}, number = {9}, pages = {1668-1681}, pmid = {37550506}, issn = {2058-5276}, support = {758161/ERC_/European Research Council/International ; }, mesh = {*Armillaria/genetics/metabolism ; Biomass ; Gene Transfer, Horizontal ; Ecosystem ; Plants ; }, abstract = {The fungal genus Armillaria contains necrotrophic pathogens and some of the largest terrestrial organisms that cause tremendous losses in diverse ecosystems, yet how they evolved pathogenicity in a clade of dominantly non-pathogenic wood degraders remains elusive. Here we show that Armillaria species, in addition to gene duplications and de novo gene origins, acquired at least 1,025 genes via 124 horizontal gene transfer events, primarily from Ascomycota. Horizontal gene transfer might have affected plant biomass degrading and virulence abilities of Armillaria, and provides an explanation for their unusual, soft rot-like wood decay strategy. Combined multi-species expression data revealed extensive regulation of horizontally acquired and wood-decay related genes, putative virulence factors and two novel conserved pathogenicity-induced small secreted proteins, which induced necrosis in planta. Overall, this study details how evolution knitted together horizontally and vertically inherited genes in complex adaptive traits of plant biomass degradation and pathogenicity in important fungal pathogens.}, } @article {pmid37549500, year = {2023}, author = {Keat-Chuan Ng, C and Linus-Lojikip, S and Mohamed, K and Hss, AS}, title = {Application of medical information system to identify dengue outbreak factors: Insights from a hyperendemic city in Malaysia.}, journal = {International journal of medical informatics}, volume = {177}, number = {}, pages = {105162}, doi = {10.1016/j.ijmedinf.2023.105162}, pmid = {37549500}, issn = {1872-8243}, mesh = {Animals ; Humans ; Cities/epidemiology ; *Dengue/epidemiology ; Malaysia/epidemiology ; Disease Outbreaks ; Information Systems ; *Zika Virus ; *Zika Virus Infection/epidemiology ; }, abstract = {BACKGROUND: Dengue is widespread globally, but it is more severe in hyperendemic regions where the virus, its vectors, and its human hosts naturally occur. The problem is particularly acute in cities, where outbreaks affect a large human population living in a wide array of socio-environmental conditions. Controlling outbreaks will rely largely on systematic data collection and analysis approaches to uncover nuances on a city-by-city basis due to the diversity of factors.

OBJECTIVE: The main objective of this study is to consolidate and analyse the dengue case dataset amassed by the e-Dengue web-based information system, developed by the Ministry of Health Malaysia, to improve our epidemiological understanding.

METHODS: We retrieved data from the e-Dengue system and integrated a total of 18,812 cases from 2012 to 2019 (8 years) with meteorological data, geoinformatics techniques, and socio-environmental observations to identify plausible factors that could have caused dengue outbreaks in Ipoh, a hyperendemic city in Malaysia.

RESULTS: The rainfall trend characterised by a linearity of R[2] > 0.99, termed the "wet-dry steps", may be the unifying factor for triggering dengue outbreaks, though it is still a hypothesis that needs further validation. Successful mapping of the dengue "reservoir" contact zones and spill-over diffusion revealed socio-environmental factors that may be controlled through preventive measures. Age is another factor to consider, as the platelet and white blood cell counts in the "below 5" age group are much greater than in other age groups.

CONCLUSIONS: Our work demonstrates the novelty of the e-Dengue system, which can identify outbreak factors at high resolution when integrated with non-medical fields. Besides dengue, the techniques and insights laid out in this paper are valuable, at large, for advancing control strategies for other mosquito-borne diseases such as malaria, chikungunya, and zika in other hyperendemic cities elsewhere globally.}, } @article {pmid37548802, year = {2023}, author = {Dong, H and Liu, Y and Cui, J and Zhu, M and Ji, W}, title = {Spatial and temporal variations of vegetation cover and its influencing factors in Shandong Province based on GEE.}, journal = {Environmental monitoring and assessment}, volume = {195}, number = {9}, pages = {1023}, pmid = {37548802}, issn = {1573-2959}, support = {42201077 and 42177453//National Natural Science Foundation of China/ ; ZR2021QD074//Natural Science Foundation of Shandong Province/ ; 17YJAZH013//the MOE Layout Foundation of Humanities and Social Sciences/ ; }, mesh = {China ; Conservation of Natural Resources ; *Ecosystem ; *Environmental Monitoring ; Soil ; Sustainable Development ; }, abstract = {Economic development has rapidly progressed since the implementation of reform and opening up policies, posing significant challenges to sustainable development, especially to vegetation, which plays a crucial role in maintaining ecosystem service functions and promoting green low-carbon transformations. In this study, we estimated the fractional vegetation cover (FVC) in Shandong Province from 2000 to 2020 using the Google Earth Engine (GEE) platform. The spatial and temporal changes in FVC were analyzed using gravity center migration analysis, trend analysis, and geographic detector, and the vegetation changes of different land use types were analyzed to reveal the internal driving mechanism of FVC changes. Our results indicate that vegetation cover in Shandong Province was in good condition during the period 2000 to 2020. The high vegetation cover classes dominated, and overall changes were relatively small, with the center of gravity of vegetation cover generally shifting towards the southwest. Land use type, soil type, population density, and GDP factors had the most significant impact on vegetation cover change in Shandong Province. The interaction of these factors enhanced the effect on vegetation cover change, with land use type and soil type having the highest degree of influence. The observational results of this study can provide data support for the policy makers to formulate new ecological restoration strategies, and the findings would help facilitate the sustainability management of regional ecosystem and natural resource planning.}, } @article {pmid37548515, year = {2024}, author = {Hakimzadeh, A and Abdala Asbun, A and Albanese, D and Bernard, M and Buchner, D and Callahan, B and Caporaso, JG and Curd, E and Djemiel, C and Brandström Durling, M and Elbrecht, V and Gold, Z and Gweon, HS and Hajibabaei, M and Hildebrand, F and Mikryukov, V and Normandeau, E and Özkurt, E and M Palmer, J and Pascal, G and Porter, TM and Straub, D and Vasar, M and Větrovský, T and Zafeiropoulos, H and Anslan, S}, title = {A pile of pipelines: An overview of the bioinformatics software for metabarcoding data analyses.}, journal = {Molecular ecology resources}, volume = {24}, number = {5}, pages = {e13847}, pmid = {37548515}, issn = {1755-0998}, support = {P20 GM103449/GM/NIGMS NIH HHS/United States ; EXC2124//Deutsche Forschungsgemeinschaft (DFG)/ ; MOBTP198//European Regional Development Fund and the programme Mobilitas Pluss/ ; //Genome Canada and Ontario Genomics/ ; U24 CA248454/CA/NCI NIH HHS/United States ; P20GM103449/GM/NIGMS NIH HHS/United States ; 21-17749S//Grantová Agentura České Republiky/ ; }, mesh = {*DNA Barcoding, Taxonomic/methods ; *Computational Biology/methods ; *Software ; High-Throughput Nucleotide Sequencing/methods ; Archaea/genetics/classification ; DNA, Environmental/genetics ; Metagenomics/methods ; Data Analysis ; Bacteria/genetics/classification ; Eukaryota/genetics/classification ; }, abstract = {Environmental DNA (eDNA) metabarcoding has gained growing attention as a strategy for monitoring biodiversity in ecology. However, taxa identifications produced through metabarcoding require sophisticated processing of high-throughput sequencing data from taxonomically informative DNA barcodes. Various sets of universal and taxon-specific primers have been developed, extending the usability of metabarcoding across archaea, bacteria and eukaryotes. Accordingly, a multitude of metabarcoding data analysis tools and pipelines have also been developed. Often, several developed workflows are designed to process the same amplicon sequencing data, making it somewhat puzzling to choose one among the plethora of existing pipelines. However, each pipeline has its own specific philosophy, strengths and limitations, which should be considered depending on the aims of any specific study, as well as the bioinformatics expertise of the user. In this review, we outline the input data requirements, supported operating systems and particular attributes of thirty-two amplicon processing pipelines with the goal of helping users to select a pipeline for their metabarcoding projects.}, } @article {pmid37548100, year = {2023}, author = {Anderson, LM and Lim, KO and Kummerfeld, E and Crosby, RD and Crow, SJ and Engel, SG and Forrest, L and Wonderlich, SA and Peterson, CB}, title = {Causal discovery analysis: A promising tool in advancing precision medicine for eating disorders.}, journal = {The International journal of eating disorders}, volume = {56}, number = {11}, pages = {2012-2021}, doi = {10.1002/eat.24040}, pmid = {37548100}, issn = {1098-108X}, support = {K23MH123910/MH/NIMH NIH HHS/United States ; 1P20GM134969/GM/NIGMS NIH HHS/United States ; R34 MH077571/MH/NIMH NIH HHS/United States ; R34MH077571/MH/NIMH NIH HHS/United States ; K23 MH123910/MH/NIMH NIH HHS/United States ; }, mesh = {Humans ; *Precision Medicine ; *Feeding and Eating Disorders/diagnosis/therapy ; Psychopathology ; }, abstract = {OBJECTIVE: Precision medicine (i.e., individually tailored treatments) represents an optimal goal for treating complex psychiatric disorders, including eating disorders. Within the eating disorders field, most treatment development efforts have been limited in their ability to identify individual-level models of eating disorder psychopathology and to develop and apply an individually tailored treatment for a given individual's personalized model of psychopathology. In addition, research is still needed to identify causal relationships within a given individual's model of eating disorder psychopathology. Addressing this limitation of the current state of precision medicine-related research in the field will allow us to progress toward advancing research and practice for eating disorders treatment.

METHOD: We present a novel set of analytic tools, causal discovery analysis (CDA) methods, which can facilitate increasingly fine-grained, person-specific models of causal relations among cognitive, behavioral, and affective symptoms.

RESULTS: CDA can advance the identification of an individual's causal model that maintains that individuals' eating disorder psychopathology.

DISCUSSION: In the current article, we (1) introduce CDA methods as a set of promising analytic tools for developing precision medicine methods for eating disorders including the potential strengths and weaknesses of CDA, (2) provide recommendations for future studies utilizing this approach, and (3) outline the potential clinical implications of using CDA to generate personalized models of eating disorder psychopathology.

PUBLIC SIGNIFICANCE STATEMENT: CDA provides a novel statistical approach for identifying causal relationships among variables of interest for a given individual. Person-specific causal models may offer a promising approach to individualized treatment planning and inform future personalized treatment development efforts for eating disorders.}, } @article {pmid37543705, year = {2023}, author = {Pakulnicka, J and Kruk, M}, title = {Regional differences in water beetle communities networks settling in dystrophic lakes in northern Poland.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {12699}, pmid = {37543705}, issn = {2045-2322}, mesh = {Humans ; *Ecosystem ; *Lakes ; Water ; Poland ; Community Networks ; }, abstract = {The relationships between the species that form the networks in small dystrophic lakes remain poorly recognised. To investigate and better understand the functioning of beetle communities in different ecosystems, we created three network models that we subjected to graph network analysis. This approach displays correlation-based networks of connections (edges) between objects (nodes) by evaluating the features of the whole network and the attributes of nodes and edges in the context of their roles, expressed by centrality metrics. We used this method to determine the importance of specific species in the networks and the interspecific relationships. Our analyses are based on faunal material collected from 25 dystrophic lakes in three regions of northern Poland. We found a total of 104 species representing different ecological elements and functional trophic groups. We have shown that the network of relationships between the biomass of species differs considerably in the three study regions. The Kashubian Lakeland had the highest cohesion and density, while the network in the Suwalki Lakeland was the thinnest and most heterogeneous, which might be related to the fractal structure and the degree of development of the studied lakes. Small-bodied predators that congregated in different clusters with species with similar ecological preferences dominated all networks. We found the highest correlations in the Masurian Lakeland, where we obtained the highest centralisation of the network. Small tyrphophiles typically occupied the central places in the network, while the periphery of the network consisted of clusters with different habitat preferences, including large predators. The species that were most important for network cohesion and density were mainly tyrphophilous species, such as Anacaena lutescens, Hygrotus decoratus, Enochrus melanocephalus and Hydroporus neglectus. The values of attributes determining the role of species in community networks were influenced by both biotic and environmental factors.}, } @article {pmid37543634, year = {2023}, author = {Fu, Y and Mason, AS and Song, M and Ni, X and Liu, L and Shi, J and Wang, T and Xiao, M and Zhang, Y and Fu, D and Yu, H}, title = {Multi-omics strategies uncover the molecular mechanisms of nitrogen, phosphorus and potassium deficiency responses in Brassica napus.}, journal = {Cellular & molecular biology letters}, volume = {28}, number = {1}, pages = {63}, pmid = {37543634}, issn = {1689-1392}, support = {LY23C130007//Zhejiang Provincial Natural Science Foundation of China/ ; 2021C02064-2//Medical Technology and Education of Zhejiang Province of China/ ; No. 2022E10012//Key Laboratory of Digital Upland Crops of Zhejiang Province/ ; }, mesh = {*Brassica napus/genetics/metabolism ; Phosphorus ; *Potassium Deficiency/genetics ; Nitrogen/metabolism ; Multiomics ; Transcriptome ; Potassium/metabolism ; *MicroRNAs/genetics/metabolism ; Gene Expression Regulation, Plant ; }, abstract = {BACKGROUND: Nitrogen (N), phosphorus (P) and potassium (K) are critical macronutrients in crops, such that deficiency in any of N, P or K has substantial effects on crop growth. However, the specific commonalities of plant responses to different macronutrient deficiencies remain largely unknown.

METHODS: Here, we assessed the phenotypic and physiological performances along with whole transcriptome and metabolomic profiles of rapeseed seedlings exposed to N, P and K deficiency stresses.

RESULTS: Quantities of reactive oxygen species were significantly increased by all macronutrient deficiencies. N and K deficiencies resulted in more severe root development responses than P deficiency, as well as greater chlorophyll content reduction in leaves (associated with disrupted chloroplast structure). Transcriptome and metabolome analyses validated the macronutrient-specific responses, with more pronounced effects of N and P deficiencies on mRNAs, microRNAs (miRNAs), circular RNAs (circRNAs) and metabolites relative to K deficiency. Tissue-specific responses also occurred, with greater effects of macronutrient deficiencies on roots compared with shoots. We further uncovered a set of common responders with simultaneous roles in all three macronutrient deficiencies, including 112 mRNAs and 10 miRNAs involved in hormonal signaling, ion transport and oxidative stress in the root, and 33 mRNAs and 6 miRNAs with roles in abiotic stress response and photosynthesis in the shoot. 27 and seven common miRNA-mRNA pairs with role in miRNA-mediated regulation of oxidoreduction processes and ion transmembrane transport were identified in all three macronutrient deficiencies. No circRNA was responsive to three macronutrient deficiency stresses, but two common circRNAs were identified for two macronutrient deficiencies. Combined analysis of circRNAs, miRNAs and mRNAs suggested that two circRNAs act as decoys for miR156 and participate in oxidoreduction processes and transmembrane transport in both N- and P-deprived roots. Simultaneously, dramatic alterations of metabolites also occurred. Associations of RNAs with metabolites were observed, and suggested potential positive regulatory roles for tricarboxylic acids, azoles, carbohydrates, sterols and auxins, and negative regulatory roles for aromatic and aspartate amino acids, glucosamine-containing compounds, cinnamic acid, and nicotianamine in plant adaptation to macronutrient deficiency.

CONCLUSIONS: Our findings revealed strategies to rescue rapeseed from macronutrient deficiency stress, including reducing the expression of non-essential genes and activating or enhancing the expression of anti-stress genes, aided by plant hormones, ion transporters and stress responders. The common responders to different macronutrient deficiencies identified could be targeted to enhance nutrient use efficiency in rapeseed.}, } @article {pmid37541986, year = {2023}, author = {Drozdovitch, V and Kukhta, T and Minenko, V and Trofimik, S and Veyalkin, I and Yauseyenka, V and Mabuchi, K and Rozhko, A}, title = {Recall of residential history and dietary habits during pregnancy and lactation in the distant past: reliability of questionnaire-based radiation doses for persons exposed in utero and early life.}, journal = {Radiation and environmental biophysics}, volume = {62}, number = {4}, pages = {465-481}, pmid = {37541986}, issn = {1432-2099}, support = {HHSN261201800015C/CA/NCI NIH HHS/United States ; HHSN261201800015C/CA/NCI NIH HHS/United States ; HHSN261201800015C/CA/NCI NIH HHS/United States ; HHSN261201800015C/CA/NCI NIH HHS/United States ; HHSN261201800015C/CA/NCI NIH HHS/United States ; HHSN261201800015C/CA/NCI NIH HHS/United States ; HHSN261201800015C/CA/NCI NIH HHS/United States ; HHSN261201800015C/CA/NCI NIH HHS/United States ; HHSN261201800015C/CA/NCI NIH HHS/United States ; }, mesh = {Female ; Pregnancy ; Humans ; Animals ; Cattle ; Radiation Dosage ; Reproducibility of Results ; *Chernobyl Nuclear Accident ; Iodine Radioisotopes ; Surveys and Questionnaires ; Lactation ; Feeding Behavior ; }, abstract = {This study evaluates the reliability of information obtained by standardized questionnaires used in by personal interviews for estimation of radiation thyroid doses of 1065 individuals in the Belarusian cohort of individuals who were exposed in utero and early life following the Chernobyl accident in April 1986. Data from two interviews conducted in 2012-2017 and in 2018-2022 with mothers, who were pregnant or gave birth shortly after the Chernobyl accident, were analysed. The most reliable answers dealt with various attributes related to residential history. In contrast, the reliability of answers regarding consumption rates of milk from privately owned cows or trade network was moderate, while the agreement in responses for consumption of milk products and leafy vegetables was fair. Information from the two interviews was used to calculate thyroid doses received by the cohort members. Specifically, 'model-based' thyroid doses due to [131]I were estimated using input data on individual residential history and food consumption reported during the personal interviews and ecological data ([131]I ground deposition in the corresponding settlements). In addition, for a subset of cohort subjects (n = 205) whose mothers were measured for [131]I thyroid activity, 'measurement-based' thyroid doses were calculated by adjusting the model-based dose using a scaling factor that is defined as the ratio of measured [131]I thyroid activity to model-based [131]I thyroid activity calculated for the date of measurement. A moderate agreement was observed for total (prenatal and postnatal) model-based thyroid doses due to [131]I intake, the arithmetic mean ± standard deviation for the Jaccard similarity coefficient ([Formula: see text]) was 0.45 ± 0.34 (median = 0.39), while measurement-based doses showed a much better agreement with a [Formula: see text] of 0.78 ± 0.29 (median = 0.93). For model-based thyroid doses from external irradiation and from ingestion of [134]Cs and [137]Cs, [Formula: see text] was 0.82 ± 0.23 (median = 0.90) and 0.84 ± 0.24 (median = 0.96), respectively. Measurement-based doses due to ingestion of radiocaesium isotopes resulted in an almost perfect agreement, [Formula: see text] was 0.91 ± 0.19 (median = 1.0). The present findings suggest that long-term memory recall can be reliable, if a person is asked about unique or important life events, such as pregnancy and childbirth occurring around the time of a nuclear reactor accident. However, the substantial difference (more than 10 times) observed for model-bases doses calculated using the two questionnaires represents an important source of human factor uncertainties that needs to be considered in any dose response analyses. Other lessons learned from this study are that (i) individual measurements of radionuclides in the human body are the most valuable source of information for estimating radiation doses, and (ii) whenever a radiation accident occurs, a sample of affected people should be asked to keep a diary, if at all possible.}, } @article {pmid37536963, year = {2023}, author = {Tobin, K and Heidari, O and Volpi, C and Sodder, S and Duncan, D}, title = {Use of geofencing interventions in population health research: a scoping review.}, journal = {BMJ open}, volume = {13}, number = {8}, pages = {e069374}, pmid = {37536963}, issn = {2044-6055}, support = {KL2 TR002317/TR/NCATS NIH HHS/United States ; R34 MH118178/MH/NIMH NIH HHS/United States ; }, mesh = {Humans ; *Population Health ; *Geographic Information Systems ; }, abstract = {OBJECTIVES: Technological advancements that use global positioning system (GPS), such as geofencing, provide the opportunity to examine place-based context in population health research. This review aimed to systematically identify, assess and synthesise the existing evidence on geofencing intervention design, acceptability, feasibility and/or impact.

DESIGN: Scoping review, using the Preferred Reporting Items for Systematic Reviews and Meta-Analyses extension for Scoping Reviews guidance for reporting.

DATA SOURCES: PubMed, CINAHL, EMBASE, Web of Science, Cochrane and PsycINFO for articles in English published up to 31 December 2021.

ELIGIBILITY CRITERIA: Articles were included if geofencing was used as a mechanism for intervention delivery.

EXCLUSION CRITERIA: (1) a component or combination of GPS, geographical information system or ecological momentary assessment was used without delivery of an intervention; (2) did not include a health or health-related outcome from the geofencing intervention; or (3) was not a peer-reviewed study.

DATA EXTRACTION AND SYNTHESIS: Several researchers independently reviewed all abstracts and full-text articles for final inclusion.

RESULTS: A total of 2171 articles were found; after exclusions, nine studies were included in the review. The majority were published in 5 years preceding the search (89%). Geofences in most studies (n=5) were fixed and programmed in the mobile application carried by participants without their input. Mechanisms of geofencing interventions were classified as direct or indirect, with five studies (56%) using direct interventions. There were several different health outcomes (from smoking to problematic alcohol use) across the five studies that used a direct geofencing intervention.

CONCLUSIONS: This scoping review found geofencing to be an emerging technology that is an acceptable and feasible intervention applied to several different populations and health outcomes. Future studies should specify the rationale for the locations that are geofenced and user input. Moreover, attention to mechanisms of actions will enable scientists to understand not only whether geofencing is an appropriate and effective intervention but why it works to achieve the outcomes observed.}, } @article {pmid37533557, year = {2023}, author = {Wang, TY and Goh, KS and Wang, LJ and Wu, LL and Wang, FY and Wu, YW}, title = {Long-Read Genome Sequencing of Abscondita cerata (Coleoptera: Lampyridae), the Endemic Firefly of Taiwan.}, journal = {Zoological studies}, volume = {62}, number = {}, pages = {e25}, pmid = {37533557}, issn = {1810-522X}, abstract = {Abscondita cerata is the most abundant and widely distributed endemic firefly species in Taiwan and is considered a key environmental and ecological indicator organism. In this study, we report the first long-read genome sequencing of Abs. cerata sequenced by Nanopore technology. The draft genome size, 967 Mb, was measured through a hybrid approach that consisted of assembling using 11.25-Gb Nanopore long reads and polishing using 9.47-Gb BGI PE100 short reads. The drafted genome was assembled into 4,855 contigs, with the N50 reaching 325.269 kb length. The assembled genome was predicted to possess 55,206 protein-coding genes, of which 20,862 (37.78%) were functionally annotated with public databases. 47.11% of the genome sequences consisted of repeat elements; among them DNA transposons accounted for the largest proportion (26.79%). A BUSCO (Benchmarking Universal Single Copy Orthologs) evaluation demonstrated that the genome and gene completeness were 84.8% and 79%, respectively. The phylogeny constructed using 1,792 single copy genes was consistent with previous studies. The comparative transcriptome between adult male head and lantern tissues revealed (1) the vision of Abs. cerata is primarily UV-sensitive to environmental twilight, which determines when it begins its nocturnal activity, (2) the major expressed OR56d receptor may be correlated to suitable humidity sensing, and (3) Luc1-type luciferase is responsible for Abs. cerata's luminescent spectrum.}, } @article {pmid37531569, year = {2023}, author = {Beer, RD}, title = {On the Proper Treatment of Dynamics in Cognitive Science.}, journal = {Topics in cognitive science}, volume = {}, number = {}, pages = {}, doi = {10.1111/tops.12686}, pmid = {37531569}, issn = {1756-8765}, abstract = {This essay examines the relevance of dynamical ideas for cognitive science. On its own, the mere mathematical idea of a dynamical system is too weak to serve as a scientific theory of anything, and dynamical approaches within cognitive science are too rich and varied to be subsumed under a single "dynamical hypothesis." Instead, after first attempting to dissect the different notions of "dynamics" and "cognition" at play, a more specific theoretical framework for cognitive science broadly construed is sketched. This framework draws upon not only dynamical ideas, but also such contemporaneous perspectives as situatedness, embodiment, ecological psychology, enaction, neuroethology/neuroscience, artificial life, and biogenic approaches. The paper ends with some methodological suggestions for pursuing this theoretical framework.}, } @article {pmid37531181, year = {2023}, author = {Murray, A and Ushakova, A and Zhu, X and Yang, Y and Xiao, Z and Brown, R and Speyer, L and Ribeaud, D and Eisner, M}, title = {Predicting Participation Willingness in Ecological Momentary Assessment of General Population Health and Behavior: Machine Learning Study.}, journal = {Journal of medical Internet research}, volume = {25}, number = {}, pages = {e41412}, pmid = {37531181}, issn = {1438-8871}, support = {/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Young Adult ; Humans ; *Ecological Momentary Assessment ; *Tobacco Use ; Machine Learning ; Research Design ; Health Behavior ; }, abstract = {BACKGROUND: Ecological momentary assessment (EMA) is widely used in health research to capture individuals' experiences in the flow of daily life. The majority of EMA studies, however, rely on nonprobability sampling approaches, leaving open the possibility of nonrandom participation concerning the individual characteristics of interest in EMA research. Knowledge of the factors that predict participation in EMA research is required to evaluate this possibility and can also inform optimal recruitment strategies.

OBJECTIVE: This study aimed to examine the extent to which being willing to participate in EMA research is related to respondent characteristics and to identify the most critical predictors of participation.

METHODS: We leveraged the availability of comprehensive data on a general young adult population pool of potential EMA participants and used and compared logistic regression, classification and regression trees, and random forest approaches to evaluate respondents' characteristic predictors of willingness to participate in the Decades-to-Minutes EMA study.

RESULTS: In unadjusted logistic regression models, gender, migration background, anxiety, attention deficit hyperactivity disorder symptoms, stress, and prosociality were significant predictors of participation willingness; in logistic regression models, mutually adjusting for all predictors, migration background, tobacco use, and social exclusion were significant predictors. Tree-based approaches also identified migration status, tobacco use, and prosociality as prominent predictors. However, overall, willingness to participate in the Decades-to-Minutes EMA study was only weakly predictable from respondent characteristics. Cross-validation areas under the curve for the best models were only in the range of 0.56 to 0.57.

CONCLUSIONS: Results suggest that migration background is the single most promising target for improving EMA participation and sample representativeness; however, more research is needed to improve prediction of participation in EMA studies in health.}, } @article {pmid37530223, year = {2023}, author = {Sun, M and Yan, H and Zhang, A and Jin, Y and Lin, C and Luo, L and Wu, B and Fan, Y and Tian, S and Cao, X and Wang, Z and Luo, J and Yang, Y and Jia, J and Zhou, P and Tang, Q and Jones, CS and Varshney, RK and Srivastava, RK and He, M and Xie, Z and Wang, X and Feng, G and Nie, G and Huang, D and Zhang, X and Zhu, F and Huang, L}, title = {Milletdb: a multi-omics database to accelerate the research of functional genomics and molecular breeding of millets.}, journal = {Plant biotechnology journal}, volume = {21}, number = {11}, pages = {2348-2357}, pmid = {37530223}, issn = {1467-7652}, mesh = {Humans ; *Millets/genetics ; *DNA Shuffling ; Genome-Wide Association Study ; Multiomics ; Genomics/methods ; }, abstract = {Millets are a class of nutrient-rich coarse cereals with high resistance to abiotic stress; thus, they guarantee food security for people living in areas with extreme climatic conditions and provide stress-related genetic resources for other crops. However, no platform is available to provide a comprehensive and systematic multi-omics analysis for millets, which seriously hinders the mining of stress-related genes and the molecular breeding of millets. Here, a free, web-accessible, user-friendly millets multi-omics database platform (Milletdb, http://milletdb.novogene.com) has been developed. The Milletdb contains six millets and their one related species genomes, graph-based pan-genomics of pearl millet, and stress-related multi-omics data, which enable Milletdb to be the most complete millets multi-omics database available. We stored GWAS (genome-wide association study) results of 20 yield-related trait data obtained under three environmental conditions [field (no stress), early drought and late drought] for 2 years in the database, allowing users to identify stress-related genes that support yield improvement. Milletdb can simplify the functional genomics analysis of millets by providing users with 20 different tools (e.g., 'Gene mapping', 'Co-expression', 'KEGG/GO Enrichment' analysis, etc.). On the Milletdb platform, a gene PMA1G03779.1 was identified through 'GWAS', which has the potential to modulate yield and respond to different environmental stresses. Using the tools provided by Milletdb, we found that the stress-related PLATZs TFs (transcription factors) family expands in 87.5% of millet accessions and contributes to vegetative growth and abiotic stress responses. Milletdb can effectively serve researchers in the mining of key genes, genome editing and molecular breeding of millets.}, } @article {pmid37529296, year = {2023}, author = {Kumar, V and Goyal, N and Prasad, A and Babu, S and Khare, K and Yadav, G}, title = {Quantification of pollen viability in Lantana camara by digital holographic microscopy.}, journal = {Quantitative plant biology}, volume = {4}, number = {}, pages = {e7}, pmid = {37529296}, issn = {2632-8828}, abstract = {Pollen grains represent the male gametes of seed plants and their viability is critical for sexual reproduction in the plant life cycle. Palynology and viability studies have traditionally been used to address a range of botanical, ecological and geological questions, but recent work has revealed the importance of pollen viability in invasion biology as well. Here, we report an efficient visual method for assessing the viability of pollen using digital holographic microscopy (DHM). Imaging data reveal that quantitative phase information provided by the technique can be correlated with viability as indicated by the outcome of the colorimetric test. We successfully test this method on pollen grains of Lantana camara, a well-known alien invasive plant in the tropical world. Our results show that pollen viability may be assessed accurately without the usual staining procedure and suggest potential applications of the DHM methodology to a number of emerging areas in plant science.}, } @article {pmid37527270, year = {2023}, author = {Kandel, AW and Sommer, C and Kanaeva, Z and Bolus, M and Bruch, AA and Groth, C and Haidle, MN and Hertler, C and Heß, J and Malina, M and Märker, M and Hochschild, V and Mosbrugger, V and Schrenk, F and Conard, NJ}, title = {The ROCEEH Out of Africa Database (ROAD): A large-scale research database serves as an indispensable tool for human evolutionary studies.}, journal = {PloS one}, volume = {18}, number = {8}, pages = {e0289513}, pmid = {37527270}, issn = {1932-6203}, mesh = {Humans ; *Artificial Intelligence ; Databases, Factual ; *Geographic Information Systems ; Software ; Africa ; }, abstract = {Large scale databases are critical for helping scientists decipher long-term patterns in human evolution. This paper describes the conception and development of such a research database and illustrates how big data can be harnessed to formulate new ideas about the past. The Role of Culture in Early Expansions of Humans (ROCEEH) is a transdisciplinary research center whose aim is to study the origins of culture and the multifaceted aspects of human expansions across Africa and Eurasia over the last three million years. To support its research, the ROCEEH team developed an online tool named the ROCEEH Out of Africa Database (ROAD) and implemented its web-based applications. ROAD integrates geographical data as well as archaeological, paleoanthropological, paleontological and paleobotanical content within a robust chronological framework. In fact, a unique feature of ROAD is its ability to dynamically link scientific data both spatially and temporally, thereby allowing its reuse in ways that were not originally conceived. The data stem from published sources spanning the last 150 years, including those generated by the research team. Descriptions of these data rely on the development of a standardized vocabulary and profit from online explanations of each table and attribute. By synthesizing legacy data, ROAD facilitates the reuse of heritage data in novel ways. Database queries yield structured information in a variety of interoperable formats. By visualizing data on maps, users can explore this vast dataset and develop their own theories. By downloading data, users can conduct further quantitative analyses, for example with Geographic Information Systems, modeling programs and artificial intelligence. In this paper, we demonstrate the innovative nature of ROAD and show how it helps scientists studying human evolution to access datasets from different fields, thereby connecting the social and natural sciences. Because it permits the reuse of "old" data in new ways, ROAD is now an indispensable tool for researchers of human evolution and paleogeography.}, } @article {pmid37526960, year = {2023}, author = {Parfitt, KM and Green, AE and Connor, TR and Neill, DR and Mahenthiralingam, E}, title = {Identification of two distinct phylogenomic lineages and model strains for the understudied cystic fibrosis lung pathogen Burkholderia multivorans.}, journal = {Microbiology (Reading, England)}, volume = {169}, number = {8}, pages = {}, pmid = {37526960}, issn = {1465-2080}, support = {/WT_/Wellcome Trust/United Kingdom ; MR/T030062/1/MRC_/Medical Research Council/United Kingdom ; 204457/Z/16/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Animals ; Mice ; *Burkholderia/classification/genetics ; *Burkholderia Infections/complications/microbiology ; *Cystic Fibrosis/complications/microbiology ; Multilocus Sequence Typing ; *Phylogeny ; Genome, Bacterial/genetics ; Mice, Inbred BALB C ; Female ; }, abstract = {Burkholderia multivorans is the dominant Burkholderia pathogen recovered from lung infection in people with cystic fibrosis. However, as an understudied pathogen there are knowledge gaps in relation to its population biology, phenotypic traits and useful model strains. A phylogenomic study of B. multivorans was undertaken using a total of 283 genomes, of which 73 were sequenced and 49 phenotypically characterized as part of this study. Average nucleotide identity analysis (ANI) and phylogenetic alignment of core genes demonstrated that the B. multivorans population separated into two distinct evolutionary clades, defined as lineage 1 (n=58 genomes) and lineage 2 (n=221 genomes). To examine the population biology of B. multivorans, a representative subgroup of 77 B. multivorans genomes (28 from the reference databases and the 49 novel short-read genome sequences) were selected based on multilocus sequence typing (MLST), isolation source and phylogenetic placement criteria. Comparative genomics was used to identify B. multivorans lineage-specific genes - ghrB_1 in lineage 1 and glnM_2 in lineage 2 - and diagnostic PCRs targeting them were successfully developed. Phenotypic analysis of 49 representative B. multivorans strains showed considerable inter-strain variance, but the majority of the isolates tested were motile and capable of biofilm formation. A striking absence of B. multivorans protease activity in vitro was observed, but no lineage-specific phenotypic differences were demonstrated. Using phylogenomic and phenotypic criteria, three model B. multivorans CF strains were identified, BCC0084 (lineage 1), BCC1272 (lineage 2a) and BCC0033 lineage 2b, and their complete genome sequences determined. B. multivorans CF strains BCC0033 and BCC0084, and the environmental reference strain, ATCC 17616, were all capable of short-term survival within a murine lung infection model. By mapping the population biology, identifying lineage-specific PCRs and model strains, we provide much needed baseline resources for future studies of B. multivorans.}, } @article {pmid37524975, year = {2023}, author = {Honeker, LK and Pugliese, G and Ingrisch, J and Fudyma, J and Gil-Loaiza, J and Carpenter, E and Singer, E and Hildebrand, G and Shi, L and Hoyt, DW and Chu, RK and Toyoda, J and Krechmer, JE and Claflin, MS and Ayala-Ortiz, C and Freire-Zapata, V and Pfannerstill, EY and Daber, LE and Meeran, K and Dippold, MA and Kreuzwieser, J and Williams, J and Ladd, SN and Werner, C and Tfaily, MM and Meredith, LK}, title = {Drought re-routes soil microbial carbon metabolism towards emission of volatile metabolites in an artificial tropical rainforest.}, journal = {Nature microbiology}, volume = {8}, number = {8}, pages = {1480-1494}, pmid = {37524975}, issn = {2058-5276}, mesh = {*Carbon/metabolism ; Carbon Dioxide/metabolism ; *Droughts ; *Rainforest ; Soil/chemistry ; *Soil Microbiology ; Tropical Climate ; *Bacteria/classification/genetics/metabolism ; Biodiversity ; Multiomics ; Gene Expression Regulation, Bacterial ; }, abstract = {Drought impacts on microbial activity can alter soil carbon fate and lead to the loss of stored carbon to the atmosphere as CO2 and volatile organic compounds (VOCs). Here we examined drought impacts on carbon allocation by soil microbes in the Biosphere 2 artificial tropical rainforest by tracking [13]C from position-specific [13]C-pyruvate into CO2 and VOCs in parallel with multi-omics. During drought, efflux of [13]C-enriched acetate, acetone and C4H6O2 (diacetyl) increased. These changes represent increased production and buildup of intermediate metabolites driven by decreased carbon cycling efficiency. Simultaneously,[13]C-CO2 efflux decreased, driven by a decrease in microbial activity. However, the microbial carbon allocation to energy gain relative to biosynthesis was unchanged, signifying maintained energy demand for biosynthesis of VOCs and other drought-stress-induced pathways. Overall, while carbon loss to the atmosphere via CO2 decreased during drought, carbon loss via efflux of VOCs increased, indicating microbially induced shifts in soil carbon fate.}, } @article {pmid37518859, year = {2024}, author = {Mueller, HM and Franzisky, BL and Messerer, M and Du, B and Lux, T and White, PJ and Carpentier, SC and Winkler, JB and Schnitzler, JP and El-Serehy, HA and Al-Rasheid, KAS and Al-Harbi, N and Alfarraj, S and Kudla, J and Kangasjärvi, J and Reichelt, M and Mithöfer, A and Mayer, KFX and Rennenberg, H and Ache, P and Hedrich, R and Geilfus, CM}, title = {Integrative multi-omics analyses of date palm (Phoenix dactylifera) roots and leaves reveal how the halophyte land plant copes with sea water.}, journal = {The plant genome}, volume = {17}, number = {1}, pages = {e20372}, doi = {10.1002/tpg2.20372}, pmid = {37518859}, issn = {1940-3372}, support = {//King Saud University/ ; (471624304;GZ: GE 3111/5-1)//German Research Foundation (German: Deutsche Forschungsgemeinschaft)/ ; }, mesh = {*Phoeniceae/genetics ; Salt-Tolerant Plants/genetics ; Multiomics ; Proteomics ; Seawater ; }, abstract = {Date palm (Phoenix dactylifera L.) is able to grow and complete its life cycle while being rooted in highly saline soils. Which of the many well-known salt-tolerance strategies are combined to fine-tune this remarkable resilience is unknown. The precise location, whether in the shoot or the root, where these strategies are employed remains uncertain, leaving us unaware of how the various known salt-tolerance mechanisms are integrated to fine-tune this remarkable resilience. To address this shortcoming, we exposed date palm to a salt stress dose equivalent to seawater for up to 4 weeks and applied integrative multi-omics analyses followed by targeted metabolomics, hormone, and ion analyses. Integration of proteomic into transcriptomic data allowed a view beyond simple correlation, revealing a remarkably high degree of convergence between gene expression and protein abundance. This sheds a clear light on the acclimatization mechanisms employed, which depend on reprogramming of protein biosynthesis. For growth in highly saline habitats, date palm effectively combines various salt-tolerance mechanisms found in both halophytes and glycophytes: "avoidance" by efficient sodium and chloride exclusion at the roots, and "acclimation" by osmotic adjustment, reactive oxygen species scavenging in leaves, and remodeling of the ribosome-associated proteome in salt-exposed root cells. Combined efficiently as in P. dactylifera L., these sets of mechanisms seem to explain the palm's excellent salt stress tolerance.}, } @article {pmid37518126, year = {2023}, author = {Makarchenko, EA and Semenchenko, AA and Palatov, DM}, title = {Fauna and taxonomy of Diamesinae (Diptera, Chironomidae) from the Caucasus, with a morphological description and DNA barcoding of new taxa and a discussion of diagnostic problems for Diamesa Meigen and Pseudodiamesa Goetghebuer.}, journal = {Zootaxa}, volume = {5271}, number = {2}, pages = {313-328}, doi = {10.11646/zootaxa.5271.2.6}, pmid = {37518126}, issn = {1175-5334}, mesh = {Male ; Animals ; *Chironomidae/genetics ; DNA Barcoding, Taxonomic ; Phylogeny ; DNA ; Databases, Nucleic Acid ; }, abstract = {As a result of the revision of adult males as well as available literature data, 26 species of the subfamily Diamesinae are registered for the Caucasus, belonging to 5 genera. Four species are recorded for the first time for this region, one species, D. elbrusica sp. nov., and one subspecies, D. sakartvella gidanica subsp. nov., are new to science and are described. Six species are classified as endemics of the Caucasus. Distribution of other species of Caucasian Diamesinae is discussed. DNA barcodes of 102 specimens and 20 species of four genera, Boreoheptagyia Brundin, Diamesa Meigen, Pseudodiamesa Goetghebuer and Syndiamesa Kieffer were obtained in this study. Of these, 12 species were deposed in the GenBank and BOLD systems for the first time. We have established that D. cinerella group includes D. kasymovi and probably D. lavillei whereas D. zernyi group includes D. vaillanti and D. valentinae. Highly supported phylogeny and results of species delimitation suggest the description of D. elbrusica sp. nov. and D. sakartvella gidanica subsp. nov. Ps. aff. branickii and Ps. aff. nivosa are new species based on DNA barcoding. The results of species delimitation show that genus Pseudodiamesa includes 10 (ASAP, GMYC), 14 (mPTP) or 21 (BOLD) distinct molecular taxonomic units (mOTUs) among which only Ps. stackelbergi have an undoubted species status that requires a large revision using both morphological and molecular approaches.}, } @article {pmid37517987, year = {2023}, author = {Wang, Y and Xue, K and Hu, R and Ding, B and Zeng, H and Li, R and Xu, B and Pang, Z and Song, X and Li, C and Du, J and Yang, X and Zhang, Z and Hao, Y and Cui, X and Guo, K and Gao, Q and Zhang, Y and Zhu, J and Sun, J and Li, Y and Jiang, L and Zhou, H and Luo, C and Zhang, Z and Gao, Q and Chen, S and Ji, B and Xu, X and Chen, H and Li, Q and Zhao, L and Xu, S and Liu, Y and Hu, L and Wu, J and Yang, Q and Dong, S and He, J and Zhao, X and Wang, S and Piao, S and Yu, G and Fu, B}, title = {Vegetation structural shift tells environmental changes on the Tibetan Plateau over 40 years.}, journal = {Science bulletin}, volume = {68}, number = {17}, pages = {1928-1937}, doi = {10.1016/j.scib.2023.07.035}, pmid = {37517987}, issn = {2095-9281}, mesh = {Humans ; *Ecosystem ; Tibet ; *Grassland ; Climate Change ; China ; }, abstract = {Structural information of grassland changes on the Tibetan Plateau is essential for understanding alterations in critical ecosystem functioning and their underlying drivers that may reflect environmental changes. However, such information at the regional scale is still lacking due to methodological limitations. Beyond remote sensing indicators only recognizing vegetation productivity, we utilized multivariate data fusion and deep learning to characterize formation-based plant community structure in alpine grasslands at the regional scale of the Tibetan Plateau for the first time and compared it with the earlier version of Vegetation Map of China for historical changes. Over the past 40 years, we revealed that (1) the proportion of alpine meadows in alpine grasslands increased from 50% to 69%, well-reflecting the warming and wetting trend; (2) dominances of Kobresia pygmaea and Stipa purpurea formations in alpine meadows and steppes were strengthened to 76% and 92%, respectively; (3) the climate factor mainly drove the distribution of Stipa purpurea formation, but not the recent distribution of Kobresia pygmaea formation that was likely shaped by human activities. Therefore, the underlying mechanisms of grassland changes over the past 40 years were considered to be formation dependent. Overall, the first exploration for structural information of plant community changes in this study not only provides a new perspective to understand drivers of grassland changes and their spatial heterogeneity at the regional scale of the Tibetan Plateau, but also innovates large-scale vegetation study paradigm.}, } @article {pmid37511196, year = {2023}, author = {Domingues, CPF and Rebelo, JS and Dionisio, F and Nogueira, T}, title = {Multi-Drug Resistance in Bacterial Genomes-A Comprehensive Bioinformatic Analysis.}, journal = {International journal of molecular sciences}, volume = {24}, number = {14}, pages = {}, pmid = {37511196}, issn = {1422-0067}, support = {UI/BD/153078/2022//Fundação para a Ciência e Tecnologia/ ; SFRH/BD/04631/2021//Fundação para a Ciência e Tecnologia/ ; UIDP/00329/2020//Fundação para a Ciência e Tecnologia/ ; }, mesh = {*Genome, Bacterial ; Plasmids/genetics ; *Anti-Bacterial Agents/pharmacology ; Computational Biology ; Drug Resistance, Multiple ; Drug Resistance, Multiple, Bacterial/genetics ; Drug Resistance, Bacterial/genetics ; }, abstract = {Antimicrobial resistance is presently one of the greatest threats to public health. The excessive and indiscriminate use of antibiotics imposes a continuous selective pressure that triggers the emergence of multi-drug resistance. We performed a large-scale analysis of closed bacterial genomes to identify multi-drug resistance considering the ResFinder antimicrobial classes. We found that more than 95% of the genomes harbor genes associated with resistance to disinfectants, glycopeptides, macrolides, and tetracyclines. On average, each genome encodes resistance to more than nine different classes of antimicrobial drugs. We found higher-than-expected co-occurrences of resistance genes in both plasmids and chromosomes for several classes of antibiotic resistance, including classes categorized as critical according to the World Health Organization (WHO). As a result of antibiotic-resistant priority pathogens, higher-than-expected co-occurrences appear in plasmids, increasing the potential for resistance dissemination. For the first time, co-occurrences of antibiotic resistance have been investigated for priority pathogens as defined by the WHO. For critically important pathogens, co-occurrences appear in plasmids, not in chromosomes, suggesting that the resistances may be epidemic and probably recent. These results hint at the need for new approaches to treating infections caused by critically important bacteria.}, } @article {pmid37508724, year = {2023}, author = {Pinto Pereira, SM and Nugawela, MD and McOwat, K and Dalrymple, E and Xu, L and Ladhani, SN and Simmons, R and Chalder, T and Swann, O and Ford, T and Heyman, I and Segal, T and Semple, MG and Rojas, NK and CLoCk Consortium, and Shafran, R and Stephenson, T}, title = {Symptom Profiles of Children and Young People 12 Months after SARS-CoV-2 Testing: A National Matched Cohort Study (The CLoCk Study).}, journal = {Children (Basel, Switzerland)}, volume = {10}, number = {7}, pages = {}, pmid = {37508724}, issn = {2227-9067}, support = {MR/P020372/1/MRC_/Medical Research Council/United Kingdom ; }, abstract = {BACKGROUND: Although 99% of children and young people have been exposed to SARS-CoV-2, the long-term prevalence of post-COVID-19 symptoms in young people is unclear. The aim of this study is to describe symptom profiles 12 months after SARS-CoV-2 testing.

METHOD: A matched cohort study of a national sample of 20,202 children and young people who took a SARS-CoV-2 PCR test between September 2020 and March 2021.

RESULTS: 12 months post-index-test, there was a difference in the number of symptoms reported by initial negatives who never tested positive (NN) compared to the other three groups who had at least one positive test (p < 0.001). Similarly, 10.2% of the NN group described five-plus symptoms at 12 months compared to 15.9-24.0% in the other three groups who had at least one positive test. The most common symptoms were tiredness, sleeping difficulties, shortness of breath, and headaches for all four groups. For all these symptoms, the initial test positives with subsequent reports of re-infection had higher prevalences than other positive groups (p < 0.001). Symptom profiles, mental health, well-being, fatigue, and quality of life did not vary by vaccination status.

CONCLUSIONS: Following the pandemic, many young people, particularly those that have had multiple SARS-CoV-2 positive tests, experience a range of symptoms that warrant consideration and potential investigation and intervention.}, } @article {pmid37508342, year = {2023}, author = {Oravec, P and Wittlinger, L and Máliš, F}, title = {Endangered Forest Communities in Central Europe: Mapping Current and Potential Distributions of Euro-Siberian Steppic Woods with Quercus spp. in South Slovak Basin.}, journal = {Biology}, volume = {12}, number = {7}, pages = {}, pmid = {37508342}, issn = {2079-7737}, support = {1/0706/20//Constantine the Philosopher University in Nitra/ ; APVV-19-0319//Technical University in Zvolen/ ; }, abstract = {In this article we focus on the issue of determining the presence and status of the priority habitat 91I0* Euro-Siberian steppic woods with Quercus spp. in the South Slovak basin. As part of the issue, we try to verify the correctness of the procedure of the State Nature Conservancy of the Slovak Republic in the search for potential habitats and areas of European importance by converting the typological map to a map of habitats. Habitat 91I0* occurs in Slovakia in the form of three subtypes, namely Thermophilous and supra-Mediterranean oak woods (Carpineto-Quercetum and Betuleto-Quercetum), Acidophilous oak forests (Quercetum), while the last-named subtype is divided into two subunits: Medio-European acidophilous oak forests-part A and Pannonic hairy greenweed sessile oak woods-part B. Due to the current unsatisfactory state of the mentioned habitats, the requirement of the State Nature Conservancy of the Slovak Republic is to find and add new areas with the occurrence of habitat 91I0* in the south of Central Slovakia. During the mapping in the Lučenecká and Rimavská basins, greater emphasis was placed on the occurrence of the subtype Thermophilic Pontic-Pannonian oak forests on loess and sand, but its presence has not been confirmed. Subsequently, we focused on the search and identification of habitats in the model area, which is the area of European importance SKUEV0957 Uderinky. The result is a map of habitats in this area, which we then compare with a typological map, which determines the reliability of the converter used by the State Nature Conservancy of the Slovak Republic.}, } @article {pmid37504804, year = {2023}, author = {Gaboutchian, AV and Knyaz, VA and Maschenko, EN and Dac, LX and Maksimov, AA and Emelyanov, AV and Korost, DV and Stepanov, NV}, title = {Measuring Dental Enamel Thickness: Morphological and Functional Relevance of Topographic Mapping.}, journal = {Journal of imaging}, volume = {9}, number = {7}, pages = {}, pmid = {37504804}, issn = {2313-433X}, abstract = {The interest in the development of dental enamel thickness measurement techniques is connected to the importance of metric data in taxonomic assessments and evolutionary research as well as in other directions of dental studies. At the same time, advances in non-destructive imaging techniques and the application of scanning methods, such as micro-focus-computed X-ray tomography, has enabled researchers to study the internal morpho-histological layers of teeth with a greater degree of accuracy and detail. These tendencies have contributed to changes in established views in different areas of dental research, ranging from the interpretation of morphology to metric assessments. In fact, a significant amount of data have been obtained using traditional metric techniques, which now should be critically reassessed using current technologies and methodologies. Hence, we propose new approaches for measuring dental enamel thickness using palaeontological material from the territories of northern Vietnam by means of automated and manually operated techniques. We also discuss method improvements, taking into account their relevance for dental morphology and occlusion. As we have shown, our approaches demonstrate the potential to form closer links between the metric data and dental morphology and provide the possibility for objective and replicable studies on dental enamel thickness through the application of automated techniques. These features are likely to be effective in more profound taxonomic research and for the development of metric and analytical systems. Our technique provides scope for its targeted application in clinical methods, which could help to reveal functional changes in the masticatory system. However, this will likely require improvements in clinically applicable imaging techniques.}, } @article {pmid37502985, year = {2023}, author = {Pekar, JE and Lytras, S and Ghafari, M and Magee, AF and Parker, E and Havens, JL and Katzourakis, A and Vasylyeva, TI and Suchard, MA and Hughes, AC and Hughes, J and Robertson, DL and Dellicour, S and Worobey, M and Wertheim, JO and Lemey, P}, title = {The recency and geographical origins of the bat viruses ancestral to SARS-CoV and SARS-CoV-2.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {37502985}, issn = {2692-8205}, support = {U19 AI135995/AI/NIAID NIH HHS/United States ; R01 AI153044/AI/NIAID NIH HHS/United States ; T15 LM011271/LM/NLM NIH HHS/United States ; R01 AI162611/AI/NIAID NIH HHS/United States ; /WT_/Wellcome Trust/United Kingdom ; R01 AI135992/AI/NIAID NIH HHS/United States ; }, abstract = {The emergence of SARS-CoV in 2002 and SARS-CoV-2 in 2019 has led to increased sampling of related sarbecoviruses circulating primarily in horseshoe bats. These viruses undergo frequent recombination and exhibit spatial structuring across Asia. Employing recombination-aware phylogenetic inference on bat sarbecoviruses, we find that the closest-inferred bat virus ancestors of SARS-CoV and SARS-CoV-2 existed just ~1-3 years prior to their emergence in humans. Phylogeographic analyses examining the movement of related sarbecoviruses demonstrate that they traveled at similar rates to their horseshoe bat hosts and have been circulating for thousands of years in Asia. The closest-inferred bat virus ancestor of SARS-CoV likely circulated in western China, and that of SARS-CoV-2 likely circulated in a region comprising southwest China and northern Laos, both a substantial distance from where they emerged. This distance and recency indicate that the direct ancestors of SARS-CoV and SARS-CoV-2 could not have reached their respective sites of emergence via the bat reservoir alone. Our recombination-aware dating and phylogeographic analyses reveal a more accurate inference of evolutionary history than performing only whole-genome or single gene analyses. These results can guide future sampling efforts and demonstrate that viral genomic fragments extremely closely related to SARS-CoV and SARS-CoV-2 were circulating in horseshoe bats, confirming their importance as the reservoir species for SARS viruses.}, } @article {pmid37499537, year = {2023}, author = {Wu, M and Liu, X and Tu, W and Xia, J and Zou, Y and Gong, X and Yu, P and Huang, WE and Wang, H}, title = {Deep insight into oriented propionate production from food waste: Microbiological interpretation and design practice.}, journal = {Water research}, volume = {243}, number = {}, pages = {120399}, doi = {10.1016/j.watres.2023.120399}, pmid = {37499537}, issn = {1879-2448}, mesh = {*Propionates ; Food ; *Refuse Disposal ; Fermentation ; Fatty Acids, Volatile ; Lactic Acid ; Butyrates ; Hydrogen-Ion Concentration ; Bioreactors ; Sewage ; Anaerobiosis ; }, abstract = {Using mixed microbial cultures (MMCs) for oriented volatile fatty acids (VFAs) refining in an open environment is a typical challenge due to the microbial diversiform and the process complexity. Especially for carbohydrate-rich waste (such as food waste), butyrate-type fermentation is usually dominant in a single-stage MMCs anaerobic process, while the production of odd-carbon VFAs (such as propionate) is difficult although it plays a significant role in chemicals industries. In this study, firstly, we gave a new perspective on the rationality of the oriented propionate production using MMCs with lactate as feedstock by conducting in-depth microbial informatics and reaction analysis. Secondly, we verified the feasibility of the "food waste-lactate-propionate" route to reverse the original butyrate-type fermentation situation and explore mechanisms for maintaining stability. In the first stage, a defined lactate fermentation microbiome was used to produce lactate-containing broth (80% of total chemical oxygen demand) at pH=4. In the second stage, an undomesticated undefined anaerobic microbiome was used to drive propionate production (45.26% ± 2.23% of total VFAs) under optimized conditions (C/N = 100:1-200:1 and pH=5.0). The low pH environment in the first stage enhanced the lactic acid bacteria to resist the invasion of non-functional flanking bacteria, making the community stable. In the second stage, the system maintained the propionate-type fermentation due to the absence of the ecological niche of the invasive lactic acid bacteria; The selection of propionate-producing specialists was a necessary but not sufficient condition for propionate-type fermentation. At last, this study proposed an enhanced engineering strategy framework for understanding elaborate MMCs fermentation.}, } @article {pmid37495700, year = {2023}, author = {Hughes, LJ and Massam, MR and Morton, O and Edwards, FA and Scheffers, BR and Edwards, DP}, title = {Global hotspots of traded phylogenetic and functional diversity.}, journal = {Nature}, volume = {620}, number = {7973}, pages = {351-357}, pmid = {37495700}, issn = {1476-4687}, mesh = {Animals ; *Biodiversity ; *Birds ; *Conservation of Natural Resources/methods/trends ; Datasets as Topic ; Endangered Species ; Europe ; Extinction, Biological ; Geographic Mapping ; *Mammals ; *Phylogeny ; Tropical Climate ; United States ; *Commerce/statistics & numerical data ; }, abstract = {Wildlife trade is a multibillion-dollar industry[1] targeting a hyperdiversity of species[2] and can contribute to major declines in abundance[3]. A key question is understanding the global hotspots of wildlife trade for phylogenetic (PD) and functional (FD) diversity, which underpin the conservation of evolutionary history[4], ecological functions[5] and ecosystem services benefiting humankind[6]. Using a global dataset of traded bird and mammal species, we identify that the highest levels of traded PD and FD are from tropical regions, where high numbers of evolutionary distinct and globally endangered species in trade occur. The standardized effect size (ses) of traded PD and FD also shows strong tropical epicentres, with additional hotspots of mammalian ses.PD in the eastern United States and ses.FD in Europe. Large-bodied, frugivorous and canopy-dwelling birds and large-bodied mammals are more likely to be traded whereas insectivorous birds and diurnally foraging mammals are less likely. Where trade drives localized extinctions[3], our results suggest substantial losses of unique evolutionary lineages and functional traits, with possible cascading effects for communities and ecosystems[5,7]. Avoiding unsustainable exploitation and lost community integrity requires targeted conservation efforts, especially in hotspots of traded phylogenetic and functional diversity.}, } @article {pmid37495016, year = {2023}, author = {Regmi, PR and Adhikaree, A and Bhattarai, U and Chhetri, S and Shakya, U and Uranw, S and Lamichhane, P and Sharma, SK}, title = {Rheumatic heart disease in school-attending Nepalese children: A descriptive analysis of the national heart screening database.}, journal = {Indian heart journal}, volume = {75}, number = {5}, pages = {363-369}, pmid = {37495016}, issn = {2213-3763}, mesh = {Humans ; *Rheumatic Heart Disease/epidemiology/diagnosis ; Nepal/epidemiology ; Cross-Sectional Studies ; Child ; Male ; Female ; Prevalence ; Adolescent ; *Mass Screening/methods ; Child, Preschool ; Echocardiography ; Databases, Factual ; Schools ; Retrospective Studies ; }, abstract = {OBJECTIVE: Rheumatic Heart Disease (RHD) remains a significant public health problem with high morbidity and mortality in children and young adults from lower-middle income countries like Nepal. However, a nation-wide database of the disease is lacking for designing effective future prevention and control programmes and strategies. The aim of our study is to estimate the prevalence of RHD in school-attending Nepalese children.

METHODS: We performed a cross-sectional descriptive analysis of a nationally representative database of Nepal Heart Foundation (NHF) national RHD screening programme which included school-attending Nepalese children between five and sixteen years of age. The screening was conducted between May 2015 and March 2020 in 236 schools, representing all seven provinces, across all three ecological zones of Nepal. Transthoracic two-dimensional echocardiography was performed in all eligible children with more than grade one murmur on cardiac auscultation. We estimated the prevalence of RHD among school-attending children as the number of RHD cases per 1000 school-attending children with a 95% confidence interval.

RESULTS: The database included a total of 107,340 children who were screened clinically, of whom 10,600 (9·9%) underwent transthoracic two-dimensional echocardiography. The overall prevalence of RHD was 2.22 cases per 1000 school-attending children (95% CI:1·94 - 2·50). The highest prevalence was observed among children living in the southern Terai ecological zone (2·89 per 1000, 95% CI (2·32-3·46)) of Nepal. Among the provinces, Karnali had the highest prevalence of RHD (3·45 per 1000, 95% CI (2·42-4·48)). Among the districts screened, Kalikot had the highest RHD prevalence (5.47 per 1000, 95% CI (3.02-7.92)).

CONCLUSION: Primordial, primary and secondary prevention programmes should pay special attention to southern Terai zone, particularly the under-privileged children from remote districts.}, } @article {pmid37494338, year = {2023}, author = {Kiyingi, M and Nankabirwa, JI and Wiltshire, CS and Nangendo, J and Kiweewa, JM and Katahoire, AR and Semitala, FC}, title = {Perspectives of people living with HIV on barriers to timely ART initiation following referral for antiretroviral therapy: A qualitative study at an urban HIV clinic in Kampala, Uganda.}, journal = {PLOS global public health}, volume = {3}, number = {7}, pages = {e0001483}, pmid = {37494338}, issn = {2767-3375}, support = {D43 TW011304/TW/FIC NIH HHS/United States ; }, abstract = {Early initiation of antiretroviral therapy (ART) after HIV diagnosis prevents HIV transmission, progression of HIV to AIDS and improves quality of life. However, little is known about the barriers to timely ART initiation among patients who test HIV positive in settings different from where they will receive HIV treatment, hence are referred in the routine setting. Therefore, we explored the perspectives of people living with HIV on barriers faced to initiate ART following HIV testing and referral for treatment. In this qualitative study, we purposively sampled and enrolled 17 patients attending the Mulago ISS clinic. We selected patients (≥18 years) who previously were received as referrals for HIV treatment and had delayed ART initiation, as ascertained from their records. We conducted in-depth interviews, which were audio recorded, transcribed and translated. We used Atlas.ti version 9 software for data management. Data analysis followed thematic and framework analysis techniques and we adopted the socio-ecological model to categorize final themes. Key themes were found at organizational level including; negative experiences at the place of HIV diagnosis attributed to inadequate counselling and support, unclear communication of HIV-positive results and ambiguous referral procedures; and, long waiting time when patients reached the HIV clinic. At individual level, the themes identified were; immediate denial with late acceptance of HIV-positive results attributed to severe emotional and psychological distress at receiving results, fear of perceived side effects and long duration on ART. At interpersonal level, we found that anticipated and enacted stigma after HIV diagnosis resulted in non-disclosure, discrimination and lack of social support. We found that challenges at entry (during HIV test) and navigation of the HIV care system in addition to individual and interpersonal factors contributed to delayed ART initiation. Interventions during HIV testing would facilitate early ART initiation among patients referred for HIV care.}, } @article {pmid37491491, year = {2023}, author = {Ma, Y and Zheng, M and Xu, F and Qian, Y and Liu, M and Zheng, X and Liu, J}, title = {Modeling and exploring the coordination relationship between green infrastructure and land use eco-efficiency: an urban agglomeration perspective.}, journal = {Environmental science and pollution research international}, volume = {30}, number = {40}, pages = {92537-92554}, pmid = {37491491}, issn = {1614-7499}, support = {42201471//National Natural Science Foundation of China/ ; 72033005//National Natural Science Foundation of China/ ; 42171113//National Natural Science Foundation of China/ ; KF-2020-05-063//Ministry of Natural Resources/ ; }, mesh = {Humans ; *Urbanization ; Cities ; Beijing ; *Sustainable Development ; Efficiency ; China ; Economic Development ; }, abstract = {In limited land space, improving the construction of infrastructure with ecological services can help to achieve the goal of promoting land use eco-efficiency (LUEE). In view of this, this study constructed interactive coordination relationship model of green infrastructure (GI) and LUEE that involves entropy method model, super-efficiency slack-based measure (SBM) model with undesirable outputs, and coupling coordination degree model. The interactive coordination relationship model can help to study and reveal the mechanisms of interaction and the coordination relationship between GI and LUEE from a land benefit and ecological perspective. We took the Beijing-Tianjin-Hebei urban agglomeration as the study area. The results showed that the assessment results of GI showed a decreasing trend from 2000 to 2020. LUEE in different cities displayed obvious variability with efficiency values ranging from 0.5666 to 2.4437. The relationship between GI and LUEE is in the stage of uncoordinated development in 53.8% of cities, mainly concentrated in the eastern and southern parts of the study area. The unnatural human activities are the critical factors affecting interactive coupling coordination degree of LUEE and GI. It is clarified that the level of coordination relationship of the two can be used as an important indicator to judge the sustainable development of urban agglomerations. Intensive use of land, optimal connection of geographic information, and localization of policies would help improve the balance and coordination between the two. This study provides interesting research ideas and novel modeling approaches for the study of green and sustainable development of urban agglomerations.}, } @article {pmid37490521, year = {2023}, author = {Schaupp, CM and Maloney, EM and Mattingly, KZ and Olker, JH and Villeneuve, DL}, title = {Comparison of in silico, in vitro, and in vivo toxicity benchmarks suggests a role for ToxCast data in ecological hazard assessment.}, journal = {Toxicological sciences : an official journal of the Society of Toxicology}, volume = {195}, number = {2}, pages = {145-154}, pmid = {37490521}, issn = {1096-0929}, support = {EPA999999/ImEPA/Intramural EPA/United States ; //United States Environmental Protection Agency Office of Research and Development/ ; //Chemical Safety for Sustainability National Research Program/ ; }, mesh = {Risk Assessment ; Animals ; *Quantitative Structure-Activity Relationship ; *Benchmarking ; Humans ; Computer Simulation ; Databases, Factual ; Toxicity Tests ; United States Environmental Protection Agency ; Ecotoxicology ; Hazardous Substances/toxicity ; United States ; }, abstract = {Large repositories of in vitro bioactivity data such as US EPA's Toxicity Forecaster (ToxCast) provide a wealth of publicly accessible toxicity information for thousands of chemicals. These data can be used to calculate point-of-departure (POD) estimates via concentration-response modeling that may serve as lower bound, protective estimates of in vivo effects. However, the data are predominantly based on mammalian models and discussions to date about their utility have largely focused on potential integration into human hazard assessment, rather than application to ecological risk assessment. The goal of the present study was to compare PODs based on (1) quantitative structure-activity relationships (QSARs), (2) the 5th centile of the activity concentration at cutoff (ACC), and (3) lower-bound cytotoxic burst (LCB) from ToxCast, with the distribution of in vivo PODs compiled in the Ecotoxicology Knowledgebase (ECOTOX). While overall correlation between ToxCast ACC5 and ECOTOX PODs for 649 chemicals was weak, there were significant associations among PODs based on LCB and ECOTOX, LCB and QSARs, and ECOTOX and QSARs. Certain classes of compounds showed moderate correlation across datasets (eg, antimicrobials/disinfectants), while others, such as organophosphate insecticides, did not. Unsurprisingly, more precise classifications of the data based on ECOTOX effect and endpoint type (eg, apical vs biochemical; acute vs chronic) had a significant effect on overall relationships. Results of this research help to define appropriate roles for data from new approach methodologies in chemical prioritization and screening of ecological hazards.}, } @article {pmid37488464, year = {2024}, author = {Andrade, MÂ and Cipriano, M and Raposo, A}, title = {ObScene database: Semantic congruency norms for 898 pairs of object-scene pictures.}, journal = {Behavior research methods}, volume = {56}, number = {4}, pages = {3058-3071}, pmid = {37488464}, issn = {1554-3528}, mesh = {Humans ; *Semantics ; Female ; Male ; Young Adult ; Adult ; *Recognition, Psychology/physiology ; Databases, Factual ; Photic Stimulation ; Pattern Recognition, Visual/physiology ; Visual Perception/physiology ; Adolescent ; }, abstract = {Research on the interaction between object and scene processing has a long history in the fields of perception and visual memory. Most databases have established norms for pictures where the object is embedded in the scene. In this study, we provide a diverse and controlled stimulus set comprising real-world pictures of 375 objects (e.g., suitcase), 245 scenes (e.g., airport), and 898 object-scene pairs (e.g., suitcase-airport), with object and scene presented separately. Our goal was twofold. First, to create a database of object and scene pictures, normed for the same variables to have comparable measures for both types of pictures. Second, to acquire normative data for the semantic relationships between objects and scenes presented separately, which offers more flexibility in the use of the pictures and allows disentangling the processing of the object and its context (the scene). Along three experiments, participants evaluated each object or scene picture on name agreement, familiarity, and visual complexity, and rated object-scene pairs on semantic congruency. A total of 125 septuplets of one scene and six objects (three congruent, three incongruent), and 120 triplets of one object and two scenes (in congruent and incongruent pairings) were built. In future studies, these objects and scenes can be used separately or combined, while controlling for their key features. Additionally, as object-scene pairs received semantic congruency ratings along the entire scale, researchers may select among a wide range of congruency values. ObScene is a comprehensive and ecologically valid database, useful for psychology and neuroscience studies of visual object and scene processing.}, } @article {pmid37484483, year = {2023}, author = {Boyes, D and , and , and , and , and , and Mulley, JF and , }, title = {The genome sequence of the Riband Wave, Idaea aversata (Linnaeus, 1758).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {45}, pmid = {37484483}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual male Idaea aversata (the Riband Wave; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 437 megabases in span. The whole assembly is scaffolded into 30 chromosomal pseudomolecules, including the assembled Z sex chromosome. The mitochondrial genome has also been assembled and is 17.5 kilobases in length. Gene annotation of this assembly on Ensembl identified 10,165 protein coding genes.}, } @article {pmid37484482, year = {2023}, author = {Boyes, D and , and , and , and , and , and Holland, PWH and , }, title = {The genome sequence of the Burnished Brass, Diachrysia chrysitis (Linnaeus, 1758).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {82}, pmid = {37484482}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual male Diachrysia chrysitis (the Burnished Brass; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 386 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the assembled Z sex chromosome. The mitochondrial genome has also been assembled and is 15.3 kilobases in length. Gene annotation of this assembly on Ensembl identified 18,320 protein coding genes.}, } @article {pmid37476650, year = {2023}, author = {Crowley, LM and Barclay, M and Roy, HE and Brown, PMJ and , and , and , and , and , and , and , }, title = {The genome sequence of the orange ladybird, Halyzia sedecimguttata (Linnaeus, 1758).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {186}, pmid = {37476650}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual Halyzia sedecimguttata (the orange ladybird, Arthropoda; Insecta; Coleoptera, Coccinellidae). The genome sequence is 919.1 megabases in span. Most of the assembly is scaffolded into 10 chromosomal pseudomolecules, including the X sex chromosome. The mitochondrial genome has also been assembled and is 21.0 kilobases in length. Gene annotation of this assembly on Ensembl identified 27,547 protein coding genes.}, } @article {pmid37475130, year = {2023}, author = {Yang, G and Cao, JM and Cui, HL and Zhan, XM and Duan, G and Zhu, YG}, title = {Artificial Sweetener Enhances the Spread of Antibiotic Resistance Genes During Anaerobic Digestion.}, journal = {Environmental science & technology}, volume = {57}, number = {30}, pages = {10919-10928}, doi = {10.1021/acs.est.2c08673}, pmid = {37475130}, issn = {1520-5851}, mesh = {*Sweetening Agents/pharmacology ; Drug Resistance, Microbial/drug effects/genetics ; Anaerobiosis/drug effects ; Genes, Bacterial ; *Gastrointestinal Microbiome/drug effects ; *Anti-Bacterial Agents/pharmacology ; }, abstract = {Artificial sweeteners have been frequently detected in the feedstocks of anaerobic digestion. As these sweeteners can lead to the shift of anaerobic microbiota in the gut similar to that caused by antibiotics, we hypothesize that they may have an antibiotic-like impact on antibiotic resistance genes (ARGs) in anaerobic digestion. However, current understanding on this topic is scarce. This investigation aimed to examine the potential impact of acesulfame, a typical artificial sweetener, on ARGs in anaerobic digestion by using metagenomics sequencing and qPCR. It was found that acesulfame increased the number of detected ARG classes and the abundance of ARGs during anaerobic digestion. The abundance of typical mobile genetic elements (MGEs) and the number of potential hosts of ARGs also increased under acesulfame exposure, suggesting the enhanced potential of horizontal gene transfer of ARGs, which was further confirmed by the correlation analysis between absolute abundances of the targeted ARGs and MGEs. The increased horizontal dissemination of ARGs may be associated with the SOS response induced by the increased ROS production, and the increased cellular membrane permeability. These findings indicate that artificial sweeteners may accelerate ARG spread through digestate disposal, thus corresponding strategies should be considered to prevent potential risks in practice.}, } @article {pmid37471436, year = {2023}, author = {Zhong, X and Xu, M and Li, T and Sun, R}, title = {Development of EST-SSRs based on the transcriptome of Castanopsis carlesii and cross-species transferability in other Castanopsis species.}, journal = {PloS one}, volume = {18}, number = {7}, pages = {e0288999}, pmid = {37471436}, issn = {1932-6203}, mesh = {Humans ; *Transcriptome/genetics ; Expressed Sequence Tags ; Genetic Markers/genetics ; *Polymorphism, Genetic ; Microsatellite Repeats/genetics ; Databases, Protein ; }, abstract = {Castanopsis carlesii (Hemsl.) Hay. is a widely distributed and dominant tree species native to subtropical China with significant ecological and economic value. Due to serious human-related disturbance, its wild resources have been increasingly reduced, and whether may result in the loss of genetic diversity. However, no population genetics studies of natural C. carlesii have been reported to date. Microsatellite markers have been a useful tool in population genetics. Therefore, we developed EST-SSR markers based on the transcriptome sequencing of C. carlesii leaves. A total of 149,380,224 clean reads were obtained, and 63,012 nonredundant unigenes with a mean length of 1,034 bp were assembled and annotated based on sequence similarity searches in the Nr, Nt, KO, SwissProt, PFAM, KOG, and GO databases. The results showed that only 5,559 (8.82%) unigenes were annotated in all seven databases, but 46,338 (73.53%) could be annotated in at least one database. A total of 31,459 potential EST-SSRs were identified in 18,690 unigenes, with an average frequency of one SSR approximately 2 kb. Among the 100 EST-SSR primer pairs designed, 49 primer pairs successfully produced the expected product by amplification, with a success rate of 49%, but only 20 primer pairs showed abundant polymorphisms. Polymorphisms were verified using 25 samples from C. carlesii in Qimen, Anhui. A total of 119 alleles were detected, with a mean number of alleles (Na) of 5.95 per locus and a mean polymorphism information content (PIC) of 0.6125. All the 20 newly developed EST-SSR markers were verified in other Castanopsis species (C. sclerophylla, C. lamontii, C. fargesii, C. eyrei and C. jucunda). Sixteen primer pairs showed successful amplification in all five Castanopsis species (80%), and the transferability ratios ranged from 90% to 100%. These developed EST-SSR markers can be applied to population genetic and germplasm evaluations of C. carlesii and related species.}, } @article {pmid37471432, year = {2023}, author = {Alwan, NA and Clutterbuck, D and Pantelic, M and Hayer, J and Fisher, L and Hishmeh, L and Heightman, M and Allsopp, G and Wootton, D and Khan, A and Hastie, C and Jackson, M and Rayner, C and Brown, D and Parrett, E and Jones, G and Smith, K and Clarke, R and Mcfarland, S and Gabbay, M and Banerjee, A and , }, title = {Long Covid active case finding study protocol: A co-produced community-based pilot within the STIMULATE-ICP study (Symptoms, Trajectory, Inequalities and Management: Understanding Long-COVID to Address and Transform Existing Integrated Care Pathways).}, journal = {PloS one}, volume = {18}, number = {7}, pages = {e0284297}, pmid = {37471432}, issn = {1932-6203}, mesh = {Humans ; *COVID-19/epidemiology ; Post-Acute COVID-19 Syndrome ; Pilot Projects ; *Delivery of Health Care, Integrated ; United Kingdom ; }, abstract = {BACKGROUND AND AIM: Long Covid is a significant public health concern with potentially negative implications for health inequalities. We know that those who are already socially disadvantaged in society are more exposed to COVID-19, experience the worst health outcomes and are more likely to suffer economically. We also know that these groups are more likely to experience stigma and have negative healthcare experiences even before the pandemic. However, little is known about disadvantaged groups' experiences of Long Covid, and preliminary evidence suggests they may be under-represented in those who access formal care. We will conduct a pilot study in a defined geographical area in London, United Kingdom to test the feasibility of a community-based approach of identifying Long Covid cases that have not been clinically diagnosed and have not been referred to Long Covid specialist services. We will explore the barriers to accessing recognition, care, and support, as well as experiences of stigma and perceived discrimination.

METHODS: This protocol and study materials were co-produced with a Community Advisory Board (CAB) made up primarily of people living with Long Covid. Working with voluntary organisations, a study leaflet will be distributed in the local community to highlight Long Covid symptoms and invite those experiencing them to participate in the study if they are not formally diagnosed. Potential participants will be assessed according to the study's inclusion criteria and offered the opportunity to participate if they fit them. Awareness of Long Covid and associated symptoms, experiences of trying to access care, as well as stigma and discrimination will be explored through qualitative interviews with participants. Upon completion of the interviews, participants will be offered a referral to the local social prescribing team to receive support that is personalised to them potentially including, but not restricted to, liaising with their primary care provider and the regional Long Covid clinic.}, } @article {pmid37469857, year = {2023}, author = {Boyes, D and Holland, PWH and , and , and , and , and , and , }, title = {The genome sequence of the Oak-tree Pug, Eupithecia dodoneata (Guenée, 1858).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {133}, pmid = {37469857}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual male Eupithecia dodoneata (the Oak-tree Pug; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 353.7 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the assembled Z sex chromosome. The mitochondrial genome has also been assembled and is 15.3 kilobases in length.}, } @article {pmid37468639, year = {2023}, author = {Caglayan, E and Ayhan, F and Liu, Y and Vollmer, RM and Oh, E and Sherwood, CC and Preuss, TM and Yi, SV and Konopka, G}, title = {Molecular features driving cellular complexity of human brain evolution.}, journal = {Nature}, volume = {620}, number = {7972}, pages = {145-153}, pmid = {37468639}, issn = {1476-4687}, support = {R24 NS092988/NS/NINDS NIH HHS/United States ; R01 MH103517/MH/NIMH NIH HHS/United States ; R01 MH126481/MH/NIMH NIH HHS/United States ; R01 HG011641/HG/NHGRI NIH HHS/United States ; T32 HL139438/HL/NHLBI NIH HHS/United States ; P51 OD011132/OD/NIH HHS/United States ; }, mesh = {Animals ; Humans ; Cell Nucleus/metabolism ; Chromatin/genetics/metabolism ; Datasets as Topic ; *Evolution, Molecular ; Genome, Human/genetics ; Genomics ; *Gyrus Cinguli/cytology/metabolism ; Macaca mulatta/genetics ; Neurons/classification/cytology ; Oligodendroglia/cytology/metabolism ; Pan troglodytes/genetics ; Single-Cell Gene Expression Analysis ; Stem Cells/cytology ; Transposases/metabolism ; Chromatin Assembly and Disassembly ; }, abstract = {Human-specific genomic changes contribute to the unique functionalities of the human brain[1-5]. The cellular heterogeneity of the human brain[6,7] and the complex regulation of gene expression highlight the need to characterize human-specific molecular features at cellular resolution. Here we analysed single-nucleus RNA-sequencing and single-nucleus assay for transposase-accessible chromatin with sequencing datasets for human, chimpanzee and rhesus macaque brain tissue from posterior cingulate cortex. We show a human-specific increase of oligodendrocyte progenitor cells and a decrease of mature oligodendrocytes across cortical tissues. Human-specific regulatory changes were accelerated in oligodendrocyte progenitor cells, and we highlight key biological pathways that may be associated with the proportional changes. We also identify human-specific regulatory changes in neuronal subtypes, which reveal human-specific upregulation of FOXP2 in only two of the neuronal subtypes. We additionally identify hundreds of new human accelerated genomic regions associated with human-specific chromatin accessibility changes. Our data also reveal that FOS::JUN and FOX motifs are enriched in the human-specifically accessible chromatin regions of excitatory neuronal subtypes. Together, our results reveal several new mechanisms underlying the evolutionary innovation of human brain at cell-type resolution.}, } @article {pmid37467926, year = {2023}, author = {Otálora, P and Guzmán, JL and Acién, FG and Berenguel, M and Reul, A}, title = {An artificial intelligence approach for identification of microalgae cultures.}, journal = {New biotechnology}, volume = {77}, number = {}, pages = {58-67}, doi = {10.1016/j.nbt.2023.07.003}, pmid = {37467926}, issn = {1876-4347}, mesh = {*Artificial Intelligence ; *Microalgae ; Neural Networks, Computer ; Biomass ; }, abstract = {In this work, a model for the characterization of microalgae cultures based on artificial neural networks has been developed. The characterization of microalgae cultures is essential to guarantee the quality of the biomass, and the objective of this work is to achieve a simple and fast method to address this issue. Data acquisition was performed using FlowCam, a device capable of capturing images of the cells detected in a culture sample, which are used as inputs by the model. The model can distinguish between 6 different genera of microalgae, having been trained with several species of each genus. It was further complemented with a classification threshold to discard unwanted objects while improving the overall accuracy of the model. The model achieved an accuracy of up to 97.27% when classifying a culture. The results demonstrate the effectiveness of the Deep Learning models for the characterization of microalgae cultures, it being a useful tool for the monitoring of microalgae cultures in large-scale production facilities while providing accurate characterization over a wide range of genera.}, } @article {pmid37467038, year = {2023}, author = {Sommerhoff, A and Ehring, T and Takano, K}, title = {Effects of Induced Mindfulness at Night on Repetitive Negative Thinking: Ecological Momentary Assessment Study.}, journal = {JMIR mental health}, volume = {10}, number = {}, pages = {e44365}, pmid = {37467038}, issn = {2368-7959}, abstract = {BACKGROUND: Repetitive negative thinking (RNT) is a cognitive risk factor for various disorders. Although brief mindfulness-based interventions (MBIs; lasting 20-30 minutes or shorter) are effective tools to reduce RNT, the effect of a minimal (5-minute) MBI remains largely unknown.

OBJECTIVE: We investigated the acute changes in RNT induced by a 10-day minimal MBI (body scan before sleeping) using an ecological momentary assessment (EMA) administered during the MBI training phase. In addition, we examined longer-term effects on the postintervention and 2-month follow-up assessments for questionnaire-based RNT and psychological distress.

METHODS: A total of 68 participants (community sample, aged 18-55 years; n=58, 85% women) were randomly allocated to either the intervention group (n=35, 51%) or the no-training control group (n=33, 49%). Both groups completed a 10-day EMA phase of RNT, during which only the intervention group performed a daily 5-minute body scan before sleeping.

RESULTS: The intervention group showed a significantly larger reduction in questionnaire-based RNT than the control group at the follow-up assessment (for growth-curve modeling analysis [GMA], dGMA=-0.91; P<.001), but this effect was not observed during the EMA phase or at the postintervention assessment. Furthermore, the intervention group showed significantly larger decreases in stress both at the postintervention (dGMA=-0.78; P<.001) and follow-up (dGMA=-0.60; P<.001) assessments than the control group. We found no intervention effects on depressive and anxiety symptoms.

CONCLUSIONS: A 5-minute body scan before sleeping reduces RNT and stress when continued for at least 10 days; however, the results suggest that this effect only appears with some time lag because no acute changes during and immediately after the intervention emerged for RNT.}, } @article {pmid37466563, year = {2023}, author = {Xavier, DR and Albuquerque, MP and Sousa-Carmo, SVT and Pinter, A}, title = {Evaluation of completeness and timeliness of data in the National Information System for Notifiable Diseases for spotted fever in the state of São Paulo, Brazil, 2007-2017.}, journal = {Epidemiologia e servicos de saude : revista do Sistema Unico de Saude do Brasil}, volume = {32}, number = {2}, pages = {e2022416}, pmid = {37466563}, issn = {2237-9622}, mesh = {Humans ; *Population Surveillance/methods ; Brazil/epidemiology ; Disease Notification ; *Spotted Fever Group Rickettsiosis ; Information Systems ; }, abstract = {OBJECTIVE: to evaluate the completeness and timeliness of notifications of cases of spotted fever (SF) held on the Notifiable Health Conditions Information System (SINAN) in São Paulo State, Brazil, from 2007 to 2017.

METHODS: this was a descriptive and ecological study of confirmed human cases of SF regarding completeness and timeliness of ten fields of the notification form (good if ≥ 90% for most variables); time series analysis was performed using the Prais-Winsten technique.

RESULTS: we analyzed 736 records; among essential fields, only "Discharge date" showed poor completeness (68.5%). Timeliness was good for the "Investigation" and "Closure" fields; other time lapses were not adequate.

CONCLUSION: in São Paulo state, data completeness was good for most variables, whereas timeliness was not adequate (except for "Closure" and "Investigation"), pointing to the need for health education and communication actions about SF.}, } @article {pmid37466561, year = {2023}, author = {Barbosa, JS and Tartaro, L and Vasconcelos, LDR and Nedel, M and Serafini, JF and Svirski, SGS and Souza, LS and Agranonik, M}, title = {Assessment of incompleteness of Mortality Information System records on deaths from external causes in the state of Rio Grande do Sul, Brazil, 2000-2019.}, journal = {Epidemiologia e servicos de saude : revista do Sistema Unico de Saude do Brasil}, volume = {32}, number = {2}, pages = {e2022301}, pmid = {37466561}, issn = {2237-9622}, mesh = {Humans ; Brazil/epidemiology ; *Suicide ; Information Systems ; Skin Pigmentation ; }, abstract = {OBJECTIVE: to evaluate the incompleteness of Mortality Information System (Sistema de Informações sobre Mortalidade - SIM) data on deaths from external causes (ECs) in the state of Rio Grande do Sul, Brazil, 2000-2019.

METHODS: This was an ecological study, using SIM data on all deaths from external causes and, specifically, from transport accident, homicides, suicides and falls; the analysis of the trend of incompleteness was performed by means of Prais-Winsten regression, with a 5% significance level.

RESULTS: A total of 146,882 deaths were evaluated; sex (0.1%), place of death (0.1%) and age (0.4%) showed the lowest incompleteness in 2019; the proportion of incompleteness showed a decreasing trend for the place of death and schooling, an increasing trend for marital status and a stable trend for age and race/skin color, among all types of death evaluated.

CONCLUSION: the variables analyzed reached a high degree of completion; with the exception of marital status and schooling, for which unsatisfactory scores persisted for deaths from ECs, both total and by subgroups.}, } @article {pmid37465614, year = {2023}, author = {Asefa, A and Reuber, V and Miehe, G and Wraase, L and Wube, T and Schabo, DG and Farwig, N}, title = {Human activities modulate reciprocal effects of a subterranean ecological engineer rodent, Tachyoryctes macrocephalus, on Afroalpine vegetation cover.}, journal = {Ecology and evolution}, volume = {13}, number = {7}, pages = {e10337}, pmid = {37465614}, issn = {2045-7758}, abstract = {Human activities, directly and indirectly, impact ecological engineering activities of subterranean rodents. As engineering activities of burrowing rodents are affected by, and reciprocally affect vegetation cover via feeding, burrowing and mound building, human influence such as settlements and livestock grazing, could have cascading effects on biodiversity and ecosystem processes such as bioturbation. However, there is limited understanding of the relationship between human activities and burrowing rodents. The aim of this study was therefore to understand how human activities influence the ecological engineering activity of the giant root-rat (Tachyoryctes macrocephalus), a subterranean rodent species endemic to the Afroalpine ecosystem of the Bale Mountains of Ethiopia. We collected data on human impact, burrowing activity and vegetation during February and March of 2021. Using path analysis, we tested (1) direct effects of human settlement on the patterns of livestock grazing intensity, (2) direct and indirect impacts of humans and livestock grazing intensity on the root-rat burrow density and (3) whether human settlement and livestock grazing influence the effects of giant root-rat burrow density on vegetation and vice versa. We found lower levels of livestock grazing intensity further from human settlement than in its proximity. We also found a significantly increased giant root-rat burrow density with increasing livestock grazing intensity. Seasonal settlement and livestock grazing intensity had an indirect negative and positive effect on giant root-rat burrow density, respectively, both via vegetation cover. Analysing the reciprocal effects of giant root-rat on vegetation, we found a significantly decreased vegetation cover with increasing density of giant root-rat burrows, and indirectly with increasing livestock grazing intensity via giant root-rat burrow density. Our results demonstrate that giant root-rats play a synanthropic engineering role that affects vegetation structure and ecosystem processes.}, } @article {pmid37463417, year = {2023}, author = {Williams, TA and Davín, AA and Morel, B and Szánthó, LL and Spang, A and Stamatakis, A and Hugenholtz, P and Szöllősi, GJ}, title = {Parameter Estimation and Species Tree Rooting Using ALE and GeneRax.}, journal = {Genome biology and evolution}, volume = {15}, number = {7}, pages = {}, pmid = {37463417}, issn = {1759-6653}, mesh = {Phylogeny ; *Algorithms ; *Evolution, Molecular ; Gene Duplication ; Bacteria/genetics ; Eukaryota ; Models, Genetic ; }, abstract = {ALE and GeneRax are tools for probabilistic gene tree-species tree reconciliation. Based on a common underlying statistical model of how gene trees evolve along species trees, these methods rely on gene vs. species tree discordance to infer gene duplication, transfer, and loss events, map gene family origins, and root species trees. Published analyses have used these methods to root species trees of Archaea, Bacteria, and several eukaryotic groups, as well as to infer ancestral gene repertoires. However, it was recently suggested that reconciliation-based estimates of duplication and transfer events using the ALE/GeneRax model were unreliable, with potential implications for species tree rooting. Here, we assess these criticisms and find that the methods are accurate when applied to simulated data and in generally good agreement with alternative methodological approaches on empirical data. In particular, ALE recovers variation in gene duplication and transfer frequencies across lineages that is consistent with the known biology of studied clades. In plants and opisthokonts, ALE recovers the consensus species tree root; in Bacteria-where there is less certainty about the root position-ALE agrees with alternative approaches on the most likely root region. Overall, ALE and related approaches are promising tools for studying genome evolution.}, } @article {pmid37461608, year = {2023}, author = {Compton, ZT and Harris, V and Mellon, W and Rupp, S and Mallo, D and Kapsetaki, SE and Wilmot, M and Kennington, R and Noble, K and Baciu, C and Ramirez, L and Peraza, A and Martins, B and Sudhakar, S and Aksoy, S and Furukawa, G and Vincze, O and Giraudeau, M and Duke, EG and Spiro, S and Flach, E and Davidson, H and Zehnder, A and Graham, TA and Troan, B and Harrison, TM and Tollis, M and Schiffman, JD and Aktipis, A and Abegglen, LM and Maley, CC and Boddy, AM}, title = {Cancer Prevalence Across Vertebrates.}, journal = {Research square}, volume = {}, number = {}, pages = {}, pmid = {37461608}, issn = {2693-5015}, support = {U54 CA217376/CA/NCI NIH HHS/United States ; T32 CA272303/CA/NCI NIH HHS/United States ; U2C CA233254/CA/NCI NIH HHS/United States ; P01 CA091955/CA/NCI NIH HHS/United States ; R01 CA140657/CA/NCI NIH HHS/United States ; }, abstract = {Cancer is pervasive across multicellular species, but what explains differences in cancer prevalence across species? Using 16,049 necropsy records for 292 species spanning three clades (amphibians, sauropsids and mammals) we found that neoplasia and malignancy prevalence increases with adult weight (contrary to Peto's Paradox) and somatic mutation rate, but decreases with gestation time. Evolution of cancer susceptibility appears to have undergone sudden shifts followed by stabilizing selection. Outliers for neoplasia prevalence include the common porpoise (<1.3%), the Rodrigues fruit bat (<1.6%) the black-footed penguin (<0.4%), ferrets (63%) and opossums (35%). Discovering why some species have particularly high or low levels of cancer may lead to a better understanding of cancer syndromes and novel strategies for the management and prevention of cancer.}, } @article {pmid37455607, year = {2023}, author = {Hutchins, L and Mc Cartney, A and Graham, N and Gillespie, R and Guzman, A}, title = {Arthropods are kin: Operationalizing Indigenous data sovereignty to respectfully utilize genomic data from Indigenous lands.}, journal = {Molecular ecology resources}, volume = {}, number = {}, pages = {}, doi = {10.1111/1755-0998.13822}, pmid = {37455607}, issn = {1755-0998}, support = {//Berkeley Food Institute Faculty Seed Grant/ ; //National Science Foundation Innovations at the Nexus of Food, Energy, and Water Systems/ ; }, abstract = {Indigenous peoples have cultivated biodiverse agroecosystems since time immemorial. The rise of metagenomics and high-throughput sequencing technologies in biodiversity studies has rapidly expanded the scale of data collection from these lands. A respectful approach to the data life cycle grounded in the sovereignty of indigenous communities is imperative to not perpetuate harm. In this paper, we operationalize an indigenous data sovereignty (IDS) framework to outline realistic considerations for genomic data that span data collection, governance, and communication. As a case study for this framework, we use arthropod genomic data collected from diversified and simplified farm sites close to and far from natural habitats within a historic Kānaka 'Ōiwi (Indigenous Hawaiian) agroecosystem. Diversified sites had the highest Operational Taxonomic Unit (OTU) richness for native and introduced arthropods. There may be a significant spillover effect between forest and farm sites, as farm sites near a natural habitat had higher OTU richness than those farther away. We also provide evidence that management factors such as the number of Polynesian crops cultivated may drive arthropod community composition. Through this case study, we emphasize the context-dependent opportunities and challenges for operationalizing IDS by utilizing participatory research methods, expanding novel data management tools through the Local Contexts Hub, and developing and nurturing community partnerships-all while highlighting the potential of agroecosystems for arthropod conservation. Overall, the workflow and the example presented here can help researchers take tangible steps to achieve IDS, which often seems elusive with the expanding use of genomic data.}, } @article {pmid37454924, year = {2023}, author = {Le, DH and Nguyen, TH and Takasu, F}, title = {Spatial metapopulation dynamics with local and global colonization.}, journal = {Journal of theoretical biology}, volume = {572}, number = {}, pages = {111579}, doi = {10.1016/j.jtbi.2023.111579}, pmid = {37454924}, issn = {1095-8541}, abstract = {We revisit a spatial metapopulation model on continuous space as a stochastic point pattern dynamics. In the model, local patches as points are distributed with a certain spatial configuration and status of each patch changes stochastically between occupied and empty: an occupied patch becomes empty by local extinction and an empty patch becomes occupied both by local and global colonization. We carry out simulation analysis and derive an analytical model in terms of singlet, pair and triplet probabilities that describe the stochastic dynamics. Using a simple closure that approximates triplet probabilities by singlet and pair probabilities, we show that equilibrium singlet and pair probabilities can be analytically derived. The derived equilibrium properties successfully describe simulation results under a certain condition where the range of local colonization and the proportion of global colonization play key roles. Our model is an extension of the classical non-spatial Levins model to a spatially explicit metapopulation model. We appeal the advantage of point pattern approach to study spatial dynamics in general ecology and call for the need to deepen our understanding of mathematical tools to explore point pattern dynamics.}, } @article {pmid37454795, year = {2023}, author = {Đokić, M and Manić, M and Đorđević, M and Gocić, M and Čupić, A and Jović, M and Dragović, R and Gajić, B and Smičiklas, I and Dragović, S}, title = {Remote sensing and nuclear techniques for high-resolution mapping and quantification of gully erosion in the highly erodible area of the Malčanska River Basin, Eastern Serbia.}, journal = {Environmental research}, volume = {235}, number = {}, pages = {116679}, doi = {10.1016/j.envres.2023.116679}, pmid = {37454795}, issn = {1096-0953}, mesh = {*Remote Sensing Technology ; *Ecosystem ; Geographic Information Systems ; Conservation of Natural Resources/methods ; Rivers ; Serbia ; Soil ; }, abstract = {Gully erosion leads to the formation of deep and wide channels that increase the risk of soil loss, flooding, and water pollution. In addition, this process reduces the productivity and viability of agricultural land and natural ecosystems. Preventing gully erosion is critical for maintaining ecological balance and preserving natural resources in certain areas. This paper presents a methodology integrating remote sensing and nuclear techniques to study gully erosion. The morphometric characterization of gullies using 360-degree camera photogrammetry was introduced as a new method in erosion research. This approach aims to investigate the suitability of unmanned aerial vehicle and terrestrial photogrammetry for modeling gullies, to study the variability of erosion processes in gullies at a small scale, and to compare the differences in erosion intensity between nearby gullies. The study's objectives include identifying the effective and economical method for gullies monitoring and providing a starting point for controlling and safeguarding gullies. Mainly erosion process was detected in the studied gullies, while deposition was identified at only 2 out of 39 sampling locations. The results showed an average soil redistribution rate of 16.2 t ha[-1] yr[-1] and coefficients of variation of 32%, 59%, and 91% for three investigated gullies. It was determined that aerial photogrammetry methods were not practical under the conditions prevailing in the study area. Highly detailed 3D models of the gullies were created using 360-degree photogrammetry. It was confirmed that the micro-relief obtained by photogrammetric modeling is an essential contribution to erosion research. The 360-degree camera photogrammetry serves as a reliable tool for analyzing the morphology of gullies and, in perspective, tracking changes in gully systems over time or monitoring the effectiveness of the applied protection measures.}, } @article {pmid37454715, year = {2023}, author = {Wu, X and Zhang, X and Chen, X and Ye, A and Cao, J and Hu, X and Zhou, W}, title = {The effects of polylactic acid bioplastic exposure on midgut microbiota and metabolite profiles in silkworm (Bombyx mori): An integrated multi-omics analysis.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {334}, number = {}, pages = {122210}, doi = {10.1016/j.envpol.2023.122210}, pmid = {37454715}, issn = {1873-6424}, mesh = {Animals ; *Bombyx ; Multiomics ; Prospective Studies ; Polyesters/toxicity/metabolism ; Biopolymers/metabolism ; *Microbiota ; Larva ; }, abstract = {Polylactic acid (PLA) is a highly common biodegradable plastic and a potential threat to health and the environment. However, limited data are available on the effects of PLA exposure in the silkworm (Bombyx mori), a model organism used in toxicity studies. In this study, silkworms with or without PLA exposure (P1: 1 mg/L, P5: 5 mg/L, P25: 25 mg/L, and P0: 0 mg/L) for the entire 5th instar period were used to investigate the impact of PLA exposure on midgut morphology, larvae growth, and survival. Mitochondrial damage was observed in the P5 and P25 groups. The weights of the P25 posterior silk gland (5th day in the 5th instar), mature larvae and pupae were all significantly lower than those of the controls (P < 0.05). Dead worm cocoon rates and larva-pupa to 5th instar larvae ratios showed a positive and negative dose-dependent manner with respect to PLA concentrations, respectively. Additionally, reactive oxygen species levels and superoxide dismutase activity of the P25 midgut were significantly higher and lower when compared with controls, respectively (P < 0.05). The molecular mechanisms underlying the effects of PLA and associated physiological responses were also investigated. In the midgut metabolome, 127 significantly different metabolites (variable importance projection >1 and P < 0.05) were identified between the P0 and P25 groups and were mainly enriched for amino acid metabolism and energy supply pathways. The 16 S rDNA data showed that PLA altered microbial richness and structural composition. Microbiota, classified into 34 genera and 63 species, were significantly altered after 25 mg/L PLA exposure (P < 0.05). Spearman's correlation results showed that Bifidobacterium catenulatum and Schaalia odontolytica played potentially vital roles during exposure, as they demonstrated stronger correlations with the significantly different metabolites than other bacterial species. In sum, PLA induced toxic effects on silkworms, especially on energy- and protein-relevant metabolism, but at high concentrations (25 mg/L). This prospective mechanistic investigation on the effects of PLA on larval toxicity provides novel insight regarding the ecological risks of biodegradable plastics in the environment.}, } @article {pmid37448139, year = {2023}, author = {Ewers, I and Rajter, L and Czech, L and Mahé, F and Stamatakis, A and Dunthorn, M}, title = {Interpreting phylogenetic placements for taxonomic assignment of environmental DNA.}, journal = {The Journal of eukaryotic microbiology}, volume = {70}, number = {5}, pages = {e12990}, doi = {10.1111/jeu.12990}, pmid = {37448139}, issn = {1550-7408}, mesh = {*DNA, Environmental ; Phylogeny ; }, abstract = {Taxonomic assignment of operational taxonomic units (OTUs) is an important bioinformatics step in analyzing environmental sequencing data. Pairwise alignment and phylogenetic-placement methods represent two alternative approaches to taxonomic assignments, but their results can differ. Here we used available colpodean ciliate OTUs from forest soils to compare the taxonomic assignments of VSEARCH (which performs pairwise alignments) and EPA-ng (which performs phylogenetic placements). We showed that when there are differences in taxonomic assignments between pairwise alignments and phylogenetic placements at the subtaxon level, there is a low pairwise similarity of the OTUs to the reference database. We then showcase how the output of EPA-ng can be further evaluated using GAPPA to assess the taxonomic assignments when there exist multiple equally likely placements of an OTU, by taking into account the sum over the likelihood weights of the OTU placements within a subtaxon, and the branch distances between equally likely placement locations. We also inferred the evolutionary and ecological characteristics of the colpodean OTUs using their placements within subtaxa. This study demonstrates how to fully analyze the output of EPA-ng, by using GAPPA in conjunction with knowledge of the taxonomic diversity of the clade of interest.}, } @article {pmid37447657, year = {2023}, author = {Li, J and Cai, Y and Gong, X and Jiang, J and Lu, Y and Meng, X and Zhang, L}, title = {Semantic Retrieval of Remote Sensing Images Based on the Bag-of-Words Association Mapping Method.}, journal = {Sensors (Basel, Switzerland)}, volume = {23}, number = {13}, pages = {}, pmid = {37447657}, issn = {1424-8220}, support = {41961063//National Natural Science Foundation of China/ ; }, mesh = {*Algorithms ; *Semantics ; Remote Sensing Technology ; Information Storage and Retrieval ; Pattern Recognition, Automated/methods ; }, abstract = {With the increasing demand for remote sensing image applications, extracting the required images from a huge set of remote sensing images has become a hot topic. The previous retrieval methods cannot guarantee the efficiency, accuracy, and interpretability in the retrieval process. Therefore, we propose a bag-of-words association mapping method that can explain the semantic derivation process of remote sensing images. The method constructs associations between low-level features and high-level semantics through visual feature word packets. An improved FP-Growth method is proposed to achieve the construction of strong association rules to semantics. A feedback mechanism is established to improve the accuracy of subsequent retrievals by reducing the semantic probability of incorrect retrieval results. The public datasets AID and NWPU-RESISC45 were used to validate these experiments. The experimental results show that the average accuracies of the two datasets reach 87.5% and 90.8%, which are 22.5% and 20.3% higher than VGG16, and 17.6% and 15.6% higher than ResNet18, respectively. The experimental results were able to validate the effectiveness of our proposed method.}, } @article {pmid37443081, year = {2023}, author = {Sharo, AG and Zou, Y and Adhikari, AN and Brenner, SE}, title = {ClinVar and HGMD genomic variant classification accuracy has improved over time, as measured by implied disease burden.}, journal = {Genome medicine}, volume = {15}, number = {1}, pages = {51}, pmid = {37443081}, issn = {1756-994X}, support = {T32 GM008295/GM/NIGMS NIH HHS/United States ; U19 HD077627/HD/NICHD NIH HHS/United States ; HD077627/NH/NIH HHS/United States ; U41 HG007346/HG/NHGRI NIH HHS/United States ; U24 HG007346/HG/NHGRI NIH HHS/United States ; }, mesh = {*Genetic Variation ; *Databases, Genetic ; Gene Frequency ; Genotype ; Genomics ; }, abstract = {BACKGROUND: Curated databases of genetic variants assist clinicians and researchers in interpreting genetic variation. Yet, these databases contain some misclassified variants. It is unclear whether variant misclassification is abating as these databases rapidly grow and implement new guidelines.

METHODS: Using archives of ClinVar and HGMD, we investigated how variant misclassification has changed over 6 years, across different ancestry groups. We considered inborn errors of metabolism (IEMs) screened in newborns as a model system because these disorders are often highly penetrant with neonatal phenotypes. We used samples from the 1000 Genomes Project (1KGP) to identify individuals with genotypes that were classified by the databases as pathogenic. Due to the rarity of IEMs, nearly all such classified pathogenic genotypes indicate likely variant misclassification in ClinVar or HGMD.

RESULTS: While the false-positive rates of both ClinVar and HGMD have improved over time, HGMD variants currently imply two orders of magnitude more affected individuals in 1KGP than ClinVar variants. We observed that African ancestry individuals have a significantly increased chance of being incorrectly indicated to be affected by a screened IEM when HGMD variants are used. However, this bias affecting genomes of African ancestry was no longer significant once common variants were removed in accordance with recent variant classification guidelines. We discovered that ClinVar variants classified as Pathogenic or Likely Pathogenic are reclassified sixfold more often than DM or DM? variants in HGMD, which has likely resulted in ClinVar's lower false-positive rate.

CONCLUSIONS: Considering misclassified variants that have since been reclassified reveals our increasing understanding of rare genetic variation. We found that variant classification guidelines and allele frequency databases comprising genetically diverse samples are important factors in reclassification. We also discovered that ClinVar variants common in European and South Asian individuals were more likely to be reclassified to a lower confidence category, perhaps due to an increased chance of these variants being classified by multiple submitters. We discuss features for variant classification databases that would support their continued improvement.}, } @article {pmid37440444, year = {2023}, author = {Pokolm, M and Kirchhain, M and Müller, D and Jordet, G and Memmert, D}, title = {Head movement direction in football - a field study on visual scanning activity during the UEFA-U17 and -U21 European Championship 2019.}, journal = {Journal of sports sciences}, volume = {41}, number = {7}, pages = {695-705}, doi = {10.1080/02640414.2023.2235160}, pmid = {37440444}, issn = {1466-447X}, mesh = {Humans ; *Soccer ; Head Movements ; Visual Perception ; Foot ; }, abstract = {Visual exploration (scanning) of one's environment is a key aspect in team sports. Based on Gibson's (1979) ecological approach of visual perception, this study aims to advance the understanding of scanning by focusing on the direction of head movements in football and its implications for subsequent on-ball actions. The video-based data analysis consisted of nine selected matches and 162 players of the Union of European Football Associations (UEFA) U17 and U21 European Championship 2019. The results indicate that the direction of the last scan prior to receiving the ball is related to the foot used for the first ball contact. This relationship was further analysed in view of the game context (direction of play and opponent pressure) and with information about the player's dominant foot. The findings reveal a relationship between the direction of the last scan before receiving the ball and the direction the game is proceeded in. Further, when a player performs the last scan to the side of their dominant foot, the probability increases that their dominant foot is used for the subsequent first ball contact. Depending on the direction of the last scan, opponent pressure had various effects on the foot used for the first contact.}, } @article {pmid37438069, year = {2023}, author = {Yao, L and Yang, Y and Wang, Z and Pan, X and Xu, L}, title = {Compliance with ecological momentary assessment programmes in the elderly: a systematic review and meta-analysis.}, journal = {BMJ open}, volume = {13}, number = {7}, pages = {e069523}, pmid = {37438069}, issn = {2044-6055}, mesh = {Aged ; Humans ; *Ecological Momentary Assessment ; *Health Status ; PubMed ; Publication Bias ; Research Personnel ; }, abstract = {OBJECTIVE: Ecological momentary assessment (EMA) refers to the repeated sampling of information about an individual's symptoms and behaviours, enabling the capture of ecologically meaningful real-time information in a timely manner. Compliance with EMA is critical in determining the validity of an assessment. However, there is limited evidence related to how the elderly comply with EMA programmes or the factors that are associated with compliance.

DESIGN: Systematic review and meta-analysis.

DATA SOURCES: PubMed, Embase, the Cochrane Library and Web of Science were searched up to 17 July 2022.

ELIGIBILITY CRITERIA: We included observational studies on EMA in the elderly reported in English.

DATA EXTRACTION AND SYNTHESIS: Two investigators independently performed screening and data extraction. Discrepancies were resolved by discussion or a third investigator. A systematic review was carried out to characterise the basic characteristics of the participants and EMA programmes. Random-effects meta-analysis was conducted to assess overall compliance and to explore factors associated with differences in compliance among the elderly.

RESULTS: A total of 20 studies with 2047 participants were included in the systematic review and meta-analysis. Meta-analysis showed that the combined compliance rate was 86.41% (95% CI: 77.38% to 92.20%; I[2]=96.4%; p<0.001). Subgroup analysis revealed high levels of heterogeneity in terms of the methods used to assess population classification, assessment method and assessment frequency, although these may not be the sources of heterogeneity. Meta-regression analysis showed that population classification and assessment period might have a significant impact on heterogeneity (p<0.05). Egger's test indicated significant publication bias (p<0.001).

CONCLUSIONS: Compliance with EMA programmes is high in the elderly. It is recommended that scholars design reasonable EMA programmes according to the health status of the elderly in the future.}, } @article {pmid37437086, year = {2023}, author = {Hua, QQH and Young, C and Pukala, TL and Martino, JC and Hoffmann, P and Gillanders, BM and Doubleday, ZA}, title = {Better late than never: Optimising the proteomic analysis of field-collected octopus.}, journal = {PloS one}, volume = {18}, number = {7}, pages = {e0288084}, pmid = {37437086}, issn = {1932-6203}, mesh = {Animals ; *Octopodiformes ; Proteomics ; Chromatography, Liquid ; Computational Biology ; Electrophoresis, Polyacrylamide Gel ; Fixatives ; }, abstract = {Proteomics, the temporal study of proteins expressed by an organism, is a powerful technique that can reveal how organisms respond to biological perturbations, such as disease and environmental stress. Yet, the use of proteomics for addressing ecological questions has been limited, partly due to inadequate protocols for the sampling and preparation of animal tissues from the field. Although RNAlater is an ideal alternative to freezing for tissue preservation in transcriptomics studies, its suitability for the field could be more broadly examined. Moreover, existing protocols require samples to be preserved immediately to maintain protein integrity, yet the effects of delays in preservation on proteomic analyses have not been thoroughly tested. Hence, we optimised a proteomic workflow for wild-caught samples. First, we conducted a preliminary in-lab test using SDS-PAGE analysis on aquaria-reared Octopus berrima confirming that RNAlater can effectively preserve proteins up to 6 h after incubation, supporting its use in the field. Subsequently, we collected arm tips from wild-caught Octopus berrima and preserved them in homemade RNAlater immediately, 3 h, and 6 h after euthanasia. Processed tissue samples were analysed by liquid chromatography tandem mass spectrometry to ascertain protein differences between time delay in tissue preservation, as well as the influence of sex, tissue type, and tissue homogenisation methods. Over 3500 proteins were identified from all tissues, with bioinformatic analysis revealing protein abundances were largely consistent regardless of sample treatment. However, nearly 10% additional proteins were detected from tissues homogenised with metal beads compared to liquid nitrogen methods, indicating the beads were more efficient at extracting proteins. Our optimised workflow demonstrates that sampling non-model organisms from remote field sites is achievable and can facilitate extensive proteomic coverage without compromising protein integrity.}, } @article {pmid37436329, year = {2023}, author = {Barros, ZDS and Rodrigues, BGM and Frota, KMG and Penha, JCD and Nascimento, FFD and Rodrigues, MTP and Mascarenhas, MDM}, title = {Syphilis detection rate trend in aged people: Brazil, 2011-2019.}, journal = {Revista brasileira de epidemiologia = Brazilian journal of epidemiology}, volume = {26}, number = {}, pages = {e230033}, pmid = {37436329}, issn = {1980-5497}, mesh = {Aged ; Humans ; Male ; Female ; *Syphilis/diagnosis/epidemiology ; Brazil/epidemiology ; Regression Analysis ; Linear Models ; Information Systems ; }, abstract = {OBJECTIVE: To analyze the trend in the detection rate of syphilis in elderly people in Brazil from 2011 to 2019.

METHODS: An ecological, time-series study with data from the Notifiable Diseases Information System. The temporal trend of syphilis detection rates was analyzed according to the Prais-Winsten linear regression method.

RESULTS: 62,765 cases of syphilis in aged people were reported. There was a growing trend in the rate of syphilis detection in aged people in Brazil. The increase was of approximately six times, with a mean increase of 25% each year (annual percent change [APC]: 25.0; 95%CI 22.1-28.1). The increase in the detection rate was identified in both genders and for all age groups, with emphasis on the increase in females (APC: 49.1; 95%CI 21.9-26.8) and in the group aged 70 to 79 years old (APC: 25.8; 95%CI 23.3-28.3). All macro-regions of the country showed an increasing trend, with emphasis on the Northeast (APC: 51.2; 95%CI 43.0-59.8) and South (APC: 49.2; 95%CI 32.3-68.3).

CONCLUSION: The growing trend in the detection rate of syphilis in aged people throughout Brazil highlights the need for planning and developing effective and multidisciplinary prevention actions and assistance adapted to this public.}, } @article {pmid37433877, year = {2023}, author = {Pairo-Castineira, E and Rawlik, K and Bretherick, AD and Qi, T and Wu, Y and Nassiri, I and McConkey, GA and Zechner, M and Klaric, L and Griffiths, F and Oosthuyzen, W and Kousathanas, A and Richmond, A and Millar, J and Russell, CD and Malinauskas, T and Thwaites, R and Morrice, K and Keating, S and Maslove, D and Nichol, A and Semple, MG and Knight, J and Shankar-Hari, M and Summers, C and Hinds, C and Horby, P and Ling, L and McAuley, D and Montgomery, H and Openshaw, PJM and Begg, C and Walsh, T and Tenesa, A and Flores, C and Riancho, JA and Rojas-Martinez, A and Lapunzina, P and , and , and , and , and Yang, J and Ponting, CP and Wilson, JF and Vitart, V and Abedalthagafi, M and Luchessi, AD and Parra, EJ and Cruz, R and Carracedo, A and Fawkes, A and Murphy, L and Rowan, K and Pereira, AC and Law, A and Fairfax, B and Hendry, SC and Baillie, JK}, title = {Author Correction: GWAS and meta-analysis identifies 49 genetic variants underlying critical COVID-19.}, journal = {Nature}, volume = {619}, number = {7971}, pages = {E61}, doi = {10.1038/s41586-023-06383-z}, pmid = {37433877}, issn = {1476-4687}, support = {MC_UU_00007/10/MRC_/Medical Research Council/United Kingdom ; MR/S01165X/1/MRC_/Medical Research Council/United Kingdom ; MR/S032304/1/MRC_/Medical Research Council/United Kingdom ; MR/V001329/1/MRC_/Medical Research Council/United Kingdom ; }, } @article {pmid37432953, year = {2023}, author = {Medina, P and Russell, SL and Corbett-Detig, R}, title = {Deep data mining reveals variable abundance and distribution of microbial reproductive manipulators within and among diverse host species.}, journal = {PloS one}, volume = {18}, number = {7}, pages = {e0288261}, pmid = {37432953}, issn = {1932-6203}, support = {R35 GM128932/GM/NIGMS NIH HHS/United States ; T32 HG008345/HG/NHGRI NIH HHS/United States ; }, mesh = {Animals ; Drosophila melanogaster/genetics ; *Arthropods ; Data Mining ; Ecology ; Reproduction ; *Wolbachia/genetics ; }, abstract = {Bacterial symbionts that manipulate the reproduction of their hosts are important factors in invertebrate ecology and evolution, and are being leveraged for host biological control. Infection prevalence restricts which biological control strategies are possible and is thought to be strongly influenced by the density of symbiont infection within hosts, termed titer. Current methods to estimate infection prevalence and symbiont titers are low-throughput, biased towards sampling infected species, and rarely measure titer. Here we develop a data mining approach to estimate symbiont infection frequencies within host species and titers within host tissues. We applied this approach to screen ~32,000 publicly available sequence samples from the most common symbiont host taxa, discovering 2,083 arthropod and 119 nematode infected samples. From these data, we estimated that Wolbachia infects approximately 44% of all arthropod and 34% of all nematode species, while other reproductive manipulators only infect 1-8% of arthropod and nematode species. Although relative titers within hosts were highly variable within and between arthropod species, a combination of arthropod host species and Wolbachia strain explained approximately 36% of variation in Wolbachia titer across the dataset. To explore potential mechanisms for host control of symbiont titer, we leveraged population genomic data from the model system Drosophila melanogaster. In this host, we found a number of SNPs associated with titer in candidate genes potentially relevant to host interactions with Wolbachia. Our study demonstrates that data mining is a powerful tool to detect bacterial infections and quantify infection intensities, thus opening an array of previously inaccessible data for further analysis in host-symbiont evolution.}, } @article {pmid37430538, year = {2023}, author = {Zhang, R and Zou, X and Deng, X and Wang, Z and Chen, Y and Lin, C and Xing, H and Dai, F}, title = {Fast and Accurate ROI Extraction for Non-Contact Dorsal Hand Vein Detection in Complex Backgrounds Based on Improved U-Net.}, journal = {Sensors (Basel, Switzerland)}, volume = {23}, number = {10}, pages = {}, pmid = {37430538}, issn = {1424-8220}, support = {IEC\NSFC\191320//International Exchanges 2019 Cost Share (NSFC)/ ; }, mesh = {*Hand/diagnostic imaging ; *Veins/diagnostic imaging ; Image Processing, Computer-Assisted ; Information Storage and Retrieval ; Normal Distribution ; }, abstract = {In response to the difficulty of traditional image processing methods to quickly and accurately extract regions of interest from non-contact dorsal hand vein images in complex backgrounds, this study proposes a model based on an improved U-Net for dorsal hand keypoint detection. The residual module was added to the downsampling path of the U-Net network to solve the model degradation problem and improve the feature information extraction ability of the network; the Jensen-Shannon (JS) divergence loss function was used to supervise the final feature map distribution so that the output feature map tended to Gaussian distribution and improved the feature map multi-peak problem; and Soft-argmax is used to calculate the keypoint coordinates of the final feature map to realize end-to-end training. The experimental results showed that the accuracy of the improved U-Net network model reached 98.6%, which was 1% better than the original U-Net network model; the improved U-Net network model file was only 1.16 M, which achieved a higher accuracy than the original U-Net network model with significantly reduced model parameters. Therefore, the improved U-Net model in this study can realize dorsal hand keypoint detection (for region of interest extraction) for non-contact dorsal hand vein images and is suitable for practical deployment in low-resource platforms such as edge-embedded systems.}, } @article {pmid37430467, year = {2023}, author = {Peltier, DMP and Carbone, MS and McIntire, CD and Robertson, N and Thompson, RA and Malone, S and LeMoine, J and Richardson, AD and McDowell, NG and Adams, HD and Pockman, WT and Trowbridge, AM}, title = {Carbon starvation following a decade of experimental drought consumes old reserves in Pinus edulis.}, journal = {The New phytologist}, volume = {240}, number = {1}, pages = {92-104}, doi = {10.1111/nph.19119}, pmid = {37430467}, issn = {1469-8137}, mesh = {*Carbon/metabolism ; *Pinus/physiology ; Droughts ; Carbohydrates/chemistry ; Starch/metabolism ; Trees/physiology ; Carbohydrate Metabolism ; }, abstract = {Shifts in the age or turnover time of non-structural carbohydrates (NSC) may underlie changes in tree growth under long-term increases in drought stress associated with climate change. But NSC responses to drought are challenging to quantify, due in part to large NSC stores in trees and subsequently long response times of NSC to climate variation. We measured NSC age (Δ[14] C) along with a suite of ecophysiological metrics in Pinus edulis trees experiencing either extreme short-term drought (-90% ambient precipitation plot, 2020-2021) or a decade of severe drought (-45% plot, 2010-2021). We tested the hypothesis that carbon starvation - consumption exceeding synthesis and storage - increases the age of sapwood NSC. One year of extreme drought had no impact on NSC pool size or age, despite significant reductions in predawn water potential, photosynthetic rates/capacity, and twig and needle growth. By contrast, long-term drought halved the age of the sapwood NSC pool, coupled with reductions in sapwood starch concentrations (-75%), basal area increment (-39%), and bole respiration rates (-28%). Our results suggest carbon starvation takes time, as tree carbon reserves appear resilient to extreme disturbance in the short term. However, after a decade of drought, trees apparently consumed old stored NSC to support metabolism.}, } @article {pmid37430226, year = {2023}, author = {Demidova, EV and Serebriiskii, IG and Vlasenkova, R and Kelow, S and Andrake, MD and Hartman, TR and Kent, T and Virtucio, J and Rosen, GL and Pomerantz, RT and Dunbrack, RL and Golemis, EA and Hall, MJ and Chen, DYT and Daly, MB and Arora, S}, title = {Correction: Candidate variants in DNA replication and repair genes in early-onset renal cell carcinoma patients referred for germline testing.}, journal = {BMC genomics}, volume = {24}, number = {1}, pages = {388}, pmid = {37430226}, issn = {1471-2164}, } @article {pmid37428511, year = {2023}, author = {Minich, M and Zhao, Q and Eickhoff, J and Moreno, MA}, title = {In the Mood for Music: Listening to Music and Other Smartphone Uses Improve Adolescent Mood.}, journal = {Cyberpsychology, behavior and social networking}, volume = {26}, number = {11}, pages = {869-873}, doi = {10.1089/cyber.2022.0344}, pmid = {37428511}, issn = {2152-2723}, mesh = {Humans ; Adolescent ; *Smartphone ; *Music ; Affect ; Ecological Momentary Assessment ; }, abstract = {Rates of adolescent mood disorders and adolescent smartphone use have risen in parallel, leading some to suggest that smartphone use might have detrimental effects on adolescents' moods. Alternatively, it is possible that adolescents turn to smartphone use when experiencing negative mood. Past experimental study suggests that certain smartphone activities can reduce adolescents' negative moods or induce more positive moods, but little is known about the effects of real-world smartphone use, which can involve many different activities. A sample of N = 253 adolescents participated in an Ecological Momentary Assessment (EMA) procedure, which assessed which smartphone activities they were engaged in at random moments throughout the day. This procedure also prompted adolescents to rate their moods before and during smartphone use. Adolescents reported mood improvements during almost all smartphone activities and did not report that moods became more negative during any smartphone activity. Mood improvements were the largest when adolescents said they were listening to music, podcasts, or audiobooks. This may suggest some adolescent smartphone use is driven by a desire to alleviate negative mood.}, } @article {pmid37427807, year = {2024}, author = {Liu, S and Gates, KM and Ferrer, E}, title = {Homogeneity Assumptions in the Analysis of Dynamic Processes.}, journal = {Multivariate behavioral research}, volume = {59}, number = {6}, pages = {1166-1176}, doi = {10.1080/00273171.2023.2225172}, pmid = {37427807}, issn = {1532-7906}, mesh = {Humans ; *Emotions ; Data Interpretation, Statistical ; Models, Statistical ; Female ; }, abstract = {With the increased use of time series data in human research, ranging from ecological momentary assessments to data passively obtained, researchers can explore dynamic processes more than ever before. An important question researchers must ask themselves is, do I think all individuals have similar processes? If not, how different, and in what ways? Dr. Peter Molenaar's work set the foundation to answer these questions by providing insight into individual-level analysis for processes that are assumed to differ across individuals in at least some aspects. Currently, such assumptions do not have a clear taxonomy regarding the degree of homogeneity in the patterns of relations among variables and the corresponding parameter values. This paper provides the language with which researchers can discuss assumptions inherent in their analyses. We define strict homogeneity as the assumption that all individuals have an identical pattern of relations as well as parameter values; pattern homogeneity assumes the same pattern of relations but parameter values can differ; weak homogeneity assumes there are some (but not all) generalizable aspects of the process; and no homogeneity explicitly assumes no population-level similarities in dynamic processes across individuals. We demonstrate these assumptions with an empirical data set of daily emotions in couples.}, } @article {pmid37425881, year = {2023}, author = {Larivière, D and Abueg, L and Brajuka, N and Gallardo-Alba, C and Grüning, B and Ko, BJ and Ostrovsky, A and Palmada-Flores, M and Pickett, BD and Rabbani, K and Balacco, JR and Chaisson, M and Cheng, H and Collins, J and Denisova, A and Fedrigo, O and Gallo, GR and Giani, AM and Gooder, GM and Jain, N and Johnson, C and Kim, H and Lee, C and Marques-Bonet, T and O'Toole, B and Rhie, A and Secomandi, S and Sozzoni, M and Tilley, T and Uliano-Silva, M and van den Beek, M and Waterhouse, RM and Phillippy, AM and Jarvis, ED and Schatz, MC and Nekrutenko, A and Formenti, G}, title = {Scalable, accessible, and reproducible reference genome assembly and evaluation in Galaxy.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {37425881}, issn = {2692-8205}, support = {U01 CA253481/CA/NCI NIH HHS/United States ; U24 CA231877/CA/NCI NIH HHS/United States ; U24 HG010263/HG/NHGRI NIH HHS/United States ; U41 HG006620/HG/NHGRI NIH HHS/United States ; }, abstract = {Improvements in genome sequencing and assembly are enabling high-quality reference genomes for all species. However, the assembly process is still laborious, computationally and technically demanding, lacks standards for reproducibility, and is not readily scalable. Here we present the latest Vertebrate Genomes Project assembly pipeline and demonstrate that it delivers high-quality reference genomes at scale across a set of vertebrate species arising over the last ~500 million years. The pipeline is versatile and combines PacBio HiFi long-reads and Hi-C-based haplotype phasing in a new graph-based paradigm. Standardized quality control is performed automatically to troubleshoot assembly issues and assess biological complexities. We make the pipeline freely accessible through Galaxy, accommodating researchers even without local computational resources and enhanced reproducibility by democratizing the training and assembly process. We demonstrate the flexibility and reliability of the pipeline by assembling reference genomes for 51 vertebrate species from major taxonomic groups (fish, amphibians, reptiles, birds, and mammals).}, } @article {pmid37415394, year = {2023}, author = {Serra, A and Mozgunov, P and Davies, G and Jaki, T}, title = {Determining the minimum duration of treatment in tuberculosis: An order restricted non-inferiority trial design.}, journal = {Pharmaceutical statistics}, volume = {22}, number = {5}, pages = {938-962}, doi = {10.1002/pst.2320}, pmid = {37415394}, issn = {1539-1612}, support = {MC_UU_00002/14/MRC_/Medical Research Council/United Kingdom ; MC_UU_00002/19/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Humans ; *Duration of Therapy ; Research Design ; *Tuberculosis/drug therapy ; Equivalence Trials as Topic ; }, abstract = {Tuberculosis (TB) is one of the biggest killers among infectious diseases worldwide. Together with the identification of drugs that can provide benefits to patients, the challenge in TB is also the optimisation of the duration of these treatments. While conventional duration of treatment in TB is 6 months, there is evidence that shorter durations might be as effective but could be associated with fewer side effects and may be associated with better adherence. Based on a recent proposal of an adaptive order-restricted superiority design that employs the ordering assumptions within various duration of the same drug, we propose a non-inferiority (typically used in TB trials) adaptive design that effectively uses the order assumption. Together with the general construction of the hypothesis testing and expression for type I and type II errors, we focus on how the novel design was proposed for a TB trial concept. We consider a number of practical aspects such as choice of the design parameters, randomisation ratios, and timings of the interim analyses, and how these were discussed with the clinical team.}, } @article {pmid37413727, year = {2023}, author = {Xing, Z and Chen, S and Xu, F and Su, X and Gou, F and Shi, Y and Chen, H and Xiang, J and Li, J and Zhao, T}, title = {Quantitative analysis of TCE biodegradation pathway in landfill cover utilizing continuous monitoring, droplet digital PCR and multi-omics sequencing technology.}, journal = {Journal of environmental management}, volume = {344}, number = {}, pages = {118509}, doi = {10.1016/j.jenvman.2023.118509}, pmid = {37413727}, issn = {1095-8630}, mesh = {*Trichloroethylene/chemistry ; Multiomics ; Biodegradation, Environmental ; Waste Disposal Facilities ; Bacteria/genetics/metabolism ; Soil ; Polymerase Chain Reaction ; Technology ; }, abstract = {The remediation of volatile chlorinated hydrocarbons in the quasi-vadose zone has become a significant challenge. We applied an integrated approach to assess the biodegradability of trichloroethylene to identify the biotransformation mechanism. The formation of the functional zone biochemical layer was assessed by analyzing the distribution of landfill gas, physical and chemical properties of cover soil, spatial-temporal variations of micro-ecology, biodegradability of landfill cover soil and distributional difference metabolic pathway. Real-time online monitoring showed that trichloroethylene continuously undergoes anaerobic dichlorination and simultaneous aerobic/anaerobic conversion-aerobic co-metabolic degradation on the vertical gradient of the landfill cover system and reduction in trans-1,2-dichloroethylene in the anoxic zone but not 1,1-dichloroethylene. PCR and diversity sequencing revealed the abundance and spatial distribution of known dichlorination-related genes within the landfill cover, with 6.61 ± 0.25 × 10[4]-6.78 ± 0.09 × 10[6] and 1.17 ± 0.78 × 10[3]-7.82 ± 0.07 × 10[5] copies per g/soil of pmoA and tceA, respectively. In addition, dominant bacteria and diversity were significantly linked with physicochemical factors, and Mesorhizobium, Pseudoxanthomonas and Gemmatimonas were responsible for biodegradation in the aerobic, anoxic and anaerobic zones. Metagenome sequencing identified 6 degradation pathways of trichloroethylene that may occur in the landfill cover; the main pathway was incomplete dechlorination accompanied by cometabolic degradation. These results indicate that the anoxic zone is important for trichloroethylene degradation.}, } @article {pmid37408609, year = {2023}, author = {Boyes, D and , and , and , and , and , and Holland, PWH and , }, title = {The genome sequence of the Spruce Carpet Moth, Thera britannica (Turner, 1925).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {114}, pmid = {37408609}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual male Thera britannica (the Spruce Carpet Moth; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 381 megabases in span. Most of the assembly is scaffolded into 19 chromosomal pseudomolecules, including the assembled Z sex chromosome. The mitochondrial genome has also been assembled and is 15.9 kilobases in length. Gene annotation of this assembly on Ensembl has identified 12,457 protein coding genes.}, } @article {pmid37407490, year = {2023}, author = {Shinohara, N and Zhao, W and Shan, Y and Ukawa, S and Ohira, H and Kawamura, T and Okabayashi, S and Wakai, K and Ando, M and Tsushita, K and Tamakoshi, A}, title = {Temporal change in the association between life satisfaction and functional decline with gender differences: an age-specific prospective cohort study.}, journal = {Environmental health and preventive medicine}, volume = {28}, number = {}, pages = {42}, pmid = {37407490}, issn = {1347-4715}, mesh = {Male ; Adult ; Humans ; Female ; Aged ; Cohort Studies ; Prospective Studies ; Sex Factors ; *Personal Satisfaction ; Age Factors ; }, abstract = {BACKGROUND: Although life satisfaction (LS) has been shown to predict mortality, research studying the relationship between LS and functional decline is scarce. This study examined the association between LS and functional decline across four time points in young-old Japanese adults.

METHODS: We analysed 1,899 community-dwelling 65-year-olds in this age-specific cohort study conducted between 2000 and 2005. The Life Satisfaction Index K was used to evaluate LS and was classified into quartiles. Functional decline was determined using the Japanese Long-Term Care Insurance (LTCI) system: 1) mild disability; 2) severe disability; 3) all-cause mortality; 4) mild or severe disability; 5) severe disability or death; 6) mild or severe disability, or death. Adjusted hazard ratios (HR) with 95% confidence intervals (CI) were calculated using the Cox proportional hazard model. The analyses were conducted in the 8[th], 10[th], 12[th], and 14[th] years to assess the effect of LS on functional decline across time points.

RESULTS: The impact of LS gradually weakened over time. In the 8[th] year (aged 72-73), a higher LS was associated with a lower risk of mild or severe disability among the women participants (adjusted HR [95% CI] = 0.30 [0.11-0.81]). However, the effect disappeared gradually (adjusted HR [95% CI] = 0.55 [0.27-1.14]) in the 10[th] year (aged 74-75), 0.72 (0.41-1.26) in the 12[th] year (aged 76-77), and 0.68 (0.41-1.14) in the 14[th] year (aged 78-79). This trend continued in severe disability or death (adjusted HR [95% CI] = 0.24 [0.06-0.70], 0.31 [0.11-0.76], 0.57 [0.28-1.14], and 0.60 [0.32-1.12]) and mild or severe disability, or death (adjusted HR [95% CI] = 0.30 [0.14-0.68], 0.46 [0.24-0.87], 0.67 [0.41-1.10], and 0.65 [0.42-1.02]) in the 8[th], 10[th], 12[th], and 14[th] years, respectively. No statistically significant association was found among men at any time points or in any classification of outcomes.

CONCLUSIONS: Higher LS scores in 65-year-old women were associated with a lower risk for functional decline in any combination of mild disability, severe disability, or death. Additionally, the effect of LS was observed to weaken over time.

TRIAL REGISTRATION: This is not an intervention survey and does not require registration.}, } @article {pmid37402922, year = {2024}, author = {Li, K and Zhou, Y and Huang, X and Xiao, H and Shan, Y}, title = {Low-carbon development pathways for resource-based cities in China under the carbon peaking and carbon neutrality goals.}, journal = {Environmental science and pollution research international}, volume = {31}, number = {7}, pages = {10213-10233}, pmid = {37402922}, issn = {1614-7499}, mesh = {*Carbon/analysis ; Cities ; *Carbon Dioxide/analysis ; Goals ; China ; Economic Development ; }, abstract = {Resource-based cities are important strategic bases for securing resources in China and have made great contributions to the country's economic development. Long-term extensive resource development has made resource-based cities an important region constraining China from achieving comprehensive low-carbon development. Therefore, it is of great significance to explore the low-carbon transition path of resource-based cities for their energy greening, industrial transformation, and high-quality economic development. This study compiled the CO2 emission inventory of resource-based cities in China from 2005 to 2017, explored the contribution to CO2 emissions from three perspectives (driver, industry, and city), and predicted the peak of CO2 emissions in resource-based cities. The results show that resource-based cities contribute 18.4% of the country's GDP and emit 44.4% of the country's CO2 and that economic growth and CO2 emissions have not yet been decoupled. The per capita CO2 emissions and emission intensity of resource-based cities are 1.8 times and 2.4 times higher than the national average, respectively. Economic growth and energy intensity are the biggest drivers and main inhibitors of CO2 emissions growth. Industrial restructuring has become the biggest inhibitor of CO2 emissions growth. Based on the different resource endowments, industrial structures, and socio-economic development levels of resource-based cities, we propose differentiated low-carbon transition pathways. This study can provide references for cities to develop differentiated low-carbon development paths under the "double carbon" target.}, } @article {pmid37396199, year = {2023}, author = {Boyes, D and Holland, PWH and , and , and , and , and , and , }, title = {The genome sequence of the Northern Deep-brown Dart, Aporophyla lueneburgensis (Freyer, 1848).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {149}, pmid = {37396199}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual female Aporophyla lueneburgensis (the Northern Deep-brown Dart; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 978.3 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.5 kilobases in length. Gene annotation of this assembly on Ensembl identified 12,580 protein coding genes.}, } @article {pmid37394173, year = {2023}, author = {Fan, W and Song, X and Liu, M and Shan, B and Ma, M and Liu, Y}, title = {Spatio-temporal evolution of resources and environmental carrying capacity and its influencing factors: A case study of Shandong Peninsula urban agglomeration.}, journal = {Environmental research}, volume = {234}, number = {}, pages = {116469}, doi = {10.1016/j.envres.2023.116469}, pmid = {37394173}, issn = {1096-0953}, mesh = {*Conservation of Natural Resources ; Cities ; Spatial Analysis ; *Economic Development ; Industry ; China ; Rivers ; Urbanization ; }, abstract = {Promoting ecological conservation and high-quality development in the Yellow River basin is an important objective in China's 14th Five-Year Plan. Understanding the spatio-temporal evolution of and factors affecting the resources and environmental carrying capacity (RECC) of the urban agglomerations is critical for boosting high-quality green-oriented development. We first combined the Driver-Pressure-State-Impact-Response (DPSIR) framework and the improved Technique for Order Preference by Similarity to Ideal Solution (TOPSIS) model to evaluate the RECC of Shandong Peninsula urban agglomeration in 2000, 2010 and 2020; we then used trend analysis and spatial autocorrelation analysis to understand the spatio-temporal evolution and distribution pattern of RECC. Furthermore, we employed Geodetector to detect the influencing factors and classified the urban agglomeration into six zones based on the weighted Voronoi diagram of RECC as well as specific conditions of the study area. The results show that the RECC of Shandong Peninsula urban agglomeration increased consistently over time, from 0.3887 in 2000 to 0.4952 in 2010 and 0.6097 in 2020, respectively. Geographically, RECC decreased gradually from the northeast coast to the southwest inland. Globally, only in 2010 the RECC presented a significant spatial positive correlation, and that in the other years were not significant. The high-high cluster was mainly located in Weifang, while the low-low cluster in Jining. Furthermore, our study reveals three key factors-advancement of industrial structure, resident consumption level, and water consumption per ten thousand yuan of industrial added value-that affected the distribution of RECC. Other factors, including the interactions between residents' consumption level and environmental regulation, residents' consumption level and advancement of industrial structure, as well as between the proportion of R&D expenditure in GDP and resident consumption level also played important roles resulting in the variation of RECC among different cities within the urban agglomeration. Accordingly, we proposed suggestions for achieving high-quality development for different zones.}, } @article {pmid37391265, year = {2023}, author = {Docherty, AB and Farrell, J and Thorpe, M and Egan, C and Dunn, S and Norman, L and Shaw, CA and Law, A and Leeming, G and Norris, L and Brooks, A and Prodan, B and MacLeod, R and Baxter, R and Morris, C and Rennie, D and Oosthuyzen, W and Semple, MG and Baillie, JK and Pius, R and Seth, S and Harrison, EM and Lone, NI}, title = {Patient emergency health-care use before hospital admission for COVID-19 and long-term outcomes in Scotland: a national cohort study.}, journal = {The Lancet. Digital health}, volume = {5}, number = {7}, pages = {e446-e457}, pmid = {37391265}, issn = {2589-7500}, support = {MC_PC_19025/MRC_/Medical Research Council/United Kingdom ; MC_PC_20004/MRC_/Medical Research Council/United Kingdom ; MC_PC_20029/MRC_/Medical Research Council/United Kingdom ; /CSO_/Chief Scientist Office/United Kingdom ; }, mesh = {Adult ; Humans ; Cohort Studies ; Retrospective Studies ; *COVID-19 Vaccines ; *COVID-19/epidemiology/therapy ; Hospitals ; }, abstract = {BACKGROUND: It is unclear what effect the pattern of health-care use before admission to hospital with COVID-19 (index admission) has on the long-term outcomes for patients. We sought to describe mortality and emergency readmission to hospital after discharge following the index admission (index discharge), and to assess associations between these outcomes and patterns of health-care use before such admissions.

METHODS: We did a national, retrospective, complete cohort study by extracting data from several national databases and linking the databases for all adult patients admitted to hospital in Scotland with COVID-19. We used latent class trajectory modelling to identify distinct clusters of patients on the basis of their emergency admissions to hospital in the 2 years before the index admission. The primary outcomes were mortality and emergency readmission up to 1 year after index admission. We used multivariable regression models to explore associations between these outcomes and patient demographics, vaccination status, level of care received in hospital, and previous emergency hospital use.

FINDINGS: Between March 1, 2020, and Oct 25, 2021, 33 580 patients were admitted to hospital with COVID-19 in Scotland. Overall, the Kaplan-Meier estimate of mortality within 1 year of index admission was 29·6% (95% CI 29·1-30·2). The cumulative incidence of emergency hospital readmission within 30 days of index discharge was 14·4% (95% CI 14·0-14·8), with the number increasing to 35·6% (34·9-36·3) patients at 1 year. Among the 33 580 patients, we identified four distinct patterns of previous emergency hospital use: no admissions (n=18 772 [55·9%]); minimal admissions (n=12 057 [35·9%]); recently high admissions (n=1931 [5·8%]), and persistently high admissions (n=820 [2·4%]). Patients with recently or persistently high admissions were older, more multimorbid, and more likely to have hospital-acquired COVID-19 than patients with no or minimal admissions. People in the minimal, recently high, and persistently high admissions groups had an increased risk of mortality and hospital readmission compared with those in the no admissions group. Compared with the no admissions group, mortality was highest in the recently high admissions group (post-hospital mortality HR 2·70 [95% CI 2·35-2·81]; p<0·0001) and the risk of readmission was highest in the persistently high admissions group (3·23 [2·89-3·61]; p<0·0001).

INTERPRETATION: Long-term mortality and readmission rates for patients hospitalised with COVID-19 were high; within 1 year, one in three patients had died and a third had been readmitted as an emergency. Patterns of hospital use before index admission were strongly predictive of mortality and readmission risk, independent of age, pre-existing comorbidities, and COVID-19 vaccination status. This increasingly precise identification of individuals at high risk of poor outcomes from COVID-19 will enable targeted support.

FUNDING: Chief Scientist Office Scotland, UK National Institute for Health Research, and UK Research and Innovation.}, } @article {pmid37389324, year = {2022}, author = {Ebdon, S and Lohse, K and , and , and , and Jansen Van Rensburg, A and , }, title = {The genome sequence of the northern brown argus, Aricia artaxerxes (Fabricius, 1793).}, journal = {Wellcome open research}, volume = {7}, number = {}, pages = {314}, pmid = {37389324}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual Aricia artaxerxes (the northern brown argus; Arthropoda; Insecta; Lepidoptera; Lycaenidae). The genome sequence is 458 megabases in span. Most of the assembly (99.99%) is scaffolded into 23 chromosomal pseudomolecules, including the assembled Z sex chromosome. The mitochondrial genome has also been assembled and is 15.8 kilobases in length. Gene annotation of this assembly on Ensembl has identified 12,688 protein coding genes.}, } @article {pmid37387279, year = {2023}, author = {Wang, QX and Feng, QY and Zhu, XQ}, title = {[Determination of bisphenols in sediment by accelerated solvent extraction and solid-phase extraction purification coupled with ultra performance liquid chromatography-tandem mass spectrometry].}, journal = {Se pu = Chinese journal of chromatography}, volume = {41}, number = {7}, pages = {582-590}, pmid = {37387279}, issn = {1872-2059}, mesh = {Humans ; *Tandem Mass Spectrometry ; Chromatography, Liquid ; Acetonitriles ; }, abstract = {Bisphenols are endocrine disruptors that are characterized with bioaccumulation, persistence, and estrogenic activity. Even low contents of bisphenols can exert adverse effects on human health and the ecological environment. Herein, a method combining accelerated solvent extraction and solid-phase extraction purification with ultra performance liquid chromatography-tandem mass spectrometry was developed for the accurate detection of bisphenol A (BPA), bisphenol B (BPB), bisphenol F (BPF), bisphenol S (BPS), bisphenol Z (BPZ), bisphenol AF (BPAF), and bisphenol AP (BPAP) in sediments. The mass spectrometric parameters of the seven bisphenols were optimized, and the response values, separation effects, and chromatographic peak shapes of the target compounds were compared under three different mobile phase conditions. The sediment samples were pretreated by accelerated solvent extraction, and orthogonal tests were used to optimize the extraction solvent, extraction temperature, and cycle number. The results showed that the use of 0.05% (v/v) ammonia and acetonitrile as the mobile phase for gradient elution could rapidly separate the seven bisphenols on an Acquity UPLC BEH C18 column (100 mm×2.1 mm, 1.7 μm). The gradient program was as follows: 0-2 min, 60%A; 2-6 min, 60%A-40%A; 6-6.5 min, 40%A; 6.5-7 min, 40%A-60%A; 7-8 min, 60%A. Orthogonal experiments indicated that the optimal extraction conditions were as follows: extraction solvent of acetonitrile, extraction temperature of 100 ℃, and cycle number of three. The seven bisphenols showed good linearity in the range of 1.0-200 μg/L, with correlation coefficients (r[2]) greater than 0.999, and the limits of detection were 0.01-0.3 ng/g. The recoveries for the seven bisphenols ranged from 74.9% to 102.8% at three spiking levels (2.0, 10, 20 ng/g), with relative standard deviations ranging from 6.2% to 10.3%. The established method was applied to detect the seven bisphenols in sediment samples collected from Luoma Lake and its inflow rivers. BPA, BPB, BPF, BPS, and BPAF were detected in the sediments of the lake, and BPA, BPF, and BPS were detected in the sediments of its inflow rivers. The detection frequency of BPA and BPF was 100%, and the contents of these bisphenols in the sediment were 11.9-38.0 ng/g and 11.0-27.3 ng/g, respectively. The developed method is simple, rapid with high accuracy and precision, and is suitable for the determination of the seven bisphenols in sediment.}, } @article {pmid37387086, year = {2023}, author = {Sijm-Eeken, M and Marcilly, R and Jaspers, M and Peute, L}, title = {Organizational and Human Factors in Green Medical Informatics - A Case Study in Dutch Hospitals.}, journal = {Studies in health technology and informatics}, volume = {305}, number = {}, pages = {537-540}, doi = {10.3233/SHTI230552}, pmid = {37387086}, issn = {1879-8365}, mesh = {Humans ; *Ethnicity ; Hospitals ; Health Facilities ; *Medical Informatics ; Organizations ; }, abstract = {Medical Informatics brings methods and solutions that could support reducing healthcare's ecological footprint. Initial frameworks for Green Medical Informatics solutions are available, however these do not address organizational and human factors. Including these factors in evaluation or analysis of (technical) interventions aimed at making healthcare more sustainable, is essential for improving usability as well as effectiveness of these interventions. Interviews with healthcare professionals from Dutch hospitals led to preliminary insights into which organizational and human factors impact the implementation and adoption of sustainable solutions. Results indicate that forming multi-disciplinary teams is considered an important factor for realizing intended outcomes in terms of reducing carbon emissions and waste. Some other key factors mentioned are formalizing tasks, allocating budget and time, creating awareness and changing protocols to promote sustainable diagnosis and treatment procedures.}, } @article {pmid37379842, year = {2023}, author = {Talley, J and Pusdekar, S and Feltenberger, A and Ketner, N and Evers, J and Liu, M and Gosh, A and Palmer, SE and Wardill, TJ and Gonzalez-Bellido, PT}, title = {Predictive saccades and decision making in the beetle-predating saffron robber fly.}, journal = {Current biology : CB}, volume = {33}, number = {14}, pages = {2912-2924.e5}, doi = {10.1016/j.cub.2023.06.019}, pmid = {37379842}, issn = {1879-0445}, mesh = {Humans ; Animals ; Saccades ; *Coleoptera ; *Crocus ; *Odonata ; Decision Making ; }, abstract = {Internal predictions about the sensory consequences of self-motion, encoded by corollary discharge, are ubiquitous in the animal kingdom, including for fruit flies, dragonflies, and humans. In contrast, predicting the future location of an independently moving external target requires an internal model. With the use of internal models for predictive gaze control, vertebrate predatory species compensate for their sluggish visual systems and long sensorimotor latencies. This ability is crucial for the timely and accurate decisions that underpin a successful attack. Here, we directly demonstrate that the robber fly Laphria saffrana, a specialized beetle predator, also uses predictive gaze control when head tracking potential prey. Laphria uses this predictive ability to perform the difficult categorization and perceptual decision task of differentiating a beetle from other flying insects with a low spatial resolution retina. Specifically, we show that (1) this predictive behavior is part of a saccade-and-fixate strategy, (2) the relative target angular position and velocity, acquired during fixation, inform the subsequent predictive saccade, and (3) the predictive saccade provides Laphria with additional fixation time to sample the frequency of the prey's specular wing reflections. We also demonstrate that Laphria uses such wing reflections as a proxy for the wingbeat frequency of the potential prey and that consecutively flashing LEDs to produce apparent motion elicits attacks when the LED flicker frequency matches that of the beetle's wingbeat cycle.}, } @article {pmid37377567, year = {2023}, author = {Schwienhorst-Stich, EM and Wabnitz, K and Geck, E and Gepp, S and Jung, L and Mumm, A and Schmid, J and Simmenroth, A and Simon, J and Eichinger, M}, title = {Initiatives promoting planetary health education in Germany: An overview.}, journal = {GMS journal for medical education}, volume = {40}, number = {3}, pages = {Doc38}, pmid = {37377567}, issn = {2366-5017}, mesh = {Germany ; *Education, Medical ; Health Education ; Curriculum ; Schools, Medical ; }, abstract = {Planetary health education focuses on the climate and ecological crises and their adverse health effects. Given the acceleration of these crises, nationwide integration of planetary health education into undergraduate and graduate education, postgraduate training and continuing education for all health professionals has repeatedly been called for. Since 2019, planetary health education has been promoted by several national initiatives in Germany that are summarized in this commentary: 1. National Working Group Planetary Health Education, 2. Manual for planetary health education, 3. Catalog of National Planetary Health Learning Objectives in the National Competency-Based Catalog of Learning Objectives for Medical Education, 4. Working Group Climate, Environment and Health Impact Assessment at the Institute for Medical and Pharmaceutical Examinations, 5. Planetary Health Report Card, and 6. PlanetMedEd study: planetary health education in medical schools in Germany. We hope these initiatives promote collaboration across institutions involved in educating and training health professionals, inter-professional cooperation as well as rapid implementation of planetary health education.}, } @article {pmid37375921, year = {2023}, author = {Qi, Y and Ma, L and Ghani, MI and Peng, Q and Fan, R and Hu, X and Chen, X}, title = {Effects of Drought Stress Induced by Hypertonic Polyethylene Glycol (PEG-6000) on Passiflora edulis Sims Physiological Properties.}, journal = {Plants (Basel, Switzerland)}, volume = {12}, number = {12}, pages = {}, pmid = {37375921}, issn = {2223-7747}, support = {2021-229, HZJD [2022]001//Guizhou Provincial Science and Technology Program/ ; Guike AA21196003//Science and Technology Base & Talent Project of Guangxi Province/ ; 2021YFD1100303-3//National Key Research and Development Program of China/ ; 2019-04//Guizhou University Cultivation Project/ ; }, abstract = {Passion fruit is known to be sensitive to drought, and in order to study the physiological and biochemical changes that occur in passion fruit seedlings under drought stress, a hypertonic polyethylene glycol (PEG) solution (5%, 10%, 15%, and 20%) was used to simulate drought stress in passion fruit seedlings. We explored the physiological changes in passion fruit seedlings under drought stress induced by PEG to elucidate their response to drought stress and provide a theoretical basis for drought-resistant cultivation of passion fruit seedlings. The results show that drought stress induced by PEG had a significant effect on the growth and physiological indices of passion fruit. Drought stress significantly decreased fresh weight, chlorophyll content, and root vitality. Conversely, the contents of soluble protein (SP), proline (Pro), and malondialdehyde (MDA) increased gradually with the increasing PEG concentration and prolonged stress duration. After nine days, the SP, Pro and MDA contents were higher in passion fruit leaves and roots under 20% PEG treatments compared with the control. Additionally, with the increase in drought time, the activities of antioxidant enzymes such as peroxidase (POD), superoxide dismutase (SOD) and catalase (CAT) showed an increasing trend and then a decreasing trend, and they reached the highest value at the sixth day of drought stress. After rehydration, SP, Pro and MDA contents in the leaves and roots of passion fruit seedlings was reduced. Among all the stress treatments, 20% PEG had the most significant effect on passion fruit seedlings. Therefore, our study demonstrated sensitive concentrations of PEG to simulate drought stress on passion fruit and revealed the physiological adaptability of passion fruit to drought stress.}, } @article {pmid37372376, year = {2023}, author = {Cheng, CC and Rivera-Colón, AG and Minhas, BF and Wilson, L and Rayamajhi, N and Vargas-Chacoff, L and Catchen, JM}, title = {Chromosome-Level Genome Assembly and Circadian Gene Repertoire of the Patagonia Blennie Eleginops maclovinus-The Closest Ancestral Proxy of Antarctic Cryonotothenioids.}, journal = {Genes}, volume = {14}, number = {6}, pages = {}, pmid = {37372376}, issn = {2073-4425}, mesh = {Humans ; Animals ; Phylogeny ; Antarctic Regions ; *Perciformes/genetics ; Fishes/genetics ; Chromosomes ; }, abstract = {The basal South American notothenioid Eleginops maclovinus (Patagonia blennie or róbalo) occupies a uniquely important phylogenetic position in Notothenioidei as the singular closest sister species to the Antarctic cryonotothenioid fishes. Its genome and the traits encoded therein would be the nearest representatives of the temperate ancestor from which the Antarctic clade arose, providing an ancestral reference for deducing polar derived changes. In this study, we generated a gene- and chromosome-complete assembly of the E. maclovinus genome using long read sequencing and HiC scaffolding. We compared its genome architecture with the more basally divergent Cottoperca gobio and the derived genomes of nine cryonotothenioids representing all five Antarctic families. We also reconstructed a notothenioid phylogeny using 2918 proteins of single-copy orthologous genes from these genomes that reaffirmed E. maclovinus' phylogenetic position. We additionally curated E. maclovinus' repertoire of circadian rhythm genes, ascertained their functionality by transcriptome sequencing, and compared its pattern of gene retention with C. gobio and the derived cryonotothenioids. Through reconstructing circadian gene trees, we also assessed the potential role of the retained genes in cryonotothenioids by referencing to the functions of the human orthologs. Our results found E. maclovinus to share greater conservation with the Antarctic clade, solidifying its evolutionary status as the direct sister and best suited ancestral proxy of cryonotothenioids. The high-quality genome of E. maclovinus will facilitate inquiries into cold derived traits in temperate to polar evolution, and conversely on the paths of readaptation to non-freezing habitats in various secondarily temperate cryonotothenioids through comparative genomic analyses.}, } @article {pmid37368895, year = {2023}, author = {Aceves-Bueno, E and Nenadovic, M and Dove, I and Atkins-Davis, C and Aceves-Bueno, JS and Trejo-Ramirez, A and Rivas-Ochoa, C and Rodriguez-Van Dyck, S and Weaver, AH}, title = {Sustaining small-scale fisheries through a nation-wide Territorial Use Rights in Fisheries system.}, journal = {PloS one}, volume = {18}, number = {6}, pages = {e0286739}, pmid = {37368895}, issn = {1932-6203}, mesh = {*Fisheries ; *Conservation of Natural Resources ; Territoriality ; Mexico ; Data Management ; Ecosystem ; }, abstract = {Territorial Use rights in Fisheries (TURFs) are used around the world to manage small-scale fisheries and they've shown varying levels of success. Our understanding of what leads to different performance levels is limited due to several reasons. Firstly, these systems are often present in areas with low monitoring capacity where data is scarce. Secondly, past research has centered on the analysis of successful cases, with little attention paid to entire systems. Thirdly, research has been ahistorical, disconnected from the development process of TURF systems. Fourthly, TURFs are often viewed as homogenous ignoring the socio-ecological conditions under which they develop. To address these gaps, the study focuses on Mexico as a case study and context. The research first presents a historical overview of the development of TURF systems in Mexico, including the institutional and legal frameworks that have shaped their evolution. The paper then presents a TURF database that maps all TURF systems in Mexico, including their geographical locations and characteristics. In addition, the study presents case studies based on identified archetypes that showcase the diversity of TURF systems in Mexico, highlighting the different types of systems and the challenges they face. By presenting a comprehensive map of all TURF systems in Mexico, this research paper aims to make an important addition to the case studies in the global literature on TURF systems and provide a valuable resource for marine resource management policymakers, researchers, and practitioners.}, } @article {pmid37366114, year = {2023}, author = {Sahoo, P and Jana, P and Kundu, S and Mishra, S and Chattopadhyay, K and Mukherjee, A and Ghosh, CK}, title = {Quercetin@Gd[3+] doped Prussian blue nanocubes induce the pyroptotic death of MDA-MB-231 cells: combinational targeted multimodal therapy, dual modal MRI, intuitive modelling of r1-r2 relaxivities.}, journal = {Journal of materials chemistry. B}, volume = {11}, number = {28}, pages = {6646-6663}, doi = {10.1039/d3tb00316g}, pmid = {37366114}, issn = {2050-7518}, mesh = {Humans ; *Quercetin/pharmacology ; MDA-MB-231 Cells ; *Triple Negative Breast Neoplasms/pathology ; Magnetic Resonance Imaging/methods ; Water ; Caspases ; }, abstract = {Quercetin (Qu), a potential bioflavonoid has gained considerable interest as a promising chemotherapeutic drug which can inhibit the proliferation of triple-negative breast cancer (TNBC) cells due to its regulation of the expression of tumor-suppressor gene metastasis and antioxidant property. Notably, Qu exhibits a very negligible cytotoxic effect on normal cells, even with high-dose treatment, while it is shows high affinity to TNBC. However, the efficiency of Qu is limited clinically due to its poor bioavailability, caused by its low aqueous solubility (2.15 μg mL[-1] at 25 °C), rapid gastrointestinal digestion and chemical instability in alkaline and neutral media. Herein, polydopamine (PDA)-coated, NH2-PEG-NH2 and hyaluronic acid (HA)-functionalized Gd[3+]-doped Prussian blue nanocubes (GPBNC) are reported as a multifunctional platform for the codelivery of Qu as a chemotherapeutic agent and GPBNC as a photodynamic (PDT) and photothermal (PTT) agent with improved therapeutic efficiency to overcome theses barriers. PDA, NH2-PEG-NH2 and HA stabilize GPBNC@Qu and facilitate bioavailability and active-targeting, while absorption of near infrared (NIR) (808 nm; 1 W cm[-2]) induces PDT and PTT activities and dual T1-T2-weighted magnetic resonance imaging (MRI) with high relaxometric parameters (r1 10.06 mM[-1] s[-1] and r2 24.96 mM[-1] s[-1] at a magnetic field of 3 T). The designed platform shows a pH-responsive Qu release profile and NIR-induced therapeutic efficiency of ∼79% in 20 minutes of irradiation, wherein N-terminal gardermin D (N-GSDMD) and a P2X7-receptor-mediated pyroptosis pathway induces cell death, corroborating the up-regulation of NLRP3, caspase-1, caspase-5, N-GSDMD, IL-1β, cleaved Pannexin-1 and P2X7 proteins. More interestingly, the increasing relaxivity values of Prussian blue nanocubes with Gd[3+] doping have been explained on the basis of Solomon-Bloembergen-Morgan theory, considering inner- and outer-sphere relaxivity, wherein crystal defects, coordinated water molecules, tumbling rate, metal to water proton distance, correlation time, magnetisation value etc. play a significant role. In summary, our study suggests that GPBNC could be a beneficial nanocarrier for theranostic purposes against TNBC, while our conceptual study clearly demonstrates the role of various factors in increasing relaxometric parameters.}, } @article {pmid37365013, year = {2023}, author = {Azzouz, DF and Chen, Z and Izmirly, PM and Chen, LA and Li, Z and Zhang, C and Mieles, D and Trujillo, K and Heguy, A and Pironti, A and Putzel, GG and Schwudke, D and Fenyo, D and Buyon, JP and Alekseyenko, AV and Gisch, N and Silverman, GJ}, title = {Longitudinal gut microbiome analyses and blooms of pathogenic strains during lupus disease flares.}, journal = {Annals of the rheumatic diseases}, volume = {82}, number = {10}, pages = {1315-1327}, pmid = {37365013}, issn = {1468-2060}, support = {R01 AR042455/AR/NIAMS NIH HHS/United States ; R24 GM137763/GM/NIGMS NIH HHS/United States ; HHSN272201400019C/AI/NIAID NIH HHS/United States ; P50 AR070591/AR/NIAMS NIH HHS/United States ; UL1 TR000038/TR/NCATS NIH HHS/United States ; P30 CA016087/CA/NCI NIH HHS/United States ; UM1 AI109565/AI/NIAID NIH HHS/United States ; }, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Symptom Flare Up ; *Lupus Erythematosus, Systemic ; *Microbiota ; Feces ; *Lupus Nephritis/genetics ; }, abstract = {OBJECTIVE: Whereas genetic susceptibility for systemic lupus erythematosus (SLE) has been well explored, the triggers for clinical disease flares remain elusive. To investigate relationships between microbiota community resilience and disease activity, we performed the first longitudinal analyses of lupus gut-microbiota communities.

METHODS: In an observational study, taxononomic analyses, including multivariate analysis of ß-diversity, assessed time-dependent alterations in faecal communities from patients and healthy controls. From gut blooms, strains were isolated, with genomes and associated glycans analysed.

RESULTS: Multivariate analyses documented that, unlike healthy controls, significant temporal community-wide ecological microbiota instability was common in SLE patients, and transient intestinal growth spikes of several pathogenic species were documented. Expansions of only the anaerobic commensal, Ruminococcus (blautia) gnavus (RG) occurred at times of high-disease activity, and were detected in almost half of patients during lupus nephritis (LN) disease flares. Whole genome sequence analysis of RG strains isolated during these flares documented 34 genes postulated to aid adaptation and expansion within a host with an inflammatory condition. Yet, the most specific feature of strains found during lupus flares was the common expression of a novel type of cell membrane-associated lipoglycan. These lipoglycans share conserved structural features documented by mass spectroscopy, and highly immunogenic repetitive antigenic-determinants, recognised by high-level serum IgG2 antibodies, that spontaneously arose, concurrent with RG blooms and lupus flares.

CONCLUSIONS: Our findings rationalise how blooms of the RG pathobiont may be common drivers of clinical flares of often remitting-relapsing lupus disease, and highlight the potential pathogenic properties of specific strains isolated from active LN patients.}, } @article {pmid37363228, year = {2023}, author = {Sauer, FG and Lange, U and Schmidt-Chanasit, J and Kiel, E and Wiatrowska, B and Myczko, Ł and Lühken, R}, title = {Overwintering Culex torrentium in abandoned animal burrows as a reservoir for arboviruses in Central Europe.}, journal = {One health (Amsterdam, Netherlands)}, volume = {16}, number = {}, pages = {100572}, pmid = {37363228}, issn = {2352-7714}, abstract = {Culex pipiens s.s./Culex torrentium belong to the most widespread mosquito taxa in Europe and are the main vectors of Sindbis, West Nile and Usutu virus. The adult overwintering females can act as reservoir for these arthropod-borne viruses (arboviruses), thus contributing to their local persistence when transmission cycles are interrupted during the winter. However, the main overwintering sites of Cx. torrentium are unknown. In a study from 2017, 3455 Cx. pipiens s.s./Cx. torrentium specimens were collected from abandoned animal burrows in Poznan, Poland. These specimens were retrospectively identified to species-level with a PCR assay, which revealed Cx. torrentium as dominant species (> 60%). Motivated by these results, we conducted a field study from February to July 2022 to systematically analyse the overwintering site patterns of Cx. pipiens s.s./Cx. torrentium. Mosquitoes were sampled using pipe traps in abandoned animal burrows (n = 20) and with aspirators in nearby anthropogenic overwintering sites (n = 23). All Cx. pipiens s.s./Cx. torrentium were screened for Flaviviridae RNA. In total, 4710 mosquitoes of five different taxa were collected from anthropogenic sites. 3977 of them were identified as Cx. p. pipiens/Cx. torrentium (Cx. p. pipiens: 85%, Cx torrentium: 1%, pools with both species: 14%). In contrast, only Cx. p. pipiens/Cx. torrentium (1688 specimens) were collected from animal burrows dominated by Cx. torrentium (52%), followed by pools with both species (40%) and Cx. p pipiens (8%). A single pool of 10 Cx. torrentium specimens collected from an animal burrow was positive for Usutu virus. The detection of Usutu virus demonstrates that Cx. torrentium can act as winter reservoir for arboviruses. Abandoned animal burrows may by the primary overwintering site for the species and should be considered in future surveillance programmes, when sampling overwintering mosquitoes.}, } @article {pmid37363059, year = {2023}, author = {Boyes, D and , and , and , and , and , and Holland, PWH and , }, title = {The genome sequence of the Mouse Moth, Amphipyra tragopoginis (Clerck 1759).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {54}, pmid = {37363059}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual male Amphipyra tragopoginis (the Mouse Moth; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 806 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the assembled Z sex chromosome. The mitochondrial genome has also been assembled and is 15.3 kilobases in length. Gene annotation of this assembly on Ensembl has identified 13,359 protein coding genes.}, } @article {pmid37359433, year = {2023}, author = {Fu, D and Abawi, F and Carneiro, H and Kerzel, M and Chen, Z and Strahl, E and Liu, X and Wermter, S}, title = {A Trained Humanoid Robot can Perform Human-Like Crossmodal Social Attention and Conflict Resolution.}, journal = {International journal of social robotics}, volume = {}, number = {}, pages = {1-16}, pmid = {37359433}, issn = {1875-4791}, abstract = {To enhance human-robot social interaction, it is essential for robots to process multiple social cues in a complex real-world environment. However, incongruency of input information across modalities is inevitable and could be challenging for robots to process. To tackle this challenge, our study adopted the neurorobotic paradigm of crossmodal conflict resolution to make a robot express human-like social attention. A behavioural experiment was conducted on 37 participants for the human study. We designed a round-table meeting scenario with three animated avatars to improve ecological validity. Each avatar wore a medical mask to obscure the facial cues of the nose, mouth, and jaw. The central avatar shifted its eye gaze while the peripheral avatars generated sound. Gaze direction and sound locations were either spatially congruent or incongruent. We observed that the central avatar's dynamic gaze could trigger crossmodal social attention responses. In particular, human performance was better under the congruent audio-visual condition than the incongruent condition. Our saliency prediction model was trained to detect social cues, predict audio-visual saliency, and attend selectively for the robot study. After mounting the trained model on the iCub, the robot was exposed to laboratory conditions similar to the human experiment. While the human performance was overall superior, our trained model demonstrated that it could replicate attention responses similar to humans.}, } @article {pmid37352503, year = {2023}, author = {Park, Y and Shimada, T and Son, SW and Park, HJ}, title = {Invasion and interaction determine population composition in an open evolving ecological system.}, journal = {Chaos (Woodbury, N.Y.)}, volume = {33}, number = {6}, pages = {}, doi = {10.1063/5.0142978}, pmid = {37352503}, issn = {1089-7682}, mesh = {*Ecosystem ; Population Dynamics ; *Models, Biological ; }, abstract = {It is well-known that interactions between species determine the population composition in an ecosystem. Conventional studies have focused on fixed population structures to reveal how interactions shape population compositions. However, interaction structures are not fixed but change over time due to invasions. Thus, invasion and interaction play an important role in shaping communities. Despite its importance, however, the interplay between invasion and interaction has not been well explored. Here, we investigate how invasion affects the population composition with interactions in open evolving ecological systems considering generalized Lotka-Volterra-type dynamics. Our results show that the system has two distinct regimes. One is characterized by low diversity with abrupt changes of dominant species in time, appearing when the interaction between species is strong and invasion slowly occurs. On the other hand, frequent invasions can induce higher diversity with slow changes in abundances despite strong interactions. It is because invasion happens before the system reaches its equilibrium, which drags the system from its equilibrium all the time. All species have similar abundances in this regime, which implies that fast invasion induces regime shift. Therefore, whether invasion or interaction dominates determines the population composition.}, } @article {pmid37352137, year = {2023}, author = {Dias Marques, V and Massago, M and da Silva, MT and Roskowski, I and de Lima, DAN and Dos Santos, L and Louro, E and Gonçalves, ST and Pedroso, RB and Obale, AM and Pelloso, SM and Vissoci, JRN and Staton, CA and Nihei, OK and Carvalho, MDB and Dutra, AC and de Andrade, L}, title = {Exploring regional disparities in lung cancer mortality in a Brazilian state: A cross-sectional ecological study.}, journal = {PloS one}, volume = {18}, number = {6}, pages = {e0287371}, pmid = {37352137}, issn = {1932-6203}, mesh = {Humans ; Adult ; Brazil/epidemiology ; Cross-Sectional Studies ; Socioeconomic Factors ; Cities ; *Lung Neoplasms/epidemiology ; }, abstract = {BACKGROUND: Lung cancer (LC) is one of the main causes of mortality in Brazil; geographic, cultural, socioeconomic and health access factors can affect the development of the disease. We explored the geospatial distribution of LC mortality, and associated factors, between 2015 and 2019, in Parana state, Brazil.

METHODS AND FINDINGS: We obtained mortality (from the Brazilian Health Informatics Department) and population rates (from the Brazilian Institute of Geography and Statistics [IBGE]) in people over 40 years old, accessibility of oncology centers by municipality, disease diagnosis rate (from Brazilian Ministry of Health), the tobacco production rate (IBGE) and Parana Municipal Performance Index (IPDM) (from Parana Institute for Economic and Social Development). Global Moran's Index and Local Indicators of Spatial Association were performed to evaluate the spatial distribution of LC mortality in Parana state. Ordinary Least Squares Regression and Geographically Weighted Regression were used to verify spatial association between LC mortality and socioeconomic indicators and health service coverage. A strong spatial autocorrelation of LC mortality was observed, with the detection of a large cluster of high LC mortality in the South of Parana state. Spatial regression analysis showed that all independent variables analyzed were directly related to LC mortality by municipality in Paraná.

CONCLUSIONS: There is a disparity in the LC mortality in Parana state, and inequality of socioeconomic and accessibility to health care services could be associated with it. Our findings may help health managers to intensify actions in regions with vulnerability in the detection and treatment of LC.}, } @article {pmid37351546, year = {2023}, author = {Boyes, D and Goate, Z and , and , and , and , and , }, title = {The genome sequence of the Lesser Swallow Prominent, Pheosia gnoma (Fabricius, 1777).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {192}, pmid = {37351546}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual male Pheosia gnoma (the Lesser Swallow Prominent; Arthropoda; Insecta; Lepidoptera; Notodontidae). The genome sequence is 271.3 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 17.0 kilobases in length. Gene annotation of this assembly on Ensembl identified 11,628 protein coding genes.}, } @article {pmid37346819, year = {2023}, author = {Boyes, D and , and , and , and , and , and Holland, PWH and , }, title = {The genome sequence of the Mother Shipton moth , Euclidia mi (Clerck, 1759).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {108}, pmid = {37346819}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual male Euclidia mi (the Mother Shipton moth; Arthropoda; Insecta; Lepidoptera; Erebidae). The genome sequence is 2,320 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the assembled Z sex chromosome. The mitochondrial genome has also been assembled and is 15.6 kilobases in length. Gene annotation of this assembly on Ensembl identified 13,454 protein coding genes.}, } @article {pmid37346773, year = {2022}, author = {Boyes, D and Sims, I and Lees, D and , and , and , and , and , and , and Dove, A and , }, title = {The genome sequence of the Kent black arches, Meganola albula (Denis & Schiffermüller, 1775).}, journal = {Wellcome open research}, volume = {7}, number = {}, pages = {310}, pmid = {37346773}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual male Meganola albula (the Kent black arches; Arthropoda; Insecta; Lepidoptera; Nolidae). The genome sequence is 405 megabases in span. Most of the assembly (99.95%) is scaffolded into 30 chromosomal pseudomolecules with the Z sex chromosome assembled. The mitochondrial genome has also been assembled and is 15.4 kilobases in length.}, } @article {pmid37344755, year = {2023}, author = {Adelisardou, F and Mederly, P and Minkina, T}, title = {Assessment of soil- and water-related ecosystem services with coupling the factors of climate and land-use change (Example of the Nitra region, Slovakia).}, journal = {Environmental geochemistry and health}, volume = {45}, number = {8}, pages = {6605-6620}, pmid = {37344755}, issn = {1573-2983}, mesh = {Humans ; *Ecosystem ; *Soil ; Water ; Slovakia ; Conservation of Natural Resources ; China ; }, abstract = {Climate and land use change can profoundly impact the provision of ecosystem services (ES) over time, particularly in the landscape of open fields along with growing urbanization and rising demand for space, food and energy. Policymakers are keen on knowing the combined effects of climate and land use change on ESs as a critical issue in human well-being. However, deep knowledge of how to identify these relationships is still lacking. This research aims to undertake a comprehensive assessment of soil- and water-related ES, and improvement in understanding how they are affected by climate and land use change. We applied the Integrated Valuation of Ecosystem Services and Trade-offs model for four ES (soil retention, nutrient delivery ratio, carbon storage, and water yield) for the years 2000 and 2018 in the Nitra region, Slovakia. We investigated the spatial and temporal changes in ES provision and determined the hotspots and coldspots of multiple ES. We found that soil retention, water yield, and carbon storage display a rising trend while the nutrient delivery ratio showed a decreasing trend over the past 18 years. Although all the mentioned services mainly attributed to land use change, the relative contribution of climate change was not deniable. Forests in the north and east and distributed urbanization and agriculture are the hotspots and coldspots for all ESs, respectively. Our results, in terms of determining the relative importance of land use and climate change and identifying the sensitive areas of ES provision, provide a scientific basis for ecosystem conservation and management priority setting at the local and regional levels.}, } @article {pmid37343095, year = {2023}, author = {Riva, F and Graco-Roza, C and Daskalova, GN and Hudgins, EJ and Lewthwaite, JMM and Newman, EA and Ryo, M and Mammola, S}, title = {Toward a cohesive understanding of ecological complexity.}, journal = {Science advances}, volume = {9}, number = {25}, pages = {eabq4207}, pmid = {37343095}, issn = {2375-2548}, mesh = {*Ecology/methods ; *Ecosystem ; Data Mining ; Bibliometrics ; Animals ; Human Activities ; }, abstract = {Ecological systems are quintessentially complex systems. Understanding and being able to predict phenomena typical of complex systems is, therefore, critical to progress in ecology and conservation amidst escalating global environmental change. However, myriad definitions of complexity and excessive reliance on conventional scientific approaches hamper conceptual advances and synthesis. Ecological complexity may be better understood by following the solid theoretical basis of complex system science (CSS). We review features of ecological systems described within CSS and conduct bibliometric and text mining analyses to characterize articles that refer to ecological complexity. Our analyses demonstrate that the study of complexity in ecology is a highly heterogeneous, global endeavor that is only weakly related to CSS. Current research trends are typically organized around basic theory, scaling, and macroecology. We leverage our review and the generalities identified in our analyses to suggest a more coherent and cohesive way forward in the study of complexity in ecology.}, } @article {pmid37343007, year = {2023}, author = {Isaacson, JE and Ye, JJ and Silva, LL and Hernandes Rocha, TA and de Andrade, L and Scheidt, JFHC and Wen, FH and Sachett, J and Monteiro, WM and Staton, CA and Vissoci, JRN and Gerardo, CJ}, title = {Antivenom access impacts severity of Brazilian snakebite envenoming: A geographic information system analysis.}, journal = {PLoS neglected tropical diseases}, volume = {17}, number = {6}, pages = {e0011305}, pmid = {37343007}, issn = {1935-2735}, support = {R21 TW011944/TW/FIC NIH HHS/United States ; }, mesh = {Humans ; *Snake Bites/epidemiology/therapy ; Antivenins/therapeutic use ; Brazil/epidemiology ; Geographic Information Systems ; Cross-Sectional Studies ; }, abstract = {BACKGROUND: Snakebite envenoming (SBE) is a neglected tropical disease capable of causing both significant disability and death. The burden of SBE is especially high in low- and middle-income countries. The aim of this study was to perform a geospatial analysis evaluating the association of sociodemographics and access to care indicators on moderate and severe cases of SBE in Brazil.

METHODS: We conducted an ecological, cross-sectional study of SBE in Brazil from 2014 to 2019 using the open access National System Identification of Notifiable Diseases (SINAN) database. We then collected a set of indicators from the Brazil Census of 2010 and performed a Principal Component Analysis to create variables related to health, economics, occupation, education, infrastructure, and access to care. Next, a descriptive and exploratory spatial analysis was conducted to evaluate the geospatial association of moderate and severe events. These variables related to events were evaluated using Geographically Weighted Poisson Regression. T-values were plotted in choropleth maps and considered statistically significant when values were <-1.96 or >+1.96.

RESULTS: We found that the North region had the highest number of SBE cases by population (47.83/100,000), death rates (0.18/100,000), moderate and severe rates (22.96/100,000), and proportion of cases that took more than three hours to reach healthcare assistance (44.11%). The Northeast and Midwest had the next poorest indicators. Life expectancy, young population structure, inequality, electricity, occupation, and more than three hours to reach healthcare were positively associated with greater cases of moderate and severe events, while income, illiteracy, sanitation, and access to care were negatively associated. The remaining indicators showed a positive association in some areas of the country and a negative association in other areas.

CONCLUSION: Regional disparities in SBE incidence and rates of poor outcomes exist in Brazil, with the North region disproportionately affected. Multiple indicators were associated with rates of moderate and severe events, such as sociodemographic and health care indicators. Any approach to improving snakebite care must work to ensure the timeliness of antivenom administration.}, } @article {pmid37340013, year = {2023}, author = {Tulis, F and Ševčík, M and Jánošíková, R and Baláž, I and Ambros, M and Zvaríková, L and Horváth, G}, title = {Author Correction: The impact of the striped field mouse's range expansion on communities of native small mammals.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {10006}, doi = {10.1038/s41598-023-36731-y}, pmid = {37340013}, issn = {2045-2322}, } @article {pmid37336403, year = {2023}, author = {Li, W and Feng, Q and Southam, G and Jin, T and Li, Z}, title = {Changes in microbial community structure during the biooxidation of iron and inorganic/organic sulfur provide prediction of acid mine drainage from coal spoil.}, journal = {The Science of the total environment}, volume = {894}, number = {}, pages = {164945}, doi = {10.1016/j.scitotenv.2023.164945}, pmid = {37336403}, issn = {1879-1026}, mesh = {*Coal ; Sulfur ; Mining ; Bacteria ; Iron ; Acids ; Oxidation-Reduction ; *Microbiota ; }, abstract = {To thoroughly investigate the formation mechanism of acid mine drainage (AMD) from coal mine spoil, this study conducted microbial shake flask experiments on gangue possessing inorganic and organic sulfur to predict the future generation of AMD. The results revealed that microbial-mediated sulfur oxidation effectively lowered the pH of leachate and increased metal ion and sulfate concentrations. The oxidation of pyrite sulfur and thiophene sulfur contributed to 70 % and 30 % of the total acid production, respectively, highlighting the importance of both processes in coal mine acidification. The abundance and diversity of the microbial community increased, with "new" iron and sulfur oxidizing bacterial species during acidification, with "new" iron and sulfur oxidizing bacterial species, such as Sulfobacillus sp. and Acidibacillus sp., emerging and constituting approximately one-third of the bacterial population. These bacteria survived desiccation and proliferated faster than A. ferrooxidans YQ-N3 when conditions favored growth.}, } @article {pmid37335075, year = {2023}, author = {Burger, J and Gochfeld, M and Giffen, N and Brown, KG and Cortes, M and Ng, K and Kosson, DS}, title = {Comparing land cover and interior forests on contaminated land and the surrounding region: Oak Ridge Reservation as a case study.}, journal = {Journal of toxicology and environmental health. Part A}, volume = {86}, number = {15}, pages = {501-517}, doi = {10.1080/15287394.2023.2223231}, pmid = {37335075}, issn = {1528-7394}, support = {P30 ES005022/ES/NIEHS NIH HHS/United States ; }, mesh = {*Conservation of Natural Resources/methods ; *Forests ; Databases, Factual ; Ecosystem ; }, abstract = {Pressure from expanding populations has resulted in a need for protection, reclamation, and restoration of damaged land to productive, beneficial health uses. The objective of this investigation was to 1) compare land cover on the Department of Energy (DOE) Oak Ridge Reservation (ORR) with the surrounding region, 2) select an indicator to evaluate ORR's protection of ecological resources, and 3) develop and implement a method to compare the amount of the indicator on ORR with the regions using National Land Cover Database (NLCD). Data demonstrated that ORR has a higher % of forests (deciduous, coniferous, mixed) than the 10 km and 30 km areas surrounding ORR, suggesting that obligations are being met to protect the ecology and environment. The findings also indicate that the interior forest at ORR is fragmented more than is the interior forest in the 30 km buffer zone, suggesting a need for DOE and managers of other lands to take into consideration the importance of intact interior forest when developing land or planning roads. The study describes the basis for specific ecological parameters such as interior forest that are important to consider when planning and executing remediation, restoration, and other management actions.}, } @article {pmid37331314, year = {2023}, author = {Liu, J and Xu, X and Zou, C and Lin, N and Zhang, K and Shan, N and Zhang, H and Liu, R}, title = {A Bayesian network-GIS probabilistic model for addressing human disturbance risk to ecological conservation redline areas.}, journal = {Journal of environmental management}, volume = {344}, number = {}, pages = {118400}, doi = {10.1016/j.jenvman.2023.118400}, pmid = {37331314}, issn = {1095-8630}, mesh = {Humans ; *Geographic Information Systems ; *Conservation of Natural Resources/methods ; Bayes Theorem ; Forests ; Models, Statistical ; China ; Ecosystem ; }, abstract = {Population growth and associated ecological space occupation are posing great risks to regional ecological security and social stability. In China, "Ecological Conservation Redline" (ECR) that prohibited urbanization and industrial construction has been proposed as a national policy to resolve spatial mismatches and management contradictions. However, unfriendly human disturbance activities (e.g., cultivation, mining, and infrastructure construction) still exist within the ECR, posing a great threat to ecological stability and safety. In this article, a Bayesian network (BN)-GIS probabilistic model is proposed to spatially and quantitatively address the human disturbance risk to the ECR at the regional scale. The Bayesian models integrate multiple human activities, ecological receptors of the ECR, and their exposure relationships for calculating the human disturbance risk. The case learning method geographic information systems (GIS) is then introduced to train BN models based on the spatial attribute of variables to evaluate the spatial distribution and correlation of risks. This approach was applied to the human disturbance risk assessment for the ECR that was delineated in 2018 in Jiangsu Province, China. The results indicated that most of the ECRs were at a low or medium human disturbance risk level, while some drinking water sources and forest parks in Lianyungang City possessed the highest risk. The sensitivity analysis result showed the ECR vulnerability, especially for cropland, that contributed most to the human disturbance risk. This spatially probabilistic method can not only enhance model's prediction precision, but also help decision-makers to determine how to establish priorities for policy design and conservation interventions. Overall, it presents a foundation for later ECR adjustments as well as for human disturbance risk supervision and management at the regional scale.}, } @article {pmid37325324, year = {2023}, author = {Douet Vannucci, V and Marchand, T and Hennequin, A and Caci, H and Staccini, P}, title = {The EPIDIA4Kids protocol for a digital epidemiology study on brain functioning in children, based on a multimodality biometry tool running on an unmodified tablet.}, journal = {Frontiers in public health}, volume = {11}, number = {}, pages = {1185565}, pmid = {37325324}, issn = {2296-2565}, mesh = {Humans ; Child ; *Mental Disorders ; Brain/diagnostic imaging ; Biometry ; }, abstract = {INTRODUCTION: Neurodevelopment and related mental disorders (NDDs) are one of the most frequent disabilities among young people. They have complex clinical phenotypes often associated with transnosographic dimensions, such as emotion dysregulation and executive dysfunction, that lead to adverse impacts in personal, social, academic, and occupational functioning. Strong overlap exists then across NDDs phenotypes that are challenging for diagnosis and therapeutic intervention. Recently, digital epidemiology uses the rapidly growing data streams from various devices to advance our understanding of health's and disorders' dynamics, both in individuals and the general population, once coupled with computational science. An alternative transdiagnostic approach using digital epidemiology may thus better help understanding brain functioning and hereby NDDs in the general population.

OBJECTIVE: The EPIDIA4Kids study aims to propose and evaluate in children, a new transdiagnostic approach for brain functioning examination, combining AI-based multimodality biometry and clinical e-assessments on an unmodified tablet. We will examine this digital epidemiology approach in an ecological context through data-driven methods to characterize cognition, emotion, and behavior, and ultimately the potential of transdiagnostic models of NDDs for children in real-life practice.

METHODS AND ANALYSIS: The EPIDIA4Kids is an uncontrolled open-label study. 786 participants will be recruited and enrolled if eligible: they are (1) aged 7 to 12 years and (2) are French speaker/reader; (3) have no severe intellectual deficiencies. Legal representative and children will complete online demographic, psychosocial and health assessments. During the same visit, children will perform additionally a paper/pencil neuro-assessments followed by a 30-min gamified assessment on a touch-screen tablet. Multi-stream data including questionnaires, video, audio, digit-tracking, will be collected, and the resulting multimodality biometrics will be generated using machine- and deep-learning algorithms. The trial will start in March 2023 and is expected to end by December 2024.

DISCUSSION: We hypothesize that the biometrics and digital biomarkers will be capable of detecting early onset symptoms of neurodevelopment compared to paper-based screening while as or more accessible in real-life practice.}, } @article {pmid37316182, year = {2023}, author = {Eliason, PH and Galarneau, JM and Kolstad, AT and Pankow, MP and West, SW and Bailey, S and Miutz, L and Black, AM and Broglio, SP and Davis, GA and Hagel, BE and Smirl, JD and Stokes, KA and Takagi, M and Tucker, R and Webborn, N and Zemek, R and Hayden, A and Schneider, KJ and Emery, CA}, title = {Prevention strategies and modifiable risk factors for sport-related concussions and head impacts: a systematic review and meta-analysis.}, journal = {British journal of sports medicine}, volume = {57}, number = {12}, pages = {749-761}, doi = {10.1136/bjsports-2022-106656}, pmid = {37316182}, issn = {1473-0480}, mesh = {Adolescent ; Child ; Humans ; *Brain Concussion/prevention & control ; *Football ; Rugby ; *Hockey ; Databases, Factual ; }, abstract = {OBJECTIVES: To evaluate prevention strategies, their unintended consequences and modifiable risk factors for sport-related concussion (SRC) and/or head impact risk.

DESIGN: This systematic review and meta-analysis was registered on PROSPERO (CRD42019152982) and conducted according to Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines.

DATA SOURCES: Eight databases (MEDLINE, CINAHL, APA PsycINFO, Cochrane (Systematic Review and Controlled Trails Registry), SPORTDiscus, EMBASE, ERIC0 were searched in October 2019 and updated in March 2022, and references searched from any identified systematic review.

ELIGIBILITY CRITERIA: Study inclusion criteria were as follows: (1) original data human research studies, (2) investigated SRC or head impacts, (3) evaluated an SRC prevention intervention, unintended consequence or modifiable risk factor, (4) participants competing in any sport, (5) analytic study design, (6) systematic reviews and meta-analyses were included to identify original data manuscripts in reference search and (7) peer-reviewed. Exclusion criteria were as follows: (1) review articles, pre-experimental, ecological, case series or case studies and (2) not written in English.

RESULTS: In total, 220 studies were eligible for inclusion and 192 studies were included in the results based on methodological criteria as assessed through the Scottish Intercollegiate Guidelines Network high ('++') or acceptable ('+') quality. Evidence was available examining protective gear (eg, helmets, headgear, mouthguards) (n=39), policy and rule changes (n=38), training strategies (n=34), SRC management strategies (n=12), unintended consequences (n=5) and modifiable risk factors (n=64). Meta-analyses demonstrated a protective effect of mouthguards in collision sports (incidence rate ratio, IRR 0.74; 95% CI 0.64 to 0.89). Policy disallowing bodychecking in child and adolescent ice hockey was associated with a 58% lower concussion rate compared with bodychecking leagues (IRR 0.42; 95% CI 0.33 to 0.53), and evidence supports no unintended injury consequences of policy disallowing bodychecking. In American football, strategies limiting contact in practices were associated with a 64% lower practice-related concussion rate (IRR 0.36; 95% CI 0.16 to 0.80). Some evidence also supports up to 60% lower concussion rates with implementation of a neuromuscular training warm-up programme in rugby. More research examining potentially modifiable risk factors (eg, neck strength, optimal tackle technique) are needed to inform concussion prevention strategies.

CONCLUSIONS: Policy and rule modifications, personal protective equipment, and neuromuscular training strategies may help to prevent SRC.

PROSPERO REGISTRATION NUMBER: CRD42019152982.}, } @article {pmid37311775, year = {2023}, author = {Nemesházi, E and Bókony, V}, title = {HerpSexDet: the herpetological database of sex determination and sex reversal.}, journal = {Scientific data}, volume = {10}, number = {1}, pages = {377}, pmid = {37311775}, issn = {2052-4463}, support = {ESP 239-B//Austrian Science Fund (Fonds zur Förderung der Wissenschaftlichen Forschung)/ ; NKFIH K-135016//Nemzeti Kutatási, Fejlesztési és Innovációs Hivatal (NKFI Office)/ ; }, mesh = {Animals ; *Animals, Wild ; Databases, Factual ; *Ecology ; Phenotype ; Species Specificity ; Sex Determination Processes ; }, abstract = {Wildlife exhibits various sex-determination systems where sex chromosomes and environmental temperatures may both contribute to individual sexual development. The causes and consequences of this variability are important questions for evolutionary ecology, especially in light of ongoing environmental change. Amphibians and reptiles are emerging as a key group for studying these questions, with new data accumulating acceleratingly. We collected empirical data from earlier databases, reviews and primary literature to create the most up-to-date database on herpetological sex determination. We named our database HerpSexDet, which currently features data on genetic and temperature-dependent sex determination as well as reports on sex reversal for a total of 192 amphibian and 697 reptile species. This dataset, which we will regularly update in the future, facilitates interspecific comparative studies on the evolution of sex determination and its consequences for species-specific traits such as life history and conservation status, and may also help guiding future research by identifying species or higher taxa that are potentially most enlightening for the study of environmentally driven sex reversal.}, } @article {pmid37307237, year = {2023}, author = {Tardelli, VS and Bianco, MCM and Patel, R and Areco, KCN and Bandiera-Paiva, P and Tardelli, AO and Segura, LE and Castaldelli-Maia, JM and Fidalgo, TM and Martins, SS}, title = {Overdose death rates in Brazil: an ecological analysis by region.}, journal = {Revista brasileira de psiquiatria (Sao Paulo, Brazil : 1999)}, volume = {45}, number = {4}, pages = {381-382}, pmid = {37307237}, issn = {1809-452X}, } @article {pmid37306048, year = {2023}, author = {Mumme, S and Middleton, AD and Ciucci, P and De Groeve, J and Corradini, A and Aikens, EO and Ossi, F and Atwood, P and Balkenhol, N and Cole, EK and Debeffe, L and Dewey, SR and Fischer, C and Gude, J and Heurich, M and Hurley, MA and Jarnemo, A and Kauffman, MJ and Licoppe, A and van Loon, E and McWhirter, D and Mong, TW and Pedrotti, L and Morellet, N and Mysterud, A and Peters, W and Proffitt, K and Saïd, S and Signer, J and Sunde, P and Starý, M and Cagnacci, F}, title = {Wherever I may roam-Human activity alters movements of red deer (Cervus elaphus) and elk (Cervus canadensis) across two continents.}, journal = {Global change biology}, volume = {29}, number = {20}, pages = {5788-5801}, doi = {10.1111/gcb.16769}, pmid = {37306048}, issn = {1365-2486}, support = {//Ågerups & Elsagårdens Säteri AB/ ; //Assmåsa Gods AB/ ; //Carl Piper/ ; Wildlife & Landscape Research Package-project 2B//Danish Forest and Nature Agency/ ; //Ersaf Lombardia and Trento/ ; //Fondazione Edmund Mach/ ; //Grand Teton Association/ ; //Halmstad University/ ; //Högestad & Christinehofs Förvaltnings AB/ ; //Holmen Skog AB/ ; //International Research School of Applied Ecology/ ; //Ittur AB/ ; //Karl-Erik Önnesjös Stiftelse för Vetenskaplig forskning och Utveckling/ ; //Kolmårdens insamlingsstiftelse/Tåby Allmänning/ ; //Marie-Claire Cronstedts Stiftelse/ ; //Office Français de la Biodiversité/ ; //Public Service of Wallonia/ ; //Region Skåne / Stiftelsen Skånska Landskap/ ; //Stelvio National Park/ ; //Stiftelsen Oscar och Lili Lamms Minne/ ; //Sveaskog/ ; 5871/2005//Swedish Association for Hunting and Wildlife Management/ ; 802-0092-11//Swedish Environmental Protection Agency/ ; //Swedish University of Agricultural Sciences/ ; //Università degli Studi di Trento/ ; //University of California Berkeley/ ; //Vectronic Aerospace GmbH/ ; //Virå Bruk AB/ ; }, mesh = {Humans ; Animals ; *Ecosystem ; *Deer/physiology ; Human Activities ; North America ; Geographic Information Systems ; }, abstract = {Human activity and associated landscape modifications alter the movements of animals with consequences for populations and ecosystems worldwide. Species performing long-distance movements are thought to be particularly sensitive to human impact. Despite the increasing anthropogenic pressure, it remains challenging to understand and predict animals' responses to human activity. Here we address this knowledge gap using 1206 Global Positioning System movement trajectories of 815 individuals from 14 red deer (Cervus elaphus) and 14 elk (Cervus canadensis) populations spanning wide environmental gradients, namely the latitudinal range from the Alps to Scandinavia in Europe, and the Greater Yellowstone Ecosystem in North America. We measured individual-level movements relative to the environmental context, or movement expression, using the standardized metric Intensity of Use, reflecting both the directionality and extent of movements. We expected movement expression to be affected by resource (Normalized Difference Vegetation Index, NDVI) predictability and topography, but those factors to be superseded by human impact. Red deer and elk movement expression varied along a continuum, from highly segmented trajectories over relatively small areas (high intensity of use), to directed transitions through restricted corridors (low intensity of use). Human activity (Human Footprint Index, HFI) was the strongest driver of movement expression, with a steep increase in Intensity of Use as HFI increased, but only until a threshold was reached. After exceeding this level of impact, the Intensity of Use remained unchanged. These results indicate the overall sensitivity of Cervus movement expression to human activity and suggest a limitation of plastic responses under high human pressure, despite the species also occurring in human-dominated landscapes. Our work represents the first comparison of metric-based movement expression across widely distributed populations of a deer genus, contributing to the understanding and prediction of animals' responses to human activity.}, } @article {pmid37302594, year = {2023}, author = {Haas, D and Ilieva, M and Fritz, T and Galler, H and Habib, J and Kriso, A and Kropsch, M and Ofner-Kopeinig, P and Reinthaler, FF and Strasser, A and Zentner, E and Schalli, M}, title = {Background concentrations of airborne, culturable fungi and dust particles in urban, rural and mountain regions.}, journal = {The Science of the total environment}, volume = {892}, number = {}, pages = {164700}, doi = {10.1016/j.scitotenv.2023.164700}, pmid = {37302594}, issn = {1879-1026}, mesh = {Humans ; *Dust ; *Environmental Monitoring/methods ; Air Microbiology ; Fungi ; Spores, Fungal ; Seasons ; }, abstract = {Geographic location and meteorological factors can affect the content of bioaerosol concentrations. This study was conducted to determine the natural background concentrations of culturable fungal spores and dust particles in three different geographical areas. Focus was given to the dominant airborne genera Cladosporium, Penicillium, Aspergillus and the species Aspergillus fumigatus. The influence of weather conditions on the microorganism concentrations in urban, rural and mountain regions were examined. Possible correlations between particle counts and culturable fungal spore concentrations were investigated. 125 measurements of the air were conducted using the air sampler MAS-100NT® and the particle counter Alphasense OPC-N3. The analyses of the collected samples were based on culture methods using different media. The highest median of fungal spore concentrations was detected in the urban region and was of 2.0 × 10[3] CFU/m[3] for xerophilic fungi and 1.7 × 10[3] CFU/m[3] for the genus Cladosporium. The concentrations of fine and coarse particles in rural and urban regions were the highest of 1.9 × 10[7] pa/m[3] and 1.3 × 10[7] pa/m[3], respectively. Little cloud cover and slight wind had a positive influence on the concentration of fungal spores. Furthermore, correlations were observed between air temperature and the concentrations of xerophilic fungi as well as the genera Cladosporium. In contrast, relative humidity correlated negatively with total fungi and Cladosporium and no correlation was found with the other fungi. For the region of Styria in summer and early autumn, the natural background concentration for xerophilic fungi ranged between 3.5 × 10[2] and 4.7 × 10[3] CFU/m[3] air. No significant differences were detected between the fungal spore concentrations in urban, rural and mountainous regions. The data of this study could be used as a reference to compare the natural background concentrations of airborne culturable fungi in further studies concerning air quality assessment.}, } @article {pmid37301186, year = {2023}, author = {Yin, Q and Wu, T and Gao, R and Wu, L and Shi, Y and Wang, X and Wang, M and Xu, Z and Zhao, Y and Su, X and Su, Y and Han, X and Yuan, L and Xiang, L and Chen, S}, title = {Multi-omics reveal key enzymes involved in the formation of phenylpropanoid glucosides in Artemisia annua.}, journal = {Plant physiology and biochemistry : PPB}, volume = {201}, number = {}, pages = {107795}, doi = {10.1016/j.plaphy.2023.107795}, pmid = {37301186}, issn = {1873-2690}, mesh = {*Artemisia annua/metabolism ; Scopoletin/chemistry/metabolism/pharmacology ; Esculin/metabolism ; Multiomics ; Molecular Docking Simulation ; *Artemisinins/metabolism ; Glucosides/metabolism ; Glucose/metabolism ; Uridine Diphosphate/metabolism ; }, abstract = {Although mainly known for producing artemisinin, Artemisia annua is enriched in phenylpropanoid glucosides (PGs) with significant bioactivities. However, the biosynthesis of A. annua PGs is insufficiently investigated. Different A. annua ecotypes from distinct growing environments accumulate varying amounts of metabolites, including artemisinin and PGs such as scopolin. UDP-glucose:phenylpropanoid glucosyltransferases (UGTs) transfers glucose from UDP-glucose in PG biosynthesis. Here, we found that the low-artemisinin ecotype GS produces a higher amount of scopolin, compared to the high-artemisinin ecotype HN. By combining transcriptome and proteome analyses, we selected 28 candidate AaUGTs from 177 annotated AaUGTs. Using AlphaFold structural prediction and molecular docking, we determined the binding affinities of 16 AaUGTs. Seven of the AaUGTs enzymatically glycosylated phenylpropanoids. AaUGT25 converted scopoletin to scopolin and esculetin to esculin. The lack of accumulation of esculin in the leaf and the high catalytic efficiency of AaUGT25 on esculetin suggest that esculetin is methylated to scopoletin, the precursor of scopolin. We also discovered that AaOMT1, a previously uncharacterized O-methyltransferase, converts esculetin to scopoletin, suggesting an alternative route for producing scopoletin, which contributes to the high-level accumulation of scopolin in A. annua leaves. AaUGT1 and AaUGT25 responded to induction of stress-related phytohormones, implying the involvement of PGs in stress responses.}, } @article {pmid37297635, year = {2023}, author = {Ojukwu, EN and Okoye, HU and Saewyc, E}, title = {Social Correlates of HIV-Risky Behaviours among African Canadian Adolescents Living in British Columbia, Canada: A Secondary Data Analysis.}, journal = {International journal of environmental research and public health}, volume = {20}, number = {11}, pages = {}, pmid = {37297635}, issn = {1660-4601}, mesh = {Humans ; Adolescent ; British Columbia/epidemiology ; *Secondary Data Analysis ; Black or African American ; Sexual Behavior ; *HIV Infections/epidemiology ; Risk-Taking ; }, abstract = {Studies have linked HIV-risky behaviours among young people to several socio-contextual factors. However, the social factors that might increase African Canadian adolescents' exposure to HIV-risky behaviours, including unprotected sex and forced or multiple-sexual partnerships, have received little or no attention in the literature. Using data from the British Columbia Adolescent Health Surveys (2003-2018) and guided by intersectionality and socio-ecological frameworks, we examined the social determinants of HIV-risky behaviours (HRB) among African Canadian adolescents in British Columbia. We observed a general decline in HRB from 2008 to 2018. However, more than half (54.5%) of the 1042 who were sexually experienced in 2018 reported having 2 or more sexual partners, and nearly half reported condom-less sex. Our results demonstrate an important need to evaluate the impacts of several social factors on health outcomes for a unique, marginalized population.}, } @article {pmid37289204, year = {2023}, author = {Brown, MJM and Walker, BE and Black, N and Govaerts, RHA and Ondo, I and Turner, R and Nic Lughadha, E}, title = {rWCVP: a companion R package for the World Checklist of Vascular Plants.}, journal = {The New phytologist}, volume = {240}, number = {4}, pages = {1355-1365}, doi = {10.1111/nph.18919}, pmid = {37289204}, issn = {1469-8137}, mesh = {*Software ; Checklist ; *Tracheophyta ; Plants ; Databases, Factual ; }, abstract = {The World Checklist of Vascular Plants (WCVP) is an extremely valuable resource that is being used to address many fundamental and applied questions in plant science, conservation, ecology and evolution. However, databases of this size require data manipulation skills that pose a barrier to many potential users. Here, we present rWCVP, an open-source R package that aims to facilitate the use of the WCVP by providing clear, intuitive functions to execute many common tasks. These functions include taxonomic name reconciliation, geospatial integration, mapping and generation of multiple different summaries of the WCVP in both data and report format. We have included extensive documentation and tutorials, providing step-by-step guides that are accessible even to users with minimal programming experience. rWCVP is available on cran and GitHub.}, } @article {pmid37278908, year = {2023}, author = {Gao, H and Wu, M and Liu, H and Ou, Y and Zhang, T and Duan, X}, title = {Unraveling the Positive Effect of Soil Moisture on the Bioaugmentation of Petroleum-Contaminated Soil Using Bioinformatics.}, journal = {Microbial ecology}, volume = {86}, number = {4}, pages = {2436-2446}, pmid = {37278908}, issn = {1432-184X}, mesh = {*Petroleum ; Soil/chemistry ; *Soil Pollutants/analysis ; Soil Microbiology ; Biodegradation, Environmental ; Hydrocarbons/metabolism ; Bacteria/genetics/metabolism ; Computational Biology ; }, abstract = {Petroleum contamination is a severe threat to the soil environment. Previous studies have demonstrated that petroleum degradation efficiency is promoted by enhancing soil moisture content (MC). However, the effects of MC on soil microbial ecological functions during bioremediation remain unclear. Here, we investigated the impacts of 5% and 15% of moisture contents on petroleum degradation, soil microbial structures and functions, and the related genes using high-throughput sequencing and gene function prediction. Results indicated that petroleum biodegradation efficiency was increased by 8.06% in the soils with 15% MC when compared to that with 5% of MC. The complexity and stability of soil microbial community structures with 15% MC were higher than those in the soils with 5% MC when hydrocarbon-degrading bacterial flora (HDBF) were inoculated into the soils. Fifteen percent of moisture content strengthened the interaction of the bacterial community network and reduced the loss of some key bacteria species including Mycobacterium, Sphingomonas, and Gemmatimonas. Some downregulated gene pathways relating to bioaugmentation were enhanced in the soils with 15% MC. The results suggested that the dynamic balances of microbial communities and the metabolic interactions by 15% MC treatment are the driving forces for the enhancement of bioremediation in petroleum-contaminated soil.}, } @article {pmid37277721, year = {2023}, author = {Zhong, H and Luo, J and Tang, L and Liao, S and Lu, Z and Lin, G and Murphy, RW and Liu, L}, title = {Association filtering and generative adversarial networks for predicting lncRNA-associated disease.}, journal = {BMC bioinformatics}, volume = {24}, number = {1}, pages = {234}, pmid = {37277721}, issn = {1471-2105}, support = {grant no. 2019FY003027//Yunnan Provincial Science and Technology Department-Yunnan University Double First-Class Joint Fund Key Projects/ ; grant no. 2022YFC2602500//National Key R&D Program of China/ ; grant no. 61862067, U1902201//National Natural Science Foundation of China/ ; grant no. 202201AT070042//Applied Basic Research Project in Yunnan Province/ ; }, mesh = {*RNA, Long Noncoding/genetics ; Algorithms ; Computational Biology/methods ; }, abstract = {BACKGROUND: Long non-coding RNA (lncRNA) closely associates with numerous biological processes, and with many diseases. Therefore, lncRNA-disease association prediction helps obtain relevant biological information and understand pathogenesis, and thus better diagnose preventable diseases.

RESULTS: Herein, we offer the LDAF_GAN method for predicting lncRNA-associated disease based on association filtering and generative adversarial networks. Experimentation used two types of data: lncRNA-disease associated data without lncRNA sequence features, and fused lncRNA sequence features. LDAF_GAN uses a generator and discriminator, and differs from the original GAN by the addition of a filtering operation and negative sampling. Filtering allows the generator output to filter out unassociated diseases before being fed into the discriminator. Thus, the results generated by the model focuses only on lncRNAs associated with disease. Negative sampling takes a portion of disease terms with 0 from the association matrix as negative samples, which are assumed to be unassociated with lncRNA. A regular term is added to the loss function to avoid producing a vector with all values of 1, which can fool the discriminator. Thus, the model requires that generated positive samples are close to 1, and negative samples are close to 0. The model achieved a superior fitting effect; LDAF_GAN had superior performance in predicting fivefold cross-validations on the two datasets with AUC values of 0.9265 and 0.9278, respectively. In the case study, LDAF_GAN predicted disease association for six lncRNAs-H19, MALAT1, XIST, ZFAS1, UCA1, and ZEB1-AS1-and with the top ten predictions of 100%, 80%, 90%, 90%, 100%, and 90%, respectively, which were reported by previous studies.

CONCLUSION: LDAF_GAN efficiently predicts the potential association of existing lncRNAs and the potential association of new lncRNAs with diseases. The results of fivefold cross-validation, tenfold cross-validation, and case studies suggest that the model has great predictive potential for lncRNA-disease association prediction.}, } @article {pmid37273367, year = {2023}, author = {Ekram, R and Nazer, MS}, title = {Hospital Admission Profile Due to Osteoarthritis: An Ecological Study.}, journal = {Cureus}, volume = {15}, number = {5}, pages = {e38435}, pmid = {37273367}, issn = {2168-8184}, abstract = {Background Osteoarthritis (OA) is also known as degenerative joint disease and is considered the major cause of joint pain and disability. Furthermore, OA is the most common, costly, and disabling form of joint diseases. The objective of this study is to explore the hospital admission profile due to OA between the period 1999 and 2019 in England and Wales. Method This is an ecological study that used health care data in the United Kingdom. Patients who were hospitalized for OA in England and Wales between 1999 and 2019 formed the study population. The Hospital Episode Statistics in England and the Patient Episode Database for Wales databases were used in this study. The difference in the admission rate during the study period was estimated using the chi-squared test. Results The admission rate during the study period increased by 112.1% for all hospital admission related to OA. The most common type of admission was related to gonarthrosis, which accounted for 46.7% of the total number of admissions for OA. The increase in admission rate across different types of admissions related to OA was not consistent. The highest increase in the admission rate was observed for polyarthrosis (604.6%). Admission rates related to OA were observed to be directly related to age. The highest increase in the admission rate during the study period was for the age group of 15-59 years (102.1%). Admission rate due to OA was higher among females compared to males. Conclusion The increase in admission rates for the various OA-related admissions was not consistent. This study found that the age range of 15 to 59 years experienced the greatest increase in admission rates. Female gender is a high risk factor for OA, especially in women around menopause.}, } @article {pmid37270983, year = {2023}, author = {Vo, HT and Vrachioli, M and Frick, F and Sauer, J and Brucet Balmana, S and Benejam Vidal, L and Mehner, T and Lemmens, P and Oertli, B and Boissezon, A and Beklioğlu, M and Dolcerocca, A and Meerhoff, M}, title = {Socio-economic or environmental benefits from pondscapes? Deriving stakeholder preferences using analytic hierarchy process and compositional data analysis.}, journal = {Journal of environmental management}, volume = {342}, number = {}, pages = {118298}, doi = {10.1016/j.jenvman.2023.118298}, pmid = {37270983}, issn = {1095-8630}, mesh = {Humans ; *Ecosystem ; *Analytic Hierarchy Process ; Biodiversity ; Ponds ; Socioeconomic Factors ; Conservation of Natural Resources ; }, abstract = {Ponds occupy a large share of standing water worldwide and play an important role in providing various ecosystem services. There are concerted efforts of the European Union either to create new ponds, or to restore and preserve existing ponds as nature-based solutions to provide benefits to ecosystem and human well-being. As part of the EU PONDERFUL project, selected pondscapes (i.e. landscapes of ponds) in eight different countries - hereafter "demo-sites", are studied to comprehensively understand their characteristics and their efficiency to provide ecosystem services. In addition, the needs and knowledge of stakeholders who own, work, research, or benefit from the pondscapes are also important, because of their capabilities to create, manage and develop the pondscapes. Therefore, we established connection with stakeholders to study their preferences and visions on the pondscapes. Using the analytic hierarchy process, this study shows that in general stakeholders in the European and Turkish demo-sites prefer environmental benefits to economic benefits, while stakeholders in the Uruguayan demo-sites rank the economic benefits higher. More specifically, in the European and Turkish demo-sites, the biodiversity benefits, i.e. life-cycle maintenance, habitat and gene pool protection, receive the highest ranking among all groups. On the other hand, stakeholders at the Uruguayan demo-sites rank provisioning benefits as the most important, because many ponds in Uruguayan demo-sites are being used for agricultural purposes. Understanding those preferences helps policy makers to address the needs of stakeholders more correctly, when considering any action or policy for the pondscapes.}, } @article {pmid37267326, year = {2023}, author = {Spencer, N and Łukasik, P and Meyer, M and Veloso, C and McCutcheon, JP}, title = {No Transcriptional Compensation for Extreme Gene Dosage Imbalance in Fragmented Bacterial Endosymbionts of Cicadas.}, journal = {Genome biology and evolution}, volume = {15}, number = {6}, pages = {}, pmid = {37267326}, issn = {1759-6653}, mesh = {Animals ; Phylogeny ; *Hemiptera/microbiology ; Symbiosis/genetics ; *Flavobacteriaceae/genetics ; *Alphaproteobacteria/genetics ; Genome, Bacterial ; Gene Dosage ; Evolution, Molecular ; }, abstract = {Bacteria that form long-term intracellular associations with host cells lose many genes, a process that often results in tiny, gene-dense, and stable genomes. Paradoxically, the some of the same evolutionary processes that drive genome reduction and simplification may also cause genome expansion and complexification. A bacterial endosymbiont of cicadas, Hodgkinia cicadicola, exemplifies this paradox. In many cicada species, a single Hodgkinia lineage with a tiny, gene-dense genome has split into several interdependent cell and genome lineages. Each new Hodgkinia lineage encodes a unique subset of the ancestral unsplit genome in a complementary way, such that the collective gene contents of all lineages match the total found in the ancestral single genome. This splitting creates genetically distinct Hodgkinia cells that must function together to carry out basic cellular processes. It also creates a gene dosage problem where some genes are encoded by only a small fraction of cells while others are much more abundant. Here, by sequencing DNA and RNA of Hodgkinia from different cicada species with different amounts of splitting-along with its structurally stable, unsplit partner endosymbiont Sulcia muelleri-we show that Hodgkinia does not transcriptionally compensate to rescue the wildly unbalanced gene and genome ratios that result from lineage splitting. We also find that Hodgkinia has a reduced capacity for basic transcriptional control independent of the splitting process. Our findings reveal another layer of degeneration further pushing the limits of canonical molecular and cell biology in Hodgkinia and may partially explain its propensity to go extinct through symbiont replacement.}, } @article {pmid37265476, year = {2023}, author = {Boyes, D and , and , and , and , and , and Hammond, J and , }, title = {The genome sequence of the Elbow-stripe Grass-veneer, Agriphila geniculea (Haworth, 1811).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {86}, pmid = {37265476}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual female Agriphila geniculea (the Elbow-stripe Grass-veneer; Arthropoda; Insecta; Lepidoptera; Crambidae). The genome sequence is 781.6 megabases in span. Most of the assembly is scaffolded into 30 chromosomal pseudomolecules, including the Z and W sex chromosomes. The mitochondrial genome has also been assembled and is 15.4 kilobases in length. Gene annotation of this assembly on Ensembl identified 22,132 protein coding genes.}, } @article {pmid37263997, year = {2023}, author = {Duncanson, L and Liang, M and Leitold, V and Armston, J and Krishna Moorthy, SM and Dubayah, R and Costedoat, S and Enquist, BJ and Fatoyinbo, L and Goetz, SJ and Gonzalez-Roglich, M and Merow, C and Roehrdanz, PR and Tabor, K and Zvoleff, A}, title = {The effectiveness of global protected areas for climate change mitigation.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {2908}, pmid = {37263997}, issn = {2041-1723}, support = {80NSSC21K0196//National Aeronautics and Space Administration (NASA)/ ; 80NSSC21K0196//National Aeronautics and Space Administration (NASA)/ ; NNL 15AA03C//National Aeronautics and Space Administration (NASA)/ ; NNL 15AA03C//National Aeronautics and Space Administration (NASA)/ ; 80NSSC21K0189//National Aeronautics and Space Administration (NASA)/ ; OAC1934389//National Science Foundation (NSF)/ ; OAC1934389//National Science Foundation (NSF)/ ; 80NSSC19K0186//National Science Foundation (NSF)/ ; OAC1934389//National Science Foundation (NSF)/ ; OAC1934389//National Science Foundation (NSF)/ ; }, abstract = {Forests play a critical role in stabilizing Earth's climate. Establishing protected areas (PAs) represents one approach to forest conservation, but PAs were rarely created to mitigate climate change. The global impact of PAs on the carbon cycle has not previously been quantified due to a lack of accurate global-scale carbon stock maps. Here we used ~412 million lidar samples from NASA's GEDI mission to estimate a total PA aboveground carbon (C) stock of 61.43 Gt (+/- 0.31), 26% of all mapped terrestrial woody C. Of this total, 9.65 + /- 0.88 Gt of additional carbon was attributed to PA status. These higher C stocks are primarily from avoided emissions from deforestation and degradation in PAs compared to unprotected forests. This total is roughly equivalent to one year of annual global fossil fuel emissions. These results underscore the importance of conservation of high biomass forests for avoiding carbon emissions and preserving future sequestration.}, } @article {pmid37263027, year = {2023}, author = {Mokarram, M and Mokarram, MJ and Najafi, A}, title = {Thermal power plants pollution assessment based on deep neural networks, remote sensing, and GIS: A real case study in Iran.}, journal = {Marine pollution bulletin}, volume = {192}, number = {}, pages = {115069}, doi = {10.1016/j.marpolbul.2023.115069}, pmid = {37263027}, issn = {1879-3363}, mesh = {Environmental Monitoring/methods ; Geographic Information Systems ; Iran ; Carbon Dioxide/analysis ; Remote Sensing Technology ; *Air Pollution/analysis ; Neural Networks, Computer ; Water/analysis ; Power Plants ; *Air Pollutants/analysis ; }, abstract = {To investigate the impact of the Bandar Abbas thermal power plant on the waters of the Persian Gulf coast, a combination of satellite images and ground data was utilized to determine the Sea Surface Temperature (SST) as a thermal index, Total Organic Carbon (TOC) and Chemical Oxygen Demand (COD) as biological indices. Additionally, measurements of SO2, O3, NO2, CO2, CO, and CH4 values in the atmosphere were taken to determine the plant's impact on air pollution. Temperature values of the water for different months were predicted using Long Short-Term Memory (LSTM), Support Vector Regression (SVR), and Cascade neural networks. The results indicate that the waters near thermal power plants exhibit the highest temperatures in July and September, with temperatures reaching approximately 50 °C. Furthermore, the SST values were found to be strongly correlated with ecological indices. The Multiple Linear Regression (MLR) analysis revealed a strong correlation between the temperature and TOC, COD, and O2 in water (RTOC[2]=0.98), [Formula: see text] , RCOD[2]=0.87 and O3, NO3, CO2, and CO in the air ([Formula: see text]). Finally, the results demonstrate that the LSTM method exhibited high accuracy in predicting the water temperature (R[2] = 0.98).}, } @article {pmid37262156, year = {2023}, author = {Gao, H and Hamp, T and Ede, J and Schraiber, JG and McRae, J and Singer-Berk, M and Yang, Y and Dietrich, ASD and Fiziev, PP and Kuderna, LFK and Sundaram, L and Wu, Y and Adhikari, A and Field, Y and Chen, C and Batzoglou, S and Aguet, F and Lemire, G and Reimers, R and Balick, D and Janiak, MC and Kuhlwilm, M and Orkin, JD and Manu, S and Valenzuela, A and Bergman, J and Rousselle, M and Silva, FE and Agueda, L and Blanc, J and Gut, M and de Vries, D and Goodhead, I and Harris, RA and Raveendran, M and Jensen, A and Chuma, IS and Horvath, JE and Hvilsom, C and Juan, D and Frandsen, P and de Melo, FR and Bertuol, F and Byrne, H and Sampaio, I and Farias, I and do Amaral, JV and Messias, M and da Silva, MNF and Trivedi, M and Rossi, R and Hrbek, T and Andriaholinirina, N and Rabarivola, CJ and Zaramody, A and Jolly, CJ and Phillips-Conroy, J and Wilkerson, G and Abee, C and Simmons, JH and Fernandez-Duque, E and Kanthaswamy, S and Shiferaw, F and Wu, D and Zhou, L and Shao, Y and Zhang, G and Keyyu, JD and Knauf, S and Le, MD and Lizano, E and Merker, S and Navarro, A and Bataillon, T and Nadler, T and Khor, CC and Lee, J and Tan, P and Lim, WK and Kitchener, AC and Zinner, D and Gut, I and Melin, A and Guschanski, K and Schierup, MH and Beck, RMD and Umapathy, G and Roos, C and Boubli, JP and Lek, M and Sunyaev, S and O'Donnell-Luria, A and Rehm, HL and Xu, J and Rogers, J and Marques-Bonet, T and Farh, KK}, title = {The landscape of tolerated genetic variation in humans and primates.}, journal = {Science (New York, N.Y.)}, volume = {380}, number = {6648}, pages = {eabn8153}, pmid = {37262156}, issn = {1095-9203}, support = {P30 AG012836/AG/NIA NIH HHS/United States ; R24 HD044964/HD/NICHD NIH HHS/United States ; R01 GM089753/GM/NIGMS NIH HHS/United States ; T32 GM007748/GM/NIGMS NIH HHS/United States ; P40 OD024628/OD/NIH HHS/United States ; }, mesh = {Animals ; Humans ; Base Sequence ; Gene Frequency ; *Genetic Variation ; *Primates/genetics ; Whole Genome Sequencing ; }, abstract = {Personalized genome sequencing has revealed millions of genetic differences between individuals, but our understanding of their clinical relevance remains largely incomplete. To systematically decipher the effects of human genetic variants, we obtained whole-genome sequencing data for 809 individuals from 233 primate species and identified 4.3 million common protein-altering variants with orthologs in humans. We show that these variants can be inferred to have nondeleterious effects in humans based on their presence at high allele frequencies in other primate populations. We use this resource to classify 6% of all possible human protein-altering variants as likely benign and impute the pathogenicity of the remaining 94% of variants with deep learning, achieving state-of-the-art accuracy for diagnosing pathogenic variants in patients with genetic diseases.}, } @article {pmid37259063, year = {2023}, author = {Ormaasen, I and Rudi, K and Diep, DB and Snipen, L}, title = {Metagenome-mining indicates an association between bacteriocin presence and strain diversity in the infant gut.}, journal = {BMC genomics}, volume = {24}, number = {1}, pages = {295}, pmid = {37259063}, issn = {1471-2164}, mesh = {*Metagenome ; Humans ; Child, Preschool ; Child ; Adolescent ; Young Adult ; Adult ; Middle Aged ; Aged ; Aged, 80 and over ; Data Mining ; *Gastrointestinal Microbiome/drug effects ; Bacteriocins/pharmacology ; Genome ; }, abstract = {BACKGROUND: Our knowledge about the ecological role of bacterial antimicrobial peptides (bacteriocins) in the human gut is limited, particularly in relation to their role in the diversification of the gut microbiota during early life. The aim of this paper was therefore to address associations between bacteriocins and bacterial diversity in the human gut microbiota. To investigate this, we did an extensive screening of 2564 healthy human gut metagenomes for the presence of predicted bacteriocin-encoding genes, comparing bacteriocin gene presence to strain diversity and age.

RESULTS: We found that the abundance of bacteriocin genes was significantly higher in infant-like metagenomes (< 2 years) compared to adult-like metagenomes (2-107 years). By comparing infant-like metagenomes with and without a given bacteriocin, we found that bacteriocin presence was associated with increased strain diversities.

CONCLUSIONS: Our findings indicate that bacteriocins may play a role in the strain diversification during the infant gut microbiota establishment.}, } @article {pmid37258861, year = {2023}, author = {Abdelsalam, NA and Elshora, H and El-Hadidi, M}, title = {Interactive Web-Based Services for Metagenomic Data Analysis and Comparisons.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2649}, number = {}, pages = {133-174}, pmid = {37258861}, issn = {1940-6029}, mesh = {*Metagenomics/methods ; Metagenome ; *Microbiota/genetics ; Ecology ; Computational Biology/methods ; Data Analysis ; }, abstract = {Recently, sequencing technologies have become readily available, and scientists are more motivated to conduct metagenomic research to unveil the potential of a myriad of ecosystems and biomes. Metagenomics studies the composition and functions of microbial communities and paves the way to multiple applications in medicine, industry, and ecology. Nonetheless, the immense amount of sequencing data of metagenomics research and the few user-friendly analysis tools and pipelines carry a new challenge to the data analysis.Web-based bioinformatics tools are now being developed to facilitate the analysis of complex metagenomic data without prior knowledge of any programming languages or special installation. Specialized web tools help answer researchers' main questions on the taxonomic classification, functional capabilities, discrepancies between two ecosystems, and the probable functional correlations between the members of a specific microbial community. With an Internet connection and a few clicks, researchers can conveniently and efficiently analyze the metagenomic datasets, summarize results, and visualize key information on the composition and the functional potential of metagenomic samples under study. This chapter provides a simple guide to a few of the fundamental web-based services used for metagenomic data analyses, such as BV-BRC, RDP, MG-RAST, MicrobiomeAnalyst, METAGENassist, and MGnify.}, } @article {pmid37258857, year = {2023}, author = {Wang, D}, title = {Metagenomics Databases for Bacteria.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2649}, number = {}, pages = {55-67}, pmid = {37258857}, issn = {1940-6029}, mesh = {Phylogeny ; *Metagenomics ; Bacteria/genetics ; Databases, Genetic ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The booming sequencing technologies have turned metagenomics into a widely used tool for microbe-related studies, especially in the areas of clinical medicine and ecology. Accordingly, the toolkit of metagenomics data analysis is growing stronger to provide multiple approaches for solving various biological questions and understanding the component and function of microbiome. As part of the toolkit, metagenomics databases play a central role in the creation and maintenance of processed data such as definition of taxonomic classifications, annotation of gene functions, sequence alignment, and phylogenetic tree inference. The availability of a large quantity of high-quality bacterial genomic sequences contributes significantly to the construction and update of metagenomics databases, which constitute the core resource for metagenomics data analysis at various scales. This chapter presents the key concepts, technical options, and challenges for metagenomics projects as well as the curation processes and versatile functions for the four representative bacterial metagenomics databases, including Greengenes, SILVA, Ribosomal Database Project (RDP), and Genome Taxonomy Database (GTDB).}, } @article {pmid37255989, year = {2023}, author = {Pauley, E and Drake, TM and Griffith, DM and Sigfrid, L and Lone, NI and Harrison, EM and Baillie, JK and Scott, JT and Walsh, TS and Semple, MG and Docherty, AB and , }, title = {Recovery from Covid-19 critical illness: A secondary analysis of the ISARIC4C CCP-UK cohort study and the RECOVER trial.}, journal = {Journal of the Intensive Care Society}, volume = {24}, number = {2}, pages = {162-169}, pmid = {37255989}, issn = {1751-1437}, support = {MC_PC_19025/MRC_/Medical Research Council/United Kingdom ; MC_PC_19026/MRC_/Medical Research Council/United Kingdom ; MC_PC_19059/MRC_/Medical Research Council/United Kingdom ; MC_UU_12014/8/MRC_/Medical Research Council/United Kingdom ; }, abstract = {BACKGROUND: We aimed to compare the prevalence and severity of fatigue in survivors of Covid-19 versus non-Covid-19 critical illness, and to explore potential associations between baseline characteristics and worse recovery.

METHODS: We conducted a secondary analysis of two prospectively collected datasets. The population included was 92 patients who received invasive mechanical ventilation (IMV) with Covid-19, and 240 patients who received IMV with non-Covid-19 illness before the pandemic. Follow-up data were collected post-hospital discharge using self-reported questionnaires. The main outcome measures were self-reported fatigue severity and the prevalence of severe fatigue (severity >7/10) 3 and 12-months post-hospital discharge.

RESULTS: Covid-19 IMV-patients were significantly younger with less prior comorbidity, and more males, than pre-pandemic IMV-patients. At 3-months, the prevalence (38.9% [7/18] vs. 27.1% [51/188]) and severity (median 5.5/10 vs 5.0/10) of fatigue were similar between the Covid-19 and pre-pandemic populations, respectively. At 6-months, the prevalence (10.3% [3/29] vs. 32.5% [54/166]) and severity (median 2.0/10 vs. 5.7/10) of fatigue were less in the Covid-19 cohort. In the total sample of IMV-patients included (i.e. all Covid-19 and pre-pandemic patients), having Covid-19 was significantly associated with less severe fatigue (severity <7/10) after adjusting for age, sex and prior comorbidity (adjusted OR 0.35 (95%CI 0.15-0.76, p=0.01).

CONCLUSION: Fatigue may be less severe after Covid-19 than after other critical illness.}, } @article {pmid37253577, year = {2023}, author = {Lee, K and McMorris, BJ and Chi, CL and Looman, WS and Burns, MK and Delaney, CW}, title = {Using data-driven analytics and ecological systems theory to identify risk and protective factors for school absenteeism among secondary students.}, journal = {Journal of school psychology}, volume = {98}, number = {}, pages = {148-180}, doi = {10.1016/j.jsp.2023.03.002}, pmid = {37253577}, issn = {1873-3506}, mesh = {Adolescent ; Humans ; Protective Factors ; *Absenteeism ; *Students ; Schools ; Forecasting ; }, abstract = {Chronic absenteeism is an administrative term defining extreme failure for students to be present at school, which can have devastating long-term impacts on students. Although numerous prior studies have investigated associated variables and interventions, there are few studies that utilize both theory-driven and data-informed approaches to investigate absenteeism. The current study applied data-driven machine learning techniques, grounded in "The Kids and Teens at School" (KiTeS) theoretical framework, to student-level data (N = 121,005) to identify risk and protective variables that are highly associated with school absences. A total of 18 risk and protective variables were identified; all 18 variables were characteristics of the microsystem or mesosystem, emphasizing school absences' proximity to variables within inner ecological systems rather than the exosystem or macrosystem. Implications for future studies and health infrastructure are discussed.}, } @article {pmid37253238, year = {2024}, author = {Borg, JM and Buskell, A and Kapitany, R and Powers, ST and Reindl, E and Tennie, C}, title = {Evolved Open-Endedness in Cultural Evolution: A New Dimension in Open-Ended Evolution Research.}, journal = {Artificial life}, volume = {30}, number = {3}, pages = {417-438}, doi = {10.1162/artl_a_00406}, pmid = {37253238}, issn = {1530-9185}, mesh = {*Cultural Evolution ; Humans ; *Biological Evolution ; }, abstract = {The goal of Artificial Life research, as articulated by Chris Langton, is "to contribute to theoretical biology by locating life-as-we-know-it within the larger picture of life-as-it-could-be." The study and pursuit of open-ended evolution in artificial evolutionary systems exemplify this goal. However, open-ended evolution research is hampered by two fundamental issues: the struggle to replicate open-endedness in an artificial evolutionary system and our assumption that we only have one system (genetic evolution) from which to draw inspiration. We argue not only that cultural evolution should be seen as another real-world example of an open-ended evolutionary system but that the unique qualities seen in cultural evolution provide us with a new perspective from which we can assess the fundamental properties of, and ask new questions about, open-ended evolutionary systems, especially with regard to evolved open-endedness and transitions from bounded to unbounded evolution. Here we provide an overview of culture as an evolutionary system, highlight the interesting case of human cultural evolution as an open-ended evolutionary system, and contextualize cultural evolution by developing a new framework of (evolved) open-ended evolution. We go on to provide a set of new questions that can be asked once we consider cultural evolution within the framework of open-ended evolution and introduce new insights that we may be able to gain about evolved open-endedness as a result of asking these questions.}, } @article {pmid37252922, year = {2023}, author = {Hassard, F and Vu, M and Rahimzadeh, S and Castro-Gutierrez, V and Stanton, I and Burczynska, B and Wildeboer, D and Baio, G and Brown, MR and Garelick, H and Hofman, J and Kasprzyk-Hordern, B and Majeed, A and Priest, S and Denise, H and Khalifa, M and Bassano, I and Wade, MJ and Grimsley, J and Lundy, L and Singer, AC and Di Cesare, M}, title = {Wastewater monitoring for detection of public health markers during the COVID-19 pandemic: Near-source monitoring of schools in England over an academic year.}, journal = {PloS one}, volume = {18}, number = {5}, pages = {e0286259}, pmid = {37252922}, issn = {1932-6203}, mesh = {Humans ; *COVID-19/epidemiology ; SARS-CoV-2/genetics ; Wastewater ; Public Health ; Pandemics ; Wastewater-Based Epidemiological Monitoring ; England/epidemiology ; RNA, Viral ; }, abstract = {BACKGROUND: Schools are high-risk settings for infectious disease transmission. Wastewater monitoring for infectious diseases has been used to identify and mitigate outbreaks in many near-source settings during the COVID-19 pandemic, including universities and hospitals but less is known about the technology when applied for school health protection. This study aimed to implement a wastewater surveillance system to detect SARS-CoV-2 and other public health markers from wastewater in schools in England.

METHODS: A total of 855 wastewater samples were collected from 16 schools (10 primary, 5 secondary and 1 post-16 and further education) over 10 months of school term time. Wastewater was analysed for SARS-CoV-2 genomic copies of N1 and E genes by RT-qPCR. A subset of wastewater samples was sent for genomic sequencing, enabling determination of the presence of SARS-CoV-2 and emergence of variant(s) contributing to COVID-19 infections within schools. In total, >280 microbial pathogens and >1200 AMR genes were screened using RT-qPCR and metagenomics to consider the utility of these additional targets to further inform on health threats within the schools.

RESULTS: We report on wastewater-based surveillance for COVID-19 within English primary, secondary and further education schools over a full academic year (October 2020 to July 2021). The highest positivity rate (80.4%) was observed in the week commencing 30th November 2020 during the emergence of the Alpha variant, indicating most schools contained people who were shedding the virus. There was high SARS-CoV-2 amplicon concentration (up to 9.2x106 GC/L) detected over the summer term (8th June - 6th July 2021) during Delta variant prevalence. The summer increase of SARS-CoV-2 in school wastewater was reflected in age-specific clinical COVID-19 cases. Alpha variant and Delta variant were identified in the wastewater by sequencing of samples collected from December to March and June to July, respectively. Lead/lag analysis between SARS-CoV-2 concentrations in school and WWTP data sets show a maximum correlation between the two-time series when school data are lagged by two weeks. Furthermore, wastewater sample enrichment coupled with metagenomic sequencing and rapid informatics enabled the detection of other clinically relevant viral and bacterial pathogens and AMR.

CONCLUSIONS: Passive wastewater monitoring surveillance in schools can identify cases of COVID-19. Samples can be sequenced to monitor for emerging and current variants of concern at the resolution of school catchments. Wastewater based monitoring for SARS-CoV-2 is a useful tool for SARS-CoV-2 passive surveillance and could be applied for case identification and containment, and mitigation in schools and other congregate settings with high risks of transmission. Wastewater monitoring enables public health authorities to develop targeted prevention and education programmes for hygiene measures within undertested communities across a broad range of use cases.}, } @article {pmid37251658, year = {2023}, author = {Boyes, D and , and , and , and , and , and Lees, D and , }, title = {The genome sequence of the long-horned flat-body, Carcina quercana (Fabricius, 1775).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {16}, pmid = {37251658}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual male Carcina quercana (the long-horned flat-body; Arthropoda; Insecta; Lepidoptera; Depressariidae). The genome sequence is 409 megabases in span. Most of the assembly (99.96%) is scaffolded into 30 chromosomal pseudomolecules, including the assembled Z sex chromosome. The complete mitochondrial genome was also assembled and is 15.3 kilobases in length. Gene annotation of this assembly on Ensembl identified 18,108 protein coding genes.}, } @article {pmid37251651, year = {2023}, author = {Dhellemmes, F and Aspillaga, E and Monk, CT}, title = {ATfiltR: A solution for managing and filtering detections from passive acoustic telemetry data.}, journal = {MethodsX}, volume = {10}, number = {}, pages = {102222}, pmid = {37251651}, issn = {2215-0161}, abstract = {Acoustic telemetry is a popular and cost-efficient method for tracking the movements of animals in the aquatic ecosystem. But data acquired via acoustic telemetry often contains spurious detections that must be identified and excluded by researchers to ensure valid results. Such data management is difficult as the amount of data collected often surpasses the capabilities of simple spreadsheet applications. ATfiltR is an open-source package programmed in R that allows users to integrate all telemetry data collected into a single file, to conditionally attribute animal data and location data to detections and to filter spurious detections based on customizable rules. Such tool will likely be useful to new researchers in acoustic telemetry and enhance results reproducibility.•ATfiltR compiles telemetry files and identifies and stores all data that was collected outside of your study period (e.g. when your receivers were on land for servicing) elsewhere.•As spurious detections are unlikely to appear sequentially in the data, ATfiltR finds all detections that occurred only once (per receiver or in the whole array) within a user-designated time period and stores them elsewhere.•ATfiltR identifies detections that are impossible given the animals' swimming speeds and the receivers detection range and stores them elsewhere.}, } @article {pmid37247155, year = {2023}, author = {Wang, Y and Lin, C and Wang, H and Wang, W and Wang, S and Zheng, R}, title = {Implementation of pollution source assessment and treatment strategy for plateau railway construction in China: an AHP-cloud model approach.}, journal = {Environmental monitoring and assessment}, volume = {195}, number = {6}, pages = {749}, pmid = {37247155}, issn = {1573-2959}, mesh = {*Analytic Hierarchy Process ; *Sewage ; Environmental Monitoring ; Environmental Pollution ; China ; }, abstract = {During the construction process of railways in the plateau region, various types of pollution sources can have serious or even irreversible impacts on the plateau ecology. To address pollution source treatment during the construction process, protect the ecological environment along the railway, and maintain the ecological balance, we collected geological and environmental data and analyzed the influencing factors of pollution sources. Taking sewage as the main research subject, we propose a new method based on the Analytic Hierarchy Process (AHP)-cloud model to classify the pollution source treatment level, establish an index system, and select the ecological environment level, sewage rate, and pollutant characteristics as the three main influencing factors. Finally, we divide the pollution source treatment level into I, II, and III, corresponding to V1 = {I-level} = {high impact}, V2 = {II-level} = {moderate impact}, and V3 = {III-level} = {low impact} . Based on the comprehensive factor weight analysis and the field engineering conditions of the studied railway in the western plateau of China, we classify the pollution source treatment level of six tunnels and propose treatment suggestions for each level. To advance the efficient implementation of environmental protection during the construction of the plateau railway, we propose three policy recommendations that can positively contribute to environmental protection and green development. This work provides theoretical and technical guidance for the treatment of pollution sources in the construction of the plateau railway, which also serves as a significant reference for other similar projects.}, } @article {pmid37244965, year = {2023}, author = {Mattalia, G and Svanberg, I and Ståhlberg, S and Kuznetsova, N and Prūse, B and Kolosova, V and Aziz, MA and Kalle, R and Sõukand, R}, title = {Outdoor activities foster local plant knowledge in Karelia, NE Europe.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {8627}, pmid = {37244965}, issn = {2045-2322}, support = {714874/ERC_/European Research Council/International ; }, mesh = {Humans ; Adult ; Child ; Europe ; Finland/epidemiology ; *Plants, Edible ; *Allergens ; Food ; }, abstract = {Wild edible plants, particularly berries, are relevant nutritional elements in the Nordic countries. In contrast to decreasing global trends, approximately 60% of the Finnish population is actively involved in (berry) foraging. We conducted 67 interviews with Finns and Karelians living in Finnish Karelia to: (a) detect the use of wild edible plants, (b) compare those results with the published data about neighbouring Russian Karelians, and (c) document the sources of local plant knowledge. The results revealed three main findings. First, we observed a similarity in wild food plant knowledge among Karelians and Finns from Karelia. Second, we detected divergences in wild food plant knowledge among Karelians living on both sides of the Finnish-Russian border. Third, the sources of local plant knowledge include vertical transmission, acquisition through literary sources, acquisition from "green" nature shops promoting healthy lifestyles, childhood foraging activities performed during the famine period following WWII, and outdoor recreational activities. We argue that the last two types of activities in particular may have influenced knowledge and connectedness with the surrounding environment and its resources at a stage of life that is crucial for shaping adult environmental behaviours. Future research should address the role of outdoor activities in maintaining (and possibly enhancing) local ecological knowledge in the Nordic countries.}, } @article {pmid37243840, year = {2024}, author = {Chaves, T and Azevedo, Á and Caldas, IM}, title = {Cheiloscopy in sex estimation: a systematic review.}, journal = {Forensic science, medicine, and pathology}, volume = {20}, number = {1}, pages = {280-292}, pmid = {37243840}, issn = {1556-2891}, support = {UIDB/04004/2020//FCT-MCTES/ ; }, mesh = {Humans ; Databases, Factual ; *Sex Determination Analysis/methods ; }, abstract = {This study aimed to conduct a systematic review to gather evidence to clarify if cheiloscopy can be used in sex estimation and identify the reasons behind the lack of consensus in the scientific community. The systematic review was performed following the PRISMA guidelines. A bibliographic survey was conducted in PubMed, Scopus, and Web of Science databases, restricted to articles published between 2010 and 2020. Studies were selected according to eligibility criteria, and then the study data were collected. The risk of bias in each study was assessed and applied as additional inclusion or exclusion criteria. The results of the articles eligible for analysis were synthesized using a descriptive approach. In the 41 included studies, several methodological flaws and variations between studies that contribute to the discrepancy in results were identified. The data gathered allowed us to conclude that there is no strong scientific evidence to support the use of cheiloscopy in sex estimation, as there is no specific pattern for each sex, which reduces the criminalistic interest of cheiloscopy in estimating this parameter.}, } @article {pmid37243228, year = {2023}, author = {Tokito, T and Kido, T and Muramatsu, K and Tokutsu, K and Okuno, D and Yura, H and Takemoto, S and Ishimoto, H and Takazono, T and Sakamoto, N and Obase, Y and Ishimatsu, Y and Fujino, Y and Yatera, K and Fushimi, K and Matsuda, S and Mukae, H}, title = {Impact of Administering Intravenous Azithromycin within 7 Days of Hospitalization for Influenza Virus Pneumonia: A Propensity Score Analysis Using a Nationwide Administrative Database.}, journal = {Viruses}, volume = {15}, number = {5}, pages = {}, pmid = {37243228}, issn = {1999-4915}, mesh = {Humans ; Azithromycin/therapeutic use ; *Influenza, Human/drug therapy ; Propensity Score ; Retrospective Studies ; *Pneumonia/drug therapy ; Hospitalization ; *Respiratory Insufficiency ; *Orthomyxoviridae ; }, abstract = {The potential antimicrobial and anti-inflammatory effectiveness of azithromycin against severe influenza is yet unclear. We retrospectively investigated the effect of intravenous azithromycin administration within 7 days of hospitalization in patients with influenza virus pneumonia and respiratory failure. Using Japan's national administrative database, we enrolled and classified 5066 patients with influenza virus pneumonia into severe, moderate, and mild groups based on their respiratory status within 7 days of hospitalization. The primary endpoints were total, 30-day, and 90-day mortality rates. The secondary endpoints were the duration of intensive-care unit management, invasive mechanical ventilation, and hospital stay. The inverse probability of the treatment weighting method with estimated propensity scores was used to minimize data collection bias. Use of intravenous azithromycin was proportional to the severity of respiratory failure (mild: 1.0%, moderate: 3.1%, severe: 14.8%). In the severe group, the 30-day mortality rate was significantly lower with azithromycin (26.49% vs. 36.65%, p = 0.038). In the moderate group, the mean duration of invasive mechanical ventilation after day 8 was shorter with azithromycin; there were no significant differences in other endpoints between the severe and moderate groups. These results suggest that intravenous azithromycin has favorable effects in patients with influenza virus pneumonia using mechanical ventilation or oxygen.}, } @article {pmid37240180, year = {2023}, author = {Lafleur, S and Bodein, A and Mbuya Malaïka Mutombo, J and Mathieu, A and Joly Beauparlant, C and Minne, X and Chandad, F and Droit, A and Houde, VP}, title = {Multi-Omics Data Integration Reveals Key Variables Contributing to Subgingival Microbiome Dysbiosis-Induced Inflammatory Response in a Hyperglycemic Microenvironment.}, journal = {International journal of molecular sciences}, volume = {24}, number = {10}, pages = {}, pmid = {37240180}, issn = {1422-0067}, support = {Biocodex Microbiota Foundation//Biocodex (France)/ ; }, mesh = {Humans ; Multiomics ; Dysbiosis/microbiology ; RNA, Ribosomal, 16S/genetics ; U937 Cells ; *Periodontitis/microbiology ; *Microbiota/genetics ; Bacteria/metabolism ; Cytokines/metabolism ; RNA-Binding Proteins ; }, abstract = {Subgingival microbiome dysbiosis promotes the development of periodontitis, an irreversible chronic inflammatory disease associated with metabolic diseases. However, studies regarding the effects of a hyperglycemic microenvironment on host-microbiome interactions and host inflammatory response during periodontitis are still scarce. Here, we investigated the impacts of a hyperglycemic microenvironment on the inflammatory response and transcriptome of a gingival coculture model stimulated with dysbiotic subgingival microbiomes. HGF-1 cells overlaid with U937 macrophage-like cells were stimulated with subgingival microbiomes collected from four healthy donors and four patients with periodontitis. Pro-inflammatory cytokines and matrix metalloproteinases were measured while the coculture RNA was submitted to a microarray analysis. Subgingival microbiomes were submitted to 16s rRNA gene sequencing. Data were analyzed using an advanced multi-omics bioinformatic data integration model. Our results show that the genes krt76, krt27, pnma5, mansc4, rab41, thoc6, tm6sf2, and znf506 as well as the pro-inflammatory cytokines IL-1β, GM-CSF, FGF2, IL-10, the metalloproteinases MMP3 and MMP8, and bacteria from the ASV 105, ASV 211, ASV 299, Prevotella, Campylobacter and Fretibacterium genera are key intercorrelated variables contributing to periodontitis-induced inflammatory response in a hyperglycemic microenvironment. In conclusion, our multi-omics integration analysis unveiled the complex interrelationships involved in the regulation of periodontal inflammation in response to a hyperglycemic microenvironment.}, } @article {pmid37232406, year = {2023}, author = {Watson, SJ and Aguirre, BA and Wright, AJ}, title = {Soil versus atmospheric drought: A test case of plant functional trait responses.}, journal = {Ecology}, volume = {104}, number = {8}, pages = {e4109}, doi = {10.1002/ecy.4109}, pmid = {37232406}, issn = {1939-9170}, mesh = {*Soil ; *Ecosystem ; Droughts ; Plants ; Plant Leaves/physiology ; }, abstract = {Climate change alters mean global surface temperatures, precipitation regimes, and atmospheric moisture. Resultant drought affects the composition and diversity of terrestrial ecosystems worldwide. To date, there have been no assessments of the combined impacts of reduced precipitation and atmospheric drying on functional trait distributions of any species in an outdoor experiment. Here, we examined whether soil and atmospheric drought affected the functional traits of a focal grass species (Poa secunda) growing in monoculture and eight-species grass communities in outdoor mesocosms. We focused on specific leaf area (SLA), leaf area, stomatal density, root:shoot ratio, and fine root:coarse root ratio responses. Leaf area and overall growth were reduced with soil drying. Root:shoot ratio only increased for P. secunda growing in monoculture under combined atmospheric and soil drought. Plant energy allocation strategy (measured using principal components) differed when P. secunda was grown in combined soil and atmospheric drought conditions compared with soil drought alone. Given a lack of outdoor manipulations of this kind, our results emphasize the importance of atmospheric drying on functional trait responses more broadly. We suggest that drought methods focused purely on soil water inputs may be imprecisely predicting drought effects on other terrestrial organisms as well (other plants, arthropods, and higher trophic levels).}, } @article {pmid37230884, year = {2023}, author = {Williams, JW and Spanbauer, TL and Heintzman, PD and Blois, J and Capo, E and Goring, SJ and Monchamp, ME and Parducci, L and Von Eggers, JM and , }, title = {Strengthening global-change science by integrating aeDNA with paleoecoinformatics.}, journal = {Trends in ecology & evolution}, volume = {38}, number = {10}, pages = {946-960}, doi = {10.1016/j.tree.2023.04.016}, pmid = {37230884}, issn = {1872-8383}, mesh = {*Biodiversity ; *DNA, Ancient ; Computational Biology ; DNA Barcoding, Taxonomic ; }, abstract = {Ancient environmental DNA (aeDNA) data are close to enabling insights into past global-scale biodiversity dynamics at unprecedented taxonomic extent and resolution. However, achieving this potential requires solutions that bridge bioinformatics and paleoecoinformatics. Essential needs include support for dynamic taxonomic inferences, dynamic age inferences, and precise stratigraphic depth. Moreover, aeDNA data are complex and heterogeneous, generated by dispersed researcher networks, with methods advancing rapidly. Hence, expert community governance and curation are essential to building high-value data resources. Immediate recommendations include uploading metabarcoding-based taxonomic inventories into paleoecoinformatic resources, building linkages among open bioinformatic and paleoecoinformatic data resources, harmonizing aeDNA processing workflows, and expanding community data governance. These advances will enable transformative insights into global-scale biodiversity dynamics during large environmental and anthropogenic changes.}, } @article {pmid37226845, year = {2023}, author = {Bizzotto, E and Bonetto, A and Marcomini, A and Vighi, M}, title = {Environmental exposure and ecotoxicological properties of a new-generation fluorosurfactant (cC6 O4): A comparison with selected legacy perfluoroalkyl acids.}, journal = {Integrated environmental assessment and management}, volume = {19}, number = {6}, pages = {1636-1648}, doi = {10.1002/ieam.4794}, pmid = {37226845}, issn = {1551-3793}, support = {//Solvay Specialty Polymers Italy S.p.A./ ; }, mesh = {Ecosystem ; Ecotoxicology ; Environmental Exposure ; *Fluorocarbons/toxicity ; Water ; *Water Pollutants, Chemical/toxicity/analysis ; }, abstract = {Cyclic C6 O4 (cC6 O4 , CAS number 1190931-27-1) is a new-generation polyfluorinated alkyl substance (PFAS) used as a polymerization aid in the synthesis of fluoropolymers, which has been produced in Italy since 2011. A review of the properties of cC6 O4 , focused on environmental distribution and ecotoxicology, was conducted. The EQuilibrium Criterion model was applied, using default environmental scenarios, to estimate environmental distribution and fate. In a situation of static thermodynamic equilibrium in a closed system (Level I), cC6 O4 distributes mainly to water (97.6%) and in a minimal amount to soil (2.3%). In a more realistic scenario (Level III), with dynamic conditions in an open system, with advection in air and water and with equal emissions in air and water, the major amount of the compound is transported through water advection. Monitoring data, mainly referring to surface and groundwater, are available for water bodies close to the production sites (maximum measured concentration 52 μg/L) as well as for a wider area in the river Po watershed with concentrations generally lower than 1 μg/L. Few values are also available for concentration in biota. Effect data indicate low toxicity on all tested organisms with no observed effect concentration (NOEC) values always higher than the maximum concentrations tested (100 mg/L for acute tests). Bioaccumulation potential is also very low. A comparison with selected widely used PFAS with five to eight C atoms indicates that cC6 O4 is substantially less dangerous to aquatic organisms. For the time being, an ecological risk for the aquatic ecosystem may be excluded even in directly exposed ecosystems. However, for a complete assessment of the suitability of cC6 O4 as a substitute for other PFAS (namely, perfluorooctanoic acid), more comprehensive chronic experiments are necessary, to produce realistic NOEC, as well as higher tier experiments (e.g., mesocosms) capable of providing ecologically relevant endpoints. Moreover, a more accurate evaluation of the environmental persistence would be necessary. Integr Environ Assess Manag 2023;19:1636-1648. © 2023 SETAC.}, } @article {pmid37226152, year = {2023}, author = {Bakó, C and Balázs, VL and Kerekes, E and Kocsis, B and Nagy, DU and Szabó, P and Micalizzi, G and Mondello, L and Krisch, J and Pethő, D and Horváth, G}, title = {Flowering phenophases influence the antibacterial and anti-biofilm effects of Thymus vulgaris L. essential oil.}, journal = {BMC complementary medicine and therapies}, volume = {23}, number = {1}, pages = {168}, pmid = {37226152}, issn = {2662-7671}, mesh = {*Oils, Volatile/pharmacology ; *Thymus Plant ; Gas Chromatography-Mass Spectrometry ; Anti-Bacterial Agents/pharmacology ; }, abstract = {BACKGROUND: Essential oils are becoming increasingly popular in medicinal applications because of their antimicrobial effect. Thymus vulgaris L. (Lamiaceae) is a well-known and widely cultivated medicinal plant, which is used as a remedy for cold, cough and gastrointestinal symptoms. Essential oil content of thyme is responsible for its antimicrobial activity, however, it has been reported that the chemical composition of essential oils influences its biological activity. In order to explore flowering phenophases influence on the chemical composition of thyme essential oil and its antibacterial and anti-biofilm activity, plant materials were collected at the beginning of flowering, in full bloom and at the end of flowering periods in 2019.

METHODS: Essential oils from fresh and dried plant materials were distilled and analyzed with gas chromatography-mass spectrometry (GC-MS) and gas chromatography-flame ionization detection (GC-FID). The antibacterial activity was performed by broth microdilution and thin layer chromatography-direct bioautography (TLC-DB) assays and the anti-biofilm effect by crystal violet assay, respectively. Scanning electron microscopy was applied to illustrate the cellular changes of bacterial cells after essential oil treatment.

RESULTS: Thymol (52.33-62.46%) was the main component in the thyme essential oils. Thyme oil distilled from fresh plant material and collected at the beginning of flowering period exerted the highest antibacterial and anti-biofilm activity against Haemophilus influenzae, H. parainfluenzae and Pseudomonas aeruginosa.

CONCLUSION: The different flowering periods of Thymus vulgaris influence the antibacterial and anti-biofilm activity of its essential oils, therefore, the collection time has to be taken into consideration and not only the full bloom, but the beginning of flowering period may provide biological active thyme essential oil.}, } @article {pmid37225998, year = {2023}, author = {Tao, F and Huang, Y and Hungate, BA and Manzoni, S and Frey, SD and Schmidt, MWI and Reichstein, M and Carvalhais, N and Ciais, P and Jiang, L and Lehmann, J and Wang, YP and Houlton, BZ and Ahrens, B and Mishra, U and Hugelius, G and Hocking, TD and Lu, X and Shi, Z and Viatkin, K and Vargas, R and Yigini, Y and Omuto, C and Malik, AA and Peralta, G and Cuevas-Corona, R and Di Paolo, LE and Luotto, I and Liao, C and Liang, YS and Saynes, VS and Huang, X and Luo, Y}, title = {Microbial carbon use efficiency promotes global soil carbon storage.}, journal = {Nature}, volume = {618}, number = {7967}, pages = {981-985}, pmid = {37225998}, issn = {1476-4687}, mesh = {*Carbon/analysis/metabolism ; *Carbon Sequestration ; Climate Change ; *Ecosystem ; Plants ; *Soil/chemistry ; *Soil Microbiology ; Datasets as Topic ; Deep Learning ; }, abstract = {Soils store more carbon than other terrestrial ecosystems[1,2]. How soil organic carbon (SOC) forms and persists remains uncertain[1,3], which makes it challenging to understand how it will respond to climatic change[3,4]. It has been suggested that soil microorganisms play an important role in SOC formation, preservation and loss[5-7]. Although microorganisms affect the accumulation and loss of soil organic matter through many pathways[4,6,8-11], microbial carbon use efficiency (CUE) is an integrative metric that can capture the balance of these processes[12,13]. Although CUE has the potential to act as a predictor of variation in SOC storage, the role of CUE in SOC persistence remains unresolved[7,14,15]. Here we examine the relationship between CUE and the preservation of SOC, and interactions with climate, vegetation and edaphic properties, using a combination of global-scale datasets, a microbial-process explicit model, data assimilation, deep learning and meta-analysis. We find that CUE is at least four times as important as other evaluated factors, such as carbon input, decomposition or vertical transport, in determining SOC storage and its spatial variation across the globe. In addition, CUE shows a positive correlation with SOC content. Our findings point to microbial CUE as a major determinant of global SOC storage. Understanding the microbial processes underlying CUE and their environmental dependence may help the prediction of SOC feedback to a changing climate.}, } @article {pmid37225767, year = {2023}, author = {Przybylska, MS and Violle, C and Vile, D and Scheepens, JF and Lacombe, B and Le Roux, X and Perrier, L and Sales-Mabily, L and Laumond, M and Vinyeta, M and Moulin, P and Beurier, G and Rouan, L and Cornet, D and Vasseur, F}, title = {AraDiv: a dataset of functional traits and leaf hyperspectral reflectance of Arabidopsis thaliana.}, journal = {Scientific data}, volume = {10}, number = {1}, pages = {314}, pmid = {37225767}, issn = {2052-4463}, support = {ANR-17-CE02-0018-01//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-17-CE02-0018-01//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-17-CE02-0018-01//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-17-CE02-0018-01//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-17-CE02-0018-01//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-17-CE02-0018-01//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-17-CE02-0018-01//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-17-CE02-0018-01//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-17-CE02-0018-01//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-17-CE02-0018-01//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-17-CE02-0018-01//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-17-CE02-0018-01//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-17-CE02-0018-01//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-17-CE02-0018-01//Agence Nationale de la Recherche (French National Research Agency)/ ; SCHE 1899/2-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; SCHE 1899/2-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; SCHE 1899/2-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; SCHE 1899/2-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; SCHE 1899/2-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; SCHE 1899/2-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; SCHE 1899/2-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; SCHE 1899/2-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; SCHE 1899/2-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; SCHE 1899/2-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; SCHE 1899/2-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; SCHE 1899/2-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; SCHE 1899/2-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; SCHE 1899/2-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; }, mesh = {Adaptation, Physiological ; *Arabidopsis/genetics ; Biological Evolution ; Databases, Factual ; Plant Leaves ; }, abstract = {Data from functional trait databases have been increasingly used to address questions related to plant diversity and trait-environment relationships. However, such databases provide intraspecific data that combine individual records obtained from distinct populations at different sites and, hence, environmental conditions. This prevents distinguishing sources of variation (e.g., genetic-based variation vs. phenotypic plasticity), a necessary condition to test for adaptive processes and other determinants of plant phenotypic diversity. Consequently, individual traits measured under common growing conditions and encompassing within-species variation across the occupied geographic range have the potential to leverage trait databases with valuable data for functional and evolutionary ecology. Here, we recorded 16 functional traits and leaf hyperspectral reflectance (NIRS) data for 721 widely distributed Arabidopsis thaliana natural accessions grown in a common garden experiment. These data records, together with meteorological variables obtained during the experiment, were assembled to create the AraDiv dataset. AraDiv is a comprehensive dataset of A. thaliana's intraspecific variability that can be explored to address questions at the interface of genetics and ecology.}, } @article {pmid37224319, year = {2022}, author = {Lohse, K and Vila, R and Hayward, A and Laetsch, DR and , and , and , and Wahlberg, N and , }, title = {The genome sequence of the high brown fritillary, Fabriciana adippe (Dennis & Schiffermüller, 1775).}, journal = {Wellcome open research}, volume = {7}, number = {}, pages = {298}, pmid = {37224319}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual female Fabriciana adippe (the high brown fritillary; Arthropoda; Insecta; Lepidoptera; Nymphalidae). The genome sequence is 485 megabases in span. Most of the assembly (99.98%) is scaffolded into 29 chromosomal pseudomolecules with the Z sex chromosome assembled. The complete mitochondrial genome was also assembled and is 15.1 kilobases in length. Gene annotation of this assembly in Ensembl identified 13,536 protein coding genes.}, } @article {pmid37224178, year = {2023}, author = {Passmore, S and Barth, W and Greenhill, SJ and Quinn, K and Sheard, C and Argyriou, P and Birchall, J and Bowern, C and Calladine, J and Deb, A and Diederen, A and Metsäranta, NP and Araujo, LH and Schembri, R and Hickey-Hall, J and Honkola, T and Mitchell, A and Poole, L and Rácz, PM and Roberts, SG and Ross, RM and Thomas-Colquhoun, E and Evans, N and Jordan, FM}, title = {Kinbank: A global database of kinship terminology.}, journal = {PloS one}, volume = {18}, number = {5}, pages = {e0283218}, pmid = {37224178}, issn = {1932-6203}, mesh = {Humans ; Female ; Male ; *Sexism ; *Anthropology ; Databases, Factual ; Family ; Interdisciplinary Studies ; }, abstract = {For a single species, human kinship organization is both remarkably diverse and strikingly organized. Kinship terminology is the structured vocabulary used to classify, refer to, and address relatives and family. Diversity in kinship terminology has been analyzed by anthropologists for over 150 years, although recurrent patterning across cultures remains incompletely explained. Despite the wealth of kinship data in the anthropological record, comparative studies of kinship terminology are hindered by data accessibility. Here we present Kinbank, a new database of 210,903 kinterms from a global sample of 1,229 spoken languages. Using open-access and transparent data provenance, Kinbank offers an extensible resource for kinship terminology, enabling researchers to explore the rich diversity of human family organization and to test longstanding hypotheses about the origins and drivers of recurrent patterns. We illustrate our contribution with two examples. We demonstrate strong gender bias in the phonological structure of parent terms across 1,022 languages, and we show that there is no evidence for a coevolutionary relationship between cross-cousin marriage and bifurcate-merging terminology in Bantu languages. Analysing kinship data is notoriously challenging; Kinbank aims to eliminate data accessibility issues from that challenge and provide a platform to build an interdisciplinary understanding of kinship.}, } @article {pmid37221394, year = {2023}, author = {Drott, MT and Park, SC and Wang, YW and Harrow, L and Keller, NP and Pringle, A}, title = {Pangenomics of the death cap mushroom Amanita phalloides, and of Agaricales, reveals dynamic evolution of toxin genes in an invasive range.}, journal = {The ISME journal}, volume = {17}, number = {8}, pages = {1236-1246}, pmid = {37221394}, issn = {1751-7370}, support = {R01 GM112739/GM/NIGMS NIH HHS/United States ; T32 ES007015/ES/NIEHS NIH HHS/United States ; }, mesh = {*Amanita/genetics ; *Agaricales/genetics ; Computational Biology ; }, abstract = {The poisonous European mushroom Amanita phalloides (the "death cap") is invading California. Whether the death caps' toxic secondary metabolites are evolving as it invades is unknown. We developed a bioinformatic pipeline to identify the MSDIN genes underpinning toxicity and probed 88 death cap genomes from an invasive Californian population and from the European range, discovering a previously unsuspected diversity of MSDINs made up of both core and accessory elements. Each death cap individual possesses a unique suite of MSDINs, and toxin genes are significantly differentiated between Californian and European samples. MSDIN genes are maintained by strong natural selection, and chemical profiling confirms MSDIN genes are expressed and result in distinct phenotypes; our chemical profiling also identified a new MSDIN peptide. Toxin genes are physically clustered within genomes. We contextualize our discoveries by probing for MSDINs in genomes from across the order Agaricales, revealing MSDIN diversity originated in independent gene family expansions among genera. We also report the discovery of an MSDIN in an Amanita outside the "lethal Amanitas" clade. Finally, the identification of an MSDIN gene and its associated processing gene (POPB) in Clavaria fumosa suggest the origin of MSDINs is older than previously suspected. The dynamic evolution of MSDINs underscores their potential to mediate ecological interactions, implicating MSDINs in the ongoing invasion. Our data change the understanding of the evolutionary history of poisonous mushrooms, emphasizing striking parallels to convergently evolved animal toxins. Our pipeline provides a roadmap for exploring secondary metabolites in other basidiomycetes and will enable drug prospecting.}, } @article {pmid37221042, year = {2023}, author = {Chaudhary, S and Wu, Y and Strongman, D and Wang, Y}, title = {CIGAF-a database and interactive platform for insect-associated trichomycete fungi.}, journal = {Database : the journal of biological databases and curation}, volume = {2023}, number = {}, pages = {}, pmid = {37221042}, issn = {1758-0463}, mesh = {Animals ; *Insecta ; Databases, Factual ; *Fungi ; Metadata ; Software ; }, abstract = {Trichomycete fungi are gut symbionts of arthropods living in aquatic habitats. The lack of a central platform with accessible collection records and associated ecological metadata has limited ecological investigations of trichomycetes. We present CIGAF (short for Collections of Insect Gut-Associated Fungi), a trichomycetes-focused digital database with interactive visualization functions enabled by the R Shiny web application. CIGAF curated 3120 collection records of trichomycetes across the globe, spanning from 1929 to 2022. CIGAF allows the exploration of nearly 100 years of field collection data through the web interface, including primary published data such as insect host information, collection site coordinates, descriptions and date of collection. When possible, specimen records are supplemented with climatic measures at collection sites. As a central platform of field collection records, multiple interactive tools allow users to analyze and plot data at various levels. CIGAF provides a comprehensive resource hub to the research community for further studies in mycology, entomology, symbiosis and biogeography.}, } @article {pmid37216923, year = {2023}, author = {Ma, Y and Liu, L and Ma, Y and Zhang, S}, title = {HONMF: integration analysis of multi-omics microbiome data via matrix factorization and hypergraph.}, journal = {Bioinformatics (Oxford, England)}, volume = {39}, number = {6}, pages = {}, pmid = {37216923}, issn = {1367-4811}, mesh = {*Multiomics ; Software ; Algorithms ; *Microbiota ; Cluster Analysis ; }, abstract = {MOTIVATION: The accumulation of multi-omics microbiome data provides an unprecedented opportunity to understand the diversity of bacterial, fungal, and viral components from different conditions. The changes in the composition of viruses, bacteria, and fungi communities have been associated with environments and critical illness. However, identifying and dissecting the heterogeneity of microbial samples and cross-kingdom interactions remains challenging.

RESULTS: We propose HONMF for the integrative analysis of multi-modal microbiome data, including bacterial, fungal, and viral composition profiles. HONMF enables identification of microbial samples and data visualization, and also facilitates downstream analysis, including feature selection and cross-kingdom association analysis between species. HONMF is an unsupervised method based on hypergraph induced orthogonal non-negative matrix factorization, where it assumes that latent variables are specific for each composition profile and integrates the distinct sets of latent variables through graph fusion strategy, which better tackles the distinct characteristics in bacterial, fungal, and viral microbiome. We implemented HONMF on several multi-omics microbiome datasets from different environments and tissues. The experimental results demonstrate the superior performance of HONMF in data visualization and clustering. HONMF also provides rich biological insights by implementing discriminative microbial feature selection and bacterium-fungus-virus association analysis, which improves our understanding of ecological interactions and microbial pathogenesis.

The software and datasets are available at https://github.com/chonghua-1983/HONMF.}, } @article {pmid37211183, year = {2023}, author = {Yokoyama, D and Kikuchi, J}, title = {Inferring microbial community assembly in an urban river basin through geo-multi-omics and phylogenetic bin-based null-model analysis of surface water.}, journal = {Environmental research}, volume = {231}, number = {Pt 3}, pages = {116202}, doi = {10.1016/j.envres.2023.116202}, pmid = {37211183}, issn = {1096-0953}, mesh = {Humans ; *Rivers ; Phylogeny ; Multiomics ; *Microbiota ; Stochastic Processes ; }, abstract = {Understanding the community assembly process is a central issue in microbial ecology. In this study, we analyzed the community assembly of particle-associated (PA) and free-living (FL) surface water microbiomes in 54 sites from the headstream to the river mouth of an urban river in Japan, the river basin of which has the highest human population density in the country. Analyses were conducted from two perspectives: (1) analysis of deterministic processes considering only environmental factors using a geo-multi-omics dataset and (2) analysis of deterministic and stochastic processes to estimate the contributions of heterogeneous selection (HeS), homogeneous selection (HoS), dispersal limitation (DL), homogenizing dispersal (HD), and drift (DR) as community assembly processes using a phylogenetic bin-based null model. The variation in microbiomes was successfully explained from a deterministic perspective by environmental factors, such as organic matter-related, nitrogen metabolism, and salinity-related parameters, using multivariate statistical analysis, network analysis, and habitat prediction. In addition, we demonstrated the dominance of stochastic processes (DL, HD, and DR) over deterministic processes (HeS and HoS) in community assembly from both deterministic and stochastic perspectives. Our analysis revealed that as the distance between two sites increased, the effect of HoS sharply decreased while the effect of HeS increased, particularly between upstream and estuary sites, indicating that the salinity gradient could potentially enhance the contribution of HeS to community assembly. Our study highlights the importance of both stochastic and deterministic processes in community assembly of PA and FL surface water microbiomes in urban riverine ecosystems.}, } @article {pmid37209314, year = {2023}, author = {Jiang, WJ and Wang, MT and Du, ZY and Li, JH and Shi, Y and Wang, X and Wu, LY and Chen, J and Zhong, M and Yang, J and Hu, BH and Huang, J}, title = {Bioinformatic and functional analysis of OsDHN2 under cadmium stress.}, journal = {Functional & integrative genomics}, volume = {23}, number = {2}, pages = {170}, pmid = {37209314}, issn = {1438-7948}, mesh = {*Cadmium/toxicity/metabolism ; Saccharomyces cerevisiae/metabolism ; Plant Proteins/genetics/metabolism ; *Oryza/genetics/metabolism ; Computational Biology ; Gene Expression Regulation, Plant ; }, abstract = {As a toxic heavy metal, cadmium (Cd) is one of the principal pollutants influencing rice productivity and food security. Despite several studies, the underlying mechanism of Cd response in plants remains largely unclear. Dehydrins are part of the late embryogenesis abundant (LEA) family which protect plants against abiotic stresses. In this study, a Cd-responsive LEA gene, OsDHN2, was functionally characterized. The chromosome localization results indicated that OsDHN2 was located on chromosome 2 of rice. Meanwhile, cis-acting elements, such as MBS (MYB binding site involved in drought-inducibility), ARE (anaerobic induction), and ABRE (abscisic acid), were present in the OsDHN2 promoter region. Expression pattern analysis also showed that OsDHN2 expression was induced in both roots and shoots under Cd stress. Overexpression of OsDHN2 improved Cd tolerance and reduced Cd concentration in yeast. Moreover, increased expression levels of SOD1, CTA1, GSH1, or CTT1 were found in transgenic yeast under Cd stress, suggesting the increased antioxidant enzymatic activities. These results suggested that OsDHN2 is a Cd-responsive gene that has the potential to improve resistance to Cd in rice.}, } @article {pmid37208222, year = {2023}, author = {de Koning, K and Broekhuijsen, J and Kühn, I and Ovaskainen, O and Taubert, F and Endresen, D and Schigel, D and Grimm, V}, title = {Digital twins: dynamic model-data fusion for ecology.}, journal = {Trends in ecology & evolution}, volume = {38}, number = {10}, pages = {916-926}, doi = {10.1016/j.tree.2023.04.010}, pmid = {37208222}, issn = {1872-8383}, mesh = {*Ecology ; Big Data ; Machine Learning ; *Computer Simulation ; }, abstract = {Digital twins (DTs) are an emerging phenomenon in the public and private sectors as a new tool to monitor and understand systems and processes. DTs have the potential to change the status quo in ecology as part of its digital transformation. However, it is important to avoid misguided developments by managing expectations about DTs. We stress that DTs are not just big models of everything, containing big data and machine learning. Rather, the strength of DTs is in combining data, models, and domain knowledge, and their continuous alignment with the real world. We suggest that researchers and stakeholders exercise caution in DT development, keeping in mind that many of the strengths and challenges of computational modelling in ecology also apply to DTs.}, } @article {pmid37207732, year = {2023}, author = {Girardi, P and Lupo, A and Mastromatteo, LY and Scrimin, S}, title = {Behavioral outcomes and exposure to perfluoroalkyl substances among children aged 6-13 years: The TEDDY child study.}, journal = {Environmental research}, volume = {231}, number = {Pt 2}, pages = {116049}, doi = {10.1016/j.envres.2023.116049}, pmid = {37207732}, issn = {1096-0953}, mesh = {Pregnancy ; Female ; Humans ; Child ; Cross-Sectional Studies ; Environmental Exposure/analysis ; *Alkanesulfonic Acids/analysis ; Alkanesulfonates/analysis ; *Fluorocarbons/analysis ; Water ; *Environmental Pollutants ; }, abstract = {BACKGROUND: Although some studies report that exposure to per- and polyfluoroalkyl substances (PFAS) during pregnancy and early life stages of a child could adversely impact neurodevelopment, literature shows mixed evidence.

OBJECTIVES: Using an ecological framework for human development, we assessed the association of risk factors for environmental PFAS exposure and childhood PFAS concentrations with behavioral difficulties among school-age children exposed to PFAS from birth, while also controlling for the important influence of the parenting and familial environment.

METHODS: The study participants included 331 school-age children (6-13 years) born in a PFAS-contaminated area in the Veneto Region (Italy). We study the associations between environmental risk factors of maternal PFAS exposure (residential time, consumption of tap water, residence in Red zone A or B), and breastfeeding duration with parent assessments of children's behavioral problems (using the Strengths and Difficulties Questionnaire [SDQ]), adjusting for socio-demographic, parenting and familial variables. The direct relationships between serum blood PFAS concentrations and SDQ scores was evaluated in a subset of children (n = 79), both with single PFAS and weighted quantile sum (WQS) regressions.

RESULTS: Poisson regression models reported positive associations between high consumption of tap water and externalizing SDQ scores (Incidence Rate Ratio [IRR]: 1.18; 95% confidence interval [CI]: 1.04-1.32) and total difficulty scores (IRR: 1.14; 95% CI: 1.02-1.26). Childhood perfluorooctane sulfonate (PFOS) and perfluorohexane sulfonate (PFHxS) were associated with higher internalizing SDQ scores (4th vs. 1st quartile, PFOS IRR: 1.54, 95% CI: 1.06-2.25), externalizing scores (4th vs. 1st quartile, PFHxS IRR: 1.59, 95% CI: 1.09-2.32), and total difficulty scores (4th vs. 1st quartile, PFOS IRR: 1.37, 95% CI: 1.05-1.71; PFHxS IRR: 1.54, 95% CI: 1.09-1.90). The WQS regressions confirmed the associations reported by single-PFAS analyses.

CONCLUSIONS: We observed cross-sectional associations of tap water consumption and childhood PFOS, and PFHxS concentrations with greater behavioral difficulties.}, } @article {pmid37207684, year = {2023}, author = {Cocker, D and Chidziwisano, K and Mphasa, M and Mwapasa, T and Lewis, JM and Rowlingson, B and Sammarro, M and Bakali, W and Salifu, C and Zuza, A and Charles, M and Mandula, T and Maiden, V and Amos, S and Jacob, ST and Kajumbula, H and Mugisha, L and Musoke, D and Byrne, R and Edwards, T and Lester, R and Elviss, N and Roberts, AP and Singer, AC and Jewell, C and Morse, T and Feasey, NA}, title = {Investigating One Health risks for human colonisation with extended spectrum β-lactamase-producing Escherichia coli and Klebsiella pneumoniae in Malawian households: a longitudinal cohort study.}, journal = {The Lancet. Microbe}, volume = {4}, number = {7}, pages = {e534-e543}, pmid = {37207684}, issn = {2666-5247}, support = {MR/S004793/1/MRC_/Medical Research Council/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; }, mesh = {Animals ; Humans ; Escherichia coli ; Klebsiella pneumoniae ; *Escherichia coli Infections/epidemiology/microbiology ; Longitudinal Studies ; *One Health ; beta-Lactamases ; *Klebsiella Infections/epidemiology/microbiology ; *Anti-Infective Agents ; Cohort Studies ; }, abstract = {BACKGROUND: Low-income countries have high morbidity and mortality from drug-resistant infections, especially from enteric bacteria such as Escherichia coli. In these settings, sanitation infrastructure is of variable and often inadequate quality, creating risks of extended-spectrum β-lactamase (ESBL)-producing Enterobacterales transmission. We aimed to describe the prevalence, distribution, and risks of ESBL-producing Enterobacterales colonisation in sub-Saharan Africa using a One Health approach.

METHODS: Between April 29, 2019, and Dec 3, 2020, we recruited 300 households in Malawi for this longitudinal cohort study: 100 each in urban, peri-urban, and rural settings. All households underwent a baseline visit and 195 were selected for longitudinal follow-up, comprising up to three additional visits over a 6 month period. Data on human health, antibiotic usage, health-seeking behaviours, structural and behavioural environmental health practices, and animal husbandry were captured alongside human, animal, and environmental samples. Microbiological processing determined the presence of ESBL-producing E coli and Klebsiella pneumoniae, and hierarchical logistic regression was performed to evaluate the risks of human ESBL-producing Enterobacterales colonisation.

FINDINGS: A paucity of environmental health infrastructure and materials for safe sanitation was identified across all sites. A total of 11 975 samples were cultured, and ESBL-producing Enterobacterales were isolated from 1190 (41·8%) of 2845 samples of human stool, 290 (29·8%) of 973 samples of animal stool, 339 (66·2%) of 512 samples of river water, and 138 (46·0%) of 300 samples of drain water. Multivariable models illustrated that human ESBL-producing E coli colonisation was associated with the wet season (adjusted odds ratio 1·66, 95% credible interval 1·38-2·00), living in urban areas (2·01, 1·26-3·24), advanced age (1·14, 1·05-1·25), and living in households where animals were observed interacting with food (1·62, 1·17-2·28) or kept inside (1·58, 1·00-2·43). Human ESBL-producing K pneumoniae colonisation was associated with the wet season (2·12, 1·63-2·76).

INTERPRETATION: There are extremely high levels of ESBL-producing Enterobacterales colonisation in humans and animals and extensive contamination of the wider environment in southern Malawi. Urbanisation and seasonality are key risks for ESBL-producing Enterobacterales colonisation, probably reflecting environmental drivers. Without adequate efforts to improve environmental health, ESBL-producing Enterobacterales transmission is likely to persist in this setting.

FUNDING: Medical Research Council, National Institute for Health and Care Research, and Wellcome Trust.

TRANSLATION: For the Chichewa translation of the abstract see Supplementary Materials section.}, } @article {pmid37205491, year = {2023}, author = {Gao, H and Hamp, T and Ede, J and Schraiber, JG and McRae, J and Singer-Berk, M and Yang, Y and Dietrich, A and Fiziev, P and Kuderna, L and Sundaram, L and Wu, Y and Adhikari, A and Field, Y and Chen, C and Batzoglou, S and Aguet, F and Lemire, G and Reimers, R and Balick, D and Janiak, MC and Kuhlwilm, M and Orkin, JD and Manu, S and Valenzuela, A and Bergman, J and Rouselle, M and Silva, FE and Agueda, L and Blanc, J and Gut, M and de Vries, D and Goodhead, I and Harris, RA and Raveendran, M and Jensen, A and Chuma, IS and Horvath, J and Hvilsom, C and Juan, D and Frandsen, P and de Melo, FR and Bertuol, F and Byrne, H and Sampaio, I and Farias, I and do Amaral, JV and Messias, M and da Silva, MNF and Trivedi, M and Rossi, R and Hrbek, T and Andriaholinirina, N and Rabarivola, CJ and Zaramody, A and Jolly, CJ and Phillips-Conroy, J and Wilkerson, G and Abee, C and Simmons, JH and Fernandez-Duque, E and Kanthaswamy, S and Shiferaw, F and Wu, D and Zhou, L and Shao, Y and Zhang, G and Keyyu, JD and Knauf, S and Le, MD and Lizano, E and Merker, S and Navarro, A and Batallion, T and Nadler, T and Khor, CC and Lee, J and Tan, P and Lim, WK and Kitchener, AC and Zinner, D and Gut, I and Melin, A and Guschanski, K and Schierup, MH and Beck, RMD and Umapathy, G and Roos, C and Boubli, JP and Lek, M and Sunyaev, S and O'Donnell, A and Rehm, H and Xu, J and Rogers, J and Marques-Bonet, T and Kai-How Farh, K}, title = {The landscape of tolerated genetic variation in humans and primates.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {37205491}, issn = {2692-8205}, support = {R01 HG010898/HG/NHGRI NIH HHS/United States ; P30 AG012836/AG/NIA NIH HHS/United States ; R24 HD044964/HD/NICHD NIH HHS/United States ; T32 GM007748/GM/NIGMS NIH HHS/United States ; P40 OD024628/OD/NIH HHS/United States ; }, abstract = {UNLABELLED: Personalized genome sequencing has revealed millions of genetic differences between individuals, but our understanding of their clinical relevance remains largely incomplete. To systematically decipher the effects of human genetic variants, we obtained whole genome sequencing data for 809 individuals from 233 primate species, and identified 4.3 million common protein-altering variants with orthologs in human. We show that these variants can be inferred to have non-deleterious effects in human based on their presence at high allele frequencies in other primate populations. We use this resource to classify 6% of all possible human protein-altering variants as likely benign and impute the pathogenicity of the remaining 94% of variants with deep learning, achieving state-of-the-art accuracy for diagnosing pathogenic variants in patients with genetic diseases.

ONE SENTENCE SUMMARY: Deep learning classifier trained on 4.3 million common primate missense variants predicts variant pathogenicity in humans.}, } @article {pmid37198478, year = {2023}, author = {Pairo-Castineira, E and Rawlik, K and Bretherick, AD and Qi, T and Wu, Y and Nassiri, I and McConkey, GA and Zechner, M and Klaric, L and Griffiths, F and Oosthuyzen, W and Kousathanas, A and Richmond, A and Millar, J and Russell, CD and Malinauskas, T and Thwaites, R and Morrice, K and Keating, S and Maslove, D and Nichol, A and Semple, MG and Knight, J and Shankar-Hari, M and Summers, C and Hinds, C and Horby, P and Ling, L and McAuley, D and Montgomery, H and Openshaw, PJM and Begg, C and Walsh, T and Tenesa, A and Flores, C and Riancho, JA and Rojas-Martinez, A and Lapunzina, P and , and , and , and , and Yang, J and Ponting, CP and Wilson, JF and Vitart, V and Abedalthagafi, M and Luchessi, AD and Parra, EJ and Cruz, R and Carracedo, A and Fawkes, A and Murphy, L and Rowan, K and Pereira, AC and Law, A and Fairfax, B and Hendry, SC and Baillie, JK}, title = {GWAS and meta-analysis identifies 49 genetic variants underlying critical COVID-19.}, journal = {Nature}, volume = {617}, number = {7962}, pages = {764-768}, pmid = {37198478}, issn = {1476-4687}, support = {MR/S032304/1/MRC_/Medical Research Council/United Kingdom ; MC_UU_00007/10/MRC_/Medical Research Council/United Kingdom ; MC_PC_19025/MRC_/Medical Research Council/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; MC_PC_20058/MRC_/Medical Research Council/United Kingdom ; MC_UU_00007/15/MRC_/Medical Research Council/United Kingdom ; MC_PC_20029/MRC_/Medical Research Council/United Kingdom ; MC_PC_20004/MRC_/Medical Research Council/United Kingdom ; MR/V001329/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Humans ; *COVID-19/genetics ; *Critical Illness ; *Genetic Predisposition to Disease/genetics ; *Genetic Variation/genetics ; *Genome-Wide Association Study ; Genotype ; Genotyping Techniques ; Monocytes/metabolism ; Phenotype ; rab GTP-Binding Proteins/genetics ; Transcriptome ; Whole Genome Sequencing ; }, abstract = {Critical illness in COVID-19 is an extreme and clinically homogeneous disease phenotype that we have previously shown[1] to be highly efficient for discovery of genetic associations[2]. Despite the advanced stage of illness at presentation, we have shown that host genetics in patients who are critically ill with COVID-19 can identify immunomodulatory therapies with strong beneficial effects in this group[3]. Here we analyse 24,202 cases of COVID-19 with critical illness comprising a combination of microarray genotype and whole-genome sequencing data from cases of critical illness in the international GenOMICC (11,440 cases) study, combined with other studies recruiting hospitalized patients with a strong focus on severe and critical disease: ISARIC4C (676 cases) and the SCOURGE consortium (5,934 cases). To put these results in the context of existing work, we conduct a meta-analysis of the new GenOMICC genome-wide association study (GWAS) results with previously published data. We find 49 genome-wide significant associations, of which 16 have not been reported previously. To investigate the therapeutic implications of these findings, we infer the structural consequences of protein-coding variants, and combine our GWAS results with gene expression data using a monocyte transcriptome-wide association study (TWAS) model, as well as gene and protein expression using Mendelian randomization. We identify potentially druggable targets in multiple systems, including inflammatory signalling (JAK1), monocyte-macrophage activation and endothelial permeability (PDE4A), immunometabolism (SLC2A5 and AK5), and host factors required for viral entry and replication (TMPRSS2 and RAB2A).}, } @article {pmid37196545, year = {2023}, author = {Yang, P and Yang, W and Wei, Z and Li, Y and Yang, Y and Wang, J}, title = {Novel targets for gastric cancer: The tumor microenvironment (TME), N6-methyladenosine (m6A), pyroptosis, autophagy, ferroptosis and cuproptosis.}, journal = {Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie}, volume = {163}, number = {}, pages = {114883}, doi = {10.1016/j.biopha.2023.114883}, pmid = {37196545}, issn = {1950-6007}, mesh = {Humans ; *Stomach Neoplasms/drug therapy ; *Ferroptosis ; Pyroptosis ; Tumor Microenvironment ; Adenosine ; Autophagy ; }, abstract = {Gastric cancer (GC) is a fatal illness, and its mortality rate is very high all over the world. At present, it is a serious health problem for any country. It is a multifactorial disease due to the rising drug resistance and the increasing global cancer burden, the treatment of GC still faces many obstacles and problems. In recent years, research on GC is being carried out continuously, and we hope to address the new targets of GC treatment through this review. At the same time, we also hope to discover new ways to fight GC and create more gospel for clinical patients. First, we discuss the descriptive tumor microenvironment (TME), N6-methyladenosine (m6A), pyroptosis, autophagy, ferroptosis, and cuproptosis. Finally, we expounded on the new or potential targets of GC treatment.}, } @article {pmid37193271, year = {2023}, author = {Mollicone, DJ and Kan, K and Coats, S and Mott, C and van Wollen, M and Hatch, A and Gallagher, J and Williams, S and Motzkin, D}, title = {Use of the psychomotor vigilance test to aid in the selection of risk controls in an air medical transport operation.}, journal = {Sleep advances : a journal of the Sleep Research Society}, volume = {4}, number = {1}, pages = {zpad003}, pmid = {37193271}, issn = {2632-5012}, abstract = {STUDY OBJECTIVES: This study evaluated the utility and ecological validity of the 3-minute psychomotor vigilance test (PVT) completed by safety-critical personnel in an air medical transport operation as part of a fatigue risk management program.

METHODS: Crewmembers in an air medical transport operation self-administered an alertness assessment incorporating a 3-minute PVT at different time points during their duty schedule. The prevalence of alertness deficits was evaluated based on a failure threshold of 12 errors considering both lapses and false starts. To evaluate the ecological validity of the PVT, the relative frequency of failed assessments was evaluated relative to crewmember position, timing of the assessment within the duty schedule, time of day, and sleep quantity in the last 24 h.

RESULTS: 2.1% of assessments were associated with a failing PVT score. Crewmember position, timing of assessment within the duty shift, time of day, and sleep quantity in the last 24 h were found to affect the relative frequency of failed assessments. Obtaining less than 7-9 h of sleep was associated with systematic increases in the failure rate (F[1, 54 612] = 168.1, p < .001). Obtaining less than 4 h of sleep was associated with a frequency of a failed assessment 2.99 times higher than the frequency of a failed assessment when obtaining 7-9 h of sleep.

CONCLUSIONS: Results provide evidence for the utility and ecological validity of the PVT as well as the suitability of the PVT failure threshold to support fatigue risk management in safety-critical operations.}, } @article {pmid37188960, year = {2023}, author = {Li, C and Wood, JC and Vu, AH and Hamilton, JP and Rodriguez Lopez, CE and Payne, RME and Serna Guerrero, DA and Gase, K and Yamamoto, K and Vaillancourt, B and Caputi, L and O'Connor, SE and Robin Buell, C}, title = {Single-cell multi-omics in the medicinal plant Catharanthus roseus.}, journal = {Nature chemical biology}, volume = {19}, number = {8}, pages = {1031-1041}, pmid = {37188960}, issn = {1552-4469}, support = {788301/ERC_/European Research Council/International ; }, mesh = {*Catharanthus/genetics ; *Plants, Medicinal/metabolism ; Multiomics ; Indole Alkaloids/metabolism ; *Antineoplastic Agents/metabolism ; Monoterpenes/metabolism ; Gene Expression Regulation, Plant ; Plant Proteins/genetics/metabolism ; }, abstract = {Advances in omics technologies now permit the generation of highly contiguous genome assemblies, detection of transcripts and metabolites at the level of single cells and high-resolution determination of gene regulatory features. Here, using a complementary, multi-omics approach, we interrogated the monoterpene indole alkaloid (MIA) biosynthetic pathway in Catharanthus roseus, a source of leading anticancer drugs. We identified clusters of genes involved in MIA biosynthesis on the eight C. roseus chromosomes and extensive gene duplication of MIA pathway genes. Clustering was not limited to the linear genome, and through chromatin interaction data, MIA pathway genes were present within the same topologically associated domain, permitting the identification of a secologanin transporter. Single-cell RNA-sequencing revealed sequential cell-type-specific partitioning of the leaf MIA biosynthetic pathway that, when coupled with a single-cell metabolomics approach, permitted the identification of a reductase that yields the bis-indole alkaloid anhydrovinblastine. We also revealed cell-type-specific expression in the root MIA pathway.}, } @article {pmid37172588, year = {2023}, author = {Gao, X and Sun, R and Jiao, N and Liang, X and Li, G and Gao, H and Wu, X and Yang, M and Chen, C and Sun, X and Chen, L and Wu, W and Cong, Y and Zhu, R and Guo, T and Liu, Z}, title = {Integrative multi-omics deciphers the spatial characteristics of host-gut microbiota interactions in Crohn's disease.}, journal = {Cell reports. Medicine}, volume = {4}, number = {6}, pages = {101050}, pmid = {37172588}, issn = {2666-3791}, mesh = {Humans ; *Crohn Disease/complications/diagnosis/pathology ; *Gastrointestinal Microbiome ; Host Microbial Interactions ; Multiomics ; Inflammation/complications ; Bacteria/genetics/metabolism ; Membrane Proteins/metabolism ; }, abstract = {Dysregulated host-microbial interactions play critical roles in initiation and perpetuation of gut inflammation in Crohn's disease (CD). However, the spatial distribution and interaction network across the intestine and its accessory tissues are still elusive. Here, we profile the host proteins and tissue microbes in 540 samples from the intestinal mucosa, submucosa-muscularis-serosa, mesenteric adipose tissues, mesentery, and mesenteric lymph nodes of 30 CD patients and spatially decipher the host-microbial interactions. We observe aberrant antimicrobial immunity and metabolic processes across multi-tissues during CD and determine bacterial transmission along with altered microbial communities and ecological patterns. Moreover, we identify several candidate interaction pairs between host proteins and microbes associated with perpetuation of gut inflammation and bacterial transmigration across multi-tissues in CD. Signature alterations in host proteins (e.g., SAA2 and GOLM1) and microbes (e.g., Alistipes and Streptococcus) are further imprinted in serum and fecal samples as potential diagnostic biomarkers, thus providing a rationale for precision diagnosis.}, } @article {pmid37172351, year = {2023}, author = {Zerouali, B and Santos, CAG and do Nascimento, TVM and Silva, RMD}, title = {A cloud-integrated GIS for forest cover loss and land use change monitoring using statistical methods and geospatial technology over northern Algeria.}, journal = {Journal of environmental management}, volume = {341}, number = {}, pages = {118029}, doi = {10.1016/j.jenvman.2023.118029}, pmid = {37172351}, issn = {1095-8630}, mesh = {Humans ; *Geographic Information Systems ; *Conservation of Natural Resources/methods ; Algeria ; Agriculture ; Environmental Monitoring/methods ; Technology ; }, abstract = {Over the last two decades, forest cover has experienced significant impacts from fires and deforestation worldwide due to direct human activities and climate change. This paper assesses trends in forest cover loss and land use and land cover changes in northern Algeria between 2000 and 2020 using datasets extracted from Google Earth Engine (GEE), such as the Hanssen Global Forest Change and MODIS Land Cover Type products (MCD12Q1). Classification was performed using the pixel-based supervised machine-learning algorithm called Random Forest (RF). Trends were analyzed using methods such as Mann-Kendall and Sen. The study area comprises 17 basins with high rainfall variability. The results indicated that the forest area decreased by 64.96%, from 3718 to 1266 km[2], during the 2000-2020 period, while the barren area increased by 40%, from 134,777 to 188,748 km[2]. The findings revealed that the Constantinois-Seybousse-Mellegue hydrographic basin was the most affected by deforestation and cover loss, exceeding 50% (with an area of 1018 km[2]), while the Seybouse River basin experienced the highest percentage of cover loss at 40%. Nonparametric tests showed that seven river basins (41%) had significantly increasing trends of forest cover loss. According to the obtained results, the forest loss situation in Algeria, especially in the northeastern part, is very alarming and requires an exceptional and urgent plan to protect forests and the ecological system against wildfires and climate change. The study provides a diagnosis that should encourage better protection and management of forest cover in Algeria.}, } @article {pmid37169855, year = {2023}, author = {Huang, L and Jin, C and Pan, Y and Zhou, L and Hu, S and Guo, Y and Meng, Y and Song, K and Pang, M and Li, H and Lin, D and Xu, X and Minor, J and Coggins, C and Jim, CY and Yan, E and Yang, Y and Tang, Z and Lindenmayer, DB}, title = {Human activities and species biological traits drive the long-term persistence of old trees in human-dominated landscapes.}, journal = {Nature plants}, volume = {9}, number = {6}, pages = {898-907}, pmid = {37169855}, issn = {2055-0278}, support = {32071652//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32025025//National Natural Science Foundation of China (National Science Foundation of China)/ ; 31988102//National Natural Science Foundation of China (National Science Foundation of China)/ ; 2022M720254//China Postdoctoral Science Foundation/ ; }, mesh = {Animals ; Humans ; *Ecosystem ; Databases, Factual ; China ; *Moths ; Plant Leaves ; }, abstract = {Old trees have many ecological and socio-cultural values. However, knowledge of the factors influencing their long-term persistence in human-dominated landscapes is limited. Here, using an extensive database (nearly 1.8 million individual old trees belonging to 1,580 species) from China, we identified which species were most likely to persist as old trees in human-dominated landscapes and where they were most likely to occur. We found that species with greater potential height, smaller leaf size and diverse human utilization attributes had the highest probability of long-term persistence. The persistence probabilities of human-associated species (taxa with diverse human utilization attributes) were relatively high in intensively cultivated areas. Conversely, the persistence probabilities of spontaneous species (taxa with no human utilization attributes and which are not cultivated) were relatively high in mountainous areas or regions inhabited by ethnic minorities. The distinctly different geographic patterns of persistence probabilities of the two groups of species were related to their dissimilar responses to heterogeneous human activities and site conditions. A small number of human-associated species dominated the current cohort of old trees, while most spontaneous species were rare and endemic. Our study revealed the potential impacts of human activities on the long-term persistence of trees and the associated shifts in species composition in human-dominated landscapes.}, } @article {pmid37166827, year = {2023}, author = {Haslbeck, J and Ryan, O and Dablander, F}, title = {Multimodality and skewness in emotion time series.}, journal = {Emotion (Washington, D.C.)}, volume = {23}, number = {8}, pages = {2117-2141}, doi = {10.1037/emo0001218}, pmid = {37166827}, issn = {1931-1516}, support = {/NWO_/Dutch Research Council/Netherlands ; }, mesh = {Humans ; Time Factors ; *Emotions ; *Ecological Momentary Assessment ; Data Management ; }, abstract = {The ability to measure emotional states in daily life using mobile devices has led to a surge of exciting new research on the temporal evolution of emotions. However, much of the potential of these data still remains untapped. In this paper, we reanalyze emotion measurements from seven openly available experience sampling methodology studies with a total of 835 individuals to systematically investigate the modality (unimodal, bimodal, and more than two modes) and skewness of within-person emotion measurements. We show that both multimodality and skewness are highly prevalent. In addition, we quantify the heterogeneity across items, individuals, and measurement designs. Our analysis reveals that multimodality is more likely in studies using an analog slider scale than in studies using a Likert scale; negatively valenced items are consistently more skewed than positive valenced items; and longer time series show a higher degree of modality in positive and a higher skew in negative items. We end by discussing the implications of our results for theorizing, measurement, and time series modeling. (PsycInfo Database Record (c) 2023 APA, all rights reserved).}, } @article {pmid37165696, year = {2024}, author = {Kudapa, H and Ghatak, A and Barmukh, R and Chaturvedi, P and Khan, A and Kale, S and Fragner, L and Chitikineni, A and Weckwerth, W and Varshney, RK}, title = {Integrated multi-omics analysis reveals drought stress response mechanism in chickpea (Cicer arietinum L.).}, journal = {The plant genome}, volume = {17}, number = {1}, pages = {e20337}, doi = {10.1002/tpg2.20337}, pmid = {37165696}, issn = {1940-3372}, support = {OPP1114827//Bill and Melinda Gates Foundation/ ; SB/S9/Z-13/2019//Department of Science and Technology, Ministry of Science and Technology, India/ ; SB/WEA-01/2017//Department of Science and Technology, Ministry of Science and Technology, India/ ; }, mesh = {*Cicer/genetics ; Multiomics ; Plant Roots/genetics ; Droughts ; Galactose/metabolism ; Uridine Diphosphate/metabolism ; }, abstract = {Drought is one of the major constraints limiting chickpea productivity. To unravel complex mechanisms regulating drought response in chickpea, we generated transcriptomics, proteomics, and metabolomics datasets from root tissues of four contrasting drought-responsive chickpea genotypes: ICC 4958, JG 11, and JG 11+ (drought-tolerant), and ICC 1882 (drought-sensitive) under control and drought stress conditions. Integration of transcriptomics and proteomics data identified enriched hub proteins encoding isoflavone 4'-O-methyltransferase, UDP-d-glucose/UDP-d-galactose 4-epimerase, and delta-1-pyrroline-5-carboxylate synthetase. These proteins highlighted the involvement of pathways such as antibiotic biosynthesis, galactose metabolism, and isoflavonoid biosynthesis in activating drought stress response mechanisms. Subsequently, the integration of metabolomics data identified six metabolites (fructose, galactose, glucose, myoinositol, galactinol, and raffinose) that showed a significant correlation with galactose metabolism. Integration of root-omics data also revealed some key candidate genes underlying the drought-responsive "QTL-hotspot" region. These results provided key insights into complex molecular mechanisms underlying drought stress response in chickpea.}, } @article {pmid37165242, year = {2023}, author = {Liao, WW and Asri, M and Ebler, J and Doerr, D and Haukness, M and Hickey, G and Lu, S and Lucas, JK and Monlong, J and Abel, HJ and Buonaiuto, S and Chang, XH and Cheng, H and Chu, J and Colonna, V and Eizenga, JM and Feng, X and Fischer, C and Fulton, RS and Garg, S and Groza, C and Guarracino, A and Harvey, WT and Heumos, S and Howe, K and Jain, M and Lu, TY and Markello, C and Martin, FJ and Mitchell, MW and Munson, KM and Mwaniki, MN and Novak, AM and Olsen, HE and Pesout, T and Porubsky, D and Prins, P and Sibbesen, JA and Sirén, J and Tomlinson, C and Villani, F and Vollger, MR and Antonacci-Fulton, LL and Baid, G and Baker, CA and Belyaeva, A and Billis, K and Carroll, A and Chang, PC and Cody, S and Cook, DE and Cook-Deegan, RM and Cornejo, OE and Diekhans, M and Ebert, P and Fairley, S and Fedrigo, O and Felsenfeld, AL and Formenti, G and Frankish, A and Gao, Y and Garrison, NA and Giron, CG and Green, RE and Haggerty, L and Hoekzema, K and Hourlier, T and Ji, HP and Kenny, EE and Koenig, BA and Kolesnikov, A and Korbel, JO and Kordosky, J and Koren, S and Lee, H and Lewis, AP and Magalhães, H and Marco-Sola, S and Marijon, P and McCartney, A and McDaniel, J and Mountcastle, J and Nattestad, M and Nurk, S and Olson, ND and Popejoy, AB and Puiu, D and Rautiainen, M and Regier, AA and Rhie, A and Sacco, S and Sanders, AD and Schneider, VA and Schultz, BI and Shafin, K and Smith, MW and Sofia, HJ and Abou Tayoun, AN and Thibaud-Nissen, F and Tricomi, FF and Wagner, J and Walenz, B and Wood, JMD and Zimin, AV and Bourque, G and Chaisson, MJP and Flicek, P and Phillippy, AM and Zook, JM and Eichler, EE and Haussler, D and Wang, T and Jarvis, ED and Miga, KH and Garrison, E and Marschall, T and Hall, IM and Li, H and Paten, B}, title = {A draft human pangenome reference.}, journal = {Nature}, volume = {617}, number = {7960}, pages = {312-324}, pmid = {37165242}, issn = {1476-4687}, support = {R01 HG006677/HG/NHGRI NIH HHS/United States ; U01 HG010961/HG/NHGRI NIH HHS/United States ; R35 GM130151/GM/NIGMS NIH HHS/United States ; U41 HG010972/HG/NHGRI NIH HHS/United States ; U01 HG010973/HG/NHGRI NIH HHS/United States ; R01 HG011649/HG/NHGRI NIH HHS/United States ; U01 HG010963/HG/NHGRI NIH HHS/United States ; R01 HG011274/HG/NHGRI NIH HHS/United States ; U24 HG009081/HG/NHGRI NIH HHS/United States ; U24 HG010262/HG/NHGRI NIH HHS/United States ; U01 HG010971/HG/NHGRI NIH HHS/United States ; U24 HG011853/HG/NHGRI NIH HHS/United States ; R01 HG010485/HG/NHGRI NIH HHS/United States ; U24 HG007497/HG/NHGRI NIH HHS/United States ; R01 HG002385/HG/NHGRI NIH HHS/United States ; ZIA HG200398/ImNIH/Intramural NIH HHS/United States ; R01 HG010169/HG/NHGRI NIH HHS/United States ; U41 HG007234/HG/NHGRI NIH HHS/United States ; OT2 OD033761/OD/NIH HHS/United States ; R01 GM123489/GM/NIGMS NIH HHS/United States ; /WT_/Wellcome Trust/United Kingdom ; }, mesh = {Humans ; Diploidy ; *Genome, Human/genetics ; Haplotypes/genetics ; Sequence Analysis, DNA ; *Genomics/standards ; Reference Standards ; Cohort Studies ; Alleles ; Genetic Variation ; }, abstract = {Here the Human Pangenome Reference Consortium presents a first draft of the human pangenome reference. The pangenome contains 47 phased, diploid assemblies from a cohort of genetically diverse individuals[1]. These assemblies cover more than 99% of the expected sequence in each genome and are more than 99% accurate at the structural and base pair levels. Based on alignments of the assemblies, we generate a draft pangenome that captures known variants and haplotypes and reveals new alleles at structurally complex loci. We also add 119 million base pairs of euchromatic polymorphic sequences and 1,115 gene duplications relative to the existing reference GRCh38. Roughly 90 million of the additional base pairs are derived from structural variation. Using our draft pangenome to analyse short-read data reduced small variant discovery errors by 34% and increased the number of structural variants detected per haplotype by 104% compared with GRCh38-based workflows, which enabled the typing of the vast majority of structural variant alleles per sample.}, } @article {pmid37162091, year = {2023}, author = {Kawano, B and Agarwal, S and Krishnamoorthy, V and Raghunathan, K and Fernandez-Moure, JS and Haines, KL}, title = {State Firearm Laws and Rate of Assault-Related Firearm Death.}, journal = {Journal of the American College of Surgeons}, volume = {237}, number = {3}, pages = {409-418}, doi = {10.1097/XCS.0000000000000753}, pmid = {37162091}, issn = {1879-1190}, mesh = {Humans ; United States/epidemiology ; Adolescent ; *Firearms ; *Wounds, Gunshot/epidemiology ; Databases, Factual ; Forecasting ; Homicide ; }, abstract = {BACKGROUND: Studying firearm-related mortality is important to reduce preventable firearm death in the US. This study aims to determine the relationship between firearm laws and assault death with firearms.

STUDY DESIGN: This ecologic study used public data from the CDC Wide-Ranging Online Data for Epidemiologic Research on decedents age 18 years or older who died from assault with firearms between 2009 and 2018 in all 50 states and Washington, DC. The outcomes were the rate of mortality per 100,000 persons from assault death by firearm used. Exposures of interest included the presence of 7 state firearm laws extracted from the RAND State Firearm Law Database. Welch's t tests were performed to compare mean mortality rate in states with each firearm law to states without each law.

RESULTS: There were 114,945 deaths from assault with firearms from 2009 to 2018. States with "stand your ground" laws had a higher assault mortality rate from all firearms and from other/unspecified firearms than states without stand your ground laws (p = 0.026; p = 0.023). States with background checks for private sales of handguns and long guns had a lower assault mortality rate from handguns and rifles, shotguns, and large firearms, respectively, than states without either law (p = 0.019; p = 0.030).

CONCLUSIONS: Stand your ground laws are correlated with a higher rate of gun-related assault death, but background checks on private sales are correlated with a lower rate. Future studies should elucidate the specific pathways by which state laws reduce, or fail to reduce, firearm-related assault death.}, } @article {pmid37162089, year = {2023}, author = {Santana, BEF and Andrade, ACS and Muraro, AP}, title = {Trend of incompleteness of maternal schooling and race/skin color variables held on the Brazilian Live Birth Information System, 2012-2020.}, journal = {Epidemiologia e servicos de saude : revista do Sistema Unico de Saude do Brasil}, volume = {32}, number = {1}, pages = {e2022725}, pmid = {37162089}, issn = {2237-9622}, mesh = {Female ; Humans ; Pregnancy ; Brazil ; *Educational Status ; *Live Birth ; Pregnancy, Multiple ; Skin Pigmentation ; Databases, Factual/standards/statistics & numerical data ; Health Information Systems ; Racial Groups ; }, abstract = {OBJECTIVE: to analyze the trend of incompleteness of the maternal schooling and race/skin color variables held on the Brazilian Live Birth Information System (SINASC) between 2012 and 2020.

METHODS: this was an ecological time series study of the incompleteness of maternal schooling and race/skin color data for Brazil, its regions and Federative Units, by means of joinpoint regression and calculation of annual percentage change (APC) and average annual percentage change.

RESULTS: a total of 26,112,301 births were registered in Brazil in the period; incompleteness of maternal schooling data decreased for Brazil (APC = -8.1%) and the Southeast (APC = -19.5%) and Midwest (APC = -17.6%) regions; as for race/skin color, there was a downward trend for Brazil (APC = -8.2%) and all regions, except the Northeast region, while nine Federative Units and the Federal District showed a stationary trend.

CONCLUSION: there was an improvement in filling out these variables on the SINASC, but with regional disparities, mainly for race/skin color.}, } @article {pmid37161334, year = {2023}, author = {Kortz, AR and Moyes, F and Pivello, VR and Pyšek, P and Dornelas, M and Visconti, P and Magurran, AE}, title = {Elevated compositional change in plant assemblages linked to invasion.}, journal = {Proceedings. Biological sciences}, volume = {290}, number = {1998}, pages = {20222450}, pmid = {37161334}, issn = {1471-2954}, mesh = {*Tracheophyta ; Biodiversity ; Databases, Factual ; Introduced Species ; }, abstract = {Alien species are widely linked to biodiversity change, but the extent to which they are associated with the reshaping of ecological communities is not well understood. One possible mechanism is that assemblages where alien species are found exhibit elevated temporal turnover. To test this, we identified assemblages of vascular plants in the BioTIME database for those assemblages in which alien species are either present or absent and used the Jaccard measure to compute compositional dissimilarity between consecutive censuses. We found that, although alien species are typically rare in invaded assemblages, their presence is associated with an increase in the average rate of compositional change. These differences in compositional change between invaded and uninvaded assemblages are not linked to differences in species richness but rather to species replacement (turnover). Rapid compositional restructuring of assemblages is a major contributor to biodiversity change, and as such, our results suggest a role for alien species in bringing this about.}, } @article {pmid37155680, year = {2023}, author = {Rokhsar, JL and Raynor, B and Sheen, J and Goldstein, ND and Levy, MZ and Castillo-Neyra, R}, title = {Modeling the impact of xenointoxication in dogs to halt Trypanosoma cruzi transmission.}, journal = {PLoS computational biology}, volume = {19}, number = {5}, pages = {e1011115}, pmid = {37155680}, issn = {1553-7358}, support = {K01 AI139284/AI/NIAID NIH HHS/United States ; T32 AI070077/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Dogs ; *Trypanosoma cruzi ; Insect Vectors ; *Chagas Disease/epidemiology/prevention & control/veterinary ; *Triatoma/parasitology ; *Insecticides/pharmacology ; Mammals ; }, abstract = {BACKGROUND: Chagas disease, a vector-borne parasitic disease caused by Trypanosoma cruzi, affects millions in the Americas. Dogs are important reservoirs of the parasite. Under laboratory conditions, canine treatment with the systemic insecticide fluralaner demonstrated efficacy in killing Triatoma infestans and T. brasiliensis, T. cruzi vectors, when they feed on dogs. This form of pest control is called xenointoxication. However, T. cruzi can also be transmitted orally when mammals ingest infected bugs, so there is potential for dogs to become infected upon consuming infected bugs killed by the treatment. Xenointoxication thereby has two contrasting effects on dogs: decreasing the number of insects feeding on the dogs but increasing opportunities for exposure to T. cruzi via oral transmission to dogs ingesting infected insects.

OBJECTIVE: Examine the potential for increased infection rates of T. cruzi in dogs following xenointoxication.

DESIGN/METHODS: We built a deterministic mathematical model, based on the Ross-MacDonald malaria model, to investigate the net effect of fluralaner treatment on the prevalence of T. cruzi infection in dogs in different epidemiologic scenarios. We drew upon published data on the change in percentage of bugs killed that fed on treated dogs over days post treatment. Parameters were adjusted to mimic three scenarios of T. cruzi transmission: high and low disease prevalence and domestic vectors, and low disease prevalence and sylvatic vectors.

RESULTS: In regions with high endemic disease prevalence in dogs and domestic vectors, prevalence of infected dogs initially increases but subsequently declines before eventually rising back to the initial equilibrium following one fluralaner treatment. In regions of low prevalence and domestic or sylvatic vectors, however, treatment seems to be detrimental. In these regions our models suggest a potential for a rise in dog prevalence, due to oral transmission from dead infected bugs.

CONCLUSION: Xenointoxication could be a beneficial and novel One Health intervention in regions with high prevalence of T. cruzi and domestic vectors. In regions with low prevalence and domestic or sylvatic vectors, there is potential harm. Field trials should be carefully designed to closely follow treated dogs and include early stopping rules if incidence among treated dogs exceeds that of controls.}, } @article {pmid37155231, year = {2023}, author = {Ondrikova, N and Harris, JP and Douglas, A and Hughes, HE and Iturriza-Gomara, M and Vivancos, R and Elliot, AJ and Cunliffe, NA and Clough, HE}, title = {Predicting Norovirus in England Using Existing and Emerging Syndromic Data: Infodemiology Study.}, journal = {Journal of medical Internet research}, volume = {25}, number = {}, pages = {e37540}, pmid = {37155231}, issn = {1438-8871}, mesh = {Humans ; Infodemiology ; *Norovirus ; England/epidemiology ; *Gastroenteritis/epidemiology ; *Caliciviridae Infections/epidemiology ; }, abstract = {BACKGROUND: Norovirus is associated with approximately 18% of the global burden of gastroenteritis and affects all age groups. There is currently no licensed vaccine or available antiviral treatment. However, well-designed early warning systems and forecasting can guide nonpharmaceutical approaches to norovirus infection prevention and control.

OBJECTIVE: This study evaluates the predictive power of existing syndromic surveillance data and emerging data sources, such as internet searches and Wikipedia page views, to predict norovirus activity across a range of age groups across England.

METHODS: We used existing syndromic surveillance and emerging syndromic data to predict laboratory data indicating norovirus activity. Two methods are used to evaluate the predictive potential of syndromic variables. First, the Granger causality framework was used to assess whether individual variables precede changes in norovirus laboratory reports in a given region or an age group. Then, we used random forest modeling to estimate the importance of each variable in the context of others with two methods: (1) change in the mean square error and (2) node purity. Finally, these results were combined into a visualization indicating the most influential predictors for norovirus laboratory reports in a specific age group and region.

RESULTS: Our results suggest that syndromic surveillance data include valuable predictors for norovirus laboratory reports in England. However, Wikipedia page views are less likely to provide prediction improvements on top of Google Trends and Existing Syndromic Data. Predictors displayed varying relevance across age groups and regions. For example, the random forest modeling based on selected existing and emerging syndromic variables explained 60% variance in the ≥65 years age group, 42% in the East of England, but only 13% in the South West region. Emerging data sets highlighted relative search volumes, including "flu symptoms," "norovirus in pregnancy," and norovirus activity in specific years, such as "norovirus 2016." Symptoms of vomiting and gastroenteritis in multiple age groups were identified as important predictors within existing data sources.

CONCLUSIONS: Existing and emerging data sources can help predict norovirus activity in England in some age groups and geographic regions, particularly, predictors concerning vomiting, gastroenteritis, and norovirus in the vulnerable populations and historical terms such as stomach flu. However, syndromic predictors were less relevant in some age groups and regions likely due to contrasting public health practices between regions and health information-seeking behavior between age groups. Additionally, predictors relevant to one norovirus season may not contribute to other seasons. Data biases, such as low spatial granularity in Google Trends and especially in Wikipedia data, also play a role in the results. Moreover, internet searches can provide insight into mental models, that is, an individual's conceptual understanding of norovirus infection and transmission, which could be used in public health communication strategies.}, } @article {pmid37155109, year = {2023}, author = {Chen, D and Zhang, Y and Feng, Q}, title = {Hydrochemical characteristics and microbial community evolution of Pinglu River affected by regional abandoned coal mine drainage, Guizhou Province, China.}, journal = {Environmental science and pollution research international}, volume = {30}, number = {27}, pages = {70671-70687}, pmid = {37155109}, issn = {1614-7499}, mesh = {Mining ; *Microbiota ; Rivers/chemistry ; Bacteria/genetics ; Water/chemistry ; Coal/analysis ; China ; *Water Pollutants, Chemical/analysis ; }, abstract = {Pinglu River in southwestern China was continuously polluted by acid mine drainage (AMD) from abandoned coal mines, and AMD has become a major source of recharge to the river (43.26% of total flow), resulting in structural changes in the physicochemical properties and microbial communities of river water and sediments. In this study, we collected abandoned coal mine drainage, river water, and river sediment samples for comprehensive analysis. Results indicated that the hydrochemical types of AMD from abandoned coal mines were mainly SO4-Ca·Mg. The pH of river water in Pinglu River decreased from upstream to downstream due to AMD, with the hydrochemical type gradually changing from SO4·HCO3-Ca·Mg to SO4-Ca·Mg. The variation of pH along the river sediments was less than that of water samples, which remained weakly alkaline. However, high-throughput sequencing revealed a gradual decrease in microbial diversity in river sediments from upstream to downstream. The core bacteria groups in the upstream sediments were mainly attributed to the phylum Proteobacteria and Actinobacteriota, mainly including Geobacter, Anaeromyxobacter, Marmoricola, and Phycicoccus. The relative abundance of Gaiella, MND1, and Pseudolabrys in sediment samples gradually increased with the confluence of AMD, and the differences in microbial communities may be attributed to pH, TOC, and TP. Results of phenotype prediction demonstrated that the relative abundance of anaerobic microorganisms in river sediment gradually decreased from upstream to downstream (from 24.77 to 12.46%), presumably due to the large amount of oligotrophic AMD converge.}, } @article {pmid37154236, year = {2023}, author = {Lin, F and Kennelly, EJ and Linington, RG and Long, C}, title = {Comprehensive Metabolite Profiling of Two Edible Garcinia Species Based on UPLC-ESI-QTOF-MS[E] Coupled with Bioactivity Assays.}, journal = {Journal of agricultural and food chemistry}, volume = {71}, number = {19}, pages = {7604-7617}, doi = {10.1021/acs.jafc.2c08372}, pmid = {37154236}, issn = {1520-5118}, mesh = {Chromatography, High Pressure Liquid ; *Garcinia ; Multivariate Analysis ; Metabolomics ; *Plants, Medicinal ; }, abstract = {In China, the endemic species Garcinia yunnanensis and native Garcinia xanthochymus are known as edible and medicinal plants. However, a systematic metabolomic and bioactivity evaluation of different plant parts from both species is lacking. In this study, comprehensive investigations of 11 plant parts of G. yunnanensis and 10 of G. xanthochymus employing UPLC-ESI-QTOF-MS[E]-based metabolomic analysis in conjunction with three bioactivity assays were undertaken. A customized chemotaxonomic-based in-house library containing 6456 compounds was constructed and coupled to the Progenesis QI informatic platform for metabolite annotations. From these two species, a total of 235 constituents were characterized using multiple criteria. Differences in metabolite profiles between the plant parts within each species were uncovered using multivariate analysis. Based on orthogonal partial least-squares discriminant analysis (OPLS-DA), 23 markers were identified as highly differential metabolites from G. xanthochymus and 20 from G. yunnanensis. Comparative assessment of the biological assays revealed the activity variations among different plant parts. The seeds of both species and G. yunnanensis latex exhibited excellent cytotoxic and antibacterial activities, while G. xanthochymus roots and G. yunnanensis arils showed strong anti-inflammatory effects. S-plot analysis identified 26 potential biomarkers for the observed activities, including the known cytotoxic agent cycloxanthochymol and the anti-inflammatory compound garcimultiflorone B, which likely explains some of the potent observed bioactivity.}, } @article {pmid37152782, year = {2023}, author = {Mori, Y and Okawara, M and Shibao, K and Kohi, S and Tamura, T and Sato, N and Fujino, Y and Fushimi, K and Matsuda, S and Hirata, K}, title = {Changes in operative trends and short-term outcomes of surgery for congenital biliary dilatation in adults using real-world data: A multilevel analysis based on a nationwide administrative database in Japan.}, journal = {Annals of gastroenterological surgery}, volume = {7}, number = {3}, pages = {471-478}, pmid = {37152782}, issn = {2475-0328}, abstract = {AIM: We aimed to evaluate the operative trends and compare the short-term outcomes between open and laparoscopic surgery for congenital biliary dilatation (CBD) in adults using real-world data from Japan.

METHODS: Data from the Japanese Diagnosis Procedure Combination database on 941 patients undergoing surgery for CBD at 357 hospitals from April 1, 2016, to March 31, 2021, were analyzed. The patients were divided into two groups: open surgery (n = 764) and laparoscopic surgery (n = 177). We performed a retrospective analysis via a multilevel analysis of the short-term surgical outcomes and costs between open and laparoscopic surgery.

RESULTS: The rate of laparoscopic surgery has been increasing annually and had almost doubled to 25% by 2021. There were no significant differences in the in-hospital mortality rate or postoperative morbidity between the two groups. The length of anesthesia was significantly longer in the laparoscopic than open surgery group (8.80 vs 6.16 hours, p < .001). The time to removal of the abdominal drain and length of hospital stay were significantly shorter in the laparoscopic than open surgery group (6.12 vs 8.35 days, p = .001 and 13.57 vs 15.79 days, p < .001, respectively). The coefficient for cost was 463 235 yen (95% confidence interval, 289 679-636 792) higher in laparoscopic than open surgery (p < .001).

CONCLUSION: The short-term results were comparable between laparoscopic and open surgery for CBD. Further investigation is needed to validate our findings and long-term outcomes.}, } @article {pmid37150648, year = {2023}, author = {Wieczorek, P and Pruc, M and Krajsman, M and Wieczorek, W and Cander, B and Szarpak, L and Navolokina, A and Matuszewski, M and Bragazzi, NL and Chirico, F and Smereka, J}, title = {Comparison of the bébé VieScope™ and direct laryngoscope for pediatric tongue oedema scenario: A simulation study.}, journal = {The American journal of emergency medicine}, volume = {69}, number = {}, pages = {207-208}, doi = {10.1016/j.ajem.2023.04.039}, pmid = {37150648}, issn = {1532-8171}, mesh = {Humans ; Child ; *Laryngoscopes ; Laryngoscopy ; Intubation, Intratracheal ; *Tongue Diseases ; Tongue ; Edema ; Manikins ; Equipment Design ; }, } @article {pmid37148803, year = {2023}, author = {Tang, Y and Hardy, TJ and Yoon, JY}, title = {Receptor-based detection of microplastics and nanoplastics: Current and future.}, journal = {Biosensors & bioelectronics}, volume = {234}, number = {}, pages = {115361}, doi = {10.1016/j.bios.2023.115361}, pmid = {37148803}, issn = {1873-4235}, mesh = {Microplastics ; Plastics ; *Biosensing Techniques ; Biological Assay ; Databases, Factual ; *Water Pollutants, Chemical ; }, abstract = {Plastic pollution is an emerging environmental concern, gaining significant attention worldwide. They are classified into microplastics (MP; defined from 1 μm to 5 mm) and smaller nanoplastics (NP; <1 μm). NPs may pose higher ecological risks than MPs. Various microscopic and spectroscopic techniques have been used to detect MPs, and the same methods have occasionally been used for NPs. However, they are not based on receptors, which provide high specificity in most biosensing applications. Receptor-based micro/nanoplastics (MNP) detection can provide high specificity, distinguishing MNPs from the environmental samples and, more importantly, identifying the plastic types. It can also offer a low limit of detection (LOD) required for environmental screening. Such receptors are expected to detect NPs specifically at the molecular level. This review categorizes the receptors into cells, proteins, peptides, fluorescent dyes, polymers, and micro/nanostructures. Detection techniques used with these receptors are also summarized and categorized. There is plenty of room for future research to test for broader classes of environmental samples and many plastic types, to lower the LOD, and to apply the current techniques for NPs. Portable and handheld MNP detection should also be demonstrated for field use since the current demonstrations primarily utilized laboratory instruments. Detection on microfluidic platforms will also be crucial in miniaturizing and automating the assay and, eventually, collecting an extensive database to support machine learning-based classification of MNP types.}, } @article {pmid37148512, year = {2023}, author = {Wang, Y}, title = {Ecological risk identification and assessment of land remediation project based on GIS technology.}, journal = {Environmental science and pollution research international}, volume = {30}, number = {27}, pages = {70493-70505}, pmid = {37148512}, issn = {1614-7499}, mesh = {Animals ; Geographic Information Systems ; *Volatile Organic Compounds ; *Environmental Restoration and Remediation ; *Environmental Pollutants ; Risk Assessment ; Technology ; Environmental Monitoring ; }, abstract = {A land remediation project involves the removal of potentially toxic chemicals from a polluted site. Lands abandoned by industry are often contaminated with heavy metals like mercury, lead, chemicals, arsenic, and other toxins like dichlorodiphenyltrichloroethane biphenyls from electronic devices, and volatile organic chemicals (VOCs) from lubricants and chemicals. Risk assessment in environmental settings requires modernized systematic methodologies due to the complexity of today's environmental problems. When people eat, drink, or work in polluted environments, they put their health at risk and may even get cancer. Integrating geospatial information systems (GIS) with pollutant dispersion models makes environmental risk assessment and early warning possible. This research thus presents a GIS-based ecological risk identification and assessment model (GIS-ERIAM) for assessing risk for efficient land rehabilitation. Environmental cleanup sites' catalog information is the source of these details. With satellite imagery, GIS makes it simple to keep an eye on the environment and track the abundance of different types of plants and animals The ecological risk assessment (ERA) model can support recognition and prioritize risk management. By integrating direct and indirect environment interactions, the risk conditions of the whole ecology and its elements have been quantified and demonstrated in the study. The numerical outcomes illustrate that the recommended GIS-ERIAM model improves the performance by 98.9%, risk level prediction by 97.3%, risk classification by 96.4%, and detection of soil degradation ratio of 95.6% compared to other existing methods.}, } @article {pmid37138127, year = {2023}, author = {Mohamadi, S and Honarmand, M and Ghazanfari, S and Hassanzadeh, R}, title = {Hotspot and accumulated hotspot analysis for assessment of groundwater quality and pollution indices using GIS in the arid region of Iran.}, journal = {Environmental science and pollution research international}, volume = {30}, number = {27}, pages = {69955-69976}, pmid = {37138127}, issn = {1614-7499}, mesh = {Water Quality ; Environmental Monitoring/methods ; Geographic Information Systems ; Iran ; *Groundwater/analysis ; Nitrates/analysis ; *Water Pollutants, Chemical/analysis ; }, abstract = {Because groundwater quality representatives for drinking usage (i.e., Schuler method, Nitrate and Groundwater Quality Index) have been abruptly changing due to extreme events induced by global climate change and over-abstracting, applying an efficient tool for their assessments is vitally important. While hotspot analysis is introduced as an efficient tool concentrating on sharp changes in groundwater quality, it has not been closely examined. Accordingly, this study is an attempt to determine the groundwater quality proxies and assess them through hotspot and accumulated hotspot analyses. To this end, a GIS-based hotspot analysis (HA) applying Getis-Ord Gi* statistics was used. The accumulated hotspot analysis was launched to identify the Groundwater Quality Index (AHA-GQI). Moreover, Schuler method (AHA-SM) was utilized to determine the maximum levels (ML) for the hottest hotspot and the lowest levels (LL) for the coldest cold-spot, and compound levels (CL). The results revealed that a significant correlation (r = 0.8) between GQI and SM was observed. However, the correlation between GQI and nitrate was not significant and the correlation between SM and nitrate was so low (r = 0.298, sig > 0.05). The results also demonstrated that using hotspot analysis on only GQI, the correlation between GQI and SM increased from 0.8 to 0.856, while using hotspot analysis on both GQI and SM increased the correlation to 0.945. Likewise, when GQI was subjected to hotspot analysis and SM underwent accumulated hotspot analysis (i.e., AHA-SM (ML)), the correlation degree increased to the highest extent (i.e., 0.958), indicating the usefulness of including the hotspot analysis and accumulated hotspot analysis in the evaluation of groundwater quality.}, } @article {pmid37134212, year = {2023}, author = {Schuler, T and King, C and Matsveru, T and Back, M and Clark, K and Chin, D and Lilian, R and Gallego, B and Coiera, E and Currow, DC}, title = {Wearable-Triggered Ecological Momentary Assessments Are Feasible in People With Advanced Cancer and Their Family Caregivers: Feasibility Study from an Outpatient Palliative Care Clinic at a Cancer Center.}, journal = {Journal of palliative medicine}, volume = {26}, number = {7}, pages = {980-985}, doi = {10.1089/jpm.2022.0535}, pmid = {37134212}, issn = {1557-7740}, mesh = {Humans ; Palliative Care ; Caregivers ; Feasibility Studies ; Ecological Momentary Assessment ; Outpatients ; *Neoplasms ; *Wearable Electronic Devices ; }, abstract = {Background: Emerging digital health approaches could play a role in better personalized palliative care. Aim: We conducted a feasibility study testing wearable sensor (WS)-triggered ecological momentary assessments (EMAs) and electronic patient-reported outcomes in community palliative care with patient-caregiver dyads. Design: All wore consumer-grade WS for five weeks. Sensor-detected "stress" (heart rate variability algorithm) that passed individualized thresholds triggered a short smartphone survey. Daily sleep surveys, weekly symptom surveys (Integrated Palliative care Outcome Scale), and a poststudy experience survey were conducted. Setting/Participants: Fifteen dyads (n = 30) were recruited from an outpatient palliative care clinic for people with cancer. Results: Daytime sensor wear-time had 73% adherence. Participants perceived value in this support. Quantity and severity of "stress" events were higher in patients. Sleep disturbance was similar but for different reasons: patients (physical symptoms) and caregivers (worrying about the patient). Conclusions: EMAs are feasible and valued in community palliative care.}, } @article {pmid37117267, year = {2023}, author = {Minhas, BF and Beck, EA and Cheng, CC and Catchen, J}, title = {Novel mitochondrial genome rearrangements including duplications and extensive heteroplasmy could underlie temperature adaptations in Antarctic notothenioid fishes.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {6939}, pmid = {37117267}, issn = {2045-2322}, mesh = {Animals ; *Genome, Mitochondrial/genetics ; Temperature ; Heteroplasmy ; Fishes/genetics ; *Perciformes/physiology ; Antarctic Regions ; }, abstract = {Mitochondrial genomes are known for their compact size and conserved gene order, however, recent studies employing long-read sequencing technologies have revealed the presence of atypical mitogenomes in some species. In this study, we assembled and annotated the mitogenomes of five Antarctic notothenioids, including four icefishes (Champsocephalus gunnari, C. esox, Chaenocephalus aceratus, and Pseudochaenichthys georgianus) and the cold-specialized Trematomus borchgrevinki. Antarctic notothenioids are known to harbor some rearrangements in their mt genomes, however the extensive duplications in icefishes observed in our study have never been reported before. In the icefishes, we observed duplications of the protein coding gene ND6, two transfer RNAs, and the control region with different copy number variants present within the same individuals and with some ND6 duplications appearing to follow the canonical Duplication-Degeneration-Complementation (DDC) model in C. esox and C. gunnari. In addition, using long-read sequencing and k-mer analysis, we were able to detect extensive heteroplasmy in C. aceratus and C. esox. We also observed a large inversion in the mitogenome of T. borchgrevinki, along with the presence of tandem repeats in its control region. This study is the first in using long-read sequencing to assemble and identify structural variants and heteroplasmy in notothenioid mitogenomes and signifies the importance of long-reads in resolving complex mitochondrial architectures. Identification of such wide-ranging structural variants in the mitogenomes of these fishes could provide insight into the genetic basis of the atypical icefish mitochondrial physiology and more generally may provide insights about their potential role in cold adaptation.}, } @article {pmid37116451, year = {2023}, author = {Barnea, O and Cohen, N and Hindi, I and Katz, C}, title = {Noticing the unutilized resource of siblinghood: Key conclusions from a scoping review about siblings in out-of-home placements.}, journal = {Child abuse & neglect}, volume = {141}, number = {}, pages = {106192}, doi = {10.1016/j.chiabu.2023.106192}, pmid = {37116451}, issn = {1873-7757}, mesh = {Child ; Humans ; *Siblings ; *Child Welfare ; Foster Home Care/methods ; Databases, Factual ; }, abstract = {BACKGROUND: Sibling bonds are often the most enduring relationship in an individual's life span. The out-of-home placement of siblings is widespread and may significantly influence children's journeys and wellbeing.

OBJECTIVE: The current scoping literature review was designed to characterize and analyze the existing knowledge regarding siblings in out-of-home placements.

METHOD: Key databases were explored using the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines, which identified 33 studies relevant to the current study's focus. The studies used quantitative, qualitative, and mixed methods and included a variety of out-of-home placement settings and sample characteristics.

RESULTS: Utilizing thematic analysis, the findings addressed three main themes: the sibling bond as a contributor to the wellbeing of children in out-of-home placements, trends in sibling placement, and difficulties in maintaining the sibling bond in out-of-home placements regarding micro, meso and exo factors.

CONCLUSION: A key conclusion from the review is that the welfare system struggles to address a child as a part of a sibling group and an extensive and multilayered relational network; hence, siblinghood is an unutilized resource in out-of-home placements. Future directions for practice, policy and research are included and discussed.}, } @article {pmid37110442, year = {2023}, author = {Maimone, G and Azzaro, M and Placenti, F and Paranhos, R and Cabral, AS and Decembrini, F and Zaccone, R and Cosenza, A and Rappazzo, AC and Patti, B and Basilone, G and Cuttitta, A and Ferreri, R and Aronica, S and Ferla, R}, title = {A Morphometric Approach to Understand Prokaryoplankton: A Study in the Sicily Channel (Central Mediterranean Sea).}, journal = {Microorganisms}, volume = {11}, number = {4}, pages = {}, pmid = {37110442}, issn = {2076-2607}, abstract = {A new understanding of plankton ecology has been obtained by studying the phenotypic traits of free-living prokaryotes in the Sicily Channel (Central Mediterranean Sea), an area characterised by oligotrophic conditions. During three cruises carried out in July 2012, January 2013 and July 2013, the volume and morphology of prokaryotic cells were assessed microscopically using image analysis in relation to environmental conditions. The study found significant differences in cell morphologies among cruises. The largest cell volumes were observed in the July 2012 cruise (0.170 ± 0.156 µm[3]), and the smallest in the January 2013 cruise (0.060 ± 0.052 µm[3]). Cell volume was negatively limited by nutrients and positively by salinity. Seven cellular morphotypes were observed among which cocci, rods and coccobacilli were the most abundant. Cocci, although they prevailed numerically, always showed the smallest volumes. Elongated shapes were positively related to temperature. Relationships between cell morphologies and environmental drivers indicated a bottom-up control of the prokaryotic community. The morphology/morphometry-based approach is a useful tool for studying the prokaryotic community in microbial ecology and should be widely applied to marine microbial populations in nature.}, } @article {pmid37107825, year = {2023}, author = {Schütt, EM and Hundsdörfer, MAJ and von Hoyningen-Huene, AJE and Lange, X and Koschmider, A and Oppelt, N}, title = {First Steps towards a near Real-Time Modelling System of Vibrio vulnificus in the Baltic Sea.}, journal = {International journal of environmental research and public health}, volume = {20}, number = {8}, pages = {}, pmid = {37107825}, issn = {1660-4601}, mesh = {Humans ; *Vibrio vulnificus ; *Vibrio Infections ; Water ; Baltic States ; Oxygen ; }, abstract = {Over the last two decades, Vibrio vulnificus infections have emerged as an increasingly serious public health threat along the German Baltic coast. To manage related risks, near real-time (NRT) modelling of V. vulnificus quantities has often been proposed. Such models require spatially explicit input data, for example, from remote sensing or numerical model products. We tested if data from a hydrodynamic, a meteorological, and a biogeochemical model are suitable as input for an NRT model system by coupling it with field samples and assessing the models' ability to capture known ecological parameters of V. vulnificus. We also identify the most important predictors for V. vulnificus in the Baltic Sea by leveraging the St. Nicolas House Analysis. Using a 27-year time series of sea surface temperature, we have investigated trends of V. vulnificus season length, which pinpoint hotspots mainly in the east of our study region. Our results underline the importance of water temperature and salinity on V. vulnificus abundance but also highlight the potential of air temperature, oxygen, and precipitation to serve as predictors in a statistical model, albeit their relationship with V. vulnificus may not be causal. The evaluated models cannot be used in an NRT model system due to data availability constraints, but promising alternatives are presented. The results provide a valuable basis for a future NRT model for V. vulnificus in the Baltic Sea.}, } @article {pmid37107056, year = {2023}, author = {Olivieri, R and Vannini, P and Corzani, A and Bianco, MT and Franchi, F and Cusi, MG and Scolletta, S and Arena, F and Basagni, C and Gusinu, R and Tumbarello, M}, title = {Rapid Decrease in Fluoroquinolones Consumption following Implementation of a Simple Antimicrobial Stewardship Bundled Intervention in a University Hospital during the COVID-19 Pandemic.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {12}, number = {4}, pages = {}, pmid = {37107056}, issn = {2079-6382}, abstract = {Fluoroquinolones (FQs) represent an class of antibiotics of medical importance, but their use has been restricted due to their ecologic impact and associated side effects. The reduction of FQs use is an important goal of antimicrobial stewardship programs (ASP). This work describes an ASP focused on overall antibiotics and FQs consumption reduction. From January 2021, an ASP was implemented in a 700-bed teaching hospital. The ASP was based on: (i) antibiotics consumption monitoring system (DDD/100 bed days); (ii) mandatory antibiotic prescription-motivation (using a dedicated informatic format) with the goal of >75% of motivated prescriptions; and (iii) data feedback and training on FQs use indications. We evaluated the impact of the intervention on overall systemic antibiotics and FQs consumption according to the objectives posed by Italian PNCAR (National Action Plan on Antimicrobial Resistance). A decrease of 6.6% in antibiotic use was observed (2019 vs. 2021). Notably, the FQs consumption fell by 48.3% from 7.1 DDD/100 bd in 2019 to 3.7 DDD/100 bd in 2021 (p < 0.001). After six months of mandatory antibiotic prescription-indication, all units achieved the target set. The study suggests that a simple, bundled ASP intervention can be rapidly effective obtaining the objectives of PNCAR on the reduction of overall antibiotics and FQs consumption.}, } @article {pmid37106771, year = {2023}, author = {Prakofjewa, J and Sartori, M and Šarka, P and Kalle, R and Pieroni, A and Sõukand, R}, title = {Boundaries Are Blurred: Wild Food Plant Knowledge Circulation across the Polish-Lithuanian-Belarusian Borderland.}, journal = {Biology}, volume = {12}, number = {4}, pages = {}, pmid = {37106771}, issn = {2079-7737}, support = {714874/ERC_/European Research Council/International ; }, abstract = {The circulation of local ecological knowledge (LEK) is a promising avenue of research for wild plant studies. To encourage the acceptance, celebration, and appreciation of biocultural diversity, which is rapidly disappearing nowadays, we need to estimate and assess multifaceted local ecological knowledge. It has direct application for local communities in informing effective policies for improving food security and building community-specific responses to environmental and social transitions. The present study draws on data collected among two ethnic groups-Lithuanians and Poles-via 200 semi-structured in-depth interviews and participant observation conducted in 2018 and 2019 in Podlasie Voivodeship (Poland), the Vilnius Region (Lithuania), and the Hrodna Region (Belarus). We aimed to observe LEK circulation in the border area through cross-ethnic and cross-country comparisons. A total of 2812 detailed use reports of wild plants were recorded. In total, 72 wild plant taxa belonging to 33 plant families were used across the food domain. Our findings show that cross-country differences were minimal, while there was some variation between the ethnic groups selected as case studies. We emphasize the need, in future studies, to combine quantitative research with qualitative approaches in order to more thoroughly identify peculiarities of cross-border circulation as a reservoir for community food resilience and biocultural diversity.}, } @article {pmid37104570, year = {2023}, author = {Osmanski, AB and Paulat, NS and Korstian, J and Grimshaw, JR and Halsey, M and Sullivan, KAM and Moreno-Santillán, DD and Crookshanks, C and Roberts, J and Garcia, C and Johnson, MG and Densmore, LD and Stevens, RD and , and Rosen, J and Storer, JM and Hubley, R and Smit, AFA and Dávalos, LM and Karlsson, EK and Lindblad-Toh, K and Ray, DA}, title = {Insights into mammalian TE diversity through the curation of 248 genome assemblies.}, journal = {Science (New York, N.Y.)}, volume = {380}, number = {6643}, pages = {eabn1430}, pmid = {37104570}, issn = {1095-9203}, support = {R01 HG002939/HG/NHGRI NIH HHS/United States ; R01 HG008742/HG/NHGRI NIH HHS/United States ; U24 HG010136/HG/NHGRI NIH HHS/United States ; }, mesh = {Animals ; Female ; Pregnancy ; *DNA Transposable Elements ; *Evolution, Molecular ; Long Interspersed Nucleotide Elements ; *Eutheria/genetics ; Datasets as Topic ; Feeding Behavior ; *Genetic Variation ; }, abstract = {We examined transposable element (TE) content of 248 placental mammal genome assemblies, the largest de novo TE curation effort in eukaryotes to date. We found that although mammals resemble one another in total TE content and diversity, they show substantial differences with regard to recent TE accumulation. This includes multiple recent expansion and quiescence events across the mammalian tree. Young TEs, particularly long interspersed elements, drive increases in genome size, whereas DNA transposons are associated with smaller genomes. Mammals tend to accumulate only a few types of TEs at any given time, with one TE type dominating. We also found association between dietary habit and the presence of DNA transposon invasions. These detailed annotations will serve as a benchmark for future comparative TE analyses among placental mammals.}, } @article {pmid37102710, year = {2023}, author = {Green, SJ and Torok, T and Allen, JE and Eloe-Fadrosh, E and Jackson, SA and Jiang, SC and Levine, SS and Levy, S and Schriml, LM and Thomas, WK and Wood, JM and Tighe, SW}, title = {Metagenomic Methods for Addressing NASA's Planetary Protection Policy Requirements on Future Missions: A Workshop Report.}, journal = {Astrobiology}, volume = {23}, number = {8}, pages = {897-907}, pmid = {37102710}, issn = {1557-8070}, mesh = {United States ; Humans ; *Planets ; *Space Flight ; Extraterrestrial Environment ; Metagenomics ; United States National Aeronautics and Space Administration ; Spacecraft ; Policy ; }, abstract = {Molecular biology methods and technologies have advanced substantially over the past decade. These new molecular methods should be incorporated among the standard tools of planetary protection (PP) and could be validated for incorporation by 2026. To address the feasibility of applying modern molecular techniques to such an application, NASA conducted a technology workshop with private industry partners, academics, and government agency stakeholders, along with NASA staff and contractors. The technical discussions and presentations of the Multi-Mission Metagenomics Technology Development Workshop focused on modernizing and supplementing the current PP assays. The goals of the workshop were to assess the state of metagenomics and other advanced molecular techniques in the context of providing a validated framework to supplement the bacterial endospore-based NASA Standard Assay and to identify knowledge and technology gaps. In particular, workshop participants were tasked with discussing metagenomics as a stand-alone technology to provide rapid and comprehensive analysis of total nucleic acids and viable microorganisms on spacecraft surfaces, thereby allowing for the development of tailored and cost-effective microbial reduction plans for each hardware item on a spacecraft. Workshop participants recommended metagenomics approaches as the only data source that can adequately feed into quantitative microbial risk assessment models for evaluating the risk of forward (exploring extraterrestrial planet) and back (Earth harmful biological) contamination. Participants were unanimous that a metagenomics workflow, in tandem with rapid targeted quantitative (digital) PCR, represents a revolutionary advance over existing methods for the assessment of microbial bioburden on spacecraft surfaces. The workshop highlighted low biomass sampling, reagent contamination, and inconsistent bioinformatics data analysis as key areas for technology development. Finally, it was concluded that implementing metagenomics as an additional workflow for addressing concerns of NASA's robotic mission will represent a dramatic improvement in technology advancement for PP and will benefit future missions where mission success is affected by backward and forward contamination.}, } @article {pmid37101136, year = {2023}, author = {Mosquera, KD and Martínez Villegas, LE and Rocha Fernandes, G and Rocha David, M and Maciel-de-Freitas, R and A Moreira, L and Lorenzo, MG}, title = {Egg-laying by female Aedes aegypti shapes the bacterial communities of breeding sites.}, journal = {BMC biology}, volume = {21}, number = {1}, pages = {97}, pmid = {37101136}, issn = {1741-7007}, mesh = {Animals ; Humans ; Female ; *Aedes ; Mosquito Vectors ; Water ; Bacteria/genetics ; Oviposition ; Larva ; }, abstract = {BACKGROUND: Aedes aegypti, the main arboviral mosquito vector, is attracted to human dwellings and makes use of human-generated breeding sites. Past research has shown that bacterial communities associated with such sites undergo compositional shifts as larvae develop and that exposure to different bacteria during larval stages can have an impact on mosquito development and life-history traits. Based on these facts, we hypothesized that female Ae. aegypti shape the bacteria communities of breeding sites during oviposition as a form of niche construction to favor offspring fitness.

RESULTS: To test this hypothesis, we first verified that gravid females can act as mechanical vectors of bacteria. We then elaborated an experimental scheme to test the impact of oviposition on breeding site microbiota. Five different groups of experimental breeding sites were set up with a sterile aqueous solution of larval food, and subsequently exposed to (1) the environment alone, (2) surface-sterilized eggs, (3) unsterilized eggs, (4) a non-egg laying female, or (5) oviposition by a gravid female. The microbiota of these differently treated sites was assessed by amplicon-oriented DNA sequencing once the larvae from the sites with eggs had completed development and formed pupae. Microbial ecology analyses revealed significant differences between the five treatments in terms of diversity. In particular, between-treatment shifts in abundance profiles were detected, showing that females induce a significant decrease in microbial alpha diversity through oviposition. In addition, indicator species analysis pinpointed bacterial taxa with significant predicting values and fidelity coefficients for the samples in which single females laid eggs. Furthermore, we provide evidence regarding how one of these indicator taxa, Elizabethkingia, exerts a positive effect on the development and fitness of mosquito larvae.

CONCLUSIONS: Ovipositing females impact the composition of the microbial community associated with a breeding site, promoting certain bacterial taxa over those prevailing in the environment. Among these bacteria, we found known mosquito symbionts and showed that they can improve offspring fitness if present in the water where eggs are laid. We deem this oviposition-mediated bacterial community shaping as a form of niche construction initiated by the gravid female.}, } @article {pmid37100861, year = {2023}, author = {Stocco, A and Pranovi, F}, title = {The paradoxical need for human intervention in the conservation of natural environments in Venice lagoon.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {6798}, pmid = {37100861}, issn = {2045-2322}, mesh = {Humans ; *Ecosystem ; *Environment ; Aquaculture ; Climate ; Geography ; Conservation of Natural Resources/methods ; }, abstract = {The Venice lagoon-the largest Mediterranean coastal lagoon-is characterized by the presence at its edges of 31 "valli da pesca", types of artificial ecosystems that mime the ecological processes of a transitional aquatic ecosystem. Constituted by a series of regulated lakes bounded by artificial embankments, the valli da pesca were established centuries ago to maximize provisioning Ecosystem Services (ESs), such as fishing and hunting. As time passed, the valli da pesca underwent an intentional isolation process leading to private management. Nonetheless, the valli da pesca are still exchanging energy and matter with the "open' lagoon and today represent an essential element within the context of lagoon conservation. This study aimed to analyze the possible effects of artificial management on both ESs supply and landscape arrangements by assessing 9 ESs (climate regulation, water purification, lifecycle support, aquaculture, waterfowl hunting, wild food, tourism, information for cognitive development, and birdwatching), along with eight landscape indicators. Obtained results suggested that the valli da pesca are today ruled under five different management strategies, according to the maximized ES. Management conditions influence the landscape pattern and achieve a series of "side effects" on the other ESs. The comparison between the managed and abandoned valli da pesca highlights the importance of anthropogenic interventions for conserving these ecosystems, as the abandoned valli da pesca show a loss of ecological gradients, landscape heterogeneity, and provisioning ESs. Nevertheless, the persistence of intrinsic geographical and morphological characteristics still prevails regardless of intentional landscape molding. The result is that the provisioning ESs capacity per unit area is higher in the abandoned valli da pesca than in the open lagoon, emphasizing the importance of these confined areas of the lagoon ecosystem. Considering the spatial distribution of multiple ESs, the provisioning ESs flow that does not occur in the abandoned valli da pesca seems to be replaced by the flow of cultural ESs. Thus, the ESs spatial pattern highlights a balancing effect between different ESs categories. The results are discussed considering the trade-offs generated by private land conservation, anthropogenic interventions, and their relevance for the ecosystem-based management of Venice lagoon.}, } @article {pmid37099856, year = {2023}, author = {Sutton, C and Prowse, J and McVey, L and Elshehaly, M and Neagu, D and Montague, J and Alvarado, N and Tissiman, C and O'Connell, K and Eyers, E and Faisal, M and Randell, R}, title = {Strategic workforce planning in health and social care - an international perspective: A scoping review.}, journal = {Health policy (Amsterdam, Netherlands)}, volume = {132}, number = {}, pages = {104827}, doi = {10.1016/j.healthpol.2023.104827}, pmid = {37099856}, issn = {1872-6054}, mesh = {Humans ; *Health Services Needs and Demand ; Workforce ; *Health Personnel ; Forecasting ; }, abstract = {Effective strategic workforce planning for integrated and co-ordinated health and social care is essential if future services are to be resourced such that skill mix, clinical practice and productivity meet population health and social care needs in timely, safe and accessible ways globally. This review presents international literature to illustrate how strategic workforce planning in health and social care has been undertaken around the world with examples of planning frameworks, models and modelling approaches. The databases Business Source Premier, CINAHL, Embase, Health Management Information Consortium, Medline and Scopus were searched for full texts, from 2005 to 2022, detailing empirical research, models or methodologies to explain how strategic workforce planning (with at least a one-year horizon) in health and/or social care has been undertaken, yielding ultimately 101 included references. The supply/demand of a differentiated medical workforce was discussed in 25 references. Nursing and midwifery were characterised as undifferentiated labour, requiring urgent growth to meet demand. Unregistered workers were poorly represented as was the social care workforce. One reference considered planning for health and social care workers. Workforce modelling was illustrated in 66 references with predilection for quantifiable projections. Increasingly needs-based approaches were called for to better consider demography and epidemiological impacts. This review's findings advocate for whole-system needs-based approaches that consider the ecology of a co-produced health and social care workforce.}, } @article {pmid37098064, year = {2023}, author = {Shea, K and Borchering, RK and Probert, WJM and Howerton, E and Bogich, TL and Li, SL and van Panhuis, WG and Viboud, C and Aguás, R and Belov, AA and Bhargava, SH and Cavany, SM and Chang, JC and Chen, C and Chen, J and Chen, S and Chen, Y and Childs, LM and Chow, CC and Crooker, I and Del Valle, SY and España, G and Fairchild, G and Gerkin, RC and Germann, TC and Gu, Q and Guan, X and Guo, L and Hart, GR and Hladish, TJ and Hupert, N and Janies, D and Kerr, CC and Klein, DJ and Klein, EY and Lin, G and Manore, C and Meyers, LA and Mittler, JE and Mu, K and Núñez, RC and Oidtman, RJ and Pasco, R and Pastore Y Piontti, A and Paul, R and Pearson, CAB and Perdomo, DR and Perkins, TA and Pierce, K and Pillai, AN and Rael, RC and Rosenfeld, K and Ross, CW and Spencer, JA and Stoltzfus, AB and Toh, KB and Vattikuti, S and Vespignani, A and Wang, L and White, LJ and Xu, P and Yang, Y and Yogurtcu, ON and Zhang, W and Zhao, Y and Zou, D and Ferrari, MJ and Pannell, D and Tildesley, MJ and Seifarth, J and Johnson, E and Biggerstaff, M and Johansson, MA and Slayton, RB and Levander, JD and Stazer, J and Kerr, J and Runge, MC}, title = {Multiple models for outbreak decision support in the face of uncertainty.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {120}, number = {18}, pages = {e2207537120}, pmid = {37098064}, issn = {1091-6490}, support = {U24 GM132013/GM/NIGMS NIH HHS/United States ; }, mesh = {Humans ; *COVID-19/epidemiology/prevention & control ; Uncertainty ; Disease Outbreaks/prevention & control ; Public Health ; Pandemics/prevention & control ; }, abstract = {Policymakers must make management decisions despite incomplete knowledge and conflicting model projections. Little guidance exists for the rapid, representative, and unbiased collection of policy-relevant scientific input from independent modeling teams. Integrating approaches from decision analysis, expert judgment, and model aggregation, we convened multiple modeling teams to evaluate COVID-19 reopening strategies for a mid-sized United States county early in the pandemic. Projections from seventeen distinct models were inconsistent in magnitude but highly consistent in ranking interventions. The 6-mo-ahead aggregate projections were well in line with observed outbreaks in mid-sized US counties. The aggregate results showed that up to half the population could be infected with full workplace reopening, while workplace restrictions reduced median cumulative infections by 82%. Rankings of interventions were consistent across public health objectives, but there was a strong trade-off between public health outcomes and duration of workplace closures, and no win-win intermediate reopening strategies were identified. Between-model variation was high; the aggregate results thus provide valuable risk quantification for decision making. This approach can be applied to the evaluation of management interventions in any setting where models are used to inform decision making. This case study demonstrated the utility of our approach and was one of several multimodel efforts that laid the groundwork for the COVID-19 Scenario Modeling Hub, which has provided multiple rounds of real-time scenario projections for situational awareness and decision making to the Centers for Disease Control and Prevention since December 2020.}, } @article {pmid37097029, year = {2023}, author = {Carrol, ED and Ranjit, S and Menon, K and Bennett, TD and Sanchez-Pinto, LN and Zimmerman, JJ and Souza, DC and Sorce, LR and Randolph, AG and Ishimine, P and Flauzino de Oliveira, C and Lodha, R and Harmon, L and Watson, RS and Schlapbach, LJ and Kissoon, N and Argent, AC and , }, title = {Operationalizing Appropriate Sepsis Definitions in Children Worldwide: Considerations for the Pediatric Sepsis Definition Taskforce.}, journal = {Pediatric critical care medicine : a journal of the Society of Critical Care Medicine and the World Federation of Pediatric Intensive and Critical Care Societies}, volume = {24}, number = {6}, pages = {e263-e271}, pmid = {37097029}, issn = {1529-7535}, support = {R01 HD105939/HD/NICHD NIH HHS/United States ; }, mesh = {Child ; Humans ; *Sepsis/diagnosis/therapy ; Hospital Mortality ; Databases, Factual ; Outcome Assessment, Health Care ; }, abstract = {Sepsis is a leading cause of global mortality in children, yet definitions for pediatric sepsis are outdated and lack global applicability and validity. In adults, the Sepsis-3 Definition Taskforce queried databases from high-income countries to develop and validate the criteria. The merit of this definition has been widely acknowledged; however, important considerations about less-resourced and more diverse settings pose challenges to its use globally. To improve applicability and relevance globally, the Pediatric Sepsis Definition Taskforce sought to develop a conceptual framework and rationale of the critical aspects and context-specific factors that must be considered for the optimal operationalization of future pediatric sepsis definitions. It is important to address challenges in developing a set of pediatric sepsis criteria which capture manifestations of illnesses with vastly different etiologies and underlying mechanisms. Ideal criteria need to be unambiguous, and capable of adapting to the different contexts in which children with suspected infections are present around the globe. Additionally, criteria need to facilitate early recognition and timely escalation of treatment to prevent progression and limit life-threatening organ dysfunction. To address these challenges, locally adaptable solutions are required, which permit individualized care based on available resources and the pretest probability of sepsis. This should facilitate affordable diagnostics which support risk stratification and prediction of likely treatment responses, and solutions for locally relevant outcome measures. For this purpose, global collaborative databases need to be established, using minimum variable datasets from routinely collected data. In summary, a "Think globally, act locally" approach is required.}, } @article {pmid37095444, year = {2023}, author = {Demidova, EV and Serebriiskii, IG and Vlasenkova, R and Kelow, S and Andrake, MD and Hartman, TR and Kent, T and Virtucio, J and Rosen, GL and Pomerantz, RT and Dunbrack, RL and Golemis, EA and Hall, MJ and Chen, DYT and Daly, MB and Arora, S}, title = {Candidate variants in DNA replication and repair genes in early-onset renal cell carcinoma patients referred for germline testing.}, journal = {BMC genomics}, volume = {24}, number = {1}, pages = {212}, pmid = {37095444}, issn = {1471-2164}, support = {R01 DK108195/GF/NIH HHS/United States ; 1UH2CA271230-01/GF/NIH HHS/United States ; R35 GM122517/GF/NIH HHS/United States ; R35 GM122517/GM/NIGMS NIH HHS/United States ; 1R01GM130889/GF/NIH HHS/United States ; P30 CA006927/CA/NCI NIH HHS/United States ; UH2 CA271230/CA/NCI NIH HHS/United States ; U01 CA164920/GF/NIH HHS/United States ; }, mesh = {Humans ; *Carcinoma, Renal Cell ; Genetic Predisposition to Disease ; DNA Replication ; Germ-Line Mutation ; *Kidney Neoplasms ; Germ Cells ; }, abstract = {BACKGROUND: Early-onset renal cell carcinoma (eoRCC) is typically associated with pathogenic germline variants (PGVs) in RCC familial syndrome genes. However, most eoRCC patients lack PGVs in familial RCC genes and their genetic risk remains undefined.

METHODS: Here, we analyzed biospecimens from 22 eoRCC patients that were seen at our institution for genetic counseling and tested negative for PGVs in RCC familial syndrome genes.

RESULTS: Analysis of whole-exome sequencing (WES) data found enrichment of candidate pathogenic germline variants in DNA repair and replication genes, including multiple DNA polymerases. Induction of DNA damage in peripheral blood monocytes (PBMCs) significantly elevated numbers of [Formula: see text]H2AX foci, a marker of double-stranded breaks, in PBMCs from eoRCC patients versus PBMCs from matched cancer-free controls. Knockdown of candidate variant genes in Caki RCC cells increased [Formula: see text]H2AX foci. Immortalized patient-derived B cell lines bearing the candidate variants in DNA polymerase genes (POLD1, POLH, POLE, POLK) had DNA replication defects compared to control cells. Renal tumors carrying these DNA polymerase variants were microsatellite stable but had a high mutational burden. Direct biochemical analysis of the variant Pol δ and Pol η polymerases revealed defective enzymatic activities.

CONCLUSIONS: Together, these results suggest that constitutional defects in DNA repair underlie a subset of eoRCC cases. Screening patient lymphocytes to identify these defects may provide insight into mechanisms of carcinogenesis in a subset of genetically undefined eoRCCs. Evaluation of DNA repair defects may also provide insight into the cancer initiation mechanisms for subsets of eoRCCs and lay the foundation for targeting DNA repair vulnerabilities in eoRCC.}, } @article {pmid37094905, year = {2023}, author = {Girón, JC and Tarasov, S and González Montaña, LA and Matentzoglu, N and Smith, AD and Koch, M and Boudinot, BE and Bouchard, P and Burks, R and Vogt, L and Yoder, M and Osumi-Sutherland, D and Friedrich, F and Beutel, RG and Mikó, I}, title = {Formalizing Invertebrate Morphological Data: A Descriptive Model for Cuticle-Based Skeleto-Muscular Systems, an Ontology for Insect Anatomy, and their Potential Applications in Biodiversity Research and Informatics.}, journal = {Systematic biology}, volume = {72}, number = {5}, pages = {1084-1100}, doi = {10.1093/sysbio/syad025}, pmid = {37094905}, issn = {1076-836X}, support = {339576//Academy of Finland/ ; //University of Helsinki/ ; MO 412/54-1//German Research Foundation/ ; }, mesh = {Animals ; Phylogeny ; *Arthropods ; Insecta ; Informatics ; Biodiversity ; }, abstract = {The spectacular radiation of insects has produced a stunning diversity of phenotypes. During the past 250 years, research on insect systematics has generated hundreds of terms for naming and comparing them. In its current form, this terminological diversity is presented in natural language and lacks formalization, which prohibits computer-assisted comparison using semantic web technologies. Here we propose a Model for Describing Cuticular Anatomical Structures (MoDCAS) which incorporates structural properties and positional relationships for standardized, consistent, and reproducible descriptions of arthropod phenotypes. We applied the MoDCAS framework in creating the ontology for the Anatomy of the Insect Skeleto-Muscular system (AISM). The AISM is the first general insect ontology that aims to cover all taxa by providing generalized, fully logical, and queryable, definitions for each term. It was built using the Ontology Development Kit (ODK), which maximizes interoperability with Uberon (Uberon multispecies anatomy ontology) and other basic ontologies, enhancing the integration of insect anatomy into the broader biological sciences. A template system for adding new terms, extending, and linking the AISM to additional anatomical, phenotypic, genetic, and chemical ontologies is also introduced. The AISM is proposed as the backbone for taxon-specific insect ontologies and has potential applications spanning systematic biology and biodiversity informatics, allowing users to: 1) use controlled vocabularies and create semiautomated computer-parsable insect morphological descriptions; 2) integrate insect morphology into broader fields of research, including ontology-informed phylogenetic methods, logical homology hypothesis testing, evo-devo studies, and genotype to phenotype mapping; and 3) automate the extraction of morphological data from the literature, enabling the generation of large-scale phenomic data, by facilitating the production and testing of informatic tools able to extract, link, annotate, and process morphological data. This descriptive model and its ontological applications will allow for clear and semantically interoperable integration of arthropod phenotypes in biodiversity studies.}, } @article {pmid37093376, year = {2023}, author = {Alam, N and Saha, S and Gupta, S and Chatterjee, A}, title = {Settlement suitability analysis of a riverine floodplain in the perspective of GIS-based multicriteria decision analysis.}, journal = {Environmental science and pollution research international}, volume = {30}, number = {24}, pages = {66002-66020}, pmid = {37093376}, issn = {1614-7499}, mesh = {Humans ; *Geographic Information Systems ; *Decision Support Techniques ; Spatial Analysis ; Sustainable Development ; Climate ; }, abstract = {Riverine floodplains are highly dynamic and the most vulnerable space on Earth particularly in flat alluvial plains of major river systems. Suitable site selection for sustainable human settlements in active floodplain areas is a critical task for decision-makers in terms of quality of lithology, ecologically fragile landmass, climate-induced hazards, immense population pressure, and environmental conservation issues. This research introduces a methodology for settlement suitability zone (SSZ) that employs GIS-based multi-criteria decision-making (MCDM) techniques. As a case study, an altered hydrological regime of the lower Ganga riparian zone was chosen to identify the SSZ as these areas are the most susceptible to riverine hazards. Twelve significant variables reflecting on topography, climate, landscape, and environment have been selected in the multi-criteria evaluation platform. The CRiteria Importance Through Intercriteria Correlation (CRITIC) method is adopted to specify the weights of the criteria and utilize an inverse distance-weighted (IDW) spatial interpolation technique to generate an SSZ map in a GIS environment. The study zone is spatially quantified into five categories, from unsuitable to high-suitable with a natural breaks (Jenks) classification method. Subsequently, the final results are validated through a receiver operating characteristics (ROC) curve using randomly selected 56 hazard-exposed location points. The outcome revealed that 8.45% of the riparian area falls under unsuitable, 21.87% under low-suitable, and 33.27% under moderate-suitable for locating human settlements. The generally suitable and high-suitable categories account for 36.40% of the total study zone. A spatial sensitivity analysis is also applied to gauge the influence of each parameter on the MCDM outcomes. The SSZ mapping results from this study can help local authorities to plan for sustainable settlement development in environmentally fragile areas.}, } @article {pmid37082718, year = {2023}, author = {Boyes, D and , and , and , and , and , and Mulley, JF and , }, title = {The genome sequence of the Birch Marble, Apotomis betuletana (Haworth, 1811).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {66}, pmid = {37082718}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual male Apotomis betuletana (the Birch Marble; Arthropoda; Insecta; Lepidoptera; Tortricidae). The genome sequence is 684 megabases in span. Most of the assembly is scaffolded into 28 chromosomal pseudomolecules with the Z sex chromosome assembled. The mitochondrial genome has also been assembled and is 15.8 kilobases in length. Gene annotation of this assembly on Ensembl identified 21,717 protein coding genes.}, } @article {pmid37078321, year = {2023}, author = {Shu, CB and Shen, YL and Liu, G and Zhang, Q and Xu, JH and Guo, Z}, title = {Impacts of Eucalyptus plantation on soil and water losses in a typical small watershed in mountainous area of southern China.}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {34}, number = {4}, pages = {1015-1023}, doi = {10.13287/j.1001-9332.202304.021}, pmid = {37078321}, issn = {1001-9332}, mesh = {*Soil ; *Eucalyptus ; Geographic Information Systems ; Forests ; China ; Conservation of Natural Resources/methods ; Environmental Monitoring/methods ; }, abstract = {Unreasonable exploitation of artificial forest causes severe soil erosion in the mountainous areas of sou-thern China. The spatial-temporal variations of soil erosion in typical small watershed with artificial forest has signifi-cant implications for artificial forest exploitation and sustainable development of mountainous ecological environment. In this study, we used revised universal soil loss equation (RUSLE) and geographic information system (GIS) to evaluate the spatial and temporal variations of soil erosion and its key drivers of Dadingshan watershed in mountainous area of western Guangdong. The results showed that the erosion modulus was 1948.1 t·km[-2]·a[-1] (belonging to light erosion) in the Dadingshan watershed. However, the spatial variation of soil erosion was substantial, with variation coefficient of 5.12. The maximal soil erosion modulus was 191127 t·km[-2]·a[-1]. Slight erosion (<500 t·km[-2]·a[-1]) accounted for 80.6% of the total watershed area. The moderate erosion and above (>2500 t·km[-2]·a[-1]) were mainly distributed in young Eucalyptus forest area with less than 30% of the vegetation coverage, which contributed nearly 75.7% of total soil erosion. During 2014-2019, the interannual variations of mean erosion of Dadingshan catchment was modest, but the spatial variation of soil erosion was large. Vegetation cover, slope, and rainfall were key drivers of such variation. The destruction of natural vegetation resulted by plantation exploitation was the primary cause of soil erosion in afforestation areas. Soil erosion significantly increased with the increases of slope gradient in the young forest area, which was aggravated by extreme rainfall. However, soil erosion gradually decreased with the increases of the age of Eucalypt plantation. Therefore, the hot spot of soil erosion was young forest areas of Eucalypt plantation with slope >25°, and the key period for soil erosion control was the first 2-3 years after Eucalyptus planting. We suggested that reasonable afforestation measures should be used in area with >25° slopes, and that the destruction of natural vegetation should be avoided on hillslope with >35° slope gradient. The road construction standards and forest management should be further improved to address the challenge of extreme rainfalls.}, } @article {pmid37076812, year = {2023}, author = {De Wolfe, TJ and Wright, ES}, title = {Multi-factorial examination of amplicon sequencing workflows from sample preparation to bioinformatic analysis.}, journal = {BMC microbiology}, volume = {23}, number = {1}, pages = {107}, pmid = {37076812}, issn = {1471-2180}, support = {T15 LM007059/LM/NLM NIH HHS/United States ; }, mesh = {Humans ; RNA, Ribosomal, 16S/genetics ; Reproducibility of Results ; Workflow ; *Microbiota/genetics ; Bacteria/genetics ; High-Throughput Nucleotide Sequencing/methods ; Computational Biology/methods ; Sequence Analysis, DNA/methods ; }, abstract = {BACKGROUND: The development of sequencing technologies to evaluate bacterial microbiota composition has allowed new insights into the importance of microbial ecology. However, the variety of methodologies used among amplicon sequencing workflows leads to uncertainty about best practices as well as reproducibility and replicability among microbiome studies. Using a bacterial mock community composed of 37 soil isolates, we performed a comprehensive methodological evaluation of workflows, each with a different combination of methodological factors spanning sample preparation to bioinformatic analysis to define sources of artifacts that affect coverage, accuracy, and biases in the resulting compositional profiles.

RESULTS: Of the workflows examined, those using the V4-V4 primer set enabled the highest level of concordance between the original mock community and resulting microbiome sequence composition. Use of a high-fidelity polymerase, or a lower-fidelity polymerase with an increased PCR elongation time, limited chimera formation. Bioinformatic pipelines presented a trade-off between the fraction of distinct community members identified (coverage) and fraction of correct sequences (accuracy). DADA2 and QIIME2 assembled V4-V4 reads amplified by Taq polymerase resulted in the highest accuracy (100%) but had a coverage of only 52%. Using mothur to assemble and denoise V4-V4 reads resulted in a coverage of 75%, albeit with marginally lower accuracy (99.5%).

CONCLUSIONS: Optimization of microbiome workflows is critical for accuracy and to support reproducibility and replicability among microbiome studies. These considerations will help reveal the guiding principles of microbial ecology and impact the translation of microbiome research to human and environmental health.}, } @article {pmid37076624, year = {2023}, author = {Klein, B and Ogbunugafor, CB and Schafer, BJ and Bhadricha, Z and Kori, P and Sheldon, J and Kaza, N and Sharma, A and Wang, EA and Eliassi-Rad, T and Scarpino, SV and Hinton, E}, title = {COVID-19 amplified racial disparities in the US criminal legal system.}, journal = {Nature}, volume = {617}, number = {7960}, pages = {344-350}, pmid = {37076624}, issn = {1476-4687}, support = {UL1 TR001863/TR/NCATS NIH HHS/United States ; }, mesh = {Humans ; Black or African American/legislation & jurisprudence/statistics & numerical data ; *COVID-19/epidemiology ; *Criminals/legislation & jurisprudence/statistics & numerical data ; *Prisoners/legislation & jurisprudence/statistics & numerical data ; United States/epidemiology ; White/legislation & jurisprudence/statistics & numerical data ; Datasets as Topic ; Hispanic or Latino/legislation & jurisprudence/statistics & numerical data ; *Racial Groups/legislation & jurisprudence/statistics & numerical data ; }, abstract = {The criminal legal system in the USA drives an incarceration rate that is the highest on the planet, with disparities by class and race among its signature features[1-3]. During the first year of the coronavirus disease 2019 (COVID-19) pandemic, the number of incarcerated people in the USA decreased by at least 17%-the largest, fastest reduction in prison population in American history[4]. Here we ask how this reduction influenced the racial composition of US prisons and consider possible mechanisms for these dynamics. Using an original dataset curated from public sources on prison demographics across all 50 states and the District of Columbia, we show that incarcerated white people benefited disproportionately from the decrease in the US prison population and that the fraction of incarcerated Black and Latino people sharply increased. This pattern of increased racial disparity exists across prison systems in nearly every state and reverses a decade-long trend before 2020 and the onset of COVID-19, when the proportion of incarcerated white people was increasing amid declining numbers of incarcerated Black people[5]. Although a variety of factors underlie these trends, we find that racial inequities in average sentence length are a major contributor. Ultimately, this study reveals how disruptions caused by COVID-19 exacerbated racial inequalities in the criminal legal system, and highlights key forces that sustain mass incarceration. To advance opportunities for data-driven social science, we publicly released the data associated with this study at Zenodo[6].}, } @article {pmid37075104, year = {2023}, author = {Skirgård, H and Haynie, HJ and Blasi, DE and Hammarström, H and Collins, J and Latarche, JJ and Lesage, J and Weber, T and Witzlack-Makarevich, A and Passmore, S and Chira, A and Maurits, L and Dinnage, R and Dunn, M and Reesink, G and Singer, R and Bowern, C and Epps, P and Hill, J and Vesakoski, O and Robbeets, M and Abbas, NK and Auer, D and Bakker, NA and Barbos, G and Borges, RD and Danielsen, S and Dorenbusch, L and Dorn, E and Elliott, J and Falcone, G and Fischer, J and Ghanggo Ate, Y and Gibson, H and Göbel, HP and Goodall, JA and Gruner, V and Harvey, A and Hayes, R and Heer, L and Herrera Miranda, RE and Hübler, N and Huntington-Rainey, B and Ivani, JK and Johns, M and Just, E and Kashima, E and Kipf, C and Klingenberg, JV and König, N and Koti, A and Kowalik, RGA and Krasnoukhova, O and Lindvall, NLM and Lorenzen, M and Lutzenberger, H and Martins, TRA and Mata German, C and van der Meer, S and Montoya Samamé, J and Müller, M and Muradoglu, S and Neely, K and Nickel, J and Norvik, M and Oluoch, CA and Peacock, J and Pearey, IOC and Peck, N and Petit, S and Pieper, S and Poblete, M and Prestipino, D and Raabe, L and Raja, A and Reimringer, J and Rey, SC and Rizaew, J and Ruppert, E and Salmon, KK and Sammet, J and Schembri, R and Schlabbach, L and Schmidt, FWP and Skilton, A and Smith, WD and de Sousa, H and Sverredal, K and Valle, D and Vera, J and Voß, J and Witte, T and Wu, H and Yam, S and Ye, J and Yong, M and Yuditha, T and Zariquiey, R and Forkel, R and Evans, N and Levinson, SC and Haspelmath, M and Greenhill, SJ and Atkinson, QD and Gray, RD}, title = {Grambank reveals the importance of genealogical constraints on linguistic diversity and highlights the impact of language loss.}, journal = {Science advances}, volume = {9}, number = {16}, pages = {eadg6175}, pmid = {37075104}, issn = {2375-2548}, mesh = {Humans ; *Language ; *Linguistics ; Cognition ; Databases, Factual ; }, abstract = {While global patterns of human genetic diversity are increasingly well characterized, the diversity of human languages remains less systematically described. Here, we outline the Grambank database. With over 400,000 data points and 2400 languages, Grambank is the largest comparative grammatical database available. The comprehensiveness of Grambank allows us to quantify the relative effects of genealogical inheritance and geographic proximity on the structural diversity of the world's languages, evaluate constraints on linguistic diversity, and identify the world's most unusual languages. An analysis of the consequences of language loss reveals that the reduction in diversity will be strikingly uneven across the major linguistic regions of the world. Without sustained efforts to document and revitalize endangered languages, our linguistic window into human history, cognition, and culture will be seriously fragmented.}, } @article {pmid37072018, year = {2023}, author = {Jackson, C and Stewart, ID and Plekhanova, T and Cunningham, PS and Hazel, AL and Al-Sheklly, B and Aul, R and Bolton, CE and Chalder, T and Chalmers, JD and Chaudhuri, N and Docherty, AB and Donaldson, G and Edwardson, CL and Elneima, O and Greening, NJ and Hanley, NA and Harris, VC and Harrison, EM and Ho, LP and Houchen-Wolloff, L and Howard, LS and Jolley, CJ and Jones, MG and Leavy, OC and Lewis, KE and Lone, NI and Marks, M and McAuley, HJC and McNarry, MA and Patel, BV and Piper-Hanley, K and Poinasamy, K and Raman, B and Richardson, M and Rivera-Ortega, P and Rowland-Jones, SL and Rowlands, AV and Saunders, RM and Scott, JT and Sereno, M and Shah, AM and Shikotra, A and Singapuri, A and Stanel, SC and Thorpe, M and Wootton, DG and Yates, T and Gisli Jenkins, R and Singh, SJ and Man, WD and Brightling, CE and Wain, LV and Porter, JC and Thompson, AAR and Horsley, A and Molyneaux, PL and Evans, RA and Jones, SE and Rutter, MK and Blaikley, JF and , }, title = {Effects of sleep disturbance on dyspnoea and impaired lung function following hospital admission due to COVID-19 in the UK: a prospective multicentre cohort study.}, journal = {The Lancet. Respiratory medicine}, volume = {11}, number = {8}, pages = {673-684}, pmid = {37072018}, issn = {2213-2619}, support = {209553/Z/17/Z/WT_/Wellcome Trust/United Kingdom ; MR/M008894/1/MRC_/Medical Research Council/United Kingdom ; MC_PC_20060/MRC_/Medical Research Council/United Kingdom ; 206330/Z/17/Z/WT_/Wellcome Trust/United Kingdom ; MC_PC_19026/MRC_/Medical Research Council/United Kingdom ; MR/T032529/1/MRC_/Medical Research Council/United Kingdom ; SP/17/16/33519/BHF_/British Heart Foundation/United Kingdom ; RE/18/3/34214/BHF_/British Heart Foundation/United Kingdom ; FS/18/13/33281/BHF_/British Heart Foundation/United Kingdom ; MC_UU_00034/6/MRC_/Medical Research Council/United Kingdom ; COV0319/DH_/Department of Health/United Kingdom ; NIHR300669/DH_/Department of Health/United Kingdom ; MC_PC_20031/MRC_/Medical Research Council/United Kingdom ; MR/S004041/1/MRC_/Medical Research Council/United Kingdom ; RP-2017-08-ST2-014/DH_/Department of Health/United Kingdom ; MR/V027859/1/MRC_/Medical Research Council/United Kingdom ; CH/16/1/32013/BHF_/British Heart Foundation/United Kingdom ; 216606/Z/19/Z/WT_/Wellcome Trust/United Kingdom ; MR/W006111/1/MRC_/Medical Research Council/United Kingdom ; NIHR203308/DH_/Department of Health/United Kingdom ; MR/V040162/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Humans ; *COVID-19/complications/epidemiology ; Prospective Studies ; Hospitalization ; *Sleep Wake Disorders/epidemiology/etiology ; Sleep/physiology ; Hospitals ; United Kingdom/epidemiology ; Lung ; }, abstract = {BACKGROUND: Sleep disturbance is common following hospital admission both for COVID-19 and other causes. The clinical associations of this for recovery after hospital admission are poorly understood despite sleep disturbance contributing to morbidity in other scenarios. We aimed to investigate the prevalence and nature of sleep disturbance after discharge following hospital admission for COVID-19 and to assess whether this was associated with dyspnoea.

METHODS: CircCOVID was a prospective multicentre cohort substudy designed to investigate the effects of circadian disruption and sleep disturbance on recovery after COVID-19 in a cohort of participants aged 18 years or older, admitted to hospital for COVID-19 in the UK, and discharged between March, 2020, and October, 2021. Participants were recruited from the Post-hospitalisation COVID-19 study (PHOSP-COVID). Follow-up data were collected at two timepoints: an early time point 2-7 months after hospital discharge and a later time point 10-14 months after hospital discharge. Sleep quality was assessed subjectively using the Pittsburgh Sleep Quality Index questionnaire and a numerical rating scale. Sleep quality was also assessed with an accelerometer worn on the wrist (actigraphy) for 14 days. Participants were also clinically phenotyped, including assessment of symptoms (ie, anxiety [Generalised Anxiety Disorder 7-item scale questionnaire], muscle function [SARC-F questionnaire], dyspnoea [Dyspnoea-12 questionnaire] and measurement of lung function), at the early timepoint after discharge. Actigraphy results were also compared to a matched UK Biobank cohort (non-hospitalised individuals and recently hospitalised individuals). Multivariable linear regression was used to define associations of sleep disturbance with the primary outcome of breathlessness and the other clinical symptoms. PHOSP-COVID is registered on the ISRCTN Registry (ISRCTN10980107).

FINDINGS: 2320 of 2468 participants in the PHOSP-COVID study attended an early timepoint research visit a median of 5 months (IQR 4-6) following discharge from 83 hospitals in the UK. Data for sleep quality were assessed by subjective measures (the Pittsburgh Sleep Quality Index questionnaire and the numerical rating scale) for 638 participants at the early time point. Sleep quality was also assessed using device-based measures (actigraphy) a median of 7 months (IQR 5-8 months) after discharge from hospital for 729 participants. After discharge from hospital, the majority (396 [62%] of 638) of participants who had been admitted to hospital for COVID-19 reported poor sleep quality in response to the Pittsburgh Sleep Quality Index questionnaire. A comparable proportion (338 [53%] of 638) of participants felt their sleep quality had deteriorated following discharge after COVID-19 admission, as assessed by the numerical rating scale. Device-based measurements were compared to an age-matched, sex-matched, BMI-matched, and time from discharge-matched UK Biobank cohort who had recently been admitted to hospital. Compared to the recently hospitalised matched UK Biobank cohort, participants in our study slept on average 65 min (95% CI 59 to 71) longer, had a lower sleep regularity index (-19%; 95% CI -20 to -16), and a lower sleep efficiency (3·83 percentage points; 95% CI 3·40 to 4·26). Similar results were obtained when comparisons were made with the non-hospitalised UK Biobank cohort. Overall sleep quality (unadjusted effect estimate 3·94; 95% CI 2·78 to 5·10), deterioration in sleep quality following hospital admission (3·00; 1·82 to 4·28), and sleep regularity (4·38; 2·10 to 6·65) were associated with higher dyspnoea scores. Poor sleep quality, deterioration in sleep quality, and sleep regularity were also associated with impaired lung function, as assessed by forced vital capacity. Depending on the sleep metric, anxiety mediated 18-39% of the effect of sleep disturbance on dyspnoea, while muscle weakness mediated 27-41% of this effect.

INTERPRETATION: Sleep disturbance following hospital admission for COVID-19 is associated with dyspnoea, anxiety, and muscle weakness. Due to the association with multiple symptoms, targeting sleep disturbance might be beneficial in treating the post-COVID-19 condition.

FUNDING: UK Research and Innovation, National Institute for Health Research, and Engineering and Physical Sciences Research Council.}, } @article {pmid37069545, year = {2023}, author = {Cai, P and Liu, S and Zhang, D and Xing, H and Han, M and Liu, D and Gong, L and Hu, QN}, title = {SynBioTools: a one-stop facility for searching and selecting synthetic biology tools.}, journal = {BMC bioinformatics}, volume = {24}, number = {1}, pages = {152}, pmid = {37069545}, issn = {1471-2105}, support = {2021YFC2103001, 2019YFA0904300//National Key Research and Development Program of China/ ; 2021YFC2103001, 2019YFA0904300//National Key Research and Development Program of China/ ; 153D31KYSB20170121//International Partnership Program of the Chinese Academy of Sciences of China/ ; }, mesh = {*Synthetic Biology ; *Computational Biology/methods ; Registries ; Databases, Factual ; Software ; }, abstract = {BACKGROUND: The rapid development of synthetic biology relies heavily on the use of databases and computational tools, which are also developing rapidly. While many tool registries have been created to facilitate tool retrieval, sharing, and reuse, no relatively comprehensive tool registry or catalog addresses all aspects of synthetic biology.

RESULTS: We constructed SynBioTools, a comprehensive collection of synthetic biology databases, computational tools, and experimental methods, as a one-stop facility for searching and selecting synthetic biology tools. SynBioTools includes databases, computational tools, and methods extracted from reviews via SCIentific Table Extraction, a scientific table-extraction tool that we built. Approximately 57% of the resources that we located and included in SynBioTools are not mentioned in bio.tools, the dominant tool registry. To improve users' understanding of the tools and to enable them to make better choices, the tools are grouped into nine modules (each with subdivisions) based on their potential biosynthetic applications. Detailed comparisons of similar tools in every classification are included. The URLs, descriptions, source references, and the number of citations of the tools are also integrated into the system.

CONCLUSIONS: SynBioTools is freely available at https://synbiotools.lifesynther.com/ . It provides end-users and developers with a useful resource of categorized synthetic biology databases, tools, and methods to facilitate tool retrieval and selection.}, } @article {pmid37069271, year = {2023}, author = {Manubens-Gil, L and Zhou, Z and Chen, H and Ramanathan, A and Liu, X and Liu, Y and Bria, A and Gillette, T and Ruan, Z and Yang, J and Radojević, M and Zhao, T and Cheng, L and Qu, L and Liu, S and Bouchard, KE and Gu, L and Cai, W and Ji, S and Roysam, B and Wang, CW and Yu, H and Sironi, A and Iascone, DM and Zhou, J and Bas, E and Conde-Sousa, E and Aguiar, P and Li, X and Li, Y and Nanda, S and Wang, Y and Muresan, L and Fua, P and Ye, B and He, HY and Staiger, JF and Peter, M and Cox, DN and Simonneau, M and Oberlaender, M and Jefferis, G and Ito, K and Gonzalez-Bellido, P and Kim, J and Rubel, E and Cline, HT and Zeng, H and Nern, A and Chiang, AS and Yao, J and Roskams, J and Livesey, R and Stevens, J and Liu, T and Dang, C and Guo, Y and Zhong, N and Tourassi, G and Hill, S and Hawrylycz, M and Koch, C and Meijering, E and Ascoli, GA and Peng, H}, title = {BigNeuron: a resource to benchmark and predict performance of algorithms for automated tracing of neurons in light microscopy datasets.}, journal = {Nature methods}, volume = {20}, number = {6}, pages = {824-835}, pmid = {37069271}, issn = {1548-7105}, support = {R01 EY031597/EY/NEI NIH HHS/United States ; MC_U105188491/MRC_/Medical Research Council/United Kingdom ; RF1 MH128693/MH/NIMH NIH HHS/United States ; R01 EY011261/EY/NEI NIH HHS/United States ; R01 EY027437/EY/NEI NIH HHS/United States ; }, mesh = {*Benchmarking ; *Microscopy/methods ; Imaging, Three-Dimensional/methods ; Neurons/physiology ; Algorithms ; }, abstract = {BigNeuron is an open community bench-testing platform with the goal of setting open standards for accurate and fast automatic neuron tracing. We gathered a diverse set of image volumes across several species that is representative of the data obtained in many neuroscience laboratories interested in neuron tracing. Here, we report generated gold standard manual annotations for a subset of the available imaging datasets and quantified tracing quality for 35 automatic tracing algorithms. The goal of generating such a hand-curated diverse dataset is to advance the development of tracing algorithms and enable generalizable benchmarking. Together with image quality features, we pooled the data in an interactive web application that enables users and developers to perform principal component analysis, t-distributed stochastic neighbor embedding, correlation and clustering, visualization of imaging and tracing data, and benchmarking of automatic tracing algorithms in user-defined data subsets. The image quality metrics explain most of the variance in the data, followed by neuromorphological features related to neuron size. We observed that diverse algorithms can provide complementary information to obtain accurate results and developed a method to iteratively combine methods and generate consensus reconstructions. The consensus trees obtained provide estimates of the neuron structure ground truth that typically outperform single algorithms in noisy datasets. However, specific algorithms may outperform the consensus tree strategy in specific imaging conditions. Finally, to aid users in predicting the most accurate automatic tracing results without manual annotations for comparison, we used support vector machine regression to predict reconstruction quality given an image volume and a set of automatic tracings.}, } @article {pmid37060443, year = {2023}, author = {Weinstein, ES and Cuthbertson, JL and Herbert, TL and Voicescu, GT and Bortolin, M and Magalini, S and Gui, D and Helou, M and Lennquist Montan, K and Montan, C and Rafalowsky, C and Ratto, G and Damele, S and Bazurro, S and Laist, I and Marzi, F and Borrello, A and Fransvea, P and Fidanzio, A and Benitez, CY and Faccincani, R and Ragazzoni, L and Caviglia, M}, title = {Advancing the scientific study of prehospital mass casualty response through a Translational Science process: the T1 scoping literature review stage.}, journal = {European journal of trauma and emergency surgery : official publication of the European Trauma Society}, volume = {49}, number = {4}, pages = {1647-1660}, pmid = {37060443}, issn = {1863-9941}, support = {101021957//European Union Horizon 2020 research and innovation program/ ; }, mesh = {Humans ; *Mass Casualty Incidents ; Translational Science, Biomedical ; Triage ; *Emergency Responders ; Databases, Factual ; }, abstract = {PURPOSE: The European Union Horizon 2020 research and innovation funding program awarded the NIGHTINGALE grant to develop a toolkit to support first responders engaged in prehospital (PH) mass casualty incident (MCI) response. To reach the projects' objectives, the NIGHTINGALE consortium used a Translational Science (TS) process. The present work is the first TS stage (T1) aimed to extract data relevant for the subsequent modified Delphi study (T2) statements.

METHODS: The authors were divided into three work groups (WGs) MCI Triage, PH Life Support and Damage Control (PHLSDC), and PH Processes (PHP). Each WG conducted simultaneous literature searches following the PRISMA extension for scoping reviews. Relevant data were extracted from the included articles and indexed using pre-identified PH MCI response themes and subthemes.

RESULTS: The initial search yielded 925 total references to be considered for title and abstract review (MCI Triage 311, PHLSDC 329, PHP 285), then 483 articles for full reference review (MCI Triage 111, PHLSDC 216, PHP 156), and finally 152 articles for the database extraction process (MCI Triage 27, PHLSDC 37, PHP 88). Most frequent subthemes and novel concepts have been identified as a basis for the elaboration of draft statements for the T2 modified Delphi study.

CONCLUSION: The three simultaneous scoping reviews allowed the extraction of relevant PH MCI subthemes and novel concepts that will enable the NIGHTINGALE consortium to create scientifically anchored statements in the T2 modified Delphi study.}, } @article {pmid37049742, year = {2023}, author = {Biswas, P and Bibi, S and Yousafi, Q and Mehmood, A and Saleem, S and Ihsan, A and Dey, D and Hasan Zilani, MN and Hasan, MN and Saleem, R and Awaji, AA and Fahmy, UA and Abdel-Daim, MM}, title = {Study of MDM2 as Prognostic Biomarker in Brain-LGG Cancer and Bioactive Phytochemicals Inhibit the p53-MDM2 Pathway: A Computational Drug Development Approach.}, journal = {Molecules (Basel, Switzerland)}, volume = {28}, number = {7}, pages = {}, pmid = {37049742}, issn = {1420-3049}, support = {RG-10-166-43//The Deanship of Scientific Research (DSR) at King Abdulaziz University (KAU), Jeddah, Saudi Arabia/ ; }, mesh = {Humans ; Tumor Suppressor Protein p53/metabolism ; Molecular Docking Simulation ; Proto-Oncogene Proteins c-mdm2/metabolism ; DNA Copy Number Variations ; Prognosis ; *Brain Neoplasms/drug therapy/genetics/metabolism ; *Glioma/drug therapy/genetics/metabolism ; Biomarkers ; Drug Development ; Brain/metabolism ; }, abstract = {An evaluation of the expression and predictive significance of the MDM2 gene in brain lower-grade glioma (LGG) cancer was carried out using onco-informatics pipelines. Several transcriptome servers were used to measure the differential expression of the targeted MDM2 gene and search mutations and copy number variations. GENT2, Gene Expression Profiling Interactive Analysis, Onco-Lnc, and PrognoScan were used to figure out the survival rate of LGG cancer patients. The protein-protein interaction networks between MDM2 gene and its co-expressed genes were constructed by Gene-MANIA tool. Identified bioactive phytochemicals were evaluated through molecular docking using Schrödinger Suite Software, with the MDM2 (PDB ID: 1RV1) target. Protein-ligand interactions were observed with key residues of the macromolecular target. A molecular dynamics simulation of the novel bioactive compounds with the targeted protein was performed. Phytochemicals targeting MDM2 protein, such as Taxifolin and (-)-Epicatechin, have been shown with more highly stable results as compared to the control drug, and hence, concluded that phytochemicals with bioactive potential might be alternative therapeutic options for the management of LGG patients. Our once informatics-based designed pipeline has indicated that the MDM2 gene may have been a predictive biomarker for LGG cancer and selected phytochemicals possessed outstanding interaction results within the macromolecular target's active site after utilizing in silico approaches. In vitro and in vivo experiments are recommended to confirm these outcomes.}, } @article {pmid37047894, year = {2023}, author = {Roberts, M and Colley, K and Currie, M and Eastwood, A and Li, KH and Avery, LM and Beevers, LC and Braithwaite, I and Dallimer, M and Davies, ZG and Fisher, HL and Gidlow, CJ and Memon, A and Mudway, IS and Naylor, LA and Reis, S and Smith, P and Stansfeld, SA and Wilkie, S and Irvine, KN}, title = {The Contribution of Environmental Science to Mental Health Research: A Scoping Review.}, journal = {International journal of environmental research and public health}, volume = {20}, number = {7}, pages = {}, pmid = {37047894}, issn = {1660-4601}, support = {/DH_/Department of Health/United Kingdom ; }, mesh = {Humans ; Mental Health ; *COVID-19 ; Pandemics ; *Environmental Science ; Environmental Exposure ; }, abstract = {Mental health is influenced by multiple complex and interacting genetic, psychological, social, and environmental factors. As such, developing state-of-the-art mental health knowledge requires collaboration across academic disciplines, including environmental science. To assess the current contribution of environmental science to this field, a scoping review of the literature on environmental influences on mental health (including conditions of cognitive development and decline) was conducted. The review protocol was developed in consultation with experts working across mental health and environmental science. The scoping review included 202 English-language papers, published between 2010 and 2020 (prior to the COVID-19 pandemic), on environmental themes that had not already been the subject of recent systematic reviews; 26 reviews on climate change, flooding, air pollution, and urban green space were additionally considered. Studies largely focused on populations in the USA, China, or Europe and involved limited environmental science input. Environmental science research methods are primarily focused on quantitative approaches utilising secondary datasets or field data. Mental health measurement was dominated by the use of self-report psychometric scales. Measures of environmental states or exposures were often lacking in specificity (e.g., limited to the presence or absence of an environmental state). Based on the scoping review findings and our synthesis of the recent reviews, a research agenda for environmental science's future contribution to mental health scholarship is set out. This includes recommendations to expand the geographical scope and broaden the representation of different environmental science areas, improve measurement of environmental exposure, prioritise experimental and longitudinal research designs, and giving greater consideration to variation between and within communities and the mediating pathways by which environment influences mental health. There is also considerable opportunity to increase interdisciplinarity within the field via the integration of conceptual models, the inclusion of mixed methods and qualitative approaches, as well as further consideration of the socio-political context and the environmental states that can help support good mental health. The findings were used to propose a conceptual model to parse contributions and connections between environmental science and mental health to inform future studies.}, } @article {pmid37046168, year = {2023}, author = {Chen, D and Feng, Q and Zhang, Y}, title = {Enrichment and response of iron-metabolizing microorganisms and metabolic genes in the contaminated area of stratified stacking coal gangue dumps, Northern China.}, journal = {Environmental science and pollution research international}, volume = {30}, number = {23}, pages = {63603-63619}, pmid = {37046168}, issn = {1614-7499}, support = {2020YFC1806501//Key Technologies Research and Development Program/ ; 41977159//National Natural Science Foundation of China/ ; }, mesh = {*Iron/analysis ; *Coal/analysis ; Environmental Pollution/analysis ; Soil/chemistry ; Sulfur/analysis ; China ; }, abstract = {In the Xishan coalfield of northern China, the stratified stacking of soil and gangue was applied to limit the acid pollution from high-sulfur coal gangue. In this study, we found that stratified stacking can effectively neutralize the acidity, with the pH value of gangue-leaching water being 6.02-8.13. In contrast to the acidic contaminated area, most of the microorganisms in the study area sediment were neutrophilic, with the main genera being Arthrobacter, Pseudorhodobacter, Pseudomonas, and Rhodoferax. A variety of iron- and sulfur-metabolizing bacteria was discovered in the gangue-leaching sediment, with the total relative abundance ranging from 4.20 to 23.75%, of which the iron-reducing bacteria (FeRB) accounted for the highest percentage. The distributions of these functional microorganisms in the samples were significantly influenced by Fe and S. The co-occurrence network analysis revealed a significant positive correlation between the iron- and sulfur-metabolizing bacteria in the sediment (93.75%), indicating a strong reciprocal symbiotic relationship between these bacteria. The iron and sulfur metabolism genes in the sediment were predicted and compared based on the Tax4Fun functional prediction method. Results showed that functional genes related to iron metabolism were highly expressed in the gangue-leaching sediment. This study enhances the understanding of iron and sulfur metabolism in gangue-leaching contaminated areas.}, } @article {pmid37043542, year = {2023}, author = {Labbé, F and Abdeladhim, M and Abrudan, J and Araki, AS and Araujo, RN and Arensburger, P and Benoit, JB and Brazil, RP and Bruno, RV and Bueno da Silva Rivas, G and Carvalho de Abreu, V and Charamis, J and Coutinho-Abreu, IV and da Costa-Latgé, SG and Darby, A and Dillon, VM and Emrich, SJ and Fernandez-Medina, D and Figueiredo Gontijo, N and Flanley, CM and Gatherer, D and Genta, FA and Gesing, S and Giraldo-Calderón, GI and Gomes, B and Aguiar, ERGR and Hamilton, JGC and Hamarsheh, O and Hawksworth, M and Hendershot, JM and Hickner, PV and Imler, JL and Ioannidis, P and Jennings, EC and Kamhawi, S and Karageorgiou, C and Kennedy, RC and Krueger, A and Latorre-Estivalis, JM and Ligoxygakis, P and Meireles-Filho, ACA and Minx, P and Miranda, JC and Montague, MJ and Nowling, RJ and Oliveira, F and Ortigão-Farias, J and Pavan, MG and Horacio Pereira, M and Nobrega Pitaluga, A and Proveti Olmo, R and Ramalho-Ortigao, M and Ribeiro, JMC and Rosendale, AJ and Sant'Anna, MRV and Scherer, SE and Secundino, NFC and Shoue, DA and da Silva Moraes, C and Gesto, JSM and Souza, NA and Syed, Z and Tadros, S and Teles-de-Freitas, R and Telleria, EL and Tomlinson, C and Traub-Csekö, YM and Marques, JT and Tu, Z and Unger, MF and Valenzuela, J and Ferreira, FV and de Oliveira, KPV and Vigoder, FM and Vontas, J and Wang, L and Weedall, GD and Zhioua, E and Richards, S and Warren, WC and Waterhouse, RM and Dillon, RJ and McDowell, MA}, title = {Genomic analysis of two phlebotomine sand fly vectors of Leishmania from the New and Old World.}, journal = {PLoS neglected tropical diseases}, volume = {17}, number = {4}, pages = {e0010862}, pmid = {37043542}, issn = {1935-2735}, support = {U54 HG003079/HG/NHGRI NIH HHS/United States ; U54 HG003273/HG/NHGRI NIH HHS/United States ; }, mesh = {Animals ; Humans ; *Phlebotomus/parasitology ; *Psychodidae/parasitology ; *Leishmania/genetics ; *Leishmaniasis, Cutaneous ; Genomics ; }, abstract = {Phlebotomine sand flies are of global significance as important vectors of human disease, transmitting bacterial, viral, and protozoan pathogens, including the kinetoplastid parasites of the genus Leishmania, the causative agents of devastating diseases collectively termed leishmaniasis. More than 40 pathogenic Leishmania species are transmitted to humans by approximately 35 sand fly species in 98 countries with hundreds of millions of people at risk around the world. No approved efficacious vaccine exists for leishmaniasis and available therapeutic drugs are either toxic and/or expensive, or the parasites are becoming resistant to the more recently developed drugs. Therefore, sand fly and/or reservoir control are currently the most effective strategies to break transmission. To better understand the biology of sand flies, including the mechanisms involved in their vectorial capacity, insecticide resistance, and population structures we sequenced the genomes of two geographically widespread and important sand fly vector species: Phlebotomus papatasi, a vector of Leishmania parasites that cause cutaneous leishmaniasis, (distributed in Europe, the Middle East and North Africa) and Lutzomyia longipalpis, a vector of Leishmania parasites that cause visceral leishmaniasis (distributed across Central and South America). We categorized and curated genes involved in processes important to their roles as disease vectors, including chemosensation, blood feeding, circadian rhythm, immunity, and detoxification, as well as mobile genetic elements. We also defined gene orthology and observed micro-synteny among the genomes. Finally, we present the genetic diversity and population structure of these species in their respective geographical areas. These genomes will be a foundation on which to base future efforts to prevent vector-borne transmission of Leishmania parasites.}, } @article {pmid37040629, year = {2023}, author = {Beauchamp, AM and Lehmann, CU and Medford, RJ and Hughes, AE}, title = {Correction: The Association of a Geographically Wide Social Media Network on Depression: County-Level Ecological Analysis.}, journal = {Journal of medical Internet research}, volume = {25}, number = {}, pages = {e47896}, doi = {10.2196/47896}, pmid = {37040629}, issn = {1438-8871}, abstract = {[This corrects the article DOI: 10.2196/43623.].}, } @article {pmid37025368, year = {2022}, author = {Lohse, K and Höök, L and Näsvall, K and Backström, N and , and , and , and , }, title = {The genome sequence of the wood white butterfly, Leptidea sinapis (Linnaeus, 1758).}, journal = {Wellcome open research}, volume = {7}, number = {}, pages = {254}, pmid = {37025368}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual male Leptidea sinapis (the wood white; Arthropoda; Insecta; Lepidoptera; Pieridae). The genome sequence is 686 megabases in span. The majority (99.99%) of the assembly is scaffolded into 48 chromosomal pseudomolecules, with three Z sex chromosomes assembled. Gene annotation of this assembly on Ensembl has identified 14,800 protein coding genes.}, } @article {pmid37022698, year = {2023}, author = {Nartker, M and Zhou, Z and Firestone, C}, title = {When will AI misclassify? Intuiting failures on natural images.}, journal = {Journal of vision}, volume = {23}, number = {4}, pages = {4}, pmid = {37022698}, issn = {1534-7362}, mesh = {Humans ; *Artificial Intelligence ; *Image Interpretation, Computer-Assisted ; }, abstract = {Machine recognition systems now rival humans in their ability to classify natural images. However, their success is accompanied by a striking failure: a tendency to commit bizarre misclassifications on inputs specifically selected to fool them. What do ordinary people know about the nature and prevalence of such classification errors? Here, five experiments exploit the recent discovery of "natural adversarial examples" to ask whether naive observers can predict when and how machines will misclassify natural images. Whereas classical adversarial examples are inputs that have been minimally perturbed to induce misclassifications, natural adversarial examples are simply unmodified natural photographs that consistently fool a wide variety of machine recognition systems. For example, a bird casting a shadow might be misclassified as a sundial, or a beach umbrella made of straw might be misclassified as a broom. In Experiment 1, subjects accurately predicted which natural images machines would misclassify and which they would not. Experiments 2 through 4 extended this ability to how the images would be misclassified, showing that anticipating machine misclassifications goes beyond merely identifying an image as nonprototypical. Finally, Experiment 5 replicated these findings under more ecologically valid conditions, demonstrating that subjects can anticipate misclassifications not only under two-alternative forced-choice conditions (as in Experiments 1-4), but also when the images appear one at a time in a continuous stream-a skill that may be of value to human-machine teams. We suggest that ordinary people can intuit how easy or hard a natural image is to classify, and we discuss the implications of these results for practical and theoretical issues at the interface of biological and artificial vision.}, } @article {pmid37022232, year = {2023}, author = {Zimmerman, S and Tierney, BT and Patel, CJ and Kostic, AD}, title = {Quantifying Shared and Unique Gene Content across 17 Microbial Ecosystems.}, journal = {mSystems}, volume = {8}, number = {2}, pages = {e0011823}, pmid = {37022232}, issn = {2379-5077}, support = {P30 DK036836/DK/NIDDK NIH HHS/United States ; R01 AI127250/AI/NIAID NIH HHS/United States ; R01 ES032470/ES/NIEHS NIH HHS/United States ; T32 DK110919/DK/NIDDK NIH HHS/United States ; }, mesh = {Humans ; *Microbiota/genetics ; Metagenome/genetics ; *Gastrointestinal Microbiome/genetics ; Metagenomics/methods ; Genome, Bacterial ; }, abstract = {Measuring microbial diversity is traditionally based on microbe taxonomy. Here, in contrast, we aimed to quantify heterogeneity in microbial gene content across 14,183 metagenomic samples spanning 17 ecologies, including 6 human associated, 7 nonhuman host associated, and 4 in other nonhuman host environments. In total, we identified 117,629,181 nonredundant genes. The vast majority of genes (66%) occurred in only one sample (i.e., "singletons"). In contrast, we found 1,864 sequences present in every metagenome, but not necessarily every bacterial genome. Additionally, we report data sets of other ecology-associated genes (e.g., abundant in only gut ecosystems) and simultaneously demonstrated that prior microbiome gene catalogs are both incomplete and inaccurately cluster microbial genetic life (e.g., at gene sequence identities that are too restrictive). We provide our results and the sets of environmentally differentiating genes described above at http://www.microbial-genes.bio. IMPORTANCE The amount of shared genetic elements has not been quantified between the human microbiome and other host- and non-host-associated microbiomes. Here, we made a gene catalog of 17 different microbial ecosystems and compared them. We show that most species shared between environment and human gut microbiomes are pathogens and that prior gene catalogs described as "nearly complete" are far from it. Additionally, over two-thirds of all genes only appear in a single sample, and only 1,864 genes (0.001%) are found in all types of metagenomes. These results highlight the large diversity between metagenomes and reveal a new, rare class of genes, those found in every type of metagenome, but not every microbial genome.}, } @article {pmid37021385, year = {2023}, author = {Riva, F and Fahrig, L}, title = {Obstruction of biodiversity conservation by minimum patch size criteria.}, journal = {Conservation biology : the journal of the Society for Conservation Biology}, volume = {37}, number = {5}, pages = {e14092}, doi = {10.1111/cobi.14092}, pmid = {37021385}, issn = {1523-1739}, mesh = {*Conservation of Natural Resources ; *Biodiversity ; Ecosystem ; Databases, Factual ; }, abstract = {Minimum patch size criteria for habitat protection reflect the conservation principle that a single large (SL) patch of habitat has higher biodiversity than several small (SS) patches of the same total area (SL > SS). Nonetheless, this principle is often incorrect, and biodiversity conservation requires placing more emphasis on protection of large numbers of small patches (SS > SL). We used a global database reporting the abundances of species across hundreds of patches to assess the SL > SS principle in systems where small patches are much smaller than the typical minimum patch size criteria applied for biodiversity conservation (i.e., ∼85% of patches <100 ha). The 76 metacommunities we examined included 4401 species in 1190 patches. From each metacommunity, we resampled species-area accumulation curves to evaluate how biodiversity responded to habitat existing as a few large patches or as many small patches. Counter to the SL > SS principle and consistent with previous syntheses, species richness accumulated more rapidly when adding several small patches (45.2% SS > SL vs. 19.9% SL > SS) to reach the same cumulative area, even for the very small patches in our data set. Responses of taxa to habitat fragmentation differed, which suggests that when a given total area of habitat is to be protected, overall biodiversity conservation will be most effective if that habitat is composed of as many small patches as possible, plus a few large ones. Because minimum patch size criteria often require larger patches than the small patches we examined, our results suggest that such criteria hinder efforts to protect biodiversity.}, } @article {pmid37021064, year = {2023}, author = {Keller, R and Spanu, A and Puhan, MA and Flahault, A and Lovis, C and Mütsch, M and Beau-Lejdstrom, R}, title = {Social media and internet search data to inform drug utilization: A systematic scoping review.}, journal = {Frontiers in digital health}, volume = {5}, number = {}, pages = {1074961}, pmid = {37021064}, issn = {2673-253X}, abstract = {INTRODUCTION: Drug utilization is currently assessed through traditional data sources such as big electronic medical records (EMRs) databases, surveys, and medication sales. Social media and internet data have been reported to provide more accessible and more timely access to medications' utilization.

OBJECTIVE: This review aims at providing evidence comparing web data on drug utilization to other sources before the COVID-19 pandemic.

METHODS: We searched Medline, EMBASE, Web of Science, and Scopus until November 25th, 2019, using a predefined search strategy. Two independent reviewers conducted screening and data extraction.

RESULTS: Of 6,563 (64%) deduplicated publications retrieved, 14 (0.2%) were included. All studies showed positive associations between drug utilization information from web and comparison data using very different methods. A total of nine (64%) studies found positive linear correlations in drug utilization between web and comparison data. Five studies reported association using other methods: One study reported similar drug popularity rankings using both data sources. Two studies developed prediction models for future drug consumption, including both web and comparison data, and two studies conducted ecological analyses but did not quantitatively compare data sources. According to the STROBE, RECORD, and RECORD-PE checklists, overall reporting quality was mediocre. Many items were left blank as they were out of scope for the type of study investigated.

CONCLUSION: Our results demonstrate the potential of web data for assessing drug utilization, although the field is still in a nascent period of investigation. Ultimately, social media and internet search data could be used to get a quick preliminary quantification of drug use in real time. Additional studies on the topic should use more standardized methodologies on different sets of drugs in order to confirm these findings. In addition, currently available checklists for study quality of reporting would need to be adapted to these new sources of scientific information.}, } @article {pmid37018807, year = {2023}, author = {Xavier, JMA and Firmino, RT and Pereira, IF and Xavier, MA and Costa, MCFD and Soares, RSC and Ribeiro, AIAM}, title = {The impact of the COVID-19 pandemic in Brazil: a study in tertiary dental care.}, journal = {Brazilian oral research}, volume = {37}, number = {}, pages = {025}, doi = {10.1590/1807-3107bor-2023.vol37.0025}, pmid = {37018807}, issn = {1807-3107}, mesh = {Humans ; *COVID-19 ; Pandemics ; Tertiary Healthcare ; Brazil ; Dental Care ; }, abstract = {The pandemic caused by coronavirus has resonated throughout different levels of health care in Brazil and, in this context, the present research aimed to evaluate this impact on tertiary dental care provided by the Unified Health System (SUS). Therefore, an ecological study was conducted with data obtained from the Hospital Information System processed by the Portal of the Department of Informatics of SUS. The sample consisted of patients of all sexes and age groups, whose Hospital Admission Authorizations (AIHs) were approved for dental tertiary care procedures from January 2015 to December 2020. Descriptive analyses and the ANOVA test with a significance level set at p < 0.05 were used. When the annual mean numbers of AIHs approved were evaluated, findings showed that on an average, the Southeast region authorized a higher number of procedures (p-value < 0.001), however, in the pandemic year (2020), a reduction of approximately 24.5% of these hospitalizations occurred throughout Brazil, with the Midwest being the region most affected (32.12%). A percentage increase occurred in the Surgical Treatment of Oral sinus/Oral nasal Fistula (16.1%), in addition to a significant decrease in performing procedures for Resection of Mouth Lesion (33.4%). In the pandemic year, there was a reduction of 14% in expenditures related to hospital services and 23.26% related to professional services. It was concluded that the data presented demonstrated a significant reduction in AIHs for tertiary dental care in the pandemic year.}, } @article {pmid37016902, year = {2025}, author = {Pandit, AA and Mahashabde, RV and Brown, CC and Acharya, M and Shoults, CC and Eswaran, H and Hayes, CJ}, title = {Association between broadband capacity and telehealth utilization among Medicare Fee-for-service beneficiaries during the COVID-19 pandemic.}, journal = {Journal of telemedicine and telecare}, volume = {31}, number = {1}, pages = {41-48}, pmid = {37016902}, issn = {1758-1109}, mesh = {Humans ; *COVID-19/epidemiology ; United States ; *Telemedicine/statistics & numerical data ; *Medicare/statistics & numerical data ; *Fee-for-Service Plans/statistics & numerical data ; Cross-Sectional Studies ; Health Services Accessibility/statistics & numerical data ; SARS-CoV-2 ; Aged ; Female ; Male ; Pandemics ; Patient Acceptance of Health Care/statistics & numerical data ; }, abstract = {BACKGROUND: Telehealth is a rapidly growing modality for expanding healthcare access, especially in the post-COVID-19 era. However, telehealth requires high-quality broadband, thus making broadband a social determinant of health. The objective of this study was to evaluate the association between broadband access and telehealth utilization across the United States during the COVID-19 pandemic.

METHODS: Using a cross-sectional, ecological study design, we merged county-level data on broadband capacity (Microsoft's Rural Broadband Initiative), telehealth utilization among Medicare Fee-for-Service beneficiaries from January through September 2020 (CareJourney), and county-level socioeconomic characteristics (Area Health Resources Files). Multivariable linear regression was used to estimate the association between broadband capacity, county-level characteristics, and telehealth utilization.

RESULTS: Among the 3107 counties, those with the greatest broadband availability (quintile 5) had 47% higher telehealth utilization compared to counties with the least broadband availability (quintile 1). In the adjusted model, a 1 standard deviation (SD) increase in broadband access was associated with a 1.54 percentage point (pp) increase in telehealth utilization (P < 0.001). Rural county designation (-1.96 pp; P < 0.001) and 1 SD increases in average Medicare beneficiary age (-1.34 pp; P = 0.001), number of nursing home beds per 1000 individuals (-0.38 pp; P = 0.002), and proportion of Native Americans/Pacific Islanders (-0.59 pp; P < 0.001) were associated with decreased telehealth utilization.

CONCLUSION: The association between broadband access and telehealth utilization and the decreased telehealth utilization in rural areas highlight the importance of broadband access for healthcare access and the need to continue investing in broadband infrastructure to promote equitable healthcare access across populations.}, } @article {pmid37011221, year = {2023}, author = {Still, CJ and Page, GFM and Rastogi, B and Griffith, DM and Aubrecht, DM and Kim, Y and Burns, SP and Hanson, CV and Kwon, H and Hawkins, L and Meinzer, FC and Sevanto, S and Roberts, DA and Goulden, M and Pau, S and Detto, M and Helliker, BR and Richardson, AD}, title = {Reply to Garen et al.: Within-canopy temperature data also do not support limited homeothermy.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {120}, number = {15}, pages = {e2302515120}, pmid = {37011221}, issn = {1091-6490}, mesh = {Temperature ; *Body Temperature Regulation ; }, } @article {pmid37010606, year = {2023}, author = {Chaves, T and Azevedo, Á and Caldas, IM}, title = {Are lip prints hereditary? A systematic review.}, journal = {International journal of legal medicine}, volume = {137}, number = {4}, pages = {1203-1214}, pmid = {37010606}, issn = {1437-1596}, support = {UIDB/04004/2020//FCT/MCTES/ ; }, mesh = {Child ; Humans ; *Lip ; *Parents ; Bibliometrics ; Databases, Factual ; }, abstract = {Hereditary lip prints have been studied by several researchers. However, the literature shows no consensus among the scientific community regarding this topic. Therefore, the aim of this study was to conduct a systematic review to gather evidence to clarify whether the surface structure of lip prints is hereditary and, consequently, if a familial relationship between individuals can be established through the analysis of lip prints. The systematic review was performed following the PRISMA (Preferred Reporting Items for Systematic reviews and Meta-Analyses) guidelines. A bibliographic survey was conducted in PubMed, Scopus, and Web of Science databases, restricted to articles published between 2010 and 2020. Studies were selected according to eligibility criteria, and then the study data were collected. The risk of bias of each study was assessed and applied as additional inclusion or exclusion criteria. The results of the articles eligible for analysis were synthesized by a descriptive approach. In the seven included studies, methodological variations, including the definition of similarity, that contribute to the heterogeneity of results were identified. The data gathered allowed to conclude that there is no strong scientific evidence to support the hypothesis of the existence of heredity in the surface structure of lip prints, since it was not proven that similarities between parents and children occur systematically in all families.}, } @article {pmid37008251, year = {2022}, author = {Boyes, D and Wright, C and , and , and , and , and , and , }, title = {The genome sequence of the peppered moth, Biston betularia Linnaeus, 1758.}, journal = {Wellcome open research}, volume = {7}, number = {}, pages = {97}, pmid = {37008251}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual male Biston betularia (the peppered moth; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 405 megabases in span. The majority of the assembly (99.99%) is scaffolded into 31 chromosomal pseudomolecules, with the Z sex chromosome assembled.Gene annotation of this assembly on Ensembl has identified 12,251 protein coding genes.}, } @article {pmid37006240, year = {2023}, author = {Yang, W and Wei, C and Cheng, J and Ding, R and Li, Y and Wang, Y and Yang, Y and Wang, J}, title = {BTG2 and SerpinB5, a novel gene pair to evaluate the prognosis of lung adenocarcinoma.}, journal = {Frontiers in immunology}, volume = {14}, number = {}, pages = {1098700}, pmid = {37006240}, issn = {1664-3224}, mesh = {Humans ; *Carcinoma, Non-Small-Cell Lung ; Molecular Docking Simulation ; *Lung Neoplasms/genetics ; *Adenocarcinoma of Lung/genetics ; Prognosis ; Tumor Microenvironment ; *Immediate-Early Proteins/genetics ; Tumor Suppressor Proteins/genetics ; }, abstract = {INTRODUCTION: Lung adenocarcinoma (LUAD), as the most frequent pathological subtype of non-small cell lung cancer, is often characterized by poor prognosis and low 5-year survival rate. Exploriton of new biomarkers and accurate molecular mechanisms for effectively predicting the prognosis of LUAD patients is still necessary. Presently, BTG2 and SerpinB5, which play important roles in tumors, are studied as a gene pair for the first time with the aim of exploring whether they can be used as potential prognostic markers.

METHODS: Using the bioinformatics method to explore whether BTG2 and SerpinB5 can become independent prognostic factors, and explore their clinical application value and whether they can be used as immunotherapeutic markers. In addition, we also verify the conclusions obtained from external datasets, molecular docking, and SqRT-PCR.

RESULTS: The results show that compared with normal lung tissue, BTG2 expression level was down-regulated and SerpinB5 was up-regulated in LUAD. Additionally, Kaplan-Meier survival analysis demonstrate that the prognosis of low expression level of BTG2 was poor, and that of high expression level of SerpinB5 was poor, suggesting that both of them can be used as independent prognostic factors. Moreover, the prognosis models of the two genes were constructed respectively in this study, and their prediction effect was verified by external data. Besides, ESTIMATE algorithm reveals the relationship between this gene pair and the immune microenvironment. Furthermore, patients with a high expression level of BTG2 and a low expression level of SerpinB5 have higher immunophenoscore for CTLA-4 and PD-1 inhibitors than patients with a low expression level of BTG2 and a high expression level of SerpinB5, indicating that such patients have a more obvious effect of immunotherapy.

DISCUSSION: Collectively, all the results demonstrate that BTG2 and SerpinB5 might serve as potential prognostic biomarkers and novel therapeutic targets for LUAD.}, } @article {pmid37004043, year = {2023}, author = {Khan, AH and Adil, M and Aziz, MA and Sõukand, R and Pieroni, A}, title = {Traditional foraging for ecological transition? Wild food ethnobotany among three ethnic groups in the highlands of the eastern Hindukush, North Pakistan.}, journal = {Journal of ethnobiology and ethnomedicine}, volume = {19}, number = {1}, pages = {9}, pmid = {37004043}, issn = {1746-4269}, mesh = {Humans ; *Ethnobotany ; Pakistan ; Ethnicity ; Plants, Edible ; *Plants, Medicinal ; }, abstract = {BACKGROUND: The Patrak Valley is home to communities, which have been inextricably linked with nature for generations, and local plant knowledge (LPK) represents an important part of their local cultural diversity. In general, globalization has come at the expense of local plant knowledge among several mountain societies, and therefore the current investigation has been undertaken to record the (possibly) last remaining wild food plant/mushroom foraging practices among Pathans, Kohistanis, and Gujjars living in the highlands of the Hindukush, North Pakistan.

METHODS: Data on the uses of wild food plants and mushrooms (WFPs) were collected through 120 semi-structured interviews. The data were cross-culturally compared among the three linguistic groups. Venn diagrams were used to visualize the comparative analysis. To determine the patterns of similarities in plant use among the different ethnic groups, we used the Jaccard similarity index (JI). The recorded data were also compared with the existing Pakistani food ethnobotanical literature.

RESULTS: A total of 68 WFPs were recorded, the majority of which were used as raw snacks and as cooked vegetables. Fruit was the most frequently reported plant part among the three researched groups. Cross-cultural comparison revealed that 37% of the used plants were commonly shared by the three studied groups. Pathans have retained rich knowledge on WFPs, and they show a comparatively closer affinity with Kohistanis is the use of WFPs compared to Gujjars. While we observed some idiosyncrasies for each of the researched groups, the distinctive plant uses among Gujjars provide insight into their food ecology, their particular human-ecological system centered on mobile pastoralism and their limited exchanges of local food/ecological knowledge due to endogamic patterns. A literature survey revealed some novel or little-known ingredients within Pakistani food ethnobotany/ethnomycology, such as Aesculus indica, Agaricus campestris, Apteranthes tuberculata, Duchesnea indica, Equisetum arvense, Eremurus himalaicus, Isodon rugosus, Morella esculenta, Sophora mollis, and Drimia indica.

CONCLUSION: The researched communities have retained important plant knowledge which could be implemented through future development programs considering that most of these traditional foraging practices fulfill environmental and social sustainability standards. Further field studies are required to thoroughly investigate the patterns of foraging among highland pastoral societies in other parts of the Hindukush region and especially their potential for the ongoing ecological transition.}, } @article {pmid37003550, year = {2023}, author = {Romero Starke, K and Schubert, M and Kaboth, P and Gerlach, J and Hegewald, J and Reusche, M and Friedemann, D and Zülke, A and Riedel-Heller, SG and Zeeb, H and Seidler, A}, title = {Traffic noise annoyance in the LIFE-adult study in Germany: Exposure-response relationships and a comparison to the WHO curves.}, journal = {Environmental research}, volume = {228}, number = {}, pages = {115815}, doi = {10.1016/j.envres.2023.115815}, pmid = {37003550}, issn = {1096-0953}, mesh = {Adult ; Humans ; *Noise, Transportation/adverse effects ; Environmental Exposure ; Germany ; Motor Vehicles ; Aircraft ; World Health Organization ; }, abstract = {BACKGROUND: Noise annoyance is the second-highest cause of lost disability-adjusted life-years due to environmental noise in Europe. Evidence on exposure-response relationships (ERRs) for traffic noise annoyance with more accurate exposure values is still needed.

OBJECTIVES: In an analysis of the population-based LIFE-Adult study in Leipzig, Germany, we aimed to investigate the effect of road, railway (train and tram), and aircraft noise on high annoyance (HA).

METHODS: Traffic exposure data was taken for 2012 and data on noise annoyance was evaluated between 2018 and 2021. HA was defined according to international standardized norms. We calculated risk estimates using logistic regression, controlling for age, sex, and socioeconomic status, and compared our ERRs with those from the last WHO review on this topic.

RESULTS: Aircraft noise had the highest relative risk for noise-related HA (OR = 12.7, 95% CI: 9.37-17.10 per 10 dB Lden increase). The road and railway traffic risk estimates were similar to each other (road: OR = 3.55, 95% CI: 2.78-4.54; railway: OR = 3.31, 95% CI: 2.77-3.97 per 10 dB Lden increase). Compared to the WHO curves, the proportion of highly annoyed individuals was somewhat lower for road and rail traffic noise, but higher for aircraft noise.

DISCUSSION: Aircraft noise is particularly annoying. There were differences between our study's ERRs and those in the WHO review, especially for aircraft noise. These differences may be partly explained by the improved accuracy of the exposure values, as we considered secondary road networks and tram noise, and by a lack of a nighttime flight ban at the Leipzig airport. Geographical, regional and climatic variations, inconsistency in HA cut-offs, as well as temporal developments in the annoyance experience may also explain the differences. Since ERRs serve as a basis for decision making in public policies, regular updates of the curves based on new evidence is recommended.}, } @article {pmid36999249, year = {2023}, author = {D'Alò, F and Zucconi, L and Onofri, S and Canini, F and Cannone, N and Malfasi, F and Morais, DK and Starke, R}, title = {Effects of 5-year experimental warming in the Alpine belt on soil Archaea: Multi-omics approaches and prospects.}, journal = {Environmental microbiology reports}, volume = {15}, number = {4}, pages = {291-297}, pmid = {36999249}, issn = {1758-2229}, mesh = {*Archaea/genetics ; *Soil/chemistry ; Multiomics ; Climate Change ; Italy ; Soil Microbiology ; }, abstract = {We currently lack a predictive understanding of how soil archaeal communities may respond to climate change, particularly in Alpine areas where warming is far exceeding the global average. Here, we characterized the abundance, structure, and function of total (by metagenomics) and active soil archaea (by metatranscriptomics) after 5-year experimental field warming (+1°C) in Italian Alpine grasslands and snowbeds. Our multi-omics approach unveiled an increasing abundance of Archaea during warming in snowbeds, which was negatively correlated with the abundance of fungi (by qPCR) and micronutrients (Ca and Mg), but positively correlated with soil water content. In the snowbeds transcripts, warming resulted in the enrichment of abundances of transcription and nucleotide biosynthesis. Our study provides novel insights into possible changes in soil Archaea composition and function in the climate change scenario.}, } @article {pmid36998243, year = {2022}, author = {Boyes, D and , and , and , and , and , and Boyes, C and , }, title = {The genome sequence of the pale mottled willow, Caradrina clavipalpis (Scopoli, 1763).}, journal = {Wellcome open research}, volume = {7}, number = {}, pages = {225}, pmid = {36998243}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual male Caradrina clavipalpis (pale mottled willow; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 474 megabases in span. The entire assembly (100%) is scaffolded into 31 chromosomal pseudomolecules with the Z sex chromosome assembled. The complete mitochondrial genome was also assembled and is 15.6 kilobases in length.}, } @article {pmid36998167, year = {2023}, author = {Sakai, K and Nagata, T and Odagami, K and Nagata, M and Mori, T and Mori, K}, title = {Supervisors' Work Engagement Is Associated With Interactivity and Carefulness in Supporting Subordinates: A Cross-sectional Study Using Text Mining in Japan.}, journal = {Journal of occupational and environmental medicine}, volume = {65}, number = {7}, pages = {e465-e471}, pmid = {36998167}, issn = {1536-5948}, mesh = {Humans ; *Work Engagement ; Cross-Sectional Studies ; Japan ; *Attitude ; Data Mining ; }, abstract = {OBJECTIVE: This study aimed to structure supervisory support and clarify the relationship between supervisors' work engagement and support for their subordinates.

METHODS: We conducted a cross-sectional study in a manufacturing company using a questionnaire survey. Supervisors provided open-ended responses regarding the provision of support for their subordinates. Using text mining, we structured these descriptions into multiple categories, assigned words to them, and analyzed frequently mentioned categories by the level of work engagement.

RESULTS: We obtained responses from 729 participants that included 13,968 words. We structured supervisory support by three categories (contents, direction, and attitude toward support) and 11 subcategories. As supervisors' work engagement increased, the rates of mentioning information retrieval, information transmission, and carefulness increased.

CONCLUSIONS: Supervisors with work engagement could communicate with each other and be careful in providing support to their subordinates.}, } @article {pmid36992446, year = {2023}, author = {Howison, M and Gillani, FS and Novitsky, V and Steingrimsson, JA and Fulton, J and Bertrand, T and Howe, K and Civitarese, A and Bhattarai, L and MacAskill, M and Ronquillo, G and Hague, J and Dunn, CW and Bandy, U and Hogan, JW and Kantor, R}, title = {An Automated Bioinformatics Pipeline Informing Near-Real-Time Public Health Responses to New HIV Diagnoses in a Statewide HIV Epidemic.}, journal = {Viruses}, volume = {15}, number = {3}, pages = {}, pmid = {36992446}, issn = {1999-4915}, support = {R01 AI136058/AI/NIAID NIH HHS/United States ; K24 AI134359/AI/NIAID NIH HHS/United States ; P30 AI042853/AI/NIAID NIH HHS/United States ; }, mesh = {Humans ; *HIV Infections/diagnosis/epidemiology ; Public Health ; Phylogeny ; Prospective Studies ; *HIV-1/genetics ; *HIV Seropositivity ; }, abstract = {Molecular HIV cluster data can guide public health responses towards ending the HIV epidemic. Currently, real-time data integration, analysis, and interpretation are challenging, leading to a delayed public health response. We present a comprehensive methodology for addressing these challenges through data integration, analysis, and reporting. We integrated heterogeneous data sources across systems and developed an open-source, automatic bioinformatics pipeline that provides molecular HIV cluster data to inform public health responses to new statewide HIV-1 diagnoses, overcoming data management, computational, and analytical challenges. We demonstrate implementation of this pipeline in a statewide HIV epidemic and use it to compare the impact of specific phylogenetic and distance-only methods and datasets on molecular HIV cluster analyses. The pipeline was applied to 18 monthly datasets generated between January 2020 and June 2022 in Rhode Island, USA, that provide statewide molecular HIV data to support routine public health case management by a multi-disciplinary team. The resulting cluster analyses and near-real-time reporting guided public health actions in 37 phylogenetically clustered cases out of 57 new HIV-1 diagnoses. Of the 37, only 21 (57%) clustered by distance-only methods. Through a unique academic-public health partnership, an automated open-source pipeline was developed and applied to prospective, routine analysis of statewide molecular HIV data in near-real-time. This collaboration informed public health actions to optimize disruption of HIV transmission.}, } @article {pmid36989356, year = {2023}, author = {Bird, N and Ormond, L and Awah, P and Caldwell, EF and Connell, B and Elamin, M and Fadlelmola, FM and Matthew Fomine, FL and López, S and MacEachern, S and Moñino, Y and Morris, S and Näsänen-Gilmore, P and Nketsia V, NK and Veeramah, K and Weale, ME and Zeitlyn, D and Thomas, MG and Bradman, N and Hellenthal, G}, title = {Dense sampling of ethnic groups within African countries reveals fine-scale genetic structure and extensive historical admixture.}, journal = {Science advances}, volume = {9}, number = {13}, pages = {eabq2616}, pmid = {36989356}, issn = {2375-2548}, support = {/WT_/Wellcome Trust/United Kingdom ; BB/R01356X/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Humans ; *Ethnicity/genetics ; Nigeria ; *Chromosomes ; Ghana ; Language ; Genetic Variation ; Genetics, Population ; }, abstract = {Previous studies have highlighted how African genomes have been shaped by a complex series of historical events. Despite this, genome-wide data have only been obtained from a small proportion of present-day ethnolinguistic groups. By analyzing new autosomal genetic variation data of 1333 individuals from over 150 ethnic groups from Cameroon, Republic of the Congo, Ghana, Nigeria, and Sudan, we demonstrate a previously underappreciated fine-scale level of genetic structure within these countries, for example, correlating with historical polities in western Cameroon. By comparing genetic variation patterns among populations, we infer that many northern Cameroonian and Sudanese groups share genetic links with multiple geographically disparate populations, likely resulting from long-distance migrations. In Ghana and Nigeria, we infer signatures of intermixing dated to over 2000 years ago, corresponding to reports of environmental transformations possibly related to climate change. We also infer recent intermixing signals in multiple African populations, including Congolese, that likely relate to the expansions of Bantu language-speaking peoples.}, } @article {pmid36981964, year = {2023}, author = {Sui, J and Zhang, G and Lin, T and Hamm, NAS and Li, C and Wu, X and Hu, K}, title = {Quantitative Evaluation of Spatial Accessibility of Various Urban Medical Services Based on Big Data of Outpatient Appointments.}, journal = {International journal of environmental research and public health}, volume = {20}, number = {6}, pages = {}, pmid = {36981964}, issn = {1660-4601}, mesh = {Child ; Humans ; *Big Data ; *Outpatients ; Health Services Accessibility ; Cities ; Catchment Area, Health ; }, abstract = {Equity of urban medical services affects human health and well-being in cities and is important in building 'just' cities. We carried out a quantitative analysis of the spatial accessibility of medical services considering the diverse demands of people of different ages, using outpatient appointment big data and refining the two-step floating catchment area (2SFCA) method. We used the traditional 2SFCA method to evaluate the overall spatial accessibility of medical services of 504 communities in Xiamen city, considering the total population and the supply of medical resources. Approximately half the communities had good access to medical services. The communities with high accessibility were mainly on Xiamen Island, and those with low accessibility were further from the central city. The refined 2SFCA method showed a more diverse and complex spatial distribution of accessibility to medical services. Overall, 209 communities had high accessibility to internal medicine services, 133 to surgery services, 50 to gynecology and obstetrics services, and 18 to pediatric services. The traditional method may over-evaluate or under-evaluate the accessibility of different types of medical services for most communities compared with the refined evaluation method. Our study can provide more precise information on urban medical service spatial accessibility to support just city development and design.}, } @article {pmid36979124, year = {2023}, author = {Schalli, M and Platzer, S and Schmutz, R and Ofner-Kopeinig, P and Reinthaler, FF and Haas, D}, title = {Dissolved Carbon Dioxide: The Lifespan of Staphylococcus aureus and Enterococcus faecalis in Bottled Carbonated Mineral Water.}, journal = {Biology}, volume = {12}, number = {3}, pages = {}, pmid = {36979124}, issn = {2079-7737}, abstract = {During the process of mineral water production, many possible contamination settings can influence the quality of bottled water. Microbial contamination can originate from different sources, for example, the ambient air, the bottles, the caps, and from the bottling machine itself. The aim of this study was to investigate the influence of three different carbon dioxide (CO2) concentrations (3.0 g/L, 5.5 g/L, and 7.0 g/L; 20 bottles each) in bottled mineral water on the bacterial growth of Staphylococcus aureus (S. aureus) and Enterococcus faecalis (Ent. faecalis). The examined mineral water was artificially contaminated before capping the bottles inside the factory. After a specific number of days, water samples were taken from freshly opened bottles and after filtration (100 mL), filters were placed on Columbia Agar with 5% Sheep blood to cultivate S. aureus and Slanetz and Bartley Agar to cultivate Ent. faecalis. The respective colony-forming units (CFU) were counted after incubation times ranging from 24 to 120 h. Colony-forming units of S. aureus were not detectable after the 16th and 27th day, whereas Ent. faecalis was not cultivable after the 5th and 13th day when stored inside the bottles. The investigation of the bottles that were stored open for a certain amount of time with CO2 bubbling out showed only single colonies for S. aureus after the 5th day and no CFUs for Ent. faecalis after the 17th day. A reduction in the two investigated bacterial strains during storage in carbonated mineral water bottles means that a proper standardized disinfection and cleaning procedure, according to valid hygiene standards of industrial bottling machines, cannot be replaced by carbonation.}, } @article {pmid36978281, year = {2023}, author = {Stanic, B and Milošević, N and Sukur, N and Samardzija Nenadov, D and Fa Nedeljkovic, S and Škrbić, S and Andric, N}, title = {An in silico toxicogenomic approach in constructing the aflatoxin B1-mediated regulatory network of hub genes in hepatocellular carcinoma.}, journal = {Toxicology mechanisms and methods}, volume = {33}, number = {7}, pages = {552-562}, doi = {10.1080/15376516.2023.2196686}, pmid = {36978281}, issn = {1537-6524}, mesh = {Humans ; *Carcinoma, Hepatocellular/chemically induced/genetics/metabolism ; *Liver Neoplasms/chemically induced/genetics/metabolism ; Aflatoxin B1/toxicity ; Toxicogenetics ; }, abstract = {Aflatoxin B1 (AFB1) can cause hepatocellular carcinoma (HCC) through a mutagenic mode of action but can also lead to global changes in gene expression; however, the AFB1 network of molecular pathways involved in HCC is not known. Here, we used toxicogenomic data from human liver cells exposed to AFB1 to infer the network of AFB1-responsive molecular pathways involved in HCC. The following computational tools: STRING, MCODE, cytoHubba, iRegulon, kinase enrichment tool KEA3, and DAVID were used to identify protein-protein interaction network, hub genes, transcription factors (TFs), upstream kinases, and biological processes (BPs). Predicted molecular events were validated with an external dataset, whereas the hub genes in HCC were validated using the UALCAN database. The results revealed an association between AFB1 and the hub genes involved in the cell cycle. We identified TFs that regulate the hub genes and linked them with upstream kinases including cyclin-dependent kinases, mitogen-activated protein kinase 1, and AKT. This approach enabled the construction of the AFB1-mediated regulatory network consisting of upstream kinases, TFs, hub genes, and BPs, thus revealing the signaling hierarchy and information flow that may contribute to AFB1-induced HCC. This could be a useful tool in predicting the molecular mechanisms involved in chemical-induced diseases when available toxicogenomic data exist.}, } @article {pmid36976982, year = {2023}, author = {Yang, D and Zhu, H and Liu, J and Zhang, Y and Wu, S and Xiong, J and Wang, F}, title = {Risk Assessment of Heavy Metals in Soils from Four Different Industrial Plants in a Medium-Sized City in North China.}, journal = {Toxics}, volume = {11}, number = {3}, pages = {}, pmid = {36976982}, issn = {2305-6304}, support = {U2003103//the Key Project of Joint Funds of the National Natural Science Foundation of China/ ; KC22075//special fund for promoting scientific and technological innovation in Xuzhou in 2022 (key research and development plan (modern agriculture) - general project/ ; No. 2020ZDPYMS10//the Fundamental Research Funds for the Central Universities/ ; }, abstract = {Laboratory experiments were carried out to analyze 39 soil samples collected from four industrial areas in Xuzhou City using inductively coupled plasma mass spectrometry and atomic fluorescence spectrometry. The descriptive statistics of heavy metals (HMs) in the soil profiles showed that the HM content at three depths was highly variable, and most coefficients of variation (CVs) showed moderate variability. The enrichment of Cd at all depths exceeded the risk screening value, and Cd pollution occurred in four plants. The enrichment of the other HMs at three depths was mainly concentrated in the pharmaceutical plant A and chemical plant C. It was found that the different HMs had different vertical distribution characteristics. For the different industrial plants, the raw materials and products not only made the spatial distribution characteristics of the HMs different, but also caused the HM types and contents to differ. The average single pollution indices of Cd in plant A, iron-steel plant B, and plant C indicated a slight pollution level. The other seven HMs in A, B, and C and all HMs in chemical plant D belonged to the safe category. The mean values of the Nemerow pollution index in the four industrial plants belonged to the warning category. The analysis showed that none of the HMs posed potential noncarcinogenic health risks, and only the carcinogenic health risks of Cr in plants A and C were unacceptable. The carcinogenic effect of Cr through the inhalation intake of resuspended soil particulates and that of Cd, Ni, and As via direct oral ingestion were the main exposure pathways.}, } @article {pmid36976384, year = {2023}, author = {Huang, F and Chen, C}, title = {GIS-based approach and multivariate statistical analysis for identifying sources of heavy metals in marine sediments from the coast of Hong Kong.}, journal = {Environmental monitoring and assessment}, volume = {195}, number = {4}, pages = {518}, pmid = {36976384}, issn = {1573-2959}, mesh = {Hong Kong ; Geographic Information Systems ; Cadmium ; Lead ; Environmental Monitoring/methods ; *Metals, Heavy/analysis ; *Mercury ; Geologic Sediments/chemistry ; Risk Assessment ; China ; *Water Pollutants, Chemical/analysis ; }, abstract = {Hong Kong is an urbanized coastal city which experiences substantially different metal loads from anthropogenic activities. This study was aimed at analyzing the spatial distribution and pollution evaluation of ten selected heavy metals (As, Cd, Cr, Cu, Pb, Hg, Ni, Zn, Fe, V) in the coastal sediments of Hong Kong. The distribution of heavy metal pollution in sediments has been analyzed using the geographic information system (GIS) technique, and their pollution degrees, corresponding potential ecological risks and source identifications, have been studied by applying the enrichment factor (EF) analysis, contamination factor (CF) analysis, potential ecological risk index (PEI), and integrated multivariate statistical methods, respectively. Firstly, the GIS technique was used to access the spatial distribution of the heavy metals; the result revealed that pollution trend of these metals was decreased from the inner to the outer coast sites of the studied area. Secondly, combining the EF analysis and CF analysis, we found that the pollution degree of heavy metals followed the order of Cu > Cr > Cd > Zn > Pb > Hg > Ni > Fe > As > V. Thirdly, the PERI calculations showed that Cd, Hg, and Cu were the most potential ecological risk factors compared to other metals. Finally, cluster analysis combined with principal component analysis showed that Cr, Cu, Hg, and Ni might originate from the industrial discharges and shipping activities. V, As, and Fe were mainly derived from the natural origin, whereas Cd, Pb, and Zn were identified from the municipal discharges and industrial wastewater. In conclusion, this work should be helpful in the establishment of strategies for contamination control and optimization of industrial structures in Hong Kong.}, } @article {pmid36972774, year = {2023}, author = {Cecchetto, M and Peruzza, L and Giubilato, E and Bernardini, I and Rovere, GD and Marcomini, A and Regoli, F and Bargelloni, L and Patarnello, T and Semenzin, E and Milan, M}, title = {An innovative index to incorporate transcriptomic data into weight of evidence approaches for environmental risk assessment.}, journal = {Environmental research}, volume = {227}, number = {}, pages = {115745}, doi = {10.1016/j.envres.2023.115745}, pmid = {36972774}, issn = {1096-0953}, mesh = {Animals ; *Transcriptome ; Gene Expression Profiling/methods ; *Mytilus/genetics ; Risk Assessment/methods ; }, abstract = {The sharp decrease in the cost of RNA-sequencing and the rapid improvement in computational analysis of eco-toxicogenomic data have brought new insights into the adverse effects of chemicals on aquatic organisms. Yet, transcriptomics is generally applied qualitatively in environmental risk assessments, hampering more effective exploitation of this evidence through multidisciplinary studies. In view of this limitation, a methodology is here presented to quantitatively elaborate transcriptional data in support to environmental risk assessment. The proposed methodology makes use of results from the application of Gene Set Enrichment Analysis to recent studies investigating the response of Mytilus galloprovincialis and Ruditapes philippinarum exposed to contaminants of emerging concern. The degree of changes in gene sets and the relevance of physiological reactions are integrated in the calculation of a hazard index. The outcome is then classified according to five hazard classes (from absent to severe), providing an evaluation of whole-transcriptome effects of chemical exposure. The application to experimental and simulated datasets proved that the method can effectively discriminate different levels of altered transcriptomic responses when compared to expert judgement (Spearman correlation coefficient of 0.96). A further application to data collected in two independent studies of Salmo trutta and Xenopus tropicalis exposed to contaminants confirmed the potential extension of the methodology to other aquatic species. This methodology can serve as a proof of concept for the integration of "genomic tools" in environmental risk assessment based on multidisciplinary investigations. To this end, the proposed transcriptomic hazard index can now be incorporated into quantitative Weight of Evidence approaches and weighed, with results from other types of analysis, to elucidate the role of chemicals in adverse ecological effects.}, } @article {pmid36972109, year = {2023}, author = {Beauchamp, AM and Lehmann, CU and Medford, RJ and Hughes, AE}, title = {The Association of a Geographically Wide Social Media Network on Depression: County-Level Ecological Analysis.}, journal = {Journal of medical Internet research}, volume = {25}, number = {}, pages = {e43623}, pmid = {36972109}, issn = {1438-8871}, support = {UL1 TR003163/TR/NCATS NIH HHS/United States ; }, mesh = {Adult ; Humans ; United States/epidemiology ; *Social Media ; Cross-Sectional Studies ; Depression/epidemiology ; Income ; Mental Health ; }, abstract = {BACKGROUND: Social connectedness decreases human mortality, improves cancer survival, cardiovascular health, and body mass, results in better-controlled glucose levels, and strengthens mental health. However, few public health studies have leveraged large social media data sets to classify user network structure and geographic reach rather than the sole use of social media platforms.

OBJECTIVE: The objective of this study was to determine the association between population-level digital social connectedness and reach and depression in the population across geographies of the United States.

METHODS: Our study used an ecological assessment of aggregated, cross-sectional population measures of social connectedness, and self-reported depression across all counties in the United States. This study included all 3142 counties in the contiguous United States. We used measures obtained between 2018 and 2020 for adult residents in the study area. The study's main exposure of interest is the Social Connectedness Index (SCI), a pair-wise composite index describing the "strength of connectedness between 2 geographic areas as represented by Facebook friendship ties." This measure describes the density and geographical reach of average county residents' social network using Facebook friendships and can differentiate between local and long-distance Facebook connections. The study's outcome of interest is self-reported depressive disorder as published by the Centers for Disease Control and Prevention.

RESULTS: On average, 21% (21/100) of all adult residents in the United States reported a depressive disorder. Depression frequency was the lowest for counties in the Northeast (18.6%) and was highest for southern counties (22.4%). Social networks in northeastern counties involved moderately local connections (SCI 5-10 the 20th percentile for n=70, 36% of counties), whereas social networks in Midwest, southern, and western counties contained mostly local connections (SCI 1-2 the 20th percentile for n=598, 56.7%, n=401, 28.2%, and n=159, 38.4%, respectively). As the quantity and distance that social connections span (ie, SCI) increased, the prevalence of depressive disorders decreased by 0.3% (SE 0.1%) per rank.

CONCLUSIONS: Social connectedness and depression showed, after adjusting for confounding factors such as income, education, cohabitation, natural resources, employment categories, accessibility, and urbanicity, that a greater social connectedness score is associated with a decreased prevalence of depression.}, } @article {pmid36966822, year = {2023}, author = {Song, W and Song, W}, title = {Cropland fallow reduces agricultural water consumption by 303 million tons annually in Gansu Province, China.}, journal = {The Science of the total environment}, volume = {879}, number = {}, pages = {163013}, doi = {10.1016/j.scitotenv.2023.163013}, pmid = {36966822}, issn = {1879-1026}, abstract = {The high-intensity utilization of global cropland causes water shortage and food crisis, which seriously affects the realization of SDG 2 (zero hunger), SDG 6 (clean water and sanitation) and SDG 15 (life on land), and threatens the sustainable social, economic and ecological development. Cropland fallow can not only improve the quality of cropland and maintain ecosystem balance, but also have a significant water-saving effect. However, in most developing countries, such as China, cropland fallow has not yet been widely promoted, and there are few reliable fallow cropland fallow identification methods, making it even more challenging to assess the water-saving effect. To remedy this deficit, we propose a framework for mapping cropland fallow and evaluating its water savings. First, we used the Landsat series of data to interpret the annual land use/cover changes in Gansu Province, China from 1991 to 2020. Subsequently, the spatial-temporal variation of cropland fallow in Gansu province (giving up farming for one to two years) was mapped. Finally, we evaluated the water-saving effect of cropland fallow using evapotranspiration, precipitation, irrigation maps, and crop-related data, instead of actual water consumption. The results showed that the mapping accuracy of fallow land in Gansu Province was 79.50 %, which was higher than that of most known fallow mapping studies. From 1993 to 2018, the average annual fallow rate in Gansu Province, China, was 10.86 %, which was at a low level in arid/semi-arid regions worldwide. More importantly, from 2003 to 2018, cropland fallow reduces annual water consumption of 303.26 million tons in Gansu Province, accounting for 3.44 % of agricultural water use in Gansu Province and equivalent to the annual water demand of 655,000 people in Gansu Province. Based on our research, we speculate that the increasing pilot projects of cropland fallow in China can bring significant water-saving effects and help achieve China's Sustainable Development Goals.}, } @article {pmid36964402, year = {2023}, author = {Dec, E and Clement, J and Cheng, K and Church, GM and Fossel, MB and Rehkopf, DH and Rosero-Bixby, L and Kobor, MS and Lin, DT and Lu, AT and Fei, Z and Guo, W and Chew, YC and Yang, X and Putra, SED and Reiner, AP and Correa, A and Vilalta, A and Pirazzini, C and Passarino, G and Monti, D and Arosio, B and Garagnani, P and Franceschi, C and Horvath, S}, title = {Centenarian clocks: epigenetic clocks for validating claims of exceptional longevity.}, journal = {GeroScience}, volume = {45}, number = {3}, pages = {1817-1835}, pmid = {36964402}, issn = {2509-2723}, support = {HHSN268201600001C/HL/NHLBI NIH HHS/United States ; HHSN268201600003C/HL/NHLBI NIH HHS/United States ; U01 AG060908/AG/NIA NIH HHS/United States ; HHSN268201800015I/HB/NHLBI NIH HHS/United States ; P30 AG012839/AG/NIA NIH HHS/United States ; HHSN268201800010I/HB/NHLBI NIH HHS/United States ; HHSN268201600002C/HL/NHLBI NIH HHS/United States ; HHSN268201600004C/HL/NHLBI NIH HHS/United States ; HHSN268201800014I/HB/NHLBI NIH HHS/United States ; R01 AG029451/AG/NIA NIH HHS/United States ; HHSN268201800013I/MD/NIMHD NIH HHS/United States ; HHSN268201800012I/HB/NHLBI NIH HHS/United States ; HHSN268201500001I/HL/NHLBI NIH HHS/United States ; HHSN268201800011I/HB/NHLBI NIH HHS/United States ; HHSN268201600018C/HL/NHLBI NIH HHS/United States ; }, mesh = {Aged, 80 and over ; Humans ; *Longevity/genetics ; *Centenarians ; DNA Methylation ; Epigenesis, Genetic/genetics ; }, abstract = {Claims surrounding exceptional longevity are sometimes disputed or dismissed for lack of credible evidence. Here, we present three DNA methylation-based age estimators (epigenetic clocks) for verifying age claims of centenarians. The three centenarian clocks were developed based on n = 7039 blood and saliva samples from individuals older than 40, including n = 184 samples from centenarians, 122 samples from semi-supercentenarians (aged 105 +), and 25 samples from supercentenarians (aged 110 +). The oldest individual was 115 years old. Our most accurate centenarian clock resulted from applying a neural network model to a training set composed of individuals older than 40. An epigenome-wide association study of age in different age groups revealed that age effects in young individuals (age < 40) are correlated (r = 0.55) with age effects in old individuals (age > 90). We present a chromatin state analysis of age effects in centenarians. The centenarian clocks are expected to be useful for validating claims surrounding exceptional old age.}, } @article {pmid36962744, year = {2023}, author = {Asaaga, FA and Purse, BV and Rahman, M and Srinivas, PN and Kalegowda, SD and Seshadri, T and Young, JC and Oommen, MA}, title = {The role of social vulnerability in improving interventions for neglected zoonotic diseases: The example of Kyasanur Forest Disease in India.}, journal = {PLOS global public health}, volume = {3}, number = {2}, pages = {e0000758}, pmid = {36962744}, issn = {2767-3375}, support = {/WT_/Wellcome Trust/United Kingdom ; MR/P024335/2/MRC_/Medical Research Council/United Kingdom ; MR/T029846/1/MRC_/Medical Research Council/United Kingdom ; }, abstract = {Forest-based communities manage many risks to health and socio-economic welfare including the increasing threat of emerging zoonoses that are expected to disproportionately affect poor and marginalised groups, and further impair their precarious livelihoods, particularly in Low-and-Middle Income (LMIC) settings. Yet, there is a relative dearth of empirical research on the vulnerability and adaptation pathways of poor and marginalised groups facing emerging zoonoses. Drawing on a survey of 229 households and a series of key-informant interviews in the Western Ghats, we examine the factors affecting vulnerability of smallholder and tribal households to Kyasanur Forest Disease (KFD), an often-fatal tick-borne viral haemorrhagic fever endemic in south India. Specifically, we investigate how different socio-demographic and institutional factors interact to shape KFD vulnerability and the strategies employed by households to adapt to disease consequences. Although surveyed households generally perceived KFD as an important health issue in the study region, there was variability in concern about contracting the disease. Overall results showed that poor access to land (AOR = 0.373, 95% CI: 0.152-0.916), being at or below the poverty line (AOR = 0.253, 95% CI: 0.094-0.685) and being headed by an older person (AOR = 1.038, 95% CI: 1.006-1.071) were all significant determinants of perceived KFD vulnerability. Furthermore, KFD vulnerability is also modulated by important extra-household factors including proximity to private hospitals (AOR = 3.281, 95% CI: 1.220-8.820), main roads (AOR = 2.144, 95% CI: 1.215-3.783) and study location (AOR = 0.226, 95% CI: 0.690-0.743). Our findings highlight how homogenous characterisation of smallholder and tribal communities and the 'techno-oriented' approach of existing interventions may further marginalise the most vulnerable and exacerbate existing inequalities. These findings are important for designing context-specific and appropriate health interventions (including the prioritisation of awareness raising, knowledge networks, livelihood diversification) that enhances the resilience of at-risk social groups within the KFD context. More broadly, our findings highlight how a focus on social vulnerability can help national and international health planners improve health interventions and prioritise among diseases with respect to neglected endemic zoonoses.}, } @article {pmid36962522, year = {2022}, author = {Sawires, R and Pearce, C and Fahey, M and Clothier, H and Gardner, K and Buttery, J}, title = {Snotwatch COVID-toes: An ecological study of chilblains and COVID-19 diagnoses in Victoria, Australia.}, journal = {PLOS global public health}, volume = {2}, number = {10}, pages = {e0000488}, pmid = {36962522}, issn = {2767-3375}, abstract = {The COVID-19 pandemic has caused widespread illness with varying clinical manifestations. One less-commonly-reported presentation of COVID-19 infection is chilblain-like lesions. We conducted an ecological analysis of chilblain presentations in comparison with confirmed and suspected COVID-19 infections in a primary care setting to establish that a relationship exists between the two. Our study collated data from three Primary Health Networks across Victoria, Australia, from 2017-2021, to understand patterns of chilblain presentations prior to and throughout the pandemic. Using a zero-inflated negative binomial regression analysis, we estimated the relationship between local minimum temperature, COVID-19 infections and the frequency of chilblain presentations. We found a 5.72 risk ratio of chilblain incidence in relation to COVID-19 infections and a 3.23 risk ratio associated with suspected COVID-19 infections. COVID-19 infections were also more strongly associated with chilblain presentations in 0-16-year-olds throughout the pandemic in Victoria. Our study statistically suggests that chilblains are significantly associated with COVID-19 infections in a primary care setting. This has major implications for clinicians aiming to diagnose COVID-19 infections or determine the cause of a presentation of chilblains. Additionally, we demonstrate the utility of large-scale primary care data in identifying an uncommon manifestation of COVID-19 infections, which will be significantly beneficial to treating physicians.}, } @article {pmid36962247, year = {2022}, author = {Asaaga, FA and Young, JC and Srinivas, PN and Seshadri, T and Oommen, MA and Rahman, M and Kiran, SK and Kasabi, GS and Narayanaswamy, D and Schäfer, SM and Burthe, SJ and August, T and Logie, M and Chanda, MM and Hoti, SL and Vanak, AT and Purse, BV}, title = {Co-production of knowledge as part of a OneHealth approach to better control zoonotic diseases.}, journal = {PLOS global public health}, volume = {2}, number = {3}, pages = {e0000075}, pmid = {36962247}, issn = {2767-3375}, support = {/WT_/Wellcome Trust/United Kingdom ; MR/P024335/2/MRC_/Medical Research Council/United Kingdom ; MR/T029846/1/MRC_/Medical Research Council/United Kingdom ; }, abstract = {There is increased global and national attention on the need for effective strategies to control zoonotic diseases. Quick, effective action is, however, hampered by poor evidence-bases and limited coordination between stakeholders from relevant sectors such as public and animal health, wildlife and forestry sectors at different scales, who may not usually work together. The OneHealth approach recognises the value of cross-sectoral evaluation of human, animal and environmental health questions in an integrated, holistic and transdisciplinary manner to reduce disease impacts and/or mitigate risks. Co-production of knowledge is also widely advocated to improve the quality and acceptability of decision-making across sectors and may be particularly important when it comes to zoonoses. This paper brings together OneHealth and knowledge co-production and reflects on lessons learned for future OneHealth co-production processes by describing a process implemented to understand spill-over and identify disease control and mitigation strategies for a zoonotic disease in Southern India (Kyasanur Forest Disease). The co-production process aimed to develop a joint decision-support tool with stakeholders, and we complemented our approach with a simple retrospective theory of change on researcher expectations of the system-level outcomes of the co-production process. Our results highlight that while co-production in OneHealth is a difficult and resource intensive process, requiring regular iterative adjustments and flexibility, the beneficial outcomes justify its adoption. A key future aim should be to improve and evaluate the degree of inter-sectoral collaboration required to achieve the aims of OneHealth. We conclude by providing guidelines based on our experience to help funders and decision-makers support future co-production processes.}, } @article {pmid36958663, year = {2023}, author = {Lima, GDS and Menegario, AA and Suarez, CA and Kamazuka, SH and Gemeiner, H and Sánchez-Sarmiento, AM and Ferioli, RB and Barreto, AS}, title = {Pelagic and estuarine birds as sentinels of metal(loid)s in the South Atlantic Ocean: Ecological niches as main factors acting on bioaccumulation.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {326}, number = {}, pages = {121452}, doi = {10.1016/j.envpol.2023.121452}, pmid = {36958663}, issn = {1873-6424}, mesh = {Humans ; Animals ; *Metals, Heavy/analysis ; Bioaccumulation ; Cadmium/analysis ; Lead/analysis ; Environmental Monitoring/methods ; Ecosystem ; *Mercury/analysis ; Birds ; Risk Assessment ; *Water Pollutants, Chemical/analysis ; }, abstract = {Activities related to the offshore exploration and production of oil and natural gas provide economic development and an essential energy source. However, besides the risk of petroleum hydrocarbon contamination, these activities can also be sources of metals and metalloids for marine organism contamination. In this research, we evaluated the potential use of two pelagic (black-browed albatross Thalassarche melanophris and yellow-nosed albatross T. chlororhynchos) and one estuarine bird species (neotropical cormorant Nannopterum brasilianus) as sentinels of contamination of As, Cd, Cr, Cu, Pb, Mn, Mo, Zn, Ni, Ba, V, and Hg in an area under influence of oil and gas activities. The analyses were carried out in samples collected from 2015 to 2022 from 97 individuals. A factor alert; an adaptation from the contamination factor is proposed to identify individuals with high concentrations that possibly suffered contamination by anthropogenic origin. Grouping all species, the metal(loid)s with the highest concentrations were in decreasing order: Zn > Cu > Mn > Hg > As > Cd > Mo > V > Cr > Ba > Ni > Pb. Similar concentrations were observed for V, Mn, Cr and Pb among the three species. Pelagic birds showed higher levels of concentrations for Hg, As and Cd. Based on the correlations and multivariate analysis performed, the results indicate that the ecological niche factor has greater relevance in the bioaccumulation of these elements compared to the habitat. Although some individuals showed high concentrations in part of the trace elements, suggesting exposure to anthropic sources, the direct influence of oil production and exploration activities was not observed, suggesting that activities on the continent are the primary contamination source. The results of this work highlight the role of seabirds as sentinels for metal(loid)s, contributing to the knowledge of the occurrence of contaminants in the South Atlantic Ocean.}, } @article {pmid36948010, year = {2023}, author = {Hao, N and Sun, P and Zhao, W and Li, X}, title = {Application of a developed triple-classification machine learning model for carcinogenic prediction of hazardous organic chemicals to the US, EU, and WHO based on Chinese database.}, journal = {Ecotoxicology and environmental safety}, volume = {255}, number = {}, pages = {114806}, doi = {10.1016/j.ecoenv.2023.114806}, pmid = {36948010}, issn = {1090-2414}, mesh = {Bayes Theorem ; Carcinogenesis ; *Carcinogens/toxicity/chemistry ; *Hazardous Substances/chemistry/toxicity ; *Machine Learning ; *Organic Chemicals/toxicity/chemistry ; Support Vector Machine ; World Health Organization ; Algorithms ; United States ; European Union ; China ; Databases, Factual ; }, abstract = {Cancer, the second largest human disease, has become a major public health problem. The prediction of chemicals' carcinogenicity before their synthesis is crucial. In this paper, seven machine learning algorithms (i.e., Random Forest (RF), Logistic Regression (LR), Support Vector Machines (SVM), Complement Naive Bayes (CNB), K-Nearest Neighbor (KNN), XGBoost, and Multilayer Perceptron (MLP)) were used to construct the carcinogenicity triple classification prediction (TCP) model (i.e., 1A, 1B, Category 2). A total of 1444 descriptors of 118 hazardous organic chemicals were calculated by Discovery Studio 2020, Sybyl X-2.0 and PaDEL-Descriptor software. The constructed carcinogenicity TCP model was evaluated through five model evaluation indicators (i.e., Accuracy, Precision, Recall, F1 Score and AUC). The model evaluation results show that Accuracy, Precision, Recall, F1 Score and AUC evaluation indicators meet requirements (greater than 0.6). The accuracy of RF, LR, XGBoost, and MLP models for predicting carcinogenicity of Category 2 is 91.67%, 79.17%, 100%, and 100%, respectively. In addition, the constructed machine learning model in this study has potential for error correction. Taking XGBoost model as an example, the predicted carcinogenicity level of 1,2,3-Trichloropropane (96-18-4) is Category 2, but the actual carcinogenicity level is 1B. But the difference between Category 2 and 1B is only 0.004, indicating that the XGBoost is one optimum model of the seven constructed machine learning models. Besides, results showed that functional groups like chlorine and benzene ring might influence the prediction of carcinogenic classification. Therefore, considering functional group characteristics of chemicals before constructing the carcinogenicity prediction model of organic chemicals is recommended. The predicted carcinogenicity of the organic chemicals using the optimum machine leaning model (i.e., XGBoost) was also evaluated and verified by the toxicokinetics. The RF and XGBoost TCP models constructed in this paper can be used for carcinogenicity detection before synthesizing new organic substances. It also provides technical support for the subsequent management of organic chemicals.}, } @article {pmid36947137, year = {2023}, author = {James, JE and Nelson, PG and Masel, J}, title = {Differential Retention of Pfam Domains Contributes to Long-term Evolutionary Trends.}, journal = {Molecular biology and evolution}, volume = {40}, number = {4}, pages = {}, pmid = {36947137}, issn = {1537-1719}, mesh = {Animals ; *Proteome ; Protein Domains ; Probability ; Hydrophobic and Hydrophilic Interactions ; Databases, Protein ; }, abstract = {Protein domains that emerged more recently in evolution have a higher structural disorder and greater clustering of hydrophobic residues along the primary sequence. It is hard to explain how selection acting via descent with modification could act so slowly as not to saturate over the extraordinarily long timescales over which these trends persist. Here, we hypothesize that the trends were created by a higher level of selection that differentially affects the retention probabilities of protein domains with different properties. This hypothesis predicts that loss rates should depend on disorder and clustering trait values. To test this, we inferred loss rates via maximum likelihood for animal Pfam domains, after first performing a set of stringent quality control methods to reduce annotation errors. Intermediate trait values, matching those of ancient domains, are associated with the lowest loss rates, making our results difficult to explain with reference to previously described homology detection biases. Simulations confirm that effect sizes are of the right magnitude to produce the observed long-term trends. Our results support the hypothesis that differential domain loss slowly weeds out those protein domains that have nonoptimal levels of disorder and clustering. The same preferences also shape the differential diversification of Pfam domains, thereby further impacting proteome composition.}, } @article {pmid36947115, year = {2023}, author = {Bautista, J and Schueller, SM}, title = {Understanding the Adoption and Use of Digital Mental Health Apps Among College Students: Secondary Analysis of a National Survey.}, journal = {JMIR mental health}, volume = {10}, number = {}, pages = {e43942}, pmid = {36947115}, issn = {2368-7959}, abstract = {BACKGROUND: Increasing rates of mental health diagnoses in college students signal the need for new opportunities to support the mental health of this population. With many mental health apps being efficacious, they may be a promising resource for college campuses to provide support to their students. However, it is important to understand why (or why not) students might want to use apps and their desired features.

OBJECTIVE: Information on students' interest in mental health apps may inform which apps are to be provided and how campuses can support their use. This study aimed to understand the interest and hesitation in app use and the relationship between mental health needs, as defined by depression, anxiety, and positive mental health, and app use.

METHODS: The web-based Healthy Minds Study collected information on mental health needs, perceptions, and service use across colleges and universities. We used a sample of 989 participants who completed the survey between 2018 and 2020 and an elective module on digital mental health. We analyzed the elective module responses using a mixed methods approach, including both descriptive and inferential statistics, along with thematic coding for open text responses.

RESULTS: The Results from this study revealed that anxiety (b=-0.07; P<.001), but not depression (b=0.03; P=.12) and positive mental health (b=-0.02; P=.17), was a significant predictor of app adoption. Prominent qualitative findings indicated that the most desired app features included tips and advice, access to resources and information, and on-demand support that involves interaction throughout the day. The participants also suggested an overall desire for human interaction to be integrated into an app. As predicted, hesitancy was encountered, and the qualitative results suggested that there was a lack of interest in the adoption of mental health app and preference.

CONCLUSIONS: The findings from this study underscore that simply providing digital mental health apps as tools may be insufficient to support their use in college campuses. Although many students were open to using a mental health app, hesitation and uncertainty were common in the participant responses. Working with colleges and universities to increase digital literacy and provide resources that allow students to gauge when app use is appropriate may be helpful when implementing mental health apps as resources in college campuses.}, } @article {pmid36946676, year = {2023}, author = {Oliveira, HC and Seabra, AB and Kondak, S and Adedokun, OP and Kolbert, Z}, title = {Multilevel approach to plant-nanomaterial relationships: from cells to living ecosystems.}, journal = {Journal of experimental botany}, volume = {74}, number = {12}, pages = {3406-3424}, pmid = {36946676}, issn = {1460-2431}, mesh = {Ecosystem ; *Mycorrhizae/physiology ; Plants ; Plant Roots/physiology ; Symbiosis/physiology ; *Nanostructures ; }, abstract = {Due to their unique properties, nanomaterials behave peculiarly in biosystems. Regarding plants, the interactions of nanomaterials can be interpreted on a spatial scale: from local interactions in cells to systemic effects on whole plants and on ecosystems. Interpreted on a time scale, the effects of nanomaterials on plants may be immediate or subsequent. At the cellular level, the composition and structure of the cell wall and membranes are modified by nanomaterials, promoting internalization. The effects of nanomaterials on germination and seedling physiology and on the primary and secondary metabolism in the shoot are realized at organ and organism levels. Nanomaterials interact with the beneficial ecological partners of plants. The effects of nanomaterials on plant growth-promoting rhizobacteria and legume-rhizobia symbiosis can be stimulating or inhibitory, depending on the concentration and type of nanomaterial. Nanomaterials exert a negative effect on arbuscular mycorrhiza, and vice versa. Pollinators are exposed to nanomaterials, which may affect plant reproduction. The substances released by the roots influence the availability of nanomaterials in the rhizosphere, and components of plant cells trigger internalization, translocation, and transformation of nanomaterials. Understanding of the multilevel and bidirectional relationship between plants and nanomaterials is of great relevance.}, } @article {pmid36939939, year = {2023}, author = {Forootan, E}, title = {GIS-based slope-adjusted curve number methods for runoff estimation.}, journal = {Environmental monitoring and assessment}, volume = {195}, number = {4}, pages = {489}, pmid = {36939939}, issn = {1573-2959}, mesh = {*Water Movements ; *Geographic Information Systems ; Environmental Monitoring/methods ; Soil ; Hydrology ; Rain ; }, abstract = {Accurate estimation of surface runoff and determination of susceptible lands to runoff generation in ungauged watersheds were the problems for hydrologic engineering which could be predicted through a simple model such as Soil Conservation Service Curve Number (SCS-CN). Due to the slope effects on this method, slope adjustment for curve number was developed to improve its precision. So, the main objectives of this study were to apply GIS-based slope SCS-CN approaches for surface runoff estimation and compare the accuracy of three slope-adjusted models including: (a) model with three empirical parameters, (b) model with two parameters slope function, and (c) model with one parameter in the region located in the central part of Iran. For this purpose, soil texture, hydrologic soil group, land use, slope, and daily rainfall volume maps were utilized. In order to provide the curve number map of the study area, land use and hydrologic soil group layers built in Arc-GIS were intersected and the curve number was determined. Then, three slope adjustment equations were used to modify curve numbers of AMC-II by employing slope map. Finally, recorded runoff data of the hydrometric station were applied to assess the performance of the models through four statistical indicators of the root mean square error (RMSE), the Nash-Sutcliffe efficiency (E), the coefficient of determination [Formula: see text], and percent bias (PB). Land use map analysis showed that rangeland was the dominant land use, whereas the soil texture map specified the greatest and smallest area belonging to loam and sandy loam textures, respectively. Although the runoff results showed the overestimation of large rainfall values and underestimation for rainfall with less than 40 mm volume in both models, the values of E (0.78), RMSE (2), PB (16), and [Formula: see text] (0.88) revealed that eq. (a) with three empirical parameters was the most accurate equation. The maximum percent of runoff generated by rainfall for eqs. (a), (b), and (c) were 68.43, 67.28, and 51.57% which showed that bareland located in south part with the slope of more than 5% was susceptible to runoff generation and should be paid attention to watershed management.}, } @article {pmid36937826, year = {2022}, author = {Wabnitz, K and Schwienhorst-Stich, EM and Asbeck, F and Fellmann, CS and Gepp, S and Leberl, J and Mezger, NCS and Eichinger, M}, title = {National Planetary Health learning objectives for Germany: A steppingstone for medical education to promote transformative change.}, journal = {Frontiers in public health}, volume = {10}, number = {}, pages = {1093720}, pmid = {36937826}, issn = {2296-2565}, mesh = {Humans ; *Education, Medical ; Curriculum ; Health Education ; Delivery of Health Care ; Germany ; }, abstract = {Physicians play an important role in adapting to and mitigating the adverse health effects of the unfolding climate and ecological crises. To fully harness this potential, future physicians need to acquire knowledge, values, skills, and leadership attributes to care for patients presenting with environmental change-related conditions and to initiate and propel transformative change in healthcare and other sectors of society including, but not limited to, the decarbonization of healthcare systems, the transition to renewable energies and the transformation of transport and food systems. Despite the potential of Planetary Health Education (PHE) to support medical students in becoming agents of change, best-practice examples of mainstreaming PHE in medical curricula remain scarce both in Germany and internationally. The process of revising and updating the Medical Licensing Regulations and the National Competency-based Catalog of Learning Objectives for Medical Education in Germany provided a window of opportunity to address this implementation challenge. In this article, we describe the development and content of national Planetary Health learning objectives for Germany. We anticipate that the learning objectives will stimulate the development and implementation of innovative Planetary Health teaching, learning and exam formats in medical schools and inform similar initiatives in other health professions. The availability of Planetary Health learning objectives in other countries will provide opportunities for cross-country and interdisciplinary exchange of experiences and validation of content, thus supporting the consolidation of Planetary Health learning objectives and the improvement of PHE for all health professionals globally.}, } @article {pmid36934309, year = {2023}, author = {Newbury, JB and Arseneault, L and Moffitt, TE and Odgers, CL and Howe, LD and Bakolis, I and Reuben, A and Danese, A and Sugden, K and Williams, B and Rasmussen, LJH and Trotta, A and Ambler, AP and Fisher, HL}, title = {Socioenvironmental Adversity and Adolescent Psychotic Experiences: Exploring Potential Mechanisms in a UK Longitudinal Cohort.}, journal = {Schizophrenia bulletin}, volume = {49}, number = {4}, pages = {1042-1054}, pmid = {36934309}, issn = {1745-1701}, support = {R01 HD077482/HD/NICHD NIH HHS/United States ; F32 ES034238/ES/NIEHS NIH HHS/United States ; /DH_/Department of Health/United Kingdom ; G1002190/MRC_/Medical Research Council/United Kingdom ; F31 ES029358/ES/NIEHS NIH HHS/United States ; 218632/Z/19/Z/WT_/Wellcome Trust/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; MR/X010791/1/MRC_/Medical Research Council/United Kingdom ; F31ES029358/ES/NIEHS NIH HHS/United States ; 204823/Z/16/Z/WT_/Wellcome Trust/United Kingdom ; MR/M020894/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Child ; Humans ; Adolescent ; Adult ; *Psychotic Disorders/epidemiology/etiology/psychology ; Cross-Sectional Studies ; Social Environment ; Longitudinal Studies ; England/epidemiology ; }, abstract = {BACKGROUND AND HYPOTHESIS: Children exposed to socioenvironmental adversities (eg, urbanicity, pollution, neighborhood deprivation, crime, and family disadvantage) are more likely to subsequently develop subclinical psychotic experiences during adolescence (eg, hearing voices, paranoia). However, the pathways through which this occurs have not been previously investigated. We hypothesized that cognitive ability and inflammation would partly explain this association.

STUDY DESIGN: Data were utilized from the Environmental-Risk Longitudinal Twin Study, a cohort of 2232 children born in 1994-1995 in England and Wales and followed to age 18. Socioenvironmental adversities were measured from birth to age 10 and classified into physical risk (defined by high urbanicity and air pollution) and socioeconomic risk (defined by high neighborhood deprivation, neighborhood disorder, and family disadvantage). Cognitive abilities (overall, crystallized, fluid, and working memory) were assessed at age 12; and inflammatory markers (C-reactive protein, interleukin-6, soluble urokinase plasminogen activator receptor) were measured at age 18 from blood samples. Participants were interviewed at age 18 regarding psychotic experiences.

STUDY RESULTS: Higher physical risk and socioeconomic risk were associated with increased odds of psychotic experiences in adolescence. The largest mediation pathways were from socioeconomic risk via overall cognitive ability and crystallized ability, which accounted for ~11% and ~19% of the association with psychotic experiences, respectively. No statistically significant pathways were found via inflammatory markers in exploratory (partially cross-sectional) analyses.

CONCLUSIONS: Cognitive ability, especially crystallized ability, may partly explain the association between childhood socioenvironmental adversity and adolescent psychotic experiences. Interventions to support cognitive development among children living in disadvantaged settings could buffer them against developing subclinical psychotic phenomena.}, } @article {pmid36932341, year = {2023}, author = {Kasmi, Y and Eschbach, E and Hanel, R}, title = {Mare-MAGE curated reference database of fish mitochondrial genes.}, journal = {BMC genomic data}, volume = {24}, number = {1}, pages = {18}, pmid = {36932341}, issn = {2730-6844}, mesh = {Animals ; Databases, Nucleic Acid ; DNA Barcoding, Taxonomic ; *Fishes/genetics ; *Genes, Mitochondrial ; }, abstract = {Biodiversity assessment approaches based on molecular biology techniques such as metabarcoding, RAD-seq, or SnaPshot sequencing are increasingly applied in assessing marine and aquatic ecosystems. Here we present a new reference database for fish meta-barcoding based on mitochondrial genes. The Mare-MAGE database contains quality-checked sequences of the mitochondrial 12S ribosomal RNA and Cytochrome c Oxidase I gene. All sequences were obtained from the National Center for Biotechnology Information- GenBank (NBCI-GenBank), the European Nucleotide Archive (ENA), AquaGene Database and BOLD database, and have undergone intensive processing. They were checked for false annotations and non-target anomalies, according to the Integrated Taxonomic Information System (ITIS) and FishBase. The dataset is compiled in ARB-Home, FASTA and Qiime2 formats, and is publicly available from the Mare-MAGE database website (http://mare-mage.weebly.com/). It includes altogether 231,333 COI and 12S rRNA gene sequences of fish, covering 19,506 species of 4,058 genera and 586 families.}, } @article {pmid36931511, year = {2023}, author = {Zhang, B and Zheng, T and Zheng, X and Jiang, S and Cao, M and Walther, M and Lu, C}, title = {Dynamics of upstream saltwater intrusion driven by tidal river in coastal aquifers.}, journal = {The Science of the total environment}, volume = {877}, number = {}, pages = {162857}, doi = {10.1016/j.scitotenv.2023.162857}, pmid = {36931511}, issn = {1879-1026}, abstract = {For the coastal aquifers, recent research have shown that the tidal has a significant effect on saltwater intrusion in the near-shore aquifer. However, it is currently unclear how the tidal river contributes to the groundwater flow and salinity distribution in the upstream aquifer of the estuary. This study examined the effects of a tidal river on the dynamic characteristics of groundwater flow and salt transport in a tidal river-coastal aquifer system using field monitoring data and numerical simulations. It was found that changes in tidal-river level led to the reversal of groundwater flow. For a tidal cycle, the maximum area of seawater intrusion is about 41.16 km[2] at the end of the high tide stage. Then the area gradually decreased to 39.02 km[2] at the end of the low tide stage. More than 2 km[2] area variation can be observed in a tidal cycle. Compared to the low tide stage, the area of SWI increased by 5 % at high tide stage. The SWI region was also spreading landward from the tidal river. In addition, we quantified the water exchange and salt flux between the tidal river and aquifer. When the tidal fell below the level of the riverbed, the water exchange rate was stabilized at about -1.6 m/h. The negative value indicated that the river was recharged by the groundwater. With the increasing of tidal water level, the water exchange rate gradually changes from negative to positive and reached the maximum value of 3.2 m/h at the beginning of the falling tide stage. The presence of a physical river dam can amplify the difference in water level between high and low tides, thereby enhancing the influence of a tidal river on water exchange and salt flux. The findings lay the foundation for gaining a comprehensive understanding of the tidal river on groundwater flow and salt transport in upstream aquifers.}, } @article {pmid36926380, year = {2022}, author = {Boyes, D and , and , and , and , and , and Parkerson, L and , }, title = {The genome sequence of the garden grass-veneer, Chrysoteuchia culmella (Linnaeus, 1758).}, journal = {Wellcome open research}, volume = {7}, number = {}, pages = {248}, pmid = {36926380}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual male Chrysoteuchia culmella (the garden grass-veneer; Arthropoda; Insecta; Lepidoptera; Crambidae). The genome sequence is 645 megabases in span. The majority of the assembly (99.81%) is scaffolded into 31 chromosomal pseudomolecules with the Z sex chromosome assembled. The complete mitochondrial genome was also assembled and is 15.4 kilobases in length. Gene annotation of this assembly on Ensembl has identified 21,251 protein coding genes.}, } @article {pmid36925815, year = {2022}, author = {Viner, AC and Malata, MP and Mtende, M and Membe-Gadama, G and Masamba, M and Makwakwa, E and Bamuya, C and Lissauer, D and Stock, SJ and Norman, JE and Reynolds, RM and Magowan, B and Freyne, B and Gadama, L and Cunningham-Burley, S and Nyondo-Mipando, L and Chipeta, E}, title = {Implementation of a novel ultrasound training programme for midwives in Malawi: A mixed methods evaluation using the RE-AIM framework.}, journal = {Frontiers in health services}, volume = {2}, number = {}, pages = {953677}, pmid = {36925815}, issn = {2813-0146}, support = {/WT_/Wellcome Trust/United Kingdom ; MR/N022556/1/MRC_/Medical Research Council/United Kingdom ; MR/T038683/1/MRC_/Medical Research Council/United Kingdom ; }, abstract = {INTRODUCTION: Despite recommendation that all women receive an ultrasound in pregnancy prior to 24 weeks', this remains unavailable to many women in low-income countries where trained practitioners are scarce. Although many programmes have demonstrated efficacy, few have achieved longterm sustainability, with a lack of information about how best to implement such programmes. This mixed-methods study aimed to evaluate the implementation of a novel education package to teach ultrasound-naive midwives in Malawi basic obstetric ultrasound, assessing its impact in the context of the Reach, Effectiveness, Adoption, Implementation and Maintenance (RE-AIM) framework.

METHODS: The study ran across six sites in Malawi between October 2020 and June 2021, encompassing three phases; pre-implementation, implementation and post-implementation. Twenty nine midwives underwent a bespoke education package with matched pre and post course surveys assessed their knowledge, attitudes and confidence and "hands on" assessments evaluating practical skills. Training evaluation forms and in-depth interviews explored their satisfaction with the package, with repeat assessment and remote image review evaluating maintenance of skills.

RESULTS: 28/29 midwives completed the training, with significant increases in knowledge, confidence and practical skills. Adherence to the education package varied, however many changes to the proposed methodology were adaptive and appeared to facilitate the efficacy of the programme. Unfortunately, despite reporting approval regarding the training itself, satisfaction regarding supervision and follow up was mixed, reflecting the difficulties encountered with providing ongoing in-person and remote support.

CONCLUSION: This programme was successful in improving trainees' knowledge, confidence and skill in performing basic obstetric ultrasound, largely on account of an adaptive approach to implementation. The maintenance of ongoing support was challenging, reflected by trainee dissatisfaction. By evaluating the success of this education package based on its implementation and not just its efficacy, we have generated new insights into the barriers to sustainable upscale, specifically those surrounding maintenance.}, } @article {pmid36921339, year = {2023}, author = {Zhang, H and Wang, X and Song, R and Ding, W and Li, F and Ji, L}, title = {Emerging Metabolic Profiles of Sulfonamide Antibiotics by Cytochromes P450: A Computational-Experimental Synergy Study on Emerging Pollutants.}, journal = {Environmental science & technology}, volume = {57}, number = {13}, pages = {5368-5379}, doi = {10.1021/acs.est.3c00071}, pmid = {36921339}, issn = {1520-5851}, mesh = {Humans ; *Anti-Bacterial Agents ; *Environmental Pollutants ; Sulfamethoxazole/metabolism ; Sulfanilamide ; Sulfonamides ; Cytochrome P-450 Enzyme System/metabolism ; Metabolome ; }, abstract = {Metabolism, especially by CYP450 enzymes, is the main reason for mediating the toxification and detoxification of xenobiotics in humans, while some uncommon metabolic pathways, especially for emerging pollutants, probably causing idiosyncratic toxicity are easily overlooked. The pollution of sulfonamide antibiotics in aqueous system has attracted increasing public attention. Hydroxylation of the central amine group can trigger a series of metabolic processes of sulfonamide antibiotics in humans; however, this work parallelly reported the coupling and fragmenting initiated by amino H-abstraction of sulfamethoxazole (SMX) catalyzed by human CYP450 enzymes. Elucidation of the emerging metabolic profiles was mapped via a multistep synergy between computations and experiments, involving preliminary DFT computations and in vitro and in vivo assays, profiling adverse effects, and rationalizing the fundamental factors via targeted computations. Especially, the confirmed SMX dimer was shown to potentially act as a metabolism disruptor in humans, while spin aromatic delocalization resulting in the low electron donor ability of amino radicals was revealed as the fundamental factor to enable coupling of sulfonamide antibiotics by CYP450 through the nonconventional nonrebound pathway. This work may further strengthen the synergistic use of computations prior to experiments to avoid wasteful experimental screening efforts in environmental chemistry and toxicology.}, } @article {pmid36921166, year = {2023}, author = {Morais, LS and Pimentel, SVT and Kawa, H and Fonseca, SC}, title = {Temporal trend of congenital syphilis in the most populous municipality of metropolitan region II of Rio de Janeiro state.}, journal = {Revista paulista de pediatria : orgao oficial da Sociedade de Pediatria de Sao Paulo}, volume = {41}, number = {}, pages = {e2021337}, pmid = {36921166}, issn = {1984-0462}, mesh = {Pregnancy ; Adolescent ; Humans ; Female ; *Syphilis, Congenital/epidemiology ; Brazil/epidemiology ; Prenatal Care ; Incidence ; Databases, Factual ; }, abstract = {OBJECTIVE: This study aimed to explore the temporal trend in congenital syphilis, according to sociodemographic and prenatal care in the city of São Gonçalo - Rio de Janeiro, from 2007 to 2018.

METHODS: Ecological time series study, with data from SINAN (Information System for Notifiable Diseases) and SINASC (Information System on Live Births databases). We calculated annual incidence (per 1,000 live births) according to sociodemographic and prenatal variables. For the same variables, we calculated trends by logarithmic regression (Joinpoint Regression), estimating the annual percentage change.

RESULTS: A total of 2,420 cases were reported from 2007 to 2018, with an increasing trend: 64.9% per year (2010-2013) and 24.9% (2013-2018). In 2018, the highest rates were in adolescents (90.6/1,000 live births), black women (87.6/1,000 live births), low-educated women (122.8/1,000 live births), and those without prenatal care (677.4/1,000 live births). The annual percentage change of these categories was, respectively, 37.3% (2010-2018), 33.5% (2012-2018), 39.9% (2014-2018), and 85.0% (2011-2015), but all categories showed a crescent trend.

CONCLUSIONS: We identified high congenital syphilis incidences and crescent trends, especially in more vulnerable groups, pointing to social and healthcare inequalities. Prenatal care needs to be more comprehensive and qualified, primarily for young, low-educated, and black women.}, } @article {pmid36920898, year = {2023}, author = {Helmer, EH and Kay, S and Marcano-Vega, H and Powers, JS and Wood, TE and Zhu, X and Gwenzi, D and Ruzycki, TS}, title = {Multiscale predictors of small tree survival across a heterogeneous tropical landscape.}, journal = {PloS one}, volume = {18}, number = {3}, pages = {e0280322}, pmid = {36920898}, issn = {1932-6203}, mesh = {*Ecosystem ; Biomass ; Wood ; Introduced Species ; *Cyclonic Storms ; Tropical Climate ; }, abstract = {Uncertainties about controls on tree mortality make forest responses to land-use and climate change difficult to predict. We tracked biomass of tree functional groups in tropical forest inventories across Puerto Rico and the U.S. Virgin Islands, and with random forests we ranked 86 potential predictors of small tree survival (young or mature stems 2.5-12.6 cm diameter at breast height). Forests span dry to cloud forests, range in age, geology and past land use and experienced severe drought and storms. When excluding species as a predictor, top predictors are tree crown ratio and height, two to three species traits and stand to regional factors reflecting local disturbance and the system state (widespread recovery, drought, hurricanes). Native species, and species with denser wood, taller maximum height, or medium typical height survive longer, but short trees and species survive hurricanes better. Trees survive longer in older stands and with less disturbed canopies, harsher geoclimates (dry, edaphically dry, e.g., serpentine substrates, and highest-elevation cloud forest), or in intervals removed from hurricanes. Satellite image phenology and bands, even from past decades, are top predictors, being sensitive to vegetation type and disturbance. Covariation between stand-level species traits and geoclimate, disturbance and neighboring species types may explain why most neighbor variables, including introduced vs. native species, had low or no importance, despite univariate correlations with survival. As forests recovered from a hurricane in 1998 and earlier deforestation, small trees of introduced species, which on average have lighter wood, died at twice the rate of natives. After hurricanes in 2017, the total biomass of trees ≥12.7 cm dbh of the introduced species Spathodea campanulata spiked, suggesting that more frequent hurricanes might perpetuate this light-wooded species commonness. If hurricane recovery favors light-wooded species while drought favors others, climate change influences on forest composition and ecosystem services may depend on the frequency and severity of extreme climate events.}, } @article {pmid36918541, year = {2023}, author = {Young, WJ and Haessler, J and Benjamins, JW and Repetto, L and Yao, J and Isaacs, A and Harper, AR and Ramirez, J and Garnier, S and van Duijvenboden, S and Baldassari, AR and Concas, MP and Duong, T and Foco, L and Isaksen, JL and Mei, H and Noordam, R and Nursyifa, C and Richmond, A and Santolalla, ML and Sitlani, CM and Soroush, N and Thériault, S and Trompet, S and Aeschbacher, S and Ahmadizar, F and Alonso, A and Brody, JA and Campbell, A and Correa, A and Darbar, D and De Luca, A and Deleuze, JF and Ellervik, C and Fuchsberger, C and Goel, A and Grace, C and Guo, X and Hansen, T and Heckbert, SR and Jackson, RD and Kors, JA and Lima-Costa, MF and Linneberg, A and Macfarlane, PW and Morrison, AC and Navarro, P and Porteous, DJ and Pramstaller, PP and Reiner, AP and Risch, L and Schotten, U and Shen, X and Sinagra, G and Soliman, EZ and Stoll, M and Tarazona-Santos, E and Tinker, A and Trajanoska, K and Villard, E and Warren, HR and Whitsel, EA and Wiggins, KL and Arking, DE and Avery, CL and Conen, D and Girotto, G and Grarup, N and Hayward, C and Jukema, JW and Mook-Kanamori, DO and Olesen, MS and Padmanabhan, S and Psaty, BM and Pattaro, C and Ribeiro, ALP and Rotter, JI and Stricker, BH and van der Harst, P and van Duijn, CM and Verweij, N and Wilson, JG and Orini, M and Charron, P and Watkins, H and Kooperberg, C and Lin, HJ and Wilson, JF and Kanters, JK and Sotoodehnia, N and Mifsud, B and Lambiase, PD and Tereshchenko, LG and Munroe, PB}, title = {Genetic architecture of spatial electrical biomarkers for cardiac arrhythmia and relationship with cardiovascular disease.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {1411}, pmid = {36918541}, issn = {2041-1723}, support = {CH/1992001/6764/BHF_/British Heart Foundation/United Kingdom ; MC_UU_00007/10/MRC_/Medical Research Council/United Kingdom ; R56 HL118277/HL/NHLBI NIH HHS/United States ; MC_PC_20029/MRC_/Medical Research Council/United Kingdom ; R01 HL105756/HL/NHLBI NIH HHS/United States ; R01 HL118277/HL/NHLBI NIH HHS/United States ; K24 HL148521/HL/NHLBI NIH HHS/United States ; MR/N025083/1/MRC_/Medical Research Council/United Kingdom ; MR/R017468/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Humans ; *Cardiovascular Diseases/genetics ; *Atrioventricular Block ; Genome-Wide Association Study ; Risk Factors ; Arrhythmias, Cardiac/genetics ; Electrocardiography/methods ; Biomarkers ; }, abstract = {The 3-dimensional spatial and 2-dimensional frontal QRS-T angles are measures derived from the vectorcardiogram. They are independent risk predictors for arrhythmia, but the underlying biology is unknown. Using multi-ancestry genome-wide association studies we identify 61 (58 previously unreported) loci for the spatial QRS-T angle (N = 118,780) and 11 for the frontal QRS-T angle (N = 159,715). Seven out of the 61 spatial QRS-T angle loci have not been reported for other electrocardiographic measures. Enrichments are observed in pathways related to cardiac and vascular development, muscle contraction, and hypertrophy. Pairwise genome-wide association studies with classical ECG traits identify shared genetic influences with PR interval and QRS duration. Phenome-wide scanning indicate associations with atrial fibrillation, atrioventricular block and arterial embolism and genetically determined QRS-T angle measures are associated with fascicular and bundle branch block (and also atrioventricular block for the frontal QRS-T angle). We identify potential biology involved in the QRS-T angle and their genetic relationships with cardiovascular traits and diseases, may inform future research and risk prediction.}, } @article {pmid36914632, year = {2023}, author = {Kohyama, TI and Sheil, D and Sun, IF and Niiyama, K and Suzuki, E and Hiura, T and Nishimura, N and Hoshizaki, K and Wu, SH and Chao, WC and Nur Hajar, ZS and Rahajoe, JS and Kohyama, TS}, title = {Contribution of tree community structure to forest productivity across a thermal gradient in eastern Asia.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {1113}, pmid = {36914632}, issn = {2041-1723}, mesh = {Humans ; *Trees ; *Forests ; Biomass ; Wood ; Asia, Eastern ; Tropical Climate ; }, abstract = {Despite their fundamental importance the links between forest productivity, diversity and climate remain contentious. We consider whether variation in productivity across climates reflects adjustment among tree species and individuals, or changes in tree community structure. We analysed data from 60 plots of humid old-growth forests spanning mean annual temperatures (MAT) from 2.0 to 26.6 °C. Comparing forests at equivalent aboveground biomass (160 Mg C ha[-1]), tropical forests ≥24 °C MAT averaged more than double the aboveground woody productivity of forests <12 °C (3.7 ± 0.3 versus 1.6 ± 0.1 Mg C ha[-1] yr[-1]). Nonetheless, species with similar standing biomass and maximum stature had similar productivity across plots regardless of temperature. We find that differences in the relative contribution of smaller- and larger-biomass species explained 86% of the observed productivity differences. Species-rich tropical forests are more productive than other forests due to the high relative productivity of many short-stature, small-biomass species.}, } @article {pmid36911337, year = {2023}, author = {Lim, T and Lee, K and Kim, RH and Ryu, J and Cha, KH and Park, SY and Koo, SY and Hwang, KT}, title = {Effects of black raspberry extract on gut microbiota, microbial metabolites, and expressions of the genes involved in cholesterol and bile acid metabolisms in rats fed excessive choline with a high-fat diet.}, journal = {Food science and biotechnology}, volume = {32}, number = {4}, pages = {577-587}, pmid = {36911337}, issn = {2092-6456}, abstract = {UNLABELLED: In our previous study, black raspberry (BR) reduced the serum levels of trimethylamine-N-oxide and cholesterol in rats fed excessive choline with a high-fat diet (HFC). We hypothesized that gut microbiota could play a crucial role in the production of trimethylamine and microbial metabolites, and BR could influence gut microbial composition. This study aimed to elucidate the role of BR on changes in gut microbiota and microbial metabolites in the rats. The phylogenetic diversity of gut microbiota was reduced in the rats fed HFC, while that in the BR-fed group was restored. The BR supplementation enriched Bifidobacterium and reduced Clostridium cluster XIVa. In the BR-fed group, most cecal bile acids and hippuric acid increased, while serum lithocholic acid was reduced. The BR supplementation upregulated Cyp7a1 and downregulated Srebf2. These results suggest that BR extract may change gut bacterial community, modulate bile acids, and regulate gene expression toward reducing cholesterol.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s10068-023-01267-4.}, } @article {pmid36911308, year = {2023}, author = {Martinez, ND}, title = {Predicting ecosystem metaphenome from community metagenome: A grand challenge for environmental biology.}, journal = {Ecology and evolution}, volume = {13}, number = {3}, pages = {e9872}, pmid = {36911308}, issn = {2045-7758}, abstract = {Elucidating how an organism's characteristics emerge from its DNA sequence has been one of the great triumphs of biology. This triumph has cumulated in sophisticated computational models that successfully predict how an organism's detailed phenotype emerges from its specific genotype. Inspired by that effort's vision and empowered by its methodologies, a grand challenge is described here that aims to predict the biotic characteristics of an ecosystem, its metaphenome, from nucleic acid sequences of all the species in its community, its metagenome. Meeting this challenge would integrate rapidly advancing abilities of environmental nucleic acids (eDNA and eRNA) to identify organisms, their ecological interactions, and their evolutionary relationships with advances in mechanistic models of complex ecosystems. Addressing the challenge would help integrate ecology and evolutionary biology into a more unified and successfully predictive science that can better help describe and manage ecosystems and the services they provide to humanity.}, } @article {pmid36901248, year = {2023}, author = {Zeng, L and Liu, C}, title = {Exploring Factors Affecting Urban Park Use from a Geospatial Perspective: A Big Data Study in Fuzhou, China.}, journal = {International journal of environmental research and public health}, volume = {20}, number = {5}, pages = {}, pmid = {36901248}, issn = {1660-4601}, support = {FJ2022C070//Social Science Foundation of Fujian, China/ ; }, mesh = {Humans ; Urban Population ; *Parks, Recreational ; *Big Data ; Cities ; China ; }, abstract = {Promoting research on urban park use is important for developing the ecological and environmental health benefits of parks. This study proposes uniquely integrated methods combined with big data to measure urban park use. It combines comprehensive geographic detectors and multiscale geographically weighted regression from a geospatial perspective to quantify the individual and interactive effects of the parks' characteristics, accessibility, and surrounding environment features on weekday and weekend park use. The study also explores the degree of influence of spatial changes. The results indicate that the park-surrounding facilities and services factor contributed most to use, while its interaction effect with park service capacity had the greatest impact on park use. The interaction effects showed binary or nonlinear enhancement. This suggests that park use should be promoted within multiple dimensions. Many influencing factors had significant changes in the geographic space, suggesting that city-level park zoning construction should be adopted. Finally, park use was found to be affected by users' subjective preference on weekends and convenience factors on weekdays. These findings provide a theoretical basis for the influencing mechanisms of urban park use, which can help urban planners and policymakers formulate more specific policies to successfully manage and plan urban parks.}, } @article {pmid36900138, year = {2023}, author = {Würstle, S and Hapfelmeier, A and Karapetyan, S and Studen, F and Isaakidou, A and Schneider, T and Schmid, RM and von Delius, S and Gundling, F and Burgkart, R and Obermeier, A and Mayr, U and Ringelhan, M and Rasch, S and Lahmer, T and Geisler, F and Turner, PE and Chan, BK and Spinner, CD and Schneider, J}, title = {Differentiation of Spontaneous Bacterial Peritonitis from Secondary Peritonitis in Patients with Liver Cirrhosis: Retrospective Multicentre Study.}, journal = {Diagnostics (Basel, Switzerland)}, volume = {13}, number = {5}, pages = {}, pmid = {36900138}, issn = {2075-4418}, support = {UL1 TR001863/TR/NCATS NIH HHS/United States ; }, abstract = {Ascitic fluid infection is a serious complication of liver cirrhosis. The distinction between the more common spontaneous bacterial peritonitis (SBP) and the less common secondary peritonitis in patients with liver cirrhosis is crucial due to the varying treatment approaches. This retrospective multicentre study was conducted in three German hospitals and analysed 532 SBP episodes and 37 secondary peritonitis episodes. Overall, >30 clinical, microbiological, and laboratory parameters were evaluated to identify key differentiation criteria. Microbiological characteristics in ascites followed by severity of illness and clinicopathological parameters in ascites were the most important predictors identified by a random forest model to distinguish between SBP and secondary peritonitis. To establish a point-score model, a least absolute shrinkage and selection operator (LASSO) regression model selected the ten most promising discriminatory features. By aiming at a sensitivity of 95% either to rule out or rule in SBP episodes, two cut-off scores were defined, dividing patients with infected ascites into a low-risk (score ≥ 45) and high-risk group (score < 25) for secondary peritonitis. Overall, the discrimination of secondary peritonitis from SBP remains challenging. Our univariable analyses, random forest model, and LASSO point score may help clinicians with the crucial differentiation between SBP and secondary peritonitis.}, } @article {pmid36899307, year = {2023}, author = {Chan, YO and Dietz, N and Zeng, S and Wang, J and Flint-Garcia, S and Salazar-Vidal, MN and Škrabišová, M and Bilyeu, K and Joshi, T}, title = {The Allele Catalog Tool: a web-based interactive tool for allele discovery and analysis.}, journal = {BMC genomics}, volume = {24}, number = {1}, pages = {107}, pmid = {36899307}, issn = {1471-2164}, support = {1920-152-0131-C//United Soybean Board/ ; 2220-152-0202//United Soybean Board/ ; }, mesh = {*Alleles ; *Internet ; *Software ; Mutation ; *Datasets as Topic ; *Glycine max/genetics ; *Zea mays/genetics ; *Arabidopsis/genetics ; Data Visualization ; Genes, Plant/genetics ; Pigmentation/genetics ; Plant Dormancy/genetics ; Gene Frequency ; Amino Acid Substitution ; Genotype ; Metadata ; *Data Mining/methods ; }, abstract = {BACKGROUND: The advancement of sequencing technologies today has made a plethora of whole-genome re-sequenced (WGRS) data publicly available. However, research utilizing the WGRS data without further configuration is nearly impossible. To solve this problem, our research group has developed an interactive Allele Catalog Tool to enable researchers to explore the coding region allelic variation present in over 1,000 re-sequenced accessions each for soybean, Arabidopsis, and maize.

RESULTS: The Allele Catalog Tool was designed originally with soybean genomic data and resources. The Allele Catalog datasets were generated using our variant calling pipeline (SnakyVC) and the Allele Catalog pipeline (AlleleCatalog). The variant calling pipeline is developed to parallelly process raw sequencing reads to generate the Variant Call Format (VCF) files, and the Allele Catalog pipeline takes VCF files to perform imputations, functional effect predictions, and assemble alleles for each gene to generate curated Allele Catalog datasets. Both pipelines were utilized to generate the data panels (VCF files and Allele Catalog files) in which the accessions of the WGRS datasets were collected from various sources, currently representing over 1,000 diverse accessions for soybean, Arabidopsis, and maize individually. The main features of the Allele Catalog Tool include data query, visualization of results, categorical filtering, and download functions. Queries are performed from user input, and results are a tabular format of summary results by categorical description and genotype results of the alleles for each gene. The categorical information is specific to each species; additionally, available detailed meta-information is provided in modal popups. The genotypic information contains the variant positions, reference or alternate genotypes, the functional effect classes, and the amino-acid changes of each accession. Besides that, the results can also be downloaded for other research purposes.

CONCLUSIONS: The Allele Catalog Tool is a web-based tool that currently supports three species: soybean, Arabidopsis, and maize. The Soybean Allele Catalog Tool is hosted on the SoyKB website (https://soykb.org/SoybeanAlleleCatalogTool/), while the Allele Catalog Tool for Arabidopsis and maize is hosted on the KBCommons website (https://kbcommons.org/system/tools/AlleleCatalogTool/Zmays and https://kbcommons.org/system/tools/AlleleCatalogTool/Athaliana). Researchers can use this tool to connect variant alleles of genes with meta-information of species.}, } @article {pmid36899120, year = {2023}, author = {Yilanci, V and Candan, G and Shah, MI}, title = {Identifying the roles of energy and economic factors on environmental degradation in MINT economies: a hesitant fuzzy analytic hierarchy process.}, journal = {Environmental science and pollution research international}, volume = {30}, number = {19}, pages = {55768-55781}, pmid = {36899120}, issn = {1614-7499}, mesh = {*Analytic Hierarchy Process ; Carbon Dioxide ; Cross-Sectional Studies ; Economic Development ; Economic Factors ; Investments ; Renewable Energy ; }, abstract = {Globally, research communities have been studying the different determinants of environmental degradation or pollution using different contexts and methods. In this study, we identify several energy and economic factors, such as energy consumption (EC), gross domestic product (GDP), energy production (EP), urbanization (URB), and foreign direct investment (FDI) as the most effective factors of environmental degradation by obtaining several environmental researchers' opinions and using the hesitant fuzzy analytic hierarchy process. In the later stage of the analysis, we use these variables as regressors of the ecological footprint (EF) as a proxy for environmental degradation. Since we find evidence of cross-sectional dependence among the members of the variables, we use second-generational panel tests. First, we test the stationarity of the variables using the cross-sectionally augmented IPS (CIPS) panel unit test. The results show that the regressors have different orders of integration. So, we employ the Durbin-Hausman panel cointegration test to test the existence of a long-run relationship between the variables. Having found a long-run relationship, we estimate the long-run coefficients using the common correlated effects mean group estimator, which reveals that energy consumption has an increasing effect on the EF in Indonesia and Turkey, while energy production has a negative impact in Mexico and Turkey. While GDP has an increasing effect in all countries, FDI has a similar effect in only Indonesia. Moreover, URB decreases the ecological footprint in Nigeria, while it increases in Turkey. Our approach to the evaluation of environmental degradation can be generalized to other regions as well as where there is a significant need to understand the roles of different drivers on environmental degradation or pollution.}, } @article {pmid36895518, year = {2022}, author = {Boyes, D and , and , and , and , and , and Lees, D and , }, title = {The genome sequence of the yellow-legged clearwing, Synanthedon vespiformis (Linnaeus, 1761).}, journal = {Wellcome open research}, volume = {7}, number = {}, pages = {233}, pmid = {36895518}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual male Synanthedon vespiformis (the yellow-legged clearwing; Arthropoda; Insecta; Lepidoptera; Sesiidae). The genome sequence is 287 megabases in span. Of the assembly, 100% is scaffolded into 31 chromosomal pseudomolecules with the Z sex chromosome assembled. The complete mitochondrial genome was also assembled and is 17.3 kilobases in length.}, } @article {pmid36894986, year = {2023}, author = {de Nies, L and Galata, V and Martin-Gallausiaux, C and Despotovic, M and Busi, SB and Snoeck, CJ and Delacour, L and Budagavi, DP and Laczny, CC and Habier, J and Lupu, PC and Halder, R and Fritz, JV and Marques, T and Sandt, E and O'Sullivan, MP and Ghosh, S and Satagopam, V and , and Krüger, R and Fagherazzi, G and Ollert, M and Hefeng, FQ and May, P and Wilmes, P}, title = {Altered infective competence of the human gut microbiome in COVID-19.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {46}, pmid = {36894986}, issn = {2049-2618}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *COVID-19 ; SARS-CoV-2/genetics ; *Microbiota ; Multiomics ; }, abstract = {BACKGROUND: Infections with SARS-CoV-2 have a pronounced impact on the gastrointestinal tract and its resident microbiome. Clear differences between severe cases of infection and healthy individuals have been reported, including the loss of commensal taxa. We aimed to understand if microbiome alterations including functional shifts are unique to severe cases or a common effect of COVID-19. We used high-resolution systematic multi-omic analyses to profile the gut microbiome in asymptomatic-to-moderate COVID-19 individuals compared to a control group.

RESULTS: We found a striking increase in the overall abundance and expression of both virulence factors and antimicrobial resistance genes in COVID-19. Importantly, these genes are encoded and expressed by commensal taxa from families such as Acidaminococcaceae and Erysipelatoclostridiaceae, which we found to be enriched in COVID-19-positive individuals. We also found an enrichment in the expression of a betaherpesvirus and rotavirus C genes in COVID-19-positive individuals compared to healthy controls.

CONCLUSIONS: Our analyses identified an altered and increased infective competence of the gut microbiome in COVID-19 patients. Video Abstract.}, } @article {pmid36893405, year = {2023}, author = {Mallinson, DC and Elwert, F and Ehrenthal, DB}, title = {Spillover Effects of Prenatal Care Coordination on Older Siblings Beyond the Mother-Infant Dyad.}, journal = {Medical care}, volume = {61}, number = {4}, pages = {206-215}, pmid = {36893405}, issn = {1537-1948}, support = {P2C HD042849/HD/NICHD NIH HHS/United States ; T32 HD007014/HD/NICHD NIH HHS/United States ; UL1 TR000427/TR/NCATS NIH HHS/United States ; UL1 TR002373/TR/NCATS NIH HHS/United States ; }, mesh = {Pregnancy ; Child ; Female ; Infant ; Humans ; Adolescent ; *Prenatal Care ; Siblings ; Mothers ; Wisconsin ; *Maternal Health Services ; }, abstract = {BACKGROUND: Pregnancy care coordination increases preventive care receipt for mothers and infants. Whether such services affect other family members' health care is unknown.

OBJECTIVE: To estimate the spillover effect of maternal exposure to Wisconsin Medicaid's Prenatal Care Coordination (PNCC) program during pregnancy with a younger sibling on the preventive care receipt for an older child.

RESEARCH DESIGN: Gain-score regressions-a sibling fixed effects strategy-estimated spillover effects while controlling for unobserved family-level confounders.

SUBJECTS: Data came from a longitudinal cohort of linked Wisconsin birth records and Medicaid claims. We sampled 21,332 sibling pairs (one older; one younger) who were born during 2008-2015, who were <4 years apart in age, and whose births were Medicaid-covered. In all, 4773 (22.4%) mothers received PNCC during pregnancy with the younger sibling.

MEASURES: The exposure was maternal PNCC receipt during pregnancy with the younger sibling (none; any). The outcome was the older sibling's number of preventive care visits or preventive care services in the younger sibling's first year of life.

RESULTS: Overall, maternal exposure to PNCC during pregnancy with the younger sibling did not affect older siblings' preventive care. However, among siblings who were 3 to <4 years apart in age, there was a positive spillover on the older sibling's receipt of care by 0.26 visits (95% CI: 0.11, 0.40 visits) and by 0.34 services (95% CI: 0.12, 0.55 services).

CONCLUSION: PNCC may only have spillover effects on siblings' preventive care in selected subpopulations but not in the broader population of Wisconsin families.}, } @article {pmid36893162, year = {2023}, author = {Rubenstein, DR and Solomon, J}, title = {Target-enriched enzymatic methyl sequencing: Flexible, scalable and inexpensive hybridization capture for quantifying DNA methylation.}, journal = {PloS one}, volume = {18}, number = {3}, pages = {e0282672}, pmid = {36893162}, issn = {1932-6203}, mesh = {*DNA Methylation ; Sequence Analysis, DNA/methods ; Reproducibility of Results ; Nucleic Acid Hybridization ; *Computational Biology ; High-Throughput Nucleotide Sequencing/methods ; CpG Islands/genetics ; }, abstract = {The increasing interest in studying DNA methylation to understand how traits or diseases develop requires new and flexible approaches for quantifying DNA methylation in a diversity of organisms. In particular, we need efficient yet cost-effective ways to measure CpG methylation states over large and complete regions of the genome. Here, we develop TEEM-Seq (target-enriched enzymatic methyl sequencing), a method that combines enzymatic methyl sequencing with a custom-designed hybridization capture bait set that can be scaled to reactions including large numbers of samples in any species for which a reference genome is available. Using DNA from a passerine bird, the superb starling (Lamprotornis superbus), we show that TEEM-Seq is able to quantify DNA methylation states similarly well to the more traditional approaches of whole-genome and reduced-representation sequencing. Moreover, we demonstrate its reliability and repeatability, as duplicate libraries from the same samples were highly correlated. Importantly, the downstream bioinformatic analysis for TEEM-Seq is the same as for any sequence-based approach to studying DNA methylation, making it simple to incorporate into a variety of workflows. We believe that TEEM-Seq could replace traditional approaches for studying DNA methylation in candidate genes and pathways, and be effectively paired with other whole-genome or reduced-representation sequencing approaches to increase project sample sizes. In addition, TEEM-Seq can be combined with mRNA sequencing to examine how DNA methylation in promoters or other regulatory regions is related to the expression of individual genes or gene networks. By maximizing the number of samples in the hybridization reaction, TEEM-Seq is an inexpensive and flexible sequence-based approach for quantifying DNA methylation in species where other capture-based methods are unavailable or too expensive, particularly for non-model organisms.}, } @article {pmid36882531, year = {2023}, author = {Wei, Z and Jian, Z and Sun, Y and Pan, F and Han, H and Liu, Q and Mei, Y}, title = {Ecological sustainability and high-quality development of the Yellow River Delta in China based on the improved ecological footprint model.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {3821}, pmid = {36882531}, issn = {2045-2322}, abstract = {Aiming at the traditional ecological footprint model, the improved ecological footprint of the carbon footprint effectively makes up for the singularity of the ecological footprint's consideration of carbon emissions, and plays an important role in promoting high-quality development and ecological sustainability. This paper selects 2015, 2018 and 2020 as important time points for the study, corrects the ecological footprint parameter factors based on net primary productivity (NPP), measures the ecological footprint after the improvement of the carbon footprint, studies the spatial and temporal variation in the ecological footprint at the 100-m grid scale with the support of IPCC greenhouse gas inventory analysis, and analyzes the current ecological conservation status of the Yellow River Delta. Additionally, in the context of a low carbon economy, the decoupling index of carbon emissions and GDP is extended to the evaluation and analysis of high-quality development. The study showed that (1) the ecological footprint of the Yellow River Delta has increased year by year, from 0.721 hm[2]·person[- 1] to 0.758 hm[2]·person[- 1], an average annual increase of 2.9%; the ecological carrying capacity has decreased from 0.40 hm[2]·person[- 1] to 0.31 hm[2]·person[- 1], an overall decrease of 28.59%. (2) The overall ecological deficit of the Yellow River Delta grid is lightly overloaded, with most of the ecological surplus occurring in the northern and eastern parts of the study area and a few moderate and heavy overloads in the center of the core area where there is a lot of built-up land and the area is small and easy to gather. (3) Based on the low-carbon economy analysis, 2015, 2017 and 2020 reach absolute decoupling and are in the ideal scenario. However, in the rest of the years, carbon emissions and economic development are still in a large contradiction, and decoupling has fluctuated and varied greatly in the last six years. The effective combination of ecological footprint and low carbon economy analysis provides an important theoretical basis for improving ecological conservation and achieving high-quality development.}, } @article {pmid36880704, year = {2023}, author = {Amato, S and Benson, JS and Stewart, B and Sarathy, A and Osler, T and Hosmer, D and An, G and Cook, A and Winchell, RJ and Malhotra, AK}, title = {Current patterns of trauma center proliferation have not led to proportionate improvements in access to care or mortality after injury: An ecologic study.}, journal = {The journal of trauma and acute care surgery}, volume = {94}, number = {6}, pages = {755-764}, pmid = {36880704}, issn = {2163-0763}, mesh = {Humans ; United States/epidemiology ; *Trauma Centers ; Income ; Geographic Information Systems ; Health Services Accessibility ; Cell Proliferation ; *Wounds and Injuries/therapy ; }, abstract = {BACKGROUND: Timely access to high-level (I/II) trauma centers (HLTCs) is essential to minimize mortality after injury. Over the last 15 years, there has been a proliferation of HLTC nationally. The current study evaluates the impact of additional HLTC on population access and injury mortality.

METHODS: A geocoded list of HLTC, with year designated, was obtained from the American Trauma Society, and 60-minute travel time polygons were created using OpenStreetMap data. Census block group population centroids, county population centroids, and American Communities Survey data from 2005 and 2020 were integrated. Age-adjusted nonoverdose injury mortality was obtained from CDC Wide-ranging Online Data for Epidemiologic Research and the Robert Wood Johnson Foundation. Geographically weighted regression models were used to identify independent predictors of HLTC access and injury mortality.

RESULTS: Over the 15-year (2005-2020) study period, the number of HLTC increased by 31.0% (445 to 583), while population access to HLTC increased by 6.9% (77.5-84.4%). Despite this increase, access was unchanged in 83.1% of counties, with a median change in access of 0.0% (interquartile range, 0.0-1.1%). Population-level age-adjusted injury mortality rates increased by 5.39 per 100,000 population during this time (60.72 to 66.11 per 100,000). Geographically weighted regression controlling for population demography and health indicators found higher median income and higher population density to be positively associated with majority (≥50%) HLTC population coverage and negatively associated with county-level nonoverdose mortality.

CONCLUSION: Over the past 15 years, the number of HLTC increased 31%, while population access to HLTC increased only 6.9%. High-level (I/II) trauma center designation is likely driven by factors other than population need. To optimize efficiency and decrease potential oversupply, the designation process should include population level metrics. Geographic information system methodology can be an effective tool to assess optimal placement.

LEVEL OF EVIDENCE: Prognostic and Epidemiological; Level IV.}, } @article {pmid36879919, year = {2022}, author = {Boyes, D and , and , and , and , and , and Parker, B and Plotkin, D and Kawahara, AY and , }, title = {The genome sequence of the sallow kitten, Furcula furcula (Clerck, 1759).}, journal = {Wellcome open research}, volume = {7}, number = {}, pages = {229}, pmid = {36879919}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual male Furcula furcula (the sallow kitten; Arthropoda; Insecta; Lepidoptera; Notodontidae). The genome sequence is 736 megabases in span. The entire assembly (100%) is scaffolded into 29 chromosomal pseudomolecules, with the Z sex chromosome assembled. The complete mitochondrial genome was also assembled and is 17.2 kilobases in length.}, } @article {pmid36875992, year = {2022}, author = {Tadrent, N and Dedeine, F and Hervé, V}, title = {SnakeMAGs: a simple, efficient, flexible and scalable workflow to reconstruct prokaryotic genomes from metagenomes.}, journal = {F1000Research}, volume = {11}, number = {}, pages = {1522}, pmid = {36875992}, issn = {2046-1402}, mesh = {*Metagenome ; Workflow ; *Software ; Metagenomics/methods ; Computational Biology ; }, abstract = {Background: Over the last decade, we have observed in microbial ecology a transition from gene-centric to genome-centric analyses. Indeed, the advent of metagenomics combined with binning methods, single-cell genome sequencing as well as high-throughput cultivation methods have contributed to the continuing and exponential increase of available prokaryotic genomes, which in turn has favored the exploration of microbial metabolisms. In the case of metagenomics, data processing, from raw reads to genome reconstruction, involves various steps and software which can represent a major technical obstacle. Methods: To overcome this challenge, we developed SnakeMAGs, a simple workflow that can process Illumina data, from raw reads to metagenome-assembled genomes (MAGs) classification and relative abundance estimate. It integrates state-of-the-art bioinformatic tools to sequentially perform: quality control of the reads (illumina-utils, Trimmomatic), host sequence removal (optional step, using Bowtie2), assembly (MEGAHIT), binning (MetaBAT2), quality filtering of the bins (CheckM, GUNC), classification of the MAGs (GTDB-Tk) and estimate of their relative abundance (CoverM). Developed with the popular Snakemake workflow management system, it can be deployed on various architectures, from single to multicore and from workstation to computer clusters and grids. It is also flexible since users can easily change parameters and/or add new rules. Results: Using termite gut metagenomic datasets, we showed that SnakeMAGs is slower but allowed the recovery of more MAGs encompassing more diverse phyla compared to another similar workflow named ATLAS. Importantly, these additional MAGs showed no significant difference compared to the other ones in terms of completeness, contamination, genome size nor relative abundance. Conclusions: Overall, it should make the reconstruction of MAGs more accessible to microbiologists. SnakeMAGs as well as test files and an extended tutorial are available at https://github.com/Nachida08/SnakeMAGs.}, } @article {pmid36877490, year = {2024}, author = {Redhead, D and McElreath, R and Ross, CT}, title = {Reliable network inference from unreliable data: A tutorial on latent network modeling using STRAND.}, journal = {Psychological methods}, volume = {29}, number = {6}, pages = {1100-1122}, doi = {10.1037/met0000519}, pmid = {36877490}, issn = {1939-1463}, support = {//Economic and Social Research Council/ ; //Max Planck Institute for Evolutionary Anthropology; Department of Human Behavior, Ecology and Culture/ ; }, mesh = {Humans ; *Models, Statistical ; *Social Networking ; Social Network Analysis ; Data Interpretation, Statistical ; Psychology/methods ; }, abstract = {Social network analysis provides an important framework for studying the causes, consequences, and structure of social ties. However, standard self-report measures-for example, as collected through the popular "name-generator" method-do not provide an impartial representation of such ties, be they transfers, interactions, or social relationships. At best, they represent perceptions filtered through the cognitive biases of respondents. Individuals may, for example, report transfers that did not really occur, or forget to mention transfers that really did. The propensity to make such reporting inaccuracies is both an individual-level and item-level characteristic-variable across members of any given group. Past research has highlighted that many network-level properties are highly sensitive to such reporting inaccuracies. However, there remains a dearth of easily deployed statistical tools that account for such biases. To address this issue, we provide a latent network model that allows researchers to jointly estimate parameters measuring both reporting biases and a latent, underlying social network. Building upon past research, we conduct several simulation experiments in which network data are subject to various reporting biases, and find that these reporting biases strongly impact fundamental network properties. These impacts are not adequately remedied using the most frequently deployed approaches for network reconstruction in the social sciences (i.e., treating either the union or the intersection of double-sampled data as the true network), but are appropriately resolved through the use of our latent network models. To make implementation of our models easier for end-users, we provide a fully documented R package, STRAND, and include a tutorial illustrating its functionality when applied to empirical food/money sharing data from a rural Colombian population. (PsycInfo Database Record (c) 2024 APA, all rights reserved).}, } @article {pmid36876314, year = {2023}, author = {Zhang, J and Qian, H}, title = {U.Taxonstand: An R package for standardizing scientific names of plants and animals.}, journal = {Plant diversity}, volume = {45}, number = {1}, pages = {1-5}, pmid = {36876314}, issn = {2468-2659}, abstract = {The scientific names of organisms are key identifiers of plants and animals. Correctly treating scientific names is a prerequisite for biodiversity research and documentation. Here, we present an R package, 'U.Taxonstand', which can standardize and harmonize scientific names in plant and animal species lists at a fast speed and at a high rate of matching success. Unlike most of other similar R packages each of which works with only one taxonomic database, U.Taxonstand can work with all taxonomic databases, as long as they are properly formatted. Multiple databases for plants and animals that can be directly used by U.Taxonstand, which include bryophytes, vascular plants, amphibians, birds, fishes, mammals, and reptiles, are available online. U.Taxonstand can be a very useful tool for botanists, zoologists, ecologists and biogeographers to standardize and harmonize scientific names of organisms.}, } @article {pmid36874580, year = {2022}, author = {Hayward, A and Lohse, K and Laetsch, DR and Vila, R and , and , and , and Taluy, E and , }, title = {The genome sequence of the silver-studded blue, Plebejus argus (Linnaeus, 1758).}, journal = {Wellcome open research}, volume = {7}, number = {}, pages = {315}, pmid = {36874580}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual male Plebejus argus (silver-studded blue; Arthropoda; Insecta; Lepidoptera; Lycaenidae). The genome sequence is 382 megabases in span. The entire assembly (100%) is scaffolded into 23 chromosomal pseudomolecules with the Z sex chromosome assembled. The complete mitochondrial genome was also assembled and is 27.4 kilobases in length. Gene annotation of this assembly on Ensembl identified 12,693 protein coding genes.}, } @article {pmid36874578, year = {2022}, author = {Boyes, D and , and , and , and , and , and Holland, PWH and , }, title = {The genome sequence of the Seraphim, Lobophora halterata (Hufnagel, 1767).}, journal = {Wellcome open research}, volume = {7}, number = {}, pages = {313}, pmid = {36874578}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual female Lobophora halterata (the Seraphim; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 315 megabases in span. The complete assembly is scaffolded into 32 chromosomal pseudomolecules with the Z and W sex chromosomes assembled. The mitochondrial genome has also been assembled and is 15.7 kilobases in length.}, } @article {pmid36874577, year = {2022}, author = {Hawkes, W and Wotton, K and , and , and , and , and , and , }, title = {The genome sequence of the dumpy grass hoverfly, Melanostoma mellinum (Linnaeus, 1758).}, journal = {Wellcome open research}, volume = {7}, number = {}, pages = {59}, pmid = {36874577}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual male Melanostoma mellinum (the dumpy grass hoverfly; Arthropoda; Insecta; Diptera; Syriphidae). The genome sequence is 731 megabases in span. The majority of the assembly (99.67%) is scaffolded into five chromosomal pseudomolecules, with the X and Y sex chromosomes assembled. The complete mitochondrial genome was also assembled and is 16.1 kilobases in length.}, } @article {pmid36874564, year = {2022}, author = {Boyes, D and Holland, PWH and , and , and , and , and , and , }, title = {The genome sequence of the large yellow underwing, Noctua pronuba (Linnaeus, 1758).}, journal = {Wellcome open research}, volume = {7}, number = {}, pages = {119}, pmid = {36874564}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual female Noctua pronuba (the large yellow underwing; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 529 megabases in span. The complete assembly is scaffolded into 32 chromosomal pseudomolecules, with the W and Z sex chromosome assembled. The mitochondrial genome was also assembled and is 15.3 kilobases in length.}, } @article {pmid36872222, year = {2023}, author = {Zhang, GZ and Chen, SL and Dong, LL}, title = {[Traditional Chinese medicine microbiomics and its research strategies].}, journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica}, volume = {48}, number = {3}, pages = {596-607}, doi = {10.19540/j.cnki.cjcmm.20221101.101}, pmid = {36872222}, issn = {1001-5302}, mesh = {Ecology ; Fermentation ; High-Throughput Nucleotide Sequencing ; *Medicine, Chinese Traditional ; *Research Design ; }, abstract = {The tight relationships between microbiome and traditional Chinese medicine(TCM)have been widely recognized. New technologies, results, and theories are emerging in the field of microbiomics in recent years with the advances in high-throughput sequencing and multi-omics technologies. Based on the previous research, the present study has proposed the concept of TCM microbiomics(TCMM), which is an interdisciplinary subject aiming at elucidating the functions and applications of microbiome in the areas of herb resources, herb processing, herb storage, and clinical effects by using modern technology of biology, ecology, and informatics. This subject essentially contains the structures, functions, interactions, molecular mechanisms, and application strategies of the microbiome associated with the quality, safety, and efficacy of TCM. Firstly, the development of the TCMM concept was summarized, with the profound understanding of TCMM on the complexity and entirety of microbiome being emphasized. Then, the research contents and applications of TCMM in promoting the sustainable development of herb resources, improving the standardization and diversification of herb fermentation, strengthening the safety of herb storage, and resolving the scientific connotation of theories and clinical efficacy of TCM are reviewed. Finally, the research strategies and methods of TCM microbiomics were elaborated from basic research, application research, and system research. TCMM is expected to promote the integrative development of TCM with frontier science and technology, thereby expanding the depth and scope of TCM study and facilitating TCM modernization.}, } @article {pmid36868417, year = {2023}, author = {Zhang, X and Shao, W and Huo, Y and Kong, Y and Zhang, W and Li, S and Zhou, W and Wu, X and Qin, F and Hu, X}, title = {The effects of short-term dietary exposure to SiO2 nanoparticle on the domesticated lepidopteran insect model silkworm (Bombyx mori): Evidence from the perspective of multi-omics.}, journal = {Chemosphere}, volume = {323}, number = {}, pages = {138257}, doi = {10.1016/j.chemosphere.2023.138257}, pmid = {36868417}, issn = {1879-1298}, mesh = {Animals ; *Bombyx/metabolism ; Silicon Dioxide/metabolism ; Multiomics ; Dietary Exposure ; *Nanoparticles/toxicity ; }, abstract = {Silicon dioxide nanoparticles (nSiO2) are one of the widely utilized nanoparticle (NPSs) materials, and exposure to nSiO2 is ubiquitous. With the increasing commercialization of nSiO2, the potential risk of nSiO2 release to the health and the ecological environment have been attracted more attention. In this study, the domesticated lepidopteran insect model silkworm (Bombyx mori) was utilized to evaluate the biological effects of dietary exposure to nSiO2. Histological investigations showed that nSiO2 exposure resulted in midgut tissue injury in a dose-dependent manner. Larval body mass and cocoon production were reduced by nSiO2 exposure. ROS burst was not triggered, and the activities of antioxidant enzymes were induced in the midgut of silkworm exposure to nSiO2. RNA-sequencing revealed that the differentially expressed genes induced by nSiO2 exposure were predominantly enriched into xenobiotics biodegradation and metabolism, lipid, and amino acid metabolism pathways. 16 S rDNA sequencing revealed that nSiO2 exposure altered the microbial diversity in the gut of the silkworm. Metabolomics analysis showed that the combined uni- and multivariate analysis identified 28 significant differential metabolites from the OPLS-DA model. These significant differential metabolites were predominantly enriched into the metabolic pathways, including purine metabolism and tyrosine metabolism and so. Spearman correlation analysis and the Sankey diagram established the relationship between microbe and metabolites, and some genera may play crucial and pleiotropic functions in the interaction between microbiome and host. These findings indicated that nSiO2 exposure could impact the dysregulation of genes related to xenobiotics metabolism, gut dysbiosis, and metabolic pathways and provided a valuable reference for assessing nSiO2 toxicity from a multi-dimensional perspective.}, } @article {pmid36868153, year = {2023}, author = {Jin, H and Zhihong, P and Jiaqing, Z and Chuxuan, L and Lu, T and Jun, J and Xinghua, L and Wenyan, G and Junkang, G and Binbin, S and Shengguo, X}, title = {Source apportionment and quantitative risk assessment of heavy metals at an abandoned zinc smelting site based on GIS and PMF models.}, journal = {Journal of environmental management}, volume = {336}, number = {}, pages = {117565}, doi = {10.1016/j.jenvman.2023.117565}, pmid = {36868153}, issn = {1095-8630}, mesh = {Humans ; Zinc/analysis ; Geographic Information Systems ; Lead ; Environmental Monitoring ; *Soil Pollutants/analysis ; *Metals, Heavy/analysis ; Soil ; China ; Risk Assessment ; Cadmium ; }, abstract = {The abandoned smelters have caused serious hazards to the surrounding environment and residents. Taking an abandoned zinc smelter in southern China as an example, a total of 245 soil samples were collected to study spatial heterogeneity, source apportionment, and source-derived risk assessment of heavy metal(loid)s (HMs) in the region. The results showed that the mean values of all HMs concentrations were higher than the local background values, with Zn, Cd, Pb, and As contamination being the most serious and their plume penetrating to the bottom layer. Four sources were identified by principal component analysis and positive matrix factorization, with their contributions to the HMs contents ranked as: surface runoff (F2, 63.2%) > surface solid waste (F1, 22.2%) > atmospheric deposition (F3, 8.5%) > parent material (F4, 6.1%). Among these, F1 was a determinant source of human health risk with a contribution rate of 60%. Therefore, F1 was considered to be the priority control factor, but it only accounted for 22.2% of HMs contents contribution. Hg dominated the ecological risk with a contribution of 91.1%. Pb (25.7%) and As (32.9%) accounted for the non-carcinogenic risk, while As (95%) dominated the carcinogenic effect. The spatial characteristics of human health risk values derived from F1 indicated that high-risk areas were mainly distributed in the casting finished products area, electrolysis area, leaching-concentration area, and fluidization roasting area. The findings highlight the significance of priority control factors (including HMs, pollution sources and functional areas) for consideration in the integrated management of this region, thus saving costs for effective soil remediation.}, } @article {pmid36866381, year = {2023}, author = {Lin, J and Yu, D and Pan, R and Cai, J and Liu, J and Zhang, L and Wen, X and Peng, X and Cernava, T and Oufensou, S and Migheli, Q and Chen, X and Zhang, X}, title = {Improved YOLOX-Tiny network for detection of tobacco brown spot disease.}, journal = {Frontiers in plant science}, volume = {14}, number = {}, pages = {1135105}, pmid = {36866381}, issn = {1664-462X}, abstract = {INTRODUCTION: Tobacco brown spot disease caused by Alternaria fungal species is a major threat to tobacco growth and yield. Thus, accurate and rapid detection of tobacco brown spot disease is vital for disease prevention and chemical pesticide inputs.

METHODS: Here, we propose an improved YOLOX-Tiny network, named YOLO-Tobacco, for the detection of tobacco brown spot disease under open-field scenarios. Aiming to excavate valuable disease features and enhance the integration of different levels of features, thereby improving the ability to detect dense disease spots at different scales, we introduced hierarchical mixed-scale units (HMUs) in the neck network for information interaction and feature refinement between channels. Furthermore, in order to enhance the detection of small disease spots and the robustness of the network, we also introduced convolutional block attention modules (CBAMs) into the neck network.

RESULTS: As a result, the YOLO-Tobacco network achieved an average precision (AP) of 80.56% on the test set. The AP was 3.22%, 8.99%, and 12.03% higher than that obtained by the classic lightweight detection networks YOLOX-Tiny network, YOLOv5-S network, and YOLOv4-Tiny network, respectively. In addition, the YOLO-Tobacco network also had a fast detection speed of 69 frames per second (FPS).

DISCUSSION: Therefore, the YOLO-Tobacco network satisfies both the advantages of high detection accuracy and fast detection speed. It will likely have a positive impact on early monitoring, disease control, and quality assessment in diseased tobacco plants.}, } @article {pmid36865376, year = {2022}, author = {Boyes, D and , and , and , and , and , and Lees, D and , }, title = {The genome sequence of the merveille du jour, Griposia aprilina (Linnaeus, 1758).}, journal = {Wellcome open research}, volume = {7}, number = {}, pages = {247}, pmid = {36865376}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual Griposia aprilina (the merveille du jour; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 720 megabases in span. The majority of the assembly (99.89%) is scaffolded into 32 chromosomal pseudomolecules with the W and Z sex chromosomes assembled. The complete mitochondrial genome was also assembled and is 15.4 kilobases in length.}, } @article {pmid36865367, year = {2022}, author = {Broad, GR and Boyes, D and , and , and , and , and , and , and , }, title = {The genome sequence of the setaceous Hebrew character, Xestia c-nigrum, (Linnaeus, 1758).}, journal = {Wellcome open research}, volume = {7}, number = {}, pages = {295}, pmid = {36865367}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual male Xestia c-nigrum (the setaceous Hebrew character; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 760 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the assembled Z sex chromosome. The mitochondrial genome has also been assembled and is 15.3 kilobases in length.}, } @article {pmid36864462, year = {2023}, author = {Keuschnig, C and Vogel, TM and Barbaro, E and Spolaor, A and Koziol, K and Björkman, MP and Zdanowicz, C and Gallet, JC and Luks, B and Layton, R and Larose, C}, title = {Selection processes of Arctic seasonal glacier snowpack bacterial communities.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {35}, pmid = {36864462}, issn = {2049-2618}, mesh = {Bayes Theorem ; *Ice Cover ; Seasons ; *Bacteria/genetics ; Biodiversity ; }, abstract = {BACKGROUND: Arctic snowpack microbial communities are continually subject to dynamic chemical and microbial input from the atmosphere. As such, the factors that contribute to structuring their microbial communities are complex and have yet to be completely resolved. These snowpack communities can be used to evaluate whether they fit niche-based or neutral assembly theories.

METHODS: We sampled snow from 22 glacier sites on 7 glaciers across Svalbard in April during the maximum snow accumulation period and prior to the melt period to evaluate the factors that drive snowpack metataxonomy. These snowpacks were seasonal, accumulating in early winter on bare ice and firn and completely melting out in autumn. Using a Bayesian fitting strategy to evaluate Hubbell's Unified Neutral Theory of Biodiversity at multiple sites, we tested for neutrality and defined immigration rates at different taxonomic levels. Bacterial abundance and diversity were measured and the amount of potential ice-nucleating bacteria was calculated. The chemical composition (anions, cations, organic acids) and particulate impurity load (elemental and organic carbon) of the winter and spring snowpack were also characterized. We used these data in addition to geographical information to assess possible niche-based effects on snow microbial communities using multivariate and variable partitioning analysis.

RESULTS: While certain taxonomic signals were found to fit the neutral assembly model, clear evidence of niche-based selection was observed at most sites. Inorganic chemistry was not linked directly to diversity, but helped to identify predominant colonization sources and predict microbial abundance, which was tightly linked to sea spray. Organic acids were the most significant predictors of microbial diversity. At low organic acid concentrations, the snow microbial structure represented the seeding community closely, and evolved away from it at higher organic acid concentrations, with concomitant increases in bacterial numbers.

CONCLUSIONS: These results indicate that environmental selection plays a significant role in structuring snow microbial communities and that future studies should focus on activity and growth. Video Abstract.}, } @article {pmid36863150, year = {2023}, author = {Liu, X and Wang, Y and Meng, X and Zhang, C and Chen, Z}, title = {Improved method for benthic ecosystem health assessment by integrating chemical indexes into multiple biological indicator species-A case study of the Baiyangdian Lake, China.}, journal = {Journal of environmental management}, volume = {335}, number = {}, pages = {117530}, doi = {10.1016/j.jenvman.2023.117530}, pmid = {36863150}, issn = {1095-8630}, mesh = {Humans ; *Ecosystem ; Lakes ; Environmental Biomarkers ; Environmental Monitoring/methods ; China ; *Metals, Heavy ; }, abstract = {A comprehensive and scientific assessment of benthic ecosystem health is key to the rational selection of endogenous pollution reduction technologies for lakes. However, current assessments are mainly limited to biological indicators and ignore the actual benthic ecosystem situations, such as the impact of eutrophication and heavy metal pollution, which may lead to the one-sidedness of the evaluation results. In this study, taking Baiyangdian Lake, the largest shallow mesotrophic-eutrophic lake in the North China Plain, as an example, the chemical assessment index and biological integrity index were first combined to estimate the biological conditions, nutritional status and heavy metal pollution of lakes. The indicator system incorporated three biological assessments (benthic index of biotic integrity (B-IBI), submerged aquatic vegetation index of biological integrity (SAV-IBI) and microbial index of biological integrity (M-IBI)) and three chemical assessments (dissolved oxygen (DO), comprehensive trophic level index (TLI) and index of geoaccumulation (Igeo)). Twenty-three attributes of B-IBI, fourteen attributes of SAV-IBI and twelve attributes of M-IBI were screened by range, responsiveness, and redundancy tests to keep the core metrics that were significantly correlated with disturbance gradients or showed strong discriminatory power between reference and impaired sites. The assessment results of B-IBI, SAV-IBI, and M-IBI showed significant differences in the response to anthropogenic activities and seasonal change, among which the submerged plants showed more significant seasonal differences. It is difficult to reach a comprehensive conclusion regarding the benthic ecosystem health status based on a single biological community. In comparison with biological indicators, the score of chemical indicators is relatively low. DO, TLI and Igeo provide an essential supplement for the benthic ecosystem health assessment of lakes with eutrophication and heavy metal pollution problems. Using the new integrated assessment method, the benthic ecosystem health of Baiyangdian Lake was rated as fair, especially the northern parts of the lake adjacent to the inflow mouth of the Fu River, which were in poor condition, indicating that the lake has experienced anthropogenic disturbance, resulting in eutrophication, heavy metal pollution and biological community degradation. Whether it's spring or summer, the integrated assessment method provides a more plausible and comprehensive view of benthic ecosystem health under the pressure of increasing human activities and changing habitat and hydrological conditions, overcoming the narrow perspective and uncertainties of the single-index method. Thus, it can assist lake managers in providing technical support for ecological indication and restoration.}, } @article {pmid36862660, year = {2023}, author = {Nanjala, R and Nyasimi, F and Masiga, D and Kibet, CK}, title = {A mentorship and incubation program using project-based learning to build a professional bioinformatics pipeline in Kenya.}, journal = {PLoS computational biology}, volume = {19}, number = {3}, pages = {e1010904}, pmid = {36862660}, issn = {1553-7358}, support = {U24 HG006941/HG/NHGRI NIH HHS/United States ; U2R TW010677/TW/FIC NIH HHS/United States ; }, mesh = {Humans ; Kenya ; *Mentors ; *Computational Biology ; Genomics ; Students ; }, abstract = {The demand for well-trained bioinformaticians to support genomics research continues to rise. Unfortunately, undergraduate training in Kenya does not prepare students for specialization in bioinformatics. Graduates are often unaware of the career opportunities in bioinformatics, and those who are may lack mentors to help them choose a specialization. The Bioinformatics Mentorship and Incubation Program seeks to bridge the gap by laying the foundation for a bioinformatics training pipeline using project-based learning. The program selects six participants through an intensive open recruitment exercise for highly competitive students to join the program for four months. The six interns undergo intensive training within the first one and a half months before being assigned to mini-projects. We track the progress of the interns weekly through code review sessions and a final presentation at the end of the four months. We have trained five cohorts, most of whom have secured master's scholarships within and outside the country and job opportunities. We demonstrate the benefit of structured mentorship using project-based learning in filling the training gap after undergraduate programs to generate well-trained bioinformaticians who are competitive in graduate programs and bioinformatics jobs.}, } @article {pmid36859647, year = {2023}, author = {Nocci, M and Villa, G and Ragazzoni, L and Tofani, L and Romagnoli, S and Baldini, G and Bertini, P and Hubloue, I and Scolletta, S and Mechi, MT and Della Corte, F}, title = {Relationship between intensive care surge capacity and hospital factors: an extensive experience.}, journal = {Internal and emergency medicine}, volume = {18}, number = {5}, pages = {1521-1532}, pmid = {36859647}, issn = {1970-9366}, mesh = {Humans ; *Surge Capacity ; *COVID-19/epidemiology ; Pandemics ; Critical Care ; Intensive Care Units ; Hospitals ; Emergency Service, Hospital ; Retrospective Studies ; }, abstract = {As a prolonged surge scenario, the COVID-19 pandemic has offered an unparalleled opportunity to improve hospital surge capacity (SC) understanding and the ability to manage it. In this study, the authors report the experience of a large hospital network and evaluate potential relationships between Intensive Care Units SC (ICU-SC) and some hospital-related variables: bed occupancy, emergency department admissions, ward admission from ED, and elective surgery procedures. Pearson's partial correlation coefficient (r) has been used to define the relationship between SC and the daily values of the above variables, collected through a dedicated digital platform that also ensured a regular quality check of the data. The observation has concerned several levels of analysis, namely two different types of SC calculation (SC base-SCb and SC actual-SCa), hospital category level and multi-hospital level, and two consecutive pandemic waves. Among the 16 hospitals observed, the correlation was shown to be moderate-positive with non-ICU bed occupancy (r/ = 0.62, r/ = 0.54), strong/moderate with ICU bed occupancy (r/ = 0.72, r/ = 0.54), and moderate with ward admissions from ED (r/ = 0.50, r/ = 0.51) On the contrary, the correlation proved to be moderate-negative with ED admissions (r/ = - 0.69, r/ = - 0.62) and low with the number of elective surgery procedures (r/ = - 0.10, r/ = - 0.16). This study identified a positive correlation between SC and three variables monitored: ICU bed occupancy, non-ICU bed occupancy, and ward admissions from ED. On the contrary, the correlation was negative for ED admission and the number of elective surgery procedures. The results have been confirmed across all levels of analysis adopted.}, } @article {pmid36859581, year = {2023}, author = {Tucker, C and Brandt, M and Hiernaux, P and Kariryaa, A and Rasmussen, K and Small, J and Igel, C and Reiner, F and Melocik, K and Meyer, J and Sinno, S and Romero, E and Glennie, E and Fitts, Y and Morin, A and Pinzon, J and McClain, D and Morin, P and Porter, C and Loeffler, S and Kergoat, L and Issoufou, BA and Savadogo, P and Wigneron, JP and Poulter, B and Ciais, P and Kaufmann, R and Myneni, R and Saatchi, S and Fensholt, R}, title = {Sub-continental-scale carbon stocks of individual trees in African drylands.}, journal = {Nature}, volume = {615}, number = {7950}, pages = {80-86}, pmid = {36859581}, issn = {1476-4687}, mesh = {*Carbon/analysis/metabolism ; *Ecosystem ; *Trees/anatomy & histology/chemistry/metabolism ; *Desert Climate ; Desiccation ; Satellite Imagery ; Africa South of the Sahara ; Machine Learning ; Wood/analysis ; Plant Roots ; Agriculture ; Environmental Restoration and Remediation ; Databases, Factual ; Biomass ; Computers ; }, abstract = {The distribution of dryland trees and their density, cover, size, mass and carbon content are not well known at sub-continental to continental scales[1-14]. This information is important for ecological protection, carbon accounting, climate mitigation and restoration efforts of dryland ecosystems[15-18]. We assessed more than 9.9 billion trees derived from more than 300,000 satellite images, covering semi-arid sub-Saharan Africa north of the Equator. We attributed wood, foliage and root carbon to every tree in the 0-1,000 mm year[-1] rainfall zone by coupling field data[19], machine learning[20-22], satellite data and high-performance computing. Average carbon stocks of individual trees ranged from 0.54 Mg C ha[-1] and 63 kg C tree[-1] in the arid zone to 3.7 Mg C ha[-1] and 98 kg tree[-1] in the sub-humid zone. Overall, we estimated the total carbon for our study area to be 0.84 (±19.8%) Pg C. Comparisons with 14 previous TRENDY numerical simulation studies[23] for our area found that the density and carbon stocks of scattered trees have been underestimated by three models and overestimated by 11 models, respectively. This benchmarking can help understand the carbon cycle and address concerns about land degradation[24-29]. We make available a linked database of wood mass, foliage mass, root mass and carbon stock of each tree for scientists, policymakers, dryland-restoration practitioners and farmers, who can use it to estimate farmland tree carbon stocks from tablets or laptops.}, } @article {pmid36859503, year = {2023}, author = {Jones, DL and Rhymes, JM and Green, E and Rimmer, C and Kevill, JL and Malham, SK and Weightman, AJ and Farkas, K}, title = {Poor air passenger knowledge of COVID-19 symptoms and behaviour undermines strategies aimed at preventing the import of SARS-CoV-2 into the UK.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {3494}, pmid = {36859503}, issn = {2045-2322}, mesh = {Adult ; Male ; Female ; Humans ; Aged ; SARS-CoV-2 ; *COVID-19 ; Pandemics ; *Air Travel ; United Kingdom ; }, abstract = {Air travel mediates transboundary movement of SARS-CoV-2. To prepare for future pandemics, we sought to understand air passenger behaviour and perceived risk during the COVID-19 pandemic. This study of UK adults (n = 2103) quantified knowledge of COVID-19 symptoms, perceived health risk of contracting COVID-19, likelihood of returning to the UK with COVID-19 symptoms, likelihood to obey self-quarantining guidelines, how safe air travellers felt when flying during the pandemic (n = 305), and perceptions towards face covering effectiveness.Overall knowledge of COVID-19 symptoms was poor. Men and younger age groups (18-44) were less informed than women and older age groups (44 +). A significant proportion (21%) of the population would likely travel back to the UK whilst displaying COVID-19 symptoms with many expressing that they would not fully comply with self-isolation guidelines. Overall, males and younger age groups had a reduced perceived personal risk from contracting COVID-19, posing a higher risk of transporting SARS-CoV-2 back to the UK. Poor passenger knowledge and behaviour undermines government guidelines and policies aimed at preventing SARS-CoV-2 entry into the UK. This supports the need for stricter, clearer and more targeted guidelines with point-of-departure viral testing and stricter quarantining upon arrival.}, } @article {pmid36858189, year = {2023}, author = {Kushwaha, B and Nagpure, NS and Srivastava, S and Pandey, M and Kumar, R and Raizada, S and Agarwal, S and Singh, M and Basheer, VS and Kumar, RG and Das, P and Das, SP and Patnaik, S and Bit, A and Srivastava, SK and Vishwakarma, AL and Joshi, CG and Kumar, D and Jena, JK}, title = {Genome size estimation and its associations with body length, chromosome number and evolution in teleost fishes.}, journal = {Gene}, volume = {864}, number = {}, pages = {147294}, doi = {10.1016/j.gene.2023.147294}, pmid = {36858189}, issn = {1879-0038}, mesh = {Animals ; Genome Size ; Evolution, Molecular ; Fishes/genetics ; Chromosomes/genetics ; Genomics ; *Perciformes/genetics ; *Catfishes/genetics ; *Cypriniformes/genetics ; Phylogeny ; }, abstract = {Precise estimation of genome size (GS) is vital for various genomic studies, such as deciding genome sequencing depth, genome assembly, biodiversity documentation, evolution, genetic disorders studies, duplication events etc. Animal Genome Size Database provides GS of over 2050 fish species, which ranges from 0.35 pg in pufferfish (Tetraodon nigroviridis) to 132.83 pg in marbled lungfish (Protopterus aethiopicus). The GS of majority of the fishes inhabiting waters of Indian subcontinent are still missing. In present study, we estimated GS of 51 freshwater teleost (31 commercially important, 7 vulnerable and 13 ornamental species) that ranged from 0.58 pg in banded gourami (Trichogaster fasciata) to 1.92 pg in scribbled goby (Awaous grammepomus). Substantial variation in GS was observed within the same fish orders (0.64-1.45 pg in cypriniformes, 0.70-1.41 pg in siluriformes and 0.58-1.92 pg in perciformes). We examined the relationship between the GS, chromosome number and body length across all the fishes. Body length was found to be associated with GS, whereas no relationship was noticed between the GS and the chromosome number. The analysis using ancestral information revealed haploid chromosome number 25, 27 and 24 for the most recent common ancestor of cypriniformes, siluriformes and perciformes, respectively. The study led to generation of new records on GS of 43 fish species and revalidated records for 8 species. The finding is valuable resource for further research in the areas of fish genomics, molecular ecology and evolutionary conservation genetics.}, } @article {pmid36852195, year = {2023}, author = {Streng, K and de Best, PA and Timen, A and Koopmans, MPG and van der Poel, WHM and Sikkema, RS}, title = {Rapid response screening for emerging zoonotic pathogens, barriers and opportunities: A study for enhanced preparedness of the Netherlands.}, journal = {One health (Amsterdam, Netherlands)}, volume = {16}, number = {}, pages = {100507}, pmid = {36852195}, issn = {2352-7714}, abstract = {BACKGROUND: Outbreaks of zoonotic emerging infectious diseases (EIDs) require rapid identification of potential reservoir hosts and mapping disease spread in these hosts to inform risk assessment and adequate control measures. Animals are often understudied when a novel EID is detected in humans and acquisition of animal samples is hampered by practical, ethical, and legal barriers, of which there is currently no clear overview. Therefore, the three aims of this study are (1) to map potentially available collections of animal samples, (2) to assess possibilities and barriers for reuse of these samples and (3) to assess possibilities and barriers for active animal and environmental sampling in the Netherlands.

METHODS: A literature search was performed to identify ongoing sampling activities and opportunities for reuse or active sampling. Semi-structured interviews with stakeholder organizations were conducted to gain further insight into the three research questions.

RESULTS: Various sample collections of surveillance, diagnostic and research activities exist in the Netherlands. Sample size, coverage, storage methods and type of samples collected differs per animal species which influences reuse suitability. Organizations are more likely to share samples, for reuse in outbreak investigations, when they have a pre-existing relationship with the requesting institute. Identified barriers for sharing were, among others, unfamiliarity with legislation and unsuitable data management systems. Active sampling of animals or the environment is possible through several routes. Related barriers are acquiring approval from animal- or property owners, conflicts with anonymization, and time needed to acquire ethical approval.

CONCLUSION: The animal sample collections identified would be very valuable for use in outbreak investigations. Barriers for sharing may be overcome by increasing familiarity with legislation, building (international) sharing networks and agreements before crises occur and developing systems for sample registration and biobanking. Proactive setting up of ethical approvals will allow for rapid animal sample collection to identify EID hosts and potential spillovers.}, } @article {pmid36850776, year = {2023}, author = {Di Paolo, S and Nijmeijer, EM and Bragonzoni, L and Gokeler, A and Benjaminse, A}, title = {Definition of High-Risk Motion Patterns for Female ACL Injury Based on Football-Specific Field Data: A Wearable Sensors Plus Data Mining Approach.}, journal = {Sensors (Basel, Switzerland)}, volume = {23}, number = {4}, pages = {}, pmid = {36850776}, issn = {1424-8220}, mesh = {Female ; Humans ; *Anterior Cruciate Ligament Injuries ; *Football ; Rotation ; Data Mining ; *Wearable Electronic Devices ; }, abstract = {The aim of the present study was to investigate if the presence of anterior cruciate ligament (ACL) injury risk factors depicted in the laboratory would reflect at-risk patterns in football-specific field data. Twenty-four female footballers (14.9 ± 0.9 year) performed unanticipated cutting maneuvers in a laboratory setting and on the football pitch during football-specific exercises (F-EX) and games (F-GAME). Knee joint moments were collected in the laboratory and grouped using hierarchical agglomerative clustering. The clusters were used to investigate the kinematics collected on field through wearable sensors. Three clusters emerged: Cluster 1 presented the lowest knee moments; Cluster 2 presented high knee extension but low knee abduction and rotation moments; Cluster 3 presented the highest knee abduction, extension, and external rotation moments. In F-EX, greater knee abduction angles were found in Cluster 2 and 3 compared to Cluster 1 (p = 0.007). Cluster 2 showed the lowest knee and hip flexion angles (p < 0.013). Cluster 3 showed the greatest hip external rotation angles (p = 0.006). In F-GAME, Cluster 3 presented the greatest knee external rotation and lowest knee flexion angles (p = 0.003). Clinically relevant differences towards ACL injury identified in the laboratory reflected at-risk patterns only in part when cutting on the field: in the field, low-risk players exhibited similar kinematic patterns as the high-risk players. Therefore, in-lab injury risk screening may lack ecological validity.}, } @article {pmid36848570, year = {2023}, author = {Stenseth, NC and Schlatte, R and Liu, X and Pielke, R and Li, R and Chen, B and Bjørnstad, ON and Kusnezov, D and Gao, GF and Fraser, C and Whittington, JD and Bai, Y and Deng, K and Gong, P and Guan, D and Xiao, Y and Xu, B and Johnsen, EB}, title = {How to avoid a local epidemic becoming a global pandemic.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {120}, number = {10}, pages = {e2220080120}, pmid = {36848570}, issn = {1091-6490}, mesh = {Humans ; Pandemics/prevention & control ; *COVID-19/epidemiology/prevention & control ; SARS-CoV-2 ; Disease Outbreaks ; *Air Travel ; }, abstract = {Here, we combine international air travel passenger data with a standard epidemiological model of the initial 3 mo of the COVID-19 pandemic (January through March 2020; toward the end of which the entire world locked down). Using the information available during this initial phase of the pandemic, our model accurately describes the main features of the actual global development of the pandemic demonstrated by the high degree of coherence between the model and global data. The validated model allows for an exploration of alternative policy efficacies (reducing air travel and/or introducing different degrees of compulsory immigration quarantine upon arrival to a country) in delaying the global spread of SARS-CoV-2 and thus is suggestive of similar efficacy in anticipating the spread of future global disease outbreaks. We show that a lesson from the recent pandemic is that reducing air travel globally is more effective in reducing the global spread than adopting immigration quarantine. Reducing air travel out of a source country has the most important effect regarding the spreading of the disease to the rest of the world. Based upon our results, we propose a digital twin as a further developed tool to inform future pandemic decision-making to inform measures intended to control the spread of disease agents of potential future pandemics. We discuss the design criteria for such a digital twin model as well as the feasibility of obtaining access to the necessary online data on international air travel.}, } @article {pmid36846939, year = {2023}, author = {Barrile, GM and Augustine, DJ and Porensky, LM and Duchardt, CJ and Shoemaker, KT and Hartway, CR and Derner, JD and Hunter, EA and Davidson, AD}, title = {A big data-model integration approach for predicting epizootics and population recovery in a keystone species.}, journal = {Ecological applications : a publication of the Ecological Society of America}, volume = {33}, number = {4}, pages = {e2827}, doi = {10.1002/eap.2827}, pmid = {36846939}, issn = {1051-0761}, mesh = {Animals ; *Ecosystem ; Big Data ; *Yersinia pestis ; Sciuridae ; Climate ; Animals, Wild ; }, abstract = {Infectious diseases pose a significant threat to global health and biodiversity. Yet, predicting the spatiotemporal dynamics of wildlife epizootics remains challenging. Disease outbreaks result from complex nonlinear interactions among a large collection of variables that rarely adhere to the assumptions of parametric regression modeling. We adopted a nonparametric machine learning approach to model wildlife epizootics and population recovery, using the disease system of colonial black-tailed prairie dogs (BTPD, Cynomys ludovicianus) and sylvatic plague as an example. We synthesized colony data between 2001 and 2020 from eight USDA Forest Service National Grasslands across the range of BTPDs in central North America. We then modeled extinctions due to plague and colony recovery of BTPDs in relation to complex interactions among climate, topoedaphic variables, colony characteristics, and disease history. Extinctions due to plague occurred more frequently when BTPD colonies were spatially clustered, in closer proximity to colonies decimated by plague during the previous year, following cooler than average temperatures the previous summer, and when wetter winter/springs were preceded by drier summers/falls. Rigorous cross-validations and spatial predictions indicated that our final models predicted plague outbreaks and colony recovery in BTPD with high accuracy (e.g., AUC generally >0.80). Thus, these spatially explicit models can reliably predict the spatial and temporal dynamics of wildlife epizootics and subsequent population recovery in a highly complex host-pathogen system. Our models can be used to support strategic management planning (e.g., plague mitigation) to optimize benefits of this keystone species to associated wildlife communities and ecosystem functioning. This optimization can reduce conflicts among different landowners and resource managers, as well as economic losses to the ranching industry. More broadly, our big data-model integration approach provides a general framework for spatially explicit forecasting of disease-induced population fluctuations for use in natural resource management decision-making.}, } @article {pmid36840322, year = {2023}, author = {Hou, H and Liu, H and Xiong, J and Wang, C and Zhang, S and Ding, Z}, title = {Comparison of Soil Bacterial Communities under Canopies of Pinus tabulaeformis and Populus euramericana in a Reclaimed Waste Dump.}, journal = {Plants (Basel, Switzerland)}, volume = {12}, number = {4}, pages = {}, pmid = {36840322}, issn = {2223-7747}, support = {No. 22BJY064//National Social Science Fund/ ; }, abstract = {To compare the effects of different remediation tree species on soil bacterial communities and provide a theoretical basis for the selection of ecosystem function promotion strategies after vegetation restoration, the characteristic changes in soil bacterial communities after Pinus tabulaeformis and Populus euramericana reclamation were explored using high-throughput sequencing and molecular ecological network methods. The results showed that: (1) With the increase in reclamation years, the reclaimed soil properties were close to the control group, and the soil properties of Pinus tabulaeformis were closer to the control group than those of P. euramericana. (2) The dominant bacteria under the canopies of P. tabulaeformis and P. euramericana was the same. Proteobacteria, Actinobacteria, Acidobacteria, Chloroflexi, Gemmatimonadetes, Planctomycetes, Bacteroidetes, and Cyanobacteria were the dominant bacteria in the restored soil, accounting for more than 95% of the total abundance. The average values of the Shannon diversity index, Simpson diversity index, Chao 1 richness estimator, and abundance-based coverage estimator of the bacterial community in the P. euramericana reclaimed soil were higher than those in the P. tabulaeformis reclaimed soil. The influence of reclamation years on the bacterial community of samples is greater than that of species types. (3) The results of ecological network construction showed that the total number of nodes, total number of connections, and average connectivity of the soil bacterial network under P. euramericana reclamation were greater than those under P. tabulaeformis reclamation. The bacterial molecular ecological network under P. euramericana was more abundant. (4) Among the dominant bacteria, the relative abundance of Actinobacteria was negatively correlated with soil pH, soil total nitrogen content, and the activities of urease, invertase, and alkaline phosphatase, while the relative abundance of Proteobacteria and Bacteroidetes was positively correlated with these environmental factors. The relationship between the soil bacterial community of P. tabulaeformis and P. euramericana and the environmental factors is not completely the same, and even the interaction between some environmental factors and bacteria is opposite.}, } @article {pmid36840309, year = {2023}, author = {Jocienė, L and Krokaitė, E and Rekašius, T and Vilčinskas, R and Judžentienė, A and Marozas, V and Kupčinskienė, E}, title = {Ionomic Parameters of Populations of Common Juniper (Juniperus communis L.) Depending on the Habitat Type.}, journal = {Plants (Basel, Switzerland)}, volume = {12}, number = {4}, pages = {}, pmid = {36840309}, issn = {2223-7747}, abstract = {For the study of the ionomic parameters of Juniperus communis needles, fourteen sites covering most of the territory of Lithuania and belonging to distinct habitats (coastal brown dunes covered with natural Scots pine forests (G), Juniperus communis scrubs (F), transition mires and quaking bogs (D), subcontinental moss Scots pine forests (G), and xero-thermophile fringes) were selected. Concentrations of macro-, micro-, and non-essential elements were analyzed in current-year needles, sampled in September. According to the concentrations of elements in J. communis needles, the differences between the most contrasting populations were as follows: up to 2-fold for Mg, N, K, Ca, and Zn; 2- to 7-fold for P, Na, Fe, Cu, Al, Cr, Ni, and Pb; and 26- to 31-fold for Mn and Cd. The concentrations of Cd, Cr, and Ni in needles of J. communis did not reach levels harmful for conifers. When compared to all other habitats (B, F, G, and E), the populations from transition mires and quaking bogs (D) had significantly lower concentrations of main nutritional elements N (12176 µg/g d. m.), P (1054 µg/g d. m.), and K (2916 µg/g d. m.). In Juniperus communis scrubs (F), a habitat protected by EUNIS, the concentration of K in the needles was highest, while Zn and Cu concentrations were the lowest. Principal component (PC) analyses using concentrations of 15 elements as variables for the discrimination of populations or habitats allowed authors to distinguish F and B habitats from the E habitat (PC1) and F and D habitats from the G habitat (PC2). Discriminating between populations, the most important variables were concentrations of P, N, Mg, Ca, Cu, and K. Discriminating between habitats, the important variables were concentrations of N and P.}, } @article {pmid36840203, year = {2023}, author = {Visztra, GV and Frei, K and Hábenczyus, AA and Soóky, A and Bátori, Z and Laborczi, A and Csikós, N and Szatmári, G and Szilassi, P}, title = {Applicability of Point- and Polygon-Based Vegetation Monitoring Data to Identify Soil, Hydrological and Climatic Driving Forces of Biological Invasions-A Case Study of Ailanthus altissima, Elaeagnus angustifolia and Robinia pseudoacacia.}, journal = {Plants (Basel, Switzerland)}, volume = {12}, number = {4}, pages = {}, pmid = {36840203}, issn = {2223-7747}, abstract = {Invasive tree species are a significant threat to native flora. They modify the environment with their allelopathic substances and inhibit the growth of native species by shading, thus reducing diversity. The most effective way to control invasive plants is to prevent their spread which requires identifying the environmental parameters promoting it. Since there are several types of invasive plant databases available, determining which database type is the most relevant for investigating the occurrence of alien plants is of great importance. In this study, we compared the efficiency and reliability of point-based (EUROSTAT Land Use and Coverage Area Frame Survey (LUCAS)) and polygon-based (National Forestry Database (NFD)) databases using geostatistical methods in ArcGIS software. We also investigated the occurrence of three invasive tree species (Ailanthus altissima, Elaeagnus angustifolia, and Robinia pseudoacacia) and their relationships with soil, hydrological, and climatic parameters such as soil organic matter content, pH, calcium carbonate content, rooting depth, water-holding capacity, distance from the nearest surface water, groundwater depth, mean annual temperature, and mean annual precipitation with generalized linear models in R-studio software. Our results show that the invasion levels of the tree species under study are generally over-represented in the LUCAS point-based vegetation maps, and the point-based database requires a dataset with a larger number of samples to be reliable. Regarding the polygon-based database, we found that the occurrence of the invasive species is generally related to the investigated soil and hydrological and climatic factors.}, } @article {pmid36836247, year = {2023}, author = {Wang, J and Qin, S and Fan, R and Peng, Q and Hu, X and Yang, L and Liu, Z and Baccelli, I and Migheli, Q and Berg, G and Chen, X and Cernava, T}, title = {Plant Growth Promotion and Biocontrol of Leaf Blight Caused by Nigrospora sphaerica on Passion Fruit by Endophytic Bacillus subtilis Strain GUCC4.}, journal = {Journal of fungi (Basel, Switzerland)}, volume = {9}, number = {2}, pages = {}, pmid = {36836247}, issn = {2309-608X}, support = {2021YFE0107700//National Key research and Development of China/ ; Guike AA21196003//Science and Technology Base & Talent Project of Guangxi Province/ ; 2019-1410;2021-229;HZJD[2022]001//Guizhou Provincial Science and Technology Program/ ; KY2021-026//Outstanding Young Scientist Program of Guizhou Province/ ; 2022-36-Z01-KF12//Guangxi Key Laboratory of Rice Genetics and Breeding Opening Research Project/ ; 111 Program; D20023//Guizhou University Cultivation Project 2019-04 and Program for Introducing Talents to Chinese Universities/ ; }, abstract = {Passion fruit (Passiflora edulis Sims) is widely cultivated in tropic and sub-tropic regions for the production of fruit, flowers, cosmetics, and for pharmacological applications. Its high economic, nutritional, and medical values elicit the market demand, and the growing areas are rapidly increasing. Leaf blight caused by Nigrospora sphaerica is a new and emerging disease of passion fruit in Guizhou, in southwest China, where the unique karst mountainous landscape and climate conditions are considered potential areas of expansion for passion fruit production. Bacillus species are the most common biocontrol and plant-growth-promotion bacteria (PGPB) resources in agricultural systems. However, little is known about the endophytic existence of Bacillus spp. in the passion fruit phyllosphere as well as their potential as biocontrol agents and PGPB. In this study, 44 endophytic strains were isolated from 15 healthy passion fruit leaves, obtained from Guangxi province, China. Through purification and molecular identification, 42 of the isolates were ascribed to Bacillus species. Their inhibitory activity against N. sphaerica was tested in vitro. Eleven endophytic Bacillus spp. strains inhibited the pathogen by >65%. All of them produced biocontrol- and plant-growth-promotion-related metabolites, including indole-3-acetic acid (IAA), protease, cellulase, phosphatase, and solubilized phosphate. Furthermore, the plant growth promotion traits of the above 11 endophytic Bacillus strains were tested on passion fruit seedlings. One isolate, coded B. subtilis GUCC4, significantly increased passion fruit stem diameter, plant height, leaf length, leaf surface, fresh weight, and dry weight. In addition, B. subtilis GUCC4 reduced the proline content, which indicated its potential to positively regulate passion fruit biochemical properties and resulted in plant growth promotion effects. Finally, the biocontrol efficiencies of B. subtilis GUCC4 against N. sphaerica were determined in vivo under greenhouse conditions. Similarly to the fungicide mancozeb and to a commercial B. subtilis-based biofungicide, B. subtilis GUCC4 significantly reduced disease severity. These results suggest that B. subtilis GUCC4 has great potential as a biological control agent and as PGPB on passion fruit.}, } @article {pmid36835681, year = {2023}, author = {Srygley, RB and Dudley, R and Hernandez, EJ and Kainz, F and Riveros, AJ and Ellington, CP}, title = {Quantifying the Aerodynamic Power Required for Flight and Testing for Adaptive Wind Drift in Passion-Vine Butterflies Heliconius sara (Lepidoptera: Nymphalidae).}, journal = {Insects}, volume = {14}, number = {2}, pages = {}, pmid = {36835681}, issn = {2075-4450}, support = {7457-03//National Geographic Society/ ; }, abstract = {Although theoretical work on optimal migration has been largely restricted to birds, relevant free-flight data are now becoming available for migratory insects. Here we report, for the first time in passion-vine butterflies, that Heliconius sara migrates directionally. To test optimal migration models for insects, we quantified the aerodynamic power curve for free-flying H. sara as they migrated across the Panama Canal. Using synchronized stereo-images from high-speed video cameras, we reconstructed three-dimensional flight kinematics of H. sara migrating naturally across the Panama Canal. We also reconstructed flight kinematics from a single-camera view of butterflies flying through a flight tunnel. We calculated the power requirements for flight for H. sara over a range of flight velocities. The relationship between aerodynamic power and velocity was "J"-shaped across the measured velocities with a minimum power velocity of 0.9 m/s and a maximum range velocity of 2.25 m/s. Migrating H. sara did not compensate for crosswind drift. Changes in airspeed with tailwind drift were consistent with the null hypothesis that H. sara did not compensate for tailwind drift, but they were also not significantly different from those predicted to maximize the migratory range of the insects.}, } @article {pmid36834418, year = {2023}, author = {Liu, J and Chen, J and Yang, Y and You, H and Han, X}, title = {Construction and Optimization of an Ecological Network in the Yellow River Source Region Based on MSPA and MCR Modelling.}, journal = {International journal of environmental research and public health}, volume = {20}, number = {4}, pages = {}, pmid = {36834418}, issn = {1660-4601}, mesh = {*Ecosystem ; Ecology ; Conservation of Natural Resources ; Rivers ; *Conservation of Water Resources ; China ; }, abstract = {The source region of the Yellow River (SRYR) is an important water conservation and farming area in China. Under the dual influence of the natural environment and external pressure, ecological patches in the region are becoming increasingly fragmented, and landscape connectivity is continuously declining, which directly affect the landscape patch pattern and SRYR sustainable development. In the SRYR, morphological spatial pattern analysis (MSPA) and landscape index methods were used to extract ecologically important sources. Based on the minimum cumulative resistance model (MCR), Linkage Mapper was used to generate a potential corridor, and then potential stepped stone patches were identified and extracted by the gravity model and betweenness centrality to build an optimal SRYR ecological network. The distribution of patches in the core area of the SRYR was fragmented, accounting for 80.53% of the total grassland area. The 10 ecological sources based on the landscape connectivity index and 15 important corridors identified based on the MCR model were mainly distributed in the central and eastern regions of the SRYR. Through betweenness centrality, 10 stepped stone patches were added, and 45 planned ecological corridors were obtained to optimize the SRYR ecological network and enhance east and west connectivity. Our research results can provide an important reference for the protection of the SRYR ecosystem, and have important guiding significance and practical value for ecological network construction in ecologically fragmented areas.}, } @article {pmid36834206, year = {2023}, author = {Li, Y and Liu, H and Su, L and Chen, S and Zhu, X and Zhang, P}, title = {Developmental Features, Influencing Factors, and Formation Mechanism of Underground Mining-Induced Ground Fissure Disasters in China: A Review.}, journal = {International journal of environmental research and public health}, volume = {20}, number = {4}, pages = {}, pmid = {36834206}, issn = {1660-4601}, mesh = {*Coal Mining ; China ; Soil ; Geology ; Pressure ; Coal ; }, abstract = {Mining-induced ground fissures are one of the major geological disasters affecting coal mines. In recent years, many effective monitoring methods have been developed to explore the developmental characteristics and nature of mining-induced ground fissures for being treated scientifically. This paper is mainly on the development law and mechanism of mining ground fissure research results which have been comprehensively combed, highlighting the development trend, including the formation condition, development features, influencing factors, and mechanical mechanism of mining-induced ground fissures. Outstanding issues are discussed and future research hot spots and trends are pointed out. The major conclusions include: (1) under the shallow coal mining condition, because the rock layer fault zone directly reaches the surface, the ground fissure usually develops seriously; (2) mining-induced ground fissures are generally divided into four types: tensile fissures, compression fissures, collapsed fissures, and sliding fissures; (3) mining-induced ground fissures are affected by the coupling effect of underground mining and surface topography. The main factors are geological mining conditions, surface deformation, and surface topography, including rock and soil structure, rock and soil mechanical properties, surface horizontal deformation, surface slope, and so on; and (4) to ensure the safety of underground mining, temporary ground fissures formed during the process of coal mining must be treated when ground fissures and rock ground fissures are connected. The results of this article make up for the deficiencies of the relevant research, provide the basis and direction for future research, and have universal applicability and scientific guiding significance.}, } @article {pmid36827177, year = {2023}, author = {Martínez-Pernía, D and Olavarría, L and Fernández-Manjón, B and Cabello, V and Henríquez, F and Robert, P and Alvarado, L and Barría, S and Antivilo, A and Velasquez, J and Cerda, M and Farías, G and Torralva, T and Ibáñez, A and Parra, MA and Gilbert, S and Slachevsky, A}, title = {The limitations and challenges in the assessment of executive dysfunction associated with real-world functioning: The opportunity of serious games.}, journal = {Applied neuropsychology. Adult}, volume = {}, number = {}, pages = {1-17}, pmid = {36827177}, issn = {2327-9109}, support = {R01 AG057234/AG/NIA NIH HHS/United States ; }, abstract = {Nowadays, there is a broad range of methods for detecting and evaluating executive dysfunction ranging from clinical interview to neuropsychological evaluation. Nevertheless, a critical issue of these assessments is the lack of correspondence of the neuropsychological test's results with real-world functioning. This paper proposes serious games as a new framework to improve the neuropsychological assessment of real-world functioning. We briefly discuss the contribution and limitations of current methods of evaluation of executive dysfunction (paper-and-pencil tests, naturalistic observation methods, and Information and Communications Technologies) to inform on daily life functioning. Then, we analyze what are the limitations of these methods to predict real-world performance: (1) A lack of appropriate instruments to investigate the complexity of real-world functioning, (2) the vast majority of neuropsychological tests assess well-structured tasks, and (3) measurement of behaviors are based on simplistic data collection and statistical analysis. This work shows how serious games offer an opportunity to develop more efficient tools to detect executive dysfunction in everyday life contexts. Serious games provide meaningful narrative stories and virtual or real environments that immerse the user in natural and social environments with social interactions. In those highly interactive game environments, the player needs to adapt his/her behavioral performance to novel and ill-structured tasks which are suited for collecting user interaction evidence. Serious games offer a novel opportunity to develop better tools to improve diagnosis of the executive dysfunction in everyday life contexts. However, more research is still needed to implement serious games in everyday clinical practice.}, } @article {pmid36826765, year = {2023}, author = {Wei, T and Guo, G and Li, H and Wang, L and Jiang, Q and Jiang, C}, title = {A novel probability integral method segmental modified model for subsidence prediction applicable to thick loose layer mining areas.}, journal = {Environmental science and pollution research international}, volume = {30}, number = {18}, pages = {52049-52061}, pmid = {36826765}, issn = {1614-7499}, support = {U21A20109//National Natural Science Foundation of China/ ; KYCX21_2294//Graduate Research and Innovation Projects of Jiangsu Province/ ; }, mesh = {*Coal Mining/methods ; *Disasters ; China ; }, abstract = {In response to the problem that the actual extent of coal mining impacts on the surface in thick loose layer mines significantly exceeds the theoretical predictions, based on the literature study, the form of influence of thick loose layer on the predicted parameters of the probability integral method is summarized and analyzed; taking into account the influence of the subsidence coefficient, the sine modification formula of the major influence radius and the logistic modification formula of the subsidence coefficient are established, respectively, and based on the characteristics of the major influence radius, a new subsidence basin demarcation point is proposed and a novel probability integral method segmental parameter modified prediction model is constructed. The simulated experiment and real data experiment results prove that the constructed probability integral method segmented parameter modified model can both reduce the convergence of surface subsidence basin edge better and take into account the predicted accuracy inside the subsidence basin. The research achievements provide scientific data support for disaster warning, pollution management, ecological restoration, and coordination between coal mining and surface city construction in thick loose layer mining areas.}, } @article {pmid36824773, year = {2023}, author = {Kapsetaki, SE and Compton, Z and Dolan, J and Harris, VK and Rupp, SM and Duke, EG and Harrison, TM and Aksoy, S and Giraudeau, M and Vincze, O and McGraw, KJ and Aktipis, A and Tollis, M and Boddy, AM and Maley, CC}, title = {Life history and cancer in birds: clutch size predicts cancer.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {36824773}, issn = {2692-8205}, support = {P01 CA091955/CA/NCI NIH HHS/United States ; R01 CA140657/CA/NCI NIH HHS/United States ; U2C CA233254/CA/NCI NIH HHS/United States ; U54 CA217376/CA/NCI NIH HHS/United States ; }, abstract = {Cancer is a disease that affects nearly all multicellular life, including birds. However, little is known about what factors explain the variance in cancer prevalence among species. Litter size is positively correlated with cancer prevalence in managed species of mammals, and larger body size, but not incubation or nestling period, is linked to tumor prevalence in wild birds. Also, birds that produce more elaborate sexual traits are expected to have fewer resources for cancer defenses and thus higher cancer prevalence. In this study, we examined whether cancer prevalence is associated with a wide variety of life history traits (clutch size, incubation length, body mass, lifespan, and the extent of sexual dimorphism) across 108 species of managed birds in 25 different zoological facilities, sanctuaries, and veterinary clinics. We found that clutch size was positively correlated with cancer and neoplasia (both benign and malignant) prevalence, even after controlling for body mass. Cancer prevalence was not associated with incubation length, body mass, lifespan, or sexual dimorphism. The positive correlations of clutch size with cancer prevalence and neoplasia prevalence suggest that there may be life-history trade-offs between reproductive investment and somatic maintenance (in the form of cancer prevention mechanisms) in managed birds.}, } @article {pmid36816807, year = {2022}, author = {Ben Aribi, H and Ding, M and Kiran, A}, title = {Gene expression data visualization tool on the o[2]S[2]PARC platform.}, journal = {F1000Research}, volume = {11}, number = {}, pages = {1267}, pmid = {36816807}, issn = {2046-1402}, mesh = {*Gene Expression Profiling ; *Computational Biology ; Data Visualization ; Gene Ontology ; Gene Expression ; }, abstract = {Background: The identification of differentially expressed genes and their associated biological processes, molecular function, and cellular components are essential for genetic disease studies because they present potential biomarkers and therapeutic targets. Methods: In this study, we developed an o[2]S[2]PARC template to instantiate an interactive pipeline for gene expression data visualization, ontological mapping, and statistical evaluation. To demonstrate the tool's usefulness, we performed a case study on a publicly available dataset. Results: The tool enables users to identify the differentially expressed genes (DEGs) and visualize them in a volcano plot format. Ontologies associated with the DEGs are assigned and visualized in barplots. Conclusions: The "Expression data visualization" template is publicly available on the o[2]S[2]PARC platform.}, } @article {pmid36821658, year = {2023}, author = {D'Emic, MD and O'Connor, PM and Sombathy, RS and Cerda, I and Pascucci, TR and Varricchio, D and Pol, D and Dave, A and Coria, RA and Curry Rogers, KA}, title = {Developmental strategies underlying gigantism and miniaturization in non-avialan theropod dinosaurs.}, journal = {Science (New York, N.Y.)}, volume = {379}, number = {6634}, pages = {811-814}, doi = {10.1126/science.adc8714}, pmid = {36821658}, issn = {1095-9203}, mesh = {Animals ; *Biological Evolution ; *Dinosaurs/anatomy & histology/classification/growth & development ; Fossils ; Phylogeny ; *Body Size ; Datasets as Topic ; }, abstract = {In amniotes, the predominant developmental strategy underlying body size evolution is thought to be adjustments to the rate of growth rather than its duration. However, most theoretical and experimental studies supporting this axiom focus on pairwise comparisons and/or lack an explicit phylogenetic framework. We present the first large-scale phylogenetic comparative analysis examining developmental strategies underlying the evolution of body size, focusing on non-avialan theropod dinosaurs. We reconstruct ancestral states of growth rate and body mass in a taxonomically rich dataset, finding that contrary to expectations, changes in the rate and duration of growth played nearly equal roles in the evolution of the vast body size disparity present in non-avialan theropods-and perhaps that of amniotes in general.}, } @article {pmid36820086, year = {2023}, author = {Huo, J and Hu, X and Bai, J and Lv, A}, title = {Multiomics analysis revealed miRNAs as potential regulators of the immune response in Carassius auratus gills to Aeromonas hydrophila infection.}, journal = {Frontiers in immunology}, volume = {14}, number = {}, pages = {1098455}, pmid = {36820086}, issn = {1664-3224}, mesh = {Animals ; *Goldfish ; Aeromonas hydrophila ; Gills ; Zebrafish/genetics ; Multiomics ; NF-kappa B/genetics ; Phylogeny ; Immunity, Innate/genetics ; *MicroRNAs/genetics ; }, abstract = {The gill of fish is an important immune organ for pathogen defense, but its microRNA (miRNA) expression and regulatory mechanism remain unclear. In this study, we report on the histopathological and immunohistochemical features of the gills of the crucian carp Carassius auratus challenged with Aeromonas hydrophila. Small RNA libraries of the gills were constructed and sequenced on the Illumina HiSeq 2000 platform. A total of 1,165 differentially expressed miRNAs (DEMs) were identified in gills, of which 539 known and 7 unknown DEMs were significantly screened (p < 0.05). Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses revealed that the potential target genes/proteins were primarily involved in 33 immune-related pathways, in which the inflammatory responses were focused on the Toll-like receptor (TLR), mitogen-activated protein kinase (MAPK), and nuclear factor kappa B (NF-κB) signaling pathways. Moreover, the expression levels of 14 key miRNAs (e.g., miR-10, miR-17, miR-26a, miR-144, miR-145, and miR-146a) and their target genes (e.g., TNFα, TLR4, NF-κB, TAB1, PI3K, and IRAK1) were verified. In addition, the protein levels based on isobaric tags for relative and absolute quantification (iTRAQ) were significantly associated with the results of the quantitative real-time PCR (qRT-PCR) analysis (p < 0.01). miR-17/pre-miR-17 were identified in the regulation expression of the NF-κB target gene, and the phylogenetic tree analysis showed that the pre-miR-17 of C. auratus with the closest similarity to the zebrafish Danio rerio is highly conserved in teleosts. This is the first report of the multi-omics analysis of the miRNAs and proteins in the gills of C. auratus infected with A. hydrophila, thus enriching knowledge on the regulation mechanism of the local immune response in Cyprinidae fish.}, } @article {pmid36815186, year = {2023}, author = {Zhou, T and Li, W}, title = {Analysis on Logistics Efficiency Measurement of New Western Land-Sea Corridor under the Background of "Double Carbon" and Ecological Environment Protection.}, journal = {Journal of environmental and public health}, volume = {2023}, number = {}, pages = {8642841}, pmid = {36815186}, issn = {1687-9813}, mesh = {*Carbon ; *Environment ; Efficiency ; Industry ; China ; Economic Development ; }, abstract = {Under the research background of ecological environment protection and "double carbon" goal, this paper applies panel data on the logistics industry from 2010 to 2019 in 12 provinces of China's new western land-sea corridor to statically measure the logistics industry's technical efficiency after taking into account the impact of different environmental elements and to analyze the dynamics trends of total factor productivity in the logistics sector. It is measured by using the three-stage SBM model and the Malmquist-Luenberger productivity index, which considers undesirable output. The findings indicate the following: (1) In the context of "double carbon," the overall technical efficiency of the logistics sector in the new western land-sea corridor seems to be relatively low; however, the average technical efficiency of the logistics sector in the southern portion of the new western land-sea corridor does seem to be higher than that of the northern part. (2) The logistics industry's technical efficiency varies greatly by region, with locations near central China having much higher technical efficiency than remote inland areas. (3) The fundamental reason for the improvement of technical efficiency in the logistics industry is pure technical efficiency, and the driving force behind the increase in total factor productivity is technological advancement. (4) Economic development, informatization development, industrial market scale, and import and export all have a substantial influence on the logistics industry's technical efficiency. Finally, depending on the findings, policy recommendations are offered.}, } @article {pmid36813959, year = {2023}, author = {Cai, S and Zhao, X and Pittelkow, CM and Fan, M and Zhang, X and Yan, X}, title = {Optimal nitrogen rate strategy for sustainable rice production in China.}, journal = {Nature}, volume = {615}, number = {7950}, pages = {73-79}, pmid = {36813959}, issn = {1476-4687}, support = {CBET-2047165//National Science Foundation/ ; CBET-2025826//National Science Foundation/ ; }, mesh = {*Agriculture/economics/methods ; China ; Fertilizers/analysis/economics ; *Nitrogen/analysis/economics/metabolism ; *Oryza/metabolism ; Soil/chemistry ; *Sustainable Development ; *Crops, Agricultural/economics/metabolism/supply & distribution ; Ecology ; Farmers ; Datasets as Topic ; Food Supply ; *Environmentalism ; }, abstract = {Avoiding excessive agricultural nitrogen (N) use without compromising yields has long been a priority for both research and government policy in China[1,2]. Although numerous rice-related strategies have been proposed[3-5], few studies have assessed their impacts on national food self-sufficiency and environmental sustainability and fewer still have considered economic risks faced by millions of smallholders. Here we established an optimal N rate strategy based on maximizing either economic (ON) or ecological (EON) performance using new subregion-specific models. Using an extensive on-farm dataset, we then assessed the risk of yield losses among smallholder farmers and the challenges of implementing the optimal N rate strategy. We find that meeting national rice production targets in 2030 is possible while concurrently reducing nationwide N consumption by 10% (6-16%) and 27% (22-32%), mitigating reactive N (Nr) losses by 7% (3-13%) and 24% (19-28%) and increasing N-use efficiency by 30% (3-57%) and 36% (8-64%) for ON and EON, respectively. This study identifies and targets subregions with disproportionate environmental impacts and proposes N rate strategies to limit national Nr pollution below proposed environmental thresholds, without compromising soil N stocks or economic benefits for smallholders. Thereafter, the preferable N strategy is allocated to each region based on the trade-off between economic risk and environmental benefit. To facilitate the adoption of the annually revised subregional N rate strategy, several recommendations were provided, including a monitoring network, fertilization quotas and smallholder subsidies.}, } @article {pmid36806940, year = {2023}, author = {Rivera-Colón, AG and Rayamajhi, N and Minhas, BF and Madrigal, G and Bilyk, KT and Yoon, V and Hüne, M and Gregory, S and Cheng, CHC and Catchen, JM}, title = {Genomics of Secondarily Temperate Adaptation in the Only Non-Antarctic Icefish.}, journal = {Molecular biology and evolution}, volume = {40}, number = {3}, pages = {}, pmid = {36806940}, issn = {1537-1719}, support = {//National Science Foundation/ ; }, mesh = {Animals ; Antarctic Regions ; *Adaptation, Physiological ; Fishes/genetics ; *Perciformes/genetics ; Genomics ; Antifreeze Proteins ; }, abstract = {White-blooded Antarctic icefishes, a family within the adaptive radiation of Antarctic notothenioid fishes, are an example of extreme biological specialization to both the chronic cold of the Southern Ocean and life without hemoglobin. As a result, icefishes display derived physiology that limits them to the cold and highly oxygenated Antarctic waters. Against these constraints, remarkably one species, the pike icefish Champsocephalus esox, successfully colonized temperate South American waters. To study the genetic mechanisms underlying secondarily temperate adaptation in icefishes, we generated chromosome-level genome assemblies of both C. esox and its Antarctic sister species, Champsocephalus gunnari. The C. esox genome is similar in structure and organization to that of its Antarctic congener; however, we observe evidence of chromosomal rearrangements coinciding with regions of elevated genetic divergence in pike icefish populations. We also find several key biological pathways under selection, including genes related to mitochondria and vision, highlighting candidates behind temperate adaptation in C. esox. Substantial antifreeze glycoprotein (AFGP) pseudogenization has occurred in the pike icefish, likely due to relaxed selection following ancestral escape from Antarctica. The canonical AFGP locus organization is conserved in C. esox and C. gunnari, but both show a translocation of two AFGP copies to a separate locus, previously unobserved in cryonotothenioids. Altogether, the study of this secondarily temperate species provides an insight into the mechanisms underlying adaptation to ecologically disparate environments in this otherwise highly specialized group.}, } @article {pmid36803728, year = {2023}, author = {Niu, L and Zhagn, L and Xi, F and Wang, J}, title = {[Influencing factors and scenario forecasting of carbon emissions in Liaoning Province, China].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {34}, number = {2}, pages = {499-509}, doi = {10.13287/j.1001-9332.202302.001}, pmid = {36803728}, issn = {1001-9332}, mesh = {*Carbon/analysis ; *Carbon Dioxide/analysis ; Economic Development ; China ; Forecasting ; }, abstract = {Liaoning is a province with large energy consumption and carbon emissions. Management of carbon emissions in Liaoning Province is crucial to realizing China's carbon peaking and carbon neutrality goals. To clarify the driving factors and trends of carbon emissions in Liaoning Province, we analyzed the impacts of six factors on carbon emissions in Liaoning Province through STIRPAT model based on carbon emission data from 1999 to 2019. The impact factors included population, urbanization rate, per-capita GDP, secondary industry ratio, energy consumption per unit GDP, and coal consumption ratio. Nine forecasting scenarios with three economic and population growth models and three emission reduction models were set up, and their carbon emission trends under the above nine forecasting scenarios were predicted. The results showed that the main driving factor of carbon emissions in Liaoning Province was per-capita GDP, and that the main inhibitor was energy consumption per unit GDP. The carbon peak year in Liaoning Province would fluctuate between 2020 and 2055 under the nine forecasting scenarios, with peak values ranging from 544 to 1088 million tons CO2. The medium economic development growth and high carbon emission reduction scenario would be the optimal carbon emission scenario in Liaoning Province. Under this forecasting scenario, Liaoning Province could achieve carbon peak (611 million tons CO2) by 2030 without affec-ting economic development through optimizing energy structure and controlling the intensity of energy consumption. Our results would be helpful for seeking the best path for carbon emission reduction in Liaoning Province and providing a reference for its realization of carbon peaking and carbon neutrality goals.}, } @article {pmid36795572, year = {2023}, author = {Wang, J and Ding, R and Ouyang, T and Gao, H and Kan, H and Li, Y and Hu, Q and Yang, Y}, title = {Systematic investigation of the mechanism of herbal medicines for the treatment of prostate cancer.}, journal = {Aging}, volume = {15}, number = {4}, pages = {1004-1024}, pmid = {36795572}, issn = {1945-4589}, mesh = {Male ; Humans ; *Drugs, Chinese Herbal/pharmacology/therapeutic use/chemistry ; Phosphatidylinositol 3-Kinases ; Reproducibility of Results ; *Prostatic Neoplasms/drug therapy/genetics ; }, abstract = {Due to various unpleasant side effects and general ineffectiveness of current treatments for prostate cancer (PCa), more and more people with PCa try to look for complementary and alternative medicine such as herbal medicine. However, since herbal medicine has multi-components, multi-targets and multi-pathways features, its underlying molecular mechanism of action is not yet known and still needs to be systematically explored. Presently, a comprehensive approach consisting of bibliometric analysis, pharmacokinetic assessment, target prediction and network construction is firstly performed to obtain PCa-related herbal medicines and their corresponding candidate compounds and potential targets. Subsequently, a total of 20 overlapping genes between DEGs in PCa patients and the target genes of the PCa-related herbs, as well as five hub genes, i.e., CCNA2, CDK2, CTH, DPP4 and SRC were determined employing bioinformatics analysis. Further, the roles of these hub genes in PCa were also investigated through survival analysis and tumour immunity analysis. Moreover, to validate the reliability of the C-T interactions and to further explore the binding modes between ingredients and their targets, the molecular dynamics (MD) simulations were carried out. Finally, based on the modularization of the biological network, four signaling pathways, i.e., PI3K-Akt, MAPK, p53 and cell cycle were integrated to further analyze the therapeutic mechanism of PCa-related herbal medicine. All the results show the mechanism of action of herbal medicines on treating PCa from the molecular to systematic levels, providing a reference for the treatment of complex diseases using TCM.}, } @article {pmid36792824, year = {2023}, author = {Woodhouse, A and Swain, A and Fagan, WF and Fraass, AJ and Lowery, CM}, title = {Late Cenozoic cooling restructured global marine plankton communities.}, journal = {Nature}, volume = {614}, number = {7949}, pages = {713-718}, pmid = {36792824}, issn = {1476-4687}, mesh = {Animals ; *Aquatic Organisms/classification/isolation & purification ; *Biodiversity ; *Cold Temperature ; Datasets as Topic ; *Foraminifera/classification/isolation & purification ; Fossils ; *Geographic Mapping ; History, Ancient ; Phylogeny ; *Phylogeography ; *Plankton/classification/isolation & purification ; *Spatio-Temporal Analysis ; Time Factors ; Hydrobiology ; }, abstract = {The geographic ranges of marine organisms, including planktonic foraminifera[1], diatoms, dinoflagellates[2], copepods[3] and fish[4], are shifting polewards owing to anthropogenic climate change[5]. However, the extent to which species will move and whether these poleward range shifts represent precursor signals that lead to extinction is unclear[6]. Understanding the development of marine biodiversity patterns over geological time and the factors that influence them are key to contextualizing these current trends. The fossil record of the macroperforate planktonic foraminifera provides a rich and phylogenetically resolved dataset that provides unique opportunities for understanding marine biogeography dynamics and how species distributions have responded to ancient climate changes. Here we apply a bipartite network approach to quantify group diversity, latitudinal specialization and latitudinal equitability for planktonic foraminifera over the past eight million years using Triton, a recently developed high-resolution global dataset of planktonic foraminiferal occurrences[7]. The results depict a global, clade-wide shift towards the Equator in ecological and morphological community equitability over the past eight million years in response to temperature changes during the late Cenozoic bipolar ice sheet formation. Collectively, the Triton data indicate the presence of a latitudinal equitability gradient among planktonic foraminiferal functional groups which is coupled to the latitudinal biodiversity gradient only through the geologically recent past (the past two million years). Before this time, latitudinal equitability gradients indicate that higher latitudes promoted community equitability across ecological and morphological groups. Observed range shifts among marine planktonic microorganisms[1,2,8] in the recent and geological past suggest substantial poleward expansion of marine communities even under the most conservative future global warming scenarios.}, } @article {pmid36792330, year = {2023}, author = {Suzuki, S and Nishikawa, Y and Okada, H and Nakayama, T}, title = {Information-seeking behaviour of community pharmacists during the COVID-19 pandemic: an ecological study.}, journal = {BMJ open}, volume = {13}, number = {2}, pages = {e062465}, pmid = {36792330}, issn = {2044-6055}, mesh = {Humans ; *COVID-19/epidemiology ; Pharmacists ; Pandemics ; Information Seeking Behavior ; *Community Pharmacy Services ; }, abstract = {OBJECTIVE: To evaluate the information-seeking behaviour of pharmacists during the COVID-19 pandemic and its relation to COVID-19 and related infections and deaths within the local prefecture.

DESIGN: Ecological study.

SETTING: Japan-47 prefectures.

METHODS: The number of accesses to a Japanese web page established by the Pharmacy Informatics Group to disseminate information about infection control and the number of infections and deaths in 47 prefectures were investigated from 6 April to 30 September 2020 using the access information on the web page and publicly available information.

RESULTS: During the first 6 months of the COVID-19 pandemic, the total number of accesses was 226 130 (range: 10 984-138 898 per month), the total number of infections was 78 761 (1738-31 857) and the total number of deaths was 1470 (39-436). The correlation between the total number of accesses and that of infections per 100 000 individuals in 47 prefectures was r=0.72 (95% CI 0.55 to 0.83, p<0.001), and between the total number of accesses and deaths per 100 000 individuals in 47 prefectures was r=0.44 (95% CI 0.17 to 0.65, p=0.002).

CONCLUSIONS: The information-seeking behaviour of community pharmacists correlated positively with infection status within the community.}, } @article {pmid36788337, year = {2023}, author = {Bayer, N and Hausmann, B and Pandey, RV and Deckert, F and Gail, LM and Strobl, J and Pjevac, P and Krall, C and Unterluggauer, L and Redl, A and Bachmayr, V and Kleissl, L and Nehr, M and Kirkegaard, R and Makristathis, A and Watzenboeck, ML and Nica, R and Staud, C and Hammerl, L and Wohlfarth, P and Ecker, RC and Knapp, S and Rabitsch, W and Berry, D and Stary, G}, title = {Correction: Disturbances in microbial skin recolonization and cutaneous immune response following allogeneic stem cell transfer.}, journal = {Leukemia}, volume = {37}, number = {3}, pages = {724}, doi = {10.1038/s41375-023-01839-7}, pmid = {36788337}, issn = {1476-5551}, } @article {pmid36787802, year = {2023}, author = {Dennis, A and Cuthbertson, DJ and Wootton, D and Crooks, M and Gabbay, M and Eichert, N and Mouchti, S and Pansini, M and Roca-Fernandez, A and Thomaides-Brears, H and Kelly, M and Robson, M and Hishmeh, L and Attree, E and Heightman, M and Banerjee, R and Banerjee, A}, title = {Multi-organ impairment and long COVID: a 1-year prospective, longitudinal cohort study.}, journal = {Journal of the Royal Society of Medicine}, volume = {116}, number = {3}, pages = {97-112}, pmid = {36787802}, issn = {1758-1095}, mesh = {Humans ; Female ; Middle Aged ; Male ; *COVID-19/epidemiology ; SARS-CoV-2 ; Post-Acute COVID-19 Syndrome ; Prospective Studies ; Quality of Life ; Longitudinal Studies ; }, abstract = {OBJECTIVES: To determine the prevalence of organ impairment in long COVID patients at 6 and 12 months after initial symptoms and to explore links to clinical presentation.

DESIGN: Prospective cohort study.

PARTICIPANTS: Individuals.

METHODS: In individuals recovered from acute COVID-19, we assessed symptoms, health status, and multi-organ tissue characterisation and function.

SETTING: Two non-acute healthcare settings (Oxford and London). Physiological and biochemical investigations were performed at baseline on all individuals, and those with organ impairment were reassessed.

MAIN OUTCOME MEASURES: Primary outcome was prevalence of single- and multi-organ impairment at 6 and 12 months post COVID-19.

RESULTS: A total of 536 individuals (mean age 45 years, 73% female, 89% white, 32% healthcare workers, 13% acute COVID-19 hospitalisation) completed baseline assessment (median: 6 months post COVID-19); 331 (62%) with organ impairment or incidental findings had follow-up, with reduced symptom burden from baseline (median number of symptoms 10 and 3, at 6 and 12 months, respectively). Extreme breathlessness (38% and 30%), cognitive dysfunction (48% and 38%) and poor health-related quality of life (EQ-5D-5L < 0.7; 57% and 45%) were common at 6 and 12 months, and associated with female gender, younger age and single-organ impairment. Single- and multi-organ impairment were present in 69% and 23% at baseline, persisting in 59% and 27% at follow-up, respectively.

CONCLUSIONS: Organ impairment persisted in 59% of 331 individuals followed up at 1 year post COVID-19, with implications for symptoms, quality of life and longer-term health, signalling the need for prevention and integrated care of long COVID.Trial Registration: ClinicalTrials.gov Identifier: NCT04369807.}, } @article {pmid36782205, year = {2023}, author = {Amin, M and Aziz, MA and Pieroni, A and Nazir, A and Al-Ghamdi, AA and Kangal, A and Ahmad, K and Abbasi, AM}, title = {Edible wild plant species used by different linguistic groups of Kohistan Upper Khyber Pakhtunkhwa (KP), Pakistan.}, journal = {Journal of ethnobiology and ethnomedicine}, volume = {19}, number = {1}, pages = {6}, pmid = {36782205}, issn = {1746-4269}, support = {RSP202R483//Abdullah Ahmed Al-Ghamdi, King Saud University/ ; RSP202R483//Abdullah Ahmed Al-Ghamdi, King Saud University/ ; }, mesh = {Humans ; Pakistan ; *Plants, Edible ; *Ethnobotany/methods ; Vegetables ; Fruit ; }, abstract = {BACKGROUND: The mountainous territory of Kohistan shelters diverse food plant species and is considered one of the important hotspots of local plant knowledge. In the era of globalization and food commodification, wild food plants (WFPs) play an important role in supporting local food systems and related local knowledge is one of the important pillars of food sustainability across the region. Since the area is populated by different cultural groups and each culture has retained particular knowledge on the local plant species, therefore, to make a cross-culturally comparison, the study was planned to record and compare the local plants knowledge among three linguistic groups viz Gujjar, Kohistani and Shina in order to not only protect the local knowledge but to determine the food cultural adaptations among these groups looking through the lens of their food ethnobotanies.

METHODS: Field ethnobotanical survey was carried out in 2020-2021 to gather the data on wild food plants. We used semi-structured interviews. Use reports were counted, and the results were visualized through Venn diagrams.

RESULTS: In total, 64 plant species belonging to 45 botanical families were documented. Among these Ajuga integrifolia, Barbarea verna, Clematis grata, Impatiens edgeworthii, Ranunculus laetus (vegetables), Parrotiopsis jacquemontiana (fruit), Indigofera tinctoria (flower), Juniperus excelsa, Primula elliptica, P. macrophylla (flavoring agent), Leontopodium himalayanum (Chewing gum), and Juniperus excelsa (snuff) were reported for the first time. The highest use reports (≥ 90) were recorded for Mentha longifolia, Amaranthus hybridus, Quercus semecarpifolia, Solanum miniatum, Oxalis corniculata, Ficus palmata, and Urtica dioica. Maximum number of wild food plant species (WFPs) were reported by Kohistani, followed by Shinaki and Gujjari linguistic groups. The percentage overlap of traditional knowledge on WFPs was highest among Kohistani and Shinaki (56.0%), followed by Shinaki and Gujjars (17.0%), and Kohistani and Gujjars (15.0%). Kohistani and Shinaki groups exhibited maximum homogeneity in traditional knowledge. However, Gujjars had more knowledge on WFPs compared to Kohistani and Shinaki. In addition, some dairy products viz. Bhorus, Bagora, Bak, Cholam, Kacha, Gurloo and Poyeen were reported also reported that are consumed orally and used in traditional cuisines.

CONCLUSIONS: The study indicates that Kohistan is one of the important spots of biocultural diversity and could be recognized as biocultural refugia. WFPs have been an integral part of the traditional food systems among the studied groups, particularly the Gujjars have reported more distinct plant uses which could be referred to their distinctive ecological experiences among others. However, social change is one of the challenges that might lead to the erosion of local plant knowledge. Moreover, intercultural negotiations among the studied groups are also a matter of concern which could homogenize the local knowledge among them. Therefore, we suggest solid policy measures to protect the local knowledge and celebrate diversity across this mountain territory.}, } @article {pmid36781356, year = {2023}, author = {Mayne, SL and DiFiore, G and Hannan, C and Nwokeji, U and Tam, V and Filograna, C and Martin, T and South, E and Mitchell, JA and Glanz, K and Fiks, AG}, title = {Feasibility and acceptability of mobile methods to assess home and neighborhood environments related to adolescent sleep.}, journal = {Sleep health}, volume = {9}, number = {3}, pages = {331-338}, pmid = {36781356}, issn = {2352-7226}, support = {K01 HL155860/HL/NHLBI NIH HHS/United States ; }, mesh = {Humans ; Male ; Adolescent ; Female ; Feasibility Studies ; *Geographic Information Systems ; *Smartphone ; Noise ; Neighborhood Characteristics ; }, abstract = {OBJECTIVE: A growing evidence base suggests home and neighborhood environmental exposures may influence adolescent sleep, but few studies have assessed these relationships using methods that account for time-varying, location-specific exposures, or multiple neighborhood contexts. This study aimed to assess the feasibility and acceptability of using smartphone global positioning system (GPS) tracking and ecological momentary assessment (EMA) to assess time-varying home and neighborhood environmental exposures hypothesized to be associated with adolescent sleep.

METHODS: Adolescents aged 15-17 years in Philadelphia completed 7 days of continuous smartphone GPS tracking, which was used to identify daily levels of exposure to geocoded neighborhood factors (eg, crime, green space). Four daily EMA surveys assessed home sleep environment (eg, noise, light), stress, health behaviors, and neighborhood perceptions. Feasibility and acceptability of GPS tracking and EMA were assessed, and distributions of daily environmental exposures were examined.

RESULTS: Among 25 teens (mean age 16, 56% male), there was a high level of GPS location data captured (median daily follow-up: 24 hours). Seventy-eight percent of EMA surveys were completed overall. Most participants (96%) reported no privacy concerns related to GPS tracking and minimal burden from EMA surveys. Exposures differed between participants' home neighborhoods and locations visited outside the home neighborhood (eg, higher crime away from home). Sleep environment disruptions were present on 29% of nights (most common: uncomfortable temperature) and were reported by 52% of adolescents.

CONCLUSIONS: Results demonstrate the feasibility and acceptability of mobile methods for assessing time-varying home and neighborhood exposures relevant to adolescent sleep for up to 1 week.}, } @article {pmid36777319, year = {2022}, author = {Glasgow, L and Lewis, R and Charles, S}, title = {The cancer epidemic in the Caribbean region: Further opportunities to reverse the disease trend.}, journal = {Lancet regional health. Americas}, volume = {13}, number = {}, pages = {100295}, pmid = {36777319}, issn = {2667-193X}, abstract = {Cancer incidence has been rising in the Caribbean and is expected to have significant adverse implications for the health of people in the region and health systems in this decade. While developed countries, for the most part, enjoy the benefits of advanced technologies and adaptive systems in cancer control and management, a different experience confronts a large segment of the Caribbean population. The region has experienced some success in enhancing cancer services, however, there is a need to address gaps in several areas through nationally and regionally tailored initiatives. This Review complements previous publications on the challenges, actions, and progress towards cancer prevention and care in Caribbean countries but also further outlines potential positive impacts that can be derived from addressing gaps pertaining to cancer education, data management, screening and risk assessment, navigation services, gender factors, and resource development. The proposed approaches encapsulate concepts of health theories that are applicable across the ecological domains. When implemented in combination, the proposals may effectively contribute to reducing the cancer burden in the region.}, } @article {pmid36775641, year = {2023}, author = {Liu, L and Zhang, WQ and Hu, FC and Pang, K and Guo, YL and Zhang, T and Li, M}, title = {[Evaluation and Optimization of Rural Sewage Treatment Technologies in the Middle Reaches of the Yangtze River Based on Group Decision Making and Analytic Hierarchy Process].}, journal = {Huan jing ke xue= Huanjing kexue}, volume = {44}, number = {2}, pages = {1191-1200}, doi = {10.13227/j.hjkx.202203043}, pmid = {36775641}, issn = {0250-3301}, mesh = {*Sewage ; *Rivers ; Analytic Hierarchy Process ; Nitrogen ; Decision Making ; China ; }, abstract = {Rural sewage treatment in the Yangtze River basin is an important link to achieve the great protection of the Yangtze River, but the existing treatment technologies are difficult to choose and have various techniques and a lack of evaluation. Therefore, this study researched and collected the case information of rural sewage treatment projects in the middle reaches of the Yangtze River, analyzed the application of each treatment technology under different collection modes and discharge standards, constructed the evaluation index system of rural sewage treatment technologies, and then conducted a classification evaluation of processing technologies for each application scenario based on group decision making and the Analytic Hierarchy Process. The results showed that:the collection modes of rural sewage in the middle reaches of the Yangtze River were mainly single village or small-scale joint village, the treatment scale was mainly concentrated below 200 m[3]·d[-1], the treatment technology was most applied by the anaerobic+ecological process (28.05%), and the application of integrated equipment was also more widely used (22.47%). The technical performance in the criterion layer had the largest weight (0.5039) in the evaluation index system, followed by those of economic benefits (0.2474), operation and management (0.1559), and environmental impact (0.0928), respectively; the four indicators of TP removal rate, ton water operation cost, ammonia nitrogen removal rate, and maintenance difficulty had higher weights. The evaluation and optimization results showed that the enhanced ecological and anaerobic+ecological treatment technologies were suitable for promotion and application in the rural areas of the middle reaches of the Yangtze River. The results of this study can provide scientific basis and reference for the selection of rural sewage treatment technologies in the middle reaches of the Yangtze River.}, } @article {pmid36771658, year = {2023}, author = {Shah, AA and Badshah, L and Khalid, N and Shah, MA and Manduzai, AK and Faiz, A and De Chiara, M and Mattalia, G and Sõukand, R and Pieroni, A}, title = {Disadvantaged Economic Conditions and Stricter Border Rules Shape Afghan Refugees' Ethnobotany: Insights from Kohat District, NW Pakistan.}, journal = {Plants (Basel, Switzerland)}, volume = {12}, number = {3}, pages = {}, pmid = {36771658}, issn = {2223-7747}, abstract = {The study of migrants' ethnobotany can help to address the diverse socio-ecological factors affecting temporal and spatial changes in local ecological knowledge (LEK). Through semi-structured and in-depth conversations with ninety interviewees among local Pathans and Afghan refugees in Kohat District, NW Pakistan, one hundred and forty-five wild plant and mushroom folk taxa were recorded. The plants quoted by Afghan refugees living inside and outside the camps tend to converge, while the Afghan data showed significant differences with those collected by local Pakistani Pathans. Interviewees mentioned two main driving factors potentially eroding folk plant knowledge: (a) recent stricter border policies have made it more difficult for refugees to visit their home regions in Afghanistan and therefore to also procure plants in their native country; (b) their disadvantaged economic conditions have forced them to engage more and more in urban activities in the host country, leaving little time for farming and foraging practices. Stakeholders should foster the exposure that refugee communities have to their plant resources, try to increase their socio-economic status, and facilitate both their settling outside the camps and their transnational movement for enhancing their use of wild plants, ultimately leading to improvements in their food security and health status.}, } @article {pmid36768056, year = {2023}, author = {Vukašinović, D and Maksimović, M and Tanasković, S and Marinković, JM and Radak, Đ and Maksimović, J and Vujčić, I and Prijović, N and Vlajinac, H}, title = {Body Mass Index and Late Adverse Outcomes after a Carotid Endarterectomy.}, journal = {International journal of environmental research and public health}, volume = {20}, number = {3}, pages = {}, pmid = {36768056}, issn = {1660-4601}, mesh = {Humans ; *Endarterectomy, Carotid/adverse effects ; *Carotid Stenosis ; Body Mass Index ; Cohort Studies ; Overweight/complications/epidemiology ; Treatment Outcome ; *Stroke/epidemiology/etiology ; Obesity/complications/epidemiology ; Retrospective Studies ; *Myocardial Infarction/epidemiology/etiology ; Risk Factors ; }, abstract = {A cohort study was conducted to examine the association of an increased body mass index (BMI) with late adverse outcomes after a carotid endarterectomy (CEA). It comprised 1597 CEAs, performed in 1533 patients at the Vascular Surgery Clinic in Belgrade, from 1 January 2012 to 31 December 2017. The follow-up lasted four years after CEA. Data for late myocardial infarction and stroke were available for 1223 CEAs, data for death for 1305 CEAs, and data for restenosis for 1162 CEAs. Logistic and Cox regressions were used in the analysis. The CEAs in patients who were overweight and obese were separately compared with the CEAs in patients with a normal weight. Out of 1223 CEAs, 413 (33.8%) were performed in patients with a normal weight, 583 (47.7%) in patients who were overweight, and 220 (18.0%) in patients who were obese. According to the logistic regression analysis, the compared groups did not significantly differ in the frequency of myocardial infarction, stroke, and death, as late major adverse outcomes (MAOs), or in the frequency of restenosis. According to the Cox and logistic regression analyses, BMI was neither a predictor for late MAOs, analyzed separately or all together, nor for restenosis. In conclusion, being overweight and being obese were not related to the occurrence of late adverse outcomes after a carotid endarterectomy.}, } @article {pmid36767964, year = {2023}, author = {Cao, H and Ou, H and Ju, W and Pan, M and Xue, H and Zhu, F}, title = {Visual Analysis of International Environmental Security Management Research (1997-2021) Based on VOSviewer and CiteSpace.}, journal = {International journal of environmental research and public health}, volume = {20}, number = {3}, pages = {}, pmid = {36767964}, issn = {1660-4601}, mesh = {Bayes Theorem ; *Agriculture ; Australia ; *Big Data ; China ; }, abstract = {To investigate the international development status and hot trends in the field of environmental security management in recent years, the published the environmental security management literature from 1997 to 2021, which was retrieved from Web of Science, with VOSviewer as the main and CiteSpace as the auxiliary, through the cooperation network of authors, scientific research institutions, and countries. The keywords were visualized by clustering, time zone analysis, and burst analysis. A total of 7596 articles were retrieved, forming six main clustering labels, including 28,144 authors. The research hotspots are from the fields of personal health, society, agriculture, ecological environment, energy, and sustainable development, as well as the development of internet environmental safety management, such as big data, Bayesian networks, and conceptual frameworks. Through cluster analysis, the cooperation of major research teams and scientific research institutions and the cooperation and development between countries were analyzed. The cooperation between scientific research institutions in various countries is relatively close. The United States currently occupies a dominant and authoritative position in this field. China has cooperated more closely with the United States, Britain, Australia, and India.}, } @article {pmid36767252, year = {2023}, author = {Liu, Q and Guo, R and Huang, Z and He, B and Li, X}, title = {The Nonlinear Impact of Mobile Human Activities on Vegetation Change in the Guangdong-Hong Kong-Macao Greater Bay Area.}, journal = {International journal of environmental research and public health}, volume = {20}, number = {3}, pages = {}, pmid = {36767252}, issn = {1660-4601}, mesh = {Humans ; Hong Kong ; Macau ; *Ecosystem ; *Urbanization ; Human Activities ; China ; }, abstract = {Vegetation is essential for ecosystem function and sustainable urban development. In the context of urbanization, the Guangdong-Hong Kong-Macao Greater Bay Area (GBA), as the typical urban-dominated region, has experienced a remarkable increase in social and economic activities. Their impact on vegetation is of great significance but unclear, as interannual flow data and linear methods have limitations. Therefore, in this study, we used human and vehicle flow data to build and simulate the indices of mobile human activity. In addition, we used partial least squares regression (PLSR), random forest (RF), and geographical detector (GD) models to analyze the impact of mobile human activities on vegetation change. The results showed that indices of mobile human and vehicle flow increased by 1.43 and 7.68 times from 2000 to 2019 in the GBA, respectively. Simultaneously, vegetation increased by approximately 64%, whereas vegetation decreased mainly in the urban areas of the GBA. Vegetation change had no significant linear correlation with mobile human activities, exhibiting a regression coefficient below 0.1 and a weight of coefficients of PLSR less than 40 between vegetation change and all the factors of human activities. However, a more significant nonlinear relationship between vegetation change and driving factors were obtained. In the RF regression model, vegetation decrease was significantly affected by mobile human activity of vehicle flow, with an importance score of 108.11. From the GD method, vegetation decrease was found to mainly interact with indices of mobile human and vehicle inflow, and the highest interaction force was 0.82. These results may support the attainment of sustainable social-ecological systems and global environmental change.}, } @article {pmid36758962, year = {2023}, author = {Lee, HE and Kim, YG and Jeong, JY and Kim, DH}, title = {Data resource profile: the Korean Community Health Status Indicators (K-CHSI) database.}, journal = {Epidemiology and health}, volume = {45}, number = {}, pages = {e2023016}, pmid = {36758962}, issn = {2092-7193}, mesh = {Humans ; Databases, Factual ; *Environment ; *Health Status Indicators ; Health Surveys ; Republic of Korea/epidemiology ; Public Health ; }, abstract = {Korean Community Health Status Indicators (K-CHSI) is a model-based database containing annual data on health outcomes and determinants at the municipal level (si/gun/gu-level regions, including mid-sized cities, counties, and districts). K-CHSI's health outcomes include overall mortality, disease incidence, prevalence rates, and self-reported health. Health determinants were measured in 5 domains: socio-demographic factors, health behaviors, social environment, physical environment, and the healthcare system. The data sources are 71 public databases, including Causes of Death Statistics, Cancer Registration Statistics, Community Health Survey, Population Census, and Census on Establishments and Statistics of Urban Plans. This dataset covers Korea's 17 metropolitan cities and provinces, with data from approximately 250 municipal regions (si/gun/gu). The current version of the database (DB version 1.3) was built using 12 years of data from 2008 to 2019. All data included in K-CHSI may be downloaded via the Korea Community Health Survey site, with no login requirement (https://chs.kdca.go.kr/chs/recsRoom/dataBaseMain.do). K-CHSI covers extensive health outcomes and health determinants at the municipal level over a period of more than 10 years, which enables ecological and time-series analyses of the relationships among various health outcomes and related factors.}, } @article {pmid36752771, year = {2023}, author = {Lippi, CA and Rund, SSC and Ryan, SJ}, title = {Characterizing the Vector Data Ecosystem.}, journal = {Journal of medical entomology}, volume = {60}, number = {2}, pages = {247-254}, pmid = {36752771}, issn = {1938-2928}, mesh = {Animals ; *Ecosystem ; *Vector Borne Diseases ; Databases, Factual ; }, abstract = {A growing body of information on vector-borne diseases has arisen as increasing research focus has been directed towards the need for anticipating risk, optimizing surveillance, and understanding the fundamental biology of vector-borne diseases to direct control and mitigation efforts. The scope and scale of this information, in the form of data, comprising database efforts, data storage, and serving approaches, means that it is distributed across many formats and data types. Data ranges from collections records to molecular characterization, geospatial data to interactions of vectors and traits, infection experiments to field trials. New initiatives arise, often spanning the effort traditionally siloed in specific research disciplines, and other efforts wane, perhaps in response to funding declines, different research directions, or lack of sustained interest. Thusly, the world of vector data - the Vector Data Ecosystem - can become unclear in scope, and the flows of data through these various efforts can become stymied by obsolescence, or simply by gaps in access and interoperability. As increasing attention is paid to creating FAIR (Findable Accessible Interoperable, and Reusable) data, simply characterizing what is 'out there', and how these existing data aggregation and collection efforts interact, or interoperate with each other, is a useful exercise. This study presents a snapshot of current vector data efforts, reporting on level of accessibility, and commenting on interoperability using an illustration to track a specimen through the data ecosystem to understand where it occurs for the database efforts anticipated to describe it (or parts of its extended specimen data).}, } @article {pmid36750720, year = {2023}, author = {Mechenich, MF and Žliobaitė, I}, title = {Eco-ISEA3H, a machine learning ready spatial database for ecometric and species distribution modeling.}, journal = {Scientific data}, volume = {10}, number = {1}, pages = {77}, pmid = {36750720}, issn = {2052-4463}, support = {314803//Academy of Finland (Suomen Akatemia)/ ; 1314803//Academy of Finland (Suomen Akatemia)/ ; }, mesh = {Animals ; Humans ; Climate Change ; *Databases, Factual ; *Ecosystem ; Geography ; Machine Learning ; Mammals ; }, abstract = {We present the Eco-ISEA3H database, a compilation of global spatial data characterizing climate, geology, land cover, physical and human geography, and the geographic ranges of nearly 900 large mammalian species. The data are tailored for machine learning (ML)-based ecological modeling, and are intended primarily for continental- to global-scale ecometric and species distribution modeling. Such models are trained on present-day data and applied to the geologic past, or to future scenarios of climatic and environmental change. Model training requires integrated global datasets, describing species' occurrence and environment via consistent observational units. The Eco-ISEA3H database incorporates data from 17 sources, and includes 3,033 variables. The database is built on the Icosahedral Snyder Equal Area (ISEA) aperture 3 hexagonal (3H) discrete global grid system (DGGS), which partitions the Earth's surface into equal-area hexagonal cells. Source data were incorporated at six nested ISEA3H resolutions, using scripts developed and made available here. We demonstrate the utility of the database in a case study analyzing the bioclimatic envelopes of ten large, widely distributed mammalian species.}, } @article {pmid36748522, year = {2022}, author = {Cunningham-Oakes, E and Pointon, T and Murphy, B and Campbell-Lee, S and Connor, TR and Mahenthiralingam, E}, title = {Novel application of metagenomics for the strain-level detection of bacterial contaminants within non-sterile industrial products - a retrospective, real-time analysis.}, journal = {Microbial genomics}, volume = {8}, number = {11}, pages = {}, pmid = {36748522}, issn = {2057-5858}, support = {MR/L015080/1/MRC_/Medical Research Council/United Kingdom ; BB/M009122/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Retrospective Studies ; *Bacteria/genetics ; *Metagenome ; Metagenomics/methods ; Workflow ; }, abstract = {The home and personal care (HPC) industry generally relies on initial cultivation and subsequent biochemical testing for the identification of microorganisms in contaminated products. This process is slow (several days for growth), labour intensive, and misses organisms which fail to revive from the harsh environment of preserved consumer products. Since manufacturing within the HPC industry is high-throughput, the process of identification of microbial contamination could benefit from the multiple cultivation-independent methodologies that have developed for the detection and analysis of microbes. We describe a novel workflow starting with automated DNA extraction directly from a HPC product, and subsequently applying metagenomic methodologies for species and strain-level identification of bacteria. The workflow was validated by application to a historic microbial contamination of a general-purpose cleaner (GPC). A single strain of Pseudomonas oleovorans was detected metagenomically within the product. The metagenome mirrored that of a contaminant isolated in parallel by a traditional cultivation-based approach. Using a dilution series of the incident sample, we also provide evidence to show that the workflow enables detection of contaminant organisms down to 100 CFU/ml of product. To our knowledge, this is the first validated example of metagenomics analysis providing confirmatory evidence of a traditionally isolated contaminant organism, in a HPC product.}, } @article {pmid36747723, year = {2023}, author = {Rokhsar, JL and Raynor, B and Sheen, J and Goldstein, ND and Levy, MZ and Castillo-Neyra, R}, title = {Modeling the impact of xenointoxication in dogs to halt Trypanosoma cruzi transmission.}, journal = {medRxiv : the preprint server for health sciences}, volume = {}, number = {}, pages = {}, pmid = {36747723}, support = {K01 AI139284/AI/NIAID NIH HHS/United States ; T32 AI070077/AI/NIAID NIH HHS/United States ; }, abstract = {BACKGROUND: Chagas disease, a vector-borne parasitic disease caused by Trypanosoma cruzi , affects millions in the Americas. Dogs are important reservoirs of the parasite. Under laboratory conditions, canine treatment with the systemic insecticide fluralaner demonstrated efficacy in killing Triatoma infestans and T. brasiliensis, T. cruzi vectors, when they feed on dogs. This form of pest control is called xenointoxication. However, T. cruzi can also be transmitted orally when mammals ingest infected bugs, so there is potential for dogs to become infected upon consuming infected bugs killed by the treatment. Xenointoxication thereby has two contrasting effects on dogs: decreasing the number of insects feeding on the dogs but increasing opportunities for exposure to T. cruzi via oral transmission to dogs ingesting infected insects.

OBJECTIVE: Examine the potential for increased infection rates of T. cruzi in dogs following xenointoxication.

DESIGN/METHODS: We built a deterministic mathematical model, based on the Ross-MacDonald malaria model, to investigate the net effect of fluralaner treatment on the prevalence of T. cruzi infection in dogs in different epidemiologic scenarios. We drew upon published data on the change in percentage of bugs killed that fed on treated dogs over days post treatment. Parameters were adjusted to mimic three scenarios of T. cruzi transmission: high and low disease prevalence and domestic vectors, and low disease prevalence and sylvatic vectors.

RESULTS: In regions with high endemic disease prevalence in dogs and domestic vectors, prevalence of infected dogs initially increases but subsequently declines before eventually rising back to the initial equilibrium following one fluralaner treatment. In regions of low prevalence and domestic or sylvatic vectors, however, treatment seems to be detrimental. In these regions our models suggest a potential for a rise in dog prevalence, due to oral transmission from dead infected bugs.

CONCLUSION: Xenointoxication could be a beneficial and novel One Health intervention in regions with high prevalence of T. cruzi and domestic vectors. In regions with low prevalence and domestic or sylvatic vectors, there is potential harm. Field trials should be carefully designed to closely follow treated dogs and include early stopping rules if incidence among treated dogs exceeds that of controls.

AUTHOR SUMMARY: Chagas disease, caused by the parasite Trypanosoma cruzi , is transmitted via triatomine insect vectors. In Latin America, dogs are a common feeding source for triatomine vectors and subsequently an important reservoir of T. cruzi . One proposed intervention to reduce T. cruzi transmission is xenointoxication: treating dogs with oral insecticide to kill triatomine vectors in order to decrease overall T. cruzi transmission. Fluralaner, commonly administered to prevent ectoparasites such as fleas and ticks, is effective under laboratory conditions against the triatomine vectors. One concern with fluralaner treatment is that rapid death of the insect vectors may make the insects more available to oral ingestion by dogs; a more effective transmission pathway than stercorarian, the usual route for T. cruzi transmission. Using a mathematical model, we explored 3 different epidemiologic scenarios: high prevalence endemic disease within a domestic T. cruzi cycle, low prevalence endemic disease within a domestic T. cruzi cycle, and low prevalence endemic disease within a semi-sylvatic T. cruzi cycle. We found a range of beneficial to detrimental effects of fluralaner xenointoxication depending on the epidemiologic scenario. Our results suggest that careful field trials should be designed and carried out before wide scale implementation of fluralaner xenointoxication to reduce T. cruzi transmission.}, } @article {pmid36746772, year = {2023}, author = {Wu, Z and Jiang, Z and Li, Z and Jiao, P and Zhai, J and Liu, S and Han, X and Zhang, S and Sun, J and Gai, Z and Qiu, C and Xu, J and Liu, H and Qin, R and Lu, R}, title = {Multi-omics analysis reveals spatiotemporal regulation and function of heteromorphic leaves in Populus.}, journal = {Plant physiology}, volume = {192}, number = {1}, pages = {188-204}, pmid = {36746772}, issn = {1532-2548}, mesh = {*Populus/physiology ; Multiomics ; Plant Leaves/metabolism ; Transcriptome/genetics ; Chromatin/metabolism ; Gene Expression Regulation, Plant ; }, abstract = {Despite the high economic and ecological importance of forests, our knowledge of the adaptive evolution of leaf traits remains very limited. Euphrates poplar (Populus euphratica), which has high tolerance to arid environment, has evolved four heteromorphic leaf forms, including narrow (linear and lanceolate) and broad (ovate and broad-ovate) leaves on different crowns. Here, we revealed the significant functional divergence of four P. euphratica heteromorphic leaves at physiological and cytological levels. Through global analysis of transcriptome and DNA methylation across tree and leaf developmental stages, we revealed that gene expression and DNA epigenetics differentially regulated key processes involving development and functional adaptation of heteromorphic leaves, such as hormone signaling pathways, cell division, and photosynthesis. Combined analysis of gene expression, methylation, ATAC-seq, and Hi-C-seq revealed longer interaction of 3D genome, hypomethylation, and open chromatin state upregulates IAA-related genes (such as PIN-FORMED1 and ANGUSTIFOLIA3) and promotes the occurrence of broad leaves while narrow leaves were associated with highly concentrated heterochromatin, hypermethylation, and upregulated abscisic acid pathway genes (such as Pyrabactin Resistance1-like10). Therefore, development of P. euphratica heteromorphic leaves along with functional divergence was regulated by differentially expressed genes, DNA methylation, chromatin accessibility, and 3D genome remodeling to adapt to the arid desert. This study advances our understanding of differential regulation on development and functional divergence of heteromorphic leaves in P. euphratica at the multi-omics level and provides a valuable resource for investigating the adaptive evolution of heteromorphic leaves in Populus.}, } @article {pmid36744611, year = {2023}, author = {Smail, EJ and Alpert, JM and Mardini, MT and Kaufmann, CN and Bai, C and Gill, TM and Fillingim, RB and Cenko, E and Zapata, R and Karnati, Y and Marsiske, M and Ranka, S and Manini, TM}, title = {Feasibility of a Smartwatch Platform to Assess Ecological Mobility: Real-Time Online Assessment and Mobility Monitor.}, journal = {The journals of gerontology. Series A, Biological sciences and medical sciences}, volume = {78}, number = {5}, pages = {821-830}, pmid = {36744611}, issn = {1758-535X}, support = {K01 AG061239/AG/NIA NIH HHS/United States ; UL1 TR001863/TR/NCATS NIH HHS/United States ; R33 AG059207/AG/NIA NIH HHS/United States ; UL1 TR001427/TR/NCATS NIH HHS/United States ; R21 AG059207/AG/NIA NIH HHS/United States ; U24 AG059624/AG/NIA NIH HHS/United States ; K01AG061239/AG/NIA NIH HHS/United States ; T32 AG062728/AG/NIA NIH HHS/United States ; P30 AG028740/AG/NIA NIH HHS/United States ; P30 AG021342/AG/NIA NIH HHS/United States ; }, mesh = {Humans ; Female ; Male ; Pilot Projects ; Feasibility Studies ; *Quality of Life ; Surveys and Questionnaires ; *Pain ; }, abstract = {BACKGROUND: Early detection of mobility decline is critical to prevent subsequent reductions in quality of life, disability, and mortality. However, traditional approaches to mobility assessment are limited in their ability to capture daily fluctuations that align with sporadic health events. We aim to describe findings from a pilot study of our Real-time Online Assessment and Mobility Monitor (ROAMM) smartwatch application, which uniquely captures multiple streams of data in real time in ecological settings.

METHODS: Data come from a sample of 31 participants (Mage = 74.7, 51.6% female) who used ROAMM for approximately 2 weeks. We describe the usability and feasibility of ROAMM, summarize prompt data using descriptive metrics, and compare prompt data with traditional survey-based questionnaires or other established measures.

RESULTS: Participants were satisfied with ROAMM's function (87.1%) and ranked the usability as "above average." Most were highly engaged (average adjusted compliance = 70.7%) and the majority reported being "likely" to enroll in a 2-year study (77.4%). Some smartwatch features were correlated with their respective traditional measurements (eg, certain GPS-derived life-space mobility features (r = 0.50-0.51, p < .05) and ecologically measured pain (r = 0.72, p = .01), but others were not (eg, ecologically measured fatigue).

CONCLUSIONS: ROAMM was usable, acceptable, and effective at measuring mobility and risk factors for mobility decline in our pilot sample. Additional work with a larger and more diverse sample is necessary to confirm associations between smartwatch-measured features and traditional measures. By monitoring multiple data streams simultaneously in ecological settings, this technology could uniquely contribute to the evolution of mobility measurement and risk factors for mobility loss.}, } @article {pmid36736631, year = {2023}, author = {LaVigne, AW and DeWeese, TL and Wright, JL and Deville, C and Yegnasubramanian, S and Alcorn, SR}, title = {Radiotherapy Deserts: The Impact of Race, Poverty, and the Rural-Urban Continuum on Density of Providers and the Use of Radiation Therapy in the US.}, journal = {International journal of radiation oncology, biology, physics}, volume = {116}, number = {1}, pages = {17-27}, doi = {10.1016/j.ijrobp.2023.01.046}, pmid = {36736631}, issn = {1879-355X}, mesh = {Aged ; Humans ; Male ; Medicare/statistics & numerical data ; *Neoplasms/economics/epidemiology/ethnology/radiotherapy ; Poverty/statistics & numerical data ; Rural Population/statistics & numerical data ; Social Class ; United States/epidemiology ; Urban Population/statistics & numerical data ; *Radiotherapy/economics/standards/statistics & numerical data ; Resource-Limited Settings/statistics & numerical data ; Race Factors/statistics & numerical data ; Health Personnel/statistics & numerical data ; Health Services Accessibility/statistics & numerical data ; Health Services Needs and Demand/statistics & numerical data ; Prostatic Neoplasms/economics/epidemiology/ethnology/radiotherapy ; Breast Neoplasms/economics/epidemiology/ethnology/radiotherapy ; Female ; Databases, Factual/statistics & numerical data ; Patient-Centered Care/statistics & numerical data ; *Healthcare Disparities/economics/ethnology/statistics & numerical data ; }, abstract = {PURPOSE: Prior efforts to characterize disparities in radiation therapy access and receipt have not comprehensively investigated interplay between race, socioeconomic status, and geography relative to oncologic outcomes. This study sought to define these complex relationships at the US county level for prostate cancer (PC) and invasive breast (BC) cancer to build a tool that facilitates identification of "radiotherapy deserts"-regions with mismatch between radiation therapy resources and oncologic need.

METHODS AND MATERIALS: An ecologic study model was constructed using national databases to evaluate 3,141 US counties. Radiation therapy resources and use densities were operationalized as physicians to persons at risk (PPR) and use to persons at risk (UPR): the number of attending radiation oncologists and Medicare beneficiaries per 100,000 persons at risk, respectively. Oncologic need was defined by "hot zone" counties with ≥2 standard deviations (SDs) above mean incidence and death rates. Univariable and multivariable logistic regressions examined links between PPR and UPR densities, epidemiologic variables, and hot zones for oncologic outcomes. Statistics are reported at a significance level of P < .05.

RESULTS: The mean (SD) PPR and UPR densities were 2.1 (5.9) and 192.6 (557.6) for PC and 1.9 (5.3) and 174.4 (501.0) for BC, respectively. Counties with high PPR and UPR densities were predominately metropolitan (odds ratio [OR], 2.9-4.4), generally with a higher percentage of Black non-Hispanic constituents (OR, 1.5-2.3). Incidence and death rate hot zones were largely nonmetropolitan (OR, 0.3-0.6), generally with a higher percentage of Black non-Hispanic constituents (OR, 3.2-6.3). Lower PPR density was associated with death rate hot zones for both types of cancer (OR, 0.8-0.9); UPR density was generally not linked to oncologic outcomes on multivariable analysis.

CONCLUSIONS: The study found that mismatch between oncologic need with PPR and UPR disproportionately affects nonmetropolitan communities with a higher percentage of Black non-Hispanic constituents. An interactive web platform (bit.ly/densitymaps) was developed to visualize "radiotherapy deserts" and drive targeted investigation of underlying barriers to care in areas of highest need, with the goal of reducing health inequities in this context.}, } @article {pmid36735127, year = {2023}, author = {Jiang, X and Sun, Y and Qu, Y and Zeng, H and Yang, J and Zhang, K and Liu, L}, title = {The development and future frontiers of global ecological restoration projects in the twenty-first century: a systematic review based on scientometrics.}, journal = {Environmental science and pollution research international}, volume = {30}, number = {12}, pages = {32230-32245}, pmid = {36735127}, issn = {1614-7499}, support = {2021YFN0113//Sichuan Provincial Science and Technology Department Project/ ; QD2022A02//Scientific Research Project of Mianyang Normal University/ ; }, mesh = {Humans ; *Publications ; *Bibliometrics ; Databases, Factual ; China ; }, abstract = {Ecological restoration projects are becoming a mainstream of research, and their studies are widely followed by scholars worldwide, yet there is no comprehensive review of this research. Nowadays, bibliometrics has attracted much attention from the scientific community, and its methodological approach allows quantitative and qualitative analysis of research performance in journals or subject areas. This paper provides a systematic and comprehensive description of the progress and hotspots of ecological restoration projects from a bibliometric perspective, based on 1173 articles in the Web of Science Core Collection (WOSCC) database. Research on ecological restoration projects has shown a positive growth trend since the twenty-first century. China and the USA are the most active countries in terms of the number of relevant articles published, and more than half of the top 10 active institutions are from China, but there is less collaboration between different countries/institutions. Research in ecological restoration projects is summarized into three main research areas: the main ecological damage problems, the impact of human beings on ecological damage, and the main methods of ecological restoration. Finally, some challenges and outlooks conducive to the rapid and balanced development of ecological restoration projects are presented, which provide valuable references and help for future researchers.}, } @article {pmid36727564, year = {2023}, author = {Kinkar, L and Korhonen, PK and Saarma, U and Wang, T and Zhu, XQ and Harliwong, I and Yang, B and Fink, JL and Wang, D and Chang, BCH and Chelomina, GN and Koehler, AV and Young, ND and Gasser, RB}, title = {Genome-wide exploration reveals distinctive northern and southern variants of Clonorchis sinensis in the Far East.}, journal = {Molecular ecology resources}, volume = {23}, number = {4}, pages = {833-843}, doi = {10.1111/1755-0998.13760}, pmid = {36727564}, issn = {1755-0998}, support = {LP180101085,LP180101334,LP190101209//Australian Research Council/ ; PRG1209//The Estonian Ministry of Education and Research/ ; 20211331-13//The Fund for Shanxi "1331 Project"/ ; 2021XG001//The Special Research Fund of Shanxi Agricultural University for High-level Talents/ ; }, mesh = {Animals ; *Clonorchis sinensis/genetics ; *Clonorchiasis/diagnosis/epidemiology/parasitology ; Genetic Variation ; Asia, Eastern ; China/epidemiology ; }, abstract = {Clonorchis sinensis is a carcinogenic liver fluke that causes clonorchiasis-a neglected tropical disease (NTD) affecting ~35 million people worldwide. No vaccine is available, and chemotherapy relies on one anthelmintic, praziquantel. This parasite has a complex life history and is known to infect a range of species of intermediate (freshwater snails and fish) and definitive (piscivorous) hosts. Despite this biological complexity and the impact of this biocarcinogenic pathogen, there has been no previous study of molecular variation in this parasite on a genome-wide scale. Here, we conducted the first extensive nuclear genomic exploration of C. sinensis individuals (n = 152) representing five distinct populations from mainland China, and one from Far East Russia, and revealed marked genetic variation within this species between "northern" and "southern" geographical regions. The discovery of this variation indicates the existence of biologically distinct variants within C. sinensis, which may have distinct epidemiology, pathogenicity and/or chemotherapic responsiveness. The detection of high heterozygosity within C. sinensis specimens suggests that this parasite has developed mechanisms to readily adapt to changing environments and/or host species during its life history/evolution. From an applied perspective, the identification of invariable genes could assist in finding new intervention targets in this parasite, given the major clinical relevance of clonorchiasis. From a technical perspective, the genomic-informatic workflow established herein will be readily applicable to a wide range of other parasites that cause NTDs.}, } @article {pmid36726097, year = {2023}, author = {Alwafi, H and Naser, AY and Ashoor, DS and Aldhahir, AM and Alqahtani, JS and Minshawi, F and Salawati, E and Samannodi, M and Dairi, MS and Alansari, AK and Ekram, R}, title = {Trends in hospital admissions and prescribing due to chronic obstructive pulmonary disease and asthma in England and Wales between 1999 and 2020: an ecological study.}, journal = {BMC pulmonary medicine}, volume = {23}, number = {1}, pages = {49}, pmid = {36726097}, issn = {1471-2466}, mesh = {Humans ; Female ; Wales/epidemiology ; *Pulmonary Disease, Chronic Obstructive/drug therapy/epidemiology ; Hospitalization ; *Asthma/drug therapy/epidemiology ; England/epidemiology ; Hospitals ; Drug Prescriptions ; *Respiratory Tract Infections/drug therapy ; }, abstract = {OBJECTIVE: To investigate the trends in hospital admissions and medication prescriptions related to asthma and chronic obstructive pulmonary disease (COPD) in England and Wales.

METHODS: An ecological study was conducted between April 1999 and April 2020 using data extracted from the hospital episode statistics database in England and the patient episode database for Wales. The Office of National Statistics mid-year population estimates for 1999 through 2020 were collected, and medication prescription data for 2004-2020 were extracted from the prescription cost analysis database.

RESULTS: The total annual number of COPD and asthma hospital admissions for various causes increased by 82.2%, from 210,525 in 1999 to 383,652 in 2020, representing a 59.1% increase in hospital admission rate (from 403.77 in 1999 to 642.42 per 100,000 persons in 2020, p < 0.05). Chronic obstructive pulmonary disease with acute lower respiratory infection accounted for 38.7% of hospital admissions. Around 34.7% of all hospital admissions involved patients aged 75 and older. Around 53.8% of all COPD and asthma hospital admissions were attributable to females. The annual number of prescriptions dispensed for COPD and asthma medications increased by 42.2%.

CONCLUSIONS: Throughout the study period, hospital admissions due to chronic obstructive pulmonary disease and asthma, as well as medication prescriptions, increased dramatically among all age groups. Hospitalization rates were higher for women. Further observational and epidemiological research is required to identify the factors contributing to increased hospitalization rates.}, } @article {pmid36725822, year = {2023}, author = {Pernet, C and Svarer, C and Blair, R and Van Horn, JD and Poldrack, RA}, title = {On the Long-term Archiving of Research Data.}, journal = {Neuroinformatics}, volume = {21}, number = {2}, pages = {243-246}, pmid = {36725822}, issn = {1559-0089}, mesh = {*Information Dissemination ; *Information Storage and Retrieval ; }, abstract = {Accessing research data at any time is what FAIR (Findable Accessible Interoperable Reusable) data sharing aims to achieve at scale. Yet, we argue that it is not sustainable to keep accumulating and maintaining all datasets for rapid access, considering the monetary and ecological cost of maintaining repositories. Here, we address the issue of cold data storage: when to dispose of data for offline storage, how can this be done while maintaining FAIR principles and who should be responsible for cold archiving and long-term preservation.}, } @article {pmid36722081, year = {2023}, author = {Ehlman, SM and Scherer, U and Bierbach, D and Francisco, F and Laskowski, KL and Krause, J and Wolf, M}, title = {Leveraging big data to uncover the eco-evolutionary factors shaping behavioural development.}, journal = {Proceedings. Biological sciences}, volume = {290}, number = {1992}, pages = {20222115}, pmid = {36722081}, issn = {1471-2954}, mesh = {Animals ; *Big Data ; *Biological Evolution ; }, abstract = {Mapping the eco-evolutionary factors shaping the development of animals' behavioural phenotypes remains a great challenge. Recent advances in 'big behavioural data' research-the high-resolution tracking of individuals and the harnessing of that data with powerful analytical tools-have vastly improved our ability to measure and model developing behavioural phenotypes. Applied to the study of behavioural ontogeny, the unfolding of whole behavioural repertoires can be mapped in unprecedented detail with relative ease. This overcomes long-standing experimental bottlenecks and heralds a surge of studies that more finely define and explore behavioural-experiential trajectories across development. In this review, we first provide a brief guide to state-of-the-art approaches that allow the collection and analysis of high-resolution behavioural data across development. We then outline how such approaches can be used to address key issues regarding the ecological and evolutionary factors shaping behavioural development: developmental feedbacks between behaviour and underlying states, early life effects and behavioural transitions, and information integration across development.}, } @article {pmid36719907, year = {2023}, author = {Turtle, L and Thorpe, M and Drake, TM and Swets, M and Palmieri, C and Russell, CD and Ho, A and Aston, S and Wootton, DG and Richter, A and de Silva, TI and Hardwick, HE and Leeming, G and Law, A and Openshaw, PJM and Harrison, EM and , and Baillie, JK and Semple, MG and Docherty, AB}, title = {Outcome of COVID-19 in hospitalised immunocompromised patients: An analysis of the WHO ISARIC CCP-UK prospective cohort study.}, journal = {PLoS medicine}, volume = {20}, number = {1}, pages = {e1004086}, pmid = {36719907}, issn = {1549-1676}, support = {205228/Z/16/Z/WT_/Wellcome Trust/United Kingdom ; MC_PC_19026/MRC_/Medical Research Council/United Kingdom ; 205228/Z/16/Z/WT_/Wellcome Trust/United Kingdom ; MC_PC_19059/MRC_/Medical Research Council/United Kingdom ; 215091/Z/18/Z/WT_/Wellcome Trust/United Kingdom ; MR/V028979/1/MRC_/Medical Research Council/United Kingdom ; MC_PC_19025/MRC_/Medical Research Council/United Kingdom ; 200927/DH_/Department of Health/United Kingdom ; MC_PC_20058/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Male ; Humans ; Female ; Middle Aged ; Aged ; *COVID-19 ; SARS-CoV-2 ; Prospective Studies ; Hospital Mortality ; Bayes Theorem ; Immunocompromised Host ; United Kingdom/epidemiology ; World Health Organization ; }, abstract = {BACKGROUND: Immunocompromised patients may be at higher risk of mortality if hospitalised with Coronavirus Disease 2019 (COVID-19) compared with immunocompetent patients. However, previous studies have been contradictory. We aimed to determine whether immunocompromised patients were at greater risk of in-hospital death and how this risk changed over the pandemic.

METHODS AND FINDINGS: We included patients > = 19 years with symptomatic community-acquired COVID-19 recruited to the ISARIC WHO Clinical Characterisation Protocol UK prospective cohort study. We defined immunocompromise as immunosuppressant medication preadmission, cancer treatment, organ transplant, HIV, or congenital immunodeficiency. We used logistic regression to compare the risk of death in both groups, adjusting for age, sex, deprivation, ethnicity, vaccination, and comorbidities. We used Bayesian logistic regression to explore mortality over time. Between 17 January 2020 and 28 February 2022, we recruited 156,552 eligible patients, of whom 21,954 (14%) were immunocompromised. In total, 29% (n = 6,499) of immunocompromised and 21% (n = 28,608) of immunocompetent patients died in hospital. The odds of in-hospital mortality were elevated for immunocompromised patients (adjusted OR 1.44, 95% CI [1.39, 1.50], p < 0.001). Not all immunocompromising conditions had the same risk, for example, patients on active cancer treatment were less likely to have their care escalated to intensive care (adjusted OR 0.77, 95% CI [0.7, 0.85], p < 0.001) or ventilation (adjusted OR 0.65, 95% CI [0.56, 0.76], p < 0.001). However, cancer patients were more likely to die (adjusted OR 2.0, 95% CI [1.87, 2.15], p < 0.001). Analyses were adjusted for age, sex, socioeconomic deprivation, comorbidities, and vaccination status. As the pandemic progressed, in-hospital mortality reduced more slowly for immunocompromised patients than for immunocompetent patients. This was particularly evident with increasing age: the probability of the reduction in hospital mortality being less for immunocompromised patients aged 50 to 69 years was 88% for men and 83% for women, and for those >80 years was 99% for men and 98% for women. The study is limited by a lack of detailed drug data prior to admission, including steroid doses, meaning that we may have incorrectly categorised some immunocompromised patients as immunocompetent.

CONCLUSIONS: Immunocompromised patients remain at elevated risk of death from COVID-19. Targeted measures such as additional vaccine doses, monoclonal antibodies, and nonpharmaceutical preventive interventions should be continually encouraged for this patient group.

TRIAL REGISTRATION: ISRCTN 66726260.}, } @article {pmid36718952, year = {2023}, author = {Freedman, AH and Harrigan, RJ and Zhen, Y and Hamilton, AM and Smith, TB}, title = {Evidence for ecotone speciation across an African rainforest-savanna gradient.}, journal = {Molecular ecology}, volume = {32}, number = {9}, pages = {2287-2300}, doi = {10.1111/mec.16867}, pmid = {36718952}, issn = {1365-294X}, support = {/EPA/EPA/United States ; }, mesh = {Animals ; *Rainforest ; Grassland ; Ecosystem ; Gene Frequency ; Biodiversity ; *Lizards/genetics ; Genetic Speciation ; }, abstract = {Accelerating climate change and habitat loss make it imperative that plans to conserve biodiversity consider species' ability to adapt to changing environments. However, in biomes where biodiversity is highest, the evolutionary mechanisms responsible for generating adaptative variation and, ultimately, new species are frequently poorly understood. African rainforests represent one such biome, as decadal debates continue concerning the mechanisms generating African rainforest biodiversity. These debates hinge on the relative importance of geographic isolation versus divergent natural selection across environmental gradients. Hindering progress is a lack of robust tests of these competing hypotheses. Because African rainforests are severely at-risk due to climate change and other anthropogenic activities, addressing this long-standing debate is critical for making informed conservation decisions. We use demographic inference and allele frequency-environment relationships to investigate mechanisms of diversification in an African rainforest skink, Trachylepis affinis, a species inhabiting the gradient between rainforest and rainforest-savanna mosaic (ecotone). We provide compelling evidence of ecotone speciation, in which gene flow has all but ceased between rainforest and ecotone populations, at a level consistent with infrequent hybridization between sister species. Parallel patterns of genomic, morphological, and physiological divergence across this environmental gradient and pronounced allele frequency-environment correlation indicate speciation is mostly probably driven by ecological divergence, supporting a central role for divergent natural selection. Our results provide strong evidence for the importance of ecological gradients in African rainforest speciation and inform conservation strategies that preserve the processes that produce and maintain biodiversity.}, } @article {pmid36716736, year = {2022}, author = {Smith, J and Alfieri, JM and Anthony, N and Arensburger, P and Athrey, GN and Balacco, J and Balic, A and Bardou, P and Barela, P and Bigot, Y and Blackmon, H and Borodin, PM and Carroll, R and Casono, MC and Charles, M and Cheng, H and Chiodi, M and Cigan, L and Coghill, LM and Crooijmans, R and Das, N and Davey, S and Davidian, A and Degalez, F and Dekkers, JM and Derks, M and Diack, AB and Djikeng, A and Drechsler, Y and Dyomin, A and Fedrigo, O and Fiddaman, SR and Formenti, G and Frantz, LAF and Fulton, JE and Gaginskaya, E and Galkina, S and Gallardo, RA and Geibel, J and Gheyas, AA and Godinez, CJP and Goodell, A and Graves, JAM and Griffin, DK and Haase, B and Han, JL and Hanotte, O and Henderson, LJ and Hou, ZC and Howe, K and Huynh, L and Ilatsia, E and Jarvis, ED and Johnson, SM and Kaufman, J and Kelly, T and Kemp, S and Kern, C and Keroack, JH and Klopp, C and Lagarrigue, S and Lamont, SJ and Lange, M and Lanke, A and Larkin, DM and Larson, G and Layos, JKN and Lebrasseur, O and Malinovskaya, LP and Martin, RJ and Martin Cerezo, ML and Mason, AS and McCarthy, FM and McGrew, MJ and Mountcastle, J and Muhonja, CK and Muir, W and Muret, K and Murphy, TD and Ng'ang'a, I and Nishibori, M and O'Connor, RE and Ogugo, M and Okimoto, R and Ouko, O and Patel, HR and Perini, F and Pigozzi, MI and Potter, KC and Price, PD and Reimer, C and Rice, ES and Rocos, N and Rogers, TF and Saelao, P and Schauer, J and Schnabel, RD and Schneider, VA and Simianer, H and Smith, A and Stevens, MP and Stiers, K and Tiambo, CK and Tixier-Boichard, M and Torgasheva, AA and Tracey, A and Tregaskes, CA and Vervelde, L and Wang, Y and Warren, WC and Waters, PD and Webb, D and Weigend, S and Wolc, A and Wright, AE and Wright, D and Wu, Z and Yamagata, M and Yang, C and Yin, ZT and Young, MC and Zhang, G and Zhao, B and Zhou, H}, title = {Fourth Report on Chicken Genes and Chromosomes 2022.}, journal = {Cytogenetic and genome research}, volume = {162}, number = {8-9}, pages = {405-528}, doi = {10.1159/000529376}, pmid = {36716736}, issn = {1424-859X}, } @article {pmid36714536, year = {2023}, author = {Astorga, F and Groom, Q and Shimabukuro, PHF and Manguin, S and Noesgaard, D and Orrell, T and Sinka, M and Hirsch, T and Schigel, D}, title = {Biodiversity data supports research on human infectious diseases: Global trends, challenges, and opportunities.}, journal = {One health (Amsterdam, Netherlands)}, volume = {16}, number = {}, pages = {100484}, pmid = {36714536}, issn = {2352-7714}, abstract = {The unprecedented generation of large volumes of biodiversity data is consistently contributing to a wide range of disciplines, including disease ecology. Emerging infectious diseases are usually zoonoses caused by multi-host pathogens. Therefore, their understanding may require the access to biodiversity data related to the ecology and the occurrence of the species involved. Nevertheless, despite several data-mobilization initiatives, the usage of biodiversity data for research into disease dynamics has not yet been fully leveraged. To explore current contribution, trends, and to identify limitations, we characterized biodiversity data usage in scientific publications related to human health, contrasting patterns of studies citing the Global Biodiversity Information Facility (GBIF) with those obtaining data from other sources. We found that the studies mainly obtained data from scientific literature and other not aggregated or standardized sources. Most of the studies explored pathogen species and, particularly those with GBIF-mediated data, tended to explore and reuse data of multiple species (>2). Data sources varied according to the taxa and epidemiological roles of the species involved. Biodiversity data repositories were mainly used for species related to hosts, reservoirs, and vectors, and barely used as a source of pathogens data, which was usually obtained from human and animal-health related institutions. While both GBIF- and not GBIF-mediated data studies explored similar diseases and topics, they presented discipline biases and different analytical approaches. Research on emerging infectious diseases may require the access to geographical and ecological data of multiple species. The One Health challenge requires interdisciplinary collaboration and data sharing, which is facilitated by aggregated repositories and platforms. The contribution of biodiversity data to understand infectious disease dynamics should be acknowledged, strengthened, and promoted.}, } @article {pmid36706978, year = {2023}, author = {Nosenko, T and Zimmer, I and Ghirardo, A and Köllner, TG and Weber, B and Polle, A and Rosenkranz, M and Schnitzler, JP}, title = {Predicting functions of putative fungal sesquiterpene synthase genes based on multiomics data analysis.}, journal = {Fungal genetics and biology : FG & B}, volume = {165}, number = {}, pages = {103779}, doi = {10.1016/j.fgb.2023.103779}, pmid = {36706978}, issn = {1096-0937}, mesh = {Multiomics ; *Sesquiterpenes/metabolism ; Genes, Fungal ; *Mycorrhizae/genetics ; Gene Expression Profiling ; }, abstract = {Sesquiterpenes (STs) are secondary metabolites, which mediate biotic interactions between different organisms. Predicting the species-specific ST repertoires can contribute to deciphering the language of communication between organisms of the same or different species. High biochemical plasticity and catalytic promiscuity of sesquiterpene synthases (STSs), however, challenge the homology-based prediction of the STS functions. Using integrated analyses of genomic, transcriptomic, volatilomic, and metabolomic data, we predict product profiles for 116 out of 146 putative STS genes identified in the genomes of 30 fungal species from different trophic groups. Our prediction method is based on the observation that STSs encoded by genes closely related phylogenetically are likely to share the initial enzymatic reactions of the ST biosynthesis pathways and, therefore, produce STs via the same reaction route. The classification by reaction routes allows to assign STs known to be emitted by a particular species to the putative STS genes from this species. Gene expression information helps to further specify these ST-to-STS assignments. Validation of the computational predictions of the STS functions using both in silico and experimental approaches shows that integrated multiomic analyses are able to correctly link cyclic STs of non-cadalane type to genes. In the process of the experimental validation, we characterized catalytic properties of several putative STS genes from the mycorrhizal fungus Laccaria bicolor. We show that the STSs encoded by the L.bicolor mycorrhiza-induced genes emit either nerolidol or α-cuprenene and α-cuparene, and discuss the possible roles of these STs in the mycorrhiza formation.}, } @article {pmid36705582, year = {2023}, author = {Bettisworth, B and Smith, SA and Stamatakis, A}, title = {Lagrange-NG: The next generation of Lagrange.}, journal = {Systematic biology}, volume = {72}, number = {1}, pages = {242-248}, pmid = {36705582}, issn = {1076-836X}, mesh = {Phylogeny ; *Software ; }, abstract = {Computing ancestral ranges via the Dispersion Extinction and Cladogensis (DEC) model of biogeography is characterized by an exponential number of states relative to the number of regions considered. This is because the DEC model requires computing a large matrix exponential, which typically accounts for up to 80% of overall runtime. Therefore, the kinds of biogeographical analyses that can be conducted under the DEC model are limited by the number of regions under consideration. In this work, we present a completely redesigned efficient version of the popular tool Lagrange which is up to 49 times faster with multithreading enabled, and is also 26 times faster when using only one thread. We call this new version Lagrange-NG (Lagrange-Next Generation). The increased computational efficiency allows Lagrange-NG to analyze datasets with a large number of regions in a reasonable amount of time, up to 12 regions in approximately 18 min. We achieve these speedups using a relatively new method of computing the matrix exponential based on Krylov subspaces. In order to validate the correctness of Lagrange-NG, we also introduce a novel metric on range distributions for trees so that researchers can assess the difference between any two range inferences. Finally, Lagrange-NG exhibits substantially higher adherence to coding quality standards. It improves a respective software quality indicator as implemented in the SoftWipe tool from average (5.5; Lagrange) to high (7.8; Lagrange-NG). Lagrange-NG is freely available under GPL2. [Biogeography; Phylogenetics; DEC Model.].}, } @article {pmid36704891, year = {2023}, author = {Crandall, ED and Toczydlowski, RH and Liggins, L and Holmes, AE and Ghoojaei, M and Gaither, MR and Wham, BE and Pritt, AL and Noble, C and Anderson, TJ and Barton, RL and Berg, JT and Beskid, SG and Delgado, A and Farrell, E and Himmelsbach, N and Queeno, SR and Trinh, T and Weyand, C and Bentley, A and Deck, J and Riginos, C and Bradburd, GS and Toonen, RJ}, title = {Importance of timely metadata curation to the global surveillance of genetic diversity.}, journal = {Conservation biology : the journal of the Society for Conservation Biology}, volume = {37}, number = {4}, pages = {e14061}, pmid = {36704891}, issn = {1523-1739}, support = {R35 GM137919/GM/NIGMS NIH HHS/United States ; }, mesh = {Humans ; *Conservation of Natural Resources ; *Metadata ; Biodiversity ; Probability ; Genetic Variation ; }, abstract = {Genetic diversity within species represents a fundamental yet underappreciated level of biodiversity. Because genetic diversity can indicate species resilience to changing climate, its measurement is relevant to many national and global conservation policy targets. Many studies produce large amounts of genome-scale genetic diversity data for wild populations, but most (87%) do not include the associated spatial and temporal metadata necessary for them to be reused in monitoring programs or for acknowledging the sovereignty of nations or Indigenous peoples. We undertook a distributed datathon to quantify the availability of these missing metadata and to test the hypothesis that their availability decays with time. We also worked to remediate missing metadata by extracting them from associated published papers, online repositories, and direct communication with authors. Starting with 848 candidate genomic data sets (reduced representation and whole genome) from the International Nucleotide Sequence Database Collaboration, we determined that 561 contained mostly samples from wild populations. We successfully restored spatiotemporal metadata for 78% of these 561 data sets (n = 440 data sets with data on 45,105 individuals from 762 species in 17 phyla). Examining papers and online repositories was much more fruitful than contacting 351 authors, who replied to our email requests 45% of the time. Overall, 23% of our email queries to authors unearthed useful metadata. The probability of retrieving spatiotemporal metadata declined significantly as age of the data set increased. There was a 13.5% yearly decrease in metadata associated with published papers or online repositories and up to a 22% yearly decrease in metadata that were only available from authors. This rapid decay in metadata availability, mirrored in studies of other types of biological data, should motivate swift updates to data-sharing policies and researcher practices to ensure that the valuable context provided by metadata is not lost to conservation science forever.}, } @article {pmid36699674, year = {2022}, author = {Siddiqui, JA and Fan, R and Naz, H and Bamisile, BS and Hafeez, M and Ghani, MI and Wei, Y and Xu, Y and Chen, X}, title = {Insights into insecticide-resistance mechanisms in invasive species: Challenges and control strategies.}, journal = {Frontiers in physiology}, volume = {13}, number = {}, pages = {1112278}, pmid = {36699674}, issn = {1664-042X}, abstract = {Threatening the global community is a wide variety of potential threats, most notably invasive pest species. Invasive pest species are non-native organisms that humans have either accidentally or intentionally spread to new regions. One of the most effective and first lines of control strategies for controlling pests is the application of insecticides. These toxic chemicals are employed to get rid of pests, but they pose great risks to people, animals, and plants. Pesticides are heavily used in managing invasive pests in the current era. Due to the overuse of synthetic chemicals, numerous invasive species have already developed resistance. The resistance development is the main reason for the failure to manage the invasive species. Developing pesticide resistance management techniques necessitates a thorough understanding of the mechanisms through which insects acquire insecticide resistance. Insects use a variety of behavioral, biochemical, physiological, genetic, and metabolic methods to deal with toxic chemicals, which can lead to resistance through continuous overexpression of detoxifying enzymes. An overabundance of enzymes causes metabolic resistance, detoxifying pesticides and rendering them ineffective against pests. A key factor in the development of metabolic resistance is the amplification of certain metabolic enzymes, specifically esterases, Glutathione S-transferase, Cytochromes p450 monooxygenase, and hydrolyses. Additionally, insect guts offer unique habitats for microbial colonization, and gut bacteria may serve their hosts a variety of useful services. Most importantly, the detoxification of insecticides leads to resistance development. The complete knowledge of invasive pest species and their mechanisms of resistance development could be very helpful in coping with the challenges and effectively developing effective strategies for the control of invasive species. Integrated Pest Management is particularly effective at lowering the risk of chemical and environmental contaminants and the resulting health issues, and it may also offer the most effective ways to control insect pests.}, } @article {pmid36699126, year = {2023}, author = {Wortel, MT and Agashe, D and Bailey, SF and Bank, C and Bisschop, K and Blankers, T and Cairns, J and Colizzi, ES and Cusseddu, D and Desai, MM and van Dijk, B and Egas, M and Ellers, J and Groot, AT and Heckel, DG and Johnson, ML and Kraaijeveld, K and Krug, J and Laan, L and Lässig, M and Lind, PA and Meijer, J and Noble, LM and Okasha, S and Rainey, PB and Rozen, DE and Shitut, S and Tans, SJ and Tenaillon, O and Teotónio, H and de Visser, JAGM and Visser, ME and Vroomans, RMA and Werner, GDA and Wertheim, B and Pennings, PS}, title = {Towards evolutionary predictions: Current promises and challenges.}, journal = {Evolutionary applications}, volume = {16}, number = {1}, pages = {3-21}, pmid = {36699126}, issn = {1752-4571}, support = {R01 AI134195/AI/NIAID NIH HHS/United States ; R01 GM104239/GM/NIGMS NIH HHS/United States ; }, abstract = {Evolution has traditionally been a historical and descriptive science, and predicting future evolutionary processes has long been considered impossible. However, evolutionary predictions are increasingly being developed and used in medicine, agriculture, biotechnology and conservation biology. Evolutionary predictions may be used for different purposes, such as to prepare for the future, to try and change the course of evolution or to determine how well we understand evolutionary processes. Similarly, the exact aspect of the evolved population that we want to predict may also differ. For example, we could try to predict which genotype will dominate, the fitness of the population or the extinction probability of a population. In addition, there are many uses of evolutionary predictions that may not always be recognized as such. The main goal of this review is to increase awareness of methods and data in different research fields by showing the breadth of situations in which evolutionary predictions are made. We describe how diverse evolutionary predictions share a common structure described by the predictive scope, time scale and precision. Then, by using examples ranging from SARS-CoV2 and influenza to CRISPR-based gene drives and sustainable product formation in biotechnology, we discuss the methods for predicting evolution, the factors that affect predictability and how predictions can be used to prevent evolution in undesirable directions or to promote beneficial evolution (i.e. evolutionary control). We hope that this review will stimulate collaboration between fields by establishing a common language for evolutionary predictions.}, } @article {pmid36696549, year = {2023}, author = {Menon, K and Sorce, LR and Argent, A and Bennett, TD and Carrol, ED and Kissoon, N and Sanchez-Pinto, LN and Schlapbach, LJ and de Souza, DC and Watson, RS and Wynn, JL and Zimmerman, JJ and Ranjit, S and , }, title = {Reporting of Social Determinants of Health in Pediatric Sepsis Studies.}, journal = {Pediatric critical care medicine : a journal of the Society of Critical Care Medicine and the World Federation of Pediatric Intensive and Critical Care Societies}, volume = {24}, number = {4}, pages = {301-310}, pmid = {36696549}, issn = {1529-7535}, support = {R01 GM128452/GM/NIGMS NIH HHS/United States ; R01 HD097081/HD/NICHD NIH HHS/United States ; R01 HD105939/HD/NICHD NIH HHS/United States ; R43 EB029863/EB/NIBIB NIH HHS/United States ; }, mesh = {Humans ; Child ; *Social Determinants of Health ; Socioeconomic Factors ; *Sepsis/epidemiology ; }, abstract = {OBJECTIVE: Standardized, consistent reporting of social determinants of health (SDOH) in studies on children with sepsis would allow for: 1) understanding the association of SDOH with illness severity and outcomes, 2) comparing populations and extrapolating study results, and 3) identification of potentially modifiable socioeconomic factors for policy makers. We, therefore, sought to determine how frequently data on SDOH were reported, which factors were collected and how these factors were defined in studies of sepsis in children.

DATA SOURCES AND SELECTION: We reviewed 106 articles (published between 2005 and 2020) utilized in a recent systematic review on physiologic criteria for pediatric sepsis.

DATA EXTRACTION: Data were extracted by two reviewers on variables that fell within the World Health Organization's SDOH categories.

DATA SYNTHESIS: SDOH were not the primary outcome in any of the included studies. Seventeen percent of articles (18/106) did not report on any SDOH, and a further 36.8% (39/106) only reported on gender/sex. Of the remaining 46.2% of articles, the most reported SDOH categories were preadmission nutritional status (35.8%, 38/106) and race/ethnicity (18.9%, 20/106). However, no two studies used the same definition of the variables reported within each of these categories. Six studies reported on socioeconomic status (3.8%, 6/106), including two from upper-middle-income and four from lower middle-income countries. Only three studies reported on parental education levels (2.8%, 3/106). No study reported on parental job security or structural conflict.

CONCLUSIONS: We found overall low reporting of SDOH and marked variability in categorizations and definitions of SDOH variables. Consistent and standardized reporting of SDOH in pediatric sepsis studies is needed to understand the role these factors play in the development and severity of sepsis, to compare and extrapolate study results between settings and to implement policies aimed at improving socioeconomic conditions related to sepsis.}, } @article {pmid36692937, year = {2023}, author = {de Angel, V and Adeleye, F and Zhang, Y and Cummins, N and Munir, S and Lewis, S and Laporta Puyal, E and Matcham, F and Sun, S and Folarin, AA and Ranjan, Y and Conde, P and Rashid, Z and Dobson, R and Hotopf, M}, title = {The Feasibility of Implementing Remote Measurement Technologies in Psychological Treatment for Depression: Mixed Methods Study on Engagement.}, journal = {JMIR mental health}, volume = {10}, number = {}, pages = {e42866}, pmid = {36692937}, issn = {2368-7959}, support = {/WT_/Wellcome Trust/United Kingdom ; MC_PC_17214/MRC_/Medical Research Council/United Kingdom ; }, abstract = {BACKGROUND: Remote measurement technologies (RMTs) such as smartphones and wearables can help improve treatment for depression by providing objective, continuous, and ecologically valid insights into mood and behavior. Engagement with RMTs is varied and highly context dependent; however, few studies have investigated their feasibility in the context of treatment.

OBJECTIVE: A mixed methods design was used to evaluate engagement with active and passive data collection via RMT in people with depression undergoing psychotherapy. We evaluated the effects of treatment on 2 different types of engagement: study attrition (engagement with study protocol) and patterns of missing data (engagement with digital devices), which we termed data availability. Qualitative interviews were conducted to help interpret the differences in engagement.

METHODS: A total of 66 people undergoing psychological therapy for depression were followed up for 7 months. Active data were gathered from weekly questionnaires and speech and cognitive tasks, and passive data were gathered from smartphone sensors and a Fitbit (Fitbit Inc) wearable device.

RESULTS: The overall retention rate was 60%. Higher-intensity treatment (χ[2]1=4.6; P=.03) and higher baseline anxiety (t56.28=-2.80, 2-tailed; P=.007) were associated with attrition, but depression severity was not (t50.4=-0.18; P=.86). A trend toward significance was found for the association between longer treatments and increased attrition (U=339.5; P=.05). Data availability was higher for active data than for passive data initially but declined at a sharper rate (90%-30% drop in 7 months). As for passive data, wearable data availability fell from a maximum of 80% to 45% at 7 months but showed higher overall data availability than smartphone-based data, which remained stable at the range of 20%-40% throughout. Missing data were more prevalent among GPS location data, followed by among Bluetooth data, then among accelerometry data. As for active data, speech and cognitive tasks had lower completion rates than clinical questionnaires. The participants in treatment provided less Fitbit data but more active data than those on the waiting list.

CONCLUSIONS: Different data streams showed varied patterns of missing data, despite being gathered from the same device. Longer and more complex treatments and clinical characteristics such as higher baseline anxiety may reduce long-term engagement with RMTs, and different devices may show opposite patterns of missingness during treatment. This has implications for the scalability and uptake of RMTs in health care settings, the generalizability and accuracy of the data collected by these methods, feature construction, and the appropriateness of RMT use in the long term.}, } @article {pmid36690591, year = {2023}, author = {Sambo, B and Bonato, M and Sperotto, A and Torresan, S and Furlan, E and Lambert, JH and Linkov, I and Critto, A}, title = {Framework for multirisk climate scenarios across system receptors with application to the Metropolitan City of Venice.}, journal = {Risk analysis : an official publication of the Society for Risk Analysis}, volume = {43}, number = {11}, pages = {2241-2261}, doi = {10.1111/risa.14097}, pmid = {36690591}, issn = {1539-6924}, support = {//Ministero degli Affari Esteri e della Cooperazione Internazionale/ ; }, abstract = {Climate change influences the frequency of extreme events that affect both human and natural systems. It requires systemic climate change adaptation to address the complexity of risks across multiple domains and tackle the uncertainties of future scenarios. This paper introduces a multirisk analysis of climate hazard, exposure, vulnerability, and risk severity, specifically designed to hotspot geographic locations and prioritize system receptors that are affected by climate-related extremes. The analysis is demonstrated for the Metropolitan City of Venice. Representative scenarios (RCP4.5 and RCP8.5) of climate threats (i.e., storm surges, pluvial flood, heat waves, and drought) are selected and represented by projections of Regional Climate Models for a 30-year period (2021-2050). A sample of results is as follows. First, an increase in the risk is largely due to drought, pluvial flood, and storm surge, depending on the areas of interest, with the overall situation worsening under the RCP8.5 scenario. Second, particular locations have colocated vulnerable receptors at higher risk, concentrated in the urban centers (e.g., housing, railways, roads) and along the coast (e.g., beaches, wetlands, primary sector). Third, risk communication of potential environmental and socio-economic losses via the multirisk maps is useful to stakeholders and public administration. Fourth, the multirisk maps recommend priorities for future investigation and risk management, such as collection of sensor data, elaboration of mitigations, and adaptation plans at hotspot locations.}, } @article {pmid36689893, year = {2023}, author = {Werneck, RA and Meinberg, MF and Passos, MZ and Brandão, WC and de Moraes, EN and da Silva-Filho, AL}, title = {Quality of information regarding abnormal uterine bleeding available online.}, journal = {European journal of obstetrics, gynecology, and reproductive biology}, volume = {282}, number = {}, pages = {83-88}, doi = {10.1016/j.ejogrb.2023.01.020}, pmid = {36689893}, issn = {1872-7654}, mesh = {Humans ; Female ; Reproducibility of Results ; *Quality of Life ; *Search Engine ; Communication ; Uterine Hemorrhage ; Internet ; }, abstract = {INTRODUCTION: The Internet and electronic devices with Internet access allow for a greater fluidity of information and speed of communication, especially in the field of health. Abnormal uterine bleeding (AUB) affects approximately 3-30% of women and can negatively impact their health and quality of life. Information regarding AUB that is available on the Internet may not be clear or accurate, rendering it difficult to understand and likely to result in delayed medical evaluation, which subsequently leads to worsening of the AUB.

OBJECTIVE: To evaluate the quality of the information regarding AUB currently available on the Internet, including information regarding treatments.

METHODS: The Google Trends website was searched for the most widely used English terms related to AUB. The identified descriptors were searched individually on the Google, Yahoo!, and Bing search engines. The first 10 results of each search were pre-selected and evaluated for inclusion in this study. Selected websites were categorically divided into two groups (news/magazine and academic) and individually analyzed by three experts using the DISCERN quality criteria (reliability, general quality, and quality of information) and the presence or absence of the Health on the Net Foundation Code of Conduct (HONcode®) seal.

RESULTS: Of the 168 websites included in this study, 60.1% were allocated to the news/magazine group and 39.9% were allocated to the academic group. Over half of the websites (54.2%) did not have the HONcode® quality seal. Websites in the academic group were more likely to include accurate information regarding AUB with greater reliability than websites in the news/magazine group. There were no statistical differences regarding the general quality of the websites. Most websites were rated as either moderate quality (70.8%) or low quality (28.6%). The HONcode® criterion was found to be a confounding factor of the analyses, as the grouping and quality results of websites without this seal were significantly associated. In addition, websites in the news/magazines group were 6.7 times more likely to provide low quality information than websites in the academic group (odds ratio: 6.7; 95% confidence interval: 2.1-21.4).

CONCLUSION: The information regarding AUB that is available on the Internet is of low to moderate quality. Academic websites present more reliable information of greater quality. The presence of the HONcode® seal is considered important to determine the quality of the content of a website, especially for news/magazine websites, and may help Internet users identify websites that contain more reliable information. Algorithms and applications that categorize the quality of information and the reliability of health content may be useful tools that can help patients clarify their symptoms for several conditions including AUB.}, } @article {pmid36685700, year = {2022}, author = {Jazayeri, SM and Pooralinaghi, M and Torres-Navarrete, Y and Oviedo-Bayas, B and Guerra, ÍE and Jácome, DH and Morán, CQ and Macias, CS and Escobar, KM and Ghafoor, SMHAS and Veiskarami, G and Jandaghi, P and Torres, ROV}, title = {Alkaloid production and response to natural adverse conditions in Peganum harmala: in silico transcriptome analyses.}, journal = {Biotechnologia}, volume = {103}, number = {4}, pages = {355-384}, pmid = {36685700}, issn = {2353-9461}, abstract = {Peganum harmala is a valuable wild plant that grows and survives under adverse conditions and produces pharmaceutical alkaloid metabolites. Using different assemblers to develop a transcriptome improves the quality of assembled transcriptome. In this study, a concrete and accurate method for detecting stress-responsive transcripts by comparing stress-related gene ontology (GO) terms and public domains was designed. An integrated transcriptome for P. harmala including 42 656 coding sequences was created by merging de novo assembled transcriptomes. Around 35 000 transcripts were annotated with more than 90% resemblance to three closely related species of Citrus, which confirmed the robustness of the assembled transcriptome; 4853 stress-responsive transcripts were identified. CYP82 involved in alkaloid biosynthesis showed a higher number of transcripts in P. harmala than in other plants, indicating its diverse alkaloid biosynthesis attributes. Transcription factors (TFs) and regulatory elements with 3887 transcripts comprised 9% of the transcriptome. Among the TFs of the integrated transcriptome, cystein2/histidine2 (C2H2) and WD40 repeat families were the most abundant. The Kyoto Encyclopedia of Genes and Genomes (KEGG) MAPK (mitogen-activated protein kinase) signaling map and the plant hormone signal transduction map showed the highest assigned genes to these pathways, suggesting their potential stress resistance. The P. harmala whole-transcriptome survey provides important resources and paves the way for functional and comparative genomic studies on this plant to discover stress-tolerance-related markers and response mechanisms in stress physiology, phytochemistry, ecology, biodiversity, and evolution. P. harmala can be a potential model for studying adverse environmental cues and metabolite biosynthesis and a major source for the production of various alkaloids.}, } @article {pmid36684825, year = {2023}, author = {Liew, CY and Labadin, J and Kok, WC and Eze, MO}, title = {A methodology framework for bipartite network modeling.}, journal = {Applied network science}, volume = {8}, number = {1}, pages = {6}, pmid = {36684825}, issn = {2364-8228}, abstract = {The graph-theoretic based studies employing bipartite network approach mostly focus on surveying the statistical properties of the structure and behavior of the network systems under the domain of complex network analysis. They aim to provide the big-picture-view insights of a networked system by looking into the dynamic interaction and relationship among the vertices. Nonetheless, incorporating the features of individual vertex and capturing the dynamic interaction of the heterogeneous local rules governing each of them in the studies is lacking. The methodology in achieving this could hardly be found. Consequently, this study intends to propose a methodology framework that considers the influence of heterogeneous features of each node to the overall network behavior in modeling real-world bipartite network system. The proposed framework consists of three main stages with principal processes detailed in each stage, and three libraries of techniques to guide the modeling activities. It is iterative and process-oriented in nature and allows future network expansion. Two case studies from the domain of communicable disease in epidemiology and habitat suitability in ecology employing this framework are also presented. The results obtained suggest that the methodology could serve as a generic framework in advancing the current state of the art of bipartite network approach.}, } @article {pmid36682374, year = {2023}, author = {Traore, T and Shanks, S and Haider, N and Ahmed, K and Jain, V and Rüegg, SR and Razavi, A and Kock, R and Erondu, N and Rahman-Shepherd, A and Yavlinsky, A and Mboera, L and Asogun, D and McHugh, TD and Elton, L and Oyebanji, O and Okunromade, O and Ansumana, R and Djingarey, MH and Ali Ahmed, Y and Diallo, AB and Balde, T and Talisuna, A and Ntoumi, F and Zumla, A and Heymann, D and Fall, IS and Dar, O}, title = {How prepared is the world? Identifying weaknesses in existing assessment frameworks for global health security through a One Health approach.}, journal = {Lancet (London, England)}, volume = {401}, number = {10377}, pages = {673-687}, doi = {10.1016/S0140-6736(22)01589-6}, pmid = {36682374}, issn = {1474-547X}, support = {001/WHO_/World Health Organization/International ; }, mesh = {Animals ; Humans ; Global Health ; Ecosystem ; Emergencies ; *COVID-19 ; *One Health ; Pandemics ; }, abstract = {The COVID-19 pandemic has exposed faults in the way we assess preparedness and response capacities for public health emergencies. Existing frameworks are limited in scope, and do not sufficiently consider complex social, economic, political, regulatory, and ecological factors. One Health, through its focus on the links among humans, animals, and ecosystems, is a valuable approach through which existing assessment frameworks can be analysed and new ways forward proposed. Although in the past few years advances have been made in assessment tools such as the International Health Regulations Joint External Evaluation, a rapid and radical increase in ambition is required. To sufficiently account for the range of complex systems in which health emergencies occur, assessments should consider how problems are defined across stakeholders and the wider sociopolitical environments in which structures and institutions operate. Current frameworks do little to consider anthropogenic factors in disease emergence or address the full array of health security hazards across the social-ecological system. A complex and interdependent set of challenges threaten human, animal, and ecosystem health, and we cannot afford to overlook important contextual factors, or the determinants of these shared threats. Health security assessment frameworks should therefore ensure that the process undertaken to prioritise and build capacity adheres to core One Health principles and that interventions and outcomes are assessed in terms of added value, trade-offs, and cobenefits across human, animal, and environmental health systems.}, } @article {pmid36669842, year = {2023}, author = {Guan, Y and Qi, Y and Zheng, L and Yang, J and Zhang, M and Zhang, Q and Ji, L}, title = {Data mining techniques for detecting signals of adverse drug reaction of cardiac therapy drugs based on Jinan adverse event reporting system database: a retrospective study.}, journal = {BMJ open}, volume = {13}, number = {1}, pages = {e068127}, pmid = {36669842}, issn = {2044-6055}, mesh = {Humans ; United States ; Retrospective Studies ; Bayes Theorem ; *Adverse Drug Reaction Reporting Systems ; *Drug-Related Side Effects and Adverse Reactions/diagnosis/epidemiology ; Data Mining ; Databases, Factual ; United States Food and Drug Administration ; }, abstract = {OBJECTIVE: Cardiac therapy drugs are widely used in the treatment of heart disease. However, the concern regarding adverse events (AEs) of cardiac therapy drugs have been rising. This study aimed to analyse cardiac therapy drug-related AEs using the Jinan adverse event reporting system (JAERS) database mining and conduct a comprehensive evaluation to provide safe medication information for patients.

DESIGN: Retrospective observational study.

SETTING: In this study, cardiac therapy drug-related AEs were detected using the JAERS database from January 2000 to March 2022.

METHODS: Reports of cardiac therapy drug-related AEs were extracted from JAERS database, and the basic information of patients, reports and common AEs were analysed. Four disproportionality analysis methods, proportional reporting ratio (PRR), reporting odds ratio (ROR), Bayesian Confidence Propagation Neural Network (BCPNN), Medicines and Healthcare products Regulatory Agency (MHRA), were used to detect cardiac therapy drug-related signals. We further checked whether the detected signals exist on drug labels in China and two developed countries, the USA and Japan.

RESULTS: In total, 168 314 AEs were reported, of which 4788 were associated with cardiac therapy drugs. Using the PRR, ROR, MHRA and BCPNN method, we detected 52 signals, 52 signals, 33 signals and 43 signals, respectively. Among the 52 signals, 14 were not included on the drug labels of China. One (isosorbide mononitrate-head bilges) was not included on the drug labels of the three countries.

CONCLUSION: We identified 14 new cardiac therapy drug signals that did not appear on drug labels in China and 1 new signal that did not appear on drug labels in 3 counties. A causal link between cardiac therapy drugs and AEs should be evaluated in further studies.}, } @article {pmid36661052, year = {2023}, author = {Acerbi, A and Burns, J and Cabuk, U and Kryczka, J and Trapp, B and Valletta, JJ and Mesoudi, A}, title = {Sentiment analysis of the Twitter response to Netflix's Our Planet documentary.}, journal = {Conservation biology : the journal of the Society for Conservation Biology}, volume = {37}, number = {4}, pages = {e14060}, doi = {10.1111/cobi.14060}, pmid = {36661052}, issn = {1523-1739}, mesh = {Humans ; *Social Media ; Planets ; Sentiment Analysis ; Conservation of Natural Resources ; Attitude ; }, abstract = {The role of nature documentaries in shaping public attitudes and behavior toward conservation and wildlife issues is unclear. We analyzed the emotional content of over 2 million tweets related to Our Planet, a major nature documentary released on Netflix, with dictionary and rule-based automatic sentiment analysis. We also compared the sentiment associated with species mentioned in Our Planet and a set of control species with similar features but not mentioned in the documentary. Tweets were largely negative in sentiment at the time of release of the series. This effect was primarily linked to the highly skewed distributions of retweets and, in particular, to a single negatively valenced and massively retweeted tweet (>150,000 retweets). Species mentioned in Our Planet were associated with more negative sentiment than the control species, and this effect coincided with a short period following the airing of the series. Our results are consistent with a general negativity bias in cultural transmission and document the difficulty of evoking positive sentiment, on social media and elsewhere, in response to environmental problems.}, } @article {pmid36656265, year = {2023}, author = {Yu, Y and Yu, X and Zhang, D and Jin, L and Huang, J and Zhu, X and Sun, J and Yu, M and Zhu, L}, title = {Biotransformation of Organophosphate Esters by Rice and Rhizosphere Microbiome: Multiple Metabolic Pathways, Mechanism, and Toxicity Assessment.}, journal = {Environmental science & technology}, volume = {57}, number = {4}, pages = {1776-1787}, doi = {10.1021/acs.est.2c07796}, pmid = {36656265}, issn = {1520-5851}, mesh = {*Oryza ; Rhizosphere ; Esters/metabolism ; *Flame Retardants/analysis ; Organophosphates ; Biotransformation ; Phosphates ; *Microbiota ; Metabolic Networks and Pathways ; Environmental Monitoring ; China ; }, abstract = {The biotransformation behavior and toxicity of organophosphate esters (OPEs) in rice and rhizosphere microbiomes were comprehensively studied by hydroponic experiments. OPEs with lower hydrophobicity were liable to be translocated acropetally, and rhizosphere microbiome could reduce the uptake and translocation of OPEs in rice tissues. New metabolites were successfully identified in rice and rhizosphere microbiome, including hydrolysis, hydroxylated, methylated, and glutathione-, glucuronide-, and sulfate-conjugated products. Rhizobacteria and plants could cooperate to form a complex ecological interaction web for OPE elimination. Furthermore, active members of the rhizosphere microbiome during OPE degradation were revealed and the metagenomic analysis indicated that most of these active populations contained OPE-degrading genes. The results of metabolomics analyses for phytotoxicity assessment implied that several key function metabolic pathways of the rice plant were found perturbed by metabolites, such as diphenyl phosphate and monophenyl phosphate. In addition, the involved metabolism mechanisms, such as the carbohydrate metabolism, amino acid metabolism and synthesis, and nucleotide metabolism in Escherichia coli, were significantly altered after exposure to the products mixture of OPEs generated by rhizosphere microbiome. This work for the first time gives a comprehensive understanding of the entire metabolism of OPEs in plants and associated microbiome, and provides support for the ongoing risk assessment of emerging contaminants and, most critically, their transformation products.}, } @article {pmid36654087, year = {2022}, author = {Yang, L and Zou, K and Gao, K and Jiang, Z}, title = {A fuzzy DRBFNN-based information security risk assessment method in improving the efficiency of urban development.}, journal = {Mathematical biosciences and engineering : MBE}, volume = {19}, number = {12}, pages = {14232-14250}, doi = {10.3934/mbe.2022662}, pmid = {36654087}, issn = {1551-0018}, mesh = {*Urban Renewal ; *Ecology/methods ; Cities ; Neural Networks, Computer ; Risk Assessment ; China ; }, abstract = {The rapid development of urban informatization is an important way for cities to achieve a higher pattern, but the accompanying information security problem become a major challenge restricting the efficiency of urban development. Therefore, effective identification and assessment of information security risks has become a key factor to improve the efficiency of urban development. In this paper, an information security risk assessment method based on fuzzy theory and neural network technology is proposed to help identify and solve the information security problem in the development of urban informatization. Combined with the theory of information ecology, this method establishes an improved fuzzy neural network model from four aspects by using fuzzy theory, neural network model and DEMATEL method, and then constructs the information security risk assessment system of smart city. According to this method, this paper analyzed 25 smart cities in China, and provided suggestions and guidance for information security control in the process of urban informatization construction.}, } @article {pmid36653564, year = {2023}, author = {Battin, TJ and Lauerwald, R and Bernhardt, ES and Bertuzzo, E and Gener, LG and Hall, RO and Hotchkiss, ER and Maavara, T and Pavelsky, TM and Ran, L and Raymond, P and Rosentreter, JA and Regnier, P}, title = {River ecosystem metabolism and carbon biogeochemistry in a changing world.}, journal = {Nature}, volume = {613}, number = {7944}, pages = {449-459}, pmid = {36653564}, issn = {1476-4687}, support = {1442439//National Science Foundation/ ; 1926426//National Science Foundation/ ; 1840243//National Science Foundation/ ; }, mesh = {*Carbon Cycle ; *Carbon Dioxide/analysis ; Carbon Sequestration ; *Ecosystem ; Greenhouse Gases/analysis ; *Rivers ; }, abstract = {River networks represent the largest biogeochemical nexus between the continents, ocean and atmosphere. Our current understanding of the role of rivers in the global carbon cycle remains limited, which makes it difficult to predict how global change may alter the timing and spatial distribution of riverine carbon sequestration and greenhouse gas emissions. Here we review the state of river ecosystem metabolism research and synthesize the current best available estimates of river ecosystem metabolism. We quantify the organic and inorganic carbon flux from land to global rivers and show that their net ecosystem production and carbon dioxide emissions shift the organic to inorganic carbon balance en route from land to the coastal ocean. Furthermore, we discuss how global change may affect river ecosystem metabolism and related carbon fluxes and identify research directions that can help to develop better predictions of the effects of global change on riverine ecosystem processes. We argue that a global river observing system will play a key role in understanding river networks and their future evolution in the context of the global carbon budget.}, } @article {pmid36651964, year = {2023}, author = {Johnson, MS and Venkataram, S and Kryazhimskiy, S}, title = {Best Practices in Designing, Sequencing, and Identifying Random DNA Barcodes.}, journal = {Journal of molecular evolution}, volume = {91}, number = {3}, pages = {263-280}, pmid = {36651964}, issn = {1432-1432}, support = {R01 GM137112/GM/NIGMS NIH HHS/United States ; 1R01GM137112/GM/NIGMS NIH HHS/United States ; 1R01GM137112/GM/NIGMS NIH HHS/United States ; }, mesh = {*DNA Barcoding, Taxonomic ; *DNA/genetics ; Sequence Analysis, DNA/methods ; Computational Biology ; High-Throughput Nucleotide Sequencing/methods ; }, abstract = {Random DNA barcodes are a versatile tool for tracking cell lineages, with applications ranging from development to cancer to evolution. Here, we review and critically evaluate barcode designs as well as methods of barcode sequencing and initial processing of barcode data. We first demonstrate how various barcode design decisions affect data quality and propose a new design that balances all considerations that we are currently aware of. We then discuss various options for the preparation of barcode sequencing libraries, including inline indices and Unique Molecular Identifiers (UMIs). Finally, we test the performance of several established and new bioinformatic pipelines for the extraction of barcodes from raw sequencing reads and for error correction. We find that both alignment and regular expression-based approaches work well for barcode extraction, and that error-correction pipelines designed specifically for barcode data are superior to generic ones. Overall, this review will help researchers to approach their barcoding experiments in a deliberate and systematic way.}, } @article {pmid36648719, year = {2023}, author = {Zhu, F and Su, T and Lei, B and Liang, Q and Zhou, Y and Liu, X and Wang, X and Zhang, D}, title = {Considerations on the impact of "source-sink" landscape pattern changes on urban thermal environment and cooling efficiency: a case study of Nanjing, China.}, journal = {Environmental science and pollution research international}, volume = {30}, number = {14}, pages = {42296-42310}, pmid = {36648719}, issn = {1614-7499}, mesh = {Humans ; Cities ; *Hot Temperature ; *Environmental Monitoring/methods ; China ; Urbanization ; }, abstract = {The urban heat island effect caused by rapid urbanization has had a great impact on human health and ecological environment. The evolution of landscape patterns often affects regional thermal characteristics at the local scale. How to rationally allocate land cover types from the perspective of urban planning is a huge challenge. This paper takes Nanjing, a typical "stove city" in China, as an example to study the impact of landscape pattern changes on the urban thermal environment. Firstly, based on the "source" landscape "/sink" landscape identified by the "source-sink" landscape index, on this basis, the contributions of the "source-sink" landscape and its effects are calculated, and the temporal and spatial evolution laws are analyzed. Second, we study the cooling effect of different characteristic landscapes. The results show that the change of landscape pattern is closely related to the urban thermal environment, and the expansion of built-up areas is the main reason for the urban thermal environment. With the development of urbanization, the "source-sink" landscape structure in most districts and counties has aggravated the heat island effect, and the ratios of "sink" and "source" landscape contribution ratios with strong levels are concentrated in the suburban areas. The results of cooling efficiency research show that the cooling range of forest land is larger than that of water bodies. At the same time, we found that the cooling efficiency of the sink landscape is the highest when the area of the sink landscape is 0.18-0.9 hm[2] and the shape index is between 1 and 4. The research results can provide feasible and practical scientific suggestions for the planning and ecological construction of Nanjing.}, } @article {pmid36648611, year = {2023}, author = {Hu, Y and Wang, X and Xu, Y and Yang, H and Tong, Z and Tian, R and Xu, S and Yu, L and Guo, Y and Shi, P and Huang, S and Yang, G and Shi, S and Wei, F}, title = {Molecular mechanisms of adaptive evolution in wild animals and plants.}, journal = {Science China. Life sciences}, volume = {66}, number = {3}, pages = {453-495}, pmid = {36648611}, issn = {1869-1889}, mesh = {*Biological Evolution ; *Adaptation, Physiological/genetics ; *Genome, Plant/genetics ; *Animals, Wild/genetics ; Biological Coevolution/genetics ; Phenotype ; Aquatic Organisms/genetics ; Ecology/methods/trends ; Computational Biology/methods ; }, abstract = {Wild animals and plants have developed a variety of adaptive traits driven by adaptive evolution, an important strategy for species survival and persistence. Uncovering the molecular mechanisms of adaptive evolution is the key to understanding species diversification, phenotypic convergence, and inter-species interaction. As the genome sequences of more and more non-model organisms are becoming available, the focus of studies on molecular mechanisms of adaptive evolution has shifted from the candidate gene method to genetic mapping based on genome-wide scanning. In this study, we reviewed the latest research advances in wild animals and plants, focusing on adaptive traits, convergent evolution, and coevolution. Firstly, we focused on the adaptive evolution of morphological, behavioral, and physiological traits. Secondly, we reviewed the phenotypic convergences of life history traits and responding to environmental pressures, and the underlying molecular convergence mechanisms. Thirdly, we summarized the advances of coevolution, including the four main types: mutualism, parasitism, predation and competition. Overall, these latest advances greatly increase our understanding of the underlying molecular mechanisms for diverse adaptive traits and species interaction, demonstrating that the development of evolutionary biology has been greatly accelerated by multi-omics technologies. Finally, we highlighted the emerging trends and future prospects around the above three aspects of adaptive evolution.}, } @article {pmid36647630, year = {2023}, author = {Watts, JD and Farina, M and Kimball, JS and Schiferl, LD and Liu, Z and Arndt, KA and Zona, D and Ballantyne, A and Euskirchen, ES and Parmentier, FW and Helbig, M and Sonnentag, O and Tagesson, T and Rinne, J and Ikawa, H and Ueyama, M and Kobayashi, H and Sachs, T and Nadeau, DF and Kochendorfer, J and Jackowicz-Korczynski, M and Virkkala, A and Aurela, M and Commane, R and Byrne, B and Birch, L and Johnson, MS and Madani, N and Rogers, B and Du, J and Endsley, A and Savage, K and Poulter, B and Zhang, Z and Bruhwiler, LM and Miller, CE and Goetz, S and Oechel, WC}, title = {Carbon uptake in Eurasian boreal forests dominates the high-latitude net ecosystem carbon budget.}, journal = {Global change biology}, volume = {29}, number = {7}, pages = {1870-1889}, doi = {10.1111/gcb.16553}, pmid = {36647630}, issn = {1365-2486}, support = {1203583//NSF/ ; 8414//Gordon and Betty Moore Foundation/ ; 80NM0018D004/NASA/NASA/United States ; 80NSSC18K0770/NASA/NASA/United States ; 19-EARTH20-0105/NASA/NASA/United States ; NNX15AT74A/NASA/NASA/United States ; 80NSSC19M0113/NASA/NASA/United States ; }, mesh = {*Ecosystem ; *Taiga ; Carbon ; Carbon Dioxide ; Tundra ; Methane ; Carbon Cycle ; }, abstract = {Arctic-boreal landscapes are experiencing profound warming, along with changes in ecosystem moisture status and disturbance from fire. This region is of global importance in terms of carbon feedbacks to climate, yet the sign (sink or source) and magnitude of the Arctic-boreal carbon budget within recent years remains highly uncertain. Here, we provide new estimates of recent (2003-2015) vegetation gross primary productivity (GPP), ecosystem respiration (Reco), net ecosystem CO2 exchange (NEE; Reco - GPP), and terrestrial methane (CH4) emissions for the Arctic-boreal zone using a satellite data-driven process-model for northern ecosystems (TCFM-Arctic), calibrated and evaluated using measurements from >60 tower eddy covariance (EC) sites. We used TCFM-Arctic to obtain daily 1-km[2] flux estimates and annual carbon budgets for the pan-Arctic-boreal region. Across the domain, the model indicated an overall average NEE sink of -850 Tg CO2 -C year[-1] . Eurasian boreal zones, especially those in Siberia, contributed to a majority of the net sink. In contrast, the tundra biome was relatively carbon neutral (ranging from small sink to source). Regional CH4 emissions from tundra and boreal wetlands (not accounting for aquatic CH4) were estimated at 35 Tg CH4 -C year[-1] . Accounting for additional emissions from open water aquatic bodies and from fire, using available estimates from the literature, reduced the total regional NEE sink by 21% and shifted many far northern tundra landscapes, and some boreal forests, to a net carbon source. This assessment, based on in situ observations and models, improves our understanding of the high-latitude carbon status and also indicates a continued need for integrated site-to-regional assessments to monitor the vulnerability of these ecosystems to climate change.}, } @article {pmid36645791, year = {2022}, author = {Marwali, EM and Kekalih, A and Yuliarto, S and Wati, DK and Rayhan, M and Valerie, IC and Cho, HJ and Jassat, W and Blumberg, L and Masha, M and Semple, C and Swann, OV and Kohns Vasconcelos, M and Popielska, J and Murthy, S and Fowler, RA and Guerguerian, AM and Streinu-Cercel, A and Pathmanathan, MD and Rojek, A and Kartsonaki, C and Gonçalves, BP and Citarella, BW and Merson, L and Olliaro, PL and Dalton, HJ and , }, title = {Paediatric COVID-19 mortality: a database analysis of the impact of health resource disparity.}, journal = {BMJ paediatrics open}, volume = {6}, number = {1}, pages = {}, pmid = {36645791}, issn = {2399-9772}, support = {MC_PC_19059/MRC_/Medical Research Council/United Kingdom ; MR/S032304/1/MRC_/Medical Research Council/United Kingdom ; 222410/Z/21/Z/WT_/Wellcome Trust/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; 215091/Z/18/Z/WT_/Wellcome Trust/United Kingdom ; 225288/Z/22/Z/WT_/Wellcome Trust/United Kingdom ; 220757/Z/20/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Adolescent ; Humans ; Child ; COVID-19 Testing ; Pandemics ; *COVID-19/epidemiology/therapy ; *Tuberculosis ; Health Resources ; }, abstract = {BACKGROUND: The impact of the COVID-19 pandemic on paediatric populations varied between high-income countries (HICs) versus low-income to middle-income countries (LMICs). We sought to investigate differences in paediatric clinical outcomes and identify factors contributing to disparity between countries.

METHODS: The International Severe Acute Respiratory and Emerging Infections Consortium (ISARIC) COVID-19 database was queried to include children under 19 years of age admitted to hospital from January 2020 to April 2021 with suspected or confirmed COVID-19 diagnosis. Univariate and multivariable analysis of contributing factors for mortality were assessed by country group (HICs vs LMICs) as defined by the World Bank criteria.

RESULTS: A total of 12 860 children (3819 from 21 HICs and 9041 from 15 LMICs) participated in this study. Of these, 8961 were laboratory-confirmed and 3899 suspected COVID-19 cases. About 52% of LMICs children were black, and more than 40% were infants and adolescent. Overall in-hospital mortality rate (95% CI) was 3.3% [=(3.0% to 3.6%), higher in LMICs than HICs (4.0% (3.6% to 4.4%) and 1.7% (1.3% to 2.1%), respectively). There were significant differences between country income groups in intervention profile, with higher use of antibiotics, antivirals, corticosteroids, prone positioning, high flow nasal cannula, non-invasive and invasive mechanical ventilation in HICs. Out of the 439 mechanically ventilated children, mortality occurred in 106 (24.1%) subjects, which was higher in LMICs than HICs (89 (43.6%) vs 17 (7.2%) respectively). Pre-existing infectious comorbidities (tuberculosis and HIV) and some complications (bacterial pneumonia, acute respiratory distress syndrome and myocarditis) were significantly higher in LMICs compared with HICs. On multivariable analysis, LMIC as country income group was associated with increased risk of mortality (adjusted HR 4.73 (3.16 to 7.10)).

CONCLUSION: Mortality and morbidities were higher in LMICs than HICs, and it may be attributable to differences in patient demographics, complications and access to supportive and treatment modalities.}, } @article {pmid36643652, year = {2023}, author = {Mugnai, F and Costantini, F and Chenuil, A and Leduc, M and Gutiérrez Ortega, JM and Meglécz, E}, title = {Be positive: customized reference databases and new, local barcodes balance false taxonomic assignments in metabarcoding studies.}, journal = {PeerJ}, volume = {11}, number = {}, pages = {e14616}, pmid = {36643652}, issn = {2167-8359}, mesh = {Databases, Factual ; *DNA Barcoding, Taxonomic ; Mediterranean Sea ; *Aquatic Organisms/genetics ; }, abstract = {BACKGROUND: In metabarcoding analyses, the taxonomic assignment is crucial to place sequencing data in biological and ecological contexts. This fundamental step depends on a reference database, which should have a good taxonomic coverage to avoid unassigned sequences. However, this goal is rarely achieved in many geographic regions and for several taxonomic groups. On the other hand, more is not necessarily better, as sequences in reference databases belonging to taxonomic groups out of the studied region/environment context might lead to false assignments.

METHODS: We investigated the effect of using several subsets of a cytochrome c oxidase subunit I (COI) reference database on taxonomic assignment. Published metabarcoding sequences from the Mediterranean Sea were assigned to taxa using COInr, which is a comprehensive, non-redundant and recent database of COI sequences obtained both from BOLD and NCBI, and two of its subsets: (i) all sequences except insects (COInr-WO-Insecta), which represent the overwhelming majority of COInr database, but are irrelevant for marine samples, and (ii) all sequences from taxonomic families present in the Mediterranean Sea (COInr-Med). Four different algorithms for taxonomic assignment were employed in parallel to evaluate differences in their output and data consistency.

RESULTS: The reduction of the database to more specific custom subsets increased the number of unassigned sequences. Nevertheless, since most of them were incorrectly assigned by the less specific databases, this is a positive outcome. Moreover, the taxonomic resolution (the lowest taxonomic level to which a sequence is attributed) of several sequences tended to increase when using customized databases. These findings clearly indicated the need for customized databases adapted to each study. However, the very high proportion of unassigned sequences points to the need to enrich the local database with new barcodes specifically obtained from the studied region and/or taxonomic group. Including novel local barcodes to the COI database proved to be very profitable: by adding only 116 new barcodes sequenced in our laboratory, thus increasing the reference database by only 0.04%, we were able to improve the resolution for ca. 0.6-1% of the Amplicon Sequence Variants (ASVs).}, } @article {pmid36642073, year = {2023}, author = {Paixão, TM and Siqueira, CEG and Tristan-Cheever, E and Fischer, FM and Martinez, MC and Christoffolete, MA and Meisinger, K and Teixeira, LR}, title = {Overweight and Obesity in Brazilian Immigrants in Massachusetts, USA: A Time Series Analysis (2009-2020).}, journal = {Obesity facts}, volume = {16}, number = {2}, pages = {109-118}, pmid = {36642073}, issn = {1662-4033}, mesh = {Adult ; Humans ; Female ; Adolescent ; Young Adult ; Middle Aged ; Male ; *Overweight/epidemiology ; Brazil/epidemiology ; Time Factors ; Obesity/epidemiology ; *Emigrants and Immigrants ; Massachusetts/epidemiology ; Prevalence ; }, abstract = {INTRODUCTION: Obesity is considered a growing public health problem by the Brazilian Ministry of Health and a global epidemic by the World Health Organization (WHO). In 2020, the Centers for Disease Control and Prevention (CDC) estimated the prevalence of adult obesity at 31.9% in the USA. The USA is one of the main destinations for Brazilian immigrants in search of better living conditions, and Massachusetts is one of the states with the highest presence of Brazilians. Changes in lifestyle and eating habits are often associated with increases in overweight and obesity in immigrants in the USA, especially Hispanics, an official classification that does not, however, include Brazilians. The aim of this study was to describe the temporal trend of overweight and obesity in Brazilian immigrants assisted by the Cambridge Health Alliance (CHA) healthcare network in Massachusetts.

METHODS: This was an ecological time series study of 128,206 records of Brazilians aged between 18 and 60 years based on hospital data from 2009 to 2020.

RESULTS: Mean age was 38.9 (SD = 10.6), and 61% of the sample were women. The prevalence of overweight and obesity was 38.4% and 25.4%, respectively. Obesity exhibited an increasing trend, while eutrophy and overweight decreased during the study period.

CONCLUSION: As little is known about the health of Brazilian immigrants in the USA, this study contributes to the literature on the subject. The observed increasing trends agree with the worldwide increase in obesity and indicate the need for future research exploring individual factors associated with immigrant acculturation.}, } @article {pmid36641462, year = {2023}, author = {Tulis, F and Ševčík, M and Jánošíková, R and Baláž, I and Ambros, M and Zvaríková, L and Horváth, G}, title = {The impact of the striped field mouse's range expansion on communities of native small mammals.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {753}, pmid = {36641462}, issn = {2045-2322}, mesh = {Animals ; *Mammals ; *Murinae ; Slovakia ; }, abstract = {Understanding species expansion as an element of the dispersal process is crucial to gaining a better comprehension of the functioning of the populations and the communities. Populations of the same species that are native in one area could be considered nonindigenous, naturalised or invasive somewhere else. The striped field mouse has been expanding its range in south-western Slovakia since 2010, although the origin of the spread has still not been clarified. In light of the striped field mouse's life history, the recent range expansion is considered to be the expansion of a native species. This study analyses the impact of the striped field mouse's expansion on the native population and small mammal communities and confronts the documented stages of striped field mouse expansion with the stages of invasion biology. Our research replicates the design and compares results from past research of small mammals prior to this expansion at the same three study areas with the same 20 study sites and control sites. Several years after expansion, the striped field mouse has a 100% frequency of occurrence in all study sites and has become the dominant species in two of the study areas. The native community is significantly affected by the striped field mouse's increasing dominance, specifically: (i) we found a re-ordering of the species rank, mainly in areas with higher dominance, and (ii) an initial positive impact on diversity and evenness during low dominance of the striped field mouse turned markedly negative after crossing the 25% dominance threshold. Results suggested that the variation in the striped field mouse's dominance is affected by the northern direction of its spread. Our findings show that establishment in a new area, spread and impact on the native community are stages possibly shared by both invasive and native species during their range expansion.}, } @article {pmid36640933, year = {2023}, author = {Gautam, P and Pandey, AK and Dubey, SK}, title = {Multi-omics approach reveals elevated potential of bacteria for biodegradation of imidacloprid.}, journal = {Environmental research}, volume = {221}, number = {}, pages = {115271}, doi = {10.1016/j.envres.2023.115271}, pmid = {36640933}, issn = {1096-0953}, mesh = {Biodegradation, Environmental ; Molecular Docking Simulation ; Multiomics ; Neonicotinoids/analysis ; *Insecticides/analysis ; Nitro Compounds/analysis/chemistry/metabolism ; Bacteria/metabolism ; *Soil Pollutants/analysis ; Soil ; }, abstract = {The residual imidacloprid, a widely used insecticide is causing serious environmental concerns. Knowledge of its biodegradation will help in assessing its residual mass in soil. In view of this, a soil microcosm-based study was performed to test the biodegradation potential of Agrobacterium sp. InxBP2. It achieved ∼88% degradation in 20 days and followed the pseudo-first-order kinetics (k = 0.0511 day[-1] and t1/2=7 days). Whole genome sequencing of Agrobacterium sp. InxBP2 revealed a genome size of 5.44 Mbp with 5179 genes. Imidacloprid degrading genes at loci K7A42_07110 (ABC transporter substrate-binding protein), K7A42_07270 (amidohydrolase family protein), K7A42_07385 (ABC transporter ATP-binding protein), K7A42_16,845 (nitronate monooxygenase family protein), and K7A42_20,660 (FAD-dependent monooxygenase) having sequence and functional similarity with known counterparts were identified. Molecular docking of proteins encoded by identified genes with their respective degradation pathway intermediates exhibited significant binding energies (-6.56 to -4.14 kcal/mol). Molecular dynamic simulation discovered consistent interactions and binding depicting high stability of docked complexes. Proteome analysis revealed differential protein expression in imidacloprid treated versus untreated samples which corroborated with the in-silico findings. Further, the detection of metabolites proved the bacterial degradation of imidacloprid. Thus, results provided a mechanistic link between imidacloprid and associated degradative genes/enzymes of Agrobacterium sp. InxBP2. These findings will be of immense significance in carrying out the lifecycle analysis and formulating strategies for the bioremediation of soils contaminated with insecticides like imidacloprid.}, } @article {pmid36639402, year = {2023}, author = {Mack, M and Stojan, R and Bock, O and Voelcker-Rehage, C}, title = {The association of executive functions and physical fitness with cognitive-motor multitasking in a street crossing scenario.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {697}, pmid = {36639402}, issn = {2045-2322}, mesh = {Female ; Humans ; Aged ; *Executive Function ; *Physical Fitness ; Exercise ; Task Performance and Analysis ; Cognition ; }, abstract = {Age-related decline in cognitive-motor multitasking performance has been attributed to declines in executive functions and physical fitness (motor coordinative fitness and cardiovascular fitness). It has been suggested that those cognitive and physical resources strongly depend on lifestyle factors such as long-term regular physical activity and cognitive engagement. Although research suggests that there is covariation between components of executive functions and physical fitness, the interdependence between these components for cognitive-motor multitasking performance is not yet clear. The aim of the study was to examine the contribution and interrelationship between executive functions, motor coordinative fitness, and cardiovascular fitness on street crossing while multitasking. We used the more ecologically valid scenario to obtain results that might be directly transferable to daily life situation. Data from 50 healthy older adults (65-75 years, 17 females, recruited in two different cities in Germany) were analyzed. Participants' executive functions (composite score including six tests), motor coordinative fitness (composite score including five tests), and cardiovascular fitness (spiroergometry), as well as their street crossing performance while multitasking were assessed. Street crossing was tested under single-task (crossing a two-line road), and multitask conditions (crossing a two-line road while typing numbers on a keypad as simulation of mobile phone use). Street crossing performance was assessed by use of cognitive outcomes (typing, crossing failures) and motor outcomes (stay time, crossing speed). Linear mixed-effects models showed beneficial main effects of executive functions for typing (p = 0.004) and crossing failures (p = 0.023), and a beneficial main effect of motor coordinative fitness for stay time (p = 0.043). Commonality analysis revealed that the proportion of variance commonly explained by executive functions, motor coordinative fitness, and cardiovascular fitness was small for all street crossing outcomes. For typing and crossing failures (cognitive outcomes), the results further showed a higher relative contribution of executive functions compared to motor coordinative fitness and cardiovascular fitness. For stay time (motor outcome), the results correspondingly revealed a higher relative contribution of motor coordinative fitness compared to executive functions and cardiovascular fitness. The findings suggest that during cognitive-motor multitasking in everyday life, task performance is determined by the components of executive functions and physical fitness related to the specific task demands. Since multitasking in everyday life includes cognitive and motor tasks, it seems to be important to maintain both executive functions and physical fitness for independent living up to old age.}, } @article {pmid36637211, year = {2023}, author = {Feldner-Busztin, D and Firbas Nisantzis, P and Edmunds, SJ and Boza, G and Racimo, F and Gopalakrishnan, S and Limborg, MT and Lahti, L and de Polavieja, GG}, title = {Dealing with dimensionality: the application of machine learning to multi-omics data.}, journal = {Bioinformatics (Oxford, England)}, volume = {39}, number = {2}, pages = {}, pmid = {36637211}, issn = {1367-4811}, support = {//European Union's Horizon 2020 research and innovation programme/ ; CEH-DNRF143//Danish National Research Foundation/ ; }, mesh = {Humans ; *Multiomics ; *Neoplasms/genetics ; Machine Learning ; Genome ; }, abstract = {MOTIVATION: Machine learning (ML) methods are motivated by the need to automate information extraction from large datasets in order to support human users in data-driven tasks. This is an attractive approach for integrative joint analysis of vast amounts of omics data produced in next generation sequencing and other -omics assays. A systematic assessment of the current literature can help to identify key trends and potential gaps in methodology and applications. We surveyed the literature on ML multi-omic data integration and quantitatively explored the goals, techniques and data involved in this field. We were particularly interested in examining how researchers use ML to deal with the volume and complexity of these datasets.

RESULTS: Our main finding is that the methods used are those that address the challenges of datasets with few samples and many features. Dimensionality reduction methods are used to reduce the feature count alongside models that can also appropriately handle relatively few samples. Popular techniques include autoencoders, random forests and support vector machines. We also found that the field is heavily influenced by the use of The Cancer Genome Atlas dataset, which is accessible and contains many diverse experiments.

All data and processing scripts are available at this GitLab repository: https://gitlab.com/polavieja_lab/ml_multi-omics_review/ or in Zenodo: https://doi.org/10.5281/zenodo.7361807.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, } @article {pmid36629615, year = {2023}, author = {Brito, MIBDS and Oliveira, ECA and Barbosa, CS and Gomes, ECS}, title = {Factors associated with severe forms and deaths from schistosomiasis and application of probabilistic linkage in databases, state of Pernambuco, Brazil, 2007-2017.}, journal = {Revista brasileira de epidemiologia = Brazilian journal of epidemiology}, volume = {26}, number = {}, pages = {e230003}, pmid = {36629615}, issn = {1980-5497}, mesh = {Humans ; Brazil/epidemiology ; *Schistosomiasis/epidemiology ; Databases, Factual ; }, abstract = {OBJECTIVE: To verify the agreement of data on severe forms and deaths from schistosomiasis recorded in the Brazilian Notifiable Diseases Information System and the Mortality Information System, sociodemographic variables with the occurrence of severe forms and deaths, and the temporal trend of the disease in the state of Pernambuco, Brazil.

METHODS: This is an ecological, descriptive, time series study with data on severe forms and deaths from schistosomiasis in Pernambuco, from 2007 to 2017. For the linkage between databases, a function was developed in python programming language, using the Soundex method. To identify sociodemographic and health factors that correlated with the dependent variables, Pearson's correlation test was applied. For trend analysis, linear regression was applied.

RESULTS: We identified 9,085 severe cases, 1,956 deaths, and 186 cases in the linkage. The correlation between the average positivity rate with the general water supply and waste collection was 0.22 and 0.26 respectively. We verified a correlation of the average cumulative mortality rate with water supply by well or spring (r=0.27), water supply by the general network (r=0.3), waste collection (r=0.42), and road urbanization (r=0.29). We found 3,153 severe forms in 2007 with a decrease trend and 205 deaths in 2010, without a trend pattern.

CONCLUSION: There is a need for greater investments in disease control and in the quality of information, especially in the record of severe forms, considering that, due to the pathophysiology of the disease, death only occurs when the individual develops the chronic form, and its notification on the Notifiable Diseases Information System is imperative.}, } @article {pmid36629614, year = {2023}, author = {Batista, JFC and Oliveira, MR and Pereira, DLM and Matos, MLSDS and Souza, IT and Menezes, MO}, title = {Spatial distribution and temporal trends of AIDS in Brazil and regions between 2005 and 2020.}, journal = {Revista brasileira de epidemiologia = Brazilian journal of epidemiology}, volume = {26}, number = {}, pages = {e230002}, pmid = {36629614}, issn = {1980-5497}, mesh = {Humans ; Adolescent ; Young Adult ; Adult ; Brazil/epidemiology ; *Acquired Immunodeficiency Syndrome/epidemiology ; Bayes Theorem ; Information Systems ; Incidence ; }, abstract = {OBJECTIVE: To analyze the spatial distribution and the temporal trend of the AIDS incidence rate in Brazil from 2005 to 2020.

METHODS: This is an ecological, temporal, and spatial study on AIDS cases in Brazil. Data from the Notifiable Diseases Information System were stratified by year of diagnosis, region of the country/municipalities of residence, and age group (over 13 years). Incidence rates were calculated for temporal estimation using the Joinpoint model, as well as Spatial Empirical Bayes (SEB) for spatial distribution, using the Kernel density estimator.

RESULTS: The incidence rate in Brazil, in 2020, was 17.69 cases per 100 thousand inhabitants. The general trend (2005-2020) was decrease in Brazil (Annual Percent Change - APC=-2.0%), in the Southeast (APC=-4.4%) and South (APC=-3.0%) regions. The North (APC=2.3%) showed an increase trend, whereas the Southeast and Midwest regions were stationary (p>0.05). Brazil, Southeast, South, and Midwest regions showed a decrease trend in most age groups. The Northeast and North regions showed an increase in the age groups of 13-29 years and 13-24 years, respectively. The Kernel estimator showed clusters with SEB above 30/10 thousand inhabitants in the states of Paraíba, Sergipe, Alagoas, Pernambuco, São Paulo, Minas Gerais, Pará, Rio Grande do Sul, and Santa Catarina.

CONCLUSION: Brazil, the Southeast, and South regions showed a decrease in the incidence rate, whereas the North region increased and the Northeast and Midwest regions were stationary. The Southeast, South, and Northeast regions presented the largest clusters of SEB.}, } @article {pmid36621304, year = {2023}, author = {Liu, X and Han, Y and Luo, L and Pan, H and Cheng, T and Zhang, Q}, title = {Multiomics analysis reveals the mechanisms underlying the different floral colors and fragrances of Rosa hybrida cultivars.}, journal = {Plant physiology and biochemistry : PPB}, volume = {195}, number = {}, pages = {101-113}, doi = {10.1016/j.plaphy.2022.12.028}, pmid = {36621304}, issn = {1873-2690}, mesh = {*Rosa/genetics/metabolism ; Odorants ; Multiomics ; Color ; Plant Breeding ; Flowers/genetics/metabolism ; Gene Expression Regulation, Plant ; }, abstract = {The color and fragrance of rose flowers affect their commercial value. However, several rose varieties with new floral colors developed by the bud mutation method lost their fragrance during the breeding process, raising the question: Is there a relationship between floral color and aroma traits? Rose cultivar 'Yellow Island' (YI) with intensely aroma and yellow petals, while its bud mutant 'Past Feeling' (PF) with light aroma and pink petals mixing some yellow, two cultivars were used to explore this question using multiomics approaches. We investigated the genomic polymorphisms between PF and YI by whole-genome resequencing. 71 differentially abundant metabolites and 155 related differentially expressed genes identified in petals between PF and YI. From this, we constructed a model of metabolic changes affecting floral color and fragrance integrating shikimate, terpenoid, carotenoid, and green leaf volatile metabolites and predicted the associated key genes and transcription factors. This study provides a reference for understanding the molecular mechanism of variation in rose floral color and aroma traits.}, } @article {pmid36620398, year = {2023}, author = {Gries, C and Hanson, PC and O'Brien, M and Servilla, M and Vanderbilt, K and Waide, R}, title = {The Environmental Data Initiative: Connecting the past to the future through data reuse.}, journal = {Ecology and evolution}, volume = {13}, number = {1}, pages = {e9592}, pmid = {36620398}, issn = {2045-7758}, abstract = {The Environmental Data Initiative (EDI) is a trustworthy, stable data repository, and data management support organization for the environmental scientist. In a bottom-up community process, EDI was built with the premise that freely and easily available data are necessary to advance the understanding of complex environmental processes and change, to improve transparency of research results, and to democratize ecological research. EDI provides tools and support that allow the environmental researcher to easily integrate data publishing into the research workflow. Almost ten years since going into production, we analyze metadata to provide a general description of EDI's collection of data and its data management philosophy and placement in the repository landscape. We discuss how comprehensive metadata and the repository infrastructure lead to highly findable, accessible, interoperable, and reusable (FAIR) data by evaluating compliance with specific community proposed FAIR criteria. Finally, we review measures and patterns of data (re)use, assuring that EDI is fulfilling its stated premise.}, } @article {pmid36618211, year = {2022}, author = {Krishnan, RA and Ravindran, RM and Vincy, VS and Arun, P and Shinu, KS and Jithesh, V and Varma, RP}, title = {Analysis of daily COVID-19 death bulletin data during the first two waves of the COVID-19 pandemic in Thiruvananthapuram district, Kerala, India.}, journal = {Journal of family medicine and primary care}, volume = {11}, number = {10}, pages = {6190-6196}, pmid = {36618211}, issn = {2249-4863}, abstract = {CONTEXT: Coronavirus disease 2019 (COVID-19) mortality trends can help discern the pattern of outbreak evolution and systemic responses.

AIM: This study aimed to explore patterns of COVID-19 deaths in Thiruvananthapuram district from 31 March 2020 to 31 December 2021.

SETTING AND DESIGN: Secondary data analysis of COVID-19 deaths in Thiruvananthapuram district was performed.

MATERIALS AND METHODS: Mortality data were obtained from the district COVID-19 control room, and deaths in the first and second waves of COVID-19 were compared.

STATISTICAL ANALYSIS: We summarised data as proportions and medians with the inter-quartile range (IQR) and performed Chi-square tests to make comparisons wherever applicable.

RESULTS: As on 31 December 2021, 4587 COVID-19 deaths were reported in Thiruvananthapuram district, with a case fatality rate of 0.91%. We observed high mortality among older persons (66.7%) and men (56.6%). The leading cause of death was bronchopneumonia (60.6%). The majority (88.5%) had co-morbidities, commonly diabetes mellitus (54.9%). The median interval from diagnosis to hospitalisation was 4 days (IQR 2-7), and that from hospitalisation to death was 2 days (IQR 0-6). The deaths reported during the second wave were four times higher than those of the first wave with a higher proportion of deaths in the absence of co-morbidities (p < 0.001). The majority of the deceased were unvaccinated. Ecological analysis with vaccine coverage data indicated 5.4 times higher mortality among unvaccinated than those who received two vaccine doses.

CONCLUSIONS: The presence of co-morbidities, an unvaccinated status, and delay in hospitalisation were important reasons for COVID-19 deaths. Primary level health providers can potentially help sustaining vaccination, expeditious referral, and monitoring of COVID-19 patients.}, } @article {pmid36617091, year = {2023}, author = {Abdallah, M and Joung, BG and Lee, WJ and Mousoulis, C and Raghunathan, N and Shakouri, A and Sutherland, JW and Bagchi, S}, title = {Anomaly Detection and Inter-Sensor Transfer Learning on Smart Manufacturing Datasets.}, journal = {Sensors (Basel, Switzerland)}, volume = {23}, number = {1}, pages = {}, pmid = {36617091}, issn = {1424-8220}, mesh = {*Commerce ; Databases, Factual ; Time Factors ; *Machine Learning ; }, abstract = {Smart manufacturing systems are considered the next generation of manufacturing applications. One important goal of the smart manufacturing system is to rapidly detect and anticipate failures to reduce maintenance cost and minimize machine downtime. This often boils down to detecting anomalies within the sensor data acquired from the system which has different characteristics with respect to the operating point of the environment or machines, such as, the RPM of the motor. In this paper, we analyze four datasets from sensors deployed in manufacturing testbeds. We detect the level of defect for each sensor data leveraging deep learning techniques. We also evaluate the performance of several traditional and ML-based forecasting models for predicting the time series of sensor data. We show that careful selection of training data by aggregating multiple predictive RPM values is beneficial. Then, considering the sparse data from one kind of sensor, we perform transfer learning from a high data rate sensor to perform defect type classification. We release our manufacturing database corpus (4 datasets) and codes for anomaly detection and defect type classification for the community to build on it. Taken together, we show that predictive failure classification can be achieved, paving the way for predictive maintenance.}, } @article {pmid36613120, year = {2023}, author = {Qin, J and Ma, M and Shi, J and Ma, S and Wu, B and Su, X}, title = {The Time-Lag Effect of Climate Factors on the Forest Enhanced Vegetation Index for Subtropical Humid Areas in China.}, journal = {International journal of environmental research and public health}, volume = {20}, number = {1}, pages = {}, pmid = {36613120}, issn = {1660-4601}, mesh = {*Ecosystem ; *Forests ; China ; Climate Change ; Temperature ; }, abstract = {Forests represent the greatest carbon reservoir in terrestrial ecosystems. Climate change drives the changes in forest vegetation growth, which in turn influences carbon sequestration capability. Exploring the dynamic response of forest vegetation to climate change is thus one of the most important scientific questions to be addressed in the precise monitoring of forest resources. This paper explores the relationship between climate factors and vegetation growth in typical forest ecosystems in China from 2007 to 2019 based on long-term meteorological monitoring data from six forest field stations in different subtropical ecological zones in China. The time-varying parameter vector autoregressive model (TVP-VAR) was used to analyze the temporal and spatial differences of the time-lag effects of climate factors, and the impact of climate change on vegetation was predicted. The enhanced vegetation index (EVI) was used to measure vegetation growth. Monthly meteorological observations and solar radiation data, including precipitation, air temperature, relative humidity, and photosynthetic effective radiation, were provided by the resource sharing service platform of the national ecological research data center. It was revealed that the time-lag effect of climate factors on the EVI vanished after a half year, and the lag accumulation tended to be steady over time. The TVP-VAR model was found to be more suitable than the vector autoregressive model (VAR). The predicted EVI values using the TVP-VAR model were close to the true values with the root mean squares error (RMSE) < 0.05. On average, each site improved its prediction accuracy by 14.81%. Therefore, the TVP-VAR model can be used to analyze the relationship of climate factors and forest EVI as well as the time-lag effect of climate factors on vegetation growth in subtropical China. The results can be used to improve the predictability of the EVI for forests and to encourage the development of intensive forest management.}, } @article {pmid36612902, year = {2022}, author = {Vlăduțu, DE and Ionescu, M and Mercuț, R and Noveri, L and Lăzărescu, G and Popescu, SM and Scrieciu, M and Manolea, HO and Iacov Crăițoiu, MM and Ionescu, AG and Mercuț, V}, title = {Ecological Momentary Assessment of Masseter Muscle Activity in Patients with Bruxism.}, journal = {International journal of environmental research and public health}, volume = {20}, number = {1}, pages = {}, pmid = {36612902}, issn = {1660-4601}, mesh = {Humans ; *Bruxism ; Masseter Muscle/physiology ; Ecological Momentary Assessment ; Electromyography ; Masticatory Muscles/physiology ; }, abstract = {According to the International Bruxism Consensus, bruxism refers to the activity of the masticatory muscles reflecting contraction disorders, regardless of whether it is during sleep (SB) or an awake (AB) state. The objective of the present study was to evaluate the activity of the masseter muscle by surface electromyographic (sEMG) recordings. This study was performed on 20 participants with self-reported “possible bruxism” (study group) and 20 participants with no self-reported bruxism (control group); all participants underwent an evaluation of the masseter muscle activity using the dia-BRUXO device, which provides numerical parameters regarding sEMG (the total duration and the type of bruxism specific events, the effort made by the masticatory muscles during the recording period, and the personal bruxism index of each participant). Participants from the study group presented more clenching events during AB, three times more frequent than the control group (p = 0.002, Mann−Whitney U test); for SB, the frequency of clenching and grinding events was comparable within the study group, being more frequent than for the control group; the mean value of the effort index was higher for AB (1.177%) than SB (0.470%) and the same for the duration index, with a mean value of 2.788% for AB and 1.054% for SB. All participants from the control group presented reduced values for all acquired parameters. Overall, the personal bruxism index in AB was approximately four times higher for the study group (2.251%) compared to the control group (0.585%) (p < 0.005, Mann−Whitney U test). Similar values were obtained for SB. All participants with “possible bruxism” from the study group presented a higher activity of the masseter muscle, which is specific for bruxism, thus being defined as “definite bruxism”.}, } @article {pmid36612815, year = {2022}, author = {Yang, X and Lei, S and Shi, Y and Wang, W}, title = {Effects of Ground Subsidence on Vegetation Chlorophyll Content in Semi-Arid Mining Area: From Leaf Scale to Canopy Scale.}, journal = {International journal of environmental research and public health}, volume = {20}, number = {1}, pages = {}, pmid = {36612815}, issn = {1660-4601}, mesh = {*Chlorophyll/analysis ; *Plants ; Plant Leaves/chemistry ; Telemetry ; Poaceae ; }, abstract = {Ground subsidence is the main cause of vegetation degradation in mining areas. It is of great significance to study the effects of ground subsidence on vegetation. At present, few studies have analyzed the effects of ground subsidence on vegetation from different scales. However, the conclusions on different scales may differ. In this experiment, chlorophyll content was used as an indicator of vegetation degradation. We conducted a long-term field survey in the Lijiahao coalfield in China. Based on field survey data and remote sensing images, we analyzed the effects of ground subsidence on chlorophyll content from two scales (leaf scale and canopy scale) and summarized the similarities and differences. We found that, regardless of leaf scale or canopy scale, the effects of subsidence on chlorophyll content have the following three characteristics: (1) mining had the least effect on chlorophyll content in the neutral area, followed by the compression area, and the greatest effect on chlorophyll content in the extension area; (2) subsidence had a slight effect on chlorophyll content of Caragana korshins, but a serious effect on chlorophyll content of Stipa baicalensis; (3) chlorophyll content was not immediately affected when the ground sank. It was the cumulative subsidence that affects chlorophyll content. The difference between leaf scale and canopy scale was that the chlorophyll content at canopy scale is more affected by mining. This means that when assessing vegetation degradation, the results obtained by remote sensing were more severe than those measured in the field. We believe that this is because the canopy chlorophyll content obtained by remote sensing is also affected by the plant canopy structure. We recommend that mining and ecological restoration should be carried out concurrently, and that ground fissures should be taken as the focus of ecological restoration. In addition, Caragana korshins ought to be widely planted. Most importantly, managers should assess the effects of ground subsidence on vegetation on different scales. However, managers need to be aware of differences at different scales.}, } @article {pmid36612520, year = {2022}, author = {Zhou, Z and Zhang, Z and Zhang, W and Luo, J and Zhang, K and Cao, Z and Wang, Z}, title = {The Impact of Residences and Roads on Wind Erosion in a Temperate Grassland Ecosystem: A Spatially Oriented Perspective.}, journal = {International journal of environmental research and public health}, volume = {20}, number = {1}, pages = {}, pmid = {36612520}, issn = {1660-4601}, mesh = {Humans ; *Ecosystem ; *Grassland ; Wind ; Conservation of Natural Resources/methods ; Environmental Monitoring/methods ; Soil ; }, abstract = {The existence of residences and roads is an important way in which human activity affects wind erosion in arid and semiarid environments. Studies assessing the impact of these elements on wind erosion have only focused on limited plots, and their threat of erosion to the surrounding environment has been ignored by many studies. This study was based on spatially overlayed analysis of independent wind erosion distribution simulated by the revised wind erosion equation (RWEQ) and remote-sensing-image-derived residence and road distribution data. Wind erosion at different distances from residences and roads was quantified at the landscape scale of a typical temperate grassland ecosystem, explicitly demonstrating the crucial impacts of both elements on wind erosion. The results showed that wind erosion weakened as the distance from residences and roads increased due to the priority pathways of human activities, and the wind erosion around the residence was more severe than around the road. Human activities in the buffer zones 0-200 m from the residences most frequently caused severe wind erosion, with a wind soil loss of 25 t ha[-1] yr[-1] and a wind soil loss of approximately 5.25 t ha[-1] yr[-1] for 0-60 m from the roads. The characteristics of wind erosion variation in the buffer zones were also affected by residence size and the environments in which the residences were located. The variation in wind erosion was closely related to the road levels. Human activities intensified wind erosion mainly by affecting the soil and vegetation around residences and roads. Ecological management should not be limited to residences and roads but should also protect the surrounding environments. The findings of this study are aimed towards a spatial perspective that can help implement rational and effective environmental management measures for the sustainability of wind-eroded ecosystems.}, } @article {pmid36607898, year = {2023}, author = {Zhang, X and Chen, X and Yue, Y and Wang, S and Zhao, B and Huang, X and Li, T and Sun, Q and Wang, J}, title = {Ecological Study on Global Health Effects due to Source-Specific Ambient Fine Particulate Matter Exposure.}, journal = {Environmental science & technology}, volume = {57}, number = {3}, pages = {1278-1291}, pmid = {36607898}, issn = {1520-5851}, mesh = {Particulate Matter/analysis ; *Air Pollutants/analysis ; Global Health ; *Air Pollution/analysis ; Databases, Factual ; Environmental Exposure ; }, abstract = {Ambient air pollution of fine particulate matter with diameters less than 2.5 μm (PM2.5) is associated with millions of premature deaths per year, recognized as a leading global health concern. The dose-response relation between ambient PM2.5 exposure and mortality risk is the most fundamental information for assessments of the health effects of PM2.5. The existing dose-response relations were generally developed based on the assumption of equal contribution to toxicity from various sources. However, the sources of PM2.5 may significantly influence health effects. In this study, we conducted an ecological study to investigate the global long-term correlation between source-specific PM2.5 exposure and cause-specific mortality risk (SPECM) based on the regional aggregate data of the publically available official health databases from 528 regions worldwide with a total registered population of 3.2 billion. The results provided preliminary epidemiological evidence for differing chronic health effects across various sources. The relative mortality risks of lung cancer and circulatory diseases were closely correlated with the primary emissions from industrial and residential combustion sources. Chronic lower respiratory diseases were mostly associated with the mass concentration of particulate matter.}, } @article {pmid36607160, year = {2023}, author = {Van Sundert, K and Leuzinger, S and Bader, MK and Chang, SX and De Kauwe, MG and Dukes, JS and Langley, JA and Ma, Z and Mariën, B and Reynaert, S and Ru, J and Song, J and Stocker, B and Terrer, C and Thoresen, J and Vanuytrecht, E and Wan, S and Yue, K and Vicca, S}, title = {When things get MESI: The Manipulation Experiments Synthesis Initiative-A coordinated effort to synthesize terrestrial global change experiments.}, journal = {Global change biology}, volume = {29}, number = {7}, pages = {1922-1938}, doi = {10.1111/gcb.16585}, pmid = {36607160}, issn = {1365-2486}, support = {PCEFP2_181115/SNSF_/Swiss National Science Foundation/Switzerland ; }, mesh = {*Ecosystem ; *Carbon Dioxide ; Biomass ; Climate Change ; Climate ; Soil ; }, abstract = {Responses of the terrestrial biosphere to rapidly changing environmental conditions are a major source of uncertainty in climate projections. In an effort to reduce this uncertainty, a wide range of global change experiments have been conducted that mimic future conditions in terrestrial ecosystems, manipulating CO2 , temperature, and nutrient and water availability. Syntheses of results across experiments provide a more general sense of ecosystem responses to global change, and help to discern the influence of background conditions such as climate and vegetation type in determining global change responses. Several independent syntheses of published data have yielded distinct databases for specific objectives. Such parallel, uncoordinated initiatives carry the risk of producing redundant data collection efforts and have led to contrasting outcomes without clarifying the underlying reason for divergence. These problems could be avoided by creating a publicly available, updatable, curated database. Here, we report on a global effort to collect and curate 57,089 treatment responses across 3644 manipulation experiments at 1145 sites, simulating elevated CO2 , warming, nutrient addition, and precipitation changes. In the resulting Manipulation Experiments Synthesis Initiative (MESI) database, effects of experimental global change drivers on carbon and nutrient cycles are included, as well as ancillary data such as background climate, vegetation type, treatment magnitude, duration, and, unique to our database, measured soil properties. Our analysis of the database indicates that most experiments are short term (one or few growing seasons), conducted in the USA, Europe, or China, and that the most abundantly reported variable is aboveground biomass. We provide the most comprehensive multifactor global change database to date, enabling the research community to tackle open research questions, vital to global policymaking. The MESI database, freely accessible at doi.org/10.5281/zenodo.7153253, opens new avenues for model evaluation and synthesis-based understanding of how global change affects terrestrial biomes. We welcome contributions to the database on GitHub.}, } @article {pmid36604610, year = {2023}, author = {Prager, M and Lundin, D and Ronquist, F and Andersson, AF}, title = {ASV portal: an interface to DNA-based biodiversity data in the Living Atlas.}, journal = {BMC bioinformatics}, volume = {24}, number = {1}, pages = {6}, pmid = {36604610}, issn = {1471-2105}, support = {2019-00242//Vetenskapsrådet/ ; }, mesh = {*DNA/genetics ; *Biodiversity ; Software ; DNA Barcoding, Taxonomic ; }, abstract = {BACKGROUND: The Living Atlas is an open source platform used to collect, visualise and analyse biodiversity data from multiple sources, and serves as the national biodiversity data hub in many countries. Although powerful, the Living Atlas has had limited functionality for species occurrence data derived from DNA sequences. As a step toward integrating this fast-growing data source into the platform, we developed the Amplicon Sequence Variant (ASV) portal: a web interface to sequence-based biodiversity observations in the Living Atlas.

RESULTS: The ASV portal allows data providers to submit denoised metabarcoding output to the Living Atlas platform via an intermediary ASV database. It also enables users to search for existing ASVs and associated Living Atlas records using the Basic Local Alignment Search Tool, or via filters on taxonomy and sequencing details. The ASV portal is a Python-Flask/jQuery web interface, implemented as a multi-container docker service, and is an integral part of the Swedish Biodiversity Data Infrastructure.

CONCLUSION: The ASV portal is a web interface that effectively integrates biodiversity data derived from DNA sequences into the Living Atlas platform.}, } @article {pmid36602254, year = {2023}, author = {Koenig, CJ and Vasquez, TS and Peterson, EB and Wollney, EN and Bylund, CL and Ho, EY}, title = {Mapping Uncharted Terrain: A Systematic Review of Complementary and Integrative Health Communication Using Observational Data in Biomedical Settings.}, journal = {Health communication}, volume = {38}, number = {14}, pages = {3147-3162}, doi = {10.1080/10410236.2022.2140080}, pmid = {36602254}, issn = {1532-7027}, mesh = {Humans ; *Health Communication ; Palliative Care ; }, abstract = {Complementary and integrative health (CIH) use is diverse and highly prevalent worldwide. Prior research of CIH communication in biomedical encounters address safety, efficacy, symptom management, and overall wellness. Observational methods are rarely used to study CIH communication and avoid recall bias, preserve ecological validity, and contextualize situated clinical communication. Following PRISMA guidelines, we systematically reviewed studies at the intersection of social scientific observational research and findings about CIH communication between clinicians, patients, and caregivers in biomedical settings. We identified international, peer-reviewed publications from seven databases between January 2010 and December 2020. Titles and abstracts were first screened for inclusion, then full studies were coded using explicit criteria. We used a standard checklist was modified to assess article quality. Ten of 11,793 studies examined CIH communication using observational methods for CIH communication in biomedical settings. Studies used a range of observational techniques, including participant and non-participant observation, which includes digital audio or video recordings. Results generated two broad sets of findings, one focused on methodological insights and another on CIH communication. Despite methodological and topic similarities, included studies addressed CIH communication as a process and as proximal and intermediate health outcomes. We recommend how observational studies of CIH communication can better highlight relationships between communication processes and health outcomes. Current research using observational methods offers an incomplete picture of CIH communication in biomedical settings. Future studies should standardize how observational techniques are reported to enhance consistency and comparability within and across biomedical settings to improve comparability.}, } @article {pmid36601075, year = {2022}, author = {Leal, JSV and Fogal, AS and Meireles, AL and Cardoso, LO and Machado, ÍE and de Menezes, MC}, title = {Health economic impacts associated with the consumption of sugar-sweetened beverages in Brazil.}, journal = {Frontiers in nutrition}, volume = {9}, number = {}, pages = {1088051}, pmid = {36601075}, issn = {2296-861X}, abstract = {INTRODUCTION: The consumption of sugar-sweetened beverages (SSBs) is among the main risk factors for non-communicable diseases (NCDs). This study aimed to estimate the financial costs of hospitalizations and procedures of high and medium complexity for NCDs attributable to the consumption of SSBs in the Brazilian Unified Health System (SUS) in 2019.

METHODS: This ecological study used data from the Global Burden of Disease (GBD) 2019 and the Department of Informatics of the Unified Health System (DATASUS). The attributable costs were estimated from the population-attributable fraction (PAF) and the costs in the treatment of chronic diseases [type 2 diabetes mellitus and ischemic heart disease (IHD)], stratified by sex, age group, level of complexity of treatment, and federative units.

RESULTS: In 2019, in Brazil, US$ 14,116,240.55 were the costs of hospitalizations and procedures of high and medium complexity in the treatment of NCDs attributable to the consumption of SSBs. These values were higher in males (US$ 8,469,265.14) and the southeast and southern regions, mainly in the state of São Paulo. However, when evaluating these results at a rate per 10,000 inhabitants, it was observed that the states of Paraná, Tocantins, and Roraima had higher costs per 10,000 inhabitants. Regarding the age groups, higher costs were observed in the older age groups.

CONCLUSION: This study revealed the high financial impact of the NCDs treatment attributed to the consumption of SSBs in Brazil and the variability among Brazilian macro-regions. The results demonstrate the urgency and need for the expansion of policies to reduce the consumption of SSBs in Brazil with strategies that consider regional particularities.}, } @article {pmid36599936, year = {2023}, author = {Juan, D and Santpere, G and Kelley, JL and Cornejo, OE and Marques-Bonet, T}, title = {Current advances in primate genomics: novel approaches for understanding evolution and disease.}, journal = {Nature reviews. Genetics}, volume = {24}, number = {5}, pages = {314-331}, pmid = {36599936}, issn = {1471-0064}, support = {R01 HG010898/HG/NHGRI NIH HHS/United States ; }, mesh = {Animals ; Humans ; *Evolution, Molecular ; *Genomics/methods ; Primates/genetics ; Genome ; Phylogeny ; Genetic Variation ; }, abstract = {Primate genomics holds the key to understanding fundamental aspects of human evolution and disease. However, genetic diversity and functional genomics data sets are currently available for only a few of the more than 500 extant primate species. Concerted efforts are under way to characterize primate genomes, genetic polymorphism and divergence, and functional landscapes across the primate phylogeny. The resulting data sets will enable the connection of genotypes to phenotypes and provide new insight into aspects of the genetics of primate traits, including human diseases. In this Review, we describe the existing genome assemblies as well as genetic variation and functional genomic data sets. We highlight some of the challenges with sample acquisition. Finally, we explore how technological advances in single-cell functional genomics and induced pluripotent stem cell-derived organoids will facilitate our understanding of the molecular foundations of primate biology.}, } @article {pmid36590525, year = {2022}, author = {Prylutskyy, Y and Nozdrenko, D and Gonchar, O and Prylutska, S and Bogutska, K and Franskevych, D and Hromovyk, B and Scharff, P and Ritter, U}, title = {C60 fullerene attenuates muscle force reduction in a rat during fatigue development.}, journal = {Heliyon}, volume = {8}, number = {12}, pages = {e12449}, pmid = {36590525}, issn = {2405-8440}, abstract = {C60 fullerene (C60) as a nanocarbon particle, compatible with biological structures, capable of penetrating through cell membranes and effectively scavenging free radicals, is widely used in biomedicine. A protective effect of C60 on the biomechanics of fast (m. gastrocnemius) and slow (m. soleus) muscle contraction in rats and the pro- and antioxidant balance of muscle tissue during the development of muscle fatigue was studied compared to the same effect of the known antioxidant N-acetylcysteine (NAC). C60 and NAC were administered intraperitoneally at doses of 1 and 150 mg kg[-1], respectively, daily for 5 days and 1 h before the start of the experiment. The following quantitative markers of muscle fatigue were used: the force of muscle contraction, the level of accumulation of secondary products of lipid peroxidation (TBARS) and the oxygen metabolite H2O2, the activity of first-line antioxidant defense enzymes (superoxide dismutase (SOD) and catalase (CAT)), and the condition of the glutathione system (reduced glutathione (GSH) content and the activity of the glutathione peroxidase (GPx) enzyme). The analysis of the muscle contraction force dynamics in rats against the background of induced muscle fatigue showed, that the effect of C60, 1 h after drug administration, was (15-17)% more effective on fast muscles than on slow muscles. A further slight increase in the effect of C60 was revealed after 2 h of drug injection, (7-9)% in the case of m. gastrocnemius and (5-6)% in the case of m. soleus. An increase in the effect of using C60 occurred within 4 days (the difference between 4 and 5 days did not exceed (3-5)%) and exceeded the effect of NAC by (32-34)%. The analysis of biochemical parameters in rat muscle tissues showed that long-term application of C60 contributed to their decrease by (10-30)% and (5-20)% in fast and slow muscles, respectively, on the 5th day of the experiment. At the same time, the protective effect of C60 was higher compared to NAC by (28-44)%. The obtained results indicate the prospect of using C60 as a potential protective nano agent to improve the efficiency of skeletal muscle function by modifying the reactive oxygen species-dependent mechanisms that play an important role in the processes of muscle fatigue development.}, } @article {pmid36581858, year = {2022}, author = {Huang, Y and Lu, W and Zeng, M and Hu, X and Su, Z and Liu, Y and Liu, Z and Yuan, J and Li, L and Zhang, X and Huang, L and Hu, W and Wang, X and Li, S and Zhang, H}, title = {Mapping the early life gut microbiome in neonates with critical congenital heart disease: multiomics insights and implications for host metabolic and immunological health.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {245}, pmid = {36581858}, issn = {2049-2618}, mesh = {Infant, Newborn ; Humans ; *Gastrointestinal Microbiome/genetics ; Multiomics ; Inflammation ; Bacteria ; *Heart Defects, Congenital ; Dysbiosis/microbiology ; }, abstract = {BACKGROUND: The early life gut microbiome is crucial in maintaining host metabolic and immune homeostasis. Though neonates with critical congenital heart disease (CCHD) are at substantial risks of malnutrition and immune imbalance, the microbial links to CCHD pathophysiology remain poorly understood. In this study, we aimed to investigate the gut microbiome in neonates with CCHD in association with metabolomic traits. Moreover, we explored the clinical implications of the host-microbe interactions in CCHD.

METHODS: Deep metagenomic sequencing and metabolomic profiling of paired fecal samples from 45 neonates with CCHD and 50 healthy controls were performed. The characteristics of gut microbiome were investigated in three dimensions (microbial abundance, functionality, and genetic variation). An in-depth analysis of gut virome was conducted to elucidate the ecological interaction between gut viral and bacterial communities. Correlations between multilevel microbial features and fecal metabolites were determined using integrated association analysis. Finally, we conducted a subgroup analysis to examine whether the interactions between gut microbiota and metabolites could mediate inflammatory responses and poor surgical prognosis.

RESULTS: Gut microbiota dysbiosis was observed in neonates with CCHD, characterized by the depletion of Bifidobacterium and overgrowth of Enterococcus, which was highly correlated with metabolomic perturbations. Genetic variations of Bifidobacterium and Enterococcus orchestrate the metabolomic perturbations in CCHD. A temperate core virome represented by Siphoviridae was identified to be implicated in shaping the gut bacterial composition by modifying microbial adaptation. The overgrowth of Enterococcus was correlated with systemic inflammation and poor surgical prognosis in subgroup analysis. Mediation analysis indicated that the overgrowth of Enterococcus could mediate gut barrier impairment and inflammatory responses in CCHD.

CONCLUSIONS: We demonstrate for the first time that an aberrant gut microbiome associated with metabolomic perturbations is implicated in immune imbalance and adverse clinical outcomes in neonates with CCHD. Our data support the importance of reconstituting optimal gut microbiome in maintaining host metabolic and immunological homeostasis in CCHD. Video Abstract.}, } @article {pmid36576353, year = {2023}, author = {Liu, C and Economo, EP and Guénard, B}, title = {GABI-I: The global ant biodiversity informatics-island database.}, journal = {Ecology}, volume = {104}, number = {4}, pages = {e3969}, doi = {10.1002/ecy.3969}, pmid = {36576353}, issn = {1939-9170}, mesh = {Animals ; *Biodiversity ; Ecology ; *Ants ; }, abstract = {Island systems are known to harbor disproportionate amounts of geographically restricted biodiversity and to experience high rates of species loss, and they ultimately represent critical systems with significant conservation values. However, knowledge of the biodiversity value of insular systems remains highly fragmented and incomplete for many groups of organisms, especially insects. This gap limits our understanding of their global significance for biodiversity and inhibits prioritization for future exploration and conservation efforts. Here, we developed a new database to present current knowledge on ants on 2678 islands globally, based on nominal species, and provide information on their native or exotic status. In total, this database contains 7010 ant species (44.6% of the known global ant fauna) that have been recorded on islands globally from 449,232 records. In addition, this database identifies 108 large islands (area > 200 km[2]) that have received no ant sampling efforts globally. This new data set provides the most comprehensive understanding of ant diversity and composition on islands globally, opening up new opportunities to address questions on a multitude of research questions and fields related to biogeography, ecology, and evolution. This data set also provides a roadmap for future exploration and conservation actions in connection with ants on islands as well as overall ant diversity, with updates available as new records and taxonomic updates are published. There are no copyright restrictions on this database and users should cite this data paper in publications when using the data.}, } @article {pmid36575453, year = {2022}, author = {Barone, M and Garelli, S and Rampelli, S and Agostini, A and Matysik, S and D'Amico, F and Krautbauer, S and Mazza, R and Salituro, N and Fanelli, F and Iozzo, P and Sanz, Y and Candela, M and Brigidi, P and Pagotto, U and Turroni, S}, title = {Multi-omics gut microbiome signatures in obese women: role of diet and uncontrolled eating behavior.}, journal = {BMC medicine}, volume = {20}, number = {1}, pages = {500}, pmid = {36575453}, issn = {1741-7015}, support = {613979//Seventh Framework Programme/ ; 245009//Seventh Framework Programme/ ; }, mesh = {Humans ; Female ; *Gastrointestinal Microbiome/genetics ; RNA, Ribosomal, 16S/genetics ; Multiomics ; Obesity/genetics ; Diet ; Feeding Behavior/physiology ; Feces/microbiology ; }, abstract = {BACKGROUND: Obesity and related co-morbidities represent a major health challenge nowadays, with a rapidly increasing incidence worldwide. The gut microbiome has recently emerged as a key modifier of human health that can affect the development and progression of obesity, largely due to its involvement in the regulation of food intake and metabolism. However, there are still few studies that have in-depth explored the functionality of the human gut microbiome in obesity and even fewer that have examined its relationship to eating behaviors.

METHODS: In an attempt to advance our knowledge of the gut-microbiome-brain axis in the obese phenotype, we thoroughly characterized the gut microbiome signatures of obesity in a well-phenotyped Italian female cohort from the NeuroFAST and MyNewGut EU FP7 projects. Fecal samples were collected from 63 overweight/obese and 37 normal-weight women and analyzed via a multi-omics approach combining 16S rRNA amplicon sequencing, metagenomics, metatranscriptomics, and lipidomics. Associations with anthropometric, clinical, biochemical, and nutritional data were then sought, with particular attention to cognitive and behavioral domains of eating.

RESULTS: We identified four compositional clusters of the gut microbiome in our cohort that, although not distinctly associated with weight status, correlated differently with eating habits and behaviors. These clusters also differed in functional features, i.e., transcriptional activity and fecal metabolites. In particular, obese women with uncontrolled eating behavior were mostly characterized by low-diversity microbial steady states, with few and poorly interconnected species (e.g., Ruminococcus torques and Bifidobacterium spp.), which exhibited low transcriptional activity, especially of genes involved in secondary bile acid biosynthesis and neuroendocrine signaling (i.e., production of neurotransmitters, indoles and ligands for cannabinoid receptors). Consistently, high amounts of primary bile acids as well as sterols were found in their feces.

CONCLUSIONS: By finding peculiar gut microbiome profiles associated with eating patterns, we laid the foundation for elucidating gut-brain axis communication in the obese phenotype. Subject to confirmation of the hypotheses herein generated, our work could help guide the design of microbiome-based precision interventions, aimed at rewiring microbial networks to support a healthy diet-microbiome-gut-brain axis, thus counteracting obesity and related complications.}, } @article {pmid36572855, year = {2022}, author = {Schwarz, J and Hemmerling, J and Kabisch, N and Galbusera, L and Heinze, M and von Peter, S and Wolff, J}, title = {Equal access to outreach mental health care? Exploring how the place of residence influences the use of intensive home treatment in a rural catchment area in Germany.}, journal = {BMC psychiatry}, volume = {22}, number = {1}, pages = {826}, pmid = {36572855}, issn = {1471-244X}, mesh = {Humans ; *Mental Health ; Ambulatory Care ; *Community Mental Health Services ; Catchment Area, Health ; Germany ; Health Services Accessibility ; }, abstract = {BACKGROUND: Internationally, intensive psychiatric home treatment has been increasingly implemented as a community-based alternative to inpatient admission. Since 2018, the so-called Inpatient Equivalent Home Treatment (IEHT; German: "Stationsäquivalente Behandlung", short: "StäB") has been introduced as a particularly intensive form of home treatment that provides at least one daily treatment contact in the service users' (SU) home environment. Prior research shows that this can be challenging in rural catchment areas. Our paper investigates to which extent the location of the SU home location within the catchment area as well as the distance between the home and the clinic influence the utilisation of inpatient treatment compared to IEHT.

METHOD: Routine data of one psychiatric hospital in the federal state of Brandenburg in Germany were analysed for the observational period 07/2018-06/2021. Two comparison groups were formed: SU receiving inpatient treatment and SU receiving IEHT. The SU places of residence were respectively anonymised and converted into geo-coordinates. A geographic information system (GIS) was used to visualise the places of residence, and car travel distances as well as travel times to the clinic were determined. Spatial analyses were performed to show the differences between comparison groups. In a more in-depth analysis, the proximity of SU residences to each other was examined as an indicator of possible clustering.

RESULTS: During the observational period, the location of 687 inpatient and 140 IEHT unique SU were mapped using the GIS. SU receiving treatment resided predominantly within the catchment area, and this proportion was slightly higher for SU receiving IEHT than for those treated in inpatient setting (95.3% vs. 84.7%). In the catchment area, the geographical distribution of SU place of residence was similar in the two groups. There was a general higher service provision in the more densely populated communities close to Berlin. SU with residence in peripheral communities were mainly treated within the inpatient setting. The mean travel times and distances to the place of residence only differed minimally between the two groups of SU (p > 0.05). The places of residence of SU treated with IEHT were located in greater proximity to each other than those of SU treated in inpatient setting (p < 0.1).

CONCLUSION: In especially peripheral parts of the examined catchment area, it may be more difficult to have access to IEHT rather than to inpatient services. The results raise questions regarding health equity and the planning of health care services and have important implications for the further development of intensive home treatment. Telehealth interventions such as blended-care approaches and an increase of flexibility in treatment intensity, e.g. eliminating the daily visit requirement, could ease the implementation of intensive home treatment especially in rural areas.}, } @article {pmid36572749, year = {2022}, author = {Kon, T and Fukuta, K and Chen, Z and Kon-Nanjo, K and Suzuki, K and Ishikawa, M and Tanaka, H and Burgess, SM and Noguchi, H and Toyoda, A and Omori, Y}, title = {Single-cell transcriptomics of the goldfish retina reveals genetic divergence in the asymmetrically evolved subgenomes after allotetraploidization.}, journal = {Communications biology}, volume = {5}, number = {1}, pages = {1404}, pmid = {36572749}, issn = {2399-3642}, mesh = {Animals ; *Goldfish/genetics ; *Transcriptome ; Genome ; Evolution, Molecular ; Gene Expression Profiling ; }, abstract = {The recent whole-genome duplication (WGD) in goldfish (Carassius auratus) approximately 14 million years ago makes it a valuable model for studying gene evolution during the early stages after WGD. We analyzed the transcriptome of the goldfish retina at the level of single-cell (scRNA-seq) and open chromatin regions (scATAC-seq). We identified a group of genes that have undergone dosage selection, accounting for 5% of the total 11,444 ohnolog pairs. We also identified 306 putative sub/neo-functionalized ohnolog pairs that are likely to be under cell-type-specific genetic variation at single-cell resolution. Diversification in the expression patterns of several ohnolog pairs was observed in the retinal cell subpopulations. The single-cell level transcriptome analysis in this study uncovered the early stages of evolution in retinal cell of goldfish after WGD. Our results provide clues for understanding the relationship between the early stages of gene evolution after WGD and the evolution of diverse vertebrate retinal functions.}, } @article {pmid36566315, year = {2022}, author = {Dualib, PM and Fernandes, G and Taddei, CR and Carvalho, CRS and Sparvoli, LG and Bittencourt, C and Silva, IT and Mattar, R and Ferreira, SRG and Dib, SA and de Almeida-Pititto, B}, title = {The gut microbiome of obese postpartum women with and without previous gestational diabetes mellitus and the gut microbiota of their babies.}, journal = {Diabetology & metabolic syndrome}, volume = {14}, number = {1}, pages = {194}, pmid = {36566315}, issn = {1758-5996}, support = {2018/14795-9//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 2018/14795-9//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; }, abstract = {BACKGROUND: The incidence of gestational diabetes mellitus (GDM) is increasing worldwide, and has been associated with some changes in the gut microbiota. Studies have shown that the maternal gut microbiota pattern with hyperglycemia can be transmitted to the offspring. The study aimed to evaluate the gut microbiota of obese postpartum women with and without previous GDM and their offspring.

METHODS: We evaluated a total of 84 puerperal women who had (n = 40) or not GDM (n = 44), and their infants were also included. Stool samples were obtained 2-6 months after delivery. The molecular profile of the fecal microbiota was obtained by sequencing V4 region of 16S rRNA gene (Illumina[®] MiSeq).

RESULTS: We found that the gut microbiota structures of the puerperal women and their infants were similar. Stratifying according to the type of delivery, the relative abundance of Victivallis genus was higher in women who had natural delivery. Exposure to exclusive breastfeeding was associated with a greater abundance of Bacteroides and Staphylococcus. The differential abundance test showed correlations to clinical and laboratory parameters. This work showed no difference in the microbiota of obese puerperal women with and without GDM and their offspring. However, breastfeeding contributed to the ecological succession of the intestinal microbiota of the offspring.

CONCLUSION: This work can contribute to understanding the potential effects of GDM and early life events on the gut microbiome of mothers and their offspring and its possible role in metabolism later in life.}, } @article {pmid36557752, year = {2022}, author = {Schalli, M and Inwinkl, SM and Platzer, S and Baumert, R and Reinthaler, FF and Ofner-Kopeinig, P and Haas, D}, title = {Cefsulodin and Vancomycin: A Supplement for Chromogenic Coliform Agar for Detection of Escherichia coli and Coliform Bacteria from Different Water Sources.}, journal = {Microorganisms}, volume = {10}, number = {12}, pages = {}, pmid = {36557752}, issn = {2076-2607}, abstract = {Background microorganism growth on Chromogenic Coliform Agar (CCA) can be challenging. For this reason, a new alternative method with a Cefsulodin/Vancomycin (CV)-supplemented CCA should be developed in this study. CCA supplemented with CV was validated according to ÖNORM EN ISO 16140-4:2021 using water from natural sources in Styria, Austria. Results show that the alternative method using the supplemented CCA has similar values in relation to sensitivity (82.2%), specificity (98.6%) and higher selectivity (59%) compared to the reference method. Repeatability and reproducibility were acceptable for the alternative method and showed similar results with the reference method. The alternative method shows a very low false positive rate and a low false negative rate paired with good performance regarding the inclusion study. The exclusion study shows the advantage of our method by suppressing background microorganisms and facilitating the process of enumeration of Escherichia coli and other coliform bacteria on CCA plates. Aeromonas hydrophila and Pseudomonas aeruginosa growth was inhibited using the supplement. To conclude, the coliform CV selective supplement combined with CCA is an appropriate tool for coliform bacteria detection in water samples.}, } @article {pmid36554991, year = {2022}, author = {Xue, Y and Lin, C and Wang, Y and Liu, W and Wan, F and Zhang, Y and Ji, L}, title = {Predicting Climate Change Effects on the Potential Distribution of Two Invasive Cryptic Species of the Bemisia tabaci Species Complex in China.}, journal = {Insects}, volume = {13}, number = {12}, pages = {}, pmid = {36554991}, issn = {2075-4450}, support = {WX145-CAS-WX2021PY-0202//14th Five-year Network Security and Informatization Plan of Chinese Academy of Sciences/ ; XDA19050200//Strategic Priority Research Program of the Chinese Academy of Sciences/ ; }, abstract = {Middle East-Asia Minor 1 (MEAM1) and Mediterranean (MED) are two invasive cryptic species of the Bemisia tabaci species complex (Hemiptera: Aleyrodidae) that cause serious damage to agricultural and horticultural crops worldwide. To explore the possible impact of climate change on their distribution, the maximum entropy (MaxEnt) model was used to predict the potential distribution ranges of MEAM1 and MED in China under current and four future climate scenarios, using shared socioeconomic pathways (SSPs), namely SSP1-2.6, SSP2-4.5, SSP3-7.0, and SSP5-8.5, over four time periods (2021-2040, 2041-2060, 2061-2080, and 2081-2100). The distribution ranges of MEAM1 and MED were extensive and similar in China under current climatic conditions, while their moderately and highly suitable habitat ranges differed. Under future climate scenarios, the areas of suitable habitat of different levels for MEAM1 and MED were predicted to increase to different degrees. However, the predicted expansion of suitable habitats varied between them, suggesting that these invasive cryptic species respond differently to climate change. Our results illustrate the difference in the effects of climate change on the geographical distribution of different cryptic species of B. tabaci and provide insightful information for further forecasting and managing the two invasive cryptic species in China.}, } @article {pmid36554882, year = {2022}, author = {Deng, F and Yang, Y and Zhao, E and Xu, N and Li, Z and Zheng, P and Han, Y and Gong, J}, title = {Urban Heat Island Intensity Changes in Guangdong-Hong Kong-Macao Greater Bay Area of China Revealed by Downscaling MODIS LST with Deep Learning.}, journal = {International journal of environmental research and public health}, volume = {19}, number = {24}, pages = {}, pmid = {36554882}, issn = {1660-4601}, mesh = {Humans ; Macau ; Hong Kong ; Cities ; *Hot Temperature ; Temperature ; *Deep Learning ; China ; Environmental Monitoring/methods ; }, abstract = {The urban heat island (UHI) effect caused by urbanization negatively impacts the ecological environment and human health. It is crucial for urban planning and social development to monitor the urban heat island effect and study its mechanism. Due to spatial and temporal resolution limitations, existing land surface temperature (LST) data obtained from remote sensing data is challenging to meet the long-term fine-scale surface temperature mapping requirement. Given the above situation, this paper introduced the ResNet-based surface temperature downscaling method to make up for the data deficiency and applied it to the study of thermal environment change in the Guangdong-Hong Kong-Macao Greater Bay Area (GBA) from 2000 to 2020. The results showed (1) the ResNet-based surface temperature downscaling method achieves high accuracy (R[2] above 0.85) and is suitable for generating 30 m-resolution surface temperature data from 1 km data; (2) the area of severe heat islands in the GBA continued to increase, increasing by 7.13 times within 20 years; and (3) except for Hong Kong and Macau, the heat island intensity of most cities showed an apparent upward trend, especially the cities with rapid urban expansion such as Guangzhou, Zhongshan, and Foshan. In general, the evolution of the heat island in the GBA diverges from the central urban area to the surrounding areas, with a phenomenon of local aggregation and the area of the intense heat island in the Guangzhou-Foshan metropolitan area is the largest. This study can enrich the downscaling research methods of surface temperature products in complex areas with surface heterogeneity and provide a reference for urban spatial planning in the GBA.}, } @article {pmid36554755, year = {2022}, author = {Chen, D and Xiong, K and Zhang, J}, title = {Progress on the Integrity Protection in the Natural World Heritage Site and Agroforestry Development in the Buffer Zone: An Implications for the World Heritage Karst.}, journal = {International journal of environmental research and public health}, volume = {19}, number = {24}, pages = {}, pmid = {36554755}, issn = {1660-4601}, mesh = {*Conservation of Natural Resources ; China ; Databases, Factual ; *Knowledge ; }, abstract = {In the face of increasing development pressure, how to fulfill the obligations under the World Cultural and Natural Heritage Convention and maintain the integrity of the Natural World Heritage Site (NWHS) is a major problem to be solved at present. Agroforestry (AF) development in the buffer zone maintains the integrity of NWHS and promotes sustainable ecological and economic development in the buffer zone. Still, few studies on the knowledge system of integrity protection of NWHS and AF development in the buffer zone research have been conducted. To fill this gap, this study conducts a systematic literature review based on 128 related articles retrieved from the Web of Science (WoS) database and the China National Knowledge Infrastructure (CNKI) database. Firstly, quantitative studies were conducted to analyze the annual numbers, content and study regions of the published literature. Secondly, the main research progress and achievements of integrity protection of WNHS and AF development in the buffer zone are classified and summarized. On this basis, this paper proposed key scientific issues that remain to be addressed in future, as well as exploring the implications for the World Heritage (WH) karst. This study is a scientific reference for the balanced development of NWHS integrity protection and AF in the buffer zone.}, } @article {pmid36554342, year = {2022}, author = {Dantas, JDC and Marinho, CDSR and Pinheiro, YT and Silva, RARD}, title = {Temporal Trend of Gestational Syphilis between 2008 and 2018 in Brazil: Association with Socioeconomic and Health Care Factors.}, journal = {International journal of environmental research and public health}, volume = {19}, number = {24}, pages = {}, pmid = {36554342}, issn = {1660-4601}, mesh = {Pregnancy ; Female ; Humans ; *Syphilis/epidemiology ; *Pregnancy Complications, Infectious/epidemiology ; *Syphilis, Congenital/epidemiology/prevention & control ; Brazil/epidemiology ; Literacy ; Delivery of Health Care ; Socioeconomic Factors ; }, abstract = {The increased number of cases in recent years has turned syphilis into a global public health problem. In 2020, 115,371 cases of acquired syphilis were reported (detection rate of 54.5 cases/100,000 inhabitants) in Brazil. In that same period, the country notified 61,441 cases of gestational syphilis (detection rate of 21.6 per 1000 live births). The number of syphilis cases points to the need to reinforce surveillance, prevention, and infection control actions, which is a worrying scenario for government organizations. This study aims to describe the temporal trend of gestational syphilis from 2008 to 2018 in Brazilian regions and to associate its detection rate with socioeconomic and health care indicators. We conducted an ecological study of temporal trends using secondary data from the Department of Informatics of the Unified Health System. The temporal trend was analyzed using the Joinpoint Regression program. The annual percent change (APC) and 95% confidence intervals (95%CI) were estimated and tested; statistical significance was assessed using the Monte Carlo permutation test. Correlations were assessed using Pearson's correlation coefficient, and statistical significance was calculated using Pearson's product-moment correlation. The gestational syphilis detection rate increased between 2008 and 2018. The South region showed the greatest trend, whereas the Midwest region presented the lowest trend. The following variables were significantly correlated with the gestational syphilis detection rate: Municipal Human Development Index, illiteracy rate, percentage of primary health care coverage, and proportion of doctors, nurses, and basic health units per inhabitant. Health policies are needed to mitigate social vulnerabilities and strengthen primary health care.}, } @article {pmid36552295, year = {2022}, author = {Sokhansanj, BA and Zhao, Z and Rosen, GL}, title = {Interpretable and Predictive Deep Neural Network Modeling of the SARS-CoV-2 Spike Protein Sequence to Predict COVID-19 Disease Severity.}, journal = {Biology}, volume = {11}, number = {12}, pages = {}, pmid = {36552295}, issn = {2079-7737}, support = {1919691//National Science Foundation/ ; 1936782//National Science Foundation/ ; 2107108//National Science Foundation/ ; }, abstract = {Through the COVID-19 pandemic, SARS-CoV-2 has gained and lost multiple mutations in novel or unexpected combinations. Predicting how complex mutations affect COVID-19 disease severity is critical in planning public health responses as the virus continues to evolve. This paper presents a novel computational framework to complement conventional lineage classification and applies it to predict the severe disease potential of viral genetic variation. The transformer-based neural network model architecture has additional layers that provide sample embeddings and sequence-wide attention for interpretation and visualization. First, training a model to predict SARS-CoV-2 taxonomy validates the architecture's interpretability. Second, an interpretable predictive model of disease severity is trained on spike protein sequence and patient metadata from GISAID. Confounding effects of changing patient demographics, increasing vaccination rates, and improving treatment over time are addressed by including demographics and case date as independent input to the neural network model. The resulting model can be interpreted to identify potentially significant virus mutations and proves to be a robust predctive tool. Although trained on sequence data obtained entirely before the availability of empirical data for Omicron, the model can predict the Omicron's reduced risk of severe disease, in accord with epidemiological and experimental data.}, } @article {pmid36547621, year = {2022}, author = {Jamal, QMS and Ahmad, V}, title = {Lysinibacilli: A Biological Factories Intended for Bio-Insecticidal, Bio-Control, and Bioremediation Activities.}, journal = {Journal of fungi (Basel, Switzerland)}, volume = {8}, number = {12}, pages = {}, pmid = {36547621}, issn = {2309-608X}, support = {QU-IF-03-01-27931//The Deputyship for Research & Innovation, Ministry of Education, Saudi Arabia/ ; }, abstract = {Microbes are ubiquitous in the biosphere, and their therapeutic and ecological potential is not much more explored and still needs to be explored more. The bacilli are a heterogeneous group of Gram-negative and Gram-positive bacteria. Lysinibacillus are dominantly found as motile, spore-forming, Gram-positive bacilli belonging to phylum Firmicutes and the family Bacillaceae. Lysinibacillus species initially came into light due to their insecticidal and larvicidal properties. Bacillus thuringiensis, a well-known insecticidal Lysinibacillus, can control many insect vectors, including a malarial vector and another, a Plasmodium vector that transmits infectious microbes in humans. Now its potential in the environment as a piece of green machinery for remediation of heavy metal is used. Moreover, some species of Lysinibacillus have antimicrobial potential due to the bacteriocin, peptide antibiotics, and other therapeutic molecules. Thus, this review will explore the biological disease control abilities, food preservative, therapeutic, plant growth-promoting, bioremediation, and entomopathogenic potentials of the genus Lysinibacillus.}, } @article {pmid36545372, year = {2022}, author = {Ruttoh, RC and Obiero, JPO and Omuto, CT and Tanui, L}, title = {Assessment of Land Cover and Land Use Change Dynamics in Kibwezi Watershed, Kenya.}, journal = {TheScientificWorldJournal}, volume = {2022}, number = {}, pages = {3944810}, pmid = {36545372}, issn = {1537-744X}, mesh = {Kenya ; *Geographic Information Systems ; *Forests ; Soil ; Trees ; Environmental Monitoring/methods ; Conservation of Natural Resources ; }, abstract = {Land use and land cover (LULC) parameters influence the hydrological and ecological processes taking place in a watershed. Understanding the changes in LULC is essential in the planning and development of management strategies for water resources. The purpose of the study was to detect changes in LULC in the Kibwezi watershed in Kenya, using geospatial approaches. Supervised and unsupervised classification techniques using remote sensing (RS) and geographical information system (GIS) were used to process Landsat imagery for 1999, 2009, and 2019 while ERDAS IMAGINE™ 14 and MS Excel software were used to derive change detection, and the Soil and Water Assessment Tool (SWAT) model was used to delineate the watershed using an in-built watershed delineation tool. The watershed was classified into ten major LULC classes, namely cropland (rainfed), cropland (irrigated), cropland (perennial), crop and shrubs/trees, closed shrublands, open shrubland, shrub grasslands, wooded shrublands, riverine woodlands, and built-up land. The results showed that LULC under shrub grassland, urban areas, and crops and shrubs increased drastically by 552.5%, 366.2%, and 357.1% respectively between 1999 and 2019 with an annual increase of 35.55%, 35.38%, and 33.86% per annum. The area under open shrubland and closed shrubland declined by73.7%, and 30.4% annually. These LULC transformations pose a negative impact on the watershed resources. There is therefore a need for proper management of the watershed for sustainable socio-economic development of the Kibwezi area.}, } @article {pmid36543718, year = {2023}, author = {Liew, F and Talwar, S and Cross, A and Willett, BJ and Scott, S and Logan, N and Siggins, MK and Swieboda, D and Sidhu, JK and Efstathiou, C and Moore, SC and Davis, C and Mohamed, N and Nunag, J and King, C and Thompson, AAR and Rowland-Jones, SL and Docherty, AB and Chalmers, JD and Ho, LP and Horsley, A and Raman, B and Poinasamy, K and Marks, M and Kon, OM and Howard, L and Wootton, DG and Dunachie, S and Quint, JK and Evans, RA and Wain, LV and Fontanella, S and de Silva, TI and Ho, A and Harrison, E and Baillie, JK and Semple, MG and Brightling, C and Thwaites, RS and Turtle, L and Openshaw, PJM and , and , }, title = {SARS-CoV-2-specific nasal IgA wanes 9 months after hospitalisation with COVID-19 and is not induced by subsequent vaccination.}, journal = {EBioMedicine}, volume = {87}, number = {}, pages = {104402}, pmid = {36543718}, issn = {2352-3964}, support = {MR/V028448/1/MRC_/Medical Research Council/United Kingdom ; MR/V027859/1/MRC_/Medical Research Council/United Kingdom ; 206330/Z/17/Z/WT_/Wellcome Trust/United Kingdom ; MC_UU_12014/12/MRC_/Medical Research Council/United Kingdom ; MC_PC_19059/MRC_/Medical Research Council/United Kingdom ; MR/S020039/1/MRC_/Medical Research Council/United Kingdom ; COV/GLA/20/05/CSO_/Chief Scientist Office/United Kingdom ; MR/W006111/1/MRC_/Medical Research Council/United Kingdom ; G0801952/MRC_/Medical Research Council/United Kingdom ; MC_PC_19025/MRC_/Medical Research Council/United Kingdom ; G1000191/MRC_/Medical Research Council/United Kingdom ; MR/W020610/1/MRC_/Medical Research Council/United Kingdom ; G0700859/MRC_/Medical Research Council/United Kingdom ; MC_PC_20031/MRC_/Medical Research Council/United Kingdom ; MR/X009297/1/MRC_/Medical Research Council/United Kingdom ; MC_PC_20060/MRC_/Medical Research Council/United Kingdom ; G0501425/MRC_/Medical Research Council/United Kingdom ; MC_PC_20002/MRC_/Medical Research Council/United Kingdom ; MC_UU_00036/2/MRC_/Medical Research Council/United Kingdom ; CH/16/1/32013/BHF_/British Heart Foundation/United Kingdom ; MC_PC_19026/MRC_/Medical Research Council/United Kingdom ; MC_UU_00008/5/MRC_/Medical Research Council/United Kingdom ; MR/S032304/1/MRC_/Medical Research Council/United Kingdom ; CH/F/21/90010/BHF_/British Heart Foundation/United Kingdom ; MC_PC_20016/MRC_/Medical Research Council/United Kingdom ; MC_PC_20058/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Adult ; Humans ; *SARS-CoV-2 ; *COVID-19/prevention & control ; COVID-19 Vaccines ; Follow-Up Studies ; Vaccination ; Hospitalization ; Immunoglobulin A ; Immunoglobulin G ; Antibodies, Viral ; Antibodies, Neutralizing ; }, abstract = {BACKGROUND: Most studies of immunity to SARS-CoV-2 focus on circulating antibody, giving limited insights into mucosal defences that prevent viral replication and onward transmission. We studied nasal and plasma antibody responses one year after hospitalisation for COVID-19, including a period when SARS-CoV-2 vaccination was introduced.

METHODS: In this follow up study, plasma and nasosorption samples were prospectively collected from 446 adults hospitalised for COVID-19 between February 2020 and March 2021 via the ISARIC4C and PHOSP-COVID consortia. IgA and IgG responses to NP and S of ancestral SARS-CoV-2, Delta and Omicron (BA.1) variants were measured by electrochemiluminescence and compared with plasma neutralisation data.

FINDINGS: Strong and consistent nasal anti-NP and anti-S IgA responses were demonstrated, which remained elevated for nine months (p < 0.0001). Nasal and plasma anti-S IgG remained elevated for at least 12 months (p < 0.0001) with plasma neutralising titres that were raised against all variants compared to controls (p < 0.0001). Of 323 with complete data, 307 were vaccinated between 6 and 12 months; coinciding with rises in nasal and plasma IgA and IgG anti-S titres for all SARS-CoV-2 variants, although the change in nasal IgA was minimal (1.46-fold change after 10 months, p = 0.011) and the median remained below the positive threshold determined by pre-pandemic controls. Samples 12 months after admission showed no association between nasal IgA and plasma IgG anti-S responses (R = 0.05, p = 0.18), indicating that nasal IgA responses are distinct from those in plasma and minimally boosted by vaccination.

INTERPRETATION: The decline in nasal IgA responses 9 months after infection and minimal impact of subsequent vaccination may explain the lack of long-lasting nasal defence against reinfection and the limited effects of vaccination on transmission. These findings highlight the need to develop vaccines that enhance nasal immunity.

FUNDING: This study has been supported by ISARIC4C and PHOSP-COVID consortia. ISARIC4C is supported by grants from the National Institute for Health and Care Research and the Medical Research Council. Liverpool Experimental Cancer Medicine Centre provided infrastructure support for this research. The PHOSP-COVD study is jointly funded by UK Research and Innovation and National Institute of Health and Care Research. The funders were not involved in the study design, interpretation of data or the writing of this manuscript.}, } @article {pmid36538553, year = {2022}, author = {Vukašinović, D and Maksimović, M and Tanasković, S and Marinković, J and Gajin, P and Ilijevski, N and Vasiljević, N and Radak, Đ and Vlajinac, H}, title = {Body mass index and early outcomes after carotid endarterectomy.}, journal = {PloS one}, volume = {17}, number = {12}, pages = {e0278298}, pmid = {36538553}, issn = {1932-6203}, mesh = {Male ; Humans ; *Endarterectomy, Carotid/adverse effects ; Body Mass Index ; Cohort Studies ; Overweight/complications ; Treatment Outcome ; Risk Factors ; Retrospective Studies ; *Stroke/complications ; Hemorrhage/etiology ; Obesity/complications ; *Diabetes Mellitus, Type 2/complications ; *Carotid Stenosis/surgery ; Risk Assessment ; }, abstract = {As the existing data on the correlation of adiposity with adverse outcomes of carotid endarterectomy (CEA) are inconsistent, the aim of the present study is to examine the correlation of an increased body mass index with 30-day complications after carotid endarterectomy. The cohort study comprises 1586 CEAs, performed at the Clinic for Vascular Surgery in Belgrade, from 2012-2017. Out of them, 550 CEAs were performed in patients with normal body mass index (18.5-24.9), 750 in overweight (25.0-29.9), and 286 in obese (≥30) patients. The association of overweight and obesity with early outcomes of carotid endarterectomy was assessed using univariate and multivariate logistic regression analysis. Overweight patients, in whom CEAs were performed, were significantly more frequently males, compared to normal weight patients-Odds Ratio (OR) 1.51 (95% confidence interval- 1.19-1.89). Moreover, overweight patients significantly more frequently had non-insulin-dependent diabetes mellitus-OR 1.44 (1.09-1.90), and more frequently used ACEI in hospital discharge therapy-OR 1.41 (1.07-1.84) than normal weight patients. Additionally, the CEAs in them were less frequently followed by bleedings-OR 0.37 (0.16-0.83). Compared to normal weight patients, obese patients were significantly younger-OR 0.98 (0.96-0.99), and with insulin-dependent and non-insulin-dependent diabetes mellitus-OR 1.83 (1.09-3.06) and OR 2.13 (1.50-3.01) respectively. They also more frequently had increased triglyceride levels-OR 1.36 (1.01-1.83), and more frequently used oral anticoagulants in therapy before the surgery-OR 2.16 (1.11-4.19). According to the results obtained, overweight and obesity were not associated with an increased death rate, transient ischemic attack (TIA), stroke, myocardial infarction, or with minor complications, and the need for reoperation after carotid endarterectomy. The only exception was bleeding, which was significantly less frequent after CEA in overweight compared to normal weight patients.}, } @article {pmid36529723, year = {2022}, author = {Liu, X and Lu, X and Yang, S and Liu, Y and Wang, W and Wei, X and Ji, H and Zhang, B and Xin, W and Wen, J and Wang, J and Chen, Q}, title = {Role of exogenous abscisic acid in freezing tolerance of mangrove Kandelia obovata under natural frost condition at near 32[°]N.}, journal = {BMC plant biology}, volume = {22}, number = {1}, pages = {593}, pmid = {36529723}, issn = {1471-2229}, mesh = {*Rhizophoraceae ; Abscisic Acid/metabolism ; Antioxidants/metabolism ; Freezing ; Proline/metabolism ; Starch/metabolism ; Sucrose/metabolism ; }, abstract = {BACKGROUND: Mangroves possess substantial ecological, social, and economic functions in tropical and subtropical coastal wetlands. Kandelia obovata is the most cold-resistance species among mangrove plants, with a widespread distribution in China that ranges from Sanya (18° 12' N) to Wenzhou (28° 20' N). Here, we explored the temporal variations in physiological status and transcriptome profiling of K. obovata under natural frost conditions at ~ 32[o]N, as well as the positive role of exogenous abscisic acid (ABA) in cold resistance.

RESULTS: The soluble sugar (SS) and proline (Pro) functioned under freezing stress, of which SS was more important for K. obovata. Consistently, up-regulated DEGs responding to low temperature were significantly annotated to glycometabolism, such as starch and sucrose metabolism and amino sugar and nucleotide sugar metabolism. Notably, the top 2 pathways of KEGG enrichment were phenylpropanoid biosynthesis and flavonoid biosynthesis. For the antioxidant system, POD in conjunction with CAT removed hydrogen peroxide, and CAT appeared to be more important. The up-regulated DEGs responding to low temperature and ABA were also found to be enriched in arginine and proline metabolism, starch and sucrose metabolism, and peroxisome. Moreover, ABA triggered the expression of P5CS and P5CR, but inhibited the ProDH expression, which might contribute to Pro accumulation. Interestingly, there was no significant change in malondialdehyde (MDA) content during the cold event (P > 0.05), suggesting foliar application of ABA effectively alleviated the adverse effects of freezing stress on K. obovata by activating the antioxidant enzyme activity and increasing osmolytes accumulation, such as Pro, and the outcome was proportional to ABA concentration.

CONCLUSIONS: This study deepened our understanding of the physiological characters and molecular mechanisms underlying the response of K. obovata to natural frost conditions and exogenous ABA at the field level, which could provide a sound theoretical foundation for expanding mangroves plantations in higher latitudes, as well as the development coastal landscape.}, } @article {pmid36528093, year = {2023}, author = {Milan, M and Bernardini, I and Bertolini, C and Dalla Rovere, G and Manuzzi, A and Pastres, R and Peruzza, L and Smits, M and Fabrello, J and Breggion, C and Sambo, A and Boffo, L and Gallocchio, L and Carrer, C and Sorrentino, F and Bettiol, C and Lodi, GC and Semenzin, E and Varagnolo, M and Matozzo, V and Bargelloni, L and Patarnello, T}, title = {Multidisciplinary long-term survey of Manila clam grown in farming sites subjected to different environmental conditions.}, journal = {The Science of the total environment}, volume = {863}, number = {}, pages = {160796}, doi = {10.1016/j.scitotenv.2022.160796}, pmid = {36528093}, issn = {1879-1026}, mesh = {Animals ; *Bivalvia/metabolism ; Seafood ; Agriculture ; Genomics ; }, abstract = {In recent years recurrent bivalve mass mortalities considerably increased around the world, causing the collapse of natural and farmed populations. Venice Lagoon has historically represented one of the major production areas of the Manila clam Ruditapes philippinarum in Europe. However, in the last 20 years a 75 % decrease in the annual production has been experienced. While climate change and anthropogenic interventions may have played a key role in natural and farmed stocks reductions, no studies investigated at multiple levels the environmental stressors affecting farmed Manila clam to date. In this work we carried out a long-term monitoring campaign on Manila clam reared in four farming sites located at different distances from the southern Venice Lagoon inlet, integrating (meta)genomic approaches (i.e. RNA-seq; microbiota characterization), biometric measurements and chemical-physical parameters. Our study allowed to characterize the molecular mechanisms adopted by this species to cope with the different environmental conditions characterizing farming sites and to propose hypotheses to explain mortality events observed in recent years. Among the most important findings, the disruption of clam's immune response, the spread of Vibrio spp., and the up-regulation of molecular pathways involved in xenobiotic metabolism suggested major environmental stressors affecting clams farmed in sites placed close to Chioggia's inlet, where highest mortality was also observed. Overall, our study provides knowledge-based tools for managing Manila clam farming on-growing areas. In addition, the collected data is a snapshot of the time immediately before the commissioning of MoSE, a system of mobile barriers aimed at protecting Venice from high tides, and will represent a baseline for future studies on the effects of MoSE on clams farming and more in general on the ecology of the Venice Lagoon.}, } @article {pmid36527397, year = {2022}, author = {Viner, A and Membe-Gadama, G and Whyte, S and Kayambo, D and Masamba, M and Martin, CJH and Magowan, B and Reynolds, RM and Stock, SJ and Freyne, B and Gadama, L}, title = {Midwife-Led Ultrasound Scanning to Date Pregnancy in Malawi: Development of a Novel Training Program.}, journal = {Journal of midwifery & women's health}, volume = {67}, number = {6}, pages = {728-734}, pmid = {36527397}, issn = {1542-2011}, support = {GHR Project: 17/63/08 DIPLOMATIC collaboration//National Institute for Health Research (NIHR)/ ; }, mesh = {Female ; Pregnancy ; Humans ; *Midwifery/education ; *Nurse Midwives/education ; Malawi ; }, abstract = {The use of ultrasound to determine gestational age is fundamental to the optimum management of pregnancy and is recommended for all women by the World Health Organization. However, this modality remains unavailable to many women in low-income countries where trained practitioners are scarce. Although previous initiatives have demonstrated efficacy in training midwives and technicians to perform antenatal ultrasound, these programs have often been too long and too complex to be realistic within the specific constraints of this context, highlighting the need for a novel and pragmatic approach. We describe the development and piloting of a bespoke course to teach midwives 3 fundamental components of early antenatal ultrasound scanning: (1) to identify the number of fetuses, (2) to confirm fetal viability, and (3) to determine gestational age. Having established that 5 days is insufficient, we propose that the minimum duration required to train ultrasound-naive midwives to competency is 10 days. Our completed program therefore consists of one and one-half days of didactic teaching, followed by 8 and one-half days of supervised hands-on practical training in which trainees are assessed on their skills. This package has subsequently been successfully implemented across 6 sites in Malawi, where 28 midwives have achieved competency. By describing the processes involved in our cross-continental collaboration, we explain how unexpected challenges helped shape and improve our program, demonstrating the value of preimplementation piloting and a pragmatic and adaptive approach.}, } @article {pmid36527232, year = {2023}, author = {Petrén, H and Köllner, TG and Junker, RR}, title = {Quantifying chemodiversity considering biochemical and structural properties of compounds with the R package chemodiv.}, journal = {The New phytologist}, volume = {237}, number = {6}, pages = {2478-2492}, doi = {10.1111/nph.18685}, pmid = {36527232}, issn = {1469-8137}, mesh = {*Phytochemicals ; *Plants ; Ecology ; Phenotype ; Databases, Factual ; }, abstract = {Plants produce large numbers of phytochemical compounds affecting plant physiology and interactions with their biotic and abiotic environment. Recently, chemodiversity has attracted considerable attention as an ecologically and evolutionary meaningful way to characterize the phenotype of a mixture of phytochemical compounds. Currently used measures of phytochemical diversity, and related measures of phytochemical dissimilarity, generally do not take structural or biosynthetic properties of compounds into account. Such properties can be indicative of the compounds' function and inform about their biosynthetic (in)dependence, and should therefore be included in calculations of these measures. We introduce the R package chemodiv, which retrieves biochemical and structural properties of compounds from databases and provides functions for calculating and visualizing chemical diversity and dissimilarity for phytochemicals and other types of compounds. Our package enables calculations of diversity that takes the richness, relative abundance and - most importantly - structural and/or biosynthetic dissimilarity of compounds into account. We illustrate the use of the package with examples on simulated and real datasets. By providing the R package chemodiv for quantifying multiple aspects of chemodiversity, we hope to facilitate investigations of how chemodiversity varies across levels of biological organization, and its importance for the ecology and evolution of plants and other organisms.}, } @article {pmid36526212, year = {2023}, author = {Zhang, Z and Fan, Y and Jiao, Z}, title = {Wetland ecological index and assessment of spatial-temporal changes of wetland ecological integrity.}, journal = {The Science of the total environment}, volume = {862}, number = {}, pages = {160741}, doi = {10.1016/j.scitotenv.2022.160741}, pmid = {36526212}, issn = {1879-1026}, mesh = {*Wetlands ; *Environmental Monitoring/methods ; Ecosystem ; Soil ; Rivers ; China ; }, abstract = {Long-term, quantitative, and dynamic monitoring of regional ecological integrity using remote sensing can provide powerful decision-making support for sustainable regional development. However, existing methods are unable to accurately evaluate the quality of the surface ecological integrity because they do not consider vegetation saturation and salinization of wetlands. In addition, the ecological fragility of wetlands is characterized by a high frequency of changes in ecological conditions over time, leading to a lack of directionality in the analysis of ecological changes over long time series. To accurately assess the surface ecological integrity, this study integrates environmental salinity (Baseline-based Soil Salinity Index, BSSI) and a new vegetation element (Improved Hyperspectral Image-based Vegetation Index, IHSVI), and proposes the wetland ecological index (WEI) for the ecological integrity assessment system. Combined with the annual ecological integrity assessment using the WEI, the Mann-Kendall test was used to obtain the nodes of long-term changes. The WEI-Mann Kendall (WEI-MK) framework indicates the direction of analysis and realizes clear long-term series change monitoring. In this study, we analyzed the spatial and temporal changes in ecological integrity in the Yellow River Delta from 1991 to 2020 based on the WEI-MK framework. The results showed that: 1) Compared with Remote Sensing-based Ecological Index (RSEI), the WEI improved the accuracy of wetland integrity evaluation to 89 %. The WEI also improved accuracy of assessments in other typical regions by approximately 10 %. 2) The selection of nodes based on the WEI-MK framework clarified the direction of environmental change analysis. The results show that although the quality of the terrestrial ecological environment has improved over the past 30 years in the Yellow River Delta, that of the marine ecological environment has gradually declined. In particular, the state of the marine ecological environment after 2016 should be of concern.}, } @article {pmid36522390, year = {2022}, author = {Acerbi, A and Snyder, WD and Tennie, C}, title = {The method of exclusion (still) cannot identify specific mechanisms of cultural inheritance.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {21680}, pmid = {36522390}, issn = {2045-2322}, support = {714658/ERC_/European Research Council/International ; }, mesh = {Animals ; Social Behavior ; *Social Learning ; Databases, Genetic ; *Hominidae ; *Cultural Evolution ; }, abstract = {The method of exclusion identifies patterns of distributions of behaviours and/or artefact forms among different groups, where these patterns are deemed unlikely to arise from purely genetic and/or ecological factors. The presence of such patterns is often used to establish whether a species is cultural or not-i.e. whether a species uses social learning or not. Researchers using or describing this method have often pointed out that the method cannot pinpoint which specific type(s) of social learning resulted in the observed patterns. However, the literature continues to contain such inferences. In a new attempt to warn against these logically unwarranted conclusions, we illustrate this error using a novel approach. We use an individual-based model, focused on wild ape cultural patterns-as these patterns are the best-known cases of animal culture and as they also contain the most frequent usage of the unwarranted inference for specific social learning mechanisms. We built a model that contained agents unable to copy specifics of behavioural or artefact forms beyond their individual reach (which we define as "copying"). We did so, as some of the previous inference claims related to social learning mechanisms revolve around copying defined in this way. The results of our model however show that non-copying social learning can already reproduce the defining-even iconic-features of observed ape cultural patterns detected by the method of exclusion. This shows, using a novel model approach, that copying processes are not necessary to produce the cultural patterns that are sometimes still used in an attempt to identify copying processes. Additionally, our model could fully control for both environmental and genetic factors (impossible in real life) and thus offers a new validity check for the method of exclusion as related to general cultural claims-a check that the method passed. Our model also led to new and additional findings, which we likewise discuss.}, } @article {pmid36522346, year = {2022}, author = {Wang, H and Harrison, SP and Li, M and Prentice, IC and Qiao, S and Wang, R and Xu, H and Mengoli, G and Peng, Y and Yang, Y}, title = {The China plant trait database version 2.}, journal = {Scientific data}, volume = {9}, number = {1}, pages = {769}, pmid = {36522346}, issn = {2052-4463}, support = {694481 GC2.0//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; 787203 REALM//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; }, mesh = {China ; Ecology ; *Ecosystem ; *Plants ; Databases, Factual ; }, abstract = {Plant functional traits represent adaptive strategies to the environment, linked to biophysical and biogeochemical processes and ecosystem functioning. Compilations of trait data facilitate research in multiple fields from plant ecology through to land-surface modelling. Here we present version 2 of the China Plant Trait Database, which contains information on morphometric, physical, chemical, photosynthetic and hydraulic traits from 1529 unique species in 140 sites spanning a diversity of vegetation types. Version 2 has five improvements compared to the previous version: (1) new data from a 4-km elevation transect on the edge of Tibetan Plateau, including alpine vegetation types not sampled previously; (2) inclusion of traits related to hydraulic processes, including specific sapwood conductance, the area ratio of sapwood to leaf, wood density and turgor loss point; (3) inclusion of information on soil properties to complement the existing data on climate and vegetation (4) assessments and flagging the reliability of individual trait measurements; and (5) inclusion of standardized templates for systematical field sampling and measurements.}, } @article {pmid36520387, year = {2023}, author = {Melayah, D and Bontemps, Z and Bruto, M and Nguyen, A and Oger, P and Hugoni, M}, title = {Metabarcoding of the Three Domains of Life in Aquatic Saline Ecosystems.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2605}, number = {}, pages = {17-35}, pmid = {36520387}, issn = {1940-6029}, mesh = {*Ecosystem ; *Archaea/genetics ; Bacteria/genetics ; High-Throughput Nucleotide Sequencing/methods ; Computational Biology/methods ; Biodiversity ; }, abstract = {High-throughput amplicon sequencing, known as metabarcoding, is a powerful technique to decipher exhaustive microbial diversity considering specific gene markers. While most of the studies investigating ecosystem functioning through microbial diversity targeted only one domain of life, either bacteria, or archaea or microeukaryotes, the remaining challenge in microbial ecology is to uncover the integrated view of microbial diversity occurring in ecosystems. Indeed, interactions occurring between the different microbial counterparts are now recognized having a great impact on stability and resilience of ecosystems. Here, we summarize protocols describing sampling, molecular, and simultaneous metabarcoding of bacteria, archaea, and microeukaryotes, as well as a bioinformatic pipeline allowing the study of exhaustive microbial diversity in natural aquatic saline samples.}, } @article {pmid36519374, year = {2023}, author = {Seidu, S and Gillies, C and Zaccardi, F and Reeves, K and Gallier, S and Khunti, K}, title = {Temporal trends in admissions for atrial fibrillation and severe bleeding in England: an 18-year longitudinal analysis.}, journal = {Scandinavian cardiovascular journal : SCJ}, volume = {57}, number = {1}, pages = {40-47}, doi = {10.1080/14017431.2022.2156597}, pmid = {36519374}, issn = {1651-2006}, mesh = {Humans ; *Atrial Fibrillation/diagnosis/epidemiology/therapy ; Anticoagulants/therapeutic use ; Administration, Oral ; Risk Factors ; Treatment Outcome ; Time Factors ; Hemorrhage/diagnosis/epidemiology ; *Stroke ; }, abstract = {Objective. Temporal trends in admissions for atrial fibrillation (AF) and severe bleeding associated with AF vary worldwide. We aimed to explore their temporal trends in England and their relation to the introduction of DOACs in 2014 in the UK. Design. This longitudinal ecological study utilised aggregated data that was extracted from the Hospital Episode Statistics database, which captured annual admissions for AF and severe bleeding associated with AF between 2001 and 2018. Trends in admissions over the study period and across age groups, gender and regions in England were assessed. Results. In total, there were 11,292,177 admissions for AF and 324,851 admissions for severe bleeding associated with AF. There was a steady rise in admissions for AF from 2001 to 2017 (204,808 to 1,109,295; p for trend<.001). A similar trend was observed for severe bleeding (4940 to 30,169; p for trend <.001), but the increase dropped slightly between 2013 and 2014 and continued thereafter. Conclusions. There was a rise in admissions for AF and severe bleeding in England between 2001 and 2018. There is little evidence that the slight drop in admissions for severe bleeding between 2013 and 2014 may have been caused by the introduction of DOACs in 2014. Contributors to these trends need urgent exploration.}, } @article {pmid36517756, year = {2022}, author = {Zhang, H and Yao, G and He, M}, title = {Transcriptome analysis of gene expression profiling from the deep sea in situ to the laboratory for the cold seep mussel Gigantidas haimaensis.}, journal = {BMC genomics}, volume = {23}, number = {1}, pages = {828}, pmid = {36517756}, issn = {1471-2164}, mesh = {Animals ; *Ecosystem ; *Mytilidae/genetics ; Gene Expression Profiling ; Transcriptome ; Gene Ontology ; }, abstract = {BACKGROUND: The deep-sea mussel Gigantidas haimaensis is a representative species from the Haima cold seep ecosystem in the South China Sea that establishes endosymbiosis with chemotrophic bacteria. During long-term evolution, G. haimaensis has adapted well to the local environment of cold seeps. Until now, adaptive mechanisms responding to environmental stresses have remained poorly understood.

RESULTS: In this study, transcriptomic analysis was performed for muscle tissue of G. haimaensis in the in situ environment (MH) and laboratory environment for 0 h (M0), 3 h (M3) and 9 h (M9), and 187,368 transcript sequences and 22,924 annotated differentially expressed genes (DEGs) were generated. Based on Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, these DEGs were enriched with a broad spectrum of biological processes and pathways, including those associated with antioxidants, apoptosis, chaperones, immunity and metabolism. Among these significantly enriched pathways, protein processing in the endoplasmic reticulum and metabolism were the most affected metabolic pathways. These results may imply that G. haimaensis struggles to support the life response to environmental change by changing gene expression profiles.

CONCLUSION: The present study provides a better understanding of the biological responses and survival strategies of the mussel G. haimaensis from deep sea in situ to the laboratory environment.}, } @article {pmid36512954, year = {2023}, author = {Kim, B and Barrington, WE and Dobra, A and Rosenberg, D and Hurvitz, P and Belza, B}, title = {Mediating role of walking between perceived and objective walkability and cognitive function in older adults.}, journal = {Health & place}, volume = {79}, number = {}, pages = {102943}, pmid = {36512954}, issn = {1873-2054}, support = {DP1 AG069874/AG/NIA NIH HHS/United States ; U01 AG006781/AG/NIA NIH HHS/United States ; U19 AG066567/AG/NIA NIH HHS/United States ; }, mesh = {Humans ; Aged ; *Exercise ; Cross-Sectional Studies ; *Environment Design ; Residence Characteristics ; Walking ; Cognition ; }, abstract = {The aim of this study was to examine the role of walking in explaining associations between perceived and objective measures of walkability and cognitive function among older adults. The study employed a cross-sectional design analyzing existing data. Data were obtained from the Adult Changes in Thought Activity Monitor study. Cognitive function and perceived walkability were measured by a survey. Objective walkability was measured using geographic information systems (GIS). Walking was measured using an accelerometer. We tested the mediating relationship based on 1,000 bootstrapped samples. Perceived walkability was associated with a 0.04 point higher cognitive function score through walking (p = 0.006). The mediating relationship accounted for 34% of the total relationship between perceived walkability and cognitive function. Walking did not have a significant indirect relationship on the association between objective walkability and cognitive function. Perceived walkability may be more relevant to walking behavior than objective walkability among older adults. Greater levels of perceived walkability may encourage older adults to undertake more walking, and more walking may in turn improve cognitive function in older adults.}, } @article {pmid36512230, year = {2023}, author = {Barlow, LD and Maciejowski, W and More, K and Terry, K and Vargová, R and Záhonová, K and Dacks, JB}, title = {Comparative Genomics for Evolutionary Cell Biology Using AMOEBAE: Understanding the Golgi and Beyond.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2557}, number = {}, pages = {431-452}, pmid = {36512230}, issn = {1940-6029}, mesh = {*Amoeba/genetics ; Reproducibility of Results ; Genomics/methods ; Biological Evolution ; Golgi Apparatus/metabolism ; Computational Biology/methods ; }, abstract = {Taking an evolutionary approach to cell biology can yield important new information about how the cell works and how it evolved to do so. This is true of the Golgi apparatus, as it is of all systems within the cell. Comparative genomics is one of the crucial first steps to this line of research, but comes with technical challenges that must be overcome for rigor and robustness. We here introduce AMOEBAE, a workflow for mid-range scale comparative genomic analyses. It allows for customization of parameters, queries, and taxonomic sampling of genomic and transcriptomics data. This protocol article covers the rationale for an evolutionary approach to cell biological study (i.e., when would AMOEBAE be useful), how to use AMOEBAE, and discussion of limitations. It also provides an example dataset, which demonstrates that the Golgi protein AP4 Epsilon is present as the sole retained subunit of the AP4 complex in basidiomycete fungi. AMOEBAE can facilitate comparative genomic studies by balancing reproducibility and speed with user-input and interpretation. It is hoped that AMOEBAE or similar tools will encourage cell biologists to incorporate an evolutionary context into their research.}, } @article {pmid36504957, year = {2022}, author = {Zhang, Y and Liu, S and Wang, Y and Wang, Y}, title = {Causal relationship between particulate matter 2.5 and hypothyroidism: A two-sample Mendelian randomization study.}, journal = {Frontiers in public health}, volume = {10}, number = {}, pages = {1000103}, pmid = {36504957}, issn = {2296-2565}, mesh = {*Particulate Matter/adverse effects ; *Genome-Wide Association Study ; Analysis of Variance ; Databases, Factual ; Polymorphism, Single Nucleotide ; }, abstract = {BACKGROUND: Epidemiological surveys have found that particulate matter 2.5 (PM2.5) plays an important role in hypothyroidism. However, due to the methodological limitations of traditional observational studies, it is difficult to make causal inferences. In the present study, we assessed the causal association between PM2.5 concentrations and risk of hypothyroidism using two-sample Mendelian randomization (TSMR).

METHODS: We performed TSMR by using aggregated data from genome-wide association studies (GWAS) on the IEU Open GWAS database. We identified seven single nucleotide polymorphisms (SNPs) associated with PM2.5 concentrations as instrumental variables (IVs). We used inverse-variance weighting (IVW) as the main analytical method, and we selected MR-Egger, weighted median, simple model, and weighted model methods for quality control.

RESULTS: MR analysis showed that PM2.5 has a positive effect on the risk of hypothyroidism: An increase of 1 standard deviation (SD) in PM2.5 concentrations increases the risk of hypothyroidism by ~10.0% (odds ratio 1.10, 95% confidence interval 1.06-1.13, P = 2.93E-08, by IVW analysis); there was no heterogeneity or pleiotropy in the results.

CONCLUSION: In conclusion, increased PM2.5 concentrations are associated with an increased risk of hypothyroidism. This study provides evidence of a causal relationship between PM2.5 and the risk of hypothyroidism, so air pollution control may have important implications for the prevention of hypothyroidism.}, } @article {pmid36503572, year = {2022}, author = {Yan, X and Si, H and Zhu, Y and Li, S and Han, Y and Liu, H and Du, R and Pope, PB and Qiu, Q and Li, Z}, title = {Integrated multi-omics of the gastrointestinal microbiome and ruminant host reveals metabolic adaptation underlying early life development.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {222}, pmid = {36503572}, issn = {2049-2618}, support = {32122083//National Natural Science Foundation of China/ ; 054575 - SuPAcow//Novo Nordisk Fonden/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; Multiomics ; *Deer/microbiology ; Rumen/microbiology ; Fatty Acids, Volatile ; }, abstract = {BACKGROUND: The gastrointestinal tract (GIT) microbiome of ruminants and its metabolic repercussions vastly influence host metabolism and growth. However, a complete understanding of the bidirectional interactions that occur across the host-microbiome axis remains elusive, particularly during the critical development stages at early life. Here, we present an integrative multi-omics approach that simultaneously resolved the taxonomic and functional attributes of microbiota from five GIT regions as well as the metabolic features of the liver, muscle, urine, and serum in sika deer (Cervus nippon) across three key early life stages.

RESULTS: Within the host, analysis of metabolites over time in serum, urine, and muscle (longissimus lumborum) showed that changes in the fatty acid profile were concurrent with gains in body weight. Additional host transcriptomic and metabolomic analysis revealed that fatty acid β-oxidation and metabolism of tryptophan and branched chain amino acids play important roles in regulating hepatic metabolism. Across the varying regions of the GIT, we demonstrated that a complex and variable community of bacteria, viruses, and archaea colonized the GIT soon after birth, whereas microbial succession was driven by the cooperative networks of hub populations. Furthermore, GIT volatile fatty acid concentrations were marked by increased microbial metabolic pathway abundances linked to mannose (rumen) and amino acids (colon) metabolism. Significant functional shifts were also revealed across varying GIT tissues, which were dominated by host fatty acid metabolism associated with reactive oxygen species in the rumen epithelium, and the intensive immune response in both small and large intestine. Finally, we reveal a possible contributing role of necroptosis and apoptosis in enhancing ileum and colon epithelium development, respectively.

CONCLUSIONS: Our findings provide a comprehensive view for the involved mechanisms in the context of GIT microbiome and ruminant metabolic growth at early life. Video Abstract.}, } @article {pmid36498115, year = {2022}, author = {Li, W and Liu, R and Sun, L and Guo, Z and Gao, J}, title = {An Investigation of Employees' Intention to Comply with Information Security System-A Mixed Approach Based on Regression Analysis and fsQCA.}, journal = {International journal of environmental research and public health}, volume = {19}, number = {23}, pages = {}, pmid = {36498115}, issn = {1660-4601}, support = {2019YFB1704103//Open Ecological Cloud ERP Platform/ ; }, mesh = {Humans ; *Intention ; *Information Systems ; Self Efficacy ; Motivation ; Regression Analysis ; }, abstract = {Employee security compliance behavior has become an important safeguard to protect the security of corporate information assets. Focusing on human factors, this paper discusses how to regulate and guide employees' compliance with information security systems through effective methods. Based on protection motivation theory (PMT), a model of employees' intention to comply with the information security system was constructed. A questionnaire survey was adopted to obtain 224 valid data points, and SPSS 26.0 was applied to verify the hypotheses underlying the research model. Then, based on the results of a regression analysis, fuzzy set qualitative comparative analysis (fsQCA) was used to explore the conditional configurations that affect employees' intention to comply with the information security system from a holistic perspective. The empirical results demonstrated that perceived severity, perceived vulnerability, response efficacy, and self-efficacy all positively influenced the employees' intention to comply with the information security system; while rewards and response costs had a negative effect. Threat appraisal had a greater effect on employees' intention to comply with the information security system compared to response appraisal. The fsQCA results showed that individual antecedent conditions are not necessary to influence employees' intention to comply with an information security system. Seven pathways exist that influence an employees' intention to comply with an information security system, with reward, self-efficacy, and response cost being the core conditions having the highest probability of occurring in each configuration of pathways, and with perceived severity and self-efficacy appearing in the core conditions of configurations with an original coverage greater than 40%. Theoretically, this study discusses the influence of the elements of PMT on employees' intention to comply with an information security system, reveals the mechanism of influence of the combination of the influencing factors on the outcome variables, and identifies the core factors and auxiliary factors in the condition configurations, providing a new broader perspective for the study of information security compliance behavior and providing some theoretical support for strengthening enterprise security management. Practically, targeted suggestions are proposed based on the research results, to increase the intention of enterprise employees to comply with information security systems, thereby improving the effectiveness of enterprise information security management and the degree of information security in enterprises.}, } @article {pmid36497480, year = {2022}, author = {Islam, MM and Poly, TN and Walther, BA and Yeh, CY and Seyed-Abdul, S and Li, YJ and Lin, MC}, title = {Deep Learning for the Diagnosis of Esophageal Cancer in Endoscopic Images: A Systematic Review and Meta-Analysis.}, journal = {Cancers}, volume = {14}, number = {23}, pages = {}, pmid = {36497480}, issn = {2072-6694}, abstract = {Esophageal cancer, one of the most common cancers with a poor prognosis, is the sixth leading cause of cancer-related mortality worldwide. Early and accurate diagnosis of esophageal cancer, thus, plays a vital role in choosing the appropriate treatment plan for patients and increasing their survival rate. However, an accurate diagnosis of esophageal cancer requires substantial expertise and experience. Nowadays, the deep learning (DL) model for the diagnosis of esophageal cancer has shown promising performance. Therefore, we conducted an updated meta-analysis to determine the diagnostic accuracy of the DL model for the diagnosis of esophageal cancer. A search of PubMed, EMBASE, Scopus, and Web of Science, between 1 January 2012 and 1 August 2022, was conducted to identify potential studies evaluating the diagnostic performance of the DL model for esophageal cancer using endoscopic images. The study was performed in accordance with PRISMA guidelines. Two reviewers independently assessed potential studies for inclusion and extracted data from retrieved studies. Methodological quality was assessed by using the QUADAS-2 guidelines. The pooled accuracy, sensitivity, specificity, positive and negative predictive value, and the area under the receiver operating curve (AUROC) were calculated using a random effect model. A total of 28 potential studies involving a total of 703,006 images were included. The pooled accuracy, sensitivity, specificity, and positive and negative predictive value of DL for the diagnosis of esophageal cancer were 92.90%, 93.80%, 91.73%, 93.62%, and 91.97%, respectively. The pooled AUROC of DL for the diagnosis of esophageal cancer was 0.96. Furthermore, there was no publication bias among the studies. The findings of our study show that the DL model has great potential to accurately and quickly diagnose esophageal cancer. However, most studies developed their model using endoscopic data from the Asian population. Therefore, we recommend further validation through studies of other populations as well.}, } @article {pmid36495963, year = {2023}, author = {Tong, H and Warren, JL and Kang, J and Li, M}, title = {Using multi-sourced big data to correlate sleep deprivation and road traffic noise: A US county-level ecological study.}, journal = {Environmental research}, volume = {220}, number = {}, pages = {115029}, doi = {10.1016/j.envres.2022.115029}, pmid = {36495963}, issn = {1096-0953}, mesh = {Humans ; *Sleep Deprivation/epidemiology ; *Noise, Transportation/adverse effects ; Bayes Theorem ; Big Data ; Sleep ; Environmental Exposure ; }, abstract = {BACKGROUND: Road traffic noise is a serious public health problem globally as it has adverse psychological and physiologic effects (i.e., sleep). Since previous studies mainly focused on individual levels, we aim to examine associations between road traffic noise and sleep deprivation on a large scale; namely, the US at county level.

METHODS: Information from a large-scale sleep survey and national traffic noise map, both obtained from government's open data, were utilized and processed with Geographic Information System (GIS) techniques. To examine the associations between traffic noise and sleep deprivation, we used a hierarchical Bayesian spatial modelling framework to simultaneously adjust for multiple socioeconomic factors while accounting for spatial correlation.

FINDINGS: With 62.90% of people not getting enough sleep, a 10 dBA increase in average sound-pressure level (SPL) or Ls10 (SPL of the relatively noisy area) in a county, was associated with a 49% (OR: 1.49; 95% CrIs:1.19-1.86) or 8% (1.08; 1.00-1.16) increase in the odds of a person in a particular county not getting enough sleep. No significant association was observed for Ls90 (SPL of the relatively quiet area). A 10% increase in noise exposure area or population ratio was associated with a 3% (1.03; 1.01-1.06) or 4% (1.04; 1.02-1.06) increase in the odds of a person within a county not getting enough sleep.

INTERPRETATION: Traffic noise can contribute to variations in sleep deprivation among counties. This study suggests that policymakers could set up different noise-management strategies for relatively quiet and noisy areas and incorporate geospatial noise indicators, such as exposure population or area ratio. Furthermore, urban planners should consider urban sprawl patterns differently in terms of noise-induced sleep problems.}, } @article {pmid36493775, year = {2023}, author = {Koptekin, D and Yüncü, E and Rodríguez-Varela, R and Altınışık, NE and Psonis, N and Kashuba, N and Yorulmaz, S and George, R and Kazancı, DD and Kaptan, D and Gürün, K and Vural, KB and Gemici, HC and Vassou, D and Daskalaki, E and Karamurat, C and Lagerholm, VK and Erdal, ÖD and Kırdök, E and Marangoni, A and Schachner, A and Üstündağ, H and Shengelia, R and Bitadze, L and Elashvili, M and Stravopodi, E and Özbaşaran, M and Duru, G and Nafplioti, A and Rose, CB and Gencer, T and Darbyshire, G and Gavashelishvili, A and Pitskhelauri, K and Çevik, Ö and Vuruşkan, O and Kyparissi-Apostolika, N and Büyükkarakaya, AM and Oğuzhanoğlu, U and Günel, S and Tabakaki, E and Aliev, A and Ibrahimov, A and Shadlinski, V and Sampson, A and Kılınç, GM and Atakuman, Ç and Stamatakis, A and Poulakakis, N and Erdal, YS and Pavlidis, P and Storå, J and Özer, F and Götherström, A and Somel, M}, title = {Spatial and temporal heterogeneity in human mobility patterns in Holocene Southwest Asia and the East Mediterranean.}, journal = {Current biology : CB}, volume = {33}, number = {1}, pages = {41-57.e15}, pmid = {36493775}, issn = {1879-0445}, mesh = {Humans ; Male ; History, Ancient ; *Racial Groups ; Iran ; *Genome, Human ; Gene Flow ; Human Migration ; Genetics, Population ; }, abstract = {We present a spatiotemporal picture of human genetic diversity in Anatolia, Iran, Levant, South Caucasus, and the Aegean, a broad region that experienced the earliest Neolithic transition and the emergence of complex hierarchical societies. Combining 35 new ancient shotgun genomes with 382 ancient and 23 present-day published genomes, we found that genetic diversity within each region steadily increased through the Holocene. We further observed that the inferred sources of gene flow shifted in time. In the first half of the Holocene, Southwest Asian and the East Mediterranean populations homogenized among themselves. Starting with the Bronze Age, however, regional populations diverged from each other, most likely driven by gene flow from external sources, which we term "the expanding mobility model." Interestingly, this increase in inter-regional divergence can be captured by outgroup-f3-based genetic distances, but not by the commonly used FST statistic, due to the sensitivity of FST, but not outgroup-f3, to within-population diversity. Finally, we report a temporal trend of increasing male bias in admixture events through the Holocene.}, } @article {pmid36478393, year = {2023}, author = {Keck, F and Couton, M and Altermatt, F}, title = {Navigating the seven challenges of taxonomic reference databases in metabarcoding analyses.}, journal = {Molecular ecology resources}, volume = {23}, number = {4}, pages = {742-755}, doi = {10.1111/1755-0998.13746}, pmid = {36478393}, issn = {1755-0998}, support = {31003A_173074//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; //Swiss Federal Office for the Environment (FOEN/BAFU)/ ; //University of Zurich Research Priority Programme in Global Change and Biodiversity/ ; }, mesh = {*DNA Barcoding, Taxonomic ; Biodiversity ; Ecology ; Databases, Nucleic Acid ; *DNA, Environmental ; }, abstract = {Assessment of biodiversity using metabarcoding data, such as from bulk or environmental DNA sampling, is becoming increasingly relevant in ecology, biodiversity sciences and monitoring. Thereby, the taxonomic identification of species from their DNA sequences relies strongly on reference databases that link genetic sequences to taxonomic names. These databases vary in completeness and availability, depending on the taxonomic group studied and the genetic region targeted. The incompleteness of reference databases is an important argument to explain the nondetection by metabarcoding of species supposedly present. However, there exist further and generally overlooked problems with reference databases that can lead to false or inaccurate inferences of taxonomic assignment. Here, we synthesize all possible problems inherent to reference databases. In particular, we identify a complete, mutually nonexclusive list of seven classes of challenges when it comes to selecting, developing and using a reference database for taxonomic assignment. These are: (i) mislabelling, (ii) sequencing errors, (iii) sequence conflict, (iv) taxonomic conflict, (v) low taxonomic resolution, (vi) missing taxa and (vii) missing intraspecific variants. For each problem identified, we provide a description of possible consequences on the taxonomic assignment process. We illustrate the respective problem with examples taken from the literature or obtained by quantitative analyses of public databases, such as GenBank or BOLD. Finally, we discuss possible solutions to the identified problems and how to navigate them. Only by raising users' awareness of the limitations of metabarcoding data and DNA reference databases will adequate interpretations of these data be achieved.}, } @article {pmid36478264, year = {2023}, author = {Mairal, M and García-Verdugo, C and Le Roux, JJ and Chau, JH and van Vuuren, BJ and Hui, C and Münzbergová, Z and Chown, SL and Shaw, JD}, title = {Multiple introductions, polyploidy and mixed reproductive strategies are linked to genetic diversity and structure in the most widespread invasive plant across Southern Ocean archipelagos.}, journal = {Molecular ecology}, volume = {32}, number = {4}, pages = {756-771}, doi = {10.1111/mec.16809}, pmid = {36478264}, issn = {1365-294X}, mesh = {Humans ; *Genetic Variation/genetics ; *Polyploidy ; Reproduction ; Geography ; Introduced Species ; Oceans and Seas ; Microsatellite Repeats/genetics ; }, abstract = {Biological invasions in remote areas that experience low human activity provide unique opportunities to elucidate processes responsible for invasion success. Here we study the most widespread invasive plant species across the isolated islands of the Southern Ocean, the annual bluegrass, Poa annua. To analyse geographical variation in genome size, genetic diversity and reproductive strategies, we sampled all major sub-Antarctic archipelagos in this region and generated microsatellite data for 470 individual plants representing 31 populations. We also estimated genome sizes for a subset of individuals using flow cytometry. Occasional events of island colonization are expected to result in high genetic structure among islands, overall low genetic diversity and increased self-fertilization, but we show that this is not the case for P. annua. Microsatellite data indicated low population genetic structure and lack of isolation by distance among the sub-Antarctic archipelagos we sampled, but high population structure within each archipelago. We identified high levels of genetic diversity, low clonality and low selfing rates in sub-Antarctic P. annua populations (contrary to rates typical of continental populations). In turn, estimates of selfing declined in populations as genetic diversity increased. Additionally, we found that most P. annua individuals are probably tetraploid and that only slight variation exists in genome size across the Southern Ocean. Our findings suggest multiple independent introductions of P. annua into the sub-Antarctic, which promoted the establishment of genetically diverse populations. Despite multiple introductions, the adoption of convergent reproductive strategies (outcrossing) happened independently in each major archipelago. The combination of polyploidy and a mixed reproductive strategy probably benefited P. annua in the Southern Ocean by increasing genetic diversity and its ability to cope with the novel environmental conditions.}, } @article {pmid36477523, year = {2022}, author = {Takemura, LS and Barbosa, ÁRG and Amaral, BS and Bosco, AAD and Lourenço, DB and Apezzato, M and Barbosa, JABA and Faria, EF and Bianco, B and Lemos, GC and Carneiro, A}, title = {Radical prostatectomies for treatment of prostate cancer: trends in a ten-year period in public health services in the city of São Paulo, Brazil.}, journal = {Einstein (Sao Paulo, Brazil)}, volume = {20}, number = {}, pages = {eAO0049}, pmid = {36477523}, issn = {2317-6385}, mesh = {United States ; Humans ; Male ; Brazil/epidemiology ; *Prostatic Neoplasms/surgery ; Health Services ; }, abstract = {OBJECTIVE: To analyze the characteristics of public health services related to radical prostatectomy, according to hospital volume of surgeries and stratified as academic and non-academic centers.

METHODS: An ecological study was conducted using a database available in TabNet platform of the Unified Health System Department of Informatics. Number of surgeries, length of hospital stay, length of stay in intensive care unit, in-hospital mortality rate, and cost of hospitalization were evaluated. The hospitals were divided into three subgroups according to surgery volume (tercile), and results were compared. The same comparisons were made among academic and non-academic centers. We considered academic centers those providing Urology residency program.

RESULTS: A total of 11,259 radical prostatectomies were performed in the city of São Paulo between 2008 and 2018. We observed a significant trend of increase in radical prostatectomies for treating prostate cancer over the years (p=0.007). The length of stay in intensive care unit, and number of deaths were not statistically different among centers with diverse surgery volume, nor between academic and non-academic centers. However, length of hospital stay was significantly shorter in academic centers (p=0.043), while cost of hospitalization was significantly higher in high-volume center compared to low- (p<0.001) and intermediate-volume centers (p<0.001).

CONCLUSION: Length of hospital stay for radical prostatectomies performed in public services in the city of São Paulo was shorter in academic centers, whereas hospitals with a high volume of surgeries showed greater cost of hospitalization.}, } @article {pmid36475098, year = {2022}, author = {Karaarslan, F and Yılmaz, H and Akkurt, HE and Kaya, FM and Şafak Yılmaz, E}, title = {Comparison of the efficacy of mud-pack and hot-pack treatments in chronic non-specific neck pain: A single-blind, randomized-controlled study.}, journal = {Turkish journal of physical medicine and rehabilitation}, volume = {68}, number = {3}, pages = {381-390}, pmid = {36475098}, issn = {2587-1250}, abstract = {OBJECTIVES: This study aims to compare the short-term efficacy of mud-pack (MP) and hot-pack (HP) treatments with the same temperature and duration on sleep, function, depression, and quality of life for chronic non-specific neck pain (CNNP) patients.

PATIENTS AND METHODS: Between December 2018 and September 2019, a total of 70 patients with CNNP diagnosis (12 males, 58 females; mean age: 50.2±9.4 years; range, 24 to 65 years) were included. The patients were divided into two groups. The MP group (n=35) had a total of 15 sessions of MP for 20 min + transcutaneous electrical nerve stimulation (TENS) for 20 min + home exercise (HE) on five days per week for three weeks. The HP group (n=35) had 15 similar sessions of HP for 20 min + TENS for 20 min + HE. The patients were assessed with the Visual Analog Scale (VAS-pain), VAS physician's and patient's global assessments, modified Neck Disability Index (mNDI), Beck Depression Inventory (BDI), Pittsburgh Sleep Quality Index (PSQI), and Short Form-36 (SF-36) measures before treatment, at the end of post-treatment third week and one month later.

RESULTS: In the MP group, there were statistically significant improvements in all parameters at the end of treatment three-week and one-month follow-up (p<0.05), apart from SF-36 Vitality/Energy (SF-36V/E) at the end of treatment and SF-36 General Health (SF-36GH) at one month. In the HP group, there were statistically significant improvements observed for all parameters (p<0.05), apart from the SF-36 Physical Role and SF-36GH at the end of treatment third week and SF-36V/E at the first-month assessment. The VAS-pain(p<0.001), mNDI (p=0.019), BDI (p=0.002), SF-36GH (p<0.001), SF-36V/E (p<0.001) and SF-36 mental health (p<0.001) showed statistically significantly superior improvements in the MP group (p<0.05).

CONCLUSION: In CNNP patients, both MP and HP treatments are effective. However, MP therapy has more positive effects on pain, function, depression, and quality of life parameters. The MP treatment may be used in addition to TENS treatment for CNNP patients.}, } @article {pmid36473660, year = {2023}, author = {Simeoni, C and Furlan, E and Pham, HV and Critto, A and de Juan, S and Trégarot, E and Cornet, CC and Meesters, E and Fonseca, C and Botelho, AZ and Krause, T and N'Guetta, A and Cordova, FE and Failler, P and Marcomini, A}, title = {Evaluating the combined effect of climate and anthropogenic stressors on marine coastal ecosystems: Insights from a systematic review of cumulative impact assessment approaches.}, journal = {The Science of the total environment}, volume = {861}, number = {}, pages = {160687}, doi = {10.1016/j.scitotenv.2022.160687}, pmid = {36473660}, issn = {1879-1026}, mesh = {*Ecosystem ; *Anthropogenic Effects ; Environmental Monitoring/methods ; Risk Assessment ; Water ; }, abstract = {Cumulative impacts increasingly threaten marine and coastal ecosystems. To address this issue, the research community has invested efforts on designing and testing different methodological approaches and tools that apply cumulative impact appraisal schemes for a sound evaluation of the complex interactions and dynamics among multiple pressures affecting marine and coastal ecosystems. Through an iterative scientometric and systematic literature review, this paper provides the state of the art of cumulative impact assessment approaches and applications. It gives a specific attention to cutting-edge approaches that explore and model inter-relations among climatic and anthropogenic pressures, vulnerability and resilience of marine and coastal ecosystems to these pressures, and the resulting changes in ecosystem services flow. Despite recent advances in computer sciences and the rising availability of big data for environmental monitoring and management, this literature review evidenced that the implementation of advanced complex system methods for cumulative risk assessment remains limited. Moreover, experts have only recently started integrating ecosystem services flow into cumulative impact appraisal frameworks, but more as a general assessment endpoint within the overall evaluation process (e.g. changes in the bundle of ecosystem services against cumulative impacts). The review also highlights a lack of integrated approaches and complex tools able to frame, explain, and model spatio-temporal dynamics of marine and coastal ecosystems' response to multiple pressures, as required under relevant EU legislation (e.g., Water Framework and Marine Strategy Framework Directives). Progress in understanding cumulative impacts, exploiting the functionalities of more sophisticated machine learning-based approaches (e.g., big data integration), will support decision-makers in the achievement of environmental and sustainability objectives.}, } @article {pmid36469956, year = {2023}, author = {Marcusson-Clavertz, D and Persson, SD and Davidson, P and Kim, J and Cardeña, E and Kuehner, C}, title = {Mind wandering and sleep in daily life: A combined actigraphy and experience sampling study.}, journal = {Consciousness and cognition}, volume = {107}, number = {}, pages = {103447}, doi = {10.1016/j.concog.2022.103447}, pmid = {36469956}, issn = {1090-2376}, mesh = {Humans ; *Ecological Momentary Assessment ; *Attention ; Actigraphy ; Sleep ; Self Report ; }, abstract = {Individuals who sleep poorly report spending more time mind wandering during the day. However, past research has relied on self-report measures of sleep or measured mind wandering during laboratory tasks, which prevents generalization to everyday contexts. We used ambulatory assessments to examine the relations between several features of sleep (duration, fragmentation, and disturbances) and mind wandering (task-unrelated, stimulus-independent, and unguided thoughts). Participants wore a wristband device that collected actigraphy and experience-sampling data across 7 days and 8 nights. Contrary to our expectations, task-unrelated and stimulus-independent thoughts were not associated with sleep either within- or between-persons (n = 164). Instead, individual differences in unguided thoughts were associated with sleep disturbances and duration, suggesting that individuals who more often experience unguided train-of-thoughts have greater sleep disturbances and sleep longer. These results highlight the need to consider the context and features of mind wandering when relating it to sleep.}, } @article {pmid36469554, year = {2022}, author = {Zhao, C and Goldman, M and Smith, BJ and Pollard, KS}, title = {Genotyping Microbial Communities with MIDAS2: From Metagenomic Reads to Allele Tables.}, journal = {Current protocols}, volume = {2}, number = {12}, pages = {e604}, pmid = {36469554}, issn = {2691-1299}, support = {R01 HL160862/HL/NHLBI NIH HHS/United States ; T32 GM067547/GM/NIGMS NIH HHS/United States ; }, mesh = {*Metagenome/genetics ; Genotype ; Alleles ; *Microbiota/genetics ; Nucleotides ; }, abstract = {The Metagenomic Intra-Species Diversity Analysis System 2 (MIDAS2) is a scalable pipeline that identifies single nucleotide variants and gene copy number variants in metagenomes using comprehensive reference databases built from public microbial genome collections (metagenotyping). MIDAS2 is the first metagenotyping tool with functionality to control metagenomic read mapping filters and to customize the reference database to the microbial community, features that improve the precision and recall of detected variants. In this article we present four basic protocols for the most common use cases of MIDAS2, along with supporting protocols for installation and use. In addition, we provide in-depth guidance on adjusting command line parameters, editing the reference database, optimizing hardware utilization, and understanding the metagenotyping results. All the steps of metagenotyping, from raw sequencing reads to population genetic analysis, are demonstrated with example data in two downloadable sequencing libraries of single-end metagenomic reads representing a mixture of multiple bacterial species. This set of protocols empowers users to accurately genotype hundreds of species in thousands of samples, providing rich genetic data for studying the evolution and strain-level ecology of microbial communities. © 2022 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Species prescreening Basic Protocol 2: Download MIDAS reference database Basic Protocol 3: Population single nucleotide variant calling Basic Protocol 4: Pan-genome copy number variant calling Support Protocol 1: Installing MIDAS2 Support Protocol 2: Command line inputs Support Protocol 3: Metagenotyping with a custom collection of genomes Support Protocol 4: Metagenotyping with advanced parameters.}, } @article {pmid36462728, year = {2023}, author = {Sosa, CC and Clavijo-Buriticá, DC and García-Merchán, VH and López-Rozo, N and Riccio-Rengifo, C and Diaz, MV and Londoño, DA and Quimbaya, MA}, title = {GOCompare: An R package to compare functional enrichment analysis between two species.}, journal = {Genomics}, volume = {115}, number = {1}, pages = {110528}, doi = {10.1016/j.ygeno.2022.110528}, pmid = {36462728}, issn = {1089-8646}, mesh = {*Aluminum ; Genomics/methods ; Computational Biology/methods ; Algorithms ; Gene Ontology ; *Arabidopsis/genetics ; }, abstract = {Functional enrichment analysis is a cornerstone in bioinformatics as it makes possible to identify functional information by using a gene list as source. Different tools are available to compare gene ontology (GO) terms, based on a directed acyclic graph structure or content-based algorithms which are time-consuming and require a priori information of GO terms. Nevertheless, quantitative procedures to compare GO terms among gene lists and species are not available. Here we present a computational procedure, implemented in R, to infer functional information derived from comparative strategies. GOCompare provides a framework for functional comparative genomics starting from comparable lists from GO terms. The program uses functional enrichment analysis (FEA) results and implement graph theory to identify statistically relevant GO terms for both, GO categories and analyzed species. Thus, GOCompare allows finding new functional information complementing current FEA approaches and extending their use to a comparative perspective. To test our approach GO terms were obtained for a list of aluminum tolerance-associated genes in Oryza sativa subsp. japonica and their orthologues in Arabidopsis thaliana. GOCompare was able to detect functional similarities for reactive oxygen species and ion binding capabilities which are common in plants as molecular mechanisms to tolerate aluminum toxicity. Consequently, the R package exhibited a good performance when implemented in complex datasets, allowing to establish hypothesis that might explain a biological process from a functional perspective, and narrowing down the possible landscapes to design wet lab experiments.}, } @article {pmid36458815, year = {2022}, author = {Yang, B and García-Carreras, B and Lessler, J and Read, JM and Zhu, H and Metcalf, CJE and Hay, JA and Kwok, KO and Shen, R and Jiang, CQ and Guan, Y and Riley, S and Cummings, DA}, title = {Long term intrinsic cycling in human life course antibody responses to influenza A(H3N2): an observational and modeling study.}, journal = {eLife}, volume = {11}, number = {}, pages = {}, pmid = {36458815}, issn = {2050-084X}, support = {MR/S004793/1/MRC_/Medical Research Council/United Kingdom ; R01 AI114703/AI/NIAID NIH HHS/United States ; R01 TW008246/TW/FIC NIH HHS/United States ; MR/J008761/1/MRC_/Medical Research Council/United Kingdom ; 200187/Z/15/Z/WT_/Wellcome Trust/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; MR/R015600/1/MRC_/Medical Research Council/United Kingdom ; R56 AG048075/AG/NIA NIH HHS/United States ; 200861/Z/16/Z/WT_/Wellcome Trust/United Kingdom ; MC_PC_19012/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Humans ; *Influenza, Human ; Influenza A Virus, H3N2 Subtype ; *Influenza Vaccines ; Antibody Formation ; Life Change Events ; Antibodies, Viral ; }, abstract = {BACKGROUND: Over a life course, human adaptive immunity to antigenically mutable pathogens exhibits competitive and facilitative interactions. We hypothesize that such interactions may lead to cyclic dynamics in immune responses over a lifetime.

METHODS: To investigate the cyclic behavior, we analyzed hemagglutination inhibition titers against 21 historical influenza A(H3N2) strains spanning 47 years from a cohort in Guangzhou, China, and applied Fourier spectrum analysis. To investigate possible biological mechanisms, we simulated individual antibody profiles encompassing known feedbacks and interactions due to generally recognized immunological mechanisms.

RESULTS: We demonstrated a long-term periodicity (about 24 years) in individual antibody responses. The reported cycles were robust to analytic and sampling approaches. Simulations suggested that individual-level cross-reaction between antigenically similar strains likely explains the reported cycle. We showed that the reported cycles are predictable at both individual and birth cohort level and that cohorts show a diversity of phases of these cycles. Phase of cycle was associated with the risk of seroconversion to circulating strains, after accounting for age and pre-existing titers of the circulating strains.

CONCLUSIONS: Our findings reveal the existence of long-term periodicities in individual antibody responses to A(H3N2). We hypothesize that these cycles are driven by preexisting antibody responses blunting responses to antigenically similar pathogens (by preventing infection and/or robust antibody responses upon infection), leading to reductions in antigen-specific responses over time until individual's increasing risk leads to an infection with an antigenically distant enough virus to generate a robust immune response. These findings could help disentangle cohort effects from individual-level exposure histories, improve our understanding of observed heterogeneous antibody responses to immunizations, and inform targeted vaccine strategy.

FUNDING: This study was supported by grants from the NIH R56AG048075 (DATC, JL), NIH R01AI114703 (DATC, BY), the Wellcome Trust 200861/Z/16/Z (SR), and 200187/Z/15/Z (SR). This work was also supported by research grants from Guangdong Government HZQB-KCZYZ-2021014 and 2019B121205009 (YG and HZ). DATC, JMR and SR acknowledge support from the National Institutes of Health Fogarty Institute (R01TW0008246). JMR acknowledges support from the Medical Research Council (MR/S004793/1) and the Engineering and Physical Sciences Research Council (EP/N014499/1). The funders had no role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript.}, } @article {pmid36456926, year = {2022}, author = {Li, Y and Wei, CM and Li, XY and Meng, DC and Gu, ZJ and Qu, SP and Huang, MJ and Huang, HQ}, title = {De novo transcriptome sequencing of Impatiens uliginosa and the analysis of candidate genes related to spur development.}, journal = {BMC plant biology}, volume = {22}, number = {1}, pages = {553}, pmid = {36456926}, issn = {1471-2229}, mesh = {*Impatiens ; Transcriptome ; Exome Sequencing ; Cell Cycle ; Databases, Protein ; }, abstract = {BACKGROUND: Spur, a structure capable of producing and storing nectar, not only plays a vital role in the pollination process but also promotes the rapid diversification of some plant lineages, which is considered a key innovation in plants. Spur is the focus of many studies, such as evolution and ecological hypothesis, but the current understanding of spur development is limited. High-throughput sequencing of Impatiens uliginosa was carried out to study the molecular mechanism of its spur development, which is believed to provide some insights into the spur development of Impatiens.

RESULTS: Transcriptomic sequencing and analysis were performed on spurs and limbs of I. uliginosa at three developmental stages. A total of 47.83 Gb of clean data were obtained, and 49,716 unigene genes were assembled. After comparison with NR, Swiss-Prot, Pfam, COG, GO and KEGG databases, a total of 27,686 genes were annotated successfully. Through comparative analysis, 19,356 differentially expressed genes were found and enriched into 208 GO terms and 146 KEGG pathways, among which plant hormone signal transduction was the most significantly enriched pathway. One thousand thirty-two transcription factors were identified, which belonged to 33 TF families such as MYB, bHLH and TCP. Twenty candidate genes that may be involved in spur development were screened and verified by qPCR, such as SBP, IAA and ABP.

CONCLUSIONS: Transcriptome data of different developmental stages of spurs were obtained, and a series of candidate genes related to spur development were identified. The importance of genes related to cell cycle, cell division, cell elongation and hormones in spur development was clarified. This study provided valuable information and resources for understanding the molecular mechanism of spur development in Impatiens.}, } @article {pmid36455989, year = {2022}, author = {Van Bortel, W and Mariën, J and Jacobs, BKM and Sinzinkayo, D and Sinarinzi, P and Lampaert, E and D'hondt, R and Mafuko, JM and De Weggheleire, A and Vogt, F and Alexander, N and Wint, W and Maes, P and Vanlerberghe, V and Leclair, C}, title = {Long-lasting insecticidal nets provide protection against malaria for only a single year in Burundi, an African highland setting with marked malaria seasonality.}, journal = {BMJ global health}, volume = {7}, number = {12}, pages = {}, pmid = {36455989}, issn = {2059-7908}, mesh = {Humans ; *Insecticides ; Burundi/epidemiology ; *Malaria/epidemiology/prevention & control ; *Health Information Systems ; Time Factors ; }, abstract = {BACKGROUND: Long-lasting insecticidal nets (LLINs) are one of the key interventions in the global fight against malaria. Since 2014, mass distribution campaigns of LLINs aim for universal access by all citizens of Burundi. In this context, we assess the impact of LLINs mass distribution campaigns on malaria incidence, focusing on the endemic highland health districts. We also explored the possible correlation between observed trends in malaria incidence with any variations in climate conditions.

METHODS: Malaria cases for 2011-2019 were obtained from the National Health Information System. We developed a generalised additive model based on a time series of routinely collected data with malaria incidence as the response variable and timing of LLIN distribution as an explanatory variable to investigate the duration and magnitude of the LLIN effect on malaria incidence. We added a seasonal and continuous-time component as further explanatory variables, and health district as a random effect to account for random natural variation in malaria cases between districts.

RESULTS: Malaria transmission in Burundian highlands was clearly seasonal and increased non-linearly over the study period. Further, a fast and steep decline of malaria incidence was noted during the first year after mass LLIN distribution (p<0.0001). In years 2 and 3 after distribution, malaria cases started to rise again to levels higher than before the control intervention.

CONCLUSION: This study highlights that LLINs did reduce the incidence in the first year after a mass distribution campaign, but in the context of Burundi, LLINs lost their impact after only 1 year.}, } @article {pmid36454025, year = {2023}, author = {Velasco, VME and Ferreira, A and Zaman, S and Noordermeer, D and Ensminger, I and Wegrzyn, JL}, title = {A long-read and short-read transcriptomics approach provides the first high-quality reference transcriptome and genome annotation for Pseudotsuga menziesii (Douglas-fir).}, journal = {G3 (Bethesda, Md.)}, volume = {13}, number = {2}, pages = {}, pmid = {36454025}, issn = {2160-1836}, mesh = {*Transcriptome ; *Pseudotsuga/genetics ; Gene Expression Profiling ; Molecular Sequence Annotation ; Base Sequence ; }, abstract = {Douglas-fir (Pseudotsuga menziesii) is native to western North America. It grows in a wide range of environmental conditions and is an important timber tree. Although there are several studies on the gene expression responses of Douglas-fir to abiotic cues, the absence of high-quality transcriptome and genome data is a barrier to further investigation. Like for most conifers, the available transcriptome and genome reference dataset for Douglas-fir remains fragmented and requires refinement. We aimed to generate a highly accurate, and complete reference transcriptome and genome annotation. We deep-sequenced the transcriptome of Douglas-fir needles from seedlings that were grown under nonstress control conditions or a combination of heat and drought stress conditions using long-read (LR) and short-read (SR) sequencing platforms. We used 2 computational approaches, namely de novo and genome-guided LR transcriptome assembly. Using the LR de novo assembly, we identified 1.3X more high-quality transcripts, 1.85X more "complete" genes, and 2.7X more functionally annotated genes compared to the genome-guided assembly approach. We predicted 666 long noncoding RNAs and 12,778 unique protein-coding transcripts including 2,016 putative transcription factors. We leveraged the LR de novo assembled transcriptome with paired-end SR and a published single-end SR transcriptome to generate an improved genome annotation. This was conducted with BRAKER2 and refined based on functional annotation, repetitive content, and transcriptome alignment. This high-quality genome annotation has 51,419 unique gene models derived from 322,631 initial predictions. Overall, our informatics approach provides a new reference Douglas-fir transcriptome assembly and genome annotation with considerably improved completeness and functional annotation.}, } @article {pmid36451580, year = {2023}, author = {Danneels, B and Blignaut, M and Marti, G and Sieber, S and Vandamme, P and Meyer, M and Carlier, A}, title = {Cyclitol metabolism is a central feature of Burkholderia leaf symbionts.}, journal = {Environmental microbiology}, volume = {25}, number = {2}, pages = {454-472}, doi = {10.1111/1462-2920.16292}, pmid = {36451580}, issn = {1462-2920}, support = {203141/Z/16/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Humans ; *Cyclitols ; *Burkholderia/genetics ; Symbiosis/genetics ; Endophytes/genetics ; Plants/microbiology ; Plant Leaves/microbiology ; Phylogeny ; }, abstract = {The symbioses between plants of the Rubiaceae and Primulaceae families with Burkholderia bacteria represent unique and intimate plant-bacterial relationships. Many of these interactions have been identified through PCR-dependent typing methods, but there is little information available about their functional and ecological roles. We assembled 17 new endophyte genomes representing endophytes from 13 plant species, including those of two previously unknown associations. Genomes of leaf endophytes belonging to Burkholderia s.l. show extensive signs of genome reduction, albeit to varying degrees. Except for one endophyte, none of the bacterial symbionts could be isolated on standard microbiological media. Despite their taxonomic diversity, all endophyte genomes contained gene clusters linked to the production of specialized metabolites, including genes linked to cyclitol sugar analog metabolism and in one instance non-ribosomal peptide synthesis. These genes and gene clusters are unique within Burkholderia s.l. and are likely horizontally acquired. We propose that the acquisition of secondary metabolite gene clusters through horizontal gene transfer is a prerequisite for the evolution of a stable association between these endophytes and their hosts.}, } @article {pmid36449461, year = {2022}, author = {van der Feltz-Cornelis, CM and Sweetman, J and Allsopp, G and Attree, E and Crooks, MG and Cuthbertson, DJ and Forshaw, D and Gabbay, M and Green, A and Heightman, M and Hillman, T and Hishmeh, L and Khunti, K and Lip, GYH and Lorgelly, P and Montgomery, H and Strain, WD and Wall, E and Watkins, C and Williams, N and Wootton, DG and Banerjee, A and , }, title = {STIMULATE-ICP-Delphi (Symptoms, Trajectory, Inequalities and Management: Understanding Long-COVID to Address and Transform Existing Integrated Care Pathways Delphi): Study protocol.}, journal = {PloS one}, volume = {17}, number = {11}, pages = {e0277936}, pmid = {36449461}, issn = {1932-6203}, mesh = {Humans ; *COVID-19/epidemiology ; Critical Pathways ; Mental Health ; *Delivery of Health Care, Integrated ; Post-Acute COVID-19 Syndrome ; }, abstract = {INTRODUCTION: As mortality rates from COVID-19 disease fall, the high prevalence of long-term sequelae (Long COVID) is becoming increasingly widespread, challenging healthcare systems globally. Traditional pathways of care for Long Term Conditions (LTCs) have tended to be managed by disease-specific specialties, an approach that has been ineffective in delivering care for patients with multi-morbidity. The multi-system nature of Long COVID and its impact on physical and psychological health demands a more effective model of holistic, integrated care. The evolution of integrated care systems (ICSs) in the UK presents an important opportunity to explore areas of mutual benefit to LTC, multi-morbidity and Long COVID care. There may be benefits in comparing and contrasting ICPs for Long COVID with ICPs for other LTCs.

METHODS AND ANALYSIS: This study aims to evaluate health services requirements for ICPs for Long COVID and their applicability to other LTCs including multi-morbidity and the overlap with medically not yet explained symptoms (MNYES). The study will follow a Delphi design and involve an expert panel of stakeholders including people with lived experience, as well as clinicians with expertise in Long COVID and other LTCs. Study processes will include expert panel and moderator panel meetings, surveys, and interviews. The Delphi process is part of the overall STIMULATE-ICP programme, aimed at improving integrated care for people with Long COVID.

ETHICS AND DISSEMINATION: Ethical approval for this Delphi study has been obtained (Research Governance Board of the University of York) as have approvals for the other STIMULATE-ICP studies. Study outcomes are likely to inform policy for ICPs across LTCs. Results will be disseminated through scientific publication, conference presentation and communications with patients and stakeholders involved in care of other LTCs and Long COVID.

REGISTRATION: Researchregistry: https://www.researchregistry.com/browse-the-registry#home/registrationdetails/6246bfeeeaaed6001f08dadc/.}, } @article {pmid36447758, year = {2022}, author = {Boyes, D and Holland, PWH and , and , and , and , and , and , }, title = {The genome sequence of the square-spot rustic, Xestia xanthographa (Schiffermuller, 1775).}, journal = {Wellcome open research}, volume = {7}, number = {}, pages = {37}, pmid = {36447758}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual male Xestia xanthographa (the square-spot rustic; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 934 megabases in span. The majority of the assembly (99.94%) is scaffolded into 31 chromosomal pseudomolecules, with the Z sex chromosome assembled.}, } @article {pmid36437091, year = {2022}, author = {Zhang, KK and He, J and Zhong, YX and Wei, QQ and Chen, F}, title = {[Identification of Soil Heavy Metal Sources Around a Copper-silver Mining Area in Ningxia Based on GIS].}, journal = {Huan jing ke xue= Huanjing kexue}, volume = {43}, number = {11}, pages = {5192-5204}, doi = {10.13227/j.hjkx.202201113}, pmid = {36437091}, issn = {0250-3301}, mesh = {Humans ; Soil ; Copper ; Silver ; *Soil Pollutants/analysis ; Geographic Information Systems ; Cadmium/analysis ; Lead/analysis ; Environmental Monitoring/methods ; *Metals, Heavy/analysis ; *Mercury/analysis ; }, abstract = {This study area was based on the catchment area of the Yaoxianzi ditch located in the arid region of western China. A total of 194 topsoil samples of 0-20 cm depth were collected using the mesh distribution method. The contents of nine heavy metals (Ni, Cu, Zn, As, Ag, Cr, Cd, Hg, and Pb) were determined using ICP-MS. The source and spatial distribution of heavy metals were analyzed using PMF and IDW. Spatial autocorrelation and clustering and outlier analysis were performed using the Spatial Statistical Analysis tool of ArcGIS. The main sources and distribution areas of heavy metals in the soil were obtained through comprehensive analysis. In the study area, the average values of Hg, Ag, Cd, and Pb were 20.48, 3.13, 2.23, and 1.12 times the background values, and the maximum values of Cd, Cu, Pb, and As were 10.92, 5.52, 2.03, and 1.39 times the filter values, respectively. The coefficients of variation of Cu, Cd, Pb, and Hg were ordered as Cu(283.23%)>Cd(224.77%)>Pb(144.40%)>Hg(67.12%) and were closely affected by human activities. The heavy metals in the soil around mining areas came from four main sources:natural parent material (32%), the mixed source of mining activities and transportation (17.1%), the mixed source of industrial activities and atmospheric sedimentation (40.3%), and the mixed source of agricultural activity and putting sandy gravel in farmland (10.6%). Cr and Ni, As and Cu, Hg, and Cd could represent these four sources of heavy metal pollution, respectively. The main sources of soil heavy metal pollution were mining activities and agricultural activities. The heavily contaminated areas were distributed in the mining areas in the south of the study area and in the planting areas in the eastern, central, and northwestern parts of the study area.}, } @article {pmid36435969, year = {2023}, author = {Kafkas, S and Ma, X and Zhang, X and Topçu, H and Navajas-Pérez, R and Wai, CM and Tang, H and Xu, X and Khodaeiaminjan, M and Güney, M and Paizila, A and Karcı, H and Zhang, X and Lin, J and Lin, H and Herrán, R and Rejón, CR and García-Zea, JA and Robles, F and Muñoz, CDV and Hotz-Wagenblatt, A and Min, XJ and Özkan, H and Motalebipour, EZ and Gozel, H and Çoban, N and Kafkas, NE and Kilian, A and Huang, H and Lv, X and Liu, K and Hu, Q and Jacygrad, E and Palmer, W and Michelmore, R and Ming, R}, title = {Pistachio genomes provide insights into nut tree domestication and ZW sex chromosome evolution.}, journal = {Plant communications}, volume = {4}, number = {3}, pages = {100497}, pmid = {36435969}, issn = {2590-3462}, mesh = {*Pistacia/genetics ; Trees/genetics ; Nuts ; Domestication ; Sex Chromosomes/genetics ; }, abstract = {Pistachio is a nut crop domesticated in the Fertile Crescent and a dioecious species with ZW sex chromosomes. We sequenced the genomes of Pistacia vera cultivar (cv.) Siirt, the female parent, and P. vera cv. Bagyolu, the male parent. Two chromosome-level reference genomes of pistachio were generated, and Z and W chromosomes were assembled. The ZW chromosomes originated from an autosome following the first inversion, which occurred approximately 8.18 Mya. Three inversion events in the W chromosome led to the formation of a 12.7-Mb (22.8% of the W chromosome) non-recombining region. These W-specific sequences contain several genes of interest that may have played a pivotal role in sex determination and contributed to the initiation and evolution of a ZW sex chromosome system in pistachio. The W-specific genes, including defA, defA-like, DYT1, two PTEN1, and two tandem duplications of six VPS13A paralogs, are strong candidates for sex determination or differentiation. Demographic history analysis of resequenced genomes suggest that cultivated pistachio underwent severe domestication bottlenecks approximately 7640 years ago, dating the domestication event close to the archeological record of pistachio domestication in Iran. We identified 390, 211, and 290 potential selective sweeps in 3 cultivar subgroups that underlie agronomic traits such as nut development and quality, grafting success, flowering time shift, and drought tolerance. These findings have improved our understanding of the genomic basis of sex determination/differentiation and horticulturally important traits and will accelerate the improvement of pistachio cultivars and rootstocks.}, } @article {pmid36429843, year = {2022}, author = {Zhang, T and Wang, B and Ge, Y and Li, C}, title = {Research on Green Space Service Space Based on Crowd Aggregation and Activity Characteristics under Big Data-Take Tacheng City as an Example.}, journal = {International journal of environmental research and public health}, volume = {19}, number = {22}, pages = {}, pmid = {36429843}, issn = {1660-4601}, mesh = {Humans ; *Parks, Recreational ; *Big Data ; Cities ; Personal Satisfaction ; }, abstract = {People-oriented planning has become the mainstream of urban space design. As an important research object of urban space, the accessibility and service level of accessibility and service level of green space as important indicators to evaluate the level of urban livability cannot be truly fed back to people's daily life. Therefore, based on big data and from the perspective of crowd activities and aggregation characteristics, this study analyzes the shortage of green space service space in Tacheng City and puts forward suggestions for improvement. The main conclusions are as follows: (1) The satisfaction of green space based on service scope covers up the imbalance of green space resources enjoyed by actual crowd activities and aggregation. (2) Although the accessibility of green space obtained by population density meets the needs in space, it cannot take care of the potential needs generated by daily crowd activities and aggregation, which leads to the overall spatial imbalance of accessibility. (3) The comprehensive analysis shows that the northeast and southwest regions are the focus of the later planning and construction. The southwest region echoes with the old urban area and attracts people's daily activities. The woodland in the northeast region, as the main green space supply, meets the potential needs of the daily population activities and aggregation of the new development urban area and the old urban area, and also serves as a place for rest and entertainment to meet the needs of the activities and aggregation of the accidental behavior of the people in the new and old urban areas after the opening up.}, } @article {pmid36421254, year = {2022}, author = {Würstle, S and Hapfelmeier, A and Karapetyan, S and Studen, F and Isaakidou, A and Schneider, T and Schmid, RM and von Delius, S and Gundling, F and Triebelhorn, J and Burgkart, R and Obermeier, A and Mayr, U and Heller, S and Rasch, S and Lahmer, T and Geisler, F and Chan, B and Turner, PE and Rothe, K and Spinner, CD and Schneider, J}, title = {A Novel Machine Learning-Based Point-Score Model as a Non-Invasive Decision-Making Tool for Identifying Infected Ascites in Patients with Hydropic Decompensated Liver Cirrhosis: A Retrospective Multicentre Study.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {11}, number = {11}, pages = {}, pmid = {36421254}, issn = {2079-6382}, support = {UL1 TR001863/TR/NCATS NIH HHS/United States ; }, abstract = {This study is aimed at assessing the distinctive features of patients with infected ascites and liver cirrhosis and developing a scoring system to allow for the accurate identification of patients not requiring abdominocentesis to rule out infected ascites. A total of 700 episodes of patients with decompensated liver cirrhosis undergoing abdominocentesis between 2006 and 2020 were included. Overall, 34 clinical, drug, and laboratory features were evaluated using machine learning to identify key differentiation criteria and integrate them into a point-score model. In total, 11 discriminatory features were selected using a Lasso regression model to establish a point-score model. Considering pre-test probabilities for infected ascites of 10%, 15%, and 25%, the negative and positive predictive values of the point-score model for infected ascites were 98.1%, 97.0%, 94.6% and 14.9%, 21.8%, and 34.5%, respectively. Besides the main model, a simplified model was generated, containing only features that are fast to collect, which revealed similar predictive values. Our point-score model appears to be a promising non-invasive approach to rule out infected ascites in clinical routine with high negative predictive values in patients with hydropic decompensated liver cirrhosis, but further external validation in a prospective study is needed.}, } @article {pmid36419146, year = {2022}, author = {Atkins, S and Heimo, L and Carter, DJ and Ribas Closa, M and Vanleeuw, L and Chenciner, L and Wambi, P and Sidney-Annerstedt, K and Egere, U and Verkuijl, S and Brands, A and Masini, T and Viney, K and Wingfield, T and Lönnroth, K and Boccia, D}, title = {The socioeconomic impact of tuberculosis on children and adolescents: a scoping review and conceptual framework.}, journal = {BMC public health}, volume = {22}, number = {1}, pages = {2153}, pmid = {36419146}, issn = {1471-2458}, support = {001/WHO_/World Health Organization/International ; MR/V004832/1/MRC_/Medical Research Council/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; }, mesh = {Child ; Humans ; Adolescent ; *Tuberculosis/epidemiology ; Social Stigma ; Databases, Factual ; Educational Status ; Knowledge ; }, abstract = {BACKGROUND: Tuberculosis (TB) has been repeatedly shown to have socioeconomic impacts in both individual-level and ecological studies; however, much less is known about this effect among children and adolescents and the extent to which being affected by TB during childhood and adolescence can have life-course implications. This paper describes the results of the development of a conceptual framework and scoping review to review the evidence on the short- and long-term socioeconomic impact of tuberculosis on children and adolescents.

OBJECTIVES: To increase knowledge of the socioeconomic impact of TB on children and adolescents.

METHODS: We developed a conceptual framework of the socioeconomic impact of TB on children and adolescents, and used scoping review methods to search for evidence supporting or disproving it. We searched four academic databases from 1 January 1990 to 6 April 2021 and conducted targeted searches of grey literature. We extracted data using a standard form and analysed data thematically.

RESULTS: Thirty-six studies (29 qualitative, five quantitative and two mixed methods studies) were included in the review. Overall, the evidence supported the conceptual framework, suggesting a severe socioeconomic impact of TB on children and adolescents through all the postulated pathways. Effects ranged from impoverishment, stigma, and family separation, to effects on nutrition and missed education opportunities. TB did not seem to exert a different socioeconomic impact when directly or indirectly affecting children/adolescents, suggesting that TB can affect this group even when they are not affected by the disease. No study provided sufficient follow-up to observe the long-term socioeconomic effect of TB in this age group.

CONCLUSION: The evidence gathered in this review reinforces our understanding of the impact of TB on children and adolescents and highlights the importance of considering effects during the entire life course. Both ad-hoc and sustainable social protection measures and strategies are essential to mitigate the socioeconomic consequences of TB among children and adolescents.}, } @article {pmid36418825, year = {2023}, author = {Debnath, J and Sahariah, D and Lahon, D and Nath, N and Chand, K and Meraj, G and Farooq, M and Kumar, P and Kanga, S and Singh, SK}, title = {Geospatial modeling to assess the past and future land use-land cover changes in the Brahmaputra Valley, NE India, for sustainable land resource management.}, journal = {Environmental science and pollution research international}, volume = {30}, number = {49}, pages = {106997-107020}, pmid = {36418825}, issn = {1614-7499}, mesh = {*Environmental Monitoring ; *Geographic Information Systems ; Remote Sensing Technology ; Agriculture ; India ; Water ; Conservation of Natural Resources ; }, abstract = {Satellite remote sensing and geographic information system (GIS) have revolutionalized the mapping, quantifying, and assessing the land surface processes, particularly analyzing the past and future land use-land cover (LULC) change patterns. Worldwide river basins have observed enormous changes in the land system dynamics as a result of anthropogenic factors such as population, urbanization, development, and agriculture. As is the scenario of various other river basins, the Brahmaputra basin, which falls in China, Bhutan, India, and Bangladesh, is also witnessing the same environmental issues. The present study has been conducted on the Brahmaputra Valley in Assam, India (a sub-basin of the larger Brahmaputra basin) and assessed its LULC changes using a maximum likelihood classification algorithm. The study also simulated the changing LULC pattern for the years 2030, 2040, and 2050 using the GIS-based cellular automata Markov model (CA-Markov) to understand the implications of the ongoing trends in the LULC change for future land system dynamics. The current rate of change of the LULC in the region was assessed using the 48 years of earth observation satellite data from 1973 to 2021. It was observed that from 1973 to 2021, the area under vegetation cover and water body decreased by 19.48 and 47.13%, respectively. In contrast, cultivated land, barren land, and built-up area increased by 7.60, 20.28, and 384.99%, respectively. It was found that the area covered by vegetation and water body has largely been transitioned to cultivated land and built-up classes. The research predicted that, by the end of 2050, the area covered by vegetation, cultivated land, and water would remain at 39.75, 32.31, and 4.91%, respectively, while the area covered by built-up areas will increase by up to 18.09%. Using the kappa index (ki) as an accuracy indicator of the simulated future LULCs, the predicted LULC of 2021 was validated against the observed LULC of 2021, and the very high ki observed validated the generated simulation LULC products. The research concludes that significant LULC changes are taking place in the study area with a decrease in vegetation cover and water body and an increase of area under built-up. Such trends will continue in the future and shall have disastrous environmental consequences unless necessary land resource management strategies are not implemented. The main factors responsible for the changing dynamics of LULC in the study area are urbanization, population growth, climate change, river bank erosion and sedimentation, and intensive agriculture. This study is aimed at providing the policy and decision-makers of the region with the necessary what-if scenarios for better decision-making. It shall also be useful in other countries of the Brahmaputra basin for transboundary integrated river basin management of the whole region.}, } @article {pmid36418120, year = {2022}, author = {Kumpik, DP and Santos-Rodriguez, R and Selwood, J and Coulthard, E and Twomey, N and Craddock, I and Ben-Shlomo, Y}, title = {A longitudinal observational study of home-based conversations for detecting early dementia: protocol for the CUBOId TV task.}, journal = {BMJ open}, volume = {12}, number = {11}, pages = {e065033}, pmid = {36418120}, issn = {2044-6055}, support = {MC_PC_16029/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Humans ; Pregnancy ; Female ; *Cognitive Dysfunction/diagnosis/psychology ; Neuropsychological Tests ; Longitudinal Studies ; Biomarkers ; *Dementia/diagnosis/psychology ; Observational Studies as Topic ; }, abstract = {INTRODUCTION: Limitations in effective dementia therapies mean that early diagnosis and monitoring are critical for disease management, but current clinical tools are impractical and/or unreliable, and disregard short-term symptom variability. Behavioural biomarkers of cognitive decline, such as speech, sleep and activity patterns, can manifest prodromal pathological changes. They can be continuously measured at home with smart sensing technologies, and permit leveraging of interpersonal interactions for optimising diagnostic and prognostic performance. Here we describe the ContinUous behavioural Biomarkers Of cognitive Impairment (CUBOId) study, which explores the feasibility of multimodal data fusion for in-home monitoring of mild cognitive impairment (MCI) and early Alzheimer's disease (AD). The report focuses on a subset of CUBOId participants who perform a novel speech task, the 'TV task', designed to track changes in ecologically valid conversations with disease progression.

METHODS AND ANALYSIS: CUBOId is a longitudinal observational study. Participants have diagnoses of MCI or AD, and controls are their live-in partners with no such diagnosis. Multimodal activity data were passively acquired from wearables and in-home fixed sensors over timespans of 8-25 months. At two time points participants completed the TV task over 5 days by recording audio of their conversations as they watched a favourite TV programme, with further testing to be completed after removal of the sensor installations. Behavioural testing is supported by neuropsychological assessment for deriving ground truths on cognitive status. Deep learning will be used to generate fused multimodal activity-speech embeddings for optimisation of diagnostic and predictive performance from speech alone.

ETHICS AND DISSEMINATION: CUBOId was approved by an NHS Research Ethics Committee (Wales REC; ref: 18/WA/0158) and is sponsored by University of Bristol. It is supported by the National Institute for Health Research Clinical Research Network West of England. Results will be reported at conferences and in peer-reviewed scientific journals.}, } @article {pmid36416261, year = {2023}, author = {Guo, S and Xu, Z and Dong, X and Hu, D and Jiang, Y and Wang, Q and Zhang, J and Zhou, Q and Liu, S and Song, W}, title = {GPSAdb: a comprehensive web resource for interactive exploration of genetic perturbation RNA-seq datasets.}, journal = {Nucleic acids research}, volume = {51}, number = {D1}, pages = {D964-D968}, pmid = {36416261}, issn = {1362-4962}, support = {I01 HX000551/HX/HSRD VA/United States ; }, mesh = {Humans ; RNA-Seq/methods ; Cell Line ; *Databases, Genetic ; *Software ; }, abstract = {Gene knock-out/down methods are commonly used to explore the functions of genes of interest, but a database that systematically collects perturbed data is not available currently. Manual curation of all the available human cell line perturbed RNA-seq datasets enabled us to develop a comprehensive human perturbation database (GPSAdb, https://www.gpsadb.com/). The current version of GPSAdb collected 3048 RNA-seq datasets associated with 1458 genes, which were knocked out/down by siRNA, shRNA, CRISPR/Cas9, or CRISPRi. The database provides full exploration of these datasets and generated 6096 new perturbed gene sets (up and down separately). GPSAdb integrated the gene sets and developed an online tool, genetic perturbation similarity analysis (GPSA), to identify candidate causal perturbations from differential gene expression data. In summary, GPSAdb is a powerful platform that aims to assist life science researchers to easily access and analyze public perturbed data and explore differential gene expression data in depth.}, } @article {pmid36414269, year = {2022}, author = {Nguyen, PY and Kanukula, R and McKenzie, JE and Alqaidoom, Z and Brennan, SE and Haddaway, NR and Hamilton, DG and Karunananthan, S and McDonald, S and Moher, D and Nakagawa, S and Nunan, D and Tugwell, P and Welch, VA and Page, MJ}, title = {Changing patterns in reporting and sharing of review data in systematic reviews with meta-analysis of the effects of interventions: cross sectional meta-research study.}, journal = {BMJ (Clinical research ed.)}, volume = {379}, number = {}, pages = {e072428}, pmid = {36414269}, issn = {1756-1833}, mesh = {Humans ; Cross-Sectional Studies ; PubMed ; *Research Design ; Systematic Reviews as Topic ; *Information Dissemination ; }, abstract = {OBJECTIVES: To examine changes in completeness of reporting and frequency of sharing data, analytical code, and other review materials in systematic reviews over time; and factors associated with these changes.

DESIGN: Cross sectional meta-research study.

POPULATION: Random sample of 300 systematic reviews with meta-analysis of aggregate data on the effects of a health, social, behavioural, or educational intervention. Reviews were indexed in PubMed, Science Citation Index, Social Sciences Citation Index, Scopus, and Education Collection in November 2020.

MAIN OUTCOME MEASURES: The extent of complete reporting and the frequency of sharing review materials in the systematic reviews indexed in 2020 were compared with 110 systematic reviews indexed in February 2014. Associations between completeness of reporting and various factors (eg, self-reported use of reporting guidelines, journal policies on data sharing) were examined by calculating risk ratios and 95% confidence intervals.

RESULTS: Several items were reported suboptimally among 300 systematic reviews from 2020, such as a registration record for the review (n=113; 38%), a full search strategy for at least one database (n=214; 71%), methods used to assess risk of bias (n=185; 62%), methods used to prepare data for meta-analysis (n=101; 34%), and source of funding for the review (n=215; 72%). Only a few items not already reported at a high frequency in 2014 were reported more frequently in 2020. No evidence indicated that reviews using a reporting guideline were more completely reported than reviews not using a guideline. Reviews published in 2020 in journals that mandated either data sharing or inclusion of data availability statements were more likely to share their review materials (eg, data, code files) than reviews in journals without such mandates (16/87 (18%) v 4/213 (2%)).

CONCLUSION: Incomplete reporting of several recommended items for systematic reviews persists, even in reviews that claim to have followed a reporting guideline. Journal policies on data sharing might encourage sharing of review materials.}, } @article {pmid36412269, year = {2022}, author = {Ebenezer, TE and Low, RS and O'Neill, EC and Huang, I and DeSimone, A and Farrow, SC and Field, RA and Ginger, ML and Guerrero, SA and Hammond, M and Hampl, V and Horst, G and Ishikawa, T and Karnkowska, A and Linton, EW and Myler, P and Nakazawa, M and Cardol, P and Sánchez-Thomas, R and Saville, BJ and Shah, MR and Simpson, AGB and Sur, A and Suzuki, K and Tyler, KM and Zimba, PV and Hall, N and Field, MC}, title = {Euglena International Network (EIN): Driving euglenoid biotechnology for the benefit of a challenged world.}, journal = {Biology open}, volume = {11}, number = {11}, pages = {}, pmid = {36412269}, issn = {2046-6390}, support = {BBS/E/J/000C0618/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/J/000PR9790/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {*Euglena/physiology ; Biotechnology ; Symbiosis ; }, abstract = {Euglenoids (Euglenida) are unicellular flagellates possessing exceptionally wide geographical and ecological distribution. Euglenoids combine a biotechnological potential with a unique position in the eukaryotic tree of life. In large part these microbes owe this success to diverse genetics including secondary endosymbiosis and likely additional sources of genes. Multiple euglenoid species have translational applications and show great promise in production of biofuels, nutraceuticals, bioremediation, cancer treatments and more exotically as robotics design simulators. An absence of reference genomes currently limits these applications, including development of efficient tools for identification of critical factors in regulation, growth or optimization of metabolic pathways. The Euglena International Network (EIN) seeks to provide a forum to overcome these challenges. EIN has agreed specific goals, mobilized scientists, established a clear roadmap (Grand Challenges), connected academic and industry stakeholders and is currently formulating policy and partnership principles to propel these efforts in a coordinated and efficient manner.}, } @article {pmid36408293, year = {2022}, author = {Ebdon, S and Bisschop, G and Lohse, K and Saccheri, I and Davies, J and , and , and , and , }, title = {The genome sequence of the orange-tip butterfly, Anthocharis cardamines (Linnaeus, 1758).}, journal = {Wellcome open research}, volume = {7}, number = {}, pages = {260}, pmid = {36408293}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual female Anthocharis cardamines (the orange-tip; Arthropoda; Insecta; Lepidoptera; Pieridae). The genome sequence is 360 megabases in span. The majority (99.74%) of the assembly is scaffolded into 31 chromosomal pseudomolecules, with the W and Z sex chromosomes assembled. Gene annotation of this assembly on Ensembl has identified 12,477 protein coding genes.}, } @article {pmid36407110, year = {2022}, author = {Michel, L and Palma, K and Cerda, M and Lagadec, R and Mayeur, H and Fuentès, M and Besseau, L and Martin, P and Magnanou, E and Blader, P and Concha, ML and Mazan, S}, title = {Diversification of habenular organization and asymmetries in teleosts: Insights from the Atlantic salmon and European eel.}, journal = {Frontiers in cell and developmental biology}, volume = {10}, number = {}, pages = {1015074}, pmid = {36407110}, issn = {2296-634X}, abstract = {Habenulae asymmetries are widespread across vertebrates and analyses in zebrafish, the reference model organism for this process, have provided insight into their molecular nature, their mechanisms of formation and their important roles in the integration of environmental and internal cues with a variety of organismal adaptive responses. However, the generality of the characteristics identified in this species remains an open question, even on a relatively short evolutionary scale, in teleosts. To address this question, we have characterized the broad organization of habenulae in the Atlantic salmon and quantified the asymmetries in each of the identified subdomains. Our results show that a highly conserved partitioning into a dorsal and a ventral component is retained in the Atlantic salmon and that asymmetries are mainly observed in the former as in zebrafish. A remarkable difference is that a prominent left-restricted pax6 positive nucleus is observed in the Atlantic salmon, but undetectable in zebrafish. This nucleus is not observed outside teleosts, and harbors a complex presence/absence pattern in this group, retaining its location and cytoarchitectonic organization in an elopomorph, the European eel. These findings suggest an ancient origin and high evolvability of this trait in the taxon. Taken together, our data raise novel questions about the variability of asymmetries across teleosts and their biological significance depending on ecological contexts.}, } @article {pmid36405737, year = {2022}, author = {Yousaf, M and Ismail, S and Ullah, A and Bibi, S}, title = {Immuno-informatics profiling of monkeypox virus cell surface binding protein for designing a next generation multi-valent peptide-based vaccine.}, journal = {Frontiers in immunology}, volume = {13}, number = {}, pages = {1035924}, pmid = {36405737}, issn = {1664-3224}, mesh = {Humans ; *Monkeypox virus ; Molecular Docking Simulation ; Membrane Proteins ; *Mpox (monkeypox) ; Vaccines, Subunit ; Epitopes, T-Lymphocyte ; }, abstract = {Monkeypox is a viral etiological agent with hallmarks analogous to those observed in smallpox cases in the past. The ongoing outbreak of Monkeypox viral infection is becoming a global health problem. Multi-valent peptide based next generation vaccines provides us a promising solution to combat these emerging infectious diseases by eliciting cell-mediated and humoral immune response. Considering the success rate of subtractive proteomics pipeline and reverse vaccinology approach, in this study, we have developed a novel, next-generation, multi-valent, in silico peptide based vaccine construct by employing cell surface binding protein. After analyzing physiochemical and biological properties of the selected target, the protein was subjected to B cell derived T cell epitope mapping. Iterative scrutinization lead to the identification of two highly antigenic, virulent, non-allergic, non-toxic, water soluble, and Interferon-gamma inducer epitopes i.e. HYITENYRN and TTSPVRENY. We estimated that the shortlisted epitopes for vaccine construction, roughly correspond to 99.74% of the world's population. UK, Finland and Sweden had the highest overall population coverage at 100% which is followed by Austria (99.99%), Germany (99.99%), France (99.98%), Poland (99.96), Croatia (99.93), Czech Republic (99.87%), Belgium (99.87), Italy (99.86%), China (97.83%), India (97.35%) and Pakistan (97.13%). The designed vaccine construct comprises of 150 amino acids with a molecular weight of 16.97242 kDa. Molecular docking studies of the modelled MEMPV (Multi-epitope Monkeypox Vaccine) with MHC I (PDB ID: 1I1Y), MHC II (PDB ID: 1KG0), and other immune mediators i.e. toll like receptors TLR3 (PDB ID: 2A0Z), and TLR4 (PDB ID: 4G8A) revealed strong binding affinity with immune receptors. Host immune simulation results predicted that the designed vaccine has strong potency to induce immune responses against target pathogen in the form of cellular and antibody-dependent immunity. Our findings suggest that the hypothesized vaccine candidate can be utilized as a potential therapeutic against Monkeypox however experimental study is required to validate the results and safe immunogenicity.}, } @article {pmid36400569, year = {2023}, author = {Wu, L and Yan, B and Han, J and Li, R and Xiao, J and He, S and Bo, X}, title = {TOXRIC: a comprehensive database of toxicological data and benchmarks.}, journal = {Nucleic acids research}, volume = {51}, number = {D1}, pages = {D1432-D1445}, pmid = {36400569}, issn = {1362-4962}, mesh = {Humans ; Benchmarking ; *Databases, Factual ; *Toxicology/methods ; Software ; }, abstract = {The toxic effects of compounds on environment, humans, and other organisms have been a major focus of many research areas, including drug discovery and ecological research. Identifying the potential toxicity in the early stage of compound/drug discovery is critical. The rapid development of computational methods for evaluating various toxicity categories has increased the need for comprehensive and system-level collection of toxicological data, associated attributes, and benchmarks. To contribute toward this goal, we proposed TOXRIC (https://toxric.bioinforai.tech/), a database with comprehensive toxicological data, standardized attribute data, practical benchmarks, informative visualization of molecular representations, and an intuitive function interface. The data stored in TOXRIC contains 113 372 compounds, 13 toxicity categories, 1474 toxicity endpoints covering in vivo/in vitro endpoints and 39 feature types, covering structural, target, transcriptome, metabolic data, and other descriptors. All the curated datasets of endpoints and features can be retrieved, downloaded and directly used as output or input to Machine Learning (ML)-based prediction models. In addition to serving as a data repository, TOXRIC also provides visualization of benchmarks and molecular representations for all endpoint datasets. Based on these results, researchers can better understand and select optimal feature types, molecular representations, and baseline algorithms for each endpoint prediction task. We believe that the rich information on compound toxicology, ML-ready datasets, benchmarks and molecular representation distribution can greatly facilitate toxicological investigations, interpretation of toxicological mechanisms, compound/drug discovery and the development of computational methods.}, } @article {pmid36399502, year = {2023}, author = {Camargo, AP and Nayfach, S and Chen, IA and Palaniappan, K and Ratner, A and Chu, K and Ritter, SJ and Reddy, TBK and Mukherjee, S and Schulz, F and Call, L and Neches, RY and Woyke, T and Ivanova, NN and Eloe-Fadrosh, EA and Kyrpides, NC and Roux, S}, title = {IMG/VR v4: an expanded database of uncultivated virus genomes within a framework of extensive functional, taxonomic, and ecological metadata.}, journal = {Nucleic acids research}, volume = {51}, number = {D1}, pages = {D733-D743}, pmid = {36399502}, issn = {1362-4962}, mesh = {*Databases, Genetic ; *Genome, Viral ; Metadata ; Metagenomics ; Software ; }, abstract = {Viruses are widely recognized as critical members of all microbiomes. Metagenomics enables large-scale exploration of the global virosphere, progressively revealing the extensive genomic diversity of viruses on Earth and highlighting the myriad of ways by which viruses impact biological processes. IMG/VR provides access to the largest collection of viral sequences obtained from (meta)genomes, along with functional annotation and rich metadata. A web interface enables users to efficiently browse and search viruses based on genome features and/or sequence similarity. Here, we present the fourth version of IMG/VR, composed of >15 million virus genomes and genome fragments, a ≈6-fold increase in size compared to the previous version. These clustered into 8.7 million viral operational taxonomic units, including 231 408 with at least one high-quality representative. Viral sequences in IMG/VR are now systematically identified from genomes, metagenomes, and metatranscriptomes using a new detection approach (geNomad), and IMG standard annotation are complemented with genome quality estimation using CheckV, taxonomic classification reflecting the latest taxonomic standards, and microbial host taxonomy prediction. IMG/VR v4 is available at https://img.jgi.doe.gov/vr, and the underlying data are available to download at https://genome.jgi.doe.gov/portal/IMG_VR.}, } @article {pmid36399496, year = {2023}, author = {Terlouw, BR and Blin, K and Navarro-Muñoz, JC and Avalon, NE and Chevrette, MG and Egbert, S and Lee, S and Meijer, D and Recchia, MJJ and Reitz, ZL and van Santen, JA and Selem-Mojica, N and Tørring, T and Zaroubi, L and Alanjary, M and Aleti, G and Aguilar, C and Al-Salihi, SAA and Augustijn, HE and Avelar-Rivas, JA and Avitia-Domínguez, LA and Barona-Gómez, F and Bernaldo-Agüero, J and Bielinski, VA and Biermann, F and Booth, TJ and Carrion Bravo, VJ and Castelo-Branco, R and Chagas, FO and Cruz-Morales, P and Du, C and Duncan, KR and Gavriilidou, A and Gayrard, D and Gutiérrez-García, K and Haslinger, K and Helfrich, EJN and van der Hooft, JJJ and Jati, AP and Kalkreuter, E and Kalyvas, N and Kang, KB and Kautsar, S and Kim, W and Kunjapur, AM and Li, YX and Lin, GM and Loureiro, C and Louwen, JJR and Louwen, NLL and Lund, G and Parra, J and Philmus, B and Pourmohsenin, B and Pronk, LJU and Rego, A and Rex, DAB and Robinson, S and Rosas-Becerra, LR and Roxborough, ET and Schorn, MA and Scobie, DJ and Singh, KS and Sokolova, N and Tang, X and Udwary, D and Vigneshwari, A and Vind, K and Vromans, SPJM and Waschulin, V and Williams, SE and Winter, JM and Witte, TE and Xie, H and Yang, D and Yu, J and Zdouc, M and Zhong, Z and Collemare, J and Linington, RG and Weber, T and Medema, MH}, title = {MIBiG 3.0: a community-driven effort to annotate experimentally validated biosynthetic gene clusters.}, journal = {Nucleic acids research}, volume = {51}, number = {D1}, pages = {D603-D610}, pmid = {36399496}, issn = {1362-4962}, support = {F32 AT011475/AT/NCCIH NIH HHS/United States ; R01 AI155694/AI/NIAID NIH HHS/United States ; U24 AT010811/AT/NCCIH NIH HHS/United States ; }, mesh = {*Genomics ; *Genome ; Multigene Family ; Biosynthetic Pathways/genetics ; }, abstract = {With an ever-increasing amount of (meta)genomic data being deposited in sequence databases, (meta)genome mining for natural product biosynthetic pathways occupies a critical role in the discovery of novel pharmaceutical drugs, crop protection agents and biomaterials. The genes that encode these pathways are often organised into biosynthetic gene clusters (BGCs). In 2015, we defined the Minimum Information about a Biosynthetic Gene cluster (MIBiG): a standardised data format that describes the minimally required information to uniquely characterise a BGC. We simultaneously constructed an accompanying online database of BGCs, which has since been widely used by the community as a reference dataset for BGCs and was expanded to 2021 entries in 2019 (MIBiG 2.0). Here, we describe MIBiG 3.0, a database update comprising large-scale validation and re-annotation of existing entries and 661 new entries. Particular attention was paid to the annotation of compound structures and biological activities, as well as protein domain selectivities. Together, these new features keep the database up-to-date, and will provide new opportunities for the scientific community to use its freely available data, e.g. for the training of new machine learning models to predict sequence-structure-function relationships for diverse natural products. MIBiG 3.0 is accessible online at https://mibig.secondarymetabolites.org/.}, } @article {pmid36394851, year = {2023}, author = {Zhang, L and Gong, R and Shi, L and Wen, M and Sun, X and Yabroff, KR and Han, X}, title = {Association of Residential Racial and Economic Segregation With Cancer Mortality in the US.}, journal = {JAMA oncology}, volume = {9}, number = {1}, pages = {122-126}, pmid = {36394851}, issn = {2374-2445}, mesh = {Male ; Female ; Humans ; Racial Groups ; Residential Segregation ; Risk Factors ; *Racism ; Health Status Disparities ; *Neoplasms ; }, abstract = {IMPORTANCE: Residential segregation is a structural risk factor for poor cancer outcomes. Previous research examining the association of residential segregation with cancer outcomes was limited by older data, restricted geographic areas, and few cancer sites. To guide targeted interventions, a comprehensive evaluation of the association between segregation and cancer outcomes is needed.

OBJECTIVE: To examine the association of residential racial and economic segregation with cancer mortality at the US county level for all cancers combined and for the 13 cancer types that represent the top 10 causes of cancer deaths in males or females.

This ecological study used county-level sociodemographic data from the 2015-2019 American Community Survey linked with 2015-2019 county-level mortality data. Data analysis was performed from September 2021 to April 2022.

EXPOSURES: Residential racial and economic segregation measured by the Index of Concentration at the Extremes (ICE) and categorized into quintiles 1 (most deprived) through 5 (most privileged).

MAIN OUTCOMES AND MEASURES: Age-adjusted cancer mortality was the outcome. Multilevel linear mixed modeling was used to calculate the adjusted mortality rate ratio (aRR).

RESULTS: A total of 3110 counties were included. The age-adjusted mortality rates of all cancers combined were 179.8, 177.3, 167.6, 159.6, and 146.1 per 100 000 population (P < .001 for trend) for the 5 ICE categories (most deprived to least deprived), respectively. Compared with the least deprived counties, aRRs for all cancers combined were 1.22 (95% CI, 1.20-1.24) for the most deprived counties, followed by 1.17 (95% CI, 1.15-1.19), 1.10 (95% CI, 1.09-1.12), and 1.06 (95% CI, 1.04-1.08) for the other 3 quintiles, respectively (P < .001 for trend). Segregation was associated with increased mortality from 12 of 13 selected cancer sites, in which aRRs ranged from 1.06 (95% CI, 1.02-1.09) for brain and other nervous system cancer to 1.49 (95% CI, 1.43-1.54) for lung and bronchus cancer.

CONCLUSIONS AND RELEVANCE: The findings of this ecological study suggest that residential racial and economic segregation is associated with higher cancer mortality at the county level, highlighting opportunities for geographically targeted cancer prevention and control efforts.}, } @article {pmid36384190, year = {2023}, author = {Liu, H and Wu, M and Gao, H and Gao, J and Wang, S}, title = {Application of [15]N tracing and bioinformatics for estimating microbial-mediated nitrogen cycle processes in oil-contaminated soils.}, journal = {Environmental research}, volume = {217}, number = {}, pages = {114799}, doi = {10.1016/j.envres.2022.114799}, pmid = {36384190}, issn = {1096-0953}, mesh = {Nitrogen Cycle ; Nitrogen/analysis ; Soil/chemistry ; *Microbiota ; Soil Microbiology ; Computational Biology ; *Soil Pollutants/analysis ; }, abstract = {Crude oil pollution can profoundly alter the nitrogen (N) cycle in the soil. Here, a 30-day incubation with [15]N tracer approach was performed to assess the impacts of crude oil concentrations (medium: 10,000 mg kg[-1]; heavy: 50,000 mg kg[-1]) on soil N cycling based on a numerical model. Results showed that crude oil pollution significantly increased the gross N-transformation rates, but the rates of oxidation of recalcitrant organic N, the immbolization of NO3[-] and the adsorption of NH4[+] changed differently as a function of hydrocarbon concentrations. There was no significant difference of the oxidation rate of recalcitrant organic N between the medium and heavy oil-contaminated soils (medium: 0.1149 mmol N kg[-1] d[-1]; heavy: 0.1299 mmol N kg[-1] d[-1]), but the rates of NO3[-] immobilization (0.1135 mmol N kg[-1] d[-1]) and NH4[+] adsorption were the highest (0.1148 mmol N kg[-1] d[-1]) in the moderately oil-contaminated soils than those in the heavy polluted soil (0.0849 mmol N kg[-1] d[-1] and 0.0034 mmol N kg[-1] d[-1], respectively). The NO3[-] immobilization rate was 2.5-fold higher than its reduction rate, indicating that NO3[-] immobilization played a more important role during the process of NO3[-] transformation. Microbial community structure analysis indicated that phyla of Actinobacteria and Ascomycota respectively promoted the immobilization of NO3[-] to recalcitrant organic N and the reduction of NO3[-] to NH4[+]. The genus of Aspergillus was related to net NH4[+] production, and the genera of Penicillium and Acremonium were responsible for oxidation of recalcitrant organic N to NO3[-].}, } @article {pmid36383289, year = {2022}, author = {McGuinness, KN and Klau, GW and Morrison, SM and Moore, EK and Seipp, J and Falkowski, PG and Nanda, V}, title = {Evaluating Mineral Lattices as Evolutionary Proxies for Metalloprotein Evolution.}, journal = {Origins of life and evolution of the biosphere : the journal of the International Society for the Study of the Origin of Life}, volume = {52}, number = {4}, pages = {263-275}, pmid = {36383289}, issn = {1573-0875}, support = {K12GM093854/NH/NIH HHS/United States ; 80NSSC18M0093//NASA Astrobiology Institute/ ; K12GM093854/NH/NIH HHS/United States ; }, mesh = {*Metalloproteins ; Minerals ; *Iron-Sulfur Proteins/chemistry/metabolism ; Sulfur/chemistry/metabolism ; Iron/chemistry ; }, abstract = {Protein coordinated iron-sulfur clusters drive electron flow within metabolic pathways for organisms throughout the tree of life. It is not known how iron-sulfur clusters were first incorporated into proteins. Structural analogies to iron-sulfide minerals present on early Earth, suggest a connection in the evolution of both proteins and minerals. The availability of large protein and mineral crystallographic structure data sets, provides an opportunity to explore co-evolution of proteins and minerals on a large-scale using informatics approaches. However, quantitative comparisons are confounded by the infinite, repeating nature of the mineral lattice, in contrast to metal clusters in proteins, which are finite in size. We address this problem using the Niggli reduction to transform a mineral lattice to a finite, unique structure that when translated reproduces the crystal lattice. Protein and reduced mineral structures were represented as quotient graphs with the edges and nodes corresponding to bonds and atoms, respectively. We developed a graph theory-based method to calculate the maximum common connected edge subgraph (MCCES) between mineral and protein quotient graphs. MCCES can accommodate differences in structural volumes and easily allows additional chemical criteria to be considered when calculating similarity. To account for graph size differences, we use the Tversky similarity index. Using consistent criteria, we found little similarity between putative ancient iron-sulfur protein clusters and iron-sulfur mineral lattices, suggesting these metal sites are not as evolutionarily connected as once thought. We discuss possible evolutionary implications of these findings in addition to suggesting an alternative proxy, mineral surfaces, for better understanding the coevolution of the geosphere and biosphere.}, } @article {pmid36378489, year = {2022}, author = {Gupta, VK and Bakshi, U and Chang, D and Lee, AR and Davis, JM and Chandrasekaran, S and Jin, YS and Freeman, MF and Sung, J}, title = {TaxiBGC: a Taxonomy-Guided Approach for Profiling Experimentally Characterized Microbial Biosynthetic Gene Clusters and Secondary Metabolite Production Potential in Metagenomes.}, journal = {mSystems}, volume = {7}, number = {6}, pages = {e0092522}, pmid = {36378489}, issn = {2379-5077}, support = {R35 GM133475/GM/NIGMS NIH HHS/United States ; }, mesh = {Humans ; Metagenome/genetics ; *Microbiota/genetics ; *Gastrointestinal Microbiome/genetics ; Computational Biology ; Multigene Family/genetics ; }, abstract = {Biosynthetic gene clusters (BGCs) in microbial genomes encode bioactive secondary metabolites (SMs), which can play important roles in microbe-microbe and host-microbe interactions. Given the biological significance of SMs and the current profound interest in the metabolic functions of microbiomes, the unbiased identification of BGCs from high-throughput metagenomic data could offer novel insights into the complex chemical ecology of microbial communities. Currently available tools for predicting BGCs from shotgun metagenomes have several limitations, including the need for computationally demanding read assembly, predicting a narrow breadth of BGC classes, and not providing the SM product. To overcome these limitations, we developed taxonomy-guided identification of biosynthetic gene clusters (TaxiBGC), a command-line tool for predicting experimentally characterized BGCs (and inferring their known SMs) in metagenomes by first pinpointing the microbial species likely to harbor them. We benchmarked TaxiBGC on various simulated metagenomes, showing that our taxonomy-guided approach could predict BGCs with much-improved performance (mean F1 score, 0.56; mean PPV score, 0.80) compared with directly identifying BGCs by mapping sequencing reads onto the BGC genes (mean F1 score, 0.49; mean PPV score, 0.41). Next, by applying TaxiBGC on 2,650 metagenomes from the Human Microbiome Project and various case-control gut microbiome studies, we were able to associate BGCs (and their SMs) with different human body sites and with multiple diseases, including Crohn's disease and liver cirrhosis. In all, TaxiBGC provides an in silico platform to predict experimentally characterized BGCs and their SM production potential in metagenomic data while demonstrating important advantages over existing techniques. IMPORTANCE Currently available bioinformatics tools to identify BGCs from metagenomic sequencing data are limited in their predictive capability or ease of use to even computationally oriented researchers. We present an automated computational pipeline called TaxiBGC, which predicts experimentally characterized BGCs (and infers their known SMs) in shotgun metagenomes by first considering the microbial species source. Through rigorous benchmarking techniques on simulated metagenomes, we show that TaxiBGC provides a significant advantage over existing methods. When demonstrating TaxiBGC on thousands of human microbiome samples, we associate BGCs encoding bacteriocins with different human body sites and diseases, thereby elucidating a possible novel role of this antibiotic class in maintaining the stability of microbial ecosystems throughout the human body. Furthermore, we report for the first time gut microbial BGC associations shared among multiple pathologies. Ultimately, we expect our tool to facilitate future investigations into the chemical ecology of microbial communities across diverse niches and pathologies.}, } @article {pmid36378100, year = {2022}, author = {Oh, AY and Rising, CJ and Gaysynsky, A and Tsakraklides, S and Huang, GC and Chou, WS and Blake, KD and Vanderpool, RC}, title = {Advancing multi-level health communication research: A Delphi study on barriers and opportunities.}, journal = {Translational behavioral medicine}, volume = {12}, number = {12}, pages = {1133-1145}, pmid = {36378100}, issn = {1613-9860}, support = {HHSN261201800002B/CA/NCI NIH HHS/United States ; HHSN261201800002C/CA/NCI NIH HHS/United States ; }, mesh = {Humans ; Delphi Technique ; *Interdisciplinary Communication ; Consensus ; Surveys and Questionnaires ; *Health Communication ; }, abstract = {Adopting a multi-level perspective that considers the many interrelated contexts influencing health could make health communication interventions more effective and equitable. However, despite increasing interest in the use of multi-level approaches, multi-level health communication (MLHC) interventions are infrequently utilized. We therefore sought to conduct a modified Delphi study to better understand how researchers conceptualize MLHC interventions and identify opportunities for advancing MLHC work. Communication and health behavior experts were invited to complete two rounds of surveys about the characteristics, benefits, pitfalls, best practices, barriers, and facilitators of MLHC interventions; the role of technology in facilitating MLHC interventions; and ways to advance MLHC intervention research (46 experts completed the first survey, 44 completed both surveys). Survey data were analyzed using a mixed-methods approach. Panelists reached consensus on two components of the proposed definition of MLHC interventions and also put forward a set of best practices for these interventions. Panelists felt that most health intervention research could benefit from a multi-level approach, and generally agreed that MLHC approaches offered certain advantages over single-level approaches. However, they also expressed concern related to the time, cost, and complexity of MLHC interventions. Although panelists felt that technology could potentially support MLHC interventions, they also recognized the potential for technology to exacerbate disparities. Finally, panelists prioritized a set of methodological advances and practical supports that would be needed to facilitate future MLHC intervention research. The results of this study point to several future directions for the field, including advancing how interactions between levels are assessed, increasing the empirical evidence base demonstrating the advantages of MLHC interventions, and identifying best practices for the use of technology. The findings also suggest that researchers may need additional support to overcome the perceived practical challenges of conducting MLHC interventions.}, } @article {pmid36374834, year = {2022}, author = {Boyle, BL and Maitner, BS and Barbosa, GGC and Sajja, RK and Feng, X and Merow, C and Newman, EA and Park, DS and Roehrdanz, PR and Enquist, BJ}, title = {Geographic name resolution service: A tool for the standardization and indexing of world political division names, with applications to species distribution modeling.}, journal = {PloS one}, volume = {17}, number = {11}, pages = {e0268162}, pmid = {36374834}, issn = {1932-6203}, mesh = {Databases, Factual ; *Biodiversity ; *Names ; Reference Standards ; }, abstract = {Massive biological databases of species occurrences, or georeferenced locations where a species has been observed, are essential inputs for modeling present and future species distributions. Location accuracy is often assessed by determining whether the observation geocoordinates fall within the boundaries of the declared political divisions. This otherwise simple validation is complicated by the difficulty of matching political division names to the correct geospatial object. Spelling errors, abbreviations, alternative codes, and synonyms in multiple languages present daunting name disambiguation challenges. The inability to resolve political division names reduces usable data, and analysis of erroneous observations can lead to flawed results. Here, we present the Geographic Name Resolution Service (GNRS), an application for correcting, standardizing, and indexing world political division names. The GNRS resolves political division names against a reference database that combines names and codes from GeoNames with geospatial object identifiers from the Global Administrative Areas Database (GADM). In a trial resolution of political division names extracted from >270 million species occurrences, only 1.9%, representing just 6% of occurrences, matched exactly to GADM political divisions in their original form. The GNRS was able to resolve, completely or in part, 92% of the remaining 378,568 political division names, or 86% of the full biodiversity occurrence dataset. In assessing geocoordinate accuracy for >239 million species occurrences, resolution of political divisions by the GNRS enabled the detection of an order of magnitude more errors and an order of magnitude more error-free occurrences. By providing a novel solution to a significant data quality impediment, the GNRS liberates a tremendous amount of biodiversity data for quantitative biodiversity research. The GNRS runs as a web service and is accessible via an API, an R package, and a web-based graphical user interface. Its modular architecture is easily integrated into existing data validation workflows.}, } @article {pmid36371952, year = {2023}, author = {Zhao, H and Liu, X and Jiang, T and Cai, C and Gu, K and Liu, Y and He, P}, title = {Activated abscisic acid pathway and C4 pathway, inhibited cell cycle progression, responses of Ulva prolifera to short term high temperature elucidated by multi-omics.}, journal = {Marine environmental research}, volume = {183}, number = {}, pages = {105796}, doi = {10.1016/j.marenvres.2022.105796}, pmid = {36371952}, issn = {1879-0291}, mesh = {*Ulva/metabolism ; Temperature ; Abscisic Acid/metabolism ; Multiomics ; Cell Cycle ; Eutrophication ; China ; }, abstract = {The annual outbreak of green tides since 2007 has destroyed coastal waters' ecological environment and caused substantial economic losses. Ulva prolifera, known as the dominant species of green tides, is influenced by temperatures. Omics-based technology was used to analyze U. prolifera under 12 h of treatment at 30 °C in the work. High temperature has the following advantages, e.g., activating the abscisic acid signaling pathway, improving the heat tolerance of U. prolifera, up-regulating metabolites such as glycolipids, glyceroyl, and glutamic acid to maintain the stability and fluidity of cells, and reducing the stimulatory effect of external stress on cells. The key genes and proteins of the tricarboxylic acid cycle, glycolysis, and pentose phosphorylation pathways were inhibited; however, the key enzyme pyruvate phospho-dikinase of the C4 pathway was up-regulated. The C4 pathway was activated in U. prolifera in response to high-temperature stress and may play a key role in photosynthesis. Besides, U. prolifera metabolizing amino acids was active. High temperature inhibited genes and proteins related to DNA replication and cell cycle in the transcriptome and proteome as well as the growth and reproduction of U. prolifera.}, } @article {pmid36365380, year = {2022}, author = {Ganie, IB and Ahmad, Z and Shahzad, A and Zaushintsena, A and Neverova, O and Ivanova, S and Wasi, A and Tahseen, S}, title = {Biotechnological Intervention and Secondary Metabolite Production in Centella asiatica L.}, journal = {Plants (Basel, Switzerland)}, volume = {11}, number = {21}, pages = {}, pmid = {36365380}, issn = {2223-7747}, support = {1144-r//Comprehensive Scientific and Technical Program/ ; }, abstract = {Centella asiatica L., commonly known as Gotu kola, Indian pennywort, and Asiatic pennyworts, is an herbaceous perennial plant that belongs to the family Apiaceae and has long been used in the traditional medicine system. The plant is known to produce a wide range of active metabolites such as triterpenoids including asiatic acid, asiaticoside, brahmoside, and madecassic acid along with other constituents including centellose, centelloside, and madecassoside, etc., which show immense pharmacological activity. Due to its beneficial role in neuroprotection activity, the plant has been considered as a brain tonic. However, limited cultivation, poor seed viability with low germination rate, and overexploitation for decades have led to severe depletion and threatened its wild stocks. The present review aimed to provide up-to-date information on biotechnological tools applied to this endangered medicinal plant for its in vitro propagation, direct or indirect regeneration, synthetic seed production, strategies for secondary metabolite productions including different elicitors. In addition, a proposed mechanism for the biosynthesis of triterpenoids is also discussed.}, } @article {pmid36362326, year = {2022}, author = {Decewicz, P and Kitowicz, M and Radlinska, M}, title = {Characteristics and Comparative Genomic Analysis of a Novel Virus, VarioGold, the First Bacteriophage of Variovorax.}, journal = {International journal of molecular sciences}, volume = {23}, number = {21}, pages = {}, pmid = {36362326}, issn = {1422-0067}, support = {no. 2017/25/B/NZ8/00472//National Science Centre (Poland)/ ; }, mesh = {*Bacteriophages ; Prophages/genetics ; Sequence Analysis, DNA ; Computational Biology ; Genomics ; Genome, Viral ; }, abstract = {Variovorax represents a widespread and ecologically significant genus of soil bacteria. Despite the ecological importance of these bacteria, our knowledge about the viruses infecting Variovorax spp. is quite poor. This study describes the isolation and characterization of the mitomycin-induced phage, named VarioGold. To the best of our knowledge, VarioGold represents the first characterized virus for this genus. Comparative genomic analyses suggested that VarioGold is distinct from currently known bacteriophages at both the nucleotide and protein levels; thus, it could be considered a new virus genus. In addition, another 37 prophages were distinguished in silico within the complete genomic sequences of Variovorax spp. that are available in public databases. The similarity networking analysis highlighted their general high diversity, which, despite clustering with previously described phages, shows their unique genetic load. Therefore, the novelty of Variovorax phages warrants the great enrichment of databases, which could, in turn, improve bioinformatic strategies for finding (pro)phages.}, } @article {pmid36357425, year = {2022}, author = {Oliveira-Rodrigues, C and Correia, AM and Valente, R and Gil, Á and Gandra, M and Liberal, M and Rosso, M and Pierce, G and Sousa-Pinto, I}, title = {Assessing data bias in visual surveys from a cetacean monitoring programme.}, journal = {Scientific data}, volume = {9}, number = {1}, pages = {682}, pmid = {36357425}, issn = {2052-4463}, mesh = {Animals ; *Cetacea/physiology ; Data Collection ; Datasets as Topic ; Bias ; }, abstract = {Long-term monitoring datasets are fundamental to understand physical and ecological responses to environmental changes, supporting management and conservation. The data should be reliable, with the sources of bias identified and quantified. CETUS Project is a cetacean monitoring programme in the Eastern North Atlantic, based on visual methods of data collection. This study aims to assess data quality and bias in the CETUS dataset, by 1) applying validation methods, through photographic confirmation of species identification; 2) creating data quality criteria to evaluate the observer's experience; and 3) assessing bias to the number of sightings collected and to the success in species identification. Through photographic validation, the species identification of 10 sightings was corrected and a new species was added to the CETUS dataset. The number of sightings collected was biased by external factors, mostly by sampling effort but also by weather conditions. Ultimately, results highlight the importance of identifying and quantifying data bias, while also yielding guidelines for data collection and processing, relevant for species monitoring programmes based on visual methods.}, } @article {pmid36352171, year = {2022}, author = {Mohsen, A and Zeidan, B and Elshemy, M}, title = {Water quality assessment of Lake Burullus, Egypt, utilizing statistical and GIS modeling as environmental hydrology applications.}, journal = {Environmental monitoring and assessment}, volume = {195}, number = {1}, pages = {93}, pmid = {36352171}, issn = {1573-2959}, mesh = {*Water Quality ; *Lakes ; Hydrology ; Geographic Information Systems ; Egypt ; Environmental Monitoring/methods ; }, abstract = {GIS is a very powerful tool for analyzing huge amount of data and connecting them with the geography; moreover, recently, there is great advancement in the field. The main objective of this study is to assess the water quality (WQ) and trophic status (TS) conditions of Lake Burullus, Egypt, using statistical modeling (PCA/FA and CA), WQ index (L-WQI), and trophic status index (Carlson TSI and TRIX) approaches, in addition to using GIS tools for building models able to automatically calculate the various indices and producing color coded maps for the lake. The results indicated that PCA/FA grouped the twenty-four WQ parameters into nine principal components explaining 72.6% of the total variance, domestic, and agriculture pollution were dominant. CA divided the twelve sampling stations into most and least polluted groups. The lake WQ was classified as a "Very Poor," according to L-WQI. Moreover, the results of the Carlson TSI and TRIX indices were coincided and classified the eutrophication levels in the lake as "Hyper-Eutrophic" and "Elevated Trophic," respectively. Based on the results of this study, Lake Burullus needs urgent plans for recovering its WQ. Pre-treatment for its drains' effluents and implementing of a periodical WQ monitoring program are highly recommended.}, } @article {pmid36350456, year = {2022}, author = {Zhang, X and Dong, X and Liu, F and Lv, T and Wu, Z and Ranagalage, M}, title = {Spatiotemporal dynamics of ecological security in a typical conservation region of southern China based on catastrophe theory and GIS.}, journal = {Environmental monitoring and assessment}, volume = {195}, number = {1}, pages = {90}, doi = {10.1007/s10661-022-10669-6}, pmid = {36350456}, issn = {1573-2959}, support = {No. GJJ200542//the Science and Technology Project of Jiangxi Education Department/ ; }, mesh = {*Ecology/methods ; *Conservation of Natural Resources/methods ; Geographic Information Systems ; Environmental Monitoring ; Ecosystem ; China ; }, abstract = {Ecological security assessment can effectively reflect the ecological status of a region and reveal its level of sustainable development. In this paper, an ecological security-oriented evaluation system was constructed, and the ecological security level of the Dongjiangyuan region from 2000 to 2020 was evaluated based on catastrophe theory and GIS. The results were as follows: (1) As shown in the land use and cover maps, by 2020, the forestland area had decreased the most, and the artificial surface area had increased the most. (2) The ecological security index of the Dongjiangyuan region showed a low trend in the artificial surface area and its surrounding areas. The quite low values of the ecological security index in 2000 and 2010 were improved in 2020 due to the increase in ecological services capacity. The increased vegetation cover from 2000 to 2020 promoted the improved ecological service capacity. (3) The rapid urbanization process in the Dongjiangyuan region resulted in a lower ecological sensitivity index value. Notably, the ecological sensitivity index of the study area had a slightly decreasing trend. (4) The spatial autocorrelation showed that the proportion of hot and cold spots from 2000 to 2020 decreased by 2.96% and 6.91%, respectively. This study can provide a scientific basis and decision-making guidance for ecological management in the Dongjiangyuan region in the future.}, } @article {pmid36348471, year = {2022}, author = {Baaijens, JA and Zulli, A and Ott, IM and Nika, I and van der Lugt, MJ and Petrone, ME and Alpert, T and Fauver, JR and Kalinich, CC and Vogels, CBF and Breban, MI and Duvallet, C and McElroy, KA and Ghaeli, N and Imakaev, M and Mckenzie-Bennett, MF and Robison, K and Plocik, A and Schilling, R and Pierson, M and Littlefield, R and Spencer, ML and Simen, BB and , and Hanage, WP and Grubaugh, ND and Peccia, J and Baym, M}, title = {Lineage abundance estimation for SARS-CoV-2 in wastewater using transcriptome quantification techniques.}, journal = {Genome biology}, volume = {23}, number = {1}, pages = {236}, pmid = {36348471}, issn = {1474-760X}, support = {T35 HL007649/HL/NHLBI NIH HHS/United States ; UL1 TR001863/TR/NCATS NIH HHS/United States ; R35 GM133700/GM/NIGMS NIH HHS/United States ; U54 GM088558/GM/NIGMS NIH HHS/United States ; TL1 TR001864/TR/NCATS NIH HHS/United States ; }, mesh = {Humans ; *SARS-CoV-2/genetics ; Wastewater ; RNA, Viral/genetics ; Transcriptome ; *COVID-19 ; }, abstract = {Effectively monitoring the spread of SARS-CoV-2 mutants is essential to efforts to counter the ongoing pandemic. Predicting lineage abundance from wastewater, however, is technically challenging. We show that by sequencing SARS-CoV-2 RNA in wastewater and applying algorithms initially used for transcriptome quantification, we can estimate lineage abundance in wastewater samples. We find high variability in signal among individual samples, but the overall trends match those observed from sequencing clinical samples. Thus, while clinical sequencing remains a more sensitive technique for population surveillance, wastewater sequencing can be used to monitor trends in mutant prevalence in situations where clinical sequencing is unavailable.}, } @article {pmid36344967, year = {2022}, author = {Toh, H and Yang, C and Formenti, G and Raja, K and Yan, L and Tracey, A and Chow, W and Howe, K and Bergeron, LA and Zhang, G and Haase, B and Mountcastle, J and Fedrigo, O and Fogg, J and Kirilenko, B and Munegowda, C and Hiller, M and Jain, A and Kihara, D and Rhie, A and Phillippy, AM and Swanson, SA and Jiang, P and Clegg, DO and Jarvis, ED and Thomson, JA and Stewart, R and Chaisson, MJP and Bukhman, YV}, title = {A haplotype-resolved genome assembly of the Nile rat facilitates exploration of the genetic basis of diabetes.}, journal = {BMC biology}, volume = {20}, number = {1}, pages = {245}, pmid = {36344967}, issn = {1741-7007}, mesh = {Humans ; Animals ; Haplotypes ; *Diabetes Mellitus, Type 2/genetics ; Murinae ; Genome ; Genomics ; }, abstract = {BACKGROUND: The Nile rat (Avicanthis niloticus) is an important animal model because of its robust diurnal rhythm, a cone-rich retina, and a propensity to develop diet-induced diabetes without chemical or genetic modifications. A closer similarity to humans in these aspects, compared to the widely used Mus musculus and Rattus norvegicus models, holds the promise of better translation of research findings to the clinic.

RESULTS: We report a 2.5 Gb, chromosome-level reference genome assembly with fully resolved parental haplotypes, generated with the Vertebrate Genomes Project (VGP). The assembly is highly contiguous, with contig N50 of 11.1 Mb, scaffold N50 of 83 Mb, and 95.2% of the sequence assigned to chromosomes. We used a novel workflow to identify 3613 segmental duplications and quantify duplicated genes. Comparative analyses revealed unique genomic features of the Nile rat, including some that affect genes associated with type 2 diabetes and metabolic dysfunctions. We discuss 14 genes that are heterozygous in the Nile rat or highly diverged from the house mouse.

CONCLUSIONS: Our findings reflect the exceptional level of genomic resolution present in this assembly, which will greatly expand the potential of the Nile rat as a model organism.}, } @article {pmid36334202, year = {2023}, author = {Tian, L and Wang, L and Zhang, X and Huang, X and Wang, F and Zhu, S and Li, X and Guan, Y}, title = {Multi-omics analysis on seasonal variations of the biofilm microbial community in a full-scale pre-denitrification biofilter.}, journal = {Environmental science and pollution research international}, volume = {30}, number = {9}, pages = {24284-24298}, pmid = {36334202}, issn = {1614-7499}, support = {21-1-4-sf-11-nsh//science and technology program for public wellbeing of qingdao/ ; }, mesh = {*Denitrification ; Bioreactors/microbiology ; Seasons ; Multiomics ; Proteomics ; *Microbiota ; Biofilms ; Nitrogen ; }, abstract = {The seasonal variations of biofilm communities in a municipal wastewater treatment plant were investigated using multi-omics techniques. The abundance of the main phyla of microorganisms varied with summer (July 2019) and winter (January 2019) samples considerably, the Bacteroidetes enriched in winter and Chloroflexi in summer. The results of metaproteomic and metagenomic showed that most of the functional microorganisms belonged to the Betaproteobacteria class, and the enrichment of Flavobacteria class in winter guaranteed the stability of denitrification performance to some extent. Seasonal variations affected the proteomic expression profiling, a total of 2835 differentially expressed proteins identified were significantly enriched in quorum sensing, two-component system, ribosome, benzoate degradation, butanoate metabolism, tricarboxylic acid cycle (TCA cycle), and cysteine and methionine metabolism pathways. With the expression of nitrogen metabolic proteins decreases in winter, the overall expression of denitrification-related enzymes in winter was much lower than that in summer, the nitrogen metabolism pathway varied significantly. Seasonal variations also induced the alteration of the biofilm metabolite profile; a total of 66 differential metabolites, 8 potential biomarkers, and 8 perturbed metabolic pathways such as TCA cycle were detected. It was found that most of the perturbed pathways are directly related to nitrogen metabolism, and several amino acids and organic acids associated with the TCA cycle were significantly perturbed, the accumulation of TCA cycle intermediates, ornithine, and L-histidine in winter might be conducive to resisting cold temperatures. Furthermore, the correlation between biofilm microbial communities and metabolites was identified by the combined analysis of metabolomic and metaproteomic. The differences of microbial community structure, function, and metabolism between winter and summer in a full-scale pre-denitrification biofilter were revealed for the first time, strengthening our understanding of the microbial ecology of biofilm communities.}, } @article {pmid36333350, year = {2022}, author = {Zhang, X and Zhang, B and Li, J and Yao, Y and Wang, J and Liu, J and Yu, F}, title = {A database of seed plants on taxonomy, geography and ecology in the Qinling-Daba Mountains and adjacent areas.}, journal = {Scientific data}, volume = {9}, number = {1}, pages = {672}, pmid = {36333350}, issn = {2052-4463}, mesh = {Humans ; *Biodiversity ; China ; Ecology ; Ecosystem ; Geography ; Plants ; *Seeds ; Databases, Factual ; }, abstract = {The Qinling-Daba Mountains span subtropical and warm temperate zones and are one of the most remarkable biodiversity hotspots in China. Establishing a complete checklist of seed plants organized by nature reserves in the Qinling-Daba Mountains and adjacent areas is an important basis for managing and utilizing plant resources. First, we collected seed plant species data from published checklists representing 58 nature reserves in the Qinling-Daba Mountains and adjacent areas; second, we comprehensively and systematically sorted and integrated these data; third, we proofread and revised the data with the help of the R language and Flora of China dataset; and finally, we set up a seed plant database containing 96148 records, including the name, order, family, genus, life form, and endemism of each species for the entirety of the Qinling-Daba Mountains. The database contains 9491 species of seed plants belonging to 1729 genera, 211 families, and 59 orders, accounting for 39% of China's seed plants.}, } @article {pmid36329351, year = {2022}, author = {Pillay, R and Watson, JEM and Hansen, AJ and Jantz, PA and Aragon-Osejo, J and Armenteras, D and Atkinson, SC and Burns, P and Ervin, J and Goetz, SJ and González-Del-Pliego, P and Robinson, NP and Supples, C and Virnig, ALS and Williams, BA and Venter, O}, title = {Humid tropical vertebrates are at lower risk of extinction and population decline in forests with higher structural integrity.}, journal = {Nature ecology & evolution}, volume = {6}, number = {12}, pages = {1840-1849}, pmid = {36329351}, issn = {2397-334X}, mesh = {Animals ; Humans ; *Tropical Climate ; *Conservation of Natural Resources ; Forests ; Biodiversity ; Vertebrates ; }, abstract = {Reducing deforestation underpins global biodiversity conservation efforts. However, this focus on retaining forest cover overlooks the multitude of anthropogenic pressures that can degrade forest quality and imperil biodiversity. We use remotely sensed indices of tropical rainforest structural condition and associated human pressures to quantify the relative importance of forest cover, structural condition and integrity (the cumulative effect of condition and pressures) on vertebrate species extinction risk and population trends across the global humid tropics. We found that tropical rainforests of high integrity (structurally intact and under low pressures) were associated with lower likelihood of species being threatened and having declining populations, compared with forest cover alone (without consideration of condition and pressures). Further, species were more likely to be threatened or have declining populations if their geographic ranges contained high proportions of degraded forest than if their ranges contained lower proportions of forest cover but of high quality. Our work suggests that biodiversity conservation policies to preserve forest integrity are now urgently required alongside ongoing efforts to halt deforestation in the hyperdiverse humid tropics.}, } @article {pmid36324785, year = {2022}, author = {Gao, Y and Gong, L and Liu, H and Kong, Y and Wu, X and Guo, Y and Hu, D}, title = {Research on the influencing factors of users' information processing in online health communities based on heuristic-systematic model.}, journal = {Frontiers in psychology}, volume = {13}, number = {}, pages = {966033}, pmid = {36324785}, issn = {1664-1078}, abstract = {With the rapid development of the Internet and the normalization of COVID-19 epidemic prevention and control, Online health communities (OHCs) have gradually become one of the important ways for people to obtain health information, and users have to go through a series of information processing when facing the massive amount of data. Understanding the factors influencing user information processing is necessary to promote users' health literacy, health knowledge popularization and health behavior shaping. Based on the Heuristic-Systematic Model (HSM), Information Ecology Theory, Privacy Trade-Off and Self-Efficacy Theory, we constructed a model of factors influencing user information processing in online health communities. We found that information quality and emotional support had indirect effects on heuristic and systematic information processing, and these effects were mediated by privacy concerns and self-efficacy. In our research model, systematic information processing was most positively influenced directly by self-efficacy. Privacy concerns had a direct negative correlation with both dual information processing pathways. Therefore, OHCs managers should develop relevant regulations to ensure the information quality in OHCs and improve privacy protection services to promote user information processing by improving users' self-efficacy and reducing their privacy concerns. Providing a user-friendly and interactive environment for users is also recommended to create more emotional support, thus facilitating more systematic information processing.}, } @article {pmid36324701, year = {2022}, author = {Boyes, D and Holland, PWH and , and , and , and , and , and , }, title = {The genome sequence of the angle shades moth, Phlogophora meticulosa (Linnaeus, 1758).}, journal = {Wellcome open research}, volume = {7}, number = {}, pages = {89}, pmid = {36324701}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual female Phlogophora meticulosa (the angle shades; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 539 megabases in span. The majority of the assembly, 95.17%, is scaffolded into 31 chromosomal pseudomolecules, with the Z sex chromosome assembled. Some unassigned scaffolds are identified as belonging to the W chromosome based on half-depth coverage and comparison to other Noctuidae W chromosomes. The mitochondrial genome was also assembled and is 15.4 kilobases in length.}, } @article {pmid36323316, year = {2022}, author = {Vatanen, T and Ang, QY and Siegwald, L and Sarker, SA and Le Roy, CI and Duboux, S and Delannoy-Bruno, O and Ngom-Bru, C and Boulangé, CL and Stražar, M and Avila-Pacheco, J and Deik, A and Pierce, K and Bullock, K and Dennis, C and Sultana, S and Sayed, S and Rahman, M and Ahmed, T and Modesto, M and Mattarelli, P and Clish, CB and Vlamakis, H and Plichta, DR and Sakwinska, O and Xavier, RJ}, title = {A distinct clade of Bifidobacterium longum in the gut of Bangladeshi children thrives during weaning.}, journal = {Cell}, volume = {185}, number = {23}, pages = {4280-4297.e12}, doi = {10.1016/j.cell.2022.10.011}, pmid = {36323316}, issn = {1097-4172}, mesh = {Infant ; Child ; Female ; Humans ; Child, Preschool ; *Bifidobacterium longum/metabolism ; Bifidobacterium/metabolism ; Weaning ; Oligosaccharides/metabolism ; Bangladesh ; Milk, Human ; Feces/microbiology ; }, abstract = {The gut microbiome has an important role in infant health and development. We characterized the fecal microbiome and metabolome of 222 young children in Dhaka, Bangladesh during the first two years of life. A distinct Bifidobacterium longum clade expanded with introduction of solid foods and harbored enzymes for utilizing both breast milk and solid food substrates. The clade was highly prevalent in Bangladesh, present globally (at lower prevalence), and correlated with many other gut taxa and metabolites, indicating an important role in gut ecology. We also found that the B. longum clades and associated metabolites were implicated in childhood diarrhea and early growth, including positive associations between growth measures and B. longum subsp. infantis, indolelactate and N-acetylglutamate. Our data demonstrate geographic, cultural, seasonal, and ecological heterogeneity that should be accounted for when identifying microbiome factors implicated in and potentially benefiting infant development.}, } @article {pmid36322519, year = {2022}, author = {Wood, ALC and Kirby, KR and Ember, CR and Silbert, S and Passmore, S and Daikoku, H and McBride, J and Paulay, F and Flory, MJ and Szinger, J and D'Arcangelo, G and Bradley, KK and Guarino, M and Atayeva, M and Rifkin, J and Baron, V and El Hajli, M and Szinger, M and Savage, PE}, title = {The Global Jukebox: A public database of performing arts and culture.}, journal = {PloS one}, volume = {17}, number = {11}, pages = {e0275469}, pmid = {36322519}, issn = {1932-6203}, mesh = {Humans ; Reproducibility of Results ; *Music ; Cross-Cultural Comparison ; Language ; Databases, Factual ; Culture ; }, abstract = {Standardized cross-cultural databases of the arts are critical to a balanced scientific understanding of the performing arts, and their role in other domains of human society. This paper introduces the Global Jukebox as a resource for comparative and cross-cultural study of the performing arts and culture. The Global Jukebox adds an extensive and detailed global database of the performing arts that enlarges our understanding of human cultural diversity. Initially prototyped by Alan Lomax in the 1980s, its core is the Cantometrics dataset, encompassing standardized codings on 37 aspects of musical style for 5,776 traditional songs from 1,026 societies. The Cantometrics dataset has been cleaned and checked for reliability and accuracy, and includes a full coding guide with audio training examples (https://theglobaljukebox.org/?songsofearth). Also being released are seven additional datasets coding and describing instrumentation, conversation, popular music, vowel and consonant placement, breath management, social factors, and societies. For the first time, all digitized Global Jukebox data are being made available in open-access, downloadable format (https://github.com/theglobaljukebox), linked with streaming audio recordings (theglobaljukebox.org) to the maximum extent allowed while respecting copyright and the wishes of culture-bearers. The data are cross-indexed with the Database of Peoples, Languages, and Cultures (D-PLACE) to allow researchers to test hypotheses about worldwide coevolution of aesthetic patterns and traditions. As an example, we analyze the global relationship between song style and societal complexity, showing that they are robustly related, in contrast to previous critiques claiming that these proposed relationships were an artifact of autocorrelation (though causal mechanisms remain unresolved).}, } @article {pmid36318246, year = {2023}, author = {Lei, B and Xu, Y and Lei, Y and Li, C and Zhou, P and Wang, L and Yang, Q and Li, X and Li, F and Liu, C and Cui, C and Chen, T and Ni, W and Hu, S}, title = {CRAMdb: a comprehensive database for composition and roles of microbiome in animals.}, journal = {Nucleic acids research}, volume = {51}, number = {D1}, pages = {D700-D707}, pmid = {36318246}, issn = {1362-4962}, mesh = {Animals ; Archaea/genetics ; Bacteria/genetics ; Fungi/genetics ; Metagenome ; Metagenomics ; *Microbiota/genetics ; *Databases, Factual ; }, abstract = {CRAMdb (a database for composition and roles of animal microbiome) is a comprehensive resource of curated and consistently annotated metagenomes for non-human animals. It focuses on the composition and roles of the microbiome in various animal species. The main goal of the CRAMdb is to facilitate the reuse of animal metagenomic data, and enable cross-host and cross-phenotype comparisons. To this end, we consistently annotated microbiomes (including 16S, 18S, ITS and metagenomics sequencing data) of 516 animals from 475 projects spanning 43 phenotype pairs to construct the database that is equipped with 9430 bacteria, 278 archaea, 2216 fungi and 458 viruses. CRAMdb provides two main contents: microbiome composition data, illustrating the landscape of the microbiota (bacteria, archaea, fungi, and viruses) in various animal species, and microbiome association data, revealing the relationships between the microbiota and various phenotypes across different animal species. More importantly, users can quickly compare the composition of the microbiota of interest cross-host or body site and the associated taxa that differ between phenotype pairs cross-host or cross-phenotype. CRAMdb is freely available at (http://www.ehbio.com/CRAMdb).}, } @article {pmid36316770, year = {2022}, author = {Ohashi, K and Osanai, T and Fujiwara, K and Tanikawa, T and Tani, Y and Takamiya, S and Sato, H and Morii, Y and Bando, K and Ogasawara, K}, title = {Spatial-temporal analysis of cerebral infarction mortality in Hokkaido, Japan: an ecological study using a conditional autoregressive model.}, journal = {International journal of health geographics}, volume = {21}, number = {1}, pages = {16}, pmid = {36316770}, issn = {1476-072X}, mesh = {Humans ; Bayes Theorem ; Japan/epidemiology ; *Stroke ; Socioeconomic Factors ; Cerebral Infarction/diagnosis/epidemiology/therapy ; }, abstract = {BACKGROUND: Accessibility to stroke treatments is a challenge that depends on the place of residence. However, recent advances in medical technology have improved health outcomes. Nevertheless, the geographic heterogeneity of medical resources may increase regional disparities. Therefore, evaluating spatial and temporal influences of the medical system on regional outcomes and advanced treatment of cerebral infarction are important from a health policy perspective. This spatial and temporal study aims to identify factors associated with mortality and to clarify regional disparities in cerebral infarction mortality at municipality level.

METHODS: This ecological study used public data between 2010 and 2020 from municipalities in Hokkaido, Japan. We applied spatial and temporal condition autoregression analysis in a Bayesian setting, with inference based on the Markov chain Monte Carlo simulation. The response variable was the number of deaths due to cerebral infarction (ICD-10 code: I63). The explanatory variables were healthcare accessibility and socioeconomic status.

RESULTS: The large number of emergency hospitals per 10,000 people (relative risk (RR) = 0.906, credible interval (Cr) = 0.861 to 0.954) was associated with low mortality. On the other hand, the large number of general hospitals per 10,000 people (RR = 1.123, Cr = 1.068 to 1.178) and longer distance to primary stroke centers (RR = 1.064, Cr = 1.014 to 1.110) were associated with high mortality. The standardized mortality ratio decreased from 2010 to 2020 in Hokkaido by approximately 44%. Regional disparity in mortality remained at the same level from 2010 to 2015, after which it narrowed by approximately 5% to 2020. After mapping, we identified municipalities with high mortality rates that emerged in Hokkaido's central and northeastern parts.

CONCLUSION: Cerebral infarction mortality rates and the disparity in Hokkaido improved during the study period (2010-2020). This study emphasized that healthcare accessibility through places such as emergency hospitals and primary stroke centers was important in determining cerebral infarction mortality at the municipality level. In addition, this study identified municipalities with high mortality rates that require healthcare policy changes. The impact of socioeconomic factors on stroke is a global challenge, and improving access to healthcare may reduce disparities in outcomes.}, } @article {pmid36316345, year = {2022}, author = {Yfantidou, S and Karagianni, C and Efstathiou, S and Vakali, A and Palotti, J and Giakatos, DP and Marchioro, T and Kazlouski, A and Ferrari, E and Girdzijauskas, Š}, title = {LifeSnaps, a 4-month multi-modal dataset capturing unobtrusive snapshots of our lives in the wild.}, journal = {Scientific data}, volume = {9}, number = {1}, pages = {663}, pmid = {36316345}, issn = {2052-4463}, support = {RAIS No 813162//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 Marie Skłodowska-Curie Actions (H2020 Excellent Science - Marie Skłodowska-Curie Actions)/ ; RAIS No 813162//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 Marie Skłodowska-Curie Actions (H2020 Excellent Science - Marie Skłodowska-Curie Actions)/ ; RAIS No 813162//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 Marie Skłodowska-Curie Actions (H2020 Excellent Science - Marie Skłodowska-Curie Actions)/ ; RAIS No 813162//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 Marie Skłodowska-Curie Actions (H2020 Excellent Science - Marie Skłodowska-Curie Actions)/ ; RAIS No 813162//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 Marie Skłodowska-Curie Actions (H2020 Excellent Science - Marie Skłodowska-Curie Actions)/ ; RAIS No 813162//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 Marie Skłodowska-Curie Actions (H2020 Excellent Science - Marie Skłodowska-Curie Actions)/ ; RAIS No 813162//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 Marie Skłodowska-Curie Actions (H2020 Excellent Science - Marie Skłodowska-Curie Actions)/ ; RAIS No 813162//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 Marie Skłodowska-Curie Actions (H2020 Excellent Science - Marie Skłodowska-Curie Actions)/ ; }, mesh = {Humans ; *Ecological Momentary Assessment ; Exercise ; *Mental Health ; Sleep ; Surveys and Questionnaires ; }, abstract = {Ubiquitous self-tracking technologies have penetrated various aspects of our lives, from physical and mental health monitoring to fitness and entertainment. Yet, limited data exist on the association between in the wild large-scale physical activity patterns, sleep, stress, and overall health, and behavioral and psychological patterns due to challenges in collecting and releasing such datasets, including waning user engagement or privacy considerations. In this paper, we present the LifeSnaps dataset, a multi-modal, longitudinal, and geographically-distributed dataset containing a plethora of anthropological data, collected unobtrusively for the total course of more than 4 months by n = 71 participants. LifeSnaps contains more than 35 different data types from second to daily granularity, totaling more than 71 M rows of data. The participants contributed their data through validated surveys, ecological momentary assessments, and a Fitbit Sense smartwatch and consented to make these data available to empower future research. We envision that releasing this large-scale dataset of multi-modal real-world data will open novel research opportunities and potential applications in multiple disciplines.}, } @article {pmid36311410, year = {2022}, author = {Nicotra, AB and Geange, SR and Bahar, NHA and Carle, H and Catling, A and Garcia, A and Harris, RJ and Head, ML and Jin, M and Whitehead, MR and Zurcher, H and Beckmann, EA}, title = {An innovative approach to using an intensive field course to build scientific and professional skills.}, journal = {Ecology and evolution}, volume = {12}, number = {10}, pages = {e9446}, pmid = {36311410}, issn = {2045-7758}, abstract = {This paper reports on the design and evaluation of Field Studies in Functional Ecology (FSFE), a two-week intensive residential field course that enables students to master core content in functional ecology alongside skills that facilitate their transition from "student" to "scientist." We provide an overview of the course structure, showing how the constituent elements have been designed and refined over successive iterations of the course. We detail how FSFE students: (1) Work closely with discipline specialists to develop a small group project that tests an hypothesis to answer a genuine scientific question in the field; (2) Learn critical skills of data management and communication; and (3) Analyze, interpret, and present their results in the format of a scientific symposium. This process is repeated in an iterative "cognitive apprenticeship" model, supported by a series of workshops that name and explicitly instruct the students in "hard" and "soft" skills (e.g., statistics and teamwork, respectively) critically relevant for research and other careers. FSFE students develop a coherent and nuanced understanding of how to approach and execute ecological studies. The sophisticated knowledge and ecological research skills that they develop during the course is demonstrated through high-quality presentations and peer-reviewed publications in an open-access, student-led journal. We outline our course structure and evaluate its efficacy to show how this novel combination of field course elements allows students to gain maximum value from their educational journey, and to develop cognitive, affective, and reflective tools to help apply their skills as scientists.}, } @article {pmid36308510, year = {2023}, author = {Sun, Y and Chang, J and Fang, J}, title = {Above- and belowground net-primary productivity: A field-based global database of grasslands.}, journal = {Ecology}, volume = {104}, number = {2}, pages = {e3904}, doi = {10.1002/ecy.3904}, pmid = {36308510}, issn = {1939-9170}, mesh = {*Ecosystem ; *Grassland ; Temperature ; Databases, Factual ; Carbon ; }, abstract = {Net primary productivity (NPP) over global grasslands is crucial for understanding the terrestrial carbon cycling and for the assessments of wild herbivores food security. During the past few decades, numerous field investigations have been conducted to estimate grassland NPP since the measuring criterion released by the International Biological Program. However, a comprehensive NPP database, particularly for belowground NPP (BNPP), in global grasslands is rare to date. Here, field NPP measurements from 438 publications (1957-2018) in global grasslands were collected, critically filtered, and incorporated in a comprehensive global database with observations for aboveground NPP (ANPP), BNPP, total NPP (TNPP), and BNPP fraction (fBNPP). Associated information on geographical locations, climatic records, grassland types, land use patterns, manipulations subjected to manipulative experiments, sampling year of study sites, as well as NPP measurement methods are also documented. This database included 2985 entries from 1785 study sites. Among them, 806 entries contained paired data of ANPP and BNPP, resulting in the 806 fBNPP data. The study sites encompassed global grasslands with latitudinal range of 54.5° S~78.9° N, longitudinal range of 157.4° W~175.8° E, and altitudes from 0 to 5168 m above sea level, covering broad climatic gradients (-17.6 to 28.8°C in mean annual temperature and 63-2052 mm in mean annual precipitation). This global database is the world's largest paired data of ANPP and BNPP field measurements in grasslands. It can be used to study the spatio-temporal patterns of NPP and its allocation, evaluate the responses of above- and below-ground carbon components to future global changes, and validate the NPP estimation by empirical or process-based models in global grasslands. The database can be freely used for noncommercial applications. We kindly request users cite this data paper when using the database, respecting all the hard work during data compilation.}, } @article {pmid36305818, year = {2023}, author = {Chen, Y and Zhang, X and Peng, X and Jin, Y and Ding, P and Xiao, J and Li, C and Wang, F and Chang, A and Yue, Q and Pu, M and Chen, P and Shen, J and Li, M and Jia, T and Wang, H and Huang, L and Guo, G and Zhang, W and Liu, H and Wang, X and Chen, D}, title = {SPEED: Single-cell Pan-species atlas in the light of Ecology and Evolution for Development and Diseases.}, journal = {Nucleic acids research}, volume = {51}, number = {D1}, pages = {D1150-D1159}, pmid = {36305818}, issn = {1362-4962}, mesh = {*Databases, Factual ; *Single-Cell Analysis ; Humans ; Animals ; Biological Evolution ; Plants/genetics ; Ecology ; }, abstract = {It is a challenge to efficiently integrate and present the tremendous amounts of single-cell data generated from multiple tissues of various species. Here, we create a new database named SPEED for single-cell pan-species atlas in the light of ecology and evolution for development and diseases (freely accessible at http://8.142.154.29 or http://speedatlas.net). SPEED is an online platform with 4 data modules, 7 function modules and 2 display modules. The 'Pan' module is applied for the interactive analysis of single cell sequencing datasets from 127 species, and the 'Evo', 'Devo', and 'Diz' modules provide comprehensive analysis of single-cell atlases on 18 evolution datasets, 28 development datasets, and 85 disease datasets. The 'C2C', 'G2G' and 'S2S' modules explore intercellular communications, genetic regulatory networks, and cross-species molecular evolution. The 'sSearch', 'sMarker', 'sUp', and 'sDown' modules allow users to retrieve specific data information, obtain common marker genes for cell types, freely upload, and download single-cell datasets, respectively. Two display modules ('HOME' and 'HELP') offer easier access to the SPEED database with informative statistics and detailed guidelines. All in all, SPEED is an integrated platform for single-cell RNA sequencing (scRNA-seq) and single-cell whole-genome sequencing (scWGS) datasets to assist the deep-mining and understanding of heterogeneity among cells, tissues, and species at multi-levels, angles, and orientations, as well as provide new insights into molecular mechanisms of biological development and pathogenesis.}, } @article {pmid36302928, year = {2022}, author = {Hammoud, R and Tognin, S and Burgess, L and Bergou, N and Smythe, M and Gibbons, J and Davidson, N and Afifi, A and Bakolis, I and Mechelli, A}, title = {Smartphone-based ecological momentary assessment reveals mental health benefits of birdlife.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {17589}, pmid = {36302928}, issn = {2045-2322}, support = {MR/S026428/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Humans ; *Ecological Momentary Assessment ; Smartphone ; Mental Health ; Retrospective Studies ; *Mobile Applications ; }, abstract = {The mental health benefits of everyday encounters with birdlife for mental health are poorly understood. Previous studies have typically relied on retrospective questionnaires or artificial set-ups with little ecological validity. In the present study, we used the Urban Mind smartphone application to examine the impact of seeing or hearing birds on self-reported mental wellbeing in real-life contexts. A sample of 1292 participants completed a total of 26,856 ecological momentary assessments between April 2018 and October 2021. Everyday encounters with birdlife were associated with time-lasting improvements in mental wellbeing. These improvements were evident not only in healthy people but also in those with a diagnosis of depression, the most common mental illness across the world. These findings have potential implications for both environmental and wildlife protection and mental healthcare policies. Specific measures, aimed at preserving and increasing everyday encounters with birdlife in urban areas, should be implemented.}, } @article {pmid36302597, year = {2023}, author = {Verbitsky, M and Krishnamurthy, S and Krithivasan, P and Hughes, D and Khan, A and Marasà, M and Vena, N and Khosla, P and Zhang, J and Lim, TY and Glessner, JT and Weng, C and Shang, N and Shen, Y and Hripcsak, G and Hakonarson, H and Ionita-Laza, I and Levy, B and Kenny, EE and Loos, RJF and Kiryluk, K and Sanna-Cherchi, S and Crosslin, DR and Furth, S and Warady, BA and Igo, RP and Iyengar, SK and Wong, CS and Parsa, A and Feldman, HI and Gharavi, AG}, title = {Genomic Disorders in CKD across the Lifespan.}, journal = {Journal of the American Society of Nephrology : JASN}, volume = {34}, number = {4}, pages = {607-618}, pmid = {36302597}, issn = {1533-3450}, support = {U01 DK066143/DK/NIDDK NIH HHS/United States ; U01 DK066174/DK/NIDDK NIH HHS/United States ; K25 DK128563/DK/NIDDK NIH HHS/United States ; UL1 TR004419/TR/NCATS NIH HHS/United States ; R21 DK119802/DK/NIDDK NIH HHS/United States ; R01 DK080099/DK/NIDDK NIH HHS/United States ; }, mesh = {Humans ; Cohort Studies ; *Longevity ; Prospective Studies ; *Renal Insufficiency, Chronic/epidemiology/genetics/complications ; Genomics ; Disease Progression ; Risk Factors ; }, abstract = {SIGNIFICANCE STATEMENT: Pathogenic structural genetic variants, also known as genomic disorders, have been associated with pediatric CKD. This study extends those results across the lifespan, with genomic disorders enriched in both pediatric and adult patients compared with controls. In the Chronic Renal Insufficiency Cohort study, genomic disorders were also associated with lower serum Mg, lower educational performance, and a higher risk of death. A phenome-wide association study confirmed the link between kidney disease and genomic disorders in an unbiased way. Systematic detection of genomic disorders can provide a molecular diagnosis and refine prediction of risk and prognosis.

BACKGROUND: Genomic disorders (GDs) are associated with many comorbid outcomes, including CKD. Identification of GDs has diagnostic utility.

METHODS: We examined the prevalence of GDs among participants in the Chronic Kidney Disease in Children (CKiD) cohort II (n =248), Chronic Renal Insufficiency Cohort (CRIC) study (n =3375), Columbia University CKD Biobank (CU-CKD; n =1986), and the Family Investigation of Nephropathy and Diabetes (FIND; n =1318) compared with 30,746 controls. We also performed a phenome-wide association analysis (PheWAS) of GDs in the electronic MEdical Records and GEnomics (eMERGE; n =11,146) cohort.

RESULTS: We found nine out of 248 (3.6%) CKiD II participants carried a GD, replicating prior findings in pediatric CKD. We also identified GDs in 72 out of 6679 (1.1%) adult patients with CKD in the CRIC, CU-CKD, and FIND cohorts, compared with 199 out of 30,746 (0.65%) GDs in controls (OR, 1.7; 95% CI, 1.3 to 2.2). Among adults with CKD, we found recurrent GDs at the 1q21.1, 16p11.2, 17q12, and 22q11.2 loci. The 17q12 GD (diagnostic of renal cyst and diabetes syndrome) was most frequent, present in 1:252 patients with CKD and diabetes. In the PheWAS, dialysis and neuropsychiatric phenotypes were the top associations with GDs. In CRIC participants, GDs were associated with lower serum magnesium, lower educational achievement, and higher mortality risk.

CONCLUSION: Undiagnosed GDs are detected both in children and adults with CKD. Identification of GDs in these patients can enable a precise genetic diagnosis, inform prognosis, and help stratify risk in clinical studies. GDs could also provide a molecular explanation for nephropathy and comorbidities, such as poorer neurocognition for a subset of patients.}, } @article {pmid36300397, year = {2022}, author = {Kulikowski, CA}, title = {50 Years of Achievements and Persistent Challenges for Biomedical and Health Informatics and John Mantas' Educational and Nursing Informatics Contributions.}, journal = {Studies in health technology and informatics}, volume = {300}, number = {}, pages = {1-11}, doi = {10.3233/SHTI220936}, pmid = {36300397}, issn = {1879-8365}, mesh = {*Nursing Informatics ; *Medical Informatics ; Cybernetics ; Expert Systems ; }, abstract = {Biomedical and Health Informatics (BMHI) have been essential catalysts for achievements in medical research and healthcare applications over the past 50 years. These include increasingly sophisticated information systems and data bases for documentation and processing, standardization of biomedical data, nomenclatures, and vocabularies to assist with large scale literature indexing and text analysis for information retrieval, and methods for computationally modeling and analyzing research and clinical data. Statistical and AI techniques for decision support, instrumentation integration, and workflow aids with improved data/information management tools are critical for scientific discoveries in the - omics revolutions with their related drug and vaccine breakthroughs and their translation to clinical and preventive healthcare. Early work on biomedical image and pattern recognition, knowledge-based expert systems, innovative database, software and simulation techniques, natural language processing and computational ontologies have all been invaluable for basic research and education. However, these methods are still in their infancy and many fundamental open scientific problems abound. Scientifically this is due to persistent limitations in understanding biological processes within complex living environments and ecologies. In clinical practice the modeling of fluid practitioner roles and methods as they adjust to novel cybernetic technologies present great opportunities but also the potential of unintended e-iatrogenic harms which must be constrained in order to adhere to ethical Hippocratic norms of responsible behavior. Balancing the art, science, and technologies of BMHI has been a hallmark of debates about the field's historical evolution. The present article reviews selected milestones, achievements, and challenges in BMHI education mainly, from a historical perspective, including some commentaries from leaders and pioneers in the field, a selection of which have been published online recently by the International Medical Informatics Association (IMIA) as the first volume of an IMIA History WG eBook. The focus of this chapter is primarily on the development of BMHI in terms of those of its educational activities which have been most significant during the first half century of IMIA, and it concentrates mainly on the leadership and contributions of John Mantas who is being honored on his retirement by the Symposia in Athens for which this chapter has been written.}, } @article {pmid36297864, year = {2022}, author = {Macchia, A and Biribicchi, C and Zaratti, C and Testa Chiari, K and D'Ambrosio, M and Toscano, D and Izzo, FC and La Russa, MF}, title = {Mattel's Barbie: Investigation of a Symbol-Analysis of Polymeric Matrices and Degradation Phenomena for Sixteen Dolls from 1959 to 1976.}, journal = {Polymers}, volume = {14}, number = {20}, pages = {}, pmid = {36297864}, issn = {2073-4360}, abstract = {Mattel's Barbie dolls are the most famous and iconic dolls since 1959. Today, they are being collected by individuals and often conserved in museum environments due to their cultural and historical significance reflecting everyday life and historical events. However, just like most museum objects made of plastics, both historical and more recent Barbies show evident degradation phenomena. Firstly, Barbies were made of plasticized polyvinyl chloride (PVC), affected by the migration of additives-mostly the plasticizers-from the bulk phase to the outermost layer, appearing as a tacky and glossy exudate. Over the years, Barbies' polymeric constituents were replaced with more stable ones, whose additives migration is limited compared to PVC, even though still occurring. Multispectral photography in visible (VIS) and ultraviolet (UV) light, microscopical observations in VIS and UV light, and Fourier Transform Infrared spectroscopy in the Attenuated Total Reflectance mode (FT-IR ATR) were performed to characterize the constituent materials of 15 Barbies produced between 1959 and 1976, bridging the information gap on their processing over the years. The micro-invasive multi-analytical approach also allowed for the characterization of the degradation products, permitting the reference of the exudated compound to the specific bulk polymer.}, } @article {pmid36297101, year = {2022}, author = {Maugeri, A and Magnano San Lio, R and Favara, G and La Rosa, MC and La Mastra, C and Riela, PM and Guarnera, L and Battiato, S and Barchitta, M and Agodi, A}, title = {Impact of Eating Context on Dietary Choices of College Students: Evidence from the HEALTHY-UNICT Project.}, journal = {Nutrients}, volume = {14}, number = {20}, pages = {}, pmid = {36297101}, issn = {2072-6643}, support = {Programma ricerca di ateneo UNICT 2020-22 linea 4, PIAno di inCEntivi per la RIcerca di Ateneo 2020/2022//University of Catania, Italy, Department of Medical and Surgical Science and Advanced Tech-nologies 'GF Ingrassia'/ ; }, mesh = {Humans ; *Diet ; *Vegetables ; Feeding Behavior ; Meals ; Students ; }, abstract = {While personal characteristics have been evaluated as determinants of dietary choices over the years, only recently studies have looked at the impact of eating context. Examining eating context, however, can be challenging. Here, we propose the use of a web-app for the Ecological Momentary Assessment of dietary habits among 138 college students from Catania (Italy) and therefore for examining the impact of eating context on dietary choices. Eating away from home was associated with lower odds of consuming vegetables, fruits, and legumes and higher odds of consuming processed meat, salty snacks, and alcoholic drinks compared with eating at home. Eating in the company of other people was associated with higher odds of consuming vegetables, red meat, fish, legumes, milk, and sugar-sweetened beverages and lower odds of consuming nuts than eating alone. This study proposed a new way to capture and assess how eating environment might affect dietary habits. Based on our results, meal location and social context have significant effects on the dietary choices of college students, pointing to the need to incorporate these aspects into further epidemiological studies.}, } @article {pmid36296237, year = {2022}, author = {Trego, A and Keating, C and Nzeteu, C and Graham, A and O'Flaherty, V and Ijaz, UZ}, title = {Beyond Basic Diversity Estimates-Analytical Tools for Mechanistic Interpretations of Amplicon Sequencing Data.}, journal = {Microorganisms}, volume = {10}, number = {10}, pages = {}, pmid = {36296237}, issn = {2076-2607}, support = {NE/L011956/1//Natural Environment Research Council/ ; EP/P029329/1//Engineering and Physical Sciences Research Council/ ; EP/V030515/1//Engineering and Physical Sciences Research Council/ ; TC/2014/0016//Enterprise Ireland/ ; 14/IA/2371/SFI_/Science Foundation Ireland/Ireland ; 16/RC/3889/SFI_/Science Foundation Ireland/Ireland ; }, abstract = {Understanding microbial ecology through amplifying short read regions, typically 16S rRNA for prokaryotic species or 18S rRNA for eukaryotic species, remains a popular, economical choice. These methods provide relative abundances of key microbial taxa, which, depending on the experimental design, can be used to infer mechanistic ecological underpinnings. In this review, we discuss recent advancements in in situ analytical tools that have the power to elucidate ecological phenomena, unveil the metabolic potential of microbial communities, identify complex multidimensional interactions between species, and compare stability and complexity under different conditions. Additionally, we highlight methods that incorporate various modalities and additional information, which in combination with abundance data, can help us understand how microbial communities respond to change in a typical ecosystem. Whilst the field of microbial informatics continues to progress substantially, our emphasis is on popular methods that are applicable to a broad range of study designs. The application of these methods can increase our mechanistic understanding of the ongoing dynamics of complex microbial communities.}, } @article {pmid36295335, year = {2022}, author = {Cherevko, AG and Krygin, AS and Ivanov, AI and Soots, RA and Antonova, IV}, title = {Benefits of Printed Graphene with Variable Resistance for Flexible and Ecological 5G Band Antennas.}, journal = {Materials (Basel, Switzerland)}, volume = {15}, number = {20}, pages = {}, pmid = {36295335}, issn = {1996-1944}, support = {FZSR-2022-0009//Ministry of Science and Higher Education of the Russian Federation/ ; 071-03-2022-001//Ministry of Digital Development, Telecommunications and Mass Media of the RF/ ; }, abstract = {The possibility of creating antennas of the 5G standard (5.2-5.9 GHz) with specified electrodynamic characteristics by printing layers of variable thickness using a graphene suspension has been substantiated experimentally and by computer simulation. A graphene suspension for screen printing on photographic paper and other flexible substrates was prepared by means of exfoliation from graphite. The relation between the graphene layer thickness and its sheet resistance was studied with the aim of determining the required thickness of the antenna conductive layer. To create a two-sided dipole, a technology has been developed for the double-sided deposition of graphene layers on photographic paper. The electrodynamic characteristics of graphene and copper antennas of identical design are compared. The antenna design corresponds to the operating frequency of 2.4 GHz. It was found that the use of graphene as a conductive layer made it possible to suppress the fundamental (first) harmonic (2.45 GHz) and to observe radiation at the second harmonic (5.75 GHz). This effect is assumed to observe in the case when the thickness of graphene is lower than that of the skin depth. The result indicates the possibility of changing the antenna electrodynamic characteristics by adjusting the graphene layer thickness.}, } @article {pmid36293641, year = {2022}, author = {Zou, H and Liu, Y and Li, B and Luo, W}, title = {Sustainable Development Efficiency of Cultural Landscape Heritage in Urban Fringe Based on GIS-DEA-MI, a Case Study of Wuhan, China.}, journal = {International journal of environmental research and public health}, volume = {19}, number = {20}, pages = {}, pmid = {36293641}, issn = {1660-4601}, support = {20YJC760145//Ministry of Education, Humanities and Social Sciences Youth Fund/ ; 20Y044//Humanities and Social Sciences Fund of Hubei Education Department/ ; XJ2021005501//Hubei University of Technology Green Industry Science and Technology Leading Program/ ; 2020EJB004//Innovation Demonstration Base of Ecological Environment Geotechnical and Ecological Restoration of Rivers and Lakes/ ; }, mesh = {Humans ; Cities ; *Conservation of Natural Resources/methods ; *Sustainable Development ; Geographic Information Systems ; Urbanization ; China ; }, abstract = {Cultural landscape heritage refers to the rare and irreplaceable cultural landscapes recognized by UNESCO and the World Heritage Committee. It is recognized as a "common works of nature and human beings" of outstanding significance and universal value, and is a type of world heritage. Dueto construction, land isincreasingly limited in urban and rural areasin the process of urbanization, and cultural landscape heritage faces a huge threat, especially larger culturallandscapeheritagelocated at the edgesof cities. However, most of the existing studies have mainly focused on the material protection of heritage but have not paid enough attention to the non-material aspects of heritage sites, failing to reveal the inseparable nature of heritage and land. Therefore, this study takes sustainable development efficiency as its analysis tool, examines two pieces of cultural landscape heritage (the Panlongcheng site and the Tomb of the King of the Ming Dynasty) in the urban edge area of Wuhan, China as examples, innovates and establishes a multidimensional evaluation method based on the GIS-DEA-Ml model, and compares the dynamic changes of the spatial development efficiency and non-spatial development efficiency of the above two cultural landscape heritage cases. The results show that: both the spatial development efficiency and non-spatial development efficiency of Panlongcheng from 2010 to 2019 are significantly higher than that of the Tomb. This method makes up for the deficiency of traditional subjective qualitative analysis. It can be used to study the development efficiency of cultural landscape heritage more objectively and comprehensively, and promote the overall sustainable development of material and intangible cultural heritage. It can provide the basis for early decision-making and post-implementation evaluation for the preservation and utilization of cultural landscape heritage under the background of urban renewal.}, } @article {pmid36293613, year = {2022}, author = {Aleni, C and Rinaldi, C and Bettio, V and Mazzucco, E and Antona, A and Meini, C and Loria, E and Bonvicini, P and Cracas, SV and Caristia, S and Rimedio, A and Faggiano, F and Ferrante, D and Capello, D}, title = {Public Attitude towards Biobanking: An Italian University Survey.}, journal = {International journal of environmental research and public health}, volume = {19}, number = {20}, pages = {}, pmid = {36293613}, issn = {1660-4601}, mesh = {Humans ; *Biological Specimen Banks ; Universities ; Attitude ; Public Opinion ; Surveys and Questionnaires ; *Biomedical Research ; }, abstract = {Biobanks have established a critical role in biomedical research by collecting, preserving, organizing, and disseminating biospecimens and related health data, contributing to precision medicine development. Participation in biobanks is influenced by several factors, such as trust in institutions and scientists, knowledge about biobanking, and the consideration of benefit sharing. Understanding public attitudes, fears, and concerns toward biobanking is fundamental to designing targeted interventions to increase trust towards biobanks. The aim of our study was to investigate the level of knowledge and perception of biobanks in students and personnel of the University of Piemonte Orientale. An online questionnaire was designed and administered via e-mail. A total of 17,758 UPO personnel and students were invited to participate in the survey, and 1521 (9.3%) subjects completed the survey. The results showed that 65.0% of the participants were aware of the term "biobank" and knew what the activity of a biobank was, and 76.3% of subjects were willing to provide biospecimens to a research biobank, whereas 67.3% of the respondents were willing to contribute, in addition to biospecimens, their health and lifestyle data. Concerns were raised about the confidentiality of the information (25.6%) and the commercial use of the samples (25.0%). In conclusion, participants were aware of the role that biobanks play in research and were eager to participate for the sake of furthering scientific research. Still, several concerns need to be addressed regarding the confidentiality of the data along with the commercial use of the samples and associated data.}, } @article {pmid36289166, year = {2022}, author = {Navidi, MN and Chatrenour, M and Seyedmohammadi, J and Khaki, BD and Moradi-Majd, N and Mirzaei, S}, title = {Ecological potential assessment and land use area estimation of agricultural lands based on multi-time images of Sentinel-2 using ANP-WLC and GIS in Bastam, Iran.}, journal = {Environmental monitoring and assessment}, volume = {195}, number = {1}, pages = {36}, pmid = {36289166}, issn = {1573-2959}, mesh = {Agriculture ; Conservation of Natural Resources/methods ; Environmental Monitoring/methods ; *Geographic Information Systems ; Iran ; Soil ; }, abstract = {The use of land-based ecological potential is a key management factor in achieving sustainable development and conserving soil and water resources. The purpose of this study is to use multi-time images of Sentinel-2 to determine the area of agricultural lands and evaluate their ecological potential in Bastam, Semnan Province, Iran. Therefore, in the first step, the most common agricultural lands (including apricot and grape orchards), field crops (including wheat and forage maize), and their phenological period were determined. Then, the information was classified using, namely support vector machine, maximum likelihood, and minimum distance. In the next step, soil, topography, and climate data were extracted according to expert opinions and the analysis of the basin's natural potential. The ecological evaluation models of the region were applied to homogeneous units, and after calculating the ecological potential index by the integrated ANP-WLC model, the ecological potential map was generated. The results of the land use classification showed that the support vector machine model and the minimum distance, respectively, had the best and worst performance with kappa coefficient of 0.82 and 0.61. The highest area of cultivated lands (3423 hectares) was estimated for wheat and the lowest (738 hectares) for forage maize. Moreover, the results of the ecological potential evaluation showed that 60% of apricot orchards, and 40.19% of the wheat fields, were in the class of good ecological potential. Overall, 2290 hectares were in the poor class, and 4030 hectares in the excellent class in terms of ecological potential.}, } @article {pmid36287517, year = {2022}, author = {Gonçalves, ICM and Freitas, RF and Aquino, EC and Carneiro, JA and Lessa, ADC}, title = {Mortality trend from falls in Brazilian older adults from 2000 to 2019.}, journal = {Revista brasileira de epidemiologia = Brazilian journal of epidemiology}, volume = {25}, number = {}, pages = {e220031}, doi = {10.1590/1980-549720220031.2}, pmid = {36287517}, issn = {1980-5497}, mesh = {Male ; Humans ; Female ; Aged ; *Accidental Falls ; Brazil/epidemiology ; *Quality of Life ; Retrospective Studies ; Information Systems ; Mortality ; }, abstract = {OBJECTIVE: To analyze the trend of mortality from falls among older adults in Brazil from 2000 to 2019.

METHODS: This is an epidemiological, analytical study with an ecological time-series design. A retrospective analysis was performed using secondary health data extracted from the Brazilian Mortality Information System in the specific period. Standardized rates of general and sex- and age-specific mortality were calculated. To observe the mortality trend, the Prais-Winsten model and the Annual Increase Rate (AIR) were used.

RESULTS: We identified 135,209 deaths resulting from falls in older adults in the period from 2000 to 2019. Mortality from falls in general, during the study period, had an upward trend (β=0.023; p<0.001; AIR=5.45%). We observed that both men (β=0.022; p<0.001; AIR=5.19%) and women (β=0.024; p<0.001; AIR=5.72%) had an upward trend. Regarding age group, the results also pointed to an upward mortality trend in all age strata, although higher in older people aged ≥80 years (β=0.027; p<0.001; AIR=6.38%).

CONCLUSION: There was an upward trend in mortality rates in Brazil during the time series studied. These findings suggest the importance of defining a line of care for this age group, focusing on promoting health in older adults and preventing the risk of falls, aiming at a reduction in the number of deaths from this cause and favoring the quality of life of this population.}, } @article {pmid36287142, year = {2022}, author = {Miller-Ter Kuile, A and Apigo, A and Bui, A and Butner, K and Childress, JN and Copeland, S and DiFiore, BP and Forbes, ES and Klope, M and Motta, CI and Orr, D and Plummer, KA and Preston, DL and Young, HS}, title = {Changes in invertebrate food web structure between high- and low-productivity environments are driven by intermediate but not top-predator diet shifts.}, journal = {Biology letters}, volume = {18}, number = {10}, pages = {20220364}, pmid = {36287142}, issn = {1744-957X}, mesh = {Animals ; *Food Chain ; *Ecosystem ; Predatory Behavior/physiology ; Invertebrates ; Diet ; }, abstract = {Predator-prey interactions shape ecosystem stability and are influenced by changes in ecosystem productivity. However, because multiple biotic and abiotic drivers shape the trophic responses of predators to productivity, we often observe patterns, but not mechanisms, by which productivity drives food web structure. One way to capture mechanisms shaping trophic responses is to quantify trophic interactions among multiple trophic groups and by using complementary metrics of trophic ecology. In this study, we combine two diet-tracing methods: diet DNA and stable isotopes, for two trophic groups (top predators and intermediate predators) in both low- and high-productivity habitats to elucidate where in the food chain trophic structure shifts in response to changes in underlying ecosystem productivity. We demonstrate that while top predators show increases in isotopic trophic position (δ[15]N) with productivity, neither their isotopic niche size nor their DNA diet composition changes. Conversely, intermediate predators show clear turnover in DNA diet composition towards a more predatory prey base in high-productivity habitats. Taking this multi-trophic approach highlights how predator identity shapes responses in predator-prey interactions across environments with different underlying productivity, building predictive power for understanding the outcomes of ongoing anthropogenic change.}, } @article {pmid36284162, year = {2022}, author = {Geneva, AJ and Park, S and Bock, DG and de Mello, PLH and Sarigol, F and Tollis, M and Donihue, CM and Reynolds, RG and Feiner, N and Rasys, AM and Lauderdale, JD and Minchey, SG and Alcala, AJ and Infante, CR and Kolbe, JJ and Schluter, D and Menke, DB and Losos, JB}, title = {Chromosome-scale genome assembly of the brown anole (Anolis sagrei), an emerging model species.}, journal = {Communications biology}, volume = {5}, number = {1}, pages = {1126}, pmid = {36284162}, issn = {2399-3642}, support = {T32 GM007103/GM/NIGMS NIH HHS/United States ; DEB-1927194//National Science Foundation (NSF)/ ; IOS-1827647//National Science Foundation (NSF)/ ; DEB-1927156//National Science Foundation (NSF)/ ; }, mesh = {Animals ; *Lizards/genetics ; Genome ; Sex Chromosomes ; Genomics ; X Chromosome ; }, abstract = {Rapid technological improvements are democratizing access to high quality, chromosome-scale genome assemblies. No longer the domain of only the most highly studied model organisms, now non-traditional and emerging model species can be genome-enabled using a combination of sequencing technologies and assembly software. Consequently, old ideas built on sparse sampling across the tree of life have recently been amended in the face of genomic data drawn from a growing number of high-quality reference genomes. Arguably the most valuable are those long-studied species for which much is already known about their biology; what many term emerging model species. Here, we report a highly complete chromosome-scale genome assembly for the brown anole, Anolis sagrei - a lizard species widely studied across a variety of disciplines and for which a high-quality reference genome was long overdue. This assembly exceeds the vast majority of existing reptile and snake genomes in contiguity (N50 = 253.6 Mb) and annotation completeness. Through the analysis of this genome and population resequence data, we examine the history of repetitive element accumulation, identify the X chromosome, and propose a hypothesis for the evolutionary history of fusions between autosomes and the X that led to the sex chromosomes of A. sagrei.}, } @article {pmid36270368, year = {2023}, author = {Derx, J and Kılıç, HS and Linke, R and Cervero-Aragó, S and Frick, C and Schijven, J and Kirschner, AKT and Lindner, G and Walochnik, J and Stalder, G and Sommer, R and Saracevic, E and Zessner, M and Blaschke, AP and Farnleitner, AH}, title = {Probabilistic fecal pollution source profiling and microbial source tracking for an urban river catchment.}, journal = {The Science of the total environment}, volume = {857}, number = {Pt 2}, pages = {159533}, doi = {10.1016/j.scitotenv.2022.159533}, pmid = {36270368}, issn = {1879-1026}, mesh = {Animals ; Humans ; Rivers ; Water Pollution/analysis ; Water Microbiology ; *Cryptosporidiosis ; Escherichia coli ; Environmental Monitoring/methods ; *Cryptosporidium ; Feces/chemistry ; Giardia ; Water/analysis ; }, abstract = {We developed an innovative approach to estimate the occurrence and extent of fecal pollution sources for urban river catchments. The methodology consists of 1) catchment surveys complemented by literature data where needed for probabilistic estimates of daily produced fecal indicator (FIBs, E. coli, enterococci) and zoonotic reference pathogen numbers (Campylobacter, Cryptosporidium and Giardia) excreted by human and animal sources in a river catchment, 2) generating a hypothesis about the dominant sources of fecal pollution and selecting a source targeted monitoring design, and 3) verifying the results by comparing measured concentrations of the informed choice of parameters (i.e. chemical tracers, C. perfringensspores, and host-associated genetic microbial source tracking (MST) markers) in the river, and by multi-parametric correlation analysis. We tested the approach at a study area in Vienna, Austria. The daily produced microbial particle numbers according to the probabilistic estimates indicated that, for the dry weather scenario, the discharge of treated wastewater (WWTP) was the primary contributor to fecal pollution. For the wet weather scenario, 80-99 % of the daily produced FIBs and pathogens resulted from combined sewer overflows (CSOs) according to the probabilistic estimates. When testing our hypothesis in the river, the measured concentrations of the human genetic fecal marker were log10 4 higher than for selected animal genetic fecal markers. Our analyses showed for the first-time statistical relationships between C. perfringens spores (used as conservative microbial tracer for communal sewage) and a human genetic fecal marker (i.e. HF183/BacR287) with the reference pathogen Giardia in river water (Spearman rank correlation: 0.78-0.83, p < 0.05. The developed approach facilitates urban water safety management and provides a robust basis for microbial fate and transport models and microbial infection risk assessment.}, } @article {pmid36264457, year = {2023}, author = {Nasiruddin, M and Islam, ARMT and Siddique, MAB and Hasanuzaman, M and Hassan, MM and Akbor, MA and Hasan, M and Islam, MS and Khan, R and Al Amin, M and Pal, SC and Idris, AM and Kumar, S}, title = {Distribution, sources, and pollution levels of toxic metal(loid)s in an urban river (Ichamati), Bangladesh using SOM and PMF modeling with GIS tool.}, journal = {Environmental science and pollution research international}, volume = {30}, number = {8}, pages = {20934-20958}, pmid = {36264457}, issn = {1614-7499}, support = {The authors extend their appreciation to the Deanship of Scientific Research at King Khalid University for funding this work through Research Group under grant number (RGP2/169/43)//King Khalid University/ ; }, mesh = {Humans ; *Metals, Heavy/analysis ; Environmental Monitoring ; Geographic Information Systems ; Rivers ; Bangladesh ; Cadmium/analysis ; Lead/analysis ; Geologic Sediments/analysis ; *Water Pollutants, Chemical/analysis ; Water Quality ; Risk Assessment ; China ; }, abstract = {Indexical assessment coupled with a self-organizing map (SOM) and positive matrix factorization (PMF) modeling of toxic metal(loid)s in sediment and water of the aquatic environment provides valuable information from the environmental management perspective. However, in northwest Bangladesh, indexical and modeling assessments of toxic metal(loid)s in surface water and sediment are still rare. Toxic metal(loid)s were measured in sediment and surface water from an urban polluted river (Ichamati) in northwest Bangladesh using an atomic absorption spectrophotometer to assess distribution, pollution levels, sources, and potential environmental risks to the aquatic environment. The mean concentrations (mg/kg) of metal(loid)s in water are as follows: Fe (871) > Mn (382) > Cr (72.4) > Zn (34.2) > Co (20.8) > Pb (17.6) > Ni (16.7) > Ag (14.9) > As (9.0) > Cu (5.63) > Cd (2.65), while in sediment, the concentration follows the order, Fe (18,725) > Mn (551) > Zn (213) > Cu (47.6) > Cr (30.2) > Ni (24.2) > Pb (23.8) > Co (9.61) > As (8.23) > Cd (0.80) > Ag (0.60). All metal concentrations were within standard guideline values except for Cr and Pb for water and Cd, Zn, Cu, Pb, and As for sediment. The outcomes of eco-environmental indices, including contamination and enrichment factors and geo-accumulation index, differed spatially, indicating that most of the sediment sites were moderately to highly polluted by Cd, Zn, and As. Cd and Zn content can trigger ecological risks. The positive matrix factorization (PMF) model recognized three probable sources of sediment, i.e., natural source (49.39%), industrial pollution (19.72%), and agricultural source (30.92%), and three possible sources of water, i.e., geogenic source (45.41%), industrial pollution (22.88%), and industrial point source (31.72%), respectively. SOM analysis identified four spatial patterns, e.g., Fe-Mn-Ag, Cd-Cu, Cr-Pb-As-Ni, and Zn-Co in water and three patterns, e.g., Mn-Co-Ni-Cr, Cd-Cu-Pb-Zn, and As-Fe-Ag in sediment. The spatial distribution of entropy water quality index values shows that the southwestern area possesses "poor" quality water. Overall, the levels of metal(loid) pollution in the investigated river surpassed a critical threshold, which might have serious consequences for the river's aquatic biota and human health in the long run.}, } @article {pmid36263952, year = {2023}, author = {Jensen, MA and Blatz, DJ and LaLone, CA}, title = {Defining the Biologically Plausible Taxonomic Domain of Applicability of an Adverse Outcome Pathway: A Case Study Linking Nicotinic Acetylcholine Receptor Activation to Colony Death.}, journal = {Environmental toxicology and chemistry}, volume = {42}, number = {1}, pages = {71-87}, pmid = {36263952}, issn = {1552-8618}, mesh = {Animals ; Bees ; *Adverse Outcome Pathways ; *Receptors, Nicotinic/genetics ; Ecotoxicology/methods ; Databases, Factual ; Amino Acid Sequence ; Risk Assessment ; }, abstract = {For the majority of developed adverse outcome pathways (AOPs), the taxonomic domain of applicability (tDOA) is typically narrowly defined with a single or a handful of species. Defining the tDOA of an AOP is critical for use in regulatory decision-making, particularly when considering protection of untested species. Structural and functional conservation are two elements that can be considered when defining the tDOA. Publicly accessible bioinformatics approaches, such as the Sequence Alignment to Predict Across Species Susceptibility (SeqAPASS) tool, take advantage of existing and growing databases of protein sequence and structural information to provide lines of evidence toward structural conservation of key events (KEs) and KE relationships (KERs) of an AOP. It is anticipated that SeqAPASS results could readily be combined with data derived from empirical toxicity studies to provide evidence of both structural and functional conservation, to define the tDOA for KEs, KERs, and AOPs. Such data could be incorporated in the AOP-Wiki as lines of evidence toward biological plausibility for the tDOA. We present a case study describing the process of using bioinformatics to define the tDOA of an AOP using an AOP linking the activation of the nicotinic acetylcholine receptor to colony death/failure in Apis mellifera. Although the AOP was developed to gain a particular biological understanding relative to A. mellifera health, applicability to other Apis bees, as well as non-Apis bees, has yet to be defined. The present study demonstrates how bioinformatics can be utilized to rapidly take advantage of existing protein sequence and structural knowledge to enhance and inform the tDOA of KEs, KERs, and AOPs, focusing on providing evidence of structural conservation across species. Environ Toxicol Chem 2023;42:71-87. © 2022 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals LLC on behalf of SETAC. This article has been contributed to by U.S. Government employees and their work is in the public domain in the USA.}, } @article {pmid36261521, year = {2022}, author = {Klunk, J and Vilgalys, TP and Demeure, CE and Cheng, X and Shiratori, M and Madej, J and Beau, R and Elli, D and Patino, MI and Redfern, R and DeWitte, SN and Gamble, JA and Boldsen, JL and Carmichael, A and Varlik, N and Eaton, K and Grenier, JC and Golding, GB and Devault, A and Rouillard, JM and Yotova, V and Sindeaux, R and Ye, CJ and Bikaran, M and Dumaine, A and Brinkworth, JF and Missiakas, D and Rouleau, GA and Steinrücken, M and Pizarro-Cerdá, J and Poinar, HN and Barreiro, LB}, title = {Evolution of immune genes is associated with the Black Death.}, journal = {Nature}, volume = {611}, number = {7935}, pages = {312-319}, pmid = {36261521}, issn = {1476-4687}, support = {P30 DK042086/DK/NIDDK NIH HHS/United States ; F32 GM140568/GM/NIGMS NIH HHS/United States ; R01 GM146051/GM/NIGMS NIH HHS/United States ; R56 AI146556/AI/NIAID NIH HHS/United States ; R01 GM134376/GM/NIGMS NIH HHS/United States ; }, mesh = {Humans ; Aminopeptidases/genetics/immunology ; *DNA, Ancient ; *Plague/genetics/immunology/microbiology/mortality ; *Yersinia pestis/immunology/pathogenicity ; *Selection, Genetic/immunology ; Europe/epidemiology/ethnology ; *Immunity/genetics ; Datasets as Topic ; *Genetic Predisposition to Disease ; London/epidemiology ; Denmark/epidemiology ; }, abstract = {Infectious diseases are among the strongest selective pressures driving human evolution[1,2]. This includes the single greatest mortality event in recorded history, the first outbreak of the second pandemic of plague, commonly called the Black Death, which was caused by the bacterium Yersinia pestis[3]. This pandemic devastated Afro-Eurasia, killing up to 30-50% of the population[4]. To identify loci that may have been under selection during the Black Death, we characterized genetic variation around immune-related genes from 206 ancient DNA extracts, stemming from two different European populations before, during and after the Black Death. Immune loci are strongly enriched for highly differentiated sites relative to a set of non-immune loci, suggesting positive selection. We identify 245 variants that are highly differentiated within the London dataset, four of which were replicated in an independent cohort from Denmark, and represent the strongest candidates for positive selection. The selected allele for one of these variants, rs2549794, is associated with the production of a full-length (versus truncated) ERAP2 transcript, variation in cytokine response to Y. pestis and increased ability to control intracellular Y. pestis in macrophages. Finally, we show that protective variants overlap with alleles that are today associated with increased susceptibility to autoimmune diseases, providing empirical evidence for the role played by past pandemics in shaping present-day susceptibility to disease.}, } @article {pmid36261519, year = {2022}, author = {Jandt, U and Bruelheide, H and Jansen, F and Bonn, A and Grescho, V and Klenke, RA and Sabatini, FM and Bernhardt-Römermann, M and Blüml, V and Dengler, J and Diekmann, M and Doerfler, I and Döring, U and Dullinger, S and Haider, S and Heinken, T and Horchler, P and Kuhn, G and Lindner, M and Metze, K and Müller, N and Naaf, T and Peppler-Lisbach, C and Poschlod, P and Roscher, C and Rosenthal, G and Rumpf, SB and Schmidt, W and Schrautzer, J and Schwabe, A and Schwartze, P and Sperle, T and Stanik, N and Storm, C and Voigt, W and Wegener, U and Wesche, K and Wittig, B and Wulf, M}, title = {More losses than gains during one century of plant biodiversity change in Germany.}, journal = {Nature}, volume = {611}, number = {7936}, pages = {512-518}, pmid = {36261519}, issn = {1476-4687}, mesh = {*Biodiversity ; Germany ; *Plants/classification ; Species Specificity ; Time Factors ; Datasets as Topic ; }, abstract = {Long-term analyses of biodiversity data highlight a 'biodiversity conservation paradox': biological communities show substantial species turnover over the past century[1,2], but changes in species richness are marginal[1,3-5]. Most studies, however, have focused only on the incidence of species, and have not considered changes in local abundance. Here we asked whether analysing changes in the cover of plant species could reveal previously unrecognized patterns of biodiversity change and provide insights into the underlying mechanisms. We compiled and analysed a dataset of 7,738 permanent and semi-permanent vegetation plots from Germany that were surveyed between 2 and 54 times from 1927 to 2020, in total comprising 1,794 species of vascular plants. We found that decrements in cover, averaged across all species and plots, occurred more often than increments; that the number of species that decreased in cover was higher than the number of species that increased; and that decrements were more equally distributed among losers than were gains among winners. Null model simulations confirmed that these trends do not emerge by chance, but are the consequence of species-specific negative effects of environmental changes. In the long run, these trends might result in substantial losses of species at both local and regional scales. Summarizing the changes by decade shows that the inequality in the mean change in species cover of losers and winners diverged as early as the 1960s. We conclude that changes in species cover in communities represent an important but understudied dimension of biodiversity change that should more routinely be considered in time-series analyses.}, } @article {pmid36261518, year = {2022}, author = {Jarvis, ED and Formenti, G and Rhie, A and Guarracino, A and Yang, C and Wood, J and Tracey, A and Thibaud-Nissen, F and Vollger, MR and Porubsky, D and Cheng, H and Asri, M and Logsdon, GA and Carnevali, P and Chaisson, MJP and Chin, CS and Cody, S and Collins, J and Ebert, P and Escalona, M and Fedrigo, O and Fulton, RS and Fulton, LL and Garg, S and Gerton, JL and Ghurye, J and Granat, A and Green, RE and Harvey, W and Hasenfeld, P and Hastie, A and Haukness, M and Jaeger, EB and Jain, M and Kirsche, M and Kolmogorov, M and Korbel, JO and Koren, S and Korlach, J and Lee, J and Li, D and Lindsay, T and Lucas, J and Luo, F and Marschall, T and Mitchell, MW and McDaniel, J and Nie, F and Olsen, HE and Olson, ND and Pesout, T and Potapova, T and Puiu, D and Regier, A and Ruan, J and Salzberg, SL and Sanders, AD and Schatz, MC and Schmitt, A and Schneider, VA and Selvaraj, S and Shafin, K and Shumate, A and Stitziel, NO and Stober, C and Torrance, J and Wagner, J and Wang, J and Wenger, A and Xiao, C and Zimin, AV and Zhang, G and Wang, T and Li, H and Garrison, E and Haussler, D and Hall, I and Zook, JM and Eichler, EE and Phillippy, AM and Paten, B and Howe, K and Miga, KH and , }, title = {Semi-automated assembly of high-quality diploid human reference genomes.}, journal = {Nature}, volume = {611}, number = {7936}, pages = {519-531}, pmid = {36261518}, issn = {1476-4687}, support = {R01 HG006677/HG/NHGRI NIH HHS/United States ; U01 HG010961/HG/NHGRI NIH HHS/United States ; R35 GM130151/GM/NIGMS NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; R01 HG010169/HG/NHGRI NIH HHS/United States ; U01 CA253481/CA/NCI NIH HHS/United States ; R01 HG011274/HG/NHGRI NIH HHS/United States ; U01 HG010971/HG/NHGRI NIH HHS/United States ; K99 HG010906/HG/NHGRI NIH HHS/United States ; R01 HG002385/HG/NHGRI NIH HHS/United States ; R01 HG010040/HG/NHGRI NIH HHS/United States ; U41 HG010972/HG/NHGRI NIH HHS/United States ; }, mesh = {Humans ; *Chromosome Mapping/standards ; *Diploidy ; *Genome, Human/genetics ; Haplotypes/genetics ; High-Throughput Nucleotide Sequencing/methods/standards ; Sequence Analysis, DNA/methods/standards ; Reference Standards ; *Genomics/methods/standards ; Chromosomes, Human/genetics ; Genetic Variation/genetics ; }, abstract = {The current human reference genome, GRCh38, represents over 20 years of effort to generate a high-quality assembly, which has benefitted society[1,2]. However, it still has many gaps and errors, and does not represent a biological genome as it is a blend of multiple individuals[3,4]. Recently, a high-quality telomere-to-telomere reference, CHM13, was generated with the latest long-read technologies, but it was derived from a hydatidiform mole cell line with a nearly homozygous genome[5]. To address these limitations, the Human Pangenome Reference Consortium formed with the goal of creating high-quality, cost-effective, diploid genome assemblies for a pangenome reference that represents human genetic diversity[6]. Here, in our first scientific report, we determined which combination of current genome sequencing and assembly approaches yield the most complete and accurate diploid genome assembly with minimal manual curation. Approaches that used highly accurate long reads and parent-child data with graph-based haplotype phasing during assembly outperformed those that did not. Developing a combination of the top-performing methods, we generated our first high-quality diploid reference assembly, containing only approximately four gaps per chromosome on average, with most chromosomes within ±1% of the length of CHM13. Nearly 48% of protein-coding genes have non-synonymous amino acid changes between haplotypes, and centromeric regions showed the highest diversity. Our findings serve as a foundation for assembling near-complete diploid human genomes at scale for a pangenome reference to capture global genetic variation from single nucleotides to structural rearrangements.}, } @article {pmid36257775, year = {2022}, author = {Peltier, DMP and Anderegg, WRL and Guo, JS and Ogle, K}, title = {Contemporary tree growth shows altered climate memory.}, journal = {Ecology letters}, volume = {25}, number = {12}, pages = {2663-2674}, doi = {10.1111/ele.14130}, pmid = {36257775}, issn = {1461-0248}, support = {1458867//Division of Biological Infrastructure/ ; 1643245//Division of Environmental Biology/ ; //National Science Foundation/ ; }, mesh = {*Trees ; *Climate Change ; Droughts ; Temperature ; }, abstract = {Trees are long-lived organisms, exhibiting temporally complex growth arising from strong climatic "memory." But conditions are becoming increasingly arid in the western USA. Using a century-long tree-ring network, we find altered climate memory across the entire range of a widespread western US conifer: growth is supported by precipitation falling further into the past (+15 months), while increasingly impacted by more recent temperature conditions (-8 months). Tree-ring datasets can be biased, so we confirm altered climate memory in a second, ecologically-sampled tree-ring network. Predicted drought responses show trees may have also become more sensitive to repeat drought. Finally, plots near sites with relatively longer precipitation memory and shorter temperature memory had significantly lower recent mortality rates (R[2] = 0.61). We argue that increased drought frequency has altered climate memory, demonstrate how non-stationarity may arise from failure to account for memory, and suggest memory length may be predictive of future tree mortality.}, } @article {pmid36255408, year = {2023}, author = {Sorokina, M and Ukubayev, T and Koichubekov, B}, title = {Tuberculosis incidence and its socioeconomic determi-nants: developing a parsimonious model.}, journal = {Annali di igiene : medicina preventiva e di comunita}, volume = {35}, number = {4}, pages = {468-479}, doi = {10.7416/ai.2022.2549}, pmid = {36255408}, issn = {1120-9135}, mesh = {Humans ; Incidence ; *Tuberculosis/epidemiology ; Socioeconomic Factors ; Linear Models ; }, abstract = {BACKGROUND: Tuberculosis is a widespread communicable disease, which is one of the top 10 causes of demise globally. Several regression models have been built, and then utilized for the Tuberculosis incidence projections. However, when fitting a multiple linear regression model, an analysis must account for multicollinearity aspects. The present study aimed to develop a parsimonious model that produces unbiased results based on socioeconomic variables as predictors of Tuberculosis incidence.

STUDY DESIGN: Ecological study.

METHODS: Data were collected from the Karaganda Regional Center of Phthisio-pulmonology and Bureau of National Statistics. By multiple linear regression model, we investigated associations between Tuberculosis incidence rate and socioeconomic determinants in Karaganda region, Kazakhstan, during 2001-2019. A Principal components analysis was performed on the socioeconomic variables with oblique rotation. Furthermore, associations of Tuberculosis incidence with the principal components derived from the Principal components analysis were assessed.

RESULTS: The incidence of Tuberculosis in Karaganda region decreased over the period of 2001-2019. Economic development and healthcare capacity were negatively correlated with Tuberculosis incidence. A multiple linear regression equation on Tuberculosis incidence (y) was developed with economic development (x1) and healthcare capacity (x2) clustering two components (utilizing Principal components analysis) to eliminate collinearity: y = 1442 - 454.3x1 - 211.4x2. The incidence of Tuberculosis decreased with the increase of economic development and healthcare capacity.

CONCLUSIONS: In conclusion, the study indicated that economic development and healthcare capacity are closely associated with the incidence of Tuberculosis. The findings support the implementation of optimal preventive measures for Tuberculosis control, including improving the level of economic status, increasing social protection, health expenditure, and strengthening health sector capacity, which are key determinants of the incidence of Tuberculosis.}, } @article {pmid36254310, year = {2022}, author = {Cui, J and Khomkrich, K}, title = {Ethnic Music Inheritance and Environmental Monitoring Using Big Data Analysis from the Cultural Perspective.}, journal = {Journal of environmental and public health}, volume = {2022}, number = {}, pages = {2485596}, pmid = {36254310}, issn = {1687-9813}, mesh = {Big Data ; China ; Data Analysis ; Environmental Monitoring ; Ethnicity/genetics ; Humans ; *Music ; }, abstract = {Ethnic music has too many expectations due to its significance to the national culture. It serves as a mirror, reflecting all the true characteristics of many geographical areas and ethnic groupings. Instilling national self-confidence and fostering national unity are essential outcomes of this. The optimal design plan for Xinjiang folk music inheritance and environmental monitoring based on big data technology is presented in this study from the standpoint of cultural ecology. Big data technology can categorize users who are interested in Xinjiang ethnic music, and after that, through customized recommendation filtering, consumers may be presented with Xinjiang ethnic music that meets their interests. Last but not least, a simulation test and analysis are performed. The algorithm's accuracy is 7.86% higher than that of the conventional algorithm, according to the simulation data. By studying and calculating the user's behavioral traits and interests, this result demonstrates in detail how the recommender system can display the user's content efficiently. However, there are numerous possibilities and varied contexts for the use of clustering techniques in recommender systems. It is crucially vital for directing the protection of ethnic music and fostering the inheritance and development of ethnic culture to conduct design study on the Xinjiang region's ethnic music heritage and development with cultural ecology as the central guiding principle. This article is from "A comprehensive study of Uygur Muqam music art with Chinese characteristics," which aims to improve the data reserve of the world and Southeast Asia on the research of Chinese Uighur Muqam art. Improve the inheritance and development of music in Xinjiang, China, and provide more detailed data to more scholars. This study adopts qualitative research methods and field survey data. The author proposes to focus on the perspective of cultural ecology, based on the use of big data technology, to improve the inheritance and development of Xinjiang national music.}, } @article {pmid36249208, year = {2022}, author = {Qamar, AI and Gronwald, L and Timmesfeld, N and Diebner, HH}, title = {Local socio-structural predictors of COVID-19 incidence in Germany.}, journal = {Frontiers in public health}, volume = {10}, number = {}, pages = {970092}, pmid = {36249208}, issn = {2296-2565}, mesh = {*COVID-19/epidemiology ; Germany/epidemiology ; Humans ; Incidence ; Risk Factors ; Socioeconomic Factors ; }, abstract = {Socio-economic conditions and social attitudes are known to represent epidemiological determinants. Credible knowledge on socio-economic driving factors of the COVID-19 epidemic is still incomplete. Based on linear random effects regression, an ecological model is derived to estimate COVID-19 incidence in German rural/urban districts from local socio-economic factors and popularity of political parties in terms of their share of vote. Thereby, records provided by Germany's public health institute (Robert Koch Institute) of weekly notified 7-day incidences per 100,000 inhabitants per district from the outset of the epidemic in 2020 up to December 1, 2021, are used to construct the dependent variable. Local socio-economic conditions including share of votes, retrieved from the Federal Statistical Office of Germany, have been used as potential risk factors. Socio-economic parameters like per capita income, proportions of protection seekers and social benefit claimants, and educational level have negligible impact on incidence. To the contrary, incidence significantly increases with population density and we observe a strong association with vote shares. Popularity of the right-wing party Alternative for Germany (AfD) bears a considerable risk of increasing COVID-19 incidence both in terms of predicting the maximum incidences during three epidemic periods (alternatively, cumulative incidences over the periods are used to quantify the dependent variable) and in a time-continuous sense. Thus, districts with high AfD popularity rank on top in the time-average regarding COVID-19 incidence. The impact of the popularity of the Free Democrats (FDP) is markedly intermittent in the course of time showing two pronounced peaks in incidence but also occasional drops. A moderate risk emanates from popularities of the Green Party (GRÜNE) and the Christian Democratic Union (CDU/CSU) compared to the other parties with lowest risk level. In order to effectively combat the COVID-19 epidemic, public health policymakers are well-advised to account for social attitudes and behavioral patterns reflected in local popularities of political parties, which are conceived as proper surrogates for these attitudes. Whilst causal relations between social attitudes and the presence of parties remain obscure, the political landscape in terms of share of votes constitutes at least viable predictive "markers" relevant for public health policy making.}, } @article {pmid36248684, year = {2022}, author = {Laroche, J and Tomassini, A and Volpe, G and Camurri, A and Fadiga, L and D'Ausilio, A}, title = {Interpersonal sensorimotor communication shapes intrapersonal coordination in a musical ensemble.}, journal = {Frontiers in human neuroscience}, volume = {16}, number = {}, pages = {899676}, pmid = {36248684}, issn = {1662-5161}, abstract = {Social behaviors rely on the coordination of multiple effectors within one's own body as well as between the interacting bodies. However, little is known about how coupling at the interpersonal level impacts coordination among body parts at the intrapersonal level, especially in ecological, complex, situations. Here, we perturbed interpersonal sensorimotor communication in violin players of an orchestra and investigated how this impacted musicians' intrapersonal movements coordination. More precisely, first section violinists were asked to turn their back to the conductor and to face the second section of violinists, who still faced the conductor. Motion capture of head and bow kinematics showed that altering the usual interpersonal coupling scheme increased intrapersonal coordination. Our perturbation also induced smaller yet more complex head movements, which spanned multiple, faster timescales that closely matched the metrical levels of the musical score. Importantly, perturbation differentially increased intrapersonal coordination across these timescales. We interpret this behavioral shift as a sensorimotor strategy that exploits periodical movements to effectively tune sensory processing in time and allows coping with the disruption in the interpersonal coupling scheme. As such, head movements, which are usually deemed to fulfill communicative functions, may possibly be adapted to help regulate own performance in time.}, } @article {pmid36247175, year = {2022}, author = {Sukma, P and Srinok, K and Papong, S and Supakata, N}, title = {Chula model for sustainable municipal solid waste management in university canteens.}, journal = {Heliyon}, volume = {8}, number = {10}, pages = {e10975}, pmid = {36247175}, issn = {2405-8440}, abstract = {Managing the large amount and variety of waste produced by university canteens is challenging. This study used life cycle assessment (LCA) to investigate sustainable municipal solid waste (MSW) management solutions for Chulalongkorn University (CU) canteens. This study assessed three scenarios for MSW management in CU canteens: the past scenario (prior to the Chula Zero Waste Project in 2016; S1); the current scenario (2017-2021, when the Chula Zero Waste Project's MSW management system was used; S2); and the future scenario (after 2021 with the new MSW management option for CU canteens under Chula Zero Waste; S3). The obtained results were characterized by eight impact categories: climate change, ozone depletion, terrestrial acidification, freshwater eutrophication, human toxicity, photochemical oxidant formation, particulate matter formation, and fossil depletion. The LCA results show that the future scenario (S3) under the Chula Zero Waste Project is sustainable for MSW management. The most environmentally sustainable MSW plan for CU canteens is to reduce, separate it at the source, and reuse materials instead of landfilling mixed waste.}, } @article {pmid36239541, year = {2023}, author = {Keck, F and Altermatt, F}, title = {Management of DNA reference libraries for barcoding and metabarcoding studies with the R package refdb.}, journal = {Molecular ecology resources}, volume = {23}, number = {2}, pages = {511-518}, doi = {10.1111/1755-0998.13723}, pmid = {36239541}, issn = {1755-0998}, support = {//Bundesamt für Umwelt/ ; 31003A_173074//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; //University of Zurich Research Priority Program Global Change and Biodiversity/ ; }, mesh = {*DNA Barcoding, Taxonomic ; *DNA/genetics ; Biodiversity ; Gene Library ; Databases, Nucleic Acid ; }, abstract = {DNA barcoding and metabarcoding are revolutionizing the study and survey of biodiversity. In order to assign taxonomic labels to the DNA sequence data retrieved, these methods are strongly dependent on comprehensive and accurate reference databases. Producing reliable databases linking biological sequences and taxonomic data can be-and often has been-done using mainstream tools such as spreadsheet software. However, spreadsheets quickly become insufficient when the amount of data increases to thousands of taxa and sequences to be matched, and validation operations become more complex and are error prone if done in a manual way. Thus, there is a clear need for providing scientists with user-friendly, reliable and powerful tools to manipulate and manage DNA reference databases in tractable, sound and efficient ways. Here, we introduce the R package refdb as an environment for semi-automatic and assisted construction of DNA reference libraries. The refdb package is a reference database manager offering a set of powerful functions to import, organize, clean, filter, audit and export the data. It is broadly applicable in metabarcoding data generally obtained in biodiversity and biomonitoring studies. We present the main features of the package and outline how refdb can speed up reference database generation, management and handling, and thus contribute to standardization and repeatability in barcoding and metabarcoding studies.}, } @article {pmid36228685, year = {2023}, author = {Seyed Hashtroudi, M and Aghadadashi, V and Mehdinia, A and Sheijooni Fumani, N}, title = {Combining theoretical concepts and Geographic Information System (GIS) to highlight source, risk, and hotspots of sedimentary PAHs: A case study of Chabahar Bay.}, journal = {Environmental research}, volume = {216}, number = {Pt 1}, pages = {114540}, doi = {10.1016/j.envres.2022.114540}, pmid = {36228685}, issn = {1096-0953}, mesh = {Geographic Information Systems ; Geologic Sediments/analysis ; Bays ; Environmental Monitoring/methods ; *Water Pollutants, Chemical/analysis ; *Polycyclic Aromatic Hydrocarbons/analysis ; Vehicle Emissions/analysis ; China ; }, abstract = {Sedimentary PAHs are regionalized variables and their levels, source, and ecological hazards must be discussed in relation to their spatial locations. Our research targeted GIS and Chabahar Bay-Iran to trace spatial variability of PAHs, improve the diagnostic ratios and receptor models in source identification, and determine hotspot of PAH-originated hazards. The entropy Voronoi map distinguished an "entropy strip" in which ∑22PAHs levels increased sharply. Different molecular signatures were individually interpolated and the indicative ratios of distinctive sources were extracted and summed by GIS. The resulting code map reduced potential disagreement among molecular signatures and highlighted the areas where petroleum inputs are prevalent. PCA-MLR analysis extracted three potential sources including fossil fuel combustion (54.36%), petrogenic inputs (29.03%), and vehicle exhaust emissions (16.61%). Interpolated risk layers were re-arranged and overlaid via Fuzzy Membership Functions. The obtained ''Fuzzy AND" map showed the hotspot of the study area in the vicinity of a seasonal estuary.}, } @article {pmid36226159, year = {2022}, author = {Boyes, D and , and , and , and , and , and Phillips, D and , }, title = {The genome sequence of the brimstone moth, Opisthograptis luteolata (Linnaeus, 1758).}, journal = {Wellcome open research}, volume = {7}, number = {}, pages = {227}, pmid = {36226159}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual male Opisthograptis luteolata (the brimstone moth; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 363 megabases in span. The majority of the assembly (99.99%) is scaffolded into 31 chromosomal pseudomolecules with the Z sex chromosome assembled. The complete mitochondrial genome was also assembled and is 16.7 kilobases in length.}, } @article {pmid36225383, year = {2022}, author = {Richardson, AD and Kong, GV and Taylor, KM and Le Moine, JM and Bowker, MA and Barber, JJ and Basler, D and Carbone, MS and Hayer, M and Koch, GW and Salvatore, MR and Sonnemaker, AW and Trilling, DE}, title = {Soil-atmosphere fluxes of CO2, CH4, and N2O across an experimentally-grown, successional gradient of biocrust community types.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {979825}, pmid = {36225383}, issn = {1664-302X}, abstract = {Biological soil crusts (biocrusts) are critical components of dryland and other ecosystems worldwide, and are increasingly recognized as novel model ecosystems from which more general principles of ecology can be elucidated. Biocrusts are often diverse communities, comprised of both eukaryotic and prokaryotic organisms with a range of metabolic lifestyles that enable the fixation of atmospheric carbon and nitrogen. However, how the function of these biocrust communities varies with succession is incompletely characterized, especially in comparison to more familiar terrestrial ecosystem types such as forests. We conducted a greenhouse experiment to investigate how community composition and soil-atmosphere trace gas fluxes of CO2, CH4, and N2O varied from early-successional light cyanobacterial biocrusts to mid-successional dark cyanobacteria biocrusts and late-successional moss-lichen biocrusts and as biocrusts of each successional stage matured. Cover type richness increased as biocrusts developed, and richness was generally highest in the late-successional moss-lichen biocrusts. Microbial community composition varied in relation to successional stage, but microbial diversity did not differ significantly among stages. Net photosynthetic uptake of CO2 by each biocrust type also increased as biocrusts developed but tended to be moderately greater (by up to ≈25%) for the mid-successional dark cyanobacteria biocrusts than the light cyanobacterial biocrusts or the moss-lichen biocrusts. Rates of soil C accumulation were highest for the dark cyanobacteria biocrusts and light cyanobacteria biocrusts, and lowest for the moss-lichen biocrusts and bare soil controls. Biocrust CH4 and N2O fluxes were not consistently distinguishable from the same fluxes measured from bare soil controls; the measured rates were also substantially lower than have been reported in previous biocrust studies. Our experiment, which uniquely used greenhouse-grown biocrusts to manipulate community composition and accelerate biocrust development, shows how biocrust function varies along a dynamic gradient of biocrust successional stages.}, } @article {pmid36224329, year = {2022}, author = {Bayer, N and Hausmann, B and Pandey, RV and Deckert, F and Gail, LM and Strobl, J and Pjevac, P and Krall, C and Unterluggauer, L and Redl, A and Bachmayr, V and Kleissl, L and Nehr, M and Kirkegaard, R and Makristathis, A and Watzenboeck, ML and Nica, R and Staud, C and Hammerl, L and Wohlfarth, P and Ecker, RC and Knapp, S and Rabitsch, W and Berry, D and Stary, G}, title = {Disturbances in microbial skin recolonization and cutaneous immune response following allogeneic stem cell transfer.}, journal = {Leukemia}, volume = {36}, number = {11}, pages = {2705-2714}, pmid = {36224329}, issn = {1476-5551}, support = {P 31494/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Humans ; *Hematopoietic Stem Cell Transplantation/adverse effects ; *Graft vs Host Disease/etiology ; *Gastrointestinal Microbiome ; Immunity ; }, abstract = {The composition of the gut microbiome influences the clinical course after allogeneic hematopoietic stem cell transplantation (HSCT), but little is known about the relevance of skin microorganisms. In a single-center, observational study, we recruited a cohort of 50 patients before undergoing conditioning treatment and took both stool and skin samples up to one year after HSCT. We could confirm intestinal dysbiosis following HSCT and report that the skin microbiome is likewise perturbed in HSCT-recipients. Overall bacterial colonization of the skin was decreased after conditioning. Particularly patients that developed acute skin graft-versus-host disease (aGVHD) presented with an overabundance of Staphylococcus spp. In addition, a loss in alpha diversity was indicative of aGVHD development already before disease onset and correlated with disease severity. Further, co-localization of CD45[+] leukocytes and staphylococci was observed in the skin of aGVHD patients even before disease development and paralleled with upregulated genes required for antigen-presentation in mononuclear phagocytes. Overall, our data reveal disturbances of the skin microbiome as well as cutaneous immune response in HSCT recipients with changes associated with cutaneous aGVHD.}, } @article {pmid36224130, year = {2022}, author = {Zhao, CH and Shen, HY and Wang, ZH and Liang, YP and Zhao, Y and Xie, H and Tang, CL}, title = {[Hydrochemical and Isotopic Characteristics in the Surface Water of the Fenhe River Basin and Influence Factors].}, journal = {Huan jing ke xue= Huanjing kexue}, volume = {43}, number = {10}, pages = {4440-4448}, doi = {10.13227/j.hjkx.202201103}, pmid = {36224130}, issn = {0250-3301}, mesh = {Calcium Sulfate ; Carbonates ; Environmental Monitoring/methods ; *Groundwater/chemistry ; Hydrogen ; Minerals ; Oxygen Isotopes ; Sulfides ; *Water Pollutants, Chemical/analysis ; Water Quality ; }, abstract = {The Fenhe River Basin is the mother river of Shanxi Province. Due to the over-exploitation of water resources and the impact of social and economic development, the ecological environment has deteriorated. After a series of treatment and protection measures, the water quality has since been improved. Mathematical statistics, Piper diagrams, Gibbs model, hydrogen and oxygen isotopes, and other methods were used to analyze the characteristics and sources of hydrochemistry in the surface water of the Fenhe River basin, which revealed the evolution process of surface water quality of the Fenhe River basin. The results showed that the content of the main hydrochemical components in the main stream surface water of Fenhe River basin increased gradually along the runoff path. The hydrochemical types of surface water of Fenhe River basin were mainly HCO3·SO4·Cl-Ca·Na·Mg and SO4·HCO3·Cl-Ca·Na·Mg. There were great differences in hydrochemical components of tributaries and karst water in the basin. There were also great differences in hydrochemical components of tributaries in the basin. The hydrochemical types of surface water of karst water were mainly SO4·HCO3-Ca·Mg. The hydrochemical composition of surface water in Fenhe River basin was mainly affected by rock weathering and evaporation crystallization, whereas rainfall had little effect. Na[+] and K[+] mainly came from the dissolution of evaporated salt rocks with Na in the surrounding loess. Ca[2+], Mg[2+], and HCO3[-] mainly came from the dissolution of carbonate rocks. SO4[2-] may have also come from the dissolution of sulfide minerals in the loess layer around Fenhe River in addition to the dissolution of gypsum. The values of δD and δ[18]O of Fenhe River surface water were gradually enriched from upstream to downstream. The characteristics of hydrogen and oxygen isotopes further showed that the surface water was mainly affected by evaporation. The results of this study can provide evidence for ecological restoration and protection and ecological civilization construction in the Fenhe River basin.}, } @article {pmid36215495, year = {2022}, author = {Zhao, J and Jin, L and Wu, D and Xie, JW and Li, J and Fu, XW and Cong, ZY and Fu, PQ and Zhang, Y and Luo, XS and Feng, XB and Zhang, G and Tiedje, JM and Li, XD}, title = {Global airborne bacterial community-interactions with Earth's microbiomes and anthropogenic activities.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {119}, number = {42}, pages = {e2204465119}, pmid = {36215495}, issn = {1091-6490}, mesh = {*Air Microbiology ; Anthropogenic Effects ; Bacteria/genetics ; Humans ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Airborne bacteria are an influential component of the Earth's microbiomes, but their community structure and biogeographic distribution patterns have yet to be understood. We analyzed the bacterial communities of 370 air particulate samples collected from 63 sites around the world and constructed an airborne bacterial reference catalog with more than 27 million nonredundant 16S ribosomal RNA (rRNA) gene sequences. We present their biogeographic pattern and decipher the interlacing of the microbiome co-occurrence network with surface environments of the Earth. While the total abundance of global airborne bacteria in the troposphere (1.72 × 10[24] cells) is 1 to 3 orders of magnitude lower than that of other habitats, the number of bacterial taxa (i.e., richness) in the atmosphere (4.71 × 10[8] to 3.08 × 10[9]) is comparable to that in the hydrosphere, and its maximum occurs in midlatitude regions, as is also observed in other ecosystems. The airborne bacterial community harbors a unique set of dominant taxa (24 species); however, its structure appears to be more easily perturbed, due to the more prominent role of stochastic processes in shaping community assembly. This is corroborated by the major contribution of surface microbiomes to airborne bacteria (averaging 46.3%), while atmospheric conditions such as meteorological factors and air quality also play a role. Particularly in urban areas, human impacts weaken the relative importance of plant sources of airborne bacteria and elevate the occurrence of potential pathogens from anthropogenic sources. These findings serve as a key reference for predicting planetary microbiome responses and the health impacts of inhalable microbiomes with future changes in the environment.}, } @article {pmid36215030, year = {2023}, author = {Yang, Z and Wang, J and Huang, Y and Wang, S and Wei, L and Liu, D and Weng, Y and Xiang, J and Zhu, Q and Yang, Z and Nie, X and Yu, Y and Yang, Z and Yang, QY}, title = {CottonMD: a multi-omics database for cotton biological study.}, journal = {Nucleic acids research}, volume = {51}, number = {D1}, pages = {D1446-D1456}, pmid = {36215030}, issn = {1362-4962}, mesh = {*Databases, Factual ; Genome ; Genomics/methods ; *Multiomics ; Phenotype ; *Gossypium/chemistry/genetics ; }, abstract = {Cotton is an important economic crop, and many loci for important traits have been identified, but it remains challenging and time-consuming to identify candidate or causal genes/variants and clarify their roles in phenotype formation and regulation. Here, we first collected and integrated the multi-omics datasets including 25 genomes, transcriptomes in 76 tissue samples, epigenome data of five species and metabolome data of 768 metabolites from four tissues, and genetic variation, trait and transcriptome datasets from 4180 cotton accessions. Then, a cotton multi-omics database (CottonMD, http://yanglab.hzau.edu.cn/CottonMD/) was constructed. In CottonMD, multiple statistical methods were applied to identify the associations between variations and phenotypes, and many easy-to-use analysis tools were provided to help researchers quickly acquire the related omics information and perform multi-omics data analysis. Two case studies demonstrated the power of CottonMD for identifying and analyzing the candidate genes, as well as the great potential of integrating multi-omics data for cotton genetic breeding and functional genomics research.}, } @article {pmid36213026, year = {2022}, author = {Wen, Y}, title = {Analysis of Regional Economy Development on Local Environmental Protection and Natural Resources Utilization from the Perspective of Big Data.}, journal = {Journal of environmental and public health}, volume = {2022}, number = {}, pages = {9461377}, pmid = {36213026}, issn = {1687-9813}, mesh = {Big Data ; China ; Cities ; *Conservation of Natural Resources ; *Economic Development ; Natural Resources ; Rivers ; }, abstract = {The ecological restoration and civilization construction is one of the key tasks in China. The economic development of different regions has different effects on the resource protection and utilization. In the face of complex natural conditions and resource-rich areas, how to carry out the ecological environment promotion work is put forward. The urbanization level of the Yangtze River region increases from 17.9% to 60.6%, showing the characteristics of rapid expansion. In the face of urban diseases such as unreasonable industrial layout, it is urgent to improve regional economy and promote green urban development from the perspective of big data. Adhering to the concept of ecological priority, the development of digital technology drove the development of local economy in 2019, accounting for 43% of the national population. While promoting the economic development, it is of great significance to ensure the efficiency of resource utilization and promote the high-quality development of common economy.}, } @article {pmid36212380, year = {2022}, author = {Shao, P and Peng, Y and Wu, Y and Wang, J and Pan, Z and Yang, Y and Aini, N and Guo, C and Shui, G and Chao, L and Tian, X and An, Q and Yang, Q and You, C and Lu, L and Zhang, X and Wang, M and Nie, X}, title = {Genome-wide association study and transcriptome analysis reveal key genes controlling fruit branch angle in cotton.}, journal = {Frontiers in plant science}, volume = {13}, number = {}, pages = {988647}, pmid = {36212380}, issn = {1664-462X}, abstract = {Fruit branch angle (FBA), a pivotal component of cotton plant architecture, is vital for field and mechanical harvesting. However, the molecular mechanism of FBA formation is poorly understood in cotton. To uncover the genetic basis for FBA formation in cotton, we performed a genome-wide association study (GWAS) of 163 cotton accessions with re-sequencing data. A total of 55 SNPs and 18 candidate genes were significantly associated with FBA trait. By combining GWAS and transcriptome analysis, four genes underlying FBA were identified. An FBA-associated candidate gene Ghi_A09G08736, which is homologous to SAUR46 in Arabidopsis thaliana, was detected in our study. In addition, transcriptomic evidence was provided to show that gravity and light were implicated in the FBA formation. This study provides new insights into the genetic architecture of FBA that informs architecture breeding in cotton.}, } @article {pmid36210994, year = {2022}, author = {Ju, X}, title = {Application of Big Data Technology to Promote Agricultural Structure Adjustment and High-Quality Development of Modern Agriculture.}, journal = {Computational intelligence and neuroscience}, volume = {2022}, number = {}, pages = {5222760}, pmid = {36210994}, issn = {1687-5273}, mesh = {*Agriculture ; *Big Data ; China ; Conservation of Natural Resources ; Remote Sensing Technology ; Technology ; }, abstract = {The implementation of the strategy of rural revitalization is a major ministerial work made by the Nineteenth National Congress of the Communist Party of China and is the general grasp of contemporary agriculture, peasants, and rural work. In recent years, with the rapid development of remote sensing technology and deep learning technology, the demand for the technology for the classification of crops on satellite remote sensing images based on deep learning technology has increased in agricultural insurance and land survey. Therefore, this paper trains one, which is 85.9%-92.8%, the accuracy of corn classification is 77%-93%, and the accuracy of forest classification is 77%-87.6%. Subsequently, the overall accuracy of classifying all directories through the multi-temporal validation data set between May 2017 and October 2017 reached 92.6%. Such a multi-time combination method can be used for monthly, timely, and efficient iteration of agricultural insurance and crop yield estimation, which will be more accurate each time. These methods can also be further applied to the growth and change monitoring of large agricultural planting areas, adding bricks and tiles to China's agricultural remote sensing. If the countryside is to be revitalized, agriculture must develop rapidly at the same time, industries must flourish, ecology must be livable, rural customs must be civilized, and life must be prosperous. Modern agriculture is a comprehensive circulation system with high yield, high quality, low consumption, ecology, environmental protection, and high efficiency. The development of modern agriculture is inseparable from the industrialization of agriculture, the globalization of agriculture, the digitization of agriculture, the integration of agriculture, the adjustment of agricultural structure, and agricultural innovation. Only the continuous development of modern agriculture can make rural revitalization enter a new journey.}, } @article {pmid36209915, year = {2022}, author = {Chetty, M and Hallinan, J and Ruz, GA and Wipat, A}, title = {Computational intelligence and machine learning in bioinformatics and computational biology.}, journal = {Bio Systems}, volume = {222}, number = {}, pages = {104792}, doi = {10.1016/j.biosystems.2022.104792}, pmid = {36209915}, issn = {1872-8324}, mesh = {*Computational Biology ; *Artificial Intelligence ; Machine Learning ; }, } @article {pmid36207680, year = {2022}, author = {Asghari-Jafarabadi, M and Gholipour, K and Khodayari-Zarnaq, R and Azmin, M and Alizadeh, G}, title = {Estimation of myocardial infarction death in Iran: artificial neural network.}, journal = {BMC cardiovascular disorders}, volume = {22}, number = {1}, pages = {438}, pmid = {36207680}, issn = {1471-2261}, mesh = {Humans ; *Hypercholesterolemia/diagnosis/epidemiology ; Iran/epidemiology ; Male ; *Myocardial Infarction/diagnosis/epidemiology ; Neural Networks, Computer ; Obesity/diagnosis/epidemiology ; Overweight ; Risk Factors ; }, abstract = {BACKGROUND: Examining past trends and predicting the future helps policymakers to design effective interventions to deal with myocardial infarction (MI) with a clear understanding of the current and future situation. The aim of this study was to estimate the death rate due to MI in Iran by artificial neural network (ANN).

METHODS: In this ecological study, the prevalence of diabetes, hypercholesterolemia over 200, hypertension, overweight and obesity were estimated for the years 2017-2025. ANN and Linear regression model were used. Also, Specialists were also asked to predict the death rate due to MI by considering the conditions of 3 conditions (optimistic, pessimistic, and probable), and the predicted process was compared with the modeling process.

RESULTS: Death rate due to MI in Iran is expected to decrease on average, while there will be a significant decrease in the prevalence of hypercholesterolemia 1.031 (- 24.81, 26.88). Also, the trend of diabetes 10.48 (111.45, - 132.42), blood pressure - 110.48 (- 174.04, - 46.91) and obesity and overweight - 35.84 (- 18.66, - 5.02) are slowly increasing. MI death rate in Iran is higher in men but is decreasing on average. Experts' forecasts are different and have predicted a completely upward trend.

CONCLUSION: The trend predicted by the modeling shows that the death rate due to MI will decrease in the future with a low slope. Improving the infrastructure for providing preventive services to reduce the risk factors for cardiovascular disease in the community is one of the priority measures in the current situation.}, } @article {pmid36202356, year = {2023}, author = {Jones, DL and Rhymes, JM and Wade, MJ and Kevill, JL and Malham, SK and Grimsley, JMS and Rimmer, C and Weightman, AJ and Farkas, K}, title = {Suitability of aircraft wastewater for pathogen detection and public health surveillance.}, journal = {The Science of the total environment}, volume = {856}, number = {Pt 2}, pages = {159162}, pmid = {36202356}, issn = {1879-1026}, mesh = {Adult ; Male ; Humans ; *Wastewater ; Public Health Surveillance ; SARS-CoV-2 ; *COVID-19/epidemiology ; Aircraft ; }, abstract = {International air travel is now widely recognised as one of the primary mechanisms responsible for the transnational movement and global spread of SARS-CoV-2. Monitoring the viral load and novel lineages within human-derived wastewater collected from aircraft and at air transport hubs has been proposed as an effective way to monitor the importation frequency of viral pathogens. The success of this approach, however, is highly dependent on the bathroom and defecation habits of air passengers during their journey. In this study of UK adults (n = 2103), we quantified the likelihood of defecation prior to departure, on the aircraft and upon arrival on both short- and long-haul flights. The results were then used to assess the likelihood of capturing the signal from infected individuals at UK travel hubs. To obtain a representative cross-section of the population, the survey was stratified by geographical region, gender, age, parenting status, and social class. We found that an individual's likelihood to defecate on short-haul flights (< 6 h in duration) was low (< 13 % of the total), but was higher on long-haul flights (< 36 %; > 6 h in duration). This behaviour pattern was higher among males and younger age groups. The maximum likelihood of defecation was prior to departure (< 39 %). Based on known SARS-CoV-2 faecal shedding rates (30-60 %) and an equal probability of infected individuals being on short- (71 % of inbound flights) and long-haul flights (29 %), we estimate that aircraft wastewater is likely to capture ca. 8-14 % of SARS-CoV-2 cases entering the UK. Monte Carlo simulations predicted that SARS-CoV-2 would be present in wastewater on 14 % of short-haul flights and 62 % of long-haul flights under current pandemic conditions. We conclude that aircraft wastewater alone is insufficient to effectively monitor all the transboundary entries of faecal-borne pathogens but can form part of a wider strategy for public heath surveillance at national borders.}, } @article {pmid36198068, year = {2022}, author = {Wanchai, V and Jenjaroenpun, P and Leangapichart, T and Arrey, G and Burnham, CM and Tümmler, MC and Delgado-Calle, J and Regenberg, B and Nookaew, I}, title = {CReSIL: accurate identification of extrachromosomal circular DNA from long-read sequences.}, journal = {Briefings in bioinformatics}, volume = {23}, number = {6}, pages = {}, pmid = {36198068}, issn = {1477-4054}, support = {P20 GM125503/GM/NIGMS NIH HHS/United States ; R37 CA251763/CA/NCI NIH HHS/United States ; T32 GM106999/GM/NIGMS NIH HHS/United States ; }, mesh = {*DNA, Circular/genetics ; *Genome ; DNA/genetics ; Eukaryotic Cells ; }, abstract = {Extrachromosomal circular DNA (eccDNA) of chromosomal origin is found in many eukaryotic species and cell types, including cancer, where eccDNAs with oncogenes drive tumorigenesis. Most studies of eccDNA employ short-read sequencing for their identification. However, short-read sequencing cannot resolve the complexity of genomic repeats, which can lead to missing eccDNA products. Long-read sequencing technologies provide an alternative to constructing complete eccDNA maps. We present a software suite, Construction-based Rolling-circle-amplification for eccDNA Sequence Identification and Location (CReSIL), to identify and characterize eccDNA from long-read sequences. CReSIL's performance in identifying eccDNA, with a minimum F1 score of 0.98, is superior to the other bioinformatic tools based on simulated data. CReSIL provides many useful features for genomic annotation, which can be used to infer eccDNA function and Circos visualization for eccDNA architecture investigation. We demonstrated CReSIL's capability in several long-read sequencing datasets, including datasets enriched for eccDNA and whole genome datasets from cells containing large eccDNA products. In conclusion, the CReSIL suite software is a versatile tool for investigating complex and simple eccDNA in eukaryotic cells.}, } @article {pmid36197407, year = {2022}, author = {Cunha, APD and Cruz, MMD}, title = {Analysis of trend in mortality due to HIV/AIDS-defining and non-HIV/AIDS defining illnesses according to sociodemographic characteristics, by Federative Unit and Brazil, 2000-2018.}, journal = {Epidemiologia e servicos de saude : revista do Sistema Unico de Saude do Brasil}, volume = {31}, number = {2}, pages = {e2022093}, pmid = {36197407}, issn = {2237-9622}, mesh = {*Acquired Immunodeficiency Syndrome/epidemiology ; Brazil/epidemiology ; Humans ; Information Systems ; Time Factors ; }, abstract = {OBJECTIVE: To analyze the temporal trend of mortality rate due to HIV/AIDS defining and non-HIV/AIDS defining illnesses in Brazil between 2000 and 2018.

METHODS: This was an ecological time series study, using data from the Mortality Information System, in Brazil and the Federative Units. Trend analysis was performed by means of Prais-Winsten regression model, according to overall mortality rate, sex, age group, marital status and race/skin color.

RESULTS: A total of 237,435 deaths were recorded in the period. In the country, defining illnesses showed higher rates (7.4 to 4.4 deaths/100,000 inhabitants in the period) than those observed among non-defining diseases (0.4 to 0.8 death/100,000 inhabitants in the period). It could be seen a decrease in overall mortality due to defining diseases (-6.3%; 95%CI -8.8;-3.8); while it increased due to non-defining diseases (11.0%; 95%CI 6.5;15.7).

CONCLUSION: There was a change in HIV/AIDS mortality profile over the years, with a decrease in deaths due to HIV/AIDS-defining diseases.}, } @article {pmid36197074, year = {2022}, author = {Gonçalves, BP and Hall, M and Jassat, W and Balan, V and Murthy, S and Kartsonaki, C and Semple, MG and Rojek, A and Baruch, J and Reyes, LF and Dasgupta, A and Dunning, J and Citarella, BW and Pritchard, M and Martín-Quiros, A and Sili, U and Baillie, JK and Aryal, D and Arabi, Y and Rashan, A and Angheben, A and Caoili, J and Carrier, FM and Harrison, EM and Gómez-Junyent, J and Figueiredo-Mello, C and Douglas, JJ and Mat Nor, MB and Chow, YP and Wong, XC and Bertagnolio, S and Thwin, SS and Streinu-Cercel, A and Salazar, L and Rishu, A and Rangappa, R and Ong, DSY and Hashmi, M and Carson, G and Diaz, J and Fowler, R and Kraemer, MUG and Wils, EJ and Horby, P and Merson, L and Olliaro, PL and , }, title = {An international observational study to assess the impact of the Omicron variant emergence on the clinical epidemiology of COVID-19 in hospitalised patients.}, journal = {eLife}, volume = {11}, number = {}, pages = {}, pmid = {36197074}, issn = {2050-084X}, support = {MC_PC_19059/MRC_/Medical Research Council/United Kingdom ; 200927/WT_/Wellcome Trust/United Kingdom ; 205228/Z/16/Z/WT_/Wellcome Trust/United Kingdom ; 222410/Z/21/Z/WT_/Wellcome Trust/United Kingdom ; 215091/Z/18/Z/WT_/Wellcome Trust/United Kingdom ; MR/S032304/1/MRC_/Medical Research Council/United Kingdom ; MC_PC_19025/MRC_/Medical Research Council/United Kingdom ; 001/WHO_/World Health Organization/International ; 225288/Z/22/Z/WT_/Wellcome Trust/United Kingdom ; 222048/Z/20/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {*COVID-19/epidemiology/virology ; Humans ; *SARS-CoV-2/genetics ; }, abstract = {BACKGROUND: Whilst timely clinical characterisation of infections caused by novel SARS-CoV-2 variants is necessary for evidence-based policy response, individual-level data on infecting variants are typically only available for a minority of patients and settings.

METHODS: Here, we propose an innovative approach to study changes in COVID-19 hospital presentation and outcomes after the Omicron variant emergence using publicly available population-level data on variant relative frequency to infer SARS-CoV-2 variants likely responsible for clinical cases. We apply this method to data collected by a large international clinical consortium before and after the emergence of the Omicron variant in different countries.

RESULTS: Our analysis, that includes more than 100,000 patients from 28 countries, suggests that in many settings patients hospitalised with Omicron variant infection less often presented with commonly reported symptoms compared to patients infected with pre-Omicron variants. Patients with COVID-19 admitted to hospital after Omicron variant emergence had lower mortality compared to patients admitted during the period when Omicron variant was responsible for only a minority of infections (odds ratio in a mixed-effects logistic regression adjusted for likely confounders, 0.67 [95% confidence interval 0.61-0.75]). Qualitatively similar findings were observed in sensitivity analyses with different assumptions on population-level Omicron variant relative frequencies, and in analyses using available individual-level data on infecting variant for a subset of the study population.

CONCLUSIONS: Although clinical studies with matching viral genomic information should remain a priority, our approach combining publicly available data on variant frequency and a multi-country clinical characterisation dataset with more than 100,000 records allowed analysis of data from a wide range of settings and novel insights on real-world heterogeneity of COVID-19 presentation and clinical outcome.

FUNDING: Bronner P. Gonçalves, Peter Horby, Gail Carson, Piero L. Olliaro, Valeria Balan, Barbara Wanjiru Citarella, and research costs were supported by the UK Foreign, Commonwealth and Development Office (FCDO) and Wellcome [215091/Z/18/Z, 222410/Z/21/Z, 225288/Z/22/Z]; and Janice Caoili and Madiha Hashmi were supported by the UK FCDO and Wellcome [222048/Z/20/Z]. Peter Horby, Gail Carson, Piero L. Olliaro, Kalynn Kennon and Joaquin Baruch were supported by the Bill & Melinda Gates Foundation [OPP1209135]; Laura Merson was supported by University of Oxford's COVID-19 Research Response Fund - with thanks to its donors for their philanthropic support. Matthew Hall was supported by a Li Ka Shing Foundation award to Christophe Fraser. Moritz U.G. Kraemer was supported by the Branco Weiss Fellowship, Google.org, the Oxford Martin School, the Rockefeller Foundation, and the European Union Horizon 2020 project MOOD (#874850). The contents of this publication are the sole responsibility of the authors and do not necessarily reflect the views of the European Commission. Contributions from Srinivas Murthy, Asgar Rishu, Rob Fowler, James Joshua Douglas, François Martin Carrier were supported by CIHR Coronavirus Rapid Research Funding Opportunity OV2170359 and coordinated out of Sunnybrook Research Institute. Contributions from Evert-Jan Wils and David S.Y. Ong were supported by a grant from foundation Bevordering Onderzoek Franciscus; and Andrea Angheben by the Italian Ministry of Health "Fondi Ricerca corrente-L1P6" to IRCCS Ospedale Sacro Cuore-Don Calabria. The data contributions of J.Kenneth Baillie, Malcolm G. Semple, and Ewen M. Harrison were supported by grants from the National Institute for Health Research (NIHR; award CO-CIN-01), the Medical Research Council (MRC; grant MC_PC_19059), and by the NIHR Health Protection Research Unit (HPRU) in Emerging and Zoonotic Infections at University of Liverpool in partnership with Public Health England (PHE) (award 200907), NIHR HPRU in Respiratory Infections at Imperial College London with PHE (award 200927), Liverpool Experimental Cancer Medicine Centre (grant C18616/A25153), NIHR Biomedical Research Centre at Imperial College London (award IS-BRC-1215-20013), and NIHR Clinical Research Network providing infrastructure support. All funders of the ISARIC Clinical Characterisation Group are listed in the appendix.}, } @article {pmid36195605, year = {2022}, author = {Peters, K and König-Ries, B}, title = {Reference bioimaging to assess the phenotypic trait diversity of bryophytes within the family Scapaniaceae.}, journal = {Scientific data}, volume = {9}, number = {1}, pages = {598}, pmid = {36195605}, issn = {2052-4463}, mesh = {Biodiversity ; *Bryophyta ; Computational Biology/methods ; *Hepatophyta ; Image Processing, Computer-Assisted/methods ; }, abstract = {Macro- and microscopic images of organisms are pivotal in biodiversity research. Despite that bioimages have manifold applications such as assessing the diversity of form and function, FAIR bioimaging data in the context of biodiversity are still very scarce, especially for difficult taxonomic groups such as bryophytes. Here, we present a high-quality reference dataset containing macroscopic and bright-field microscopic images documenting various phenotypic characters of the species belonging to the liverwort family of Scapaniaceae occurring in Europe. To encourage data reuse in biodiversity and adjacent research areas, we annotated the imaging data with machine-actionable metadata using community-accepted semantics. Furthermore, raw imaging data are retained and any contextual image processing like multi-focus image fusion and stitching were documented to foster good scientific practices through source tracking and provenance. The information contained in the raw images are also of particular interest for machine learning and image segmentation used in bioinformatics and computational ecology. We expect that this richly annotated reference dataset will encourage future studies to follow our principles.}, } @article {pmid36195601, year = {2022}, author = {Pottier, P and Lin, HY and Oh, RRY and Pollo, P and Rivera-Villanueva, AN and Valdebenito, JO and Yang, Y and Amano, T and Burke, S and Drobniak, SM and Nakagawa, S}, title = {A comprehensive database of amphibian heat tolerance.}, journal = {Scientific data}, volume = {9}, number = {1}, pages = {600}, pmid = {36195601}, issn = {2052-4463}, support = {Scientia Doctoral Scholarship//University of New South Wales (UNSW Australia)/ ; Scientia Doctoral Scholarship//University of New South Wales (UNSW Australia)/ ; Scientia Doctoral Scholarship//University of New South Wales (UNSW Australia)/ ; DFG-FZT 118, 202548816//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; FT180100354//Department of Education and Training | Australian Research Council (ARC)/ ; DE180100202//Department of Education and Training | Australian Research Council (ARC)/ ; DP200100367//Department of Education and Training | Australian Research Council (ARC)/ ; }, mesh = {*Amphibians ; Animals ; Databases, Factual ; Hot Temperature ; Temperature ; *Thermotolerance ; }, abstract = {Rising temperatures represent a significant threat to the survival of ectothermic animals. As such, upper thermal limits represent an important trait to assess the vulnerability of ectotherms to changing temperatures. For instance, one may use upper thermal limits to estimate current and future thermal safety margins (i.e., the proximity of upper thermal limits to experienced temperatures), use this trait together with other physiological traits in species distribution models, or investigate the plasticity and evolvability of these limits for buffering the impacts of changing temperatures. While datasets on thermal tolerance limits have been previously compiled, they sometimes report single estimates for a given species, do not present measures of data dispersion, and are biased towards certain parts of the globe. To overcome these limitations, we systematically searched the literature in seven languages to produce the most comprehensive dataset to date on amphibian upper thermal limits, spanning 3,095 estimates across 616 species. This resource will represent a useful tool to evaluate the vulnerability of amphibians, and ectotherms more generally, to changing temperatures.}, } @article {pmid36194325, year = {2023}, author = {Zhou, Y and Hu, Z and Geng, Q and Ma, J and Liu, J and Wang, M and Wang, Y}, title = {Monitoring and analysis of desertification surrounding Qinghai Lake (China) using remote sensing big data.}, journal = {Environmental science and pollution research international}, volume = {30}, number = {7}, pages = {17420-17436}, pmid = {36194325}, issn = {1614-7499}, mesh = {Humans ; *Remote Sensing Technology ; *Conservation of Natural Resources/methods ; Lakes ; Big Data ; Environmental Monitoring/methods ; China ; }, abstract = {Desertification is one of the most serious ecological environmental problems in the world. Monitoring the spatiotemporal dynamics of desertification is crucial for its control. The region around Qinghai Lake, in the northeastern part of the Qinghai-Tibet Plateau in China, is a special ecological function area and a climate change sensitive area, making its environmental conditions a great concern. Using cloud computing via Google Earth Engine (GEE), we collected Landsat 5 TM, Landsat 8 OLI/TIRS, and MODIS Albedo images from 2000 to 2020 in the region around Qinghai Lake, acquired land surface albedo (Albedo), and normalized vegetation index (NDVI) to build a remote sensing monitoring model of desertification. Our results showed that the desertification difference index based on the Albedo-NDVI feature space could reflect the degree of desertification in the region around Qinghai Lake. GEE offers significant advantages, such as massive data processing and long-term dynamic monitoring. The desertification land area fluctuated downward in the study area from 2000 to 2020, and the overall desertification status improved. Natural factors, such as climate change from warm-dry to warm-wet and decreased wind speed, and human factors improved the desertification situation. The findings indicate that desertification in the region around Qinghai Lake has been effectively controlled, and the overall desertification trend is improving.}, } @article {pmid36191222, year = {2022}, author = {Yang, L and Constantino, SM and Grenfell, BT and Weber, EU and Levin, SA and Vasconcelos, VV}, title = {Sociocultural determinants of global mask-wearing behavior.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {119}, number = {41}, pages = {e2213525119}, pmid = {36191222}, issn = {1091-6490}, mesh = {*COVID-19/epidemiology/prevention & control ; Humans ; *Masks ; *Pandemics/prevention & control ; Public Policy ; Risk ; SARS-CoV-2 ; Social Conditions ; }, abstract = {Behavioral responses influence the trajectories of epidemics. During the COVID-19 pandemic, nonpharmaceutical interventions (NPIs) reduced pathogen transmission and mortality worldwide. However, despite the global pandemic threat, there was substantial cross-country variation in the adoption of protective behaviors that is not explained by disease prevalence alone. In particular, many countries show a pattern of slow initial mask adoption followed by sharp transitions to high acceptance rates. These patterns are characteristic of behaviors that depend on social norms or peer influence. We develop a game-theoretic model of mask wearing where the utility of wearing a mask depends on the perceived risk of infection, social norms, and mandates from formal institutions. In this model, increasing pathogen transmission or policy stringency can trigger social tipping points in collective mask wearing. We show that complex social dynamics can emerge from simple individual interactions and that sociocultural variables and local policies are important for recovering cross-country variation in the speed and breadth of mask adoption. These results have implications for public health policy and data collection.}, } @article {pmid36188695, year = {2022}, author = {Zhang, W}, title = {Design of Urban Garden Landscape Visualization System Based on GIS and Remote Sensing Technology.}, journal = {Computational intelligence and neuroscience}, volume = {2022}, number = {}, pages = {9592376}, pmid = {36188695}, issn = {1687-5273}, mesh = {Cities ; Environmental Monitoring/methods ; Gardens ; *Geographic Information Systems ; Hot Temperature ; *Remote Sensing Technology ; }, abstract = {Urban green ecological space is an important manifestation of the environmental characteristics of a green city. The research results show that the urban green ecological space has obvious cooling and humidity effects, which are very important for reducing the urban heat island effect. Remote sensing technology describes the slow-release effects of urban green parks in different seasons from the two perspectives of thermal slow-release intensity and thermal slow-release distance. In this paper, UAV remote sensing is used to extract the internal and external factors of the urban green environment characteristics and to identify the main factors that affect the slow-release heat effect and seasonal changes of the urban green environment. In addition, it analyzes the factors that affect the urban environmental temperature within the environmental temperature slow-release range of urban green space, establishes a model to predict the environmental temperature within the thermal slow-release range outside the park, and realizes the largest thermal slow release in the urban greening ecological space. These are new technologies created in the context of digitization, which include image understanding and synthesis, which involve the use of computer graphics and image processing technology to convert data into graphics or images displayed on the screen to achieve an interactive process.}, } @article {pmid36187697, year = {2022}, author = {Ekpenyong, N and Heitz Tokpa, K and Nwankwo, O and O'Donnell, D and Rodriguez Franco, D and Berté, S and Amani Kouassi, S and Eteng, G and Undelikwo, V and Auer, C and Guessan Bi, GB and Oyo-Ita, A and Bosch-Capblanch, X}, title = {Using and improving the PHISICC paper-based tools in the health facility laboratories: Examples of Human Centered Design taking systems thinking into practice, in Côte d'Ivoire and Nigeria.}, journal = {Frontiers in public health}, volume = {10}, number = {}, pages = {916397}, pmid = {36187697}, issn = {2296-2565}, mesh = {Cote d'Ivoire ; Health Facilities ; Humans ; *Laboratories ; Nigeria ; Systems Analysis ; *Universal Design ; }, abstract = {BACKGROUND: Health workers in low- and middle-income countries are increasingly demanded to collect more and more data to report them to higher levels of the health information system (HIS), in detriment of useful data for clinical and public health decision-making, potentially compromising the quality of their health care provison. In order to support health workers' decision-making, we engaged with partners in Côte d'Ivoire, Mozambique and Nigeria in a research project to conceive, design, produce, implement and test paper-based health information tools: the PHISICC tools. Our aim was to understand the use of PHISICC tools by health workers and to improve them based on their feedback.

METHODS: The design Health Facility Laboratories (HF Labs) in Côte d'Ivoire and in Nigeria were set up after months of use of PHISICC tools. Activities were structured in three phases or 'sprints' of co-creative research. We used a transdisciplinary approach, including anthropology and Human Centered Design (HCD), observations, shadowing, structured interviews and co-creation.

RESULTS: Health workers appreciated the standardization of the tools across different health care areas, with a common visual language that optimized use. Several design issues were raised, in terms of formats and contents. They strongly appreciated how the PHISICC registers guided their clinical decision-making and how it facilitated tallying and counting for monthly reporting. However, adherence to new procedures was not universal. The co-creation sessions resulted in modifications to the PHISICC tools of out-patient care and postnatal care.

DISCUSSION: Although health systems and systemic thinking allowed the teams to embrace complexity, it was the HCD approach that actually produced a shift in researchers' mind-set: from HIS as data management tools to HIS as quality of care instruments. HCD allowed navigating the complexity of health systems interventions due to its capacity to operate change: it not only allowed us to understand how the PHISICC tools were used but also how to further improve them. In the absence of (or even with) an analytical health systems framework, HCD approaches can work in real-life situations for the ideation, testing and implementation of interventions to improve health systems and health status outcomes.}, } @article {pmid36179444, year = {2022}, author = {Chin, JM and Growns, B and Sebastian, J and Page, MJ and Nakagawa, S}, title = {The transparency and reproducibility of systematic reviews in forensic science.}, journal = {Forensic science international}, volume = {340}, number = {}, pages = {111472}, doi = {10.1016/j.forsciint.2022.111472}, pmid = {36179444}, issn = {1872-6283}, mesh = {*Benchmarking ; Databases, Factual ; *Forensic Sciences ; Reproducibility of Results ; Systematic Reviews as Topic ; }, abstract = {Systematic reviews are indispensable tools for both reliably informing decision-makers about the state of the field and for identifying areas that need further study. Their value, however, depends on their transparency and reproducibility. Readers should be able to determine what was searched for and when, where the authors searched, and whether that search was predetermined or evolved based on what was found. In this article, we measured the transparency and reproducibility of systematic reviews in forensic science, a field where courts, policymakers, and legislators count on systematic reviews to make informed decisions. In a sample of 100 systematic reviews published between 2018 and 2021, we found that completeness of reporting varied markedly. For instance, 50 % of reviews claimed to follow a reporting guideline and such statements were only modestly related to compliance with that reporting guideline. As to specific reporting items, 82 % reported all of the databases searched, 22 % reported the review's full Boolean search logic, and just 7 % reported the review was registered. Among meta-analyses (n = 23), only one stated data was available and none stated the analytic code was available. After considering the results, we end with recommendations for improved regulation of reporting practices, especially among journals. Our results may serve as a useful benchmark as the field evolves.}, } @article {pmid36175492, year = {2022}, author = {Leonardi, M and Boschin, F and Boscato, P and Manica, A}, title = {Following the niche: the differential impact of the last glacial maximum on four European ungulates.}, journal = {Communications biology}, volume = {5}, number = {1}, pages = {1038}, pmid = {36175492}, issn = {2399-3642}, mesh = {Animals ; Archaeology ; Databases, Factual ; *Deer ; Ecosystem ; Horses ; Species Specificity ; Sus scrofa ; Swine ; }, abstract = {Predicting the effects of future global changes on species requires a better understanding of the ecological niche dynamics in response to climate; the large climatic fluctuations of the last 50,000 years can be used as a natural experiment to that aim. Here we test whether the realized niche of horse, aurochs, red deer, and wild boar changed between 47,000 and 7500 years ago using paleoecological modelling over an extensive archaeological database. We show that they all changed their niche, with species-specific responses to climate fluctuations. We also suggest that they survived the climatic turnovers thanks to their flexibility and by expanding their niche in response to the extinction of competitors and predators. Irrespective of the mechanism behind such processes, the fact that species with long generation times can change their niche over thousands of years cautions against assuming it to stay constant both when reconstructing the past and predicting the future.}, } @article {pmid36174014, year = {2022}, author = {Porter, TM and Hajibabaei, M}, title = {MetaWorks: A flexible, scalable bioinformatic pipeline for high-throughput multi-marker biodiversity assessments.}, journal = {PloS one}, volume = {17}, number = {9}, pages = {e0274260}, pmid = {36174014}, issn = {1932-6203}, mesh = {Animals ; *Biodiversity ; Biomarkers ; *Computational Biology ; Ecology ; Eukaryota ; }, abstract = {Multi-marker metabarcoding is increasingly being used to generate biodiversity information across different domains of life from microbes to fungi to animals such as for molecular ecology and biomonitoring applications in different sectors from academic research to regulatory agencies and industry. Current popular bioinformatic pipelines support microbial and fungal marker analysis, while ad hoc methods are often used to process animal metabarcode markers from the same study. MetaWorks provides a harmonized processing environment, pipeline, and taxonomic assignment approach for demultiplexed Illumina reads for all biota using a wide range of metabarcoding markers such as 16S, ITS, and COI. A Conda environment is provided to quickly gather most of the programs and dependencies for the pipeline. Several workflows are provided such as: taxonomically assigning exact sequence variants, provides an option to generate operational taxonomic units, and facilitates single-read processing. Pipelines are automated using Snakemake to minimize user intervention and facilitate scalability. All pipelines use the RDP classifier to provide taxonomic assignments with confidence measures. We extend the functionality of the RDP classifier for taxonomically assigning 16S (bacteria), ITS (fungi), and 28S (fungi), to also support COI (eukaryotes), rbcL (eukaryotes, land plants, diatoms), 12S (fish, vertebrates), 18S (eukaryotes, diatoms) and ITS (fungi, plants). MetaWorks properly handles ITS by trimming flanking conserved rRNA gene regions as well as protein coding genes by providing two options for removing obvious pseudogenes. MetaWorks can be downloaded from https://github.com/terrimporter/MetaWorks and quickstart instructions, pipeline details, and a tutorial for new users can be found at https://terrimporter.github.io/MetaWorksSite.}, } @article {pmid36172318, year = {2022}, author = {Yin, G and Liu, J}, title = {Research on Movement Analysis and Guidance in Dance Learning Based on Data Mining.}, journal = {Computational intelligence and neuroscience}, volume = {2022}, number = {}, pages = {9327442}, pmid = {36172318}, issn = {1687-5273}, mesh = {Data Mining ; Humans ; *Learning ; *Movement ; Students ; }, abstract = {In dance, we must understand the essential meaning of dance movements from the inside and express them on the basis of dance. Therefore, in the process of developing new dance teaching methods, it is necessary to improve the basic education of dance students, so that they can express the emotions conveyed by dance through body language and movements, and improve dance expression ability. In this context, we made the research and reached the following conclusions: (1) the number of frames of different dance types is also different, and the number of frames to be learned is also increasing. The dance with the highest number of frames is Latin2, which has 3635 frames, and the dance with the highest number of frames that need to be learned is also Latin2, which requires 2519 frames to learn. (2) The data mining method is still the highest among the three methods, and the accuracy of the complete teaching method is 82%, which is the lowest among the three methods, and the accuracy of the decentralized teaching method is 87%. No matter in the test set or the mixed test set, the curve values of deep mining are very stable. First of all, human movements emphasize that in dance, the essential meaning of dance movements needs to be understood from the inside and expressed through the foundation of dance. Therefore, when developing new dance teaching methods, it is necessary to strengthen the basic dance training of students so that students can express the emotions conveyed by dance through body language and movements and improve their dance expression ability. We conduct research in this ecological environment. Different types of dance learning process using different frames, different types of dance in the algorithm transport have different recognition methods, using better and different algorithms can achieve the best performance. Both groups in the Hip Hop dance had a shorter average learning time than both groups in the Latin dance.}, } @article {pmid36171318, year = {2023}, author = {Wen, C and Zhen, Z and Zhang, L and Yan, C}, title = {A bibliometric analysis of river health based on publications in the last three decades.}, journal = {Environmental science and pollution research international}, volume = {30}, number = {6}, pages = {15400-15413}, pmid = {36171318}, issn = {1614-7499}, support = {XDA23030203//Strategic Priority Research Program of the Chinese Academy of Sciences/ ; }, mesh = {Humans ; *Rivers ; *Bibliometrics ; Australia ; China ; Databases, Factual ; Publications ; }, abstract = {Rivers are a vital part of the earth's environment and the basis for human survival. River health has been widely concerned by scholars and practitioners, and the number of studies in this area is increasing. In order to examine the evolution of river health research and identify the research frontiers, a total of 675 articles were retrieved from the Web of Science Core Collection database, and CiteSpace was used for bibliometrics. The results revealed that the research on river health is multidisciplinary. Freshwater Biology and Ecological Indicators were two of the most influential journals. Researchers and institutions from America, Australia, and China were the core research forces, and a certain gap was observed between developed and developing countries in river health. The most productive institution was Michigan State University, followed by Griffith University and Hohai University. There are three development trends in river health: (1) Research scale is expanding; (2) Research methods are diversified and interdisciplinary; and (3) Evaluation index is more comprehensive and systematic. The frontier of river health had been expanded from the connotation of river health to the evaluation methods, evaluation indexes, and comprehensive river ecological research. Overall, research on river health is a well-developed and promising research field. This study provides a framework in the river health field for new researchers and helps scholars to identify further potential perspectives on collaborators, research frontiers, hotspots, and research trends.}, } @article {pmid36169445, year = {2022}, author = {Martins, ACM and Giordani, F and Gonçalves, MC and Guaraldo, L and Rozenfeld, S}, title = {[Deaths from adverse drug events in Brazil: Mortality Information System as a source of information].}, journal = {Cadernos de saude publica}, volume = {38}, number = {8}, pages = {e00291221}, doi = {10.1590/0102-311XPT291221}, pmid = {36169445}, issn = {1678-4464}, mesh = {Aged ; Brazil/epidemiology ; Child ; *Drug-Related Side Effects and Adverse Reactions ; Humans ; Information Systems ; Middle Aged ; Psychotropic Drugs/adverse effects ; Retrospective Studies ; }, abstract = {Adverse drug events (ADEs) are harmful events caused by medication, and some of which can lead to death. Death records are an important source of information when using codes from the 10th revision of the International Classification of Diseases (ICD-10) suggestive of ADE. This study aimed to identify the ADEs registered in Brazililian Mortality Information System (SIM), analyzing data distribution by year, age group, and type of event. This is an ecological study with retrospective data collection, identifying ADEs in the SIM, using the ICD-10 codes. The study included deaths that occurred in Brazil from 2008 to 2016. An increase in the number of deaths associated with ADE was observed from 2008 to 2016, with a mortality rate per 1 million inhabitants ranging from 8.70 to 14.40 in the period. Most events corresponded to mental and behavioral disorders due to the use of psychotropic drugs. Most deaths (12,311) related to ADE codes were identified in several chapters of the ICD-10. Chapter XX, about adverse events, allowed the identification of a smaller number of deaths (4,893). Higher event rates were observed among individuals aged 60 years and over (39.8/1 million) and children younger than one year (22.0/1 million). The identification of ADE-related deaths on the SIM is an important strategy for addressing undesirable drug-related events. Deaths related to the use of psychotropic drugs were the most frequent ADE-related deaths and the elderly were the age group most affected by ADEs.}, } @article {pmid36167554, year = {2022}, author = {Kim, J and Lee, C and Ko, BJ and Yoo, DA and Won, S and Phillippy, AM and Fedrigo, O and Zhang, G and Howe, K and Wood, J and Durbin, R and Formenti, G and Brown, S and Cantin, L and Mello, CV and Cho, S and Rhie, A and Kim, H and Jarvis, ED}, title = {False gene and chromosome losses in genome assemblies caused by GC content variation and repeats.}, journal = {Genome biology}, volume = {23}, number = {1}, pages = {204}, pmid = {36167554}, issn = {1474-760X}, support = {207492/Z/17/Z/WT_/Wellcome Trust/United Kingdom ; /HHMI/Howard Hughes Medical Institute/United States ; R03 NS115145/NS/NINDS NIH HHS/United States ; ZIA HG200398/ImNIH/Intramural NIH HHS/United States ; R03 NS059755/NS/NINDS NIH HHS/United States ; WT206194/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Animals ; Base Composition/genetics ; Chromosomes ; *Genome/genetics ; Sequence Analysis, DNA ; *Vertebrates/genetics ; }, abstract = {BACKGROUND: Many short-read genome assemblies have been found to be incomplete and contain mis-assemblies. The Vertebrate Genomes Project has been producing new reference genome assemblies with an emphasis on being as complete and error-free as possible, which requires utilizing long reads, long-range scaffolding data, new assembly algorithms, and manual curation. A more thorough evaluation of the recent references relative to prior assemblies can provide a detailed overview of the types and magnitude of improvements.

RESULTS: Here we evaluate new vertebrate genome references relative to the previous assemblies for the same species and, in two cases, the same individuals, including a mammal (platypus), two birds (zebra finch, Anna's hummingbird), and a fish (climbing perch). We find that up to 11% of genomic sequence is entirely missing in the previous assemblies. In the Vertebrate Genomes Project zebra finch assembly, we identify eight new GC- and repeat-rich micro-chromosomes with high gene density. The impact of missing sequences is biased towards GC-rich 5'-proximal promoters and 5' exon regions of protein-coding genes and long non-coding RNAs. Between 26 and 60% of genes include structural or sequence errors that could lead to misunderstanding of their function when using the previous genome assemblies.

CONCLUSIONS: Our findings reveal novel regulatory landscapes and protein coding sequences that have been greatly underestimated in previous assemblies and are now present in the Vertebrate Genomes Project reference genomes.}, } @article {pmid36167140, year = {2023}, author = {Tölgyesi, C and Hábenczyus, AA and Kelemen, A and Török, P and Valkó, O and Deák, B and Erdős, L and Tóth, B and Csikós, N and Bátori, Z}, title = {How to not trade water for carbon with tree planting in water-limited temperate biomes?.}, journal = {The Science of the total environment}, volume = {856}, number = {Pt 1}, pages = {158960}, doi = {10.1016/j.scitotenv.2022.158960}, pmid = {36167140}, issn = {1879-1026}, mesh = {*Ecosystem ; *Carbon ; Water ; Sand ; Forests ; Soil ; }, abstract = {The most widespread nature-based solution for mitigating climate change is tree planting. When realized as forest restoration in historically forested biomes, it can efficiently contribute to the sequestration of atmospheric carbon and can also entail significant biodiversity and ecosystem service benefits. Conversely, tree planting in naturally open biomes can have adverse effects, of which water shortage due to increased evapotranspiration is among the most alarming ones. Here we assessed how soil texture affects the strength of the trade-off between tree cover and water balance in the forest-steppe biome, where the global pressure for afforestation is threatening with increasing tree cover above historical levels. Here we monitored vertical soil moisture dynamics in four stands in each of the most common forest types of lowland Hungary on well-drained, sandy (natural poplar groves, and Robinia and pine plantations) and on poorly drained, silty-clayey soils (natural oak stands and Robinia plantations), and neighboring grasslands. We found that forests on sand retain moisture in the topsoil (approx. 20 cm) throughout the year, but a thick dry layer develops below that during the vegetation period, significantly impeding groundwater recharge. Neighboring sandy grasslands showed an opposite pattern, with often dry topsoil but intact moisture reserves below, allowing deep percolation. In contrast, forests on silty-clayey soils did not desiccate lower soil layers compared neighboring grasslands, which in turn showed moisture patterns similar to sandy grasslands. We conclude that, in water-limited temperate biomes where landscape-wide water regime depends on deep percolation, soil texture should drive the spatial allocation of tree-based climate mitigation efforts. On sand, the establishment of new forests should be kept to a minimum and grassland restoration should be preferred. The trade-off between water and carbon is less pronounced on silty-clayey soils, making forest patches and wooded rangelands viable targets for both climate mitigation and ecosystem restoration.}, } @article {pmid36166925, year = {2023}, author = {Koo, SY and Hwang, KT and Hwang, S and Choi, KY and Park, YJ and Choi, JH and Truong, TQ and Kim, SM}, title = {Nanoencapsulation enhances the bioavailability of fucoxanthin in microalga Phaeodactylum tricornutum extract.}, journal = {Food chemistry}, volume = {403}, number = {}, pages = {134348}, doi = {10.1016/j.foodchem.2022.134348}, pmid = {36166925}, issn = {1873-7072}, mesh = {Humans ; Mice ; Animals ; Biological Availability ; *Microalgae/metabolism ; Caco-2 Cells ; Xanthophylls/metabolism ; }, abstract = {The marine carotenoid fucoxanthin (FX) has various health benefits but suffers from poor bioavailability. We hypothesize that the bioavailability of FX in microalga Phaeodactylum tricornutum extract (PE) could be improved through nanoencapsulation. Here, we developed two types of nanoparticles: one consisting of alginate and casein (A-C-PE, 246 nm diameter, 79.6% encapsulation efficiency) and the other A-C-PE coated with chitosan (CS-A-C-PE, 258 nm, 78.1%). Both types of nanoparticles incorporating PE showed controlled FX release during simulated gastrointestinal digestion, as well as 1.8-fold improvement of membrane permeability in Caco-2/TC7 cells compared to non-encapsulated PE. Pharmacokinetic behavior of two FX metabolites (fucoxanthinol and amarouciaxanthin A) in mouse plasma was monitored after oral administration. The results showed that 31.8-332.1% more FX metabolites from the nanoparticles were absorbed into plasma than those from PE. In conclusion, encapsulation of PE in both types of nanoparticles significantly promoted the bioavailability of FX.}, } @article {pmid36157711, year = {2022}, author = {Mihaljevic, JR and Borkovec, S and Ratnavale, S and Hocking, TD and Banister, KE and Eppinger, JE and Hepp, C and Doerry, E}, title = {SPARSEMODr: Rapidly simulate spatially explicit and stochastic models of COVID-19 and other infectious diseases.}, journal = {Biology methods & protocols}, volume = {7}, number = {1}, pages = {bpac022}, pmid = {36157711}, issn = {2396-8923}, abstract = {Building realistically complex models of infectious disease transmission that are relevant for informing public health is conceptually challenging and requires knowledge of coding architecture that can implement key modeling conventions. For example, many of the models built to understand COVID-19 dynamics have included stochasticity, transmission dynamics that change throughout the epidemic due to changes in host behavior or public health interventions, and spatial structures that account for important spatio-temporal heterogeneities. Here we introduce an R package, SPARSEMODr, that allows users to simulate disease models that are stochastic and spatially explicit, including a model for COVID-19 that was useful in the early phases of the epidemic. SPARSEMOD stands for SPAtial Resolution-SEnsitive Models of Outbreak Dynamics, and our goal is to demonstrate particular conventions for rapidly simulating the dynamics of more complex, spatial models of infectious disease. In this report, we outline the features and workflows of our software package that allow for user-customized simulations. We believe the example models provided in our package will be useful in educational settings, as the coding conventions are adaptable, and will help new modelers to better understand important assumptions that were built into sophisticated COVID-19 models.}, } @article {pmid36155927, year = {2023}, author = {Russo, A and Blettner, M and Merzenich, H and Wollschlaeger, D and Erdmann, F and Gianicolo, E}, title = {Incidence of childhood leukemia before and after shut down of nuclear power plants in Germany in 2011: A population-based register study during 2004 to 2019.}, journal = {International journal of cancer}, volume = {152}, number = {5}, pages = {913-920}, doi = {10.1002/ijc.34303}, pmid = {36155927}, issn = {1097-0215}, mesh = {Child ; Humans ; *Nuclear Power Plants ; Incidence ; Case-Control Studies ; *Leukemia/epidemiology ; Germany/epidemiology ; }, abstract = {The association between leukemia and proximity to nuclear-power-plants (NPPs) has been assessed in several countries with inconsistent results. A case-control study from Germany had shown an increased risk for childhood leukemia (diagnoses 1980-2003) near NPPs. Germany began shutting down nuclear reactors in 2011, following the Fukushima disaster. We tested whether the previously observed association between leukemia and proximity to NPP persisted despite the shutdown. We used an ecological study design to investigate the incidence of leukemia during 2004 to 2019 in children aged 0 to 14 years living near NPPs where at least one reactor was shut down in 2011. We defined study and control areas as municipalities whose surface area was at least 75% within 10 km or between 10 and 50 km of NPPs, respectively. We calculated age-standardized rates and incidence rate ratios (IRR) using control-areas as the reference. We also computed standardized incidence ratios (SIR) separately for each NPP using incidence rates of the German population as a reference. IRR decreased from 1.20 (95% confidence interval: 0.81-1.77) in 2004 to 2011 to 1.12 (0.75-1.68) in 2012 to 2019. Analyses of single plants showed an excess of childhood leukemia during 2004 to 2019 for the Unterweser-NPP, based only on three cases, and the Krümmel-NPP (n = 14; SIR: 1.98, 1.17-3.35). We found slightly decreasing of leukemia incidence rate ratios after the shutdown of nuclear reactors in 2011. Due to the small number of cases, risk estimates have large uncertainty. Further research including a longer follow-up is warranted. The consistent excess of incidence cases around Krümmel may require analytical epidemiological analysis.}, } @article {pmid36149894, year = {2022}, author = {Zhang, L and Chen, L and Yu, XA and Duvallet, C and Isazadeh, S and Dai, C and Park, S and Frois-Moniz, K and Duarte, F and Ratti, C and Alm, EJ and Ling, F}, title = {MicrobiomeCensus estimates human population sizes from wastewater samples based on inter-individual variability in gut microbiomes.}, journal = {PLoS computational biology}, volume = {18}, number = {9}, pages = {e1010472}, pmid = {36149894}, issn = {1553-7358}, mesh = {*COVID-19 ; *Gastrointestinal Microbiome/genetics ; Humans ; Pandemics ; Population Density ; Sewage ; Wastewater ; }, abstract = {The metagenome embedded in urban sewage is an attractive new data source to understand urban ecology and assess human health status at scales beyond a single host. Analyzing the viral fraction of wastewater in the ongoing COVID-19 pandemic has shown the potential of wastewater as aggregated samples for early detection, prevalence monitoring, and variant identification of human diseases in large populations. However, using census-based population size instead of real-time population estimates can mislead the interpretation of data acquired from sewage, hindering assessment of representativeness, inference of prevalence, or comparisons of taxa across sites. Here, we show that taxon abundance and sub-species diversisty in gut-associated microbiomes are new feature space to utilize for human population estimation. Using a population-scale human gut microbiome sample of over 1,100 people, we found that taxon-abundance distributions of gut-associated multi-person microbiomes exhibited generalizable relationships with respect to human population size. Here and throughout this paper, the human population size is essentially the sample size from the wastewater sample. We present a new algorithm, MicrobiomeCensus, for estimating human population size from sewage samples. MicrobiomeCensus harnesses the inter-individual variability in human gut microbiomes and performs maximum likelihood estimation based on simultaneous deviation of multiple taxa's relative abundances from their population means. MicrobiomeCensus outperformed generic algorithms in data-driven simulation benchmarks and detected population size differences in field data. New theorems are provided to justify our approach. This research provides a mathematical framework for inferring population sizes in real time from sewage samples, paving the way for more accurate ecological and public health studies utilizing the sewage metagenome.}, } @article {pmid36141528, year = {2022}, author = {Emelyanova, A and Savolainen, A and Oksanen, A and Nieminen, P and Loginova, O and Abass, K and Rautio, A}, title = {Research on Selected Wildlife Infections in the Circumpolar Arctic-A Bibliometric Review.}, journal = {International journal of environmental research and public health}, volume = {19}, number = {18}, pages = {}, pmid = {36141528}, issn = {1660-4601}, mesh = {Alaska/epidemiology ; Animals ; *Animals, Wild ; Arctic Regions ; Bibliometrics ; *Communicable Diseases/epidemiology/veterinary ; Humans ; Mammals ; }, abstract = {One Health, a multidisciplinary approach to public health, which integrates human, animal, and environmental studies, is prudent for circumpolar Arctic health research. The objective of our bibliometric review was to identify and compare research in select infectious diseases in Arctic wildlife species with importance to human health indexed in English language databases (PubMed, Scopus) and the Russian database eLibrary.ru. Included articles (in English and Russian languages) needed to meet the following criteria: (1) data comes from the Arctic, (2) articles report original research or surveillance reports, (3) articles were published between 1990 and 2018, and (4) research relates to naturally occurring infections. Of the included articles (total n = 352), most were from Russia (n = 131, 37%), Norway (n = 58, 16%), Canada (n = 39, 11%), and Alaska (n = 39, 11%). Frequently reported infectious agents among selected mammals were Trichinella spp. (n = 39), Brucella spp. (n = 25), rabies virus (n = 11), Echinococcus spp. (n = 10), and Francisella tularensis (n = 9). There were 25 articles on anthrax in eLibrary.ru, while there were none in the other two databases. We identified future directions where opportunities for further research, collaboration, systematic reviews, or monitoring programs are possible and needed.}, } @article {pmid36138772, year = {2022}, author = {Botella, C and Bonnet, P and Hui, C and Joly, A and Richardson, DM}, title = {Dynamic Species Distribution Modeling Reveals the Pivotal Role of Human-Mediated Long-Distance Dispersal in Plant Invasion.}, journal = {Biology}, volume = {11}, number = {9}, pages = {}, pmid = {36138772}, issn = {2079-7737}, support = {//DSI-NRF Centre of Excellence for Invasion Biology/ ; 89967//Millennium Trust, the National Research Foundation of South Africa/ ; CZ.02.2.69/0.0/0.0/18_053/0017850//Mobility 2020 project (Ministry of Education, Youth and Sports of the Czech Republic)/ ; RVO 67985939//long-term research development project (Czech Academy of Sciences)/ ; }, abstract = {Plant invasions generate massive ecological and economic costs worldwide. Predicting their spatial dynamics is crucial to the design of effective management strategies and the prevention of invasions. Earlier studies highlighted the crucial role of long-distance dispersal in explaining the speed of many invasions. In addition, invasion speed depends highly on the duration of its lag phase, which may depend on the scaling of fecundity with age, especially for woody plants, even though empirical proof is still rare. Bayesian dynamic species distribution models enable the fitting of process-based models to partial and heterogeneous observations using a state-space modeling approach, thus offering a tool to test such hypotheses on past invasions over large spatial scales. We use such a model to explore the roles of long-distance dispersal and age-structured fecundity in the transient invasion dynamics of Plectranthus barbatus, a woody plant invader in South Africa. Our lattice-based model accounts for both short and human-mediated long-distance dispersal, as well as age-structured fecundity. We fitted our model on opportunistic occurrences, accounting for the spatio-temporal variations of the sampling effort and the variable detection rates across datasets. The Bayesian framework enables us to integrate a priori knowledge on demographic parameters and control identifiability issues. The model revealed a massive wave of spatial spread driven by human-mediated long-distance dispersal during the first decade and a subsequent drastic population growth, leading to a global equilibrium in the mid-1990s. Without long-distance dispersal, the maximum population would have been equivalent to 30% of the current equilibrium population. We further identified the reproductive maturity at three years old, which contributed to the lag phase before the final wave of population growth. Our results highlighted the importance of the early eradication of weedy horticultural alien plants around urban areas to hamper and delay the invasive spread.}, } @article {pmid36130600, year = {2022}, author = {Bidel, F and Bennett, NC and Wardill, TJ}, title = {Octopus bimaculoides' arm recruitment and use during visually evoked prey capture.}, journal = {Current biology : CB}, volume = {32}, number = {21}, pages = {4727-4733.e3}, doi = {10.1016/j.cub.2022.08.080}, pmid = {36130600}, issn = {1879-0445}, mesh = {Animals ; *Octopodiformes/physiology ; Movement/physiology ; Extremities/physiology ; Adaptation, Physiological ; }, abstract = {Octopus' limb hyper-redundancy complicates traditional motor control system theory due to its extensive sensory inputs, subsequent decision-making, and arm coordination. Octopuses are thought to reduce flexibility control complexity by relying on highly stereotypical motor primitives (e.g., reaching[1][,][2][,][3][,][4] and crawling[5]) and multi-level processes to coordinate movement,[6][,][7] utilizing extensive peripheral nervous system (PNS) processing.[2][,][8][,][9] Division of labor along the anterior-posterior axis[10] and limb specialization of the four anterior arms in T-maze food retrieval[11] further simplify control. However, specific arm recruitment and coordination during visually guided reaching behavior remains poorly understood. Here, we investigated visually evoked Octopus bimaculoides' prey capture capabilities[12][,][13] by eliciting and examining prey-specific arm recruitment. When striking crabs, octopuses preferred synchronous arm recruitment, while sequential arm recruitment with a characteristic swaying movement is employed for shrimp. Such behavioral selection aligns with specific prey escape strategies and the octopus' flexible arm biomechanical constraints. Although side bias existed, we found significant bilateral symmetry, with one side being functionally a mirror of the other rather than anterior arm use being functionally equal and differing to posterior arm use. Among arms, the second limb is unequivocally dominant for goal-directed monocularly driven prey capture. Although the eight arms share gross anatomy and are considered equipotential,[10][,][14] such arm use for specific actions could reflect subtle evolutionary adaptations. Finally, we quantitatively show, corroborating earlier observations,[10][,][15] that octopuses employ a dimension reduction strategy by actively deciding to recruit adjacent arms over other available arms during either sequential or synchronous visually evoked prey attack.}, } @article {pmid36130260, year = {2022}, author = {Sun, D and Ding, S and Cai, P and Zhang, D and Han, M and Hu, QN}, title = {BioBulkFoundary: a customized webserver for exploring biosynthetic potentials of bulk chemicals.}, journal = {Bioinformatics (Oxford, England)}, volume = {38}, number = {22}, pages = {5137-5138}, doi = {10.1093/bioinformatics/btac640}, pmid = {36130260}, issn = {1367-4811}, support = {2020YFA0908300//National Key Research and Development Program of China/ ; 153D31KYSB20170121//CAS International Partnership Programme of the Chinese Academy of Sciences of China/ ; }, mesh = {*Metabolic Engineering/methods ; *Synthetic Biology ; Databases, Factual ; }, abstract = {SUMMARY: Advances in metabolic engineering have boosted the production of bulk chemicals, resulting in tons of production volumes of some bulk chemicals with very low prices. A decrease in the production cost and overproduction of bulk chemicals makes it necessary and desirable to explore the potential to synthesize higher-value products from them. It is also useful and important for society to explore the use of design methods involving synthetic biology to increase the economic value of these bulk chemicals. Therefore, we developed 'BioBulkFoundary', which provides an elaborate analysis of the biosynthetic potential of bulk chemicals based on the state-of-art exploration of pathways to synthesize value-added chemicals, along with associated comprehensive technology and economic database into a user-friendly framework.

Freely available on the web at http://design.rxnfinder.org/biobulkfoundary/.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, } @article {pmid36127081, year = {2022}, author = {Barrigon, ML and Porras-Segovia, A and Courtet, P and Lopez-Castroman, J and Berrouiguet, S and Pérez-Rodríguez, MM and Artes, A and , and Baca-Garcia, E}, title = {Smartphone-based Ecological Momentary Intervention for secondary prevention of suicidal thoughts and behaviour: protocol for the SmartCrisis V.2.0 randomised clinical trial.}, journal = {BMJ open}, volume = {12}, number = {9}, pages = {e051807}, pmid = {36127081}, issn = {2044-6055}, mesh = {Ecological Momentary Assessment ; Humans ; Randomized Controlled Trials as Topic ; Secondary Prevention ; *Smartphone ; Suicidal Ideation ; *Telemedicine ; }, abstract = {INTRODUCTION: Suicide is one of the leading public health issues worldwide. Mobile health can help us to combat suicide through monitoring and treatment. The SmartCrisis V.2.0 randomised clinical trial aims to evaluate the effectiveness of a smartphone-based Ecological Momentary Intervention to prevent suicidal thoughts and behaviour.

METHODS AND ANALYSIS: The SmartCrisis V.2.0 study is a randomised clinical trial with two parallel groups, conducted among patients with a history of suicidal behaviour treated at five sites in France and Spain. The intervention group will be monitored using Ecological Momentary Assessment (EMA) and will receive an Ecological Momentary Intervention called 'SmartSafe' in addition to their treatment as usual (TAU). TAU will consist of mental health follow-up of the patient (scheduled appointments with a psychiatrist) in an outpatient Suicide Prevention programme, with predetermined clinical appointments according to the Brief Intervention Contact recommendations (1, 2, 4, 7 and 11 weeks and 4, 6, 9 and 12 months). The control group would receive TAU and be monitored using EMA.

ETHICS AND DISSEMINATION: This study has been approved by the Ethics Committee of the University Hospital Fundación Jiménez Díaz. It is expected that, in the near future, our mobile health intervention and monitoring system can be implemented in routine clinical practice. Results will be disseminated through peer-reviewed journals and psychiatric congresses. Reference number EC005-21_FJD. Participants gave informed consent to participate in the study before taking part.

TRIAL REGISTRATION NUMBER: NCT04775160.}, } @article {pmid36123315, year = {2022}, author = {Fontana, F and Alessandri, G and Tarracchini, C and Bianchi, MG and Rizzo, SM and Mancabelli, L and Lugli, GA and Argentini, C and Vergna, LM and Anzalone, R and Longhi, G and Viappiani, A and Taurino, G and Chiu, M and Turroni, F and Bussolati, O and van Sinderen, D and Milani, C and Ventura, M}, title = {Designation of optimal reference strains representing the infant gut bifidobacterial species through a comprehensive multi-omics approach.}, journal = {Environmental microbiology}, volume = {24}, number = {12}, pages = {5825-5839}, pmid = {36123315}, issn = {1462-2920}, mesh = {Humans ; Infant ; *Bifidobacterium/genetics ; *Multiomics ; Reproducibility of Results ; Feces/microbiology ; Metagenomics ; Bacteria ; }, abstract = {The genomic era has resulted in the generation of a massive amount of genetic data concerning the genomic diversity of bacterial taxa. As a result, the microbiological community is increasingly looking for ways to define reference bacterial strains to perform experiments that are representative of the entire bacterial species. Despite this, there is currently no established approach allowing a reliable identification of reference strains based on a comprehensive genomic, ecological, and functional context. In the current study, we developed a comprehensive multi-omics approach that will allow the identification of the optimal reference strains using the Bifidobacterium genus as test case. Strain tracking analysis based on 1664 shotgun metagenomics datasets of healthy infant faecal samples were employed to identify bifidobacterial strains suitable for in silico and in vitro analyses. Subsequently, an ad hoc bioinformatic tool was developed to screen local strain collections for the most suitable species-representative strain alternative. The here presented approach was validated using in vitro trials followed by metagenomics and metatranscriptomics analyses. Altogether, these results demonstrated the validity of the proposed model for reference strain selection, thus allowing improved in silico and in vitro investigations both in terms of cross-laboratory reproducibility and relevance of research findings.}, } @article {pmid36120670, year = {2022}, author = {Liu, X and Wang, J and Rui, X and Zhang, J}, title = {Application of GIS Technology-Supported Cross Media Fusion Method Based on Deep Learning in Landscape Performance Evaluation.}, journal = {Computational intelligence and neuroscience}, volume = {2022}, number = {}, pages = {8339895}, pmid = {36120670}, issn = {1687-5273}, mesh = {Algorithms ; *Deep Learning ; Geographic Information Systems ; Humans ; Neural Networks, Computer ; Technology ; }, abstract = {GIS technology can provide reasonable and sustainable data support for landscape planning and ecological development and make wetland landscape planning consider the spatial layout of landscape and the optimal allocation of resources more. The key technologies of cross media intelligence mainly focus on intelligent information retrieval, analysis and reasoning, knowledge map construction, and intelligent storage. Convolutional neural network (CNN), as one of the representative algorithms of deep learning, plays an important role in retrieving landscape data and extracting image and text features across media. Further retrieval of media data, in-depth text processing, and image feature data extraction are realized by using deep learning technology, and comprehensive in-depth analysis is carried out by combining landscape plane images, three-dimensional images, and vector information in GIS technology. Provide quantitative information for the evaluation system of human landscape, economy, history, and region, so as to formulate a scientific and reasonable performance evaluation system.}, } @article {pmid36114727, year = {2022}, author = {Ma, X and Zhu, X and Xie, Q and Jin, J and Zhou, Y and Luo, Y and Liu, Y and Tian, J and Zhao, Y}, title = {Monitoring nature's calendar from space: Emerging topics in land surface phenology and associated opportunities for science applications.}, journal = {Global change biology}, volume = {28}, number = {24}, pages = {7186-7204}, pmid = {36114727}, issn = {1365-2486}, mesh = {*Ecosystem ; Seasons ; *Climate Change ; Carbon ; Water ; }, abstract = {Vegetation phenology has been viewed as the nature's calendar and an integrative indicator of plant-climate interactions. The correct representation of vegetation phenology is important for models to accurately simulate the exchange of carbon, water, and energy between the vegetated land surface and the atmosphere. Remote sensing has advanced the monitoring of vegetation phenology by providing spatially and temporally continuous data that together with conventional ground observations offers a unique contribution to our knowledge about the environmental impact on ecosystems as well as the ecological adaptations and feedback to global climate change. Land surface phenology (LSP) is defined as the use of satellites to monitor seasonal dynamics in vegetated land surfaces and to estimate phenological transition dates. LSP, as an interdisciplinary subject among remote sensing, ecology, and biometeorology, has undergone rapid development over the past few decades. Recent advances in sensor technologies, as well as data fusion techniques, have enabled novel phenology retrieval algorithms that refine phenology details at even higher spatiotemporal resolutions, providing new insights into ecosystem dynamics. As such, here we summarize the recent advances in LSP and the associated opportunities for science applications. We focus on the remaining challenges, promising techniques, and emerging topics that together we believe will truly form the very frontier of the global LSP research field.}, } @article {pmid36112603, year = {2022}, author = {Miller, JC and Satheesh Babu, AK and Petersen, C and Wankhade, UD and Robeson, MS and Putich, MN and Mueller, JE and O'Farrell, AS and Cho, JM and Chintapalli, SV and Jalili, T and Symons, JD and Anandh Babu, PV}, title = {Gut Microbes Are Associated with the Vascular Beneficial Effects of Dietary Strawberry on Metabolic Syndrome-Induced Vascular Inflammation.}, journal = {Molecular nutrition & food research}, volume = {66}, number = {22}, pages = {e2200112}, pmid = {36112603}, issn = {1613-4133}, support = {R03 AG052848/AG/NIA NIH HHS/United States ; R01 AT010247/AT/NCCIH NIH HHS/United States ; R01 HL141540/HL/NHLBI NIH HHS/United States ; P30 DK020579/DK/NIDDK NIH HHS/United States ; R03AGO52848/HL/NHLBI NIH HHS/United States ; }, mesh = {Male ; Mice ; Animals ; *Fragaria/chemistry ; *Metabolic Syndrome/etiology/drug therapy ; *Gastrointestinal Microbiome ; Mice, Inbred C57BL ; Diet, High-Fat/adverse effects ; Inflammation ; }, abstract = {SCOPE: Metabolic syndrome (MetS) alters the gut microbial ecology and increases the risk of cardiovascular disease. This study investigates whether strawberry consumption reduces vascular complications in an animal model of MetS and identifies whether this effect is associated with changes in the composition of gut microbes.

METHODS AND RESULTS: Seven-week-old male mice consume diets with 10% (C) or 60% kcal from fat (high-fat diet fed mice; HF) for 12 weeks and subgroups are fed a 2.35% freeze-dried strawberry supplemented diet (C+SB or HF+SB). This nutritional dose is equivalent to ≈160 g of strawberry. After 12 weeks treatment, vascular inflammation is enhanced in HF versus C mice as shown by an increased monocyte binding to vasculature, elevated serum chemokines, and increased mRNA expression of inflammatory molecules. However, strawberry supplementation suppresses vascular inflammation in HF+SB versus HF mice. Metabolic variables, blood pressure, and indices of vascular function were similar among the groups. Further, the abundance of opportunistic microbe is decreased in HF+SB. Importantly, circulating chemokines are positively associated with opportunistic microbes and negatively associated with the commensal microbes (Bifidobacterium and Facalibaculum).

CONCLUSION: Dietary strawberry decreases the abundance of opportunistic microbe and this is associated with a decrease in vascular inflammation resulting from MetS.}, } @article {pmid36112284, year = {2023}, author = {Badapalli, PK and Kottala, RB and Madiga, R and Golla, V}, title = {An integrated approach for the assessment and monitoring of land degradation and desertification in semi-arid regions using physico-chemical and geospatial modeling techniques.}, journal = {Environmental science and pollution research international}, volume = {30}, number = {55}, pages = {116751-116764}, pmid = {36112284}, issn = {1614-7499}, mesh = {*Conservation of Natural Resources ; *Ecosystem ; Environmental Monitoring/methods ; Geographic Information Systems ; Soil ; }, abstract = {Land degradation (LD) and desertification are serious ecological, environmental, and social-economic threats in the world, and there is a demanding need to develop accountable and reproducible techniques to assess them at different scales. This study assesses LD and desertification with the help of remote sensing (RS) and geographical information system (GIS) in the study region for the period past 29 years, i.e., from 1990 to 2019. The severity of LD and desertification was assessed quantitatively by collecting twelve soil samples in the study region and analyzing the eleven soil physico-chemical parameters and these values have made correlated with digital number (DN) values with LANDSAT 8 OLI/TIRS satellite image. The land cover analysis of LANDSAT imagery revealed that the water body slightly increased from 0.29% in 1990 to 0.46% in 2019, and built-up-land increased from 2.87% in 1990 to 5.31% in 2019. Vegetation decreased from 52.03% in 1990 to 28.57%. Fallow land, degraded land, and desertified lands increased at alarming rates, respectively 13.71% to 26.35, 18.57% to 22.31%, and 12.53% to 17.00%. It is also established that the multi-temporal analysis of change detection data can provide a sophisticated measure of ecosystem health and variation, and that, over the last 29 years, considerable progress has been made in the respective research.}, } @article {pmid36111781, year = {2022}, author = {Eyre, MT and Souza, FN and Carvalho-Pereira, TSA and Nery, N and de Oliveira, D and Cruz, JS and Sacramento, GA and Khalil, H and Wunder, EA and Hacker, KP and Hagan, JE and Childs, JE and Reis, MG and Begon, M and Diggle, PJ and Ko, AI and Giorgi, E and Costa, F}, title = {Linking rattiness, geography and environmental degradation to spillover Leptospira infections in marginalised urban settings: An eco-epidemiological community-based cohort study in Brazil.}, journal = {eLife}, volume = {11}, number = {}, pages = {}, pmid = {36111781}, issn = {2050-084X}, support = {U01 AI088752/AI/NIAID NIH HHS/United States ; F31 AI114245/NH/NIH HHS/United States ; 102330/Z/13/Z/WT_/Wellcome Trust/United Kingdom ; F31 AI114245/AI/NIAID NIH HHS/United States ; R01 TW009504/TW/FIC NIH HHS/United States ; R01 AI052473/NH/NIH HHS/United States ; R01 TW009504/NH/NIH HHS/United States ; R25 TW009338/NH/NIH HHS/United States ; UL1 TR001863/TR/NCATS NIH HHS/United States ; R01 AI052473/AI/NIAID NIH HHS/United States ; R25 TW009338/TW/FIC NIH HHS/United States ; U01 AI088752/NH/NIH HHS/United States ; /WT_/Wellcome Trust/United Kingdom ; 001/WHO_/World Health Organization/International ; 964635/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Adult ; Animals ; Brazil/epidemiology ; Cohort Studies ; Epidemiologic Studies ; Geography ; Humans ; *Leptospirosis/epidemiology ; Male ; *Poverty Areas ; Rats ; Zoonoses/epidemiology ; }, abstract = {BACKGROUND: Zoonotic spillover from animal reservoirs is responsible for a significant global public health burden, but the processes that promote spillover events are poorly understood in complex urban settings. Endemic transmission of Leptospira, the agent of leptospirosis, in marginalised urban communities occurs through human exposure to an environment contaminated by bacteria shed in the urine of the rat reservoir. However, it is unclear to what extent transmission is driven by variation in the distribution of rats or by the dispersal of bacteria in rainwater runoff and overflow from open sewer systems.

METHODS: We conducted an eco-epidemiological study in a high-risk community in Salvador, Brazil, by prospectively following a cohort of 1401 residents to ascertain serological evidence for leptospiral infections. A concurrent rat ecology study was used to collect information on the fine-scale spatial distribution of 'rattiness', our proxy for rat abundance and exposure of interest. We developed and applied a novel geostatistical framework for joint spatial modelling of multiple indices of disease reservoir abundance and human infection risk.

RESULTS: The estimated infection rate was 51.4 (95%CI 40.4, 64.2) infections per 1000 follow-up events. Infection risk increased with age until 30 years of age and was associated with male gender. Rattiness was positively associated with infection risk for residents across the entire study area, but this effect was stronger in higher elevation areas (OR 3.27 95% CI 1.68, 19.07) than in lower elevation areas (OR 1.14 95% CI 1.05, 1.53).

CONCLUSIONS: These findings suggest that, while frequent flooding events may disperse bacteria in regions of low elevation, environmental risk in higher elevation areas is more localised and directly driven by the distribution of local rat populations. The modelling framework developed may have broad applications in delineating complex animal-environment-human interactions during zoonotic spillover and identifying opportunities for public health intervention.

FUNDING: This work was supported by the Oswaldo Cruz Foundation and Secretariat of Health Surveillance, Brazilian Ministry of Health, the National Institutes of Health of the United States (grant numbers F31 AI114245, R01 AI052473, U01 AI088752, R01 TW009504 and R25 TW009338); the Wellcome Trust (102330/Z/13/Z), and by the Fundação de Amparo à Pesquisa do Estado da Bahia (FAPESB/JCB0020/2016). MTE was supported by a Medical Research UK doctorate studentship. FBS participated in this study under a FAPESB doctorate scholarship.}, } @article {pmid36109660, year = {2022}, author = {Negesse, A and Woyraw, W and Temesgen, H and Teka, Y and Yismaw, L and Akalu, TY and Deml, YA and Sume, BW and Negesse, Y and Taddege, T and Kidie, WD and Teym, A and Asmare, B and Hune, Y and Damte, D and Getaneh, T and Gebre, T and Tilahun, B and Tenagne, A and Tegegne, E and Birhanu, MY and Mekonen, H and Shiferaw, M and Kassahun, W and Desalegn, BB}, title = {Spatial exploration of non-resilience to food insecurity, its association with COVID-19 and household coping strategies in East Gojjam districts, Northwest Ethiopia, 2020.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {15511}, pmid = {36109660}, issn = {2045-2322}, mesh = {Adaptation, Psychological ; *COVID-19/epidemiology ; Cross-Sectional Studies ; Ethiopia/epidemiology ; Family Characteristics ; Food Insecurity ; *Food Supply ; Humans ; Male ; Pandemics ; Socioeconomic Factors ; }, abstract = {The coronavirus disease-2019 (COVID-19) pandemic has posed a significant multifaceted threat to the global community. Ethiopia, as a Sub-Saharan African country, is suffering from chronic food insecurity, and the emergence of such a pandemic will exacerbate the situation. As a result, this study investigated the spatial variation of non-resilience to food insecurity, its relationship with COVID-19, and household coping strategies to become resilient in the long run among households in the East Gojjam Zone of Northwest Ethiopia. From September 22 to December 24, 2020, an agro-ecological-based cross-sectional study of 3532 households was conducted to assess the spatial distribution and associated factors of non-resilience to household food insecurity. The enumeration areas (EAs) and households were chosen using a multistage sampling technique. Data were gathered using a semi-structured questionnaire and checklist using an Android device loaded with an Open Data Kit (ODK) template. Binary logistic regression was used to identify the specific factors associated with household non-resilience to food insecurity. A thematic analysis was conducted to investigate the opportunities and challenges of resilience for household food insecurity. Nearly two-thirds (62.5%) of the households were farmers, 67.9% lived in rural areas, and nearly three-quarters (73.8%) earned less than or equal to ETB 2100 per month. Males headed more than four-fifths of the households (81.7%). We found that nearly two-thirds of the households (60.02%), 95% CI 58.40, 61.64) were food insecure. After bivariate logistic regression, we found that households who were divorced (AOR = 2.54 (1.65, 3.87)), daily laborers (AOR = 2.37 (1.15, 4.87)), government employees (AOR = 2.06 (1.05, 4.05)), residents of highland and hot areas (AOR = 11.5 (5.37, 16.77)) and lowland areas (AOR = 1.35 (1.02, 3.15)) were frustrated by COVID-19 (AOR = 1.23 (1.02, 1.50)) and price inflation (1.89 (AOR = 1.42, 2.56))) were at higher odds of being non-resilient to household food insecurity at a 95% confidence level. Geospatial hot spot analysis revealed that Kurar kebele (the lowest government administrative unit) in Dejen District and Debre Markos town were the red-hotspot areas of household non-resilience to food insecurity. Less than a quarter of the households attempted to cope with food insecurity by adjusting their food consumption, while more than 60% of the households chose none of the coping strategies tested. According to the thematic analysis, the degree of poverty (lack of asset ownership), the COVID-19 pandemic, farm decreased variety, and low crop productivity were identified as challenges to coping with the hardship of resilience to food insecurity. During the COVID-19 pandemic and public emergency, the proportion of households that were unprepared for food insecurity reached its peak. It was recognized that a segment of the population with low economic capacity was more vulnerable to food insecurity and less resilient. Tough developmental gains will be undermined in this case. As a result, each responsible body and stakeholder should develop and implement solid corrective plans for the local context.}, } @article {pmid36109545, year = {2022}, author = {Domma, F and Condino, F and Franceschi, S and De Luca, DL and Biondi, D}, title = {On the extreme hydrologic events determinants by means of Beta-Singh-Maddala reparameterization.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {15537}, pmid = {36109545}, issn = {2045-2322}, mesh = {*Hydrology ; }, abstract = {In previous studies, beta-k distribution and distribution functions strongly related to that, have played important roles in representing extreme events. Among these distributions, the Beta-Singh-Maddala turned out to be adequate for modelling hydrological extreme events. Starting from this distribution, the aim of the paper is to express the model as a function of indexes of hydrological interest and simultaneously investigate on their dependence with a set of explanatory variables in such a way to explore on possible determinants of extreme hydrologic events. Finally, an application to a real hydrologic dataset is considered in order to show the potentiality of the proposed model in describing data and in understanding effects of covariates on frequently adopted hydrological indicators.}, } @article {pmid36108049, year = {2022}, author = {Tegally, H and San, JE and Cotten, M and Moir, M and Tegomoh, B and Mboowa, G and Martin, DP and Baxter, C and Lambisia, AW and Diallo, A and Amoako, DG and Diagne, MM and Sisay, A and Zekri, AN and Gueye, AS and Sangare, AK and Ouedraogo, AS and Sow, A and Musa, AO and Sesay, AK and Abias, AG and Elzagheid, AI and Lagare, A and Kemi, AS and Abar, AE and Johnson, AA and Fowotade, A and Oluwapelumi, AO and Amuri, AA and Juru, A and Kandeil, A and Mostafa, A and Rebai, A and Sayed, A and Kazeem, A and Balde, A and Christoffels, A and Trotter, AJ and Campbell, A and Keita, AK and Kone, A and Bouzid, A and Souissi, A and Agweyu, A and Naguib, A and Gutierrez, AV and Nkeshimana, A and Page, AJ and Yadouleton, A and Vinze, A and Happi, AN and Chouikha, A and Iranzadeh, A and Maharaj, A and Batchi-Bouyou, AL and Ismail, A and Sylverken, AA and Goba, A and Femi, A and Sijuwola, AE and Marycelin, B and Salako, BL and Oderinde, BS and Bolajoko, B and Diarra, B and Herring, BL and Tsofa, B and Lekana-Douki, B and Mvula, B and Njanpop-Lafourcade, BM and Marondera, BT and Khaireh, BA and Kouriba, B and Adu, B and Pool, B and McInnis, B and Brook, C and Williamson, C and Nduwimana, C and Anscombe, C and Pratt, CB and Scheepers, C and Akoua-Koffi, CG and Agoti, CN and Mapanguy, CM and Loucoubar, C and Onwuamah, CK and Ihekweazu, C and Malaka, CN and Peyrefitte, C and Grace, C and Omoruyi, CE and Rafaï, CD and Morang'a, CM and Erameh, C and Lule, DB and Bridges, DJ and Mukadi-Bamuleka, D and Park, D and Rasmussen, DA and Baker, D and Nokes, DJ and Ssemwanga, D and Tshiabuila, D and Amuzu, DSY and Goedhals, D and Grant, DS and Omuoyo, DO and Maruapula, D and Wanjohi, DW and Foster-Nyarko, E and Lusamaki, EK and Simulundu, E and Ong'era, EM and Ngabana, EN and Abworo, EO and Otieno, E and Shumba, E and Barasa, E and Ahmed, EB and Ahmed, EA and Lokilo, E and Mukantwari, E and Philomena, E and Belarbi, E and Simon-Loriere, E and Anoh, EA and Manuel, E and Leendertz, F and Taweh, FM and Wasfi, F and Abdelmoula, F and Takawira, FT and Derrar, F and Ajogbasile, FV and Treurnicht, F and Onikepe, F and Ntoumi, F and Muyembe, FM and Ragomzingba, FEZ and Dratibi, FA and Iyanu, FA and Mbunsu, GK and Thilliez, G and Kay, GL and Akpede, GO and van Zyl, GU and Awandare, GA and Kpeli, GS and Schubert, G and Maphalala, GP and Ranaivoson, HC and Omunakwe, HE and Onywera, H and Abe, H and Karray, H and Nansumba, H and Triki, H and Kadjo, HAA and Elgahzaly, H and Gumbo, H and Mathieu, H and Kavunga-Membo, H and Smeti, I and Olawoye, IB and Adetifa, IMO and Odia, I and Ben Boubaker, IB and Muhammad, IA and Ssewanyana, I and Wurie, I and Konstantinus, IS and Halatoko, JWA and Ayei, J and Sonoo, J and Makangara, JC and Tamfum, JM and Heraud, JM and Shaffer, JG and Giandhari, J and Musyoki, J and Nkurunziza, J and Uwanibe, JN and Bhiman, JN and Yasuda, J and Morais, J and Kiconco, J and Sandi, JD and Huddleston, J and Odoom, JK and Morobe, JM and Gyapong, JO and Kayiwa, JT and Okolie, JC and Xavier, JS and Gyamfi, J and Wamala, JF and Bonney, JHK and Nyandwi, J and Everatt, J and Nakaseegu, J and Ngoi, JM and Namulondo, J and Oguzie, JU and Andeko, JC and Lutwama, JJ and Mogga, JJH and O'Grady, J and Siddle, KJ and Victoir, K and Adeyemi, KT and Tumedi, KA and Carvalho, KS and Mohammed, KS and Dellagi, K and Musonda, KG and Duedu, KO and Fki-Berrajah, L and Singh, L and Kepler, LM and Biscornet, L and de Oliveira Martins, L and Chabuka, L and Olubayo, L and Ojok, LD and Deng, LL and Ochola-Oyier, LI and Tyers, L and Mine, M and Ramuth, M and Mastouri, M and ElHefnawi, M and Mbanne, M and Matsheka, MI and Kebabonye, M and Diop, M and Momoh, M and Lima Mendonça, MDL and Venter, M and Paye, MF and Faye, M and Nyaga, MM and Mareka, M and Damaris, MM and Mburu, MW and Mpina, MG and Owusu, M and Wiley, MR and Tatfeng, MY and Ayekaba, MO and Abouelhoda, M and Beloufa, MA and Seadawy, MG and Khalifa, MK and Matobo, MM and Kane, M and Salou, M and Mbulawa, MB and Mwenda, M and Allam, M and Phan, MVT and Abid, N and Rujeni, N and Abuzaid, N and Ismael, N and Elguindy, N and Top, NM and Dia, N and Mabunda, N and Hsiao, NY and Silochi, NB and Francisco, NM and Saasa, N and Bbosa, N and Murunga, N and Gumede, N and Wolter, N and Sitharam, N and Ndodo, N and Ajayi, NA and Tordo, N and Mbhele, N and Razanajatovo, NH and Iguosadolo, N and Mba, N and Kingsley, OC and Sylvanus, O and Femi, O and Adewumi, OM and Testimony, O and Ogunsanya, OA and Fakayode, O and Ogah, OE and Oludayo, OE and Faye, O and Smith-Lawrence, P and Ondoa, P and Combe, P and Nabisubi, P and Semanda, P and Oluniyi, PE and Arnaldo, P and Quashie, PK and Okokhere, PO and Bejon, P and Dussart, P and Bester, PA and Mbala, PK and Kaleebu, P and Abechi, P and El-Shesheny, R and Joseph, R and Aziz, RK and Essomba, RG and Ayivor-Djanie, R and Njouom, R and Phillips, RO and Gorman, R and Kingsley, RA and Neto Rodrigues, RMDESA and Audu, RA and Carr, RAA and Gargouri, S and Masmoudi, S and Bootsma, S and Sankhe, S and Mohamed, SI and Femi, S and Mhalla, S and Hosch, S and Kassim, SK and Metha, S and Trabelsi, S and Agwa, SH and Mwangi, SW and Doumbia, S and Makiala-Mandanda, S and Aryeetey, S and Ahmed, SS and Ahmed, SM and Elhamoumi, S and Moyo, S and Lutucuta, S and Gaseitsiwe, S and Jalloh, S and Andriamandimby, SF and Oguntope, S and Grayo, S and Lekana-Douki, S and Prosolek, S and Ouangraoua, S and van Wyk, S and Schaffner, SF and Kanyerezi, S and Ahuka-Mundeke, S and Rudder, S and Pillay, S and Nabadda, S and Behillil, S and Budiaki, SL and van der Werf, S and Mashe, T and Mohale, T and Le-Viet, T and Velavan, TP and Schindler, T and Maponga, TG and Bedford, T and Anyaneji, UJ and Chinedu, U and Ramphal, U and George, UE and Enouf, V and Nene, V and Gorova, V and Roshdy, WH and Karim, WA and Ampofo, WK and Preiser, W and Choga, WT and Ahmed, YA and Ramphal, Y and Bediako, Y and Naidoo, Y and Butera, Y and de Laurent, ZR and , and Ouma, AEO and von Gottberg, A and Githinji, G and Moeti, M and Tomori, O and Sabeti, PC and Sall, AA and Oyola, SO and Tebeje, YK and Tessema, SK and de Oliveira, T and Happi, C and Lessells, R and Nkengasong, J and Wilkinson, E}, title = {The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance.}, journal = {Science (New York, N.Y.)}, volume = {378}, number = {6615}, pages = {eabq5358}, pmid = {36108049}, issn = {1095-9203}, support = {MR/J01477X/1/MRC_/Medical Research Council/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; MR/P028071/1/MRC_/Medical Research Council/United Kingdom ; MC_UU_12014/12/MRC_/Medical Research Council/United Kingdom ; U54 TW012041/TW/FIC NIH HHS/United States ; MC_UU_00027/1/MRC_/Medical Research Council/United Kingdom ; MC_PC_20045/MRC_/Medical Research Council/United Kingdom ; MC_PC_19026/MRC_/Medical Research Council/United Kingdom ; U19 AI089696/AI/NIAID NIH HHS/United States ; U01 HG007480/HG/NHGRI NIH HHS/United States ; K24 AI131924/AI/NIAID NIH HHS/United States ; MC_PC_20001/MRC_/Medical Research Council/United Kingdom ; K24 AI131928/AI/NIAID NIH HHS/United States ; U2R TW010673/TW/FIC NIH HHS/United States ; U01 AI151698/AI/NIAID NIH HHS/United States ; U19 AI129387/AI/NIAID NIH HHS/United States ; 001/WHO_/World Health Organization/International ; U01 AI151812/AI/NIAID NIH HHS/United States ; U54 HG007480/HG/NHGRI NIH HHS/United States ; }, mesh = {Africa/epidemiology ; *COVID-19/epidemiology/virology ; *Epidemiological Monitoring ; Genomics ; Humans ; *Pandemics ; *SARS-CoV-2/genetics ; }, abstract = {Investment in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing in Africa over the past year has led to a major increase in the number of sequences that have been generated and used to track the pandemic on the continent, a number that now exceeds 100,000 genomes. Our results show an increase in the number of African countries that are able to sequence domestically and highlight that local sequencing enables faster turnaround times and more-regular routine surveillance. Despite limitations of low testing proportions, findings from this genomic surveillance study underscore the heterogeneous nature of the pandemic and illuminate the distinct dispersal dynamics of variants of concern-particularly Alpha, Beta, Delta, and Omicron-on the continent. Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve while the continent faces many emerging and reemerging infectious disease threats. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century.}, } @article {pmid36107252, year = {2022}, author = {Lukasová, V and Bičárová, S and Buchholcerová, A and Adamčíková, K}, title = {Low sensitivity of Pinus mugo to surface ozone pollution in the subalpine zone of continental Europe.}, journal = {International journal of biometeorology}, volume = {66}, number = {11}, pages = {2311-2324}, pmid = {36107252}, issn = {1432-1254}, support = {VEGA 2/0093/21//Agentúra Ministerstva Školstva, Vedy, Výskumu a Športu SR/ ; }, mesh = {Humans ; *Ozone/analysis ; *Air Pollutants/analysis ; *Pinus ; Environmental Monitoring ; Plant Leaves ; Polyesters/analysis/pharmacology ; }, abstract = {High altitudes have been exposed to enhanced levels of surface ozone (O3) concentrations over recent decades compared to the pre-industrial era. The responses of vegetation to this toxic pollutant are species-specific and depend on the climate conditions. In this paper, we explored the reaction of Pinus mugo (P. mugo) to O3-induced stress in the continental climate of an ozone-rich mountain area in the High Tatra Mountains (Western Carpathians). The effects of O3 doses modelled by a deposition model, O3 concentrations and other factors on P. mugo were identified from (a) satellite-based data via NDVI (normalised differenced vegetation index) over 2000-2020 and (b) visible injury on needle samples gathered from P. mugo individuals at ground-truth sites in 2019 and 2020. Analysing the NDVI trend, we observed non-significant changes (p > 0.05) in the greenness of P. mugo despite growing in an environment with the average seasonal O3 concentration around 51.6 ppbv, the maximum hourly concentrations more than 90 ppbv and increasing trend of O3 doses by 0.1 mmol m[-2] PLA (plant leaf area) year[-1]. The visible O3 injury of samples collected at study sites was low (mean injury observed on 1-10% of needles' surface), and the symptoms of injury caused by other biotic and abiotic factors prevailed over those caused by O3. In addition, the correlation analyses between NDVI and the climatic factors indicated a significant (p < 0.05) and positive relationship with photosynthetic active radiation (R = 0.45) in July, and with stomatal conductance (R = 0.52) and temperature factor (R = 0.43) in August. Therefore, we concluded that the positive effect of climate conditions, which support the growth processes of P. mugo, may suppress the negative effect of the mean O3 doses of 17.8 mmol m[-2] PLA accumulated over the growing season.}, } @article {pmid36107138, year = {2023}, author = {Bassing, SB and DeVivo, M and Ganz, TR and Kertson, BN and Prugh, LR and Roussin, T and Satterfield, L and Windell, RM and Wirsing, AJ and Gardner, B}, title = {Are we telling the same story? Comparing inferences made from camera trap and telemetry data for wildlife monitoring.}, journal = {Ecological applications : a publication of the Ecological Society of America}, volume = {33}, number = {1}, pages = {e2745}, doi = {10.1002/eap.2745}, pmid = {36107138}, issn = {1051-0761}, mesh = {Animals ; *Animals, Wild ; *Ecosystem ; Geographic Information Systems ; Surveys and Questionnaires ; Telemetry ; }, abstract = {Estimating habitat and spatial associations for wildlife is common across ecological studies and it is well known that individual traits can drive population dynamics and vice versa. Thus, it is commonly assumed that individual- and population-level data should represent the same underlying processes, but few studies have directly compared contemporaneous data representing these different perspectives. We evaluated the circumstances under which data collected from Lagrangian (individual-level) and Eulerian (population-level) perspectives could yield comparable inference to understand how scalable information is from the individual to the population. We used Global Positioning System (GPS) collar (Lagrangian) and camera trap (Eulerian) data for seven species collected simultaneously in eastern Washington (2018-2020) to compare inferences made from different survey perspectives. We fit the respective data streams to resource selection functions (RSFs) and occupancy models and compared estimated habitat- and space-use patterns for each species. Although previous studies have considered whether individual- and population-level data generated comparable information, ours is the first to make this comparison for multiple species simultaneously and to specifically ask whether inferences from the two perspectives differed depending on the focal species. We found general agreement between the predicted spatial distributions for most paired analyses, although specific habitat relationships differed. We hypothesize the discrepancies arose due to differences in statistical power associated with camera and GPS-collar sampling, as well as spatial mismatches in the data. Our research suggests data collected from individual-based sampling methods can capture coarse population-wide patterns for a diversity of species, but results differ when interpreting specific wildlife-habitat relationships.}, } @article {pmid36103465, year = {2022}, author = {Nam, S and Jeon, S and Lee, SJ and Ash, G and Nelson, LE and Granger, DA}, title = {Real-time racial discrimination, affective states, salivary cortisol and alpha-amylase in Black adults.}, journal = {PloS one}, volume = {17}, number = {9}, pages = {e0273081}, pmid = {36103465}, issn = {1932-6203}, support = {R25 MH067127/MH/NIMH NIH HHS/United States ; }, mesh = {Adult ; Cross-Sectional Studies ; Humans ; *Hydrocortisone ; *Racism/psychology ; Retrospective Studies ; Saliva ; Stress, Psychological/psychology ; alpha-Amylases ; }, abstract = {Perceived racial discrimination has been associated with the autonomic nervous system (ANS) and hypothalamic-pituitary-adrenal (HPA) axis activities-two major stress response systems. To date, most studies have used cross-sectional data that captured retrospective measures of the racial discrimination associated with current physiological stress responses. The purpose of this study was to examine the relationship between racial discrimination measured in real-time and physiological stress responses. Twelve healthy Black adults completed baseline surveys and self-collected saliva samples 4x/day for 4 days to measure cortisol and alpha amylase (AA) as a proxy of HPA and ANS systems, respectively. Real-time racial discrimination was measured using ecological momentary assessments (EMA) sent to participants 5x/day for 7 days. Multilevel models were conducted to examine the relationship between racial discrimination and stress responses. In multilevel models, the previous day's racial discrimination was significantly associated with the next day's cortisol level at wakening (β = 0.81, partial r = 0.74, p<0.01) and diurnal slope (β = -0.85, partial r = -0.73, p<0.01). Also, microaggressions were significantly associated with the diurnal cortisol slope in the same day, indicating that on the day when people reported more microaggressions than usual, a flatter diurnal slope of cortisol was observed (β = -0.50, partial r = -0.64, p<0.01). The concurrent use of salivary biomarkers and EMA was feasible methods to examine the temporal relationship between racial discrimination and physiological stress responses. The within-person approach may help us understand the concurrent or lagged effects of racial discrimination on the stress responses. Further studies are needed to confirm the observed findings with a large sample size and to improve stress related health outcomes in racial/ethnic minorities.}, } @article {pmid36102834, year = {2022}, author = {Débarre, F and Lecoeur, E and Guimier, L and Jauffret-Roustide, M and Jannot, AS}, title = {The French Covid-19 vaccination policy did not solve vaccination inequities: a nationwide study on 64.5 million people.}, journal = {European journal of public health}, volume = {32}, number = {5}, pages = {825-830}, pmid = {36102834}, issn = {1464-360X}, mesh = {*COVID-19/epidemiology/prevention & control ; *COVID-19 Vaccines ; Emigration and Immigration ; Humans ; Policy ; Vaccination ; }, abstract = {BACKGROUND: To encourage Covid-19 vaccination, France introduced during the Summer 2021 a 'Sanitary Pass', which morphed into a 'Vaccine Pass' in early 2022. While the sanitary pass led to an increase in Covid-19 vaccination rates, spatial heterogeneities in vaccination rates remained. To identify potential determinants of these heterogeneities and evaluate the French sanitary and vaccine passes' efficacies in reducing them, we used a data-driven approach on exhaustive nationwide data, gathering 141 socio-economic, political and geographic indicators.

METHODS: We considered the association between vaccination rates and each indicator at different time points: before the sanitary pass announcement (week 2021-W27), before the sanitary pass came into force (week 2021-W31) and 1 month after (week 2021-W35) and the equivalent dates for the vaccine pass (weeks 2021-W49, 2022-W03 and 2022-W07).

RESULTS: The indicators most associated with vaccination rates were the share of local income coming from unemployment benefits, overcrowded households rate, immigrants rate and vote for an 'anti-establishment' candidate at the 2017 Presidential election. These associations increase over time. Consequently, living in a district below the median of such indicator decreases the probability to be vaccinated by about 30% at the end of the studied period, and this probability gradually decreases by deciles of these indicators.

CONCLUSIONS: Our analysis reveals that factors related to poverty, immigration and trust in the government are strong determinants of vaccination rate, and that vaccination inequities tended to increase after the introduction of the French sanitary and vaccination passes.}, } @article {pmid36100598, year = {2022}, author = {Metz, S and Huber, P and Mateus-Barros, E and Junger, PC and de Melo, M and Bagatini, IL and Izaguirre, I and Câmara Dos Reis, M and Llames, ME and Accattatis, V and Quiroga, MV and Devercelli, M and Schiaffino, MR and Niño-García, JP and Bastidas Navarro, M and Modenutti, B and Vieira, H and Saraceno, M and Sabio Y García, CA and Pereira, E and González-Revello, A and Piccini, C and Unrein, F and Alonso, C and Sarmento, H}, title = {A georeferenced rRNA amplicon database of aquatic microbiomes from South America.}, journal = {Scientific data}, volume = {9}, number = {1}, pages = {565}, pmid = {36100598}, issn = {2052-4463}, mesh = {Bacteria/genetics ; Databases, Genetic ; High-Throughput Nucleotide Sequencing ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; South America ; Water Microbiology ; }, abstract = {The biogeography of bacterial communities is a key topic in Microbial Ecology. Regarding continental water, most studies are carried out in the northern hemisphere, leaving a gap on microorganism's diversity patterns on a global scale. South America harbours approximately one third of the world's total freshwater resources, and is one of these understudied regions. To fill this gap, we compiled 16S rRNA amplicon sequencing data of microbial communities across South America continental water ecosystems, presenting the first database µSudAqua[db]. The database contains over 866 georeferenced samples from 9 different ecoregions with contextual environmental information. For its integration and validation we constructed a curated database (µSudAqua[db.sp]) using samples sequenced by Illumina MiSeq platform with commonly used prokaryote universal primers. This comprised ~60% of the total georeferenced samples of the µSudAqua[db]. This compilation was carried out in the scope of the µSudAqua collaborative network and represents one of the most complete databases of continental water microbial communities from South America.}, } @article {pmid36095758, year = {2022}, author = {Golovatch, S and Vandenspiegel, D}, title = {Carinobolus gen. nov. and Costabolus gen. nov., two new, remarkably crested, monospecific genera of spirobolidan millipedes from West Africa, with the proposal of a new tribe, Amblybolini tribus nova (Diplopoda, Spirobolida, Pachybolidae).}, journal = {Zootaxa}, volume = {5150}, number = {1}, pages = {97-110}, doi = {10.11646/zootaxa.5150.1.5}, pmid = {36095758}, issn = {1175-5334}, mesh = {Africa, Western ; Animals ; *Arthropods ; }, abstract = {Two new genera, Carinobolus gen. nov. and Costabolus gen. nov., both belonging to the very large, widespread, pantropical family Pachybolidae, are described based on Carinobolus complex sp. nov. and Costabolus baculus sp. nov., respectively. Chiefly based on the posterior gonopod being distinctly articulated at midlength, both new genera seem to be especially similar to Amblybolus Keeton, 1964a (three species in western Africa) and Atlanticobolus Hoffman, 1979 (one species from an island off the Brazilian coast), all of them meriting a separate tribal category, Amblybolini tribus nova. A key is proposed to distinguish all four presently accepted genera of the new tribe. The new genera and species are clearly distinguished in showing unusually strongly crested/ribbed metazonae, a character that is only very seldom observed in Pachybolidae generally, and apparently unique among Afrotropical members. Being rather similar in many respects, both new genera and species differ from each other sufficiently well in gonopodal and leg structure, even though both come from forests in southeastern Nigeria close to the border to Cameroon.}, } @article {pmid36095211, year = {2022}, author = {Still, CJ and Page, G and Rastogi, B and Griffith, DM and Aubrecht, DM and Kim, Y and Burns, SP and Hanson, CV and Kwon, H and Hawkins, L and Meinzer, FC and Sevanto, S and Roberts, D and Goulden, M and Pau, S and Detto, M and Helliker, B and Richardson, AD}, title = {No evidence of canopy-scale leaf thermoregulation to cool leaves below air temperature across a range of forest ecosystems.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {119}, number = {38}, pages = {e2205682119}, pmid = {36095211}, issn = {1091-6490}, mesh = {*Carbon/metabolism ; *Carbon Cycle ; *Forests ; *Plant Leaves/anatomy & histology/metabolism ; Temperature ; }, abstract = {Understanding and predicting the relationship between leaf temperature (Tleaf) and air temperature (Tair) is essential for projecting responses to a warming climate, as studies suggest that many forests are near thermal thresholds for carbon uptake. Based on leaf measurements, the limited leaf homeothermy hypothesis argues that daytime Tleaf is maintained near photosynthetic temperature optima and below damaging temperature thresholds. Specifically, leaves should cool below Tair at higher temperatures (i.e., > ∼25-30°C) leading to slopes <1 in Tleaf/Tair relationships and substantial carbon uptake when leaves are cooler than air. This hypothesis implies that climate warming will be mitigated by a compensatory leaf cooling response. A key uncertainty is understanding whether such thermoregulatory behavior occurs in natural forest canopies. We present an unprecedented set of growing season canopy-level leaf temperature (Tcan) data measured with thermal imaging at multiple well-instrumented forest sites in North and Central America. Our data do not support the limited homeothermy hypothesis: canopy leaves are warmer than air during most of the day and only cool below air in mid to late afternoon, leading to Tcan/Tair slopes >1 and hysteretic behavior. We find that the majority of ecosystem photosynthesis occurs when canopy leaves are warmer than air. Using energy balance and physiological modeling, we show that key leaf traits influence leaf-air coupling and ultimately the Tcan/Tair relationship. Canopy structure also plays an important role in Tcan dynamics. Future climate warming is likely to lead to even greater Tcan, with attendant impacts on forest carbon cycling and mortality risk.}, } @article {pmid36094211, year = {2022}, author = {Njoroge, SM and Madé, LF and von Mentzer, A and Kulohoma, BW and Kamanu, TK and Ouko, TT and Kiiru, J and Ward, MJ and Thomson, NR and Fèvre, EM and Woolhouse, M and Kariuki, S}, title = {Draft Genome Sequence of an Enterotoxigenic Escherichia coli Strain Carrying Genes for Colonization Surface Antigen 13 and a Heat-Labile Toxin.}, journal = {Microbiology resource announcements}, volume = {11}, number = {10}, pages = {e0041622}, pmid = {36094211}, issn = {2576-098X}, support = {G1100783/1//UKRI | Medical Research Council (MRC)/ ; BB/L019019/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; WT103953MA//Wellcome Trust (WT)/ ; G1100783/MRC_/Medical Research Council/United Kingdom ; R01 AI099525/AI/NIAID NIH HHS/United States ; MR/R015090/1/MRC_/Medical Research Council/United Kingdom ; }, abstract = {Here, we report the draft genome of ESEI_597, an enterotoxigenic Escherichia coli (ETEC) strain harboring genes encoding colonization surface antigen 13 (CS13) and a heat-labile toxin. The ESEI_597 strain was isolated from an 8-month-old child living in Korogocho, Kenya, in 2013.}, } @article {pmid36090080, year = {2022}, author = {Chang, Y and Chen, F and Zhu, Y and You, Y and Cheng, Y and Ma, J}, title = {Influence of revegetation on soil microbial community and its assembly process in the open-pit mining area of the Loess Plateau, China.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {992816}, pmid = {36090080}, issn = {1664-302X}, abstract = {Vegetation recovery is an important marker of ecosystem health in the mining area. Clarifying the influence of vegetation recovery on the characteristics of soil microbial community and its assembly process can improve our understanding of the ecological resilience and self-maintaining mechanism in the open-pit mining area. For this purpose, we employed MiSeq high-throughput sequencing coupled with null model analysis to determine the composition, molecular ecological network characteristics, key bacterial and fungal clusters, and the assembly mechanism of the soil microbial communities in shrubs (BL), coniferous forest (CF), broad-leaved forests (BF), mixed forest (MF), and the control plot (CK, the poplar plantation nearby that had been continuously grown for over 30 a without disturbance). The results showed that the vegetation restoration model had a significant influence on the α-diversity of the microbial community (p < 0.05). Compared with CK, Sobs and Shannon index of MF and CF have increased by 35.29, 3.50, and 25.18%, 1.05%, respectively, whereas there was no significant difference in the α-diversity of fungal community among different vegetation restoration types, Actinobacteria, Chloroflexi, Proteobacteria, and Acidobacteria were the dominant phyla. The diversity of the first two phyla was significantly higher than those of CK. However, the diversity of the last two phyla was dramatically lower than those of CK (p < 0.05). Ascomycota and Basidiomycota were dominant phyla in the fungal community. The abundance and diversity of Ascomycota were significantly higher than those of CK, while the abundance and diversity of the latter were considerably lower than those of CK (p < 0.05). The stochastic process governed the assembly of the soil microbial community, and the contribution rate to the bacterial community construction of CK, CF, BF, and MF was 100.0%. Except for MF, where the soil fungal community assembly was governed by the deterministic process, all other fungal communities were governed by the stochastic process. Proteobacteria and Acidobacteria are key taxa of the bacterial network, while Mortierellales, Thelebolales, Chaetothyriales, and Hypocreales are the key taxa of the fungal network. All these results might provide the theoretical foundation for restoring the fragile ecosystem in the global mining region.}, } @article {pmid36089013, year = {2023}, author = {Lyu, Y and Wu, Z and Wu, H and Pang, X and Qin, K and Wang, B and Ding, S and Chen, D and Chen, J}, title = {Tracking long-term population exposure risks to PM2.5 and ozone in urban agglomerations of China 2015-2021.}, journal = {The Science of the total environment}, volume = {854}, number = {}, pages = {158599}, doi = {10.1016/j.scitotenv.2022.158599}, pmid = {36089013}, issn = {1879-1026}, mesh = {Humans ; *Air Pollutants/analysis ; Particulate Matter/analysis ; *Ozone ; Pandemics ; *COVID-19/epidemiology ; *Air Pollution/analysis ; China/epidemiology ; }, abstract = {China has experienced severe air pollution in the past decade, especially PM2.5 and emerging ozone pollution recently. In this study, we comprehensively analyzed long-term population exposure risks to PM2.5 and ozone in urban agglomerations of China during 2015-2021 regarding two-stage clean-air actions based on the Ministry of Ecology and the Environment (MEE) air monitoring network. Overall, the ratio of the population living in the regions exceeding the Chinese National Ambient Air Quality Standard (35 μg/m[3]) decreases by 29.9 % for PM2.5 from 2015 to 2021, driven by high proportions in the Middle Plain (MP, 42.3 %) and Lan-Xi (35.0 %) regions. However, this ratio almost remains unchanged for ozone and even increases by 1.5 % in the MP region. As expected, the improved air quality leads to 234.7 × 10[3] avoided premature mortality (ΔMort), mainly ascribed to the reduction in PM2.5 concentration. COVID-19 pandemic may influence the annual variation of PM2.5-related ΔMort as it affects the shape of the population exposure curve to become much steeper. Although all eleven urban agglomerations share stroke (43.6 %) and ischaemic heart disease (IHD, 30.1 %) as the two largest contributors to total ΔMort, cause-specific ΔMort is highly regional heterogeneous, in which ozone-related ΔMort is significantly higher (21 %) in the Tibet region than other urban agglomeration. Despite ozone-related ΔMort being one order of magnitude lower than PM2.5-related ΔMort from 2015 to 2021, ozone-related ΔMort is predicted to increase in major urban agglomerations initially along with a continuous decline for PM2.5-related ΔMort from 2020 to 2060, highlighting the importance of ozone control. Coordinated controls of PM2.5 and O3 are warranted for reducing health burdens in China during achieving carbon neutrality.}, } @article {pmid36088355, year = {2022}, author = {Mull, CG and Pacoureau, N and Pardo, SA and Ruiz, LS and García-Rodríguez, E and Finucci, B and Haack, M and Harry, A and Judah, AB and VanderWright, W and Yin, JS and Kindsvater, HK and Dulvy, NK}, title = {Sharkipedia: a curated open access database of shark and ray life history traits and abundance time-series.}, journal = {Scientific data}, volume = {9}, number = {1}, pages = {559}, pmid = {36088355}, issn = {2052-4463}, mesh = {Animals ; Conservation of Natural Resources ; Databases, Factual ; Internationality ; *Life History Traits ; *Sharks ; }, abstract = {A curated database of shark and ray biological data is increasingly necessary both to support fisheries management and conservation efforts, and to test the generality of hypotheses of vertebrate macroecology and macroevolution. Sharks and rays are one of the most charismatic, evolutionary distinct, and threatened lineages of vertebrates, comprising around 1,250 species. To accelerate shark and ray conservation and science, we developed Sharkipedia as a curated open-source database and research initiative to make all published biological traits and population trends accessible to everyone. Sharkipedia hosts information on 58 life history traits from 274 sources, for 170 species, from 39 families, and 12 orders related to length (n = 9 traits), age (8), growth (12), reproduction (19), demography (5), and allometric relationships (5), as well as 871 population time-series from 202 species. Sharkipedia relies on the backbone taxonomy of the IUCN Red List and the bibliography of Shark-References. Sharkipedia has profound potential to support the rapidly growing data demands of fisheries management, international trade regulation as well as anchoring vertebrate macroecology and macroevolution.}, } @article {pmid36085224, year = {2023}, author = {Gul, S and Bibi, T and Rahim, S and Gul, Y and Niaz, A and Mumtaz, S and Shedayi, AA}, title = {Spatio-temporal change detection of land use and land cover in Malakand Division Khyber Pakhtunkhwa, Pakistan, using remote sensing and geographic information system.}, journal = {Environmental science and pollution research international}, volume = {30}, number = {4}, pages = {10982-10994}, pmid = {36085224}, issn = {1614-7499}, mesh = {*Geographic Information Systems ; *Remote Sensing Technology ; Pakistan ; Conservation of Natural Resources ; Environmental Monitoring/methods ; Agriculture ; }, abstract = {The land use land cover (LULC) change due to the rapidly growing population is a common feature of the urban area. The rapidly growing population in Malakand Division is a greater threat to the LULC of the area due to its negative impact on environment and ecology. This research aims to detect the variations in LULC from 1991 to 2017 in the Malakand Division, Khyber Pakhtunkhwa (KP) province of Pakistan. The study relies on secondary dataset downloaded from the US Geological Survey (1991, 2001, 2011, and 2017 imageries) and the United Nations Office for the Coordination of Humanitarian Affairs (UN OCHA) website. Maximum likelihood technique under supervised image classification was opted to analyze the LULC changes in between 1991 and 2017. The results were based on six major land use classes including agriculture built-up area, vegetation cover, water bodies, snow cover, and barren land. The results from 1991 to 2017 show a substantial reduction in snow cover and barren land which is consequence of climate change. A known change has been recorded in built-up area which shows an increase from 1.02 to 6.2% with a change of 5.18% of the total land. The vegetation cover water bodies were also showing increase in area. The vegetation cover increased from 28.89 to 44.67% while barren land decreased from 45.68 to 40.29% of the total area. Furthermore, the built-up area increased from 1.02 to 6.2%, whereas water covers increased from 0.63% (1991) to 0.86% (2017) of the total area. The study concludes that there is an immense need for planning to preserve the natural habitat for sustainable development in the area.}, } @article {pmid36074761, year = {2022}, author = {Cappellato, M and Baruzzo, G and Di Camillo, B}, title = {Investigating differential abundance methods in microbiome data: A benchmark study.}, journal = {PLoS computational biology}, volume = {18}, number = {9}, pages = {e1010467}, pmid = {36074761}, issn = {1553-7358}, mesh = {*Benchmarking ; Computational Biology/methods ; High-Throughput Nucleotide Sequencing/methods ; *Microbiota ; Reproducibility of Results ; }, abstract = {The development of increasingly efficient and cost-effective high throughput DNA sequencing techniques has enhanced the possibility of studying complex microbial systems. Recently, researchers have shown great interest in studying the microorganisms that characterise different ecological niches. Differential abundance analysis aims to find the differences in the abundance of each taxa between two classes of subjects or samples, assigning a significance value to each comparison. Several bioinformatic methods have been specifically developed, taking into account the challenges of microbiome data, such as sparsity, the different sequencing depth constraint between samples and compositionality. Differential abundance analysis has led to important conclusions in different fields, from health to the environment. However, the lack of a known biological truth makes it difficult to validate the results obtained. In this work we exploit metaSPARSim, a microbial sequencing count data simulator, to simulate data with differential abundance features between experimental groups. We perform a complete comparison of recently developed and established methods on a common benchmark with great effort to the reliability of both the simulated scenarios and the evaluation metrics. The performance overview includes the investigation of numerous scenarios, studying the effect on methods' results on the main covariates such as sample size, percentage of differentially abundant features, sequencing depth, feature variability, normalisation approach and ecological niches. Mainly, we find that methods show a good control of the type I error and, generally, also of the false discovery rate at high sample size, while recall seem to depend on the dataset and sample size.}, } @article {pmid36071746, year = {2022}, author = {Prenzel, F and Treudler, R and Lipek, T and Vom Hove, M and Kage, P and Kuhs, S and Kaiser, T and Bastl, M and Bumberger, J and Genuneit, J and Hornick, T and Klotz, S and Zarnowski, J and Boege, M and Zebralla, V and Simon, JC and Dunker, S}, title = {Invasive Growth of Ailanthus altissima Trees is Associated with a High Rate of Sensitization in Atopic Patients.}, journal = {Journal of asthma and allergy}, volume = {15}, number = {}, pages = {1217-1226}, pmid = {36071746}, issn = {1178-6965}, abstract = {PURPOSE: Ailanthus altissima is one of the world's most invasive species with a globally problematic spread. Pollen is dispersed locally and partially airborne. We aimed at investigating if (i) A. altissima pollen can be detected in relevant quantity in the air and if (ii) sensitization to A. altissima can be detected in patients with seasonal exacerbation of atopic diseases.

PATIENTS AND METHODS: We recorded distribution of A. altissima in Leipzig, Germany. In 2019 and 2020, pollen was collected with a Hirst-type pollen trap placed on the roof of the University Hospital. Specific IgE investigations were performed in children and adults with history of atopic diseases with deterioration between May and July. We analysed specific IgE for A. altissima, Alternaria sp., birch, grasses, profilins, polcalcins and crossreacting carbohydrates.

RESULTS: We found abundant growth of A. altissima and pollen was detected from early June to mid-July with a maximum pollen concentration of 31 pollen/m[3]. Out of 138 patients (63 female, 69 children/adolescents), 95 (69%) had seasonal allergic rhinitis, 84 (61%) asthma, and 43 (31%) atopic dermatitis. Sensitization to A. altissima was shown in 59 (42%). There were no significant differences between age groups. In 59% of patients sensitized (35/59), there was no sensitization to possibly cross-reacting structures.

CONCLUSION: Sensitization to A. altissima pollen could be detected in 42% of our patients with atopic diseases, suggesting allergenic potential of this neophyte. In the context of further spread with climate change, eradication strategies and population-based sensitization studies are needed.}, } @article {pmid36071164, year = {2022}, author = {Arostegui, MC and Gaube, P and Woodworth-Jefcoats, PA and Kobayashi, DR and Braun, CD}, title = {Anticyclonic eddies aggregate pelagic predators in a subtropical gyre.}, journal = {Nature}, volume = {609}, number = {7927}, pages = {535-540}, pmid = {36071164}, issn = {1476-4687}, mesh = {Animals ; Cyclonic Storms ; Datasets as Topic ; *Ecosystem ; Fisheries ; Food Chain ; Nutrients/analysis ; Pacific Ocean ; *Predatory Behavior ; Tropical Climate ; *Water ; *Water Movements ; }, abstract = {Ocean eddies are coherent, rotating features that can modulate pelagic ecosystems across many trophic levels. These mesoscale features, which are ubiquitous at mid-latitudes[1], may increase productivity of nutrient-poor regions[2,3], accumulate prey[4] and modulate habitat conditions in the water column[5]. However, in nutrient-poor subtropical gyres-the largest marine biome-the role of eddies in modulating behaviour throughout the pelagic predator community remains unknown despite predictions for these gyres to expand[6] and pelagic predators to become increasingly important for food security[7]. Using a large-scale fishery dataset in the North Pacific Subtropical Gyre, we show a pervasive pattern of increased pelagic predator catch inside anticyclonic eddies relative to cyclones and non-eddy areas. Our results indicate that increased mesopelagic prey abundance in anticyclone cores[4,8] may be attracting diverse predators, forming ecological hotspots where these predators aggregate and exhibit increased abundance. In this energetically quiescent gyre, we expect that isolated mesoscale features (and the habitat conditions in them) exhibit primacy over peripheral submesoscale dynamics in structuring the foraging opportunities of pelagic predators. Our finding that eddies influence coupling of epi- to mesopelagic communities corroborates the growing evidence that deep scattering layer organisms are vital prey for a suite of commercially important predator species[9] and, thus, provide valuable ecosystem services.}, } @article {pmid36071118, year = {2022}, author = {Brown, JM and Bossomaier, T and Barnett, L}, title = {Information flow in first-order potts model phase transition.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {15145}, pmid = {36071118}, issn = {2045-2322}, mesh = {Entropy ; *Hot Temperature ; Phase Transition ; Thermodynamics ; }, abstract = {Phase transitions abound in nature and society, and, from species extinction to stock market collapse, their prediction is of widespread importance. In earlier work we showed that Global Transfer Entropy, a general measure of information flow, was found to peaks away from the transition on the disordered side for the Ising model, a canonical second order transition. Here we show that (a) global transfer entropy also peaks on the disordered side of the transition of finite first order transitions, such as ecology dynamics on coral reefs, which have latent heat and no correlation length divergence, and (b) analysis of information flow across state boundaries unifies both transition orders. We obtain the first information-theoretic result for the high-order Potts model and the first demonstration of early warning of a first order transition. The unexpected earlier finding that global transfer entropy peaks on the disordered side of a transition is also found for finite first order systems, albeit not in the thermodynamic limit. By noting that the interface length of clusters in each phase is the dominant region of information flow, we unify the information theoretic behaviour of first and second order transitions.}, } @article {pmid36058075, year = {2022}, author = {Maloney, KO and Buchanan, C and Jepsen, RD and Krause, KP and Cashman, MJ and Gressler, BP and Young, JA and Schmid, M}, title = {Explainable machine learning improves interpretability in the predictive modeling of biological stream conditions in the Chesapeake Bay Watershed, USA.}, journal = {Journal of environmental management}, volume = {322}, number = {}, pages = {116068}, doi = {10.1016/j.jenvman.2022.116068}, pmid = {36058075}, issn = {1095-8630}, mesh = {Agriculture ; *Bays ; Ecosystem ; Environmental Monitoring/methods ; Machine Learning ; *Rivers ; }, abstract = {Anthropogenic alterations have resulted in widespread degradation of stream conditions. To aid in stream restoration and management, baseline estimates of conditions and improved explanation of factors driving their degradation are needed. We used random forests to model biological conditions using a benthic macroinvertebrate index of biotic integrity for small, non-tidal streams (upstream area ≤200 km[2]) in the Chesapeake Bay watershed (CBW) of the mid-Atlantic coast of North America. We utilized several global and local model interpretation tools to improve average and site-specific model inferences, respectively. The model was used to predict condition for 95,867 individual catchments for eight periods (2001, 2004, 2006, 2008, 2011, 2013, 2016, 2019). Predicted conditions were classified as Poor, FairGood, or Uncertain to align with management needs and individual reach lengths and catchment areas were summed by condition class for the CBW for each period. Global permutation and local Shapley importance values indicated percent of forest, development, and agriculture in upstream catchments had strong impacts on predictions. Development and agriculture negatively influenced stream condition for model average (partial dependence [PD] and accumulated local effect [ALE] plots) and local (individual condition expectation and Shapley value plots) levels. Friedman's H-statistic indicated large overall interactions for these three land covers, and bivariate global plots (PD and ALE) supported interactions among agriculture and development. Total stream length and catchment area predicted in FairGood conditions decreased then increased over the 19-years (length/area: 66.6/65.4% in 2001, 66.3/65.2% in 2011, and 66.6/65.4% in 2019). Examination of individual catchment predictions between 2001 and 2019 showed those predicted to have the largest decreases in condition had large increases in development; whereas catchments predicted to exhibit the largest increases in condition showed moderate increases in forest cover. Use of global and local interpretative methods together with watershed-wide and individual catchment predictions support conservation practitioners that need to identify widespread and localized patterns, especially acknowledging that management actions typically take place at individual-reach scales.}, } @article {pmid36053136, year = {2022}, author = {Kelleher, K and McGinnity, P and Howard, BJ and Boyer, P and Vidal, M and Bildstein, OM}, title = {The use of the IAEA MARIS database in determining the variability of sediment distribution coefficients in the marine environment and potential implications for marine dispersion modelling.}, journal = {Journal of radiological protection : official journal of the Society for Radiological Protection}, volume = {42}, number = {3}, pages = {}, doi = {10.1088/1361-6498/ac8a53}, pmid = {36053136}, issn = {1361-6498}, mesh = {Geologic Sediments ; Information Systems ; *Radioactivity ; Seawater ; *Water Pollutants, Radioactive/analysis ; }, abstract = {A prototype tool has been developed for deriving sediment distribution coefficients,Kd, in the marine environment by harvesting simultaneous measurements of activity concentrations of radionuclides in seawater and sediments based on the International Atomic Energy Agency's Marine Radioactivity Information System (MARIS). As a case study, theKdvariability in the Baltic Sea was investigated as this region has been extensively monitored by HELCOM since 1984 resulting in a comprehensive dataset with good spatial and temporal coverage and required ancillary parameters. The prototype tool was used to derive a dataset ofin-situapparentKd(a)values derived from measurements of seawater and sediment in quasi-equilibrium conditions from the Baltic Sea over a period of approximately 35 years. For Cs, a comprehensive analysis of the Baltic SeaKd(a)dataset was undertaken, focusing on the temporal trend ofKd(a)and comparing the results toKdvalues derived elsewhere. For Sr and Pu, for which there were fewer data records available a more rudimentary analysis was carried out. The CsKd(a)median values derived from[137]Cs data in this study were estimated to be 2154 l kg[-1]for seabed sediment and 10 000 l kg[-1]for suspended sediment. The value derived for seabed sediment is in good agreement with the previously recommended ocean margin CsKdvalue of 4000 l kg[-1]. The analysis demonstrated the important distinction in the Baltic Sea betweenKdvalues for seabed sediment and suspended sediments, which differed by an order of magnitude. The analysis also highlighted the dependence ofKdvalues on the variation in both the salinity of seawater and the type of seabed sediment. Such variability can significantly influence outcomes when modelling the behaviour of radionuclides in marine dispersion modelling.}, } @article {pmid36051895, year = {2022}, author = {Boyes, D and , and , and , and , and , and Gibbs, M and , }, title = {The genome sequence of the clay, Mythimna ferrago (Fabricius, 1787).}, journal = {Wellcome open research}, volume = {7}, number = {}, pages = {177}, pmid = {36051895}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual female Mythimna ferrago (the clay; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 861 megabases in span. The majority of the assembly (99.98%) is scaffolded into 32 chromosomal pseudomolecules, with the W and Z chromosomes assembled. The complete mitochondrial genome was also assembled and is 15.3 kilobases in length. Gene annotation of this assembly on Ensembl has identified 14,075 protein coding genes.}, } @article {pmid36050321, year = {2022}, author = {Young, WJ and Lahrouchi, N and Isaacs, A and Duong, T and Foco, L and Ahmed, F and Brody, JA and Salman, R and Noordam, R and Benjamins, JW and Haessler, J and Lyytikäinen, LP and Repetto, L and Concas, MP and van den Berg, ME and Weiss, S and Baldassari, AR and Bartz, TM and Cook, JP and Evans, DS and Freudling, R and Hines, O and Isaksen, JL and Lin, H and Mei, H and Moscati, A and Müller-Nurasyid, M and Nursyifa, C and Qian, Y and Richmond, A and Roselli, C and Ryan, KA and Tarazona-Santos, E and Thériault, S and van Duijvenboden, S and Warren, HR and Yao, J and Raza, D and Aeschbacher, S and Ahlberg, G and Alonso, A and Andreasen, L and Bis, JC and Boerwinkle, E and Campbell, A and Catamo, E and Cocca, M and Cutler, MJ and Darbar, D and De Grandi, A and De Luca, A and Ding, J and Ellervik, C and Ellinor, PT and Felix, SB and Froguel, P and Fuchsberger, C and Gögele, M and Graff, C and Graff, M and Guo, X and Hansen, T and Heckbert, SR and Huang, PL and Huikuri, HV and Hutri-Kähönen, N and Ikram, MA and Jackson, RD and Junttila, J and Kavousi, M and Kors, JA and Leal, TP and Lemaitre, RN and Lin, HJ and Lind, L and Linneberg, A and Liu, S and MacFarlane, PW and Mangino, M and Meitinger, T and Mezzavilla, M and Mishra, PP and Mitchell, RN and Mononen, N and Montasser, ME and Morrison, AC and Nauck, M and Nauffal, V and Navarro, P and Nikus, K and Pare, G and Patton, KK and Pelliccione, G and Pittman, A and Porteous, DJ and Pramstaller, PP and Preuss, MH and Raitakari, OT and Reiner, AP and Ribeiro, ALP and Rice, KM and Risch, L and Schlessinger, D and Schotten, U and Schurmann, C and Shen, X and Shoemaker, MB and Sinagra, G and Sinner, MF and Soliman, EZ and Stoll, M and Strauch, K and Tarasov, K and Taylor, KD and Tinker, A and Trompet, S and Uitterlinden, A and Völker, U and Völzke, H and Waldenberger, M and Weng, LC and Whitsel, EA and Wilson, JG and Avery, CL and Conen, D and Correa, A and Cucca, F and Dörr, M and Gharib, SA and Girotto, G and Grarup, N and Hayward, C and Jamshidi, Y and Järvelin, MR and Jukema, JW and Kääb, S and Kähönen, M and Kanters, JK and Kooperberg, C and Lehtimäki, T and Lima-Costa, MF and Liu, Y and Loos, RJF and Lubitz, SA and Mook-Kanamori, DO and Morris, AP and O'Connell, JR and Olesen, MS and Orini, M and Padmanabhan, S and Pattaro, C and Peters, A and Psaty, BM and Rotter, JI and Stricker, B and van der Harst, P and van Duijn, CM and Verweij, N and Wilson, JF and Arking, DE and Ramirez, J and Lambiase, PD and Sotoodehnia, N and Mifsud, B and Newton-Cheh, C and Munroe, PB}, title = {Genetic analyses of the electrocardiographic QT interval and its components identify additional loci and pathways.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {5144}, pmid = {36050321}, issn = {2041-1723}, support = {MR/N025083/1/MRC_/Medical Research Council/United Kingdom ; R01 HL139731/HL/NHLBI NIH HHS/United States ; /DH_/Department of Health/United Kingdom ; MC_UU_00007/10/MRC_/Medical Research Council/United Kingdom ; R01 HL105756/HL/NHLBI NIH HHS/United States ; T32 HL007604/HL/NHLBI NIH HHS/United States ; K24 HL148521/HL/NHLBI NIH HHS/United States ; MR/R010676/1/MRC_/Medical Research Council/United Kingdom ; R01 HL142825/HL/NHLBI NIH HHS/United States ; R01 DK107786/DK/NIDDK NIH HHS/United States ; K23 HL127704/HL/NHLBI NIH HHS/United States ; R01 DK110113/DK/NIDDK NIH HHS/United States ; U01 AG068221/AG/NIA NIH HHS/United States ; R01 HL128914/HL/NHLBI NIH HHS/United States ; R01 HL141989/HL/NHLBI NIH HHS/United States ; R01 HL143070/HL/NHLBI NIH HHS/United States ; U54 GM115428/GM/NIGMS NIH HHS/United States ; MR/R017468/1/MRC_/Medical Research Council/United Kingdom ; T32 HL139439/HL/NHLBI NIH HHS/United States ; R01 HL142302/HL/NHLBI NIH HHS/United States ; R01 HL138737/HL/NHLBI NIH HHS/United States ; K24 HL105780/HL/NHLBI NIH HHS/United States ; U01 HG007416/HG/NHGRI NIH HHS/United States ; U24 AG051129/AG/NIA NIH HHS/United States ; R01 DK124097/DK/NIDDK NIH HHS/United States ; MR/S019669/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {*Arrhythmias, Cardiac/genetics ; Death, Sudden, Cardiac ; *Electrocardiography/methods ; Genetic Testing ; Humans ; Male ; }, abstract = {The QT interval is an electrocardiographic measure representing the sum of ventricular depolarization and repolarization, estimated by QRS duration and JT interval, respectively. QT interval abnormalities are associated with potentially fatal ventricular arrhythmia. Using genome-wide multi-ancestry analyses (>250,000 individuals) we identify 177, 156 and 121 independent loci for QT, JT and QRS, respectively, including a male-specific X-chromosome locus. Using gene-based rare-variant methods, we identify associations with Mendelian disease genes. Enrichments are observed in established pathways for QT and JT, and previously unreported genes indicated in insulin-receptor signalling and cardiac energy metabolism. In contrast for QRS, connective tissue components and processes for cell growth and extracellular matrix interactions are significantly enriched. We demonstrate polygenic risk score associations with atrial fibrillation, conduction disease and sudden cardiac death. Prioritization of druggable genes highlight potential therapeutic targets for arrhythmia. Together, these results substantially advance our understanding of the genetic architecture of ventricular depolarization and repolarization.}, } @article {pmid36048827, year = {2022}, author = {Omoru, OB and Pereira, F and Janga, SC and Manzourolajdad, A}, title = {A Putative long-range RNA-RNA interaction between ORF8 and Spike of SARS-CoV-2.}, journal = {PloS one}, volume = {17}, number = {9}, pages = {e0260331}, pmid = {36048827}, issn = {1932-6203}, support = {R01 GM123314/GM/NIGMS NIH HHS/United States ; }, mesh = {*COVID-19 ; Genome, Viral ; Humans ; RNA, Viral/genetics ; *SARS-CoV-2/genetics ; *Spike Glycoprotein, Coronavirus/genetics ; *Viral Proteins/genetics ; }, abstract = {SARS-CoV-2 has affected people worldwide as the causative agent of COVID-19. The virus is related to the highly lethal SARS-CoV-1 responsible for the 2002-2003 SARS outbreak in Asia. Research is ongoing to understand why both viruses have different spreading capacities and mortality rates. Like other beta coronaviruses, RNA-RNA interactions occur between different parts of the viral genomic RNA, resulting in discontinuous transcription and production of various sub-genomic RNAs. These sub-genomic RNAs are then translated into other viral proteins. In this work, we performed a comparative analysis for novel long-range RNA-RNA interactions that may involve the Spike region. Comparing in-silico fragment-based predictions between reference sequences of SARS-CoV-1 and SARS-CoV-2 revealed several predictions amongst which a thermodynamically stable long-range RNA-RNA interaction between (23660-23703 Spike) and (28025-28060 ORF8) unique to SARS-CoV-2 was observed. The patterns of sequence variation using data gathered worldwide further supported the predicted stability of the sub-interacting region (23679-23690 Spike) and (28031-28042 ORF8). Such RNA-RNA interactions can potentially impact viral life cycle including sub-genomic RNA production rates.}, } @article {pmid36044830, year = {2023}, author = {Niestroj, SC and Steden, S and Boecker, M and Brodkin, ES and Konrad, K}, title = {The Development and Validation of the First German Open Scale of Social Information Processing.}, journal = {Psychopathology}, volume = {56}, number = {1-2}, pages = {52-63}, doi = {10.1159/000525950}, pmid = {36044830}, issn = {1423-033X}, mesh = {Male ; Child ; Female ; Adolescent ; Humans ; *Social Behavior ; *Cognition ; Aggression/psychology ; Social Perception ; Emotions ; }, abstract = {INTRODUCTION: This study introduces the first German Open Scale of Social Information Processing (GOSSIP) and evaluates its psychometric properties. Even though social information processing (SIP) and its important role in developmental psychopathology is a rising field of interest, model-based standardized assessment tools are still scarce.

METHODS: GOSSIP was developed to assess SI processes in boys and girls aged eight to 21 years. First, 61 vignettes (combinations of pictures and short written descriptions of the situation depicted) were evaluated by an expert group and piloted with 48 healthy participants (aged 8-21). The best-rated vignettes were then implemented in a Web-based application. 191 participants completed GOSSIP. Of those, 76 answered additional questionnaires to assess their social skills and psychopathology. Internal consistencies for the emotional and cognitive GOSSIP scales were determined. Latent profile analysis (LPA) was used to identify subgroups of children and adolescents characterized by specific SIP profiles (i.e., patterns of emotional, cognitive, and behavioral responses to the GOSSIP). Furthermore, the external validity of the participants' attribution tendencies in GOSSIP was evaluated in real life by smartphone-based Ecological Momentary Assessments (EMA).

RESULTS: The internal consistencies for the emotional and cognitive scales (angry, ashamed, physical aggression, pro-social response, revenge, and outcome expectancy) were good to excellent. The scales of hostile interpretation, relation aggression, sadness, and exclusion showed borderline/acceptable internal consistency. Correlation analysis confirmed convergent validity with self-reported social skills and external validity with ratings of aggressive and pro-social behaviors. The LPA revealed three profiles as the best fit of the data. The first group is named "aggressors," the second "social-emotional group," and a third named "ashamed-internalizing group." However, no significant association was found between the attribution tendencies derived from GOSSIP and EMA data.

DISCUSSION/CONCLUSION: GOSSIP is the first model-based German Web-based assessment for several SIP mechanisms that showed overall adequate psychometric properties. GOSSIP can be used to classify individuals into SIP profiles that differ in terms of their cognitive and emotional response tendencies and therefore could contribute to the development of targeted interventions. Integrating assessments of emotional responses into GOSSIP revealed an important role of "shame" in SIP and the development of psychopathology. Furthermore, the lack of external validity between GOSSIP and EMA calls into question how attribution tendencies are best assessed in future studies.}, } @article {pmid36041271, year = {2022}, author = {Sokhansanj, BA and Rosen, GL}, title = {Predicting COVID-19 disease severity from SARS-CoV-2 spike protein sequence by mixed effects machine learning.}, journal = {Computers in biology and medicine}, volume = {149}, number = {}, pages = {105969}, pmid = {36041271}, issn = {1879-0534}, mesh = {*COVID-19/epidemiology ; Humans ; Machine Learning ; Mutation ; Phylogeny ; Retrospective Studies ; SARS-CoV-2 ; Severity of Illness Index ; *Spike Glycoprotein, Coronavirus/genetics ; }, abstract = {Epidemiological studies show that COVID-19 variants-of-concern, like Delta and Omicron, pose different risks for severe disease, but they typically lack sequence-level information for the virus. Studies which do obtain viral genome sequences are generally limited in time, location, and population scope. Retrospective meta-analyses require time-consuming data extraction from heterogeneous formats and are limited to publicly available reports. Fortuitously, a subset of GISAID, the global SARS-CoV-2 sequence repository, includes "patient status" metadata that can indicate whether a sequence record is associated with mild or severe disease. While GISAID lacks data on comorbidities relevant to severity, such as obesity and chronic disease, it does include metadata for age and sex to use as additional attributes in modeling. With these caveats, previous efforts have demonstrated that genotype-patient status models can be fit to GISAID data, particularly when country-of-origin is used as an additional feature. But are these models robust and biologically meaningful? This paper shows that, in fact, temporal and geographic biases in sequences submitted to GISAID, as well as the evolving pandemic response, particularly reduction in severe disease due to vaccination, create complex issues for model development and interpretation. This paper poses a potential solution: efficient mixed effects machine learning using GPBoost, treating country as a random effect group. Training and validation using temporally split GISAID data and emerging Omicron variants demonstrates that GPBoost models are more predictive of the impact of spike protein mutations on patient outcomes than fixed effect XGBoost, LightGBM, random forests, and elastic net logistic regression models.}, } @article {pmid36039768, year = {2024}, author = {De Calheiros Velozo, J and Habets, J and George, SV and Niemeijer, K and Minaeva, O and Hagemann, N and Herff, C and Kuppens, P and Rintala, A and Vaessen, T and Riese, H and Delespaul, P}, title = {Designing daily-life research combining experience sampling method with parallel data.}, journal = {Psychological medicine}, volume = {54}, number = {1}, pages = {98-107}, doi = {10.1017/S0033291722002367}, pmid = {36039768}, issn = {1469-8978}, mesh = {Humans ; *Ecological Momentary Assessment ; *Life Change Events ; Research Design ; }, abstract = {BACKGROUND: Ambulatory monitoring is gaining popularity in mental and somatic health care to capture an individual's wellbeing or treatment course in daily-life. Experience sampling method collects subjective time-series data of patients' experiences, behavior, and context. At the same time, digital devices allow for less intrusive collection of more objective time-series data with higher sampling frequencies and for prolonged sampling periods. We refer to these data as parallel data. Combining these two data types holds the promise to revolutionize health care. However, existing ambulatory monitoring guidelines are too specific to each data type, and lack overall directions on how to effectively combine them.

METHODS: Literature and expert opinions were integrated to formulate relevant guiding principles.

RESULTS: Experience sampling and parallel data must be approached as one holistic time series right from the start, at the study design stage. The fluctuation pattern and volatility of the different variables of interest must be well understood to ensure that these data are compatible. Data have to be collected and operationalized in a manner that the minimal common denominator is able to answer the research question with regard to temporal and disease severity resolution. Furthermore, recommendations are provided for device selection, data management, and analysis. Open science practices are also highlighted throughout. Finally, we provide a practical checklist with the delineated considerations and an open-source example demonstrating how to apply it.

CONCLUSIONS: The provided considerations aim to structure and support researchers as they undertake the new challenges presented by this exciting multidisciplinary research field.}, } @article {pmid36039277, year = {2022}, author = {Stokes, J and Bower, P and Guthrie, B and Mercer, SW and Rice, N and Ryan, AM and Sutton, M}, title = {Cuts to local government spending, multimorbidity and health-related quality of life: A longitudinal ecological study in England.}, journal = {The Lancet regional health. Europe}, volume = {19}, number = {}, pages = {100436}, pmid = {36039277}, issn = {2666-7762}, support = {MR/T027517/1/MRC_/Medical Research Council/United Kingdom ; }, abstract = {BACKGROUND: Population health has stagnated or is declining in many high-income countries. We analysed whether nationally administered austerity cuts in England were associated with prevalence of multimorbidity (individuals with two or more long-term conditions) and health-related quality of life.

METHODS: We conducted an observational, longitudinal study on 147 local authorities in England. We examined associations of changes in spending over time (2009/10-2017/18), in total and by budget line, with (i) prevalence of multimorbidity, 2+ conditions (2011/12-2017/18), and (ii) health-related quality of life (EQ-5D-5L) score (2012/13-2016/17). We estimated linear, log-log regression models, incorporating local authority fixed-effects, time-varying demographic and socio-economic confounders, and time trends.

FINDINGS: All local authorities experienced real spending cuts, varying from 42% (Barking and Dagenham) to 0·3% (Sefton). A 1% cut in per capita total service expenditure was associated with a 0·10% (95% CI 0·03 to 0·16) increase in prevalence of multimorbidity. We found no association (0·003%; 95% CI -0·01 to 0·01) with health-related quality of life. By budget line, after controlling for other spending, a 1% cut in public health expenditure was associated with a 0·15% (95% CI 0·11 to 0·20) increase in prevalence of multimorbidity, and a 1% cut in adult social care expenditure was associated with a 0·01% (95% CI 0·002 to 0·02) decrease in average health-related quality of life.

INTERPRETATION: Fiscal austerity is associated with worse multimorbidity and health-related quality of life. Policymakers should consider the potential health consequences of local government expenditure cuts and knock-on effects for health systems.

FUNDING: Medical Research Council.}, } @article {pmid36037884, year = {2022}, author = {Luoma, E and Laurila-Pant, M and Altarriba, E and Nevalainen, L and Helle, I and Granhag, L and Lehtiniemi, M and Srėbalienė, G and Olenin, S and Lehikoinen, A}, title = {A multi-criteria decision analysis model for ship biofouling management in the Baltic Sea.}, journal = {The Science of the total environment}, volume = {852}, number = {}, pages = {158316}, doi = {10.1016/j.scitotenv.2022.158316}, pmid = {36037884}, issn = {1879-1026}, mesh = {*Biofouling/prevention & control ; Ships ; Carbon Dioxide ; Bayes Theorem ; Water ; Decision Support Techniques ; }, abstract = {Biofouling of ship hulls form a vector for the introduction of non-indigenous organisms worldwide. Through increasing friction, the organisms attached to ships' hulls increase the fuel consumption, leading to both higher fuel costs and air emissions. At the same time, ship biofouling management causes both ecological risks and monetary costs. All these aspects should be considered case-specifically in the search of sustainable management strategies. Applying Bayesian networks, we developed a multi-criteria decision analysis model to compare biofouling management strategies in the Baltic Sea, given the characteristics of a ship, its operating profile and operational environment, considering the comprehensive environmental impact and the monetary costs. The model is demonstrated for three scenarios (SC1-3) and sub-scenarios (A-C), comparing the alternative biofouling management strategies in relation to NIS (non-indigenous species) introduction risk, eco-toxicological risk due to biocidal coating, carbon dioxide emissions and costs related to fuel consumption, in-water cleaning and hull coating. The scenarios demonstrate that by the careful consideration of the hull fouling management strategy, both money and environment can be saved. We suggest biocidal-free coating with a regular in-water cleaning using a capture system is generally the lowest-risk option. The best biocidal-free coating type and the optimal in-water cleaning interval should be evaluated case-specifically, though. In some cases, however, biocidal coating remains a justifiable option.}, } @article {pmid36036236, year = {2022}, author = {Strobl, MR and Vollmann, U and Eckl-Dorna, J and Radakovics, A and Ibl, V and Schnurer, M and Brenner, M and Dermendjiev, G and Weckwerth, W and Neumüller, M and Frommlet, F and Demir, H and Bublin, M and Müller, C and Bohle, B}, title = {Identification of apple cultivars hypoallergenic for birch pollen-allergic individuals by a multidisciplinary in vitro and in vivo approach.}, journal = {Clinical and translational allergy}, volume = {12}, number = {8}, pages = {e12186}, pmid = {36036236}, issn = {2045-7022}, support = {P 32953/FWF_/Austrian Science Fund FWF/Austria ; P33891 (to VI), W1212, P32953, I4437//Austrian Science Funds/ ; ÖNB17947//Austrian Jubiläumsfond/ ; //Medical University of Vienna/ ; //Danube Allergy Research Cluster/ ; }, abstract = {BACKGROUND: Birch pollen-related apple allergy is the most frequent IgE-mediated food allergy in Central-Northern Europe with Mal d 1 as major allergen. Its concentration in apples varies with the cultivar and storage time. Year-round appealing, hypoallergenic cultivars still are needed to satisfy the nutritional needs of affected individuals. We characterized three promising cultivars by multidisciplinary in vitro assays including long-term storage and by clinical challenges of allergic individuals before and after the birch pollen season.

METHODS: Proteins were extracted from fruits of 'Santana', 'Golden Delicious' (GD), and three genuine cultivars in November 2018 and April 2019. Mal d 1-levels were analysed by mass spectrometry, SDS-PAGE, immunoblotting, competitive ELISA, and basophil activation tests. Twenty-eight allergic individuals underwent single-blinded open food challenges and skin testing with the cultivars and birch pollen in November 2018 and May 2019. Allergen-specific IgE-levels were determined.

RESULTS: After storage all cultivars except 'Santana' were of appealing appearance and taste. Their Mal d 1 content had increased, also reflected by significantly amplified basophil activation and stronger reactions in clinical challenges. Besides, individuals showed boosted reactivity after pollen exposure indicated by enhanced allergen-specific IgE-levels and skin reactions to birch pollen. Still, all cultivars remained significantly less allergenic than GD and comparable to Santana in November 2018 in all assessments except for skin testing.

CONCLUSIONS: Combined expertise in pomology and allergology identified promising new cultivars for allergic consumers. The evaluation of hypoallergenic apples should incorporate long-term storage and birch pollen exposure. Basophil activation tests may be suitable in the selection of promising cultivars for oral challenges.}, } @article {pmid36035686, year = {2022}, author = {Del Vecchio, S and Sharma, SK and Pavan, M and Acosta, ATR and Bacchetta, G and de Bello, F and Isermann, M and Michalet, R and Buffa, G}, title = {Within-species variation of seed traits of dune engineering species across a European climatic gradient.}, journal = {Frontiers in plant science}, volume = {13}, number = {}, pages = {978205}, pmid = {36035686}, issn = {1664-462X}, abstract = {Within-species variation is a key component of biodiversity and linking it to climatic gradients may significantly improve our understanding of ecological processes. High variability can be expected in plant traits, but it is unclear to which extent it varies across populations under different climatic conditions. Here, we investigated seed trait variability and its environmental dependency across a latitudinal gradient of two widely distributed dune-engineering species (Thinopyrum junceum and Calamagrostis arenaria). Seed germination responses against temperature and seed mass were compared within and among six populations exposed to a gradient of temperature and precipitation regimes (Spiekeroog, DE; Bordeaux, FR; Valencia, ES; Cagliari, IT, Rome, IT; Venice, IT). Seed germination showed opposite trends in response to temperature experienced during emergence in both species: with some expectation, in populations exposed to severe winters, seed germination was warm-cued, whereas in populations from warm sites with dry summer, seed germination was cold-cued. In C. arenaria, variability in seed germination responses disappeared once the seed coat was incised. Seed mass from sites with low precipitation was smaller than that from sites with higher precipitation and was better explained by rainfall continentality than by aridity in summer. Within-population variability in seed germination accounted for 5 to 54%, while for seed mass it was lower than 40%. Seed trait variability can be considerable both within- and among-populations even at broad spatial scale. The variability may be hardly predictable since it only partially correlated with the analyzed climatic variables, and with expectation based on the climatic features of the seed site of origin. Considering seed traits variability in the analysis of ecological processes at both within- and among-population levels may help elucidate unclear patterns of species dynamics, thereby contributing to plan adequate measures to counteract biodiversity loss.}, } @article {pmid36033213, year = {2022}, author = {Pho, AT and Mangal, S and Bakken, S}, title = {Human Papillomavirus Vaccination Among Transgender and Gender Diverse People in the United States: An Integrative Review.}, journal = {Transgender health}, volume = {7}, number = {4}, pages = {303-313}, pmid = {36033213}, issn = {2688-4887}, abstract = {OBJECTIVE: This integrative review explores the barriers to and facilitators for human papillomavirus (HPV) vaccination among adult transgender and gender diverse (TGD) people in the United States.

DATA SOURCE: A systematic search of electronic databases included PubMed/MEDLINE, CINAHL, and EMBASE from 1985 to 2020.

Inclusion criteria included studies from the United States that described HPV vaccination barriers or facilitators and included adult TGD participants, both quantitative and qualitative studies. Exclusion criteria were studies that reported only HPV vaccine prevalence, non-English/non-U.S. studies, and studies limited to pediatric populations.

DATA EXTRACTION: Two investigators used Covidence software to screen studies and manage data extraction. Quality of the quantitative studies was appraised using a checklist proposed by the Joanna Briggs Institute (JBI); qualitative studies were appraised using quality criteria informed by the literature.

DATA SYNTHESIS: The Social Ecological Model guided the review to organize barriers to and facilitators for HPV vaccination at the patient-, provider-, and system-levels.

RESULTS: Database searches and hand-searching yielded 843 citations. After screening, eight articles were retained in the review. Seven were cross-sectional studies and one was a qualitative focus-group. All retained quantitative studies met six of the eight JBI quality checklist items.

CONCLUSION: The low proportion of TGD participants in the retained studies highlights a gap in knowledge about HPV vaccination among this population. Future studies of HPV vaccination should recruit TGD people to better represent their perspectives.}, } @article {pmid36032727, year = {2022}, author = {Kenzie, ES and Parks, EL and Carney, N and Wakeland, W}, title = {System dynamics modeling for traumatic brain injury: Mini-review of applications.}, journal = {Frontiers in bioengineering and biotechnology}, volume = {10}, number = {}, pages = {854358}, pmid = {36032727}, issn = {2296-4185}, abstract = {Traumatic brain injury (TBI) is a highly complex phenomenon involving a cascade of disruptions across biomechanical, neurochemical, neurological, cognitive, emotional, and social systems. Researchers and clinicians urgently need a rigorous conceptualization of brain injury that encompasses nonlinear and mutually causal relations among the factors involved, as well as sources of individual variation in recovery trajectories. System dynamics, an approach from systems science, has been used for decades in fields such as management and ecology to model nonlinear feedback dynamics in complex systems. In this mini-review, we summarize some recent uses of this approach to better understand acute injury mechanisms, recovery dynamics, and care delivery for TBI. We conclude that diagram-based approaches like causal-loop diagramming have the potential to support the development of a shared paradigm of TBI that incorporates social support aspects of recovery. When developed using adequate data from large-scale studies, simulation modeling presents opportunities for improving individualized treatment and care delivery.}, } @article {pmid36030325, year = {2022}, author = {Cooney, DB and Rossine, FW and Morris, DH and Levin, SA}, title = {A PDE Model for Protocell Evolution and the Origin of Chromosomes via Multilevel Selection.}, journal = {Bulletin of mathematical biology}, volume = {84}, number = {10}, pages = {109}, doi = {10.1007/s11538-022-01062-y}, pmid = {36030325}, issn = {1522-9602}, mesh = {*Artificial Cells ; Chromosomes ; Genome ; Mathematical Concepts ; Models, Biological ; }, abstract = {The evolution of complex cellular life involved two major transitions: the encapsulation of self-replicating genetic entities into cellular units and the aggregation of individual genes into a collectively replicating genome. In this paper, we formulate a minimal model of the evolution of proto-chromosomes within protocells. We model a simple protocell composed of two types of genes: a "fast gene" with an advantage for gene-level self-replication and a "slow gene" that replicates more slowly at the gene level, but which confers an advantage for protocell-level reproduction. Protocell-level replication capacity depends on cellular composition of fast and slow genes. We use a partial differential equation to describe how the composition of genes within protocells evolves over time under within-cell and between-cell competition, considering an infinite population of protocells that each contain infinitely many genes. We find that the gene-level advantage of fast replicators casts a long shadow on the multilevel dynamics of protocell evolution: no level of between-protocell competition can produce coexistence of the fast and slow replicators when the two genes are equally needed for protocell-level reproduction. By introducing a "dimer replicator" consisting of a linked pair of the slow and fast genes, we show analytically that coexistence between the two genes can be promoted in pairwise multilevel competition between fast and dimer replicators, and provide numerical evidence for coexistence in trimorphic competition between fast, slow, and dimer replicators. Our results suggest that dimerization, or the formation of a simple chromosome-like dimer replicator, can help to overcome the shadow of lower-level selection and work in concert with deterministic multilevel selection in protocells featuring high gene copy number to allow for the coexistence of two genes that are complementary at the protocell level but compete at the level of individual gene-level replication. These results for the PDE model complement existing results on the benefits of dimerization in the case of low genetic copy number, for which it has been shown that genetic linkage can help to overcome the stochastic loss of necessary genetic templates.}, } @article {pmid36016080, year = {2022}, author = {Yousaf, M and Ullah, A and Sarosh, N and Abbasi, SW and Ismail, S and Bibi, S and Hasan, MM and Albadrani, GM and Talaat Nouh, NA and Abdulhakim, JA and Abdel-Daim, MM and Bin Emran, T}, title = {Design of Multi-Epitope Vaccine for Staphylococcus saprophyticus: Pan-Genome and Reverse Vaccinology Approach.}, journal = {Vaccines}, volume = {10}, number = {8}, pages = {}, pmid = {36016080}, issn = {2076-393X}, support = {PNURSP2022R30//This research was supported by Princess Nourah bint Abdulrahman University Researchers Supporting Project number (PNURSP2022R30), Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia./ ; }, abstract = {Staphylococcus saprophyticus is a Gram-positive coccus responsible for the occurrence of cystitis in sexually active, young females. While effective antibiotics against this organism exist, resistant strains are on the rise. Therefore, prevention via vaccines appears to be a viable solution to address this problem. In comparison to traditional techniques of vaccine design, computationally aided vaccine development demonstrates marked specificity, efficiency, stability, and safety. In the present study, a novel, multi-epitope vaccine construct was developed against S. saprophyticus by targeting fully sequenced proteomes of its five different strains, which were examined using a pangenome and subtractive proteomic strategy to characterize prospective vaccination targets. The three immunogenic vaccine targets which were utilized to map the probable immune epitopes were verified by annotating the entire proteome. The predicted epitopes were further screened on the basis of antigenicity, allergenicity, water solubility, toxicity, virulence, and binding affinity towards the DRB*0101 allele, resulting in 11 potential epitopes, i.e., DLKKQKEKL, NKDLKKQKE, QDKLKDKSD, NVMDNKDLE, TSGTPDSQA, NANSDGSSS, GSDSSSSNN, DSSSSNNDS, DSSSSDRNN, SSSDRNNGD, and SSDDKSKDS. All these epitopes have the efficacy to cover 99.74% of populations globally. Finally, shortlisted epitopes were joined together with linkers and three different adjuvants to find the most stable and immunogenic vaccine construct. The top-ranked vaccine construct was further scrutinized on the basis of its physicochemical characterization and immunological profile. The non-allergenic and antigenic features of modeled vaccine constructs were initially validated and then subjected to docking with immune receptor major histocompatibility complex I and II (MHC-I and II), resulting in strong contact. In silico cloning validations yielded a codon adaptation index (CAI) value of 1 and an ideal percentage of GC contents (46.717%), indicating a putative expression of the vaccine in E. coli. Furthermore, immune simulation demonstrated that, after injecting the proposed MEVC, powerful antibodies were produced, resulting in the sharpest peaks of IgM + IgG formation (>11,500) within 5 to 15 days. Experimental testing against S. saprophyticus can evaluate the safety and efficacy of these prophylactic vaccination designs.}, } @article {pmid36016053, year = {2022}, author = {Tropea, M and Fedele, G and De Luca, R and Miriello, D and De Rango, F}, title = {Automatic Stones Classification through a CNN-Based Approach.}, journal = {Sensors (Basel, Switzerland)}, volume = {22}, number = {16}, pages = {}, pmid = {36016053}, issn = {1424-8220}, mesh = {Bayes Theorem ; Cluster Analysis ; Machine Learning ; *Neural Networks, Computer ; *Support Vector Machine ; }, abstract = {This paper presents an automatic recognition system for classifying stones belonging to different Calabrian quarries (Southern Italy). The tool for stone recognition has been developed in the SILPI project (acronym of "Sistema per l'Identificazione di Lapidei Per Immagini"), financed by POR Calabria FESR-FSE 2014-2020. Our study is based on the Convolutional Neural Network (CNNs) that is used in literature for many different tasks such as speech recognition, neural language processing, bioinformatics, image classification and much more. In particular, we propose a two-stage hybrid approach based on the use of a model of Deep Learning (DL), in our case the CNN, in the first stage and a model of Machine Learning (ML) in the second one. In this work, we discuss a possible solution to stones classification which uses a CNN for the feature extraction phase and the Softmax or Multinomial Logistic Regression (MLR), Support Vector Machine (SVM), k-Nearest Neighbors (kNN), Random Forest (RF) and Gaussian Naive Bayes (GNB) ML techniques in order to perform the classification phase basing our study on the approach called Transfer Learning (TL). We show the image acquisition process in order to collect adequate information for creating an opportune database of the stone typologies present in the Calabrian quarries, also performing the identification of quarries in the considered region. Finally, we show a comparison of different DL and ML combinations in our Two-Stage Hybrid Model solution.}, } @article {pmid36007741, year = {2022}, author = {Ali, A and Farhan, SB and Zhang, Y and Nasir, J and Farhan, H and Zamir, UB and Gao, H}, title = {Changes in temporal pattern and spatial distribution of environmental pollutants in 8 Asian countries owing to COVID-19 pandemic.}, journal = {Chemosphere}, volume = {308}, number = {Pt 1}, pages = {136075}, pmid = {36007741}, issn = {1879-1298}, mesh = {*Air Pollutants/analysis ; *Air Pollution/analysis ; *COVID-19/epidemiology ; Carbon Monoxide/analysis ; Environmental Monitoring/methods ; *Environmental Pollutants ; Formaldehyde ; Humans ; Nitrogen Dioxide/analysis ; *Ozone/analysis ; Pakistan ; Pandemics ; Particulate Matter/analysis ; Sulfur Dioxide/analysis ; }, abstract = {This study investigated the changes in air pollutant's concentration, spatio-temporal distribution and sensitivity of changes in air pollutant's concentration during pre and post COVID-19 outbreak. We employed Google Earth Engine Platform to access remote sensing datasets of air pollutants across Asian continent. Air pollution and cumulative confirmed-COVID cases data of Asian countries (Afghanistan, Bangladesh, China, India, Iran, Iraq, Pakistan, and Saudi Arabia) have been collected and analyzed for 2019 and 2020. The results indicate that aerosol index (AI) and nitrogen dioxide (NO2) is significantly reduced during COVID outbreak i.e. in year 2020. In addition, we found significantly positive (P < 0.05, 95% confidence interval, two-tailed) correlation between changes in AI and NO2 concentration for net active-COVID case increment in almost each country. For other atmospheric gases i.e. carbon monoxide (CO), formaldehyde (HCHO), ozone (O3), and Sulfur dioxide (SO2), insignificant and/or significant negative correlation is also observed. These results suggest that the atmospheric concentration of AI and NO2 are good indicators of human activities. Furthermore, the changes in O3 shows significantly negative correlation for net active-COVID case increment. In conclusion, we observed significant positive environmental impact of COVID-19 restrictions in Asia. This study would help and assist environmentalist and policy makers in restraining air pollution by implementing efficient restrictions on human activities with minimal economic loss.}, } @article {pmid36007087, year = {2022}, author = {Wang, Y and Cai, G and Yang, L and Zhang, N and Du, M}, title = {Monitoring of urban ecological environment including air quality using satellite imagery.}, journal = {PloS one}, volume = {17}, number = {8}, pages = {e0266759}, pmid = {36007087}, issn = {1932-6203}, mesh = {*Air Pollution ; China ; Environment ; Environmental Monitoring/methods ; Remote Sensing Technology ; *Satellite Imagery ; }, abstract = {Rapid urbanisation has highlighted problems in the urban ecological environment and stimulated research on the evaluation of urban environments. In previous studies, key factors such as greenness, wetness, and temperature were extracted from satellite images to assess the urban ecological environment. Although air pollution has become increasingly serious as urbanisation proceeds, information on air pollution is not included in existing models. The Sentinel-5P satellite launched by the European Space Agency in 2017 is a reliable data source for monitoring air quality. By making full use of images from Landsat 8, Sentinel-2A, and Sentinel-5P, this work attempts to construct a new remote sensing monitoring index for urban ecology by adding air quality information to the existing remote sensing ecological index. The proposed index was tested in the Beijing metropolitan area using satellite data from 2020. The results obtained using the proposed index differ greatly in the central urban region and near large bodies of water from those obtained using the existing remote sensing monitoring model, indicating that air quality plays a significant role in evaluating the urban ecological environment. Because the model constructed in this study integrates information on vegetation, soil, humidity, heat, and air quality, it can comprehensively and objectively reflect the quality of the urban ecological environment. Consequently, the proposed remote sensing index provides a new approach to effectively monitoring the urban ecological environment.}, } @article {pmid35999898, year = {2021}, author = {Waterhouse, RM and Adam-Blondon, AF and Agosti, D and Baldrian, P and Balech, B and Corre, E and Davey, RP and Lantz, H and Pesole, G and Quast, C and Glöckner, FO and Raes, N and Sandionigi, A and Santamaria, M and Addink, W and Vohradsky, J and Nunes-Jorge, A and Willassen, NP and Lanfear, J}, title = {Recommendations for connecting molecular sequence and biodiversity research infrastructures through ELIXIR.}, journal = {F1000Research}, volume = {10}, number = {}, pages = {}, pmid = {35999898}, issn = {2046-1402}, support = {BB/CSP1720/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/T/000PR9817/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/P016855/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/T/000PR9783/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/CCG1720/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/T/000PR9814/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {*Biodiversity ; *Biological Science Disciplines ; Computational Biology ; Europe ; }, abstract = {Threats to global biodiversity are increasingly recognised by scientists and the public as a critical challenge. Molecular sequencing technologies offer means to catalogue, explore, and monitor the richness and biogeography of life on Earth. However, exploiting their full potential requires tools that connect biodiversity infrastructures and resources. As a research infrastructure developing services and technical solutions that help integrate and coordinate life science resources across Europe, ELIXIR is a key player. To identify opportunities, highlight priorities, and aid strategic thinking, here we survey approaches by which molecular technologies help inform understanding of biodiversity. We detail example use cases to highlight how DNA sequencing is: resolving taxonomic issues; Increasing knowledge of marine biodiversity; helping understand how agriculture and biodiversity are critically linked; and playing an essential role in ecological studies. Together with examples of national biodiversity programmes, the use cases show where progress is being made but also highlight common challenges and opportunities for future enhancement of underlying technologies and services that connect molecular and wider biodiversity domains. Based on emerging themes, we propose key recommendations to guide future funding for biodiversity research: biodiversity and bioinformatic infrastructures need to collaborate closely and strategically; taxonomic efforts need to be aligned and harmonised across domains; metadata needs to be standardised and common data management approaches widely adopted; current approaches need to be scaled up dramatically to address the anticipated explosion of molecular data; bioinformatics support for biodiversity research needs to be enabled and sustained; training for end users of biodiversity research infrastructures needs to be prioritised; and community initiatives need to be proactive and focused on enabling solutions. For sequencing data to deliver their full potential they must be connected to knowledge: together, molecular sequence data collection initiatives and biodiversity research infrastructures can advance global efforts to prevent further decline of Earth's biodiversity.}, } @article {pmid36002452, year = {2022}, author = {Yang, C and Liu, H and Li, Q and Wang, X and Ma, W and Liu, C and Fang, X and Tang, Y and Shi, T and Wang, Q and Xu, Y and Zhang, J and Li, X and Xu, G and Chen, J and Su, M and Wang, S and Wu, J and Huang, L and Li, X and Wu, G}, title = {Human expansion into Asian highlands in the 21st Century and its effects.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {4955}, pmid = {36002452}, issn = {2041-1723}, mesh = {Asia ; Asia, Southeastern ; *Asian People ; *Ecosystem ; Humans ; }, abstract = {Most intensive human activities occur in lowlands. However, sporadic reports indicate that human activities are expanding in some Asian highlands. Here we investigate the expansions of human activities in highlands and their effects over Asia from 2000 to 2020 by combining earth observation data and socioeconomic data. We find that ∼23% of human activity expansions occur in Asian highlands and ∼76% of these expansions in highlands comes from ecological lands, reaching 95% in Southeast Asia. The expansions of human activities in highlands intensify habitat fragmentation and result in large ecological costs in low and lower-middle income countries, and they also support Asian developments. We estimate that cultivated land net growth in the Asian highlands contributed approximately 54% in preventing the net loss of the total cultivated land. Moreover, the growth of highland artificial surfaces may provide living and working spaces for ∼40 million people. Our findings suggest that highland developments hold dual effects and provide new insight for regional sustainable developments.}, } @article {pmid36002035, year = {2024}, author = {Polanowska, KE and Iwański, S and Leśniak, MM and Seniów, J}, title = {Computer-assisted training of executive functions in adult patients with non-progressive acquired brain damage - a pilot study on efficacy of a new therapeutic application.}, journal = {Applied neuropsychology. Adult}, volume = {31}, number = {6}, pages = {1180-1191}, doi = {10.1080/23279095.2022.2114354}, pmid = {36002035}, issn = {2327-9109}, mesh = {Humans ; *Executive Function/physiology ; Male ; Pilot Projects ; Female ; Middle Aged ; Adult ; *Brain Injuries/complications/rehabilitation ; *Therapy, Computer-Assisted ; Aged ; Problem Solving/physiology ; Activities of Daily Living ; Social Skills ; }, abstract = {Executive dysfunction is most often caused by post-traumatic or post-stroke damage to the prefrontal regions of the brain. The aim of this study was to compare the efficacy of two computer-assisted therapy programs for executive dysfunctions in patients with acquired brain injury. Patients were trained using either a newly developed application ExeSystem (designed to help improve the ability to manage and control one's own behavior by performing tasks imitating natural, everyday situations) or a combination of two commercial applications RehaCom and CogniPlus. Data collected after a three-week period of therapy conducted in two 15-person groups of participants indicated comparable efficacy of both therapy programs in improving quality of daily functioning, executive attention, as well as planning and problem-solving but not memory. The improvement in social competence (p = .028) was the only advantage of therapy with the ExeSystem. Therapeutic interactions using computer programs were shown to be positively evaluated by patients (p < .01). This study confirmed at least equal efficacy of computer-based executive function therapy using ExeSystem compared to RehaCom and CogniPlus. However, despite the implementation of a more ecological and comprehensive approach to the content of a new application, the benefits of this approach were limited.}, } @article {pmid36001546, year = {2022}, author = {Diodato, N and Borrelli, P and Panagos, P and Bellocchi, G}, title = {Global assessment of storm disaster-prone areas.}, journal = {PloS one}, volume = {17}, number = {8}, pages = {e0272161}, pmid = {36001546}, issn = {1932-6203}, mesh = {*Disasters ; Geographic Information Systems ; Humans ; Hydrology ; *Rain ; Soil ; }, abstract = {BACKGROUND: Advances in climate change research contribute to improved forecasts of hydrological extremes with potentially severe impacts on human societies and natural landscapes. Rainfall erosivity density (RED), i.e. rainfall erosivity (MJ mm hm-2 h-1 yr-1) per rainfall unit (mm), is a measure of rainstorm aggressiveness and a proxy indicator of damaging hydrological events.

METHODS AND FINDINGS: Here, using downscaled RED data from 3,625 raingauges worldwide and log-normal ordinary kriging with probability mapping, we identify damaging hydrological hazard-prone areas that exceed warning and alert thresholds (1.5 and 3.0 MJ hm-2 h-1, respectively). Applying exceedance probabilities in a geographical information system shows that, under current climate conditions, hazard-prone areas exceeding a 50% probability cover ~31% and ~19% of the world's land at warning and alert states, respectively.

CONCLUSION: RED is identified as a key driver behind the spatial growth of environmental disruption worldwide (with tropical Latin America, South Africa, India and the Indian Archipelago most affected).}, } @article {pmid36001047, year = {2023}, author = {Shaffer, M and Thurimella, K and Sterrett, JD and Lozupone, CA}, title = {SCNIC: Sparse correlation network investigation for compositional data.}, journal = {Molecular ecology resources}, volume = {23}, number = {1}, pages = {312-325}, pmid = {36001047}, issn = {1755-0998}, support = {T15 LM009451/LM/NLM NIH HHS/United States ; 4 T15 LM009451-10//U.S. National Library of Medicine/ ; //National Science Foundation/ ; }, mesh = {*Software ; Algorithms ; *Microbiota ; }, abstract = {Microbiome studies are often limited by a lack of statistical power due to small sample sizes and a large number of features. This problem is exacerbated in correlative studies of multi-omic datasets. Statistical power can be increased by finding and summarizing modules of correlated observations, which is one dimensionality reduction method. Additionally, modules provide biological insight as correlated groups of microbes can have relationships among themselves. To address these challenges, we developed SCNIC: Sparse Cooccurrence Network Investigation for compositional data. SCNIC is open-source software that can generate correlation networks and detect and summarize modules of highly correlated features. Modules can be formed using either the Louvain Modularity Maximization (LMM) algorithm or a Shared Minimum Distance algorithm (SMD) that we newly describe here and relate to LMM using simulated data. We applied SCNIC to two published datasets and we achieved increased statistical power and identified microbes that not only differed across groups, but also correlated strongly with each other, suggesting shared environmental drivers or cooperative relationships among them. SCNIC provides an easy way to generate correlation networks, identify modules of correlated features and summarize them for downstream statistical analysis. Although SCNIC was designed considering properties of microbiome data, such as compositionality and sparsity, it can be applied to a variety of data types including metabolomics data and used to integrate multiple data types. SCNIC allows for the identification of functional microbial relationships at scale while increasing statistical power through feature reduction.}, } @article {pmid36000659, year = {2022}, author = {Santos, JS and Cruz, AJS and Ruas, CM and Pereira Júnior, EA and Mattos, FF and Klevens, M and Abreu, MHNG}, title = {Factors associated with the use of a public information system of dentist-prescribed antibiotics in Minas Gerais, Brazil.}, journal = {Ciencia & saude coletiva}, volume = {27}, number = {9}, pages = {3741-3750}, doi = {10.1590/1413-81232022279.07422022}, pmid = {36000659}, issn = {1678-4561}, mesh = {*Anti-Bacterial Agents ; Brazil ; *Dentists ; Humans ; Information Systems ; Socioeconomic Factors ; }, abstract = {This article aims to investigate the association between socioeconomic factors, health care organizations, and the use of a management and monitoring system for the dispensing of antibiotics prescribed by dentists in public health services in Minas Gerais, Brazil. This is an ecological-epidemiological study that analyzed secondary data from the Integrated Pharmaceutical Care Management System (SIGAF) of the Department of Health of the state of MG, Brazil, in 2017. Thirteen independent variables were analyzed to assess their influence on municipal adherence to SIGAF system considering dental prescriptions of antibiotics. Descriptive statistical analyses were performed, and the Classification and Regression Tree technique was used to identify the municipal variables associated with the outcome. A total of 57,279 antibiotic courses prescribed by dentists and recorded in SIGAF were examined. Socioeconomic factors were not associated with the use of SIGAF to record these prescriptions. Oral healthcare coverage was positively associated with the use of SIGAF for the dispensing of antibiotics prescribed by dentists. Dental Specialties Center were negatively associated with the outcome. Municipalities with high oral healthcare coverage and those without a Dental Specialties Center were more likely to use SIGAF.}, } @article {pmid35999848, year = {2022}, author = {Kopperud, BT and Lidgard, S and Liow, LH}, title = {Enhancing georeferenced biodiversity inventories: automated information extraction from literature records reveal the gaps.}, journal = {PeerJ}, volume = {10}, number = {}, pages = {e13921}, pmid = {35999848}, issn = {2167-8359}, mesh = {Animals ; *Biodiversity ; *Bryozoa ; Information Storage and Retrieval ; }, abstract = {We use natural language processing (NLP) to retrieve location data for cheilostome bryozoan species (text-mined occurrences (TMO)) in an automated procedure. We compare these results with data combined from two major public databases (DB): the Ocean Biodiversity Information System (OBIS), and the Global Biodiversity Information Facility (GBIF). Using DB and TMO data separately and in combination, we present latitudinal species richness curves using standard estimators (Chao2 and the Jackknife) and range-through approaches. Our combined DB and TMO species richness curves quantitatively document a bimodal global latitudinal diversity gradient for extant cheilostomes for the first time, with peaks in the temperate zones. A total of 79% of the georeferenced species we retrieved from TMO (N = 1,408) and DB (N = 4,549) are non-overlapping. Despite clear indications that global location data compiled for cheilostomes should be improved with concerted effort, our study supports the view that many marine latitudinal species richness patterns deviate from the canonical latitudinal diversity gradient (LDG). Moreover, combining online biodiversity databases with automated information retrieval from the published literature is a promising avenue for expanding taxon-location datasets.}, } @article {pmid35990172, year = {2022}, author = {Xiao, H and Xu, Z and Ren, J and Zhou, Y and Lin, R and Bao, S and Zhang, L and Lu, S and Lee, CKM and Liu, J}, title = {Navigating Chinese cities to achieve sustainable development goals by 2030.}, journal = {Innovation (Cambridge (Mass.))}, volume = {3}, number = {5}, pages = {100288}, pmid = {35990172}, issn = {2666-6758}, abstract = {Achieving the 17 United Nations sustainable development goals (SDGs) in China largely depends on the transition of cities toward sustainable development. However, significant knowledge gaps exist in evaluating the SDG index at the city scale and in understanding how to simulate pathways to achieve the 17 SDGs for Chinese cities by 2030. This study aimed to quantify the SDG index of 285 Chinese cities and developed a forecasting model to simulate the performance of each SDG in each city until 2030 using varied scenarios. The results indicated that although the SDG index in Chinese cities increased by 33.97% during 2005-2016, Chinese cities, which continued their past paths, achieved an average of only five SDGs by 2030. To promote the joint achievement of all SDGs, we designed different paths for all SDGs of each of the 285 cities and simulated their SDG index until 2030. Under the scenarios, 216 Chinese cities (75.79%) could achieve 9-13 more SDGs in 2030 and the overall SDG index can improve from 74.57 in 2030 to 97.49 (target score 100) by adopting more intensive path adjustment. We lastly determined a cost-effective path for each SDG of each city to promote joint achievement of all SDGs by 2030. The proposed simulation model and cost-effective path serve as a foundation for other countries to simulate SDG progress and develop pathways for achieving SDGs in the future.}, } @article {pmid35990120, year = {2022}, author = {Zhang, H}, title = {The Impact of Tax Reduction and Fee Reduction Based on Big Data Algorithm on the High-Quality Development of the Real Economy under the Action of Coupling Effect or Substitution Effect.}, journal = {Computational intelligence and neuroscience}, volume = {2022}, number = {}, pages = {2828687}, pmid = {35990120}, issn = {1687-5273}, mesh = {Algorithms ; *Big Data ; China ; Ecology ; *Economic Development ; }, abstract = {The basic idea of the mass of medical growth is to adhere to local market price thinking with a Chinese touch and follow the development policy of "quality first, efficiency first." It insists on properly handling a series of important relationships betwixt socialism and market economy, the first to drive the rich later, the government and the market, equality and efficiency, short-term growth and long-term development, China and the international economy, ecology and growth of the region. Under the guidance of the qualitative thinking theory, it combines the strategic goals of China's economic qualitative development and actively draws on the research results of other countries. It uses big data algorithms to focus on the impact of qualitative development on tax and income reduction in the real economy. It conducts research experiments on the impact of tax reduction and fee reduction based on big data algorithms on the top-notch growth of the real economy. Its experimental data show that: in 2018, the share of primary, tertiary, and primary sector in China's dimensional economy top-notch growth coordination index was 7.2%, 40.7%, and 52.2%, respectively. Its contribution rate to economic growth was 4.2%, 36.1%, and 59.7%, respectively. From these data, it can be concluded that the top-notch growth of the real economy is getting better and better under the influence of tax reduction and fee reduction by big data algorithms.}, } @article {pmid35983321, year = {2022}, author = {Zhu, Y and Ge, X and Wang, L and You, Y and Cheng, Y and Ma, J and Chen, F}, title = {Biochar rebuilds the network complexity of rare and abundant microbial taxa in reclaimed soil of mining areas to cooperatively avert cadmium stress.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {972300}, pmid = {35983321}, issn = {1664-302X}, abstract = {Understanding the interactions between the soil microbial communities and species is critical in the remediation of heavy metal-contaminated soil. Biochar has been widely applied as a stabilizer in the in situ remediation of cadmium (Cd)-contaminated soils in mining areas. However, the rebuilding of the microbial taxa of rare and abundant species by biochar and their cooperative resistance to Cd stress remains elusive. In this pursuit, the present study envisaged the effects of two types of biochars viz., poplar bark biochar (PB) and thiourea-modified poplar bark biochar (TP) on the rare and abundant bacterial and fungal taxa by using pot experiments. The results demonstrated that the PB and TP treatments significantly reduced the leached Cd content, by 35.13 and 68.05%, respectively, compared with the control group (CK), in the reclaimed soil of the mining area. The application of biochar significantly improved the physicochemical properties like pH and Soil Organic Matter (SOM) of the soil. It was observed that TP treatment was superior to the PB and CK groups in increasing the diversity of the soil abundant and rare species of microbial taxa. Compared with the CK group, the application of PB and TP enhanced and elevated the complexity of the microbial networks of rare and abundant taxa, increased the number and types of network core microorganisms, reshaped the network core microorganisms and hubs, and boosted the microbial resistance to Cd stress. Our results indicate the response of rare and abundant microbial taxa to biochar application and the mechanism of their synergistic remediation of Cd-contaminated soil, thereby providing technical feasibility for in situ remediation of Cd-contaminated soil in mining areas.}, } @article {pmid35977400, year = {2022}, author = {IJdema, F and De Smet, J and Crauwels, S and Lievens, B and Van Campenhout, L}, title = {Meta-analysis of larvae of the black soldier fly (Hermetia illucens) microbiota based on 16S rRNA gene amplicon sequencing.}, journal = {FEMS microbiology ecology}, volume = {98}, number = {9}, pages = {}, pmid = {35977400}, issn = {1574-6941}, mesh = {Animals ; Bacteria/genetics ; *Diptera/microbiology ; Genes, rRNA ; Larva/microbiology ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Black soldier fly larvae (BSFL) belong to the most widely reared insects as an alternative protein source at industrial scale. Bacteria in the larval gut can provide benefits for the animal, though some bacteria can also be pathogenic for the insect. Accurate characterization of the BSFL microbiota is important for the production of BSFL in terms of yield and microbiological safety. In this study, 16S ribosomal RNA gene sequence data sets from 11 studies were re-analysed to gain better insights in the BSFL gut microbiota, potential factors that influence their composition, and differences between the gut and the whole larvae microbiota. A core gut microbiota was found consisting of members of Enterococcus, Klebsiella, Morganella, Providencia, and Scrofimicrobium. Further, the factors 'Study', 'Age' and 'Feed' (i.e. rearing substrate of the larvae) significantly affected the microbiota gut composition. When compared to whole larvae, a significantly lower diversity was found for gut samples, suggesting that the larvae harboured additional microbes on their cuticle or in the insect body. Universal choices in insect sample type, primer selection and bio-informatics analysis pipeline can strengthen future meta-analyses and improve our understanding of the BSFL gut microbiota towards the optimization of insect rearing conditions and substrates.}, } @article {pmid35975694, year = {2022}, author = {Orlando, CG and Possell, M and Price, C and Banks, PB and Mercorelli, L and McArthur, C}, title = {A new conceptual and quantitative approach to exploring and defining potential open-access olfactory information.}, journal = {The New phytologist}, volume = {236}, number = {4}, pages = {1605-1619}, pmid = {35975694}, issn = {1469-8137}, mesh = {*Odorants ; *Plants/chemistry ; Reproducibility of Results ; Trees/chemistry ; }, abstract = {All organisms emit odour, providing 'open-access' olfactory information for any receiver with the right sensory apparatus. Characterizing open-access information emitted by groups of organisms, such as plant species, provides the means to answer significant questions about ecological interactions and their evolution. We present a new conceptual framework defining information reliability and a practical method to characterize and recover information from amongst olfactory noise. We quantified odour emissions from two tree species, one focal group and one outgroup, to demonstrate our approach using two new R statistical functions. We explore the consequences of relaxing or tightening criteria defining information and, from thousands of odour combinations, we identify and quantify those few likely to be informative. Our method uses core general principles characterizing information while incorporating knowledge of how receivers detect and discriminate odours. We can now map information in consistency-precision reliability space, explore the concept of information, and test information-noise boundaries, and between cues and signals.}, } @article {pmid35974327, year = {2022}, author = {Garza, DR and von Meijenfeldt, FAB and van Dijk, B and Boleij, A and Huynen, MA and Dutilh, BE}, title = {Nutrition or nature: using elementary flux modes to disentangle the complex forces shaping prokaryote pan-genomes.}, journal = {BMC ecology and evolution}, volume = {22}, number = {1}, pages = {101}, pmid = {35974327}, issn = {2730-7182}, mesh = {Archaea/genetics ; Bacteria/genetics ; *Evolution, Molecular ; *Genome, Bacterial/genetics ; Genomics ; Humans ; Phylogeny ; Prokaryotic Cells ; }, abstract = {BACKGROUND: Microbial pan-genomes are shaped by a complex combination of stochastic and deterministic forces. Even closely related genomes exhibit extensive variation in their gene content. Understanding what drives this variation requires exploring the interactions of gene products with each other and with the organism's external environment. However, to date, conceptual models of pan-genome dynamics often represent genes as independent units and provide limited information about their mechanistic interactions.

RESULTS: We simulated the stochastic process of gene-loss using the pooled genome-scale metabolic reaction networks of 46 taxonomically diverse bacterial and archaeal families as proxies for their pan-genomes. The frequency by which reactions are retained in functional networks when stochastic gene loss is simulated in diverse environments allowed us to disentangle the metabolic reactions whose presence depends on the metabolite composition of the external environment (constrained by "nutrition") from those that are independent of the environment (constrained by "nature"). By comparing the frequency of reactions from the first group with their observed frequencies in bacterial and archaeal families, we predicted the metabolic niches that shaped the genomic composition of these lineages. Moreover, we found that the lineages that were shaped by a more diverse metabolic niche also occur in more diverse biomes as assessed by global environmental sequencing datasets.

CONCLUSION: We introduce a computational framework for analyzing and interpreting pan-reactomes that provides novel insights into the ecological and evolutionary drivers of pan-genome dynamics.}, } @article {pmid35972961, year = {2022}, author = {Ramírez-Castañeda, V and Westeen, EP and Frederick, J and Amini, S and Wait, DR and Achmadi, AS and Andayani, N and Arida, E and Arifin, U and Bernal, MA and Bonaccorso, E and Bonachita Sanguila, M and Brown, RM and Che, J and Condori, FP and Hartiningtias, D and Hiller, AE and Iskandar, DT and Jiménez, RA and Khelifa, R and Márquez, R and Martínez-Fonseca, JG and Parra, JL and Peñalba, JV and Pinto-García, L and Razafindratsima, OH and Ron, SR and Souza, S and Supriatna, J and Bowie, RCK and Cicero, C and McGuire, JA and Tarvin, RD}, title = {A set of principles and practical suggestions for equitable fieldwork in biology.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {119}, number = {34}, pages = {e2122667119}, pmid = {35972961}, issn = {1091-6490}, mesh = {*Bioethical Issues ; *Biology/ethics ; Humans ; }, abstract = {Field biology is an area of research that involves working directly with living organisms in situ through a practice known as "fieldwork." Conducting fieldwork often requires complex logistical planning within multiregional or multinational teams, interacting with local communities at field sites, and collaborative research led by one or a few of the core team members. However, existing power imbalances stemming from geopolitical history, discrimination, and professional position, among other factors, perpetuate inequities when conducting these research endeavors. After reflecting on our own research programs, we propose four general principles to guide equitable, inclusive, ethical, and safe practices in field biology: be collaborative, be respectful, be legal, and be safe. Although many biologists already structure their field programs around these principles or similar values, executing equitable research practices can prove challenging and requires careful consideration, especially by those in positions with relatively greater privilege. Based on experiences and input from a diverse group of global collaborators, we provide suggestions for action-oriented approaches to make field biology more equitable, with particular attention to how those with greater privilege can contribute. While we acknowledge that not all suggestions will be applicable to every institution or program, we hope that they will generate discussions and provide a baseline for training in proactive, equitable fieldwork practices.}, } @article {pmid35972940, year = {2022}, author = {Vimercati, G and Probert, AF and Volery, L and Bernardo-Madrid, R and Bertolino, S and Céspedes, V and Essl, F and Evans, T and Gallardo, B and Gallien, L and González-Moreno, P and Grange, MC and Hui, C and Jeschke, JM and Katsanevakis, S and Kühn, I and Kumschick, S and Pergl, J and Pyšek, P and Rieseberg, L and Robinson, TB and Saul, WC and Sorte, CJB and Vilà, M and Wilson, JRU and Bacher, S}, title = {The EICAT+ framework enables classification of positive impacts of alien taxa on native biodiversity.}, journal = {PLoS biology}, volume = {20}, number = {8}, pages = {e3001729}, pmid = {35972940}, issn = {1545-7885}, support = {I 4011/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {*Biodiversity ; Ecosystem ; Human Activities ; Humans ; *Introduced Species ; }, abstract = {Species introduced through human-related activities beyond their native range, termed alien species, have various impacts worldwide. The IUCN Environmental Impact Classification for Alien Taxa (EICAT) is a global standard to assess negative impacts of alien species on native biodiversity. Alien species can also positively affect biodiversity (for instance, through food and habitat provisioning or dispersal facilitation) but there is currently no standardized and evidence-based system to classify positive impacts. We fill this gap by proposing EICAT+, which uses 5 semiquantitative scenarios to categorize the magnitude of positive impacts, and describes underlying mechanisms. EICAT+ can be applied to all alien taxa at different spatial and organizational scales. The application of EICAT+ expands our understanding of the consequences of biological invasions and can inform conservation decisions.}, } @article {pmid35969597, year = {2022}, author = {Ramasawmy, M and Mu, Y and Clutterbuck, D and Pantelic, M and Lip, GYH and van der Feltz-Cornelis, C and Wootton, D and Williams, NH and Montgomery, H and Mallinson Cookson, R and Attree, E and Gabbay, M and Heightman, M and Alwan, NA and Banerjee, A and Lorgelly, P and , }, title = {STIMULATE-ICP-CAREINEQUAL (Symptoms, Trajectory, Inequalities and Management: Understanding Long-COVID to Address and Transform Existing Integrated Care Pathways) study protocol: Defining usual care and examining inequalities in Long Covid support.}, journal = {PloS one}, volume = {17}, number = {8}, pages = {e0271978}, pmid = {35969597}, issn = {1932-6203}, support = {COV-LT2-0043/DH_/Department of Health/United Kingdom ; }, mesh = {*COVID-19/complications/epidemiology/therapy ; Critical Pathways ; *Delivery of Health Care, Integrated ; Humans ; Longitudinal Studies ; Post-Acute COVID-19 Syndrome ; }, abstract = {INTRODUCTION: Individuals with Long Covid represent a new and growing patient population. In England, fewer than 90 Long Covid clinics deliver assessment and treatment informed by NICE guidelines. However, a paucity of clinical trials or longitudinal cohort studies means that the epidemiology, clinical trajectory, healthcare utilisation and effectiveness of current Long Covid care are poorly documented, and that neither evidence-based treatments nor rehabilitation strategies exist. In addition, and in part due to pre-pandemic health inequalities, access to referral and care varies, and patient experience of the Long Covid care pathways can be poor. In a mixed methods study, we therefore aim to: (1) describe the usual healthcare, outcomes and resource utilisation of individuals with Long Covid; (2) assess the extent of inequalities in access to Long Covid care, and specifically to understand Long Covid patients' experiences of stigma and discrimination.

METHODS AND ANALYSIS: A mixed methods study will address our aims. Qualitative data collection from patients and health professionals will be achieved through surveys, interviews and focus group discussions, to understand their experience and document the function of clinics. A patient cohort study will provide an understanding of outcomes and costs of care. Accessible data will be further analysed to understand the nature of Long Covid, and the care received.

ETHICS AND DISSEMINATION: Ethical approval was obtained from South Central-Berkshire Research Ethics Committee (reference 303958). The dissemination plan will be decided by the patient and public involvement and engagement (PPIE) group members and study Co-Is, but will target 1) policy makers, and those responsible for commissioning and delivering Long Covid services, 2) patients and the public, and 3) academics.}, } @article {pmid35964757, year = {2022}, author = {Loli, M and Kefalas, G and Dafis, S and Mitoulis, SA and Schmidt, F}, title = {Bridge-specific flood risk assessment of transport networks using GIS and remotely sensed data.}, journal = {The Science of the total environment}, volume = {850}, number = {}, pages = {157976}, doi = {10.1016/j.scitotenv.2022.157976}, pmid = {35964757}, issn = {1879-1026}, mesh = {*Floods ; *Geographic Information Systems ; Hydrology ; Reproducibility of Results ; Risk Assessment ; }, abstract = {A novel framework for the expedient assessment of flood risk to transportation networks focused on the response of the most critical and vulnerable infrastructure assets, the bridges, is developed, validated and applied. Building upon the recent French guidelines on scour risk (CEREMA, 2019), this paper delivers a thorough methodology, that incorporates three key, risk parameters: (i) the hydrodynamic loading, a hazard component of equal significance to scour, for the assessment of hazard; (ii) the correlation of select scour indicators with a new index relating to flow velocity, a primary measure of the adverse impacts of flow-structure interaction, enabling a more accurate and automated, assessment of bridge susceptibility to scour; (iii) the use of a new, comprehensive indicator, namely the Indicator of Flood Hazard Intensity (IFHI) which incorporates, in a simple yet efficient way, the key parameters controlling the severity of flood impact on bridges, namely flow velocity, floodwater height, flow obstruction, and sediment type. The framework is implemented for the analysis of flood risk in a case study area, considering an inventory of 117 bridges of diverse construction characteristics, which were affected by a major flood that impacted Greece in September 2020. The reliability of the method is validated against an extensive record of inspected and documented bridge damages. Regional scale analysis is facilitated by the adoption of the Multi-Criteria Decision-Making method for flood hazard indexing, considering geomorphological, meteorological, hydrological, and land use/cover data, based on the processing of remotely sensed imagery and openly available geospatial datasets in GIS.}, } @article {pmid35964726, year = {2022}, author = {Karimian, H and Zou, W and Chen, Y and Xia, J and Wang, Z}, title = {Landscape ecological risk assessment and driving factor analysis in Dongjiang river watershed.}, journal = {Chemosphere}, volume = {307}, number = {Pt 3}, pages = {135835}, doi = {10.1016/j.chemosphere.2022.135835}, pmid = {35964726}, issn = {1879-1298}, mesh = {China ; *Environmental Monitoring/methods ; Factor Analysis, Statistical ; Humans ; Risk Assessment ; *Rivers ; Urbanization ; }, abstract = {The ecological and environmental quality of Dongjiang river watershed has great influence on Guangdong, Hong Kong and Macao. The landscape ecological risk assessment model could effectively monitor and assess environmental quality. In this study, spatial autocorrelation and geographic detector methods were used to explore the spatial characteristics of landscape ecological risk and their driving factors in the Dongjiang river watershed for four decades. The results showed that the ecological risks of Dongjiang River Source Watershed are mainly classified as low and intermediate, which are distributed in the hilly regions and the marginal mountainous regions at the junction of the Xunwu and Dingnan counties. From 1980 to 2018, the area of regions with the low ecological risk increased by 587.01 km [2]. The size of regions with moderate, high and severe ecological risk decreased by 165.6 km [2], 258.82 km[2] and 162.58 km[2], respectively. Moreover, landscape ecological risk values exhibited an apparent spatial dependency, and high-risk areas cluster together. Among influencing factors, population density has the most significant impact on the change of landscape ecological risk in the Dongjiang river watershed, followed by elevation (DEM), human interface, vegetation index (NDVI), and urbanization level. However, the interaction of driving factors has a greater impact on the ecological risk of the Dongjiang river watershed than a single driving factor. The research provides good knowledge for environmental quality management, and the proposed methods can be used for other regions.}, } @article {pmid35960845, year = {2022}, author = {Amend, AS and Swift, SOI and Darcy, JL and Belcaid, M and Nelson, CE and Buchanan, J and Cetraro, N and Fraiola, KMS and Frank, K and Kajihara, K and McDermot, TG and McFall-Ngai, M and Medeiros, M and Mora, C and Nakayama, KK and Nguyen, NH and Rollins, RL and Sadowski, P and Sparagon, W and Téfit, MA and Yew, JY and Yogi, D and Hynson, NA}, title = {A ridge-to-reef ecosystem microbial census reveals environmental reservoirs for animal and plant microbiomes.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {119}, number = {33}, pages = {e2204146119}, pmid = {35960845}, issn = {1091-6490}, support = {P20 GM125508/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Bacteria ; *Ecosystem ; *Microbiota ; *Plants/microbiology ; }, abstract = {Microbes are found in nearly every habitat and organism on the planet, where they are critical to host health, fitness, and metabolism. In most organisms, few microbes are inherited at birth; instead, acquiring microbiomes generally involves complicated interactions between the environment, hosts, and symbionts. Despite the criticality of microbiome acquisition, we know little about where hosts' microbes reside when not in or on hosts of interest. Because microbes span a continuum ranging from generalists associating with multiple hosts and habitats to specialists with narrower host ranges, identifying potential sources of microbial diversity that can contribute to the microbiomes of unrelated hosts is a gap in our understanding of microbiome assembly. Microbial dispersal attenuates with distance, so identifying sources and sinks requires data from microbiomes that are contemporary and near enough for potential microbial transmission. Here, we characterize microbiomes across adjacent terrestrial and aquatic hosts and habitats throughout an entire watershed, showing that the most species-poor microbiomes are partial subsets of the most species-rich and that microbiomes of plants and animals are nested within those of their environments. Furthermore, we show that the host and habitat range of a microbe within a single ecosystem predicts its global distribution, a relationship with implications for global microbial assembly processes. Thus, the tendency for microbes to occupy multiple habitats and unrelated hosts enables persistent microbiomes, even when host populations are disjunct. Our whole-watershed census demonstrates how a nested distribution of microbes, following the trophic hierarchies of hosts, can shape microbial acquisition.}, } @article {pmid35960769, year = {2022}, author = {Ali, MA and Iqbal, MS and Ahmad, KS and Akbar, M and Mehmood, A and Hussain, SA and Arshad, N and Munir, S and Masood, H and Ahmad, T and Kaloi, GM and Islam, M}, title = {Plant species diversity assessment and monitoring in catchment areas of River Chenab, Punjab, Pakistan.}, journal = {PloS one}, volume = {17}, number = {8}, pages = {e0272654}, pmid = {35960769}, issn = {1932-6203}, mesh = {Biodiversity ; *Ecosystem ; Humans ; Pakistan ; Plants ; Potassium ; *Rivers ; Soil/chemistry ; Trees ; }, abstract = {BACKGROUND: Biodiversity data is crucial for sustainable development and making decisions regarding natural resources and its conservation. The study goal was to use quantitative ecological approaches to determine the species richness and diversity of wild flora and the ultimate impact of environmental factors on vegetation dynamics.

METHODS: Quadrats having sizes of 1×1 for herbs, 5×5 for shrubs, and 10×10 m2 for trees were used. Various phytosociological characteristics were investigated in association with a wide variety of environmental variables. Soil analysis based on texture, moisture, pH, electrical conductivity (EC), organic matter (OM), available potassium (K), and phosphorus (P) were examined. The existing state of vegetation along the River Chenab was assessed using SWOT analysis and a future conservation strategy was devised.

RESULTS: One hundred twenty different plant speies were divided into 51 families including 92 dicots, 17 monocots, 6 pteridophytes and 1 bryophyte species. Herbs accounted for 89 followed by shrubs (16 species) and trees (15 species). Correlation analysis revealed a highly positive correlation between relative density and relative frequency (0.956**). Shannon and Simpson's diversity indices elaborated that site 3 and 7 with clay loamy soil had non-significant alpha diversity and varies from site to site. Diversity analysis showed that site 10 was most diverse (22.25) in terms of species richness. The principal coordinate analysis expressed that different environmental variables including OM, soil pH, P, K, and EC affect vegetation significantly, therefore, loamy soil showed presence and dispersal of more vegetation as compared to loam, sandy and sandy loam soils. Further, 170 ppm of available potassium had significant affect on plant diversity and distribution.

CONCLUSION: Asteraceae family was found dominant as dicot while poaceae among monocot. Adhatoda vasica was one of the unique species and found in Head Maralla site. For evenness, site 3 had maximum value 0.971. Most of the soil represented loamy soil texture where site 2 and 4 possess high soil moisture content. SWOT analysis revealed strengths as people prefered plants for medicine, food and economic purposes. In weakness, agricultural practices, soil erosion and flooding affected the vegetation. In opportunities, Forest and Irrigation Departments were planting plants for the restoration of ecosystem. Threats include anthropogenic activities overgrazing, urbanization and road infrastructure at Head Maralla, habitat fragmentation at Head Khanki, and extensive fish farming at Head Qadirabad. Future conservation efforts should be concentrated on SWOT analysis outcome in terms of stopping illegal consumption of natural resources, restoration of plant biodiversity through reforestation, designating protected areas and multiplying rare species locally.}, } @article {pmid35959935, year = {2023}, author = {Stahlke, AR and Chang, J and Tembrock, LR and Sim, SB and Chudalayandi, S and Geib, SM and Scheffler, BE and Perera, OP and Gilligan, TM and Childers, AK and Hackett, KJ and Coates, BS}, title = {A Chromosome-Scale Genome Assembly of a Helicoverpa zea Strain Resistant to Bacillus thuringiensis Cry1Ac Insecticidal Protein.}, journal = {Genome biology and evolution}, volume = {15}, number = {3}, pages = {}, pmid = {35959935}, issn = {1759-6653}, mesh = {Animals ; *Insecticides/pharmacology ; *Bacillus thuringiensis/genetics ; Zea mays ; Sex Chromosomes ; *Lepidoptera ; Bacterial Proteins/genetics ; Plants, Genetically Modified ; Hemolysin Proteins/genetics ; *Moths/genetics ; Pest Control, Biological ; Larva ; }, abstract = {Helicoverpa zea (Lepidoptera: Noctuidae) is an insect pest of major cultivated crops in North and South America. The species has adapted to different host plants and developed resistance to several insecticidal agents, including Bacillus thuringiensis (Bt) insecticidal proteins in transgenic cotton and maize. Helicoverpa zea populations persist year-round in tropical and subtropical regions, but seasonal migrations into temperate zones increase the geographic range of associated crop damage. To better understand the genetic basis of these physiological and ecological characteristics, we generated a high-quality chromosome-level assembly for a single H. zea male from Bt-resistant strain, HzStark_Cry1AcR. Hi-C data were used to scaffold an initial 375.2 Mb contig assembly into 30 autosomes and the Z sex chromosome (scaffold N50 = 12.8 Mb and L50 = 14). The scaffolded assembly was error-corrected with a novel pipeline, polishCLR. The mitochondrial genome was assembled through an improved pipeline and annotated. Assessment of this genome assembly indicated 98.8% of the Lepidopteran Benchmark Universal Single-Copy Ortholog set were complete (98.5% as complete single copy). Repetitive elements comprised approximately 29.5% of the assembly with the plurality (11.2%) classified as retroelements. This chromosome-scale reference assembly for H. zea, ilHelZeax1.1, will facilitate future research to evaluate and enhance sustainable crop production practices.}, } @article {pmid35955104, year = {2022}, author = {Zhou, X and Shen, D and Gu, X}, title = {Influences of Land Policy on Urban Ecological Corridors Governance: A Case Study from Shanghai.}, journal = {International journal of environmental research and public health}, volume = {19}, number = {15}, pages = {}, pmid = {35955104}, issn = {1660-4601}, mesh = {Agriculture ; China ; Cities ; Conservation of Natural Resources ; Ecosystem ; *Forests ; *Policy ; }, abstract = {The analysis of land use change (LUC) characteristics and the impact of policies related to urban ecological space is required to improve spatial planning and to support decision making regarding green infrastructure (GI) investment. This study employed Geo-informatic Tupu analysis and Fluctuation Potential Tupu analysis methods to analyze the characteristics of LUC in an urban ecological corridor (EC). To help understand the influence of land use policy on GI governance and support the optimization of spatial planning, we proposed a situation-structure-implementation-outcome (SSIO) policy cascade analysis framework. SSIO takes "place" as its starting point, then couples the local policy with the governance structure to promote the sustainability of urban commons governance. The results show that the land use type within an EC in the city is mainly cultivated land. However, between 2009 and 2019, cultivated land, construction land, and facility agricultural land all showed a decreasing trend, while forest land and garden land types underwent increasing trends. The LUC Tupu unit highlights the transition from cultivated land to forest land. Forest land has the greatest increase in area and accounts for 52.34% of the area of increasing land use. Cultivated land shows the greatest decrease in area and accounts for 70.30% of the area of decreasing trends. Based on the local policy situation of the metropolis, a land policy governance mechanism can be constructed by the establishment of a governance structure with local government as the core, using land consolidation as the platform, taking ecological spatial planning and inefficient construction land reduction as typical policy tools, and experimentally integrating the concept of Nature-based Solutions (NbS). In general, these findings may be applicable to other rapidly urbanizing cities around the world that are developing complex land use policies for ecological space governance.}, } @article {pmid35954991, year = {2022}, author = {Wang, Q and Yang, K and Li, L and Zhu, Y}, title = {Assessing the Terrain Gradient Effect of Landscape Ecological Risk in the Dianchi Lake Basin of China Using Geo-Information Tupu Method.}, journal = {International journal of environmental research and public health}, volume = {19}, number = {15}, pages = {}, pmid = {35954991}, issn = {1660-4601}, mesh = {China ; *Conservation of Natural Resources ; Ecosystem ; Geographic Information Systems ; *Lakes ; Risk Assessment/methods ; }, abstract = {The assessment of landscape ecological risk (LER) in different terrain gradients is beneficial to ecological environmental protection and risk management in different terrain gradients. Due to the impact of urban expansion, the landscape pattern of the Dianchi Lake basin (DLB) changed obviously, resulting in significant spatial difference of LER. At present, the LER assessment of the DLB is not clear, and the evolution mechanism of LER in different terrain gradients has not been revealed. Based on the LER assessment model, the geo-information Tupu method, the terrain niche gradient, and distribution index, this paper analyzed the LER and its terrain gradient effect in the DLB of China. The conclusions are as follows: (1) Since 1995, the land use type has mainly changed from grassland and cultivated land to construction land in the DLB of China. (2) The LERs in the DLB of China were mainly low, med low, and med high due to the transformation of land use type. The dominance distribution of the low and high LER was obviously constrained by terrain gradient. While the dominance distribution of med-low LER expanded to med-high terrain gradient, the dominance distribution of the med-high LER decreased to med-low terrain gradient. (3) The Tupu LERs were mainly a stable type of "medium" risk and anaphase change type of "med-high to medium" risk. The dominant distribution regions of the stable type, the prophase change type, and the continuous change type were relatively stable; the anaphase and middle change type expanded to the higher terrain gradient, and the repeated change type decreased to the med-high terrain gradient. In the process of ecological risk management and protection in the DLB, attention should be paid to the water area structure and LER control in med-high and high terrain gradients.}, } @article {pmid35954559, year = {2022}, author = {Lamberti-Castronuovo, A and Valente, M and Aleni, C and Hubloue, I and Ragazzoni, L and Barone-Adesi, F}, title = {Using Ambulatory Care Sensitive Conditions to Assess Primary Health Care Performance during Disasters: A Systematic Review.}, journal = {International journal of environmental research and public health}, volume = {19}, number = {15}, pages = {}, pmid = {35954559}, issn = {1660-4601}, mesh = {Ambulatory Care ; Ambulatory Care Sensitive Conditions ; Databases, Factual ; *Disasters ; Hospitalization ; Humans ; *Primary Health Care ; }, abstract = {Ambulatory care sensitive conditions (ACSCs) are health conditions for which appropriate primary care intervention could prevent hospital admission. ACSC hospitalization rates are a well-established parameter for assessing the performance of primary health care (PHC). Although this indicator has been extensively used to monitor the performance of PHC systems in peacetime, its consideration during disasters has been neglected. The World Health Organization (WHO) has acknowledged the importance of PHC in guaranteeing continuity of care during and after a disaster for avoiding negative health outcomes. We conducted a systematic review to evaluate the extent and nature of research activity on the use of ACSCs during disasters, with an eye toward finding innovative ways to assess the level of PHC function at times of crisis. Online databases were searched to identify papers. A final list of nine publications was retrieved. The analysis of the reviewed articles confirmed that ACSCs can serve as a useful indicator of PHC performance during disasters, with several caveats that must be considered. The reviewed articles cover several disaster scenarios and a wide variety of methodologies showing the connection between ACSCs and health system performance. The strengths and weaknesses of using different methodologies are explored and recommendations are given for using ACSCs to assess PHC performance during disasters.}, } @article {pmid35951711, year = {2022}, author = {Nishimura, T and Tokuda, IT and Miyachi, S and Dunn, JC and Herbst, CT and Ishimura, K and Kaneko, A and Kinoshita, Y and Koda, H and Saers, JPP and Imai, H and Matsuda, T and Larsen, ON and Jürgens, U and Hirabayashi, H and Kojima, S and Fitch, WT}, title = {Evolutionary loss of complexity in human vocal anatomy as an adaptation for speech.}, journal = {Science (New York, N.Y.)}, volume = {377}, number = {6607}, pages = {760-763}, doi = {10.1126/science.abm1574}, pmid = {35951711}, issn = {1095-9203}, mesh = {Animals ; *Biological Evolution ; Humans ; *Larynx/anatomy & histology ; *Phonation ; Phonetics ; *Primates ; *Speech ; Speech Acoustics ; *Vocal Cords/anatomy & histology ; }, abstract = {Human speech production obeys the same acoustic principles as vocal production in other animals but has distinctive features: A stable vocal source is filtered by rapidly changing formant frequencies. To understand speech evolution, we examined a wide range of primates, combining observations of phonation with mathematical modeling. We found that source stability relies upon simplifications in laryngeal anatomy, specifically the loss of air sacs and vocal membranes. We conclude that the evolutionary loss of vocal membranes allows human speech to mostly avoid the spontaneous nonlinear phenomena and acoustic chaos common in other primate vocalizations. This loss allows our larynx to produce stable, harmonic-rich phonation, ideally highlighting formant changes that convey most phonetic information. Paradoxically, the increased complexity of human spoken language thus followed simplification of our laryngeal anatomy.}, } @article {pmid35947263, year = {2023}, author = {Liu, S and Zhang, Y and Cai, J}, title = {Operation of high-speed rail and reduction of corporate pollution: evidence from China.}, journal = {Environmental science and pollution research international}, volume = {30}, number = {2}, pages = {3562-3575}, pmid = {35947263}, issn = {1614-7499}, mesh = {Humans ; China ; *Asian People ; Databases, Factual ; *Economic Development ; Environmental Pollution ; }, abstract = {As an environmentally friendly means of transport, the high-speed rail (HSR) is conducive to promoting corporate performance. An innovative approach extends the impact of HSR networks on pollution emissions from the regional level to the micro-enterprise level. Based on the quasi-natural experiment of the opening of HSR, a difference-in-difference model is used to investigate the impact of HSR on enterprise pollution emission levels and its action mechanism by using the matched data from the Chinese Enterprise Pollution Emission Database, the Chinese Industrial Enterprise Database, and the Chinese City Statistical Yearbook from 2000 to 2010. The results show that opening HSR significantly reduces the enterprises' pollution emission level, while reducing the number of polluting enterprises and transportation costs as well as improving the innovation capacity of enterprises are the corresponding action mechanisms. The impact of HSR on the enterprises' pollution emission varies with industry intensity, population size, and regional economic development level. The conclusions not only provide important insights to increase the ecological quality of China's environment through transportation infrastructure upgrades but also bring some guidance to more developing countries to improve their air environment.}, } @article {pmid35946638, year = {2022}, author = {Andrade, GM and Gil, AO and Barbosa, ARG and Teles, SB and Amaral, BS and Monteiro, J and Apezzato, M and Bianco, B and Lemos, GC and Carneiro, A}, title = {Analysis of adrenalectomy for the treatment of adrenal diseases performed by the Public Health Service in São Paulo between 2008 and 2019.}, journal = {Revista do Colegio Brasileiro de Cirurgioes}, volume = {49}, number = {}, pages = {e20223320}, pmid = {35946638}, issn = {1809-4546}, mesh = {*Adrenalectomy/methods ; Brazil ; Hospitals, High-Volume ; Humans ; Length of Stay ; *Surgeons ; }, abstract = {INTRODUCTION: treating benign (hormonally active or nonfunctional) and malignant adrenal cancer includes adrenalectomy. The expertise of surgeons and surgery performed by high-volume surgeons were associated with fewer complications and lower cost. We aimed to describe and compare the number of surgeries, mortality rate, and length of hospital stay for adrenalectomies performed between 2008 and 2019 in the public health system of São Paulo.

METHODS: this was an ecological study. The data were collected using the TabNet Platform of the Unified Health System Department of Informatics. Outcomes analyzed included the number of surgeries performed, mortality rate during hospital stay, and length of hospital stay. Public hospitals in Sao Paulo were divided into three subgroups according to the surgical volume of adrenalectomies performed as well as hospitals with and without a residency program in Urology, and the results were compared among them.

RESULTS: a total of 943 adrenalectomies were performed in Sao Paulo between 2008 and 2019. Mortality rates during hospital stay according to hospital surgical volume were no reported deaths in low-volume, 0.015% in intermediate-volume, and 0.004% in high-volume hospitals. The average length of the ICU stay was 1.03 days in low-volume, 2.8 in intermediate-volume, and 1.12 in high-volume hospitals (analysis between intermediate and high volume centers with statistical significance, p=0.016).

CONCLUSIONS: despite no statistically significant differences among the groups analyzed, mortality rates were very low in all groups. ICU stay was shorter in high-volume centers than in intermediate-volume centers.}, } @article {pmid35933453, year = {2022}, author = {Wang, Z and Yang, S and Luo, L and Guo, X and Deng, B and Zhao, Z and Rui, J and Yu, S and Zhao, B and Wang, Y and Chen, J and Sun, Y and Chen, T and Feng, X}, title = {Epidemiological characteristics of severe fever with thrombocytopenia syndrome and its relationship with meteorological factors in Liaoning Province, China.}, journal = {Parasites & vectors}, volume = {15}, number = {1}, pages = {283}, pmid = {35933453}, issn = {1756-3305}, mesh = {China/epidemiology ; Humans ; Incidence ; Male ; Meteorological Concepts ; *Severe Fever with Thrombocytopenia Syndrome ; Temperature ; }, abstract = {BACKGROUND: Severe fever with thrombocytopenia syndrome (SFTS), one kind of tick-borne acute infectious disease, is caused by a novel bunyavirus. The relationship between meteorological factors and infectious diseases is a hot topic of current research. Liaoning Province has reported a high incidence of SFTS in recent years. However, the epidemiological characteristics of SFTS and its relationship with meteorological factors in the province remain largely unexplored.

METHODS: Data on reported SFTS cases were collected from 2011 to 2019. Epidemiological characteristics of SFTS were analyzed. Spearman's correlation test and generalized linear models (GLM) were used to identify the relationship between meteorological factors and the number of SFTS cases.

RESULTS: From 2011 to 2019, the incidence showed an overall upward trend in Liaoning Province, with the highest incidence in 2019 (0.35/100,000). The incidence was slightly higher in males (55.9%, 438/783), and there were more SFTS patients in the 60-69 age group (31.29%, 245/783). Dalian City and Dandong City had the largest number of cases of SFTS (87.99%, 689/783). The median duration from the date of illness onset to the date of diagnosis was 8 days [interquartile range (IQR): 4-13 days]. Spearman correlation analysis and GLM showed that the number of SFTS cases was positively correlated with monthly average rainfall (rs = 0.750, P < 0.001; β = 0.285, P < 0.001), monthly average relative humidity (rs = 0.683, P < 0.001; β = 0.096, P < 0.001), monthly average temperature (rs = 0.822, P < 0.001; β = 0.154, P < 0.001), and monthly average ground temperature (rs = 0.810, P < 0.001; β = 0.134, P < 0.001), while negatively correlated with monthly average air pressure (rs = -0.728, P < 0.001; β = -0.145, P < 0.001), and monthly average wind speed (rs = -0.272, P < 0.05; β = -1.048, P < 0.001). By comparing both correlation coefficients and regression coefficients between the number of SFTS cases (dependent variable) and meteorological factors (independent variables), no significant differences were observed when considering immediate cases and cases with lags of 1 to 5 weeks for dependent variables. Based on the forward and backward stepwise GLM regression, the monthly average air pressure, monthly average temperature, monthly average wind speed, and time sequence were selected as relevant influences on the number of SFTS cases.

CONCLUSION: The annual incidence of SFTS increased year on year in Liaoning Province. Incidence of SFTS was affected by several meteorological factors, including monthly average air pressure, monthly average temperature, and monthly average wind speed.}, } @article {pmid35933090, year = {2022}, author = {Sun, Z and Wang, Y and Song, Z and Zhang, H and Wang, Y and Liu, K and Ma, M and Wang, P and Fang, Y and Cai, D and Li, G and Fang, Y}, title = {DNA methylation in transposable elements buffers the connection between three-dimensional chromatin organization and gene transcription upon rice genome duplication.}, journal = {Journal of advanced research}, volume = {42}, number = {}, pages = {41-53}, pmid = {35933090}, issn = {2090-1224}, mesh = {*DNA Transposable Elements/genetics ; *Oryza/genetics ; DNA Methylation ; Gene Duplication ; Chromatin/genetics ; Transcription, Genetic/genetics ; }, abstract = {INTRODUCTION: Polyploidy is a major force in plant evolution and the domestication of cultivated crops.

OBJECTIVES: The study aimed to explore the relationship and underlying mechanism between three-dimensional (3D) chromatin organization and gene transcription upon rice genome duplication.

METHODS: The 3D chromatin structures between diploid (2C) and autotetraploid (4C) rice were compared using high-throughput chromosome conformation capture (Hi-C) analysis. The study combined genetics, transcriptomics, whole-genome bisulfite sequencing (WGBS-seq) and 3D genomics approaches to uncover the mechanism for DNA methylation in modulating gene transcription through 3D chromatin architectures upon rice genome duplication.

RESULTS: We found that 4C rice presents weakened intra-chromosomal interactions compared to its 2C progenitor in some chromosomes. In addition, we found that changes of 3D chromatin organizations including chromatin compartments, topologically associating domains (TADs), and loops, are uncorrelated with gene transcription. Moreover, DNA methylations in the regulatory sequences of genes in compartment A/B switched regions and TAD boundaries are unrelated to their expression. Importantly, although there was no significant difference in the methylation levels in transposable elements (TEs) in differentially expressed gene (DEG) and non-DEG promoters between 2C and 4C rice, we found that the hypermethylated TEs across genes in compartment A/B switched regions and TAD boundaries may suppress the expression of these genes.

CONCLUSION: The study proposed that the rice genome doubling might modulate TE methylation to buffer the effects of chromatin architecture on gene transcription in compartment A/B switched regions and TAD boundaries, resulting in the disconnection between 3D chromatin structure alteration and gene transcription upon rice genome duplication.}, } @article {pmid35932855, year = {2022}, author = {Zhang, X and Manzanedo, RD and Lv, P and Xu, C and Hou, M and Huang, X and Rademacher, T}, title = {Reduced diurnal temperature range mitigates drought impacts on larch tree growth in North China.}, journal = {The Science of the total environment}, volume = {848}, number = {}, pages = {157808}, doi = {10.1016/j.scitotenv.2022.157808}, pmid = {35932855}, issn = {1879-1026}, mesh = {China ; Climate Change ; Droughts ; Forests ; *Larix ; Temperature ; Trees ; }, abstract = {Forests are facing climate changes such as warmer temperatures, accelerated snowmelt, increased drought, as well as changing diurnal temperature ranges (DTR) and cloud cover regimes. How tree growth is influenced by the changes in daily to monthly temperatures and its associations with droughts has been extensively investigated, however, few studies have focused on how changes in sub-daily temperatures i.e., DTR, influence tree growth during drought events. Here, we used a network of Larix principis-rupprechtii tree-ring data from 1989 to 2018, covering most of the distribution of planted larch across North China, to investigate how DTR, cloud cover and their interactions influence the relationship between drought stress and tree growth. DTR showed a negative correlation with larch growth in 95 % of sites (rmean = -0.30, significant in 42 % of sites). Cloud cover was positively correlated with growth in 87 % of sites (rmean = 0.13, significant in 5 % of sites). Enhanced tree growth was found at lower DTR in the absence of severe drought. Our findings highlight that in the absence of severe droughts, reduced DTR benefits tree growth, while increased cloud cover tended to benefit tree growth only during severe drought periods. Given how DTR influences drought impacts on tree growth, net tree growth was found to be larger in regions with smaller DTR.}, } @article {pmid35930452, year = {2024}, author = {Li, T and Chen, X and Wang, X and Zhao, L and Zhou, X and Zou, A and Ikhumhen, HO}, title = {Grid computing method for atmospheric environmental capacity coupled with ventilation coefficient using CALPUFF simulation and GIS spatial analysis technology.}, journal = {Environmental technology}, volume = {45}, number = {2}, pages = {294-305}, doi = {10.1080/09593330.2022.2109993}, pmid = {35930452}, issn = {1479-487X}, mesh = {*Air Pollution/prevention & control ; Particulate Matter ; Geographic Information Systems ; *Air Pollutants/analysis ; China ; Spatial Analysis ; Environmental Monitoring/methods ; }, abstract = {Atmospheric environmental issues have evolved from point source pollution to regional pollution, leading to controlling specific air pollutant emissions. A-value method has been found suitable for estimating large-scale atmospheric environmental capacity rather than small-scale, resulting in the inaccuracy of developing air pollution control strategy. This study proposed a grid computing method based on the CALPUFF modelling system and GIS spatial analysis tool. The meteorological data from the MM5 model were used to simulate the spatial distribution of air pollutants. The meteorological flow field data was used to simulate the ventilation coefficient. The A value was revised with the simulated to achieve accurate results of atmospheric environment capacity. The credibility was verified by applying this method to Fengtai District, Beijing, China. The research area was divided into small partitions via the ArcGIS spatial analysis tool. The simulation results agreed well with the observation data from actual monitoring stations, even for the PM10 concentration with the most significant error (MRE: 7.05%-13.28%, RMSE: 11.62-17.89, R[2]: 0.84-0.90). The GIS spatial analysis tools were applied to match the underlying surface types and overcome the restrictions of administrative boundary management. The study proposed four schemes to achieve differentiated air pollutant emission reduction and develop suitable control strategies. Furthermore, this method can be applied on different scales of natural geographic boundaries and realize the precise spatial management of atmospheric environmental capacity.}, } @article {pmid35930070, year = {2022}, author = {Chakraborty, H and Kayal, T and Lianthuamluaia, L and Sarkar, UK and Das, AK and Chakraborty, S and Sahoo, BK and Mondal, K and Mandal, S and Das, BK}, title = {Use of geographical information systems (GIS) in assessing ecological profile, fish community structure and production of a large reservoir of Himachal Pradesh.}, journal = {Environmental monitoring and assessment}, volume = {194}, number = {9}, pages = {643}, doi = {10.1007/s10661-022-10292-5}, pmid = {35930070}, issn = {1573-2959}, mesh = {Animals ; *Biodiversity ; Ecosystem ; Environmental Monitoring ; Fishes ; *Geographic Information Systems ; Water ; }, abstract = {The present study demonstrates the spatial analysis and mapping of fish and different measures of environmental parameters and fish diversity of Pong reservoir, Himachal Pradesh, using Kriging spatial interpolation methods for geographical information system mapping. Seasonal data on environmental parameters, potential fish habitat and fish diversity was collected from lentic (dam), lentic (reservoir), transitional and lotic zone of the reservoir.. Important environmental parameters like water temperature, dissolved oxygen, electrical conductivity, water depth and transparency showed variations across the different zones of the reservoir. The sediment of the reservoir was sandy clay loam in nature as per texture analysis. Fish species richness, Shannon index and evenness index showed a similarity of the lotic and lentic (reservoir) zones of the reservoir. Six potential fish breeding grounds were identified in the reservoir indicating high conservation significance. The analysis of data showed a declining trend in fish production from 456.9 tonnes during the decade 1976-1987 to 347.91 tonnes during 2009-2020. The factors like anthropogenic climate change, predation of a stocked fish juvenile by water birds, undersized fish stocking and unscientific management are the probable reasons for the decreasing fish production. The spatial variation pattern of the water spread area, environmental parameters, fish catch and potential fish breeding grounds depicted in the GIS platform can be used as an important information base by the policy makers for fisheries management. The stocking of large size fish as a stocking material and adequate protection of the potential fish breeding grounds are the key advisories for the sustainable enhancement of fisheries as well as conservation.}, } @article {pmid35927942, year = {2022}, author = {Rademacher, T and Fonti, P and LeMoine, JM and Fonti, MV and Bowles, F and Chen, Y and Eckes-Shephard, AH and Friend, AD and Richardson, AD}, title = {Insights into source/sink controls on wood formation and photosynthesis from a stem chilling experiment in mature red maple.}, journal = {The New phytologist}, volume = {236}, number = {4}, pages = {1296-1309}, doi = {10.1111/nph.18421}, pmid = {35927942}, issn = {1469-8137}, mesh = {*Acer ; Wood/physiology ; Photosynthesis ; Trees/physiology ; Carbon/analysis ; Plant Leaves/physiology ; }, abstract = {Whether sources or sinks control wood growth remains debated with a paucity of evidence from mature trees in natural settings. Here, we altered carbon supply rate in stems of mature red maples (Acer rubrum) within the growing season by restricting phloem transport using stem chilling; thereby increasing carbon supply above and decreasing carbon supply below the restrictions, respectively. Chilling successfully altered nonstructural carbon (NSC) concentrations in the phloem without detectable repercussions on bulk NSC in stems and roots. Ring width responded strongly to local variations in carbon supply with up to seven-fold differences along the stem of chilled trees; however, concurrent changes in the structural carbon were inconclusive at high carbon supply due to large local variability of wood growth. Above chilling-induced bottlenecks, we also observed higher leaf NSC concentrations, reduced photosynthetic capacity, and earlier leaf coloration and fall. Our results indicate that the cambial sink is affected by carbon supply, but within-tree feedbacks can downregulate source activity, when carbon supply exceeds demand. Such feedbacks have only been hypothesized in mature trees. Consequently, these findings constitute an important advance in understanding source-sink dynamics, suggesting that mature red maples operate close to both source- and sink-limitation in the early growing season.}, } @article {pmid35927319, year = {2022}, author = {Jang, SK and Evans, L and Fialkowski, A and Arnett, DK and Ashley-Koch, AE and Barnes, KC and Becker, DM and Bis, JC and Blangero, J and Bleecker, ER and Boorgula, MP and Bowden, DW and Brody, JA and Cade, BE and Jenkins, BWC and Carson, AP and Chavan, S and Cupples, LA and Custer, B and Damrauer, SM and David, SP and de Andrade, M and Dinardo, CL and Fingerlin, TE and Fornage, M and Freedman, BI and Garrett, ME and Gharib, SA and Glahn, DC and Haessler, J and Heckbert, SR and Hokanson, JE and Hou, L and Hwang, SJ and Hyman, MC and Judy, R and Justice, AE and Kaplan, RC and Kardia, SLR and Kelly, S and Kim, W and Kooperberg, C and Levy, D and Lloyd-Jones, DM and Loos, RJF and Manichaikul, AW and Gladwin, MT and Martin, LW and Nouraie, M and Melander, O and Meyers, DA and Montgomery, CG and North, KE and Oelsner, EC and Palmer, ND and Payton, M and Peljto, AL and Peyser, PA and Preuss, M and Psaty, BM and Qiao, D and Rader, DJ and Rafaels, N and Redline, S and Reed, RM and Reiner, AP and Rich, SS and Rotter, JI and Schwartz, DA and Shadyab, AH and Silverman, EK and Smith, NL and Smith, JG and Smith, AV and Smith, JA and Tang, W and Taylor, KD and Telen, MJ and Vasan, RS and Gordeuk, VR and Wang, Z and Wiggins, KL and Yanek, LR and Yang, IV and Young, KA and Young, KL and Zhang, Y and Liu, DJ and Keller, MC and Vrieze, S}, title = {Rare genetic variants explain missing heritability in smoking.}, journal = {Nature human behaviour}, volume = {6}, number = {11}, pages = {1577-1586}, pmid = {35927319}, issn = {2397-3374}, support = {HHSN268201800003I/HL/NHLBI NIH HHS/United States ; HHSN268201800007I/HL/NHLBI NIH HHS/United States ; R01 HL119443/HL/NHLBI NIH HHS/United States ; HHSN268201700001I/HL/NHLBI NIH HHS/United States ; R01 DA037904/DA/NIDA NIH HHS/United States ; R01 HG011035/HG/NHGRI NIH HHS/United States ; R01 AG058921/AG/NIA NIH HHS/United States ; HHSN268201500014C/HL/NHLBI NIH HHS/United States ; R01 HL120393/HL/NHLBI NIH HHS/United States ; HHSN268201500001I/HL/NHLBI NIH HHS/United States ; N01HC85081/HL/NHLBI NIH HHS/United States ; HHSN268201800005I/HL/NHLBI NIH HHS/United States ; U19 CA203654/CA/NCI NIH HHS/United States ; R03 OD032630/OD/NIH HHS/United States ; R01 EB015611/EB/NIBIB NIH HHS/United States ; U01 HL120393/HL/NHLBI NIH HHS/United States ; R01 HL153805/HL/NHLBI NIH HHS/United States ; N01HC55222/HL/NHLBI NIH HHS/United States ; R01 HL113338/HL/NHLBI NIH HHS/United States ; HHSN268201800012I/HB/NHLBI NIH HHS/United States ; 75N92019D00031/HL/NHLBI NIH HHS/United States ; N01HC85082/HL/NHLBI NIH HHS/United States ; F32 HL085989/HL/NHLBI NIH HHS/United States ; HHSN268201700005I/HL/NHLBI NIH HHS/United States ; R01 HL105756/HL/NHLBI NIH HHS/United States ; R01 HL113323/HL/NHLBI NIH HHS/United States ; HHSN268201700004I/HL/NHLBI NIH HHS/United States ; R35 HL135818/HL/NHLBI NIH HHS/United States ; R01 HG008983/HG/NHGRI NIH HHS/United States ; HHSN268201800001C/HL/NHLBI NIH HHS/United States ; IK2 CX001780/CX/CSRD VA/United States ; HHSN268201200036C/HL/NHLBI NIH HHS/United States ; HHSN268201800011I/HB/NHLBI NIH HHS/United States ; U01 HL089856/HL/NHLBI NIH HHS/United States ; HHSN268201700003I/HL/NHLBI NIH HHS/United States ; HHSN268201800010I/HB/NHLBI NIH HHS/United States ; HHSN268200800007C/HL/NHLBI NIH HHS/United States ; 75N92021D00006/HL/NHLBI NIH HHS/United States ; U01 HL054457/HL/NHLBI NIH HHS/United States ; R01 DK071891/DK/NIDDK NIH HHS/United States ; R01 HL085571/HL/NHLBI NIH HHS/United States ; R01 MH100141/MH/NIMH NIH HHS/United States ; HHSN268201700002I/HL/NHLBI NIH HHS/United States ; R01 HL117626/HL/NHLBI NIH HHS/United States ; N01HC85080/HL/NHLBI NIH HHS/United States ; HHSN268201800006I/HL/NHLBI NIH HHS/United States ; R01 NS058700/NS/NINDS NIH HHS/United States ; R01 HL087660/HL/NHLBI NIH HHS/United States ; HHSN268201800013I/MD/NIMHD NIH HHS/United States ; U01 HL089897/HL/NHLBI NIH HHS/United States ; HHSN268201100007I/HL/NHLBI NIH HHS/United States ; HHSN268201800004I/HL/NHLBI NIH HHS/United States ; R01 DA044283/DA/NIDA NIH HHS/United States ; U01 HL054464/HL/NHLBI NIH HHS/United States ; N01HC85086/HL/NHLBI NIH HHS/United States ; N01HC85079/HL/NHLBI NIH HHS/United States ; }, mesh = {*Genome-Wide Association Study ; Gene Frequency ; *Polymorphism, Single Nucleotide/genetics ; Phenotype ; Smoking/genetics ; }, abstract = {Common genetic variants explain less variation in complex phenotypes than inferred from family-based studies, and there is a debate on the source of this 'missing heritability'. We investigated the contribution of rare genetic variants to tobacco use with whole-genome sequences from up to 26,257 unrelated individuals of European ancestries and 11,743 individuals of African ancestries. Across four smoking traits, single-nucleotide-polymorphism-based heritability ([Formula: see text]) was estimated from 0.13 to 0.28 (s.e., 0.10-0.13) in European ancestries, with 35-74% of it attributable to rare variants with minor allele frequencies between 0.01% and 1%. These heritability estimates are 1.5-4 times higher than past estimates based on common variants alone and accounted for 60% to 100% of our pedigree-based estimates of narrow-sense heritability ([Formula: see text], 0.18-0.34). In the African ancestry samples, [Formula: see text] was estimated from 0.03 to 0.33 (s.e., 0.09-0.14) across the four smoking traits. These results suggest that rare variants are important contributors to the heritability of smoking.}, } @article {pmid35925968, year = {2022}, author = {Xu, W and Yi, J and Shuai, J and Yu, Z and Cheng, J}, title = {Dynamic evaluation of the ecological civilization of Jiangxi Province: GIS and AHP approaches.}, journal = {PloS one}, volume = {17}, number = {8}, pages = {e0271768}, pmid = {35925968}, issn = {1932-6203}, mesh = {China ; Cities ; *Civilization ; Conservation of Natural Resources ; Ecosystem ; Environment ; *Geographic Information Systems ; Humans ; }, abstract = {Faced with the increasingly severe ecological environment, China promotes the construction of ecological civilization vigorously. Therefore, it is of great significance to adopt scientific, effective and comprehensive methods to evaluate development status of ecological civilization. Based on the panel data from 2010 to 2014, this paper employs GIS and AHP methods to dynamically examine the level of ecological civilization construction in Jiangxi Province. The results indicate that: (1) The ecological civilization construction in Jiangxi Province is 13.23% higher than the national average, whereas there is an imbalance in the development of different cities within the province; (2) The ecological civilization construction in the whole province rises first and then falls; (3) The performances of the cities vary in different dimensions of the construction of ecological civilization that cities in Jiangxi province perform well in the dimension of ecological environment, but perform poorly in the dimension of social development. Finally, we put forward policy recommendations for improving ecological environment to realize harmonious development between human and nature.}, } @article {pmid35925662, year = {2022}, author = {Martinez, GJ and Grover, T and Mattingly, SM and Mark, G and D'Mello, S and Aledavood, T and Akbar, F and Robles-Granda, P and Striegel, A}, title = {Alignment Between Heart Rate Variability From Fitness Trackers and Perceived Stress: Perspectives From a Large-Scale In Situ Longitudinal Study of Information Workers.}, journal = {JMIR human factors}, volume = {9}, number = {3}, pages = {e33754}, pmid = {35925662}, issn = {2292-9495}, support = {R21 NR018972/NR/NINR NIH HHS/United States ; }, abstract = {BACKGROUND: Stress can have adverse effects on health and well-being. Informed by laboratory findings that heart rate variability (HRV) decreases in response to an induced stress response, recent efforts to monitor perceived stress in the wild have focused on HRV measured using wearable devices. However, it is not clear that the well-established association between perceived stress and HRV replicates in naturalistic settings without explicit stress inductions and research-grade sensors.

OBJECTIVE: This study aims to quantify the strength of the associations between HRV and perceived daily stress using wearable devices in real-world settings.

METHODS: In the main study, 657 participants wore a fitness tracker and completed 14,695 ecological momentary assessments (EMAs) assessing perceived stress, anxiety, positive affect, and negative affect across 8 weeks. In the follow-up study, approximately a year later, 49.8% (327/657) of the same participants wore the same fitness tracker and completed 1373 EMAs assessing perceived stress at the most stressful time of the day over a 1-week period. We used mixed-effects generalized linear models to predict EMA responses from HRV features calculated over varying time windows from 5 minutes to 24 hours.

RESULTS: Across all time windows, the models explained an average of 1% (SD 0.5%; marginal R[2]) of the variance. Models using HRV features computed from an 8 AM to 6 PM time window (namely work hours) outperformed other time windows using HRV features calculated closer to the survey response time but still explained a small amount (2.2%) of the variance. HRV features that were associated with perceived stress were the low frequency to high frequency ratio, very low frequency power, triangular index, and SD of the averages of normal-to-normal intervals. In addition, we found that although HRV was also predictive of other related measures, namely, anxiety, negative affect, and positive affect, it was a significant predictor of stress after controlling for these other constructs. In the follow-up study, calculating HRV when participants reported their most stressful time of the day was less predictive and provided a worse fit (R[2]=0.022) than the work hours time window (R[2]=0.032).

CONCLUSIONS: A significant but small relationship between perceived stress and HRV was found. Thus, although HRV is associated with perceived stress in laboratory settings, the strength of that association diminishes in real-life settings. HRV might be more reflective of perceived stress in the presence of specific and isolated stressors and research-grade sensing. Relying on wearable-derived HRV alone might not be sufficient to detect stress in naturalistic settings and should not be considered a proxy for perceived stress but rather a component of a complex phenomenon.}, } @article {pmid35924138, year = {2022}, author = {McCall, T and Asuzu, K and Oladele, CR and Leung, TI and Wang, KH}, title = {A Socio-Ecological Approach to Addressing Digital Redlining in the United States: A Call to Action for Health Equity.}, journal = {Frontiers in digital health}, volume = {4}, number = {}, pages = {897250}, pmid = {35924138}, issn = {2673-253X}, support = {R01 LM013477/LM/NLM NIH HHS/United States ; }, abstract = {Physical distancing requirements due to the coronavirus (COVID-19) pandemic has increased the need for broadband internet access. The World Health Organization defines social determinants of health as non-medical factors that impact health outcomes by affecting the conditions in which people are born, grow, work, live, and age. By this definition broadband internet access is a social determinant of health. Digital redlining-the systematic process by which specific groups are deprived of equal access to digital tools such as the internet-creates inequities in access to educational and employment opportunities, as well as healthcare and health information. Although it is known that internet service providers systematically exclude low-income communities from broadband service, little has been done to stop this discriminatory practice. In this paper, we seek to amplify the call to action against the practice of digital redlining in the United States, describe how it contributes to health disparities broadly and within the context of the COVID-19 pandemic, and use a socio-ecological framework to propose short- and long-term actions to address this inequity.}, } @article {pmid35923402, year = {2022}, author = {Derx, J and Demeter, K and Linke, R and Cervero-Aragó, S and Lindner, G and Stalder, G and Schijven, J and Sommer, R and Walochnik, J and Kirschner, AKT and Komma, J and Blaschke, AP and Farnleitner, AH}, title = {Corrigendum: Genetic microbial source tracking support QMRA modeling for a riverine wetland drinking water resource.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {973379}, doi = {10.3389/fmicb.2022.973379}, pmid = {35923402}, issn = {1664-302X}, abstract = {[This corrects the article DOI: 10.3389/fmicb.2021.668778.].}, } @article {pmid35922501, year = {2022}, author = {Kreibich, H and Van Loon, AF and Schröter, K and Ward, PJ and Mazzoleni, M and Sairam, N and Abeshu, GW and Agafonova, S and AghaKouchak, A and Aksoy, H and Alvarez-Garreton, C and Aznar, B and Balkhi, L and Barendrecht, MH and Biancamaria, S and Bos-Burgering, L and Bradley, C and Budiyono, Y and Buytaert, W and Capewell, L and Carlson, H and Cavus, Y and Couasnon, A and Coxon, G and Daliakopoulos, I and de Ruiter, MC and Delus, C and Erfurt, M and Esposito, G and François, D and Frappart, F and Freer, J and Frolova, N and Gain, AK and Grillakis, M and Grima, JO and Guzmán, DA and Huning, LS and Ionita, M and Kharlamov, M and Khoi, DN and Kieboom, N and Kireeva, M and Koutroulis, A and Lavado-Casimiro, W and Li, HY and LLasat, MC and Macdonald, D and Mård, J and Mathew-Richards, H and McKenzie, A and Mejia, A and Mendiondo, EM and Mens, M and Mobini, S and Mohor, GS and Nagavciuc, V and Ngo-Duc, T and Thao Nguyen Huynh, T and Nhi, PTT and Petrucci, O and Nguyen, HQ and Quintana-Seguí, P and Razavi, S and Ridolfi, E and Riegel, J and Sadik, MS and Savelli, E and Sazonov, A and Sharma, S and Sörensen, J and Arguello Souza, FA and Stahl, K and Steinhausen, M and Stoelzle, M and Szalińska, W and Tang, Q and Tian, F and Tokarczyk, T and Tovar, C and Tran, TVT and Van Huijgevoort, MHJ and van Vliet, MTH and Vorogushyn, S and Wagener, T and Wang, Y and Wendt, DE and Wickham, E and Yang, L and Zambrano-Bigiarini, M and Blöschl, G and Di Baldassarre, G}, title = {The challenge of unprecedented floods and droughts in risk management.}, journal = {Nature}, volume = {608}, number = {7921}, pages = {80-86}, pmid = {35922501}, issn = {1476-4687}, mesh = {Climate Change/statistics & numerical data ; Datasets as Topic ; *Droughts/prevention & control/statistics & numerical data ; *Extreme Weather ; *Floods/prevention & control/statistics & numerical data ; Humans ; Hydrology ; Internationality ; *Risk Management/methods/statistics & numerical data/trends ; }, abstract = {Risk management has reduced vulnerability to floods and droughts globally[1,2], yet their impacts are still increasing[3]. An improved understanding of the causes of changing impacts is therefore needed, but has been hampered by a lack of empirical data[4,5]. On the basis of a global dataset of 45 pairs of events that occurred within the same area, we show that risk management generally reduces the impacts of floods and droughts but faces difficulties in reducing the impacts of unprecedented events of a magnitude not previously experienced. If the second event was much more hazardous than the first, its impact was almost always higher. This is because management was not designed to deal with such extreme events: for example, they exceeded the design levels of levees and reservoirs. In two success stories, the impact of the second, more hazardous, event was lower, as a result of improved risk management governance and high investment in integrated management. The observed difficulty of managing unprecedented events is alarming, given that more extreme hydrological events are projected owing to climate change[3].}, } @article {pmid35921404, year = {2022}, author = {Kass, JM and Guénard, B and Dudley, KL and Jenkins, CN and Azuma, F and Fisher, BL and Parr, CL and Gibb, H and Longino, JT and Ward, PS and Chao, A and Lubertazzi, D and Weiser, M and Jetz, W and Guralnick, R and Blatrix, R and Lauriers, JD and Donoso, DA and Georgiadis, C and Gomez, K and Hawkes, PG and Johnson, RA and Lattke, JE and MacGown, JA and Mackay, W and Robson, S and Sanders, NJ and Dunn, RR and Economo, EP}, title = {The global distribution of known and undiscovered ant biodiversity.}, journal = {Science advances}, volume = {8}, number = {31}, pages = {eabp9908}, pmid = {35921404}, issn = {2375-2548}, mesh = {Animals ; *Ants/physiology ; Biodiversity ; Ecosystem ; Invertebrates ; Phylogeny ; Vertebrates ; }, abstract = {Invertebrates constitute the majority of animal species and are critical for ecosystem functioning and services. Nonetheless, global invertebrate biodiversity patterns and their congruences with vertebrates remain largely unknown. We resolve the first high-resolution (~20-km) global diversity map for a major invertebrate clade, ants, using biodiversity informatics, range modeling, and machine learning to synthesize existing knowledge and predict the distribution of undiscovered diversity. We find that ants and different vertebrate groups have distinct features in their patterns of richness and rarity, underscoring the need to consider a diversity of taxa in conservation. However, despite their phylogenetic and physiological divergence, ant distributions are not highly anomalous relative to variation among vertebrate clades. Furthermore, our models predict that rarity centers largely overlap (78%), suggesting that general forces shape endemism patterns across taxa. This raises confidence that conservation of areas important for small-ranged vertebrates will benefit invertebrates while providing a "treasure map" to guide future discovery.}, } @article {pmid35915718, year = {2022}, author = {Aziz, MA and Mattalia, G and Sulaiman, N and Shah, AA and Polesny, Z and Kalle, R and Sõukand, R and Pieroni, A}, title = {The nexus between traditional foraging and its sustainability: a qualitative assessment among a few selected Eurasian case studies.}, journal = {Environment, development and sustainability}, volume = {}, number = {}, pages = {1-26}, pmid = {35915718}, issn = {1573-2975}, support = {714874/ERC_/European Research Council/International ; }, abstract = {Plant foraging is an important human ecological phenomenon being studied by a number of contemporary ethnobiologists as well as by a few social anthropologists among rural communities and, more recently, in urban environments. The sustainability dimension of foraging is, however, largely unexplored. We analyse a few case studies from recent field research and qualitatively assess both the environmental and social sustainability of diverse patterns of traditional foraging practices in three distinct human ecological environments (horticulturalism-, forestry-, and pastoralism-driven) located in the Eastern Mediterranean, Eastern Europe, and North Pakistan, i.e. we address the question of when does traditional foraging become unsustainable and what factors may influence this. The main findings are multidimensional. First, in all case studies, we sometimes observed competitive foraging among the gatherers of certain wild food plants potentially causing ecological degradation; such unsustainable practices seem to be linked to the market pressure on certain species. However, also customs and norms promoted by states can be detrimental (former Soviet Union), as well as climate change (Eastern Europe), and marginalisation of some minority groups (Pakistan). Second, in the Mediterranean Syrian context, wild food plant resources are largely represented by widely available weedy "wild" vegetables, normally (but not exclusively) collected by women, and usually easily accessible; only very few wild food plants seem to be threatened due to specific market demands or to disequilibria created by household economic instabilities due to the recent war. We also argue that unsustainable foraging is enhanced by the abandonment of daily practices and continuous interaction with the natural environment and by the increasingly uneven distribution of active practical knowledge on wild food plants among the middle-aged and younger population. Facilitating the transmission of sustainable foraging knowledge and practices could be therefore crucial, also for coping with food insecurity in times of crisis; but for that to occur, holistic environmental and food educational frameworks, appropriate policies for fostering community-based biodiversity conservation and also social cohesion and communal management of lands should be seriously considered as well. Moreover, future gastronomic and eco-tourism initiatives, if organised in a thoughtful manner, could represent a positive turning point not only for the local small-scale economies of the considered rural communities but also for helping them to dynamically preserve the entire socio-ecological system underpinned in plant foraging and ultimately to better adapt to the current global crisis.}, } @article {pmid35910222, year = {2022}, author = {Li, L and Lan, LY and Huang, L and Ye, C and Andrade, J and Wilson, PC}, title = {Selecting Representative Samples From Complex Biological Datasets Using K-Medoids Clustering.}, journal = {Frontiers in genetics}, volume = {13}, number = {}, pages = {954024}, pmid = {35910222}, issn = {1664-8021}, abstract = {Rapid growth of single-cell sequencing techniques enables researchers to investigate almost millions of cells with diverse properties in a single experiment. Meanwhile, it also presents great challenges for selecting representative samples from massive single-cell populations for further experimental characterization, which requires a robust and compact sampling with balancing diverse properties of different priority levels. The conventional sampling methods fail to generate representative and generalizable subsets from a massive single-cell population or more complicated ensembles. Here, we present a toolkit called Cookie which can efficiently select out the most representative samples from a massive single-cell population with diverse properties. This method quantifies the relationships/similarities among samples using their Manhattan distances by vectorizing all given properties and then determines an appropriate sample size by evaluating the coverage of key properties from multiple candidate sizes, following by a k-medoids clustering to group samples into several clusters and selects centers from each cluster as the most representatives. Comparison of Cookie with conventional sampling methods using a single-cell atlas dataset, epidemiology surveillance data, and a simulated dataset shows the high efficacy, efficiency, and flexibly of Cookie. The Cookie toolkit is implemented in R and is freely available at https://wilsonimmunologylab.github.io/Cookie/.}, } @article {pmid35904963, year = {2023}, author = {Smyth, JM and Zawadzki, MJ and Marcusson-Clavertz, D and Scott, SB and Johnson, JA and Kim, J and Toledo, MJ and Stawski, RS and Sliwinski, MJ and Almeida, DM}, title = {Computing Components of Everyday Stress Responses: Exploring Conceptual Challenges and New Opportunities.}, journal = {Perspectives on psychological science : a journal of the Association for Psychological Science}, volume = {18}, number = {1}, pages = {110-124}, pmid = {35904963}, issn = {1745-6924}, support = {UH2 AG052167/AG/NIA NIH HHS/United States ; UH3 AG052167/AG/NIA NIH HHS/United States ; }, mesh = {Humans ; *Stress, Psychological/psychology ; *Exercise/psychology ; }, abstract = {Repeated assessments in everyday life enables collecting ecologically valid data on dynamic, within-persons processes. These methods have widespread utility and application and have been extensively used for the study of stressors and stress responses. Enhanced conceptual sophistication of characterizing intraindividual stress responses in everyday life would help advance the field. This article provides a pragmatic overview of approaches, opportunities, and challenges when intensive ambulatory methods are applied to study everyday stress responses in "real time." We distinguish between three stress-response components (i.e., reactivity, recovery, and pileup) and focus on several fundamental questions: (a) What is the appropriate stress-free resting state (or "baseline") for an individual in everyday life? (b) How does one index the magnitude of the initial response to a stressor (reactivity)? (c) Following a stressor, how can recovery be identified (e.g., when the stress response has completed)? and (d) Because stressors may not occur in isolation, how can one capture the temporal clustering of stressors and/or stress responses (pileup)? We also present initial ideas on applying this approach to intervention research. Although we focus on stress responses, these issues may inform many other dynamic intraindividual constructs and behaviors (e.g., physical activity, physiological processes, other subjective states) captured in ambulatory assessment.}, } @article {pmid35902858, year = {2022}, author = {Plekhanova, T and Rowlands, AV and Evans, RA and Edwardson, CL and Bishop, NC and Bolton, CE and Chalmers, JD and Davies, MJ and Daynes, E and Dempsey, PC and Docherty, AB and Elneima, O and Greening, NJ and Greenwood, SA and Hall, AP and Harris, VC and Harrison, EM and Henson, J and Ho, LP and Horsley, A and Houchen-Wolloff, L and Khunti, K and Leavy, OC and Lone, NI and Marks, M and Maylor, B and McAuley, HJC and Nolan, CM and Poinasamy, K and Quint, JK and Raman, B and Richardson, M and Sargeant, JA and Saunders, RM and Sereno, M and Shikotra, A and Singapuri, A and Steiner, M and Stensel, DJ and Wain, LV and Whitney, J and Wootton, DG and Brightling, CE and Man, WD and Singh, SJ and Yates, T and , }, title = {Device-assessed sleep and physical activity in individuals recovering from a hospital admission for COVID-19: a multicentre study.}, journal = {The international journal of behavioral nutrition and physical activity}, volume = {19}, number = {1}, pages = {94}, pmid = {35902858}, issn = {1479-5868}, support = {MR/V020536/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Accelerometry/methods ; Aftercare ; Aged ; *COVID-19 ; *Diabetes Mellitus, Type 2/therapy ; Exercise ; Female ; Hospitalization ; Hospitals ; Humans ; Male ; Patient Discharge ; Sleep ; }, abstract = {BACKGROUND: The number of individuals recovering from severe COVID-19 is increasing rapidly. However, little is known about physical behaviours that make up the 24-h cycle within these individuals. This study aimed to describe physical behaviours following hospital admission for COVID-19 at eight months post-discharge including associations with acute illness severity and ongoing symptoms.

METHODS: One thousand seventy-seven patients with COVID-19 discharged from hospital between March and November 2020 were recruited. Using a 14-day wear protocol, wrist-worn accelerometers were sent to participants after a five-month follow-up assessment. Acute illness severity was assessed by the WHO clinical progression scale, and the severity of ongoing symptoms was assessed using four previously reported data-driven clinical recovery clusters. Two existing control populations of office workers and individuals with type 2 diabetes were comparators.

RESULTS: Valid accelerometer data from 253 women and 462 men were included. Women engaged in a mean ± SD of 14.9 ± 14.7 min/day of moderate-to-vigorous physical activity (MVPA), with 12.1 ± 1.7 h/day spent inactive and 7.2 ± 1.1 h/day asleep. The values for men were 21.0 ± 22.3 and 12.6 ± 1.7 h /day and 6.9 ± 1.1 h/day, respectively. Over 60% of women and men did not have any days containing a 30-min bout of MVPA. Variability in sleep timing was approximately 2 h in men and women. More severe acute illness was associated with lower total activity and MVPA in recovery. The very severe recovery cluster was associated with fewer days/week containing continuous bouts of MVPA, longer total sleep time, and higher variability in sleep timing. Patients post-hospitalisation with COVID-19 had lower levels of physical activity, greater sleep variability, and lower sleep efficiency than a similarly aged cohort of office workers or those with type 2 diabetes.

CONCLUSIONS: Those recovering from a hospital admission for COVID-19 have low levels of physical activity and disrupted patterns of sleep several months after discharge. Our comparative cohorts indicate that the long-term impact of COVID-19 on physical behaviours is significant.}, } @article {pmid35902604, year = {2022}, author = {Röhr, S and Pabst, A and Baber, R and Engel, C and Glaesmer, H and Hinz, A and Schroeter, ML and Witte, AV and Zeynalova, S and Villringer, A and Löffler, M and Riedel-Heller, SG}, title = {Social determinants and lifestyle factors for brain health: implications for risk reduction of cognitive decline and dementia.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {12965}, pmid = {35902604}, issn = {2045-2322}, mesh = {Adult ; Aged ; Brain ; *Cognitive Dysfunction/epidemiology/prevention & control/psychology ; *Dementia/epidemiology/prevention & control/psychology ; Female ; Humans ; Life Style ; Male ; Middle Aged ; Risk Factors ; Risk Reduction Behavior ; Social Determinants of Health ; }, abstract = {Substantial evidence indicates a huge potential for risk reduction of cognitive decline and dementia based on modifiable health and lifestyle factors. To maximize the chances for risk reduction, it is useful to investigate associations of social determinants and lifestyle for brain health. We computed the "LIfestyle for BRAin health" (LIBRA) score for baseline participants of the Leipzig Research Centre for Civilization Diseases (LIFE) Adult Study, a population-based urban cohort in Germany. LIBRA predicts dementia in midlife and early late life populations, comprising 12 modifiable risk factors (heart disease, kidney disease, diabetes, obesity, hypertension, hypercholesterolemia, alcohol consumption, smoking, physical inactivity, diet, depression, cognitive inactivity). Associations of social determinants (living situation, marital status, social isolation, education, net equivalence income, occupational status, socioeconomic status/SES, employment) with LIBRA were inspected using age- and sex-adjusted multivariable linear regression analysis. Z-standardization and sampling weights were applied. Participants (n = 6203) were M = 57.4 (SD = 10.6, range 40-79) years old and without dementia, 53.0% were women. Except for marital status, all considered social determinants were significantly associated with LIBRA. Beta coefficients for the association with higher LIBRA scores were most pronounced for low SES (β = 0.80, 95% CI [0.72-0.88]; p < 0.001) and middle SES (β = 0.55, 95% CI [0.47-0.62]; p < 0.001). Social determinants, particularly socioeconomic factors, are associated with lifestyle for brain health, and should thus be addressed in risk reduction strategies for cognitive decline and dementia. A social-ecological public health perspective on risk reduction might be more effective and equitable than focusing on individual lifestyle behaviors alone.}, } @article {pmid35902586, year = {2022}, author = {McManamay, RA and George, R and Morrison, RR and Ruddell, BL}, title = {Mapping hydrologic alteration and ecological consequences in stream reaches of the conterminous United States.}, journal = {Scientific data}, volume = {9}, number = {1}, pages = {450}, pmid = {35902586}, issn = {2052-4463}, abstract = {Environmental flows are critical for balancing societal water needs with that of riverine ecosystems; however, data limitations often hinder the development of predictive relationships between anthropogenic modifications to streamflow regimes and ecological responses - these relationships are the basis for setting regional water policy standards for rivers. Herein, we present and describe a comprehensive dataset of modeled hydrologic alteration and consequences for native fish biodiversity, both mapped at the stream-reach resolution for the conterminous U.S. Using empirical observations of reference conditions and anthropogenically altered streamflow at over 7000 stream gauges, we developed a predictive model of hydrologic alteration, which was extended to >2.6 million stream reaches. We then used a previous nationwide assessment of ecological responses to hydrologic alteration to predict fish biodiversity loss in stream reaches resulting from streamflow modification. Validation efforts suggested hydrologic alteration models had satisfactory performance, whereas modeled ecological responses were susceptible to compounded errors. The dataset could ameliorate regional data deficits for setting environmental flow standards while providing tools for prioritizing streamflow protection or restoration.}, } @article {pmid35900894, year = {2022}, author = {Marino, JL and Tait, RJ and Straker, LM and Schofield, DJ and Doherty, DA and Ivers, RQ and Graham, PL and Steinbeck, K and Lymer, S and Sanci, LA and Patton, GC and Liu, B and Brooks, FM and Kang, MS and Hickey, M and Cunich, M and Bista, S and Skinner, SR}, title = {Health, social and economic implications of adolescent risk behaviours/states: protocol for Raine Study Gen2 cohort data linkage study.}, journal = {Longitudinal and life course studies : international journal}, volume = {13}, number = {4}, pages = {647-666}, doi = {10.1332/175795921X16424353247247}, pmid = {35900894}, issn = {1757-9597}, mesh = {Child ; Humans ; Adolescent ; Female ; Pregnancy ; Young Adult ; Adult ; Prospective Studies ; *Risk-Taking ; *Substance-Related Disorders/epidemiology ; Cohort Studies ; Information Storage and Retrieval ; }, abstract = {BACKGROUND: Risk-taking behaviours are a major contributor to youth morbidity and mortality. Vulnerability to these negative outcomes is constructed from individual behaviour including risk-taking, and from social context, ecological determinants, early life experience, developmental capacity and mental health, contributing to a state of higher risk. However, although risk-taking is part of normal adolescent development, there is no systematic way to distinguish young people with a high probability of serious adverse outcomes, hindering the capacity to screen and intervene. This study aims to explore the association between risk behaviours/states in adolescence and negative health, social and economic outcomes through young adulthood.

METHODS: The Raine Study is a prospective cohort study which recruited pregnant women in 1989-91, in Perth, Western Australia. The offspring cohort (N = 2,868) was followed up at regular intervals from 1 to 27 years of age. These data will be linked to State government health and welfare administrative data. We will empirically examine relationships across multiple domains of risk (for example, substance use, sexual behaviour, driving) with health and social outcomes (for instance, road-crash injury, educational underachievement). Microsimulation models will measure the impact of risk-taking on educational attainment and labour force outcomes.

DISCUSSION: Comprehensive preventive child health programmes and policy prioritise a healthy start to life. This is the first linkage study focusing on adolescence to adopt a multi-domain approach, and to integrate health economic modelling. This approach captures a more complete picture of health and social impacts of risk behaviour/​states in adolescence and young adulthood.}, } @article {pmid35900623, year = {2023}, author = {Sharma, N and Kaushal, A and Yousuf, A and Sood, A and Kaur, S and Sharda, R}, title = {Geospatial technology for assessment of soil erosion and prioritization of watersheds using RUSLE model for lower Sutlej sub-basin of Punjab, India.}, journal = {Environmental science and pollution research international}, volume = {30}, number = {1}, pages = {515-531}, pmid = {35900623}, issn = {1614-7499}, mesh = {Humans ; *Soil ; *Soil Erosion ; Conservation of Natural Resources/methods ; Environmental Monitoring/methods ; Geographic Information Systems ; India ; Technology ; }, abstract = {Erosion of soil by water coupled with human activities is considered as one of the most serious agents of land degradation, posing severe threat to agricultural productivity, soil health, water quality, and ecological setup. The assessment of soil erosion and recognition of problematic watersheds are pre-requisite for management of erosion hazards. In the present study, Revised Universal Soil Loss Equation (RUSLE) integrated with remote sensing (RS) and geographic information system (GIS) has been used to assess the soil erosion in lower Sutlej River basin of Punjab, India, and prioritize the watersheds for implementation of land and water conservation measures. The total basin area was about 8577 km[2] which was divided into 14 sub-watersheds with the area ranging from 357.8 to 1354 km[2]. The data on rainfall (IMD gridded data), soil characteristics (FAO soil map), topography (ALOS PALSAR DEM) and land use (ESRI land use and land cover map) were prepared in the form of raster layers and overlaid together to determine the average annual soil loss. The results revealed that the average annual soil loss varied from 1.26 to 25 t ha[-1], whereas total soil loss was estimated to be 2,441,639 tonnes. The spatial distribution map of soil erosion showed that about 94.4% and 4.7% of the total area suffered from very slight erosion (0-5 t ha[-1] year[-1]) and slight erosion (5-10 t ha[-1] year[-1]), respectively, whereas 0.11% (9.38 km[2]) experienced very severe soil loss (> 25 t ha[-1] year[-1]). Based on estimated average annual soil loss of sub-watersheds, WS8 was assigned the highest priority for implementation of soil and water conservation measures (323.5 t ha[-1] year[-1]), followed by WS9 (303.8 t ha[-1] year[-1]), whereas WS2 was given last priority owing to its lowest value of soil loss (122.02 t ha[-1] year[-1]). The present study urges that conservation strategies should be carried out in accordance with the priority ranking of diverse watersheds. These findings can certainly be used to implement soil conservation plans and management practices in order to diminish soil loss in the river basin.}, } @article {pmid35900003, year = {2022}, author = {Arruda, CL and Ferreira D'Agostini Marin, D and Depieri Michels, B and Martins Rosa, V and Iser, BPM}, title = {Maternal mortality in South region of Brazil: an analysis from 2000 to 2018.}, journal = {Journal of obstetrics and gynaecology : the journal of the Institute of Obstetrics and Gynaecology}, volume = {42}, number = {7}, pages = {2715-2721}, doi = {10.1080/01443615.2022.2099737}, pmid = {35900003}, issn = {1364-6893}, mesh = {Pregnancy ; Female ; Humans ; Adult ; *Maternal Mortality ; Brazil/epidemiology ; *Maternal Death ; Educational Status ; Linear Models ; Cause of Death ; }, abstract = {This study characterises maternal mortality in southern Brazil and verifies its trends between 2000 and 2018. It is an ecological time-series study, analysing secondary data from the Department of Informatics of the Unified Health System. The trend of the maternal mortality ratio (MMR) was calculated using generalised linear regression, and the ratios of the rates according to women's characteristics, with a confidence interval (CI) of 95%. The MMR in the South region went from 53.4 to 36.8 deaths per 100,000 live births from 2000 to 2018, a reduction trend of 1.2 percentage points per year. Mortality was directly related to increasing age (p < .001) and inversely related to schooling (p < .001) and predominated in non-white women (p < .001). The main cause of death was direct causes, including hypertensive disorders. Despite the reduction trend in maternal mortality in southern Brazil, the MMR observed is constantly above the recommended by the World Health Organisation.Impact StatementWhat is already known on this subject? The Maternal Mortality Ratio (MMR) is an indicator that allows an analysis of women's health in relation to the socio-economic and care characteristics of the region where they live. Between 2000 and 2015, Brazil had presented a high MMR, with around 50 deaths per 100,000 live births, while WHO considers a reasonably adequate MMR of fewer than 20 deaths per 100,000 live births.What do the results of this study add? This study updates data about MMR in the Southern Region of Brazil, the one which has the lowest rates in the country, but with variable values between the states. There was a reduction in MMR in southern Brazil between 2000 and 2018 but higher rates for women over 30 years old and in a situation of social vulnerability, as low-income and non-white women. Santa Catarina State presented stable values in the period and remained below the RMM averages of the other states during all years.What are the implications of these findings for clinical practice and/or further research? Comparing previous and current Maternal Mortality Rates in the regional context is important to adapt public health policies for the most affected population. Maternal death is still a reality for single and low-income women, who have greater difficulty in access to health care. Strategies in the Unified Health System are needed to tackle this problem.}, } @article {pmid35896546, year = {2022}, author = {Moon, M and Richardson, AD and Milliman, T and Friedl, MA}, title = {A high spatial resolution land surface phenology dataset for AmeriFlux and NEON sites.}, journal = {Scientific data}, volume = {9}, number = {1}, pages = {448}, pmid = {35896546}, issn = {2052-4463}, support = {1702697//NSF | BIO | Division of Environmental Biology (DEB)/ ; 1065029//NSF | BIO | Division of Environmental Biology (DEB)/ ; 1702627//NSF | BIO | Division of Environmental Biology (DEB)/ ; SC0016011//U.S. Department of Energy (DOE)/ ; 80NSSC18K0334//National Aeronautics and Space Administration (NASA)/ ; }, abstract = {Vegetation phenology is a key control on water, energy, and carbon fluxes in terrestrial ecosystems. Because vegetation canopies are heterogeneous, spatially explicit information related to seasonality in vegetation activity provides valuable information for studies that use eddy covariance measurements to study ecosystem function and land-atmosphere interactions. Here we present a land surface phenology (LSP) dataset derived at 3 m spatial resolution from PlanetScope imagery across a range of plant functional types and climates in North America. The dataset provides spatially explicit information related to the timing of phenophase changes such as the start, peak, and end of vegetation activity, along with vegetation index metrics and associated quality assurance flags for the growing seasons of 2017-2021 for 10 × 10 km windows centred over 104 eddy covariance towers at AmeriFlux and National Ecological Observatory Network (NEON) sites. These LSP data can be used to analyse processes controlling the seasonality of ecosystem-scale carbon, water, and energy fluxes, to evaluate predictions from land surface models, and to assess satellite-based LSP products.}, } @article {pmid35893025, year = {2022}, author = {Masarovič, R and Zvaríková, M and Zvarík, M and Majzlan, O and Prokop, P and Fedor, P}, title = {Changes in Diversity and Structure of Thrips (Thysanoptera) Assemblages in the Spruce Forest Stands of High Tatra Mts. after a Windthrow Calamity.}, journal = {Insects}, volume = {13}, number = {8}, pages = {}, pmid = {35893025}, issn = {2075-4450}, support = {VEGA 1/0286/20//Scientific Grant Agency of the Ministry of Education of the Slovak Republic/ ; }, abstract = {Strong winds, fire, and subsequent forest management impact arthropod communities. We monitored the diversity and changes in the community structure of forest thrips assemblages in the context of secondary succession and anthropogenic impact. There were eight study plots that were affected to varying degrees by the mentioned disturbances that were selected in the Central European spruce (Picea abies (L.) Karst.) forests in Slovakia. The soil photoeclectors were used to obtain thrips in the study plots during two vegetation seasons. The thrips assemblages and their attributes were analyzed by non-metric multidimensional scaling (NMDS). The significant changes in community structure, composition, stratification, species richness, and diversity of thrips assemblages that were caused by natural- (wind) and human-induced disturbance (forestry and fire) were observed in our research. Our analyses revealed a clear relationship between different thrips assemblages and impacted environment. Moreover, our results indicate that silvicolous thrips species may be useful for indicating changes and disturbances in forest ecological systems.}, } @article {pmid35891501, year = {2022}, author = {Hufsky, F and Abecasis, A and Agudelo-Romero, P and Bletsa, M and Brown, K and Claus, C and Deinhardt-Emmer, S and Deng, L and Friedel, CC and Gismondi, MI and Kostaki, EG and Kühnert, D and Kulkarni-Kale, U and Metzner, KJ and Meyer, IM and Miozzi, L and Nishimura, L and Paraskevopoulou, S and Pérez-Cataluña, A and Rahlff, J and Thomson, E and Tumescheit, C and van der Hoek, L and Van Espen, L and Vandamme, AM and Zaheri, M and Zuckerman, N and Marz, M}, title = {Women in the European Virus Bioinformatics Center.}, journal = {Viruses}, volume = {14}, number = {7}, pages = {}, pmid = {35891501}, issn = {1999-4915}, support = {646891/ERC_/European Research Council/International ; 721367/MCCC_/Marie Curie/United Kingdom ; 220814/WT_/Wellcome Trust/United Kingdom ; MC_UU_12014/1/MRC_/Medical Research Council/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; }, mesh = {*Computational Biology ; Europe ; Female ; Humans ; *Research Personnel/statistics & numerical data ; *Viruses/genetics ; }, abstract = {Viruses are the cause of a considerable burden to human, animal and plant health, while on the other hand playing an important role in regulating entire ecosystems. The power of new sequencing technologies combined with new tools for processing "Big Data" offers unprecedented opportunities to answer fundamental questions in virology. Virologists have an urgent need for virus-specific bioinformatics tools. These developments have led to the formation of the European Virus Bioinformatics Center, a network of experts in virology and bioinformatics who are joining forces to enable extensive exchange and collaboration between these research areas. The EVBC strives to provide talented researchers with a supportive environment free of gender bias, but the gender gap in science, especially in math-intensive fields such as computer science, persists. To bring more talented women into research and keep them there, we need to highlight role models to spark their interest, and we need to ensure that female scientists are not kept at lower levels but are given the opportunity to lead the field. Here we showcase the work of the EVBC and highlight the achievements of some outstanding women experts in virology and viral bioinformatics.}, } @article {pmid35886637, year = {2022}, author = {Cen, Y and Zhang, B and Luo, J and Deng, Q and Liu, H and Wang, L}, title = {Influence of Topographic Factors on the Characteristics of Gully Systems in Mountainous Areas of Ningnan Dry-Hot Valley, SW China.}, journal = {International journal of environmental research and public health}, volume = {19}, number = {14}, pages = {}, pmid = {35886637}, issn = {1660-4601}, mesh = {China ; *Conservation of Natural Resources/methods ; Ecosystem ; Geographic Information Systems ; *Soil ; }, abstract = {A gully system is an important indicator that reflects the development of regional topography and landforms, and topography is one of the most important factors affecting the development of gullies. However, at present, research on the impact of topography on the development of gully systems in the mountainous area of Ningnan dry-hot valley still needs to be strengthened. In order to study the characteristics of gullies and the influence of topography on the development of gully systems, based on both the visual interpretation of remote sensing images and field investigations, five topographic factors (elevation, slope gradient, aspect, relief, and dissection) were employed and three gully erosion indexes (gully length, density, and frequency) were calculated. The geographical information system was used in this study to carry out the spatial analysis, Ward’s hierarchical clustering and correlation analysis. Results showed that the development of gully systems is greatly affected by the degree of relief and dissection, and there is a significant positive correlation (p < 0.01; p < 0.05), while elevation, slope gradient and aspect have little influence on it. Analysis of the gully systems showed that the gully erosion is the most intense in the area with an elevation of 2800−3200 m and slope gradients ≥ 38°. Furthermore, the degree of erosion on shady slopes was greater than that on sunny slopes. These results will help us to understand the spatial distribution and formation of gully systems in mountainous areas.}, } @article {pmid35886522, year = {2022}, author = {Chen, M and Zheng, L and Zhang, D and Li, J}, title = {Spatio-Temporal Evolution and Obstacle Factors Analysis of Tourism Ecological Security in Huanggang Dabieshan UNESCO Global Geopark.}, journal = {International journal of environmental research and public health}, volume = {19}, number = {14}, pages = {}, pmid = {35886522}, issn = {1660-4601}, mesh = {China ; *Conservation of Natural Resources/methods ; Ecosystem ; Humans ; Industry ; *Tourism ; UNESCO ; }, abstract = {The United Nations Educational, Scientific and Cultural Organization (UNESCO) Global Geoparks (UGGp) and geotourism activities not only improve people's scientific quality by popularizing geoscience knowledge, but also play important roles in protecting precious geoheritages and promoting the development of regional economies. However, tourism activities also have a negative impact on the local ecological environment, placing the regional ecological system under great pressure. Therefore, this paper constructed a tourism ecological security evaluation indicator system suitable for geoparks by using the "Driving-Pressure-State-Impact-Response" (DPSIR) model. The spatial autocorrelation and obstacle degree model are used to analyze the spatio-temporal characteristics and influencing factors of the tourism ecological security index (TESI) of Huanggang Dabieshan UGGp in 2000, 2005, 2010, 2015 and 2018, respectively. The results indicate that the TESI of the study area has gradually improved from 2000 to 2018. Spatially, the level of TESI presents a gradient distribution from the townships where the main scenic spots are located to the surrounding townships. The main obstacle factors affecting TESI include: per capita tourism income, proportion of comprehensive tourism revenue in GDP, per capita net income of rural residents, proportion of tertiary industry in GDP, coverage of nature reserves, planning integrity of geopark, informatization of geopark, growth rate of tourists, comprehensive utilization rate of solid waste, etc. The influencing factors of TESI varied from time to time. Balancing the conflict between local tourism activities and environmental protection, encouraging the participation of local communities, and strengthening science popularization for the local public will effectively improve the tourism ecological security of geoparks.}, } @article {pmid35885950, year = {2022}, author = {Kolobkov, DS and Sviridova, DA and Abilev, SK and Kuzovlev, AN and Salnikova, LE}, title = {Genes and Diseases: Insights from Transcriptomics Studies.}, journal = {Genes}, volume = {13}, number = {7}, pages = {}, pmid = {35885950}, issn = {2073-4425}, mesh = {*Gene Expression Profiling ; Gene Ontology ; Humans ; Phenotype ; *Transcriptome/genetics ; }, abstract = {Results of expression studies can be useful to clarify the genotype-phenotype relationship. However, according to data from recent literature, there is a large group of genes that are revealed as differentially expressed (DE) in many studies, regardless of the biological context. Additional analyses could shed more light on the relationships between genes, their differential expression, and diseases. We generated a set of 9972 disease genes from five gene-phenotype databases (OMIM, ORPHANET, DDG2P, DisGeNet and MalaCards) and a report of the International Union of Immunological Societies. To study transcriptomics of disease and non-disease genes in healthy tissues, we obtained data from the Human Protein Atlas (HPA) website. We analyzed the dependency between expression in healthy tissues and gene occurrence in Gene Expression Omnibus series using tools within the Enrichr libraries. The results of expression studies were annotated with Gene Ontology (GO) and Human Phenotype Ontology (HPO) terms. Using transcriptomics analysis of healthy tissues, we validated the previous findings of higher expression levels of disease genes in pathologically linked tissues compared to other tissues. Preferentially DE genes were generally highly expressed in one or multiple tissues and were enriched for disease genes. According to the results of GO enrichment analyses, both down- and up-regulated DE genes most often took part in immune response, translation and tissue-specific processes. A connection between DE-related pathology and the diversity of HPO terms was found. Investigating a link between expression and phenotype contributes to understanding the mode of development and progression of human diseases.}, } @article {pmid35883471, year = {2022}, author = {Zhang, Y and Jin, J and Huang, B and Ying, H and He, J and Jiang, L}, title = {Selenium Metabolism and Selenoproteins in Prokaryotes: A Bioinformatics Perspective.}, journal = {Biomolecules}, volume = {12}, number = {7}, pages = {}, pmid = {35883471}, issn = {2218-273X}, mesh = {Archaea/genetics/metabolism ; *Computational Biology ; Humans ; Prokaryotic Cells ; *Selenium/metabolism ; Selenoproteins/genetics/metabolism ; }, abstract = {Selenium (Se) is an important trace element that mainly occurs in the form of selenocysteine in selected proteins. In prokaryotes, Se is also required for the synthesis of selenouridine and Se-containing cofactor. A large number of selenoprotein families have been identified in diverse prokaryotic organisms, most of which are thought to be involved in various redox reactions. In the last decade or two, computational prediction of selenoprotein genes and comparative genomics of Se metabolic pathways and selenoproteomes have arisen, providing new insights into the metabolism and function of Se and their evolutionary trends in bacteria and archaea. This review aims to offer an overview of recent advances in bioinformatics analysis of Se utilization in prokaryotes. We describe current computational strategies for the identification of selenoprotein genes and generate the most comprehensive list of prokaryotic selenoproteins reported to date. Furthermore, we highlight the latest research progress in comparative genomics and metagenomics of Se utilization in prokaryotes, which demonstrates the divergent and dynamic evolutionary patterns of different Se metabolic pathways, selenoprotein families, and selenoproteomes in sequenced organisms and environmental samples. Overall, bioinformatics analyses of Se utilization, function, and evolution may contribute to a systematic understanding of how this micronutrient is used in nature.}, } @article {pmid35882317, year = {2022}, author = {Chen, X and Jiang, L and Xia, Y and Wang, L and Ye, J and Hou, T and Zhang, Y and Li, M and Li, Z and Song, Z and Li, J and Jiang, Y and Li, P and Zhang, X and Zhang, Y and Rosenfeld, D and Seinfeld, JH and Yu, S}, title = {Quantifying on-road vehicle emissions during traffic congestion using updated emission factors of light-duty gasoline vehicles and real-world traffic monitoring big data.}, journal = {The Science of the total environment}, volume = {847}, number = {}, pages = {157581}, doi = {10.1016/j.scitotenv.2022.157581}, pmid = {35882317}, issn = {1879-1026}, mesh = {*Air Pollutants/analysis ; *Air Pollution/analysis ; Big Data ; Environmental Monitoring ; Gasoline/analysis ; Motor Vehicles ; Vehicle Emissions/analysis ; }, abstract = {Light-duty gasoline vehicles (LDGVs) have made up >90 % of vehicle fleets in China since 2019, moreover, with a high annual growth rate (> 10 %) since 2017. Hence, accurate estimates of air pollutant emissions of these fast-changing LDGVs are vital for air quality management, human healthcare, and ecological protection. However, this issue is poorly quantified due to insufficient reserves of timely updated LDGV emission factors, which are dependent on real-world activity levels. Here we constructed a big dataset of explicit emission profiles (e.g., emission factors and accumulated mileages) for 159,051 LDGVs based on an official I/M database by matching real-time traffic dynamics via real-world traffic monitoring (e.g., traffic volumes and speeds). Consequently, we provide robust evidence that the emission factors of these LDGVs follow a clear heavy-tailed distribution. The top 10 % emitters contributed >60 % to the total fleet emissions, while the bottom 50 % contributed <10 %. Such emission factors were effectively reduced by 75.7-86.2 % as official emission standards upgraded gradually (i.e., from China 2 to China 5) within 13 years from 2004 to 2017. Nevertheless, such achievements would be offset once traffic congestion occurred. In the real world, the typical traffic congestions (i.e., vehicle speed <5 km/h) can lead to emissions 5- 9 times higher than those on non-congested roads (i.e., vehicle speed >50 km/h). These empirical analyses enabled us to propose future traffic scenarios that could harmonize emission standards and traffic congestion. Practical approaches on vehicle emission controls under realistic conditions are proposed, which would provide new insights for future urban vehicle emission management.}, } @article {pmid35881864, year = {2022}, author = {Özdemir, V}, title = {Call for Papers: COVID-19 Systems Biology, Multi-Omics Integration, and Digital Technologies in Ecology, Health, and Society.}, journal = {Omics : a journal of integrative biology}, volume = {26}, number = {9}, pages = {471-472}, doi = {10.1089/omi.2022.0094}, pmid = {35881864}, issn = {1557-8100}, mesh = {*COVID-19/epidemiology ; Computational Biology ; Digital Technology ; Genomics ; Humans ; *Systems Biology ; }, } @article {pmid35881010, year = {2022}, author = {Worobey, M and Levy, JI and Malpica Serrano, L and Crits-Christoph, A and Pekar, JE and Goldstein, SA and Rasmussen, AL and Kraemer, MUG and Newman, C and Koopmans, MPG and Suchard, MA and Wertheim, JO and Lemey, P and Robertson, DL and Garry, RF and Holmes, EC and Rambaut, A and Andersen, KG}, title = {The Huanan Seafood Wholesale Market in Wuhan was the early epicenter of the COVID-19 pandemic.}, journal = {Science (New York, N.Y.)}, volume = {377}, number = {6609}, pages = {951-959}, pmid = {35881010}, issn = {1095-9203}, support = {U19 AI135995/AI/NIAID NIH HHS/United States ; R01 AI153044/AI/NIAID NIH HHS/United States ; MC_UU_12014/12/MRC_/Medical Research Council/United Kingdom ; MC_PC_19026/MRC_/Medical Research Council/United Kingdom ; R01 AI132223/AI/NIAID NIH HHS/United States ; U54 CA260581/CA/NCI NIH HHS/United States ; T15 LM011271/LM/NLM NIH HHS/United States ; /WT_/Wellcome Trust/United Kingdom ; R01 AI132244/AI/NIAID NIH HHS/United States ; R01 AI135992/AI/NIAID NIH HHS/United States ; R01 AI136056/AI/NIAID NIH HHS/United States ; U19 AI142790/AI/NIAID NIH HHS/United States ; T32 AI007244/AI/NIAID NIH HHS/United States ; F32 AI152341/AI/NIAID NIH HHS/United States ; 75N93021C00015/AI/NIAID NIH HHS/United States ; UL1 TR002550/TR/NCATS NIH HHS/United States ; U01 AI151812/AI/NIAID NIH HHS/United States ; U54 HG007480/HG/NHGRI NIH HHS/United States ; }, mesh = {Animals ; *COVID-19/epidemiology/transmission/virology ; China/epidemiology ; Humans ; *Pandemics ; *SARS-CoV-2/isolation & purification ; *Seafood/virology ; *Viral Zoonoses/epidemiology/transmission/virology ; }, abstract = {Understanding how severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in 2019 is critical to preventing future zoonotic outbreaks before they become the next pandemic. The Huanan Seafood Wholesale Market in Wuhan, China, was identified as a likely source of cases in early reports, but later this conclusion became controversial. We show here that the earliest known COVID-19 cases from December 2019, including those without reported direct links, were geographically centered on this market. We report that live SARS-CoV-2-susceptible mammals were sold at the market in late 2019 and that within the market, SARS-CoV-2-positive environmental samples were spatially associated with vendors selling live mammals. Although there is insufficient evidence to define upstream events, and exact circumstances remain obscure, our analyses indicate that the emergence of SARS-CoV-2 occurred through the live wildlife trade in China and show that the Huanan market was the epicenter of the COVID-19 pandemic.}, } @article {pmid35881005, year = {2022}, author = {Pekar, JE and Magee, A and Parker, E and Moshiri, N and Izhikevich, K and Havens, JL and Gangavarapu, K and Malpica Serrano, LM and Crits-Christoph, A and Matteson, NL and Zeller, M and Levy, JI and Wang, JC and Hughes, S and Lee, J and Park, H and Park, MS and Ching Zi Yan, K and Lin, RTP and Mat Isa, MN and Noor, YM and Vasylyeva, TI and Garry, RF and Holmes, EC and Rambaut, A and Suchard, MA and Andersen, KG and Worobey, M and Wertheim, JO}, title = {The molecular epidemiology of multiple zoonotic origins of SARS-CoV-2.}, journal = {Science (New York, N.Y.)}, volume = {377}, number = {6609}, pages = {960-966}, pmid = {35881005}, issn = {1095-9203}, support = {U19 AI135995/AI/NIAID NIH HHS/United States ; R01 AI153044/AI/NIAID NIH HHS/United States ; R01 AI132223/AI/NIAID NIH HHS/United States ; U54 CA260581/CA/NCI NIH HHS/United States ; T15 LM011271/LM/NLM NIH HHS/United States ; T32 AI007244/AI/NIAID NIH HHS/United States ; /WT_/Wellcome Trust/United Kingdom ; R01 AI132244/AI/NIAID NIH HHS/United States ; R01 AI135992/AI/NIAID NIH HHS/United States ; R01 AI136056/AI/NIAID NIH HHS/United States ; U19 AI142790/AI/NIAID NIH HHS/United States ; 75N93021C00015/AI/NIAID NIH HHS/United States ; UL1 TR002550/TR/NCATS NIH HHS/United States ; U01 AI151812/AI/NIAID NIH HHS/United States ; U54 HG007480/HG/NHGRI NIH HHS/United States ; }, mesh = {Animals ; *COVID-19/epidemiology/transmission/virology ; Computer Simulation ; Genetic Variation ; Genomics/methods ; Humans ; Molecular Epidemiology ; *Pandemics ; Phylogeny ; *SARS-CoV-2/classification/genetics/isolation & purification ; *Viral Zoonoses/epidemiology/virology ; }, abstract = {Understanding the circumstances that lead to pandemics is important for their prevention. We analyzed the genomic diversity of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) early in the coronavirus disease 2019 (COVID-19) pandemic. We show that SARS-CoV-2 genomic diversity before February 2020 likely comprised only two distinct viral lineages, denoted "A" and "B." Phylodynamic rooting methods, coupled with epidemic simulations, reveal that these lineages were the result of at least two separate cross-species transmission events into humans. The first zoonotic transmission likely involved lineage B viruses around 18 November 2019 (23 October to 8 December), and the separate introduction of lineage A likely occurred within weeks of this event. These findings indicate that it is unlikely that SARS-CoV-2 circulated widely in humans before November 2019 and define the narrow window between when SARS-CoV-2 first jumped into humans and when the first cases of COVID-19 were reported. As with other coronaviruses, SARS-CoV-2 emergence likely resulted from multiple zoonotic events.}, } @article {pmid35880005, year = {2022}, author = {Macharia, PM and Ray, N and Gitonga, CW and Snow, RW and Giorgi, E}, title = {Combining school-catchment area models with geostatistical models for analysing school survey data from low-resource settings: Inferential benefits and limitations.}, journal = {Spatial statistics}, volume = {51}, number = {}, pages = {100679}, pmid = {35880005}, issn = {2211-6753}, support = {212176/WT_/Wellcome Trust/United Kingdom ; 079080/WT_/Wellcome Trust/United Kingdom ; 081829/WT_/Wellcome Trust/United Kingdom ; 203077/WT_/Wellcome Trust/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; }, abstract = {School-based sampling has been used to inform targeted responses for malaria and neglected tropical diseases. Standard geostatistical methods for mapping disease prevalence use the school location to model spatial correlation, which is questionable since exposure to the disease is more likely to occur in the residential location. In this paper, we propose to overcome the limitations of standard geostatistical methods by introducing a modelling framework that accounts for the uncertainty in the location of the residence of the students. By using cost distance and cost allocation models to define spatial accessibility and in absence of any information on the travel mode of students to school, we consider three school catchment area models that assume walking only, walking and bicycling and, walking and motorized transport. We illustrate the use of this approach using two case studies of malaria in Kenya and compare it with the standard approach that uses the school locations to build geostatistical models. We argue that the proposed modelling framework presents several inferential benefits, such as the ability to combine data from multiple surveys some of which may also record the residence location, and to deal with ecological bias when estimating the effects of malaria risk factors. However, our results show that invalid assumptions on the modes of travel to school can worsen the predictive performance of geostatistical models. Future research in this area should focus on collecting information on the modes of transportation to school which can then be used to better parametrize the catchment area models.}, } @article {pmid35877609, year = {2022}, author = {Wangithi, C and Muriithi, BW and Diiro, G and Dubois, T and Mohamed, S and Lattorff, MG and Ngowi, BV and Abdel-Rahman, EM and Adan, M and Kassie, M}, title = {Synergies of integrated pest and pollinator management in avocado farming in East Africa: An ex-ante economic analysis.}, journal = {PloS one}, volume = {17}, number = {7}, pages = {e0271241}, pmid = {35877609}, issn = {1932-6203}, mesh = {Agriculture ; Humans ; *Persea ; Pest Control ; Pollination ; Tanzania ; }, abstract = {Using synthetic pesticides to manage pests can threaten pollination services, affecting the productivity of pollination-dependent crops such as avocado. The need to mitigate this negative externality has led to the emergence of the concept of integrated pest and pollinator management (IPPM) to achieve both pest and pollinator management, leading to complementary or synergistic benefits for yield and quality of the harvest. This paper aims to evaluate the potential economic and welfare impact of IPPM in avocado production systems in Kenya and Tanzania. We utilize both primary and secondary data and employed the economic surplus model. On average the potential economic gain from the adoption of IPPM is US$ 66 million annually in Kenya, with a benefit-cost ratio (BCR) of 13:1, while in Tanzania US$ 1.4 million per year, with a BCR of 34:1. The potential benefits from IPPM intervention gains are expected to reduce the number of poor people in Kenya and Tanzania by 10,464 and 1,255 people per year respectively. The findings conclude that policies that enhance the adoption of IPPM can fast-track economic development and therefore improve the livelihoods of various actors across the avocado value chain.}, } @article {pmid35875359, year = {2022}, author = {Constant, A and Clark, A and Kirchhoff, M and Friston, KJ}, title = {Extended active inference: Constructing predictive cognition beyond skulls.}, journal = {Mind & language}, volume = {37}, number = {3}, pages = {373-394}, pmid = {35875359}, issn = {0268-1064}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {Cognitive niche construction is the process whereby organisms create and maintain cause-effect models of their niche as guides for fitness influencing behavior. Extended mind theory claims that cognitive processes extend beyond the brain to include predictable states of the world. Active inference and predictive processing in cognitive science assume that organisms embody predictive (i.e., generative) models of the world optimized by standard cognitive functions (e.g., perception, action, learning). This paper presents an active inference formulation that views cognitive niche construction as a cognitive function aimed at optimizing organisms' generative models. We call that process of optimization extended active inference.}, } @article {pmid35874548, year = {2022}, author = {Czapanskiy, MF and Beltran, RS}, title = {How Reproducibility Will Accelerate Discovery Through Collaboration in Physio-Logging.}, journal = {Frontiers in physiology}, volume = {13}, number = {}, pages = {917976}, pmid = {35874548}, issn = {1664-042X}, abstract = {What new questions could ecophysiologists answer if physio-logging research was fully reproducible? We argue that technical debt (computational hurdles resulting from prioritizing short-term goals over long-term sustainability) stemming from insufficient cyberinfrastructure (field-wide tools, standards, and norms for analyzing and sharing data) trapped physio-logging in a scientific silo. This debt stifles comparative biological analyses and impedes interdisciplinary research. Although physio-loggers (e.g., heart rate monitors and accelerometers) opened new avenues of research, the explosion of complex datasets exceeded ecophysiology's informatics capacity. Like many other scientific fields facing a deluge of complex data, ecophysiologists now struggle to share their data and tools. Adapting to this new era requires a change in mindset, from "data as a noun" (e.g., traits, counts) to "data as a sentence", where measurements (nouns) are associate with transformations (verbs), parameters (adverbs), and metadata (adjectives). Computational reproducibility provides a framework for capturing the entire sentence. Though usually framed in terms of scientific integrity, reproducibility offers immediate benefits by promoting collaboration between individuals, groups, and entire fields. Rather than a tax on our productivity that benefits some nebulous greater good, reproducibility can accelerate the pace of discovery by removing obstacles and inviting a greater diversity of perspectives to advance science and society. In this article, we 1) describe the computational challenges facing physio-logging scientists and connect them to the concepts of technical debt and cyberinfrastructure, 2) demonstrate how other scientific fields overcame similar challenges by embracing computational reproducibility, and 3) present a framework to promote computational reproducibility in physio-logging, and bio-logging more generally.}, } @article {pmid35873380, year = {2022}, author = {Lim, T and Lee, K and Kim, RH and Cha, KH and Koo, SY and Moon, EC and Hwang, KT}, title = {Black raspberry extract can lower serum LDL cholesterol via modulation of gut microbial composition and serum bile acid profile in rats fed trimethylamine-N-oxide with a high-fat diet.}, journal = {Food science and biotechnology}, volume = {31}, number = {8}, pages = {1041-1051}, pmid = {35873380}, issn = {2092-6456}, abstract = {UNLABELLED: Blood trimethylamine-N-oxide (TMAO) has been associated with cardiovascular disease. Black raspberry (Rubus occidentalis, BR) has been regarded to be beneficial for cardiovascular health. This study aimed to investigate how BR extract affects serum lipid profile, gut microbial composition, metabolites in rats fed TMAO with a high-fat diet. Dietary TMAO increased serum LDL cholesterol, while BR extract decreased its level. α-Diversity of gut microbiota was not changed; however, in the rats fed TMAO, Macellibacteroides and Mucispirillum were enriched, while Ruminococcaceae was reduced. The BR supplementation could restore Macellibacteroides, Clostridium, and Ruminococcaceae. The BR supplementation increased cecal hippuric acid and serum farnesoid X receptor-antagonistic bile acids, including ursodeoxycholic acid (UDCA), tauro-α-muricholic acid, and tauro-UDCA. The BR supplementation tended to upregulate Cyp7a1 and Abcg5 expressions while downregulating Srebf2 and Hmgcr expressions. BR extract affects the gut bacterial community and microbial metabolites, lowering serum LDL cholesterol in rats with elevated serum TMAO.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s10068-022-01079-y.}, } @article {pmid35870534, year = {2022}, author = {Hossain Bhuiyan, MA and Chandra Karmaker, S and Saha, BB}, title = {Nexus between potentially toxic elements' accumulation and seasonal/anthropogenic influences on mangrove sediments and ecological risk in Sundarbans, Bangladesh: An approach from GIS, self-organizing map, conditional inference tree and random forest models.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {309}, number = {}, pages = {119765}, doi = {10.1016/j.envpol.2022.119765}, pmid = {35870534}, issn = {1873-6424}, mesh = {Bangladesh ; Cadmium/analysis ; China ; Ecosystem ; Environmental Monitoring/methods ; Geographic Information Systems ; Geologic Sediments ; Humans ; Lead/analysis ; *Metals, Heavy/analysis ; Risk Assessment/methods ; Seasons ; *Water Pollutants, Chemical/analysis ; }, abstract = {Mangroves play a vital role in protecting the coastal community from the climate change effect and in the restoration of the coastal ecosystem. This research has been designed to determine the spatial and seasonal changes of potentially toxic elements' (PTEs) concentration in sediments and their potential source contribution among the different human-driven processes in Sundarbans, Bangladesh. Different pollution evaluation indices, random forest (RF) model, conditional inference tree (CIT), self-organizing map (SOM), geographical information system (GIS), and principal component analysis (PCA) were used for the interpretation of sources and risk assessment of PTEs. The mean concentration of PTEs both in winter and monsoon seasons has fallen below the threshold effect level but exceeded the rare effect level of marine sediments quality standards. Results showed that the PTEs were significantly enriched (EF > 1.00 < 70.00) in sediments, whereas the Cd enrichment (7.00% samples) was very alarming (EF = 60-70). Except for Zn and Cd, other PTEs were enriched in 30-60% samples. The highest geoaccumulation and contamination factors for Cd were observed in 46-72% of samples. The ecological risk (ER) factors showed similar results where Cd showed strong to very strong factors (ER = 110-2218) in 80% of samples. The CIT explained the natural/geogenic and anthropogenic sources of pollution, where the higher CIT values for Cd indicated industrial, aquaculture, and coal-based thermal powerplant. The RF model provided that shrimp firms, power plants, industry, and seaport were recognized as the influential sources for Zn, Pb, Cr, Cd, and As in sediments. Though Pb and As were found as the most significant pollutants, Cd was identified as a severe threat to ecology and public health. Based on CIT, RF, SOM and PCA the order of PTEs in mangroves sediment were:industrial/urban > aquaculture/shrimpfirm > powerplant > seaportoperation > tourism > geogenic/natural. The present study will help the policymakers for effective and sustainable management of the mangrove ecosystem.}, } @article {pmid35868837, year = {2022}, author = {Nishizawa, N and Okawara, M and Mori, M and Fujino, Y and Matsuda, S and Fushimi, K and Tanaka, F}, title = {Postoperative cerebral infarction risk is related to lobectomy site in lung cancer: a retrospective cohort study of nationwide data in Japan.}, journal = {BMJ open respiratory research}, volume = {9}, number = {1}, pages = {}, pmid = {35868837}, issn = {2052-4439}, mesh = {Cerebral Infarction/epidemiology/etiology/surgery ; Humans ; Japan/epidemiology ; *Lung Neoplasms/complications/epidemiology/surgery ; *Pneumonectomy/adverse effects/methods ; Postoperative Complications/epidemiology/etiology ; Retrospective Studies ; }, abstract = {OBJECTIVES: To determine the incidence of cerebral infarction after lobectomy at different sites using inpatient data from a diagnosis procedure combination database.

DESIGN: Retrospective cohort study.

SETTING: Data were retrieved from the Japanese diagnosis procedure combination inpatient database for patients who underwent lobectomies for lung cancer between April 2018 and March 2020.

PARTICIPANTS: The analysis included 37 352 patients from 556 institutions who underwent lobectomies for lung cancer.

MAIN OUTCOMES AND MEASURES: The occurrence of cerebral infarction after lobectomy during hospitalisation was estimated using multilevel logistic regression models adjusted for sex, age, body mass index, smoking history, activity of daily living, surgical approach (thoracotomy or video-assisted), clinical cancer stage, comorbidities and hospital-level factors to describe the association between cerebral infarction and different lobectomy sites.

RESULTS: Overall cerebral infarction after lobectomy occurred in 99 patients (0.27%): 29 with left upper lobectomy (0.39%), 19 with left lower lobectomy (0.34%), 32 with right upper lobectomy (0.24%), 6 with right middle lobectomy (0.21%) and 13 with right lower lobectomy (0.16%). The multilevel multivariate logistic regression analysis revealed high ORs for the left upper lobectomy and left lower lobectomy groups. In both univariate and multivariate analyses, left upper lobectomy had the highest OR for the occurrence of cerebral infarction compared with lobectomies at other sites.

CONCLUSIONS AND RELEVANCE: Left upper lobectomy had the highest OR for the occurrence of cerebral infarction after lung cancer lobectomy during hospitalisation. There is an urgent need to investigate the specific mechanisms underlying postoperative cerebral infarction after left upper lobectomy and to establish preventive measures such as altering surgical methods, using radiological examinations for early detection and better use of anticoagulants.}, } @article {pmid35866021, year = {2022}, author = {Singh, P and Irisarri, I and Torres-Dowdall, J and Thallinger, GG and Svardal, H and Lemmon, EM and Lemmon, AR and Koblmüller, S and Meyer, A and Sturmbauer, C}, title = {Phylogenomics of trophically diverse cichlids disentangles processes driving adaptive radiation and repeated trophic transitions.}, journal = {Ecology and evolution}, volume = {12}, number = {7}, pages = {e9077}, pmid = {35866021}, issn = {2045-7758}, abstract = {Cichlid fishes of the tribe Tropheini are a striking case of adaptive radiation, exemplifying multiple trophic transitions between herbivory and carnivory occurring in sympatry with other established cichlid lineages. Tropheini evolved highly specialized eco-morphologies to exploit similar trophic niches in different ways repeatedly and rapidly. To better understand the evolutionary history and trophic adaptations of this lineage, we generated a dataset of 532 targeted loci from 21 out of the 22 described Tropheini species. We resolved the Tropheini into seven monophyletic genera and discovered one to be polyphyletic. The polyphyletic genus, Petrochromis, represents three convergent origins of the algae grazing trophic specialization. This repeated evolution of grazing may have been facilitated by adaptive introgression as we found evidence for gene flow among algae grazing genera. We also found evidence of gene flow among algae browsing genera, but gene flow was restricted between herbivorous and carnivorous genera. Furthermore, we observed no evidence supporting a hybrid origin of this radiation. Our molecular evolutionary analyses suggest that opsin genes likely evolved in response to selection pressures associated with trophic ecology in the Tropheini. We found surprisingly little evidence of positive selection in coding regions of jaw-shaping genes in this trophically diverse lineage. This suggests low degrees of freedom for further change in these genes, and possibly a larger role for regulatory variation in driving jaw adaptations. Our study emphasizes Tropheini cichlids as an important model for studying the evolution of trophic specialization and its role in speciation.}, } @article {pmid35865637, year = {2022}, author = {Dwivedi, D and Santos, ALD and Barnard, MA and Crimmins, TM and Malhotra, A and Rod, KA and Aho, KS and Bell, SM and Bomfim, B and Brearley, FQ and Cadillo-Quiroz, H and Chen, J and Gough, CM and Graham, EB and Hakkenberg, CR and Haygood, L and Koren, G and Lilleskov, EA and Meredith, LK and Naeher, S and Nickerson, ZL and Pourret, O and Song, HS and Stahl, M and Taş, N and Vargas, R and Weintraub-Leff, S}, title = {Biogeosciences Perspectives on Integrated, Coordinated, Open, Networked (ICON) Science.}, journal = {Earth and space science (Hoboken, N.J.)}, volume = {9}, number = {3}, pages = {e2021EA002119}, pmid = {35865637}, issn = {2333-5084}, support = {P01 ES028939/ES/NIEHS NIH HHS/United States ; }, abstract = {This article is composed of three independent commentaries about the state of Integrated, Coordinated, Open, Networked (ICON) principles in the American Geophysical Union Biogeosciences section, and discussion on the opportunities and challenges of adopting them. Each commentary focuses on a different topic: (a) Global collaboration, technology transfer, and application (Section 2), (b) Community engagement, community science, education, and stakeholder involvement (Section 3), and (c) Field, experimental, remote sensing, and real-time data research and application (Section 4). We discuss needs and strategies for implementing ICON and outline short- and long-term goals. The inclusion of global data and international community engagement are key to tackling grand challenges in biogeosciences. Although recent technological advances and growing open-access information across the world have enabled global collaborations to some extent, several barriers, ranging from technical to organizational to cultural, have remained in advancing interoperability and tangible scientific progress in biogeosciences. Overcoming these hurdles is necessary to address pressing large-scale research questions and applications in the biogeosciences, where ICON principles are essential. Here, we list several opportunities for ICON, including coordinated experimentation and field observations across global sites, that are ripe for implementation in biogeosciences as a means to scientific advancements and social progress.}, } @article {pmid35864989, year = {2022}, author = {Simoes, J and Bulla, J and Neff, P and Pryss, R and Marcrum, SC and Langguth, B and Schlee, W}, title = {Daily Contributors of Tinnitus Loudness and Distress: An Ecological Momentary Assessment Study.}, journal = {Frontiers in neuroscience}, volume = {16}, number = {}, pages = {883665}, pmid = {35864989}, issn = {1662-4548}, abstract = {BACKGROUND: Tinnitus is a heterogeneous condition which may be associated with moderate to severe disability, but the reasons why only a subset of individuals is burdened by the condition are not fully clear. Ecological momentary assessment (EMA) allows a better understanding of tinnitus by capturing the fluctuations of tinnitus symptoms, such as distress and loudness, and psychological processes, such as emotional arousal, overall stress, mood, and concentration and how these variables interact over time. Whether any of those variables have an influence over the next day, that is, whether any of these variables are auto- or cross-correlated, is still unanswered.

OBJECTIVES: Assess whether behavioral and symptom-related data from tinnitus users from the TrackYourTinnitus (TYT) mobile app have an impact on tinnitus loudness and distress on subsequent days.

METHODS: Anonymized data was collected from 278 users of the iOS or Android TYT apps between 2014 and 2020. Tinnitus-related distress, tinnitus loudness, concentration level, mood, emotional arousal, and overall stress level were assessed using either a slider or the Wong-Baker Pain FACES scale via a daily survey. Three modeling strategies were used to investigate whether tinnitus loudness and distress are affected by previous days symptoms or psychological processes: auto- and cross correlations, regressions with elastic net regularization, and subgrouping within group iterative multiple model estimation (S-GIMME).

RESULTS: No autocorrelation or cross-correlation was observed at the group level between the variables assessed. However, application of the regression models with elastic net regularization identified individualized predictors of tinnitus loudness and distress for most participants, with the models including contemporaneous and lagged information from the previous day. S-GIMME corroborated these findings by identifying individualized predictors of tinnitus loudness and distress from the previous day.

DISCUSSION: We showed that tinnitus loudness and tinnitus distress are affected by the contemporaneous and lagged dynamics of behavioral and emotional processes measured through EMA. These effects were seen at the group, and individual levels. The relevance EMA and the implications of the insights derived from it for tinnitus care are discussed, especially considering current trends toward the individualization of tinnitus care.}, } @article {pmid35864391, year = {2022}, author = {Zhu, Q and Ruan, M and Hu, Z and Ye, C}, title = {Addition of carbon sources and nutrient salts can inhibit gangue acidification by changing microbial community structure.}, journal = {Environmental science and pollution research international}, volume = {29}, number = {60}, pages = {90046-90057}, pmid = {35864391}, issn = {1614-7499}, mesh = {*Carbon ; Sodium Lactate ; RNA, Ribosomal, 16S ; China ; *Microbiota ; }, abstract = {Acidic pollution from gangue oxidation has become a primary environmental problem in coal mining areas in China. The use of microorganisms to remediate acidic pollution in coal gangue piles has been indicated to be effective, but environmental differences and carbon sources in different mining areas have become important factors restricting microbial activity. Instead of the addition of new functional bacteria to gangue piles, carbon sources and nutrient salts were added to recently discharged gangue to enhance the activity of beneficial bacteria in the indigenous microbial community. The changes in pH and electrical conductivity (EC) of the gangue leachate as well as the composition and abundance of the functional microbial community on the surface of the gangue were analyzed by leaching simulation experiments and 16S rRNA sequencing. The results showed that the addition of a carbon source maintained the pH of the gangue leachate at 6.31~6.65 in 14 d, which was significantly higher than that of the control group, but the pH of the leachate decreased significantly after the addition of the carbon source was stopped. The most effective treatment is adding a low concentration of nutrient salt (20% concentration) and sodium lactate (0.02 g/L) to the gangue first, and then adding sodium lactate (0.1 mg/L) every 7 days. The addition of carbon sources and nutrient salts changed the microbial community composition on the surface of the gangue, and the species diversity index decreased. The dominant genera in the experimental group were Listeria, Arthrobacter, and Enterococcus. The functional gene types in the experimental and control groups were almost the same, but their relative abundance changed. The abundance of functional genes related to the sulfur cycle increased substantially in the experimental group, and the abundance of genes involved in the nitrogen and carbon cycles also increased, albeit to different degrees.}, } @article {pmid35863666, year = {2023}, author = {Liao, PJ and Ting, MK and Kuo, CF and Ding, YH and Lin, CM and Hsu, KH}, title = {Kinship analysis of type 2 diabetes mellitus familial aggregation in Taiwan.}, journal = {Biomedical journal}, volume = {46}, number = {4}, pages = {100549}, pmid = {35863666}, issn = {2320-2890}, mesh = {*Diabetes Mellitus, Type 2/genetics ; Taiwan ; Humans ; Family ; Pedigree ; Male ; Female ; Sex Factors ; Age Factors ; Risk ; Gene-Environment Interaction ; Adult ; Middle Aged ; Aged ; Aged, 80 and over ; }, abstract = {BACKGROUND: Family disease history plays a vital role in type 2 diabetes mellitus (T2DM) risk. However, the familial aggregation of T2DM among different kinship relatives warrants further investigation.

METHODS: This nationwide kinship relationship study collected 2000-2016 data of two to five generations of the Taiwanese population from the National Health Insurance Research Database. Approximately 4 million family trees were constructed from the records of 20, 890, 264 Taiwanese residents during the study period. T2DM was diagnosed on the basis of ICD-9-CM codes 250.x0 or 250.x2, with three consecutive related prescriptions. The Cox proportional hazard model was used for statistical analysis.

RESULTS: Compared with their counterparts, individuals who had first-degree relatives with T2DM were more likely to develop T2DM during the follow-up period (hazard ratio [HR], 2.37-27.75), followed by individuals who had second-degree relatives with T2DM (HR, 1.29-1.88). T2DM relative risk was higher in those with an affected mother than in those with affected father. The HR for T2DM was 20.32 (95%CI = 15.64-26.42) among male individuals with an affected twin brother, whereas among female individuals with an affected twin sister, it was 60.07 (95%CI = 40.83-88.36). The HRs presented a dose-response relationship with the number of affected family members.

CONCLUSION: The study suggests a significant familial aggregation of T2DM occurrence; these findings could aid in identifying the high-risk group for T2DM and designing early intervention strategies and treatment plans.}, } @article {pmid35859343, year = {2022}, author = {Treerat, P and McGuire, B and Palmer, E and Dahl, EM and Karstens, L and Merritt, J and Kreth, J}, title = {Oral microbiome diversity: The curious case of Corynebacterium sp. isolation.}, journal = {Molecular oral microbiology}, volume = {37}, number = {5}, pages = {167-179}, pmid = {35859343}, issn = {2041-1014}, support = {R01 DE022083/DE/NIDCR NIH HHS/United States ; R56 DE021726/DE/NIDCR NIH HHS/United States ; R01 DE018893/DE/NIDCR NIH HHS/United States ; R01 DE029492/DE/NIDCR NIH HHS/United States ; R01 DE021726/DE/NIDCR NIH HHS/United States ; R35 DE028252/DE/NIDCR NIH HHS/United States ; }, mesh = {Actinomyces/genetics ; *Corynebacterium/genetics ; DNA, Bacterial/genetics ; Fatty Acids ; *Microbiota/genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Streptococcus sanguis/genetics ; }, abstract = {Oral microbiome sequencing efforts revealed the presence of hundreds of different microbes. Interindividual differences at strain and species resolution suggest that microbiome diversity could lead to mechanistically distinct gene regulation as well as species-related differences in phenotypes. Commonly, gene regulation and related phenotypes are studied in a few selected strains of a particular species with conclusions that are mostly generalized. The aim of this study was to isolate several species of Corynebacterium using an established protocol that led to the previous isolation of C. durum. Characterization of C. durum interspecies interactions revealed a specific mechanism for chain elongation in Streptococcus sanguinis that was the result of corynebacterial fatty acid production and secretion. While the protocol was successfully applied to isolate what we presumed to be additional Corynebacterium based on several phenotypic traits that seem to be identical to C. durum, genome sequencing of the newly isolated strains placed them closer to Actinomyces. Both Corynebacterium and Actinomyces are suborders of the Actinobacteridae and related species. Our study suggests to take several comprehensive strategies into consideration when taxonomically identifying closely related microorganisms. Furthermore, it seems to be important to test common core phenotypes in bacterial ecology to understand the behavior of specific groups of microbes, rather than simply relying upon genome sequence homology to establish relationships in the microbiome.}, } @article {pmid35858960, year = {2022}, author = {Raja, NB and Dimitrijević, D and Krause, MC and Kiessling, W}, title = {Ancient Reef Traits, a database of trait information for reef-building organisms over the Phanerozoic.}, journal = {Scientific data}, volume = {9}, number = {1}, pages = {425}, pmid = {35858960}, issn = {2052-4463}, support = {KI 806/17-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; KI 806/17-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; }, mesh = {Animals ; *Anthozoa ; Biological Evolution ; *Coral Reefs ; Databases, Factual ; Fossils ; Phenotype ; }, abstract = {Trait-based approaches are increasingly relevant to understand ecological and evolutionary patterns. A comprehensive trait database for extant reef corals is already available and widely used to reveal vulnerabilities to environmental disturbances including climate change. However, the lack of similar trait compilations for extinct reef builders prevents the derivation of generalities from the fossil record and to address similar questions. Here we present the Ancient Reef Traits Database (ARTD), which aims to compile trait information of various reef-building organisms in one single repository. ARTD contains specimen-level data from both published and unpublished resources. In this first version, we release 15 traits for 505 genera and 1129 species, comprising a dataset of 17,841 trait values of Triassic to mid-Holocene scleractinian corals, the dominant reef-builders in the modern ocean. Other trait data, including for other reef-building organisms, are currently being collated.}, } @article {pmid35857750, year = {2022}, author = {Debnath, J and Meraj, G and Das Pan, N and Chand, K and Debbarma, S and Sahariah, D and Gualtieri, C and Kanga, S and Singh, SK and Farooq, M and Sahu, N and Kumar, P}, title = {Integrated remote sensing and field-based approach to assess the temporal evolution and future projection of meanders: A case study on River Manu in North-Eastern India.}, journal = {PloS one}, volume = {17}, number = {7}, pages = {e0271190}, pmid = {35857750}, issn = {1932-6203}, mesh = {Geographic Information Systems ; India ; *Remote Sensing Technology ; *Rivers ; Soil ; }, abstract = {A common phenomenon associated with alluvial rivers is their meander evolution, eventually forming cutoffs. Point bar deposits and ox-bow lakes are the products of lateral bend migration and meander cutoff. The present study focuses on identifying the meanders of River Manu and their cutoffs. Moreover, this study compares the temporal evolution and predicts the progress of selected meanders of River Manu. In the present research, the Survey of India topographical map, satellite imagery, and geographic information system (GIS) technique were used to examine the evolution of the Manu River meander. Subsequently, a field visit was done to the selected cutoffs and meanders of River Manu to ascertain the present status and collect data. It has been observed that many cutoffs have undergone temporal changes, and their sizes have decreased. Some have become dried or converted to agricultural fields. The width of River Manu has decreased in all the selected bends from 1932 to 2017. The sinuosity index has changed from 2.04 (1932) to 1.90 (2017), and the length of the river has decreased by 7 km in 85 years (1932-2017). The decrease in length is evident from lowering the number of meanders. Uniformity coefficient and coefficient of curvature of the bank soil samples were calculated, indicating that the soil is poorly graded and falls under the cohesionless category. Based on cross-section analysis, sediment discharge, grain-size analysis of the bank material, channel planform change, and radius of curvature, it can be stated that almost all the selected bends have the probability of future cutoff. The highest probabilities were observed in bend 3 (Jalai) and bend 4 (Chhontail). This work is aimed to provide planners with decisions regarding the construction of roads and bridges in areas that show the huge dynamicity of river meandering.}, } @article {pmid35855607, year = {2022}, author = {Bledsoe, EK and Burant, JB and Higino, GT and Roche, DG and Binning, SA and Finlay, K and Pither, J and Pollock, LS and Sunday, JM and Srivastava, DS}, title = {Data rescue: saving environmental data from extinction.}, journal = {Proceedings. Biological sciences}, volume = {289}, number = {1979}, pages = {20220938}, pmid = {35855607}, issn = {1471-2954}, abstract = {Historical and long-term environmental datasets are imperative to understanding how natural systems respond to our changing world. Although immensely valuable, these data are at risk of being lost unless actively curated and archived in data repositories. The practice of data rescue, which we define as identifying, preserving, and sharing valuable data and associated metadata at risk of loss, is an important means of ensuring the long-term viability and accessibility of such datasets. Improvements in policies and best practices around data management will hopefully limit future need for data rescue; these changes, however, do not apply retroactively. While rescuing data is not new, the term lacks formal definition, is often conflated with other terms (i.e. data reuse), and lacks general recommendations. Here, we outline seven key guidelines for effective rescue of historically collected and unmanaged datasets. We discuss prioritization of datasets to rescue, forming effective data rescue teams, preparing the data and associated metadata, and archiving and sharing the rescued materials. In an era of rapid environmental change, the best policy solutions will require evidence from both contemporary and historical sources. It is, therefore, imperative that we identify and preserve valuable, at-risk environmental data before they are lost to science.}, } @article {pmid35855596, year = {2022}, author = {Sieben, AJ and Mihaljevic, JR and Shoemaker, LG}, title = {Quantifying mechanisms of coexistence in disease ecology.}, journal = {Ecology}, volume = {103}, number = {12}, pages = {e3819}, doi = {10.1002/ecy.3819}, pmid = {35855596}, issn = {1939-9170}, mesh = {*Ecosystem ; *Plants ; Models, Biological ; Ecology ; }, abstract = {Pathogen coexistence depends on ecological processes operating at both within and between-host scales, making it difficult to quantify which processes may promote or prevent coexistence. Here, we propose that adapting modern coexistence theory-traditionally applied in plant communities-to pathogen systems provides an exciting approach for examining mechanisms of coexistence operating across different spatial scales. We first overview modern coexistence theory and its mechanistic decomposition; we subsequently adapt the framework to quantify how spatial variation in pathogen density, host resources and immunity, and their interaction may promote pathogen coexistence. We apply this derivation to an example two pathogen, multiscale model comparing two scenarios with generalist and strain-specific immunity: one with demographic equivalency among pathogens and one with demographic trade-offs among pathogens. We then show how host-pathogen feedbacks generate spatial heterogeneity that promote pathogen coexistence and decompose those mechanisms to quantify how each spatial heterogeneity contributes to that coexistence. Specifically, coexistence of demographically equivalent pathogens occurs due to spatial variation in host resources, immune responses, and pathogen aggregation. With a competition-colonization trade-off, the superior colonizer requires spatial heterogeneity to coexist, whereas the superior competitor does not. Finally, we suggest ways forward for linking theory and empirical tests of coexistence in disease systems.}, } @article {pmid35854053, year = {2022}, author = {Schäfer, B and Beck, C and Rhys, H and Soteriou, H and Jennings, P and Beechey, A and Heppell, CM}, title = {Machine learning approach towards explaining water quality dynamics in an urbanised river.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {12346}, pmid = {35854053}, issn = {2045-2322}, support = {Marie-Sklodowska-Curie Grant agreement No 840825/MCCC_/Marie Curie/United Kingdom ; }, mesh = {Ecosystem ; Environmental Monitoring/methods ; Humans ; Machine Learning ; Rivers ; *Water Pollutants, Chemical/analysis ; *Water Quality ; }, abstract = {Human activities alter river water quality and quantity, with consequences for the ecosystems of urbanised rivers. Quantifying the role of human-induced drivers in controlling spatio-temporal patterns in water quality is critical to develop successful strategies for improving the ecological health of urban rivers. Here, we analyse high-frequency electrical conductivity and temperature data collected from the River Chess in South-East England during a Citizen Science project. Utilizing machine learning, we find that boosted trees outperform GAM and accurately describe water quality dynamics with less than 1% error. SHapley Additive exPlanations reveal the importance of and the (inter)dependencies between the individual variables, such as river level and Wastewater Treatment Works (WWTW) outflow. WWTW outflows give rise to diurnal variations in electrical conductivity, which are detectable throughout the year, and to an increase in average water temperature of 1 [Formula: see text] in a 2 km reach downstream of the wastewater treatment works during low flows. Overall, we showcase how high-frequency water quality measurements initiated by a Citizen Science project, together with machine learning techniques, can help untangle key drivers of water quality dynamics in an urbanised chalk stream.}, } @article {pmid35850342, year = {2022}, author = {Cao, X and Chen, W and Ge, X and Chen, X and Wang, J and Ding, J}, title = {Multidimensional soil salinity data mining and evaluation from different satellites.}, journal = {The Science of the total environment}, volume = {846}, number = {}, pages = {157416}, doi = {10.1016/j.scitotenv.2022.157416}, pmid = {35850342}, issn = {1879-1026}, mesh = {Data Mining ; Environmental Monitoring/methods ; Remote Sensing Technology ; *Salinity ; *Soil ; }, abstract = {Soil salinization, a common land degradation mode, restricts the ecological environment and is a global issue due to climate change. Accurately, quickly and effectively monitoring soil salinity is critical for governmental institutions that develop hazard prevention and mitigation strategies. Remote sensing (RS) technology provides a viable alternative to traditional field work due to its large area coverage, abundant spectral information and nearly constant observations. Key issues in RS-based soil salinity monitoring include the lack of both data-mining techniques for obtaining spectral band information and comprehensive considerations of synergies among different spectra. The main objective of this study was to provide in-depth explorations of data mining and integration algorithms from different satellites to multidimensionally evaluate soil salinity models. The Ebinur Lake Wetland Reserve (Xinjiang Province, China) was selected as a case study. First, ground-measured visible and near infrared (VIS-NIR) spectral data were combined with the RS band to simulate Landsat 8 (L8) and Sentinel 2 (S2) and 3 (S3) data. Second, one-dimensional RS bands and 15 soil salinity and vegetation indices were selected, and 15 spectral data transformations (reciprocal, differential, absorbance, etc.) were obtained. Two- and three-dimensional spectral indices were constructed, and the response relationships between different spectral indices and soil electrical conductivity (EC) were comprehensively explored. Finally, an integrated multidimensional algorithm was used to estimate soil salinity in high-performance models for the three satellites. The results showed that all data-mining-based model combinations performed well for all satellites (R[2] > 0.80). However, with multidimensional model combinations, S3 presented the highest predictive capability (R[2] = 0.89, RMSE = 2.57 mS·cm[-1], RPD = 2.05), followed by S2 (R[2] = 0.86, RMSE = 2.71 mS·cm[-1], RPD = 1.90) and L8 (R[2] = 0.85, RMSE = 2.84 mS·cm[-1], RPD = 1.87). Therefore, data mining with integration algorithms in model combinations performs significantly better than previous models and could be considered a promising method for obtaining improved results from soil salinity susceptibility models in similar cases.}, } @article {pmid35845917, year = {2022}, author = {Hemanand, D and Mishra, N and Premalatha, G and Mavaluru, D and Vajpayee, A and Kushwaha, S and Sahile, K}, title = {Applications of Intelligent Model to Analyze the Green Finance for Environmental Development in the Context of Artificial Intelligence.}, journal = {Computational intelligence and neuroscience}, volume = {2022}, number = {}, pages = {2977824}, pmid = {35845917}, issn = {1687-5273}, mesh = {*Artificial Intelligence ; Carbon ; *Financial Management ; Industry ; Investments ; }, abstract = {Green finance can be referred to as financial investments made on sustainable projects and policies that focus on a sustainable economy. The procedures include promoting renewable energy sources, energy efficiency, water sanitation, industrial pollution control, transportation pollution control, reduction of deforestation, and carbon emissions, etc. Mainly, these green finance initiatives are carried out by private and public agents like business organizations, banks, international organizations, government organizations, etc. Green finance provides a financial solution to create a positive impact on society and leads to environmental development. In the age of artificial intelligence, all industries adopt AI technologies. In this research, we see the applications of the intelligent model to examine the green finance for ecological advancement with regard to artificial intelligence. Feasible transportation and energy proficiency and power transmission are two significant fields to be advanced and focused on minimizing the carbon impression in these industries. Renewable sources like solar energies for power generation and electric vehicles are to be researched and developed. This R&D requires a considerable fund supply, thus comes the green finance. Globally, green finance plays a vital role in creating a sustainable environment. In this research, for performing the green finance analysis, financial maximally filtered graph (FMFG) algorithm is implemented in different domains. The proposed algorithm is compared with the neural model and observed that the proposed model has obtained 98.85% of accuracy which is higher than the neural model.}, } @article {pmid35841531, year = {2022}, author = {Agius, PA and Cutts, JC and Song, P and Rudan, I and Rudan, D and Aboyans, V and McDermott, MM and Criqui, MH and Fowkes, FGR and Fowkes, FJI}, title = {The Global Epidemiological Transition in Cardiovascular Diseases: Unrecognised Impact of Endemic Infections on Peripheral Artery Disease.}, journal = {Journal of epidemiology and global health}, volume = {12}, number = {3}, pages = {219-223}, pmid = {35841531}, issn = {2210-6014}, mesh = {*Cardiovascular Diseases/epidemiology ; Humans ; *Noncommunicable Diseases ; *Peripheral Arterial Disease/epidemiology/etiology ; Prevalence ; Risk Factors ; }, abstract = {An epidemiological transition in the prevalence of peripheral artery disease (PAD) is taking place especially in low- and middle-income countries (LMICs) where an ageing population and adoption of western lifestyles are associated with an increase in PAD. We discuss the limited evidence which suggests that infection, potentially mediated by inflammation, may be a risk factor for PAD, and show by means of an ecological analysis that country-level prevalence of the major endemic infections of HIV, tuberculosis and malaria are associated with the prevalence of PAD. While further research is required, we propose that scientists and health authorities pay more attention to the interplay between communicable and non-communicable diseases, and we suggest that limiting the occurrence of endemic infections might have some effect on slowing the epidemiological transition in PAD.}, } @article {pmid35840893, year = {2022}, author = {Mack, M and Stojan, R and Bock, O and Voelcker-Rehage, C}, title = {Cognitive-motor multitasking in older adults: a randomized controlled study on the effects of individual differences on training success.}, journal = {BMC geriatrics}, volume = {22}, number = {1}, pages = {581}, pmid = {35840893}, issn = {1471-2318}, mesh = {Aged ; *Cognition ; Exercise ; Exercise Therapy/methods ; Humans ; *Individuality ; Walking ; }, abstract = {BACKGROUND: Multitasking is an essential part of our everyday life, but performance declines typically in older age. Many studies have investigated the beneficial effects of cognitive, motor and combined cognitive-motor training on multitasking performance in older adults. Previous work, however, has not regarded interindividual differences in cognitive functioning and motor fitness that may affect training benefits. The current study aims to identify whether different training programs may have differential effects on multitasking performance depending on the initial level of cognitive functioning and motor fitness.

METHODS: We conduct a 12-week single-blinded randomized controlled trial. A total of N = 150 healthy older adults are assigned to either a single cognitive, a single motor, or a simultaneous cognitive-motor training. Participants are trained twice per week for 45 min. A comprehensive test battery assesses cognitive functions, motor and cardiovascular fitness, and realistic multitasking during walking and driving in two virtual environments. We evaluate how multitasking performance is related not only to the training program, but also to participants' initial levels of cognitive functioning and motor fitness.

DISCUSSION: We expect that multitasking performance in participants with lower initial competence in either one or both domains (cognitive functioning, motor fitness) benefits more from single-task training (cognitive training and/or motor training). In contrast, multitasking performance in participants with higher competence in both domains should benefit more from multitask training (simultaneous cognitive-motor training). The results may help to identify whether tailored training is favorable over standardized one-size-fits all training approaches to improve multitasking in older adults. In addition, our findings will advance the understanding of factors that influence training effects on multitasking.

TRIAL REGISTRATION: DRKS (German Clinical Trials Register), DRKS00022407. Registered 26/08/2020 - Retrospectively registered at https://www.drks.de/drks_web/setLocale_EN.do.}, } @article {pmid35834176, year = {2022}, author = {Gokyar, S and Voss, HU and Taracila, V and Robb, FJL and Bernico, M and Kelley, D and Ballon, DJ and Winkler, SA}, title = {A pathway towards a two-dimensional, bore-mounted, volume body coil concept for ultra high-field magnetic resonance imaging.}, journal = {NMR in biomedicine}, volume = {35}, number = {12}, pages = {e4802}, doi = {10.1002/nbm.4802}, pmid = {35834176}, issn = {1099-1492}, support = {R00 EB024341/EB/NIBIB NIH HHS/United States ; }, mesh = {Male ; Humans ; *Magnetic Resonance Imaging/methods ; *Radio Waves ; Phantoms, Imaging ; Head ; Brain/diagnostic imaging ; }, abstract = {Lack of a body-sized, bore-mounted, radiofrequency (RF) body coil for ultrahigh field (UHF) magnetic resonance imaging (MRI) is one of the major drawbacks of UHF, hampering the clinical potential of the technology. Transmit field (B1) nonuniformity and low specific absorption rate (SAR) efficiencies in UHF MRI are two challenges to be overcome. To address these problems, and ultimately provide a pathway for the full clinical potential of the modality, we have designed and simulated two-dimensional cylindrical high-pass ladder (2D c-HPL) architectures for clinical bore-size dimensions, and demonstrated a simplified proof of concept with a head-sized prototype at 7 T. A new dispersion relation has been derived and electromagnetic simulations were used to verify coil modes. The coefficient of variation (CV) for brain, cerebellum, heart, and prostate tissues after B1 [+] shimming in silico is reported and compared with previous works. Three prototypes were designed in simulation: a head-sized, body-sized, and long body-sized coil. The head-sized coil showed a CV of 12.3%, a B1 [+] efficiency of 1.33 μT/√W, and a SAR efficiency of 2.14 μT/√(W/kg) for brain simulations. The body-sized 2D c-HPL coil was compared with same-sized transverse electromagnetic (TEM) and birdcage coils in silico with a four-port circularly polarized mode excitation. Improved B1 [+] uniformity (26.9%) and SAR efficiency (16% and 50% better than birdcage and TEM coils, respectively) in spherical phantoms was observed. We achieved a CV of 12.3%, 4.9%, 16.7%, and 2.8% for the brain, cerebellum, heart, and prostate, respectively. Preliminary imaging results for the head-sized coil show good agreement between simulation and experiment. Extending the 1D birdcage coil concept to 2D c-HPLs provides improved B1 [+] uniformity and SAR efficiency.}, } @article {pmid35833012, year = {2022}, author = {Ramirez-Delgado, D and Cicala, F and Gonzalez-Sanchez, RA and Avalos-Tellez, R and Solana-Arellano, E and Licea-Navarro, A}, title = {Multi-locus evaluation of gastrointestinal bacterial communities from Zalophus californianus pups in the Gulf of California, México.}, journal = {PeerJ}, volume = {10}, number = {}, pages = {e13235}, pmid = {35833012}, issn = {2167-8359}, mesh = {Animals ; *Sea Lions/genetics ; RNA, Ribosomal, 16S/genetics ; Mexico ; Bacteria/genetics ; Computational Biology ; }, abstract = {BACKGROUND: The gastrointestinal (GI) bacterial communities of sea lions described to date have occasionally revealed large intraspecific variability, which may originate from several factors including different methodological approaches. Indeed, GI bacterial community surveys commonly rely on the use of a single hypervariable region (HR) of 16S rRNA, which may result in misleading structural interpretations and limit comparisons among studies. Here, we considered a multi-locus analysis by targeting six HRs of 16S rRNA with the aims of (i) comprehensively assessing the GI bacterial consortium in rectal samples from Zalophus californianus pups and (ii) elucidating structural variations among the tested HRs. In addition, we evaluated which HRs may be most suitable for identifying intrinsic, structurally related microbiome characteristics, such as geographic variations or functional capabilities.

METHODS: We employed a Short MUltiple Regions Framework (SMURF) approach using the Ion 16S™ Metagenomic Kit. This kit provides different proprietary primers designed to target six HRs of the 16S rRNA gene. To date, the only analytical pipeline available for this kit is the Ion Reporter™ Software of Thermo Fisher Scientific. Therefore, we propose an in-house pipeline to use with open-access tools, such as QIIME2 and PICRUSt 2, in downstream bioinformatic analyses.

RESULTS: As hypothesized, distinctive bacterial community profiles were observed for each analyzed HR. A higher number of bacterial taxa were detected with the V3 and V6-V7 regions. Conversely, the V8 and V9 regions were less informative, as we detected a lower number of taxa. The synergistic information of these HRs suggests that the GI microbiota of Zalophus californianus pups is predominated by five bacterial phyla: Proteobacteria (~50%), Bacteroidetes (~20%), Firmicutes (~18%), Fusobacteria (~7%), and Epsilonbacteraeota (~4%). Notably, our results differ at times from previously reported abundance profiles, which may promote re-evaluations of the GI bacterial compositions in sea lions and other pinniped species that have been reported to date. Moreover, consistent geographic differences were observed only with the V3, V4, and V6-V7 regions. In addition, these HRs also presented higher numbers of predicted molecular pathways, although no significant functional changes were apparent. Together, our results suggests that multi-locus analysis should be encouraged in GI microbial surveys, as single-locus approaches may result in misleading structural results that hamper the identification of structurally related microbiome features.}, } @article {pmid35830166, year = {2022}, author = {Konstantyner, TCRO and Martins, CB and Góis, AFT and Castro, BVC and Konstantyner, T}, title = {Trend in the incidence rates of accidents with venomous animals in children and adolescents in Brazil (2007-2019).}, journal = {Revista paulista de pediatria : orgao oficial da Sociedade de Pediatria de Sao Paulo}, volume = {41}, number = {}, pages = {e2021272}, pmid = {35830166}, issn = {1984-0462}, mesh = {*Accidents ; Animals ; Brazil/epidemiology ; Humans ; Incidence ; Information Systems ; *Venoms ; }, abstract = {OBJECTIVE: To estimate the temporal trend of the incidence rates of accidents with venomous animals in children and adolescents in Brazil.

METHODS: An ecological time-series study was carried out between 2007 and 2019. Data were obtained from the Brazilian Information System on Diseases of Compulsory Declaration (Sistema de Informação de Agravos de Notificação - SINAN). The time series of incidence rates of accidents with venomous animals were stratified by age group (children aged 0 to 9 years and adolescents aged 10 to 19 years), Brazilian macro-regions (North, Northeast, Midwest, Southeast, and South), and type of accident (snake, scorpion, spider, and caterpillar). For trend analysis, the Prais-Winsten model and the Annual Percent Change (APC) were used.

RESULTS: The time series of the incidence rate of accidents with venomous animals in children and adolescents from the North, Northeast, Midwest, and Southeast macro-regions and in children from the South region showed an upward trend. The average annual incidence rates were higher in the age group of 10 to 19 years, except for the South macro-region. Accidents with scorpions, snakes, and spiders, in this order, were the most frequent; the trends in the time series stratified by type of animal varied according to the geographic macro-region.

CONCLUSIONS: There was an upward trend in the incidence rate of accidents with venomous animals in children and adolescents in Brazil, except for adolescents in the South macro-region of the country.}, } @article {pmid35829803, year = {2023}, author = {Kapp, JM and Micheas, L and Holmes, S and Stormont, M and Reinke, WM}, title = {Prevalence of Poor Mental Health Days and Adverse Childhood Experience Reporting in U.S. Adults Before and After COVID-19.}, journal = {Community mental health journal}, volume = {59}, number = {2}, pages = {233-242}, pmid = {35829803}, issn = {1573-2789}, mesh = {Adult ; Humans ; Mental Health ; *Adverse Childhood Experiences ; Prevalence ; *COVID-19/epidemiology ; *Mental Disorders/epidemiology ; }, abstract = {This is the first study of US adults to examine change in the prevalence of psychological burden (i.e., self-reported poor mental health days in the past 30 days, and ACEs recollections) before compared to after COVID-19 started. We analyzed the prevalence of self-reported poor mental health days, and ACEs recollections from 17 states using the Behavioral Risk Factor Surveillance System. Adjusted models identified an increase in prevalence from before compared to after COVID-19 onset in those married or partnered reporting 48% more poor mental health days in the past 30 days; persons of color reporting living with anyone with mental illness during childhood by 73% and reporting more ACEs by 35%; those employed or self-employed reporting childhood sexual abuse by 45%. This ecological-level analysis revealed population-level changes in psychological well-being reporting of U.S. adults from before compared to after the pandemic onset.}, } @article {pmid37745777, year = {2022}, author = {Boyes, D and , and , and , and , and , and Godfray, C and Holland, PWH and , }, title = {The genome sequence of the dun-bar pinion, Cosmia trapezina (Linnaeus, 1758).}, journal = {Wellcome open research}, volume = {7}, number = {}, pages = {189}, pmid = {37745777}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual male Cosmia trapezina (dun-bar pinion; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 825 megabases in span. The majority of the assembly (99.87%) is scaffolded into 32 chromosomal pseudomolecules with the Z chromosome assembled. The complete mitochondrial genome was also assembled and is 15.4 kilobases in length.}, } @article {pmid35817763, year = {2022}, author = {Brophy, JK and Matthews, GJ}, title = {Reference database of teeth images from the Family Bovidae.}, journal = {Scientific data}, volume = {9}, number = {1}, pages = {396}, pmid = {35817763}, issn = {2052-4463}, mesh = {Animals ; *Cattle ; Databases, Factual ; *Fossils ; Paleodontology ; Tooth/diagnostic imaging ; }, abstract = {Researchers typically rely on fossils from the Family Bovidae to generate African paleoenvironmental reconstructions due to their strict ecological tendencies. Bovids have dominated the southern African fauna for the past four million years and, therefore, dominate the fossil faunal assemblages, especially isolated teeth. Traditionally, researchers reference modern and fossil comparative collections to identify teeth. However, researchers are limited by the specific type and number of bovids at each institution. B.O.V.I.D. (Bovidae Occlusal Visual IDentification) is a repository of images of the occlusal surface of bovid teeth. The dataset currently includes extant bovids from 7 tribes and 20 species (~3900). B.O.V.I.D. contains two scaled images per specimen: a color and a black and white (binarized) image. The database is a useful reference for identifying bovid teeth. The large sample size also allows one to observe the natural variation that exists in each taxa. The binarized images can be used in statistical shape analyses, such as taxonomic classification. B.O.V.I.D. is a valuable supplement to other methods for taxonomically identifying bovid teeth.}, } @article {pmid35817397, year = {2022}, author = {Gloria-Soria, A and Faraji, A and Hamik, J and White, G and Amsberry, S and Donahue, M and Buss, B and Pless, E and Cosme, LV and Powell, JR}, title = {Origins of high latitude introductions of Aedes aegypti to Nebraska and Utah during 2019.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {103}, number = {}, pages = {105333}, doi = {10.1016/j.meegid.2022.105333}, pmid = {35817397}, issn = {1567-7257}, mesh = {*Aedes/genetics ; Animals ; Humans ; *Mosquito Vectors/genetics ; Nebraska/epidemiology ; Utah/epidemiology ; Yellow Fever ; Zika Virus ; Zika Virus Infection ; }, abstract = {Aedes aegypti (L.), the yellow fever mosquito, is also an important vector of dengue and Zika viruses, and an invasive species in North America. Aedes aegypti inhabits tropical and sub-tropical areas of the world and in North America is primarily distributed throughout the southern US states and Mexico. The northern range of Ae. aegypti is limited by cold winter months and establishment in these areas has been mostly unsuccessful. However, frequent introductions of Ae. aegypti to temperate, non-endemic areas during the warmer months can lead to seasonal activity and disease outbreaks. Two Ae. aegypti incursions were reported in the late summer of 2019 into York, Nebraska and Moab, Utah. These states had no history of established populations of this mosquito and no evidence of previous seasonal activity. We genotyped a subset of individuals from each location at 12 microsatellite loci and ~ 14,000 single nucleotide polymorphic markers to determine their genetic affinities to other populations worldwide and investigate their potential source of introduction. Our results support a single origin for each of the introductions from different sources. Aedes aegypti from Utah likely derived from Tucson, Arizona, or a nearby location. Nebraska specimen results were not as conclusive, but point to an origin from southcentral or southeastern US. In addition to an effective, efficient, and sustainable control of invasive mosquitoes, such as Ae. aegypti, identifying the potential routes of introduction will be key to prevent future incursions and assess their potential health threat based on the ability of the source population to transmit a particular virus and its insecticide resistance profile, which may complicate vector control.}, } @article {pmid35816807, year = {2022}, author = {Wu, X and Zhou, Q and Mu, L and Hu, X}, title = {Machine learning in the identification, prediction and exploration of environmental toxicology: Challenges and perspectives.}, journal = {Journal of hazardous materials}, volume = {438}, number = {}, pages = {129487}, doi = {10.1016/j.jhazmat.2022.129487}, pmid = {35816807}, issn = {1873-3336}, mesh = {Algorithms ; Databases, Factual ; *Ecotoxicology ; Hazardous Substances ; *Machine Learning ; }, abstract = {Over the past few decades, data-driven machine learning (ML) has distinguished itself from hypothesis-driven studies and has recently received much attention in environmental toxicology. However, the use of ML in environmental toxicology remains in the early stages, with knowledge gaps, technical bottlenecks in data quality, high-dimensional/heterogeneous/small-sample data analysis and model interpretability, and a lack of an in-depth understanding of environmental toxicology. Given the above problems, we review the recent progress in the literature and highlight state-of-the-art toxicological studies using ML (such as learning and predicting toxicity in complicated biosystems and multiple-factor environmental scenarios of long-term and large-scale pollution). Beyond predicting simple biological endpoints by integrating untargeted omics and adverse outcome pathways, ML development should focus on revealing toxicological mechanisms. The integration of data-driven ML with other methods (e.g., omics analysis and adverse outcome pathway frameworks) endows ML with widely promising application in revealing toxicological mechanisms. High-quality databases and interpretable algorithms are urgently needed for toxicology and environmental science. Addressing the core issues and future challenges for ML in this review may narrow the knowledge gap between environmental toxicity and computational science and facilitate the control of environmental risk in the future.}, } @article {pmid35810285, year = {2022}, author = {Borges, G and Garcia, JA and Pirkis, J and Spittal, MJ and Gunnell, D and Sinyor, M and John, A}, title = {A state level analyses of suicide and the COVID-19 pandemic in Mexico.}, journal = {BMC psychiatry}, volume = {22}, number = {1}, pages = {460}, pmid = {35810285}, issn = {1471-244X}, mesh = {*COVID-19/epidemiology ; Humans ; Interrupted Time Series Analysis ; Mexico/epidemiology ; Pandemics ; *Suicide ; }, abstract = {BACKGROUND: While suicide rates in high- and middle-income countries appeared stable in the early stages of the pandemic, we know little about within-country variations. We sought to investigate the impact of COVID-19 on suicide in Mexico's 32 states and to identify factors that may have contributed to observed variations between states.

METHODS: Interrupted time-series analysis to model the trend in monthly suicides before COVID-19 (from Jan 1, 2010, to March 31, 2020), comparing the expected number of suicides derived from the model with the observed number for the remainder of the year (April 1 to December 31, 2020) for each of Mexico's 32 states. Next, we modeled state-level trends using linear regression to study likely contributing factors at ecological level.

RESULTS: Suicide increased slightly across Mexico during the first nine months of the pandemic (RR 1.03; 95%CI 1.01-1.05). Suicides remained stable in 19 states, increase in seven states (RR range: 1.12-2.04) and a decrease in six states (RR range: 0.46-0.88). Suicide RR at the state level was positively associated with population density in 2020 and state level suicide death rate in 2019.

CONCLUSIONS: The COVID-19 pandemic had a differential effect on suicide death within the 32 states of Mexico. Higher population density and higher suicide rates in 2019 were associated with increased suicide. As the country struggles to cope with the ongoing pandemic, efforts to improve access to primary care and mental health care services (including suicide crisis intervention services) in these settings should be given priority.}, } @article {pmid35808154, year = {2022}, author = {Han, J and Xu, C and An, Z and Qian, K and Tan, W and Wang, D and Fang, Q}, title = {PRAPNet: A Parallel Residual Atrous Pyramid Network for Polyp Segmentation.}, journal = {Sensors (Basel, Switzerland)}, volume = {22}, number = {13}, pages = {}, pmid = {35808154}, issn = {1424-8220}, support = {2019YFC0117800//the National Key Research and Development Program of China/ ; }, mesh = {Colonoscopy ; Deep Learning ; Humans ; *Image Processing, Computer-Assisted/methods ; *Intestinal Polyps/diagnostic imaging ; *Neural Networks, Computer ; }, abstract = {In a colonoscopy, accurate computer-aided polyp detection and segmentation can help endoscopists to remove abnormal tissue. This reduces the chance of polyps developing into cancer, which is of great importance. In this paper, we propose a neural network (parallel residual atrous pyramid network or PRAPNet) based on a parallel residual atrous pyramid module for the segmentation of intestinal polyp detection. We made full use of the global contextual information of the different regions by the proposed parallel residual atrous pyramid module. The experimental results showed that our proposed global prior module could effectively achieve better segmentation results in the intestinal polyp segmentation task compared with the previously published results. The mean intersection over union and dice coefficient of the model in the Kvasir-SEG dataset were 90.4% and 94.2%, respectively. The experimental results outperformed the scores achieved by the seven classical segmentation network models (U-Net, U-Net++, ResUNet++, praNet, CaraNet, SFFormer-L, TransFuse-L).}, } @article {pmid35805698, year = {2022}, author = {Eichinger, M and Bechtoldt, M and Bui, ITM and Grund, J and Keller, J and Lau, AG and Liu, S and Neuber, M and Peter, F and Pohle, C and Reese, G and Schäfer, F and Heinzel, S}, title = {Evaluating the Public Climate School-A School-Based Programme to Promote Climate Awareness and Action in Students: Protocol of a Cluster-Controlled Pilot Study.}, journal = {International journal of environmental research and public health}, volume = {19}, number = {13}, pages = {}, pmid = {35805698}, issn = {1660-4601}, mesh = {Adolescent ; Humans ; Peer Group ; Pilot Projects ; Program Evaluation ; Randomized Controlled Trials as Topic ; School Health Services ; *Schools ; *Students ; }, abstract = {Introduction: School-based programmes may promote knowledge and skills required to address climate change and better health and well-being in adolescents, yet evidence of their effectiveness is limited. In preparation for evaluating the Public Climate School, a school-based intervention to promote climate awareness and action in adolescents, we conduct a pilot study intended to assess procedures for participant recruitment, retention, and data collection, data quality issues and to provide preliminary parameter estimates to guide sample size calculations. Methods and analysis: This unblinded, cluster-controlled pilot study targets students in twelve classes from grades seven to thirteen in German public schools. Seven and five classes were allocated to the intervention and waitlist control arms, respectively. The intervention consisted of (1) live lessons on YouTube, (2) climate-related challenges of the day, (3) workshops and (4) peer exchange sessions. Waitlist control classes participated three weeks later. Measures included the proportion of students completing baseline and follow-up surveys, a comparison of baseline characteristics between students in the retained subsample and those lost to follow-up, proportions of students completing online and paper-pencil-based surveys and problems during data collection based on information reported by teachers. Data quality was assessed as proportions of missing data, associations between missingness and sociodemographic measures using logistic regression models and basic psychometric properties of scales including ceiling effects and internal consistency. Intentions to reduce one's ecological footprint, the primary outcome, and all secondary outcomes for effect estimation were assessed one week pre- and post-intervention from November to December 2021 using items adapted from internationally used instruments and will be investigated using generalised linear mixed models and intention-to-treat analyses. Conclusions: The pilot study will lay the methodological groundwork for a large-scale cluster-randomised effectiveness and process evaluation of the Public Climate School. If proven effective and rolled out more broadly, the Public Climate School has the potential to contribute meaningfully to national climate mitigation and adaptation efforts by reaching a substantial share of adolescents in public schools, including those traditionally less involved in climate action.}, } @article {pmid35795771, year = {2022}, author = {Zhai, Y and Li, W}, title = {Evaluation and Change Analysis of Ecosystem Service Value of China's Northeast Tiger-Leopard National Park Based on Big Data Land Use Change.}, journal = {Computational intelligence and neuroscience}, volume = {2022}, number = {}, pages = {6270731}, pmid = {35795771}, issn = {1687-5273}, mesh = {Animals ; Big Data ; China ; Conservation of Natural Resources/methods ; Ecosystem ; *Panthera ; Parks, Recreational ; *Tigers ; }, abstract = {The aim of the construction of Northeast Tiger-Leopard National Park is to protect the integrity of endangered wild animals and natural resources. There is a close relationship between land use and ecosystem service value. Improving the quality of ecological environment is the demand of ecological civilization construction. Therefore, this paper aims to evaluate and analyze the ecosystem service value of Tiger and Leopard Park, which is particularly based on big data land use change. Firstly, using ArcGIS software as the support, we have discussed the impact of the dynamic trend of land use change, transfer matrix, and sensitivity coefficient on ecosystem services in different periods of Tiger and Leopard Park. Secondly, we constructed an evaluation model based on the ecological service value method, which is primarily based on geographical conditions and surface coverage. We have completed the value evaluation and change analysis of ecosystem service in Tiger and Leopard Park by analyzing the generation process of ecosystem service data and information characteristics, as well as the ecosystem classification standard of Tiger and Leopard Park and equivalent factor of ecosystem service value per unit area. Simulation experiments show that the method proposed in this paper can reflect the service value of the ecosystem of the Tiger and Leopard Park, lay the foundation for the construction of ecotourism, and promote the green and sustainable development of the regional ecosystem of the Tiger and Leopard Park.}, } @article {pmid35795770, year = {2022}, author = {Zhou, Z and Wang, H and Hu, Q and Zhou, M}, title = {GIS Multimedia Technology in Regional Construction Land Suitability Evaluation in Mountainous Villages and Towns.}, journal = {Computational intelligence and neuroscience}, volume = {2022}, number = {}, pages = {8305285}, pmid = {35795770}, issn = {1687-5273}, mesh = {Cities ; Cluster Analysis ; *Geographic Information Systems ; Information Technology ; *Multimedia ; }, abstract = {In order to explore the suitability evaluation of regional construction land in mountainous villages and towns, a method based on GIS technology is proposed. Supported by GIS and RS technology, the Delphi method is used to determine the natural, socioeconomic, and ecological security factors affecting the ecological suitability of regional construction land in mountainous villages and towns, and analytic hierarchy process is used to calculate the weight of relevant influencing factors. Following the principle of giving priority to ecological protection, a set of ecological suitability evaluation model system and method of regional construction land in mountainous villages and towns are established, based on which the basic ecological control areas of mountainous villages and towns in the study area are divided, so as to provide suggestions for rational and effective planning of land resources in mountainous villages and towns. The experimental results show that the K-means clustering method is divided into five categories: the most suitable land, the more suitable land, the basically suitable land, the unsuitable land, and the unavailable land. Finally, according to the suitability grade system of construction land, it is reclassified, the unsuitable land and unavailable land are divided into basic ecological control areas, the most suitable land and more suitable land are divided into construction control areas, and the basically suitable land is listed as ecological buffer areas. It is proved that the basic ecological control area determined by the model method is basically consistent with the current basic ecological control line of a city, which shows that the model is practical and scientific.}, } @article {pmid35794151, year = {2022}, author = {Riley, M and Meagher, P and Huveneers, C and Leto, J and Peddemors, VM and Slip, D and West, J and Bradshaw, CJA}, title = {The Australian Shark-Incident Database for quantifying temporal and spatial patterns of shark-human conflict.}, journal = {Scientific data}, volume = {9}, number = {1}, pages = {378}, pmid = {35794151}, issn = {2052-4463}, mesh = {Animals ; *Bites and Stings/epidemiology ; Databases, Factual ; Fisheries ; Humans ; Northern Territory ; *Sharks ; }, abstract = {We describe the Australian Shark-Incident Database, formerly known as the Australian Shark-Attack File, which contains comprehensive reports of 1,196 shark bites that have occurred in Australia over 231 years (1791-2022). Data were collated by the Taronga Conservation Society Australia using purpose-designed questionnaires provided to shark-bite victims or witnesses, media reports, and information provided by the department responsible for fisheries in each Australian state (including the Northern Territory). The dataset includes provoked and unprovoked bites from fresh, brackish, and marine waters in Australia. Data span 22 suspected shark species. This dataset will be publicly available, and can be used by analysts to decipher environmental, biological, and social patterns of shark bites in Australia. The information will aid scientists, conservationists, authorities, and members of the public to make informed decisions when implementing or selecting mitigation measures.}, } @article {pmid35792777, year = {2022}, author = {Nascimento, MID and Przibilski, ALF and Coelho, CSG and Leite, KFA and Makenze, M and Jesus, SB}, title = {Mortality attributed to sickle cell disease in children and adolescents in Brazil, 2000-2019.}, journal = {Revista de saude publica}, volume = {56}, number = {}, pages = {65}, pmid = {35792777}, issn = {1518-8787}, mesh = {Adolescent ; Adult ; *Anemia, Sickle Cell ; Brazil/epidemiology ; Child ; Child, Preschool ; Data Collection ; Female ; Humans ; Infant, Newborn ; *Information Systems ; Male ; Young Adult ; }, abstract = {OBJECTIVE: Estimate rates and describe mortality trends attributed to sickle cell disease in children and adolescents in Brazil from 2000 to 2019.

METHODS: This is an ecological study of the time-trend of mortality rates that used the autoregressive method, proposed by Prais-Winsten, to evaluate trends in the estimated rates of sickle cell disease deaths in children and adolescents in Brazil. Deaths with code D57 were obtained from the Mortality Information System, considering age groups (0-4, 5-9, 10-14, 15-19 years) and were used to estimate age-specific and standardized rates by gender and age.

RESULTS: From 2000 to 2019, Brazil had 2,422 deaths from sickle cell disease in people under 20 years of age, with higher frequency in the Northeast (40.46%), followed by the Southeast (39.02%), Midwest (9.58%), North (7.84%), and South (3.10%). The main victims were people of Black skin/race (78.73%). In Brazil, the global standardized average rate was 0.20/100,000 people-year, with an elevation trend (annual percentage change - APC = 5.44%; confidence interval - 95%CI: 2.57-8.39). The pattern was repeated in males (APC = 4.38%; 95%CI: 2.17-6.64) and females (APC = 6.96%; 95%CI: 3.05-11.01). Elaborating age-specific rates showed that the range up to four years experienced the highest rates, without distinction by region. The age group of 15 and 19 years was the second most affected in Brazil and in the Northeast, Southeast, and Midwest regions.

CONCLUSION: Deaths due to sickle cell disorders showed an elevation trend in children and adolescents. Considering that the magnitude of deaths was more evident in the first years (0-4) and late adolescence (15-19), the study suggests that age-specific approaches may impact the control of fatal outcomes caused by sickle cell disease in Brazil.}, } @article {pmid35791567, year = {2022}, author = {Ma, J and Dong, WX and Zhu, YF and Xiao, D and Chen, F}, title = {[Characteristics and Assembly Process of Reclaimed Soil Microbial Communities in Eastern Plain Mining Areas].}, journal = {Huan jing ke xue= Huanjing kexue}, volume = {43}, number = {7}, pages = {3844-3853}, doi = {10.13227/j.hjkx.202110018}, pmid = {35791567}, issn = {0250-3301}, mesh = {Acidobacteria ; Bacteroidetes ; *Microbiota ; RNA, Ribosomal, 16S ; *Soil ; }, abstract = {Understanding how soil microorganisms respond to land reclamation is essential to evaluating the success of ecological restoration actions in disturbed mine soil. However, the microbiological mechanism referred to as productivity reconstruction of the reclaimed soil is still unclear. To shed light on this mechanism, a total of 75 soil samples were collected for 16S rRNA amplicon high-throughput sequencing. The five sampling sites contained four reclamation plots (reclaimed 8 a, 11 a, 14 a, and 17 a) and 1 non-reclaimed plot, which served as the control sampling site. The microbial community composition, potential functions, and assembly mechanisms were also analyzed. The results showed that:①the richness of the microbial community increased with the reclamation time and was higher than that of the control site. However, the community diversity and evenness decreased with the increasing reclamation year (P<0.05). ②Acidobacteria, Chloroflexi, Proteobacteria, and Bacteroidetes dominated in the reclaimed soil, and the relative abundances of the first two phyla were significantly higher than that of the control (P<0.05), whereas the latter two presented the opposite trends (P<0.05). ③ Eight functions, including coenzyme transport and metabolism, translation, ribosomal structure, and biogenesis, showed a positive succession in the reclamation sites and enhanced with increasing reclamation years. ④ The molecular ecological networks of the microbial community in the plain mining area were well modular, whereas the key microbial groups belonged to the Acidobacteria and Bacteroidetes. The microbial communities were dominantly assembled with the deterministic process, and the homogeneous selection contributed the most, which might have been mainly controlled by the local special environment. The results presented herein will undoubtedly aid in the establishment of success indicators of ecological restoration activities in disturbed mining soil. These findings also provide the theoretical basis for improving the productivity and ecological services of reclaimed soil.}, } @article {pmid35791366, year = {2022}, author = {Zheng, C and Yang, X and Liu, Z and Liu, K and Huang, Y}, title = {Spatial distribution of soil nutrients and evaluation of cultivated land in Xuwen county.}, journal = {PeerJ}, volume = {10}, number = {}, pages = {e13239}, pmid = {35791366}, issn = {2167-8359}, mesh = {*Soil/chemistry ; *Agriculture ; Geographic Information Systems ; Nutrients ; Phosphorus ; Nitrogen/analysis ; }, abstract = {It is of great significance to promote the quantitative research of soil science and the implementation of precision agriculture. On this basis, taking Xuwen County as the research object, this paper comprehensively analyzed the soil characteristics of cultivated land in Xuwen County and clarify the soil nutrient content and spatial distribution characteristics of cultivated land in Xuwen County, this paper comprehensively applied the methods of geostatistics, geographic information system (GIS) and fuzzy mathematics, and referred to the cultivated land quality grade standard (GB/T 33469-2016), to analyze the soil characteristics and evaluate the soil fertility of this region. The results show that the optimal interpolation model of soil pH and available phosphorus (AP) is a Gaussian model, and the optimal interpolation model of soil organic matter (SOM), available nitrogen (AN) and available potassium (AK) is a J-Bessel model. In addition, the spatial correlation of AK is weak, whereas pH, SOM, AN and AP show moderate spatial correlation. The proportion of excellent, good, average, medium and poor comprehensive fertility index are 26.00%, 32.67%, 19.33%, 19.00% and 3.00%, respectively. The overall level of soil fertility in Xuwen County is above the average, and the fertility quality presents an obvious trend of high in the South and low in the North. Areas that above average fertility are mainly distributed in Maichen Town, Qujie Town, Nanshan Town and Chengbei Town. The results can provide theoretical basis for improving the utilization rate of chemical fertilizer, fine management of cultivated land and ecological environment in this region, which can help in decision-making of precision fertilization.}, } @article {pmid35790740, year = {2022}, author = {Beninde, J and Toffelmier, EM and Andreas, A and Nishioka, C and Slay, M and Soto, A and Bueno, JP and Gonzalez, G and Pham, HV and Posta, M and Pace, JL and Shaffer, HB}, title = {CaliPopGen: A genetic and life history database for the fauna and flora of California.}, journal = {Scientific data}, volume = {9}, number = {1}, pages = {380}, pmid = {35790740}, issn = {2052-4463}, support = {R25 GM055052/GM/NIGMS NIH HHS/United States ; BE 6887/1-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; }, mesh = {Animals ; California ; *Databases, Factual ; Ecosystem ; Fishes/genetics ; *Genetics, Population ; Humans ; Microsatellite Repeats ; }, abstract = {CaliPopGen is a database of population genetic data for native and naturalized eukaryotic species in California, USA. It summarizes the published literature (1985-2020) for 5,453 unique populations with genetic data from more than 187,394 individuals and 448 species (513 species plus subspecies) across molecular markers including allozymes, RFLPs, mtDNA, microsatellites, nDNA, and SNPs. Terrestrial habitats accounted for the majority (46.4%) of the genetic data. Taxonomic groups with the greatest representation were Magnoliophyta (20.31%), Insecta (13.4%), and Actinopterygii (12.85%). CaliPopGen also reports life-history data for most included species to enable analyses of the drivers of genetic diversity across the state. The large number of populations and wide taxonomic breadth will facilitate explorations of ecological patterns and processes across the varied geography of California. CaliPopGen covers all terrestrial and marine ecoregions of California and has a greater density of species and georeferenced populations than any previously published population genetic database. It is thus uniquely suited to inform conservation management at the regional and state levels across taxonomic groups.}, } @article {pmid35789323, year = {2022}, author = {Baranasic, D and Hörtenhuber, M and Balwierz, PJ and Zehnder, T and Mukarram, AK and Nepal, C and Várnai, C and Hadzhiev, Y and Jimenez-Gonzalez, A and Li, N and Wragg, J and D'Orazio, FM and Relic, D and Pachkov, M and Díaz, N and Hernández-Rodríguez, B and Chen, Z and Stoiber, M and Dong, M and Stevens, I and Ross, SE and Eagle, A and Martin, R and Obasaju, O and Rastegar, S and McGarvey, AC and Kopp, W and Chambers, E and Wang, D and Kim, HR and Acemel, RD and Naranjo, S and Łapiński, M and Chong, V and Mathavan, S and Peers, B and Sauka-Spengler, T and Vingron, M and Carninci, P and Ohler, U and Lacadie, SA and Burgess, SM and Winata, C and van Eeden, F and Vaquerizas, JM and Gómez-Skarmeta, JL and Onichtchouk, D and Brown, BJ and Bogdanovic, O and van Nimwegen, E and Westerfield, M and Wardle, FC and Daub, CO and Lenhard, B and Müller, F}, title = {Multiomic atlas with functional stratification and developmental dynamics of zebrafish cis-regulatory elements.}, journal = {Nature genetics}, volume = {54}, number = {7}, pages = {1037-1050}, pmid = {35789323}, issn = {1546-1718}, support = {U24 HG002659/HG/NHGRI NIH HHS/United States ; BB/R015457/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; MC_UP_1102/1/MRC_/Medical Research Council/United Kingdom ; MC_EX_MR/S300007/1/MRC_/Medical Research Council/United Kingdom ; 106955/WT_/Wellcome Trust/United Kingdom ; P61715/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; MC_UP_1605/10/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Animals ; Chromatin/genetics ; *Databases, Genetic ; *Gene Expression Regulation, Developmental ; *Genome/genetics ; *Genomics ; Humans ; Mice ; Molecular Sequence Annotation ; Organogenesis/genetics ; *Regulatory Sequences, Nucleic Acid/genetics ; *Zebrafish/embryology/genetics ; *Zebrafish Proteins/genetics ; }, abstract = {Zebrafish, a popular organism for studying embryonic development and for modeling human diseases, has so far lacked a systematic functional annotation program akin to those in other animal models. To address this, we formed the international DANIO-CODE consortium and created a central repository to store and process zebrafish developmental functional genomic data. Our data coordination center (https://danio-code.zfin.org) combines a total of 1,802 sets of unpublished and re-analyzed published genomic data, which we used to improve existing annotations and show its utility in experimental design. We identified over 140,000 cis-regulatory elements throughout development, including classes with distinct features dependent on their activity in time and space. We delineated the distinct distance topology and chromatin features between regulatory elements active during zygotic genome activation and those active during organogenesis. Finally, we matched regulatory elements and epigenomic landscapes between zebrafish and mouse and predicted functional relationships between them beyond sequence similarity, thus extending the utility of zebrafish developmental genomics to mammals.}, } @article {pmid35788820, year = {2022}, author = {Li, J and Miao, B and Wang, S and Dong, W and Xu, H and Si, C and Wang, W and Duan, S and Lou, J and Bao, Z and Zeng, H and Yang, Z and Cheng, W and Zhao, F and Zeng, J and Liu, XS and Wu, R and Shen, Y and Chen, Z and Chen, S and Wang, M and , }, title = {Hiplot: a comprehensive and easy-to-use web service for boosting publication-ready biomedical data visualization.}, journal = {Briefings in bioinformatics}, volume = {23}, number = {4}, pages = {}, doi = {10.1093/bib/bbac261}, pmid = {35788820}, issn = {1477-4054}, mesh = {Computational Biology/methods ; Data Visualization ; Genomics ; Humans ; *Software ; *User-Computer Interface ; }, abstract = {Complex biomedical data generated during clinical, omics and mechanism-based experiments have increasingly been exploited through cloud- and visualization-based data mining techniques. However, the scientific community still lacks an easy-to-use web service for the comprehensive visualization of biomedical data, particularly high-quality and publication-ready graphics that allow easy scaling and updatability according to user demands. Therefore, we propose a community-driven modern web service, Hiplot (https://hiplot.org), with concise and top-quality data visualization applications for the life sciences and biomedical fields. This web service permits users to conveniently and interactively complete a few specialized visualization tasks that previously could only be conducted by senior bioinformatics or biostatistics researchers. It covers most of the daily demands of biomedical researchers with its equipped 240+ biomedical data visualization functions, involving basic statistics, multi-omics, regression, clustering, dimensional reduction, meta-analysis, survival analysis, risk modelling, etc. Moreover, to improve the efficiency in use and development of plugins, we introduced some core advantages on the client-/server-side of the website, such as spreadsheet-based data importing, cross-platform command-line controller (Hctl), multi-user plumber workers, JavaScript Object Notation-based plugin system, easy data/parameters, results and errors reproduction and real-time updates mode. Meanwhile, using demo/real data sets and benchmark tests, we explored statistical parameters, cancer genomic landscapes, disease risk factors and the performance of website based on selected native plugins. The statistics of visits and user numbers could further reflect the potential impact of this web service on relevant fields. Thus, researchers devoted to life and data sciences would benefit from this emerging and free web service.}, } @article {pmid35787295, year = {2022}, author = {Zeng, J and Tu, Q and Yu, X and Qian, L and Wang, C and Shu, L and Liu, F and Liu, S and Huang, Z and He, J and Yan, Q and He, Z}, title = {PCycDB: a comprehensive and accurate database for fast analysis of phosphorus cycling genes.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {101}, pmid = {35787295}, issn = {2049-2618}, mesh = {Bacteria/genetics ; Databases, Factual ; Metagenome/genetics ; *Microbiota ; *Phosphorus ; }, abstract = {BACKGROUND: Phosphorus (P) is one of the most essential macronutrients on the planet, and microorganisms (including bacteria and archaea) play a key role in P cycling in all living things and ecosystems. However, our comprehensive understanding of key P cycling genes (PCGs) and microorganisms (PCMs) as well as their ecological functions remains elusive even with the rapid advancement of metagenome sequencing technologies. One of major challenges is a lack of a comprehensive and accurately annotated P cycling functional gene database.

RESULTS: In this study, we constructed a well-curated P cycling database (PCycDB) covering 139 gene families and 10 P metabolic processes, including several previously ignored PCGs such as pafA encoding phosphate-insensitive phosphatase, ptxABCD (phosphite-related genes), and novel aepXVWPS genes for 2-aminoethylphosphonate transporters. We achieved an annotation accuracy, positive predictive value (PPV), sensitivity, specificity, and negative predictive value (NPV) of 99.8%, 96.1%, 99.9%, 99.8%, and 99.9%, respectively, for simulated gene datasets. Compared to other orthology databases, PCycDB is more accurate, more comprehensive, and faster to profile the PCGs. We used PCycDB to analyze P cycling microbial communities from representative natural and engineered environments and showed that PCycDB could apply to different environments.

CONCLUSIONS: We demonstrate that PCycDB is a powerful tool for advancing our understanding of microbially driven P cycling in the environment with high coverage, high accuracy, and rapid analysis of metagenome sequencing data. The PCycDB is available at https://github.com/ZengJiaxiong/Phosphorus-cycling-database . Video Abstract.}, } @article {pmid35785929, year = {2022}, author = {Nocci, M and Ragazzoni, L and Barone-Adesi, F and Hubloue, I and Romagnoli, S and Peris, A and Bertini, P and Scolletta, S and Cipollini, F and Mechi, MT and Della Corte, F}, title = {Dynamic assessment of surge capacity in a large hospital network during COVID-19 pandemic.}, journal = {Minerva anestesiologica}, volume = {88}, number = {11}, pages = {928-938}, doi = {10.23736/S0375-9393.22.16460-6}, pmid = {35785929}, issn = {1827-1596}, mesh = {Humans ; *Surge Capacity ; *COVID-19 ; Pandemics ; Hospital Bed Capacity ; Intensive Care Units ; Hospitals ; }, abstract = {BACKGROUND: The COVID-19 pandemic has provided an unprecedented scenario to deepen knowledge of surge capacity (SC), assessment of which remains a challenge. This study reports a large-scale experience of a multi-hospital network, with the aim of evaluating the characteristics of different hospitals involved in the response and of measuring a real-time SC based on two complementary modalities (actual, base) referring to the intensive care units (ICU).

METHODS: Data analysis referred to two consecutive pandemic waves (March-December 2020). Regarding SC, two different levels of analysis are considered: single hospital category (referring to a six-level categorization based on the number of hospital beds) and multi-hospital wide (referring to the response of the entire hospital network).

RESULTS: During the period of 114 days, the analysis revealed a key role of the biggest hospitals (>Category-4) in terms of involvement in the pandemic response. In terms of SC, Category-4 hospitals showed the highest mean SC values, irrespective of the calculation method and level of analysis. At the multi-hospital level, the analysis revealed an overall ICU-SC (base) of 84.4% and an ICU-SC (actual) of 106.5%.

CONCLUSIONS: The results provide benchmarks to better understand ICU hospital response capacity, highlighting the need for a more flexible approach to SC definition.}, } @article {pmid35783389, year = {2022}, author = {Glaser, K and Van, AT and Pushkareva, E and Barrantes, I and Karsten, U}, title = {Microbial Communities in Biocrusts Are Recruited From the Neighboring Sand at Coastal Dunes Along the Baltic Sea.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {859447}, pmid = {35783389}, issn = {1664-302X}, abstract = {Biological soil crusts occur worldwide as pioneer communities stabilizing the soil surface. In coastal primary sand dunes, vascular plants cannot sustain due to scarce nutrients and the low-water-holding capacity of the sand sediment. Thus, besides planted dune grass, biocrusts are the only vegetation there. Although biocrusts can reach high coverage rates in coastal sand dunes, studies about their biodiversity are rare. Here, we present a comprehensive overview of the biodiversity of microorganisms in such biocrusts and the neighboring sand from sampling sites along the Baltic Sea coast. The biodiversity of Bacteria, Cyanobacteria, Fungi, and other microbial Eukaryota were assessed using high-throughput sequencing (HTS) with a mixture of universal and group-specific primers. The results showed that the biocrusts recruit their microorganisms mainly from the neighboring sand rather than supporting a universal biocrust microbiome. Although in biocrusts the taxa richness was lower than in sand, five times more co-occurrences were identified using network analysis. This study showed that by comparing neighboring bare surface substrates with biocrusts holds the potential to better understand biocrust development. In addition, the target sequencing approach helps outline potential biotic interactions between different microorganisms groups and identify key players during biocrust development.}, } @article {pmid35779528, year = {2022}, author = {de Ferran, V and Figueiró, HV and de Jesus Trindade, F and Smith, O and Sinding, MS and Trinca, CS and Lazzari, GZ and Veron, G and Vianna, JA and Barbanera, F and Kliver, S and Serdyukova, N and Bulyonkova, T and Ryder, OA and Gilbert, MTP and Koepfli, KP and Eizirik, E}, title = {Phylogenomics of the world's otters.}, journal = {Current biology : CB}, volume = {32}, number = {16}, pages = {3650-3658.e4}, doi = {10.1016/j.cub.2022.06.036}, pmid = {35779528}, issn = {1879-0445}, mesh = {Animals ; Base Sequence ; *Otters/genetics ; Phylogeny ; }, abstract = {Comparative whole-genome analyses hold great power to illuminate commonalities and differences in the evolution of related species that share similar ecologies. The mustelid subfamily Lutrinae includes 13 currently recognized extant species of otters,[1-5] a semiaquatic group whose evolutionary history is incompletely understood. We assembled a dataset comprising 24 genomes from all living otter species, 14 of which were newly sequenced. We used this dataset to infer phylogenetic relationships and divergence times, to characterize patterns of genome-wide genealogical discordance, and to investigate demographic history and current genomic diversity. We found that genera Lutra, Aonyx, Amblonyx, and Lutrogale form a coherent clade that should be synonymized under Lutra, simplifying the taxonomic structure of the subfamily. The poorly known tropical African Aonyx congicus and the more widespread Aonyx capensis were found to be reciprocally monophyletic (having diverged 440,000 years ago), supporting the validity of the former as a distinct species. We observed variable changes in effective population sizes over time among otters within and among continents, although several species showed similar trends of expansions and declines during the last 100,000 years. This has led to different levels of genomic diversity assessed by overall heterozygosity, genome-wide SNV density, and run of homozygosity burden. Interestingly, there were cases in which diversity metrics were consistent with the current threat status (mostly based on census size), highlighting the potential of genomic data for conservation assessment. Overall, our results shed light on otter evolutionary history and provide a framework for further in-depth comparative genomic studies targeting this group.}, } @article {pmid35779167, year = {2022}, author = {Güneri, FD and Karaarslan, F and Forestıer, FBE and Forestıer, RJ and Odabaşı, E}, title = {Publication activity in water treatments: Web of Science-based bibliometric analysis of the last two decades.}, journal = {International journal of biometeorology}, volume = {66}, number = {9}, pages = {1829-1839}, pmid = {35779167}, issn = {1432-1254}, mesh = {*Bibliometrics ; Databases, Factual ; Efficiency ; *Mineral Waters ; Turkey ; }, abstract = {We evaluated the quantity and quality of scientific publications linked with water treatments using the Web of Science (WoS) database. The WoS was searching by using the following terms "hydrotherapy," "balneotherapy," "spa therapy," "spa treatment," "creno-balneotherapy," "water treatments," and "aqua therapy," on February 10th, 2022. The recorded data were the total number of articles, year of articles, country of articles, journal, document type, index data, and citation data. Also, the studies performed with natural source mineral water were marked to make a further subgroup analysis through quality and quantity. We obtained 816 articles; 667 (81.74%) were original research articles, and 149 (18.26%) were review articles. A statistically significant and increasing trend was shown in the publication about water treatments (p < 0.01). About three-quarters of the trials were sourced from high-income countries. Italy (n = 98; 12.01%); Turkey (n = 75; 9.19%); Australia (n = 65; 7.97%); Brazil (n = 46; 5.64%); and France (n = 38; 4.66%) were the most productive countries. Calculating the number of articles per million population, Hungary (3.38), Australia (2.53), and Italy (1.64) ranked in the top three. According to 100 billion dollars GDP, the top three countries were Brazil (24.41), Hungary (21.15), and Turkey (10.41). In the average citation calculation, the Netherlands (60.84), Israel (29.86), and Australia (29.06) were in the top three. The International Journal of Biometeorology was the leading journal for publication trials about water treatments. In the subgroup analysis, we found the total number of studies performed with natural source mineral water and non-specified source water trials as 430 and 386, respectively. We also presented that the natural source and non-specified water trials had a statistically significant and increasing trend between 2000 and 2021 (p < 0.01 and p < 0.01, respectively). The trials performed with natural source water mainly were sourced from Italy (n = 79; 18.37%), Turkey (n = 61; 14.19%), France (n = 38; 8.84%), Poland (n = 30; 6.98%), and Hungary (n = 29; 6.74%), the trials performed with non-specified water were sourced from Australia (n = 61; 15.80%), Brazil (n = 46; 11.92%), USA (n = 27; 6.99%), Italy (n = 19; 4.92%), and England (n = 18; 4.66%). The top journal of the natural source water trials was the International Journal of Biometeorology (n = 65; 15.12%), and for the non-specified water trials, it was the International Journal of Sports Physiology (n = 12; 3.11%).Our study presented an increasing trend in trial publications regarding water treatments between 2000 and 2021. Most of the trials were from high and upper-middle-income countries. We suggest that by demonstrating global productivity worldwide, our results can create more scientific attention on this topic and may promote the quantity and quality of the trials.}, } @article {pmid35778947, year = {2022}, author = {Tercel, MPTG and Cuff, JP}, title = {The complex epistemological challenge of data curation in dietary metabarcoding: Comment on "The precautionary principle and dietary DNA metabarcoding: Commonly used abundance thresholds change ecological interpretation" by Littleford-Colquhoun et al. (2022).}, journal = {Molecular ecology}, volume = {31}, number = {22}, pages = {5653-5659}, doi = {10.1111/mec.16576}, pmid = {35778947}, issn = {1365-294X}, mesh = {*DNA Barcoding, Taxonomic/methods ; *Data Curation ; Diet ; DNA/genetics ; }, abstract = {In their article, Littleford-Colquhoun et al. (2022) advise against using arbitrary relative read abundance (RRA) thresholds (i.e., minimum sequence copy thresholds) for removing low-abundance sequences since they can increase false negative rates in dietary DNA metabarcoding data sets. The main criticisms presented against these widespread methods are that they (i) are arbitrary, often existing as standard values or defined based on researcher-selected delineations, (ii) are subjective, varying between studies and contexts, and, most problematically, (iii) result in the exclusion of true positives, particularly rarely consumed taxa, to the detriment of ecological insight. We commend the authors for presenting a refreshing and timely perspective on this often neglected topic, which is certainly in need of greater discussion following over a decade of significant advances in dietary metabarcoding. In this complex epistemological problem of false positives versus false negatives, we feel that several of the points raised deserve additional discussion. We address these aspects below, including measured approaches to data filtration and consistent representation of RRAs, and we welcome any further discourse to solidify or refute the concepts therein.}, } @article {pmid35776271, year = {2022}, author = {Thirumurthy, S and Jayanthi, M and Samynathan, M and Duraisamy, M and Kabiraj, S and Vijayakumar, S and Anbazhahan, N}, title = {Assessment of spatial-temporal changes in water bodies and its influencing factors using remote sensing and GIS - a model study in the southeast coast of India.}, journal = {Environmental monitoring and assessment}, volume = {194}, number = {8}, pages = {548}, pmid = {35776271}, issn = {1573-2959}, mesh = {Environmental Monitoring ; *Geographic Information Systems ; India ; *Remote Sensing Technology ; Water ; }, abstract = {Concerns have been raised about the threat of ecological imbalance due to the loss of water bodies in densely populated areas. The present study explored the changes in water bodies in terms of area, number, and size in northern districts of Tamil Nadu, India, between 1978 and 2018 using satellite data, geographic information system, spatial analysis, ground truth verification, and field validation. The analysis indicated that the water bodies' area has reduced by 3027 ha and 4363 ha in the Kancheepuram and Tiruvallur Districts, respectively. Almost 179 water bodies have entirely disappeared, and 628 water bodies have been partly converted for other purposes. Of the disappeared water bodies, small, medium, and large water bodies account for 53, 93, and 33, respectively. The main reason for the changes in water bodies was the conversion to agriculture and buildings. Overall, the water bodies' area and number have been reduced by 9% and 12%, respectively, while the population has grown by 37%. The water bodies lost due to anthropogenic activities demand the scientific inventory of water bodies and integrated water resources management at a state or national level with strict monitoring regulations to protect them.}, } @article {pmid35775972, year = {2022}, author = {Feeney, MA and Newitt, JT and Addington, E and Algora-Gallardo, L and Allan, C and Balis, L and Birke, AS and Castaño-Espriu, L and Charkoudian, LK and Devine, R and Gayrard, D and Hamilton, J and Hennrich, O and Hoskisson, PA and Keith-Baker, M and Klein, JG and Kruasuwan, W and Mark, DR and Mast, Y and McHugh, RE and McLean, TC and Mohit, E and Munnoch, JT and Murray, J and Noble, K and Otani, H and Parra, J and Pereira, CF and Perry, L and Pintor-Escobar, L and Pritchard, L and Prudence, SMM and Russell, AH and Schniete, JK and Seipke, RF and Sélem-Mojica, N and Undabarrena, A and Vind, K and van Wezel, GP and Wilkinson, B and Worsley, SF and Duncan, KR and Fernández-Martínez, LT and Hutchings, MI}, title = {ActinoBase: tools and protocols for researchers working on Streptomyces and other filamentous actinobacteria.}, journal = {Microbial genomics}, volume = {8}, number = {7}, pages = {}, pmid = {35775972}, issn = {2057-5858}, support = {BB/T001038/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/R022054/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/T004126/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/N023544/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/V000993/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/V017586/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/T008075/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/T014962/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/S016651/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/W000628/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/T015446/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/S00811X/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/P005292/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/F009429/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/J/000PR9790/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; G0801721/MRC_/Medical Research Council/United Kingdom ; BB/M011216/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {*Actinobacteria/genetics ; Anti-Bacterial Agents ; *Streptomyces/genetics ; }, abstract = {Actinobacteria is an ancient phylum of Gram-positive bacteria with a characteristic high GC content to their DNA. The ActinoBase Wiki is focused on the filamentous actinobacteria, such as Streptomyces species, and the techniques and growth conditions used to study them. These organisms are studied because of their complex developmental life cycles and diverse specialised metabolism which produces many of the antibiotics currently used in the clinic. ActinoBase is a community effort that provides valuable and freely accessible resources, including protocols and practical information about filamentous actinobacteria. It is aimed at enabling knowledge exchange between members of the international research community working with these fascinating bacteria. ActinoBase is an anchor platform that underpins worldwide efforts to understand the ecology, biology and metabolic potential of these organisms. There are two key differences that set ActinoBase apart from other Wiki-based platforms: [1] ActinoBase is specifically aimed at researchers working on filamentous actinobacteria and is tailored to help users overcome challenges working with these bacteria and [2] it provides a freely accessible resource with global networking opportunities for researchers with a broad range of experience in this field.}, } @article {pmid35775333, year = {2022}, author = {Partezani, AD and Duarte-Santos, HO and Amaral, BS and Gomes Barbosa, AR and Apezzato, M and Brunhara, J and Bianco, B and Lemos, GC and Carneiro, A}, title = {Outcomes of nephrectomy for renal cell carcinoma: An ecologic retrospective study in a middle-income country.}, journal = {Archivio italiano di urologia, andrologia : organo ufficiale [di] Societa italiana di ecografia urologica e nefrologica}, volume = {94}, number = {2}, pages = {129-133}, doi = {10.4081/aiua.2022.2.129}, pmid = {35775333}, issn = {2282-4197}, mesh = {Brazil ; *Carcinoma, Renal Cell/surgery ; Humans ; *Kidney Neoplasms/surgery ; Nephrectomy/methods ; Retrospective Studies ; Treatment Outcome ; }, abstract = {OBJECTIVE: The aim of this study was to describe and compare the outcomes and indirect costs of oncological radical (RN) and partial nephrectomies (PN) in hospitals from the São Paulo public health system, Brazil.

MATERIALS AND METHODS: An ecologic retrospective study was performed from 2008 to 2019, using the TabNet Platform of the Brazilian Unified Health System Department of Informatics. Hospitals were classified according to volume of surgeries (low and high-volume, and also into four quartiles according to volume of surgeries), and with or without medical residency program in urology. The results were compared between groups.

RESULTS: In the period analyzed were performed 2.606 RN in 16 hospitals. Data available for PN ranged only from 2013-2019 and included 1.223 surgeries comprising 15 hospitals. Overall mortality rates were 0.41% for PN and 2.87% for RN. The length of hospital stay was significantly higher in low-volume hospitals for both RN and PN (8.97 vs. 5.62 days, p = 0.001, and 7.75 vs. 4.37 days, p = 0.001, respectively), and also for the RN in hospitals without residency program in Urology (9.37 vs. 6.54 days, p = 0.03). When the volume of surgeries was divided into four quartiles, the length of hospital stay and ICU hospitalization days were significantly higher in the first quartile hospitals for RN (p = 0.016) and PN (p = 0.009), respectively. The mortality rates and indirect costs were not different considering PN and RN in the different types of hospitals.

CONCLUSIONS: The length of hospital stay was significantly lower for both PN and RN in high-volume hospitals, and also for RN in hospitals with residency program in Urology.}, } @article {pmid35773545, year = {2022}, author = {Sarkar, I and Dey, P and Rathore, SS and Singh, GD and Singh, RP}, title = {Global genomic and proteomic analysis indicates co-evolution of Neisseria species and with their human host.}, journal = {World journal of microbiology & biotechnology}, volume = {38}, number = {9}, pages = {149}, pmid = {35773545}, issn = {1573-0972}, mesh = {Computational Biology ; Genome, Bacterial/genetics ; Genomics ; Humans ; *Neisseria/genetics ; *Proteomics ; }, abstract = {Neisseria, a genus from the beta-proteobacteria class, is of potential clinical importance. This genus contains both pathogenic and commensal strains. Gonorrhea and meningitis are two major diseases caused by pathogens belonging to this genus. With the increased use of antimicrobial agents against these pathogens they have evolved the antimicrobial resistance capacity making these diseases nearly untreatable. The set of anti-bacterial resistance genes (resistome) and genes associated with signal processing (secretomes) are crucial for the host-microbial interaction. With the virtue of whole-genome sequences and computational biology, it is now possible to study the genomic and proteomic riddles of Neisseria along with their comprehensive evolutionary and metabolic profiling. We have studied relative synonymous codon usage, amino acid usage, reverse ecology, comparative genomics, evolutionary analysis and pathogen-host (Neisseria-human) interaction through bioinformatics analysis. Our analysis revealed the co-evolution of Neisseria genomes with the human host. Moreover, the co-occurrence of Neisseria and humans has been supported through reverse ecology analysis. A differential pattern of the evolutionary rate of resistomes and secretomes was evident among the pathogenic and commensal strains. Comparative genomics supported the presence of virulent genes in both pathogenic and commensal strains of the select genus. Our analysis also indicated a transition from commensal to pathogenic Neisseria strains through the long run of evolution.}, } @article {pmid35773456, year = {2022}, author = {Nelder, MP and Russell, CB and Johnson, S and Li, Y and Cronin, K and Cawston, T and Patel, SN}, title = {American dog ticks along their expanding range edge in Ontario, Canada.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {11063}, pmid = {35773456}, issn = {2045-2322}, mesh = {Animals ; Data Collection ; Dogs ; *Ixodes ; New Jersey ; Ontario/epidemiology ; *Rhipicephalus sanguineus ; }, abstract = {The American dog tick, Dermacentor variabilis, is a tick of public and veterinary health importance in North America. Using passive tick surveillance data, we document distribution changes for the American dog tick in Ontario, Canada, from 2010 through 2018. Dermacentor variabilis submissions from the public were geocoded and aggregated-from large to small administrative geographies-by health region, public health unit (PHU) and Forward Sortation Area (FSA). PHU hot spots with high rates of D. variabilis submissions were (1) Brant County, Haldimand-Norfolk and Niagara Regional in the Central West region and (2) Lambton and Winsor-Essex County in the South West region. The number of established D. variabilis populations with ≥ 6 submissions per year increased significantly during the study at regional (PHUs: 22 to 31) and local (FSAs: 27 to 91) scales. The range of D. variabilis increased similarly to the positive control (Ixodes scapularis) during the study and in contrast to the static range of the negative control (Ixodes cookei). Submission hot spots were in warmer, low elevation areas with poorly drained soils, compared to the province's low submission areas. Dermacentor variabilis is spreading in Ontario and continued research into their vector ecology is required to assess medicoveterinary health risks.}, } @article {pmid35770028, year = {2022}, author = {Xiao, D and He, H and Yan, X and Keita, M and Diaz, ND and Chen, D and Ma, J and Zhang, Y and Li, J and Julien, EO and Yan, X}, title = {Dataset of response characteristics of H2-producing bacteria consortium to β-lactams, aminoglycosides, macrolides, quinolones antibiotics.}, journal = {Data in brief}, volume = {43}, number = {}, pages = {108354}, pmid = {35770028}, issn = {2352-3409}, abstract = {Antibiotics on H2 producing bacteria shall be considered as being one of the critical elements in biological H2 production utilizing livestock manure as raw resources. Despite the fact that the manure stands a significance role in bio-fermentation, the possibility of antibiotics being contained in excreta shall not be eliminated. Findings of whether the above saying might threaten the safety of bio-H2 production needs to be further studied. The experiment subjects include: six single and three combined antibiotics were tested and analyzed by the application of the gradient experiment method. Along with the H2 production rate, CHO content, pH and OD600 were used to analyze the effects of various antibiotics introduction on the hydrolysis, fermentation and H2 production. To a further extent, four typical representative samples were selected for biodiversity analysis from the single antibiotic experiment groups. Amounting more than 6000 pieces of data were obtained in a series of experiments. Data suggested that remarkable measure of antibiotics have various degrees of H2 production inhibition, while some antibiotics, Penicillin G, Streptomycin Sulfate, and their compound antibiotics, could promote the growth of Ethanoligenens sp. and improve H2 yield in the contrary. Correspondent to the transition of key metabolic intermediates and end products, the mechanism of each antibiotic type and dose on H2 production were summarized as follows: the main inhibitory mechanisms were: (1) board-spectrum inhibition, (2) partial inhibition, (3) H2 consumption enhancement; and the enhancement mechanisms were: (1) enhance the growth of H2-producing bacteria, (2) enhanced starch hydrolysis, (3) inhibitory H2 consumption or release of acid inhibition. Meanwhile, data analysis found that the effect of antibiotics on H2 producing was not only related to type, but also to dosage. Even one kind of antibiotic may have completely opposite effects on H2-producing bacteria under different dosage conditions. Inhibition of H2 yield was highest with Levofloxacin at 6.15 mg/L, gas production was reduced by 88.77%; and enhancement of H2 yield was highest with Penicillin G at 7.20 mg/L, the gas production increased by 72.90%.}, } @article {pmid35767644, year = {2022}, author = {Tietje, M and Antonelli, A and Baker, WJ and Govaerts, R and Smith, SA and Eiserhardt, WL}, title = {Global variation in diversification rate and species richness are unlinked in plants.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {119}, number = {27}, pages = {e2120662119}, pmid = {35767644}, issn = {1091-6490}, mesh = {Biodiversity ; Climate ; Datasets as Topic ; Ecosystem ; *Extinction, Biological ; *Genetic Speciation ; Phylogeny ; *Plants/classification/genetics ; }, abstract = {Species richness varies immensely around the world. Variation in the rate of diversification (speciation minus extinction) is often hypothesized to explain this pattern, while alternative explanations invoke time or ecological carrying capacities as drivers. Focusing on seed plants, the world's most important engineers of terrestrial ecosystems, we investigated the role of diversification rate as a link between the environment and global species richness patterns. Applying structural equation modeling to a comprehensive distribution dataset and phylogenetic tree covering all circa 332,000 seed plant species and 99.9% of the world's terrestrial surface (excluding Antarctica), we test five broad hypotheses postulating that diversification serves as a mechanistic link between species richness and climate, climatic stability, seasonality, environmental heterogeneity, or the distribution of biomes. Our results show that the global patterns of species richness and diversification rate are entirely independent. Diversification rates were not highest in warm and wet climates, running counter to the Metabolic Theory of Ecology, one of the dominant explanations for global gradients in species richness. Instead, diversification rates were highest in edaphically diverse, dry areas that have experienced climate change during the Neogene. Meanwhile, we confirmed climate and environmental heterogeneity as the main drivers of species richness, but these effects did not involve diversification rates as a mechanistic link, calling for alternative explanations. We conclude that high species richness is likely driven by the antiquity of wet tropical areas (supporting the "tropical conservatism hypothesis") or the high ecological carrying capacity of warm, wet, and/or environmentally heterogeneous environments.}, } @article {pmid35767535, year = {2022}, author = {Wild, TA and Koblitz, JC and Dechmann, DKN and Dietz, C and Meboldt, M and Wikelski, M}, title = {Micro-sized open-source and low-cost GPS loggers below 1 g minimise the impact on animals while collecting thousands of fixes.}, journal = {PloS one}, volume = {17}, number = {6}, pages = {e0267730}, pmid = {35767535}, issn = {1932-6203}, mesh = {Animals ; Animals, Wild ; Dogs ; *Ecology/methods ; *Geographic Information Systems ; Movement ; }, abstract = {GPS-enabled loggers have been proven as valuable tools for monitoring and understanding animal movement, behaviour and ecology. While the importance of recording accurate location estimates is well established, deployment on many, especially small species, has been limited by logger mass and cost. We developed an open-source and low-cost 0.65 g GPS logger with a simple smartphone-compatible user interface, that can record more than 10,000 GPS fixes on a single 30 mAh battery charge (resulting mass including battery: 1.3 g). This low-budget 'TickTag' (currently 32 USD) allows scientists to scale-up studies while becoming a 'wearable' for larger animals and simultaneously enabling high-definition studies on small animals. Tests on two different species (domestic dog, Canis lupus familiaris and greater mouse-eared bats, Myotis myotis) showed that our combination of optimised hardware design and software-based recording strategies increases the number of achievable GPS fixes per g device mass compared to existing micro-sized solutions. We propose that due to the open-source access, as well as low cost and mass, the TickTag fills a technological gap in wildlife ecology and will open up new possibilities for wildlife research and conservation.}, } @article {pmid35767189, year = {2022}, author = {Drozdovitch, V and Kukhta, T and Trofimik, S and Melo, DR and Viarenich, K and Podgaiskaya, M and Minenko, V}, title = {Doses from external irradiation and ingestion of [134]Cs, [137]Cs and [90]Sr of the population of Belarus accumulated over 35 years after the Chernobyl accident.}, journal = {Radiation and environmental biophysics}, volume = {61}, number = {3}, pages = {445-464}, pmid = {35767189}, issn = {1432-2099}, support = {Z99 CA999999/ImNIH/Intramural NIH HHS/United States ; }, mesh = {Animals ; Cattle ; Cesium Radioisotopes ; *Chernobyl Nuclear Accident ; Eating ; Female ; Radiation Dosage ; Republic of Belarus ; Strontium Radioisotopes ; }, abstract = {This study considers the exposure of the population of the most contaminated Gomel and Mogilev Oblasts in Belarus to prolonged sources of irradiation resulting from the Chernobyl accident. Dose reconstruction methods were developed and applied in this study to estimate the red bone-marrow doses (RBMs) from (i) external irradiation from gamma-emitting radionuclides deposited on the ground and (ii) [134]Cs, [137]Cs and [90]Sr ingestion with locally produced foodstuffs. The mean population-weighted RBM doses accumulated during 35 years after the Chernobyl accident were 12 and 5.7 mGy for adult residents in Gomel and Mogilev Oblasts, respectively, while doses for youngest age groups were 20-40% lower. The highest mean area-specific RBM doses for adults accumulated in 1986-2021 were 63, 56 and 46 mGy in Narovlya, Vetka and Korma raions in Gomel Oblast, respectively. For most areas, external irradiation was the predominant pathway of exposure (60-70% from the total dose), except for areas with an extremely high aggregated [137]Cs soil to cow's milk transfer coefficient (≥ 5.0 Bq L[-1] per kBq m[-2]), where the contribution of [134]Cs and [137]Cs ingestion to the total RBM dose was more than 70%. The contribution of [90]Sr intake to the total RBM dose did not exceed 4% for adults and 10% for newborns in most raion in Gomel and Mogilev Oblasts. The validity of the doses estimated in this study was assessed by comparison with doses obtained from measurements by thermoluminescence dosimeters and whole-body counters done in 1987-2015. The methodology developed in this study can be used to calculate doses to target organs other than RBM such as thyroid and breast doses. The age-dependent and population-weighted doses estimated in this study are useful for ecological epidemiological studies, for projection of radiation risk, and for justification of analytical epidemiological studies in populations exposed to Chernobyl fallout.}, } @article {pmid35766770, year = {2022}, author = {Caló, RDS and Souza, RAG and Alves, MR and Lima, FCDS and Galvão, ND and Souza, BDSN and Aguilar, LB}, title = {Trends in the incidence of colorectal cancer in Greater Cuiabá, Mato Grosso (Brazil), from 2000 to 2016.}, journal = {Revista brasileira de epidemiologia = Brazilian journal of epidemiology}, volume = {25}, number = {Supl 1}, pages = {e220013}, doi = {10.1590/1980-549720220013.supl.1}, pmid = {35766770}, issn = {1980-5497}, mesh = {Adult ; Aged ; Female ; Humans ; Male ; Middle Aged ; Brazil/epidemiology ; *Colorectal Neoplasms/epidemiology ; Incidence ; *Information Systems ; }, abstract = {OBJECTIVE: To analyze the temporal incidence trend of colorectal cancer (CRC), according to sex and age, in the Greater Cuiabá, Mato Grosso, Brazil, from 2000 to 2016.

METHODS: Ecological time series study, with cases of CRC (C18 to C21) diagnosed from 2000 to 2016, of residents of the Greater Cuiabá (Cuiabá and Várzea Grande), in Mato Grosso. The information on the cases was obtained from the Population-Based Cancer Registry and population data from the Brazilian Institute of Geography and Statistics (IBGE). The rates were adjusted by world population. The age groups considered ranged from 30 to 39 years, 40 to 49 years, 50 to 59 years, 60 to 69 years, 70 to 79 years and 80 years and older. Joinpoint regression was used to analyze the trend of incidence.

RESULTS: A total of 1,715 cases of CRC were registered with information on sex and age, with an adjusted rate of 16.4 new cases/100,000 men and 16.1 new cases/100,000 women. Men presented trend of increasing incidence rates in the age group of 70 to 79 years, with increase of 4.0% per year, while women presented trend of increase in the age group 50 to 59 years, with increase of 2.7% per year.

CONCLUSION: Older men showed a more significant trend towards an increase in the incidence of CRC, but in women this occurred in a younger age group, highlighting the importance of considering age related information in the analyzes of occurrence of the disease in this population.}, } @article {pmid35766767, year = {2022}, author = {Oliveira, JFP and Lima, FCDS and Galvão, ND and Souza, PCF}, title = {Cancer Incidence in Mato Grosso state, Brazil: analysis of population-based registries (2007 a 2011).}, journal = {Revista brasileira de epidemiologia = Brazilian journal of epidemiology}, volume = {25}, number = {Supl 1}, pages = {e220010}, doi = {10.1590/1980-549720220010.supl.1}, pmid = {35766767}, issn = {1980-5497}, mesh = {Brazil/epidemiology ; Female ; Humans ; Incidence ; *Information Systems ; Male ; *Neoplasms/epidemiology ; Registries ; }, abstract = {OBJECTIVE: To analyze five types of cancer health region in the state of Mato Grosso according to sex.

METHODS: A descriptive ecological study of the health regions of Mato Grosso state using two data sets on the incidence of population-based cancer registries in Mato Grosso - inland and Cuiabá. Age-adjusted annual incidence rates were calculated for the world population in 1960, according to sex, for the period comprising 2007 to 2011.

RESULTS: Although we are still facing problems related to data completeness and quality, the most common cancer types were prostate, female breast, cervix, lung, colorectal and stomach cancer in the state of Mato Grosso from 2007 to 2011. The most frequent types among men were prostate and lung cancer. Among women, breast and cervix cancer were the most frequent ones. The highest incidence rates of cancer per 100,000 inhabitants were found in health regions Tangará da Serra, Sinop, Rondonópolis, and Porto Alegre do Norte.

CONCLUSIONS: Identifying the main types of cancer is important for the improvement of cancer prevention and control actions, as well as to understand its magnitude and impact on society. We must continue to improve the quality of information available in population-based cancer records in the state of Mato Grosso, Brazil.}, } @article {pmid35766764, year = {2022}, author = {Carvalho, AE and Souza, RAG and Galvão, ND and Melanda, FN and Caló, RDS and Souza, BDSN and Lima, FCDS and Aguilar, LB}, title = {Colorectal cancer mortality trend in Mato Grosso, Brazil, 2000 to 2019.}, journal = {Revista brasileira de epidemiologia = Brazilian journal of epidemiology}, volume = {25}, number = {Supl 1}, pages = {e220007}, doi = {10.1590/1980-549720220007.supl.1}, pmid = {35766764}, issn = {1980-5497}, mesh = {Female ; Humans ; Male ; Brazil/epidemiology ; *Colorectal Neoplasms ; Geography ; *Information Systems ; }, abstract = {OBJECTIVE: To analyze the time series of colorectal cancer (CRC) mortality, according to sex and age group, in Mato Grosso, Brazil, from 2000 to 2019.

METHODS: Ecological time series study, with standardized mortality rates from CRC (C18 to C21) among residents of Mato Grosso. Information on deaths was provided by the Mato Grosso State Health Department, comprising the Mortality Information System and demographic information obtained from the Brazilian Institute of Geography and Statistics. The joinpoint regression analysis was used in the analysis of temporal trend.

RESULTS: A total of 2,406 deaths from CRC were identified in Mato Grosso between 2000 and 2019. The highest rates were found among the age group from 60 to 79 years. There was an increasing trend in mortality rates among men due to CRC for almost all age groups, with the exception of those aged 40 to 49 years and 80 years and older. For women, there was a significant increase in the age groups from 50 to 59 years and 80 years and older.

CONCLUSION: The results showed an increase in mortality rates from CRC in the state of Mato Grosso, from 2000 to 2019, in certain age groups for both sexes, but especially for men. Knowledge about the evolution of mortality can provide data on the epidemiological situation of cancer at the local level and, thus, contribute to the development of actions to control and prevent this disease.}, } @article {pmid35766762, year = {2022}, author = {Modesto, VC and Evangelista, FM and Soares, MR and Alves, MR and Neves, MABD and Corrêa, MLM and Sousa, NFDSE and Galvão, ND and Andrade, ACS}, title = {Cancer mortality in the State of Mato Grosso from 2000 to 2015: temporal trend and regional differences.}, journal = {Revista brasileira de epidemiologia = Brazilian journal of epidemiology}, volume = {25}, number = {Supl 1}, pages = {e220005}, doi = {10.1590/1980-549720220005.supl.1}, pmid = {35766762}, issn = {1980-5497}, mesh = {Brazil/epidemiology ; Humans ; *Information Systems ; *Liver Neoplasms ; Male ; Time Factors ; }, abstract = {OBJECTIVE: To analyze the trend of standardized cancer mortality rate in the state of Mato Grosso according to health regions, from 2000 to 2015.

METHODS: Ecological time series study with data on deaths by cancer from the Mortality Information System. The rates were standardized using direct method and calculated by year and health regions. The annual percentage changes (APC) and respective confidence interval (95%CI) were obtained through simple linear regression. Thematic maps were built to show the spatial distribution of rates.

RESULTS: There were 28,525 deaths by cancer registered in Mato Grosso, with the main types being lung, prostate, stomach, breast and liver cancer. The highest mortality rates were found in regions Médio Norte, Baixada Cuiabana and Sul Mato-Grossense. From 2000 to 2015, an upward trend was seen in the mortality rate by cancer in Mato Grosso (APC=0.81%; 95%CI 0.38-1.26), and in four health regions, Garças Araguaia (APC=2.27%; 95%CI 1.46-3.08), Sul Mato-Grossense (APC=1.12%; 95%CI 0.28-1.97), Teles Pires (APC=1.93%; 95%CI 0,11-3,74) and Vale dos Arinos (APC=2.61%; 95%CI 1.10-4.70), while the other regions remained stable.

CONCLUSION: In the state of Mato Grosso and in the four health regions, cancer mortality rate showed a growing trend. The results point to the need to consider regional differences when thinking about actions for cancer prevention, control and assistance.}, } @article {pmid35766761, year = {2022}, author = {Aguilar, LB and Gomes, CV and Lima Neto, GS and Montenegro, LHF and Oliveira, JCS and Galvão, ND and Melanda, FN and Alves, MR and Souza, BDSN}, title = {Mortality trend of cancer and main types according to macroregion in the state of Mato Grosso, Brazil, 2000 to 2015.}, journal = {Revista brasileira de epidemiologia = Brazilian journal of epidemiology}, volume = {25}, number = {Supl 1}, pages = {e220004}, doi = {10.1590/1980-549720220004.supl.1}, pmid = {35766761}, issn = {1980-5497}, mesh = {Brazil/epidemiology ; *Colorectal Neoplasms ; Humans ; *Information Systems ; Male ; Time Factors ; }, abstract = {OBJECTIVE: To describe the mortality trend from all cancers and the five main ones in the state of Mato Grosso, Brazil, from 2000 to 2015.

METHODS: This is a descriptive, ecological, time series study, with data referring to deaths of residents of Mato Grosso due to cancer (ICD-10 codes C00 to C97), from the Mortality Information System (SIM). Time trend analyses of the standardized mortality rate from all cancers and five specific cancers (lung, prostate, breast, colorectal and cervical) for the state and according to macroregion (South, West, North, East and Center-North) were performed using linear regression (p<0.05).

RESULTS: From 2000 to 2015, 28,525 deaths from all cancers in residents of the state of Mato Grosso were recorded. An increasing trend was observed for all cancers, in addition to lung, breast and colorectal cancers. The South and North macroregions showed an increasing trend for all cancers, breast and colorectal, and Center-North for breast and colorectal. East showed an increasing trend for all cancers, prostate and colorectal, and decreasing for cervical.

CONCLUSION: In the state of Mato Grosso, there was an increasing trend in mortality for all cancers and from specific ones, with emphasis on breast and colorectal cancer in most macroregions.}, } @article {pmid35766760, year = {2022}, author = {Souza, BDSN and Lima, DV and Caló, RDS and Oliveira, JCS and Andrade, ACS and Oliveira, LR and Galvão, ND}, title = {Trend of incompleteness of cancer death records in the Mortality Information System database, state of Mato Grosso, Brazil, 2000 to 2016.}, journal = {Revista brasileira de epidemiologia = Brazilian journal of epidemiology}, volume = {25}, number = {Supl 1}, pages = {e220003}, doi = {10.1590/1980-549720220003.supl.1}, pmid = {35766760}, issn = {1980-5497}, mesh = {Brazil/epidemiology ; Databases, Factual ; *Death Certificates ; Humans ; Information Systems ; *Neoplasms ; }, abstract = {OBJECTIVE: To describe the trend of incompleteness of cancer death records in the Mortality Information System (SIM, in Portuguese) database, state of Mato Grosso, Brazil, 2000 to 2016.

METHODS: This is a descriptive, ecological, time series study of records of death from cancer of people living in the state of Mato Grosso (codes C00 to C97 of the 10th revision of the International Statistical Classification of Diseases and Related Health Problems - ICD-10), collected from SIM. To asses incompleteness in the filling of the variables of race/skin color, education, marital status, occupation and underlying cause of death, the relative frequency was calculated in the percentage of null values. The time trend analyzes of the incomplete percentage of categories and variables of interest was performed using linear regression (p<0.05).

RESULTS: From 2000 to 2016, there were 31,097 deaths from cancer among residents of the state of Mato Grosso. Race/skin color, marital status and occupation presented a stable trend of incompleteness; education and underlying cause of death were decreasing. An increasing trend was observed in the categories ignored (marital status) and retired (occupation); a decreasing trend was observed for blank (education), unidentified and housewife (occupation), and C76-other and ill-defined sites and C80-without specification of site (underlying cause of death). Incompleteness of occupation was classified as very poor, with emphasis on housewife and retired. For the remaining variables and categories, the classification was excellent or good.

CONCLUSIONS: Although most of the indicators showed satisfactory trend and classification, the marital status and occupation variables stood out for indicating poorer quality in the records.}, } @article {pmid35764639, year = {2022}, author = {Dong, B and Liu, Y and Mu, W and Jiang, Z and Pandey, P and Hong, T and Olesen, B and Lawrence, T and O'Neil, Z and Andrews, C and Azar, E and Bandurski, K and Bardhan, R and Bavaresco, M and Berger, C and Burry, J and Carlucci, S and Chvatal, K and De Simone, M and Erba, S and Gao, N and Graham, LT and Grassi, C and Jain, R and Kumar, S and Kjærgaard, M and Korsavi, S and Langevin, J and Li, Z and Lipczynska, A and Mahdavi, A and Malik, J and Marschall, M and Nagy, Z and Neves, L and O'Brien, W and Pan, S and Park, JY and Pigliautile, I and Piselli, C and Pisello, AL and Rafsanjani, HN and Rupp, RF and Salim, F and Schiavon, S and Schwee, J and Sonta, A and Touchie, M and Wagner, A and Walsh, S and Wang, Z and Webber, DM and Yan, D and Zangheri, P and Zhang, J and Zhou, X and Zhou, X}, title = {A Global Building Occupant Behavior Database.}, journal = {Scientific data}, volume = {9}, number = {1}, pages = {369}, pmid = {35764639}, issn = {2052-4463}, support = {1883-RP//American Society of Heating, Refrigerating and Air-Conditioning Engineers (ASHRAE)/ ; }, abstract = {This paper introduces a database of 34 field-measured building occupant behavior datasets collected from 15 countries and 39 institutions across 10 climatic zones covering various building types in both commercial and residential sectors. This is a comprehensive global database about building occupant behavior. The database includes occupancy patterns (i.e., presence and people count) and occupant behaviors (i.e., interactions with devices, equipment, and technical systems in buildings). Brick schema models were developed to represent sensor and room metadata information. The database is publicly available, and a website was created for the public to access, query, and download specific datasets or the whole database interactively. The database can help to advance the knowledge and understanding of realistic occupancy patterns and human-building interactions with building systems (e.g., light switching, set-point changes on thermostats, fans on/off, etc.) and envelopes (e.g., window opening/closing). With these more realistic inputs of occupants' schedules and their interactions with buildings and systems, building designers, energy modelers, and consultants can improve the accuracy of building energy simulation and building load forecasting.}, } @article {pmid35763352, year = {2022}, author = {Stuart, KC and Edwards, RJ and Cheng, Y and Warren, WC and Burt, DW and Sherwin, WB and Hofmeister, NR and Werner, SJ and Ball, GF and Bateson, M and Brandley, MC and Buchanan, KL and Cassey, P and Clayton, DF and De Meyer, T and Meddle, SL and Rollins, LA}, title = {Transcript- and annotation-guided genome assembly of the European starling.}, journal = {Molecular ecology resources}, volume = {22}, number = {8}, pages = {3141-3160}, pmid = {35763352}, issn = {1755-0998}, support = {RGP0030/2015//Human Sciences Frontier Programme/ ; BB/P013759/1//Roslin Institute Strategic Grant funding from the UK Biotechnology and Biological Sciences Research Council/ ; //University of New South Wales Scientia Fellowship/ ; LP160100610//Australian Research Council/ ; LP18010072//Australian Research Council/ ; P013759/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; Australia ; Genome/genetics ; Genomics ; Molecular Sequence Annotation ; *Starlings/genetics ; }, abstract = {The European starling, Sturnus vulgaris, is an ecologically significant, globally invasive avian species that is also suffering from a major decline in its native range. Here, we present the genome assembly and long-read transcriptome of an Australian-sourced European starling (S. vulgaris vAU), and a second, North American, short-read genome assembly (S. vulgaris vNA), as complementary reference genomes for population genetic and evolutionary characterization. S. vulgaris vAU combined 10× genomics linked-reads, low-coverage Nanopore sequencing, and PacBio Iso-Seq full-length transcript scaffolding to generate a 1050 Mb assembly on 6222 scaffolds (7.6 Mb scaffold N50, 94.6% busco completeness). Further scaffolding against the high-quality zebra finch (Taeniopygia guttata) genome assigned 98.6% of the assembly to 32 putative nuclear chromosome scaffolds. Species-specific transcript mapping and gene annotation revealed good gene-level assembly and high functional completeness. Using S. vulgaris vAU, we demonstrate how the multifunctional use of PacBio Iso-Seq transcript data and complementary homology-based annotation of sequential assembly steps (assessed using a new tool, saaga) can be used to assess, inform, and validate assembly workflow decisions. We also highlight some counterintuitive behaviour in traditional busco metrics, and present buscomp, a complementary tool for assembly comparison designed to be robust to differences in assembly size and base-calling quality. This work expands our knowledge of avian genomes and the available toolkit for assessing and improving genome quality. The new genomic resources presented will facilitate further global genomic and transcriptomic analysis on this ecologically important species.}, } @article {pmid35761171, year = {2022}, author = {Wang, H and Zhang, X and Ding, S and Huang, Y and Wang, S and Chen, H and Chen, Y and Li, Y}, title = {VisProDom: an interactive Shiny/R application for displaying protein domains with transcriptional features.}, journal = {BMC genomics}, volume = {23}, number = {1}, pages = {472}, pmid = {35761171}, issn = {1471-2164}, support = {31701439//National Natural Science Foundation of China/ ; }, mesh = {Databases, Factual ; *Genome ; Genomics ; Protein Domains ; *Software ; }, abstract = {BACKGROUND: Both the protein domains and transcript structures influence protein functional variation. The genomic location of both protein domains and transcript structural features can be described using the genomic coordinates of their encoded sequences. However, the coordinates of protein domains and transcriptional features often differ greatly, and it is difficult to view them in combination at the genome-wide level. In this paper, we describe the development of a new tool that allows users to visualize domains and transcript features together, using either built-in or uploaded genome datasets, and export publication-ready figures. RESULTS: We developed a user-friendly, independent R package and Shiny web application named "VisProDom". VisProDom consists of a genome-wide database containing entire annotated transcripts merged with annotated protein domains from the Pfam database. The built-in dataset includes 82 files, which merge genome general feature format (GFF) annotations with rpsblast tabular outputs from protein sequence searches in the Pfam database. Multiple genomes can be simultaneously screened for protein domains or transcript names. VisProDom includes step-by-step introductions and clickable elements for ease of use.

CONCLUSION: VisProDom can display hundreds of transcripts alongside protein domains and export figures in a publication-ready format. This makes it a valuable tool for molecular evolution and comparative genomics.}, } @article {pmid35759658, year = {2022}, author = {Abrahms, B and Rafiq, K and Jordan, NR and McNutt, JW}, title = {Long-term, climate-driven phenological shift in a tropical large carnivore.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {119}, number = {27}, pages = {e2121667119}, pmid = {35759658}, issn = {1091-6490}, mesh = {Animals ; *Canidae/physiology ; *Climate Change ; Datasets as Topic ; Ecosystem ; *Endangered Species ; Seasons ; Temperature ; }, abstract = {Understanding the degree to which animals are shifting their phenology to track optimal conditions as the climate changes is essential to predicting ecological responses to global change. Species at low latitudes or high trophic levels are theoretically expected to exhibit weaker phenological responses than other species, but limited research on tropical systems or on top predators impedes insight into the contexts in which these predictions are upheld. Moreover, a lack of phenological studies on top predators limits understanding of how climate change impacts propagate through entire ecosystems. Using a 30-y dataset on endangered African wild dogs (Lycaon pictus), we examined changes in reproductive phenology and temperatures during birthing and denning over time, as well as potential fitness consequences of these changes. We hypothesized that their phenology would shift to track a stable thermal range over time. Data from 60 packs and 141 unique pack-years revealed that wild dogs have delayed parturition by 7 days per decade on average in response to long-term warming. This shift has led to temperatures on birthing dates remaining relatively stable but, contrary to expectation, has led to increased temperatures during denning periods. Increased denning temperatures were associated with reduced reproductive success, suggesting that a continued phenological shift in the species may become maladaptive. Such results indicate that climate-driven shifts could be more widespread in upper trophic levels than previously appreciated, and they extend theoretical understanding of the species traits and environmental contexts in which large phenological shifts can be expected to occur as the climate changes.}, } @article {pmid35757606, year = {2022}, author = {Ali, EOM and Babalghith, AO and Bahathig, AOS and Dafalla, OM and Al-Maghamsi, IW and Mustafa, NEAG and Al-Zahrani, AAA and Al-Mahmoudi, SMY and Abdel-Latif, ME}, title = {Detection of Dengue Virus From Aedes aegypti (Diptera, Culicidae) in Field-Caught Samples From Makkah Al-Mokarramah, Kingdom of Saudi Arabia, Using RT-PCR.}, journal = {Frontiers in public health}, volume = {10}, number = {}, pages = {850851}, pmid = {35757606}, issn = {2296-2565}, mesh = {*Aedes ; Animals ; *Dengue/diagnosis/epidemiology ; *Dengue Virus/genetics ; Female ; Mosquito Vectors ; Reverse Transcriptase Polymerase Chain Reaction ; Saudi Arabia ; }, abstract = {Dengue fever (DF) is endemic to Makkah and Jeddah, the Kingdom of Saudi Arabia (KSA). However, until recently, the circulation of dengue virus (DENV) in Aedes mosquitoes in these areas was unknown. Serological surveillance of DENV in Ae aegypti is a powerful tool for early detection of dengue outbreaks and essential for developing effective control strategies. Therefore, this research aimed to examine a sample of adult Ae aegypti mosquitoes from Makkah, KSA, to detect DENV. In total, 1295 Ae aegypti mosquitoes were collected from the field from target areas of Makkah with a high incidence and prevalence of DF. The samples were divided into 259 coded pools (five mosquitoes in each) and preserved in 1.5 mL plastic tubes. The tubes were labeled, capped, and stored at-86°C until use. RT-PCR was used to detect DENV in the samples. All positive pools were confirmed by RT-PCR. The RT-PCR products were analyzed by gel electrophoresis (1.5% agarose in Tris-acetate EDTA buffer), stained with ethidium bromide, and visualized. DENV was isolated from six female Ae Aegypti collected from six pools (out of 259 pools). No other viruses were detected. Only five of the nine target localities had positive pools. Samples from the remaining four localities yielded negative results. Four DENV-positive mosquitoes were collected at the aquatic stages, and two were collected at the adult stage. These results show the circulation of DENV in adult mosquitoes and offspring, indicating vertical transmission of DENV. In conclusion, this study found that, in Makkah, DENV is circulating in dengue vectors with a high significance rate, suggesting the possibility of a dengue outbreak in the future; therefore, a sensitive surveillance system is vital to predict the outbreak and for early intervention and control.}, } @article {pmid35757168, year = {2022}, author = {Rosenberg, G and Auffenberg, K and Bank, R and Bieler, R and Bouchet, P and Herbert, D and Köhler, F and Neubauer, TA and Neubert, E and Páll-Gergely, B and Richling, I and Schneider, S}, title = {Adapting mark-recapture methods to estimating accepted species-level diversity: a case study with terrestrial Gastropoda.}, journal = {PeerJ}, volume = {10}, number = {}, pages = {e13139}, pmid = {35757168}, issn = {2167-8359}, mesh = {Animals ; *Gastropoda ; Mollusca ; Fossils ; Databases, Factual ; Research Design ; }, abstract = {We introduce a new method of estimating accepted species diversity by adapting mark-recapture methods to comparisons of taxonomic databases. A taxonomic database should become more complete over time, so the error bar on an estimate of its completeness and the known diversity of the taxon it treats will decrease. Independent databases can be correlated, so we use the time course of estimates comparing them to understand the effect of correlation. If a later estimate is significantly larger than an earlier one, the databases are positively correlated, if it is significantly smaller, they are negatively correlated, and if the estimate remains roughly constant, then the correlations have averaged out. We tested this method by estimating how complete MolluscaBase is for accepted names of terrestrial gastropods. Using random samples of names from an independent database, we determined whether each name led to a name accepted in MolluscaBase. A sample tested in August 2020 found that 16.7% of tested names were missing; one in July 2021 found 5.3% missing. MolluscaBase grew by almost 3,000 accepted species during this period, reaching 27,050 species. The estimates ranged from 28,409 ± 365 in 2021 to 29,063 ± 771 in 2020. All estimates had overlapping 95% confidence intervals, indicating that correlations between the databases did not cause significant problems. Uncertainty beyond sampling error added 475 ± 430 species, so our estimate for accepted terrestrial gastropods species at the end of 2021 is 28,895 ± 630 species. This estimate is more than 4,000 species higher than previous ones. The estimate does not account for ongoing flux of species into and out of synonymy, new discoveries, or changing taxonomic methods and concepts. The species naming curve for terrestrial gastropods is still far from reaching an asymptote, and combined with the additional uncertainties, this means that predicting how many more species might ultimately be recognized is presently not feasible. Our methods can be applied to estimate the total number of names of Recent mollusks (as opposed to names currently accepted), the known diversity of fossil mollusks, and known diversity in other phyla.}, } @article {pmid35755650, year = {2022}, author = {Li, Y and Miao, Y and Zhang, J and Cammarano, D and Li, S and Liu, X and Tian, Y and Zhu, Y and Cao, W and Cao, Q}, title = {Improving Estimation of Winter Wheat Nitrogen Status Using Random Forest by Integrating Multi-Source Data Across Different Agro-Ecological Zones.}, journal = {Frontiers in plant science}, volume = {13}, number = {}, pages = {890892}, pmid = {35755650}, issn = {1664-462X}, abstract = {Timely and accurate estimation of plant nitrogen (N) status is crucial to the successful implementation of precision N management. It has been a great challenge to non-destructively estimate plant N status across different agro-ecological zones (AZs). The objective of this study was to use random forest regression (RFR) models together with multi-source data to improve the estimation of winter wheat (Triticum aestivum L.) N status across two AZs. Fifteen site-year plot and farmers' field experiments involving different N rates and 19 cultivars were conducted in two AZs from 2015 to 2020. The results indicated that RFR models integrating climatic and management factors with vegetation index (R[2] = 0.72-0.86) outperformed the models by only using the vegetation index (R[2] = 0.36-0.68) and performed well across AZs. The Pearson correlation coefficient-based variables selection strategy worked well to select 6-7 key variables for developing RFR models that could achieve similar performance as models using full variables. The contributions of climatic and management factors to N status estimation varied with AZs and N status indicators. In higher-latitude areas, climatic factors were more important to N status estimation, especially water-related factors. The addition of climatic factors significantly improved the performance of the RFR models for N nutrition index estimation. Climatic factors were important for the estimation of the aboveground biomass, while management variables were more important to N status estimation in lower-latitude areas. It is concluded that integrating multi-source data using RFR models can significantly improve the estimation of winter wheat N status indicators across AZs compared to models only using one vegetation index. However, more studies are needed to develop unmanned aerial vehicles and satellite remote sensing-based machine learning models incorporating multi-source data for more efficient monitoring of crop N status under more diverse soil, climatic, and management conditions across large regions.}, } @article {pmid35754095, year = {2022}, author = {Balfour, NJ and Castellanos, MC and Goulson, D and Philippides, A and Johnson, C}, title = {DoPI: The Database of Pollinator Interactions.}, journal = {Ecology}, volume = {103}, number = {11}, pages = {e3801}, pmid = {35754095}, issn = {1939-9170}, mesh = {Animals ; Databases, Factual ; Ecosystem ; Flowers ; *Insecta ; *Plants ; Pollination ; }, abstract = {Despite the importance of pollinating insects to natural environments and agriculture, there have been few attempts to unite the existing plant-pollinator interaction datasets into a single depository using a common format. Accordingly, we have created one of the world's first online, open-access, and searchable pollinator-plant interaction databases. DoPI (The Database of Pollinator Interactions) was built from a systematic review of the scientific literature and unpublished datasets requested from researchers and organizations. We collated records of interactions between British plant and insect flower-visitor species (or genera), together with associated metadata (date, location, habitat, source publication) when available. The dataset currently (December 2021) contains 101,539 records, detailing over 320,000 interactions. The number of interactions (i.e., the number of times a pairwise species interaction was recorded per occasion) varies considerably among records, averaging 3.6. These include records from 1888 pollinator species and 1241 plant species, totaling >17,000 pairwise species interactions. By combining a large volume of information in a single repository, DoPI can be used to answer fundamental ecological questions on the dynamics of pollination interactions in space and time, as well as applied questions in conservation practice. We hope this dynamic database will be a useful tool not only for researchers, but also for conservationists, funding agencies, governmental departments, beekeepers, agronomists, and gardeners. We request that this paper is cited when using the data in publications and individual studies when appropriate. Researchers and organizations are encouraged to add further data in the future. The database can be accessed at: https://www.dopi.org.uk/.}, } @article {pmid35753285, year = {2022}, author = {Feng, Y and Cheng, X and Lu, Y and Wang, H and Chen, D and Luo, C and Liu, H and Gao, S and Lei, T and Huang, C and Yu, X}, title = {Gas chromatography-mass spectrometry analysis of floral fragrance-related compounds in scented rose (Rosa hybrida) varieties and a subsequent evaluation on the basis of the analytical hierarchy process.}, journal = {Plant physiology and biochemistry : PPB}, volume = {185}, number = {}, pages = {368-377}, doi = {10.1016/j.plaphy.2022.06.007}, pmid = {35753285}, issn = {1873-2690}, mesh = {Analytic Hierarchy Process ; Flowers ; Gas Chromatography-Mass Spectrometry/methods ; Odorants/analysis ; *Oils, Volatile ; *Rosa/chemistry ; *Volatile Organic Compounds/analysis ; }, abstract = {Scented rose (Rosa hybrida) varieties are valued as ornamentals, but they also contain volatile organic compounds (VOCs) that produce pleasant aromas. In plants, aromas are produced via metabolism during growth, and each aroma compound has a unique function. In this study, the floral aroma compounds of diverse scented rose varieties were analyzed and classified. The VOCs of different rose varieties were qualitatively and quantitatively analyzed via headspace solid-phase microextraction combined with gas chromatography and mass spectrometry. The test materials were the mature flowers of 55 scented rose varieties that were cultivated under identical conditions. Seventeen important aroma compounds were selected and an analytical hierarchy process (AHP)-based method was developed to identify the most suitable essential oil resources, aromatherapy resources, and healthcare resources. A floral fragrance evaluation model was established for the comprehensive evaluation of the scented rose varieties. The 55 varieties were classified into three grades according to their suitability for each use. 'Soeur Emmanuelle', 'Wollerton Old Hall', 'Accademia', and 'Tianmidemeng' were revealed to be suitable essential oil, aromatherapy, and healthcare resources. On the basis of their aroma compound types, the fifty-five rose varieties were divided into eight groups. The results of this study provide the theoretical basis for the classification of rose flower aromas as well as the rational use of diverse rose varieties to further develop the rose industry.}, } @article {pmid35752802, year = {2022}, author = {Darcy, JL and Amend, AS and Swift, SOI and Sommers, PS and Lozupone, CA}, title = {specificity: an R package for analysis of feature specificity to environmental and higher dimensional variables, applied to microbiome species data.}, journal = {Environmental microbiome}, volume = {17}, number = {1}, pages = {34}, pmid = {35752802}, issn = {2524-6372}, support = {5 T15 LM009451-12/NH/NIH HHS/United States ; 1255972//National Science Foundation/ ; }, abstract = {BACKGROUND: Understanding the factors that influence microbes' environmental distributions is important for determining drivers of microbial community composition. These include environmental variables like temperature and pH, and higher-dimensional variables like geographic distance and host species phylogeny. In microbial ecology, "specificity" is often described in the context of symbiotic or host parasitic interactions, but specificity can be more broadly used to describe the extent to which a species occupies a narrower range of an environmental variable than expected by chance. Using a standardization we describe here, Rao's (Theor Popul Biol, 1982. https://doi.org/10.1016/0040-5809(82)90004-1, Sankhya A, 2010. https://doi.org/10.1007/s13171-010-0016-3) Quadratic Entropy can be conveniently applied to calculate specificity of a feature, such as a species, to many different environmental variables.

RESULTS: We present our R package specificity for performing the above analyses, and apply it to four real-life microbial data sets to demonstrate its application. We found that many fungi within the leaves of native Hawaiian plants had strong specificity to rainfall and elevation, even though these variables showed minimal importance in a previous analysis of fungal beta-diversity. In Antarctic cryoconite holes, our tool revealed that many bacteria have specificity to co-occurring algal community composition. Similarly, in the human gut microbiome, many bacteria showed specificity to the composition of bile acids. Finally, our analysis of the Earth Microbiome Project data set showed that most bacteria show strong ontological specificity to sample type. Our software performed as expected on synthetic data as well.

CONCLUSIONS: specificity is well-suited to analysis of microbiome data, both in synthetic test cases, and across multiple environment types and experimental designs. The analysis and software we present here can reveal patterns in microbial taxa that may not be evident from a community-level perspective. These insights can also be visualized and interactively shared among researchers using specificity's companion package, specificity.shiny.}, } @article {pmid35749381, year = {2022}, author = {Favila, N and Madrigal-Trejo, D and Legorreta, D and Sánchez-Pérez, J and Espinosa-Asuar, L and Eguiarte, LE and Souza, V}, title = {MicNet toolbox: Visualizing and unraveling a microbial network.}, journal = {PloS one}, volume = {17}, number = {6}, pages = {e0259756}, pmid = {35749381}, issn = {1932-6203}, mesh = {Cluster Analysis ; Computational Biology/methods ; Microbial Consortia ; *Microbiota ; *Software ; }, abstract = {Applications of network theory to microbial ecology are an emerging and promising approach to understanding both global and local patterns in the structure and interplay of these microbial communities. In this paper, we present an open-source python toolbox which consists of two modules: on one hand, we introduce a visualization module that incorporates the use of UMAP, a dimensionality reduction technique that focuses on local patterns, and HDBSCAN, a clustering technique based on density; on the other hand, we have included a module that runs an enhanced version of the SparCC code, sustaining larger datasets than before, and we couple the resulting networks with network theory analyses to describe the resulting co-occurrence networks, including several novel analyses, such as structural balance metrics and a proposal to discover the underlying topology of a co-occurrence network. We validated the proposed toolbox on 1) a simple and well described biological network of kombucha, consisting of 48 ASVs, and 2) we validate the improvements of our new version of SparCC. Finally, we showcase the use of the MicNet toolbox on a large dataset from Archean Domes, consisting of more than 2,000 ASVs. Our toolbox is freely available as a github repository (https://github.com/Labevo/MicNetToolbox), and it is accompanied by a web dashboard (http://micnetapplb-1212130533.us-east-1.elb.amazonaws.com) that can be used in a simple and straightforward manner with relative abundance data. This easy-to-use implementation is aimed to microbial ecologists with little to no experience in programming, while the most experienced bioinformatics will also be able to manipulate the source code's functions with ease.}, } @article {pmid35748824, year = {2022}, author = {Mehta, TK and Penso-Dolfin, L and Nash, W and Roy, S and Di-Palma, F and Haerty, W}, title = {Evolution of miRNA-Binding Sites and Regulatory Networks in Cichlids.}, journal = {Molecular biology and evolution}, volume = {39}, number = {7}, pages = {}, pmid = {35748824}, issn = {1537-1719}, support = {BB/J004669//BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/P016774/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/T/000PR9817/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/CSP17270/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/CCG1720/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; Binding Sites ; *Cichlids/genetics ; Evolution, Molecular ; Gene Regulatory Networks ; *MicroRNAs/genetics ; Phylogeny ; }, abstract = {The divergence of regulatory regions and gene regulatory network (GRN) rewiring is a key driver of cichlid phenotypic diversity. However, the contribution of miRNA-binding site turnover has yet to be linked to GRN evolution across cichlids. Here, we extend our previous studies by analyzing the selective constraints driving evolution of miRNA and transcription factor (TF)-binding sites of target genes, to infer instances of cichlid GRN rewiring associated with regulatory binding site turnover. Comparative analyses identified increased species-specific networks that are functionally associated to traits of cichlid phenotypic diversity. The evolutionary rewiring is associated with differential models of miRNA- and TF-binding site turnover, driven by a high proportion of fast-evolving polymorphic sites in adaptive trait genes compared with subsets of random genes. Positive selection acting upon discrete mutations in these regulatory regions is likely to be an important mechanism in rewiring GRNs in rapidly radiating cichlids. Regulatory variants of functionally associated miRNA- and TF-binding sites of visual opsin genes differentially segregate according to phylogeny and ecology of Lake Malawi species, identifying both rewired, for example, clade-specific and conserved network motifs of adaptive trait associated GRNs. Our approach revealed several novel candidate regulators, regulatory regions, and three-node motifs across cichlid genomes with previously reported associations to known adaptive evolutionary traits.}, } @article {pmid35748425, year = {2022}, author = {Pelletier, TA and Parsons, DJ and Decker, SK and Crouch, S and Franz, E and Ohrstrom, J and Carstens, BC}, title = {phylogatR: Phylogeographic data aggregation and repurposing.}, journal = {Molecular ecology resources}, volume = {22}, number = {8}, pages = {2830-2842}, pmid = {35748425}, issn = {1755-0998}, support = {DBI-1911293//National Science Foundation/ ; DBI-1910623//National Science Foundation/ ; }, mesh = {*Data Aggregation ; *Ecology/methods ; Ecosystem ; Humans ; Phylogeography ; Software ; }, abstract = {Patterns of genetic diversity within species contain information the history of that species, including how they have responded to historical climate change and how easily the organism is able to disperse across its habitat. More than 40,000 phylogeographic and population genetic investigations have been published to date, each collecting genetic data from hundreds of samples. Despite these millions of data points, meta-analyses are challenging because the synthesis of results across hundreds of studies, each using different methods and forms of analysis, is a daunting and time-consuming task. It is more efficient to proceed by repurposing existing data and using automated data analysis. To facilitate data repurposing, we created a database (phylogatR) that aggregates data from different sources and conducts automated multiple sequence alignments and data curation to provide users with nearly ready-to-analyse sets of data for thousands of species. Two types of scientific research will be made easier by phylogatR: large meta-analyses of thousands of species that can address classic questions in evolutionary biology and ecology, and student- or citizen- science based investigations that will introduce a broad range of people to the analysis of genetic data. phylogatR enhances the value of existing data via the creation of software and web-based tools that enable these data to be recycled and reanalysed and increase accessibility to big data for research laboratories and classroom instructors with limited computational expertise and resources.}, } @article {pmid35748219, year = {2022}, author = {Weyrich, A and Joel, M and Lewin, G and Hofmann, T and Frericks, M}, title = {Review of the state of science and evaluation of currently available in silico prediction models for reproductive and developmental toxicity: A case study on pesticides.}, journal = {Birth defects research}, volume = {114}, number = {14}, pages = {812-842}, pmid = {35748219}, issn = {2472-1727}, mesh = {Computer Simulation ; Databases, Factual ; *Pesticides/toxicity ; Quantitative Structure-Activity Relationship ; Reproduction ; }, abstract = {BACKGROUND: In silico methods for toxicity prediction have increased significantly in recent years due to the 3Rs principle. This also applies to predicting reproductive toxicology, which is one of the most critical factors in pesticide approval. The widely used quantitative structure-activity relationship (QSAR) models use experimental toxicity data to create a model that relates experimentally observed toxicity to molecular structures to predict toxicity. Aim of the study was to evaluate the available prediction models for developmental and reproductive toxicity regarding their strengths and weaknesses in a pesticide database.

METHODS: The reproductive toxicity of 315 pesticides, which have a GHS classification by ECHA, was compared with the prediction of different in silico models: VEGA, OECD (Q)SAR Toolbox, Leadscope Model Applier, and CASE Ultra by MultiCASE.

RESULTS: In all models, a large proportion (up to 77%) of all pesticides were outside the chemical space of the model. Analysis of the prediction of remaining pesticides revealed a balanced accuracy of the models between 0.48 and 0.66.

CONCLUSION: Overall, predictions were only meaningful in rare cases and therefore always require evaluation by an expert. The critical factors were the underlying data and determination of molecular similarity, which offer great potential for improvement.}, } @article {pmid35747132, year = {2022}, author = {Li, W and Guo, Y}, title = {A Secure Private Cloud Storage Platform for English Education Resources Based on IoT Technology.}, journal = {Computational and mathematical methods in medicine}, volume = {2022}, number = {}, pages = {8453470}, pmid = {35747132}, issn = {1748-6718}, mesh = {*Big Data ; *Cloud Computing ; Humans ; Technology ; }, abstract = {The contemporary ubiquitous "cloud" network knowledge and information resources, as well as ecological pedagogy theory, have enlarged teaching research's perspective, widened teaching research's innovation area, and created practical options for English classroom reform. Cloud education relies on the Internet of Things, cloud computing, and big data to have a huge impact on the English learning process. The key to the integration of English education resources is the storage of huge amount of English teaching data. Applying the technology and methods of cloud storage to the construction of English education resource integration can effectively save the educational resources of schools, improve the utilization rate of English education resources, and thus enhance the teaching level of English subjects. In this work, we examine the existing state of English education resource building and teaching administration and offer a way for creating a "private cloud" of English education materials. We not only examined the architecture and three-layer modules of cloud computing in depth, but we also analyzed the "private cloud" technology and built the cloud structure of English teaching materials on this foundation. We hope that this paper can help and inspire us to solve the problems of uneven distribution, irregular management, and difficult sharing in the construction of English education resources.}, } @article {pmid35743915, year = {2022}, author = {Vargová, B and Majláth, I and Kurimský, J and Cimbala, R and Zbojovský, J and Tryjanowski, P and Majláthová, V}, title = {Locomotor Activity of Ixodes ricinus Females in 900 MHz Electromagnetic Field.}, journal = {Life (Basel, Switzerland)}, volume = {12}, number = {6}, pages = {}, pmid = {35743915}, issn = {2075-1729}, support = {APVV-17-0372//Slovak Research and Development Agency/ ; }, abstract = {Mobile telecommunications technologies have become an indispensable part of people's lives of all ages around the world. They affect personal life and social interactions and are a work tool in the work routine. Network availability requirements and the quality of the Internet connection are constantly increasing, to which telecommunications providers are responding. Humans and wildlife live in the permanent presence of electromagnetic radiation with just a minor knowledge of the impact this radiation has. The aim of our study was to investigate the effect of a 900 MHz electromagnetic field (EMF) on the locomotor behavior of female Ixodes ricinus ticks under laboratory conditions. Experiments were performed in the radiation-shielded tube (RST) test and radiation-shielded circular open-field arena placed in an anechoic chamber. Altogether, 480 female I. ricinus ticks were tested. In the RST arena, no differences in preference for irradiated and shielded parts of experimental modules were observed; in the open-field arena, the time spent and the trajectory passed was significantly longer in the part exposed to the EMF.}, } @article {pmid35742413, year = {2022}, author = {Maturkanič, P and Tomanová Čergeťová, I and Konečná, I and Thurzo, V and Akimjak, A and Hlad, Ľ and Zimny, J and Roubalová, M and Kurilenko, V and Toman, M and Petrikovič, J and Petrikovičová, L}, title = {Well-Being in the Context of COVID-19 and Quality of Life in Czechia.}, journal = {International journal of environmental research and public health}, volume = {19}, number = {12}, pages = {}, pmid = {35742413}, issn = {1660-4601}, mesh = {Adolescent ; *COVID-19/epidemiology ; Czech Republic/epidemiology ; Female ; Humans ; Male ; *Quality of Life ; Religion ; Surveys and Questionnaires ; }, abstract = {The present study focuses on exploring the differences and relationship between well-being and experience of pastoral and psychological service of religious denomination based on religious affiliation during the first wave of the pandemic in Czechia. Our research has been focused on the investigation, comparison, and correlation between the level of well-being and pastoral and psychological service. The research sample (n = 1126) consisted of the Czech health population with age over 16 years, of which 42.4% were men (n = 478) and 57.5% were women (n = 648). From the perspective of religiosity, the study sample was divided in terms of religion into two groups-51.9% participants with religious affiliation (n = 584) and 48.1% participants without religious affiliation (n = 542). The level of well-being was identified by means of The Satisfaction with Life Scale (Diener, Emmons, Larsen, & Griffin, 1985). The level of experience with pastoral and psychological service was measured using our non-standardised questionnaire. The results confirmed the differences between the variables of well-being and positive experience with pastoral and psychological service based on religious affiliation. Moreover, we confirmed the hypothesis of a positive correlation between well-being and positive experience with pastoral and psychological service in Czechia.}, } @article {pmid35739750, year = {2022}, author = {Li, S and Shen, W and Lian, S and Wu, Y and Qu, Y and Deng, Y}, title = {DARHD: A sequence database for aromatic ring-hydroxylating dioxygenase analysis and primer evaluation.}, journal = {Journal of hazardous materials}, volume = {436}, number = {}, pages = {129230}, doi = {10.1016/j.jhazmat.2022.129230}, pmid = {35739750}, issn = {1873-3336}, mesh = {Amino Acid Sequence ; Bacteria/metabolism ; Biodegradation, Environmental ; Databases, Nucleic Acid ; *Dioxygenases/genetics/metabolism ; Phylogeny ; *Polycyclic Aromatic Hydrocarbons/metabolism ; }, abstract = {Biodegradation of aromatic compounds is ubiquitous in the environment and important for controlling organic pollutants. Aromatic ring-hydroxylating dioxygenases (ARHDs) are responsible for the first and rate-limiting step of aerobic biodegradation of aromatic compounds. The ARHD α subunit is a good biomarker for studying functional microorganisms in the environment, however their diversity and corresponding primer coverage are unclear, both of which require a comprehensive sequence database for the ARHD α subunit. Here amino acid sequences of the ARHD α subunit were collected, and a total of 103 sequences were selected as seed sequences that were distributed in 72 bacterial genera with 34 gene names. Based on both homolog search and keyword confirmation against the GenBank, a sequence database of ARHD (DARHD) has been established and 6367 highly credible sequences were retrieved. DARHD contained 407 bacterial genera capable of degrading 38 aromatic substrates, and intricate relationships among the gene name, aromatic substrate and microbial taxa were observed. Thereafter, a total of 136 pairs of primers were collected and assessed. Results showed coverages of most published primers were low. Our research provides new insights for understanding the diversity of ARHD α subunit, and gives guidance on the design and application of primers in the future.}, } @article {pmid37546168, year = {2022}, author = {Boyes, D and , and , and , and , and , and Lewin, T and , }, title = {The genome sequence of the double-striped pug, Gymnoscelis rufifasciata (Haworth, 1809).}, journal = {Wellcome open research}, volume = {7}, number = {}, pages = {135}, pmid = {37546168}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual female Gymnoscelis rufifasciata (the double-striped pug; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 352 megabases in span. The majority of the assembly (99.82%) is scaffolded into 32 chromosomal pseudomolecules, with the W and Z sex chromosomes assembled. The mitochondrial genome was also assembled, and is 15.4 kilobases in length.}, } @article {pmid37953928, year = {2022}, author = {Boyes, D and , and , and , and , and , and Turner, R and , }, title = {The genome sequence of the rosy rustic, Hydraecia micacea (Esper, 1789).}, journal = {Wellcome open research}, volume = {7}, number = {}, pages = {131}, pmid = {37953928}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual female Hydraecia micacea (the rosy rustic; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 562 megabases in span. The majority of the assembly (99.98%) is scaffolded into 32 chromosomal pseudomolecules, with the W and Z sex chromosomes assembled. The mitochondrial genome was also assembled, and is 16.3 kilobases in length.}, } @article {pmid37928611, year = {2022}, author = {Boyes, D and , and , and , and , and , and Phillips, D and , }, title = {The genome sequence of the black arches, Lymantria monacha (Linnaeus, 1758).}, journal = {Wellcome open research}, volume = {7}, number = {}, pages = {128}, pmid = {37928611}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual male Lymantria monacha (the black arches; Arthropoda; Insecta; Lepidoptera; Erebidae). The genome sequence is 916 megabases in span. The majority of the assembly (99.99%) is scaffolded into 28 chromosomal pseudomolecules, with the Z sex chromosome assembled. The mitochondrial genome was also assembled, and is 15.6 kilobases in length.}, } @article {pmid36873714, year = {2021}, author = {Hawkes, W and Wotton, K and , and , and , and , and , and , }, title = {The genome sequence of the tapered dronefly, Eristalis pertinax (Scopoli, 1763).}, journal = {Wellcome open research}, volume = {6}, number = {}, pages = {292}, pmid = {36873714}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual male Eristalis pertinax (the tapered dronefly; Arthropoda; Insecta; Diptera; Syriphidae). The genome sequence is 487 megabases in span. The majority of the assembly (95.23%) is scaffolded into seven chromosomal pseudomolecules, with the X and Y sex chromosomes assembled. The complete mitochondrial genome was also assembled and is 17.2 kilobases in length.}, } @article {pmid36873713, year = {2021}, author = {Boyes, D and Holland, PWH and , and , and , and , and , and , }, title = {The genome sequence of the swallow prominent, Pheosia tremula (Clerck, 1759).}, journal = {Wellcome open research}, volume = {6}, number = {}, pages = {335}, pmid = {36873713}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual male Pheosia tremula (the swallow prominent; Arthropoda; Insecta; Lepidoptera; Notodontidae). The genome sequence is 290 megabases in span. The majority of the assembly, 99.94%, is scaffolded into 31 chromosomal pseudomolecules, with the Z sex chromosome assembled.}, } @article {pmid37744128, year = {2021}, author = {Otto, EC and Held, BW and Gould, TJ and Blanchette, RA}, title = {Fungal Diversity in Multiple Post-harvest Aged Red Pine Stumps and Their Potential Influence on Heterobasidion Root Rot in Managed Stands Across Minnesota.}, journal = {Frontiers in fungal biology}, volume = {2}, number = {}, pages = {782181}, pmid = {37744128}, issn = {2673-6128}, abstract = {Thinning operations that occur in managed red pine (Pinus resinosa) stands, create tree stumps that can serve as a habitat for fungi, especially Heterobasidion irregulare, the cause of a serious root disease. Different fungi can colonize stumps early and the community of fungi can change over time as initial fungal species become replaced. Samples were collected from both the native and non-native range of red pine from stumps that were cut at different time periods. Stumps that were harvested at 0-1, 2-3, 5-6, and 10-12 years before sampling were used to provide data on the diversity of fungi that colonize tree stumps and how these communities can change over time as well as how they influence colonization of H. irregulare. Traditional culturing methods and Illumina MiSeq sequencing were used to identify the fungi in the samples. Of particular interest was Phlebiopsis gigantea, which can colonize cut stumps and prevent H. irregulare from becoming established. Overall, P. gigantea was the most abundant fungus isolated and sequenced via Illumina MiSeq. Results show that Phlebiopsis gigantea was isolated from 90% of all stumps sampled for sites harvested within 3 years of sampling in the native range of red pine compared to 33% in the non-native range. For Illumina MiSeq, 5,940 total amplicon sequence variants (ASVs) were detected. P. gigantea represented 14% of the total reads and composed 19% of the reads in the native range and 8% in non-native range of red pine. Furthermore, P. gigantea represented 38% of the reads for stumps that were harvested within 3 years of sampling in the native range of red pine compared to 14% in the non-native range. These results help demonstrate that a higher amount of P. gigantea is present in the native range of red pine and could be acting as a native biological control agent. Additional fungi, including Resinicium bicolor, Hypochnicium cremicolor, Leptographium spp., and others identified at different cutting times are also discussed. Finally, different diversity indices revealed similar, but slightly higher diversity for southern sites via Shannon and Simpson Diversity indices. Beta diversity demonstrated a similar species composition in stumps harvested at different times with these stumps being grouped together based on harvesting years.}, } @article {pmid36866282, year = {2021}, author = {Hawkes, W and Wotton, K and Smith, M and , and , and , and , and , and , and , }, title = {The genome sequence of the two-banded wasp hoverfly, Chrysotoxum bicinctum (Linnaeus, 1758).}, journal = {Wellcome open research}, volume = {6}, number = {}, pages = {321}, pmid = {36866282}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual female Chrysotoxum bicinctum (the two-banded wasp hoverfly; Arthropoda; Insecta; Diptera; Syriphidae). The genome sequence is 913 megabases in span. The majority of the assembly (98.81%) is scaffolded into five chromosomal pseudomolecules, with the X sex chromosome assembled.}, } @article {pmid36570104, year = {2021}, author = {Saxena, A and Dutta, A and Fischer, HW and Keleman Saxena, A and Jantz, P}, title = {Forest livelihoods and a "green recovery" from the COVID-19 pandemic: Insights and emerging research priorities from India.}, journal = {Forest policy and economics}, volume = {131}, number = {}, pages = {102550}, pmid = {36570104}, issn = {1389-9341}, abstract = {For those concerned with the future of forests, the COVID-19 pandemic has simultaneously offered cause for great concern, and renewed hope. On one hand, the pandemic is occurring at a time when forests are already under unprecedented pressures from climate change, amplifying concerns about unsustainable forest extraction in the name of economic recovery. On the other hand, however, the crisis has helped to gather momentum around the notion of a "green recovery," including setting aside additional land for forest conservation. Drawing insights from past and ongoing research in India, we highlight an issue that exemplifies the tension between these two poles: the role of forests as social safety nets for rural communities in developing countries. It is well established that forests can provide critical resources for rural livelihoods, especially in times of crisis, and preliminary reports suggest that these resources have become even more important in the context of India's COVID lockdowns, and mass return migration from urban to rural areas. As the second wave of the pandemic continues to unfold in India, we highlight some key research priorities, including: 1) understanding how and to what extent forest-dependent communities and industries are changing their use of wood- and non-wood resources in the context of return migration and economic stress; 2) tracking shifts in forest cover, structure, and composition that may result from increased extractive pressures; 3) assessing the role of institutions, whether local, national, or international, in mediating these outcomes. Drawing on these observations, we suggest some key principles for integrating forest-based livelihoods into "green recovery," founded on principles that articulate forests as complex and integrated social-ecological systems, prioritize equity, and build on past learnings of community-based forest management.}, } @article {pmid36866281, year = {2021}, author = {Boyes, D and Holland, PWH and , and , and , and , and , and , }, title = {The genome sequence of the snout, Hypena proboscidalis (Linnaeus, 1758).}, journal = {Wellcome open research}, volume = {6}, number = {}, pages = {236}, pmid = {36866281}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual female Hypena proboscidalis (the snout; Arthropoda; Insecta; Lepidoptera; Erebidae). The genome sequence is 637 megabases in span. The majority of the assembly is scaffolded into 31 chromosomal pseudomolecules, with the Z sex chromosome assembled.}, } @article {pmid36777713, year = {2021}, author = {Dussex, N and van der Valk, T and Morales, HE and Wheat, CW and Díez-Del-Molino, D and von Seth, J and Foster, Y and Kutschera, VE and Guschanski, K and Rhie, A and Phillippy, AM and Korlach, J and Howe, K and Chow, W and Pelan, S and Mendes Damas, JD and Lewin, HA and Hastie, AR and Formenti, G and Fedrigo, O and Guhlin, J and Harrop, TWR and Le Lec, MF and Dearden, PK and Haggerty, L and Martin, FJ and Kodali, V and Thibaud-Nissen, F and Iorns, D and Knapp, M and Gemmell, NJ and Robertson, F and Moorhouse, R and Digby, A and Eason, D and Vercoe, D and Howard, J and Jarvis, ED and Robertson, BC and Dalén, L}, title = {Population genomics of the critically endangered kākāpō.}, journal = {Cell genomics}, volume = {1}, number = {1}, pages = {100002}, pmid = {36777713}, issn = {2666-979X}, abstract = {The kākāpō is a flightless parrot endemic to New Zealand. Once common in the archipelago, only 201 individuals remain today, most of them descending from an isolated island population. We report the first genome-wide analyses of the species, including a high-quality genome assembly for kākāpō, one of the first chromosome-level reference genomes sequenced by the Vertebrate Genomes Project (VGP). We also sequenced and analyzed 35 modern genomes from the sole surviving island population and 14 genomes from the extinct mainland population. While theory suggests that such a small population is likely to have accumulated deleterious mutations through genetic drift, our analyses on the impact of the long-term small population size in kākāpō indicate that present-day island kākāpō have a reduced number of harmful mutations compared to mainland individuals. We hypothesize that this reduced mutational load is due to the island population having been subjected to a combination of genetic drift and purging of deleterious mutations, through increased inbreeding and purifying selection, since its isolation from the mainland ∼10,000 years ago. Our results provide evidence that small populations can survive even when isolated for hundreds of generations. This work provides key insights into kākāpō breeding and recovery and more generally into the application of genetic tools in conservation efforts for endangered species.}, } @article {pmid35935893, year = {2021}, author = {Crous, PW and Cowan, DA and Maggs-Kölling, G and Yilmaz, N and Thangavel, R and Wingfield, MJ and Noordeloos, ME and Dima, B and Brandrud, TE and Jansen, GM and Morozova, OV and Vila, J and Shivas, RG and Tan, YP and Bishop-Hurley, S and Lacey, E and Marney, TS and Larsson, E and Le Floch, G and Lombard, L and Nodet, P and Hubka, V and Alvarado, P and Berraf-Tebbal, A and Reyes, JD and Delgado, G and Eichmeier, A and Jordal, JB and Kachalkin, AV and Kubátová, A and Maciá-Vicente, JG and Malysheva, EF and Papp, V and Rajeshkumar, KC and Sharma, A and Spetik, M and Szabóová, D and Tomashevskaya, MA and Abad, JA and Abad, ZG and Alexandrova, AV and Anand, G and Arenas, F and Ashtekar, N and Balashov, S and Bañares, Á and Baroncelli, R and Bera, I and Biketova, AY and Blomquist, CL and Boekhout, T and Boertmann, D and Bulyonkova, TM and Burgess, TI and Carnegie, AJ and Cobo-Diaz, JF and Corriol, G and Cunnington, JH and da Cruz, MO and Damm, U and Davoodian, N and de A Santiago, ALCM and Dearnaley, J and de Freitas, LWS and Dhileepan, K and Dimitrov, R and Di Piazza, S and Fatima, S and Fuljer, F and Galera, H and Ghosh, A and Giraldo, A and Glushakova, AM and Gorczak, M and Gouliamova, DE and Gramaje, D and Groenewald, M and Gunsch, CK and Gutiérrez, A and Holdom, D and Houbraken, J and Ismailov, AB and Istel, Ł and Iturriaga, T and Jeppson, M and Jurjević, Ž and Kalinina, LB and Kapitonov, VI and Kautmanová, I and Khalid, AN and Kiran, M and Kiss, L and Kovács, Á and Kurose, D and Kušan, I and Lad, S and Læssøe, T and Lee, HB and Luangsa-Ard, JJ and Lynch, M and Mahamedi, AE and Malysheva, VF and Mateos, A and Matočec, N and Mešić, A and Miller, AN and Mongkolsamrit, S and Moreno, G and Morte, A and Mostowfizadeh-Ghalamfarsa, R and Naseer, A and Navarro-Ródenas, A and Nguyen, TTT and Noisripoom, W and Ntandu, JE and Nuytinck, J and Ostrý, V and Pankratov, TA and Pawłowska, J and Pecenka, J and Pham, THG and Polhorský, A and Pošta, A and Raudabaugh, DB and Reschke, K and Rodríguez, A and Romero, M and Rooney-Latham, S and Roux, J and Sandoval-Denis, M and Smith, MT and Steinrucken, TV and Svetasheva, TY and Tkalčec, Z and van der Linde, EJ and V D Vegte, M and Vauras, J and Verbeken, A and Visagie, CM and Vitelli, JS and Volobuev, SV and Weill, A and Wrzosek, M and Zmitrovich, IV and Zvyagina, EA and Groenewald, JZ}, title = {Fungal Planet description sheets: 1182-1283.}, journal = {Persoonia}, volume = {46}, number = {}, pages = {313-528}, pmid = {35935893}, issn = {0031-5850}, abstract = {Novel species of fungi described in this study include those from various countries as follows: Algeria, Phaeoacremonium adelophialidum from Vitis vinifera. Antarctica, Comoclathris antarctica from soil. Australia, Coniochaeta salicifolia as endophyte from healthy leaves of Geijera salicifolia, Eremothecium peggii in fruit of Citrus australis, Microdochium ratticaudae from stem of Sporobolus natalensis, Neocelosporium corymbiae on stems of Corymbia variegata, Phytophthora kelmanii from rhizosphere soil of Ptilotus pyramidatus, Pseudosydowia backhousiae on living leaves of Backhousia citriodora, Pseudosydowia indooroopillyensis, Pseudosydowia louisecottisiae and Pseudosydowia queenslandica on living leaves of Eucalyptus sp. Brazil, Absidia montepascoalis from soil. Chile, Ilyonectria zarorii from soil under Maytenus boaria. Costa Rica, Colletotrichum filicis from an unidentified fern. Croatia, Mollisia endogranulata on deteriorated hardwood. Czech Republic, Arcopilus navicularis from tea bag with fruit tea, Neosetophoma buxi as endophyte from Buxus sempervirens, Xerochrysium bohemicum on surface of biscuits with chocolate glaze and filled with jam. France, Entoloma cyaneobasale on basic to calcareous soil, Fusarium aconidiale from Triticum aestivum, Fusarium juglandicola from buds of Juglans regia. Germany, Tetraploa endophytica as endophyte from Microthlaspi perfoliatum roots. India, Castanediella ambae on leaves of Mangifera indica, Lactifluus kanadii on soil under Castanopsis sp., Penicillium uttarakhandense from soil. Italy, Penicillium ferraniaense from compost. Namibia, Bezerromyces gobabebensis on leaves of unidentified succulent, Cladosporium stipagrostidicola on leaves of Stipagrostis sp., Cymostachys euphorbiae on leaves of Euphorbia sp., Deniquelata hypolithi from hypolith under a rock, Hysterobrevium walvisbayicola on leaves of unidentified tree, Knufia hypolithi and Knufia walvisbayicola from hypolith under a rock, Lapidomyces stipagrostidicola on leaves of Stipagrostis sp., Nothophaeotheca mirabibensis (incl. Nothophaeotheca gen. nov.) on persistent inflorescence remains of Blepharis obmitrata, Paramyrothecium salvadorae on twigs of Salvadora persica, Preussia procaviicola on dung of Procavia sp., Sordaria equicola on zebra dung, Volutella salvadorae on stems of Salvadora persica. Netherlands, Entoloma ammophilum on sandy soil, Entoloma pseudocruentatum on nutrient poor (acid) soil, Entoloma pudens on plant debris, amongst grasses. New Zealand, Amorocoelophoma neoregeliae from leaf spots of Neoregelia sp., Aquilomyces metrosideri and Septoriella callistemonis from stem discolouration and leaf spots of Metrosideros sp., Cadophora neoregeliae from leaf spots of Neoregelia sp., Flexuomyces asteliae (incl. Flexuomyces gen. nov.) and Mollisia asteliae from leaf spots of Astelia chathamica, Ophioceras freycinetiae from leaf spots of Freycinetia banksii, Phaeosphaeria caricis-sectae from leaf spots of Carex secta. Norway, Cuphophyllus flavipesoides on soil in semi-natural grassland, Entoloma coracis on soil in calcareous Pinus and Tilia forests, Entoloma cyaneolilacinum on soil semi-natural grasslands, Inocybe norvegica on gravelly soil. Pakistan, Butyriboletus parachinarensis on soil in association with Quercus baloot. Poland, Hyalodendriella bialowiezensis on debris beneath fallen bark of Norway spruce Picea abies. Russia, Bolbitius sibiricus on à moss covered rotting trunk of Populus tremula, Crepidotus wasseri on debris of Populus tremula, Entoloma isborscanum on soil on calcareous grasslands, Entoloma subcoracis on soil in subalpine grasslands, Hydropus lecythiocystis on rotted wood of Betula pendula, Meruliopsis faginea on fallen dead branches of Fagus orientalis, Metschnikowia taurica from fruits of Ziziphus jujube, Suillus praetermissus on soil, Teunia lichenophila as endophyte from Cladonia rangiferina. Slovakia, Hygrocybe fulgens on mowed grassland, Pleuroflammula pannonica from corticated branches of Quercus sp. South Africa, Acrodontium burrowsianum on leaves of unidentified Poaceae, Castanediella senegaliae on dead pods of Senegalia ataxacantha, Cladophialophora behniae on leaves of Behnia sp., Colletotrichum cliviigenum on leaves of Clivia sp., Diatrype dalbergiae on bark of Dalbergia armata, Falcocladium heteropyxidicola on leaves of Heteropyxis canescens, Lapidomyces aloidendricola as epiphyte on brown stem of Aloidendron dichotomum, Lasionectria sansevieriae and Phaeosphaeriopsis sansevieriae on leaves of Sansevieria hyacinthoides, Lylea dalbergiae on Diatrype dalbergiae on bark of Dalbergia armata, Neochaetothyrina syzygii (incl. Neochaetothyrina gen. nov.) on leaves of Syzygium chordatum, Nothophaeomoniella ekebergiae (incl. Nothophaeomoniella gen. nov.) on leaves of Ekebergia pterophylla, Paracymostachys euphorbiae (incl. Paracymostachys gen. nov.) on leaf litter of Euphorbia ingens, Paramycosphaerella pterocarpi on leaves of Pterocarpus angolensis, Paramycosphaerella syzygii on leaf litter of Syzygium chordatum, Parateichospora phoenicicola (incl. Parateichospora gen. nov.) on leaves of Phoenix reclinata, Seiridium syzygii on twigs of Syzygium chordatum, Setophoma syzygii on leaves of Syzygium sp., Starmerella xylocopis from larval feed of an Afrotropical bee Xylocopa caffra, Teratosphaeria combreti on leaf litter of Combretum kraussii, Teratosphaericola leucadendri on leaves of Leucadendron sp., Toxicocladosporium pterocarpi on pods of Pterocarpus angolensis. Spain, Cortinarius bonachei with Quercus ilex in calcareus soils, Cortinarius brunneovolvatus under Quercus ilex subsp. ballota in calcareous soil, Extremopsis radicicola (incl. Extremopsis gen. nov.) from root-associated soil in a wet heathland, Russula quintanensis on acidic soils, Tubaria vulcanica on volcanic lapilii material, Tuber zambonelliae in calcareus soil. Sweden, Elaphomyces borealis on soil under Pinus sylvestris and Betula pubescens. Tanzania, Curvularia tanzanica on inflorescence of Cyperus aromaticus. Thailand, Simplicillium niveum on Ophiocordyceps camponoti-leonardi on underside of unidentified dicotyledonous leaf. USA, Calonectria californiensis on leaves of Umbellularia californica, Exophiala spartinae from surface sterilised roots of Spartina alterniflora, Neophaeococcomyces oklahomaensis from outside wall of alcohol distillery. Vietnam, Fistulinella aurantioflava on soil. Morphological and culture characteristics are supported by DNA barcodes. Citation: Crous PW, Cowan DA, Maggs-Kölling, et al. 2021. Fungal Planet description sheets: 1182-1283. Persoonia 46: 313-528. https://doi.org/10.3767/persoonia.2021.46.11.}, } @article {pmid36568028, year = {2021}, author = {Huss, M and Brander, M and Kassie, M and Ehlert, U and Bernauer, T}, title = {Improved storage mitigates vulnerability to food-supply shocks in smallholder agriculture during the COVID-19 pandemic.}, journal = {Global food security}, volume = {28}, number = {}, pages = {100468}, pmid = {36568028}, issn = {2211-9124}, abstract = {Millions of smallholder farmers in low-income countries are highly vulnerable to food-supply shocks, and reducing this vulnerability remains challenging in view of climatic changes. Restrictions to limit the spread of the COVID-19 pandemic produced a severe supply-side shock in rural areas of Sub-Saharan Africa, including through frictions in agricultural markets. We use a large-scale field experiment to examine the effects of improved on-farm storage on household food security during COVID-19 restrictions. Based on text message survey data we find that the prevalence of food insecurity increased in control group households during COVID-19 restrictions (coinciding with the agricultural lean season). In treatment households, equipped with an improved on-farm storage technology and training in its use, food insecurity was lower during COVID-19 restrictions. This underscores the benefits of improved on-farm storage for mitigating vulnerability to food-supply shocks. These insights are relevant for the larger, long-term question of climate change adaptation, and also regarding trade-offs between public health protection and food security.}, } @article {pmid36659170, year = {2020}, author = {Gong, P and Chen, B and Li, X and Liu, H and Wang, J and Bai, Y and Chen, J and Chen, X and Fang, L and Feng, S and Feng, Y and Gong, Y and Gu, H and Huang, H and Huang, X and Jiao, H and Kang, Y and Lei, G and Li, A and Li, X and Li, X and Li, Y and Li, Z and Li, Z and Liu, C and Liu, C and Liu, M and Liu, S and Mao, W and Miao, C and Ni, H and Pan, Q and Qi, S and Ren, Z and Shan, Z and Shen, S and Shi, M and Song, Y and Su, M and Ping Suen, H and Sun, B and Sun, F and Sun, J and Sun, L and Sun, W and Tian, T and Tong, X and Tseng, Y and Tu, Y and Wang, H and Wang, L and Wang, X and Wang, Z and Wu, T and Xie, Y and Yang, J and Yang, J and Yuan, M and Yue, W and Zeng, H and Zhang, K and Zhang, N and Zhang, T and Zhang, Y and Zhao, F and Zheng, Y and Zhou, Q and Clinton, N and Zhu, Z and Xu, B}, title = {Mapping essential urban land use categories in China (EULUC-China): preliminary results for 2018.}, journal = {Science bulletin}, volume = {65}, number = {3}, pages = {182-187}, doi = {10.1016/j.scib.2019.12.007}, pmid = {36659170}, issn = {2095-9281}, } @article {pmid36595968, year = {2018}, author = {Martínková, N and Pikula, J and Zukal, J and Kovacova, V and Bandouchova, H and Bartonička, T and Botvinkin, AD and Brichta, J and Dundarova, H and Kokurewicz, T and Irwin, NR and Linhart, P and Orlov, OL and Piacek, V and Škrabánek, P and Tiunov, MP and Zahradníková, A}, title = {Hibernation temperature-dependent Pseudogymnoascus destructans infection intensity in Palearctic bats.}, journal = {Virulence}, volume = {9}, number = {1}, pages = {1734-1750}, pmid = {36595968}, issn = {2150-5608}, abstract = {White-nose syndrome (WNS) is a fungal disease caused by Pseudogymnoascus destructans that is devastating to Nearctic bat populations but tolerated by Palearctic bats. Temperature is a factor known to be important for fungal growth and bat choice of hibernation. Here we investigated the effect of temperature on the pathogenic fungal growth in the wild across the Palearctic. We modelled body surface temperature of bats with respect to fungal infection intensity and disease severity and were able to relate this to the mean annual surface temperature at the site. Bats that hibernated at lower temperatures had less fungal growth and fewer skin lesions on their wings. Contrary to expectation derived from laboratory P. destructans culture experiments, natural infection intensity peaked between 5 and 6°C and decreased at warmer hibernating temperature. We made predictive maps based on bat species distributions, temperature and infection intensity and disease severity data to determine not only where P. destructans will be found but also where the infection will be invasive to bats across the Palearctic. Together these data highlight the mechanistic model of the interplay between environmental and biological factors, which determine progression in a wildlife disease.}, } @article {pmid35738644, year = {2022}, author = {Knauer, J and Terhorst, Y and Philippi, P and Kallinger, S and Eiler, S and Kilian, R and Waldmann, T and Moshagen, M and Bader, M and Baumeister, H}, title = {Effectiveness and cost-effectiveness of a web-based routine assessment with integrated recommendations for action for depression and anxiety (RehaCAT+): protocol for a cluster randomised controlled trial for patients with elevated depressive symptoms in rehabilitation facilities.}, journal = {BMJ open}, volume = {12}, number = {6}, pages = {e061259}, pmid = {35738644}, issn = {2044-6055}, mesh = {Anxiety/therapy ; Cost-Benefit Analysis ; *Depression/psychology ; Humans ; Internet ; *Quality of Life ; Randomized Controlled Trials as Topic ; }, abstract = {INTRODUCTION: The integration of a web-based computer-adaptive patient-reported outcome test (CAT) platform with persuasive design optimised features including recommendations for action into routine healthcare could provide a promising way to translate reliable diagnostic results into action. This study aims to evaluate the effectiveness and cost-effectiveness of such a platform for depression and anxiety (RehaCAT+) compared with the standard diagnostic system (RehaCAT) in cardiological and orthopaedic health clinics in routine care.

METHODS AND ANALYSIS: A two-arm, pragmatic, cluster-randomised controlled trial will be conducted. Twelve participating rehabilitation clinics in Germany will be randomly assigned to a control (RehaCAT) or experimental group (RehaCAT+) in a 1:1 design. A total sample of 1848 participants will be recruited across all clinics. The primary outcome, depression severity at 12 months follow-up (T3), will be assessed using the CAT Patient-Reported Outcome Measurement Information System Emotional Distress-Depression Item set. Secondary outcomes are depression at discharge (T1) and 6 months follow-up (T2) as well as anxiety, satisfaction with participation in social roles and activities, pain impairment, fatigue, sleep, health-related quality of life, self-efficacy, physical functioning, alcohol, personality and health economic-specific general quality of life and socioeconomic cost and benefits at T1-3. User behaviour, acceptance, facilitating and hindering factors will be assessed with semistructured qualitative interviews. Additionally, a smart sensing substudy will be conducted, with daily ecological momentary assessments and passive collection of smartphone usage variables. Data analysis will follow the intention-to-treat principle with additional per-protocol analyses. Cost-effectiveness analyses will be conducted from a societal perspective and the perspective of the statutory pension insurance.

ETHICS AND DISSEMINATION: The study will be conducted according to the Declaration of Helsinki. The Ethics Committee of Ulm University, has approved the study (on 24 February 2021 ref. 509/20). Written informed consent will be obtained for all participants. Results will be published via peer-reviewed journals.

TRIAL REGISTRATION NUMBER: DRKS00027447.}, } @article {pmid35737561, year = {2023}, author = {Swerdlow, BA and Sandel, DB and Johnson, SL}, title = {Shame on me for needing you: A multistudy examination of links between receiving interpersonal emotion regulation and experiencing shame.}, journal = {Emotion (Washington, D.C.)}, volume = {23}, number = {3}, pages = {737-752}, doi = {10.1037/emo0001109}, pmid = {35737561}, issn = {1931-1516}, support = {/MH/NIMH NIH HHS/United States ; }, mesh = {Humans ; *Emotions/physiology ; *Emotional Regulation ; Shame ; Hostility ; Data Management ; }, abstract = {Recent theory and research have drawn attention to interpersonal dimensions of emotion regulation. Yet, few empirical investigations of the outcomes of interpersonal emotion regulation have been conducted. We propose that one negative affective outcome of received interpersonal emotion regulation of conceptual and practical interest is shame. In the present series of studies, participants from six disparate samples reported on experiences of receiving interpersonal emotion regulation using autobiographical recall and ecological sampling paradigms (total analyzed n = 1,868; total analyzed k = 2,515 instances of receiving interpersonal emotion regulation). We sought to quantify the frequency and distinctiveness of shame as an outcome of receiving interpersonal emotion regulation. We used an exploratory-confirmatory approach to identify robust and generalizable correlates of shame. We considered individual (e.g., trait external shame-proneness), situational (e.g., desire for regulation), relational (e.g., perceived closeness with the provider), and interaction-specific (e.g., perceptions of provider hostility) variables. Our results indicate that it is not uncommon for people to experience receiving interpersonal emotion regulation as shame-inducing, and these perceptions are distinct from their evaluations of the overall helpfulness of the interaction. An internal mini meta-analysis showed that the strongest correlates of shame across studies and samples were individual differences in nonacceptance of negative emotions and expressive suppression and interaction-specific ratings of provider responsiveness and hostility. We discuss the conceptual, methodological, and practical implications of these findings for studying interpersonal emotion regulation and shame. (PsycInfo Database Record (c) 2023 APA, all rights reserved).}, } @article {pmid35735943, year = {2022}, author = {Da Costa, HVV and Vieira do Bonfim, C and Fusco, W and Moreira, MM and Maciano de Paula Neto, F}, title = {Impact of the COVID-19 pandemic on the number of births in Pernambuco Brazil.}, journal = {Geospatial health}, volume = {17}, number = {s1}, pages = {}, doi = {10.4081/gh.2022.1069}, pmid = {35735943}, issn = {1970-7096}, mesh = {Brazil/epidemiology ; *COVID-19/epidemiology ; Forecasting ; Humans ; Pandemics ; Time Factors ; }, abstract = {This study aimed at analysing the potential effects of the COVID-19 pandemic on the time series and spatial patterns of live births in the state of Pernambuco, Brazil, from 2010 to 2021. This is an ecological study that applied intervention analysis in time series, with the goal to identify how projected data behaved in relation to observed data in the months December 2020 to November 2021, i.e. months representing conceptions from March2020 to April 2021. For the state of Pernambuco, a discrepancy up to +5.7% was found between the observed and projected data, while the respective difference for the São Francisco mesoregion showed the opposite trend with maximum discrepancy of -9%. The results did not indicate a clear change in the number of live births but supported the expected continuation of the downward trend of the previous years. Considering the importance of the number of live births in the context of demography, economy and public health, monitoring must be maintained to analyse the possible future impact of the COVID-19 pandemic on live birth projections.}, } @article {pmid35733262, year = {2022}, author = {Qiu, Z and Espinoza, B and Vasconcelos, VV and Chen, C and Constantino, SM and Crabtree, SA and Yang, L and Vullikanti, A and Chen, J and Weibull, J and Basu, K and Dixit, A and Levin, SA and Marathe, MV}, title = {Understanding the coevolution of mask wearing and epidemics: A network perspective.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {119}, number = {26}, pages = {e2123355119}, pmid = {35733262}, issn = {1091-6490}, support = {R01 GM109718/GM/NIGMS NIH HHS/United States ; 75D30119C05935//HHS | Centers for Disease Control and Prevention (CDC)/ ; 1R01GM109718//HHS | National Institutes of Health (NIH)/ ; }, mesh = {*Epidemics/prevention & control ; Humans ; *Masks ; }, abstract = {Nonpharmaceutical interventions (NPIs) such as mask wearing can be effective in mitigating the spread of infectious diseases. Therefore, understanding the behavioral dynamics of NPIs is critical for characterizing the dynamics of disease spread. Nevertheless, standard infection models tend to focus only on disease states, overlooking the dynamics of "beneficial contagions," e.g., compliance with NPIs. In this work, we investigate the concurrent spread of disease and mask-wearing behavior over multiplex networks. Our proposed framework captures both the competing and complementary relationships between the dueling contagion processes. Further, the model accounts for various behavioral mechanisms that influence mask wearing, such as peer pressure and fear of infection. Our results reveal that under the coupled disease-behavior dynamics, the attack rate of a disease-as a function of transition probability-exhibits a critical transition. Specifically, as the transmission probability exceeds a critical threshold, the attack rate decreases abruptly due to sustained mask-wearing responses. We empirically explore the causes of the critical transition and demonstrate the robustness of the observed phenomena. Our results highlight that without proper enforcement of NPIs, reductions in the disease transmission probability via other interventions may not be sufficient to reduce the final epidemic size.}, } @article {pmid35733118, year = {2022}, author = {Sawires, R and Kuldorff, M and Fahey, M and Clothier, H and Buttery, J}, title = {Snotwatch: an ecological analysis of the relationship between febrile seizures and respiratory virus activity.}, journal = {BMC pediatrics}, volume = {22}, number = {1}, pages = {359}, pmid = {35733118}, issn = {1471-2431}, mesh = {Child ; Humans ; Infant ; *Influenza, Human/complications/diagnosis/epidemiology ; *Seizures, Febrile/epidemiology/etiology ; Victoria/epidemiology ; *Virus Diseases/complications ; *Viruses ; }, abstract = {BACKGROUND: Febrile seizures are the commonest type of seizure in occurring in the first few years of life, mostly affecting children aged six months to five years old. While largely benign, the incidence of each febrile seizure increases the risk of recurrence, afebrile seizures and epilepsy. Viruses are the most frequent cause of febrile illnesses in which a febrile seizure occurs. Febrile seizure presentation patterns appear to follow a seasonal trend.

AIMS: To identify patterns of febrile seizure incidence across different seasons with specific viral activity, and to establish a framework for analysing virus circulation data with common illnesses within a shared region and population.

SETTING: Our study was a study of febrile seizure presentations in Victoria, Australia and respiratory virus detection.

PARTICIPANTS: We obtained independent datasets of emergency department febrile seizure presentations at Monash Health and all respiratory multiplex PCR tests performed at Monash Health from January 2010-December 2019 to observe common trends in virus circulation and febrile seizure incidence.

STUDY DESIGN: Trends were studied temporally through mixed effects Poisson regression analysis of the monthly incidence of febrile seizures and the rate of positive PCR tests. Peak viral seasons (95th centile incidence) were compared to median viral circulation (50th centile incidence) to calculate peak season risk ratios.

RESULTS: We found a 1.75-2.06 annual risk ratio of febrile seizure incidence in June-September. Temporal analysis of our data showed this peak in febrile seizures was attributable to circulating viruses in this season, and virus modelling showed correlation with increased rates of positive Influenza A (1.48 peak season risk ratio), Influenza B (1.31 peak season risk ratio), Human metapneumovirus (1.19 peak season risk ratio) and Respiratory Syncytial Virus (1.53 peak season risk ratio) on PCR testing.

CONCLUSION: Our ecological study statistically demonstrates the recognised winter peak in febrile seizure incidence and ascribes the seasonal relationship to several viral infections which affect the community, including a novel association with Human metapneumovirus.}, } @article {pmid35732838, year = {2022}, author = {Zhao, Y and Niu, Z and Zhong, Q and Wang, L and He, S and Xu, M and Wang, J}, title = {Preparation and Characterization of Red Mud/Fly Ash Composite Material (RFCM) for Phosphate Removal.}, journal = {Bulletin of environmental contamination and toxicology}, volume = {109}, number = {1}, pages = {169-179}, pmid = {35732838}, issn = {1432-0800}, support = {51602344//National Natural Science Foundation of China/ ; 51974314//National Natural Science Foundation of China/ ; BK20160241//Natural Science Foundation of Jiangsu Province/ ; 2014QNA35//Fundamental Research Funds for the Central Universities/ ; }, mesh = {Adsorption ; Aluminum Oxide ; *Coal Ash ; Industrial Waste/analysis ; *Phosphates/chemistry ; }, abstract = {In this study, a new red mud/fly ash composite material (RFCM) for phosphate removal was prepared by granulation and activation methods, using bauxite residue (red mud, RM) as the main raw material, adding with some fly ash and a few adhesives. The effects of different types of RM and adhesives on RFCM for phosphate removal were discussed. It was found that RFCM prepared from sintering red mud and cement waste performed better on phosphate removal than that prepared from Bayer red mud and common industrial adhesives. After calcination activated at appropriate temperature around 800-900℃, the specific surface area of RFCM increased, and new substances with hydroxyl (-OH) appeared on the surface of RFCM, which were the functional groups for phosphate removal. Mechanism of RFCM for phosphate removal was speculated as a combination of physical adsorption, chemical adsorption and chemical precipitation, which mainly depended on ligand exchange and chemical reaction. This research will provide a potential application of bauxite residue in environmental remediation.}, } @article {pmid35732736, year = {2022}, author = {Paoli, L and Ruscheweyh, HJ and Forneris, CC and Hubrich, F and Kautsar, S and Bhushan, A and Lotti, A and Clayssen, Q and Salazar, G and Milanese, A and Carlström, CI and Papadopoulou, C and Gehrig, D and Karasikov, M and Mustafa, H and Larralde, M and Carroll, LM and Sánchez, P and Zayed, AA and Cronin, DR and Acinas, SG and Bork, P and Bowler, C and Delmont, TO and Gasol, JM and Gossert, AD and Kahles, A and Sullivan, MB and Wincker, P and Zeller, G and Robinson, SL and Piel, J and Sunagawa, S}, title = {Biosynthetic potential of the global ocean microbiome.}, journal = {Nature}, volume = {607}, number = {7917}, pages = {111-118}, pmid = {35732736}, issn = {1476-4687}, support = {835067/ERC_/European Research Council/International ; }, mesh = {Bacteria/classification/genetics ; *Biosynthetic Pathways/genetics ; Genomics ; *Microbiota/genetics ; Multigene Family/genetics ; *Oceans and Seas ; Phylogeny ; }, abstract = {Natural microbial communities are phylogenetically and metabolically diverse. In addition to underexplored organismal groups[1], this diversity encompasses a rich discovery potential for ecologically and biotechnologically relevant enzymes and biochemical compounds[2,3]. However, studying this diversity to identify genomic pathways for the synthesis of such compounds[4] and assigning them to their respective hosts remains challenging. The biosynthetic potential of microorganisms in the open ocean remains largely uncharted owing to limitations in the analysis of genome-resolved data at the global scale. Here we investigated the diversity and novelty of biosynthetic gene clusters in the ocean by integrating around 10,000 microbial genomes from cultivated and single cells with more than 25,000 newly reconstructed draft genomes from more than 1,000 seawater samples. These efforts revealed approximately 40,000 putative mostly new biosynthetic gene clusters, several of which were found in previously unsuspected phylogenetic groups. Among these groups, we identified a lineage rich in biosynthetic gene clusters ('Candidatus Eudoremicrobiaceae') that belongs to an uncultivated bacterial phylum and includes some of the most biosynthetically diverse microorganisms in this environment. From these, we characterized the phospeptin and pythonamide pathways, revealing cases of unusual bioactive compound structure and enzymology, respectively. Together, this research demonstrates how microbiomics-driven strategies can enable the investigation of previously undescribed enzymes and natural products in underexplored microbial groups and environments.}, } @article {pmid35730806, year = {2022}, author = {Barbosa, ÁRG and Takemura, LS and Amaral, BS and Wroclawski, ML and Alfer, W and Gil, AO and Monteiro, J and Lourenço, DB and Cha, JD and Apezzato, M and Barbosa, JABA and Bianco, B and Lemos, GC and Carneiro, A}, title = {Benign prostatic hyperplasia surgical treatment trends in the Public Health System in São Paulo, Brazil.}, journal = {Einstein (Sao Paulo, Brazil)}, volume = {20}, number = {}, pages = {eAO6880}, pmid = {35730806}, issn = {2317-6385}, mesh = {Brazil/epidemiology ; Humans ; *Laser Therapy/methods ; Male ; Prostatectomy ; *Prostatic Hyperplasia/surgery ; Public Health ; Retrospective Studies ; *Transurethral Resection of Prostate/methods ; Treatment Outcome ; }, abstract = {OBJECTIVE: To describe and compare the number of surgeries, mortality rate, length of hospital stay, and costs of transurethral resection of the prostate and open prostatectomy for the treatment of benign prostatic hyperplasia, between 2008 and 2018, in the Public Health System in São Paulo, Brazil.

METHODS: Ecological and retrospective study using data from the informatics department of the Brazilian Public Health System database. Procedure codes were "open prostatectomy" and "transurethral resection of the prostate." The outcomes analyzed were compared between transurethral resection of the prostate and open prostatectomy according to the hospital surgical volume and presence or absence of a residency program.

RESULTS: A total of 18,874 surgeries were analyzed (77% transurethral resection of the prostate) and overall mortality was not statistically different between procedures. Intermediate and high-volume centers had shorter length of hospital stay than low-volume centers for transurethral resection of the prostate (3.28, 3.02, and 6.58 days, respectively, p=0.01 and p=0.004). Length of hospital stay was also shorter for open prostatectomy in high-volume compared to low-volume centers (4.86 versus 10.76 days, p=0.036). Intrahospital mortality was inversely associated with surgical volume for transurethral resection of the prostate. Centers with residency program had shorter length of hospital stay considering open prostatectomy and less mortality regarding transurethral resection of the prostate. Open prostatectomy was 64% more expensive than transurethral resection of the prostate.

CONCLUSION: The findings suggest the importance of investing in specialized centers, which could be potential referral centers for surgical cases.}, } @article {pmid35727537, year = {2022}, author = {Terraneo, TI and Mariappan, KG and Forsman, Z and Arrigoni, R}, title = {Mitochondrial Genome of Nonmodel Marine Metazoans by Next-Generation Sequencing (NGS).}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2498}, number = {}, pages = {1-18}, pmid = {35727537}, issn = {1940-6029}, mesh = {Animals ; Computational Biology ; DNA ; Gene Library ; *Genome, Mitochondrial ; High-Throughput Nucleotide Sequencing/methods ; Sequence Analysis, DNA/methods ; }, abstract = {Mitochondrial genomes (mtgenome) represent an important source of information for addressing fundamental evolutionary, phylogeographic, systematic, and ecological questions in marine organisms. In the last two decades the advent of high-throughput next-generation sequencing (NGS) has provided an unprecedented possibility to access large amount of genomic data and, as such, there has been a rapid growth in mtgenome resources and studies. In particular, NGS strategies represent a great advantage for investigating nonmodel marine organisms for which no or limited genomic resources are available. Here, we describe a routinely used standardized protocol to obtain mtgenome of nonmodel marine organisms by NGS. The protocol is composed of five main steps, including DNA extraction, DNA fragmentation, library preparation, high-throughput sequencing, and bioinformatic analyses. Each of the first three steps is followed by size/quality and concentration validations. The advantages of the described protocol rely on the assumption that no a priori information on mtgenome of the studied organism is needed and on its versatility as researchers may choose several kits for DNA extraction and library preparation and adopt different methods for DNA fragmentation depending on their needs, experience, and suppliers.}, } @article {pmid35724975, year = {2022}, author = {Prajapati, J and Singh, A and Patil, K and Bhowmick, AR and Mukherjee, A and Huang, Y and Banerjee, AK}, title = {An occurrence data set for invasive and naturalized alien plants in India.}, journal = {Ecology}, volume = {103}, number = {11}, pages = {e3794}, doi = {10.1002/ecy.3794}, pmid = {35724975}, issn = {1939-9170}, mesh = {*Introduced Species ; *Ecosystem ; Plants ; Biodiversity ; Databases, Factual ; }, abstract = {India has numerous invasive alien plant species (IAPSs), which seriously impact biodiversity, ecosystem services, and economic development. The availability of reliable occurrence records of IAPSs is of great importance for their successful management, prediction of distribution across time and space, and other research and development efforts. Global databases of occurrence data, like the Global Biodiversity Information Facility (GBIF), are often not exhaustive, especially for India, and poorly represent the actual distribution of IAPSs in the country. Our objective in creating this data set was threefold: (1) to compile occurrence data for the invasive and naturalized alien plant species of India, (2) to collect spatial and temporal information associated with occurrence records, and (3) to share the data in an accessible format so every record is traceable to its sources and allow users to submit data to increase the resolution of the data set. To achieve these objectives, we extracted data from 3137 literature records and 357 herbarium sheets. For each occurrence record, we curated information for 20 variables, which were arranged in a table with the Darwin Core (DwC) terms as column names. All data were subjected to technical validation before being included in the database. A total of 12,347 occurrence records were obtained for 362 species (195 invasive aliens and 167 naturalized aliens). The number of collected occurrence records was much higher for the invasive aliens (73.7%) than for the naturalized alien species (26.3%). Our data set will supplement the GBIF data by 60.39%, and occurrence records will be added for 64 invasive and naturalized alien plant species. The data set, as a part of the larger database of the Indian Alien Flora Information (ILORA) database, is made available without any restrictions on use as long as this data paper is properly cited. We have also made provisions for users to submit occurrence-related data following a data standard. The users are encouraged to cite the original reference when using a specific data record. The data set is expected to assist a wide range of stakeholders involved in India's scientific research, policy formulation, and decision-making related to IAPSs.}, } @article {pmid35716808, year = {2022}, author = {Thomas, AC and Wintemute, G and Nathens, AB and Subacius, H and Stey, AM and Bilimoria, KY and Campbell, BT}, title = {The association between gun shows and firearm injuries: An analysis of 259 gun shows across 23 US cities.}, journal = {Preventive medicine}, volume = {161}, number = {}, pages = {107110}, doi = {10.1016/j.ypmed.2022.107110}, pmid = {35716808}, issn = {1096-0260}, mesh = {Cities ; Commerce ; Databases, Factual ; *Firearms ; Humans ; *Wounds, Gunshot/epidemiology ; }, abstract = {Guns shows are estimated to account for 4-9% of firearm sales in the US. Increased regulation of firearm sales at gun shows has been proposed as one approach to reducing firearm injury rates. This study evaluated the association between gun shows and local firearm injury rates. Data regarding the date and location of gun shows from 2017 to 2019 were abstracted from the Big Show Journal. Firearm injury rates were estimated using discharges from trauma centers serving counties within a 25-mile radius of each gun show. Clinical data were derived from the National Trauma Databank (NTDB). We used Poisson regression modeling to adjust for potential confounders including seasonality. We evaluated injury rates before and after 259 gun shows in 23 US locations using firearm injury data from 36 trauma centers. There were 1513 hospitalizations for firearm injuries pre-gun show and 1526 post-gun show. The adjusted mean 2-week rate of all-cause firearm injury per 1,000,000 person-years was 1.79 (1.16-2.76) before and 1.82 (1.18-2.83) after a gun show, with an incident rate ratio of 1.02 (0.94, 1.08). The adjusted mean 2-week rate did not vary significantly by intent after a gun show, (p = 0.24). Within two weeks after a gun show, rates of hospitalization for all-cause firearm injury do not increase significantly within the surrounding communities. The relatively small increase in available firearms after a show and the short time horizon evaluated may account for the absence of an association between gun show firearm sales and local firearm injury rates.}, } @article {pmid35715815, year = {2022}, author = {Belichenko, O and Kolosova, V and Kalle, R and Sõukand, R}, title = {Green pharmacy at the tips of your toes: medicinal plants used by Setos and Russians of Pechorsky District, Pskov Oblast (NW Russia).}, journal = {Journal of ethnobiology and ethnomedicine}, volume = {18}, number = {1}, pages = {46}, pmid = {35715815}, issn = {1746-4269}, support = {714874//HORIZON EUROPE European Research Council/ ; 714874//HORIZON EUROPE European Research Council/ ; 714874//HORIZON EUROPE European Research Council/ ; }, mesh = {Ethnobotany ; Humans ; Medicine, Traditional ; *Pharmacy ; *Plants, Medicinal ; Russia ; Toes ; }, abstract = {BACKGROUND: While the hybridization of ecological knowledge has attracted substantial attention from researchers, the coexistence of local and allopathic medicinal traditions in literate societies widely exposed to centralized schooling and medical services has not yet been investigated. To this end, we studied the current and remembered local ethnomedical practices of Setos and neighboring Russians at the border with Estonia.

METHODS: During 2018-2019, we carried out 62 semi-structured interviews in the Pechorsky District of Pskov Oblast, NW Russia. For cross-border comparison, we utilized the data from 71 interviews carried out at the same time among Setos in Estonia. The Jaccard Similarity Index and qualitative comparison were used to analyze the data.

RESULTS: The study participants mentioned 819 uses of 112 taxa belonging to 54 families. More than two-thirds of the uses (565) were quoted by 36 Russian interviewees, while the remaining third (254) were quoted by 26 Seto interviewees, with the top 3 in both groups being Viburnum opulus, Rubus idaeus, and Plantago major. The Seto intraethnic similarity index was lower (0.43) than the interethnic similarity in Estonia (0.52) and comparable to the interethnic similarity in Russia (0.43). Setos in Russia and local Russians rely more on wild plants (86% and 80% of medicinal plants, respectively), while Setos in Estonia and Estonians show less preference to them (63% and 61%, respectively). Nevertheless, Setos tend to source wild plants available in their gardens (33% of plants for Setos in Estonia and 38% in Russia), while Russians prefer to source them in the wild (38%).

CONCLUSIONS: The preference of both groups in Russia for wild plants over cultivated and purchased plants was inspired by the overall plant literacy, access to nature, and one-to-many knowledge transfer favoring wild plants. Setos in Russia reported a narrower and more homogenous set of plants transferred vertically. However, due to atomization and the erosion of horizontal connections, there are singular plant uses among Setos that overlap with the local Russian set of medicinal plants and differ qualitatively from that of Setos in Estonia.}, } @article {pmid35715445, year = {2022}, author = {Donaldson, DR and Koepke, JW}, title = {A focus groups study on data sharing and research data management.}, journal = {Scientific data}, volume = {9}, number = {1}, pages = {345}, pmid = {35715445}, issn = {2052-4463}, support = {RE-37-19-0082-19//Institute of Museum and Library Services (IMLS)/ ; }, mesh = {*Data Management ; Focus Groups ; Humans ; *Information Dissemination ; Metadata ; Research Personnel ; }, abstract = {Data sharing can accelerate scientific discovery while increasing return on investment beyond the researcher or group that produced them. Data repositories enable data sharing and preservation over the long term, but little is known about scientists' perceptions of them and their perspectives on data management and sharing practices. Using focus groups with scientists from five disciplines (atmospheric and earth science, computer science, chemistry, ecology, and neuroscience), we asked questions about data management to lead into a discussion of what features they think are necessary to include in data repository systems and services to help them implement the data sharing and preservation parts of their data management plans. Participants identified metadata quality control and training as problem areas in data management. Additionally, participants discussed several desired repository features, including: metadata control, data traceability, security, stable infrastructure, and data use restrictions. We present their desired repository features as a rubric for the research community to encourage repository utilization. Future directions for research are discussed.}, } @article {pmid35708657, year = {2023}, author = {Wang, T and Smith, DA and Campbell, C and Freeman, O and Moysova, Z and Noble, T and Várnai, KA and Harris, S and Salih, H and Roadknight, G and Little, S and Glampson, B and Mercuri, L and Papadimitriou, D and Jones, CR and Taylor, V and Chaudhry, A and Phan, H and Borca, F and Olza, J and Warricker, F and Romão, L and Ramlakhan, D and English, L and Klenerman, P and Andersson, M and Collier, J and Stockdale, AJ and Todd, S and McIntyre, K and Frankland, A and Nastouli, E and Khakoo, SI and Gelson, W and Cooke, GS and Woods, K and Davies, J and Barnes, E and Matthews, PC}, title = {Cohort Profile: The National Institute for Health Research Health Informatics Collaborative: Hepatitis B Virus (NIHR HIC HBV) research dataset.}, journal = {International journal of epidemiology}, volume = {52}, number = {1}, pages = {e27-e37}, pmid = {35708657}, issn = {1464-3685}, support = {/WT_/Wellcome Trust/United Kingdom ; 29725/CRUK_/Cancer Research UK/United Kingdom ; 110110/WT_/Wellcome Trust/United Kingdom ; /DH_/Department of Health/United Kingdom ; }, mesh = {Humans ; Hepatitis B virus ; *Hepatitis B/epidemiology ; Hepatitis B Surface Antigens ; *Medical Informatics ; }, } @article {pmid35708643, year = {2022}, author = {Perry, A and McGaugh, SE and Keene, AC and Blackmon, H}, title = {CaveCrawler: an interactive analysis suite for cavefish bioinformatics.}, journal = {G3 (Bethesda, Md.)}, volume = {12}, number = {8}, pages = {}, pmid = {35708643}, issn = {2160-1836}, support = {R35 GM138098/GM/NIGMS NIH HHS/United States ; R21 NS122166/NS/NINDS NIH HHS/United States ; R01 CA127872/CA/NCI NIH HHS/United States ; }, mesh = {Animals ; Biological Evolution ; Caves ; *Characidae/genetics ; *Computational Biology ; Genome ; }, abstract = {The growing use of genomics in diverse organisms provides the basis for identifying genomic and transcriptional differences across species and experimental conditions. Databases containing genomic and functional data have played critical roles in the development of numerous genetic models but most emerging models lack such databases. The Mexican tetra, Astyanax mexicanus exists as 2 morphs: surface-dwelling and cave-dwelling. There exist at least 30 cave populations, providing a system to study convergent evolution. We have generated a web-based analysis suite that integrates datasets from different studies to identify how gene transcription and genetic markers of selection differ between populations and across experimental contexts. Results of diverse studies can be analyzed in conjunction with other genetic data (e.g. Gene Ontology information), to enable biological inference from cross-study patterns and identify future avenues of research. Furthermore, the framework that we have built for A. mexicanus can be adapted for other emerging model systems.}, } @article {pmid35708073, year = {2022}, author = {Weinstein, BG and Garner, L and Saccomanno, VR and Steinkraus, A and Ortega, A and Brush, K and Yenni, G and McKellar, AE and Converse, R and Lippitt, CD and Wegmann, A and Holmes, ND and Edney, AJ and Hart, T and Jessopp, MJ and Clarke, RH and Marchowski, D and Senyondo, H and Dotson, R and White, EP and Frederick, P and Ernest, SKM}, title = {A general deep learning model for bird detection in high-resolution airborne imagery.}, journal = {Ecological applications : a publication of the Ecological Society of America}, volume = {32}, number = {8}, pages = {e2694}, doi = {10.1002/eap.2694}, pmid = {35708073}, issn = {1051-0761}, mesh = {Humans ; Animals ; *Deep Learning ; Ecosystem ; Artificial Intelligence ; Neural Networks, Computer ; Birds ; }, abstract = {Advances in artificial intelligence for computer vision hold great promise for increasing the scales at which ecological systems can be studied. The distribution and behavior of individuals is central to ecology, and computer vision using deep neural networks can learn to detect individual objects in imagery. However, developing supervised models for ecological monitoring is challenging because it requires large amounts of human-labeled training data, requires advanced technical expertise and computational infrastructure, and is prone to overfitting. This limits application across space and time. One solution is developing generalized models that can be applied across species and ecosystems. Using over 250,000 annotations from 13 projects from around the world, we develop a general bird detection model that achieves over 65% recall and 50% precision on novel aerial data without any local training despite differences in species, habitat, and imaging methodology. Fine-tuning this model with only 1000 local annotations increases these values to an average of 84% recall and 69% precision by building on the general features learned from other data sources. Retraining from the general model improves local predictions even when moderately large annotation sets are available and makes model training faster and more stable. Our results demonstrate that general models for detecting broad classes of organisms using airborne imagery are achievable. These models can reduce the effort, expertise, and computational resources necessary for automating the detection of individual organisms across large scales, helping to transform the scale of data collection in ecology and the questions that can be addressed.}, } @article {pmid35707246, year = {2022}, author = {Xiao, D and Keita, M and Zhang, C and Wang, E and Diaz, ND and Wu, J and He, H and Ma, J and Julien, EO}, title = {Dataset of coal bio-gasification and coalbed methane stimulation by single well nutrition injection in Qinshui anthracite coalbed methane wells.}, journal = {Data in brief}, volume = {43}, number = {}, pages = {108353}, pmid = {35707246}, issn = {2352-3409}, abstract = {In-situ coal bio-gasification can be defined as one of the coal bio-mining methodology that fully utilizes the methanogenic bacteria in coal to review the current findings, namely anaerobic digestion of organic components. The following experiment has been done in regards, one vertical well and one multi-branch horizontal well were used as experiment wells and two vertical wells were used as control wells, the pilot test was carried out with single well nutrition injection method. By applying the above mentioned method, the concentration of Cl[-] ion and number altered in Methanogen spp. were used to trace nutrition diffusion. Furthermore, technical implementation results analysis has been made with the observation of CH4 production changes and coal bed biome evolution. Gas production rates in each well were monitored by using the FLLQ gas roots flow mete. The concentration of CH4 and CO2 were evaluated by using the Agilent 7890A gas chromatograph, on the other hand, concentrations of Cl[-] were determined by the application of ICS-1100 ion chromatography system. The F420 fluorescence method was adopted to test for the presence of methanogenic bacteria. In the interim of the completion stage, the study stated that the bacterial diversity of underground water of Z-7H well has a high pass sequence with the experimental period of 814 days. Gas production data in Z-159 and Z-7H wells showed the gasification of coal lasted 635 and 799 days, yielded 74817 m[3] and 251754 m[3] coalbed methane, respectively. Furthermore, experimental data presented that one time nutrition injection in anthracite coalbed methane wells achieved an average of 717 days of continuous gas production among all experimental wells. The above fore-said study dedicated the significance of native bacterial fermentation, as it proven the fact that anthracite can be applied to accomplish coal bio-gasification and coalbed methane production stimulation in-situ.}, } @article {pmid35707189, year = {2022}, author = {Chen, G and Tang, P and Wang, H}, title = {Boundary Determination of Lake-Type Wetland Park Based on GIS Multifactor Analysis.}, journal = {Computational intelligence and neuroscience}, volume = {2022}, number = {}, pages = {6161491}, pmid = {35707189}, issn = {1687-5273}, mesh = {China ; Conservation of Natural Resources ; *Ecosystem ; Environmental Monitoring ; Geographic Information Systems ; Humans ; Remote Sensing Technology ; *Wetlands ; }, abstract = {One key carrier for wetland resource protection is wetland park, the main form of which includes lake-type wetland park. To determine the management and control boundary of lake-type wetland parks scientifically and reasonably is of great significance to the sustainable protection and utilization of wetland resources. From the perspective of landscape architecture, and landscape ecology, this paper studies the boundary determination of Changdang Lake National Wetland Park (the Park) based on satellite remote sensing information technology and GIS technology and in virtue of Analytic Hierarchy Process (AHP). In this study, 12 subindicators were selected from three levels including visual control, human geography, and ecological control. The weight of each indicator was determined by AHP, and then the influencing factors were transformed into graphic data by using GIS technology. Finally, the Park's boundary was determined by factor superposition analysis based on the weight. The research shows that the newly defined management and control boundary are about 340 sq.km, which effectively integrates the human and natural ecological resources around the lake area, makes the development of the surrounding areas harmonious, ensures the integrity of the lake area ecosystem, and facilitates the sustainable development of wetland resources.}, } @article {pmid35705152, year = {2022}, author = {Chen, Y and Su, J and Zhao, H and Li, JY and Wang, J and Wang, Q and Yin, J and Jin, L}, title = {In-situ biochar amendment mitigates dietary risks of heavy metals and PAHs in aquaculture products.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {308}, number = {}, pages = {119615}, doi = {10.1016/j.envpol.2022.119615}, pmid = {35705152}, issn = {1873-6424}, mesh = {Animals ; Aquaculture ; Charcoal ; Environmental Monitoring ; Geologic Sediments/chemistry ; *Metals, Heavy/analysis ; *Polycyclic Aromatic Hydrocarbons/analysis ; Water ; *Water Pollutants, Chemical/analysis ; }, abstract = {Heavy metals (HMs) and polycyclic aromatic hydrocarbons (PAHs) are two common contaminant groups of concern in aquaculture products. While biochar amendment can be one of the solutions to immobilize these contaminant in pond sediment, its in situ effectiveness in mitigating the bioavailability, tissue residue, and dietary risk of these contaminants is yet to be tested. In this study, we added wheat straw biochar in sediments of three aquaculture ponds with polyculture of fish and shrimps and employed passive sampling techniques (i.e., diffusive gradient in thin film for HMs and polydimethylsiloxane for PAHs) to assess the diffusion flux and bioavailability throughout the culturing cycle. Reduction in HM concentrations in organisms by biochar after 28 weeks ranged from 17% to 65% for benthic organisms and from 6.0% to 47% for fish. ΣTHQs values of HMs dropped from 2.5 to 2.1 and 1.2 to 0.91 for the two organisms with the initial ΣTHQs value above 1.0. The decrease rates of both the concentrations and ΣTHQs values followed the order of Cu > Cr > Pb > Cd, which was closely correlated with the speciation of HMs in the sediments. ΣPAHs values dropped significantly at the growth stage (20[th] week) and the mature stage (28[th] week), and, on average, by 34% across all the organisms. Carcinogenic PAHs in aquaculture products decreased dramatically at the seedling stage (12[th] week), while there was no significant change observed for the Incremental Lifetime Cancer Risk values. By comparing the freely-dissolved concentrations in pore water of sediments and the overlying water, consistently enhanced diffusion fluxes of HMs and PAHs from water to sediment over the whole culturing cycle were obtained. Our results demonstrated the in situ applicability of biochar amendment to remediating chemical pollution in aquaculture environment and safeguarding quality of aquatic products.}, } @article {pmid35699571, year = {2022}, author = {Mangal, S and Park, L and Reading Turchioe, M and Choi, J and Niño de Rivera, S and Myers, A and Goyal, P and Dugdale, L and Masterson Creber, R}, title = {Building trust in research through information and intent transparency with health information: representative cross-sectional survey of 502 US adults.}, journal = {Journal of the American Medical Informatics Association : JAMIA}, volume = {29}, number = {9}, pages = {1535-1545}, pmid = {35699571}, issn = {1527-974X}, support = {R00 NR019124/NR/NINR NIH HHS/United States ; R00 NR016275/NR/NINR NIH HHS/United States ; }, mesh = {Adult ; Cross-Sectional Studies ; Female ; Health Services Research ; Humans ; *Physicians ; Surveys and Questionnaires ; *Trust ; }, abstract = {OBJECTIVE: Participation in healthcare research shapes health policy and practice; however, low trust is a barrier to participation. We evaluated whether returning health information (information transparency) and disclosing intent of data use (intent transparency) impacts trust in research.

MATERIALS AND METHODS: We conducted an online survey with a representative sample of 502 US adults. We assessed baseline trust and change in trust using 6 use cases representing the Social-Ecological Model. We assessed descriptive statistics and associations between trust and sociodemographic variables using logistic and multinomial regression.

RESULTS: Most participants (84%) want their health research information returned. Black/African American participants were more likely to increase trust in research with individual information transparency (odds ratio (OR) 2.06 [95% confidence interval (CI): 1.06-4.34]) and with intent transparency when sharing with chosen friends and family (3.66 [1.98-6.77]), doctors and nurses (1.96 [1.10-3.65]), or health tech companies (1.87 [1.02-3.40]). Asian, Native American or Alaska Native, Native Hawaiian or Pacific Islander, Multirace, and individuals with a race not listed, were more likely to increase trust when sharing with health policy makers (1.88 [1.09-3.30]). Women were less likely to increase trust when sharing with friends and family (0.55 [0.35-0.87]) or health tech companies (0.46 [0.31-0.70]).

DISCUSSION: Participants wanted their health information returned and would increase their trust in research with transparency when sharing health information.

CONCLUSION: Trust in research is influenced by interrelated factors. Future research should recruit diverse samples with lower baseline trust levels to explore changes in trust, with variation on the type of information shared.}, } @article {pmid35695566, year = {2022}, author = {Sajid, M and Srivastava, S and Yadav, RK and Singh, H and Singh, S and Bharadwaj, M}, title = {Composition and Ecological Functionality of Fungal Communities Associated with Smokeless Tobacco Products Mainly Consumed in India.}, journal = {Microbiology spectrum}, volume = {10}, number = {4}, pages = {e0227321}, pmid = {35695566}, issn = {2165-0497}, mesh = {Bacteria/genetics ; Carcinogens/analysis ; India ; *Mycobiome ; *Nitrosamines/analysis ; *Tobacco, Smokeless/analysis ; }, abstract = {The microbial communities present in smokeless tobacco products (STPs) perform critical steps in the synthesis of carcinogens, mainly tobacco-specific nitrosamines (TSNAs). Most studies emphasize the bacterial component, and the mycobiome of STPs has not been well characterized. In this study, we investigated the fungal communities in the different categories of STPs by sequencing the internal transcribed spacer (ITS) rRNA region of the fungal genome. The ecological character of the fungal community associated with STPs was determined by using FUNGuild. Our results indicated that Ascomycota and Basidiomycota were the most abundant fungal phyla across all STPs. The predominant fungal genera in STPs were Pichia, Sterigmatomyces, and Mortierella. The α-diversity varied significantly across the STPs based on observed, Fisher, and Shannon indices. Using SparCC cooccurrence network analysis, significant positive correlations of 58.5% and negative connections of 41.5% were obtained among fungal genera identified in STPs. Furthermore, the functional predictions by FUNGuild determined that STPs possessed high abundances of saprotroph and pathotroph-saprotroph-symbiotroph fungal trophic groups. At the functional guild level, the qiwam samples contained high abundances of soil saprotrophs, while plant pathogens were prevalent in pan-masala samples. These results suggest that various fungal populations reside in STPs and interrelate with each other and can contribute to the synthesis of TSNAs. This study has established the basis for future large-scale investigations of STP-associated mycobiota and the impact of such mycobiota in oral carcinogenesis in STP users via inflammation and carcinogens (TSNAs and mycotoxins). IMPORTANCE Smokeless tobacco products (STPs) contain complex microbial communities that influence the synthesis of carcinogens, such as tobacco-specific nitrosamines (TSNAs). Research on STP-associated bacterial populations revealed connections between bacterial metabolism and TSNA synthesis. The abundance of the fungal population may also have an impact on the production of TSNAs. This study examined STPs popularly used in India, and diverse fungal communities were identified in these STPs. Pichia, Sterigmatomyces, and Mortierella were the predominant fungal genera in the STPs. High abundances of saprotroph and pathotroph-saprotroph-symbiotroph trophic groups in STPs could affect the degradation of tobacco products and the synthesis of TSNAs.}, } @article {pmid35694197, year = {2022}, author = {Boyes, D and , and , and , and , and , and Lewin, T and , }, title = {The genome sequence of the pebble prominent, Notodonta ziczac (Linnaeus, 1758).}, journal = {Wellcome open research}, volume = {7}, number = {}, pages = {111}, pmid = {35694197}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual male Notodonta ziczac (the pebble prominent; Arthropoda; Insecta; Lepidoptera; Notodontidae). The genome sequence is 352 megabases in span. The majority of the assembly (99.66%) is scaffolded into 31 chromosomal pseudomolecules, with the Z sex chromosome assembled. The mitochondrial genome was also assembled, and is 18.3 kilobases in length.}, } @article {pmid35693972, year = {2022}, author = {van Doorn, M and Nijhuis, LA and Monsanto, A and van Amelsvoort, T and Popma, A and Jaspers, MWM and Noordzij, ML and Öry, FG and Alvarez-Jimenez, M and Nieman, DH}, title = {Usability, Feasibility, and Effect of a Biocueing Intervention in Addition to a Moderated Digital Social Therapy-Platform in Young People With Emerging Mental Health Problems: A Mixed-Method Approach.}, journal = {Frontiers in psychiatry}, volume = {13}, number = {}, pages = {871813}, pmid = {35693972}, issn = {1664-0640}, abstract = {INTRODUCTION: To optimize treatment, it is of utmost importance to take into account the myriad of biological, social, and psychological changes that young people go through during adolescence which make them more vulnerable for developing mental health problems. Biocueing, a non-invasive method to transform physiological parameters into an observable signal, could strengthen stress- and emotion regulation by cueing physiologically unusual values in daily life. The aim of this study is to investigate the usability, feasibility, and exploratory effect of biocueing in addition to ENgage YOung people earlY (ENYOY), a moderated digital social therapy-platform, in young people with emerging mental health complaints.

METHODS: A user-centered mixed-method design was used. A focus group was conducted to optimize the ENYOY-platform and biocueing intervention. Biocueing was operationalized by a smartwatch and the Sense-IT app. A within-subjects design was used; 10 days for all participants 'biofeedback off' (control), followed by 10 days 'biofeedback on' (experimental). Emotional awareness and perceived stress were measured using ecological momentary assessment. Eight individuals participated. User-friendliness, usability, and acceptance were assessed using a qualitative design.

RESULTS: Findings from the focus group resulted in several adaptations of the biocueing intervention to the ENYOY-platform and vice versa. The average measurement compliance rate was 78.8%. Level-one findings showed different individual effects on perceived stress and emotional awareness. Level-two analyses showed no overall effects on perceived stress (B = -0.020, p = 0.562) and overall positive effects on emotional awareness (B = 0.030, p = 0.048) with small effect sizes (Improvement Rate Difference = 0.05-0.35). The intervention was found to be acceptable and showed moderate usability. Participants indicated they experienced improvements in reflection on feelings and changes in behavior, such as pausing and evaluating the situation.

CONCLUSION: These preliminary results show that biocueing could be a promising addition to digital treatment platforms and help young people become more emotionally aware. Improvements should be made regarding the usability and acceptability of the smartwatch, as well as more extensive integration of the biocueing intervention with a digital treatment platform. It would be relevant to gain a better understanding of which individuals would benefit most from an additional biocueing intervention.}, } @article {pmid35690703, year = {2022}, author = {Satrovic, E and Adedoyin, FF}, title = {An empirical assessment of electricity consumption and environmental degradation in the presence of economic complexities.}, journal = {Environmental science and pollution research international}, volume = {29}, number = {52}, pages = {78330-78344}, pmid = {35690703}, issn = {1614-7499}, mesh = {*Carbon Dioxide ; *Economic Development ; Carbon Footprint ; Electricity ; }, abstract = {To a large extent, the theories and concepts behind the effect of ecological footprint have been the paramount concern of the recent literature. Since the rising and falling of environmental degradation have been a continuous issue since the first phase of development, determinants such as economic complexity may play a critical role in achieving long-term sustainable development in the framework of environmental Kuznets curve (EKC) paradigm. Therefore, this research expands on the notion of an EKC paradigm for the world's top ten most complex economies by considering four variables, such as real GDP per capita, electricity consumption, trade openness, and a new putative factor of environmental obstacle, the economic complexity index (ECI). This is one of the first studies to look at the impact of ECI on the ecological footprint of a specific sample from 1998 to 2017. The findings demonstrate a continuous inverted U-shaped link between real GDP per capita, the square of real GDP per capita, and ecological footprint. The EKC hypothesis is found to be valid in the long term in the examined complex economies. The findings of the panel autoregressive distributed lag (ARDL) of the pooled mean group (PMG) and fully modified ordinary least squares (FMOLS) estimations demonstrate that in the long term, electric power usage contributed to the carbon footprints. Furthermore, the economic complexity index and trade openness increase environmental performance over time. To determine if there is causation between the variables, we employ the panel vector error correction model (VECM) framework. Particularly, the results show unidirectional causality running from electric power consumption to ecological footprint and bidirectional causal relationship between (1) economic growth and ecological footprint; (2) square of economic growth and ecological footprint; (3) economic complexity index and ecological footprint; and (4) trade openness and ecological footprint.}, } @article {pmid35686764, year = {2022}, author = {Yan, YY and Yin, SS and He, Q and Qin, K and Zhang, RQ}, title = {[Trend Changes in Ozone Pollution and Sensitivity Analysis of Ozone in Henan Province].}, journal = {Huan jing ke xue= Huanjing kexue}, volume = {43}, number = {6}, pages = {2947-2956}, doi = {10.13227/j.hjkx.202108287}, pmid = {35686764}, issn = {0250-3301}, mesh = {*Air Pollutants/analysis ; *Air Pollution/analysis ; China ; Cities ; Environmental Monitoring/methods ; *Ozone/analysis ; Seasons ; }, abstract = {Based on air quality station data and satellite remote sensing data, the interannual variation characteristics and seasonal variation trends of near-surface ozone (O3) in Henan province were studied, and the variation in O3 sensitivity was analyzed. The results showed that the O3 concentration near the surface of Henan province increased first and then decreased from 2015 to 2020. The highest O3 concentration was found in 2018, and the annual mean of the maximum daily 8 h moving mean (MDA8) of O3 was 110.70 μg·m[-3]. The difference in MDA8 values among different stations gradually decreased. From 2015 to 2020, the average monthly MDA8 in Henan province showed an upward trend, with a growth rate of 2.46 μg·(m[3]·a)[-1]. According to the MK trend test, except for in Luohe, Nanyang, and Pingdingshan, the rising trend in other cities was significant (P<0.05). The concentration of MDA8 in the four seasons also showed an increasing trend during the 6 years as follows:autumn (19.31%)>winter (17.09%)>spring (16.82%)>summer (7.24%). From 2015 to 2019, the high value of tropospheric NO2 was concentrated in the northwest of Henan province, and the concentration showed a decreasing trend with a decreasing rate of 0.34×10[15] molecules·(cm[2]·a)[-1], whereas the tropospheric HCHO showed a slow rising trend with an annual growth rate of 0.19×10[15] molecules·(cm[2]·a)[-1], with a higher concentration in the northern urban area. The O3 sensitivity control area from 2015 to 2019 showed that most of the eastern part of Henan province belonged to the VOCs limited category.}, } @article {pmid35684257, year = {2022}, author = {Gašparovičová, P and Ševčík, M and David, S}, title = {The Prediction of Distribution of the Invasive Fallopia Taxa in Slovakia.}, journal = {Plants (Basel, Switzerland)}, volume = {11}, number = {11}, pages = {}, pmid = {35684257}, issn = {2223-7747}, abstract = {Invasive species are now considered the second biggest threat for biodiversity and have adverse environmental, economic and social impacts. Understanding its spatial distribution and dynamics is crucial for the development of tools for large-scale mapping, monitoring and management. The aim of this study was to predict the distribution of invasive Fallopia taxa in Slovakia and to identify the most important predictors of spreading of these species. We designed models of species distribution for invasive species of Fallopia—Fallopia japonica—Japanese knotweed, Fallopia sachalinensis—Sakhalin knotweed and their hybrid Fallopia × bohemica—Czech knotweed. We designed 12 models—generalized linear model (GLM), generalized additive model (GAM), classification and regression trees (CART), boosted regression trees (BRT), multivariate adaptive regression spline (MARS), random forests (RF), support vector machine (SVM), artificial neural networks (ANN), maximum entropy (Maxent), penalized maximum likelihood GLM (GLMNET), domain, and radial basis function network (RBF). The accuracy of the models was evaluated using occurrence data for the presence and absence of species. The final simplified logistic regression model showed the three most important prediction variables lead by distances from roads and rails, then type of soil and distances from water bodies. The probability of invasive Fallopia species occurrence was evaluated using Pearson’s chi-squared test (χ21). It significantly decreases with increasing distance from transport lines (χ21 = 118.85, p < 0.001) and depends on soil type (χ21 = 49.56, p < 0.001) and the distance from the water, where increasing the distance decrease the probability (χ21 = 8.95, p = 0.003).}, } @article {pmid35684255, year = {2022}, author = {Chao, L and Pan, Z and Wang, J and Wu, Y and Shui, G and Aini, N and Tang, B and Guo, C and Han, P and Shao, P and Tian, X and Chang, X and An, Q and Ma, C and You, C and Zhu, L and Nie, X}, title = {Genetic Mapping and Analysis of a Compact Plant Architecture and Precocious Mutant in Upland Cotton.}, journal = {Plants (Basel, Switzerland)}, volume = {11}, number = {11}, pages = {}, pmid = {35684255}, issn = {2223-7747}, support = {NO.2021CB028//the Fund for the Innovation Leadership Program in Sciences and Technologies for Young and Middle-aged Scientists of Xinjiang production and Construction Corps, China/ ; NO.31760402//National Natural Science Foundation of China/ ; NO.2021NY01//Major science and technology project plan/ ; NO.2020CB017//Science and Technology Innovation Talents Program/ ; }, abstract = {With the promotion and popularization of machine cotton-picking, more and more attention has been paid to the selection of early-maturity varieties with compact plant architecture. The type of fruit branch is one of the most important factors affecting plant architecture and early maturity of cotton. Heredity analysis of the cotton fruit branch is beneficial to the breeding of machine-picked cotton. Phenotype analysis showed that the types of fruit branches in cotton are controlled by a single recessive gene. Using an F2 population crossed with Huaxin102 (normal branch) and 04N-11 (nulliplex branch), BSA (Bulked Segregant Analysis) resequencing analysis and GhNB gene cloning in 04N-11, and allelic testing, showed that fruit branch type was controlled by the GhNB gene, located on chromosome D07. Ghnb5, a new recessive genotype of GhNB, was found in 04N-11. Through candidate gene association analysis, SNP 20_15811516_SNV was found to be associated with plant architecture and early maturity in the Xinjiang natural population. The GhNB gene, which is related to early maturity and the plant architecture of cotton, is a branch-type gene of cotton. The 20_15811516_SNV marker, obtained from the Xinjiang natural population, was used for the assisted breeding of machine-picked cotton varieties.}, } @article {pmid35682045, year = {2022}, author = {Ma, L and Hong, Y and Chen, X}, title = {Can Green Economy and Ecological Welfare Achieve Synergistic Development? The Perspective of the "Two Mountains" Theory.}, journal = {International journal of environmental research and public health}, volume = {19}, number = {11}, pages = {}, pmid = {35682045}, issn = {1660-4601}, mesh = {China ; Cities ; *Conservation of Energy Resources ; Economic Development ; *Efficiency ; Sustainable Development ; Urbanization ; }, abstract = {China's high-speed economic growth and severe environmental problems have resulted in a poor Environmental Performance Index and have affected China's sustainable development and ecological welfare improvement. Therefore, exploring whether there is a certain relationship between the two and their influencing factors is an important way and a breakthrough to solve the problems regarding green economic progress and ecological welfare enhancement. To this end, by using the undesirable slack-based measure (SBM) model, this paper measures the ecological welfare performance and the green economic efficiency of 11 cities in Zhejiang Province, China, from 2000 to 2019. Through the methods of spatiotemporal evolution, coefficient of variation, coupling coordination degree, and the Tobit model, we found that: (1) The development trend of urban green economic efficiency and ecological welfare performance were both in a "U" shape that first fell and then rose; (2) The coupling coordination degree between green economic efficiency and ecological welfare performance showed a wave-like upward trend as a whole and most cities have entered a more advanced coupling coordination stage during the study period. The coefficient of variation revealed a downward trend; (3) The urbanization level, industrial structure, and government investment can promote the regional coordinated development, while the industrialization degree and the opening level had a negative impact on it; (4) The "Two Mountains" theory was beneficial to the improvement of regional urban green economic efficiency and ecological welfare performance and their coordinated development both in theory and practice. Finally, according to the findings, we offer relevant suggestions on making good use of the country's preferential policies and informatization means from the perspective of the regional coordinated development.}, } @article {pmid35678830, year = {2022}, author = {Zhao, Y and Wang, J and Yang, B and Zhong, Q and Wang, L and Niu, Z and Xin, H and Zhang, W}, title = {Performance of Red Mud/Biochar Composite Material (RMBC) as Heavy Metal Passivator in Pb-Contaminated Soil.}, journal = {Bulletin of environmental contamination and toxicology}, volume = {109}, number = {1}, pages = {30-43}, pmid = {35678830}, issn = {1432-0800}, support = {51602344//National Natural Science Foundation of China/ ; 51974314//National Natural Science Foundation of China/ ; 2014QNA35//Fundamental Research Funds for the Central Universities/ ; Open Fund of Key Laboratory for Advanced Technology in Environmental Protection of Jiangsu Province//Open Fund of Key Laboratory for Advanced Technology in Environmental Protection of Jiangsu Province/ ; BE2020773//Jiangsu province Key R & D Program: Social Development Project/ ; BK20191480//Natural Science Foundation of Jiangsu Province/ ; }, mesh = {Charcoal/chemistry ; Lead ; *Metals, Heavy/analysis ; Soil/chemistry ; *Soil Pollutants/analysis ; }, abstract = {Red mud/biochar composite material (RMBC), which was applied as heavy metal passivator in this research, was prepared with red mud (the bauxite residue) and cornstalk under anoxic sintering condition. Based on the batch experiments in Pb contaminated soil, the passivating properties of several materials, including red mud (RM), biochar (BC), RMBC and phosphate-containing RMBC (PRMBC), were investigated in comparison with each other. Some interesting results are as follows: through anoxic thermal activation, a rough and porous structure of RMBC was obtained. Substances such as Fe3O4 and metal-organic complexes generated in RMBC provided effective sites for Pb passivation; and the mechanisms were speculated as the precipitation between Pb[2+] and the carbonate (or hydroxide), as well as the complexation reaction between Pb and metal organic complexes through ligand bonding. The pot experiments showed the promotion effects of four passivators on the growth of red onion were in the following order: PRMBC > RMBC > BC > RM. PRMBC stabilized Pb content in soil significantly due to the formation of insoluble substances, with the minimum transfer factor and bioconcentration factor for plant growth. The evidences above implied the composite materials (PRMBC and RMBC) would be potential passivators for heavy metal-contaminated soil.}, } @article {pmid35676946, year = {2022}, author = {Fan, L}, title = {Big Data Technology Oriented to Wetland Resource Ecosystem Value Evaluation.}, journal = {Computational intelligence and neuroscience}, volume = {2022}, number = {}, pages = {6815102}, pmid = {35676946}, issn = {1687-5273}, mesh = {Big Data ; China ; Conservation of Natural Resources/methods ; *Ecosystem ; Technology ; *Wetlands ; }, abstract = {In order to study a big data technology research for the evaluation of wetland resource ecosystem value. This paper proposes a wetland dimension oriented to the evaluation of wetland ecosystem services space attribute through big data coupling analysis framework. The framework used China's coastal wetlands as a case for empirical research and summarized the future direction of the research on the value evaluation of wetland ecosystem services in the era of big data. The result shows: Wetland Ecosystem Observation Network can obtain long-term series of dynamic data, remote sensing Earth observation can realize the integrated observation of space, space, and Earth, the combination of the two will help to build a wetland ecological big data observation system. The service value of China's coastal wetland ecosystem is 5010.32 × 108 yuan. The research results can effectively solve the problem of geographical heterogeneity and have reference value for the protection and management of the wetland ecosystem.}, } @article {pmid35672133, year = {2022}, author = {Arif, S and MacNeil, MA}, title = {Predictive models aren't for causal inference.}, journal = {Ecology letters}, volume = {25}, number = {8}, pages = {1741-1745}, doi = {10.1111/ele.14033}, pmid = {35672133}, issn = {1461-0248}, mesh = {Causality ; *Confounding Factors, Epidemiologic ; Data Interpretation, Statistical ; }, abstract = {Ecologists often rely on observational data to understand causal relationships. Although observational causal inference methodologies exist, predictive techniques such as model selection based on information criterion (e.g. AIC) remains a common approach used to understand ecological relationships. However, predictive approaches are not appropriate for drawing causal conclusions. Here, we highlight the distinction between predictive and causal inference and show how predictive techniques can lead to biased causal estimates. Instead, we encourage ecologists to valid causal inference methods such as the backdoor criterion, a graphical rule that can be used to determine causal relationships across observational studies.}, } @article {pmid35669667, year = {2022}, author = {Wang, Y}, title = {Research on Performance Optimization Algorithm of Resource and Environment Audit Based on Computer Technology.}, journal = {Computational intelligence and neuroscience}, volume = {2022}, number = {}, pages = {4288729}, doi = {10.1155/2022/4288729}, pmid = {35669667}, issn = {1687-5273}, mesh = {*Algorithms ; *Artificial Intelligence ; Big Data ; Computers ; Humans ; Technology ; }, abstract = {With the rapid development of the economy and society, the sustainable development of resources and environment has been paid more and more attention. As an important part of the national environmental supervision system, resources and environmental audits have attracted great attention from the society. In order to explore the application effect of intelligent networking technology in resource and environment audit, this study carries out monitoring sampling, information collection, and later data processing optimization in resource and environment audit projects through the reference of artificial intelligence technology and method and combined with Internet of things big data analysis, which brings new Turks to the development of natural resource and environment audit and helps to improve the efficiency of audit work. Through the application of new technology in the sampling process of environmental information, the staff use new technology to collect, analyze, and mine data and explore how the new technology can promote the efficiency of resource and environmental audit and better promote the construction of ecological civilization.}, } @article {pmid35668508, year = {2022}, author = {Hickson, J and Athayde, LFA and Miranda, TG and Junior, PAS and Dos Santos, AC and da Cunha Galvão, LM and da Câmara, ACJ and Bartholomeu, DC and de Souza, RCM and Murta, SMF and Nahum, LA}, title = {Trypanosoma cruzi iron superoxide dismutases: insights from phylogenetics to chemotherapeutic target assessment.}, journal = {Parasites & vectors}, volume = {15}, number = {1}, pages = {194}, pmid = {35668508}, issn = {1756-3305}, support = {CAPES - DCB: 23038.004631/2014-80//Coordination for the Improvement of Higher Education Personnel/ ; SMFM: VPPCB-007-FIO-18-2-94//INOVA FIOCRUZ program - Oswaldo Cruz Foundation/ ; FAPEMIG: SMFM: CBB-PPM//Minas Gerais Research Funding Foundation/ ; APQ-02816-21//Minas Gerais Research Funding Foundation/ ; CBB-AUC 00030-15//Minas Gerais Research Funding Foundation/ ; FAPEMIG DCB: APQ-01822-18//Minas Gerais Research Funding Foundation/ ; FAPEMIG RCMS: AUC-00030-15//Minas Gerais Research Funding Foundation/ ; CNPq: SMFM: 304158/2019-4//National Council for Scientific and Technological Development/ ; FIOCRUZ/VPEIC: JH: graduate student fellowship: no grant number//FIOCRUZ Vice-Presidency of Education, Information and Communication/ ; CAPES/PNPD: PASJ: 88882.317220/2019-01//Graduate Program in Health Sciences, Fiocruz Minas/ ; }, mesh = {Antioxidants ; Bayes Theorem ; *Chagas Disease/parasitology ; Humans ; Phylogeny ; Superoxide Dismutase/genetics ; Superoxides ; *Trypanosoma cruzi/genetics ; }, abstract = {BACKGROUND: Components of the antioxidant defense system in Trypanosoma cruzi are potential targets for new drug development. Superoxide dismutases (SODs) constitute key components of antioxidant defense systems, removing excess superoxide anions by converting them into oxygen and hydrogen peroxide. The main goal of the present study was to investigate the genes coding for iron superoxide dismutase (FeSOD) in T. cruzi strains from an evolutionary perspective.

METHODS: In this study, molecular biology methods and phylogenetic studies were combined with drug assays. The FeSOD-A and FeSOD-B genes of 35 T. cruzi strains, belonging to six discrete typing units (Tcl-TcVI), from different hosts and geographical regions were amplified by PCR and sequenced using the Sanger method. Evolutionary trees were reconstructed based on Bayesian inference and maximum likelihood methods. Drugs that potentially interacted with T. cruzi FeSODs were identified and tested against the parasites.

RESULTS: Our results suggest that T. cruzi FeSOD types are members of distinct families. Gene copies of FeSOD-A (n = 2), FeSOD-B (n = 4) and FeSOD-C (n = 4) were identified in the genome of the T. cruzi reference clone CL Brener. Phylogenetic inference supported the presence of two functional variants of each FeSOD type across the T. cruzi strains. Phylogenetic trees revealed a monophyletic group of FeSOD genes of T. cruzi TcIV strains in both distinct genes. Altogether, our results support the hypothesis that gene duplication followed by divergence shaped the evolution of T. cruzi FeSODs. Two drugs, mangafodipir and polaprezinc, that potentially interact with T. cruzi FeSODs were identified and tested in vitro against amastigotes and trypomastigotes: mangafodipir had a low trypanocidal effect and polaprezinc was inactive.

CONCLUSIONS: Our study contributes to a better understanding of the molecular biodiversity of T. cruzi FeSODs. Herein we provide a successful approach to the study of gene/protein families as potential drug targets.}, } @article {pmid35665284, year = {2022}, author = {Wu, H and Cheng, M}, title = {Trust of Information during the Dissemination of Popular Science Web Videos in the New Media Era.}, journal = {Computational intelligence and neuroscience}, volume = {2022}, number = {}, pages = {1746472}, pmid = {35665284}, issn = {1687-5273}, mesh = {Information Dissemination ; *Social Media ; *Trust ; Video Recording ; }, abstract = {Web videos have gradually replaced text, voice, pictures, and other information carriers to become an important way of information dissemination in the new media era. As digital technology brings a new dissemination ecology, the original dissemination trust theory and its framework are facing the crisis of explanatory power failure. This paper considers the popular science web video as an object of study. It analyses and interprets the development of popular science web videos based on the evolution of dissemination form and the basic principle of social trust, from perspectives such as mediology, informatics, and sociology. To maintain or improve the trust relationship in web videos, it's necessary to find positive incentive and reverse punishment, and establish a trust certification and regulation mechanism. In this way, active dissemination and sharing of information can be promoted for a more vigorous society and culture. Moreover, this paper explores a new way of web video development from the perspective of trust.}, } @article {pmid35658270, year = {2022}, author = {Plaza, A and Castillo, M and Naulin, PI}, title = {Seed and seedling interactions in three tree species from Mediterranean forests as a knowledge base for ecological restoration.}, journal = {Journal of environmental management}, volume = {316}, number = {}, pages = {115241}, doi = {10.1016/j.jenvman.2022.115241}, pmid = {35658270}, issn = {1095-8630}, mesh = {Ecosystem ; Forests ; Germination/physiology ; Humans ; Knowledge Bases ; Plant Extracts ; *Seedlings ; Seeds ; *Trees ; }, abstract = {The ecosystems of the Mediterranean regions are severely threatened by human activity, and although we have made progress in physical restoration measures, little is known about the interactions between the plants of these biomes. The objective of this study is to contribute to document interactions between seeds and seedlings of three woody species native to Chile (P. chilensis, Q. saponaria and A. caven), which could be used for restoration actions (e.g., after forest fires). In a first experiment, we evaluated the germination response, the initial elongation and the interactions between the seedlings that germinate exposed to the chemical compounds of the other species. In a second experiment, we compared the survival and growth of seedlings in monospecific versus bispecific mixtures, using a substrate similar to that which is present after a wildfire. Seed extracts of teguments promoted germination of P. chilensis, but cotyledons and whole seed extracts inhibited germination of only one species, Q. saponaria, with very high intensity. The effects of the extracts on initial seedling elongation were more variable, including five inhibitions and one facilitation. Negative effects on germination and elongation included two cases of autotoxicity. The survival of seedlings grown in mixtures showed only two differences between monospecific and bispecific mixtures, both positive, constituting a reciprocal effect between two species. Only in one case was there a significant difference in seedling growth, which was root growth inhibition. Indeed, these results reveal an interaction between species, the type and intensity of which varies according to the condition of the seed or seedling. The negative effect found in seedling root growth reflects an allelopathic interaction that conditions a vital aspect for the establishment of these species, so this information is an opportunity to improve the establishment conditions in future reforestation projects, by avoiding particular species or promoting their proportion in plantation mixtures, either by planting or direct seeding.}, } @article {pmid35656925, year = {2023}, author = {Figus, C and Stephens, NB and Sorrentino, R and Bortolini, E and Arrighi, S and Higgins, OA and Lugli, F and Marciani, G and Oxilia, G and Romandini, M and Silvestrini, S and Baruffaldi, F and Belcastro, MG and Bernardini, F and Festa, A and Hajdu, T and Mateovics-László, O and Pap, I and Szeniczey, T and Tuniz, C and Ryan, TM and Benazzi, S}, title = {Morphologies in-between: The impact of the first steps on the human talus.}, journal = {Anatomical record (Hoboken, N.J. : 2007)}, volume = {306}, number = {1}, pages = {124-142}, pmid = {35656925}, issn = {1932-8494}, mesh = {Humans ; *Walking ; X-Ray Microtomography ; }, abstract = {OBJECTIVE: The development of bipedalism is a very complex activity that contributes to shaping the anatomy of the foot. The talus, which starts ossifying in utero, may account for the developing stages from the late gestational phase onwards. Here, we explore the early development of the talus in both its internal and external morphology to broaden the knowledge of the anatomical changes that occur during early development.

MATERIALS AND METHODS: The sample consists of high-resolution microCT scans of 28 modern juvenile tali (from 36 prenatal weeks to 2 years), from a broad chronological range from the Late Roman period to the 20th century. We applied geometric morphometric and whole-bone trabecular analysis to investigate the early talar morphological changes.

RESULTS: In the youngest group (<6 postnatal months), the immature external shell is accompanied by an isotropic internal structure, with thin and densely packed trabeculae. After the initial attempts of locomotion, bone volume fraction decreases, while anisotropy and trabecular thickness increase. These internal changes correspond to the maturation of the external shell, which is now more defined and shows the development of the articular surfaces.

DISCUSSION: The internal and external morphology of the human talus reflects the diverse load on the foot during the initial phases of the bipedal locomotion, with the youngest group potentially reflecting the lack of readiness of the human talus to bear forces and perform bipedal walking. These results highlight the link between mechanical loading and bone development in the human talus during the acquisition of bipedalism, providing new insight into the early phases of talar development.}, } @article {pmid35654905, year = {2022}, author = {Herberstein, ME and McLean, DJ and Lowe, E and Wolff, JO and Khan, MK and Smith, K and Allen, AP and Bulbert, M and Buzatto, BA and Eldridge, MDB and Falster, D and Fernandez Winzer, L and Griffith, SC and Madin, JS and Narendra, A and Westoby, M and Whiting, MJ and Wright, IJ and Carthey, AJR}, title = {AnimalTraits - a curated animal trait database for body mass, metabolic rate and brain size.}, journal = {Scientific data}, volume = {9}, number = {1}, pages = {265}, pmid = {35654905}, issn = {2052-4463}, mesh = {Animals ; *Basal Metabolism ; *Body Weight ; *Brain ; *Databases, Factual ; Ecology ; Organ Size ; Phenotype ; }, abstract = {Trait databases have become important resources for large-scale comparative studies in ecology and evolution. Here we introduce the AnimalTraits database, a curated database of body mass, metabolic rate and brain size, in standardised units, for terrestrial animals. The database has broad taxonomic breadth, including tetrapods, arthropods, molluscs and annelids from almost 2000 species and 1000 genera. All data recorded in the database are sourced from their original empirical publication, and the original metrics and measurements are included with each record. This allows for subsequent data transformations as required. We have included rich metadata to allow users to filter the dataset. The additional R scripts we provide will assist researchers with aggregating standardised observations into species-level trait values. Our goals are to provide this resource without restrictions, to keep the AnimalTraits database current, and to grow the number of relevant traits in the future.}, } @article {pmid35644269, year = {2022}, author = {Grover, E and Paull, S and Kechris, K and Buchwald, A and James, K and Liu, Y and Carlton, EJ}, title = {Predictors of bovine Schistosoma japonicum infection in rural Sichuan, China.}, journal = {International journal for parasitology}, volume = {52}, number = {8}, pages = {485-496}, pmid = {35644269}, issn = {1879-0135}, support = {R01 AI068854/AI/NIAID NIH HHS/United States ; R01 AI134673/AI/NIAID NIH HHS/United States ; R21 AI115288/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Cattle ; China/epidemiology ; Cross-Sectional Studies ; Humans ; Prevalence ; Schistosoma ; *Schistosoma japonicum ; *Schistosomiasis/epidemiology ; *Schistosomiasis japonica/epidemiology/veterinary ; Snails ; Swine ; Water ; }, abstract = {In China, bovines are believed to be the most common animal source of human schistosomiasis infections, though little is known about what factors promote bovine infections. The current body of literature features inconsistent, and sometimes contradictory results, and to date, few studies have looked beyond physical characteristics to identify the broader environmental conditions that predict bovine schistosomiasis. Because schistosomiasis is a sanitation-related, water-borne disease transmitted by many animals, we hypothesised that several environmental factors - such as the lack of improved sanitation systems, or participation in agricultural production that is water-intensive - could promote schistosomiasis infection in bovines. Using data collected as part of a repeat cross-sectional study conducted in rural villages in Sichuan, China from 2007 to 2016, we used a Random Forests, machine learning approach to identify the best physical and environmental predictors of bovine Schistosoma japonicum infection. Candidate predictors included: (i) physical/biological characteristics of bovines, (ii) human sources of environmental schistosomes, (iii) socio-economic indicators, (iv) animal reservoirs, and (v) agricultural practices. The density of bovines in a village and agricultural practices such as the area of rice and dry summer crops planted, and the use of night soil as an agricultural fertilizer, were among the top predictors of bovine S. japonicum infection in all collection years. Additionally, human infection prevalence, pig ownership and bovine age were found to be strong predictors of bovine infection in at least 1 year. Our findings highlight that presumptively treating bovines in villages with high bovine density or human infection prevalence may help to interrupt transmission. Furthermore, village-level predictors were stronger predictors of bovine infection than household-level predictors, suggesting future investigations may need to apply a broad ecological lens to identify potential underlying sources of persistent transmission.}, } @article {pmid35643307, year = {2022}, author = {Inoue, K and Muramatsu, K and Nishimura, T and Fujino, Y and Matsuda, S and Fushimi, K and Kamochi, M}, title = {Association between early diagnosis of and inpatient mortality from invasive pulmonary aspergillosis among patients without immunocompromised host factors: a nationwide observational study.}, journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases}, volume = {122}, number = {}, pages = {279-284}, doi = {10.1016/j.ijid.2022.05.048}, pmid = {35643307}, issn = {1878-3511}, mesh = {Aged ; Antifungal Agents/therapeutic use ; Cross-Sectional Studies ; Early Diagnosis ; Humans ; Immunocompromised Host ; Inpatients ; *Invasive Pulmonary Aspergillosis/complications/diagnosis/drug therapy ; Retrospective Studies ; }, abstract = {OBJECTIVES: The incidence of invasive pulmonary aspergillosis (IPA) among patients without immunocompromised host factors (ICHF) has been described extensively. However, its diagnosis remains challenging. To date, no study has statistically confirmed the efficacy of early IPA diagnosis in patients without ICHF.

METHODS: We conducted a cross-sectional study on mortality from IPA among patients without ICHF, using the Japanese Diagnosis Procedure Combination National Inpatient Database (April 2014-March 2018). The early diagnosis group was defined according to antifungal therapy initiation within 7 days of hospital admission. The delayed diagnosis group was defined according to antifungal therapy initiation between 8 and 28 days of the hospitalization. Associations were estimated using multivariate logistic regression.

RESULTS: A total of 423 patients were registered (early diagnosis group, n = 262, 62%). The early diagnosis group had a lower mortality rate (30%) than the delayed diagnosis group (42%). The early diagnosis group that was treated with voriconazole was associated with lower odds of mortality (odds ratio 0.55, 95% confidence interval 0.31-0.99, P = 0.047). An age of ≥65 years and mechanical ventilation were associated with a higher mortality rate.

CONCLUSION: Early diagnosis along with optimal antifungal treatment are crucial for achieving favorable outcomes among patients with IPA without ICHF.}, } @article {pmid35643184, year = {2022}, author = {Suresh, KP and Sengupta, PP and Jacob, SS and Sathyanarayana, MKG and Patil, SS and Swarnkar, CP and Singh, D}, title = {Exploration of machine learning models to predict the environmental and remote sensing risk factors of haemonchosis in sheep flocks of Rajasthan, India.}, journal = {Acta tropica}, volume = {233}, number = {}, pages = {106542}, doi = {10.1016/j.actatropica.2022.106542}, pmid = {35643184}, issn = {1873-6254}, mesh = {Animals ; *Haemonchiasis ; India/epidemiology ; Machine Learning ; *Nematode Infections ; Remote Sensing Technology ; Risk Factors ; Seasons ; Sheep ; *Sheep Diseases/epidemiology ; }, abstract = {Globally haemonchosis in sheep is a known devastating disease imposing considerable economic loss. Understanding the environmental risk factors and their role is essentially required to manage the disease successfully. In this study, 14 years' disease data was analysed to predict the risk factors responsible for the occurrence of the disease. Season-wise analysis revealed high incidence during monsoon and post-monsoon and least in winter and summer seasons. The linear discriminant analysis (LDA) revealed the significant environmental and remote sensing risk factors contributing to haemonchosis incidence as enhanced vegetation index, leaf area index, potential evapotranspiration and specific humidity. Further, significant ecological and environmental risk factors identified using LDA were subjected to the climate-disease modelling and risk maps were generated. Basic reproduction number (R0) was estimated and was ranged from 0.76 to 2.08 for >1000 egg per gram of faeces (EPG) in four districts whereas R0 values of 1.09-1.69 for >2000 EPG in three districts indicating the severity of the infection. The random forest and adaptive boosting models emerged out as best fitted models for both the EPG groups. The results of the study will help to focus on high-risk areas of haemonchosis in sheep to implement the available control strategies and better animal production globally.}, } @article {pmid35642818, year = {2022}, author = {Chen, A and Yang, X and Guo, J and Zhang, M and Xing, X and Yang, D and Xu, B and Jiang, L}, title = {Dynamic of land use, landscape, and their impact on ecological quality in the northern sand-prevention belt of China.}, journal = {Journal of environmental management}, volume = {317}, number = {}, pages = {115351}, doi = {10.1016/j.jenvman.2022.115351}, pmid = {35642818}, issn = {1095-8630}, mesh = {China ; *Conservation of Natural Resources ; *Ecosystem ; Forests ; Poaceae ; Sand ; }, abstract = {Changes in land use and landscapes have a direct impact on the regional eco-environment. It is of great importance to understand the change pattern of land use, landscapes, and their mechanism on the ecological quality, especially ecologically fragile areas. The northern sand-prevention belt (NSPB) is an important ecologically fragile area in China, which has a large influence on the ecological security of the entire country. Based on the land use data of the NSPB in 2000, 2010, and 2018, we studied the spatio-temporal characteristics of land-use change and change in landscape patterns. The ecological quality represented by the remote sensing-based desertification index (RSDI) was calculated using satellite images. The effects of land use and landscape patterns on RSDI were analyzed by geographic detector and geographically weighted regression. Important results include the following: (1) Land-use change in the study area was high during 2000-2010 but slower in 2010-2018. Grassland was the largest land-use type in the NSPB, and varied greatly in terms of total change and spatial location. The major change was the conversion between dense and moderate grass, with 64,860 km[2] of dense grass turning into moderate grass, and 48,505 km[2] changing the other way. (2) Among the four landscape metrics, patch density, area-weighted mean fractal dimension, and edge density increased, whereas the aggregation index decreased, which indicated that the landscape was developing towards heterogeneity, fragmentation, complexity, and aggregation. Spatially, the landscape metrics presented a strip distribution in the east of the NSPB. (3) The effects of various land-use types on ecological quality, from high to low, were unused land, woodland, dense grass, cropland, moderate grass, built-up land, sparse grass, and waterbody. The areas where the ecological quality was greatly affected by the landscape patterns were concentrated in the agro-pastoral ecotone and the forest-steppe ecotone. The results of this study reveal the trends of land use and landscape patterns in the NSPB over 18 years and can help to understand their mechanism on ecological quality, which is of significance for the management of this area.}, } @article {pmid35641949, year = {2022}, author = {Botero-Mesa, S and Coelho, FC and Nwosu, K and Wicht, B and Venkatasubramanian, A and Wagner, O and Valera, C and Nguimbis, B and Câmara, D and Reis, I and Bianchi, L and Mahdiani, M and Onsimbie, PA and Diallo, PAN and Jacques, L and Muloliwa, AM and Bougma, M and Mukavhi, L and Kaneria, A and Peruvemba, R and Gupta, A and Triulzi, I and James, A and Carrara, V and Ngambi, W and Habibi, Z and Adhanom, MT and Rodriguez Velásquez, S and Sestito, P and Kousil, T and Biru, L and Vivacqua, D and Dalal, J and Mian, A and Roelens, M and Orel, E and Hofer, CB and Wangara, F and Mboussou, F and Mlanda, T and Bukhari, A and Lee, TM and Ngom, R and Stoll, B and Chimbetete, C and Abbate, J and Impouma, B and Keiser, O}, title = {Leveraging human resources for outbreak analysis: lessons from an international collaboration to support the sub-Saharan African COVID-19 response.}, journal = {BMC public health}, volume = {22}, number = {1}, pages = {1073}, pmid = {35641949}, issn = {1471-2458}, support = {001/WHO_/World Health Organization/International ; }, mesh = {Africa South of the Sahara/epidemiology ; *COVID-19/epidemiology ; Disease Outbreaks/prevention & control ; Humans ; Public Health ; Workforce ; }, abstract = {Emerging infectious diseases are a growing threat in sub-Saharan African countries, but the human and technical capacity to quickly respond to outbreaks remains limited. Here, we describe the experience and lessons learned from a joint project with the WHO Regional Office for Africa (WHO AFRO) to support the sub-Saharan African COVID-19 response.In June 2020, WHO AFRO contracted a number of consultants to reinforce the COVID-19 response in member states by providing actionable epidemiological analysis. Given the urgency of the situation and the magnitude of work required, we recruited a worldwide network of field experts, academics and students in the areas of public health, data science and social science to support the effort. Most analyses were performed on a merged line list of COVID-19 cases using a reverse engineering model (line listing built using data extracted from national situation reports shared by countries with the Regional Office for Africa as per the IHR (2005) obligations). The data analysis platform The Renku Project (https://renkulab.io) provided secure data storage and permitted collaborative coding.Over a period of 6 months, 63 contributors from 32 nations (including 17 African countries) participated in the project. A total of 45 in-depth country-specific epidemiological reports and data quality reports were prepared for 28 countries. Spatial transmission and mortality risk indices were developed for 23 countries. Text and video-based training modules were developed to integrate and mentor new members. The team also began to develop EpiGraph Hub, a web application that automates the generation of reports similar to those we created, and includes more advanced data analyses features (e.g. mathematical models, geospatial analyses) to deliver real-time, actionable results to decision-makers.Within a short period, we implemented a global collaborative approach to health data management and analyses to advance national responses to health emergencies and outbreaks. The interdisciplinary team, the hands-on training and mentoring, and the participation of local researchers were key to the success of this initiative.}, } @article {pmid35641668, year = {2022}, author = {Esen, F}, title = {Determining the effects of geomorphological factors on the distribution of land use and plant cover by different statistical methods.}, journal = {Environmental monitoring and assessment}, volume = {194}, number = {7}, pages = {465}, pmid = {35641668}, issn = {1573-2959}, mesh = {Agriculture ; *Environmental Monitoring/methods ; Geographic Information Systems ; *Plants ; }, abstract = {The aim of this study is to determine the role of geomorphological factors in land use and plant cover organization. For this purpose, the relationship between geomorphological factors such as geomorphological unit, elevation, slope, aspect, and curvature with land use and plant cover was analyzed using GIS (Geographical Information Systems) techniques and statistical methods (zonal analysis, correlation analysis, regression analysis). Using zonal analysis, the boundaries of both land use patterns and plant species are clearly drawn according to geomorphological factors. Using correlation analysis, the direction and intensity of the relationship between each geomorphological factor with land use patterns and plant species were determined. Finally, regression analysis method was used to determine the impact rate of geomorphological factors on land use patterns and plant cover. Thus, the effects of geomorphological factors on the distribution of both land use patterns and the each plant species were explained in detail. When the results of all three analyses are evaluated in general, the elevation is very strong, the slope strong, the aspect medium, the geomorphological unit weak, and the curvature has a very weak effect on the distribution of land use patterns and the plant species in the research area. The data obtained from the study will contribute to the planning and implementation of activities such as forest, agriculture, land use, water management to be carried out by local administrations and decision-makers. In addition, it will form a scientific basis for the sustainability of forest existence in harmony with the ecological conditions of Göksun Plain and its surroundings.}, } @article {pmid35639883, year = {2022}, author = {Dong, X and Penrice-Randal, R and Goldswain, H and Prince, T and Randle, N and Donovan-Banfield, I and Salguero, FJ and Tree, J and Vamos, E and Nelson, C and Clark, J and Ryan, Y and Stewart, JP and Semple, MG and Baillie, JK and Openshaw, PJM and Turtle, L and Matthews, DA and Carroll, MW and Darby, AC and Hiscox, JA}, title = {Analysis of SARS-CoV-2 known and novel subgenomic mRNAs in cell culture, animal model, and clinical samples using LeTRS, a bioinformatic tool to identify unique sequence identifiers.}, journal = {GigaScience}, volume = {11}, number = {}, pages = {}, pmid = {35639883}, issn = {2047-217X}, support = {MR/W005611/1/MRC_/Medical Research Council/United Kingdom ; MC_PC_19059/MRC_/Medical Research Council/United Kingdom ; 75F40120C00085/FD/FDA HHS/United States ; MC_PC_19027/MRC_/Medical Research Council/United Kingdom ; MC_PC_19025/MRC_/Medical Research Council/United Kingdom ; 215091/Z/18/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Animals ; *COVID-19 ; Cell Culture Techniques ; Computational Biology ; Humans ; Mammals/genetics ; Models, Animal ; RNA, Messenger/genetics ; *SARS-CoV-2/genetics ; }, abstract = {Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has a complex strategy for the transcription of viral subgenomic mRNAs (sgmRNAs), which are targets for nucleic acid diagnostics. Each of these sgmRNAs has a unique 5' sequence, the leader-transcriptional regulatory sequence gene junction (leader-TRS junction), that can be identified using sequencing. High-resolution sequencing has been used to investigate the biology of SARS-CoV-2 and the host response in cell culture and animal models and from clinical samples. LeTRS, a bioinformatics tool, was developed to identify leader-TRS junctions and can be used as a proxy to quantify sgmRNAs for understanding virus biology. LeTRS is readily adaptable for other coronaviruses such as Middle East respiratory syndrome coronavirus or a future newly discovered coronavirus. LeTRS was tested on published data sets and novel clinical samples from patients and longitudinal samples from animal models with coronavirus disease 2019. LeTRS identified known leader-TRS junctions and identified putative novel sgmRNAs that were common across different mammalian species. This may be indicative of an evolutionary mechanism where plasticity in transcription generates novel open reading frames, which can then subject to selection pressure. The data indicated multiphasic abundance of sgmRNAs in two different animal models. This recapitulates the relative sgmRNA abundance observed in cells at early points in infection but not at late points. This pattern is reflected in some human nasopharyngeal samples and therefore has implications for transmission models and nucleic acid-based diagnostics. LeTRS provides a quantitative measure of sgmRNA abundance from sequencing data. This can be used to assess the biology of SARS-CoV-2 (or other coronaviruses) in clinical and nonclinical samples, especially to evaluate different variants and medical countermeasures that may influence viral RNA synthesis.}, } @article {pmid35639882, year = {2022}, author = {Salim, JA and Saraiva, AM and Zermoglio, PF and Agostini, K and Wolowski, M and Drucker, DP and Soares, FM and Bergamo, PJ and Varassin, IG and Freitas, L and Maués, MM and Rech, AR and Veiga, AK and Acosta, AL and Araujo, AC and Nogueira, A and Blochtein, B and Freitas, BM and Albertini, BC and Maia-Silva, C and Nunes, CEP and Pires, CSS and Dos Santos, CF and Queiroz, EP and Cartolano, EA and de Oliveira, FF and Amorim, FW and Fontúrbel, FE and da Silva, GV and Consolaro, H and Alves-Dos-Santos, I and Machado, IC and Silva, JS and Aleixo, KP and Carvalheiro, LG and Rocca, MA and Pinheiro, M and Hrncir, M and Streher, NS and Ferreira, PA and de Albuquerque, PMC and Maruyama, PK and Borges, RC and Giannini, TC and Brito, VLG}, title = {Data standardization of plant-pollinator interactions.}, journal = {GigaScience}, volume = {11}, number = {}, pages = {}, pmid = {35639882}, issn = {2047-217X}, mesh = {Animals ; Biodiversity ; *Ecosystem ; Phylogeny ; *Pollination ; Reference Standards ; }, abstract = {BACKGROUND: Animal pollination is an important ecosystem function and service, ensuring both the integrity of natural systems and human well-being. Although many knowledge shortfalls remain, some high-quality data sets on biological interactions are now available. The development and adoption of standards for biodiversity data and metadata has promoted great advances in biological data sharing and aggregation, supporting large-scale studies and science-based public policies. However, these standards are currently not suitable to fully support interaction data sharing.

RESULTS: Here we present a vocabulary of terms and a data model for sharing plant-pollinator interactions data based on the Darwin Core standard. The vocabulary introduces 48 new terms targeting several aspects of plant-pollinator interactions and can be used to capture information from different approaches and scales. Additionally, we provide solutions for data serialization using RDF, XML, and DwC-Archives and recommendations of existing controlled vocabularies for some of the terms. Our contribution supports open access to standardized data on plant-pollinator interactions.

CONCLUSIONS: The adoption of the vocabulary would facilitate data sharing to support studies ranging from the spatial and temporal distribution of interactions to the taxonomic, phenological, functional, and phylogenetic aspects of plant-pollinator interactions. We expect to fill data and knowledge gaps, thus further enabling scientific research on the ecology and evolution of plant-pollinator communities, biodiversity conservation, ecosystem services, and the development of public policies. The proposed data model is flexible and can be adapted for sharing other types of interactions data by developing discipline-specific vocabularies of terms.}, } @article {pmid35633848, year = {2022}, author = {McDonald, PJ and Brown, RM and Kraus, F and Bowles, P and Arifin, U and Eliades, SJ and Fisher, RN and Gaulke, M and Grismer, LL and Ineich, I and Karin, BR and Meneses, CG and Richards, SJ and Sanguila, MB and Siler, CD and Oliver, PM}, title = {Cryptic extinction risk in a western Pacific lizard radiation.}, journal = {Biodiversity and conservation}, volume = {31}, number = {8-9}, pages = {2045-2062}, pmid = {35633848}, issn = {0960-3115}, abstract = {UNLABELLED: Cryptic ecologies, the Wallacean Shortfall of undocumented species' geographical ranges and the Linnaean Shortfall of undescribed diversity, are all major barriers to conservation assessment. When these factors overlap with drivers of extinction risk, such as insular distributions, the number of threatened species in a region or clade may be underestimated, a situation we term 'cryptic extinction risk'. The genus Lepidodactylus is a diverse radiation of insular and arboreal geckos that occurs across the western Pacific. Previous work on Lepidodactylus showed evidence of evolutionary displacement around continental fringes, suggesting an inherent vulnerability to extinction from factors such as competition and predation. We sought to (1) comprehensively review status and threats, (2) estimate the number of undescribed species, and (3) estimate extinction risk in data deficient and candidate species, in Lepidodactylus. From our updated IUCN Red List assessment, 60% of the 58 recognized species are threatened (n = 15) or Data Deficient (n = 21), which is higher than reported for most other lizard groups. Species from the smaller and isolated Pacific islands are of greatest conservation concern, with most either threatened or Data Deficient, and all particularly vulnerable to invasive species. We estimated 32 undescribed candidate species and linear modelling predicted that an additional 18 species, among these and the data deficient species, are threatened with extinction. Focusing efforts to resolve the taxonomy and conservation status of key taxa, especially on small islands in the Pacific, is a high priority for conserving this remarkably diverse, yet poorly understood, lizard fauna. Our data highlight how cryptic ecologies and cryptic diversity combine and lead to significant underestimation of extinction risk.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s10531-022-02412-x.}, } @article {pmid35633719, year = {2022}, author = {Gevi, F and Leo, P and Cassaro, A and Pacelli, C and de Vera, JP and Rabbow, E and Timperio, AM and Onofri, S}, title = {Metabolomic Profile of the Fungus Cryomyces antarcticus Under Simulated Martian and Space Conditions as Support for Life-Detection Missions on Mars.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {749396}, pmid = {35633719}, issn = {1664-302X}, abstract = {The identification of traces of life beyond Earth (e.g., Mars, icy moons) is a challenging task because terrestrial chemical-based molecules may be destroyed by the harsh conditions experienced on extraterrestrial planetary surfaces. For this reason, studying the effects on biomolecules of extremophilic microorganisms through astrobiological ground-based space simulation experiments is significant to support the interpretation of the data that will be gained and collected during the ongoing and future space exploration missions. Here, the stability of the biomolecules of the cryptoendolithic black fungus Cryomyces antarcticus, grown on two Martian regolith analogues and on Antarctic sandstone, were analysed through a metabolomic approach, after its exposure to Science Verification Tests (SVTs) performed in the frame of the European Space Agency (ESA) Biology and Mars Experiment (BIOMEX) project. These tests are building a set of ground-based experiments performed before the space exposure aboard the International Space Station (ISS). The analysis aimed to investigate the effects of different mineral mixtures on fungal colonies and the stability of the biomolecules synthetised by the fungus under simulated Martian and space conditions. The identification of a specific group of molecules showing good stability after the treatments allow the creation of a molecular database that should support the analysis of future data sets that will be collected in the ongoing and next space exploration missions.}, } @article {pmid35630464, year = {2022}, author = {Papale, M and Rizzo, C and Giannarelli, S and Caruso, G and Amalfitano, S and Aspholm, PE and Maimone, G and Miserocchi, S and Rappazzo, AC and Lo Giudice, A and Azzaro, M}, title = {Benthic Microbial Communities in a Seasonally Ice-Covered Sub-Arctic River (Pasvik River, Norway) Are Shaped by Site-Specific Environmental Conditions.}, journal = {Microorganisms}, volume = {10}, number = {5}, pages = {}, pmid = {35630464}, issn = {2076-2607}, support = {262693//INTERACT Transnational Access EU Program/ ; }, abstract = {The Pasvik River experiences chemical, physical, and biological stressors due to the direct discharges of domestic sewage from settlements located within the catchment and runoff from smelter and mine wastes. Sediments, as a natural repository of organic matter and associated contaminants, are of global concern for the possible release of pollutants in the water column, with detrimental effects on aquatic organisms. The present study was aimed at characterizing the riverine benthic microbial community and evaluating its ecological role in relation to the contamination level. Sediments were sampled along the river during two contrasting environmental periods (i.e., beginning and ongoing phases of ice melting). Microbial enzymatic activities, cell abundance, and morphological traits were evaluated, along with the phylogenetic community composition. Amplified 16S rRNA genes from bacteria were sequenced using a next-generation approach. Sediments were also analyzed for a variety of chemical features, namely particulate material characteristics and concentration of polychlorobiphenyls, polycyclic aromatic hydrocarbons, and pesticides. Riverine and brackish sites did not affect the microbial community in terms of main phylogenetic diversity (at phylum level), morphometry, enzymatic activities, and abundance. Instead, bacterial diversity in the river sediments appeared to be influenced by the micro-niche conditions, with differences in the relative abundance of selected taxa. In particular, our results highlighted the occurrence of bacterial taxa directly involved in the C, Fe, and N cycles, as well as in the degradation of organic pollutants and toxic compounds.}, } @article {pmid35628215, year = {2022}, author = {Kozicki, M and Pawlaczyk, A and Adamska, A and Szynkowska-Jóźwik, MI and Sąsiadek-Andrzejczak, E}, title = {Golden and Silver-Golden Chitosan Hydrogels and Fabrics Modified with Golden Chitosan Hydrogels.}, journal = {International journal of molecular sciences}, volume = {23}, number = {10}, pages = {}, pmid = {35628215}, issn = {1422-0067}, mesh = {*Chitosan/chemistry ; Hydrogels/chemistry ; Microscopy, Electron, Scanning ; *Silver/chemistry ; Textiles ; }, abstract = {Golden and silver-golden chitosan hydrogels and hydrogel-modified textiles of potential biomedical applications are investigated in this work. The hydrogels are formed by reactions of chitosan with HAuCl4·xH2O. For above the critical concentration of chitosan (c*), chitosan-Au hydrogels were prepared. For chitosan concentrations lower than c*, chitosan-Au nano- and microgels were formed. To characterise chitosan-Au structures, sol-gel analysis, UV-Vis spectrophotometry and dynamic light scattering were performed. Au concentration in the hydrogels was determined by the flame atomic absorption spectrophotometry. Colloidal chitosan-Au solutions were used for the modification of fabrics. The Au content in the modified fabrics was quantified by inductively coupled plasma mass spectrometry technique. Scanning electron microscopy with energy dispersion X-ray spectrometer was used to analyse the samples. Reflectance spectrophotometry was applied to examine the colour of the fabrics. The formation of chitosan-Au-Ag hydrogels by the competitive reaction of Au and Ag ions with the chitosan macromolecules is reported.}, } @article {pmid35627689, year = {2022}, author = {Xu, D and Lin, W and Gao, J and Jiang, Y and Li, L and Gao, F}, title = {PM2.5 Exposure and Health Risk Assessment Using Remote Sensing Data and GIS.}, journal = {International journal of environmental research and public health}, volume = {19}, number = {10}, pages = {}, pmid = {35627689}, issn = {1660-4601}, mesh = {China ; *Geographic Information Systems ; Particulate Matter/analysis ; *Remote Sensing Technology ; Risk Assessment ; }, abstract = {Assessing personal exposure risk from PM2.5 air pollution poses challenges due to the limited availability of high spatial resolution data for PM2.5 and population density. This study introduced a seasonal spatial-temporal method of modeling PM2.5 distribution characteristics at a 1-km grid level based on remote sensing data and Geographic Information Systems (GIS). The high-accuracy population density data and the relative exposure risk model were used to assess the relationship between exposure to PM2.5 air pollution and public health. The results indicated that the spatial-temporal PM2.5 concentration could be simulated by MODIS images and GIS method and could provide high spatial resolution data sources for exposure risk assessment. PM2.5 air pollution risks were most serious in spring and winter, and high risks of environmental health hazards were mostly concentrated in densely populated areas in Shanghai-Hangzhou Bay, China. Policies to control the total population and pollution discharge need follow the principle of adaptation to local conditions in high-risk areas. Air quality maintenance and ecological maintenance should be carried out in low-risk areas to reduce exposure risk and improve environmental health.}, } @article {pmid35624681, year = {2022}, author = {Baszyński, J and Kamiński, P and Bogdzińska, M and Mroczkowski, S and Szymański, M and Wasilow, K and Stanek, E and Hołderna-Bona, K and Brodzka, S and Bilski, R and Tkachenko, H and Kurhaluk, N and Stuczyński, T and Lorek, M and Woźniak, A}, title = {Enzymatic Antioxidant Defense and Polymorphic Changes in Male Infertility.}, journal = {Antioxidants (Basel, Switzerland)}, volume = {11}, number = {5}, pages = {}, pmid = {35624681}, issn = {2076-3921}, abstract = {The intensification of oxidative stress and destabilization of the antioxidative defenses of an organism is a consequence of many environmental factors. We considered aspects conditioning male reproductive potential and the functionality of enzymatic antioxidative mechanisms, i.e., superoxide dismutase (SOD), catalase (CAT), glutathione peroxidase (GPx) and glutathione reductase (GR), and their correlations with Li, Be, B, Na, Mg, Al, P, K, Ca, Ti, V, Cr, Mn, Fe, Co, Ni, Cu, Zn, As, Se, Sr, Mo, Ag, Cd, Sn, Sb, Ba, Hg, Tl, Pb, and malondialdehyde (MDA), as well as genetic polymorphism IL-4v.C589T (rs2243250) in men with infertility (n = 76). A healthy normozoospermic control (n = 87) was also used. We assessed the impact of negative changes driven by oxidative stress on enzymatic antioxidative mechanisms as well as the role of MDA in the overall process. On this basis, we infer connections between disturbances in enzymatic antioxidative defense and reproductive potential. Based on a molecular analysis of the polymorphism of gene IL-4v.C589T (rs2243250) (chromosome 5) (PCR-RFLP), we considered the relationships among particular genotypes with the possibility of occurrence of male infertility. Concentrations of chemical elements were measured in the blood. The activity of antioxidants and MDA levels were measured in serum. In the infertile group, higher GPx activity was noted (6.56 nmoL·min[-1]·mL[-1], control: 4.31 nmoL·min[-1]·mL[-1]; p = 0.004), while GR achieved a greater level in the control (17.74 nmoL·min[-1]·mL[-1], infertile: 15.97 nmoL·min[-1]·mL[-1], p = 0.043), which implies diversified efficiency of the first and second lines of defense. The polymorphism of IL-4v.C589T (rs2243250) was not directly connected with infertility because there were not any differences in the frequency of genotypes between the infertile and control group (p = 0.578). An analysis of genotypes CC and TT (polymorphism IL-4v.C589T (rs2243250)) indicated numerous correlations between antioxidants, chemical elements and MDA. Therefore, chemical economy, antioxidative defense and genetic conditions are connected and jointly shape male reproductive potential. Chemical elements influence antioxidative defense and male fertility; the most important modulators appeared to be Na, Ba, Al and B. The polymorphism of gene IL-4v.C589T (rs2243250) has a limited influence on antioxidative defense and the metabolism of chemical elements.}, } @article {pmid35622850, year = {2022}, author = {Madzík, P and Falát, L}, title = {State-of-the-art on analytic hierarchy process in the last 40 years: Literature review based on Latent Dirichlet Allocation topic modelling.}, journal = {PloS one}, volume = {17}, number = {5}, pages = {e0268777}, pmid = {35622850}, issn = {1932-6203}, mesh = {Algorithms ; *Analytic Hierarchy Process ; Databases, Factual ; *Ecosystem ; Fuzzy Logic ; }, abstract = {Although there are several articles that have carried out a systematic literature review of the analytical hierarchy process (AHP), many of them work with a limited number of analyzed documents. This article presents a computer-aided systematic literature review of articles related to AHP. The objectives are: (i) to identify AHP usage and research impact in different subject areas; (ii) to identify trends in the popularity of the AHP from the first introduction of the method in 1980 to the present; (iii) to identify the most common topics related to AHP and topic development over time. We process 35,430 documents related to AHP, published between 1980 and 2021, retrieved from the Scopus database. We provide detailed statistics about research interest, research impact in particular subject areas over the analyzed time period. We use Latent Dirichlet Allocation (LDA) using Gibbs sampling to perform topic modeling based on the corpus of abstracts. We identify nine topics related to AHP: Ecology & Ecosystems; Multi-criteria decision-making; Production and performance management; Sustainable development; Computer network, optimization and algorithms; Service quality; Fuzzy logic; Systematic evaluation; Risk assessment. We also present the individual topics trends over time and point out the possible future direction of AHP.}, } @article {pmid35620757, year = {2022}, author = {Kraemer, R and Remmler, P and Bumberger, J and Kabisch, N}, title = {Running a dense air temperature measurement field campaign at the urban neighbourhood level: Protocol and lessons learned.}, journal = {MethodsX}, volume = {9}, number = {}, pages = {101719}, pmid = {35620757}, issn = {2215-0161}, abstract = {The cooling capacity of urban green spaces constitutes a key measure for cities to mitigate heat events, which is gaining importance in climate change adaptation and mitigation. In this protocol article, we present details on two field campaigns aiming at collecting dense air temperature data in two urban inner city parks in Leipzig, Germany, under unprecedented heat and drought conditions. We introduce all the steps required to plan and conduct qualified fieldwork in environmental research, including study design, technical and logistical preparations, on-site work and data management steps from data acquisition, transfer into research outcomes to dissemination. We further share valuable lessons learned before, during and after fieldwork that helped us improve our work and that could support and improve similar future project campaigns.}, } @article {pmid35618868, year = {2022}, author = {Mammola, S and Pavlek, M and Huber, BA and Isaia, M and Ballarin, F and Tolve, M and Čupić, I and Hesselberg, T and Lunghi, E and Mouron, S and Graco-Roza, C and Cardoso, P}, title = {A trait database and updated checklist for European subterranean spiders.}, journal = {Scientific data}, volume = {9}, number = {1}, pages = {236}, pmid = {35618868}, issn = {2052-4463}, support = {882221//European Commission (EC)/ ; 882221//European Commission (EC)/ ; }, mesh = {Animals ; *Databases, Factual ; Ecosystem ; Europe ; *Spiders ; }, abstract = {Species traits are an essential currency in ecology, evolution, biogeography, and conservation biology. However, trait databases are unavailable for most organisms, especially those living in difficult-to-access habitats such as caves and other subterranean ecosystems. We compiled an expert-curated trait database for subterranean spiders in Europe using both literature data (including grey literature published in many different languages) and direct morphological measurements whenever specimens were available to us. We started by updating the checklist of European subterranean spiders, now including 512 species across 20 families, of which at least 192 have been found uniquely in subterranean habitats. For each of these species, we compiled 64 traits. The trait database encompasses morphological measures, including several traits related to subterranean adaptation, and ecological traits referring to habitat preference, dispersal, and feeding strategies. By making these data freely available, we open up opportunities for exploring different research questions, from the quantification of functional dimensions of subterranean adaptation to the study of spatial patterns in functional diversity across European caves.}, } @article {pmid35618416, year = {2022}, author = {Krieger, G and Lupo, O and Wittkopp, P and Barkai, N}, title = {Evolution of transcription factor binding through sequence variations and turnover of binding sites.}, journal = {Genome research}, volume = {32}, number = {6}, pages = {1099-1111}, pmid = {35618416}, issn = {1549-5469}, mesh = {Binding Sites ; Chromatin Immunoprecipitation ; *Computational Biology/methods ; Protein Binding ; Saccharomyces cerevisiae/genetics/metabolism ; *Transcription Factors/genetics/metabolism ; }, abstract = {Variations in noncoding regulatory sequences play a central role in evolution. Interpreting such variations, however, remains difficult even in the context of defined attributes such as transcription factor (TF) binding sites. Here, we systematically link variations in cis-regulatory sequences to TF binding by profiling the allele-specific binding of 27 TFs expressed in a yeast hybrid, in which two related genomes are present within the same nucleus. TFs localize preferentially to sites containing their known consensus motifs but occupy only a small fraction of the motif-containing sites available within the genomes. Differential binding of TFs to the orthologous alleles was well explained by variations that alter motif sequence, whereas differences in chromatin accessibility between alleles were of little apparent effect. Motif variations that abolished binding when present in only one allele were still bound when present in both alleles, suggesting evolutionary compensation, with a potential role for sequence conservation at the motif's vicinity. At the level of the full promoter, we identify cases of binding-site turnover, in which binding sites are reciprocally gained and lost, yet most interspecific differences remained uncompensated. Our results show the flexibility of TFs to bind imprecise motifs and the fast evolution of TF binding sites between related species.}, } @article {pmid35617745, year = {2022}, author = {Antony, S and Unnikrishnan, K and Aswin, S and Dev, VV and Arun, V and Krishnan, KA}, title = {Heavy metals in coral reef sediments of Kavaratti Island, India: An integrated quality assessment using GIS and pollution indicators.}, journal = {Marine pollution bulletin}, volume = {180}, number = {}, pages = {113721}, doi = {10.1016/j.marpolbul.2022.113721}, pmid = {35617745}, issn = {1879-3363}, mesh = {Cadmium/analysis ; China ; Coral Reefs ; Environmental Monitoring/methods ; Geographic Information Systems ; Geologic Sediments ; Lead/analysis ; *Metals, Heavy/analysis ; Risk Assessment ; *Water Pollutants, Chemical/analysis ; }, abstract = {The present study aims to document the contamination levels and ecological risks of heavy metals in the sediments of Kavaratti lagoon, India. A total of 15 sediment samples were collected for the analysis of Al, Pb, Cd, Cu, Cr, Mn, Ni and Zn. The decreasing trend of heavy metals was observed in the lagoon sediment as Pb > Zn > Al > Mn > Ni > Cr > Cd > Cu. The Geo-accumulation index (Igeo) results indicate that Cu, Cr, Mn, Ni and Zn were uncontaminated, while Cd was strong to extremely contaminated and Al and Pb were moderately contaminated. The enrichment factors (EF) of Cd and Pb range from moderate to extremely high (EF > 1) indicating that they have anthropogenic origin on Kavaratti Island. The Contamination factor (Cf) indicated that Cd, Pb and Al belong to a high risk of contamination (Cf > 6). The pollution load index (PLI) value near one suggested that a moderate level of pollution occurs in the study area. The modified degree of contamination (mCd) shows that Al, Cd and Pb have an ultra- higher degree of contamination (mCd ≤ 32). The potential ecological risk (RI) index confirmed that Pb and Cd have considerable to the serious thread of ecological risk (RI > 600). Additionally, multivariate statistical analysis and pollution indexes showed that the Kavaratti lagoon is moderate to considerably polluted by heavy metals. Diesel-based power generation, activities related to shipping, untreated sewage, fishing and tourism activities are the main anthropogenic sources of heavy metal pollution on Kavaratti Island.}, } @article {pmid35617403, year = {2022}, author = {Bonnet, T and Morrissey, MB and de Villemereuil, P and Alberts, SC and Arcese, P and Bailey, LD and Boutin, S and Brekke, P and Brent, LJN and Camenisch, G and Charmantier, A and Clutton-Brock, TH and Cockburn, A and Coltman, DW and Courtiol, A and Davidian, E and Evans, SR and Ewen, JG and Festa-Bianchet, M and de Franceschi, C and Gustafsson, L and Höner, OP and Houslay, TM and Keller, LF and Manser, M and McAdam, AG and McLean, E and Nietlisbach, P and Osmond, HL and Pemberton, JM and Postma, E and Reid, JM and Rutschmann, A and Santure, AW and Sheldon, BC and Slate, J and Teplitsky, C and Visser, ME and Wachter, B and Kruuk, LEB}, title = {Genetic variance in fitness indicates rapid contemporary adaptive evolution in wild animals.}, journal = {Science (New York, N.Y.)}, volume = {376}, number = {6596}, pages = {1012-1016}, doi = {10.1126/science.abk0853}, pmid = {35617403}, issn = {1095-9203}, mesh = {*Adaptation, Biological/genetics ; Animals ; *Animals, Wild/genetics ; *Biological Evolution ; Birds/genetics ; Datasets as Topic ; *Genetic Fitness ; Genetic Variation ; Mammals/genetics ; Population Dynamics ; Selection, Genetic ; }, abstract = {The rate of adaptive evolution, the contribution of selection to genetic changes that increase mean fitness, is determined by the additive genetic variance in individual relative fitness. To date, there are few robust estimates of this parameter for natural populations, and it is therefore unclear whether adaptive evolution can play a meaningful role in short-term population dynamics. We developed and applied quantitative genetic methods to long-term datasets from 19 wild bird and mammal populations and found that, while estimates vary between populations, additive genetic variance in relative fitness is often substantial and, on average, twice that of previous estimates. We show that these rates of contemporary adaptive evolution can affect population dynamics and hence that natural selection has the potential to partly mitigate effects of current environmental change.}, } @article {pmid35616633, year = {2022}, author = {Rutz, A and Sorokina, M and Galgonek, J and Mietchen, D and Willighagen, E and Gaudry, A and Graham, JG and Stephan, R and Page, R and Vondrášek, J and Steinbeck, C and Pauli, GF and Wolfender, JL and Bisson, J and Allard, PM}, title = {The LOTUS initiative for open knowledge management in natural products research.}, journal = {eLife}, volume = {11}, number = {}, pages = {}, pmid = {35616633}, issn = {2050-084X}, support = {P50 AT000155/AT/NCCIH NIH HHS/United States ; U41 AT008706/AT/NCCIH NIH HHS/United States ; }, mesh = {*Biological Products ; Computational Biology ; Databases, Factual ; Knowledge ; *Knowledge Management ; }, abstract = {Contemporary bioinformatic and chemoinformatic capabilities hold promise to reshape knowledge management, analysis and interpretation of data in natural products research. Currently, reliance on a disparate set of non-standardized, insular, and specialized databases presents a series of challenges for data access, both within the discipline and for integration and interoperability between related fields. The fundamental elements of exchange are referenced structure-organism pairs that establish relationships between distinct molecular structures and the living organisms from which they were identified. Consolidating and sharing such information via an open platform has strong transformative potential for natural products research and beyond. This is the ultimate goal of the newly established LOTUS initiative, which has now completed the first steps toward the harmonization, curation, validation and open dissemination of 750,000+ referenced structure-organism pairs. LOTUS data is hosted on Wikidata and regularly mirrored on https://lotus.naturalproducts.net. Data sharing within the Wikidata framework broadens data access and interoperability, opening new possibilities for community curation and evolving publication models. Furthermore, embedding LOTUS data into the vast Wikidata knowledge graph will facilitate new biological and chemical insights. The LOTUS initiative represents an important advancement in the design and deployment of a comprehensive and collaborative natural products knowledge base.}, } @article {pmid35615290, year = {2022}, author = {Adhikari, JN and Bhattarai, BP and Rokaya, MB and Thapa, TB}, title = {Land use/land cover changes in the central part of the Chitwan Annapurna Landscape, Nepal.}, journal = {PeerJ}, volume = {10}, number = {}, pages = {e13435}, pmid = {35615290}, issn = {2167-8359}, mesh = {*Conservation of Natural Resources ; Nepal ; *Environmental Monitoring/methods ; Geographic Information Systems ; Remote Sensing Technology ; }, abstract = {BACKGROUND: Land use/land cover assessment and monitoring of the land cover dynamics are essential to know the ecological, physical and anthropogenic processes in the landscape. Previous studies have indicated changes in the landscape of mid-hills of Nepal in the past few decades. But there is a lack of study in the Chitwan Annapurna Landscape; hence, this study was carried out to fill in study gap that existed in the area.

METHODS: This study evaluates land use/land cover dynamics between 2000 to 2020 in the central part of the Chitwan Annapurna Landscape, Nepal by using Landsat images. The Landsat images were classified into eight different classes using remote sensing and geographic information system (GIS). The accuracy assessment of classified images was evaluated by calculating actual accuracy, producer's accuracy, user's accuracy and kappa coefficient based on the ground-truthing points for 2020 and Google Earth and topographic maps for images of 2010 and 2000.

RESULTS: The results of land use/land cover analysis of Landsat image 2020 showed that the study area was composed of grassland (1.73%), barren area (1.76%), riverine forest (1.93%), water body (1.97%), developed area (4.13%), Sal dominated forest (15.4%), cropland (28.13%) and mixed forest (44.95%). The results of land cover change between 2000 to 2020 indicated an overall increase in Sal dominated forest (7.6%), developed area (31.34%), mixed forest (37.46%) and decrease in riverine forest (11.29%), barren area (20.03%), croplands (29.87%) and grasslands (49.71%). The classification of the images of 2000, 2010 and 2020 had 81%, 81.6% and 84.77% overall accuracy, respectively. This finding can be used as a baseline information for the development of a proper management plan to protect wildlife habitats and forecasting possible future changes, if needed.}, } @article {pmid35614412, year = {2022}, author = {Kim, MS and Yu, J}, title = {Text mining for identifying the nature of online questions about non-suicidal self-injury.}, journal = {BMC public health}, volume = {22}, number = {1}, pages = {1041}, pmid = {35614412}, issn = {1471-2458}, mesh = {Data Mining ; Humans ; Risk Factors ; *Self-Injurious Behavior/epidemiology ; Suicidal Ideation ; }, abstract = {OBJECTIVE: The internet provides convenient access to information about non-suicidal self-injury (NSSI) owing to its accessibility and anonymity. This study aimed to explore the distribution of topics regarding NSSI posted on the internet and yearly trends in the derived topics using text mining.

METHODS: We searched for the keyword "non-suicidal self-injury" (Ja-Hae in Korean) in the Naver Q&A using the statistical package R. We analyzed 7893 NSSI-related questions posted between 2009 and 2018. Text mining was performed using latent Dirichlet allocation (LDA) on the dataset to determine associations between phrases and thus identify common themes in posts about NSSI.

RESULTS: In the LDA, we selected the following 10 most common topics: anger, family troubles, collecting information on NSSI, stress, concerns regarding NSSI scarring, ways to help a non-suicidal self-injurious friend, depression, medical advice, ways to perform or stop NSSI, and prejudices and thoughts regarding non-suicidal self-injurious people.

CONCLUSIONS: This study provides valuable information on the nature of NSSI questions posted online. In future research, developing websites that provide NSSI information and support or guidance on effectively communicating with NSSI is necessary.}, } @article {pmid35605833, year = {2022}, author = {Bernardini, I and Fabrello, J and Vecchiato, M and Ferraresso, S and Babbucci, M and Peruzza, L and Rovere, GD and Masiero, L and Marin, MG and Bargelloni, L and Gambaro, A and Patarnello, T and Matozzo, V and Milan, M}, title = {Effects of environmental concentrations of the fragrance amyl salicylate on the mediterranean mussel Mytilus galloprovincialis.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {307}, number = {}, pages = {119502}, doi = {10.1016/j.envpol.2022.119502}, pmid = {35605833}, issn = {1873-6424}, mesh = {Animals ; *Microbiota ; *Mytilus/metabolism ; Odorants/analysis ; Salicylates/toxicity ; Water/metabolism ; *Water Pollutants, Chemical/analysis ; }, abstract = {Amyl salicylate (AS) is a fragrance massively used as a personal care product and following the discharged in wastewaters may end up in the aquatic environment representing a potential threat for the ecosystem and living organisms. AS was recently detected in water of the Venice Lagoon, a vulnerable area continuously subjected to the income of anthropogenic chemicals. The lagoon is a relevant area for mollusc farming, including the Mediterranean mussels (Mytilus galloprovincialis) having an important economic and ecological role. Despite high levels of AS occurred in water of the Lagoon of Venice, no studies investigated the possible consequences of AS exposures on species inhabiting this ecosystem to date. For the first time, we applied a multidisciplinary approach to investigate the potential effects of the fragrance AS on Mediterranean mussels. To reach such a goal, bioaccumulation, cellular, biochemical, and molecular analyses (RNA-seq and microbiota characterization) were measured in mussels treated for 7 and 14 days with different AS Venice lagoon environmental levels (0.1 and 0.5 μg L[-1]). Despite chemical investigations suggested low AS bioaccumulation capability, cellular and molecular analyses highlighted the disruption of several key cellular processes after the prolonged exposures to the high AS concentration. Among them, potential immunotoxicity and changes in transcriptional regulation of pathways involved in energy metabolism, stress response, apoptosis and cell death regulations have been observed. Conversely, exposure to the low AS concentration demonstrated weak transcriptional changes and transient increased representation of opportunistic pathogens, as Arcobacter genus and Vibrio aestuarianus. Summarizing, this study provides the first overview on the effects of AS on one of the most widely farmed mollusk species.}, } @article {pmid35605726, year = {2022}, author = {Ma, J and Chen, F and Zhu, Y and Li, X and Yu, H and Sun, Y}, title = {Joint effects of microplastics and ciprofloxacin on their toxicity and fates in wheat: A hydroponic study.}, journal = {Chemosphere}, volume = {303}, number = {Pt 2}, pages = {135023}, doi = {10.1016/j.chemosphere.2022.135023}, pmid = {35605726}, issn = {1879-1298}, mesh = {Anti-Bacterial Agents ; Chlorophyll A/analysis ; Ciprofloxacin/analysis/toxicity ; Hydroponics ; *Microplastics ; Plastics/toxicity ; Polystyrenes/analysis ; Triticum ; *Water Pollutants, Chemical/analysis/toxicity ; }, abstract = {The toxicological impacts of microplastics (MPs) and antibiotics in the soil environment have gradually drawn widespread attention, while little research has focused on the combined pollution of MPs and antibiotics on plants. In this work, a 21-day hydroponic study was conducted to test the hypothesis that polystyrene MPs (0.1, 1 and 10 μm particle sizes, 50 mg/L) and ciprofloxacin (CIP) (1.0 and 5.0 mg/L) had a joint toxicity to wheat seedlings and they could be absorbed by wheat. Plant samples were taken for analyses after 21 days of exposure. The results showed that 0.1 and 1 μm MP could enter wheat roots but only the former could translocate to aerial parts. Moreover, 0.1 μm MP showed a greater toxicity effect than 1 μm MP, whereas 10 μm MP exhibited little toxicity on wheat. The dosing of 0.1 μm MP significantly increased the toxic effects of CIP to wheat. Compared to the control treatment (without MPs and CIP), 0.1 μm MPs-5.0 mg/L CIP treatment resulted in inhibition of root length and weight by 60.1% and 44.3%, respectively, while the contents of chlorophyll a and chlorophyll b decreased by 36.3% and 44.6%, respectively. The presence of CIP (5.0 mg/L) potentially aggravated the combined toxicity. The exposure of 0.1 μm MP significantly reduced root superoxide distumase activity but increased root malondialdehyde content. The amount of CIP in wheat tissues carried by MPs was negligible compared with the uptake quantity of CIP by wheat.}, } @article {pmid35605195, year = {2022}, author = {Zhao, F and Tian, S and Wu, Q and Li, Z and Ye, L and Zhuang, Y and Wang, M and Xie, Y and Zou, S and Teng, W and Tong, Y and Tang, D and Mahato, AK and Benhamed, M and Liu, Z and Zhang, Y}, title = {Utility of Triti-Map for bulk-segregated mapping of causal genes and regulatory elements in Triticeae.}, journal = {Plant communications}, volume = {3}, number = {4}, pages = {100304}, pmid = {35605195}, issn = {2590-3462}, mesh = {*Evolution, Molecular ; *Genome, Plant ; Plant Breeding ; Poaceae/genetics ; Triticum/genetics ; }, abstract = {Triticeae species, including wheat, barley, and rye, are critical for global food security. Mapping agronomically important genes is crucial for elucidating molecular mechanisms and improving crops. However, Triticeae includes many wild relatives with desirable agronomic traits, and frequent introgressions occurred during Triticeae evolution and domestication. Thus, Triticeae genomes are generally large and complex, making the localization of genes or functional elements that control agronomic traits challenging. Here, we developed Triti-Map, which contains a suite of user-friendly computational packages specifically designed and optimized to overcome the obstacles of gene mapping in Triticeae, as well as a web interface integrating multi-omics data from Triticeae for the efficient mining of genes or functional elements that control particular traits. The Triti-Map pipeline accepts both DNA and RNA bulk-segregated sequencing data as well as traditional QTL data as inputs for locating genes and elucidating their functions. We illustrate the usage of Triti-Map with a combination of bulk-segregated ChIP-seq data to detect a wheat disease-resistance gene with its promoter sequence that is absent from the reference genome and clarify its evolutionary process. We hope that Triti-Map will facilitate gene isolation and accelerate Triticeae breeding.}, } @article {pmid35601625, year = {2022}, author = {Asci, F and Scardapane, S and Zampogna, A and D'Onofrio, V and Testa, L and Patera, M and Falletti, M and Marsili, L and Suppa, A}, title = {Handwriting Declines With Human Aging: A Machine Learning Study.}, journal = {Frontiers in aging neuroscience}, volume = {14}, number = {}, pages = {889930}, pmid = {35601625}, issn = {1663-4365}, abstract = {BACKGROUND: Handwriting is an acquired complex cognitive and motor skill resulting from the activation of a widespread brain network. Handwriting therefore may provide biologically relevant information on health status. Also, handwriting can be collected easily in an ecological scenario, through safe, cheap, and largely available tools. Hence, objective handwriting analysis through artificial intelligence would represent an innovative strategy for telemedicine purposes in healthy subjects and people affected by neurological disorders.

MATERIALS AND METHODS: One-hundred and fifty-six healthy subjects (61 males; 49.6 ± 20.4 years) were enrolled and divided according to age into three subgroups: Younger adults (YA), middle-aged adults (MA), and older adults (OA). Participants performed an ecological handwriting task that was digitalized through smartphones. Data underwent the DBNet algorithm for measuring and comparing the average stroke sizes in the three groups. A convolutional neural network (CNN) was also used to classify handwriting samples. Lastly, receiver operating characteristic (ROC) curves and sensitivity, specificity, positive, negative predictive values (PPV, NPV), accuracy and area under the curve (AUC) were calculated to report the performance of the algorithm.

RESULTS: Stroke sizes were significantly smaller in OA than in MA and YA. The CNN classifier objectively discriminated YA vs. OA (sensitivity = 82%, specificity = 80%, PPV = 78%, NPV = 79%, accuracy = 77%, and AUC = 0.84), MA vs. OA (sensitivity = 84%, specificity = 56%, PPV = 78%, NPV = 73%, accuracy = 74%, and AUC = 0.7), and YA vs. MA (sensitivity = 75%, specificity = 82%, PPV = 79%, NPV = 83%, accuracy = 79%, and AUC = 0.83).

DISCUSSION: Handwriting progressively declines with human aging. The effect of physiological aging on handwriting abilities can be detected remotely and objectively by using machine learning algorithms.}, } @article {pmid35594026, year = {2022}, author = {Ren, S and Shen, B}, title = {5G, Big Data, and AI for Smart City and Prevention of Virus Infection.}, journal = {Advances in experimental medicine and biology}, volume = {1368}, number = {}, pages = {189-214}, pmid = {35594026}, issn = {0065-2598}, mesh = {Artificial Intelligence ; *Big Data ; *COVID-19/prevention & control ; Cities ; Humans ; Technology ; }, abstract = {With the development of urbanization, artificial intelligence, communication technology, and the Internet of Things, cities have evolved a new ecology from traditional city structures, that is, smart city. Combining 5G and big data, the applications of smart cities have been extended to every aspect of residents' lives. Based on the popularization of communication equipment and sensors, the great improvement in data transmission and processing technology, the production efficiency in medical field, industrial field, and security field has been improved. This chapter introduces the current research related to smart cities, including its architecture, technologies, and equipment involved. Then it discussed the challenges and opportunities of explainable artificial intelligence (XAI), which is the next important development direction of AI, especially in the medical field, where patients and medical personnel have non-negligible needs for the interpretability of AI models. Then, taking COVID-19 as an example, it discussed how smart cities play a role during virus infection and introduced the specific applications designed so far. Finally, it discussed the shortcomings of the current situation and the aspects that can be improved in the future.}, } @article {pmid35590257, year = {2022}, author = {Zhu, Y and Chen, L and Hong, X and Shi, H and Li, X}, title = {Revealing the novel complexity of plant long non-coding RNA by strand-specific and whole transcriptome sequencing for evolutionarily representative plant species.}, journal = {BMC genomics}, volume = {23}, number = {Suppl 4}, pages = {381}, pmid = {35590257}, issn = {1471-2164}, support = {2019YFA0904601//National Key Research and Development Program of China/ ; 31701137, 31972881, 31900470//National Natural Science Foundation of China/ ; }, mesh = {Computational Biology/methods ; DNA Transposable Elements ; *RNA, Long Noncoding/genetics ; RNA, Messenger ; RNA, Plant/genetics ; Sequence Analysis, RNA ; Transcriptome ; Exome Sequencing ; }, abstract = {BACKGROUND: Previous studies on plant long noncoding RNAs (lncRNAs) lacked consistency and suffered from many factors like heterogeneous data sources and experimental protocols, different plant tissues, inconsistent bioinformatics pipelines, etc. For example, the sequencing of RNAs with poly(A) tails excluded a large portion of lncRNAs without poly(A), and use of regular RNA-sequencing technique did not distinguish transcripts' direction for lncRNAs. The current study was designed to systematically discover and analyze lncRNAs across eight evolutionarily representative plant species, using strand-specific (directional) and whole transcriptome sequencing (RiboMinus) technique.

RESULTS: A total of 39,945 lncRNAs (25,350 lincRNAs and 14,595 lncNATs) were identified, which showed molecular features of lncRNAs that are consistent across divergent plant species but different from those of mRNA. Further, transposable elements (TEs) were found to play key roles in the origination of lncRNA, as significantly large number of lncRNAs were found to contain TEs in gene body and promoter region, and transcription of many lncRNAs was driven by TE promoters. The lncRNA sequences were divergent even in closely related species, and most plant lncRNAs were genus/species-specific, amid rapid turnover in evolution. Evaluated with PhastCons scores, plant lncRNAs showed similar conservation level to that of intergenic sequences, suggesting that most lincRNAs were young and with short evolutionary age. INDUCED BY PHOSPHATE STARVATION (IPS) was found so far to be the only plant lncRNA group with conserved motifs, which may play important roles in the adaptation of terrestrial life during migration from aquatic to terrestrial. Most highly and specially expressed lncRNAs formed co-expression network with coding genes, and their functions were believed to be closely related to their co-expression genes.

CONCLUSION: The study revealed novel features and complexity of lncRNAs in plants through systematic analysis, providing important insights into the origination and evolution of plant lncRNAs.}, } @article {pmid35587983, year = {2022}, author = {Feng, Y and Schmid, B and Loreau, M and Forrester, DI and Fei, S and Zhu, J and Tang, Z and Zhu, J and Hong, P and Ji, C and Shi, Y and Su, H and Xiong, X and Xiao, J and Wang, S and Fang, J}, title = {Multispecies forest plantations outyield monocultures across a broad range of conditions.}, journal = {Science (New York, N.Y.)}, volume = {376}, number = {6595}, pages = {865-868}, doi = {10.1126/science.abm6363}, pmid = {35587983}, issn = {1095-9203}, mesh = {Biodiversity ; *Datasets as Topic ; *Environmental Restoration and Remediation ; *Forestry ; *Forests ; *Trees ; }, abstract = {Multispecies tree planting has long been applied in forestry and landscape restoration in the hope of providing better timber production and ecosystem services; however, a systematic assessment of its effectiveness is lacking. We compiled a global dataset of matched single-species and multispecies plantations to evaluate the impact of multispecies planting on stand growth. Average tree height, diameter at breast height, and aboveground biomass were 5.4, 6.8, and 25.5% higher, respectively, in multispecies stands compared with single-species stands. These positive effects were mainly the result of interspecific complementarity and were modulated by differences in leaf morphology and leaf life span, stand age, planting density, and temperature. Our results have implications for designing afforestation and reforestation strategies and bridging experimental studies of biodiversity-ecosystem functioning relationships with real-world practices.}, } @article {pmid35587493, year = {2022}, author = {Tadmor-Levi, R and Borovski, T and Marcos-Hadad, E and Shapiro, J and Hulata, G and Golani, D and David, L}, title = {Establishing and using a genetic database for resolving identification of fish species in the Sea of Galilee, Israel.}, journal = {PloS one}, volume = {17}, number = {5}, pages = {e0267021}, pmid = {35587493}, issn = {1932-6203}, mesh = {Animals ; DNA ; *DNA Barcoding, Taxonomic ; Databases, Genetic ; Fishes/genetics ; *Fresh Water ; Israel ; Phylogeny ; }, abstract = {Freshwaters are a very valuable resource in arid areas, such as Mediterranean countries. Freshwater systems are vulnerable ecological habitats, significantly disturbed globally and especially in arid areas. The Sea of Galilee is the largest surface freshwater body in the Middle East. It is an isolated habitat supporting unique fish populations, including endemic species and populations on the edge of their distribution range. Using the Sea of Galilee for water supply, fishing and recreation has been placing pressure on these fish populations. Therefore, efficient monitoring and effective actions can make a difference in the conservation of these unique fish populations. To set a baseline and develop molecular tools to do so, in this study, DNA barcoding was used to establish a database of molecular species identification based on sequences of Cytochrome C Oxidase subunit I gene. DNA barcodes for 22 species were obtained and deposited in Barcode of Life Database. Among these, 12 barcodes for 10 species were new to the database and different from those already there. Barcode sequences were queried against the database and similar barcodes from the same and closely related species were obtained. Disagreements between morphological and molecular species identification were identified for five species, which were further studied by phylogenetic and genetic distances analyses. These analyses suggested the Sea of Galilee contained hybrid fish of some species and other species for which the species definition should be reconsidered. Notably, the cyprinid fish defined as Garra rufa, should be considered as Garra jordanica. Taken together, along with data supporting reconsideration of species definition, this study sets the basis for further using molecular tools for monitoring fish populations, understanding their ecology, and effectively managing their conservation in this unique and important habitat and in the region.}, } @article {pmid35585229, year = {2022}, author = {Łopucki, R and Klich, D and Kociuba, P}, title = {Detection of spatial avoidance between sousliks and moles by combining field observations, remote sensing and deep learning techniques.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {8264}, pmid = {35585229}, issn = {2045-2322}, mesh = {Animals ; *Deep Learning ; Ecosystem ; *Moles ; Remote Sensing Technology ; Sciuridae ; }, abstract = {Nowadays, remote sensing is being increasingly applied in ecology and conservation, and even underground animals can successfully be studied if they leave clear signs of their presence in the environment. In this work, by combining a field study, analysis of high-resolution aerial images, and machine learning techniques, we investigated the interspecies relationships of two small burrowing mammals: the spotted souslik Spermophilus suslicus and the European mole Talpa europaea. The study was conducted for 3 years (2018-2020) at a 105-ha grass airfield where both species coexist (Poland). Both field studies and the analysis of aerial imagery showed that, in the period of low population numbers, the souslik avoided coexistence with the European mole, and the presence of the mole was found to reduce the area of the habitat suitable for the souslik. The presence of other burrowing species may be an important element in the habitat selectivity of the souslik, but this has not yet been included in the conservation guidelines for this species. We discuss the contribution of our results to the knowledge of the ecology of burrowing mammals and their interspecies relationships. We also assess the possibility of using remote sensing and deep learning methods in ecology and conservation of small burrowing mammals.}, } @article {pmid35584207, year = {2022}, author = {Xue, W and Chen, B and Hong, D and Yu, J and Liu, G}, title = {Research on the Comprehensive Evaluation Method for the Automatic Recognition of Raman Spectrum under Multidimensional Constraint.}, journal = {Analytical chemistry}, volume = {94}, number = {21}, pages = {7628-7636}, doi = {10.1021/acs.analchem.2c00852}, pmid = {35584207}, issn = {1520-6882}, mesh = {*Algorithms ; Databases, Factual ; *Spectrum Analysis, Raman/methods ; }, abstract = {Raman spectrum contains abundant substance information with fingerprint characteristics. However, due to the huge variety of substances and their complex characteristic information, it is difficult to recognize the Raman spectrum accurately. Starting from dimensions like the Raman shift, the relative peak intensity, and the overall hit ratio of characteristic peaks, we extracted and recognized the characteristics in the Raman spectrum and analyzed these characteristics from local and global perspectives and then proposed a comprehensive evaluation method for the recognition of Raman spectrum on the basis of the data fusion of the recognition results under multidimensional constraint. Based on the common spectrum database of the normal Raman and surface-enhanced Raman of thousands of substances, we analyzed the performance of the evaluation method. It shows that even for the identification of spectra from instruments of low technical specifications, the automatic recognition rate of the sample can reach 98% and above, a great improvement compared with that of the common identification algorithms, which proves the effectiveness of the comprehensive evaluation method under multidimensional constraint.}, } @article {pmid35582905, year = {2022}, author = {Rodino, KG and Peaper, DR and Kelly, BJ and Bushman, F and Marques, A and Adhikari, H and Tu, ZJ and Marrero Rolon, R and Westblade, LF and Green, DA and Berry, GJ and Wu, F and Annavajhala, MK and Uhlemann, AC and Parikh, BA and McMillen, T and Jani, K and Babady, NE and Hahn, AM and Koch, RT and Grubaugh, ND and , and Rhoads, DD}, title = {Partial ORF1ab Gene Target Failure with Omicron BA.2.12.1.}, journal = {Journal of clinical microbiology}, volume = {60}, number = {6}, pages = {e0060022}, pmid = {35582905}, issn = {1098-660X}, support = {CDC BAA 200-2021-10986//HHS | Centers for Disease Control and Prevention (CDC)/ ; K23 AI121485/AI/NIAID NIH HHS/United States ; UL1 TR001863/TR/NCATS NIH HHS/United States ; 75D30120C09570//HHS | Centers for Disease Control and Prevention (CDC)/ ; P30 CA008748/CA/NCI NIH HHS/United States ; 75D30121C11102/000HCVL1-2021-55232//HHS | Centers for Disease Control and Prevention (CDC)/ ; R61 HL137063/HL/NHLBI NIH HHS/United States ; R01 AI140442/AI/NIAID NIH HHS/United States ; 75N93021C00015/AI/NIAID NIH HHS/United States ; L30 AI120149/AI/NIAID NIH HHS/United States ; R33 HL137063/HL/NHLBI NIH HHS/United States ; U01 DA053949/DA/NIDA NIH HHS/United States ; P30 AI045008/AI/NIAID NIH HHS/United States ; }, mesh = {Base Sequence ; *COVID-19 ; Humans ; Mutation ; *SARS-CoV-2/genetics ; }, abstract = {Mutations in the genome of SARS-CoV-2 can affect the performance of molecular diagnostic assays. In some cases, such as S-gene target failure, the impact can serve as a unique indicator of a particular SARS-CoV-2 variant and provide a method for rapid detection. Here, we describe partial ORF1ab gene target failure (pOGTF) on the cobas SARS-CoV-2 assays, defined by a ≥2-thermocycle delay in detection of the ORF1ab gene compared to that of the E-gene. We demonstrate that pOGTF is 98.6% sensitive and 99.9% specific for SARS-CoV-2 lineage BA.2.12.1, an emerging variant in the United States with spike L452Q and S704L mutations that may affect transmission, infectivity, and/or immune evasion. Increasing rates of pOGTF closely mirrored rates of BA.2.12.1 sequences uploaded to public databases, and, importantly, increasing local rates of pOGTF also mirrored increasing overall test positivity. Use of pOGTF as a proxy for BA.2.12.1 provides faster tracking of the variant than whole-genome sequencing and can benefit laboratories without sequencing capabilities.}, } @article {pmid35582795, year = {2022}, author = {Farrell, MJ and Brierley, L and Willoughby, A and Yates, A and Mideo, N}, title = {Past and future uses of text mining in ecology and evolution.}, journal = {Proceedings. Biological sciences}, volume = {289}, number = {1975}, pages = {20212721}, pmid = {35582795}, issn = {1471-2954}, support = {MR/T027355/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {*Data Mining ; Language ; Machine Learning ; *Natural Language Processing ; Reproducibility of Results ; }, abstract = {Ecology and evolutionary biology, like other scientific fields, are experiencing an exponential growth of academic manuscripts. As domain knowledge accumulates, scientists will need new computational approaches for identifying relevant literature to read and include in formal literature reviews and meta-analyses. Importantly, these approaches can also facilitate automated, large-scale data synthesis tasks and build structured databases from the information in the texts of primary journal articles, books, grey literature, and websites. The increasing availability of digital text, computational resources, and machine-learning based language models have led to a revolution in text analysis and natural language processing (NLP) in recent years. NLP has been widely adopted across the biomedical sciences but is rarely used in ecology and evolutionary biology. Applying computational tools from text mining and NLP will increase the efficiency of data synthesis, improve the reproducibility of literature reviews, formalize analyses of research biases and knowledge gaps, and promote data-driven discovery of patterns across ecology and evolutionary biology. Here we present recent use cases from ecology and evolution, and discuss future applications, limitations and ethical issues.}, } @article {pmid35582791, year = {2022}, author = {Roche, DG and Berberi, I and Dhane, F and Lauzon, F and Soeharjono, S and Dakin, R and Binning, SA}, title = {Slow improvement to the archiving quality of open datasets shared by researchers in ecology and evolution.}, journal = {Proceedings. Biological sciences}, volume = {289}, number = {1975}, pages = {20212780}, pmid = {35582791}, issn = {1471-2954}, mesh = {Data Accuracy ; Data Collection ; *Ecology ; Humans ; *Information Dissemination ; }, abstract = {Many leading journals in ecology and evolution now mandate open data upon publication. Yet, there is very little oversight to ensure the completeness and reusability of archived datasets, and we currently have a poor understanding of the factors associated with high-quality data sharing. We assessed 362 open datasets linked to first- or senior-authored papers published by 100 principal investigators (PIs) in the fields of ecology and evolution over a period of 7 years to identify predictors of data completeness and reusability (data archiving quality). Datasets scored low on these metrics: 56.4% were complete and 45.9% were reusable. Data reusability, but not completeness, was slightly higher for more recently archived datasets and PIs with less seniority. Journal open data policy, PI gender and PI corresponding author status were unrelated to data archiving quality. However, PI identity explained a large proportion of the variance in data completeness (27.8%) and reusability (22.0%), indicating consistent inter-individual differences in data sharing practices by PIs across time and contexts. Several PIs consistently shared data of either high or low archiving quality, but most PIs were inconsistent in how well they shared. One explanation for the high intra-individual variation we observed is that PIs often conduct research through students and postdoctoral researchers, who may be responsible for the data collection, curation and archiving. Levels of data literacy vary among trainees and PIs may not regularly perform quality control over archived files. Our findings suggest that research data management training and culture within a PI's group are likely to be more important determinants of data archiving quality than other factors such as a journal's open data policy. Greater incentives and training for individual researchers at all career stages could improve data sharing practices and enhance data transparency and reusability.}, } @article {pmid35576571, year = {2022}, author = {Wonkam, A and Munung, NS and Dandara, C and Esoh, KK and Hanchard, NA and Landoure, G}, title = {Five Priorities of African Genomics Research: The Next Frontier.}, journal = {Annual review of genomics and human genetics}, volume = {23}, number = {}, pages = {499-521}, doi = {10.1146/annurev-genom-111521-102452}, pmid = {35576571}, issn = {1545-293X}, support = {U01 HG009716/HG/NHGRI NIH HHS/United States ; U24 HL135600/HL/NHLBI NIH HHS/United States ; U01 MH127692/MH/NIMH NIH HHS/United States ; U54 HG009790/HG/NHGRI NIH HHS/United States ; U01 HG007044/HG/NHGRI NIH HHS/United States ; H3A/18/001/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Biological Evolution ; *Black People ; Computational Biology ; *Genomics ; Humans ; Pharmacogenetics ; }, abstract = {To embrace the prospects of accurately diagnosing thousands of monogenic conditions, predicting disease risks for complex traits or diseases, tailoring treatment to individuals' pharmacogenetic profiles, and potentially curing some diseases, research into African genomic variation is a scientific imperative. African genomes harbor millions of uncaptured variants accumulated over 300,000 years of modern humans' evolutionary history, with successive waves of admixture, migration, and natural selection combining with extensive ecological diversity to create a broad and exceptional genomic complexity. Harnessing African genomic complexity, therefore, will require sustained commitment and equitable collaboration from the scientific community and funding agencies. African governments must support academic public research and industrial partnerships that build the necessary genetic medicine workforce, utilize the emerging genomic big data to develop expertise in computer science and bioinformatics, and evolve national and globalgovernance frameworks that recognize the ethical implications of data-driven genomic research and empower its application in African social, cultural, economic, and religious contexts.}, } @article {pmid35576088, year = {2022}, author = {Schulz, S and Möllerke, A}, title = {MACE - An Open Access Data Repository of Mass Spectra for Chemical Ecology.}, journal = {Journal of chemical ecology}, volume = {48}, number = {7-8}, pages = {589-597}, pmid = {35576088}, issn = {1573-1561}, mesh = {*Access to Information ; Databases, Factual ; Gas Chromatography-Mass Spectrometry/methods ; Mass Spectrometry ; }, abstract = {MACE is an open access collection of electron impact (EI) mass spectra for coupled gas chromatography-mass spectrometry (GC/MS) that serves as an add-on database, comprising curated spectra not present in widely available commercial mass spectral libraries, such as the NIST or WILEY databases. The spectra are stored as text files that allow easy integration into individual GC/MS systems. The article describes the concept of MACE, the data structure, how to contribute, and its usage. MACE is designed as a community effort and will require contributions from the community to be successful.}, } @article {pmid35573805, year = {2022}, author = {Record, S and Jarzyna, MA and Hardiman, B and Richardson, AD}, title = {Open data facilitate resilience in science during the COVID-19 pandemic.}, journal = {Frontiers in ecology and the environment}, volume = {20}, number = {2}, pages = {76-77}, pmid = {35573805}, issn = {1540-9295}, } @article {pmid35569357, year = {2022}, author = {Proskuryakova, L}, title = {The interaction of environmental systems and human development in a time of wild cards. A big data enhanced foresight study.}, journal = {Journal of environmental management}, volume = {316}, number = {}, pages = {115169}, doi = {10.1016/j.jenvman.2022.115169}, pmid = {35569357}, issn = {1095-8630}, mesh = {*Big Data ; Climate Change ; Conservation of Natural Resources ; Economic Development ; *Ecosystem ; Humans ; }, abstract = {The article contributes to the research discussion around the human-natural and social-ecological systems by identification of a comprehensive list of global trends related to integrated interaction between environmental systems and human development, including climate change, pollution, new quality of economic growth, and challenges for education and healthcare. The foresight study behind it encompasses a combination of quantitative (big data) and qualitative (expert) methods. This approach allows for a systemic vision of structural shifts, assessing their probability and impact. The outcomes of the study include the list of global environmental and human development trends and factors classified by STEEPV categories, their effects that split into opportunities and threats, and an assessment of their inter-relation and mutual impact. Policy implications focus on possible areas of intervention for sustainable growth.}, } @article {pmid35568273, year = {2022}, author = {Ruz, GA and Ashlock, D and Allmendinger, R and Fogel, GB}, title = {Editorial: 2020 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology (IEEE CIBCB 2020).}, journal = {Bio Systems}, volume = {218}, number = {}, pages = {104698}, doi = {10.1016/j.biosystems.2022.104698}, pmid = {35568273}, issn = {1872-8324}, mesh = {*Artificial Intelligence ; *Computational Biology ; }, } @article {pmid35565046, year = {2022}, author = {da Silva Paiva, L and de Alcantara Sousa, LV and Oliveira, FR and de Carvalho, LEW and Raimundo, RD and Correa, JA and de Abreu, LC and Adami, F}, title = {Temporal Trend of the Prevalence of Modifiable Risk Factors of Stroke: An Ecological Study of Brazilians between 2006 and 2012.}, journal = {International journal of environmental research and public health}, volume = {19}, number = {9}, pages = {}, pmid = {35565046}, issn = {1660-4601}, mesh = {Brazil/epidemiology ; *Diabetes Mellitus/epidemiology ; Humans ; *Hypertension/epidemiology ; Obesity/epidemiology ; Overweight/epidemiology ; Prevalence ; Risk Factors ; *Stroke/epidemiology ; }, abstract = {Stroke is one of the leading causes of death worldwide, including in Brazil. This study aimed to analyze the temporal trend of the prevalence of modifiable risk factors of stroke from 2006 to 2012. This ecological study was conducted by secondary analysis in May 2018, using data from the surveillance of risk factors and protection for chronic diseases by telephone inquiry (VIGITEL) available in the Department of Informatics of the Unified Health System (DATASUS). The modifiable risk factors of stroke in Brazilians were systemic arterial hypertension, diabetes mellitus, abusive alcohol consumption, overweight, and obesity. Overall, there was a significant increase in the risk factors of diabetes (β = 0.30, P = 0.001, r2 = 0.99), overweight (β = 0.50, P = 0.002, r2 = 0.98), and obesity (β = 0.88, P < 0.001, r2 = 0.96). However, there was a stability in the prevalence of hypertension (β = 0.25, P = 0.320, r2 = 0.88) and alcohol abuse (β = 0.32, P = 0.116, r2 = 0.49). There was an increase in the prevalence of diabetes mellitus, overweight, and obesity, but stability in systemic arterial hypertension and abusive alcohol consumption in the Brazilian population.}, } @article {pmid35564957, year = {2022}, author = {Wang, T and Yang, Z and Chen, X and Han, F}, title = {Bibliometric Analysis and Literature Review of Tourism Destination Resilience Research.}, journal = {International journal of environmental research and public health}, volume = {19}, number = {9}, pages = {}, pmid = {35564957}, issn = {1660-4601}, mesh = {*Bibliometrics ; Databases, Factual ; Forecasting ; Publications ; *Tourism ; United States ; }, abstract = {The application of resilience thinking to tourism destination research is a new perspective on sustainable tourism and has gradually become a popular research topic. Some literature has been conducted on tourism destination resilience, but there has not been a comprehensive review and analysis of the whole field. This study was based on the literature from 2000 to 2021 in the Web of Science core collection database. The collaboration analysis, literature co-citation analysis, keyword co-occurrence, burst detection analysis in CiteSpace, and qualitative analysis were adopted to conduct a holistic tourism destination resilience research review. The results indicated that the United States, Australia, China, and the United Kingdom were the primary countries involved in tourism destination resilience research. Five hot research themes were obtained. (1) concept and connotation of tourism destination resilience, (2) drivers of tourism destination resilience, (3) sustainable management framework and practices, (4) perception of tourism destination resilience, and (5) the resilience of the tourism community. Furthermore, four research gaps and future directions were proposed in this study, including the theoretical framework of tourism destination resilience, assessment of tourism destination resilience, sustainable management and resilience, and application of advanced technology in tourism destination resilience. This study assists researchers in understanding the development and future research directions in tourism destination resilience research.}, } @article {pmid35564261, year = {2022}, author = {Nozdrenko, D and Prylutska, S and Bogutska, K and Cherepanov, V and Senenko, A and Vygovska, O and Khrapatyi, S and Ritter, U and Prylutskyy, Y and Piosik, J}, title = {Analysis of Biomechanical and Biochemical Markers of Rat Muscle Soleus Fatigue Processes Development during Long-Term Use of C60 Fullerene and N-Acetylcysteine.}, journal = {Nanomaterials (Basel, Switzerland)}, volume = {12}, number = {9}, pages = {}, pmid = {35564261}, issn = {2079-4991}, abstract = {The development of an effective therapy aimed at restoring muscle dysfunctions in clinical and sports medicine, as well as optimizing working activity in general remains an urgent task today. Modern nanobiotechnologies are able to solve many clinical and social health problems, in particular, they offer new therapeutic approaches using biocompatible and bioavailable nanostructures with specific bioactivity. Therefore, the nanosized carbon molecule, C60 fullerene, as a powerful antioxidant, is very attractive. In this study, a comparative analysis of the dynamic of muscle soleus fatigue processes in rats was conducted using 50 Hz stimulation for 5 s with three consistent pools after intraperitoneal administration of the following antioxidants: C60 fullerene (a daily dose of 1 mg/kg one hour prior to the start of the experiment) and N-acetylcysteine (NAC; a daily dose of 150 mg/kg one hour prior to the start of the experiment) during five days. Changes in the integrated power of muscle contraction, levels of the maximum and minimum contraction force generation, time of reduction of the contraction force by 50% of its maximum value, achievement of the maximum force response, and delay of the beginning of a single contraction force response were analyzed as biomechanical markers of fatigue processes. Levels of creatinine, creatine phosphokinase, lactate, and lactate dehydrogenase, as well as pro- and antioxidant balance (thiobarbituric acid reactive substances, hydrogen peroxide, reduced glutathione, and catalase activity) in the blood of rats were analyzed as biochemical markers of fatigue processes. The obtained data indicate that applied therapeutic drugs have the most significant effects on the 2nd and especially the 3rd stimulation pools. Thus, the application of C60 fullerene has a (50-80)% stronger effect on the resumption of muscle biomechanics after the beginning of fatigue than NAC on the first day of the experiment. There is a clear trend toward a positive change in all studied biochemical parameters by about (12-15)% after therapeutic administration of NAC and by (20-25)% after using C60 fullerene throughout the experiment. These findings demonstrate the promise of using C60 fullerenes as potential therapeutic nanoagents that can reduce or adjust the pathological conditions of the muscular system that occur during fatigue processes in skeletal muscles.}, } @article {pmid35560159, year = {2022}, author = {Reijnders, MJMF and Waterhouse, RM}, title = {CrowdGO: Machine learning and semantic similarity guided consensus Gene Ontology annotation.}, journal = {PLoS computational biology}, volume = {18}, number = {5}, pages = {e1010075}, pmid = {35560159}, issn = {1553-7358}, mesh = {*Computational Biology/methods ; Consensus ; Gene Ontology ; Machine Learning ; Molecular Sequence Annotation ; *Semantics ; }, abstract = {Characterising gene function for the ever-increasing number and diversity of species with annotated genomes relies almost entirely on computational prediction methods. These software are also numerous and diverse, each with different strengths and weaknesses as revealed through community benchmarking efforts. Meta-predictors that assess consensus and conflict from individual algorithms should deliver enhanced functional annotations. To exploit the benefits of meta-approaches, we developed CrowdGO, an open-source consensus-based Gene Ontology (GO) term meta-predictor that employs machine learning models with GO term semantic similarities and information contents. By re-evaluating each gene-term annotation, a consensus dataset is produced with high-scoring confident annotations and low-scoring rejected annotations. Applying CrowdGO to results from a deep learning-based, a sequence similarity-based, and two protein domain-based methods, delivers consensus annotations with improved precision and recall. Furthermore, using standard evaluation measures CrowdGO performance matches that of the community's best performing individual methods. CrowdGO therefore offers a model-informed approach to leverage strengths of individual predictors and produce comprehensive and accurate gene functional annotations.}, } @article {pmid35560102, year = {2023}, author = {Li, J and Dong, Z and Lu, S and Wang, SJ and Yan, WJ and Ma, Y and Liu, Y and Huang, C and Fu, X}, title = {CAS(ME)[3]: A Third Generation Facial Spontaneous Micro-Expression Database With Depth Information and High Ecological Validity.}, journal = {IEEE transactions on pattern analysis and machine intelligence}, volume = {45}, number = {3}, pages = {2782-2800}, doi = {10.1109/TPAMI.2022.3174895}, pmid = {35560102}, issn = {1939-3539}, mesh = {Female ; Humans ; Male ; Young Adult ; Algorithms ; Bias ; *Databases, Factual/standards ; Datasets as Topic/standards ; *Emotions ; *Facial Expression ; Photic Stimulation ; Reproducibility of Results ; Sample Size ; Supervised Machine Learning/standards ; Video Recording ; Visual Perception ; }, abstract = {Micro-expression (ME) is a significant non-verbal communication clue that reveals one person's genuine emotional state. The development of micro-expression analysis (MEA) has just gained attention in the last decade. However, the small sample size problem constrains the use of deep learning on MEA. Besides, ME samples distribute in six different databases, leading to database bias. Moreover, the ME database development is complicated. In this article, we introduce a large-scale spontaneous ME database: CAS(ME) [3]. The contribution of this article is summarized as follows: (1) CAS(ME) [3] offers around 80 hours of videos with over 8,000,000 frames, including manually labeled 1,109 MEs and 3,490 macro-expressions. Such a large sample size allows effective MEA method validation while avoiding database bias. (2) Inspired by psychological experiments, CAS(ME) [3] provides the depth information as an additional modality unprecedentedly, contributing to multi-modal MEA. (3) For the first time, CAS(ME) [3] elicits ME with high ecological validity using the mock crime paradigm, along with physiological and voice signals, contributing to practical MEA. (4) Besides, CAS(ME) [3] provides 1,508 unlabeled videos with more than 4,000,000 frames, i.e., a data platform for unsupervised MEA methods. (5) Finally, we demonstrate the effectiveness of depth information by the proposed depth flow algorithm and RGB-D information.}, } @article {pmid35554909, year = {2022}, author = {Khan, MS and Yousafi, Q and Bibi, S and Azhar, M and Ihsan, A}, title = {Bioinformatics-Based Approaches to Study Virus-Host Interactions During SARS-CoV-2 Infection.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2452}, number = {}, pages = {197-212}, pmid = {35554909}, issn = {1940-6029}, mesh = {*COVID-19 ; Computational Biology ; Host Microbial Interactions ; Host-Pathogen Interactions/genetics ; Humans ; Proteins ; SARS-CoV-2/genetics ; }, abstract = {As the knowledge of biomolecules is increasing from the last decades, it is helping the researchers to understand the unsolved issues regarding virology. Recent technologies in high-throughput sequencing are providing the swift generation of SARS-CoV-2 genomic data with the basic inside of viral infection. Owing to various virus-host protein interactions, high-throughput technologies are unable to provide complete details of viral pathogenesis. Identifying the virus-host protein interactions using bioinformatics approaches can assist in understanding the mechanism of SARS-CoV-2 infection and pathogenesis. In this chapter, recent integrative bioinformatics approaches are discussed to help the virologists and computational biologists in the identification of structurally similar proteins of human and SARS-CoV-2 virus, and to predict the potential of virus-host interactions. Considering experimental and time limitations for effective viral drug development, computational aided drug design (CADD) can reduce the gap between drug prediction and development. More research with respect to evolutionary solutions could be helpful to make a new pipeline for virus-host protein-protein interactions and provide more understanding to disclose the cases of host switch, and also expand the virulence of the pathogen and host range in developing viral infections.}, } @article {pmid35552640, year = {2022}, author = {Qin, D and Bo, W and Zheng, X and Hao, Y and Li, B and Zheng, J and Liang, G}, title = {DFBP: a comprehensive database of food-derived bioactive peptides for peptidomics research.}, journal = {Bioinformatics (Oxford, England)}, volume = {38}, number = {12}, pages = {3275-3280}, doi = {10.1093/bioinformatics/btac323}, pmid = {35552640}, issn = {1367-4811}, support = {32172196//National Natural Science Foundation of China/ ; 2107619//NSF/ ; //Faculty Research Fellowship from the University of Akron/ ; CSTC2019JCYJ-MSXMX0527//Natural Science Foundation of Chongqing/ ; }, mesh = {*Peptides/chemistry ; Databases, Factual ; Structure-Activity Relationship ; }, abstract = {MOTIVATION: Food-derived bioactive peptides (FBPs) have demonstrated their significance in pharmaceuticals, diets and nutraceuticals, benefiting public health and global ecology. While significant efforts have been made to discover FBPs and to elucidate the underlying bioactivity mechanisms, there is lack of a systemic study of sequence-structure-activity relationship of FBPs in a large dataset.

RESULTS: Here, we construct a database of food-derived bioactive peptides (DFBP), containing a total of 6276 peptide entries in 31 types from different sources. Further, we develop a series of analysis tools for function discovery/repurposing, traceability, multifunctional bioactive exploration and physiochemical property assessment of peptides. Finally, we apply this database and data-mining techniques to discover new FBPs as potential drugs for cardiovascular diseases. The DFBP serves as a useful platform for not only the fundamental understanding of sequence-structure-activity of FBPs but also the design, discovery, and repurposing of peptide-based drugs, vaccines, materials and food ingredients.

DFBP service can be accessed freely via http://www.cqudfbp.net/. All data are incorporated into the article and its online supplementary material.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, } @article {pmid35549599, year = {2023}, author = {Truong, M and Yeganeh, L and Cartwright, A and Ward, E and Ibrahim, J and Cuschieri, D and Dawson, M and Bugeja, L}, title = {Domestic/Family Homicide: A Systematic Review of Empirical Evidence.}, journal = {Trauma, violence & abuse}, volume = {24}, number = {3}, pages = {1908-1928}, doi = {10.1177/15248380221082084}, pmid = {35549599}, issn = {1552-8324}, mesh = {Humans ; United States ; *Homicide ; Risk Factors ; Sexual Partners ; Databases, Factual ; Protective Factors ; *Intimate Partner Violence ; }, abstract = {BACKGROUND: Domestic/family homicide (D/FH) is a global social, economic and public health problem. To date, the research studies into risk factors associated with D/FH has largely focused on intimate partner homicide (IPH). A more contemporary approach recognizes that D/FH extends beyond the intimate partner relationship. This systematic review sought to identify and quantify the individual, relationship, community and societal factors in the empirical evidence literature on D/FH.

METHODS: Eight electronic databases were searched from January 1999 to December 2020. Published journal articles on studies of D/FH were included if the study included victims and/or perpetrator of D/FH, reported risk and/or protective factors associated with D/FH, reported primary data and was published in English. Factors were descriptively synthesized by the categories of the social ecological model and D/FH sub-type.

RESULTS: Three hundred and forty published articles met the inclusion criteria. From 1999 to 2020 the number of articles on D/FH increased globally from 10 to 40 respectively, declining to 23 in 2020. Almost half of the articles examined populations located in the Americas (160, 47.1%), predominately the United States and the majority of articles used quantitative designs (277, 81.5%). The forms of homicide more commonly studied were intimate partner (171, 50.3%), and filicide (98, 28.8%). Approximately 90% of articles reported individual victim and perpetrator factors, 64.7% examined relationship factors, 17.9% examined community factors and 15.6% examined societal factors.

CONCLUSION: To inform universal and targeted D/FH elimination and prevention strategies, more research across different regions and a greater emphasis on community and societal-level factors is needed.}, } @article {pmid35549363, year = {2023}, author = {Wylie, MS and Colasante, T and De France, K and Lin, L and Hollenstein, T}, title = {Momentary emotion regulation strategy use and success: Testing the influences of emotion intensity and habitual strategy use.}, journal = {Emotion (Washington, D.C.)}, volume = {23}, number = {2}, pages = {375-386}, doi = {10.1037/emo0001074}, pmid = {35549363}, issn = {1931-1516}, support = {//Natural Sciences and Engineering Research Council/ ; }, mesh = {Humans ; Female ; Young Adult ; Adult ; Male ; *Emotional Regulation/physiology ; Emotions/physiology ; Ecological Momentary Assessment ; Data Management ; }, abstract = {Successful emotion regulation (ER) is important for a wide range of psychosocial outcomes. Specific ER strategies have been identified as being more or less likely to be successful. However, recent evidence suggests significant individual differences in the association between strategy implementation and ER success. Indeed, 2 key factors may play an important role in moderating the link between ER strategy use and ER success in the moment: (a) the intensity of the specific emotional experience, and (b) the relative frequency in using a given ER strategy. Experience-sampling across 14-days (N = 304, Mage = 19.14, % female = 87.5) was used to assess whether emotion intensity and trait ER strategy use were differentially associated with perceived regulatory success depending on which ER strategy was used. Multilevel modeling revealed that more intense emotions were associated with lower perceived success for all strategies. Additionally, habitual reappraisal predicted greater success and habitual rumination predicted lower success. We discuss the possibility that results reflected intensity-based ER strategy choices and add to the growing call to abandon the reductive labeling of ER strategies as either "adaptive" or "maladaptive." (PsycInfo Database Record (c) 2023 APA, all rights reserved).}, } @article {pmid35544870, year = {2022}, author = {Aragão, CMC and Mascarenhas, MDM}, title = {Temporal trend of adolescent intentional self-harm notifications in the school environment, Brazil, 2011-2018.}, journal = {Epidemiologia e servicos de saude : revista do Sistema Unico de Saude do Brasil}, volume = {31}, number = {1}, pages = {e2021820}, doi = {10.1590/S1679-49742022000100028}, pmid = {35544870}, issn = {2237-9622}, mesh = {Adolescent ; Brazil/epidemiology ; Female ; Humans ; Information Systems ; Linear Models ; Male ; Schools ; *Self-Injurious Behavior/epidemiology ; }, abstract = {OBJECTIVE: To analyze the trend of adolescent intentional self-harm notifications in the school environment, Brazil, 2011 to 2018.

METHODS: This was an ecological time series study, with data from the Notifiable Health Conditions Information System, using the Prais-Winsten linear regression model.

RESULTS: A total of 1,989 cases were notified. Notification rates ranged from 0.09 to 2.75/100,000 inhabitants, with an increasing trend, both in females (APC= 66.0%; 95%CI 39.0;98.3) and male (APC = 55.2%; 95%CI 29.9;85.4). The North region showed a stationary trend, while the Southeast and South regions showed an increasing trend, especially Rio de Janeiro (APC = 85.5%; 95%CI 58.0;117.8) and Paraná (APC = 73.6%; 95%CI 41.9;112.3). In the Midwest region, only the state of Mato Grosso do Sul showed a rising trend (APC = 54.5%; 95%CI 16.9;104.2).

CONCLUSION: There was an increasing trend in adolescent intentional self-harm notifications in the school environment in Brazil, during the study period.}, } @article {pmid35544285, year = {2022}, author = {Kieft, K and Adams, A and Salamzade, R and Kalan, L and Anantharaman, K}, title = {vRhyme enables binning of viral genomes from metagenomes.}, journal = {Nucleic acids research}, volume = {50}, number = {14}, pages = {e83}, pmid = {35544285}, issn = {1362-4962}, support = {R35 GM137828/GM/NIGMS NIH HHS/United States ; R35 GM143024/GM/NIGMS NIH HHS/United States ; T15 LM007359/LM/NLM NIH HHS/United States ; U19 AI142720/AI/NIAID NIH HHS/United States ; }, mesh = {*Genome, Viral ; High-Throughput Nucleotide Sequencing ; Humans ; *Metagenome ; Metagenomics ; Sequence Analysis, DNA ; Software ; }, abstract = {Genome binning has been essential for characterization of bacteria, archaea, and even eukaryotes from metagenomes. Yet, few approaches exist for viruses. We developed vRhyme, a fast and precise software for construction of viral metagenome-assembled genomes (vMAGs). vRhyme utilizes single- or multi-sample coverage effect size comparisons between scaffolds and employs supervised machine learning to identify nucleotide feature similarities, which are compiled into iterations of weighted networks and refined bins. To refine bins, vRhyme utilizes unique features of viral genomes, namely a protein redundancy scoring mechanism based on the observation that viruses seldom encode redundant genes. Using simulated viromes, we displayed superior performance of vRhyme compared to available binning tools in constructing more complete and uncontaminated vMAGs. When applied to 10,601 viral scaffolds from human skin, vRhyme advanced our understanding of resident viruses, highlighted by identification of a Herelleviridae vMAG comprised of 22 scaffolds, and another vMAG encoding a nitrate reductase metabolic gene, representing near-complete genomes post-binning. vRhyme will enable a convention of binning uncultivated viral genomes and has the potential to transform metagenome-based viral ecology.}, } @article {pmid35537509, year = {2022}, author = {Xu, N and Zhang, Z and Shen, Y and Zhang, Q and Liu, Z and Yu, Y and Wang, Y and Lei, C and Ke, M and Qiu, D and Lu, T and Chen, Y and Xiong, J and Qian, H}, title = {Compare the performance of multiple binary classification models in microbial high-throughput sequencing datasets.}, journal = {The Science of the total environment}, volume = {837}, number = {}, pages = {155807}, doi = {10.1016/j.scitotenv.2022.155807}, pmid = {35537509}, issn = {1879-1026}, mesh = {Algorithms ; *Artificial Intelligence ; High-Throughput Nucleotide Sequencing ; Machine Learning ; *Neural Networks, Computer ; Support Vector Machine ; }, abstract = {The development of machine learning and deep learning provided solutions for predicting microbiota response on environmental change based on microbial high-throughput sequencing. However, there were few studies specifically clarifying the performance and practical of two types of binary classification models to find a better algorithm for the microbiota data analysis. Here, for the first time, we evaluated the performance, accuracy and running time of the binary classification models built by three machine learning methods - random forest (RF), support vector machine (SVM), logistic regression (LR), and one deep learning method - back propagation neural network (BPNN). The built models were based on the microbiota datasets that removed low-quality variables and solved the class imbalance problem. Additionally, we optimized the models by tuning. Our study demonstrated that dataset pre-processing was a necessary process for model construction. Among these 4 binary classification models, BPNN and RF were the most suitable methods for constructing microbiota binary classification models. Using these 4 models to predict multiple microbial datasets, BPNN showed the highest accuracy and the most robust performance, while the RF method was ranked second. We also constructed the optimal models by adjusting the epochs of BPNN and the n_estimators of RF for six times. The evaluation related to performances of models provided a road map for the application of artificial intelligence to assess microbial ecology.}, } @article {pmid35535680, year = {2022}, author = {Engelhardt, EK and Biber, MF and Dolek, M and Fartmann, T and Hochkirch, A and Leidinger, J and Löffler, F and Pinkert, S and Poniatowski, D and Voith, J and Winterholler, M and Zeuss, D and Bowler, DE and Hof, C}, title = {Consistent signals of a warming climate in occupancy changes of three insect taxa over 40 years in central Europe.}, journal = {Global change biology}, volume = {28}, number = {13}, pages = {3998-4012}, doi = {10.1111/gcb.16200}, pmid = {35535680}, issn = {1365-2486}, mesh = {Animals ; Biodiversity ; *Butterflies ; Climate ; Climate Change ; Ecosystem ; Europe ; *Odonata ; }, abstract = {Recent climate and land-use changes are having substantial impacts on biodiversity, including population declines, range shifts, and changes in community composition. However, few studies have compared these impacts among multiple taxa, particularly because of a lack of standardized time series data over long periods. Existing data sets are typically of low resolution or poor coverage, both spatially and temporally, thereby limiting the inferences that can be drawn from such studies. Here, we compare climate and land-use driven occupancy changes in butterflies, grasshoppers, and dragonflies using an extensive data set of highly heterogeneous observation data collected in the central European region of Bavaria (Germany) over a 40-year period. Using occupancy models, we find occupancies (the proportion of sites occupied by a species in each year) of 37% of species have decreased, 30% have increased and 33% showed no significant trend. Butterflies and grasshoppers show strongest declines with 41% of species each. By contrast, 52% of dragonfly species increased. Temperature preference and habitat specificity appear as significant drivers of species trends. We show that cold-adapted species across all taxa have declined, whereas warm-adapted species have increased. In butterflies, habitat specialists have decreased, while generalists increased or remained stable. The trends of habitat generalists and specialists both in grasshoppers and semi-aquatic dragonflies, however did not differ. Our findings indicate strong and consistent effects of climate warming across insect taxa. The decrease of butterfly specialists could hint towards a threat from land-use change, as especially butterfly specialists' occurrence depends mostly on habitat quality and area. Our study not only illustrates how these taxa showed differing trends in the past but also provides hints on how we might mitigate the detrimental effects of human development on their diversity in the future.}, } @article {pmid35534559, year = {2022}, author = {Howe, LJ and Nivard, MG and Morris, TT and Hansen, AF and Rasheed, H and Cho, Y and Chittoor, G and Ahlskog, R and Lind, PA and Palviainen, T and van der Zee, MD and Cheesman, R and Mangino, M and Wang, Y and Li, S and Klaric, L and Ratliff, SM and Bielak, LF and Nygaard, M and Giannelis, A and Willoughby, EA and Reynolds, CA and Balbona, JV and Andreassen, OA and Ask, H and Baras, A and Bauer, CR and Boomsma, DI and Campbell, A and Campbell, H and Chen, Z and Christofidou, P and Corfield, E and Dahm, CC and Dokuru, DR and Evans, LM and de Geus, EJC and Giddaluru, S and Gordon, SD and Harden, KP and Hill, WD and Hughes, A and Kerr, SM and Kim, Y and Kweon, H and Latvala, A and Lawlor, DA and Li, L and Lin, K and Magnus, P and Magnusson, PKE and Mallard, TT and Martikainen, P and Mills, MC and Njølstad, PR and Overton, JD and Pedersen, NL and Porteous, DJ and Reid, J and Silventoinen, K and Southey, MC and Stoltenberg, C and Tucker-Drob, EM and Wright, MJ and , and , and Hewitt, JK and Keller, MC and Stallings, MC and Lee, JJ and Christensen, K and Kardia, SLR and Peyser, PA and Smith, JA and Wilson, JF and Hopper, JL and Hägg, S and Spector, TD and Pingault, JB and Plomin, R and Havdahl, A and Bartels, M and Martin, NG and Oskarsson, S and Justice, AE and Millwood, IY and Hveem, K and Naess, Ø and Willer, CJ and Åsvold, BO and Koellinger, PD and Kaprio, J and Medland, SE and Walters, RG and Benjamin, DJ and Turley, P and Evans, DM and Davey Smith, G and Hayward, C and Brumpton, B and Hemani, G and Davies, NM}, title = {Within-sibship genome-wide association analyses decrease bias in estimates of direct genetic effects.}, journal = {Nature genetics}, volume = {54}, number = {5}, pages = {581-592}, pmid = {35534559}, issn = {1546-1718}, support = {MC_UU_00011/6/MRC_/Medical Research Council/United Kingdom ; R01 HL109946/HL/NHLBI NIH HHS/United States ; MR/T030852/1/MRC_/Medical Research Council/United Kingdom ; MC_UU_12026/2/MRC_/Medical Research Council/United Kingdom ; 208806/Z/17/Z/WT_/Wellcome Trust/United Kingdom ; MC_UU_00017/1/MRC_/Medical Research Council/United Kingdom ; MC_U137686851/MRC_/Medical Research Council/United Kingdom ; MC_UU_00007/10/MRC_/Medical Research Council/United Kingdom ; MC_PC_13049/MRC_/Medical Research Council/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; MC_PC_14135/MRC_/Medical Research Council/United Kingdom ; R01 AG042568/AG/NIA NIH HHS/United States ; MC_UU_00011/1/MRC_/Medical Research Council/United Kingdom ; R24 AG065184/AG/NIA NIH HHS/United States ; 212946/Z/18/Z/WT_/Wellcome Trust/United Kingdom ; MR/R026408/1/MRC_/Medical Research Council/United Kingdom ; P2C HD042849/HD/NICHD NIH HHS/United States ; R56 AG042568/AG/NIA NIH HHS/United States ; }, mesh = {*Genome-Wide Association Study ; Humans ; Mendelian Randomization Analysis ; Multifactorial Inheritance/genetics ; Phenotype ; *Polymorphism, Single Nucleotide/genetics ; }, abstract = {Estimates from genome-wide association studies (GWAS) of unrelated individuals capture effects of inherited variation (direct effects), demography (population stratification, assortative mating) and relatives (indirect genetic effects). Family-based GWAS designs can control for demographic and indirect genetic effects, but large-scale family datasets have been lacking. We combined data from 178,086 siblings from 19 cohorts to generate population (between-family) and within-sibship (within-family) GWAS estimates for 25 phenotypes. Within-sibship GWAS estimates were smaller than population estimates for height, educational attainment, age at first birth, number of children, cognitive ability, depressive symptoms and smoking. Some differences were observed in downstream SNP heritability, genetic correlations and Mendelian randomization analyses. For example, the within-sibship genetic correlation between educational attainment and body mass index attenuated towards zero. In contrast, analyses of most molecular phenotypes (for example, low-density lipoprotein-cholesterol) were generally consistent. We also found within-sibship evidence of polygenic adaptation on taller height. Here, we illustrate the importance of family-based GWAS data for phenotypes influenced by demographic and indirect genetic effects.}, } @article {pmid35533868, year = {2022}, author = {Lencioni, V and Stella, E and Zanoni, MG and Bellin, A}, title = {On the delay between water temperature and invertebrate community response to warming climate.}, journal = {The Science of the total environment}, volume = {837}, number = {}, pages = {155759}, doi = {10.1016/j.scitotenv.2022.155759}, pmid = {35533868}, issn = {1879-1026}, mesh = {Animals ; Climate ; Climate Change ; Ecosystem ; Ice Cover ; *Invertebrates ; Rivers ; Temperature ; *Water ; }, abstract = {We evaluated the effect of global warming on invertebrate communities at high altitudes using data from the Careser system. We procured data on air temperature, which was obtained over 50 years at altitudes above 2600 m a.s.l., and data on water temperature, which was available for approximately 30 years. We sampled thrice in the past 20 years (2001, 2014, 2018) at three sampling sites (CR0-metakryal, CR1-hypokryal, CR2-glacio-rhithral) of the Careser glacier-fed stream and its main non-glacial tributary (CR1bis-krenal). Warmer climates were observed in the last decade compared to the 1980s, with a mean maximum summer air temperature (mTmax) increase of 1.7 °C at 2642 m a.s.l. and 1.8 °C at 2858 m a.s.l. Compared to air temperatures, the rise in water temperature was delayed by approximately 20 years; water mTmax started to increase in 2003, reaching 8.1 °C at 2642 m a.s.l. and 2.4 °C at 2858 m a.s.l in the year 2020. The invertebrate community exhibited a delayed response approximately 13 years from the water warming; there was a sequential increase in the number of taxa, Shannon diversity, and after 17 years, functional diversity. In the kryal sites, taxonomical and functional diversity changed more consistently than in the glacio-rhithral site in the same period, due to the arrival of taxa that were previously absent upstream and bearers of entirely new traits. Progressive taxonomical homogenisation was evident with decreasing glacial influence, mainly between glacio-rhithral and krenal sites. The numbers of Diamesa steinboecki, an insect that was adapted to the cold, declined in summer (water mTmax >6 °C and air mTmax >12 °C). This study highlights the mode and time of response of stream invertebrate communities to global warming in alpine streams and provides guidelines for analysing changes in the stream invertebrate communities of other glacial systems in alpine regions.}, } @article {pmid35531376, year = {2022}, author = {Relph, KA and Russell, CD and Fairfield, CJ and Turtle, L and de Silva, TI and Siggins, MK and Drake, TM and Thwaites, RS and Abrams, S and Moore, SC and Hardwick, HE and Oosthuyzen, W and Harrison, EM and Docherty, AB and Openshaw, PJM and Baillie, JK and Semple, MG and Ho, A and , }, title = {Procalcitonin Is Not a Reliable Biomarker of Bacterial Coinfection in People With Coronavirus Disease 2019 Undergoing Microbiological Investigation at the Time of Hospital Admission.}, journal = {Open forum infectious diseases}, volume = {9}, number = {5}, pages = {ofac179}, pmid = {35531376}, issn = {2328-8957}, support = {MC_PC_19026/MRC_/Medical Research Council/United Kingdom ; 205228/Z/16/Z/WT_/Wellcome Trust/United Kingdom ; MC_PC_19059/MRC_/Medical Research Council/United Kingdom ; MR/S032304/1/MRC_/Medical Research Council/United Kingdom ; MC_PC_19025/MRC_/Medical Research Council/United Kingdom ; }, abstract = {Admission procalcitonin measurements and microbiology results were available for 1040 hospitalized adults with coronavirus disease 2019 (from 48 902 included in the International Severe Acute Respiratory and Emerging Infections Consortium World Health Organization Clinical Characterisation Protocol UK study). Although procalcitonin was higher in bacterial coinfection, this was neither clinically significant (median [IQR], 0.33 [0.11-1.70] ng/mL vs 0.24 [0.10-0.90] ng/mL) nor diagnostically useful (area under the receiver operating characteristic curve, 0.56 [95% confidence interval, .51-.60]).}, } @article {pmid35526396, year = {2022}, author = {Coolen, JWP and Vanaverbeke, J and Dannheim, J and Garcia, C and Birchenough, SNR and Krone, R and Beermann, J}, title = {Generalized changes of benthic communities after construction of wind farms in the southern North Sea.}, journal = {Journal of environmental management}, volume = {315}, number = {}, pages = {115173}, doi = {10.1016/j.jenvman.2022.115173}, pmid = {35526396}, issn = {1095-8630}, mesh = {Biodiversity ; *Energy-Generating Resources ; Farms ; Humans ; North Sea ; *Wind ; }, abstract = {Over the last years, the development of offshore renewable energy installations such as offshore wind farms led to an increasing number of man-made structures in marine environments. Since 2009, benthic impact monitoring programs were carried out in wind farms installed in the southern North Sea. We collated and analyzed data sets from three major monitoring programs. Our analysis considered a total of 2849 sampling points converted to a set of biodiversity response metrics. We analyzed biodiversity changes related to the implementation of offshore wind farms and generalized the correlation of these changes with spatial and temporal patterns. Our results demonstrate that depth, season and distance to structure (soft-bottom community) consistently determined diversity indicators and abundance parameters, whereas the age and the country affiliation were significantly related to some but not all indices. The water depth was the most important structuring factor for fouling communities while seasonal effects were driving most of the observed changes in soft-sediment communities. We demonstrate that a meta-analysis can provide an improved level of understanding of ecological patterns on large-scale effects of anthropogenic structures on marine biodiversity, which were not visible in single monitoring studies. We believe that meta-analyses should become an indispensable tool for management of offshore wind farm effects in the future, particularly in the view of the foreseen development of offshore renewable energies. This might lead to a better picture and more comprehensive view on potential alterations. However, this requires a modern open-source data policy and data management, across institutions and across national borders.}, } @article {pmid35525040, year = {2022}, author = {Luo, J and Sun, Z and Lu, L and Xiong, Z and Cui, L and Mao, Z}, title = {Rapid expansion of coastal aquaculture ponds in Southeast Asia: Patterns, drivers and impacts.}, journal = {Journal of environmental management}, volume = {315}, number = {}, pages = {115100}, doi = {10.1016/j.jenvman.2022.115100}, pmid = {35525040}, issn = {1095-8630}, mesh = {Aquaculture ; Asia, Southeastern ; *Ecosystem ; Geographic Information Systems ; *Ponds ; }, abstract = {Aquaculture pond is one of the most important land use types and a main income source in coastal zones in Southeast Asia. However, the fast expansion of aquaculture ponds threatens coastal ecosystems - an issue that Sustainable Development Goals (SDGs)14 seeks to address. Investigating expansion patterns is essential for exploring the drivers and understanding its impacts, and thus the focus of the sustainable management of aquaculture. This study aims to assess the spatio-temporal expansion patterns of aquaculture ponds with multitemporal remote sensing images and geographic information system in the coastal zone of Southeast Asia over a 25-year period (1990-2015), to understanding how globalization and economic policies may have contributed to such changes. The results show that, in 2015, total area of coastal aquaculture ponds was about 23,245 km[2], and 79% of coastal aquaculture ponds distributed within 15 km from the coastline. And the amount has expanded about 2.6 times in the past 25 years. Vietnam has the largest area of aquaculture in 2015 and the highest annual increasing rate, accounting for 40.28% and 298.5 km[2]/y, followed by Indonesia (31.50% and 156.8 km[2]/y), Thailand (10.79% and 64.8 km[2]/y), Myanmar (8.76% and 61.1 km[2]/y). The expansion pattern of aquaculture ponds in the region altered from outlying to edge-expansion from the year of 2000. The main drivers of rapid expansion lie to the intensified local fisher policies as a result of economic globalization. While development of aquaculture has enhanced family income, it has also led to significant reduction of mangrove and coastal water pollution (eutrophication). With the prevailing antagonism between aquaculture expansion and ecosystem conversion, our research call for the local government's attention to sustainable management of aquaculture. This will be the key to reduce food safety risk and simultaneously prevent inevitable damages to coastal ecosystems, as stipulated by SDGs 2 and 14.}, } @article {pmid35523985, year = {2022}, author = {Martínez-García, PJ and Mas-Gómez, J and Wegrzyn, J and Botía, JA}, title = {Bioinformatic approach for the discovery of cis-eQTL signals during fruit ripening of a woody species as grape (Vitis vinifera L.).}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {7481}, pmid = {35523985}, issn = {2045-2322}, mesh = {Computational Biology ; Fruit/metabolism ; Gene Expression Profiling ; Gene Expression Regulation, Plant ; Indoleacetic Acids/metabolism ; *Vitis/metabolism ; }, abstract = {Expression quantitative trait loci (eQTLs) are associations between genetic variants, such as Single Nucleotide Polymorphisms (SNPs), and gene expression. eQTLs are an important tool to understand the genetic variance of gene expression of complex phenotypes. eQTLs analyses are common in biomedical models but are scarce in woody crop species such as fruit trees or grapes. In this study, a comprehensive bioinformatic analysis was conducted leveraging with expression data from two different growth stages, around ripening onset, of 10 genotypes of grape (Vitis vinifera L.). A total of 2170 cis-eQTL were identified in 212 gene modulated at ripening onset. The 48% of these DEGs have a known function. Among the annotated protein-coding genes, terpene synthase, auxin-regulatory factors, GRFS, ANK_REP_REGION domain-containing protein, Kinesin motor domain-containing protein and flavonol synthase were noted. This new inventory of cis-eQTLs influencing gene expression during fruit ripening will be an important resource to examine variation for this trait and will help to elucidate the complex genetic architecture underlying this process in grape.}, } @article {pmid35511143, year = {2022}, author = {Shoemaker, WR and Polezhaeva, E and Givens, KB and Lennon, JT}, title = {Seed banks alter the molecular evolutionary dynamics of Bacillus subtilis.}, journal = {Genetics}, volume = {221}, number = {2}, pages = {}, pmid = {35511143}, issn = {1943-2631}, mesh = {*Bacillus subtilis/genetics ; Evolution, Molecular ; Humans ; *Seed Bank ; }, abstract = {Fluctuations in the availability of resources constrain the growth and reproduction of individuals, which subsequently affects the evolution of their respective populations. Many organisms contend with such fluctuations by entering a reversible state of reduced metabolic activity, a phenomenon known as dormancy. This pool of dormant individuals (i.e. a seed bank) does not reproduce and is expected to act as an evolutionary buffer, though it is difficult to observe this effect directly over an extended evolutionary timescale. Through genetic manipulation, we analyze the molecular evolutionary dynamics of Bacillus subtilis populations in the presence and absence of a seed bank over 700 days. The ability of these bacteria to enter a dormant state increased the accumulation of genetic diversity over time and altered the trajectory of mutations, findings that were recapitulated using simulations based on a mathematical model of evolutionary dynamics. While the ability to form a seed bank did not alter the degree of negative selection, we found that it consistently altered the direction of molecular evolution across genes. Together, these results show that the ability to form a seed bank can affect the direction and rate of molecular evolution over an extended evolutionary timescale.}, } @article {pmid35510784, year = {2022}, author = {Jasper, RJ and McDonald, TK and Singh, P and Lu, M and Rougeux, C and Lind, BM and Yeaman, S}, title = {Evaluating the accuracy of variant calling methods using the frequency of parent-offspring genotype mismatch.}, journal = {Molecular ecology resources}, volume = {22}, number = {7}, pages = {2524-2533}, pmid = {35510784}, issn = {1755-0998}, support = {RGPIN/03950-2017//NSERC Discovery/ ; 20150252//Alberta Innovates/ ; }, mesh = {Computational Biology ; Genotype ; *High-Throughput Nucleotide Sequencing/methods ; Mutation ; *Polymorphism, Single Nucleotide ; Software ; }, abstract = {The use of next-generation sequencing (NGS) data sets has increased dramatically over the last decade, but there have been few systematic analyses quantifying the accuracy of the commonly used variant caller programs. Here we used a familial design consisting of diploid tissue from a single lodgepole pine (Pinus contorta) parent and the maternally derived haploid tissue from 106 full-sibling offspring, where mismatches could only arise due to mutation or bioinformatic error. Given the rarity of mutation, we used the rate of mismatches between parent and offspring genotype calls to infer the single nucleotide polymorphism (SNP) genotyping error rates of FreeBayes, HaplotypeCaller, SAMtools, UnifiedGenotyper, and VarScan. With baseline filtering HaplotypeCaller and UnifiedGenotyper yielded more SNPs and higher error rates by one to two orders of magnitude, whereas FreeBayes, SAMtools and VarScan yielded lower numbers of SNPs and more modest error rates. To facilitate comparison between variant callers we standardized each SNP set to the same number of SNPs using additional filtering, where UnifiedGenotyper consistently produced the smallest proportion of genotype errors, followed by HaplotypeCaller, VarScan, SAMtools, and FreeBayes. Additionally, we found that error rates were minimized for SNPs called by more than one variant caller. Finally, we evaluated the performance of various commonly used filtering metrics on SNP calling. Our analysis provides a quantitative assessment of the accuracy of five widely used variant calling programs and offers valuable insights into both the choice of variant caller program and the choice of filtering metrics, especially for researchers using non-model study systems.}, } @article {pmid35510429, year = {2022}, author = {Cheng, X and Xie, H and Zhang, K and Wen, J}, title = {Enabling Medicago truncatula forward genetics: identification of genetic crossing partner for R108 and development of mapping resources for Tnt1 mutants.}, journal = {The Plant journal : for cell and molecular biology}, volume = {111}, number = {2}, pages = {608-616}, doi = {10.1111/tpj.15797}, pmid = {35510429}, issn = {1365-313X}, mesh = {Databases, Nucleic Acid ; Genes, Plant ; Genetic Testing ; *Medicago truncatula/genetics ; Mutagenesis, Insertional ; }, abstract = {Though Medicago truncatula Tnt1 mutants are widely used by researchers in the legume community, they are mainly used for reverse genetics because of the availability of the BLAST-searchable large-scale flanking sequence tags database. However, these mutants should have also been used extensively for forward genetic screens, an effort that has been hindered due to the lack of a compatible genetic crossing partner for the M. truncatula genotype R108, from which Tnt1 mutants were generated. In this study, we selected three Medicago HapMap lines (HM017, HM018 and HM022) and performed reciprocal genetic crosses with R108. After phenotypic analyses in F1 and F2 progenies, HM017 was identified as a compatible crossing partner with R108. By comparing the assembled genomic sequences of HM017 and R108, we developed and confirmed 318 Indel markers evenly distributed across the eight chromosomes of the M. truncatula genome. To validate the effectiveness of these markers, by employing the map-based cloning approach, we cloned the causative gene in the dwarf mutant crs isolated from the Tnt1 mutant population, identifying it as gibberellin 3-β-dioxygenase 1, using some of the confirmed Indel markers. The primer sequences and the size difference of each marker were made available for users in the web-based database. The identification of the crossing partner for R108 and the generation of Indel markers will enhance the forward genetics and the overall usage of the Tnt1 mutants.}, } @article {pmid35505773, year = {2022}, author = {Boyes, D and , and , and , and , and , and Sivess, L and , }, title = {The genome sequence of the small elephant hawk moth, Deilephila porcellus (Linnaeus, 1758).}, journal = {Wellcome open research}, volume = {7}, number = {}, pages = {80}, pmid = {35505773}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual male Deilephila porcellus (the small elephant hawk moth; Arthropoda; Insecta; Lepidoptera; Sphingidae). The genome sequence is 402 megabases in span. The majority of the assembly (99.99%) is scaffolded into 29 chromosomal pseudomolecules, with the Z sex chromosome assembled.}, } @article {pmid35504469, year = {2022}, author = {Zhu, Y and Wang, L and You, Y and Cheng, Y and Ma, J and Chen, F}, title = {Enhancing network complexity and function of soil bacteria by thiourea-modified biochar under cadmium stress in post-mining area.}, journal = {Chemosphere}, volume = {302}, number = {}, pages = {134811}, doi = {10.1016/j.chemosphere.2022.134811}, pmid = {35504469}, issn = {1879-1298}, mesh = {Bacteria/metabolism ; Biodegradation, Environmental ; *Cadmium/analysis ; Charcoal/chemistry ; Soil/chemistry ; *Soil Pollutants/analysis ; Thiourea ; }, abstract = {Cadmium (Cd) pollution cause severe stress to soil microorganisms and biochar utilized for its ability to immobilize Cd in the soil effectively. However, the influence of biochar on the structure and function of the bacterial network under Cd stress is unclear. This research reports a pot experiment conducted to investigate the impact of 2.0% Italian poplar bark biochar (PB), 2.0% thiourea-modified biochar (TP), and control treatment (CK) on the complexity, stability and functional properties of the bacterial community under Cd stress. The results showed that: (1) Biochar increased the diversity of soil bacterial consortia under Cd stress (p < 0.05), and the diversity index demonstrated as order of CK < PB < TP; (2) Compared with CK network, the nodes number of PB and TP treatments networks were much higher, while the modularity and transitivity increased by 0.04% and 37.6%, 2.45% and 1.12%, respectively. The biochar amendment increased the stability and complexity of the network; (3) PICRUSt2 prediction results show that Xenobiotics biodegradation and metabolism membrane transport of TP treatment increased 62.52% and 53.62% compared with CK, respectively, which could be related to the decrease in Cd content according to principal component analysis. (4) The reduction of leaching Cd content caused network complexity and bacterial function changes by biochar amendment. TP amendment enhanced the complexity and stability of soil bacterial community under Cd stress, which will provide a scientific basis for in situ remediations of Cd-contaminated soils.}, } @article {pmid35504313, year = {2022}, author = {Carvalho, GML and Silva, DF and Xavier, LDA and Soares, JVR and Ramos, VDV and Madureira, AP and Lima, MA and Tonelli, GB and Paz, GF and Rêgo, FD and Andrade-Filho, JD and Margonari, C}, title = {Sand fly bioecological aspects and risk mapping of leishmaniasis by geographical information systems approach in a mineral exploration area of Brazil.}, journal = {Acta tropica}, volume = {232}, number = {}, pages = {106491}, doi = {10.1016/j.actatropica.2022.106491}, pmid = {35504313}, issn = {1873-6254}, mesh = {Animals ; Brazil/epidemiology ; DNA ; Dogs ; Female ; Geographic Information Systems ; Insect Vectors/genetics ; *Leishmaniasis/epidemiology ; Male ; Minerals ; *Phlebotomus/genetics ; *Psychodidae/genetics ; }, abstract = {Epidemiological studies of leishmaniasis in areas of great human influence and environmental change serve as important tools for the implementation of effective control plans. Mining is currently a major economic activity in Brazil with the municipality of Pains, in the state of Minas Gerais, being one of the main lime producing municipalities in the country. This study aimed to map areas of potential transmission risks within the municipality of Pains using an epidemiological approach in association with the ecological study of sand flies. Twelve samplings carried out between May 2015 and April 2016 collected a total of 12,728 sandflies, comprising 2,854 females (22.42%) and 9,874 males (77.58%), of 20 species belonging to ten genera. The most abundant species was Lutzomyia longipalpis (80%). Leishmania DNA was detected in seven pools of female sand flies with an infection rate of 0.37%. Geoprocessing and the use of maps revealed that vector sand flies are distributed throughout the urban area, as are cases of canine and human leishmaniasis. However, the greatest abundances of sand flies were at sampling points at the border of the urban area. Higher densities of sand flies and the presence of Leishmania DNA may be correlated with extensive degradation by limestone mining. Integrated and multidisciplinary research approaches are necessary to better understand how the impacts of environmental change influence these insect vectors of leishmaniasis.}, } @article {pmid35502341, year = {2022}, author = {Qing, J and Song, W and Tian, L and Samuel, SB and Li, Y}, title = {Potential Small Molecules for Therapy of Lupus Nephritis Based on Genetic Effect and Immune Infiltration.}, journal = {BioMed research international}, volume = {2022}, number = {}, pages = {2259164}, pmid = {35502341}, issn = {2314-6141}, mesh = {Computational Biology ; Female ; Gene Expression ; Genes, Regulator ; Humans ; *Lupus Erythematosus, Systemic/genetics ; *Lupus Nephritis/drug therapy/genetics ; Male ; Membrane Proteins/genetics ; RNA-Binding Proteins/genetics ; }, abstract = {Lupus nephritis (LN) is the most common and significant complication of systemic lupus erythematosus (SLE) due to its poor prognosis and mortality rates in SLE patients. There is a critical need for new drugs as the pathogenesis of LN remains to be elucidated and immunosuppressive therapy comes with many deficiencies. In this study, 23 hub genes (IFI6, PLSCR1, XAF1, IFI16, IFI44, MX1, IFI44L, IFIT3, IFIT2, IFI27, DDX58, EIF2AK2, IFITM1, RTP4, IFITM3, TRIM22, PARP12, IFIH1, OAS1, HERC6, RSAD2, DDX60, and MX2) were identified through bioinformatics and network analysis and are closely related to interferon production and function. Interestingly, immune cell infiltration analysis and correlation analysis demonstrate a positive correlation between the expression of 23 hub genes and monocyte infiltration in glomeruli and M2 macrophage infiltration in the tubulointerstitium of LN patients. Additionally, the CTD database, DsigDB database, and DREIMT database were used to explore the bridging role of genes in chemicals and LN as well as the potential influence of these chemicals on immune cells. After comparison and discussion, six small molecules (Acetohexamide, Suloctidil, Terfenadine, Prochlorperazine, Mefloquine, and Triprolidine) were selected for their potential ability in treating lupus nephritis.}, } @article {pmid35501433, year = {2022}, author = {Wilk, BK and Szopińska, M and Sobaszek, M and Pierpaoli, M and Błaszczyk, A and Luczkiewicz, A and Fudala-Ksiazek, S}, title = {Electrochemical oxidation of landfill leachate using boron-doped diamond anodes: pollution degradation rate, energy efficiency and toxicity assessment.}, journal = {Environmental science and pollution research international}, volume = {29}, number = {43}, pages = {65625-65641}, pmid = {35501433}, issn = {1614-7499}, support = {RX-15/13/2017//wojewódzki fundusz ochrony środowiska i gospodarki wodnej w gdańsku/ ; }, mesh = {Ammonia/analysis ; *Boron/analysis ; Chlorine/analysis ; Conservation of Energy Resources ; Electrodes ; Oxidants ; Oxidation-Reduction ; Sulfates/analysis ; Wastewater/analysis ; *Water Pollutants, Chemical/analysis ; }, abstract = {Electrochemical oxidation (EO), due to high efficiency and small carbon footprint, is regarded as an attractive option for on-site treatment of highly contaminated wastewater. This work shows the effectiveness of EO using three boron-doped diamond electrodes (BDDs) in sustainable management of landfill leachate (LL). The effect of the applied current density (25-100 mA cm[-2]) and boron doping concentration (B/C ratio: 500 ppm, 10,000 ppm and 15,000 ppm) on the performance of EO was investigated. It was found that, of the electrodes used, the one most effective at COD, BOD20 and ammonia removal (97.1%, 98.8% and 62%, respectively) was the electrode with the lowest boron doping. Then, to better elucidate the ecological role of LLs, before and after EO, cultivation of faecal bacteria and microscopic analysis of total (prokaryotic) cell number, together with ecotoxicity assay (Daphnia magna, Thamnocephalus platyurus and Artemia salina) were combined for the two better-performing electrodes. The EO process was very effective at bacterial cell inactivation using each of the two anodes, even within 2 h of contact time. In a complex matrix of LLs, this is probably a combined effect of electrogenerated oxidants (hydroxyl radicals, active chlorine and sulphate radicals), which may penetrate into the bacterial cells and/or react with cellular components. The toxicity of EO-treated LLs proved to be lower than that of raw ones. Since toxicity drops with increased boron doping, it is believed that appropriate electrolysis parameters can diminish the toxicity effect without compromising the nutrient-removal and disinfection capability, although salinity of LLs and related multistep-oxidation pathways needs to be further elucidated.}, } @article {pmid35488501, year = {2022}, author = {Chen, Y and Rademacher, T and Fonti, P and Eckes-Shephard, AH and LeMoine, JM and Fonti, MV and Richardson, AD and Friend, AD}, title = {Inter-annual and inter-species tree growth explained by phenology of xylogenesis.}, journal = {The New phytologist}, volume = {235}, number = {3}, pages = {939-952}, pmid = {35488501}, issn = {1469-8137}, mesh = {Carbohydrates ; Ecosystem ; *Pinus ; *Quercus ; Seasons ; *Tracheophyta ; Wood ; Xylem ; }, abstract = {Wood formation determines major long-term carbon (C) accumulation in trees and therefore provides a crucial ecosystem service in mitigating climate change. Nevertheless, we lack understanding of how species with contrasting wood anatomical types differ with respect to phenology and environmental controls on wood formation. In this study, we investigated the seasonality and rates of radial growth and their relationships with climatic factors, and the seasonal variations of stem nonstructural carbohydrates (NSC) in three species with contrasting wood anatomical types (red oak: ring-porous; red maple: diffuse-porous; white pine: coniferous) in a temperate mixed forest during 2017-2019. We found that the high ring width variability observed in both red oak and red maple was caused more by changes in growth duration than growth rate. Seasonal radial growth patterns did not vary following transient environmental factors for all three species. Both angiosperm species showed higher concentrations and lower inter-annual fluctuations of NSC than the coniferous species. Inter-annual variability of ring width varied by species with contrasting wood anatomical types. Due to the high dependence of annual ring width on growth duration, our study highlights the critical importance of xylem formation phenology for understanding and modelling the dynamics of wood formation.}, } @article {pmid35483251, year = {2022}, author = {Xiao, D and He, H and Yan, X and Díaz, ND and Chen, D and Ma, J and Zhang, Y and Li, J and Keita, M and Julien, EO and Yan, X}, title = {The response regularity of biohydrogen production by anthracite H2-producing bacteria consortium to six conventional veterinary antibiotics.}, journal = {Journal of environmental management}, volume = {315}, number = {}, pages = {115088}, doi = {10.1016/j.jenvman.2022.115088}, pmid = {35483251}, issn = {1095-8630}, mesh = {Anti-Bacterial Agents/pharmacology ; Bacteria ; Bioreactors/microbiology ; *Coal ; Fermentation ; *Hydrogen/analysis ; }, abstract = {The impact of antibiotics on H2-producing bacteria must be considered in the industrialization of biological H2 production using livestock manure as raw resources. However, whether antibiotics that may be contained in excreta will threaten the safety of biohydrogen production needs to be researched. This study explored the impact characteristics and mechanism of six single antibiotics and three groups of compound antibiotics on H2 production. Experiments confirmed that most antibiotics have different degrees of H2 production inhibition, while some antibiotics, which like Penicillin G, Streptomycin Sulfate, and their compound antibiotics, could promote the growth of Ethanoligenens sp. and improve H2 yield on the contrary. Comprehensive analysis shows that the main inhibitory mechanisms were: (1) board-spectrum inhibition, (2) partial inhibition, (3) H2 consumption enhancement; and the enhancement mechanisms were: (1) enhance the growth of H2-producing bacteria, (2) enhanced starch hydrolysis, (3) inhibitory H2 consumption or release of acid inhibition. Meanwhile, experiment found that the effect of antibiotics on H2 producing was not only related to type, but also to dosage. Even one kind of antibiotic may have completely opposite effects on H2-producing bacteria under different dosage conditions. Inhibition of H2 yield was highest with Levofloxacin at 6.15 mg/L, gas production was reduced by 88.77%; and enhancement of H2 yield was highest with Penicillin G at 7.20 mg/L, the gas production increased by 72.90%. In the selection of raw material, the type and content of antibiotics demand a detailed investigation and analysis to ensure that the sustainability of H2 yield.}, } @article {pmid35478198, year = {2022}, author = {Millar, JE and Neyton, L and Seth, S and Dunning, J and Merson, L and Murthy, S and Russell, CD and Keating, S and Swets, M and Sudre, CH and Spector, TD and Ourselin, S and Steves, CJ and Wolf, J and Docherty, AB and Harrison, EM and Openshaw, PJM and Semple, MG and Baillie, JK and , }, title = {Distinct clinical symptom patterns in patients hospitalised with COVID-19 in an analysis of 59,011 patients in the ISARIC-4C study.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {6843}, pmid = {35478198}, issn = {2045-2322}, support = {MC_PC_19025/MRC_/Medical Research Council/United Kingdom ; MC_PC_19059/MRC_/Medical Research Council/United Kingdom ; MC_PC_20058/MRC_/Medical Research Council/United Kingdom ; MR/S032304/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {*COVID-19 ; Confusion ; Cough ; Dyspnea ; Fatigue ; Female ; Fever ; Humans ; Prospective Studies ; }, abstract = {COVID-19 is clinically characterised by fever, cough, and dyspnoea. Symptoms affecting other organ systems have been reported. However, it is the clinical associations of different patterns of symptoms which influence diagnostic and therapeutic decision-making. In this study, we applied clustering techniques to a large prospective cohort of hospitalised patients with COVID-19 to identify clinically meaningful sub-phenotypes. We obtained structured clinical data on 59,011 patients in the UK (the ISARIC Coronavirus Clinical Characterisation Consortium, 4C) and used a principled, unsupervised clustering approach to partition the first 25,477 cases according to symptoms reported at recruitment. We validated our findings in a second group of 33,534 cases recruited to ISARIC-4C, and in 4,445 cases recruited to a separate study of community cases. Unsupervised clustering identified distinct sub-phenotypes. First, a core symptom set of fever, cough, and dyspnoea, which co-occurred with additional symptoms in three further patterns: fatigue and confusion, diarrhoea and vomiting, or productive cough. Presentations with a single reported symptom of dyspnoea or confusion were also identified, alongside a sub-phenotype of patients reporting few or no symptoms. Patients presenting with gastrointestinal symptoms were more commonly female, had a longer duration of symptoms before presentation, and had lower 30-day mortality. Patients presenting with confusion, with or without core symptoms, were older and had a higher unadjusted mortality. Symptom sub-phenotypes were highly consistent in replication analysis within the ISARIC-4C study. Similar patterns were externally verified in patients from a study of self-reported symptoms of mild disease. The large scale of the ISARIC-4C study enabled robust, granular discovery and replication. Clinical interpretation is necessary to determine which of these observations have practical utility. We propose that four sub-phenotypes are usefully distinct from the core symptom group: gastro-intestinal disease, productive cough, confusion, and pauci-symptomatic presentations. Importantly, each is associated with an in-hospital mortality which differs from that of patients with core symptoms.}, } @article {pmid35469881, year = {2022}, author = {Chen, L and Zhou, M and Wang, J and Zhang, Z and Duan, C and Wang, X and Zhao, S and Bai, X and Li, Z and Li, Z and Fang, L}, title = {A global meta-analysis of heavy metal(loid)s pollution in soils near copper mines: Evaluation of pollution level and probabilistic health risks.}, journal = {The Science of the total environment}, volume = {835}, number = {}, pages = {155441}, doi = {10.1016/j.scitotenv.2022.155441}, pmid = {35469881}, issn = {1879-1026}, mesh = {Adult ; Cadmium/analysis ; Child ; China ; Copper/analysis ; Environmental Monitoring ; Environmental Pollution/analysis ; Humans ; *Metals, Heavy/analysis ; Risk Assessment ; Soil ; *Soil Pollutants/analysis ; }, abstract = {With the rapid development of the mining industry, the pollution of heavy metal(loid)s in soils near copper (Cu) mining sites is a significant concern worldwide. However, the pollution status and probabilistic health risks of heavy metal(loid)s of soils associated with Cu mines, have rarely been studied on a global scale. In this study, eight heavy metal(loid) concentrations in soil samples taken near 102 Cu mining sites worldwide were obtained through a literature review. Based on this database, the heavy metal(loid) pollution and ecological risk in soils near Cu mines were evaluated. Most of the study sites exceeded the moderately to heavily polluted levels of Cu and Cd; compared to other regions, higher pollution levels were observed at sites in Oman, China, Australia, and the United Kingdom. Soil pollution by Cd, Pb, and Zn at agricultural sites was higher than that in non-agricultural sites. In addition, these heavy metal(loid)s produced a high ecological risk to soils around Cu mining sites in which the contribution of Cd, Cu, and As reached up to 46.5%, 21.7%, and 18.4%, respectively. The mean hazard indices of the eight heavy metal(loid)s were 0.209 and 0.979 for adults and children, respectively. The Monte Carlo simulation further predicted that 1.40% and 29.9% of non-carcinogenic risk values for adults and children, respectively, exceeded the safe level of 1.0. Moreover, 84.5% and 91.0% of the total cancer risk values for adults and children, respectively, exceeded the threshold of 1E-04. Arsenic was the main contributor to non-carcinogenic risk, while Cu had the highest exceedance of carcinogenic risk. Our findings indicate that the control of Cu, Cd, and As should be prioritized because of their high incidence and significant risks in soils near Cu mines. These results provide valuable inputs for policymakers in designing effective strategies for reducing the exposure of heavy metal(loid)s in this area worldwide.}, } @article {pmid35468590, year = {2022}, author = {Pokolm, M and Rein, R and Müller, D and Nopp, S and Kirchhain, M and Aksum, KM and Jordet, G and Memmert, D}, title = {Modeling Players' Scanning Activity in Football.}, journal = {Journal of sport & exercise psychology}, volume = {44}, number = {4}, pages = {263-271}, doi = {10.1123/jsep.2020-0299}, pmid = {35468590}, issn = {1543-2904}, mesh = {Humans ; *Soccer/physiology/psychology ; *Visual Perception/physiology ; }, abstract = {The purpose of this study was to develop and test models of scanning activity in football. Gibson's ecological approach of visual perception and exploratory activity provided the theoretical framework for the models. The video-based data analysis consisted of 17 selected matches and 239 players of the Union of European Football Associations (UEFA) U17 and U19 European Championship 2018 and the UEFA U17 and U21 European Championship 2019. The results showed a positive relation between scanning frequency and successful passes, as well as changes in body orientation. Scanning frequency was also related to a player's appearances in national teams and to opponent pressure. Opponent pressure had a large effect on pass result and the player's body orientation. Previous research on the relation between scanning frequency and performance was extended by several contextual predictors. Future research should focus on gaining a deeper understanding of the relation between scanning frequency and further contextual variables related to scanning.}, } @article {pmid35466253, year = {2022}, author = {Wanieck, K and Hamann, L and Bartz, M and Uttich, E and Hollermann, M and Drack, M and Beismann, H}, title = {Biomimetics Linked to Classical Product Development: An Interdisciplinary Endeavor to Develop a Technical Standard.}, journal = {Biomimetics (Basel, Switzerland)}, volume = {7}, number = {2}, pages = {}, pmid = {35466253}, issn = {2313-7673}, abstract = {Biomimetics is a well-known approach for technical innovation. However, most of its influence remains in the academic field. One option for increasing its application in the practice of technical design is to enhance the use of the biomimetic process with a step-by-step standard, building a bridge to common engineering procedures. This article presents the endeavor of an interdisciplinary expert panel from the fields of biology, engineering science, and industry to develop a standard that links biomimetics to the classical processes of product development and engineering design. This new standard, VDI 6220 Part 2, proposes a process description that is compatible and connectable to classical approaches in engineering design. The standard encompasses both the solution-based and the problem-driven process of biomimetics. It is intended to be used in any product development process for more biomimetic applications in the future.}, } @article {pmid35464909, year = {2022}, author = {Mader, R and Muñoz Madero, C and Aasmäe, B and Bourély, C and Broens, EM and Busani, L and Callens, B and Collineau, L and Crespo-Robledo, P and Damborg, P and Filippitzi, ME and Fitzgerald, W and Heuvelink, A and van Hout, J and Kaspar, H and Norström, M and Pedersen, K and Pohjanvirta, T and Pokludova, L and Dal Pozzo, F and Slowey, R and Teixeira Justo, C and Urdahl, AM and Vatopoulos, A and Zafeiridis, C and Madec, JY and Amat, JP}, title = {Review and Analysis of National Monitoring Systems for Antimicrobial Resistance in Animal Bacterial Pathogens in Europe: A Basis for the Development of the European Antimicrobial Resistance Surveillance Network in Veterinary Medicine (EARS-Vet).}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {838490}, pmid = {35464909}, issn = {1664-302X}, abstract = {The monitoring of antimicrobial resistance (AMR) in bacterial pathogens of animals is not currently coordinated at European level. To fill this gap, experts of the European Union Joint Action on Antimicrobial Resistance and Healthcare Associated Infections (EU-JAMRAI) recommended building the European Antimicrobial Resistance Surveillance network in Veterinary medicine (EARS-Vet). In this study, we (i) identified national monitoring systems for AMR in bacterial pathogens of animals (both companion and food-producing) among 27 countries affiliated to EU-JAMRAI, (ii) described their structures and operations, and (iii) analyzed their respective strengths, weaknesses, opportunities and threats (SWOT). Twelve countries reported having at least one national monitoring system in place, representing an opportunity to launch EARS-Vet, but highlighting important gaps in AMR data generation in Europe. In total, 15 national monitoring systems from 11 countries were described and analyzed. They displayed diverse structures and operations, but most of them shared common weaknesses (e.g., data management and representativeness) and common threats (e.g., economic vulnerability and data access), which could be addressed collectively under EARS-Vet. This work generated useful information to countries planning to build or improve their system, by learning from others' experience. It also enabled to advance on a pragmatic harmonization strategy: EARS-Vet shall follow the European Committee on Antimicrobial Susceptibility Testing (EUCAST) standards, collect quantitative data and interpret AMR data using epidemiological cut-off values.}, } @article {pmid35462782, year = {2022}, author = {Matsubayashi, S and Nakadai, K and Suzuki, R and Ura, T and Hasebe, M and Okuno, HG}, title = {Auditory Survey of Endangered Eurasian Bittern Using Microphone Arrays and Robot Audition.}, journal = {Frontiers in robotics and AI}, volume = {9}, number = {}, pages = {854572}, pmid = {35462782}, issn = {2296-9144}, abstract = {Bioacoustics monitoring has become increasingly popular for studying the behavior and ecology of vocalizing birds. This study aims to verify the practical effectiveness of localization technology for auditory monitoring of endangered Eurasian bittern (Botaurus stellaris) which inhabits wetlands in remote areas with thick vegetation. Their crepuscular and highly secretive nature, except during the breeding season when they vocalize advertisement calls, make them difficult to monitor. Because of the increasing rates of habitat loss, surveying accurate numbers and their habitat needs are both important conservation tasks. We investigated the feasibility of localizing their booming calls, at a low frequency range between 100-200 Hz, using microphone arrays and robot audition HARK (Honda Research Institute, Audition for Robots with Kyoto University). We first simulated sound source localization of actual bittern calls for microphone arrays of radii 10 cm, 50 cm, 1 m, and 10 m, under different noise levels. Second, we monitored bitterns in an actual field environment using small microphone arrays (height = 12 cm; width = 8 cm), in the Sarobetsu Mire, Hokkaido Island, Japan. The simulation results showed that the spectral detectability was higher for larger microphone arrays, whereas the temporal detectability was higher for smaller microphone arrays. We identified that false detection in smaller microphone arrays, which was coincidentally generated in the calculation proximate to the transfer function for the opposite side. Despite technical limitations, we successfully localized booming calls of at least two males in a reverberant wetland, surrounded by thick vegetation and riparian trees. This study is the first case of localizing such rare birds using small-sized microphone arrays in the field, thereby presenting how this technology could contribute to auditory surveys of population numbers, behaviors, and microhabitat selection, all of which are difficult to investigate using other observation methods. This methodology is not only useful for the better understanding of bitterns, but it can also be extended to investigate other rare nocturnal birds with low-frequency vocalizations, without direct ringing or tagging. Our results also suggest a future necessity for a robust localization system to avoid reverberation and echoing in the field, resulting in the false detection of the target birds.}, } @article {pmid35462586, year = {2023}, author = {Zhan, Y and Chang, Y and Tao, Y and Zhang, H and Lin, Y and Deng, J and Ma, T and Ding, G and Wei, Y and Li, J}, title = {Insight into the dynamic microbial community and core bacteria in composting from different sources by advanced bioinformatics methods.}, journal = {Environmental science and pollution research international}, volume = {30}, number = {4}, pages = {8956-8966}, pmid = {35462586}, issn = {1614-7499}, mesh = {Animals ; Sheep ; Soil ; *Composting ; Manure/analysis ; *Refuse Disposal ; Bacteria/genetics ; Computational Biology ; *Microbiota ; Vegetables ; Chickens ; }, abstract = {Microbial communities are important for high composting efficiency and good quality composts. This study was conducted to compare the changes of physicochemical and bacterial characteristics in composting from different raw materials, including chicken manure (CM), duck manure (DM), sheep manure (SM), food waste (FW), and vegetable waste (VW). The role and interactions of core bacteria and their contribution to maturity in diverse composts were analyzed by advanced bioinformatics methods combined sequencing with co-occurrence network and structural equation modeling (SEM). Results indicated that there were obviously different bacterial composition and diversity in composting from diverse sources. FW had a low pH and different physiochemical characteristics compared to other composts but they all achieved similar maturity products. Redundancy analysis suggested total organic carbon, phosphorus, and temperature governed the composition of microbial species but key factors were different in diverse composts. Network analysis showed completely different interactions of core bacterial community from diverse composts but Thermobifida was the ubiquitous core bacteria in composting bacterial network. Sphaerobacter and Lactobacillus as core genus were presented in the starting mesophilic and thermophilic phases of composting from manure (CM, DM, SM) and municipal solid waste (FW, VW), respectively. SEM indicated core bacteria had the positive, direct, and the biggest (> 80%) effects on composting maturity. Therefore, this study presents theoretical basis to identify and enhance the core bacteria for improving full-scale composting efficiency facing more and more organic wastes.}, } @article {pmid35459797, year = {2022}, author = {Wyngaard, GA and Skern-Mauritzen, R and Malde, K and Prendergast, R and Peruzzi, S}, title = {The salmon louse genome may be much larger than sequencing suggests.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {6616}, pmid = {35459797}, issn = {2045-2322}, support = {R15 GM104868/GM/NIGMS NIH HHS/United States ; 1R15GM104868/NH/NIH HHS/United States ; }, mesh = {Animals ; *Copepoda/genetics ; *Fish Diseases/genetics ; Genome ; Norway ; Transcriptome ; }, abstract = {The genome size of organisms impacts their evolution and biology and is often assumed to be characteristic of a species. Here we present the first published estimates of genome size of the ecologically and economically important ectoparasite, Lepeophtheirus salmonis (Copepoda, Caligidae). Four independent L. salmonis genome assemblies of the North Atlantic subspecies Lepeophtheirus salmonis salmonis, including two chromosome level assemblies, yield assemblies ranging from 665 to 790 Mbps. These genome assemblies are congruent in their findings, and appear very complete with Benchmarking Universal Single-Copy Orthologs analyses finding > 92% of expected genes and transcriptome datasets routinely mapping > 90% of reads. However, two cytometric techniques, flow cytometry and Feulgen image analysis densitometry, yield measurements of 1.3-1.6 Gb in the haploid genome. Interestingly, earlier cytometric measurements reported genome sizes of 939 and 567 Mbps in L. salmonis salmonis samples from Bay of Fundy and Norway, respectively. Available data thus suggest that the genome sizes of salmon lice are variable. Current understanding of eukaryotic genome dynamics suggests that the most likely explanation for such variability involves repetitive DNA, which for L. salmonis makes up ≈ 60% of the genome assemblies.}, } @article {pmid35459255, year = {2022}, author = {Jiang, H and Fan, G and Zhang, D and Zhang, S and Fan, Y}, title = {Evaluation of eco-environmental quality for the coal-mining region using multi-source data.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {6623}, pmid = {35459255}, issn = {2045-2322}, mesh = {China ; Coal ; *Coal Mining/methods ; Conservation of Natural Resources ; Environmental Monitoring/methods ; Geographic Information Systems ; Humans ; Reproducibility of Results ; }, abstract = {The contradiction between the exploitation of coal resources and the protection of the ecological environment in western China is becoming increasingly prominent. Reasonable ecological environment evaluation is the premise for alleviating this contradiction. First, this paper evaluates the eco-environment of Ibei coalfield by combining the genetic projection pursuit model and geographic information system (GIS) and using remote sensing image data and other statistical data of this area. The powerful spatial analysis function of GIS and the advantages of the genetic projection pursuit model in weight calculation have been fully used to improve the reliability of the evaluation results. Furthermore, spatial autocorrelation is used to analyze the spatial characteristics of ecological environment quality in the mining area and plan the specific governance scope. The geographic detector is used to determine the driving factors of the eco-environment of the mining area. The results show that Ibei Coalfield presents a spatially heterogeneous eco-environment pattern. The high-intensity mining area (previously mined area of Ili No.4 Coal Mine) has the worst ecological environment quality, followed by the coal reserve area of Ili No.4 Coal Mine and the planned survey area of Ili No.5 Coal Mine. The eco-environment quality (EEQ) of the study area is affected by both human and natural factors. Mining intensity and surface subsidence are the main human factors affecting the ecological environment in the study area. The main natural factors affecting the ecological environment in the study area are annual average precipitation, elevation, annual average evaporation, NDVI and land use type. Meanwhile, the interaction effect of any two indicators is greater than that of a single indicator. It is also indicated that the eco-environment of the mining area is nonlinearly correlated to impact indicators. The spatial autocorrelation analysis shows three areas that should be treated strategically that are the management area, close attention area and protective area. Corresponding management measures are put forward for different regions. This paper can provide scientific references for mining area eco-environmental protection, which is significant for the sustainability of coal mine projects.}, } @article {pmid35457703, year = {2022}, author = {Oselladore, F and Bernarello, V and Cacciatore, F and Cornello, M and Boscolo Brusà, R and Sfriso, A and Bonometto, A}, title = {Changes in Macrozoobenthos Community after Aquatic Plant Restoration in the Northern Venice Lagoon (IT).}, journal = {International journal of environmental research and public health}, volume = {19}, number = {8}, pages = {}, pmid = {35457703}, issn = {1660-4601}, mesh = {Animals ; *Biodiversity ; *Ecosystem ; Environmental Monitoring/methods ; Invertebrates ; }, abstract = {Responses of the macrozoobenthic community to an ecological restoration activity in the northern Venice lagoon were studied, within the scope of the project LIFE SEagrass RESTOration aimed at recreating aquatic phanerogam meadows largely reduced in recent decades. Transplants were successful in almost all project areas. Macrozoobenthos was sampled in eight stations before (2014) and after (2015, 2016, 2017) transplanting activities. An increase in abundance and fluctuations in richness and univariate ecological indices (Shannon's, Margalef's, Pielou's indices) resulted during the years. Comparing non-vegetated and vegetated samples in 2017, every index except Pielou's increased in the latter. Multivariate analysis (hierarchical cluster analysis, MDS, PERMDISP, SIMPER) grouped samples by localization rather than years, with differences between stations due to the abundance of common species. In 2017, results were also grouped by the presence or absence of aquatic plants, with differences in the abundance of grazer and filter-feeding species. Results of ecological index M-AMBI depicted conditions from moderate to good ecological status (sensu Dir.2000/60/EC) with similar fluctuations, as presented by univariate indices from 2014 to 2017. Responses of the macrozoobenthic community were more evident when comparing vegetated and non-vegetated samples, with the vegetated areas sustaining communities with greater abundance and diversity than non-vegetated samples, thus demonstrating the supporting function of aquatic plants to benthic communities.}, } @article {pmid35457308, year = {2022}, author = {Cai, Z and Lei, S and Zhao, Y and Gong, C and Wang, W and Du, C}, title = {Spatial Distribution and Migration Characteristics of Heavy Metals in Grassland Open-Pit Coal Mine Dump Soil Interface.}, journal = {International journal of environmental research and public health}, volume = {19}, number = {8}, pages = {}, pmid = {35457308}, issn = {1660-4601}, mesh = {China ; Coal/analysis ; Environmental Monitoring/methods ; Grassland ; *Metals, Heavy/analysis ; Soil ; *Soil Pollutants/analysis ; }, abstract = {The open-pit coal mine dump in the study area contains many low-concentration heavy metal pollutants, which may cause pollution to the soil interface. Firstly, statistical analysis and geostatistical spatial interpolation methods described heavy metal pollution's spatial distribution. The mine dump heavy metal pollution distribution is strongly random due to disorderly piles, but it is closely related to slope soil erosion. Furthermore, the soil deposition area is where pollutants accumulate. For example, all heavy metal elements converge at the bottom of the dump. Usually, the pollution in the lower part is higher than that in the upper part; the pollution in the lower step is higher than the upper step; the pollution in the soil deposition locations such as flat plate and slope bottom is higher than the soil erosion locations such as slope tip and middle slope. Finally, the hyperspectral remote sensing method described heavy metals pollution's migration characteristics, that the pollutants could affect the soil interface by at least 1 km. This study provides a basis for preventing and controlling critical parts of mine dump heavy metal pollution and pollution path control.}, } @article {pmid35453730, year = {2022}, author = {Navega, D and Costa, E and Cunha, E}, title = {Adult Skeletal Age-at-Death Estimation through Deep Random Neural Networks: A New Method and Its Computational Analysis.}, journal = {Biology}, volume = {11}, number = {4}, pages = {}, pmid = {35453730}, issn = {2079-7737}, abstract = {Age-at-death assessment is a crucial step in the identification process of skeletal human remains. Nonetheless, in adult individuals this task is particularly difficult to achieve with reasonable accuracy due to high variability in the senescence processes. To improve the accuracy of age-at-estimation, in this work we propose a new method based on a multifactorial macroscopic analysis and deep random neural network models. A sample of 500 identified skeletons was used to establish a reference dataset (age-at-death: 19-101 years old, 250 males and 250 females). A total of 64 skeletal traits are covered in the proposed macroscopic technique. Age-at-death estimation is tackled from a function approximation perspective and a regression approach is used to infer both point and prediction interval estimates. Based on cross-validation and computational experiments, our results demonstrate that age estimation from skeletal remains can be accurately (~6 years mean absolute error) inferred across the entire adult age span and informative estimates and prediction intervals can be obtained for the elderly population. A novel software tool, DRNNAGE, was made available to the community.}, } @article {pmid35449394, year = {2023}, author = {Swann, OV and Pollock, L and Holden, KA and Munro, APS and Bennett, A and Williams, TC and Turtle, L and Fairfield, CJ and Drake, TM and Faust, SN and Sinha, IP and Roland, D and Whittaker, E and Ladhani, SN and Nguyen-Van-Tam, JS and Girvan, M and Donohue, C and Donegan, C and Spencer, RG and Hardwick, HE and Openshaw, PJM and Baillie, JK and Harrison, EM and Docherty, AB and Semple, MG and , }, title = {Comparison of UK paediatric SARS-CoV-2 admissions across the first and second pandemic waves.}, journal = {Pediatric research}, volume = {93}, number = {1}, pages = {207-216}, pmid = {35449394}, issn = {1530-0447}, support = {MC_PC_19025/MRC_/Medical Research Council/United Kingdom ; MC_PC_19059/MRC_/Medical Research Council/United Kingdom ; MC_PC_20058/MRC_/Medical Research Council/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; }, mesh = {Humans ; Child ; Adolescent ; SARS-CoV-2 ; *COVID-19/epidemiology ; Pandemics ; Prospective Studies ; *Coronavirus Infections ; United Kingdom/epidemiology ; }, abstract = {BACKGROUND: We hypothesised that the clinical characteristics of hospitalised children and young people (CYP) with SARS-CoV-2 in the UK second wave (W2) would differ from the first wave (W1) due to the alpha variant (B.1.1.7), school reopening and relaxation of shielding.

METHODS: Prospective multicentre observational cohort study of patients <19 years hospitalised in the UK with SARS-CoV-2 between 17/01/20 and 31/01/21. Clinical characteristics were compared between W1 and W2 (W1 = 17/01/20-31/07/20,W2 = 01/08/20-31/01/21).

RESULTS: 2044 CYP < 19 years from 187 hospitals. 427/2044 (20.6%) with asymptomatic/incidental SARS-CoV-2 were excluded from main analysis. 16.0% (248/1548) of symptomatic CYP were admitted to critical care and 0.8% (12/1504) died. 5.6% (91/1617) of symptomatic CYP had Multisystem Inflammatory Syndrome in Children (MIS-C). After excluding CYP with MIS-C, patients in W2 had lower Paediatric Early Warning Scores (PEWS, composite vital sign score), lower antibiotic use and less respiratory and cardiovascular support than W1. The proportion of CYP admitted to critical care was unchanged. 58.0% (938/1617) of symptomatic CYP had no reported comorbidity. Patients without co-morbidities were younger (42.4%, 398/938, <1 year), had lower PEWS, shorter length of stay and less respiratory support.

CONCLUSIONS: We found no evidence of increased disease severity in W2 vs W1. A large proportion of hospitalised CYP had no comorbidity.

IMPACT: No evidence of increased severity of COVID-19 admissions amongst children and young people (CYP) in the second vs first wave in the UK, despite changes in variant, relaxation of shielding and return to face-to-face schooling. CYP with no comorbidities made up a significant proportion of those admitted. However, they had shorter length of stays and lower treatment requirements than CYP with comorbidities once those with MIS-C were excluded. At least 20% of CYP admitted in this cohort had asymptomatic/incidental SARS-CoV-2 infection. This paper was presented to SAGE to inform CYP vaccination policy in the UK.}, } @article {pmid35448861, year = {2022}, author = {Csenki, Z and Risa, A and Sárkány, D and Garai, E and Bata-Vidács, I and Baka, E and Szekeres, A and Varga, M and Ács, A and Griffitts, J and Bakos, K and Bock, I and Szabó, I and Kriszt, B and Urbányi, B and Kukolya, J}, title = {Comparison Evaluation of the Biological Effects of Sterigmatocystin and Aflatoxin B1 Utilizing SOS-Chromotest and a Novel Zebrafish (Danio rerio) Embryo Microinjection Method.}, journal = {Toxins}, volume = {14}, number = {4}, pages = {}, pmid = {35448861}, issn = {2072-6651}, mesh = {Aflatoxin B1/toxicity ; *Aflatoxins ; Animals ; Escherichia coli ; Microinjections ; *Sterigmatocystin/toxicity ; Zebrafish ; }, abstract = {Aflatoxin B1 (AFB1) is a potent mycotoxin and natural carcinogen. The primary producers of AFB1 are Aspergillus flavus and A. parasiticus. Sterigmatocystin (STC), another mycotoxin, shares its biosynthetic pathway with aflatoxins. While there are abundant data on the biological effects of AFB1, STC is not well characterised. According to published data, AFB1 is more harmful to biological systems than STC. It has been suggested that STC is about one-tenth as potent a mutagen as AFB1 as measured by the Ames test. In this research, the biological effects of S9 rat liver homogenate-activated and non-activated STC and AFB1 were compared using two different biomonitoring systems, SOS-Chromotest and a recently developed microinjection zebrafish embryo method. When comparing the treatments, activated STC caused the highest mortality and number of DNA strand breaks across all injected volumes. Based on the E. coli SOS-Chromotest, the two toxins exerted the same genotoxicities. Moreover, according to the newly developed zebrafish microinjection method, STC appeared more toxic than AFB1. The scarce information correlating AFB1 and STC toxicity suggests that AFB1 is a more potent genotoxin than STC. Our findings contradict this assumption and illustrate the need for more complex biomonitoring systems for mycotoxin risk assessment.}, } @article {pmid35448792, year = {2022}, author = {Prakofjewa, J and Anegg, M and Kalle, R and Simanova, A and Prūse, B and Pieroni, A and Sõukand, R}, title = {Diverse in Local, Overlapping in Official Medical Botany: Critical Analysis of Medicinal Plant Records from the Historic Regions of Livonia and Courland in Northeast Europe, 1829-1895.}, journal = {Plants (Basel, Switzerland)}, volume = {11}, number = {8}, pages = {}, pmid = {35448792}, issn = {2223-7747}, support = {714874/ERC_/European Research Council/International ; }, abstract = {Works on historical ethnobotany can help shed light on past plant uses and humankind's relationships with the environment. We analyzed medicinal plant uses from the historical regions of Livonia and Courland in Northeast Europe based on three studies published within the 19th century by medical doctors researching local ethnomedicine. The sources were manually searched, and information extracted and entered into a database. In total, there were 603 detailed reports of medicinal plant use, which refer to 219 taxa belonging to 69 families and one unidentified local taxon. Dominant families were Asteraceae (14%), Solanaceae (7%), Rosaceae (6%), and Apiaceae (5%). The majority of use reports were attributed to the treatment of four disease categories: digestive (24%), skin (22%), respiratory (11%), and general (11%). The small overlapping portion (14 taxa mentioned by all three authors and another 27 taxa named by two authors) contained a high proportion of taxa (46%) mentioned in Dioscorides, which were widespread during that period in scholarly practice. Despite the shared flora, geographical vicinity, and culturally similar backgrounds, the medicinal use of plants in historical Courland and Livonia showed high biocultural diversity and reliance on wild taxa. We encourage researchers to study and re-evaluate the historical ethnobotanical literature and provide some suggestions on how to do this effectively.}, } @article {pmid35448419, year = {2022}, author = {Picone, M and Distefano, GG and Marchetto, D and Russo, M and Baccichet, M and Zangrando, R and Gambaro, A and Volpi Ghirardini, A}, title = {Inhibition of Larval Development of Marine Copepods Acartia tonsa by Neonicotinoids.}, journal = {Toxics}, volume = {10}, number = {4}, pages = {}, pmid = {35448419}, issn = {2305-6304}, support = {Not applicable//Consortium for Coordination of Research activities Concerning the Venice Lagoon System/ ; }, abstract = {Neonicotinoids (NEOs) are neurotoxic pesticides widely used in agriculture due to their high effectiveness against pest insects. Despite their widespread use, very little is known about their toxicity towards marine organisms, including sensitive and ecologically relevant taxa such as copepods. Thus, we investigated the toxicity of five widely used NEOs, including acetamiprid (ACE), clothianidin (CLO), imidacloprid (IMI), thiacloprid (THI), and thiamethoxam (TMX), to assess their ability to inhibit the larval development of the copepod Acartia tonsa. The more toxic NEOs were ACE (EC50 = 0.73 μg L[-1]), TMX (EC50 = 1.71 μg L[-1]) and CLO (EC50 = 1.90 μg L[-1]), while the less toxic compound was IMI (EC50 = 8.84 μg L[-1]). Early life-stage mortality was unaffected by NEOs at all of the tested concentrations. The calculated toxicity data indicated that significant effects due to ACE (EC20 = 0.12 μg L[-1]), THI (EC20 = 0.88 μg L[-1]) and TMX (EC20 = 0.18 μg L[-1]) are observed at concentrations lower than established chronic aquatic life benchmarks reported by USEPA for freshwater invertebrates. Nevertheless, since environmental concentrations of NEOs are generally lower than the threshold concentrations we calculated for A. tonsa, the effects may be currently of concern only in estuaries receiving wastewater discharges or experiencing intense runoff from agriculture.}, } @article {pmid35442313, year = {2022}, author = {Mota, FM and Ferreira Júnior, MA and Cardoso, AIQ and Pompeo, CM and Frota, OP and Tsuha, DH and Souza, AS}, title = {Analysis of the temporal trend of mortality from sickle cell anemia in Brazil.}, journal = {Revista brasileira de enfermagem}, volume = {75}, number = {4}, pages = {e20210640}, doi = {10.1590/0034-7167-2021-0640}, pmid = {35442313}, issn = {1984-0446}, mesh = {Adult ; *Anemia, Sickle Cell/complications/epidemiology ; Brazil/epidemiology ; Female ; Humans ; Incidence ; *Information Systems ; Male ; }, abstract = {OBJECTIVES: To analyze the temporal trend of mortality from sickle cell anemia in Brazil, by region, in the period 1997-2017.

METHODS: epidemiological study, with an ecological design, with a temporal trend, carried out with data from the Mortality Information System. For descriptive analysis, absolute and relative frequencies were used. In the correlation analysis, the ANOVA test was used, followed by Tukey's post-test. The temporal trend was obtained using the cubic polynomial regression test.

RESULTS: 6,813 deaths from sickle cell anemia were registered. Brown individuals (50.87%) were more frequent, with a predominance of males (50.4%), aged between 25 and 34 years and a higher incidence of deaths in the Midwest (0.25/100 thousand inhabitants). The time curve showed an increasing trend of deaths in the country between 1997 and 2015 (R2 = 0.98).

CONCLUSIONS: sickle cell anemia showed increasing mortality in the 21 years analyzed and alerts health professionals and managers.}, } @article {pmid35440731, year = {2022}, author = {Stratmann, T}, title = {The ProkaBioDen database, a global database of benthic prokaryotic biomasses and densities in the marine realm.}, journal = {Scientific data}, volume = {9}, number = {1}, pages = {179}, pmid = {35440731}, issn = {2052-4463}, support = {856.18.003//Nederlandse Organisatie voor Wetenschappelijk Onderzoek (Netherlands Organisation for Scientific Research)/ ; VI.Veni.212.211//Nederlandse Organisatie voor Wetenschappelijk Onderzoek (Netherlands Organisation for Scientific Research)/ ; 019.182EN.012//Nederlandse Organisatie voor Wetenschappelijk Onderzoek (Netherlands Organisation for Scientific Research)/ ; }, mesh = {*Archaea ; *Bacteria ; Biomass ; Databases, Factual ; Geologic Sediments/microbiology ; }, abstract = {Benthic prokaryotes include Bacteria and Archaea and dominate densities of marine benthos. They play major roles in element cycles and heterotrophic, chemoautotrophic, and phototrophic carbon production. To understand how anthropogenic disturbances and climate change might affect these processes, better estimates of prokaryotic biomasses and densities are required. Hence, I developed the ProkaBioDen database, the largest open-access database of benthic prokaryotic biomasses and densities in marine surface sediments. In total, the database comprises 1,089 georeferenced benthic prokaryotic biomass and 1,875 density records extracted from 85 and 112 studies, respectively. I identified all references applying the procedures for systematic reviews and meta analyses and report prokaryotic biomasses as g C cm[-3] sediment, g C g[-1] sediment, and g C m[-2]. Density records are presented as cell cm[-3] sediment, cell g[-1] sediment/ sulfide/ vent precipitate, and cell m[-2]. This database should serve as reference to close sampling gaps in the future.}, } @article {pmid35438376, year = {2022}, author = {Sütçüoğlu, GG and Önaç, AK}, title = {A site selection model proposal for sustainable urban regeneration: case study of Karşıyaka, İzmir, Turkey.}, journal = {Environmental monitoring and assessment}, volume = {194}, number = {5}, pages = {378}, pmid = {35438376}, issn = {1573-2959}, mesh = {Cities ; *Environmental Monitoring ; *Geographic Information Systems ; Turkey ; Urban Renewal ; }, abstract = {Cities that have become the most crowded living spaces in all over the world are facing numerous problems and challenges such as environmental pollution, heavy traffic, urban dilapidation, lack of facility provision, and economic decline. Urban regeneration, which is an important agenda for both academia and politicians, aims to address these urban problems which are mostly caused by overpopulation. As the urban regeneration is a complex issue that requires to consider numerous components, regeneration initiatives cannot always achieve sustainable urban applications, which are causing new urban and social problems. Previous research have mainly focused on one aspect of urban renewal, in which a comprehensive perspective is lacking by just considering the physical aspects of the regeneration areas while lacking the social aspects and current global issues such as climate change and urban adaptation. A multi-criteria decision-making process for site selection and sustainable regeneration plan would contribute to better regeneration outcomes. Therefore, this study proposes a multi-criteria decision-making process which combines the analytical hierarchy process (AHP) and geographical ınformation system (GIS) at site selection phase of urban regeneration on a case study that includes all the physical and social components of the study area as well as focusing on sustaining ecological, economic, and social features.}, } @article {pmid35437414, year = {2022}, author = {Simon, ADF and Adamczyk, EM and Basman, A and Chu, JWF and Gartner, HN and Fletcher, K and Gibbs, CJ and Gibbs, DM and Gilmore, SR and Harbo, RM and Harris, LH and Humphrey, E and Lamb, A and Lambert, P and McDaniel, N and Scott, J and Starzomski, BM}, title = {Toward an atlas of Salish Sea biodiversity: the flora and fauna of Galiano Island, British Columbia, Canada. Part I. Marine zoology.}, journal = {Biodiversity data journal}, volume = {10}, number = {}, pages = {e76050}, pmid = {35437414}, issn = {1314-2828}, abstract = {BACKGROUND: Based on records dating from 1859 to 2021, we provide an overview of the marine animal diversity reported for Galiano Island, British Columbia, Canada. More than 650 taxa are represented by 20,000 species occurrence records in this curated dataset, which includes dive records documented through the Pacific Marine Life Surveys, museum voucher specimens, ecological data and crowd-sourced observations from the BC Cetacean Sightings Network and iNaturalist.

NEW INFORMATION: We describe Galiano Island's marine animal diversity in relation to the Salish Sea's overall biodiversity and quantify the proportional contributions of different types of sampling effort to our current local knowledge. Overviews are provided for each taxonomic group in a format intended to be accessible to amateur naturalists interested in furthering research into the region's marine biodiversity. In summary, we find that the Pacific Marine Life Surveys, a regional community science diving initiative, account for 60% of novel records reported for Galiano Island. Voucher specimens account for 19% and crowd-sourced biodiversity data 18% of novel records, respectively, with the remaining 3% of reports coming from other sources. These findings shed light on the complementarity of different types of sampling effort and demonstrate the potential for community science to contribute to the global biodiversity research community. We present a biodiversity informatics framework that is designed to enable these practices by supporting collaboration among researchers and communities in the collection, curation and dissemination of biodiversity data.}, } @article {pmid35434770, year = {2022}, author = {Yocom, L and Ogle, K and Peltier, D and Szejner, P and Liu, Y and Monson, RK}, title = {Tree growth sensitivity to climate varies across a seasonal precipitation gradient.}, journal = {Oecologia}, volume = {198}, number = {4}, pages = {933-946}, pmid = {35434770}, issn = {1432-1939}, support = {1065790//national science foundation/ ; 1458867//national science foundation/ ; 1754430//national science foundation/ ; }, mesh = {Climate Change ; *Forests ; *Pinus ponderosa ; Seasons ; Temperature ; }, abstract = {Spatial patterns of precipitation in the southwestern United States result in a complex gradient from winter-to-summer moisture dominance that influences tree growth. In response, tree growth exhibits seasonal-to-annual variability that is evident in the growth of whole tree rings, and in sub-annual sections such as earlywood and latewood. We evaluated the influence of precipitation and temperature on the growth of Pinus ponderosa trees in 11 sites in the southwestern US. Precipitation during the year of growth and the prior year accounted for about half of the climate influence on annual growth, with the other half reflecting conditions 2-4 years prior to growth, indicating that individual trees do indeed exhibit multi-year "memory" of climate. Trees in wetter sites exhibited weaker influence of past precipitation inputs, but longer memory of climatic variability. Conversely, trees in dry sites exhibited shorter memory of long-term climatic variability, but greater sensitivity to past precipitation effects. These results are consistent with the existence of complex interactions between endogenous (phenotype) effects and exogenous (climate) effects in controlling climate memory in trees. After accounting for climate, residual variability in latewood growth was negatively correlated with earlywood growth, indicating a potential tradeoff between latewood versus earlywood growth. This study provides new insights that will assist the accurate prediction of woody biomass growth and forest carbon sequestration across a southwestern US precipitation gradient.}, } @article {pmid35433514, year = {2022}, author = {Franklin, S and Aitken, SL and Shi, Y and Sahasrabhojane, PV and Robinson, S and Peterson, CB and Daver, N and Ajami, NA and Kontoyiannis, DP and Shelburne, SA and Galloway-Peña, J}, title = {Oral and Stool Microbiome Coalescence and Its Association With Antibiotic Exposure in Acute Leukemia Patients.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {848580}, pmid = {35433514}, issn = {2235-2988}, support = {K01 AI143881/AI/NIAID NIH HHS/United States ; P30 CA016672/CA/NCI NIH HHS/United States ; T32 CA096520/CA/NCI NIH HHS/United States ; }, mesh = {Anti-Bacterial Agents/pharmacology/therapeutic use ; Feces/microbiology ; *Gastrointestinal Microbiome ; Humans ; *Leukemia, Myeloid, Acute/complications/drug therapy ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Failure to maintain segregation of oral and gut microbial communities has been linked to several diseases. We sought to characterize oral-fecal microbiome community coalescence, ectopic extension of oral bacteria, clinical variables contributing to this phenomenon, and associated infectious consequences by analyzing the 16S rRNA V4 sequences of longitudinal fecal (n=551) and oral (n=737) samples from 97 patients with acute myeloid leukemia (AML) receiving induction chemotherapy (IC). Clustering observed in permutation based multivariate analysis of variance (PERMANOVA) of Bray-Curtis dissimilarity and PCoA plot of UniFrac distances between intra-patient longitudinal oral-stool sample pairs suggested potential oral-stool microbial community coalescence. Bray-Curtis dissimilarities and UniFrac distances were used to create an objective definition of microbial community coalescence. We determined that only 23 of the 92 patients exhibited oral-stool community coalescence. This was validated through a linear mixed model which determined that patients who experienced coalescence had an increased proportion of shared to unique OTUs between their oral-stool sample pairs over time compared to non-coalesced patients. Evaluation of longitudinal microbial characteristics revealed that patients who experienced coalescence had increased stool abundance of Streptococcus and Stenotrophomonas compared to non-coalesced patients. When treated as a time-varying covariate, each additional day of linezolid (HR 1.15, 95% CI 1.06 - 1.24, P <0.001), meropenem (HR 1.13, 95% CI 1.05 - 1.21, P = 0.001), metronidazole (HR 1.13, 95% CI 1.05 - 1.21, P = 0.001), and cefepime (HR 1.10, 95% CI 1.01 - 1.18, P = 0.021) increased the hazard of oral-stool microbial community coalescence. Levofloxacin receipt was associated with a lower risk of microbiome community coalescence (HR 0.75, 95% CI 0.61 - 0.93, P = 0.009). By the time of neutrophil recovery, the relative abundance of Bacteroidia (P<0.001), Fusobacteria (P=0.012), and Clostridia (P=0.013) in the stool were significantly lower in patients with oral-gut community coalescence. Exhibiting oral-stool community coalescence was associated with the occurrence of infections prior to neutrophil recovery (P=0.002), as well as infections during the 90 days post neutrophil recovery (P=0.027). This work elucidates specific antimicrobial effects on microbial ecology and furthers the understanding of oral/intestinal microbial biogeography and its implications for adverse clinical outcomes.}, } @article {pmid35432266, year = {2022}, author = {Ji, C and Huang, J and Yu, H and Tian, Y and Rao, X and Zhang, X}, title = {Do the Reclaimed Fungal Communities Succeed Toward the Original Structure in Eco-Fragile Regions of Coal Mining Disturbances? A Case Study in North China Loess-Aeolian Sand Area.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {770715}, pmid = {35432266}, issn = {1664-302X}, abstract = {Mining activity has caused serious environmental damage, particularly for soil ecosystems. How the soil fungal community evolves in mine reclamation and what are the succession patterns of molecular ecological networks still needs to be studied in depth. We used high-throughput sequencing to explore the changes in soil fungal communities, molecular ecological networks, and interactions with soil environmental factors in five different ages (the including control group) during 14 years of reclamation in eco-fragile mines. The results showed that the abundance and diversity of soil fungi after 14 years of reclamation were close to, but still lower than, those in the undisturbed control area, but the dominant phylum was Ascomycota. Soil nitrate-N, C/N ratio, pH, and water content significantly affected the fungal community with increasing reclamation ages. Moreover, we found that Mortierellomycota, despite its high relative abundance, had little significant connectivity with other species in the molecular ecological network. Fungal molecular ecological networks evolve with increasing ages of reclamation, with larger modules, more positive connections, and tighter networks, forming large modules of more than 60 nodes by age 9. The large modules were composed mainly of Ascomycota and Basidiomycota, which can form mycorrhiza with plant roots, and are not only capable of degrading pollution but are also "encouraged" by most (more than 64%) physicochemical factors in the soil environment. The results can provide a basis for scientific mine ecological restoration, especially for eco-fragile regions.}, } @article {pmid35429140, year = {2022}, author = {Furlan, E and Derepasko, D and Torresan, S and Pham, HV and Fogarin, S and Critto, A}, title = {Ecosystem services at risk in Italy from coastal inundation under extreme sea level scenarios up to 2050: A spatially resolved approach supporting climate change adaptation.}, journal = {Integrated environmental assessment and management}, volume = {18}, number = {6}, pages = {1564-1577}, doi = {10.1002/ieam.4620}, pmid = {35429140}, issn = {1551-3793}, support = {//SAVEMEDCOASTS Project/ ; }, mesh = {*Ecosystem ; *Climate Change ; Sea Level Rise ; Biodiversity ; Italy ; }, abstract = {According to the latest projections of the Intergovernmental Panel on Climate Change, at the end of the century, coastal zones and low-lying ecosystems will be increasingly threatened by rising global mean sea levels. In order to support integrated coastal zone management and advance the basic "source-pathway-receptor-consequence" approach focused on traditional receptors (e.g., population, infrastructure, and economy), a novel risk framework is proposed able to evaluate potential risks of loss or degradation of ecosystem services (ESs) due to projected extreme sea level scenarios in the Italian coast. Three risk scenarios for the reference period (1969-2010) and future time frame up to 2050 under RCP4.5 and RCP8.5 are developed by integrating extreme water-level projections related to changing climate conditions, with vulnerability information about the topography, distance from coastlines, and presence of artificial protections. A risk assessment is then performed considering the potential effects of the spatial-temporal variability of inundations and land use on the supply level and spatial distribution of ESs. The results of the analysis are summarized into a spatially explicit risk index, useful to rank coastal areas more prone to ESs losses or degradation due to coastal inundation at the national scale. Overall, the Northern Adriatic coast is scored at high risk of ESs loss or degradation in the future scenario. Other small coastal strips with medium risk scores are the Eastern Puglia coast, Western Sardinia, and Tuscany's coast. The ESs Coastal Risk Index provides an easy-to-understand screening assessment that could support the prioritization of areas for coastal adaptation at the national scale. Moreover, this index allows the direct evaluation of the public value of ecosystems and supports more effective territorial planning and environmental management decisions. In particular, it could support the mainstreaming of ecosystem-based approaches (e.g., ecological engineering and green infrastructures) to mitigate the risks of climate change and extreme events while protecting ecosystems and biodiversity. Integr Environ Assess Manag 2022;18:1564-1577. © 2021 SETAC.}, } @article {pmid35420897, year = {2022}, author = {Reich, NG and Lessler, J and Funk, S and Viboud, C and Vespignani, A and Tibshirani, RJ and Shea, K and Schienle, M and Runge, MC and Rosenfeld, R and Ray, EL and Niehus, R and Johnson, HC and Johansson, MA and Hochheiser, H and Gardner, L and Bracher, J and Borchering, RK and Biggerstaff, M}, title = {Collaborative Hubs: Making the Most of Predictive Epidemic Modeling.}, journal = {American journal of public health}, volume = {112}, number = {6}, pages = {839-842}, pmid = {35420897}, issn = {1541-0048}, support = {U01IP001137/ACL/ACL HHS/United States ; U01 IP001121/IP/NCIRD CDC HHS/United States ; U24 GM132013/GM/NIGMS NIH HHS/United States ; R01 GM140564/GM/NIGMS NIH HHS/United States ; U01 IP001137/IP/NCIRD CDC HHS/United States ; NU38OT000297/CC/CDC HHS/United States ; U01 IP001122/IP/NCIRD CDC HHS/United States ; /WT_/Wellcome Trust/United Kingdom ; R35 GM119582/GM/NIGMS NIH HHS/United States ; 210758/Z/18/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {*Epidemics ; Humans ; }, } @article {pmid35416792, year = {2022}, author = {Wang, M and Li, S and Zheng, T and Li, N and Shi, Q and Zhuo, X and Ding, R and Huang, Y}, title = {Big Data Health Care Platform With Multisource Heterogeneous Data Integration and Massive High-Dimensional Data Governance for Large Hospitals: Design, Development, and Application.}, journal = {JMIR medical informatics}, volume = {10}, number = {4}, pages = {e36481}, pmid = {35416792}, issn = {2291-9694}, abstract = {BACKGROUND: With the advent of data-intensive science, a full integration of big data science and health care will bring a cross-field revolution to the medical community in China. The concept big data represents not only a technology but also a resource and a method. Big data are regarded as an important strategic resource both at the national level and at the medical institutional level, thus great importance has been attached to the construction of a big data platform for health care.

OBJECTIVE: We aimed to develop and implement a big data platform for a large hospital, to overcome difficulties in integrating, calculating, storing, and governing multisource heterogeneous data in a standardized way, as well as to ensure health care data security.

METHODS: The project to build a big data platform at West China Hospital of Sichuan University was launched in 2017. The West China Hospital of Sichuan University big data platform has extracted, integrated, and governed data from different departments and sections of the hospital since January 2008. A master-slave mode was implemented to realize the real-time integration of multisource heterogeneous massive data, and an environment that separates heterogeneous characteristic data storage and calculation processes was built. A business-based metadata model was improved for data quality control, and a standardized health care data governance system and scientific closed-loop data security ecology were established.

RESULTS: After 3 years of design, development, and testing, the West China Hospital of Sichuan University big data platform was formally brought online in November 2020. It has formed a massive multidimensional data resource database, with more than 12.49 million patients, 75.67 million visits, and 8475 data variables. Along with hospital operations data, newly generated data are entered into the platform in real time. Since its launch, the platform has supported more than 20 major projects and provided data service, storage, and computing power support to many scientific teams, facilitating a shift in the data support model-from conventional manual extraction to self-service retrieval (which has reached 8561 retrievals per month).

CONCLUSIONS: The platform can combine operation systems data from all departments and sections in a hospital to form a massive high-dimensional high-quality health care database that allows electronic medical records to be used effectively and taps into the value of data to fully support clinical services, scientific research, and operations management. The West China Hospital of Sichuan University big data platform can successfully generate multisource heterogeneous data storage and computing power. By effectively governing massive multidimensional data gathered from multiple sources, the West China Hospital of Sichuan University big data platform provides highly available data assets and thus has a high application value in the health care field. The West China Hospital of Sichuan University big data platform facilitates simpler and more efficient utilization of electronic medical record data for real-world research.}, } @article {pmid35412148, year = {2022}, author = {Mori, Y and Okawara, M and Fujimoto, K and Oba, T and Sato, N and Kohi, S and Tamura, T and Nagata, J and Fujino, Y and Fushimi, K and Matsuda, S and Shibao, K and Hirata, K}, title = {Evaluation of cholecystectomy in older individuals using real-world data: a multilevel analysis based on a nationwide administrative database in Japan.}, journal = {Journal of gastroenterology}, volume = {57}, number = {6}, pages = {433-440}, pmid = {35412148}, issn = {1435-5922}, mesh = {*Activities of Daily Living ; Aged ; Aged, 80 and over ; *Cholecystectomy ; Humans ; Japan/epidemiology ; Length of Stay ; Multilevel Analysis ; Postoperative Complications/epidemiology ; Retrospective Studies ; Treatment Outcome ; }, abstract = {BACKGROUND: In the present study, we aimed to evaluate the clinical outcomes of cholecystectomy in older individuals.

METHODS: In this retrospective study, data from the Japanese Diagnosis Procedure Combination database on 96,620 patients who had undergone cholecystectomy at 1060 hospitals from 2018 to 2020 were analyzed. Patients were divided into five age groups: < 75, 75-79, 80-84, 85-89, and ≥ 90 years. Associations between postoperative outcomes and age group were investigated by logistic regression analysis. Mean differences between age groups in time to postoperative recovery and cost were also compared.

RESULTS: Older patients had higher rates of poor scores for activities of daily living and preoperative comorbidity. Compared with the youngest age group (< 75 years), the odds ratios for in-hospital mortality were 3.00 (95% confidence interval, 1.74-5.19), 7.54 (4.73-12.01), 13.47 (8.21-22.14), and 27.64 (15.56-49.09), in the 75-79, 80-84, 85-89, and ≥ 90-year-old age group, respectively (all p < 0.001). Furthermore, the length of postoperative hospital stay and rates of postoperative complications, postoperative reintubation, and reoperation with general anesthesia increased significantly in parallel with increasing age, the highest rates being in the ≥ 90 year-old age group.

CONCLUSIONS: Our real-world data highlight the worse postoperative outcomes, including a higher mortality rate, in older patients undergoing cholecystectomy. Care should be taken when considering the indications for surgery in such patients.}, } @article {pmid35398990, year = {2022}, author = {DeRaad, DA}, title = {snpfiltr: An R package for interactive and reproducible SNP filtering.}, journal = {Molecular ecology resources}, volume = {22}, number = {6}, pages = {2443-2453}, doi = {10.1111/1755-0998.13618}, pmid = {35398990}, issn = {1755-0998}, mesh = {Computational Biology/methods ; Genomics/methods ; *Polymorphism, Single Nucleotide ; Sequence Analysis ; *Software ; }, abstract = {Here, I describe the R package snpfiltr and demonstrate its functionality as the backbone of a customizable, reproducible single nucleotide polymorphism (SNP) filtering pipeline implemented exclusively via the widely adopted R programming language. SNPfiltR extends existing SNP filtering functionalities by automating the visualization of key parameters such as sequencing depth, quality, and missing data proportion, allowing users to visually optimize and implement filtering thresholds within a single, cohesive work session. All SNPfiltR functions require vcfr objects as input, which can be easily generated by reading a SNP data set stored in standard variant call format (vcf) into an R working environment using the function read.vcfR() from the R package vcfr. Performance and accuracy benchmarking reveal that for moderately sized SNP data sets (up to 50 M genotypes, plus associated quality information), SNPfiltR performs filtering with comparable accuracy and efficiency to current state of the art command-line-based programs. These results indicate that for most reduced-representation genomic data sets, SNPfiltR is an ideal choice for investigating, visualizing, and filtering SNPs as part of a user friendly bioinformatic pipeline. The snpfiltr package can be downloaded from CRAN with the command install.packages("snpfiltr"), and the current development version is available from GitHub at: (github.com/DevonDeRaad/SNPfiltR). Thorough documentation for SNPfiltR, including multiple comprehensive vignettes detailing realistic use-cases, is available at the website: devonderaad.github.io/SNPfiltR/.}, } @article {pmid35398432, year = {2022}, author = {Zheng, F and Xu, S and Chai, W and Liu, D and Lu, H}, title = {Fermentation liquid as a carbon source for wastewater nitrogen removal reduced nitrogenous disinfection byproduct formation potentials of the effluent.}, journal = {The Science of the total environment}, volume = {832}, number = {}, pages = {155115}, doi = {10.1016/j.scitotenv.2022.155115}, pmid = {35398432}, issn = {1879-1026}, mesh = {Carbon ; Denitrification ; Disinfection ; Fermentation ; Nitrogen/analysis ; Sewage ; Wastewater/analysis ; *Water Pollutants, Chemical/analysis ; *Water Purification ; }, abstract = {Sludge alkaline fermentation liquid (SAFL) is an alternative to sodium acetate (NaAc) in enhancing wastewater nitrogen removal. Upon SAFL addition, dissolved organic nitrogen (DON) can be externally introduced or biologically synthesized during nitrogen removal, which is an important precursor to toxic nitrogenous disinfection by-products (N-DBPs). This study aims to evaluate the effects of different carbon source addition on effluent DON concentration, composition, and N-DBP formation potentials. A lab-scale A[2]O system treating real municipal wastewater was operated with NaAc or SAFL as external carbon sources. DON molecules and potential N-DBP precursors were identified by Orbitrap mass spectrometry. Subsequently, major microorganisms contributing to DON biosynthesis were suggested based on metagenomics. It was found that effluent DON was higher with SAFL as the carbon source than NaAc (1.51 ± 0.24 v.s. 0.56 ± 0.08 mg N/L, p < 0.05). Nevertheless, dichloroacetonitrile and nitrosamine formation potentials (7.14 ± 1.02 and 1.57 ± 0.07 μg/mg DON-N, respectively) of the effluent with SAFL addition were 42.79 ± 2.42% and 54.89 ± 1.70% lower than those of NaAc. Protein- and lignin-like compounds were the most abundant DON molecules in the effluent, where alanine, glycine and tyrosine were important precursors to N-DBPs. Azonexus and Flavobacterium spp. were positively correlated with these precursors, and possessed key genes involved in precursor synthesis. SAFL is a promising carbon source, not only for achieving efficient inorganic nitrogen and DON removals, but also for reducing N-DBP formation potentials of chlorinated effluent.}, } @article {pmid35396580, year = {2022}, author = {Trubetskoy, V and Pardiñas, AF and Qi, T and Panagiotaropoulou, G and Awasthi, S and Bigdeli, TB and Bryois, J and Chen, CY and Dennison, CA and Hall, LS and Lam, M and Watanabe, K and Frei, O and Ge, T and Harwood, JC and Koopmans, F and Magnusson, S and Richards, AL and Sidorenko, J and Wu, Y and Zeng, J and Grove, J and Kim, M and Li, Z and Voloudakis, G and Zhang, W and Adams, M and Agartz, I and Atkinson, EG and Agerbo, E and Al Eissa, M and Albus, M and Alexander, M and Alizadeh, BZ and Alptekin, K and Als, TD and Amin, F and Arolt, V and Arrojo, M and Athanasiu, L and Azevedo, MH and Bacanu, SA and Bass, NJ and Begemann, M and Belliveau, RA and Bene, J and Benyamin, B and Bergen, SE and Blasi, G and Bobes, J and Bonassi, S and Braun, A and Bressan, RA and Bromet, EJ and Bruggeman, R and Buckley, PF and Buckner, RL and Bybjerg-Grauholm, J and Cahn, W and Cairns, MJ and Calkins, ME and Carr, VJ and Castle, D and Catts, SV and Chambert, KD and Chan, RCK and Chaumette, B and Cheng, W and Cheung, EFC and Chong, SA and Cohen, D and Consoli, A and Cordeiro, Q and Costas, J and Curtis, C and Davidson, M and Davis, KL and de Haan, L and Degenhardt, F and DeLisi, LE and Demontis, D and Dickerson, F and Dikeos, D and Dinan, T and Djurovic, S and Duan, J and Ducci, G and Dudbridge, F and Eriksson, JG and Fañanás, L and Faraone, SV and Fiorentino, A and Forstner, A and Frank, J and Freimer, NB and Fromer, M and Frustaci, A and Gadelha, A and Genovese, G and Gershon, ES and Giannitelli, M and Giegling, I and Giusti-Rodríguez, P and Godard, S and Goldstein, JI and González Peñas, J and González-Pinto, A and Gopal, S and Gratten, J and Green, MF and Greenwood, TA and Guillin, O and Gülöksüz, S and Gur, RE and Gur, RC and Gutiérrez, B and Hahn, E and Hakonarson, H and Haroutunian, V and Hartmann, AM and Harvey, C and Hayward, C and Henskens, FA and Herms, S and Hoffmann, P and Howrigan, DP and Ikeda, M and Iyegbe, C and Joa, I and Julià, A and Kähler, AK and Kam-Thong, T and Kamatani, Y and Karachanak-Yankova, S and Kebir, O and Keller, MC and Kelly, BJ and Khrunin, A and Kim, SW and Klovins, J and Kondratiev, N and Konte, B and Kraft, J and Kubo, M and Kučinskas, V and Kučinskiene, ZA and Kusumawardhani, A and Kuzelova-Ptackova, H and Landi, S and Lazzeroni, LC and Lee, PH and Legge, SE and Lehrer, DS and Lencer, R and Lerer, B and Li, M and Lieberman, J and Light, GA and Limborska, S and Liu, CM and Lönnqvist, J and Loughland, CM and Lubinski, J and Luykx, JJ and Lynham, A and Macek, M and Mackinnon, A and Magnusson, PKE and Maher, BS and Maier, W and Malaspina, D and Mallet, J and Marder, SR and Marsal, S and Martin, AR and Martorell, L and Mattheisen, M and McCarley, RW and McDonald, C and McGrath, JJ and Medeiros, H and Meier, S and Melegh, B and Melle, I and Mesholam-Gately, RI and Metspalu, A and Michie, PT and Milani, L and Milanova, V and Mitjans, M and Molden, E and Molina, E and Molto, MD and Mondelli, V and Moreno, C and Morley, CP and Muntané, G and Murphy, KC and Myin-Germeys, I and Nenadić, I and Nestadt, G and Nikitina-Zake, L and Noto, C and Nuechterlein, KH and O'Brien, NL and O'Neill, FA and Oh, SY and Olincy, A and Ota, VK and Pantelis, C and Papadimitriou, GN and Parellada, M and Paunio, T and Pellegrino, R and Periyasamy, S and Perkins, DO and Pfuhlmann, B and Pietiläinen, O and Pimm, J and Porteous, D and Powell, J and Quattrone, D and Quested, D and Radant, AD and Rampino, A and Rapaport, MH and Rautanen, A and Reichenberg, A and Roe, C and Roffman, JL and Roth, J and Rothermundt, M and Rutten, BPF and Saker-Delye, S and Salomaa, V and Sanjuan, J and Santoro, ML and Savitz, A and Schall, U and Scott, RJ and Seidman, LJ and Sharp, SI and Shi, J and Siever, LJ and Sigurdsson, E and Sim, K and Skarabis, N and Slominsky, P and So, HC and Sobell, JL and Söderman, E and Stain, HJ and Steen, NE and Steixner-Kumar, AA and Stögmann, E and Stone, WS and Straub, RE and Streit, F and Strengman, E and Stroup, TS and Subramaniam, M and Sugar, CA and Suvisaari, J and Svrakic, DM and Swerdlow, NR and Szatkiewicz, JP and Ta, TMT and Takahashi, A and Terao, C and Thibaut, F and Toncheva, D and Tooney, PA and Torretta, S and Tosato, S and Tura, GB and Turetsky, BI and Üçok, A and Vaaler, A and van Amelsvoort, T and van Winkel, R and Veijola, J and Waddington, J and Walter, H and Waterreus, A and Webb, BT and Weiser, M and Williams, NM and Witt, SH and Wormley, BK and Wu, JQ and Xu, Z and Yolken, R and Zai, CC and Zhou, W and Zhu, F and Zimprich, F and Atbaşoğlu, EC and Ayub, M and Benner, C and Bertolino, A and Black, DW and Bray, NJ and Breen, G and Buccola, NG and Byerley, WF and Chen, WJ and Cloninger, CR and Crespo-Facorro, B and Donohoe, G and Freedman, R and Galletly, C and Gandal, MJ and Gennarelli, M and Hougaard, DM and Hwu, HG and Jablensky, AV and McCarroll, SA and Moran, JL and Mors, O and Mortensen, PB and Müller-Myhsok, B and Neil, AL and Nordentoft, M and Pato, MT and Petryshen, TL and Pirinen, M and Pulver, AE and Schulze, TG and Silverman, JM and Smoller, JW and Stahl, EA and Tsuang, DW and Vilella, E and Wang, SH and Xu, S and , and , and , and , and Adolfsson, R and Arango, C and Baune, BT and Belangero, SI and Børglum, AD and Braff, D and Bramon, E and Buxbaum, JD and Campion, D and Cervilla, JA and Cichon, S and Collier, DA and Corvin, A and Curtis, D and Forti, MD and Domenici, E and Ehrenreich, H and Escott-Price, V and Esko, T and Fanous, AH and Gareeva, A and Gawlik, M and Gejman, PV and Gill, M and Glatt, SJ and Golimbet, V and Hong, KS and Hultman, CM and Hyman, SE and Iwata, N and Jönsson, EG and Kahn, RS and Kennedy, JL and Khusnutdinova, E and Kirov, G and Knowles, JA and Krebs, MO and Laurent-Levinson, C and Lee, J and Lencz, T and Levinson, DF and Li, QS and Liu, J and Malhotra, AK and Malhotra, D and McIntosh, A and McQuillin, A and Menezes, PR and Morgan, VA and Morris, DW and Mowry, BJ and Murray, RM and Nimgaonkar, V and Nöthen, MM and Ophoff, RA and Paciga, SA and Palotie, A and Pato, CN and Qin, S and Rietschel, M and Riley, BP and Rivera, M and Rujescu, D and Saka, MC and Sanders, AR and Schwab, SG and Serretti, A and Sham, PC and Shi, Y and St Clair, D and Stefánsson, H and Stefansson, K and Tsuang, MT and van Os, J and Vawter, MP and Weinberger, DR and Werge, T and Wildenauer, DB and Yu, X and Yue, W and Holmans, PA and Pocklington, AJ and Roussos, P and Vassos, E and Verhage, M and Visscher, PM and Yang, J and Posthuma, D and Andreassen, OA and Kendler, KS and Owen, MJ and Wray, NR and Daly, MJ and Huang, H and Neale, BM and Sullivan, PF and Ripke, S and Walters, JTR and O'Donovan, MC and , }, title = {Mapping genomic loci implicates genes and synaptic biology in schizophrenia.}, journal = {Nature}, volume = {604}, number = {7906}, pages = {502-508}, pmid = {35396580}, issn = {1476-4687}, support = {R01 MH116281/MH/NIMH NIH HHS/United States ; 5R01 MH101519/NH/NIH HHS/United States ; 085475/B/08/Z/WT_/Wellcome Trust/United Kingdom ; R01 MH124873/MH/NIMH NIH HHS/United States ; U01 MH109536/MH/NIMH NIH HHS/United States ; R01 MH101519/MH/NIMH NIH HHS/United States ; MC_UU_00007/10/MRC_/Medical Research Council/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; MR/L010305/1/MRC_/Medical Research Council/United Kingdom ; G0901310/MRC_/Medical Research Council/United Kingdom ; 085475/Z/08/Z/WT_/Wellcome Trust/United Kingdom ; R01 MH119243/MH/NIMH NIH HHS/United States ; G0800509/MRC_/Medical Research Council/United Kingdom ; R01 MH106575/MH/NIMH NIH HHS/United States ; G1100583/MRC_/Medical Research Council/United Kingdom ; R37 NS036715/NS/NINDS NIH HHS/United States ; K01 MH121659/MH/NIMH NIH HHS/United States ; U01 MH109514/MH/NIMH NIH HHS/United States ; }, mesh = {Alleles ; Genetic Predisposition to Disease/genetics ; *Genome-Wide Association Study ; Genomics ; Humans ; Polymorphism, Single Nucleotide/genetics ; *Schizophrenia/genetics ; }, abstract = {Schizophrenia has a heritability of 60-80%[1], much of which is attributable to common risk alleles. Here, in a two-stage genome-wide association study of up to 76,755 individuals with schizophrenia and 243,649 control individuals, we report common variant associations at 287 distinct genomic loci. Associations were concentrated in genes that are expressed in excitatory and inhibitory neurons of the central nervous system, but not in other tissues or cell types. Using fine-mapping and functional genomic data, we identify 120 genes (106 protein-coding) that are likely to underpin associations at some of these loci, including 16 genes with credible causal non-synonymous or untranslated region variation. We also implicate fundamental processes related to neuronal function, including synaptic organization, differentiation and transmission. Fine-mapped candidates were enriched for genes associated with rare disruptive coding variants in people with schizophrenia, including the glutamate receptor subunit GRIN2A and transcription factor SP4, and were also enriched for genes implicated by such variants in neurodevelopmental disorders. We identify biological processes relevant to schizophrenia pathophysiology; show convergence of common and rare variant associations in schizophrenia and neurodevelopmental disorders; and provide a resource of prioritized genes and variants to advance mechanistic studies.}, } @article {pmid35396482, year = {2022}, author = {Meyer, F and Fritz, A and Deng, ZL and Koslicki, D and Lesker, TR and Gurevich, A and Robertson, G and Alser, M and Antipov, D and Beghini, F and Bertrand, D and Brito, JJ and Brown, CT and Buchmann, J and Buluç, A and Chen, B and Chikhi, R and Clausen, PTLC and Cristian, A and Dabrowski, PW and Darling, AE and Egan, R and Eskin, E and Georganas, E and Goltsman, E and Gray, MA and Hansen, LH and Hofmeyr, S and Huang, P and Irber, L and Jia, H and Jørgensen, TS and Kieser, SD and Klemetsen, T and Kola, A and Kolmogorov, M and Korobeynikov, A and Kwan, J and LaPierre, N and Lemaitre, C and Li, C and Limasset, A and Malcher-Miranda, F and Mangul, S and Marcelino, VR and Marchet, C and Marijon, P and Meleshko, D and Mende, DR and Milanese, A and Nagarajan, N and Nissen, J and Nurk, S and Oliker, L and Paoli, L and Peterlongo, P and Piro, VC and Porter, JS and Rasmussen, S and Rees, ER and Reinert, K and Renard, B and Robertsen, EM and Rosen, GL and Ruscheweyh, HJ and Sarwal, V and Segata, N and Seiler, E and Shi, L and Sun, F and Sunagawa, S and Sørensen, SJ and Thomas, A and Tong, C and Trajkovski, M and Tremblay, J and Uritskiy, G and Vicedomini, R and Wang, Z and Wang, Z and Wang, Z and Warren, A and Willassen, NP and Yelick, K and You, R and Zeller, G and Zhao, Z and Zhu, S and Zhu, J and Garrido-Oter, R and Gastmeier, P and Hacquard, S and Häußler, S and Khaledi, A and Maechler, F and Mesny, F and Radutoiu, S and Schulze-Lefert, P and Smit, N and Strowig, T and Bremges, A and Sczyrba, A and McHardy, AC}, title = {Critical Assessment of Metagenome Interpretation: the second round of challenges.}, journal = {Nature methods}, volume = {19}, number = {4}, pages = {429-440}, pmid = {35396482}, issn = {1548-7105}, mesh = {Archaea/genetics ; *Metagenome ; *Metagenomics/methods ; Reproducibility of Results ; Sequence Analysis, DNA ; Software ; }, abstract = {Evaluating metagenomic software is key for optimizing metagenome interpretation and focus of the Initiative for the Critical Assessment of Metagenome Interpretation (CAMI). The CAMI II challenge engaged the community to assess methods on realistic and complex datasets with long- and short-read sequences, created computationally from around 1,700 new and known genomes, as well as 600 new plasmids and viruses. Here we analyze 5,002 results by 76 program versions. Substantial improvements were seen in assembly, some due to long-read data. Related strains still were challenging for assembly and genome recovery through binning, as was assembly quality for the latter. Profilers markedly matured, with taxon profilers and binners excelling at higher bacterial ranks, but underperforming for viruses and Archaea. Clinical pathogen detection results revealed a need to improve reproducibility. Runtime and memory usage analyses identified efficient programs, including top performers with other metrics. The results identify challenges and guide researchers in selecting methods for analyses.}, } @article {pmid35395669, year = {2022}, author = {Shaffer, HB and Toffelmier, E and Corbett-Detig, RB and Escalona, M and Erickson, B and Fiedler, P and Gold, M and Harrigan, RJ and Hodges, S and Luckau, TK and Miller, C and Oliveira, DR and Shaffer, KE and Shapiro, B and Sork, VL and Wang, IJ}, title = {Landscape Genomics to Enable Conservation Actions: The California Conservation Genomics Project.}, journal = {The Journal of heredity}, volume = {113}, number = {6}, pages = {577-588}, doi = {10.1093/jhered/esac020}, pmid = {35395669}, issn = {1465-7333}, mesh = {*Ecosystem ; Phylogeny ; *Biodiversity ; Genomics ; Fresh Water ; California ; Conservation of Natural Resources ; }, abstract = {The California Conservation Genomics Project (CCGP) is a unique, critically important step forward in the use of comprehensive landscape genetic data to modernize natural resource management at a regional scale. We describe the CCGP, including all aspects of project administration, data collection, current progress, and future challenges. The CCGP will generate, analyze, and curate a single high-quality reference genome and 100-150 resequenced genomes for each of 153 species projects (representing 235 individual species) that span the ecological and phylogenetic breadth of California's marine, freshwater, and terrestrial ecosystems. The resulting portfolio of roughly 20 000 resequenced genomes will be analyzed with identical informatic and landscape genomic pipelines, providing a comprehensive overview of hotspots of within-species genomic diversity, potential and realized corridors connecting these hotspots, regions of reduced diversity requiring genetic rescue, and the distribution of variation critical for rapid climate adaptation. After 2 years of concerted effort, full funding ($12M USD) has been secured, species identified, and funds distributed to 68 laboratories and 114 investigators drawn from all 10 University of California campuses. The remaining phases of the CCGP include completion of data collection and analyses, and delivery of the resulting genomic data and inferences to state and federal regulatory agencies to help stabilize species declines. The aspirational goals of the CCGP are to identify geographic regions that are critical to long-term preservation of California biodiversity, prioritize those regions based on defensible genomic criteria, and provide foundational knowledge that informs management strategies at both the individual species and ecosystem levels.}, } @article {pmid35395011, year = {2022}, author = {Wang, H and Zhu, Y and Wang, J and Han, H and Niu, J and Chen, X}, title = {Modeling of spatial pattern and influencing factors of cultivated land quality in Henan Province based on spatial big data.}, journal = {PloS one}, volume = {17}, number = {4}, pages = {e0265613}, pmid = {35395011}, issn = {1932-6203}, mesh = {Agriculture ; *Big Data ; China ; City Planning ; Conservation of Natural Resources ; *Pesticides ; Urbanization ; }, abstract = {The quality of cultivated land determines the production capacity of cultivated land and the level of regional development, and also directly affects the food security and ecological safety of the country. This paper starts from the perspective of spatial pattern of cultivated land quality and uses spatial autocorrelation analysis to study the spatial aggregation characteristics and differences of cultivated land quality in Henan Province at the county level scale, and also uses bivariate spatial autocorrelation to analyze the influence of neighboring influences on the quality of cultivated land in the target area. The spatial autoregressive model was used to further analyze the driving factors affecting the quality of cultivated land, and the influence of cultivated land area index was coupled in the process of rating analysis, which was finally used as a basis to propose more precise measures for the protection of cultivated land zoning. The results show that: (1) The quality of cultivated land in Henan Province has a strong spatial correlation (global Moran's I≈0.710) and shows an obvious aggregation pattern in spatial distribution; positive correlation types (high-high and low-low) are concentrated in north-central and western mountainous areas of Henan Province, respectively; negative correlation types are discrete. The negative correlation types are distributed in a discrete manner. (2) The bivariate spatial autocorrelation results show that Slope (Moran's I≈-0.505), Irrigation guarantee rate (IGR, 0.354), Urbanization rate (-0.255), Total agricultural machinery power (TAMP, 0.331) and Pesticide use (0.214) are the main influencing factors. (3) According to the absolute values of the regression coefficients, it can be seen that the magnitude of the influence of different factors on the quality of cultivated land is: Slope (0.089) >IGR (0.025) > Urbanization rate (0.002) > TAMP (0.001) > Pesticide use (1.96e-006). (4) Based on the spatial pattern presented by the spatial autocorrelation results, we proposed corresponding protection zoning measures to provide more scientific reference decisions and technical support for the implementation of refined cultivated land management in Henan Province.}, } @article {pmid35393619, year = {2022}, author = {Hasnin, S and Saltzman, JA and Dev, DA}, title = {Correlates of children's dietary intake in childcare settings: A systematic review.}, journal = {Nutrition reviews}, volume = {80}, number = {5}, pages = {1247-1273}, doi = {10.1093/nutrit/nuab123}, pmid = {35393619}, issn = {1753-4887}, mesh = {Adult ; Child ; Child Care ; Child, Preschool ; Diet, Healthy ; Eating ; Feeding Behavior ; Humans ; *Pediatric Obesity/epidemiology/etiology/prevention & control ; }, abstract = {CONTEXT: Children consume up to two-thirds of their daily dietary requirements in full-time childcare, making the setting a critical vector for preventing childhood obesity.

OBJECTIVE: To summarize the ecological correlates of children's dietary intake in childcare settings that were identified and categorized using the Six-Cs developmental ecological model of contributors to overweight and obesity in childhood.

DATA SOURCES: A literature search was conducted in 4 electronic databases.

STUDY SELECTION: English-language, peer-reviewed publications that investigated at least 1 correlate of children's (ages 2-6 years) dietary intake in childcare settings and measured children's actual consumption of foods and beverages from food groups were included.

DATA EXTRACTION: Correlates were categorized into child, clan, community, and country groups.

RESULTS: A total of 55 studies, which examined 29 correlates, were reviewed. Correlates identified included child's age, sex, characteristics of food provision (namely, food composition, foods and beverages served, portion sizes), repeated exposure, nutrition education, book reading, peer influence, meal service type, and childcare teachers' responsive feeding practices. Policies and participation in Head Start and the Child and Adult Care Food Program could not be determined as correlates of children's dietary intake, owing to a lack of evidence.

CONCLUSION: This review produced a list of correlates to consider in designing interventions to improve children's dietary intake in childcare settings. The correlates could contribute to development of lifelong healthy eating habits, thereby preventing childhood obesity.}, } @article {pmid35391019, year = {2022}, author = {Vandenspiegel, D and Golovatch, SI and Rutherford, MG}, title = {The millipede genus Pandirodesmus Silvestri, 1932 in Trinidad and Tobago, Caribbean, with the description of P. jaggernauthi sp. nov. from Trinidad (Diplopoda, Polydesmida, Chelodesmidae, Pandirodesmini).}, journal = {Zootaxa}, volume = {5104}, number = {4}, pages = {567-576}, doi = {10.11646/zootaxa.5104.4.6}, pmid = {35391019}, issn = {1175-5334}, mesh = {Animals ; *Arthropods ; Caribbean Region ; Surveys and Questionnaires ; Trinidad and Tobago ; }, abstract = {During several collecting surveys for terrestrial micro-molluscs across Trinidad and Tobago, millipedes of the genus Pandirodesmus were taken by MR on both islands. Samples of P. rutherfordi Shelley Smith, 2015, from Tobago, were recovered in addition to those containing a new species from Trinidad: Pandirodesmus jaggernauthi sp. nov. Additional records, illustrations, and descriptive notes are given for P. rutherfordi. A key is presented to all three species of the genus, and their distributions are mapped.}, } @article {pmid35389344, year = {2022}, author = {Villanueva, EMF and Lim, PK and Lim, JJJ and Lim, SC and Lau, PY and Koh, KTS and Tan, E and Kairon, RS and See, WA and Liao, JX and Hee, KM and Vijay, V and Maitra, I and Boon, CJ and Fo, K and Wang, YT and Jaya, R and Hew, LA and Lim, YY and Lee, WQ and Lee, ZQ and Foo, H and Dos Santos, AL and Mutwil, M}, title = {Protist.guru: A Comparative Transcriptomics Database for Protists.}, journal = {Journal of molecular biology}, volume = {434}, number = {11}, pages = {167502}, doi = {10.1016/j.jmb.2022.167502}, pmid = {35389344}, issn = {1089-8638}, mesh = {*Databases, Genetic ; *Eukaryota/genetics ; Gene Expression Profiling ; Sequence Analysis, DNA ; *Transcriptome/genetics ; }, abstract = {During the last few decades, the study of microbial ecology has been enabled by molecular and genomic data. DNA sequencing has revealed the surprising extent of microbial diversity and how microbial processes run global ecosystems. However, significant gaps in our understanding of the microbial world remain, and one example is that microbial eukaryotes, or protists, are still largely neglected. To address this gap, we used gene expression data from 17 protist species to create protist.guru: an online database equipped with tools for identifying co-expressed genes, gene families, and co-expression clusters enriched for specific biological functions. Here, we show how our database can be used to reveal genes involved in essential pathways, such as the synthesis of secondary carotenoids in Haematococcus lacustris. We expect protist.guru to serve as a valuable resource for protistologists, as well as a catalyst for discoveries and new insights into the biological processes of microbial eukaryotes. AVAILABILITY: The database and co-expression networks are freely available from http://protist.guru/. The expression matrices and sample annotations are found in the supplementary data.}, } @article {pmid35388071, year = {2022}, author = {Galbraith, E and Li, J and Rio-Vilas, VJD and Convertino, M}, title = {In.To. COVID-19 socio-epidemiological co-causality.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {5831}, pmid = {35388071}, issn = {2045-2322}, support = {001/WHO_/World Health Organization/International ; }, mesh = {*COVID-19/epidemiology ; Communication ; Humans ; Reproducibility of Results ; SARS-CoV-2 ; *Social Media ; }, abstract = {Social media can forecast disease dynamics, but infoveillance remains focused on infection spread, with little consideration of media content reliability and its relationship to behavior-driven epidemiological outcomes. Sentiment-encoded social media indicators have been poorly developed for expressed text to forecast healthcare pressure and infer population risk-perception patterns. Here we introduce Infodemic Tomography (InTo) as the first web-based interactive infoveillance cybertechnology that forecasts and visualizes spatio-temporal sentiments and healthcare pressure as a function of social media positivity (i.e., Twitter here), considering both epidemic information and potential misinformation. Information spread is measured on volume and retweets, and the Value of Misinformation (VoMi) is introduced as the impact on forecast accuracy where misinformation has the highest dissimilarity in information dynamics. We validated InTo for COVID-19 in New Delhi and Mumbai by inferring distinct socio-epidemiological risk-perception patterns. We forecast weekly hospitalization and cases using ARIMA models and interpolate spatial hospitalization using geostatistical kriging on inferred risk perception curves between tweet positivity and epidemiological outcomes. Geospatial tweet positivity tracks accurately [Formula: see text]60[Formula: see text] of hospitalizations and forecasts hospitalization risk hotspots along risk aversion gradients. VoMi is higher for risk-prone areas and time periods, where misinformation has the highest non-linear predictability, with high incidence and positivity manifesting popularity-seeking social dynamics. Hospitalization gradients, VoMi, effective healthcare pressure and spatial model-data gaps can be used to predict hospitalization fluxes, misinformation, healthcare capacity gaps and surveillance uncertainty. Thus, InTo is a participatory instrument to better prepare and respond to public health crises by extracting and combining salient epidemiological and social surveillance at any desired space-time scale.}, } @article {pmid35384998, year = {2022}, author = {Covre, ER and Pereira, ND and Oliveira, NN and Charlo, PB and Oliveira, MLF and Oliveira, RR and Carreira, L and Facchini, LA and Vissoci, JRN and Salci, MA}, title = {Spatial correlation of covid-19 with intensive care unit beds in Paraná.}, journal = {Revista de saude publica}, volume = {56}, number = {}, pages = {14}, pmid = {35384998}, issn = {1518-8787}, mesh = {Brazil/epidemiology ; *COVID-19/epidemiology ; Government Programs ; Humans ; Intensive Care Units ; Spatial Analysis ; }, abstract = {OBJECTIVE: To analyze the spatial correlation between confirmed cases of covid-19 and the intensive care unit beds exclusive to the disease in municipalities of Paraná.

METHODS: This is an epidemiological study of ecological type which used data from the Epidemiological Report provided by the Department of Health of Paraná on the confirmed cases of covid-19 from March 12, 2020, to January 18, 2021. The number of intensive care beds exclusive to covid-19 in each municipality of Paraná was obtained by the Cadastro Nacional de Estabelecimentos de Saúde (CNES - National Registry of Health Establishments), provided online by the Departamento de Informática do Sistema Único de Saúde (Datasus - Informatics Department of the Brazilian Unified Health System). The Bivariate Moran's Index (local and global) was used to analyze the intensive care bed variable and spatial correlation, with a 5% significance level. LISA Map was used to identify critical and transition areas.

RESULTS: In the analyzed period, we found 499,777 confirmed cases of covid-19 and 1,029 intensive care beds exclusive to the disease in Paraná. We identified a positive spatial autocorrelation between the confirmed cases of covid-19 (0.404-p ≤ 0.001) and intensive care beds exclusive to the disease (0.085-p ≤ 0.001) and disparities between the regions of Paraná.

CONCLUSION: Spatial analysis indicated that confirmed cases of covid-19 are related to the distribution of intensive care beds exclusive to the disease in Paraná, allowing us to find priority areas of care in the state regarding the dissemination and control of the disease.}, } @article {pmid35383841, year = {2022}, author = {Ma, Y and He, S and Gu, T and Liu, Y and He, S and Jiang, Z}, title = {LncRNA: a new perspective on the study of neurological diseases.}, journal = {Biochemical Society transactions}, volume = {50}, number = {2}, pages = {951-963}, doi = {10.1042/BST20211181}, pmid = {35383841}, issn = {1470-8752}, mesh = {Computational Biology/methods ; Gene Regulatory Networks ; Humans ; *MicroRNAs/metabolism ; *Nervous System Diseases/genetics ; *RNA, Long Noncoding/genetics/metabolism ; RNA, Messenger/metabolism ; }, abstract = {Long non-coding RNAs (lncRNAs) are a class of non-coding RNA with a length greater than 200 nt. It has a mRNA-like structure, formed by splicing after transcription, and contains a polyA tail and a promoter, of whom promoter plays a role by binding transcription factors. LncRNAs' sequences are low in conservation, and other species can only find a handful of the same lncRNAs as humans, and there are different splicing ways during the differentiation of identical species, with spatiotemporal expression specificity. With developing high-throughput sequencing and bioinformatics, found that more and more lncRNAs associated with nervous system disease. This article deals with the regulation of certain lncRNAs in the nervous system disease, by mean of to understand its mechanism of action, and the pathogenesis of some neurological diseases have a fresh understanding, deposit a foundation for resulting research and clinical treatment of disease.}, } @article {pmid35383183, year = {2022}, author = {Tanalgo, KC and Tabora, JAG and de Oliveira, HFM and Haelewaters, D and Beranek, CT and Otálora-Ardila, A and Bernard, E and Gonçalves, F and Eriksson, A and Donnelly, M and González, JM and Ramos, HF and Rivas, AC and Webala, PW and Deleva, S and Dalhoumi, R and Maula, J and Lizarro, D and Aguirre, LF and Bouillard, N and Quibod, MNRM and Barros, J and Turcios-Casco, MA and Martínez, M and Ordoñez-Mazier, DI and Orellana, JAS and Ordoñez-Trejo, EJ and Ordoñez, D and Chornelia, A and Lu, JM and Xing, C and Baniya, S and Muylaert, RL and Dias-Silva, LH and Ruadreo, N and Hughes, AC}, title = {DarkCideS 1.0, a global database for bats in karsts and caves.}, journal = {Scientific data}, volume = {9}, number = {1}, pages = {155}, pmid = {35383183}, issn = {2052-4463}, mesh = {Animals ; Biodiversity ; *Chiroptera ; Databases, Factual ; Ecosystem ; }, abstract = {Understanding biodiversity patterns as well as drivers of population declines, and range losses provides crucial baselines for monitoring and conservation. However, the information needed to evaluate such trends remains unstandardised and sparsely available for many taxonomic groups and habitats, including the cave-dwelling bats and cave ecosystems. We developed the DarkCideS 1.0 (https://darkcides.org/), a global database of bat caves and species synthesised from publicly available information and datasets. The DarkCideS 1.0 is by far the largest database for cave-dwelling bats, which contains information for geographical location, ecological status, species traits, and parasites and hyperparasites for 679 bat species are known to occur in caves or use caves in part of their life histories. The database currently contains 6746 georeferenced occurrences for 402 cave-dwelling bat species from 2002 cave sites in 46 countries and 12 terrestrial biomes. The database has been developed to be collaborative and open-access, allowing continuous data-sharing among the community of bat researchers and conservation biologists to advance bat research and comparative monitoring and prioritisation for conservation.}, } @article {pmid35373179, year = {2022}, author = {Scherer, EA and Metcalf, SA and Whicker, CL and Bartels, SM and Grabinski, M and Kim, SJ and Sweeney, MA and Lemley, SM and Lavoie, H and Xie, H and Bissett, PG and Dallery, J and Kiernan, M and Lowe, MR and Onken, L and Prochaska, JJ and Stoeckel, LE and Poldrack, RA and MacKinnon, DP and Marsch, LA}, title = {Momentary Influences on Self-Regulation in Two Populations With Health Risk Behaviors: Adults Who Smoke and Adults Who Are Overweight and Have Binge-Eating Disorder.}, journal = {Frontiers in digital health}, volume = {4}, number = {}, pages = {798895}, pmid = {35373179}, issn = {2673-253X}, support = {P30 DA029926/DA/NIDA NIH HHS/United States ; UH2 DA041713/DA/NIDA NIH HHS/United States ; UH3 DA041713/DA/NIDA NIH HHS/United States ; }, abstract = {INTRODUCTION: Self-regulation has been implicated in health risk behaviors and is a target of many health behavior interventions. Despite most prior research focusing on self-regulation as an individual-level trait, we hypothesize that self-regulation is a time-varying mechanism of health and risk behavior that may be influenced by momentary contexts to a substantial degree. Because most health behaviors (e.g., eating, drinking, smoking) occur in the context of everyday activities, digital technologies may help us better understand and influence these behaviors in real time. Using a momentary self-regulation measure, the current study (which was part of a larger multi-year research project on the science of behavior change) used ecological momentary assessment (EMA) to assess if self-regulation can be engaged and manipulated on a momentary basis in naturalistic, non-laboratory settings.

METHODS: This one-arm, open-label exploratory study prospectively collected momentary data for 14 days from 104 participants who smoked regularly and 81 participants who were overweight and had binge-eating disorder. Four times per day, participants were queried about momentary self-regulation, emotional state, and social and environmental context; recent smoking and exposure to smoking cues (smoking sample only); and recent eating, binge eating, and exposure to binge-eating cues (binge-eating sample only). This study used a novel, momentary self-regulation measure comprised of four subscales: momentary perseverance, momentary sensation seeking, momentary self-judgment, and momentary mindfulness. Participants were also instructed to engage with Laddr, a mobile application that provides evidence-based health behavior change tools via an integrated platform. The association between momentary context and momentary self-regulation was explored via mixed-effects models. Exploratory assessments of whether recent Laddr use (defined as use within 12 h of momentary responses) modified the association between momentary context and momentary self-regulation were performed via mixed-effects models.

RESULTS: Participants (mean age 35.2; 78% female) in the smoking and binge-eating samples contributed a total of 3,233 and 3,481 momentary questionnaires, respectively. Momentary self-regulation subscales were associated with several momentary contexts, in the combined as well as smoking and binge-eating samples. For example, in the combined sample momentary perseverance was associated with location, positively associated with positive affect, and negatively associated with negative affect, stress, and tiredness. In the smoking sample, momentary perseverance was positively associated with momentary difficulty in accessing cigarettes, caffeine intake, and momentary restraint in smoking, and negatively associated with temptation and urge to smoke. In the binge-eating sample, momentary perseverance was positively associated with difficulty in accessing food and restraint in eating, and negatively associated with urge to binge eat. While recent Laddr use was not associated directly with momentary self-regulation subscales, it did modify several of the contextual associations, including challenging contexts.

CONCLUSIONS: Overall, this study provides preliminary evidence that momentary self-regulation may vary in response to differing momentary contexts in samples from two exemplar populations with risk behaviors. In addition, the Laddr application may modify some of these relationships. These findings demonstrate the possibility of measuring momentary self-regulation in a trans-diagnostic way and assessing the effects of momentary, mobile interventions in context. Health behavior change interventions may consider measuring and targeting momentary self-regulation in addition to trait-level self-regulation to better understand and improve health risk behaviors. This work will be used to inform a later stage of research focused on assessing the transdiagnostic mediating effect of momentary self-regulation on medical regimen adherence and health outcomes.

CLINICAL TRIAL REGISTRATION: ClinicalTrials.gov, Identifier: NCT03352713.}, } @article {pmid35372638, year = {2022}, author = {Wan, TTH and Matthews, S and Luh, H and Zeng, Y and Wang, Z and Yang, L}, title = {A Proposed Multi-Criteria Optimization Approach to Enhance Clinical Outcomes Evaluation for Diabetes Care: A Commentary.}, journal = {Health services research and managerial epidemiology}, volume = {9}, number = {}, pages = {23333928221089125}, pmid = {35372638}, issn = {2333-3928}, abstract = {There are several challenges in diabetes care management including optimizing the currently used therapies, educating patients on selfmanagement, and improving patient lifestyle and systematic healthcare barriers. The purpose of performing a systems approach to implementation science aided by artificial intelligence techniques in diabetes care is two-fold: 1) to explicate the systems approach to formulate predictive analytics that will simultaneously consider multiple input and output variables to generate an ideal decision-making solution for an optimal outcome; and 2) to incorporate contextual and ecological variations in practicing diabetes care coupled with specific health educational interventions as exogenous variables in prediction. A similar taxonomy of modeling approaches proposed by Brennon et al (2006) is formulated to examining the determinants of diabetes care outcomes in program evaluation. The discipline-free methods used in implementation science research, applied to efficiency and quality-of-care analysis are presented. Finally, we illustrate a logically formulated predictive analytics with efficiency and quality criteria included for evaluation of behavioralchange intervention programs, with the time effect included, in diabetes care and research.}, } @article {pmid35371039, year = {2022}, author = {Chang, ML and Cheng, JS and Chuang, YH and Pao, LH and Wu, TS and Chen, SC and Chang, MY and Chien, RN}, title = {Evolution of Cryoglobulinemia in Direct-Acting Antiviral-Treated Asian Hepatitis C Patients With Sustained Virological Responses: A 4-Year Prospective Cohort Study.}, journal = {Frontiers in immunology}, volume = {13}, number = {}, pages = {823160}, pmid = {35371039}, issn = {1664-3224}, mesh = {Antiviral Agents/therapeutic use ; *Cryoglobulinemia/complications ; Cryoglobulins ; Hepacivirus ; *Hepatitis C/complications/drug therapy ; *Hepatitis C, Chronic/complications/drug therapy ; Humans ; Immunoglobulin G/therapeutic use ; Immunoglobulin M ; Prospective Studies ; Recurrence ; *Vasculitis/drug therapy ; }, abstract = {BACKGROUND: How cryoglobulinemia evolves after sustained virological response (SVR) following direct-acting antiviral (DAA) treatment in Asian hepatitis C virus (HCV)-infected patients remains elusive.

METHODS: A prospective cohort study was conducted in 422 Taiwanese patients (358 completed DAA therapy and 353 experienced SVRs). Serum cryoglobulins were surveyed at baseline and every 3-6 months posttherapy.

RESULTS: Of 422, 227 (53.8%) had cryoglobulinemia, 8 (1.89%) had cryoglobulinemic vasculitis. Of 227, 54 (23.8%), 57 (25.1%) and 116 (51.1%) had 1, 2 and 3 cryoglobulins, respectively; those with 3 cryoglobulins had the highest alanine aminotransferase, immunoglobulin G (IgG) and fibrosis-4 index. During a 4-year follow-up, among SVR patients, cryoglobulinemia rates decreased from 56.4% to 15.4%, single cryoglobulin rates increased (21.6% to 63.9%) and 3 cryoglobulin rates decreased (55.7% to 11.1%). Compared with baseline values, among SVR patients with baseline cryoglobulinemia, complement component 4 levels increased, and IgG and IgM levels decreased until 48 weeks posttherapy for those without posttherapy cryoglobulinemia. All 8 cryoglobulinemic vasculitis patients exhibited SVRs; 5 (62.5%) achieved complete clinical response 12 weeks posttherapy, of whom, 2 (40%) experienced clinical relapse 24~48 weeks posttherapy. Baseline IgM levels were associated with posttherapy cryoglobulinemia in SVR patients (cut-off values at 12, 24, 48 weeks and 4 years posttherapy: 130, 105, 118 and 168 mg/dL, respectively).

CONCLUSIONS: Among DAA-treated SVR patients, in 4 years, cryoglobulinemia rates decreased from 56.4% to 15.4%, multiple cryoglobulin rates decreased, cryoglobulinemia signals reversed, 62.5% of cryoglobulinemic vasculitis patients achieved complete clinical response (40% had relapse), and baseline IgM levels indicated posttherapy cryoglobulinemia.}, } @article {pmid35367982, year = {2022}, author = {Santos, HSB and Do, T and Parolo, CCF and Poloni, JF and Maltz, M and Arthur, RA and Damé-Teixeira, N}, title = {Streptococcus mutans Gene Expression and Functional Profile in Root Caries: An RNA-Seq Study.}, journal = {Caries research}, volume = {56}, number = {2}, pages = {116-128}, doi = {10.1159/000524196}, pmid = {35367982}, issn = {1421-976X}, mesh = {Biofilms ; *Dental Caries/genetics ; Gene Expression ; Humans ; RNA-Seq ; *Root Caries ; Streptococcus mutans/genetics/metabolism ; }, abstract = {The literature is still scarce on studies describing Streptococcus mutans global gene expression under clinical conditions such as those found on complex biofilms from sound root surfaces (SRS) and carious root surfaces (RC). This study aimed to investigate the S. mutans gene expression and functional profile within the metatranscriptome of biofilms from SRS and from RC in an attempt to identify enriched functional signatures potentially associated with the healthy-to-disease transitioning process. Total RNA was extracted, and prepared libraries (SRS = 10 and RC = 9) were paired-end sequenced using the Illumina HiSeq2500. A read count assigned to each gene of the S. mutans UA159 strain was obtained. Differentially expressed genes (DEG) between SRS and RC were identified using the DESeq2 R package, and weighted gene co-expression network analysis (WGCNA) was performed to explore and identify functional modules related to SRS and RC. We found seventeen DEG between SRS and RC samples, with three overexpressed in RC and related to membrane protein, alanyl-tRNA synthetase, and GTP-binding protein, with the remaining ones overexpressed in SRS samples and related to hypothetical protein, transposon integrase, histidine kinase, putative transporter, bacteriocin immunity protein, response regulator, 6-phospho-beta-galactosidase, purine metabolism, and transcriptional regulator. Key-functional modules were identified for SRS and RC conditions based on WGCNA, being 139 hub genes found on SRS key-module and 17 genes on RC key-module. Functional analysis of S. mutans within the metatranscriptome of biofilms from sound root and from carious root revealed a similar pattern of gene expression, and only a few genes have been differentially expressed between biofilms from SRS and those from root carious lesions. However, S. mutans presented a greater functional abundance in the carious lesion samples. Some functional patterns related to sugar (starch, sucrose, fructose, mannose, and lactose) and heterofermentative metabolisms, to cell-wall biosynthesis, and to acid tolerance stress seem to be enriched on carious root surfaces, conferring ecological advantages to S. mutans. Altogether, the present data suggest that a functional signature may be associated with carious root lesions.}, } @article {pmid35365676, year = {2022}, author = {O'Sullivan, J and Lowe, CG and Sosa-Nishizaki, O and Jorgensen, SJ and Anderson, JM and Farrugia, TJ and García-Rodríguez, E and Lyons, K and McKinzie, MK and Oñate-González, EC and Weng, K and White, CF and Winkler, C and Van Houtan, KS}, title = {A biologging database of juvenile white sharks from the northeast Pacific.}, journal = {Scientific data}, volume = {9}, number = {1}, pages = {142}, pmid = {35365676}, issn = {2052-4463}, mesh = {Animals ; Databases, Factual ; *Ecosystem ; *Sharks ; Telemetry ; }, abstract = {Species occurrence records are vital data streams in marine conservation with a wide range of important applications. From 2001-2020, the Monterey Bay Aquarium led an international research collaboration to understand the life cycle, ecology, and behavior of white sharks (Carcharodon carcharias) in the southern California Current. The collaboration was devoted to tagging juveniles with animal-borne sensors, also known as biologging. Here we report the full data records from 59 pop-up archival (PAT) and 20 smart position and temperature transmitting (SPOT) tags that variously recorded pressure, temperature, and light-level data, and computed depth and geolocations for 63 individuals. Whether transmitted or from recovered devices, raw data files from successful deployments (n = 70) were auto-ingested from the manufacturer into the United States (US) Animal Telemetry Network's (ATN) Data Assembly Center (DAC). There they have attributed a full suite of metadata, visualized within their public-facing data portal, compiled for permanent archive under the DataONE Research Workspace member node, and are accessible for download from the ATN data portal.}, } @article {pmid35363913, year = {2023}, author = {Zhu, M and Wang, Z and Yang, Y and Wang, Z and Mu, W and Liu, J}, title = {Multi-omics reveal differentiation and maintenance of dimorphic flowers in an alpine plant on the Qinghai-Tibet Plateau.}, journal = {Molecular ecology}, volume = {32}, number = {6}, pages = {1411-1424}, doi = {10.1111/mec.16449}, pmid = {35363913}, issn = {1365-294X}, support = {XDB31000000//Chinese Academy of Sciences Key Project/ ; 2019QZKK0502//Chinese Academy of Sciences Key Project/ ; lzujbky- 2019//Fundamental Research Funds for the Central Universities/ ; BP0719040//International Collaboration 111 Programme/ ; 31590821//National Natural Science Foundation of China/ ; 91731301//National Natural Science Foundation of China/ ; 2017YFC0505203//National Key Research and Development Program of China/ ; }, mesh = {Tibet ; *Multiomics ; *Plants/genetics ; Transcriptome/genetics ; Flowers/genetics ; }, abstract = {Dimorphic flowers growing on a single individual plant play a critical role in extreme adaption and reproductive assurance in plants and have high ecological and evolutionary significance. However, the omics bases underlying such a differentiation and maintenance remain largely unknown. We aimed to investigate this through genomic, transcriptome and metabolomic analyses of dimorphic flowers in an alpine biennial, Sinoswertia tetraptera (Gentianaceae). A high-quality chromosome-level genome sequence (903 Mb) was first assembled for S. tetraptera with 31,359 protein-coding genes annotated. Two rounds of recent independent whole-genome duplication (WGD) were revealed. Numerous genes from the recent species-specific WGD were found to be differentially expressed in the two types of flowers, and this may have helped contribute to the origin of this innovative trait. The genes with contrasting expressions between flowers were related to biosynthesis of hormones, floral pigments (carotenoids and flavonoids) and iridoid compounds, which are involved in both flower development and colour. Metabolomic analyses similarly suggested differential concentrations of these chemicals in the two types of flowers. The expression interactions between multiple genes may together lead to contrasting morphology and chemical concentration and open versus closed pollination of the dimorphic flowers in this species for reproductive assurance.}, } @article {pmid35362663, year = {2023}, author = {Demofonti, A and Carpino, G and Tagliamonte, NL and Baldini, G and Bramato, L and Zollo, L}, title = {Design of a modular and compliant wrist module for upper limb prosthetics.}, journal = {Anatomical record (Hoboken, N.J. : 2007)}, volume = {306}, number = {4}, pages = {764-776}, doi = {10.1002/ar.24911}, pmid = {35362663}, issn = {1932-8494}, mesh = {*Wrist ; Artificial Limbs ; *Equipment Design ; Humans ; *Prostheses and Implants ; Range of Motion, Articular ; Torque ; Hand/physiology ; Wrist Joint ; }, abstract = {In the last decades, there have been great efforts in the development of advanced polyarticulated prosthetic hands; in contrast, prosthetic wrists have drawn less interest. Nevertheless, increasing the dexterity of the wrist improves handling skills because the wrist allows the prepositioning of the hand before carrying out a task, avoiding the onset of unwanted trunk or shoulders compensatory movements and potential onset or exacerbation of articular injuries. This study presents a novel 2-degree-of-freedom prosthetic wrist module with active pronation/supination and passive elastic flexion/extension. This system is suitable to be included in hand prostheses to improve anthropomorphism and produce a more physiological motion. The first submodule within the socket is able to rotate a prosthetic hand and an external load of 3 kg at 2.6 rad/s. The second one can guarantee a range of motion of ±75° with a centering elastic torque (compliant mode) or it can keep firms grasps (fixed mode). Compliant mode is based on a Scotch-Yoke mechanism converting wrist flexion/extension into the linear motion of a crossbeam acting on compression springs, while fixed mode is achieved by means of a piston that can be engaged/disengaged. The whole module fits with anthropometry and the modular design ensures the proposed system can be used in a stand-alone way and adapted to different hand prostheses. This device is expected to favor a more physiological dexterity with respect to simpler fixed prostheses that can potentially induce harmful motion of body districts not naturally involved in the reaching and grasping tasks.}, } @article {pmid35360357, year = {2022}, author = {Tardy, O and Vincenot, CE and Bouchard, C and Ogden, NH and Leighton, PA}, title = {Context-dependent host dispersal and habitat fragmentation determine heterogeneity in infected tick burdens: an agent-based modelling study.}, journal = {Royal Society open science}, volume = {9}, number = {3}, pages = {220245}, pmid = {35360357}, issn = {2054-5703}, abstract = {As the incidence of tick-borne diseases has sharply increased over the past decade, with serious consequences for human and animal health, there is a need to identify ecological drivers contributing to heterogeneity in tick-borne disease risk. In particular, the relative importance of animal host dispersal behaviour in its three context-dependent phases of emigration, transfer and settlement is relatively unexplored. We built a spatially explicit agent-based model to investigate how the host dispersal process, in concert with the tick and host demographic processes, habitat fragmentation and the pathogen transmission process, affects infected tick distributions among hosts. A sensitivity analysis explored the impacts of different input parameters on infected tick burdens on hosts and infected tick distributions among hosts. Our simulations indicate that ecological predictors of infected tick burdens differed among the post-egg life stages of ticks, with tick attachment and detachment, tick questing activity and pathogen transmission dynamics identified as key processes, in a coherent way. We also found that the type of host settlement strategy and the proportion of habitat suitable for hosts determined super-spreading of infected ticks. We developed a theoretical mechanistic framework that can serve as a first step towards applied studies of on-the-ground public health intervention strategies.}, } @article {pmid35359763, year = {2022}, author = {Gavurova, B and Ivankova, V and Rigelsky, M and Mudarri, T and Miovsky, M}, title = {Somatic Symptoms, Anxiety, and Depression Among College Students in the Czech Republic and Slovakia: A Cross-Sectional Study.}, journal = {Frontiers in public health}, volume = {10}, number = {}, pages = {859107}, pmid = {35359763}, issn = {2296-2565}, mesh = {Anxiety/epidemiology/psychology ; Anxiety Disorders/epidemiology ; *COVID-19/epidemiology ; Cross-Sectional Studies ; Czech Republic/epidemiology ; Depression/epidemiology/psychology ; Female ; Humans ; *Medically Unexplained Symptoms ; Pandemics ; Slovakia/epidemiology ; Students/psychology ; }, abstract = {Studying in college can be a challenging time for many students, which can affect their mental health. In addition to academic pressure and stressful tasks, another aggravating factor in student life is the ongoing coronavirus disease 2019 (COVID-19) pandemic. The aim of the study was to examine the prevalence of anxiety, depression, and somatic symptoms in Czech and Slovak college students during the COVID-19 pandemic and to evaluate possible socio-demographic determinants of mental health problems. A total of 3,099 respondents participated in this cross-sectional study (Czech Republic: 1,422, Slovakia: 1,677). The analyzes included the Patient Health Questionnaire for somatic symptoms (PHQ-15), the Generalized Anxiety Disorder instrument (GAD-7), and the Patient Health Questionnaire for depression (PHQ-9). Socio-demographic factors were gender, age, family structure, marital status, form of study, degree of study, year of study, field of study, distance between home and college, residence, and housing during the semester. Among Czech students, prevalence of somatic complaints, anxiety and depression was 72.2, 40.3, and 52%, respectively. Among Slovak students, prevalence of somatic complaints, anxiety and depression was 69.5, 34.6, and 47%, respectively. During the COVID-19 pandemic, the most severe mental health problems were identified in a non-negligible part of the sample (Czech Republic: PHQ-15 = 10.1%, GAD-7 = 4.9%, PHQ-9 = 3.4%; Slovakia: PHQ-15 = 7.4%, GAD-7 = 3.5%, PHQ-9 = 2.7%). Regarding the differences between the analyzed countries, a significantly higher score in somatic symptoms, anxiety, and depression was identified in the Czech Republic. Significant differences in mental disorders were found in most socio-demographic characteristics. The main results of the logistic regression analysis revealed that risk factors for mental health disorders in Czech and Slovak students were female gender, younger age, third degree of study, and study of Informatics, Mathematics, Information and Communication Technologies (ICT). Especially in the case of these high-risk groups of students, public policies should consider a response to impending problems. The findings are an appeal for a proactive approach to improving the mental health of students and for the implementation of effective prevention programs, which are more than necessary in the Czech and Slovak college environment.}, } @article {pmid35357911, year = {2022}, author = {Altemose, N and Logsdon, GA and Bzikadze, AV and Sidhwani, P and Langley, SA and Caldas, GV and Hoyt, SJ and Uralsky, L and Ryabov, FD and Shew, CJ and Sauria, MEG and Borchers, M and Gershman, A and Mikheenko, A and Shepelev, VA and Dvorkina, T and Kunyavskaya, O and Vollger, MR and Rhie, A and McCartney, AM and Asri, M and Lorig-Roach, R and Shafin, K and Lucas, JK and Aganezov, S and Olson, D and de Lima, LG and Potapova, T and Hartley, GA and Haukness, M and Kerpedjiev, P and Gusev, F and Tigyi, K and Brooks, S and Young, A and Nurk, S and Koren, S and Salama, SR and Paten, B and Rogaev, EI and Streets, A and Karpen, GH and Dernburg, AF and Sullivan, BA and Straight, AF and Wheeler, TJ and Gerton, JL and Eichler, EE and Phillippy, AM and Timp, W and Dennis, MY and O'Neill, RJ and Zook, JM and Schatz, MC and Pevzner, PA and Diekhans, M and Langley, CH and Alexandrov, IA and Miga, KH}, title = {Complete genomic and epigenetic maps of human centromeres.}, journal = {Science (New York, N.Y.)}, volume = {376}, number = {6588}, pages = {eabl4178}, pmid = {35357911}, issn = {1095-9203}, support = {U24 HG010263/HG/NHGRI NIH HHS/United States ; U01 HG010961/HG/NHGRI NIH HHS/United States ; DP2 MH119424/MH/NIMH NIH HHS/United States ; R35 GM139653/GM/NIGMS NIH HHS/United States ; R21 CA240199/CA/NCI NIH HHS/United States ; OT2 OD026682/OD/NIH HHS/United States ; R01 GM074728/GM/NIGMS NIH HHS/United States ; R21 CA238758/CA/NCI NIH HHS/United States ; U01 HG010971/HG/NHGRI NIH HHS/United States ; P20 GM103546/GM/NIGMS NIH HHS/United States ; R01 GM132600/GM/NIGMS NIH HHS/United States ; R01 GM124041/GM/NIGMS NIH HHS/United States ; T32 GM007445/GM/NIGMS NIH HHS/United States ; U41 HG010972/HG/NHGRI NIH HHS/United States ; F31 HG011205/HG/NHGRI NIH HHS/United States ; F32 GM134558/GM/NIGMS NIH HHS/United States ; R01 HG010169/HG/NHGRI NIH HHS/United States ; R01 GM129263/GM/NIGMS NIH HHS/United States ; U41 HG007234/HG/NHGRI NIH HHS/United States ; U01 CA253481/CA/NCI NIH HHS/United States ; U24 HG007234/HG/NHGRI NIH HHS/United States ; R01 HG011274/HG/NHGRI NIH HHS/United States ; U24 HG006620/HG/NHGRI NIH HHS/United States ; R01 HG002939/HG/NHGRI NIH HHS/United States ; R01 AG054712/AG/NIA NIH HHS/United States ; U24 HG010136/HG/NHGRI NIH HHS/United States ; R01 HG010329/HG/NHGRI NIH HHS/United States ; R21 HG010548/HG/NHGRI NIH HHS/United States ; U24 HG011853/HG/NHGRI NIH HHS/United States ; R01 GM123312/GM/NIGMS NIH HHS/United States ; R01 HG009190/HG/NHGRI NIH HHS/United States ; R01 GM117420/GM/NIGMS NIH HHS/United States ; R01 HG010485/HG/NHGRI NIH HHS/United States ; R24 DK106766/DK/NIDDK NIH HHS/United States ; }, mesh = {Centromere/*genetics ; *Chromosome Mapping ; *Epigenesis, Genetic ; Evolution, Molecular ; *Genome, Human ; Genomics ; Humans ; Repetitive Sequences, Nucleic Acid ; }, abstract = {Existing human genome assemblies have almost entirely excluded repetitive sequences within and near centromeres, limiting our understanding of their organization, evolution, and functions, which include facilitating proper chromosome segregation. Now, a complete, telomere-to-telomere human genome assembly (T2T-CHM13) has enabled us to comprehensively characterize pericentromeric and centromeric repeats, which constitute 6.2% of the genome (189.9 megabases). Detailed maps of these regions revealed multimegabase structural rearrangements, including in active centromeric repeat arrays. Analysis of centromere-associated sequences uncovered a strong relationship between the position of the centromere and the evolution of the surrounding DNA through layered repeat expansions. Furthermore, comparisons of chromosome X centromeres across a diverse panel of individuals illuminated high degrees of structural, epigenetic, and sequence variation in these complex and rapidly evolving regions.}, } @article {pmid35357313, year = {2022}, author = {Thorpe, D and Fouyaxis, J and Lipschitz, JM and Nielson, A and Li, W and Murphy, SA and Bidargaddi, N}, title = {Cost and Effort Considerations for the Development of Intervention Studies Using Mobile Health Platforms: Pragmatic Case Study.}, journal = {JMIR formative research}, volume = {6}, number = {3}, pages = {e29988}, pmid = {35357313}, issn = {2561-326X}, support = {K23 MH120324/MH/NIMH NIH HHS/United States ; }, abstract = {BACKGROUND: The research marketplace has seen a flood of open-source or commercial mobile health (mHealth) platforms that can collect and use user data in real time. However, there is a lack of practical literature on how these platforms are developed, integrated into study designs, and adopted, including important information around cost and effort considerations.

OBJECTIVE: We intend to build critical literacy in the clinician-researcher readership into the cost, effort, and processes involved in developing and operationalizing an mHealth platform, focusing on Intui, an mHealth platform that we developed.

METHODS: We describe the development of the Intui mHealth platform and general principles of its operationalization across sites.

RESULTS: We provide a worked example in the form of a case study. Intui was operationalized in the design of a behavioral activation intervention in collaboration with a mental health service provider. We describe the design specifications of the study site, the developed software, and the cost and effort required to build the final product.

CONCLUSIONS: Study designs, researcher needs, and technical considerations can impact effort and costs associated with the use of mHealth platforms. Greater transparency from platform developers about the impact of these factors on practical considerations relevant to end users such as clinician-researchers is crucial to increasing critical literacy around mHealth, thereby aiding in the widespread use of these potentially beneficial technologies and building clinician confidence in these tools.}, } @article {pmid35356560, year = {2022}, author = {Reeve, S and Deane, DC and McGrannachan, C and Horner, G and Hui, C and McGeoch, M}, title = {Rare, common, alien and native species follow different rules in an understory plant community.}, journal = {Ecology and evolution}, volume = {12}, number = {3}, pages = {e8734}, pmid = {35356560}, issn = {2045-7758}, abstract = {Biological invasions are a leading threat to biodiversity globally. Increasingly, ecosystems experience multiple introductions, which can have significant effects on patterns of diversity. The way these communities assemble will depend partly on whether rare and common alien species respond to environmental predictors in the same manner as rare and common native species, but this is not well understood. To examine this question across four national parks in south-eastern Australia, we sampled the understory plant community of eucalypt-dominated dry forest subject to multiple plant introductions. The drivers of diversity and turnover in alien and native species of contrasting frequency of occurrence (low, intermediate, and high) were each tested individually. We found alien species diversity and turnover were both strongly associated with abiotic conditions (e.g., soil pH), while distance had little influence because of the greater extent of occurrence and more homogeneous composition of common aliens. In contrast, native species diversity was not associated with abiotic conditions and their turnover was as strongly influenced by distance as by abiotic conditions. In both alien and native species, however, the most important predictors of turnover changed with frequency of occurrence. Although local coexistence appears to be facilitated by life history trade-offs, species richness of aliens and natives was negatively correlated and native species might face greater competition in areas with more neutral soils (e.g., pH > ~5.5) where alien richness and relative frequency were both highest. We conclude that diversity and turnover in the generally more widespread alien species are mainly driven by species sorting along an environmental gradient associated with pH and nutrient availability, whereas turnover of native species is driven by more neutral processes associated with dispersal limitation. We show alien and native plant species respond to different environmental factors, as do rare and common species within each component.}, } @article {pmid35351593, year = {2022}, author = {Pan, SF and Ji, XH and Xie, YH and Liu, SH and Tian, FX and Liu, XL}, title = {Influence of soil properties on cadmium accumulation in vegetables: Thresholds, prediction and pathway models based on big data.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {304}, number = {}, pages = {119225}, doi = {10.1016/j.envpol.2022.119225}, pmid = {35351593}, issn = {1873-6424}, mesh = {Big Data ; *Cadmium/analysis ; China ; Soil/chemistry ; *Soil Pollutants/analysis ; Vegetables/chemistry ; }, abstract = {Soil properties, such as soil pH, soil organic matter (SOM), cation exchange capacity (CEC), are the most important factors affecting cadmium (Cd) accumulation in vegetables. In this study, we conducted big data mining of 31,342 soil and vegetable samples to examine the influence of soil properties (soil pH, SOM, CEC, Zn and Mn content) on the accumulation of Cd in root, solanaceous, and leafy vegetables in Hunan Province, China. Specifically, the Cd accumulation capability was in the following order: leafy vegetables > root vegetables > solanaceous vegetables. The soil property thresholds for safety production in vegetables were determined by establishing nonlinear models between Cd bioaccumulation factor (BCF) and the individual soil property, and were 6.5 (pH), 30.0 g/kg (SOM), 13.0 cmol/kg (CEC), 100-140 mg/kg (Zn), and 300-400 mg/kg (Mn). When soil property values were higher than the thresholds, Cd accumulation in vegetables tended to be stable. Prediction models showed that pH and soil Zn were the leading factors influencing Cd accumulation in root vegetables, explaining 87% of the variance; pH, SOM, soil Zn and Mn explained 68% of the variance in solanaceous vegetables; pH and SOM were the main contributors in leafy vegetables, explaining 65% of the variance. Further, variance partitioning analysis (VPA) revealed that the interaction effect of the corresponding key soil properties contributed mostly to BCF. Meanwhile, partial least squares (PLS) path modeling was employed to analyze the path and the interactive effects of soil properties on Cd BCF. pH and SOM were found to be the biggest two players affecting BCF in PLS-models, and the most substantial interactive influence paths of soil properties on BCF were different among the three types of vegetables.}, } @article {pmid35349783, year = {2022}, author = {Smith, SP and Shahamatdar, S and Cheng, W and Zhang, S and Paik, J and Graff, M and Haiman, C and Matise, TC and North, KE and Peters, U and Kenny, E and Gignoux, C and Wojcik, G and Crawford, L and Ramachandran, S}, title = {Enrichment analyses identify shared associations for 25 quantitative traits in over 600,000 individuals from seven diverse ancestries.}, journal = {American journal of human genetics}, volume = {109}, number = {5}, pages = {871-884}, pmid = {35349783}, issn = {1537-6605}, support = {75N92021D00005/WH/WHI NIH HHS/United States ; N01HC65236/HL/NHLBI NIH HHS/United States ; T32 GM128596/GM/NIGMS NIH HHS/United States ; 75N92021D00001/HL/NHLBI NIH HHS/United States ; N01HC65233/HL/NHLBI NIH HHS/United States ; N01HC65237/HL/NHLBI NIH HHS/United States ; 75N92021D00003/WH/WHI NIH HHS/United States ; N01 HC065236/HC/NHLBI NIH HHS/United States ; R01 GM118652/GM/NIGMS NIH HHS/United States ; 75N92021D00004/WH/WHI NIH HHS/United States ; MC_QA137853/MRC_/Medical Research Council/United Kingdom ; MC_PC_17228/MRC_/Medical Research Council/United Kingdom ; 75N92021D00002/HL/NHLBI NIH HHS/United States ; R35 GM139628/GM/NIGMS NIH HHS/United States ; N01HC65235/HL/NHLBI NIH HHS/United States ; N01 HC065237/HC/NHLBI NIH HHS/United States ; N01HC65234/HL/NHLBI NIH HHS/United States ; }, mesh = {*Genome-Wide Association Study/methods ; Humans ; Multifactorial Inheritance ; Phenotype ; *Polymorphism, Single Nucleotide/genetics ; Racial Groups ; }, abstract = {Since 2005, genome-wide association (GWA) datasets have been largely biased toward sampling European ancestry individuals, and recent studies have shown that GWA results estimated from self-identified European individuals are not transferable to non-European individuals because of various confounding challenges. Here, we demonstrate that enrichment analyses that aggregate SNP-level association statistics at multiple genomic scales-from genes to genomic regions and pathways-have been underutilized in the GWA era and can generate biologically interpretable hypotheses regarding the genetic basis of complex trait architecture. We illustrate examples of the robust associations generated by enrichment analyses while studying 25 continuous traits assayed in 566,786 individuals from seven diverse self-identified human ancestries in the UK Biobank and the Biobank Japan as well as 44,348 admixed individuals from the PAGE consortium including cohorts of African American, Hispanic and Latin American, Native Hawaiian, and American Indian/Alaska Native individuals. We identify 1,000 gene-level associations that are genome-wide significant in at least two ancestry cohorts across these 25 traits as well as highly conserved pathway associations with triglyceride levels in European, East Asian, and Native Hawaiian cohorts.}, } @article {pmid35347145, year = {2022}, author = {Mammola, S and Malumbres-Olarte, J and Arabesky, V and Barrales-Alcalá, DA and Barrion-Dupo, AL and Benamú, MA and Bird, TL and Bogomolova, M and Cardoso, P and Chatzaki, M and Cheng, RC and Chu, TA and Classen-Rodríguez, LM and Čupić, I and Dhiya'ulhaq, NU and Picard, AD and El-Hennawy, HK and Elverici, M and Fukushima, CS and Ganem, Z and Gavish-Regev, E and Gonnye, NT and Hacala, A and Haddad, CR and Hesselberg, T and Ho, TAT and Into, T and Isaia, M and Jayaraman, D and Karuaera, N and Khalap, R and Khalap, K and Kim, D and Korhonen, T and Kralj-Fišer, S and Land, H and Lin, SW and Loboda, S and Lowe, E and Lubin, Y and Martínez, A and Mbo, Z and Miličić, M and Kioko, GM and Nanni, V and Norma-Rashid, Y and Nwankwo, D and Painting, CJ and Pang, A and Pantini, P and Pavlek, M and Pearce, R and Petcharad, B and Pétillon, J and Raberahona, OC and Saarinen, JA and Segura-Hernández, L and Sentenská, L and Uhl, G and Walker, L and Warui, CM and Wiśniewski, K and Zamani, A and Scott, C and Chuang, A}, title = {An expert-curated global database of online newspaper articles on spiders and spider bites.}, journal = {Scientific data}, volume = {9}, number = {1}, pages = {109}, pmid = {35347145}, issn = {2052-4463}, mesh = {Animals ; Databases, Factual ; Humans ; Language ; Newspapers as Topic ; *Spider Bites ; *Spider Venoms ; *Spiders ; }, abstract = {Mass media plays an important role in the construction and circulation of risk perception associated with animals. Widely feared groups such as spiders frequently end up in the spotlight of traditional and social media. We compiled an expert-curated global database on the online newspaper coverage of human-spider encounters over the past ten years (2010-2020). This database includes information about the location of each human-spider encounter reported in the news article and a quantitative characterisation of the content-location, presence of photographs of spiders and bites, number and type of errors, consultation of experts, and a subjective assessment of sensationalism. In total, we collected 5348 unique news articles from 81 countries in 40 languages. The database refers to 211 identified and unidentified spider species and 2644 unique human-spider encounters (1121 bites and 147 as deadly bites). To facilitate data reuse, we explain the main caveats that need to be made when analysing this database and discuss research ideas and questions that can be explored with it.}, } @article {pmid35346493, year = {2022}, author = {Ricke, SC and Dittoe, DK and Brown, JA and Thompson, DR}, title = {Practical opportunities for microbiome analyses and bioinformatics in poultry processing.}, journal = {Poultry science}, volume = {101}, number = {5}, pages = {101787}, pmid = {35346493}, issn = {1525-3171}, mesh = {Animals ; Chickens/genetics/microbiology ; Computational Biology ; Food Microbiology ; *Microbiota ; *Poultry/microbiology ; }, abstract = {Poultry processing is undergoing changes both in operations as well as microbial methodologies. Traditionally, microbial data has been gathered through a series of culturing methods using liquid media and plating for isolation and enumeration. Both foodborne pathogens and nonpathogenic bacterial populations are estimated to assess food safety risks as well as the potential for spoilage. Bacterial loads from carcasses are important for estimating processing control and the effectiveness of antimicrobial applications. However, these culture-based approaches may only provide part of the microbial ecology landscape associated with chicken carcasses and the subsequent changes that occur in these populations during processing. Newer molecular-based approaches, such as 16S sequencing of the microbiota, offer a means to retrieve a more comprehensive microbial compositional profile. However, such approaches also result in large data sets which must be analyzed and interpreted. As more data is generated, this will require not only bioinformatic programs to process the data but appropriate educational forums to present the processed data to a broad audience.}, } @article {pmid35346441, year = {2022}, author = {Pruilh, S and Jannot, AS and Allassonnière, S}, title = {Spatio-temporal mixture process estimation to detect dynamical changes in population.}, journal = {Artificial intelligence in medicine}, volume = {126}, number = {}, pages = {102258}, pmid = {35346441}, issn = {1873-2860}, mesh = {Algorithms ; *COVID-19/epidemiology ; Humans ; Models, Statistical ; }, abstract = {Population monitoring is a challenge in many areas such as public health and ecology. We propose a method to model and monitor population distributions over space and time, in order to build an alert system for spatio-temporal data changes. Assuming that mixture models can correctly model populations, we propose a new version of the Expectation-Maximization (EM) algorithm to better estimate the number of clusters and their parameters at the same time. This algorithm is compared to existing methods on several simulated datasets. We then combine the algorithm with a temporal statistical model, allowing for the detection of dynamical changes in population distributions, and call the result a spatio-temporal mixture process (STMP). We test STMPs on synthetic data, and consider several different behaviors of the distributions, to fit this process. Finally, we validate STMPs on a real data set of positive diagnosed patients to coronavirus disease 2019. We show that our pipeline correctly models evolving real data and detects epidemic changes.}, } @article {pmid35344735, year = {2022}, author = {Swets, MC and Russell, CD and Harrison, EM and Docherty, AB and Lone, N and Girvan, M and Hardwick, HE and , and Visser, LG and Openshaw, PJM and Groeneveld, GH and Semple, MG and Baillie, JK}, title = {SARS-CoV-2 co-infection with influenza viruses, respiratory syncytial virus, or adenoviruses.}, journal = {Lancet (London, England)}, volume = {399}, number = {10334}, pages = {1463-1464}, pmid = {35344735}, issn = {1474-547X}, support = {MC_PC_19059/MRC_/Medical Research Council/United Kingdom ; MC_PC_19025/MRC_/Medical Research Council/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; MC_G1001212/MRC_/Medical Research Council/United Kingdom ; MC_PC_20058/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Adenoviridae ; *COVID-19 ; *Coinfection ; Humans ; *Influenza, Human/complications ; *Respiratory Syncytial Virus, Human ; SARS-CoV-2 ; }, } @article {pmid35343018, year = {2022}, author = {Graves, TA and Yarnall, MJ and Johnston, AN and Preston, TM and Chong, GW and Cole, EK and Janousek, WM and Cross, PC}, title = {Eyes on the herd: Quantifying ungulate density from satellite, unmanned aerial systems, and GPScollar data.}, journal = {Ecological applications : a publication of the Ecological Society of America}, volume = {32}, number = {5}, pages = {e2600}, doi = {10.1002/eap.2600}, pmid = {35343018}, issn = {1051-0761}, mesh = {Animals ; Animals, Wild ; *Deer ; Geographic Information Systems ; Satellite Imagery ; Snow ; }, abstract = {Novel approaches to quantifying density and distributions could help biologists adaptively manage wildlife populations, particularly if methods are accurate, consistent, cost-effective, rapid, and sensitive to change. Such approaches may also improve research on interactions between density and processes of interest, such as disease transmission across multiple populations. We assess how satellite imagery, unmanned aerial system (UAS) imagery, and Global Positioning System (GPS) collar data vary in characterizing elk density, distribution, and count patterns across times with and without supplemental feeding at the National Elk Refuge (NER) in the US state of Wyoming. We also present the first comparison of satellite imagery data with traditional counts for ungulates in a temperate system. We further evaluate seven different aggregation metrics to identify the most consistent and sensitive metrics for comparing density and distribution across time and populations. All three data sources detected higher densities and aggregation locations of elk during supplemental feeding than non-feeding at the NER. Kernel density estimates (KDEs), KDE polygon areas, and the first quantile of interelk distances detected differences with the highest sensitivity and were most highly correlated across data sources. Both UAS and satellite imagery provide snapshots of density and distribution patterns of most animals in the area at lower cost than GPS collars. While satellite-based counts were lower than traditional counts, aggregation metrics matched those from UAS and GPS data sources when animals appeared in high contrast to the landscape, including brown elk against new snow in open areas. UAS counts of elk were similar to traditional ground-based counts on feed grounds and are the best data source for assessing changes in small spatial extents. Satellite, UAS, or GPS data can provide appropriate data for assessing density and changes in density from adaptive management actions. For the NER, where high elk densities are beneath controlled airspace, GPS collar data will be most useful for evaluating how management actions, including changes in the dates of supplemental feeding, influence elk density and aggregation across large spatial extents. Using consistent and sensitive measures of density may improve research on the drivers and effects of density within and across a wide range of species.}, } @article {pmid35341043, year = {2022}, author = {Stowell, D}, title = {Computational bioacoustics with deep learning: a review and roadmap.}, journal = {PeerJ}, volume = {10}, number = {}, pages = {e13152}, pmid = {35341043}, issn = {2167-8359}, mesh = {Animals ; *Acoustics ; *Deep Learning ; Ecosystem ; Signal Processing, Computer-Assisted ; Vocalization, Animal ; }, abstract = {Animal vocalisations and natural soundscapes are fascinating objects of study, and contain valuable evidence about animal behaviours, populations and ecosystems. They are studied in bioacoustics and ecoacoustics, with signal processing and analysis an important component. Computational bioacoustics has accelerated in recent decades due to the growth of affordable digital sound recording devices, and to huge progress in informatics such as big data, signal processing and machine learning. Methods are inherited from the wider field of deep learning, including speech and image processing. However, the tasks, demands and data characteristics are often different from those addressed in speech or music analysis. There remain unsolved problems, and tasks for which evidence is surely present in many acoustic signals, but not yet realised. In this paper I perform a review of the state of the art in deep learning for computational bioacoustics, aiming to clarify key concepts and identify and analyse knowledge gaps. Based on this, I offer a subjective but principled roadmap for computational bioacoustics with deep learning: topics that the community should aim to address, in order to make the most of future developments in AI and informatics, and to use audio data in answering zoological and ecological questions.}, } @article {pmid35340018, year = {2022}, author = {Murphy, B and Grimshaw, S and Hoptroff, M and Paterson, S and Arnold, D and Cawley, A and Adams, SE and Falciani, F and Dadd, T and Eccles, R and Mitchell, A and Lathrop, WF and Marrero, D and Yarova, G and Villa, A and Bajor, JS and Feng, L and Mihalov, D and Mayes, AE}, title = {Alteration of barrier properties, stratum corneum ceramides and microbiome composition in response to lotion application on cosmetic dry skin.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {5223}, pmid = {35340018}, issn = {2045-2322}, mesh = {*Ceramides/metabolism ; Epidermis/metabolism ; *Microbiota ; RNA, Ribosomal, 16S/genetics/metabolism ; Skin/chemistry ; }, abstract = {Xerosis, commonly referred to as dry skin, is a common dermatological condition affecting almost a third of the population. Successful treatment of the condition traditionally involves the application of cosmetic products facilitating the moisturisation of the skin with a range of ingredients including glycerol and fatty acids. While the effectiveness of these treatments is not in question, limited information exists on the impact on the skin microbiome following use of these products and the improvement in skin hydration. Here, we describe improvements in skin barrier properties together with increased levels of cholesterol, ceramides and long-chain fatty acids following application of Body Lotion. Concomitant alterations in the skin microbiome are also seen via 16S rRNA metataxonomics, in combination with both traditional and novel informatics analysis. Following 5 weeks of lotion use, beneficial skin bacteria are increased, with improvements in microbiome functional potential, and increases in pathways associated with biosynthesis of multiple long chain fatty acids.}, } @article {pmid35338150, year = {2022}, author = {Bolotov, IN and Gofarov, MY and Koshkin, ES and Gorbach, VV and Bakhaev, YI and Berlov, OE and Gordeev, SY and Kolosova, YS and Kondakov, AV and Korshunov, AV and Potapov, GS and Sinev, SY and Sleptsov, SS and Spitsyn, VM and Strelnikov, EG and Timchenko, AV and Haverinen, R and Nupponen, K and Saarenmaa, H}, title = {A nearly complete database on the records and ecology of the rarest boreal tiger moth from 1840s to 2020.}, journal = {Scientific data}, volume = {9}, number = {1}, pages = {107}, pmid = {35338150}, issn = {2052-4463}, mesh = {Animals ; Climate Change ; Databases, Factual ; *Moths ; *Taiga ; }, abstract = {Global environmental changes may cause dramatic insect declines but over century-long time series of certain species' records are rarely available for scientific research. The Menetries' Tiger Moth (Arctia menetriesii) appears to be the most enigmatic example among boreal insects. Although it occurs throughout the entire Eurasian taiga biome, it is so rare that less than 100 specimens were recorded since its original description in 1846. Here, we present the database, which contains nearly all available information on the species' records collected from 1840s to 2020. The data on A. menetriesii records (N = 78) through geographic regions, environments, and different timeframes are compiled and unified. The database may serve as the basis for a wide array of future research such as the distribution modeling and predictions of range shifts under climate changes. It represents a unique example of a more than century-long dataset of distributional, ecological, and phenological data designed for an exceptionally rare but widespread boreal insect, which primarily occurs in hard-to-reach, uninhabited areas of Eurasia.}, } @article {pmid35337897, year = {2022}, author = {Mohammad Sham, N and Anual, ZF and Shaharudin, R}, title = {GIS based interpolation method to urinary metal concentrations in Malaysia.}, journal = {Food and chemical toxicology : an international journal published for the British Industrial Biological Research Association}, volume = {163}, number = {}, pages = {112949}, doi = {10.1016/j.fct.2022.112949}, pmid = {35337897}, issn = {1873-6351}, mesh = {Adult ; *Arsenic ; Cadmium ; China ; Cross-Sectional Studies ; Environmental Monitoring ; Geographic Information Systems ; Humans ; Lead ; Malaysia ; *Metals, Heavy/analysis ; Nickel ; Risk Assessment ; *Soil Pollutants/analysis ; }, abstract = {Recently, there has been an increasing ecological and global public health concern associated with environmental contamination by arsenic (As), cadmium (Cd), nickel (Ni) and lead (Pb). This study aims to visualize distribution of these heavy metals concentration in urine of 817 Malaysian adults in Malaysia. This cross-sectional study compiled urine samples from October 2017 to March 2018. Spatial inverse distance weighted (IDW) interpolation method was used to derive a map which illustrate the distribution of these metals from urine samples. Moran's I Index was used to assess the spatial autocorrelation of these metals between the study area. The mean concentration for Ni and Cd was highest in Perak while for As and Pb, they were predominantly in East Coast region (Terengganu and Kelantan). Moran's I index showed significant spatial autocorrelation exist in the study area for all metals except for Pb (p-value<0.05). According to IDW, people in North East and Western regions had the highest concentrations for As and Cd. Individuals in Central region were less exposed than those in North region. These techniques can assist health authorities a better prediction in assessing exposure to heavy metals in population of an area to prioritize their control and preventive measure.}, } @article {pmid35331756, year = {2022}, author = {Fernández-García, V and Beltrán-Marcos, D and Fernández-Guisuraga, JM and Marcos, E and Calvo, L}, title = {Predicting potential wildfire severity across Southern Europe with global data sources.}, journal = {The Science of the total environment}, volume = {829}, number = {}, pages = {154729}, doi = {10.1016/j.scitotenv.2022.154729}, pmid = {35331756}, issn = {1879-1026}, mesh = {*Burns ; Europe ; *Fires ; Humans ; Information Storage and Retrieval ; *Wildfires ; }, abstract = {The large environmental and socioeconomic impacts of wildfires in Southern Europe require the development of efficient generalizable tools for fire danger analysis and proactive environmental management. With this premise, we aimed to study the influence of different environmental variables on burn severity, as well as to develop accurate and generalizable models to predict burn severity. To address these objectives, we selected 23 wildfires (131,490 ha) across Southern Europe. Using satellite imagery and geospatial data available at the planetary scale, we spatialized burn severity as well as 20 pre-burn environmental variables, which were grouped into climatic, topographic, fuel load-type, fuel load-moisture and fuel continuity predictors. We sampled all variables and divided the data into three independent datasets: a training dataset, used to perform univariant regression models, random forest (RF) models by groups of variables, and RF models including all predictors (full and parsimonious models); a second dataset to analyze interpolation capacity within the training wildfires; and a third dataset to study extrapolation capacity to independent wildfires. Results showed that all environmental variables determined burn severity, which increased towards the mildest climatic conditions, sloping terrain, high fuel loads, and coniferous vegetation. In general, the highest predictive and generalization capacities were found for fuel load proxies obtained though multispectral imagery, both in the individual analysis and by groups of variables. The full and parsimonious models outperformed all, the individual models, models by groups, and formerly developed predictive models of burn severity, as they were able to explain up to 95%, 59% and 25% of variance when applied to the training, interpolation and extrapolation datasets respectively. Our study is a benchmark for progress in the prediction of fire danger, provides operational tools for the identification of areas at risk, and sets the basis for the design of pre-burn management actions.}, } @article {pmid35331375, year = {2022}, author = {Orban, AM and Rühl, M}, title = {Identification of volatile producing enzymes in higher fungi: Combining analytical and bioinformatic methods.}, journal = {Methods in enzymology}, volume = {664}, number = {}, pages = {221-242}, doi = {10.1016/bs.mie.2021.12.007}, pmid = {35331375}, issn = {1557-7988}, mesh = {Computational Biology ; Fungi/genetics/metabolism ; *Volatile Organic Compounds/metabolism ; }, abstract = {Filamentous fungi harbor the genetic potential for the biosynthesis of several secondary metabolites including various volatile organic compounds (VOCs). Nonetheless, under standard laboratory conditions, many of these VOCs are not formed. Furthermore, little is known about enzymes involved in the production of fungal VOCs. To tap these interesting topics, we developed an approach to identify enzymes putatively involved in the fungal VOC biosynthesis. In this chapter, we highlight different fungal cultivation methods and techniques for the extraction of VOCs, including a method that allows the noninvasive analysis of VOCs. In addition using terpene synthases as an example, it is depicted how enzymes putatively involved in VOC synthesis can be identified by means of bioinformatic approaches. Transcriptomic data of chosen genes combined with volatilome data obtained during different developmental stages is demonstrated as a powerful tool to identify enzymes putatively involved in fungal VOC biosynthesis. Especially with regard to subsequent enzyme characterization, this procedure is a target-oriented way to save time and efforts by considering only the most important enzymes.}, } @article {pmid35330083, year = {2022}, author = {Nozdrenko, D and Prylutska, S and Bogutska, K and Nurishchenko, NY and Abramchuk, O and Motuziuk, O and Prylutskyy, Y and Scharff, P and Ritter, U}, title = {Effect of C60 Fullerene on Recovery of Muscle Soleus in Rats after Atrophy Induced by Achillotenotomy.}, journal = {Life (Basel, Switzerland)}, volume = {12}, number = {3}, pages = {}, pmid = {35330083}, issn = {2075-1729}, support = {№21БП018-01Р//Ministry of Education and Science of Ukraine/ ; }, abstract = {Biomechanical and biochemical changes in the muscle soleus of rats during imitation of hind limbs unuse were studied in the model of the Achilles tendon rupture (Achillotenotomy). Oral administration of water-soluble C60 fullerene at a dose of 1 mg/kg was used as a therapeutic agent throughout the experiment. Changes in the force of contraction and the integrated power of the muscle, the time to reach the maximum force response, the mechanics of fatigue processes development, in particular, the transition from dentate to smooth tetanus, as well as the levels of pro- and antioxidant balance in the blood of rats on days 15, 30 and 45 after injury were described. The obtained results indicate a promising prospect for C60 fullerene use as a powerful antioxidant for reducing and correcting pathological conditions of the muscular system arising from skeletal muscle atrophy.}, } @article {pmid35328906, year = {2022}, author = {Xu, X and Chen, Q and Zhu, Z}, title = {Evolutionary Overview of Land Consolidation Based on Bibliometric Analysis in Web of Science from 2000 to 2020.}, journal = {International journal of environmental research and public health}, volume = {19}, number = {6}, pages = {}, pmid = {35328906}, issn = {1660-4601}, mesh = {*Bibliometrics ; China ; Databases, Factual ; *Ecosystem ; Soil ; United States ; }, abstract = {Land consolidation is widely used as a powerful tool for land use management in many countries. In order to objectively reveal the current research status in the field of land consolidation, this paper uses the Bibliometrix and Biblioshiny software packages, and VOSviewer to analyze the literature in the field of land consolidation in the last 20 years of the Web of Science Core Collection Database. The results show that: (1) In the past two decades, the annual publication of papers on land consolidation rose. It can be divided into three stages: 2000-2007 for the embryonic period, 2008-2012 for the long-term, and 2013-2020 for the high-yield period. (2) Land consolidation studies covered 68 countries or regions. The top three countries were China, Poland, and the United States. China and the United States played an important role in international cooperation in the field of land consolidation, and Turkey mainly conducted independent research in the field of land consolidation. (3) Land consolidation, reclamation, China, remote sensing, and land fragmentation were the high-frequency keywords in the field of land consolidation in recent years. (4) The research focusing on the field of land consolidation involved its development course, its impact on ecosystem services, and the evaluation of its benefits. (5) The theme of land consolidation studies was shunted and evolved over time, and nine evolution paths could be summarized in the studies of cultivated land fragmentation, development course of land consolidation, and impacts of land consolidation on soil. Finally, this paper predicted the future research directions of land consolidation: exploring new methods for evaluating the benefits of land consolidation, the scale effects of the impact of land consolidation on ecosystem services, research on the mechanism and comprehensive effects of land consolidation on soil, research on land consolidation and rural revitalization, and land consolidation theory research.}, } @article {pmid35326848, year = {2022}, author = {Jepsen, K and Falk, W and Brune, F and Cosgarea, R and Fimmers, R and Bekeredjian-Ding, I and Jepsen, S}, title = {Prevalence and Antibiotic Susceptibility Trends of Selected Enterobacteriaceae, Enterococci, and Candida albicans in the Subgingival Microbiota of German Periodontitis Patients: A Retrospective Surveillance Study.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {11}, number = {3}, pages = {}, pmid = {35326848}, issn = {2079-6382}, abstract = {The periodontal microbiota is ecologically diverse and may facilitate colonization by bacteria of enteric origin (Enterobacteriaceae, Enterococci) and co-infections with Candida albicans, possibly producing subgingival biofilms with high antimicrobial tolerance. This retrospective surveillance study followed periodontitis-associated superinfection profiles in a large patient sample. From 2008 to 2015, biofilm samples from deep periodontal pockets were collected from a total of 16,612 German adults diagnosed with periodontitis. The presence of selected Enterobacteriaceae, Enterococci, and Candida albicans was confirmed in overnight cultures. Antimicrobial susceptibility of these clinical isolates was tested by disk diffusion with antibiotics routinely used for treatment of oral infections, e.g., amoxicillin (AML), amoxicillin/clavulanic acid (AMC), doxycycline (DO), and ciprofloxacin (CIP). The mean annual prevalence of patients harboring Enterobacteriaceae in periodontal plaques was 11.5% in total and ranged from 2.5% for Enterobacter cloacae to 3.6% for Klebsiella oxytoca, 1.1% for Klebsiella pneumoniae, 2.8% for Serratia marcescens, and 1.5% for Serratia liquefaciens. In comparison, the mean detection rates for microbiota typically found in the oral cavity were higher, e.g., 5.6% for Enterococcus spp. and 21.8% for Candida albicans. Among the Enterobacteriaceae, species harboring intrinsic resistance to AML (Enterobacter spp., Klebsiella spp., Serratia spp.) were predominant. Non-susceptibility to AMC was observed for Serratia spp. and Enterobacter cloacae. By contrast, Enterococcus spp. only showed non-susceptibility to DO and CIP. Trends for increasing resistance were found to AML in Serratia liquefaciens and to DO in Enterococcus spp. Trend analysis showed decreasing resistance to AMC in Serratia liquefaciens and Klebsiella oxytoca; and to DO in Serratia marcescens, liquefaciens, and Enterobacter cloacae. This study confirms the low but consistent presence of Enterobacteriaceae and Enterococci among the subgingival microbiota recovered from periodontitis specimen. Although their pathogenetic role in periodontal lesions remains unclear, their presence in the oral cavity should be recognized as a potential reservoir for development and spread of antibiotic resistance in light of antibiotic usage in oral infections.}, } @article {pmid35319247, year = {2022}, author = {Kollath, DR and Mihaljevic, JR and Barker, BM}, title = {PM10 and Other Climatic Variables Are Important Predictors of Seasonal Variability of Coccidioidomycosis in Arizona.}, journal = {Microbiology spectrum}, volume = {10}, number = {2}, pages = {e0148321}, pmid = {35319247}, issn = {2165-0497}, mesh = {Animals ; Arizona/epidemiology ; Coccidioides ; *Coccidioidomycosis/epidemiology ; Humans ; Mammals ; Seasons ; United States ; }, abstract = {Coccidioidomycosis (Valley fever) is a disease caused by the fungal pathogens Coccidioides immitis and Coccidioides posadasii that are endemic to the southwestern United States and parts of Mexico and South America. Throughout the range where the pathogens are endemic, there are seasonal patterns of infection rates that are associated with certain climatic variables. Previous studies that looked at annual and monthly relationships of coccidioidomycosis and climate suggest that infection numbers are linked with precipitation and temperature fluctuations; however, these analytic methods may miss important nonlinear, nonmonotonic seasonal relationships between the response (Valley fever cases) and explanatory variables (climate) influencing disease outbreaks. To improve our current knowledge and to retest relationships, we used case data from three counties of high endemicity in southern Arizona paired with climate data to construct a generalized additive statistical model that explores which meteorological parameters are most useful in predicting Valley fever incidence throughout the year. We then use our model to forecast the pattern of Valley fever cases by month. Our model shows that maximum monthly temperature, average PM10, and total precipitation 1 month prior to reported cases (lagged model) were all significant in predicting Valley fever cases. Our model fits Valley fever case data in the region of endemicity of southern Arizona and captures the seasonal relationships that predict when the public is at higher risk of being infected. This study builds on and retests relationships described by previous studies regarding climate variables that are important for predicting risk of infection and understanding this fungal pathogen. IMPORTANCE The inhalation of environmental infectious propagules from the fungal pathogens Coccidioides immitis and Coccidioides posadasii by susceptible mammals can result in coccidioidomycosis (Valley fever). Arizona is known to be a region where the pathogen is hyperendemic, and reported cases are increasing throughout the western United States. Coccidioides spp. are naturally occurring fungi in arid soils. Little is known about ecological factors that influence the growth of these fungi, and a higher environmental burden may result in increases in human exposure and therefore case rates. By examining case and climate data from Arizona and using generalized additive statistical models, we were able to examine the relationship between disease outbreaks and climatic variables and predict seasonal time points of increased infection risk.}, } @article {pmid35318148, year = {2022}, author = {Nunes, IJG and Feltes, BC and David, MZ and Dorn, M}, title = {Gene Expression Variation Analysis (GEVA): A new R package to evaluate variations in differential expression in multiple biological conditions.}, journal = {Journal of biomedical informatics}, volume = {129}, number = {}, pages = {104053}, doi = {10.1016/j.jbi.2022.104053}, pmid = {35318148}, issn = {1532-0480}, mesh = {Cluster Analysis ; *Gene Expression Profiling/methods ; Programming Languages ; *Software ; Transcriptome ; }, abstract = {Nowadays, there are thousands of publicly available gene expression datasets which can be analyzed in silico using specialized software or the R programming language. However, transcriptomic studies consider experimental conditions individually, giving one independent result per comparison. Here we describe the Gene Expression Variation Analysis (GEVA), a new R package that accepts multiple differential expression analysis results as input and performs multiple statistical steps, such as weighted summarization, quantiles partition, and clustering to find genes whose differential expression varied less across all experiments. The experimental conditions can be divided into groups, which we call factors, where additional ANOVA (Fisher's and Levene's) tests are applied to identify differentially expressed genes in response either specifically to one factor or dependently to all factors. The final results present three possible classifications for relevant genes: similar, factor-dependent, and factor-specific. To validate these results subsequently to the GEVA's development, 28 transcriptomic datasets were tested using 11 different combinations of the available parameters, including several clustering, quantiles, and summarization methods. The final classifications were validated using knockout studies from different organisms, as they lack genes whose differential expression is expected. Although some of the final classifications differed depending on the parameters' choice, the test results from the default parameters corroborated with the published experimental studies regarding the selected datasets. Thus, we conclude that GEVA can effectively find similarities between groups of biological conditions, and therefore could be a robust alternative for multiple comparison analyses.}, } @article {pmid35317857, year = {2022}, author = {Murakami, T and Takeuchi, N and Mori, H and Hirose, Y and Edwards, A and Irvine-Fynn, T and Li, Z and Ishii, S and Segawa, T}, title = {Metagenomics reveals global-scale contrasts in nitrogen cycling and cyanobacterial light-harvesting mechanisms in glacier cryoconite.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {50}, pmid = {35317857}, issn = {2049-2618}, mesh = {*Cyanobacteria/genetics ; Ecosystem ; *Ice Cover/microbiology ; Metagenomics ; Nitrogen/metabolism ; Phycoerythrin/metabolism ; }, abstract = {BACKGROUND: Cryoconite granules are mineral-microbial aggregates found on glacier surfaces worldwide and are hotspots of biogeochemical reactions in glacier ecosystems. However, despite their importance within glacier ecosystems, the geographical diversity of taxonomic assemblages and metabolic potential of cryoconite communities around the globe remain unclear. In particular, the genomic content of cryoconite communities on Asia's high mountain glaciers, which represent a substantial portion of Earth's ice masses, has rarely been reported. Therefore, in this study, to elucidate the taxonomic and ecological diversities of cryoconite bacterial consortia on a global scale, we conducted shotgun metagenomic sequencing of cryoconite acquired from a range of geographical areas comprising Polar (Arctic and Antarctic) and Asian alpine regions.

RESULTS: Our metagenomic data indicate that compositions of both bacterial taxa and functional genes are particularly distinctive for Asian cryoconite. Read abundance of the genes responsible for denitrification was significantly more abundant in Asian cryoconite than the Polar cryoconite, implying that denitrification is more enhanced in Asian glaciers. The taxonomic composition of Cyanobacteria, the key primary producers in cryoconite communities, also differs between the Polar and Asian samples. Analyses on the metagenome-assembled genomes and fluorescence emission spectra reveal that Asian cryoconite is dominated by multiple cyanobacterial lineages possessing phycoerythrin, a green light-harvesting component for photosynthesis. In contrast, Polar cryoconite is dominated by a single cyanobacterial species Phormidesmis priestleyi that does not possess phycoerythrin. These findings suggest that the assemblage of cryoconite bacterial communities respond to regional- or glacier-specific physicochemical conditions, such as the availability of nutrients (e.g., nitrate and dissolved organic carbon) and light (i.e., incident shortwave radiation).

CONCLUSIONS: Our genome-resolved metagenomics provides the first characterization of the taxonomic and metabolic diversities of cryoconite from contrasting geographical areas, highlighted by the distinct light-harvesting approaches of Cyanobacteria and nitrogen utilization between Polar and Asian cryoconite, and implies the existence of environmental controls on the assemblage of cryoconite communities. These findings deepen our understanding of the biodiversity and biogeochemical cycles of glacier ecosystems, which are susceptible to ongoing climate change and glacier decline, on a global scale. Video abstract.}, } @article {pmid35317834, year = {2022}, author = {Stryamets, N and Prakofjewa, J and Mattalia, G and Kalle, R and Pruse, B and Zocchi, DM and Sõukand, R and Pieroni, A and Fontefrancesco, MF}, title = {Why the ongoing occupation of Ukraine matters to ethnobiology.}, journal = {Journal of ethnobiology and ethnomedicine}, volume = {18}, number = {1}, pages = {21}, pmid = {35317834}, issn = {1746-4269}, mesh = {Environment ; Humans ; *Knowledge ; *Medicine, Traditional ; Occupations ; Ukraine ; }, abstract = {Ethnobiology and ethnomedicine investigate the continuously changing complex and inextricable relations among culture, nature, and health. Since the emergence of modern ethnobiology a few decades ago, its essence and mission have been the study of biocultural diversities and the centers of its inquiries have been and are local communities and their co-evolutionary interrelationships between natural environments and social systems. At the core of ethnobiologists' work there are not only conceptualizations of and reflections on others' views about nature and the universe, but also a robust commitment to advocacy in defense of these assemblages of local ecological knowledge, practices, and beliefs (LEK). Homogenization processes and therefore erosion of LEK have occurred throughout history in different ways: from colonialism to industrialization, and from financialization to globalization; however, we cannot forget the role played by centripetal states and even dictatorships in this process, nor the associated political ideology of nationalism, which has often elicited and justified policies aimed at standardizing diversities within state borders. Our research groups have been working since eight years together with local communities in Ukrainian rural areas and documented a remarkable erosion of LEK during the Soviet times, yet an extraordinary surviving biocultural diversity occurs; the ongoing military occupation of Ukraine could further threaten this heritage. While citizens' attention now should be on effectively supporting those who are experiencing hardships during this traumatic time, ethnobiologists will be called hopefully soon to directly participate in rebuilding the biocultural "cobwebs" damaged by the military operations.}, } @article {pmid35311562, year = {2022}, author = {Sokhansanj, BA and Rosen, GL}, title = {Mapping Data to Deep Understanding: Making the Most of the Deluge of SARS-CoV-2 Genome Sequences.}, journal = {mSystems}, volume = {7}, number = {2}, pages = {e0003522}, pmid = {35311562}, issn = {2379-5077}, mesh = {Humans ; *SARS-CoV-2/genetics ; *COVID-19 ; Pandemics/prevention & control ; High-Throughput Nucleotide Sequencing ; }, abstract = {Next-generation sequencing has been essential to the global response to the COVID-19 pandemic. As of January 2022, nearly 7 million severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequences are available to researchers in public databases. Sequence databases are an abundant resource from which to extract biologically relevant and clinically actionable information. As the pandemic has gone on, SARS-CoV-2 has rapidly evolved, involving complex genomic changes that challenge current approaches to classifying SARS-CoV-2 variants. Deep sequence learning could be a potentially powerful way to build complex sequence-to-phenotype models. Unfortunately, while they can be predictive, deep learning typically produces "black box" models that cannot directly provide biological and clinical insight. Researchers should therefore consider implementing emerging methods for visualizing and interpreting deep sequence models. Finally, researchers should address important data limitations, including (i) global sequencing disparities, (ii) insufficient sequence metadata, and (iii) screening artifacts due to poor sequence quality control.}, } @article {pmid35301629, year = {2022}, author = {Sarkar, A and Wang, H and Rahman, A and Memon, WH and Qian, L}, title = {A bibliometric analysis of sustainable agriculture: based on the Web of Science (WOS) platform.}, journal = {Environmental science and pollution research international}, volume = {29}, number = {26}, pages = {38928-38949}, pmid = {35301629}, issn = {1614-7499}, support = {71973105//national natural science foundation of china/ ; }, mesh = {Agriculture ; *Bibliometrics ; Databases, Factual ; *Publications ; Soil ; }, abstract = {The global trends of sustainable agriculture (SA) have expanded dramatically through many scholarly studies in this area. Many literary works have focused on several aspects of sustainable agriculture (SA), such as the effectiveness of pesticide management, impacts on cultivation and enhancement, quantifying with soil, water, and air, agro-ecological activities, ecological aspects, and other areas of focus. The review offers a structured bibliometric and network evaluation that will profoundly observe the recent trends of SA, which other studies in this field have not comprehensively analyzed before. The study's prime objectives are to investigate the progress, trends and themes, and provide a comprehensive mapping of the field of sustainable agriculture. The study utilizes the Web of Science core collection database to search, filter, and extract the published article from 1992-2020. The review commences by exploring over 3000 journal articles, those then filtered into some well-recognized matrix of impacts and published by impactful journals, institutions, and authors. The results indicate a stable growth in publications since 2006, with a sharp improvement from 2010. Thematic assessment of key concepts by exploring the abstract discovered a robust emphasis on quantitative resource associations within a strong subjective focus with farm capacities and inner-sectorial dominations. We reveal how the outcome may assist the sectors to facilitate better understandings and comprehend the challenging transitions based on brainstorming to action formulation.}, } @article {pmid35300703, year = {2022}, author = {Ruiz Cuenca, P and Key, S and Lindblade, KA and Vythilingam, I and Drakeley, C and Fornace, K}, title = {Is there evidence of sustained human-mosquito-human transmission of the zoonotic malaria Plasmodium knowlesi? A systematic literature review.}, journal = {Malaria journal}, volume = {21}, number = {1}, pages = {89}, pmid = {35300703}, issn = {1475-2875}, support = {001/WHO_/World Health Organization/International ; Global Malaria Programme/WHO_/World Health Organization/International ; 221963/Z/20/Z//Wellcome Trust and Royal Society/ ; }, mesh = {Animals ; Asia, Southeastern/epidemiology ; *Culicidae ; Humans ; *Malaria/epidemiology ; *Plasmodium knowlesi ; Zoonoses/epidemiology ; }, abstract = {BACKGROUND: The zoonotic malaria parasite Plasmodium knowlesi has emerged across Southeast Asia and is now the main cause of malaria in humans in Malaysia. A critical priority for P. knowlesi surveillance and control is understanding whether transmission is entirely zoonotic or is also occurring through human-mosquito-human transmission.

METHODS: A systematic literature review was performed to evaluate existing evidence which refutes or supports the occurrence of sustained human-mosquito-human transmission of P. knowlesi. Possible evidence categories and study types which would support or refute non-zoonotic transmission were identified and ranked. A literature search was conducted on Medline, EMBASE and Web of Science using a broad search strategy to identify any possible published literature. Results were synthesized using the Synthesis Without Meta-analysis (SWiM) framework, using vote counting to combine the evidence within specific categories.

RESULTS: Of an initial 7,299 studies screened, 131 studies were included within this review: 87 studies of P. knowlesi prevalence in humans, 14 studies in non-human primates, 13 studies in mosquitoes, and 29 studies with direct evidence refuting or supporting non-zoonotic transmission. Overall, the evidence showed that human-mosquito-human transmission is biologically possible, but there is limited evidence of widespread occurrence in endemic areas. Specific areas of research were identified that require further attention, notably quantitative analyses of potential transmission dynamics, epidemiological and entomological surveys, and ecological studies into the sylvatic cycle of the disease.

CONCLUSION: There are key questions about P. knowlesi that remain within the areas of research that require more attention. These questions have significant implications for malaria elimination and eradication programs. This paper considers limited but varied research and provides a methodological framework for assessing the likelihood of different transmission patterns for emerging zoonotic diseases.}, } @article {pmid35298643, year = {2022}, author = {Rodríguez-López, CE and Jiang, Y and Kamileen, MO and Lichman, BR and Hong, B and Vaillancourt, B and Buell, CR and O'Connor, SE}, title = {Phylogeny-Aware Chemoinformatic Analysis of Chemical Diversity in Lamiaceae Enables Iridoid Pathway Assembly and Discovery of Aucubin Synthase.}, journal = {Molecular biology and evolution}, volume = {39}, number = {4}, pages = {}, pmid = {35298643}, issn = {1537-1719}, mesh = {Cheminformatics ; *Iridoid Glucosides/chemistry/metabolism ; Iridoids/metabolism ; *Lamiaceae/genetics/metabolism ; Phylogeny ; }, abstract = {Countless reports describe the isolation and structural characterization of natural products, yet this information remains disconnected and underutilized. Using a cheminformatics approach, we leverage the reported observations of iridoid glucosides with the known phylogeny of a large iridoid producing plant family (Lamiaceae) to generate a set of biosynthetic pathways that best explain the extant iridoid chemical diversity. We developed a pathway reconstruction algorithm that connects iridoid reports via reactions and prunes this solution space by considering phylogenetic relationships between genera. We formulate a model that emulates the evolution of iridoid glucosides to create a synthetic data set, used to select the parameters that would best reconstruct the pathways, and apply them to the iridoid data set to generate pathway hypotheses. These computationally generated pathways were then used as the basis by which to select and screen biosynthetic enzyme candidates. Our model was successfully applied to discover a cytochrome P450 enzyme from Callicarpa americana that catalyzes the oxidation of bartsioside to aucubin, predicted by our model despite neither molecule having been observed in the genus. We also demonstrate aucubin synthase activity in orthologues of Vitex agnus-castus, and the outgroup Paulownia tomentosa, further strengthening the hypothesis, enabled by our model, that the reaction was present in the ancestral biosynthetic pathway. This is the first systematic hypothesis on the epi-iridoid glucosides biosynthesis in 25 years and sets the stage for streamlined work on the iridoid pathway. This work highlights how curation and computational analysis of widely available structural data can facilitate hypothesis-based gene discovery.}, } @article {pmid35298256, year = {2022}, author = {Ferreira, RL and Bernard, E and da Cruz Júnior, FW and Piló, LB and Calux, A and Souza-Silva, M and Barlow, J and Pompeu, PS and Cardoso, P and Mammola, S and García, AM and Jeffery, WR and Shear, W and Medellín, RA and Wynne, JJ and Borges, PAV and Kamimura, Y and Pipan, T and Hajna, NZ and Sendra, A and Peck, S and Onac, BP and Culver, DC and Hoch, H and Flot, JF and Stoch, F and Pavlek, M and Niemiller, ML and Manchi, S and Deharveng, L and Fenolio, D and Calaforra, JM and Yager, J and Griebler, C and Nader, FH and Humphreys, WF and Hughes, AC and Fenton, B and Forti, P and Sauro, F and Veni, G and Frumkin, A and Gavish-Regev, E and Fišer, C and Trontelj, P and Zagmajster, M and Delic, T and Galassi, DMP and Vaccarelli, I and Komnenov, M and Gainett, G and da Cunha Tavares, V and Kováč, Ľ and Miller, AZ and Yoshizawa, K and Di Lorenzo, T and Moldovan, OT and Sánchez-Fernández, D and Moutaouakil, S and Howarth, F and Bilandžija, H and Dražina, T and Kuharić, N and Butorac, V and Lienhard, C and Cooper, SJB and Eme, D and Strauss, AM and Saccò, M and Zhao, Y and Williams, P and Tian, M and Tanalgo, K and Woo, KS and Barjakovic, M and McCracken, GF and Simmons, NB and Racey, PA and Ford, D and Labegalini, JA and Colzato, N and Ramos Pereira, MJ and Aguiar, LMS and Moratelli, R and Du Preez, G and Pérez-González, A and Reboleira, ASPS and Gunn, J and Mc Cartney, A and Bobrowiec, PED and Milko, D and Kinuthia, W and Fischer, E and Meierhofer, MB and Frick, WF}, title = {Brazilian cave heritage under siege.}, journal = {Science (New York, N.Y.)}, volume = {375}, number = {6586}, pages = {1238-1239}, doi = {10.1126/science.abo1973}, pmid = {35298256}, issn = {1095-9203}, } @article {pmid35296832, year = {2022}, author = {Hemmerling, F and Piel, J}, title = {Strategies to access biosynthetic novelty in bacterial genomes for drug discovery.}, journal = {Nature reviews. Drug discovery}, volume = {21}, number = {5}, pages = {359-378}, pmid = {35296832}, issn = {1474-1784}, mesh = {Bacteria/genetics/metabolism ; *Biological Products/chemistry ; *Computational Biology ; Drug Discovery ; Genome, Bacterial ; Genomics ; Humans ; }, abstract = {Bacteria provide a rich source of natural products with potential therapeutic applications, such as novel antibiotic classes or anticancer drugs. Bioactivity-guided screening of bacterial extracts and characterization of biosynthetic pathways for drug discovery is now complemented by the availability of large (meta)genomic collections, placing researchers into the postgenomic, big-data era. The progress in next-generation sequencing and the rise of powerful computational tools provide unprecedented insights into unexplored taxa, ecological niches and 'biosynthetic dark matter', revealing diverse and chemically distinct natural products in previously unstudied bacteria. In this Review, we discuss such sources of new chemical entities and the implications for drug discovery with a particular focus on the strategies that have emerged in recent years to identify and access novelty.}, } @article {pmid35295279, year = {2022}, author = {Li, P}, title = {Research on Ecoenvironmental Quality Evaluation System Based on Big Data Analysis.}, journal = {Computational intelligence and neuroscience}, volume = {2022}, number = {}, pages = {5191223}, pmid = {35295279}, issn = {1687-5273}, mesh = {Big Data ; Data Analysis ; *Ecosystem ; Environment ; *Remote Sensing Technology ; }, abstract = {Comprehensive and objective evaluation of ecological environment quality is of great significance to regional sustainable development. In this study, Landsat remote sensing images of 1991, 2000, 2004, 2010, 2013, 2018, and 2019 are selected to evaluate the changes of ecological environment quality in the Headwaters of Dongjiangyuan River by using remote sensing ecological index RSEI. The influencing factors of ecological environment change in Dongjiangyuan River are also discussed. The results showed that, from 1991 to 2019, the ecoenvironmental quality of the Dongjiangyuan River showed a good trend of development. Humidity index, greenness index, and dryness index all fluctuated in a small range; the greenness and dryness showed an overall increase. The average temperature in the Headwaters of the Dongjiangyuan River presents a rising trend. This study establishes the evaluation system of ecological environment quality from two dimensions of time and space and gives the change rule of environmental quality quantitatively, which provides the theoretical basis for the ecological environment management of Dongjiangyuan River.}, } @article {pmid35291055, year = {2022}, author = {Hung, CM and Tsao, SH and Chiang, PL and Wu, SP and Tuanmu, MN and Juang, JY}, title = {Functional connections between bird eggshell stiffness and nest characteristics through risk of egg collision in nests.}, journal = {Ecology letters}, volume = {25}, number = {6}, pages = {1421-1431}, pmid = {35291055}, issn = {1461-0248}, support = {AS-CDA-111-L07//Academia Sinica/ ; AS-CDA-108-L05//Academia Sinica/ ; 106-2221-E-002-141-MY3//Ministry of Science and Technology, Taiwan/ ; 108-2621-B-001-008-MY3//Ministry of Science and Technology, Taiwan/ ; //National Taiwan University/ ; }, mesh = {Animals ; Birds/physiology ; Body Temperature Regulation ; Ecosystem ; *Egg Shell/physiology ; *Nesting Behavior/physiology ; }, abstract = {Eggs and nests are two critical traits for the ecological success of birds. Their functional interactions, however, remain unclear. Here, we examined the functional connections between egg stiffness and nest attachment, site and structure for 1350 avian species. We revealed high eggshell stiffness for eggs in nests with a pensile attachment, located on non-tree vegetation or having a domed shape, suggesting that birds produce stiffer eggs in response to higher egg-collision risk in unstable or enclosed nests. Interdependence models suggested that the evolution of eggshell stiffness was more likely to be driven by than drive that of nest characters. Our results implied a trade-off between investment in competing for established nesting niches and producing stiff eggs to explore novel niches with high collision risk, possibly mediated by predation or thermoregulation. This study highlights an overlooked connection between nests and eggshells that may have broadened the ecological niches of birds.}, } @article {pmid35286014, year = {2022}, author = {Tindall, D and McLevey, J and Koop-Monteiro, Y and Graham, A}, title = {Big data, computational social science, and other recent innovations in social network analysis.}, journal = {Canadian review of sociology = Revue canadienne de sociologie}, volume = {59}, number = {2}, pages = {271-288}, doi = {10.1111/cars.12377}, pmid = {35286014}, issn = {1755-618X}, mesh = {*Big Data ; Semantic Web ; *Social Network Analysis ; Social Networking ; Social Sciences ; }, abstract = {While sociologists have studied social networks for about one hundred years, recent developments in data, technology, and methods of analysis provide opportunities for social network analysis (SNA) to play a prominent role in the new research world of big data and computational social science (CSS). In our review, we focus on four broad topics: (1) Collecting Social Network Data from the Web, (2) Non-traditional and Bipartite/Multi-mode Networks, including Discourse and Semantic Networks, and Social-Ecological Networks, (3) Recent Developments in Statistical Inference for Networks, and (4) Ethics in Computational Network Research.}, } @article {pmid35284876, year = {2021}, author = {Young, ND and Kinkar, L and Stroehlein, AJ and Korhonen, PK and Stothard, JR and Rollinson, D and Gasser, RB}, title = {Mitochondrial genome of Bulinus truncatus (Gastropoda: Lymnaeoidea): Implications for snail systematics and schistosome epidemiology.}, journal = {Current research in parasitology & vector-borne diseases}, volume = {1}, number = {}, pages = {100017}, pmid = {35284876}, issn = {2667-114X}, abstract = {Many freshwater snails of the genus Bulinus act as intermediate hosts in the life-cycles of schistosomes in Africa and adjacent regions. Currently, 37 species of Bulinus representing four groups are recognised. The mitochondrial cytochrome c oxidase subunit 1 (cox1) gene has shown utility for identifying and differentiating Bulinus species and groups, but taxonomic relationships based on genetic data are not entirely consistent with those inferred using morphological and biological features. To underpin future systematic studies of members of the genus, we characterised here the mitochondrial genome of Bulinus truncatus (from a defined laboratory strain) using a combined second- and third-generation sequencing and informatics approach, enabling taxonomic comparisons with other planorbid snails for which mitochondrial (mt) genomes were available. Analyses showed consistency in gene order and length among mitochondrial genomes of representative planorbid snails, with the lowest and highest nucleotide diversities being in the cytochrome c oxidase and nicotinamide dehydrogenase subunit genes, respectively. This first mt genome for a representative of the genus Bulinus should provide a useful resource for future investigations of the systematics, population genetics, epidemiology and/or ecology of Bulinus and related snails. The sequencing and informatic workflow employed here should find broad applicability to a range of other snail intermediate hosts of parasitic trematodes.}, } @article {pmid35277593, year = {2022}, author = {Tao, T and Shi, Y and Gilbert, KM and Liu, X}, title = {Spatiotemporal variations of air pollutants based on ground observation and emission sources over 19 Chinese urban agglomerations during 2015-2019.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {4293}, pmid = {35277593}, issn = {2045-2322}, mesh = {*Air Pollutants/analysis ; *Air Pollution/analysis ; China ; Environmental Monitoring/methods ; Particulate Matter/analysis ; }, abstract = {The "comparative attitude" of urban agglomerations involves multidimensional perspectives such as infrastructure, ecological protection, and air pollution. Based on monitoring station data, comparative studies of multispatial, multitimescale and multiemission pollution sources of air quality on 19 urban agglomerations during the 13th Five-Year Plan period in China were explored by mathematical statistics. The comparison results are all visualized and show that clean air days gradually increased and occurred mainly in summer, especially in South and Southwest China. PM2.5, PM10 and O3 were still the main primary pollutants. PM2.5 is mainly concentrated in December, January and February, and PM10 is mainly concentrated in October-November and March-April. The O3 pollution in the Pearl River Delta and Beibu Gulf urban agglomerations located in the south is mainly concentrated from August to November, which is different from others from May to September. Second, from 2015 to 2019, the increasing rate of O3 concentration in any hour is higher than that of particulate matter (PM). Diurnal trends in O3 concentration in all directions also showed a single peak, with the largest increments that appeared between 13:00 and 16:00, while the spatial distribution of this peak was significantly regional, earlier in the east but later in the west. Third, this analysis indicated that the annual average air quality index (AQI) showed a gradually decreasing trend outward, taking the Central Plain urban agglomeration as the center. The ambient air pollutants are gradually moving southward and mainly concentrated in the Central Plains urban agglomeration from 2015 to 2019. Furthermore, in each urban agglomeration, the cumulative emission of PM2.5 is consisted of the four average emissions, which is approximately 2.5 times of that of PM10, and industries are the main sources of PM2.5, PM10 and VOCs (volatile organic compounds). VOCs and NOX increased in half of the urban agglomerations, which are the reasons for the increase in ozone pollution. The outcomes of this study will provide targeted insights on pollution prevention in urban agglomerations in the future.}, } @article {pmid35275994, year = {2022}, author = {Norris, T and Razieh, C and Yates, T and Zaccardi, F and Gillies, CL and Chudasama, YV and Rowlands, A and Davies, MJ and McCann, GP and Banerjee, A and Docherty, AB and Openshaw, PJM and Baillie, JK and Semple, MG and Lawson, CA and Khunti, K}, title = {Admission Blood Glucose Level and Its Association With Cardiovascular and Renal Complications in Patients Hospitalized With COVID-19.}, journal = {Diabetes care}, volume = {45}, number = {5}, pages = {1132-1140}, pmid = {35275994}, issn = {1935-5548}, support = {MC_PC_19025/MRC_/Medical Research Council/United Kingdom ; MR/V020536/1/MRC_/Medical Research Council/United Kingdom ; MC_PC_19059/MRC_/Medical Research Council/United Kingdom ; CO-CIN-01/DH_/Department of Health/United Kingdom ; }, mesh = {Adult ; Aged ; Blood Glucose ; *COVID-19/complications/epidemiology ; *Heart Failure ; Humans ; Ischemia ; Kidney ; Prospective Studies ; *Stroke/epidemiology/etiology ; }, abstract = {OBJECTIVE: To investigate the association between admission blood glucose levels and risk of in-hospital cardiovascular and renal complications.

RESEARCH DESIGN AND METHODS: In this multicenter prospective study of 36,269 adults hospitalized with COVID-19 between 6 February 2020 and 16 March 2021 (N = 143,266), logistic regression models were used to explore associations between admission glucose level (mmol/L and mg/dL) and odds of in-hospital complications, including heart failure, arrhythmia, cardiac ischemia, cardiac arrest, coagulation complications, stroke, and renal injury. Nonlinearity was investigated using restricted cubic splines. Interaction models explored whether associations between glucose levels and complications were modified by clinically relevant factors.

RESULTS: Cardiovascular and renal complications occurred in 10,421 (28.7%) patients; median admission glucose level was 6.7 mmol/L (interquartile range 5.8-8.7) (120.6 mg/dL [104.4-156.6]). While accounting for confounders, for all complications except cardiac ischemia and stroke, there was a nonlinear association between glucose and cardiovascular and renal complications. For example, odds of heart failure, arrhythmia, coagulation complications, and renal injury decreased to a nadir at 6.4 mmol/L (115 mg/dL), 4.9 mmol/L (88.2 mg/dL), 4.7 mmol/L (84.6 mg/dL), and 5.8 mmol/L (104.4 mg/dL), respectively, and increased thereafter until 26.0 mmol/L (468 mg/dL), 50.0 mmol/L (900 mg/dL), 8.5 mmol/L (153 mg/dL), and 32.4 mmol/L (583.2 mg/dL). Compared with 5 mmol/L (90 mg/dL), odds ratios at these glucose levels were 1.28 (95% CI 0.96, 1.69) for heart failure, 2.23 (1.03, 4.81) for arrhythmia, 1.59 (1.36, 1.86) for coagulation complications, and 2.42 (2.01, 2.92) for renal injury. For most complications, a modifying effect of age was observed, with higher odds of complications at higher glucose levels for patients age <69 years. Preexisting diabetes status had a similar modifying effect on odds of complications, but evidence was strongest for renal injury, cardiac ischemia, and any cardiovascular/renal complication.

CONCLUSIONS: Increased odds of cardiovascular or renal complications were observed for admission glucose levels indicative of both hypo- and hyperglycemia. Admission glucose could be used as a marker for risk stratification of high-risk patients. Further research should evaluate interventions to optimize admission glucose on improving COVID-19 outcomes.}, } @article {pmid35274171, year = {2022}, author = {Fural, Ş and Kükrer, S and Cürebal, İ and Aykır, D}, title = {Ecological degradation and non-carcinogenic health risks of potential toxic elements: a GIS-based spatial analysis for Doğancı Dam (Turkey).}, journal = {Environmental monitoring and assessment}, volume = {194}, number = {4}, pages = {269}, pmid = {35274171}, issn = {1573-2959}, support = {2019 - 030//Balikesir Üniversitesi/ ; }, mesh = {Environmental Monitoring ; Geographic Information Systems ; *Metals, Heavy/analysis/toxicity ; Risk Assessment ; *Soil Pollutants/analysis ; Spatial Analysis ; Turkey ; }, abstract = {This study was carried out to determine the ecological degradation and non-carcinogenic health risks at Doğancı Dam, Bursa, Turkey. Potentially toxic element (PTE) concentrations (ppm) were as follows: Fe (55.030) > Al (27.220) > Mn (1053) > Cr (181) > Ni (180) > Zn (95) > Cu (62) > As (17) > Pb (11) > Cd (0.20) > Hg (0.108). As, Pb, Cd, and Hg were enriched anthropogenically, while other PTEs were of natural origin. The contamination severity index (CSI) indicated a moderate PTE contamination in the dam, mostly due to lithogenic effects. According to the modified hazard quotient (mHQ), ecological risk was identified at the level of extreme severity for Ni of lithological origin, of high severity for Cr of considerable severity for As of anthropogenic origin, and of moderate severity for Cu. According to the ecological contamination index (ECI), the dam had an ecological risk of a slight-to-moderate contamination. Health risk index showed no non-carcinogenic health risks in the dam. Mining, highways, and agricultural activities were identified as the primary anthropogenic drivers to be monitored. The ongoing anthropogenic activities in the Nilüfer Stream basin and natural factors affect the ecological degradation and non-carcinogenic health risk level of the dam.}, } @article {pmid35268740, year = {2022}, author = {Maiti, P and Sharma, P and Nand, M and Bhatt, ID and Ramakrishnan, MA and Mathpal, S and Joshi, T and Pant, R and Mahmud, S and Simal-Gandara, J and Alshehri, S and Ghoneim, MM and Alruwaily, M and Awadh, AAA and Alshahrani, MM and Chandra, S}, title = {Integrated Machine Learning and Chemoinformatics-Based Screening of Mycotic Compounds against Kinesin Spindle ProteinEg5 for Lung Cancer Therapy.}, journal = {Molecules (Basel, Switzerland)}, volume = {27}, number = {5}, pages = {}, pmid = {35268740}, issn = {1420-3049}, mesh = {Machine Learning ; *Lung Neoplasms/drug therapy/metabolism ; Humans ; Cell Line, Tumor ; *Kinesins/antagonists & inhibitors/chemistry ; *Secondary Metabolism ; *Fungi/chemistry/metabolism ; *Cheminformatics/methods ; *Antineoplastic Agents/chemistry/pharmacology/therapeutic use ; Molecular Dynamics Simulation ; Protein Conformation ; Ligands ; Protein Binding ; }, abstract = {Among the various types of cancer, lung cancer is the second most-diagnosed cancer worldwide. The kinesin spindle protein, Eg5, is a vital protein behind bipolar mitotic spindle establishment and maintenance during mitosis. Eg5 has been reported to contribute to cancer cell migration and angiogenesis impairment and has no role in resting, non-dividing cells. Thus, it could be considered as a vital target against several cancers, such as renal cancer, lung cancer, urothelial carcinoma, prostate cancer, squamous cell carcinoma, etc. In recent years, fungal secondary metabolites from the Indian Himalayan Region (IHR) have been identified as an important lead source in the drug development pipeline. Therefore, the present study aims to identify potential mycotic secondary metabolites against the Eg5 protein by applying integrated machine learning, chemoinformatics based in silico-screening methods and molecular dynamic simulation targeting lung cancer. Initially, a library of 1830 mycotic secondary metabolites was screened by a predictive machine-learning model developed based on the random forest algorithm with high sensitivity (1) and an ROC area of 0.99. Further, 319 out of 1830 compounds screened with active potential by the model were evaluated for their drug-likeness properties by applying four filters simultaneously, viz., Lipinski's rule, CMC-50 like rule, Veber rule, and Ghose filter. A total of 13 compounds passed from all the above filters were considered for molecular docking, functional group analysis, and cell line cytotoxicity prediction. Finally, four hit mycotic secondary metabolites found in fungi from the IHR were screened viz., (-)-Cochlactone-A, Phelligridin C, Sterenin E, and Cyathusal A. All compounds have efficient binding potential with Eg5, containing functional groups like aromatic rings, rings, carboxylic acid esters, and carbonyl and with cell line cytotoxicity against lung cancer cell lines, namely, MCF-7, NCI-H226, NCI-H522, A549, and NCI H187. Further, the molecular dynamics simulation study confirms the docked complex rigidity and stability by exploring root mean square deviations, root mean square fluctuations, and radius of gyration analysis from 100 ns simulation trajectories. The screened compounds could be used further to develop effective drugs against lung and other types of cancer.}, } @article {pmid35264543, year = {2022}, author = {Yokoyama-Sato, Y and Nishioka, T and Naganuma, Y and Takahashi, M and Nakagawa, A and Yoda, N and Sasaki, K and Takahashi, N and Tominaga, T and Iikubo, M}, title = {Effectiveness of an actuator-driven pulsed water jet for removal of softened carious dentin.}, journal = {Dental materials journal}, volume = {41}, number = {4}, pages = {527-533}, doi = {10.4012/dmj.2021-234}, pmid = {35264543}, issn = {1881-1361}, mesh = {*Dental Caries/therapy ; Dentin ; Hardness ; Humans ; Water ; }, abstract = {The aim of this study was to assess the utility of an actuator-driven pulsed water jet (ADPJ) as a hardness-dependent carious dentin removal device by using different outputs. Thirty-six plane surface dental caries samples were treated with the ADPJ at 150, 200, and 250 voltage (12 teeth each). The Knoop hardness number (KHN) and Ca/P mass ratio were measured at 70 μm from the deepest point of the removing groove. Furthermore, three other teeth samples were manually treated with the ADPJ at the three above mentioned voltages (one tooth each) for 1 min. The KHN and Ca/P mass ratio were measured at 70 μm from the surface of the residual dentin part. In both the KHN and Ca/P mass ratio, higher residual dentin depended on the applied voltage of ADPJ. The ADPJ enabled the removal of softened carious dentin in an applied voltage-dependent manner.}, } @article {pmid35263561, year = {2022}, author = {Jetz, W and Tertitski, G and Kays, R and Mueller, U and Wikelski, M and , }, title = {Biological Earth observation with animal sensors.}, journal = {Trends in ecology & evolution}, volume = {37}, number = {4}, pages = {293-298}, doi = {10.1016/j.tree.2021.11.011}, pmid = {35263561}, issn = {1872-8383}, mesh = {Animals ; Conservation of Natural Resources ; *Earth, Planet ; *Ecosystem ; Movement ; }, abstract = {Space-based tracking technology using low-cost miniature tags is now delivering data on fine-scale animal movement at near-global scale. Linked with remotely sensed environmental data, this offers a biological lens on habitat integrity and connectivity for conservation and human health; a global network of animal sentinels of environmental change.}, } @article {pmid35262228, year = {2022}, author = {Olker, JH and Elonen, CM and Pilli, A and Anderson, A and Kinziger, B and Erickson, S and Skopinski, M and Pomplun, A and LaLone, CA and Russom, CL and Hoff, D}, title = {The ECOTOXicology Knowledgebase: A Curated Database of Ecologically Relevant Toxicity Tests to Support Environmental Research and Risk Assessment.}, journal = {Environmental toxicology and chemistry}, volume = {41}, number = {6}, pages = {1520-1539}, pmid = {35262228}, issn = {1552-8618}, support = {EPA999999/ImEPA/Intramural EPA/United States ; }, mesh = {Databases, Factual ; *Ecotoxicology/methods ; Humans ; Knowledge Bases ; Risk Assessment/methods ; *Toxicity Tests/methods ; }, abstract = {The need for assembled existing and new toxicity data has accelerated as the amount of chemicals introduced into commerce continues to grow and regulatory mandates require safety assessments for a greater number of chemicals. To address this evolving need, the ECOTOXicology Knowledgebase (ECOTOX) was developed starting in the 1980s and is currently the world's largest compilation of curated ecotoxicity data, providing support for assessments of chemical safety and ecological research through systematic and transparent literature review procedures. The recently released version of ECOTOX (Ver 5, www.epa.gov/ecotox) provides single-chemical ecotoxicity data for over 12,000 chemicals and ecological species with over one million test results from over 50,000 references. Presented is an overview of ECOTOX, detailing the literature review and data curation processes within the context of current systematic review practices and discussing how recent updates improve the accessibility and reusability of data to support the assessment, management, and research of environmental chemicals. Relevant and acceptable toxicity results are identified from studies in the scientific literature, with pertinent methodological details and results extracted following well-established controlled vocabularies and newly extracted toxicity data added quarterly to the public website. Release of ECOTOX, Ver 5, included an entirely redesigned user interface with enhanced data queries and retrieval options, visualizations to aid in data exploration, customizable outputs for export and use in external applications, and interoperability with chemical and toxicity databases and tools. This is a reliable source of curated ecological toxicity data for chemical assessments and research and continues to evolve with accessible and transparent state-of-the-art practices in literature data curation and increased interoperability to other relevant resources. Environ Toxicol Chem 2022;41:1520-1539. © 2022 SETAC. This article has been contributed to by US Government employees and their work is in the public domain in the USA.}, } @article {pmid35259638, year = {2022}, author = {Woo, S and Yum, S}, title = {Transcriptional response of the azooxanthellate octocoral Scleronephthya gracillimum to seawater acidification and thermal stress.}, journal = {Comparative biochemistry and physiology. Part D, Genomics & proteomics}, volume = {42}, number = {}, pages = {100978}, doi = {10.1016/j.cbd.2022.100978}, pmid = {35259638}, issn = {1878-0407}, mesh = {Acclimatization/genetics ; Animals ; *Anthozoa/genetics/metabolism ; Gene Ontology ; Hydrogen-Ion Concentration ; Seawater ; }, abstract = {The stress responses to increased seawater temperature and marine acidification were investigated using a microarray to reveal transcriptional changes in S. gracillimum. For the study, corals were exposed to different stress experiments; high temperature only (26 °C, 28 °C and 30 °C), low-pH only (pH 7.5, pH 7.0 and pH 6.5) and dual stress experiments (28 °C + pH 7.8, 28 °C + pH 7.5 and 28 °C + pH 7.0), mortality and morphological changes in 24 h exposure experiments were investigated. The survival rates of each experimental group were observed. The gene expression changes in single and dual stress exposed coals were measured and the differentially expressed genes were classified with gene ontology analysis. The top three enriched gene ontology terms of DEGs in response to dual stress were metal ion binding (23.4%), extracellular region (17.2%), and calcium ion binding (12.8%). The gene showing the greatest increase in expression as a response to the dual stress was hemagglutinin/amebocyte aggregation factor, followed by interferon-inducible GTPase 5 and the gene showing the greatest decrease as a response to the dual stress was Fas-associating death domain-containing protein, followed by oxidase 2. These results represented the transcriptomic study focused on the stress responses of the temperate asymbiotic soft coral exposed to single and dual stresses. The combined effect of thermal and acidification stress on corals triggered the negative regulation of ion binding and extracellular matrix coding genes and these genes might serve as a basis for research into coral-specific adaptations to stress responses and global climate change.}, } @article {pmid35258467, year = {2022}, author = {Elavsky, S and Blahošová, J and Lebedíková, M and Tkaczyk, M and Tancos, M and Plhák, J and Sotolář, O and Smahel, D}, title = {Researching the Links Between Smartphone Behavior and Adolescent Well-being With the FUTURE-WP4 (Modeling the Future: Understanding the Impact of Technology on Adolescent's Well-being Work Package 4) Project: Protocol for an Ecological Momentary Assessment Study.}, journal = {JMIR research protocols}, volume = {11}, number = {3}, pages = {e35984}, pmid = {35258467}, issn = {1929-0748}, abstract = {BACKGROUND: Smartphone ownership has increased among teens within the last decade, with up to 89% of adolescents owning a smartphone and engaging daily with the online world through it. Although the results of recent meta-analyses suggest that engaging digital technology plays only a small role in adolescent well-being, parents, professionals, and policymakers remain concerned about the impact that the instant connectivity of smartphones has on adolescent well-being.

OBJECTIVE: Herein, we introduce the protocol of a research study investigating the associations between adolescent smartphone use and different facets of well-being (social, physical, and psychological), with the aim to apply innovative methods to address the limitations of existing empirical studies.

METHODS: This 12-month prospective study of adolescents uses a repeated measurement-burst design with the ecological momentary assessment methodology. Adolescents (N=203; age range 13-17 years) complete baseline assessments through online questionnaires, four 14-day intensive data collection bursts, and an online questionnaire at the end of the study. As part of the 4 measurement bursts, adolescent smartphone behavior is assessed objectively by passive data collection of smartphone data logs and through self-reports in short questionnaires administered via a custom-built Android app.

RESULTS: The protocol describes the study objectives, research tools (including the development of the Android app and specialized software), and process (including pilot studies, the main study, and targets for machine learning approaches). Two of the 203 enrolled participants provided no data during the first data collection burst of the main study. Preliminary analyses of the data from the first data collection burst indicated an acceptable level of compliance (72.25%) with the daily questionnaires. The design of the study will allow for the assessment of both within- and between-person variabilities in smartphone behavior, as well as short-term variation and long-term change in smartphone behavior and how it impacts the indicators of social, physical, and psychological well-being.

CONCLUSIONS: The innovative methods applied in this study (objective smartphone logs, ecological momentary assessment, and machine learning) will allow for a more nuanced assessment of the links between smartphone use and well-being, informing strategies to help adolescents navigate the online world more constructively in terms of the development of their physical, social, and psychological well-being.

DERR1-10.2196/35984.}, } @article {pmid35255492, year = {2022}, author = {Kousathanas, A and Pairo-Castineira, E and Rawlik, K and Stuckey, A and Odhams, CA and Walker, S and Russell, CD and Malinauskas, T and Wu, Y and Millar, J and Shen, X and Elliott, KS and Griffiths, F and Oosthuyzen, W and Morrice, K and Keating, S and Wang, B and Rhodes, D and Klaric, L and Zechner, M and Parkinson, N and Siddiq, A and Goddard, P and Donovan, S and Maslove, D and Nichol, A and Semple, MG and Zainy, T and Maleady-Crowe, F and Todd, L and Salehi, S and Knight, J and Elgar, G and Chan, G and Arumugam, P and Patch, C and Rendon, A and Bentley, D and Kingsley, C and Kosmicki, JA and Horowitz, JE and Baras, A and Abecasis, GR and Ferreira, MAR and Justice, A and Mirshahi, T and Oetjens, M and Rader, DJ and Ritchie, MD and Verma, A and Fowler, TA and Shankar-Hari, M and Summers, C and Hinds, C and Horby, P and Ling, L and McAuley, D and Montgomery, H and Openshaw, PJM and Elliott, P and Walsh, T and Tenesa, A and , and , and , and Fawkes, A and Murphy, L and Rowan, K and Ponting, CP and Vitart, V and Wilson, JF and Yang, J and Bretherick, AD and Scott, RH and Hendry, SC and Moutsianas, L and Law, A and Caulfield, MJ and Baillie, JK}, title = {Whole-genome sequencing reveals host factors underlying critical COVID-19.}, journal = {Nature}, volume = {607}, number = {7917}, pages = {97-103}, pmid = {35255492}, issn = {1476-4687}, support = {RC4 AG039029/AG/NIA NIH HHS/United States ; MC_PC_17228/MRC_/Medical Research Council/United Kingdom ; P30 ES010126/ES/NIEHS NIH HHS/United States ; U01 AG009740/AG/NIA NIH HHS/United States ; UL1 TR001878/TR/NCATS NIH HHS/United States ; 223164/Z/21/Z/WT_/Wellcome Trust/United Kingdom ; MC_EX_MR/M009203/1/MRC_/Medical Research Council/United Kingdom ; MC_PC_19059/MRC_/Medical Research Council/United Kingdom ; MR/R026408/1/MRC_/Medical Research Council/United Kingdom ; MR/N02995X/1/MRC_/Medical Research Council/United Kingdom ; MC_PC_20004/MRC_/Medical Research Council/United Kingdom ; MR/M009203/1/MRC_/Medical Research Council/United Kingdom ; MC_UU_00007/10/MRC_/Medical Research Council/United Kingdom ; 204979/Z/16/Z/WT_/Wellcome Trust/United Kingdom ; MC_PC_20058/MRC_/Medical Research Council/United Kingdom ; S10 OD026880/OD/NIH HHS/United States ; MC_UU_12008/1/MRC_/Medical Research Council/United Kingdom ; MC_PC_20029/MRC_/Medical Research Council/United Kingdom ; S10 OD030463/OD/NIH HHS/United States ; MC_PC_19025/MRC_/Medical Research Council/United Kingdom ; RC2 AG036495/AG/NIA NIH HHS/United States ; /WT_/Wellcome Trust/United Kingdom ; MC_QA137853/MRC_/Medical Research Council/United Kingdom ; MC_PC_14089/MRC_/Medical Research Council/United Kingdom ; }, mesh = {ATP-Binding Cassette Transporters ; *COVID-19/genetics/mortality/pathology/virology ; Cell Adhesion Molecules ; Critical Care ; *Critical Illness/mortality ; E-Selectin ; Factor VIII ; Fucosyltransferases ; *Genome, Human/genetics ; Genome-Wide Association Study ; *Host-Pathogen Interactions/genetics ; Humans ; Interleukin-10 Receptor beta Subunit ; Lectins, C-Type ; Mucin-1 ; Nerve Tissue Proteins ; Phospholipid Transfer Proteins ; Receptors, Cell Surface ; Repressor Proteins ; SARS-CoV-2/pathogenicity ; *Whole Genome Sequencing ; Galactoside 2-alpha-L-fucosyltransferase ; }, abstract = {Critical COVID-19 is caused by immune-mediated inflammatory lung injury. Host genetic variation influences the development of illness requiring critical care[1] or hospitalization[2-4] after infection with SARS-CoV-2. The GenOMICC (Genetics of Mortality in Critical Care) study enables the comparison of genomes from individuals who are critically ill with those of population controls to find underlying disease mechanisms. Here we use whole-genome sequencing in 7,491 critically ill individuals compared with 48,400 controls to discover and replicate 23 independent variants that significantly predispose to critical COVID-19. We identify 16 new independent associations, including variants within genes that are involved in interferon signalling (IL10RB and PLSCR1), leucocyte differentiation (BCL11A) and blood-type antigen secretor status (FUT2). Using transcriptome-wide association and colocalization to infer the effect of gene expression on disease severity, we find evidence that implicates multiple genes-including reduced expression of a membrane flippase (ATP11A), and increased expression of a mucin (MUC1)-in critical disease. Mendelian randomization provides evidence in support of causal roles for myeloid cell adhesion molecules (SELE, ICAM5 and CD209) and the coagulation factor F8, all of which are potentially druggable targets. Our results are broadly consistent with a multi-component model of COVID-19 pathophysiology, in which at least two distinct mechanisms can predispose to life-threatening disease: failure to control viral replication; or an enhanced tendency towards pulmonary inflammation and intravascular coagulation. We show that comparison between cases of critical illness and population controls is highly efficient for the detection of therapeutically relevant mechanisms of disease.}, } @article {pmid35254646, year = {2022}, author = {Johnson, MS and Adams, VM and Byrne, J and Harris, RMB}, title = {The benefits of Q + PPGIS for coupled human-natural systems research: A systematic review.}, journal = {Ambio}, volume = {51}, number = {8}, pages = {1819-1836}, pmid = {35254646}, issn = {1654-7209}, mesh = {*Community Participation ; Ecosystem ; *Geographic Information Systems ; Humans ; }, abstract = {Managing complex problems in socio-ecological systems (SES) requires innovative approaches, which account for multiple scales, large datasets, and diverse lived experiences. By combining two commonly utilized mixed-methods, public participation GIS (PPGIS) and Q-method (Q), Q + PPGIS has the potential to reveal competing agendas and reduce conflict, but its benefits and weaknesses are comparatively understudied. Using a systematic review, we evaluated how different studies have employed and implemented the Q + PPGIS method. We found 16 studies, comprising 30 publications, with considerable variation in their geographic foci, research disciplines, and addressed SES challenges. These studies exhibit a lack of cohesion between methodological design and implementation and the absence of a consistent application of the method. Nonetheless, Q + PPGIS offers a tool that can guide policy, better inform stakeholders, and reduce conflict based on misconceptions. Resolving the shortcomings identified here will broaden Q + PPGIS utility in geographically situating and representing multiple realities within complex socio-ecological systems challenges.}, } @article {pmid35252591, year = {2021}, author = {Boyes, D and Holland, PWH and , and , and , and , and , and , }, title = {The genome sequence of the peach blossom moth, Thyatira batis (Linnaeus, 1758).}, journal = {Wellcome open research}, volume = {6}, number = {}, pages = {267}, pmid = {35252591}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual male Thyatira batis (the peach-blossom moth; Arthropoda; Insecta; Lepidoptera; Drepanidae). The genome sequence is 315 megabases in span. The majority of the assembly (99.68%) is scaffolded into 31 chromosomal pseudomolecules, with the Z sex chromosome assembled. The mitochondrial genome was also assembled and is 15.4 kilobases in length. Gene annotation of this assembly on Ensembl has identified 12,238 protein coding genes.}, } @article {pmid35249934, year = {2022}, author = {Sekoguchi, S and Ikegami, K and Ando, H and Yoshitake, H and Baba, H and Ishigaki, Y and Moritake, T and Myojo, T and Ogami, A}, title = {Visualization of Dust Generation in Outdoor Workplaces Using A Wearable Particle Monitor and Global Navigation Satellite System.}, journal = {Journal of UOEH}, volume = {44}, number = {1}, pages = {1-13}, doi = {10.7888/juoeh.44.1}, pmid = {35249934}, issn = {0387-821X}, mesh = {*Dust/analysis ; Environmental Monitoring ; Particle Size ; *Wearable Electronic Devices ; Workplace ; }, abstract = {We manufactured a wearable particle monitor (WPM), which is a simple and low-cost dust monitor. We aimed to evaluate the usefulness of the device by using it and location information of a Global Navigation Satellite System (GNSS) to measure dust generation in outdoor workplaces. We used nine WPMs and a particle counter KC-52 to measure in parallel the dust concentration diffusing standard particles in a dust exposure apparatus to evaluate the measurability of the WPM, and visualized dust generation in outdoor workplaces to evaluate its usability. We obtained location information using a GNSS in parallel with measuring with the WPM. The measured values of the WPM followed the measured values of the KC-52, with a strong correlation of the values between the KC-52 and each WPM. The discrepancy among devices tended to increase, however, because the measured values of the WPMs increased. For outdoor measurements, we could create a heat map of the relative values of dust generation by combining two data of the WPM and the GNSS. The methods of using the WPM could overview the conditions needed to produce dust emissions in dust-generating workplaces.}, } @article {pmid35247724, year = {2022}, author = {Friedman, J and Montero, F and Bourgois, P and Wahbi, R and Dye, D and Goodman-Meza, D and Shover, C}, title = {Xylazine spreads across the US: A growing component of the increasingly synthetic and polysubstance overdose crisis.}, journal = {Drug and alcohol dependence}, volume = {233}, number = {}, pages = {109380}, pmid = {35247724}, issn = {1879-0046}, support = {K08 DA048163/DA/NIDA NIH HHS/United States ; R01 DA049644/DA/NIDA NIH HHS/United States ; T32 DA035165/DA/NIDA NIH HHS/United States ; K01 DA050771/DA/NIDA NIH HHS/United States ; T32 GM008042/GM/NIGMS NIH HHS/United States ; }, mesh = {Analgesics, Opioid/adverse effects ; *Drug Overdose/epidemiology ; Fentanyl ; Heroin ; Humans ; *Substance Abuse, Intravenous ; Xylazine ; }, abstract = {BACKGROUND: Sharp exacerbations of the US overdose crisis are linked to polysubstance use of synthetic compounds. Xylazine is a veterinary tranquilizer, long noted in the street opioid supply of Puerto Rico, and more recently Philadelphia. Yet its national trends, geographic distribution, and health risks are poorly characterized.

METHODS: In this sequential mixed-methods study, xylazine was increasingly observed by ethnographers in Philadelphia among drug-sellers and people who inject drugs (PWID). Subsequently, we systematically searched for records describing xylazine-present overdose mortality across the US and assessed time trends and overlap with other drugs.

RESULTS: In 10 jurisdictions - representing all four US Census Regions - xylazine was increasingly present in overdose deaths, rising from 0.36% of deaths in 015m 6.7% in 2020. The highest xylazine prevalence data was observed in Philadelphia, (25.8% of deaths), followed by Maryland (19.3%) and Connecticut (10.2%). Illicitly-manufactured-fentanyls were present in 98.4% of xylazine-present-overdose-deaths - suggesting a strong ecological link - as well as cocaine (45.4%), benzodiazepines (28.4%), heroin (23.3%), and alcohol (19.7%). PWID in Philadelphia described xylazine as a sought-after adulterant that lengthens the short duration of fentanyl injections. They also linked it to increased risk of soft tissue infection and naloxone-resistant overdose.

CONCLUSIONS: Xylazine is increasingly present in overdose deaths, linked to the proliferation of illicitly-manufactured-fentanyls. Ethnographic accounts associate it with profound risks for PWID. Nevertheless, many jurisdictions do not routinely test for xylazine, and it is not comprehensively tracked nationally. Further efforts are needed to provide PWID with services that can help minimize additional risks associated with a shifting drug supply.}, } @article {pmid35240359, year = {2022}, author = {Wechsler, K and Bock, O and Schubert, T and Koch, I}, title = {Dual-task interference in simulated car driving: The psychological refractory period effect when not only the second, but also the first task is ecologically relevant.}, journal = {Applied ergonomics}, volume = {102}, number = {}, pages = {103722}, doi = {10.1016/j.apergo.2022.103722}, pmid = {35240359}, issn = {1872-9126}, mesh = {*Automobile Driving/psychology ; Automobiles ; Humans ; *Pedestrians ; Reaction Time ; Refractory Period, Psychological ; }, abstract = {The psychological refractory period (PRP) effect denotes the finding that shortening the temporal interval between two tasks leads to increased reaction time in the second task. Earlier work in driving simulators confirmed the emergence of a PRP effect even if the second task (T2) was ecologically relevant, such as in a car-braking task. Here we evaluate the PRP effect if the first task (T1) is ecologically relevant as well. In a driving simulator, participants had to warn pedestrians against crossing the street (T1), and had to brake when the lead car braked (T2). As the temporal interval between tasks decreased, reaction time in T2 increased, confirming once more the emergence of a PRP effect. The PRP effect in our study was larger than in previous studies where T1 was artificial rather than ecologically relevant. This suggests that an ecologically relevant T1 is processed more elaborately, resulting in stronger interference with T2.}, } @article {pmid35239835, year = {2022}, author = {Rocha, CAO and Santana, GBA and Leal, TC and Paiva, JPS and Silva, LFD and Santos, LG and Nunes, BEBR and Carmo, RFD and Souza, CDF}, title = {Impact of the COVID-19 pandemic on compulsory notification of meningitis during the first wave of the pandemic in Brazil: an ecological study using P-score.}, journal = {Sao Paulo medical journal = Revista paulista de medicina}, volume = {140}, number = {2}, pages = {305-309}, pmid = {35239835}, issn = {1806-9460}, mesh = {Brazil/epidemiology ; *COVID-19/epidemiology ; Disease Notification ; Humans ; *Meningitis/epidemiology ; Pandemics/prevention & control ; }, abstract = {BACKGROUND: Meningitis is listed as one of the diseases requiring compulsory notification in Brazil. It can affect all age groups and also has no seasonality. Cases can be recorded in all months of the year and in all states of Brazil. Despite its importance, the obligation of immediate notification may have been compromised by the coronavirus disease 2019 (COVID-19) pandemic.

OBJECTIVE: To analyze the immediate impact of the COVID-19 pandemic on compulsory notifications of meningitis in Brazil and its states during the first wave of the pandemic.

DESIGN AND SETTING: This was an ecological study involving all confirmed cases of meningitis in Brazil, in its regions and in its states.

METHODS: Data for the months from 2015 to 2020 were obtained from the database of the Notifiable Diseases Information System (Sistema de Informação de Agravos de Notificação, SINAN), in the Department of Informatics of the National Health System (Departamento de Informática do Sistema Único de Saúde, DATASUS). The P-score was used to obtain the percentage change in the numbers of cases reported in 2020.

RESULTS: A 45.7% reduction in notifications of meningitis in Brazil was observed. Regarding the regions and the states, with the exception of Roraima, all of them showed a negative P-score, with decreasing curves each month.

CONCLUSION: The pandemic caused a negative impact on meningitis notifications in Brazil.}, } @article {pmid35238933, year = {2022}, author = {Oliveira, CR and Niccolai, LM and Sheikha, H and Elmansy, L and Kalinich, CC and Grubaugh, ND and Shapiro, ED and , }, title = {Assessment of Clinical Effectiveness of BNT162b2 COVID-19 Vaccine in US Adolescents.}, journal = {JAMA network open}, volume = {5}, number = {3}, pages = {e220935}, pmid = {35238933}, issn = {2574-3805}, support = {K23 AI159518/AI/NIAID NIH HHS/United States ; T35 HL007649/HL/NHLBI NIH HHS/United States ; UL1 TR001863/TR/NCATS NIH HHS/United States ; }, mesh = {Adolescent ; BNT162 Vaccine/*administration & dosage ; COVID-19/diagnosis/*prevention & control ; COVID-19 Nucleic Acid Testing ; Case-Control Studies ; Connecticut ; Female ; Humans ; Male ; Retrospective Studies ; SARS-CoV-2/*immunology ; United States/epidemiology ; *Vaccine Efficacy ; }, abstract = {IMPORTANCE: The emergence of the B.1.617.2 (Delta) variant of SARS-CoV-2 has led to increases in both infections and hospitalizations among adolescents. Little is known about the effectiveness of the BNT162b2 vaccine in adolescents in the general population, as opposed to a clinical trial population.

OBJECTIVE: To estimate the effectiveness of the BNT162b2 vaccine in adolescents aged 12 to 18 years.

This was a matched case-control study among adolescents (aged 12-18 years) who had results from a SARS-CoV-2 reverse transcription-polymerase chain reaction (RT-PCR) test. Immunization histories, relevant clinical data, and RT-PCR test results were obtained from the Yale New Haven Health System's medical records between June 1, 2021, and August 15, 2021, when the Delta variant caused 92% of infections in Connecticut. Case participants were defined as adolescents who had a positive test result and an associated medical encounter. Control participants were defined as those who had a negative test result and were matched to a case participant by age, county of residence, and date of testing.

EXPOSURES: Adolescents were defined as fully immunized if they had received 2 doses of vaccine at least 14 days before focal time.

MAIN OUTCOMES AND MEASURES: The primary outcome measured was SARS-CoV-2 infection confirmed by RT-PCR. The vaccine's effectiveness (VE) was estimated using matched odds ratios from conditional logistic regression models. Secondary measures included estimated VE by clinical symptoms, number of vaccine doses received, and elapsed time from immunization.

RESULTS: A total of 6901 adolescents were tested for SARS-CoV-2. The final sample comprised 186 case participants and 356 matched control participants. The median age was 14 (IQR, 13-16) years, 262 (48%) identified as female, 81 (15%) as Black, 82 (15%) as Hispanic, and 297 (55%) as White. Overall, 134 (25%) were fully immunized (case participants, 10 [5%]; control participants, 124 [35%]). The median time between immunization and the SARS-CoV-2 test was 62 days (range, 17-129 days). Within 4 months of receiving 2 doses, VE against any infection was estimated to be 91% (95% CI, 80%-96%); against asymptomatic infection, 85% (95% CI, 57%-95%). Effectiveness after a single dose was estimated to be 74% (95% CI, 18%-92%).

CONCLUSIONS AND RELEVANCE: In this retrospective case-control study of US adolescents, 2 doses of BNT162b2 vaccine appeared to provide excellent protection for at least 4 months after immunization against both symptomatic and asymptomatic SARS-CoV-2 infections.}, } @article {pmid35238791, year = {2022}, author = {Zhang, P and Fonnesbeck, C and Schmidt, DC and White, J and Kleinberg, S and Mulvaney, SA}, title = {Using Momentary Assessment and Machine Learning to Identify Barriers to Self-management in Type 1 Diabetes: Observational Study.}, journal = {JMIR mHealth and uHealth}, volume = {10}, number = {3}, pages = {e21959}, pmid = {35238791}, issn = {2291-5222}, support = {DP3 DK097706/DK/NIDDK NIH HHS/United States ; UL1 TR000445/TR/NCATS NIH HHS/United States ; }, mesh = {Adolescent ; Blood Glucose Self-Monitoring ; *Diabetes Mellitus, Type 1/psychology/therapy ; Humans ; Machine Learning ; Retrospective Studies ; *Self-Management ; Young Adult ; }, abstract = {BACKGROUND: For adolescents living with type 1 diabetes (T1D), completion of multiple daily self-management tasks, such as monitoring blood glucose and administering insulin, can be challenging because of psychosocial and contextual barriers. These barriers are hard to assess accurately and specifically by using traditional retrospective recall. Ecological momentary assessment (EMA) uses mobile technologies to assess the contexts, subjective experiences, and psychosocial processes that surround self-management decision-making in daily life. However, the rich data generated via EMA have not been frequently examined in T1D or integrated with machine learning analytic approaches.

OBJECTIVE: The goal of this study is to develop a machine learning algorithm to predict the risk of missed self-management in young adults with T1D. To achieve this goal, we train and compare a number of machine learning models through a learned filtering architecture to explore the extent to which EMA data were associated with the completion of two self-management behaviors: mealtime self-monitoring of blood glucose (SMBG) and insulin administration.

METHODS: We analyzed data from a randomized controlled pilot study using machine learning-based filtering architecture to investigate whether novel information related to contextual, psychosocial, and time-related factors (ie, time of day) relate to self-management. We combined EMA-collected contextual and insulin variables via the MyDay mobile app with Bluetooth blood glucose data to construct machine learning classifiers that predicted the 2 self-management behaviors of interest.

RESULTS: With 1231 day-level SMBG frequency counts for 45 participants, demographic variables and time-related variables were able to predict whether daily SMBG was below the clinical threshold of 4 times a day. Using the 1869 data points derived from app-based EMA data of 31 participants, our learned filtering architecture method was able to infer nonadherence events with high accuracy and precision. Although the recall score is low, there is high confidence that the nonadherence events identified by the model are truly nonadherent.

CONCLUSIONS: Combining EMA data with machine learning methods showed promise in the relationship with risk for nonadherence. The next steps include collecting larger data sets that would more effectively power a classifier that can be deployed to infer individual behavior. Improvements in individual self-management insights, behavioral risk predictions, enhanced clinical decision-making, and just-in-time patient support in diabetes could result from this type of approach.}, } @article {pmid35234307, year = {2022}, author = {Abreu, SN and Jesus, F and Domingues, I and Baptista, F and Pereira, JL and Serpa, D and Soares, AMVM and Martins, RE and Oliveira E Silva, M}, title = {Automated Counting of Daphnid Neonates, Artemia Nauplii, and Zebrafish Eggs: A Proof of Concept.}, journal = {Environmental toxicology and chemistry}, volume = {41}, number = {6}, pages = {1451-1458}, doi = {10.1002/etc.5323}, pmid = {35234307}, issn = {1552-8618}, mesh = {Animals ; Artemia ; *Cladocera ; Daphnia ; Ecotoxicology ; *Water Pollutants, Chemical ; Zebrafish ; }, abstract = {In aquatic invertebrate (e.g., daphnids and Artemia sp.) and zebrafish cultures, in ecotoxicological bioassays, or when addressing complex population-level experimental designs, the counting of an organism's progeny is often required. This counting process is laborious, repetitive, and time-consuming, potentially posing health hazards to the operators, and necessarily entailing a higher likelihood of human error. We present an experimental evaluation of a computer-based device for counting neonates (Daphnia magna, Daphnia longispina, and Ceriodaphnia sp.), nauplii (Artemia salina and Artemia franciscana), and zebrafish (Danio rerio) eggs. Manual counts by an experienced technician were compared with the corresponding automated counts achieved by the computer-based counting device. A minimum of 55 counts/species was performed, with the number of counted organisms being up to a maximum of 150 neonates of Ceriodaphnia dubia, 200 neonates of D. magna and D. longispina, 200 nauplii of A. franciscana and A. salina, and 500 zebrafish eggs. Manual and automated counts were both performed in culture medium solutions of 50 ml of volume. Automated counts showed a mean relative acccuracy of 98.9% (97.9%-99.4%) and a relative standard deviation of 1.72%. The results demonstrate that the computer-based device can be used for accurately counting these aquatic organisms. This computer-based counting might be extended to other organisms of similar size, thus facilitating reproduction and life-cycle ecotoxicity tests. Environ Toxicol Chem 2022;41:1451-1458. © 2022 SETAC.}, } @article {pmid35230855, year = {2022}, author = {Auerbach, RP and Srinivasan, A and Kirshenbaum, JS and Mann, JJ and Shankman, SA}, title = {Geolocation features differentiate healthy from remitted depressed adults.}, journal = {Journal of psychopathology and clinical science}, volume = {131}, number = {4}, pages = {341-349}, pmid = {35230855}, issn = {2769-755X}, support = {P50 MH090964/MH/NIMH NIH HHS/United States ; R01 MH119771/MH/NIMH NIH HHS/United States ; R21 MH112330/MH/NIMH NIH HHS/United States ; }, mesh = {Adult ; *Depression/epidemiology/etiology ; Ecological Momentary Assessment ; Geographic Information Systems ; *Health Status ; Humans ; *Mobile Applications ; Recurrence ; Secondary Prevention ; Self Report ; *Smartphone ; }, abstract = {Depression recurrence is debilitating, and there is a pressing need to develop clinical tools that detect the reemergence of symptoms with the aim of bridging patients to treatment before recurrences. At baseline, remitted depressed adults (n = 22) and healthy controls (n = 24) were administered clinical interviews and completed self-report symptom measures. Then, smartphone apps were installed on personal smartphones to acquire geolocation data over 21 days and ecological momentary assessment of positive and negative affect during the initial 14-day period. Compared with healthy controls, remitted depressed adults exhibited reduced circadian routine (regularity of one's daily routine) and lower average daily distance traveled. Further, reduced distance traveled associated with greater daily negative affect after controlling for depression severity; however, this effect was not more pronounced among remitted adults. A least absolute shrinkage and selection operator (LASSO) regression indicated that a linear combination of circadian routine, average distance traveled, and baseline depression severity classified remitted depressed individuals with 72% accuracy; outperforming models restricted to either geolocation or clinical measures alone. Mobile sensing approaches hold enormous promise to improve clinical care for depressive disorders. Although barriers remain, leveraging technological advancements related to real-time monitoring can improve treatment for depressed patients and potentially, reduce high rates of recurrence. (PsycInfo Database Record (c) 2022 APA, all rights reserved).}, } @article {pmid35224212, year = {2021}, author = {Boyes, D and Holland, PWH and , and , and , and , and , and , }, title = {The genome sequence of the lime hawk-moth, Mimas tiliae (Linnaeus, 1758).}, journal = {Wellcome open research}, volume = {6}, number = {}, pages = {357}, pmid = {35224212}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual male Mimas tiliae (the lime hawk-moth; Arthropoda; Insecta; Lepidoptera; Sphingidae). The genome sequence is 478 megabases in span. The complete assembly is scaffolded into 29 chromosomal pseudomolecules, with the Z sex chromosome assembled.}, } @article {pmid35219603, year = {2022}, author = {Suenaga, H and Aida, J and Kumasaka, A and Shibamoto, A and Sato, S and Shinohara, Y and Hatakeyama, T and Yamaguchi, H and Sasaki, K and Takahashi, T and Koseki, T and Peck, C and Iikubo, M}, title = {Impact of Dental Referral Prior to Elective Surgery on Postoperative Outcomes.}, journal = {Journal of the American Medical Directors Association}, volume = {23}, number = {4}, pages = {638-645.e2}, doi = {10.1016/j.jamda.2022.01.071}, pmid = {35219603}, issn = {1538-9375}, mesh = {*Elective Surgical Procedures ; Humans ; Length of Stay ; Postoperative Complications/prevention & control ; Postoperative Period ; *Preoperative Care/methods ; Referral and Consultation ; Retrospective Studies ; }, abstract = {OBJECTIVES: Oral bacteria may contribute to postoperative infectious complications including postoperative pneumonia or surgical site infection. The aim of this study was to investigate the impact of preoperative dental care on postoperative outcomes among surgical patients under general anesthesia.

DESIGN: Retrospective cohort study.

SETTING AND PARTICIPANTS: We analyzed clinical records of major surgical patients at a university hospital between 2016 and 2018. Subjects were categorized into either the preoperative dental care group, those being referred to dentists by their surgeons based on an individual surgeon's judgment for dental care before surgery, or the control group.

METHODS: The primary outcome was postoperative infectious complications. Secondary outcomes were postoperative inflammation markers (C-reactive protein and fever), and economic outcomes (postoperative length of hospital stay and medical expenses). As the main analysis, the average treatment effects of the preoperative dental care were obtained from the augmented inverse-probability weighting (AIPW) method with consideration of demographics and perioperative risk factors to estimate causal effect of the intervention from the observational data. Then, stratified analyses by age and surgical sites were conducted with the inverse-probability weighting and linear regression methods, respectively.

RESULTS: In the AIPW estimation, compared with the control group, the care group saw a significantly lower rate of postoperative infection (average treatment effect -3.02) and shorter fever duration (-2.79 days). The stratified analysis by age revealed significant positive impact of dental care in all age groups, including the highest treatment effects observed among patients younger than 60. Also, treatment effect was observed in wider surgical sites than previously known.

CONCLUSION/IMPLICATIONS: This study indicates a significant impact of preoperative dental care on preventing postoperative infection and inflammation. Along with old age or certain types of surgeries in which advantages of dental referral have been already known, preoperative dental referral could be beneficial for broader types of patients.}, } @article {pmid35215949, year = {2022}, author = {Schmidt-Chanasit, J and Agboli, E and Jöst, H}, title = {Special Issue "Mosquito-Borne Virus Ecology".}, journal = {Viruses}, volume = {14}, number = {2}, pages = {}, pmid = {35215949}, issn = {1999-4915}, mesh = {Aedes/physiology/virology ; Animals ; Arbovirus Infections/prevention & control/transmission/virology ; Arboviruses/physiology ; *Ecology ; Humans ; Mosquito Vectors/physiology/*virology ; }, abstract = {Mosquito-borne viruses (MBVs), also known as moboviruses, are associated mainly with mosquitoes and are able to infect humans and other vertebrates [...].}, } @article {pmid35212739, year = {2022}, author = {Zhang, Y and Wu, D and Wang, Y and Xu, X}, title = {Two types of C-terminal regions of RNA-binding proteins play distinct roles in stress tolerance of Synechocystis sp. PCC 6803.}, journal = {FEMS microbiology letters}, volume = {369}, number = {1}, pages = {}, pmid = {35212739}, issn = {1574-6968}, mesh = {Computational Biology ; Phylogeny ; RNA-Binding Proteins/genetics ; Salt Tolerance ; *Synechocystis/genetics ; }, abstract = {In the phylogenetic tree of RRM-type Rbps (RNA-binding proteins) in cyanobacteria, Rbp1 of Synechocystis 6803, with a single RRM (RNA recognition motif) region and a C-terminal glycine-rich region, and Rbp2, without the C-terminal region, both belong to the cluster I, whereas Rbp3 with a different type of C-terminal region is in the cluster II. Rbp1 is required for the cold adaptability of the cyanobacterium, and Rbp3 is for salt tolerance. Here, we report that the C-terminal region of Rbp1 is not required for the cold adaptability function but the C-terminal region of Rbp3 can direct the RRM of Rbp1 to the salt tolerance function. Bioinformatic and experimental analyses indicate that Rbps in cyanobacteria should be classified as two types. It is the first report for the distinct roles of C-terminal regions of Rbps in stress tolerance of cyanobacteria.}, } @article {pmid35211700, year = {2021}, author = {Alegana, VA and Macharia, PM and Muchiri, S and Mumo, E and Oyugi, E and Kamau, A and Chacky, F and Thawer, S and Molteni, F and Rutazanna, D and Maiteki-Sebuguzi, C and Gonahasa, S and Noor, AM and Snow, RW}, title = {Plasmodium falciparum parasite prevalence in East Africa: Updating data for malaria stratification.}, journal = {PLOS global public health}, volume = {1}, number = {12}, pages = {e0000014}, pmid = {35211700}, issn = {2767-3375}, support = {211208/WT_/Wellcome Trust/United Kingdom ; 211208/Z/18/Z/WT_/Wellcome Trust/United Kingdom ; 107769/WT_/Wellcome Trust/United Kingdom ; 212176/WT_/Wellcome Trust/United Kingdom ; 203077/WT_/Wellcome Trust/United Kingdom ; EP-C-15-003/EPA/EPA/United States ; /WT_/Wellcome Trust/United Kingdom ; }, abstract = {The High Burden High Impact (HBHI) strategy for malaria encourages countries to use multiple sources of available data to define the sub-national vulnerabilities to malaria risk, including parasite prevalence. Here, a modelled estimate of Plasmodium falciparum from an updated assembly of community parasite survey data in Kenya, mainland Tanzania, and Uganda is presented and used to provide a more contemporary understanding of the sub-national malaria prevalence stratification across the sub-region for 2019. Malaria prevalence data from surveys undertaken between January 2010 and June 2020 were assembled form each of the three countries. Bayesian spatiotemporal model-based approaches were used to interpolate space-time data at fine spatial resolution adjusting for population, environmental and ecological covariates across the three countries. A total of 18,940 time-space age-standardised and microscopy-converted surveys were assembled of which 14,170 (74.8%) were identified after 2017. The estimated national population-adjusted posterior mean parasite prevalence was 4.7% (95% Bayesian Credible Interval 2.6-36.9) in Kenya, 10.6% (3.4-39.2) in mainland Tanzania, and 9.5% (4.0-48.3) in Uganda. In 2019, more than 12.7 million people resided in communities where parasite prevalence was predicted ≥ 30%, including 6.4%, 12.1% and 6.3% of Kenya, mainland Tanzania and Uganda populations, respectively. Conversely, areas that supported very low parasite prevalence (<1%) were inhabited by approximately 46.2 million people across the sub-region, or 52.2%, 26.7% and 10.4% of Kenya, mainland Tanzania and Uganda populations, respectively. In conclusion, parasite prevalence represents one of several data metrics for disease stratification at national and sub-national levels. To increase the use of this metric for decision making, there is a need to integrate other data layers on mortality related to malaria, malaria vector composition, insecticide resistance and bionomic, malaria care-seeking behaviour and current levels of unmet need of malaria interventions.}, } @article {pmid35210936, year = {2022}, author = {Marqués, L and Peltier, DMP and Camarero, JJ and Zavala, MA and Madrigal-González, J and Sangüesa-Barreda, G and Ogle, K}, title = {Disentangling the Legacies of Climate and Management on Tree Growth.}, journal = {Ecosystems (New York, N.Y.)}, volume = {25}, number = {1}, pages = {215-235}, pmid = {35210936}, issn = {1432-9840}, abstract = {UNLABELLED: Legacies of past climate conditions and historical management govern forest productivity and tree growth. Understanding how these processes interact and the timescales over which they influence tree growth is critical to assess forest vulnerability to climate change. Yet, few studies address this issue, likely because integrated long-term records of both growth and forest management are uncommon. We applied the stochastic antecedent modelling (SAM) framework to annual tree-ring widths from mixed forests to recover the ecological memory of tree growth. We quantified the effects of antecedent temperature and precipitation up to 4 years preceding the year of ring formation and integrated management effects with records of harvesting intensity from historical forest management archives. The SAM approach uncovered important time periods most influential to growth, typically the warmer and drier months or seasons, but variation among species and sites emerged. Silver fir responded primarily to past climate conditions (25-50 months prior to the year of ring formation), while European beech and Scots pine responded mostly to climate conditions during the year of ring formation and the previous year, although these responses varied among sites. Past management and climate interacted in such a way that harvesting promoted growth in young silver fir under wet and warm conditions and in old European beech under drier and cooler conditions. Our study shows that the ecological memory associated with climate legacies and historical forest management is species-specific and context-dependent, suggesting that both aspects are needed to properly evaluate forest functioning under climate change.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s10021-021-00650-8.}, } @article {pmid35210695, year = {2022}, author = {Schaafsma, FL and David, CL and Kohlbach, D and Ehrlich, J and Castellani, G and Lange, BA and Vortkamp, M and Meijboom, A and Fortuna-Wünsch, A and Immerz, A and Cantzler, H and Klasmeier, A and Zakharova, N and Schmidt, K and Van de Putte, AP and van Franeker, JA and Flores, H}, title = {Allometric relationships of ecologically important Antarctic and Arctic zooplankton and fish species.}, journal = {Polar biology}, volume = {45}, number = {2}, pages = {203-224}, pmid = {35210695}, issn = {0722-4060}, abstract = {UNLABELLED: Allometric relationships between body properties of animals are useful for a wide variety of purposes, such as estimation of biomass, growth, population structure, bioenergetic modelling and carbon flux studies. This study summarizes allometric relationships of zooplankton and nekton species that play major roles in polar marine food webs. Measurements were performed on 639 individuals of 15 species sampled during three expeditions in the Southern Ocean (winter and summer) and 2374 individuals of 14 species sampled during three expeditions in the Arctic Ocean (spring and summer). The information provided by this study fills current knowledge gaps on relationships between length and wet/dry mass of understudied animals, such as various gelatinous zooplankton, and of animals from understudied seasons and maturity stages, for example, for the krill Thysanoessa macrura and larval Euphausia superba caught in winter. Comparisons show that there is intra-specific variation in length-mass relationships of several species depending on season, e.g. for the amphipod Themisto libellula. To investigate the potential use of generalized regression models, comparisons between sexes, maturity stages or age classes were performed and are discussed, such as for the several krill species and T. libellula. Regression model comparisons on age classes of the fish E. antarctica were inconclusive about their general use. Other allometric measurements performed on carapaces, eyes, heads, telsons, tails and otoliths provided models that proved to be useful for estimating length or mass in, e.g. diet studies. In some cases, the suitability of these models may depend on species or developmental stages.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s00300-021-02984-4.}, } @article {pmid35208836, year = {2022}, author = {Šmigová, J and Šnábel, V and Cavallero, S and Šmiga, Ľ and Šoltys, J and Papaj, J and Papajová, I}, title = {Neglected Diseases-Parasitic Infections among Slovakian Children from Different Populations and Genotypes of Giardia duodenalis.}, journal = {Microorganisms}, volume = {10}, number = {2}, pages = {}, pmid = {35208836}, issn = {2076-2607}, support = {APVV-18-0351//Slovak Research and Development Agency/ ; VEGA 2/0138/21//Scientific Grant Agency of the Ministry of Education of the Slovak Republic/ ; }, abstract = {Children are most prone to parasitic infections. The objectives of the study were to examine the occurrence of parasitic infections in children from different populations and to perform molecular characterization of human Giardia duodenalis isolates. We examined 631 stool samples from Roma and non-Roma children for the presence of parasitic developmental stages. Samples were collected from three eastern Slovakia districts. The ages of the children ranged from 1 months to 17 years. Subsequently, the molecular characterization of human G. duodenalis isolates by PCR detected triosephosphate isomerase (tpi) and beta-giardin (bg) genes was performed. The overall prevalence of parasitic infection was 19.8%. Ascaris lumbricoides eggs were the most frequent, with an occurrence of about 13.8%. G. duodenalis cysts were present in 6.3% of samples. G. duodenalis isolates obtained from 13 children were subjected to DNA sequencing with tpi and bg genes. Five isolates were categorized as bearing subassemblage BIII, the three isolates as subassemblage BIV, one person was infected with a mixture of subassemblages BIII and BIV, four children had subassemblage AII, and one isolate revealed a structure corresponding with subassemblage AI. Our work is proof that poverty and poor hygiene contribute the most to public health problems associated with neglected parasitic diseases.}, } @article {pmid35205315, year = {2022}, author = {Venkatraman, S and Balasubramanian, B and Pongchaikul, P and Tohtong, R and Chutipongtanate, S}, title = {Molecularly Guided Drug Repurposing for Cholangiocarcinoma: An Integrative Bioinformatic Approach.}, journal = {Genes}, volume = {13}, number = {2}, pages = {}, pmid = {35205315}, issn = {2073-4425}, mesh = {*Bile Duct Neoplasms/drug therapy/genetics ; Bile Ducts, Intrahepatic/metabolism/pathology ; Carcinogenesis/genetics ; *Cholangiocarcinoma/drug therapy/genetics/metabolism ; Computational Biology ; Drug Repositioning ; Gene Expression Regulation, Neoplastic ; Humans ; Prognosis ; Tumor Microenvironment ; }, abstract = {BACKGROUND: Cholangiocarcinoma (CCA) has a complex immune microenvironment architecture, thus possessing challenges in its characterization and treatment. This study aimed to repurpose FDA-approved drugs for cholangiocarcinoma by transcriptomic-driven bioinformatic approach.

METHODS: Cox-proportional univariate regression was applied to 3017 immune-related genes known a priori to identify a list of mortality-associated genes, so-called immune-oncogenic gene signature, in CCA tumor-derived RNA-seq profiles of two independent cohorts. Unsupervised clustering stratified CCA tumors into two groups according to the immune-oncogenic gene signature expression, which then confirmed its clinical relevance by Kaplan-Meier curve. Molecularly guided drug repurposing was performed by an integrative connectivity map-prioritized drug-gene network analysis.

RESULTS: The immune-oncogenic gene signature consists of 26 mortality-associated immune-related genes. Patients with high-expression signature had a poorer overall survival (log-rank p < 0.001), while gene enrichment analysis revealed cell-cycle checkpoint regulation and inflammatory-immune response signaling pathways affected this high-risk group. The integrative drug-gene network identified eight FDA-approved drugs as promising candidates, including Dasatinib a multi-kinase inhibitor currently investigated for advanced CCA with isocitrate-dehydrogenase mutations.

CONCLUSION: This study proposes the use of the immune-oncogenic gene signature to identify high-risk CCA patients. Future preclinical and clinical studies are required to elucidate the therapeutic efficacy of the molecularly guided drugs as the adjunct therapy, aiming to improve the survival outcome.}, } @article {pmid35202783, year = {2022}, author = {Vickers, DM and Baral, S and Mishra, S and Kwong, JC and Sundaram, M and Katz, A and Calzavara, A and Maheu-Giroux, M and Buckeridge, DL and Williamson, T}, title = {Stringency of containment and closures on the growth of SARS-CoV-2 in Canada prior to accelerated vaccine roll-out.}, journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases}, volume = {118}, number = {}, pages = {73-82}, pmid = {35202783}, issn = {1878-3511}, mesh = {*COVID-19/epidemiology/prevention & control ; Canada/epidemiology ; Humans ; Pandemics/prevention & control ; SARS-CoV-2 ; *Vaccines ; }, abstract = {BACKGROUND: Many studies have examined the effectiveness of non-pharmaceutical interventions (NPIs) on SARS-CoV-2 transmission worldwide. However, less attention has been devoted to understanding the limits of NPIs across the course of the pandemic and along a continuum of their stringency. In this study, we explore the relationship between the growth of SARS-CoV-2 cases and an NPI stringency index across Canada before the accelerated vaccine roll-out.

METHODS: We conducted an ecological time-series study of daily SARS-CoV-2 case growth in Canada from February 2020 to February 2021. Our outcome was a back-projected version of the daily growth ratio in a stringency period (i.e., a 10-point range of the stringency index) relative to the last day of the previous period. We examined the trends in case growth using a linear mixed-effects model accounting for stringency period, province, and mobility in public domains.

RESULTS: Case growth declined rapidly by 20-60% and plateaued within the first month of the first wave, irrespective of the starting values of the stringency index. When stringency periods increased, changes in case growth were not immediate and were faster in the first wave than in the second. In the first wave, the largest decreasing trends from our mixed effects model occurred in both early and late stringency periods, depending on the province, at a geometric mean index value of 30⋅1 out of 100. When compared with the first wave, the stringency periods in the second wave possessed little association with case growth.

CONCLUSIONS: The minimal association in the first wave, and the lack thereof in the second, is compatible with the hypothesis that NPIs do not, per se, lead to a decline in case growth. Instead, the correlations we observed might be better explained by a combination of underlying behaviors of the populations in each province and the natural dynamics of SARS-CoV-2. Although there exist alternative explanations for the equivocal relationship between NPIs and case growth, the onus of providing evidence shifts to demonstrating how NPIs can consistently have flat association, despite incrementally high stringency.}, } @article {pmid35202411, year = {2022}, author = {Chiarello, M and McCauley, M and Villéger, S and Jackson, CR}, title = {Ranking the biases: The choice of OTUs vs. ASVs in 16S rRNA amplicon data analysis has stronger effects on diversity measures than rarefaction and OTU identity threshold.}, journal = {PloS one}, volume = {17}, number = {2}, pages = {e0264443}, pmid = {35202411}, issn = {1932-6203}, mesh = {Animals ; Bias ; *Biodiversity ; Bivalvia/microbiology ; Cluster Analysis ; DNA, Bacterial ; *Data Analysis ; Datasets as Topic ; *Gastrointestinal Microbiome ; *Genetic Variation ; Invertebrates/*microbiology ; RNA, Ribosomal, 16S/*genetics ; Rivers/microbiology ; Sequence Analysis, DNA ; }, abstract = {Advances in the analysis of amplicon sequence datasets have introduced a methodological shift in how research teams investigate microbial biodiversity, away from sequence identity-based clustering (producing Operational Taxonomic Units, OTUs) to denoising methods (producing amplicon sequence variants, ASVs). While denoising methods have several inherent properties that make them desirable compared to clustering-based methods, questions remain as to the influence that these pipelines have on the ecological patterns being assessed, especially when compared to other methodological choices made when processing data (e.g. rarefaction) and computing diversity indices. We compared the respective influences of two widely used methods, namely DADA2 (a denoising method) vs. Mothur (a clustering method) on 16S rRNA gene amplicon datasets (hypervariable region v4), and compared such effects to the rarefaction of the community table and OTU identity threshold (97% vs. 99%) on the ecological signals detected. We used a dataset comprising freshwater invertebrate (three Unionidae species) gut and environmental (sediment, seston) communities sampled in six rivers in the southeastern USA. We ranked the respective effects of each methodological choice on alpha and beta diversity, and taxonomic composition. The choice of the pipeline significantly influenced alpha and beta diversities and changed the ecological signal detected, especially on presence/absence indices such as the richness index and unweighted Unifrac. Interestingly, the discrepancy between OTU and ASV-based diversity metrics could be attenuated by the use of rarefaction. The identification of major classes and genera also revealed significant discrepancies across pipelines. Compared to the pipeline's effect, OTU threshold and rarefaction had a minimal impact on all measurements.}, } @article {pmid35199413, year = {2022}, author = {Berner, LT and Goetz, SJ}, title = {Satellite observations document trends consistent with a boreal forest biome shift.}, journal = {Global change biology}, volume = {28}, number = {10}, pages = {3275-3292}, pmid = {35199413}, issn = {1365-2486}, mesh = {Climate Change ; *Ecosystem ; Forests ; *Taiga ; Trees ; }, abstract = {The boreal forest biome is a major component of Earth's biosphere and climate system that is projected to shift northward due to continued climate change over the coming century. Indicators of a biome shift will likely first be evident along the climatic margins of the boreal forest and include changes in vegetation productivity, mortality, and recruitment, as well as overall vegetation greenness. However, the extent to which a biome shift is already underway remains unclear because of the local nature of most field studies, sparsity of systematic ground-based ecological monitoring, and reliance on coarse resolution satellite observations. Here, we evaluated early indicators of a boreal forest biome shift using four decades of moderate resolution (30 m) satellite observations and biogeoclimatic spatial datasets. Specifically, we quantified interannual trends in annual maximum vegetation greenness using an ensemble of vegetation indices derived from Landsat observations at 100,000 sample sites in areas without signs of recent disturbance. We found vegetation greenness increased (greened) at 38 [29, 42] % and 22 [15, 26] % of sample sites from 1985 to 2019 and 2000 to 2019, whereas vegetation greenness decreased (browned) at 13 [9, 15] % and 15 [13, 19] % of sample sites during these respective periods [95% Monte Carlo confidence intervals]. Greening was thus 3.0 [2.6, 3.5] and 1.5 [0.8, 2.0] times more common than browning and primarily occurred in cold sparsely treed areas with high soil nitrogen and moderate summer warming. Conversely, browning primarily occurred in the climatically warmest margins of both the boreal forest biome and major forest types (e.g., evergreen conifer forests), especially in densely treed areas where summers became warmer and drier. These macroecological trends reflect underlying shifts in vegetation productivity, mortality, and recruitment that are consistent with early stages of a boreal biome shift.}, } @article {pmid35194141, year = {2022}, author = {Chandrakumar, I and Gauthier, NPG and Nelson, C and Bonsall, MB and Locher, K and Charles, M and MacDonald, C and Krajden, M and Manges, AR and Chorlton, SD}, title = {BugSplit enables genome-resolved metagenomics through highly accurate taxonomic binning of metagenomic assemblies.}, journal = {Communications biology}, volume = {5}, number = {1}, pages = {151}, pmid = {35194141}, issn = {2399-3642}, mesh = {*Algorithms ; Bacteria/classification/*genetics ; COVID-19/epidemiology/prevention & control/virology ; Computational Biology/*methods ; Humans ; Internet ; Metagenome/*genetics ; Metagenomics/*methods ; Nanopore Sequencing/*methods ; Pandemics/prevention & control ; Reproducibility of Results ; SARS-CoV-2/classification/genetics/physiology ; }, abstract = {A large gap remains between sequencing a microbial community and characterizing all of the organisms inside of it. Here we develop a novel method to taxonomically bin metagenomic assemblies through alignment of contigs against a reference database. We show that this workflow, BugSplit, bins metagenome-assembled contigs to species with a 33% absolute improvement in F1-score when compared to alternative tools. We perform nanopore mNGS on patients with COVID-19, and using a reference database predating COVID-19, demonstrate that BugSplit's taxonomic binning enables sensitive and specific detection of a novel coronavirus not possible with other approaches. When applied to nanopore mNGS data from cases of Klebsiella pneumoniae and Neisseria gonorrhoeae infection, BugSplit's taxonomic binning accurately separates pathogen sequences from those of the host and microbiota, and unlocks the possibility of sequence typing, in silico serotyping, and antimicrobial resistance prediction of each organism within a sample. BugSplit is available at https://bugseq.com/academic .}, } @article {pmid35193403, year = {2022}, author = {Gross, CP and Duffy, JE and Hovel, KA and Kardish, MR and Reynolds, PL and Boström, C and Boyer, KE and Cusson, M and Eklöf, J and Engelen, AH and Eriksson, BK and Fodrie, FJ and Griffin, JN and Hereu, CM and Hori, M and Hughes, AR and Ivanov, MV and Jorgensen, P and Kruschel, C and Lee, KS and Lefcheck, J and McGlathery, K and Moksnes, PO and Nakaoka, M and O'Connor, MI and O'Connor, NE and Olsen, JL and Orth, RJ and Peterson, BJ and Reiss, H and Rossi, F and Ruesink, J and Sotka, EE and Thormar, J and Tomas, F and Unsworth, R and Voigt, EP and Whalen, MA and Ziegler, SL and Stachowicz, JJ}, title = {The biogeography of community assembly: latitude and predation drive variation in community trait distribution in a guild of epifaunal crustaceans.}, journal = {Proceedings. Biological sciences}, volume = {289}, number = {1969}, pages = {20211762}, pmid = {35193403}, issn = {1471-2954}, mesh = {Animals ; Crustacea ; Ecosystem ; Oceans and Seas ; *Predatory Behavior ; *Zosteraceae ; }, abstract = {While considerable evidence exists of biogeographic patterns in the intensity of species interactions, the influence of these patterns on variation in community structure is less clear. Studying how the distributions of traits in communities vary along global gradients can inform how variation in interactions and other factors contribute to the process of community assembly. Using a model selection approach on measures of trait dispersion in crustaceans associated with eelgrass (Zostera marina) spanning 30° of latitude in two oceans, we found that dispersion strongly increased with increasing predation and decreasing latitude. Ocean and epiphyte load appeared as secondary predictors; Pacific communities were more overdispersed while Atlantic communities were more clustered, and increasing epiphytes were associated with increased clustering. By examining how species interactions and environmental filters influence community structure across biogeographic regions, we demonstrate how both latitudinal variation in species interactions and historical contingency shape these responses. Community trait distributions have implications for ecosystem stability and functioning, and integrating large-scale observations of environmental filters, species interactions and traits can help us predict how communities may respond to environmental change.}, } @article {pmid35193392, year = {2022}, author = {Escamilla Molgora, JM and Sedda, L and Diggle, PJ and Atkinson, PM}, title = {A taxonomic-based joint species distribution model for presence-only data.}, journal = {Journal of the Royal Society, Interface}, volume = {19}, number = {187}, pages = {20210681}, pmid = {35193392}, issn = {1742-5662}, mesh = {Bayes Theorem ; *Biodiversity ; *Ecosystem ; }, abstract = {Species distribution models (SDMs) are an important class of model for mapping taxa spatially and are a key tool for tackling biodiversity loss. However, most common SDMs depend on presence-absence data and, despite the accumulation and exponential growth of biological occurrence data across the globe, the available data are predominantly presence-only (i.e. they lack real absences). Although presence-only SDMs do exist, they inevitably require assumptions about absences of the considered taxa and they are specified mostly for single species and, thus, do not exploit fully the information in related taxa. This greatly limits the utility of global biodiversity databases such as GBIF. Here, we present a Bayesian-based SDM for multiple species that operates directly on presence-only data by exploiting the joint distribution between the multiple ecological processes and, crucially, identifies the sampling effort per taxa which allows inference on absences. The model was applied to two case studies. One, focusing on taxonomically diverse taxa over central Mexico and another focusing on the monophyletic family Cactacea over continental Mexico. In both cases, the model was able to identify the ecological and sampling effort processes for each taxon using only the presence observations, environmental and anthropological data.}, } @article {pmid35190562, year = {2022}, author = {Fu, Z and Ciais, P and Prentice, IC and Gentine, P and Makowski, D and Bastos, A and Luo, X and Green, JK and Stoy, PC and Yang, H and Hajima, T}, title = {Atmospheric dryness reduces photosynthesis along a large range of soil water deficits.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {989}, pmid = {35190562}, issn = {2041-1723}, mesh = {*Air ; Datasets as Topic ; *Droughts ; Ecological Parameter Monitoring/statistics & numerical data ; Europe ; Neural Networks, Computer ; *Photosynthesis ; Plant Leaves/physiology ; Soil/*chemistry ; Vapor Pressure ; Water/analysis/chemistry ; }, abstract = {Both low soil water content (SWC) and high atmospheric dryness (vapor pressure deficit, VPD) can negatively affect terrestrial gross primary production (GPP). The sensitivity of GPP to soil versus atmospheric dryness is difficult to disentangle, however, because of their covariation. Using global eddy-covariance observations, here we show that a decrease in SWC is not universally associated with GPP reduction. GPP increases in response to decreasing SWC when SWC is high and decreases only when SWC is below a threshold. By contrast, the sensitivity of GPP to an increase of VPD is always negative across the full SWC range. We further find canopy conductance decreases with increasing VPD (irrespective of SWC), and with decreasing SWC on drier soils. Maximum photosynthetic assimilation rate has negative sensitivity to VPD, and a positive sensitivity to decreasing SWC when SWC is high. Earth System Models underestimate the negative effect of VPD and the positive effect of SWC on GPP such that they should underestimate the GPP reduction due to increasing VPD in future climates.}, } @article {pmid35186498, year = {2022}, author = {Reijnders, MJMF}, title = {Wei2GO: weighted sequence similarity-based protein function prediction.}, journal = {PeerJ}, volume = {10}, number = {}, pages = {e12931}, pmid = {35186498}, issn = {2167-8359}, mesh = {*Software ; *Algorithms ; Molecular Sequence Annotation ; Proteins/genetics ; Databases, Protein ; }, abstract = {BACKGROUND: Protein function prediction is an important part of bioinformatics and genomics studies. There are many different predictors available, however most of these are in the form of web-servers instead of open-source locally installable versions. Such local versions are necessary to perform large scale genomics studies due to the presence of limitations imposed by web servers such as queues, prediction speed, and updatability of databases.

METHODS: This paper describes Wei2GO: a weighted sequence similarity and python-based open-source protein function prediction software. It uses DIAMOND and HMMScan sequence alignment searches against the UniProtKB and Pfam databases respectively, transfers Gene Ontology terms from the reference protein to the query protein, and uses a weighing algorithm to calculate a score for the Gene Ontology annotations.

RESULTS: Wei2GO is compared against the Argot2 and Argot2.5 web servers, which use a similar concept, and DeepGOPlus which acts as a reference. Wei2GO shows an increase in performance according to precision and recall curves, Fmax scores, and Smin scores for biological process and molecular function ontologies. Computational time compared to Argot2 and Argot2.5 is decreased from several hours to several minutes.

AVAILABILITY: Wei2GO is written in Python 3, and can be found at https://gitlab.com/mreijnders/Wei2GO.}, } @article {pmid35184239, year = {2022}, author = {Pandey, HK and Singh, VK and Singh, SK}, title = {Multi-criteria decision making and Dempster-Shafer model-based delineation of groundwater prospect zones from a semi-arid environment.}, journal = {Environmental science and pollution research international}, volume = {29}, number = {31}, pages = {47740-47758}, pmid = {35184239}, issn = {1614-7499}, support = {NRDMS/01/267/2019//Natural Resources Data Management System/ ; }, mesh = {Decision Making ; Desert Climate ; Environmental Monitoring/methods ; *Geographic Information Systems ; *Groundwater ; Hydrology ; }, abstract = {The present study illustrates the delineation of the groundwater potential zones in one of the most critical and drought-affected areas under Bundelkhand region of Uttar Pradesh (India). Hydrological evaluations were carried out using GIS tools and remote sensing data which ultimately yielded several thematic maps, such as lineament density, land use/land cover, drainage density, lithology, slope, geomorphology, topographic wetness index (TWI), DEM, and soil. Thematic layers were assigned relative weightages as per their groundwater potential prospects under multi-criteria decision making (MCDM) method through analytical hierarchy process (AHP). To recognize the groundwater potential zone, weighted overlay analysis was also performed. Additionally, for testing of the Dempster-Shafer model, 16 wells in the study area have been selected. Based on the probability of the groundwater occurrence, the belief factor was equated to delineate groundwater potential zones which illustrate five different potential zones. According to the AHP model, the northwest side of the study area is characterized with very high potential zones whereas the northeast and southeast regions constitute medium and low groundwater potential zones respectively. According to the DS model, very high groundwater potential zones constitute 17% and the remaining area falls under low potential. Overall accuracy of the DS model is higher than AHP model.}, } @article {pmid35182532, year = {2022}, author = {He, W and Meng, H and Han, J and Zhou, G and Zheng, H and Zhang, S}, title = {Spatiotemporal PM2.5 estimations in China from 2015 to 2020 using an improved gradient boosting decision tree.}, journal = {Chemosphere}, volume = {296}, number = {}, pages = {134003}, doi = {10.1016/j.chemosphere.2022.134003}, pmid = {35182532}, issn = {1879-1298}, mesh = {*Air Pollutants/analysis ; *Air Pollution/analysis ; China ; Decision Trees ; Environmental Monitoring/methods ; Humans ; Particulate Matter/analysis ; }, abstract = {Fine particulate matter (PM2.5) with spatiotemporal continuity can provide important basis for the assessment of adverse effects on human health. In recent years, researchers have done a lot of work on the surface PM2.5 simulation. However, due to the limitations of data and models, it is difficult to accurately evaluate the spatial and temporal PM2.5 variations on a fine scale. In this study, we adopted the multi-angle implementation of atmospheric correction (MAIAC) aerosol products, and proposed a spatiotemporal model based on the gradient boosting decision tree (GBDT) algorithm to retrieve PM2.5 concentration across China from 2015 to 2020 at 1-km resolution. Our model achieved excellent performance, with overall CV-R[2] of 0.92, and annual CV-R[2] of 0.90-0.93. In addition, the model can also be used for evaluation on different time scales. Compared with previous studies, the model developed in our study performed better and more stable, which showed the highest accuracies in PM2.5 estimation works at 1-km resolution. During the study period, the overall national PM2.5 pollution showed a downward trend, with the annual mean concentration dropping from 42.42 μg/m[3] to 27.91 μg/m[3]. The largest decrease occurred in Beijing-Tianjin-Hebei (BTH), with a trend of -5.17 μg/m[3]/yr, while it remains the most polluted region. The area meeting the secondary national air quality standard (<35 μg/m[3]) increased from ∼34% to ∼79%. These results indicate that the atmospheric environment has improved significantly. Moreover, different regions have different time nodes for the start of the continuous standard-met day during the year, and the duration is different as well. Overall, this study can provide reliable large-scale PM2.5 estimations.}, } @article {pmid35178228, year = {2022}, author = {Yang, J and Chen, M}, title = {Construction of Sports and Health Data Resources and Transformation of Teachers' Orientation Based on Web Database.}, journal = {Journal of healthcare engineering}, volume = {2022}, number = {}, pages = {4372406}, pmid = {35178228}, issn = {2040-2309}, mesh = {*Data Management ; Humans ; Physical Education and Training ; Schools ; *Sports ; Students ; }, abstract = {In the intelligent era, emerging information technology helps to transform the information society into an intelligent society and the educational system into a new educational ecology. Teachers must change their roles to be competent for future education and teaching as a result of social transformation, technology application, and education development. Simultaneously, figuring out how to sort sports health data and analyze students' physical health information with a low error rate is an urgent problem that needs to be solved. Data management skills are an unavoidable requirement of the current state of school physical education. Sports health information management will become easier as computer technology advances and the country places a greater emphasis on computer networks. This paper proposes a Web database-based sports health data management system. This paper can help schools understand the relationship between important factors and indicators that affect students' health in order to guide them in making timely changes to their physical education programs. Provide a reasonable sports health plan based on scientific analysis and evaluation to achieve the goal of improving students' physical quality and reducing workload.}, } @article {pmid35176378, year = {2022}, author = {Choo, SW and Chong, JL and Gaubert, P and Hughes, AC and O'Brien, S and Chaber, AL and Antunes, A and Platto, S and Sun, NC and Yu, L and Koepfli, KP and Suwal, TL and Thakur, M and Ntie, S and Panjang, E and Kumaran, JV and Mahmood, T and Heighton, SP and Dorji, D and Gonedelé, BS and Nelson, BR and Djagoun, CAMS and Loh, IH and Kaspal, P and Pauklin, S and Michelena, T and Zhu, H and Lipovich, L and Tian, X and Deng, S and Mason, CE and Hu, J and White, R and Jakubovics, NS and Wee, WY and Tan, TK and Wong, KT and Paterson, S and Chen, M and Zhang, Y and Othman, RY and Brown, LC and Shen, B and Shui, G and Ang, MY and Zhao, Y and Li, Y and Zhang, B and Chong, CT and Meng, Y and Wong, A and Su, J and Omar, H and Shen, H and Tan, CH and Xu, H and Paterson, IC and Wang, M and Chan, CK and Zhang, S and Dutta, A and Tee, TS and Juvigny-Khenafou, NPD and Mutha, NVR and Aziz, MA}, title = {A collective statement in support of saving pangolins.}, journal = {The Science of the total environment}, volume = {824}, number = {}, pages = {153666}, doi = {10.1016/j.scitotenv.2022.153666}, pmid = {35176378}, issn = {1879-1026}, support = {25064/CRUK_/Cancer Research UK/United Kingdom ; }, mesh = {Animals ; *Pangolins ; }, } @article {pmid35175823, year = {2022}, author = {Nathan, R and Monk, CT and Arlinghaus, R and Adam, T and Alós, J and Assaf, M and Baktoft, H and Beardsworth, CE and Bertram, MG and Bijleveld, AI and Brodin, T and Brooks, JL and Campos-Candela, A and Cooke, SJ and Gjelland, KØ and Gupte, PR and Harel, R and Hellström, G and Jeltsch, F and Killen, SS and Klefoth, T and Langrock, R and Lennox, RJ and Lourie, E and Madden, JR and Orchan, Y and Pauwels, IS and Říha, M and Roeleke, M and Schlägel, UE and Shohami, D and Signer, J and Toledo, S and Vilk, O and Westrelin, S and Whiteside, MA and Jarić, I}, title = {Big-data approaches lead to an increased understanding of the ecology of animal movement.}, journal = {Science (New York, N.Y.)}, volume = {375}, number = {6582}, pages = {eabg1780}, doi = {10.1126/science.abg1780}, pmid = {35175823}, issn = {1095-9203}, mesh = {Animal Migration ; Animals ; Animals, Wild/*physiology ; *Behavior, Animal ; *Big Data ; Data Collection ; *Ecology ; Ecosystem ; *Environment ; *Movement ; Spatio-Temporal Analysis ; }, abstract = {Understanding animal movement is essential to elucidate how animals interact, survive, and thrive in a changing world. Recent technological advances in data collection and management have transformed our understanding of animal "movement ecology" (the integrated study of organismal movement), creating a big-data discipline that benefits from rapid, cost-effective generation of large amounts of data on movements of animals in the wild. These high-throughput wildlife tracking systems now allow more thorough investigation of variation among individuals and species across space and time, the nature of biological interactions, and behavioral responses to the environment. Movement ecology is rapidly expanding scientific frontiers through large interdisciplinary and collaborative frameworks, providing improved opportunities for conservation and insights into the movements of wild animals, and their causes and consequences.}, } @article {pmid35171691, year = {2022}, author = {Altinli, M and Leggewie, M and Badusche, M and Gyanwali, R and Scherer, C and Schulze, J and Sreenu, VB and Fegebank, M and Zibrat, B and Fuss, J and Junglen, S and Schnettler, E}, title = {Antiviral RNAi Response against the Insect-Specific Agua Salud Alphavirus.}, journal = {mSphere}, volume = {7}, number = {1}, pages = {e0100321}, pmid = {35171691}, issn = {2379-5042}, mesh = {*Aedes/genetics/virology ; *Alphavirus/genetics ; Animals ; Antiviral Agents ; *Arboviruses/physiology ; Cell Line ; *Insect Viruses ; *MicroRNAs ; Mosquito Vectors/virology ; RNA Interference ; RNA, Double-Stranded ; RNA, Small Interfering/genetics ; }, abstract = {Arboviruses transmitted by mosquitoes are responsible for the death of millions of people each year. In addition to arboviruses, many insect-specific viruses (ISVs) have been discovered in mosquitoes in the last decade. ISVs, in contrast to arboviruses transmitted by mosquitoes to vertebrates, cannot replicate in vertebrate cells even when they are evolutionarily closely related to arboviruses. The alphavirus genus includes many arboviruses, although only a few ISVs have been discovered from this genus so far. Here, we investigate the interactions of a recently isolated insect-specific alphavirus, Agua Salud alphavirus (ASALV), with its mosquito host. RNA interference (RNAi) is one of the essential antiviral responses against arboviruses, although there is little knowledge on the interactions of RNAi with ISVs. Through the knockdown of transcripts of the different key RNAi pathway (small interfering RNA [siRNA], microRNA [miRNA], and P-element-induced wimpy testis [PIWI]-interacting RNA [piRNA]) proteins, we show the antiviral role of Ago2 (siRNA), Ago1 (miRNA), and Piwi4 proteins against ASALV in Aedes aegypti-derived cells. ASALV replication was increased in Dicer2 and Ago2 knockout cells, confirming the antiviral role of the siRNA pathway. In infected cells, mainly ASALV-specific siRNAs are produced, while piRNA-like small RNAs, with the characteristic nucleotide bias resulting from ping-pong amplification, are produced only in Dicer2 knockout cells. Taken together, ASALV interactions with the mosquito RNAi response differ from those of arthropod-borne alphaviruses in some aspects, although they also share some commonalities. Further research is needed to understand whether the identified differences can be generalized to other insect-specific alphaviruses. IMPORTANCE Mosquitoes are efficient vectors for many arboviruses that cause emergent infectious diseases in humans. Many insect-specific viruses (ISVs) that can infect mosquitoes but cannot infect vertebrates have been discovered in the last decade. ISVs have attracted great attention due to their potential use in mosquito or arbovirus control, by either decreasing mosquito fitness or restricting arbovirus replication and transmission to humans. However, ISV-mosquito interactions are not well understood. RNA interference (RNAi) is the most important innate immune response against many arboviruses, while it is unknown if it is antiviral against ISVs. Here, we investigate in detail the antiviral effect of the RNAi response in mosquitoes against an ISV for the first time. Using a recently isolated insect-specific alphavirus, we show that the regulation of virus replication was different from that for arthropod-borne alphaviruses despite some similarities. The differences in mosquito-virus interactions could drive the different transmission modes, which could eventually drive the evolution of arboviruses. Hence, an understanding of mosquito-ISV interactions can shed light on the ecology and evolution of both ISVs and the medically important arboviruses.}, } @article {pmid35165328, year = {2022}, author = {Melnikov, VR and Christopoulos, GI and Krzhizhanovskaya, VV and Lees, MH and Sloot, PMA}, title = {Behavioural thermal regulation explains pedestrian path choices in hot urban environments.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {2441}, pmid = {35165328}, issn = {2045-2322}, mesh = {*Adaptation, Psychological ; Adult ; Bayes Theorem ; *Choice Behavior ; Cities ; Computational Biology/methods ; Female ; *Heat-Shock Response ; *Hot Temperature ; Humans ; Male ; Middle Aged ; Pedestrians/*psychology ; Trees ; *Tropical Climate ; *Urban Population ; Young Adult ; }, abstract = {Due to phenomena such as urban heat islands, outdoor thermal comfort of the cities' residents emerges as a growing concern. A major challenge for mega-cities in changing climate is the design of urban spaces that ensure and promote pedestrian thermal comfort. Understanding pedestrian behavioural adaptation to urban thermal environments is critically important to attain this goal. Current research in pedestrian behaviour lacks controlled experimentation, which limits the quantitative modelling of such complex behaviour. Combining well-controlled experiments with human participants and computational methods inspired by behavioural ecology and decision theory, we examine the effect of sun exposure on route choice in a tropical city. We find that the distance walked in the shade is discounted by a factor of 0.86 compared to the distance walked in the sun, and that shadows cast by buildings have a stronger effect than trees. The discounting effect is mathematically formalised and thus allows quantification of the behaviour that can be used in understanding pedestrian behaviour in changing urban climates. The results highlight the importance of assessment of climate through human responses to it and point the way forward to explore scenarios to mitigate pedestrian heat stress.}, } @article {pmid35163220, year = {2022}, author = {Botti, V and Marrone, S and Cannistraro, S and Bizzarri, AR}, title = {Interaction between miR4749 and Human Serum Albumin as Revealed by Fluorescence, FRET, Atomic Force Spectroscopy and Computational Modelling.}, journal = {International journal of molecular sciences}, volume = {23}, number = {3}, pages = {}, pmid = {35163220}, issn = {1422-0067}, support = {24450//Italian Association for Cancer Research/ ; }, mesh = {Binding Sites/drug effects ; Circular Dichroism/methods ; Computational Biology/methods ; Fluorescence ; Fluorescence Resonance Energy Transfer/methods ; Humans ; MicroRNAs/*chemistry/*genetics ; Molecular Docking Simulation/methods ; Molecular Dynamics Simulation ; Protein Binding/physiology ; Serum Albumin, Human/*chemistry/metabolism/ultrastructure ; Spectrometry, Fluorescence/methods ; Thermodynamics ; }, abstract = {The interaction of Human Serum Albumin (HSA) with the microRNA, miR4749, was investigated by Atomic Force Spectrscopy (AFS), static and time-resolved fluorescence spectroscopy and by computational methods. The formation of a HSA/miR4749 complex with an affinity of about 10[4] M[-1] has been assessed through a Stern-Volmer analysis of steady-state fluorescence quenching of the lone Trp residue (Trp214) emission of HSA. Förster Resonance Energy Transfer (FRET) measurements of fluorescence lifetime of the HSA/miR4749 complex were carried out in the absence and in the presence of an acceptor chromophore linked to miR4749. This allowed us to determine a distance of 4.3 ± 0.5 nm between the lone Trp of HSA and the dye bound to miR4749 5p-end. Such a distance was exploited for a screening of the possible binding sites between HSA and miR4749, as predicted by computational docking. Such an approach, further refined by binding free energy calculations, led us to the identification of a consistent model for the structure of the HSA/miR4749 complex in which a positively charged HSA pocket accommodates the negatively charged miRNA molecule. These results designate native HSA as a suitable miRNA carrier under physiological conditions for delivering to appropriate targets.}, } @article {pmid35157858, year = {2022}, author = {Wang, W and Tian, P and Zhang, J and Agathokleous, E and Xiao, L and Koike, T and Wang, H and He, X}, title = {Big data-based urban greenness in Chinese megalopolises and possible contribution to air quality control.}, journal = {The Science of the total environment}, volume = {824}, number = {}, pages = {153834}, doi = {10.1016/j.scitotenv.2022.153834}, pmid = {35157858}, issn = {1879-1026}, mesh = {*Air Pollutants/analysis ; *Air Pollution/analysis ; Big Data ; China ; Cities ; Environmental Monitoring ; Humans ; Nitrogen Dioxide/analysis ; Particulate Matter/analysis ; Quality Control ; }, abstract = {Urban greenness is essential for people's daily lives, while its contribution to air quality control is unclear. In this study, Streetview big data of urban greenness and air quality data (Air Quality Index, PM2.5, PM10, SO2, NO2, O3, CO) from 206 monitoring stations from 27 provincial capital cities in China were analyzed. The national averages for the sky, ground and middle-level (shrub and short trees) view greenness were 5.4%, 5.5%, and 15.4%, respectively, and the sky:ground:middle ratio was 2:2:6. Street-view/bird-view greenness ratio averaged at 1.1. Large inter-city variations were observed in all the greenness parameters, and the weak associations between all street-view parameters and bird-eye greenspace percentage (21%-73%) indicate their representatives of different aspects of green infrastructures. All air quality parameters were higher in winter than in summer, except O3. Over 90% of air quality variation could be explained by socioeconomics and geoclimates, suggesting that air quality control in China should first reduce efflux from social economics, while geoclimatic-oriented ventilation facilitation design is also critical. For different air quality components, greenness had most significant associations with NO2, O3 and CO, and street-view/bird-view ratio was the most powerful indicator of all greenness parameters. Pooled-data analysis at national level showed that street-view greenness was responsible for 2.3% of the air quality variations in the summer and 3.6% in the winter; however, when separated into different regions (North-South China; East-West China), the explaining power increased up to 16.2%. Increased NO2 was accompanied with decreased O3, indicating NO titration effect. The higher O3 aligned with the higher street-view greenness, showing the greenness-related precursor risk for O3 pollution. Our study manifested that big internet data could identify the association of greenness and air pollution from street view scale, which can favor urban greenness management and evaluation in other regions where street-view data are available.}, } @article {pmid35157146, year = {2022}, author = {Xu, Y and Wang, X and Cui, G and Li, K and Liu, Y and Li, B and Yao, Z}, title = {Source apportionment and ecological and health risk mapping of soil heavy metals based on PMF, SOM, and GIS methods in Hulan River Watershed, Northeastern China.}, journal = {Environmental monitoring and assessment}, volume = {194}, number = {3}, pages = {181}, pmid = {35157146}, issn = {1573-2959}, support = {41861124004//National Natural Science Foundation of China/ ; 42001107//National Natural Science Foundation of China/ ; }, mesh = {Adult ; Child ; China ; Environmental Monitoring ; Geographic Information Systems ; Humans ; *Metals, Heavy/analysis ; Risk Assessment ; Rivers ; Soil ; *Soil Pollutants/analysis ; }, abstract = {Heavy metals in agricultural soils not only affect the food security and soil security, but also endanger the human health through the food chain. Based on the incorporation of index analysis, positive matrix factorization (PMF), self-organizing map (SOM), and geostatistical methods, this research performed the assessment of source apportionment and ecological and health risks of soil heavy metals in Hulan River Watershed, Northeastern China. According to the Pollution Load Index (PLI), 83.08% of the soil samples were slightly or mildly polluted, and 1.54% of the soil samples were severely polluted. The ecological risk index (EI) showed that about 80.77% and 60.77% of the soil samples were beyond the low risk level for Hg and Cd, respectively. In this research, the non-carcinogenic and carcinogenic risk indices for children were higher than adult males and adult females. Four potential sources were revealed based on the PMF and SOM analysis including atmospheric deposition and industrial emission; transportation source; agricultural source; and a combination of agricultural, industrial, and natural sources. Considerable and high ecological risk from Hg existed in the area close to the coal steam-electric plant, and considerable and high ecological risk from Cd existed in the Hulan River estuary area. The eastern part of the study area experienced higher non-carcinogenic and carcinogenic risks for adults and children than the western part of the study area. The source apportionment and ecological and health risk mapping provide important role in reducing pollution sources. Zonal pollution control and soil restoration measures should be performed in the areas with high ecological and health risks.}, } @article {pmid35157026, year = {2022}, author = {Pandey, P and Arora, S and Rosen, GL}, title = {MetaMutationalSigs: comparison of mutational signature refitting results made easy.}, journal = {Bioinformatics (Oxford, England)}, volume = {38}, number = {8}, pages = {2344-2347}, pmid = {35157026}, issn = {1367-4811}, support = {P50 DE030707/DE/NIDCR NIH HHS/United States ; 1936791//NSF/ ; //Fox Chase Cancer Center Risk Assessment Program Funds/ ; //DOD W81XWH-18-1-0148 award and a CEP award from the Yale Head and Neck Cancer NIH SPORE/ ; }, mesh = {Humans ; Mutation ; *Software ; *Neoplasms/genetics ; }, abstract = {MOTIVATION: The analysis of mutational signatures is becoming increasingly common in cancer genetics, with emerging implications in cancer evolution, classification, treatment decision and prognosis. Recently, several packages have been developed for mutational signature analysis, with each using different methodology and yielding significantly different results. Because of the non-trivial differences in tools' refitting results, researchers may desire to survey and compare the available tools, in order to objectively evaluate the results for their specific research question, such as which mutational signatures are prevalent in different cancer types.

RESULTS: Due to the need for effective comparison of refitting mutational signatures, we introduce a user-friendly software that can aggregate and visually present results from different refitting packages.

MetaMutationalSigs is implemented using R and python and is available for installation using Docker and available at: https://github.com/EESI/MetaMutationalSigs.}, } @article {pmid35150681, year = {2022}, author = {Mizuta, K and Grunwald, S and Bacon, AR and Cropper, WP and Phillips, MA and Moss, CB and Gonzalez-Benecke, CA and Markewitz, D and Clingensmith, CM and Xiong, X}, title = {Holistic aboveground ecological productivity efficiency modeling using data envelopment analysis in the southeastern U.S.}, journal = {The Science of the total environment}, volume = {824}, number = {}, pages = {153802}, doi = {10.1016/j.scitotenv.2022.153802}, pmid = {35150681}, issn = {1879-1026}, mesh = {*Ecosystem ; Forests ; *Soil ; Southeastern United States ; }, abstract = {Aboveground net primary productivity (ANPP) of an ecosystem is among the most important metrics of valued ecosystem services. Measuring the efficiency scores of ecological production (ESEP) based on ANPP using relevant variables is valuable for identifying inefficient sites. The efficiency scores computed by the Data Envelopment Analysis (DEA) may be influenced by the number of input variables incorporated into the models and two DEA settings-orientations and returns-to-scales (RTSs). Therefore, the objectives were threefold to: (1) identify soil-environmental variables relevant to ANPP, (2) assess the sensitivity of ESEP to the number of input variables and DEA settings, and (3) assess local management relations with ESEP. The ANPP rates were calculated for pine forests in the southeastern U.S. where 10 management types were used. This was followed by an all-relevant variable selection technique based on 696 variables that cover biotic, pedogenic, climatic, geological, and topographical factors. Five minimal-optimal variable selection techniques were further applied to create five parsimonious sets that contain a different number of variables used as DEA inputs. After setting ANPP as the output variable, two DEA orientations (input/output) and six RTS were applied to compute ESEP. The variable selection methods succeeded in objectively identifying the major factors relevant to ANPP variation. The site index showed the highest correlation with ANPP (r = 0.39), while various precipitation factors were negatively correlated (r = - 0.15~ - 0.29, p < 0.01). Parsimonious ESEP models observed a decrease in score variances as the number of input variables increased. Various RTS produced similar scores across orientations. Of the DEA settings, an output orientation with decreasing RTS produced the most progressive ESEP with large variation. Results also suggested that macro- and micronutrient fertilization is the best combination of management strategies to achieve high ESEP. This holistic benchmark approach can be applied to other ecological functions in diverse regions.}, } @article {pmid35136536, year = {2021}, author = {Whegang Youdom, S and Tonnang, HEZ and Choukem, SP}, title = {Modelling and projections of the COVID-19 epidemic and the potential impact of social distancing in Cameroon.}, journal = {Journal of public health in Africa}, volume = {12}, number = {2}, pages = {1479}, pmid = {35136536}, issn = {2038-9922}, abstract = {The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) disease (COVID-19) pandemic continues to be a global health problem with a significant impact in Cameroon. The aim of this study was to improve the understanding of the spread of COVID-19 and enhance disease control strategies. We assessed the SIRD (susceptible, infected, recovered and death) model to describe COVID-19 reported cases in Cameroon from March 7 to May 31, 2020, and study the impact of social distancing. We assessed changes in the basic reproduction number (R0) on a phaseadjusted process and forecasted the longterm epidemic trend. Daily incidence data was fitted to a log-linear model before each peak of the epidemic with the purpose of studying the effective mechanism of variation of the reproduction number Re. Before the first peak of the epidemic, R0 was estimated as 6.8. Social distancing and restricted measures contributed to reduce the value to 3.24 by April 30 but remained greater than 1 (R0=2.43) by May 22 when the initial measures implemented by the government to control the spread of the disease were relaxed. The estimated number of infections ranged 13,703-18,456 by May 31, and will continue increasing throughout June 2020 with more than 20,000 cases expected by the end of June 2020, suggesting that the pandemic is still in the growth phase. Longterm prediction showed a flattened curve towards April 2021. Preventive measures initially implemented by the government of Cameroon should be strictly maintained and reinforced to reduce Re to 0.5.}, } @article {pmid35134065, year = {2022}, author = {Engelstad, P and Jarnevich, CS and Hogan, T and Sofaer, HR and Pearse, IS and Sieracki, JL and Frakes, N and Sullivan, J and Young, NE and Prevéy, JS and Belamaric, P and LaRoe, J}, title = {INHABIT: A web-based decision support tool for invasive plant species habitat visualization and assessment across the contiguous United States.}, journal = {PloS one}, volume = {17}, number = {2}, pages = {e0263056}, pmid = {35134065}, issn = {1932-6203}, mesh = {Conservation of Natural Resources/*methods ; Decision Making ; Decision Support Techniques ; Ecosystem ; Internet ; Introduced Species/*statistics & numerical data ; Plant Dispersal/*physiology ; Plants/classification ; Software ; United States ; }, abstract = {Narrowing the communication and knowledge gap between producers and users of scientific data is a longstanding problem in ecological conservation and land management. Decision support tools (DSTs), including websites or interactive web applications, provide platforms that can help bridge this gap. DSTs can most effectively disseminate and translate research results when producers and users collaboratively and iteratively design content and features. One data resource seldom incorporated into DSTs are species distribution models (SDMs), which can produce spatial predictions of habitat suitability. Outputs from SDMs can inform management decisions, but their complexity and inaccessibility can limit their use by resource managers or policy makers. To overcome these limitations, we present the Invasive Species Habitat Tool (INHABIT), a novel, web-based DST built with R Shiny to display spatial predictions and tabular summaries of habitat suitability from SDMs for invasive plants across the contiguous United States. INHABIT provides actionable science to support the prevention and management of invasive species. Two case studies demonstrate the important role of end user feedback in confirming INHABIT's credibility, utility, and relevance.}, } @article {pmid35131424, year = {2022}, author = {Ganser, MH and Santoferrara, LF and Agatha, S}, title = {Molecular signature characters complement taxonomic diagnoses: A bioinformatic approach exemplified by ciliated protists (Ciliophora, Oligotrichea).}, journal = {Molecular phylogenetics and evolution}, volume = {170}, number = {}, pages = {107433}, doi = {10.1016/j.ympev.2022.107433}, pmid = {35131424}, issn = {1095-9513}, support = {I 3268/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {*Ciliophora ; *Computational Biology ; Humans ; Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA ; }, abstract = {Traditionally, taxa following the botanical or zoological codes of nomenclature are diagnosed mainly by morphological characters, although integrative taxonomy advocates including additional features. While many taxonomic studies include DNA sequence analyses, a systematic integration of diagnostic molecular characters (signature characters) is still rare. Here, we suggest a practical guideline for the detection and evaluation of signature characters that provides the means necessary to complement diagnoses and facilitates identifications. The guideline comprises generally applicable criteria exemplified by a case study on an ecologically important group of planktonic protists, the Oligotrichea. The detection of signature characters and their discrete states in multiple sequence alignments is facilitated by the recently developed tool DeSignate. Moreover, we introduce a novel bioinformatic approach to test the influence of different alignment programs on the consistency of signature characters. Our workflow enabled detection of consensus signature characters for most tested taxa and inclusion of such characters in the diagnoses of three orders, eight families, and two genera in the Oligotrichea. The suggested approach is a step towards an integrative taxonomy linking reliable molecular sequence data to organisms' traits.}, } @article {pmid35130830, year = {2022}, author = {Dreier, M and Meola, M and Berthoud, H and Shani, N and Wechsler, D and Junier, P}, title = {High-throughput qPCR and 16S rRNA gene amplicon sequencing as complementary methods for the investigation of the cheese microbiota.}, journal = {BMC microbiology}, volume = {22}, number = {1}, pages = {48}, pmid = {35130830}, issn = {1471-2180}, mesh = {Bacteria/classification/*genetics/isolation & purification ; Cheese/*microbiology ; Computational Biology ; DNA, Bacterial/genetics ; High-Throughput Nucleotide Sequencing/*methods ; High-Throughput Screening Assays/methods ; Microbiota/*genetics ; RNA, Ribosomal, 16S/*genetics ; Real-Time Polymerase Chain Reaction/*methods ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: Next-generation sequencing (NGS) methods and especially 16S rRNA gene amplicon sequencing have become indispensable tools in microbial ecology. While they have opened up new possibilities for studying microbial communities, they also have one drawback, namely providing only relative abundances and thus compositional data. Quantitative PCR (qPCR) has been used for years for the quantification of bacteria. However, this method requires the development of specific primers and has a low throughput. The constraint of low throughput has recently been overcome by the development of high-throughput qPCR (HT-qPCR), which allows for the simultaneous detection of the most prevalent bacteria in moderately complex systems, such as cheese and other fermented dairy foods. In the present study, the performance of the two approaches, NGS and HT-qPCR, was compared by analyzing the same DNA samples from 21 Raclette du Valais protected designation of origin (PDO) cheeses. Based on the results obtained, the differences, accuracy, and usefulness of the two approaches were studied in detail.

RESULTS: The results obtained using NGS (non-targeted) and HT-qPCR (targeted) show considerable agreement in determining the microbial composition of the cheese DNA samples studied, albeit the fundamentally different nature of these two approaches. A few inconsistencies in species detection were observed, particularly for less abundant ones. The detailed comparison of the results for 15 bacterial species/groups measured by both methods revealed a considerable bias for certain bacterial species in the measurements of the amplicon sequencing approach. We identified as probable origin to this PCR bias due to primer mismatches, variations in the number of copies for the 16S rRNA gene, and bias introduced in the bioinformatics analysis.

CONCLUSION: As the normalized microbial composition results of NGS and HT-qPCR agreed for most of the 21 cheese samples analyzed, both methods can be considered as complementary and reliable for studying the microbial composition of cheese. Their combined application proved to be very helpful in identifying potential biases and overcoming methodological limitations in the quantitative analysis of the cheese microbiota.}, } @article {pmid35129838, year = {2022}, author = {Manu, R and Corre, MD and Aleeje, A and Mwanjalolo, MJG and Babweteera, F and Veldkamp, E and van Straaten, O}, title = {Responses of tree growth and biomass production to nutrient addition in a semi-deciduous tropical forest in Africa.}, journal = {Ecology}, volume = {103}, number = {6}, pages = {e3659}, doi = {10.1002/ecy.3659}, pmid = {35129838}, issn = {1939-9170}, mesh = {Biomass ; Carbon ; *Forests ; Nutrients ; Soil ; *Trees/growth & development ; *Tropical Climate ; Uganda ; Water ; }, abstract = {Experimental evidence of nutrient limitations on primary productivity in Afrotropical forests is rare and globally underrepresented yet are crucial for understanding constraints to terrestrial carbon uptake. In an ecosystem-scale nutrient manipulation experiment, we assessed the early responses of tree growth rates among different tree sizes, taxonomic species, and at a community level in a humid tropical forest in Uganda. Following a full factorial design, we established 32 (eight treatments × four replicates) experimental plots of 40 × 40 m each. We added nitrogen (N), phosphorus (P), potassium (K), their combinations (NP, NK, PK, and NPK), and control at the rates of 125 kg N ha[-1] year[-1] , 50 kg P ha[-1] year[-1] and 50 kg K ha[-1] year[-1] , split into four equal applications, and measured stem growth of more than 15,000 trees with diameter at breast height (dbh) ≥1 cm. After 2 years, the response of tree stem growth to nutrient additions was dependent on tree sizes, species and leaf habit but not community wide. First, tree stem growth increased under N additions, primarily among medium-sized trees (10-30 cm dbh), and in trees of Lasiodiscus mildbraedii in the second year of the experiment. Second, K limitation was evident in semi-deciduous trees, which increased stem growth by 46% in +K than -K treatments, following a strong, prolonged dry season during the first year of the experiment. This highlights the key role of K in stomatal regulation and maintenance of water balance in trees, particularly under water-stressed conditions. Third, the role of P in promoting tree growth and carbon accumulation rates in this forest on highly weathered soils was rather not pronounced; nonetheless, mortality among saplings (1-5 cm dbh) was reduced by 30% in +P than in -P treatments. Although stem growth responses to nutrient interaction effects were positive or negative (likely depending on nutrient combinations and climate variability), our results underscore the fact that, in a highly diverse forest ecosystem, multiple nutrients and not one single nutrient regulate tree growth and aboveground carbon uptake due to varying nutrient requirements and acquisition strategies of different tree sizes, species, and leaf habits.}, } @article {pmid35128952, year = {2022}, author = {Antezana, G and Venning, A and Smith, D and Bidargaddi, N}, title = {Do young men and women differ in well-being apps usage? Findings from a randomised trial.}, journal = {Health informatics journal}, volume = {28}, number = {1}, pages = {14604582211064825}, doi = {10.1177/14604582211064825}, pmid = {35128952}, issn = {1741-2811}, mesh = {Adolescent ; Cross-Sectional Studies ; Female ; Humans ; Logistic Models ; Male ; *Mobile Applications ; Qualitative Research ; Surveys and Questionnaires ; }, abstract = {Introduction: The potential of mobile applications (apps) as a resource to support well-being in young people is hampered by low usage. Suggested reasons for this vary from technical issues to users' psychological and personal characteristics like gender, mood and perceptions on well-being. Objectives: To identify and understand predictive variables related to the use of well-being apps by young people in the context of the 'Online Wellbeing Centre' (OWC) Randomised Controlled Trial (a study assessing changes in well-being of young people who use well-being apps). Methods: A cross-sectional analysis using binary logistic regression was conducted, taking into account previous app usage of participants at baseline versus demographic, ecological momentary assessments, and well-being variables, of data collected in the OWC-RCT. To explore predictors further, follow-up post-RCT surveys were coded to better understand user's predisposition towards apps. Results: Mood (p < 0.006) and gender (p < 0.03) are significantly associated with the use of well-being apps. Female participants with elevated mood were more likely to use well-being apps before signing up into the study. Two themes were identified from participants at follow-up that related to the design of the app and engagement of the app user. Females were more likely to focus on the purpose of app, whereas males were more likely to focus on specific goals and features (e.g. tracking) offered by the app. Females were able to mention the link between well-being and app usage. Conclusion: Personal characteristics explain engagement with well-being apps, with mood and gender significant in the current sample. Further qualitative research may help identify other individual characteristics that explain why and how young people use well-being apps and the impact of these on a user's health.}, } @article {pmid35128811, year = {2022}, author = {Tahara, M and Ishimaru, T and Fujino, Y and Fushimi, K and Matsuda, S and Mukae, H and Yatera, K}, title = {A new scoring system for predicting in-hospital death after lung cancer surgery (the SABCIP score) using a Japanese nationwide administrative database.}, journal = {Thoracic cancer}, volume = {13}, number = {6}, pages = {870-875}, pmid = {35128811}, issn = {1759-7714}, mesh = {Aged ; Databases, Factual ; Hospital Mortality ; Humans ; Japan/epidemiology ; *Lung Neoplasms/surgery ; Male ; Retrospective Studies ; }, abstract = {BACKGROUND: We aimed to develop and validate a new risk scoring tool for predicting in-hospital mortality after lung cancer surgery.

METHODS: We retrospectively identified patients admitted for lung cancer surgery from a nationwide administrative database in Japan and randomly divided them into derivation and validation cohorts. In the derivation cohort, we performed logistic regression analysis to determine predictive variables and developed a risk scoring tool by proportionally weighting the regression coefficients and assigning points to each variable. In both cohorts, we evaluated the predictive performance of the score using the c-index and showed the in-hospital mortality at each risk score.

RESULTS: In total, 64 175 patients (32 170 and 32 005 patients in the derivation and validation cohort, respectively) were enrolled, including 115 (0.4%) and 119 (0.4%) in-hospital patient deaths in the derivation and validation cohorts, respectively. Following the multivariate regression analysis, we selected six variables to create the SABCIP score, a risk scoring tool named after the parameters on which it is based, namely male sex, age ≥ 75 years, body mass index <18.5, clinical stage ≥3, interstitial lung disease, and procedure type (sleeve resection, chest wall resection, or pneumonectomy). The c-index of the score was 0.82 and 0.80 in the derivation and validation cohorts, respectively, which represents a better or equal discrimination performance compared with previous scoring tools. In-hospital mortality increased as the score increased in both cohorts.

CONCLUSION: The SABCIP score is a simple and useful predictor of in-hospital mortality in patients after lung cancer surgery.}, } @article {pmid35127311, year = {2022}, author = {Arain, MA and Xu, B and Brodeur, JJ and Khomik, M and Peichl, M and Beamesderfer, E and Restrepo-Couple, N and Thorne, R}, title = {Heat and drought impact on carbon exchange in an age-sequence of temperate pine forests.}, journal = {Ecological processes}, volume = {11}, number = {1}, pages = {7}, pmid = {35127311}, issn = {2192-1709}, abstract = {BACKGROUND: Most North American temperate forests are plantation or regrowth forests, which are actively managed. These forests are in different stages of their growth cycles and their ability to sequester atmospheric carbon is affected by extreme weather events. In this study, the impact of heat and drought events on carbon sequestration in an age-sequence (80, 45, and 17 years as of 2019) of eastern white pine (Pinus strobus L.) forests in southern Ontario, Canada was examined using eddy covariance flux measurements from 2003 to 2019.

RESULTS: Over the 17-year study period, the mean annual values of net ecosystem productivity (NEP) were 180 ± 96, 538 ± 177 and 64 ± 165 g C m[-2] yr[-1] in the 80-, 45- and 17-year-old stands, respectively, with the highest annual carbon sequestration rate observed in the 45-year-old stand. We found that air temperature (Ta) was the dominant control on NEP in all three different-aged stands and drought, which was a limiting factor for both gross ecosystem productivity (GEP) and ecosystems respiration (RE), had a smaller impact on NEP. However, the simultaneous occurrence of heat and drought events during the early growing seasons or over the consecutive years had a significant negative impact on annual NEP in all three forests. We observed a similar trend of NEP decline in all three stands over three consecutive years that experienced extreme weather events, with 2016 being a hot and dry, 2017 being a dry, and 2018 being a hot year. The youngest stand became a net source of carbon for all three of these years and the oldest stand became a small source of carbon for the first time in 2018 since observations started in 2003. However, in 2019, all three stands reverted to annual net carbon sinks.

CONCLUSIONS: Our study results indicate that the timing, frequency and concurrent or consecutive occurrence of extreme weather events may have significant implications for carbon sequestration in temperate conifer forests in Eastern North America. This study is one of few globally available to provide long-term observational data on carbon exchanges in different-aged temperate plantation forests. It highlights interannual variability in carbon fluxes and enhances our understanding of the responses of these forest ecosystems to extreme weather events. Study results will help in developing climate resilient and sustainable forestry practices to offset atmospheric greenhouse gas emissions and improving simulation of carbon exchange processes in terrestrial ecosystem models.}, } @article {pmid35126486, year = {2022}, author = {Shi, L and Zhou, J and Zhou, X}, title = {Evaluation of Regional Ecological Efficiency and Intelligent Decision Support for Sustainable Development Based on Environmental Big Data.}, journal = {Computational intelligence and neuroscience}, volume = {2022}, number = {}, pages = {2820426}, pmid = {35126486}, issn = {1687-5273}, mesh = {Big Data ; China ; *Economic Development ; Ecosystem ; *Sustainable Development ; Urbanization ; }, abstract = {To promote urbanization in the next stage, it is of great significance to explore the ecological efficiency of green ecological regions and advance the sustainable development of a social economic system. However, spatial heterogeneity has not been fully considered in the existing evaluation models or methods for regional ecological efficiency (REE), and the corresponding decisions on sustainable development are not the optimal solutions. To solve the problems, this paper explores the evaluation of REE and intelligent decision support for sustainable development by analyzing environmental big data. Firstly, the spatiotemporal evolution of REE was examined based on environmental big data to clarify the spatial layout of REE and the sources of the spatial differences. Next, a multiobjective optimal decision-making model was established for the sustainable development of a regional ecosystem, and the solving method was presented for the model. The proposed model was proved valid through experiments.}, } @article {pmid35123321, year = {2022}, author = {Chitty, KM and Raubenheimer, J and Cairns, R and Kirby, KA and Buckley, NA}, title = {Deliberate self-poisoning in Australian adolescents is increased on school days.}, journal = {Journal of psychiatric research}, volume = {148}, number = {}, pages = {103-109}, doi = {10.1016/j.jpsychires.2022.01.045}, pmid = {35123321}, issn = {1879-1379}, mesh = {Adolescent ; Australia/epidemiology ; Female ; Humans ; Male ; Racial Groups ; Schools ; *Self-Injurious Behavior/epidemiology ; *Suicide, Attempted ; }, abstract = {Deliberate self-poisoning (DSP) in adolescents is increasing dramatically. Life at school is one of the most important life influences for this age group. This study aimed to investigate whether the frequency of DSP is higher during school term compared to holidays and whether this difference has become greater over time. This is an ecological study using Poisons Information Centre (PIC) data for all DSPs in 10-19 year olds from New South Wales, Tasmania and Australian Capital Territory that occurred between 2005 and 2018. For each call, the date of the poisoning was assigned as 'term' or 'holiday'. To control for population growth, calls were expressed as per 100,000 of the population per day. Multivariable Poisson regression was performed to investigate the combined impact of various predictors (state, sex, year, holiday/term, day of week, age) on call number. 26,432 calls were included in the analysis (73.6% female, 24.1% male and 2.3% unknown). Poisson regression showed significant effects for all predictors, with an increased likelihood of DSP during the school term compared with holidays and on Monday-Thursday compared with Saturday but only during the school term. DSP doubled between 2012 and 2017 and the disparity between DSP that occurs during term vs. holiday increased over that time frame. We conclude that some of the increase in DSP is likely due to school-specific stressors, hence the school environment is the ideal setting for self-harm prevention initiatives.}, } @article {pmid35122167, year = {2022}, author = {Gaddam, VK and Myneni, TK and Kulkarni, AV and Zhang, Y}, title = {Assessment of runoff in Chandra river basin of Western Himalaya using Remote Sensing and GIS Techniques.}, journal = {Environmental monitoring and assessment}, volume = {194}, number = {3}, pages = {145}, pmid = {35122167}, issn = {1573-2959}, mesh = {Climate Change ; Environmental Monitoring ; Geographic Information Systems ; Hydrology ; Remote Sensing Technology ; *Rivers ; *Snow ; }, abstract = {The runoff of Chandra river basin in the Himalayan India was assessed using a hydrological model combined with satellite remote sensing observations. During a test period between 2000 and 2015, in situ measurements of runoff and meteorological parameters were conducted in the glacial catchment areas of Sutridhaka and Chhotashigri. A good agreement was found between the observed and predicted runoff (correlation R[2] > 0.8). The hydrological model was then used to simulate the runoff of Chandra River for a period of 2000 to 2015. Almost 68% of the predicted runoff occurred during the ablation period (May to September). A sensitivity study of the Chandra basin hydrology to a predicted warming climate of 1 to 4 K, toward the end of the century suggests that increased production of glacial melt water would have more impact on runoff than potential increase in precipitation. During the monsoon months (of June to August), increased runoff is predicted due to enhanced glacial melting but the runoff in other months to be lower than present mean runoff, except for the summer months (March to July).}, } @article {pmid35120462, year = {2022}, author = {Shrestha, AMS and B Guiao, JE and R Santiago, KC}, title = {Assembly-free rapid differential gene expression analysis in non-model organisms using DNA-protein alignment.}, journal = {BMC genomics}, volume = {23}, number = {1}, pages = {97}, pmid = {35120462}, issn = {1471-2164}, mesh = {DNA ; *Gene Expression Profiling ; High-Throughput Nucleotide Sequencing ; Molecular Sequence Annotation ; RNA-Seq ; Sequence Analysis, RNA ; *Transcriptome ; }, abstract = {BACKGROUND: RNA-seq is being increasingly adopted for gene expression studies in a panoply of non-model organisms, with applications spanning the fields of agriculture, aquaculture, ecology, and environment. For organisms that lack a well-annotated reference genome or transcriptome, a conventional RNA-seq data analysis workflow requires constructing a de-novo transcriptome assembly and annotating it against a high-confidence protein database. The assembly serves as a reference for read mapping, and the annotation is necessary for functional analysis of genes found to be differentially expressed. However, assembly is computationally expensive. It is also prone to errors that impact expression analysis, especially since sequencing depth is typically much lower for expression studies than for transcript discovery.

RESULTS: We propose a shortcut, in which we obtain counts for differential expression analysis by directly aligning RNA-seq reads to the high-confidence proteome that would have been otherwise used for annotation. By avoiding assembly, we drastically cut down computational costs - the running time on a typical dataset improves from the order of tens of hours to under half an hour, and the memory requirement is reduced from the order of tens of Gbytes to tens of Mbytes. We show through experiments on simulated and real data that our pipeline not only reduces computational costs, but has higher sensitivity and precision than a typical assembly-based pipeline. A Snakemake implementation of our workflow is available at: https://bitbucket.org/project_samar/samar .

CONCLUSIONS: The flip side of RNA-seq becoming accessible to even modestly resourced labs has been that the time, labor, and infrastructure cost of bioinformatics analysis has become a bottleneck. Assembly is one such resource-hungry process, and we show here that it can be avoided for quick and easy, yet more sensitive and precise, differential gene expression analysis in non-model organisms.}, } @article {pmid35119923, year = {2022}, author = {Le Duc, D and Velluva, A and Cassatt-Johnstone, M and Olsen, RA and Baleka, S and Lin, CC and Lemke, JR and Southon, JR and Burdin, A and Wang, MS and Grunewald, S and Rosendahl, W and Joger, U and Rutschmann, S and Hildebrandt, TB and Fritsch, G and Estes, JA and Kelso, J and Dalén, L and Hofreiter, M and Shapiro, B and Schöneberg, T}, title = {Genomic basis for skin phenotype and cold adaptation in the extinct Steller's sea cow.}, journal = {Science advances}, volume = {8}, number = {5}, pages = {eabl6496}, pmid = {35119923}, issn = {2375-2548}, mesh = {Animals ; Cattle ; *Dugong ; Female ; Mammals ; Mice ; Phenotype ; }, abstract = {Steller's sea cow, an extinct sirenian and one of the largest Quaternary mammals, was described by Georg Steller in 1741 and eradicated by humans within 27 years. Here, we complement Steller's descriptions with paleogenomic data from 12 individuals. We identified convergent evolution between Steller's sea cow and cetaceans but not extant sirenians, suggesting a role of several genes in adaptation to cold aquatic (or marine) environments. Among these are inactivations of lipoxygenase genes, which in humans and mouse models cause ichthyosis, a skin disease characterized by a thick, hyperkeratotic epidermis that recapitulates Steller's sea cows' reportedly bark-like skin. We also found that Steller's sea cows' abundance was continuously declining for tens of thousands of years before their description, implying that environmental changes also contributed to their extinction.}, } @article {pmid35113936, year = {2022}, author = {Ilic-Zivojinovic, J and Krdzic, I and Jovanovic, A and Vukasinovic, D and Ilic, B and Gavrilovic, A and Soldatovic, I}, title = {Transcultural adaptation and validation of the Serbian version of the colorectal-specific quality of life questionnaire FACT-C.}, journal = {PloS one}, volume = {17}, number = {2}, pages = {e0263110}, pmid = {35113936}, issn = {1932-6203}, mesh = {*Adaptation, Physiological ; Aged ; Colorectal Neoplasms/*psychology/therapy ; Combined Modality Therapy ; *Cultural Characteristics ; Female ; Humans ; *Language ; Male ; *Quality of Life ; Reproducibility of Results ; Surveys and Questionnaires ; Translations ; }, abstract = {OBJECTIVE: Transcultural adaptation and validation of the FACT-C questionnaire to Serbian language.

METHODS: The study included 131 patients with colorectal cancer. Translation included standard forward and backward translation from original language to Serbian and back. Pilot testing of the questionnaire was conducted on 10 patients with diagnosed colorectal cancer. The questionnaires EORTC-QLQ-C30 and DASS will be used as validated tools to evaluate validity of examined, FACT-C questionnaire.

RESULTS: The FACT-C demonstrated satisfactory construct validity using Cronbach's alpha. Satisfactory concurrent validity was demonstrated using correlations with EORTC-QLQ-C30 and DASS questionnaires. High reproducibility was demonstrated using repeated questionnaires on 30 patients two weeks after the first interview.

CONCLUSION: The Serbian version of the FACT-C was demonstrated to have satisfactory applicability, reliability and validity in Serbian patients with colorectal cancer. It can be considered as a valid colorectal cancer specific health related quality of life tool for the Serbian population.}, } @article {pmid35107336, year = {2022}, author = {Liu, KT and Gong, YN and Huang, CG and Huang, PN and Yu, KY and Lee, HC and Lee, SC and Chiang, HJ and Kung, YA and Lin, YT and Hsiao, MJ and Huang, PW and Huang, SY and Wu, HT and Wu, CC and Kuo, RL and Chen, KF and Hung, CT and Oguntuyo, KY and Stevens, CS and Kowdle, S and Chiu, HP and Lee, B and Chen, GW and Shih, SR}, title = {Quantifying Neutralizing Antibodies in Patients with COVID-19 by a Two-Variable Generalized Additive Model.}, journal = {mSphere}, volume = {7}, number = {1}, pages = {e0088321}, pmid = {35107336}, issn = {2379-5042}, support = {MOST 109-2634-F-182-001//Ministry of Science and Technology, Taiwan (MOST)/ ; 110-2222-E-182-004//Ministry of Science and Technology, Taiwan (MOST)/ ; 1U01AI151698-01//HHS | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; 75N93021C00045/AI/NIAID NIH HHS/United States ; CORPG3K0241//Chang Gung Memorial Hospital (CGMH)/ ; CMRPG2H0323//Chang Gung Memorial Hospital (CGMH)/ ; 109-2221-E-182-043-MY2//Ministry of Science and Technology, Taiwan (MOST)/ ; 109-2314-B-182-036//MOST | Institute for Information Industry, Ministry of Science and Technology, Taiwan (III)/ ; U01 AI151698/AI/NIAID NIH HHS/United States ; HHSN272201400007C/AI/NIAID NIH HHS/United States ; }, mesh = {Antibodies, Neutralizing/*blood ; Biomarkers/blood ; COVID-19/blood/diagnosis/*immunology ; Case-Control Studies ; *Enzyme-Linked Immunosorbent Assay ; Humans ; *Models, Immunological ; *Models, Statistical ; Neutralization Tests/*methods ; Regression Analysis ; SARS-CoV-2/*immunology ; }, abstract = {Considering the urgent demand for faster methods to quantify neutralizing antibody titers in patients with coronavirus (CoV) disease 2019 (COVID-19), developing an analytical model or method to replace the conventional virus neutralization test (NT) is essential. Moreover, a "COVID-19 immunity passport" is currently being proposed as a certification for people who travel internationally. Therefore, an enzyme-linked immunosorbent assay (ELISA) was designed to detect severe acute respiratory syndrome CoV 2 (SARS-CoV-2)-neutralizing antibodies in serum, which is based on the binding affinity of SARS-CoV-2 viral spike protein 1 (S1) and the viral spike protein receptor-binding domain (RBD) to antibodies. The RBD is considered the major binding region of neutralizing antibodies. Furthermore, S1 covers the RBD and several other regions, which are also important for neutralizing antibody binding. In this study, we assessed 144 clinical specimens, including those from patients with PCR-confirmed SARS-CoV-2 infections and healthy donors, using both the NT and ELISA. The ELISA results analyzed by spline regression and the two-variable generalized additive model precisely reflected the NT value, and the correlation between predicted and actual NT values was as high as 0.917. Therefore, our method serves as a surrogate to quantify neutralizing antibody titer. The analytic method and platform used in this study present a new perspective for serological testing of SARS-CoV-2 infection and have clinical potential to assess vaccine efficacy. IMPORTANCE Herein, we present a new approach for serological testing for SARS-CoV-2 antibodies using innovative laboratory methods that demonstrate a combination of biology and mathematics. The traditional virus neutralization test is the gold standard method; however, it is time-consuming and poses a risk to medical personnel. Thus, there is a demand for methods that rapidly quantify neutralizing antibody titers in patients with COVID-19 or examine vaccine efficacy at a biosafety level 2 containment facility. Therefore, we used a two-variable generalized additive model to analyze the results of the enzyme-linked immunosorbent assay and found the method to serve as a surrogate to quantify neutralizing antibody titers. This methodology has potential for clinical use in assessing vaccine efficacy.}, } @article {pmid35104413, year = {2022}, author = {Zavarin, M and Chang, E and Wainwright, H and Parham, N and Kaukuntla, R and Zouabe, J and Deinhart, A and Genetti, V and Shipman, S and Bok, F and Brendler, V}, title = {Community Data Mining Approach for Surface Complexation Database Development.}, journal = {Environmental science & technology}, volume = {56}, number = {4}, pages = {2827-2838}, doi = {10.1021/acs.est.1c07109}, pmid = {35104413}, issn = {1520-5851}, mesh = {Adsorption ; *Carbonates ; Data Mining ; Databases, Factual ; *Minerals ; }, abstract = {This paper presents a comprehensive data-to-model workflow, including a findable, accessible, interoperable, reusable (FAIR) community sorption database (newly developed LLNL Surface Complexation/Ion Exchange (L-SCIE) database) along with a data fitting workflow to efficiently optimize surface complexation reaction constants with multiple surface complexation model (SCM) constructs. This workflow serves as a universal framework to mine, compile, and analyze large numbers of published sorption data as well as to estimate reaction constants for parameterizing reactive transport models. The framework includes (1) data digitization from published papers, (2) data unification including unit conversions, and (3) data-model integration and reaction constant estimation using geochemical software PHREEQC coupled with the universal parameter estimation code PEST. We demonstrate our approach using an analysis of U(VI) sorption to quartz based on a first L-SCIE implementation, concluding that a multisite SCM construct with carbonate surface species yielded the best fit to community data. Surface complexation reaction constants extracted from this approach captured all available sorption data available in the literature and provided insight into previously published reaction constants and surface complexation model constructs. The L-SCIE sorption database presented herein allows for automating this approach across a wide range of metals and minerals and implementing novel machine learning approaches to reactive transport in the future.}, } @article {pmid35101414, year = {2022}, author = {de Almeida, TM and Neto, IR and Consalter, R and Brum, FT and Rojas, EAG and da Costa-Ribeiro, MCV}, title = {Predictive modeling of sand fly distribution incriminated in the transmission of Leishmania (Viannia) braziliensis and the incidence of Cutaneous Leishmaniasis in the state of Paraná, Brazil.}, journal = {Acta tropica}, volume = {229}, number = {}, pages = {106335}, doi = {10.1016/j.actatropica.2022.106335}, pmid = {35101414}, issn = {1873-6254}, mesh = {Animals ; Brazil/epidemiology ; Incidence ; Insect Vectors ; *Leishmania braziliensis ; *Leishmaniasis, Cutaneous/epidemiology ; *Psychodidae ; }, abstract = {Southern Brazil concentrates a considerable number of cases of cutaneous leishmaniasis reported since 1980, and Paraná is the state that most records CL cases in the region. The main sand fly species incriminated as vectors of Leishmania (Viannia) braziliensis (Vianna,1911) are Migonemyia (Migonemyia) migonei (França, 1920), Nyssomyia (Nyssomyia) neivai (Pinto, 1926) and Nyssomyia (Nyssomyia) whitmani (Antunes & Coutinho, 1936). In this study, we evaluated areas with climatic suitability for the distribution of these vectors and correlated these data with CL incidence in the state. The occurrence points of Mg. migonei, Ny. neivai, and Ny. whitmani were extracted from a literature review and field data. For CL analysis in the state of Paraná, data were obtained from the Informatics Department of the Unified Health System of Brazil (DATASUS), covering the period from 2001 to 2019. The layers of bioclimatic variables from the WorldClim database were used in the study. Species distribution modeling was developed using the MaxEnt Software version 3.4.4. ArcGIS software version 10.5 was used to develop suitability maps and the graphical representation of disease incidence. The AUC values were acceptable for all models (> 0,8). Bioclimatic variables BIO13 and BIO14 were the most influential in the distribution of Mg. migonei, while BIO19 and BIO6 were the variables that most influenced the distribution of Ny. neivai, and Ny. whitmani was most influenced by variables BIO5 and BIO9. During 19 years, 4992 cases of CL were reported in the state by 286 municipalities (71,6%). Northern Paraná showed the highest number of areas with very high and high climatic suitability for the occurrence of these species, coinciding with the highest number of CL cases. The modeling tools allowed analyzing the association between climatic variables and the geographical distribution of CL in the state. Moreover, they provided a better understanding of the climatic conditions related to the distribution of different species, favoring the monitoring of risk areas, the implementation of preventive measures, risk awareness, early and accurate diagnosis, and consequent timely treatment.}, } @article {pmid35098917, year = {2022}, author = {Cunningham-Oakes, E and Trivett, H}, title = {Applied Bioinformatics and Public Health Microbiology: challenges, discoveries and innovations during a pandemic.}, journal = {Microbial genomics}, volume = {8}, number = {1}, pages = {}, pmid = {35098917}, issn = {2057-5858}, support = {/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Bacterial Infections/*epidemiology/microbiology/prevention & control ; COVID-19/*epidemiology/prevention & control/virology ; Computational Biology/*methods ; Humans ; Microbiological Techniques/*methods ; Public Health/*methods ; }, abstract = {The eighth Applied Bioinformatics and Public Health Microbiology (ABPHM) conference showcased the recent acceleration of bioinformatic approaches used in public health settings. This included approaches for the surveillance of infectious diseases, understanding microbial evolution and diversity and pathogen interactions. Overall, the meeting highlighted the importance of data-driven approaches used by scientists during the COVID-19 pandemic.}, } @article {pmid35098619, year = {2022}, author = {Shin, YJ and Midgley, GF and Archer, ERM and Arneth, A and Barnes, DKA and Chan, L and Hashimoto, S and Hoegh-Guldberg, O and Insarov, G and Leadley, P and Levin, LA and Ngo, HT and Pandit, R and Pires, APF and Pörtner, HO and Rogers, AD and Scholes, RJ and Settele, J and Smith, P}, title = {Actions to halt biodiversity loss generally benefit the climate.}, journal = {Global change biology}, volume = {28}, number = {9}, pages = {2846-2874}, pmid = {35098619}, issn = {1365-2486}, mesh = {Biodiversity ; Climate Change ; *Conservation of Natural Resources ; Ecosystem ; Humans ; *Quality of Life ; }, abstract = {The two most urgent and interlinked environmental challenges humanity faces are climate change and biodiversity loss. We are entering a pivotal decade for both the international biodiversity and climate change agendas with the sharpening of ambitious strategies and targets by the Convention on Biological Diversity and the United Nations Framework Convention on Climate Change. Within their respective Conventions, the biodiversity and climate interlinked challenges have largely been addressed separately. There is evidence that conservation actions that halt, slow or reverse biodiversity loss can simultaneously slow anthropogenic mediated climate change significantly. This review highlights conservation actions which have the largest potential for mitigation of climate change. We note that conservation actions have mainly synergistic benefits and few antagonistic trade-offs with climate change mitigation. Specifically, we identify direct co-benefits in 14 out of the 21 action targets of the draft post-2020 global biodiversity framework of the Convention on Biological Diversity, notwithstanding the many indirect links that can also support both biodiversity conservation and climate change mitigation. These relationships are context and scale-dependent; therefore, we showcase examples of local biodiversity conservation actions that can be incentivized, guided and prioritized by global objectives and targets. The close interlinkages between biodiversity, climate change mitigation, other nature's contributions to people and good quality of life are seldom as integrated as they should be in management and policy. This review aims to re-emphasize the vital relationships between biodiversity conservation actions and climate change mitigation in a timely manner, in support to major Conferences of Parties that are about to negotiate strategic frameworks and international goals for the decades to come.}, } @article {pmid35098469, year = {2022}, author = {Yuan, Q and Wu, H and Zhao, Y and Zhang, Y and Yao, R and Zhao, Y and Yang, W}, title = {Ecosystem health of the Beiyun River basin (Beijing, China) as evaluated by the method of combination of AHP and PCA.}, journal = {Environmental science and pollution research international}, volume = {29}, number = {26}, pages = {39116-39130}, pmid = {35098469}, issn = {1614-7499}, mesh = {*Analytic Hierarchy Process ; Beijing ; China ; *Ecosystem ; Environmental Monitoring ; Humans ; Principal Component Analysis ; }, abstract = {Ecosystem services provided by river ecosystems rely on healthy ecosystem structure and ecological processes. The Beijing-Tianjin-Hebei urban is a typical water-deficient area. As an important part of the urban-rural integration construction, evaluating the health status of the Beiyun River Basin and discovering the weak links in the water environment are the basis for improving the health of the basin. In this study, analytic hierarchy process (AHP) was used to establish an evaluation index system for the Beiyun River Basin from 5 aspects including water quality, biology, ecology, hydrology, and social functions, and the principal component analysis (PCA) was then used to assign weights to the index layer. The evaluation results showed that the health evaluation results of the Beiyun River Basin in 2019 are "sub-healthy," and the overall health status is getting worse from northwest to southeast. In the middle reaches of the region, the evaluation result is "healthy," followed by the upstream, and the downstream is the worst. The results showed that areas with less human interference or orderly intervention are in better health. High eutrophication level, low bio-diversity, and low vegetation coverage are the main indicators that leads to poor ecosystem health in the Beiyun River Basin. For the comprehensive management of the Beiyun River, the improvement of water quality and habitat ecological restoration are key actions to the health of the upstream ecosystem. The improvement of the health status of the downstream should focus on equal emphasis on water quality and quantity, restoration of biodiversity, and improvement of the quality of the riparian ecological environment.}, } @article {pmid35098379, year = {2022}, author = {Yao, S and Zheng, C and Wang, B and Chen, P}, title = {A two-step ensemble learning for predicting protein hot spot residues from whole protein sequence.}, journal = {Amino acids}, volume = {54}, number = {5}, pages = {765-776}, pmid = {35098379}, issn = {1438-2199}, support = {62072002//National Natural Science Foundation of China/ ; 61773360//National Natural Science Foundation of China/ ; 61672035//National Natural Science Foundation of China/ ; U19A2064//National Natural Science Foundation of China/ ; }, mesh = {Amino Acid Sequence ; Databases, Protein ; *Machine Learning ; Protein Binding ; *Proteins/chemistry ; }, abstract = {Protein hot spot residues are functional sites in protein-protein interactions. Biological experimental methods are traditionally used to identify hot spot residues, which is laborious and time-consuming. Thus a variety of computational methods were widely used in recent years. Despite the success of computational methods in hot spot identification, most of them are impractical in reality because they can recognize hot spot residues only from known protein-protein interface residues. Therefore, identifying hot spots from whole protein sequence is a meaningful and interesting issue. However, it will bring extreme imbalance between positive and negative samples. Hot spot residues only account for about 1-2% of whole protein sequences. To address the issue, this paper proposes a two-step ensemble model for identifying hot spot residues from extremely unbalanced data set. The model is composed of 134 classifiers constructed by base KNN and SVM. Compared to the previous methods, our model yields good performance with an F1 score of 0.593 on the BID test set. Furthermore, to validate the robustness of our model, it was tested on other three independent test sets and also achieved good predictions. More importantly, the performance of our model tested on unbalanced data set is comparable with other methods tested on balanced hot spot data set.}, } @article {pmid35096768, year = {2021}, author = {Jiao, Z and Yang, J and Long, X and Lu, Y and Guo, Z and Peng, Y and Huang, X and Yin, Y and Song, C and Zhang, P}, title = {CRISPR/Cas12a-Assisted Visual Logic-Gate Detection of Pathogenic Microorganisms Based on Water-Soluble DNA-Binding AIEgens.}, journal = {Frontiers in chemistry}, volume = {9}, number = {}, pages = {801972}, pmid = {35096768}, issn = {2296-2646}, abstract = {Here, we developed a rapid, visual and double-checked Logic Gate detection platform for detection of pathogenic microorganisms by aggregation-induced emission luminogens (AIEgens) in combination with Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/CRISPR associated (Cas). DNA light-up AIEgens (1,1,2,2-tetrakis[4-(2-bromo-ethoxy) phenyl]ethene, TTAPE) was non-emissive but the emission was turned on in the presence of large amount of DNA produced by recombinase polymerase amplification (RPA). When CRISPR/Cas12a was added, all long-stranded DNA were cut leading to the emission quenched. Thus, a method that can directly observe the emission changes with the naked eye has been successfully constructed. The detection is speedy within only 20 min, and has strong specificity to the target. The result can be judged by Logic Gate. Only when the output signal is (1,0), does it represent the presence of pathogenic microorganisms in the test object. Finally, the method was applied to the detect pathogenic microorganisms in environmental water samples, which proved that this method has high selectivity, specificity and applicability for the detection of pathogenic microorganisms in environmental water samples.}, } @article {pmid35087540, year = {2021}, author = {Wang, S and Han, Z and Turchini, GM and Wang, X and Fang, Z and Chen, N and Xie, R and Zhang, H and Li, S}, title = {Effects of Dietary Phospholipids on Growth Performance, Digestive Enzymes Activity and Intestinal Health of Largemouth Bass (Micropterus salmoides) Larvae.}, journal = {Frontiers in immunology}, volume = {12}, number = {}, pages = {827946}, pmid = {35087540}, issn = {1664-3224}, mesh = {Animals ; Bass/*physiology ; Computational Biology/methods ; *Dietary Supplements ; *Digestion ; Enzymes/*metabolism ; Gastrointestinal Microbiome ; Intestines/*physiology ; Larva ; Phospholipids/administration & dosage/*metabolism ; }, abstract = {While the beneficial roles of dietary phospholipids on health status and overall performances of fish larvae have been well demonstrated, the underlying mechanisms remain unclear. To address this gap, the present study was conducted to investigate the effects of dietary phospholipids on growth performance, intestinal development, immune response and microbiota of larval largemouth bass (Micropterus salmoides). Five isonitrogenous and isolipidic micro-diets were formulated to contain graded inclusion levels of phospholipids (1.69, 3.11, 5.23, 7.43 and 9.29%). Results showed that the supplementation of dietary phospholipids linearly improved the growth performance of largemouth bass larvae. The inclusion of dietary phospholipids increased the activity of digestive enzymes, such as lipase, trypsin and alkaline phosphatase, and promoted the expression of tight junction proteins including ZO-1, claudin-4 and claudin-5. Additionally, dietary phospholipids inclusion alleviated the accumulation of intestinal triacylglycerols, and further elevated the activity of lysozyme. Dietary phospholipids inhibited the transcription of some pro-inflammatory cytokines, including il-1β, and tnf-α, but promoted the expression of anti-inflammatory cytokines tgf-β, with these modifications being suggested to be mediated by the p38MAPK/Nf-κB pathway. The analysis of bacterial 16S rRNA V3-4 region indicated that the intestinal microbiota profile was significantly altered at the genus level with dietary phospholipids inclusion, including a decreased richness of pathogenic bacteria genera Klebsiella in larval intestine. In summary, it was showed that largemouth bass larvae have a specific requirement for dietary phospholipids, and this study provided novel insights on how dietary phospholipids supplementation contributes to improving the growth performance, digestive tract development and intestinal health.}, } @article {pmid35086564, year = {2022}, author = {Wu, D and Jin, L and Xie, J and Liu, H and Zhao, J and Ye, D and Li, XD}, title = {Inhalable antibiotic resistomes emitted from hospitals: metagenomic insights into bacterial hosts, clinical relevance, and environmental risks.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {19}, pmid = {35086564}, issn = {2049-2618}, mesh = {*Anti-Bacterial Agents/pharmacology ; Bacteria/genetics ; Genes, Bacterial ; Hospitals ; Humans ; *Metagenome/genetics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {BACKGROUND: Threats of antimicrobial resistance (AMR) to human health are on the rise worldwide. Airborne fine particulate matter (PM2.5), especially those emitted from hospitals, could serve as a substantial yet lesser-known environmental medium of inhalable antibiotic resistomes. A genome-centric understanding of the hosting bacterial taxa, mobility potential, and consequent risks of the resistomes is needed to reveal the health relevance of PM2.5-associated AMR from clinical settings.

RESULTS: Compared to urban ambient air PM2.5, the hospital samples harbored nearly twice the abundance of antibiotic resistantance genes (ARGs, ~ 0.2 log10(ARGs/16S rRNA gene)) in the summer and winter sampled. The profiled resistome was closely correlated with the human-source-influenced (~ 30% of the contribution) bacterial community (Procrustes test, P < 0.001), reflecting the potential antibiotic-resistant bacteria (PARB), such as the human commensals Staphylococcus spp. and Corynebacterium spp. Despite the reduced abundance and diversity of the assembled metagenomes from summer to winter, the high horizontal transfer potential of ARGs, such as the clinically relevant blaOXA and bacA, in the human virulent PARB remained unaffected in the hospital air PM samples. The occurring patterns of β-lactam resistance genes and their hosting genomes in the studied hospital-emitting PM2.5 were closely related to the in-ward β-lactam-resistant infections (SEM, std = 0.62, P < 0.01). Featured with more abundant potentially virulent PARB (2.89 genome copies/m[3]-air), the hospital samples had significantly higher resistome risk index scores than the urban ambient air samples, indicating that daily human exposure to virulent PARB via the inhalation of PM2.5 was ten times greater than from the ingestion of drinking water.

CONCLUSIONS: The significance of AMR in the studied hospital-emitting PM2.5 was highlighted by the greater abundance of ARGs, the prevalence of potentially virulent PARB, and the close association with hospital in-ward β-lactam infections. A larger-scale multi-source comparison of genome-resolved antibiotic resistomes is needed to provide a more holistic understanding to evaluate the importance of airborne AMR from the "One-Health" perspective. Video Abstract.}, } @article {pmid35082293, year = {2022}, author = {Fetters, AM and Cantalupo, PG and Wei, N and Robles, MTS and Stanley, A and Stephens, JD and Pipas, JM and Ashman, TL}, title = {The pollen virome of wild plants and its association with variation in floral traits and land use.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {523}, pmid = {35082293}, issn = {2041-1723}, mesh = {Amino Acid Sequence ; Animals ; Ecology ; Flowers ; Genome, Viral ; *Phenotype ; Phylogeny ; Plants/*virology ; Pollen/*virology ; Pollination ; Seeds ; *Virome/genetics ; Viruses/classification/genetics ; }, abstract = {Pollen is a unique vehicle for viral spread. Pollen-associated viruses hitchhike on or within pollen grains and are transported to other plants by pollinators. They are deposited on flowers and have a direct pathway into the plant and next generation via seeds. To discover the diversity of pollen-associated viruses and identify contributing landscape and floral features, we perform a species-level metagenomic survey of pollen from wild, visually asymptomatic plants, located in one of four regions in the United States of America varying in land use. We identify many known and novel pollen-associated viruses, half belonging to the Bromoviridae, Partitiviridae, and Secoviridae viral families, but many families are represented. Across the regions, species harbor more viruses when surrounded by less natural and more human-modified environments than the reverse, but we note that other region-level differences may also covary with this. When examining the novel connection between virus richness and floral traits, we find that species with multiple, bilaterally symmetric flowers and smaller, spikier pollen harbored more viruses than those with opposite traits. The association of viral diversity with floral traits highlights the need to incorporate plant-pollinator interactions as a driver of pollen-associated virus transport into the study of plant-viral interactions.}, } @article {pmid35077330, year = {2021}, author = {Praça, GM and Chagas, MH and Bredt, SGT and Andrade, AGP and Custódio, IJO and Rochael, M}, title = {The influence of the offside rule on players' positional dynamics in soccer small-sided games.}, journal = {Science & medicine in football}, volume = {5}, number = {2}, pages = {144-149}, doi = {10.1080/24733938.2020.1819559}, pmid = {35077330}, issn = {2473-4446}, mesh = {*Athletic Performance/physiology ; *Football ; Geographic Information Systems ; *Soccer/physiology ; *Space Flight ; }, abstract = {BACKGROUND: Previous studies on soccer small-sided games (SSGs) chose between with and without offside rule conditions without evidence-based criteria. The current study aimed to compare the positional dynamics of 3v3 SSGs with and without the offside rule.

METHODS: Twenty-four Brazilian U-17 national-level soccer players were recruited. They were split into eight teams and played SSGs with and without the offside rule . Positional data were gathered by a Global Positioning System, and teams' length, width, the length per width ratio (LPWratio), stretch index and players' spatial exploration index were calculated. Data were compared between the experimental conditions by a paired t-test.

RESULTS: Results showed that SSGs with the offside rule presented lower values of length (~16.63%, large effect), the LPWratio (~19.74%, large effect), and players' spatial exploration (~4.13%, small-to-moderate effect).

CONCLUSION: We conclude that the offside rule impacts players' positional behavior in SSGs, inducing a less exploratory behavior mainly in the width axis. For this reason, we recommend caution when interpreting previous results on SSG when the offside rule was not applied since adopting this rule might elicit different responses to the players . Coaches can manipulate this rule aiming to achieve specific tactical goals for the training session.}, } @article {pmid35073506, year = {2022}, author = {De Menezes, A and Nunes, AC and Pimenta, DN and Lotta, G and Nkya, T and Krieger, MM and Schall, B and Wenham, C}, title = {Examining the Intersection between Gender, Community Health Workers, and Vector Control Policies: A Text Mining Literature Review.}, journal = {The American journal of tropical medicine and hygiene}, volume = {106}, number = {3}, pages = {768-774}, pmid = {35073506}, issn = {1476-1645}, support = {218750/Z/19/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {*Community Health Workers ; Data Mining ; Delivery of Health Care ; Female ; Humans ; Male ; Policy ; Pregnancy ; *Text Messaging ; }, abstract = {Gender intersects with healthcare systems; this is equally true for arboviral vector control efforts. However, there is as yet no comprehensive analysis as to how vector control is gendered. Hence, our objective is to provide the first thematic scoping and spatial distribution of the literature on gender, community health workers, and vector control. The authors use a systematic review approach to collect the academic literature on gender, community health workers, and vector control in Web of Science, Scopus, and PubMed (7,367 articles). After applying the exclusion criteria, 2,812 articles were analyzed using machine learning techniques: text mining and quantitative text analysis. The authors use topic modeling to assess the thematic scope of the literature and analyze the spatial distribution of themes. Our results show that the literature's spatial scope is strongly represented by the global south as research was conducted mainly in Latin America, Africa, and Asia, places with greater incidence of vector-borne disease and with health systems, which incorporate community healthcare workers. However, there are significant spatial heterogeneities in where and how research is conducted. The topic analysis reveals that the literature predominantly considers issues of sex (e.g., pregnancy) and gender as it relates motherhood. Gendered considerations occur upon implementation of vector control policies, rather than being mainstreamed into their development and delivery. There is a need to deepen the analysis to allow for gendered aspects to be understood beyond binary sex differences and/or reproductive health.}, } @article {pmid35073313, year = {2022}, author = {Bogdanowski, A and Banitz, T and Muhsal, LK and Kost, C and Frank, K}, title = {McComedy: A user-friendly tool for next-generation individual-based modeling of microbial consumer-resource systems.}, journal = {PLoS computational biology}, volume = {18}, number = {1}, pages = {e1009777}, pmid = {35073313}, issn = {1553-7358}, mesh = {Computational Biology/*methods ; *Microbiota ; Software ; *User-Computer Interface ; }, abstract = {Individual-based modeling is widely applied to investigate the ecological mechanisms driving microbial community dynamics. In such models, the population or community dynamics emerge from the behavior and interplay of individual entities, which are simulated according to a predefined set of rules. If the rules that govern the behavior of individuals are based on generic and mechanistically sound principles, the models are referred to as next-generation individual-based models. These models perform particularly well in recapitulating actual ecological dynamics. However, implementation of such models is time-consuming and requires proficiency in programming or in using specific software, which likely hinders a broader application of this powerful method. Here we present McComedy, a modeling tool designed to facilitate the development of next-generation individual-based models of microbial consumer-resource systems. This tool allows flexibly combining pre-implemented building blocks that represent physical and biological processes. The ability of McComedy to capture the essential dynamics of microbial consumer-resource systems is demonstrated by reproducing and furthermore adding to the results of two distinct studies from the literature. With this article, we provide a versatile tool for developing next-generation individual-based models that can foster understanding of microbial ecology in both research and education.}, } @article {pmid35072879, year = {2022}, author = {Li, D and Huai, W and Guo, Y and Liu, M}, title = {Flow characteristics in partially vegetated channel with homogeneous and heterogeneous layouts.}, journal = {Environmental science and pollution research international}, volume = {29}, number = {25}, pages = {38186-38197}, pmid = {35072879}, issn = {1614-7499}, support = {52020105006//National Natural Science Foundation of China/ ; 11872285//National Natural Science Foundation of China/ ; 2018HLG01//Open Funding of State Key Laboratory of Water Resources and Hydropower Engineering Science (WRHES), Wuhan University/ ; }, mesh = {*Rivers ; }, abstract = {This study presents the experimental results of the flow characteristics, such as the flow adjustment, velocity profiles, mixing layer, and the momentum exchange, in the partially vegetated channel with homogeneous and heterogeneous layouts. Three cases are considered, including two homogeneous canopies with uniform sparse and dense vegetation patches respectively, and a heterogeneous canopy consisting of alternating patches of both densities. Results show that heterogeneous canopy requires a longer adjustment distance to reach the quasi-equilibrium region, compared with the homogenous canopy of the same density. In heterogeneous canopy flow, the mixing layer width and the momentum thickness fluctuates with the alternation of vegetation density. The increased values for these two parameters compared to those values for the homogeneous canopies indicate that the greater resistance and momentum loss occur for the heterogeneous layout. A wavy region of the enhanced in-plane turbulence kinetic energy (TKE) is observed in the heterogeneous canopy, suggesting a comparatively more chaotic flow condition, whereas the contours of in-plane TKE are smooth in homogeneous canopies. The presence of the coherent structures in heterogeneous canopy is identified by spectral analysis and the quasi-periodic fluctuations of velocities. The Reynolds stress associated with the coherent structures is found to be the dominator of the contribution to the total Reynolds stress. The comparison between the homogenous canopies of different density is also conducted. These results will be of practical importance for the design of vegetation layouts in water ecological restoration projects and for river management.}, } @article {pmid35072653, year = {2021}, author = {Leskanicova, A and Babincak, M and Mochnacky, F and Pipova Kokosova, N and Kukelova, D and Urbanska, N and Kolesarova, M and Macekova, D and Kostolny, J and Kiskova, T}, title = {Sex-dependent differences in stress-induced depression in Wistar rats are accompanied predominantly by changes in phosphatidylcholines and sphingomyelins.}, journal = {Journal of physiology and pharmacology : an official journal of the Polish Physiological Society}, volume = {72}, number = {4}, pages = {}, doi = {10.26402/jpp.2021.4.14}, pmid = {35072653}, issn = {1899-1505}, mesh = {Animals ; *COVID-19 ; Depression ; Female ; Humans ; Male ; Phosphatidylcholines ; Pregnancy ; Rats ; Rats, Wistar ; SARS-CoV-2 ; *Sphingomyelins ; }, abstract = {With a high annual and lifetime prevalence, depression is becoming the leading contributor to the global disease burden. During the COVID-19 crisis, the depression and mood disorders accelerated significantly. Despite the growing evidence, the precise underlying mechanisms of depression disorders (DD) remain unknown. When studying DD in humans, there are many uncontrollable factors such as medication history, age of the patient or living conditions. In this regard, animal models provide an essential step for examining neural circuitry or molecular and cellular pathways in a controlled environment. As far as we know, women have a consistently higher prevalence of DD than men. Thus, the aim of our study was to evaluate sex-related changes in blood metabolites in a model of stress-induced depression in Wistar rats. Pregnant females were stressed using restriction of mobility in the final week of the pregnancy three times a day for 45 minutes each, three following days. After the birth, the progeny aged 60 days was stressed repeatedly. The perturbation in overall energy metabolism as well as in lipid metabolism was found. While in males, phosphatidylcholines (the most phosphatidylcholine with acyl-alkyl residue sum C40:4 - PC ae C40:4), sphingomyelins, and acylcarnitines were changed, in females, lipid metabolism perturbation was seen with the most critical alteration in hydroxysphingomyelin with acyl residue sum C16:1 (SM OH C16:1). Our results confirm that the animal model may be used further in the research of depression. Our results may provide an essential insight into the sex-dependent pathogenesis of depression and contribute to the search for effective treatment and prevention of depression with respect to sex.}, } @article {pmid35071799, year = {2021}, author = {Boyes, D and Crowley, L and Holland, PWH and , and , and , and , and , and , }, title = {The genome sequence of the spectacle, Abrostola tripartita Hufnagel, 1766.}, journal = {Wellcome open research}, volume = {6}, number = {}, pages = {330}, pmid = {35071799}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual male Abrostola tripartita (the spectacle; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 381 megabases in span. The majority of the assembly (99.99%) is scaffolded into 31 chromosomal pseudomolecules, with the Z sex chromosome assembled.}, } @article {pmid35064124, year = {2022}, author = {Krueger, CJ and Janzen, FJ}, title = {ROSIE, a database of reptilian offspring sex ratios and sex-determining mechanisms, beginning with Testudines.}, journal = {Scientific data}, volume = {9}, number = {1}, pages = {22}, pmid = {35064124}, issn = {2052-4463}, support = {1744592//National Science Foundation (NSF)/ ; }, mesh = {Animals ; Databases, Factual ; Ecology ; Sex Determination Processes ; *Sex Ratio ; Temperature ; *Turtles ; }, abstract = {In contrast to genotypic sex determination (GSD), temperature-dependent sex determination (TSD) in amniotic vertebrates eludes intuitive connections to Fisherian sex-ratio theory. Attempts to draw such connections have driven over 50 years of research on the evolution of sex-determining mechanisms (SDM), perhaps most prominently among species in the order Testudines. Despite regular advancements in our understanding of this topic, no efforts have been published compiling the entirety of data on the relationships between incubation temperature and offspring sex in any taxonomic group. Here, we present the Reptilian Offspring Sex and Incubation Environment (ROSIE) database, a comprehensive set of over 7,000 individual measurements of offspring sex ratios in the order Testudines as well as SDM classifications for 149 species. As the name suggests, we plan to expand the taxonomic coverage of ROSIE to include all non-avian reptiles and will regularly release updates to maintain its comprehensive nature. This resource will enable crucial future research probing the ecology and evolution of SDM, including the presumed sensitivity of TSD to rapid environmental change.}, } @article {pmid35063580, year = {2022}, author = {Becerra, AG and Gutiérrez, M and Lahoz-Beltra, R}, title = {Computing within bacteria: Programming of bacterial behavior by means of a plasmid encoding a perceptron neural network.}, journal = {Bio Systems}, volume = {213}, number = {}, pages = {104608}, doi = {10.1016/j.biosystems.2022.104608}, pmid = {35063580}, issn = {1872-8324}, mesh = {Bacteria/genetics ; Biotechnology ; Humans ; *Neural Networks, Computer ; Plasmids/genetics ; *Synthetic Biology ; }, abstract = {In nature, bacteria exhibit a limited repertoire of behaviors in response to environmental changes. Synthetic biology has now opened up the possibility of programming cells or unicellular organisms in order to enable them to perform certain tasks, which would allow the programming of 'intelligent' bacteria. Many of the theoretical ideas that Liberman proposed last century, for example his seminal idea that a cell is a computer, are now being put into practice with bacterial colonies in both wet and in silico experiments.These bacteria may one day be used to solve a wide range of problems whose solution requires their adaptation to external changes either within a bioreactor, organ or tissue of a patient or through the design of microbial-synthetic consortia oriented to their use in bioprocesses to produce medicines, biofuels or biomaterials. In this work, we show the possibility of programming synthetic bacteria with a previously trained perceptron neural network. First, we illustrate how a colony of bacteria endowed with a perceptron is able to solve an optimization problem in silico. Secondly, we study by means of in silico simulations how a perceptron can be applied to program behaviors in bacteria leading to social interactions and to the formation of complex communities that in the future would be useful in biotechnology. Finally, we go a step further, and study how the above perceptron designed to program bacterial behavior is implemented in a genetic circuit designed for this purpose. Once the genetic circuit was obtained, it was engineered into a plasmid.}, } @article {pmid35062523, year = {2022}, author = {Zhu, L and Boissy, P and Duval, C and Zou, G and Jog, M and Montero-Odasso, M and Speechley, M}, title = {How Long Should GPS Recording Lengths Be to Capture the Community Mobility of An Older Clinical Population? A Parkinson's Example.}, journal = {Sensors (Basel, Switzerland)}, volume = {22}, number = {2}, pages = {}, pmid = {35062523}, issn = {1424-8220}, support = {200907AMG-208147-AML-CFEB-56596/CAPMC/CIHR/Canada ; Ontario Graduate Scholarship//Government of Ontario/ ; Joseph Scott Studentship//Parkwood Hospital/ ; }, mesh = {Aged ; Geographic Information Systems ; Humans ; *Parkinson Disease/diagnosis ; *Wearable Electronic Devices ; }, abstract = {Wearable global position system (GPS) technology can help those working with older populations and people living with movement disorders monitor and maintain their mobility level. Health research using GPS often employs inconsistent recording lengths due to the lack of a standard minimum GPS recording length for a clinical context. Our work aimed to recommend a GPS recording length for an older clinical population. Over 14 days, 70 older adults with Parkinson's disease wore the wireless inertial motion unit with GPS (WIMU-GPS) during waking hours to capture daily "time outside", "trip count", "hotspots count" and "area size travelled". The longest recording length accounting for weekend and weekdays was ≥7 days of ≥800 daily minutes of data (14 participants with 156, 483.9 min recorded). We compared the error rate generated when using data based on recording lengths shorter than this sample. The smallest percentage errors were observed across all outcomes, except "hotspots count", with daily recordings ≥500 min (8.3 h). Eight recording days will capture mobility variability throughout days of the week. This study adds empirical evidence to the sensor literature on the required minimum duration of GPS recording.}, } @article {pmid35061792, year = {2022}, author = {Guo, Z and Lv, L and Liu, D and He, X and Wang, W and Feng, Y and Islam, MS and Wang, Q and Chen, W and Liu, Z and Wu, S and Abied, A}, title = {A global meta-analysis of animal manure application and soil microbial ecology based on random control treatments.}, journal = {PloS one}, volume = {17}, number = {1}, pages = {e0262139}, pmid = {35061792}, issn = {1932-6203}, mesh = {Animals ; Bacteria/genetics/isolation & purification ; Betaproteobacteria/genetics/isolation & purification ; Biomass ; Databases, Factual ; Fungi/genetics/isolation & purification ; Manure/*analysis/microbiology ; RNA, Ribosomal, 16S/genetics/metabolism ; RNA, Ribosomal, 18S/genetics/metabolism ; *Soil Microbiology ; }, abstract = {The processes involved in soil domestication have altered the soil microbial ecology. We examined the question of whether animal manure application affects the soil microbial ecology of farmlands. The effects of global animal manure application on soil microorganisms were subjected to a meta-analysis based on randomized controlled treatments. A total of 2303 studies conducted in the last 30 years were incorporated into the analysis, and an additional 45 soil samples were collected and sequenced to obtain 16S rRNA and 18S rRNA data. The results revealed that manure application increased soil microbial biomass. Manure application alone increased bacterial diversity (M-Z: 7.546 and M-I: 8.68) and inhibited and reduced fungal diversity (M-Z: -1.15 and M-I: -1.03). Inorganic fertilizer replaced cattle and swine manure and provided nutrients to soil microorganisms. The soil samples of the experimental base were analyzed, and the relative abundances of bacteria and fungi were altered compared with no manure application. Manure increased bacterial diversity and reduced fungal diversity. Mrakia frigida and Betaproteobacteriales, which inhibit other microorganisms, increased significantly in the domesticated soil. Moreover, farm sewage treatments resulted in a bottleneck in the manure recovery rate that should be the focus of future research. Our results suggest that the potential risks of restructuring the microbial ecology of cultivated land must be considered.}, } @article {pmid35059459, year = {2022}, author = {Ahmed, S and Ibrahim, M and Nantasenamat, C and Nisar, MF and Malik, AA and Waheed, R and Ahmed, MZ and Ojha, SC and Alam, MK}, title = {Pragmatic Applications and Universality of DNA Barcoding for Substantial Organisms at Species Level: A Review to Explore a Way Forward.}, journal = {BioMed research international}, volume = {2022}, number = {}, pages = {1846485}, pmid = {35059459}, issn = {2314-6141}, mesh = {Arabidopsis/*genetics ; *Bacteria/classification/genetics ; *DNA Barcoding, Taxonomic ; DNA, Bacterial/*genetics ; DNA, Fungal/*genetics ; DNA, Plant/*genetics ; *Fungi/classification/genetics ; }, abstract = {DNA barcodes are regarded as hereditary succession codes that serve as a recognition marker to address several queries relating to the identification, classification, community ecology, and evolution of certain functional traits in organisms. The mitochondrial cytochrome c oxidase 1 (CO1) gene as a DNA barcode is highly efficient for discriminating vertebrate and invertebrate animal species. Similarly, different specific markers are used for other organisms, including ribulose bisphosphate carboxylase (rbcL), maturase kinase (matK), transfer RNA-H and photosystem II D1-ApbsArabidopsis thaliana (trnH-psbA), and internal transcribed spacer (ITS) for plant species; 16S ribosomal RNA (16S rRNA), elongation factor Tu gene (Tuf gene), and chaperonin for bacterial strains; and nuclear ITS for fungal strains. Nevertheless, the taxon coverage of reference sequences is far from complete for genus or species-level identification. Applying the next-generation sequencing approach to the parallel acquisition of DNA barcode sequences could greatly expand the potential for library preparation or accurate identification in biodiversity research. Overall, this review articulates on the DNA barcoding technology as applied to different organisms, its universality, applicability, and innovative approach to handling DNA-based species identification.}, } @article {pmid35058458, year = {2022}, author = {van Woesik, R and Kratochwill, C}, title = {A global coral-bleaching database, 1980-2020.}, journal = {Scientific data}, volume = {9}, number = {1}, pages = {20}, pmid = {35058458}, issn = {2052-4463}, support = {OCE 1829393//National Science Foundation (NSF)/ ; OCE 1829393//National Science Foundation (NSF)/ ; }, mesh = {Animals ; *Anthozoa ; Coral Reefs ; Databases, Factual ; *Ecosystem ; Symbiosis ; Temperature ; }, abstract = {Coral reefs are the world's most diverse marine ecosystems that provide resources and services that benefit millions of people globally. Yet, coral reefs have recently experienced an increase in the frequency and intensity of thermal-stress events that are causing coral bleaching. Coral bleaching is a result of the breakdown of the symbiosis between corals and their symbiotic microalgae, causing the loss of pigments and symbionts, giving corals a pale, bleached appearance. Bleaching can be temporary or fatal for corals, depending on the species, the geographic location, historical conditions, and on local and regional influences. Indeed, marine heat waves are the greatest threat to corals worldwide. Here we compile a Global Coral-Bleaching Database (GCBD) that encompasses 34,846 coral bleaching records from 14,405 sites in 93 countries, from 1980-2020. The GCBD provides vital information on the presence or absence of coral bleaching along with site exposure, distance to land, mean turbidity, cyclone frequency, and a suite of sea-surface temperature metrics at the times of survey.}, } @article {pmid35057511, year = {2022}, author = {Barchitta, M and Maugeri, A and Favara, G and Magnano San Lio, R and Riela, PM and Guarnera, L and Battiato, S and Agodi, A}, title = {Development of a Web-App for the Ecological Momentary Assessment of Dietary Habits among College Students: The HEALTHY-UNICT Project.}, journal = {Nutrients}, volume = {14}, number = {2}, pages = {}, pmid = {35057511}, issn = {2072-6643}, support = {PIAno di inCEntivi per la RIcerca di Ateneo 2020/2022//University of Catania/ ; }, mesh = {Adult ; Diet/*methods ; Ecological Momentary Assessment/*statistics & numerical data ; *Feeding Behavior ; Female ; *Health Behavior ; Humans ; Italy ; Male ; *Mobile Applications ; Pilot Projects ; Program Development/*methods ; Students/statistics & numerical data ; Surveys and Questionnaires ; Universities ; Young Adult ; }, abstract = {The transition from adolescence to adulthood is a critical period for the development of healthy behaviors. Yet, it is often characterized by unhealthy food choices. Considering the current pandemic scenario, it is also essential to assess the effects of coronavirus disease-19 (COVID-19) on lifestyles and diet, especially among young people. However, the assessment of dietary habits and their determinants is a complex issue that requires innovative approaches and tools, such as those based on the ecological momentary assessment (EMA). Here, we describe the first phases of the "HEALTHY-UNICT" project, which aimed to develop and validate a web-app for the EMA of dietary data among students from the University of Catania, Italy. The pilot study included 138 students (mean age 24 years, SD = 4.2; 75.4% women), who used the web-app for a week before filling out a food frequency questionnaire with validation purposes. Dietary data obtained through the two tools showed moderate correlations, with the lowest value for butter and margarine and the highest for pizza (Spearman's correlation coefficients of 0.202 and 0.699, respectively). According to the cross-classification analysis, the percentage of students classified into the same quartile ranged from 36.9% for vegetable oil to 58.1% for pizza. In line with these findings, the weighted-kappa values ranged from 0.15 for vegetable oil to 0.67 for pizza, and most food categories showed values above 0.4. This web-app showed good usability among students, assessed through a 19-item usability scale. Moreover, the web-app also had the potential to evaluate the effect of the COVID-19 pandemic on students' behaviors and emotions, showing a moderate impact on sedentary activities, level of stress, and depression. These findings, although interesting, might be confirmed by the next phases of the HEALTHY-UNICT project, which aims to characterize lifestyles, dietary habits, and their relationship with anthropometric measures and emotions in a larger sample of students.}, } @article {pmid35055095, year = {2022}, author = {Yuan, Y and Zhang, M and Li, J and Yang, C and Abubakar, YS and Chen, X and Zheng, W and Wang, Z and Zheng, H and Zhou, J}, title = {The Small GTPase FgRab1 Plays Indispensable Roles in the Vegetative Growth, Vesicle Fusion, Autophagy and Pathogenicity of Fusarium graminearum.}, journal = {International journal of molecular sciences}, volume = {23}, number = {2}, pages = {}, pmid = {35055095}, issn = {1422-0067}, support = {31870136//National Natural Science Foundation of China/ ; 31670142//National Natural Science Foundation of China/ ; 2020J06047//Natural Science Foundation of Fujian Province/ ; }, mesh = {Autophagy/*genetics ; Computational Biology/methods ; Disease Susceptibility ; Endoplasmic Reticulum/metabolism ; Fusarium/classification/*physiology ; Genomics/methods ; Golgi Apparatus/metabolism ; Host-Pathogen Interactions ; Phenotype ; Phylogeny ; Plant Diseases/*microbiology ; Protein Transport ; Virulence ; rab1 GTP-Binding Proteins/*genetics/metabolism ; }, abstract = {Rab GTPases are key regulators of membrane and intracellular vesicle transports. However, the biological functions of FgRab1 are still unclear in the devastating wheat pathogen Fusarium graminearum. In this study, we generated constitutively active (CA) and dominant-negative (DN) forms of FgRAB1 from the wild-type PH-1 background for functional analyses. Phenotypic analyses of these mutants showed that FgRab1 is important for vegetative growth, cell wall integrity and hyphal branching. Compared to the PH-1 strain, the number of spores produced by the Fgrab1DN strain was significantly reduced, with obviously abnormal conidial morphology. The number of septa in the conidia of the Fgrab1DN mutant was fewer than that observed in the PH-1 conidia. Fgrab1DN was dramatically reduced in its ability to cause Fusarium head blight symptoms on wheat heads. GFP-FgRab1 was observed to partly localize to the Golgi apparatus, endoplasmic reticulum and Spitzenkörper. Furthermore, we found that FgRab1 inactivation blocks not only the transport of the v-SNARE protein FgSnc1 from the Golgi to the plasma membrane but also the fusion of endocytic vesicles with their target membranes and general autophagy. In summary, our results indicate that FgRab1 plays vital roles in vegetative growth, conidiogenesis, pathogenicity, autophagy, vesicle fusion and trafficking in F. graminearum.}, } @article {pmid35054796, year = {2022}, author = {Yamagata, M}, title = {Towards Tabula Gallus.}, journal = {International journal of molecular sciences}, volume = {23}, number = {2}, pages = {}, pmid = {35054796}, issn = {1422-0067}, mesh = {Animals ; Biological Evolution ; Chick Embryo ; Chickens/genetics/*physiology ; Computational Biology ; Connectome ; Epigenesis, Genetic ; Transcriptome/genetics ; }, abstract = {The Tabula Gallus is a proposed project that aims to create a map of every cell type in the chicken body and chick embryos. Chickens (Gallus gallus) are one of the most recognized model animals that recapitulate the development and physiology of mammals. The Tabula Gallus will generate a compendium of single-cell transcriptome data from Gallus gallus, characterize each cell type, and provide tools for the study of the biology of this species, similar to other ongoing cell atlas projects (Tabula Muris and Tabula Sapiens/Human Cell Atlas for mice and humans, respectively). The Tabula Gallus will potentially become an international collaboration between many researchers. This project will be useful for the basic scientific study of Gallus gallus and other birds (e.g., cell biology, molecular biology, developmental biology, neuroscience, physiology, oncology, virology, behavior, ecology, and evolution). It will eventually be beneficial for a better understanding of human health and diseases.}, } @article {pmid35049824, year = {2022}, author = {Götz, S and Raoult, CMC and Reiter, K and Wensch-Dorendorf, M and von Borell, E}, title = {Lying, Feeding and Activity Preference of Weaned Piglets for LED-Illuminated vs. Dark Pen Compartments.}, journal = {Animals : an open access journal from MDPI}, volume = {12}, number = {2}, pages = {}, pmid = {35049824}, issn = {2076-2615}, support = {820 204//Landwirtschaftliche Rentenbank/ ; }, abstract = {Little is known on the effect of light on pig behaviour. The choice behaviour of weaned piglets kept under two different light-emitting diode (LED) illuminance levels was investigated: 32 piglets (in two batches) were housed in a preference test room composed of two identical double pen units. One side of the pen unit was permanently illuminated with 600 lux, while the other was darkened to almost 0 lux (~0 lx); by using a passageway, piglets could move between the two sides. The "lying", "eating" and "activity" behaviours were evaluated during three days in the first, third and fifth experimental week based on video recordings and a 5-min time sampling method. At first, piglets preferred to stay in the 600 lux illuminated compartments. Then, this preference decreased for the "eating" and "activity" behaviours and reversed for the "lying" behaviour, with the darkened compartments being preferred. The results also show that pen soiling was higher under 600 lux, but feed consumption was not affected by the illuminance. Since pigs choose between the two illuminance levels to perform specific behaviours, illuminance could be used to divide the pens into functional areas and, thus, help in meeting pigs' behavioural needs.}, } @article {pmid35045851, year = {2022}, author = {Okui, T and Park, J}, title = {Analysis of regional differences in the amount of hypnotic and anxiolytic prescriptions in Japan using nationwide claims data.}, journal = {BMC psychiatry}, volume = {22}, number = {1}, pages = {44}, pmid = {35045851}, issn = {1471-244X}, mesh = {Adult ; *Anti-Anxiety Agents/therapeutic use ; Databases, Factual ; Drug Prescriptions ; Humans ; Hypnotics and Sedatives/therapeutic use ; Japan ; }, abstract = {BACKGROUND: In Japan, there has been no investigation of regional differences in the number or amount of prescriptions of anxiolytics or hypnotics. Attributes related to the high amount of prescriptions for these drugs are unknown. We investigated recent trends and regional differences in the amount of prescriptions of hypnotics and anxiolytics in Japan and identified factors associated with these regional differences.

METHODS: The National Database of Health Insurance Claims and Specific Health Checkups of Japan (NDB) Open data from 2015 to 2018 were used. We calculated diazepam-equivalent doses (mg) for each drug and the total amount of prescriptions per capita for hypnotics and anxiolytics by sex and age. In addition, we calculated the standardized claim ratio (SCR) of the amount of prescriptions by prefecture. We investigated factors associated with regional differences in the SCRs of hypnotics and anxiolytics using the prefectures' medical, socioeconomic, and physical characteristics by an ecological study using a linear mixed-effects model.

RESULTS: The amount of prescriptions of hypnotics and anxiolytics, specifically, the amount of prescriptions of benzodiazepine receptor agonists (BZRAs), decreased in many of the adult age groups from 2015 to 2018. The regression analysis revealed that the number of medical clinics per capita, the number of public assistance recipients per capita, the proportion of persons whose HbA1c ≥ 6.5%, and the proportion of persons whose BMI ≥25 kg/m[2] were positively and significantly associated with the SCR of hypnosis. In contrast, the number of public assistance recipients per capita and the proportion of persons whose BMI ≥25 kg/m[2] were positively and significantly associated with the SCR of anxiolytics.

CONCLUSIONS: Factors associated with prescription amount of hypnotics and anxiolytics were revealed in this study, and a further study is needed for investigating causal relationships between the prescriptions amount and the associated factors using individual data.}, } @article {pmid35043296, year = {2022}, author = {Chen, Y and Xiong, K and Ren, X and Cheng, C}, title = {An overview of ecological vulnerability: a bibliometric analysis based on the Web of Science database.}, journal = {Environmental science and pollution research international}, volume = {29}, number = {9}, pages = {12984-12996}, pmid = {35043296}, issn = {1614-7499}, mesh = {*Bibliometrics ; China ; Databases, Factual ; *Efficiency ; }, abstract = {Ecological vulnerability has become one of the hot issues of ecology and environmental science under global change and sustainable development scenarios. However, no study quantitatively analyzes the global scientific performance and hot research areas in this field by adopting the bibliometric method. Based on 935 pieces of literature retrieved from the Web of Science database, we comprehensively analyzed the research on ecological vulnerability in terms of growth trend, research content, publication journal and country, and co-occurrence network of keywords. The results showed that research on ecological vulnerability had experienced rapid growth since 2000, while ecological vulnerability research at the World Heritage sites was still embryonic. The top two productive countries in ecological vulnerability research were America and China, and the top two productive journals were Ecological Indicators and Regional Environmental Change. Study on ecological vulnerability was mainly classified as empirical evaluation and regional synthesis, whereas theoretical research is rare. Based on the summary of the main progress and achievements in ecological vulnerability research, we proposed five scientific issues that remain to be resolved in the field of ecological vulnerability. Overall, this study could shed light on a comprehensive and systematic understanding of ecological vulnerability and provide directions for future research on ecological vulnerability in a rapidly changing world.}, } @article {pmid35042937, year = {2022}, author = {Luo, Q and Chen, Z and Xu, T and Huang, D and Hou, H and Hong, C and Zhan, F and Guo, H and Lin, Z and Guo, X and Chen, L and Ji, ZL}, title = {Construction of integrative transcriptome to boost systematic exploration of Bougainvillea.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {923}, pmid = {35042937}, issn = {2045-2322}, mesh = {Computational Biology/methods ; Flowers/genetics ; Gene Expression/genetics ; Gene Expression Profiling/*methods ; Gene Expression Regulation, Plant/genetics ; Genome/genetics ; Genomics/methods ; Nyctaginaceae/*genetics ; Sequence Analysis, RNA/methods ; Transcriptome/*genetics ; }, abstract = {Members of the genus Bougainvillea are rich sources of natural dyes, pigments, and traditional medicines. They are also commonly used as ornamentals in roadside landscape construction. However, the horticultural development of Bougainvillea flowers with extended growth periods and coloration is not always feasible. One reason is limited molecular knowledge and no genomic information for Bougainvillea. Here, we compiled an integrative transcriptome of all expressed transcripts for Bougainvillea × buttiana Miss Manila by integrating 20 Illumina-sequencing RNA transcriptomes. The integrative transcriptome consisted of 97,623 distinct transcripts. Of these, 47,006 were protein-coding, 31,109 were non-coding, and 19,508 were unannotated. In addition, we affirmed that the integrative transcriptome could serve as a surrogate reference to the genome in aiding accurate transcriptome assembly. For convenience, we curated the integrative transcriptome database for Bougainvillea, namely InTransBo, which can be freely accessed at http://www.bio-add.org/InTransBo/index.jsp . To the best of our knowledge, the present study is the most comprehensive genomic resource for Bougainvillea up-to-date. The integrative transcriptome helps fill the genomic gap and elucidate the transcriptional nature of Bougainvillea. It may also advance progress in the precise regulation of flowering in horticulture. The same strategy can be readily applied toward the systematic exploration of other plant species lacking complete genomic information.}, } @article {pmid35042854, year = {2022}, author = {Tyrrell, P and Amoke, I and Betjes, K and Broekhuis, F and Buitenwerf, R and Carroll, S and Hahn, N and Haywood, D and Klaassen, B and Løvschal, M and Macdonald, D and Maiyo, K and Mbithi, H and Mwangi, N and Ochola, C and Odire, E and Ondrusek, V and Ratemo, J and Pope, F and Russell, S and Sairowua, W and Sigilai, K and Stabach, JA and Svenning, JC and Stone, E and du Toit, JT and Western, G and Wittemyer, G and Wall, J}, title = {Landscape Dynamics (landDX) an open-access spatial-temporal database for the Kenya-Tanzania borderlands.}, journal = {Scientific data}, volume = {9}, number = {1}, pages = {8}, pmid = {35042854}, issn = {2052-4463}, mesh = {Agriculture ; Animals ; *Animals, Wild ; *Biodiversity ; Conservation of Natural Resources ; Databases, Factual ; *Grassland ; Kenya ; Livestock ; Mammals ; Spatio-Temporal Analysis ; Tanzania ; }, abstract = {The savannas of the Kenya-Tanzania borderland cover >100,000 km[2] and is one of the most important regions globally for biodiversity conservation, particularly large mammals. The region also supports >1 million pastoralists and their livestock. In these systems, resources for both large mammals and pastoralists are highly variable in space and time and thus require connected landscapes. However, ongoing fragmentation of (semi-)natural vegetation by smallholder fencing and expansion of agriculture threatens this social-ecological system. Spatial data on fences and agricultural expansion are localized and dispersed among data owners and databases. Here, we synthesized data from several research groups and conservation NGOs and present the first release of the Landscape Dynamics (landDX) spatial-temporal database, covering ~30,000 km[2] of southern Kenya. The data includes 31,000 livestock enclosures, nearly 40,000 kilometres of fencing, and 1,500 km[2] of agricultural land. We provide caveats and interpretation of the different methodologies used. These data are useful to answer fundamental ecological questions, to quantify the rate of change of ecosystem function and wildlife populations, for conservation and livestock management, and for local and governmental spatial planning.}, } @article {pmid35042809, year = {2022}, author = {Sherkow, JS and Barker, KB and Braverman, I and Cook-Deegan, R and Durbin, R and Easter, CL and Goldstein, MM and Hudson, M and Kress, WJ and Lewin, HA and Mathews, DJH and McCarthy, C and McCartney, AM and da Silva, M and Torrance, AW and Greely, HT}, title = {Ethical, legal, and social issues in the Earth BioGenome Project.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {119}, number = {4}, pages = {}, pmid = {35042809}, issn = {1091-6490}, support = {207492/Z/17/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Animals ; Biosecurity/ethics/legislation & jurisprudence ; Endangered Species/*legislation & jurisprudence ; *Ethics, Research ; *Genomics/ethics/legislation & jurisprudence ; Humans ; }, abstract = {The Earth BioGenome Project (EBP) is an audacious endeavor to obtain whole-genome sequences of representatives from all eukaryotic species on Earth. In addition to the project's technical and organizational challenges, it also faces complicated ethical, legal, and social issues. This paper, from members of the EBP's Ethical, Legal, and Social Issues (ELSI) Committee, catalogs these ELSI concerns arising from EBP. These include legal issues, such as sample collection and permitting; the applicability of international treaties, such as the Convention on Biological Diversity and the Nagoya Protocol; intellectual property; sample accessioning; and biosecurity and ethical issues, such as sampling from the territories of Indigenous peoples and local communities, the protection of endangered species, and cross-border collections, among several others. We also comment on the intersection of digital sequence information and data rights. More broadly, this list of ethical, legal, and social issues for large-scale genomic sequencing projects may be useful in the consideration of ethical frameworks for future projects. While we do not-and cannot-provide simple, overarching solutions for all the issues raised here, we conclude our perspective by beginning to chart a path forward for EBP's work.}, } @article {pmid35042803, year = {2022}, author = {Kress, WJ and Soltis, DE and Kersey, PJ and Wegrzyn, JL and Leebens-Mack, JH and Gostel, MR and Liu, X and Soltis, PS}, title = {Green plant genomes: What we know in an era of rapidly expanding opportunities.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {119}, number = {4}, pages = {}, pmid = {35042803}, issn = {1091-6490}, mesh = {Base Sequence/*genetics ; Biodiversity ; Biological Evolution ; DNA Transposable Elements/genetics ; Ecology ; Ecosystem ; Embryophyta/genetics ; Evolution, Molecular ; Genome ; Genome, Plant/genetics ; Genomics/methods/*trends ; Information Dissemination/methods ; Information Storage and Retrieval/methods ; Phylogeny ; Plants/genetics ; Viridiplantae/*genetics ; }, abstract = {Green plants play a fundamental role in ecosystems, human health, and agriculture. As de novo genomes are being generated for all known eukaryotic species as advocated by the Earth BioGenome Project, increasing genomic information on green land plants is essential. However, setting standards for the generation and storage of the complex set of genomes that characterize the green lineage of life is a major challenge for plant scientists. Such standards will need to accommodate the immense variation in green plant genome size, transposable element content, and structural complexity while enabling research into the molecular and evolutionary processes that have resulted in this enormous genomic variation. Here we provide an overview and assessment of the current state of knowledge of green plant genomes. To date fewer than 300 complete chromosome-scale genome assemblies representing fewer than 900 species have been generated across the estimated 450,000 to 500,000 species in the green plant clade. These genomes range in size from 12 Mb to 27.6 Gb and are biased toward agricultural crops with large branches of the green tree of life untouched by genomic-scale sequencing. Locating suitable tissue samples of most species of plants, especially those taxa from extreme environments, remains one of the biggest hurdles to increasing our genomic inventory. Furthermore, the annotation of plant genomes is at present undergoing intensive improvement. It is our hope that this fresh overview will help in the development of genomic quality standards for a cohesive and meaningful synthesis of green plant genomes as we scale up for the future.}, } @article {pmid35042802, year = {2022}, author = {Lawniczak, MKN and Durbin, R and Flicek, P and Lindblad-Toh, K and Wei, X and Archibald, JM and Baker, WJ and Belov, K and Blaxter, ML and Marques Bonet, T and Childers, AK and Coddington, JA and Crandall, KA and Crawford, AJ and Davey, RP and Di Palma, F and Fang, Q and Haerty, W and Hall, N and Hoff, KJ and Howe, K and Jarvis, ED and Johnson, WE and Johnson, RN and Kersey, PJ and Liu, X and Lopez, JV and Myers, EW and Pettersson, OV and Phillippy, AM and Poelchau, MF and Pruitt, KD and Rhie, A and Castilla-Rubio, JC and Sahu, SK and Salmon, NA and Soltis, PS and Swarbreck, D and Thibaud-Nissen, F and Wang, S and Wegrzyn, JL and Zhang, G and Zhang, H and Lewin, HA and Richards, S}, title = {Standards recommendations for the Earth BioGenome Project.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {119}, number = {4}, pages = {}, pmid = {35042802}, issn = {1091-6490}, support = {WT108749/Z/15/Z/WT_/Wellcome Trust/United Kingdom ; 207492/Z/17/Z/WT_/Wellcome Trust/United Kingdom ; /HHMI/Howard Hughes Medical Institute/United States ; /WT_/Wellcome Trust/United Kingdom ; BBS/E/T/000PR9817/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; Base Sequence/*genetics ; Biodiversity ; Eukaryota/*genetics ; Genomics/methods/*standards ; Humans ; Reference Standards ; Reference Values ; Sequence Analysis, DNA/methods/standards ; }, abstract = {A global international initiative, such as the Earth BioGenome Project (EBP), requires both agreement and coordination on standards to ensure that the collective effort generates rapid progress toward its goals. To this end, the EBP initiated five technical standards committees comprising volunteer members from the global genomics scientific community: Sample Collection and Processing, Sequencing and Assembly, Annotation, Analysis, and IT and Informatics. The current versions of the resulting standards documents are available on the EBP website, with the recognition that opportunities, technologies, and challenges may improve or change in the future, requiring flexibility for the EBP to meet its goals. Here, we describe some highlights from the proposed standards, and areas where additional challenges will need to be met.}, } @article {pmid35042386, year = {2022}, author = {Gunner, RM and Wilson, RP and Holton, MD and Hopkins, P and Bell, SH and Marks, NJ and Bennett, NC and Ferreira, S and Govender, D and Viljoen, P and Bruns, A and van Schalkwyk, OL and Bertelsen, MF and Duarte, CM and van Rooyen, MC and Tambling, CJ and Göppert, A and Diesel, D and Scantlebury, DM}, title = {Decision rules for determining terrestrial movement and the consequences for filtering high-resolution global positioning system tracks: a case study using the African lion (Panthera leo).}, journal = {Journal of the Royal Society, Interface}, volume = {19}, number = {186}, pages = {20210692}, pmid = {35042386}, issn = {1742-5662}, mesh = {Animals ; Animals, Wild ; Ecology ; *Geographic Information Systems ; *Lions ; Movement ; }, abstract = {The combined use of global positioning system (GPS) technology and motion sensors within the discipline of movement ecology has increased over recent years. This is particularly the case for instrumented wildlife, with many studies now opting to record parameters at high (infra-second) sampling frequencies. However, the detail with which GPS loggers can elucidate fine-scale movement depends on the precision and accuracy of fixes, with accuracy being affected by signal reception. We hypothesized that animal behaviour was the main factor affecting fix inaccuracy, with inherent GPS positional noise (jitter) being most apparent during GPS fixes for non-moving locations, thereby producing disproportionate error during rest periods. A movement-verified filtering (MVF) protocol was constructed to compare GPS-derived speed data with dynamic body acceleration, to provide a computationally quick method for identifying genuine travelling movement. This method was tested on 11 free-ranging lions (Panthera leo) fitted with collar-mounted GPS units and tri-axial motion sensors recording at 1 and 40 Hz, respectively. The findings support the hypothesis and show that distance moved estimates were, on average, overestimated by greater than 80% prior to GPS screening. We present the conceptual and mathematical protocols for screening fix inaccuracy within high-resolution GPS datasets and demonstrate the importance that MVF has for avoiding inaccurate and biased estimates of movement.}, } @article {pmid35041659, year = {2022}, author = {Campeau, W and Simons, AM and Stevens, B}, title = {The evolutionary maintenance of Lévy flight foraging.}, journal = {PLoS computational biology}, volume = {18}, number = {1}, pages = {e1009490}, pmid = {35041659}, issn = {1553-7358}, mesh = {Algorithms ; Animals ; Appetitive Behavior/*physiology ; Computational Biology ; *Evolution, Molecular ; *Genetic Fitness/genetics/physiology ; *Models, Biological ; *Models, Statistical ; Population Dynamics ; Selection, Genetic/genetics/physiology ; }, abstract = {Lévy flight is a type of random walk that characterizes the behaviour of many natural phenomena studied across a multiplicity of academic disciplines; within biology specifically, the behaviour of fish, birds, insects, mollusks, bacteria, plants, slime molds, t-cells, and human populations. The Lévy flight foraging hypothesis states that because Lévy flights can maximize an organism's search efficiency, natural selection should result in Lévy-like behaviour. Empirical and theoretical research has provided ample evidence of Lévy walks in both extinct and extant species, and its efficiency across models with a diversity of resource distributions. However, no model has addressed the maintenance of Lévy flight foraging through evolutionary processes, and existing models lack ecological breadth. We use numerical simulations, including lineage-based models of evolution with a distribution of move lengths as a variable and heritable trait, to test the Lévy flight foraging hypothesis. We include biological and ecological contexts such as population size, searching costs, lifespan, resource distribution, speed, and consider both energy accumulated at the end of a lifespan and averaged over a lifespan. We demonstrate that selection often results in Lévy-like behaviour, although conditional; smaller populations, longer searches, and low searching costs increase the fitness of Lévy-like behaviour relative to Brownian behaviour. Interestingly, our results also evidence a bet-hedging strategy; Lévy-like behaviour reduces fitness variance, thus maximizing geometric mean fitness over multiple generations.}, } @article {pmid35038864, year = {2022}, author = {Xie, J and Jin, L and Wu, D and Pruden, A and Li, X}, title = {Inhalable Antibiotic Resistome from Wastewater Treatment Plants to Urban Areas: Bacterial Hosts, Dissemination Risks, and Source Contributions.}, journal = {Environmental science & technology}, volume = {56}, number = {11}, pages = {7040-7051}, doi = {10.1021/acs.est.1c07023}, pmid = {35038864}, issn = {1520-5851}, mesh = {*Anti-Bacterial Agents/pharmacology ; Bacteria/genetics ; Genes, Bacterial ; Humans ; Particulate Matter ; Wastewater/microbiology ; *Water Purification ; }, abstract = {Antibiotic resistance genes (ARGs) are commonly detected in the atmosphere, but questions remain regarding their sources and relative contributions, bacterial hosts, and corresponding human health risks. Here, we conducted a qPCR- and metagenomics-based investigation of inhalable fine particulate matter (PM2.5) at a large wastewater treatment plant (WWTP) and in the ambient air of Hong Kong, together with an in-depth analysis of published data of other potential sources in the area. PM2.5 was observed with increasing enrichment of total ARGs along the coastal-urban-WWTP gradient and clinically relevant ARGs commonly identified in urban and WWTP sites, illustrating anthropogenic impacts on the atmospheric accumulation of ARGs. With certain kinds of putative antibiotic-resistant pathogens detected in urban and WWTP PM2.5, a comparable proportion of ARGs that co-occurred with MGEs was found between the atmosphere and WWTP matrices. Despite similar emission rates of bacteria and ARGs within each WWTP matrix, about 11-13% of the bacteria and >57% of the relevant ARGs in urban and WWTP PM2.5 were attributable to WWTPs. Our study highlights the importance of WWTPs in disseminating bacteria and ARGs to the ambient air from a quantitative perspective and, thus, the need to control potential sources of inhalation exposure to protect the health of urban populations.}, } @article {pmid35037140, year = {2022}, author = {Chen, L and Wang, J and Guo, X and Wu, H and He, H and Fang, L}, title = {Pollution characteristics and health risk assessment of potentially toxic elements in soils around China's gold mines: a meta-analysis.}, journal = {Environmental geochemistry and health}, volume = {44}, number = {11}, pages = {3765-3777}, pmid = {35037140}, issn = {1573-2983}, support = {41977031//the national natural science foundation of china/ ; }, mesh = {Child ; Adult ; Humans ; Soil ; *Metals, Heavy/toxicity/analysis ; *Soil Pollutants/toxicity/analysis ; Gold/toxicity/analysis ; Cadmium/analysis ; Lead/analysis ; Environmental Monitoring/methods ; Risk Assessment ; *Mercury/analysis ; China ; }, abstract = {Since toxic element pollution is widespread in soils near gold mines due to increasing mining activities, the adverse effects of potentially toxic elements (PTEs) in the soils on ecological systems and human health cannot be ignored. However, assessments of PTE pollution in soils and their ecological-health risks on a national scale are still limited. Here, the concentrations of eight PTEs in soils near gold mines throughout China were obtained from published articles. Based on these data, the pollution levels and ecological-health risks of the eight PTEs in soils were comprehensively estimated. The results showed that the average contents of As, Cr, Cd, Pb, Hg, Cu, Ni, and Zn were 81.62, 79.82, 1.04, 206.03, 2.05, 40.82, 71.82, and 130.42 mg kg[-1], respectively, which exceeded the corresponding background values for soils. Most of the examined soils were heavily polluted by Hg and Cd, and higher pollution levels were found in the Henan and Shaanxi Provinces than in other regions. The average potential ecological risk value of all PTEs was 2534.71, indicating the presence of very high risks. Contribution of Hg to the potential ecological risk was more than 80%. For adults, all hazard index (HI) values of noncarcinogenic risks were below the safe level of 1.00. For children, none of the HI values exceeded the safe level, with the exception of As (HI = 1.81); nevertheless, four PTEs (As, Cr, Cu, and Ni) presented unacceptable carcinogenic risks. This study provides scientific basis for controlling PTE contamination and reducing the health risks in soils near gold mines worldwide.}, } @article {pmid35032255, year = {2022}, author = {Marcusson-Clavertz, D and Sliwinski, MJ and Buxton, OM and Kim, J and Almeida, DM and Smyth, JM}, title = {Relationships between daily stress responses in everyday life and nightly sleep.}, journal = {Journal of behavioral medicine}, volume = {45}, number = {4}, pages = {518-532}, pmid = {35032255}, issn = {1573-3521}, support = {R01 AG039409/AG/NIA NIH HHS/United States ; UH2 AG052167/AG/NIA NIH HHS/United States ; R01 AG026728/AG/NIA NIH HHS/United States ; UH3 AG052167/AG/NIA NIH HHS/United States ; R01 AG042595/AG/NIA NIH HHS/United States ; UL1 TR001073/TR/NCATS NIH HHS/United States ; P01 AG003949/AG/NIA NIH HHS/United States ; R01 HL067990/HL/NHLBI NIH HHS/United States ; }, mesh = {Ecological Momentary Assessment ; Emotions/physiology ; Humans ; Sleep/physiology ; *Sleep Initiation and Maintenance Disorders ; *Stress, Psychological/psychology ; }, abstract = {Stress and sleep are related, but the nature and time course of this relation is not well understood. We explored the within-person associations of three components of emotional responses to everyday stressors, indexed by negative affect, reactivity (initial response to a stressor), recovery (persistence of the post-stressor response), and pile-up (accumulation of stress episodes), with sleep indicators. We conducted coordinated analyses of data in several studies employing ecological momentary assessments, which captured naturally occurring, self-reported stress and sleep. We defined proximal reactivity as the emotional response to the stressor moment in question compared to an immediate pre-stressor state, and distal reactivity as the emotional response to the stressor moment in question compared to a typical stressor-free state for that person. Results in two of three studies showed that people reported significantly lower sleep quality following days on which they experienced higher levels of distal reactivity to stressors. Days with greater distal reactivity also predicted significantly more difficulty falling asleep in one of two studies. There was no clear association between proximal reactivity and subsequent sleep. Associations of recovery or pile-up with subsequent sleep emerged only in single studies. Poorer sleep quality was significantly related to higher next day levels of negative affect in all three studies, but there were no consistent relations between sleep and next day stress reactivity, recovery, or pile-up. These exploratory analyses suggest that distal reactivity is associated with a heightened risk of experiencing poor sleep quality the following night, and as such the former may serve as a candidate for potential targets for the remediation of the negative effects of stress on sleep.}, } @article {pmid35028427, year = {2021}, author = {Boyes, D and Crowley, L and Holland, PWH and , and , and , and , and , and , }, title = {The genome sequence of the sycamore, Acronicta aceris (Linnaeus, 1758).}, journal = {Wellcome open research}, volume = {6}, number = {}, pages = {326}, pmid = {35028427}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual female Acronicta aceris (the sycamore; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 466 megabases in span. The complete assembly is scaffolded into 32 chromosomal pseudomolecules, with the W and Z sex chromosome assembled.}, } @article {pmid35022463, year = {2022}, author = {García-García, D and Morales, E and Fonfría, ES and Vigo, I and Bordehore, C}, title = {Caveats on COVID-19 herd immunity threshold: the Spain case.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {598}, pmid = {35022463}, issn = {2045-2322}, support = {COVID-19 2020-41.30.6P.0016//Universidad de Alicante/ ; COVID-19 2020-41.30.6P.0016//Universidad de Alicante/ ; COVID-19 2020-41.30.6P.0016//Universidad de Alicante/ ; 2020-41.30.6O.00.01//Montgó-Dénia Research Station (University of Alicante-Ajuntament de Dénia)/ ; 41.30.6O.00.01//Montgó-Dénia Research Station (University of Alicante-Generalitat Valenciana -Conselleria de Agricultura, Desarrollo Rural, Emergencia Climática y Transición Ecológica-)/ ; }, mesh = {COVID-19/*immunology ; Data Interpretation, Statistical ; Differential Threshold ; Humans ; *Immunity, Herd ; Models, Biological ; Spain ; }, abstract = {After a year of living with the COVID-19 pandemic and its associated consequences, hope looms on the horizon thanks to vaccines. The question is what percentage of the population needs to be immune to reach herd immunity, that is to avoid future outbreaks. The answer depends on the basic reproductive number, R0, a key epidemiological parameter measuring the transmission capacity of a disease. In addition to the virus itself, R0 also depends on the characteristics of the population and their environment. Additionally, the estimate of R0 depends on the methodology used, the accuracy of data and the generation time distribution. This study aims to reflect on the difficulties surrounding R0 estimation, and provides Spain with a threshold for herd immunity, for which we considered the different combinations of all the factors that affect the R0 of the Spanish population. Estimates of R0 range from 1.39 to 3.10 for the ancestral SARS-CoV-2 variant, with the largest differences produced by the method chosen to estimate R0. With these values, the herd immunity threshold (HIT) ranges from 28.1 to 67.7%, which would have made 70% a realistic upper bound for Spain. However, the imposition of the delta variant (B.1.617.2 lineage) in late summer 2021 may have expanded the range of R0 to 4.02-8.96 and pushed the upper bound of the HIT to 90%.}, } @article {pmid35021588, year = {2022}, author = {Zhao, Y and Wang, N and Luo, Y and He, H and Wu, L and Wang, H and Wang, Q and Wu, J}, title = {Quantification of ecosystem services supply-demand and the impact of demographic change on cultural services in Shenzhen, China.}, journal = {Journal of environmental management}, volume = {304}, number = {}, pages = {114280}, doi = {10.1016/j.jenvman.2021.114280}, pmid = {35021588}, issn = {1095-8630}, mesh = {Carbon Sequestration ; China ; *Conservation of Natural Resources ; Demography ; *Ecosystem ; }, abstract = {Previous studies on the supply and demand of ecosystem services (ES) mainly focused on inter-annual changes, and no studies have explored the impact of demographic change on the ES supply and demand on fine-grained time scales. Thus, taking Shenzhen as an example, the status of ES supply and demand, as well as diurnal population changes and their impacts on cultural services were analyzed at different time periods using mobile phone signaling data, ecological supply-demand ratio (ESDR), Geo-Informatic Tupu, InVEST model and buffer zone. The results showed that the population declines successively on workdays, weekends and holidays, and that the daytime population is greater than the nighttime. Water yield services can basically meet the demand in terms of quantity and spatial distribution, however, carbon sequestration and cultural services showed the opposite results. The main type of ESDR changes in cultural services are the mutual conversion of deficit and balance, and these are concentrated in areas with high forest coverage and small populations, but frequent population changes. In addition, when the fixed population is too large, the use of time-varying population data will conceal the impact of demographic changes on ES supply and demand, and other data are needed for auxiliary analysis. Overall, this study provides a new research perspective for the ES supply and demand and can provide a theoretical basis for refined sustainable urban management.}, } @article {pmid35021210, year = {2022}, author = {Morel, B and Schade, P and Lutteropp, S and Williams, TA and Szöllősi, GJ and Stamatakis, A}, title = {SpeciesRax: A Tool for Maximum Likelihood Species Tree Inference from Gene Family Trees under Duplication, Transfer, and Loss.}, journal = {Molecular biology and evolution}, volume = {39}, number = {2}, pages = {}, pmid = {35021210}, issn = {1537-1719}, mesh = {*Algorithms ; *Gene Duplication ; Models, Genetic ; Pedigree ; Phylogeny ; }, abstract = {Species tree inference from gene family trees is becoming increasingly popular because it can account for discordance between the species tree and the corresponding gene family trees. In particular, methods that can account for multiple-copy gene families exhibit potential to leverage paralogy as informative signal. At present, there does not exist any widely adopted inference method for this purpose. Here, we present SpeciesRax, the first maximum likelihood method that can infer a rooted species tree from a set of gene family trees and can account for gene duplication, loss, and transfer events. By explicitly modeling events by which gene trees can depart from the species tree, SpeciesRax leverages the phylogenetic rooting signal in gene trees. SpeciesRax infers species tree branch lengths in units of expected substitutions per site and branch support values via paralogy-aware quartets extracted from the gene family trees. Using both empirical and simulated data sets we show that SpeciesRax is at least as accurate as the best competing methods while being one order of magnitude faster on large data sets at the same time. We used SpeciesRax to infer a biologically plausible rooted phylogeny of the vertebrates comprising 188 species from 31,612 gene families in 1 h using 40 cores. SpeciesRax is available under GNU GPL at https://github.com/BenoitMorel/GeneRax and on BioConda.}, } @article {pmid35021103, year = {2022}, author = {Trimèche, M and Boussoffara, T and Chelbi, I and Cherni, S and Zhioua, S and Msallem, N and Labidi, I and Zhioua, E}, title = {Effects of multiple feedings on sensitized rabbits on the fitness of Phlebotomus papatasi (Diptera: Psychodidae).}, journal = {Acta tropica}, volume = {228}, number = {}, pages = {106303}, doi = {10.1016/j.actatropica.2022.106303}, pmid = {35021103}, issn = {1873-6254}, mesh = {Animals ; Antibodies ; Female ; *Leishmania ; *Leishmaniasis, Cutaneous ; *Phlebotomus ; *Psychodidae ; Rabbits ; }, abstract = {In the present study, we evaluated the effects of antibodies anti-sandfly saliva on the fecundity of Phlebotomus papatasi, vector of zoonotic cutaneous leishmaniasis in the Old World. Rabbits were repeatedly exposed to sandfly bites. Immune sera showed increased levels of anti-sandfly saliva antibody compared to the pre-exposition period. The analysis of biological parameters revealed no decline on the feeding success of females P. papatasi fed on rabbits repeatedly exposed to sandfly bites. Our results showed that anti-sandfly saliva antibodies of rabbits are not detrimental to the fitness of females P. papatasi. Thus, rabbits did not acquire resistance to sandflies following repeated exposures, and that contribute in maintaining a high density of P. papatasi. To control sandfly infestations and Leishmania transmission, more studies are needed for a better understanding of the mechanisms governing the resistance of hosts to bites of sandflies.}, } @article {pmid35013360, year = {2022}, author = {Henniges, MC and Powell, RF and Mian, S and Stace, CA and Walker, KJ and Gornall, RJ and Christenhusz, MJM and Brown, MR and Twyford, AD and Hollingsworth, PM and Jones, L and de Vere, N and Antonelli, A and Leitch, AR and Leitch, IJ}, title = {A taxonomic, genetic and ecological data resource for the vascular plants of Britain and Ireland.}, journal = {Scientific data}, volume = {9}, number = {1}, pages = {1}, pmid = {35013360}, issn = {2052-4463}, support = {NE/L002485/1//RCUK | Natural Environment Research Council (NERC)/ ; }, mesh = {*Biodiversity ; Databases as Topic ; Ecosystem ; Introduced Species ; Ireland ; Tracheophyta/*classification ; United Kingdom ; }, abstract = {The vascular flora of Britain and Ireland is among the most extensively studied in the world, but the current knowledge base is fragmentary, with taxonomic, ecological and genetic information scattered across different resources. Here we present the first comprehensive data repository of native and alien species optimized for fast and easy online access for ecological, evolutionary and conservation analyses. The inventory is based on the most recent reference flora of Britain and Ireland, with taxon names linked to unique Kew taxon identifiers and DNA barcode data. Our data resource for 3,227 species and 26 traits includes existing and unpublished genome sizes, chromosome numbers and life strategy and life-form assessments, along with existing data on functional traits, species distribution metrics, hybrid propensity, associated biomes, realized niche description, native status and geographic origin of alien species. This resource will facilitate both fundamental and applied research and enhance our understanding of the flora's composition and temporal changes to inform conservation efforts in the face of ongoing climate change and biodiversity loss.}, } @article {pmid35013190, year = {2022}, author = {Rimbach, R and Yamada, Y and Sagayama, H and Ainslie, PN and Anderson, LF and Anderson, LJ and Arab, L and Baddou, I and Bedu-Addo, K and Blaak, EE and Blanc, S and Bonomi, AG and Bouten, CVC and Bovet, P and Buchowski, MS and Butte, NF and Camps, SGJA and Close, GL and Cooper, JA and Das, SK and Dugas, LR and Ekelund, U and Entringer, S and Forrester, T and Fudge, BW and Goris, AH and Gurven, M and Hambly, C and El Hamdouchi, A and Hoos, MB and Hu, S and Joonas, N and Joosen, AM and Katzmarzyk, P and Kempen, KP and Kimura, M and Kraus, WE and Kushner, RF and Lambert, EV and Leonard, WR and Lessan, N and Martin, CK and Medin, AC and Meijer, EP and Morehen, JC and Morton, JP and Neuhouser, ML and Nicklas, TA and Ojiambo, RM and Pietiläinen, KH and Pitsiladis, YP and Plange-Rhule, J and Plasqui, G and Prentice, RL and Rabinovich, RA and Racette, SB and Raichlen, DA and Ravussin, E and Reynolds, RM and Roberts, SB and Schuit, AJ and Sjödin, AM and Stice, E and Urlacher, SS and Valenti, G and Van Etten, LM and Van Mil, EA and Wells, JCK and Wilson, G and Wood, BM and Yanovski, J and Yoshida, T and Zhang, X and Murphy-Alford, AJ and Loechl, CU and Luke, AH and Rood, J and Schoeller, DA and Westerterp, KR and Wong, WW and Speakman, JR and Pontzer, H and , }, title = {Total energy expenditure is repeatable in adults but not associated with short-term changes in body composition.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {99}, pmid = {35013190}, issn = {2041-1723}, support = {P30 DK072476/DK/NIDDK NIH HHS/United States ; R01 CA119171/CA/NCI NIH HHS/United States ; R01 DK080763/DK/NIDDK NIH HHS/United States ; UL1 TR001414/TR/NCATS NIH HHS/United States ; }, mesh = {Adipose Tissue/*metabolism ; Adult ; Bayes Theorem ; Body Composition/*physiology ; Child ; Databases, Factual ; Energy Metabolism/*physiology ; Female ; Humans ; Isotope Labeling ; Longitudinal Studies ; Male ; Middle Aged ; Water/*metabolism ; Weight Gain/physiology ; }, abstract = {Low total energy expenditure (TEE, MJ/d) has been a hypothesized risk factor for weight gain, but repeatability of TEE, a critical variable in longitudinal studies of energy balance, is understudied. We examine repeated doubly labeled water (DLW) measurements of TEE in 348 adults and 47 children from the IAEA DLW Database (mean ± SD time interval: 1.9 ± 2.9 y) to assess repeatability of TEE, and to examine if TEE adjusted for age, sex, fat-free mass, and fat mass is associated with changes in weight or body composition. Here, we report that repeatability of TEE is high for adults, but not children. Bivariate Bayesian mixed models show no among or within-individual correlation between body composition (fat mass or percentage) and unadjusted TEE in adults. For adults aged 20-60 y (N = 267; time interval: 7.4 ± 12.2 weeks), increases in adjusted TEE are associated with weight gain but not with changes in body composition; results are similar for subjects with intervals >4 weeks (N = 53; 29.1 ± 12.8 weeks). This suggests low TEE is not a risk factor for, and high TEE is not protective against, weight or body fat gain over the time intervals tested.}, } @article {pmid35011537, year = {2022}, author = {Zhu, T and Zhang, M and Su, H and Li, M and Wang, Y and Jin, L and Li, M}, title = {Integrated Metabolomic and Transcriptomic Analysis Reveals Differential Mechanism of Flavonoid Biosynthesis in Two Cultivars of Angelica sinensis.}, journal = {Molecules (Basel, Switzerland)}, volume = {27}, number = {1}, pages = {}, pmid = {35011537}, issn = {1420-3049}, support = {81360615 and 32160083//National Natural Science Foundation of China/ ; 20JR5RA182//Innovation Base and Talent Plan of Gansu Province of China/ ; GSSYLXM-05//Double First-Class initiative projects of Gansu Province of China/ ; 2021KCZD-4//Gansu University of Chinese Medicine/ ; 202103003//Assurance Project of Ecological Planting and Quality of Daodi Herbs/ ; }, mesh = {Angelica sinensis/*genetics/*metabolism ; Anthocyanins/metabolism ; Biosynthetic Pathways ; Computational Biology/methods ; Flavonoids/*biosynthesis ; Gene Expression Profiling ; *Gene Expression Regulation, Plant ; *Metabolome ; Metabolomics/methods ; Molecular Sequence Annotation ; *Transcriptome ; }, abstract = {Angelica sinensis is a traditional Chinese medicinal plant that has been primarily used as a blood tonic. It largely relies on its bioactive metabolites, which include ferulic acid, volatile oils, polysaccharides and flavonoids. In order to improve the yield and quality of A. sinensis, the two cultivars Mingui 1 (M1), with a purple stem, and Mingui 2 (M2), with a green stem, have been selected in the field. Although a higher root yield and ferulic acid content in M1 than M2 has been observed, the differences of flavonoid biosynthesis and stem-color formation are still limited. In this study, the contents of flavonoids and anthocyanins were determined by spectrophotometer, the differences of flavonoids and transcripts in M1 and M2 were conducted by metabolomic and transcriptomic analysis, and the expression level of candidate genes was validated by qRT-PCR. The results showed that the contents of flavonoids and anthocyanins were 1.5- and 2.6-fold greater in M1 than M2, respectively. A total of 26 differentially accumulated flavonoids (DAFs) with 19 up-regulated (UR) and seven down-regulated (DR) were obtained from the 131 identified flavonoids (e.g., flavonols, flavonoid, isoflavones, and anthocyanins) in M1 vs. M2. A total 2210 differentially expressed genes (DEGs) were obtained from the 34,528 full-length isoforms in M1 vs. M2, and 29 DEGs with 24 UR and 5 DR were identified to be involved in flavonoid biosynthesis, with 25 genes (e.g., CHS1, CHI3, F3H, DFR, ANS, CYPs and UGTs) mapped on the flavonoid biosynthetic pathway and four genes (e.g., RL1, RL6, MYB90 and MYB114) belonging to transcription factors. The differential accumulation level of flavonoids is coherent with the expression level of candidate genes. Finally, the network of DAFs regulated by DEGs was proposed. These findings will provide references for flavonoid production and cultivars selection of A. sinensis.}, } @article {pmid35010641, year = {2021}, author = {Kim, M and You, S and You, JS and Kim, SY and Park, JH}, title = {Income-Related Mortality Inequalities and Its Social Factors among Middle-Aged and Older Adults at the District Level in Aging Seoul: An Ecological Study Using Administrative Big Data.}, journal = {International journal of environmental research and public health}, volume = {19}, number = {1}, pages = {}, pmid = {35010641}, issn = {1660-4601}, support = {2020-CR-15//Seoul Institute/ ; }, mesh = {Aged ; Aging ; Big Data ; Female ; *Health Status Disparities ; Humans ; Income ; Male ; Middle Aged ; Mortality ; Seoul/epidemiology ; *Social Factors ; Socioeconomic Factors ; }, abstract = {This study investigated income-related health inequality at sub-national level, focusing on mortality inequality among middle-aged and older adults (MOAs). Specifically, we examined income-related mortality inequality and its social factors among MOAs across 25 districts in Seoul using administrative big data from the National Health Insurance Service (NHIS). We obtained access to the NHIS's full-population micro-data on both incomes and demographic variables for the entire residents of Seoul. Slope Index of Inequality (SII) and Relative Index of Inequality (RII) were calculated. The effects of social attributes of districts on SIIs and RIIs were examined through ordinary least squares and spatial regressions. There were clear income-related mortality gradients. Cross-district variance of mortality rates was greater among the lowest income group. SIIs were smaller in wealthier districts. Weak spatial correlation was found in SIIs among men. Lower RIIs were linked to lower Gini coefficients of income for both genders. SIIs (men) were associated with higher proportions of special occupational pensioners and working population. Lower SIIs and RIIs (women) were associated with higher proportions of female household heads. The results suggest that increasing economic activities, targeting households with female heads, reforming public pensions, and reducing income inequality among MOAs can be good policy directions.}, } @article {pmid35007287, year = {2022}, author = {Papadopoulou, M and Hildenbrandt, H and Sankey, DWE and Portugal, SJ and Hemelrijk, CK}, title = {Self-organization of collective escape in pigeon flocks.}, journal = {PLoS computational biology}, volume = {18}, number = {1}, pages = {e1009772}, pmid = {35007287}, issn = {1553-7358}, mesh = {Animals ; Columbidae/*physiology ; Computational Biology ; Computer Simulation ; Escape Reaction/*physiology ; *Mass Behavior ; Species Specificity ; }, abstract = {Bird flocks under predation demonstrate complex patterns of collective escape. These patterns may emerge by self-organization from local interactions among group-members. Computational models have been shown to be valuable for identifying what behavioral rules may govern such interactions among individuals during collective motion. However, our knowledge of such rules for collective escape is limited by the lack of quantitative data on bird flocks under predation in the field. In the present study, we analyze the first GPS trajectories of pigeons in airborne flocks attacked by a robotic falcon in order to build a species-specific model of collective escape. We use our model to examine a recently identified distance-dependent pattern of collective behavior: the closer the prey is to the predator, the higher the frequency with which flock members turn away from it. We first extract from the empirical data of pigeon flocks the characteristics of their shape and internal structure (bearing angle and distance to nearest neighbors). Combining these with information on their coordination from the literature, we build an agent-based model adjusted to pigeons' collective escape. We show that the pattern of turning away from the predator with increased frequency when the predator is closer arises without prey prioritizing escape when the predator is near. Instead, it emerges through self-organization from a behavioral rule to avoid the predator independently of their distance to it. During this self-organization process, we show how flock members increase their consensus over which direction to escape and turn collectively as the predator gets closer. Our results suggest that coordination among flock members, combined with simple escape rules, reduces the cognitive costs of tracking the predator while flocking. Such escape rules that are independent of the distance to the predator can now be investigated in other species. Our study showcases the important role of computational models in the interpretation of empirical findings of collective behavior.}, } @article {pmid35003918, year = {2021}, author = {La Manna, G and Picciulin, M and Crobu, A and Perretti, F and Ronchetti, F and Manghi, M and Ruiu, A and Ceccherelli, G}, title = {Marine soundscape and fish biophony of a Mediterranean marine protected area.}, journal = {PeerJ}, volume = {9}, number = {}, pages = {e12551}, pmid = {35003918}, issn = {2167-8359}, abstract = {BACKGROUND: Marine soundscape is the aggregation of sound sources known as geophony, biophony, and anthrophony. The soundscape analysis, in terms of collection and analysis of acoustic signals, has been proposed as a tool to evaluate the specific features of ecological assemblages and to estimate their acoustic variability over space and time. This study aimed to characterise the Capo Caccia-Isola Piana Marine Protected Area (Italy, Western Mediterranean Sea) soundscape over short temporal (few days) and spatial scales (few km) and to quantify the main anthropogenic and biological components, with a focus on fish biophonies.

METHODS: Within the MPA, three sites were chosen each in a different protection zone (A for the integral protection, B as the partial protection, and C as the general protection). In each site, two underwater autonomous acoustic recorders were deployed in July 2020 at a depth of about 10 m on rocky bottoms. To characterise the contribution of both biophonies and anthrophonies, sea ambient noise (SAN) levels were measured as sound pressure level (SPL dB re: 1 μ Pa-rms) at eight 1/3 octave bands, centred from 125 Hz to 16 kHz, and biological and anthropogenic sounds were noted. Fish sounds were classified and counted following a catalogue of known fish sounds from the Mediterranean Sea based on the acoustic characteristic of sound types. A contemporary fish visual census had been carried out at the test sites.

RESULTS: SPL were different by site, time (day vs. night), and hour. SPLs bands centred at 125, 250, and 500 Hz were significantly higher in the daytime, due to the high number of boats per minute whose noise dominated the soundscapes. The loudest man-made noise was found in the A zone, followed by the B and the C zone, confirming that MPA current regulations do not provide protection from acoustic pollution. The dominant biological components of the MPA soundscape were the impulsive sounds generated by some invertebrates, snapping shrimps and fish. The vast majority of fish sounds were recorded at the MPA site characterized by the highest sound richness, abundance, and Shannon-Wiener index, coherently with the results of a fish visual census. Moreover, the acoustic monitoring detected a sound associated with a cryptic species (Ophidion spp.) never reported in the study area before, further demonstrating the usefulness of passive acoustic monitoring as a complementary technique to species census. This study provides baseline data to detect future changes of the marine soundscapes and some suggestions to reduce the impact of noise on marine biodiversity.}, } @article {pmid35003672, year = {2021}, author = {Raiho, AM and Nicklen, EF and Foster, AC and Roland, CA and Hooten, MB}, title = {Bridging implementation gaps to connect large ecological datasets and complex models.}, journal = {Ecology and evolution}, volume = {11}, number = {24}, pages = {18271-18287}, pmid = {35003672}, issn = {2045-7758}, abstract = {Merging robust statistical methods with complex simulation models is a frontier for improving ecological inference and forecasting. However, bringing these tools together is not always straightforward. Matching data with model output, determining starting conditions, and addressing high dimensionality are some of the complexities that arise when attempting to incorporate ecological field data with mechanistic models directly using sophisticated statistical methods. To illustrate these complexities and pragmatic paths forward, we present an analysis using tree-ring basal area reconstructions in Denali National Park (DNPP) to constrain successional trajectories of two spruce species (Picea mariana and Picea glauca) simulated by a forest gap model, University of Virginia Forest Model Enhanced-UVAFME. Through this process, we provide preliminary ecological inference about the long-term competitive dynamics between slow-growing P. mariana and relatively faster-growing P. glauca. Incorporating tree-ring data into UVAFME allowed us to estimate a bias correction for stand age with improved parameter estimates. We found that higher parameter values for P. mariana minimum growth under stress and P. glauca maximum growth rate were key to improving simulations of coexistence, agreeing with recent research that faster-growing P. glauca may outcompete P. mariana under climate change scenarios. The implementation challenges we highlight are a crucial part of the conversation for how to bring models together with data to improve ecological inference and forecasting.}, } @article {pmid35001266, year = {2022}, author = {Ruhela, M and Sharma, K and Bhutiani, R and Chandniha, SK and Kumar, V and Tyagi, K and Ahamad, F and Tyagi, I}, title = {GIS-based impact assessment and spatial distribution of air and water pollutants in mining area.}, journal = {Environmental science and pollution research international}, volume = {29}, number = {21}, pages = {31486-31500}, pmid = {35001266}, issn = {1614-7499}, mesh = {*Air Pollutants/analysis ; *Air Pollution/analysis ; Environmental Monitoring/methods ; Geographic Information Systems ; Iron ; Nitrogen Dioxide ; Particulate Matter/analysis ; *Water Pollutants ; }, abstract = {Mining is a significant part of the transforming economy, which is generally considered as essential as well as social evil at the same time. It is one of the potential contributors to air and water pollution and possesses long-term impact on their quality. Keeping in view the exponential mining activities, we have selected an iron mine area in Bailadila, Chhattisgarh, India, as a sampling site and investigated the impact of mining activities on the air as well as water quality by setting up seven air quality and thirty water quality monitoring stations. From the results obtained, it was observed that concentration of air pollutants such as SO2, NO2, PM2.5 and PM10 for the year 2015 lies in the range of 11.5-13.0 µg/m[3], 11.5-13.0 µg/m[3], 24.9-33.4 ppm and 61.6-74.2 ppm, respectively, while for the year 2018, it lies in the range of 10.3-11.7 µg/m[3], 10.5-14.7 µg/m[3], 18.3-50.8 ppm and 23.7-60.7 ppm, respectively. Furthermore, results obtained revealed that air pollutants such as SO2, NO2, PM2.5 and PM10 were within the permissible limits but they contributed towards the light air pollution (air pollution index: 25-50) at all the air monitoring stations. Moreover, PM10 was considered as criterion pollutant in the Bailadila, Chhattisgarh region. On the other hand, it was observed that groundwater quality was deteriorated in the subsequent years. Most of the water quality parameters were in the permissible limits except iron (Fe). Moreover, on the basis of water quality indexing, water quality was classified as "poor" in ~ 30% of the sites and "very poor" in ~ 34% sites. The water quality was "unhealthy for drinking" in 3% and 6% sites in the year 2015 and 2018, respectively.}, } @article {pmid35000017, year = {2022}, author = {Reddy, BSN and V, SP and Pramada, SK}, title = {Suitability of different precipitation data sources for hydrological analysis: a study from Western Ghats, India.}, journal = {Environmental monitoring and assessment}, volume = {194}, number = {2}, pages = {75}, pmid = {35000017}, issn = {1573-2959}, mesh = {*Environmental Monitoring ; *Hydrology ; Information Storage and Retrieval ; Rain ; Retrospective Studies ; }, abstract = {For hydrological analysis, it is essential to have continuous and long-term precipitation data. However, the precipitation data from rain gauge stations are often insufficient and not continuous. At present, ground-based gridded data and satellite-based gridded data are often used as an alternative. However, these data sets have to be evaluated for their suitability in hydrological studies. The current study compared three different rainfall data sources with the observed station data for the Kallada River basin of Kerala, India. The ground-based gridded rainfall data from the India Meteorological Department (IMD), the high-resolution satellite product Tropical Rainfall Measuring Mission (TRMM 3B43, version 7), and the reanalysis data Modern-Era Retrospective Analysis for Research and Applications (MERRA) are used in the analysis. The correlation coefficient, normalized root mean square error, Nash-Sutcliffe efficiency, modified index of agreement, and volumetric efficiency are used as performance indicators. The performance indicator's weights are based on the entropy method. The multi-criteria decision-making techniques like compromise programming and Preference Ranking Organization Method (PROMETHEE II) are used for ranking the precipitation data sources. It is found that IMD ground-based gridded data is ranked 1 among the three data sets. The IMD ground-based gridded data are not homogeneous based on the absolute homogeneity test, even though they had the highest rank. The IMD gridded data are further corrected based on double mass curve analysis. The corrected data were analyzed using the precipitation concentration index (PCI) to assess the temporal variation in precipitation, and it was found that the location falls under a uniform distribution zone.}, } @article {pmid34995483, year = {2022}, author = {Conwill, A and Kuan, AC and Damerla, R and Poret, AJ and Baker, JS and Tripp, AD and Alm, EJ and Lieberman, TD}, title = {Anatomy promotes neutral coexistence of strains in the human skin microbiome.}, journal = {Cell host & microbe}, volume = {30}, number = {2}, pages = {171-182.e7}, pmid = {34995483}, issn = {1934-6069}, support = {DP2 GM140922/GM/NIGMS NIH HHS/United States ; }, mesh = {*Acne Vulgaris/microbiology ; Humans ; *Microbiota ; Propionibacterium acnes/genetics ; Skin/microbiology ; Whole Genome Sequencing ; }, abstract = {What enables strains of the same species to coexist in a microbiome? Here, we investigate whether host anatomy can explain strain co-residence of Cutibacterium acnes, the most abundant species on human skin. We reconstruct on-person evolution and migration using whole-genome sequencing of C. acnes colonies acquired from healthy subjects, including from individual skin pores, and find considerable spatial structure at the level of pores. Although lineages (sets of colonies separated by <100 mutations) with in vitro fitness differences coexist within centimeter-scale regions, each pore is dominated by a single lineage. Moreover, colonies from a pore typically have identical genomes. An absence of adaptive signatures suggests a genotype-independent source of low within-pore diversity. We therefore propose that pore anatomy imposes random single-cell bottlenecks; the resulting population fragmentation reduces competition and promotes coexistence. Our findings suggest that therapeutic interventions involving pore-dwelling species might focus on removing resident populations over optimizing probiotic fitness.}, } @article {pmid34993820, year = {2022}, author = {Fawad, M and Ullah, F and Irshad, M and Shah, W and Mahmood, Q and Ahmad, I}, title = {Marble waste site suitability assessment using the GIS-based AHP model.}, journal = {Environmental science and pollution research international}, volume = {29}, number = {19}, pages = {28386-28401}, pmid = {34993820}, issn = {1614-7499}, mesh = {Analytic Hierarchy Process ; Calcium Carbonate ; Decision Support Techniques ; *Geographic Information Systems ; *Refuse Disposal/methods ; Waste Disposal Facilities ; Water ; }, abstract = {Site suitability with regards to environmental protection, public concerns, and the legitimate prerequisite is a basic issue that has been tended to in this study. By and large, marble waste is being unloaded on accessible open spaces or released in water to the close by waterways in the territory, Mohmand marble zone (Shabqadar), Khyber Pakhtunkhwa, Pakistan. Suitability assessment for marble waste collection and disposal was carried out through the integrated approach of analytical hierarchy process (AHP) and geographic information system (GIS) to limit the ecological dangers, public, and government concerns related to marble waste. The available land use was ordered into three main land use classes followed by six sub-classes including water bodies and agriculture (environmental), settlement and social site (social), and marble units and roads (economic). These sub-classes in the investigation region were organized through pairwise correlation and weighted sum analysis, AHP procedure. The AHP results were interpreted through GIS tools of digitization, buffering, and overlay in ArcMap, ArcGIS. The integrated AHP and GIS outcomes were consolidated to get the optimum results of the study, marble waste collection, and disposal options. It was concluded that priority should be given to water bodies followed by agricultural land while protecting the available land use classes from marble waste hazards. The percent priority values calculated are 32.33%, 30.50%, 12.16%, 10.66%, 8.50%, and 6% for water bodies, agricultural land, settlements, marble processing units, roads, and cultural sites respectively. The sequence of priority of the land use values are waterbodies > agriculture > settlement > marble industries > road > cultural site. The proposed integrated model is helpful in site suitability for waste management by the authorities and decision-makers associated with waste management.}, } @article {pmid34990828, year = {2022}, author = {Mallinson, DC and Elwert, F}, title = {Estimating sibling spillover effects with unobserved confounding using gain-scores.}, journal = {Annals of epidemiology}, volume = {67}, number = {}, pages = {73-80}, pmid = {34990828}, issn = {1873-2585}, support = {UL1 TR000427/TR/NCATS NIH HHS/United States ; P2C HD042849/HD/NICHD NIH HHS/United States ; P30 AG017266/AG/NIA NIH HHS/United States ; R24 HD042849/HD/NICHD NIH HHS/United States ; P2C HD047873/HD/NICHD NIH HHS/United States ; UL1 TR002373/TR/NCATS NIH HHS/United States ; R24 HD047873/HD/NICHD NIH HHS/United States ; T32 HD007014/HD/NICHD NIH HHS/United States ; }, mesh = {Child ; Humans ; Infant, Newborn ; *Premature Birth ; Regression Analysis ; Research Design ; *Siblings ; United States ; Wisconsin ; }, abstract = {PURPOSE: A growing area of research in epidemiology is the identification of health-related sibling spillover effects, or the effect of one individual's exposure on their sibling's outcome. The health within families may be confounded by unobserved factors, rendering identification of sibling spillovers challenging.

METHODS: We demonstrate a gain-score (fixed effects) regression method for identifying exposure-to-outcome spillover effects within sibling pairs in linear models. The method identifies the exposure-to-outcome spillover effect if only one sibling's exposure affects the other's outcome, and it identifies the difference between the spillover effects if both siblings' exposures affect the others' outcomes. The method fails with outcome-to-exposure spillover or with outcome-to-outcome spillover. Analytic results, Monte Carlo simulations, and a brief application demonstrate the method and its limitations.

RESULTS: We estimate the spillover effect of a child's preterm birth on an older sibling's literacy skills, measured by the Phonological Awareness Literacy Screening-Kindergarten test. We analyze 20,010 sibling pairs from a population-wide, Wisconsin-based (United States) birth cohort. Without covariate adjustment, we estimate that preterm birth modestly decreases an older sibling's test score.

CONCLUSIONS: Gain-scores are a promising strategy for identifying exposure-to-outcome spillover effects in sibling pairs while controlling for sibling-invariant unobserved confounding.}, } @article {pmid34990484, year = {2022}, author = {Gestuveo, RJ and Parry, R and Dickson, LB and Lequime, S and Sreenu, VB and Arnold, MJ and Khromykh, AA and Schnettler, E and Lambrechts, L and Varjak, M and Kohl, A}, title = {Mutational analysis of Aedes aegypti Dicer 2 provides insights into the biogenesis of antiviral exogenous small interfering RNAs.}, journal = {PLoS pathogens}, volume = {18}, number = {1}, pages = {e1010202}, pmid = {34990484}, issn = {1553-7374}, support = {/WT_/Wellcome Trust/United Kingdom ; MC_UU_12014/8/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Aedes/genetics/*immunology/*virology ; Alphavirus Infections/*immunology ; Animals ; DNA Mutational Analysis ; Mosquito Vectors/virology ; RNA, Small Interfering/immunology ; RNA, Viral/immunology ; Ribonuclease III/genetics/*immunology ; Semliki forest virus ; }, abstract = {The exogenous small interfering RNA (exo-siRNA) pathway is a key antiviral mechanism in the Aedes aegypti mosquito, a widely distributed vector of human-pathogenic arboviruses. This pathway is induced by virus-derived double-stranded RNAs (dsRNA) that are cleaved by the ribonuclease Dicer 2 (Dcr2) into predominantly 21 nucleotide (nt) virus-derived small interfering RNAs (vsiRNAs). These vsiRNAs are used by the effector protein Argonaute 2 within the RNA-induced silencing complex to cleave target viral RNA. Dcr2 contains several domains crucial for its activities, including helicase and RNase III domains. In Drosophila melanogaster Dcr2, the helicase domain has been associated with binding to dsRNA with blunt-ended termini and a processive siRNA production mechanism, while the platform-PAZ domains bind dsRNA with 3' overhangs and subsequent distributive siRNA production. Here we analyzed the contributions of the helicase and RNase III domains in Ae. aegypti Dcr2 to antiviral activity and to the exo-siRNA pathway. Conserved amino acids in the helicase and RNase III domains were identified to investigate Dcr2 antiviral activity in an Ae. aegypti-derived Dcr2 knockout cell line by reporter assays and infection with mosquito-borne Semliki Forest virus (Togaviridae, Alphavirus). Functionally relevant amino acids were found to be conserved in haplotype Dcr2 sequences from field-derived Ae. aegypti across different continents. The helicase and RNase III domains were critical for silencing activity and 21 nt vsiRNA production, with RNase III domain activity alone determined to be insufficient for antiviral activity. Analysis of 21 nt vsiRNA sequences (produced by functional Dcr2) to assess the distribution and phasing along the viral genome revealed diverse yet highly consistent vsiRNA pools, with predominantly short or long sequence overlaps including 19 nt overlaps (the latter representing most likely true Dcr2 cleavage products). Combined with the importance of the Dcr2 helicase domain, this suggests that the majority of 21 nt vsiRNAs originate by processive cleavage. This study sheds new light on Ae. aegypti Dcr2 functions and properties in this important arbovirus vector species.}, } @article {pmid34989689, year = {2022}, author = {Bouldin, ED and Delgado, R and Peacock, K and Hale, W and Roghani, A and Trevino, AY and Viny, M and Wetter, DW and Pugh, MJ}, title = {Military Injuries-Understanding Posttraumatic Epilepsy, Health, and Quality-of-Life Effects of Caregiving: Protocol for a Longitudinal Mixed Methods Observational Study.}, journal = {JMIR research protocols}, volume = {11}, number = {1}, pages = {e30975}, pmid = {34989689}, issn = {1929-0748}, abstract = {BACKGROUND: Veterans with posttraumatic epilepsy (PTE), particularly those with comorbidities associated with epilepsy or traumatic brain injury (TBI), have poorer health status and higher symptom burden than their peers without PTE. One area that has been particularly poorly studied is that of the role of caregivers in the health of veterans with PTE and the impact caring for someone with PTE has on the caregivers themselves.

OBJECTIVE: In this study, we aim to address the following: describe and compare the health and quality of life of veterans and caregivers of veterans with and without PTE; evaluate the change in available supports and unmet needs for services among caregivers of post-9/11 veterans with PTE over a 2-year period and to compare support and unmet needs with those without PTE; and identify veteran and caregiver characteristics associated with the 2-year health trajectories of caregivers and veterans with PTE compared with veterans without PTE.

METHODS: We conducted a prospective cohort study of the health and quality of life among 4 groups of veterans and their caregivers: veterans with PTE, nontraumatic epilepsy, TBI only, and neither epilepsy nor TBI. We will recruit participants from previous related studies and collect information about both the veterans and their primary informal caregivers on health, quality of life, unmet needs for care, PTE and TBI symptoms and treatment, relationship, and caregiver experience. Data sources will include existing data supplemented with primary data, such as survey data collected at baseline, intermittent brief reporting using ecological momentary assessment, and qualitative interviews. We will make both cross-sectional and longitudinal comparisons, using veteran-caregiver dyads, along with qualitative findings to better understand risk and promotive factors for quality of life and health among veterans and caregivers, as well as the bidirectional impact of caregivers and care recipients on one another.

RESULTS: This study was approved by the institutional review boards of the University of Utah and Salt Lake City Veterans Affairs and is under review by the Human Research Protection Office of the United States Army Medical Research and Development Command. The Service Member, Veteran, and Caregiver Community Stakeholders Group has been formed and the study questionnaire will be finalized once the panel reviews it. We anticipate the start of recruitment and primary data collection by January 2022.

CONCLUSIONS: New national initiatives aim to incorporate the caregiver into the veteran's treatment plan; however, we know little about the impact of caregiving-both positive and negative-on the caregivers themselves and on the veterans for whom they provide care. We will identify specific needs in this understudied population, which will inform clinicians, patients, families, and policy makers about the specific impact and needs to equip caregivers in caring for veterans at home.

PRR1-10.2196/30975.}, } @article {pmid34989252, year = {2021}, author = {Ardalan, A and Yamane, N and Rao, AK and Montes, J and Goldman, S}, title = {Analysis of gait synchrony and balance in neurodevelopmental disorders using computer vision techniques.}, journal = {Health informatics journal}, volume = {27}, number = {4}, pages = {14604582211055650}, doi = {10.1177/14604582211055650}, pmid = {34989252}, issn = {1741-2811}, mesh = {Child ; Computers ; *Gait ; Humans ; *Neurodevelopmental Disorders ; Research Design ; }, abstract = {Gait tasks are commonly administered during motor assessments of children with neurodevelopmental disorders (NDDs). Gait analyses are often conducted in laboratory settings using costly and cumbersome experiments. In this paper, we propose a computational pipeline using computer vision techniques as an ecological and precise method to quantify gait in children with NDDs with challenging behaviors. We analyzed videos of 15 probands (PB) and 12 typically developing (TD) siblings, engaged in a preferred-pace walking task, using pose estimation software to track points of interest on their bodies over time. Analyzing the extracted information revealed that PB children had significantly less whole-body gait synchrony and poorer balance compared to their TD siblings. Our work offers a cost-effective method while preserving the validity of its results. This remote approach increases access to more diverse and distant cohorts and thus lowers barriers to research participation, further enriching our understanding of motor outcomes in NDDs.}, } @article {pmid34976041, year = {2021}, author = {Feng, B}, title = {Dynamic Analysis of College Physical Education Teaching Quality Evaluation Based on Network under the Big Data.}, journal = {Computational intelligence and neuroscience}, volume = {2021}, number = {}, pages = {5949167}, pmid = {34976041}, issn = {1687-5273}, mesh = {Artificial Intelligence ; *Big Data ; Humans ; *Physical Education and Training ; Students ; Universities ; }, abstract = {Improving the quality of college physical education is of great significance to facilitating the integrated development of students' psyches and physical. Establishing a more systematic, effective, and social training needs of education quality evaluation hierarchy is also the centerpiece of the college physical culture education administration. Massive information technology provides new conception and methods to this, and supply advantage sustains for furtherance the education ecology development. Based on the network education system, this paper uses big data to quantify the evaluation indexes of physical education teaching, so as to actualize the timely dynamic evaluation of the process that is physical teaching and learning. This essay constructs the evaluation index system of college physical education teaching quality by combining mensurable and qualitative methods. On the basis of previous studies, an evaluation model of college physical education teaching quality based on artificial intelligence mass data calculation is designed. The experiment authenticates that the model evaluation risk coefficient is 1.93 lower than the optimized model. The experiment also proves that the model is conducive to elevating the education quality.}, } @article {pmid34972511, year = {2021}, author = {Tilahun, B and Derseh, L and Atinafu, A and Mamuye, A and Mariam, TH and Mohammed, M and Hiwot, TG and Endehabtu, BF}, title = {Level and contributing factors of health data quality and information use in two districts in Northwest Ethiopia: social-ecological perspective.}, journal = {BMC medical informatics and decision making}, volume = {21}, number = {1}, pages = {373}, pmid = {34972511}, issn = {1472-6947}, mesh = {Cross-Sectional Studies ; *Data Accuracy ; Delivery of Health Care ; Ethiopia ; *Health Facilities ; Humans ; }, abstract = {BACKGROUND: The health management information system has been implemented at all levels of healthcare delivery to ensure quality data production and information use in Ethiopia. Including the capacity-building activities and provision of infrastructure, various efforts have been made to improve the production and use of quality health data though the result is still unsatisfactory. This study aimed to examine the quality of health data and use in Wogera and Tach-Armacheho districts and understand its barriers and facilitators.

METHODS: The study utilized a mixed-method; for the quantitative approach, institution-based cross-sectional study was conducted to determine the quality of health data and use by 95 departments in the two districts. The qualitative approach involved 16 in-depth interviewees from Wogera district. A descriptive Phenomenological design was used to explore factors influencing the quality and use of health data. The quantitative data were expressed descriptively with tables, graphs, and percent whereas the qualitative data were analyzed with content analysis guided by the social-ecological model framework.

RESULT: The average levels of information use for Wogera and Tach-Armacheho districts were estimated at 29 and 35.9, respectively. The overall average level of accuracy of reports for six different health services in the HCs of Wogera and Tach Armacheho districts were 0.95 and 0.86, respectively. The qualitatively identified factors that influence the production and use of quality health data include valuing data, getting staff training, being a patriotic staff, and getting supportive supervision, were identified from individual-level characteristics; similarly, coaching, supportive supervision, and peer-to-peer learning from relational/interpersonal level characteristics, and organizational culture, incentive, infrastructure establishing accountability, and staff turnover, were identified from organizational level characteristics.

CONCLUSION: The quality of data and routine information utilization was low and were influenced by a number of actors presented in and around the health system including individual, interpersonal, and organizational characteristics. Incentive affects data quality and information use directly or indirectly after modifying factors at all levels of the social-ecological model. Therefore, interventions should gear towards addressing multiple social-ecological factors of the health system concomitantly or intervene on incentive which has a multifaceted effect on the outcome.}, } @article {pmid34968387, year = {2021}, author = {Cunniffe, NJ and Taylor, NP and Hamelin, FM and Jeger, MJ}, title = {Epidemiological and ecological consequences of virus manipulation of host and vector in plant virus transmission.}, journal = {PLoS computational biology}, volume = {17}, number = {12}, pages = {e1009759}, pmid = {34968387}, issn = {1553-7358}, support = {/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; Computational Biology ; Genetic Fitness ; Host-Pathogen Interactions ; *Insect Vectors/genetics/physiology/virology ; Models, Biological ; *Plant Diseases/statistics & numerical data/virology ; *Plant Viruses/genetics/pathogenicity ; }, abstract = {Many plant viruses are transmitted by insect vectors. Transmission can be described as persistent or non-persistent depending on rates of acquisition, retention, and inoculation of virus. Much experimental evidence has accumulated indicating vectors can prefer to settle and/or feed on infected versus noninfected host plants. For persistent transmission, vector preference can also be conditional, depending on the vector's own infection status. Since viruses can alter host plant quality as a resource for feeding, infection potentially also affects vector population dynamics. Here we use mathematical modelling to develop a theoretical framework addressing the effects of vector preferences for landing, settling and feeding-as well as potential effects of infection on vector population density-on plant virus epidemics. We explore the consequences of preferences that depend on the host (infected or healthy) and vector (viruliferous or nonviruliferous) phenotypes, and how this is affected by the form of transmission, persistent or non-persistent. We show how different components of vector preference have characteristic effects on both the basic reproduction number and the final incidence of disease. We also show how vector preference can induce bistability, in which the virus is able to persist even when it cannot invade from very low densities. Feedbacks between plant infection status, vector population dynamics and virus transmission potentially lead to very complex dynamics, including sustained oscillations. Our work is supported by an interactive interface https://plantdiseasevectorpreference.herokuapp.com/. Our model reiterates the importance of coupling virus infection to vector behaviour, life history and population dynamics to fully understand plant virus epidemics.}, } @article {pmid34966925, year = {2021}, author = {Lange, M and Alako, BTF and Cochrane, G and Ghaffar, M and Mascher, M and Habekost, PK and Hillebrand, U and Scholz, U and Schorch, F and Freitag, J and Scholz, AH}, title = {Quantitative monitoring of nucleotide sequence data from genetic resources in context of their citation in the scientific literature.}, journal = {GigaScience}, volume = {10}, number = {12}, pages = {}, pmid = {34966925}, issn = {2047-217X}, mesh = {Base Sequence ; *Data Mining ; Databases, Nucleic Acid ; Europe ; *Nucleotides ; }, abstract = {BACKGROUND: Linking nucleotide sequence data (NSD) to scientific publication citations can enhance understanding of NSD provenance, scientific use, and reuse in the community. By connecting publications with NSD records, NSD geographical provenance information, and author geographical information, it becomes possible to assess the contribution of NSD to infer trends in scientific knowledge gain at the global level.

FINDINGS: We extracted and linked records from the European Nucleotide Archive to citations in open-access publications aggregated at Europe PubMed Central. A total of 8,464,292 ENA accessions with geographical provenance information were associated with publications. We conducted a data quality review to uncover potential issues in publication citation information extraction and author affiliation tagging and developed and implemented best-practice recommendations for citation extraction. We constructed flat data tables and a data warehouse with an interactive web application to enable ad hoc exploration of NSD use and summary statistics.

CONCLUSIONS: The extraction and linking of NSD with associated publication citations enables transparency. The quality review contributes to enhanced text mining methods for identifier extraction and use. Furthermore, the global provision and use of NSD enable scientists worldwide to join literature and sequence databases in a multidimensional fashion. As a concrete use case, we visualized statistics of country clusters concerning NSD access in the context of discussions around digital sequence information under the United Nations Convention on Biological Diversity.}, } @article {pmid34965549, year = {2021}, author = {Kuriata, MS and Vasylenko, VV and Ivanova, OM and Kramarenko, MS and Lytvynets, LO and Morozov, VV and Misсhenko, LP and Boiko, ZN and Buderatska, VB and Chepurny, MI and Kukush, AG}, title = {RECONSTRUCTION, VERIFICATION AND ANALYSIS OF RESULTS OF WBC MEASUREMENTS DATED 1986 THAT WERE INPUTTED TO ELECTRONIC DATABASE IN 2019-2021.}, journal = {Problemy radiatsiinoi medytsyny ta radiobiolohii}, volume = {26}, number = {}, pages = {199-218}, doi = {10.33145/2304-8336-2021-26-199-218}, pmid = {34965549}, issn = {2313-4607}, mesh = {*Chernobyl Nuclear Accident ; Data Accuracy ; Data Collection/statistics & numerical data/trends ; Databases, Factual/*statistics & numerical data/*trends ; Epidemiological Monitoring ; Forecasting ; Humans ; Radiation Exposure/*statistics & numerical data ; Radiation Monitoring/*statistics & numerical data ; Radiometry/*statistics & numerical data ; Registries ; Ukraine ; Whole-Body Counting/*statistics & numerical data ; }, abstract = {UNLABELLED: Objective of research is to improve the electronic database of WBC measurements dated 1986 by inputting of newinformation from paper carriers, reconstruction of information gaps, verification and analysis of new entered data,revision of internal exposure doses that are based on results of WBC measurements dated 1986.

MATERIALS AND METHODS: In 2013-2015 during a revision of databases (DB) of WBC measurements results dated1986-2014, it was discovered a great amount of paper carriers with information about WBC measurements, includ-ing the ones dated 1986, that were not inputted to the electronic DB. The paper carriers were systematized andordered by the following indicators: place of residence of a person and place of WBC measurement, institution andoperator that made the measurement, measurement device and date of measurement. For a comfortable inputtingof the information to the electronic DB, it was additionally created a form which exists as an option in existing program complex Silbody (Version 19.0.9). In the revised DB of WBC measurements dated 1986 internal exposure dosesfrom radio-cesium of Chornobyl origin were computed based on an ecological and dosimetric model for radio-cesiummigration in environment and a model for radio-cesium metabolism in human body. In the work, mathematical andstatistical methods of research were used.

RESULTS: In 2019-2021 additionally 35,319 notes were inputted to the electronic DB of WBC measurement dated1986, and as a result its volume increased in 2.2 times. Mostly those are data on results concerning residents of Kyiv,Zhytomyr, Donetsk, Cherkasy, Odessa, Ivano-Frankivsk, and Rivne Oblasts. It was established the information onmeasurement devices and respectively on the minimal detected activity (MDA) for 27,119 notes (76.7 % of all newentered). Information is reconstructed about the body mass of all persons under investigation. Evaluation is madefor values of intake of incorporated radionuclides 137Cs and 134Cs for all new entered to DB. Quality of reconstructedinformation was analyzed. To group 1, «qualitative», it was classified 18,598 notes (53 % of all new entered), measurements in 1986 (including new entered). Dose not exceeding 1 mSv was obtained by 80 % of adults (older than20), as well as 73 % of persons younger than 20.

CONCLUSION: To DB of WBC measurements, it was additionally inputted 35,319 notes on results of measurementsdated 1986. New entered information is verified and distributed by the quality groups. Individual exposure dosesevaluated based on those data can be used for further scientific research.}, } @article {pmid34965548, year = {2021}, author = {Drozdovitch, V and Yauseyenka, VV and Minenko, VF and Veyalkin, IV and Kukhta, TS and Grakovitch, RI and Trofimik, S and Polyanskaya, ON and Starastsenka, L and Cahoon, EK and Hatch, M and Little, MP and Brenner, AV and Ostroumova, E and Mabuchi, K and Rozhko, AV}, title = {THYROID SCREENING AND RELIABILITY OF RADIATION THYROID DOSES FOR THE BELARUSIAN IN UTERO COHORT.}, journal = {Problemy radiatsiinoi medytsyny ta radiobiolohii}, volume = {26}, number = {}, pages = {188-198}, pmid = {34965548}, issn = {2313-4607}, support = {HHSN261201300002C/CA/NCI NIH HHS/United States ; HHSN261201800015I/CA/NCI NIH HHS/United States ; Z99 CA999999/ImNIH/Intramural NIH HHS/United States ; HHSN261201800015C/CA/NCI NIH HHS/United States ; 001/WHO_/World Health Organization/International ; }, mesh = {Adult ; *Chernobyl Nuclear Accident ; Cohort Studies ; Female ; Fetus/*radiation effects ; Humans ; Infant, Newborn ; Longitudinal Studies ; Male ; Maternal Exposure/statistics & numerical data ; Neoplasms, Radiation-Induced/epidemiology ; Pregnancy ; *Pregnant Women ; Prenatal Exposure Delayed Effects ; *Radiation Dosage ; Radioactive Fallout/*adverse effects ; Reproducibility of Results ; Republic of Belarus ; Thyroid Gland/*physiopathology/*radiation effects ; Thyroid Nodule/epidemiology/etiology/*physiopathology ; Ukraine ; }, abstract = {OBJECTIVE: To describe the status and results of thyroid disease screening and assessment of reliability of radiationthyroid doses in the Belarusian in utero cohort of 2,965 individuals exposed to Chernobyl (Chornobyl) fallout.

MATERIALS AND METHODS: Thyroid screening examinations are currently underway including thyroid palpation by anendocrinologist, ultrasonographic examination by an ultrasonographer and analysis of blood samples for diagnosisof hypo- and hyperthyroidism, autoimmune thyroiditis, thyroid function tests (thyroid-stimulating hormone [TSH],thyroxine [T4], thyroid peroxidase antibody [anti-TPO], and thyroglobulin antibodies [anti-TG]). Reliability of (i)information from 780 pairs of questionnaires obtained during the first and second interviews of the mothers and (ii)thyroid doses, which were calculated for the cohort members using this information, is evaluated.

RESULTS: As of 15 August 2021, 1,267 in utero exposed study subjects had been screened. A single thyroid nodule wasdiagnosed in 167 persons (13.2 % of the total) and multiple thyroid nodules in 101 persons (8.0 %): 189 (14.9 %)persons had nodules detected for the first time at the screening while 79 (6.2 %) persons had nodules detected pre-viously (pre-screening nodules). Fifty-nine out of 268 subjects (22.0 %) with a suspicious thyroid nodule werereferred to fine needle aspiration biopsy, and among them 33 (55.9 %) were biopsied. Reasonable agreement wasobserved for modelqbased doses calculated for the Belarusian in utero cohort members using data from the two inter-views (Spearman's rank-correlation coefficient rs = 0.74, p < 0.001), while measurementqbased doses yielded almost per-fect agreement (rs = 0.99, p < 0.001).

CONCLUSIONS: During the thyroid screening, at least one thyroid nodule was identified in 268 of 1,267 (21.2 %) inutero exposed cohort members. Seven thyroid cancer cases were identified in the cohort, including 5 pre-screeningcases and 2 cases detected during the screening. Ongoing research on this unique cohort will provide importantinformation on adverse health effects following prenatal and postnatal exposure to radioiodine and radiocesium iso-topes, for which available epidemiological data are scant.}, } @article {pmid34962958, year = {2021}, author = {Ren, W and Zhao, J and Ma, X and Wang, X}, title = {Analysis of the spatial differentiation and scale effects of the three-dimensional architectural landscape in Xi'an, China.}, journal = {PloS one}, volume = {16}, number = {12}, pages = {e0261846}, pmid = {34962958}, issn = {1932-6203}, mesh = {*Architecture ; China ; Cities ; *City Planning ; Climate ; Conservation of Natural Resources ; *Ecology ; Ecosystem ; Geographic Information Systems ; Geography ; Models, Theoretical ; Principal Component Analysis ; Software ; Spatial Analysis ; Sustainable Development ; Urban Renewal ; }, abstract = {Three-dimensional landscape patterns are an effective means to study the relationship between landscape pattern evolution and eco-environmental effects. This paper selects six districts in Xi'an as the study area to examine the spatial distribution characteristics of the three-dimensional architectural landscape in the city's main urban area using three-dimensional information on the buildings in 2020 with the support of GIS. In this study, two new architectural landscape indices-landscape height variable coefficient and building rugosity index-were employed in landscape pattern analysis, whilst a system of rigorous and comprehensive three-dimensional architectural landscape metrics was established using principal component analysis. A mathematical model of weighted change of landscape metrics based on the objective weighting method was applied to carry out scale analysis of the landscape patterns. Spatial statistical analysis and spatial autocorrelation analysis were conducted to comprehensively study the differentiation of three-dimensional architectural landscape spatial patterns. The results show that the characteristic scale of the three-dimensional landscape pattern in Xi'an's main urban area is around 8 km. Moreover, the three-dimensional landscape of the buildings in this area is spatially positively correlated, exhibiting a high degree of spatial autocorrelation whilst only showing small spatial differences. The layout of the architectural landscape pattern is disorderly and chaotic within the second ring, whilst the clustering of patch types occurs near the third ring. Moreover, the building density in the Beilin, Lianhu, and Xincheng districts is large, the building height types are rich, and the roughness of the underlying surface is high, such that these are key areas to be improved through urban renewal. The height, volume, density, morphological heterogeneity, and vertical roughness of the architectural landscape vary amongst functional areas within the study area. This paper is the first to apply the study of spatial heterogeneity of three-dimensional landscape patterns to Xi'an. It does so in order to provide a quantitative basis for urban landscape ecological design for urban renewal and the rational planning of built-up areas, which will promote the sustainable development of the city's urban environment.}, } @article {pmid34961822, year = {2021}, author = {Zhang, F and Wang, X and Yu, G and Gao, J and Niu, H and Zhao, J}, title = {Detection and Genotyping of Francisella tularensis in Animal Hosts and Vectors from Six Different Natural Landscape Areas, Gansu Province, China.}, journal = {Computational and mathematical methods in medicine}, volume = {2021}, number = {}, pages = {6820864}, pmid = {34961822}, issn = {1748-6718}, mesh = {Animals ; Animals, Wild/*microbiology ; China/epidemiology ; Computational Biology ; DNA, Bacterial/genetics ; Disease Vectors ; Francisella tularensis/classification/*genetics/*isolation & purification ; Genotype ; Host Specificity ; Humans ; Microsatellite Repeats ; Rodentia/microbiology ; Ticks/microbiology ; Tularemia/epidemiology/transmission/veterinary ; }, abstract = {OBJECTIVE: Tularemia, also known as hare fever, is caused by the bacterium Francisella tularensis (F. tularensis) transmitted through diseased wild animals, blood sucking insects, or contaminated water or food, which is distributed worldwide. The purpose of this study was to investigate F. tularensis infection in animal hosts and vectors from six different natural landscape areas in Gansu Province and to identify the genotypes of the detected F. tularensis.

METHODS: Rodents were captured by snap traps, and ticks were collected by dragging a cloth over the vegetation or from domestic animals. After species identification, DNA was isolated from the captured animals and detected by nested PCR assays targeting the F. tularensis fopA gene. The positive samples were further amplified to discriminate the species, and another two short-sequence tandem repeat regions (SSTR) were amplified to identify their genotypes. All positive fragments were sequenced and analyzed by ClustalX (5.0) and DNAClub software.

RESULTS: A total of 407 rodents of 12 species were captured, among which six rodent species were positive for F. tularensis, with an overall prevalence of 3.93%. The geographical difference in infection rate was statistically significant. At the SSTR9 locus, there were 7 genotypes among positive rodent samples. A total of 1864 ticks were tested for evidence of tularemia by nested PCR assays, 69 of which were positive, with an average positive rate of 3.70% for F. tularensis in ticks. The positive rates were significantly different among different regions. Seven genotypes were identified at the SSTR9 locus, one of which seemed dominant in positive tick samples. All positive samples had the same genotype at the SSTR16 locus.

CONCLUSION: There is natural infection of F. tularensis among animal vectors and hosts in Gansu Province, with diverse genotypes.}, } @article {pmid34961277, year = {2021}, author = {Sukhikh, S and Asyakina, L and Korobenkov, M and Skrypnik, L and Pungin, A and Ivanova, S and Larichev, T and Larina, V and Krol, O and Ulrikh, E and Chupakhin, E and Babich, O}, title = {Chemical Composition and Content of Biologically Active Substances Found in Cotinus coggygria, Dactylorhiza maculata, Platanthera chlorantha Growing in Various Territories.}, journal = {Plants (Basel, Switzerland)}, volume = {10}, number = {12}, pages = {}, pmid = {34961277}, issn = {2223-7747}, support = {19-72-30009//Russian Science Foundation/ ; }, abstract = {Medicinal plants (Cotinus coggygria, Dactylorhiza maculata, Platanthera chlorantha) growing in various territories (Kaliningrad, Moscow, and Minsk regions) were the objects of research. This paper presents a study of the chemical composition of these plants. To analyze the qualitative and quantitative composition of biologically active substances, the method of high-performance liquid chromatography was used. Atomic absorption spectrometry was used to study the content of trace elements. The content of organic acids and vitamins was determined by capillary electrophoresis using the Kapel-105/105M capillary electrophoresis system with high negative polarity. Extracts of medicinal plants were obtained on a Soxhlet apparatus using 70% ethanol as an extractant. It was found that among the biologically active substances in the plants under discussion, hyperoside, rutin (C. coggygria), Ferulic acid and Gallic acid (D. maculata), triene hydrocarbon (3,7-Dimethyl-1,3,6-octatriene), unsaturated alcohol (3,7-Dimethyl-2,6-octadien-1-ol), and benzyl acetate (P. chlorantha) prevailed. Samples of these medicinal plants contained trace elements (phosphorus, potassium, calcium, sodium, magnesium, and sulfur) and many aliphatic organic acids (succinic acid, benzoic acid, fumaric acid, citric acid, oxalic acid, and tartaric acid). The largest amount of biologically active substances and secondary metabolites of the studied plants from the Eastern Baltic is associated with climatic and ecological differences from other regions. The composition of these plants determines the potential of their use in feed additives for livestock and poultry as part of measures to improve the quality of livestock products. The use of medicinal plants for the production of feed additives is relevant in terms of improving regional economies, as well as improving the quality of life and nation's health by providing ecologically clean livestock products.}, } @article {pmid34960394, year = {2021}, author = {Ciampittiello, M and Manca, D and Dresti, C and Grisoni, S and Lami, A and Saidi, H}, title = {Meteo-Hydrological Sensors within the Lake Maggiore Catchment: System Establishment, Functioning and Data Validation.}, journal = {Sensors (Basel, Switzerland)}, volume = {21}, number = {24}, pages = {}, pmid = {34960394}, issn = {1424-8220}, support = {281- 120//POR-FESR 2007-2013 - Bando IOD - Attività I.1.3 Innovazione e PMI/ ; not present//Scientific collaboration agreement between CNR IRSA and CNR IRPI/ ; }, mesh = {*Ecosystem ; Environmental Monitoring ; Human Activities ; Humans ; Hydrology ; *Lakes ; Meteorology ; }, abstract = {Climate change and human activities have a strong impact on lakes and their catchments, so to understand ongoing processes it is fundamental to monitor environmental variables with a spatially well-distributed and high frequency network and efficiently share data. An effective sharing and interoperability of environmental information between technician and end-user fosters an in-depth knowledge of the territory and its critical environmental issues. In this paper, we present the approaches and the results obtained during the PITAGORA project (Interoperable Technological Platform for Acquisition, Management and Organization of Environmental data, related to the lake basin). PITAGORA was aimed at developing both instruments and data management, including pre-processing and quality control of raw data to ensure that data are findable, accessible, interoperable, and reusable (FAIR principles). The main results show that the developed instrumentation is low-cost, easily implementable and reliable, and can be applied to the measurement of diverse environmental parameters such as meteorological, hydrological, physico-chemical, and geological. The flexibility of the solutions proposed make our system adaptable to different monitoring purposes, research, management, and civil protection. The real time access to environmental information can improve management of a territory and ecosystems, safety of the population, and sustainable socio-economic development.}, } @article {pmid34951964, year = {2022}, author = {Henriksen, RA and Jenjaroenpun, P and Sjøstrøm, IB and Jensen, KR and Prada-Luengo, I and Wongsurawat, T and Nookaew, I and Regenberg, B}, title = {Circular DNA in the human germline and its association with recombination.}, journal = {Molecular cell}, volume = {82}, number = {1}, pages = {209-217.e7}, pmid = {34951964}, issn = {1097-4164}, support = {P20 GM125503/GM/NIGMS NIH HHS/United States ; }, mesh = {Alu Elements ; *Chromosomes, Human ; DNA, Circular/genetics/*metabolism ; Evolution, Molecular ; Gene Expression Regulation, Developmental ; Humans ; Male ; *Meiosis ; Mutation ; *Recombination, Genetic ; Spermatozoa/*metabolism ; }, abstract = {Extrachromosomal circular DNA (eccDNA) is common in somatic tissue, but its existence and effects in the human germline are unexplored. We used microscopy, long-read DNA sequencing, and new analytic methods to document thousands of eccDNAs from human sperm. EccDNAs derived from all genomic regions and mostly contained a single DNA fragment, although some consisted of multiple fragments. The generation of eccDNA inversely correlates with the meiotic recombination rate, and chromosomes with high coding-gene density and Alu element abundance form the least eccDNA. Analysis of insertions in human genomes further indicates that eccDNA can persist in the human germline when the circular molecules reinsert themselves into the chromosomes. Our results suggest that eccDNA has transient and permanent effects on the germline. They explain how differences in the physical and genetic map might arise and offer an explanation of how Alu elements coevolved with genes to protect genome integrity against deleterious mutations producing eccDNA.}, } @article {pmid34948556, year = {2021}, author = {Vasile, GG and Tenea, AG and Dinu, C and Iordache, AMM and Gheorghe, S and Mureseanu, M and Pascu, LF}, title = {Bioavailability, Accumulation and Distribution of Toxic Metals (As, Cd, Ni and Pb) and Their Impact on Sinapis alba Plant Nutrient Metabolism.}, journal = {International journal of environmental research and public health}, volume = {18}, number = {24}, pages = {}, pmid = {34948556}, issn = {1660-4601}, mesh = {Biological Availability ; Cadmium/toxicity ; Lead ; *Metals, Heavy/analysis/toxicity ; Nutrients ; Sinapis ; Soil ; *Soil Pollutants/analysis/toxicity ; }, abstract = {This study presents the behavior of white mustard seedlings Sinapis alba grown for three months in laboratory polluted soil containing As, Cd, Ni and Pb. Four different experiments were performed in which As was combined with the other three toxic metals in different combinations (As, AsCd, AsCdNi, AsCdNiPb), keeping the same concentrations of As and Cd in all tests and following the national soil quality regulations. The effects of these metals were monitored by the analytical control of metal concentrations in soil and plants, bioavailability tests of mobile metal fractions using three different extracting solutions (DTPA + TEA + CaCl2-DTPA, DTPA + CaCl2-CAT, and CH3COONH4 + EDTA-EDTA) and calculation of bioaccumulation and translocation factors. Additionally, micro, and macro-nutrients both in soil and plant (root, stem, leaves, flowers and seeds) were analyzed in order to evaluate the impact of toxic metals on plant nutrient metabolism. Metals were significantly and differently accumulated in the plant tissues, especially under AsCdNi and AsCdNiPb treatments. Significant differences (p < 0.05) in the concentration of both As and Cd were highlighted. Translocation could be influenced by the presence of other toxic metals, such as Cd, but also of essential metals, through the competition and antagonism processes existing in plant tissues. Significantly, more Cd and Ni levels were detected in leaves and flowers. Cd was also detected in seeds above the WHO limit, but the results are not statistically significant (p > 0.05). The extraction of metallic nutrients (Zn, Cu, Mn, Ni, Mg, K, Fe, Ca, Cr) in the plant was not influenced by the presence of toxic metal combinations, on the contrary, their translocation was more efficient in the aerial parts of the plants. No phytotoxic effects were recorded during the exposure period. The most efficient methods of metal extraction from soil were for As-CAT; Cd-all methods; Pb and Ni-DTPA. The Pearson correlations (r) between applied extraction methods and metal detection in plants showed positive correlations for all toxic metals as follows: As-CAT > DTPA > EDTA, Cd-DTPA > CAT > EDTA, Ni-EDTA = DTPA > CAT, Pb-EDTA = DTPA = CAT). The results revealed that Sinapis alba has a good ability to accumulate the most bioavailable metals Cd and Ni, to stabilize As at the root level and to block Pb in soil.}, } @article {pmid34948531, year = {2021}, author = {Jin, T and Meng, Q and Li, X and Zhou, L}, title = {Fluorescence Characteristics of Coalbed Methane Produced Water and Its Influence on Freshwater Bacteria in the South Qinshui Basin, China.}, journal = {International journal of environmental research and public health}, volume = {18}, number = {24}, pages = {}, pmid = {34948531}, issn = {1660-4601}, mesh = {Bacteria/genetics ; China ; Factor Analysis, Statistical ; Fluorescence ; Fresh Water ; Humic Substances/analysis ; *Methane ; Spectrometry, Fluorescence ; *Water Pollutants, Chemical/analysis ; }, abstract = {Production of coalbed methane (CBM) resources commonly requires using hydraulic fracturing and chemical production well additives. Concern exists for the existence of chemical compounds in CBM produced water, due to the risk of environmental receptor contamination. In this study, parallel factor method analysis (PARAFAC), fluorescence index, and the fluorescence area integral methods were used to analyse the properties of CBM produced water sampled from Shizhuang Block (one of the most active CBM-producing regions in the Qinshui Basin). A culture experiment was designed to determine the effect of discharged CBM produced water on microorganisms in freshwater. Water quality analysis shows the hydrochemistry of most water samples as Na-HCO3 type produced water of CBM appears as a generally weak alkaline (pH 8.69 ± 0.185) with high salinity, high alkalinity, and a high chemical oxygen demand (COD) value. Three individual components were identified by using parallel factor method analysis as humic-like components (C1), fulvic-like components (C2), and amino acid-like substances (C3). The fluorescence characteristic index comprehensively explains that the fluorescent substances in CBM produced water has the characteristics of a low degree of humification and a high recent self-generating source. The region integration results of characteristic peaks show that tyrosine-like and tryptophan-like materials account for more than 67% of fluorescent substances in CBM produced water. The addition of produced water from coalbed methane promotes the growth of freshwater bacteria, and this process is accompanied by the decrease of the proportion of fulvic acid, humic acid, and the increase of the proportion of soluble microbial metabolites. This paper proposes a convenient method for organic matter identification of CBM produced water and provides some theoretical support and reference for the improvement of CBM water treatment and utilization.}, } @article {pmid34632092, year = {2021}, author = {Boyes, DH and Holland, PWH and , and , and , and , and , and , }, title = {The genome sequence of the yellow-tail moth, Euproctis similis (Fuessly, 1775).}, journal = {Wellcome open research}, volume = {6}, number = {}, pages = {227}, pmid = {34632092}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; 206194/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual male Euproctis similis (the yellow-tail; Arthropoda; Insecta; Lepidoptera; Lymantriidae). The genome sequence is 508 megabases in span. Over 99% of the assembly is scaffolded into 22 chromosomal pseudomolecules, with the Z sex chromosome assembled. The complete mitochondrial genome, 15.5 kb in length, was also assembled.}, } @article {pmid34941865, year = {2021}, author = {Thindwa, D and Wolter, N and Pinsent, A and Carrim, M and Ojal, J and Tempia, S and Moyes, J and McMorrow, M and Kleynhans, J and Gottberg, AV and French, N and , and Cohen, C and Flasche, S}, title = {Estimating the contribution of HIV-infected adults to household pneumococcal transmission in South Africa, 2016-2018: A hidden Markov modelling study.}, journal = {PLoS computational biology}, volume = {17}, number = {12}, pages = {e1009680}, pmid = {34941865}, issn = {1553-7358}, support = {208812/Z/17/Z/WT_/Wellcome Trust/United Kingdom ; /DH_/Department of Health/United Kingdom ; }, mesh = {Adolescent ; Adult ; Algorithms ; Carrier State/epidemiology/transmission ; Child ; Child, Preschool ; Computational Biology ; Female ; *HIV Infections/complications/epidemiology ; Humans ; Male ; Markov Chains ; Middle Aged ; Models, Statistical ; *Pneumococcal Infections/complications/epidemiology/transmission ; South Africa/epidemiology ; Streptococcus pneumoniae ; Young Adult ; }, abstract = {Human immunodeficiency virus (HIV) infected adults are at a higher risk of pneumococcal colonisation and disease, even while receiving antiretroviral therapy (ART). To help evaluate potential indirect effects of vaccination of HIV-infected adults, we assessed whether HIV-infected adults disproportionately contribute to household transmission of pneumococci. We constructed a hidden Markov model to capture the dynamics of pneumococcal carriage acquisition and clearance observed during a longitudinal household-based nasopharyngeal swabbing study, while accounting for sample misclassifications. Households were followed-up twice weekly for approximately 10 months each year during a three-year study period for nasopharyngeal carriage detection via real-time PCR. We estimated the effect of participant's age, HIV status, presence of a HIV-infected adult within the household and other covariates on pneumococcal acquisition and clearance probabilities. Of 1,684 individuals enrolled, 279 (16.6%) were younger children (<5 years-old) of whom 4 (1.5%) were HIV-infected and 726 (43.1%) were adults (≥18 years-old) of whom 214 (30.4%) were HIV-infected, most (173, 81.2%) with high CD4+ count. The observed range of pneumococcal carriage prevalence across visits was substantially higher in younger children (56.9-80.5%) than older children (5-17 years-old) (31.7-50.0%) or adults (11.5-23.5%). We estimate that 14.4% (95% Confidence Interval [CI]: 13.7-15.0) of pneumococcal-negative swabs were false negatives. Daily carriage acquisition probabilities among HIV-uninfected younger children were similar in households with and without HIV-infected adults (hazard ratio: 0.95, 95%CI: 0.91-1.01). Longer average carriage duration (11.4 days, 95%CI: 10.2-12.8 vs 6.0 days, 95%CI: 5.6-6.3) and higher median carriage density (622 genome equivalents per millilitre, 95%CI: 507-714 vs 389, 95%CI: 311.1-435.5) were estimated in HIV-infected vs HIV-uninfected adults. The use of ART and antibiotics substantially reduced carriage duration in all age groups, and acquisition rates increased with household size. Although South African HIV-infected adults on ART have longer carriage duration and density than their HIV-uninfected counterparts, they show similar patterns of pneumococcal acquisition and onward transmission.}, } @article {pmid34941548, year = {2021}, author = {Bartlett Ellis, R and Wright, J and Miller, LS and Jake-Schoffman, D and Hekler, EB and Goldstein, CM and Arigo, D and Nebeker, C}, title = {Lessons Learned: Beta-Testing the Digital Health Checklist for Researchers Prompts a Call to Action by Behavioral Scientists.}, journal = {Journal of medical Internet research}, volume = {23}, number = {12}, pages = {e25414}, pmid = {34941548}, issn = {1438-8871}, support = {K23 HL136657/HL/NHLBI NIH HHS/United States ; }, mesh = {*COVID-19 ; *Checklist ; Ethics Committees, Research ; Humans ; Retrospective Studies ; SARS-CoV-2 ; }, abstract = {Digital technologies offer unique opportunities for health research. For example, Twitter posts can support public health surveillance to identify outbreaks (eg, influenza and COVID-19), and a wearable fitness tracker can provide real-time data collection to assess the effectiveness of a behavior change intervention. With these opportunities, it is necessary to consider the potential risks and benefits to research participants when using digital tools or strategies. Researchers need to be involved in the risk assessment process, as many tools in the marketplace (eg, wellness apps, fitness sensors) are underregulated. However, there is little guidance to assist researchers and institutional review boards in their evaluation of digital tools for research purposes. To address this gap, the Digital Health Checklist for Researchers (DHC-R) was developed as a decision support tool. A participatory research approach involving a group of behavioral scientists was used to inform DHC-R development. Scientists beta-tested the checklist by retrospectively evaluating the technologies they had chosen for use in their research. This paper describes the lessons learned because of their involvement in the beta-testing process and concludes with recommendations for how the DHC-R could be useful for a variety of digital health stakeholders. Recommendations focus on future research and policy development to support research ethics, including the development of best practices to advance safe and responsible digital health research.}, } @article {pmid34938590, year = {2021}, author = {Latombe, G and Richardson, DM and McGeoch, MA and Altwegg, R and Catford, JA and Chase, JM and Courchamp, F and Esler, KJ and Jeschke, JM and Landi, P and Measey, J and Midgley, GF and Minoarivelo, HO and Rodger, JG and Hui, C}, title = {Mechanistic reconciliation of community and invasion ecology.}, journal = {Ecosphere (Washington, D.C)}, volume = {12}, number = {2}, pages = {e03359}, pmid = {34938590}, issn = {2150-8925}, abstract = {Community and invasion ecology have mostly grown independently. There is substantial overlap in the processes captured by different models in the two fields, and various frameworks have been developed to reduce this redundancy and synthesize information content. Despite broad recognition that community and invasion ecology are interconnected, a process-based framework synthesizing models across these two fields is lacking. Here we review 65 representative community and invasion models and propose a common framework articulated around six processes (dispersal, drift, abiotic interactions, within-guild interactions, cross-guild interactions, and genetic changes). The framework is designed to synthesize the content of the two fields, provide a general perspective on their development, and enable their comparison. The application of this framework and of a novel method based on network theory reveals some lack of coherence between the two fields, despite some historical similarities. Community ecology models are characterized by combinations of multiple processes, likely reflecting the search for an overarching theory to explain community assembly and structure, drawing predominantly on interaction processes, but also accounting largely for the other processes. In contrast, most models in invasion ecology invoke fewer processes and focus more on interactions between introduced species and their novel biotic and abiotic environment. The historical dominance of interaction processes and their independent developments in the two fields is also reflected in the lower level of coherence for models involving interactions, compared to models involving dispersal, drift, and genetic changes. It appears that community ecology, with a longer history than invasion ecology, has transitioned from the search for single explanations for patterns observed in nature to investigate how processes may interact mechanistically, thereby generating and testing hypotheses. Our framework paves the way for a similar transition in invasion ecology, to better capture the dynamics of multiple alien species introduced in complex communities. Reciprocally, applying insights from invasion to community ecology will help us understand and predict the future of ecological communities in the Anthropocene, in which human activities are weakening species' natural boundaries. Ultimately, the successful integration of the two fields could advance a predictive ecology that is urgently required in a rapidly changing world.}, } @article {pmid34934063, year = {2021}, author = {Shvetz, C and Gu, F and Drodge, J and Torous, J and Guimond, S}, title = {Validation of an ecological momentary assessment to measure processing speed and executive function in schizophrenia.}, journal = {NPJ schizophrenia}, volume = {7}, number = {1}, pages = {64}, pmid = {34934063}, issn = {2334-265X}, support = {K23 MH116130/MH/NIMH NIH HHS/United States ; K23MH116130//U.S. Department of Health & Human Services | NIH | National Institute of Mental Health (NIMH)/ ; }, abstract = {Cognitive impairments are a core feature of schizophrenia that have negative impacts on functional outcomes. However, it remains challenging to assess these impairments in clinical settings. Smartphone apps provide the opportunity to measure cognitive impairments in an accessible way; however, more research is needed to validate these cognitive assessments in schizophrenia. We assessed the initial accessibility, validity, and reliability of a smartphone-based cognitive test to measure cognition in schizophrenia. A total of 29 individuals with schizophrenia and 34 controls were included in the analyses. Participants completed the standard pen-and-paper Trail Making Tests (TMT) A and B, and smartphone-based versions, Jewels Trail Tests (JTT) A and B, at the single in-lab visit. Participants were asked to complete the JTT remotely once per week for three months. We also investigated how subjective sleep quality and mood may affect cognitive performance longitudinally. In-lab and remote JTT scores moderately and positively correlated with in-lab TMT scores. Moderate test-retest reliability was observed across the in-lab, first remote, and last remote completion times of the JTT. Additionally, individuals with schizophrenia had significantly lower performance compared to controls on both the in-lab JTT and TMT. Self-reported mood had a significant effect on JTT A performance over time but no other significant relationships were found remotely. Our results support the initial accessibility, validity and reliability of using the JTT to measure cognition in schizophrenia. Future research to develop additional smartphone-based cognitive tests as well as with larger samples and in other psychiatric populations are warranted.}, } @article {pmid34932588, year = {2021}, author = {Gumede, SB and de Wit, JBF and Venter, WDF and Lalla-Edward, ST}, title = {Study protocol: Strengthening understanding of effective adherence strategies for first-line and second-line antiretroviral therapy (ART) in selected rural and urban communities in South Africa.}, journal = {PloS one}, volume = {16}, number = {12}, pages = {e0261107}, pmid = {34932588}, issn = {1932-6203}, support = {/WT_/Wellcome Trust/United Kingdom ; UG3 HL156388/HL/NHLBI NIH HHS/United States ; }, mesh = {Adolescent ; Adult ; Aged ; Aged, 80 and over ; Anti-Retroviral Agents/*therapeutic use ; Clinical Trials, Phase I as Topic ; Clinical Trials, Phase II as Topic ; Clinical Trials, Phase III as Topic ; Clinical Trials, Phase IV as Topic ; Female ; HIV/*drug effects ; HIV Infections/*drug therapy/epidemiology/virology ; Humans ; Male ; Medication Adherence/*statistics & numerical data ; Middle Aged ; Randomized Controlled Trials as Topic ; Retrospective Studies ; Rural Population ; South Africa/epidemiology ; Urban Population ; *Viral Load ; Young Adult ; }, abstract = {Multiple factors make adherence to antiretroviral therapy (ART) a complex process. This study aims to describe the barriers and facilitators to adherence for patients receiving first-line and second-line ART, identify different adherence strategies utilized and make recommendations for an improved adherence strategy. This mixed method parallel convergent study will be conducted in seven high volume public health facilities in Gauteng and one in Limpopo province in South Africa. The study consists of four phases; a retrospective secondary data analysis of a large cohort of patients on ART (using TIER.Net, an ART patient and data management system for recording and monitoring patients on ART and tuberculosis (TB)) from seven Johannesburg inner-city public health facilities (Gauteng province); a secondary data analysis of the Intensified Treatment Monitoring Accumulation (ITREMA) trial (a randomized control trial which ran from June 2015 to January 2019) conducted at the Ndlovu Medical Center (Limpopo province); in-depth interviews with people living with Human Immunodeficiency Virus (PLHIV) who are taking ART (in both urban and rural settings); and a systematic review of the impact of treatment adherence interventions for chronic conditions in sub-Saharan Africa. Data will be collected on demographics, socio-economic status, treatment support, retention in care status, disclosure, stigma, clinical markers (CD4 count and viral load (VL)), self-reported adherence information, intrapersonal, and interpersonal factors, community networks, and policy level factors. The systematic review will follow the Preferred Reporting Items for Systematic Reviews and Meta-Analysis (PRISMA) reporting and Population, Interventions, Comparisons and Outcomes (PICO) criteria. Analyses will involve tests of association (Chi-square and t-test), thematic analysis (deductive and inductive approaches) and network meta-analysis. Using an integrated multilevel socio-ecological framework this study will describe the factors associated with adherence for PLHIV who are taking first-line or second-line ART. Implementing evidence-based adherence approaches, when taken up, will improve patient's overall health outcomes. Our study results will provide guidance regarding context-specific intervention strategies to improve ART adherence.}, } @article {pmid34932572, year = {2021}, author = {Diaz-Colunga, J and Diaz-Uriarte, R}, title = {Conditional prediction of consecutive tumor evolution using cancer progression models: What genotype comes next?.}, journal = {PLoS computational biology}, volume = {17}, number = {12}, pages = {e1009055}, pmid = {34932572}, issn = {1553-7358}, mesh = {Computational Biology/*methods ; Disease Progression ; Evolution, Molecular ; Genotype ; Humans ; *Models, Genetic ; Mutation/genetics ; *Neoplasms/genetics/pathology ; }, abstract = {Accurate prediction of tumor progression is key for adaptive therapy and precision medicine. Cancer progression models (CPMs) can be used to infer dependencies in mutation accumulation from cross-sectional data and provide predictions of tumor progression paths. However, their performance when predicting complete evolutionary trajectories is limited by violations of assumptions and the size of available data sets. Instead of predicting full tumor progression paths, here we focus on short-term predictions, more relevant for diagnostic and therapeutic purposes. We examine whether five distinct CPMs can be used to answer the question "Given that a genotype with n mutations has been observed, what genotype with n + 1 mutations is next in the path of tumor progression?" or, shortly, "What genotype comes next?". Using simulated data we find that under specific combinations of genotype and fitness landscape characteristics CPMs can provide predictions of short-term evolution that closely match the true probabilities, and that some genotype characteristics can be much more relevant than global features. Application of these methods to 25 cancer data sets shows that their use is hampered by a lack of information needed to make principled decisions about method choice. Fruitful use of these methods for short-term predictions requires adapting method's use to local genotype characteristics and obtaining reliable indicators of performance; it will also be necessary to clarify the interpretation of the method's results when key assumptions do not hold.}, } @article {pmid34930971, year = {2021}, author = {Hammoud, R and Tognin, S and Bakolis, I and Ivanova, D and Fitzpatrick, N and Burgess, L and Smythe, M and Gibbons, J and Davidson, N and Mechelli, A}, title = {Lonely in a crowd: investigating the association between overcrowding and loneliness using smartphone technologies.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {24134}, pmid = {34930971}, issn = {2045-2322}, support = {MR/S026428/1/MRC_/Medical Research Council/United Kingdom ; /DH_/Department of Health/United Kingdom ; }, abstract = {Loneliness is a major public health concern with links to social and environmental factors. Previous studies have typically investigated loneliness as a stable emotional state using retrospective cross-sectional designs. Yet people experience different levels of loneliness throughout the day depending on their surrounding environment. In the present study, we investigated the associations between loneliness and social and environmental factors (i.e. overcrowding, population density, social inclusivity and contact with nature) in real-time. Ecological momentary assessment data was collected from participants using the Urban Mind smartphone application. Data from 756 participants who completed 16,602 assessments between April 2018 and March 2020 were used in order to investigate associations between momentary feeling of loneliness, the social environment (i.e. overcrowding, social inclusivity, population density) and the built environment (i.e. contact with nature) using multilevel modelling. Increased overcrowding and population density were associated with higher levels of loneliness; in contrast, social inclusivity and contact with nature were associated with lower levels of loneliness. These associations remained significant after adjusting for age, gender, ethnicity, education and occupation. The positive association between social inclusivity and lower levels of loneliness was more pronounced when participants were in contact with nature, indicating an interaction between the social and built environment on loneliness. The feeling of loneliness changes in relation to both social and environmental factors. Our findings have potential implications for public health strategies and interventions aimed at reducing the burden of loneliness on society. Specific measures, which would increase social inclusion and contact with nature while reducing overcrowding, should be implemented, especially in densely populated cities.}, } @article {pmid34922131, year = {2022}, author = {Chen, F and Ma, J and Zhu, Y and Li, X and Yu, H and Sun, Y}, title = {Biodegradation performance and anti-fouling mechanism of an ICME/electro-biocarriers-MBR system in livestock wastewater (antibiotic-containing) treatment.}, journal = {Journal of hazardous materials}, volume = {426}, number = {}, pages = {128064}, doi = {10.1016/j.jhazmat.2021.128064}, pmid = {34922131}, issn = {1873-3336}, mesh = {Animals ; Anti-Bacterial Agents ; *Biofouling/prevention & control ; Bioreactors ; Carbon ; Electrolysis ; Hydrogen Peroxide ; Iron ; Livestock ; Membranes, Artificial ; *Wastewater ; }, abstract = {Livestock wastewater is an important reservoir of antibiotic resistance genes (ARGs) and antibiotic residues. Membrane fouling is one of the most challenging problems confining the operation and application of membrane bioreactor (MBR). In this work, a novel iron-carbon micro-electrolysis (ICME)/electro-biocarriers-MBR system was established to explore the performance of pollutant removal and anti-fouling for an actual livestock wastewater. A light-weight porous ceramsite (bulk density 0.98 g/cm[3]) was used as the MBR biocarriers. The electrons generated from iron corrosion in the ICME tank traveled through external wires to the stainless steel membrane modules of MBR and the protons were transferred from the MBR tank to the ICME tank through a salt bridge, thus producing a spontaneous electric field. Under the optimized conditions, the system exhibited chemical oxygen demand removal of 76.0%, total suspended solids removal of 100%, antibiotic removal of 86.4%, NH4[+]-N removal of 91.1%, and ARGs reduction of 6-8 orders of magnitude. The quality of the final effluent can reach the national Class I-A discharge criteria. Adding ceramsite could not only effectively improve biodegradation performance but also alleviate membrane fouling through the migration and enrichment of microbial flora to the ceramsite. The self-generated electric field had no significant improvement effect on pollutant removal, but exhibited good anti-membrane fouling behavior which could be ascribed to (i) oxidization of membrane foulants by the electrochemical products (such as H2O2 and •OH radicals), and (ii) electrostatic repulsion of negatively charged foulants and bacterial cells. The bacterial community structure and diversity were studied using high-throughput pyrosequencing, and the results demonstrated the roles of electric field and biocarriers in enrichment of anti-fouling communities and repulsion of biofouling-creating communities.}, } @article {pmid34921678, year = {2022}, author = {Allen-Perkins, A and Magrach, A and Dainese, M and Garibaldi, LA and Kleijn, D and Rader, R and Reilly, JR and Winfree, R and Lundin, O and McGrady, CM and Brittain, C and Biddinger, DJ and Artz, DR and Elle, E and Hoffman, G and Ellis, JD and Daniels, J and Gibbs, J and Campbell, JW and Brokaw, J and Wilson, JK and Mason, K and Ward, KL and Gundersen, KB and Bobiwash, K and Gut, L and Rowe, LM and Boyle, NK and Williams, NM and Joshi, NK and Rothwell, N and Gillespie, RL and Isaacs, R and Fleischer, SJ and Peterson, SS and Rao, S and Pitts-Singer, TL and Fijen, T and Boreux, V and Rundlöf, M and Viana, BF and Klein, AM and Smith, HG and Bommarco, R and Carvalheiro, LG and Ricketts, TH and Ghazoul, J and Krishnan, S and Benjamin, FE and Loureiro, J and Castro, S and Raine, NE and de Groot, GA and Horgan, FG and Hipólito, J and Smagghe, G and Meeus, I and Eeraerts, M and Potts, SG and Kremen, C and García, D and Miñarro, M and Crowder, DW and Pisanty, G and Mandelik, Y and Vereecken, NJ and Leclercq, N and Weekers, T and Lindstrom, SAM and Stanley, DA and Zaragoza-Trello, C and Nicholson, CC and Scheper, J and Rad, C and Marks, EAN and Mota, L and Danforth, B and Park, M and Bezerra, ADM and Freitas, BM and Mallinger, RE and Oliveira da Silva, F and Willcox, B and Ramos, DL and D da Silva E Silva, F and Lázaro, A and Alomar, D and González-Estévez, MA and Taki, H and Cariveau, DP and Garratt, MPD and Nabaes Jodar, DN and Stewart, RIA and Ariza, D and Pisman, M and Lichtenberg, EM and Schüepp, C and Herzog, F and Entling, MH and Dupont, YL and Michener, CD and Daily, GC and Ehrlich, PR and Burns, KLW and Vilà, M and Robson, A and Howlett, B and Blechschmidt, L and Jauker, F and Schwarzbach, F and Nesper, M and Diekötter, T and Wolters, V and Castro, H and Gaspar, H and Nault, BA and Badenhausser, I and Petersen, JD and Tscharntke, T and Bretagnolle, V and Willis Chan, DS and Chacoff, N and Andersson, GKS and Jha, S and Colville, JF and Veldtman, R and Coutinho, J and Bianchi, FJJA and Sutter, L and Albrecht, M and Jeanneret, P and Zou, Y and Averill, AL and Saez, A and Sciligo, AR and Vergara, CH and Bloom, EH and Oeller, E and Badano, EI and Loeb, GM and Grab, H and Ekroos, J and Gagic, V and Cunningham, SA and Åström, J and Cavigliasso, P and Trillo, A and Classen, A and Mauchline, AL and Montero-Castaño, A and Wilby, A and Woodcock, BA and Sidhu, CS and Steffan-Dewenter, I and Vogiatzakis, IN and Herrera, JM and Otieno, M and Gikungu, MW and Cusser, SJ and Nauss, T and Nilsson, L and Knapp, J and Ortega-Marcos, JJ and González, JA and Osborne, JL and Blanche, R and Shaw, RF and Hevia, V and Stout, J and Arthur, AD and Blochtein, B and Szentgyorgyi, H and Li, J and Mayfield, MM and Woyciechowski, M and Nunes-Silva, P and Halinski de Oliveira, R and Henry, S and Simmons, BI and Dalsgaard, B and Hansen, K and Sritongchuay, T and O'Reilly, AD and Chamorro García, FJ and Nates Parra, G and Magalhães Pigozo, C and Bartomeus, I}, title = {CropPol: A dynamic, open and global database on crop pollination.}, journal = {Ecology}, volume = {103}, number = {3}, pages = {e3614}, doi = {10.1002/ecy.3614}, pmid = {34921678}, issn = {1939-9170}, support = {BB/I000348/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; Bees ; Crops, Agricultural ; *Ecosystem ; Flowers ; Insecta ; *Pollination ; }, abstract = {Seventy five percent of the world's food crops benefit from insect pollination. Hence, there has been increased interest in how global change drivers impact this critical ecosystem service. Because standardized data on crop pollination are rarely available, we are limited in our capacity to understand the variation in pollination benefits to crop yield, as well as to anticipate changes in this service, develop predictions, and inform management actions. Here, we present CropPol, a dynamic, open, and global database on crop pollination. It contains measurements recorded from 202 crop studies, covering 3,394 field observations, 2,552 yield measurements (i.e., berry mass, number of fruits, and fruit density [kg/ha], among others), and 47,752 insect records from 48 commercial crops distributed around the globe. CropPol comprises 32 of the 87 leading global crops and commodities that are pollinator dependent. Malus domestica is the most represented crop (32 studies), followed by Brassica napus (22 studies), Vaccinium corymbosum (13 studies), and Citrullus lanatus (12 studies). The most abundant pollinator guilds recorded are honey bees (34.22% counts), bumblebees (19.19%), flies other than Syrphidae and Bombyliidae (13.18%), other wild bees (13.13%), beetles (10.97%), Syrphidae (4.87%), and Bombyliidae (0.05%). Locations comprise 34 countries distributed among Europe (76 studies), North America (60), Latin America and the Caribbean (29), Asia (20), Oceania (10), and Africa (7). Sampling spans three decades and is concentrated on 2001-2005 (21 studies), 2006-2010 (40), 2011-2015 (88), and 2016-2020 (50). This is the most comprehensive open global data set on measurements of crop flower visitors, crop pollinators and pollination to date, and we encourage researchers to add more datasets to this database in the future. This data set is released for non-commercial use only. Credits should be given to this paper (i.e., proper citation), and the products generated with this database should be shared under the same license terms (CC BY-NC-SA).}, } @article {pmid34921205, year = {2021}, author = {Molina-Venegas, R}, title = {Conserving evolutionarily distinct species is critical to safeguard human well-being.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {24187}, pmid = {34921205}, issn = {2045-2322}, mesh = {Biodiversity ; *Biological Evolution ; Conservation of Natural Resources ; Databases, Factual ; Eating ; Hazard Analysis and Critical Control Points ; Humans ; Phylogeny ; Plants/classification ; }, abstract = {Although there is growing interest in safeguarding the Tree of Life to preserve the human benefits that are directly provided by biodiversity, their evolutionary distribution remains unknown, which has hampered our understanding of the potential of phylodiversity indicators to evince them. Here, I drew on a global review of plant benefits and comprehensive phylogenetic information to breakdown their evolutionary distribution and thereby show why the commonly used Phylogenetic Diversity and Evolutionary Distinctiveness indicators can unequivocally help to preserve these natural services. Beneficial species clumped within phylogenetically overdispersed genera and closely related species often contributed very few and redundant benefits, suggesting that multiple plant lineages are required to maintain a wide variety of services. Yet, a reduced number of species stood out as multi-beneficial and evolutionarily distinct plants relative to both the entire phylogeny and the subset of beneficial species, and they collectively contributed a higher-than-expected number of records for most types of benefits. In addition to providing a clear mechanistic understanding for the recently proved success of Phylogenetic Diversity in capturing plant benefits, these findings stress the decisive role that conservation programmes aimed at protecting evolutionarily distinct taxa will play in safeguarding the beneficial potential of biodiversity for the future.}, } @article {pmid34916500, year = {2021}, author = {Abrahms, B and Teitelbaum, CS and Mueller, T and Converse, SJ}, title = {Ontogenetic shifts from social to experiential learning drive avian migration timing.}, journal = {Nature communications}, volume = {12}, number = {1}, pages = {7326}, pmid = {34916500}, issn = {2041-1723}, mesh = {*Animal Migration ; Animals ; Behavior, Animal ; Biological Ontologies ; Birds/*physiology ; Climate Change ; Learning ; Seasons ; }, abstract = {Migrating animals may benefit from social or experiential learning, yet whether and how these learning processes interact or change over time to produce observed migration patterns remains unexplored. Using 16 years of satellite-tracking data from 105 reintroduced whooping cranes, we reveal an interplay between social and experiential learning in migration timing. Both processes dramatically improved individuals' abilities to dynamically adjust their timing to track environmental conditions along the migration path. However, results revealed an ontogenetic shift in the dominant learning process, whereby subadult birds relied on social information, while mature birds primarily relied on experiential information. These results indicate that the adjustment of migration phenology in response to the environment is a learned skill that depends on both social context and individual age. Assessing how animals successfully learn to time migrations as environmental conditions change is critical for understanding intraspecific differences in migration patterns and for anticipating responses to global change.}, } @article {pmid34915868, year = {2021}, author = {Xu, Y and Lu, JH and Zhang, JD and Liu, DK and Wang, Y and Niu, QD and Huang, DD}, title = {Transcriptome revealed the molecular mechanism of Glycyrrhiza inflata root to maintain growth and development, absorb and distribute ions under salt stress.}, journal = {BMC plant biology}, volume = {21}, number = {1}, pages = {599}, pmid = {34915868}, issn = {1471-2229}, mesh = {Absorption, Physicochemical ; Gene Expression Regulation, Plant ; Gene Ontology ; Glycyrrhiza/*growth & development/metabolism ; High-Throughput Nucleotide Sequencing ; *Ion Transport ; Plant Roots/*growth & development/metabolism ; RNA-Seq ; *Salt Stress ; Salt Tolerance ; Sodium/metabolism ; Transcriptome ; }, abstract = {BACKGROUND: Soil salinization extensively hampers the growth, yield, and quality of crops worldwide. The most effective strategies to counter this problem are a) development of crop cultivars with high salt tolerance and b) the plantation of salt-tolerant crops. Glycyrrhiza inflata, a traditional Chinese medicinal and primitive plant with salt tolerance and economic value, is among the most promising crops for improving saline-alkali wasteland. However, the underlying molecular mechanisms for the adaptive response of G. inflata to salinity stress remain largely unknown.

RESULT: G. inflata retained a high concentration of Na[+] in roots and maintained the absorption of K[+], Ca[2+], and Mg[2+] under 150 mM NaCl induced salt stress. Transcriptomic analysis of G. inflata roots at different time points of salt stress (0 min, 30 min, and 24 h) was performed, which resulted in 70.77 Gb of clean data. Compared with the control, we detected 2645 and 574 differentially expressed genes (DEGs) at 30 min and 24 h post-salt-stress induction, respectively. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses revealed that G. inflata response to salt stress post 30 min and 24 h was remarkably distinct. Genes that were differentially expressed at 30 min post-salt stress induction were enriched in signal transduction, secondary metabolite synthesis, and ion transport. However, genes that were differentially expressed at 24 h post-salt-stress induction were enriched in phenylpropane biosynthesis and metabolism, fatty acid metabolism, glycerol metabolism, hormone signal transduction, wax, cutin, and cork biosynthesis. Besides, a total of 334 transcription factors (TFs) were altered in response to 30 min and 24 h of salt stress. Most of these TFs belonged to the MYB, WRKY, AP2-EREBP, C2H2, bHLH, bZIP, and NAC families.

CONCLUSION: For the first time, this study elucidated the salt tolerance in G. inflata at the molecular level, including the activation of signaling pathways and genes that regulate the absorption and distribution of ions and root growth in G. inflata under salt stress conditions. These findings enhanced our understanding of the G. inflata salt tolerance and provided a theoretical basis for cultivating salt-tolerant crop varieties.}, } @article {pmid34915300, year = {2022}, author = {Ramiadantsoa, T and Metcalf, CJE and Raherinandrasana, AH and Randrianarisoa, S and Rice, BL and Wesolowski, A and Randriatsarafara, FM and Rasambainarivo, F}, title = {Existing human mobility data sources poorly predicted the spatial spread of SARS-CoV-2 in Madagascar.}, journal = {Epidemics}, volume = {38}, number = {}, pages = {100534}, pmid = {34915300}, issn = {1878-0067}, support = {DP2 LM013102/LM/NLM NIH HHS/United States ; R01 AI160780/AI/NIAID NIH HHS/United States ; DP21 LM013102/NH/NIH HHS/United States ; }, mesh = {*COVID-19/epidemiology ; Humans ; Information Storage and Retrieval ; Madagascar/epidemiology ; Pandemics ; *SARS-CoV-2 ; United States ; }, abstract = {For emerging epidemics such as the COVID-19 pandemic, quantifying travel is a key component of developing accurate predictive models of disease spread to inform public health planning. However, in many LMICs, traditional data sets on travel such as commuting surveys as well as non-traditional sources such as mobile phone data are lacking, or, where available, have only rarely been leveraged by the public health community. Evaluating the accuracy of available data to measure transmission-relevant travel may be further hampered by limited reporting of suspected and laboratory confirmed infections. Here, we leverage case data collected as part of a COVID-19 dashboard collated via daily reports from the Malagasy authorities on reported cases of SARS-CoV-2 across the 22 regions of Madagascar. We compare the order of the timing of when cases were reported with predictions from a SARS-CoV-2 metapopulation model of Madagascar informed using various measures of connectivity including a gravity model based on different measures of distance, Internal Migration Flow data, and mobile phone data. Overall, the models based on mobile phone connectivity and the gravity-based on Euclidean distance best predicted the observed spread. The ranks of the regions most remote from the capital were more difficult to predict but interestingly, regions where the mobile phone connectivity model was more accurate differed from those where the gravity model was most accurate. This suggests that there may be additional features of mobility or connectivity that were consistently underestimated using all approaches but are epidemiologically relevant. This work highlights the importance of data availability and strengthening collaboration among different institutions with access to critical data - models are only as good as the data that they use, so building towards effective data-sharing pipelines is essential.}, } @article {pmid34903666, year = {2021}, author = {Bussotti, G and Piel, L and Pescher, P and Domagalska, MA and Rajan, KS and Cohen-Chalamish, S and Doniger, T and Hiregange, DG and Myler, PJ and Unger, R and Michaeli, S and Späth, GF}, title = {Genome instability drives epistatic adaptation in the human pathogen Leishmania.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {118}, number = {51}, pages = {}, pmid = {34903666}, issn = {1091-6490}, mesh = {Adaptation, Physiological/*genetics ; *Epistasis, Genetic ; Gene Dosage ; Genetic Fitness ; *Genome, Protozoan ; *Genomic Instability ; Humans ; Leishmania/*genetics ; Leishmaniasis/parasitology ; }, abstract = {How genome instability is harnessed for fitness gain despite its potential deleterious effects is largely elusive. An ideal system to address this important open question is provided by the protozoan pathogen Leishmania, which exploits frequent variations in chromosome and gene copy number to regulate expression levels. Using ecological genomics and experimental evolution approaches, we provide evidence that Leishmania adaptation relies on epistatic interactions between functionally associated gene copy number variations in pathways driving fitness gain in a given environment. We further uncover posttranscriptional regulation as a key mechanism that compensates for deleterious gene dosage effects and provides phenotypic robustness to genetically heterogenous parasite populations. Finally, we correlate dynamic variations in small nucleolar RNA (snoRNA) gene dosage with changes in ribosomal RNA 2'-O-methylation and pseudouridylation, suggesting translational control as an additional layer of parasite adaptation. Leishmania genome instability is thus harnessed for fitness gain by genome-dependent variations in gene expression and genome-independent compensatory mechanisms. This allows for polyclonal adaptation and maintenance of genetic heterogeneity despite strong selective pressure. The epistatic adaptation described here needs to be considered in Leishmania epidemiology and biomarker discovery and may be relevant to other fast-evolving eukaryotic cells that exploit genome instability for adaptation, such as fungal pathogens or cancer.}, } @article {pmid34900321, year = {2021}, author = {Bahramian, B and Afshari, A and Kiani, B and Sani, MA and Hashemi, M}, title = {The prevalence of foodborne parasites in raw vegetables in Iran: a comprehensive systematic review and meta-analysis.}, journal = {Journal of environmental health science & engineering}, volume = {19}, number = {2}, pages = {2027-2045}, pmid = {34900321}, issn = {2052-336X}, abstract = {UNLABELLED: Foodborne parasites in raw vegetables could cause parasitic infections in humans. An effective approach to the reduction of pathogenic microorganisms in vegetables involves identifying the main sources of contamination and the ecology of the involved microorganisms. This review aimed to evaluate the prevalence of foodborne parasites in raw vegetables in Iran. According to the reviewed studies, the prevalence rate of Ascaris spp., Giardia spp., Toxocara spp., Fasciola, Trichuris, Cryptosporidium, Dicrocoeliasis, Taenia spp., and Entamoeba histolytica was 6 % (95 % CI: 5-8 %), 6 % (95 % CI: 5-7 %), 6 % (95 % CI: 4-7 %), 2 % (95 % CI: 1-2 %), 1 % (95 % CI: 1-2 %), 10 % (95 % CI: 6-15 %), 2 % (95 % CI: 1-3 %), 5 % (95 % CI: 4-6 %), and 3 % (95 % CI: 2-4 %), respectively. According to the standard deviation map, Ilam province was one of the high-risk areas in terms of food-borne parasites in raw vegetables (3 SD < prevalence < 4 SD). Given the key role of raw vegetables in human parasitic contamination, governments must implement more stringent programs for effective wastewater treatment, preventing domestic and wild animals from entering farms, not using human and animal manure on farms, using ready-to-eat packaged vegetables, food safety training for households, implementation of GMP and HACCP in the factory vegetable packaging are required in this regard, especially in the high-risk areas of Iran, such as Ilam province.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s40201-021-00714-w.}, } @article {pmid34899100, year = {2021}, author = {Boonmee, S and Wanasinghe, DN and Calabon, MS and Huanraluek, N and Chandrasiri, SKU and Jones, GEB and Rossi, W and Leonardi, M and Singh, SK and Rana, S and Singh, PN and Maurya, DK and Lagashetti, AC and Choudhary, D and Dai, YC and Zhao, CL and Mu, YH and Yuan, HS and He, SH and Phookamsak, R and Jiang, HB and Martín, MP and Dueñas, M and Telleria, MT and Kałucka, IL and Jagodziński, AM and Liimatainen, K and Pereira, DS and Phillips, AJL and Suwannarach, N and Kumla, J and Khuna, S and Lumyong, S and Potter, TB and Shivas, RG and Sparks, AH and Vaghefi, N and Abdel-Wahab, MA and Abdel-Aziz, FA and Li, GJ and Lin, WF and Singh, U and Bhatt, RP and Lee, HB and Nguyen, TTT and Kirk, PM and Dutta, AK and Acharya, K and Sarma, VV and Niranjan, M and Rajeshkumar, KC and Ashtekar, N and Lad, S and Wijayawardene, NN and Bhat, DJ and Xu, RJ and Wijesinghe, SN and Shen, HW and Luo, ZL and Zhang, JY and Sysouphanthong, P and Thongklang, N and Bao, DF and Aluthmuhandiram, JVS and Abdollahzadeh, J and Javadi, A and Dovana, F and Usman, M and Khalid, AN and Dissanayake, AJ and Telagathoti, A and Probst, M and Peintner, U and Garrido-Benavent, I and Bóna, L and Merényi, Z and Boros, L and Zoltán, B and Stielow, JB and Jiang, N and Tian, CM and Shams, E and Dehghanizadeh, F and Pordel, A and Javan-Nikkhah, M and Denchev, TT and Denchev, CM and Kemler, M and Begerow, D and Deng, CY and Harrower, E and Bozorov, T and Kholmuradova, T and Gafforov, Y and Abdurazakov, A and Xu, JC and Mortimer, PE and Ren, GC and Jeewon, R and Maharachchikumbura, SSN and Phukhamsakda, C and Mapook, A and Hyde, KD}, title = {Fungal diversity notes 1387-1511: taxonomic and phylogenetic contributions on genera and species of fungal taxa.}, journal = {Fungal diversity}, volume = {111}, number = {1}, pages = {1-335}, pmid = {34899100}, issn = {1560-2745}, support = {P 31038/FWF_/Austrian Science Fund FWF/Austria ; }, abstract = {This article is the 13th contribution in the Fungal Diversity Notes series, wherein 125 taxa from four phyla, ten classes, 31 orders, 69 families, 92 genera and three genera incertae sedis are treated, demonstrating worldwide and geographic distribution. Fungal taxa described and illustrated in the present study include three new genera, 69 new species, one new combination, one reference specimen and 51 new records on new hosts and new geographical distributions. Three new genera, Cylindrotorula (Torulaceae), Scolecoleotia (Leotiales genus incertae sedis) and Xenovaginatispora (Lindomycetaceae) are introduced based on distinct phylogenetic lineages and unique morphologies. Newly described species are Aspergillus lannaensis, Cercophora dulciaquae, Cladophialophora aquatica, Coprinellus punjabensis, Cortinarius alutarius, C. mammillatus, C. quercoflocculosus, Coryneum fagi, Cruentomycena uttarakhandina, Cryptocoryneum rosae, Cyathus uniperidiolus, Cylindrotorula indica, Diaporthe chamaeropicola, Didymella azollae, Diplodia alanphillipsii, Dothiora coronicola, Efibula rodriguezarmasiae, Erysiphe salicicola, Fusarium queenslandicum, Geastrum gorgonicum, G. hansagiense, Helicosporium sexualis, Helminthosporium chiangraiensis, Hongkongmyces kokensis, Hydrophilomyces hydraenae, Hygrocybe boertmannii, Hyphoderma australosetigerum, Hyphodontia yunnanensis, Khaleijomyces umikazeana, Laboulbenia divisa, Laboulbenia triarthronis, Laccaria populina, Lactarius pallidozonarius, Lepidosphaeria strobelii, Longipedicellata megafusiformis, Lophiotrema lincangensis, Marasmius benghalensis, M. jinfoshanensis, M. subtropicus, Mariannaea camelliae, Melanographium smilaxii, Microbotryum polycnemoides, Mimeomyces digitatus, Minutisphaera thailandensis, Mortierella solitaria, Mucor harpali, Nigrograna jinghongensis, Odontia huanrenensis, O. parvispina, Paraconiothyrium ajrekarii, Parafuscosporella niloticus, Phaeocytostroma yomensis, Phaeoisaria synnematicus, Phanerochaete hainanensis, Pleopunctum thailandicum, Pleurotheciella dimorphospora, Pseudochaetosphaeronema chiangraiense, Pseudodactylaria albicolonia, Rhexoacrodictys nigrospora, Russula paravioleipes, Scolecoleotia eriocamporesi, Seriascoma honghense, Synandromyces makranczyi, Thyridaria aureobrunnea, Torula lancangjiangensis, Tubeufia longihelicospora, Wicklowia fusiformispora, Xenovaginatispora phichaiensis and Xylaria apiospora. One new combination, Pseudobactrodesmium stilboideus is proposed. A reference specimen of Comoclathris permunda is designated. New host or distribution records are provided for Acrocalymma fici, Aliquandostipite khaoyaiensis, Camarosporidiella laburni, Canalisporium caribense, Chaetoscutula juniperi, Chlorophyllum demangei, C. globosum, C. hortense, Cladophialophora abundans, Dendryphion hydei, Diaporthe foeniculina, D. pseudophoenicicola, D. pyracanthae, Dictyosporium pandanicola, Dyfrolomyces distoseptatus, Ernakulamia tanakae, Eutypa flavovirens, E. lata, Favolus septatus, Fusarium atrovinosum, F. clavum, Helicosporium luteosporum, Hermatomyces nabanheensis, Hermatomyces sphaericoides, Longipedicellata aquatica, Lophiostoma caudata, L. clematidis-vitalbae, Lophiotrema hydei, L. neoarundinaria, Marasmiellus palmivorus, Megacapitula villosa, Micropsalliota globocystis, M. gracilis, Montagnula thailandica, Neohelicosporium irregulare, N. parisporum, Paradictyoarthrinium diffractum, Phaeoisaria aquatica, Poaceascoma taiwanense, Saproamanita manicata, Spegazzinia camelliae, Submersispora variabilis, Thyronectria caudata, T. mackenziei, Tubeufia chiangmaiensis, T. roseohelicospora, Vaginatispora nypae, Wicklowia submersa, Xanthagaricus necopinatus and Xylaria haemorrhoidalis. The data presented herein are based on morphological examination of fresh specimens, coupled with analysis of phylogenetic sequence data to better integrate taxa into appropriate taxonomic ranks and infer their evolutionary relationships.}, } @article {pmid34890403, year = {2021}, author = {Horvatić, S and Malavasi, S and Vukić, J and Šanda, R and Marčić, Z and Ćaleta, M and Lorenzoni, M and Mustafić, P and Buj, I and Onorato, L and Ivić, L and Cavraro, F and Zanella, D}, title = {Correlation between acoustic divergence and phylogenetic distance in soniferous European gobiids (Gobiidae; Gobius lineage).}, journal = {PloS one}, volume = {16}, number = {12}, pages = {e0260810}, pmid = {34890403}, issn = {1932-6203}, mesh = {Acoustics ; Animals ; Fishes/*classification/genetics/*physiology ; Genetic Variation ; Phylogeny ; Sequence Analysis, DNA ; Sound ; Species Specificity ; Stochastic Processes ; Vocalization, Animal/*physiology ; }, abstract = {In fish, species identity can be encoded by sounds, which have been thoroughly investigated in European gobiids (Gobiidae, Gobius lineage). Recent evolutionary studies suggest that deterministic and/or stochastic forces could generate acoustic differences among related animal species, though this has not been investigated in any teleost group to date. In the present comparative study, we analysed the sounds from nine soniferous gobiids and quantitatively assessed their acoustic variability. Our interspecific acoustic study, incorporating for the first time the representative acoustic signals from the majority of soniferous gobiids, suggested that their sounds are truly species-specific (92% of sounds correctly classified into exact species) and each taxon possesses a unique set of spectro-temporal variables. In addition, we reconstructed phylogenetic relationships from a concatenated molecular dataset consisting of multiple molecular markers to track the evolution of acoustic signals in soniferous gobiids. The results of this study indicated that the genus Padogobius is polyphyletic, since P. nigricans was nested within the Ponto-Caspian clade, while the congeneric P. bonelli turned out to be a sister taxon to the remaining investigated soniferous species. Lastly, by extracting the acoustic and genetic distance matrices, sound variability and genetic distance were correlated for the first time to assess whether sound evolution follows a similar phylogenetic pattern. The positive correlation between the sound variability and genetic distance obtained here emphasizes that certain acoustic features from representative sounds could carry the phylogenetic signal in soniferous gobiids. Our study was the first attempt to evaluate the mutual relationship between acoustic variation and genetic divergence in any teleost fish.}, } @article {pmid34889891, year = {2021}, author = {Jia, C and Yang, T and Yanagimoto, T and Gao, T}, title = {Comprehensive Draft Genome Analyses of Three Rockfishes (Scorpaeniformes, Sebastiscus) via Genome Survey Sequencing.}, journal = {Current issues in molecular biology}, volume = {43}, number = {3}, pages = {2048-2058}, pmid = {34889891}, issn = {1467-3045}, support = {2019YFD0901303//National Key R&D Program of China/ ; No. 41776171//National Natural Science Foundation of China/ ; }, mesh = {Animals ; Computational Biology/methods ; *Genome ; *Genomics/methods ; Microsatellite Repeats ; Perciformes/classification/*genetics ; Phylogeny ; *Sequence Analysis, DNA ; *Whole Genome Sequencing ; }, abstract = {Sebastiscus species, marine rockfishes, are of essential economic value. However, the genomic data of this genus is lacking and incomplete. Here, whole genome sequencing of all species of Sebastiscus was conducted to provide fundamental genomic information. The genome sizes were estimated to be 802.49 Mb (S. albofasciatus), 786.79 Mb (S. tertius), and 776.00 Mb (S. marmoratus) by using k-mer analyses. The draft genome sequences were initially assembled, and genome-wide microsatellite motifs were identified. The heterozygosity, repeat ratios, and numbers of microsatellite motifs all suggested possibly that S. tertius is more closely related to S. albofasciatus than S. marmoratus at the genetic level. Moreover, the complete mitochondrial genome sequences were assembled from the whole genome data and the phylogenetic analyses genetically supported the validation of Sebastiscus species. This study provides an important genome resource for further studies of Sebastiscus species.}, } @article {pmid34887912, year = {2021}, author = {Guo, T and Yu, H}, title = {Evaluation of Ecological Water Consumption in Yanhe River Basin Based on Big Data.}, journal = {Computational intelligence and neuroscience}, volume = {2021}, number = {}, pages = {2201964}, pmid = {34887912}, issn = {1687-5273}, mesh = {Big Data ; China ; *Drinking ; *Rivers ; Water ; Water Resources ; }, abstract = {Starting from the main eco-environmental problems faced by water environment, taking Yanhe River Basin as an example, this paper discusses the theoretical connotation and evaluation calculation method of eco-environmental water consumption. In order to study the eco-environmental water consumption of Yanhe River Basin, a runoff driving factor mining method based on big data analysis is established in this paper. Aiming at the problem that the statistical law and genetic law of runoff change frequently in changing environment, the mining technology method of runoff key driving factors is proposed by combining traditional methods with big data analysis. The characteristic factors that have no significant impact on runoff change are removed, the implicit characteristic factors affecting runoff change are extracted, the driving relationship of hydrological, meteorological, and vegetation characteristic factors on ecological water consumption change is identified, and the key driving factors of ecological water consumption change are extracted, which lays a data foundation for ecological water consumption prediction based on machine learning. The economic water consumption based on eco-environmental water consumption in Yanhe River Basin in the future is predicted (including water demand in three aspects of industry, agriculture, and life); that is, the prediction is to meet the economic water demand on the basis of ensuring that the water consumption of ecological environment will not be occupied, which can effectively ensure the improvement of ecological environment function in Yanhe River Basin and is conducive to the sustainable utilization of water resources in Yanhe River Basin. The research is only based on a small watershed such as Yanhe River Basin, and the purpose of the research is to provide a reference for ecological environment protection and sustainable utilization of water resources in the Loess Plateau, even in the arid, semiarid, and semihumid areas of North China.}, } @article {pmid34887434, year = {2021}, author = {Goswami, K and Shope, AJ and Tokarev, V and Wright, JR and Unverdorben, LV and Ly, T and Chen See, J and McLimans, CJ and Wong, HT and Lock, L and Clarkson, S and Parvizi, J and Lamendella, R}, title = {Comparative meta-omics for identifying pathogens associated with prosthetic joint infection.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {23749}, pmid = {34887434}, issn = {2045-2322}, mesh = {Aged ; Aged, 80 and over ; Arthritis, Infectious/diagnosis/*etiology ; Biodiversity ; Computational Biology/methods ; Female ; Gene Expression Profiling ; Humans ; Male ; Metagenome ; Metagenomics/*methods ; Middle Aged ; Prosthesis-Related Infections/diagnosis/*etiology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Prosthetic joint infections (PJI) are economically and personally costly, and their incidence has been increasing in the United States. Herein, we compared 16S rRNA amplicon sequencing (16S), shotgun metagenomics (MG) and metatranscriptomics (MT) in identifying pathogens causing PJI. Samples were collected from 30 patients, including 10 patients undergoing revision arthroplasty for infection, 10 patients receiving revision for aseptic failure, and 10 patients undergoing primary total joint arthroplasty. Synovial fluid and peripheral blood samples from the patients were obtained at time of surgery. Analysis revealed distinct microbial communities between primary, aseptic, and infected samples using MG, MT, (PERMANOVA p = 0.001), and 16S sequencing (PERMANOVA p < 0.01). MG and MT had higher concordance with culture (83%) compared to 0% concordance of 16S results. Supervised learning methods revealed MT datasets most clearly differentiated infected, primary, and aseptic sample groups. MT data also revealed more antibiotic resistance genes, with improved concordance results compared to MG. These data suggest that a differential and underlying microbial ecology exists within uninfected and infected joints. This study represents the first application of RNA-based sequencing (MT). Further work on larger cohorts will provide opportunities to employ deep learning approaches to improve accuracy, predictive power, and clinical utility.}, } @article {pmid34886005, year = {2021}, author = {Zhang, Y and Xu, C and Dai, H and Jia, X}, title = {Psychological Distress and Adolescents' Cyberbullying under Floods and the COVID-19 Pandemic: Parent-Child Relationships and Negotiable Fate as Moderators.}, journal = {International journal of environmental research and public health}, volume = {18}, number = {23}, pages = {}, pmid = {34886005}, issn = {1660-4601}, mesh = {Adolescent ; *COVID-19 ; *Cyberbullying ; Female ; Floods ; Humans ; Male ; Pandemics ; Parent-Child Relations ; *Psychological Distress ; SARS-CoV-2 ; }, abstract = {Since the outbreak of coronavirus disease 2019 (COVID-19), adolescents in 70 countries have suffered the COVID-19 pandemic and flood disasters simultaneously. Although antecedent cyberbullying variables have attracted significant research attention, the effects of psychological distress and the potential mechanisms of cyberbullying among adolescents under multiple disasters remains unclear. Based on social-ecological system theory, this study examines the moderating effects of parent-child relationships and the negotiable fate on the relationship between psychological distress and cyberbullying. A total of 1204 middle school students (52.4% boys) who suffered from floods and the COVID-19 pandemic from Zhengzhou City, China, are the participants. The results reveal that psychological distress was positively related to adolescent cyberbullying during a disaster. Parent-child relationships and negotiable fate significantly moderate the relationship between psychological distress and cyberbullying. Specifically, high parent-child relationships and a high negotiable fate could protect adolescents from the negative effects of psychological distress of cyberbullying. For adolescents with low or high parent-child relationships and low negotiable fate, the links between psychological distress and cyberbullying are stronger. These findings underline the significance of considering the interaction of psychological distress, parent-child relationships, and negotiable fate when examining adolescents' cyberbullying during disasters.}, } @article {pmid34884449, year = {2021}, author = {Song, T and Yu, Y and Zhang, M and Zhou, H and Zhang, S and Yu, M and Zhou, J and Cheng, J and Xiang, J and Yang, S and Zhang, X}, title = {A Wheat TaTOE1-B1 Transcript TaTOE1-B1-3 Can Delay the Flowering Time of Transgenic Arabidopsis.}, journal = {International journal of molecular sciences}, volume = {22}, number = {23}, pages = {}, pmid = {34884449}, issn = {1422-0067}, support = {32171992//National Natural Science Foundation of China/ ; 31671693//National Natural Science Foundation of China/ ; 2016YFD0101802//National Key Research and Development Program of China/ ; 2019ZDLNY04-05//Key Research and Development Project of Shaanxi Province/ ; }, mesh = {Alternative Splicing ; Arabidopsis/genetics/*physiology ; Cloning, Molecular ; Computational Biology ; Evolution, Molecular ; Flowers/genetics/physiology ; Gene Expression Regulation, Plant ; Plant Proteins/genetics/metabolism ; Plants, Genetically Modified/physiology ; Transcription Factors/*genetics/metabolism ; Triticum/genetics/*metabolism ; }, abstract = {Flowering time is one of the most important agronomic traits in wheat production. A proper flowering time might contribute to the reduction or avoidance of biotic and abiotic stresses, adjust plant architecture, and affect the yield and quality of grain. In this study, TaTOE1-B1 in wheat produced three transcripts (TaTOE1-B1-1, TaTOE1-B1-2, and TaTOE1-B1-3) by alternative splicing. Compared to the longest transcript, TaTOE1-B1-1, TaTOE1-B1-3 has a deletion in the sixth exon (1219-1264 bp). Under long-day conditions, the heterologous overexpression of the TaTOE1-B1-3 gene delayed flowering, prolonged the vegetative growth time, and enlarged the vegetative body of Arabidopsis, but that of TaTOE1-B1-1 did not. As typical AP2 family members, TaTOE1-B1-1 and TaTOE1-B1-3 are mainly located in the nucleus and have transcriptional activation activities; the transcriptional activation region of TaTOE1-B1-3 is located in the C-terminal. In TaTOE1-B1-3 overexpression lines, the expression of flowering-related AtFT and AtSOC1 genes is significantly downregulated. In addition, this study confirms the protein-protein interaction between TaTOE1-B1-3 and TaPIFI, which may play an important role in flowering inhibition. These results provide a theoretical basis for the precise regulation of wheat flowering time.}, } @article {pmid34882714, year = {2021}, author = {Noble, PM and Appleton, C and Radford, AD and Nenadic, G}, title = {Using topic modelling for unsupervised annotation of electronic health records to identify an outbreak of disease in UK dogs.}, journal = {PloS one}, volume = {16}, number = {12}, pages = {e0260402}, pmid = {34882714}, issn = {1932-6203}, support = {BB/N019547/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; Data Curation ; Disease Outbreaks/*veterinary ; Dog Diseases/*epidemiology ; Dogs ; Electronic Health Records ; Gastroenteritis/epidemiology/*veterinary ; Population Surveillance ; United Kingdom/epidemiology ; Unsupervised Machine Learning ; }, abstract = {A key goal of disease surveillance is to identify outbreaks of known or novel diseases in a timely manner. Such an outbreak occurred in the UK associated with acute vomiting in dogs between December 2019 and March 2020. We tracked this outbreak using the clinical free text component of anonymised electronic health records (EHRs) collected from a sentinel network of participating veterinary practices. We sourced the free text (narrative) component of each EHR supplemented with one of 10 practitioner-derived main presenting complaints (MPCs), with the 'gastroenteric' MPC identifying cases involved in the disease outbreak. Such clinician-derived annotation systems can suffer from poor compliance requiring retrospective, often manual, coding, thereby limiting real-time usability, especially where an outbreak of a novel disease might not present clinically as a currently recognised syndrome or MPC. Here, we investigate the use of an unsupervised method of EHR annotation using latent Dirichlet allocation topic-modelling to identify topics inherent within the clinical narrative component of EHRs. The model comprised 30 topics which were used to annotate EHRs spanning the natural disease outbreak and investigate whether any given topic might mirror the outbreak time-course. Narratives were annotated using the Gensim Library LdaModel module for the topic best representing the text within them. Counts for narratives labelled with one of the topics significantly matched the disease outbreak based on the practitioner-derived 'gastroenteric' MPC (Spearman correlation 0.978); no other topics showed a similar time course. Using artificially injected outbreaks, it was possible to see other topics that would match other MPCs including respiratory disease. The underlying topics were readily evaluated using simple word-cloud representations and using a freely available package (LDAVis) providing rapid insight into the clinical basis of each topic. This work clearly shows that unsupervised record annotation using topic modelling linked to simple text visualisations can provide an easily interrogable method to identify and characterise outbreaks and other anomalies of known and previously un-characterised diseases based on changes in clinical narratives.}, } @article {pmid34879058, year = {2021}, author = {Rubio-Teves, M and Díez-Hermano, S and Porrero, C and Sánchez-Jiménez, A and Prensa, L and Clascá, F and García-Amado, M and Villacorta-Atienza, JA}, title = {Benchmarking of tools for axon length measurement in individually-labeled projection neurons.}, journal = {PLoS computational biology}, volume = {17}, number = {12}, pages = {e1009051}, pmid = {34879058}, issn = {1553-7358}, mesh = {Animals ; Axons/*physiology ; Benchmarking ; Computational Biology/*methods ; Databases, Factual ; Imaging, Three-Dimensional/*methods ; Mice ; Neurons/*cytology ; Tomography ; }, abstract = {Projection neurons are the commonest neuronal type in the mammalian forebrain and their individual characterization is a crucial step to understand how neural circuitry operates. These cells have an axon whose arborizations extend over long distances, branching in complex patterns and/or in multiple brain regions. Axon length is a principal estimate of the functional impact of the neuron, as it directly correlates with the number of synapses formed by the axon in its target regions; however, its measurement by direct 3D axonal tracing is a slow and labor-intensive method. On the contrary, axon length estimations have been recently proposed as an effective and accessible alternative, allowing a fast approach to the functional significance of the single neuron. Here, we analyze the accuracy and efficiency of the most used length estimation tools-design-based stereology by virtual planes or spheres, and mathematical correction of the 2D projected-axon length-in contrast with direct measurement, to quantify individual axon length. To this end, we computationally simulated each tool, applied them over a dataset of 951 3D-reconstructed axons (from NeuroMorpho.org), and compared the generated length values with their 3D reconstruction counterparts. The evaluated reliability of each axon length estimation method was then balanced with the required human effort, experience and know-how, and economic affordability. Subsequently, computational results were contrasted with measurements performed on actual brain tissue sections. We show that the plane-based stereological method balances acceptable errors (~5%) with robustness to biases, whereas the projection-based method, despite its accuracy, is prone to inherent biases when implemented in the laboratory. This work, therefore, aims to provide a constructive benchmark to help guide the selection of the most efficient method for measuring specific axonal morphologies according to the particular circumstances of the conducted research.}, } @article {pmid34878090, year = {2021}, author = {Giacomet, CL and Santos, MS and Berra, TZ and Alves, YM and Alves, LS and Costa, FBPD and Ramos, ACV and Crispim, JA and Monroe, AA and Pinto, IC and Fiorati, RC and Arcoverde, MAM and Gomes, D and Freitas, GL and Yamamura, M and Arcêncio, RA}, title = {Temporal trend of tuberculosis incidence and its spatial distribution in Macapá - Amapá.}, journal = {Revista de saude publica}, volume = {55}, number = {}, pages = {96}, pmid = {34878090}, issn = {1518-8787}, mesh = {Brazil ; Humans ; Incidence ; Information Systems ; Seasons ; *Tuberculosis/diagnosis/epidemiology ; }, abstract = {OBJECTIVE: To evaluate the temporal trend of tuberculosis incidence after the implementation of the rapid molecular test (RMT-TB), to identify whether tuberculosis presents seasonal variation and to classify the territory according to case density and risk areas in Macapá, Amapá.

METHODS: Ecological study of tuberculosis cases registered in the Sistema de Informação de Agravos de Notificação (SINAN - Information System for Notifiable Diseases) between 2001 and 2017. We used the Prais-Winsten test to classify the temporal trend of incidence and the interrupted time series to identify changes in the temporal trend before and after the implementation of the rapid molecular test, and to verify seasonality in the municipality. The Kernel estimator was used to classify case density and scan statistics to identify areas of tuberculosis risk.

RESULTS: A total of 1,730 cases were identified, with a decreasing temporal trend of tuberculosis incidence (-0.27% per month, 95%CI -0.13 to -0.41). The time series showed no change in level after the implementation of the GeneXpert®MTB/RIF molecular test; however, the incidence increased in the post-test period (+2.09% per month, 95%CI 0.92 to 3.27). Regarding the seasonal variation, it showed growth (+13.7%/month, 95%CI 4.71 to 23.87) from December to June, the rainy season - called amazon winter season -, and decrease (-9.21% per month, CI95% -1.37 to -16.63) in the other periods. We classified areas with high density of cases in the Central and Northern districts using Kernel and identified three protection clusters, SC1 (RR = 0.07), SC2 (RR = 0.23) and SC3 (RR = 0.36), and a high-risk cluster, SC4 (RR = 1.47), with the scan statistics.

CONCLUSION: The temporal trend of tuberculosis incidence was decreasing in the time series; however, detection increased after the introduction of RMT-TB, and tuberculosis showed seasonal behavior. The case distribution was heterogeneous, with a tendency to concentrate in vulnerable and risk territories, evidencing a pattern of disease inequality in the territory.}, } @article {pmid34877561, year = {2021}, author = {Wang, F and Harindintwali, JD and Yuan, Z and Wang, M and Wang, F and Li, S and Yin, Z and Huang, L and Fu, Y and Li, L and Chang, SX and Zhang, L and Rinklebe, J and Yuan, Z and Zhu, Q and Xiang, L and Tsang, DCW and Xu, L and Jiang, X and Liu, J and Wei, N and Kästner, M and Zou, Y and Ok, YS and Shen, J and Peng, D and Zhang, W and Barceló, D and Zhou, Y and Bai, Z and Li, B and Zhang, B and Wei, K and Cao, H and Tan, Z and Zhao, LB and He, X and Zheng, J and Bolan, N and Liu, X and Huang, C and Dietmann, S and Luo, M and Sun, N and Gong, J and Gong, Y and Brahushi, F and Zhang, T and Xiao, C and Li, X and Chen, W and Jiao, N and Lehmann, J and Zhu, YG and Jin, H and Schäffer, A and Tiedje, JM and Chen, JM}, title = {Technologies and perspectives for achieving carbon neutrality.}, journal = {Innovation (Cambridge (Mass.))}, volume = {2}, number = {4}, pages = {100180}, pmid = {34877561}, issn = {2666-6758}, abstract = {Global development has been heavily reliant on the overexploitation of natural resources since the Industrial Revolution. With the extensive use of fossil fuels, deforestation, and other forms of land-use change, anthropogenic activities have contributed to the ever-increasing concentrations of greenhouse gases (GHGs) in the atmosphere, causing global climate change. In response to the worsening global climate change, achieving carbon neutrality by 2050 is the most pressing task on the planet. To this end, it is of utmost importance and a significant challenge to reform the current production systems to reduce GHG emissions and promote the capture of CO2 from the atmosphere. Herein, we review innovative technologies that offer solutions achieving carbon (C) neutrality and sustainable development, including those for renewable energy production, food system transformation, waste valorization, C sink conservation, and C-negative manufacturing. The wealth of knowledge disseminated in this review could inspire the global community and drive the further development of innovative technologies to mitigate climate change and sustainably support human activities.}, } @article {pmid34877560, year = {2021}, author = {Xu, Y and Liu, X and Cao, X and Huang, C and Liu, E and Qian, S and Liu, X and Wu, Y and Dong, F and Qiu, CW and Qiu, J and Hua, K and Su, W and Wu, J and Xu, H and Han, Y and Fu, C and Yin, Z and Liu, M and Roepman, R and Dietmann, S and Virta, M and Kengara, F and Zhang, Z and Zhang, L and Zhao, T and Dai, J and Yang, J and Lan, L and Luo, M and Liu, Z and An, T and Zhang, B and He, X and Cong, S and Liu, X and Zhang, W and Lewis, JP and Tiedje, JM and Wang, Q and An, Z and Wang, F and Zhang, L and Huang, T and Lu, C and Cai, Z and Wang, F and Zhang, J}, title = {Artificial intelligence: A powerful paradigm for scientific research.}, journal = {Innovation (Cambridge (Mass.))}, volume = {2}, number = {4}, pages = {100179}, pmid = {34877560}, issn = {2666-6758}, abstract = {Artificial intelligence (AI) coupled with promising machine learning (ML) techniques well known from computer science is broadly affecting many aspects of various fields including science and technology, industry, and even our day-to-day life. The ML techniques have been developed to analyze high-throughput data with a view to obtaining useful insights, categorizing, predicting, and making evidence-based decisions in novel ways, which will promote the growth of novel applications and fuel the sustainable booming of AI. This paper undertakes a comprehensive survey on the development and application of AI in different aspects of fundamental sciences, including information science, mathematics, medical science, materials science, geoscience, life science, physics, and chemistry. The challenges that each discipline of science meets, and the potentials of AI techniques to handle these challenges, are discussed in detail. Moreover, we shed light on new research trends entailing the integration of AI into each scientific discipline. The aim of this paper is to provide a broad research guideline on fundamental sciences with potential infusion of AI, to help motivate researchers to deeply understand the state-of-the-art applications of AI-based fundamental sciences, and thereby to help promote the continuous development of these fundamental sciences.}, } @article {pmid34876514, year = {2021}, author = {Vasconcelos, VV and Constantino, SM and Dannenberg, A and Lumkowsky, M and Weber, E and Levin, S}, title = {Segregation and clustering of preferences erode socially beneficial coordination.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {118}, number = {50}, pages = {}, pmid = {34876514}, issn = {1091-6490}, abstract = {Polarization on various issues has increased in many Western democracies over the last decades, leading to divergent beliefs, preferences, and behaviors within societies. We develop a model to investigate the effects of polarization on the likelihood that a society will coordinate on a welfare-improving action in a context in which collective benefits are acquired only if enough individuals take that action. We examine the impacts of different manifestations of polarization: heterogeneity of preferences, segregation of the social network, and the interaction between the two. In this context, heterogeneity captures differential perceived benefits from coordinating, which can lead to different intentions and sensitivity regarding the intentions of others. Segregation of the social network can create a bottleneck in information flows about others' preferences, as individuals may base their decisions only on their close neighbors. Additionally, heterogeneous preferences can be evenly distributed in the population or clustered in the local network, respectively reflecting or systematically departing from the views of the broader society. The model predicts that heterogeneity of preferences alone is innocuous and it can even be beneficial, while segregation can hamper coordination, mainly when local networks distort the distribution of valuations. We base these results on a multimethod approach including an online group experiment with 750 individuals. We randomize the range of valuations associated with different choice options and the information respondents have about others. The experimental results reinforce the idea that, even in a situation in which all could stand to gain from coordination, polarization can impede social progress.}, } @article {pmid34876508, year = {2021}, author = {Santos, FP and Lelkes, Y and Levin, SA}, title = {Link recommendation algorithms and dynamics of polarization in online social networks.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {118}, number = {50}, pages = {}, pmid = {34876508}, issn = {1091-6490}, abstract = {The level of antagonism between political groups has risen in the past years. Supporters of a given party increasingly dislike members of the opposing group and avoid intergroup interactions, leading to homophilic social networks. While new connections offline are driven largely by human decisions, new connections on online social platforms are intermediated by link recommendation algorithms, e.g., "People you may know" or "Whom to follow" suggestions. The long-term impacts of link recommendation in polarization are unclear, particularly as exposure to opposing viewpoints has a dual effect: Connections with out-group members can lead to opinion convergence and prevent group polarization or further separate opinions. Here, we provide a complex adaptive-systems perspective on the effects of link recommendation algorithms. While several models justify polarization through rewiring based on opinion similarity, here we explain it through rewiring grounded in structural similarity-defined as similarity based on network properties. We observe that preferentially establishing links with structurally similar nodes (i.e., sharing many neighbors) results in network topologies that are amenable to opinion polarization. Hence, polarization occurs not because of a desire to shield oneself from disagreeable attitudes but, instead, due to the creation of inadvertent echo chambers. When networks are composed of nodes that react differently to out-group contacts, either converging or polarizing, we find that connecting structurally dissimilar nodes moderates opinions. Overall, our study sheds light on the impacts of social-network algorithms and unveils avenues to steer dynamics of radicalization and polarization in online social networks.}, } @article {pmid34874249, year = {2021}, author = {Bohr, LL and Youngblom, MA and Eldholm, V and Pepperell, CS}, title = {Genome reorganization during emergence of host-associated Mycobacterium abscessus.}, journal = {Microbial genomics}, volume = {7}, number = {12}, pages = {}, pmid = {34874249}, issn = {2057-5858}, support = {R01 AI113287/AI/NIAID NIH HHS/United States ; T32 AI055396/AI/NIAID NIH HHS/United States ; }, mesh = {Adaptation, Physiological ; Australia ; Chromosomes, Bacterial/*genetics ; Databases, Genetic ; Denmark ; Gene Transfer, Horizontal ; High-Throughput Nucleotide Sequencing ; Humans ; Mycobacterium Infections, Nontuberculous/*microbiology ; Mycobacterium abscessus/*classification/genetics/isolation & purification ; Netherlands ; Norway ; Phylogeny ; Phylogeography ; Plasmids/*genetics ; Prophages/*genetics ; Recombination, Genetic ; United Kingdom ; Whole Genome Sequencing/*methods ; }, abstract = {Mycobacterium abscessus is a rapid growing, free-living species of bacterium that also causes lung infections in humans. Human infections are usually acquired from the environment; however, dominant circulating clones (DCCs) have emerged recently in both M. abscessus subsp. massiliense and subsp. abscessus that appear to be transmitted among humans and are now globally distributed. These recently emerged clones are potentially informative about the ecological and evolutionary mechanisms of pathogen emergence and host adaptation. The geographical distribution of DCCs has been reported, but the genomic processes underlying their transition from environmental bacterium to human pathogen are not well characterized. To address this knowledge gap, we delineated the structure of M. abscessus subspecies abscessus and massiliense using genomic data from 200 clinical isolates of M. abscessus from seven geographical regions. We identified differences in overall patterns of lateral gene transfer (LGT) and barriers to LGT between subspecies and between environmental and host-adapted bacteria. We further characterized genome reorganization that accompanied bacterial host adaptation, inferring selection pressures acting at both genic and intergenic loci. We found that both subspecies encode an expansive pangenome with many genes at rare frequencies. Recombination appears more frequent in M. abscessus subsp. massiliense than in subsp. abscessus, consistent with prior reports. We found evidence suggesting that phage are exchanged between subspecies, despite genetic barriers evident elsewhere throughout the genome. Patterns of LGT differed according to niche, with less LGT observed among host-adapted DCCs versus environmental bacteria. We also found evidence suggesting that DCCs are under distinct selection pressures at both genic and intergenic sites. Our results indicate that host adaptation of M. abscessus was accompanied by major changes in genome evolution, including shifts in the apparent frequency of LGT and impacts of selection. Differences were evident among the DCCs as well, which varied in the degree of gene content remodelling, suggesting they were placed differently along the evolutionary trajectory toward host adaptation. These results provide insight into the evolutionary forces that reshape bacterial genomes as they emerge into the pathogenic niche.}, } @article {pmid34873159, year = {2021}, author = {Daru, BH and Davies, TJ and Willis, CG and Meineke, EK and Ronk, A and Zobel, M and Pärtel, M and Antonelli, A and Davis, CC}, title = {Widespread homogenization of plant communities in the Anthropocene.}, journal = {Nature communications}, volume = {12}, number = {1}, pages = {6983}, pmid = {34873159}, issn = {2041-1723}, mesh = {Africa ; *Algorithms ; Asia ; Australia ; *Biodiversity ; *Databases, Factual ; Ecosystem ; Europe ; Geography ; Human Activities ; Human Migration ; Humans ; *Models, Theoretical ; North America ; *Phylogeny ; Plants/*classification/genetics ; }, abstract = {Native biodiversity decline and non-native species spread are major features of the Anthropocene. Both processes can drive biotic homogenization by reducing trait and phylogenetic differences in species assemblages between regions, thus diminishing the regional distinctiveness of biotas and likely have negative impacts on key ecosystem functions. However, a global assessment of this phenomenon is lacking. Here, using a dataset of >200,000 plant species, we demonstrate widespread and temporal decreases in species and phylogenetic turnover across grain sizes and spatial extents. The extent of homogenization within major biomes is pronounced and is overwhelmingly explained by non-native species naturalizations. Asia and North America are major sources of non-native species; however, the species they export tend to be phylogenetically close to recipient floras. Australia, the Pacific and Europe, in contrast, contribute fewer species to the global pool of non-natives, but represent a disproportionate amount of phylogenetic diversity. The timeline of most naturalisations coincides with widespread human migration within the last ~500 years, and demonstrates the profound influence humans exert on regional biotas beyond changes in species richness.}, } @article {pmid34871304, year = {2021}, author = {Civantos-Gómez, I and García-Algarra, J and García-Callejas, D and Galeano, J and Godoy, O and Bartomeus, I}, title = {Fine scale prediction of ecological community composition using a two-step sequential Machine Learning ensemble.}, journal = {PLoS computational biology}, volume = {17}, number = {12}, pages = {e1008906}, pmid = {34871304}, issn = {1553-7358}, mesh = {Algorithms ; Biota/*physiology ; Computational Biology ; *Machine Learning ; *Models, Biological ; Plants ; }, abstract = {Prediction is one of the last frontiers in ecology. Indeed, predicting fine-scale species composition in natural systems is a complex challenge as multiple abiotic and biotic processes operate simultaneously to determine local species abundances. On the one hand, species intrinsic performance and their tolerance limits to different abiotic pressures modulate species abundances. On the other hand, there is growing recognition that species interactions play an equally important role in limiting or promoting such abundances within ecological communities. Here, we present a joint effort between ecologists and data scientists to use data-driven models to predict species abundances using reasonably easy to obtain data. We propose a sequential data-driven modeling approach that in a first step predicts the potential species abundances based on abiotic variables, and in a second step uses these predictions to model the realized abundances once accounting for species competition. Using a curated data set over five years we predict fine-scale species abundances in a highly diverse annual plant community. Our models show a remarkable spatial predictive accuracy using only easy-to-measure variables in the field, yet such predictive power is lost when temporal dynamics are taken into account. This result suggests that predicting future abundances requires longer time series analysis to capture enough variability. In addition, we show that these data-driven models can also suggest how to improve mechanistic models by adding missing variables that affect species performance such as particular soil conditions (e.g. carbonate availability in our case). Robust models for predicting fine-scale species composition informed by the mechanistic understanding of the underlying abiotic and biotic processes can be a pivotal tool for conservation, especially given the human-induced rapid environmental changes we are experiencing. This objective can be achieved by promoting the knowledge gained with classic modelling approaches in ecology and recently developed data-driven models.}, } @article {pmid34869819, year = {2021}, author = {Markovic, S and Rodic, A and Salom, I and Milicevic, O and Djordjevic, M and Djordjevic, M}, title = {COVID-19 severity determinants inferred through ecological and epidemiological modeling.}, journal = {One health (Amsterdam, Netherlands)}, volume = {13}, number = {}, pages = {100355}, pmid = {34869819}, issn = {2352-7714}, abstract = {Understanding variations in the severity of infectious diseases is essential for planning proper mitigation strategies. Determinants of COVID-19 clinical severity are commonly assessed by transverse or longitudinal studies of the fatality counts. However, the fatality counts depend both on disease clinical severity and transmissibility, as more infected also lead to more deaths. Instead, we use epidemiological modeling to propose a disease severity measure that accounts for the underlying disease dynamics. The measure corresponds to the ratio of population-averaged mortality and recovery rates (m/r), is independent of the disease transmission dynamics (i.e., the basic reproduction number), and has a direct mechanistic interpretation. We use this measure to assess demographic, medical, meteorological, and environmental factors associated with the disease severity. For this, we employ an ecological regression study design and analyze different US states during the first disease outbreak. Principal Component Analysis, followed by univariate, and multivariate analyses based on machine learning techniques, is used for selecting important predictors. The usefulness of the introduced severity measure and the validity of the approach are confirmed by the fact that, without using prior knowledge from clinical studies, we recover the main significant predictors known to influence disease severity, in particular age, chronic diseases, and racial factors. Additionally, we identify long-term pollution exposure and population density as not widely recognized (though for the pollution previously hypothesized) significant predictors. The proposed measure is applicable for inferring severity determinants not only of COVID-19 but also of other infectious diseases, and the obtained results may aid a better understanding of the present and future epidemics. Our holistic, systematic investigation of disease severity at the human-environment intersection by epidemiological dynamical modeling and machine learning ecological regressions is aligned with the One Health approach. The obtained results emphasize a syndemic nature of COVID-19 risks.}, } @article {pmid34868877, year = {2021}, author = {Sakhare, A and Stradford, J and Ravichandran, R and Deng, R and Ruiz, J and Subramanian, K and Suh, J and Pa, J}, title = {Simultaneous Exercise and Cognitive Training in Virtual Reality Phase 2 Pilot Study: Impact on Brain Health and Cognition in Older Adults.}, journal = {Brain plasticity (Amsterdam, Netherlands)}, volume = {7}, number = {2}, pages = {111-130}, pmid = {34868877}, issn = {2213-6312}, abstract = {BACKGROUND: Aerobic exercise and environmental enrichment have been shown to enhance brain function. Virtual reality (VR) is a promising method for combining these activities in a meaningful and ecologically valid way.

OBJECTIVE: The purpose of this Phase 2 pilot study was to calculate relative change and effect sizes to assess the impact of simultaneous exercise and cognitive training in VR on brain health and cognition in older adults.

METHODS: Twelve cognitively normal older adults (64.7±8.8 years old, 8 female) participated in a 12-week intervention, 3 sessions/week for 25-50 minutes/session at 50-80% HRmax. Participants cycled on a custom-built stationary exercise bike while wearing a VR head-mounted display and navigating novel virtual environments to train spatial memory. Brain and cognitive changes were assessed using MRI imaging and a cognitive battery.

RESULTS: Medium effect size (ES) improvements in cerebral flow and brain structure were observed. Pulsatility, a measure of peripheral vascular resistance, decreased 10.5% (ES(d) = 0.47). Total grey matter volume increased 0.73% (ES(r) = 0.38), while thickness of the superior parietal lobule, a region associated with spatial orientation, increased 0.44% (ES(r) = 0.30). Visual memory discrimination related to pattern separation showed a large improvement of 68% (ES(η p [2]) = 0.43). Cognitive flexibility (Trail Making Test B) (ES(r) = 0.42) and response inhibition (ES(W) = 0.54) showed medium improvements of 14% and 34%, respectively.

CONCLUSIONS: Twelve weeks of simultaneous exercise and cognitive training in VR elicits positive changes in brain volume, vascular resistance, memory, and executive function with moderate-to-large effect sizes in our pilot study.}, } @article {pmid34868617, year = {2021}, author = {Cushnan, D and Berka, R and Bertolli, O and Williams, P and Schofield, D and Joshi, I and Favaro, A and Halling-Brown, M and Imreh, G and Jefferson, E and Sebire, NJ and Reilly, G and Rodrigues, JCL and Robinson, G and Copley, S and Malik, R and Bloomfield, C and Gleeson, F and Crotty, M and Denton, E and Dickson, J and Leeming, G and Hardwick, HE and Baillie, K and Openshaw, PJ and Semple, MG and Rubin, C and Howlett, A and Rockall, AG and Bhayat, A and Fascia, D and Sudlow, C and , and Jacob, J}, title = {Towards nationally curated data archives for clinical radiology image analysis at scale: Learnings from national data collection in response to a pandemic.}, journal = {Digital health}, volume = {7}, number = {}, pages = {20552076211048654}, pmid = {34868617}, issn = {2055-2076}, support = {/WT_/Wellcome Trust/United Kingdom ; MC_PC_19025/MRC_/Medical Research Council/United Kingdom ; MC_PC_19059/MRC_/Medical Research Council/United Kingdom ; MR/S010351/1/MRC_/Medical Research Council/United Kingdom ; }, abstract = {The prevalence of the coronavirus SARS-CoV-2 disease has resulted in the unprecedented collection of health data to support research. Historically, coordinating the collation of such datasets on a national scale has been challenging to execute for several reasons, including issues with data privacy, the lack of data reporting standards, interoperable technologies, and distribution methods. The coronavirus SARS-CoV-2 disease pandemic has highlighted the importance of collaboration between government bodies, healthcare institutions, academic researchers and commercial companies in overcoming these issues during times of urgency. The National COVID-19 Chest Imaging Database, led by NHSX, British Society of Thoracic Imaging, Royal Surrey NHS Foundation Trust and Faculty, is an example of such a national initiative. Here, we summarise the experiences and challenges of setting up the National COVID-19 Chest Imaging Database, and the implications for future ambitions of national data curation in medical imaging to advance the safe adoption of artificial intelligence in healthcare.}, } @article {pmid34864095, year = {2022}, author = {Shahid, M and Azfaralariff, A and Zubair, M and Abdulkareem Najm, A and Khalili, N and Law, D and Firasat, S and Fazry, S}, title = {In silico study of missense variants of FANCA, FANCC and FANCG genes reveals high risk deleterious alleles predisposing to Fanconi anemia pathogenesis.}, journal = {Gene}, volume = {812}, number = {}, pages = {146104}, doi = {10.1016/j.gene.2021.146104}, pmid = {34864095}, issn = {1879-0038}, mesh = {Binding Sites ; Computational Biology/*methods ; Fanconi Anemia/*genetics ; Fanconi Anemia Complementation Group A Protein/chemistry/*genetics ; Fanconi Anemia Complementation Group C Protein/chemistry/*genetics ; Fanconi Anemia Complementation Group G Protein/chemistry/*genetics ; Genetic Association Studies ; Genetic Predisposition to Disease ; Humans ; Models, Molecular ; *Mutation, Missense ; Protein Conformation ; Protein Stability ; }, abstract = {Among the 22 Fanconi anemia (FA) reported genes, 90% of mutational spectra were found in three genes, namely FANCA (64%), FANCC (12%) and FANCG (8%). Therefore, this study aimed to identify the high-risk deleterious variants in three selected genes (FANCA, FANCC, and FANCG) through various computational approaches. The missense variant datasets retrieved from the UCSC genome browser were analyzed for their pathogenicity, stability, and phylogenetic conservancy. A total of 23 alterations, of which 16 in FANCA, 6 in FANCC and one variant in FANCG, were found to be highly deleterious. The native and mutant structures were generated, which demonstrated a profound impact on the respective proteins. Besides, their pathway analysis predicted many other pathways in addition to the Fanconi anemia pathway, homologous recombination, and mismatch repair pathways. Hence, this is the first comprehensive study that can be useful for understanding the genetic signatures in the development of FA.}, } @article {pmid34863336, year = {2022}, author = {Kokaliaris, C and Garba, A and Matuska, M and Bronzan, RN and Colley, DG and Dorkenoo, AM and Ekpo, UF and Fleming, FM and French, MD and Kabore, A and Mbonigaba, JB and Midzi, N and Mwinzi, PNM and N'Goran, EK and Polo, MR and Sacko, M and Tchuem Tchuenté, LA and Tukahebwa, EM and Uvon, PA and Yang, G and Wiesner, L and Zhang, Y and Utzinger, J and Vounatsou, P}, title = {Effect of preventive chemotherapy with praziquantel on schistosomiasis among school-aged children in sub-Saharan Africa: a spatiotemporal modelling study.}, journal = {The Lancet. Infectious diseases}, volume = {22}, number = {1}, pages = {136-149}, pmid = {34863336}, issn = {1474-4457}, support = {001/WHO_/World Health Organization/International ; }, mesh = {Adolescent ; Africa South of the Sahara/epidemiology ; Animals ; Anthelmintics/*therapeutic use ; Chemoprevention ; Child ; Child, Preschool ; Cross-Sectional Studies ; Databases, Factual ; Humans ; Praziquantel/administration & dosage/*therapeutic use ; Prevalence ; Schistosoma haematobium/*drug effects ; Schistosoma mansoni/*drug effects ; Schistosomiasis/classification/*drug therapy/epidemiology ; Schools ; *Spatio-Temporal Analysis ; }, abstract = {BACKGROUND: Over the past 20 years, schistosomiasis control has been scaled up. Preventive chemotherapy with praziquantel is the main intervention. We aimed to assess the effect of preventive chemotherapy on schistosomiasis prevalence in sub-Saharan Africa, comparing 2000-10 with 2011-14 and 2015-19.

METHODS: In this spatiotemporal modelling study, we analysed survey data from school-aged children (aged 5-14 years) in 44 countries across sub-Saharan Africa. The data were extracted from the Global Neglected Tropical Diseases database and augmented by 2018 and 2019 survey data obtained from disease control programmes. Bayesian geostatistical models were fitted to Schistosoma haematobium and Schistosoma mansoni survey data. The models included data on climatic predictors obtained from satellites and other open-source environmental databases and socioeconomic predictors obtained from various household surveys. Temporal changes in Schistosoma species prevalence were estimated by a categorical variable with values corresponding to the three time periods (2000-10, 2011-14, and 2015-19) during which preventive chemotherapy interventions were scaled up.

FINDINGS: We identified 781 references with relevant geolocated schistosomiasis survey data for 2000-19. There were 19 166 unique survey locations for S haematobium and 23 861 for S mansoni, of which 77% (14 757 locations for S haematobium and 18 372 locations for S mansoni) corresponded to 2011-19. Schistosomiasis prevalence among school-aged children in sub-Saharan Africa decreased from 23·0% (95% Bayesian credible interval 22·1-24·1) in 2000-10 to 9·6% (9·1-10·2) in 2015-19, an overall reduction of 58·3%. The reduction of S haematobium was 67·9% (64·6-71·1) and that of S mansoni 53·6% (45·2-58·3) when comparing 2000-10 with 2015-19.

INTERPRETATION: Our model-based estimates suggest that schistosomiasis prevalence in sub-Saharan Africa has decreased considerably, most likely explained by the scale-up of preventive chemotherapy. There is a need to consolidate gains in the control of schistosomiasis by means of preventive chemotherapy, coupled with other interventions to interrupt disease transmission.

FUNDING: European Research Council and WHO.}, } @article {pmid34862646, year = {2022}, author = {Kropf, S and Antweiler, K and Glimm, E}, title = {Use of multivariate distance measures for high-dimensional data in tests for difference, superiority, equivalence and non-inferiority.}, journal = {Biometrical journal. Biometrische Zeitschrift}, volume = {64}, number = {3}, pages = {577-597}, doi = {10.1002/bimj.202000367}, pmid = {34862646}, issn = {1521-4036}, abstract = {Tests based on pairwise distance measures for multivariate sample vectors are common in ecological studies but are usually restricted to two-sided tests for differences. In this paper, we investigate extensions to tests for superiority, equivalence and non-inferiority.}, } @article {pmid34861418, year = {2022}, author = {Huang, Z and Gao, N and Zhang, S and Xing, J and Hou, J}, title = {Investigating the toxically homogenous effects of three lanthanides on zebrafish.}, journal = {Comparative biochemistry and physiology. Toxicology & pharmacology : CBP}, volume = {253}, number = {}, pages = {109251}, doi = {10.1016/j.cbpc.2021.109251}, pmid = {34861418}, issn = {1532-0456}, mesh = {Animals ; Ecotoxicology ; Gene Expression Regulation/drug effects ; Gene Ontology ; Gene Regulatory Networks ; Lanthanoid Series Elements/*toxicity ; Sequence Analysis, RNA ; Toxicity Tests, Acute ; Water Pollutants, Chemical/toxicity ; *Zebrafish/genetics ; Zebrafish Proteins/*genetics ; }, abstract = {The adverse effects of rare earth elements (REEs) have been increasingly reported in the past decades and have raised concern about their environmental toxicities. However, the available data is insufficient to elucidate the toxic effects, mechanisms, and whether the toxicity across all REEs is uniform. In this study, zebrafish were exposed to 0, 0.8, 1.6, 3.2, 6.4, 12.8 and 25.6 mg/L Ln(NO3)3•6H2O to test the acute toxicity of La(III), Ce(III), and Nd(III). LC50 of the three lanthanides was compared to the extent of the impact on gene expression. We carried out the functionally grouped network-based transcriptome analysis using gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) to explore the molecular mechanisms. The acute toxicity test showed that LC50 of La(III), Ce(III), and Nd(III) were 2.53, 2.03, and 2.76 mg/L, respectively. Consistent with acute toxicity, Ce(III) caused a little more DEGs than La(III) and Nd(III). Some biological processes such as metabolism of xenobiotics, oocyte meiosis, steroid biosynthesis, DNA replication, and p53 signaling pathway were affected following exposure of all the three lanthanides. Ce(III) also induced changes in the chemokine-mediated signaling pathway. The results indicated that the lethality is comparable, and the toxic patterns are similar across the three lanthanides. This study gives comparative research on the toxicities of three lanthanides to model organism zebrafish.}, } @article {pmid34857747, year = {2021}, author = {Yang, X and Baskin, CC and Baskin, JM and Pakeman, RJ and Huang, Z and Gao, R and Cornelissen, JHC}, title = {Global patterns of potential future plant diversity hidden in soil seed banks.}, journal = {Nature communications}, volume = {12}, number = {1}, pages = {7023}, pmid = {34857747}, issn = {2041-1723}, mesh = {Altitude ; *Biodiversity ; Databases, Factual ; Ecosystem ; *Models, Statistical ; Plant Dispersal/*physiology ; Plants/classification ; Seed Bank ; Seeds/classification/*physiology ; Soil ; }, abstract = {Soil seed banks represent a critical but hidden stock for potential future plant diversity on Earth. Here we compiled and analyzed a global dataset consisting of 15,698 records of species diversity and density for soil seed banks in natural plant communities worldwide to quantify their environmental determinants and global patterns. Random forest models showed that absolute latitude was an important predictor for diversity of soil seed banks. Further, climate and soil were the major determinants of seed bank diversity, while net primary productivity and soil characteristics were the main predictors of seed bank density. Moreover, global mapping revealed clear spatial patterns for soil seed banks worldwide; for instance, low densities may render currently species-rich low latitude biomes (such as tropical rain-forests) less resilient to major disturbances. Our assessment provides quantitative evidence of how environmental conditions shape the distribution of soil seed banks, which enables a more accurate prediction of the resilience and vulnerabilities of plant communities and biomes under global changes.}, } @article {pmid34853345, year = {2021}, author = {Costa, JS and Hahn, S and Araújo, PM and Dhanjal-Adams, KL and Rocha, AD and Alves, JA}, title = {Linking migratory performance to breeding phenology and productivity in an Afro-Palearctic long-distance migrant.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {23258}, pmid = {34853345}, issn = {2045-2322}, mesh = {Africa, Western ; Animal Distribution ; *Animal Migration ; Animals ; Bees ; Birds/*physiology ; Europe ; *Feeding Behavior ; Female ; Geographic Information Systems ; Geography ; Male ; Population Dynamics ; *Reproduction ; *Seasons ; Spain ; Time Factors ; }, abstract = {Understanding the relationship between migratory performance and fitness is crucial for predicting population dynamics of migratory species. In this study, we used geolocators to explore migration performance (speed and duration of migratory movements, migratory timings) and its association with breeding phenology and productivity in an Afro-Palearctic insectivore, the European bee-eater (Merops apiaster), breeding in Iberian Peninsula. Bee-eaters migrated at higher travel speeds and had shorter travel duration in spring compared to autumn. Individuals that departed earlier or spent fewer days in-flight arrived earlier to the breeding areas. Our results show overall positive, but year-specific, linkages between arrival and laying dates. In one year, laying was earlier and productivity was higher, remaining constant throughout the season, while in the subsequent year productivity was lower and, importantly, declined with laying date. These results suggest that arriving earlier can be advantageous for bee-eaters, as in years when breeding conditions are favourable, early and late breeders produce high and similar number of fledglings, but when conditions are unfavourable only early breeders experience high productivity levels.}, } @article {pmid34848787, year = {2021}, author = {Dal Pont, G and Duarte Ritter, C and Agostinis, AO and Stica, PV and Horodesky, A and Cozer, N and Balsanelli, E and Netto, OSM and Henn, C and Ostrensky, A and Pie, MR}, title = {Monitoring fish communities through environmental DNA metabarcoding in the fish pass system of the second largest hydropower plant in the world.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {23167}, pmid = {34848787}, issn = {2045-2322}, mesh = {Animals ; Biodiversity ; Brazil ; Computational Biology/methods ; *Conservation of Natural Resources ; DNA Barcoding, Taxonomic/*methods ; DNA, Environmental ; Ecology ; Ecosystem ; Environmental Monitoring/methods ; Fishes/*genetics/*physiology ; Freshwater Biology ; Geography ; Humans ; *Power Plants ; Rivers ; }, abstract = {The Itaipu Hydroelectric Power Plant is the second largest in the world in power generation. The artificial barrier created by its dam imposes an obstacle for fish migration. Thus, in 2002, a fish pass system, named Piracema Channel, was built to allow fish to access areas upstream of the reservoir. We tested the potential of environmental DNA metabarcoding to monitor the impact of both the dam and associated fish pass system in the Paraná River fish communities and to compare it with traditional monitoring methods. Using a fragment of the 12S gene, we characterized richness and community composition based on amplicon sequence variants, operational taxonomic units, and zero-radius OTUs. We combined GenBank and in-house data for taxonomic assignment. We found that different bioinformatics approaches showed similar results. Also, we found a decrease in fish diversity from 2019 to 2020 probably due to the recent extreme drought experienced in southeastern Brazil. The highest alpha diversity was recorded in the mouth of the fish pass system, located in a protected valley with the highest environmental heterogeneity. Despite the clear indication that the reference databases need to be continuously improved, our results demonstrate the analytical efficiency of the metabarcoding to monitor fish species.}, } @article {pmid34843472, year = {2021}, author = {Osone, Y and Hashimoto, S and Kenzo, T}, title = {Verification of our empirical understanding of the physiology and ecology of two contrasting plantation species using a trait database.}, journal = {PloS one}, volume = {16}, number = {11}, pages = {e0254599}, pmid = {34843472}, issn = {1932-6203}, mesh = {Chamaecyparis/*physiology ; Climate Change ; Cryptomeria/*physiology ; Databases, Factual ; *Droughts ; *Ecosystem ; *Forests ; Trees ; }, abstract = {The effects of climate change on forest ecosystems take on increasing importance more than ever. Information on plant traits is a powerful predictor of ecosystem dynamics and functioning. We reviewed the major ecological traits, such as foliar gas exchange and nutrients, xylem morphology and drought tolerance, of Cryptomeria japonica and Chamaecyparis obtusa, which are major timber species in East Asia, especially in Japan, by using a recently developed functional trait database for both species (SugiHinokiDB). Empirically, C. obtusa has been planted under drier conditions, whereas C. japonica, which grows faster but thought to be less drought tolerant, has been planted under wetter conditions. Our analysis generally support the empirical knowledge: The maximum photosynthetic rate, stomatal conductance, foliar nutrient content and soil-to-foliage hydraulic conductance were higher in C. japonica than in C. obtusa. In contrast, the foliar turgor loss point and xylem pressure corresponding to 50% conductivity, which indicate drought tolerance, were lower in C. obtusa and are consistent with the drier habitat of C. obtusa. Ontogenetic shifts were also observed; as the age and height of the trees increased, foliar nutrient concentrations, foliar minimum midday water potential and specific leaf area decreased in C. japonica, suggesting that nutrient and water limitation occurs with the growth. In C. obtusa, the ontogenetic shits of these foliar traits were less pronounced. Among the Cupressaceae worldwide, the drought tolerance of C. obtusa, as well as C. japonica, was not as high. This may be related to the fact that the Japanese archipelago has historically not been subjected to strong dryness. The maximum photosynthetic rate showed intermediate values within the family, indicating that C. japonica and C. obtusa exhibit relatively high growth rates in the Cupressaceae family, and this is thought to be the reason why they have been selected as economically suitable timber species in Japanese forestry. This study clearly demonstrated that the plant trait database provides us a promising opportunity to verify out empirical knowledge of plantation management and helps us to understand effect of climate change on plantation forests by using trait-based modelling.}, } @article {pmid34839580, year = {2022}, author = {Li, F and Rane, RV and Luria, V and Xiong, Z and Chen, J and Li, Z and Catullo, RA and Griffin, PC and Schiffer, M and Pearce, S and Lee, SF and McElroy, K and Stocker, A and Shirriffs, J and Cockerell, F and Coppin, C and Sgrò, CM and Karger, A and Cain, JW and Weber, JA and Santpere, G and Kirschner, MW and Hoffmann, AA and Oakeshott, JG and Zhang, G}, title = {Phylogenomic analyses of the genus Drosophila reveals genomic signals of climate adaptation.}, journal = {Molecular ecology resources}, volume = {22}, number = {4}, pages = {1559-1581}, pmid = {34839580}, issn = {1755-0998}, support = {R01 HD091846/HD/NICHD NIH HHS/United States ; //Australia's Science and Industry Endowment Fund/ ; 152453KYSB20170002//International Partnership Program of Chinese Academy of Sciences/ ; //Australian Research Council and their Laureate Fellowship Scheme/ ; CF16-0663//Carlsbergfondet/ ; 25900//Villum Fonden/ ; XDB31020000//Strategic Priority Research Program of the Chinese Academy of Sciences/ ; ID 100010434//"la Caixa" Foundation/ ; PID2019-104700GA-I00//Ministerio de Ciencia e Innovación, Spain/ ; R01 HD073104/HD/NICHD NIH HHS/United States ; }, mesh = {Adaptation, Physiological/genetics ; Animals ; *Drosophila/genetics ; *Genome ; Genomics ; Humans ; Phylogeny ; }, abstract = {Many Drosophila species differ widely in their distributions and climate niches, making them excellent subjects for evolutionary genomic studies. Here, we have developed a database of high-quality assemblies for 46 Drosophila species and one closely related Zaprionus. Fifteen of the genomes were newly sequenced, and 20 were improved with additional sequencing. New or improved annotations were generated for all 47 species, assisted by new transcriptomes for 19. Phylogenomic analyses of these data resolved several previously ambiguous relationships, especially in the melanogaster species group. However, it also revealed significant phylogenetic incongruence among genes, mainly in the form of incomplete lineage sorting in the subgenus Sophophora but also including asymmetric introgression in the subgenus Drosophila. Using the phylogeny as a framework and taking into account these incongruences, we then screened the data for genome-wide signals of adaptation to different climatic niches. First, phylostratigraphy revealed relatively high rates of recent novel gene gain in three temperate pseudoobscura and five desert-adapted cactophilic mulleri subgroup species. Second, we found differing ratios of nonsynonymous to synonymous substitutions in several hundred orthologues between climate generalists and specialists, with trends for significantly higher ratios for those in tropical and lower ratios for those in temperate-continental specialists respectively than those in the climate generalists. Finally, resequencing natural populations of 13 species revealed tropics-restricted species generally had smaller population sizes, lower genome diversity and more deleterious mutations than the more widespread species. We conclude that adaptation to different climates in the genus Drosophila has been associated with large-scale and multifaceted genomic changes.}, } @article {pmid34837836, year = {2022}, author = {Li, Y and Huang, H and Zhang, X}, title = {Identification of catabolic pathway for 1-deoxy-D-sorbitol in Bacillus licheniformis.}, journal = {Biochemical and biophysical research communications}, volume = {586}, number = {}, pages = {81-86}, doi = {10.1016/j.bbrc.2021.11.072}, pmid = {34837836}, issn = {1090-2104}, mesh = {Aldehyde-Lyases/genetics/*metabolism ; Bacillus licheniformis/classification/genetics/*metabolism ; Bacterial Proteins/genetics/*metabolism ; Computational Biology/methods ; Gene Expression Regulation, Bacterial ; Glycerol/chemistry/metabolism ; Mannitol/chemistry/metabolism ; Metabolism/*genetics ; Operon ; Phylogeny ; Sorbitol/analogs & derivatives/*metabolism ; }, abstract = {1-Deoxy-D-sorbitol, the 1-deoxy analogue of D-sorbitol, has been detected in human urine as well as in natural herbs and spices. Although there are sporadic reports about 1-deoxy-D-sorbitol dehydrogenase, the complete catabolic pathway of 1-deoxy-D-sorbitol remains unsolved. Informed by the promiscuous activities of fructose-6-phosphate aldolase (FSA) which is involved in the sorbitol (glucitol) utilization (gut) operon and guided by the large scale bioinformatics analysis, we predicted and then experimentally verified the gut operon encoded by Bacillus licheniformis ATCC14580 is responsible for the catabolism of both D-sorbitol and 1-deoxy-D-sorbitol by in vitro activity assays of pathway enzymes, in vivo growth phenotypes, and transcriptomic studies. Moreover, the phylogenetic distribution analysis suggests that the D-sorbitol and 1-deoxy-D-sorbitol catabolic gene cluster is mostly conserved in members of Firmicutes phylum.}, } @article {pmid34837514, year = {2022}, author = {Strnadová, K and Pfeiferová, L and Přikryl, P and Dvořánková, B and Vlčák, E and Frýdlová, J and Vokurka, M and Novotný, J and Šáchová, J and Hradilová, M and Brábek, J and Šmigová, J and Rösel, D and Smetana, K and Kolář, M and Lacina, L}, title = {Exosomes produced by melanoma cells significantly influence the biological properties of normal and cancer-associated fibroblasts.}, journal = {Histochemistry and cell biology}, volume = {157}, number = {2}, pages = {153-172}, pmid = {34837514}, issn = {1432-119X}, support = {No. 19-05048S//Czech Science Foundation project/ ; project CZ.02.1.01/0.0/0.0/16_019/0000785 "Centre for Tumour Ecology-Research of the Cancer Microenvironment Supporting Cancer Growth Spread"//Operational Programme "Research, Development and Education"/ ; PROGRESS Q28//Univerzita Karlova v Praze/ ; CZ.02.1.01/0.0/0.0/16_013/0001775//ERDF/ ; CZ.02.1.01/0.0/0.0/18_046/0016045//ERDF/ ; LM2018129//MEYS/ ; }, mesh = {Exosomes/*metabolism ; Fibroblasts/*metabolism/pathology ; Humans ; Melanoma, Experimental/*metabolism/pathology ; Tumor Cells, Cultured ; }, abstract = {The incidence of cutaneous malignant melanoma is increasing worldwide. While the treatment of initial stages of the disease is simple, the advanced disease frequently remains fatal despite novel therapeutic options . This requires identification of novel therapeutic targets in melanoma. Similarly to other types of tumours, the cancer microenvironment plays a prominent role and determines the biological properties of melanoma. Importantly, melanoma cell-produced exosomes represent an important tool of intercellular communication within this cancer ecosystem. We have focused on potential differences in the activity of exosomes produced by melanoma cells towards melanoma-associated fibroblasts and normal dermal fibroblasts. Cancer-associated fibroblasts were activated by the melanoma cell-produced exosomes significantly more than their normal counterparts, as assessed by increased transcription of genes for inflammation-supporting cytokines and chemokines, namely IL-6 or IL-8. We have observed that the response is dependent on the duration of the stimulus via exosomes and also on the quantity of exosomes. Our study demonstrates that melanoma-produced exosomes significantly stimulate the tumour-promoting proinflammatory activity of cancer-associated fibroblasts. This may represent a potential new target of oncologic therapy .}, } @article {pmid34837107, year = {2022}, author = {Adedoyin, FF and Alola, UV and Bekun, FV}, title = {On the nexus between globalization, tourism, economic growth, and biocapacity: evidence from top tourism destinations.}, journal = {Environmental science and pollution research international}, volume = {29}, number = {17}, pages = {24995-25005}, pmid = {34837107}, issn = {1614-7499}, mesh = {Carbon Dioxide ; *Economic Development ; Internationality ; *Tourism ; }, abstract = {Several studies have investigated the relationship between tourism, consumption of energy, globalization, and ecological footprint. However, the role of biocapacity alongside tourism development in environmental sustainability is yet to be documented in the extant literature. No doubt, the biocapacity of a country, its level of tourist's arrival, as well as globalization all contribute immensely to ecological footprint. Consequently, this study looks at long-run and causality connections with a special focus on bio-capacity. The study uses the pooled mean group-autoregressive distributed lag model (PMG-ARDL) methodology to test the causality relationship during 2016 international tourists' receipt from world tourism organization data files for 10 tourism destinations. Empirical result based on the panel PMG-ARDL confirms the environmental Kuznets curve (EKC) hypothesis for the 10 tourism destinations countries investigated. Furthermore, the panel ARDL estimator was used to estimate the short-run and long-run relationships simultaneously between biocapacity, tourist arrivals, GDP per capita, globalization, and ecological footprints. While the Dumitrescu and Hurlin panel causality test was used to establish causality relationships among the highlighted variables. The trade-off between economic growth and environmental quality suggests that tourist arrival dampens environmental quality. In addition, the study finds that growing biocapacity affects ecological footprints negatively. Furthermore, an increase in tourism-related activities, globalization, and economic production has the potential to damage the quality of the environment. To this end, given the study results, there is a need to pursue green tourism which can reduce environmental degradation and destruction of land caused by multiple tourism-related transportation and construction of tourist facilities respectively in the top ten tourist destination countries.}, } @article {pmid34835321, year = {2021}, author = {Pushkareva, E and Barrantes, I and Leinweber, P and Karsten, U}, title = {Microbial Diversity in Subarctic Biocrusts from West Iceland following an Elevation Gradient.}, journal = {Microorganisms}, volume = {9}, number = {11}, pages = {}, pmid = {34835321}, issn = {2076-2607}, support = {FP7/2007-2013//Seventh Framework Programme/ ; KA899/33-1//Deutsche Forschungsgemeinschaft/ ; }, abstract = {Biological soil crusts (biocrusts) are essential communities of organisms in the Icelandic soil ecosystem, as they prevent erosion and cryoturbation and provide nutrients to vascular plants. However, biocrust microbial composition in Iceland remains understudied. To address this gap in knowledge, we applied high-throughput sequencing to study microbial community composition in biocrusts collected along an elevation gradient (11-157 m a.s.l.) stretching away perpendicular to the marine coast. Four groups of organisms were targeted: bacteria and cyanobacteria (16S rRNA gene), fungi (transcribed spacer region), and other eukaryotes (18S rRNA gene). The amplicon sequencing of the 16S rRNA gene revealed the dominance of Proteobacteria, Bacteroidetes, and Actinobacteria. Within the cyanobacteria, filamentous forms from the orders Synechococcales and Oscillatoriales prevailed. Furthermore, fungi in the biocrusts were dominated by Ascomycota, while the majority of reads obtained from sequencing of the 18S rRNA gene belonged to Archaeplastida. In addition, microbial photoautotrophs isolated from the biocrusts were assigned to the cyanobacterial genera Phormidesmis, Microcoleus, Wilmottia, and Oscillatoria and to two microalgal phyla Chlorophyta and Charophyta. In general, the taxonomic diversity of microorganisms in the biocrusts increased following the elevation gradient and community composition differed among the sites, suggesting that microclimatic and soil parameters might shape biocrust microbiota.}, } @article {pmid34835128, year = {2021}, author = {Cebriá-Mendoza, M and Bracho, MA and Arbona, C and Larrea, L and Díaz, W and Sanjuán, R and Cuevas, JM}, title = {Exploring the Diversity of the Human Blood Virome.}, journal = {Viruses}, volume = {13}, number = {11}, pages = {}, pmid = {34835128}, issn = {1999-4915}, mesh = {*Genome, Viral ; Healthy Volunteers ; Humans ; Spain ; *Virome ; Viruses/*isolation & purification ; }, abstract = {Metagenomics is greatly improving our ability to discover new viruses, as well as their possible associations with disease. However, metagenomics has also changed our understanding of viruses in general. The vast expansion of currently known viral diversity has revealed a large fraction of non-pathogenic viruses, and offers a new perspective in which viruses function as important components of many ecosystems. In this vein, studies of the human blood virome are often motivated by the search for new viral diseases, especially those associated with blood transfusions. However, these studies have revealed the common presence of apparently non-pathogenic viruses in blood, particularly human anelloviruses and, to a lower extent, human pegiviruses (HPgV). To shed light on the diversity of the human blood virome, we subjected pooled plasma samples from 587 healthy donors in Spain to a viral enrichment protocol, followed by massive parallel sequencing. This showed that anelloviruses were clearly the major component of the blood virome and showed remarkable diversity. In total, we assembled 332 complete or near-complete anellovirus genomes, 50 of which could be considered new species. HPgV was much less frequent, but we, nevertheless, recovered 17 different isolates that we subsequently used for characterizing the diversity of this virus. In-depth investigation of the human blood virome should help to elucidate the ecology of these viruses, and to unveil potentially associated diseases.}, } @article {pmid34834835, year = {2021}, author = {Love, NLR and Bonnet, P and Goëau, H and Joly, A and Mazer, SJ}, title = {Machine Learning Undercounts Reproductive Organs on Herbarium Specimens but Accurately Derives Their Quantitative Phenological Status: A Case Study of Streptanthus tortuosus.}, journal = {Plants (Basel, Switzerland)}, volume = {10}, number = {11}, pages = {}, pmid = {34834835}, issn = {2223-7747}, abstract = {Machine learning (ML) can accelerate the extraction of phenological data from herbarium specimens; however, no studies have assessed whether ML-derived phenological data can be used reliably to evaluate ecological patterns. In this study, 709 herbarium specimens representing a widespread annual herb, Streptanthus tortuosus, were scored both manually by human observers and by a mask R-CNN object detection model to (1) evaluate the concordance between ML and manually-derived phenological data and (2) determine whether ML-derived data can be used to reliably assess phenological patterns. The ML model generally underestimated the number of reproductive structures present on each specimen; however, when these counts were used to provide a quantitative estimate of the phenological stage of plants on a given sheet (i.e., the phenological index or PI), the ML and manually-derived PI's were highly concordant. Moreover, herbarium specimen age had no effect on the estimated PI of a given sheet. Finally, including ML-derived PIs as predictor variables in phenological models produced estimates of the phenological sensitivity of this species to climate, temporal shifts in flowering time, and the rate of phenological progression that are indistinguishable from those produced by models based on data provided by human observers. This study demonstrates that phenological data extracted using machine learning can be used reliably to estimate the phenological stage of herbarium specimens and to detect phenological patterns.}, } @article {pmid34833734, year = {2021}, author = {Makarov, M and Aslamov, I and Gnatovsky, R}, title = {Environmental Monitoring of the Littoral Zone of Lake Baikal Using a Network of Automatic Hydro-Meteorological Stations: Development and Trial Run.}, journal = {Sensors (Basel, Switzerland)}, volume = {21}, number = {22}, pages = {}, pmid = {34833734}, issn = {1424-8220}, support = {075-15-2020-787//Ministry of Science and Higher Education of the Russian Federation/ ; }, mesh = {Chlorophyll A ; *Environmental Monitoring ; *Lakes ; Meteorology ; Temperature ; }, abstract = {An automatic hydro-meteorological station (AHMS) was designed to monitor the littoral zone of Lake Baikal in areas with high anthropogenic pressure. The developed AHMS was installed near the Bolshiye Koty settlement (southern basin). This AHMS is the first experience focused on obtaining the necessary competencies for the development of a monitoring network of the Baikal natural territory. To increase the flexibility of adjustment and repeatability, we developed AHMS as a low-cost modular system. AHMS is equipped with a weather station and sensors measuring water temperature, pH, dissolved oxygen, redox potential, conductivity, chlorophyll-a, and turbidity. This article describes the main AHMS functions (hardware and software) and measures taken to ensure data quality control. We present the results of the first two periods of its operation. The data acquired during this periods have demonstrated that, to obtain accurate measurements and to detect and correct errors that were mainly due to biofouling of the sensors and calibration bias, a correlation between AHMS and laboratory studies is necessary for parameters such as pH and chlorophyll-a. The gained experience should become the basis for the further development of the monitoring network of the Baikal natural territory.}, } @article {pmid34833612, year = {2021}, author = {Chen, C and Ye, S and Bai, Z and Wang, J and Zhang, Z and Ablameyko, S}, title = {Intelligent Mining of Urban Ventilation Corridors Based on High-Precision Oblique Photographic Images.}, journal = {Sensors (Basel, Switzerland)}, volume = {21}, number = {22}, pages = {}, pmid = {34833612}, issn = {1424-8220}, support = {LGJ19F020002//Zhejiang Province Basic Public Welfare Research Program Project/ ; }, mesh = {China ; Cities ; *City Planning ; *Hot Temperature ; Urbanization ; Ventilation ; }, abstract = {With the advancement of urbanization and the impact of industrial pollution, the issue of urban ventilation has attracted increasing attention. Research on urban ventilation corridors is a hotspot in the field of urban planning. Traditional studies on ventilation corridors mostly focus on qualitative or simulated research on urban climate issues such as the intensified urban heat island effect, serious environmental pollution, and insufficient climate adaptability. Based on the high-precision urban remote sensing image data obtained by aeromagnetic oblique photography, this paper calculates the frontal area density of the city with reference to the urban wind statistics. Based on the existing urban patterns, template matching technology was used to automatically excavate urban ventilation corridors, which provides scientific and reasonable algorithmic support for the rapid construction of potential urban ventilation corridor paths. It also provides technical methods and decision basis for low-carbon urban planning, ecological planning and microclimate optimization design. This method was proved to be effective through experiments in Deqing city, Zhejiang Province, China.}, } @article {pmid34831741, year = {2021}, author = {Arrogante-Funes, P and Bruzón, AG and Arrogante-Funes, F and Ramos-Bernal, RN and Vázquez-Jiménez, R}, title = {Integration of Vulnerability and Hazard Factors for Landslide Risk Assessment.}, journal = {International journal of environmental research and public health}, volume = {18}, number = {22}, pages = {}, pmid = {34831741}, issn = {1660-4601}, mesh = {*Disasters ; Ecosystem ; Geographic Information Systems ; Humans ; *Landslides ; Risk Assessment ; }, abstract = {Among the numerous natural hazards, landslides are one of the greatest, as they can cause enormous loss of life and property, and affect the natural ecosystem and their services. Landslides are disasters that cause damage to anthropic activities and innumerable loss of human life, globally. The landslide risk assessed by the integration of susceptibility and vulnerability maps has recently become a manner of studying sites prone to landslide events and managing these regions well. Developing countries, where the impact of landslides is frequent, need risk assessment tools that enable them to address these disasters, starting with their prevention, with free spatial data and appropriate models. Our study shows a heuristic risk model by integrating a susceptibility map made by AutoML and a vulnerability one that is made considering ecological vulnerability and socio-economic vulnerability. The input data used in the State of Guerrero (México) approach uses spatial data, such as remote sensing, or official Mexican databases. This aspect makes this work adaptable to other parts of the world because the cost is low, and the frequency adaptation is high. Our results show a great difference between the distribution of vulnerability and susceptibility zones in the study area, and even between the socio-economic and ecological vulnerabilities. For instance, the highest ecological vulnerability is in the mountainous zone in Guerrero, and the highest socio-economic vulnerability values are found around settlements and roads. Therefore, the final risk assessment map is an integrated index that considers susceptibility and vulnerability and would be a good first attempt to challenge landslide disasters.}, } @article {pmid34830331, year = {2021}, author = {Zhang, J and Yu, P and Zhao, Y and Zhou, Q and Yang, J and Hu, Q and Liu, T and Bao, C and Su, S and Gui, JF}, title = {Global Analysis of Transcriptome and Translatome Revealed That Coordinated WNT and FGF Regulate the Carapacial Ridge Development of Chinese Soft-Shell Turtle.}, journal = {International journal of molecular sciences}, volume = {22}, number = {22}, pages = {}, pmid = {34830331}, issn = {1422-0067}, support = {31802273//National Natural Science Foundation of China/ ; gxyqZD2021097//Excellent Young Talents Fund Program of Higher Education Institutions of Anhui Province/ ; [2021]711//Fishery Industrial System of Anhui Province, China/ ; 18030701173//Major Science and Technology Project of Anhui Province/ ; 2016FB16//Open Project of State Key Laboratory of Freshwater Ecology and Biotechnology/ ; }, mesh = {Animal Shells/growth & development/*metabolism ; Animals ; Biological Evolution ; Body Patterning/*genetics ; China ; Embryo, Nonmammalian ; Gene Expression Profiling ; Gene Expression Regulation, Developmental ; Gene Ontology ; Gene Regulatory Networks ; MAP Kinase Kinase 4/genetics ; Molecular Sequence Annotation ; *Protein Biosynthesis ; Receptors, Fibroblast Growth Factor/*genetics/metabolism ; *Transcriptome ; Turtles/classification/*genetics/growth & development ; Wnt Signaling Pathway ; Wnt-5a Protein/*genetics/metabolism ; }, abstract = {The turtle carapace is composed of severely deformed fused dorsal vertebrae, ribs, and bone plates. In particular, the lateral growth in the superficial layer of turtle ribs in the dorsal trunk causes an encapsulation of the scapula and pelvis. The recent study suggested that the carapacial ridge (CR) is a new model of epithelial-mesenchymal transition which is essential for the arrangement of the ribs. Therefore, it is necessary to explore the regulatory mechanism of carapacial ridge development to analyze the formation of the turtle shell. However, the current understanding of the regulatory network underlying turtle carapacial ridge development is poor due to the lack of both systematic gene screening at different carapacial ridge development stages and gene function verification studies. In this study, we obtained genome-wide gene transcription and gene translation profiles using RNA sequencing and ribosome nascent-chain complex mRNA sequencing from carapacial ridge tissues of Chinese soft-shell turtle at different development stages. A correlation analysis of the transcriptome and translatome revealed that there were 129, 670, and 135 codifferentially expressed genes, including homodirection and opposite-direction differentially expressed genes, among three comparison groups, respectively. The pathway enrichment analysis of codifferentially expressed genes from the Kyoto Encyclopedia of Genes and Genomes showed dynamic changes in signaling pathways involved in carapacial ridge development. Especially, the results revealed that the Wnt signaling pathway and MAPK signaling pathway may play important roles in turtle carapacial ridge development. In addition, Wnt and Fgf were expressed during the carapacial ridge development. Furthermore, we discovered that Wnt5a regulated carapacial ridge development through the Wnt5a/JNK pathway. Therefore, our studies uncover that the morphogenesis of the turtle carapace might function through the co-operation between conserved WNT and FGF signaling pathways. Consequently, our findings revealed the dynamic signaling pathways acting on the carapacial ridge development of Chinese soft-shell turtle and provided new insights into uncover the molecular mechanism underlying turtle shell morphogenesis.}, } @article {pmid34826482, year = {2022}, author = {Alcántara, I and Somma, A and Chalar, G and Fabre, A and Segura, A and Achkar, M and Arocena, R and Aubriot, L and Baladán, C and Barrios, M and Bonilla, S and Burwood, M and Calliari, DL and Calvo, C and Capurro, L and Carballo, C and Céspedes-Payret, C and Conde, D and Corrales, N and Cremella, B and Crisci, C and Cuevas, J and De Giacomi, S and De León, L and Delbene, L and Díaz, I and Fleitas, V and González-Bergonzoni, I and González-Madina, L and González-Piana, M and Goyenola, G and Gutiérrez, O and Haakonsson, S and Iglesias, C and Kruk, C and Lacerot, G and Langone, J and Lepillanca, F and Lucas, C and Martigani, F and Martínez de la Escalera, G and Meerhoff, M and Nogueira, L and Olano, H and Pacheco, JP and Panario, D and Piccini, C and Quintans, F and Teixeira de Mello, F and Terradas, L and Tesitore, G and Vidal, L and García-Rodríguez, F}, title = {A reply to "Relevant factors in the eutrophication of the Uruguay River and the Río Negro".}, journal = {The Science of the total environment}, volume = {818}, number = {}, pages = {151854}, doi = {10.1016/j.scitotenv.2021.151854}, pmid = {34826482}, issn = {1879-1026}, mesh = {*Black or African American ; Environmental Monitoring ; Eutrophication ; Harmful Algal Bloom ; Humans ; Phosphorus/analysis ; Reproducibility of Results ; *Rivers ; Uruguay ; }, abstract = {A recent paper by Beretta-Blanco and Carrasco-Letelier (2021) claims that agricultural eutrophication is not one of the main causes for cyanobacterial blooms in rivers and artificial reservoirs. By combining rivers of markedly different hydrological characteristics e.g., presence/absence and number of dams, river discharge and geological setting, the study speculates about the role of nutrients for modulating phytoplankton chlorophyll-a. Here, we identified serious flaws, from erratic and inaccurate data manipulation. The study did not define how erroneous original dataset values were treated, how the variables below the detection/quantification limit were numerically introduced, lack of mandatory variables for river studies such as flow and rainfall, arbitrary removal of pH > 7.5 values (which were not outliers), and finally how extreme values of other environmental variables were included. In addition, we identified conceptual and procedural mistakes such as biased construction/evaluation of model prediction capability. The study trained the model using pooled data from a short restricted lotic section of the (large) Uruguay River and from both lotic and reservoir domains of the Negro River, but then tested predictability within the (small) Cuareim River. Besides these methodological considerations, the article shows misinterpretations of the statistical correlation of cause and effect neglecting basic limnological knowledge of the ecology of harmful algal blooms (HABs) and international research on land use effects on freshwater quality. The argument that pH is a predictor variable for HABs neglects overwhelming basic paradigms of carbon fluxes and change in pH because of primary productivity. As a result, the article introduces the notion that HABs formation are not related to agricultural land use and water residence time and generate a great risk for the management of surface waterbodies. This reply also emphasizes the need for good practices of open data management, especially for public databases in view of external reproducibility.}, } @article {pmid34825535, year = {2021}, author = {Nath, A and Venkatesh, S and Vindhya, J and Balan, S and Metgud, CS}, title = {Prevalence of intimate partner violence among pregnant women attending a public sector hospital in Bengaluru, southern India.}, journal = {The National medical journal of India}, volume = {34}, number = {3}, pages = {132-137}, doi = {10.25259/NMJI_309_19}, pmid = {34825535}, issn = {2583-150X}, mesh = {Adolescent ; Adult ; Female ; Hospitals, Public ; Humans ; India/epidemiology ; *Intimate Partner Violence ; Pregnancy ; Pregnancy Outcome ; *Pregnant Women ; Prevalence ; Public Sector ; Risk Factors ; Young Adult ; }, abstract = {Background Intimate partner violence (IPV) is recognized as an important public health problem globally as well as in India. It may result in adverse physical and mental health consequences for the victim or unfavourable pregnancy outcomes if it happens during pregnancy. The possible risk factors for IPV can be explained by four levels of ecological factors: individual, partner, household and community. We estimated the prevalence of IPV and its association with selected ecological risk factors among pregnant women availing of antenatal care at a public sector hospital in Bengaluru, southern India. Methods We included 350 women above the age of 18 years with a confirmed pregnancy of less than 24 weeks and having no obstetric complication. We used the Conflict Tactics Scale to determine the presence of IPV. The risk factors measured were-individual level: respondent's age, education, occupation, gravidity, planned or unplanned pregnancy, substance abuse, presence of depression and anxiety; partner-related: spouse's education, occupation and marital discord; household/community-related: socioeconomic status, social support, religion and consanguinity. Results The prevalence of IPV was 3.7%. Factors that were significantly associated on multivariate analysis were higher age (above 20 years) (adjusted odds ratio [AOR] 1.82 [1.12-2.97], p=0.016) and presence of depression (AOR 6.84 [1.76-26.61], p=0.005). Conclusion The prevalence of IPV was less in our study population compared to figures reported from other Indian study settings.}, } @article {pmid34825399, year = {2022}, author = {Jaworski, L and Sauer, F and Jansen, S and Tannich, E and Schmidt-Chanasit, J and Kiel, E and Lühken, R}, title = {Artificial resting sites: An alternative sampling method for adult mosquitoes.}, journal = {Medical and veterinary entomology}, volume = {36}, number = {2}, pages = {139-148}, doi = {10.1111/mve.12559}, pmid = {34825399}, issn = {1365-2915}, mesh = {*Aedes ; Animals ; Carbon Dioxide ; *Culex ; Female ; Male ; Mosquito Control/methods ; Mosquito Vectors ; }, abstract = {Mosquito collections are commonly conducted with baited traps predominantly attracting host-seeking females. In contrast, resting sites are generally colonized by a broader range of the mosquito population, including a higher proportion of males and blood-engorged females. This study evaluates the sampling success of different artificial resting sites, attached to a deciduous or coniferous tree at different heights. As standard sampling method, carbon dioxide-baited Biogents Sentinel traps (BG traps) were operated in parallel. BG traps caught a higher number of specimens compared to the resting sites. However, the proportion of blood-engorged females and males was higher in resting sites. More Culiseta spp. specimens were collected in resting sites compared to BG traps, but less Aedes spp. specimens. In general, fewer specimens and species were recorded in small resting sites and at top height level compared to medium or large resting sites at medium or ground level. The proportion of males was highest at the ground, while the proportion of engorged females was highest at medium and top level. Due to the higher proportion of blood-engorged females, artificial resting sites are especially useful for studies of host-feeding patterns or xenosurveillance. Low costs and efforts allow a cost-effective increase of the number of resting sites per sampling site to collect more mosquitoes.}, } @article {pmid34819495, year = {2021}, author = {Hafner, L and Pichon, M and Burucoa, C and Nusser, SHA and Moura, A and Garcia-Garcera, M and Lecuit, M}, title = {Listeria monocytogenes faecal carriage is common and depends on the gut microbiota.}, journal = {Nature communications}, volume = {12}, number = {1}, pages = {6826}, pmid = {34819495}, issn = {2041-1723}, mesh = {Animals ; Carrier State/diagnosis/*epidemiology/microbiology ; DNA, Bacterial/isolation & purification ; Datasets as Topic ; Disease Models, Animal ; Feces/microbiology ; Gastrointestinal Microbiome/*genetics ; Humans ; Listeria monocytogenes/genetics/*isolation & purification/pathogenicity ; Male ; Metagenomics/statistics & numerical data ; Mice ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Virulence ; }, abstract = {Listeria genus comprises two pathogenic species, L. monocytogenes (Lm) and L. ivanovii, and non-pathogenic species. All can thrive as saprophytes, whereas only pathogenic species cause systemic infections. Identifying Listeria species' respective biotopes is critical to understand the ecological contribution of Listeria virulence. In order to investigate the prevalence and abundance of Listeria species in various sources, we retrieved and analyzed 16S rRNA datasets from MG-RAST metagenomic database. 26% of datasets contain Listeria sensu stricto sequences, and Lm is the most prevalent species, most abundant in soil and host-associated environments, including 5% of human stools. Lm is also detected in 10% of human stool samples from an independent cohort of 900 healthy asymptomatic donors. A specific microbiota signature is associated with Lm faecal carriage, both in humans and experimentally inoculated mice, in which it precedes Lm faecal carriage. These results indicate that Lm faecal carriage is common and depends on the gut microbiota, and suggest that Lm faecal carriage is a crucial yet overlooked consequence of its virulence.}, } @article {pmid34811423, year = {2021}, author = {Alberdi, A and Martin Bideguren, G and Aizpurua, O}, title = {Diversity and compositional changes in the gut microbiota of wild and captive vertebrates: a meta-analysis.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {22660}, pmid = {34811423}, issn = {2045-2322}, support = {DNRF143//Danmarks Grundforskningsfond/ ; }, mesh = {Animals ; Animals, Wild ; Animals, Zoo/*microbiology ; Bacteria/classification ; Cluster Analysis ; Computational Biology ; Ecology ; *Gastrointestinal Microbiome ; Humans ; Mammals/*microbiology ; Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/metabolism ; Species Specificity ; Vertebrates ; }, abstract = {The gut microbiota is recognised as an essential asset for the normal functioning of animal biology. When wild animals are moved into captivity, the modified environmental pressures are expected to rewire the gut microbiota, yet whether this transition follows similar patterns across vertebrates is still unresolved due to the absence of systematic multi-species analyses. We performed a meta-analysis of gut microbiota profiles of 322 captive and 322 wild specimens from 24 vertebrate species. Our analyses yielded no overall pattern of diversity and compositional variation between wild and captive vertebrates, but a heterogeneous landscape of responses, which differed depending on the components of diversity considered. Captive populations showed enrichment patterns of human-associated microorganisms, and the minimal host phylogenetic signal suggests that changes between wild and captive populations are mainly driven by case-specific captivity conditions. Finally, we show that microbiota differences between wild and captive populations can impact evolutionary and ecological inferences that rely on hierarchical clustering-based comparative analyses of gut microbial communities across species.}, } @article {pmid34810237, year = {2022}, author = {Knight, SR and Gupta, RK and Ho, A and Pius, R and Buchan, I and Carson, G and Drake, TM and Dunning, J and Fairfield, CJ and Gamble, C and Green, CA and Halpin, S and Hardwick, HE and Holden, KA and Horby, PW and Jackson, C and Mclean, KA and Merson, L and Nguyen-Van-Tam, JS and Norman, L and Olliaro, PL and Pritchard, MG and Russell, CD and Shaw, CA and Sheikh, A and Solomon, T and Sudlow, C and Swann, OV and Turtle, LCW and Openshaw, PJM and Baillie, JK and Docherty, A and Semple, MG and Noursadeghi, M and Harrison, EM and , and , }, title = {Prospective validation of the 4C prognostic models for adults hospitalised with COVID-19 using the ISARIC WHO Clinical Characterisation Protocol.}, journal = {Thorax}, volume = {77}, number = {6}, pages = {606-615}, pmid = {34810237}, issn = {1468-3296}, support = {MC_PC_19026/MRC_/Medical Research Council/United Kingdom ; MC_PC_19059/MRC_/Medical Research Council/United Kingdom ; MC_UU_12014/9/MRC_/Medical Research Council/United Kingdom ; 200 907/DH_/Department of Health/United Kingdom ; MR/S032304/1/MRC_/Medical Research Council/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; 200 927/DH_/Department of Health/United Kingdom ; 215091/Z/18/Z/WT_/Wellcome Trust/United Kingdom ; CO-CIN-01/DH_/Department of Health/United Kingdom ; IS-BRC-1215-20013/DH_/Department of Health/United Kingdom ; 201 385/DH_/Department of Health/United Kingdom ; MR/V001329/1/MRC_/Medical Research Council/United Kingdom ; 205228/Z/16/Z/WT_/Wellcome Trust/United Kingdom ; MC_PC_19025/MRC_/Medical Research Council/United Kingdom ; MC_PC_15001/MRC_/Medical Research Council/United Kingdom ; 207511/Z/17/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Adolescent ; Adult ; *COVID-19/therapy ; Hospital Mortality ; Humans ; Observational Studies as Topic ; Prognosis ; SARS-CoV-2 ; State Medicine ; World Health Organization ; }, abstract = {PURPOSE: To prospectively validate two risk scores to predict mortality (4C Mortality) and in-hospital deterioration (4C Deterioration) among adults hospitalised with COVID-19.

METHODS: Prospective observational cohort study of adults (age ≥18 years) with confirmed or highly suspected COVID-19 recruited into the International Severe Acute Respiratory and emerging Infections Consortium (ISARIC) WHO Clinical Characterisation Protocol UK (CCP-UK) study in 306 hospitals across England, Scotland and Wales. Patients were recruited between 27 August 2020 and 17 February 2021, with at least 4 weeks follow-up before final data extraction. The main outcome measures were discrimination and calibration of models for in-hospital deterioration (defined as any requirement of ventilatory support or critical care, or death) and mortality, incorporating predefined subgroups.

RESULTS: 76 588 participants were included, of whom 27 352 (37.4%) deteriorated and 12 581 (17.4%) died. Both the 4C Mortality (0.78 (0.77 to 0.78)) and 4C Deterioration scores (pooled C-statistic 0.76 (95% CI 0.75 to 0.77)) demonstrated consistent discrimination across all nine National Health Service regions, with similar performance metrics to the original validation cohorts. Calibration remained stable (4C Mortality: pooled slope 1.09, pooled calibration-in-the-large 0.12; 4C Deterioration: 1.00, -0.04), with no need for temporal recalibration during the second UK pandemic wave of hospital admissions.

CONCLUSION: Both 4C risk stratification models demonstrate consistent performance to predict clinical deterioration and mortality in a large prospective second wave validation cohort of UK patients. Despite recent advances in the treatment and management of adults hospitalised with COVID-19, both scores can continue to inform clinical decision making.

TRIAL REGISTRATION NUMBER: ISRCTN66726260.}, } @article {pmid34807904, year = {2021}, author = {Walker, M and Chandrasegaran, K and Vinauger, C and Robert, MA and Childs, LM}, title = {Modeling the effects of Aedes aegypti's larval environment on adult body mass at emergence.}, journal = {PLoS computational biology}, volume = {17}, number = {11}, pages = {e1009102}, pmid = {34807904}, issn = {1553-7358}, mesh = {Aedes/anatomy & histology/*growth & development/virology ; Animals ; Body Size ; Computational Biology ; Environment ; Female ; Food ; Larva/growth & development ; Mathematical Concepts ; *Models, Biological ; Mosquito Vectors/anatomy & histology/growth & development/virology ; Time Factors ; }, abstract = {Mosquitoes vector harmful pathogens that infect millions of people every year, and developing approaches to effectively control mosquitoes is a topic of great interest. However, the success of many control measures is highly dependent upon ecological, physiological, and life history traits of mosquito species. The behavior of mosquitoes and their potential to vector pathogens can also be impacted by these traits. One trait of interest is mosquito body mass, which depends upon many factors associated with the environment in which juvenile mosquitoes develop. Our experiments examined the impact of larval density on the body mass of Aedes aegypti mosquitoes, which are important vectors of dengue, Zika, yellow fever, and other pathogens. To investigate the interactions between the larval environment and mosquito body mass, we built a discrete time mathematical model that incorporates body mass, larval density, and food availability and fit the model to our experimental data. We considered three categories of model complexity informed by data, and selected the best model within each category using Akaike's Information Criterion. We found that the larval environment is an important determinant of the body mass of mosquitoes upon emergence. Furthermore, we found that larval density has greater impact on body mass of adults at emergence than on development time, and that inclusion of density dependence in the survival of female aquatic stages in models is important. We discuss the implications of our results for the control of Aedes mosquitoes and on their potential to spread disease.}, } @article {pmid34805552, year = {2021}, author = {Boyes, D and Holland, PWH and , and , and , and , and , and , }, title = {The genome sequence of the white ermine, Spilosoma lubricipeda Linnaeus 1758.}, journal = {Wellcome open research}, volume = {6}, number = {}, pages = {271}, pmid = {34805552}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual male Spilosoma lubricipeda (the white ermine; Arthropoda; Insecta; Lepidoptera; Erebidae). The genome sequence is 587 megabases in span. The majority of the assembly is scaffolded into 30 chromosomal pseudomolecules, with the Z sex chromosome assembled.}, } @article {pmid34793127, year = {2022}, author = {Schwarz, C and Mathieu, J and Laverde Gomez, JA and Yu, P and Alvarez, PJJ}, title = {Renaissance for Phage-Based Bacterial Control.}, journal = {Environmental science & technology}, volume = {56}, number = {8}, pages = {4691-4701}, doi = {10.1021/acs.est.1c06232}, pmid = {34793127}, issn = {1520-5851}, mesh = {Bacteria/genetics ; *Bacteriophages/genetics ; Computational Biology ; *Microbiota ; Sequence Analysis, DNA ; }, abstract = {Bacteriophages (phages) are an underutilized biological resource with vast potential for pathogen control and microbiome editing. Phage research and commercialization have increased rapidly in biomedical and agricultural industries, but adoption has been limited elsewhere. Nevertheless, converging advances in DNA sequencing, bioinformatics, microbial ecology, and synthetic biology are now poised to broaden phage applications beyond pathogen control toward the manipulation of microbial communities for defined functional improvements. Enhancements in sequencing combined with network analysis make it now feasible to identify and disrupt microbial associations to elicit desirable shifts in community structure or function, indirectly modulate species abundance, and target hub or keystone species to achieve broad functional shifts. Sequencing and bioinformatic advancements are also facilitating the use of temperate phages for safe gene delivery applications. Finally, integration of synthetic biology stands to create novel phage chassis and modular genetic components. While some fundamental, regulatory, and commercialization barriers to widespread phage use remain, many major challenges that have impeded the field now have workable solutions. Thus, a new dawn for phage-based (chemical-free) precise biocontrol and microbiome editing is on the horizon to enhance, suppress, or modulate microbial activities important for public health, food security, and more sustainable energy production and water reuse.}, } @article {pmid34791539, year = {2021}, author = {Demir, S and Demirel, Ö and Okatan, A}, title = {An ecological restoration assessment integrating multi-criteria decision analysis with landscape sensitivity analysis for a hydroelectric power plant project: the Tokat-Niksar case.}, journal = {Environmental monitoring and assessment}, volume = {193}, number = {12}, pages = {818}, pmid = {34791539}, issn = {1573-2959}, mesh = {*Conservation of Natural Resources ; Decision Support Techniques ; *Ecosystem ; Environmental Monitoring ; Power Plants ; }, abstract = {Due to Turkey's reliance on imported electricity, it has been using hydroelectric power plants (HPPs) to cover some of its electrical energy needs since 2011. However, HPP projects, which do not take landscape sensitivity into account, cause the ecological integrity of the basins and the ecosystem structure to deteriorate. This study presents the Tokat-Niksar HPP project field example in Turkey's Central Black Sea region with its steep slopes, rich forest and creek vegetation, protected endemic plants and wildlife, cultural heritage dating back to 3000 BC agricultural activities, and long-established local culture. The study, in fact, aims to develop a landscape restoration plan that considers the sensitivity of landscapes in the HPP project area. For this purpose, a landscape sensitivity analysis consisting of water, habitat, visibility, erosion functions, and multi-criteria decision analysis (MCDA) determining priority of functions conducted with experts were performed. According to the results, the water function was found to have the highest, and the visibility the lowest priority in the ranking. Consequently, 1st, 2nd, 3rd, and 4th-degree sensitive areas with very high, high, and moderate landscape sensitivity were determined by weighted sum function by considering the priority of each landscape function, and accordingly, a five-stage landscape restoration model was developed including soil protection, areas to be protected, erosion control, vegetation screening, and creek reclamation. This study presents a framework for sustainable landscape restoration solutions in the town by combining landscape sensitivity analysis via MCDA.}, } @article {pmid34787724, year = {2021}, author = {Lu, Q and Bian, Z and Tsuchiya, N}, title = {Assessment of heavy metal pollution and ecological risk in river water and sediments in a historically metal mined watershed, Northeast Japan.}, journal = {Environmental monitoring and assessment}, volume = {193}, number = {12}, pages = {814}, pmid = {34787724}, issn = {1573-2959}, support = {2018K085C//Postdoctoral Science Foundation of Jiangsu Province/ ; }, mesh = {China ; Environmental Monitoring ; Geologic Sediments ; Japan ; *Metals, Heavy/analysis ; Risk Assessment ; Rivers ; Water ; *Water Pollutants, Chemical/analysis ; }, abstract = {Mining legacies continue to impact the geochemical cycles in historically mined watersheds after mine closure. The Hokuroku District in Northeast Japan is a famous metal mining area with a long mining history; however, studies on the distribution mechanisms and pollution characteristics of heavy metals in these historically mined watersheds after the boom period of mining activities are lacking. This study aims to provide fundamental insights into the effects of the mining activities and hydrological conditions on heavy metal pollution in the Kosaka watershed, Hokuroku District. Sampling was performed in terms of watershed segmentation, and the outlet of the tributary within each sub-watershed was also sampled to capture the diffusional pollution status. The distributions of Zn, Cu, Cd, Pb and As in river water and sediments, as well as their pollution characteristics and ecological risks, were analysed under different hydrological conditions. Our findings provide evidence of the ecological risk in surface water induced by Zn, Cu and Pb pollution in the Kosaka River system. In a high proportion of the sub-watershed, there was moderate to strong enrichment in Cd, Cu and Zn in the river sediments. The sub-watersheds with high pollution levels and ecological risk were highly consistent with the sub-watersheds encompassing abandoned mine sites. Suspended particles carried large amounts of Pb and Cu, especially on rainy days. The heavy metal contents in river water were very sensitive to occasional rainfall events; rainy days posed the most risk to organisms in the Kosaka River, followed by the low-water-level season and the high-water-level season.}, } @article {pmid34785977, year = {2021}, author = {Chamanara, J and Gaikwad, J and Gerlach, R and Algergawy, A and Ostrowski, A and König-Ries, B}, title = {BEXIS2: A FAIR-aligned data management system for biodiversity, ecology and environmental data.}, journal = {Biodiversity data journal}, volume = {9}, number = {}, pages = {e72901}, pmid = {34785977}, issn = {1314-2828}, abstract = {BACKGROUND: Obtaining fit-to-use data associated with diverse aspects of biodiversity, ecology and environment is challenging since often it is fragmented, sub-optimally managed and available in heterogeneous formats. Recently, with the universal acceptance of the FAIR data principles, the requirements and standards of data publications have changed substantially. Researchers are encouraged to manage the data as per the FAIR data principles and ensure that the raw data, metadata, processed data, software, codes and associated material are securely stored and the data be made available with the completion of the research.

NEW INFORMATION: We have developed BEXIS2 as an open-source community-driven web-based research data management system to support research data management needs of mid to large-scale research projects with multiple sub-projects and up to several hundred researchers. BEXIS2 is a modular and extensible system providing a range of functions to realise the complete data lifecycle from data structure design to data collection, data discovery, dissemination, integration, quality assurance and research planning. It is an extensible and customisable system that allows for the development of new functions and customisation of its various components from database schemas to the user interface layout, elements and look and feel.During the development of BEXIS2, we aimed to incorporate key aspects of what is encoded in FAIR data principles. To investigate the extent to which BEXIS2 conforms to these principles, we conducted the self-assessment using the FAIR indicators, definitions and criteria provided in the FAIR Data Maturity Model. Even though the FAIR data maturity model is developed initially to judge the conformance of datasets, the self-assessment results indicated that BEXIS2 remarkably conforms and supports FAIR indicators. BEXIS2 strongly conforms to the indicators Findability and Accessibility. The indicator Interoperability is moderately supported as of now; however, for many of the lesssupported facets, we have concrete plans for improvement. Reusability (as defined by the FAIR data principles) is partially achieved.This paper also illustrates community deployment examples of the BEXIS2 instances as success stories to exemplify its capacity to meet the biodiversity and ecological data management needs of differently sized projects and serve as an organisational research data management system.}, } @article {pmid34782652, year = {2021}, author = {Xie, C and An, W and Liu, S and Huang, Y and Yang, Z and Lin, J and Zheng, X}, title = {Comparative genomic study on the complete plastomes of four officinal Ardisia species in China.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {22239}, pmid = {34782652}, issn = {2045-2322}, support = {81903741//National Natural Science Foundation of China/ ; }, mesh = {Ardisia/*classification/*genetics ; China ; Computational Biology/methods ; *Genome, Chloroplast ; *Genomics/methods ; Phylogeny ; Polymorphism, Genetic ; Sequence Analysis, DNA ; Exome Sequencing ; }, abstract = {Ardisia Sw. (Primulaceae) is naturally distributed in tropical and subtropical areas. Most of them possess edible and medicinal values and are popular in clinical and daily use in China. However, ambiguous species delineation and genetic information limit the development and utilization of this genus. In this study, the chloroplast genomes of four Ardisia species, namely A. gigantifolia Stapf, A. crenata Sims, A. villosa Roxb. and A. mamillata Hance, were sequenced, annotated, and analyzed comparatively. All the four chloroplast genomes possess a typical quadripartite structure, and each of the genomes is about 156 Kb in size. The structure and gene content of the Ardisia plastomes were conservative and showed low sequence divergence. Furthermore, we identified five mutation hotspots as candidate DNA barcodes for Ardisia, namely, trnT-psbD, ndhF-rpl32, rpl32-ccsA, ccsA-ndhD and ycf1. Phylogenetic analysis based on the whole-chloroplast genomes data showed that Ardisia was sister to Tapeinosperma Hook. f. In addition, the results revealed a great topological profile of Ardisia's with strong support values, which matches their geographical distribution patterns. Summarily, our results provide useful information for investigations on taxonomic differences, molecular identification, and phylogenetic relationships of Ardisia plants.}, } @article {pmid34780468, year = {2021}, author = {Sarmashghi, S and Balaban, M and Rachtman, E and Touri, B and Mirarab, S and Bafna, V}, title = {Estimating repeat spectra and genome length from low-coverage genome skims with RESPECT.}, journal = {PLoS computational biology}, volume = {17}, number = {11}, pages = {e1009449}, pmid = {34780468}, issn = {1553-7358}, support = {R01 GM114362/GM/NIGMS NIH HHS/United States ; }, mesh = {*Algorithms ; Animals ; Computational Biology ; Computer Simulation ; Databases, Genetic/statistics & numerical data ; *Genome ; Genomics/*statistics & numerical data ; Humans ; Invertebrates/classification/genetics ; Least-Squares Analysis ; Linear Models ; Mammals/classification/genetics ; Models, Genetic ; Phylogeny ; Plants/classification/genetics ; *Repetitive Sequences, Nucleic Acid ; *Software ; Vertebrates/classification/genetics ; }, abstract = {The cost of sequencing the genome is dropping at a much faster rate compared to assembling and finishing the genome. The use of lightly sampled genomes (genome-skims) could be transformative for genomic ecology, and results using k-mers have shown the advantage of this approach in identification and phylogenetic placement of eukaryotic species. Here, we revisit the basic question of estimating genomic parameters such as genome length, coverage, and repeat structure, focusing specifically on estimating the k-mer repeat spectrum. We show using a mix of theoretical and empirical analysis that there are fundamental limitations to estimating the k-mer spectra due to ill-conditioned systems, and that has implications for other genomic parameters. We get around this problem using a novel constrained optimization approach (Spline Linear Programming), where the constraints are learned empirically. On reads simulated at 1X coverage from 66 genomes, our method, REPeat SPECTra Estimation (RESPECT), had 2.2% error in length estimation compared to 27% error previously achieved. In shotgun sequenced read samples with contaminants, RESPECT length estimates had median error 4%, in contrast to other methods that had median error 80%. Together, the results suggest that low-pass genomic sequencing can yield reliable estimates of the length and repeat content of the genome. The RESPECT software will be publicly available at https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_shahab-2Dsarmashghi_RESPECT.git&d=DwIGAw&c=-35OiAkTchMrZOngvJPOeA&r=ZozViWvD1E8PorCkfwYKYQMVKFoEcqLFm4Tg49XnPcA&m=f-xS8GMHKckknkc7Xpp8FJYw_ltUwz5frOw1a5pJ81EpdTOK8xhbYmrN4ZxniM96&s=717o8hLR1JmHFpRPSWG6xdUQTikyUjicjkipjFsKG4w&e=.}, } @article {pmid34780461, year = {2021}, author = {Li, R and Ranipeta, A and Wilshire, J and Malczyk, J and Duong, M and Guralnick, R and Wilson, A and Jetz, W}, title = {A cloud-based toolbox for the versatile environmental annotation of biodiversity data.}, journal = {PLoS biology}, volume = {19}, number = {11}, pages = {e3001460}, pmid = {34780461}, issn = {1545-7885}, support = {80NSSC17K0282/ImNASA/Intramural NASA/United States ; 80NSSC18K0435/ImNASA/Intramural NASA/United States ; }, mesh = {Animals ; *Biodiversity ; Birds/physiology ; *Cloud Computing ; Databases as Topic ; Satellite Communications ; Seasons ; Spatio-Temporal Analysis ; Species Specificity ; Temperature ; Time Factors ; }, abstract = {A vast range of research applications in biodiversity sciences requires integrating primary species, genetic, or ecosystem data with other environmental data. This integration requires a consideration of the spatial and temporal scale appropriate for the data and processes in question. But a versatile and scale flexible environmental annotation of biodiversity data remains constrained by technical hurdles. Existing tools have streamlined the intersection of occurrence records with gridded environmental data but have remained limited in their ability to address a range of spatial and temporal grains, especially for large datasets. We present the Spatiotemporal Observation Annotation Tool (STOAT), a cloud-based toolbox for flexible biodiversity-environment annotations. STOAT is optimized for large biodiversity datasets and allows user-specified spatial and temporal resolution and buffering in support of environmental characterizations that account for the uncertainty and scale of data and of relevant processes. The tool offers these services for a growing set of near global, remotely sensed, or modeled environmental data, including Landsat, MODIS, EarthEnv, and CHELSA. STOAT includes a user-friendly, web-based dashboard that provides tools for annotation task management and result visualization, linked to Map of Life, and a dedicated R package (rstoat) for programmatic access. We demonstrate STOAT functionality with several examples that illustrate phenological variation and spatial and temporal scale dependence of environmental characteristics of birds at a continental scale. We expect STOAT to facilitate broader exploration and assessment of the scale dependence of observations and processes in ecology.}, } @article {pmid34776776, year = {2021}, author = {Ambarlı, D and Simons, NK and Wehner, K and Kämper, W and Gossner, MM and Nauss, T and Neff, F and Seibold, S and Weisser, W and Blüthgen, N}, title = {Animal-Mediated Ecosystem Process Rates in Forests and Grasslands are Affected by Climatic Conditions and Land-Use Intensity.}, journal = {Ecosystems (New York, N.Y.)}, volume = {24}, number = {2}, pages = {467-483}, pmid = {34776776}, issn = {1432-9840}, abstract = {Decomposition, vegetation regeneration, and biological control are essential ecosystem functions, and animals are involved in the underlying processes, such as dung removal, seed removal, herbivory, and predation. Despite evidence for declines of animal diversity and abundance due to climate change and land-use intensification, we poorly understand how animal-mediated processes respond to these global change drivers. We experimentally measured rates of four ecosystem processes in 134 grassland and 149 forest plots in Germany and tested their response to climatic conditions and land-use intensity, that is, grazing, mowing, and fertilization in grasslands and the proportion of harvested wood, non-natural trees, and deadwood origin in forests. For both climate and land use, we distinguished between short-term effects during the survey period and medium-term effects during the preceding years. Forests had significantly higher process rates than grasslands. In grasslands, the climatic effects on the process rates were similar or stronger than land-use effects, except for predation; land-use intensity negatively affected several process rates. In forests, the land-use effects were more pronounced than the climatic effects on all processes except for predation. The proportion of non-natural trees had the greatest impact on the process rates in forests. The proportion of harvested wood had negative effects, whereas the proportion of anthropogenic deadwood had positive effects on some processes. The effects of climatic conditions and land-use intensity on process rates mirror climatic and habitat effects on animal abundance, activity, and resource quality. Our study demonstrates that land-use changes and interventions affecting climatic conditions will have substantial impacts on animal-mediated ecosystem processes.}, } @article {pmid34773908, year = {2022}, author = {Liu, Y and Song, L and Wang, W and Jian, X and Chen, WQ}, title = {Developing a GIS-based model to quantify spatiotemporal pattern of home appliances and e-waste generation-A case study in Xiamen, China.}, journal = {Waste management (New York, N.Y.)}, volume = {137}, number = {}, pages = {150-157}, doi = {10.1016/j.wasman.2021.10.039}, pmid = {34773908}, issn = {1879-2456}, mesh = {China ; Cities ; *Electronic Waste/analysis ; Geographic Information Systems ; Humans ; *Waste Management ; }, abstract = {The growing amount of electronic waste (e-waste) poses considerable risks to the environment and human health, especially when treated inadequately. However, it is difficult to assess the significance of these issues without quantitative understanding of spatiotemporal patterns of e-waste generation. This paper proposes a new model to estimate in-use stock of electric household appliances (HAs) and e-waste generation at the level of 1 km × 1 km grids by coupling geographic information system (GIS) and material flow analysis (MFA). We took Xiamen, a rapidly urbanized city in China, as a case and the results showed that demands for HAs increased from 1980, peaked in 2016, and then declined. In-use HAs exhibited a logistic growth and significantly increased in both spatial extent and intensity. E-waste generation kept rising until 2019, and its spatial center expanded outward from downtown to suburban areas. Our study highlights that a dynamic and spatial model is useful for designing effective policies for e-waste management by providing spatiotemporal details of e-waste types and generation magnitudes and explicitly recognizing generation hotspots in cities.}, } @article {pmid34773248, year = {2022}, author = {Gann, ER and Truchon, AR and Papoulis, SE and Dyhrman, ST and Gobler, CJ and Wilhelm, SW}, title = {Aureococcus anophagefferens (Pelagophyceae) genomes improve evaluation of nutrient acquisition strategies involved in brown tide dynamics.}, journal = {Journal of phycology}, volume = {58}, number = {1}, pages = {146-160}, doi = {10.1111/jpy.13221}, pmid = {34773248}, issn = {1529-8817}, mesh = {Harmful Algal Bloom ; Nitrogen/metabolism ; Nutrients ; *Stramenopiles/genetics/metabolism ; }, abstract = {The pelagophyte Aureococcus anophagefferens causes harmful brown tide blooms in marine embayments on three continents. Aureococcus anophagefferens was the first harmful algal bloom species to have its genome sequenced, an advance that evidenced genes important for adaptation to environmental conditions that prevail during brown tides. To expand the genomic tools available for this species, genomes for four strains were assembled, including three newly sequenced strains and one assembled from publicly available data. These genomes ranged from 57.11 to 73.62 Mb, encoding 13,191-17,404 potential proteins. All strains shared ~90% of their encoded proteins as determined by homology searches and shared most functional orthologs as determined by KEGG, although each strain also possessed coding sequences with unique functions. Like the original reference genome, the genomes assembled in this study possessed genes hypothesized to be important in bloom proliferation, including genes involved in organic compound metabolism and growth at low light. Cross-strain informatics and culture experiments suggest that the utilization of purines is a potentially important source of organic nitrogen for brown tides. Analyses of metatranscriptomes from a brown tide event demonstrated that use of a single genome yielded a lower read mapping percentage (~30% of library reads) as compared to a database generated from all available genomes (~43%), suggesting novel information about bloom ecology can be gained from expanding genomic space. This work demonstrates the continued need to sequence ecologically relevant algae to understand the genomic potential and their ecology in the environment.}, } @article {pmid34773098, year = {2022}, author = {Arnold, BJ and Huang, IT and Hanage, WP}, title = {Horizontal gene transfer and adaptive evolution in bacteria.}, journal = {Nature reviews. Microbiology}, volume = {20}, number = {4}, pages = {206-218}, pmid = {34773098}, issn = {1740-1534}, mesh = {*Bacteria/genetics ; Computational Biology ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Genome, Bacterial/genetics ; Genomics ; Phylogeny ; }, abstract = {Horizontal gene transfer (HGT) is arguably the most conspicuous feature of bacterial evolution. Evidence for HGT is found in most bacterial genomes. Although HGT can considerably alter bacterial genomes, not all transfer events may be biologically significant and may instead represent the outcome of an incessant evolutionary process that only occasionally has a beneficial purpose. When adaptive transfers occur, HGT and positive selection may result in specific, detectable signatures in genomes, such as gene-specific sweeps or increased transfer rates for genes that are ecologically relevant. In this Review, we first discuss the various mechanisms whereby HGT occurs, how the genetic signatures shape patterns of genomic variation and the distinct bioinformatic algorithms developed to detect these patterns. We then discuss the evolutionary theory behind HGT and positive selection in bacteria, and discuss the approaches developed over the past decade to detect transferred DNA that may be involved in adaptation to new environments.}, } @article {pmid34771416, year = {2021}, author = {Islam, MM and Poly, TN and Walther, BA and Lin, MC and Li, YJ}, title = {Artificial Intelligence in Gastric Cancer: Identifying Gastric Cancer Using Endoscopic Images with Convolutional Neural Network.}, journal = {Cancers}, volume = {13}, number = {21}, pages = {}, pmid = {34771416}, issn = {2072-6694}, abstract = {Gastric cancer (GC) is one of the most newly diagnosed cancers and the fifth leading cause of death globally. Identification of early gastric cancer (EGC) can ensure quick treatment and reduce significant mortality. Therefore, we aimed to conduct a systematic review with a meta-analysis of current literature to evaluate the performance of the CNN model in detecting EGC. We conducted a systematic search in the online databases (e.g., PubMed, Embase, and Web of Science) for all relevant original studies on the subject of CNN in EGC published between 1 January 2010, and 26 March 2021. The Quality Assessment of Diagnostic Accuracy Studies-2 was used to assess the risk of bias. Pooled sensitivity, specificity, positive likelihood ratio, negative likelihood ratio, and diagnostic odds ratio were calculated. Moreover, a summary receiver operating characteristic curve (SROC) was plotted. Of the 171 studies retrieved, 15 studies met inclusion criteria. The application of the CNN model in the diagnosis of EGC achieved a SROC of 0.95, with corresponding sensitivity of 0.89 (0.88-0.89), and specificity of 0.89 (0.89-0.90). Pooled sensitivity and specificity for experts endoscopists were 0.77 (0.76-0.78), and 0.92 (0.91-0.93), respectively. However, the overall SROC for the CNN model and expert endoscopists was 0.95 and 0.90. The findings of this comprehensive study show that CNN model exhibited comparable performance to endoscopists in the diagnosis of EGC using digital endoscopy images. Given its scalability, the CNN model could enhance the performance of endoscopists to correctly stratify EGC patients and reduce work load.}, } @article {pmid34770185, year = {2021}, author = {Bezerra, IMP and Ramos, JLS and Pianissola, MC and Adami, F and Rocha, JBFD and Ribeiro, MAL and de Castro, MR and Bezerra, JDF and Smiderle, FRN and Sousa, LVA and Siqueira, CE and de Abreu, LC}, title = {Perinatal Mortality Analysis in Espírito Santo, Brazil, 2008 to 2017.}, journal = {International journal of environmental research and public health}, volume = {18}, number = {21}, pages = {}, pmid = {34770185}, issn = {1660-4601}, mesh = {Adolescent ; Adult ; Brazil/epidemiology ; Child ; Female ; Humans ; Infant ; Infant Mortality ; Infant, Newborn ; *Perinatal Death ; *Perinatal Mortality ; Pregnancy ; Prenatal Care ; Young Adult ; }, abstract = {This is an ecological and time-series study using secondary data on perinatal mortality and its components from 2008 to 2017 in Espírito Santo, Brazil. The data were collected from the Mortality Information System (SIM) and Live Births Information System (SINASC) of the Unified Health System Informatics Department (DATASUS) in June 2019. The perinatal mortality rate (×1000 total births) was calculated. Time series were constructed from the perinatal mortality rate for the regions and Espírito Santo. To analyze the trend, the Prais-Winsten model was used. From 2008 to 2017 there were 8132 perinatal deaths (4939 fetal and 3193 early neonatal) out of a total of 542,802 births, a perinatal mortality rate of 15.0/1000 total births. The fetal/early neonatal ratio was 1.5:1, with a strong positive correlation early neonatal mortality rate, perinatal mortality rate, r (9) = 0.8893, with a significance level of p = 0.000574. The presence of differences in trends by health region was observed. Risk factors that stood out were as follows: mother's age ranging between 10 and 19 or 40 and 49 years old, with no education, a gestational age between 22 and 36 weeks, triple and double pregnancy, and a birth weight below 2499 g. Among the causes of death, 49.70% of deaths were concentrated in category of the tenth edition of the International Classification of Diseases, fetuses and newborns affected by maternal factors and complications of pregnancy, labor, and delivery (P00-P04), and 11.03% were in the category of intrauterine hypoxia and birth asphyxia (P20-P21), both related to proper care during pregnancy and childbirth. We observed a slow reduction in the perinatal mortality rate in the state of Espírito Santo from 2008 to 2017.}, } @article {pmid34770038, year = {2021}, author = {Huang, Y and Liu, H and Zhang, L and Li, S and Wang, W and Ren, Z and Zhou, Z and Ma, X}, title = {The Psychological and Behavioral Patterns of Online Psychological Help-Seekers before and during COVID-19 Pandemic: A Text Mining-Based Longitudinal Ecological Study.}, journal = {International journal of environmental research and public health}, volume = {18}, number = {21}, pages = {}, pmid = {34770038}, issn = {1660-4601}, mesh = {Anxiety ; *COVID-19 ; Data Mining ; Depression ; Humans ; *Pandemics ; SARS-CoV-2 ; }, abstract = {Online mental health service (OMHS) platforms have contributed significantly to the public's mental health during the COVID-19 pandemic in China. However, it remains unclear why the public used OMHS platforms for psychological help-seeking (PHS) behavior and how PHS behavior varied across different stages of the COVID-19 pandemic. Based on the ecological PHS behavior data from two OMHS platforms, we extracted population, psychological problems, and influential factors of PHS behavior by text mining and time series analysis methods. Seven top-ranked psychological problems (i.e., depression and anxiety, lack of interest, suicidal tendencies, social phobia, feelings of being worried and afraid, suffering, anger) and seven influential factors (i.e., interpersonal relationships, love, family, work, psychotherapy, personal characteristics, marriage) were found. The online PHS behaviors related to different psychological problems and influential factors remained a growing trend before 2020 and have been increasing significantly due to the COVID-19 outbreak. Four main stages were found during the pandemic according to the changes in the online PHS population: sharp growth, significant decline, slight rebound, and slow decline. This study identified large-scale, spontaneous PHS behaviors among the online public during the COVID-19 pandemic and the various psychological problems and influential factors that varied across different stages of the pandemic, suggesting that the government and health practitioners should adopt effective policies and strategies to prevent and intervene in mental health problems for the online public.}, } @article {pmid34766911, year = {2021}, author = {Martinez, GJ and Mattingly, SM and Robles-Granda, P and Saha, K and Sirigiri, A and Young, J and Chawla, N and De Choudhury, M and D'Mello, S and Mark, G and Striegel, A}, title = {Predicting Participant Compliance With Fitness Tracker Wearing and Ecological Momentary Assessment Protocols in Information Workers: Observational Study.}, journal = {JMIR mHealth and uHealth}, volume = {9}, number = {11}, pages = {e22218}, pmid = {34766911}, issn = {2291-5222}, mesh = {*Ecological Momentary Assessment ; Exercise ; *Fitness Trackers ; Humans ; Research Design ; Surveys and Questionnaires ; }, abstract = {BACKGROUND: Studies that use ecological momentary assessments (EMAs) or wearable sensors to track numerous attributes, such as physical activity, sleep, and heart rate, can benefit from reductions in missing data. Maximizing compliance is one method of reducing missing data to increase the return on the heavy investment of time and money into large-scale studies.

OBJECTIVE: This paper aims to identify the extent to which compliance can be prospectively predicted from individual attributes and initial compliance.

METHODS: We instrumented 757 information workers with fitness trackers for 1 year and conducted EMAs in the first 56 days of study participation as part of an observational study. Their compliance with the EMA and fitness tracker wearing protocols was analyzed. Overall, 31 individual characteristics (eg, demographics and personalities) and behavioral variables (eg, early compliance and study portal use) were considered, and 14 variables were selected to create beta regression models for predicting compliance with EMAs 56 days out and wearable compliance 1 year out. We surveyed study participation and correlated the results with compliance.

RESULTS: Our modeling indicates that 16% and 25% of the variance in EMA compliance and wearable compliance, respectively, could be explained through a survey of demographics and personality in a held-out sample. The likelihood of higher EMA and wearable compliance was associated with being older (EMA: odds ratio [OR] 1.02, 95% CI 1.00-1.03; wearable: OR 1.02, 95% CI 1.01-1.04), speaking English as a first language (EMA: OR 1.38, 95% CI 1.05-1.80; wearable: OR 1.39, 95% CI 1.05-1.85), having had a wearable before joining the study (EMA: OR 1.25, 95% CI 1.04-1.51; wearable: OR 1.50, 95% CI 1.23-1.83), and exhibiting conscientiousness (EMA: OR 1.25, 95% CI 1.04-1.51; wearable: OR 1.34, 95% CI 1.14-1.58). Compliance was negatively associated with exhibiting extraversion (EMA: OR 0.74, 95% CI 0.64-0.85; wearable: OR 0.67, 95% CI 0.57-0.78) and having a supervisory role (EMA: OR 0.65, 95% CI 0.54-0.79; wearable: OR 0.66, 95% CI 0.54-0.81). Furthermore, higher wearable compliance was negatively associated with agreeableness (OR 0.68, 95% CI 0.56-0.83) and neuroticism (OR 0.85, 95% CI 0.73-0.98). Compliance in the second week of the study could help explain more variance; 62% and 66% of the variance in EMA compliance and wearable compliance, respectively, was explained. Finally, compliance correlated with participants' self-reflection on the ease of participation, usefulness of our compliance portal, timely resolution of issues, and compensation adequacy, suggesting that these are avenues for improving compliance.

CONCLUSIONS: We recommend conducting an initial 2-week pilot to measure trait-like compliance and identify participants at risk of long-term noncompliance, performing oversampling based on participants' individual characteristics to avoid introducing bias in the sample when excluding data based on noncompliance, using an issue tracking portal, and providing special care in troubleshooting to help participants maintain compliance.}, } @article {pmid34764244, year = {2021}, author = {Santora, JA and Rogers, TL and Cimino, MA and Sakuma, KM and Hanson, KD and Dick, EJ and Jahncke, J and Warzybok, P and Field, JC}, title = {Diverse integrated ecosystem approach overcomes pandemic-related fisheries monitoring challenges.}, journal = {Nature communications}, volume = {12}, number = {1}, pages = {6492}, pmid = {34764244}, issn = {2041-1723}, support = {80NSSC17K0574/NASA/NASA/United States ; 80NSSC20M0001/NASA/NASA/United States ; NA15NMF4270308//NOAA/ ; }, mesh = {Animals ; Biodiversity ; COVID-19/*epidemiology/transmission/virology ; Conservation of Natural Resources/*methods ; Databases, Factual ; Ecosystem ; Environmental Monitoring/methods ; Fisheries/*statistics & numerical data ; Fishes ; Food Chain ; Models, Statistical ; SARS-CoV-2/isolation & purification/*pathogenicity ; }, abstract = {The COVID-19 pandemic caused unprecedented cancellations of fisheries and ecosystem-assessment surveys, resulting in a recession of observations needed for management and conservation globally. This unavoidable reduction of survey data poses challenges for informing biodiversity and ecosystem functioning, developing future stock assessments of harvested species, and providing strategic advice for ecosystem-based management. We present a diversified framework involving integration of monitoring data with empirical models and simulations to inform ecosystem status within the California Current Large Marine Ecosystem. We augment trawl observations collected from a limited fisheries survey with survey effort reduction simulations, use of seabird diets as indicators of fish abundance, and krill species distribution modeling trained on past observations. This diversified approach allows for evaluation of ecosystem status during data-poor situations, especially during the COVID-19 era. The challenges to ecosystem monitoring imposed by the pandemic may be overcome by preparing for unexpected effort reduction, linking disparate ecosystem indicators, and applying new species modeling techniques.}, } @article {pmid34752878, year = {2022}, author = {Chen, L and Wang, J and Beiyuan, J and Guo, X and Wu, H and Fang, L}, title = {Environmental and health risk assessment of potentially toxic trace elements in soils near uranium (U) mines: A global meta-analysis.}, journal = {The Science of the total environment}, volume = {816}, number = {}, pages = {151556}, doi = {10.1016/j.scitotenv.2021.151556}, pmid = {34752878}, issn = {1879-1026}, mesh = {Adult ; Child ; China ; Environmental Monitoring ; Humans ; *Metals, Heavy/analysis ; Risk Assessment ; Soil ; *Soil Pollutants/analysis ; *Trace Elements ; *Uranium ; }, abstract = {Soil pollution by potentially toxic trace elements (PTEs) near uranium (U) mines arouses a growing interest worldwide. However, nearly all studies have focused on a single site or only a few sites, which may not fully represent the soil pollution status at the global scale. In this study, data of U, Cd, Cr, Pb, Cu, Zn, As, Mn, and Ni contents in U mine-associated soils were collected and screened from published articles (2006-2021). Assessments of pollution levels, distributions, ecological, and human health risks of the nine PTEs were analysed. The results revealed that the average contents of the U, Cd, Cr, Pb, Cu, Zn, As, Mn, and Ni were 39.88-, 55.33-, 0.88-, 3.81-, 3.12-, 3.07-, 9.26-, 1.83-, and 1.17-fold greater than those in the upper continental crust, respectively. The pollution assessment showed that most of the studied soils were heavily polluted by U and Cd. Among them, the U mine-associated soils in France, Portugal, and Bulgaria exhibited significantly higher pollution levels of U and Cd when compared to other regions. The average potential ecological risk value for all PTEs was 3358.83, which indicated the presence of remarkably high risks. Among the PTEs, Cd and U contributed more to the potential ecological risk than the other elements. The health risk assessment showed that oral ingestion was the main exposure route for soil PTEs; and the hazard index (HI) values for children were higher than those for adult males and females. For adult males and females, all hazard index values for the noncarcinogenic risks were below the safe level of 1.00. For children, none of the HI values exceeded the safe level, with the exception of U (HI = 3.56) and As (HI = 1.83), but Cu presented unacceptable carcinogenic risks. This study provides a comprehensive analysis that demonstrates the urgent necessity for treating PTE pollution in U mine-associated soils worldwide.}, } @article {pmid34751666, year = {2021}, author = {Slovak, P and Ford, BQ and Widen, S and Daudén Roquet, C and Theofanopoulou, N and Gross, JJ and Hankin, B and Klasnja, P}, title = {An In Situ, Child-Led Intervention to Promote Emotion Regulation Competence in Middle Childhood: Protocol for an Exploratory Randomized Controlled Trial.}, journal = {JMIR research protocols}, volume = {10}, number = {11}, pages = {e28914}, pmid = {34751666}, issn = {1929-0748}, support = {MR/T041897/1/MRC_/Medical Research Council/United Kingdom ; }, abstract = {BACKGROUND: Emotion regulation is a key transdiagnostic risk factor for a range of psychopathologies, making it a prime target for both prevention and treatment interventions in childhood. Existing interventions predominantly rely on workshops or in-person therapy-based approaches, limiting the ability to promote emotion regulation competence for children in everyday settings and at scale. Purrble is a newly developed, inexpensive, socially assistive robot-in the form of an interactive plush toy-that uses haptic feedback to support in-the-moment emotion regulation. It is accessible to children as needed in their daily lives, without the need for a priori training. Although qualitative data from previous studies show high engagement in situ and anecdotal evidence of the robot being incorporated into children's emotion regulation routines, there is no quantitative evidence of the intervention's impact on child outcomes.

OBJECTIVE: The aim of this study is to examine the efficacy of a new intervention model for child-led emotion regulation-Purrble-that can be deployed across prevention and treatment contexts.

METHODS: Overall, 134 children aged 8 to 10 years will be selected from an enriched nonclinical North American population; for inclusion, the cutoff for the parents' rating of child dysregulation will be ≥10 points in the total difficulties score on the Strengths and Difficulties Questionnaire. This cutoff was selected to obtain a measurable, but not necessarily clinical, level of the child's emotion regulatory difficulties. The selected families will be randomly assigned with .5 probability to receive either a Purrble or an active control (noninteractive plush toy). The primary outcome will be a daily ecological momentary assessment measure of child emotion regulation capability (as reported by parents) over a period of 4 weeks. Exploratory analyses will investigate the intervention impact on secondary outcomes of child emotion regulation, collected weekly over the same 4-week period, with follow-ups at 1 month and 6 months postdeployment. Quantitative data will be analyzed on an intent-to-treat basis. A proportion of families (approximately 30% of the sample) will be interviewed after deployment as part of the process analysis.

RESULTS: The study is funded by the UKRI Future Leaders Fellowship (MR/T041897/1) and an in-kind contribution from the Committee for Children. This study received ethical approval from the Pearl institutional review board (#18-CFC-101). Participant recruitment started in February 2021, with the 1-month deployment in April-May 2021. The results of this analysis will be published in 2022.

CONCLUSIONS: This study will be the first quantitative evaluation of the efficacy of an innovative, proof-of-concept intervention model for an in situ, child-led emotion regulation intervention. Insights into the trajectory of daily changes, complemented with weekly questionnaire batteries and postdeployment interviews, will result in an in-depth understanding of whether and how the hypothesized intervention logic model works, leading to further intervention optimization.

TRIAL REGISTRATION: ClinicalTrials.gov NCT04810455; http://clinicaltrials.gov/ct2/show/NCT04810455.

PRR1-10.2196/28914.}, } @article {pmid34749696, year = {2021}, author = {Naser, AY and Mansour, MM and Alanazi, AFR and Sabha, O and Alwafi, H and Jalal, Z and Paudyal, V and Dairi, MS and Salawati, EM and Alqahtan, JS and Alaamri, S and Mustafa Ali, MK}, title = {Hospital admission trends due to respiratory diseases in England and Wales between 1999 and 2019: an ecologic study.}, journal = {BMC pulmonary medicine}, volume = {21}, number = {1}, pages = {356}, pmid = {34749696}, issn = {1471-2466}, mesh = {Adolescent ; Adult ; Aged ; Aged, 80 and over ; Child ; Databases, Factual ; England/epidemiology ; Hospitalization/*statistics & numerical data/*trends ; Humans ; Male ; Middle Aged ; Respiratory Tract Diseases/*epidemiology ; Sex Distribution ; Wales/epidemiology ; Young Adult ; }, abstract = {BACKGROUND: Identifying trends of hospital admissions for respiratory diseases is crucial for public health and research to guide future clinical improvements for better outcomes. This study aims to define the trends of respiratory disease-related hospital admissions (RRHA) in England and Wales between 1999 and 2019.

METHODS: An ecological study was conducted using hospital admission data taken from the Hospital Episode Statistics database in England and the Patient Episode Database for Wales. Hospital admissions data for respiratory diseases were extracted for the period between April 1999 and March 2019. The trend in hospital admissions was assessed using a Poisson model.

RESULTS: Hospital admission rate increased by 104.7% [from 1535.05 (95% CI 1531.71-1538.38) in 1999 to 3142.83 (95% CI 3138.39-3147.26) in 2019 per 100,000 persons, trend test, p < 0.01]. The most common causes were influenza and pneumonia, chronic lower respiratory diseases, other acute lower respiratory infections, which accounted for 26.6%, 26.4%, and 14.9%, respectively. The age group 75 years and above accounted for 34.1% of the total number of hospital admissions. Males contributed to 50.5% of the total number of hospital admissions. Hospital admission rate in females increased by 119.8% [from 1442.18 (95% CI 1437.66-1446.70) in 1999 to 3169.38 (95% CI 3163.11-3175.64) in 2019 per 100,000 persons, trend test, p < 0.001]. Hospital admission rate increased by 92.9% in males [from 1633.25 (95% CI 1628.32-1638.17) in 1999 to 3149.78 (95% CI 3143.46-3156.09) in 2019 per 100,000 persons, trend test, p < 0.001].

CONCLUSION: During the study period, hospital admissions rate due to respiratory diseases increased sharply. The rates of hospital admissions were higher among males for the vast majority of respiratory diseases. Further observational studies are warranted to identify risk factors for these hospital admissions and to offer relevant interventions to mitigate the risk.}, } @article {pmid34749211, year = {2021}, author = {Fridman, M and Krasko, O and Levin, L and Veyalkin, I and Lam, AK}, title = {Comparative pathological characteristics of papillary thyroid carcinoma with second primary non-thyroid malignancies in the region affected by the Chernobyl accident.}, journal = {Pathology, research and practice}, volume = {228}, number = {}, pages = {153658}, doi = {10.1016/j.prp.2021.153658}, pmid = {34749211}, issn = {1618-0631}, mesh = {Adolescent ; Adult ; *Chernobyl Nuclear Accident ; Cohort Studies ; Female ; Humans ; Male ; Middle Aged ; Neoplasms, Radiation-Induced/*pathology ; Neoplasms, Second Primary/etiology/*pathology ; Thyroid Cancer, Papillary/etiology/*pathology ; Thyroid Neoplasms/etiology/*pathology ; Young Adult ; }, abstract = {The aim was to study the pathological features of papillary thyroid carcinoma diagnosed with or before second primary malignancy in patients exposed to post-Chernobyl exposure. The patients selected (n = 6559) were those exposed to radiation at the age of ≤ 18 years old and developed papillary thyroid carcinoma during the years 1990-2020. Of these, 2.1% (n = 140) had second primary malignancies. To compare the histopathological characteristics of papillary thyroid carcinoma in the group under analysis, 91% (n = 128) with sufficient data were included in further analysis. The control group was formed by matching patients with age at exposure to radiation, age at surgery, gender, and place of residence. Median age at exposure was 14 years old for both groups. Besides, no difference in tumour extension and histological features of papillary thyroid carcinoma was noted between patients with synchronous or metachronous primary malignant tumours. Nevertheless, the time lag to the diagnosis of papillary thyroid carcinoma was shortened in the group with metachronous when compared to patients with synchronous second primaries (p < 0.001). Independent differences between patients with second primaries and their matched peers included tumour size {OR (95%CI) = 0.89 (0.45; 1.04)}, multiple tumours {OR (95% CI) = 1.46 (0.86; 2.42)}, lymphatic vessel invasion (OR (95%CI) 0.92 (0.61; 1.53)), blood vessel invasion (OR (95%CI) 0.41 (0.10; 1.23) and presence of numerous psammomas (OR (95%CI) 0.73 (0.39; 1.31)). The possible influence of radiative iodine treatment for development of second primaries was analysed for the group of patients with metachronous malignancies using the same approach (84 patients were compared to 252 matched patients). Independent differences also included tumour size {OR (95% CI) 0.77 (0.45; 1.30)}, lymphatic vessel invasion {OR (95%CI) 0.75(0.43; 1.28)}, blood vessel invasion {OR (95%CI) 0.17 (0.01; 0.87)} . Besides, multiple tumours were revealed more frequently in patients with metachronous primaries (OR (95%CI) 1.92 (1.0; 3.62)). To conclude, patients exposed to Chernobyl irradiation with the development of papillary thyroid carcinoma and second primary malignancy have less biological aggressive pathological characteristics of their thyroid cancers. Accordingly, these patients were less frequently treated with post-surgical radioactive iodine. Thus, 131I-irradiation may have negligible impact on the development of second primaries.}, } @article {pmid34748971, year = {2022}, author = {Xiao, J and Luo, SS and Du, JH and Liu, QY and Huang, Y and Wang, WF and Chen, XL and Chen, XH and Liu, H and Zhou, XY and Zhao, YZ and Wang, HL}, title = {Transcriptomic analysis of gills in nitrite-tolerant and -sensitive families of Litopenaeus vannamei.}, journal = {Comparative biochemistry and physiology. Toxicology & pharmacology : CBP}, volume = {253}, number = {}, pages = {109212}, doi = {10.1016/j.cbpc.2021.109212}, pmid = {34748971}, issn = {1532-0456}, mesh = {Animals ; Ecotoxicology ; Energy Metabolism/drug effects/genetics ; Gene Expression Profiling ; Gene Expression Regulation/drug effects ; Gene Ontology ; Gills/*physiology ; Nitrites/*toxicity ; Penaeidae/*drug effects/*genetics/physiology ; Reproducibility of Results ; Sequence Analysis, RNA ; Stress, Physiological/drug effects/*genetics/immunology ; Water Pollutants, Chemical/toxicity ; }, abstract = {Nitrite stress is a major environmental factor that limits aquatic animal growth, reproduction and survival. Even so, some shrimps still can withstand somewhat high concentrations of nitrite environment. However, few studies have been conducted about the tolerance molecular mechanism of Litopenaeus vannamei in the high concentration nitrite. To identify the genes and pathways involved in the regulation of nitrite tolerance, we performed comparative transcriptomic analysis in the L. vannamei nitrite-tolerant (NT) and nitrite-sensitive (NS) families, and untreated shrimps were used as the control group. After 24 h of nitrite exposure (NaNO2, 112.5 mg/L), a total of 1521 and 868 differentially expressed genes (DEGs) were obtained from NT compared with NS and control group, respectively. Functional enrichment analysis revealed that most of these DEGs were involved in immune defense, energy metabolism processes and endoplasmic reticulum (ER) stress. During nitrite stress, energy metabolism in NT was significantly enhanced by activating the related genes expression of oxidative phosphorylation (OXPHOS) pathway and tricarboxylic acid (TCA) cycle. Meanwhile, some DEGs involved in innate immunity- related genes and pathways, and ER stress responses also were highly expressed in NT. Therefore, we speculate that accelerated energy metabolism, higher expression of immunity and ER related genes might be the important adaptive strategies for NT in relative to NS under nitrite stress. These results will provide new insights on the potential tolerant molecular mechanisms and the breeding of new varieties of nitrite tolerant L. vannamei.}, } @article {pmid34748936, year = {2022}, author = {Tilikj, N and Novo, M}, title = {How to resist soil desiccation: Transcriptional changes in a Mediterranean earthworm during aestivation.}, journal = {Comparative biochemistry and physiology. Part A, Molecular & integrative physiology}, volume = {264}, number = {}, pages = {111112}, doi = {10.1016/j.cbpa.2021.111112}, pmid = {34748936}, issn = {1531-4332}, mesh = {Animals ; Desert Climate ; Desiccation ; Down-Regulation ; Droughts ; Ecosystem ; Estivation/*genetics/*physiology ; Gene Expression Profiling ; Gene Ontology ; Mediterranean Region ; Oligochaeta/*genetics/*physiology ; Soil/chemistry ; Spain ; Stress, Physiological/genetics/physiology ; Transcription, Genetic ; }, abstract = {Earthworms have a central role in ministering the terrestrial ecosystems and are proving to have an important role in modulating the effects climate change has on soil. Aestivation is a form of dormancy employed by the organisms living in deserts and arid environments, when confronted with prolonged periods of drought. Understanding global metabolic adjustments required for withstanding the harsh conditions of the ever more severe Iberian drought, we performed a global transcriptomic exploration of the endogeic earthworm Carpetania matritensis during aestivation. There were a total of 6352 differentially expressed transcripts in the aestivating group, with 65% being downregulated. Based on GO and KEGG enrichment analyses, downregulated genes seem to be indicative of an overall metabolic depression during aestivation. Indeed we noted a reduction of protein turnover and macromolecule metabolism coupled with suppression of genes involved in digestion. Upregulated genes, namely antioxidant genes and DNA repair genes showed clear signs of abiotic stress caused by ROS generation. Abiotic stress led to transcriptomic changes of genes involved in immune response, mostly affecting the NF-kb signaling pathway as well as changes in apoptotic genes indicating the necessity of investigating these processes in a tissue specific manner. Lastly we uncovered a possible mechanism for water retention by nitrogenous waste accumulation. This study provides the first ever transcriptomic investigation done on aestivating earthworms and as such serves as a general framework for investigation on other earthworm species and other soil invertebrates, which is becoming increasingly important with the current scenario of climate change.}, } @article {pmid34748540, year = {2021}, author = {Lechón-Alonso, P and Clegg, T and Cook, J and Smith, TP and Pawar, S}, title = {The role of competition versus cooperation in microbial community coalescence.}, journal = {PLoS computational biology}, volume = {17}, number = {11}, pages = {e1009584}, pmid = {34748540}, issn = {1553-7358}, mesh = {Biological Evolution ; Computational Biology ; Computer Simulation ; Humans ; Mathematical Concepts ; Microbial Interactions/*physiology ; Microbiota/*physiology ; *Models, Biological ; }, abstract = {New microbial communities often arise through the mixing of two or more separately assembled parent communities, a phenomenon that has been termed "community coalescence". Understanding how the interaction structures of complex parent communities determine the outcomes of coalescence events is an important challenge. While recent work has begun to elucidate the role of competition in coalescence, that of cooperation, a key interaction type commonly seen in microbial communities, is still largely unknown. Here, using a general consumer-resource model, we study the combined effects of competitive and cooperative interactions on the outcomes of coalescence events. To do so, we simulate coalescence events between pairs of communities with different degrees of competition for shared carbon resources and cooperation through cross-feeding on leaked metabolic by-products (facilitation). We also study how structural and functional properties of post-coalescence communities evolve when they are subjected to repeated coalescence events. We find that in coalescence events, the less competitive and more cooperative parent communities contribute a higher proportion of species to the new community because of their superior ability to deplete resources and resist invasions. Consequently, when a community is subjected to repeated coalescence events, it gradually evolves towards being less competitive and more cooperative, as well as more speciose, robust and efficient in resource use. Encounters between microbial communities are becoming increasingly frequent as a result of anthropogenic environmental change, and there is great interest in how the coalescence of microbial communities affects environmental and human health. Our study provides new insights into the mechanisms behind microbial community coalescence, and a framework to predict outcomes based on the interaction structures of parent communities.}, } @article {pmid34748536, year = {2021}, author = {Zamberletti, P and Sabir, K and Opitz, T and Bonnefon, O and Gabriel, E and Papaïx, J}, title = {More pests but less pesticide applications: Ambivalent effect of landscape complexity on conservation biological control.}, journal = {PLoS computational biology}, volume = {17}, number = {11}, pages = {e1009559}, pmid = {34748536}, issn = {1553-7358}, mesh = {Agriculture/methods/statistics & numerical data ; Animals ; Computational Biology ; Computer Simulation ; Conservation of Natural Resources/methods/statistics & numerical data ; Crops, Agricultural/growth & development/parasitology ; Ecosystem ; Pest Control/methods/statistics & numerical data ; Pest Control, Biological/*methods/statistics & numerical data ; Pesticides/*pharmacology ; Plant Diseases/parasitology/prevention & control ; Predatory Behavior ; }, abstract = {In agricultural landscapes, the amount and organization of crops and semi-natural habitats (SNH) have the potential to promote a bundle of ecosystem services due to their influence on ecological community at multiple spatio-temporal scales. SNH are relatively undisturbed and are often source of complementary resources and refuges, therefore supporting more diverse and abundant natural pest enemies. However, the nexus of SNH proportion and organization with pest suppression is not trivial. It is thus crucial to understand how the behavior of pest and natural enemy species, the underlying landscape structure, and their interaction, may influence conservation biological control (CBC). Here, we develop a generative stochastic landscape model to simulate realistic agricultural landscape compositions and configurations of fields and linear elements. Generated landscapes are used as spatial support over which we simulate a spatially explicit predator-prey dynamic model. We find that increased SNH presence boosts predator populations by sustaining high predator density that regulates and keeps pest density below the pesticide application threshold. However, predator presence over all the landscape helps to stabilize the pest population by keeping it under this threshold, which tends to increase pest density at the landscape scale. In addition, the joint effect of SNH presence and predator dispersal ability among hedge and field interface results in a stronger pest regulation, which also limits pest growth. Considering properties of both fields and linear elements, such as local structure and geometric features, provides deeper insights for pest regulation; for example, hedge presence at crop field boundaries clearly strengthens CBC. Our results highlight that the integration of species behaviors and traits with landscape structure at multiple scales is necessary to provide useful insights for CBC.}, } @article {pmid34746021, year = {2021}, author = {Kang, X and Deng, DM and Crielaard, W and Brandt, BW}, title = {Reprocessing 16S rRNA Gene Amplicon Sequencing Studies: (Meta)Data Issues, Robustness, and Reproducibility.}, journal = {Frontiers in cellular and infection microbiology}, volume = {11}, number = {}, pages = {720637}, pmid = {34746021}, issn = {2235-2988}, mesh = {*Computational Biology ; Genes, rRNA ; *High-Throughput Nucleotide Sequencing ; RNA, Ribosomal, 16S/genetics ; Reproducibility of Results ; Sequence Analysis, DNA ; }, abstract = {High-throughput sequencing technology provides an efficient method for evaluating microbial ecology. Different bioinformatics pipelines can be used to convert 16S ribosomal RNA gene amplicon sequencing data into an operational taxonomic unit (OTU) table that is used to analyze microbial communities. It is important to assess the robustness of these pipelines, each with specific algorithms and/or parameters, and their influence on the outcome of statistical tests. Articles with publicly available datasets on the oral microbiome were searched for, and five datasets were retrieved. These were from studies on changes in microbiota related to smoking, oral cancer, caries, diabetes, or periodontitis. Next, the data was processed with four pipelines based on VSEARCH, USEARCH, mothur, and UNOISE3. OTU tables were rarefied, and differences in α-diversity and β-diversity were tested for different groups in a dataset. Finally, these results were checked for consistency among these example pipelines. Of articles that deposited data, only 57% made all sequencing and metadata available. When processing the datasets, issues were encountered, caused by read characteristics and differences between tools and their defaults in combination with a lack of detail in the methodology of the articles. In general, the four mainstream pipelines provided similar results, but importantly, P-values sometimes differed between pipelines beyond the significance threshold. Our results indicated that for published articles, the description of bioinformatics methods and data deposition should be improved, and regarding reproducibility, that analysis of multiple subsamples is required when using rarefying as library-size normalization method.}, } @article {pmid34745591, year = {2021}, author = {Lyon, V and LeRouge, C and Fruhling, A and Thompson, M}, title = {Home testing for COVID-19 and other virus outbreaks: The complex system of translating to communities.}, journal = {Health systems (Basingstoke, England)}, volume = {10}, number = {4}, pages = {298-317}, pmid = {34745591}, issn = {2047-6965}, support = {U54 GM115458/GM/NIGMS NIH HHS/United States ; }, abstract = {Home testing is an emerging innovation that can enable nations and health care systems to safely and efficiently test large numbers of patients to manage COVID-19 and other viral outbreaks. In this position paper, we explore the process of moving home testing across the translational continuum from labs to households, and ultimately into practice and communities for optimal public health impact. We focus on the four translational science drivers to accelerate the implementation of systems-wide home testing programmes 1) collaboration and team science, 2) technology, 3) multilevel interventions, and 4) knowledge integration. We use the Socio Ecological Model (SEM) as a framework to illustrate our vision for the ideal future state of a comprehensive system of stakeholders utilising tech-enabled home testing for COVID-19 and other virus outbreaks, and we suggest SEM as a tool to address key translational readiness and response questions.}, } @article {pmid34741974, year = {2021}, author = {Ma, Z and Wang, X and Li, M and Zhou, D and Chen, J}, title = {An ecological comparison study on the causal association between leptospirosis and moyamoya disease in Hubei, China, 2017-2019.}, journal = {Clinical neurology and neurosurgery}, volume = {210}, number = {}, pages = {107007}, doi = {10.1016/j.clineuro.2021.107007}, pmid = {34741974}, issn = {1872-6968}, mesh = {Adolescent ; Adult ; Aged ; Aged, 80 and over ; Animals ; Cattle ; Child ; Child, Preschool ; China/epidemiology ; Databases, Factual/trends ; *Ecosystem ; Female ; Humans ; Infant ; Leptospirosis/*diagnosis/*epidemiology ; Male ; Middle Aged ; Moyamoya Disease/*diagnosis/*epidemiology ; Registries ; Risk Factors ; Swine ; Young Adult ; }, abstract = {OBJECTIVE: The importance of environmental factors (especially leptospirosis) of moyamoya disease (MMD) has not been clarified. Here we investigated the epidemiological characteristics of MMD in Hubei province, China.

METHODS: We conducted a population-based study to describe the epidemiologic characteristics of MMD in Hubei province between 2017 and 2019. The regional clusters of the hot spots (high incidence) and cold spots (low incidence) of MMD were identified using the spatial statistical method. To evaluate the role of leptospirosis in MMD, we performed an ecological comparison study to evaluate whether the socioeconomic and environmental variables of hot spots are more suitable for leptospirosis spread.

RESULTS: The average annual sex and age adjusted incidence of MMD was 3.07 per 100,000 person-years from 2017 to 2019. The middle-aged had apparently higher incidence of MMD than the children. There existed an obvious geographic distribution difference of MMD at county level. The hot spots were identified mainly in the low mountainous and hilly terrain, while cold spots were located in the Jianghan Plains. Compared to cold spots, the hot spots had larger cattle density (32.0 vs 3.1, p = 0.002), higher percentages of rice field (85.6% vs 47.0%, p = 0.007), and lower elevation (33.6 vs 157.4, p < 0.001) CONCLUSIONS: There exists geographic distribution difference of MMD in Hubei province and was likely to be caused by leptospirosis in the early years. The MMD in China is dominant by middle-aged adults, which might be driven from leptospirosis outbreaks in the last century.}, } @article {pmid34735469, year = {2021}, author = {Ibrahium, SM and Farghali, AA and Mahmoud, R and Wahba, AA and El-Ashram, S and Mahran, HA and Aboelhadid, SM}, title = {New insight on some selected nanoparticles as an effective adsorbent toward diminishing the health risk of deltamethrin contaminated water.}, journal = {PloS one}, volume = {16}, number = {11}, pages = {e0258749}, pmid = {34735469}, issn = {1932-6203}, mesh = {Acaricides/chemistry/toxicity ; Adsorption/drug effects ; Animals ; Environmental Restoration and Remediation ; Humans ; Hydroxides/chemistry/pharmacology ; Insecticides/*adverse effects/chemistry ; Kinetics ; Nanocomposites/chemistry ; Nanoparticles/*chemistry ; Nitriles/*adverse effects/chemistry ; Pyrethrins/*adverse effects/chemistry ; Water/chemistry ; Water Pollutants, Chemical/adverse effects/*chemistry ; Water Purification ; }, abstract = {Deltamethrin is a widely used insecticide that kills a wide variety of insects and ticks. Deltamethrin resistance develops as a result of intensive, repeated use, as well as increased environmental contamination and a negative impact on public health. Its negative impact on aquatic ecology and human health necessitated the development of a new technique for environmental remediation and wastewater treatment, such as the use of nanotechnology. The co-precipitation method was used to create Zn-Fe/LDH, Zn-AL-GA/LDH, and Fe-oxide nanoparticles (NPs), which were then characterized using XRD, FT-IR, FE-SEM, and HR-TEM. The kinetic study of adsorption test revealed that these NPs were effective at removing deltamethrin from wastewater. The larval packet test, which involved applying freshly adsorbed deltamethrin nanocomposites (48 hours after adsorption), and the comet assay test were used to confirm that deltamethrin had lost its acaricidal efficacy. The kinetics of the deltamethrin adsorption process was investigated using several kinetic models at pH 7, initial concentration of deltamethrin 40 ppm and temperature 25°C. Within the first 60 min, the results indicated efficient adsorption performance in deltamethrin removal, the maximum adsorption capacity was 27.56 mg/L, 17.60 mg/L, and 3.06 mg/L with the Zn-Al LDH/GA, Zn-Fe LDH, and Fe Oxide, respectively. On tick larvae, the results of the freshly adsorbed DNC bioassay revealed larval mortality. This suggests that deltamethrin's acaricidal activity is still active. However, applying DNCs to tick larvae 48 hours after adsorption had no lethal effect, indicating that deltamethrin had lost its acaricidal activity. The latter result corroborated the results of the adsorption test's kinetic study. Furthermore, the comet assay revealed that commercial deltamethrin caused 28.51% DNA damage in tick cells, which was significantly higher than any DNC. In conclusion, the NPs used play an important role in deltamethrin decontamination in water, resulting in reduced public health risk. As a result, these NPs could be used as a method of environmental remediation.}, } @article {pmid34733117, year = {2021}, author = {Mandeville, CP and Koch, W and Nilsen, EB and Finstad, AG}, title = {Open Data Practices among Users of Primary Biodiversity Data.}, journal = {Bioscience}, volume = {71}, number = {11}, pages = {1128-1147}, pmid = {34733117}, issn = {0006-3568}, abstract = {Presence-only biodiversity data are increasingly relied on in biodiversity, ecology, and conservation research, driven by growing digital infrastructures that support open data sharing and reuse. Recent reviews of open biodiversity data have clearly documented the value of data sharing, but the extent to which the biodiversity research community has adopted open data practices remains unclear. We address this question by reviewing applications of presence-only primary biodiversity data, drawn from a variety of sources beyond open databases, in the indexed literature. We characterize how frequently researchers access open data relative to data from other sources, how often they share newly generated or collated data, and trends in metadata documentation and data citation. Our results indicate that biodiversity research commonly relies on presence-only data that are not openly available and neglects to make such data available. Improved data sharing and documentation will increase the value, reusability, and reproducibility of biodiversity research.}, } @article {pmid34731206, year = {2021}, author = {Pittarello, M and Ravetto Enri, S and Lonati, M and Lombardi, G}, title = {Slope and distance from buildings are easy-to-retrieve proxies for estimating livestock site-use intensity in alpine summer pastures.}, journal = {PloS one}, volume = {16}, number = {11}, pages = {e0259120}, pmid = {34731206}, issn = {1932-6203}, mesh = {Animals ; Conservation of Natural Resources/*methods ; Geographic Information Systems ; Grassland ; Herbivory/*physiology ; Italy ; Livestock/*physiology ; Remote Sensing Technology ; }, abstract = {Regardless of the issue, most of the research carried out on summer pastures of European Alps had to consider the effects of grazing management, as it is an intrinsic component of alpine environment. The management intensity of grazing livestock is measured in terms of livestock stocking rate, but not always a direct measure of it is easily retrievable. Therefore, the aim of the research was to test the reliability of proxies easily retrievable from open data sources (i.e. slope and distance from buildings) in approximating the pastoral site-use intensity. To test the proxies' effectiveness two different approaches were used. With the first one, the proxies' reliability was assessed in a case-study conducted at farm scale by using the number of positions gathered with GPS collars, which are a reliable measure of livestock site-use intensity. With the second, the proxies' reliability was assessed by means of five Vegetation Ecological Groups (VEGs), used as a tool for indirect quantification of livestock site-use intensity at regional scale (thirty-two alpine valleys of the Western Italian Alps, Piedmont Region-Italy). At farm scale, distance from buildings and slope were both reliable predictors of the number of GPS locations as assessed with a Generalized Additive Model. Results of Generalized Linear Models at the regional scale showed that the values of both the slope and the distance from buildings were able to separate VEGs along the same site-use intensity gradient assessed by modelling the number of GPS locations at farm scale. By testing proxies' reliability both with a direct (i.e. GPS collar positions) and indirect (i.e. VEGs) measurement of livestock site-use intensity, results indicated that slope and distance from buildings can be considered effective surrogates of site-use intensity gradient in alpine grasslands managed under livestock grazing. Therefore, when the level of site-use intensity in research carried out in alpine summer pastures is not directly available, a reliable solution consists in the use of the terrain slope and the distance from buildings, which are also easily retrievable from open data sources or computable.}, } @article {pmid34730664, year = {2021}, author = {Dantas, ESO and Farias, YMF and Rezende, EB and Silva, GWDS and Silva, PGD and Meira, KC}, title = {Estimates of suicide mortality in women residents in northeast brazilian states from 1996 to 2018.}, journal = {Ciencia & saude coletiva}, volume = {26}, number = {10}, pages = {4795-4804}, doi = {10.1590/1413-812320212610.29552020}, pmid = {34730664}, issn = {1678-4561}, mesh = {Asphyxia ; Brazil/epidemiology ; Female ; Humans ; Information Systems ; Mortality ; *Suicide ; }, abstract = {The objective of this study was to analyze the temporal trend of suicide mortality in women in the states of Northeastern Brazil. This is an ecological study of a time series stratified by states in Northeast Brazil from 1996 to 2018, with data extracted from the Mortality Information System (SIM). The temporal trend was evaluated by negative binomial regression (p values≤0.05). There was a higher proportion of deaths in black and brown women (73.9%), single (57.3%), with the place of death occurring in the home (53.4%). Hanging and strangulation stood out as the perpetration means (47.6%). Most states showed an upward temporal trend, except for Pernambuco, Rio Grande do Norte, Sergipe and Maranhão, which showed a steady trend (p>0.05). An upward temporal trend was identified in the analysis of deaths by suicide in women in five states in northeastern Brazil between 1996 and 2018. The information presented can support planning and decision-making for the prevention of suicide among women in northeastern Brazil.}, } @article {pmid34725368, year = {2021}, author = {Gutierrez, LE and Elorriaga, N and Gibbons, L and Melendi, S and Chaparro, M and Calandrelli, M and Lanas, F and Mores, N and Ponzo, J and Poggio, R and Berrueta, M and Irazola, V}, title = {Attributes of the food and physical activity built environments from the Southern Cone of Latin America.}, journal = {Scientific data}, volume = {8}, number = {1}, pages = {291}, pmid = {34725368}, issn = {2052-4463}, support = {109059-016//International Development Research Centre (Centre de recherches pour le développement international)/ ; 109059-016//International Development Research Centre (Centre de recherches pour le développement international)/ ; 107730-001//International Development Research Centre (Centre de recherches pour le développement international)/ ; 107730-001//International Development Research Centre (Centre de recherches pour le développement international)/ ; 109059-016//International Development Research Centre (Centre de recherches pour le développement international)/ ; 107730-001//International Development Research Centre (Centre de recherches pour le développement international)/ ; }, mesh = {*Built Environment ; *Exercise ; *Food ; Humans ; Latin America ; Noncommunicable Diseases/epidemiology ; Obesity/epidemiology ; Residence Characteristics ; Risk Factors ; Socioeconomic Factors ; }, abstract = {Previous studies have shown the influence of the physical and social environments on the development of obesity and non-communicable diseases (NCD). An obesogenic environment promotes higher dietary energy intakes and sedentary behaviors while limiting opportunities or incentives for active living. This paper presents a dataset with key attributes of the food and physical activity built environment, including green spaces, quality of streets and sidewalks, and different types of food retail outlets in four cities of the Southern Cone of Latin America. A total of 139 representative neighborhoods randomly selected from: Marcos Paz and Bariloche (Argentina), Temuco (Chile) and Canelones-Barros Blancos (Uruguay) were evaluated, where standardized community walks were conducted for direct observation of the built environment. This dataset will contribute valuable data to the evaluation of obesogenic environments in the region, and could be linked to additional ecological information about risk factors for NCDs and socio-economic features from other sources. Understanding environmental influences on cardiovascular risk factors and individual habits may help explain NCD outcomes and plan urban policies.}, } @article {pmid34724822, year = {2021}, author = {Wu, R and Davison, MR and Nelson, WC and Graham, EB and Fansler, SJ and Farris, Y and Bell, SL and Godinez, I and Mcdermott, JE and Hofmockel, KS and Jansson, JK}, title = {DNA Viral Diversity, Abundance, and Functional Potential Vary across Grassland Soils with a Range of Historical Moisture Regimes.}, journal = {mBio}, volume = {12}, number = {6}, pages = {e0259521}, pmid = {34724822}, issn = {2150-7511}, mesh = {Bacteria/virology ; Bacteriophages ; Computational Biology ; *DNA Viruses/genetics ; Ecosystem ; Genome, Viral ; *Grassland ; Lysogeny ; Metagenome ; Metagenomics ; Sequence Analysis, DNA ; Soil ; *Soil Microbiology ; Washington ; }, abstract = {Soil viruses are abundant, but the influence of the environment and climate on soil viruses remains poorly understood. Here, we addressed this gap by comparing the diversity, abundance, lifestyle, and metabolic potential of DNA viruses in three grassland soils with historical differences in average annual precipitation, low in eastern Washington (WA), high in Iowa (IA), and intermediate in Kansas (KS). Bioinformatics analyses were applied to identify a total of 2,631 viral contigs, including 14 complete viral genomes from three deep metagenomes (1 terabase [Tb] each) that were sequenced from bulk soil DNA. An additional three replicate metagenomes (∼0.5 Tb each) were obtained from each location for statistical comparisons. Identified viruses were primarily bacteriophages targeting dominant bacterial taxa. Both viral and host diversity were higher in soil with lower precipitation. Viral abundance was also significantly higher in the arid WA location than in IA and KS. More lysogenic markers and fewer clustered regularly interspaced short palindromic repeats (CRISPR) spacer hits were found in WA, reflecting more lysogeny in historically drier soil. More putative auxiliary metabolic genes (AMGs) were also detected in WA than in the historically wetter locations. The AMGs occurring in 18 pathways could potentially contribute to carbon metabolism and energy acquisition in their hosts. Structural equation modeling (SEM) suggested that historical precipitation influenced viral life cycle and selection of AMGs. The observed and predicted relationships between soil viruses and various biotic and abiotic variables have value for predicting viral responses to environmental change. IMPORTANCE Soil viruses are abundant but poorly understood. Because soil viruses regulate the dynamics of their hosts and potentially key processes in soil ecology, it is important to understand them better. Here, we leveraged massive DNA sequencing to unearth previously unknown soil viruses. We found that soil viruses differed across a historical gradient of precipitation. We compared soil viruses from Iowa, which is traditionally wetter, to those from Washington, which is traditionally drier, and from Kansas, which is intermediate. This study provides strong evidence that changes in historical precipitation impact not only the types of soil viruses but also their functional potential.}, } @article {pmid34723959, year = {2021}, author = {Giannari, D and Ho, CH and Mahadevan, R}, title = {A gap-filling algorithm for prediction of metabolic interactions in microbial communities.}, journal = {PLoS computational biology}, volume = {17}, number = {11}, pages = {e1009060}, pmid = {34723959}, issn = {1553-7358}, mesh = {*Algorithms ; Bacteroidetes/metabolism ; Bifidobacterium adolescentis/metabolism ; Computational Biology ; Computer Simulation ; Databases, Factual ; Escherichia coli/metabolism ; Faecalibacterium prausnitzii/metabolism ; Gastrointestinal Microbiome/physiology ; Humans ; *Metabolic Networks and Pathways ; Microbiota/*physiology ; *Models, Biological ; Peptococcaceae/metabolism ; Synthetic Biology ; }, abstract = {The study of microbial communities and their interactions has attracted the interest of the scientific community, because of their potential for applications in biotechnology, ecology and medicine. The complexity of interspecies interactions, which are key for the macroscopic behavior of microbial communities, cannot be studied easily experimentally. For this reason, the modeling of microbial communities has begun to leverage the knowledge of established constraint-based methods, which have long been used for studying and analyzing the microbial metabolism of individual species based on genome-scale metabolic reconstructions of microorganisms. A main problem of genome-scale metabolic reconstructions is that they usually contain metabolic gaps due to genome misannotations and unknown enzyme functions. This problem is traditionally solved by using gap-filling algorithms that add biochemical reactions from external databases to the metabolic reconstruction, in order to restore model growth. However, gap-filling algorithms could evolve by taking into account metabolic interactions among species that coexist in microbial communities. In this work, a gap-filling method that resolves metabolic gaps at the community level was developed. The efficacy of the algorithm was tested by analyzing its ability to resolve metabolic gaps on a synthetic community of auxotrophic Escherichia coli strains. Subsequently, the algorithm was applied to resolve metabolic gaps and predict metabolic interactions in a community of Bifidobacterium adolescentis and Faecalibacterium prausnitzii, two species present in the human gut microbiota, and in an experimentally studied community of Dehalobacter and Bacteroidales species of the ACT-3 community. The community gap-filling method can facilitate the improvement of metabolic models and the identification of metabolic interactions that are difficult to identify experimentally in microbial communities.}, } @article {pmid34722694, year = {2021}, author = {Mattalia, G and Belichenko, O and Kalle, R and Kolosova, V and Kuznetsova, N and Prakofjewa, J and Stryamets, N and Pieroni, A and Volpato, G and Sõukand, R}, title = {Multifarious Trajectories in Plant-Based Ethnoveterinary Knowledge in Northern and Southern Eastern Europe.}, journal = {Frontiers in veterinary science}, volume = {8}, number = {}, pages = {710019}, pmid = {34722694}, issn = {2297-1769}, abstract = {Over the last century in the European context, animal production has been transformed by the dynamics of centralization and decentralization due to political and economic factors. These processes have influenced knowledge related to healing and ensuring the welfare of domestic animals. Therefore, our study aimed to document and compare current and past ethnoveterinary practices, and to identify trajectories in ethnoveterinary knowledge in study regions from both northern and southern Eastern Europe. In the summers of 2018 and 2019, we conducted 476 interviews, recording the use of 94 plant taxa, 67 of which were wild and 24 were cultivated. We documented 452 use reports, 24 of which were related to the improvement of the quality or quantity of meat and milk, while the other 428 involved ethnoveterinary practices for treating 10 domestic animal taxa. Cattle were the most mentioned target of ethnoveterinary treatments across all the study areas, representing about 70% of all use reports. Only four plant species were reported in five or more countries (Artemisia absinthium, Hypericum spp., Linum usitatissimum, Quercus robur). The four study regions located in Northern and Southern Eastern Europe did not present similar ethnoveterinary knowledge trajectories. Bukovinian mountain areas appeared to hold a living reservoir of ethnoveterinary knowledge, unlike the other regions. Setomaa (especially Estonian Setomaa) and Dzukija showed an erosion of ethnoveterinary knowledge with many uses reported in the past but no longer in use. The current richness of ethnoveterinary knowledge reported in Bukovina could have been developed and maintained through its peculiar geographical location in the Carpathian Mountains and fostered by the intrinsic relationship between the mountains and local pastoralists and by its unbroken continuity of management even during the Soviet era. Finally, our results show some patterns common to several countries and to the veterinary medicine promoted during the time of the Soviet Union. However, the Soviet Union and its centralized animal breeding system, resulted in a decline of ethnoveterinary knowledge as highly specialized veterinary doctors worked in almost every village. Future research should examine the complex networks of sources from where farmers derive their ethnoveterinary knowledge.}, } @article {pmid34722103, year = {2021}, author = {Garett, R and Young, SD}, title = {Geolocation, ethics, and HIV research.}, journal = {Health and technology}, volume = {11}, number = {6}, pages = {1305-1309}, pmid = {34722103}, issn = {2190-7188}, support = {R01 AI132030/AI/NIAID NIH HHS/United States ; R01 MH106415/MH/NIMH NIH HHS/United States ; R33 AT010606/AT/NCCIH NIH HHS/United States ; R34 DA054511/DA/NIDA NIH HHS/United States ; }, abstract = {The HIV epidemic continues to disproportionally affect marginalized populations. Digital tools, including global positioning system and ecologic momentary assessment, have been studied as methods for improving data collection and interventions among HIV-affected communities. Although people living with HIV and populations at high risk have found it acceptable to use digital technologies for HIV research, concerns over privacy and trust have also been expressed. This paper explores and describes the use of geolocation technology data (e.g., location-based social media) in HIV research as well as the ethical and implementation considerations that warrant examination prior to use. Transparent and clear language in consent forms might improve participant trust in the project and investigators' ability to keep participant data secure and private. With respect to institutional review boards, a committee member who is knowledgeable about digital technologies and consumer protections may offer guidance in assessing adequate protections in study protocols. As technology used in research continues to evolve, investigators and the research community must continue to examine the ethical challenges that emerge to address participant concerns.}, } @article {pmid34714989, year = {2021}, author = {Hatami, F and Beamish, E and Davies, A and Rigby, R and Dondelinger, F}, title = {A hierarchical Bayesian approach for detecting global microbiome associations.}, journal = {Statistical applications in genetics and molecular biology}, volume = {20}, number = {3}, pages = {85-100}, pmid = {34714989}, issn = {1544-6115}, mesh = {Animals ; Bayes Theorem ; *Gastrointestinal Microbiome ; *Inflammatory Bowel Diseases ; Mice ; *Microbiota ; Phylogeny ; }, abstract = {The human gut microbiome has been shown to be associated with a variety of human diseases, including cancer, metabolic conditions and inflammatory bowel disease. Current approaches for detecting microbiome associations are limited by relying on specific measures of ecological distance, or only allowing for the detection of associations with individual bacterial species, rather than the whole microbiome. In this work, we develop a novel hierarchical Bayesian model for detecting global microbiome associations. Our method is not dependent on a choice of distance measure, and is able to incorporate phylogenetic information about microbial species. We perform extensive simulation studies and show that our method allows for consistent estimation of global microbiome effects. Additionally, we investigate the performance of the model on two real-world microbiome studies: a study of microbiome-metabolome associations in inflammatory bowel disease, and a study of associations between diet and the gut microbiome in mice. We show that we can use the method to reliably detect associations in real-world datasets with varying numbers of samples and covariates.}, } @article {pmid34713030, year = {2020}, author = {Egger, ST and Knorr, M and Bobes, J and Bernstein, A and Seifritz, E and Vetter, S}, title = {Real-Time Assessment of Stress and Stress Response Using Digital Phenotyping: A Study Protocol.}, journal = {Frontiers in digital health}, volume = {2}, number = {}, pages = {544418}, pmid = {34713030}, issn = {2673-253X}, abstract = {Background: Stress is a complex phenomenon that may have a negative influence on health and well-being; consequently, it plays a pivotal role in mental health. Although the incidence of mental disorders has been continuously rising, development of prevention and treatment methods has been rather slow. Through the ubiquitous presence of smartphones and wearable devices, people can monitor stress parameters in everyday life. However, the reliability and validity of such monitoring are still unsatisfactory. Methods: The aim of this trial is to find a relationship between psychological stress and saliva cortisol levels on the one hand and physiological parameters measured by smartphones in combination with a commercially available wearable device on the other. Participants include cohorts of individuals with and without a psychiatric disorder. The study is conducted in two settings: one naturalistic and one a controlled laboratory environment, combining ecological momentary assessment (EMA) and digital phenotyping (DP). EMA is used for the assessment of challenging and stressful situations coincidentally happening during a whole observation week. DP is used during a controlled stress situation with the Trier Social Stress Test (TSST) as a standardized psychobiological paradigm. Initially, participants undergo a complete psychological screening and profiling using a standardized psychometric test battery. EMA uses a smartphone application, and the participants keep a diary about their daily routine, activities, well-being, sleep, and difficult and stressful situations they may encounter. DP is conducted through wearable devices able to continuously monitor physiological parameters (i.e., heart rate, heart rate variability, skin conductivity, temperature, movement and acceleration). Additionally, saliva cortisol samples are repeatedly taken. The TSST is conducted with continuous measurement of the same parameters measured during the EMA. Discussion: We aim to identify valid and reliable digital biomarkers for stress and stress reactions. Furthermore, we expect to find a way of early detection of psychological stress in order to evolve new opportunities for interventions reducing stress. That may allow us to find new ways of treating and preventing mental disorders. Trial Registration: The competing ethics committee of the Canton of Zurich, Switzerland, approved the study protocol V05.1 May 28, 2019 [BASEC: 2019-00814]; the trial was registered at ClinicalTrials.gov [NCT04100213] on September 19, 2019.}, } @article {pmid34710096, year = {2021}, author = {Howerton, E and Ferrari, MJ and Bjørnstad, ON and Bogich, TL and Borchering, RK and Jewell, CP and Nichols, JD and Probert, WJM and Runge, MC and Tildesley, MJ and Viboud, C and Shea, K}, title = {Synergistic interventions to control COVID-19: Mass testing and isolation mitigates reliance on distancing.}, journal = {PLoS computational biology}, volume = {17}, number = {10}, pages = {e1009518}, pmid = {34710096}, issn = {1553-7358}, mesh = {COVID-19/epidemiology/*prevention & control ; COVID-19 Testing/methods ; Communicable Disease Control/methods ; Computational Biology ; Computer Simulation ; Cost-Benefit Analysis ; Humans ; Models, Biological ; Pandemics/*prevention & control ; Physical Distancing ; *SARS-CoV-2 ; }, abstract = {Stay-at-home orders and shutdowns of non-essential businesses are powerful, but socially costly, tools to control the pandemic spread of SARS-CoV-2. Mass testing strategies, which rely on widely administered frequent and rapid diagnostics to identify and isolate infected individuals, could be a potentially less disruptive management strategy, particularly where vaccine access is limited. In this paper, we assess the extent to which mass testing and isolation strategies can reduce reliance on socially costly non-pharmaceutical interventions, such as distancing and shutdowns. We develop a multi-compartmental model of SARS-CoV-2 transmission incorporating both preventative non-pharmaceutical interventions (NPIs) and testing and isolation to evaluate their combined effect on public health outcomes. Our model is designed to be a policy-guiding tool that captures important realities of the testing system, including constraints on test administration and non-random testing allocation. We show how strategic changes in the characteristics of the testing system, including test administration, test delays, and test sensitivity, can reduce reliance on preventative NPIs without compromising public health outcomes in the future. The lowest NPI levels are possible only when many tests are administered and test delays are short, given limited immunity in the population. Reducing reliance on NPIs is highly dependent on the ability of a testing program to identify and isolate unreported, asymptomatic infections. Changes in NPIs, including the intensity of lockdowns and stay at home orders, should be coordinated with increases in testing to ensure epidemic control; otherwise small additional lifting of these NPIs can lead to dramatic increases in infections, hospitalizations and deaths. Importantly, our results can be used to guide ramp-up of testing capacity in outbreak settings, allow for the flexible design of combined interventions based on social context, and inform future cost-benefit analyses to identify efficient pandemic management strategies.}, } @article {pmid34709312, year = {2021}, author = {Yamada, ABF and Freitas, PL and Silva, RFD and Souto, FJD}, title = {Trends and spatial distribution of Hepatitis D in the North of Brazil, 2009-2018: an ecological study.}, journal = {Epidemiologia e servicos de saude : revista do Sistema Unico de Saude do Brasil}, volume = {30}, number = {4}, pages = {e2020867}, doi = {10.1590/S1679-49742021000400014}, pmid = {34709312}, issn = {2237-9622}, mesh = {Brazil/epidemiology ; Environment ; *Hepatitis D/epidemiology ; Humans ; Incidence ; Information Systems ; }, abstract = {OBJECTIVE: To analyze the annual incidence of hepatitis D cases in both Brazil and the Brazilian Northern region between 2009 and 2018.

METHODS: This was an ecological study of hepatitis cases notified on the Notifiable Health Conditions Information System (SINAN), analyzed by sex, age groups, and Northern region states. Temporal trend analysis was performed using the Prais-Winsten method to estimate incident rate annual percent change (APC).

RESULTS: In the period studied, 2,710 cases were reported in Brazil, 74.5% of them in the Northern region and 71.5% in Amazonas, Acre and Rondonia alone. APC showed a downward trend in Brazil as a whole (-21.6% - 95%CI -3.8;-36.2%), in the Northern region (-28.5% - 95%CI -5.2;-46.1%,), in Amazonas (-34.1% - 95%CI -0.8;-56.2%) and in Acre (-37.6% - 95%CI -18.0;-52.6%). Cases decreased in age groups below 40 years old.

CONCLUSION: There was a downward trend in incidence in the Western Amazon, impacting incidence in Brazil as a whole. This fall was led by younger people, probably due to hepatitis B vaccination.}, } @article {pmid34708689, year = {2021}, author = {Hofmann, SM and Klotzsche, F and Mariola, A and Nikulin, V and Villringer, A and Gaebler, M}, title = {Decoding subjective emotional arousal from EEG during an immersive virtual reality experience.}, journal = {eLife}, volume = {10}, number = {}, pages = {}, pmid = {34708689}, issn = {2050-084X}, mesh = {Adult ; *Arousal ; *Electroencephalography ; Emotions/*physiology ; Female ; Humans ; Male ; *Virtual Reality ; Young Adult ; }, abstract = {Immersive virtual reality (VR) enables naturalistic neuroscientific studies while maintaining experimental control, but dynamic and interactive stimuli pose methodological challenges. We here probed the link between emotional arousal, a fundamental property of affective experience, and parieto-occipital alpha power under naturalistic stimulation: 37 young healthy adults completed an immersive VR experience, which included rollercoaster rides, while their EEG was recorded. They then continuously rated their subjective emotional arousal while viewing a replay of their experience. The association between emotional arousal and parieto-occipital alpha power was tested and confirmed by (1) decomposing the continuous EEG signal while maximizing the comodulation between alpha power and arousal ratings and by (2) decoding periods of high and low arousal with discriminative common spatial patterns and a long short-term memory recurrent neural network. We successfully combine EEG and a naturalistic immersive VR experience to extend previous findings on the neurophysiology of emotional arousal towards real-world neuroscience.}, } @article {pmid34708327, year = {2021}, author = {de Medeiros Azevedo, T and Aburjaile, FF and Ferreira-Neto, JRC and Pandolfi, V and Benko-Iseppon, AM}, title = {The endophytome (plant-associated microbiome): methodological approaches, biological aspects, and biotech applications.}, journal = {World journal of microbiology & biotechnology}, volume = {37}, number = {12}, pages = {206}, pmid = {34708327}, issn = {1573-0972}, mesh = {Agricultural Inoculants ; Agriculture ; Biotechnology/*methods ; Computational Biology ; *Endophytes ; Humans ; Metagenomics/methods ; *Microbiota ; Plant Roots/microbiology ; Plants/*microbiology ; Soil ; Soil Microbiology ; }, abstract = {Similar to other organisms, plants establish interactions with a variety of microorganisms in their natural environment. The plant microbiome occupies the host plant's tissues, either internally or on its surfaces, showing interactions that can assist in its growth, development, and adaptation to face environmental stresses. The advance of metagenomics and metatranscriptomics approaches has strongly driven the study and recognition of plant microbiome impacts. Research in this regard provides comprehensive information about the taxonomic and functional aspects of microbial plant communities, contributing to a better understanding of their dynamics. Evidence of the plant microbiome's functional potential has boosted its exploitation to develop more ecological and sustainable agricultural practices that impact human health. Although microbial inoculants' development and use are promising to revolutionize crop production, interdisciplinary studies are needed to identify new candidates and promote effective practical applications. On the other hand, there are challenges in understanding and analyzing complex data generated within a plant microbiome project's scope. This review presents aspects about the complex structuring and assembly of the microbiome in the host plant's tissues, metagenomics, and metatranscriptomics approaches for its understanding, covering descriptions of recent studies concerning metagenomics to characterize the microbiome of non-model plants under different aspects. Studies involving bio-inoculants, isolated from plant microbial communities, capable of assisting in crops' productivity, are also reviewed.}, } @article {pmid34707831, year = {2021}, author = {Preble, JH and Vincenot, CE and Saito, K and Ohte, N}, title = {Roosting ecology of endangered plant-roosting bats on Okinawa Island: Implications for bat-friendly forestry practices.}, journal = {Ecology and evolution}, volume = {11}, number = {20}, pages = {13961-13971}, pmid = {34707831}, issn = {2045-7758}, abstract = {Roosting information is crucial to guiding bat conservation and bat-friendly forestry practices. The Ryukyu tube-nosed bat Murina ryukyuana (Endangered) and Yanbaru whiskered bat Myotis yanbarensis (Critically Endangered) are forest-dwelling bats endemic to the central Ryukyu Archipelago, Japan. Despite their threatened status, little is known about the roosting ecology of these species and the characteristics of natural maternity roosts are unknown. To inform sustainable forestry practices and conservation management, we radio-tracked day roosts of both species in the subtropical forests of Okinawa's Kunigami Village District. We compared roost and roost site characteristics statistically between M. ryukyuana nonmaternity roosts (males or nonreproductive females), maternity roosts, and all M. yanbarensis roosts. Generalized linear models were used to investigate roost site selection by M. ryukyuana irrespective of sex and age class. Lastly, we compiled data on phenology from this and prior studies. Nonreproductive M. ryukyuana roosted alone and primarily in understory foliage. Murina ryukyuana maternity roosts were limited to stands >50 years old, and ~60% were in foliage. Myotis yanbarensis roosted almost entirely in cavities along gulch bottoms and only in stands >70 years old (~1/3 of Kunigami's total forest area). Murina ryukyuana maternity roosts were higher (4.3 ± 0.6 m) than conspecific nonmaternity roosts (2.3 ± 0.5 m; p < .001) and M. yanbarensis roosts (2.7 ± 0.5 m; not significant). Model results were inconclusive. Both species appear to be obligate plant roosters throughout their life cycle, but the less flexible roosting preferences of M. yanbarensis may explain its striking rarity. To conserve these threatened bats, we recommend the following forestry practices: (a) reduce clearing of understory vegetation, (b) refrain from removing trees along streams, (c) promote greater tree cavity densities by protecting old-growth forests and retaining snags, and (d) refrain from removing trees or understory between April and July, while bats are pupping.}, } @article {pmid34705816, year = {2021}, author = {Pettersson, S and Nilsson Jacobi, M}, title = {Spatial heterogeneity enhance robustness of large multi-species ecosystems.}, journal = {PLoS computational biology}, volume = {17}, number = {10}, pages = {e1008899}, pmid = {34705816}, issn = {1553-7358}, mesh = {Animals ; Biodiversity ; Computational Biology ; Ecology ; *Ecosystem ; Humans ; *Models, Biological ; }, abstract = {Understanding ecosystem stability and functioning is a long-standing goal in theoretical ecology, with one of the main tools being dynamical modelling of species abundances. With the help of spatially unresolved (well-mixed) population models and equilibrium dynamics, limits to stability and regions of various ecosystem robustness have been extensively mapped in terms of diversity (number of species), types of interactions, interaction strengths, varying interaction networks (for example plant-pollinator, food-web) and varying structures of these networks. Although many insights have been gained, the impact of spatial extension is not included in this body of knowledge. Recent studies of spatially explicit modelling on the other hand have shown that stability limits can be crossed and diversity increased for systems with spatial heterogeneity in species interactions and/or chaotic dynamics. Here we show that such crossing and diversity increase can appear under less strict conditions. We find that the mere possibility of varying species abundances at different spatial locations make possible the preservation or increase in diversity across previous boundaries thought to mark catastrophic transitions. In addition, we introduce and make explicit a multitude of different dynamics a spatially extended complex system can use to stabilise. This expanded stabilising repertoire of dynamics is largest at intermediate levels of dispersal. Thus we find that spatially extended systems with intermediate dispersal are more robust, in general have higher diversity and can stabilise beyond previous stability boundaries, in contrast to well-mixed systems.}, } @article {pmid34702250, year = {2021}, author = {Boedeker, W and Watts, M and Clausing, P and Marquez, E}, title = {Response to: "letter to the editor regarding the article "the global distribution of acute unintentional pesticide poisoning: estimations based on a systematic review"" by Dunn et al. 2021 in BMC public health.}, journal = {BMC public health}, volume = {21}, number = {1}, pages = {1943}, pmid = {34702250}, issn = {1471-2458}, mesh = {Humans ; Information Storage and Retrieval ; *Pesticides ; *Public Health ; }, abstract = {In a correspondence to BMC Public Health, Dunn et al. (Dunn SE, Reed J and Neumann C. BMC Public Health (n.d)) respond to our review on the occurrence of unintentional, acute pesticide poisoning (UAPP). Based on a systematic review and further data sources we estimated that about 385 million cases of UAPP occur annually world-wide including around 11,000 fatalities (Boedeker W. et al. BMC Public Health:1875, 2020).}, } @article {pmid34698527, year = {2021}, author = {Cui, Z and Huntley, RB and Schultes, NP and Kakar, KU and Yang, CH and Zeng, Q}, title = {Expression of the Type III Secretion System Genes in Epiphytic Erwinia amylovora Cells on Apple Stigmas Benefits Endophytic Infection at the Hypanthium.}, journal = {Molecular plant-microbe interactions : MPMI}, volume = {34}, number = {10}, pages = {1119-1127}, doi = {10.1094/MPMI-06-21-0152-R}, pmid = {34698527}, issn = {0894-0282}, mesh = {*Erwinia amylovora/genetics ; *Malus ; Plant Diseases ; Type III Secretion Systems ; Virulence Factors ; }, abstract = {Erwinia amylovora causes fire blight on rosaceous plants. One of the major entry points of E. amylovora into hosts is flowers, where E. amylovora proliferates epiphytically on stigmatic and hypanthium surfaces and, subsequently, causes endophytic infection at the hypanthium. The type III secretion system (T3SS) is an important virulence factor in E. amylovora. Although the role of T3SS during endophytic infection is well characterized, its expression during epiphytic colonization and role in the subsequent infection is less understood. Here, we investigated T3SS gene expression in epiphytic E. amylovora on stigma and hypanthium of apple flowers under different relative humidities (RH). On stigma surfaces, T3SS was expressed in a high percentage of E. amylovora cells, and its expression promoted epiphytic growth. On hypanthium surfaces, however, T3SS was expressed in fewer E. amylovora cells than on the stigma, and displayed no correlation with epiphytic growth, even though T3SS expression is essential for infection. E. amylovora cells grown on stigmatic surfaces and then flushed down to the hypanthium displayed a higher level of T3SS expression than cells grown on the hypanthium surface alone. Furthermore, E. amylovora cells precultured on stigma had a higher potential to infect flowers than E. amylovora cells precultured in a T3SS-repressive medium. This suggests that T3SS induction during the stigmatic epiphytic colonization may be beneficial for subsequent infection. Finally, epiphytic expression of T3SS was influenced by RH. Higher percentage of stigmatic E. amylovora cells expressed T3SS under high RH than under low RH.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.}, } @article {pmid34698117, year = {2021}, author = {Kim, MJ and Lee, KH and Park, JS and Jeong, JS and Jeong, NR and Lee, W and Kim, I}, title = {Complete Mitochondrial Genomes of Metcalfa pruinosa and Salurnis marginella (Hemiptera: Flatidae): Genomic Comparison and Phylogenetic Inference in Fulgoroidea.}, journal = {Current issues in molecular biology}, volume = {43}, number = {3}, pages = {1391-1418}, pmid = {34698117}, issn = {1467-3045}, support = {PJ01338901//Cooperative Research Program for Agriculture Science and Technology Development, Rural Development Administration, Republic of Korea/ ; }, mesh = {Animals ; Base Sequence ; Computational Biology/methods ; Conserved Sequence ; DNA Barcoding, Taxonomic ; DNA, Ribosomal Spacer ; Gene Rearrangement ; Genes, Insect ; Genes, Mitochondrial ; Genetic Variation ; *Genome, Mitochondrial ; *Genomics ; Hemiptera/*classification/*genetics ; High-Throughput Nucleotide Sequencing ; Molecular Sequence Annotation ; Nucleotide Motifs ; *Phylogeny ; }, abstract = {The complete mitochondrial genomes (mitogenomes) of two DNA barcode-defined haplotypes of Metcalfa pruinosa and one of Salurnis marginella (Hemiptera: Flatidae) were sequenced and compared to those of other Fulgoroidea species. Furthermore, the mitogenome sequences were used to reconstruct phylogenetic relationships among fulgoroid families. The three mitogenomes, including that of the available species of Flatidae, commonly possessed distinctive structures in the 1702-1836 bp A+T-rich region, such as two repeat regions at each end and a large centered nonrepeat region. All members of the superfamily Fulgoroidea, including the Flatidae, consistently possessed a motiflike sequence (TAGTA) at the ND1 and trnS2 junction. The phylogenetic analyses consistently recovered the familial relationships of (((((Ricaniidae + Issidae) + Flatidae) + Fulgoridae) + Achilidae) + Derbidae) in the amino acid-based analysis, with the placement of Cixiidae and Delphacidae as the earliest-derived lineages of fulgoroid families, whereas the monophyly of Delphacidae was not congruent between tree-constructing algorithms.}, } @article {pmid34697381, year = {2021}, author = {Swift, BMC and Barron, ES and Christley, R and Corbetta, D and Grau-Roma, L and Jewell, C and O'Cathail, C and Mitchell, A and Phoenix, J and Prosser, A and Rees, C and Sorley, M and Verin, R and Bennett, M}, title = {Tuberculosis in badgers where the bovine tuberculosis epidemic is expanding in cattle in England.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {20995}, pmid = {34697381}, issn = {2045-2322}, mesh = {Animal Diseases/*epidemiology/*microbiology ; Animals ; Cattle ; England/epidemiology ; Geography, Medical ; Incidence ; Mustelidae/*microbiology ; Prevalence ; Public Health Surveillance ; Tuberculosis/*veterinary ; Tuberculosis, Bovine/*epidemiology/microbiology ; }, abstract = {Bovine tuberculosis (bTB) is an important animal health and economic problem for the cattle industry and a potential zoonotic threat. Wild badgers (Meles meles) play a role on its epidemiology in some areas of high prevalence in cattle, particularly in the UK and Republic of Ireland and increasingly in parts of mainland Europe. However, little is known about the involvement of badgers in areas on the spatial edge of the cattle epidemic, where increasing prevalence in cattle is seen. Here we report the findings of a study of found-dead (mainly road-killed) badgers in six counties on the edge of the English epidemic of bTB in cattle. The overall prevalence of Mycobacterium tuberculosis complex (MTC) infection detected in the study area was 51/610 (8.3%, 95% CI 6.4-11%) with the county-level prevalence ranging from 15 to 4-5%. The MTC spoligotypes of recovered from badgers and cattle varied: in the northern part of the study area spoligotype SB0129 predominated in both cattle and badgers, but elsewhere there was a much wider range of spoligotypes found in badgers than in cattle, in which infection was mostly with the regional cattle spoligotype. The low prevalence of MTC in badgers in much of the study area, and, relative to in cattle, the lower density of sampling, make firm conclusions difficult to draw. However, with the exception of Cheshire (north-west of the study area), little evidence was found to link the expansion of the bTB epidemic in cattle in England to widespread badger infection.}, } @article {pmid34696369, year = {2021}, author = {Hasiów-Jaroszewska, B and Boezen, D and Zwart, MP}, title = {Metagenomic Studies of Viruses in Weeds and Wild Plants: A Powerful Approach to Characterise Variable Virus Communities.}, journal = {Viruses}, volume = {13}, number = {10}, pages = {}, pmid = {34696369}, issn = {1999-4915}, mesh = {Biodiversity ; Computational Biology/methods ; DNA Viruses/genetics ; Genome, Viral/genetics ; High-Throughput Nucleotide Sequencing/methods ; Metagenome/genetics ; Metagenomics/*methods ; Plant Weeds/*genetics/*virology ; Plants/genetics/virology ; Viruses/classification/genetics ; Viruses, Unclassified/genetics ; }, abstract = {High throughput sequencing (HTS) has revolutionised virus detection and discovery, allowing for the untargeted characterisation of whole viromes. Viral metagenomics studies have demonstrated the ubiquity of virus infection - often in the absence of disease symptoms - and tend to discover many novel viruses, highlighting the small fraction of virus biodiversity described to date. The majority of the studies using high-throughput sequencing to characterise plant viromes have focused on economically important crops, and only a small number of studies have considered weeds and wild plants. Characterising the viromes of wild plants is highly relevant, as these plants can affect disease dynamics in crops, often by acting as viral reservoirs. Moreover, the viruses in unmanaged systems may also have important effects on wild plant populations and communities. Here, we review metagenomic studies on weeds and wild plants to show the benefits and limitations of this approach and identify knowledge gaps. We consider key genomics developments that are likely to benefit the field in the near future. Although only a small number of HTS studies have been performed on weeds and wild plants, these studies have already discovered many novel viruses, demonstrated unexpected trends in virus distributions, and highlighted the potential of metagenomics as an approach.}, } @article {pmid34696031, year = {2021}, author = {Kovanič, Ľ and Ambriško, Ľ and Marasová, D and Blišťan, P and Kasanický, T and Cehlár, M}, title = {Long-Exposure RGB Photography with a Fixed Stand for the Measurement of a Trajectory of a Dynamic Impact Device in Real Scale.}, journal = {Sensors (Basel, Switzerland)}, volume = {21}, number = {20}, pages = {}, pmid = {34696031}, issn = {1424-8220}, support = {VEGA 1/0429/18//NATIONAL RESEARCH AGENCY OF SLOVAKIA/ ; VEGA 1/0588/21//Scientific Grant Agency of The Ministry of Education, Science, Research and Sport of the Slovak Republic/ ; 004TUKE-4/2019//Cultural and Educational Agency of The Ministry of Education, Science, Research and Sport of the Slovak Republic/ ; 055TUKE-4/2021//Cultural and Educational Agency of The Ministry of Education, Science, Research and Sport of the Slovak Republic (KEGA)/ ; APVV-18-0351//Slovak Research and Development Agency/ ; }, abstract = {The present manuscript proposes a novel method for the measurement of a trajectory of a falling impact hammer in the dynamic loading of conveyor belts and the determination of their impact resistance. The proposed method has been experimentally tested and the results of the measurements are presented in this manuscript. The proposed method is based on the long-exposure photography with a long-duration opened shutter of the Nikon D5000 DSLR camera. Results of the experimental research were compared with direct reference measurements performed using the L-GAGE LT3 laser distance sensor. Differences between values, obtained by the new method and by the reference measurements were up to ±3 mm. The standard deviation identified in all the experiments was 1 mm.}, } @article {pmid34695025, year = {2021}, author = {Wenbo, L and Qiyan, F and Haoqian, L and Di, C and Xiangdong, L}, title = {Passive treatment test of acid mine drainage from an abandoned coal mine in Kaili Guizhou, China.}, journal = {Water science and technology : a journal of the International Association on Water Pollution Research}, volume = {84}, number = {8}, pages = {1981-1996}, doi = {10.2166/wst.2021.405}, pmid = {34695025}, issn = {0273-1223}, mesh = {Acids ; Coal ; Hydrogen-Ion Concentration ; Metals ; *Mining ; Sulfates ; *Water Pollutants, Chemical/analysis ; }, abstract = {Discharge of acid mine drainage (AMD) from abandoned coal mines of the YuDong catchment in Kaili City, Guizhou Province, China, has severely damaged local ecological environments. In this study, a laboratory-scale dispersed alkaline substrate (DAS) was studied for the treatment of simulated AMD. The experimental conditions and reaction mechanisms were preliminarily explored. The treatment effect and variation law of vertical effluent water quality of the experimental conditions were thoroughly analysed. The results indicated that small-sized limestone (diameter 5-7 mm) having a 20:1 mixture ratio with shavings and minimum HRT of 20 hours result in increasing effluent pH from 3.5 to 6.6, achieving 66.2% and 99.1% removal of Fe and Al, respectively. There were obvious differences in each reaction layer for the removal of various pollutants from AMD along the depth by DAS, the main reaction zone was first 20-30 cm of the reaction column. The removal process of metal ions and sulfate was accompanied by bio-mineralization reaction. This test provided a valuable support for the local practical engineering applications, enriched the AMD processing technology experimental cases, and provided reference for the treatment technology of similar polluted areas.}, } @article {pmid34683705, year = {2021}, author = {Horak, I and Prylutska, S and Krysiuk, I and Luhovskyi, S and Hrabovsky, O and Tverdokhleb, N and Franskevych, D and Rumiantsev, D and Senenko, A and Evstigneev, M and Drobot, L and Matyshevska, O and Ritter, U and Piosik, J and Prylutskyy, Y}, title = {Nanocomplex of Berberine with C60 Fullerene Is a Potent Suppressor of Lewis Lung Carcinoma Cells Invasion In Vitro and Metastatic Activity In Vivo.}, journal = {Materials (Basel, Switzerland)}, volume = {14}, number = {20}, pages = {}, pmid = {34683705}, issn = {1996-1944}, support = {2020.02/0060//National Research Foundation of Ukraine/ ; }, abstract = {Effective targeting of metastasis is considered the main problem in cancer therapy. The development of herbal alkaloid Berberine (Ber)-based anticancer drugs is limited due to Ber' low effective concentration, poor membrane permeability, and short plasma half-life. To overcome these limitations, we used Ber noncovalently bound to C60 fullerene (C60). The complexation between C60 and Ber molecules was evidenced with computer simulation. The aim of the present study was to estimate the effect of the free Ber and C60-Ber nanocomplex in a low Ber equivalent concentration on Lewis lung carcinoma cells (LLC) invasion potential, expression of epithelial-to-mesenchymal transition (EMT) markers in vitro, and the ability of cancer cells to form distant lung metastases in vivo in a mice model of LLC. It was shown that in contrast to free Ber its nanocomplex with C60 demonstrated significantly higher efficiency to suppress invasion potential, to downregulate the level of EMT-inducing transcription factors SNAI1, ZEB1, and TWIST1, to unblock expression of epithelial marker E-cadherin, and to repress cancer stem cells-like markers. More importantly, a relatively low dose of C60-Ber nanocomplex was able to suppress lung metastasis in vivo. These findings indicated that сomplexation of natural alkaloid Ber with C60 can be used as an additional therapeutic strategy against aggressive lung cancer.}, } @article {pmid34678259, year = {2022}, author = {Firouraghi, N and Mohammadi, A and Hamer, DH and Bergquist, R and Mostafavi, SM and Shamsoddini, A and Raouf-Rahmati, A and Fakhar, M and Moghaddas, E and Kiani, B}, title = {Spatio-temporal visualisation of cutaneous leishmaniasis in an endemic, urban area in Iran.}, journal = {Acta tropica}, volume = {225}, number = {}, pages = {106181}, doi = {10.1016/j.actatropica.2021.106181}, pmid = {34678259}, issn = {1873-6254}, mesh = {Bayes Theorem ; Cluster Analysis ; Humans ; Incidence ; Iran/epidemiology ; *Leishmaniasis, Cutaneous/epidemiology ; Spatio-Temporal Analysis ; }, abstract = {INTRODUCTION: Cutaneous Leishmaniasis (CL) is a significant public health concern worldwide. Iran is among the most CL-affected countries, being one of the six most endemic countries in the world. This study aimed to provide a spatio-temporal visualisation of CL cases in an endemic urban area in north-eastern Iran identifying high-risk and low-risk areas during the period 2016-2019.

METHODS: This ecological study was conducted in the city of Mashhad, north-eastern Iran. All cases (n=2425) were diagnosed based on clinical findings and parasitological tests. The patient data were aggregated at the census tract level (the highest resolution available). CL incidence rates were subjected to Empirical Bayesian smoothing across the census tracts followed by spatial autocorrelation analysis to identify clusters and outliers. Spatial scan statistic was used to explore the purely temporal, purely spatial and spatio-temporal trend of the disease. In all instances, the null hypothesis of no clusters was rejected at p ≤0.05.

RESULTS: The overall crude incidence rate decreased from 34.6 per 100,000 individuals in 2016 to 19.9 per 100,000 in 2019. Cluster analysis identified high-risk areas in south-western Mashhad and low-risk areas in the north-eastern areas. Purely time scan statistics identified March to July as the time period with highest risk for CL occurrence. One most likely purely high-risk spatial cluster and six secondary purely high-risk spatial clusters were identified. Further, two spatio-temporal high-risk clusters, one in the north of the city from April to August and a second in the south-western part from March to September were observed.

CONCLUSIONS: Significant spatial, temporal and spatio-temporal patterns of CL distribution were observed in the study area, which should be considered when designing tailored interventions, such as effective resource allocation models, informed control plans and implementation of efficient surveillance systems. Furthermore, this study generated new hypotheses to test potential relationships between socio-economic and environmental risk factors and incidence of CL in high-risk areas.}, } @article {pmid34677966, year = {2021}, author = {Hanna, GS and Choo, YM and Harbit, R and Paeth, H and Wilde, S and Mackle, J and Verga, JU and Wolf, BJ and Thomas, OP and Croot, P and Cray, J and Thomas, C and Li, LZ and Hardiman, G and Hu, JF and Wang, X and Patel, D and Schinazi, RF and O'Keefe, BR and Hamann, MT}, title = {Contemporary Approaches to the Discovery and Development of Broad-Spectrum Natural Product Prototypes for the Control of Coronaviruses.}, journal = {Journal of natural products}, volume = {84}, number = {11}, pages = {3001-3007}, pmid = {34677966}, issn = {1520-6025}, support = {P30 AI050409/AI/NIAID NIH HHS/United States ; F31 AT011158/AT/NCCIH NIH HHS/United States ; U01 DA045300/DA/NIDA NIH HHS/United States ; U54 MD010706/MD/NIMHD NIH HHS/United States ; R01 AT007318/AT/NCCIH NIH HHS/United States ; }, mesh = {Antiviral Agents/*pharmacology ; Betacoronavirus/*drug effects ; Biological Products/*pharmacology ; Computational Biology ; Databases, Chemical ; Databases, Protein ; *Drug Discovery ; Ligands ; Mass Spectrometry ; Protein Interaction Mapping ; SARS-CoV-2/drug effects ; }, abstract = {The pressing need for SARS-CoV-2 controls has led to a reassessment of strategies to identify and develop natural product inhibitors of zoonotic, highly virulent, and rapidly emerging viruses. This review article addresses how contemporary approaches involving computational chemistry, natural product (NP) and protein databases, and mass spectrometry (MS) derived target-ligand interaction analysis can be utilized to expedite the interrogation of NP structures while minimizing the time and expense of extraction, purification, and screening in BioSafety Laboratories (BSL)3 laboratories. The unparalleled structural diversity and complexity of NPs is an extraordinary resource for the discovery and development of broad-spectrum inhibitors of viral genera, including Betacoronavirus, which contains MERS, SARS, SARS-CoV-2, and the common cold. There are two key technological advances that have created unique opportunities for the identification of NP prototypes with greater efficiency: (1) the application of structural databases for NPs and target proteins and (2) the application of modern MS techniques to assess protein-ligand interactions directly from NP extracts. These approaches, developed over years, now allow for the identification and isolation of unique antiviral ligands without the immediate need for BSL3 facilities. Overall, the goal is to improve the success rate of NP-based screening by focusing resources on source materials with a higher likelihood of success, while simultaneously providing opportunities for the discovery of novel ligands to selectively target proteins involved in viral infection.}, } @article {pmid34677716, year = {2022}, author = {Wang, J and Wang, T and Wang, Q and Tang, X and Ren, Y and Zheng, H and Liu, K and Yang, L and Jiang, H and Li, Y and Liu, Q and Zou, D and Zheng, H}, title = {QTL mapping and candidate gene mining of flag leaf size traits in Japonica rice based on linkage mapping and genome-wide association study.}, journal = {Molecular biology reports}, volume = {49}, number = {1}, pages = {63-71}, pmid = {34677716}, issn = {1573-4978}, support = {(LH2019C035)//Natural Science Foundation Joint Guide Project of Heilongjiang/ ; YS20B05//5511 Science and Technology Innovation Talent Project of Jiangxi Province/ ; 2021YYYF037//Application R & D Project of Heilongjiang Academy of Agricultural Science/ ; LBH-Z16188//Heilongjiang Provincial Postdoctoral Science Foundation/ ; }, mesh = {Chromosome Mapping/*methods ; DNA Shuffling ; Data Mining/*methods ; Gene Expression Regulation, Plant ; Genome-Wide Association Study ; Haplotypes ; Oryza/*anatomy & histology/genetics ; Phenotype ; Plant Leaves/anatomy & histology/genetics ; Plant Proteins/genetics ; *Quantitative Trait Loci ; }, abstract = {BACKGROUND: As one of the most important factors of the japonica rice plant, leaf shape affects the photosynthesis and carbohydrate accumulation directly. Mining and using new leaf shape related genes/QTLs can further enrich the theory of molecular breeding and accelerate the breeding process of japonica rice.

METHODS: In the present study, 2 RILs and a natural population with 295 japonica rice varieties were used to map QTLs for flag leaf length (FL), flag leaf width (FW) and flag leaf area (FLA) by linkage analysis and genome-wide association study (GWAS) throughout 2 years.

RESULTS: A total of 64 QTLs were detected by 2 ways, and pleiotropic QTLs qFL2 (Chr2_33,332,579) and qFL10 (Chr10_10,107,835; Chr10_10,230,100) consisted of overlapping QTLs mapped by linkage analysis and GWAS throughout the 2 years were identified.

CONCLUSIONS: The candidate genes LOC_Os02g54254, LOC_Os02g54550, LOC_Os10g20160, LOC_Os10g20240, LOC_Os10g20260 were obtained, filtered by linkage disequilibrium (LD), and haplotype analysis. LOC_Os10g20160 (SD-RLK-45) showed outstanding characteristics in quantitative real-time PCR (qRT-PCR) analysis in leaf development period, belongs to S-domain receptor-like protein kinases gene and probably to be a main gene regulating flag leaf width of japonica rice. The results of this study provide valuable resources for mining the main genes/QTLs of japonica rice leaf development and molecular breeding of japonica rice ideal leaf shape.}, } @article {pmid34677568, year = {2021}, author = {Hirose, Y and Ohtsubo, Y and Misawa, N and Yonekawa, C and Nagao, N and Shimura, Y and Fujisawa, T and Kanesaki, Y and Katoh, H and Katayama, M and Yamaguchi, H and Yoshikawa, H and Ikeuchi, M and Eki, T and Nakamura, Y and Kawachi, M}, title = {Genome sequencing of the NIES Cyanobacteria collection with a focus on the heterocyst-forming clade.}, journal = {DNA research : an international journal for rapid publication of reports on genes and genomes}, volume = {28}, number = {6}, pages = {}, pmid = {34677568}, issn = {1756-1663}, support = {//Japan Agency for Medical Research and Development/ ; 19K06707//Grant-in-Aid for Scientific Research (C)/ ; //Japan Society for the Promotion of Science (JSPS)/ ; }, mesh = {Base Sequence ; *Cyanobacteria/genetics ; *Ecosystem ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Cyanobacteria are a diverse group of Gram-negative prokaryotes that perform oxygenic photosynthesis. Cyanobacteria have been used for research on photosynthesis and have attracted attention as a platform for biomaterial/biofuel production. Cyanobacteria are also present in almost all habitats on Earth and have extensive impacts on global ecosystems. Given their biological, economical, and ecological importance, the number of high-quality genome sequences for Cyanobacteria strains is limited. Here, we performed genome sequencing of Cyanobacteria strains in the National Institute for Environmental Studies microbial culture collection in Japan. We sequenced 28 strains that can form a heterocyst, a morphologically distinct cell that is specialized for fixing nitrogen, and 3 non-heterocystous strains. Using Illumina sequencing of paired-end and mate-pair libraries with in silico finishing, we constructed highly contiguous assemblies. We determined the phylogenetic relationship of the sequenced genome assemblies and found potential difficulties in the classification of certain heterocystous clades based on morphological observation. We also revealed a bias on the sequenced strains by the phylogenetic analysis of the 16S rRNA gene including unsequenced strains. Genome sequencing of Cyanobacteria strains deposited in worldwide culture collections will contribute to understanding the enormous genetic and phenotypic diversity within the phylum Cyanobacteria.}, } @article {pmid34674330, year = {2021}, author = {G Ribeiro, P and Torres Jiménez, MF and Andermann, T and Antonelli, A and Bacon, CD and Matos-Maraví, P}, title = {A bioinformatic platform to integrate target capture and whole genome sequences of various read depths for phylogenomics.}, journal = {Molecular ecology}, volume = {30}, number = {23}, pages = {6021-6035}, pmid = {34674330}, issn = {1365-294X}, support = {2017-04980//Swedish Research Council/ ; 2019-04739//Swedish Research Council/ ; //Swedish Foundation for Strategic Research/ ; //Royal Botanic Gardens, Kew/ ; GJ20-18566Y//Grant Agency of the Czech Republic/ ; MARIPOSAS-704035//Marie Skłodowska-Curie Fellowship of the European Commission/ ; }, mesh = {*Computational Biology ; *Genome ; High-Throughput Nucleotide Sequencing ; Phylogeny ; Whole Genome Sequencing ; }, abstract = {The increasing availability of short-read whole genome sequencing (WGS) provides unprecedented opportunities to study ecological and evolutionary processes. Although loci of interest can be extracted from WGS data and combined with target sequence data, this requires suitable bioinformatic workflows. Here, we test different assembly and locus extraction strategies and implement them into secapr, a pipeline that processes short-read data into multilocus alignments for phylogenetics and molecular ecology analyses. We integrate the processing of data from low-coverage WGS (<30×) and target sequence capture into a flexible framework, while optimizing de novo contig assembly and loci extraction. Specifically, we test different assembly strategies by contrasting their ability to recover loci from targeted butterfly protein-coding genes, using four data sets: a WGS data set across different average coverages (10×, 5× and 2×) and a data set for which these loci were enriched prior to sequencing via target sequence capture. Using the resulting de novo contigs, we account for potential errors within contigs and infer phylogenetic trees to evaluate the ability of each assembly strategy to recover species relationships. We demonstrate that choosing multiple sizes of kmer simultaneously for assembly results in the highest yield of extracted loci from de novo assembled contigs, while data sets derived from sequencing read depths as low as 5× recovers the expected species relationships in phylogenetic trees. By making the tested assembly approaches available in the secapr pipeline, we hope to inspire future studies to incorporate complementary data and make an informed choice on the optimal assembly strategy.}, } @article {pmid34671161, year = {2021}, author = {Wang, Y and Pedersen, MW and Alsos, IG and De Sanctis, B and Racimo, F and Prohaska, A and Coissac, E and Owens, HL and Merkel, MKF and Fernandez-Guerra, A and Rouillard, A and Lammers, Y and Alberti, A and Denoeud, F and Money, D and Ruter, AH and McColl, H and Larsen, NK and Cherezova, AA and Edwards, ME and Fedorov, GB and Haile, J and Orlando, L and Vinner, L and Korneliussen, TS and Beilman, DW and Bjørk, AA and Cao, J and Dockter, C and Esdale, J and Gusarova, G and Kjeldsen, KK and Mangerud, J and Rasic, JT and Skadhauge, B and Svendsen, JI and Tikhonov, A and Wincker, P and Xing, Y and Zhang, Y and Froese, DG and Rahbek, C and Bravo, DN and Holden, PB and Edwards, NR and Durbin, R and Meltzer, DJ and Kjær, KH and Möller, P and Willerslev, E}, title = {Late Quaternary dynamics of Arctic biota from ancient environmental genomics.}, journal = {Nature}, volume = {600}, number = {7887}, pages = {86-92}, pmid = {34671161}, issn = {1476-4687}, support = {207492/Z/17/Z/WT_/Wellcome Trust/United Kingdom ; /ERC_/European Research Council/International ; 207492/WT_/Wellcome Trust/United Kingdom ; WT220023/WT_/Wellcome Trust/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; 069906/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Animals ; Arctic Regions ; *Biota ; Climate Change/history ; DNA, Ancient/*analysis ; DNA, Environmental/*analysis ; Databases, Genetic ; Datasets as Topic ; Extinction, Biological ; Geologic Sediments ; Grassland ; Greenland ; Haplotypes/genetics ; Herbivory/genetics ; History, Ancient ; Humans ; Lakes ; Mammoths ; *Metagenomics ; Mitochondria/genetics ; Perissodactyla ; Permafrost ; Phylogeny ; Plants/genetics ; Population Dynamics ; Rain ; Siberia ; Spatio-Temporal Analysis ; Wetlands ; }, abstract = {During the last glacial-interglacial cycle, Arctic biotas experienced substantial climatic changes, yet the nature, extent and rate of their responses are not fully understood[1-8]. Here we report a large-scale environmental DNA metagenomic study of ancient plant and mammal communities, analysing 535 permafrost and lake sediment samples from across the Arctic spanning the past 50,000 years. Furthermore, we present 1,541 contemporary plant genome assemblies that were generated as reference sequences. Our study provides several insights into the long-term dynamics of the Arctic biota at the circumpolar and regional scales. Our key findings include: (1) a relatively homogeneous steppe-tundra flora dominated the Arctic during the Last Glacial Maximum, followed by regional divergence of vegetation during the Holocene epoch; (2) certain grazing animals consistently co-occurred in space and time; (3) humans appear to have been a minor factor in driving animal distributions; (4) higher effective precipitation, as well as an increase in the proportion of wetland plants, show negative effects on animal diversity; (5) the persistence of the steppe-tundra vegetation in northern Siberia enabled the late survival of several now-extinct megafauna species, including the woolly mammoth until 3.9 ± 0.2 thousand years ago (ka) and the woolly rhinoceros until 9.8 ± 0.2 ka; and (6) phylogenetic analysis of mammoth environmental DNA reveals a previously unsampled mitochondrial lineage. Our findings highlight the power of ancient environmental metagenomics analyses to advance understanding of population histories and long-term ecological dynamics.}, } @article {pmid34666168, year = {2022}, author = {Phillips, MJ and Westerman, M and Cascini, M}, title = {The value of updating GenBank accessions for supermatrix phylogeny: The case of the New Guinean marsupial carnivore genus Myoictis.}, journal = {Molecular phylogenetics and evolution}, volume = {166}, number = {}, pages = {107328}, doi = {10.1016/j.ympev.2021.107328}, pmid = {34666168}, issn = {1095-9513}, mesh = {Animals ; Cell Nucleus/genetics ; Databases, Nucleic Acid ; *Marsupialia ; New Guinea ; Phylogeny ; }, abstract = {Erroneous taxonomic attributions in GenBank accessions can mislead phylogenetic inference and appear to be widespread within genera. We investigate the influence of taxonomic misattributions for reconstructing the phylogeny of three-striped dasyures, which include four recognized Myoictis species (Marsupialia: Dasyuridae) that are distributed across New Guinea and nearby islands. Molecular phylogenetic studies that have focused on dasyurids consistently resolve the interrelationships of these small carnivores, grouping M. leucura with M. wavicus, and placing M. wallacei and M. melas as successively deeper divergences from these. Two recent marsupial and mammalian supermatrix phylogenies instead favour an alternative Myoictis topology that is discordant with each of these relationships. We add new nuclear and mitochondrial sequences and employ randomized accession resampling that shows the supermatrix topologies are an artefact of several outdated taxonomic attributions in GenBank. Updating these accessions brings agreement across Myoictis phylogenies with randomly resampled accessions. We encourage authors to update GenBank taxonomic attributions and we argue that an option is needed for flagging accessions that are not demonstrably incorrect, but that provide anomalous results. This would serve both as a caution for future supermatrix construction and to highlight accessions of potentially significant biological interest for further study.}, } @article {pmid34665841, year = {2021}, author = {Ellepola, G and Herath, J and Manamendra-Arachchi, K and Wijayathilaka, N and Senevirathne, G and Pethiyagoda, R and Meegaskumbura, M}, title = {Molecular species delimitation of shrub frogs of the genus Pseudophilautus (Anura, Rhacophoridae).}, journal = {PloS one}, volume = {16}, number = {10}, pages = {e0258594}, pmid = {34665841}, issn = {1932-6203}, mesh = {Amphibian Proteins/genetics ; Animals ; Anura/*classification/genetics ; DNA Barcoding, Taxonomic/*methods ; Databases, Genetic ; Homeodomain Proteins/*genetics ; India ; Phylogeny ; Phylogeography ; RNA, Ribosomal/*genetics ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, DNA ; }, abstract = {Sri Lanka is an amphibian hotspot of global significance. Its anuran fauna is dominated by the shrub frogs of the genus Pseudophilautus. Except for one small clade of four species in Peninsular India, these cool-wet adapted frogs, numbering some 59 extant species, are distributed mainly across the montane and lowland rain forests of the island. With species described primarily by morphological means, the diversification has never yet been subjected to a molecular species delimitation analysis, a procedure now routinely applied in taxonomy. Here we test the species boundaries of Pseudophilautus in the context of the phylogenetic species concept (PSC). We use all the putative species for which credible molecular data are available (nDNA-Rag-1; mt-DNA- 12S rRNA, 16S rRNA) to build a well resolved phylogeny, which is subjected to species delimitation analyses. The ABGD, bPTP, mPTP and bGMYC species delimitation methods applied to the 16S rRNA frog barcoding gene (for all species), 12S rRNA and Rag-1 nDNA grouped P. procax and P. abundus; P. hallidayi and P. fergusonianus; P. reticulatus and P. pappilosus; P. pleurotaenia and P. hoipolloi; P. hoffmani and P. asankai; P. silvaticus and P. limbus; P. dilmah and P. hankeni; P. fulvus and P. silus.. Surprisingly, all analyses recovered 14 unidentified potential new species as well. The geophylogeny affirms a distribution across the island's aseasonal 'wet zone' and its three principal hill ranges, suggestive of allopatric speciation playing a dominant role, especially between mountain masses. Among the species that are merged by the delimitation analyses, a pattern leading towards a model of parapatric speciation emerges-ongoing speciation in the presence of gene flow. This delimitation analysis reinforces the species hypotheses, paving the way to a reasonable understanding of Sri Lankan Pseudophilautus, enabling both deeper analyses and conservation efforts of this remarkable diversification. http://zoobank.org/urn:lsid:zoobank.org:pub:DA869B6B-870A-4ED3-BF5D-5AA3F69DDD27.}, } @article {pmid34664915, year = {2021}, author = {Fujishima, K and Sasai, T and Hibino, Y and Nishizawa, H}, title = {Morphology, Diet, and Reproduction of Coastal Hydrophis Sea Snakes (Elapidae: Hydrophiinae) at Their Northern Distribution Limit.}, journal = {Zoological science}, volume = {38}, number = {5}, pages = {405-415}, doi = {10.2108/zs210010}, pmid = {34664915}, issn = {0289-0003}, mesh = {Animals ; Animals, Newborn/anatomy & histology ; Diet/veterinary ; Elapidae/*anatomy & histology/classification/*physiology ; Female ; Litter Size ; Male ; Sex Characteristics ; Species Specificity ; }, abstract = {The Ryukyu Archipelago represents the northern distribution limit for hydrophiine sea snakes, the largest group of marine reptiles. Ryukyuan sea snakes may have developed distinct local adaptations in morphology and ecology, but they have been poorly studied. We examined preserved specimens of 111 Hydrophismelanocephalusand 61 Hydrophis ornatusfrom the Ryukyu Archipelago to obtain data on morphology, diet, and reproduction. Sexual size dimorphism was detected in H. melanocephalus (mean ± standard deviation of adult snout-vent length: SVL, females 1062 ± 141 mm vs. males 959 ± 96 mm) but not in H. ornatus. Female H. melanocephalus had larger head widths and shorter tail lengths relative to SVL compared to males. Relative girth was low in neonates of both species (1.0-1.3), but increased in adults to about 1.7-2.6 in H. melanocephalus and 1.3-1.8 in female H. ornatus. Stomach contents of H. melanocephalus consisted of ophichthid and congrid eels, a sand diver, and gobies, whereas in H. ornatus, gobies and a goat fish were found. Litter size of three reproductive H. melanocephalus ranged from five to seven, and parturition seems to occur from August to October. Litter size of six H. ornatus ranged from two to seven, and was correlated with maternal SVL. Parturition in H. ornatus probably occurs around November. Different selective forces related to locomotion, feeding and predation risk, which influence the pregnant mother and neonates, may have resulted in having few, long but slender offspring that show positive allometric growth in hind-body girth.}, } @article {pmid34662503, year = {2022}, author = {Darolti, I and Mank, JE}, title = {A bioinformatic toolkit to simultaneously identify sex and sex-linked regions.}, journal = {Molecular ecology resources}, volume = {22}, number = {2}, pages = {455-457}, doi = {10.1111/1755-0998.13530}, pmid = {34662503}, issn = {1755-0998}, support = {680951//ERC/ ; }, mesh = {*Computational Biology ; *Genome ; Genomics ; Sex Chromosomes/genetics ; }, abstract = {Sex chromosomes are strange things, and often exhibit unusual patterns of diversity, rates of evolution, and gene regulation (Bachtrog et al., 2011, Mank, 2013). These unique features mean that although sex chromosomes are often a relatively small proportion of the genome, they are best identified and assessed separately from the autosomal majority when carrying out genomic analyses. However, identifying and partitioning genomic regions into sex-linked and autosomal in non-model species can often be quite difficult. In this issue of Molecular Ecology Resources, Nursyifa et al. (2021) provide a useful method that combines sequencing depth information with clustering models to assign sex to samples at the same time as identifying sex-linked scaffolds. This method gives robust results even with more challenging or low-quality data, and thus is particularly promising in studies of non-model organisms.}, } @article {pmid34661677, year = {2022}, author = {Sullivan, MK and Lees, JS and Drake, TM and Docherty, AB and Oates, G and Hardwick, HE and Russell, CD and Merson, L and Dunning, J and Nguyen-Van-Tam, JS and Openshaw, P and Harrison, EM and Baillie, JK and , and Semple, MG and Ho, A and Mark, PB}, title = {Acute kidney injury in patients hospitalized with COVID-19 from the ISARIC WHO CCP-UK Study: a prospective, multicentre cohort study.}, journal = {Nephrology, dialysis, transplantation : official publication of the European Dialysis and Transplant Association - European Renal Association}, volume = {37}, number = {2}, pages = {271-284}, pmid = {34661677}, issn = {1460-2385}, support = {MR/V001671/1/MRC_/Medical Research Council/United Kingdom ; MC_PC_19026/MRC_/Medical Research Council/United Kingdom ; MC_PC_19059/MRC_/Medical Research Council/United Kingdom ; MC_UU_12014/9/MRC_/Medical Research Council/United Kingdom ; MC_PC_19025/MRC_/Medical Research Council/United Kingdom ; MC_PC_15001/MRC_/Medical Research Council/United Kingdom ; 200927/WT_/Wellcome Trust/United Kingdom ; PCL/20/10/CSO_/Chief Scientist Office/United Kingdom ; MR/S032304/1/MRC_/Medical Research Council/United Kingdom ; MR/R502121/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {*Acute Kidney Injury/epidemiology/etiology ; *COVID-19 ; Cohort Studies ; Hospital Mortality ; Humans ; Male ; Prospective Studies ; Retrospective Studies ; Risk Factors ; SARS-CoV-2 ; United Kingdom ; World Health Organization ; }, abstract = {BACKGROUND: Acute kidney injury (AKI) is common in coronavirus disease 2019 (COVID-19). This study investigated adults hospitalized with COVID-19 and hypothesized that risk factors for AKI would include comorbidities and non-White race.

METHODS: A prospective multicentre cohort study was performed using patients admitted to 254 UK hospitals with COVID-19 between 17 January 2020 and 5 December 2020.

RESULTS: Of 85 687 patients, 2198 (2.6%) received acute kidney replacement therapy (KRT). Of 41 294 patients with biochemistry data, 13 000 (31.5%) had biochemical AKI: 8562 stage 1 (65.9%), 2609 stage 2 (20.1%) and 1829 stage 3 (14.1%). The main risk factors for KRT were chronic kidney disease (CKD) [adjusted odds ratio (aOR) 3.41: 95% confidence interval 3.06-3.81], male sex (aOR 2.43: 2.18-2.71) and Black race (aOR 2.17: 1.79-2.63). The main risk factors for biochemical AKI were admission respiratory rate >30 breaths per minute (aOR 1.68: 1.56-1.81), CKD (aOR 1.66: 1.57-1.76) and Black race (aOR 1.44: 1.28-1.61). There was a gradated rise in the risk of 28-day mortality by increasing severity of AKI: stage 1 aOR 1.58 (1.49-1.67), stage 2 aOR 2.41 (2.20-2.64), stage 3 aOR 3.50 (3.14-3.91) and KRT aOR 3.06 (2.75-3.39). AKI rates peaked in April 2020 and the subsequent fall in rates could not be explained by the use of dexamethasone or remdesivir.

CONCLUSIONS: AKI is common in adults hospitalized with COVID-19 and it is associated with a heightened risk of mortality. Although the rates of AKI have fallen from the early months of the pandemic, high-risk patients should have their kidney function and fluid status monitored closely.}, } @article {pmid34655508, year = {2022}, author = {Ng, TC and Teo, CH and Toh, JY and Dunn, AG and Ng, CJ and Ang, TF and Abdullah, A and Syed, A and Lim, HM and Yin, K and Liew, CS}, title = {Factors influencing healthcare seeking in patients with dengue: Systematic review.}, journal = {Tropical medicine & international health : TM & IH}, volume = {27}, number = {1}, pages = {13-27}, doi = {10.1111/tmi.13695}, pmid = {34655508}, issn = {1365-3156}, mesh = {*Dengue ; *Healthcare Disparities ; Humans ; *Patient Acceptance of Health Care ; *Primary Health Care ; }, abstract = {OBJECTIVE: Delays in seeking healthcare for dengue are associated with poor health outcomes. Despite this, the factors influencing such delays remain unclear, rendering interventions to improve healthcare seeking for dengue ineffective. This systematic review aimed to synthesise the factors influencing healthcare seeking of patients with dengue and form a comprehensive framework.

METHODS: This review included both qualitative and quantitative studies. Studies were obtained by searching five databases, contacting field experts and performing backward reference searches. The best-fit meta-synthesis approach was used during data synthesis, where extracted data were fitted into the social-ecological model. Sub-analyses were conducted to identify the commonly reported factors and their level of statistical significance.

RESULTS: Twenty studies were selected for meta-synthesis. Eighteen factors influencing healthcare seeking in dengue were identified and categorised under four domains: individual (11 factors), interpersonal (one factor), organisational (four factors) and community (two factors). The most reported factors were knowledge of dengue, access to healthcare, quality of health service and resource availability. Overall, more barriers to dengue health seeking than facilitators were found. History of dengue infection and having knowledge of dengue were found to be ambiguous as they both facilitated and hindered dengue healthcare seeking. Contrary to common belief, women were less likely to seek help for dengue than men.

CONCLUSIONS: The factors affecting dengue healthcare-seeking behaviour are diverse, can be ambiguous and are found across multiple social-ecological levels. Understanding these complexities is essential for the development of effective interventions to improve dengue healthcare-seeking behaviour.}, } @article {pmid34654896, year = {2021}, author = {García-Olivares, V and Muñoz-Barrera, A and Lorenzo-Salazar, JM and Zaragoza-Trello, C and Rubio-Rodríguez, LA and Díaz-de Usera, A and Jáspez, D and Iñigo-Campos, A and González-Montelongo, R and Flores, C}, title = {A benchmarking of human mitochondrial DNA haplogroup classifiers from whole-genome and whole-exome sequence data.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {20510}, pmid = {34654896}, issn = {2045-2322}, mesh = {Benchmarking ; Computational Biology/*methods ; DNA, Mitochondrial/*classification ; Genome, Mitochondrial ; Haplotypes ; Humans ; Whole Genome Sequencing ; }, abstract = {The mitochondrial genome (mtDNA) is of interest for a range of fields including evolutionary, forensic, and medical genetics. Human mitogenomes can be classified into evolutionary related haplogroups that provide ancestral information and pedigree relationships. Because of this and the advent of high-throughput sequencing (HTS) technology, there is a diversity of bioinformatic tools for haplogroup classification. We present a benchmarking of the 11 most salient tools for human mtDNA classification using empirical whole-genome (WGS) and whole-exome (WES) short-read sequencing data from 36 unrelated donors. We also assessed the best performing tool in third-generation long noisy read WGS data obtained with nanopore technology for a subset of the donors. We found that, for short-read WGS, most of the tools exhibit high accuracy for haplogroup classification irrespective of the input file used for the analysis. However, for short-read WES, Haplocheck and MixEmt were the most accurate tools. Based on the performance shown for WGS and WES, and the accompanying qualitative assessment, Haplocheck stands out as the most complete tool. For third-generation HTS data, we also showed that Haplocheck was able to accurately retrieve mtDNA haplogroups for all samples assessed, although only after following assembly-based approaches (either based on a referenced-based assembly or a hybrid de novo assembly). Taken together, our results provide guidance for researchers to select the most suitable tool to conduct the mtDNA analyses from HTS data.}, } @article {pmid34654839, year = {2021}, author = {Rodríguez, J and Killick, DR and Ressel, L and Espinosa de Los Monteros, A and Santana, A and Beck, S and Cian, F and McKay, JS and Noble, PJ and Pinchbeck, GL and Singleton, DA and Radford, AD}, title = {A text-mining based analysis of 100,000 tumours affecting dogs and cats in the United Kingdom.}, journal = {Scientific data}, volume = {8}, number = {1}, pages = {266}, pmid = {34654839}, issn = {2052-4463}, support = {BB/N019547/1//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; BB/N019547/1//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; BB/N019547/1//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; BB/N019547/1//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; }, mesh = {Animals ; Cat Diseases/*epidemiology ; Cats ; *Data Mining ; Dog Diseases/*epidemiology ; Dogs ; Neoplasms/epidemiology/*veterinary ; United Kingdom/epidemiology ; }, abstract = {Cancer is a major reason for veterinary consultation, especially in companion animals. Cancer surveillance plays a key role in prevention but opportunities for such surveillance in companion animals are limited by the lack of suitable veterinary population health infrastructures. In this paper we describe a pathology-based animal tumour registry (PTR) developed within the Small Animal Veterinary Surveillance Network (SAVSNET) built from electronic pathology records (EPR) submitted to this network. From an original collection of 180232 free text (non-structured) EPRs reported between April 2018 and June 2019, we used specific text-mining methodologies to identify 109895 neoplasias. These data were normalized to describe both the tumour (type and location) and the animal (breed, neutering status and veterinary practice postcode). The resulting PTR, the largest of its kind for companion animals to date, is an important research resource being able to facilitate a wide array of research in areas including surveillance, clinical decision making and comparative cancer biology.}, } @article {pmid34651181, year = {2021}, author = {Pekár, S and Wolff, JO and Černecká, Ľ and Birkhofer, K and Mammola, S and Lowe, EC and Fukushima, CS and Herberstein, ME and Kučera, A and Buzzatto, BA and Djoudi, EA and Domenech, M and Enciso, AV and Piñanez Espejo, YMG and Febles, S and García, LF and Gonçalves-Souza, T and Isaia, M and Lafage, D and Líznarová, E and Macías-Hernández, N and Magalhães, I and Malumbres-Olarte, J and Michálek, O and Michalik, P and Michalko, R and Milano, F and Munévar, A and Nentwig, W and Nicolosi, G and Painting, CJ and Pétillon, J and Piano, E and Privet, K and Ramírez, MJ and Ramos, C and Řezáč, M and Ridel, A and Růžička, V and Santos, I and Sentenská, L and Walker, L and Wierucka, K and Zurita, GA and Cardoso, P}, title = {The World Spider Trait database: a centralized global open repository for curated data on spider traits.}, journal = {Database : the journal of biological databases and curation}, volume = {2021}, number = {}, pages = {}, pmid = {34651181}, issn = {1758-0463}, mesh = {Animals ; *Arthropods ; Databases, Factual ; Ecosystem ; Phenotype ; *Spiders/genetics ; }, abstract = {Spiders are a highly diversified group of arthropods and play an important role in terrestrial ecosystems as ubiquitous predators, which makes them a suitable group to test a variety of eco-evolutionary hypotheses. For this purpose, knowledge of a diverse range of species traits is required. Until now, data on spider traits have been scattered across thousands of publications produced for over two centuries and written in diverse languages. To facilitate access to such data, we developed an online database for archiving and accessing spider traits at a global scale. The database has been designed to accommodate a great variety of traits (e.g. ecological, behavioural and morphological) measured at individual, species or higher taxonomic levels. Records are accompanied by extensive metadata (e.g. location and method). The database is curated by an expert team, regularly updated and open to any user. A future goal of the growing database is to include all published and unpublished data on spider traits provided by experts worldwide and to facilitate broad cross-taxon assays in functional ecology and comparative biology. Database URL:https://spidertraits.sci.muni.cz/.}, } @article {pmid34650271, year = {2022}, author = {Hoffmann, MA and Nothias, LF and Ludwig, M and Fleischauer, M and Gentry, EC and Witting, M and Dorrestein, PC and Dührkop, K and Böcker, S}, title = {High-confidence structural annotation of metabolites absent from spectral libraries.}, journal = {Nature biotechnology}, volume = {40}, number = {3}, pages = {411-421}, pmid = {34650271}, issn = {1546-1696}, support = {R01 GM107550/GM/NIGMS NIH HHS/United States ; P41 GM103484/GM/NIGMS NIH HHS/United States ; U19 AG063744/AG/NIA NIH HHS/United States ; R03 CA211211/CA/NCI NIH HHS/United States ; }, mesh = {Databases, Factual ; Humans ; Metabolome ; *Metabolomics/methods ; Molecular Structure ; *Tandem Mass Spectrometry ; }, abstract = {Untargeted metabolomics experiments rely on spectral libraries for structure annotation, but, typically, only a small fraction of spectra can be matched. Previous in silico methods search in structure databases but cannot distinguish between correct and incorrect annotations. Here we introduce the COSMIC workflow that combines in silico structure database generation and annotation with a confidence score consisting of kernel density P value estimation and a support vector machine with enforced directionality of features. On diverse datasets, COSMIC annotates a substantial number of hits at low false discovery rates and outperforms spectral library search. To demonstrate that COSMIC can annotate structures never reported before, we annotated 12 natural bile acids. The annotation of nine structures was confirmed by manual evaluation and two structures using synthetic standards. In human samples, we annotated and manually validated 315 molecular structures currently absent from the Human Metabolome Database. Application of COSMIC to data from 17,400 metabolomics experiments led to 1,715 high-confidence structural annotations that were absent from spectral libraries.}, } @article {pmid34650153, year = {2021}, author = {Boršová, K and Paul, ED and Kováčová, V and Radvánszka, M and Hajdu, R and Čabanová, V and Sláviková, M and Ličková, M and Lukáčiková, Ľ and Belák, A and Roussier, L and Kostičová, M and Líšková, A and Maďarová, L and Štefkovičová, M and Reizigová, L and Nováková, E and Sabaka, P and Koščálová, A and Brejová, B and Staroňová, E and Mišík, M and Vinař, T and Nosek, J and Čekan, P and Klempa, B}, title = {Surveillance of SARS-CoV-2 lineage B.1.1.7 in Slovakia using a novel, multiplexed RT-qPCR assay.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {20494}, pmid = {34650153}, issn = {2045-2322}, support = {COVID-20-0116//Agentúra na Podporu Výskumu a Vývoja/ ; PP-COVID-20-0017//Agentúra na Podporu Výskumu a Vývoja/ ; 871029//Horizon 2020 Framework Programme/ ; }, mesh = {Alleles ; COVID-19/*diagnosis/epidemiology/*virology ; COVID-19 Nucleic Acid Testing/*methods ; Humans ; Multiplex Polymerase Chain Reaction/*methods ; Mutation ; Prevalence ; RNA, Viral/genetics ; SARS-CoV-2/*genetics/isolation & purification ; Slovakia/epidemiology ; }, abstract = {The emergence of a novel SARS-CoV-2 B.1.1.7 variant sparked global alarm due to increased transmissibility, mortality, and uncertainty about vaccine efficacy, thus accelerating efforts to detect and track the variant. Current approaches to detect B.1.1.7 include sequencing and RT-qPCR tests containing a target assay that fails or results in reduced sensitivity towards the B.1.1.7 variant. Since many countries lack genomic surveillance programs and failed assays detect unrelated variants containing similar mutations as B.1.1.7, we used allele-specific PCR, and judicious placement of LNA-modified nucleotides to develop an RT-qPCR test that accurately and rapidly differentiates B.1.1.7 from other SARS-CoV-2 variants. We validated the test on 106 clinical samples with lineage status confirmed by sequencing and conducted a country-wide surveillance study of B.1.1.7 prevalence in Slovakia. Our multiplexed RT-qPCR test showed 97% clinical sensitivity and retesting 6,886 SARS-CoV-2 positive samples obtained during three campaigns performed within one month, revealed pervasive spread of B.1.1.7 with an average prevalence of 82%. Labs can easily implement this test to rapidly scale B.1.1.7 surveillance efforts and it is particularly useful in countries with high prevalence of variants possessing only the ΔH69/ΔV70 deletion because current strategies using target failure assays incorrectly identify these as putative B.1.1.7 variants.}, } @article {pmid34650048, year = {2021}, author = {Risely, A and Wilhelm, K and Clutton-Brock, T and Manser, MB and Sommer, S}, title = {Diurnal oscillations in gut bacterial load and composition eclipse seasonal and lifetime dynamics in wild meerkats.}, journal = {Nature communications}, volume = {12}, number = {1}, pages = {6017}, pmid = {34650048}, issn = {2041-1723}, mesh = {Animals ; Bacteria/genetics ; *Bacterial Load ; Biodiversity ; *Circadian Rhythm ; Clostridium ; Computational Biology ; DNA, Bacterial ; Ecology ; *Gastrointestinal Microbiome/genetics ; Humans ; Pilot Projects ; RNA, Ribosomal, 16S/genetics ; *Seasons ; }, abstract = {Circadian rhythms in gut microbiota composition are crucial for metabolic function, yet the extent to which they govern microbial dynamics compared to seasonal and lifetime processes remains unknown. Here, we investigate gut bacterial dynamics in wild meerkats (Suricata suricatta) over a 20-year period to compare diurnal, seasonal, and lifetime processes in concert, applying ratios of absolute abundance. We found that diurnal oscillations in bacterial load and composition eclipsed seasonal and lifetime dynamics. Diurnal oscillations were characterised by a peak in Clostridium abundance at dawn, were associated with temperature-constrained foraging schedules, and did not decay with age. Some genera exhibited seasonal fluctuations, whilst others developed with age, although we found little support for microbial senescence in very old meerkats. Strong microbial circadian rhythms in this species may reflect the extreme daily temperature fluctuations typical of arid-zone climates. Our findings demonstrate that accounting for circadian rhythms is essential for future gut microbiome research.}, } @article {pmid34649323, year = {2021}, author = {Bonilla-Bedoya, S and López-Ulloa, M and Mora-Garcés, A and Macedo-Pezzopane, JE and Salazar, L and Herrera, MÁ}, title = {Urban soils as a spatial indicator of quality for urban socio-ecological systems.}, journal = {Journal of environmental management}, volume = {300}, number = {}, pages = {113556}, doi = {10.1016/j.jenvman.2021.113556}, pmid = {34649323}, issn = {1095-8630}, mesh = {Cities ; Ecosystem ; Environmental Monitoring ; *Metals, Heavy/analysis ; Soil ; *Soil Pollutants/analysis ; }, abstract = {The development of criteria and indicators to quantify the transition to sustainability of the urban socio-ecological systems quality is determinant for planning policies and the 21st century urban agenda. This study models the spatial variation in the concentration and distribution of some macronutrients, micronutrients, and trace nutrients in the soil of a high-altitude city in the Andes. Meanwhile, machine learning methods were employed to study some interactions between the different dimensions that constitute an urban socio-ecosystem that caused these variations. We proposed a methodology that considered two phases: a) field work to collect data on 300 soil samples; laboratory analysis to measure the concentrations of 24 macronutrients, micronutrients, and trace nutrients; and the design of geophysical, spectral, and urban co-variables; b) statistical and geo-informatics analysis, where multivariate analysis grouped the elements into factors; and, machine learning integrated with co-variables was applied to derive the intensity of each factor across the city. Multivariate statistics described the variation in soil co-concentrations with a moderate percentage (42%). Four factors were determined that grouped some of the analyzed elements, as follows: F1 (Zn, S, Cu, Pb, Ni, and Cr), F2 (Ba, Ag, K, In, and Mg), F3 (B, V, Li, and Sr), and F4 (Si and Mn). The percentage R[2] out-of-bag of the spatial model were: F1 = 20%, F2 = 8%, F3 = 14%, and F4 = 10%. Our outputs show that the enrichment and contamination by anthropogenic factors, such as the increase in population density, land use, road network, and traffic generated by fossil fuel vehicles, should be prioritized in urban planning decisions.}, } @article {pmid34648487, year = {2021}, author = {Grundler, MC and Rabosky, DL}, title = {Rapid increase in snake dietary diversity and complexity following the end-Cretaceous mass extinction.}, journal = {PLoS biology}, volume = {19}, number = {10}, pages = {e3001414}, pmid = {34648487}, issn = {1545-7885}, mesh = {Animals ; *Biodiversity ; Databases as Topic ; *Diet ; *Extinction, Biological ; Models, Biological ; Multivariate Analysis ; Phenotype ; Phylogeny ; Snakes/*physiology ; Time Factors ; }, abstract = {The Cenozoic marked a period of dramatic ecological opportunity in Earth history due to the extinction of non-avian dinosaurs as well as to long-term physiographic changes that created new biogeographic theaters and new habitats. Snakes underwent massive ecological diversification during this period, repeatedly evolving novel dietary adaptations and prey preferences. The evolutionary tempo and mode of these trophic ecological changes remain virtually unknown, especially compared with co-radiating lineages of birds and mammals that are simultaneously predators and prey of snakes. Here, we assemble a dataset on snake diets (34,060 observations on the diets of 882 species) to investigate the history and dynamics of the multidimensional trophic niche during the global radiation of snakes. Our results show that per-lineage dietary niche breadths remained remarkably constant even as snakes diversified to occupy disparate outposts of dietary ecospace. Rapid increases in dietary diversity and complexity occurred in the early Cenozoic, and the overall rate of ecospace expansion has slowed through time, suggesting a potential response to ecological opportunity in the wake of the end-Cretaceous mass extinction. Explosive bursts of trophic innovation followed colonization of the Nearctic and Neotropical realms by a group of snakes that today comprises a majority of living snake diversity. Our results indicate that repeated transformational shifts in dietary ecology are important drivers of adaptive radiation in snakes and provide a framework for analyzing and visualizing the evolution of complex ecological phenotypes on phylogenetic trees.}, } @article {pmid34645885, year = {2021}, author = {Tiburcio, SRG and Macrae, A and Peixoto, RS and da Costa Rachid, CTC and Mansoldo, FRP and Alviano, DS and Alviano, CS and Ferreira, DF and de Queiroz Venâncio, F and Ferreira, DF and Vermelho, AB}, title = {Sulphate-reducing bacterial community structure from produced water of the Periquito and Galo de Campina onshore oilfields in Brazil.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {20311}, pmid = {34645885}, issn = {2045-2322}, mesh = {Biodiversity ; Biofilms ; Biotechnology ; Brazil ; DNA, Ribosomal/metabolism ; Databases, Genetic ; Desulfovibrionales/genetics ; Ecology ; Enterobacteriaceae/genetics ; Gammaproteobacteria/genetics ; Geography ; Hydrogen Sulfide/chemistry ; *Microbiota ; *Oil and Gas Fields ; RNA, Ribosomal, 16S/genetics ; Sulfates/*chemistry ; Water ; *Water Microbiology ; }, abstract = {Sulphate-reducing bacteria (SRB) cause fouling, souring, corrosion and produce H2S during oil and gas production. Produced water obtained from Periquito (PQO) and Galo de Campina (GC) onshore oilfields in Brazil was investigated for SRB. Produced water with Postgate B, Postgate C and Baars media was incubated anaerobically for 20 days. DNA was extracted, 16S rDNA PCR amplified and fragments were sequenced using Illumina TruSeq. 4.2 million sequence reads were analysed and deposited at NCBI SAR accession number SRP149784. No significant differences in microbial community composition could be attributed to the different media but significant differences in the SRB were observed between the two oil fields. The dominant bacterial orders detected from both oilfields were Desulfovibrionales, Pseudomonadales and Enterobacteriales. The genus Pseudomonas was found predominantly in the GC oilfield and Pleomorphominas and Shewanella were features of the PQO oilfield. 11% and 7.6% of the sequences at GC and PQO were not classified at the genus level but could be partially identified at the order level. Relative abundances changed for Desulfovibrio from 29.8% at PQO to 16.1% at GC. Clostridium varied from 2.8% at PQO and 2.4% at GC. These data provide the first description of SRB from onshore produced water in Brazil and reinforce the importance of Desulfovibrionales, Pseudomonadales, and Enterobacteriales in produced water globally. Identifying potentially harmful microbes is an important first step in developing microbial solutions that prevent their proliferation.}, } @article {pmid34644777, year = {2021}, author = {Amorim, EKR and Matozinhos, FP and Araújo, LA and Silva, TPRD}, title = {Trend in cases of gestational and congenital syphilis in Minas Gerais, Brazil, 2009-2019: an ecological study.}, journal = {Epidemiologia e servicos de saude : revista do Sistema Unico de Saude do Brasil}, volume = {30}, number = {4}, pages = {e2021128}, doi = {10.1590/S1679-49742021000400006}, pmid = {34644777}, issn = {2237-9622}, mesh = {Brazil/epidemiology ; Female ; Humans ; Incidence ; Information Systems ; Pregnancy ; *Syphilis/epidemiology ; *Syphilis, Congenital/epidemiology ; }, abstract = {OBJECTIVE: To analyze the trend of notifications of gestational and congenital syphilis in Minas Gerais, Brazil, from 2009 to 2019.

METHODS: This was an ecological time series study which took the state of Minas Gerais as its unit of analysis, based on data reported on the Notifiable Health Conditions Information System (SINAN). The Prais-Winsten autoregressive model was used to verify trends.

RESULTS: 20,348 cases of gestational syphilis and 11,173 cases of congenital syphilis were reported. Average percentage annual increase was 36.7% (95%CI 32.5;41.0), for gestational syphilis incidence rates, and 32.8% (95%CI 28.0;37.8) for congenital syphilis incidence rates (p<0.001).

CONCLUSION: The temporal trend analysis showed that gestational and congenital syphilis incidence rates had significant increasing trends, which may be related to inadequate treatment or failure to treat syphilis during pregnancy.}, } @article {pmid34644118, year = {2021}, author = {Rodger, JG and Bennett, JM and Razanajatovo, M and Knight, TM and van Kleunen, M and Ashman, TL and Steets, JA and Hui, C and Arceo-Gómez, G and Burd, M and Burkle, LA and Burns, JH and Durka, W and Freitas, L and Kemp, JE and Li, J and Pauw, A and Vamosi, JC and Wolowski, M and Xia, J and Ellis, AG}, title = {Widespread vulnerability of flowering plant seed production to pollinator declines.}, journal = {Science advances}, volume = {7}, number = {42}, pages = {eabd3524}, pmid = {34644118}, issn = {2375-2548}, abstract = {Despite evidence of pollinator declines from many regions across the globe, the threat this poses to plant populations is not clear because plants can often produce seeds without animal pollinators. Here, we quantify pollinator contribution to seed production by comparing fertility in the presence versus the absence of pollinators for a global dataset of 1174 plant species. We estimate that, without pollinators, a third of flowering plant species would produce no seeds and half would suffer an 80% or more reduction in fertility. Pollinator contribution to plant reproduction is higher in plants with tree growth form, multiple reproductive episodes, more specialized pollination systems, and tropical distributions, making these groups especially vulnerable to reduced service from pollinators. These results suggest that, without mitigating efforts, pollinator declines have the potential to reduce reproduction for most plant species, increasing the risk of population declines.}, } @article {pmid34638623, year = {2021}, author = {Hafeez, M and Li, X and Ullah, F and Zhang, Z and Zhang, J and Huang, J and Khan, MM and Chen, L and Ren, X and Zhou, S and Fernández-Grandon, GM and Zalucki, MP and Lu, Y}, title = {Behavioral and Physiological Plasticity Provides Insights into Molecular Based Adaptation Mechanism to Strain Shift in Spodoptera frugiperda.}, journal = {International journal of molecular sciences}, volume = {22}, number = {19}, pages = {}, pmid = {34638623}, issn = {1422-0067}, support = {2020C02003//The Key R&D Program of Zhejiang Province/ ; 233952//China National Postdoctoral Science foundation/ ; }, mesh = {Adaptation, Physiological/genetics ; Animals ; China ; Crops, Agricultural/parasitology ; Digestive System Physiological Phenomena ; Feeding Behavior/physiology ; Female ; Gene Ontology ; Genes, Insect ; Herbivory/genetics/physiology ; Host Adaptation/genetics/physiology ; Host Specificity/genetics/physiology ; Host-Parasite Interactions/genetics/physiology ; Larva/physiology ; Male ; Oryza/parasitology ; Oviposition/physiology ; Spodoptera/*genetics/pathogenicity/*physiology ; Transcriptome ; Zea mays/parasitology ; }, abstract = {How herbivorous insects adapt to host plants is a key question in ecological and evolutionary biology. The fall armyworm, (FAW) Spodoptera frugiperda (J.E. Smith), although polyphagous and a major pest on various crops, has been reported to have a rice and corn (maize) feeding strain in its native range in the Americas. The species is highly invasive and has recently established in China. We compared behavioral changes in larvae and adults of a corn population (Corn) when selected on rice (Rice) and the molecular basis of these adaptational changes in midgut and antennae based on a comparative transcriptome analysis. Larvae of S. frugiperda reared on rice plants continuously for 20 generations exhibited strong feeding preference for with higher larval performance and pupal weight on rice than on maize plants. Similarly, females from the rice selected population laid significantly more eggs on rice as compared to females from maize population. The most highly expressed DEGs were shown in the midgut of Rice vs. Corn. A total of 6430 DEGs were identified between the populations mostly in genes related to digestion and detoxification. These results suggest that potential adaptations for feeding on rice crops, may contribute to the current rapid spread of fall armyworm on rice crops in China and potentially elsewhere. Consistently, highly expressed DEGs were also shown in antennae; a total of 5125 differentially expressed genes (DEGs) s were identified related to the expansions of major chemosensory genes family in Rice compared to the Corn feeding population. These results not only provide valuable insight into the molecular mechanisms in host plants adaptation of S. frugiperda but may provide new gene targets for the management of this pest.}, } @article {pmid34638269, year = {2021}, author = {Yu, Y and Matsuyama, R and Tsunematsu, M and Kakehashi, M}, title = {Quantifying the Effects of Medical Examination and Possible Risk Factors against the Incidence of Cervical Cancer in a Low Human Papillomavirus Vaccination Coverage: An Ecological Study in Japan.}, journal = {Cancers}, volume = {13}, number = {19}, pages = {}, pmid = {34638269}, issn = {2072-6694}, support = {18K17321, 18H03026,19KK0242,and 21K17250//Japan Society for the Promotion of Science/ ; }, abstract = {Cervical cancer (CC) is one of the most common gynecological malignancies in females, mainly caused by human papillomavirus (HPV). In countries with lower HPV vaccine coverage, such as Japan, medical examination may play a key role in decreasing CC incidence. This study aimed to quantify the effect of medical examination on cervical cancer (CC) incidence in Japan, considering the effects of possible risk factors. By collecting Japan's Prefectural data on CC incidence (2013-2017), incidence of sexually transmitted diseases (STDs; Chlamydia, Herpes, Condyloma, and Gonorrhea; 1993-2012), screening and detailed examination rate against CC (2013-2016), smoking rate (2001-2013), economic status (disposable income and economic surplus; 2014-2015), and education status (2015), we analyzed associations among them using Pearson's correlation coefficients. Additionally, assuming that the incidence of STDs reflects the frequency of risky sexual behavior at the co-infection point with HPV, we constructed generalized linear models to predict CC incidence, taking a 5-20-year time-lag between incidences of STDs and the CC incidence. Against CC incidence, Chlamydia in females and Gonorrhea in males with a 15-year time-lag showed positive associations, while Condyloma in both genders with a 15-year time-lag, screening rate, economic status, and smoking rate showed negative associations. An increase in screening test rate by 10% was estimated to decrease CC incidence by 9.6%. This means that screening tests decrease CC incidence effectively, but not drastically, suggesting the need for additional countermeasures for CC prevention.}, } @article {pmid34637742, year = {2021}, author = {Lofgren, LA and Stajich, JE}, title = {Fungal biodiversity and conservation mycology in light of new technology, big data, and changing attitudes.}, journal = {Current biology : CB}, volume = {31}, number = {19}, pages = {R1312-R1325}, pmid = {34637742}, issn = {1879-0445}, support = {R01 AI130128/AI/NIAID NIH HHS/United States ; }, mesh = {Attitude ; Big Data ; Biodiversity ; *Ecosystem ; Fungi/genetics ; Humans ; *Mycology ; Technology ; }, abstract = {Fungi have successfully established themselves across seemingly every possible niche, substrate, and biome. They are fundamental to biogeochemical cycling, interspecies interactions, food production, and drug bioprocessing, as well as playing less heroic roles as difficult to treat human infections and devastating plant pathogens. Despite community efforts to estimate and catalog fungal diversity, we have only named and described a minute fraction of the fungal world. The identification, characterization, and conservation of fungal diversity is paramount to preserving fungal bioresources, and to understanding and predicting ecosystem cycling and the evolution and epidemiology of fungal disease. Although species and ecosystem conservation are necessarily the foundation of preserving this diversity, there is value in expanding our definition of conservation to include the protection of biological collections, ecological metadata, genetic and genomic data, and the methods and code used for our analyses. These definitions of conservation are interdependent. For example, we need metadata on host specificity and biogeography to understand rarity and set priorities for conservation. To aid in these efforts, we need to draw expertise from diverse fields to tie traditional taxonomic knowledge to data obtained from modern -omics-based approaches, and support the advancement of diverse research perspectives. We also need new tools, including an updated framework for describing and tracking species known only from DNA, and the continued integration of functional predictions to link genetic diversity to functional and ecological diversity. Here, we review the state of fungal diversity research as shaped by recent technological advancements, and how changing viewpoints in taxonomy, -omics, and systematics can be integrated to advance mycological research and preserve fungal biodiversity.}, } @article {pmid34636724, year = {2021}, author = {Di, C and Murga Moreno, J and Salazar-Tortosa, DF and Lauterbur, ME and Enard, D}, title = {Decreased recent adaptation at human mendelian disease genes as a possible consequence of interference between advantageous and deleterious variants.}, journal = {eLife}, volume = {10}, number = {}, pages = {}, pmid = {34636724}, issn = {2050-084X}, support = {R35 GM142677/GM/NIGMS NIH HHS/United States ; }, mesh = {Databases, Genetic ; Evolution, Molecular ; Genetic Diseases, Inborn/*genetics ; *Genetic Variation ; Genome, Human/*genetics ; Humans ; }, abstract = {Advances in genome sequencing have improved our understanding of the genetic basis of human diseases, and thousands of human genes have been associated with different diseases. Recent genomic adaptation at disease genes has not been well characterized. Here, we compare the rate of strong recent adaptation in the form of selective sweeps between mendelian, non-infectious disease genes and non-disease genes across distinct human populations from the 1000 Genomes Project. We find that mendelian disease genes have experienced far less selective sweeps compared to non-disease genes especially in Africa. Investigating further the possible causes of the sweep deficit at disease genes, we find that this deficit is very strong at disease genes with both low recombination rates and with high numbers of associated disease variants, but is almost non-existent at disease genes with higher recombination rates or lower numbers of associated disease variants. Because segregating recessive deleterious variants have the ability to interfere with adaptive ones, these observations strongly suggest that adaptation has been slowed down by the presence of interfering recessive deleterious variants at disease genes. These results suggest that disease genes suffer from a transient inability to adapt as fast as the rest of the genome.}, } @article {pmid34634795, year = {2022}, author = {Zhou, S and Liu, B and Han, Y and Wang, Y and Chen, L and Wu, Z and Yang, J}, title = {ZOVER: the database of zoonotic and vector-borne viruses.}, journal = {Nucleic acids research}, volume = {50}, number = {D1}, pages = {D943-D949}, pmid = {34634795}, issn = {1362-4962}, mesh = {Animals ; Chiroptera/virology ; Communicable Diseases, Emerging/*epidemiology/transmission/virology ; Culicidae/virology ; *Databases, Factual ; Datasets as Topic ; Disease Vectors/classification ; Epidemiological Monitoring ; Host-Pathogen Interactions ; Humans ; Internet ; Molecular Sequence Annotation ; Rodentia/virology ; *Software ; Ticks/virology ; Virus Diseases/*epidemiology/transmission/virology ; Viruses/classification/genetics/*pathogenicity ; Zoonoses/*epidemiology/transmission/virology ; }, abstract = {Emerging infectious diseases significantly threaten global public health and socioeconomic security. The majority of emerging infectious disease outbreaks are caused by zoonotic/vector-borne viruses. Bats and rodents are the two most important reservoir hosts of many zoonotic viruses that can cross species barriers to infect humans, whereas mosquitos and ticks are well-established major vectors of many arboviral diseases. Moreover, some emerging zoonotic diseases require a vector to spread or are intrinsically vector-borne and zoonotically transmitted. In this study, we present a newly upgraded database of zoonotic and vector-borne viruses designated ZOVER (http://www.mgc.ac.cn/ZOVER). It incorporates two previously released databases, DBatVir and DRodVir, for bat- and rodent-associated viruses, respectively, and further collects up-to-date knowledge on mosquito- and tick-associated viruses to establish a comprehensive online resource for zoonotic and vector-borne viruses. Additionally, it integrates a set of online visualization tools for convenient comparative analyses to facilitate the discovery of potential patterns of virome diversity and ecological characteristics between/within different viral hosts/vectors. The ZOVER database will be a valuable resource for virologists, zoologists and epidemiologists to better understand the diversity and dynamics of zoonotic and vector-borne viruses and conduct effective surveillance to monitor potential interspecies spillover for efficient prevention and control of future emerging zoonotic diseases.}, } @article {pmid34634737, year = {2021}, author = {Wang, X and Zhang, C and Wang, C and Liu, G and Wang, H}, title = {GIS-based for prediction and prevention of environmental geological disaster susceptibility: From a perspective of sustainable development.}, journal = {Ecotoxicology and environmental safety}, volume = {226}, number = {}, pages = {112881}, doi = {10.1016/j.ecoenv.2021.112881}, pmid = {34634737}, issn = {1090-2414}, mesh = {China ; Cities ; *Disasters ; Environment ; *Geographic Information Systems ; Humans ; Sustainable Development ; }, abstract = {Geological disasters seriously threaten the safety of human life, property, ecological resources, and the environment. Effective control of geological disasters is the focus of achieving sustainable social development. The Helong City (Jilin Province, China) was selected as the case study. Combined with GIS technology, a new integrated prediction model of geological disaster susceptibility was developed to improve the accuracy of geological disaster assessment, reduce the cost of geological disaster treatment, and ensure the sustainable development of ecological environment. The research results showed that elevation and normalized difference vegetation index (NDVI) were the key factors affecting susceptibility. Compared with the conventional model, the accuracy of the developing integrated model FR-DT and FR-RF was improved by more than 6%, and the disaster points were more concentrated in the high susceptibility zone. Statistical results of disaster treatment cost estimation and gross domestic product (GDP) value showed that the integrated model can save about 10% of treatment cost, and the ratio of total GDP/disaster governance cost was higher. The performance of the integrated model FR-DT and FR-RF had obvious advantages over the conventional model in terms of prediction accuracy, prevention pertinence, and prevention cost. These research results promote the advancement of geological disaster prevention and control technology, ensure the safety of the geological environment, and are of great significance to the sustainable development of the regional economy.}, } @article {pmid34633184, year = {2021}, author = {Xue, J and Derks, RJE and Hoang, L and Giera, M and Siuzdak, G}, title = {Proteomics with Enhanced In-Source Fragmentation/Annotation: Applying XCMS-EISA Informatics and Q-MRM High-Sensitivity Quantification.}, journal = {Journal of the American Society for Mass Spectrometry}, volume = {32}, number = {11}, pages = {2644-2654}, pmid = {34633184}, issn = {1879-1123}, support = {R35 GM130385/GM/NIGMS NIH HHS/United States ; }, mesh = {Ions/analysis/chemistry ; Molecular Sequence Annotation/*methods ; Peptide Fragments/*analysis/*chemistry ; Proteomics/*methods ; Sensitivity and Specificity ; }, abstract = {Enhanced in-source fragmentation/annotation (EISA) has recently been shown to produce fragment ions that match tandem mass spectrometry data across a wide range of small molecules. EISA has been developed to facilitate data-dependent acquisition (DDA), data-independent acquisiton (DIA), and multiple-reaction monitoring (MRM), enabling molecular identifications in untargeted metabolomics and targeted quantitative single-quadrupole MRM (Q-MRM) analyses. Here, EISA has been applied to peptide-based proteomic analysis using optimized in-source fragmentation to generate fragmentation patterns for a mixture of 38 peptides, which were comparable to the b- and y-type fragment ions typically observed in tandem MS experiments. The optimal in-source fragmentation conditions at which high-abundance peptide fragments and precursor ions coexist were compared with automated data-dependent acquisition (DDA) in the same quadrupole time-of-flight (QTOF-MS) mass spectrometer, generating a significantly higher fragment percentage of peptides from both singly and doubly charged b- and y-type fragment (b[+], y[+], b[2+], and y[2+]) ions. Higher fragment percentages were also observed for these fragment ion series over linear ion trap instrumentation. An XCMS-EISA annotation/deconvolution program was developed, making use of the retention time and peak shape continuity between precursor fragment ions, to perform automated proteomic data analysis on the enhanced in-source fragments. Post-translational modification (PTM) characterization on peptides was demonstrated with EISA, producing fragment ions corresponding to a neutral loss of phosphoric acid with greater intensity than observed with DDA on a QTOF-MS. Moreover, Q-MRM demonstrated the ability to use EISA for peptide quantification. The availability of more sophisticated in-source fragmentation informatics, beyond XCMS-EISA, will further enable EISA for sensitive autonomous identification and Q-MRM quantitative analyses in proteomics.}, } @article {pmid34630072, year = {2021}, author = {Chang, CM and Wu, PC and Lin, JR and Jan Wu, YJ and Luo, SF and Hsue, YT and Lan, JL and Pan, TL and Wu, YT and Yu, KH and Wei, YH and Chang, HH}, title = {Herbal Formula SS-1 Increases Tear Secretion for Sjögren's Syndrome.}, journal = {Frontiers in pharmacology}, volume = {12}, number = {}, pages = {645437}, pmid = {34630072}, issn = {1663-9812}, abstract = {Background: Sjögren's syndrome (SS) is an autoimmune inflammatory disease that primarily affects the exocrine glands, leading to glandular dysfunction. The hallmark symptoms of SS are dry eyes and mouth, compromising the quality of life of patients and decreasing their capacity to perform their daily activities. Objective: This study aims to evaluate the efficacy of the herbal formula SS-1 for its potential therapeutic benefits for patients with Sjögren's syndrome. Materials and Methods: The bioactivity profile of SS-1 was determined using four different SS-1 concentrations across 12 human primary cell systems of the BioMAP profile. After that, a randomized, double-blind, crossover, placebo-controlled trial was performed including 57 patients treated with SS-1 for 28 weeks. Results: Biologically multiplexed activity profiling in cell-based models indicated that SS-1 exerted anti-proliferative activity in B cells and promoted anti-inflammatory and immunomodulatory activity. In the clinical trial, Schirmer's test results revealed significant improvements in both eyes, with increases of 3.42 mm (95% CI, 2.44-4.41 mm) and 3.45 mm (95% CI, 2.32-4.59 mm), respectively, and a significant reduction in artificial tear use, which was -1.38 times/day, 95% CI, -1.95 to -0.81 times/day. Moreover, the increases in B-cell activating factor (BAFF) and B-cell maturation antigen (BCMA) levels were dampened by 53.20% (295.29 versus 555.02 pg/ml) and 58.33% (99.16 versus 169.99 pg/ml), respectively. Conclusion: SS-1 treatment significantly inhibited B-cell maturation antigen. No serious drug-related adverse effects were observed. Oral SS-1 administration may be a complementary treatment for Sjögren's syndrome.}, } @article {pmid34628147, year = {2021}, author = {Pitacco, V and Mistri, M and Granata, T and Moruzzi, L and Meloni, ML and Massara, F and Sfriso, A and Sfriso, AA and Munari, C}, title = {Habitat heterogeneity: A confounding factor for the effect of pollutants on macrobenthic community in coastal waters.}, journal = {Marine environmental research}, volume = {172}, number = {}, pages = {105499}, doi = {10.1016/j.marenvres.2021.105499}, pmid = {34628147}, issn = {1879-0291}, mesh = {Animals ; Ecosystem ; Environmental Monitoring ; *Environmental Pollutants ; Geologic Sediments ; *Invertebrates ; Metals ; }, abstract = {Discrepancies were found between Ecological Status of sediments evaluated though the analysis of macrobenthic community and chemical analyses along a heavily trafficked and contaminated maritime seaway in Tyrrhenian Sea. Chemical analyses showed some sites highly contaminated by PAHs and metals with values exceeding thresholds for Good Chemical status and representing potential toxicological risk for benthic animals. Conversely, macrobenthic communities were highly rich and diverse, with Ecological Status (through M-AMBI) Good and High at each site. Sampling depth, total organic carbon, and total nitrogen were the major factors influencing biotic indices (AMBI, M-AMBI, S, H), even if concentrations of PAHs and metals (V, As, and Fe) contributed in explaining a part of indices variability. Habitat heterogeneity of sampled sites is likely acting as a confounding factor for two reasons: (1) high variability of environmental parameters leads to high richness and diversity, to which M-AMBI is sensitive, and (2) environmental parameters explained part of the variability of indices, together with contaminants. Our results suggested the importance of considering natural variability as a fundamental step of environmental impact assessment, for the correct interpretation of biotic indices.}, } @article {pmid34627532, year = {2021}, author = {van der Wal, JM and van Borkulo, CD and Deserno, MK and Breedvelt, JJF and Lees, M and Lokman, JC and Borsboom, D and Denys, D and van Holst, RJ and Smidt, MP and Stronks, K and Lucassen, PJ and van Weert, JCM and Sloot, PMA and Bockting, CL and Wiers, RW}, title = {Advancing urban mental health research: from complexity science to actionable targets for intervention.}, journal = {The lancet. Psychiatry}, volume = {8}, number = {11}, pages = {991-1000}, doi = {10.1016/S2215-0366(21)00047-X}, pmid = {34627532}, issn = {2215-0374}, support = {U01_AG09740-13S2/AG/NIA NIH HHS/United States ; P01_AG005842/AG/NIA NIH HHS/United States ; P01_AG08291/AG/NIA NIH HHS/United States ; P30_AG12815/AG/NIA NIH HHS/United States ; R21_AG025169/AG/NIA NIH HHS/United States ; Y1-AG-4553-01/AG/NIA NIH HHS/United States ; IAG_BSR06-11/AG/NIA NIH HHS/United States ; OGHA_04-064/GD/OGDP CDC HHS/United States ; HHSN271201300071C/AG/NIA NIH HHS/United States ; }, mesh = {Adult ; Anxiety Disorders/diagnosis/epidemiology ; COVID-19/diagnosis/epidemiology/*psychology/virology ; Depressive Disorder/diagnosis/epidemiology ; Ecosystem ; Female ; Health Status Indicators ; Humans ; Male ; Mental Disorders/diagnosis/*epidemiology/psychology/therapy ; Mental Health/*standards/trends ; Meta-Analysis as Topic ; Prevalence ; SARS-CoV-2/genetics ; Social Network Analysis ; Substance-Related Disorders/diagnosis/epidemiology ; Systems Analysis ; Urban Health/*standards/trends ; }, abstract = {Urbanisation and common mental disorders (CMDs; ie, depressive, anxiety, and substance use disorders) are increasing worldwide. In this Review, we discuss how urbanicity and risk of CMDs relate to each other and call for a complexity science approach to advance understanding of this interrelationship. We did an ecological analysis using data on urbanicity and CMD burden in 191 countries. We found a positive, non-linear relationship with a higher CMD prevalence in more urbanised countries, particularly for anxiety disorders. We also did a review of meta-analytic studies on the association between urban factors and CMD risk. We identified factors relating to the ambient, physical, and social urban environment and showed differences per diagnosis of CMDs. We argue that factors in the urban environment are likely to operate as a complex system and interact with each other and with individual city inhabitants (including their psychological and neurobiological characteristics) to shape mental health in an urban context. These interactions operate on various timescales and show feedback loop mechanisms, rendering system behaviour characterised by non-linearity that is hard to predict over time. We present a conceptual framework for future urban mental health research that uses a complexity science approach. We conclude by discussing how complexity science methodology (eg, network analyses, system-dynamic modelling, and agent-based modelling) could enable identification of actionable targets for treatment and policy, aimed at decreasing CMD burdens in an urban context.}, } @article {pmid34626884, year = {2021}, author = {Russo, S and Besmer, MD and Blumensaat, F and Bouffard, D and Disch, A and Hammes, F and Hess, A and Lürig, M and Matthews, B and Minaudo, C and Morgenroth, E and Tran-Khac, V and Villez, K}, title = {The value of human data annotation for machine learning based anomaly detection in environmental systems.}, journal = {Water research}, volume = {206}, number = {}, pages = {117695}, doi = {10.1016/j.watres.2021.117695}, pmid = {34626884}, issn = {1879-2448}, mesh = {Algorithms ; *Data Curation ; Humans ; *Machine Learning ; }, abstract = {Anomaly detection is the process of identifying unexpected data samples in datasets. Automated anomaly detection is either performed using supervised machine learning models, which require a labelled dataset for their calibration, or unsupervised models, which do not require labels. While academic research has produced a vast array of tools and machine learning models for automated anomaly detection, the research community focused on environmental systems still lacks a comparative analysis that is simultaneously comprehensive, objective, and systematic. This knowledge gap is addressed for the first time in this study, where 15 different supervised and unsupervised anomaly detection models are evaluated on 5 different environmental datasets from engineered and natural aquatic systems. To this end, anomaly detection performance, labelling efforts, as well as the impact of model and algorithm tuning are taken into account. As a result, our analysis reveals the relative strengths and weaknesses of the different approaches in an objective manner without bias for any particular paradigm in machine learning. Most importantly, our results show that expert-based data annotation is extremely valuable for anomaly detection based on machine learning.}, } @article {pmid34624284, year = {2022}, author = {Mishra, M and Acharyya, T and Chand, P and Santos, CAG and Silva, RMD and Santos, CACD and Pradhan, S and Kar, D}, title = {Response of long- to short-term tidal inlet morphodynamics on the ecological ramification of Chilika lake, the tropical Ramsar wetland in India.}, journal = {The Science of the total environment}, volume = {807}, number = {Pt 2}, pages = {150769}, doi = {10.1016/j.scitotenv.2021.150769}, pmid = {34624284}, issn = {1879-1026}, mesh = {Bays ; *Cyclonic Storms ; India ; Lakes ; *Wetlands ; }, abstract = {The long- to short-term morphodynamic response in low-lying coastal wetlands raises serious concerns worldwide about the loss of their biodiversity and ecological ramifications due to change in tidal amplitude and cyclonic events. One such place worth studying is Chilika lake, India, a prominent Ramsar site, the largest brackish water lagoon in Asia, and the second-largest coastal lagoon in the world. It experiences frequent cyclone landfalls and strong littoral drift that tends to open/close the tidal inlet. The goal of this study was to analyze the response of slow onset events such as long- (1952-2020) to short-term (~annual scale from 1989 to 2020) tidal inlet movement, shoreline change (1990-2020 with almost every five-year interval), spit morphodynamics (~annual scale from 1989 to 2020) on ecological ramification in Chilika lake as well as the implications of sudden onset event such as cyclonic landfall. In this study, we used the Digital Shoreline Change Analysis System (DSAS) to compute the statistics of shoreline change rate by calculating end point rate (EPR) values for short-term shoreline change (1990, 1995, 2000, 2005, 2011, 2016, and 2020) and weighted linear regression (WLR) for long-term shoreline change (1990-2020). The results show that Chilika lake experienced both erosion and accretion processes with a remarkably high erosion rate of 19.87 m year[-1] and accretion of 16.91 m year[-1] during a long-term scale (1990-2020). The average erosion and accretion rates were 2.25 m year[-1] and 4.67 m year[-1], respectively, during the past three decades (1990-2020). The short-term analysis suggests that the highest mean erosion of 4.37 m year[-1] occurred during 2005-2011, mainly due to cyclonic storms, reduction in sediment discharge, and lunar eclipse, which induced tide with very high amplitude in August 2008. Overall, the annual scale analysis of tidal inlet shows a shifting trend towards the northward side even after the artificial opening of an inlet in 2000. It can be ascribed mainly to the prevalent direction of longshore drift along this coast. This study observed that the landfall of cyclones significantly affects the spit morphodynamics and opening of the tidal inlet, which defines the inflow of the seawater into the lagoon and further substantial impacts on the ecological ramification. The current study's methodology can be extended to comprehend the response of long- to short-term changes of the tidal inlet, shoreline, and spit morphodynamics on the ecological ramification of coastal lagoons worldwide along with impacts of sudden-onset events caused by cyclonic landfall.}, } @article {pmid34623501, year = {2022}, author = {Odabasi, E and Turan, M}, title = {The importance of body core temperature evaluation in balneotherapy.}, journal = {International journal of biometeorology}, volume = {66}, number = {1}, pages = {25-33}, pmid = {34623501}, issn = {1432-1254}, mesh = {*Balneology ; Temperature ; }, abstract = {It is not wrong to say that there are no application standards or best practices in balneotherapy considering traditional applications. There is not enough information about how changes in body temperature, duration, and frequency of exposure to heat affect therapeutic outcomes of balneotherapeutic applications. Body core temperature (BCT) is probably the best parameter for expressing the heat load of the body and can be used to describe the causal relationship between heat exposure and its effects. There are several reasons to take BCT changes into account; for example, it can be used for individualized treatment planning, defining the consequences of thermal effects, developing disease-specific approaches, avoiding adverse effects, and designing clinical trials. The reasons why BCT changes should be considered instead of conventional measures will be discussed while explaining the effects of balneotherapy in this article, along with a discussion of BCT measurement in balneotherapy practice.}, } @article {pmid34621536, year = {2021}, author = {Delclos, PJ and Adhikari, K and Hassan, O and Cambric, JE and Matuk, AG and Presley, RI and Tran, J and Sriskantharajah, V and Meisel, RP}, title = {Thermal tolerance and preference are both consistent with the clinal distribution of house fly proto-Y chromosomes.}, journal = {Evolution letters}, volume = {5}, number = {5}, pages = {495-506}, pmid = {34621536}, issn = {2056-3744}, abstract = {Selection pressures can vary within localized areas and across massive geographical scales. Temperature is one of the best studied ecologically variable abiotic factors that can affect selection pressures across multiple spatial scales. Organisms rely on physiological (thermal tolerance) and behavioral (thermal preference) mechanisms to thermoregulate in response to environmental temperature. In addition, spatial heterogeneity in temperatures can select for local adaptation in thermal tolerance, thermal preference, or both. However, the concordance between thermal tolerance and preference across genotypes and sexes within species and across populations is greatly understudied. The house fly, Musca domestica, is a well-suited system to examine how genotype and environment interact to affect thermal tolerance and preference. Across multiple continents, house fly males from higher latitudes tend to carry the male-determining gene on the Y chromosome, whereas those from lower latitudes usually have the male determiner on the third chromosome. We tested whether these two male-determining chromosomes differentially affect thermal tolerance and preference as predicted by their geographical distributions. We identify effects of genotype and developmental temperature on male thermal tolerance and preference that are concordant with the natural distributions of the chromosomes, suggesting that temperature variation across the species range contributes to the maintenance of the polymorphism. In contrast, female thermal preference is bimodal and largely independent of congener male genotypes. These sexually dimorphic thermal preferences suggest that temperature-dependent mating dynamics within populations could further affect the distribution of the two chromosomes. Together, the differences in thermal tolerance and preference across sexes and male genotypes suggest that different selection pressures may affect the frequencies of the male-determining chromosomes across different spatial scales.}, } @article {pmid34614003, year = {2021}, author = {Rinkert, A and Misiewicz, TM and Carter, BE and Salmaan, A and Whittall, JB}, title = {Bird nests as botanical time capsules: DNA barcoding identifies the contents of contemporary and historical nests.}, journal = {PloS one}, volume = {16}, number = {10}, pages = {e0257624}, pmid = {34614003}, issn = {1932-6203}, mesh = {Animals ; Botany ; Computational Biology ; DNA Barcoding, Taxonomic ; DNA, Plant/analysis/genetics ; *Ecosystem ; *Nesting Behavior ; Plants/classification/*genetics ; *Sparrows/physiology ; }, abstract = {Bird nests in natural history collections are an abundant yet vastly underutilized source of genetic information. We sequenced the nuclear ribosomal internal transcribed spacer to identify plant species used as nest material in two contemporary (2003 and 2018) and two historical (both 1915) nest specimens constructed by Song Sparrows (Melospiza melodia) and Savannah Sparrows (Passerculus sandwichensis). A total of 13 (22%) samples yielded single, strong bands that could be identified using GenBank resources: six plants (Angiospermae), six green algae (Chlorophyta), and one ciliate (Ciliophora). Two native plant species identified in the nests included Festuca microstachys, which was introduced to the nest collection site by restoration practitioners, and Rosa californica, identified in a nest collected from a lost habitat that existed about 100 years ago. Successful sequencing was correlated with higher sample mass and DNA quality, suggesting future studies should select larger pieces of contiguous material from nests and materials that appear to have been fresh when incorporated into the nest. This molecular approach was used to distinguish plant species that were not visually identifiable, and did not require disassembling the nest specimens as is a traditional practice with nest material studies. The many thousands of nest specimens in natural history collections hold great promise as sources of genetic information to address myriad ecological questions.}, } @article {pmid34610848, year = {2021}, author = {Pfrengle, S and Neukamm, J and Guellil, M and Keller, M and Molak, M and Avanzi, C and Kushniarevich, A and Montes, N and Neumann, GU and Reiter, E and Tukhbatova, RI and Berezina, NY and Buzhilova, AP and Korobov, DS and Suppersberger Hamre, S and Matos, VMJ and Ferreira, MT and González-Garrido, L and Wasterlain, SN and Lopes, C and Santos, AL and Antunes-Ferreira, N and Duarte, V and Silva, AM and Melo, L and Sarkic, N and Saag, L and Tambets, K and Busso, P and Cole, ST and Avlasovich, A and Roberts, CA and Sheridan, A and Cessford, C and Robb, J and Krause, J and Scheib, CL and Inskip, SA and Schuenemann, VJ}, title = {Mycobacterium leprae diversity and population dynamics in medieval Europe from novel ancient genomes.}, journal = {BMC biology}, volume = {19}, number = {1}, pages = {220}, pmid = {34610848}, issn = {1741-7007}, support = {/WT_/Wellcome Trust/United Kingdom ; 200368/Z/15/Z/WT_/Wellcome Trust/United Kingdom ; 2000368/Z/15/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Europe ; Genome, Bacterial/genetics ; Humans ; Leprosy/genetics ; *Mycobacterium leprae/genetics ; Population Dynamics ; }, abstract = {BACKGROUND: Hansen's disease (leprosy), widespread in medieval Europe, is today mainly prevalent in tropical and subtropical regions with around 200,000 new cases reported annually. Despite its long history and appearance in historical records, its origins and past dissemination patterns are still widely unknown. Applying ancient DNA approaches to its major causative agent, Mycobacterium leprae, can significantly improve our understanding of the disease's complex history. Previous studies have identified a high genetic continuity of the pathogen over the last 1500 years and the existence of at least four M. leprae lineages in some parts of Europe since the Early Medieval period.

RESULTS: Here, we reconstructed 19 ancient M. leprae genomes to further investigate M. leprae's genetic variation in Europe, with a dedicated focus on bacterial genomes from previously unstudied regions (Belarus, Iberia, Russia, Scotland), from multiple sites in a single region (Cambridgeshire, England), and from two Iberian leprosaria. Overall, our data confirm the existence of similar phylogeographic patterns across Europe, including high diversity in leprosaria. Further, we identified a new genotype in Belarus. By doubling the number of complete ancient M. leprae genomes, our results improve our knowledge of the past phylogeography of M. leprae and reveal a particularly high M. leprae diversity in European medieval leprosaria.

CONCLUSIONS: Our findings allow us to detect similar patterns of strain diversity across Europe with branch 3 as the most common branch and the leprosaria as centers for high diversity. The higher resolution of our phylogeny tree also refined our understanding of the interspecies transfer between red squirrels and humans pointing to a late antique/early medieval transmission. Furthermore, with our new estimates on the past population diversity of M. leprae, we gained first insights into the disease's global history in relation to major historic events such as the Roman expansion or the beginning of the regular transatlantic long distance trade. In summary, our findings highlight how studying ancient M. leprae genomes worldwide improves our understanding of leprosy's global history and can contribute to current models of M. leprae's worldwide dissemination, including interspecies transmissions.}, } @article {pmid34608637, year = {2021}, author = {Freschet, GT and Pagès, L and Iversen, CM and Comas, LH and Rewald, B and Roumet, C and Klimešová, J and Zadworny, M and Poorter, H and Postma, JA and Adams, TS and Bagniewska-Zadworna, A and Bengough, AG and Blancaflor, EB and Brunner, I and Cornelissen, JHC and Garnier, E and Gessler, A and Hobbie, SE and Meier, IC and Mommer, L and Picon-Cochard, C and Rose, L and Ryser, P and Scherer-Lorenzen, M and Soudzilovskaia, NA and Stokes, A and Sun, T and Valverde-Barrantes, OJ and Weemstra, M and Weigelt, A and Wurzburger, N and York, LM and Batterman, SA and Gomes de Moraes, M and Janeček, Š and Lambers, H and Salmon, V and Tharayil, N and McCormack, ML}, title = {A starting guide to root ecology: strengthening ecological concepts and standardising root classification, sampling, processing and trait measurements.}, journal = {The New phytologist}, volume = {232}, number = {3}, pages = {973-1122}, pmid = {34608637}, issn = {1469-8137}, mesh = {Databases, Factual ; Ecology ; *Ecosystem ; Phenotype ; *Plants ; }, abstract = {In the context of a recent massive increase in research on plant root functions and their impact on the environment, root ecologists currently face many important challenges to keep on generating cutting-edge, meaningful and integrated knowledge. Consideration of the below-ground components in plant and ecosystem studies has been consistently called for in recent decades, but methodology is disparate and sometimes inappropriate. This handbook, based on the collective effort of a large team of experts, will improve trait comparisons across studies and integration of information across databases by providing standardised methods and controlled vocabularies. It is meant to be used not only as starting point by students and scientists who desire working on below-ground ecosystems, but also by experts for consolidating and broadening their views on multiple aspects of root ecology. Beyond the classical compilation of measurement protocols, we have synthesised recommendations from the literature to provide key background knowledge useful for: (1) defining below-ground plant entities and giving keys for their meaningful dissection, classification and naming beyond the classical fine-root vs coarse-root approach; (2) considering the specificity of root research to produce sound laboratory and field data; (3) describing typical, but overlooked steps for studying roots (e.g. root handling, cleaning and storage); and (4) gathering metadata necessary for the interpretation of results and their reuse. Most importantly, all root traits have been introduced with some degree of ecological context that will be a foundation for understanding their ecological meaning, their typical use and uncertainties, and some methodological and conceptual perspectives for future research. Considering all of this, we urge readers not to solely extract protocol recommendations for trait measurements from this work, but to take a moment to read and reflect on the extensive information contained in this broader guide to root ecology, including sections I-VII and the many introductions to each section and root trait description. Finally, it is critical to understand that a major aim of this guide is to help break down barriers between the many subdisciplines of root ecology and ecophysiology, broaden researchers' views on the multiple aspects of root study and create favourable conditions for the inception of comprehensive experiments on the role of roots in plant and ecosystem functioning.}, } @article {pmid34608378, year = {2021}, author = {Voigt, K and James, TY and Kirk, PM and Santiago, ALCMA and Waldman, B and Griffith, GW and Fu, M and Radek, R and Strassert, JFH and Wurzbacher, C and Jerônimo, GH and Simmons, DR and Seto, K and Gentekaki, E and Hurdeal, VG and Hyde, KD and Nguyen, TTT and Lee, HB}, title = {Early-diverging fungal phyla: taxonomy, species concept, ecology, distribution, anthropogenic impact, and novel phylogenetic proposals.}, journal = {Fungal diversity}, volume = {109}, number = {1}, pages = {59-98}, pmid = {34608378}, issn = {1560-2745}, abstract = {The increasing number of new fungal species described from all over the world along with the use of genetics to define taxa, has dramatically changed the classification system of early-diverging fungi over the past several decades. The number of phyla established for non-Dikarya fungi has increased from 2 to 17. However, to date, both the classification and phylogeny of the basal fungi are still unresolved. In this article, we review the recent taxonomy of the basal fungi and re-evaluate the relationships among early-diverging lineages of fungal phyla. We also provide information on the ecology and distribution in Mucoromycota and highlight the impact of chytrids on amphibian populations. Species concepts in Chytridiomycota, Aphelidiomycota, Rozellomycota, Neocallimastigomycota are discussed in this paper. To preserve the current application of the genus Nephridiophaga (Chytridiomycota: Nephridiophagales), a new type species, Nephridiophaga blattellae, is proposed.}, } @article {pmid34608157, year = {2021}, author = {Hurlbert, AH and Olsen, AM and Sawyer, MM and Winner, PM}, title = {The Avian Diet Database as a source of quantitative information on bird diets.}, journal = {Scientific data}, volume = {8}, number = {1}, pages = {260}, pmid = {34608157}, issn = {2052-4463}, support = {EF-1702708//National Science Foundation (NSF)/ ; }, mesh = {Animals ; *Birds ; *Databases, Factual ; Diet/*veterinary ; Ecosystem ; North America ; Seasons ; }, abstract = {This data paper describes a compilation of 73,075 quantitative diet data records for 759 primarily North American bird species, providing standardized information not just on the diet itself, but on the context for that diet information including the year, season, location, and habitat type of each study. The methods used for collecting and cleaning these data are described, and we present tools for summarizing and visualizing diet information by bird species or prey.}, } @article {pmid34607270, year = {2021}, author = {Stoffel, M and Neubauer, AB and Ditzen, B}, title = {How to assess and interpret everyday life salivary cortisol measures: A tutorial on practical and statistical considerations.}, journal = {Psychoneuroendocrinology}, volume = {133}, number = {}, pages = {105391}, doi = {10.1016/j.psyneuen.2021.105391}, pmid = {34607270}, issn = {1873-3360}, mesh = {Biomarkers/analysis ; Data Interpretation, Statistical ; Humans ; *Hydrocortisone/analysis ; Research Design ; *Saliva/chemistry ; Stress, Psychological/metabolism ; }, abstract = {Salivary cortisol has been the central marker in psychoneuroendocrinological stress research for three decades. Given the technological possibilities to assess data in ecologically valid circumstances, many studies have implemented longitudinal assessments of salivary cortisol in study participants' everyday life. Such studies bear the potential to understand real-life associations of cortisol with psychological traits, states, and health variables. Furthermore, changes in the neuroendocrine regulation and in cortisol reactivity can be used to evaluate the effects of behavioral interventions in real-life circumstances. While standardized paradigms have been developed to measure cortisol in laboratory settings, there is high heterogeneity in the assessment, statistical processing, and interpretation of everyday life cortisol measures. This methodological tutorial aims at summarizing important knowledge which had been accumulated during the past two decades and which could be used to set up an ambulatory assessment study focusing on salivary cortisol in everyday life. Practical advice for possible strategies at all stages of the research process is outlined in detail. Additionally, an example on how to statistically process cortisol data in a multilevel framework (including syntax) is provided. In these analyses, we investigate within- and between-person research questions regarding the association between stress and cortisol in daily life. Thus, the present work (a) can be used as tutorial for setting up everyday life studies focusing on the assessment of salivary cortisol, and (b) can be useful to avoid inconsistencies in study planning, data assessment and data processing in future studies.}, } @article {pmid34602364, year = {2021}, author = {Doherty, JF and Chai, X and Cope, LE and de Angeli Dutra, D and Milotic, M and Ni, S and Park, E and Filion, A}, title = {The rise of big data in disease ecology.}, journal = {Trends in parasitology}, volume = {37}, number = {12}, pages = {1034-1037}, doi = {10.1016/j.pt.2021.09.003}, pmid = {34602364}, issn = {1471-5007}, mesh = {*Big Data ; *Ecology ; }, abstract = {Big data have become readily available to explore patterns in large-scale disease ecology. However, the rate at which these public databases are exploited remains unknown. We highlight trends in big data usage in disease ecology during the past decade and encourage researchers to integrate big data into their study framework.}, } @article {pmid34601904, year = {2021}, author = {Santos, FP and Pacheco, JM and Santos, FC}, title = {The complexity of human cooperation under indirect reciprocity.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {376}, number = {1838}, pages = {20200291}, pmid = {34601904}, issn = {1471-2970}, mesh = {Biological Evolution ; *Cooperative Behavior ; Game Theory ; Humans ; *Models, Psychological ; Morals ; Social Norms ; }, abstract = {Indirect reciprocity (IR) is a key mechanism to understand cooperation among unrelated individuals. It involves reputations and complex information processing, arising from social interactions. By helping someone, individuals may improve their reputation, which may be shared in a population and change the predisposition of others to reciprocate in the future. The reputation of individuals depends, in turn, on social norms that define a good or bad action, offering a computational and mathematical appealing way of studying the evolution of moral systems. Over the years, theoretical and empirical research has unveiled many features of cooperation under IR, exploring norms with varying degrees of complexity and information requirements. Recent results suggest that costly reputation spread, interaction observability and empathy are determinants of cooperation under IR. Importantly, such characteristics probably impact the level of complexity and information requirements for IR to sustain cooperation. In this review, we present and discuss those recent results. We provide a synthesis of theoretical models and discuss previous conclusions through the lens of evolutionary game theory and cognitive complexity. We highlight open questions and suggest future research in this domain. This article is part of the theme issue 'The language of cooperation: reputation and honest signalling'.}, } @article {pmid34599334, year = {2021}, author = {Westfall, AK and Telemeco, RS and Grizante, MB and Waits, DS and Clark, AD and Simpson, DY and Klabacka, RL and Sullivan, AP and Perry, GH and Sears, MW and Cox, CL and Cox, RM and Gifford, ME and John-Alder, HB and Langkilde, T and Angilletta, MJ and Leaché, AD and Tollis, M and Kusumi, K and Schwartz, TS}, title = {A chromosome-level genome assembly for the eastern fence lizard (Sceloporus undulatus), a reptile model for physiological and evolutionary ecology.}, journal = {GigaScience}, volume = {10}, number = {10}, pages = {}, pmid = {34599334}, issn = {2047-217X}, mesh = {Animals ; Chromosomes/genetics ; Genome ; Genomics ; *Lizards/genetics ; Synteny ; }, abstract = {BACKGROUND: High-quality genomic resources facilitate investigations into behavioral ecology, morphological and physiological adaptations, and the evolution of genomic architecture. Lizards in the genus Sceloporus have a long history as important ecological, evolutionary, and physiological models, making them a valuable target for the development of genomic resources.

FINDINGS: We present a high-quality chromosome-level reference genome assembly, SceUnd1.0 (using 10X Genomics Chromium, HiC, and Pacific Biosciences data), and tissue/developmental stage transcriptomes for the eastern fence lizard, Sceloporus undulatus. We performed synteny analysis with other snake and lizard assemblies to identify broad patterns of chromosome evolution including the fusion of micro- and macrochromosomes. We also used this new assembly to provide improved reference-based genome assemblies for 34 additional Sceloporus species. Finally, we used RNAseq and whole-genome resequencing data to compare 3 assemblies, each representing an increased level of cost and effort: Supernova Assembly with data from 10X Genomics Chromium, HiRise Assembly that added data from HiC, and PBJelly Assembly that added data from Pacific Biosciences sequencing. We found that the Supernova Assembly contained the full genome and was a suitable reference for RNAseq and single-nucleotide polymorphism calling, but the chromosome-level scaffolds provided by the addition of HiC data allowed synteny and whole-genome association mapping analyses. The subsequent addition of PacBio data doubled the contig N50 but provided negligible gains in scaffold length.

CONCLUSIONS: These new genomic resources provide valuable tools for advanced molecular analysis of an organism that has become a model in physiology and evolutionary ecology.}, } @article {pmid34597593, year = {2021}, author = {Owen, SV and Wenner, N and Dulberger, CL and Rodwell, EV and Bowers-Barnard, A and Quinones-Olvera, N and Rigden, DJ and Rubin, EJ and Garner, EC and Baym, M and Hinton, JCD}, title = {Prophages encode phage-defense systems with cognate self-immunity.}, journal = {Cell host & microbe}, volume = {29}, number = {11}, pages = {1620-1633.e8}, pmid = {34597593}, issn = {1934-6069}, support = {/WT_/Wellcome Trust/United Kingdom ; R35 GM133700/GM/NIGMS NIH HHS/United States ; }, mesh = {*Bacteriophages/genetics ; Genome, Bacterial ; *Prophages/genetics ; Salmonella ; }, abstract = {Temperate phages are pervasive in bacterial genomes, existing as vertically inherited islands termed prophages. Prophages are vulnerable to predation of their host bacterium by exogenous phages. Here, we identify BstA, a family of prophage-encoded phage-defense proteins in diverse Gram-negative bacteria. BstA localizes to sites of exogenous phage DNA replication and mediates abortive infection, suppressing the competing phage epidemic. During lytic replication, the BstA-encoding prophage is not itself inhibited by BstA due to self-immunity conferred by the anti-BstA (aba) element, a short stretch of DNA within the bstA locus. Inhibition of phage replication by distinct BstA proteins from Salmonella, Klebsiella, and Escherichia prophages is generally interchangeable, but each possesses a cognate aba element. The specificity of the aba element ensures that immunity is exclusive to the replicating prophage, preventing exploitation by variant BstA-encoding phages. The BstA protein allows prophages to defend host cells against exogenous phage attack without sacrificing the ability to replicate lytically.}, } @article {pmid34593851, year = {2021}, author = {Guenay-Greunke, Y and Bohan, DA and Traugott, M and Wallinger, C}, title = {Handling of targeted amplicon sequencing data focusing on index hopping and demultiplexing using a nested metabarcoding approach in ecology.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {19510}, pmid = {34593851}, issn = {2045-2322}, support = {P 28578/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Animals ; Coleoptera/classification/genetics ; Computational Biology/*methods ; *DNA Barcoding, Taxonomic ; *Ecology/methods ; Gene Library ; *High-Throughput Nucleotide Sequencing ; *Sequence Analysis, DNA ; Software ; }, abstract = {High-throughput sequencing platforms are increasingly being used for targeted amplicon sequencing because they enable cost-effective sequencing of large sample sets. For meaningful interpretation of targeted amplicon sequencing data and comparison between studies, it is critical that bioinformatic analyses do not introduce artefacts and rely on detailed protocols to ensure that all methods are properly performed and documented. The analysis of large sample sets and the use of predefined indexes create challenges, such as adjusting the sequencing depth across samples and taking sequencing errors or index hopping into account. However, the potential biases these factors introduce to high-throughput amplicon sequencing data sets and how they may be overcome have rarely been addressed. On the example of a nested metabarcoding analysis of 1920 carabid beetle regurgitates to assess plant feeding, we investigated: (i) the variation in sequencing depth of individually tagged samples and the effect of library preparation on the data output; (ii) the influence of sequencing errors within index regions and its consequences for demultiplexing; and (iii) the effect of index hopping. Our results demonstrate that despite library quantification, large variation in read counts and sequencing depth occurred among samples and that the sequencing error rate in bioinformatic software is essential for accurate adapter/primer trimming and demultiplexing. Moreover, setting an index hopping threshold to avoid incorrect assignment of samples is highly recommended.}, } @article {pmid34593819, year = {2021}, author = {Falster, D and Gallagher, R and Wenk, EH and Wright, IJ and Indiarto, D and Andrew, SC and Baxter, C and Lawson, J and Allen, S and Fuchs, A and Monro, A and Kar, F and Adams, MA and Ahrens, CW and Alfonzetti, M and Angevin, T and Apgaua, DMG and Arndt, S and Atkin, OK and Atkinson, J and Auld, T and Baker, A and von Balthazar, M and Bean, A and Blackman, CJ and Bloomfield, K and Bowman, DMJS and Bragg, J and Brodribb, TJ and Buckton, G and Burrows, G and Caldwell, E and Camac, J and Carpenter, R and Catford, JA and Cawthray, GR and Cernusak, LA and Chandler, G and Chapman, AR and Cheal, D and Cheesman, AW and Chen, SC and Choat, B and Clinton, B and Clode, PL and Coleman, H and Cornwell, WK and Cosgrove, M and Crisp, M and Cross, E and Crous, KY and Cunningham, S and Curran, T and Curtis, E and Daws, MI and DeGabriel, JL and Denton, MD and Dong, N and Du, P and Duan, H and Duncan, DH and Duncan, RP and Duretto, M and Dwyer, JM and Edwards, C and Esperon-Rodriguez, M and Evans, JR and Everingham, SE and Farrell, C and Firn, J and Fonseca, CR and French, BJ and Frood, D and Funk, JL and Geange, SR and Ghannoum, O and Gleason, SM and Gosper, CR and Gray, E and Groom, PK and Grootemaat, S and Gross, C and Guerin, G and Guja, L and Hahs, AK and Harrison, MT and Hayes, PE and Henery, M and Hochuli, D and Howell, J and Huang, G and Hughes, L and Huisman, J and Ilic, J and Jagdish, A and Jin, D and Jordan, G and Jurado, E and Kanowski, J and Kasel, S and Kellermann, J and Kenny, B and Kohout, M and Kooyman, RM and Kotowska, MM and Lai, HR and Laliberté, E and Lambers, H and Lamont, BB and Lanfear, R and van Langevelde, F and Laughlin, DC and Laugier-Kitchener, BA and Laurance, S and Lehmann, CER and Leigh, A and Leishman, MR and Lenz, T and Lepschi, B and Lewis, JD and Lim, F and Liu, U and Lord, J and Lusk, CH and Macinnis-Ng, C and McPherson, H and Magallón, S and Manea, A and López-Martinez, A and Mayfield, M and McCarthy, JK and Meers, T and van der Merwe, M and Metcalfe, DJ and Milberg, P and Mokany, K and Moles, AT and Moore, BD and Moore, N and Morgan, JW and Morris, W and Muir, A and Munroe, S and Nicholson, Á and Nicolle, D and Nicotra, AB and Niinemets, Ü and North, T and O'Reilly-Nugent, A and O'Sullivan, OS and Oberle, B and Onoda, Y and Ooi, MKJ and Osborne, CP and Paczkowska, G and Pekin, B and Guilherme Pereira, C and Pickering, C and Pickup, M and Pollock, LJ and Poot, P and Powell, JR and Power, SA and Prentice, IC and Prior, L and Prober, SM and Read, J and Reynolds, V and Richards, AE and Richardson, B and Roderick, ML and Rosell, JA and Rossetto, M and Rye, B and Rymer, PD and Sams, MA and Sanson, G and Sauquet, H and Schmidt, S and Schönenberger, J and Schulze, ED and Sendall, K and Sinclair, S and Smith, B and Smith, R and Soper, F and Sparrow, B and Standish, RJ and Staples, TL and Stephens, R and Szota, C and Taseski, G and Tasker, E and Thomas, F and Tissue, DT and Tjoelker, MG and Tng, DYP and de Tombeur, F and Tomlinson, K and Turner, NC and Veneklaas, EJ and Venn, S and Vesk, P and Vlasveld, C and Vorontsova, MS and Warren, CA and Warwick, N and Weerasinghe, LK and Wells, J and Westoby, M and White, M and Williams, NSG and Wills, J and Wilson, PG and Yates, C and Zanne, AE and Zemunik, G and Ziemińska, K}, title = {AusTraits, a curated plant trait database for the Australian flora.}, journal = {Scientific data}, volume = {8}, number = {1}, pages = {254}, pmid = {34593819}, issn = {2052-4463}, support = {FT160100113//Department of Education and Training | Australian Research Council (ARC)/ ; DE170100208//Department of Education and Training | Australian Research Council (ARC)/ ; }, mesh = {Australia ; *Databases, Factual ; *Phenotype ; Plant Physiological Phenomena ; *Plants ; }, abstract = {We introduce the AusTraits database - a compilation of values of plant traits for taxa in the Australian flora (hereafter AusTraits). AusTraits synthesises data on 448 traits across 28,640 taxa from field campaigns, published literature, taxonomic monographs, and individual taxon descriptions. Traits vary in scope from physiological measures of performance (e.g. photosynthetic gas exchange, water-use efficiency) to morphological attributes (e.g. leaf area, seed mass, plant height) which link to aspects of ecological variation. AusTraits contains curated and harmonised individual- and species-level measurements coupled to, where available, contextual information on site properties and experimental conditions. This article provides information on version 3.0.2 of AusTraits which contains data for 997,808 trait-by-taxon combinations. We envision AusTraits as an ongoing collaborative initiative for easily archiving and sharing trait data, which also provides a template for other national or regional initiatives globally to fill persistent gaps in trait knowledge.}, } @article {pmid34591916, year = {2021}, author = {Wu, ST and Hsieh, YT and Huang, SC and Wei, CH and Chen, CT and Chen, JC}, title = {Perceptions of tourists of the resources, ecological service functions and recreation value of the Guanwu National Forest Recreation Area.}, journal = {PloS one}, volume = {16}, number = {9}, pages = {e0257835}, pmid = {34591916}, issn = {1932-6203}, mesh = {Conservation of Natural Resources/*methods ; Ecosystem ; Geographic Information Systems ; Humans ; Perception ; Public Opinion ; Taiwan ; Travel/*psychology ; }, abstract = {This study surveyed visitor perceptions of the resources of the Guanwu National Forest Recreation Area (GNFRA) in Taiwan', their perceptions toward the ecosystem service functions of the GNFRA, their expectations and opinions on its management, and their recreational activities. Independent sample t-tests and one-way analysis of variance (ANOVA) were used to examine the influences of the backgrounds of respondents on their perceptions toward the ecosystem service functions of the GNFRA. The importance-performance analysis (IPA) method was used to explore evaluations by tourists on the management of the GNRFA. Finally, a global positioning system (GPS) was used to process records of recreational activities by tourists within the GNFRA to understand the movement of tourists during their recreational activities within the GNRFA. The results showed that visitors to the GNRFA regarded its recreational resources to be valuable and that they had a high willingness to revisit. The visitors also showed a certain understanding of the ecosystem services provided by the forest ecosystem. There were significant differences in perceptions of ecosystem services among visitors of different backgrounds. In addition, the results of IPA showed the "importance" of perceptions and "performance" within the opinions of tourists on the management of the forest recreation area. The records of recreational activities by tourists showed that they experienced the most benefits when experiencing picturesque scenery along walking trails. The results of this study can contribute to future management of the GNRFA.}, } @article {pmid34587157, year = {2021}, author = {Zelnik, YR and Mau, Y and Shachak, M and Meron, E}, title = {High-integrity human intervention in ecosystems: Tracking self-organization modes.}, journal = {PLoS computational biology}, volume = {17}, number = {9}, pages = {e1009427}, pmid = {34587157}, issn = {1553-7358}, mesh = {Animal Husbandry ; Animals ; Biomass ; Climate Change ; Computational Biology ; Computer Simulation ; Conservation of Natural Resources/*methods/*statistics & numerical data ; Conservation of Water Resources/methods/statistics & numerical data ; Droughts ; Ecology/*organization & administration/*statistics & numerical data ; *Ecosystem ; Grassland ; Herbivory ; Humans ; Remote Sensing Technology/statistics & numerical data ; Stochastic Processes ; }, abstract = {Humans play major roles in shaping and transforming the ecology of Earth. Unlike natural drivers of ecosystem change, which are erratic and unpredictable, human intervention in ecosystems generally involves planning and management, but often results in detrimental outcomes. Using model studies and aerial-image analysis, we argue that the design of a successful human intervention form calls for the identification of the self-organization modes that drive ecosystem change, and for studying their dynamics. We demonstrate this approach with two examples: grazing management in drought-prone ecosystems, and rehabilitation of degraded vegetation by water harvesting. We show that grazing can increase the resilience to droughts, rather than imposing an additional stress, if managed in a spatially non-uniform manner, and that fragmental restoration along contour bunds is more resilient than the common practice of continuous restoration in vegetation stripes. We conclude by discussing the need for additional studies of self-organization modes and their dynamics.}, } @article {pmid34586901, year = {2021}, author = {Fernandes-Martins, MC and Keller, LM and Munro-Ehrlich, M and Zimlich, KR and Mettler, MK and England, AM and Clare, R and Surya, K and Shock, EL and Colman, DR and Boyd, ES}, title = {Ecological Dichotomies Arise in Microbial Communities Due to Mixing of Deep Hydrothermal Waters and Atmospheric Gas in a Circumneutral Hot Spring.}, journal = {Applied and environmental microbiology}, volume = {87}, number = {23}, pages = {e0159821}, pmid = {34586901}, issn = {1098-5336}, support = {CSP 504081//Department of Energy/ ; EAR-1820658//National Science Foundation (NSF)/ ; }, mesh = {*Atmosphere ; Carbon ; *Hot Springs/microbiology ; Metagenomics ; *Microbiota ; Oxygen ; Wyoming ; }, abstract = {Little is known of how the confluence of subsurface and surface processes influences the assembly and habitability of hydrothermal ecosystems. To address this knowledge gap, the geochemical and microbial composition of a high-temperature, circumneutral hot spring in Yellowstone National Park was examined to identify the sources of solutes and their effect on the ecology of microbial inhabitants. Metagenomic analysis showed that populations comprising planktonic and sediment communities are archaeal dominated, are dependent on chemical energy (chemosynthetic), share little overlap in their taxonomic composition, and are differentiated by their inferred use of/tolerance to oxygen and mode of carbon metabolism. The planktonic community is dominated by putative aerobic/aerotolerant autotrophs, while the taxonomic composition of the sediment community is more evenly distributed and comprised of anaerobic heterotrophs. These observations are interpreted to reflect sourcing of the spring by anoxic, organic carbon-limited subsurface hydrothermal fluids and ingassing of atmospheric oxygen that selects for aerobic/aerotolerant organisms that have autotrophic capabilities in the water column. Autotrophy and consumption of oxygen by the planktonic community may influence the assembly of the anaerobic and heterotrophic sediment community. Support for this inference comes from higher estimated rates of genome replication in planktonic populations than sediment populations, indicating faster growth in planktonic populations. Collectively, these observations provide new insight into how mixing of subsurface waters and atmospheric oxygen create dichotomy in the ecology of hot spring communities and suggest that planktonic and sediment communities may have been less differentiated taxonomically and functionally prior to the rise of oxygen at ∼2.4 billion years ago (Gya). IMPORTANCE Understanding the source and availability of energy capable of supporting life in hydrothermal environments is central to predicting the ecology of microbial life on early Earth when volcanic activity was more widespread. Little is known of the substrates supporting microbial life in circumneutral to alkaline springs, despite their relevance to early Earth habitats. Using metagenomic and informatics approaches, water column and sediment habitats in a representative circumneutral hot spring in Yellowstone were shown to be dichotomous, with the former largely hosting aerobic/aerotolerant autotrophs and the latter primarily hosting anaerobic heterotrophs. This dichotomy is attributed to influx of atmospheric oxygen into anoxic deep hydrothermal spring waters. These results indicate that the ecology of microorganisms in circumneutral alkaline springs sourced by deep hydrothermal fluids was different prior to the rise of atmospheric oxygen ∼2.4 Gya, with planktonic and sediment communities likely to be less differentiated than contemporary circumneutral hot springs.}, } @article {pmid34586500, year = {2021}, author = {Cassaro, A and Pacelli, C and Aureli, L and Catanzaro, I and Leo, P and Onofri, S}, title = {Antarctica as a reservoir of planetary analogue environments.}, journal = {Extremophiles : life under extreme conditions}, volume = {25}, number = {5-6}, pages = {437-458}, pmid = {34586500}, issn = {1433-4909}, mesh = {Antarctic Regions ; Exobiology ; Extraterrestrial Environment ; Extreme Environments ; *Mars ; *Planets ; }, abstract = {One of the main objectives of astrobiological research is the investigation of the habitability of other planetary bodies. Since space exploration missions are expensive and require long-term organization, the preliminary study of terrestrial environments is an essential step to prepare and support exploration missions. The Earth hosts a multitude of extreme environments whose characteristics resemble celestial bodies in our Solar System. In these environments, the physico-chemical properties partly match extraterrestrial environments and could clarify limits and adaptation mechanisms of life, the mineralogical or geochemical context, and support and interpret data sent back from planetary bodies. One of the best terrestrial analogues is Antarctica, whose conditions lie on the edge of habitability. It is characterized by a cold and dry climate (Onofri et al., Nova Hedwigia 68:175-182, 1999), low water availability, strong katabatic winds, salt concentration, desiccation, and high radiation. Thanks to the harsh conditions like those in other celestial bodies, Antarctica offers good terrestrial analogues for celestial body (Mars or icy moons; Léveillé, CR Palevol 8:637-648, https://doi.org/10.1016/j.crpv.2009.03.005 , 2009). The continent could be distinguished into several habitats, each with characteristics similar to those existing on other bodies. Here, we reported a description of each simulated parameter within the habitats, in relation to each of the simulated extraterrestrial environments.}, } @article {pmid34584090, year = {2021}, author = {Hannula, SE and Heinen, R and Huberty, M and Steinauer, K and De Long, JR and Jongen, R and Bezemer, TM}, title = {Persistence of plant-mediated microbial soil legacy effects in soil and inside roots.}, journal = {Nature communications}, volume = {12}, number = {1}, pages = {5686}, pmid = {34584090}, issn = {2041-1723}, mesh = {Computational Biology ; Endophytes/*physiology ; Grassland ; Microbiota/*physiology ; Plant Roots/growth & development/*microbiology ; Poaceae/*growth & development/microbiology ; *Soil Microbiology ; }, abstract = {Plant-soil feedbacks are shaped by microbial legacies that plants leave in the soil. We tested the persistence of these legacies after subsequent colonization by the same or other plant species using 6 typical grassland plant species. Soil fungal legacies were detectable for months, but the current plant effect on fungi amplified in time. By contrast, in bacterial communities, legacies faded away rapidly and bacteria communities were influenced strongly by the current plant. However, both fungal and bacterial legacies were conserved inside the roots of the current plant species and their composition significantly correlated with plant growth. Hence, microbial soil legacies present at the time of plant establishment play a vital role in shaping plant growth even when these legacies have faded away in the soil due the growth of the current plant species. We conclude that soil microbiome legacies are reversible and versatile, but that they can create plant-soil feedbacks via altering the endophytic community acquired during early ontogeny.}, } @article {pmid34583207, year = {2021}, author = {Brant, BJ and Singleton, DA and Noble, PJM and Radford, AD}, title = {Seasonality and risk factors for grass seed foreign bodies in dogs.}, journal = {Preventive veterinary medicine}, volume = {197}, number = {}, pages = {105499}, doi = {10.1016/j.prevetmed.2021.105499}, pmid = {34583207}, issn = {1873-1716}, support = {BB/N019547/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; *Dog Diseases/epidemiology/etiology ; Dogs ; *Foreign Bodies/veterinary ; Plant Breeding ; Poaceae ; Risk Factors ; Seeds ; }, abstract = {Grass seed foreign bodies (GSFBs) are a familiar presentation, especially in dogs, associated with a variety of clinical signs depending on site of penetration and extent of migration. Seasonality and risk factors for GSFB occurrence were investigated using electronic health records from a sentinel voluntary network of 245 veterinary practices in the United Kingdom between 17th March 2014 and 18th September 2020. Clinical narrative text mining of 4,580,503 canine consultations produced a final case dataset of 1,037 consultations where GSFBs had been recorded in individual dogs. Cases of GSFBs were recorded in all months, with 940 (90.6 %) recorded between June and September. In particular, the odds of GSFBs in July was almost 176 times more than that of January (Odds ratio, OR, 175.6, 95 % Confidence interval, CI, 43.5-707.7, P < 0.001). Compared to the retriever breed type, spaniel breed types were 7.7 times more likely to present with a GSFB (CI 5.4-11.0, P < 0.001). Other significant risk factors associated with recorded GSFBs for this population included being male (OR = 1.4, CI 1.2-1.6, P < 0.001), and geographical location. When compared to the South East of England, risk was lowest in Wales (OR = 0.1, CI 0.0-0.3, P=<0.001), and highest in the East of England (OR = 1.9, 1.2-2.9, P = 0.003), and overall risk in urban areas was reduced (OR = 0.8, CI 0.7-1.0, P = 0.024). These observations provide a number of areas for temporally targeted health campaigns at specific types of dogs, to reduce the impact of GSFBs on canine welfare.}, } @article {pmid34574999, year = {2021}, author = {Pasdar, Z and Pana, TA and Ewers, KD and Szlachetka, WA and Perdomo-Lampignano, JA and Gamble, DT and Bhattacharya, S and Carter, B and Myint, PK}, title = {An Ecological Study Assessing the Relationship between Public Health Policies and Severity of the COVID-19 Pandemic.}, journal = {Healthcare (Basel, Switzerland)}, volume = {9}, number = {9}, pages = {}, pmid = {34574999}, issn = {2227-9032}, abstract = {Reliance on government-led policies have heightened during the COVID-19 pandemic. Further research on the policies associated with outcomes other than mortality rates remains warranted. We aimed to determine associations between government public health policies on the severity of the COVID-19 pandemic. This ecological study including countries reporting ≥25 daily COVID-related deaths until end May 2020, utilised public data on policy indicators described by the Blavatnik school of Government. Associations between policy indicators and severity of the pandemic (mean mortality rate, time to peak, peak deaths per 100,000, cumulative deaths after peak per 100,000 and ratio of mean slope of the descending curve to mean slope of the ascending curve) were measured using Spearman rank-order tests. Analyses were stratified for age, income and region. Among 22 countries, containment policies such as school closures appeared effective in younger populations (rs = -0.620, p = 0.042) and debt/contract relief in older populations (rs = -0.743, p = 0.009) when assessing peak deaths per 100,000. In European countries, containment policies were generally associated with good outcomes. In non-European countries, school closures were associated with mostly good outcomes (rs = -0.757, p = 0.049 for mean mortality rate). In high-income countries, health system policies were generally effective, contrasting to low-income countries. Containment policies may be effective in younger populations or in high-income or European countries. Health system policies have been most effective in high-income countries.}, } @article {pmid34574756, year = {2021}, author = {Tao, Y and Wang, Q and Zou, Y}, title = {Simulation and Analysis of Urban Production-Living-Ecological Space Evolution Based on a Macro-Micro Joint Decision Model.}, journal = {International journal of environmental research and public health}, volume = {18}, number = {18}, pages = {}, pmid = {34574756}, issn = {1660-4601}, mesh = {China ; Cities ; *City Planning ; Computer Simulation ; *Conservation of Natural Resources ; Ecosystem ; Humans ; Urban Renewal ; }, abstract = {The precise simulation of urban space evolution and grasping of the leading factors are the most important basis for urban space planning. However, the simulation ability of current models is lacking when it comes to complicated/unpredictable urban space changes, resulting in flawed government decision-making and wasting of urban resources. In this study, a macro-micro joint decision model was proposed to improve the ability of urban space evolution simulation. The simulation objects were unified into production, living and ecological space to realize "multiple planning in one". For validation of the proposed model and method, remote sensing images, geographic information and socio-economic data of Xuzhou, China from 2000 to 2020 were collected and tested. The results showed that the simulation precision of the cellular automata (CA) model was about 87% (Kappa coefficient), which improved to 89% if using a CA and multi-agent system (MAS) joint model. The simulation precision could be better than 92% using the prosed model. The result of factor weight determination indicated that the micro factors affected the evolution of production and living space more than the macro factors, while the macro factors had more influence on the evolution of ecological space than the micro factors. Therefore, active policies should be formulated to strengthen the ideological guidance towards micro individuals (e.g., a resident, farmer, or entrepreneur), and avoid disordered development of living and production space. In addition, ecological space planning should closely link with the local environment and natural conditions, to improve urban ecological carrying capacity and realize urban sustainable development.}, } @article {pmid34566545, year = {2021}, author = {Yousafi, Q and Amin, H and Bibi, S and Rafi, R and Khan, MS and Ali, H and Masroor, A}, title = {Subtractive Proteomics and Immuno-informatics Approaches for Multi-peptide Vaccine Prediction Against Klebsiella oxytoca and Validation Through In Silico Expression.}, journal = {International journal of peptide research and therapeutics}, volume = {27}, number = {4}, pages = {2685-2701}, pmid = {34566545}, issn = {1573-3149}, abstract = {Klebsiella oxytoca is a gram-negative bacterium. It is opportunistic in nature and causes hospital acquired infections. Subtractive proteomics and reverse vaccinology approaches were employed to screen out the best proteins for vaccine designing. Whole proteome of K. oxytoca strain ATCC 8724, consisting of 5483 proteins, was used for designing the vaccine. Total 1670 cytotoxic T lymphocyte (CTL) epitope were predicted through NetCTL while 1270 helper T lymphocyte (HTL) epitopes were predicted through IEDB server. The epitopes were screened for non-toxicity, allergenicity, antigenicity and water solubility. After epitope screening 300 CTL and 250 HTL epitopes were submitted to IFN-γ epitope server to predict their Interferon-γ induction response. The selected IFN-γ positive epitopes were tested for their binding affinity with MHCI-DRB1 by MHCPred. The 15 CTL and 13 HTL epitopes were joined by linkers AAY and GPGPG respectively in vaccine construct. Chain C of Pam3CSK4 (PDB ID; 2Z7X) was linked to the vaccine construct as an adjuvant. A 450aa long vaccine construct was submitted to I-TASSER server for 3D structure prediction. Thirteen Linear B cells were predicted by ABCPred server and 10 sets of discontinues epitopes for 3D vaccine structure were predicted by DiscoTope server. The modeled 3D vaccine construct was docked with human Toll-like receptor 2 (PDB ID: 6NIG) by PatchDock. The docked complexes were refined by FireDock. The selected docked complex showed five hydrogen bonds and one salt bridge. The vaccine sequence was reverse transcribed to get nucleotide sequence for In silico cloning. The reverse transcribed sequence strand was cloned in pET28a(+) expression vector. A clone containing 6586 bp was constructed including the 450 bp of query gene sequence.}, } @article {pmid34564253, year = {2021}, author = {Thomaes, A and Barbalat, S and Bardiani, M and Bower, L and Campanaro, A and Fanega Sleziak, N and Gonçalo Soutinho, J and Govaert, S and Harvey, D and Hawes, C and Kadej, M and Méndez, M and Meriguet, B and Rink, M and Rossi De Gasperis, S and Ruyts, S and Jelaska, LŠ and Smit, J and Smolis, A and Snegin, E and Tagliani, A and Vrezec, A}, title = {The European Stag Beetle (Lucanus cervus) Monitoring Network: International Citizen Science Cooperation Reveals Regional Differences in Phenology and Temperature Response.}, journal = {Insects}, volume = {12}, number = {9}, pages = {}, pmid = {34564253}, issn = {2075-4450}, support = {Saving threatened great stag beetles across Europe//PEOPLE'S TRUST FOR ENDANGERED SPECIES/ ; P1-0255//Ministry of Environment and Spatial Planning of Republic of Slovenia/ ; Network Ecological Monitoring//ministry of Ministry of Agriculture, Nature and Food Quality/ ; Network Ecological Monitoring//province of Gelderland/ ; LIFE17 ESC/IT/001 "ESC360"//Life/ ; }, abstract = {To address the decline in biodiversity, international cooperation in monitoring of threatened species is needed. Citizen science can play a crucial role in achieving this challenging goal, but most citizen science projects have been established at national or regional scales. Here we report on the establishment and initial findings of the European Stag Beetle Monitoring Network (ESBMN), an international network of stag beetle (Lucanus cervus) monitoring schemes using the same protocol. The network, started in 2016, currently includes 14 countries (see results) but with a strong variation in output regarding the number of transects (148 successful transects in total) and transect walks (1735). We found differences across European regions in the number of stag beetles recorded, related to phenology and temperature, but not for time of transect start. Furthermore, the initial experiences of the ESBMN regarding international cooperation, citizen science approach, and drop-out of volunteers is discussed. An international standardised protocol that allows some local variation is essential for international collaboration and data management, and analysis is best performed at the international level, whereas recruiting, training, and maintaining volunteers is best organised locally. In conclusion, we appeal for more joint international citizen science-based monitoring initiatives assisting international red-listing and conservation actions.}, } @article {pmid34562356, year = {2021}, author = {Upham, NS and Poelen, JH and Paul, D and Groom, QJ and Simmons, NB and Vanhove, MPM and Bertolino, S and Reeder, DM and Bastos-Silveira, C and Sen, A and Sterner, B and Franz, NM and Guidoti, M and Penev, L and Agosti, D}, title = {Liberating host-virus knowledge from biological dark data.}, journal = {The Lancet. Planetary health}, volume = {5}, number = {10}, pages = {e746-e750}, pmid = {34562356}, issn = {2542-5196}, support = {R01 AI151144/AI/NIAID NIH HHS/United States ; R21 AI164268/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; *COVID-19/epidemiology/virology ; *Host Microbial Interactions ; Humans ; *Information Storage and Retrieval ; SARS-CoV-2 ; Zoonoses ; }, abstract = {Connecting basic data about bats and other potential hosts of SARS-CoV-2 with their ecological context is crucial to the understanding of the emergence and spread of the virus. However, when lockdowns in many countries started in March, 2020, the world's bat experts were locked out of their research laboratories, which in turn impeded access to large volumes of offline ecological and taxonomic data. Pandemic lockdowns have brought to attention the long-standing problem of so-called biological dark data: data that are published, but disconnected from digital knowledge resources and thus unavailable for high-throughput analysis. Knowledge of host-to-virus ecological interactions will be biased until this challenge is addressed. In this Viewpoint, we outline two viable solutions: first, in the short term, to interconnect published data about host organisms, viruses, and other pathogens; and second, to shift the publishing framework beyond unstructured text (the so-called PDF prison) to labelled networks of digital knowledge. As the indexing system for biodiversity data, biological taxonomy is foundational to both solutions. Building digitally connected knowledge graphs of host-pathogen interactions will establish the agility needed to quickly identify reservoir hosts of novel zoonoses, allow for more robust predictions of emergence, and thereby strengthen human and planetary health systems.}, } @article {pmid34559439, year = {2022}, author = {Bramness, JG and Hjellvik, V and Stubhaug, A and Skurtveit, S}, title = {Possible opioid-saving effect of cannabis-based medicine using individual-based data from the Norwegian Prescription Database.}, journal = {Basic & clinical pharmacology & toxicology}, volume = {130}, number = {1}, pages = {84-92}, doi = {10.1111/bcpt.13660}, pmid = {34559439}, issn = {1742-7843}, support = {320360//Norwegian Research Council/ ; }, mesh = {Adult ; Aged ; Analgesics/administration & dosage ; Analgesics, Opioid/*administration & dosage ; Cannabidiol/*administration & dosage ; Databases, Factual ; Dronabinol/*administration & dosage ; Drug Combinations ; Female ; Humans ; Male ; Middle Aged ; Norway ; Opioid-Related Disorders/epidemiology ; Practice Patterns, Physicians'/*statistics & numerical data ; }, abstract = {Some ecological studies have shown that areas with higher use of cannabis may have lower opioid use and fewer opioid-related problems. Newer studies are questioning this finding. Few individually based studies have been performed. Using data from the Norwegian Prescription Database, this study investigated the individual level effect of prescribed cannabis extract (Sativex®) in prescription opioid users on their opioid use in the following year. Looking at all those filling a prescription for Sativex®, opioid use was only marginally lowered in the follow-up period. Some Sativex® users, however, filled more prescriptions for Sativex® and were able to reduce their opioid use substantially. Further studies are needed to elucidate more details on these patients, so as to know who can benefit from such cannabis-based extracts in reducing their opioid use.}, } @article {pmid34556766, year = {2021}, author = {Kouba, M and Bartoš, L and Bartošová, J and Hongisto, K and Korpimäki, E}, title = {Long-term trends in the body condition of parents and offspring of Tengmalm's owls under fluctuating food conditions and climate change.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {18893}, pmid = {34556766}, issn = {2045-2322}, mesh = {Animals ; Climate Change ; Datasets as Topic ; Ecological Parameter Monitoring/*statistics & numerical data ; Female ; Finland ; Forests ; Male ; Physical Fitness/*physiology ; Population Dynamics/statistics & numerical data/trends ; Predatory Behavior ; Reproduction ; Seasons ; Strigiformes/*physiology ; }, abstract = {Physical condition is important for the ability to resist various parasites and diseases as well as in escaping predators thus contributing to reproductive success, over-winter survival and possible declines in wildlife populations. However, in-depth research on trends in body condition is rare because decades-long datasets are not available for a majority of species. We analysed the long-term dataset of offspring covering 34 years, male parents (40 years) and female parents (42 years) to find out whether the decline of Tengmalm's owl population in western Finland is attributable to either decreased adult and/or juvenile body condition in interaction with changing weather conditions and density estimates of main foods. We found that body condition of parent owl males and females declined throughout the 40-year study period whereas the body condition of owlets at the fledging stage very slightly increased. The body condition of parent owls increased with augmenting depth of snow cover in late winter (January to March), and that of offspring improved with increasing precipitation in late spring (May to June). We conclude that the decreasing trend of body condition of parent owl males and females is important factor probably inducing reduced adult survival and reduced reproduction success thus contributing to the long-term decline of the Tengmalm's owl study population. The very slightly increasing trend of body condition of offspring is obviously not able to compensate the overall decline of Tengmalm's owl population, because the number of offspring in turn simultaneously decreased considerably in the long-term. The ongoing climate change appeared to work in opposite ways in this case because declining depth of snow cover will make the situation worse but increased precipitation will improve. We suggest that the main reasons for long-term decline of body condition of parent owls are interactive or additive effects of reduced food resources and increased overall predation risk due to habitat degradation (loss and fragmentation of mature and old-growth forests due to clear-felling) subsequently leading to decline of Tengmalm's owl study population.}, } @article {pmid34556492, year = {2021}, author = {Wild, JM and Porter, JC and Molyneaux, PL and George, PM and Stewart, I and Allen, RJ and Aul, R and Baillie, JK and Barratt, SL and Beirne, P and Bianchi, SM and Blaikley, JF and Brooke, J and Chaudhuri, N and Collier, G and Denneny, EK and Docherty, A and Fabbri, L and Gibbons, MA and Gleeson, FV and Gooptu, B and Hall, IP and Hanley, NA and Heightman, M and Hillman, TE and Johnson, SR and Jones, MG and Khan, F and Lawson, R and Mehta, P and Mitchell, JA and Platé, M and Poinasamy, K and Quint, JK and Rivera-Ortega, P and Semple, M and Simpson, AJ and Smith, D and Spears, M and Spencer, LG and Stanel, SC and Thickett, DR and Thompson, AAR and Walsh, SL and Weatherley, ND and Weeks, ME and Wootton, DG and Brightling, CE and Chambers, RC and Ho, LP and Jacob, J and Piper Hanley, K and Wain, LV and Jenkins, RG}, title = {Understanding the burden of interstitial lung disease post-COVID-19: the UK Interstitial Lung Disease-Long COVID Study (UKILD-Long COVID).}, journal = {BMJ open respiratory research}, volume = {8}, number = {1}, pages = {}, pmid = {34556492}, issn = {2052-4439}, support = {MC_PC_19059/MRC_/Medical Research Council/United Kingdom ; MR/W006111/1/MRC_/Medical Research Council/United Kingdom ; G1000861/MRC_/Medical Research Council/United Kingdom ; SP/14/6/31350/BHF_/British Heart Foundation/United Kingdom ; MC_PC_20022/MRC_/Medical Research Council/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; MR/S019669/1/MRC_/Medical Research Council/United Kingdom ; FS/18/13/33281/BHF_/British Heart Foundation/United Kingdom ; MR/M008894/1/MRC_/Medical Research Council/United Kingdom ; MR/V027859/1/MRC_/Medical Research Council/United Kingdom ; MR/T032529/1/MRC_/Medical Research Council/United Kingdom ; MC_PC_19025/MRC_/Medical Research Council/United Kingdom ; }, mesh = {COVID-19/*complications ; Humans ; Longitudinal Studies ; *Lung Diseases, Interstitial/epidemiology ; Observational Studies as Topic ; Pandemics ; Prospective Studies ; United Kingdom/epidemiology ; Post-Acute COVID-19 Syndrome ; }, abstract = {INTRODUCTION: The COVID-19 pandemic has led to over 100 million cases worldwide. The UK has had over 4 million cases, 400 000 hospital admissions and 100 000 deaths. Many patients with COVID-19 suffer long-term symptoms, predominantly breathlessness and fatigue whether hospitalised or not. Early data suggest potentially severe long-term consequence of COVID-19 is development of long COVID-19-related interstitial lung disease (LC-ILD).

METHODS AND ANALYSIS: The UK Interstitial Lung Disease Consortium (UKILD) will undertake longitudinal observational studies of patients with suspected ILD following COVID-19. The primary objective is to determine ILD prevalence at 12 months following infection and whether clinically severe infection correlates with severity of ILD. Secondary objectives will determine the clinical, genetic, epigenetic and biochemical factors that determine the trajectory of recovery or progression of ILD. Data will be obtained through linkage to the Post-Hospitalisation COVID platform study and community studies. Additional substudies will conduct deep phenotyping. The Xenon MRI investigation of Alveolar dysfunction Substudy will conduct longitudinal xenon alveolar gas transfer and proton perfusion MRI. The POST COVID-19 interstitial lung DiseasE substudy will conduct clinically indicated bronchoalveolar lavage with matched whole blood sampling. Assessments include exploratory single cell RNA and lung microbiomics analysis, gene expression and epigenetic assessment.

ETHICS AND DISSEMINATION: All contributing studies have been granted appropriate ethical approvals. Results from this study will be disseminated through peer-reviewed journals.

CONCLUSION: This study will ensure the extent and consequences of LC-ILD are established and enable strategies to mitigate progression of LC-ILD.}, } @article {pmid34555011, year = {2021}, author = {Camacho Mateu, J and Sireci, M and Muñoz, MA}, title = {Phenotypic-dependent variability and the emergence of tolerance in bacterial populations.}, journal = {PLoS computational biology}, volume = {17}, number = {9}, pages = {e1009417}, pmid = {34555011}, issn = {1553-7358}, mesh = {Adaptation, Physiological ; *Anti-Bacterial Agents/pharmacology ; Bacteria/drug effects ; *Bacterial Physiological Phenomena ; Biological Evolution ; Computational Biology ; Computer Simulation ; Drug Tolerance ; Microbiota/drug effects/physiology ; Models, Biological ; Phenotype ; Stress, Physiological ; *Drug Resistance, Bacterial ; }, abstract = {Ecological and evolutionary dynamics have been historically regarded as unfolding at broadly separated timescales. However, these two types of processes are nowadays well-documented to intersperse much more tightly than traditionally assumed, especially in communities of microorganisms. Advancing the development of mathematical and computational approaches to shed novel light onto eco-evolutionary problems is a challenge of utmost relevance. With this motivation in mind, here we scrutinize recent experimental results showing evidence of rapid evolution of tolerance by lag in bacterial populations that are periodically exposed to antibiotic stress in laboratory conditions. In particular, the distribution of single-cell lag times-i.e., the times that individual bacteria from the community remain in a dormant state to cope with stress-evolves its average value to approximately fit the antibiotic-exposure time. Moreover, the distribution develops right-skewed heavy tails, revealing the presence of individuals with anomalously large lag times. Here, we develop a parsimonious individual-based model mimicking the actual demographic processes of the experimental setup. Individuals are characterized by a single phenotypic trait: their intrinsic lag time, which is transmitted with variation to the progeny. The model-in a version in which the amplitude of phenotypic variations grows with the parent's lag time-is able to reproduce quite well the key empirical observations. Furthermore, we develop a general mathematical framework allowing us to describe with good accuracy the properties of the stochastic model by means of a macroscopic equation, which generalizes the Crow-Kimura equation in population genetics. Even if the model does not account for all the biological mechanisms (e.g., genetic changes) in a detailed way-i.e., it is a phenomenological one-it sheds light onto the eco-evolutionary dynamics of the problem and can be helpful to design strategies to hinder the emergence of tolerance in bacterial communities. From a broader perspective, this work represents a benchmark for the mathematical framework designed to tackle much more general eco-evolutionary problems, thus paving the road to further research avenues.}, } @article {pmid34552242, year = {2021}, author = {Migliavacca, M and Musavi, T and Mahecha, MD and Nelson, JA and Knauer, J and Baldocchi, DD and Perez-Priego, O and Christiansen, R and Peters, J and Anderson, K and Bahn, M and Black, TA and Blanken, PD and Bonal, D and Buchmann, N and Caldararu, S and Carrara, A and Carvalhais, N and Cescatti, A and Chen, J and Cleverly, J and Cremonese, E and Desai, AR and El-Madany, TS and Farella, MM and Fernández-Martínez, M and Filippa, G and Forkel, M and Galvagno, M and Gomarasca, U and Gough, CM and Göckede, M and Ibrom, A and Ikawa, H and Janssens, IA and Jung, M and Kattge, J and Keenan, TF and Knohl, A and Kobayashi, H and Kraemer, G and Law, BE and Liddell, MJ and Ma, X and Mammarella, I and Martini, D and Macfarlane, C and Matteucci, G and Montagnani, L and Pabon-Moreno, DE and Panigada, C and Papale, D and Pendall, E and Penuelas, J and Phillips, RP and Reich, PB and Rossini, M and Rotenberg, E and Scott, RL and Stahl, C and Weber, U and Wohlfahrt, G and Wolf, S and Wright, IJ and Yakir, D and Zaehle, S and Reichstein, M}, title = {The three major axes of terrestrial ecosystem function.}, journal = {Nature}, volume = {598}, number = {7881}, pages = {468-472}, pmid = {34552242}, issn = {1476-4687}, mesh = {*Carbon Cycle ; Carbon Dioxide/metabolism ; Climate ; Datasets as Topic ; *Ecosystem ; Humidity ; Plants/classification/*metabolism ; Principal Component Analysis ; *Water Cycle ; }, abstract = {The leaf economics spectrum[1,2] and the global spectrum of plant forms and functions[3] revealed fundamental axes of variation in plant traits, which represent different ecological strategies that are shaped by the evolutionary development of plant species[2]. Ecosystem functions depend on environmental conditions and the traits of species that comprise the ecological communities[4]. However, the axes of variation of ecosystem functions are largely unknown, which limits our understanding of how ecosystems respond as a whole to anthropogenic drivers, climate and environmental variability[4,5]. Here we derive a set of ecosystem functions[6] from a dataset of surface gas exchange measurements across major terrestrial biomes. We find that most of the variability within ecosystem functions (71.8%) is captured by three key axes. The first axis reflects maximum ecosystem productivity and is mostly explained by vegetation structure. The second axis reflects ecosystem water-use strategies and is jointly explained by variation in vegetation height and climate. The third axis, which represents ecosystem carbon-use efficiency, features a gradient related to aridity, and is explained primarily by variation in vegetation structure. We show that two state-of-the-art land surface models reproduce the first and most important axis of ecosystem functions. However, the models tend to simulate more strongly correlated functions than those observed, which limits their ability to accurately predict the full range of responses to environmental changes in carbon, water and energy cycling in terrestrial ecosystems[7,8].}, } @article {pmid34550967, year = {2021}, author = {Zhao, Z and Woloszynek, S and Agbavor, F and Mell, JC and Sokhansanj, BA and Rosen, GL}, title = {Learning, visualizing and exploring 16S rRNA structure using an attention-based deep neural network.}, journal = {PLoS computational biology}, volume = {17}, number = {9}, pages = {e1009345}, pmid = {34550967}, issn = {1553-7358}, mesh = {Algorithms ; Computational Biology ; Databases, Genetic ; *Deep Learning ; Gastrointestinal Microbiome/genetics ; Host Microbial Interactions/genetics ; Humans ; Inflammatory Bowel Diseases/microbiology ; Microbiota/*genetics ; Natural Language Processing ; *Neural Networks, Computer ; Phenotype ; Prevotella/classification/genetics/isolation & purification ; Proof of Concept Study ; RNA, Ribosomal, 16S/classification/*genetics ; }, abstract = {Recurrent neural networks with memory and attention mechanisms are widely used in natural language processing because they can capture short and long term sequential information for diverse tasks. We propose an integrated deep learning model for microbial DNA sequence data, which exploits convolutional neural networks, recurrent neural networks, and attention mechanisms to predict taxonomic classifications and sample-associated attributes, such as the relationship between the microbiome and host phenotype, on the read/sequence level. In this paper, we develop this novel deep learning approach and evaluate its application to amplicon sequences. We apply our approach to short DNA reads and full sequences of 16S ribosomal RNA (rRNA) marker genes, which identify the heterogeneity of a microbial community sample. We demonstrate that our implementation of a novel attention-based deep network architecture, Read2Pheno, achieves read-level phenotypic prediction. Training Read2Pheno models will encode sequences (reads) into dense, meaningful representations: learned embedded vectors output from the intermediate layer of the network model, which can provide biological insight when visualized. The attention layer of Read2Pheno models can also automatically identify nucleotide regions in reads/sequences which are particularly informative for classification. As such, this novel approach can avoid pre/post-processing and manual interpretation required with conventional approaches to microbiome sequence classification. We further show, as proof-of-concept, that aggregating read-level information can robustly predict microbial community properties, host phenotype, and taxonomic classification, with performance at least comparable to conventional approaches. An implementation of the attention-based deep learning network is available at https://github.com/EESI/sequence_attention (a python package) and https://github.com/EESI/seq2att (a command line tool).}, } @article {pmid34545526, year = {2022}, author = {Roumiani, A and Mofidi, A}, title = {Predicting ecological footprint based on global macro indicators in G-20 countries using machine learning approaches.}, journal = {Environmental science and pollution research international}, volume = {29}, number = {8}, pages = {11736-11755}, pmid = {34545526}, issn = {1614-7499}, mesh = {*Anthropogenic Effects ; Databases, Factual ; Linear Models ; *Machine Learning ; *Neural Networks, Computer ; }, abstract = {Paying attention to human activities in terms of land grazing infrastructure, crops, forest products, and carbon impact, the so-called ecological impact (EF) is one of the most important economic issues in the world. For the present study, global database data were used. The ability of the penalized regression (RR) approaches (including Ridge, Lasso and Elastic Net) and artificial neural network (ANN) to predict EF indices in the G-20 countries over the past two decades (1999-2018) was illustrated and compared. For this purpose, 10-fold cross-validation was used to evaluate the predictive performance and determine the penalty parameter for PR models. According to the results, the predictive performance compared to linear regression improved somewhat using the penalized methods. Using the elastic net model, more global macro indices were selected than Lasso. Although Lasso selected only a few indicators, it had better predictive performance among PR ns models. In addition to relative improvement in the predictive performance of PR methods, their interest in selecting a subset of indicators by shrinking coefficients and creating a parsimonious model was evident and significant. As a result, PR methods would be preferred, using variable selection and interpretive considerations to predictive performance alone. On the other hand, ANN models with higher determination coefficients (R[2]) and lower RMSE values performed significantly better than PR and OLS and showed that they were more accurate in predicting EF. Therefore, ANN could provide considerable and appropriate predictions for EF indicators in the G-20 countries.}, } @article {pmid34545216, year = {2021}, author = {Albrecht, J and Peters, MK and Becker, JN and Behler, C and Classen, A and Ensslin, A and Ferger, SW and Gebert, F and Gerschlauer, F and Helbig-Bonitz, M and Kindeketa, WJ and Kühnel, A and Mayr, AV and Njovu, HK and Pabst, H and Pommer, U and Röder, J and Rutten, G and Schellenberger Costa, D and Sierra-Cornejo, N and Vogeler, A and Vollstädt, MGR and Dulle, HI and Eardley, CD and Howell, KM and Keller, A and Peters, RS and Kakengi, V and Hemp, C and Zhang, J and Manning, P and Mueller, T and Bogner, C and Böhning-Gaese, K and Brandl, R and Hertel, D and Huwe, B and Kiese, R and Kleyer, M and Leuschner, C and Kuzyakov, Y and Nauss, T and Tschapka, M and Fischer, M and Hemp, A and Steffan-Dewenter, I and Schleuning, M}, title = {Species richness is more important for ecosystem functioning than species turnover along an elevational gradient.}, journal = {Nature ecology & evolution}, volume = {5}, number = {12}, pages = {1582-1593}, pmid = {34545216}, issn = {2397-334X}, mesh = {Animals ; *Biodiversity ; *Ecosystem ; Plants ; Tanzania ; }, abstract = {Many experiments have shown that biodiversity enhances ecosystem functioning. However, we have little understanding of how environmental heterogeneity shapes the effect of diversity on ecosystem functioning and to what extent this diversity effect is mediated by variation in species richness or species turnover. This knowledge is crucial to scaling up the results of experiments from local to regional scales. Here we quantify the diversity effect and its components-that is, the contributions of variation in species richness and species turnover-for 22 ecosystem functions of microorganisms, plants and animals across 13 major ecosystem types on Mt Kilimanjaro, Tanzania. Environmental heterogeneity across ecosystem types on average increased the diversity effect from explaining 49% to 72% of the variation in ecosystem functions. In contrast to our expectation, the diversity effect was more strongly mediated by variation in species richness than by species turnover. Our findings reveal that environmental heterogeneity strengthens the relationship between biodiversity and ecosystem functioning and that species richness is a stronger driver of ecosystem functioning than species turnover. Based on a broad range of taxa and ecosystem functions in a non-experimental system, these results are in line with predictions from biodiversity experiments and emphasize that conserving biodiversity is essential for maintaining ecosystem functioning.}, } @article {pmid34543307, year = {2021}, author = {Pestle, WJ and Hubbell, C and Hubbe, M}, title = {(DIGSS) Determination of Intervals using Georeferenced Survey Simulation: An R package for subsurface survey.}, journal = {PloS one}, volume = {16}, number = {9}, pages = {e0257386}, pmid = {34543307}, issn = {1932-6203}, mesh = {Algorithms ; Archaeology/*methods ; Artifacts ; Computational Biology/*methods ; Computer Simulation ; Environmental Monitoring/*methods ; Environmental Pollution ; Geology ; Humans ; Models, Statistical ; Programming Languages ; Software ; Statistics as Topic ; }, abstract = {Systematic survey is a crucial component of the archaeological field endeavor. In low visibility areas, systematic subsurface testing is required, most often in the form of shovel test pits or "STPs". Decisions about the interval between STPs, and the size of such units, impact significantly both the effectiveness of survey for site location and the efficiency of such prospection efforts, and yet "cookie-cutter" survey strategies are often employed without a thorough examination of their costs and benefits. In this work, we present a simulation-based method (DIGSS, Determination of Intervals using Georeferenced Survey Simulation) by which archaeologists can simulate the effectiveness and efficiency of different survey strategies for both prospective and retrospective applications. Beyond permitting the design and implementation of survey strategies that both maximize the possibility of site detection in a given region and that husband precious resources (money and time), this method permits the generation of post hoc correction factors that make direct comparison of previous surveys possible. While DIGSS was designed with archaeological applications (artifacts and sites) in mind, it has potential ramifications in other fields of study where discrete spatial sampling is used as a means of determining the presence, absence, or abundance of discontinuous assemblages materials of interest in a survey region. As such, we can envision potential application in the fields of geology, ecology, and environmental/pollution monitoring.}, } @article {pmid34538136, year = {2021}, author = {De Baets, K and Huntley, JW and Scarponi, D and Klompmaker, AA and Skawina, A}, title = {Phanerozoic parasitism and marine metazoan diversity: dilution versus amplification.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {376}, number = {1837}, pages = {20200366}, pmid = {34538136}, issn = {1471-2970}, mesh = {Animals ; *Biodiversity ; *Biological Evolution ; Databases, Factual ; Fossils ; Invertebrates/*parasitology ; Marine Biology ; Paleontology ; Parasites/*physiology ; Vertebrates/*parasitology ; }, abstract = {Growing evidence suggests that biodiversity mediates parasite prevalence. We have compiled the first global database on occurrences and prevalence of marine parasitism throughout the Phanerozoic and assess the relationship with biodiversity to test if there is support for amplification or dilution of parasitism at the macroevolutionary scale. Median prevalence values by era are 5% for the Paleozoic, 4% for the Mesozoic, and a significant increase to 10% for the Cenozoic. We calculated period-level shareholder quorum sub-sampled (SQS) estimates of mean sampled diversity, three-timer (3T) origination rates, and 3T extinction rates for the most abundant host clades in the Paleobiology Database to compare to both occurrences of parasitism and the more informative parasite prevalence values. Generalized linear models (GLMs) of parasite occurrences and SQS diversity measures support both the amplification (all taxa pooled, crinoids and blastoids, and molluscs) and dilution hypotheses (arthropods, cnidarians, and bivalves). GLMs of prevalence and SQS diversity measures support the amplification hypothesis (all taxa pooled and molluscs). Though likely scale-dependent, parasitism has increased through the Phanerozoic and clear patterns primarily support the amplification of parasitism with biodiversity in the history of life. This article is part of the theme issue 'Infectious disease macroecology: parasite diversity and dynamics across the globe'.}, } @article {pmid34536956, year = {2021}, author = {Drozdovitch, V and Minenko, V and Kukhta, T and Viarenich, K and Trofimik, S and Rogounovitch, T and Nakayama, T and Drozd, V and Veyalkin, I and Mitsutake, N and Ostroumova, E and Saenko, V}, title = {Thyroid dose estimates for the genome-wide association study of thyroid cancer in persons exposed in Belarus to 131I after the Chernobyl accident.}, journal = {Journal of radiation research}, volume = {}, number = {}, pages = {}, doi = {10.1093/jrr/rrab082}, pmid = {34536956}, issn = {1349-9157}, support = {/NH/NIH HHS/United States ; 001/WHO_/World Health Organization/International ; }, abstract = {The Chernobyl accident on 26 April 1986 led to a sharp increase in thyroid cancer (TC) incidence in the individuals exposed to radiation in childhood. The major risk factor for TC was exposure to Iodine-131 (131I). Here, we estimated the thyroid doses due to 131I intake for 2041 participants of the genome-wide association study of TC in Belarusian people exposed to radioactive fallout from the Chernobyl accident. The following parameter-values specially developed in this study were used to estimate individual thyroid doses: (i) scaling factors for adjustment of the model-based doses, (ii) age and gender diet to characterize 131I intake, and (iii) area-, age- and gender-specific S-values for the thyroid gland per 131I decay in the thyroid. The most reliable doses were calculated for 103 people with measured 131I thyroid activity (the arithmetic mean of 1.2 Gy, median 0.52 Gy), and 275 individuals with detailed residential history and dietary data (the arithmetic mean of 0.41 Gy, median 0.24 Gy). The arithmetic mean of thyroid doses among all study participants was 0.23 Gy (median 0.082 Gy); the highest individual dose was 9.0 Gy. Special attention was paid to the reliability and validity of the obtained estimates, in particular for the individuals without 131I thyroid activity measurements and individual data on residential history and diet, by comparing those with the doses from other post-Chernobyl epidemiological studies. Overall, the doses estimated in the current study were in reasonable agreement with previously reported thyroid doses. These doses will be used in the genome-wide association study of TC in people exposed in Belarus to 131I after the Chernobyl accident.}, } @article {pmid34535466, year = {2021}, author = {Hippisley-Cox, J and Coupland, CA and Mehta, N and Keogh, RH and Diaz-Ordaz, K and Khunti, K and Lyons, RA and Kee, F and Sheikh, A and Rahman, S and Valabhji, J and Harrison, EM and Sellen, P and Haq, N and Semple, MG and Johnson, PWM and Hayward, A and Nguyen-Van-Tam, JS}, title = {Risk prediction of covid-19 related death and hospital admission in adults after covid-19 vaccination: national prospective cohort study.}, journal = {BMJ (Clinical research ed.)}, volume = {374}, number = {}, pages = {n2244}, pmid = {34535466}, issn = {1756-1833}, support = {MR/V028367/1/MRC_/Medical Research Council/United Kingdom ; MR/K023241/1/MRC_/Medical Research Council/United Kingdom ; MC_PC_13043/MRC_/Medical Research Council/United Kingdom ; MR/K006525/1/MRC_/Medical Research Council/United Kingdom ; MC_PC_19025/MRC_/Medical Research Council/United Kingdom ; MR/S017968/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Adult ; Aged ; Aged, 80 and over ; BNT162 Vaccine ; COVID-19/immunology/*mortality ; COVID-19 Vaccines/*administration & dosage/immunology ; ChAdOx1 nCoV-19 ; Comorbidity ; Databases, Factual ; Female ; Hospitalization/*statistics & numerical data ; Humans ; Male ; Middle Aged ; Prospective Studies ; Risk Assessment ; SARS-CoV-2 ; United Kingdom/epidemiology ; Vaccination/*statistics & numerical data ; }, abstract = {OBJECTIVES: To derive and validate risk prediction algorithms to estimate the risk of covid-19 related mortality and hospital admission in UK adults after one or two doses of covid-19 vaccination.

DESIGN: Prospective, population based cohort study using the QResearch database linked to data on covid-19 vaccination, SARS-CoV-2 results, hospital admissions, systemic anticancer treatment, radiotherapy, and the national death and cancer registries.

SETTINGS: Adults aged 19-100 years with one or two doses of covid-19 vaccination between 8 December 2020 and 15 June 2021.

MAIN OUTCOME MEASURES: Primary outcome was covid-19 related death. Secondary outcome was covid-19 related hospital admission. Outcomes were assessed from 14 days after each vaccination dose. Models were fitted in the derivation cohort to derive risk equations using a range of predictor variables. Performance was evaluated in a separate validation cohort of general practices.

RESULTS: Of 6 952 440 vaccinated patients in the derivation cohort, 5 150 310 (74.1%) had two vaccine doses. Of 2031 covid-19 deaths and 1929 covid-19 hospital admissions, 81 deaths (4.0%) and 71 admissions (3.7%) occurred 14 days or more after the second vaccine dose. The risk algorithms included age, sex, ethnic origin, deprivation, body mass index, a range of comorbidities, and SARS-CoV-2 infection rate. Incidence of covid-19 mortality increased with age and deprivation, male sex, and Indian and Pakistani ethnic origin. Cause specific hazard ratios were highest for patients with Down's syndrome (12.7-fold increase), kidney transplantation (8.1-fold), sickle cell disease (7.7-fold), care home residency (4.1-fold), chemotherapy (4.3-fold), HIV/AIDS (3.3-fold), liver cirrhosis (3.0-fold), neurological conditions (2.6-fold), recent bone marrow transplantation or a solid organ transplantation ever (2.5-fold), dementia (2.2-fold), and Parkinson's disease (2.2-fold). Other conditions with increased risk (ranging from 1.2-fold to 2.0-fold increases) included chronic kidney disease, blood cancer, epilepsy, chronic obstructive pulmonary disease, coronary heart disease, stroke, atrial fibrillation, heart failure, thromboembolism, peripheral vascular disease, and type 2 diabetes. A similar pattern of associations was seen for covid-19 related hospital admissions. No evidence indicated that associations differed after the second dose, although absolute risks were reduced. The risk algorithm explained 74.1% (95% confidence interval 71.1% to 77.0%) of the variation in time to covid-19 death in the validation cohort. Discrimination was high, with a D statistic of 3.46 (95% confidence interval 3.19 to 3.73) and C statistic of 92.5. Performance was similar after each vaccine dose. In the top 5% of patients with the highest predicted covid-19 mortality risk, sensitivity for identifying covid-19 deaths within 70 days was 78.7%.

CONCLUSION: This population based risk algorithm performed well showing high levels of discrimination for identifying those patients at highest risk of covid-19 related death and hospital admission after vaccination.}, } @article {pmid34534224, year = {2021}, author = {Stringer, DN and Bertozzi, T and Meusemann, K and Delean, S and Guzik, MT and Tierney, SM and Mayer, C and Cooper, SJB and Javidkar, M and Zwick, A and Austin, AD}, title = {Development and evaluation of a custom bait design based on 469 single-copy protein-coding genes for exon capture of isopods (Philosciidae: Haloniscus).}, journal = {PloS one}, volume = {16}, number = {9}, pages = {e0256861}, pmid = {34534224}, issn = {1932-6203}, mesh = {Animals ; Arthropod Proteins/classification/*genetics/metabolism ; Datasets as Topic ; *Exons ; Gene Expression ; Genetic Loci ; Genetics, Population ; *Genome ; High-Throughput Nucleotide Sequencing ; Introns ; Isopoda/classification/*genetics ; *Open Reading Frames ; Phylogeny ; }, abstract = {Transcriptome-based exon capture approaches, along with next-generation sequencing, are allowing for the rapid and cost-effective production of extensive and informative phylogenomic datasets from non-model organisms for phylogenetics and population genetics research. These approaches generally employ a reference genome to infer the intron-exon structure of targeted loci and preferentially select longer exons. However, in the absence of an existing and well-annotated genome, we applied this exon capture method directly, without initially identifying intron-exon boundaries for bait design, to a group of highly diverse Haloniscus (Philosciidae), paraplatyarthrid and armadillid isopods, and examined the performance of our methods and bait design for phylogenetic inference. Here, we identified an isopod-specific set of single-copy protein-coding loci, and a custom bait design to capture targeted regions from 469 genes, and analysed the resulting sequence data with a mapping approach and newly-created post-processing scripts. We effectively recovered a large and informative dataset comprising both short (<100 bp) and longer (>300 bp) exons, with high uniformity in sequencing depth. We were also able to successfully capture exon data from up to 16-year-old museum specimens along with more distantly related outgroup taxa, and efficiently pool multiple samples prior to capture. Our well-resolved phylogenies highlight the overall utility of this methodological approach and custom bait design, which offer enormous potential for application to future isopod, as well as broader crustacean, molecular studies.}, } @article {pmid34533750, year = {2022}, author = {Tella, A and Balogun, AL}, title = {GIS-based air quality modelling: spatial prediction of PM10 for Selangor State, Malaysia using machine learning algorithms.}, journal = {Environmental science and pollution research international}, volume = {29}, number = {57}, pages = {86109-86125}, pmid = {34533750}, issn = {1614-7499}, mesh = {Humans ; Geographic Information Systems ; Bayes Theorem ; Cities ; Malaysia ; Sustainable Growth ; *Air Pollution/analysis ; *Air Pollutants/analysis ; Particulate Matter/analysis ; Machine Learning ; Algorithms ; }, abstract = {Rapid urbanization has caused severe deterioration of air quality globally, leading to increased hospitalization and premature deaths. Therefore, accurate prediction of air quality is crucial for mitigation planning to support urban sustainability and resilience. Although some studies have predicted air pollutants such as particulate matter (PM) using machine learning algorithms (MLAs), there is a paucity of studies on spatial hazard assessment with respect to the air quality index (AQI). Incorporating PM in AQI studies is crucial because of its easily inhalable micro-size which has adverse impacts on ecology, environment, and human health. Accurate and timely prediction of the air quality index can ensure adequate intervention to aid air quality management. Therefore, this study undertakes a spatial hazard assessment of the air quality index using particulate matter with a diameter of 10 μm or lesser (PM10) in Selangor, Malaysia, by developing four machine learning models: eXtreme Gradient Boosting (XGBoost), random forest (RF), K-nearest neighbour (KNN), and Naive Bayes (NB). Spatially processed data such as NDVI, SAVI, BU, LST, Ws, slope, elevation, and road density was used for the modelling. The model was trained with 70% of the dataset, while 30% was used for cross-validation. Results showed that XGBoost has the highest overall accuracy and precision of 0.989 and 0.995, followed by random forest (0.989, 0.993), K-nearest neighbour (0.987, 0.984), and Naive Bayes (0.917, 0.922), respectively. The spatial air quality maps were generated by integrating the geographical information system (GIS) with the four MLAs, which correlated with Malaysia's air pollution index. The maps indicate that air quality in Selangor is satisfactory and posed no threats to health. Nevertheless, the two algorithms with the best performance (XGBoost and RF) indicate that a high percentage of the air quality is moderate. The study concludes that successful air pollution management policies such as green infrastructure practice, improvement of energy efficiency, and restrictions on heavy-duty vehicles can be adopted in Selangor and other Southeast Asian cities to prevent deterioration of air quality in the future.}, } @article {pmid34530225, year = {2021}, author = {Ma, X and Du, Y and Peng, W and Zhang, S and Liu, X and Wang, S and Yuan, S and Kolditz, O}, title = {Modeling the impacts of plants and internal organic carbon on remediation performance in the integrated vertical flow constructed wetland.}, journal = {Water research}, volume = {204}, number = {}, pages = {117635}, doi = {10.1016/j.watres.2021.117635}, pmid = {34530225}, issn = {1879-2448}, mesh = {*Carbon ; Nitrogen ; Oxygen ; Reproducibility of Results ; *Wetlands ; }, abstract = {The integrated vertical flow (IVF) constructed wetland consists of two or more chambers with heterogeneous flow patterns and strong aeration capability, possesses favorable remediation performance. The Constructed Wetland Model No.1 (CWM1) embedded in the OpenGeoSys # IPHREEQC was applied to investigate the wetland plant effects on treatment efficiency. Two fundamental functions of the plant roots (i) the radial oxygen loss (ROL) and (ii) exudation of internal organic carbon (IOC), are developed and implemented in the model to simulate the treating processes of planted laboratory-scale IVF wetlands fed by the synthetic wastewater. The good agreement between simulated results and measurements of the planted IVF wetland and the unplanted filters mimicking wetland demonstrates the combined effects of ROL and IOC and the model reliability. In summer the ammonia (NH4-N) and total nitrogen (TN) removals are high as above 90% in both IVF wetlands, and in winter they decline significantly to around 55% and 45% in unplanted wetland, contrastively to about 85% and 78% in the planted wetland. The nitrogen removal - COD/N ratio relation curves of IVF wetlands are proposed and obtained by modeling to evaluate organic carbon loading status. Based on the curves, the COD/N ratios of unplanted and planted wetlands are about 3∼7 and 3∼10 gCOD/gN for high TN removal respectively. Planted wetlands can tolerate a wider range of COD/N ratio influents than unplanted ones. The ROL in the unplanted wetland promotes COD and NH4-N removal, while may inhibit denitrification under low-temperature conditions. The single addition of IOC enhances the oxygen-consuming and restrains the nitrification under the full loaded COD condition. Summing up all organic carbon releases from substrate and roots as IOC, the quantification of IOC acts on nitrogen treatment was simulated and compared with the external organic carbon (EOC) loading from influent. IOC performs higher efficiency on TN removal than EOC at the same organic loading rates. The results provide the thoughts of the solution for low TN removal in the carbon deficient constructed wetlands.}, } @article {pmid34527601, year = {2021}, author = {Altinli, M and Schnettler, E and Sicard, M}, title = {Symbiotic Interactions Between Mosquitoes and Mosquito Viruses.}, journal = {Frontiers in cellular and infection microbiology}, volume = {11}, number = {}, pages = {694020}, pmid = {34527601}, issn = {2235-2988}, mesh = {Animals ; *Arboviruses ; *Culicidae ; Female ; Humans ; *Insect Viruses ; Metagenomics ; *Viruses ; }, abstract = {Mosquitoes not only transmit human and veterinary pathogens called arboviruses (arthropod-borne viruses) but also harbor mosquito-associated insect-specific viruses (mosquito viruses) that cannot infect vertebrates. In the past, studies investigating mosquito viruses mainly focused on highly pathogenic interactions that were easier to detect than those without visible symptoms. However, the recent advances in viral metagenomics have highlighted the abundance and diversity of viruses which do not generate mass mortality in host populations. Over the last decade, this has facilitated the rapid growth of virus discovery in mosquitoes. The circumstances around the discovery of mosquito viruses greatly affected how they have been studied so far. While earlier research mainly focused on the pathogenesis caused by DNA and some double-stranded RNA viruses during larval stages, more recently discovered single-stranded RNA mosquito viruses were heavily studied for their putative interference with arboviruses in female adults. Thus, many aspects of mosquito virus interactions with their hosts and host-microbiota are still unknown. In this context, considering mosquito viruses as endosymbionts can help to identify novel research areas, in particular in relation to their long-term interactions with their hosts (e.g. relationships during all life stages, the stability of the associations at evolutionary scales, transmission routes and virulence evolution) and the possible context-dependent range of interactions (i.e. beneficial to antagonistic). Here, we review the symbiotic interactions of mosquito viruses considering different aspects of their ecology, such as transmission, host specificity, host immune system and interactions with other symbionts within the host cellular arena. Finally, we highlight related research gaps in mosquito virus research.}, } @article {pmid34526557, year = {2021}, author = {Ogushi, F and Kertész, J and Kaski, K and Shimada, T}, title = {Ecology of the digital world of Wikipedia.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {18371}, pmid = {34526557}, issn = {2045-2322}, abstract = {Wikipedia, a paradigmatic example of online knowledge space is organized in a collaborative, bottom-up way with voluntary contributions, yet it maintains a level of reliability comparable to that of traditional encyclopedias. The lack of selected professional writers and editors makes the judgement about quality and trustworthiness of the articles a real challenge. Here we show that a self-consistent metrics for the network defined by the edit records captures well the character of editors' activity and the articles' level of complexity. Using our metrics, one can better identify the human-labeled high-quality articles, e.g., "featured" ones, and differentiate them from the popular and controversial articles. Furthermore, the dynamics of the editor-article system is also well captured by the metrics, revealing the evolutionary pathways of articles and diverse roles of editors. We demonstrate that the collective effort of the editors indeed drives to the direction of article improvement.}, } @article {pmid34522345, year = {2021}, author = {Remeš, V and Remešová, E and Friedman, NR and Matysioková, B and Rubáčová, L}, title = {Functional diversity of avian communities increases with canopy height: From individual behavior to continental-scale patterns.}, journal = {Ecology and evolution}, volume = {11}, number = {17}, pages = {11839-11851}, pmid = {34522345}, issn = {2045-7758}, abstract = {Vegetation complexity is an important predictor of animal species diversity. Specifically, taller vegetation should provide more potential ecological niches and thus harbor communities with higher species richness and functional diversity (FD). Resource use behavior is an especially important functional trait because it links species to their resource base with direct relevance to niche partitioning. However, it is unclear how exactly the diversity of resource use behavior changes with vegetation complexity. To address this question, we studied avian FD in relation to vegetation complexity along a continental-scale vegetation gradient. We quantified foraging behavior of passerine birds in terms of foraging method and substrate use at 21 sites (63 transects) spanning 3,000 km of woodlands and forests in Australia. We also quantified vegetation structure on 630 sampling points at the same sites. Additionally, we measured morphological traits for all 111 observed species in museum collections. We calculated individual-based, abundance-weighted FD in morphology and foraging behavior and related it to species richness and vegetation complexity (indexed by canopy height) using structural equation modeling, rarefaction analyses, and distance-based metrics. FD of morphology and foraging methods was best predicted by species richness. However, FD of substrate use was best predicted by canopy height (ranging 10-30 m), but only when substrates were categorized with fine resolution (17 categories), not when categorized coarsely (8 categories). These results suggest that, first, FD might increase with vegetation complexity independently of species richness, but whether it does so depends on the studied functional trait. Second, patterns found might be shaped by how finely we categorize functional traits. More complex vegetation provided larger "ecological space" with more resources, allowing the coexistence of more species with disproportionately more diverse foraging substrate use. We suggest that the latter pattern was driven by nonrandom accumulation of functionally distinct species with increasing canopy height.}, } @article {pmid34518574, year = {2021}, author = {de Santana, CD and Parenti, LR and Dillman, CB and Coddington, JA and Bastos, DA and Baldwin, CC and Zuanon, J and Torrente-Vilara, G and Covain, R and Menezes, NA and Datovo, A and Sado, T and Miya, M}, title = {The critical role of natural history museums in advancing eDNA for biodiversity studies: a case study with Amazonian fishes.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {18159}, pmid = {34518574}, issn = {2045-2322}, mesh = {Animals ; *Biodiversity ; DNA Barcoding, Taxonomic ; DNA, Environmental/*analysis ; Data Analysis ; Databases, Genetic ; Fishes/classification/*genetics ; *Museums ; Phylogeny ; Rivers ; South America ; Species Specificity ; Surveys and Questionnaires ; }, abstract = {Ichthyological surveys have traditionally been conducted using whole-specimen, capture-based sampling with varied but conventional fishing gear. Recently, environmental DNA (eDNA) metabarcoding has emerged as a complementary, and possible alternative, approach to whole-specimen methodologies. In the tropics, where much of the diversity remains undescribed, vast reaches continue unexplored, and anthropogenic activities are constant threats; there have been few eDNA attempts for ichthyological inventories. We tested the discriminatory power of eDNA using MiFish primers with existing public reference libraries and compared this with capture-based methods in two distinct ecosystems in the megadiverse Amazon basin. In our study, eDNA provided an accurate snapshot of the fishes at higher taxonomic levels and corroborated its effectiveness to detect specialized fish assemblages. Some flaws in fish metabarcoding studies are routine issues addressed in natural history museums. Thus, by expanding their archives and adopting a series of initiatives linking collection-based research, training and outreach, natural history museums can enable the effective use of eDNA to survey Earth's hotspots of biodiversity before taxa go extinct. Our project surveying poorly explored rivers and using DNA vouchered archives to build metabarcoding libraries for Neotropical fishes can serve as a model of this protocol.}, } @article {pmid34516542, year = {2021}, author = {Ma, S and Ren, B and Mallick, H and Moon, YS and Schwager, E and Maharjan, S and Tickle, TL and Lu, Y and Carmody, RN and Franzosa, EA and Janson, L and Huttenhower, C}, title = {A statistical model for describing and simulating microbial community profiles.}, journal = {PLoS computational biology}, volume = {17}, number = {9}, pages = {e1008913}, pmid = {34516542}, issn = {1553-7358}, support = {P30 DK043351/DK/NIDDK NIH HHS/United States ; R24 DK110499/DK/NIDDK NIH HHS/United States ; U19 AI110820/AI/NIAID NIH HHS/United States ; }, mesh = {Algorithms ; Benchmarking ; Computational Biology/methods ; Computer Simulation ; *Microbiota ; *Models, Statistical ; }, abstract = {Many methods have been developed for statistical analysis of microbial community profiles, but due to the complex nature of typical microbiome measurements (e.g. sparsity, zero-inflation, non-independence, and compositionality) and of the associated underlying biology, it is difficult to compare or evaluate such methods within a single systematic framework. To address this challenge, we developed SparseDOSSA (Sparse Data Observations for the Simulation of Synthetic Abundances): a statistical model of microbial ecological population structure, which can be used to parameterize real-world microbial community profiles and to simulate new, realistic profiles of known structure for methods evaluation. Specifically, SparseDOSSA's model captures marginal microbial feature abundances as a zero-inflated log-normal distribution, with additional model components for absolute cell counts and the sequence read generation process, microbe-microbe, and microbe-environment interactions. Together, these allow fully known covariance structure between synthetic features (i.e. "taxa") or between features and "phenotypes" to be simulated for method benchmarking. Here, we demonstrate SparseDOSSA's performance for 1) accurately modeling human-associated microbial population profiles; 2) generating synthetic communities with controlled population and ecological structures; 3) spiking-in true positive synthetic associations to benchmark analysis methods; and 4) recapitulating an end-to-end mouse microbiome feeding experiment. Together, these represent the most common analysis types in assessment of real microbial community environmental and epidemiological statistics, thus demonstrating SparseDOSSA's utility as a general-purpose aid for modeling communities and evaluating quantitative methods. An open-source implementation is available at http://huttenhower.sph.harvard.edu/sparsedossa2.}, } @article {pmid34508077, year = {2021}, author = {Oidtman, RJ and Omodei, E and Kraemer, MUG and Castañeda-Orjuela, CA and Cruz-Rivera, E and Misnaza-Castrillón, S and Cifuentes, MP and Rincon, LE and Cañon, V and Alarcon, P and España, G and Huber, JH and Hill, SC and Barker, CM and Johansson, MA and Manore, CA and Reiner, RC and Rodriguez-Barraquer, I and Siraj, AS and Frias-Martinez, E and García-Herranz, M and Perkins, TA}, title = {Trade-offs between individual and ensemble forecasts of an emerging infectious disease.}, journal = {Nature communications}, volume = {12}, number = {1}, pages = {5379}, pmid = {34508077}, issn = {2041-1723}, support = {/WT_/Wellcome Trust/United Kingdom ; 220414/Z/20/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Colombia/epidemiology ; Communicable Diseases, Emerging/*epidemiology ; Data Interpretation, Statistical ; Datasets as Topic ; Epidemics/*statistics & numerical data ; *Epidemiological Monitoring ; Forecasting/methods ; Humans ; Models, Statistical ; Spatio-Temporal Analysis ; Uncertainty ; Zika Virus Infection/*epidemiology ; }, abstract = {Probabilistic forecasts play an indispensable role in answering questions about the spread of newly emerged pathogens. However, uncertainties about the epidemiology of emerging pathogens can make it difficult to choose among alternative model structures and assumptions. To assess the potential for uncertainties about emerging pathogens to affect forecasts of their spread, we evaluated the performance 16 forecasting models in the context of the 2015-2016 Zika epidemic in Colombia. Each model featured a different combination of assumptions about human mobility, spatiotemporal variation in transmission potential, and the number of virus introductions. We found that which model assumptions had the most ensemble weight changed through time. We additionally identified a trade-off whereby some individual models outperformed ensemble models early in the epidemic, but on average the ensembles outperformed all individual models. Our results suggest that multiple models spanning uncertainty across alternative assumptions are necessary to obtain robust forecasts for emerging infectious diseases.}, } @article {pmid34505241, year = {2021}, author = {Xu, M and Yang, M and Xie, D and Ni, J and Meng, J and Wang, Q and Gao, M and Wu, C}, title = {Research trend analysis of composting based on Web of Science database.}, journal = {Environmental science and pollution research international}, volume = {28}, number = {42}, pages = {59528-59541}, pmid = {34505241}, issn = {1614-7499}, support = {2018YFC1900904//national key r&d program of china/ ; 51978047//national natural science foundation of china/ ; }, mesh = {Agriculture ; Bibliometrics ; *Composting ; Databases, Factual ; Solid Waste ; }, abstract = {Bibliometric analysis was used in this study for the quantitative evaluation of current research trends on composting. The research articles indexed from the Science Citation Index-Expanded in Web of Science database published from 2000 to 2019 were investigated. The USA, China and Spain were the top three countries considering the number of papers. Amongst the research institutes, CSIC of Spain, Chinese Academy of Sciences and Agriculture & Agri-Food Canada ranked the top three in total publication amount. Journals that published a significant number of literature regarding topics of composting included Environmental Sciences & Ecology, Agriculture and Engineering. In terms of research content, keywords such as heavy metal, heavy metal and biodegradation appeared frequently. In addition, the analysis of keywords revealed the following research hotspots in future studies: investigation of heavy metal passivator, optimisation of composting conditioner, development of all kinds of microorganisms, rational management of the composting process and improvement of solid waste life cycle assessment. To some extent, it helps to understand the current global status and trends of the related research.}, } @article {pmid34504229, year = {2021}, author = {Gavashelishvili, A and Yanchukov, A and Tarkhnishvili, D and Murtskhvaladze, M and Akhvlediani, I and Kazancı, C}, title = {Landscape genetics and the genetic legacy of Upper Paleolithic and Mesolithic hunter-gatherers in the modern Caucasus.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {17985}, pmid = {34504229}, issn = {2045-2322}, mesh = {Chromosomes, Human, Y/genetics ; DNA/genetics/isolation & purification ; Databases, Genetic ; Genetic Drift ; Genetic Variation ; *Genome, Human ; Genomics/*methods ; *Genotype ; Georgia (Republic) ; History, 21st Century ; History, Ancient ; Human Migration/*history ; Humans ; Male ; Pedigree ; Refugees/history ; Russia ; Turkey ; White People/*genetics ; }, abstract = {This study clarifies the role of refugia and landscape permeability in the formation of the current genetic structure of peoples of the Caucasus. We report novel genome-wide data for modern individuals from the Caucasus, and analyze them together with available Paleolithic and Mesolithic individuals from Eurasia and Africa in order (1) to link the current and ancient genetic structures via landscape permeability, and (2) thus to identify movement paths between the ancient refugial populations and the Caucasus. The ancient genetic ancestry is best explained by landscape permeability implying that human movement is impeded by terrain ruggedness, swamps, glaciers and desert. Major refugial source populations for the modern Caucasus are those of the Caucasus, Anatolia, the Balkans and Siberia. In Rugged areas new genetic signatures take a long time to form, but once they do so, they remain for a long time. These areas act as time capsules harboring genetic signatures of ancient source populations and making it possible to help reconstruct human history based on patterns of variation today.}, } @article {pmid34504119, year = {2021}, author = {Trigos-Peral, G and Juhász, O and Kiss, PJ and Módra, G and Tenyér, A and Maák, I}, title = {Wood ants as biological control of the forest pest beetles Ips spp.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {17931}, pmid = {34504119}, issn = {2045-2322}, mesh = {Altitude ; Animals ; Ants/*physiology ; Biodiversity ; Climate Change ; Coleoptera/*physiology ; Conservation of Natural Resources/methods ; *Forests ; Hungary ; Pest Control, Biological/*methods ; Poland ; Population Dynamics ; Slovakia ; *Trees ; }, abstract = {Climate change is one of the major threats to biodiversity, but its impact varies among the species. Bark beetles (Ips spp.), as well as other wood-boring pests of European forests, show escalating numbers in response to the changes driven by climate change and seriously affect the survival of the forests through the massive killing of trees. Many methods were developed to control these wood-boring beetles, however, their implementation can be detrimental for other forest specialists. Ants are widely used for biological pest-control, so in our study, we aimed to test the effect of Formica polyctena on the control of the wood-boring beetles. The results show that the proportion of infested trees is significantly reduced by the increase of the number of F. polyctena nests, with a strong effect on those infested by Ips species. We also show that the boring beetle community is shaped by different biotic and abiotic factors, including the presence of F. polyctena nests. However, the boring beetle infestation was not related to the latitude, altitude and age of the forests. Based on our results, we assert the effectiveness of the red wood ants as biological pest control and the importance of their conservation to keep the health of the forests.}, } @article {pmid34502161, year = {2021}, author = {Stravoravdis, S and Marra, RE and LeBlanc, NR and Crouch, JA and Hulvey, JP}, title = {Evidence for the Role of CYP51A and Xenobiotic Detoxification in Differential Sensitivity to Azole Fungicides in Boxwood Blight Pathogens.}, journal = {International journal of molecular sciences}, volume = {22}, number = {17}, pages = {}, pmid = {34502161}, issn = {1422-0067}, mesh = {Azoles/*pharmacology ; Buxus/*drug effects/*genetics/*microbiology ; Computational Biology/methods ; Cytochrome P-450 Enzyme System/*genetics ; Drug Resistance, Fungal ; Ergosterol/metabolism ; Fungal Proteins/*genetics ; Fungicides, Industrial/*pharmacology ; Gene Expression Profiling ; Genome, Fungal ; Genomics/methods ; Hypocreales/drug effects ; Inactivation, Metabolic/genetics ; Microbial Sensitivity Tests ; Plant Diseases/microbiology ; Transcriptome ; }, abstract = {Boxwood blight, a fungal disease of ornamental plants (Buxus spp.), is caused by two sister species, Calonectria pseudonaviculata (Cps) and C. henricotiae (Che). Compared to Cps, Che is documented to display reduced sensitivity to fungicides, including the azole class of antifungals, which block synthesis of a key fungal membrane component, ergosterol. A previous study reported an ergosterol biosynthesis gene in Cps, CYP51A, to be a pseudogene, and RNA-Seq data confirm that a functional CYP51A is expressed only in Che. The lack of additional ergosterol biosynthesis genes showing significant differential expression suggests that the functional CYP51A in Che could contribute to reduced azole sensitivity when compared to Cps. RNA-Seq and bioinformatic analyses found that following azole treatment, 55 genes in Cps, belonging to diverse pathways, displayed a significant decrease in expression. Putative xenobiotic detoxification genes overexpressed in tetraconazole-treated Che encoded predicted monooxygenase and oxidoreductase enzymes. In summary, expression of a functional CYP51A gene and overexpression of predicted xenobiotic detoxification genes appear likely to contribute to differential fungicide sensitivity in these two sister taxa.}, } @article {pmid34501863, year = {2021}, author = {Barhoumi, W and Chelbi, I and Fares, W and Zhioua, S and Abbas, M and Derbali, M and Ramalho-Ortigao, M and Zhioua, E}, title = {Risk Assessment of the Role of the Ecotones in the Transmission of Zoonotic Cutaneous Leishmaniasis in Central Tunisia.}, journal = {International journal of environmental research and public health}, volume = {18}, number = {17}, pages = {}, pmid = {34501863}, issn = {1660-4601}, mesh = {Animals ; *Leishmania major ; *Leishmaniasis, Cutaneous/epidemiology ; *Phlebotomus ; Risk Assessment ; Tunisia/epidemiology ; }, abstract = {Zoonotic cutaneous leishmaniasis (ZCL), endemic in Central and Southern Tunisia, is caused by Leishmania major (Kinetoplastida: Trypanosomatidae), which is transmitted by the sand fly Phlebotomus papatasi. In Tunisia, the fat sand rat Psammomys obesus and the desert jird Meriones shawi are the principal reservoir hosts of L. major. The presence of the P. papatasi vector of the L. major etiologic agent of ZCL was assessed in the vicinity of villages in endemic areas of Central Tunisia. The study was performed from September through October 2019, a period corresponding to the main peak of activity of P. papatasi. Sand flies were collected from rodent burrows located at the ecotone level, which is the transition zone between the natural environment and human settlement. Sand flies were identified to species level and tested for the presence of L. major by PCR. Our entomological survey showed that P. papatasi is the most abundant sand fly species associated with rodent burrows, and this abundance is even higher in ecotones primarily occupied by P. obesus in comparison to ecotones occupied by M. shawi. Infections with Leishmania major were detected only in P. papatasi, with an overall minimum infection rate (MIR) of 2.64%. No significant difference was observed between the MIRs in ecotones of P. obesus and of M. shawi. Incidence of ZCL in the studied areas ranged from 200 to 700 cases per 100,000 inhabitants, with a mean incidence of 385.41 per 100,000. Higher ZCL incidence was identified in ecotones of M. shawi compared to ecotones of P. obesus. ZCL cases are positively correlated with the MIRs. Considering the short flight range of P. papatasi, increases in its densities associated with burrows of P. obesus or M. shawi at the ecotone level expand the overlap of infected vectors with communities and subsequently increase ZCL incidence. Therefore, control measures should target P. papatasi populations at the ecotones.}, } @article {pmid34497788, year = {2021}, author = {Stosovic, D and Vasiljevic, N and Jovanovic, V and Cirkovic, A and Paunovic, K and Davidovic, D}, title = {Dietary Habits of Older Adults in Serbia: Findings From the National Health Survey.}, journal = {Frontiers in public health}, volume = {9}, number = {}, pages = {610873}, pmid = {34497788}, issn = {2296-2565}, mesh = {Animals ; Cross-Sectional Studies ; *Diet ; *Feeding Behavior ; Health Surveys ; Serbia/epidemiology ; }, abstract = {Objectives: Adults aged 65 years and older comprise one fifth of the Serbian population. Many of them have multiple, often diet-related comorbidities. We aimed to investigate their dietary habits by comparing them with younger adults' and to determine the relation of the differing ones to demographic, socioeconomic and health factors. Methods: We performed a secondary analysis of 2013 Serbian National Health Survey data on 14,082 adults. Binary logistic regression was used to determine dietary habits associated with older age (≥65 years) compared to younger age (18-64 years) and to assess their independent predictors in older adults. Results: Older adults more often reported everyday breakfast (OR = 2.085, 95%CI = 1.622-2.680) and brown/wholegrain bread consumption (OR = 1.681, 95% CI = 1.537-1.839), while using margarine (OR = 0.578, 95%CI = 0.397-0.839), discretionary salt (sometimes: OR = 0.648, 95%CI = 0.596-0.705, almost always: OR = 0.522, 95%CI = 0.445-0.614) and consuming fish (two or more times a week: OR = 0.465, 95%CI = 0.383-0.566) less frequently than younger adults. This was mainly positively related to urban environment, affluence, higher education and poor health. Conclusion: Using nationally representative data, we found that older adults reported healthier dietary habits compared to younger adults, which requires timely public health action.}, } @article {pmid34496132, year = {2022}, author = {Creedy, TJ and Andújar, C and Meramveliotakis, E and Noguerales, V and Overcast, I and Papadopoulou, A and Morlon, H and Vogler, AP and Emerson, BC and Arribas, P}, title = {Coming of age for COI metabarcoding of whole organism community DNA: Towards bioinformatic harmonisation.}, journal = {Molecular ecology resources}, volume = {22}, number = {3}, pages = {847-861}, pmid = {34496132}, issn = {1755-0998}, support = {810729//Horizon 2020 Framework Programme/ ; }, mesh = {Animals ; Biodiversity ; *Computational Biology ; DNA/genetics ; *DNA Barcoding, Taxonomic/methods ; Ecology ; }, abstract = {Metabarcoding of DNA extracted from community samples of whole organisms (whole organism community DNA, wocDNA) is increasingly being applied to terrestrial, marine and freshwater metazoan communities to provide rapid, accurate and high resolution data for novel molecular ecology research. The growth of this field has been accompanied by considerable development that builds on microbial metabarcoding methods to develop appropriate and efficient sampling and laboratory protocols for whole organism metazoan communities. However, considerably less attention has focused on ensuring bioinformatic methods are adapted and applied comprehensively in wocDNA metabarcoding. In this study we examined over 600 papers and identified 111 studies that performed COI metabarcoding of wocDNA. We then systematically reviewed the bioinformatic methods employed by these papers to identify the state-of-the-art. Our results show that the increasing use of wocDNA COI metabarcoding for metazoan diversity is characterised by a clear absence of bioinformatic harmonisation, and the temporal trends show little change in this situation. The reviewed literature showed (i) high heterogeneity across pipelines, tasks and tools used, (ii) limited or no adaptation of bioinformatic procedures to the nature of the COI fragment, and (iii) a worrying underreporting of tasks, software and parameters. Based upon these findings we propose a set of recommendations that we think the metabarcoding community should consider to ensure that bioinformatic methods are appropriate, comprehensive and comparable. We believe that adhering to these recommendations will improve the long-term integrative potential of wocDNA COI metabarcoding for biodiversity science.}, } @article {pmid34495960, year = {2021}, author = {Li, C and Av-Shalom, TV and Tan, JWG and Kwah, JS and Chng, KR and Nagarajan, N}, title = {BEEM-Static: Accurate inference of ecological interactions from cross-sectional microbiome data.}, journal = {PLoS computational biology}, volume = {17}, number = {9}, pages = {e1009343}, pmid = {34495960}, issn = {1553-7358}, mesh = {Biomass ; Cross-Sectional Studies ; Datasets as Topic ; *Ecosystem ; *Gastrointestinal Microbiome ; Humans ; }, abstract = {BEEM-Static provides new opportunities for mining ecologically interpretable interactions and systems insights from the growing corpus of microbiome data.}, } @article {pmid34494031, year = {2021}, author = {Baaijens, JA and Zulli, A and Ott, IM and Petrone, ME and Alpert, T and Fauver, JR and Kalinich, CC and Vogels, CBF and Breban, MI and Duvallet, C and McElroy, K and Ghaeli, N and Imakaev, M and Mckenzie-Bennett, M and Robison, K and Plocik, A and Schilling, R and Pierson, M and Littlefield, R and Spencer, M and Simen, BB and , and Hanage, WP and Grubaugh, ND and Peccia, J and Baym, M}, title = {Variant abundance estimation for SARS-CoV-2 in wastewater using RNA-Seq quantification.}, journal = {medRxiv : the preprint server for health sciences}, volume = {}, number = {}, pages = {}, pmid = {34494031}, support = {UL1 TR001863/TR/NCATS NIH HHS/United States ; T32 AI007535/AI/NIAID NIH HHS/United States ; R35 GM133700/GM/NIGMS NIH HHS/United States ; U54 GM088558/GM/NIGMS NIH HHS/United States ; TL1 TR001864/TR/NCATS NIH HHS/United States ; }, abstract = {Effectively monitoring the spread of SARS-CoV-2 variants is essential to efforts to counter the ongoing pandemic. Wastewater monitoring of SARS-CoV-2 RNA has proven an effective and efficient technique to approximate COVID-19 case rates in the population. Predicting variant abundances from wastewater, however, is technically challenging. Here we show that by sequencing SARS-CoV-2 RNA in wastewater and applying computational techniques initially used for RNA-Seq quantification, we can estimate the abundance of variants in wastewater samples. We show by sequencing samples from wastewater and clinical isolates in Connecticut U.S.A. between January and April 2021 that the temporal dynamics of variant strains broadly correspond. We further show that this technique can be used with other wastewater sequencing techniques by expanding to samples taken across the United States in a similar timeframe. We find high variability in signal among individual samples, and limited ability to detect the presence of variants with clinical frequencies <10%; nevertheless, the overall trends match what we observed from sequencing clinical samples. Thus, while clinical sequencing remains a more sensitive technique for population surveillance, wastewater sequencing can be used to monitor trends in variant prevalence in situations where clinical sequencing is unavailable or impractical.}, } @article {pmid34493743, year = {2021}, author = {Emelianova, K and Martínez Martínez, A and Campos-Dominguez, L and Kidner, C}, title = {Multi-tissue transcriptome analysis of two Begonia species reveals dynamic patterns of evolution in the chalcone synthase gene family.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {17773}, pmid = {34493743}, issn = {2045-2322}, mesh = {Acyltransferases/*genetics ; Amino Acid Sequence ; Base Sequence ; Begoniaceae/classification/*genetics/metabolism ; *Biological Evolution ; Evolution, Molecular ; *Gene Duplication ; Gene Ontology ; Genetic Variation ; Genome, Plant ; Molecular Sequence Annotation ; Multigene Family ; Organ Specificity ; Phylogeny ; Plant Proteins/*genetics ; Plant Structures/metabolism ; RNA, Plant/biosynthesis/genetics ; Sequence Alignment ; Sequence Homology, Amino Acid ; Species Specificity ; *Transcriptome ; }, abstract = {Begonia is an important horticultural plant group, as well as one of the most speciose Angiosperm genera, with over 2000 described species. Genus wide studies of genome size have shown that Begonia has a highly variable genome size, and analysis of paralog pairs has previously suggested that Begonia underwent a whole genome duplication. We address the contribution of gene duplication to the generation of diversity in Begonia using a multi-tissue RNA-seq approach. We chose to focus on chalcone synthase (CHS), a gene family having been shown to be involved in biotic and abiotic stress responses in other plant species, in particular its importance in maximising the use of variable light levels in tropical plants. We used RNA-seq to sample six tissues across two closely related but ecologically and morphologically divergent species, Begonia conchifolia and B. plebeja, yielding 17,012 and 19,969 annotated unigenes respectively. We identified the chalcone synthase gene family members in our Begonia study species, as well as in Hillebrandia sandwicensis, the monotypic sister genus to Begonia, Cucumis sativus, Arabidopsis thaliana, and Zea mays. Phylogenetic analysis suggested the CHS gene family has high duplicate turnover, all members of CHS identified in Begonia arising recently, after the divergence of Begonia and Cucumis. Expression profiles were similar within orthologous pairs, but we saw high inter-ortholog expression variation. Sequence analysis showed relaxed selective constraints on some ortholog pairs, with substitutions at conserved sites. Evidence of pseudogenisation and species specific duplication indicate that lineage specific differences are already beginning to accumulate since the divergence of our study species. We conclude that there is evidence for a role of gene duplication in generating diversity through sequence and expression divergence in Begonia.}, } @article {pmid34491200, year = {2021}, author = {, and Jha, SG and Borowsky, AT and Cole, BJ and Fahlgren, N and Farmer, A and Huang, SC and Karia, P and Libault, M and Provart, NJ and Rice, SL and Saura-Sanchez, M and Agarwal, P and Ahkami, AH and Anderton, CR and Briggs, SP and Brophy, JA and Denolf, P and Di Costanzo, LF and Exposito-Alonso, M and Giacomello, S and Gomez-Cano, F and Kaufmann, K and Ko, DK and Kumar, S and Malkovskiy, AV and Nakayama, N and Obata, T and Otegui, MS and Palfalvi, G and Quezada-Rodríguez, EH and Singh, R and Uhrig, RG and Waese, J and Van Wijk, K and Wright, RC and Ehrhardt, DW and Birnbaum, KD and Rhee, SY}, title = {Vision, challenges and opportunities for a Plant Cell Atlas.}, journal = {eLife}, volume = {10}, number = {}, pages = {}, pmid = {34491200}, issn = {2050-084X}, support = {R01 GM123259/GM/NIGMS NIH HHS/United States ; R35 GM138143/GM/NIGMS NIH HHS/United States ; }, mesh = {Agriculture ; Chlamydomonas reinhardtii ; Chloroplasts ; Computational Biology ; Image Processing, Computer-Assisted ; *Plant Cells/physiology ; Plant Development ; Plants/classification/genetics ; Zea mays ; }, abstract = {With growing populations and pressing environmental problems, future economies will be increasingly plant-based. Now is the time to reimagine plant science as a critical component of fundamental science, agriculture, environmental stewardship, energy, technology and healthcare. This effort requires a conceptual and technological framework to identify and map all cell types, and to comprehensively annotate the localization and organization of molecules at cellular and tissue levels. This framework, called the Plant Cell Atlas (PCA), will be critical for understanding and engineering plant development, physiology and environmental responses. A workshop was convened to discuss the purpose and utility of such an initiative, resulting in a roadmap that acknowledges the current knowledge gaps and technical challenges, and underscores how the PCA initiative can help to overcome them.}, } @article {pmid34487888, year = {2021}, author = {Jin, H and Nath, SS and Schneider, S and Junghaenel, D and Wu, S and Kaplan, C}, title = {An informatics approach to examine decision-making impairments in the daily life of individuals with depression.}, journal = {Journal of biomedical informatics}, volume = {122}, number = {}, pages = {103913}, doi = {10.1016/j.jbi.2021.103913}, pmid = {34487888}, issn = {1532-0480}, mesh = {Decision Making ; *Depression/diagnosis ; Humans ; Informatics ; *Mental Disorders ; Mental Health ; Pilot Projects ; }, abstract = {Mental health informatics studies methods that collect, model, and interpret a wide variety of data to generate useful information with theoretical or clinical relevance to improve mental health and mental health care. This article presents a mental health informatics approach that is based on the decision-making theory of depression, whereby daily life data from a natural sequential decision-making task are collected and modeled using a reinforcement learning method. The model parameters are then estimated to uncover specific aspects of decision-making impairment in individuals with depression. Empirical results from a pilot study conducted to examine decision-making impairments in the daily lives of university students with depression are presented to illustrate this approach. Future research can apply and expand on this approach to investigate a variety of daily life situations and psychiatric conditions and to facilitate new informatics applications. Using this approach in mental health research may generate useful information with both theoretical and clinical relevance and high ecological validity.}, } @article {pmid34473760, year = {2021}, author = {Tercek, MT and Thoma, D and Gross, JE and Sherrill, K and Kagone, S and Senay, G}, title = {Historical changes in plant water use and need in the continental United States.}, journal = {PloS one}, volume = {16}, number = {9}, pages = {e0256586}, pmid = {34473760}, issn = {1932-6203}, mesh = {Amphibians/*physiology ; Animals ; Climate Change ; Datasets as Topic ; *Forests ; History, 20th Century ; History, 21st Century ; *Models, Statistical ; Parks, Recreational ; Plant Transpiration/*physiology ; Plants/*metabolism ; Seasons ; Temperature ; United States ; Water/*chemistry ; }, abstract = {A robust method for characterizing the biophysical environment of terrestrial vegetation uses the relationship between Actual Evapotranspiration (AET) and Climatic Water Deficit (CWD). These variables are usually estimated from a water balance model rather than measured directly and are often more representative of ecologically-significant changes than temperature or precipitation. We evaluate trends and spatial patterns in AET and CWD in the Continental United States (CONUS) during 1980-2019 using a gridded water balance model. The western US had linear regression slopes indicating increasing CWD and decreasing AET (drying), while the eastern US had generally opposite trends. When limits to plant performance characterized by AET and CWD are exceeded, vegetation assemblages change. Widespread increases in aridity throughout the west portends shifts in the distribution of plants limited by available moisture. A detailed look at Sequoia National Park illustrates the high degree of fine-scale spatial variability that exists across elevation and topographical gradients. Where such topographical and climatic diversity exists, appropriate use of our gridded data will require sub-setting to an appropriate area and analyzing according to categories of interest such as vegetation communities or across obvious physical gradients. Recent studies have successfully applied similar water balance models to fire risk and forest structure in both western and eastern U.S. forests, arid-land spring discharge, amphibian colonization and persistence in wetlands, whitebark pine mortality and establishment, and the distribution of arid-land grass species and landscape scale vegetation condition. Our gridded dataset is available free for public use. Our findings illustrate how a simple water balance model can identify important trends and patterns at site to regional scales. However, at finer scales, environmental heterogeneity is driving a range of responses that may not be simply characterized by a single trend.}, } @article {pmid34469515, year = {2021}, author = {Sundell, D and Öhrman, C and Svensson, D and Karlsson, E and Brindefalk, B and Myrtennäs, K and Ahlinder, J and Antwerpen, MH and Walter, MC and Forsman, M and Stenberg, P and Sjödin, A}, title = {FlexTaxD: flexible modification of taxonomy databases for improved sequence classification.}, journal = {Bioinformatics (Oxford, England)}, volume = {37}, number = {21}, pages = {3932-3933}, doi = {10.1093/bioinformatics/btab621}, pmid = {34469515}, issn = {1367-4811}, mesh = {*Software ; Databases, Factual ; }, abstract = {SUMMARY: The Flexible Taxonomy Database framework provides a method for modification and merging official and custom taxonomic databases to create improved databases. Using such databases will increase accuracy and precision of existing methods to classify sequence reads.

Source code is freely available at https://github.com/FOI-Bioinformatics/flextaxd and installable through Bioconda.}, } @article {pmid34468725, year = {2021}, author = {Varliero, G and Rafiq, M and Singh, S and Summerfield, A and Sgouridis, F and Cowan, DA and Barker, G}, title = {Microbial characterisation and Cold-Adapted Predicted Protein (CAPP) database construction from the active layer of Greenland's permafrost.}, journal = {FEMS microbiology ecology}, volume = {97}, number = {10}, pages = {}, pmid = {34468725}, issn = {1574-6941}, mesh = {Greenland ; Metagenome ; Metagenomics ; *Permafrost ; Soil Microbiology ; }, abstract = {Permafrost represents a reservoir for the biodiscovery of cold-adapted proteins which are advantageous in industrial and medical settings. Comparisons between different thermo-adapted proteins can give important information for cold-adaptation bioengineering. We collected permafrost active layer samples from 34 points along a proglacial transect in southwest Greenland. We obtained a deep read coverage assembly (>164x) from nanopore and Illumina sequences for the purposes of i) analysing metagenomic and metatranscriptomic trends of the microbial community of this area, and ii) creating the Cold-Adapted Predicted Protein (CAPP) database. The community showed a similar taxonomic composition in all samples along the transect, with a solid permafrost-shaped community, rather than microbial trends typical of proglacial systems. We retrieved 69 high- and medium-quality metagenome-assembled clusters, 213 complete biosynthetic gene clusters and more than three million predicted proteins. The latter constitute the CAPP database that can provide cold-adapted protein sequence information for protein- and taxon-focused amino acid sequence modifications for the future bioengineering of cold-adapted enzymes. As an example, we focused on the enzyme polyphenol oxidase, and demonstrated how sequence variation information could inform its protein engineering.}, } @article {pmid34463736, year = {2022}, author = {Gauld, JS and Olgemoeller, F and Heinz, E and Nkhata, R and Bilima, S and Wailan, AM and Kennedy, N and Mallewa, J and Gordon, MA and Read, JM and Heyderman, RS and Thomson, NR and Diggle, PJ and Feasey, NA}, title = {Spatial and Genomic Data to Characterize Endemic Typhoid Transmission.}, journal = {Clinical infectious diseases : an official publication of the Infectious Diseases Society of America}, volume = {74}, number = {11}, pages = {1993-2000}, pmid = {34463736}, issn = {1537-6591}, support = {//Wellcome Trust/United Kingdom ; R01 AI160780/AI/NIAID NIH HHS/United States ; 206454/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Cohort Studies ; Genomics ; Humans ; Nucleotides ; Salmonella typhi/genetics ; *Typhoid Fever/microbiology ; }, abstract = {BACKGROUND: Diverse environmental exposures and risk factors have been implicated in the transmission of Salmonella Typhi, but the dominant transmission pathways through the environment to susceptible humans remain unknown. Here, we use spatial, bacterial genomic, and hydrological data to refine our view of typhoid transmission in an endemic setting.

METHODS: A total of 546 patients presenting to Queen Elizabeth Central Hospital in Blantyre, Malawi, with blood culture-confirmed typhoid fever between April 2015 and January 2017 were recruited to a cohort study. The households of a subset of these patients were geolocated, and 256 S. Typhi isolates were whole-genome sequenced. Pairwise single-nucleotide variant distances were incorporated into a geostatistical modeling framework using multidimensional scaling.

RESULTS: Typhoid fever was not evenly distributed across Blantyre, with estimated minimum incidence ranging across the city from <15 to >100 cases per 100 000 population per year. Pairwise single-nucleotide variant distance and physical household distances were significantly correlated (P = .001). We evaluated the ability of river catchment to explain the spatial patterns of genomics observed, finding that it significantly improved the fit of the model (P = .003). We also found spatial correlation at a smaller spatial scale, of households living <192 m apart.

CONCLUSIONS: These findings reinforce the emerging view that hydrological systems play a key role in the transmission of typhoid fever. By combining genomic and spatial data, we show how multifaceted data can be used to identify high incidence areas, explain the connections between them, and inform targeted environmental surveillance, all of which will be critical to shape local and regional typhoid control strategies.}, } @article {pmid34459069, year = {2021}, author = {Mendy, A and Wu, X and Keller, JL and Fassler, CS and Apewokin, S and Mersha, TB and Xie, C and Pinney, SM}, title = {Air pollution and the pandemic: Long-term PM2.5 exposure and disease severity in COVID-19 patients.}, journal = {Respirology (Carlton, Vic.)}, volume = {26}, number = {12}, pages = {1181-1187}, pmid = {34459069}, issn = {1440-1843}, support = {R01 HL132344/HL/NHLBI NIH HHS/United States ; K08CA237735//US NIH/ ; K08 CA237735/CA/NCI NIH HHS/United States ; P30 ES006096/ES/NIEHS NIH HHS/United States ; 5UL1TR001425-03//National Center for Advancing Translational Sciences of the National Institute of Health (NIH)/ ; UL1 TR001425/TR/NCATS NIH HHS/United States ; T32ES010957/ES/NIEHS NIH HHS/United States ; T32 ES010957/ES/NIEHS NIH HHS/United States ; }, mesh = {Adult ; Aged ; Aged, 80 and over ; *Air Pollutants/adverse effects/analysis ; Air Pollution/*adverse effects/analysis ; COVID-19/*epidemiology/etiology ; Environmental Exposure/*adverse effects ; Female ; Hospitalization/*statistics & numerical data ; Humans ; Male ; Middle Aged ; Pandemics ; Particulate Matter/*adverse effects/analysis ; SARS-CoV-2 ; Severity of Illness Index ; }, abstract = {BACKGROUND AND OBJECTIVE: Ecological studies have suggested an association between exposure to particulate matter ≤2.5 μm (PM2.5) and coronavirus disease 2019 (COVID-19) severity. However, these findings are yet to be validated in individual-level studies. We aimed to determine the association of long-term PM2.5 exposure with hospitalization among individual patients infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).

METHODS: We estimated the 10-year (2009-2018) PM2.5 exposure at the residential zip code of COVID-19 patients diagnosed at the University of Cincinnati healthcare system between 13 March 2020 and 30 September 2020. Logistic regression was used to determine the odds ratio (OR) and 95% CI for COVID-19 hospitalizations associated with PM2.5 , adjusting for socioeconomic characteristics and comorbidities.

RESULTS: Among the 14,783 COVID-19 patients included in our study, 13.6% were hospitalized; the geometric mean (SD) PM2.5 was 10.48 (1.12) μg/m[3] . In adjusted analysis, 1 μg/m[3] increase in 10-year annual average PM2.5 was associated with 18% higher hospitalization (OR: 1.18, 95% CI: 1.11-1.26). Likewise, 1 μg/m[3] increase in PM2.5 estimated for the year 2018 was associated with 14% higher hospitalization (OR: 1.14, 95% CI: 1.08-1.21).

CONCLUSION: Long-term PM2.5 exposure is associated with increased hospitalization in COVID-19. Therefore, more stringent COVID-19 prevention measures may be needed in areas with higher PM2.5 exposure to reduce the disease morbidity and healthcare burden.}, } @article {pmid34454937, year = {2022}, author = {Zhong, C and Yang, Q and Liang, J and Ma, H}, title = {Fuzzy comprehensive evaluation with AHP and entropy methods and health risk assessment of groundwater in Yinchuan Basin, northwest China.}, journal = {Environmental research}, volume = {204}, number = {Pt A}, pages = {111956}, doi = {10.1016/j.envres.2021.111956}, pmid = {34454937}, issn = {1096-0953}, mesh = {Adult ; Analytic Hierarchy Process ; Child ; China ; Entropy ; Environmental Monitoring ; Fuzzy Logic ; *Groundwater ; Humans ; Risk Assessment ; *Water Pollutants, Chemical/analysis ; Water Quality ; }, abstract = {Water quality evaluation and health risk assessment are not only the basis of environmental protection work, but also of great significance to water environment supervision and management. In this paper, the fuzzy comprehensive evaluation for water quality was improved by using the analytic hierarchy process (AHP) and Entropy, and a health risk assessment model based on triangular fuzzy theory was developed. The evaluation results show 5 water categories: Class-1 (n = 1, 2%), Class-2 (n = 14, 32%), Class-3 (n = 15, 34%), Class-4 (n = 8, 18%) and Class-5 (n = 6, 14%), manifesting about 67% of the phreatic water can be used for drinking purposes in the research area. The Chadha diagram provides hydrochemical facies of the phreatic water are mainly NaCl type (n = 16, 36%) and Ca-Mg-Na type (n = 15, 34%). Fluorine as non-carcinogenic factor in health risk assessment, showing moderate correlation with SO4[2][-] (r = 0.54) and low correlation with Na+ (r = 0.38) in Pearson correlation analysis. The order of non-carcinogenic risk per year is as follow: Class-2, Class-3, All, Class-4 and Class-5 with the mean of 0.29, 0.51, 0.67, 0.86 and 1.55 × 10[-8] for adults, 0.54, 0.95, 1.27, 1.58 and 2.89 × 10[-8] for children. Compare with adults, children undertake higher health risk, in research area. Particularly, the region accepting Class-5 water supplement encounter high non-carcinogenic risk, where risk level is 2.24 and 2.28 times to the average risk level for adults and children, respectively. This paper provides insights into solving uncertainties in groundwater management and environmental protection, as well as into fuzzy logic techniques addressing pollution.}, } @article {pmid34454383, year = {2021}, author = {Mishra, M and Acharyya, T and Kar, D and Debanath, M and Santos, CAG and Silva, RMD and Kamal, AHM and Sahu, JK and Idris, MH}, title = {Geo-ecological cues for mass nesting synchronization of Olive Ridley turtles along Rushikulya estuary in Odisha, east coast of India.}, journal = {Marine pollution bulletin}, volume = {172}, number = {}, pages = {112881}, doi = {10.1016/j.marpolbul.2021.112881}, pmid = {34454383}, issn = {1879-3363}, mesh = {Animals ; Cues ; Ecosystem ; Estuaries ; India ; Nesting Behavior ; *Turtles ; }, abstract = {In this study, we have analyzed how geo-ecological cues for endangered Olive Ridley turtles' mass nesting behavior got modified by impact of four severe cyclones during 2010-2019 that made landfall in the vicinity of Rushikulya estuary, which is one of the largest mass nesting congregation (arribada) sites in the world. Analyzing last 10 years of shoreline dynamics, we show that even the slightest modification in beach morphology influenced their nesting behavior in Rushikulya rookery. Shoreline change analysis showed periodic phases of high/low erosion and the northward longshore sediment movement, which becomes impeded by the southern spit, the length of which increased by about 1800 m. During the analyzed period, the nesting behavior of Olive Ridley turtle was greatly influenced by changes in land use and land cover pattern around the Rushikulya rookery. Such reductions in tree cover and marshy land areas were majorly driven by anthropogenic activities and extreme weather events, such as cyclones. We also report increased mortality of turtles, no or false mass nesting events due to significant loss and/or erosion of the nesting sites due to cyclones. The results indicate that conservation of Olive Ridley turtles should be more holistic, or ecosystem centric, rather than species centric. It is important to maintain the ecological integrity of their habitat for highly synchronized mass nesting event and eventually their survival.}, } @article {pmid34453008, year = {2021}, author = {Che, Y and Yang, Y and Xu, X and Břinda, K and Polz, MF and Hanage, WP and Zhang, T}, title = {Reply to Partridge et al.: Complementary bioinformatics and experimental approaches to investigate the transfer of AMR genes.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {118}, number = {35}, pages = {}, pmid = {34453008}, issn = {1091-6490}, mesh = {*Computational Biology ; }, } @article {pmid34450871, year = {2021}, author = {Guo, J and Zhang, M and Shang, Q and Liu, F and Wu, A and Li, X}, title = {River Basin Cyberinfrastructure in the Big Data Era: An Integrated Observational Data Control System in the Heihe River Basin.}, journal = {Sensors (Basel, Switzerland)}, volume = {21}, number = {16}, pages = {}, pmid = {34450871}, issn = {1424-8220}, support = {2016YFC0500105//the National Key R&D Program of China/ ; XDA20060602//The Strategic Priority Research Program of the Chinese Academy of Sciences/ ; }, mesh = {Big Data ; China ; *Conservation of Natural Resources ; Hydrology ; *Rivers ; }, abstract = {River basin cyberinfrastructure with the Internet of Things (IoT) as the core has brought watershed data science into the big data era, greatly improving data acquisition and sharing efficiency. However, challenges in analyzing, processing, and applying very large quantities of observational data remain. Given the observational needs in watershed research, we studied the construction of river basin cyberinfrastructure and developed an integrated observational data control system (IODCS). The IODCS is an important platform for processing large quantities of observational data, including automated collection, storage, analysis, processing, and release. This paper presents various aspects of the IODCS in detail, including the system's overall design, function realization, big data analysis methods, and integrated models. We took the middle reaches of the Heihe River Basin (HRB) as the application research area to show the performance of the developed system. Since the system began operation, it has automatically received, analyzed, and stored more than 1.4 billion observational data records, with an average of more than 14 million observational data records processed per month and up to 21,011 active users. The demonstrated results show that the IODCS can effectively leverage the processing capability of massive observational data and provide a new perspective for facilitating ecological and hydrological scientific research on the HRB.}, } @article {pmid34449023, year = {2022}, author = {He, D and Hou, K and Wen, JF and Wu, SQ and Wu, ZP}, title = {A coupled study of ecological security and land use change based on GIS and entropy method-a typical region in Northwest China, Lanzhou.}, journal = {Environmental science and pollution research international}, volume = {29}, number = {4}, pages = {6347-6359}, pmid = {34449023}, issn = {1614-7499}, support = {19JK0369//Education Department of Shaanxi Province/ ; 42007415//National Natural Science Foundation of China/ ; }, mesh = {China ; Cities ; *Conservation of Natural Resources ; Ecosystem ; Entropy ; *Geographic Information Systems ; Urbanization ; }, abstract = {Due to rapid population growth, industrialization, and urbanization, it is particularly important to address the increasingly serious ecological security issues in the process of urbanization, while it is important to grasp the impact of changes in land use structure on ecological security for scientific planning and to aid decision-making. As a typical valley basin industrialized city in northwest China, Lanzhou has complex geomorphology and climate with distinct regional characteristics, and the relationship between land use and ecological security is complex. In order to understand the current status and influencing factors of ecological security in various regions of Lanzhou, and to explore the intrinsic connection between ecological security and land use, this study constructed an ecological security evaluation index system based on the pressure-state-response (PSR) model with 14 secondary factors including natural, social, and economic factors. Based on the entropy method, GIS was used to analyze the trend of ecological security in each district and to clarify the coupling relationship between ecological security and land use change in Lanzhou City. The results show that the ecological security index (ESI) of Xigu District, a typical heavy industrial area, increased from 0.26 to 0.35, and the ESI of Yuzhong County, an agricultural development area, increased from 0.51 to 0.55 from 2000 to 2017. Low ESI was mainly distributed in areas with developed heavy industry, while high ESI was mainly found in areas with favorable natural conditions and mainly agricultural development. Economic factors were the leading factors affecting the ecological security of Lanzhou. In general, changes in land use structure and ecological security were inextricably linked, and the two influence and interact with each other. These results could provide some reference for the study of ecological security development and land use change in typical river valley cities and also provide a new path for other cities to study ecological security and the conservation of the ecological environment.}, } @article {pmid34448977, year = {2021}, author = {McEvoy, JF and Kishbaugh, JC and Valitutto, MT and Aung, O and Tun, KYN and Win, YT and Maw, MT and Thein, WZ and Win, HH and Chit, AM and Vodzak, ME and Murray, S}, title = {Movements of Indian Flying Fox in Myanmar as a Guide to Human-Bat Interface Sites.}, journal = {EcoHealth}, volume = {18}, number = {2}, pages = {204-216}, pmid = {34448977}, issn = {1612-9210}, mesh = {Animals ; Animals, Wild ; *Chiroptera/virology ; Cluster Analysis ; Ecosystem ; Geographic Information Systems ; Humans ; Mouth/virology ; Myanmar ; Rectum/virology ; Zoonoses/prevention & control/*transmission ; }, abstract = {Frugivorous bats play a vital role in tropical ecosystems as pollinators and seed dispersers but are also important vectors of zoonotic diseases. Myanmar sits at the intersection of numerous bioregions and contains habitats that are important for many endangered and endemic species. This rapidly developing country also forms a connection between hotspots of emerging human diseases. We deployed Global Positioning System collars to track the movements of 10 Indian flying fox (Pteropus giganteus) in the agricultural landscapes of central Myanmar. We used clustering analysis to identify foraging sites and high-utilization areas. As part of a larger viral surveillance study in bats of Myanmar, we also collected oral and rectal swab samples from 29 bats to test for key emerging viral diseases in this colony. There were no positive results detected for our chosen viruses. We analyzed their foraging movement behavior and evaluated selected foraging sites for their potential as human-wildlife interface sites.}, } @article {pmid34446481, year = {2021}, author = {Carter, ED and Leslie, HH and Marchant, T and Amouzou, A and Munos, MK}, title = {Methodological considerations for linking household and healthcare provider data for estimating effective coverage: a systematic review.}, journal = {BMJ open}, volume = {11}, number = {8}, pages = {e045704}, pmid = {34446481}, issn = {2044-6055}, mesh = {*Family Characteristics ; Health Facilities ; *Health Personnel ; Health Services ; Humans ; Information Storage and Retrieval ; }, abstract = {OBJECTIVE: To assess existing knowledge related to methodological considerations for linking population-based surveys and health facility data to generate effective coverage estimates. Effective coverage estimates the proportion of individuals in need of an intervention who receive it with sufficient quality to achieve health benefit.

DESIGN: Systematic review of available literature.

DATA SOURCES: Medline, Carolina Population Health Center and Demographic and Health Survey publications and handsearch of related or referenced works of all articles included in full text review. The search included publications from 1 January 2000 to 29 March 2021.

ELIGIBILITY CRITERIA: Publications explicitly evaluating (1) the suitability of data, (2) the implications of the design of existing data sources and (3) the impact of choice of method for combining datasets to obtain linked coverage estimates.

RESULTS: Of 3805 papers reviewed, 70 publications addressed relevant issues. Limited data suggest household surveys can be used to identify sources of care, but their validity in estimating intervention need was variable. Methods for collecting provider data and constructing quality indices were diverse and presented limitations. There was little empirical data supporting an association between structural, process and outcome quality. Few studies addressed the influence of the design of common data sources on linking analyses, including imprecise household geographical information system data, provider sampling design and estimate stability. The most consistent evidence suggested under certain conditions, combining data based on geographical proximity or administrative catchment (ecological linking) produced similar estimates to linking based on the specific provider utilised (exact match linking).

CONCLUSIONS: Linking household and healthcare provider data can leverage existing data sources to generate more informative estimates of intervention coverage and care. However, existing evidence on methods for linking data for effective coverage estimation are variable and numerous methodological questions remain. There is need for additional research to develop evidence-based, standardised best practices for these analyses.}, } @article {pmid34445220, year = {2021}, author = {Bartas, M and Brázda, V and Volná, A and Červeň, J and Pečinka, P and Zawacka-Pankau, JE}, title = {The Changes in the p53 Protein across the Animal Kingdom Point to Its Involvement in Longevity.}, journal = {International journal of molecular sciences}, volume = {22}, number = {16}, pages = {}, pmid = {34445220}, issn = {1422-0067}, support = {18-15548S//Czech Science Foundation/ ; ZIP//Warsaw University's Integrated Development Programme/ ; }, mesh = {Animals ; *Databases, Genetic ; *Gene Dosage ; *Longevity ; *Models, Molecular ; Protein Domains ; Protein Structure, Secondary ; Species Specificity ; Tumor Suppressor Protein p53/chemistry/genetics/metabolism ; }, abstract = {Recently, the quest for the mythical fountain of youth has produced extensive research programs that aim to extend the healthy lifespan of humans. Despite advances in our understanding of the aging process, the surprisingly extended lifespan and cancer resistance of some animal species remain unexplained. The p53 protein plays a crucial role in tumor suppression, tissue homeostasis, and aging. Long-lived, cancer-free African elephants have 20 copies of the TP53 gene, including 19 retrogenes (38 alleles), which are partially active, whereas humans possess only one copy of TP53 and have an estimated cancer mortality rate of 11-25%. The mechanism through which p53 contributes to the resolution of the Peto's paradox in Animalia remains vague. Thus, in this work, we took advantage of the available datasets and inspected the p53 amino acid sequence of phylogenetically related organisms that show variations in their lifespans. We discovered new correlations between specific amino acid deviations in p53 and the lifespans across different animal species. We found that species with extended lifespans have certain characteristic amino acid substitutions in the p53 DNA-binding domain that alter its function, as depicted from the Phenotypic Annotation of p53 Mutations, using the PROVEAN tool or SWISS-MODEL workflow. In addition, the loop 2 region of the human p53 DNA-binding domain was identified as the longest region that was associated with longevity. The 3D model revealed variations in the loop 2 structure in long-lived species when compared with human p53. Our findings show a direct association between specific amino acid residues in p53 protein, changes in p53 functionality, and the extended animal lifespan, and further highlight the importance of p53 protein in aging.}, } @article {pmid34445017, year = {2021}, author = {Dore, MP and Parodi, G and Portoghese, M and Errigo, A and Pes, GM}, title = {Water Quality and Mortality from Coronary Artery Disease in Sardinia: A Geospatial Analysis.}, journal = {Nutrients}, volume = {13}, number = {8}, pages = {}, pmid = {34445017}, issn = {2072-6643}, mesh = {Cause of Death ; Coronary Artery Disease/diagnosis/*mortality ; Databases, Factual ; Geographic Mapping ; Humans ; Italy/epidemiology ; Mineral Waters/*analysis ; Natural Springs/*analysis ; Prognosis ; Protective Factors ; Risk Assessment ; Risk Factors ; Time Factors ; *Water Quality ; *Water Supply ; }, abstract = {The role of water hardness on human health is still debated, ranging from beneficial to harmful. Before the rise of drinking bottled water, it was a common habit to obtain supplies of drinking water directly from spring-fed public fountains. According to the geographic location, spring waters are characterized by a variable content of mineral components. In this ecological study, for the first time in Sardinia, Italy, the spatial association between spring water quality/composition and standardized mortality ratio (SMR) for coronary artery disease (CAD) in the decade from 1981 to 1991 was investigated using data retrieved from published databases. In a total of 377 municipalities, 9918 deaths due to CAD, including acute myocardial infarction (AMI), ICD-9 code 410, and ischemic heart disease (IHD), ICD-9 code 411-414, were retrieved. A conditional autoregressive model with spatially structured random effects for each municipality was used. The average SMR for CAD in municipalities with a predominantly "soft" (<30 mg/L) or "hard" (≥30 mg/L) water was, respectively, 121.4 ± 59.1 vs. 104.7 ± 38.2 (p = 0.025). More specifically, an inverse association was found between elevated calcium content in spring water and cardiovascular mortality (AMI: r = -0.123, p = 0.032; IHD: r = -0.146, p = 0.009) and borderline significance for magnesium (AMI: r = -0.131, p = 0.054; IHD: r = -0.138, p = 0.074) and bicarbonate (IHD: r = -0.126, p = 0.058), whereas weak positive correlations were detected for sodium and chloride. The lowest CAD mortality was observed in geographic areas (North-West: SMR 0.92; South-East: SMR 0.88), where calcium- and bicarbonate-rich mineral waters were consumed. Our results, within the limitation of an ecological study, confirm the beneficial role of waters with high content in calcium and bicarbonate against coronary artery disease.}, } @article {pmid34444194, year = {2021}, author = {Yan, S and Tang, J}, title = {Optimization of Green Space Planning to Improve Ecosystem Services Efficiency: The Case of Chongqing Urban Areas.}, journal = {International journal of environmental research and public health}, volume = {18}, number = {16}, pages = {}, pmid = {34444194}, issn = {1660-4601}, mesh = {China ; Cities ; City Planning ; Conservation of Natural Resources ; *Ecosystem ; Geographic Information Systems ; *Parks, Recreational ; Wetlands ; }, abstract = {This paper applied landscape indexes to evaluate the size, form, and structure of green spaces in the mountainous city of Chongqing and found that green spaces benefit from certain advantages in size, but the network suffered from low heterogeneity and limited interconnectivity. To ensure the integrity and continuity of ecological processes and improve the efficiency of ecosystem services (ES), the authors used Geographic Information System (GIS) software to conduct adaptability evaluation and adjacent buffer analysis for the existing green spaces, wetlands, rivers, and other landscapes with relatively high capacity for ES. We designed a comprehensive map of potential areas for UGS expansion by superimposing the maps obtained from adaptability evaluation and buffer analysis. We also proposed some strategies that respect, consider, and evaluate aspects and special features of urban environment to optimize green space planning and improve ES efficiency, such as protection of important areas, development of green corridors, and careful consideration of ecological processes and complex functions in urban areas. Based on these strategies, the paper put forth suggestions for green space planning to improve ES efficiency that can function as foundation for subsequent green space planning.}, } @article {pmid34440287, year = {2021}, author = {Schwabe, M and Griep, S and Schmidtberg, H and Plarre, R and Goesmann, A and Vilcinskas, A and Vogel, H and Brinkrolf, K}, title = {Next-Generation Sequencing Analysis of the Tineola bisselliella Larval Gut Transcriptome Reveals Candidate Enzymes for Keratin Digestion.}, journal = {Genes}, volume = {12}, number = {8}, pages = {}, pmid = {34440287}, issn = {2073-4425}, mesh = {Animals ; Gene Ontology ; High-Throughput Nucleotide Sequencing/*methods ; Keratins/*metabolism ; Larva/*genetics ; Lepidoptera/*genetics/growth & development ; *Transcriptome ; }, abstract = {The clothes moth Tineola bisselliella is one of a few insects that can digest keratin, leading to the destruction of clothing, textiles and artwork. The mechanism of keratin digestion is not yet fully understood, partly reflecting the lack of publicly available genomic and transcriptomic data. Here we present a high-quality gut transcriptome of T. bisselliella generated from larvae reared on keratin-rich and keratin-free diets. The overall transcriptome consists of 428,221 contigs that were functionally annotated and screened for candidate enzymes involved in keratin utilization. As a mechanism for keratin digestion, we identified cysteine synthases, cystathionine β-synthases and cystathionine γ-lyases. These enzymes release hydrogen sulfite, which may reduce the disulfide bonds in keratin. The dataset also included 27 differentially expressed contigs with trypsin domains, among which 20 were associated with keratin feeding. Finally, we identified seven collagenases that were upregulated on the keratin-rich diet. In addition to this enzymatic repertoire potentially involved in breaking down keratin, our analysis of poly(A)-enriched and poly(A)-depleted transcripts suggested that T. bisselliella larvae possess an unstable intestinal microbiome that may nevertheless contribute to keratin digestion.}, } @article {pmid34439761, year = {2021}, author = {Bertini, L and Cozzolino, F and Proietti, S and Falconieri, GS and Iacobucci, I and Salvia, R and Falabella, P and Monti, M and Caruso, C}, title = {What Antarctic Plants Can Tell Us about Climate Changes: Temperature as a Driver for Metabolic Reprogramming.}, journal = {Biomolecules}, volume = {11}, number = {8}, pages = {}, pmid = {34439761}, issn = {2218-273X}, mesh = {Antarctic Regions ; Antioxidants ; Cell Wall ; Chromatography, Liquid ; *Climate Change ; Computational Biology ; Global Warming ; Oxidation-Reduction ; Oxidative Stress ; Photosynthesis ; *Plant Physiological Phenomena ; Protein Isoforms ; Proteomics/*methods ; *Reactive Oxygen Species ; *Stress, Physiological ; Tandem Mass Spectrometry ; Temperature ; Up-Regulation ; }, abstract = {Global warming is strongly affecting the maritime Antarctica climate and the consequent melting of perennial snow and ice covers resulted in increased colonization by plants. Colobanthus quitensis is a vascular plant highly adapted to the harsh environmental conditions of Antarctic Peninsula and understanding how the plant is responding to global warming is a new challenging target for modern cell physiology. To this aim, we performed differential proteomic analysis on C. quitensis plants grown in natural conditions compared to plants grown for one year inside open top chambers (OTCs) which determine an increase of about 4 °C at midday, mimicking the effect of global warming. A thorough analysis of the up- and downregulated proteins highlighted an extensive metabolism reprogramming leading to enhanced photoprotection and oxidative stress control as well as reduced content of cell wall components. Overall, OTCs growth seems to be advantageous for C. quitensis plants which could benefit from a better CO2 diffusion into the mesophyll and a reduced ROS-mediated photodamage.}, } @article {pmid34434823, year = {2021}, author = {Oliver, AE and Newbold, LK and Gweon, HS and Read, DS and Woodcock, BA and Pywell, RF}, title = {Integration of DNA extraction, metabarcoding and an informatics pipeline to underpin a national citizen science honey monitoring scheme.}, journal = {MethodsX}, volume = {8}, number = {}, pages = {101303}, pmid = {34434823}, issn = {2215-0161}, abstract = {Worldwide honeybees (Apis mellifera L.) are one of the most widely kept domesticated animals, supporting domestic and commercial livelihoods through the production of honey and wax, as well as in the delivery of pollination services to crops. Quantifying which plant species are foraged upon by honeybees provides insights into their nutritional status as well as patterns of landscape scale habitat utilization. Here we outline a rapid and reproducible methodology for identifying environmental DNA (eDNA) originating principally from pollen grains suspended within honey. The process is based on a DNA extraction incorporating vacuum filtration prior to universal eukaryotic internal transcribed spacer 2 region (ITS2) amplicon generation, sequencing and identification. To provide a pre-cursor to sequence phylotyping, we outline systems for error-corrected processing amplicon sequence variant abundance tables that removes chimeras. This methodology underpins the new UK National Honey Monitoring Scheme.•We compare the efficacy and speed of centrifugation and filtration systems for removing pollen from honey samples as a precursor to plant DNA barcoding.•We introduce the 'HONEYPI' informatics pipeline, an open access resource implemented in python 2.7, to ensure long-term reproducibility during the process of amplicon sequence variant classification.}, } @article {pmid34433947, year = {2021}, author = {Cuni-Sanchez, A and Sullivan, MJP and Platts, PJ and Lewis, SL and Marchant, R and Imani, G and Hubau, W and Abiem, I and Adhikari, H and Albrecht, T and Altman, J and Amani, C and Aneseyee, AB and Avitabile, V and Banin, L and Batumike, R and Bauters, M and Beeckman, H and Begne, SK and Bennett, AC and Bitariho, R and Boeckx, P and Bogaert, J and Bräuning, A and Bulonvu, F and Burgess, ND and Calders, K and Chapman, C and Chapman, H and Comiskey, J and de Haulleville, T and Decuyper, M and DeVries, B and Dolezal, J and Droissart, V and Ewango, C and Feyera, S and Gebrekirstos, A and Gereau, R and Gilpin, M and Hakizimana, D and Hall, J and Hamilton, A and Hardy, O and Hart, T and Heiskanen, J and Hemp, A and Herold, M and Hiltner, U and Horak, D and Kamdem, MN and Kayijamahe, C and Kenfack, D and Kinyanjui, MJ and Klein, J and Lisingo, J and Lovett, J and Lung, M and Makana, JR and Malhi, Y and Marshall, A and Martin, EH and Mitchard, ETA and Morel, A and Mukendi, JT and Muller, T and Nchu, F and Nyirambangutse, B and Okello, J and Peh, KS and Pellikka, P and Phillips, OL and Plumptre, A and Qie, L and Rovero, F and Sainge, MN and Schmitt, CB and Sedlacek, O and Ngute, ASK and Sheil, D and Sheleme, D and Simegn, TY and Simo-Droissart, M and Sonké, B and Soromessa, T and Sunderland, T and Svoboda, M and Taedoumg, H and Taplin, J and Taylor, D and Thomas, SC and Timberlake, J and Tuagben, D and Umunay, P and Uzabaho, E and Verbeeck, H and Vleminckx, J and Wallin, G and Wheeler, C and Willcock, S and Woods, JT and Zibera, E}, title = {High aboveground carbon stock of African tropical montane forests.}, journal = {Nature}, volume = {596}, number = {7873}, pages = {536-542}, pmid = {34433947}, issn = {1476-4687}, mesh = {Africa ; *Attitude ; Biomass ; Carbon/*analysis ; *Carbon Sequestration ; Climate Change ; Conservation of Natural Resources ; Datasets as Topic ; Geographic Mapping ; *Rainforest ; Trees/*metabolism ; *Tropical Climate ; }, abstract = {Tropical forests store 40-50 per cent of terrestrial vegetation carbon[1]. However, spatial variations in aboveground live tree biomass carbon (AGC) stocks remain poorly understood, in particular in tropical montane forests[2]. Owing to climatic and soil changes with increasing elevation[3], AGC stocks are lower in tropical montane forests compared with lowland forests[2]. Here we assemble and analyse a dataset of structurally intact old-growth forests (AfriMont) spanning 44 montane sites in 12 African countries. We find that montane sites in the AfriMont plot network have a mean AGC stock of 149.4 megagrams of carbon per hectare (95% confidence interval 137.1-164.2), which is comparable to lowland forests in the African Tropical Rainforest Observation Network[4] and about 70 per cent and 32 per cent higher than averages from plot networks in montane[2,5,6] and lowland[7] forests in the Neotropics, respectively. Notably, our results are two-thirds higher than the Intergovernmental Panel on Climate Change default values for these forests in Africa[8]. We find that the low stem density and high abundance of large trees of African lowland forests[4] is mirrored in the montane forests sampled. This carbon store is endangered: we estimate that 0.8 million hectares of old-growth African montane forest have been lost since 2000. We provide country-specific montane forest AGC stock estimates modelled from our plot network to help to guide forest conservation and reforestation interventions. Our findings highlight the need for conserving these biodiverse[9,10] and carbon-rich ecosystems.}, } @article {pmid34432124, year = {2021}, author = {Havenga, M and Wingfield, BD and Wingfield, MJ and Dreyer, LL and Roets, F and Aylward, J}, title = {Genetic response to nitrogen starvation in the aggressive Eucalyptus foliar pathogen Teratosphaeria destructans.}, journal = {Current genetics}, volume = {67}, number = {6}, pages = {981-990}, pmid = {34432124}, issn = {1432-0983}, support = {11824//national research foundation of south africa/ ; 98353//sarchi chair in fungal genomics/ ; }, mesh = {Ascomycota/*physiology ; Computational Biology/methods ; Eucalyptus/*microbiology ; Fungal Proteins/genetics ; Gene Expression Profiling ; *Gene Expression Regulation, Fungal ; *Host-Pathogen Interactions ; Nitrogen/*metabolism ; Plant Diseases/*microbiology ; RNA-Seq ; Secondary Metabolism/genetics ; Transcriptome ; }, abstract = {Teratosphaeria destructans is one of the most aggressive foliar pathogens of Eucalyptus. The biological factors underpinning T. destructans infections, which include shoot and leaf blight on young trees, have never been interrogated. Thus, the means by which the pathogen modifies its host environment to overcome host defences remain unknown. By applying transcriptome sequencing, the aim of this study was to compare gene expression in a South African isolate of T. destructans grown on nitrogen-deficient and complete media. This made it possible to identify upregulated genes in a nitrogen-starved environment, often linked to the pathogenicity of the fungus. The results support the hypothesis that nitrogen starvation in T. destructans likely mirrors an in planta genetic response. This is because 45% of genes that were highly upregulated under nitrogen starvation have previously been reported to be associated with infection in other pathogen systems. These included several CAZymes, fungal effector proteins, peptidases, kinases, toxins, lipases and proteins associated with detoxification of toxic compounds. Twenty-five secondary metabolites were identified and expressed in both nitrogen-deficient and complete conditions. Additionally, the most highly expressed genes in both growth conditions had pathogenicity-related functions. This study highlights the large number of expressed genes associated with pathogenicity and overcoming plant defences. As such, the generated baseline knowledge regarding pathogenicity and aggressiveness in T. destructans is a valuable reference for future in planta work.}, } @article {pmid34432068, year = {2021}, author = {Ubalde-Lopez, M and Garani-Papadatos, T and Scelo, G and Casas, M and Lissåker, C and Peters, S and Nohr, EA and Albin, M and Lucas, R and Papantoniou, K and Polańska, K and Ramlau-Hansen, CH and Šarac, J and Selander, J and Skröder, H and Vasileiou, E and Kogevinas, M and Bültmann, U and Mehlum, IS and Maule, M}, title = {Working life, health and well-being of parents: a joint effort to uncover hidden treasures in European birth cohorts.}, journal = {Scandinavian journal of work, environment & health}, volume = {47}, number = {7}, pages = {550-560}, pmid = {34432068}, issn = {1795-990X}, mesh = {*Birth Cohort ; Databases, Factual ; *Employment ; Europe ; Female ; Humans ; Infant, Newborn ; Pregnancy ; }, abstract = {OBJECTIVE: Birth cohorts collect valuable and under-utilized information on employment and health of parents before and during pregnancy, at birth, and sometimes after birth. In this discussion paper, we examine how these data could be exploited to study the complex relationships and interactions between parenthood, work, and health among parents themselves.

METHODS: Using a web-based database of birth cohorts, we summarize information on maternal employment and health conditions and other potentially related variables in cohorts spread throughout Europe. This provided information on what data are available and could be used in future studies, and what was missing if specific questions are to be addressed, exploiting the opportunity to explore work-health associations across heterogenous geographical and social contexts.

RESULTS: We highlight the many potentialities provided by birth cohorts and identify gaps that need to be addressed to adopt a life-course approach and investigate topics specific to the peri-pregnancy period, such as psychosocial aspects. We address the technical difficulties implied by data harmonization and the ethical challenges related to the repurposing of data, and provide scientific, ecological and economic arguments in favor of improving the value of data already available as a result of a serious investment in human and material resources.

CONCLUSIONS: There is a hidden treasure in birth cohorts that deserves to be brought out to study the relationships between employment and health among working parents in a time when the boundaries between work and life are being stretched more than ever before.}, } @article {pmid34430295, year = {2021}, author = {Abdullah, MM and Al-Ali, ZM and Srinivasan, S}, title = {The use of UAV-based remote sensing to estimate biomass and carbon stock for native desert shrubs.}, journal = {MethodsX}, volume = {8}, number = {}, pages = {101399}, pmid = {34430295}, issn = {2215-0161}, abstract = {Unmanned Aerial Vehicles (UAVs) have started to receive more attention in the ecological field in the past 15 years, as they provide very high-resolution imagery that ranges from meters to millimeters. Very high-resolution multispectral imagery obtained from UAVs can help in assessing and monitoring native desert vegetation. Thus, this study use UAVs to develop a method to estimate the biomass and carbon stock of native desert shrubs. The method integrates different techniques and software to monitor native plants' coverage, biomass, and carbon stock. The techniques used in this work are also applicable for other native desert shrubs in the region and could support ecosystem managers in assessing and monitoring arid ecosystems and restoration and revegetation programs. A three-stage image and data management are discussed, including: (1) fieldwork and image acquisition using UAVs, (2) image pre-processing, and (3) image processing using different techniques and software.•Determining shrub biomass is not restricted to multispectral data only but could be applicable for RGB data since it mainly depends on the DSM and DTM.•Allometric parameters could help in estimating desert shrub biomass which could be measured easily and rapidly using UAV imagery.•SVM Supervised classification could help in distinguishing between native shrubs and grasses.}, } @article {pmid34427865, year = {2022}, author = {Song, R and Li, D and Chang, A and Tao, M and Qin, Y and Keller, AA and Suh, S}, title = {Accelerating the pace of ecotoxicological assessment using artificial intelligence.}, journal = {Ambio}, volume = {51}, number = {3}, pages = {598-610}, pmid = {34427865}, issn = {1654-7209}, support = {83557901//U.S. Environmental Protection Agency/ ; }, mesh = {*Artificial Intelligence ; Databases, Factual ; Ecotoxicology ; Risk Assessment ; *Water Pollutants, Chemical/toxicity ; }, abstract = {Species Sensitivity Distribution (SSD) is a key metric for understanding the potential ecotoxicological impacts of chemicals. However, SSDs have been developed to estimate for only handful of chemicals due to the scarcity of experimental toxicity data. Here we present a novel approach to expand the chemical coverage of SSDs using Artificial Neural Network (ANN). We collected over 2000 experimental toxicity data in Lethal Concentration 50 (LC50) for 8 aquatic species and trained an ANN model for each of the 8 aquatic species based on molecular structure. The R[2] values of resulting ANN models range from 0.54 to 0.75 (median R[2] = 0.69). We applied the predicted LC50 values to fit SSD curves using bootstrapping method, generating SSDs for 8424 chemicals in the ToX21 database. The dataset is expected to serve as a screening-level reference SSD database for understanding potential ecotoxicological impacts of chemicals.}, } @article {pmid34427520, year = {2021}, author = {Birer-Williams, CMC and Chu, RK and Anderton, CR and Wright, ES}, title = {SubTap, a Versatile 3D Printed Platform for Eavesdropping on Extracellular Interactions.}, journal = {mSystems}, volume = {6}, number = {4}, pages = {e0090221}, pmid = {34427520}, issn = {2379-5077}, support = {DP2 AI145058/AI/NIAID NIH HHS/United States ; 1DP2AI145058-01//HHS | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; EMSL 50808//DOE | NNSA | LDRD | Pacific Northwest National Laboratory (PNNL)/ ; }, abstract = {Communication within the microbiome occurs through an immense diversity of small molecules. Capturing these microbial interactions is a significant challenge due to the complexity of the exometabolome and its sensitivity to environmental stimuli. Traditional methods for acquiring exometabolomic data from interacting microorganisms are limited by their low throughput or lack of sampling depth. To address this challenge, we introduce subtapping (short for substrate tapping), a technique for tapping into extracellular metabolites that are being transferred through the growth substrate during coculture. High-throughput subtapping is made possible by a new coculturing platform, named SubTap, that we engineered to resemble a 96-well plate. The three-dimensional (3D) printed SubTap platform captures the exometabolome in an agar compartment that connects physically separated growth chambers, which permits cell growth without competition for space. We show how SubTap facilitates replicable and quick detection of exometabolites via direct infusion mass spectrometry analysis. Using bacterial isolates from the soil, we apply SubTap to characterize the effects of growth medium, growth duration, and mixed versus unmixed coculturing on the exometabolome. Finally, we demonstrate SubTap's versatility by interrogating microbial interactions in multicultures with up to four strains. IMPORTANCE Improvements in experimental techniques and instrumentation have led to the discovery that the microbiome plays an essential role in human and environmental health. Nevertheless, there remain major impediments to conducting large-scale interrogations of the microbiome in a high-throughput manner, particularly in the field of exometabolomics. Existing methods to coculture microorganisms and interrogate their interactions are labor-intensive and low throughput. This inspired us to develop a solution for coculturing that was (i) open source, (ii) inexpensive, (iii) scalable, (iv) customizable, and (v) compatible with existing mass spectrometry instrumentation. Here, we present SubTap-a 3D printed coculturing platform that permits tapping directly into the growth substrate between physically separated, but interconnected, growth compartments. SubTap allows multiculture (with up to four distinct growth compartments) in spatially mixed or unmixed configurations and enables repeatable results with mass spectrometry, as shown by our validation with known compounds and cultures of one to four organisms.}, } @article {pmid34427185, year = {2021}, author = {Heinze, S and El Jundi, B and Berg, BG and Homberg, U and Menzel, R and Pfeiffer, K and Hensgen, R and Zittrell, F and Dacke, M and Warrant, E and Pfuhl, G and Rybak, J and Tedore, K}, title = {A unified platform to manage, share, and archive morphological and functional data in insect neuroscience.}, journal = {eLife}, volume = {10}, number = {}, pages = {}, pmid = {34427185}, issn = {2050-084X}, mesh = {Animals ; *Biomedical Research ; Brain/anatomy & histology/*physiology ; Computer Graphics ; Data Mining ; *Databases, Factual ; *Information Management ; *Information Storage and Retrieval ; Insecta/anatomy & histology/*physiology ; Internet ; *Nervous System Physiological Phenomena ; *Neurosciences ; User-Computer Interface ; }, abstract = {Insect neuroscience generates vast amounts of highly diverse data, of which only a small fraction are findable, accessible and reusable. To promote an open data culture, we have therefore developed the InsectBrainDatabase (IBdb), a free online platform for insect neuroanatomical and functional data. The IBdb facilitates biological insight by enabling effective cross-species comparisons, by linking neural structure with function, and by serving as general information hub for insect neuroscience. The IBdb allows users to not only effectively locate and visualize data, but to make them widely available for easy, automated reuse via an application programming interface. A unique private mode of the database expands the IBdb functionality beyond public data deposition, additionally providing the means for managing, visualizing, and sharing of unpublished data. This dual function creates an incentive for data contribution early in data management workflows and eliminates the additional effort normally associated with publicly depositing research data.}, } @article {pmid34426640, year = {2021}, author = {Braga, J and Samir, C and Fradi, A and Feunteun, Y and Jakata, K and Zimmer, VA and Zipfel, B and Thackeray, JF and Macé, M and Wood, BA and Grine, FE}, title = {Cochlear shape distinguishes southern African early hominin taxa with unique auditory ecologies.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {17018}, pmid = {34426640}, issn = {2045-2322}, mesh = {Animals ; Cochlea/*anatomy & histology ; Fossils ; Hearing/*physiology ; Hominidae/*classification ; *Phylogeny ; Principal Component Analysis ; South Africa ; }, abstract = {Insights into potential differences among the bony labyrinths of Plio-Pleistocene hominins may inform their evolutionary histories and sensory ecologies. We use four recently-discovered bony labyrinths from the site of Kromdraai to significantly expand the sample for Paranthropus robustus. Diffeomorphometry, which provides detailed information about cochlear shape, reveals size-independent differences in cochlear shape between P. robustus and Australopithecus africanus that exceed those among modern humans and the African apes. The cochlea of P. robustus is distinctive and relatively invariant, whereas cochlear shape in A. africanus is more variable, resembles that of early Homo, and shows a degree of morphological polymorphism comparable to that evinced by modern species. The curvature of the P. robustus cochlea is uniquely derived and is consistent with enhanced sensitivity to low-frequency sounds. Combined with evidence for selection, our findings suggest that sound perception shaped distinct ecological adaptations among southern African early hominins.}, } @article {pmid34426354, year = {2021}, author = {Scowen, M and Athanasiadis, IN and Bullock, JM and Eigenbrod, F and Willcock, S}, title = {The current and future uses of machine learning in ecosystem service research.}, journal = {The Science of the total environment}, volume = {799}, number = {}, pages = {149263}, doi = {10.1016/j.scitotenv.2021.149263}, pmid = {34426354}, issn = {1879-1026}, mesh = {Big Data ; *Ecosystem ; *Machine Learning ; }, abstract = {Machine learning (ML) expands traditional data analysis and presents a range of opportunities in ecosystem service (ES) research, offering rapid processing of 'big data' and enabling significant advances in data description and predictive modelling. Descriptive ML techniques group data with little or no prior domain specific assumptions; they can generate hypotheses and automatically sort data prior to other analyses. Predictive ML techniques allow for the predictive modelling of highly non-linear systems where casual mechanisms are poorly understood, as is often the case for ES. We conducted a review to explore how ML is used in ES research and to identify and quantify trends in the different ML approaches that are used. We reviewed 308 peer-reviewed publications and identified that ES studies implemented machine learning techniques in data description (64%; n = 308) and predictive modelling (44%), with some papers containing both categories. Classification and Regression Trees were the most popular techniques (60%), but unsupervised learning techniques were also used for descriptive tasks such as clustering to group or split data without prior assumptions (19%). Whilst there are examples of ES publications that apply ML with rigour, many studies do not have robust or repeatable methods. Some studies fail to report model settings (43%) or software used (28%), and many studies do not report carrying out any form of model hyperparameter tuning (67%) or test model generalisability (59%). Whilst studies use ML to analyse very large and complex datasets, ES research is generally not taking full advantage of the capacity of ML to model big data (1138 medium number of data points; 13 median quantity of variables). There is great further opportunity to utilise ML in ES research, to make better use of big data and to develop detailed modelling of spatial-temporal dynamics that meet stakeholder demands.}, } @article {pmid34424472, year = {2022}, author = {Pakhchanian, H and Raiker, R and Kardeş, S and Bilal, M and Alam, K and Khan, A and Hutson, W and Thakkar, S and Singh, S}, title = {Impact of COVID-19 on interest in hepato-pancreato-biliary diseases.}, journal = {Environmental science and pollution research international}, volume = {29}, number = {4}, pages = {5771-5776}, pmid = {34424472}, issn = {1614-7499}, mesh = {*COVID-19 ; Humans ; Infodemiology ; Pandemics ; SARS-CoV-2 ; }, abstract = {An important gap of knowledge exists regarding the public interest in hepato-pancreato-biliary (HPB) diseases during the coronavirus disease 2019 (COVID-19) pandemic. We aimed to understand the public interest in HPB diseases in the COVID-19 era. In this infodemiology study, we performed a comparative analysis of Google search volume of HPB terms in 2020-2021 and compared it to a similar time frame (2016-2019) in 3 periods to assess how trends in patient seeking behavior of HPB terms changed during the course of the pandemic in the USA and worldwide. Our analysis showed a substantial decrease in search volume of HPB diseases and procedure terms early in the pandemic. However, search volumes appeared to revert back to pre-pandemic years closer to the 1-year mark in USA and worldwide. Patients may have initially neglected HPB-related issues during the early phase of the COVID-19 pandemic, which could lead to worse outcomes. While HPB-related terms reverted closer to pre-pandemic levels later in the pandemic, further research is needed to assess the long-term impacts.}, } @article {pmid34411700, year = {2021}, author = {Lee, CY and Lee, YF and Lai, LC and Tsai, MH and Lu, TP and Chuang, EY}, title = {MiDSystem: A comprehensive online system for de novo assembly and analysis of microbial genomes.}, journal = {New biotechnology}, volume = {65}, number = {}, pages = {42-52}, doi = {10.1016/j.nbt.2021.08.002}, pmid = {34411700}, issn = {1876-4347}, mesh = {*Genome, Bacterial ; Metagenome ; *Metagenomics ; Online Systems ; }, abstract = {The substantial reduction in experimental cost of next-generation sequencing techniques makes it feasible to assemble a bacterial genome of unknown species de novo and acquire substantial genetic information from environmental samples. Many bioinformatics tools and algorithms have also been developed for prokaryotes, but complex parameter settings and command line-based user interfaces cause a significant entry barrier for novices. Efficient construction of pipelines that integrate all the available genomic data poses a major challenge to the understanding of unknown pathogens. MiDSystem is a comprehensive online system for analyzing genomic data from microbiomes. With a user-friendly interface, MiDSystem supports both de novo assembly and metagenomic analysis pipelines. It is designed to automatically analyze whole genome shotgun sequencing data of bacteria submitted by users. Multiple analytical steps can be performed directly on the system, and the results generated from the embedded tools are visualized in an online summary report to make it more interpretable. Constructing a genome de novo has gradually become the foundation of bacterial studies. Taking both single species and metagenomic samples into consideration, MiDSystem can greatly reduce the time and effort for analysis of bacterial genomic data. Use of MiDSystem will enable more focus to be placed on understanding the etiology of bacterial infections and microorganism ecologies.}, } @article {pmid34410336, year = {2021}, author = {Bernard, M and Rué, O and Mariadassou, M and Pascal, G}, title = {FROGS: a powerful tool to analyse the diversity of fungi with special management of internal transcribed spacers.}, journal = {Briefings in bioinformatics}, volume = {22}, number = {6}, pages = {}, doi = {10.1093/bib/bbab318}, pmid = {34410336}, issn = {1477-4054}, mesh = {DNA Barcoding, Taxonomic/*methods ; *DNA, Ribosomal Spacer ; Databases, Genetic ; Fungi/*classification/*genetics/metabolism ; Metagenomics/methods ; RNA, Ribosomal, 16S ; Software ; User-Computer Interface ; Web Browser ; Workflow ; }, abstract = {Fungi are present in all environments. They fulfil important ecological functions and play a crucial role in the food industry. Their accurate characterization is thus indispensable, particularly through metabarcoding. The most frequently used markers to monitor fungi are ITSs. These markers are the best documented in public databases but have one main weakness: polymerase chain reaction amplification may produce non-overlapping reads in a significant fraction of the fungi. When these reads are filtered out, traditional metabarcoding pipelines lose part of the information and consequently produce biased pictures of the composition and structure of the environment under study. We developed a solution that enables processing of the entire set of reads including both overlapping and non-overlapping, thus providing a more accurate picture of fungal communities. Our comparative tests using simulated and real data demonstrated the effectiveness of our solution, which can be used by both experts and non-specialists on a command line or through the Galaxy-based web interface.}, } @article {pmid34408318, year = {2021}, author = {Leigh, DM and van Rees, CB and Millette, KL and Breed, MF and Schmidt, C and Bertola, LD and Hand, BK and Hunter, ME and Jensen, EL and Kershaw, F and Liggins, L and Luikart, G and Manel, S and Mergeay, J and Miller, JM and Segelbacher, G and Hoban, S and Paz-Vinas, I}, title = {Opportunities and challenges of macrogenetic studies.}, journal = {Nature reviews. Genetics}, volume = {22}, number = {12}, pages = {791-807}, pmid = {34408318}, issn = {1471-0064}, mesh = {Animals ; Biodiversity ; Databases, Genetic ; Genetic Techniques ; *Genetic Variation ; *Genetics ; Genetics, Population ; Humans ; Phylogeography ; Workflow ; }, abstract = {The rapidly emerging field of macrogenetics focuses on analysing publicly accessible genetic datasets from thousands of species to explore large-scale patterns and predictors of intraspecific genetic variation. Facilitated by advances in evolutionary biology, technology, data infrastructure, statistics and open science, macrogenetics addresses core evolutionary hypotheses (such as disentangling environmental and life-history effects on genetic variation) with a global focus. Yet, there are important, often overlooked, limitations to this approach and best practices need to be considered and adopted if macrogenetics is to continue its exciting trajectory and reach its full potential in fields such as biodiversity monitoring and conservation. Here, we review the history of this rapidly growing field, highlight knowledge gaps and future directions, and provide guidelines for further research.}, } @article {pmid34407145, year = {2021}, author = {Edwards, T and Jones, CB and Perkins, SE and Corcoran, P}, title = {Passive citizen science: The role of social media in wildlife observations.}, journal = {PloS one}, volume = {16}, number = {8}, pages = {e0255416}, pmid = {34407145}, issn = {1932-6203}, mesh = {*Social Media ; *Citizen Science ; Animals ; *Biodiversity ; Animals, Wild ; United Kingdom ; Introduced Species ; }, abstract = {Citizen science plays an important role in observing the natural environment. While conventional citizen science consists of organized campaigns to observe a particular phenomenon or species there are also many ad hoc observations of the environment in social media. These data constitute a valuable resource for 'passive citizen science'-the use of social media that are unconnected to any particular citizen science program, but represent an untapped dataset of ecological value. We explore the value of passive citizen science, by evaluating species distributions using the photo sharing site Flickr. The data are evaluated relative to those submitted to the National Biodiversity Network (NBN) Atlas, the largest collection of species distribution data in the UK. Our study focuses on the 1500 best represented species on NBN, and common invasive species within UK, and compares the spatial and temporal distribution with NBN data. We also introduce an innovative image verification technique that uses the Google Cloud Vision API in combination with species taxonomic data to determine the likelihood that a mention of a species on Flickr represents a given species. The spatial and temporal analyses for our case studies suggest that the Flickr dataset best reflects the NBN dataset when considering a purely spatial distribution with no time constraints. The best represented species on Flickr in comparison to NBN are diurnal garden birds as around 70% of the Flickr posts for them are valid observations relative to the NBN. Passive citizen science could offer a rich source of observation data for certain taxonomic groups, and/or as a repository for dedicated projects. Our novel method of validating Flickr records is suited to verifying more extensive collections, including less well-known species, and when used in combination with citizen science projects could offer a platform for accurate identification of species and their location.}, } @article {pmid34407125, year = {2021}, author = {Natori, Y and Hino, A}, title = {Global identification and mapping of socio-ecological production landscapes with the Satoyama Index.}, journal = {PloS one}, volume = {16}, number = {8}, pages = {e0256327}, pmid = {34407125}, issn = {1932-6203}, mesh = {Agriculture/ethics/*organization & administration ; Biodiversity ; Conservation of Natural Resources/*methods ; Datasets as Topic ; Ecosystem ; Humans ; Internationality ; *Models, Statistical ; }, abstract = {Production landscapes play an important role in conserving biodiversity outside protected areas. Socio-ecological production landscapes (SEPL) are places where people use for primary production that conserve biodiversity. Such places can be found around the world, but a lack of geographic information on SEPL has resulted in their potential for conservation being neglected in policies and programs. We tested the global applicability of the Satoyama Index for identifying SEPL in multi-use cultural landscapes using global land use/cover data and two datasets of known SEPL. We found that the Satoyama Index, which was developed with a focus on biodiversity and tested in Japan, could be used globally to identify landscapes resulting from complex interactions between people and nature with statistical significance. This makes SEPL more relevant in the global conservation discourse. As the Satoyama Index mapping revealed that approximately 80% of SEPL occur outside recognized conservation priorities, such as protected areas and key biodiversity areas, identifying SEPL under the scheme of other area-based conservation measures (OECM) may bring more conservation attention to SEPL. Based on the issues identified in the SEPL mapping, we discuss ways that could improve the Satoyama Index mapping at global scale with the longitudinal temporal dimension and at more local scale with spatial and thematic resolution.}, } @article {pmid34406207, year = {2021}, author = {Nunes, HRC and Murta-Nascimento, C and Lima, MCP}, title = {Impact of the Dry Law on road traffic mortality in Brazilian states: an interrupted time series analysis.}, journal = {Revista brasileira de epidemiologia = Brazilian journal of epidemiology}, volume = {24}, number = {}, pages = {e210045}, doi = {10.1590/1980-549720210045}, pmid = {34406207}, issn = {1980-5497}, mesh = {*Accidents, Traffic ; Brazil/epidemiology ; Geography ; Humans ; *Information Systems ; Interrupted Time Series Analysis ; }, abstract = {OBJECTIVE: To assess the impact of 2008 Public Law number 11,705, also known as Dry Law (DL-08), on mortality from road traffic accidents (RTA), in each of the 27 Brazilian Federative Units (BFUs).

METHODS: Ecological study of interrupted time series with RTA data from 2002 to 2015, totalizing 168 months. Data were obtained from the Mortality Information System, the Brazilian Institute of Geography and Statistics, and from the National Traffic Department. Autoregressive integrated moving average (ARIMA) models were adjusted to assess the impact of DL-08 in each BFUs.

RESULTS: After the implementation of the DL-08, there was a significant decrease in mortality from RTA in the state of Santa Catarina (pre DL-08 = 2.60 ± 0.30 and post DL-08 = 2.32 ± 0.35; p < 0.001) and in the Federal District (pre DL-08 = 2.22 ± 0.40 and post DL-08 = 1.76 ± 0.35; p = 0.002), a significant increase in mortality in the states of Acre, Amazonas, Rondônia, Maranhão, Piauí, Ceará, Rio Grande do Norte, Paraíba, Pernambuco, Alagoas, Sergipe and Mato Grosso, and a stability in the other states. The sensitivity analysis conducted over a shorter time series with 24 months showed results similar to those obtained with the 168-month series for most of the 27 BFUs.

CONCLUSION: The DL-08 had a heterogeneous impact on mortality from traffic accidents on BFUs.}, } @article {pmid34405324, year = {2022}, author = {Chen, F and Muhammad, FG and Khan, ZI and Ahmad, K and Nadeem, M and Mahmood, S and Awan, MUF and Munir, M and Malik, IS and Ashfaq, A and Sultana, R and Maqsood, A and Saqlain, L and Naeem, M and Ma, J}, title = {Ecological risk assessment of heavy metal chromium in a contaminated pastureland area in the Central Punjab, Pakistan: soils vs plants vs ruminants.}, journal = {Environmental science and pollution research international}, volume = {29}, number = {3}, pages = {4170-4179}, pmid = {34405324}, issn = {1614-7499}, mesh = {Animals ; Chromium ; Environmental Monitoring ; Female ; *Metals, Heavy/analysis ; Pakistan ; Risk Assessment ; Ruminants ; Soil ; *Soil Pollutants/analysis ; }, abstract = {Grazing animals act as a bioindicator to study the heavy metal status in the pasture lands because excessive amount of toxic metals in the animal diet either disturb their normal activity or deposit the contaminants into their tissues. The aim of this study was to appraise the chromium status in soil and pasture crops with respect to the nutritional requirement of grazing animals. Three different sites were selected to collect soil, forages, and animal samples from District Jhang. All the samples were processed through atomic absorption spectrophotometer to analyze the chromium concentration in them. Chromium concentration was varied as 0.703-4.20 mg/kg in soil, 0.45-2.85 mg/kg in forages, and 0.588-2.37 mg/kg in all collected animal samples. Both the soil and forage samples displayed the maximum chromium concentration in the Capparis decidua, whereas animal samples revealed maximum concentration in animal blood. Results of pollution load index (0.078 to 0.463 mg/kg) exhibited that all the sample values are less than unity while enrichment factor (1.57-8.25mg/kg) showed that significant level of chromium is enriched in these sites. The maximum value of daily intake (0.0007-0.0055mg/kg/day) and health risk index (0.0004-0.00370055mg/kg/day) was observed in the buffalo that feed on the Capparis decidua. Bio-concentration factor (0.398-2.09mg/kg) value was the maximum in the Medicago sativa. It is concluded that all the animal samples showed chromium concentration beyond their standards. Thus, proper measures should be taken to reduce the metal contamination in these areas that ultimately lessen the availability of toxic metals to grazing animals.}, } @article {pmid34404811, year = {2021}, author = {Sabatini, FM and Bluhm, H and Kun, Z and Aksenov, D and Atauri, JA and Buchwald, E and Burrascano, S and Cateau, E and Diku, A and Duarte, IM and Fernández López, ÁB and Garbarino, M and Grigoriadis, N and Horváth, F and Keren, S and Kitenberga, M and Kiš, A and Kraut, A and Ibisch, PL and Larrieu, L and Lombardi, F and Matovic, B and Melu, RN and Meyer, P and Midteng, R and Mikac, S and Mikoláš, M and Mozgeris, G and Panayotov, M and Pisek, R and Nunes, L and Ruete, A and Schickhofer, M and Simovski, B and Stillhard, J and Stojanovic, D and Szwagrzyk, J and Tikkanen, OP and Toromani, E and Volosyanchuk, R and Vrška, T and Waldherr, M and Yermokhin, M and Zlatanov, T and Zagidullina, A and Kuemmerle, T}, title = {European primary forest database v2.0.}, journal = {Scientific data}, volume = {8}, number = {1}, pages = {220}, pmid = {34404811}, issn = {2052-4463}, support = {658876//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; ETN-WIE-FZS-001//Zoologische Gesellschaft Frankfurt (Frankfurt Zoological Society)/ ; ETN-WIE-FZS-001//Zoologische Gesellschaft Frankfurt (Frankfurt Zoological Society)/ ; }, mesh = {*Conservation of Natural Resources ; Databases, Factual ; Europe ; *Forests ; }, abstract = {Primary forests, defined here as forests where the signs of human impacts, if any, are strongly blurred due to decades without forest management, are scarce in Europe and continue to disappear. Despite these losses, we know little about where these forests occur. Here, we present a comprehensive geodatabase and map of Europe's known primary forests. Our geodatabase harmonizes 48 different, mostly field-based datasets of primary forests, and contains 18,411 individual patches (41.1 Mha) spread across 33 countries. When available, we provide information on each patch (name, location, naturalness, extent and dominant tree species) and the surrounding landscape (biogeographical regions, protection status, potential natural vegetation, current forest extent). Using Landsat satellite-image time series (1985-2018) we checked each patch for possible disturbance events since primary forests were identified, resulting in 94% of patches free of significant disturbances in the last 30 years. Although knowledge gaps remain, ours is the most comprehensive dataset on primary forests in Europe, and will be useful for ecological studies, and conservation planning to safeguard these unique forests.}, } @article {pmid34403763, year = {2021}, author = {Skern-Mauritzen, R and Malde, K and Eichner, C and Dondrup, M and Furmanek, T and Besnier, F and Komisarczuk, AZ and Nuhn, M and Dalvin, S and Edvardsen, RB and Klages, S and Huettel, B and Stueber, K and Grotmol, S and Karlsbakk, E and Kersey, P and Leong, JS and Glover, KA and Reinhardt, R and Lien, S and Jonassen, I and Koop, BF and Nilsen, F}, title = {The salmon louse genome: Copepod features and parasitic adaptations.}, journal = {Genomics}, volume = {113}, number = {6}, pages = {3666-3680}, doi = {10.1016/j.ygeno.2021.08.002}, pmid = {34403763}, issn = {1089-8646}, mesh = {Acclimatization ; Animals ; *Copepoda/genetics/parasitology ; *Fish Diseases/genetics ; *Parasites/genetics ; Transcriptome ; }, abstract = {Copepods encompass numerous ecological roles including parasites, detrivores and phytoplankton grazers. Nonetheless, copepod genome assemblies remain scarce. Lepeophtheirus salmonis is an economically and ecologically important ectoparasitic copepod found on salmonid fish. We present the 695.4 Mbp L. salmonis genome assembly containing ≈60% repetitive regions and 13,081 annotated protein-coding genes. The genome comprises 14 autosomes and a ZZ-ZW sex chromosome system. Assembly assessment identified 92.4% of the expected arthropod genes. Transcriptomics supported annotation and indicated a marked shift in gene expression after host attachment, including apparent downregulation of genes related to circadian rhythm coinciding with abandoning diurnal migration. The genome shows evolutionary signatures including loss of genes needed for peroxisome biogenesis, presence of numerous FNII domains, and an incomplete heme homeostasis pathway suggesting heme proteins to be obtained from the host. Despite repeated development of resistance against chemical treatments L. salmonis exhibits low numbers of many genes involved in detoxification.}, } @article {pmid34402267, year = {2021}, author = {Li, ZY and Wang, JQ and Li, CF and Zhang, XB and Yang, HJ and Huang, LQ and Yang, B}, title = {[Strategies for efficacy and function positioning of new resources of Chinese materia medica].}, journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica}, volume = {46}, number = {14}, pages = {3455-3464}, doi = {10.19540/j.cnki.cjcmm.20210502.102}, pmid = {34402267}, issn = {1001-5302}, mesh = {China ; Data Mining ; *Drugs, Chinese Herbal/pharmacology ; Humans ; *Materia Medica ; Medicine, Chinese Traditional ; }, abstract = {Chinese materia medica(CMM) serves as an important cornerstone for the development of traditional Chinese medicine(TCM) culture and industry due to its unique ecological,medical,economic,scientific and technological,and cultural values. The supply shortage and unstable quality of some CMM resources have hindered the development of TCM. Ensuring the sustainable use of CMM resources has become essential for the development of TCM in China. Enriching CMM resources is the key to ensuring the sustainable utilization of TCM resources in China,which can be achieved via expanding the medicinal parts,developing the substitutes,seeking for analogues,exploring the ethnic and folk medicines,or introducing foreign medicinal materials. CMM efficacy or function positioning plays a very important role in the transformation of new CMM resources. The strategies and methods for efficacy or function positioning of new CMM resources,including analogy,plant genetic relationship exploration,medicinal property deduction,ethnobotanical investigation,text mining,network pharmacology,and structure-activity relationship exploration,were systematically proposed in this study based on CMM theory,textual research,and modern methodologies. This paper is expected to provide a theoretical reference for the continuous enrichment and development of CMM resources and the high-quality development of TCM culture and industry.}, } @article {pmid34401744, year = {2021}, author = {Pintor, AFV and Ray, N and Longbottom, J and Bravo-Vega, CA and Yousefi, M and Murray, KA and Ediriweera, DS and Diggle, PJ}, title = {Addressing the global snakebite crisis with geo-spatial analyses - Recent advances and future direction.}, journal = {Toxicon: X}, volume = {11}, number = {}, pages = {100076}, pmid = {34401744}, issn = {2590-1710}, support = {001/WHO_/World Health Organization/International ; MR/R015600/1/MRC_/Medical Research Council/United Kingdom ; }, abstract = {Venomous snakebite is a neglected tropical disease that annually leads to hundreds of thousands of deaths or long-term physical and mental ailments across the developing world. Insufficient data on spatial variation in snakebite risk, incidence, human vulnerability, and accessibility of medical treatment contribute substantially to ineffective on-ground management. There is an urgent need to collect data, fill knowledge gaps and address on-ground management problems. The use of novel, and transdisciplinary approaches that take advantage of recent advances in spatio-temporal models, 'big data', high performance computing, and fine-scale spatial information can add value to snakebite management by strategically improving our understanding and mitigation capacity of snakebite. We review the background and recent advances on the topic of snakebite related geospatial analyses and suggest avenues for priority research that will have practical on-ground applications for snakebite management and mitigation. These include streamlined, targeted data collection on snake distributions, snakebites, envenomings, venom composition, health infrastructure, and antivenom accessibility along with fine-scale models of spatio-temporal variation in snakebite risk and incidence, intraspecific venom variation, and environmental change modifying human exposure. These measures could improve and 'future-proof' antivenom production methods, antivenom distribution and stockpiling systems, and human-wildlife conflict management practices, while simultaneously feeding into research on venom evolution, snake taxonomy, ecology, biogeography, and conservation.}, } @article {pmid34399373, year = {2021}, author = {Yang, X and Liu, S and Jia, C and Liu, Y and Yu, C}, title = {Vulnerability assessment and management planning for the ecological environment in urban wetlands.}, journal = {Journal of environmental management}, volume = {298}, number = {}, pages = {113540}, doi = {10.1016/j.jenvman.2021.113540}, pmid = {34399373}, issn = {1095-8630}, mesh = {China ; Cities ; City Planning ; Conservation of Natural Resources ; *Ecosystem ; Geographic Information Systems ; *Wetlands ; }, abstract = {As a special ecosystem in cities, urban wetland parks have important environmental regulation and social service functions. This paper proposes a new methodology of urban wetland planning and management based on the vulnerability of the ecological environment. The Jixi National Wetland Park (JNWP) was taken as the research area to analyze the ecological, geological and environmental factors that affect urban wetlands. A remote sensing image, digital elevation model, and environmental quality interpolation processing were used to generate the factor layer, and a comprehensive evaluation index system was established. The fuzzy Delphi analytic hierarchy process (FDAHP) method was used to calculate the comprehensive weight of each evaluation factor. A model to evaluate the ecological environment vulnerability of the JNWP was established. Then, an improved k-means clustering algorithm was used to classify the ecological environment of the study area. The ecological environment vulnerability of the wetland was evaluated. The results showed that the vulnerability of the ecological environment in the study area could be divided into five levels, including very low, low, medium, high and very high vulnerability areas. According to the vulnerability level and the results of k-means++ cluster analysis, the JNWP is divided into five areas. The wetland buffer zone is the main factor that determines the distribution of ecological environment vulnerability in urban wetlands. However, cultivated land development and ecological environmental restoration are the main factors that determine the evolution of ecological environment vulnerability in urban wetlands. The FDAHP and geographic information systems (GIS), combined with cluster analysis, are effective methods to evaluate the vulnerability of the ecological environment of urban wetlands, which provides a scientific and accurate methodology for the management and sustainable development of urban wetlands.}, } @article {pmid34396479, year = {2022}, author = {Karabulut, Aİ and Yazici-Karabulut, B and Derin, P and Yesilnacar, MI and Cullu, MA}, title = {Landfill siting for municipal solid waste using remote sensing and geographic information system integrated analytic hierarchy process and simple additive weighting methods from the point of view of a fast-growing metropolitan area in GAP area of Turkey.}, journal = {Environmental science and pollution research international}, volume = {29}, number = {3}, pages = {4044-4061}, pmid = {34396479}, issn = {1614-7499}, mesh = {Analytic Hierarchy Process ; Geographic Information Systems ; Humans ; *Refuse Disposal ; Remote Sensing Technology ; *Solid Waste ; Turkey ; Waste Disposal Facilities ; }, abstract = {The site selection process for municipal solid wastes (MSW) plays an important role in environmental impact studies by allowing the use of environmental design criteria in city and country planning. This process also includes the subject of urban planning due to its impact on the economy, ecology, and environmental health of the region. Urban growth is a phenomenon that is difficult to stop or limit in line with environmental, social, and economic changes and development. Therefore, the selection of solid waste landfill is of great importance in terms of ensuring a sustainable urban future. In the study, Landsat 5 and Landsat 8 satellite images, base map, soil, and geology maps were used for the integration of geospatial data. Each layer specified in the map has been formed using the spatial analysis potential of the ArcGIS10.5 software. In these digitized layers, weight scoring was made using the comparison matrix and the final suitability map was produced. All digital layers established in the generated maps were arranged according to the analytical hierarchy method (AHP) and subjected to the simple additive weighting (SAW) method. The results indicated that 13.51% of the total area was suitable for a sanitary landfill. As a result of this study, urban growth, population projection, and domestic solid waste volume of Sanliurfa province were determined. According to the 25-year population projection, the population in 2045 was approximately 4,471,938 people, and the cumulative waste volume was 27,415,627 m[3]. In addition, as a result of accepting the wastes of three metropolitan districts and seven district municipalities to the sanitary landfill, only "first candidate area" is the most and has been deemed appropriate. Given the ecological and environmental challenges (proximity to the city center, etc.) associated with the existing MSW sanitary landfill facility in Sanliurfa, the results of this study show that the geographic information system (GIS) integrated AHP and SAW method is an effective tool to assist decision makers to properly plan towards achieving a sustainable environment.}, } @article {pmid34392439, year = {2021}, author = {Zhao, Y and Lyu, X and Xiao, W and Tian, S and Zhang, J and Hu, Z and Fu, Y}, title = {Evaluation of the soil profile quality of subsided land in a coal mining area backfilled with river sediment based on monitoring wheat growth biomass with UAV systems.}, journal = {Environmental monitoring and assessment}, volume = {193}, number = {9}, pages = {576}, pmid = {34392439}, issn = {1573-2959}, support = {2012BAC04B03//National Science and Technology Program during the Twelfth Five-year Plan Period/ ; 41771542//National Natural Science Foundation of China/ ; 41401609//National Natural Science Foundation of China/ ; 41807511//National Natural Science Foundation of China/ ; 42071250//national natural science foundation of china/ ; }, mesh = {Biomass ; *Coal Mining ; Environmental Monitoring ; Rivers ; *Soil ; Triticum ; }, abstract = {Underground coal mining leads to land subsidence, and the situation is particularly serious in the Coal-Grain Complex in eastern China, causing the crop production to be reduced or to be taken out. Backfilling with Yellow River sediment is one of the effective methods to solve the land subsidence in this area, but a key issue is how to select the optimal soil reconstruction profile so that the crop yield after backfilling and reclamation is unaffected. The main purpose of this study is to verify the feasibility of selecting the optimal soil reconstruction profile by rapid monitoring of crop growth and judging soil quality with the aid of unmanned aerial vehicle systems (UAVs). A control treatment and 13 experimental treatments were established for the study area. The control treatment consisted of using 30 cm topsoil and 90 cm subsoil and the topsoil is a proxy for native (undisturbed) soil from the study sites. All other treatments consisted of using varying combinations of subsoil and sediment overlain by 30 cm of topsoil. The vegetation indices from the UAV multispectral images, and the plant height and vegetation coverage from the UAV RGB images were used for estimation of the winter wheat biomass in a random forest regression. The results showed that the random forest regression model yielded accurate estimation of the aboveground biomass. Furthermore, knowledge of plant height and vegetation coverage improved the accuracy of prediction such that crop growth was well characterized. The optimal soil profile consisted of 0.3 m topsoil + 0.2 m subsoil + 0.2 m sediment + 0.2 m subsoil + 0.3 m sediment. A fast and effective airborne monitoring method for soil quality was established, thus providing greatly improved monitoring efficiency.}, } @article {pmid34391505, year = {2021}, author = {Read, JM and Green, CA and Harrison, EM and Docherty, AB and Funk, S and Harrison, J and Girvan, M and Hardwick, HE and Turtle, L and Dunning, J and Nguyen-Van-Tam, JS and Openshaw, PJ and Baillie, JK and Semple, MG and , }, title = {Hospital-acquired SARS-CoV-2 infection in the UK's first COVID-19 pandemic wave.}, journal = {Lancet (London, England)}, volume = {398}, number = {10305}, pages = {1037-1038}, pmid = {34391505}, issn = {1474-547X}, support = {/WT_/Wellcome Trust/United Kingdom ; MC_PC_19025/MRC_/Medical Research Council/United Kingdom ; MC_PC_19059/MRC_/Medical Research Council/United Kingdom ; MR/V038613/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {COVID-19/epidemiology/*transmission ; Cross Infection/*epidemiology ; Hospitals/*classification/statistics & numerical data ; Humans ; Pandemics/statistics & numerical data ; *SARS-CoV-2 ; United Kingdom/epidemiology ; }, } @article {pmid34387818, year = {2022}, author = {Chen, F and Saqlain, L and Ma, J and Khan, ZI and Ahmad, K and Ashfaq, A and Sultana, R and Muhammad, FG and Maqsood, A and Naeem, M and Malik, IS and Munir, M and Nadeem, M and Yang, Y}, title = {Evaluation of potential ecological risk and prediction of zinc accumulation and its transfer in soil plants and ruminants: public health implications.}, journal = {Environmental science and pollution research international}, volume = {29}, number = {3}, pages = {3386-3393}, pmid = {34387818}, issn = {1614-7499}, mesh = {Animals ; Cattle ; Environmental Monitoring ; Female ; *Metals, Heavy/analysis ; Public Health ; Risk Assessment ; Ruminants ; Sheep ; Soil ; *Soil Pollutants/analysis ; Zinc ; }, abstract = {Present work evaluated the zinc (Zn) concentration in soil, forage, blood plasma, hair, and feces samples of cows, buffaloes, and sheep taken from Mianwali, Punjab, Pakistan. The concentration of Zn was found in the ranged of 21.82-35.09mg/kg, 32.59-42.17mg/kg, 0.927-2.48mg/l, 1.03-2.84mg/kg, and 0.923-1.98mg/kg in soil, forage, blood plasma, hair, and feces samples, respectively. The Zn concentration in soil, forage, blood, hair, and feces was safer compared to standard limits. Statistical analysis described that values for BCF, PLI, EF, DIM, and HRI ranged 1.03-1.57mg/kg, 0.486-0.782mg/kg, 0.457-0.696mg/kg, 0.048-0.08mg/kg, and 0.160-0.272mg/kg, respectively. It can be concluded from the present work that Zn concentration was safe in soil, forages, and animal samples. BCF was noticed as greater than 1 while PLI, EF, DIM, and HRI were found less than 1, so regular heavy metal analysis was required to appraise the contamination level in environment.}, } @article {pmid34387347, year = {2022}, author = {Caetano-Anollés, K and Ewers, B and Iyer, S and Lucas, JR and Pavlic, TP and Seale, AP and Zeng, Y}, title = {A Minimal Framework for Describing Living Systems: A Multi-Dimensional View of Life Across Scales.}, journal = {Integrative and comparative biology}, volume = {61}, number = {6}, pages = {2053-2065}, doi = {10.1093/icb/icab172}, pmid = {34387347}, issn = {1557-7023}, mesh = {Animals ; Humans ; *Life Cycle Stages ; }, abstract = {The almost limitless complexity of biology has led to two general approaches to understanding biological phenomena. One approach is dominated by reductionism in which high-level phenomena of whole systems are viewed as emerging from relatively simple and generally understood interactions at a substantially lower level. Although this approach is theoretically general, it can become intractable in practice when attempting to simultaneously explain a wide range of systems. A second approach is for specialists to investigate biological phenomena within one of many different hierarchical levels of description that are separated to decouple from concerns at other levels. Although this approach reduces the explanatory burden on specialists that operate within each level, it also reduces integration from insights gained at other levels. Thus, as beneficial as these approaches have been, they limit the scope and integration of knowledge across scales of biological organization to the detriment of a truly synoptic view of life. The challenge is to find a theoretical and experimental framework that facilitates a broader understanding of the hierarchy of life-providing permeability for the exchange of ideas among disciplinary specialists without discounting the peculiarities that have come to define those disciplines. For this purpose, coarse-grained, scale-invariant properties, and resources need to be identified that describe the characteristic features of a living system at all spatiotemporal scales. The approach will be aided by a common vernacular that underscores the realities of biological connections across a wide range of scales. Therefore, in this vision paper, we propose a conceptual approach based on four identified resources-energy, conductance, storage, and information (ECSI)-to reintegrate biological studies with the aim of unifying life sciences under resource limitations. We argue that no functional description of a living system is complete without accounting for at least all four of these resources. Thus, making these resources explicit will help to identify commonalities to aid in transdisciplinary discourse as well as opportunities for integrating among the differently scoped areas of specialized inquiry. The proposed conceptual framework for living systems should be valid across all scales and may uncover potential limitations of existing hypotheses and help researchers develop new hypotheses addressing fundamental processes of life without having to resort to reductionism.}, } @article {pmid34386785, year = {2021}, author = {Sigfrid, L and Drake, TM and Pauley, E and Jesudason, EC and Olliaro, P and Lim, WS and Gillesen, A and Berry, C and Lowe, DJ and McPeake, J and Lone, N and Munblit, D and Cevik, M and Casey, A and Bannister, P and Russell, CD and Goodwin, L and Ho, A and Turtle, L and O'Hara, ME and Hastie, C and Donohue, C and Spencer, RG and Donegan, C and Gummery, A and Harrison, J and Hardwick, HE and Hastie, CE and Carson, G and Merson, L and Baillie, JK and Openshaw, P and Harrison, EM and Docherty, AB and Semple, MG and Scott, JT and , }, title = {Long Covid in adults discharged from UK hospitals after Covid-19: A prospective, multicentre cohort study using the ISARIC WHO Clinical Characterisation Protocol.}, journal = {The Lancet regional health. Europe}, volume = {8}, number = {}, pages = {100186}, pmid = {34386785}, issn = {2666-7762}, support = {MC_PC_19059/MRC_/Medical Research Council/United Kingdom ; MC_UU_12014/9/MRC_/Medical Research Council/United Kingdom ; MC_UU_12014/8/MRC_/Medical Research Council/United Kingdom ; MC_PC_19025/MRC_/Medical Research Council/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; MC_PC_15001/MRC_/Medical Research Council/United Kingdom ; MC_PC_19026/MRC_/Medical Research Council/United Kingdom ; MR/N003403/1/MRC_/Medical Research Council/United Kingdom ; }, abstract = {BACKGROUND: This study sought to establish the long-term effects of Covid-19 following hospitalisation.

METHODS: 327 hospitalised participants, with SARS-CoV-2 infection were recruited into a prospective multicentre cohort study at least 3 months post-discharge. The primary outcome was self-reported recovery at least ninety days after initial Covid-19 symptom onset. Secondary outcomes included new symptoms, disability (Washington group short scale), breathlessness (MRC Dyspnoea scale) and quality of life (EQ5D-5L).

FINDINGS: 55% of participants reported not feeling fully recovered. 93% reported persistent symptoms, with fatigue the most common (83%), followed by breathlessness (54%). 47% reported an increase in MRC dyspnoea scale of at least one grade. New or worse disability was reported by 24% of participants. The EQ5D-5L summary index was significantly worse following acute illness (median difference 0.1 points on a scale of 0 to 1, IQR: -0.2 to 0.0). Females under the age of 50 years were five times less likely to report feeling recovered (adjusted OR 5.09, 95% CI 1.64 to 15.74), were more likely to have greater disability (adjusted OR 4.22, 95% CI 1.12 to 15.94), twice as likely to report worse fatigue (adjusted OR 2.06, 95% CI 0.81 to 3.31) and seven times more likely to become more breathless (adjusted OR 7.15, 95% CI 2.24 to 22.83) than men of the same age.

INTERPRETATION: Survivors of Covid-19 experienced long-term symptoms, new disability, increased breathlessness, and reduced quality of life. These findings were present in young, previously healthy working age adults, and were most common in younger females.

FUNDING: National Institute for Health Research, UK Medical Research Council, Wellcome Trust, Department for International Development and the Bill and Melinda Gates Foundation.}, } @article {pmid34382939, year = {2021}, author = {Hughes, AC and Marshall, BM and Strine, CT}, title = {Gaps in global wildlife trade monitoring leave amphibians vulnerable.}, journal = {eLife}, volume = {10}, number = {}, pages = {}, pmid = {34382939}, issn = {2050-084X}, mesh = {Africa, Central ; *Amphibians/classification/physiology ; Animals ; *Animals, Wild/classification/physiology ; *Biodiversity ; China ; Commerce ; Databases, Factual ; Endangered Species ; Internationality ; Reptiles ; South America ; Species Specificity ; }, abstract = {As the biodiversity crisis continues, we must redouble efforts to understand and curb pressures pushing species closer to extinction. One major driver is the unsustainable trade of wildlife. Trade in internationally regulated species gains the most research attention, but this only accounts for a minority of traded species and we risk failing to appreciate the scale and impacts of unregulated legal trade. Despite being legal, trade puts pressure on wild species via direct collection, introduced pathogens, and invasive species. Smaller species-rich vertebrates, such as reptiles, fish, and amphibians, may be particularly vulnerable to trading because of gaps in regulations, small distributions, and demand of novel species. Here, we combine data from five sources: online web searches in six languages, Convention on International Trade in Endangered Species (CITES) trade database, Law Enforcement Management Information System (LEMIS) trade inventory, IUCN assessments, and a recent literature review, to characterise the global trade in amphibians, and also map use by purpose including meat, pets, medicinal, and for research. We show that 1215 species are being traded (17% of amphibian species), almost three times previous recorded numbers, 345 are threatened, and 100 Data Deficient or unassessed. Traded species origin hotspots include South America, China, and Central Africa; sources indicate 42% of amphibians are taken from the wild. Newly described species can be rapidly traded (mean time lag of 6.5 years), including threatened and unassessed species. The scale and limited regulation of the amphibian trade, paired with the triptych of connected pressures (collection, pathogens, invasive species), warrants a re-examination of the wildlife trade status quo, application of the precautionary principle in regard to wildlife trade, and a renewed push to achieve global biodiversity goals.}, } @article {pmid34380583, year = {2022}, author = {Bommarito, C and Wahl, M and Thieltges, DW and Pansch, C and Zucchetta, M and Pranovi, F}, title = {Biotic and abiotic drivers affect parasite richness, prevalence and abundance in Mytilus galloprovincialis along the Northern Adriatic Sea.}, journal = {Parasitology}, volume = {149}, number = {1}, pages = {15-23}, pmid = {34380583}, issn = {1469-8161}, mesh = {Animals ; Humans ; *Mytilus ; *Parasites ; *Parasitic Diseases ; Prevalence ; Salinity ; }, abstract = {Although it is generally known that a combination of abiotic and biotic drivers shapes the distribution and abundance of parasites, our understanding of the interplay of these factors remains to be assessed for most marine host species. The present field survey investigated spatial patterns of richness, prevalence and abundance of parasites in Mytilus galloprovincialis along the coast of the northern Adriatic Sea. Herein, the relationships between biotic (host size, density and local parasite richness of mussel population) and abiotic (eutrophication and salinity) drivers and parasite richness of mussel individuals, prevalence and abundance were analysed. Local parasite richness was the most relevant factor driving parasite species richness in mussel individuals. Prevalence was mainly driven by eutrophication levels in three out of four parasite species analysed. Similarly, abundance was driven mainly by eutrophication in two parasite species. Mussel size, density and salinity had only minor contributions to the best fitting models. This study highlights that the influence of abiotic and biotic drivers on parasite infections in mussels can be differentially conveyed, depending on the infection measure applied, i.e. parasite richness, prevalence or abundance. Furthermore, it stresses the importance of eutrophication as a major factor influencing parasite prevalence and abundance in mussels in the Adriatic Sea.}, } @article {pmid34378981, year = {2021}, author = {Molina, L and Udaondo, Z and Montero-Curiel, M and Wittich, RM and García-Puente, A and Segura, A}, title = {Clover Root Exudates Favor Novosphingobium sp. HR1a Establishment in the Rhizosphere and Promote Phenanthrene Rhizoremediation.}, journal = {mSphere}, volume = {6}, number = {4}, pages = {e0041221}, pmid = {34378981}, issn = {2379-5042}, mesh = {Biodegradation, Environmental ; Medicago/*chemistry/drug effects ; Phenanthrenes/analysis/*metabolism/pharmacology ; Plant Extracts/pharmacology ; Plant Roots/*chemistry ; Soil Microbiology ; Sphingomonadaceae/drug effects/*physiology ; }, abstract = {Rhizoremediation is based on the ability of microorganisms to metabolize nutrients from plant root exudates and, thereby, to cometabolize or even mineralize toxic environmental contaminants. Novosphingobium sp. HR1a is a bacterial strain able to degrade a wide variety of polycyclic aromatic hydrocarbons (PAHs). Here, we have demonstrated that the number of CFU in microcosms vegetated with clover was almost 2 orders of magnitude higher than that in nonvegetated microcosms or microcosms vegetated with rye-grass or grass. Strain HR1a was able to eliminate 92% of the phenanthrene in the microcosms with clover after 9 days. We have studied the molecular basis of the interaction between strain HR1a and clover by phenomic, metabolomic, and transcriptomic analyses. By measuring the relative concentrations of several metabolites exudated by clover both in the presence and in the absence of the bacteria, we identified some compounds that were probably consumed in the rhizosphere; the transcriptomic analyses confirmed the expression of genes involved in the catabolism of these compounds. By using a transcriptional fusion of the green fluorescent protein (GFP) to the promoter of the gene encoding the dioxygenase involved in the degradation of PAHs, we have demonstrated that this gene is induced at higher levels in clover microcosms than in nonvegetated microcosms. Therefore, the positive interaction between clover and Novosphingobium sp. HR1a during rhizoremediation is a result of the bacterial utilization of different carbon and nitrogen sources released during seedling development and the capacity of clover exudates to induce the PAH degradation pathway. IMPORTANCE The success of an eco-friendly and cost-effective strategy for soil decontamination is conditioned by the understanding of the ecology of plant-microorganism interactions. Although many studies have been published about the bacterial metabolic capacities in the rhizosphere and about rhizoremediation of contaminants, there are fewer studies dealing with the integration of bacterial metabolic capacities in the rhizosphere during PAH bioremediation, and some aspects still remain controversial. Some authors have postulated that the presence of easily metabolizable carbon sources in root exudates might repress the expression of genes required for contaminant degradation, while others found that specific rhizosphere compounds can induce such genes. Novosphingobium sp. HR1a, which is our model organism, has two characteristics desirable in bacteria for use in remediation: its ubiquity and the capacity to degrade a wide variety of contaminants. We have demonstrated that this bacterium consumes several rhizospheric compounds without repression of the genes required for the mineralization of PAHs. In fact, some compounds even induced their expression.}, } @article {pmid34375331, year = {2021}, author = {Giles, JR and Cummings, DAT and Grenfell, BT and Tatem, AJ and Erbach-Schoenberg, EZ and Metcalf, C and Wesolowski, A}, title = {Trip duration drives shift in travel network structure with implications for the predictability of spatial disease spread.}, journal = {PLoS computational biology}, volume = {17}, number = {8}, pages = {e1009127}, pmid = {34375331}, issn = {1553-7358}, support = {DP2 LM013102/LM/NLM NIH HHS/United States ; R01 AI160780/AI/NIAID NIH HHS/United States ; }, mesh = {Cell Phone Use/statistics & numerical data ; Communicable Diseases/epidemiology/*transmission ; Computational Biology ; Computer Simulation ; Disease Outbreaks/statistics & numerical data ; Epidemics/statistics & numerical data ; Geographic Information Systems/statistics & numerical data ; Humans ; Models, Biological ; Models, Statistical ; Namibia/epidemiology ; Population Density ; Spatio-Temporal Analysis ; Time Factors ; Travel/*statistics & numerical data ; Urban Population/statistics & numerical data ; }, abstract = {Human travel is one of the primary drivers of infectious disease spread. Models of travel are often used that assume the amount of travel to a specific destination decreases as cost of travel increases with higher travel volumes to more populated destinations. Trip duration, the length of time spent in a destination, can also impact travel patterns. We investigated the spatial patterns of travel conditioned on trip duration and find distinct differences between short and long duration trips. In short-trip duration travel networks, trips are skewed towards urban destinations, compared with long-trip duration networks where travel is more evenly spread among locations. Using gravity models to inform connectivity patterns in simulations of disease transmission, we show that pathogens with shorter generation times exhibit initial patterns of spatial propagation that are more predictable among urban locations. Further, pathogens with a longer generation time have more diffusive patterns of spatial spread reflecting more unpredictable disease dynamics.}, } @article {pmid34372527, year = {2021}, author = {Banko, A and Petrovic, G and Miljanovic, D and Loncar, A and Vukcevic, M and Despot, D and Cirkovic, A}, title = {Comparison and Sensitivity Evaluation of Three Different Commercial Real-Time Quantitative PCR Kits for SARS-CoV-2 Detection.}, journal = {Viruses}, volume = {13}, number = {7}, pages = {}, pmid = {34372527}, issn = {1999-4915}, mesh = {COVID-19/diagnosis/epidemiology/*virology ; COVID-19 Nucleic Acid Testing/*methods ; Cross-Sectional Studies ; Humans ; RNA, Viral/genetics/isolation & purification ; *Reagent Kits, Diagnostic ; Real-Time Polymerase Chain Reaction/*methods ; SARS-CoV-2/genetics/*isolation & purification ; Sensitivity and Specificity ; Serbia/epidemiology ; }, abstract = {Real-time reverse transcription polymerase chain reaction (RT-qPCR) is the most sensitive and specific assay and, therefore, is the "gold standard" diagnostic method for the diagnosis of SARS-CoV-2 infection. The aim of this study was to compare and analyze the detection performance of three different commercially available SARS-CoV-2 nucleic acid detection kits: Sansure Biotech, GeneFinder[TM], and TaqPath[TM] on 354 randomly selected samples from hospitalized COVID-19 patients. All PCR reactions were performed using the same RNA isolates and one real-time PCR machine. The final result of the three evaluated kits was not statistically different (p = 0.107), and also had a strong positive association and high Cohen's κ coefficient. In contrast, the average Ct values that refer to the ORF1ab and N gene amplification were significantly different (p < 0.001 and p < 0.001, respectively), with the lowest obtained by the TaqPath[TM] for the ORF1ab and by the Sansure Biotech for the N gene. The results show a high similarity in the analytical sensitivities for SARS-CoV-2 detection, which indicates that the diagnostic accuracy of the three assays is comparable. However, the SanSure Biotech kit showed a bit better diagnostic performance. Our findings suggest that the imperative for improvement should address the determination of cut-off Ct values and rapid modification of the primer sets along with the appearance of new variants.}, } @article {pmid34371221, year = {2021}, author = {Li, J and Chen, X and Kurban, A and Van de Voorde, T and De Maeyer, P and Zhang, C}, title = {Identification of conservation priorities in the major basins of Central Asia: Using an integrated GIS-based ordered weighted averaging approach.}, journal = {Journal of environmental management}, volume = {298}, number = {}, pages = {113442}, doi = {10.1016/j.jenvman.2021.113442}, pmid = {34371221}, issn = {1095-8630}, mesh = {Asia ; China ; *Conservation of Natural Resources ; *Ecosystem ; Geographic Information Systems ; Humans ; Soil ; }, abstract = {Ecosystem services (ESs) provided by the major basins of Central Asia are critical to human well-being and have attracted the attention of the international community. The identification of conservation priorities is of great significance for the maintenance and protection of key ESs. In this study, we quantified the spatiotemporal changes of net primary productivity (NPP), soil conservation (SC), water yield (WY) and habitat quality (HQ) in the major basins of Central Asia from 1995 to 2015. In addition, a GIS-based ordered weighted averaging (OWA) multi-criterion valuation method was adopted to identify potential conservation areas under 11 scenarios. Conservation priorities were determined by comparing the conservation efficiency under each scenario. Then, a broad range of indicators were considered to distinguish the driving factors affecting ESs in conservation priorities. The results show that the average conservation efficiency in the Issyk-Kul Basin was the highest, followed by the Am Darya Basin, Ili-Balkhash Basin and Syr Darya Basin. We observed that the conservation efficiency of the four ESs declined continuously in the Ili-Balkhash Basin from 1995 to 2015, while it changed steadily in the other three basins. Correlation analysis indicated that natural factors (e.g., precipitation and topography) were the main driving factors of WY, SR and NPP in conservation priorities, while HQ was more affected by socio-economic factors (e.g., population density and both cropland and urban percentages). The identification of conservation priorities and their driving factors plays an important role in ensuring the ecological security of the lower reaches, regulating the regional water balance and stabilizing the climate pattern.}, } @article {pmid34363887, year = {2021}, author = {Paudel, YP and Hu, Z and Khatiwada, JR and Fan, L and Pradhan, S and Liu, B and Qin, W}, title = {Chloroplast genome analysis of Chrysotila dentata.}, journal = {Gene}, volume = {804}, number = {}, pages = {145871}, doi = {10.1016/j.gene.2021.145871}, pmid = {34363887}, issn = {1879-0038}, mesh = {Chloroplasts/*genetics ; Computational Biology/methods ; Evolution, Molecular ; Genes, Plant ; Genome ; Haptophyta/*genetics ; High-Throughput Nucleotide Sequencing/methods ; Inverted Repeat Sequences/genetics ; Microsatellite Repeats/genetics ; Phylogeny ; RNA, Ribosomal/genetics ; Sequence Analysis, DNA/methods ; Whole Genome Sequencing/methods ; }, abstract = {Chrysotila dentata is an ecologically important marine alga contributing to the coccolith formation. In this study, a complete chloroplast (cp DNA) genome of Chrysotila dentata was sequenced by using Illumina Hiseq and was analyzed with the help of a bioinformatics tool CPGAVAS2. The circular chloroplast genome of Chrysotila dentata has a size of 109,017 bp with two inverted repeats (IRs) regions (4513 bp each) which is a common feature in most land plants and algal species. The Chrysotila dentata cp genome consists of 61 identified protein-coding genes, 30 tRNA genes and 6 rRNAs with 21 microsatellites. The phylogenetic relationship with other select algal species revealed a close phylogeny of Chrysotila dentata with Phaeocystis antarctica. This is the first report of the cp genome analysis of genus Chrysotila and the results from this study will be helpful for understanding the genetic structure and function of chloroplast in other species of Chrysotila.}, } @article {pmid34362321, year = {2021}, author = {Asaaga, FA and Young, JC and Oommen, MA and Chandarana, R and August, J and Joshi, J and Chanda, MM and Vanak, AT and Srinivas, PN and Hoti, SL and Seshadri, T and Purse, BV}, title = {Operationalising the "One Health" approach in India: facilitators of and barriers to effective cross-sector convergence for zoonoses prevention and control.}, journal = {BMC public health}, volume = {21}, number = {1}, pages = {1517}, pmid = {34362321}, issn = {1471-2458}, support = {MR/P024335/2/MRC_/Medical Research Council/United Kingdom ; MR/S012893/2/MRC_/Medical Research Council/United Kingdom ; MR/S012893/1/MRC_/Medical Research Council/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; MR/T029846/1/MRC_/Medical Research Council/United Kingdom ; MR/P024335/1/MRC_/Medical Research Council/United Kingdom ; /BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; Humans ; India ; *One Health ; Zoonoses/epidemiology/prevention & control ; }, abstract = {BACKGROUND: There is a strong policy impetus for the One Health cross-sectoral approach to address the complex challenge of zoonotic diseases, particularly in low/lower middle income countries (LMICs). Yet the implementation of this approach in LMIC contexts such as India has proven challenging, due partly to the relatively limited practical guidance and understanding on how to foster and sustain cross-sector collaborations. This study addresses this gap by exploring the facilitators of and barriers to successful convergence between the human, animal and environmental health sectors in India.

METHODS: A mixed methods study was conducted using a detailed content review of national policy documents and in-depth semi-structured interview data on zoonotic disease management in India. In total, 29 policy documents were reviewed and 15 key informant interviews were undertaken with national and state level policymakers, disease managers and experts operating within the human-animal-environment interface of zoonotic disease control.

RESULTS: Our findings suggest that there is limited policy visibility of zoonotic diseases, although global zoonoses, especially those identified to be of pandemic potential by international organisations (e.g. CDC, WHO and OIE) rather than local, high burden endemic diseases, have high recognition in the existing policy agenda setting. Despite the widespread acknowledgement of the importance of cross-sectoral collaboration, a myriad of factors operated to either constrain or facilitate the success of cross-sectoral convergence at different stages (i.e. information-sharing, undertaking common activities and merging resources and infrastructure) of cross-sectoral action. Importantly, participants identified the lack of supportive policies, conflicting departmental priorities and limited institutional capacities as major barriers that hamper effective cross-sectoral collaboration on zoonotic disease control. Building on existing informal inter-personal relationships and collaboration platforms were suggested by participants as the way forward.

CONCLUSION: Our findings point to the importance of strengthening existing national policy frameworks as a first step for leveraging cross-sectoral capacity for improved disease surveillance and interventions. This requires the contextual adaptation of the One Health approach in a manner that is sensitive to the underlying socio-political, institutional and cultural context that determines and shapes outcomes of cross-sector collaborative arrangements.}, } @article {pmid34360355, year = {2021}, author = {Fu, J and Zhang, S}, title = {Functional Assessment and Coordination Characteristics of Production, Living, Ecological Function-A Case Study of Henan Province, China.}, journal = {International journal of environmental research and public health}, volume = {18}, number = {15}, pages = {}, pmid = {34360355}, issn = {1660-4601}, mesh = {China ; Cities ; *Spatial Analysis ; }, abstract = {Multifunctional state assessment was the basis of time sequence design of territory spatial development and overall utilisation. This study aimed to identify the ecological-production-living (PLE) territory spatial function to provide a basis for territory spatial planning. It took Henan Province as the research area. This study developed a methodology to assess differentiation characteristics for PLE function, a method that integrates functional merging and geographic information technology. We used the coordination degree model and spatial autocorrelation analysis to reveal the coordination of spatial functions of the province. The results were as follows: (1) During the study period, the land production function of main grain-producing areas decreased slowly, and production and living function values of the Central Plains urban agglomeration with Zhengzhou as the centre were in an upward trend. The characteristics of urban-rural dualization were prominent, and ecological function value decreased year by year. (2) The laws of territorial spatial functions had different manifestations in different stages (1990-2005 and 2005-2018). By different characteristic laws, the change in production function in the later period was bigger than that in the previous period. The living function maintained a good continuity expansion characteristic before and after. The spatial regularity distribution characteristics of ecological function were weak, and the overall environment became worse than before. (3) The territory space of middle and low coordination function types was the most important type, and the aggregation was relatively weak. Xuchang County and Weihui City showed better states of functional coordination aggregation. Lushi County, Xinxian County, and Shangcheng County, which were in the western and southern mountainous and hilly areas, showed low-low aggregation characteristics. Thus, the government will strengthen targeted control over territorial space. This study provides a reference for the overall deployment of the development and utilisation of territory space in Henan Province.}, } @article {pmid34356817, year = {2021}, author = {Cheng, H and Bowler, C and Xing, X and Bulone, V and Shao, Z and Duan, D}, title = {Full-Length Transcriptome of Thalassiosira weissflogii as a Reference Resource and Mining of Chitin-Related Genes.}, journal = {Marine drugs}, volume = {19}, number = {7}, pages = {}, pmid = {34356817}, issn = {1660-3397}, support = {41806175//National Natural Science Foundation of China/ ; YQ2018NO06//Youth Project of Marine Biology and Biotechnology Laboratory in Pilot National Laboratory for Marine Science and Technology/ ; }, mesh = {Animals ; Biosynthetic Pathways ; Chitin/*genetics ; Data Mining ; Diatoms/genetics ; Transcriptome ; }, abstract = {β-Chitin produced by diatoms is expected to have significant economic and ecological value due to its structure, which consists of parallel chains of chitin, its properties and the high abundance of diatoms. Nevertheless, few studies have functionally characterised chitin-related genes in diatoms owing to the lack of omics-based information. In this study, we first compared the chitin content of three representative Thalassiosira species. Cell wall glycosidic linkage analysis and chitin/chitosan staining assays showed that Thalassiosira weissflogii was an appropriate candidate chitin producer. A full-length (FL) transcriptome of T. weissflogii was obtained via PacBio sequencing. In total, the FL transcriptome comprised 23,362 annotated unigenes, 710 long non-coding RNAs (lncRNAs), 363 transcription factors (TFs), 3113 alternative splicing (AS) events and 3295 simple sequence repeats (SSRs). More specifically, 234 genes related to chitin metabolism were identified and the complete biosynthetic pathways of chitin and chitosan were explored. The information presented here will facilitate T. weissflogii molecular research and the exploitation of β-chitin-derived high-value enzymes and products.}, } @article {pmid34356057, year = {2021}, author = {Tarek, M and Abdelzaher, H and Kobeissy, F and El-Fawal, HAN and Salama, MM and Abdelnaser, A}, title = {Bioinformatics Analysis of Allele Frequencies and Expression Patterns of ACE2, TMPRSS2 and FURIN in Different Populations and Susceptibility to SARS-CoV-2.}, journal = {Genes}, volume = {12}, number = {7}, pages = {}, pmid = {34356057}, issn = {2073-4425}, support = {1/CX/CSRD VA/United States ; }, mesh = {*Alleles ; *Angiotensin-Converting Enzyme 2/biosynthesis/genetics ; *COVID-19/enzymology/genetics ; Computational Biology ; *Databases, Nucleic Acid ; Female ; *Furin/biosynthesis/genetics ; *Gene Expression Regulation, Enzymologic ; *Gene Frequency ; *Genetic Predisposition to Disease ; Humans ; Male ; SARS-CoV-2/genetics/*metabolism ; *Serine Endopeptidases/biosynthesis/genetics ; }, abstract = {The virus responsible for the COVID-19 global health crisis, SARS-CoV-2, has been shown to utilize the ACE2 protein as an entry point to its target cells. The virus has been shown to rely on the actions of TMPRSS2 (a serine protease), as well as FURIN (a peptidase), for the critical priming of its spike protein. It has been postulated that variations in the sequence and expression of SARS-CoV-2's receptor (ACE2) and the two priming proteases (TMPRSS2 and FURIN) may be critical in contributing to SARS-CoV-2 infectivity. This study aims to examine the different expression levels of FURIN in various tissues and age ranges in light of ACE2 and TMPRSS2 expression levels using the LungMAP database. Furthermore, we retrieved expression quantitative trait loci (eQTLs) of the three genes and their annotation. We analyzed the frequency of the retrieved variants in data from various populations and compared it to the Egyptian population. We highlight FURIN's potential interplay with the immune response to SARS-CoV-2 and showcase a myriad of variants of the three genes that are differentially expressed across populations. Our findings provide insights into potential genetic factors that impact SARS-CoV-2 infectivity in different populations and shed light on the varying expression patterns of FURIN.}, } @article {pmid34355643, year = {2021}, author = {Perez-Gelvez, YNC and Camus, AC and Bridger, R and Wells, L and Rhodes, OE and Bergmann, CW}, title = {Effects of chronic exposure to low levels of IR on Medaka (Oryzias latipes): a proteomic and bioinformatic approach.}, journal = {International journal of radiation biology}, volume = {97}, number = {10}, pages = {1485-1501}, doi = {10.1080/09553002.2021.1962570}, pmid = {34355643}, issn = {1362-3095}, mesh = {Animals ; Chromatography, Liquid ; Computational Biology ; *Oryzias ; Proteomics ; Radiation, Ionizing ; Tandem Mass Spectrometry ; }, abstract = {PURPOSE: Chronic exposure to ionizing radiation (IR) at low doses (<100 mGy) has been insufficiently studied to understand fully the risk to health. Relatively little knowledge exists regarding how species and healthy tissues respond at the protein level to chronic exposure to low doses of IR, and mass spectrometric-based profiling of protein expression is a powerful tool for studying changes in protein abundance.

MATERIALS AND METHODS: SDS gel electrophoresis, LC-MS/MS mass spectrometry-based approaches and bioinformatic data analytics were used to detect proteomic changes following chronic exposure to moderate/low doses of radiation in adults and normally developed Medaka fish (Oryzias latipes).

RESULTS: Significant variations in the abundance of proteins involved in thyroid hormone signaling and lipid metabolism were detected, which could be related to the gonadal regression phenotype observed after 21.04 mGy and 204.3 mGy/day exposure. The global proteomic change was towards overexpression of proteins in muscle and skin, while the opposite effect was observed in internal organs.

CONCLUSION: The present study provides information on the impacts of biologically relevant low doses of IR, which will be useful in future research for the identification of potential biomarkers of IR exposure and allow for a better assessment of radiation biosafety regulations.}, } @article {pmid34353948, year = {2021}, author = {Hufford, MB and Seetharam, AS and Woodhouse, MR and Chougule, KM and Ou, S and Liu, J and Ricci, WA and Guo, T and Olson, A and Qiu, Y and Della Coletta, R and Tittes, S and Hudson, AI and Marand, AP and Wei, S and Lu, Z and Wang, B and Tello-Ruiz, MK and Piri, RD and Wang, N and Kim, DW and Zeng, Y and O'Connor, CH and Li, X and Gilbert, AM and Baggs, E and Krasileva, KV and Portwood, JL and Cannon, EKS and Andorf, CM and Manchanda, N and Snodgrass, SJ and Hufnagel, DE and Jiang, Q and Pedersen, S and Syring, ML and Kudrna, DA and Llaca, V and Fengler, K and Schmitz, RJ and Ross-Ibarra, J and Yu, J and Gent, JI and Hirsch, CN and Ware, D and Dawe, RK}, title = {De novo assembly, annotation, and comparative analysis of 26 diverse maize genomes.}, journal = {Science (New York, N.Y.)}, volume = {373}, number = {6555}, pages = {655-662}, pmid = {34353948}, issn = {1095-9203}, support = {S10 OD028632/OD/NIH HHS/United States ; }, mesh = {Centromere/genetics ; Chromosome Mapping ; Chromosomes, Plant ; DNA Methylation ; Disease Resistance/genetics ; Genes, Plant ; Genetic Variation ; *Genome, Plant ; Genotype ; High-Throughput Nucleotide Sequencing ; *Molecular Sequence Annotation ; Multifactorial Inheritance/genetics ; Phenotype ; Plant Diseases ; Polymorphism, Single Nucleotide ; Regulatory Sequences, Nucleic Acid ; Sequence Analysis, DNA ; Tetraploidy ; Transcriptome ; Whole Genome Sequencing ; Zea mays/*genetics ; }, abstract = {We report de novo genome assemblies, transcriptomes, annotations, and methylomes for the 26 inbreds that serve as the founders for the maize nested association mapping population. The number of pan-genes in these diverse genomes exceeds 103,000, with approximately a third found across all genotypes. The results demonstrate that the ancient tetraploid character of maize continues to degrade by fractionation to the present day. Excellent contiguity over repeat arrays and complete annotation of centromeres revealed additional variation in major cytological landmarks. We show that combining structural variation with single-nucleotide polymorphisms can improve the power of quantitative mapping studies. We also document variation at the level of DNA methylation and demonstrate that unmethylated regions are enriched for cis-regulatory elements that contribute to phenotypic variation.}, } @article {pmid34352463, year = {2021}, author = {Zhu, Y and Liu, S and Yi, Y and Xie, F and Grünwald, R and Miao, W and Wu, K and Qi, M and Gao, Y and Singh, D}, title = {Overview of terrestrial water storage changes over the Indus River Basin based on GRACE/GRACE-FO solutions.}, journal = {The Science of the total environment}, volume = {799}, number = {}, pages = {149366}, doi = {10.1016/j.scitotenv.2021.149366}, pmid = {34352463}, issn = {1879-1026}, mesh = {Environmental Monitoring ; *Groundwater ; Hydrology ; *Rivers ; Water ; }, abstract = {Water resources are under severe stress in the highly populated Indus River Basin due to the increased consumption of water across different sectors and climate change. Coping with these challenges, requires a clear understanding on hydrological processes and anthropogenic activities, and how these are influencing recharging and spatiotemporal availability of groundwater in the basin. The present study aims to investigate the natural and anthropogenic impact on Terrestrial Water Storage (TWS) over the Indus River Basin by using a series of statistical methods and the observation data from the Gravity Recovery and Climate Experiment (GRACE) and Follow-On (GRACE-FO). Our results show that (i) TWS Anomaly (TWSA) experienced a significant decrease from 2002 to 2020, particularly in the MUIP; (ii) the UIB showed a weak decreasing trend in TWSA as a result of the accelerated glacier melting; (iii) there was significant loss of groundwater (1.57 mm/month) caused by ineffective water management and over-exploitation; and (iv) assisted by favorable meteorological conditions, the precipitation presented a positive trend against the weakness of the Westerlies, which exerted the positive influence on TWSA.}, } @article {pmid34351581, year = {2022}, author = {Wang, Q and Zhang, Y and Feng, Q and Hu, G and Gao, Z and Meng, Q and Zhu, X}, title = {Occurrence, distribution, and risk assessment of bisphenol analogues in Luoma Lake and its inflow rivers in Jiangsu Province, China.}, journal = {Environmental science and pollution research international}, volume = {29}, number = {1}, pages = {1430-1445}, pmid = {34351581}, issn = {1614-7499}, support = {2018002//The Environmental protection research project of Jiangsu Province/ ; }, mesh = {Benzhydryl Compounds/analysis ; China ; Ecosystem ; Humans ; Lakes ; Risk Assessment ; *Rivers ; *Water Pollutants, Chemical/analysis ; }, abstract = {Bisphenol analogs (BPs) are widely used in industrial and commercial products and have been detected in surface water, sediment, sewage, and sludge. The presence of BPs in the natural environment poses threats to the aquatic ecosystem and human health. The concentration, distribution, seasonal variation, and risk assessment of BPA and BPA structural analogs including BPB, BPF, BPS, BPZ, BPAF, and BPAP in surface water and sediment during dry season and flood season in Luoma Lake and its inflow rivers in Jiangsu Province, China, were investigated in this study. The detection frequency of BPA and BPF was 100%. Although the use of BPA is restricted, BPA is still the dominant BPs in surface water and sediment. The concentration of BPs in surface water during flood season was higher than that in dry season. The concentrations of BPs in Fangting River, Zhongyun River, and Bulao River were higher than those in Luoma Lake. The average concentrations of BPs in surface water were in the order of BPA > BPF> BPS> BPB > BPZ > BPAF> BPAP. Compared with other studies, the concentration of BPs in Luoma Lake was moderate. There is no significant spatial distribution and difference in seasonal variation of BPs concentration in sediment (p > 0.05). Compared with other studies, the contamination of BPs in sediment of Luoma Lake was relatively low. Risk quotient (RQ) was used to evaluate the ecological risk of BPs in water environment, and the 17β estradiol equivalent (EEQ) method was used to estimate the estrogenic activity of BPs. The risk assessment showed no high ecological risk (RQ < 1.0) and estrogenic risk (EEQ < 1.0 ng/L) in dry season and flood season. The estimated RQ and EEQt indicated that the ecological and human health impacts were negligible in the short term.}, } @article {pmid34351016, year = {2021}, author = {Munblit, D and Bobkova, P and Spiridonova, E and Shikhaleva, A and Gamirova, A and Blyuss, O and Nekliudov, N and Bugaeva, P and Andreeva, M and DunnGalvin, A and Comberiati, P and Apfelbacher, C and Genuneit, J and Avdeev, S and Kapustina, V and Guekht, A and Fomin, V and Svistunov, AA and Timashev, P and Subbot, VS and Royuk, VV and Drake, TM and Hanson, SW and Merson, L and Carson, G and Horby, P and Sigfrid, L and Scott, JT and Semple, MG and Warner, JO and Vos, T and Olliaro, P and Glybochko, P and Butnaru, D and , }, title = {Incidence and risk factors for persistent symptoms in adults previously hospitalized for COVID-19.}, journal = {Clinical and experimental allergy : journal of the British Society for Allergy and Clinical Immunology}, volume = {51}, number = {9}, pages = {1107-1120}, pmid = {34351016}, issn = {1365-2222}, support = {MC_PC_19026/MRC_/Medical Research Council/United Kingdom ; MC_PC_19059/MRC_/Medical Research Council/United Kingdom ; INT 2021/RSM C 19 01//UK Embassy in Moscow/ ; MC_UU_12014/8/MRC_/Medical Research Council/United Kingdom ; 20-04-60063//Russian Foundation for Basic Research/ ; }, mesh = {Adolescent ; Adult ; *Aftercare ; Aged ; Aged, 80 and over ; COVID-19/*epidemiology ; *COVID-19 Testing ; Female ; Follow-Up Studies ; *Hospitalization ; Humans ; Incidence ; Male ; Middle Aged ; Risk Factors ; Russia/epidemiology ; *SARS-CoV-2 ; *Surveys and Questionnaires ; *COVID-19 Drug Treatment ; }, abstract = {BACKGROUND: The long-term sequalae of COVID-19 remain poorly characterized. We assessed persistent symptoms in previously hospitalized patients with COVID-19 and assessed potential risk factors.

METHODS: Data were collected from patients discharged from 4 hospitals in Moscow, Russia between 8 April and 10 July 2020. Participants were interviewed via telephone using an ISARIC Long-term Follow-up Study questionnaire.

RESULTS: 2,649 of 4755 (56%) discharged patients were successfully evaluated, at median 218 (IQR 200, 236) days post-discharge. COVID-19 diagnosis was clinical in 1291 and molecular in 1358. Most cases were mild, but 902 (34%) required supplemental oxygen and 68 (2.6%) needed ventilatory support. Median age was 56 years (IQR 46, 66) and 1,353 (51.1%) were women. Persistent symptoms were reported by 1247 (47.1%) participants, with fatigue (21.2%), shortness of breath (14.5%) and forgetfulness (9.1%) the most common symptoms and chronic fatigue (25%) and respiratory (17.2%) the most common symptom categories. Female sex was associated with any persistent symptom category OR 1.83 (95% CI 1.55 to 2.17) with association being strongest for dermatological (3.26, 2.36 to 4.57) symptoms. Asthma and chronic pulmonary disease were not associated with persistent symptoms overall, but asthma was associated with neurological (1.95, 1.25 to 2.98) and mood and behavioural changes (2.02, 1.24 to 3.18), and chronic pulmonary disease was associated with chronic fatigue (1.68, 1.21 to 2.32).

CONCLUSIONS: Almost half of adults admitted to hospital due to COVID-19 reported persistent symptoms 6 to 8 months after discharge. Fatigue and respiratory symptoms were most common, and female sex was associated with persistent symptoms.}, } @article {pmid34349739, year = {2021}, author = {Jones, B and Goodall, T and George, PBL and Gweon, HS and Puissant, J and Read, DS and Emmett, BA and Robinson, DA and Jones, DL and Griffiths, RI}, title = {Beyond Taxonomic Identification: Integration of Ecological Responses to a Soil Bacterial 16S rRNA Gene Database.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {682886}, pmid = {34349739}, issn = {1664-302X}, abstract = {High-throughput sequencing 16S rRNA gene surveys have enabled new insights into the diversity of soil bacteria, and furthered understanding of the ecological drivers of abundances across landscapes. However, current analytical approaches are of limited use in formalizing syntheses of the ecological attributes of taxa discovered, because derived taxonomic units are typically unique to individual studies and sequence identification databases only characterize taxonomy. To address this, we used sequences obtained from a large nationwide soil survey (GB Countryside Survey, henceforth CS) to create a comprehensive soil specific 16S reference database, with coupled ecological information derived from survey metadata. Specifically, we modeled taxon responses to soil pH at the OTU level using hierarchical logistic regression (HOF) models, to provide information on both the shape of landscape scale pH-abundance responses, and pH optima (pH at which OTU abundance is maximal). We identify that most of the soil OTUs examined exhibited a non-flat relationship with soil pH. Further, the pH optima could not be generalized by broad taxonomy, highlighting the need for tools and databases synthesizing ecological traits at finer taxonomic resolution. We further demonstrate the utility of the database by testing against geographically dispersed query 16S datasets; evaluating efficacy by quantifying matches, and accuracy in predicting pH responses of query sequences from a separate large soil survey. We found that the CS database provided good coverage of dominant taxa; and that the taxa indicating soil pH in a query dataset corresponded with the pH classifications of top matches in the CS database. Furthermore we were able to predict query dataset community structure, using predicted abundances of dominant taxa based on query soil pH data and the HOF models of matched CS database taxa. The database with associated HOF model outputs is released as an online portal for querying single sequences of interest (https://shiny-apps.ceh.ac.uk/ID-TaxER/), and flat files are made available for use in bioinformatic pipelines. The further development of advanced informatics infrastructures incorporating modeled ecological attributes along with new functional genomic information will likely facilitate large scale exploration and prediction of soil microbial functional biodiversity under current and future environmental change scenarios.}, } @article {pmid34349287, year = {2021}, author = {Vaidyanathan, G}, title = {The world's species are playing musical chairs: how will it end?.}, journal = {Nature}, volume = {596}, number = {7870}, pages = {22-25}, pmid = {34349287}, issn = {1476-4687}, mesh = {Animals ; Anthozoa ; *Biodiversity ; Biomass ; *Conservation of Natural Resources ; Databases, Factual ; *Ecology ; Endangered Species/*statistics & numerical data ; Environmental Science ; Europe ; Forestry ; Human Activities ; Insecta ; Islands ; North America ; }, } @article {pmid34346485, year = {2021}, author = {Nadel, BB and Oliva, M and Shou, BL and Mitchell, K and Ma, F and Montoya, DJ and Mouton, A and Kim-Hellmuth, S and Stranger, BE and Pellegrini, M and Mangul, S}, title = {Systematic evaluation of transcriptomics-based deconvolution methods and references using thousands of clinical samples.}, journal = {Briefings in bioinformatics}, volume = {22}, number = {6}, pages = {}, pmid = {34346485}, issn = {1477-4054}, support = {R01 CA229618/CA/NCI NIH HHS/United States ; U01 HG007598/HG/NHGRI NIH HHS/United States ; }, mesh = {Algorithms ; Computational Biology/methods ; Computer Simulation ; Gene Expression Profiling/methods ; Humans ; *Transcriptome ; }, abstract = {Estimating cell type composition of blood and tissue samples is a biological challenge relevant in both laboratory studies and clinical care. In recent years, a number of computational tools have been developed to estimate cell type abundance using gene expression data. Although these tools use a variety of approaches, they all leverage expression profiles from purified cell types to evaluate the cell type composition within samples. In this study, we compare 12 cell type quantification tools and evaluate their performance while using each of 10 separate reference profiles. Specifically, we have run each tool on over 4000 samples with known cell type proportions, spanning both immune and stromal cell types. A total of 12 of these represent in vitro synthetic mixtures and 300 represent in silico synthetic mixtures prepared using single-cell data. A final 3728 clinical samples have been collected from the Framingham cohort, for which cell populations have been quantified using electrical impedance cell counting. When tools are applied to the Framingham dataset, the tool Estimating the Proportions of Immune and Cancer cells (EPIC) produces the highest correlation, whereas Gene Expression Deconvolution Interactive Tool (GEDIT) produces the lowest error. The best tool for other datasets is varied, but CIBERSORT and GEDIT most consistently produce accurate results. We find that optimal reference depends on the tool used, and report suggested references to be used with each tool. Most tools return results within minutes, but on large datasets runtimes for CIBERSORT can exceed hours or even days. We conclude that deconvolution methods are capable of returning high-quality results, but that proper reference selection is critical.}, } @article {pmid34341920, year = {2022}, author = {Oto, OA and Kardeş, S and Guller, N and Safak, S and Dirim, AB and Başhan, Y and Demir, E and Artan, AS and Yazıcı, H and Turkmen, A}, title = {Impact of the COVID-19 pandemic on interest in renal diseases.}, journal = {Environmental science and pollution research international}, volume = {29}, number = {1}, pages = {711-718}, pmid = {34341920}, issn = {1614-7499}, mesh = {*COVID-19 ; Humans ; Infodemiology ; *Kidney Diseases/epidemiology ; Pandemics ; SARS-CoV-2 ; Search Engine ; }, abstract = {There is an information gap about the public's interest in nephrological diseases in the COVID-19 era. The objective was to identify public interest in kidney diseases during the pandemic. In this infodemiology study, Google Trends was queried for a total of 50 search queries corresponding to a broad spectrum of nephrological diseases and the term "nephrologist." Two time intervals of 2020 (March 15-July 4 and July 5-October 31) were compared to similar time intervals of 2016-2019 for providing information on interest in different phases of the pandemic. Compared to the prior 4 years, analyses showed significant decreases in relative search volume (RSV) in the majority (76%) of search queries on March 15-July 4, 2020 period. However, RSV of the majority of search queries (≈70%) on July 5-October 31, 2020 period was not significantly different from similar periods of the previous 4 years, with an increase in search terms of amyloidosis, kidney biopsy, hematuria, chronic kidney disease, hypertension, nephrolithiasis, acute kidney injury, and Fabry disease. During the early pandemic, there have been significant decreases in search volumes for many nephrological diseases. However, this trend reversed in the period from July 5 to October 31, 2020, implying the increased need for information on kidney diseases. The results of this study enable us to understand how COVID-19 impacted the interest in kidney diseases and demands/needs for kidney diseases by the general public during the pandemic.}, } @article {pmid34340549, year = {2021}, author = {Mullins, AJ and Webster, G and Kim, HJ and Zhao, J and Petrova, YD and Ramming, CE and Jenner, M and Murray, JAH and Connor, TR and Hertweck, C and Challis, GL and Mahenthiralingam, E}, title = {Discovery of the Pseudomonas Polyyne Protegencin by a Phylogeny-Guided Study of Polyyne Biosynthetic Gene Cluster Diversity.}, journal = {mBio}, volume = {12}, number = {4}, pages = {e0071521}, pmid = {34340549}, issn = {2150-7511}, support = {BB/M009122/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; MR/L015080/1/MRC_/Medical Research Council/United Kingdom ; BB/S007652/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/K002341/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/R012121/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/S008020/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Biosynthetic Pathways/*genetics ; Evolution, Molecular ; Genome, Bacterial ; Genomics ; *Multigene Family ; *Phylogeny ; Polyynes/*classification/*metabolism ; Pseudomonas/*genetics/*metabolism ; }, abstract = {Natural products that possess alkyne or polyyne moieties have been isolated from a variety of biological sources and possess a broad a range of bioactivities. In bacteria, the basic biosynthesis of polyynes is known, but their biosynthetic gene cluster (BGC) distribution and evolutionary relationship to alkyne biosynthesis have not been addressed. Through comprehensive genomic and phylogenetic analyses, the distribution of alkyne biosynthesis gene cassettes throughout bacteria was explored, revealing evidence of multiple horizontal gene transfer events. After investigation of the evolutionary connection between alkyne and polyyne biosynthesis, a monophyletic clade was identified that possessed a conserved seven-gene cassette for polyyne biosynthesis that built upon the conserved three-gene cassette for alkyne biosynthesis. Further diversity mapping of the conserved polyyne gene cassette revealed a phylogenetic subclade for an uncharacterized polyyne BGC present in several Pseudomonas species, designated pgn. Pathway mutagenesis and high-resolution analytical chemistry showed the Pseudomonas protegens pgn BGC directed the biosynthesis of a novel polyyne, protegencin. Exploration of the biosynthetic logic behind polyyne production, through BGC mutagenesis and analytical chemistry, highlighted the essentiality of a triad of desaturase proteins and a thioesterase in both the P. protegens pgn and Trinickia caryophylli (formerly Burkholderia caryophylli) caryoynencin pathways. We have unified and expanded knowledge of polyyne diversity and uniquely demonstrated that alkyne and polyyne biosynthetic gene clusters are evolutionarily related and widely distributed within bacteria. The systematic mapping of conserved biosynthetic genes across the available bacterial genomic diversity proved to be a fruitful method for discovering new natural products and better understanding polyyne biosynthesis. IMPORTANCE Natural products bearing alkyne (triple carbon bond) or polyyne (multiple alternating single and triple carbon bonds) moieties exhibit a broad range of important biological activities. Polyyne metabolites have been implicated in important ecological roles such as cepacin mediating biological control of plant pathogens and caryoynencin protecting Lagriinae beetle eggs against pathogenic fungi. After further phylogenetic exploration of polyyne diversity, we identified a novel gene cluster in Pseudomonas bacteria with known biological control abilities and proved it was responsible for synthesizing a new polyyne metabolite, protegencin. The evolutionary analysis of polyyne pathways showed that multiple biosynthetic genes were conserved, and using mutagenesis, their essentiality was demonstrated. Our research provides a foundation for the future modification of polyyne metabolites and has identified a novel polyyne, protegencin, with potential bioactive roles of ecological and agricultural importance.}, } @article {pmid34340091, year = {2021}, author = {Wang, M and Tian, P and Wang, L and Yu, Z and Du, T and Chen, Q and Guan, X and Guo, Y and Zhang, M and Tang, C and Chang, Y and Shi, J and Liang, J and Cao, X and Zhang, L}, title = {High contribution of vehicle emissions to fine particulate pollutions in Lanzhou, Northwest China based on high-resolution online data source appointment.}, journal = {The Science of the total environment}, volume = {798}, number = {}, pages = {149310}, doi = {10.1016/j.scitotenv.2021.149310}, pmid = {34340091}, issn = {1879-1026}, mesh = {*Air Pollutants/analysis ; China ; Coal/analysis ; Dust/analysis ; Environmental Monitoring ; Information Storage and Retrieval ; Minerals ; Particulate Matter/analysis ; Seasons ; *Vehicle Emissions/analysis ; }, abstract = {The quantitative estimation of urban particulate matter (PM) sources is essential but limited because of various reasons. The hourly online data of PM2.5, organic carbon (OC), elemental carbon (EC), water-soluble ions, and elements from December 2019 to November 2020 was used to conduct PM source appointment, with an emphasis on the contribution of vehicle emissions to fine PM pollution in downtown Lanzhou, Northwest China. Vehicle emissions, secondary formation, mineral dust, and coal combustion were found to be the major PM sources using the positive matrix factorization model. The seasonal mean PM2.5 were estimated to be 72.8, 39.2, 24.3, and 43.6 μg·m[-3] and vehicle emissions accounted for 35.7%, 25.8%, 30.0%, and 56.6% in winter, spring, summer, and autumn, respectively. Vehicle emissions were the largest source of PM considering the high PM pollution in winter and its significantly large contribution in autumn. Furthermore, the contribution of vehicle emissions increased with increasing PM in winter and autumn. Vehicle emissions were also the most important source of EC, accounting for 70.3%, 91.0%, 83.5%, and 93.7% of the total EC in winter, spring, summer, and autumn, respectively. With the reduction in industrial emissions and increase in vehicle numbers in China in recent years, vehicle emissions are going to be the largest source of urban PM pollution. To sustainably improve air quality in Lanzhou and other Chinese cities, efforts should be made to control vehicle emissions such as promoting clean-energy vehicles and encouraging public transportation.}, } @article {pmid34340076, year = {2021}, author = {Fernandes, ACP and Terêncio, DPS and Pacheco, FAL and Fernandes, LFS}, title = {A combined GIS-MCDA approach to prioritize stream water quality interventions, based on the contamination risk and intervention complexity.}, journal = {The Science of the total environment}, volume = {798}, number = {}, pages = {149322}, doi = {10.1016/j.scitotenv.2021.149322}, pmid = {34340076}, issn = {1879-1026}, mesh = {Decision Support Techniques ; Environmental Monitoring ; Geographic Information Systems ; *Rivers ; *Water Quality ; }, abstract = {Water management decisions are complex ever since they are dependent on adopted politics, social objectives, environmental impacts, and economic determinants. To adequately address hydric resources issues, it is crucial to rely on scientific data and models guiding decision-makers. The present study brings a new methodology, consisting of a combined GIS-MCDA, to prioritize catchments that require environmental interventions to improve surface water quality. A Portuguese catchment, Ave River Basin, was selected to test this methodology due to the low water quality. First, it was calculated the contamination risk of each catchment, based on a GIS-MCDA using point source pressures, landscape metrics, and diffuse emissions as criteria. This analysis was compared to local data of ecological and chemical status through ANOVA and the Tukey test. The results showed the efficiency of the method since the contamination risk was lower for catchments under a good status and higher in catchments with a lower classification. In a second task, it was calculated the intervention complexity using a different GIS-MCDA. For this approach, it was chosen five criteria that condition environmental interventions, population density, slope, percentage of burned areas, Strahler order, and the number of effluent discharge sites. Both multicriteria methods were combined in a graphical analysis to rank the catchments intervention priority, subdividing the prioritization into four categories from 1st to 4th[,] giving a higher preference for catchments with high contamination risk and low intervention complexity. As a result, catchments with a good status were dominantly placed under low intervention priority, and catchments with a lower ecological status were classified as a high priority, 1st and 2nd. In total, 248 catchments were spatially ranked, which is an essential finding for decision-makers, that are willing to safeguard the catchment water quality.}, } @article {pmid34339460, year = {2021}, author = {Ensley, R and Hansen, RD and Morales-Aguilar, C and Thompson, J}, title = {Geomorphology of the Mirador-Calakmul Karst Basin: A GIS-based approach to hydrogeologic mapping.}, journal = {PloS one}, volume = {16}, number = {8}, pages = {e0255496}, pmid = {34339460}, issn = {1932-6203}, mesh = {Environmental Monitoring/*methods ; Geographic Information Systems/*statistics & numerical data ; Groundwater/*analysis ; Guatemala ; Hydrology ; Natural Springs/*analysis ; Remote Sensing Technology/*methods ; Rivers/*chemistry ; }, abstract = {This paper classifies the karst landscapes of the Petén Plateau and defines the Mirador-Calakmul Karst Basin by illustrating the distribution of its karst hydrologic features. Archaeological and spatial research of the Mirador-Calakmul area of Guatemala and Mexico has shown it to be a karst basin with geopolitical implications. Current research characterizes the karst landscapes of the Petén Plateau, maps the distribution of karst hydrologic features, and delineates the basin in geomorphological terms. To further this aim, multiple forms of remote sensing data including orthophotographs, a satellite Digital Elevation Model, satellite multispectral images, and Light Detection and Ranging (LiDAR) data have been integrated to interpret the karst features in the study area. Outcrop study and thin section analysis of the upper Buena Vista Formation document that the dominant lithologies are a shallow water algal boundstone interbedded with terrestrial caliche. Karst landforms have been mapped over the Petén Plateau and we identify five karst landscapes, the largest of which is a fluviokarst landscape dominated by karst valleys. We further map karst hydrologic features including seasonal swamps, dolines, intermittent lakes, intermittent streams, solution-enhanced fractures, and springs all of which are characteristic of drainage basins. Boundaries of the karst basin are mapped from multiple lines of evidence including distribution of the karst valleys, a line of springs along the western boundary of the fluviokarst landscape, and a surface drainage analysis. We capture and classify hydrologic data points and develop a regional groundwater map that indicates subsurface flow from east to west within the basin. A drainage map illustrates the extensive system of karst valleys, boundaries, and inferred groundwater flow paths of the Mirador-Calakmul Karst Basin. It was within this geomorphological setting that the ancient Maya developed an extensive civilization during the Middle and Late Preclassic periods (1000 BCE-150 CE).}, } @article {pmid34339067, year = {2021}, author = {Hagmann, RK and Hessburg, PF and Prichard, SJ and Povak, NA and Brown, PM and Fulé, PZ and Keane, RE and Knapp, EE and Lydersen, JM and Metlen, KL and Reilly, MJ and Sánchez Meador, AJ and Stephens, SL and Stevens, JT and Taylor, AH and Yocom, LL and Battaglia, MA and Churchill, DJ and Daniels, LD and Falk, DA and Henson, P and Johnston, JD and Krawchuk, MA and Levine, CR and Meigs, GW and Merschel, AG and North, MP and Safford, HD and Swetnam, TW and Waltz, AEM}, title = {Evidence for widespread changes in the structure, composition, and fire regimes of western North American forests.}, journal = {Ecological applications : a publication of the Ecological Society of America}, volume = {31}, number = {8}, pages = {e02431}, pmid = {34339067}, issn = {1939-5582}, mesh = {Ecosystem ; *Fires ; Forests ; Humans ; North America ; *Wildfires ; }, abstract = {Implementation of wildfire- and climate-adaptation strategies in seasonally dry forests of western North America is impeded by numerous constraints and uncertainties. After more than a century of resource and land use change, some question the need for proactive management, particularly given novel social, ecological, and climatic conditions. To address this question, we first provide a framework for assessing changes in landscape conditions and fire regimes. Using this framework, we then evaluate evidence of change in contemporary conditions relative to those maintained by active fire regimes, i.e., those uninterrupted by a century or more of human-induced fire exclusion. The cumulative results of more than a century of research document a persistent and substantial fire deficit and widespread alterations to ecological structures and functions. These changes are not necessarily apparent at all spatial scales or in all dimensions of fire regimes and forest and nonforest conditions. Nonetheless, loss of the once abundant influence of low- and moderate-severity fires suggests that even the least fire-prone ecosystems may be affected by alteration of the surrounding landscape and, consequently, ecosystem functions. Vegetation spatial patterns in fire-excluded forested landscapes no longer reflect the heterogeneity maintained by interacting fires of active fire regimes. Live and dead vegetation (surface and canopy fuels) is generally more abundant and continuous than before European colonization. As a result, current conditions are more vulnerable to the direct and indirect effects of seasonal and episodic increases in drought and fire, especially under a rapidly warming climate. Long-term fire exclusion and contemporaneous social-ecological influences continue to extensively modify seasonally dry forested landscapes. Management that realigns or adapts fire-excluded conditions to seasonal and episodic increases in drought and fire can moderate ecosystem transitions as forests and human communities adapt to changing climatic and disturbance regimes. As adaptation strategies are developed, evaluated, and implemented, objective scientific evaluation of ongoing research and monitoring can aid differentiation of warranted and unwarranted uncertainties.}, } @article {pmid34335498, year = {2021}, author = {Derx, J and Demeter, K and Linke, R and Cervero-Aragó, S and Lindner, G and Stalder, G and Schijven, J and Sommer, R and Walochnik, J and Kirschner, AKT and Komma, J and Blaschke, AP and Farnleitner, AH}, title = {Genetic Microbial Source Tracking Support QMRA Modeling for a Riverine Wetland Drinking Water Resource.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {668778}, pmid = {34335498}, issn = {1664-302X}, abstract = {Riverine wetlands are important natural habitats and contain valuable drinking water resources. The transport of human- and animal-associated fecal pathogens into the surface water bodies poses potential risks to water safety. The aim of this study was to develop a new integrative modeling approach supported by microbial source tracking (MST) markers for quantifying the transport pathways of two important reference pathogens, Cryptosporidium and Giardia, from external (allochthonous) and internal (autochthonous) fecal sources in riverine wetlands considering safe drinking water production. The probabilistic-deterministic model QMRAcatch (v 1.1 python backwater) was modified and extended to account for short-time variations in flow and microbial transport at hourly time steps. As input to the model, we determined the discharge rates, volumes and inundated areas of the backwater channel based on 2-D hydrodynamic flow simulations. To test if we considered all relevant fecal pollution sources and transport pathways, we validated QMRAcatch using measured concentrations of human, ruminant, pig and bird associated MST markers as well as E. coli in a Danube wetland area from 2010 to 2015. For the model validation, we obtained MST marker decay rates in water from the literature, adjusted them within confidence limits, and simulated the MST marker concentrations in the backwater channel, resulting in mean absolute errors of < 0.7 log10 particles/L (Kruskal-Wallis p > 0.05). In the scenarios, we investigated (i) the impact of river discharges into the backwater channel (allochthonous sources), (ii) the resuspension of pathogens from animal fecal deposits in inundated areas, and (iii) the pathogen release from animal fecal deposits after rainfall (autochthonous sources). Autochthonous and allochthonous human and animal sources resulted in mean loads and concentrations of Cryptosporidium and Giardia (oo)cysts in the backwater channel of 3-13 × 10[9] particles/hour and 0.4-1.2 particles/L during floods and rainfall events, and in required pathogen treatment reductions to achieve safe drinking water of 5.0-6.2 log10. The integrative modeling approach supports the sustainable and proactive drinking water safety management of alluvial backwater areas.}, } @article {pmid34333677, year = {2021}, author = {Liang, Y and Zhang, J and Xiao, X and Xing, M and Lu, Y and Wang, L}, title = {Risk Assessment of Heavy Metals in Overlapped Areas of Farmland and Coal Resources in Xuzhou, China.}, journal = {Bulletin of environmental contamination and toxicology}, volume = {107}, number = {6}, pages = {1065-1069}, pmid = {34333677}, issn = {1432-0800}, support = {DYGX-2020-027//Open sharing fund project for large instruments and equipment of China University of Mining and Technology/ ; }, mesh = {Adult ; Child ; China ; Coal ; Environmental Monitoring ; Farms ; Humans ; *Metals, Heavy/analysis ; Risk Assessment ; Soil ; *Soil Pollutants/analysis ; }, abstract = {Heavy metals (As, Cu, Cd, Cr, Pb, Zn, Hg) in soil of a typical overlapped area of farmland and coal resources (OAFCR) in Xuzhou were investigated, meanwhile the pollution levels and risks of there were discussed. The results are: Pollution Load Index (PLI) showed no heavy metals (HMs) pollution; 3.74% of soil samples were above moderately accumulated with Hg; the ecological risk (Er) values followed the order: Hg > Cd > Cu > As > Pb > Cr > Zn, and there has a moderate degree of potential ecological risk (PER) with the mean PER of 184.26; the non-carcinogenic risk of all seven HMs to human beings is acceptable, and the carcinogenic risk caused by As, Cd and Cr can be tolerated; the exposure ways both of carcinogenic and non-carcinogenic is: oral > dermal > inhalation, while children are suffering higher health risks than adults.}, } @article {pmid34330207, year = {2021}, author = {Jiang, F and Jiang, Y and Wang, W and Xiao, C and Lin, R and Xie, T and Sung, WK and Li, S and Jakovlić, I and Chen, J and Du, X}, title = {A chromosome-level genome assembly of Cairina moschata and comparative genomic analyses.}, journal = {BMC genomics}, volume = {22}, number = {1}, pages = {581}, pmid = {34330207}, issn = {1471-2164}, mesh = {Animals ; Birds ; Chromosomes ; *Ducks/genetics ; Genome ; *Genomics ; Humans ; }, abstract = {BACKGROUND: The Muscovy duck (Cairina moschata) is an economically important duck species, with favourable growth and carcass composition parameters in comparison to other ducks. However, limited genomic resources for Muscovy duck hinder our understanding of its evolution and genetic diversity.

RESULTS: We combined linked-reads sequencing technology and reference-guided methods for de novo genome assembly. The final draft assembly was 1.12 Gbp with 29 autosomes, one sex chromosome and 4,583 unlocalized scaffolds with an N50 size of 77.35 Mb. Based on universal single-copy orthologues (BUSCO), the draft genome assembly completeness was estimated to be 93.30 %. Genome annotation identified 15,580 genes, with 15,537 (99.72 %) genes annotated in public databases. We conducted comparative genomic analyses and found that species-specific and rapidly expanding gene families (compared to other birds) in Muscovy duck are mainly involved in Calcium signaling, Adrenergic signaling in cardiomyocytes, and GnRH signaling pathways. In comparison to the common domestic duck (Anas platyrhynchos), we identified 104 genes exhibiting strong signals of adaptive evolution (Ka/Ks > 1). Most of these genes were associated with immune defence pathways (e.g. IFNAR1 and TLR5). This is indicative of the existence of differences in the immune responses between the two species. Additionally, we combined divergence and polymorphism data to demonstrate the "faster-Z effect" of chromosome evolution.

CONCLUSIONS: The chromosome-level genome assembly of Muscovy duck and comparative genomic analyses provide valuable resources for future molecular ecology studies, as well as the evolutionary arms race between the host and influenza viruses.}, } @article {pmid34327587, year = {2021}, author = {Qiao, Y and Li, S and Zhang, J and Liu, Q and Wang, Q and Chen, H and Ma, ZS}, title = {Integrated diversity and shared species analyses of human viromes.}, journal = {Archives of virology}, volume = {166}, number = {10}, pages = {2743-2749}, pmid = {34327587}, issn = {1432-8798}, support = {#GREKF19-07//State Key Laboratory of Genetic Resources and Evolution/ ; #GREKF20-06//State Key Laboratory of Genetic Resources and Evolution/ ; }, mesh = {*Biodiversity ; Databases, Genetic ; Genome, Viral/genetics ; Health Status ; Humans ; Rural Population ; Urban Population ; *Virome/genetics ; }, abstract = {Diversity analysis has been performed routinely on microbiomes, including human viromes. Shared species analysis has been conducted only rarely, but it can be a powerful supplement to diversity analysis. In the present study, we conducted integrated diversity and shared species analyses of human viromes by reanalyzing three published datasets of human viromes with more than 250 samples from healthy vs. diseased individuals and/or rural vs. urban individuals. We found significant differences in the virome diversity measured in the Hill numbers between the healthy and diseased individuals, with diseased individuals exhibiting higher virome diversity than healthy individuals, and rural individual exhibiting higher virome diversity than urban individuals. We applied both "read randomization" and "sample randomization" algorithms to perform shared species analysis. With the more conservative sample randomization algorithm, the observed number of shared species was significantly smaller than the expected shared species in 50% (8 of 16) of the comparisons. These results suggest that integrated diversity and shared species analysis can offer more comprehensive insights in comparing human virome samples than standard diversity analysis alone with potentially powerful applications in differentiating the effects of diseases or other meta-factors.}, } @article {pmid34326450, year = {2021}, author = {Schmidt, M and Maixner, F and Hotz, G and Pap, I and Szikossy, I and Pálfi, G and Zink, A and Wagner, W}, title = {DNA methylation profiling in mummified human remains from the eighteenth-century.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {15493}, pmid = {34326450}, issn = {2045-2322}, mesh = {Adult ; Body Remains ; Computational Biology/methods ; CpG Islands ; DNA/*analysis ; *DNA Methylation ; Ecology ; Epigenesis, Genetic ; *Epigenome ; Epigenomics ; Female ; Genetic Techniques ; Humans ; Hungary ; Lung/metabolism ; *Mummies ; Oligonucleotide Array Sequence Analysis ; Switzerland ; Temperature ; }, abstract = {Reconstruction of ancient epigenomes by DNA methylation (DNAm) can shed light into the composition of cell types, disease states, and age at death. However, such analysis is hampered by impaired DNA quality and little is known how decomposition affects DNAm. In this study, we determined if EPIC Illumina BeadChip technology is applicable for specimens from mummies of the eighteenth century CE. Overall, the signal intensity on the microarray was extremely low, but for one of two samples we were able to detect characteristic DNAm signals in a subset of CG dinucleotides (CpGs), which were selected with a stringent processing pipeline. Using only these CpGs we could train epigenetic signatures with reference DNAm profiles of multiple tissues and our predictions matched the fact that the specimen was lung tissue from a 28-year-old woman. Thus, we provide proof of principle that Illumina BeadChips are applicable for DNAm profiling in ancient samples.}, } @article {pmid34325695, year = {2021}, author = {Olafson, PU and Aksoy, S and Attardo, GM and Buckmeier, G and Chen, X and Coates, CJ and Davis, M and Dykema, J and Emrich, SJ and Friedrich, M and Holmes, CJ and Ioannidis, P and Jansen, EN and Jennings, EC and Lawson, D and Martinson, EO and Maslen, GL and Meisel, RP and Murphy, TD and Nayduch, D and Nelson, DR and Oyen, KJ and Raszick, TJ and Ribeiro, JMC and Robertson, HM and Rosendale, AJ and Sackton, TB and Saelao, P and Swiger, SL and Sze, SH and Tarone, AM and Taylor, DB and Warren, WC and Waterhouse, RM and Weirauch, MT and Werren, JH and Wilson, RK and Zdobnov, EM and Benoit, JB}, title = {Publisher Correction: The genome of the stable fly, Stomoxys calcitrans, reveals potential mechanisms underlying reproduction, host interactions, and novel targets for pest control.}, journal = {BMC biology}, volume = {19}, number = {1}, pages = {150}, pmid = {34325695}, issn = {1741-7007}, } @article {pmid34324531, year = {2021}, author = {Li, Y and Xie, J and Jiang, R and Yan, D}, title = {Application of edge computing and GIS in ecological water requirement prediction and optimal allocation of water resources in irrigation area.}, journal = {PloS one}, volume = {16}, number = {7}, pages = {e0254547}, pmid = {34324531}, issn = {1932-6203}, mesh = {*Geographic Information Systems ; *Water Resources ; *Agricultural Irrigation/methods ; *Water Supply ; Models, Theoretical ; Conservation of Natural Resources/methods ; Water Quality ; Conservation of Water Resources/methods ; }, abstract = {The purposes are to use water resources efficiently and ensure the sustainable development of social water resources. The edge computing technology and GIS (Geographic Information Science) image data are combined from the perspective of sustainable development. A prediction model for the water resources in the irrigation area is constructed. With the goal of maximizing comprehensive benefits, the optimal allocation of water quality and quantity of water resources is determined. Finally, the actual effect of the model is verified through specific instance data in a province. Results demonstrate that the proposed irrigation area ecological prediction model based on edge computing and GIS images can provide better performance than other state of the art models on water resources prediction. Specifically, the accuracy can remain above 90%. The proposed model for ecological water demand prediction in the irrigation area and optimal allocation of water resources is based on the principle of quality water supply. The optimal allocation of water resources reveals the sustainable development ideas and the requirements of the optimal allocation model, which is very reasonable. The improvement of the system is effective and feasible, and the optimal allocation results are reasonable. This allocation model aims at the water quality and quantity conditions, water conservancy project conditions, and specific water demand requirements in the study area. The calculation results have great practicability and a strong guiding significance for the sustainable utilization and management of the irrigation area.}, } @article {pmid34323751, year = {2021}, author = {Senanayake, S and Pradhan, B and Huete, A and Brennan, J}, title = {Proposing an ecologically viable and economically sound farming system using a matrix-based geo-informatics approach.}, journal = {The Science of the total environment}, volume = {794}, number = {}, pages = {148788}, doi = {10.1016/j.scitotenv.2021.148788}, pmid = {34323751}, issn = {1879-1026}, mesh = {*Agriculture ; Conservation of Natural Resources ; Farms ; Informatics ; *Soil ; Sri Lanka ; }, abstract = {Healthy farming systems play a vital role in improving agricultural productivity and sustainable food production. The present study aimed to propose an efficient framework to evaluate ecologically viable and economically sound farming systems using a matrix-based analytic hierarchy process (AHP) and weighted linear combination method with geo-informatics tools. The proposed framework has been developed and tested in the Central Highlands of Sri Lanka. Results reveal that more than 50% of farming systems demonstrated moderate status in terms of ecological and economic aspects. However, two vulnerable farming systems on the western slopes of the Central Highlands, named WL1a and WM1a, were identified as very poor status. These farming systems should be a top priority for restoration planning and soil conservation to prevent further deterioration. Findings indicate that a combination of ecologically viable (nine indicators) and economical sound (four indicators) criteria are a practical method to scrutinize farming systems and decision making on soil conservation and sustainable land management. In addition, this research introduces a novel approach to delineate the farming systems based on agro-ecological regions and cropping areas using geo-informatics technology. This framework and methodology can be employed to evaluate the farming systems of other parts of the country and elsewhere to identify ecologically viable and economically sound farming systems concerning soil erosion hazards. The proposed approach addresses a new dimension of the decision-making process by evaluating the farming systems relating to soil erosion hazards and suggests introducing policies on priority-based planning for conservation with low-cost strategies for sustainable land management.}, } @article {pmid34319975, year = {2021}, author = {Garcia, JA and Lohmueller, KE}, title = {Negative linkage disequilibrium between amino acid changing variants reveals interference among deleterious mutations in the human genome.}, journal = {PLoS genetics}, volume = {17}, number = {7}, pages = {e1009676}, pmid = {34319975}, issn = {1553-7404}, support = {R35 GM119856/GM/NIGMS NIH HHS/United States ; }, mesh = {Alleles ; Biological Evolution ; Databases, Genetic ; Gene Frequency/genetics ; Genome, Human/genetics ; Genotype ; Haplotypes/*genetics ; Humans ; Linkage Disequilibrium/*genetics ; Models, Statistical ; Mutation/*genetics ; Mutation Rate ; Polymorphism, Single Nucleotide/genetics ; Selection, Genetic/genetics ; }, abstract = {Evolutionary forces like Hill-Robertson interference and negative epistasis can lead to deleterious mutations being found on distinct haplotypes. However, the extent to which these forces depend on the selection and dominance coefficients of deleterious mutations and shape genome-wide patterns of linkage disequilibrium (LD) in natural populations with complex demographic histories has not been tested. In this study, we first used forward-in-time simulations to predict how negative selection impacts LD. Under models where deleterious mutations have additive effects on fitness, deleterious variants less than 10 kb apart tend to be carried on different haplotypes relative to pairs of synonymous SNPs. In contrast, for recessive mutations, there is no consistent ordering of how selection coefficients affect LD decay, due to the complex interplay of different evolutionary effects. We then examined empirical data of modern humans from the 1000 Genomes Project. LD between derived alleles at nonsynonymous SNPs is lower compared to pairs of derived synonymous variants, suggesting that nonsynonymous derived alleles tend to occur on different haplotypes more than synonymous variants. This result holds when controlling for potential confounding factors by matching SNPs for frequency in the sample (allele count), physical distance, magnitude of background selection, and genetic distance between pairs of variants. Lastly, we introduce a new statistic HR(j) which allows us to detect interference using unphased genotypes. Application of this approach to high-coverage human genome sequences confirms our finding that nonsynonymous derived alleles tend to be located on different haplotypes more often than are synonymous derived alleles. Our findings suggest that interference may play a pervasive role in shaping patterns of LD between deleterious variants in the human genome, and consequently influences genome-wide patterns of LD.}, } @article {pmid34319970, year = {2021}, author = {Rubin, IN and Ispolatov, I and Doebeli, M}, title = {Evolution to alternative levels of stable diversity leaves areas of niche space unexplored.}, journal = {PLoS computational biology}, volume = {17}, number = {7}, pages = {e1008650}, pmid = {34319970}, issn = {1553-7358}, mesh = {*Biodiversity ; *Biological Evolution ; Computational Biology ; *Ecosystem ; Genetic Fitness ; *Models, Biological ; Mutation ; }, abstract = {One of the oldest and most persistent questions in ecology and evolution is whether natural communities tend to evolve toward saturation and maximal diversity. Robert MacArthur's classical theory of niche packing and the theory of adaptive radiations both imply that populations will diversify and fully partition any available niche space. However, the saturation of natural populations is still very much an open area of debate and investigation. Additionally, recent evolutionary theory suggests the existence of alternative evolutionary stable states (ESSs), which implies that some stable communities may not be fully saturated. Using models with classical Lotka-Volterra ecological dynamics and three formulations of evolutionary dynamics (a model using adaptive dynamics, an individual-based model, and a partial differential equation model), we show that following an adaptive radiation, communities can often get stuck in low diversity states when limited by mutations of small phenotypic effect. These low diversity metastable states can also be maintained by limited resources and finite population sizes. When small mutations and finite populations are considered together, it is clear that despite the presence of higher-diversity stable states, natural populations are likely not fully saturating their environment and leaving potential niche space unfilled. Additionally, within-species variation can further reduce community diversity from levels predicted by models that assume species-level homogeneity.}, } @article {pmid34315906, year = {2021}, author = {Tedersoo, L and Küngas, R and Oras, E and Köster, K and Eenmaa, H and Leijen, Ä and Pedaste, M and Raju, M and Astapova, A and Lukner, H and Kogermann, K and Sepp, T}, title = {Data sharing practices and data availability upon request differ across scientific disciplines.}, journal = {Scientific data}, volume = {8}, number = {1}, pages = {192}, pmid = {34315906}, issn = {2052-4463}, abstract = {Data sharing is one of the cornerstones of modern science that enables large-scale analyses and reproducibility. We evaluated data availability in research articles across nine disciplines in Nature and Science magazines and recorded corresponding authors' concerns, requests and reasons for declining data sharing. Although data sharing has improved in the last decade and particularly in recent years, data availability and willingness to share data still differ greatly among disciplines. We observed that statements of data availability upon (reasonable) request are inefficient and should not be allowed by journals. To improve data sharing at the time of manuscript acceptance, researchers should be better motivated to release their data with real benefits such as recognition, or bonus points in grant and job applications. We recommend that data management costs should be covered by funding agencies; publicly available research data ought to be included in the evaluation of applications; and surveillance of data sharing should be enforced by both academic publishers and funders. These cross-discipline survey data are available from the plutoF repository.}, } @article {pmid34314425, year = {2021}, author = {Chelbi, I and Maghraoui, K and Zhioua, S and Cherni, S and Labidi, I and Satoskar, A and Hamilton, JGC and Zhioua, E}, title = {Enhanced attraction of sand fly vectors of Leishmania infantum to dogs infected with zoonotic visceral leishmaniasis.}, journal = {PLoS neglected tropical diseases}, volume = {15}, number = {7}, pages = {e0009647}, pmid = {34314425}, issn = {1935-2735}, support = {/WT_/Wellcome Trust/United Kingdom ; R21 AI130485/AI/NIAID NIH HHS/United States ; 209336/Z/17/7/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Animals ; Dog Diseases/*parasitology/transmission ; Dogs ; Feeding Behavior/*physiology ; Female ; Insect Vectors ; *Leishmania infantum ; Leishmaniasis, Visceral/parasitology/transmission/*veterinary ; Male ; Phlebotomus/*physiology ; Zoonoses ; }, abstract = {BACKGROUND: The sand fly Phlebotomus perniciosus is the main vector of Leishmania infantum, etiological agent of zoonotic visceral leishmaniasis in the Western Mediterranean basin. Dogs are the main reservoir host of this disease. The main objective of this study was to determine, under both laboratory and field conditions, if dogs infected with L. infantum, were more attractive to female P. perniciosus than uninfected dogs.

We carried out a series of host choice experiments and found that infected dogs were significantly more attractive to P. perniciosus than uninfected dogs in the laboratory as well as in the field. Significantly more P. perniciosus fed on infected dogs than on uninfected dogs. However, the fecundity of P. perniciosus fed on infected dogs was adversely impacted compared to uninfected dogs by lowering the number of laid eggs. Phlebotomus perfiliewi, the second most abundant sand fly species in the field site and a competent vector of L. infantum had similar trends of attractivity as P. perniciosus toward infected dogs under field conditions.

CONCLUSIONS: The results strongly suggest that L. infantum causes physiological changes in the reservoir host which lead to the host becoming more attractive to both male and female P. perniciosus. These changes are likely to improve the chance of successful transmission because of increased contact with infected hosts and therefore, infected dogs should be particularly targeted in the control of zoonotic visceral leishmaniasis in North Africa.}, } @article {pmid34313464, year = {2021}, author = {Li, YX and Rao, YZ and Qi, YL and Qu, YN and Chen, YT and Jiao, JY and Shu, WS and Jiang, H and Hedlund, BP and Hua, ZS and Li, WJ}, title = {Deciphering Symbiotic Interactions of "Candidatus Aenigmarchaeota" with Inferred Horizontal Gene Transfers and Co-occurrence Networks.}, journal = {mSystems}, volume = {6}, number = {4}, pages = {e0060621}, pmid = {34313464}, issn = {2379-5077}, support = {91951205//National Natural Science Foundation of China (NSFC)/ ; 91751206//National Natural Science Foundation of China (NSFC)/ ; }, abstract = {"Candidatus Aenigmarchaeota" ("Ca. Aenigmarchaeota") represents one of the earliest proposed evolutionary branches within the Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, and Nanohaloarchaeota (DPANN) superphylum. However, their ecological roles and potential host-symbiont interactions are still poorly understood. Here, eight metagenome-assembled genomes (MAGs) were reconstructed from hot spring ecosystems, and further in-depth comparative and evolutionary genomic analyses were conducted on these MAGs and other genomes downloaded from public databases. Although with limited metabolic capacities, we reported that "Ca. Aenigmarchaeota" in thermal environments harbor more genes related to carbohydrate metabolism than "Ca. Aenigmarchaeota" in nonthermal environments. Evolutionary analyses suggested that members from the Thaumarchaeota, Aigarchaeota, Crenarchaeota, and Korarchaeota (TACK) superphylum and Euryarchaeota contribute substantially to the niche expansion of "Ca. Aenigmarchaeota" via horizontal gene transfer (HGT), especially genes related to virus defense and stress responses. Based on co-occurrence network results and recent genetic exchanges among community members, we conjectured that "Ca. Aenigmarchaeota" may be symbionts associated with one MAG affiliated with the genus Pyrobaculum, though host specificity might be wide and variable across different "Ca. Aenigmarchaeota" organisms. This study provides significant insight into possible DPANN-host interactions and ecological roles of "Ca. Aenigmarchaeota." IMPORTANCE Recent advances in sequencing technology promoted the blowout discovery of super tiny microbes in the Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, and Nanohaloarchaeota (DPANN) superphylum. However, the unculturable properties of the majority of microbes impeded our investigation of their behavior and symbiotic lifestyle in the corresponding community. By integrating horizontal gene transfer (HGT) detection and co-occurrence network analysis on "Candidatus Aenigmarchaeota" ("Ca. Aenigmarchaeota"), we made one of the first attempts to infer their putative interaction partners and further decipher the potential functional and genetic interactions between the symbionts. We revealed that HGTs contributed by members from the Thaumarchaeota, Aigarchaeota, Crenarchaeota, and Korarchaeota (TACK) superphylum and Euryarchaeota conferred "Ca. Aenigmarchaeota" with the ability to survive under different environmental stresses, such as virus infection, high temperature, and oxidative stress. This study demonstrates that the interaction partners might be inferable by applying informatics analyses on metagenomic sequencing data.}, } @article {pmid34312673, year = {2022}, author = {D'Orangeville, L and Itter, M and Kneeshaw, D and Munger, JW and Richardson, AD and Dyer, JM and Orwig, DA and Pan, Y and Pederson, N}, title = {Peak radial growth of diffuse-porous species occurs during periods of lower water availability than for ring-porous and coniferous trees.}, journal = {Tree physiology}, volume = {42}, number = {2}, pages = {304-316}, pmid = {34312673}, issn = {1758-4469}, mesh = {Climate Change ; Droughts ; Forests ; Porosity ; *Tracheophyta ; *Trees ; Water ; Xylem ; }, abstract = {Climate models project warmer summer temperatures will increase the frequency and heat severity of droughts in temperate forests of Eastern North America. Hotter droughts are increasingly documented to affect tree growth and forest dynamics, with critical impacts on tree mortality, carbon sequestration and timber provision. The growing acknowledgement of the dominant role of drought timing on tree vulnerability to water deficit raises the issue of our limited understanding of radial growth phenology for most temperate tree species. Here, we use well-replicated dendrometer band data sampled frequently during the growing season to assess the growth phenology of 610 trees from 15 temperate species over 6 years. Patterns of diameter growth follow a typical logistic shape, with growth rates reaching a maximum in June, and then decreasing until process termination. On average, we find that diffuse-porous species take 16-18 days less than other wood-structure types to put on 50% of their annual diameter growth. However, their peak growth rate occurs almost a full month later than ring-porous and conifer species (ca. 24 ± 4 days; mean ± 95% credible interval). Unlike other species, the growth phenology of diffuse-porous species in our dataset is highly correlated with their spring foliar phenology. We also find that the later window of growth in diffuse-porous species, coinciding with peak evapotranspiration and lower water availability, exposes them to a higher water deficit of 88 ± 19 mm (mean ± SE) during their peak growth than ring-porous and coniferous species (15 ± 35 mm and 30 ± 30 mm, respectively). Given the high climatic sensitivity of wood formation, our findings highlight the importance of wood porosity as one predictor of species climatic sensitivity to the projected intensification of the drought regime in the coming decades.}, } @article {pmid34310597, year = {2021}, author = {Shuang, L and Ximing, C and Jie, S}, title = {Research on the degree of coupling of the Internet development level and agricultural--Ecological efficiency based on 2009-2018 data from 13 major grain-producing areas in China.}, journal = {PloS one}, volume = {16}, number = {7}, pages = {e0254078}, pmid = {34310597}, issn = {1932-6203}, mesh = {Agriculture/economics/*trends ; China ; *Ecology ; Edible Grain/*growth & development ; Humans ; Internet/economics/*trends ; Sustainable Development/economics ; }, abstract = {Agricultural informatization and agricultural green development are important components of modern agricultural development, and coordination between the two is an important foundation for achieving sustainable agricultural development. This paper uses data from the 13 major grain producing areas in China from 2009 to 2018 to analyze the coordination of the Internet development level and the agricultural ecological-efficiency, and it further investigates the degree of coupling and coordination between the two. The results of theis study are as follows.(1) The Internet development level of China's 13 main grain production areas has been continuously improving. The average Internet penetration rate increased from 0.25 in 2008 to 0.54 in 2018. (2) The agricultural ecological efficiency of China's main grain production areas has gradually improved. The average value of agricultural ecological efficiency increased from 0.45 in 2009 to 0.79 in 2018. (3) The Internet development level in China's main grain production areas and the continuous improvement of coordination and degree of coupling of the agricultural ecological efficiency show that the interaction between them has led to continuous improvements in the agricultural informatization development and agricultural green development. However, the coordination between the two still has significant room for growth, and there is a certain gap between the different regions.}, } @article {pmid34307821, year = {2021}, author = {Walden, HDS and Lo, MM and Maunsell, FP and Traore, KF and Reuss, SM and Young, A and Diouf, B and Seck, M and Adesogan, AT and Hernandez, JA}, title = {Anemia and intestinal parasites in farmers and family members and sheep in two agro-ecological zones in Senegal.}, journal = {One health (Amsterdam, Netherlands)}, volume = {13}, number = {}, pages = {100260}, pmid = {34307821}, issn = {2352-7714}, abstract = {The burden of anemia in Senegal is high, particularly in children and women in rural households. The main objectives of the study reported here were (i) to measure and compare the prevalence of anemia and intestinal parasitic infections in farmers and family members and sheep in two agro-ecological zones in Senegal and (ii) to examine the association between anemia and age or sex in farmers and family members. The study was conducted in Mpal (250 km from Dakar, the capital city) and Diawara (700 km from Dakar, a remote location near the Malian border). In humans, the prevalence of anemia was higher in Diawara (64/86 = 74%), compared to Mpal (13/29 = 45%) (p < 0.01). Using logistic regression, the odds of anemia were 20.3, 5.7, and 3.2 times higher in children 1-4 years old, children 5-12 years-old, and teenagers 13-19 years old, respectively, compared to adults 20-60 years old, after controlling for study site and sex (p < 0.05). In Diawara, the odds of anemia were 2.9 times higher in women, compared to men, after controlling for age (p = 0.06). The prevalence of intestinal parasites (Giardia sp.) was the same (7%) at both locations. In sheep, the prevalence of low packed cell volume (PCV) and low body condition was higher in Diawara (48/60 = 60% and 11/60 = 18%, respectively), compared to Mpal (23/46 = 50% and 0/46 = 0%, respectively) (p < 0.05). Clinical anemia was associated (p < 0.01) with low PCV and a positive diagnosis of H. contortus. Overall, the prevalence of anemia was higher in farmers and family members and owned sheep in Diawara. In addition, anemia was more common in children and women, an indication that intra-household food allocation may be regulated in favor of men and older age groups. The consequences of livestock affected with anemia and undernutrition can be significant. High morbidity and mortality in livestock can lead to low household income, inadequate household access to and individual consumption of animal source foods, and subsequent risk of anemia in children and women in rural households in Senegal.}, } @article {pmid34303237, year = {2021}, author = {Liu, C and Yang, M and Hou, Y and Xue, X}, title = {Ecosystem service multifunctionality assessment and coupling coordination analysis with land use and land cover change in China's coastal zones.}, journal = {The Science of the total environment}, volume = {797}, number = {}, pages = {149033}, doi = {10.1016/j.scitotenv.2021.149033}, pmid = {34303237}, issn = {1879-1026}, mesh = {China ; Cities ; *Conservation of Natural Resources ; *Ecosystem ; Forests ; Humans ; }, abstract = {Ecosystem services (ESs) have received widespread attention worldwide for their potential to solve sustainability issues. However, extensive land use and land cover change (LUCC) driven by human activities has raised concerns regarding its impacts on ESs, especially in coastal zones. More importantly, spatial-temporal changes, their coupling relationships with LUCC, and their underlying drivers have not been thoroughly analyzed. This study focuses on China's coastal zones to investigate the spatial-temporal changes of ecosystem service multifunctionality (ESM) from 2000 to 2018. Coupling coordination degree (CCD) analysis of the relationship between ESM and comprehensive intensity of land use was applied to identify coastal cities with low-level coordination and their main drivers in 2018. The results show that: (1) the proportion with high levels of ESM decreased by 1.01% from 2000 to 2010 and then increased by 3.29% from 2010 to 2018; (2) the ESM of China's coastal zones present significant spatial heterogeneity, and the low levels of ESM are mainly distributed in the north and urban areas, while most areas in the southern coastal zones have high levels of ESM; (3) forest land is the leading land cover type for ESM, and China's forest conservation policies significantly contribute to the increase in ESM; (4) the CCD of most cities in the southern coastal zones, apart from Shanghai and the Pearl River Delta, is at a relatively high level and experiences no significant changes, while most cities in the northern coastal zones display an improving trend; (5) the land use type, landform type, and leaf area index are the determinants of ESM, and the annual average temperature, population density, and surface elevation are the greatest influences on the CCD. The findings of this study can inform ecological conservation and landscape planning and are beneficial to the sustainable development of coastal zones in China.}, } @article {pmid34302167, year = {2022}, author = {Peltier, DMP and Guo, J and Nguyen, P and Bangs, M and Wilson, M and Samuels-Crow, K and Yocom, LL and Liu, Y and Fell, MK and Shaw, JD and Auty, D and Schwalm, C and Anderegg, WRL and Koch, GW and Litvak, ME and Ogle, K}, title = {Temperature memory and non-structural carbohydrates mediate legacies of a hot drought in trees across the southwestern USA.}, journal = {Tree physiology}, volume = {42}, number = {1}, pages = {71-85}, doi = {10.1093/treephys/tpab091}, pmid = {34302167}, issn = {1758-4469}, mesh = {Carbohydrates ; Climate Change ; *Droughts ; Temperature ; *Trees/physiology ; }, abstract = {Trees are long-lived organisms that integrate climate conditions across years or decades to produce secondary growth. This integration process is sometimes referred to as 'climatic memory.' While widely perceived, the physiological processes underlying this temporal integration, such as the storage and remobilization of non-structural carbohydrates (NSC), are rarely explicitly studied. This is perhaps most apparent when considering drought legacies (perturbed post-drought growth responses to climate), and the physiological mechanisms underlying these lagged responses to climatic extremes. Yet, drought legacies are likely to become more common if warming climate brings more frequent drought. To quantify the linkages between drought legacies, climate memory and NSC, we measured tree growth (via tree ring widths) and NSC concentrations in three dominant species across the southwestern USA. We analyzed these data with a hierarchical mixed effects model to evaluate the time-scales of influence of past climate (memory) on tree growth. We then evaluated the role of climate memory and the degree to which variation in NSC concentrations were related to forward-predicted growth during the hot 2011-2012 drought and subsequent 4-year recovery period. Populus tremuloides exhibited longer climatic memory compared to either Pinus edulis or Juniperus osteosperma, but following the 2011-2012 drought, P. tremuloides trees with relatively longer memory of temperature conditions showed larger (more negative) drought legacies. Conversely, Pinus edulis trees with longer temperature memory had smaller (less negative) drought legacies. For both species, higher NSC concentrations followed more negative (larger) drought legacies, though the relevant NSC fraction differed between P. tremuloides and P. edulis. Our results suggest that differences in tree NSC are also imprinted upon tree growth responses to climate across long time scales, which also underlie tree resilience to increasingly frequent drought events under climate change.}, } @article {pmid34299846, year = {2021}, author = {Beierle, F and Schobel, J and Vogel, C and Allgaier, J and Mulansky, L and Haug, F and Haug, J and Schlee, W and Holfelder, M and Stach, M and Schickler, M and Baumeister, H and Cohrdes, C and Deckert, J and Deserno, L and Edler, JS and Eichner, FA and Greger, H and Hein, G and Heuschmann, P and John, D and Kestler, HA and Krefting, D and Langguth, B and Meybohm, P and Probst, T and Reichert, M and Romanos, M and Störk, S and Terhorst, Y and Weiß, M and Pryss, R}, title = {Corona Health-A Study- and Sensor-Based Mobile App Platform Exploring Aspects of the COVID-19 Pandemic.}, journal = {International journal of environmental research and public health}, volume = {18}, number = {14}, pages = {}, pmid = {34299846}, issn = {1660-4601}, support = {01KX2021//German Federal Ministry of Education and Research/ ; 428318753//German Research Foundation/ ; 01EO1501//German Federal Ministry of Education and Research/ ; HE 4566/5-1//German Research Foundation/ ; }, mesh = {*COVID-19 ; Ecological Momentary Assessment ; Humans ; *Mobile Applications ; Pandemics/prevention & control ; SARS-CoV-2 ; }, abstract = {Physical and mental well-being during the COVID-19 pandemic is typically assessed via surveys, which might make it difficult to conduct longitudinal studies and might lead to data suffering from recall bias. Ecological momentary assessment (EMA) driven smartphone apps can help alleviate such issues, allowing for in situ recordings. Implementing such an app is not trivial, necessitates strict regulatory and legal requirements, and requires short development cycles to appropriately react to abrupt changes in the pandemic. Based on an existing app framework, we developed Corona Health, an app that serves as a platform for deploying questionnaire-based studies in combination with recordings of mobile sensors. In this paper, we present the technical details of Corona Health and provide first insights into the collected data. Through collaborative efforts from experts from public health, medicine, psychology, and computer science, we released Corona Health publicly on Google Play and the Apple App Store (in July 2020) in eight languages and attracted 7290 installations so far. Currently, five studies related to physical and mental well-being are deployed and 17,241 questionnaires have been filled out. Corona Health proves to be a viable tool for conducting research related to the COVID-19 pandemic and can serve as a blueprint for future EMA-based studies. The data we collected will substantially improve our knowledge on mental and physical health states, traits and trajectories as well as its risk and protective factors over the course of the COVID-19 pandemic and its diverse prevention measures.}, } @article {pmid34299819, year = {2021}, author = {Ali, EOM and Babalghith, AO and Bahathig, AOS and Toulah, FHS and Bafaraj, TG and Al-Mahmoudi, SMY and Alhazmi, AMF and Abdel-Latif, ME}, title = {Prevalence of Larval Breeding Sites and Seasonal Variations of Aedes aegypti Mosquitoes (Diptera: Culicidae) in Makkah Al-Mokarramah, Saudi Arabia.}, journal = {International journal of environmental research and public health}, volume = {18}, number = {14}, pages = {}, pmid = {34299819}, issn = {1660-4601}, mesh = {*Aedes ; Animals ; *Dengue/epidemiology ; Larva ; Prevalence ; Saudi Arabia/epidemiology ; Seasons ; }, abstract = {Since 1994, dengue fever (DF) transmission rates have increased significantly in Saudi Arabia (KSA). Climatic, geographic, and demographic conditions make KSA especially suitable for DF's spread. Still, there are insufficient strategies for controlling the Aedes species that transmit DF virus (DENV). To develop effective management strategies, it is necessary to identify Aedes species and the ecological habitat of larvae in Makkah Al-Mokarramah, KSA. We conducted a longitudinal survey of Aedes mosquitoes in 14 localities from January 2015 to December 2015. World Health Organization (WHO) inspection kits for larvae were used to detect and sample larvae, along with pictorial keys. A total of 42,981 potential Aedes larval breeding sites were surveyed. A total of 5403 (12.6%) sites had at least one water source positive for Aedes aegypti (Linnaeus) mosquitoes. Among the total of 15,133 water sources surveyed within the sampled sites, 1815 (12.0%) were positive for Aedes aegypti. Aedes aegypti was the only Aedes species identified in the course of the survey. The presence of such a large immature population may indicate an imminent outbreak of DF in the near future unless proper implementation of control and elimination of Aedes&nbsp;aegypti are undertaken. Additionally, the adaptation of Aedes&nbsp;aegypti to the arid climate of Makkah needs further investigation.}, } @article {pmid34299001, year = {2021}, author = {Volná, A and Bartas, M and Karlický, V and Nezval, J and Kundrátová, K and Pečinka, P and Špunda, V and Červeň, J}, title = {G-Quadruplex in Gene Encoding Large Subunit of Plant RNA Polymerase II: A Billion-Year-Old Story.}, journal = {International journal of molecular sciences}, volume = {22}, number = {14}, pages = {}, pmid = {34299001}, issn = {1422-0067}, support = {SGS07/PrF/2020; SGS02/PrF/2021; SGS01/PrF/2020; SGS11/PrF/2021//University of Ostrava/ ; 18-23702S//Czech Science Foundation/ ; QK1810391//National Agency for Agricultural Research (NAZV) of Czech Republic/ ; CZ.02.1.01/0.0/0.0/16_019/0000797//SustES - Adaptation strategies for sustainable ecosystem services and food security under adverse environmental conditions/ ; }, mesh = {Amino Acid Sequence ; Arabidopsis/chemistry/genetics/radiation effects ; Circular Dichroism ; Computational Biology ; Evolution, Molecular ; *G-Quadruplexes/radiation effects ; Gene Expression Regulation, Plant/genetics ; Glaucophyta/chemistry/genetics/radiation effects ; Phylogeny ; Plant Proteins/*chemistry/genetics/radiation effects ; Plants/*chemistry/genetics/radiation effects ; RNA Polymerase II/*chemistry/genetics ; Rhodophyta/chemistry/genetics/radiation effects ; Sequence Alignment ; Ultraviolet Rays ; }, abstract = {G-quadruplexes have long been perceived as rare and physiologically unimportant nucleic acid structures. However, several studies have revealed their importance in molecular processes, suggesting their possible role in replication and gene expression regulation. Pathways involving G-quadruplexes are intensively studied, especially in the context of human diseases, while their involvement in gene expression regulation in plants remains largely unexplored. Here, we conducted a bioinformatic study and performed a complex circular dichroism measurement to identify a stable G-quadruplex in the gene RPB1, coding for the RNA polymerase II large subunit. We found that this G-quadruplex-forming locus is highly evolutionarily conserved amongst plants sensu lato (Archaeplastida) that share a common ancestor more than one billion years old. Finally, we discussed a new hypothesis regarding G-quadruplexes interacting with UV light in plants to potentially form an additional layer of the regulatory network.}, } @article {pmid34297727, year = {2021}, author = {Xu, Z and Asakawa, S}, title = {A model explaining mRNA level fluctuations based on activity demands and RNA age.}, journal = {PLoS computational biology}, volume = {17}, number = {7}, pages = {e1009188}, pmid = {34297727}, issn = {1553-7358}, mesh = {Computational Biology ; Computer Simulation ; *Models, Biological ; *RNA Stability/genetics/physiology ; RNA, Fungal/genetics/metabolism ; RNA, Messenger/genetics/*metabolism ; Saccharomyces cerevisiae/cytology/genetics/metabolism ; Saccharomyces cerevisiae Proteins/genetics/metabolism ; Single-Cell Analysis ; Transcription, Genetic ; Transcriptome ; }, abstract = {Cellular RNA levels typically fluctuate and are influenced by different transcription rates and RNA degradation rates. However, the understanding of the fundamental relationships between RNA abundance, environmental stimuli, RNA activities, and RNA age distributions is incomplete. Furthermore, the rates of RNA degradation and transcription are difficult to measure in transcriptomic experiments in living organisms, especially in studies involving humans. A model based on activity demands and RNA age was developed to explore the mechanisms of RNA level fluctuations. Using single-cell time-series gene expression experimental data, we assessed the transcription rates, RNA degradation rates, RNA life spans, RNA demand, accumulated transcription levels, and accumulated RNA degradation levels. This model could also predict RNA levels under simulation backgrounds, such as stimuli that induce regular oscillations in RNA abundance, stable RNA levels over time that result from long-term shortage of total RNA activity or from uncontrollable transcription, and relationships between RNA/protein levels and metabolic rates. This information contributes to existing knowledge.}, } @article {pmid34296999, year = {2021}, author = {Woolf, TB and Goheer, A and Holzhauer, K and Martinez, J and Coughlin, JW and Martin, L and Zhao, D and Song, S and Ahmad, Y and Sokolinskyi, K and Remayeva, T and Clark, JM and Bennett, W and Lehmann, H}, title = {Development of a Mobile App for Ecological Momentary Assessment of Circadian Data: Design Considerations and Usability Testing.}, journal = {JMIR formative research}, volume = {5}, number = {7}, pages = {e26297}, pmid = {34296999}, issn = {2561-326X}, support = {P30 DK072488/DK/NIDDK NIH HHS/United States ; }, abstract = {BACKGROUND: Collecting data on daily habits across a population of individuals is challenging. Mobile-based circadian ecological momentary assessment (cEMA) is a powerful frame for observing the impact of daily living on long-term health.

OBJECTIVE: In this paper, we (1) describe the design, testing, and rationale for specifications of a mobile-based cEMA app to collect timing of eating and sleeping data and (2) compare cEMA and survey data collected as part of a 6-month observational cohort study. The ultimate goal of this paper is to summarize our experience and lessons learned with the Daily24 mobile app and to highlight the pros and cons of this data collection modality.

METHODS: Design specifications for the Daily24 app were drafted by the study team based on the research questions and target audience for the cohort study. The associated backend was optimized to provide real-time data to the study team for participant monitoring and engagement. An external 8-member advisory board was consulted throughout the development process, and additional test users recruited as part of a qualitative study provided feedback through in-depth interviews.

RESULTS: After ≥4 days of at-home use, 37 qualitative study participants provided feedback on the app. The app generally received positive feedback from test users for being fast and easy to use. Test users identified several bugs and areas where modifications were necessary to in-app text and instructions and also provided feedback on the engagement strategy. Data collected through the mobile app captured more variability in eating windows than data collected through a one-time survey, though at a significant cost.

CONCLUSIONS: Researchers should consider the potential uses of a mobile app beyond the initial data collection when deciding whether the time and monetary expenditure are advisable for their situation and goals.}, } @article {pmid34294906, year = {2021}, author = {Upadhyaya, NM and Mago, R and Panwar, V and Hewitt, T and Luo, M and Chen, J and Sperschneider, J and Nguyen-Phuc, H and Wang, A and Ortiz, D and Hac, L and Bhatt, D and Li, F and Zhang, J and Ayliffe, M and Figueroa, M and Kanyuka, K and Ellis, JG and Dodds, PN}, title = {Genomics accelerated isolation of a new stem rust avirulence gene-wheat resistance gene pair.}, journal = {Nature plants}, volume = {7}, number = {9}, pages = {1220-1228}, pmid = {34294906}, issn = {2055-0278}, mesh = {Australia ; Disease Resistance/*genetics ; Gene Expression Regulation, Fungal ; Gene Expression Regulation, Plant ; Genes, Fungal ; Genes, Plant ; Genetic Variation ; Genomics ; Genotype ; Plant Diseases/*microbiology ; Puccinia/*genetics/*isolation & purification/*pathogenicity ; Triticum/*genetics/microbiology ; Virulence/*genetics ; }, abstract = {Stem rust caused by the fungus Puccinia graminis f. sp. tritici (Pgt) is a devastating disease of the global staple crop wheat. Although this disease was largely controlled in the latter half of the twentieth century, new virulent strains of Pgt, such as Ug99, have recently evolved[1,2]. These strains have caused notable losses worldwide and their continued spread threatens global wheat production. Breeding for disease resistance provides the most cost-effective control of wheat rust diseases[3]. A number of rust resistance genes have been characterized in wheat and most encode immune receptors of the nucleotide-binding leucine-rich repeat (NLR) class[4], which recognize pathogen effector proteins known as avirulence (Avr) proteins[5]. However, only two Avr genes have been identified in Pgt so far, AvrSr35 and AvrSr50 (refs. [6,7]), and none in other cereal rusts[8,9]. The Sr27 resistance gene was first identified in a wheat line carrying an introgression of the 3R chromosome from Imperial rye[10]. Although not deployed widely in wheat, Sr27 is widespread in the artificial crop species Triticosecale (triticale), which is a wheat-rye hybrid and is a host for Pgt[11,12]. Sr27 is effective against Ug99 (ref. [13]) and other recent Pgt strains[14,15]. Here, we identify both the Sr27 gene in wheat and the corresponding AvrSr27 gene in Pgt and show that virulence to Sr27 can arise experimentally and in the field through deletion mutations, copy number variation and expression level polymorphisms at the AvrSr27 locus.}, } @article {pmid34294116, year = {2021}, author = {Herman, EK and Greninger, A and van der Giezen, M and Ginger, ML and Ramirez-Macias, I and Miller, HC and Morgan, MJ and Tsaousis, AD and Velle, K and Vargová, R and Záhonová, K and Najle, SR and MacIntyre, G and Muller, N and Wittwer, M and Zysset-Burri, DC and Eliáš, M and Slamovits, CH and Weirauch, MT and Fritz-Laylin, L and Marciano-Cabral, F and Puzon, GJ and Walsh, T and Chiu, C and Dacks, JB}, title = {Genomics and transcriptomics yields a system-level view of the biology of the pathogen Naegleria fowleri.}, journal = {BMC biology}, volume = {19}, number = {1}, pages = {142}, pmid = {34294116}, issn = {1741-7007}, mesh = {Animals ; Disease Models, Animal ; Genomics ; Mice ; *Naegleria fowleri/genetics ; Transcriptome ; Trogocytosis ; }, abstract = {BACKGROUND: The opportunistic pathogen Naegleria fowleri establishes infection in the human brain, killing almost invariably within 2 weeks. The amoeba performs piece-meal ingestion, or trogocytosis, of brain material causing direct tissue damage and massive inflammation. The cellular basis distinguishing N. fowleri from other Naegleria species, which are all non-pathogenic, is not known. Yet, with the geographic range of N. fowleri advancing, potentially due to climate change, understanding how this pathogen invades and kills is both important and timely.

RESULTS: Here, we report an -omics approach to understanding N. fowleri biology and infection at the system level. We sequenced two new strains of N. fowleri and performed a transcriptomic analysis of low- versus high-pathogenicity N. fowleri cultured in a mouse infection model. Comparative analysis provides an in-depth assessment of encoded protein complement between strains, finding high conservation. Molecular evolutionary analyses of multiple diverse cellular systems demonstrate that the N. fowleri genome encodes a similarly complete cellular repertoire to that found in free-living N. gruberi. From transcriptomics, neither stress responses nor traits conferred from lateral gene transfer are suggested as critical for pathogenicity. By contrast, cellular systems such as proteases, lysosomal machinery, and motility, together with metabolic reprogramming and novel N. fowleri proteins, are all implicated in facilitating pathogenicity within the host. Upregulation in mouse-passaged N. fowleri of genes associated with glutamate metabolism and ammonia transport suggests adaptation to available carbon sources in the central nervous system.

CONCLUSIONS: In-depth analysis of Naegleria genomes and transcriptomes provides a model of cellular systems involved in opportunistic pathogenicity, uncovering new angles to understanding the biology of a rare but highly fatal pathogen.}, } @article {pmid34291384, year = {2022}, author = {Hennessy, EA and Acabchuk, RL and Arnold, PA and Dunn, AG and Foo, YZ and Johnson, BT and Geange, SR and Haddaway, NR and Nakagawa, S and Mapanga, W and Mengersen, K and Page, MJ and Sánchez-Tójar, A and Welch, V and McGuinness, LA}, title = {Ensuring Prevention Science Research is Synthesis-Ready for Immediate and Lasting Scientific Impact.}, journal = {Prevention science : the official journal of the Society for Prevention Research}, volume = {23}, number = {5}, pages = {809-820}, pmid = {34291384}, issn = {1573-6695}, support = {K01 AA028536/AA/NIAAA NIH HHS/United States ; DRF-2018–11-ST2-048/DH_/Department of Health/United Kingdom ; }, mesh = {*Health Services Research ; Humans ; }, abstract = {When seeking to inform and improve prevention efforts and policy, it is important to be able to robustly synthesize all available evidence. But evidence sources are often large and heterogeneous, so understanding what works, for whom, and in what contexts can only be achieved through a systematic and comprehensive synthesis of evidence. Many barriers impede comprehensive evidence synthesis, which leads to uncertainty about the generalizability of intervention effectiveness, including inaccurate titles/abstracts/keywords terminology (hampering literature search efforts), ambiguous reporting of study methods (resulting in inaccurate assessments of study rigor), and poorly reported participant characteristics, outcomes, and key variables (obstructing the calculation of an overall effect or the examination of effect modifiers). To address these issues and improve the reach of primary studies through their inclusion in evidence syntheses, we provide a set of practical guidelines to help prevention scientists prepare synthesis-ready research. We use a recent mindfulness trial as an empirical example to ground the discussion and demonstrate ways to ensure the following: (1) primary studies are discoverable; (2) the types of data needed for synthesis are present; and (3) these data are readily synthesizable. We highlight several tools and practices that can aid authors in these efforts, such as using a data-driven approach for crafting titles, abstracts, and keywords or by creating a repository for each project to host all study-related data files. We also provide step-by-step guidance and software suggestions for standardizing data design and public archiving to facilitate synthesis-ready research.}, } @article {pmid34289256, year = {2021}, author = {Dávila-Lara, A and Reichelt, M and Wang, D and Vogel, H and Mithöfer, A}, title = {Proof of anthocyanins in the carnivorous plant genus Nepenthes.}, journal = {FEBS open bio}, volume = {11}, number = {9}, pages = {2576-2585}, pmid = {34289256}, issn = {2211-5463}, mesh = {Anthocyanins/*analysis/biosynthesis/chemistry/isolation & purification ; Carnivorous Plant/*chemistry/classification/genetics ; Chemical Fractionation ; Chromatography, High Pressure Liquid ; Computational Biology/methods ; Gene Expression Profiling ; Gene Expression Regulation, Plant ; Molecular Structure ; Phylogeny ; *Pigmentation ; Spectrometry, Mass, Electrospray Ionization ; Transcriptome ; }, abstract = {Yellow to red colored betalains are a chemotaxonomic feature of Caryophyllales, while in most other plant taxa, anthocyanins are responsible for these colors. The carnivorous plant family Nepenthaceae belongs to Caryophyllales; here, red-pigmented tissues seem to attract insect prey. Strikingly, the chemical nature of red color in Nepenthes has never been elucidated. Although belonging to Caryophyllales, in Nepenthes, some molecular evidence supports the presence of anthocyanins rather than betalains. However, there was previously no direct chemical proof of this. Using ultra-high-performance liquid chromatography-electrospray ionization-high-resolution mass spectrometry, we identified cyanidin glycosides in Nepenthes species and tissues. Further, we reveal the existence of a complete set of constitutively expressed anthocyanin biosynthetic genes in Nepenthes. Thus, here we finally conclude the long-term open question regarding red pigmentation in Nepenthaceae.}, } @article {pmid34288531, year = {2022}, author = {Miralles, A and Ducasse, J and Brouillet, S and Flouri, T and Fujisawa, T and Kapli, P and Knowles, LL and Kumari, S and Stamatakis, A and Sukumaran, J and Lutteropp, S and Vences, M and Puillandre, N}, title = {SPART: A versatile and standardized data exchange format for species partition information.}, journal = {Molecular ecology resources}, volume = {22}, number = {1}, pages = {430-438}, doi = {10.1111/1755-0998.13470}, pmid = {34288531}, issn = {1755-0998}, support = {865101//H2020 European Research Council/ ; VE247/20-1//Deutsche Forschungsgemeinschaft/ ; }, abstract = {A wide range of data types can be used to delimit species and various computer-based tools dedicated to this task are now available. Although these formalized approaches have significantly contributed to increase the objectivity of species delimitation (SD) under different assumptions, they are not routinely used by alpha-taxonomists. One obvious shortcoming is the lack of interoperability among the various independently developed SD programs. Given the frequent incongruences between species partitions inferred by different SD approaches, researchers applying these methods often seek to compare these alternative species partitions to evaluate the robustness of the species boundaries. This procedure is excessively time consuming at present, and the lack of a standard format for species partitions is a major obstacle. Here, we propose a standardized format, SPART, to enable compatibility between different SD tools exporting or importing partitions. This format reports the partitions and describes, for each of them, the assignment of individuals to the "inferred species". The syntax also allows support values to be optionally reported, as well as original trees and the full command lines used in the respective SD analyses. Two variants of this format are proposed, overall using the same terminology but presenting the data either optimized for human readability (matricial SPART) or in a format in which each partition forms a separate block (SPART.XML). ABGD, DELINEATE, GMYC, PTP and TR2 have already been adapted to output SPART files and a new version of LIMES has been developed to import, export, merge and split them.}, } @article {pmid34287660, year = {2021}, author = {Zhu, H and Ma, Y and Guo, Q}, title = {Expression stability of internal reference gene in response to Trichoderma polysporum infection in Avena fatua L.}, journal = {Current genetics}, volume = {67}, number = {6}, pages = {909-918}, pmid = {34287660}, issn = {1432-0983}, support = {2019-ZJ-7057//QingHai Department of Science and Technology/ ; }, mesh = {Avena/*genetics/*microbiology ; Computational Biology/methods ; Gene Expression Profiling ; *Gene Expression Regulation, Plant ; *Genes, Plant ; Host-Pathogen Interactions/*genetics ; Hypocreales/*genetics ; RNA Stability ; Transcriptome ; }, abstract = {Trichoderma polysporum was a pathogenic fungi which showed strong pathogenicity to Avena fatua L. in recent study. The stress response of A. fatua to T. polysporum is mediated by the regulation of gene expression. Quantification of the expression of genes requires normalizing RT-qPCR data using reference genes with stable expression in the system studied as internal standards. To construct a RT-qPCR system suitable for response of A. fatua to T. polysporum, and screen stable internal reference genes, GeNorm, NormFinder, BestKeeper and RefFinde were used to perform SYBR Green-based RT-qPCR analysis on eight candidate internal reference genes (18S, 28S, TUA, UBC, ACT, GAPDH, TBP and EF-1α) in A. fatua samples after inoculation of T. polysporum Strain HZ-31. The results showed that TBP, 18S and UBC were the most stable internal reference genes, TBP and TUA, TBP and GAPDH, 18S and TBP, UBC and 18S were the most suitable combination of the two internal reference genes, which could be used as internal reference genes for functional gene expression analysis during the interaction between T. polysporum and A. fatua. This is the first study describing a set of reference genes with a stable expression under fungi stress in A. fatua. These genes are also candidate reference genes of choice for studies seeking to identify stress-responsive genes in A. fatua.}, } @article {pmid34286299, year = {2021}, author = {Coutinho, FH and Zaragoza-Solas, A and López-Pérez, M and Barylski, J and Zielezinski, A and Dutilh, BE and Edwards, R and Rodriguez-Valera, F}, title = {RaFAH: Host prediction for viruses of Bacteria and Archaea based on protein content.}, journal = {Patterns (New York, N.Y.)}, volume = {2}, number = {7}, pages = {100274}, pmid = {34286299}, issn = {2666-3899}, support = {RC2 DK116713/DK/NIDDK NIH HHS/United States ; }, abstract = {Culture-independent approaches have recently shed light on the genomic diversity of viruses of prokaryotes. One fundamental question when trying to understand their ecological roles is: which host do they infect? To tackle this issue we developed a machine-learning approach named Random Forest Assignment of Hosts (RaFAH), that uses scores to 43,644 protein clusters to assign hosts to complete or fragmented genomes of viruses of Archaea and Bacteria. RaFAH displayed performance comparable with that of other methods for virus-host prediction in three different benchmarks encompassing viruses from RefSeq, single amplified genomes, and metagenomes. RaFAH was applied to assembled metagenomic datasets of uncultured viruses from eight different biomes of medical, biotechnological, and environmental relevance. Our analyses led to the identification of 537 sequences of archaeal viruses representing unknown lineages, whose genomes encode novel auxiliary metabolic genes, shedding light on how these viruses interfere with the host molecular machinery. RaFAH is available at https://sourceforge.net/projects/rafah/.}, } @article {pmid34286134, year = {2021}, author = {Shalash, AS and Rösler, TW and Abdelrahman, IY and Abulmakarem, HS and Müller, SH and Hopfner, F and Kuhlenbäumer, G and Höglinger, GU and Salama, M}, title = {Atypical pantothenate kinase-associated neurodegeneration with variable phenotypes in an Egyptian family.}, journal = {Heliyon}, volume = {7}, number = {7}, pages = {e07469}, pmid = {34286134}, issn = {2405-8440}, abstract = {Pantothenate kinase-associated neurodegeneration (PKAN) is a rare hereditary neurodegenerative disease characterized by an accumulation of iron within the brain. In the present report, we describe a family with 4 affected siblings presenting with variable clinical manifestations, e.g., parkinsonian features, dystonia and slow disease progression over 5 years. Exome sequencing revealed a causative variant in the pantothenate kinase 2 gene (PANK2). Variant NM_024960.6:c.710C > T was homozygous in all affected subjects. Our report describes the first genetically confirmed cases of PKAN in the Egyptian population. Studying genetics of neurodegenerative diseases in different ethnicities is very important for determining clinical phenotypes and understanding pathomechanisms of these diseases.}, } @article {pmid34285264, year = {2021}, author = {Hill, JE and Kellner, KF and Kluever, BM and Avery, ML and Humphrey, JS and Tillman, EA and DeVault, TL and Belant, JL}, title = {Landscape transformations produce favorable roosting conditions for turkey vultures and black vultures.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {14793}, pmid = {34285264}, issn = {2045-2322}, mesh = {Animals ; Behavior, Animal/*physiology ; Ecosystem ; Falconiformes/*physiology ; Geographic Information Systems ; Human Activities ; North America ; Remote Sensing Technology/*methods ; Satellite Imagery ; Seasons ; }, abstract = {Recent increases in turkey vulture (Cathartes aura) and black vulture (Coragyps atratus) populations in North America have been attributed in part to their success adapting to human-modified landscapes. However, the capacity for such landscapes to generate favorable roosting conditions for these species has not been thoroughly investigated. We assessed the role of anthropogenic and natural landscape elements on roosting habitat selection of 11 black and 7 turkey vultures in coastal South Carolina, USA using a GPS satellite transmitter dataset derived from previous research. Our dataset spanned 2006-2012 and contained data from 7916 nights of roosting. Landscape fragmentation, as measured by land cover richness, influenced roosting probability for both species in all seasons, showing either a positive relationship or peaking at intermediate values. Roosting probability of turkey vultures was maximized at intermediate road densities in three of four seasons, and black vultures showed a positive relationship with roads in fall, but no relationship throughout the rest of the year. Roosting probability of both species declined with increasing high density urban cover throughout most of the year. We suggest that landscape transformations lead to favorable roosting conditions for turkey vultures and black vultures, which has likely contributed to their recent proliferations across much of the Western Hemisphere.}, } @article {pmid34284227, year = {2021}, author = {Ge, Y and Chen, Z and Handel, A and Martinez, L and Xiao, Q and Li, C and Chen, E and Pan, J and Li, Y and Ling, F and Shen, Y}, title = {The impact of social distancing, contact tracing, and case isolation interventions to suppress the COVID-19 epidemic: A modeling study.}, journal = {Epidemics}, volume = {36}, number = {}, pages = {100483}, pmid = {34284227}, issn = {1878-0067}, mesh = {*COVID-19 ; Contact Tracing ; *Epidemics ; Humans ; Physical Distancing ; SARS-CoV-2 ; }, abstract = {INTRODUCTION: Most countries are dependent on nonpharmaceutical public health interventions such as social distancing, contact tracing, and case isolation to mitigate COVID-19 spread until medicines or vaccines widely available. Minimal research has been performed on the independent and combined impact of each of these interventions based on empirical case data.

METHODS: We obtained data from all confirmed COVID-19 cases from January 7th to February 22nd 2020 in Zhejiang Province, China, to fit an age-stratified compartmental model using human contact information before and during the outbreak. The effectiveness of social distancing, contact tracing, and case isolation was studied and compared in simulation. We also simulated a two-phase reopening scenario to assess whether various strategies combining nonpharmaceutical interventions are likely to achieve population-level control of a second-wave epidemic.

RESULTS: Our study sample included 1,218 symptomatic cases with COVID-19, of which 664 had no inter-province travel history. Results suggest that 36.5 % (95 % CI, 12.8-57.1) of contacts were quarantined, and approximately five days (95 % CI, 2.2-11.0) were needed to detect and isolate a case. As contact networks would increase after societal and economic reopening, avoiding a second wave without strengthening nonpharmaceutical interventions compared to the first wave it would be exceedingly difficult.

CONCLUSIONS: Continuous attention and further improvement of nonpharmaceutical interventions are needed in second-wave prevention. Specifically, contact tracing merits further attention.}, } @article {pmid34282833, year = {2021}, author = {Bai, Y and Meng, Y and Luo, J and Wang, H and Li, G and Li, C}, title = {Full-length transcriptome assembly of andrias davidianus (amphibia: caudata) skin via hybrid sequencing.}, journal = {Bioscience reports}, volume = {41}, number = {8}, pages = {}, pmid = {34282833}, issn = {1573-4935}, mesh = {Amphibian Proteins/*genetics/metabolism ; Animals ; Databases, Genetic ; Female ; *Gene Expression Profiling ; Gene Expression Regulation ; Gene Regulatory Networks ; High-Throughput Nucleotide Sequencing ; RNA, Long Noncoding/genetics/metabolism ; *Single-Cell Analysis ; Skin/cytology/*metabolism ; Transcription Factors/genetics/metabolism ; *Transcriptome ; Urodela/*genetics/metabolism ; }, abstract = {The Chinese giant salamander, Andrias davidianus, is the largest amphibian species in the world; it is thus an economically and ecologically important species. The skin of A. davidianus exhibits complex adaptive structural and functional adaptations to facilitate survival in aquatic and terrestrial ecosystems. Here, we report the first full-length amphibian transcriptome from the dorsal skin of A. davidianus, which was assembled using hybrid sequencing and the PacBio and Illumina platforms. A total of 153,038 transcripts were hybrid assembled (mean length of 2039 bp and N50 of 2172 bp), and 133,794 were annotated in at least one database (nr, Swiss-Prot, KEGG, KOGs, GO, and nt). A total of 58,732, 68,742, and 115,876 transcripts were classified into 24 KOG categories, 1903 GO term categories, and 46 KEGG pathways (level 2), respectively. A total of 207,627 protein-coding regions, 785 transcription factors, 27,237 potential long non-coding RNAs, and 8299 simple sequence repeats were also identified. The hybrid-assembled transcriptome recovered more full-length transcripts, had a higher N50 contig length, and a higher annotation rate of unique genes compared with that assembled in previous studies using next-generation sequencing. The high-quality full-length reference gene set generated in this study will help elucidate the genetic characteristics of A. davidianus skin and aid the identification of functional skin proteins.}, } @article {pmid34281113, year = {2021}, author = {Catelan, D and Giangreco, M and Biggeri, A and Barbone, F and Monasta, L and Ricci, G and Romano, F and Rosolen, V and Zito, G and Ronfani, L}, title = {Spatial Patterns of Endometriosis Incidence. A Study in Friuli Venezia Giulia (Italy) in the Period 2004-2017.}, journal = {International journal of environmental research and public health}, volume = {18}, number = {13}, pages = {}, pmid = {34281113}, issn = {1660-4601}, mesh = {Adolescent ; Adult ; Bayes Theorem ; Databases, Factual ; *Endometriosis/epidemiology ; Female ; Humans ; Incidence ; Italy/epidemiology ; Middle Aged ; Young Adult ; }, abstract = {BACKGROUND: Diagnosis of endometriosis and evaluation of incidence data are complex tasks because the disease is identified laparoscopically and confirmed histologically. Incidence estimates reported in literature are widely inconsistent, presumably reflecting geographical variability of risk and the difficulty of obtaining reliable data.

METHODS: We retrieved incident cases of endometriosis in women aged 15-50 years using hospital discharge records and pathology databases of the Friuli Venezia Giulia region in the calendar period 2004-2017. We studied the spatial pattern of endometriosis incidence applying Bayesian approaches to Disease Mapping, and profiled municipalities at higher risk controlling for multiple comparisons using both q-values and a fully Bayesian approach.

RESULTS: 4125 new cases of endometriosis were identified in the age range 15 to 50 years in the period 2004-2017. The incidence rate (x100 000) is 111 (95% CI 110-112), with a maximum of 160 in the age group 31-35 years. The geographical distribution of endometriosis incidence showed a very strong north-south spatial gradient. We consistently identified a group of five neighboring municipalities at higher risk (RR 1.31 95% CI 1.13; 1.52), even accounting for ascertainment bias.

CONCLUSIONS: The cluster of 5 municipalities in the industrialized and polluted south-east part of the region is suggestive. However, due to the ecologic nature of the present study, information on the patients' characteristics and exposure histories are limited. Individual studies, including biomonitoring, and life-course studies are necessary to better evaluate our findings.}, } @article {pmid34280204, year = {2021}, author = {Schaber, KL and Morrison, AC and Elson, WH and Astete-Vega, H and Córdova-López, JJ and Ríos López, EJ and Flores, WLQ and Santillan, ASV and Scott, TW and Waller, LA and Kitron, U and Barker, CM and Perkins, TA and Rothman, AL and Vazquez-Prokopec, GM and Elder, JP and Paz-Soldan, VA}, title = {The impact of dengue illness on social distancing and caregiving behavior.}, journal = {PLoS neglected tropical diseases}, volume = {15}, number = {7}, pages = {e0009614}, pmid = {34280204}, issn = {1935-2735}, support = {P01 AI098670/AI/NIAID NIH HHS/United States ; }, mesh = {Adolescent ; Adult ; Caregivers/*psychology ; Child ; Data Collection ; Dengue/epidemiology/*psychology/*transmission ; Female ; Humans ; Male ; Peru/epidemiology ; *Physical Distancing ; Young Adult ; }, abstract = {BACKGROUND: Human mobility among residential locations can drive dengue virus (DENV) transmission dynamics. Recently, it was shown that individuals with symptomatic DENV infection exhibit significant changes in their mobility patterns, spending more time at home during illness. This change in mobility is predicted to increase the risk of acquiring infection for those living with or visiting the ill individual. It has yet to be considered, however, whether social contacts are also changing their mobility, either by socially distancing themselves from the infectious individual or increasing contact to help care for them. Social, or physical, distancing and caregiving could have diverse yet important impacts on DENV transmission dynamics; therefore, it is necessary to better understand the nature and frequency of these behaviors including their effect on mobility.

Through community-based febrile illness surveillance and RT-PCR infection confirmation, 67 DENV positive (DENV+) residents were identified in the city of Iquitos, Peru. Using retrospective interviews, data were collected on visitors and home-based care received during the illness. While 15% of participants lost visitors during their illness, 22% gained visitors; overall, 32% of all individuals (particularly females) received visitors while symptomatic. Caregiving was common (90%), particularly caring by housemates (91%) and caring for children (98%). Twenty-eight percent of caregivers changed their behavior enough to have their work (and, likely, mobility patterns) affected. This was significantly more likely when caring for individuals with low "health-related quality of well-being" during illness (Fisher's Exact, p = 0.01).

CONCLUSIONS/SIGNIFICANCE: Our study demonstrates that social contacts of individuals with dengue modify their patterns of visitation and caregiving. The observed mobility changes could impact a susceptible individual's exposure to virus or a presymptomatic/clinically inapparent individual's contribution to onward transmission. Accounting for changes in social contact mobility is imperative in order to get a more accurate understanding of DENV transmission.}, } @article {pmid34280179, year = {2021}, author = {Whitlock, AOB and Juliano, JJ and Mideo, N}, title = {Immune selection suppresses the emergence of drug resistance in malaria parasites but facilitates its spread.}, journal = {PLoS computational biology}, volume = {17}, number = {7}, pages = {e1008577}, pmid = {34280179}, issn = {1553-7358}, mesh = {Animals ; Antimalarials/*pharmacology/therapeutic use ; Computational Biology ; Drug Resistance/*immunology ; *Host-Parasite Interactions/drug effects/immunology ; Humans ; *Malaria, Falciparum/drug therapy/immunology/parasitology/transmission ; Models, Biological ; *Plasmodium falciparum/drug effects/immunology ; }, abstract = {Although drug resistance in Plasmodium falciparum typically evolves in regions of low transmission, resistance spreads readily following introduction to regions with a heavier disease burden. This suggests that the origin and the spread of resistance are governed by different processes, and that high transmission intensity specifically impedes the origin. Factors associated with high transmission, such as highly immune hosts and competition within genetically diverse infections, are associated with suppression of resistant lineages within hosts. However, interactions between these factors have rarely been investigated and the specific relationship between adaptive immunity and selection for resistance has not been explored. Here, we developed a multiscale, agent-based model of Plasmodium parasites, hosts, and vectors to examine how host and parasite dynamics shape the evolution of resistance in populations with different transmission intensities. We found that selection for antigenic novelty ("immune selection") suppressed the evolution of resistance in high transmission settings. We show that high levels of population immunity increased the strength of immune selection relative to selection for resistance. As a result, immune selection delayed the evolution of resistance in high transmission populations by allowing novel, sensitive lineages to remain in circulation at the expense of the spread of a resistant lineage. In contrast, in low transmission settings, we observed that resistant strains were able to sweep to high population prevalence without interference. Additionally, we found that the relationship between immune selection and resistance changed when resistance was widespread. Once resistance was common enough to be found on many antigenic backgrounds, immune selection stably maintained resistant parasites in the population by allowing them to proliferate, even in untreated hosts, when resistance was linked to a novel epitope. Our results suggest that immune selection plays a role in the global pattern of resistance evolution.}, } @article {pmid34279216, year = {2021}, author = {Kim, BY and Wang, JR and Miller, DE and Barmina, O and Delaney, E and Thompson, A and Comeault, AA and Peede, D and D'Agostino, ERR and Pelaez, J and Aguilar, JM and Haji, D and Matsunaga, T and Armstrong, EE and Zych, M and Ogawa, Y and Stamenković-Radak, M and Jelić, M and Veselinović, MS and Tanasković, M and Erić, P and Gao, JJ and Katoh, TK and Toda, MJ and Watabe, H and Watada, M and Davis, JS and Moyle, LC and Manoli, G and Bertolini, E and Košťál, V and Hawley, RS and Takahashi, A and Jones, CD and Price, DK and Whiteman, N and Kopp, A and Matute, DR and Petrov, DA}, title = {Highly contiguous assemblies of 101 drosophilid genomes.}, journal = {eLife}, volume = {10}, number = {}, pages = {}, pmid = {34279216}, issn = {2050-084X}, support = {R35 GM122592/GM/NIGMS NIH HHS/United States ; F32 GM135998/GM/NIGMS NIH HHS/United States ; T32 GM132022/GM/NIGMS NIH HHS/United States ; R01 GM121750/GM/NIGMS NIH HHS/United States ; R35 GM118165/GM/NIGMS NIH HHS/United States ; R35 GM119816/GM/NIGMS NIH HHS/United States ; R01 GM125715/GM/NIGMS NIH HHS/United States ; K01 DK119582/DK/NIDDK NIH HHS/United States ; T32 GM128596/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Cell Line ; Chromosomes ; Computational Biology/methods ; Drosophila melanogaster/*genetics ; Female ; Genome ; *Genome Size ; Genomics/*methods ; High-Throughput Nucleotide Sequencing/methods ; Nanopores ; }, abstract = {Over 100 years of studies in Drosophila melanogaster and related species in the genus Drosophila have facilitated key discoveries in genetics, genomics, and evolution. While high-quality genome assemblies exist for several species in this group, they only encompass a small fraction of the genus. Recent advances in long-read sequencing allow high-quality genome assemblies for tens or even hundreds of species to be efficiently generated. Here, we utilize Oxford Nanopore sequencing to build an open community resource of genome assemblies for 101 lines of 93 drosophilid species encompassing 14 species groups and 35 sub-groups. The genomes are highly contiguous and complete, with an average contig N50 of 10.5 Mb and greater than 97% BUSCO completeness in 97/101 assemblies. We show that Nanopore-based assemblies are highly accurate in coding regions, particularly with respect to coding insertions and deletions. These assemblies, along with a detailed laboratory protocol and assembly pipelines, are released as a public resource and will serve as a starting point for addressing broad questions of genetics, ecology, and evolution at the scale of hundreds of species.}, } @article {pmid34274064, year = {2021}, author = {Drake, TM and Riad, AM and Fairfield, CJ and Egan, C and Knight, SR and Pius, R and Hardwick, HE and Norman, L and Shaw, CA and McLean, KA and Thompson, AAR and Ho, A and Swann, OV and Sullivan, M and Soares, F and Holden, KA and Merson, L and Plotkin, D and Sigfrid, L and de Silva, TI and Girvan, M and Jackson, C and Russell, CD and Dunning, J and Solomon, T and Carson, G and Olliaro, P and Nguyen-Van-Tam, JS and Turtle, L and Docherty, AB and Openshaw, PJ and Baillie, JK and Harrison, EM and Semple, MG and , }, title = {Characterisation of in-hospital complications associated with COVID-19 using the ISARIC WHO Clinical Characterisation Protocol UK: a prospective, multicentre cohort study.}, journal = {Lancet (London, England)}, volume = {398}, number = {10296}, pages = {223-237}, pmid = {34274064}, issn = {1474-547X}, support = {G0701652/MRC_/Medical Research Council/United Kingdom ; MR/V001671/1/MRC_/Medical Research Council/United Kingdom ; MC_UU_12014/12/MRC_/Medical Research Council/United Kingdom ; MC_PC_19026/MRC_/Medical Research Council/United Kingdom ; MC_PC_19059/MRC_/Medical Research Council/United Kingdom ; MC_UU_12014/9/MRC_/Medical Research Council/United Kingdom ; MR/S032304/1/MRC_/Medical Research Council/United Kingdom ; MC_UU_12014/8/MRC_/Medical Research Council/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; MC_UU_12014/10/MRC_/Medical Research Council/United Kingdom ; MC_PC_15001/MRC_/Medical Research Council/United Kingdom ; 205228/Z/16/Z/WT_/Wellcome Trust/United Kingdom ; MC_PC_19025/MRC_/Medical Research Council/United Kingdom ; FS/18/13/33281/BHF_/British Heart Foundation/United Kingdom ; 215091/Z/18/Z/WT_/Wellcome Trust/United Kingdom ; 109965/Z/15/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Age Factors ; Aged ; COVID-19/*complications/epidemiology ; Cardiovascular Diseases ; Clinical Protocols/*standards ; *Comorbidity ; Female ; *Hospital Mortality ; *Hospitalization ; Hospitals ; Humans ; Male ; Nervous System Diseases ; Prospective Studies ; Respiratory Tract Diseases ; SARS-CoV-2 ; United Kingdom/epidemiology ; World Health Organization ; }, abstract = {BACKGROUND: COVID-19 is a multisystem disease and patients who survive might have in-hospital complications. These complications are likely to have important short-term and long-term consequences for patients, health-care utilisation, health-care system preparedness, and society amidst the ongoing COVID-19 pandemic. Our aim was to characterise the extent and effect of COVID-19 complications, particularly in those who survive, using the International Severe Acute Respiratory and Emerging Infections Consortium WHO Clinical Characterisation Protocol UK.

METHODS: We did a prospective, multicentre cohort study in 302 UK health-care facilities. Adult patients aged 19 years or older, with confirmed or highly suspected SARS-CoV-2 infection leading to COVID-19 were included in the study. The primary outcome of this study was the incidence of in-hospital complications, defined as organ-specific diagnoses occurring alone or in addition to any hallmarks of COVID-19 illness. We used multilevel logistic regression and survival models to explore associations between these outcomes and in-hospital complications, age, and pre-existing comorbidities.

FINDINGS: Between Jan 17 and Aug 4, 2020, 80 388 patients were included in the study. Of the patients admitted to hospital for management of COVID-19, 49·7% (36 367 of 73 197) had at least one complication. The mean age of our cohort was 71·1 years (SD 18·7), with 56·0% (41 025 of 73 197) being male and 81·0% (59 289 of 73 197) having at least one comorbidity. Males and those aged older than 60 years were most likely to have a complication (aged ≥60 years: 54·5% [16 579 of 30 416] in males and 48·2% [11 707 of 24 288] in females; aged <60 years: 48·8% [5179 of 10 609] in males and 36·6% [2814 of 7689] in females). Renal (24·3%, 17 752 of 73 197), complex respiratory (18·4%, 13 486 of 73 197), and systemic (16·3%, 11 895 of 73 197) complications were the most frequent. Cardiovascular (12·3%, 8973 of 73 197), neurological (4·3%, 3115 of 73 197), and gastrointestinal or liver (0·8%, 7901 of 73 197) complications were also reported.

INTERPRETATION: Complications and worse functional outcomes in patients admitted to hospital with COVID-19 are high, even in young, previously healthy individuals. Acute complications are associated with reduced ability to self-care at discharge, with neurological complications being associated with the worst functional outcomes. COVID-19 complications are likely to cause a substantial strain on health and social care in the coming years. These data will help in the design and provision of services aimed at the post-hospitalisation care of patients with COVID-19.

FUNDING: National Institute for Health Research and the UK Medical Research Council.}, } @article {pmid34273858, year = {2021}, author = {de Vries, JJC and Brown, JR and Fischer, N and Sidorov, IA and Morfopoulou, S and Huang, J and Munnink, BBO and Sayiner, A and Bulgurcu, A and Rodriguez, C and Gricourt, G and Keyaerts, E and Beller, L and Bachofen, C and Kubacki, J and Samuel, C and Florian, L and Dennis, S and Beer, M and Hoeper, D and Huber, M and Kufner, V and Zaheri, M and Lebrand, A and Papa, A and van Boheemen, S and Kroes, ACM and Breuer, J and Lopez-Labrador, FX and Claas, ECJ}, title = {Benchmark of thirteen bioinformatic pipelines for metagenomic virus diagnostics using datasets from clinical samples.}, journal = {Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology}, volume = {141}, number = {}, pages = {104908}, pmid = {34273858}, issn = {1873-5967}, support = {206478/WT_/Wellcome Trust/United Kingdom ; 206478/Z/17/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Benchmarking ; *Computational Biology ; High-Throughput Nucleotide Sequencing ; Humans ; Metagenomics ; *Viruses/genetics ; }, abstract = {INTRODUCTION: Metagenomic sequencing is increasingly being used in clinical settings for difficult to diagnose cases. The performance of viral metagenomic protocols relies to a large extent on the bioinformatic analysis. In this study, the European Society for Clinical Virology (ESCV) Network on NGS (ENNGS) initiated a benchmark of metagenomic pipelines currently used in clinical virological laboratories.

METHODS: Metagenomic datasets from 13 clinical samples from patients with encephalitis or viral respiratory infections characterized by PCR were selected. The datasets were analyzed with 13 different pipelines currently used in virological diagnostic laboratories of participating ENNGS members. The pipelines and classification tools were: Centrifuge, DAMIAN, DIAMOND, DNASTAR, FEVIR, Genome Detective, Jovian, MetaMIC, MetaMix, One Codex, RIEMS, VirMet, and Taxonomer. Performance, characteristics, clinical use, and user-friendliness of these pipelines were analyzed.

RESULTS: Overall, viral pathogens with high loads were detected by all the evaluated metagenomic pipelines. In contrast, lower abundance pathogens and mixed infections were only detected by 3/13 pipelines, namely DNASTAR, FEVIR, and MetaMix. Overall sensitivity ranged from 80% (10/13) to 100% (13/13 datasets). Overall positive predictive value ranged from 71-100%. The majority of the pipelines classified sequences based on nucleotide similarity (8/13), only a minority used amino acid similarity, and 6 of the 13 pipelines assembled sequences de novo. No clear differences in performance were detected that correlated with these classification approaches. Read counts of target viruses varied between the pipelines over a range of 2-3 log, indicating differences in limit of detection.

CONCLUSION: A wide variety of viral metagenomic pipelines is currently used in the participating clinical diagnostic laboratories. Detection of low abundant viral pathogens and mixed infections remains a challenge, implicating the need for standardization and validation of metagenomic analysis for clinical diagnostic use. Future studies should address the selective effects due to the choice of different reference viral databases.}, } @article {pmid34273183, year = {2021}, author = {Biancolini, D and Vascellari, V and Melone, B and Blackburn, TM and Cassey, P and Scrivens, SL and Rondinini, C}, title = {DAMA: the global Distribution of Alien Mammals database.}, journal = {Ecology}, volume = {102}, number = {11}, pages = {e03474}, doi = {10.1002/ecy.3474}, pmid = {34273183}, issn = {1939-9170}, mesh = {Animals ; Biodiversity ; Databases, Factual ; Ecology ; *Introduced Species ; *Mammals ; }, abstract = {We developed the DAMA (Distribution of Alien Mammals) database, a comprehensive source reporting the global distribution of the 230 species of mammals that have established self-sustaining and free-ranging populations outside their native range due to direct or indirect human action. Every alien range is accompanied by information on its invasion stage, pathway, method of introduction, and date of introduction. We collected information from 827 different sources (scientific literature, books, risk assessments, reports, online biodiversity databases and websites), and used it to draw alien range maps for these species following the IUCN mapping framework. DAMA comprises 2,726 range polygons, covering 199 countries, 2,190 level 1 administrative areas, and 11 zoogeographic realms for the period 21500 BC-AD 2017. The most represented orders among introduced mammal species are Rodentia (n = 58, 25.22%), Cetartiodactyla (n = 49 species, 21.30%), Carnivora (n = 30 species, 13.04%), Diprotodontia (n = 28, 12.17%), and Primates (n = 26, 11.30%). Mammal species have been frequently introduced for hunting (n = 100), pet trade (n = 57), conservation (n = 51), and fauna improvement (n = 42). The majority of range polygons are placed on islands (n = 2,196, 80.56%), encompass populations that have moved beyond establishment and into the invasion stage (n = 1,655, 60.71%), and originated from 1500 AD to the present (n = 1,496, 54.88%). Despite inheriting literature biases towards more studied regions (e.g., developed countries), DAMA is the most up-to-date picture of alien mammal global distribution and can be used to investigate their invasion ecology across different biogeographical regions. There are no copyright or proprietary restrictions; IUCN range maps were modified into a derivative work according to the IUCN's terms of service.}, } @article {pmid34272616, year = {2021}, author = {Salnikova, LE and Kolobkov, DS and Sviridova, DA and Abilev, SK}, title = {An overview of germline variations in genes of primary immunodeficiences through integrative analysis of ClinVar, HGMD[®] and dbSNP databases.}, journal = {Human genetics}, volume = {140}, number = {9}, pages = {1379-1393}, pmid = {34272616}, issn = {1432-1203}, support = {0112-2019-0002//Ministry of Education and Science of Russia/ ; }, mesh = {*Databases, Genetic ; Female ; *Genetic Predisposition to Disease ; Humans ; Male ; *Polymorphism, Single Nucleotide ; Primary Immunodeficiency Diseases/*genetics ; }, abstract = {Primary immunodeficiencies (PID) are a diverse group of genetic disorders caused by inadequate development and function of immune system. Identifying genetic etiology is important for genetic counselling and treatment decisions. Clinical relevance of genetic variants is a complex problem depending on gene-specific and variant specific genotype-phenotype interactions. To address this challenge, we aimed to characterize the pathogenic landscape of PID genes by combining the analysis of germline variations reported in ClinVar and HGMD[®] and identification of damaging variations available in dbSNP. We generated a joint ClinVar/HGMD database, which included 111,940 variants, among them 32,452 were classified as pathogenic/likely pathogenic. From a total of 5,415,794 bi- or multiallelic variants in PID genes recorded in dbSNP, we retrieved 38,291 high impact (HI) biallelic variants with presumably disruptive impact in the protein, of them 25,500 variants were not present in ClinVar/HGMD. Using a functional prediction algorithm, we additionally identified 28,507 deleterious and 56,016 neutral missense variants among dbSNP variants and created a collection of damaging and neutral variations in PID genes, not currently present in ClinVar/HGMD, with their allele frequencies and mappings to protein domains. The distribution of pathogenic variants from ClinVar/HGMD, HI variants and deleterious missense variants from dbSNP was analyzed in the context of hereditary pattern and gene specific metrics, such as pLI and haploinsufficiency. Our report summarized data on complex gene-specific variability in PID genes and might be useful for the identification of the most promising variants and gene regions for further study.}, } @article {pmid34271370, year = {2021}, author = {Hallard, RI and Wells, A and Aadahl, V and Emsley, R and Pratt, D}, title = {Metacognition, rumination and suicidal ideation: An experience sampling test of the self-regulatory executive function model.}, journal = {Psychiatry research}, volume = {303}, number = {}, pages = {114083}, doi = {10.1016/j.psychres.2021.114083}, pmid = {34271370}, issn = {1872-7123}, mesh = {Anxiety ; Ecological Momentary Assessment ; Executive Function ; Humans ; *Metacognition ; *Suicidal Ideation ; }, abstract = {A relationship between rumination and suicidal ideation is well-evidenced. A role for thought suppression has also been suggested but under-explored. The present study assessed the relative contribution of rumination and a range of thought control strategies in the understanding of suicidal ideation, within the theoretical framework of the self-regulatory executive function (S-REF) model (Wells & Matthews, 2015). Twenty-four participants who had experienced suicidal ideation in the last two months completed trait-level measures of metacognitive beliefs and momentary sampling measures of thought control strategy use, rumination and suicidal ideation over six days. Maladaptive thought control strategy use (worry and punishment), alongside rumination, predicted suicidal ideation. Adaptive strategies (distraction, social control and reappraisal) emerged as negative predictors. Metacognitive beliefs about the need to control thoughts predicted the use of punishment- but not worry-based thought control strategies. Thought control strategy use is as important in the development of suicidal ideation as rumination. The S-REF model represents a promising new approach to understanding these processes in the development of suicidal ideation.}, } @article {pmid34268018, year = {2021}, author = {Caballero, M and Lauer, E and Bennett, J and Zaman, S and McEvoy, S and Acosta, J and Jackson, C and Townsend, L and Eckert, A and Whetten, RW and Loopstra, C and Holliday, J and Mandal, M and Wegrzyn, JL and Isik, F}, title = {Toward genomic selection in Pinus taeda: Integrating resources to support array design in a complex conifer genome.}, journal = {Applications in plant sciences}, volume = {9}, number = {6}, pages = {e11439}, pmid = {34268018}, issn = {2168-0450}, abstract = {PREMISE: An informatics approach was used for the construction of an Axiom genotyping array from heterogeneous, high-throughput sequence data to assess the complex genome of loblolly pine (Pinus taeda).

METHODS: High-throughput sequence data, sourced from exome capture and whole genome reduced-representation approaches from 2698 trees across five sequence populations, were analyzed with the improved genome assembly and annotation for the loblolly pine. A variant detection, filtering, and probe design pipeline was developed to detect true variants across and within populations. From 8.27 million variants, a total of 642,275 were evaluated and 423,695 of those were screened across a range-wide population.

RESULTS: The final informatics and screening approach delivered an Axiom array representing 46,439 high-confidence variants to the forest tree breeding and genetics community. Based on the annotated reference genome, 34% were located in or directly upstream or downstream of genic regions.

DISCUSSION: The Pita50K array represents a genome-wide resource developed from sequence data for an economically important conifer, loblolly pine. It uniquely integrates independent projects that assessed trees sampled across the native range. The challenges associated with the large and repetitive genome are addressed in the development of this resource.}, } @article {pmid34267646, year = {2021}, author = {Stojan, R and Kaushal, N and Bock, OL and Hudl, N and Voelcker-Rehage, C}, title = {Benefits of Higher Cardiovascular and Motor Coordinative Fitness on Driving Behavior Are Mediated by Cognitive Functioning: A Path Analysis.}, journal = {Frontiers in aging neuroscience}, volume = {13}, number = {}, pages = {686499}, pmid = {34267646}, issn = {1663-4365}, abstract = {Driving is an important skill for older adults to maintain an independent lifestyle, and to preserve the quality of life. However, the ability to drive safely in older adults can be compromised by age-related cognitive decline. Performing an additional task during driving (e.g., adjusting the radio) increases cognitive demands and thus might additionally impair driving performance. Cognitive functioning has been shown to be positively related to physical activity/fitness such as cardiovascular and motor coordinative fitness. As such, a higher fitness level might be associated with higher cognitive resources and may therefore benefit driving performance under dual-task conditions. For the first time, the present study investigated whether this association of physical fitness and cognitive functioning causes an indirect relationship between physical fitness and dual-task driving performance through cognitive functions. Data from 120 healthy older adults (age: 69.56 ± 3.62, 53 female) were analyzed. Participants completed tests on cardiovascular fitness (cardiorespiratory capacity), motor coordinative fitness (composite score: static balance, psychomotor speed, bimanual dexterity), and cognitive functions (updating, inhibition, shifting, cognitive processing speed). Further, they performed a virtual car driving scenario where they additionally engaged in cognitively demanding tasks that were modeled after typical real-life activities during driving (typing or reasoning). Structural equation modeling (path analysis) was used to investigate whether cardiovascular and motor coordinative fitness were indirectly associated with lane keeping (i.e., variability in lateral position) and speed control (i.e., average velocity) while dual-task driving via cognitive functions. Both cardiovascular and motor coordinative fitness demonstrated the hypothesized indirect effects on dual-task driving. Motor coordinative fitness showed a significant indirect effect on lane keeping, while cardiovascular fitness demonstrated a trend-level indirect effect on speed control. Moreover, both fitness domains were positively related to different cognitive functions (processing speed and/or updating), and cognitive functions (updating or inhibition), in turn, were related to dual-task driving. These findings indicate that cognitive benefits associated with higher fitness may facilitate driving performance. Given that driving with lower cognitive capacity can result in serious consequences, this study emphasizes the importance for older adults to engage in a physically active lifestyle as it might serve as a preventive measure for driving safety.}, } @article {pmid34267263, year = {2021}, author = {Ekpenyong, ME and Edoho, ME and Inyang, UG and Uzoka, FM and Ekaidem, IS and Moses, AE and Emeje, MO and Tatfeng, YM and Udo, IJ and Anwana, ED and Etim, OE and Geoffery, JI and Dan, EA}, title = {A hybrid computational framework for intelligent inter-continent SARS-CoV-2 sub-strains characterization and prediction.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {14558}, pmid = {34267263}, issn = {2045-2322}, mesh = {COVID-19/epidemiology/transmission/*virology ; Computational Biology/methods ; DNA, Viral/genetics ; Databases, Genetic ; Forecasting/methods ; Genome, Viral ; Humans ; Machine Learning ; Mutation ; Phylogeny ; SARS-CoV-2/classification/*genetics/pathogenicity ; Sequence Analysis, DNA/*methods ; Whole Genome Sequencing/methods ; }, abstract = {Whereas accelerated attention beclouded early stages of the coronavirus spread, knowledge of actual pathogenicity and origin of possible sub-strains remained unclear. By harvesting the Global initiative on Sharing All Influenza Data (GISAID) database (https://www.gisaid.org/), between December 2019 and January 15, 2021, a total of 8864 human SARS-CoV-2 complete genome sequences processed by gender, across 6 continents (88 countries) of the world, Antarctica exempt, were analyzed. We hypothesized that data speak for itself and can discern true and explainable patterns of the disease. Identical genome diversity and pattern correlates analysis performed using a hybrid of biotechnology and machine learning methods corroborate the emergence of inter- and intra- SARS-CoV-2 sub-strains transmission and sustain an increase in sub-strains within the various continents, with nucleotide mutations dynamically varying between individuals in close association with the virus as it adapts to its host/environment. Interestingly, some viral sub-strain patterns progressively transformed into new sub-strain clusters indicating varying amino acid, and strong nucleotide association derived from same lineage. A novel cognitive approach to knowledge mining helped the discovery of transmission routes and seamless contact tracing protocol. Our classification results were better than state-of-the-art methods, indicating a more robust system for predicting emerging or new viral sub-strain(s). The results therefore offer explanations for the growing concerns about the virus and its next wave(s). A future direction of this work is a defuzzification of confusable pattern clusters for precise intra-country SARS-CoV-2 sub-strains analytics.}, } @article {pmid34267209, year = {2021}, author = {Chen, F and Chen, Z and Chen, M and Chen, G and Huang, Q and Yang, X and Yin, H and Chen, L and Zhang, W and Lin, H and Ou, M and Wang, L and Chen, Y and Lin, C and Xu, W and Yin, G}, title = {Reduced stress-associated FKBP5 DNA methylation together with gut microbiota dysbiosis is linked with the progression of obese PCOS patients.}, journal = {NPJ biofilms and microbiomes}, volume = {7}, number = {1}, pages = {60}, pmid = {34267209}, issn = {2055-5008}, mesh = {Adult ; Biodiversity ; Biomarkers ; Case-Control Studies ; Computational Biology ; *DNA Methylation ; Disease Susceptibility ; *Dysbiosis ; Female ; *Gastrointestinal Microbiome ; Humans ; Metabolome ; Metabolomics/methods ; Middle Aged ; Obesity ; Polycystic Ovary Syndrome/diagnosis/*etiology/*metabolism ; *Stress, Physiological ; Tacrolimus Binding Proteins/*genetics ; Young Adult ; }, abstract = {Polycystic ovary syndrome (PCOS) is a common endocrine disease in females that is characterized by hyperandrogenemia, chronic anovulation, and polycystic ovaries. However, the exact etiology and pathogenesis of PCOS are still unknown. The aim of this study was to clarify the bacterial, stress status, and metabolic differences in the gut microbiomes of healthy individuals and patients with high body mass index (BMI) PCOS (PCOS-HB) and normal BMI PCOS (PCOS-LB), respectively. Here, we compared the gut microbiota characteristics of PCOS-HB, PCOS-LB, and healthy controls by 16S rRNA gene sequencing, FK506-binding protein 5 (FKBP5) DNA methylation and plasma metabolite determination. Clinical parameter comparisons indicated that PCOS patients had higher concentrations of total testosterone, androstenedione, dehydroepiandrosterone sulfate, luteinizing hormone, and HOMA-IR while lower FKBP5 DNA methylation. Significant differences in bacterial diversity and community were observed between the PCOS and healthy groups but not between the PCOS-HB and PCOS-LB groups. Bacterial species number was negatively correlated with insulin concentrations (both under fasting status and 120 min after glucose load) and HOMA-IR but positively related to FKBP5 DNA methylation. Compared to the healthy group, both PCOS groups had significant changes in bacterial genera, including Prevotella_9, Dorea, Maihella, and Slackia, and plasma metabolites, including estrone sulfate, lysophosphatidyl choline 18:2, and phosphatidylcholine (22:6e/19:1). The correlation network revealed the complicated interaction of the clinical index, bacterial genus, stress indices, and metabolites. Our work links the stress responses and gut microbiota characteristics of PCOS disease, which might afford perspectives to understand the progression of PCOS.}, } @article {pmid34265094, year = {2021}, author = {Monteiro, J and Pratas, D and Videira, A and Pereira, F}, title = {Revisiting the Neurospora crassa mitochondrial genome.}, journal = {Letters in applied microbiology}, volume = {73}, number = {4}, pages = {495-505}, doi = {10.1111/lam.13538}, pmid = {34265094}, issn = {1472-765X}, support = {SFRH/BD/124406/2016//Fundação para a Ciência e a Tecnologia (FCT)/ ; CI-CTTI-94-ARH/2019//Fundação para a Ciência e a Tecnologia (FCT)/ ; }, mesh = {DNA, Fungal ; DNA, Mitochondrial/genetics ; *Genome, Mitochondrial ; *Neurospora/genetics ; *Neurospora crassa/genetics ; }, abstract = {The mitochondrial genome of Neurospora crassa has been less studied than its nuclear counterpart, yet it holds great potential for understanding the diversity and evolution of this important fungus. Here we describe a new mitochondrial DNA (mtDNA) complete sequence of a N. crassa wild type strain. The genome with 64 839 bp revealed 21 protein-coding genes and several hypothetical open reading frames with no significant homology to any described gene. Five large repetitive regions were identified across the genome, including partial or complete genes. The largest repeated region holds a partial nd2 section that was also detected in Neurospora intermedia, suggesting a rearrangement that occurred before the N. crassa speciation. Interestingly, N. crassa has a palindrome adjacent to the partial nd2 repeated region possibly related to the genomic rearrangement, which is absent in N. intermedia. Finally, we compared the sequences of the three available N. crassa complete mtDNAs and found low levels of intraspecific variability. Most differences among strains were due to small indels in noncoding regions. The revisiting of the N. crassa mtDNA forms the basis for future studies on mitochondrial genome organization and variability.}, } @article {pmid34264935, year = {2021}, author = {Markkula, G and Uludağ, Z and Wilkie, RM and Billington, J}, title = {Accumulation of continuously time-varying sensory evidence constrains neural and behavioral responses in human collision threat detection.}, journal = {PLoS computational biology}, volume = {17}, number = {7}, pages = {e1009096}, pmid = {34264935}, issn = {1553-7358}, support = {/WT_/Wellcome Trust/United Kingdom ; 204825/Z/16/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Adult ; Brain/*physiology ; Computational Biology ; Decision Making/*physiology ; Electroencephalography ; Female ; Humans ; Male ; Middle Aged ; Models, Neurological ; Space Perception/*physiology ; Task Performance and Analysis ; Time Factors ; Young Adult ; }, abstract = {Evidence accumulation models provide a dominant account of human decision-making, and have been particularly successful at explaining behavioral and neural data in laboratory paradigms using abstract, stationary stimuli. It has been proposed, but with limited in-depth investigation so far, that similar decision-making mechanisms are involved in tasks of a more embodied nature, such as movement and locomotion, by directly accumulating externally measurable sensory quantities of which the precise, typically continuously time-varying, magnitudes are important for successful behavior. Here, we leverage collision threat detection as a task which is ecologically relevant in this sense, but which can also be rigorously observed and modelled in a laboratory setting. Conventionally, it is assumed that humans are limited in this task by a perceptual threshold on the optical expansion rate-the visual looming-of the obstacle. Using concurrent recordings of EEG and behavioral responses, we disprove this conventional assumption, and instead provide strong evidence that humans detect collision threats by accumulating the continuously time-varying visual looming signal. Generalizing existing accumulator model assumptions from stationary to time-varying sensory evidence, we show that our model accounts for previously unexplained empirical observations and full distributions of detection response. We replicate a pre-response centroparietal positivity (CPP) in scalp potentials, which has previously been found to correlate with accumulated decision evidence. In contrast with these existing findings, we show that our model is capable of predicting the onset of the CPP signature rather than its buildup, suggesting that neural evidence accumulation is implemented differently, possibly in distinct brain regions, in collision detection compared to previously studied paradigms.}, } @article {pmid34262682, year = {2021}, author = {Rocchini, D and Thouverai, E and Marcantonio, M and Iannacito, M and Da Re, D and Torresani, M and Bacaro, G and Bazzichetto, M and Bernardi, A and Foody, GM and Furrer, R and Kleijn, D and Larsen, S and Lenoir, J and Malavasi, M and Marchetto, E and Messori, F and Montaghi, A and Moudrý, V and Naimi, B and Ricotta, C and Rossini, M and Santi, F and Santos, MJ and Schaepman, ME and Schneider, FD and Schuh, L and Silvestri, S and Ŝímová, P and Skidmore, AK and Tattoni, C and Tordoni, E and Vicario, S and Zannini, P and Wegmann, M}, title = {rasterdiv-An Information Theory tailored R package for measuring ecosystem heterogeneity from space: To the origin and back.}, journal = {Methods in ecology and evolution}, volume = {12}, number = {6}, pages = {1093-1102}, pmid = {34262682}, issn = {2041-210X}, abstract = {Ecosystem heterogeneity has been widely recognized as a key ecological indicator of several ecological functions, diversity patterns and change, metapopulation dynamics, population connectivity or gene flow.In this paper, we present a new R package-rasterdiv-to calculate heterogeneity indices based on remotely sensed data. We also provide an ecological application at the landscape scale and demonstrate its power in revealing potentially hidden heterogeneity patterns.The rasterdiv package allows calculating multiple indices, robustly rooted in Information Theory, and based on reproducible open-source algorithms.}, } @article {pmid34261051, year = {2021}, author = {Wollschläger, D and Auvinen, A and Blettner, M and Zeeb, H}, title = {Methodological considerations for interrupted time series analysis in radiation epidemiology: an overview.}, journal = {Journal of radiological protection : official journal of the Society for Radiological Protection}, volume = {41}, number = {4}, pages = {}, doi = {10.1088/1361-6498/ac149c}, pmid = {34261051}, issn = {1361-6498}, mesh = {Forecasting ; Interrupted Time Series Analysis ; *Research Design ; }, abstract = {Interrupted time series analysis (ITSA) is a method that can be applied to evaluate health outcomes in populations exposed to ionizing radiation following major radiological events. Using aggregated time series data, ITSA evaluates whether the time trend of a health indicator shows a change associated with the radiological event. That is, ITSA checks whether there is a statistically significant discrepancy between the projection of a pre-event trend and the data empirically observed after the event. Conducting ITSA requires one to consider specific methodological issues due to unique threats to internal validity that make ITSA prone to bias. We here discuss the strengths and limitations of ITSA with respect to bias and confounding, data quality, and statistical aspects. We provide recommendations to strengthen the robustness of ITSA studies and reduce their susceptibility to producing spurious results as a consequence of arbitrary modelling decisions.}, } @article {pmid34260961, year = {2021}, author = {Levi, A and Barnett-Itzhaki, Z}, title = {Effects of chronic exposure to ambient air pollutants, demographic, and socioeconomic factors on COVID-19 morbidity: The Israeli case study.}, journal = {Environmental research}, volume = {202}, number = {}, pages = {111673}, pmid = {34260961}, issn = {1096-0953}, mesh = {*Air Pollutants/adverse effects/analysis ; *Air Pollution/adverse effects/analysis ; *COVID-19/epidemiology ; Environmental Exposure/adverse effects/analysis ; Humans ; Israel/epidemiology ; Morbidity ; Particulate Matter/adverse effects/analysis ; Socioeconomic Factors ; }, abstract = {BACKGROUND: Recent studies conducted in several OECD countries have shown that chronic exposure to elevated levels of air pollutants (especially PM2.5, PM10 and NOx), might negatively impact COVID-19 morbidity and mortality rates. The aim of this study was to examine the association between chronic exposure to air pollution in Israeli cities and towns, their demographic and socioeconomic status, and COVID-19 morbidity, during the three local morbidity waves.

METHODS: We examined the associations between: (a) annual average concentrations of NOx, CO, PM10, PM2.5 and SO2 in 2016-2019, and demographic and socioeconomic parameters, and (b) COVID-19 positive cases in 279 Israeli cities and towns, in the four state-wide morbidity peaks: 1[st] wave peak: March 31[st], 2020; 2[nd] wave peaks: July 24[th] and September 27[th], 2020, and the 3[rd] wave peak: January 17[th], 2021, which occurred after the beginning of the nationwide vaccination campaign. These associations were calculated using both Spearman correlations and multivariate linear regressions.

RESULTS: We found statistically significant positive correlations between the concentrations of most pollutants in 2016-19 and COVID-19 morbidity rate at the first three timepoints but not the 4t[h] (January 17[th], 2021). Population density and city/town total population were also positively associated with the COVID-19 morbidity rates at these three timepoints, but not the 4[th], in which socioeconomic parameters were more dominant - we found a statistically significant negative correlation between socioeconomic cluster and COVID-19 morbidity. In addition, all multivariate models including PM2.5 concentrations were statistically significant, and PM2.5 concentrations were positively associated with the COVID-19 morbidity rates in all models.

CONCLUSIONS: We found a nationwide association between population chronic exposure to five main air pollutants in Israeli cities and towns, and COVID-19 morbidity rates during two of the three morbidity waves experienced in Israel. The widespread morbidity that was related to socioeconomic factors during the 3[rd] wave, emphasizes the need for special attention to morbidity prevention in socioeconomically vulnerable populations and especially in large household communities. Nevertheless, this ecological study has several limitations, such as the inability to draw conclusions about causality or mechanisms of action. The growing body of evidence, regarding association between exacerbated COVID-19 morbidity and mortality rates and long-term chronic exposure to elevated concentrations of air pollutants should serve as a wake-up call to policy makers regarding the urgent need to reduce air pollution and its harmful effects.}, } @article {pmid34260303, year = {2021}, author = {Feller, FM and Wöhlbrand, L and Holert, J and Schnaars, V and Elsner, L and Mohn, WW and Rabus, R and Philipp, B}, title = {Proteome, Bioinformatic, and Functional Analyses Reveal a Distinct and Conserved Metabolic Pathway for Bile Salt Degradation in the Sphingomonadaceae.}, journal = {Applied and environmental microbiology}, volume = {87}, number = {19}, pages = {e0098721}, pmid = {34260303}, issn = {1098-5336}, mesh = {Bacterial Proteins/genetics/metabolism ; Bile Acids and Salts/*metabolism ; Biodegradation, Environmental ; Computational Biology ; Metabolic Networks and Pathways ; Proteome ; Sphingomonadaceae/genetics/*metabolism ; }, abstract = {Bile salts are amphiphilic steroids with digestive functions in vertebrates. Upon excretion, bile salts are degraded by environmental bacteria. Degradation of the bile salt steroid skeleton resembles the well-studied pathway for other steroids, like testosterone, while specific differences occur during side chain degradation and the initiating transformations of the steroid skeleton. Of the latter, two variants via either Δ[1,4]- or Δ[4,6]-3-ketostructures of the steroid skeleton exist for 7-hydroxy bile salts. While the Δ[1,4] variant is well known from many model organisms, the Δ[4,6] variant involving a 7-hydroxysteroid dehydratase as a key enzyme has not been systematically studied. Here, combined proteomic, bioinformatic, and functional analyses of the Δ[4,6] variant in Sphingobium sp. strain Chol11 were performed. They revealed a degradation of the steroid rings similar to that of the Δ[1,4] variant except for the elimination of the 7-OH as a key difference. In contrast, differential production of the respective proteins revealed a putative gene cluster for the degradation of the C5 carboxylic side chain encoding a CoA ligase, an acyl-CoA dehydrogenase, a Rieske monooxygenase, and an amidase but lacking most canonical genes known from other steroid-degrading bacteria. Bioinformatic analyses predicted the Δ[4,6] variant to be widespread among the Sphingomonadaceae, which was verified for three type strains which also have the predicted side chain degradation cluster. A second amidase in the side chain degradation gene cluster of strain Chol11 was shown to cleave conjugated bile salts while having low similarity to known bile salt hydrolases. This study identifies members of the Sphingomonadaceae that are remarkably well adapted to the utilization of bile salts via a partially distinct metabolic pathway. IMPORTANCE This study highlights the biochemical diversity of bacterial degradation of steroid compounds, in particular bile salts. Furthermore, it substantiates and advances knowledge of a variant pathway for degradation of steroids by sphingomonads, a group of environmental bacteria that are well known for their broad metabolic capabilities. Biodegradation of bile salts is a critical process due to the high input of these compounds from manure into agricultural soils and wastewater treatment plants. In addition, these results may also be relevant for the biotechnological production of bile salts or other steroid compounds with pharmaceutical functions.}, } @article {pmid34258685, year = {2021}, author = {Carpio, LE and Sanz, Y and Gozalbes, R and Barigye, SJ}, title = {Computational strategies for the discovery of biological functions of health foods, nutraceuticals and cosmeceuticals: a review.}, journal = {Molecular diversity}, volume = {25}, number = {3}, pages = {1425-1438}, pmid = {34258685}, issn = {1573-501X}, support = {INNTAL32/19/002//Agencia Valenciana de la Investigación/ ; 893810//H2020 Marie Skłodowska-Curie Actions/ ; }, mesh = {Algorithms ; Cheminformatics/*methods ; Cosmeceuticals/*chemistry/pharmacology ; Databases, Chemical ; Dietary Supplements/*analysis ; Functional Food/*analysis ; Humans ; Machine Learning ; *Models, Molecular ; Molecular Docking Simulation ; Molecular Dynamics Simulation ; *Quantitative Structure-Activity Relationship ; }, abstract = {Scientific and consumer interest in healthy foods (also known as functional foods), nutraceuticals and cosmeceuticals has increased in the recent years, leading to an increased presence of these products in the market. However, the regulations across different countries that define the type of claims that may be made, and the degree of evidence required to support these claims, are rather inconsistent. Moreover, there is also controversy on the effectiveness and biological mode of action of many of these products, which should undergo an exhaustive approval process to guarantee the consumer rights. Computational approaches constitute invaluable tools to facilitate the discovery of bioactive molecules and provide biological plausibility on the mode of action of these products. Indeed, methodologies like QSAR, docking or molecular dynamics have been used in drug discovery protocols for decades and can now aid in the discovery of bioactive food components. Thanks to these approaches, it is possible to search for new functions in food constituents, which may be part of our daily diet, and help to prevent disorders like diabetes, hypercholesterolemia or obesity. In the present manuscript, computational studies applied to this field are reviewed to illustrate the potential of these approaches to guide the first screening steps and the mechanistic studies of nutraceutical, cosmeceutical and functional foods.}, } @article {pmid34253732, year = {2021}, author = {Mehrshad, M and Lopez-Fernandez, M and Sundh, J and Bell, E and Simone, D and Buck, M and Bernier-Latmani, R and Bertilsson, S and Dopson, M}, title = {Energy efficiency and biological interactions define the core microbiome of deep oligotrophic groundwater.}, journal = {Nature communications}, volume = {12}, number = {1}, pages = {4253}, pmid = {34253732}, issn = {2041-1723}, mesh = {Biodiversity ; Databases, Genetic ; *Energy Metabolism ; Gene Expression Regulation ; Groundwater/*microbiology ; Isoelectric Point ; Metagenome ; *Microbiota/genetics ; Phylogeny ; Transcription, Genetic ; Transcriptome/genetics ; }, abstract = {While oligotrophic deep groundwaters host active microbes attuned to the low-end of the bioenergetics spectrum, the ecological constraints on microbial niches in these ecosystems and their consequences for microbiome convergence are unknown. Here, we provide a genome-resolved, integrated omics analysis comparing archaeal and bacterial communities in disconnected fracture fluids of the Fennoscandian Shield in Europe. Leveraging a dataset that combines metagenomes, single cell genomes, and metatranscriptomes, we show that groundwaters flowing in similar lithologies offer fixed niches that are occupied by a common core microbiome. Functional expression analysis highlights that these deep groundwater ecosystems foster diverse, yet cooperative communities adapted to this setting. We suggest that these communities stimulate cooperation by expression of functions related to ecological traits, such as aggregate or biofilm formation, while alleviating the burden on microorganisms producing compounds or functions that provide a collective benefit by facilitating reciprocal promiscuous metabolic partnerships with other members of the community. We hypothesize that an episodic lifestyle enabled by reversible bacteriostatic functions ensures the subsistence of the oligotrophic deep groundwater microbiome.}, } @article {pmid34253230, year = {2021}, author = {Palatini, U and Masri, RA and Cosme, LV and Koren, S and Thibaud-Nissen, F and Biedler, JK and Krsticevic, F and Johnston, JS and Halbach, R and Crawford, JE and Antoshechkin, I and Failloux, AB and Pischedda, E and Marconcini, M and Ghurye, J and Rhie, A and Sharma, A and Karagodin, DA and Jenrette, J and Gamez, S and Miesen, P and Masterson, P and Caccone, A and Sharakhova, MV and Tu, Z and Papathanos, PA and Van Rij, RP and Akbari, OS and Powell, J and Phillippy, AM and Bonizzoni, M}, title = {Author Correction: Improved reference genome of the arboviral vector Aedes albopictus.}, journal = {Genome biology}, volume = {22}, number = {1}, pages = {205}, pmid = {34253230}, issn = {1474-760X}, } @article {pmid34252299, year = {2021}, author = {Jones, S and Kay, K and Hodel, EM and Gruenberg, M and Lerch, A and Felger, I and Hastings, I}, title = {Should Deep-Sequenced Amplicons Become the New Gold Standard for Analyzing Malaria Drug Clinical Trials?.}, journal = {Antimicrobial agents and chemotherapy}, volume = {65}, number = {10}, pages = {e0043721}, pmid = {34252299}, issn = {1098-6596}, support = {MR/L022508/1/MRC_/Medical Research Council/United Kingdom ; UWSC9757//Malaria Modelling Consortium/ ; 1032350//Bill and Melinda Gates Foundation (BMGF)/ ; G1100522/MRC_/Medical Research Council/United Kingdom ; G1100522//UKRI | Medical Research Council (MRC)/ ; 310030_159580/SNSF_/Swiss National Science Foundation/Switzerland ; }, mesh = {*Antimalarials/therapeutic use ; Humans ; *Malaria/drug therapy ; *Malaria, Falciparum/drug therapy ; *Pharmaceutical Preparations ; Plasmodium falciparum/genetics ; }, abstract = {Regulatory clinical trials are required to ensure the continued supply and deployment of effective antimalarial drugs. Patient follow-up in such trials typically lasts several weeks, as the drugs have long half-lives and new infections often occur during this period. "Molecular correction" is therefore used to distinguish drug failures from new infections. The current WHO-recommended method for molecular correction uses length-polymorphic alleles at highly diverse loci but is inherently poor at detecting low-density clones in polyclonal infections. This likely leads to substantial underestimates of failure rates, delaying the replacement of failing drugs with potentially lethal consequences. Deep-sequenced amplicons (AmpSeq) substantially increase the detectability of low-density clones and may offer a new "gold standard" for molecular correction. Pharmacological simulation of clinical trials was used to evaluate the suitability of AmpSeq for molecular correction. We investigated the impact of factors such as the number of amplicon loci analyzed, the informatics criteria used to distinguish genotyping "noise" from real low-density signals, the local epidemiology of malaria transmission, and the potential impact of genetic signals from gametocytes. AmpSeq greatly improved molecular correction and provided accurate drug failure rate estimates. The use of 3 to 5 amplicons was sufficient, and simple, nonstatistical criteria could be used to classify recurrent infections as drug failures or new infections. These results suggest AmpSeq is strongly placed to become the new standard for molecular correction in regulatory trials, with potential extension into routine surveillance once the requisite technical support becomes established.}, } @article {pmid34244702, year = {2021}, author = {Mahé, F and Czech, L and Stamatakis, A and Quince, C and de Vargas, C and Dunthorn, M and Rognes, T}, title = {Swarm v3: towards tera-scale amplicon clustering.}, journal = {Bioinformatics (Oxford, England)}, volume = {38}, number = {1}, pages = {267-269}, pmid = {34244702}, issn = {1367-4811}, support = {BBS/E/T/000PR9817/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; GBMF5275//Gordon and Betty Moore Foundation/ ; #DU1319/5-1//Klaus Tschira Foundation, and the Deutsche Forschungsgemeinschaft/ ; }, mesh = {*Software ; Cluster Analysis ; }, abstract = {MOTIVATION: Previously we presented swarm, an open-source amplicon clustering programme that produces fine-scale molecular operational taxonomic units (OTUs) that are free of arbitrary global clustering thresholds. Here, we present swarm v3 to address issues of contemporary datasets that are growing towards tera-byte sizes.

RESULTS: When compared with previous swarm versions, swarm v3 has modernized C++ source code, reduced memory footprint by up to 50%, optimized CPU-usage and multithreading (more than 7 times faster with default parameters), and it has been extensively tested for its robustness and logic.

Source code and binaries are available at https://github.com/torognes/swarm.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, } @article {pmid34244416, year = {2021}, author = {Toda, Y and Ko, MC and Liang, Q and Miller, ET and Rico-Guevara, A and Nakagita, T and Sakakibara, A and Uemura, K and Sackton, T and Hayakawa, T and Sin, SYW and Ishimaru, Y and Misaka, T and Oteiza, P and Crall, J and Edwards, SV and Buttemer, W and Matsumura, S and Baldwin, MW}, title = {Early origin of sweet perception in the songbird radiation.}, journal = {Science (New York, N.Y.)}, volume = {373}, number = {6551}, pages = {226-231}, doi = {10.1126/science.abf6505}, pmid = {34244416}, issn = {1095-9203}, mesh = {Amino Acids ; Animals ; Avian Proteins/chemistry/metabolism ; *Biological Evolution ; Birds/physiology ; Carbohydrates ; Diet ; Feeding Behavior ; *Plant Nectar ; Protein Multimerization ; Receptors, G-Protein-Coupled/*chemistry/*metabolism ; Songbirds/*physiology ; Sucrose ; *Taste Perception ; }, abstract = {Early events in the evolutionary history of a clade can shape the sensory systems of descendant lineages. Although the avian ancestor may not have had a sweet receptor, the widespread incidence of nectar-feeding birds suggests multiple acquisitions of sugar detection. In this study, we identify a single early sensory shift of the umami receptor (the T1R1-T1R3 heterodimer) that conferred sweet-sensing abilities in songbirds, a large evolutionary radiation containing nearly half of all living birds. We demonstrate sugar responses across species with diverse diets, uncover critical sites underlying carbohydrate detection, and identify the molecular basis of sensory convergence between songbirds and nectar-specialist hummingbirds. This early shift shaped the sensory biology of an entire radiation, emphasizing the role of contingency and providing an example of the genetic basis of convergence in avian evolution.}, } @article {pmid34243703, year = {2021}, author = {Lin, CW and Hong, Y and Liu, J}, title = {Aggregation-and-Attention Network for brain tumor segmentation.}, journal = {BMC medical imaging}, volume = {21}, number = {1}, pages = {109}, pmid = {34243703}, issn = {1471-2342}, mesh = {Algorithms ; Brain Neoplasms/*diagnostic imaging ; Diagnosis, Computer-Assisted ; Glioma/*diagnostic imaging ; Humans ; Magnetic Resonance Imaging/*methods ; *Neural Networks, Computer ; Supervised Machine Learning ; }, abstract = {BACKGROUND: Glioma is a malignant brain tumor; its location is complex and is difficult to remove surgically. To diagnosis the brain tumor, doctors can precisely diagnose and localize the disease using medical images. However, the computer-assisted diagnosis for the brain tumor diagnosis is still the problem because the rough segmentation of the brain tumor makes the internal grade of the tumor incorrect.

METHODS: In this paper, we proposed an Aggregation-and-Attention Network for brain tumor segmentation. The proposed network takes the U-Net as the backbone, aggregates multi-scale semantic information, and focuses on crucial information to perform brain tumor segmentation. To this end, we proposed an enhanced down-sampling module and Up-Sampling Layer to compensate for the information loss. The multi-scale connection module is to construct the multi-receptive semantic fusion between encoder and decoder. Furthermore, we designed a dual-attention fusion module that can extract and enhance the spatial relationship of magnetic resonance imaging and applied the strategy of deep supervision in different parts of the proposed network.

RESULTS: Experimental results show that the performance of the proposed framework is the best on the BraTS2020 dataset, compared with the-state-of-art networks. The performance of the proposed framework surpasses all the comparison networks, and its average accuracies of the four indexes are 0.860, 0.885, 0.932, and 1.2325, respectively.

CONCLUSIONS: The framework and modules of the proposed framework are scientific and practical, which can extract and aggregate useful semantic information and enhance the ability of glioma segmentation.}, } @article {pmid34241945, year = {2022}, author = {Dubé, MG and Dunlop, JM and Davidson, C and Beausoleil, DL and Hazewinkel, RRO and Wyatt, F}, title = {History, overview, and governance of environmental monitoring in the oil sands region of Alberta, Canada.}, journal = {Integrated environmental assessment and management}, volume = {18}, number = {2}, pages = {319-332}, pmid = {34241945}, issn = {1551-3793}, support = {//Oil Sands Monitoring Program/ ; }, mesh = {Alberta ; *Environmental Monitoring/methods ; *Oil and Gas Fields ; }, abstract = {Over the past decades, concerns regarding the local and cumulative impacts of oil sands development have been increasing. These concerns reflect the industry's emissions, land disturbance, water use, and the resulting impacts to Indigenous Rights. Effective environmental management is essential to address and ultimately manage these concerns. A series of ambient regional monitoring programs in the oil sands region (OSR) have struggled with scope and governance. In the last 10 years, monitoring has evolved from a regulatory-driven exercise implemented by industry into a focused, collaborative, multistakeholder program that attempts to integrate rigorous science from a multitude of disciplines and ways of knowing. Monitoring in the region continues to grapple with leadership, governance, data management, scope, and effective analysis and reporting. This special series, "A Decade of Research and Monitoring in the Oil Sands Region of Alberta, Canada," provides a series of critical reviews that synthesize 10 years of published monitoring results to identify patterns of consistent ecological responses or effects, significant gaps in knowledge, and recommendations for improved monitoring, assessment, and management of the region. The special series considered over 300 peer-reviewed papers and represents the first integrated critical review of the published literature from the region. This introductory paper of the series introduces the history of ambient environmental monitoring in the OSR and discusses historic and ongoing challenges with the environmental monitoring effort. While significant progress has been made in areas of governance, expanded geographical scope, and inclusion of Indigenous communities in monitoring in the region, significant issues remain regarding a lack of integrated reporting on environmental conditions, public access to data, and continuity of monitoring efforts over time. Integr Environ Assess Manag 2022;18:319-332. © 2021 The Authors. Integrated Environmental Assessment and Management published by Wiley Periodicals LLC on behalf of Society of Environmental Toxicology & Chemistry (SETAC).}, } @article {pmid34241589, year = {2021}, author = {Neukirchen, S and Sousa, FL}, title = {DiSCo: a sequence-based type-specific predictor of Dsr-dependent dissimilatory sulphur metabolism in microbial data.}, journal = {Microbial genomics}, volume = {7}, number = {7}, pages = {}, pmid = {34241589}, issn = {2057-5858}, mesh = {Archaea/enzymology/*genetics ; Archaeal Proteins/genetics/metabolism ; Bacteria/enzymology/*genetics ; Bacterial Proteins/genetics/metabolism ; Computational Biology/*methods ; Genome, Archaeal/genetics ; Genome, Bacterial/genetics ; Genomics/methods ; Hydrogensulfite Reductase/genetics/*metabolism ; Oxidation-Reduction ; Sulfur/*metabolism ; }, abstract = {Current methods in comparative genomic analyses for metabolic potential prediction of proteins involved in, or associated with the Dsr (dissimilatory sulphite reductase)-dependent dissimilatory sulphur metabolism are both time-intensive and computationally challenging, especially when considering metagenomic data. We developed DiSCo, a Dsr-dependent dissimilatory sulphur metabolism classification tool, which automatically identifies and classifies the protein type from sequence data. It takes user-supplied protein sequences and lists the identified proteins and their classification in terms of protein family and predicted type. It can also extract the sequence data from user-input to serve as basis for additional downstream analyses. DiSCo provides the metabolic functional prediction of proteins involved in Dsr-dependent dissimilatory sulphur metabolism with high levels of accuracy in a fast manner. We ran DiSCo against a dataset composed of over 190 thousand (meta)genomic records and efficiently mapped Dsr-dependent dissimilatory sulphur proteins in 1798 lineages across both prokaryotic domains. This allowed the identification of new micro-organisms belonging to Thaumarchaeota and Spirochaetes lineages with the metabolic potential to use the Dsr-pathway for energy conservation. DiSCo is implemented in Perl 5 and freely available under the GNU GPLv3 at https://github.com/Genome-Evolution-and-Ecology-Group-GEEG/DiSCo.}, } @article {pmid34236030, year = {2021}, author = {Guo, W and Zhan, X and Jiang, F and Xi, Y}, title = {[Bioinformatics analysis, prokaryotic expression and biological activity of HSP70 domain-containing proteins derived from pollen of Populus deltoides].}, journal = {Xi bao yu fen zi mian yi xue za zhi = Chinese journal of cellular and molecular immunology}, volume = {37}, number = {8}, pages = {710-715}, pmid = {34236030}, issn = {1007-8738}, mesh = {Allergens ; Animals ; Blotting, Western ; Computational Biology ; Epitopes ; Mice ; Pollen/genetics ; *Populus/genetics ; }, abstract = {Objective To study the bioinformatics characteristics of HSP70 domain proteins derived from pollen of Populus deltoides (P. deltoides), optimize the prokaryotic expression methods, and identify the biological activity of these proteins. Methods Physicochemical characteristics of three kinds of HSP70 domain-containing proteins were analyzed by bioinformatics software. The T/B cell epitopes of these proteins were predicted by Immune Epitope Database and Analysis Resource (IEDB). According to the amino acid sequence provided by Uniprot database, their nucleotide sequences were synthesized and cloned into pET28a(+) plasmid for prokaryotic expression. Protein expression was detected by SDS-PAGE, then the expressed products were purified by nickel column and identified by Western blotting. The protein concentration was measured by protein quantitative kit. Then the three proteins were used as antigens to prepare mouse asthma models, and the concentration of serum total IgE antibody was determined by ELISA. Results The bioinformatics analysis showed that the relative molecular mass (Mr) of B9N9W6, B9GX02 and A0A2K2AYN8 were 71 900, 94 600 and 75 200, respectively. The 13 T-cell epitopes and 14 B-cell epitopes were identified in the three proteins which had high hydrophilia and stability. SDS-PAGE analysis revealed that the genes encoding the three proteins were expressed with three specific bands of approximately Mr 72 000, 95 000 and 75 000, respectively. Western blotting showed the specific bands at the corresponding sites. ELISA showed that the IgE level in the extract group and the A0A2K2AYN8 group were higher than that in the PBS group. Compared with the A0A2K2AYN8 group, the IgE concentration in the B9N9W6 group and B9GX02 group increased significantly. Conclusion The soluble HSP70 domain-containing proteins A0A2K2AYN8, B9GX02 and B9N9W6 derived from pollen of P. deltoides can be expressed as well as purified, and have the biological activity of producing IgE antibodies.}, } @article {pmid34235698, year = {2021}, author = {Cao, Y and Cui, Y and Yu, X and Li, T and Chang, IS and Wu, J}, title = {Bibliometric analysis of phosphogypsum research from 1990 to 2020 based on literatures and patents.}, journal = {Environmental science and pollution research international}, volume = {28}, number = {47}, pages = {66845-66857}, pmid = {34235698}, issn = {1614-7499}, support = {2018YFC1903604//National Basic Research Program of China (973 Program)/ ; }, mesh = {*Bibliometrics ; Calcium Sulfate ; Databases, Factual ; Phosphorus ; *Publications ; Technology ; }, abstract = {The demand together with the urgency of phosphogypsum (PG) treatment will pose significant challenges for many countries. This research aims to explore the research progress of PG, including basic status, cooperation situation, research fields, and development trends, based on the Web of Science database through bibliometric analysis of publications (articles and patents) from 1990 to 2020. The results show that academic research on PG originated early, but the number of patents grew quickly. China is a global leader in terms of the number of publications and plays a significant role in international cooperation. The knowledge of PG has remained concentrated in the fields of natural radioactivity, cement paste backfilling, soil, crystal morphology, and synthetic gas. However, academic hotspots focus on the microstructure of chemical processes and various environmental impacts; patents and hot technologies are based on the production of refractory materials, ceramics, surface materials, cement mortar, and composite materials. The academic frontiers of PG will be centered on exploiting the methods of recovering rare earth elements from PG, the conditions of ion solidification/stabilization in PG, the impact of reaction conditions on product quality, and the reaction mechanism at the micro-level. The frontiers of patents need to focus on the improvement of manufacturing equipment, new wall materials, and chemically modified polymer materials. Envisaging the number of articles and patents to be published in the future, architectural research has a large room for improvement. This paper conducts an in-depth analysis of PG and provides information on the technological development prospects and opportunities, which is helpful for researchers engaged in PG management.}, } @article {pmid34234337, year = {2021}, author = {Gomez, M and Mejia, A and Ruddell, BL and Rushforth, RR}, title = {Supply chain diversity buffers cities against food shocks.}, journal = {Nature}, volume = {595}, number = {7866}, pages = {250-254}, pmid = {34234337}, issn = {1476-4687}, mesh = {Cities/statistics & numerical data ; Food/*statistics & numerical data ; Food Supply/*methods ; Humans ; Models, Statistical ; Probability ; Reproducibility of Results ; *Risk Management ; United States ; }, abstract = {Food supply shocks are increasing worldwide[1,2], particularly the type of shock wherein food production or distribution loss in one location propagates through the food supply chain to other locations[3,4]. Analogous to biodiversity buffering ecosystems against external shocks[5,6], ecological theory suggests that food supply chain diversity is crucial for managing the risk of food shock to human populations[7,8]. Here we show that boosting a city's food supply chain diversity increases the resistance of a city to food shocks of mild to moderate severity by up to 15 per cent. We develop an intensity-duration-frequency model linking food shock risk to supply chain diversity. The empirical-statistical model is based on annual food inflow observations from all metropolitan areas in the USA during the years 2012 to 2015, years when most of the country experienced moderate to severe droughts. The model explains a city's resistance to food shocks of a given frequency, intensity and duration as a monotonically declining function of the city's food inflow supply chain's Shannon diversity. This model is simple, operationally useful and addresses any kind of hazard. Using this method, cities can improve their resistance to food supply shocks with policies that increase the food supply chain's diversity.}, } @article {pmid34234328, year = {2021}, author = {Queiroz, N and Humphries, NE and Couto, A and Vedor, M and da Costa, I and Sequeira, AMM and Mucientes, G and Santos, AM and Abascal, FJ and Abercrombie, DL and Abrantes, K and Acuña-Marrero, D and Afonso, AS and Afonso, P and Anders, D and Araujo, G and Arauz, R and Bach, P and Barnett, A and Bernal, D and Berumen, ML and Lion, SB and Bezerra, NPA and Blaison, AV and Block, BA and Bond, ME and Bonfil, R and Braun, CD and Brooks, EJ and Brooks, A and Brown, J and Byrne, ME and Campana, SE and Carlisle, AB and Chapman, DD and Chapple, TK and Chisholm, J and Clarke, CR and Clua, EG and Cochran, JEM and Crochelet, EC and Dagorn, L and Daly, R and Cortés, DD and Doyle, TK and Drew, M and Duffy, CAJ and Erikson, T and Espinoza, E and Ferreira, LC and Ferretti, F and Filmalter, JD and Fischer, GC and Fitzpatrick, R and Fontes, J and Forget, F and Fowler, M and Francis, MP and Gallagher, AJ and Gennari, E and Goldsworthy, SD and Gollock, MJ and Green, JR and Gustafson, JA and Guttridge, TL and Guzman, HM and Hammerschlag, N and Harman, L and Hazin, FHV and Heard, M and Hearn, AR and Holdsworth, JC and Holmes, BJ and Howey, LA and Hoyos, M and Hueter, RE and Hussey, NE and Huveneers, C and Irion, DT and Jacoby, DMP and Jewell, OJD and Johnson, R and Jordan, LKB and Joyce, W and Keating Daly, CA and Ketchum, JT and Klimley, AP and Kock, AA and Koen, P and Ladino, F and Lana, FO and Lea, JSE and Llewellyn, F and Lyon, WS and MacDonnell, A and Macena, BCL and Marshall, H and McAllister, JD and Meÿer, MA and Morris, JJ and Nelson, ER and Papastamatiou, YP and Peñaherrera-Palma, C and Pierce, SJ and Poisson, F and Quintero, LM and Richardson, AJ and Rogers, PJ and Rohner, CA and Rowat, DRL and Samoilys, M and Semmens, JM and Sheaves, M and Shillinger, G and Shivji, M and Singh, S and Skomal, GB and Smale, MJ and Snyders, LB and Soler, G and Soria, M and Stehfest, KM and Thorrold, SR and Tolotti, MT and Towner, A and Travassos, P and Tyminski, JP and Vandeperre, F and Vaudo, JJ and Watanabe, YY and Weber, SB and Wetherbee, BM and White, TD and Williams, S and Zárate, PM and Harcourt, R and Hays, GC and Meekan, MG and Thums, M and Irigoien, X and Eguiluz, VM and Duarte, CM and Sousa, LL and Simpson, SJ and Southall, EJ and Sims, DW}, title = {Reply to: Caution over the use of ecological big data for conservation.}, journal = {Nature}, volume = {595}, number = {7866}, pages = {E20-E28}, pmid = {34234328}, issn = {1476-4687}, mesh = {*Big Data ; Conservation of Natural Resources ; *Ecology ; }, } @article {pmid34234327, year = {2021}, author = {Harry, AV and Braccini, JM}, title = {Caution over the use of ecological big data for conservation.}, journal = {Nature}, volume = {595}, number = {7866}, pages = {E17-E19}, pmid = {34234327}, issn = {1476-4687}, mesh = {*Big Data ; Conservation of Natural Resources ; *Ecology ; }, } @article {pmid34228729, year = {2021}, author = {Ackley, C and Elsheikh, M and Zaman, S}, title = {Scoping review of Neglected Tropical Disease Interventions and Health Promotion: A framework for successful NTD interventions as evidenced by the literature.}, journal = {PLoS neglected tropical diseases}, volume = {15}, number = {7}, pages = {e0009278}, pmid = {34228729}, issn = {1935-2735}, support = {/DH_/Department of Health/United Kingdom ; }, mesh = {Animals ; Data Management ; Health Promotion/*methods ; Humans ; Neglected Diseases/*epidemiology/prevention & control ; Public Health/education ; Tropical Medicine/*education ; }, abstract = {BACKGROUND: Neglected Tropical Diseases (NTDs) affect more than one billion people globally. A Public Library of Science (PLOS) journal dedicated to NTDs lists almost forty NTDs, while the WHO prioritises twenty NTDs. A person can be affected by more than one disease at the same time from a range of infectious and non-infectious agents. Many of these diseases are preventable, and could be eliminated with various public health, health promotion and medical interventions. This scoping review aims to determine the extent of the body of literature on NTD interventions and health promotion activities, and to provide an overview of their focus while providing recommendations for best practice going forward. This scoping review includes both the identification of relevant articles through the snowball method and an electronic database using key search terms. A two-phased screening process was used to assess the relevance of studies identified in the search-an initial screening review followed by data characterization using the Critical Appraisal Skills Program (CASP). Studies were eligible for inclusion if they broadly described the characteristics, methods, and approaches of (1) NTD interventions and/or (2) community health promotion.

PRINCIPAL FINDINGS: 90 articles met the CASP criteria partially or fully and then underwent a qualitative synthesis to be included in the review. 75 articles specifically focus on NTD interventions and approaches to their control, treatment, and elimination, while 15 focus specifically on health promotion and provide a grounding in health promotion theories and perspectives. 29 of the articles provided a global perspective to control, treatment, or elimination of NTDs through policy briefs or literature reviews. 19 of the articles focused on providing strategies for NTDs more generally while 12 addressed multiple NTDs or their interaction with other infectious diseases. Of the 20 NTDs categorized by the WHO and the expanded NTD list identified by PLOS NTDs, several NTDs did not appear in the database search on NTD interventions and health promotion, including yaws, fascioliasis, and chromoblastomycosis.

CONCLUSIONS: Based on the literature we have identified the four core components of best practices including programmatic interventions, multi sectoral and multi-level interventions, adopting a social and ecological model and clearly defining 'community.' NTD interventions tend to centre on mass drug administration (MDA), particularly because NTDs were branded as such based on their being amenable to MDA. However, there remains a need for intervention approaches that also include multiple strategies that inform a larger multi-disease and multi-sectoral programme. Many NTD strategies include a focus on WASH and should also incorporate the social and ecological determinants of NTDs, suggesting a preventative and systems approach to health, not just a treatment-based approach. Developing strong communities and incorporating social rehabilitation at the sublocation level (e.g. hospital) could benefit several NTDs and infectious diseases through a multi-disease, multi-sectoral, and multi-lateral approach. Finally, it is important the 'community' is clearly defined in each intervention, and that community members are included in intervention activities and viewed as assets to interventions.}, } @article {pmid34226152, year = {2021}, author = {Askar, M and Cañadas, RN and Svendsen, K}, title = {An introduction to network analysis for studies of medication use.}, journal = {Research in social & administrative pharmacy : RSAP}, volume = {17}, number = {12}, pages = {2054-2061}, doi = {10.1016/j.sapharm.2021.06.021}, pmid = {34226152}, issn = {1934-8150}, mesh = {Aged ; Databases, Factual ; Drug Interactions ; *Drug Prescriptions ; *Electronic Prescribing ; Humans ; Social Networking ; }, abstract = {BACKGROUND: Network Analysis (NA) is a method that has been used in various disciplines such as Social sciences and Ecology for decades. So far, NA has not been used extensively in studies of medication use. Only a handful of papers have used NA in Drug Prescription Networks (DPN). We provide an introduction to NA terminology alongside a guide to creating and extracting results from the medication networks.

OBJECTIVE: To introduce the readers to NA as a tool to study medication use by demonstrating how to apply different NA measures on 3 generated medication networks.

METHODS: We used the Norwegian Prescription Database (NorPD) to create a network that describes the co-medication in elderly persons in Norway on January 1, 2013. We used the Norwegian Electronic Prescription Support System (FEST) to create another network of severe drug-drug interactions (DDIs). Lastly, we created a network combining the two networks to show the actual use of drugs with severe DDIs. We used these networks to elucidate how to apply and interpret different network measures in medication networks.

RESULTS: Interactive network graphs are made available online, Stata and R syntaxes are provided. Various useful network measures for medication networks were applied such as network topological features, modularity analysis and centrality measures. Edge lists data used to generate the networks are openly available for readers in an open data repository to explore and use.

CONCLUSION: We believe that NA can be a useful tool in medication use studies. We have provided information and hopefully inspiration for other researchers to use NA in their own projects. While network analyses are useful for exploring and discovering structures in medication use studies, it also has limitations. It can be challenging to interpret and it is not suitable for hypothesis testing.}, } @article {pmid34220784, year = {2021}, author = {Miljanovic, D and Milicevic, O and Loncar, A and Abazovic, D and Despot, D and Banko, A}, title = {The First Molecular Characterization of Serbian SARS-CoV-2 Isolates From a Unique Early Second Wave in Europe.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {691154}, pmid = {34220784}, issn = {1664-302X}, abstract = {March 6, 2020 is considered as the official date of the beginning of the COVID-19 epidemic in Serbia. In late spring and early summer 2020, Europe recorded a decline in the rate of SARS-CoV-2 infection and subsiding of the first wave. This trend lasted until the fall, when the second wave of the epidemic began to appear. Unlike the rest of Europe, Serbia was hit by the second wave of the epidemic a few months earlier. Already in June 2020, newly confirmed cases had risen exponentially. As the COVID-19 pandemic is the first pandemic in which there has been instant sharing of genomic information on isolates around the world, the aim of this study was to analyze whole SARS-CoV-2 viral genomes from Serbia, to identify circulating variants/clade/lineages, and to explore site-specific mutational patterns in the unique early second wave of the European epidemic. This analysis of Serbian isolates represents the first publication from Balkan countries, which demonstrates the importance of specificities of local transmission especially when preventive measures differ among countries. One hundred forty-eight different genome variants among 41 Serbian isolates were detected in this study. One unique and seven extremely rare mutations were identified, with locally specific continuous dominance of the 20D clade. At the same time, amino acid substitutions of newly identified variants of concern were found in our isolates from October 2020. Future research should be focused on functional characterization of novel mutations in order to understand the exact role of these variations.}, } @article {pmid34219394, year = {2021}, author = {Pauling, CD and Finke, DL and Anderson, DM}, title = {Interrelationship of soil moisture and temperature to sylvatic plague cycle among prairie dogs in the Western United States.}, journal = {Integrative zoology}, volume = {16}, number = {6}, pages = {852-867}, doi = {10.1111/1749-4877.12567}, pmid = {34219394}, issn = {1749-4877}, support = {//University of Missouri Research and Creative Works Program/ ; }, mesh = {Animals ; Climate Change ; Databases, Factual ; Plague/epidemiology/*veterinary ; Sciuridae/*microbiology ; Soil/*chemistry ; *Temperature ; United States/epidemiology ; Water/*chemistry ; Yersinia pestis/physiology ; }, abstract = {Plague, caused by Yersinia pestis, is a flea-borne disease that is endemic in areas throughout the world due to its successful maintenance in a sylvatic cycle, mainly in areas with temperate climates. Burrowing rodents are thought to play a key role in the enzootic maintenance as well as epizootic outbreaks of plague. In the United States, prairie dogs (Cynomys), rodents (Muridae), and ground squirrels (Spermophilus) are susceptible to infection and are parasitized by fleas that transmit plague. In particular, prairie dogs can experience outbreaks that rapidly spread, which can lead to extirpation of colonies. A number of ecological parameters, including climate, are associated with these epizootics. In this study, we asked whether soil parameters, primarily moisture and temperature, are associated with outbreaks of plague in black-tailed prairie dogs and Gunnison's prairie dogs in the Western United States, and at what depth these associations were apparent. We collected publicly available county-level information on the occurrence of population declines or colony extirpation, while historical soil data was collected from SCAN and USCRN stations in counties and states where prairie dogs have been located. The analysis suggests that soil moisture at lower depths correlates with colony die-offs, in addition to temperature near the surface, with key differences within the landscape ecology that impact the occurrence of plague. Overall, the model suggests that the burrow environment may play a significant role in the epizootic spread of disease amongst black-tailed and Gunnison's prairie dogs.}, } @article {pmid34218159, year = {2021}, author = {Justus, J and Wakil, S}, title = {The algorithmic turn in conservation biology: Characterizing progress in ethically-driven sciences.}, journal = {Studies in history and philosophy of science}, volume = {88}, number = {}, pages = {181-192}, doi = {10.1016/j.shpsa.2021.05.013}, pmid = {34218159}, issn = {0039-3681}, mesh = {Algorithms ; *Biodiversity ; Biology ; *Conservation of Natural Resources/methods ; Geographic Information Systems ; }, abstract = {As a discipline distinct from ecology, conservation biology emerged in the 1980s as a rigorous science focused on protecting biodiversity. Two algorithmic breakthroughs in information processing made this possible: place-prioritization algorithms and geographical information systems. They provided defensible, data-driven methods for designing reserves to conserve biodiversity that obviated the need for largely intuitive and highly problematic appeals to ecological theory at the time. But the scientific basis of these achievements and whether they constitute genuine scientific progress has been criticized. We counter by pointing out important inaccuracies about the science and rejecting the apparent theory-first focus. More broadly, the case study reveals significant limitations of the predominant epistemic-semantic conceptions of scientific progress and the considerable merits of pragmatic, practically-oriented accounts.}, } @article {pmid34217245, year = {2021}, author = {Mercaldo, R and Whalen, C and Kakaire, R and Nakkonde, D and Handel, A and Sekandi, JN}, title = {Community drivers of tuberculosis diagnostic delay in Kampala, Uganda: a retrospective cohort study.}, journal = {BMC infectious diseases}, volume = {21}, number = {1}, pages = {641}, pmid = {34217245}, issn = {1471-2334}, mesh = {Adolescent ; Adult ; Aged ; Aged, 80 and over ; *Delayed Diagnosis ; Female ; Health Knowledge, Attitudes, Practice ; Health Services Accessibility/*statistics & numerical data ; Humans ; Male ; Middle Aged ; Patient Acceptance of Health Care ; Public Health ; Retrospective Studies ; Time-to-Treatment/*statistics & numerical data ; Tuberculosis/*diagnosis/*prevention & control ; Uganda ; Young Adult ; }, abstract = {BACKGROUND: Recent approaches to TB control have focused on identifying and treating active cases to halt further transmission. Patients with TB symptoms often delay to seek care, get appropriate diagnosis, and initiate effective treatment. These delays are partly influenced by whom the patients contact within their community network. We aimed to evaluate the community drivers of diagnostic delay in an urban setting in Uganda.

METHODS: In this study we analyze data from a retrospective cohort of 194 TB patients in Kampala, Uganda. We characterized the patterns of contacts made by patients seeking care for TB symptoms. The main outcome of interest was total community contact delay, defined as the time patients spent seeking care before visiting a provider capable of diagnosing TB.

RESULTS: Visits to health providers without access to appropriate diagnostic services accounted for 56% of contacts made by cohort members, and were significantly associated with community contact delay, as were symptoms common to other prevalent illnesses, such as bone and joint pain.

CONCLUSIONS: Education programs aimed at primary care providers, as well as other community members, may benefit case identification, by informing them of rarer symptoms of TB, potential for co-infections of TB and other prevalent diseases, and the availability of diagnostic services.}, } @article {pmid34215191, year = {2021}, author = {Apuli, RP and Richards, T and Rendón-Anaya, M and Karacic, A and Rönnberg-Wästljung, AC and Ingvarsson, PK}, title = {The genetic basis of adaptation in phenology in an introduced population of Black Cottonwood (Populus trichocarpa, Torr. & Gray).}, journal = {BMC plant biology}, volume = {21}, number = {1}, pages = {317}, pmid = {34215191}, issn = {1471-2229}, mesh = {Adaptation, Physiological/*genetics ; Gene Ontology ; Genetic Association Studies ; Inheritance Patterns/genetics ; *Introduced Species ; Phenotype ; Populus/*genetics/*physiology ; Quantitative Trait, Heritable ; Seasons ; }, abstract = {BACKGROUND: Entering and exiting winter dormancy present important trade-offs between growth and survival at northern latitudes. Many forest trees display local adaptation across latitude in traits associated with these phenology transitions. Transfers of a species outside its native range introduce the species to novel combinations of environmental conditions potentially requiring different combinations of alleles to optimize growth and survival. In this study, we performed genome wide association analyses and a selection scan in a P. trichocarpa mapping population derived from crossings between clones collected across the native range and introduced into Sweden. GWAS analyses were performed using phenotypic data collected across two field seasons and in a controlled phytotron experiment.

RESULTS: We uncovered 584 putative candidate genes associated with spring and autumn phenology traits as well as with growth. Many regions harboring variation significantly associated with the initiation of leaf shed and leaf autumn coloring appeared to have been evolving under positive selection in the native environments of P. trichocarpa. A comparison between the candidate genes identified with results from earlier GWAS analyses performed in the native environment found a smaller overlap for spring phenology traits than for autumn phenology traits, aligning well with earlier observations that spring phenology transitions have a more complex genetic basis than autumn phenology transitions.

CONCLUSIONS: In a small and structured introduced population of P. trichocarpa, we find complex genetic architectures underlying all phenology and growth traits, and identify multiple putative candidate genes despite the limitations of the study population.}, } @article {pmid34214077, year = {2021}, author = {Weinstein, BG and Graves, SJ and Marconi, S and Singh, A and Zare, A and Stewart, D and Bohlman, SA and White, EP}, title = {A benchmark dataset for canopy crown detection and delineation in co-registered airborne RGB, LiDAR and hyperspectral imagery from the National Ecological Observation Network.}, journal = {PLoS computational biology}, volume = {17}, number = {7}, pages = {e1009180}, pmid = {34214077}, issn = {1553-7358}, mesh = {Algorithms ; Benchmarking ; *Databases, Factual ; Ecosystem ; Environmental Monitoring/*methods ; *Forests ; Image Processing, Computer-Assisted/*methods ; Optical Imaging ; *Trees/classification/physiology ; }, abstract = {Broad scale remote sensing promises to build forest inventories at unprecedented scales. A crucial step in this process is to associate sensor data into individual crowns. While dozens of crown detection algorithms have been proposed, their performance is typically not compared based on standard data or evaluation metrics. There is a need for a benchmark dataset to minimize differences in reported results as well as support evaluation of algorithms across a broad range of forest types. Combining RGB, LiDAR and hyperspectral sensor data from the USA National Ecological Observatory Network's Airborne Observation Platform with multiple types of evaluation data, we created a benchmark dataset to assess crown detection and delineation methods for canopy trees covering dominant forest types in the United States. This benchmark dataset includes an R package to standardize evaluation metrics and simplify comparisons between methods. The benchmark dataset contains over 6,000 image-annotated crowns, 400 field-annotated crowns, and 3,000 canopy stem points from a wide range of forest types. In addition, we include over 10,000 training crowns for optional use. We discuss the different evaluation data sources and assess the accuracy of the image-annotated crowns by comparing annotations among multiple annotators as well as overlapping field-annotated crowns. We provide an example submission and score for an open-source algorithm that can serve as a baseline for future methods.}, } @article {pmid34209491, year = {2021}, author = {Inui, T and Hanley, B and Tee, ES and Nishihira, J and Tontisirin, K and Van Dael, P and Eggersdorfer, M}, title = {The Role of Micronutrients in Ageing Asia: What Can Be Implemented with the Existing Insights.}, journal = {Nutrients}, volume = {13}, number = {7}, pages = {}, pmid = {34209491}, issn = {2072-6643}, mesh = {Aged ; Aged, 80 and over ; *Aging ; Asia, Southeastern/epidemiology ; Dietary Supplements ; Elder Nutritional Physiological Phenomena ; Fatty Acids, Omega-3 ; Female ; Humans ; Life Expectancy/trends ; Male ; *Micronutrients ; Minerals ; Noncommunicable Diseases/*epidemiology ; *Nutrition Policy ; Nutritional Status ; *Population Health ; Quality of Life ; Trace Elements ; Vitamins ; }, abstract = {Life expectancy as a measure of population health does not reflect years of healthy life. The average life expectancy in the Asia-Pacific region has more than doubled since 1900 and is now above 70 years. In the Asia-Pacific region, the proportion of aged people in the population is expected to double between 2017 and 2050. Increased life expectancy leads to an increase in non-communicable diseases, which consequently affects quality of life. Suboptimal nutritional status is a contributing factor to the prevalence and severity of non-communicable diseases, including cardiovascular, cognitive, musculoskeletal, immune, metabolic and ophthalmological functions. We have reviewed the published literature on nutrition and healthy ageing as it applies to the Asia-Pacific region, focusing on vitamins, minerals/trace elements and omega-3 fatty acids. Optimal nutritional status needs to start before a senior age is reached and before the consequences of the disease process are irreversible. Based on the nutritional status and health issues in the senior age in the region, micronutrients of particular importance are vitamins A, D, E, C, B-12, zinc and omega-3 fatty acids. The present paper substantiates the creation of micronutrient guidelines and proposes actions to support the achievement of optimal nutritional status as contribution to healthy ageing for Asia-Pacific populations.}, } @article {pmid34208807, year = {2021}, author = {Salman, A and Sigodo, KO and Al-Ghadban, F and Al-Lahou, B and Alnashmi, M and Hermassi, S and Chun, S}, title = {Effects of COVID-19 Lockdown on Physical Activity and Dietary Behaviors in Kuwait: A Cross-Sectional Study.}, journal = {Nutrients}, volume = {13}, number = {7}, pages = {}, pmid = {34208807}, issn = {2072-6643}, mesh = {Adult ; COVID-19/*epidemiology/prevention & control ; Cigarette Smoking/epidemiology ; Communicable Disease Control/*methods ; Cross-Sectional Studies ; Diet/*methods/statistics & numerical data ; *Exercise ; *Feeding Behavior ; Female ; Health Behavior ; Humans ; Kuwait/epidemiology ; Life Style ; Male ; Middle Aged ; Pandemics ; SARS-CoV-2 ; Sleep ; Surveys and Questionnaires ; Vegetables ; Young Adult ; }, abstract = {The Coronavirus disease (COVID-19) pandemic has brought about drastic measures that have significantly altered the norms of daily living. These measures have affected human behaviors in disparate ways. This study seeks to understand the impact of the pandemic on physical activity and dietary behavior among adults living in Kuwait. A cross-sectional survey was conducted between 18 June and 15 July 2020, using a questionnaire disseminated through social media, including WhatsApp and Facebook. The target population was individuals aged 21 years or older living in the State of Kuwait. The study included 679 respondents; 57.9% were females, and 67.7% were Kuwaiti nationals. Both genders reported an increased consumption of vegetables, fruits, and carbohydrates, and a decreased consumption of fish and sugary drinks. Compared to males, females reported eating more during the outbreak than their pre-pandemic eating behaviors (32.3% vs. 35.9%, p < 0.05). Approximately one-third of respondents (33.1%) reported performing less than 30 min of physical activity or exercise in a week, and 36.4% of respondents rated their quality of sleep as 'poor' or 'very poor'. The rate of smoking cigarettes among males was significantly higher than in females (40.6% vs. 5.3%, p < 0.001). Physical activity was positively correlated with vegetable consumption and quality of sleep. Quality of sleep was negatively correlated with the consumption of sweets and snacks, just as the consumption of vegetables was negatively correlated with the consumption of sugary drinks. The overall negative impact of the COVID-19 pandemic in Kuwait necessitates the development of health promotion interventions to support positive physical activity and dietary behaviors using alternative coping strategies among the residents of Kuwait.}, } @article {pmid34207456, year = {2021}, author = {Prūse, B and Simanova, A and Mežaka, I and Kalle, R and Prakofjewa, J and Holsta, I and Laizāne, S and Sõukand, R}, title = {Active Wild Food Practices among Culturally Diverse Groups in the 21st Century across Latgale, Latvia.}, journal = {Biology}, volume = {10}, number = {6}, pages = {}, pmid = {34207456}, issn = {2079-7737}, support = {Nr. 1.1.1.1/18/A/ 043//European Regional Development Fund/ ; }, abstract = {Local ecological knowledge (LEK), including but not limited to the use of wild food plants, plays a large role in sustainable natural resource management schemes, primarily due to the synergy between plants and people. There are calls for the study of LEK in culturally diverse areas due to a loss of knowledge, the active practice of utilizing wild plants in various parts of the world, and a decline in biodiversity. An ethnobotanical study in a border region of Latvia, characterised by diverse natural landscapes and people with deep spiritual attachments to nature, provided an opportunity for such insight, as well as the context to analyse wild food plant usages among different sociocultural groups, allowing us to explore the differences among these groups. Semi-structured interviews were carried out as part of a wider ethnobotanical field study to obtain information about wild food plants and their uses. The list of wild food plant uses, derived from 72 interviews, revealed a high level of homogenisation (in regards to knowledge) among the study groups, and that many local uses of wild food plants are still actively practiced. People did not gather plants as a recreational activity but rather as a source of diet diversification. The results provide evidence of the importance of safeguarding ecological and cultural diversity due to high local community dependency on natural resources.}, } @article {pmid34206965, year = {2021}, author = {Rebelo, JS and Domingues, CPF and Dionisio, F and Gomes, MC and Botelho, A and Nogueira, T}, title = {COVID-19 Lockdowns May Reduce Resistance Genes Diversity in the Human Microbiome and the Need for Antibiotics.}, journal = {International journal of molecular sciences}, volume = {22}, number = {13}, pages = {}, pmid = {34206965}, issn = {1422-0067}, support = {PTDC/BIA-MIC/28824/2017//Fundação para a Ciência e a Tecnologia/ ; UIDP/00329/2020//Fundação para a Ciência e a Tecnologia/ ; }, mesh = {Algorithms ; Anti-Bacterial Agents/*pharmacology/therapeutic use ; Bacterial Infections/drug therapy ; COVID-19/pathology/virology ; Databases, Factual ; Drug Resistance, Microbial/*drug effects/genetics ; *Genetic Variation ; Humans ; Physical Distancing ; Quarantine ; SARS-CoV-2/isolation & purification ; }, abstract = {Recently, much attention has been paid to the COVID-19 pandemic. Yet bacterial resistance to antibiotics remains a serious and unresolved public health problem that kills hundreds of thousands of people annually, being an insidious and silent pandemic. To contain the spreading of the SARS-CoV-2 virus, populations confined and tightened hygiene measures. We performed this study with computer simulations and by using mobility data of mobile phones from Google in the region of Lisbon, Portugal, comprising 3.7 million people during two different lockdown periods, scenarios of 40 and 60% mobility reduction. In the simulations, we assumed that the network of physical contact between people is that of a small world and computed the antibiotic resistance in human microbiomes after 180 days in the simulation. Our simulations show that reducing human contacts drives a reduction in the diversity of antibiotic resistance genes in human microbiomes. Kruskal-Wallis and Dunn's pairwise tests show very strong evidence (p < 0.000, adjusted using the Bonferroni correction) of a difference between the four confinement regimes. The proportion of variability in the ranked dependent variable accounted for by the confinement variable was η[2] = 0.148, indicating a large effect of confinement on the diversity of antibiotic resistance. We have shown that confinement and hygienic measures, in addition to reducing the spread of pathogenic bacteria in a human network, also reduce resistance and the need to use antibiotics.}, } @article {pmid34206938, year = {2021}, author = {Yuan, D and Zhang, J and Wang, J and Cui, X and Liu, F and Zhang, Y}, title = {Robustly Adaptive EKF PDR/UWB Integrated Navigation Based on Additional Heading Constraint.}, journal = {Sensors (Basel, Switzerland)}, volume = {21}, number = {13}, pages = {}, pmid = {34206938}, issn = {1424-8220}, support = {No. E2020402086//Hebei Natural Science Foundation Ecological Smart Mine Joint Fund/ ; }, abstract = {At present, GNSS (Global Navigation Satellite System) positioning technology is widely used for outdoor positioning services because of its high-precision positioning characteristics. However, in indoor environments, effective position information cannot be provided, because of the signals being obscured. In order to improve the accuracy and continuity of indoor positioning systems, in this paper, we propose a PDR/UWB (Pedestrian Dead Reckoning and Ultra Wide Band) integrated navigation algorithm based on an adaptively robust EKF (Extended Kalman Filter) to address the problem of error accumulation in the PDR algorithm and gross errors in the location results of the UWB in non-line-of-sight scenarios. First, the basic principles of UWB and PDR location algorithms are given. Then, we propose a loose combination of the PDR and UWB algorithms by using the adaptively robust EKF. By using the robust factor to adjust the weight of the observation value to resist the influence of the gross error, and by adjusting the variance of the system adaptively according to the positioning scene, the algorithm can improve the robustness and heading factor of the PDR algorithm, which is constrained by indoor maps. Finally, the effectiveness of the algorithm is verified by the measured data. The experimental results showed that the algorithm can not only reduce the accumulation of PDR errors, but can also resist the influence of gross location errors under non-line-of-sight UWB scenarios.}, } @article {pmid34203872, year = {2021}, author = {Martín-delosReyes, LM and Lardelli-Claret, P and García-Cuerva, L and Rivera-Izquierdo, M and Jiménez-Mejías, E and Martínez-Ruiz, V}, title = {Effect of Periodic Vehicle Inspection on Road Crashes and Injuries: A Systematic Review.}, journal = {International journal of environmental research and public health}, volume = {18}, number = {12}, pages = {}, pmid = {34203872}, issn = {1660-4601}, mesh = {*Accidents, Traffic ; Case-Control Studies ; Databases, Factual ; Humans ; *Wounds and Injuries/epidemiology ; }, abstract = {This systematic review was conducted to determine the effect of periodic motor vehicle inspections on road crashes and injuries, compared to less exposure to periodic inspections or no inspections. The Medline, Web of Science, and Scopus databases were used to search the literature. Ecological studies were specifically excluded. A reverse search of the results with these databases and of other identified narrative reviews was also performed. Of the 5065 unique references initially extracted, only six of them met the inclusion criteria and were selected for review: one experimental study, two cohort studies with an internal comparison group, two cohort studies without a comparison group, and one case-control study. Two authors independently extracted the information and assessed the quality of each study. Due to the heterogeneity of the designs and the intervention or comparison groups used, quantitative synthesis of the results was not attempted. Except for the case-control study, which showed a significant association between road crashes and the absence of a valid vehicle inspection certificate, the other studies showed either a small reduction in crash rates (around 9%), no association, or a higher crash rate in vehicles with more inspections. In all observational studies, the risk of residual confounding bias was significant and could have explained the results. Therefore, although the research reviewed here suggests that periodic inspection may be associated with a slight reduction in road crashes, the marked heterogeneity along with probable residual confounding in most reports prevented us from establishing causality for this association.}, } @article {pmid34202710, year = {2021}, author = {Ji, C and Huang, J and Tian, Y and Liu, Y and Barvor, JB and Shao, X and Li, Z}, title = {Feasibility Study on the Application of Microbial Agent Modified Water-Jet Loom Sludge for the Restoration of Degraded Soil in Mining Areas.}, journal = {International journal of environmental research and public health}, volume = {18}, number = {13}, pages = {}, pmid = {34202710}, issn = {1660-4601}, mesh = {Biomass ; Ecosystem ; Feasibility Studies ; *Sewage ; *Soil ; Soil Microbiology ; Water ; }, abstract = {Open-pit mining causes soil damage and affects the health of the ecosystem. In the arid grassland mining areas, the soil is severely sanded, water-starved, and saline, thus making it difficult for plants and microorganisms to survive. Water-jet loom sludge can be used to improve the quality as it contains a lot of clay and is rich in organic matter, which provides a material basis for microorganism activity. To explore the effects of microbial agent-modified water-jet loom sludge on the restoration of degraded soil in grassland mining areas, four pot trials were set up, i.e., for untreated soil, the application of a microbial agent alone, the application of water-jet loom sludge alone, and the combined application of water-jet loom sludge and the microbial agent. The results show that (1) microbial agent-modified sludge can improve soil water-holding capacity and aggregate stability; (2) the nutrient content of the restored soil fraction increased significantly, and the pH of the original saline soil decreased from 9.06 to 7.84; (3) this method significantly increased plant biomass and microbial biomass carbon and enhanced the abundance and diversity of fungi and bacteria. The three treatments had different results in different soil properties, and the effect of the combined water-jet loom sludge and microbial agent treatment on soil remediation was significantly better than the individual application of either.}, } @article {pmid34202619, year = {2021}, author = {Zhang, Y and Chang, Y and Yu, K and Zhang, L and Li, X}, title = {Difference Analysis of Ecological Vulnerability and Zoning Changes of National Energy and Chemical Bases Using FAHP Method.}, journal = {International journal of environmental research and public health}, volume = {18}, number = {13}, pages = {}, pmid = {34202619}, issn = {1660-4601}, mesh = {China ; *Conservation of Natural Resources ; *Ecosystem ; Geographic Information Systems ; Human Activities ; Humans ; Soil ; }, abstract = {Ecological vulnerability zoning research is an important basis for taking targeted regional ecological environment restoration and governance measures. This study analyzes the ecological vulnerability pattern and trend in the National Energy and Chemical Base (NECB) in the typical region of the Loess Plateau using GIS (Geographic Information System) data and the fuzzy analytic hierarchy process (FAHP) approach. Based on the human activity-natural environment factor index system, 13 factors representing human activities, socioeconomics, meteorology, soil and topography are selected to build an ecological vulnerability index (EVI) system in the NECB region, which aims at identifying the regional features of eco-environment and major environmental problems in the Loess Plateau. By calculating ecological vulnerability zoning, a model of ecological vulnerability trend change is constructed to quantitatively study the overall temporal and spatial variation of ecological vulnerability. The results indicate that the medium and heavy levels of ecological vulnerability index were mostly distributed in the areas with developed energy and chemical industries, and the slight and light levels were distributed in the southern area and developed agricultural regions. A comprehensive ecological vulnerability index had a score of 2.3207 in 2015 and 2.441 in 2000, indicating that the ecological security gradually improved. Nevertheless, highly intense human activities accelerated the degradation of regional eco-environment in recent years.}, } @article {pmid34199822, year = {2021}, author = {Lyatuu, I and Loss, G and Farnham, A and Lyatuu, GW and Fink, G and Winkler, MS}, title = {Associations between Natural Resource Extraction and Incidence of Acute and Chronic Health Conditions: Evidence from Tanzania.}, journal = {International journal of environmental research and public health}, volume = {18}, number = {11}, pages = {}, pmid = {34199822}, issn = {1660-4601}, mesh = {*Health Facilities ; *Health Information Systems ; Humans ; Incidence ; Natural Resources ; Tanzania/epidemiology ; }, abstract = {Natural resource extraction projects are often accompanied by complex environmental and social-ecological changes. In this paper, we evaluated the association between commodity extraction and the incidence of diseases. We retrieved council (district)-level outpatient data from all public and private health facilities from the District Health Information System (DHIS2). We combined this information with population data from the 2012 national population census and a geocoded list of resource extraction projects from the Geological Survey of Tanzania (GST). We used Poisson regression with random effects and cluster-robust standard errors to estimate the district-level associations between the presence of three types of commodity extraction (metals, gemstone, and construction materials) and the total number of patients in each disease category in each year. Metal extraction was associated with reduced incidence of several diseases, including chronic diseases (IRR = 0.61, CI: 0.47-0.80), mental health disorders (IRR = 0.66, CI: 0.47-0.92), and undernutrition (IRR = 0.69, CI: 0.55-0.88). Extraction of construction materials was associated with an increased incidence of chronic diseases (IRR = 1.47, CI: 1.15-1.87). This study found that the presence of natural resources commodity extraction is significantly associated with changes in disease-specific patient volumes reported in Tanzania's DHIS2. These associations differed substantially between commodities, with the most protective effects shown from metal extraction.}, } @article {pmid34197728, year = {2021}, author = {Wilmers, CC and Nisi, AC and Ranc, N}, title = {COVID-19 suppression of human mobility releases mountain lions from a landscape of fear.}, journal = {Current biology : CB}, volume = {31}, number = {17}, pages = {3952-3955.e3}, pmid = {34197728}, issn = {1879-0445}, mesh = {Animals ; Automobile Driving/statistics & numerical data ; *Behavior, Animal ; COVID-19/*prevention & control ; California ; Cities ; Ecosystem ; Fear ; Female ; Geographic Information Systems ; Humans ; Male ; Physical Distancing ; *Puma ; Quarantine ; }, abstract = {Humans have outsized effects on ecosystems, in part by initiating trophic cascades that impact all levels of the food chain.[1][,][2] Theory suggests that disease outbreaks can reverse these impacts by modifying human behavior,[3][,][4] but this has not yet been tested. The COVID-19 pandemic provided a natural experiment to test whether a virus could subordinate humans to an intermediate link in the trophic chain, releasing a top carnivore from a landscape of fear. Shelter-in-place orders in the Bay Area of California led to a 50% decline in human mobility, which resulted in a relaxation of mountain lion aversion to urban areas. Rapid changes in human mobility thus appear to act quickly on food web functions, suggesting an important pathway by which emerging infectious diseases will impact not only human health but ecosystems as well.}, } @article {pmid34197520, year = {2021}, author = {Pham, TA and Pham, TM and Dang, GTH and Nguyen, DT and Du, QVV}, title = {Mapping the potential aggregation values of ecotourism landscapes from stakeholder survey, structural equation modeling and GIS: Case study of Moc Chau site, Vietnam.}, journal = {PloS one}, volume = {16}, number = {7}, pages = {e0253908}, pmid = {34197520}, issn = {1932-6203}, mesh = {*Ecology ; Geographic Information Systems ; Geography ; Latent Class Analysis ; Spatial Analysis ; *Tourism ; Vietnam ; }, abstract = {The primary aim of this study is to propose a potential landscape value assessment from different dimensions rather than the traditional approach of a composite indicator. The method used in this study is the combination of data collection from stakeholder survey, score measurement for landscape value dimensions using Structural Equation Modeling (SEM), and spatial representation with the support of Geographic Information System (GIS). From a large-scale (n = 400) investigation in the Moc Chau district, the statistical data extracted from the survey provides input data for the score determination process. SEM analysis shows that each landscape site has 11 determinants influencing the landscape value assessment. Using the RMSE comparison (for validation) with different interpolation methods, the ordinary kriging method is chosen to model the aggregation landscape value map of Moc Chau District. About 24.97% total area of the study area has great potential for tourism development, being mainly distributed in the center of a high mountainous area. This approach can be used as a model to advocate local and regional assessment and enhance value-based management in other territories in Vietnam and beyond.}, } @article {pmid34197512, year = {2021}, author = {Dunham, KD and Osnas, EE and Frost, CJ and Fischer, JB and Grand, JB}, title = {Assessing recovery of spectacled eiders using a Bayesian decision analysis.}, journal = {PloS one}, volume = {16}, number = {7}, pages = {e0253895}, pmid = {34197512}, issn = {1932-6203}, mesh = {Alaska ; Animals ; Bayes Theorem ; *Decision Making, Organizational ; *Decision Support Techniques ; *Ducks ; Ecological Parameter Monitoring/statistics & numerical data ; Endangered Species/*legislation & jurisprudence/statistics & numerical data ; United States ; Yukon Territory ; }, abstract = {Assessing species status and making classification decisions under the Endangered Species Act is a critical step towards effective species conservation. However, classification decisions are liable to two errors: i) failing to classify a species as threatened or endangered that should be classified (underprotection), or ii) classifying a species as threatened or endangered when it is not warranted (overprotection). Recent surveys indicate threatened spectacled eider populations are increasing in western Alaska, prompting the U.S. Fish and Wildlife Service to reconsider the federal listing status. There are multiple criteria set for assessing spectacled eider status, and here we focus on the abundance and decision analysis criteria. We estimated population metrics using state-space models for Alaskan breeding populations of spectacled eiders. We projected abundance over 50 years using posterior estimates of abundance and process variation to estimate the probability of quasi-extinction. The decision analysis maps the risk of quasi-extinction to the loss associated with making a misclassification error (i.e., underprotection) through a loss function. Our results indicate that the Yukon Kuskokwim Delta breeding population in western Alaska has met the recovery criteria but the Arctic Coastal Plain population in northern Alaska has not. The methods employed here provide an example of accounting for uncertainty and incorporating value judgements in such a way that the decision-makers may understand the risk of committing a misclassification error. Incorporating the abundance threshold and decision analysis in the reclassification criteria greatly increases the transparency and defensibility of the classification decision, a critical aspect for making effective decisions about species management and conservation.}, } @article {pmid34197484, year = {2021}, author = {Tovo, A and Stivanello, S and Maritan, A and Suweis, S and Favaro, S and Formentin, M}, title = {Upscaling human activity data: A statistical ecology approach.}, journal = {PloS one}, volume = {16}, number = {7}, pages = {e0253461}, pmid = {34197484}, issn = {1932-6203}, mesh = {*Big Data ; Computer Communication Networks/*statistics & numerical data ; *Datasets as Topic ; Electronic Mail/*statistics & numerical data ; Humans ; Social Media/*statistics & numerical data ; }, abstract = {Big data require new techniques to handle the information they come with. Here we consider four datasets (email communication, Twitter posts, Wikipedia articles and Gutenberg books) and propose a novel statistical framework to predict global statistics from random samples. More precisely, we infer the number of senders, hashtags and words of the whole dataset and how their abundances (i.e. the popularity of a hashtag) change through scales from a small sample of sent emails per sender, posts per hashtag and word occurrences. Our approach is grounded on statistical ecology as we map inference of human activities into the unseen species problem in biodiversity. Our findings may have applications to resource management in emails, collective attention monitoring in Twitter and language learning process in word databases.}, } @article {pmid34194016, year = {2021}, author = {Dance, A}, title = {Beyond coronavirus: the virus discoveries transforming biology.}, journal = {Nature}, volume = {595}, number = {7865}, pages = {22-25}, pmid = {34194016}, issn = {1476-4687}, mesh = {Animals ; Carbon/analysis ; *Classification ; Databases, Genetic ; Datasets as Topic ; Ecosystem ; Genome, Viral/genetics ; Giant Viruses/genetics/isolation & purification ; Host Microbial Interactions ; Humans ; Metagenome/genetics ; Permafrost/chemistry/microbiology/virology ; *SARS-CoV-2/genetics ; Species Specificity ; Terminology as Topic ; Virology/*trends ; Viruses/*classification/genetics/*isolation & purification ; Wastewater/microbiology/virology ; }, } @article {pmid34192775, year = {2022}, author = {Vadaq, N and Schirmer, M and Tunjungputri, RN and Vlamakis, H and Chiriac, C and Ardiansyah, E and Gasem, MH and Joosten, LAB and de Groot, PG and Xavier, RJ and Netea, MG and van der Ven, AJ and de Mast, Q}, title = {Untargeted Plasma Metabolomics and Gut Microbiome Profiling Provide Novel Insights into the Regulation of Platelet Reactivity in Healthy Individuals.}, journal = {Thrombosis and haemostasis}, volume = {122}, number = {4}, pages = {529-539}, doi = {10.1055/a-1541-3706}, pmid = {34192775}, issn = {2567-689X}, mesh = {Adult ; *Gastrointestinal Microbiome ; Healthy Volunteers ; Humans ; Metabolome ; Metabolomics/methods ; Plasma ; }, abstract = {BACKGROUND: Considerable variation exists in platelet reactivity to stimulation among healthy individuals. Various metabolites and metabolic pathways influence platelet reactivity, but a comprehensive overview of these associations is missing. The gut microbiome has a strong influence on the plasma metabolome. Here, we investigated the association of platelet reactivity with results of untargeted plasma metabolomics and gut microbiome profiling.

METHODS: We used data from a cohort of 534 healthy adult Dutch volunteers (the 500 Functional Genomics study). Platelet activation and reactivity were measured by the expression of the alpha-granule protein P-selectin and the binding of fibrinogen to the activated integrin αIIbβ3, both in unstimulated blood and after ex vivo stimulation with platelet agonists. Plasma metabolome was measured using an untargeted metabolic profiling approach by quadrupole time-of-flight mass spectrometry. Gut microbiome data were measured by shotgun metagenomic sequencing from stool samples.

RESULTS: Untargeted metabolomics yielded 1,979 metabolites, of which 422 were identified to play a role in a human metabolic pathway. Overall, 92/422 (21.8%) metabolites were significantly associated with at least one readout of platelet reactivity. The majority of associations involved lipids, especially members of eicosanoids, including prostaglandins and leukotrienes. Dietary-derived polyphenols were also found to inhibit platelet reactivity. Validation of metabolic pathways with functional microbial profiles revealed two overlapping metabolic pathways ("alanine, aspartate, and glutamate metabolism" and "arginine biosynthesis") that were associated with platelet reactivity.

CONCLUSION: This comprehensive overview is an resource for understanding the regulation of platelet reactivity by the plasma metabolome and the possible contribution of the gut microbiota.}, } @article {pmid34191820, year = {2021}, author = {Hölzchen, E and Hertler, C and Mateos, A and Rodríguez, J and Berndt, JO and Timm, IJ}, title = {Discovering the opposite shore: How did hominins cross sea straits?.}, journal = {PloS one}, volume = {16}, number = {6}, pages = {e0252885}, pmid = {34191820}, issn = {1932-6203}, mesh = {Animals ; *Biological Evolution ; Emigration and Immigration/*statistics & numerical data ; Hominidae ; Humans ; *Models, Theoretical ; *Oceans and Seas ; Population Dynamics ; *Swimming ; }, abstract = {Understanding hominin expansions requires the comprehension of movement processes at different scales. In many models of hominin expansion these processes are viewed as being determined by large-scale effects, such as changes in climate and vegetation spanning continents and thousands or even millions of years. However, these large-scale patterns of expansions also need to be considered as possibly resulting from the accumulation of small-scale decisions of individual hominins. Moving on a continental scale may for instance involve crossing a water barrier. We present a generalized agent-based model for simulating the crossing of a water barrier where the agents represent the hominin individuals. The model can be configured to represent a variety of movement modes across water. Here, we compare four different behavioral scenarios in conjunction with a set of water barrier configurations, in which agents move in water by either paddling, drifting, swimming or rafting. We introduce the crossing-success-rate (CSR) to quantify the performance in water crossing. Our study suggests that more focus should be directed towards the exploration of behavioral models for hominins, as directionality may be a more powerful factor for crossing a barrier than environmental opportunities alone. A prerequisite for this is to perceive the opposite shore. Furthermore, to provide a comprehensive understanding of hominin expansions, the CSR allows for the integration of results obtained from small-scale simulations into large-scale models for hominin expansion.}, } @article {pmid34191613, year = {2021}, author = {Özdemir, V and Springer, S and Yıldırım, A and Biçer, Ş and Kendirci, A and Şardaş, S and Kılıç, H and Hekim, N and Kunej, T and Arga, KY and Dzobo, K and Wang, W and Geanta, M and Brand, A and Bayram, M}, title = {Thanatechnology and the Living Dead: New Concepts in Digital Transformation and Human-Computer Interaction.}, journal = {Omics : a journal of integrative biology}, volume = {25}, number = {7}, pages = {401-407}, doi = {10.1089/omi.2021.0100}, pmid = {34191613}, issn = {1557-8100}, mesh = {Big Data ; Computers ; Humans ; *Pandemics ; *Social Media ; Technology ; }, abstract = {In a digital society, shall we be the authors of our own experience, not only during our lifetime but also after we die? We ask this question because dying and bereavement have become even harder, and much less private, in the digital age. New big data-driven digital industries and technologies are on the rise, with promises of interactive 3D avatars and storage of digital memories of the deceased, so they can continue to exist online as the "living dead" in a digital afterlife. Famous rock and roll icons like Roy Orbison, Frank Zappa, Ronnie James Dio, and Amy Winehouse have famously been turned into holograms that can once again give "live" performances on the touring circuit, often pulling in large audiences. Death studies, dying, and grief have become virtual in the 21st century. We live in truly unprecedented times for human-computer interactions. Thanatology is the scientific study of death, dying, loss, and grief. In contrast to the biological study of biological aging (cellular senescence) and programmed cell death (apoptosis), thanatology employs multiple professional lenses, medical, psychological, physical, spiritual, ethical, descriptive, and normative. In 1997, Carla Sofka introduced the term thanatechnology as "technological mechanisms such as interactive videodiscs and computer programs that are used to access information or aid in learning about thanatology topics." Onward to 2021, the advent of social media, the Internet of Things, and sensors that digitize and archive nearly every human movement and experience are taking thanatechnology, and by extension, digital transformation, to new heights. For example, what happens to digital remains of persons once they cease to exist physically? This article offers a critical study and snapshot of this nascent field, and the "un-disciplinary" sociotechnical issues digital thanatechnologies raise in relation to big data. We also discuss how best to critically govern this new frontier in systems science and the digital society. We suggest that new policy narratives such as (1) the right to nonparticipation in relation to information and communication technologies and (2) the planetary public goods deserve further attention to democratize thanatechnology and big data. To the extent that systems science often depends on data from online platforms, for example, in times of pandemics and ecological crises, "critical thanatechnology studies," introduced in this article, is a timely and essential field of scholarship with broad importance for systems science and planetary health.}, } @article {pmid34187896, year = {2021}, author = {Skalenko, KS and Li, L and Zhang, Y and Vvedenskaya, IO and Winkelman, JT and Cope, AL and Taylor, DM and Shah, P and Ebright, RH and Kinney, JB and Zhang, Y and Nickels, BE}, title = {Promoter-sequence determinants and structural basis of primer-dependent transcription initiation in Escherichia coli.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {118}, number = {27}, pages = {}, pmid = {34187896}, issn = {1091-6490}, support = {R01 GM041376/GM/NIGMS NIH HHS/United States ; R37 GM041376/GM/NIGMS NIH HHS/United States ; R35 GM124976/GM/NIGMS NIH HHS/United States ; R35 GM133777/GM/NIGMS NIH HHS/United States ; R35 GM118059/GM/NIGMS NIH HHS/United States ; }, mesh = {Base Sequence ; Binding Sites ; Chromosomes, Bacterial/genetics ; DNA Primers/*metabolism ; Escherichia coli/*genetics ; Gene Expression Regulation, Bacterial ; *Promoter Regions, Genetic ; RNA, Messenger/genetics/metabolism ; Transcription Initiation Site ; *Transcription Initiation, Genetic ; }, abstract = {Chemical modifications of RNA 5'-ends enable "epitranscriptomic" regulation, influencing multiple aspects of RNA fate. In transcription initiation, a large inventory of substrates compete with nucleoside triphosphates for use as initiating entities, providing an ab initio mechanism for altering the RNA 5'-end. In Escherichia coli cells, RNAs with a 5'-end hydroxyl are generated by use of dinucleotide RNAs as primers for transcription initiation, "primer-dependent initiation." Here, we use massively systematic transcript end readout (MASTER) to detect and quantify RNA 5'-ends generated by primer-dependent initiation for ∼4[10] (∼1,000,000) promoter sequences in E. coli The results show primer-dependent initiation in E. coli involves any of the 16 possible dinucleotide primers and depends on promoter sequences in, upstream, and downstream of the primer binding site. The results yield a consensus sequence for primer-dependent initiation, YTSS-2NTSS-1NTSSWTSS+1, where TSS is the transcription start site, NTSS-1NTSS is the primer binding site, Y is pyrimidine, and W is A or T. Biochemical and structure-determination studies show that the base pair (nontemplate-strand base:template-strand base) immediately upstream of the primer binding site (Y:RTSS-2, where R is purine) exerts its effect through the base on the DNA template strand (RTSS-2) through interchain base stacking with the RNA primer. Results from analysis of a large set of natural, chromosomally encoded Ecoli promoters support the conclusions from MASTER. Our findings provide a mechanistic and structural description of how TSS-region sequence hard-codes not only the TSS position but also the potential for epitranscriptomic regulation through primer-dependent transcription initiation.}, } @article {pmid34186981, year = {2021}, author = {Bartels, PJ and Nelson, DR and Kaczmarek, Ł}, title = {An updated species list for "Smoky Bears": Tardigrades of the Great Smoky Mountains National Park, USA.}, journal = {Zootaxa}, volume = {4980}, number = {2}, pages = {256268}, doi = {10.11646/zootaxa.4980.2.2}, pmid = {34186981}, issn = {1175-5334}, mesh = {Animals ; Databases, Factual ; North Carolina ; Parks, Recreational ; Tardigrada/*classification ; Tennessee ; }, abstract = {One of the largest inventories of tardigrades ever conducted occurred from 20002010 in the Great Smoky Mountains National Park, USA. Over 16,000 specimens were catalogued, 85 species were identified, 11 species new to science were described, and 16 other possible new species await further study. More than 20 papers have resulted from the GSMNP tardigrade inventory, making the Smokies the most thoroughly studied area in North America for tardigrades. Several species lists have been published over this 20-year period, but many taxonomic revisions and new identifications have led to significant changes to the list. Biogeographical studies citing species records from earlier studies could yield serious errors. Here we update the species list from the Smokies to accommodate the many recent changes in tardigrade taxonomy, we re-analyze some species in light of delineations of cryptic species groups that have occurred recently via integrative taxonomy, and we provide a table of all synonyms that have been used in previous publications. We also make available, for the first time, the Smokies tardigrade database, complete with all locations, elevations, and substrates.}, } @article {pmid34185805, year = {2021}, author = {Rujumba, J and Akugizibwe, M and Basta, NE and Banura, C}, title = {Why don't adolescent girls in a rural Uganda district initiate or complete routine 2-dose HPV vaccine series: Perspectives of adolescent girls, their caregivers, healthcare workers, community health workers and teachers.}, journal = {PloS one}, volume = {16}, number = {6}, pages = {e0253735}, pmid = {34185805}, issn = {1932-6203}, mesh = {Adolescent ; Child ; Female ; Humans ; Young Adult ; *Caregivers ; *Community Health Workers ; *Educational Personnel ; *Health Knowledge, Attitudes, Practice ; *Papillomavirus Vaccines/administration & dosage ; *Patient Acceptance of Health Care ; Schools ; Uganda ; }, abstract = {INTRODUCTION: Vaccination with the 2-dose HPV vaccine series among adolescent girls in Uganda remains low after almost 5 years since the vaccine was included into the routine national immunization program and barriers are not well understood.

OBJECTIVE: We explored barriers that prevent eligible girls from initiating or completing the recommended 2-dose HPV vaccine series in Oyam District, Northern Uganda.

METHODS: A qualitative study was conducted in Oyam District, Northern Uganda. Forty interviews were conducted with adolescent girls, their caregivers, Village Health Team Members, health workers and school administrators involved in HPV vaccination. All interviews were audio recorded and transcribed. NVivo version 11 was used for data management and content thematic approach for analysis guided by the Social Ecological Model.

RESULTS: At individual level, low levels of knowledge about the vaccine, girls' frequent mobility between vaccine doses, school absenteeism and drop out, fear of injection pain and discouragement from caregivers or peers were key barriers. At the health facilities level, reported barriers included: few healthcare workers, inadequate knowledge about HPV vaccine, limited social mobilization and community engagement to promote the vaccine, limited availability of the HPV vaccine, unreliable transportation, lack of reminder strategies after the first dose of the vaccine, lack of vaccination strategy for out-of-school girls and un-friendly behaviour of some healthcare workers. Concerns about safety and efficacy of the vaccine, negative religious and cultural beliefs against vaccination, rumors and misconceptions about the vaccine, mistrust in government intentions to introduce the new vaccine targeting girls, busy schedules and the gendered nature of care work were key community level barriers.

CONCLUSION: Our study revealed an interplay of barriers at individual, health facility and community levels, which prevent initiation and completion of HPV vaccination among adolescent girls. Strengthening HIV vaccination programs and ensuring high uptake requires providing appropriate information to the girls plus the community, school and health facility stakeholders; addressing cold chain challenges as well as adequate training of vaccinators to enable them respond to rumors about HPV vaccination.}, } @article {pmid34184225, year = {2021}, author = {Yang, C and Nan, J and Li, J and Lin, Y and Yu, J and Wu, J and Shen, X}, title = {The role of mechanical harvesting on the recession of aquatic vegetation under an extreme water level increase in a eutrophic shallow lake.}, journal = {Environmental science and pollution research international}, volume = {28}, number = {43}, pages = {61682-61695}, pmid = {34184225}, issn = {1614-7499}, support = {PCRRIC16005//State Key Laboratory of Pollution Control and Resource Reuse/ ; 2017ZX07205//Major Science and Technology Program for Water Pollution Control and Treatment/ ; SZWK2020WJD001 and SZSY2018WJG033//Bereau of Water Resource of Wujiang District/ ; }, mesh = {Ecosystem ; *Lakes ; *Water ; Water Quality ; }, abstract = {Mechanical harvesting is quick and effective way to remove nuisance macrophytes and improve recreational use and aesthetics in shallow lake. However, applying mechanical harvesting to macrophytes in eutrophic shallow lake with weak resilience and strong perturbation raises concerns of the public and scientific communities. A combination of field investigation and remote sensing was used to determine the potential driving factors of macrophyte degradation in a eutrophic shallow lake from 2014 to 2017, including a comparative analysis of preserved and harvested areas to determine the impacts of mechanical harvesting. Over 95% of macrophytes had disappeared by 2017 in both preserved and harvested areas, with no significant difference in macrophyte distribution area or decline rate between the two by that time. The decline rate in the harvested area (76.7%) was slightly higher than in the preserved area (61.7%) in 2016 after performing the mechanical harvesting in 2015. The results demonstrate that mechanical harvesting is not the definitive driving factor for macrophyte loss, but it could accelerate the decline process. Bottom light availability (Secchi disk depth to water level), which decreased from 0.70 to 0.29 in 2015 and from 0.70 to 0.21 in 2016, is more likely the driving factor, caused by extreme water level increase events in two consecutive years (2015 and 2016) and decreased water clarity. Maintaining water clarity and low water level is crucial for macrophyte restoration.}, } @article {pmid34182782, year = {2021}, author = {Murareanu, BM and Sukhdeo, R and Qu, R and Jiang, J and Reinke, AW}, title = {Generation of a Microsporidia Species Attribute Database and Analysis of the Extensive Ecological and Phenotypic Diversity of Microsporidia.}, journal = {mBio}, volume = {12}, number = {3}, pages = {e0149021}, pmid = {34182782}, issn = {2150-7511}, mesh = {Animals ; *Databases, Factual ; *Ecology ; *Genetic Variation ; Host Specificity ; Humans ; Microsporidia/classification/*genetics ; *Phenotype ; }, abstract = {Microsporidia are a large group of fungus-related obligate intracellular parasites. Though many microsporidia species have been identified over the past 160 years, depiction of the full diversity of this phylum is lacking. To systematically describe the characteristics of these parasites, we created a database of 1,440 species and their attributes, including the hosts they infect and spore characteristics. We find that microsporidia have been reported to infect 16 metazoan and 4 protozoan phyla, with smaller phyla being underrepresented. Most species are reported to infect only a single host, but those that are generalists are also more likely to infect a broader set of host tissues. Strikingly, polar tubes are threefold longer in species that infect tissues besides the intestine, suggesting that polar tube length is a determinant of tissue specificity. Phylogenetic analysis revealed four clades which each contain microsporidia that infect hosts from all major habitats. Although related species are more likely to infect similar hosts, we observe examples of changes in host specificity and convergent evolution. Taken together, our results show that microsporidia display vast diversity in their morphology and the hosts they infect, illustrating the flexibility of these parasites to evolve new traits. IMPORTANCE Microsporidia are a large group of parasites that cause death and disease in humans and many agriculturally important animal species. To fully understand the diverse properties of these parasites, we curated species reports from the last 160 years. Using these data, we describe when and where microsporidia were identified and what types of animals and host tissues these parasites infect. Microsporidia infect hosts using a conserved apparatus known as the polar tube. We observe that the length of this tube is correlated with the tissues that are being infected, suggesting that the polar tube controls where within the animals that the parasite infects. Finally, we show that microsporidia species often exist in multiple environments and are flexible in their ability to evolve new traits. Our study provides insight into the ecology and evolution of microsporidia and provides a useful resource to further understand these fascinating parasites.}, } @article {pmid34181792, year = {2022}, author = {Mairal, M and Chown, SL and Shaw, J and Chala, D and Chau, JH and Hui, C and Kalwij, JM and Münzbergová, Z and Jansen van Vuuren, B and Le Roux, JJ}, title = {Human activity strongly influences genetic dynamics of the most widespread invasive plant in the sub-Antarctic.}, journal = {Molecular ecology}, volume = {31}, number = {6}, pages = {1649-1665}, doi = {10.1111/mec.16045}, pmid = {34181792}, issn = {1365-294X}, mesh = {Antarctic Regions ; Ecosystem ; *Gene Flow ; Genetic Variation/genetics ; Human Activities ; Humans ; Islands ; *Microsatellite Repeats/genetics ; }, abstract = {The link between the successful establishment of alien species and propagule pressure is well-documented. Less known is how humans influence the post-introduction dynamics of invasive alien populations. The latter requires studying parallel invasions by the same species in habitats that are differently impacted by humans. We analysed microsatellite and genome size variation, and then compared the genetic diversity and structure of invasive Poa annua L. on two sub-Antarctic islands: human-occupied Marion Island and unoccupied Prince Edward Island. We also carried out niche modelling to map the potential distribution of the species on both islands. We found high levels of genetic diversity and evidence for extensive admixture between genetically distinct lineages of P. annua on Marion Island. By contrast, the Prince Edward Island populations showed low genetic diversity, no apparent admixture, and had smaller genomes. On both islands, high genetic diversity was apparent at human landing sites, and on Marion Island, also around human settlements, suggesting that these areas received multiple introductions and/or acted as initial introduction sites and secondary sources (bridgeheads) for invasive populations. More than 70 years of continuous human activity associated with a meteorological station on Marion Island led to a distribution of this species around human settlements and along footpaths, which facilitates ongoing gene flow among geographically separated populations. By contrast, this was not the case for Prince Edward Island, where P. annua populations showed high genetic structure. The high levels of genetic variation and admixture in P. annua facilitated by human activity, coupled with high habitat suitability on both islands, suggest that P. annua is likely to increase its distribution and abundance in the future.}, } @article {pmid34181762, year = {2021}, author = {Folk, RA and Siniscalchi, CM}, title = {Biodiversity at the global scale: the synthesis continues.}, journal = {American journal of botany}, volume = {108}, number = {6}, pages = {912-924}, doi = {10.1002/ajb2.1694}, pmid = {34181762}, issn = {1537-2197}, mesh = {*Biodiversity ; *Ecology ; Phylogeny ; Plants ; }, abstract = {Traditionally, the generation and use of biodiversity data and their associated specimen objects have been primarily the purview of individuals and small research groups. While deposition of data and specimens in herbaria and other repositories has long been the norm, throughout most of their history, these resources have been accessible only to a small community of specialists. Through recent concerted efforts, primarily at the level of national and international governmental agencies over the last two decades, the pace of biodiversity data accumulation has accelerated, and a wider array of biodiversity scientists has gained access to this massive accumulation of resources, applying them to an ever-widening compass of research pursuits. We review how these new resources and increasing access to them are affecting the landscape of biodiversity research in plants today, focusing on new applications across evolution, ecology, and other fields that have been enabled specifically by the availability of these data and the global scope that was previously beyond the reach of individual investigators. We give an overview of recent advances organized along three lines: broad-scale analyses of distributional data and spatial information, phylogenetic research circumscribing large clades with comprehensive taxon sampling, and data sets derived from improved accessibility of biodiversity literature. We also review synergies between large data resources and more traditional data collection paradigms, describe shortfalls and how to overcome them, and reflect on the future of plant biodiversity analyses in light of increasing linkages between data types and scientists in our field.}, } @article {pmid34180607, year = {2021}, author = {Bruggeling, CE and Garza, DR and Achouiti, S and Mes, W and Dutilh, BE and Boleij, A}, title = {Optimized bacterial DNA isolation method for microbiome analysis of human tissues.}, journal = {MicrobiologyOpen}, volume = {10}, number = {3}, pages = {e1191}, pmid = {34180607}, issn = {2045-8827}, mesh = {Bacteria/classification/*genetics/*isolation & purification ; Biopsy ; Colon/microbiology/pathology ; DNA, Bacterial/genetics/*isolation & purification ; Humans ; Metagenomics ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Recent advances in microbiome sequencing have rendered new insights into the role of the microbiome in human health with potential clinical implications. Unfortunately, the presence of host DNA in tissue isolates has hampered the analysis of host-associated bacteria. Here, we present a DNA isolation protocol for tissue, optimized on biopsies from resected human colons (~2-5 mm in size), which includes reduction of human DNA without distortion of relative bacterial abundance at the phylum level. We evaluated which concentrations of Triton and saponin lyse human cells and leave bacterial cells intact, in combination with DNAse treatment to deplete released human DNA. Saponin at a concentration of 0.0125% in PBS lysed host cells, resulting in a 4.5-fold enrichment of bacterial DNA while preserving the relative abundance of Firmicutes, Bacteroidetes, γ-Proteobacteria, and Actinobacteria assessed by qPCR. Our optimized protocol was validated in the setting of two large clinical studies on 521 in vivo acquired colon biopsies of 226 patients using shotgun metagenomics. The resulting bacterial profiles exhibited alpha and beta diversities that are similar to the diversities found by 16S rRNA amplicon sequencing. A direct comparison between shotgun metagenomics and 16S rRNA amplicon sequencing of 15 forceps tissue biopsies showed similar bacterial profiles and a similar Shannon diversity index between the sequencing methods. Hereby, we present the first protocol for enriching bacterial DNA from tissue biopsies that allows efficient isolation of all bacteria. Our protocol facilitates analysis of a wide spectrum of bacteria of clinical tissue samples improving their applicability for microbiome research.}, } @article {pmid34178741, year = {2020}, author = {Mihailovic, N and Vasiljevic, D and Milicic, V and Luketina Sunjka, M and Radovanovi, S and Milicic, B and Kocic, S}, title = {Discrepancy between Admission and Discharge Diagnoses in Central Serbia: Analysis by the Groups of International Classification of Diseases, 10th Revision.}, journal = {Iranian journal of public health}, volume = {49}, number = {12}, pages = {2348-2355}, pmid = {34178741}, issn = {2251-6093}, abstract = {BACKGROUND: Repeated research while using the same methodology can be useful and it can enable relevant conclusions in the same health care system. The aim of our study was to perform comparative analysis of the agreement between admission and discharge diagnostic groups in period 2014-2017 with period 2006-2013 in the Clinical Center of Kragujevac, Serbia.

METHODS: The 5% simple, random sample was made from the basic set of all hospital reports from Clinical Centre Kragujevac, Serbia, in the period 01.01. 2014 - 31.12. 2017 (n=10228). The first four digits of ICD-10 codes at admission and discharge were compared for agreement. We used discharge diagnosis as a "golden standard". Statistical analysis was performed using Cohen's Kappa statistic.

RESULTS: In the period 2014-2017, agreement between diagnosis among the most ICD10 groups increased in comparison with the period 2006-2013. Disagreements between diagnosis in the period 2014-2017 in comparation with period 2006-2013 was associated with increased length of stay in the hospital (7.5 vs. 9.1 days, P<0.01), patients were younger (54 vs 49.6 yr, P<0.01), number of males declined (26.3% vs 16.2%, P<0.05), kappa value decreased in XV ICD10 group and XI ICD10 group and kappa value increased in XIV ICD10 group.

CONCLUSION: Agreement between admission and discharge diagnosis among the most ICD10 diagnostic groups increased. Introduction of a new web application has increased the quality of data, but interpreting it requires the skill of researchers. Further research should identify modifiable causes of discrepancy between admission and discharge diagnoses.}, } @article {pmid34177836, year = {2021}, author = {Solon, AJ and Mastrangelo, C and Vimercati, L and Sommers, P and Darcy, JL and Gendron, EMS and Porazinska, DL and Schmidt, SK}, title = {Gullies and Moraines Are Islands of Biodiversity in an Arid, Mountain Landscape, Asgard Range, Antarctica.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {654135}, pmid = {34177836}, issn = {1664-302X}, abstract = {Cold, dry, and nutrient-poor, the McMurdo Dry Valleys of Antarctica are among the most extreme terrestrial environments on Earth. Numerous studies have described microbial communities of low elevation soils and streams below glaciers, while less is known about microbial communities in higher elevation soils above glaciers. We characterized microbial life in four landscape features (habitats) of a mountain in Taylor Valley. These habitats varied significantly in soil moisture and include moist soils of a (1) lateral glacial moraine, (2) gully that terminates at the moraine, and very dry soils on (3) a southeastern slope and (4) dry sites near the gully. Using rRNA gene PCR amplicon sequencing of Bacteria and Archaea (16S SSU) and eukaryotes (18S SSU), we found that all habitat types harbored significantly different bacterial and eukaryotic communities and that these differences were most apparent when comparing habitats that had macroscopically visible soil crusts (gully and moraine) to habitats with no visible crusts (near gully and slope). These differences were driven by a relative predominance of Actinobacteria and a Colpodella sp. in non-crust habitats, and by phototrophic bacteria and eukaryotes (e.g., a moss) and predators (e.g., tardigrades) in habitats with biological soil crusts (gully and moraine). The gully and moraine also had significantly higher 16S and 18S ESV richness than the other two habitat types. We further found that many of the phototrophic bacteria and eukaryotes of the gully and moraine share high sequence identity with phototrophs from moist and wet areas elsewhere in the Dry Valleys and other cold desert ecosystems. These include a Moss (Bryum sp.), several algae (e.g., a Chlorococcum sp.) and cyanobacteria (e.g., Nostoc and Phormidium spp.). Overall, the results reported here broaden the diversity of habitat types that have been studied in the Dry Valleys of Antarctica and suggest future avenues of research to more definitively understand the biogeography and factors controlling microbial diversity in this unique ecosystem.}, } @article {pmid34174780, year = {2021}, author = {Kishore, K and Jaswal, V and Verma, M and Koushal, V}, title = {Exploring the Utility of Google Mobility Data During the COVID-19 Pandemic in India: Digital Epidemiological Analysis.}, journal = {JMIR public health and surveillance}, volume = {7}, number = {8}, pages = {e29957}, pmid = {34174780}, issn = {2369-2960}, mesh = {COVID-19/*epidemiology/*transmission ; *Cell Phone ; *Geographic Information Systems ; Humans ; India/epidemiology ; *Pandemics ; Travel/*statistics & numerical data ; }, abstract = {BACKGROUND: Association between human mobility and disease transmission has been established for COVID-19, but quantifying the levels of mobility over large geographical areas is difficult. Google has released Community Mobility Reports (CMRs) containing data about the movement of people, collated from mobile devices.

OBJECTIVE: The aim of this study is to explore the use of CMRs to assess the role of mobility in spreading COVID-19 infection in India.

METHODS: In this ecological study, we analyzed CMRs to determine human mobility between March and October 2020. The data were compared for the phases before the lockdown (between March 14 and 25, 2020), during lockdown (March 25-June 7, 2020), and after the lockdown (June 8-October 15, 2020) with the reference periods (ie, January 3-February 6, 2020). Another data set depicting the burden of COVID-19 as per various disease severity indicators was derived from a crowdsourced API. The relationship between the two data sets was investigated using the Kendall tau correlation to depict the correlation between mobility and disease severity.

RESULTS: At the national level, mobility decreased from -38% to -77% for all areas but residential (which showed an increase of 24.6%) during the lockdown compared to the reference period. At the beginning of the unlock phase, the state of Sikkim (minimum cases: 7) with a -60% reduction in mobility depicted more mobility compared to -82% in Maharashtra (maximum cases: 1.59 million). Residential mobility was negatively correlated (-0.05 to -0.91) with all other measures of mobility. The magnitude of the correlations for intramobility indicators was comparatively low for the lockdown phase (correlation ≥0.5 for 12 indicators) compared to the other phases (correlation ≥0.5 for 45 and 18 indicators in the prelockdown and unlock phases, respectively). A high correlation coefficient between epidemiological and mobility indicators was observed for the lockdown and unlock phases compared to the prelockdown phase.

CONCLUSIONS: Mobile-based open-source mobility data can be used to assess the effectiveness of social distancing in mitigating disease spread. CMR data depicted an association between mobility and disease severity, and we suggest using this technique to supplement future COVID-19 surveillance.}, } @article {pmid34171977, year = {2022}, author = {Biçer, Ş and Yıldırım, A}, title = {Digital Death and Thanatechnology: New Ways of Thinking About Data (Im)Mortality and Digital Transformation.}, journal = {Omics : a journal of integrative biology}, volume = {26}, number = {2}, pages = {88-92}, doi = {10.1089/omi.2021.0096}, pmid = {34171977}, issn = {1557-8100}, mesh = {*Artificial Intelligence ; Big Data ; Digital Technology ; Humans ; *Internet ; Pandemics ; }, abstract = {Digital technologies such as the Internet of Things and artificial intelligence are changing how we live and do research, for example, the ways in which patient-reported outcomes and phenomics big data are curated and analyzed. Digital transformation is everywhere and is reshaping data (im)mortality in a wide range of sectors in medicine, engineering, journalism, and beyond. In this context, thanatechnology is a term introduced by Carla Sofka over two decades ago, referring to "any kind of technology that can be used to deal with death, dying, grief, loss, and illness." The field of thanatechnology has become relevant in the digital age as social media is full of accounts from dead individuals, whereas digital media is often harnessed as a source of data and metadata, and in times of pandemics and normalcy. Emerging macroscale analyses forecast billions of social media user accounts from deceased persons in the current century. What happens to digital remains of persons once they cease to exist physically? Digital death, or its absence in the case of deceased individuals, becomes a challenge for both data availability and veracity, and confound research and public health services. Data (im)mortality and digital death are also relevant for research on past events of significance for public health, for example, to discern the history of pandemics and ecological threats. This article examines and calls for new ways of thinking about digital death and thanatechnology as integral dimensions of digital transformation in medicine, new media studies, and society in the 21st century.}, } @article {pmid34171302, year = {2021}, author = {Souilmi, Y and Lauterbur, ME and Tobler, R and Huber, CD and Johar, AS and Moradi, SV and Johnston, WA and Krogan, NJ and Alexandrov, K and Enard, D}, title = {An ancient viral epidemic involving host coronavirus interacting genes more than 20,000 years ago in East Asia.}, journal = {Current biology : CB}, volume = {31}, number = {16}, pages = {3504-3514.e9}, pmid = {34171302}, issn = {1879-0445}, support = {R01 AI120694/AI/NIAID NIH HHS/United States ; U19 AI135990/AI/NIAID NIH HHS/United States ; R01 AI122747/AI/NIAID NIH HHS/United States ; U19 AI135972/AI/NIAID NIH HHS/United States ; P01 AI063302/AI/NIAID NIH HHS/United States ; P50 AI150476/AI/NIAID NIH HHS/United States ; R01 AI143292/AI/NIAID NIH HHS/United States ; }, mesh = {Coronavirus/*genetics ; Coronavirus Infections/*history/virology ; Datasets as Topic ; Evolution, Molecular ; Asia, Eastern/epidemiology ; Gene Frequency ; Genetic Predisposition to Disease ; Genome, Human/*genetics ; Genome, Viral/genetics ; Genome-Wide Association Study ; History, Ancient ; Host Microbial Interactions/*genetics ; Human Genome Project ; Humans ; Mutation ; Pandemics/*history ; Phylogeny ; Selection, Genetic ; }, abstract = {The current severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has emphasized the vulnerability of human populations to novel viral pressures, despite the vast array of epidemiological and biomedical tools now available. Notably, modern human genomes contain evolutionary information tracing back tens of thousands of years, which may help identify the viruses that have impacted our ancestors-pointing to which viruses have future pandemic potential. Here, we apply evolutionary analyses to human genomic datasets to recover selection events involving tens of human genes that interact with coronaviruses, including SARS-CoV-2, that likely started more than 20,000 years ago. These adaptive events were limited to the population ancestral to East Asian populations. Multiple lines of functional evidence support an ancient viral selective pressure, and East Asia is the geographical origin of several modern coronavirus epidemics. An arms race with an ancient coronavirus, or with a different virus that happened to use similar interactions as coronaviruses with human hosts, may thus have taken place in ancestral East Asian populations. By learning more about our ancient viral foes, our study highlights the promise of evolutionary information to better predict the pandemics of the future. Importantly, adaptation to ancient viral epidemics in specific human populations does not necessarily imply any difference in genetic susceptibility between different human populations, and the current evidence points toward an overwhelming impact of socioeconomic factors in the case of coronavirus disease 2019 (COVID-19).}, } @article {pmid34170938, year = {2021}, author = {Hartmann, SA and Hochradel, K and Greule, S and Günther, F and Luedtke, B and Schauer-Weisshahn, H and Brinkmann, R}, title = {Collision risk of bats with small wind turbines: Worst-case scenarios near roosts, commuting and hunting structures.}, journal = {PloS one}, volume = {16}, number = {6}, pages = {e0253782}, pmid = {34170938}, issn = {1932-6203}, mesh = {Animals ; Chiroptera/*physiology ; *Conservation of Natural Resources ; *Models, Biological ; Renewable Energy ; }, abstract = {Small wind turbines (SWTs) have become increasingly common within the last decade, but their impact on wildlife, especially bats, is largely unknown. We conducted an operational experiment by sequentially placing a mobile SWT with five different operational modes at six sites of high bat activity, including roosts, commuting structures, and highly frequented hunting areas. Bat flight trajectories around the SWT were documented at each site during five consecutive nights using a specifically designed high-spatial-resolution 3D camera. The recordings showed high bat activity levels close to the SWT (7,065 flight trajectories within a 10-m radius). The minimum distance to the rotor of each trajectory varied between 0 and 18 m, with a mean of 4.6 m across all sites. Linear mixed models created to account for site differences showed that, compared to a reference pole without a SWT, bats flew 0.4 m closer to the rotor (95% CI 0.3-0.6 m) if it was out of operation and 0.3 m closer (95% CI 0.1-0.4 m) if it was moving slowly. Exploratory behavior was frequently observed, with many bats deviating from their original flight trajectory to approach the rotor. Among 7,850 documented trajectories, 176 crossed the rotor, including 65 while it was in motion. The collision of one P. pygmaeus individual occurred during the experiment. These results demonstrate that, despite the generally strong ability of bats to evade moving rotor blades, bat casualties at SWTs placed at sites of high bat activity can reach or exceed the current threshold levels set for large wind turbines. As SWTs provide less energy than large turbines, their negative impact on bats should be minimized by avoidance measures such as a bat-friendly site selection or curtailment algorithms.}, } @article {pmid34166051, year = {2022}, author = {Wenzel, M and Rowland, Z and Kubiak, T}, title = {How much variance can event intensity and emotion regulation strategies explain in momentary affect in daily life?.}, journal = {Emotion (Washington, D.C.)}, volume = {22}, number = {8}, pages = {1969-1979}, doi = {10.1037/emo0000816}, pmid = {34166051}, issn = {1931-1516}, support = {//Stipendienstiftung Rheinland-Pfalz/ ; //Johannes Gutenberg Mainz University/ ; }, mesh = {Humans ; *Emotional Regulation ; Emotions/physiology ; Ecological Momentary Assessment ; Data Management ; }, abstract = {Research based on the process model of emotion regulation has largely focused on affective outcomes of four prominent emotion regulation strategies: distraction, rumination, reappraisal, and suppression. We identified two areas that are relatively understudied regarding the prediction of affect in daily life: (a) comparing the importance of these four strategies to the subjective experience of event intensity and (b) including additional emotion regulation strategies that focus more on positive than negative affect. In two ecological momentary assessment data sets (Nindividuals = 299), we found that event intensity explained an average of 14.8% (4.9% to 25.9%) of the total variance in momentary affect above the variance explained by emotion regulation strategies. In turn, emotion regulation strategies explained an average of 8.3% (2.4% to 19.6%) in additional total variance in momentary affect. The added predictive power of emotion regulation strategies above event intensity was improved when strategies more specific to positive affect (ΔR[2] = 5.1%) were included. These results highlight avenues for future research that include strategies that focus on the selection and modification of an emotionally relevant situation and on positive affect. (PsycInfo Database Record (c) 2022 APA, all rights reserved).}, } @article {pmid34162873, year = {2021}, author = {Scherlach, K and Hertweck, C}, title = {Mining and unearthing hidden biosynthetic potential.}, journal = {Nature communications}, volume = {12}, number = {1}, pages = {3864}, pmid = {34162873}, issn = {2041-1723}, mesh = {Biological Products/chemistry/metabolism ; Biosynthetic Pathways/genetics ; Computational Biology/*methods ; Data Mining/*methods ; Drug Discovery/methods ; Genome, Bacterial/*genetics ; Genome, Plant/*genetics ; Genomics/*methods ; Molecular Structure ; Secondary Metabolism/genetics ; }, abstract = {Genetically encoded small molecules (secondary metabolites) play eminent roles in ecological interactions, as pathogenicity factors and as drug leads. Yet, these chemical mediators often evade detection, and the discovery of novel entities is hampered by low production and high rediscovery rates. These limitations may be addressed by genome mining for biosynthetic gene clusters, thereby unveiling cryptic metabolic potential. The development of sophisticated data mining methods and genetic and analytical tools has enabled the discovery of an impressive array of previously overlooked natural products. This review shows the newest developments in the field, highlighting compound discovery from unconventional sources and microbiomes.}, } @article {pmid34161793, year = {2021}, author = {Frank, A and Subbey, S and Kobras, M and Gjøsæter, H}, title = {Population dynamic regulators in an empirical predator-prey system.}, journal = {Journal of theoretical biology}, volume = {527}, number = {}, pages = {110814}, doi = {10.1016/j.jtbi.2021.110814}, pmid = {34161793}, issn = {1095-8541}, mesh = {Animals ; Biomass ; *Ecosystem ; Fishes ; Food Chain ; Models, Biological ; Population Dynamics ; *Predatory Behavior ; }, abstract = {Capelin (Mallotus villosus) is a short-lived (1-4 years) fish species, that plays a crucial role by dominating the intermediate trophic level in the Barents Sea. Several episodes of extreme biomass decline (collapse) have been observed during the last three decades. We postulate that these collapses might be regulated by food availability (bottom-up effect) and/or by time discrepancy between capelin feeding and abundance of its prey (match-mismatch hypothesis). This paper investigates our postulate using a model consisting of a set of coupled differential equations to describe the predator-prey system, with a single delay term, τ, in description of the predator dynamics. We derive theoretical conditions on τ, as well as determine how changes in these conditions define different stability regimes of the system. Unconstrained optimization is used to calculate optimal model parameters by fitting the predator-prey model to empirical data. The optimization results are combined with those from the theoretical analysis, to make inference about the empirical system stability. Our results show that Hopf bifurcation occurs in the predatory-prey system when τ exceeds a theoretically derived value τ[∗]>0. This value represents the critical time for prey availability in advance of the optimal predator growth period.Set into an ecological context, our findings provide mathematical evidence for validity of the match-mismatch hypothesis and a bottom-up effect for capelin.}, } @article {pmid34161736, year = {2021}, author = {Huber, C and Müller, E and Schulze, T and Brack, W and Krauss, M}, title = {Improving the Screening Analysis of Pesticide Metabolites in Human Biomonitoring by Combining High-Throughput In Vitro Incubation and Automated LC-HRMS Data Processing.}, journal = {Analytical chemistry}, volume = {93}, number = {26}, pages = {9149-9157}, doi = {10.1021/acs.analchem.1c00972}, pmid = {34161736}, issn = {1520-6882}, mesh = {Biological Monitoring ; Chromatography, Liquid ; Databases, Factual ; Humans ; Mass Spectrometry ; *Pesticides/analysis ; }, abstract = {There is a current need to monitor human exposure to a large number of pesticides and other chemicals of emerging concern (CECs). This requires screening analysis with high confidence for these compounds and their metabolites in complex matrices, which is hampered by the fact that no reference standards are available for most metabolites. We address this challenge by a high-throughput workflow based on incubation of pesticides (or other CECs) with human liver S9, followed by solid-phase extraction, liquid chromatography-high-resolution mass spectrometry (LC-HRMS) analysis, and automated data processing to generate a database (retention time, precursor m/z, and MS[2] spectral library) for the annotation in human samples. The metabolite prioritization consists of statistical comparisons and mass defect and m/z range filtering to obtain a subset of probable phase I metabolites, for which molecular formulas and likely metabolic transformation are retrieved. We tested the workflow on 22 pesticides, for which we could determine 91 metabolite molecular formulas which are only partly covered by the literature and/or predicted by in silico metabolization. Our workflow allows for an efficient generation of metabolite reference information, which can be used directly for annotating LC-HRMS data from human samples. A full structure elucidation of individual metabolites can be limited to those being actually present in human samples.}, } @article {pmid34161323, year = {2021}, author = {Mishra, AP and Harper, NS and Schnupp, JWH}, title = {Exploring the distribution of statistical feature parameters for natural sound textures.}, journal = {PloS one}, volume = {16}, number = {6}, pages = {e0238960}, pmid = {34161323}, issn = {1932-6203}, mesh = {Acoustic Stimulation/methods ; Acoustics ; Auditory Perception/*physiology ; Cochlea/physiology ; Databases, Factual ; Humans ; Models, Statistical ; Noise ; Principal Component Analysis/methods ; Psychoacoustics ; *Sound ; }, abstract = {Sounds like "running water" and "buzzing bees" are classes of sounds which are a collective result of many similar acoustic events and are known as "sound textures". A recent psychoacoustic study using sound textures has reported that natural sounding textures can be synthesized from white noise by imposing statistical features such as marginals and correlations computed from the outputs of cochlear models responding to the textures. The outputs being the envelopes of bandpass filter responses, the 'cochlear envelope'. This suggests that the perceptual qualities of many natural sounds derive directly from such statistical features, and raises the question of how these statistical features are distributed in the acoustic environment. To address this question, we collected a corpus of 200 sound textures from public online sources and analyzed the distributions of the textures' marginal statistics (mean, variance, skew, and kurtosis), cross-frequency correlations and modulation power statistics. A principal component analysis of these parameters revealed a great deal of redundancy in the texture parameters. For example, just two marginal principal components, which can be thought of as measuring the sparseness or burstiness of a texture, capture as much as 64% of the variance of the 128 dimensional marginal parameter space, while the first two principal components of cochlear correlations capture as much as 88% of the variance in the 496 correlation parameters. Knowledge of the statistical distributions documented here may help guide the choice of acoustic stimuli with high ecological validity in future research.}, } @article {pmid34160409, year = {2021}, author = {Ciulla, MM and Re, D and Gilardoni, E and D'Amato, A and Altomare, A and Baron, G and Carugo, S and Aldini, G}, title = {PHoral: Effects of carnosine supplementation on quantity/quality of oral salivae in healthy volunteer and in subjects affected by common oral pathologies.}, journal = {Medicine}, volume = {100}, number = {25}, pages = {e26369}, pmid = {34160409}, issn = {1536-5964}, mesh = {Administration, Buccal ; Adolescent ; Adult ; Cardiovascular Diseases/etiology/prevention & control ; Carnosine/*administration & dosage ; Dental Caries/complications/*diet therapy/prevention & control ; Dietary Supplements ; Gingivitis/*diet therapy/microbiology/prevention & control ; Healthy Volunteers ; Humans ; Hydrogen-Ion Concentration ; Male ; Microbiota/physiology ; Mouth Mucosa/microbiology ; Periodontitis/*diet therapy/microbiology/prevention & control ; Saliva/*chemistry/metabolism ; Tablets ; Young Adult ; }, abstract = {BACKGROUND: Diseases of the oral cavity (OC) with an infectious trigger such as caries and periodontal disease are extremely common in the general population and can also have effects at the cardiovascular level. The oral salivary flow, with its buffering capacity, is able to regulate the pH of the OC and, therefore, significantly contribute to the ecological balance of the microenvironment in which the oral microbiome (OM) develops. On the other side, when the quality/quantity of salivary flow is altered it is supposed the disruption of this balance with the potential increase in oral pathogens and triggered diseases. Among the endogenous substances able to exert a significant effect on the salivary flow and its characteristics, carnosine (Car), a dipeptide originally isolated in skeletal muscle, represents, thanks to the known buffering properties, a promising principle.

METHODS: We aimed this protocol to evaluate the quantitative/qualitative characteristics of the salivary flow in healthy volunteer subjects (n = 20) and in subjects suffering from common OC pathologies (n = 40), before and after 7 days of supplementation with SaliflussTM (Metis Healthcare srl, Milan, Italy), a Class I medical device on the market as 400 mg mucoadhesive oral tablets that has Car as the main ingredient.

DISCUSSION: Combining the characteristics of saliva with the OM and comparing them with OC pathologies, we expect to clarify their reciprocal relationship and, using quantitative proteomics techniques, to help clarify the mechanism of action of Car.}, } @article {pmid34159217, year = {2021}, author = {Brook, DL and Hetrick, AT and Chettri, SR and Schalkoff, CA and Sibley, AL and Lancaster, KE and Go, VF and Miller, WC and Kline, DM}, title = {The Relationship Between Hepatitis C Virus Rates and Office-Based Buprenorphine Access in Ohio.}, journal = {Open forum infectious diseases}, volume = {8}, number = {6}, pages = {ofab242}, pmid = {34159217}, issn = {2328-8957}, support = {F30 DA050423/DA/NIDA NIH HHS/United States ; K01 DA048174/DA/NIDA NIH HHS/United States ; }, abstract = {BACKGROUND: The United States is experiencing an epidemic of hepatitis C virus (HCV) infections due to injection drug use, primarily of opioids and predominantly in rural areas. Buprenorphine, a medication for opioid use disorder, may indirectly prevent HCV transmission. We assessed the relationship of HCV rates and office-based buprenorphine prescribing in Ohio.

METHODS: We conducted an ecological study of the county-level (n = 88) relationship between HCV case rates and office-based buprenorphine prescribing in Ohio. We fit adjusted negative binomial models between the county-level acute and total HCV incidence rates during 2013-2017 and 1) the number of patients in each county that could be served by office-based buprenorphine (prescribing capacity) and 2) the number served by office-based buprenorphine (prescribing frequency) from January-March, 2018.

RESULTS: For each 10% increase in acute HCV rate, office-based buprenorphine prescribing capacity differed by 1% (95% CI: -1%, 3%). For each 10% increase in total HCV rate, office-based buprenorphine prescribing capacity was 12% (95% CI: 7%, 17%) higher. For each 10% increase in acute HCV rate, office-based buprenorphine prescribing frequency was 1% (95% CI: -1%, 3%) higher. For each 10% increase in total HCV rate, office-based buprenorphine prescribing frequency was 14% (95% CI: 7%, 20%) higher.

CONCLUSIONS: Rural counties in Ohio have less office-based buprenorphine and higher acute HCV rates versus urban counties, but a similar relationship between office-based buprenorphine prescribing and HCV case rates. To adequately prevent and control HCV rates, certain rural counties may need more office-based buprenorphine prescribing in areas with high HCV case rates.}, } @article {pmid34158546, year = {2021}, author = {Akond, Z and Ahsan, MA and Alam, M and Mollah, MNH}, title = {Robustification of GWAS to explore effective SNPs addressing the challenges of hidden population stratification and polygenic effects.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {13060}, pmid = {34158546}, issn = {2045-2322}, mesh = {Computer Simulation ; Flowers/genetics/physiology ; Gene Expression Profiling ; Gene Expression Regulation, Plant ; Gene Ontology ; Genes, Plant ; *Genome-Wide Association Study ; Genotype ; Humans ; Linear Models ; Multifactorial Inheritance/*genetics ; Oryza/genetics/physiology ; Phenotype ; Polymorphism, Single Nucleotide/*genetics ; }, abstract = {Genome-wide association studies (GWAS) play a vital role in identifying important genes those is associated with the phenotypic variations of living organisms. There are several statistical methods for GWAS including the linear mixed model (LMM) which is popular for addressing the challenges of hidden population stratification and polygenic effects. However, most of these methods including LMM are sensitive to phenotypic outliers that may lead the misleading results. To overcome this problem, in this paper, we proposed a way to robustify the LMM approach for reducing the influence of outlying observations using the β-divergence method. The performance of the proposed method was investigated using both synthetic and real data analysis. Simulation results showed that the proposed method performs better than both linear regression model (LRM) and LMM approaches in terms of powers and false discovery rates in presence of phenotypic outliers. On the other hand, the proposed method performed almost similar to LMM approach but much better than LRM approach in absence of outliers. In the case of real data analysis, our proposed method identified 11 SNPs that are significantly associated with the rice flowering time. Among the identified candidate SNPs, some were involved in seed development and flowering time pathways, and some were connected with flower and other developmental processes. These identified candidate SNPs could assist rice breeding programs effectively. Thus, our findings highlighted the importance of robust GWAS in identifying candidate genes.}, } @article {pmid34157255, year = {2021}, author = {McElwain, J}, title = {Jennifer McElwain.}, journal = {Current biology : CB}, volume = {31}, number = {12}, pages = {R772-R774}, doi = {10.1016/j.cub.2021.05.028}, pmid = {34157255}, issn = {1879-0445}, mesh = {Big Data ; Botany/*history ; Earth Sciences/history ; Fossils ; Greenland ; History, 20th Century ; History, 21st Century ; Ireland ; Literature, Modern ; Paleontology/*history ; }, abstract = {Interview with Jennifer McElwain, who performs plant experiments in controlled atmospheric, light and climatic conditions at Trinity College Dublin to assess how these factors have influenced plant evolution and ecology throughout Earth's history.}, } @article {pmid34156297, year = {2021}, author = {Carper, DL and Weston, DJ and Barde, A and Timm, CM and Lu, TY and Burdick, LH and Jawdy, SS and Klingeman, DM and Robeson, MS and Veach, AM and Cregger, MA and Kalluri, UC and Schadt, CW and Podar, M and Doktycz, MJ and Pelletier, DA}, title = {Cultivating the Bacterial Microbiota of Populus Roots.}, journal = {mSystems}, volume = {6}, number = {3}, pages = {e0130620}, pmid = {34156297}, issn = {2379-5077}, support = {//U.S. Department of Energy (DOE)/ ; }, abstract = {The integral role of microbial communities in plant growth and health is now widely recognized, and, increasingly, the constituents of the microbiome are being defined. While phylogenetic surveys have revealed the taxa present in a microbiome and show that this composition can depend on, and respond to, environmental perturbations, the challenge shifts to determining why particular microbes are selected and how they collectively function in concert with their host. In this study, we targeted the isolation of representative bacterial strains from environmental samples of Populus roots using a direct plating approach and compared them to amplicon-based sequencing analysis of root samples. The resulting culture collection contains 3,211 unique isolates representing 10 classes, 18 orders, 45 families, and 120 genera from 6 phyla, based on 16S rRNA gene sequence analysis. The collection accounts for ∼50% of the natural community of plant-associated bacteria as determined by phylogenetic analysis. Additionally, a representative set of 553 had their genomes sequenced to facilitate functional analyses. The top sequence variants in the amplicon data, identified as Pseudomonas, had multiple representatives within the culture collection. We then explore a simplified microbiome, comprised of 10 strains representing abundant taxa from environmental samples, and tested for their ability to reproducibly colonize Populus root tissue. The 10-member simplified community was able to reproducibly colonize on Populus roots after 21 days, with some taxa found in surface-sterilized aboveground tissue. This study presents a comprehensive collection of bacteria isolated from Populus for use in exploring microbial function and community inoculation experiments to understand basic concepts of plant and environmental selection. IMPORTANCE Microbial communities play an integral role in the health and survival of their plant hosts. Many studies have identified key members in these communities and led to the use of synthetic communities for elucidating their function; however, these studies are limited by the available cultured bacterial representatives. Here, we present a bacterial culture collection comprising 3,211 isolates that is representative of the root community of Populus. We then demonstrate the ability to examine underlying microbe-microbe interactions using a synthetic community approach. This culture collection will allow for the greater exploration of the microbial community function through targeted experimentation and manipulation.}, } @article {pmid34155233, year = {2021}, author = {Zhang, H and Yue, P and Tong, X and Bai, J and Yang, J and Guo, J}, title = {mRNA-seq and miRNA-seq profiling analyses reveal molecular mechanisms regulating induction of fruiting body in Ophiocordyceps sinensis.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {12944}, pmid = {34155233}, issn = {2045-2322}, mesh = {Computational Biology/methods ; Cordyceps/*genetics/metabolism ; Fruiting Bodies, Fungal/*genetics ; Gene Expression Profiling ; Gene Expression Regulation, Fungal ; Gene Ontology ; MicroRNAs/*genetics ; Models, Biological ; RNA, Messenger/*genetics ; *Transcriptome ; }, abstract = {Ophiocordyceps sinensis has been a source of valuable materials in traditional Asian medicine for over two thousand years. With recent global warming and overharvest, however, the availability of these wild fungi has decreased dramatically. While fruiting body of O. sinensis has been artificially cultivated, the molecular mechanisms that govern the induction of fruiting body at the transcriptional and post-transcriptional levels are unclear. In this study, we carried out both mRNA and small RNA sequencing to identify crucial genes and miRNA-like RNAs (milRNAs) involved in the development of fruiting body. A total of 2875 differentially expressed genes (DEGs), and 71 differentially expressed milRNAs (DEMs) were identified among the mycoparasite complex, the sclerotium (ST) and the fruiting body stage. Functional enrichment and Gene Set Enrichment Analysis indicated that the ST had increased oxidative stress and energy metabolism and that mitogen-activated protein kinase signaling might induce the formation of fruiting body. Integrated analysis of DEGs and DEMs revealed that n_os_milR16, n_os_milR21, n_os_milR34, and n_os_milR90 could be candidate milRNAs that regulate the induction of fruiting body. This study provides transcriptome-wide insight into the molecular basis of fruiting body formation in O. Sinensis and identifies potential candidate genes for improving induction rate.}, } @article {pmid34152039, year = {2021}, author = {Glombik, M and Copetti, D and Bartos, J and Stoces, S and Zwierzykowski, Z and Ruttink, T and Wendel, JF and Duchoslav, M and Dolezel, J and Studer, B and Kopecky, D}, title = {Reciprocal allopolyploid grasses (Festuca × Lolium) display stable patterns of genome dominance.}, journal = {The Plant journal : for cell and molecular biology}, volume = {107}, number = {4}, pages = {1166-1182}, pmid = {34152039}, issn = {1365-313X}, mesh = {Crops, Agricultural ; Databases, Genetic ; Festuca/*genetics/growth & development ; Gene Expression Profiling ; *Gene Expression Regulation, Plant ; *Genome, Plant ; Lolium/*genetics/growth & development ; *Polyploidy ; Regulatory Sequences, Nucleic Acid ; Sequence Analysis, RNA ; }, abstract = {Allopolyploidization entailing the merger of two distinct genomes in a single hybrid organism, is an important process in plant evolution and a valuable tool in breeding programs. Newly established hybrids often experience massive genomic perturbations, including karyotype reshuffling and gene expression modifications. These phenomena may be asymmetric with respect to the two progenitors, with one of the parental genomes being "dominant." Such "genome dominance" can manifest in several ways, including biased homoeolog gene expression and expression level dominance. Here we employed a k-mer-based approach to study gene expression in reciprocal Festuca pratensis Huds. × Lolium multiflorum Lam. allopolyploid grasses. Our study revealed significantly more genes where expression mimicked that of the Lolium parent compared with the Festuca parent. This genome dominance was heritable to successive generation and its direction was only slightly modified by environmental conditions and plant age. Our results suggest that Lolium genome dominance was at least partially caused by its more efficient trans-acting gene expression regulatory factors. Unraveling the mechanisms responsible for propagation of parent-specific traits in hybrid crops contributes to our understanding of allopolyploid genome evolution and opens a way to targeted breeding strategies.}, } @article {pmid34151345, year = {2022}, author = {Tanner, RL and Grover, N and Anderson, ML and Crocker, KC and Dutta, S and Horner, AM and Hough, LE and Moore, TY and Rosen, GL and S Whitney, K and Summers, AP}, title = {Examining Cultural Structures and Functions in Biology.}, journal = {Integrative and comparative biology}, volume = {61}, number = {6}, pages = {2282-2293}, doi = {10.1093/icb/icab140}, pmid = {34151345}, issn = {1557-7023}, mesh = {Animals ; *Biology ; }, abstract = {Scientific culture and structure organize biological sciences in many ways. We make choices concerning the systems and questions we study. Our research then amplifies these choices into factors that influence the directions of future research by shaping our hypotheses, data analyses, interpretation, publication venues, and dissemination via other methods. But our choices are shaped by more than objective curiosity-we are influenced by cultural paradigms reinforced by societal upbringing and scientific indoctrination during training. This extends to the systems and data that we consider to be ethically obtainable or available for study, and who is considered qualified to do research, ask questions, and communicate about research. It is also influenced by the profitability of concepts like open-access-a system designed to improve equity, but which enacts gatekeeping in unintended but foreseeable ways. Creating truly integrative biology programs will require more than intentionally developing departments or institutes that allow overlapping expertise in two or more subfields of biology. Interdisciplinary work requires the expertise of large and diverse teams of scientists working together-this is impossible without an authentic commitment to addressing, not denying, racism when practiced by individuals, institutions, and cultural aspects of academic science. We have identified starting points for remedying how our field has discouraged and caused harm, but we acknowledge there is a long path forward. This path must be paved with field-wide solutions and institutional buy-in: our solutions must match the scale of the problem. Together, we can integrate-not reintegrate-the nuances of biology into our field.}, } @article {pmid34148204, year = {2021}, author = {Omodior, O and Saeedpour-Parizi, MR and Rahman, MK and Azad, A and Clay, K}, title = {Using convolutional neural networks for tick image recognition - a preliminary exploration.}, journal = {Experimental & applied acarology}, volume = {84}, number = {3}, pages = {607-622}, pmid = {34148204}, issn = {1572-9702}, mesh = {Amblyomma ; Animals ; Female ; *Ixodes ; *Ixodidae ; Male ; Neural Networks, Computer ; Nymph ; }, abstract = {Smartphone cameras and digital devices are increasingly used in the capture of tick images by the public as citizen scientists, and rapid advances in deep learning and computer vision has enabled brand new image recognition models to be trained. However, there is currently no web-based or mobile application that supports automated classification of tick images. The purpose of this study was to compare the accuracy of a deep learning model pre-trained with millions of annotated images in Imagenet, against a shallow custom-build convolutional neural network (CNN) model for the classification of common hard ticks present in anthropic areas from northeastern USA. We created a dataset of approximately 2000 images of four tick species (Ixodes scapularis, Dermacentor variabilis, Amblyomma americanum and Haemaphysalis sp.), two sexes (male, female) and two life stages (adult, nymph). We used these tick images to train two separate CNN models - ResNet-50 and a simple shallow custom-built. We evaluated our models' performance on an independent subset of tick images not seen during training. Compared to the ResNet-50 model, the small shallow custom-built model had higher training (99.7%) and validation (99.1%) accuracies. When tested with new tick image data, the shallow custom-built model yielded higher mean prediction accuracy (80%), greater confidence of true detection (88.7%) and lower mean response time (3.64 s). These results demonstrate that, with limited data size for model training, a simple shallow custom-built CNN model has great prospects for use in the classification of common hard ticks present in anthropic areas from northeastern USA.}, } @article {pmid34146566, year = {2021}, author = {Baumgartner, M and Lang, M and Holley, H and Crepaz, D and Hausmann, B and Pjevac, P and Moser, D and Haller, F and Hof, F and Beer, A and Orgler, E and Frick, A and Khare, V and Evstatiev, R and Strohmaier, S and Primas, C and Dolak, W and Köcher, T and Klavins, K and Rath, T and Neurath, MF and Berry, D and Makristathis, A and Muttenthaler, M and Gasche, C}, title = {Mucosal Biofilms Are an Endoscopic Feature of Irritable Bowel Syndrome and Ulcerative Colitis.}, journal = {Gastroenterology}, volume = {161}, number = {4}, pages = {1245-1256.e20}, pmid = {34146566}, issn = {1528-0012}, support = {714366/ERC_/European Research Council/International ; }, mesh = {Austria ; Bacteria/*growth & development/metabolism/ultrastructure ; Biofilms/*growth & development ; Case-Control Studies ; Colitis, Ulcerative/metabolism/*microbiology/pathology ; Colon/metabolism/*microbiology/pathology ; *Colonoscopy ; Deep Learning ; *Gastrointestinal Microbiome ; Germany ; Humans ; Image Interpretation, Computer-Assisted ; Intestinal Mucosa/metabolism/*microbiology/pathology ; Irritable Bowel Syndrome/metabolism/*microbiology/pathology ; Metabolomics ; Microscopy, Confocal ; Microscopy, Electron, Scanning ; Predictive Value of Tests ; Ribotyping ; }, abstract = {BACKGROUND & AIMS: Irritable bowel syndrome (IBS) and inflammatory bowel diseases result in a substantial reduction in quality of life and a considerable socioeconomic impact. In IBS, diagnosis and treatment options are limited, but evidence for involvement of the gut microbiome in disease pathophysiology is emerging. Here we analyzed the prevalence of endoscopically visible mucosal biofilms in gastrointestinal disease and associated changes in microbiome composition and metabolism.

METHODS: The presence of mucosal biofilms was assessed in 1426 patients at 2 European university-based endoscopy centers. One-hundred and seventeen patients were selected for in-depth molecular and microscopic analysis using 16S ribosomal RNA gene amplicon-sequencing of colonic biopsies and fecal samples, confocal microscopy with deep learning-based image analysis, scanning electron microscopy, metabolomics, and in vitro biofilm formation assays.

RESULTS: Biofilms were present in 57% of patients with IBS and 34% of patients with ulcerative colitis compared with 6% of controls (P < .001). These yellow-green adherent layers of the ileum and right-sided colon were microscopically confirmed to be dense bacterial biofilms. 16S-sequencing links the presence of biofilms to a dysbiotic gut microbiome, including overgrowth of Escherichia coli and Ruminococcus gnavus. R. gnavus isolates cultivated from patient biofilms also formed biofilms in vitro. Metabolomic analysis found an accumulation of bile acids within biofilms that correlated with fecal bile acid excretion, linking this phenotype with a mechanism of diarrhea.

CONCLUSIONS: The presence of mucosal biofilms is an endoscopic feature in a subgroup of IBS and ulcerative colitis with disrupted bile acid metabolism and bacterial dysbiosis. They provide novel insight into the pathophysiology of IBS and ulcerative colitis, illustrating that biofilm can be seen as a tipping point in the development of dysbiosis and disease.}, } @article {pmid34144010, year = {2021}, author = {Sun, Y and Li, H}, title = {Data mining for evaluating the ecological compensation, static and dynamic benefits of returning farmland to forest.}, journal = {Environmental research}, volume = {201}, number = {}, pages = {111524}, doi = {10.1016/j.envres.2021.111524}, pmid = {34144010}, issn = {1096-0953}, mesh = {Bayes Theorem ; China ; *Conservation of Natural Resources ; Data Mining ; *Ecosystem ; Farms ; Forests ; }, abstract = {Based on data mining technology, this paper incorporates Bayesian networks to examine ecosystem data in order to investigate the static and dynamic benefits of returning farmland to forests and ecological compensation. The restricted network structure is suggested to reduce training costs and simplify model structure. Simultaneously, in order to increase prediction accuracy over a single model, ensemble learning is utilized to train multiple models to solve the same problem. Furthermore, based on data mining, this article explores the ecosystem's development purpose, constituent elements, and static framework, illustrates its operation and evolution mechanism, and constructs an evaluation system for returning farmland to forest and ecological compensation. Finally, this article incorporates current situation to determine the static and dynamic benefits, and then systematically verifies it using experiments and mathematical statistics. The research findings indicate that the impact of the framework built in this paper meets the standards of the construction model which could be used in practice.}, } @article {pmid34143768, year = {2021}, author = {Prost, V and Gazut, S and Brüls, T}, title = {A zero inflated log-normal model for inference of sparse microbial association networks.}, journal = {PLoS computational biology}, volume = {17}, number = {6}, pages = {e1009089}, pmid = {34143768}, issn = {1553-7358}, mesh = {Algorithms ; Computational Biology ; Computer Simulation ; Metagenome ; Metagenomics/statistics & numerical data ; Microbial Consortia/genetics/physiology ; *Microbiota/genetics/physiology ; *Models, Biological ; Multivariate Analysis ; Normal Distribution ; Synthetic Biology ; }, abstract = {The advent of high-throughput metagenomic sequencing has prompted the development of efficient taxonomic profiling methods allowing to measure the presence, abundance and phylogeny of organisms in a wide range of environmental samples. Multivariate sequence-derived abundance data further has the potential to enable inference of ecological associations between microbial populations, but several technical issues need to be accounted for, like the compositional nature of the data, its extreme sparsity and overdispersion, as well as the frequent need to operate in under-determined regimes. The ecological network reconstruction problem is frequently cast into the paradigm of Gaussian Graphical Models (GGMs) for which efficient structure inference algorithms are available, like the graphical lasso and neighborhood selection. Unfortunately, GGMs or variants thereof can not properly account for the extremely sparse patterns occurring in real-world metagenomic taxonomic profiles. In particular, structural zeros (as opposed to sampling zeros) corresponding to true absences of biological signals fail to be properly handled by most statistical methods. We present here a zero-inflated log-normal graphical model (available at https://github.com/vincentprost/Zi-LN) specifically aimed at handling such "biological" zeros, and demonstrate significant performance gains over state-of-the-art statistical methods for the inference of microbial association networks, with most notable gains obtained when analyzing taxonomic profiles displaying sparsity levels on par with real-world metagenomic datasets.}, } @article {pmid34140494, year = {2021}, author = {Borko, Š and Trontelj, P and Seehausen, O and Moškrič, A and Fišer, C}, title = {A subterranean adaptive radiation of amphipods in Europe.}, journal = {Nature communications}, volume = {12}, number = {1}, pages = {3688}, pmid = {34140494}, issn = {2041-1723}, mesh = {*Adaptation, Physiological ; Amphipoda/*anatomy & histology/*genetics/physiology ; Animals ; Biodiversity ; *Biological Evolution ; Databases, Chemical ; Ecosystem ; Europe ; Europe, Eastern ; Evolution, Molecular ; *Genetic Speciation ; Phenotype ; Phylogeny ; }, abstract = {Adaptive radiations are bursts of evolutionary species diversification that have contributed to much of the species diversity on Earth. An exception is modern Europe, where descendants of ancient adaptive radiations went extinct, and extant adaptive radiations are small, recent and narrowly confined. However, not all legacy of old radiations has been lost. Subterranean environments, which are dark and food-deprived, yet buffered from climate change, have preserved ancient lineages. Here we provide evidence of an entirely subterranean adaptive radiation of the amphipod genus Niphargus, counting hundreds of species. Our modelling of lineage diversification and evolution of morphological and ecological traits using a time-calibrated multilocus phylogeny suggests a major adaptive radiation, comprised of multiple subordinate adaptive radiations. Their spatio-temporal origin coincides with the uplift of carbonate massifs in South-Eastern Europe 15 million years ago. Emerging subterranean environments likely provided unoccupied, predator-free space, constituting ecological opportunity, a key trigger of adaptive radiation. This discovery sheds new light on the biodiversity of Europe.}, } @article {pmid34140471, year = {2021}, author = {Boyero, L and López-Rojo, N and Tonin, AM and Pérez, J and Correa-Araneda, F and Pearson, RG and Bosch, J and Albariño, RJ and Anbalagan, S and Barmuta, LA and Basaguren, A and Burdon, FJ and Caliman, A and Callisto, M and Calor, AR and Campbell, IC and Cardinale, BJ and Jesús Casas, J and Chará-Serna, AM and Chauvet, E and Ciapała, S and Colón-Gaud, C and Cornejo, A and Davis, AM and Degebrodt, M and Dias, ES and Díaz, ME and Douglas, MM and Encalada, AC and Figueroa, R and Flecker, AS and Fleituch, T and García, EA and García, G and García, PE and Gessner, MO and Gómez, JE and Gómez, S and Gonçalves, JF and Graça, MAS and Gwinn, DC and Hall, RO and Hamada, N and Hui, C and Imazawa, D and Iwata, T and Kariuki, SK and Landeira-Dabarca, A and Laymon, K and Leal, M and Marchant, R and Martins, RT and Masese, FO and Maul, M and McKie, BG and Medeiros, AO and Erimba, CMM and Middleton, JA and Monroy, S and Muotka, T and Negishi, JN and Ramírez, A and Richardson, JS and Rincón, J and Rubio-Ríos, J and Dos Santos, GM and Sarremejane, R and Sheldon, F and Sitati, A and Tenkiano, NSD and Tiegs, SD and Tolod, JR and Venarsky, M and Watson, A and Yule, CM}, title = {Impacts of detritivore diversity loss on instream decomposition are greatest in the tropics.}, journal = {Nature communications}, volume = {12}, number = {1}, pages = {3700}, pmid = {34140471}, issn = {2041-1723}, mesh = {Animals ; Biodiversity ; Biomass ; *Biota ; Body Size ; Chironomidae/physiology ; Climate ; *Ecosystem ; Ephemeroptera/physiology ; Insecta/physiology ; Plant Leaves/chemistry ; Rainforest ; *Rivers/chemistry/microbiology/parasitology/virology ; Tropical Climate ; Tundra ; }, abstract = {The relationship between detritivore diversity and decomposition can provide information on how biogeochemical cycles are affected by ongoing rates of extinction, but such evidence has come mostly from local studies and microcosm experiments. We conducted a globally distributed experiment (38 streams across 23 countries in 6 continents) using standardised methods to test the hypothesis that detritivore diversity enhances litter decomposition in streams, to establish the role of other characteristics of detritivore assemblages (abundance, biomass and body size), and to determine how patterns vary across realms, biomes and climates. We observed a positive relationship between diversity and decomposition, strongest in tropical areas, and a key role of abundance and biomass at higher latitudes. Our results suggest that litter decomposition might be altered by detritivore extinctions, particularly in tropical areas, where detritivore diversity is already relatively low and some environmental stressors particularly prevalent.}, } @article {pmid34138866, year = {2021}, author = {Gardner, BJ and Kilpatrick, AM}, title = {Contact tracing efficiency, transmission heterogeneity, and accelerating COVID-19 epidemics.}, journal = {PLoS computational biology}, volume = {17}, number = {6}, pages = {e1009122}, pmid = {34138866}, issn = {1553-7358}, mesh = {*COVID-19/epidemiology/prevention & control/transmission ; Computational Biology ; *Contact Tracing ; Epidemics/*statistics & numerical data ; Humans ; Models, Biological ; SARS-CoV-2 ; }, abstract = {Simultaneously controlling COVID-19 epidemics and limiting economic and societal impacts presents a difficult challenge, especially with limited public health budgets. Testing, contact tracing, and isolating/quarantining is a key strategy that has been used to reduce transmission of SARS-CoV-2, the virus that causes COVID-19 and other pathogens. However, manual contact tracing is a time-consuming process and as case numbers increase a smaller fraction of cases' contacts can be traced, leading to additional virus spread. Delays between symptom onset and being tested (and receiving results), and a low fraction of symptomatic cases being tested and traced can also reduce the impact of contact tracing on transmission. We examined the relationship between increasing cases and delays and the pathogen reproductive number Rt, and the implications for infection dynamics using deterministic and stochastic compartmental models of SARS-CoV-2. We found that Rt increased sigmoidally with the number of cases due to decreasing contact tracing efficacy. This relationship results in accelerating epidemics because Rt initially increases, rather than declines, as infections increase. Shifting contact tracers from locations with high and low case burdens relative to capacity to locations with intermediate case burdens maximizes their impact in reducing Rt (but minimizing total infections may be more complicated). Contact tracing efficacy decreased sharply with increasing delays between symptom onset and tracing and with lower fraction of symptomatic infections being tested. Finally, testing and tracing reductions in Rt can sometimes greatly delay epidemics due to the highly heterogeneous transmission dynamics of SARS-CoV-2. These results demonstrate the importance of having an expandable or mobile team of contact tracers that can be used to control surges in cases. They also highlight the synergistic value of high capacity, easy access testing and rapid turn-around of testing results, and outreach efforts to encourage symptomatic cases to be tested immediately after symptom onset.}, } @article {pmid34137037, year = {2021}, author = {Ogle, K and Liu, Y and Vicca, S and Bahn, M}, title = {A hierarchical, multivariate meta-analysis approach to synthesising global change experiments.}, journal = {The New phytologist}, volume = {231}, number = {6}, pages = {2382-2394}, doi = {10.1111/nph.17562}, pmid = {34137037}, issn = {1469-8137}, mesh = {Bayes Theorem ; Carbon Dioxide ; *Climate Change ; *Ecosystem ; Soil ; }, abstract = {Meta-analyses enable synthesis of results from globally distributed experiments to draw general conclusions about the impacts of global change factors on ecosystem function. Traditional meta-analyses, however, are challenged by the complexity and diversity of experimental results. We illustrate how several key issues can be addressed by a multivariate, hierarchical Bayesian meta-analysis (MHBM) approach applied to information extracted from published studies. We applied an MHBM to log-response ratios for aboveground biomass (AB, n = 300), belowground biomass (BB, n = 205) and soil CO2 exchange (SCE, n = 544), representing 100 studies. The MHBM accounted for study duration, climate effects and covariation among the AB, BB and SCE responses to elevated CO2 (eCO2) and/or warming. The MHBM revealed significant among-study covariation in the AB and BB responses to experimental treatments. The MHBM imputed missing duration (4.2%) and climate (6%) data, and revealed that climate context governs how eCO2 and warming impact ecosystem function. Predictions identified biomes that may be particularly sensitive to eCO2 or warming, but that are under-represented in global change experiments. The MHBM approach offers a flexible and powerful tool for synthesising disparate experimental results reported across multiple studies, sites and response variables.}, } @article {pmid34135869, year = {2021}, author = {Almada-Érix, CN and Almada, CN and Cabral, L and Barros de Medeiros, VP and Roquetto, AR and Santos-Junior, VA and Fontes, M and Gonçalves, AESS and Dos Santos, A and Lollo, PC and Magnani, M and Sant'Ana, AS}, title = {Orange Juice and Yogurt Carrying Probiotic Bacillus coagulans GBI-30 6086: Impact of Intake on Wistar Male Rats Health Parameters and Gut Bacterial Diversity.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {623951}, pmid = {34135869}, issn = {1664-302X}, abstract = {This study aimed to investigate the impact of the food matrix (orange juice and yogurt) on the effects of the spore-forming probiotic microorganism Bacillus coagulans GBI-30 6086 in health parameters and gastrointestinal tract (gut) bacterial diversity in Wistar male rats. Rats (n = 48) were randomly distributed into six groups. The groups were the Control (which received sterile distilled water), Juice (which received orange juice), Yogurt (which received yogurt), Probiotic Bacillus (which received B. coagulans GBI-30 6086 in distilled water), Probiotic Juice (which received orange juice with B. coagulans GBI-30 6086), and Probiotic Yogurt (which received yogurt with B. coagulans GBI-30 6086). Each animal belonging to the different groups was treated for 21 days. The daily administration of probiotic juice or probiotic yogurt did not affect the rats' food or body weight. Rats fed with Probiotic Yogurt showed lower glucose and triglycerides levels (p < 0.05) in comparison to the control group (p < 0.05), while no changes in these parameters were observed in the rats fed with Probiotic Juice. Rats fed with Probiotic Yogurt showed a higher gut bacterial diversity than the control group (p < 0.05), and higher abundance (p < 0.05) of Vibrionales, Enterobacteriales, Burkholderiales, Erysipelotrichales, and Bifidobacteriales compared to all other groups. No changes were observed in the expression levels of antioxidant enzymes or heat shock protein 70 of rats fed with probiotic yogurt or probiotic juice. Results reveal that the consumption of yogurt containing B. coagulans GBI-30 6086 decreases triglycerides and glucose levels and positively impacts the gut bacterial ecology in healthy rats. These animal model findings indicate that the matrix also impacts the functionality of foods carrying spore-forming probiotics. Besides, this research indicates that yogurt is also a suitable food carrier of Bacillus coagulans GBI-30 6086.}, } @article {pmid34134032, year = {2021}, author = {Ryu, SM and Nguyen, QN and Lee, S and Kwon, H and Kwon, J and Lee, H and Kwon, SL and Lee, J and Hwang, BY and Yim, JH and Guo, Y and Kim, JJ and Kang, KS and Lee, D}, title = {Chemical constituents from basidiomycete Basidioradulum radula culture medium and their cytotoxic effect on human prostate cancer DU-145 cells.}, journal = {Bioorganic chemistry}, volume = {114}, number = {}, pages = {105064}, doi = {10.1016/j.bioorg.2021.105064}, pmid = {34134032}, issn = {1090-2120}, mesh = {Animals ; Antineoplastic Agents/chemistry/isolation & purification/*pharmacology ; Apoptosis/drug effects ; Basidiomycota/*chemistry ; Cell Proliferation/drug effects ; Cyclophosphamide ; Dose-Response Relationship, Drug ; Drug Screening Assays, Antitumor ; Humans ; Mice ; Mice, Inbred C57BL ; Molecular Structure ; Spleen/drug effects ; Structure-Activity Relationship ; Tumor Cells, Cultured ; }, abstract = {Eight new naphtho[1,2-c]furan derivatives (1-8) along with six known analogues (9-14) were isolated from culture medium of the basidiomycete Basidioradulum radula. The structures of these compounds were identified using spectroscopic analysis, and their absolute configurations were resolved using X-ray diffraction, ECD, and VCD. Compounds 7 and 14 inhibited the cell viability of human prostate cancer DU-145 cells with IC50 values of 7.54 ± 0.03 μM and 5.04 ± 0.03 μM, respectively. At 8 μM, compounds 7 and 14 increased the percentage of apoptotic cells and upregulated the protein expression related to the apoptosis caspase pathways in DU-145 cells. Furthermore, the hallmarks of cells undergoing apoptosis, such as chromatin condensation, were also observed at this concentration. However, compound 7 and 14 showed no effect on the proliferation of splenocytes isolated from cyclophosphamide-induce immunosuppressed mice.}, } @article {pmid34129717, year = {2021}, author = {Jucker, T and Amano, T and Bell, A and Garnett, EE and Geffert, JL and Guth, MK and Hacket-Pain, A and Luke, SH and Mumby, HS and Nunes, M and Rademacher, T and Rose, DC and Schleicher, J and Simmons, BI and Zabala, A and Mukherjee, N}, title = {Steps to diversify priority-setting research in conservation: reflections on de Gracia 2021.}, journal = {Conservation biology : the journal of the Society for Conservation Biology}, volume = {35}, number = {4}, pages = {1324-1326}, doi = {10.1111/cobi.13790}, pmid = {34129717}, issn = {1523-1739}, mesh = {*Biodiversity ; *Conservation of Natural Resources ; Ecosystem ; }, } @article {pmid34129629, year = {2021}, author = {Molina-Venegas, R and Rodríguez, MÁ and Pardo-de-Santayana, M and Mabberley, DJ}, title = {A global database of plant services for humankind.}, journal = {PloS one}, volume = {16}, number = {6}, pages = {e0253069}, pmid = {34129629}, issn = {1932-6203}, mesh = {Agriculture/legislation & jurisprudence ; Data Curation ; Data Management ; Databases, Factual ; Human Activities ; Humans ; Tracheophyta/*classification ; }, abstract = {Humanity faces the challenge of conserving the attributes of biodiversity that may be essential to secure human wellbeing. Among all the organisms that are beneficial to humans, plants stand out as the most important providers of natural resources. Therefore, identifying plant uses is critical to preserve the beneficial potential of biodiversity and to promote basic and applied research on the relationship between plants and humans. However, much of this information is often uncritical, contradictory, of dubious value or simply not readily accessible to the great majority of scientists and policy makers. Here, we compiled a genus-level dataset of plant-use records for all accepted vascular plant taxa (13489 genera) using the information gathered in the 4th Edition of Mabberley's plant-book, the most comprehensive global review of plant classification and their uses published to date. From 1974 to 2017 all the information was systematically gathered, evaluated, and synthesized by David Mabberley, who reviewed over 1000 botanical sources including modern Floras, monographs, periodicals, handbooks, and authoritative websites. Plant uses were arranged across 28 standard categories of use following the Economic Botany Data Collection Standard guidelines, which resulted in a binary classification of 9478 plant-use records pertaining human and animal nutrition, materials, fuels, medicine, poisons, social and environmental uses. Of all the taxa included in the dataset, 33% were assigned to at least one category of use, the most common being "ornamental" (26%), "medicine" (16%), "human food" (13%) and "timber" (8%). In addition to a readily available binary matrix for quantitative analyses, we provide a control text matrix that links the former to the description of the uses in Mabberley's plant-book. We hope this dataset will serve to establish synergies between scientists and policy makers interested in plant-human interactions and to move towards the complete compilation and classification of the nature's contributions to people upon which the wellbeing of future generations may depend.}, } @article {pmid34127003, year = {2021}, author = {Unosson, J and Kabéle, M and Boman, C and Nyström, R and Sadiktsis, I and Westerholm, R and Mudway, IS and Purdie, E and Raftis, J and Miller, MR and Mills, NL and Newby, DE and Blomberg, A and Sandström, T and Bosson, JA}, title = {Acute cardiovascular effects of controlled exposure to dilute Petrodiesel and biodiesel exhaust in healthy volunteers: a crossover study.}, journal = {Particle and fibre toxicology}, volume = {18}, number = {1}, pages = {22}, pmid = {34127003}, issn = {1743-8977}, support = {SP/15/8/31575/BHF_/British Heart Foundation/United Kingdom ; FS/16/14/32023/BHF_/British Heart Foundation/United Kingdom ; CH/09/002/26360/BHF_/British Heart Foundation/United Kingdom ; WT103782AIA/WT_/Wellcome Trust/United Kingdom ; CH/F/21/90010/BHF_/British Heart Foundation/United Kingdom ; MR/S019669/1/MRC_/Medical Research Council/United Kingdom ; CH/09/002/BHF_/British Heart Foundation/United Kingdom ; }, mesh = {*Air Pollution ; *Biofuels/toxicity ; Cross-Over Studies ; Female ; Humans ; Male ; Particulate Matter/*toxicity ; Vasodilation ; Vehicle Emissions/analysis/*toxicity ; }, abstract = {BACKGROUND: Air pollution derived from combustion is associated with considerable cardiorespiratory morbidity and mortality in addition to environmental effects. Replacing petrodiesel with biodiesel may have ecological benefits, but impacts on human health remain unquantified. The objective was to compare acute cardiovascular effects of blended and pure biodiesel exhaust exposure against known adverse effects of petrodiesel exhaust (PDE) exposure in human subjects. In two randomized controlled double-blind crossover studies, healthy volunteers were exposed to PDE or biodiesel exhaust for one hour. In study one, 16 subjects were exposed, on separate occasions, to PDE and 30% rapeseed methyl ester biodiesel blend (RME30) exhaust, aiming at PM10 300 μg/m[3]. In study two, 19 male subjects were separately exposed to PDE and exhaust from a 100% RME fuel (RME100) using similar engine load and exhaust dilution. Generated exhaust was analyzed for physicochemical composition and oxidative potential. Following exposure, vascular endothelial function was assessed using forearm venous occlusion plethysmography and ex vivo thrombus formation was assessed using a Badimon chamber model of acute arterial injury. Biomarkers of inflammation, platelet activation and fibrinolysis were measured in the blood.

RESULTS: In study 1, PDE and RME30 exposures were at comparable PM levels (314 ± 27 μg/m[3]; (PM10 ± SD) and 309 ± 30 μg/m[3] respectively), whereas in study 2, the PDE exposure concentrations remained similar (310 ± 34 μg/m[3]), but RME100 levels were lower in PM (165 ± 16 μg/m[3]) and PAHs, but higher in particle number concentration. Compared to PDE, PM from RME had less oxidative potential. Forearm infusion of the vasodilators acetylcholine, bradykinin, sodium nitroprusside and verapamil resulted in dose-dependent increases in blood flow after all exposures. Vasodilatation and ex vivo thrombus formation were similar following exposure to exhaust from petrodiesel and the two biodiesel formulations (RME30 and RME100). There were no significant differences in blood biomarkers or exhaled nitric oxide levels between exposures.

CONCLUSIONS: Despite differences in PM composition and particle reactivity, controlled exposure to biodiesel exhaust was associated with similar cardiovascular effects to PDE. We suggest that the potential adverse health effects of biodiesel fuel emissions should be taken into account when evaluating future fuel policies.

TRIAL REGISTRATION: ClinicalTrials.gov, NCT01337882 /NCT01883466. Date of first enrollment March 11, 2011, registered April 19, 2011, i.e. retrospectively registered.}, } @article {pmid34125841, year = {2021}, author = {Sandhu, SK and Bayliss, CD and Morozov, AY}, title = {How does feedback from phage infections influence the evolution of phase variation in Campylobacter?.}, journal = {PLoS computational biology}, volume = {17}, number = {6}, pages = {e1009067}, pmid = {34125841}, issn = {1553-7358}, mesh = {Animals ; Bacteriophage Receptors/*genetics/physiology ; Campylobacter Infections/microbiology/*therapy/virology ; Campylobacter jejuni/*genetics/*virology ; Computational Biology ; Computer Simulation ; Evolution, Molecular ; Gene Expression Regulation, Bacterial ; Genes, Bacterial ; Humans ; Microbial Interactions/genetics/physiology ; Microsatellite Repeats ; Models, Biological ; Mutation ; *Phage Therapy/methods/statistics & numerical data ; }, abstract = {Campylobacter jejuni (C. jejuni) causes gastroenteritis following the consumption of contaminated poultry meat, resulting in a large health and economic burden worldwide. Phage therapy is a promising technique for eradicating C. jejuni from poultry flocks and chicken carcasses. However, C. jejuni can resist infections by some phages through stochastic, phase-variable ON/OFF switching of the phage receptors mediated by simple sequence repeats (SSR). While selection strength and exposure time influence the evolution of SSR-mediated phase variation (PV), phages offer a more complex evolutionary environment as phage replication depends on having a permissive host organism. Here, we build and explore several continuous culture bacteria-phage computational models, each analysing different phase-variable scenarios calibrated to the experimental SSR rates of C. jejuni loci and replication parameters for the F336 phage. We simulate the evolution of PV rates via the adaptive dynamics framework for varying levels of selective pressures that act on the phage-resistant state. Our results indicate that growth reducing counter-selection on a single PV locus results in the stable maintenance of the phage, while compensatory selection between bacterial states affects the evolutionary stable mutation rates (i.e. very high and very low mutation rates are evolutionarily disadvantageous), whereas, in the absence of either selective pressure the evolution of PV rates results in mutation rates below the basal values. Contrastingly, a biologically-relevant model with two phase-variable loci resulted in phage extinction and locking of the bacteria into a phage-resistant state suggesting that another counter-selective pressure is required, instance, the use of a distinct phage whose receptor is an F336-phage-resistant state. We conclude that a delicate balance between counter-selection and phage-attack can result in both the evolution of phase-variable phage receptors and persistence of PV-receptor-specific phage.}, } @article {pmid34108816, year = {2021}, author = {Varotsos, CA and Krapivin, VF and Xue, Y and Soldatov, V and Voronova, T}, title = {COVID-19 pandemic decision support system for a population defense strategy and vaccination effectiveness.}, journal = {Safety science}, volume = {142}, number = {}, pages = {105370}, pmid = {34108816}, issn = {0925-7535}, abstract = {The year 2020 ended with a significant COVID-19 pandemic, which traumatized almost many countries where the lockdowns were restored, and numerous emotional social protests erupted. According to the World Health Organization, the global epidemiological situation in the first months of 2021 deteriorated. In this paper, the decision-making supporting system (DMSS) is proposed to be an epidemiological prediction tool. COVID-19 trends in several countries and regions, take into account the big data clouds for important geophysical and socio-ecological characteristics and the expected potentials of the medical service, including vaccination and restrictions on population migration both within the country and international traffic. These parameters for numerical simulations are estimated from officially delivered data that allows the verification of theoretical results. The numerical simulations of the transition and the results of COVID-19 are mainly based on the deterministic approach and the algorithm for processing statistical data based on the instability indicator. DMSS has been shown to help predict the effects of COVID-19 depending on the protection strategies against COVID-19 including vaccination. Numerical simulations have shown that DMSS provides results using accompanying information in the appropriate scenario.}, } @article {pmid34107928, year = {2021}, author = {Leclerc, QJ and Fuller, NM and Keogh, RH and Diaz-Ordaz, K and Sekula, R and Semple, MG and , and , and Atkins, KE and Procter, SR and Knight, GM}, title = {Importance of patient bed pathways and length of stay differences in predicting COVID-19 hospital bed occupancy in England.}, journal = {BMC health services research}, volume = {21}, number = {1}, pages = {566}, pmid = {34107928}, issn = {1472-6963}, support = {G0701652/MRC_/Medical Research Council/United Kingdom ; 206471/Z/17/Z/WT_/Wellcome Trust/United Kingdom ; MC_PC_19059/MRC_/Medical Research Council/United Kingdom ; 218554/Z/19//WT_/Wellcome Trust/United Kingdom ; MR/N013638/1/MRC_/Medical Research Council/United Kingdom ; BB/M009513/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; MR/S032304/1/MRC_/Medical Research Council/United Kingdom ; MR/P014658/1/MRC_/Medical Research Council/United Kingdom ; MC_PC_19025/MRC_/Medical Research Council/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; MR/S003975/1/MRC_/Medical Research Council/United Kingdom ; MR/S017968/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {*Bed Occupancy ; *COVID-19 ; England ; Humans ; Length of Stay ; SARS-CoV-2 ; }, abstract = {BACKGROUND: Predicting bed occupancy for hospitalised patients with COVID-19 requires understanding of length of stay (LoS) in particular bed types. LoS can vary depending on the patient's "bed pathway" - the sequence of transfers of individual patients between bed types during a hospital stay. In this study, we characterise these pathways, and their impact on predicted hospital bed occupancy.

METHODS: We obtained data from University College Hospital (UCH) and the ISARIC4C COVID-19 Clinical Information Network (CO-CIN) on hospitalised patients with COVID-19 who required care in general ward or critical care (CC) beds to determine possible bed pathways and LoS. We developed a discrete-time model to examine the implications of using either bed pathways or only average LoS by bed type to forecast bed occupancy. We compared model-predicted bed occupancy to publicly available bed occupancy data on COVID-19 in England between March and August 2020.

RESULTS: In both the UCH and CO-CIN datasets, 82% of hospitalised patients with COVID-19 only received care in general ward beds. We identified four other bed pathways, present in both datasets: "Ward, CC, Ward", "Ward, CC", "CC" and "CC, Ward". Mean LoS varied by bed type, pathway, and dataset, between 1.78 and 13.53 days. For UCH, we found that using bed pathways improved the accuracy of bed occupancy predictions, while only using an average LoS for each bed type underestimated true bed occupancy. However, using the CO-CIN LoS dataset we were not able to replicate past data on bed occupancy in England, suggesting regional LoS heterogeneities.

CONCLUSIONS: We identified five bed pathways, with substantial variation in LoS by bed type, pathway, and geography. This might be caused by local differences in patient characteristics, clinical care strategies, or resource availability, and suggests that national LoS averages may not be appropriate for local forecasts of bed occupancy for COVID-19.

TRIAL REGISTRATION: The ISARIC WHO CCP-UK study ISRCTN66726260 was retrospectively registered on 21/04/2020 and designated an Urgent Public Health Research Study by NIHR.}, } @article {pmid34106993, year = {2021}, author = {Kong, JD and Tekwa, EW and Gignoux-Wolfsohn, SA}, title = {Social, economic, and environmental factors influencing the basic reproduction number of COVID-19 across countries.}, journal = {PloS one}, volume = {16}, number = {6}, pages = {e0252373}, pmid = {34106993}, issn = {1932-6203}, mesh = {Age Factors ; Basic Reproduction Number/*statistics & numerical data ; COVID-19/economics/*epidemiology/transmission/virology ; Databases, Factual ; Global Health ; Humans ; Income/*statistics & numerical data ; Models, Statistical ; Pandemics ; SARS-CoV-2/isolation & purification ; Social Media/*statistics & numerical data ; Socioeconomic Factors ; Urban Population/statistics & numerical data ; }, abstract = {OBJECTIVE: To assess whether the basic reproduction number (R0) of COVID-19 is different across countries and what national-level demographic, social, and environmental factors other than interventions characterize initial vulnerability to the virus.

METHODS: We fit logistic growth curves to reported daily case numbers, up to the first epidemic peak, for 58 countries for which 16 explanatory covariates are available. This fitting has been shown to robustly estimate R0 from the specified period. We then use a generalized additive model (GAM) to discern both linear and nonlinear effects, and include 5 random effect covariates to account for potential differences in testing and reporting that can bias the estimated R0.

FINDINGS: We found that the mean R0 is 1.70 (S.D. 0.57), with a range between 1.10 (Ghana) and 3.52 (South Korea). We identified four factors-population between 20-34 years old (youth), population residing in urban agglomerates over 1 million (city), social media use to organize offline action (social media), and GINI income inequality-as having strong relationships with R0, across countries. An intermediate level of youth and GINI inequality are associated with high R0, (n-shape relationships), while high city population and high social media use are associated with high R0. Pollution, temperature, and humidity did not have strong relationships with R0 but were positive.

CONCLUSION: Countries have different characteristics that predispose them to greater intrinsic vulnerability to COVID-19. Studies that aim to measure the effectiveness of interventions across locations should account for these baseline differences in social and demographic characteristics.}, } @article {pmid34103103, year = {2021}, author = {Doherty, JF and Filion, A and Bennett, J and Raj Bhattarai, U and Chai, X and de Angeli Dutra, D and Donlon, E and Jorge, F and Milotic, M and Park, E and Sabadel, AJM and Thomas, LJ and Poulin, R}, title = {The people vs science: can passively crowdsourced internet data shed light on host-parasite interactions?.}, journal = {Parasitology}, volume = {148}, number = {11}, pages = {1313-1319}, pmid = {34103103}, issn = {1469-8161}, mesh = {Animals ; Canada ; Crowdsourcing/*statistics & numerical data ; Databases, Factual/statistics & numerical data ; Demography ; Female ; Helminths/*physiology ; *Host-Parasite Interactions ; Humans ; Internet/*statistics & numerical data ; Male ; Photography ; Population Density ; Seasons ; Time Factors ; United States ; }, abstract = {Every internet search query made out of curiosity by anyone who observed something in nature, as well as every photo uploaded to the internet, constitutes a data point of potential use to scientists. Researchers have now begun to exploit the vast online data accumulated through passive crowdsourcing for studies in ecology and epidemiology. Here, we demonstrate the usefulness of iParasitology, i.e. the use of internet data for tests of parasitological hypotheses, using hairworms (phylum Nematomorpha) as examples. These large worms are easily noticeable by people in general, and thus likely to generate interest on the internet. First, we show that internet search queries (collated with Google Trends) and photos uploaded to the internet (specifically, to the iNaturalist platform) point to parts of North America with many sightings of hairworms by the public, but few to no records in the scientific literature. Second, we demonstrate that internet searches predict seasonal peaks in hairworm abundance that accurately match scientific data. Finally, photos uploaded to the internet by non-scientists can provide reliable data on the host taxa that hairworms most frequently parasitize, and also identify hosts that appear to have been neglected by scientific studies. Our findings suggest that for any parasite group likely to be noticeable by non-scientists, information accumulating through internet search activity, photo uploads, social media or any other format available online, represents a valuable source of data that can complement traditional scientific data sources in parasitology.}, } @article {pmid34100767, year = {2021}, author = {Mascheroni, A and Choe, EK and Luo, Y and Marazza, M and Ferlito, C and Caverzasio, S and Mezzanotte, F and Kaelin-Lang, A and Faraci, F and Puiatti, A and Ratti, PL}, title = {The SleepFit Tablet Application for Home-Based Clinical Data Collection in Parkinson Disease: User-Centric Development and Usability Study.}, journal = {JMIR mHealth and uHealth}, volume = {9}, number = {6}, pages = {e16304}, pmid = {34100767}, issn = {2291-5222}, mesh = {*COVID-19 ; Data Collection ; Humans ; Pandemics ; *Parkinson Disease/drug therapy ; Quality of Life ; SARS-CoV-2 ; }, abstract = {BACKGROUND: Parkinson disease (PD) is a common, multifaceted neurodegenerative disorder profoundly impacting patients' autonomy and quality of life. Assessment in real-life conditions of subjective symptoms and objective metrics of mobility and nonmotor symptoms such as sleep disturbance is strongly advocated. This information would critically guide the adaptation of antiparkinsonian medications and nonpharmacological interventions. Moreover, since the spread of the COVID-19 pandemic, health care practices are being reshaped toward a more home-based care. New technologies could play a pivotal role in this new approach to clinical care. Nevertheless, devices and information technology tools might be unhandy for PD patients, thus dramatically limiting their widespread employment.

OBJECTIVE: The goals of the research were development and usability evaluation of an application, SleepFit, for ecological momentary assessment of objective and subjective clinical metrics at PD patients' homes, and as a remote tool for researchers to monitor patients and integrate and manage data.

METHODS: An iterative and user-centric strategy was employed for the development of SleepFit. The core structure of SleepFit consists of (1) an electronic finger-tapping test; (2) motor, sleepiness, and emotional subjective scales; and (3) a sleep diary. Applicable design, ergonomic, and navigation principles have been applied while tailoring the application to the specific patient population. Three progressively enhanced versions of the application (alpha, v1.0, v2.0) were tested by a total of 56 patients with PD who were asked to perform multiple home assessments 4 times per day for 2 weeks. Patient compliance was calculated as the proportion of completed tasks out of the total number of expected tasks. Satisfaction on the latest version (v2.0) was evaluated as potential willingness to use SleepFit again after the end of the study.

RESULTS: From alpha to v1.0, SleepFit was improved in graphics, ergonomics, and navigation, with automated flows guiding the patients in performing tasks throughout the 24 hours, and real-time data collection and consultation were made possible thanks to a remote web portal. In v2.0, the kiosk-mode feature restricts the use of the tablet to the SleepFit application only, thus preventing users from accidentally exiting the application. A total of 52 (4 dropouts) patients were included in the analyses. Overall compliance (all versions) was 88.89% (5707/6420). SleepFit was progressively enhanced and compliance increased from 87.86% (2070/2356) to 89.92% (2899/3224; P=.04). Among the patients who used v2.0, 96% (25/26) declared they would use SleepFit again.

CONCLUSIONS: SleepFit can be considered a state-of-the-art home-based system that increases compliance in PD patients, ensures high-quality data collection, and works as a handy tool for remote monitoring and data management in clinical research. Thanks to its user-friendliness and modular structure, it could be employed in other clinical studies with minimum adaptation efforts.

TRIAL REGISTRATION: ClinicalTrials.gov NCT02723396; https://clinicaltrials.gov/ct2/show/NCT02723396.}, } @article {pmid34100002, year = {2021}, author = {Russell, CD and Fairfield, CJ and Drake, TM and Turtle, L and Seaton, RA and Wootton, DG and Sigfrid, L and Harrison, EM and Docherty, AB and de Silva, TI and Egan, C and Pius, R and Hardwick, HE and Merson, L and Girvan, M and Dunning, J and Nguyen-Van-Tam, JS and Openshaw, PJM and Baillie, JK and Semple, MG and Ho, A and , }, title = {Co-infections, secondary infections, and antimicrobial use in patients hospitalised with COVID-19 during the first pandemic wave from the ISARIC WHO CCP-UK study: a multicentre, prospective cohort study.}, journal = {The Lancet. Microbe}, volume = {2}, number = {8}, pages = {e354-e365}, pmid = {34100002}, issn = {2666-5247}, support = {G0701652/MRC_/Medical Research Council/United Kingdom ; MC_UU_12014/12/MRC_/Medical Research Council/United Kingdom ; MC_PC_19026/MRC_/Medical Research Council/United Kingdom ; MC_PC_19059/MRC_/Medical Research Council/United Kingdom ; MC_UU_12014/9/MRC_/Medical Research Council/United Kingdom ; MR/S032304/1/MRC_/Medical Research Council/United Kingdom ; MC_UU_12014/8/MRC_/Medical Research Council/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; MC_UU_12014/10/MRC_/Medical Research Council/United Kingdom ; MC_PC_15001/MRC_/Medical Research Council/United Kingdom ; 205228/Z/16/Z/WT_/Wellcome Trust/United Kingdom ; MC_PC_19025/MRC_/Medical Research Council/United Kingdom ; 215091/Z/18/Z/WT_/Wellcome Trust/United Kingdom ; 109965/Z/15/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Aged ; Aged, 80 and over ; *Anti-Infective Agents ; *COVID-19/epidemiology ; *Coinfection/drug therapy ; Female ; Humans ; Male ; Middle Aged ; Pandemics ; Prospective Studies ; *Respiratory Tract Infections/epidemiology ; SARS-CoV-2 ; United Kingdom/epidemiology ; World Health Organization ; }, abstract = {BACKGROUND: Microbiological characterisation of co-infections and secondary infections in patients with COVID-19 is lacking, and antimicrobial use is high. We aimed to describe microbiologically confirmed co-infections and secondary infections, and antimicrobial use, in patients admitted to hospital with COVID-19.

METHODS: The International Severe Acute Respiratory and Emerging Infections Consortium (ISARIC) WHO Clinical Characterisation Protocol UK (CCP-UK) study is an ongoing, prospective cohort study recruiting inpatients from 260 hospitals in England, Scotland, and Wales, conducted by the ISARIC Coronavirus Clinical Characterisation Consortium. Patients with a confirmed or clinician-defined high likelihood of SARS-CoV-2 infection were eligible for inclusion in the ISARIC WHO CCP-UK study. For this specific study, we excluded patients with a recorded negative SARS-CoV-2 test result and those without a recorded outcome at 28 days after admission. Demographic, clinical, laboratory, therapeutic, and outcome data were collected using a prespecified case report form. Organisms considered clinically insignificant were excluded.

FINDINGS: We analysed data from 48 902 patients admitted to hospital between Feb 6 and June 8, 2020. The median patient age was 74 years (IQR 59-84) and 20 786 (42·6%) of 48 765 patients were female. Microbiological investigations were recorded for 8649 (17·7%) of 48 902 patients, with clinically significant COVID-19-related respiratory or bloodstream culture results recorded for 1107 patients. 762 (70·6%) of 1080 infections were secondary, occurring more than 2 days after hospital admission. Staphylococcus aureus and Haemophilus influenzae were the most common pathogens causing respiratory co-infections (diagnosed ≤2 days after admission), with Enterobacteriaceae and S aureus most common in secondary respiratory infections. Bloodstream infections were most frequently caused by Escherichia coli and S aureus. Among patients with available data, 13 390 (37·0%) of 36 145 had received antimicrobials in the community for this illness episode before hospital admission and 39 258 (85·2%) of 46 061 patients with inpatient antimicrobial data received one or more antimicrobials at some point during their admission (highest for patients in critical care). We identified frequent use of broad-spectrum agents and use of carbapenems rather than carbapenem-sparing alternatives.

INTERPRETATION: In patients admitted to hospital with COVID-19, microbiologically confirmed bacterial infections are rare, and more likely to be secondary infections. Gram-negative organisms and S aureus are the predominant pathogens. The frequency and nature of antimicrobial use are concerning, but tractable targets for stewardship interventions exist.

FUNDING: National Institute for Health Research (NIHR), UK Medical Research Council, Wellcome Trust, UK Department for International Development, Bill & Melinda Gates Foundation, EU Platform for European Preparedness Against (Re-)emerging Epidemics, NIHR Health Protection Research Unit (HPRU) in Emerging and Zoonotic Infections at University of Liverpool, and NIHR HPRU in Respiratory Infections at Imperial College London.}, } @article {pmid34096870, year = {2021}, author = {Nam, S and Jeon, S and Ash, G and Whittemore, R and Vlahov, D}, title = {Racial Discrimination, Sedentary Time, and Physical Activity in African Americans: Quantitative Study Combining Ecological Momentary Assessment and Accelerometers.}, journal = {JMIR formative research}, volume = {5}, number = {6}, pages = {e25687}, pmid = {34096870}, issn = {2561-326X}, support = {UL1 TR001863/TR/NCATS NIH HHS/United States ; }, abstract = {BACKGROUND: A growing number of studies indicate that exposure to social stress, such as perceived racial discrimination, may contribute to poor health, health behaviors, and health disparities. Increased physical activity (PA) may buffer the impact of social stress resulting from racial discrimination. However, to date, data on the relationship between racial discrimination and PA have been mixed. Part of the reason is that the effect of perceived racial discrimination on PA has primarily been examined in cross-sectional studies that captured retrospective measures of perceived racial discrimination associated with individuals' current PA outcomes. The association between real-time perceived racial discrimination and PA among African Americans remains unclear.

OBJECTIVE: The purpose of this study is to examine the relationship among demographic, anthropometric and clinical, and psychological factors with lifetime racial discrimination and examine the within- and between-person associations between daily real-time racial discrimination and PA outcomes (total energy expenditure, sedentary time, and moderate-to-vigorous PA patterns) measured by ecological momentary assessment (EMA) and accelerometers in healthy African Americans.

METHODS: This pilot study used an intensive, observational, case-crossover design of African Americans (n=12) recruited from the community. After participants completed baseline surveys, they were asked to wear an accelerometer for 7 days to measure their PA levels. EMA was sent to participants 5 times per day for 7 days to assess daily real-time racial discrimination. Multilevel models were used to examine the within- and between-person associations of daily racial discrimination on PA.

RESULTS: More EMA-reported daily racial discrimination was associated with younger age (r=0.75; P=.02). Daily EMA-reported microaggression was associated with depressive symptoms (r=0.66; P=.05), past race-related events (r=0.82; P=.004), and lifetime discrimination (r=0.78; P=.01). In the within-person analyses, the day-level association of racial discrimination and sedentary time was significant (β=.30, SE 0.14; P=.03), indicating that on occasions when participants reported more racial discrimination than usual, more sedentary time was observed. Between-person associations of racial discrimination (β=-.30, SE 0.28; P=.29) or microaggression (β=-.34, SE 0.36; P=.34) with total energy expenditure were suggestive but inconclusive.

CONCLUSIONS: Concurrent use of EMA and accelerometers is a feasible method to examine the relationship between racial discrimination and PA in real time. Examining daily processes at the within-person level has the potential to elucidate the mechanisms of which racial discrimination may have on health and health behaviors and to guide the development of personalized interventions for increasing PA in racial ethnic minorities. Future studies with a precision health approach, incorporating within- and between-person associations, are warranted to further elucidate the effects of racial discrimination and PA.

RR2-10.1002/nur.22068.}, } @article {pmid34090126, year = {2021}, author = {Duncan, GE and Hurvitz, PM and Moudon, AV and Avery, AR and Tsang, S}, title = {Measurement of neighborhood-based physical activity bouts.}, journal = {Health & place}, volume = {70}, number = {}, pages = {102595}, pmid = {34090126}, issn = {1873-2054}, support = {P2C HD042828/HD/NICHD NIH HHS/United States ; R01 AG042176/AG/NIA NIH HHS/United States ; }, mesh = {Accelerometry ; Adult ; *Exercise ; Geographic Information Systems ; Humans ; *Residence Characteristics ; }, abstract = {This study examined how buffer type (shape), size, and the allocation of activity bouts inside buffers that delineate the neighborhood spatially produce different estimates of neighborhood-based physical activity. A sample of 375 adults wore a global positioning system (GPS) data logger and accelerometer over 2 weeks under free-living conditions. Analytically, the amount of neighborhood physical activity measured objectively varies substantially, not only due to buffer shape and size, but by how GPS-based activity bouts are identified with respect to containment within neighborhood buffers. To move the "neighborhood-effects" literature forward, it is critical to delineate the spatial extent of the neighborhood, given how different ways of measuring GPS-based activity containment will result in different levels of physical activity across different buffer types and sizes.}, } @article {pmid34083778, year = {2021}, author = {Medema, MH and de Rond, T and Moore, BS}, title = {Mining genomes to illuminate the specialized chemistry of life.}, journal = {Nature reviews. Genetics}, volume = {22}, number = {9}, pages = {553-571}, pmid = {34083778}, issn = {1471-0064}, support = {F32 GM129960/GM/NIGMS NIH HHS/United States ; R01 GM085770/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Bacteria/*genetics ; Biological Products/*chemistry/metabolism/therapeutic use ; Computational Biology/methods ; Drug Discovery/*methods ; Fungi/*genetics ; *Genome ; Genomics/*methods ; Humans ; Plants/*genetics ; }, abstract = {All organisms produce specialized organic molecules, ranging from small volatile chemicals to large gene-encoded peptides, that have evolved to provide them with diverse cellular and ecological functions. As natural products, they are broadly applied in medicine, agriculture and nutrition. The rapid accumulation of genomic information has revealed that the metabolic capacity of virtually all organisms is vastly underappreciated. Pioneered mainly in bacteria and fungi, genome mining technologies are accelerating metabolite discovery. Recent efforts are now being expanded to all life forms, including protists, plants and animals, and new integrative omics technologies are enabling the increasingly effective mining of this molecular diversity.}, } @article {pmid34083578, year = {2021}, author = {Carlisle, AB and Allan, EA and Kim, SL and Meyer, L and Port, J and Scherrer, S and O'Sullivan, J}, title = {Integrating multiple chemical tracers to elucidate the diet and habitat of Cookiecutter Sharks.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {11809}, pmid = {34083578}, issn = {2045-2322}, mesh = {*Animal Nutritional Physiological Phenomena ; Animals ; Computational Biology/methods ; DNA, Environmental ; Ecology ; *Ecosystem ; Environment ; Female ; *Food Chain ; High-Throughput Nucleotide Sequencing ; Male ; Population Dynamics ; Radioactive Tracers ; Seasons ; *Sharks ; }, abstract = {The Cookiecutter shark (Isistius brasiliensis) is an ectoparasitic, mesopelagic shark that is known for removing plugs of tissue from larger prey, including teleosts, chondrichthyans, cephalopods, and marine mammals. Although this species is widely distributed throughout the world's tropical and subtropical oceanic waters, like many deep-water species, it remains very poorly understood due to its mesopelagic distribution. We used a suite of biochemical tracers, including stable isotope analysis (SIA), fatty acid analysis (FAA), and environmental DNA (eDNA), to investigate the trophic ecology of this species in the Central Pacific around Hawaii. We found that large epipelagic prey constituted a relatively minor part of the overall diet. Surprisingly, small micronektonic and forage species (meso- and epipelagic) are the most important prey group for Cookiecutter sharks across the studied size range (17-43 cm total length), with larger mesopelagic species or species that exhibit diel vertical migration also being important prey. These results were consistent across all the tracer techniques employed. Our results indicate that Cookiecutter sharks play a unique role in pelagic food webs, feeding on prey ranging from the largest apex predators to small, low trophic level species, in particular those that overlap with the depth distribution of the sharks throughout the diel cycle. We also found evidence of a potential shift in diet and/or habitat with size and season. Environmental DNA metabarcoding revealed new prey items for Cookiecutter sharks while also demonstrating that eDNA can be used to identify recent prey in stomachs frozen for extended periods. Integrating across chemical tracers is a powerful tool for investigating the ecology of elusive and difficult to study species, such as meso- and bathypelagic chondrichthyans, and can increase the amount of information gained from small sample sizes. Better resolving the foraging ecology of these mesopelagic predators is critical for effective conservation and management of these taxa and ecosystems, which are intrinsically vulnerable to overfishing and exploitation.}, } @article {pmid34081744, year = {2021}, author = {Colella, JP and Bates, J and Burneo, SF and Camacho, MA and Carrion Bonilla, C and Constable, I and D'Elía, G and Dunnum, JL and Greiman, S and Hoberg, EP and Lessa, E and Liphardt, SW and Londoño-Gaviria, M and Losos, E and Lutz, HL and Ordóñez Garza, N and Peterson, AT and Martin, ML and Ribas, CC and Struminger, B and Torres-Pérez, F and Thompson, CW and Weksler, M and Cook, JA}, title = {Leveraging natural history biorepositories as a global, decentralized, pathogen surveillance network.}, journal = {PLoS pathogens}, volume = {17}, number = {6}, pages = {e1009583}, pmid = {34081744}, issn = {1553-7374}, mesh = {Animals ; Animals, Wild ; Biodiversity ; Biological Specimen Banks/*organization & administration/standards/supply & distribution/trends ; COVID-19/epidemiology ; *Communicable Disease Control/methods/organization & administration/standards ; Communicable Diseases, Emerging/epidemiology/microbiology/*prevention & control/virology ; Community Networks/*organization & administration/standards/supply & distribution/trends ; Disaster Planning/methods/organization & administration/standards ; Geography ; Global Health/standards/trends ; Humans ; Medical Countermeasures ; Pandemics/prevention & control ; Public Health ; Public Health Surveillance/*methods ; Risk Assessment ; SARS-CoV-2/physiology ; Zoonoses/epidemiology/prevention & control ; }, abstract = {The Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) pandemic reveals a major gap in global biosecurity infrastructure: a lack of publicly available biological samples representative across space, time, and taxonomic diversity. The shortfall, in this case for vertebrates, prevents accurate and rapid identification and monitoring of emerging pathogens and their reservoir host(s) and precludes extended investigation of ecological, evolutionary, and environmental associations that lead to human infection or spillover. Natural history museum biorepositories form the backbone of a critically needed, decentralized, global network for zoonotic pathogen surveillance, yet this infrastructure remains marginally developed, underutilized, underfunded, and disconnected from public health initiatives. Proactive detection and mitigation for emerging infectious diseases (EIDs) requires expanded biodiversity infrastructure and training (particularly in biodiverse and lower income countries) and new communication pipelines that connect biorepositories and biomedical communities. To this end, we highlight a novel adaptation of Project ECHO's virtual community of practice model: Museums and Emerging Pathogens in the Americas (MEPA). MEPA is a virtual network aimed at fostering communication, coordination, and collaborative problem-solving among pathogen researchers, public health officials, and biorepositories in the Americas. MEPA now acts as a model of effective international, interdisciplinary collaboration that can and should be replicated in other biodiversity hotspots. We encourage deposition of wildlife specimens and associated data with public biorepositories, regardless of original collection purpose, and urge biorepositories to embrace new specimen sources, types, and uses to maximize strategic growth and utility for EID research. Taxonomically, geographically, and temporally deep biorepository archives serve as the foundation of a proactive and increasingly predictive approach to zoonotic spillover, risk assessment, and threat mitigation.}, } @article {pmid34078898, year = {2021}, author = {Liu, Y and Wang, B and Shu, S and Li, Z and Song, C and Liu, D and Niu, Y and Liu, J and Zhang, J and Liu, H and Hu, Z and Huang, B and Liu, X and Liu, W and Jiang, L and Alami, MM and Zhou, Y and Ma, Y and He, X and Yang, Y and Zhang, T and Hu, H and Barker, MS and Chen, S and Wang, X and Nie, J}, title = {Analysis of the Coptis chinensis genome reveals the diversification of protoberberine-type alkaloids.}, journal = {Nature communications}, volume = {12}, number = {1}, pages = {3276}, pmid = {34078898}, issn = {2041-1723}, mesh = {Berberine Alkaloids/*metabolism ; Biosynthetic Pathways/genetics ; Coptis/chemistry/*genetics/metabolism ; Cytochrome P-450 Enzyme System/*genetics/metabolism ; Drugs, Chinese Herbal ; Gene Duplication ; Gene Expression Regulation, Plant ; Gene Ontology ; *Genome, Plant ; Molecular Sequence Annotation ; Phylogeny ; Plant Proteins/*genetics/metabolism ; Plants, Medicinal ; }, abstract = {Chinese goldthread (Coptis chinensis Franch.), a member of the Ranunculales, represents an important early-diverging eudicot lineage with diverse medicinal applications. Here, we present a high-quality chromosome-scale genome assembly and annotation of C. chinensis. Phylogenetic and comparative genomic analyses reveal the phylogenetic placement of this species and identify a single round of ancient whole-genome duplication (WGD) shared by the Ranunculaceae. We characterize genes involved in the biosynthesis of protoberberine-type alkaloids in C. chinensis. In particular, local genomic tandem duplications contribute to member amplification of a Ranunculales clade-specific gene family of the cytochrome P450 (CYP) 719. The functional versatility of a key CYP719 gene that encodes the (S)-canadine synthase enzyme involved in the berberine biosynthesis pathway may play critical roles in the diversification of other berberine-related alkaloids in C. chinensis. Our study provides insights into the genomic landscape of early-diverging eudicots and provides a valuable model genome for genetic and applied studies of Ranunculales.}, } @article {pmid34078235, year = {2021}, author = {Aksum, KM and Pokolm, M and Bjørndal, CT and Rein, R and Memmert, D and Jordet, G}, title = {Scanning activity in elite youth football players.}, journal = {Journal of sports sciences}, volume = {39}, number = {21}, pages = {2401-2410}, doi = {10.1080/02640414.2021.1935115}, pmid = {34078235}, issn = {1466-447X}, mesh = {Adolescent ; Age Factors ; Athletic Performance/physiology/*psychology ; *Competitive Behavior/physiology ; Eye-Tracking Technology ; Head/physiology ; Humans ; Linear Models ; Male ; Movement ; Soccer/physiology/*psychology ; Time and Motion Studies ; *Visual Perception/physiology ; }, abstract = {The purpose of this study was to analyse the scanning behaviour of elite youth football players across different playing positions and age groups during high-level matches. Data was obtained by filming the 2018 UEFA European U17 and U19 Championship semi-finals and finals. A total of 53 outfield players from the four teams that reached the finals were analysed in both their respective semi-final and final matches, resulting in a total of 1686 attacking play situations. Ecological psychology provided us with the theoretical rationale for the study and informed our research hypotheses and interpretations. We found that U19 players performed more scans than U17 players. A positive relationship between scan frequency and pass success was also found. The results further suggest that opponent pressure and pitch position are both critical contextual factors that may influence scanning behaviour. In addition, central midfielders and central defenders were found to have higher scan frequencies than players in other positions. Our results support and extend previous research, suggesting that playing positions and age groups are important factors that impact visual perception and specifically scanning in football. Potential implications for coaches and recommendations for future studies are discussed.}, } @article {pmid34076241, year = {2021}, author = {Queirós, P and Delogu, F and Hickl, O and May, P and Wilmes, P}, title = {Mantis: flexible and consensus-driven genome annotation.}, journal = {GigaScience}, volume = {10}, number = {6}, pages = {}, pmid = {34076241}, issn = {2047-217X}, support = {863664/ERC_/European Research Council/International ; }, mesh = {Consensus ; *Data Mining ; Metagenome ; Molecular Sequence Annotation ; Reproducibility of Results ; *Software ; }, abstract = {BACKGROUND: The rapid development of the (meta-)omics fields has produced an unprecedented amount of high-resolution and high-fidelity data. Through the use of these datasets we can infer the role of previously functionally unannotated proteins from single organisms and consortia. In this context, protein function annotation can be described as the identification of regions of interest (i.e., domains) in protein sequences and the assignment of biological functions. Despite the existence of numerous tools, challenges remain in terms of speed, flexibility, and reproducibility. In the big data era, it is also increasingly important to cease limiting our findings to a single reference, coalescing knowledge from different data sources, and thus overcoming some limitations in overly relying on computationally generated data from single sources.

RESULTS: We implemented a protein annotation tool, Mantis, which uses database identifiers intersection and text mining to integrate knowledge from multiple reference data sources into a single consensus-driven output. Mantis is flexible, allowing for the customization of reference data and execution parameters, and is reproducible across different research goals and user environments. We implemented a depth-first search algorithm for domain-specific annotation, which significantly improved annotation performance compared to sequence-wide annotation. The parallelized implementation of Mantis results in short runtimes while also outputting high coverage and high-quality protein function annotations.

CONCLUSIONS: Mantis is a protein function annotation tool that produces high-quality consensus-driven protein annotations. It is easy to set up, customize, and use, scaling from single genomes to large metagenomes. Mantis is available under the MIT license at https://github.com/PedroMTQ/mantis.}, } @article {pmid34076209, year = {2021}, author = {Gusmão, AC and Meira, TC and Ferrite, S}, title = {Factors associated with notification of noise-induced hearing loss in Brazil, 2013-2015: an ecological study.}, journal = {Epidemiologia e servicos de saude : revista do Sistema Unico de Saude do Brasil}, volume = {30}, number = {2}, pages = {e2020607}, doi = {10.1590/S1679-49742021000200018}, pmid = {34076209}, issn = {2237-9622}, mesh = {Brazil/epidemiology ; *Hearing Loss, Noise-Induced/epidemiology ; Humans ; Information Systems ; *Noise, Occupational/adverse effects ; *Occupational Health ; }, abstract = {OBJECTIVE: To investigate factors associated with the notification of noise-induced hearing loss (NIHL), on the Notifiable Health Conditions Information System (SINAN) in Brazil.

METHODS: This was an ecological study to estimate the proportion of municipalities that had notified NIHL. Logistic regression models were used to identify associated factors.

RESULTS: Between 2013-2015, 277 (5.0%) municipalities notified NIHL. Notification was more prevalent among municipalities in an Occupational Health Referral Center (CEREST) coverage area (OR=1.62 - 95%CI 1.02;2.59) or those that had a CEREST in their territory (OR=4.37 - 95CI% 2.75;6.93), those that were closer to the state capital (OR=1.43 - 95%CI 1.06;1.92) and those with a high human development index (OR=2.35 - 95%CI 1.16;4.75). Among the municipalities located in a CEREST coverage area, notification was more frequent when there was a speech-language-hearing professional in the team (OR=1.96 - 95%CI - 1.47;2.63) and when employee turnover was low (OR=1.88 - 95%CI 1.40;2.52).

CONCLUSION: Contextual factors influence NIHL notification, particularly the presence of CERESTs and their qualification.}, } @article {pmid34074278, year = {2021}, author = {Nielsen, JH and Melendez-Torres, GJ and Rotevatn, TA and Peven, K and Fonager, K and Overgaard, C}, title = {How do reminder systems in follow-up screening for women with previous gestational diabetes work? - a realist review.}, journal = {BMC health services research}, volume = {21}, number = {1}, pages = {535}, pmid = {34074278}, issn = {1472-6963}, support = {/WT_/Wellcome Trust/United Kingdom ; }, mesh = {*Diabetes Mellitus, Type 2/diagnosis/epidemiology ; *Diabetes, Gestational/diagnosis/epidemiology ; Female ; Follow-Up Studies ; Humans ; Postpartum Period ; Pregnancy ; Reminder Systems ; }, abstract = {BACKGROUND: Women with previous gestational diabetes have an increased risk of developing type 2 diabetes later in life. Recommendations therefore urge these women to participate in follow-up screening, 4-12 weeks postpartum and every 1-3 years thereafter. We sought to theorize how reminder interventions to support early detection of diabetes work, for whom, and in what circumstances.

METHODS: We used a method informed by realist review and synthesis. A systematic, iterative search in six electronic databases (PubMed, MEDLINE Ovid, The Cochrane Library, CINAHL, EMBASE) had a primary focus on experimental intervention studies and included additional information in relation to identified intervention studies. Analysis inductively identified context-mechanism-outcome configurations present in the evidence.

RESULTS: We located 16 articles eligible for inclusion. A cross-case comparison identified seven grouped context-mechanism-outcome configurations leading to intervention mechanisms relating to changes in women's reasoning and behavior. Configurations were thematically ordered in relation to Systems Resources, Women's Circumstances, and Continuity of Care. These were mapped onto a socio-ecological model and discussed according to identified middle-range theories.

CONCLUSION: Our findings adds to the body of evidence, that reminders have the potential to be effective in increasing participation in the recommended follow-up screening. Our study may assist researchers and policy and decision makers to analyze and judge if reminders are feasible and/or likely to succeed in their specific context. Further research into the perspective of socially disadvantaged and overweight women is needed to avoid unintended consequences such as social inequality in service use and stigmatization in future programs.}, } @article {pmid34074043, year = {2021}, author = {Yoneda, Y and Yamamoto, K and Makino, A and Tanaka, Y and Meng, XY and Hashimoto, J and Shin-Ya, K and Satoh, N and Fujie, M and Toyama, T and Mori, K and Ike, M and Morikawa, M and Kamagata, Y and Tamaki, H}, title = {Novel Plant-Associated Acidobacteria Promotes Growth of Common Floating Aquatic Plants, Duckweeds.}, journal = {Microorganisms}, volume = {9}, number = {6}, pages = {}, pmid = {34074043}, issn = {2076-2607}, support = {JPMJAL1108//Japan Science and Technology Agency/ ; JPMJER1502//Japan Science and Technology Agency/ ; JP19H05683//Japan Society for the Promotion of Science/ ; }, abstract = {Duckweeds are small, fast growing, and starch- and protein-rich aquatic plants expected to be a next generation energy crop and an excellent biomaterial for phytoremediation. Despite such an importance, very little is known about duckweed-microbe interactions that would be a key biological factor for efficient industrial utilization of duckweeds. Here we first report the duckweed growth promoting ability of bacterial strains belonging to the phylum Acidobacteria, the members of which are known to inhabit soils and terrestrial plants, but their ecological roles and plant-microbe interactions remain largely unclear. Two novel Acidobacteria strains, F-183 and TBR-22, were successfully isolated from wild duckweeds and phylogenetically affiliated with subdivision 3 and 6 of the phylum, respectively, based on 16S rRNA gene sequence analysis. In the co-culture experiments with aseptic host plants, the F-183 and TBR-22 strains visibly enhanced growth (frond number) of six duckweed species (subfamily Lemnoideae) up to 1.8-5.1 times and 1.6-3.9 times, respectively, compared with uninoculated controls. Intriguingly, both strains also increased the chlorophyll content of the duckweed (Lemna aequinoctialis) up to 2.4-2.5 times. Under SEM observation, the F-183 and TBR-22 strains were epiphytic and attached to the surface of duckweed. Taken together, our findings suggest that indigenous plant associated Acidobacteria contribute to a healthy growth of their host aquatic plants.}, } @article {pmid34073261, year = {2021}, author = {Ahmed, EH and Brooks, E and Sloan, S and Schlotter, S and Jeney, F and Hale, C and Mao, C and Zhang, X and McLaughlin, E and Shindiapina, P and Shire, S and Das, M and Prouty, A and Lozanski, G and Mamuye, AT and Abebe, T and Alinari, L and Caligiuri, MA and Baiocchi, RA}, title = {Targeted Delivery of BZLF1 to DEC205 Drives EBV-Protective Immunity in a Spontaneous Model of EBV-Driven Lymphoproliferative Disease.}, journal = {Vaccines}, volume = {9}, number = {6}, pages = {}, pmid = {34073261}, issn = {2076-393X}, support = {P30 CA016058/CA/NCI NIH HHS/United States ; T32CA090223/NH/NIH HHS/United States ; 1RC2CA148348-01/NH/NIH HHS/United States ; }, abstract = {Epstein-Barr virus (EBV) is a human herpes virus that infects over 90% of the world's population and is linked to development of cancer. In immune-competent individuals, EBV infection is mitigated by a highly efficient virus-specific memory T-cell response. Risk of EBV-driven cancers increases with immune suppression (IS). EBV-seronegative recipients of solid organ transplants are at high risk of developing post-transplant lymphoproliferative disease (PTLD) due to iatrogenic IS. While reducing the level of IS may improve EBV-specific immunity and regression of PTLD, patients are at high risk for allograft rejection and need for immune-chemotherapy. Strategies to prevent PTLD in this vulnerable patient population represents an unmet need. We have previously shown that BZLF1-specific cytotoxic T-cell (CTL) expansion following reduced IS correlated with immune-mediated PTLD regression and improved patient survival. We have developed a vaccine to bolster EBV-specific immunity to the BZLF1 protein and show that co-culture of dendritic cells (DCs) loaded with a αDEC205-BZLF1 fusion protein with peripheral blood mononuclear cells (PMBCs) leads to expansion and increased cytotoxic activity of central-effector memory CTLs against EBV-transformed B-cells. Human-murine chimeric Hu-PBL-SCID mice were vaccinated with DCs loaded with αDEC205-BZLF1 or control to assess prevention of fatal human EBV lymphoproliferative disease. Despite a profoundly immunosuppressive environment, vaccination with αDEC205-BZLF1 stimulated clonal expansion of antigen-specific T-cells that produced abundant IFNγ and significantly prolonged survival. These results support preclinical and clinical development of vaccine approaches using BZLF1 as an immunogen to harness adaptive cellular responses and prevent PTLD in vulnerable patient populations.}, } @article {pmid34073246, year = {2021}, author = {Feng, X and Yan, W and Wang, A and Ma, R and Chen, X and Lin, TH and Chen, YL and Wei, S and Jin, T and Jiao, N and Zhang, R}, title = {A Novel Broad Host Range Phage Infecting Alteromonas.}, journal = {Viruses}, volume = {13}, number = {6}, pages = {}, pmid = {34073246}, issn = {1999-4915}, mesh = {Alteromonas/*virology ; Bacteriophages/isolation & purification/*physiology/ultrastructure ; Computational Biology/methods ; Genome, Viral ; Genomics/methods ; *Host Specificity ; Models, Molecular ; Molecular Sequence Annotation ; Open Reading Frames ; Phylogeny ; Protein Conformation ; Structure-Activity Relationship ; Viral Proteins/chemistry/genetics ; }, abstract = {Bacteriophages substantially contribute to bacterial mortality in the ocean and play critical roles in global biogeochemical processes. Alteromonas is a ubiquitous bacterial genus in global tropical and temperate waters, which can cross-protect marine cyanobacteria and thus has important ecological benefits. However, little is known about the biological and ecological features of Alteromonas phages (alterophages). Here, we describe a novel alterophage vB_AmeP-R8W (R8W), which belongs to the Autographiviridae family and infects the deep-clade Alteromonas mediterranea. R8W has an equidistant and icosahedral head (65 ± 1 nm in diameter) and a short tail (12 ± 2 nm in length). The genome size of R8W is 48,825 bp, with a G + C content of 40.55%. R8W possesses three putative auxiliary metabolic genes encoding proteins involved in nucleotide metabolism and DNA binding: thymidylate synthase, nucleoside triphosphate pyrophosphohydrolase, and PhoB. R8W has a rapid lytic cycle with a burst size of 88 plaque-forming units/cell. Notably, R8W has a wide host range, such that it can infect 35 Alteromonas strains; it exhibits a strong specificity for strains isolated from deep waters. R8W has two specific receptor binding proteins and a compatible holin-endolysin system, which contribute to its wide host range. The isolation of R8W will contribute to the understanding of alterophage evolution, as well as the phage-host interactions and ecological importance of alterophages.}, } @article {pmid34070673, year = {2021}, author = {Cadar, D and Schmidt-Chanasit, J and Tappe, D}, title = {Genomic and Micro-Evolutionary Features of Mammalian 2 orthobornavirus (Variegated Squirrel Bornavirus 1, VSBV-1).}, journal = {Microorganisms}, volume = {9}, number = {6}, pages = {}, pmid = {34070673}, issn = {2076-2607}, support = {01KI2005C//German Federal Ministry of Education and Research/ ; }, abstract = {Mammalian 2 orthobornavirus (VSBV-1) is an emerging zoonotic pathogen discovered in several exotic squirrel species and associated with fatal human encephalitis. The dynamics of VSBV-1 spread and evolution in its presumed natural hosts are unknown. Here, we present the phylogeny, micro-evolution, cross-species transmission and spread of VSBV-1 at a temporal and spatial resolution within the limits of animal husbandry. The results showed that VSBV-1 can be classified into six distinct groups and that the most recent common ancestor of the known German strains emerged at least 20 years ago. We here demonstrate that the genetic diversity of the VSBV-1 groups is shaped primarily by in situ evolution and most of the amino acid changes are deleterious polymorphisms removed by purifying selection. Evidence of adaptive evolution has been found in the G and L genes which might have an influence on transmission fitness. Furthermore, there was also evidence for some form of adaptive changes in the glycoprotein which suggests that many sites might be subjected to positive pressure evolving under episodic directional selection, indicating past occurrence of positive selection. Host switching events were detected as dominant evolutionary mechanisms driving the virus-host associations. Virus spread by animal trade followed by subsequent local micro-evolution in zoos and holdings is responsible for diversifying strains. Time-resolved phylogeny indicated that Prevost's squirrels might be the original squirrel species carrying and seeding the virus in Germany. This study provides the first insight into the ecology and micro-evolutionary dynamics of this novel viral pathogen in the captive exotic squirrel population under artificial ecological conditions (zoos and animal husbandry) and co-housing of different squirrel species.}, } @article {pmid34069990, year = {2021}, author = {Ansorge, R and Birolo, G and James, SA and Telatin, A}, title = {Dadaist2: A Toolkit to Automate and Simplify Statistical Analysis and Plotting of Metabarcoding Experiments.}, journal = {International journal of molecular sciences}, volume = {22}, number = {10}, pages = {}, pmid = {34069990}, issn = {1422-0067}, support = {BB/R012490/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; MR/T030062/1/MRC_/Medical Research Council/United Kingdom ; BB/R506552/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/F/000PR10353/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; MR/T030062/1//UK Research and Innovation/ ; }, mesh = {Algorithms ; Cluster Analysis ; Computational Biology/methods ; DNA Barcoding, Taxonomic/*statistics & numerical data ; Data Interpretation, Statistical ; High-Throughput Nucleotide Sequencing ; Metadata ; Metagenomics/*statistics & numerical data ; Microbiota/*genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Software ; }, abstract = {The taxonomic composition of microbial communities can be assessed using universal marker amplicon sequencing. The most common taxonomic markers are the 16S rDNA for bacterial communities and the internal transcribed spacer (ITS) region for fungal communities, but various other markers are used for barcoding eukaryotes. A crucial step in the bioinformatic analysis of amplicon sequences is the identification of representative sequences. This can be achieved using a clustering approach or by denoising raw sequencing reads. DADA2 is a widely adopted algorithm, released as an R library, that denoises marker-specific amplicons from next-generation sequencing and produces a set of representative sequences referred to as 'Amplicon Sequence Variants' (ASV). Here, we present Dadaist2, a modular pipeline, providing a complete suite for the analysis that ranges from raw sequencing reads to the statistics of numerical ecology. Dadaist2 implements a new approach that is specifically optimised for amplicons with variable lengths, such as the fungal ITS. The pipeline focuses on streamlining the data flow from the command line to R, with multiple options for statistical analysis and plotting, both interactive and automatic.}, } @article {pmid34059668, year = {2021}, author = {Clark, RL and Connors, BM and Stevenson, DM and Hromada, SE and Hamilton, JJ and Amador-Noguez, D and Venturelli, OS}, title = {Design of synthetic human gut microbiome assembly and butyrate production.}, journal = {Nature communications}, volume = {12}, number = {1}, pages = {3254}, pmid = {34059668}, issn = {2041-1723}, support = {R01 EB030340/EB/NIBIB NIH HHS/United States ; R35 GM124774/GM/NIGMS NIH HHS/United States ; T32 GM008349/GM/NIGMS NIH HHS/United States ; T32 HG002760/HG/NHGRI NIH HHS/United States ; }, mesh = {Anaerobiosis ; Bacteria/genetics/isolation & purification/*metabolism ; Bacteriological Techniques/*methods ; Butyrates/*metabolism ; Computational Biology ; DNA, Bacterial/isolation & purification ; Gastrointestinal Microbiome/*physiology ; Genome, Bacterial ; Humans ; Hydrogen Sulfide/metabolism ; Hydrogen-Ion Concentration ; Industrial Microbiology/methods ; Metabolic Engineering ; Sequence Analysis, DNA ; }, abstract = {The capability to design microbiomes with predictable functions would enable new technologies for applications in health, agriculture, and bioprocessing. Towards this goal, we develop a model-guided approach to design synthetic human gut microbiomes for production of the health-relevant metabolite butyrate. Our data-driven model quantifies microbial interactions impacting growth and butyrate production separately, providing key insights into ecological mechanisms driving butyrate production. We use our model to explore a vast community design space using a design-test-learn cycle to identify high butyrate-producing communities. Our model can accurately predict community assembly and butyrate production across a wide range of species richness. Guided by the model, we identify constraints on butyrate production by high species richness and key molecular factors driving butyrate production, including hydrogen sulfide, environmental pH, and resource competition. In sum, our model-guided approach provides a flexible and generalizable framework for understanding and accurately predicting community assembly and metabolic functions.}, } @article {pmid34058184, year = {2021}, author = {Picornell, A and Oteros, J and Ruiz-Mata, R and Recio, M and Trigo, MM and Martínez-Bracero, M and Lara, B and Serrano-García, A and Galán, C and García-Mozo, H and Alcázar, P and Pérez-Badia, R and Cabezudo, B and Romero-Morte, J and Rojo, J}, title = {Methods for interpolating missing data in aerobiological databases.}, journal = {Environmental research}, volume = {200}, number = {}, pages = {111391}, doi = {10.1016/j.envres.2021.111391}, pmid = {34058184}, issn = {1096-0953}, mesh = {Databases, Factual ; *Pollen ; Seasons ; }, abstract = {Missing data is a common problem in scientific research. The availability of extensive environmental time series is usually laborious and difficult, and sometimes unexpected failures are not detected until samples are processed. Consequently, environmental databases frequently have some gaps with missing data in it. Applying an interpolation method before starting the data analysis can be a good solution in order to complete this missing information. Nevertheless, there are several different approaches whose accuracy should be considered and compared. In this study, data from 6 aerobiological sampling stations were used as an example of environmental data series to assess the accuracy of different interpolation methods. For that, observed daily pollen/spore concentration data series were randomly removed, interpolated by using different methods and then, compared with the observed data to measure the errors produced. Different periods, gap sizes, interpolation methods and bioaerosols were considered in order to check their influence in the interpolation accuracy. The moving mean interpolation method obtained the highest success rate as average. By using this method, a success rate of the 70% was obtained when the risk classes used in the alert systems of the pollen information platforms were taken into account. In general, errors were mostly greater when there were high oscillations in the concentrations of biotic particles during consecutive days. That is the reason why the pre-peak and peak periods showed the highest interpolation errors. The errors were also higher when gaps longer than 5 days were considered. So, for completing long periods of missing data, it would be advisable to test other methodological approaches. A new Variation Index based on the behaviour of the pollen/spore season (measurement of the variability of the concentrations every 2 consecutive days) was elaborated, which allows to estimate the potential error before the interpolation is applied.}, } @article {pmid34057165, year = {2021}, author = {Todorovic, J and Terzic-Supic, Z and Divjak, J and Stamenkovic, Z and Mandic-Rajcevic, S and Kocic, S and Ukropina, S and Markovic, R and Radulovic, O and Arnaut, A and Piperac, P and Mirkovic, M and Nesic, D}, title = {Validation of the Study Burnout Inventory and the Copenhagen Burnout Inventory for the use among medical students.}, journal = {International journal of occupational medicine and environmental health}, volume = {34}, number = {6}, pages = {737-745}, doi = {10.13075/ijomeh.1896.01726}, pmid = {34057165}, issn = {1896-494X}, mesh = {Burnout, Psychological ; Humans ; Reproducibility of Results ; Serbia/epidemiology ; *Students, Medical ; }, abstract = {OBJECTIVES: The aim of this study was to assess the validity and reliability of the Serbian versions of the Copenhagen Burnout Inventory (CBI) and the Study Burnout Inventory (SBI) among fifth-year medical students at 5 universities in Serbia.

MATERIAL AND METHODS: The study included 573 fifthyear medical students at 5 universities in Serbia. The research instrument consisted of SBI and CBI. The reliability of these instruments was assessed using an internal consistency measure (Cronbach's α), an intra-class coefficient (ICC) and factor analysis.

RESULTS: Cronbach's α for SBI was 0.83, including for exhaustion 0.73, for cynicism 0.70, and for inadequacy 0.48. The test-retest reliability (ICC) was 0.75. Cronbach's α for personal burnout on CBI was 0.89, for the faculty-related burnout 0.86, and for the faculty-members-related burnout 0.92. Cronbach's α for CBI was 0.93. The factor analysis for SBI showed 2 factors and for CBI 3 factors.

CONCLUSIONS: This study revealed that the Serbian versions of both SBI and CBI could be used for the assessment of burnout in this population. Int J Occup Med Environ Health. 2021;34(6):737-45.}, } @article {pmid34056519, year = {2021}, author = {Leroux, A and Rzasa-Lynn, R and Crainiceanu, C and Sharma, T}, title = {Wearable Devices: Current Status and Opportunities in Pain Assessment and Management.}, journal = {Digital biomarkers}, volume = {5}, number = {1}, pages = {89-102}, pmid = {34056519}, issn = {2504-110X}, support = {T32 AG000247/AG/NIA NIH HHS/United States ; }, abstract = {INTRODUCTION: We investigated the possibilities and opportunities for using wearable devices that measure physical activity and physiometric signals in conjunction with ecological momentary assessment (EMA) data to improve the assessment and treatment of pain.

METHODS: We considered studies with cross-sectional and longitudinal designs as well as interventional or observational studies correlating pain scores with measures derived from wearable devices. A search was also performed on studies that investigated physical activity and physiometric signals among patients with pain.

RESULTS: Few studies have assessed the possibility of incorporating wearable devices as objective tools for contextualizing pain and physical function in free-living environments. Of the studies that have been conducted, most focus solely on physical activity and functional outcomes as measured by a wearable accelerometer. Several studies report promising correlations between pain scores and signals derived from wearable devices, objectively measured physical activity, and physical function. In addition, there is a known association between physiologic signals that can be measured by wearable devices and pain, though studies using wearable devices to measure these signals and associate them with pain in free-living environments are limited.

CONCLUSION: There exists a great opportunity to study the complex interplay between physiometric signals, physical function, and pain in a real-time fashion in free-living environments. The literature supports the hypothesis that wearable devices can be used to develop reproducible biosignals that correlate with pain. The combination of wearable devices and EMA will likely lead to the development of clinically meaningful endpoints that will transform how we understand and treat pain patients.}, } @article {pmid34054617, year = {2021}, author = {Baumeister, H and Bauereiss, N and Zarski, AC and Braun, L and Buntrock, C and Hoherz, C and Idrees, AR and Kraft, R and Meyer, P and Nguyen, TBD and Pryss, R and Reichert, M and Sextl, T and Steinhoff, M and Stenzel, L and Steubl, L and Terhorst, Y and Titzler, I and Ebert, DD}, title = {Clinical and Cost-Effectiveness of PSYCHOnlineTHERAPY: Study Protocol of a Multicenter Blended Outpatient Psychotherapy Cluster Randomized Controlled Trial for Patients With Depressive and Anxiety Disorders.}, journal = {Frontiers in psychiatry}, volume = {12}, number = {}, pages = {660534}, pmid = {34054617}, issn = {1664-0640}, abstract = {Introduction: Internet- and mobile-based interventions (IMIs) and their integration into routine psychotherapy (i.e., blended therapy) can offer a means of complementing psychotherapy in a flexible and resource optimized way. Objective: The present study will evaluate the non-inferiority, cost-effectiveness, and safety of two versions of integrated blended psychotherapy for depression and anxiety compared to standard cognitive behavioral therapy (CBT). Methods: A three-armed multicenter cluster-randomized controlled non-inferiority trial will be conducted comparing two implementations of blended psychotherapy (PSYCHOnlineTHERAPYfix/flex) compared to CBT. Seventy-five outpatient psychotherapists with a CBT-license will be randomized in a 1:1:1 ratio. Each of them is asked to include 12 patients on average with depressive or anxiety disorders resulting in a total sample size of N = 900. All patients receive up to a maximum of 16 psychotherapy sessions, either as routine CBT or alternating with Online self-help sessions (fix: 8/8; flex: 0-16). Assessments will be conducted at patient study inclusion (pre-treatment) and 6, 12, 18, and 24 weeks and 12 months post-inclusion. The primary outcome is depression and anxiety severity at 18 weeks post-inclusion (post-treatment) using the Patient Health Questionnaire Anxiety and Depression Scale. Secondary outcomes are depression and anxiety remission, treatment response, health-related quality of life, patient satisfaction, working alliance, psychotherapy adherence, and patient safety. Additionally, several potential moderators and mediators including patient characteristics and attitudes toward the interventions will be examined, complemented by ecological day-to-day digital behavior variables via passive smartphone sensing as part of an integrated smart-sensing sub-study. Data-analysis will be performed on an intention-to-treat basis with additional per-protocol analyses. In addition, cost-effectiveness and cost-utility analyses will be conducted from a societal and a public health care perspective. Additionally, qualitative interviews on acceptance, feasibility, and optimization potential will be conducted and analyzed. Discussion: PSYCHOnlineTHERAPY will provide evidence on blended psychotherapy in one of the largest ever conducted psychotherapy trials. If shown to be non-inferior and cost-effective, PSYCHOnlineTHERAPY has the potential to innovate psychotherapy in the near future by extending the ways of conducting psychotherapy. The rigorous health care services approach will facilitate a timely implementation of blended psychotherapy into standard care. Trial Registration: The trial is registered in the German Clinical Trials Register (DRKS00023973; date of registration: December 28th 2020).}, } @article {pmid34048482, year = {2021}, author = {Kadykalo, AN and Kelly, LA and Berberi, A and Reid, JL and Findlay, CS}, title = {Research effort devoted to regulating and supporting ecosystem services by environmental scientists and economists.}, journal = {PloS one}, volume = {16}, number = {5}, pages = {e0252463}, pmid = {34048482}, issn = {1932-6203}, mesh = {Conservation of Natural Resources ; Databases, Factual ; *Ecosystem ; Environmental Science ; Peer Review, Research ; }, abstract = {The economic valuation of ecosystem services in part reflects the desire to use conventional economic tools (markets and economic instruments) to conserve ecosystem services. However, for regulating and supporting ecosystem services that depend on ecosystem structure and function, estimation of economic value requires estimates of the current level of underlying ecological functions first. This primary step is in principle, the job of environmental scientists, not economists. Here, we provide a coarse-level quantitative assessment of the relationship between the research effort expended by environmental scientists (on the biophysical values) and economists (on the monetary values) on 15 different regulating and supporting services in 32 ecosystem types using peer-reviewed article hits retrieved from bibliographic databases as a measure of research effort. We find a positive, moderately strong (r = 0.69) correlation between research efforts in the two domains, a result that, while encouraging, is likely to reflect serendipity rather than the deliberate design of integrated environmental science-economics research programs. Our results suggest that compared to environmental science research effort economic valuation is devoted to a smaller, less diverse set of ecosystem services but a broader, more diverse, set of ecosystem types. The two domains differed more with respect to the ecosystem services that are the major focus of research effort than they did with respect to the ecosystem types of principal research interest. For example, carbon sequestration, erosion regulation, and nutrient cycling receive more relative research effort in the environmental sciences; air quality regulation in economic valuations. For both domains, cultivated areas, wetlands, and urban/semi-urban ecosystem types received relatively large research effort, while arctic and mountain tundra, cave and subterranean, cryosphere, intertidal/littoral zone, and kelp forest ecosystem types received negligible research effort. We suggest ways and means by which the field of sustainability science may be improved by the design and implementation of a searchable database of environmental science and economic valuation literature as well as a global ecosystem service research network and repository that explicitly links research on the estimation and prediction of biophysical ecosystem functions with that of the social sciences and other knowledge systems. These suggestions would, at least in principle, facilitate a more efficient research agenda between economists and environmental scientists and aid management, regulatory and judicial decision-makers.}, } @article {pmid34046832, year = {2021}, author = {Chen, D and Feng, Q and Liang, H}, title = {Effects of long-term discharge of acid mine drainage from abandoned coal mines on soil microorganisms: microbial community structure, interaction patterns, and metabolic functions.}, journal = {Environmental science and pollution research international}, volume = {28}, number = {38}, pages = {53936-53952}, pmid = {34046832}, issn = {1614-7499}, support = {41977159//National Natural Science Foundation of China/ ; }, mesh = {Biodegradation, Environmental ; Coal ; Hydrogen-Ion Concentration ; *Microbiota ; *Soil ; }, abstract = {More than twenty abandoned coal mines in the Yudong River Basin of Guizhou Province have discharged acid mine drainage (AMD) for a long time. The revelation of microbial community composition, interaction patterns, and metabolic functions can contribute to a better understanding of such ecosystems, which in its turn can be helpful in the development of strategies aiming at the ecological remediation of AMD pollution. In this study, reference and contaminated soil samples were collected along the AMD flow path for high-throughput sequencing. Results showed that the long-term AMD pollution promoted the evolution of γ-Proteobacteria, and the acidophilic iron-oxidizing bacteria Ferrovum (relative abundance of 15.50%) and iron-reducing bacteria Metallibacterium (9.87%) belonging to this class became the dominant genera. Co-occurrence analysis revealed that the proportion of positive correlations among bacteria increased from 51.02 (reference soil) to 75.16% (contaminated soil), suggesting that acidic pollution promotes the formation of mutualistic interaction networks of microorganisms. Metabolic function prediction (Tax4Fun) revealed that AMD contamination enhanced microbial functions such as translation, repair, and biosynthesis of peptidoglycan and lipopolysaccharide, etc., which may be an adaptive mechanism for microbial survival in extremely acidic environment. In addition, acidic pollution promoted the high expression of nitrogen-fixing genes in soil, and the discovery of autotrophic nitrogen-fixing bacteria such as Ferrovum highlights the possibility of using this taxon for bioremediation of AMD pollution.}, } @article {pmid34043242, year = {2021}, author = {Rademacher, T and Fonti, P and LeMoine, JM and Fonti, MV and Basler, D and Chen, Y and Friend, AD and Seyednasrollah, B and Eckes-Shephard, AH and Richardson, AD}, title = {Manipulating phloem transport affects wood formation but not local nonstructural carbon reserves in an evergreen conifer.}, journal = {Plant, cell & environment}, volume = {44}, number = {8}, pages = {2506-2521}, doi = {10.1111/pce.14117}, pmid = {34043242}, issn = {1365-3040}, mesh = {Biological Transport ; Carbon/*metabolism ; Carbon Dioxide/metabolism ; Cell Wall/metabolism ; Massachusetts ; Phloem/*metabolism ; Pinus/*growth & development/*metabolism ; Plant Cells/metabolism ; Plant Roots/metabolism ; Plant Stems/metabolism ; Wood/*growth & development/metabolism ; Xylem/metabolism ; }, abstract = {How variations in carbon supply affect wood formation remains poorly understood in particular in mature forest trees. To elucidate how carbon supply affects carbon allocation and wood formation, we attempted to manipulate carbon supply to the cambial region by phloem girdling and compression during the mid- and late-growing season and measured effects on structural development, CO2 efflux and nonstructural carbon reserves in stems of mature white pines. Wood formation and stem CO2 efflux varied with a location relative to treatment (i.e., above or below the restriction). We observed up to twice as many tracheids formed above versus below the treatment after the phloem transport manipulation, whereas the cell-wall area decreased only slightly below the treatments, and cell size did not change relative to the control. Nonstructural carbon reserves in the xylem, needles and roots were largely unaffected by the treatments. Our results suggest that low and high carbon supply affects wood formation, primarily through a strong effect on cell proliferation, and respiration, but local nonstructural carbon concentrations appear to be maintained homeostatically. This contrasts with reports of decoupling of source activity and wood formation at the whole-tree or ecosystem level, highlighting the need to better understand organ-specific responses, within-tree feedbacks, as well as phenological and ontogenetic effects on sink-source dynamics.}, } @article {pmid34042352, year = {2021}, author = {Han, L and Huo, H and Liu, Z and Zhao, YH and Zhu, HL and Chen, R and Zhao, ZL}, title = {[Spatial and temporal variations of vegetation coverage in the middle section of Yellow River Basin based on terrain gradient:Taking Yan'an City as an example.].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {32}, number = {5}, pages = {1581-1592}, doi = {10.13287/j.1001-9332.202105.014}, pmid = {34042352}, issn = {1001-9332}, mesh = {China ; Cities ; *Ecosystem ; Environmental Monitoring ; *Rivers ; }, abstract = {Vegetation restoration is an important requirement for ecological protection and high-quality development in the Yellow River Basin. In-depth understanding the temporal and spatial differentiation of vegetation has important practical significance. With the four Landsat TM/OLI remote sensing images as the data source, the pixel binary model was used to estimate vegetation coverage. The transfer matrix, geological information map, and the center of gravity migration model were used to analyze the temporal and spatial variations of vegetation coverage in Yan'an City in the middle of the Yellow River Basin from 1988 to 2018. The spatial variation of vegetation cover to elevation and slope was explored using terrain distribution index combined with terrain data. The results showed that vegetation coverage in Yan'an was low in the north region and high in the south region. The vegetation coverage increased significantly due to policy changes. From 1988 to 2018, the vegetation change pattern in Yan'an was dominated by continuous improvement and stability. Vegetation coverage increased in about 50% of the area. 83% of the study area with high vegetation coverage remained stable. At each elevation and slope level, the advantage of high vegetation cove-rage increased with time. At each slope level, vegetation cover increased with slope. The transition direction of vegetation cover of different levels in Yan'an was basically consistent with the overall spatial change trend of vegetation cover, with the overall shift being from north to west. The vegetation construction in Yan'an has achieved remarkable results, though the vegetation coverage in the north still needs to be improved. Optimizing vegetation types and structures is an important direction for future vegetation construction.}, } @article {pmid34041231, year = {2021}, author = {Ortiz, Y and Carrión, J and Lahoz-Beltrá, R and Gutiérrez, M}, title = {A Framework for Implementing Metaheuristic Algorithms Using Intercellular Communication.}, journal = {Frontiers in bioengineering and biotechnology}, volume = {9}, number = {}, pages = {660148}, pmid = {34041231}, issn = {2296-4185}, abstract = {Metaheuristics (MH) are Artificial Intelligence procedures that frequently rely on evolution. MH approximate difficult problem solutions, but are computationally costly as they explore large solution spaces. This work pursues to lay the foundations of general mappings for implementing MH using Synthetic Biology constructs in cell colonies. Two advantages of this approach are: harnessing large scale parallelism capability of cell colonies and, using existing cell processes to implement basic dynamics defined in computational versions. We propose a framework that maps MH elements to synthetic circuits in growing cell colonies to replicate MH behavior in cell colonies. Cell-cell communication mechanisms such as quorum sensing (QS), bacterial conjugation, and environmental signals map to evolution operators in MH techniques to adapt to growing colonies. As a proof-of-concept, we implemented the workflow associated to the framework: automated MH simulation generators for the gro simulator and two classes of algorithms (Simple Genetic Algorithms and Simulated Annealing) encoded as synthetic circuits. Implementation tests show that synthetic counterparts mimicking MH are automatically produced, but also that cell colony parallelism speeds up the execution in terms of generations. Furthermore, we show an example of how our framework is extended by implementing a different computational model: The Cellular Automaton.}, } @article {pmid34037104, year = {2021}, author = {Andrade, RLM and Spala, MR and Silva, G and Ribeiro, FAS and Bertolde, AI and Dantas, A and Silva, RC and Morellato, SA and Ramalho, WM}, title = {Compulsorily notifiable diseases and health problems and socio-environmental conditions: an ecological study, Espírito Santo, Brazil, 2011-2015.}, journal = {Epidemiologia e servicos de saude : revista do Sistema Unico de Saude do Brasil}, volume = {30}, number = {2}, pages = {e2020324}, doi = {10.1590/S1679-49742021000200019}, pmid = {34037104}, issn = {2237-9622}, mesh = {*Ambulatory Care ; Brazil/epidemiology ; Educational Status ; Female ; Humans ; *Information Systems ; Research ; }, abstract = {OBJECTIVE: To analyze association between climatic-environmental conditions and occurrence of compulsorily notifiable diseases and health problems, in the state of Espírito Santo, Brazil, 2011-2015.

METHODS: This was an ecological study of municipality clusters calculated based on cases confirmed on the Notifiable Health Conditions Information System for the period 2011-2015.

RESULTS: Notifications were more frequent among females (51.1%); people of brown race/skin color (31.7%); in the 20-49 year age group (48.1%) and in the Metropolitan Health Region (60.3%). The factors associated with health problems were ambulatory care sensitive conditions (p-value<0.001); education development index (p-value<0.001); temperature (p-value=0.019) and degree of urbanization (p-value=0.004). Diseases were associated with population density (p-value<0.001); temperature (p-value<0.001), humidity (p-value<0.001) and altitude (p-value=0.005).

CONCLUSION: Health problems were positively associated with ambulatory care sensitive conditions, the education development index and temperature; but negatively associated with degree of urbanization. Diseases were positively associated with the factors mentioned.}, } @article {pmid34030983, year = {2021}, author = {Miller, KE and Polaszek, A and Evans, DM}, title = {A dearth of data: fitting parasitoids into ecological networks.}, journal = {Trends in parasitology}, volume = {37}, number = {10}, pages = {863-874}, doi = {10.1016/j.pt.2021.04.012}, pmid = {34030983}, issn = {1471-5007}, mesh = {Animals ; DNA Barcoding, Taxonomic ; Databases, Genetic ; *Ecosystem ; *Host-Parasite Interactions/physiology ; }, abstract = {Studying parasitoids can provide insights into global diversity estimates, climate change impacts, and agroecosystem service provision. However, this potential remains largely untapped due to a lack of data on how parasitoids interact with other organisms. Ecological networks are a useful tool for studying and exploiting the impacts of parasitoids, but their construction is hindered by the magnitude of undescribed parasitoid species, a sparse knowledge of host ranges, and an under-representation of parasitoids within DNA-barcode databases (we estimate <5% have a barcode). Here, we advocate the use of DNA metabarcoding to construct the host-parasitoid component of multilayer networks. While the incorporation of parasitoids into network-based analyses has far ranging applications, we focus on its potential for assessing ecosystem service provision within agroecosystems.}, } @article {pmid34029315, year = {2021}, author = {Kalm, K and Norris, D}, title = {Sequence learning recodes cortical representations instead of strengthening initial ones.}, journal = {PLoS computational biology}, volume = {17}, number = {5}, pages = {e1008969}, pmid = {34029315}, issn = {1553-7358}, support = {MC_UU_00005/11/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Computational Biology/*methods ; Humans ; *Learning ; Magnetic Resonance Imaging ; Memory ; }, abstract = {We contrast two computational models of sequence learning. The associative learner posits that learning proceeds by strengthening existing association weights. Alternatively, recoding posits that learning creates new and more efficient representations of the learned sequences. Importantly, both models propose that humans act as optimal learners but capture different statistics of the stimuli in their internal model. Furthermore, these models make dissociable predictions as to how learning changes the neural representation of sequences. We tested these predictions by using fMRI to extract neural activity patterns from the dorsal visual processing stream during a sequence recall task. We observed that only the recoding account can explain the similarity of neural activity patterns, suggesting that participants recode the learned sequences using chunks. We show that associative learning can theoretically store only very limited number of overlapping sequences, such as common in ecological working memory tasks, and hence an efficient learner should recode initial sequence representations.}, } @article {pmid34028527, year = {2021}, author = {Ahlquist, KD and Bañuelos, MM and Funk, A and Lai, J and Rong, S and Villanea, FA and Witt, KE}, title = {Our Tangled Family Tree: New Genomic Methods Offer Insight into the Legacy of Archaic Admixture.}, journal = {Genome biology and evolution}, volume = {13}, number = {7}, pages = {}, pmid = {34028527}, issn = {1759-6653}, support = {T32 GM007601/GM/NIGMS NIH HHS/United States ; R35 GM139628/GM/NIGMS NIH HHS/United States ; T32 GM128596/GM/NIGMS NIH HHS/United States ; R35 GM128946/GM/NIGMS NIH HHS/United States ; R01 GM127472/GM/NIGMS NIH HHS/United States ; R01 GM118652/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Genome, Human ; Genomics ; *Hominidae/genetics ; Humans ; *Neanderthals/genetics ; Pedigree ; }, abstract = {The archaic ancestry present in the human genome has captured the imagination of both scientists and the wider public in recent years. This excitement is the result of new studies pushing the envelope of what we can learn from the archaic genetic information that has survived for over 50,000 years in the human genome. Here, we review the most recent ten years of literature on the topic of archaic introgression, including the current state of knowledge on Neanderthal and Denisovan introgression, as well as introgression from other as-yet unidentified archaic populations. We focus this review on four topics: 1) a reimagining of human demographic history, including evidence for multiple admixture events between modern humans, Neanderthals, Denisovans, and other archaic populations; 2) state-of-the-art methods for detecting archaic ancestry in population-level genomic data; 3) how these novel methods can detect archaic introgression in modern African populations; and 4) the functional consequences of archaic gene variants, including how those variants were co-opted into novel function in modern human populations. The goal of this review is to provide a simple-to-access reference for the relevant methods and novel data, which has changed our understanding of the relationship between our species and its siblings. This body of literature reveals the large degree to which the genetic legacy of these extinct hominins has been integrated into the human populations of today.}, } @article {pmid34022649, year = {2021}, author = {Rice, WL and Park, S}, title = {Big data spatial analysis of campers' landscape preferences: Examining demand for amenities.}, journal = {Journal of environmental management}, volume = {292}, number = {}, pages = {112773}, doi = {10.1016/j.jenvman.2021.112773}, pmid = {34022649}, issn = {1095-8630}, mesh = {*Big Data ; *Recreation ; Rivers ; Spatial Analysis ; }, abstract = {Outdoor recreation decision-making has received significant research interest over the last fifty years. In the context of campsite choice, this previous research has almost exclusively used stated preference data and aspatial methods to understand decision-making. This present research seeks to understand how recreationists reach decisions on the selection of campsites and what aspects of the recreational setting drive demand through an examination of a big dataset of revealed preference data using a spatial regression. Specifically, we examine which managerial, social, and ecological aspects of the setting influence demand for campsites in Zion National Park's (USA) Watchman Campground using reservation data from the Recreation Information Database (RIDB). Results indicate that price, access to electricity, ease of access, and proximity to the Virgin River are significantly predictive of demand. Study implications for park management, including campsite allocation and distributive justice, are provided. Additionally, implications for future research methodology, including the use of transaction-style big data in protected area management research, are discussed.}, } @article {pmid34021761, year = {2021}, author = {Halder, S and Ghosh, S and Chattopadhyay, J and Chatterjee, S}, title = {Bistability in cell signalling and its significance in identifying potential drug-targets.}, journal = {Bioinformatics (Oxford, England)}, volume = {37}, number = {22}, pages = {4156-4163}, doi = {10.1093/bioinformatics/btab395}, pmid = {34021761}, issn = {1367-4811}, mesh = {*Signal Transduction ; *Protein Interaction Domains and Motifs ; Computational Biology ; }, abstract = {MOTIVATION: Bistability is one of the salient dynamical features in various all-or-none kinds of decision-making processes. The presence of bistability in a cell signalling network plays a key role in input-output (I/O) relation. Our study is aiming to capture and emphasize the role of motif structure influencing the I/O relation between two nodes in the context of bistability. Here, a model-based analysis is made to investigate the critical conditions responsible for the emergence of different bistable protein-protein interaction (PPI) motifs and their possible applications to find the potential drug-targets.

RESULTS: The global sensitivity analysis is used to identify sensitive parameters and their role in maintaining the bistability. Additionally, the bistable switching through hysteresis is explored to develop an understanding of the underlying mechanisms involved in the cell signalling processes, when significant motifs exhibiting bistability have emerged. Further, we elaborate the application of the results by the implication of the emerged PPI motifs to identify potential drug-targets in three cancer networks, which is validated with existing databases. The influence of stochastic perturbations that could hinder desired functionality of any signalling networks is also described here.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, } @article {pmid34021563, year = {2021}, author = {Wright, ES and Gupta, R and Vetsigian, KH}, title = {Multi-stable bacterial communities exhibit extreme sensitivity to initial conditions.}, journal = {FEMS microbiology ecology}, volume = {97}, number = {6}, pages = {}, doi = {10.1093/femsec/fiab073}, pmid = {34021563}, issn = {1574-6941}, mesh = {Bacteria/genetics ; *Microbiota ; *Models, Biological ; Population Dynamics ; }, abstract = {Microbial communities can have dramatically different compositions even among similar environments. This might be due to the existence of multiple alternative stable states, yet there exists little experimental evidence supporting this possibility. Here, we gathered a large collection of absolute population abundances capturing population dynamics in one- to four-strain communities of soil bacteria with a complex life cycle in a feast-or-famine environment. This dataset led to several observations: (i) some pairwise competitions resulted in bistability with a separatrix near a 1:1 initial ratio across a range of population densities; (ii) bistability propagated to multi-stability in multispecies communities; and (iii) replicate microbial communities reached different stable states when starting close to initial conditions separating basins of attraction, indicating finite-sized regions where the dynamics are unpredictable. The generalized Lotka-Volterra equations qualitatively captured most competition outcomes but were unable to quantitatively recapitulate the observed dynamics. This was partly due to complex and diverse growth dynamics in monocultures that ranged from Allee effects to nonmonotonic behaviors. Overall, our results highlight that multi-stability might be generic in multispecies communities and, combined with ecological noise, can lead to unpredictable community assembly, even in simple environments.}, } @article {pmid34021210, year = {2021}, author = {Hu, M and Li, J and Hou, M and Liu, X and Cui, S and Yang, X and Liu, L and Jiang, X and Mu, G}, title = {Transcriptomic and metabolomic joint analysis reveals distinct flavonoid biosynthesis regulation for variegated testa color development in peanut (Arachis hypogaea L.).}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {10721}, pmid = {34021210}, issn = {2045-2322}, mesh = {Arachis/*physiology ; Computational Biology/methods ; Flavonoids/*biosynthesis ; Gene Expression Regulation, Plant ; Gene Ontology ; Gene Regulatory Networks ; Genetic Association Studies ; *Metabolomics/methods ; Models, Biological ; Phenotype ; *Plant Development ; Plant Physiological Phenomena ; Plant Proteins/genetics/metabolism ; *Transcriptome ; }, abstract = {Peanut is one of the important oil and economic crops, among which the variegated testa peanut is a unique member. The molecular mechanisms underlying the pigment synthesis in variegated testa are still unclear. Differentially expressed genes (DEGs) in the flavonoid metabolism pathway in pigmented areas indicated that there were 27 DEGs highly related to the synthesis of variegated testa color among 1,050 DEGs. Of these 27, 13 were up-regulated and 14 were down-regulated, including 3 PALs, 1 C4H, 2 CHSs, 1 F3H, 1 F3'H, 2 DFRs, 2 LARs, 2 IAAs, 4 bHLHs, and 9 MYBs. GO (Gene Ontology) analysis indicated that DEGs were similarly enriched in three branches. KEGG (Kyoto Encyclopedia of Genes and Genomes) analysis suggested flavonoid biosynthesis is the most direct metabolic pathway for the synthesis of testa variegation. The liquid chromatography-tandem mass spectrometry (LC-MS/MS) results showed that cyanidin and delphinidin were the primary metabolites that caused the color differences between the pigmented and the non-pigmented areas. Through the verification of 20 DEGs via qPCR, the results were consistent with transcriptome sequencing in four comparison groups. The results in this study lay the foundation for revealing the molecular regulation mechanisms of flavonoid synthesis in variegated testa peanut.}, } @article {pmid34019115, year = {2021}, author = {Drackett, L and Dragićević, S}, title = {Suitability Analysis of Acoustic Refugia for Endangered Killer Whales (Orcinus orca) Using the GIS-based Logic Scoring of Preference Method.}, journal = {Environmental management}, volume = {68}, number = {2}, pages = {262-278}, pmid = {34019115}, issn = {1432-1009}, support = {RGPIN-2017-03939//Natural Sciences and Engineering Research Council of Canada/ ; }, mesh = {Acoustics ; Animals ; Canada ; Geographic Information Systems ; Logic ; Refugium ; *Whale, Killer ; }, abstract = {An emerging priority in marine noise pollution research is identifying marine "acoustic refugia" where noise levels are relatively low and good-quality habitat is available to acoustically sensitive species. The endangered Southern Resident population of killer whales (Orcinus orca) that inhabits the transboundary Salish Sea in Canada and the USA are affected by noise pollution. Geographic Information Systems (GIS) and spatial multicriteria evaluation (MCE) methods have been used to operationalize suitability analysis in ecology and conservation for site selection problems. However, commonly used methods lack the ability to represent complex logical relationships between input criteria. Therefore, the objective of this study is to apply a more advanced MCE method, known as Logic Scoring of Preference (LSP), to identify acoustic refugia for killer whales in the Salish Sea. This GIS-based LSP-MCE approach considers multiple input criteria by combining input data representing killer whale habitat requirements with noise pollution and other factors to identify suitable acoustic refugia. The results indicate the locations of suitable acoustic refugia and how they are affected by noise pollution from marine vessels in three scenarios developed to represent different levels of vessel traffic. Identifying acoustic refugia can contribute to efforts to reduce the effect of marine noise pollution on killer whale populations by highlighting high-priority areas in which to implement policies such as traffic-limiting measures or marine protected areas. Moreover, the proposed LSP-MCE procedure combines criteria in a stepwise manner that can support environmental management decision-making processes and can be applied to other marine suitability analysis contexts.}, } @article {pmid34014965, year = {2021}, author = {Jia, WJ and Wang, MF and Zhou, CH and Yang, QH}, title = {Analysis of the spatial association of geographical detector-based landslides and environmental factors in the southeastern Tibetan Plateau, China.}, journal = {PloS one}, volume = {16}, number = {5}, pages = {e0251776}, pmid = {34014965}, issn = {1932-6203}, mesh = {*Geographic Information Systems ; *Rivers ; Tibet ; }, abstract = {Steep canyons surrounded by high mountains resulting from large-scale landslides characterize the study area located in the southeastern part of the Tibetan Plateau. A total of 1766 large landslides were identified based on integrated remote sensing interpretations utilizing multisource satellite images and topographic data that were dominated by 3 major regional categories, namely, rockslides, rock falls, and flow-like landslides. The geographical detector method was applied to quantitatively unveil the spatial association between the landslides and 12 environmental factors through computation of the q values based on spatially stratified heterogeneity. Meanwhile, a certainty factor (CF) model was used for comparison. The results indicate that the q values of the 12 influencing factors vary obviously, and the dominant factors are also different for the 3 types of landslides, with annual mean precipitation (AMP) being the dominant factor for rockslide distribution, elevation being the dominant factor for rock fall distribution and lithology being the dominant factor for flow-like distribution. Integrating the results of the factor detector and ecological detector, the AMP, annual mean temperature (AMT), elevation, river density, fault distance and lithology have a stronger influence on the spatial distribution of landslides than other factors. Furthermore, the factor interactions can significantly enhance their interpretability of landslides, and the top 3 dominant interactions were revealed. Based on statistics of landslide discrepancies with respect to diverse stratification of each factor, the high-risk zones were identified for 3 types of landslides, and the results were contrasted with the CF model. In conclusion, our method provides an objective framework for landslide prevention and mitigation through quantitative, spatial and statistical analyses in regions with complex terrain.}, } @article {pmid34014945, year = {2021}, author = {Stokes, AC and Lundberg, DJ and Elo, IT and Hempstead, K and Bor, J and Preston, SH}, title = {COVID-19 and excess mortality in the United States: A county-level analysis.}, journal = {PLoS medicine}, volume = {18}, number = {5}, pages = {e1003571}, pmid = {34014945}, issn = {1549-1676}, support = {P2C HD044964/HD/NICHD NIH HHS/United States ; R01 AG060115/AG/NIA NIH HHS/United States ; }, mesh = {Black or African American/statistics & numerical data ; Aged ; COVID-19/*mortality ; Comorbidity ; Cross-Sectional Studies ; Databases, Factual ; Diabetes Mellitus/epidemiology ; Educational Status ; Hispanic or Latino/statistics & numerical data ; Humans ; Income ; *Mortality ; Race Factors ; SARS-CoV-2 ; United States/epidemiology ; White People/statistics & numerical data ; }, abstract = {BACKGROUND: Coronavirus Disease 2019 (COVID-19) excess deaths refer to increases in mortality over what would normally have been expected in the absence of the COVID-19 pandemic. Several prior studies have calculated excess deaths in the United States but were limited to the national or state level, precluding an examination of area-level variation in excess mortality and excess deaths not assigned to COVID-19. In this study, we take advantage of county-level variation in COVID-19 mortality to estimate excess deaths associated with the pandemic and examine how the extent of excess mortality not assigned to COVID-19 varies across subsets of counties defined by sociodemographic and health characteristics.

METHODS AND FINDINGS: In this ecological, cross-sectional study, we made use of provisional National Center for Health Statistics (NCHS) data on direct COVID-19 and all-cause mortality occurring in US counties from January 1 to December 31, 2020 and reported before March 12, 2021. We used data with a 10-week time lag between the final day that deaths occurred and the last day that deaths could be reported to improve the completeness of data. Our sample included 2,096 counties with 20 or more COVID-19 deaths. The total number of residents living in these counties was 319.1 million. On average, the counties were 18.7% Hispanic, 12.7% non-Hispanic Black, and 59.6% non-Hispanic White. A total of 15.9% of the population was older than 65 years. We first modeled the relationship between 2020 all-cause mortality and COVID-19 mortality across all counties and then produced fully stratified models to explore differences in this relationship among strata of sociodemographic and health factors. Overall, we found that for every 100 deaths assigned to COVID-19, 120 all-cause deaths occurred (95% CI, 116 to 124), implying that 17% (95% CI, 14% to 19%) of excess deaths were ascribed to causes of death other than COVID-19 itself. Our stratified models revealed that the percentage of excess deaths not assigned to COVID-19 was substantially higher among counties with lower median household incomes and less formal education, counties with poorer health and more diabetes, and counties in the South and West. Counties with more non-Hispanic Black residents, who were already at high risk of COVID-19 death based on direct counts, also reported higher percentages of excess deaths not assigned to COVID-19. Study limitations include the use of provisional data that may be incomplete and the lack of disaggregated data on county-level mortality by age, sex, race/ethnicity, and sociodemographic and health characteristics.

CONCLUSIONS: In this study, we found that direct COVID-19 death counts in the US in 2020 substantially underestimated total excess mortality attributable to COVID-19. Racial and socioeconomic inequities in COVID-19 mortality also increased when excess deaths not assigned to COVID-19 were considered. Our results highlight the importance of considering health equity in the policy response to the pandemic.}, } @article {pmid34011982, year = {2021}, author = {Rabosky, DL and Benson, RBJ}, title = {Ecological and biogeographic drivers of biodiversity cannot be resolved using clade age-richness data.}, journal = {Nature communications}, volume = {12}, number = {1}, pages = {2945}, pmid = {34011982}, issn = {2041-1723}, mesh = {Animals ; *Biodiversity ; *Biological Evolution ; Data Interpretation, Statistical ; *Ecosystem ; Extinction, Biological ; Fossils ; Genetic Speciation ; Mathematical Concepts ; *Models, Biological ; Paleontology/methods/statistics & numerical data ; Phylogeny ; Phylogeography ; Time Factors ; }, abstract = {Estimates of evolutionary diversification rates - speciation and extinction - have been used extensively to explain global biodiversity patterns. Many studies have analyzed diversification rates derived from just two pieces of information: a clade's age and its extant species richness. This "age-richness rate" (ARR) estimator provides a convenient shortcut for comparative studies, but makes strong assumptions about the dynamics of species richness through time. Here we demonstrate that use of the ARR estimator in comparative studies is problematic on both theoretical and empirical grounds. We prove mathematically that ARR estimates are non-identifiable: there is no information in the data for a single clade that can distinguish a process with positive net diversification from one where net diversification is zero. Using paleontological time series, we demonstrate that the ARR estimator has no predictive ability for real datasets. These pathologies arise because the ARR inference procedure yields "point estimates" that have been computed under a saturated statistical model with zero degrees of freedom. Although ARR estimates remain useful in some contexts, they should be avoided for comparative studies of diversification and species richness.}, } @article {pmid34008793, year = {2021}, author = {Broday, GA and Kluthcovsky, ACGC}, title = {INFANT MORTALITY AND FAMILY HEALTH STRATEGY IN THE 3RD HEALTH REGIONAL OF PARANÁ, FROM 2005 TO 2016.}, journal = {Revista paulista de pediatria : orgao oficial da Sociedade de Pediatria de Sao Paulo}, volume = {40}, number = {}, pages = {e2020122}, pmid = {34008793}, issn = {1984-0462}, mesh = {Adolescent ; Adult ; Brazil/epidemiology ; Family Health/*standards ; Female ; Humans ; Infant ; *Infant Mortality ; Infant, Newborn ; Information Systems ; Live Birth/*epidemiology ; Male ; Population Surveillance ; Spatial Analysis ; Young Adult ; }, abstract = {OBJECTIVE: To analyze the temporal trend in infant mortality and in populational coverage by the Family Health Strategy and associated factors with infant mortality in the municipalities of the 3rd Health Regional of Paraná, Southern Brazil.

METHODS: Ecological time series study, with data from the Mortality Information System (Sistema de Informação Sobre Mortalidade - SIM), the Live Birth Information System (Sistema de Informação Sobre Nascidos Vivos - SINASC) and the Support Room for Strategic Management (Sala de Apoio à Gestão Estratégica - SAGE), from 2005 to 2016. Trends were calculated using polynomial regression. The associated factors with infant mortality were maternal, perinatal and obstetric variables. The significance level adopted was 5%.

RESULTS: Between 2005 and 2016, there were 115,796 births and 1,575 deaths of children under 1 year of age. Considering the municipalities together, the populational coverage by the Family Health Strategy went from 43.8% in 2005 to 66.4% in 2016 and the infant mortality from 17.1/1,000 live births in 2005 to 10.7/1,000 live births in 2016. The trend over time of populational coverage by the Family Health Strategy was crescent and of infant mortality was decrescent, for most municipalities. The factors associated with greater chances of death in children under 1 year of age were preterm gestational age (Odds Ratio - OR=15.05; 95% confidence interval - 95CI% 13.54-16.72), low birth weight (OR=15.14; 95%CI 13.61-16.84), multiple gestation (OR=4.51; 95%CI 3.74-5.45) and mother with up to 7 years of study (OR=1.93; 95%CI 1.74-2.14).

CONCLUSIONS: Crescent trend in coverage by the Family Health Strategy was accompanied by a decrescent trend in infant mortality. The results can be a source of information for the strengthening of mother-child health actions, considering local and regional specificities.}, } @article {pmid34006840, year = {2021}, author = {Karatayev, VA and Vasconcelos, VV and Lafuite, AS and Levin, SA and Bauch, CT and Anand, M}, title = {A well-timed shift from local to global agreements accelerates climate change mitigation.}, journal = {Nature communications}, volume = {12}, number = {1}, pages = {2908}, pmid = {34006840}, issn = {2041-1723}, abstract = {Recent attempts at cooperating on climate change mitigation highlight the limited efficacy of large-scale negotiations, when commitment to mitigation is costly and initially rare. Deepening existing voluntary mitigation pledges could require more stringent, legally-binding agreements that currently remain untenable at the global scale. Building-blocks approaches promise greater success by localizing agreements to regions or few-nation summits, but risk slowing mitigation adoption globally. Here, we show that a well-timed policy shift from local to global legally-binding agreements can dramatically accelerate mitigation compared to using only local, only global, or both agreement types simultaneously. This highlights the scale-specific roles of mitigation incentives: local agreements promote and sustain mitigation commitments in early-adopting groups, after which global agreements rapidly draw in late-adopting groups. We conclude that focusing negotiations on local legally-binding agreements and, as these become common, a renewed pursuit of stringent, legally-binding world-wide agreements could best overcome many current challenges facing climate mitigation.}, } @article {pmid34003850, year = {2021}, author = {Manoharan, L and Cattrall, JWS and Harris, C and Newell, K and Thomson, B and Pritchard, MG and Bannister, PG and Sigfrid, L and Solomon, T and Horby, PW and Carson, G and Olliaro, P}, title = {Evaluating clinical characteristics studies produced early in the Covid-19 pandemic: A systematic review.}, journal = {PloS one}, volume = {16}, number = {5}, pages = {e0251250}, pmid = {34003850}, issn = {1932-6203}, support = {/WT_/Wellcome Trust/United Kingdom ; MR/V033441/1/MRC_/Medical Research Council/United Kingdom ; 215091/Z/18/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {C-Reactive Protein/analysis ; COVID-19/complications/epidemiology/*pathology/virology ; Cough/epidemiology/etiology ; Databases, Factual ; Fever/epidemiology/etiology ; Headache/epidemiology/etiology ; Humans ; Lymphopenia/etiology ; Pandemics ; SARS-CoV-2/isolation & purification ; }, abstract = {OBJECTIVES: Clinical characterisation studies have been essential in helping inform research, diagnosis and clinical management efforts, particularly early in a pandemic. This systematic review summarises the early literature on clinical characteristics of patients admitted to hospital, and evaluates the quality of evidence produced during the initial stages of the pandemic.

METHODS: MEDLINE, EMBASE and Global Health databases were searched for studies published from January 1st 2020 to April 28th 2020. Studies which reported on at least 100 hospitalised patients with Covid-19 of any age were included. Data on clinical characteristics were independently extracted by two review authors. Study design specific critical appraisal tools were used to evaluate included studies: the Newcastle Ottawa scale for cohort and cross sectional studies, Joanna Briggs Institute checklist for case series and the Cochrane collaboration tool for assessing risk of bias in randomised trials.

RESULTS: The search yielded 78 studies presenting data on 77,443 people. Most studies (82%) were conducted in China. No studies included patients from low- and middle-income countries. The overall quality of included studies was low to moderate, and the majority of studies did not include a control group. Fever and cough were the most commonly reported symptoms early in the pandemic. Laboratory and imaging findings were diverse with lymphocytopenia and ground glass opacities the most common findings respectively. Clinical data in children and vulnerable populations were limited.

CONCLUSIONS: The early Covid-19 literature had moderate to high risk of bias and presented several methodological issues. Early clinical characterisation studies should aim to include different at-risk populations, including patients in non-hospital settings. Pandemic preparedness requires collection tools to ensure observational studies are methodologically robust and will help produce high-quality data early on in the pandemic to guide clinical practice and public health policy.

REVIEW REGISTRATION: Available at https://osf.io/mpafn.}, } @article {pmid34002532, year = {2021}, author = {Pawlowski, S and Moeller, M and Miller, IB and Kellermann, MY and Schupp, PJ and Petersen-Thiery, M}, title = {UV filters used in sunscreens-A lack in current coral protection?.}, journal = {Integrated environmental assessment and management}, volume = {17}, number = {5}, pages = {926-939}, doi = {10.1002/ieam.4454}, pmid = {34002532}, issn = {1551-3793}, mesh = {Animals ; *Anthozoa ; Aquatic Organisms ; Ecotoxicology ; Risk Assessment ; *Sunscreening Agents/toxicity ; }, abstract = {Ultraviolet (UV) filters used in sunscreens are among the anthropogenic substances that may enter the marine environment by both indirect (via wastewater) and direct pathways (leisure activities). Owing to the recent global decline in coral population, the impact of those UV filters on the coral health is currently under increased investigation. First results from scientists suggest that some of the filters may be toxic to various coral life stages, but an initial cross comparison with existing data from other freshwater organisms does not indicate that corals are specifically more susceptible to UV filters than other standard species. In fact, the available data leading to this conclusion is still vague and based on toxicity and bioaccumulation tests with corals, which are both still at the research stage. To facilitate a proper hazard assessment, robust experimental procedures for coral ecotoxicological studies are considered mandatory. In other words, additional steps should be taken to standardize and validate such new test systems to generate reliable results, which then can be used in regulatory decision making. Furthermore, to facilitate a more detailed and site-specific environmental risk assessment in the marine area, an application-based exposure scenario must be developed. Until these data and tools become available, environmental hazard and risk assessments may be carried out using existing data from freshwater organisms and existing tonnage-based exposure scenarios as a potential surrogate. Integr Environ Assess Manag 2021;17:926-939. © 2021 SETAC.}, } @article {pmid34002172, year = {2021}, author = {Green, MA and García-Fiñana, M and Barr, B and Burnside, G and Cheyne, CP and Hughes, D and Ashton, M and Sheard, S and Buchan, IE}, title = {Evaluating social and spatial inequalities of large scale rapid lateral flow SARS-CoV-2 antigen testing in COVID-19 management: An observational study of Liverpool, UK (November 2020 to January 2021).}, journal = {The Lancet regional health. Europe}, volume = {6}, number = {}, pages = {100107}, pmid = {34002172}, issn = {2666-7762}, support = {MR/R024847/1/MRC_/Medical Research Council/United Kingdom ; }, abstract = {BACKGROUND: Large-scale asymptomatic testing of communities in Liverpool (UK) for SARS-CoV-2 was used as a public health tool for containing COVID-19. The aim of the study is to explore social and spatial inequalities in uptake and case-detection of rapid lateral flow SARS-CoV-2 antigen tests (LFTs) offered to people without symptoms of COVID-19.

METHODS: Linked pseudonymised records for asymptomatic residents in Liverpool who received a LFT for COVID-19 between 6th November 2020 to 31st January 2021 were accessed using the Combined Intelligence for Population Health Action resource. Bayesian Hierarchical Poisson Besag, York, and Mollié models were used to estimate ecological associations for uptake and positivity of testing.

FINDINGS: 214 525 residents (43%) received a LFT identifying 5192 individuals as positive cases of COVID-19 (1.3% of tests were positive). Uptake was highest in November when there was military assistance. High uptake was observed again in the week preceding Christmas and was sustained into a national lockdown. Overall uptake were lower among males (e.g. 40% uptake over the whole period), Black Asian and other Minority Ethnic groups (e.g. 27% uptake for 'Mixed' ethnicity) and in the most deprived areas (e.g. 32% uptake in most deprived areas). These population groups were also more likely to have received positive tests for COVID-19. Models demonstrated that uptake and repeat testing were lower in areas of higher deprivation, areas located further from test sites and areas containing populations less confident in the using Internet technologies. Positive tests were spatially clustered in deprived areas.

INTERPRETATION: Large-scale voluntary asymptomatic community testing saw social, ethnic, digital and spatial inequalities in uptake. COVID-19 testing and support to isolate need to be more accessible to the vulnerable communities most impacted by the pandemic, including non-digital means of access.

FUNDING: Department of Health and Social Care (UK) and Economic and Social Research Council.}, } @article {pmid34001609, year = {2021}, author = {Bohutínská, M and Vlček, J and Yair, S and Laenen, B and Konečná, V and Fracassetti, M and Slotte, T and Kolář, F}, title = {Genomic basis of parallel adaptation varies with divergence in Arabidopsis and its relatives.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {118}, number = {21}, pages = {}, pmid = {34001609}, issn = {1091-6490}, mesh = {Adaptation, Physiological/*genetics ; Animals ; Arabidopsis/classification/*genetics/metabolism/radiation effects ; *Biological Evolution ; Cold Temperature ; Gene Ontology ; Genetic Drift ; Genetic Introgression ; *Genetic Variation ; *Genome, Plant ; Herbivory/physiology ; Models, Genetic ; Molecular Sequence Annotation ; Plant Proteins/*genetics/metabolism ; Radiation, Ionizing ; Stress, Physiological ; }, abstract = {Parallel adaptation provides valuable insight into the predictability of evolutionary change through replicated natural experiments. A steadily increasing number of studies have demonstrated genomic parallelism, yet the magnitude of this parallelism varies depending on whether populations, species, or genera are compared. This led us to hypothesize that the magnitude of genomic parallelism scales with genetic divergence between lineages, but whether this is the case and the underlying evolutionary processes remain unknown. Here, we resequenced seven parallel lineages of two Arabidopsis species, which repeatedly adapted to challenging alpine environments. By combining genome-wide divergence scans with model-based approaches, we detected a suite of 151 genes that show parallel signatures of positive selection associated with alpine colonization, involved in response to cold, high radiation, short season, herbivores, and pathogens. We complemented these parallel candidates with published gene lists from five additional alpine Brassicaceae and tested our hypothesis on a broad scale spanning ∼0.02 to 18 My of divergence. Indeed, we found quantitatively variable genomic parallelism whose extent significantly decreased with increasing divergence between the compared lineages. We further modeled parallel evolution over the Arabidopsis candidate genes and showed that a decreasing probability of repeated selection on the same standing or introgressed alleles drives the observed pattern of divergence-dependent parallelism. We therefore conclude that genetic divergence between populations, species, and genera, affecting the pool of shared variants, is an important factor in the predictability of genome evolution.}, } @article {pmid34001434, year = {2021}, author = {Shen, W and Ren, H}, title = {TaxonKit: A practical and efficient NCBI taxonomy toolkit.}, journal = {Journal of genetics and genomics = Yi chuan xue bao}, volume = {48}, number = {9}, pages = {844-850}, doi = {10.1016/j.jgg.2021.03.006}, pmid = {34001434}, issn = {1673-8527}, mesh = {*Software ; *Classification/methods ; United States ; National Library of Medicine (U.S.) ; Computational Biology/methods ; }, abstract = {The National Center for Biotechnology Information (NCBI) Taxonomy is widely applied in biomedical and ecological studies. Typical demands include querying taxonomy identifier (TaxIds) by taxonomy names, querying complete taxonomic lineages by TaxIds, listing descendants of given TaxIds, and others. However, existed tools are either limited in functionalities or inefficient in terms of runtime. In this work, we present TaxonKit, a command-line toolkit for comprehensive and efficient manipulation of NCBI Taxonomy data. TaxonKit comprises seven core subcommands providing functions, including TaxIds querying, listing, filtering, lineage retrieving and reformatting, lowest common ancestor computation, and TaxIds change tracking. The practical functions, competitive processing performance, scalability with different scales of datasets and good accessibility can facilitate taxonomy data manipulations. TaxonKit provides free access under the permissive MIT license on GitHub, Brewsci, and Bioconda. The documents are also available at https://bioinf.shenwei.me/taxonkit/.}, } @article {pmid34000238, year = {2021}, author = {Docherty, AB and Mulholland, RH and Lone, NI and Cheyne, CP and De Angelis, D and Diaz-Ordaz, K and Donegan, C and Drake, TM and Dunning, J and Funk, S and García-Fiñana, M and Girvan, M and Hardwick, HE and Harrison, J and Ho, A and Hughes, DM and Keogh, RH and Kirwan, PD and Leeming, G and Nguyen Van-Tam, JS and Pius, R and Russell, CD and Spencer, RG and Tom, BD and Turtle, L and Openshaw, PJ and Baillie, JK and Harrison, EM and Semple, MG and , }, title = {Changes in in-hospital mortality in the first wave of COVID-19: a multicentre prospective observational cohort study using the WHO Clinical Characterisation Protocol UK.}, journal = {The Lancet. Respiratory medicine}, volume = {9}, number = {7}, pages = {773-785}, pmid = {34000238}, issn = {2213-2619}, support = {MC_PC_19004/MRC_/Medical Research Council/United Kingdom ; G0701652/MRC_/Medical Research Council/United Kingdom ; MC_PC_19026/MRC_/Medical Research Council/United Kingdom ; MC_PC_19059/MRC_/Medical Research Council/United Kingdom ; MR/R024847/1/MRC_/Medical Research Council/United Kingdom ; MR/S032304/1/MRC_/Medical Research Council/United Kingdom ; MC_UU_00002/2/MRC_/Medical Research Council/United Kingdom ; MC_PC_19025/MRC_/Medical Research Council/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; MR/S017968/1/MRC_/Medical Research Council/United Kingdom ; 109965/Z/15/Z/WT_/Wellcome Trust/United Kingdom ; MC_UU_12014/9/MRC_/Medical Research Council/United Kingdom ; MC_UU_00002/11/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Aged ; Aged, 80 and over ; COVID-19/epidemiology/*mortality ; Clinical Protocols ; Cohort Studies ; Female ; *Hospital Mortality ; Humans ; Male ; Middle Aged ; Prospective Studies ; United Kingdom/epidemiology ; World Health Organization ; }, abstract = {BACKGROUND: Mortality rates in hospitalised patients with COVID-19 in the UK appeared to decline during the first wave of the pandemic. We aimed to quantify potential drivers of this change and identify groups of patients who remain at high risk of dying in hospital.

METHODS: In this multicentre prospective observational cohort study, the International Severe Acute Respiratory and Emerging Infections Consortium WHO Clinical Characterisation Protocol UK recruited a prospective cohort of patients with COVID-19 admitted to 247 acute hospitals in England, Scotland, and Wales during the first wave of the pandemic (between March 9 and Aug 2, 2020). We included all patients aged 18 years and older with clinical signs and symptoms of COVID-19 or confirmed COVID-19 (by RT-PCR test) from assumed community-acquired infection. We did a three-way decomposition mediation analysis using natural effects models to explore associations between week of admission and in-hospital mortality, adjusting for confounders (demographics, comorbidities, and severity of illness) and quantifying potential mediators (level of respiratory support and steroid treatment). The primary outcome was weekly in-hospital mortality at 28 days, defined as the proportion of patients who had died within 28 days of admission of all patients admitted in the observed week, and it was assessed in all patients with an outcome. This study is registered with the ISRCTN Registry, ISRCTN66726260.

FINDINGS: Between March 9, and Aug 2, 2020, we recruited 80 713 patients, of whom 63 972 were eligible and included in the study. Unadjusted weekly in-hospital mortality declined from 32·3% (95% CI 31·8-32·7) in March 9 to April 26, 2020, to 16·4% (15·0-17·8) in June 15 to Aug 2, 2020. Reductions in mortality were observed in all age groups, in all ethnic groups, for both sexes, and in patients with and without comorbidities. After adjustment, there was a 32% reduction in the risk of mortality per 7-week period (odds ratio [OR] 0·68 [95% CI 0·65-0·71]). The higher proportions of patients with severe disease and comorbidities earlier in the first wave (March and April) than in June and July accounted for 10·2% of this reduction. The use of respiratory support changed during the first wave, with gradually increased use of non-invasive ventilation over the first wave. Changes in respiratory support and use of steroids accounted for 22·2%, OR 0·95 (0·94-0·95) of the reduction in in-hospital mortality.

INTERPRETATION: The reduction in in-hospital mortality in patients with COVID-19 during the first wave in the UK was partly accounted for by changes in the case-mix and illness severity. A significant reduction in in-hospital mortality was associated with differences in respiratory support and critical care use, which could partly reflect accrual of clinical knowledge. The remaining improvement in in-hospital mortality is not explained by these factors, and could be associated with changes in community behaviour, inoculum dose, and hospital capacity strain.

FUNDING: National Institute for Health Research and the Medical Research Council.}, } @article {pmid33997800, year = {2021}, author = {Drake, TM and Fairfield, CJ and Pius, R and Knight, SR and Norman, L and Girvan, M and Hardwick, HE and Docherty, AB and Thwaites, RS and Openshaw, PJM and Baillie, JK and Harrison, EM and Semple, MG and , }, title = {Non-steroidal anti-inflammatory drug use and outcomes of COVID-19 in the ISARIC Clinical Characterisation Protocol UK cohort: a matched, prospective cohort study.}, journal = {The Lancet. Rheumatology}, volume = {3}, number = {7}, pages = {e498-e506}, pmid = {33997800}, issn = {2665-9913}, support = {G0701652/MRC_/Medical Research Council/United Kingdom ; MR/T031565/1/MRC_/Medical Research Council/United Kingdom ; MC_PC_19059/MRC_/Medical Research Council/United Kingdom ; MR/S032304/1/MRC_/Medical Research Council/United Kingdom ; MC_PC_19025/MRC_/Medical Research Council/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; MC_PC_15001/MRC_/Medical Research Council/United Kingdom ; 109965/Z/15/Z/WT_/Wellcome Trust/United Kingdom ; }, abstract = {BACKGROUND: Early in the pandemic it was suggested that pre-existing use of non-steroidal anti-inflammatory drugs (NSAIDs) could lead to increased disease severity in patients with COVID-19. NSAIDs are an important analgesic, particularly in those with rheumatological disease, and are widely available to the general public without prescription. Evidence from community studies, administrative data, and small studies of hospitalised patients suggest NSAIDs are not associated with poorer COVID-19 outcomes. We aimed to characterise the safety of NSAIDs and identify whether pre-existing NSAID use was associated with increased severity of COVID-19 disease.

METHODS: This prospective, multicentre cohort study included patients of any age admitted to hospital with a confirmed or highly suspected SARS-CoV-2 infection leading to COVID-19 between Jan 17 and Aug 10, 2020. The primary outcome was in-hospital mortality, and secondary outcomes were disease severity at presentation, admission to critical care, receipt of invasive ventilation, receipt of non-invasive ventilation, use of supplementary oxygen, and acute kidney injury. NSAID use was required to be within the 2 weeks before hospital admission. We used logistic regression to estimate the effects of NSAIDs and adjust for confounding variables. We used propensity score matching to further estimate effects of NSAIDS while accounting for covariate differences in populations.

RESULTS: Between Jan 17 and Aug 10, 2020, we enrolled 78 674 patients across 255 health-care facilities in England, Scotland, and Wales. 72 179 patients had death outcomes available for matching; 40 406 (56·2%) of 71 915 were men, 31 509 (43·8%) were women. In this cohort, 4211 (5·8%) patients were recorded as taking systemic NSAIDs before admission to hospital. Following propensity score matching, balanced groups of NSAIDs users and NSAIDs non-users were obtained (4205 patients in each group). At hospital admission, we observed no significant differences in severity between exposure groups. After adjusting for explanatory variables, NSAID use was not associated with worse in-hospital mortality (matched OR 0·95, 95% CI 0·84-1·07; p=0·35), critical care admission (1·01, 0·87-1·17; p=0·89), requirement for invasive ventilation (0·96, 0·80-1·17; p=0·69), requirement for non-invasive ventilation (1·12, 0·96-1·32; p=0·14), requirement for oxygen (1·00, 0·89-1·12; p=0·97), or occurrence of acute kidney injury (1·08, 0·92-1·26; p=0·33).

INTERPRETATION: NSAID use is not associated with higher mortality or increased severity of COVID-19. Policy makers should consider reviewing issued advice around NSAID prescribing and COVID-19 severity.

FUNDING: National Institute for Health Research and Medical Research Council.}, } @article {pmid33987687, year = {2022}, author = {Figueiredo, G and Gomes, M and Covas, C and Mendo, S and Caetano, T}, title = {The Unexplored Wealth of Microbial Secondary Metabolites: the Sphingobacteriaceae Case Study.}, journal = {Microbial ecology}, volume = {83}, number = {2}, pages = {470-481}, pmid = {33987687}, issn = {1432-184X}, support = {SFRH/BD/98446/2013//Fundação para a Ciência e a Tecnologia/ ; CEECIND/01463/2017//Fundação para a Ciência e a Tecnologia/ ; UIDP/50017/2020+UIDB/50017/2020//Fundação para a Ciência e a Tecnologia/ ; }, mesh = {*Actinobacteria/genetics ; *Bacteroidetes/genetics ; Computational Biology ; Genomics/methods ; Humans ; Multigene Family ; }, abstract = {Research on secondary metabolites (SMs) has been mostly focused on Gram-positive bacteria, especially Actinobacteria. The association of genomics with robust bioinformatics tools revealed the neglected potential of Gram-negative bacteria as promising sources of new SMs. The family Sphingobacteriaceae belongs to the phylum Bacteroidetes having representatives in practically all environments including humans, rhizosphere, soils, wastewaters, among others. Some genera of this family have demonstrated great potential as plant growth promoters, bioremediators and producers of some value-added compounds such as carotenoids and antimicrobials. However, to date, Sphingobacteriaceae's SMs are still poorly characterized, and likewise, little is known about their chemistry. This study revealed that Sphingobacteriaceae pangenome encodes a total of 446 biosynthetic gene clusters (BGCs), which are distributed across 85 strains, highlighting the great potential of this bacterial family to produce SMs. Pedobacter, Mucilaginibacter and Sphingobacterium were the genera with the highest number of BGCs, especially those encoding the biosynthesis of ribosomally synthesized and post-translationally modified peptides (RiPPs), terpenes, polyketides and nonribosomal peptides (NRPs). In Mucilaginibacter and Sphingobacterium genera, M. lappiensis ATCC BAA-1855, Mucilaginibacter sp. OK098 (both with 11 BGCs) and Sphingobacterium sp. 21 (6 BGCs) are the strains with the highest number of BGCs. Most of the BGCs found in these two genera did not have significant hits with the MIBiG database. These results strongly suggest that the bioactivities and environmental functions of these compounds, especially RiPPs, PKs and NRPs, are still unknown. Among RiPPs, two genera encoded the production of class I and class III lanthipeptides. The last are associated with LanKC proteins bearing uncommon lyase domains, whose dehydration mechanism deserves further investigation. This study translated genomics into functional information that unveils the enormous potential of environmental Gram-negative bacteria to produce metabolites with unknown chemistries, bioactivities and, more importantly, unknown ecological roles.}, } @article {pmid33987031, year = {2021}, author = {Diazgranados, M and Tovar, C and Etherington, TR and Rodríguez-Zorro, PA and Castellanos-Castro, C and Galvis Rueda, M and Flantua, SGA}, title = {Ecosystem services show variable responses to future climate conditions in the Colombian páramos.}, journal = {PeerJ}, volume = {9}, number = {}, pages = {e11370}, pmid = {33987031}, issn = {2167-8359}, abstract = {BACKGROUND: The páramos, the high-elevation ecosystems of the northern Andes, are well-known for their high species richness and provide a variety of ecosystem services to local subsistence-based communities and regional urbanizations. Climate change is expected to negatively affect the provision of these services, but the level of this impact is still unclear. Here we assess future climate change impact on the ecosystem services provided by the critically important páramos of the department of Boyacá in Colombia, of which over 25% of its territory is páramo.

METHODS: We first performed an extensive literature review to identify useful species of Boyacá, and selected 103 key plant species that, based on their uses, support the provision of ecosystem services in the páramos. We collated occurrence information for each key species and using a Mahalanobis distance approach we applied climate niche modelling for current and future conditions.

RESULTS: We show an overall tendency of reduction in area for all ecosystem services under future climate conditions (mostly a loss of 10% but reaching up to a loss of 40%), but we observe also increases, and responses differ in intensity loss. Services such as Food for animals, Material and Medicinal, show a high range of changes that includes both positive and negative outcomes, while for Food for humans the responses are mostly substantially negative. Responses are less extreme than those projected for individual species but are often complex because a given ecosystem service is provided by several species. As the level of functional or ecological redundancy between species is not yet known, there is an urgency to expand our knowledge on páramos ecosystem services for more species. Our results are crucial for decision-makers, social and conservation organizations to support sustainable strategies to monitor and mitigate the potential consequences of climate change for human livelihoods in mountainous settings.}, } @article {pmid33986630, year = {2021}, author = {Johnson, N and Druckenmiller, ML and Danielsen, F and Pulsifer, PL}, title = {The Use of Digital Platforms for Community-Based Monitoring.}, journal = {Bioscience}, volume = {71}, number = {5}, pages = {452-466}, pmid = {33986630}, issn = {0006-3568}, abstract = {Environmental observing programs that are based on Indigenous and local knowledge increasingly use digital technologies. Digital platforms may improve data management in community-based monitoring (CBM) programs, but little is known about how their use translates into tangible results. Drawing on published literature and a survey of 18 platforms, we examine why and how digital platforms are used in CBM programs and illuminate potential challenges and opportunities. Digital platforms make it easy to collect, archive, and share CBM data, facilitate data use, and support understanding larger-scale environmental patterns through interlinking with other platforms. Digital platforms, however, also introduce new challenges, with implications for the sustainability of CBM programs and communities' abilities to maintain control of their own data. We expect that increased data access and strengthened technical capacity will create further demand within many communities for ethically developed platforms that aid in both local and larger-scale decision-making.}, } @article {pmid33984880, year = {2021}, author = {Queirós, P and Novikova, P and Wilmes, P and May, P}, title = {Unification of functional annotation descriptions using text mining.}, journal = {Biological chemistry}, volume = {402}, number = {8}, pages = {983-990}, doi = {10.1515/hsz-2021-0125}, pmid = {33984880}, issn = {1437-4315}, mesh = {*Data Mining/methods ; Molecular Sequence Annotation ; Proteins/metabolism/chemistry ; Humans ; Databases, Protein ; }, abstract = {A common approach to genome annotation involves the use of homology-based tools for the prediction of the functional role of proteins. The quality of functional annotations is dependent on the reference data used, as such, choosing the appropriate sources is crucial. Unfortunately, no single reference data source can be universally considered the gold standard, thus using multiple references could potentially increase annotation quality and coverage. However, this comes with challenges, particularly due to the introduction of redundant and exclusive annotations. Through text mining it is possible to identify highly similar functional descriptions, thus strengthening the confidence of the final protein functional annotation and providing a redundancy-free output. Here we present UniFunc, a text mining approach that is able to detect similar functional descriptions with high precision. UniFunc was built as a small module and can be independently used or integrated into protein function annotation pipelines. By removing the need to individually analyse and compare annotation results, UniFunc streamlines the complementary use of multiple reference datasets.}, } @article {pmid33984684, year = {2021}, author = {Nesoff, ED and Milam, AJ and Morrison, C and Weir, BW and Branas, CC and Furr-Holden, DM and Knowlton, AR and Martins, SS}, title = {Alcohol outlets, drug paraphernalia sales, and neighborhood drug overdose.}, journal = {The International journal on drug policy}, volume = {95}, number = {}, pages = {103289}, pmid = {33984684}, issn = {1873-4758}, support = {R01CE002682/ACL/ACL HHS/United States ; R49 CE003094/CE/NCIPC CDC HHS/United States ; R01 CE002682/CE/NCIPC CDC HHS/United States ; U49 CE000728/CE/NCIPC CDC HHS/United States ; U54 MD011227/MD/NIMHD NIH HHS/United States ; R49CE003094/ACL/ACL HHS/United States ; T32 DA031099/DA/NIDA NIH HHS/United States ; K01 DA049900/DA/NIDA NIH HHS/United States ; K01 AA026327/AA/NIAAA NIH HHS/United States ; R34 DA034314/DA/NIDA NIH HHS/United States ; }, mesh = {Alcohol Drinking ; Alcoholic Beverages ; Cross-Sectional Studies ; *Drug Overdose/epidemiology ; Humans ; *Pharmaceutical Preparations ; }, abstract = {BACKGROUND: Alcohol outlets have been associated with various forms of injury and may contribute to neighborhood disparities in drug overdose. Few studies have examined the associations between alcohol outlets and drug overdose. This study investigated whether alcohol outlets were associated with the neighborhood drug overdose rate and whether the sale of drug paraphernalia contributes to this association.

METHODS: A cross-sectional ecological spatial analysis was conducted within census block groups in Baltimore City (n = 653). Outcomes were counts of EMS calls for any drug overdose in 2015 (n = 3,856). Exposures of interest were counts of alcohol outlets licensed for off-premise and on-premise consumption and the proportion of off-premise outlets selling drug paraphernalia (e.g., blunt wrappers, baggies, pipes). Negative binomial regression was used to assess the relationship between outlet count and overdose rate, and if paraphernalia sales altered this relationship, controlling for other neighborhood factors. Spatial autocorrelation was assessed and regression inference adjusted accordingly.

RESULTS: Each additional off-premise alcohol outlet was associated with a 16.6% increase in the neighborhood overdose rate (IRR=1.17, 95%CI=(1.11, 1.23)), adjusted for other neighborhood variables. On-premise alcohol outlets were not significantly associated with overdose rate when adjusting for off-premise alcohol outlets (IRR=1.01, 95% CI=(0.97, 1.06)). The proportion of off-premise outlets that sold drug paraphernalia was negatively associated with overdose rate (IRR=0.55, 95% CI=(0.41, 0.74)) and did not alter the relationship between off-premise outlets and overdose.

CONCLUSION: This study provides preliminary public health evidence for informing policy decisions about alcohol outlet licensing and zoning. Alcohol outlets could be potential community partners for harm reduction strategies such as health communication in identifying overdose symptoms or Good Samaritan Laws.}, } @article {pmid33983959, year = {2021}, author = {Sahneh, F and Balk, MA and Kisley, M and Chan, CK and Fox, M and Nord, B and Lyons, E and Swetnam, T and Huppenkothen, D and Sutherland, W and Walls, RL and Quinn, DP and Tarin, T and LeBauer, D and Ribes, D and Birnie, DP and Lushbough, C and Carr, E and Nearing, G and Fischer, J and Tyle, K and Carrasco, L and Lang, M and Rose, PW and Rushforth, RR and Roy, S and Matheson, T and Lee, T and Brown, CT and Teal, TK and Papeș, M and Kobourov, S and Merchant, N}, title = {Ten simple rules to cultivate transdisciplinary collaboration in data science.}, journal = {PLoS computational biology}, volume = {17}, number = {5}, pages = {e1008879}, pmid = {33983959}, issn = {1553-7358}, mesh = {Computational Biology ; *Cooperative Behavior ; *Data Science/ethics/organization & administration/trends ; Humans ; *Interdisciplinary Communication ; *Interprofessional Relations ; Intersectoral Collaboration ; }, } @article {pmid33983918, year = {2021}, author = {Sukumaran, J and Holder, MT and Knowles, LL}, title = {Incorporating the speciation process into species delimitation.}, journal = {PLoS computational biology}, volume = {17}, number = {5}, pages = {e1008924}, pmid = {33983918}, issn = {1553-7358}, mesh = {Algorithms ; Animals ; Computational Biology ; Computer Simulation ; Gene Flow ; *Genetic Speciation ; Genetics, Population ; *Models, Genetic ; Models, Statistical ; Phylogeny ; Software ; Species Specificity ; Time Factors ; }, abstract = {The "multispecies" coalescent (MSC) model that underlies many genomic species-delimitation approaches is problematic because it does not distinguish between genetic structure associated with species versus that of populations within species. Consequently, as both the genomic and spatial resolution of data increases, a proliferation of artifactual species results as within-species population lineages, detected due to restrictions in gene flow, are identified as distinct species. The toll of this extends beyond systematic studies, getting magnified across the many disciplines that rely upon an accurate framework of identified species. Here we present the first of a new class of approaches that addresses this issue by incorporating an extended speciation process for species delimitation. We model the formation of population lineages and their subsequent development into independent species as separate processes and provide for a way to incorporate current understanding of the species boundaries in the system through specification of species identities of a subset of population lineages. As a result, species boundaries and within-species lineages boundaries can be discriminated across the entire system, and species identities can be assigned to the remaining lineages of unknown affinities with quantified probabilities. In addition to the identification of species units in nature, the primary goal of species delimitation, the incorporation of a speciation model also allows us insights into the links between population and species-level processes. By explicitly accounting for restrictions in gene flow not only between, but also within, species, we also address the limits of genetic data for delimiting species. Specifically, while genetic data alone is not sufficient for accurate delimitation, when considered in conjunction with other information we are able to not only learn about species boundaries, but also about the tempo of the speciation process itself.}, } @article {pmid33982340, year = {2021}, author = {Huaraca Huasco, W and Riutta, T and Girardin, CAJ and Hancco Pacha, F and Puma Vilca, BL and Moore, S and Rifai, SW and Del Aguila-Pasquel, J and Araujo Murakami, A and Freitag, R and Morel, AC and Demissie, S and Doughty, CE and Oliveras, I and Galiano Cabrera, DF and Durand Baca, L and Farfán Amézquita, F and Silva Espejo, JE and da Costa, ACL and Oblitas Mendoza, E and Quesada, CA and Evouna Ondo, F and Edzang Ndong, J and Jeffery, KJ and Mihindou, V and White, LJT and N'ssi Bengone, N and Ibrahim, F and Addo-Danso, SD and Duah-Gyamfi, A and Djaney Djagbletey, G and Owusu-Afriyie, K and Amissah, L and Mbou, AT and Marthews, TR and Metcalfe, DB and Aragão, LEO and Marimon-Junior, BH and Marimon, BS and Majalap, N and Adu-Bredu, S and Abernethy, KA and Silman, M and Ewers, RM and Meir, P and Malhi, Y}, title = {Fine root dynamics across pantropical rainforest ecosystems.}, journal = {Global change biology}, volume = {27}, number = {15}, pages = {3657-3680}, doi = {10.1111/gcb.15677}, pmid = {33982340}, issn = {1365-2486}, support = {321131/ERC_/European Research Council/International ; }, mesh = {Africa ; Biomass ; *Ecosystem ; Forests ; Plant Roots ; *Rainforest ; Soil ; South America ; Trees ; Tropical Climate ; }, abstract = {Fine roots constitute a significant component of the net primary productivity (NPP) of forest ecosystems but are much less studied than aboveground NPP. Comparisons across sites and regions are also hampered by inconsistent methodologies, especially in tropical areas. Here, we present a novel dataset of fine root biomass, productivity, residence time, and allocation in tropical old-growth rainforest sites worldwide, measured using consistent methods, and examine how these variables are related to consistently determined soil and climatic characteristics. Our pantropical dataset spans intensive monitoring plots in lowland (wet, semi-deciduous, and deciduous) and montane tropical forests in South America, Africa, and Southeast Asia (n = 47). Large spatial variation in fine root dynamics was observed across montane and lowland forest types. In lowland forests, we found a strong positive linear relationship between fine root productivity and sand content, this relationship was even stronger when we considered the fractional allocation of total NPP to fine roots, demonstrating that understanding allocation adds explanatory power to understanding fine root productivity and total NPP. Fine root residence time was a function of multiple factors: soil sand content, soil pH, and maximum water deficit, with longest residence times in acidic, sandy, and water-stressed soils. In tropical montane forests, on the other hand, a different set of relationships prevailed, highlighting the very different nature of montane and lowland forest biomes. Root productivity was a strong positive linear function of mean annual temperature, root residence time was a strong positive function of soil nitrogen content in montane forests, and lastly decreasing soil P content increased allocation of productivity to fine roots. In contrast to the lowlands, environmental conditions were a better predictor for fine root productivity than for fractional allocation of total NPP to fine roots, suggesting that root productivity is a particularly strong driver of NPP allocation in tropical mountain regions.}, } @article {pmid33979640, year = {2021}, author = {Babaie, E and Alesheikh, AA and Tabasi, M}, title = {Spatial prediction of human brucellosis (HB) using a GIS-based adaptive neuro-fuzzy inference system (ANFIS).}, journal = {Acta tropica}, volume = {220}, number = {}, pages = {105951}, doi = {10.1016/j.actatropica.2021.105951}, pmid = {33979640}, issn = {1873-6254}, mesh = {Animals ; Brucellosis/*epidemiology ; Climate ; Cluster Analysis ; *Fuzzy Logic ; *Geographic Information Systems ; Humans ; Incidence ; Linear Models ; Models, Statistical ; *Neural Networks, Computer ; *Spatial Analysis ; }, abstract = {OBJECTIVE: This study pursues three main objectives: 1) exploring the spatial distribution patterns of human brucellosis (HB); 2) identifying parameters affecting the disease spread; and 3) modeling and predicting the spatial distribution of HB cases in 2012-2016 and 2017-2018, respectively, in rural districts of Mazandaran province, Iran.

METHODS: We collected data on the disease incidence, demography, ecology, climate, topography, and vegetation. Using the Global Moran's I statistic, we measured spatial autocorrelation between log (number of HB cases). We applied the Getis-Ord Gi[*] statistic to identify areas with high and low risk of the disease. To investigate the relationships between the factors affecting the incidence of HB as input variables together and the factors with the log (number of HB cases) as an output variable, we used the statistical linear regression model and the Pearson correlation coefficient. Then, we implemented a GIS-based adaptive neuro-fuzzy inference system (ANFIS) with two subtractive clustering and fuzzy c-means (FCM) clustering methods to model and predict the spatial distribution of HB.

RESULTS: Global Moran's I spatial autocorrelation analysis indicated that the type of HB distribution is clustered in all years except 2014 and 2017, which are random. According to the Getis-Ord Gi[*] analysis, the location of the hot spots varied during 2012-2018. In 2012 and 2013, most of the hot spots were seen in the west of the province. While in 2018, they were mostly concentrated in the eastern regions of the province. The linear regression model indicated that the parameters affecting the incidence of HB are independent of each other and can explain only 25.3% of the total changes in the log (number of HB cases). The results of the Pearson correlation coefficient showed that there were positive relationships between vegetation, log (population), and the number of sheep and cattle (p-value < 0.05). The above-mentioned factors had the strongest positive correlation with the log (number of HB cases) (p-value < 0.01). These results may be due to the fact that vegetation regions are suitable for livestock grazing, attracting large crowds of people. Therefore, this will increase HB cases. We compared the results of subtractive clustering and FCM clustering methods by evaluation criteria (e.g., linear correlation coefficient (LCC) and mean absolute error (MAE)) in two phases of development and assessment of the ANFIS model. In the assessment phase, we predicted the spatial distribution of log (number of HB cases) in 2017 and 2018 by subtractive clustering (R[2] = 0.699, LCC or R = 0.692, MAE = 0.509, MSE = 0.455) and by FCM clustering (R[2] = 0.704, LCC or R = 0.697, MAE = 0.512, MSE = 0.448) that showed FCM clustering outperformed the subtractive clustering.

CONCLUSION: The findings may have important implications for public health. The emergence of the hot spots in the east of the province can be a warning to the health system. Health authorities can use the findings of this study to predict the spread of HB and perform HB prevention programs. They can also investigate the factors affecting the prevalence of the disease, identify high-risk areas, and ultimately allocate resources to high-risk regions.}, } @article {pmid33979341, year = {2021}, author = {Dias Louro, MA and Bettencourt-Dias, M and Bank, C}, title = {Patterns of selection against centrosome amplification in human cell lines.}, journal = {PLoS computational biology}, volume = {17}, number = {5}, pages = {e1008765}, pmid = {33979341}, issn = {1553-7358}, mesh = {Biological Evolution ; Cell Line ; Cell Proliferation ; Centrioles/genetics/pathology ; Centrosome/*pathology ; Computational Biology ; Humans ; Mathematical Concepts ; *Models, Biological ; Mutation ; Neoplasms/genetics/pathology ; Nonlinear Dynamics ; Selection, Genetic ; }, abstract = {The presence of extra centrioles, termed centrosome amplification, is a hallmark of cancer. The distribution of centriole numbers within a cancer cell population appears to be at an equilibrium maintained by centriole overproduction and selection, reminiscent of mutation-selection balance. It is unknown to date if the interaction between centriole overproduction and selection can quantitatively explain the intra- and inter-population heterogeneity in centriole numbers. Here, we define mutation-selection-like models and employ a model selection approach to infer patterns of centriole overproduction and selection in a diverse panel of human cell lines. Surprisingly, we infer strong and uniform selection against any number of extra centrioles in most cell lines. Finally we assess the accuracy and precision of our inference method and find that it increases non-linearly as a function of the number of sampled cells. We discuss the biological implications of our results and how our methodology can inform future experiments.}, } @article {pmid33978473, year = {2021}, author = {Varga, C and John, P and Cooke, M and Majowicz, SE}, title = {Area-Level Clustering of Shiga Toxin-Producing Escherichia coli Infections and Their Socioeconomic and Demographic Factors in Ontario, Canada: An Ecological Study.}, journal = {Foodborne pathogens and disease}, volume = {18}, number = {7}, pages = {438-447}, doi = {10.1089/fpd.2020.2918}, pmid = {33978473}, issn = {1556-7125}, mesh = {Adolescent ; Adult ; Aged ; Aged, 80 and over ; Child ; Child, Preschool ; Cluster Analysis ; Escherichia coli Infections/*epidemiology ; Female ; Geographic Information Systems ; Humans ; Infant ; Infant, Newborn ; Logistic Models ; Male ; Middle Aged ; Ontario/epidemiology ; Retrospective Studies ; Shiga-Toxigenic Escherichia coli/*isolation & purification ; Socioeconomic Factors ; Young Adult ; }, abstract = {Shiga toxin-producing Escherichia coli (STEC) infections are an important health burden for human populations in Ontario and worldwide. We assessed 452 STEC cases that were reported to Ontario's reportable disease surveillance system between 2015 and 2017. A retrospective scan statistic using a Poisson model was used to detect high-rate STEC clusters at the forward sortation area (FSA; the first three digits of a postal code) level. A significant spatial cluster in the southwest region of Ontario was identified. A case-case logistic regression analysis was applied to compare FSA-level socioeconomic and demographic characteristics among STEC cases included inside the spatial cluster with cases outside of the cluster. Cases included in the spatial cluster had higher odds of living in FSAs with a low median family income, low proportion of lone-parent families, and low proportion of the visible minority population. In addition, STEC cases inside the cluster had higher odds of coming from rural FSAs. Our study demonstrated that STEC cases were spatially clustered in Ontario and their clustering was associated with FSA-level socioeconomic and demographic determinants of cases.}, } @article {pmid33975966, year = {2021}, author = {Chuckran, PF and Fofanov, V and Hungate, BA and Morrissey, EM and Schwartz, E and Walkup, J and Dijkstra, P}, title = {Rapid Response of Nitrogen Cycling Gene Transcription to Labile Carbon Amendments in a Soil Microbial Community.}, journal = {mSystems}, volume = {6}, number = {3}, pages = {}, pmid = {33975966}, issn = {2379-5077}, abstract = {Episodic inputs of labile carbon (C) to soil can rapidly stimulate nitrogen (N) immobilization by soil microorganisms. However, the transcriptional patterns that underlie this process remain unclear. In order to better understand the regulation of N cycling in soil microbial communities, we conducted a 48-h laboratory incubation with agricultural soil where we stimulated the uptake of inorganic N by amending the soil with glucose. We analyzed the metagenome and metatranscriptome of the microbial communities at four time points that corresponded with changes in N availability. The relative abundances of genes remained largely unchanged throughout the incubation. In contrast, glucose addition rapidly increased the transcription of genes encoding ammonium and nitrate transporters, enzymes responsible for N assimilation into biomass, and genes associated with the N regulatory network. This upregulation coincided with an increase in transcripts associated with glucose breakdown and oxoglutarate production, demonstrating a connection between C and N metabolism. When concentrations of ammonium were low, we observed a transient upregulation of genes associated with the nitrogen-fixing enzyme nitrogenase. Transcripts for nitrification and denitrification were downregulated throughout the incubation, suggesting that dissimilatory transformations of N may be suppressed in response to labile C inputs in these soils. These results demonstrate that soil microbial communities can respond rapidly to changes in C availability by drastically altering the transcription of N cycling genes.IMPORTANCE A large portion of activity in soil microbial communities occurs in short time frames in response to an increase in C availability, affecting the biogeochemical cycling of nitrogen. These changes are of particular importance as nitrogen represents both a limiting nutrient for terrestrial plants as well as a potential pollutant. However, we lack a full understanding of the short-term effects of labile carbon inputs on the metabolism of microbes living in soil. Here, we found that soil microbial communities responded to labile carbon addition by rapidly transcribing genes encoding proteins and enzymes responsible for inorganic nitrogen acquisition, including nitrogen fixation. This work demonstrates that soil microbial communities respond within hours to carbon inputs through altered gene expression. These insights are essential for an improved understanding of the microbial processes governing soil organic matter production, decomposition, and nutrient cycling in natural and agricultural ecosystems.}, } @article {pmid33975908, year = {2021}, author = {Che, Y and Yang, Y and Xu, X and Břinda, K and Polz, MF and Hanage, WP and Zhang, T}, title = {Reply to Shaw: Challenges for enrichment analysis of AMR gene-bearing plasmids.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {118}, number = {21}, pages = {}, pmid = {33975908}, issn = {1091-6490}, mesh = {*Drug Resistance, Bacterial ; Plasmids/genetics ; }, } @article {pmid33975267, year = {2021}, author = {Li, X and Hui, N and Yang, Y and Ma, J and Luo, Z and Chen, F}, title = {Short-term effects of land consolidation of dryland-to-paddy conversion on soil CO2 flux.}, journal = {Journal of environmental management}, volume = {292}, number = {}, pages = {112691}, doi = {10.1016/j.jenvman.2021.112691}, pmid = {33975267}, issn = {1095-8630}, mesh = {Agriculture ; Carbon/analysis ; Carbon Dioxide/analysis ; China ; *Oryza ; *Soil ; }, abstract = {To improve grain production capacity, many areas in the world are shifting from rainfed agriculture to irrigated agriculture. One example of such land consolidation is dryland-to-paddy conversion. The conversion of land use pattern largely affects the stability of farmland soil, especially the soil carbon cycle. However, the mutual feedback mechanisms between carbon flux variation and environmental factors during the farmland consolidation process are still poorly known. Located in the Huang-Huai-Hai Plain China, Xuzhou is a typical area where dryland-to-paddy conversion are most widely distributed. Therefore, in this study, we have carried out dryland-to-paddy conversion by setting up two isolated rectangular fields one group planting corn in dryland (DL) and another group planting in paddy field (PF) in Xuzhou. Here, we determined the effect of dryland-to-paddy consolidation on soil CO2 flux in two isolated rectangular fields - the dryland (DL) cultivated with corn and the paddy field (PF) cultivated with rice. Our results showed that the soil carbon flux and temperature followed similar unimodal curves with greater soil CO2 flux of in PF than in DL. Surprisingly, the land conversion significantly reduced soil microbial biomass carbon and easily oxidized organic carbon by 28.55% and 29.09%, respectively. The structural equation modeling results demonstrated that the changes in soil environmental factors, including temperature, and fungal OTU numbers, were the primary drivers for the soil CO2 flux and soil carbon pool (P < 0.05). Overall, this study improves the understanding of the ecological impact of dryland-to-paddy conversion, providing insights into low-carbon agriculture and climate mitigation.}, } @article {pmid33974954, year = {2021}, author = {Lima, J and Manning, T and Rutherford, KM and Baima, ET and Dewhurst, RJ and Walsh, P and Roehe, R}, title = {Taxonomic annotation of 16S rRNA sequences of pig intestinal samples using MG-RAST and QIIME2 generated different microbiota compositions.}, journal = {Journal of microbiological methods}, volume = {186}, number = {}, pages = {106235}, doi = {10.1016/j.mimet.2021.106235}, pmid = {33974954}, issn = {1872-8359}, support = {BB/N01720X/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/S006567/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; Bacteria/*classification/genetics/*isolation & purification ; Computational Biology/*methods ; DNA, Bacterial/genetics ; *Gastrointestinal Microbiome ; Intestines/*microbiology ; Molecular Sequence Annotation/*methods ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Swine/microbiology ; }, abstract = {Environmental microbiome studies rely on fast and accurate bioinformatics tools to characterize the taxonomic composition of samples based on the 16S rRNA gene. MetaGenome Rapid Annotation using Subsystem Technology (MG-RAST) and Quantitative Insights Into Microbial Ecology 2 (QIIME2) are two of the most popular tools available to perform this task. Their underlying algorithms differ in many aspects, and therefore the comparison of the pipelines provides insights into their best use and interpretation of the outcomes. Both of these bioinformatics tools are based on several specialized algorithms pipelined together, but whereas MG-RAST is a user-friendly webserver that clusters rRNA sequences based on their similarity to create Operational Taxonomic Units (OTU), QIIME2 employs DADA2 in the construction of Amplicon Sequence Variants (ASV) by applying an error model that considers the abundance of each sequence and its similarity to other sequences. Taxonomic compositions obtained from the analyses of amplicon sequences of DNA from swine intestinal gut and faecal microbiota samples using MG-RAST and QIIME2 were compared at domain-, phylum-, family- and genus-levels in terms of richness, relative abundance and diversity. We found significant differences between the microbiota profiles obtained from each pipeline. At domain level, bacteria were relatively more abundant using QIIME2 than MG-RAST; at phylum level, seven taxa were identified exclusively by QIIME2; at family level, samples processed in QIIME2 showed higher evenness and richness (assessed by Shannon and Simpson indices). The genus-level compositions obtained from each pipeline were used in partial least squares-discriminant analyses (PLS-DA) to discriminate between sample collection sites (caecum, colon and faeces). The results showed that different genera were found to be significant for the models, based on the Variable Importance in Projection, e.g. when using sequencing data processed by MG-RAST, the three most important genera were Acetitomaculum, Ruminococcus and Methanosphaera, whereas when data was processed using QIIME2, these were Candidatus Methanomethylophilus, Sphaerochaeta and Anaerorhabdus. Furthermore, the application of differential filtering procedures before the PLS-DA revealed higher accuracy when using non-restricted datasets obtained from MG-RAST, whereas datasets obtained from QIIME2 resulted in more accurate discrimination of sample collection sites after removing genera with low relative abundances (<1%) from the datasets. Our results highlight the differences in taxonomic compositions of samples obtained from the two separate pipelines, while underlining the impact on downstream analyses, such as biomarkers identification.}, } @article {pmid33972780, year = {2021}, author = {Turakhia, Y and Thornlow, B and Hinrichs, AS and De Maio, N and Gozashti, L and Lanfear, R and Haussler, D and Corbett-Detig, R}, title = {Ultrafast Sample placement on Existing tRees (UShER) enables real-time phylogenetics for the SARS-CoV-2 pandemic.}, journal = {Nature genetics}, volume = {53}, number = {6}, pages = {809-816}, pmid = {33972780}, issn = {1546-1718}, support = {U41 HG002371/HG/NHGRI NIH HHS/United States ; R35 GM128932/GM/NIGMS NIH HHS/United States ; 5U41HG002371-19//U.S. Department of Health & Human Services | NIH | National Human Genome Research Institute (NHGRI)/ ; DP200103151//Department of Education and Training | Australian Research Council (ARC)/ ; T32 HG008345/HG/NHGRI NIH HHS/United States ; 2020-0000000020//Center for Information Technology Research in the Interest of Society (CITRIS)/ ; R35GM128932//U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; T32HG008345//U.S. Department of Health & Human Services | NIH | National Human Genome Research Institute (NHGRI)/ ; R01 HG010485/HG/NHGRI NIH HHS/United States ; F31HG010584//U.S. Department of Health & Human Services | NIH | National Human Genome Research Institute (NHGRI)/ ; F31 HG010584/HG/NHGRI NIH HHS/United States ; }, mesh = {Algorithms ; COVID-19/*epidemiology/*virology ; Computational Biology/*methods/standards ; Databases, Genetic ; Genome, Viral ; Humans ; Molecular Sequence Annotation ; Mutation ; *Phylogeny ; SARS-CoV-2/*classification/*genetics ; *Software ; Web Browser ; }, abstract = {As the SARS-CoV-2 virus spreads through human populations, the unprecedented accumulation of viral genome sequences is ushering in a new era of 'genomic contact tracing'-that is, using viral genomes to trace local transmission dynamics. However, because the viral phylogeny is already so large-and will undoubtedly grow many fold-placing new sequences onto the tree has emerged as a barrier to real-time genomic contact tracing. Here, we resolve this challenge by building an efficient tree-based data structure encoding the inferred evolutionary history of the virus. We demonstrate that our approach greatly improves the speed of phylogenetic placement of new samples and data visualization, making it possible to complete the placements under the constraints of real-time contact tracing. Thus, our method addresses an important need for maintaining a fully updated reference phylogeny. We make these tools available to the research community through the University of California Santa Cruz SARS-CoV-2 Genome Browser to enable rapid cross-referencing of information in new virus sequences with an ever-expanding array of molecular and structural biology data. The methods described here will empower research and genomic contact tracing for SARS-CoV-2 specifically for laboratories worldwide.}, } @article {pmid33972615, year = {2021}, author = {Singh, G and Brass, A and Cruickshank, SM and Knight, CG}, title = {Cage and maternal effects on the bacterial communities of the murine gut.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {9841}, pmid = {33972615}, issn = {2045-2322}, mesh = {ATP Binding Cassette Transporter, Subfamily B/genetics ; Adolescent ; Adult ; Age Factors ; Animals ; Colitis/genetics/*microbiology ; Colon/microbiology ; DNA, Bacterial/isolation & purification ; Disease Models, Animal ; Feces/microbiology ; *Gastrointestinal Microbiome ; Humans ; Intestinal Mucosa/microbiology ; Male ; Mice ; Mice, Knockout ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Findings from gut microbiome studies are strongly influenced by both experimental and analytical factors that can unintentionally bias their interpretation. Environment is also critical. Both co-housing and maternal effects are expected to affect microbiomes and have the potential to confound other manipulated factors, such as genetics. We therefore analysed microbiome data from a mouse experiment using littermate controls and tested differences among genotypes (wildtype versus colitis prone-mdr1a[-/-]), gut niches (stool versus mucus), host ages (6 versus 18 weeks), social groups (co-housed siblings of different genotypes) and maternal influence. We constructed a 16S phylogenetic tree from bacterial communities, fitting random forest models using all 428,234 clades identified. Models discriminated all criteria except host genotype, where no community differences were found. Host social groups differed in abundant, low-level, taxa whereas intermediate phylogenetic and abundance scales distinguished ages and niches. Thus, a carefully controlled experiment treating evolutionary clades of microbes equivalently without reference to taxonomy, clearly identifies whether and how gut microbial communities are distinct across ecologically important factors (niche and host age) and other experimental factors, notably cage effects and maternal influence. These findings highlight the importance of considering such environmental factors in future microbiome studies.}, } @article {pmid33966825, year = {2021}, author = {Liu, C and Hu, B and Cheng, Y and Guo, Y and Yao, W and Qian, H}, title = {In-depth analysis of the mechanisms of aloe polysaccharides on mitigating subacute colitis in mice via microbiota informatics.}, journal = {Carbohydrate polymers}, volume = {265}, number = {}, pages = {118041}, doi = {10.1016/j.carbpol.2021.118041}, pmid = {33966825}, issn = {1879-1344}, mesh = {Akkermansia/drug effects ; Aloe/*chemistry ; Animals ; Anti-Inflammatory Agents/pharmacology ; Colitis, Ulcerative/*drug therapy/metabolism ; Colon/drug effects ; Computational Biology/methods ; Dextran Sulfate/adverse effects ; Fatty Acids, Volatile/metabolism ; Gastrointestinal Microbiome/*drug effects ; Inflammation/drug therapy/metabolism ; Latent Class Analysis ; Male ; Mice ; Mice, Inbred C57BL ; Phosphorus-Oxygen Lyases/metabolism ; Polysaccharides/chemistry/*pharmacology ; }, abstract = {Aloe polysaccharides (APs) are indigestible bioactive polysaccharides, while can be fermented by colonic microbiota. Although plant polysaccharides can alleviate subacute ulcerative colitis (SUC), the mechanisms APs regulated SUC via colonic microbiota have not been fully explored. Hence, to elucidate the complex interactions between the novel APs, colonic microbiota, SCFAs, and inflammation, the SUC mouse model and in-depth analysis were performed, including multiple bioinformatics analysis and structural equation modeling (SEM). After APs intervention, SCFAs and SCFAs-producing genus, including Akkermansia and Blautia, were increased in colon, and the colonic inflammation and barrier dysfunction were alleviated significantly in SUC mice. Spearman analysis found positive correlations between microbiota and SCFAs. PICRUSt2 and KEGG analysis revealed 6-pyruvoyltetra hydropterin synthase in folate biosynthesis metabolism pathway was activated, while phosphotransferase system was inhibited. SEM results further proved APs was beneficial to gut micro-ecological balance in mice via SCFAs metabolism and anti-inflammatory functions. Together, APs could be exploited to alleviate SUC as dietary therapeutics.}, } @article {pmid33963496, year = {2021}, author = {Knief, U and Forstmeier, W}, title = {Violating the normality assumption may be the lesser of two evils.}, journal = {Behavior research methods}, volume = {53}, number = {6}, pages = {2576-2590}, pmid = {33963496}, issn = {1554-3528}, mesh = {Data Interpretation, Statistical ; Humans ; Monte Carlo Method ; Normal Distribution ; *Reproducibility of Results ; Sample Size ; }, abstract = {When data are not normally distributed, researchers are often uncertain whether it is legitimate to use tests that assume Gaussian errors, or whether one has to either model a more specific error structure or use randomization techniques. Here we use Monte Carlo simulations to explore the pros and cons of fitting Gaussian models to non-normal data in terms of risk of type I error, power and utility for parameter estimation. We find that Gaussian models are robust to non-normality over a wide range of conditions, meaning that p values remain fairly reliable except for data with influential outliers judged at strict alpha levels. Gaussian models also performed well in terms of power across all simulated scenarios. Parameter estimates were mostly unbiased and precise except if sample sizes were small or the distribution of the predictor was highly skewed. Transformation of data before analysis is often advisable and visual inspection for outliers and heteroscedasticity is important for assessment. In strong contrast, some non-Gaussian models and randomization techniques bear a range of risks that are often insufficiently known. High rates of false-positive conclusions can arise for instance when overdispersion in count data is not controlled appropriately or when randomization procedures ignore existing non-independencies in the data. Hence, newly developed statistical methods not only bring new opportunities, but they can also pose new threats to reliability. We argue that violating the normality assumption bears risks that are limited and manageable, while several more sophisticated approaches are relatively error prone and particularly difficult to check during peer review. Scientists and reviewers who are not fully aware of the risks might benefit from preferentially trusting Gaussian mixed models in which random effects account for non-independencies in the data.}, } @article {pmid33963474, year = {2021}, author = {Zhumakayev, AR and Vörös, M and Szekeres, A and Rakk, D and Vágvölgyi, C and Szűcs, A and Kredics, L and Škrbić, BD and Hatvani, L}, title = {Comprehensive characterization of stress tolerant bacteria with plant growth-promoting potential isolated from glyphosate-treated environment.}, journal = {World journal of microbiology & biotechnology}, volume = {37}, number = {6}, pages = {94}, pmid = {33963474}, issn = {1573-0972}, support = {HUSRB/1602/41/0031//Hungary-Serbia IPA Cross-border Co-operation Programme/ ; HUSRB/1602/41/0031//Hungary-Serbia IPA Cross-border Co-operation Programme/ ; SHE-15651-001/2017//Stipendium Hungaricum Scholarship Programme/ ; }, mesh = {Glycine/*analogs & derivatives/pharmacology ; Hydrogen-Ion Concentration ; Indoleacetic Acids/metabolism ; Solanum lycopersicum/*growth & development/microbiology ; Metals, Heavy/pharmacology ; Pseudomonas/*isolation & purification/metabolism/physiology ; RNA, Ribosomal, 16S/genetics ; Rhizobiaceae/*isolation & purification/metabolism/physiology ; Seeds/growth & development/microbiology ; Siderophores/metabolism ; Soil Microbiology ; Stress, Physiological ; Glyphosate ; }, abstract = {The application of plant growth-promoting bacteria in agricultural systems is an efficient and environment-friendly strategy to improve crop yields and maintain soil quality. However, as different soils have diverse and specific ecological characteristics and may represent adverse abiotic conditions, in vivo application requires the careful selection of the desired beneficial microorganisms. In this study we report Ensifer adhaerens SZMC 25856 and Pseudomonas resinovorans SZMC 25875 isolates recovered from glyphosate-treated soil to possess yet undiscovered plant growth-enhancing potential. The strains were found to promote the growth of tomato seedlings significantly, to have the ability of synthesizing indole-3-acetic acid and siderophores, to tolerate pH in the range of 6.59-7.96, salinity up to 12.5 g L[-1] NaCl and drought up to 125 g L[-1] polyethylene glycol 6000, as well as to survive in the presence of various pesticides including glyphosate, diuron, chlorotoluron, carbendazim and thiabendazole, and heavy metals such as Al, Fe, Mn, Zn, Pb and Cu. The plant growth-promoting traits of the examined E. adhaerens and P. resinovorans isolates and their tolerance to numerous abiotic stress factors make them promising candidates for application in different agricultural environments, including soils polluted with glyphosate.}, } @article {pmid33962815, year = {2021}, author = {Ge, Y and Li, N and Fu, Y and Yu, X and Xiao, Y and Tang, Z and Xiao, J and Wu, JL and Jiang, ZH}, title = {Deciphering superior quality of Pu-erh tea from thousands of years' old trees based on the chemical profile.}, journal = {Food chemistry}, volume = {358}, number = {}, pages = {129602}, doi = {10.1016/j.foodchem.2021.129602}, pmid = {33962815}, issn = {1873-7072}, mesh = {Antioxidants/*analysis/chemistry ; Caffeine/analysis ; Camellia sinensis/*chemistry ; Cheminformatics ; Chromatography, High Pressure Liquid ; Flavonoids/analysis ; Food Analysis/methods ; Food Quality ; Humans ; Hydroxybenzoates/analysis ; Mass Spectrometry ; Taste ; Tea/*chemistry ; Time Factors ; Trees ; }, abstract = {Pu-erh teas from thousands of years' old trees (TPT) equip with both superior flavors and powerful antioxidative capacities. With UHPLC-Q-TOF-MS approach, TPTs' chemical profiles were characterized by comparing with Pu-erh teas from ecological trees (EPT). TPTs are discovered to possess higher contents of amino acids, fatty acids, phenolic acids, nucleosides and nucleobases but lower contents of flavonoids and caffeine congeners based on 117 discriminative constituents from 305 identified ones. Particularly, a series of caffeic acid congeners including ten new hydroxycinnamic acid depsides with higher contents in TPTs are discovered, and caffeic acid with a fold change of 638 is the foremost discriminative component. Furthermore, distinguishing constituent proportion including caffeic acid congeners in TPTs are found to take great responsibilities for their more powerful antioxidative abilities and superior flavors especially more aroma and pleasant bitterness. This research provides information for deciphering formation of TPTs' superior qualities based on chemical profile.}, } @article {pmid33961346, year = {2021}, author = {Baptiste, YM}, title = {Digital Feast and Physical Famine: The Altered Ecosystem of Anatomy Education due to the Covid-19 Pandemic.}, journal = {Anatomical sciences education}, volume = {14}, number = {4}, pages = {399-407}, pmid = {33961346}, issn = {1935-9780}, mesh = {Anatomy/*education ; *COVID-19 ; *Cadaver ; Ecology ; Education, Distance ; Humans ; Visible Human Projects ; }, abstract = {This article explores the effects of the coronavirus disease 2019 (Covid-19) pandemic on the evolution of both physical and digital cadavers within the unique ecosystem of the anatomy laboratory. A physical cadaver is a traditional and established learning tool in anatomy education, whereas a digital cadaver is a relatively recent phenomenon. The Covid-19 pandemic presented a major disturbance and disruption to all levels and types of education, including anatomy education. This article constructs a conceptual metaphor between a typical anatomy laboratory and an ecosystem, and considers the affordances, constraints, and changing roles of physical and digital cadavers within anatomy education through an ecological lens. Adaptation of physical and digital cadavers during the disturbance is analyzed, and the resiliency of digital cadaver technology is recognized. The evolving role of the digital cadaver is considered in terms of increasing accessibility and inclusivity within the anatomy laboratory ecosystem of the future.}, } @article {pmid33961222, year = {2021}, author = {Wang, Z and Liang, JL and Huang, LN and Mengoni, A and Shu, WS}, title = {Metagenomic Assembly: Reconstructing Genomes from Metagenomes.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2242}, number = {}, pages = {139-152}, pmid = {33961222}, issn = {1940-6029}, mesh = {Databases, Genetic ; High-Throughput Nucleotide Sequencing ; *Metagenome ; *Metagenomics ; Phylogeny ; Research Design ; *Sequence Analysis, DNA ; Software ; Workflow ; }, abstract = {Assembly of metagenomic sequence data into microbial genomes is of critical importance for disentangling community complexity and unraveling the functional capacity of microorganisms. The rapid development of sequencing technology and novel assembly algorithms have made it possible to reliably reconstruct hundreds to thousands of microbial genomes from raw sequencing reads through metagenomic assembly. In this chapter, we introduce a routinely used metagenomic assembly workflow including read quality filtering, assembly, contig/scaffold binning, and postassembly check for genome completeness and contamination. We also describe a case study to reconstruct near-complete microbial genomes from metagenomes using our workflow.}, } @article {pmid33956885, year = {2021}, author = {Ortega-Andrade, HM and Rodes Blanco, M and Cisneros-Heredia, DF and Guerra Arévalo, N and López de Vargas-Machuca, KG and Sánchez-Nivicela, JC and Armijos-Ojeda, D and Cáceres Andrade, JF and Reyes-Puig, C and Quezada Riera, AB and Székely, P and Rojas Soto, OR and Székely, D and Guayasamin, JM and Siavichay Pesántez, FR and Amador, L and Betancourt, R and Ramírez-Jaramillo, SM and Timbe-Borja, B and Gómez Laporta, M and Webster Bernal, JF and Oyagata Cachimuel, LA and Chávez Jácome, D and Posse, V and Valle-Piñuela, C and Padilla Jiménez, D and Reyes-Puig, JP and Terán-Valdez, A and Coloma, LA and Pérez Lara, MB and Carvajal-Endara, S and Urgilés, M and Yánez Muñoz, MH}, title = {Red List assessment of amphibian species of Ecuador: A multidimensional approach for their conservation.}, journal = {PloS one}, volume = {16}, number = {5}, pages = {e0251027}, pmid = {33956885}, issn = {1932-6203}, mesh = {*Amphibians ; Animals ; Anura ; Bufonidae ; Conservation of Natural Resources/methods ; Databases as Topic ; Ecosystem ; Ecuador ; *Endangered Species/statistics & numerical data ; }, abstract = {Ecuador is one of the most biodiverse countries in the world, but faces severe pressures and threats to its natural ecosystems. Numerous species have declined and require to be objectively evaluated and quantified, as a step towards the development of conservation strategies. Herein, we present an updated National Red List Assessment for amphibian species of Ecuador, with one of the most detailed and complete coverages for any Ecuadorian taxonomic group to date. Based on standardized methodologies that integrate taxonomic work, spatial analyses, and ecological niche modeling, we assessed the extinction risk and identified the main threats for all Ecuadorian native amphibians (635 species), using the IUCN Red List Categories and Criteria. Our evaluation reveals that 57% (363 species) are categorized as Threatened, 12% (78 species) as Near Threatened, 4% (26 species) as Data Deficient, and 27% (168 species) as Least Concern. Our assessment almost doubles the number of threatened species in comparison with previous evaluations. In addition to habitat loss, the expansion of the agricultural/cattle raising frontier and other anthropogenic threats (roads, human settlements, and mining/oil activities) amplify the incidence of other pressures as relevant predictors of ecological integrity. Potential synergic effects with climate change and emergent diseases (apparently responsible for the sudden declines), had particular importance amongst the threats sustained by Ecuadorian amphibians. Most threatened species are distributed in montane forests and paramo habitats of the Andes, with nearly 10% of them occurring outside the National System of Protected Areas of the Ecuadorian government. Based on our results, we recommend the following actions: (i) An increase of the National System of Protected Areas to include threatened species. (ii) Supporting the ex/in-situ conservation programs to protect species considered like Critically Endangered and Endangered. (iii) Focalizing research efforts towards the description of new species, as well as species currently categorized as Data Deficient (DD) that may turn out to be threatened. The implementation of the described actions is challenging, but urgent, given the current conservation crisis faced by amphibians.}, } @article {pmid33955689, year = {2021}, author = {Huettmann, F and Hueffer, K}, title = {The ecological niche of reported rabies cases in Canada is similar to Alaska.}, journal = {Zoonoses and public health}, volume = {68}, number = {6}, pages = {677-683}, pmid = {33955689}, issn = {1863-2378}, mesh = {Alaska/epidemiology ; Animals ; *Animals, Wild ; Canada/epidemiology ; Demography ; Ecosystem ; Geographic Information Systems ; Humans ; *Livestock ; *Models, Biological ; *Pets ; Rabies/epidemiology/*veterinary ; Viral Zoonoses ; }, abstract = {The ecology of rabies in the circumpolar North is still not well understood. We use machine learning, a geographic information system and data explicit in time and space obtained for reported rabies cases and predictors in Canada to develop an ecological niche model for the distribution of reported rabies cases in the American north (Alaska and Canada). The ecological niche model based on reported rabies cases in Canada predicted reported rabies cases in Alaska, suggesting a rather robust inference and even similar drivers on a continental scale. As found in Alaska, proximity to human infrastructure-specifically along the coast-was a strong predictor in the detection of rabies cases in Canada. Also, this finding highlights the need for a more systematic landscape sampling for rabies infection model predictions to better understand and tackle the ecology of this important zoonotic disease on a landscape scale at some distance from human infrastructure in wilderness areas.}, } @article {pmid33948558, year = {2021}, author = {Santos, FP and Levin, SA and Vasconcelos, VV}, title = {Biased perceptions explain collective action deadlocks and suggest new mechanisms to prompt cooperation.}, journal = {iScience}, volume = {24}, number = {4}, pages = {102375}, pmid = {33948558}, issn = {2589-0042}, abstract = {When individuals face collective action problems, their expectations about others' willingness to contribute affect their motivation to cooperate. Individuals, however, often misperceive the cooperation levels in a population. In the context of climate action, people underestimate the pro-climate positions of others. Designing incentives to enable cooperation and a sustainable future must thereby consider how social perception biases affect collective action. We propose a theoretical model and investigate the effect of social perception bias in non-linear public goods games. We show that different types of bias play a distinct role in cooperation dynamics. False uniqueness (underestimating own views) and false consensus (overestimating own views) both explain why communities get locked in suboptimal states. Such dynamics also impact the effectiveness of typical monetary incentives, such as fees. Our work contributes to understanding how targeting biases, e.g., by changing the information available to individuals, can comprise a fundamental mechanism to prompt collective action.}, } @article {pmid33947700, year = {2021}, author = {Fouks, B and Brand, P and Nguyen, HN and Herman, J and Camara, F and Ence, D and Hagen, DE and Hoff, KJ and Nachweide, S and Romoth, L and Walden, KKO and Guigo, R and Stanke, M and Narzisi, G and Yandell, M and Robertson, HM and Koeniger, N and Chantawannakul, P and Schatz, MC and Worley, KC and Robinson, GE and Elsik, CG and Rueppell, O}, title = {The genomic basis of evolutionary differentiation among honey bees.}, journal = {Genome research}, volume = {31}, number = {7}, pages = {1203-1215}, pmid = {33947700}, issn = {1549-5469}, support = {R15 GM102753/GM/NIGMS NIH HHS/United States ; R21 AG046837/AG/NIA NIH HHS/United States ; U54 HG003273/HG/NHGRI NIH HHS/United States ; }, abstract = {In contrast to the western honey bee, Apis mellifera, other honey bee species have been largely neglected despite their importance and diversity. The genetic basis of the evolutionary diversification of honey bees remains largely unknown. Here, we provide a genome-wide comparison of three honey bee species, each representing one of the three subgenera of honey bees, namely the dwarf (Apis florea), giant (A. dorsata), and cavity-nesting (A. mellifera) honey bees with bumblebees as an outgroup. Our analyses resolve the phylogeny of honey bees with the dwarf honey bees diverging first. We find that evolution of increased eusocial complexity in Apis proceeds via increases in the complexity of gene regulation, which is in agreement with previous studies. However, this process seems to be related to pathways other than transcriptional control. Positive selection patterns across Apis reveal a trade-off between maintaining genome stability and generating genetic diversity, with a rapidly evolving piRNA pathway leading to genomes depleted of transposable elements, and a rapidly evolving DNA repair pathway associated with high recombination rates in all Apis species. Diversification within Apis is accompanied by positive selection in several genes whose putative functions present candidate mechanisms for lineage-specific adaptations, such as migration, immunity, and nesting behavior.}, } @article {pmid33946876, year = {2021}, author = {Wei, G and Sun, H and Wei, H and Qin, T and Yang, Y and Xu, X and Zhao, S}, title = {Detecting the Mechanism behind the Transition from Fixed Two-Dimensional Patterned Sika Deer (Cervus nippon) Dermal Papilla Cells to Three-Dimensional Pattern.}, journal = {International journal of molecular sciences}, volume = {22}, number = {9}, pages = {}, pmid = {33946876}, issn = {1422-0067}, mesh = {AC133 Antigen/biosynthesis/genetics ; Alkaline Phosphatase/biosynthesis/genetics ; Animals ; Biomarkers ; Cell Aggregation ; Cell Culture Techniques ; Cell Division ; Cells, Cultured ; Deer/*anatomy & histology/genetics ; Gene Expression Regulation ; Gene Ontology ; Hair ; Hair Follicle/*cytology/growth & development/metabolism ; Mesoderm/cytology ; SOXB1 Transcription Factors/biosynthesis/genetics ; Species Specificity ; Spheroids, Cellular/cytology/metabolism ; Transcriptome ; Versicans/biosynthesis/genetics ; }, abstract = {The hair follicle dermal papilla is critical for hair generation and de novo regeneration. When cultured in vitro, dermal papilla cells from different species demonstrate two distinguishable growth patterns under the conventional culture condition: a self-aggregative three dimensional spheroidal (3D) cell pattern and a two dimensional (2D) monolayer cell pattern, correlating with different hair inducing properties. Whether the loss of self-aggregative behavior relates to species-specific differences or the improper culture condition remains unclear. Can the fixed 2D patterned dermal papilla cells recover the self-aggregative behavior and 3D pattern also remains undetected. Here, we successfully constructed the two growth patterns using sika deer (Cervus nippon) dermal papilla cells and proved it was the culture condition that determined the dermal papilla growth pattern. The two growth patterns could transit mutually as the culture condition was exchanged. The fixed 2D patterned sika deer dermal papilla cells could recover the self-aggregative behavior and transit back to 3D pattern, accompanied by the restoration of hair inducing capability when the culture condition was changed. In addition, the global gene expressions during the transition from 2D pattern to 3D pattern were compared to detect the potential regulating genes and pathways involved in the recovery of 3D pattern and hair inducing capability.}, } @article {pmid33945265, year = {2021}, author = {Wang, Y and Ouyang, W and Lin, C and Zhu, W and Critto, A and Tysklind, M and Wang, X and He, M and Wang, B and Wu, H}, title = {Higher Fine Particle Fraction in Sediment Increased Phosphorus Flux to Estuary in Restored Yellow River Basin.}, journal = {Environmental science & technology}, volume = {55}, number = {10}, pages = {6783-6790}, doi = {10.1021/acs.est.1c00135}, pmid = {33945265}, issn = {1520-5851}, mesh = {China ; Environmental Monitoring ; Estuaries ; Geologic Sediments ; Phosphorus/analysis ; *Rivers ; *Water Pollutants, Chemical/analysis ; }, abstract = {River delta-front estuaries (DEs) are vital interfaces for fluxes between terrestrial and marine environments. However, deep uncertainty exists in estimating the sedimentary pollutant flux from terrestrial environments in DEs due, in part, to a lack of direct measurements in these dynamic and complicated regions and uncertainty in the calculation method. Due to its high sediment content, the Yellow River (YR) has a strong ability to adsorb phosphorus; therefore, it reliably reflects estuarine sedimentary processes. Here, through the comprehensive analysis of field samples, monitoring data and remote sensing images, we conclude that riverine fine particles control the deltaic estuary pollution status and that particle size is the key factor. Based on the stable relationships between phosphorus and heavy metals, with r[2] values of 0.990, 0.992, and 0.639 for As, Cd, and Cr, respectively, we estimated that the P flux reached 22.68 g/m[2] yr in 2017. Analysis of the YR high-silt sediment load, which has a strong phosphorus adsorption ability and constitutes a substantial fraction of global fluvial sediment transport, revealed a negative correlation between the riverine sediment load and the estuarine phosphorus flux.}, } @article {pmid33937774, year = {2020}, author = {Ben-Zeev, D and Buck, B and Chander, A and Brian, R and Wang, W and Atkins, D and Brenner, CJ and Cohen, T and Campbell, A and Munson, J}, title = {Mobile RDoC: Using Smartphones to Understand the Relationship Between Auditory Verbal Hallucinations and Need for Care.}, journal = {Schizophrenia bulletin open}, volume = {1}, number = {1}, pages = {sgaa060}, pmid = {33937774}, issn = {2632-7899}, abstract = {OBJECTIVE: Auditory verbal hallucinations (AVH) are common in multiple clinical populations but also occur in individuals who are otherwise considered healthy. Adopting the National Institute of Mental Health's Research Domain Criteria (RDoC) framework, the aim of the current study was to integrate a variety of measures to evaluate whether AVH experience varies across clinical and nonclinical individuals.

METHODS: A total of 384 people with AVH from 41 US states participated in the study; 295 participants (77%) who received inpatient, outpatient, or combination treatments for AVH and 89 participants (23%) who never received care. Participants used a multi-modal smartphone data collection system to report on their AVH experiences and co-occurring psychological states multiple times daily, over 30 days. In parallel, smartphone sensors recorded their physical activity, geolocation, and calling and texting behavior continuously.

RESULTS: The clinical sample experienced AVH more frequently than the nonclinical group and rated their AVH as significantly louder and more powerful. They experienced more co-occurring negative affect and were more socially withdrawn, spending significantly more time at home and significantly less time near other people. Participants with a history of inpatient care also rated their AVH as infused with significantly more negative content. The groups did not differ in their physical activity or use of their smartphones for digital communication.

CONCLUSION: Smartphone-assisted remote data collection revealed real-time/real-place phenomenological, affective, and behavioral differences between clinical and nonclinical samples of people who experience AVH. The study provided strong support for the application of RDoC-informed approaches in psychosis research.}, } @article {pmid33934723, year = {2021}, author = {Aime, MC and Miller, AN and Aoki, T and Bensch, K and Cai, L and Crous, PW and Hawksworth, DL and Hyde, KD and Kirk, PM and Lücking, R and May, TW and Malosso, E and Redhead, SA and Rossman, AY and Stadler, M and Thines, M and Yurkov, AM and Zhang, N and Schoch, CL}, title = {How to publish a new fungal species, or name, version 3.0.}, journal = {IMA fungus}, volume = {12}, number = {1}, pages = {11}, pmid = {33934723}, issn = {2210-6340}, support = {1010662//U.S. Department of Agriculture/ ; Intramural Research Program//U.S. National Library of Medicine/ ; DEB 1452971//National Science Foundation/ ; }, abstract = {It is now a decade since The International Commission on the Taxonomy of Fungi (ICTF) produced an overview of requirements and best practices for describing a new fungal species. In the meantime the International Code of Nomenclature for algae, fungi, and plants (ICNafp) has changed from its former name (the International Code of Botanical Nomenclature) and introduced new formal requirements for valid publication of species scientific names, including the separation of provisions specific to Fungi and organisms treated as fungi in a new Chapter F. Equally transformative have been changes in the data collection, data dissemination, and analytical tools available to mycologists. This paper provides an updated and expanded discussion of current publication requirements along with best practices for the description of new fungal species and publication of new names and for improving accessibility of their associated metadata that have developed over the last 10 years. Additionally, we provide: (1) model papers for different fungal groups and circumstances; (2) a checklist to simplify meeting (i) the requirements of the ICNafp to ensure the effective, valid and legitimate publication of names of new taxa, and (ii) minimally accepted standards for description; and, (3) templates for preparing standardized species descriptions.}, } @article {pmid33934278, year = {2021}, author = {Olsson, S and Lorenzo, Z and Zabal-Aguirre, M and Piotti, A and Vendramin, GG and González-Martínez, SC and Grivet, D}, title = {Evolutionary history of the mediterranean Pinus halepensis-brutia species complex using gene-resequencing and transcriptomic approaches.}, journal = {Plant molecular biology}, volume = {106}, number = {4-5}, pages = {367-380}, pmid = {33934278}, issn = {1573-5028}, support = {CGL2011-30182-C02-01/02//Agencia Estatal de Investigación/ ; }, mesh = {DNA, Plant ; Datasets as Topic ; *Evolution, Molecular ; Genetic Markers ; Genetic Variation ; Genetics, Population ; Phylogeny ; Pinus/classification/*genetics ; Sequence Analysis, DNA ; Transcriptome ; }, abstract = {Complementary gene-resequencing and transcriptomic approaches reveal contrasted evolutionary histories in a species complex. Pinus halepensis and Pinus brutia are closely related species that can intercross, but occupy different geographical ranges and bioclimates. To study the evolution of this species complex and to provide genomic resources for further research, we produce and analyze two new complementary sets of genetic resources: (i) a set of 172 re-sequenced genomic target loci analyzed in 45 individuals, and (ii) a set of 11 transcriptome assemblies. These two datasets provide insights congruent with previous studies: P. brutia displays high level of genetic diversity and no genetic sub-structure, while P. halepensis shows three main genetic clusters, the western Mediterranean and North African clusters displaying much lower genetic diversity than the eastern Mediterranean cluster, the latter cluster having similar genetic diversity to P. brutia. In addition, these datasets provide new insights on the timing of the species-complex history: the two species would have split at the end of the tertiary, and the changing climatic conditions of the Mediterranean region at the end of the Tertiary-beginning of the Quaternary, together with the distinct species tolerance to harsh climatic conditions would have resulted in different geographic distributions, demographic histories and genetic patterns of the two pines. The multiple glacial-interglacial cycles during the Quaternary would have led to the expansion of P. brutia in the Middle East, while P. halepensis would have been through bottlenecks. The last glaciations, from 0.6 Mya on, would have affected further the Western genetic pool of P. halepensis.}, } @article {pmid33933034, year = {2021}, author = {Woods, LM and Rachet, B and Morris, M and Bhaskaran, K and Coleman, MP}, title = {Are socio-economic inequalities in breast cancer survival explained by peri-diagnostic factors?.}, journal = {BMC cancer}, volume = {21}, number = {1}, pages = {485}, pmid = {33933034}, issn = {1471-2407}, support = {/WT_/Wellcome Trust/United Kingdom ; 11415/CRUK_/Cancer Research UK/United Kingdom ; 18525/CRUK_/Cancer Research UK/United Kingdom ; 29018/CRUK_/Cancer Research UK/United Kingdom ; }, mesh = {Adolescent ; Adult ; Aged ; Aged, 80 and over ; Alcohol Drinking/epidemiology ; Breast Neoplasms/diagnosis/*mortality/pathology/surgery ; Comorbidity ; Databases, Factual/statistics & numerical data ; England/epidemiology ; Female ; Health Services Needs and Demand/*statistics & numerical data ; *Health Status ; Humans ; Middle Aged ; Poverty Areas ; Primary Health Care/*statistics & numerical data ; Proportional Hazards Models ; Registries/statistics & numerical data ; Retrospective Studies ; Smoking/epidemiology ; *Socioeconomic Factors ; Survival Analysis ; Time-to-Treatment ; Young Adult ; }, abstract = {BACKGROUND: Patients living in more deprived localities have lower cancer survival in England, but the role of individual health status at diagnosis and the utilisation of primary health care in explaining these differentials has not been widely considered. We set out to evaluate whether pre-existing individual health status at diagnosis and primary care consultation history (peri-diagnostic factors) could explain socio-economic differentials in survival amongst women diagnosed with breast cancer.

METHODS: We conducted a retrospective cohort study of women aged 15-99 years diagnosed in England using linked routine data. Ecologically-derived measures of income deprivation were combined with individually-linked data from the English National Cancer Registry, Clinical Practice Research Datalink (CPRD) and Hospital Episodes Statistics (HES) databases. Smoking status, alcohol consumption, BMI, comorbidity, and consultation histories were derived for all patients. Time to breast surgery was derived for women diagnosed after 2005. We estimated net survival and modelled the excess hazard ratio of breast cancer death using flexible parametric models. We accounted for missing data using multiple imputation.

RESULTS: Net survival was lower amongst more deprived women, with a single unit increase in deprivation quintile inferring a 4.4% (95% CI 1.4-8.8) increase in excess mortality. Peri-diagnostic co-variables varied by deprivation but did not explain the differentials in multivariable analyses.

CONCLUSIONS: These data show that socio-economic inequalities in survival cannot be explained by consultation history or by pre-existing individual health status, as measured in primary care. Differentials in the effectiveness of treatment, beyond those measuring the inclusion of breast surgery and the timing of surgery, should be considered as part of the wider effort to reduce inequalities in premature mortality.}, } @article {pmid33929583, year = {2021}, author = {Tsakiroglou, AM and Astley, S and Dave, M and Fergie, M and Harkness, E and Rosenberg, A and Sperrin, M and West, C and Byers, R and Linton, K}, title = {Immune infiltrate diversity confers a good prognosis in follicular lymphoma.}, journal = {Cancer immunology, immunotherapy : CII}, volume = {70}, number = {12}, pages = {3573-3585}, pmid = {33929583}, issn = {1432-0851}, support = {IS-BRC-1215-20007//Manchester Biomedical Research Centre/ ; }, mesh = {Biomarkers/metabolism ; Biomarkers, Tumor/immunology ; Cohort Studies ; Female ; Fluorescent Antibody Technique/methods ; Humans ; Kaplan-Meier Estimate ; Lymphocytes, Tumor-Infiltrating/drug effects/immunology ; Lymphoma, Follicular/drug therapy/*immunology/*pathology ; Male ; Prognosis ; Progression-Free Survival ; Rituximab/therapeutic use ; Tumor Microenvironment/drug effects/immunology ; }, abstract = {BACKGROUND: Follicular lymphoma (FL) prognosis is influenced by the composition of the tumour microenvironment. We tested an automated approach to quantitatively assess the phenotypic and spatial immune infiltrate diversity as a prognostic biomarker for FL patients.

METHODS: Diagnostic biopsies were collected from 127 FL patients initially treated with rituximab-based therapy (52%), radiotherapy (28%), or active surveillance (20%). Tissue microarrays were constructed and stained using multiplex immunofluorescence (CD4, CD8, FOXP3, CD21, PD-1, CD68, and DAPI). Subsequently, sections underwent automated cell scoring and analysis of spatial interactions, defined as cells co-occurring within 30 μm. Shannon's entropy, a metric describing species biodiversity in ecological habitats, was applied to quantify immune infiltrate diversity of cell types and spatial interactions. Immune infiltrate diversity indices were tested in multivariable Cox regression and Kaplan-Meier analysis for overall (OS) and progression-free survival (PFS).

RESULTS: Increased diversity of cell types (HR = 0.19 95% CI 0.06-0.65, p = 0.008) and cell spatial interactions (HR = 0.39, 95% CI 0.20-0.75, p = 0.005) was associated with favourable OS, independent of the Follicular Lymphoma International Prognostic Index. In the rituximab-treated subset, the favourable trend between diversity and PFS did not reach statistical significance.

CONCLUSION: Multiplex immunofluorescence and Shannon's entropy can objectively quantify immune infiltrate diversity and generate prognostic information in FL. This automated approach warrants validation in additional FL cohorts, and its applicability as a pre-treatment biomarker to identify high-risk patients should be further explored. The multiplex image dataset generated by this study is shared publicly to encourage further research on the FL microenvironment.}, } @article {pmid33924490, year = {2021}, author = {Holland, I and DeVille, NV and Browning, MHEM and Buehler, RM and Hart, JE and Hipp, JA and Mitchell, R and Rakow, DA and Schiff, JE and White, MP and Yin, J and James, P}, title = {Measuring Nature Contact: A Narrative Review.}, journal = {International journal of environmental research and public health}, volume = {18}, number = {8}, pages = {}, pmid = {33924490}, issn = {1660-4601}, support = {P30 ES025128/ES/NIEHS NIH HHS/United States ; P30 ES000002/ES/NIEHS NIH HHS/United States ; MC_UU_12017/10/MRC_/Medical Research Council/United Kingdom ; T32 ES007069/ES/NIEHS NIH HHS/United States ; R01 ES028712/ES/NIEHS NIH HHS/United States ; SPHSU10/CSO_/Chief Scientist Office/United Kingdom ; R00 CA201542/CA/NCI NIH HHS/United States ; R01 HL150119/HL/NHLBI NIH HHS/United States ; SPHSU19/CSO_/Chief Scientist Office/United Kingdom ; MC_UU_00022/4/MRC_/Medical Research Council/United Kingdom ; }, mesh = {*City Planning ; Cross-Sectional Studies ; *Geographic Information Systems ; Humans ; Residence Characteristics ; Surveys and Questionnaires ; }, abstract = {While many studies suggest evidence for the health benefits of nature, there is currently no standardized method to measure time spent in nature or nature contact, nor agreement on how best to define nature contact in research. The purpose of this review is to summarize how nature contact has been measured in recent health research and provide insight into current metrics of exposure to nature at individual and population scales. The most common methods include surrounding greenness, questionnaires, and global positioning systems (GPS) tracking. Several national-level surveys exist, though these are limited by their cross-sectional design, often measuring only a single component of time spent in nature, and poor links to measures of health. In future research, exposure assessment combining the quantifying (e.g., time spent in nature and frequency of visits to nature) and qualifying (e.g., greenness by the normalized difference of vegetation index (NDVI) and ratings on perception by individuals) aspects of current methods and leveraging innovative methods (e.g., experience sampling methods, ecological momentary assessment) will provide a more comprehensive understanding of the health effects of nature exposure and inform health policy and urban planning.}, } @article {pmid33924187, year = {2021}, author = {Warns, FK and Gültas, M and van Asten, AL and Scholz, T and Gerken, M}, title = {Is There a Link between Suckling and Manipulation Behavior during Rearing in Pigs?.}, journal = {Animals : an open access journal from MDPI}, volume = {11}, number = {4}, pages = {}, pmid = {33924187}, issn = {2076-2615}, abstract = {Inadequate possibilities to perform oral manipulation behavior for pigs can lead to misdirection and thus tail biting. Our study aimed to analyze manipulation behaviors of weaner pigs with focus on tail biting and the relationship with agonistic characteristics of the piglets during suckling. We analyzed the individual manipulation behavior of 188 weaner pigs. General health condition and tail lesions were determined weekly. Correlations were estimated between weight at weaning and at the end of rearing period, frequency of manipulative rearing behaviors and Dominance and social tension index based on suckling behavior. Principal component and cluster analyses were performed to identify groups of piglets which showed similar suckling and rearing behaviors. Tail biting increased at the middle and end of rearing with switching roles of biters and victims. Tail lesions were correlated with received tail biting behavior but occurred with a delay of more than a week. The frequency of performed tail biting was correlated with dominance index (rs = -0.256, p < 0.01) and weaning weight (rs = -0.199, p < 0.05). We assume that performed tail biting is more often observed in pigs who show mainly submissive behavior in teat disputes.}, } @article {pmid33924156, year = {2021}, author = {Raza, A and Su, W and Gao, A and Mehmood, SS and Hussain, MA and Nie, W and Lv, Y and Zou, X and Zhang, X}, title = {Catalase (CAT) Gene Family in Rapeseed (Brassica napus L.): Genome-Wide Analysis, Identification, and Expression Pattern in Response to Multiple Hormones and Abiotic Stress Conditions.}, journal = {International journal of molecular sciences}, volume = {22}, number = {8}, pages = {}, pmid = {33924156}, issn = {1422-0067}, support = {N/A//This work was supported by the Science and Technology Innovation Project of the Chinese Academy of Agricultural Sciences./ ; }, mesh = {Brassica napus/classification/*genetics/metabolism ; Catalase/*genetics/metabolism ; Computational Biology ; Conserved Sequence ; Gene Expression Profiling ; Gene Expression Regulation, Plant/*drug effects ; Genome-Wide Association Study ; *Multigene Family ; Nucleotide Motifs ; Organ Specificity ; Phylogeny ; Plant Growth Regulators/*pharmacology ; Promoter Regions, Genetic ; Reactive Oxygen Species/metabolism ; Stress, Physiological/*genetics ; Synteny ; *Transcriptome ; }, abstract = {Catalase (CAT) is an antioxidant enzyme expressed by the CAT gene family and exists in almost all aerobic organisms. Environmental stresses induce the generation of reactive oxygen species (ROS) that eventually hinder plant growth and development. The CAT enzyme translates the hydrogen peroxide (H2O2) to water (H2O) and reduce the ROS levels to shelter the cells' death. So far, the CAT gene family has not been reported in rapeseed (Brassica napus L.). Therefore, a genome-wide comprehensive analysis was conducted to classify the CAT genes in the rapeseed genome. The current study identified 14 BnCAT genes in the rapeseed genome. Based on phylogenetic and synteny analysis, the BnCATs belong to four groups (Groups I-IV). A gene structure and conserved motif analysis showed that Group I, Group II, and Group IV possess almost the same intron/exon pattern, and an equal number of motifs, while Group III contains diverse structures and contain 15 motifs. By analyzing the cis-elements in the promoters, we identified five hormone-correlated responsive elements and four stress-related responsive elements. Further, six putative bna-miRNAs were also identified, targeting three genes (BnCAT4, BnCAT6, and BnCAT8). Gene ontology (GO) enrichment analysis showed that the BnCAT genes were largely related to cellular organelles, ROS response, stimulus response, stress response, and antioxidant enzymes. Almost 10 BnCAT genes showed higher expression levels in different tissues, i.e., root, leaf, stem, and silique. The expression analysis showed that BnCAT1-BnCAT3 and BnCAT11-BnCAT13 were significantly upregulated by cold, salinity, abscisic acid (ABA), and gibberellic acid (GA) treatment, but not by drought and methyl jasmonate (MeJA). Notably, most of the genes were upregulated by waterlogging stress, except BnCAT6, BnCAT9, and BnCAT10. Our results opened new windows for future investigations and provided insights into the CAT family genes in rapeseed.}, } @article {pmid33919681, year = {2021}, author = {Shen, H and Zhang, Y and Zheng, C and Wang, B and Chen, P}, title = {A Cascade Graph Convolutional Network for Predicting Protein-Ligand Binding Affinity.}, journal = {International journal of molecular sciences}, volume = {22}, number = {8}, pages = {}, pmid = {33919681}, issn = {1422-0067}, mesh = {Databases, Protein ; Ligands ; Models, Theoretical ; *Neural Networks, Computer ; Protein Binding ; Proteins/*metabolism ; }, abstract = {Accurate prediction of binding affinity between protein and ligand is a very important step in the field of drug discovery. Although there are many methods based on different assumptions and rules do exist, prediction performance of protein-ligand binding affinity is not satisfactory so far. This paper proposes a new cascade graph-based convolutional neural network architecture by dealing with non-Euclidean irregular data. We represent the molecule as a graph, and use a simple linear transformation to deal with the sparsity problem of the one-hot encoding of original data. The first stage adopts ARMA graph convolutional neural network to learn the characteristics of atomic space in the protein-ligand complex. In the second stage, one variant of the MPNN graph convolutional neural network is introduced with chemical bond information and interactive atomic features. Finally, the architecture passes through the global add pool and the fully connected layer, and outputs a constant value as the predicted binding affinity. Experiments on the PDBbind v2016 data set showed that our method is better than most of the current methods. Our method is also comparable to the state-of-the-art method on the data set, and is more intuitive and simple.}, } @article {pmid33918473, year = {2021}, author = {Gao, B and Chi, L and Zhu, Y and Shi, X and Tu, P and Li, B and Yin, J and Gao, N and Shen, W and Schnabl, B}, title = {An Introduction to Next Generation Sequencing Bioinformatic Analysis in Gut Microbiome Studies.}, journal = {Biomolecules}, volume = {11}, number = {4}, pages = {}, pmid = {33918473}, issn = {2218-273X}, support = {R01 AA020703/AA/NIAAA NIH HHS/United States ; P30 DK120515/DK/NIDDK NIH HHS/United States ; R01 AA024726/AA/NIAAA NIH HHS/United States ; R37 AA020703/AA/NIAAA NIH HHS/United States ; P50 AA011999/AA/NIAAA NIH HHS/United States ; U01 AA026939/AA/NIAAA NIH HHS/United States ; }, mesh = {Bacteria/genetics ; Computational Biology/*methods ; Fungi/genetics ; *Gastrointestinal Microbiome ; High-Throughput Nucleotide Sequencing ; Humans ; RNA, Ribosomal, 16S/chemistry/metabolism ; RNA, Ribosomal, 18S/chemistry/metabolism ; Viruses/genetics ; }, abstract = {The gut microbiome is a microbial ecosystem which expresses 100 times more genes than the human host and plays an essential role in human health and disease pathogenesis. Since most intestinal microbial species are difficult to culture, next generation sequencing technologies have been widely applied to study the gut microbiome, including 16S rRNA, 18S rRNA, internal transcribed spacer (ITS) sequencing, shotgun metagenomic sequencing, metatranscriptomic sequencing and viromic sequencing. Various software tools were developed to analyze different sequencing data. In this review, we summarize commonly used computational tools for gut microbiome data analysis, which extended our understanding of the gut microbiome in health and diseases.}, } @article {pmid33917500, year = {2021}, author = {Aziz, MA and Ullah, Z and Al-Fatimi, M and De Chiara, M and Sõukand, R and Pieroni, A}, title = {On the Trail of an Ancient Middle Eastern Ethnobotany: Traditional Wild Food Plants Gathered by Ormuri Speakers in Kaniguram, NW Pakistan.}, journal = {Biology}, volume = {10}, number = {4}, pages = {}, pmid = {33917500}, issn = {2079-7737}, abstract = {An ethnobotanical field study focusing on traditional wild food botanical taxa was carried out in Kaniguram, South Waziristan, Pakistan, among Ormur (or Burki or Baraki) peoples, which represent a diasporic minority group, as well as among the surrounding Pashtuns. Through sixty semi-structured interviews, fifty-two wild food plants (taxa) were recorded, and they were primarily used raw as snacks and cooked as vegetables. Comparative analysis found a remarkable overlap of the quoted plant uses between the two studied groups, which may reflect complex socio-cultural adaptations Ormur speakers faced. Ormur people retain a rich knowledge of anthropogenic weeds and the phytonyms reveal important commonalities with Persian and Kurdish phytonyms, which may indicate their possible horticultural-driven human ecological origin from the Middle East. Some novel or rare food uses of Cirsiumarvense, Nannorrhops ritchiana, Periploca aphylla, Perovskia atriplicifolia, Viscum album,Oxalis corniculata and Withania coagulans were documented. Since the Ormuri language represents a moribund language, still spoken by only a few thousand speakers in NW Pakistan and Afghanistan, it is recommended that the traditional bio-cultural and gastronomical heritage of this minority group be appropriately protected and bolstered in future rural development programs.}, } @article {pmid33914830, year = {2021}, author = {Parra-Galindo, MA and Soto-Sedano, JC and Mosquera-Vásquez, T and Roda, F}, title = {Pathway-based analysis of anthocyanin diversity in diploid potato.}, journal = {PloS one}, volume = {16}, number = {4}, pages = {e0250861}, pmid = {33914830}, issn = {1932-6203}, mesh = {Anthocyanins/*biosynthesis ; *Biosynthetic Pathways ; Computational Biology/methods ; Coumaric Acids/metabolism ; Diploidy ; Gene Expression Regulation, Plant ; Genome-Wide Association Study/*methods ; Methionine/metabolism ; Phenylalanine Ammonia-Lyase/genetics ; Plant Proteins/genetics ; *Polymorphism, Single Nucleotide ; Quantitative Trait Loci ; Solanum tuberosum/genetics/*metabolism ; }, abstract = {Anthocyanin biosynthesis is one of the most studied pathways in plants due to the important ecological role played by these compounds and the potential health benefits of anthocyanin consumption. Given the interest in identifying new genetic factors underlying anthocyanin content we studied a diverse collection of diploid potatoes by combining a genome-wide association study and pathway-based analyses. By using an expanded SNP dataset, we identified candidate genes that had not been associated with anthocyanin variation in potatoes, namely a Myb transcription factor, a Leucoanthocyanidin dioxygenase gene and a vacuolar membrane protein. Importantly, a genomic region in chromosome 10 harbored the SNPs with strongest associations with anthocyanin content in GWAS. Some of these SNPs were associated with multiple anthocyanin compounds and therefore could underline the existence of pleiotropic genes or anthocyanin biosynthetic clusters. We identified multiple anthocyanin homologs in this genomic region, including four transcription factors and five enzymes that could be governing anthocyanin variation. For instance, a SNP linked to the phenylalanine ammonia-lyase gene, encoding the first enzyme in the phenylpropanoid biosynthetic pathway, was associated with all of the five anthocyanins measured. Finally, we combined a pathway analysis and GWAS of other agronomic traits to identify pathways related to anthocyanin biosynthesis in potatoes. We found that methionine metabolism and the production of sugars and hydroxycinnamic acids are genetically correlated to anthocyanin biosynthesis. The results contribute to the understanding of anthocyanins regulation in potatoes and can be used in future breeding programs focused on nutraceutical food.}, } @article {pmid33911920, year = {2021}, author = {Nasser, M and Okely, M and Nasif, O and Alharbi, S and GadAllah, S and Al-Obaid, S and Enan, R and Bala, M and Al-Ashaal, S}, title = {Spatio-temporal analysis of Egyptian flower mantis Blepharopsis mendica (order: mantodea), with notes of its future status under climate change.}, journal = {Saudi journal of biological sciences}, volume = {28}, number = {4}, pages = {2049-2055}, pmid = {33911920}, issn = {1319-562X}, abstract = {Egyptian flower mantis Blepharopsis mendica (Order: Mantodea) is a widespread mantis species throughout the southwest Palearctic region. The ecological and geographical distribution of such interesting species is rarely known. So, through this work, habitat suitability models for its distribution through Egyptian territory were created using MaxEnt software from 90 occurrence records. One topographic (altitude) and eleven bioclimatic variables influencing the species distribution were selected to generate the models. The predicted distribution in Egypt was focused on the Delta, South Sinai, the north-eastern part of the country, and some areas in the west including Siwa Oasis. Temporal analysis between the two periods (1900-1961) and (1961-2017) show current reduction of this species distribution through Delta and its surrounding areas, may be due to urbanization. On the other hand, it increases in newly protected areas of South Sinai. Under the future climate change scenario, the MaxEnt model predicted the habitat gains for B. mendica in RCP 2.6 for 2070 and loss of habitat in RCP 8.5 for the same year. Our results can be used as a basis for conserving this species not only in Egypt, but also throughout the whole of its range, also, it show how the using of geo-information could help in studying animal ecology.}, } @article {pmid33911273, year = {2021}, author = {Rhie, A and McCarthy, SA and Fedrigo, O and Damas, J and Formenti, G and Koren, S and Uliano-Silva, M and Chow, W and Fungtammasan, A and Kim, J and Lee, C and Ko, BJ and Chaisson, M and Gedman, GL and Cantin, LJ and Thibaud-Nissen, F and Haggerty, L and Bista, I and Smith, M and Haase, B and Mountcastle, J and Winkler, S and Paez, S and Howard, J and Vernes, SC and Lama, TM and Grutzner, F and Warren, WC and Balakrishnan, CN and Burt, D and George, JM and Biegler, MT and Iorns, D and Digby, A and Eason, D and Robertson, B and Edwards, T and Wilkinson, M and Turner, G and Meyer, A and Kautt, AF and Franchini, P and Detrich, HW and Svardal, H and Wagner, M and Naylor, GJP and Pippel, M and Malinsky, M and Mooney, M and Simbirsky, M and Hannigan, BT and Pesout, T and Houck, M and Misuraca, A and Kingan, SB and Hall, R and Kronenberg, Z and Sović, I and Dunn, C and Ning, Z and Hastie, A and Lee, J and Selvaraj, S and Green, RE and Putnam, NH and Gut, I and Ghurye, J and Garrison, E and Sims, Y and Collins, J and Pelan, S and Torrance, J and Tracey, A and Wood, J and Dagnew, RE and Guan, D and London, SE and Clayton, DF and Mello, CV and Friedrich, SR and Lovell, PV and Osipova, E and Al-Ajli, FO and Secomandi, S and Kim, H and Theofanopoulou, C and Hiller, M and Zhou, Y and Harris, RS and Makova, KD and Medvedev, P and Hoffman, J and Masterson, P and Clark, K and Martin, F and Howe, K and Flicek, P and Walenz, BP and Kwak, W and Clawson, H and Diekhans, M and Nassar, L and Paten, B and Kraus, RHS and Crawford, AJ and Gilbert, MTP and Zhang, G and Venkatesh, B and Murphy, RW and Koepfli, KP and Shapiro, B and Johnson, WE and Di Palma, F and Marques-Bonet, T and Teeling, EC and Warnow, T and Graves, JM and Ryder, OA and Haussler, D and O'Brien, SJ and Korlach, J and Lewin, HA and Howe, K and Myers, EW and Durbin, R and Phillippy, AM and Jarvis, ED}, title = {Towards complete and error-free genome assemblies of all vertebrate species.}, journal = {Nature}, volume = {592}, number = {7856}, pages = {737-746}, pmid = {33911273}, issn = {1476-4687}, support = {U41 HG002371/HG/NHGRI NIH HHS/United States ; U41 HG007234/HG/NHGRI NIH HHS/United States ; MR/T021985/1/MRC_/Medical Research Council/United Kingdom ; R01 HG010485/HG/NHGRI NIH HHS/United States ; BBS/E/T/000PR9817/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; ZIA HG200398/ImNIH/Intramural NIH HHS/United States ; 207492/Z/17/Z/WT_/Wellcome Trust/United Kingdom ; R01 GM130691/GM/NIGMS NIH HHS/United States ; /WT_/Wellcome Trust/United Kingdom ; R21 DC014432/DC/NIDCD NIH HHS/United States ; R44 HG008118/HG/NHGRI NIH HHS/United States ; }, mesh = {Animals ; Birds ; Gene Library ; *Genome ; Genome Size ; Genome, Mitochondrial ; Genomics/*methods ; Haplotypes ; High-Throughput Nucleotide Sequencing ; Molecular Sequence Annotation ; Sequence Alignment ; Sequence Analysis, DNA ; Sex Chromosomes/genetics ; Vertebrates/*genetics ; }, abstract = {High-quality and complete reference genome assemblies are fundamental for the application of genomics to biology, disease, and biodiversity conservation. However, such assemblies are available for only a few non-microbial species[1-4]. To address this issue, the international Genome 10K (G10K) consortium[5,6] has worked over a five-year period to evaluate and develop cost-effective methods for assembling highly accurate and nearly complete reference genomes. Here we present lessons learned from generating assemblies for 16 species that represent six major vertebrate lineages. We confirm that long-read sequencing technologies are essential for maximizing genome quality, and that unresolved complex repeats and haplotype heterozygosity are major sources of assembly error when not handled correctly. Our assemblies correct substantial errors, add missing sequence in some of the best historical reference genomes, and reveal biological discoveries. These include the identification of many false gene duplications, increases in gene sizes, chromosome rearrangements that are specific to lineages, a repeated independent chromosome breakpoint in bat genomes, and a canonical GC-rich pattern in protein-coding genes and their regulatory regions. Adopting these lessons, we have embarked on the Vertebrate Genomes Project (VGP), an international effort to generate high-quality, complete reference genomes for all of the roughly 70,000 extant vertebrate species and to help to enable a new era of discovery across the life sciences.}, } @article {pmid33911077, year = {2021}, author = {Miao, J and Feng, Q and Li, Y and Zhao, Q and Zhou, C and Lu, H and Fan, D and Yan, J and Lu, Y and Tian, Q and Li, W and Weng, Q and Zhang, L and Zhao, Y and Huang, T and Li, L and Huang, X and Sang, T and Han, B}, title = {Chromosome-scale assembly and analysis of biomass crop Miscanthus lutarioriparius genome.}, journal = {Nature communications}, volume = {12}, number = {1}, pages = {2458}, pmid = {33911077}, issn = {2041-1723}, mesh = {Base Composition/genetics ; Biomass ; Cell Wall/metabolism ; Centromere/genetics ; Chloroplasts/genetics ; Chromosomes, Plant/*genetics ; Computational Biology ; Genetic Variation/genetics ; Genome, Plant/*genetics ; High-Throughput Nucleotide Sequencing ; Ion Transport/genetics ; Photosynthesis/genetics ; Phylogeny ; Poaceae/classification/*genetics ; Sequence Analysis, DNA ; Sequence Homology ; Sorghum/genetics ; Telomere/genetics ; }, abstract = {Miscanthus, a rhizomatous perennial plant, has great potential for bioenergy production for its high biomass and stress tolerance. We report a chromosome-scale assembly of Miscanthus lutarioriparius genome by combining Oxford Nanopore sequencing and Hi-C technologies. The 2.07-Gb assembly covers 96.64% of the genome, with contig N50 of 1.71 Mb. The centromere and telomere sequences are assembled for all 19 chromosomes and chromosome 10, respectively. Allotetraploid origin of the M. lutarioriparius is confirmed using centromeric satellite repeats. The tetraploid genome structure and several chromosomal rearrangements relative to sorghum are clearly demonstrated. Tandem duplicate genes of M. lutarioriparius are functional enriched not only in terms related to stress response, but cell wall biosynthesis. Gene families related to disease resistance, cell wall biosynthesis and metal ion transport are greatly expanded and evolved. The expansion of these families may be an important genomic basis for the enhancement of remarkable traits of M. lutarioriparius.}, } @article {pmid33910227, year = {2021}, author = {Yang, C and Zhou, Y and Marcus, S and Formenti, G and Bergeron, LA and Song, Z and Bi, X and Bergman, J and Rousselle, MMC and Zhou, C and Zhou, L and Deng, Y and Fang, M and Xie, D and Zhu, Y and Tan, S and Mountcastle, J and Haase, B and Balacco, J and Wood, J and Chow, W and Rhie, A and Pippel, M and Fabiszak, MM and Koren, S and Fedrigo, O and Freiwald, WA and Howe, K and Yang, H and Phillippy, AM and Schierup, MH and Jarvis, ED and Zhang, G}, title = {Evolutionary and biomedical insights from a marmoset diploid genome assembly.}, journal = {Nature}, volume = {594}, number = {7862}, pages = {227-233}, pmid = {33910227}, issn = {1476-4687}, support = {F30 MH112351/MH/NIMH NIH HHS/United States ; T32 GM007739/GM/NIGMS NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; }, mesh = {Animals ; Biomedical Research ; Callithrix/*genetics ; DNA Copy Number Variations ; *Diploidy ; *Evolution, Molecular ; Female ; Genome/*genetics ; Genomics/*standards ; Germ-Line Mutation/genetics ; Haplotypes/genetics ; Heterozygote ; Humans ; INDEL Mutation/genetics ; Male ; Reference Standards ; Selection, Genetic ; Sex Differentiation/genetics ; Y Chromosome/genetics ; }, abstract = {The accurate and complete assembly of both haplotype sequences of a diploid organism is essential to understanding the role of variation in genome functions, phenotypes and diseases[1]. Here, using a trio-binning approach, we present a high-quality, diploid reference genome, with both haplotypes assembled independently at the chromosome level, for the common marmoset (Callithrix jacchus), an primate model system that is widely used in biomedical research[2,3]. The full spectrum of heterozygosity between the two haplotypes involves 1.36% of the genome-much higher than the 0.13% indicated by the standard estimation based on single-nucleotide heterozygosity alone. The de novo mutation rate is 0.43 × 10[-8] per site per generation, and the paternal inherited genome acquired twice as many mutations as the maternal. Our diploid assembly enabled us to discover a recent expansion of the sex-differentiation region and unique evolutionary changes in the marmoset Y chromosome. In addition, we identified many genes with signatures of positive selection that might have contributed to the evolution of Callithrix biological features. Brain-related genes were highly conserved between marmosets and humans, although several genes experienced lineage-specific copy number variations or diversifying selection, with implications for the use of marmosets as a model system.}, } @article {pmid33910068, year = {2021}, author = {Szabó, B and Lang, Z and Kövér, S and Bakonyi, G}, title = {The inter-individual variance can provide additional information for the ecotoxicologists beside the mean.}, journal = {Ecotoxicology and environmental safety}, volume = {217}, number = {}, pages = {112260}, doi = {10.1016/j.ecoenv.2021.112260}, pmid = {33910068}, issn = {1090-2414}, mesh = {Animals ; Arthropods/*physiology ; Clutch Size ; Insecticides/*toxicity ; Phenotype ; Pyrethrins/*toxicity ; Reproduction/drug effects ; }, abstract = {The hypothesis that the inter-individual parameter variability is an unexploited area of ecotoxicology was proposed several decades ago. Although some illustrative examples were presented to support this hypothesis in the last decades, it has never been tested on an extensive, coherent database. In this study, variance changes of 105 dose-response curves were analysed. All data originated from the same experiment, where the effects of the insecticide Trebon EC were investigated in a dose-response manner on 15 traits of the collembolan Folsomia candida in four subsequent generations and two types of insecticide treatments. A consistent relationship between inter-individual variance and insecticide application was found in 2 (first clutch size and growth-reproduction trade-off) out of the 15 of the parameters. Contrary to the mean, the variance of the first clutch size showed consistent differences compared to the control. Furthermore, the variance of the growth-reproduction trade-off was consistently different from the control except in one case (F3 generation of the transgenerational treatment). Higher first clutch size variances were found in F1 and a lower one in the F2 and F3 generations than in that of the control. This overall pattern of the variance changes of the first clutch size and the trade-off seems to be a quick response to the insecticide application. In the short term, we have found that variance increased with insecticide treatment (P and F1 generation), because phenotypic variance generally increases due to environmental stress. Disruptive selection could be another mechanism between the more detoxification less reproduction strategy and the more reproduction less detoxification strategy. However, in the later generations (F2-F3) the variance decreases compared to the control, which could be because on short term selection stronger on the viability parameters and in long-term selection on reproduction becomes stronger. According to our results, analysis of the variance changes of some parameters may give information about the effects of the pesticide even when the mean does not predict any impact. Testing variance changes are important in ecotoxicology because variance change can signalise toxicant impact even when the mean does not change in certain cases.}, } @article {pmid33909693, year = {2021}, author = {Freedman, R and Brown, JA and Caldow, C and Caselle, JE}, title = {Species-specific thermal classification schemes can improve climate related marine resource decisions.}, journal = {PloS one}, volume = {16}, number = {4}, pages = {e0250792}, pmid = {33909693}, issn = {1932-6203}, mesh = {Animals ; Biota ; California ; Climate Change ; Conservation of Natural Resources/*methods ; Databases, Factual ; Decision Making ; Fishes/*classification ; Humans ; Kelp/*classification ; Species Specificity ; Temperature ; }, abstract = {Global climate change increasingly contributes to large changes in ecosystem structure. Timely management of rapidly changing marine ecosystems must be matched with methods to rapidly quantify and assess climate driven impacts to ecological communities. Here we create a species-specific, classification system for fish thermal affinities, using three quantifiable datasets and expert opinion. Multiple sources of information limit potential data bias and avoid misclassification. Using a temperate kelp forest fish community in California, USA as a test case for this new methodology, we found the majority of species had high classification agreement across all four data sources (n = 78) but also a number of low agreement species (2 sources disagree from the others, n = 47). For species with low agreement, use of just one dataset to classify species, as is commonly done, would lead to high risk of misclassification. Differences in species classification between individual datasets and our composite classification were apparent. Applying different thermal classifications, lead to different conclusions when quantifying 'warm' and 'cool' species density responses to a marine heatwave. Managers can use this classification approach as a tool to generate accurate, timely and simple information for resource management.}, } @article {pmid33907795, year = {2021}, author = {Patwary, ZP and Paul, NA and Nishitsuji, K and Campbell, AH and Shoguchi, E and Zhao, M and Cummins, SF}, title = {Application of omics research in seaweeds with a focus on red seaweeds.}, journal = {Briefings in functional genomics}, volume = {20}, number = {3}, pages = {148-161}, doi = {10.1093/bfgp/elab023}, pmid = {33907795}, issn = {2041-2657}, mesh = {Biodiversity ; *Seaweed ; }, abstract = {Targeted 'omics' research for seaweeds, utilizing various computational and informatics frameworks, has the potential to rapidly develop our understanding of biological processes at the molecular level and contribute to solutions for the most pressing environmental and social issues of our time. Here, a systematic review into the current status of seaweed omics research was undertaken to evaluate the biological diversity of seaweed species investigated (red, green and brown phyla), the levels to which the work was undertaken (from full genome to transcripts, proteins or metabolites) and the field of research to which it has contributed. We report that from 1994 to 2021 the majority of seaweed omics research has been performed on the red seaweeds (45% of total studies), with more than half of these studies based upon two genera Pyropia and Gracilaria. A smaller number of studies examined brown seaweed (key genera Saccharina and Sargassum) and green seaweed (primarily Ulva). Overall, seaweed omics research is most highly associated with the field of evolution (46% of total studies), followed by the fields of ecology, natural products and their biosynthesis, omics methodology and seaweed-microbe interactions. Synthesis and specific outcomes derived from omics studies in the red seaweeds are provided. Together, these studies have provided a broad-scale interrogation of seaweeds, facilitating our ability to answer fundamental queries and develop applied outcomes. Crucial to the next steps will be establishing analytical tools and databases that can be more broadly utilized by practitioners and researchers across the globe because of their shared interest in the key seaweed genera.}, } @article {pmid33907064, year = {2023}, author = {Ibayashi, K and Fujino, Y and Mimaki, M and Fujimoto, K and Matsuda, S and Goto, YI}, title = {Estimation of the Number of Patients With Mitochondrial Diseases: A Descriptive Study Using a Nationwide Database in Japan.}, journal = {Journal of epidemiology}, volume = {33}, number = {2}, pages = {68-75}, pmid = {33907064}, issn = {1349-9092}, mesh = {Male ; Female ; Humans ; Adult ; Middle Aged ; Japan/epidemiology ; Prevalence ; Databases, Factual ; Tokyo ; *Mitochondrial Diseases/epidemiology ; }, abstract = {BACKGROUND: To provide a better healthcare system for patients with mitochondrial diseases, it is important to understand the basic epidemiology of these conditions, including the number of patients affected. However, little information about them has appeared in Japan to date.

METHODS: To gather data of patients with mitochondrial diseases, we estimated the number of patients with mitochondrial diseases from April 2018 through March 2019 using a national Japanese health care claims database, the National Database (NDB). Further, we calculated the prevalence of patients, and sex ratio, age class, and geographical distribution.

RESULTS: From April 2018 through March 2019, the number of patients with mitochondrial diseases was 3,629, and the prevalence was 2.9 (95% confidence interval [CI], 2.8-3.0) per 100,000 general population. The ratio of females and males was 53 to 47, and the most frequent age class was 40-49 years old. Tokyo had the greatest number of patients with mitochondrial diseases, at 477, whereas Yamanashi had the fewest, at 13. Kagoshima had the highest prevalence of patients with mitochondrial diseases, 8.4 (95% CI, 7.1-10.0) per 100,000 population, whereas Yamanashi had the lowest, 1.6 (95% CI, 0.8-2.7).

CONCLUSION: The number of patients with mitochondrial diseases estimated by this study, 3,269, was more than double that indicated by the Japanese government. This result may imply that about half of all patients are overlooked for reasons such as low severity of illness, suggesting that the Japanese healthcare system needs to provide additional support for these patients.}, } @article {pmid33900611, year = {2021}, author = {Ramakrishnan, M and Yrjälä, K and Satheesh, V and Zhou, MB}, title = {Bamboo Transposon Research: Current Status and Perspectives.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2250}, number = {}, pages = {257-270}, pmid = {33900611}, issn = {1940-6029}, mesh = {DNA Transposable Elements/*genetics ; Databases, Genetic ; Gene Expression Regulation, Plant ; Genetic Variation ; Genome Size/genetics ; Genome, Plant/*genetics ; Genomics/*methods ; Internet ; Plant Breeding/economics/methods ; Ploidies ; Sasa/classification/*genetics ; Species Specificity ; }, abstract = {Bamboo, a fast-growing non-timber forest plant with many uses, is a valuable species for green development. However, bamboo flowering is very infrequent, extending, in general, for up to 120 years. Ecologically, bamboo species are generally better adapted to various environments than other grasses. Therefore, the species deserves a special status in what could be called Ecological Bioeconomy. An understanding of the genetic processes of bamboo can help us sustainably develop and manage bamboo forests. Transposable elements (TEs), jumping genes or transposons, are major genetic elements in plant genomes. The rapid development of the bamboo reference genome, at the chromosome level, reveals that TEs occupy over 63.24% of the genome. This is higher than found in rice, Brachypodium, and sorghum. The bamboo genome contains diverse families of TEs, which play a significant role in bamboo's biological processes including growth and development. TEs provide important clues for understanding the evolution of the bamboo genome. In this chapter, we briefly describe the current status of research on TEs in the bamboo genome, their regulation, and transposition mechanisms. Perspectives for future research are also provided.}, } @article {pmid33900597, year = {2021}, author = {Wang, L and Cho, J and Satheesh, V}, title = {Bioinformatics Analysis Guides to LTR Retrotransposon-Derived Extrachromosomal Linear DNAs Identified by ALE-seq.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2250}, number = {}, pages = {111-114}, pmid = {33900597}, issn = {1940-6029}, mesh = {Computational Biology/*methods ; *Retroelements ; Sequence Analysis, DNA/methods ; Software ; *Terminal Repeat Sequences ; }, abstract = {ALE-seq is a method devised to identify pre-integration intermediates of LTR retrotransposons called extrachromosomal linear DNA, which can be used to predict retrotransposition activity. We describe here a bioinformatic methodology to process reads obtained from the ALE-seq protocol for the effective annotation of novel and active retroelements.}, } @article {pmid33900591, year = {2021}, author = {Su, W and Ou, S and Hufford, MB and Peterson, T}, title = {A Tutorial of EDTA: Extensive De Novo TE Annotator.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2250}, number = {}, pages = {55-67}, pmid = {33900591}, issn = {1940-6029}, mesh = {Benchmarking ; Computational Biology/*methods ; *DNA Transposable Elements ; DNA, Plant/genetics ; Evolution, Molecular ; Molecular Sequence Annotation ; Plants/*genetics ; Software ; Workflow ; }, abstract = {Transposable elements (TEs) are important contributors to genome structure and evolution. With the growth of sequencing technologies, various computational pipelines and software programs have been developed to facilitate TE identification and annotation. These computational tools can be categorized into three types based on their underlying approach: homology-based, structural-based, and de novo methods. Each of these tools has advantages and disadvantages. In this chapter, we introduce EDTA (Extensive de novo TE Annotator), a new comprehensive pipeline composed of high-quality tools to identify and annotate all types of TEs. The development of EDTA is based on the benchmarking results of a collection of TE annotation methods. The selected programs are evaluated by their ability to identify true TEs as well as to exclude false candidates. Here, we present an overview of the EDTA pipeline and a detailed manual for its use. The source code of EDTA is available at https://github.com/oushujun/EDTA .}, } @article {pmid33893361, year = {2021}, author = {Ahlinder, J and Giles, BE and García-Gil, MR}, title = {Life stage-specific inbreeding depression in long-lived Pinaceae species depends on population connectivity.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {8834}, pmid = {33893361}, issn = {2045-2322}, mesh = {Datasets as Topic ; Genes, Plant ; *Inbreeding ; Life Cycle Stages ; Pinaceae/embryology/genetics/*physiology ; Species Specificity ; }, abstract = {Inbreeding depression (ID) is a fundamental selective pressure that shapes mating systems and population genetic structures in plants. Although it has been shown that ID varies over the life stages of shorter-lived plants, less is known about how the fitness effects of inbreeding vary across life stages in long-lived species. We conducted a literature survey in the Pinaceae, a tree family known to harbour some of the highest mutational loads ever reported. Using a meta-regression model, we investigated distributions of inbreeding depression over life stages, adjusting for effects of inbreeding levels and the genetic differentiation of populations within species. The final dataset contained 147 estimates of ID across life stages from 41 studies. 44 Fst estimates were collected from 40 peer-reviewed studies for the 18 species to aid genetic differentiation modelling. Partitioning species into fragmented and well-connected groups using Fst resulted in the best way (i.e. trade-off between high goodness-of-fit of the model to the data and reduced model complexity) to incorporate genetic connectivity in the meta-regression analysis. Inclusion of a life stage term and its interaction with the inbreeding coefficient (F) dramatically increased model precision. We observed that the correlation between ID and F was significant at the earliest life stage. Although partitioning of species populations into fragmented and well-connected groups explained little of the between-study heterogeneity, the inclusion of an interaction between life stage and population differentiation revealed that populations with fragmented distributions suffered lower inbreeding depression at early embryonic stages than species with well-connected populations. There was no evidence for increased ID in late life stages in well-connected populations, although ID tended to increase across life stages in the fragmented group. These findings suggest that life stage data should be included in inbreeding depression studies and that inbreeding needs to be managed over life stages in commercial populations of long-lived plants.}, } @article {pmid33893182, year = {2021}, author = {Tweed, EJ and Thomson, RM and Lewer, D and Sumpter, C and Kirolos, A and Southworth, PM and Purba, AK and Aldridge, RW and Hayward, A and Story, A and Hwang, SW and Katikireddi, SV}, title = {Health of people experiencing co-occurring homelessness, imprisonment, substance use, sex work and/or severe mental illness in high-income countries: a systematic review and meta-analysis.}, journal = {Journal of epidemiology and community health}, volume = {75}, number = {10}, pages = {1010-1018}, pmid = {33893182}, issn = {1470-2738}, support = {218105/Z/19/Z/WT_/Wellcome Trust/United Kingdom ; MC_UU_00022/2/MRC_/Medical Research Council/United Kingdom ; 206602/WT_/Wellcome Trust/United Kingdom ; SPHSU15/CSO_/Chief Scientist Office/United Kingdom ; 203919/Z/16/Z/WT_/Wellcome Trust/United Kingdom ; 206602/Z/17/Z/WT_/Wellcome Trust/United Kingdom ; SCAF/15/02/CSO_/Chief Scientist Office/United Kingdom ; MC_UU_12017/13/MRC_/Medical Research Council/United Kingdom ; SPHSU13/CSO_/Chief Scientist Office/United Kingdom ; DRF-2018-11-ST2-016/DH_/Department of Health/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; CAF/17/11/CSO_/Chief Scientist Office/United Kingdom ; SPHSU17/CSO_/Chief Scientist Office/United Kingdom ; MC_UU_12017/15/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Developed Countries ; *Ill-Housed Persons ; Humans ; *Mental Disorders/epidemiology ; Observational Studies as Topic ; Quality of Life ; Sex Work ; *Substance-Related Disorders/epidemiology ; }, abstract = {BACKGROUND: People affected by homelessness, imprisonment, substance use, sex work or severe mental illness experience substantial excess ill health and premature death. Though these experiences often co-occur, health outcomes associated with their overlap have not previously been reviewed. We synthesised existing evidence on mortality, morbidity, self-rated health and quality of life among people affected by more than one of these experiences.

METHODS: In this systematic review and meta-analysis, we searched Medline, Embase, and PsycINFO for peer-reviewed English-language observational studies from high-income countries published between 1 January 1998 and 11 June 2018. Two authors undertook independent screening, with risk of bias assessed using a modified Newcastle-Ottawa Scale. Findings were summarised by narrative synthesis and random-effect meta-analysis.

RESULTS: From 15 976 citations, 2517 studies underwent full-text screening, and 444 were included. The most common exposure combinations were imprisonment/substance use (31% of data points) and severe mental illness/substance use (27%); only 1% reported outcomes associated with more than two exposures. Infections were the most common outcomes studied, with blood-borne viruses accounting for 31% of all data points. Multiple exposures were associated with poorer outcomes in 80% of data points included (sign test for effect direction, p<0.001). Meta-analysis suggested increased all-cause mortality among people with multiple versus fewer exposures (HR: 1.57 and 95% CI: 1.38 to 1.77), though heterogeneity was high.

CONCLUSION: People affected by multiple exclusionary processes experience profound health inequalities, though there are important gaps in the research landscape. Addressing the health needs of these populations is likely to require co-ordinated action across multiple sectors, such as healthcare, criminal justice, drug treatment, housing and social security.

PROSPERO REGISTRATION NUMBER: CRD42018097189.}, } @article {pmid33888580, year = {2021}, author = {Everson, KM and Gray, LN and Jones, AG and Lawrence, NM and Foley, ME and Sovacool, KL and Kratovil, JD and Hotaling, S and Hime, PM and Storfer, A and Parra-Olea, G and Percino-Daniel, R and Aguilar-Miguel, X and O'Neill, EM and Zambrano, L and Shaffer, HB and Weisrock, DW}, title = {Geography is more important than life history in the recent diversification of the tiger salamander complex.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {118}, number = {17}, pages = {}, pmid = {33888580}, issn = {1091-6490}, support = {T32 GM070449/GM/NIGMS NIH HHS/United States ; }, mesh = {Ambystoma/*genetics/*metabolism ; Ambystoma mexicanum/genetics ; Animals ; Databases, Genetic ; Gene Flow ; Genetics, Population/methods ; Geography ; Larva/genetics ; Metamorphosis, Biological/genetics ; North America ; Phylogeny ; }, abstract = {The North American tiger salamander species complex, including its best-known species, the Mexican axolotl, has long been a source of biological fascination. The complex exhibits a wide range of variation in developmental life history strategies, including populations and individuals that undergo metamorphosis; those able to forego metamorphosis and retain a larval, aquatic lifestyle (i.e., paedomorphosis); and those that do both. The evolution of a paedomorphic life history state is thought to lead to increased population genetic differentiation and ultimately reproductive isolation and speciation, but the degree to which it has shaped population- and species-level divergence is poorly understood. Using a large multilocus dataset from hundreds of samples across North America, we identified genetic clusters across the geographic range of the tiger salamander complex. These clusters often contain a mixture of paedomorphic and metamorphic taxa, indicating that geographic isolation has played a larger role in lineage divergence than paedomorphosis in this system. This conclusion is bolstered by geography-informed analyses indicating no effect of life history strategy on population genetic differentiation and by model-based population genetic analyses demonstrating gene flow between adjacent metamorphic and paedomorphic populations. This fine-scale genetic perspective on life history variation establishes a framework for understanding how plasticity, local adaptation, and gene flow contribute to lineage divergence. Many members of the tiger salamander complex are endangered, and the Mexican axolotl is an important model system in regenerative and biomedical research. Our results chart a course for more informed use of these taxa in experimental, ecological, and conservation research.}, } @article {pmid33883743, year = {2021}, author = {Réjou-Méchain, M and Mortier, F and Bastin, JF and Cornu, G and Barbier, N and Bayol, N and Bénédet, F and Bry, X and Dauby, G and Deblauwe, V and Doucet, JL and Doumenge, C and Fayolle, A and Garcia, C and Kibambe Lubamba, JP and Loumeto, JJ and Ngomanda, A and Ploton, P and Sonké, B and Trottier, C and Vimal, R and Yongo, O and Pélissier, R and Gourlet-Fleury, S}, title = {Unveiling African rainforest composition and vulnerability to global change.}, journal = {Nature}, volume = {593}, number = {7857}, pages = {90-94}, pmid = {33883743}, issn = {1476-4687}, mesh = {Acclimatization ; Africa, Central ; Datasets as Topic ; Flowers ; Global Warming/*statistics & numerical data ; Human Activities ; Humans ; Population Growth ; *Rainforest ; Seasons ; Sustainable Development ; Temperature ; Trees/*classification/growth & development ; }, abstract = {Africa is forecasted to experience large and rapid climate change[1] and population growth[2] during the twenty-first century, which threatens the world's second largest rainforest. Protecting and sustainably managing these African forests requires an increased understanding of their compositional heterogeneity, the environmental drivers of forest composition and their vulnerability to ongoing changes. Here, using a very large dataset of 6 million trees in more than 180,000 field plots, we jointly model the distribution in abundance of the most dominant tree taxa in central Africa, and produce continuous maps of the floristic and functional composition of central African forests. Our results show that the uncertainty in taxon-specific distributions averages out at the community level, and reveal highly deterministic assemblages. We uncover contrasting floristic and functional compositions across climates, soil types and anthropogenic gradients, with functional convergence among types of forest that are floristically dissimilar. Combining these spatial predictions with scenarios of climatic and anthropogenic global change suggests a high vulnerability of the northern and southern forest margins, the Atlantic forests and most forests in the Democratic Republic of the Congo, where both climate and anthropogenic threats are expected to increase sharply by 2085. These results constitute key quantitative benchmarks for scientists and policymakers to shape transnational conservation and management strategies that aim to provide a sustainable future for central African forests.}, } @article {pmid33883555, year = {2021}, author = {Broennimann, O and Petitpierre, B and Chevalier, M and González-Suárez, M and Jeschke, JM and Rolland, J and Gray, SM and Bacher, S and Guisan, A}, title = {Distance to native climatic niche margins explains establishment success of alien mammals.}, journal = {Nature communications}, volume = {12}, number = {1}, pages = {2353}, pmid = {33883555}, issn = {2041-1723}, mesh = {Animals ; Bayes Theorem ; *Climate ; Databases, Factual ; Ecosystem ; *Introduced Species ; *Mammals ; *Models, Biological ; Population Dynamics ; }, abstract = {One key hypothesis explaining the fate of exotic species introductions posits that the establishment of a self-sustaining population in the invaded range can only succeed within conditions matching the native climatic niche. Yet, this hypothesis remains untested for individual release events. Using a dataset of 979 introductions of 173 mammal species worldwide, we show that climate-matching to the realized native climatic niche, measured by a new Niche Margin Index (NMI), is a stronger predictor of establishment success than most previously tested life-history attributes and historical factors. Contrary to traditional climatic suitability metrics derived from species distribution models, NMI is based on niche margins and provides a measure of how distant a site is inside or, importantly, outside the niche. Besides many applications in research in ecology and evolution, NMI as a measure of native climatic niche-matching in risk assessments could improve efforts to prevent invasions and avoid costly eradications.}, } @article {pmid33880762, year = {2021}, author = {Zeng, T and Yu, X and Chen, Z}, title = {Applying artificial intelligence in the microbiome for gastrointestinal diseases: A review.}, journal = {Journal of gastroenterology and hepatology}, volume = {36}, number = {4}, pages = {832-840}, doi = {10.1111/jgh.15503}, pmid = {33880762}, issn = {1440-1746}, support = {2017SHZDZX01//Shanghai Municipal Science and Technology Major Project/ ; 61803360//National Natural Science Foundation of China/ ; 11871456//National Natural Science Foundation of China/ ; XDB38050200//Strategic Priority Research Program of Chinese Academy of Sciences/ ; }, mesh = {Artificial Intelligence/*trends ; *Big Data ; Datasets as Topic ; Gastrointestinal Diseases/*etiology/*microbiology ; *Gastrointestinal Microbiome ; Information Storage and Retrieval/*methods ; }, abstract = {For a long time, gut bacteria have been recognized for their important roles in the occurrence and progression of gastrointestinal diseases like colorectal cancer, and the ever-increasing amounts of microbiome data combined with other high-quality clinical and imaging datasets are leading the study of gastrointestinal diseases into an era of biomedical big data. The "omics" technologies used for microbiome analysis continuously evolve, and the machine learning or artificial intelligence technologies are key to extract the relevant information from microbiome data. This review intends to provide a focused summary of recent research and applications of microbiome big data and to discuss the use of artificial intelligence to combat gastrointestinal diseases.}, } @article {pmid33879798, year = {2021}, author = {Whon, TW and Ahn, SW and Yang, S and Kim, JY and Kim, YB and Kim, Y and Hong, JM and Jung, H and Choi, YE and Lee, SH and Roh, SW}, title = {ODFM, an omics data resource from microorganisms associated with fermented foods.}, journal = {Scientific data}, volume = {8}, number = {1}, pages = {113}, pmid = {33879798}, issn = {2052-4463}, support = {KE2101-2//World Institute of Kimchi (WIK)/ ; }, mesh = {Archaea/genetics ; Bacteria/genetics ; Data Management/*methods ; *Databases, Genetic ; Fermented Foods/*microbiology ; *Metagenome ; Viruses/genetics ; }, abstract = {ODFM is a data management system that integrates comprehensive omics information for microorganisms associated with various fermented foods, additive ingredients, and seasonings (e.g. kimchi, Korean fermented vegetables, fermented seafood, solar salt, soybean paste, vinegar, beer, cheese, sake, and yogurt). The ODFM archives genome, metagenome, metataxonome, and (meta)transcriptome sequences of fermented food-associated bacteria, archaea, eukaryotic microorganisms, and viruses; 131 bacterial, 38 archaeal, and 28 eukaryotic genomes are now available to users. The ODFM provides both the Basic Local Alignment Search Tool search-based local alignment function as well as average nucleotide identity-based genetic relatedness measurement, enabling gene diversity and taxonomic analyses of an input query against the database. Genome sequences and annotation results of microorganisms are directly downloadable, and the microbial strains registered in the archive library will be available from our culture collection of fermented food-associated microorganisms. The ODFM is a comprehensive database that covers the genomes of an entire microbiome within a specific food ecosystem, providing basic information to evaluate microbial isolates as candidate fermentation starters for fermented food production.}, } @article {pmid33877954, year = {2021}, author = {Kobayashi, K and Jo, T and Mimura, W and Suzukawa, M and Ohshima, N and Tanaka, G and Akazawa, M and Matsui, H and Fushimi, K and Yasunaga, H and Nagase, T and Nagai, H}, title = {Interrupted time-series analyses of routine vaccination program for elderly pneumonia patients in Japan; an ecological study using aggregated nationwide inpatient data.}, journal = {Human vaccines & immunotherapeutics}, volume = {17}, number = {8}, pages = {2661-2669}, pmid = {33877954}, issn = {2164-554X}, mesh = {Aged ; Humans ; Immunization Programs ; Inpatients ; Japan/epidemiology ; *Pneumococcal Infections ; Pneumococcal Vaccines ; *Pneumonia, Pneumococcal/epidemiology/prevention & control ; Vaccination ; }, abstract = {A national routine pneumococcal pneumonia immunization program started in Japan in 2014. It targeted the population aged ≥65 years and used a 23-valent pneumococcal polysaccharide vaccine; PPSV23. However, its effectiveness was not well defined because of the lack of a comprehensive database on the PPSV23 vaccination status of each subject. We used interrupted time-series analyses to assess the changes in the incidence and prognosis of elderly patients hospitalized for pneumonia before and after initiation of the program. First, we estimated the PPSV23 coverage rates in subjects aged ≥65 years based on the number of shipped PPSV23 syringes and the estimated population in each prefecture. The estimated coverage rates reached around 40% in 2014 for the 3 Tohoku prefectures, while those in the other prefectures remained below 20%. After the national routine immunization program started, the estimated coverage rate increased significantly in every prefecture and exceeded 40% in 2017. Next, we aggregated the data extracted from the Japanese Diagnosis Procedure Combination database from April 2011 through February 2017 for hospitalized pneumonia patients aged ≥65 years. The data included data from 655,746 patients, excluding those in the 3 Tohoku prefectures. Interrupted time-series analyses found no change in the incidence of hospitalized pneumonia patients and in-hospital mortality after the vaccination program, but there was a decrease in the in-hospital mortality of pneumonia patients with severe comorbidities defined by the modified Charlson comorbidity index. These results suggest an association between the vaccination program and an improved outcome in hospitalized elderly pneumonia patients with severe comorbidities in Japan.}, } @article {pmid33872774, year = {2021}, author = {Monticelli, M and Mele, BH and Andreotti, G and Cubellis, MV and Riccio, G}, title = {Why does SARS-CoV-2 hit in different ways? Host genetic factors can influence the acquisition or the course of COVID-19.}, journal = {European journal of medical genetics}, volume = {64}, number = {6}, pages = {104227}, pmid = {33872774}, issn = {1878-0849}, mesh = {COVID-19/*genetics/*immunology ; Data Mining ; Gene Frequency ; *Genetic Predisposition to Disease ; Genetic Variation ; Host Microbial Interactions ; Humans ; *Immunity, Innate ; Mannose-Binding Lectin/genetics/immunology ; Polymorphism, Single Nucleotide ; Risk Factors ; SARS-CoV-2/*pathogenicity ; Serine Endopeptidases/genetics/immunology ; Tumor Necrosis Factor Receptor Superfamily, Member 7/genetics/immunology ; }, abstract = {The identification of high-risk factors for the infection by SARS-CoV-2 and the negative outcome of COVID-19 is crucial. The genetic background of the host might account for individual responses to SARS-CoV-2 infection besides age and comorbidities. A list of candidate polymorphisms is needed to drive targeted screens, given the existence of frequent polymorphisms in the general population. We carried out text mining in the scientific literature to draw up a list of genes referable to the term "SARS-CoV*". We looked for frequent mutations that are likely to affect protein function in these genes. Ten genes, mostly involved in innate immunity, and thirteen common variants were identified, for some of these the involvement in COVID-19 is supported by publicly available epidemiological data. We looked for available data on the population distribution of these variants and we demonstrated that the prevalence of five of them, Arg52Cys (rs5030737), Gly54Asp (rs1800450) and Gly57Glu (rs1800451) in MBL2, Ala59Thr (rs25680) in CD27, and Val197Met (rs12329760) in TMPRSS2, correlates with the number of cases and/or deaths of COVID-19 observed in different countries. The association of the TMPRSS2 variant provides epidemiological evidence of the usefulness of transmembrane protease serine 2 inhibitors for the cure of COVID-19. The identified genetic variants represent a basis for the design of a cost-effective assay for population screening of genetic risk factors in the COVID-19 pandemic.}, } @article {pmid33871638, year = {2021}, author = {Muyle, A and Ross-Ibarra, J and Seymour, DK and Gaut, BS}, title = {Gene body methylation is under selection in Arabidopsis thaliana.}, journal = {Genetics}, volume = {218}, number = {2}, pages = {}, pmid = {33871638}, issn = {1943-2631}, mesh = {Alleles ; Arabidopsis/*genetics ; Cytosine/metabolism ; *DNA Methylation ; Datasets as Topic ; *Epigenesis, Genetic ; Gene Expression Profiling ; *Gene Expression Regulation, Plant ; Genes, Plant ; Plant Leaves ; *Selection, Genetic ; }, abstract = {In plants, mammals and insects, some genes are methylated in the CG dinucleotide context, a phenomenon called gene body methylation (gbM). It has been controversial whether this phenomenon has any functional role. Here, we took advantage of the availability of 876 leaf methylomes in Arabidopsis thaliana to characterize the population frequency of methylation at the gene level and to estimate the site-frequency spectrum of allelic states. Using a population genetics model specifically designed for epigenetic data, we found that genes with ancestral gbM are under significant selection to remain methylated. Conversely, ancestrally unmethylated genes were under selection to remain unmethylated. Repeating the analyses at the level of individual cytosines confirmed these results. Estimated selection coefficients were small, on the order of 4 Nes = 1.4, which is similar to the magnitude of selection acting on codon usage. We also estimated that A. thaliana is losing gbM threefold more rapidly than gaining it, which could be due to a recent reduction in the efficacy of selection after a switch to selfing. Finally, we investigated the potential function of gbM through its link with gene expression. Across genes with polymorphic methylation states, the expression of gene body methylated alleles was consistently and significantly higher than unmethylated alleles. Although it is difficult to disentangle genetic from epigenetic effects, our work suggests that gbM has a small but measurable effect on fitness, perhaps due to its association to a phenotype-like gene expression.}, } @article {pmid35707452, year = {2021}, author = {Werbin, ZR and Hackos, B and Lopez-Nava, J and Dietze, MC and Bhatnagar, JM}, title = {The National Ecological Observatory Network's soil metagenomes: assembly and basic analysis.}, journal = {F1000Research}, volume = {10}, number = {}, pages = {299}, pmid = {35707452}, issn = {2046-1402}, mesh = {Computational Biology/methods ; *Metagenome ; Metagenomics/methods ; Neon ; *Soil ; }, abstract = {The largest dataset of soil metagenomes has recently been released by the National Ecological Observatory Network (NEON), which performs annual shotgun sequencing of soils at 47 sites across the United States. NEON serves as a valuable educational resource, thanks to its open data and programming tutorials, but there is currently no introductory tutorial for accessing and analyzing the soil shotgun metagenomic dataset. Here, we describe methods for processing raw soil metagenome sequencing reads using a bioinformatics pipeline tailored to the high complexity and diversity of the soil microbiome. We describe the rationale, necessary resources, and implementation of steps such as cleaning raw reads, taxonomic classification, assembly into contigs or genomes, annotation of predicted genes using custom protein databases, and exporting data for downstream analysis. The workflow presented here aims to increase the accessibility of NEON's shotgun metagenome data, which can provide important clues about soil microbial communities and their ecological roles.}, } @article {pmid33866357, year = {2021}, author = {Nachtigall, PG and Rautsaw, RM and Ellsworth, SA and Mason, AJ and Rokyta, DR and Parkinson, CL and Junqueira-de-Azevedo, ILM}, title = {ToxCodAn: a new toxin annotator and guide to venom gland transcriptomics.}, journal = {Briefings in bioinformatics}, volume = {22}, number = {5}, pages = {}, doi = {10.1093/bib/bbab095}, pmid = {33866357}, issn = {1477-4054}, mesh = {*Algorithms ; Animals ; Computational Biology/*methods ; Gene Expression Profiling/*methods ; High-Throughput Nucleotide Sequencing/methods ; Phylogeny ; Snake Venoms/chemistry/*genetics/metabolism ; Snakes/classification/*genetics/metabolism ; Species Specificity ; Toxins, Biological/chemistry/*genetics/metabolism ; }, abstract = {MOTIVATION: Next-generation sequencing has become exceedingly common and has transformed our ability to explore nonmodel systems. In particular, transcriptomics has facilitated the study of venom and evolution of toxins in venomous lineages; however, many challenges remain. Primarily, annotation of toxins in the transcriptome is a laborious and time-consuming task. Current annotation software often fails to predict the correct coding sequence and overestimates the number of toxins present in the transcriptome. Here, we present ToxCodAn, a python script designed to perform precise annotation of snake venom gland transcriptomes. We test ToxCodAn with a set of previously curated transcriptomes and compare the results to other annotators. In addition, we provide a guide for venom gland transcriptomics to facilitate future research and use Bothrops alternatus as a case study for ToxCodAn and our guide.

RESULTS: Our analysis reveals that ToxCodAn provides precise annotation of toxins present in the transcriptome of venom glands of snakes. Comparison with other annotators demonstrates that ToxCodAn has better performance with regard to run time ($>20x$ faster), coding sequence prediction ($>3x$ more accurate) and the number of toxins predicted (generating $>4x$ less false positives). In this sense, ToxCodAn is a valuable resource for toxin annotation. The ToxCodAn framework can be expanded in the future to work with other venomous lineages and detect novel toxins.}, } @article {pmid33863805, year = {2021}, author = {Hao, Y and Mabry, ME and Edger, PP and Freeling, M and Zheng, C and Jin, L and VanBuren, R and Colle, M and An, H and Abrahams, RS and Washburn, JD and Qi, X and Barry, K and Daum, C and Shu, S and Schmutz, J and Sankoff, D and Barker, MS and Lyons, E and Pires, JC and Conant, GC}, title = {The contributions from the progenitor genomes of the mesopolyploid Brassiceae are evolutionarily distinct but functionally compatible.}, journal = {Genome research}, volume = {31}, number = {5}, pages = {799-810}, pmid = {33863805}, issn = {1549-5469}, mesh = {Evolution, Molecular ; *Genome ; Genome, Plant ; Humans ; Hybridization, Genetic ; Phylogeny ; *Polyploidy ; }, abstract = {The members of the tribe Brassiceae share a whole-genome triplication (WGT), and one proposed model for its formation is a two-step pair of hybridizations producing hexaploid descendants. However, evidence for this model is incomplete, and the evolutionary and functional constraints that drove evolution after the hexaploidy are even less understood. Here, we report a new genome sequence of Crambe hispanica, a species sister to most sequenced Brassiceae. Using this new genome and three others that share the hexaploidy, we traced the history of gene loss after the WGT using the Polyploidy Orthology Inference Tool (POInT). We confirm the two-step formation model and infer that there was a significant temporal gap between those two allopolyploidizations, with about a third of the gene losses from the first two subgenomes occurring before the arrival of the third. We also, for the 90,000 individual genes in our study, make parental subgenome assignments, inferring, with measured uncertainty, from which of the progenitor genomes of the allohexaploidy each gene derives. We further show that each subgenome has a statistically distinguishable rate of homoeolog losses. There is little indication of functional distinction between the three subgenomes: the individual subgenomes show no patterns of functional enrichment, no excess of shared protein-protein or metabolic interactions between their members, and no biases in their likelihood of having experienced a recent selective sweep. We propose a "mix and match" model of allopolyploidy, in which subgenome origin drives homoeolog loss propensities but where genes from different subgenomes function together without difficulty.}, } @article {pmid33862346, year = {2021}, author = {Allen, T and Wilson, S and Cohen, DD and Taberner, M}, title = {Drill design using the 'control-chaos continuum': Blending science and art during return to sport following knee injury in elite football.}, journal = {Physical therapy in sport : official journal of the Association of Chartered Physiotherapists in Sports Medicine}, volume = {50}, number = {}, pages = {22-35}, doi = {10.1016/j.ptsp.2021.02.011}, pmid = {33862346}, issn = {1873-1600}, mesh = {Athletic Injuries/*rehabilitation ; Exercise Therapy/*methods ; Geographic Information Systems ; Humans ; Knee Injuries/*rehabilitation ; *Return to Sport ; Running ; Soccer/*injuries ; }, abstract = {Establishing the level of risk, planning and adapting the return to sport (RTS) process following a complex knee injury involves drawing on a combination of relevant high-quality evidence and practitioner experience. On-pitch rehabilitation is a critical element of this process, providing an effective transition from rehabilitation to team training. The 'control-chaos continuum' (CCC) is an adaptable framework for on-pitch rehabilitation moving from high control to high chaos, progressively increasing running load demands and incorporating greater perceptual and neurocognitive challenges within sport-specific drills. Drills are a key element of the CCC, and are designed to ensure specificity, ecological validity and maintaining player interest. We showcase drill progression through the phases of the CCC, highlighting the use of constraints to create drills that incorporate the physical, technical, tactical and injury-specific needs of the player. We also provide recommendations to help practitioners create training session content using the CCC to help replicate the demands of team training within their own environment.}, } @article {pmid33862123, year = {2021}, author = {Qiu, S and Zhong, C and Zhao, B and Li, G and Wang, J and Jehan, S and Li, J and Zhao, X and Li, D and Sui, G}, title = {Transcriptome analysis of signaling pathways targeted by Ellagic acid in hepatocellular carcinoma cells.}, journal = {Biochimica et biophysica acta. General subjects}, volume = {1865}, number = {7}, pages = {129911}, doi = {10.1016/j.bbagen.2021.129911}, pmid = {33862123}, issn = {1872-8006}, mesh = {Apoptosis ; Biomarkers, Tumor/genetics/*metabolism ; Carcinoma, Hepatocellular/drug therapy/genetics/*metabolism/pathology ; Cell Proliferation ; Computational Biology ; Ellagic Acid/*pharmacology ; Gene Expression Regulation, Neoplastic/*drug effects ; Gene Regulatory Networks ; Hep G2 Cells ; Humans ; Liver Neoplasms/drug therapy/genetics/*metabolism/pathology ; RNA-Seq ; Transcriptome/*drug effects ; }, abstract = {BACKGROUND: Ellagic acid (EA) possesses prominent inhibitory activities against various cancers, including hepatocellular carcinoma (HCC). Our recent study demonstrated EA's activities in reducing HCC cell proliferation and tumor formation. However, the mechanisms of EA to exert its anticancer activities and its primary targets in cancer cells have not been systematically explored.

METHODS: Cell proliferation assay and flow cytometric analysis were used to examine the effects of EA treatment on viability and apoptosis, respectively, of HepG2 cells. RNA-seq studies and associated pathway analyses by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) were employed to determine EA's primary targets. Differentially expressed genes (DEG) in EA-treated HepG2 cells were verified by RT-qPCR and Western blot. Integrative analyses of the RNA-seq dataset with a TCGA dataset derived from HCC patients were conducted to verify EA-targeted genes and signaling pathways. Interaction network analysis of the DEGs, shRNA-mediated knockdown, cell viability assay, and colony formation assay were used to validate EA's primary targets.

RESULTS: EA reduced cell viability, caused DNA damage, and induced cell cycle arrest at G1 phase of HepG2 cells. We identified 5765 DEGs encoding proteins with over 2.0-fold changes in EA-treated HepG2 cells by DESeq2. These DEGs showed significant enrichment in the pathways regulating DNA replication and cell cycle progression. As primary targets, p21 was significantly upregulated, while MCM2-7 were uniformly downregulated in response to EA treatment. Consistently, p21 knockdown desensitized liver cells to EA in cell viability and colony formation assays.

CONCLUSION: EA induced G1 phase arrest and promoted apoptosis of HCC cells through activating the p21 gene and downregulating the MCM2-7 genes, respectively.

GENERAL SIGNIFICANCE: The discoveries in this study provide helpful insights into developing novel strategies in the therapeutic treatment of HCC patients.}, } @article {pmid33862097, year = {2021}, author = {Wang, KL and Chen, SN and Huo, HJ and Nie, P}, title = {Identification and expression analysis of sixteen Toll-like receptor genes, TLR1, TLR2a, TLR2b, TLR3, TLR5M, TLR5S, TLR7-9, TLR13a-c, TLR14, TLR21-23 in mandarin fish Siniperca chuatsi.}, journal = {Developmental and comparative immunology}, volume = {121}, number = {}, pages = {104100}, doi = {10.1016/j.dci.2021.104100}, pmid = {33862097}, issn = {1879-0089}, mesh = {Animals ; Computational Biology ; Fish Diseases/*immunology ; Fish Proteins/genetics/*metabolism ; Fishes/genetics/*immunology ; Gene Expression Profiling ; Head Kidney/cytology/immunology/metabolism ; Immunity, Innate ; Lipopolysaccharides/immunology ; Lymphocytes/immunology/metabolism ; Phylogeny ; Poly I-C/immunology ; Protein Domains/genetics ; Sequence Analysis, DNA ; Toll-Like Receptors/genetics/*metabolism ; Up-Regulation/immunology ; }, abstract = {Toll-like receptors (TLRs), as a family of pattern recognition receptors (PRRs), possess specific pathogen-related molecular pattern (PAMP) recognition spectrum in inducing immune responses. In this study, sixteen TLRs were identified and characterized in mandarin fish (Siniperca chuatsi). All these TLRs consist of leucine-rich repeats (LRRs), a transmembrane domain and a Toll/interleukin-I receptor (TIR) domain, with the exception of TLR5S which lacks TIR domain, and they can be clustered into five branches, i.e. TLR1 subfamily, TLR3 subfamily, TLR5 subfamily, TLR7 subfamily and TLR11 subfamily in phylogenetic tree. These TLR genes were expressed in all tested tissues and had high expression levels in immune-related tissues such as head-kidney and spleen or mucosa-related tissues such as intestine and pyloric caecum. The transcripts of TLR2a, TLR2b, TLR3, TLR13a, TLR14, TLR22 and TLR23 were all significantly up-regulated after stimulation with poly(I:C); TLR1, TLR2a, TLR2b, TLR3, TLR5M, TLR5S, TLR13a and TLR13b transcripts were all significantly up-regulated after stimulation with PGN; and TLR2a, TLR2b, TLR5M, TLR5S, TLR7, TLR8, TLR9, TLR13c, TLR14 and TLR22 transcripts were all significantly up-regulated after stimulation with LPS in isolated head kidney lymphocytes of mandarin fish. The findings in this study may provide a valuable basis for functional study on TLR genes in mandarin fish.}, } @article {pmid33861764, year = {2021}, author = {Fatemi, M and Rezaei-Moghaddam, K and Karami, E and Hayati, D and Wackernagel, M}, title = {An integrated approach of Ecological Footprint (EF) and Analytical Hierarchy Process (AHP) in human ecology: A base for planning toward sustainability.}, journal = {PloS one}, volume = {16}, number = {4}, pages = {e0250167}, pmid = {33861764}, issn = {1932-6203}, mesh = {Agriculture ; Analytic Hierarchy Process ; Conservation of Natural Resources/*methods ; Ecological and Environmental Phenomena ; Ecology ; Farmers ; Humans ; Iran ; Natural Resources ; Pilot Projects ; Reproducibility of Results ; Surveys and Questionnaires ; Sustainable Development/economics/*trends ; }, abstract = {Environmental challenges to natural resources have been attributed to human behavior and traditional agricultural production techniques. Natural resource degradation in agriculture has always been a prime concern in agro ecological research and sustainability analysis. There are many techniques for assessing environmental performance; one of which, ecological footprint (EF), assesses human pressure on the environment and natural resources. The main purpose of this study was calculation of ecological indices including biocapacity (BC) and EF of rural areas of Fars province of Iran. The study was accomplished using survey and structured interviews consisting of three main questionnaires in two different steps. Different agricultural stakeholders, including farmers (for the first step) as well as the policymakers, extension managers and authorities (for the second step) were interviewed. Based on multi-stage stratified random sampling, 50 villages and 423 farmers were selected. Face validity and reliability of the questionnaires were assessed by a panel of specialists as well as conducting a pilot study, respectively. The paradigmatic perspectives of agricultural policy makers and managers (22 individuals) were also analyzed using another specific questionnaire by Analytical Hierarchy Process (AHP). Findings revealed that most of the studied villages faced a critical environmental condition due to the results of ecological indicator which was calculated in the study. According to the four main components of human ecology (POET model) including Population, Organization, Environment and Technology, village groups that differed in terms of sustainability level also showed significantly differences due to population, social participation, use of green technologies and attitude towards diverse environmental management paradigms. The causal model also revealed that population, green technology, social participation and attitude toward frontier economics, which were in accordance with the elements of human ecology model, were the main factors affecting the ecological index. Finally, AHP results determined the dominant economic perspectives of agricultural authorities. A paradigm shift toward the comprehensive paradigm of eco-development plus consideration of the results of the ecological indicator calculation as the base of agricultural planning at the local level were recommended.}, } @article {pmid33860294, year = {2021}, author = {Schweizer, RM and Saarman, N and Ramstad, KM and Forester, BR and Kelley, JL and Hand, BK and Malison, RL and Ackiss, AS and Watsa, M and Nelson, TC and Beja-Pereira, A and Waples, RS and Funk, WC and Luikart, G}, title = {Big Data in Conservation Genomics: Boosting Skills, Hedging Bets, and Staying Current in the Field.}, journal = {The Journal of heredity}, volume = {112}, number = {4}, pages = {313-327}, doi = {10.1093/jhered/esab019}, pmid = {33860294}, issn = {1465-7333}, support = {DOB-1639014//National Science Foundation/ ; IOS-NSF 1755411//National Science Foundation/ ; }, mesh = {*Big Data ; Biological Evolution ; *Conservation of Natural Resources ; Genetics, Population ; Genomics ; Humans ; }, abstract = {A current challenge in the fields of evolutionary, ecological, and conservation genomics is balancing production of large-scale datasets with additional training often required to handle such datasets. Thus, there is an increasing need for conservation geneticists to continually learn and train to stay up-to-date through avenues such as symposia, meetings, and workshops. The ConGen meeting is a near-annual workshop that strives to guide participants in understanding population genetics principles, study design, data processing, analysis, interpretation, and applications to real-world conservation issues. Each year of ConGen gathers a diverse set of instructors, students, and resulting lectures, hands-on sessions, and discussions. Here, we summarize key lessons learned from the 2019 meeting and more recent updates to the field with a focus on big data in conservation genomics. First, we highlight classical and contemporary issues in study design that are especially relevant to working with big datasets, including the intricacies of data filtering. We next emphasize the importance of building analytical skills and simulating data, and how these skills have applications within and outside of conservation genetics careers. We also highlight recent technological advances and novel applications to conservation of wild populations. Finally, we provide data and recommendations to support ongoing efforts by ConGen organizers and instructors-and beyond-to increase participation of underrepresented minorities in conservation and eco-evolutionary sciences. The future success of conservation genetics requires both continual training in handling big data and a diverse group of people and approaches to tackle key issues, including the global biodiversity-loss crisis.}, } @article {pmid33859237, year = {2021}, author = {Ma, ZS}, title = {A unified survival-analysis approach to insect population development and survival times.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {8223}, pmid = {33859237}, issn = {2045-2322}, mesh = {Animals ; Aphids/growth & development/physiology ; Computational Biology ; Entomology/methods ; Insecta/*growth & development/physiology ; Longevity/*physiology ; Probability ; Proportional Hazards Models ; Survival Analysis ; Survival Rate ; Time Factors ; Triticum/parasitology ; }, abstract = {There are two major categories of observation data in studying time-dependent processes: one is the time-series data, and the other is the perhaps lesser-recognized but similarly prevalent time-to-event data (also known as survival or failure time). Examples in entomology include molting times and death times of insects, waiting times of predators before the next attack or the hiding times of preys. A particular challenge in analyzing time-to-event data is the observation censoring, or the incomplete observation of survival times, dealing which is a unique advantage of survival analysis statistics. Even with a perfectly designed experiment being conducted perfectly, such 'naturally' censoring may still be unavoidable due to the natural processes, including the premature death in the observation of insect development, the variability in instarship, or simply the continuous nature of time process and the discrete nature of sampling intervals. Here we propose to apply the classic Cox proportional hazards model for modeling both insect development and survival rates (probabilities) with a unified survival analysis approach. We demonstrated the advantages of the proposed approach with the development and survival datasets of 1800 Russian wheat aphids from their births to deaths, observed under 25 laboratory treatments of temperatures and plant growth stages.}, } @article {pmid33858386, year = {2021}, author = {Kiani, B and Hashemi Amin, F and Bagheri, N and Bergquist, R and Mohammadi, AA and Yousefi, M and Faraji, H and Roshandel, G and Beirami, S and Rahimzadeh, H and Hoseini, B}, title = {Association between heavy metals and colon cancer: an ecological study based on geographical information systems in North-Eastern Iran.}, journal = {BMC cancer}, volume = {21}, number = {1}, pages = {414}, pmid = {33858386}, issn = {1471-2407}, mesh = {Colonic Neoplasms/*epidemiology/*etiology ; Disease Susceptibility ; Female ; Geographic Information Systems ; Geography, Medical ; Humans ; Iran/epidemiology ; Male ; Metals, Heavy/*adverse effects ; Population Surveillance ; Spatial Analysis ; Trace Elements ; }, abstract = {BACKGROUND: Colorectal cancer has increased in Middle Eastern countries and exposure to environmental pollutants such as heavy metals has been implicated. However, data linking them to this disease are generally lacking. This study aimed to explore the spatial pattern of age-standardized incidence rate (ASR) of colon cancer and its potential association with the exposure level of the amount of heavy metals existing in rice produced in north-eastern Iran.

METHODS: Cancer data were drawn from the Iranian population-based cancer registry of Golestan Province, north-eastern Iran. Samples of 69 rice milling factories were analysed for the concentration levels of cadmium, nickel, cobalt, copper, selenium, lead and zinc. The inverse distance weighting (IDW) algorithm was used to interpolate the concentration of this kind of heavy metals on the surface of the study area. Exploratory regression analysis was conducted to build ordinary least squares (OLS) models including every possible combination of the candidate explanatory variables and chose the most useful ones to show the association between heavy metals and the ASR of colon cancer.

RESULTS: The highest concentrations of heavy metals were found in the central part of the province and particularly counties with higher amount of cobalt were shown to be associated with higher ASR of men with colon cancer. In contrast, selenium concentrations were higher in areas with lower ASR of colon cancer in men. A significant regression equation for men with colon cancer was found (F(4,137) = 38.304, P < .000) with an adjusted R[2] of 0.77. The predicted ASR of men colon cancer was - 58.36 with the coefficients for cobalt = 120.33; cadmium = 80.60; selenium = - 6.07; nickel = - 3.09; and zinc = - 0.41. The association of copper and lead with colon cancer in men was not significant. We did not find a significant outcome for colon cancer in women.

CONCLUSION: Increased amounts of heavy metals in consumed rice may impact colon cancer incidence, both positively and negatively. While there were indications of an association between high cobalt concentrations and an increased risk for colon cancer, we found that high selenium concentrations might instead decrease the risk. Further investigations are needed to clarify if there are ecological or other reasons for these discrepancies. Regular monitoring of the amount of heavy metals in consumed rice is recommended.}, } @article {pmid33857642, year = {2021}, author = {Sheehan, MJ and Miller, SE}, title = {The promises and challenges of archiving insect behavior and natural history in a changing world.}, journal = {Current opinion in insect science}, volume = {45}, number = {}, pages = {115-120}, pmid = {33857642}, issn = {2214-5753}, support = {DP2 GM128202/GM/NIGMS NIH HHS/United States ; F32 GM101863/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; *Behavior, Animal ; *Data Curation ; *Ecology ; *Entomology ; *Ethology ; *Insecta ; *Life History Traits ; Natural History ; }, abstract = {Insect behavioral ecologists are not routinely archiving their behavioral media files and natural history observations. This is especially problematic because most behaviors are not preserved by the physical specimens stored in typical natural history collections. Improving the reporting and archiving of insect behavior and natural history data holds the promise of allowing scientists to track real-time responses of animals to global change and will preserve aspects of natural history that might otherwise be lost due to extinctions. Here we argue that behavioral ecologists should work to preserve and archive raw media files and field notes related to behavior and natural history of their study organisms. One major mechanism to incentivize archiving of such data would be for journals to develop policies for archiving of natural history data that is the focus of the paper or ancillary information collected about study subjects. Buy in from researchers, journals, and funding agencies will be needed to make substantial changes in data archiving.}, } @article {pmid33857526, year = {2021}, author = {Diego, D and Hannisdal, B and Dahle, H}, title = {On how the power supply shapes microbial survival.}, journal = {Mathematical biosciences}, volume = {338}, number = {}, pages = {108615}, doi = {10.1016/j.mbs.2021.108615}, pmid = {33857526}, issn = {1879-3134}, mesh = {Electric Power Supplies ; *Microbial Viability ; *Microbiota/physiology ; *Models, Biological ; Population Dynamics ; }, abstract = {Understanding how environmental factors affect microbial survival is an important open problem in microbial ecology. Patterns of microbial community structure have been characterized across a wide range of different environmental settings, but the mechanisms generating these patterns remain poorly understood. Here, we use mathematical modelling to investigate fundamental connections between chemical power supply to a system and patterns of microbial survival. We reveal a complex set of interdependences between power supply and distributions of survival probability across microbial habitats, in a case without interspecific resource competition. We also find that different properties determining power supply, such as substrate fluxes and Gibbs energies of reactions, affect microbial survival in fundamentally different ways. Moreover, we show how simple connections between power supply and growth can give rise to complex patterns of microbial survival across physicochemical gradients, such as pH gradients. Our findings show the importance of taking energy fluxes into account in order to reveal fundamental connections between microbial survival and environmental conditions, and to obtain a better understanding of microbial population dynamics in natural environments.}, } @article {pmid33855273, year = {2021}, author = {Zhang, B and Hughes, RM and Davis, WS and Cao, C}, title = {Big data challenges in overcoming China's water and air pollution: relevant data and indicators.}, journal = {SN applied sciences}, volume = {3}, number = {4}, pages = {469}, pmid = {33855273}, issn = {2523-3971}, abstract = {Big data are potentially useful for environmental management planning and actions that can be directed toward pollution control. China is using big data approaches to help reduce its current levels of pollution. However, also needed are better environmental indicators, measurement technologies, data management and reporting, and adaptive management and enforcement. Based on continental-extent monitoring and assessment programs in Europe and the USA, we recommend three major programmatic changes for China. (1) Establish long-term systemic environmental and human health objectives and indicators. (2) Adopt national standard methods for survey designs, sampling and analytical protocols, statistical analyses, and collaborative sampling programs. (3) Provide a transparent process for reporting and correcting data errors.}, } @article {pmid33854906, year = {2021}, author = {Shams-White, MM and D'Angelo, H and Perez, LG and Dwyer, LA and Stinchcomb, DG and Oh, AY}, title = {A national examination of neighborhood socio-economic disparities in built environment correlates of youth physical activity.}, journal = {Preventive medicine reports}, volume = {22}, number = {}, pages = {101358}, pmid = {33854906}, issn = {2211-3355}, abstract = {Adolescents in the U.S. do not meet current physical activity guidelines. Ecological models of physical activity posit that factors across multiple levels may support physical activity by promoting walkability, such as the neighborhood built environment and neighborhood socioeconomic status (nSES). We examined associations between neighborhood built environment factors and adolescent moderate-to-vigorous physical activity (MVPA), and whether nSES moderated associations. Data were drawn from a national sample of adolescents (12-17 years, N = 1295) surveyed in 2014. MVPA (minutes/week) were estimated from self-report validated by accelerometer data. Adolescents' home addresses were geocoded and linked to Census data from which a nSES Index and home neighborhood factors were derived using factor analysis (high density, older homes, short auto commutes). Multiple linear regression models examined associations between neighborhood factors and MVPA, and tested interactions between quintiles of nSES and each neighborhood factor, adjusting for socio-demographics. Living in higher density neighborhoods (B(SE): 9.22 (2.78), p = 0.001) and neighborhoods with more older homes (4.42 (1.85), p = 0.02) were positively associated with adolescent MVPA. Living in neighborhoods with shorter commute times was negatively associated with MVPA (-5.11 (2.34), p = 0.03). Positive associations were found between MVPA and the high density and older homes neighborhood factors, though associations were not consistent across quintiles. In conclusion, living in neighborhoods with walkable attributes was associated with greater adolescent MVPA, though the effects were not distributed equally across nSES. Adolescents living in lower SES neighborhoods may benefit more from physical activity interventions and environmental supports that provide opportunities to be active beyond neighborhood walkability.}, } @article {pmid33854233, year = {2021}, author = {Choin, J and Mendoza-Revilla, J and Arauna, LR and Cuadros-Espinoza, S and Cassar, O and Larena, M and Ko, AM and Harmant, C and Laurent, R and Verdu, P and Laval, G and Boland, A and Olaso, R and Deleuze, JF and Valentin, F and Ko, YC and Jakobsson, M and Gessain, A and Excoffier, L and Stoneking, M and Patin, E and Quintana-Murci, L}, title = {Genomic insights into population history and biological adaptation in Oceania.}, journal = {Nature}, volume = {592}, number = {7855}, pages = {583-589}, pmid = {33854233}, issn = {1476-4687}, mesh = {Adaptation, Biological/*genetics ; Animals ; Australia ; *Biological Evolution ; Datasets as Topic ; Asia, Eastern ; Genetic Introgression ; *Genetics, Population ; Genome, Human/*genetics ; *Genomics ; History, Ancient ; Human Migration/*history ; Humans ; *Islands ; Neanderthals/genetics ; Oceania ; Pacific Ocean ; Taiwan ; }, abstract = {The Pacific region is of major importance for addressing questions regarding human dispersals, interactions with archaic hominins and natural selection processes[1]. However, the demographic and adaptive history of Oceanian populations remains largely uncharacterized. Here we report high-coverage genomes of 317 individuals from 20 populations from the Pacific region. We find that the ancestors of Papuan-related ('Near Oceanian') groups underwent a strong bottleneck before the settlement of the region, and separated around 20,000-40,000 years ago. We infer that the East Asian ancestors of Pacific populations may have diverged from Taiwanese Indigenous peoples before the Neolithic expansion, which is thought to have started from Taiwan around 5,000 years ago[2-4]. Additionally, this dispersal was not followed by an immediate, single admixture event with Near Oceanian populations, but involved recurrent episodes of genetic interactions. Our analyses reveal marked differences in the proportion and nature of Denisovan heritage among Pacific groups, suggesting that independent interbreeding with highly structured archaic populations occurred. Furthermore, whereas introgression of Neanderthal genetic information facilitated the adaptation of modern humans related to multiple phenotypes (for example, metabolism, pigmentation and neuronal development), Denisovan introgression was primarily beneficial for immune-related functions. Finally, we report evidence of selective sweeps and polygenic adaptation associated with pathogen exposure and lipid metabolism in the Pacific region, increasing our understanding of the mechanisms of biological adaptation to island environments.}, } @article {pmid33850654, year = {2021}, author = {Zablocki, O and Michelsen, M and Burris, M and Solonenko, N and Warwick-Dugdale, J and Ghosh, R and Pett-Ridge, J and Sullivan, MB and Temperton, B}, title = {VirION2: a short- and long-read sequencing and informatics workflow to study the genomic diversity of viruses in nature.}, journal = {PeerJ}, volume = {9}, number = {}, pages = {e11088}, pmid = {33850654}, issn = {2167-8359}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {Microbes play fundamental roles in shaping natural ecosystem properties and functions, but do so under constraints imposed by their viral predators. However, studying viruses in nature can be challenging due to low biomass and the lack of universal gene markers. Though metagenomic short-read sequencing has greatly improved our virus ecology toolkit-and revealed many critical ecosystem roles for viruses-microdiverse populations and fine-scale genomic traits are missed. Some of these microdiverse populations are abundant and the missed regions may be of interest for identifying selection pressures that underpin evolutionary constraints associated with hosts and environments. Though long-read sequencing promises complete virus genomes on single reads, it currently suffers from high DNA requirements and sequencing errors that limit accurate gene prediction. Here we introduce VirION2, an integrated short- and long-read metagenomic wet-lab and informatics pipeline that updates our previous method (VirION) to further enhance the utility of long-read viral metagenomics. Using a viral mock community, we first optimized laboratory protocols (polymerase choice, DNA shearing size, PCR cycling) to enable 76% longer reads (now median length of 6,965 bp) from 100-fold less input DNA (now 1 nanogram). Using a virome from a natural seawater sample, we compared viromes generated with VirION2 against other library preparation options (unamplified, original VirION, and short-read), and optimized downstream informatics for improved long-read error correction and assembly. VirION2 assemblies combined with short-read based data ('enhanced' viromes), provided significant improvements over VirION libraries in the recovery of longer and more complete viral genomes, and our optimized error-correction strategy using long- and short-read data achieved 99.97% accuracy. In the seawater virome, VirION2 assemblies captured 5,161 viral populations (including all of the virus populations observed in the other assemblies), 30% of which were uniquely assembled through inclusion of long-reads, and 22% of the top 10% most abundant virus populations derived from assembly of long-reads. Viral populations unique to VirION2 assemblies had significantly higher microdiversity means, which may explain why short-read virome approaches failed to capture them. These findings suggest the VirION2 sample prep and workflow can help researchers better investigate the virosphere, even from challenging low-biomass samples. Our new protocols are available to the research community on protocols.io as a 'living document' to facilitate dissemination of updates to keep pace with the rapid evolution of long-read sequencing technology.}, } @article {pmid33846912, year = {2021}, author = {Liu, H and Jiang, Y and Misa, R and Gao, J and Xia, M and Preusse, A and Sroka, A and Jiang, Y}, title = {Ecological environment changes of mining areas around Nansi lake with remote sensing monitoring.}, journal = {Environmental science and pollution research international}, volume = {28}, number = {32}, pages = {44152-44164}, pmid = {33846912}, issn = {1614-7499}, support = {CHN/1101176STP//Alexander von Humboldt-Stiftung/ ; 2016YFC0501105//National Research and Development Project/ ; 2018-TD-MS052//China Coal Technology & Engineering Group Project/ ; }, mesh = {China ; *Coal Mining ; Environmental Monitoring ; *Lakes ; Remote Sensing Technology ; }, abstract = {Underground mining activity has existed for more than 100 years in Nansi lake. Coal mining not only plays a supporting role in local social and economic development but also has a significant impact on the ecological environment in the region. Landsat series remote sensing data (1988~2019) are used to research the impact of coal mining on the ecological environment in Nansi lake. Then support vector machine (SVM) classifier is applied to extract the water area of the upstream lake from 1988 to 2019, and ecological environment and spatiotemporal variation characteristics are analyzed by Remote Sensing Ecology Index (RSEI). The results illustrate that the water area change is associated with annual precipitation. In terms of ecological quality, the area of poor ecological quality areas increased by 101.782 km[2], while the area of good and excellent quality areas decreased by 218.988 km[2] from 2009 to 2019. So compared with 2009, the ecological quality of the lake is worse in 2019, and then the reason for this change is due to large-scale underground mining. Therefore, the coal mines from the natural reserve may be closed or limited to the mining boundary for protecting the lake's ecological environment.}, } @article {pmid33844692, year = {2021}, author = {Michaelson, V and Pilato, KA and Davison, CM}, title = {Family as a health promotion setting: A scoping review of conceptual models of the health-promoting family.}, journal = {PloS one}, volume = {16}, number = {4}, pages = {e0249707}, pmid = {33844692}, issn = {1932-6203}, support = {MOP 341188//CIHR/Canada ; MOP 97962//CIHR/Canada ; }, mesh = {Child ; Culture ; Databases, Factual ; Delivery of Health Care/*methods ; Ecosystem ; Family/*psychology ; Health Promotion/*methods ; Humans ; Models, Theoretical ; }, abstract = {BACKGROUND: The family is a key setting for health promotion. Contemporary health promoting family models can establish scaffolds for shaping health behaviors and can be useful tools for education and health promotion.

OBJECTIVES: The objective of this scoping review is to provide details as to how conceptual and theoretical models of the health promoting potential of the family are being used in health promotion contexts.

DESIGN: Guided by PRISMA ScR guidelines, we used a three-step search strategy to find relevant papers. This included key-word searching electronic databases (Medline, PSycINFO, Embase, and CINAHL), searching the reference lists of included studies, and intentionally searching for grey literature (in textbooks, dissertations, thesis manuscripts and reports.).

RESULTS: After applying inclusion and exclusion criteria, the overall search generated 113 included manuscripts/chapters with 118 unique models. Through our analysis of these models, three main themes were apparent: 1) ecological factors are central components to most models or conceptual frameworks; 2) models were attentive to cultural and other diversities, allowing room for a wide range of differences across family types, and for different and ever-expanding social norms and roles; and 3) the role of the child as a passive recipient of their health journey rather than as an active agent in promoting their own family health was highlighted as an important gap in many of the identified models.

CONCLUSIONS: This review contributes a synthesis of contemporary literature in this area and supports the priority of ecological frameworks and diversity of family contexts. It encourages researchers, practitioners and family stakeholders to recognize the value of the child as an active agent in shaping the health promoting potential of their family context.}, } @article {pmid33840129, year = {2021}, author = {Peng, Y and Li, JS and Zhang, K and Liu, YF and Li, XP and Zhang, H and Gong, L and Liu, LQ and Lü, ZM and Liu, BJ}, title = {Identification of a large dataset of SNPs in hair-fin anchovy (Setipinna tenuifilis) based on RAD-seq.}, journal = {Animal genetics}, volume = {52}, number = {3}, pages = {371-374}, doi = {10.1111/age.13062}, pmid = {33840129}, issn = {1365-2052}, support = {41806156//National Natural Science Foundation of China/ ; 31702321//Zhejiang Provincial Natural Science Foundation of China/ ; LY20C190008//Zhejiang Provincial Natural Science Foundation of China/ ; LMB20201005//Open Foundation from the Key Laboratory of Tropical Marine Bio-resources and Ecology, Chinese Academy of Sciences/ ; 2020C21016//Science and Technology Project of Zhoushan/ ; 20200201//Open Foundation from Marine Sciences in the First-Class Subjects of Zhejiang; Starting Research Fund from the Zhejiang Ocean University/ ; 20200202//Open Foundation from Marine Sciences in the First-Class Subjects of Zhejiang; Starting Research Fund from the Zhejiang Ocean University/ ; }, mesh = {Animals ; China ; Datasets as Topic ; Fishes/*genetics ; *Genetics, Population ; Pacific Ocean ; *Polymorphism, Single Nucleotide ; Sequence Analysis, DNA ; }, abstract = {Hair-fin anchovy (Setipinna tenuifilis) is an economically important fish distributed in the West Indian Ocean and the Northwest Pacific Ocean. In this study, 154 individuals in eight populations of S. tenuifilis were sequenced and 850 million raw reads were obtained using restriction site-associated DNA sequencing (RAD-seq). First, we identified 14 012 044 hypothetical SNP markers. A dataset of 199 903 high-quality SNPs was collected after further screening. These SNPs have a strong ability to test the genetic diversity between the eight populations. The differentiation and genetic law between samples were explored based on SNPs in populations of S. tenuifilis. The results of this study will provide data for protecting the genetic resources of the species.}, } @article {pmid33839662, year = {2021}, author = {Damiani, M and Roux, P and Loiseau, E and Lamouroux, N and Pella, H and Morel, M and Rosenbaum, RK}, title = {A high-resolution life cycle impact assessment model for continental freshwater habitat change due to water consumption.}, journal = {The Science of the total environment}, volume = {782}, number = {}, pages = {146664}, doi = {10.1016/j.scitotenv.2021.146664}, pmid = {33839662}, issn = {1879-1026}, abstract = {Global value chains and climate change have a significant impact on water resources and increasingly threaten freshwater ecosystems. Recent methodological proposals for life cycle impact assessment (LCIA), evaluate water use impacts on freshwater habitats based on river hydraulic parameters alterations. However, they are limited to French rivers due to lack of global data and models. On this basis, this article proposes an approach to compute regionalized characterization factors for modeling river habitat change potential (HCP) induced by water consumption, potentially applicable worldwide. A simplified model is developed for fish guilds and invertebrates. Based on French datasets, it establishes a relationship between HCP and river hydraulic parameters. A methodology to derive discharge and hydraulic geometry at the reach scale is proposed and applied to European and Middle Eastern rivers below 60°N latitude. Regionalized HCPs are calculated at the river reach scale and aggregated at watershed. Then, the impact of agricultural water use in contrasted European and Middle Eastern countries is evaluated comparing the outcomes from the HCP and the Available Water Remaining (AWARE) models at the national scale, considering water supply mix data. The same analysis is carried out on selected river basins. Finally, result consistency, uncertainty and global applicability of the overall approach are discussed. The study demonstrates the reproducibility of the impact model developed for French rivers on any hydrographic network where comparable ecological, hydrological and hydraulic conditions are met. Furthermore, it highlights the need to characterize impacts at a higher spatial resolution in areas where HCP is higher. Large scale quantification of HCP opens the way to the operationalization of mechanistic LCIA models in which the habitat preferences of freshwater species are taken into account to assess the impacts of water consumption on biodiversity.}, } @article {pmid33839192, year = {2021}, author = {Bohálová, N and Cantara, A and Bartas, M and Kaura, P and Šťastný, J and Pečinka, P and Fojta, M and Mergny, JL and Brázda, V}, title = {Analyses of viral genomes for G-quadruplex forming sequences reveal their correlation with the type of infection.}, journal = {Biochimie}, volume = {186}, number = {}, pages = {13-27}, doi = {10.1016/j.biochi.2021.03.017}, pmid = {33839192}, issn = {1638-6183}, mesh = {DNA, Viral/genetics/metabolism ; *Databases, Nucleic Acid ; *G-Quadruplexes ; *Genome, Viral ; Humans ; *Virus Diseases/genetics/metabolism ; *Viruses/genetics/metabolism ; }, abstract = {G-quadruplexes contribute to the regulation of key molecular processes. Their utilization for antiviral therapy is an emerging field of contemporary research. Here we present comprehensive analyses of the presence and localization of putative G-quadruplex forming sequences (PQS) in all viral genomes currently available in the NCBI database (including subviral agents). The G4Hunter algorithm was applied to a pool of 11,000 accessible viral genomes representing 350 Mbp in total. PQS frequencies differ across evolutionary groups of viruses, and are enriched in repeats, replication origins, 5'UTRs and 3'UTRs. Importantly, PQS presence and localization is connected to viral lifecycles and corresponds to the type of viral infection rather than to nucleic acid type; while viruses routinely causing persistent infections in Metazoa hosts are enriched for PQS, viruses causing acute infections are significantly depleted for PQS. The unique localization of PQS identifies the importance of G-quadruplex-based regulation of viral replication and life cycle, providing a tool for potential therapeutic targeting.}, } @article {pmid33837760, year = {2021}, author = {Bartas, M and Goswami, P and Lexa, M and Červeň, J and Volná, A and Fojta, M and Brázda, V and Pečinka, P}, title = {Letter to the Editor: Significant mutation enrichment in inverted repeat sites of new SARS-CoV-2 strains.}, journal = {Briefings in bioinformatics}, volume = {22}, number = {5}, pages = {}, pmid = {33837760}, issn = {1477-4054}, support = {18-18699S//Czech Science Foundation/ ; }, mesh = {COVID-19/virology ; Genome, Viral ; Humans ; *Mutation ; SARS-CoV-2/*genetics ; }, abstract = {In a recently published paper, we have found that SARS-CoV-2 hot-spot mutations are significantly associated with inverted repeat loci and CG dinucleotides. However, fast-spreading strains with new mutations (so-called mink farm mutations, England mutations and Japan mutations) have been recently described. We used the new datasets to check the positioning of mutation sites in genomes of the new SARS-CoV-2 strains. Using an open-access Palindrome analyzer tool, we found mutations in these new strains to be significantly enriched in inverted repeat loci.}, } @article {pmid33836121, year = {2021}, author = {Hong, SL and Lemey, P and Suchard, MA and Baele, G}, title = {Bayesian Phylogeographic Analysis Incorporating Predictors and Individual Travel Histories in BEAST.}, journal = {Current protocols}, volume = {1}, number = {4}, pages = {e98}, pmid = {33836121}, issn = {2691-1299}, support = {U19 AI135995/AI/NIAID NIH HHS/United States ; 725422-ReservoirDOCS/ERC_/European Research Council/International ; AI135995/NH/NIH HHS/United States ; R01 AI153044/AI/NIAID NIH HHS/United States ; 874850/ERC_/European Research Council/International ; 206298/Z/17/Z/WT_/Wellcome Trust/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; }, mesh = {Bayes Theorem ; COVID-19/*epidemiology/genetics/transmission/*virology ; Computational Biology/methods ; Databases, Nucleic Acid ; Humans ; Phylogeny ; Phylogeography/methods ; SARS-CoV-2/classification/*genetics/isolation & purification ; Sequence Analysis, DNA/methods ; Software ; Travel/*statistics & numerical data ; United States/epidemiology ; }, abstract = {Advances in sequencing technologies have tremendously reduced the time and costs associated with sequence generation, making genomic data an important asset for routine public health practices. Within this context, phylogenetic and phylogeographic inference has become a popular method to study disease transmission. In a Bayesian context, these approaches have the benefit of accommodating phylogenetic uncertainty, and popular implementations provide the possibility to parameterize the transition rates between locations as a function of epidemiological and ecological data to reconstruct spatial spread while simultaneously identifying the main factors impacting the spatial spread dynamics. Recent developments enable researchers to make use of travel history data of infected individuals in the reconstruction of pathogen spread, offering increased inference accuracy and mitigating sampling bias. Here, we describe a detailed workflow to reconstruct the spatial spread of a pathogen through Bayesian phylogeographic analysis in discrete space using these novel approaches, implemented in BEAST. The individual protocols focus on how to incorporate molecular data, covariates of spread, and individual travel history data into the analysis. © 2021 Wiley Periodicals LLC. Basic Protocol 1: Creating a SARS-CoV-2 MSA using sequences from GISAID Basic Protocol 2: Setting up a discrete trait phylogeographic reconstruction in BEAUti Basic Protocol 3: Phylogeographic reconstruction incorporating travel history information Basic Protocol 4: Visualizing ancestral spatial trajectories for specific taxa.}, } @article {pmid33836018, year = {2021}, author = {Machado, AF and Ritter, CD and Miranda, CL and Bredin, YK and Ramos Pereira, MJ and Duarte, L}, title = {Potential mammalian species for investigating the past connections between Amazonia and the Atlantic Forest.}, journal = {PloS one}, volume = {16}, number = {4}, pages = {e0250016}, pmid = {33836018}, issn = {1932-6203}, mesh = {Animal Distribution/classification/*physiology ; Animals ; Biodiversity ; Brazil ; Databases, Genetic ; Ecosystem ; Forests ; Mammals/classification ; Phylogeny ; Phylogeography/*methods ; South America ; }, abstract = {Much evidence suggests that Amazonia and the Atlantic Forest were connected through at least three dispersion routes in the past: the Eastern route, the central route, and the Western route. However, few studies have assessed the use of these routes based on multiple species. Here we present a compilation of mammal species that potentially have dispersed between the two forest regions and which may serve to investigate these connections. We evaluate the present-day geographic distributions of mammals occurring in both Amazonia and the Atlantic Forest and the likely connective routes between these forests. We classified the species per habitat occupancy (strict forest specialists, species that prefer forest habitat, or generalists) and compiled the genetic data available for each species. We found 127 mammalian species presently occurring in both Amazonia and the Atlantic Forest for which, substantial genetic data was available. Hence, highlighting their potential for phylogeographic studies investigating the past connections between the two forests. Differently from what was previously proposed, the present-day geographic distribution of mammal species found in both Amazonia and the Atlantic Forest points to more species in the eastern portion of the dry diagonal (and adjoining forested habitats). The Central route was associated with the second most species. Although it remains to be seen how this present-day geography reflects the paleo dispersal routes, our results show the potential of using mammal species to investigate and bring new insights about the past connections between Amazonia and the Atlantic Forest.}, } @article {pmid33835712, year = {2021}, author = {Brandt, MI and Trouche, B and Quintric, L and Günther, B and Wincker, P and Poulain, J and Arnaud-Haond, S}, title = {Bioinformatic pipelines combining denoising and clustering tools allow for more comprehensive prokaryotic and eukaryotic metabarcoding.}, journal = {Molecular ecology resources}, volume = {21}, number = {6}, pages = {1904-1921}, doi = {10.1111/1755-0998.13398}, pmid = {33835712}, issn = {1755-0998}, support = {AP2016-228//Ifremer/ ; ANR-10-INBS-09//France Génomique/ ; //Genoscope-CEA/ ; }, mesh = {Animals ; Archaea/*classification ; Bacteria/*classification ; Bayes Theorem ; Biodiversity ; Cluster Analysis ; *Computational Biology ; *DNA Barcoding, Taxonomic ; *DNA, Environmental ; Ecosystem ; Eukaryota/*classification ; Geologic Sediments ; Seawater ; }, abstract = {Environmental DNA metabarcoding is a powerful tool for studying biodiversity. However, bioinformatic approaches need to adjust to the diversity of taxonomic compartments targeted as well as to each barcode gene specificities. We built and tested a pipeline based on read correction with DADA2 allowing analysing metabarcoding data from prokaryotic (16S) and eukaryotic (18S, COI) life compartments. We implemented the option to cluster amplicon sequence variants (ASVs) into operational taxonomic units (OTUs) with swarm, a network-based clustering algorithm, and the option to curate ASVs/OTUs using LULU. Finally, taxonomic assignment was implemented via the Ribosomal Database Project Bayesian classifier (RDP) and BLAST. We validated this pipeline with ribosomal and mitochondrial markers using metazoan mock communities and 42 deep-sea sediment samples. The results show that ASVs and OTUs describe different levels of biotic diversity, the choice of which depends on the research questions. They underline the advantages and complementarity of clustering and LULU-curation for producing metazoan biodiversity inventories at a level approaching the one obtained using morphological criteria. While clustering removes intraspecific variation, LULU effectively removes spurious clusters, originating from errors or intragenomic variability. Swarm clustering affected alpha and beta diversity differently depending on genetic marker. Specifically, d-values > 1 appeared to be less appropriate with 18S for metazoans. Similarly, increasing LULU's minimum ratio level proved essential to avoid losing species in sample-poor data sets. Comparing BLAST and RDP underlined that accurate assignments of deep-sea species can be obtained with RDP, but highlighted the need for a concerted effort to build comprehensive, ecosystem-specific databases.}, } @article {pmid33835454, year = {2021}, author = {D'Antonio, M and Libro, P and Picardi, E and Pesole, G and Castrignanò, T}, title = {RAP: A Web Tool for RNA-Seq Data Analysis.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2284}, number = {}, pages = {393-415}, pmid = {33835454}, issn = {1940-6029}, mesh = {Animals ; Computational Biology/methods ; Data Analysis ; Gene Expression Profiling/methods ; High-Throughput Nucleotide Sequencing/methods ; Humans ; *Internet ; Polyadenylation ; RNA-Seq/*methods/statistics & numerical data ; Sequence Analysis, RNA/methods ; *Software ; Transcriptome ; Exome Sequencing ; }, abstract = {Since 1950 main studies of RNA regarded its role in the protein synthesis. Later insights showed that only a small portion of RNA codes for proteins where the rest could have different functional roles. With the advent of Next Generation Sequencing (NGS) and in particular with RNA-seq technology the cost of sequencing production dropped down. Among the NGS application areas, the transcriptome analysis, that is, the analysis of transcripts in a cell, their quantification for a specific developmental stage or treatment condition, became more and more adopted in the laboratories. As a consequence in the last decade new insights were gained in the understanding of both transcriptome complexity and involvement of RNA molecules in cellular processes. For what concerns computational advances, bioinformatics research developed new methods for analyzing RNA-seq data. The comparison among transcriptome profiles from several samples is often a difficult task for nonexpert programmers. Here, in this chapter, we introduce RAP (RNA-Seq Analysis Pipeline), a completely automated web tool for transcriptome analysis. It is a user-friendly web tool implementing a detailed transcriptome workflow to detect differential expressed genes and transcript, identify spliced junctions and constitutive or alternative polyadenylation sites and predict gene fusion events. Through the web interface the researchers can get all this information without any knowledge of the underlying High Performance Computing infrastructure.}, } @article {pmid33835447, year = {2021}, author = {Lo Giudice, C and Mansi, L and Flati, T and Gioiosa, S and Chillemi, G and Libro, P and Castrignanò, T and Pesole, G and Picardi, E}, title = {RNA Editing Detection in HPC Infrastructures.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2284}, number = {}, pages = {253-270}, pmid = {33835447}, issn = {1940-6029}, mesh = {Animals ; Computational Biology/methods ; *Computing Methodologies ; Databases, Genetic ; Datasets as Topic ; Genomics ; High-Throughput Nucleotide Sequencing ; Humans ; Neoplasms/genetics ; Nervous System Diseases/genetics ; Neurodegenerative Diseases/genetics ; RNA Editing/*physiology ; Sequence Analysis, RNA/*methods ; Software ; Transcriptome ; }, abstract = {RNA editing by A-to-I deamination is a relevant co/posttranscriptional modification carried out by ADAR enzymes. In humans, it has pivotal cellular effects and its deregulation has been linked to a variety of human disorders including neurological and neurodegenerative diseases and cancer. Despite its biological relevance, the detection of RNA editing variants in large transcriptome sequencing experiments (RNAseq) is yet a challenging computational task. To drastically reduce computing times we have developed a novel REDItools version able to identify A-to-I events in huge amount of RNAseq data employing High Performance Computing (HPC) infrastructures.Here we show how to use REDItools v2 in HPC systems.}, } @article {pmid33833441, year = {2021}, author = {Feng, S and Stiller, J and Deng, Y and Armstrong, J and Fang, Q and Reeve, AH and Xie, D and Chen, G and Guo, C and Faircloth, BC and Petersen, B and Wang, Z and Zhou, Q and Diekhans, M and Chen, W and Andreu-Sánchez, S and Margaryan, A and Howard, JT and Parent, C and Pacheco, G and Sinding, MS and Puetz, L and Cavill, E and Ribeiro, ÂM and Eckhart, L and Fjeldså, J and Hosner, PA and Brumfield, RT and Christidis, L and Bertelsen, MF and Sicheritz-Ponten, T and Tietze, DT and Robertson, BC and Song, G and Borgia, G and Claramunt, S and Lovette, IJ and Cowen, SJ and Njoroge, P and Dumbacher, JP and Ryder, OA and Fuchs, J and Bunce, M and Burt, DW and Cracraft, J and Meng, G and Hackett, SJ and Ryan, PG and Jønsson, KA and Jamieson, IG and da Fonseca, RR and Braun, EL and Houde, P and Mirarab, S and Suh, A and Hansson, B and Ponnikas, S and Sigeman, H and Stervander, M and Frandsen, PB and van der Zwan, H and van der Sluis, R and Visser, C and Balakrishnan, CN and Clark, AG and Fitzpatrick, JW and Bowman, R and Chen, N and Cloutier, A and Sackton, TB and Edwards, SV and Foote, DJ and Shakya, SB and Sheldon, FH and Vignal, A and Soares, AER and Shapiro, B and González-Solís, J and Ferrer-Obiol, J and Rozas, J and Riutort, M and Tigano, A and Friesen, V and Dalén, L and Urrutia, AO and Székely, T and Liu, Y and Campana, MG and Corvelo, A and Fleischer, RC and Rutherford, KM and Gemmell, NJ and Dussex, N and Mouritsen, H and Thiele, N and Delmore, K and Liedvogel, M and Franke, A and Hoeppner, MP and Krone, O and Fudickar, AM and Milá, B and Ketterson, ED and Fidler, AE and Friis, G and Parody-Merino, ÁM and Battley, PF and Cox, MP and Lima, NCB and Prosdocimi, F and Parchman, TL and Schlinger, BA and Loiselle, BA and Blake, JG and Lim, HC and Day, LB and Fuxjager, MJ and Baldwin, MW and Braun, MJ and Wirthlin, M and Dikow, RB and Ryder, TB and Camenisch, G and Keller, LF and DaCosta, JM and Hauber, ME and Louder, MIM and Witt, CC and McGuire, JA and Mudge, J and Megna, LC and Carling, MD and Wang, B and Taylor, SA and Del-Rio, G and Aleixo, A and Vasconcelos, ATR and Mello, CV and Weir, JT and Haussler, D and Li, Q and Yang, H and Wang, J and Lei, F and Rahbek, C and Gilbert, MTP and Graves, GR and Jarvis, ED and Paten, B and Zhang, G}, title = {Author Correction: Dense sampling of bird diversity increases power of comparative genomics.}, journal = {Nature}, volume = {592}, number = {7856}, pages = {E24}, doi = {10.1038/s41586-021-03473-8}, pmid = {33833441}, issn = {1476-4687}, support = {U01 HG010971/HG/NHGRI NIH HHS/United States ; U01 HL137183/HL/NHLBI NIH HHS/United States ; }, } @article {pmid33831583, year = {2021}, author = {Ismail, R and Baaity, Z and Csóka, I}, title = {Regulatory status quo and prospects for biosurfactants in pharmaceutical applications.}, journal = {Drug discovery today}, volume = {26}, number = {8}, pages = {1929-1935}, doi = {10.1016/j.drudis.2021.03.029}, pmid = {33831583}, issn = {1878-5832}, mesh = {Antiviral Agents/*pharmacology ; *COVID-19/prevention & control ; COVID-19 Vaccines/*pharmacology ; *Drug Discovery/methods/trends ; Drug and Narcotic Control/organization & administration ; Ecological and Environmental Phenomena ; Humans ; Nanostructures ; Pharmaceutical Preparations/classification ; *SARS-CoV-2/drug effects/physiology ; Surface-Active Agents/*pharmacology ; *COVID-19 Drug Treatment ; }, abstract = {The concept of going 'green' and 'cold' has led to utilizing renewable resources for the synthesis of microbial biosurfactants that are both patient and eco-friendly. In this review, we shed light on the potential and regulatory aspects of biosurfactants in pharmaceutical applications and how they can significantly contribute to novel concepts for the Coronavirus 2019 (COVID-19) vaccine and future treatment. We emphasize that more specific guidelines should be formulated to regulate the approval of biosurfactants for human use. It is also crucial to implement a risk-based approach from the early research and development (R&D) phase in addition to establishing more robust standardized techniques and assays to evaluate the characteristics of biosurfactants.}, } @article {pmid33830905, year = {2021}, author = {Li, Y and O'Donnell, AC and Ochman, H}, title = {Discriminating arboviral species.}, journal = {The Journal of general virology}, volume = {102}, number = {4}, pages = {}, pmid = {33830905}, issn = {1465-2099}, support = {R35 GM118038/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Arbovirus Infections/*virology ; *Arboviruses/classification/genetics ; Culicidae/*virology ; Databases, Genetic ; *Flavivirus/classification/genetics ; Mosquito Vectors/*virology ; }, abstract = {Mosquito-borne arboviruses, including a diverse array of alphaviruses and flaviviruses, lead to hundreds of millions of human infections each year. Current methods for species-level classification of arboviruses adhere to guidelines prescribed by the International Committee on Taxonomy of Viruses (ICTV), and generally apply a polyphasic approach that might include information about viral vectors, hosts, geographical distribution, antigenicity, levels of DNA similarity, disease association and/or ecological characteristics. However, there is substantial variation in the criteria used to define viral species, which can lead to the establishment of artificial boundaries between species and inconsistencies when inferring their relatedness, variation and evolutionary history. In this study, we apply a single, uniform principle - that underlying the Biological Species Concept (BSC) - to define biological species of arboviruses based on recombination between genomes. Given that few recombination events have been documented in arboviruses, we investigate the incidence of recombination within and among major arboviral groups using an approach based on the ratio of homoplastic sites (recombinant alleles) to non-homoplastic sites (vertically transmitted alleles). This approach supports many ICTV-designations but also recognizes several cases in which a named species comprises multiple biological species. These findings demonstrate that this metric may be applied to all lifeforms, including viruses, and lead to more consistent and accurate delineation of viral species.}, } @article {pmid33828196, year = {2021}, author = {Spiesman, BJ and Gratton, C and Hatfield, RG and Hsu, WH and Jepsen, S and McCornack, B and Patel, K and Wang, G}, title = {Assessing the potential for deep learning and computer vision to identify bumble bee species from images.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {7580}, pmid = {33828196}, issn = {2045-2322}, mesh = {Animals ; *Artificial Intelligence ; Bees/*anatomy & histology/*classification ; Conservation of Natural Resources ; Databases, Factual ; *Deep Learning ; Ecosystem ; Image Processing, Computer-Assisted ; Neural Networks, Computer ; North America ; Pigmentation ; Pollination ; Species Specificity ; }, abstract = {Pollinators are undergoing a global decline. Although vital to pollinator conservation and ecological research, species-level identification is expensive, time consuming, and requires specialized taxonomic training. However, deep learning and computer vision are providing ways to open this methodological bottleneck through automated identification from images. Focusing on bumble bees, we compare four convolutional neural network classification models to evaluate prediction speed, accuracy, and the potential of this technology for automated bee identification. We gathered over 89,000 images of bumble bees, representing 36 species in North America, to train the ResNet, Wide ResNet, InceptionV3, and MnasNet models. Among these models, InceptionV3 presented a good balance of accuracy (91.6%) and average speed (3.34 ms). Species-level error rates were generally smaller for species represented by more training images. However, error rates also depended on the level of morphological variability among individuals within a species and similarity to other species. Continued development of this technology for automatic species identification and monitoring has the potential to be transformative for the fields of ecology and conservation. To this end, we present BeeMachine, a web application that allows anyone to use our classification model to identify bumble bees in their own images.}, } @article {pmid33825910, year = {2021}, author = {Gu, D and Song, Z and Kang, H and Mao, Y and Feng, Q}, title = {Occurrence, Profiles and Ecological Risk of Bisphenol Analogues in a Municipal Sewage Treatment Plant.}, journal = {Bulletin of environmental contamination and toxicology}, volume = {106}, number = {6}, pages = {1044-1049}, pmid = {33825910}, issn = {1432-0800}, support = {41673120//National Natural Science Foundation of China/ ; 2018002//Research on Environmental Safety Monitoring, Assessment and Early Warning Technology of Centralized Drinking Water Source/ ; }, mesh = {Beijing ; Benzhydryl Compounds/analysis ; China ; Phenols ; *Sewage/analysis ; Tandem Mass Spectrometry ; *Water Pollutants, Chemical/analysis ; }, abstract = {Due to the strict control on bisphenol A (BPA) in many countries, bisphenol analogues (BPs) are being widely used as alternative materials to manufacture epoxy resins and polycarbonate plastics, resulting in their occurrence in sewage treatment plants (STPs). In this study, the occurrence and distribution of 7 BPs in a large-scale STP in Beijing China was investigated. Wastewater samples were collected from the influents and effluents of each processing unit, and extracted by solid-phase extraction. Target compounds were quantified by ultra-performance liquid chromatography tandem mass spectrometry (HPLC-MS/MS). The total concentrations of seven BPs (ΣBPs) were 400.42 ± 48.12 ng/L in the raw sewage, 438.60 ± 46.50 ng/L in the primary effluent, 17.21 ± 13.12 ng/L in the secondary effluent, and 11.33 ± 4.84 ng/L in the tertiary effluent, respectively. Bisphenol S (BPS) and BPA were the predominant congener in raw sewage with an overall contribution of 29.32% and 70.22% to the ΣBPs, indicating that there was a large amount of BPS and BPA consumption in the study area. During a one-week sampling period, ΣBPs changed slightly at the same sampling site. It was found that high removal efficiencies were achieved for BPs in anoxic and oxic secondary clarifier treatment units, suggesting that biodegradation and sorption played major roles in BPs elimination in the STP. After tertiary treatment, all BPs except BPA were completely removed, suggesting the necessity to investigate the fate and toxicity of BPA in the aquatic environment.}, } @article {pmid33818967, year = {2021}, author = {Navidpour, S and Jahanifard, E and Hosseini-Vasoukolaei, N}, title = {Species Composition and Spatial Distribution of Scorpions Based on Eco-Environmental Variables in Provinces Along with the Oman Sea and the Persian Gulf in Iran: A GIS-Based Approach.}, journal = {Archives of Razi Institute}, volume = {76}, number = {1}, pages = {149-160}, pmid = {33818967}, issn = {2008-9872}, mesh = {Animals ; *Geographic Information Systems ; Indian Ocean ; Iran/epidemiology ; Oman ; *Scorpions ; Species Specificity ; }, abstract = {Scorpions are venomous arachnids with major medical health importance in Iran, specifically in the Southwest. In total, three families of scorpions, including Scorpionidae, Hemiscorpiidae, and Buthidae were reported in Iran. This study was conducted on scorpion ecology to determine the species composition and the dispersion of scorpions based on the ecological and environmental variables in combination with the Geographic Information System (GIS) in Khuzestan, Hormozgan, and Bushehr Provinces along with the Oman Sea and the Persian Gulf in Iran. Scorpions were collected from Hormozgan, Khuzestan, and Bushehr Provinces, Iran using the Ultra Violet light. The specimens were then identified according to their morphological characters utilizing reliable keys. To determine the relationship between the eco-environmental variables and the spatial distribution of species, the GPS points of the collected scorpions were recorded, and the scorpion shapefile was overlaid on digital elevation model, slope, land use, temperature, rainfall, soil texture, and bioclimatic maps. Totally, 25 specimens were reported in three families of Scorpionidae, Hemiscorpiidae, and Buthidae. Furthermore, Razianus zarudnyi, Androctonus crassicauda, Buthacus macrocentrus, Mesobuthus eupeus phillipsii, Odontobuthus bidentatus, and Hemiscorpius lepturus were the common species collected from Hormozgan, Khuzestan, and Bushehr Provinces, Iran. The results of the current study showed that a large number of species preferred the sand texture due to ecomorphological adaptation. Moreover, the poor rangeland vegetation cover was preferred by the majority of the scorpion species, including S. maurus townsendi. According to the results, the combination of the ecological factors related to the suitable habitat of different species of scorpion and GIS will provide the dispersal areas of each species. Furthermore, such databases can be comprehensive and valuable guides for health authorities to reduce and manage scorpion envenomation.}, } @article {pmid33815930, year = {2021}, author = {da Silva, GAP and Kock, KS}, title = {Effect of seasonality in hospitalizations and deaths from acute myocardial infarction in southern Brazil from 2009 to 2018.}, journal = {American journal of cardiovascular disease}, volume = {11}, number = {1}, pages = {148-154}, pmid = {33815930}, issn = {2160-200X}, abstract = {INTRODUCTION: Acute myocardial infarction (AMI) is one of the main causes of morbidity and mortality in Brazil and worldwide. Seasonality and climate change seem to be associated with hospitalization for AMI.

OBJECTIVE: to analyze the effect that seasonality and temperature have on the number of hospitalizations and deaths due to AMI, stratified by gender and age group, from 2009 to 2018 in a region of southern Brazil.

METHODS: An Ecological study, composed of cases of hospitalizations and deaths by AMI in the Association of Municipalities of the Laguna Region (AMUREL), SC, Brazil. Data on AMI were collected by the Department of Informatics of the Unified Health System (DATASUS) and data on average monthly temperature (degrees Celsius) of the Laguna region (SC, Brazil) were provided by the National Institute of Meteorology (INMET). The data analysis was performed through linear regression and ANOVA test with Tukey post-hoc.

RESULTS: 2947 hospitalizations were analyzed. The monthly average hospitalization per AMI was 24.6±8.1 cases (7.0±2.2/100,000 inhabitants) with a lethality of 14.4±6.8%. The results showed that there is no difference in AMI hospitalization between the months of the year, but showed a significant negative correlation between temperature and AMI hospitalizations (r=-0.219; P=0.022; β=-0.165). It was also shown that men and elderly had more cases of AMI hospitalization, but women and elderly had more lethality. When the lethality rate was analyzed during the study period, there was a significant negative correlation, indicating the reduction of AMI deaths with time.

CONCLUSION: There was an association between temperature reduction and AMI hospitalization, where each 6°C reduction in temperature was related to an increase of 1 hospitalization per AMI/100,000 inhabitants. It is hoped that the results may assist in the formulation of public environmental policies for the prevention of risk factors for AMI.}, } @article {pmid33810462, year = {2021}, author = {Bohálová, N and Cantara, A and Bartas, M and Kaura, P and Šťastný, J and Pečinka, P and Fojta, M and Brázda, V}, title = {Tracing dsDNA Virus-Host Coevolution through Correlation of Their G-Quadruplex-Forming Sequences.}, journal = {International journal of molecular sciences}, volume = {22}, number = {7}, pages = {}, pmid = {33810462}, issn = {1422-0067}, support = {18-15548S//Grantová Agentura České Republiky/ ; CZ.02.1.01/0.0/0.0/15_003/0000477//ERDF/ ; }, mesh = {Archaea/virology ; Bacteria/virology ; Computational Biology/*methods ; DNA/*genetics ; *G-Quadruplexes ; Gene Expression Regulation ; Genome ; *Genome, Viral ; Humans ; Viral Proteins/*genetics ; Viruses/genetics ; }, abstract = {The importance of gene expression regulation in viruses based upon G-quadruplex may point to its potential utilization in therapeutic targeting. Here, we present analyses as to the occurrence of putative G-quadruplex-forming sequences (PQS) in all reference viral dsDNA genomes and evaluate their dependence on PQS occurrence in host organisms using the G4Hunter tool. PQS frequencies differ across host taxa without regard to GC content. The overlay of PQS with annotated regions reveals the localization of PQS in specific regions. While abundance in some, such as repeat regions, is shared by all groups, others are unique. There is abundance within introns of Eukaryota-infecting viruses, but depletion of PQS in introns of bacteria-infecting viruses. We reveal a significant positive correlation between PQS frequencies in dsDNA viruses and corresponding hosts from archaea, bacteria, and eukaryotes. A strong relationship between PQS in a virus and its host indicates their close coevolution and evolutionarily reciprocal mimicking of genome organization.}, } @article {pmid33809683, year = {2021}, author = {Ren, J and Long, Y and Liu, R and Song, G and Li, Q and Cui, Z}, title = {Characterization of Biological Pathways Regulating Acute Cold Resistance of Zebrafish.}, journal = {International journal of molecular sciences}, volume = {22}, number = {6}, pages = {}, pmid = {33809683}, issn = {1422-0067}, support = {2018YFD0900302-2//National Key R&D Program of China/ ; 31772836//National Natural Science Foundation of China/ ; 2021GDASYL-20210102003//Special Fund Project for Guangdong Academy of Sciences to Build Domestic First-class Research institutions/ ; 2016305//Youth Innovation Promotion Association of Chinese Academy of Sciences/ ; 2020B0202080005//Key-Area Research and Development Program of Guangdong Province/ ; }, mesh = {*Adaptation, Physiological/genetics ; Animals ; Biomarkers/metabolism ; Cluster Analysis ; *Cold Temperature ; Gene Expression Profiling ; Gene Expression Regulation ; Gene Ontology ; Larva/genetics ; *Signal Transduction/genetics ; Survival Analysis ; Transcription, Genetic ; Transcriptome/genetics ; Zebrafish/genetics/*physiology ; Zebrafish Proteins/genetics/metabolism ; }, abstract = {Low temperature stress represents a major threat to the lives of both farmed and wild fish species. However, biological pathways determining the development of cold resistance in fish remain largely unknown. Zebrafish larvae at 96 hpf were exposed to lethal cold stress (10 °C) for different time periods to evaluate the adverse effects at organism, tissue and cell levels. Time series RNA sequencing (RNA-seq) experiments were performed to delineate the transcriptomic landscape of zebrafish larvae under cold stress and during the subsequent rewarming phase. The genes regulated by cold stress were characterized by progressively enhanced or decreased expression, whereas the genes associated with rewarming were characterized by rapid upregulation upon return to normal temperature (28 °C). Genes such as trib3, dusp5 and otud1 were identified as the representative molecular markers of cold-induced damages through network analysis. Biological pathways involved in cold stress responses were mined from the transcriptomic data and their functions in regulating cold resistance were validated using specific inhibitors. The autophagy, FoxO and MAPK (mitogen-activated protein kinase) signaling pathways were revealed to be survival pathways for enhancing cold resistance, while apoptosis and necroptosis were the death pathways responsible for cold-induced mortality. Functional mechanisms of the survival-enhancing factors Foxo1, ERK (extracellular signal-regulated kinase) and p38 MAPK were further characterized by inhibiting their activities upon cold stress and analyzing gene expression though RNA-seq. These factors were demonstrated to determine the cold resistance of zebrafish through regulating apoptosis and p53 signaling pathway. These findings have provided novel insights into the stress responses elicited by lethal cold and shed new light on the molecular mechanisms underlying cold resistance of fish.}, } @article {pmid33808463, year = {2021}, author = {Pushkareva, E and Sommer, V and Barrantes, I and Karsten, U}, title = {Diversity of Microorganisms in Biocrusts Surrounding Highly Saline Potash Tailing Piles in Germany.}, journal = {Microorganisms}, volume = {9}, number = {4}, pages = {}, pmid = {33808463}, issn = {2076-2607}, support = {20016/462//Deutsche Bundesstiftung Umwelt/ ; }, abstract = {Potash tailing piles located in Germany represent extremely hypersaline locations that negatively affect neighbouring environments and limit the development of higher vegetation. However, biocrusts, as cryptogamic covers, inhabit some of these areas and provide essential ecological functions, but, nevertheless, they remain poorly described. Here, we applied high-throughput sequencing (HTS) and targeted four groups of microorganisms: bacteria, cyanobacteria, fungi and other eukaryotes. The sequencing of the 16S rRNA gene revealed the dominance of Proteobacteria, Cyanobacteria and Actinobacteria. Additionally, we applied yanobacteria-specific primers for a detailed assessment of the cyanobacterial community, which was dominated by members of the filamentous orders Synechococcales and Oscillatoriales. Furthermore, the majority of reads in the studied biocrusts obtained by sequencing of the 18S rRNA gene belonged to eukaryotic microalgae. In addition, sequencing of the internal rDNA transcribed spacer region (ITS) showed the dominance of Ascomycota within the fungal community. Overall, these molecular data provided the first detailed overview of microorganisms associated with biocrusts inhabiting highly saline potash tailing piles and showed the dissimilarities in microbial diversity among the samples.}, } @article {pmid33807576, year = {2021}, author = {Elsohaby, I and Samy, A and Elmoslemany, A and Alorabi, M and Alkafafy, M and Aldoweriej, A and Al-Marri, T and Elbehiry, A and Fayez, M}, title = {Migratory Wild Birds as a Potential Disseminator of Antimicrobial-Resistant Bacteria around Al-Asfar Lake, Eastern Saudi Arabia.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {10}, number = {3}, pages = {}, pmid = {33807576}, issn = {2079-6382}, support = {TURSP-2020-57//Taif University/ ; }, abstract = {Migratory wild birds acquire antimicrobial-resistant (AMR) bacteria from contaminated habitats and then act as reservoirs and potential spreaders of resistant elements through migration. However, the role of migratory wild birds as antimicrobial disseminators in the Arabian Peninsula desert, which represents a transit point for birds migrating all over Asia, Africa, and Europe not yet clear. Therefore, the present study objective was to determine antimicrobial-resistant bacteria in samples collected from migratory wild birds around Al-Asfar Lake, located in Al-Ahsa Oasis, Eastern Saudi Arabia, with a particular focus on Escherichia coli virulence and resistance genes. Cloacal swabs were collected from 210 migratory wild birds represent four species around Al-Asfar. E. coli, Staphylococcus, and Salmonella spp. have been recovered from 90 (42.9%), 37 (17.6%), and 5 (2.4%) birds, respectively. Out of them, 19 (14.4%) were a mixed infection. All samples were subjected to AMR phenotypic characterization, and results revealed (14-41%) and (16-54%) of E. coli and Staphylococcus spp. isolates were resistant to penicillins, sulfonamides, aminoglycoside, and tetracycline antibiotics. Multidrug-resistant (MDR) E. coli and Staphylococcus spp. were identified in 13 (14.4%) and 7 (18.9%) isolates, respectively. However, none of the Salmonella isolates were MDR. Of the 90 E. coli isolates, only 9 (10%) and 5 (5.6%) isolates showed the presence of eaeA and stx2 virulence-associated genes, respectively. However, both eaeA and stx2 genes were identified in four (4.4%) isolates. None of the E. coli isolates carried the hlyA and stx1 virulence-associated genes. The E. coli AMR associated genes blaCTX-M, blaTEM, blaSHV, aac(3)-IV, qnrA, and tet(A) were identified in 7 (7.8%), 5 (5.6%), 1 (1.1%), 8 (8.9%), 4 (4.4%), and 6 (6.7%) isolates, respectively. While the mecA gene was not detected in any of the Staphylococcus spp. isolates. Regarding migratory wild bird species, bacterial recovery, mixed infection, MDR, and AMR index were relatively higher in aquatic-associated species. Overall, the results showed that migratory wild birds around Al-Asfar Lake could act as a reservoir for AMR bacteria enabling them to have a potential role in maintaining, developing, and disseminating AMR bacteria. Furthermore, results highlight the importance of considering migratory wild birds when studying the ecology of AMR.}, } @article {pmid33806786, year = {2021}, author = {Peters, K and Balcke, G and Kleinenkuhnen, N and Treutler, H and Neumann, S}, title = {Untargeted In Silico Compound Classification-A Novel Metabolomics Method to Assess the Chemodiversity in Bryophytes.}, journal = {International journal of molecular sciences}, volume = {22}, number = {6}, pages = {}, pmid = {33806786}, issn = {1422-0067}, support = {322031L0107//Bundesministerium für Bildung, Wissenschaft und Forschung/ ; }, mesh = {Biodiversity ; Bryophyta/*chemistry/classification/genetics ; Cluster Analysis ; *Computational Biology/methods ; Metabolome ; *Metabolomics/methods ; Phylogeny ; Phytochemicals/*chemistry/*classification ; }, abstract = {In plant ecology, biochemical analyses of bryophytes and vascular plants are often conducted on dried herbarium specimen as species typically grow in distant and inaccessible locations. Here, we present an automated in silico compound classification framework to annotate metabolites using an untargeted data independent acquisition (DIA)-LC/MS-QToF-sequential windowed acquisition of all theoretical fragment ion mass spectra (SWATH) ecometabolomics analytical method. We perform a comparative investigation of the chemical diversity at the global level and the composition of metabolite families in ten different species of bryophytes using fresh samples collected on-site and dried specimen stored in a herbarium for half a year. Shannon and Pielou's diversity indices, hierarchical clustering analysis (HCA), sparse partial least squares discriminant analysis (sPLS-DA), distance-based redundancy analysis (dbRDA), ANOVA with post-hoc Tukey honestly significant difference (HSD) test, and the Fisher's exact test were used to determine differences in the richness and composition of metabolite families, with regard to herbarium conditions, ecological characteristics, and species. We functionally annotated metabolite families to biochemical processes related to the structural integrity of membranes and cell walls (proto-lignin, glycerophospholipids, carbohydrates), chemical defense (polyphenols, steroids), reactive oxygen species (ROS) protection (alkaloids, amino acids, flavonoids), nutrition (nitrogen- and phosphate-containing glycerophospholipids), and photosynthesis. Changes in the composition of metabolite families also explained variance related to ecological functioning like physiological adaptations of bryophytes to dry environments (proteins, peptides, flavonoids, terpenes), light availability (flavonoids, terpenes, carbohydrates), temperature (flavonoids), and biotic interactions (steroids, terpenes). The results from this study allow to construct chemical traits that can be attributed to biogeochemistry, habitat conditions, environmental changes and biotic interactions. Our classification framework accelerates the complex annotation process in metabolomics and can be used to simplify biochemical patterns. We show that compound classification is a powerful tool that allows to explore relationships in both molecular biology by "zooming in" and in ecology by "zooming out". The insights revealed by our framework allow to construct new research hypotheses and to enable detailed follow-up studies.}, } @article {pmid33803866, year = {2021}, author = {Marques, I and Fernandes, I and Paulo, OS and Lidon, FC and DaMatta, FM and Ramalho, JC and Ribeiro-Barros, AI}, title = {A Transcriptomic Approach to Understanding the Combined Impacts of Supra-Optimal Temperatures and CO2 Revealed Different Responses in the Polyploid Coffea arabica and Its Diploid Progenitor C. canephora.}, journal = {International journal of molecular sciences}, volume = {22}, number = {6}, pages = {}, pmid = {33803866}, issn = {1422-0067}, support = {No 727934 (project BreedCAFS)//European Union's Horizon 2020/ ; PTDC/ASP-AGR/31257/2017//Fundação para a Ciência e a Tecnologia (FCT), Portugal/ ; UIDB/00239/2020//Research Unit CEF/ ; UIDP/04035/2020 GeoBioTec//Research Unit GeoBioTec/ ; sn//Conselho Nacional de Desenvolvimento Científico e Tecnológico, Brazil (CNPq)/ ; APEMIG, project CRA-RED-00053-16//Fundação de Amparo à Pesquisa do Estado de Minas Gerais, Brazil/ ; }, mesh = {Carbon Dioxide/*pharmacology ; Coffea/drug effects/*genetics ; *Diploidy ; *Gene Expression Regulation, Plant/drug effects ; Gene Ontology ; Genotype ; Photosynthesis/drug effects ; *Polyploidy ; *Temperature ; Transcriptome/drug effects/*genetics ; }, abstract = {Understanding the effect of extreme temperatures and elevated air (CO2) is crucial for mitigating the impacts of the coffee industry. In this work, leaf transcriptomic changes were evaluated in the diploid C. canephora and its polyploid C. arabica, grown at 25 °C and at two supra-optimal temperatures (37 °C, 42 °C), under ambient (aCO2) or elevated air CO2 (eCO2). Both species expressed fewer genes as temperature rose, although a high number of differentially expressed genes (DEGs) were observed, especially at 42 °C. An enrichment analysis revealed that the two species reacted differently to the high temperatures but with an overall up-regulation of the photosynthetic machinery until 37 °C. Although eCO2 helped to release stress, 42 °C had a severe impact on both species. A total of 667 photosynthetic and biochemical related-DEGs were altered with high temperatures and eCO2, which may be used as key probe genes in future studies. This was mostly felt in C. arabica, where genes related to ribulose-bisphosphate carboxylase (RuBisCO) activity, chlorophyll a-b binding, and the reaction centres of photosystems I and II were down-regulated, especially under 42°C, regardless of CO2. Transcriptomic changes showed that both species were strongly affected by the highest temperature, although they can endure higher temperatures (37 °C) than previously assumed.}, } @article {pmid33801727, year = {2021}, author = {Zaborowska, J and Łabiszak, B and Perry, A and Cavers, S and Wachowiak, W}, title = {Candidate Genes for the High-Altitude Adaptations of Two Mountain Pine Taxa.}, journal = {International journal of molecular sciences}, volume = {22}, number = {7}, pages = {}, pmid = {33801727}, issn = {1422-0067}, support = {UMO-2017/27/B/NZ9/00159//Narodowe Centrum Nauki/ ; NE/K012177/1//Natural Environment Research Council/ ; BB/L012243/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {*Adaptation, Biological ; Alleles ; *Altitude ; Bayes Theorem ; Biological Evolution ; Cluster Analysis ; Computational Biology ; Conservation of Natural Resources ; *Genes, Plant ; Genetic Variation ; Genome ; Genotype ; Geography ; High-Throughput Nucleotide Sequencing ; Pinus/*genetics ; Polymorphism, Single Nucleotide ; RNA, Messenger/metabolism ; Spain ; Species Specificity ; Transcriptome ; }, abstract = {Mountain plants, challenged by vegetation time contractions and dynamic changes in environmental conditions, developed adaptations that help them to balance their growth, reproduction, survival, and regeneration. However, knowledge regarding the genetic basis of species adaptation to higher altitudes remain scarce for most plant species. Here, we attempted to identify such corresponding genomic regions of high evolutionary importance in two closely related European pines, Pinus mugo and P. uncinata, contrasting them with a reference lowland relative-P. sylvestris. We genotyped 438 samples at thousands of single nucleotide polymorphism (SNP) markers, tested their genetic differentiation and population structure followed by outlier detection and gene ontology annotations. Markers clearly differentiated the species and uncovered patterns of population structure in two of them. In P. uncinata three Pyrenean sites were grouped together, while two outlying populations constituted a separate cluster. In P. sylvestris, Spanish population appeared distinct from the remaining four European sites. Between mountain pines and the reference species, 35 candidate genes for altitude-dependent selection were identified, including such encoding proteins responsible for photosynthesis, photorespiration and cell redox homeostasis, regulation of transcription, and mRNA processing. In comparison between two mountain pines, 75 outlier SNPs were found in proteins involved mainly in the gene expression and metabolism.}, } @article {pmid33800973, year = {2021}, author = {San-Eufrasio, B and Bigatton, ED and Guerrero-Sánchez, VM and Chaturvedi, P and Jorrín-Novo, JV and Rey, MD and Castillejo, MÁ}, title = {Proteomics Data Analysis for the Identification of Proteins and Derived Proteotypic Peptides of Potential Use as Putative Drought Tolerance Markers for Quercus ilex.}, journal = {International journal of molecular sciences}, volume = {22}, number = {6}, pages = {}, pmid = {33800973}, issn = {1422-0067}, mesh = {*Acclimatization ; Biomarkers ; Computational Biology ; *Data Analysis ; *Droughts ; Peptides/*metabolism ; Plant Proteins/metabolism ; Proteolysis ; *Proteome ; *Proteomics/methods ; Quercus/*physiology ; }, abstract = {Drought is one of the main causes of mortality in holm oak (Quercus ilex) seedlings used in reforestation programs. Although this species shows high adaptability to the extreme climate conditions prevailing in Southern Spain, its intrinsic genetic variability may play a role in the differential response of some populations and individuals. The aim of this work was to identify proteins and derived proteotypic peptides potentially useful as putative markers for drought tolerance in holm oak by using a targeted post-acquisition proteomics approach. For this purpose, we used a set of proteins identified by shotgun (LC-MSMS) analysis in a drought experiment on Q. ilex seedlings from four different provenances (viz. the Andalusian provinces Granada, Huelva, Cadiz and Seville). A double strategy involving the quantification of proteins and target peptides by shotgun analysis and post-acquisition data analysis based on proteotypic peptides was used. To this end, an initial list of proteotypic peptides from proteins highly represented under drought conditions was compiled that was used in combination with the raw files from the shotgun experiment to quantify the relative abundance of the fragment's ion peaks with the software Skyline. The most abundant peptides under drought conditions in at least two populations were selected as putative markers of drought tolerance. A total of 30 proteins and 46 derived peptides belonging to the redox, stress-related, synthesis,-folding and degradation, and primary and secondary metabolism functional groups were thus identified. Two proteins (viz., subtilisin and chaperone GrpE protein) were found at increased levels in three populations, which make them especially interesting for validation drought tolerance markers in subsequent experiments.}, } @article {pmid33794796, year = {2021}, author = {Moghaddam, VK and Dickerson, AS and Bazrafshan, E and Seyedhasani, SN and Najafi, F and Hadei, M and Momeni, J and Moradi, G and Sarmadi, M}, title = {Socioeconomic determinants of global distribution of multiple sclerosis: an ecological investigation based on Global Burden of Disease data.}, journal = {BMC neurology}, volume = {21}, number = {1}, pages = {145}, pmid = {33794796}, issn = {1471-2377}, support = {SRC-97-114//Torbat Heydariyeh University of Medical Sciences/ ; }, mesh = {Databases, Factual ; Educational Status ; Female ; *Global Burden of Disease ; Global Health ; Humans ; Incidence ; Income ; Male ; Multiple Sclerosis/*epidemiology ; Prevalence ; Quality-Adjusted Life Years ; *Socioeconomic Factors ; United Nations ; }, abstract = {BACKGROUND: Socioeconomic factors may be involved in risk of multiple sclerosis (MS), either indirectly or as confounding factors. In this study two comprehensive indicators reflecting socioeconomic differences, including the Human Development Index (HDI) and Prosperity Index (PI), were used to assess the impact of these factors on the worldwide distribution of MS.

METHODS: The data for this global ecological study were obtained from three comprehensive databases including the Global Burden of Disease (as the source of MS indices), United Nations Development Programme (source for HDI) and the Legatum Institute Database for PI. MS indices (including prevalence, incidence, mortality, and disability-adjusted life years) were all analyzed in the form of age- and sex-standardized. Correlation and regression analyses were used to investigate the relationship between HDI and PI and their subsets with MS indices.

RESULTS: All MS indices were correlated with HDI and PI. It was also found that developed countries had significantly higher prevalence and incidence rates of MS than developing countries. Education and governance from the PI, and gross national income and expected years of schooling from the HDI were more associated with MS. Education was significantly related to MS indices (p < 0.01) in both developed and developing countries.

CONCLUSION: In general, the difference in income and the socioeconomic development globally have created a landscape for MS that should be studied in more detail in future studies.}, } @article {pmid33794130, year = {2021}, author = {Özdemir, V}, title = {Digital Is Political: Why We Need a Feminist Conceptual Lens on Determinants of Digital Health.}, journal = {Omics : a journal of integrative biology}, volume = {25}, number = {4}, pages = {249-254}, doi = {10.1089/omi.2021.0020}, pmid = {33794130}, issn = {1557-8100}, mesh = {Artificial Intelligence/trends ; Big Data ; COVID-19/*epidemiology ; Delivery of Health Care/ethics ; Digital Technology/*organization & administration ; Female ; *Feminism ; Healthcare Disparities/*ethics ; Humans ; Pandemics/*prevention & control ; Politics ; Public Health/trends ; SARS-CoV-2/*pathogenicity ; }, abstract = {Digital health is a rapidly emerging field that offers several promising potentials: health care delivery remotely, in urban and rural areas, in any time zone, and in times of pandemics and ecological crises. Digital health encompasses electronic health, computing science, big data, artificial intelligence, and the Internet of Things, to name but a few technical components. Digital health is part of a vision for systems medicine. The advances in digital health have been, however, uneven and highly variable across communities, countries, medical specialties, and societal contexts. This article critically examines the determinants of digital health (DDH). DDH describes and critically responds to inequities and differences in digital health theory and practice across people, places, spaces, and time. DDH is not limited to studying variability in design and access to digital technologies. DDH is situated within a larger context of the political determinants of health. Hence, this article presents an analysis of DDH, as seen through political science, and the feminist studies of technology and society. A feminist lens would strengthen systems-driven, historically and critically informed governance for DDH. This would be a timely antidote against unchecked destructive/extractive governance narratives (e.g., technocracy and patriarchy) that produce and reproduce the health inequities. Moreover, feminist framing of DDH can help cultivate epistemic competence to detect and reject false equivalences in how we understand the emerging digital world(s). False equivalence, very common in the current pandemic and post-truth era, is a type of flawed reasoning in decision-making where equal weight is given to arguments with concrete material evidence, and those that are conjecture, untrue, or unjust. A feminist conceptual lens on DDH would help remedy what I refer to in this article as "the normative deficits" in science and technology policy that became endemic with the rise of neoliberal governance since the 1980s in particular. In this context, it is helpful to recall the feminist writer Ursula K. Le Guin. Le Guin posed "what if?" questions, to break free from oppressive narratives such as patriarchy and re-imagine technology futures. It is time to envision an emancipated, equitable, and more democratic world by asking "what if we lived in a feminist world?" That would be truly awesome, for everyone, women and men, children, youth, and future generations, to steer digital technologies and the new field of DDH toward broadly relevant, ethical, experiential, democratic, and socially responsive health outcomes.}, } @article {pmid33793560, year = {2021}, author = {Burthe, SJ and Schäfer, SM and Asaaga, FA and Balakrishnan, N and Chanda, MM and Darshan, N and Hoti, SL and Kiran, SK and Seshadri, T and Srinivas, PN and Vanak, AT and Purse, BV}, title = {Reviewing the ecological evidence base for management of emerging tropical zoonoses: Kyasanur Forest Disease in India as a case study.}, journal = {PLoS neglected tropical diseases}, volume = {15}, number = {4}, pages = {e0009243}, pmid = {33793560}, issn = {1935-2735}, support = {MR/P024335/2/MRC_/Medical Research Council/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; IA/CPHI/16/1/502648/WTDBT_/DBT-Wellcome Trust India Alliance/India ; MR/P024335/1/MRC_/Medical Research Council/United Kingdom ; /BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; Animals, Wild ; Disease Reservoirs/*veterinary/virology ; Ecosystem ; Encephalitis Viruses, Tick-Borne/*isolation & purification/physiology ; India/epidemiology ; Kyasanur Forest Disease/epidemiology/*veterinary/virology ; *Mammals ; Zoonoses/*epidemiology/virology ; }, abstract = {Zoonoses disproportionately affect tropical communities and are associated with human modification and use of ecosystems. Effective management is hampered by poor ecological understanding of disease transmission and often focuses on human vaccination or treatment. Better ecological understanding of multi-vector and multi-host transmission, social and environmental factors altering human exposure, might enable a broader suite of management options. Options may include "ecological interventions" that target vectors or hosts and require good knowledge of underlying transmission processes, which may be more effective, economical, and long lasting than conventional approaches. New frameworks identify the hierarchical series of barriers that a pathogen needs to overcome before human spillover occurs and demonstrate how ecological interventions may strengthen these barriers and complement human-focused disease control. We extend these frameworks for vector-borne zoonoses, focusing on Kyasanur Forest Disease Virus (KFDV), a tick-borne, neglected zoonosis affecting poor forest communities in India, involving complex communities of tick and host species. We identify the hierarchical barriers to pathogen transmission targeted by existing management. We show that existing interventions mainly focus on human barriers (via personal protection and vaccination) or at barriers relating to Kyasanur Forest Disease (KFD) vectors (tick control on cattle and at the sites of host (monkey) deaths). We review the validity of existing management guidance for KFD through literature review and interviews with disease managers. Efficacy of interventions was difficult to quantify due to poor empirical understanding of KFDV-vector-host ecology, particularly the role of cattle and monkeys in the disease transmission cycle. Cattle are hypothesised to amplify tick populations. Monkeys may act as sentinels of human infection or are hypothesised to act as amplifying hosts for KFDV, but the spatial scale of risk arising from ticks infected via monkeys versus small mammal reservoirs is unclear. We identified 19 urgent research priorities for refinement of current management strategies or development of ecological interventions targeting vectors and host barriers to prevent disease spillover in the future.}, } @article {pmid33793260, year = {2021}, author = {Rothermich, K and Schoen Simmons, E and Rao Makarla, P and Benson, L and Plyler, E and Kim, H and Henssel Joergensen, G}, title = {Tracking nonliteral language processing using audiovisual scenarios.}, journal = {Canadian journal of experimental psychology = Revue canadienne de psychologie experimentale}, volume = {75}, number = {2}, pages = {211-220}, doi = {10.1037/cep0000223}, pmid = {33793260}, issn = {1878-7290}, mesh = {*Cues ; Humans ; Intention ; *Language ; }, abstract = {Recognizing sarcasm and jocularity during face-to-face communication requires the integration of verbal, paralinguistic, and nonverbal cues, yet most previous research on nonliteral language processing has been carried out using written or static stimuli. In the current study, we examined the processing of dynamic literal and nonliteral intentions using eye tracking. Participants (N = 37) viewed short, ecologically valid video vignettes and were asked to identify the speakers' intention. Participants had greater difficulty identifying jocular statements as insincere in comparison to sarcastic statements and spent significantly more time looking at faces during nonliteral versus literal social interactions. Finally, participants took longer to shift their attention from one talker to the other talker during interactions that conveyed literal positive intentions compared with jocular and literal negative intentions. These findings currently support the Standard Pragmatic Model and the Parallel-Constraint-Satisfaction Model of nonliteral language processing. (PsycInfo Database Record (c) 2021 APA, all rights reserved).}, } @article {pmid33788864, year = {2021}, author = {Khalil, H and Santana, R and de Oliveira, D and Palma, F and Lustosa, R and Eyre, MT and Carvalho-Pereira, T and Reis, MG and Ko, AI and Diggle, PJ and Alzate Lopez, Y and Begon, M and Costa, F}, title = {Poverty, sanitation, and Leptospira transmission pathways in residents from four Brazilian slums.}, journal = {PLoS neglected tropical diseases}, volume = {15}, number = {3}, pages = {e0009256}, pmid = {33788864}, issn = {1935-2735}, support = {MR/P024084/1/MRC_/Medical Research Council/United Kingdom ; UL1 TR001863/TR/NCATS NIH HHS/United States ; 102330/Z/13/Z/WT_/Wellcome Trust/United Kingdom ; R01 TW009504/TW/FIC NIH HHS/United States ; }, mesh = {Adult ; Brazil/epidemiology ; Cross-Sectional Studies ; Female ; Humans ; Leptospirosis/*epidemiology/etiology/transmission ; Male ; Middle Aged ; *Poverty ; *Poverty Areas ; *Sanitation ; Social Class ; }, abstract = {Residents of urban slums suffer from a high burden of zoonotic diseases due to individual, socioeconomic, and environmental factors. We conducted a cross-sectional sero-survey in four urban slums in Salvador, Brazil, to characterize how poverty and sanitation contribute to the transmission of rat-borne leptospirosis. Sero-prevalence in the 1,318 participants ranged between 10.0 and 13.3%. We found that contact with environmental sources of contamination, rather than presence of rat reservoirs, is what leads to higher risk for residents living in areas with inadequate sanitation. Further, poorer residents may be exposed away from the household, and ongoing governmental interventions were not associated with lower transmission risk. Residents at higher risk were aware of their vulnerability, and their efforts improved the physical environment near their household, but did not reduce their infection chances. This study highlights the importance of understanding the socioeconomic and environmental determinants of risk, which ought to guide intervention efforts.}, } @article {pmid33788018, year = {2021}, author = {Morris, MRJ and Smith, SJ and Rosebush, J and Rogers, SM}, title = {Mitochondrial volume density and evidence for its role in adaptive divergence in response to thermal tolerance in threespine stickleback.}, journal = {Journal of comparative physiology. B, Biochemical, systemic, and environmental physiology}, volume = {191}, number = {4}, pages = {657-668}, pmid = {33788018}, issn = {1432-136X}, mesh = {Acclimatization ; Adaptation, Physiological ; Animals ; Lakes ; Mitochondrial Size ; *Smegmamorpha ; }, abstract = {Phenotypic plasticity is predicted to permit persistence in new environments, and may subsequently evolve to enhance fitness. Colonizing environments with lower winter temperatures can lead to the evolution of lower critical thermal minima; the corresponding physiological traits associated with temperature tolerance are predicted to involve mitochondrial function. Threespine stickleback (Gasterosteus aculeatus) have colonized freshwater lakes along the Pacific Northwest. These freshwater populations are known to exhibit cold-induced increases in mitochondrial volume density in pectoral muscle, but whether such plasticity evolved before or after colonization is uncertain. Here, we measure critical thermal minima (CTmin) in one marine and one freshwater population of threespine stickleback, and mitochondrial volume density in pectoral and cardiac tissue of both populations acclimated to different temperature treatments (6.2, 14.5 and 20.6 ℃). Mitochondrial volume density increased with cold acclimation in pectoral muscle; cardiac muscle was non-plastic but had elevated mitochondrial volume densities compared to pectoral muscle across all temperature treatments. There were no differences in the levels of plasticity between marine and freshwater stickleback, but neither were there differences in CTmin. Importantly, marine stickleback exhibited plasticity under low-salinity conditions, suggesting that marine stickleback had at least one necessary phenotype for persistence in freshwater environments before colonization occurred.}, } @article {pmid33787289, year = {2021}, author = {Lui, B and Zheng, M and Ogogo, J and White, RS}, title = {Data limitations of administrative databases in examining healthcare disparities in anesthesiology.}, journal = {Journal of comparative effectiveness research}, volume = {10}, number = {7}, pages = {533-535}, doi = {10.2217/cer-2020-0290}, pmid = {33787289}, issn = {2042-6313}, mesh = {*Anesthesiology ; Data Management ; Databases, Factual ; *Healthcare Disparities ; Humans ; }, } @article {pmid33785827, year = {2021}, author = {Vosnjak, M and Sircelj, H and Hudina, M and Usenik, V}, title = {Response of chloroplast pigments, sugars and phenolics of sweet cherry leaves to chilling.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {7210}, pmid = {33785827}, issn = {2045-2322}, mesh = {Acclimatization ; Chloroplasts/chemistry/*metabolism ; *Cold-Shock Response ; Phenols/analysis/*metabolism ; Pigments, Biological/analysis/metabolism ; Plant Leaves/chemistry/physiology ; Prunus avium/chemistry/*physiology ; Sugars/analysis/*metabolism ; }, abstract = {The aim of the present study was to evaluate the effect of post-flowering chilling of sweet cherry (Prunus avium L.) on the content of biochemical parameters in the leaf (chloroplast pigments, sugars and phenolics). The effect of chilling was investigated in two experiments. Potted 2-year-old trees of cv. 'Grace Star' and 'Schneiders' were exposed to one, two or three consecutive overnight chillings at an average air temperature of 4.7 °C (Experiment I), but in the following year only trees of 'Grace Star' were chilled at 2.2 °C (Experiment II), 3 to 7 weeks after flowering. The analysis of the biochemical parameters was performed by high performance liquid chromatography combined with electrospray ionization mass spectrometry. Chilling at 4.7 °C caused little or no stress, while 2.2 °C induced more intense stress with increased zeaxanthin, sugar and phenolic content in leaves, while exposure of trees to higher temperatures and closer to flowering showed no changes. Two or three consecutive overnight chilling periods increased the phenolic content and enhanced the accumulation of zeaxanthin in the leaves. Sucrose, sorbitol, fructose, total sugar, and total flavonoid content in leaves increased within 48 h after chilling. Zeaxanthin epoxidized within 24 h after one and 48 h after one and two consecutive overnight chillings.}, } @article {pmid33785734, year = {2021}, author = {Moro, E and Frank, MR and Pentland, A and Rutherford, A and Cebrian, M and Rahwan, I}, title = {Universal resilience patterns in labor markets.}, journal = {Nature communications}, volume = {12}, number = {1}, pages = {1972}, pmid = {33785734}, issn = {2041-1723}, abstract = {Cities are the innovation centers of the US economy, but technological disruptions can exclude workers and inhibit a middle class. Therefore, urban policy must promote the jobs and skills that increase worker pay, create employment, and foster economic resilience. In this paper, we model labor market resilience with an ecologically-inspired job network constructed from the similarity of occupations' skill requirements. This framework reveals that the economic resilience of cities is universally and uniquely determined by the connectivity within a city's job network. US cities with greater job connectivity experienced lower unemployment during the Great Recession. Further, cities that increase their job connectivity see increasing wage bills, and workers of embedded occupations enjoy higher wages than their peers elsewhere. Finally, we show how job connectivity may clarify the augmenting and deleterious impact of automation in US cities. Policies that promote labor connectivity may grow labor markets and promote economic resilience.}, } @article {pmid33784860, year = {2021}, author = {Todorov, OS and Blomberg, SP and Goswami, A and Sears, K and Drhlík, P and Peters, J and Weisbecker, V}, title = {Testing hypotheses of marsupial brain size variation using phylogenetic multiple imputations and a Bayesian comparative framework.}, journal = {Proceedings. Biological sciences}, volume = {288}, number = {1947}, pages = {20210394}, pmid = {33784860}, issn = {1471-2954}, mesh = {Animals ; Bayes Theorem ; Biological Evolution ; Female ; *Marsupialia/genetics ; Organ Size ; Phylogeny ; Pregnancy ; }, abstract = {Considerable controversy exists about which hypotheses and variables best explain mammalian brain size variation. We use a new, high-coverage dataset of marsupial brain and body sizes, and the first phylogenetically imputed full datasets of 16 predictor variables, to model the prevalent hypotheses explaining brain size evolution using phylogenetically corrected Bayesian generalized linear mixed-effects modelling. Despite this comprehensive analysis, litter size emerges as the only significant predictor. Marsupials differ from the more frequently studied placentals in displaying a much lower diversity of reproductive traits, which are known to interact extensively with many behavioural and ecological predictors of brain size. Our results therefore suggest that studies of relative brain size evolution in placental mammals may require targeted co-analysis or adjustment of reproductive parameters like litter size, weaning age or gestation length. This supports suggestions that significant associations between behavioural or ecological variables with relative brain size may be due to a confounding influence of the extensive reproductive diversity of placental mammals.}, } @article {pmid33780473, year = {2021}, author = {Jiang, W and Liu, L and Xiao, H and Zhu, S and Li, W and Liu, Y}, title = {Composition and distribution of vegetation in the water level fluctuating zone of the Lantsang cascade reservoir system using UAV multispectral imagery.}, journal = {PloS one}, volume = {16}, number = {3}, pages = {e0247682}, pmid = {33780473}, issn = {1932-6203}, mesh = {Biodiversity ; China ; Conservation of Natural Resources/*methods ; Ecosystem ; Geographic Information Systems ; Humans ; Lakes ; Plant Development/*physiology ; Plants/*classification ; Power Plants ; Remote Sensing Technology/*instrumentation ; Rivers ; Spatial Analysis ; }, abstract = {With the development of a large number of tall dams and large cascade reservoir projects in the Lantsang River Basin, a large water level fluctuating zone (WLFZ) containing cascading reservoirs has formed. This newborn ecosystem is related to the sustainable development of hydropower projects, and has become a new problem to be studied urgently. Taking WLFZs in the Huangdeng, Xiaowan and Nuozhadu Reservoirs in the Lantsang River Basin as study areas, this study used multi-spectral remote-sensing field data obtained with unmanned aerial vehicles (UAVs) to ascertain the species types, coverage, distribution characteristics, dominant species and pioneer species of naturally restored vegetation. The considered data were subjected to UAV data processing, vegetation classification using multi-spectral images and a geographic information system (GIS) terrain-distribution analysis. Results show that: Polygonum Plebeium, Cynodon dactylon, Xanthium sibiricum, Ageratum conyzoides, Eleusine indica, Digitaria sanguinalis and Verbena officinalis are the dominant species of vegetation that could be naturally restored in the WLFZ; the vegetation coverage and the number of species are significantly positively correlated with the age and restoration periods of the WLFZ; the vegetation coverage of each study area increases at first, and then decreases, as a function of elevation; gentle slopes about 0-25°are more suitable for vegetation restoration. This study provides first-hand data on the natural restoration of vegetation in WLFZs, and gives a useful reference for its ecological restoration as a consequence of hydropower cascade development in the Lantsang River Basin. Finally, the study demonstrates that light UAV remote sensing is an attractive choice for investigating vegetation in reservoir WLFZs.}, } @article {pmid33779842, year = {2021}, author = {Shalash, AS and Rösler, TW and Salama, M and Pendziwiat, M and Müller, SH and Hopfner, F and Höglinger, GU and Kuhlenbäumer, G}, title = {Evidence for pathogenicity of variant ATM Val1729Leu in a family with ataxia telangiectasia.}, journal = {Neurogenetics}, volume = {22}, number = {2}, pages = {143-147}, pmid = {33779842}, issn = {1364-6753}, mesh = {Ataxia Telangiectasia/*genetics ; Causality ; Egypt ; Female ; Genotype ; Humans ; Male ; *Mutation, Missense ; Pedigree ; Phenotype ; *Point Mutation ; Exome Sequencing ; alpha-Fetoproteins/genetics ; }, abstract = {Ataxia telangiectasia is a rare autosomal recessive multisystem disorder caused by mutations in the gene of ATM serine/threonine kinase. It is characterized by neurodegeneration, leading to severe ataxia, immunodeficiency, increased cancer susceptibility, and telangiectasia. Here, we discovered a co-segregation of two ATM gene variants with ataxia telangiectasia in an Egyptian family. While one of these variants (NM_000051.4(ATM_i001):p.(Val128*)) has previously been reported as pathogenic, the other one (NM_000051.4(ATM_i001):p.(Val1729Leu)) is regarded as a variant of uncertain significance. Our findings in this family provide additional evidence for causality of the second variant and argue that its status should be changed to pathogenic.}, } @article {pmid33779835, year = {2022}, author = {Kardeş, S and Erdem, A and Gürdal, H}, title = {Public interest in musculoskeletal symptoms and disorders during the COVID-19 pandemic : Infodemiology study.}, journal = {Zeitschrift fur Rheumatologie}, volume = {81}, number = {3}, pages = {247-252}, pmid = {33779835}, issn = {1435-1250}, mesh = {*COVID-19/epidemiology ; Humans ; Infodemiology ; *Musculoskeletal Diseases/epidemiology ; Pandemics ; Search Engine ; United States/epidemiology ; }, abstract = {OBJECTIVE: The goal was to assess public interest in a wide range of musculoskeletal symptoms and disorders during the coronavirus disease 2019 (COVID-19) pandemic.

METHODS: We searched Google Trends for 118 search queries within the United States. We compared two timeframes of 2020 (March 15-July 4 and July 5-October 31) to similar timeframes over the four prior years (2016-2019).

RESULTS: In the early pandemic, March 15-July 4, a statistically significant decrease in relative search volume of the majority of queries (60%) was detected, with a significant increase in only 2 queries (i.e. myalgia and toe swelling). In the phase July through October, a statistically significant decrease was detected in only 22% of search queries; there was no difference for 60% of search queries between 2020 and 2016-2019 suggesting a return to their prior levels for most of search queries. Interestingly, the search volume of 18% of search queries (i.e. fatigue, joint pain, muscle pain, myalgia, spondylosis, radiculopathy, myelopathy, neck pain, neck strain, lower back strain, sciatica, shoulder pain, frozen shoulder, elbow pain, lateral epicondylitis, wrist pain, carpal tunnel, hand pain, finger pain, trigger finger, and Morton's neuroma) was significantly increased compared with the four prior years.

CONCLUSION: Public interest focused on COVID-19 and sought online information for COVID-19 symptoms in the early pandemic. In the period July through October, there was an upward trend in musculoskeletal symptoms and some colloquial terms/well-known musculoskeletal conditions coupled with a downward trend in general musculoskeletal disorder terms and certain specific diagnoses. This information may help rheumatologists understand public interest in musculoskeletal symptoms and disorders and address the needs of patients to mitigate the negative impact of the pandemic on outcomes.}, } @article {pmid33772033, year = {2021}, author = {Brlík, V and Šilarová, E and Škorpilová, J and Alonso, H and Anton, M and Aunins, A and Benkö, Z and Biver, G and Busch, M and Chodkiewicz, T and Chylarecki, P and Coombes, D and de Carli, E and Del Moral, JC and Derouaux, A and Escandell, V and Eskildsen, DP and Fontaine, B and Foppen, RPB and Gamero, A and Gregory, RD and Harris, S and Herrando, S and Hristov, I and Husby, M and Ieronymidou, C and Jiquet, F and Kålås, JA and Kamp, J and Kmecl, P and Kurlavičius, P and Lehikoinen, A and Lewis, L and Lindström, Å and Manolopoulos, A and Martí, D and Massimino, D and Moshøj, C and Nellis, R and Noble, D and Paquet, A and Paquet, JY and Portolou, D and Ramírez, I and Redel, C and Reif, J and Ridzoň, J and Schmid, H and Seaman, B and Silva, L and Soldaat, L and Spasov, S and Staneva, A and Szép, T and Florenzano, GT and Teufelbauer, N and Trautmann, S and van der Meij, T and van Strien, A and van Turnhout, C and Vermeersch, G and Vermouzek, Z and Vikstrøm, T and Voříšek, P and Weiserbs, A and Klvaňová, A}, title = {Long-term and large-scale multispecies dataset tracking population changes of common European breeding birds.}, journal = {Scientific data}, volume = {8}, number = {1}, pages = {21}, pmid = {33772033}, issn = {2052-4463}, support = {07.0202/2017/755630/SUB/ENV.D2//European Commission (EC)/ ; 07.0202/2017/755630/SUB/ENV.D2//European Commission (EC)/ ; 07.0202/2017/755630/SUB/ENV.D2//European Commission (EC)/ ; 07.0202/2017/755630/SUB/ENV.D2//European Commission (EC)/ ; 07.0202/2017/755630/SUB/ENV.D2//European Commission (EC)/ ; 07.0202/2017/755630/SUB/ENV.D2//European Commission (EC)/ ; }, mesh = {Animals ; *Birds ; Conservation of Natural Resources ; Databases, Factual ; Europe ; Population Dynamics ; }, abstract = {Around fifteen thousand fieldworkers annually count breeding birds using standardized protocols in 28 European countries. The observations are collected by using country-specific and standardized protocols, validated, summarized and finally used for the production of continent-wide annual and long-term indices of population size changes of 170 species. Here, we present the database and provide a detailed summary of the methodology used for fieldwork and calculation of the relative population size change estimates. We also provide a brief overview of how the data are used in research, conservation and policy. We believe this unique database, based on decades of bird monitoring alongside the comprehensive summary of its methodology, will facilitate and encourage further use of the Pan-European Common Bird Monitoring Scheme results.}, } @article {pmid33771867, year = {2021}, author = {Boyero, L and Pérez, J and López-Rojo, N and Tonin, AM and Correa-Araneda, F and Pearson, RG and Bosch, J and Albariño, RJ and Anbalagan, S and Barmuta, LA and Beesley, L and Burdon, FJ and Caliman, A and Callisto, M and Campbell, IC and Cardinale, BJ and Casas, JJ and Chará-Serna, AM and Ciapała, S and Chauvet, E and Colón-Gaud, C and Cornejo, A and Davis, AM and Degebrodt, M and Dias, ES and Díaz, ME and Douglas, MM and Elosegi, A and Encalada, AC and de Eyto, E and Figueroa, R and Flecker, AS and Fleituch, T and Frainer, A and França, JS and García, EA and García, G and García, P and Gessner, MO and Giller, PS and Gómez, JE and Gómez, S and Gonçalves, JF and Graça, MAS and Hall, RO and Hamada, N and Hepp, LU and Hui, C and Imazawa, D and Iwata, T and Junior, ESA and Kariuki, S and Landeira-Dabarca, A and Leal, M and Lehosmaa, K and M'Erimba, C and Marchant, R and Martins, RT and Masese, FO and Camden, M and McKie, BG and Medeiros, AO and Middleton, JA and Muotka, T and Negishi, JN and Pozo, J and Ramírez, A and Rezende, RS and Richardson, JS and Rincón, J and Rubio-Ríos, J and Serrano, C and Shaffer, AR and Sheldon, F and Swan, CM and Tenkiano, NSD and Tiegs, SD and Tolod, JR and Vernasky, M and Watson, A and Yegon, MJ and Yule, CM}, title = {Latitude dictates plant diversity effects on instream decomposition.}, journal = {Science advances}, volume = {7}, number = {13}, pages = {}, pmid = {33771867}, issn = {2375-2548}, abstract = {Running waters contribute substantially to global carbon fluxes through decomposition of terrestrial plant litter by aquatic microorganisms and detritivores. Diversity of this litter may influence instream decomposition globally in ways that are not yet understood. We investigated latitudinal differences in decomposition of litter mixtures of low and high functional diversity in 40 streams on 6 continents and spanning 113° of latitude. Despite important variability in our dataset, we found latitudinal differences in the effect of litter functional diversity on decomposition, which we explained as evolutionary adaptations of litter-consuming detritivores to resource availability. Specifically, a balanced diet effect appears to operate at lower latitudes versus a resource concentration effect at higher latitudes. The latitudinal pattern indicates that loss of plant functional diversity will have different consequences on carbon fluxes across the globe, with greater repercussions likely at low latitudes.}, } @article {pmid33767284, year = {2021}, author = {Clontz, LM and Pepin, KM and VerCauteren, KC and Beasley, JC}, title = {Behavioral state resource selection in invasive wild pigs in the Southeastern United States.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {6924}, pmid = {33767284}, issn = {2045-2322}, mesh = {Animals ; *Feeding Behavior ; Female ; Geographic Information Systems ; *Introduced Species ; Male ; Remote Sensing Technology ; Seasons ; South Carolina ; Sus scrofa/*psychology ; }, abstract = {Elucidating correlations between wild pig (Sus scrofa) behavior and landscape attributes can aid in the advancement of management strategies for controlling populations. Using GPS data from 49 wild pigs in the southeastern U.S., we used hidden Markov models to define movement path characteristics and assign behaviors (e.g., resting, foraging, travelling). We then explored the connection between these behaviors and resource selection for both sexes between two distinct seasons based on forage availability (i.e., low forage, high forage). Females demonstrated a crepuscular activity pattern in the high-forage season and a variable pattern in the low-forage season, while males exhibited nocturnal activity patterns across both seasons. Wild pigs selected for bottomland hardwoods and dense canopy cover in all behavioral states in both seasons. Males selected for diversity in vegetation types while foraging in the low-forage season compared to the high-forage season and demonstrated an increased use of linear anthropogenic features across seasons while traveling. Wild pigs can establish populations and home ranges in an array of landscapes, but our results demonstrate male and female pigs exhibit clear differences in movement behavior and there are key resources associated with common behaviors that can be targeted to improve the efficiency of management programs.}, } @article {pmid33767257, year = {2021}, author = {Randhawa, N and Mailhot, H and Lang, DT and Martínez-López, B and Gilardi, K and Mazet, JAK}, title = {Fine scale infectious disease modeling using satellite-derived data.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {6946}, pmid = {33767257}, issn = {2045-2322}, mesh = {Disease Outbreaks ; *Disease Transmission, Infectious ; *Geographic Information Systems ; Humans ; Influenza Vaccines ; Influenza, Human/epidemiology/prevention & control/*transmission ; *Models, Theoretical ; Rwanda/epidemiology ; *Satellite Imagery ; Vaccination ; }, abstract = {Innovative tools for modeling infectious agents are essential for better understanding disease spread given the inherent complexity of changing and interacting ecological, environmental, and demographic factors. We leveraged fine-scale satellite data on urban areas to build a road-connected geospatial network upon which to model disease spread. This model was tested by simulating the spread of the 2009 pandemic influenza in Rwanda and also used to determine the effects of vaccination regimens on outbreak spread and impact. Our results were comparable to data collected during the actual pandemic in Rwanda, determining the initial places affected after outbreak introduction in Kigali. They also highlighted the effectiveness of preventing outbreaks by targeting mitigation efforts at points of outbreak origin. This modeling approach can be valuable for planning and control purposes in real-time disease situations, providing helpful baseline scenarios during initial phases of outbreaks, and can be applied to other infectious diseases where high population mobility promotes rapid disease propagation.}, } @article {pmid33764467, year = {2021}, author = {Modica, MV and Ahmad, R and Ainsworth, S and Anderluh, G and Antunes, A and Beis, D and Caliskan, F and Serra, MD and Dutertre, S and Moran, Y and Nalbantsoy, A and Oukkache, N and Pekar, S and Remm, M and von Reumont, BM and Sarigiannis, Y and Tarallo, A and Tytgat, J and Undheim, EAB and Utkin, Y and Verdes, A and Violette, A and Zancolli, G}, title = {The new COST Action European Venom Network (EUVEN)-synergy and future perspectives of modern venomics.}, journal = {GigaScience}, volume = {10}, number = {3}, pages = {}, pmid = {33764467}, issn = {2047-217X}, mesh = {*Venoms ; }, abstract = {Venom research is a highly multidisciplinary field that involves multiple subfields of biology, informatics, pharmacology, medicine, and other areas. These different research facets are often technologically challenging and pursued by different teams lacking connection with each other. This lack of coordination hampers the full development of venom investigation and applications. The COST Action CA19144-European Venom Network was recently launched to promote synergistic interactions among different stakeholders and foster venom research at the European level.}, } @article {pmid33762616, year = {2021}, author = {Peebles, K and Mittler, JE and Goodreau, SM and Murphy, JT and Reid, MC and Abernethy, N and Gottlieb, GS and Barnabas, RV and Herbeck, JT}, title = {Risk compensation after HIV-1 vaccination may accelerate viral adaptation and reduce cost-effectiveness: a modeling study.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {6798}, pmid = {33762616}, issn = {2045-2322}, support = {R01 AI108490/AI/NIAID NIH HHS/United States ; R01 AI150467/AI/NIAID NIH HHS/United States ; R21 HD075662/HD/NICHD NIH HHS/United States ; R01 HD068395/HD/NICHD NIH HHS/United States ; }, mesh = {AIDS Vaccines/*administration & dosage/immunology ; Cost-Benefit Analysis ; Drug Resistance, Viral ; HIV Infections/immunology/*prevention & control/virology ; HIV-1/isolation & purification/*physiology ; Humans ; *Models, Theoretical ; Risk Assessment ; Vaccination ; }, abstract = {Pathogen populations can evolve in response to selective pressure from vaccine-induced immune responses. For HIV, models predict that viral adaptation, either via strain replacement or selection on de novo mutation, may rapidly reduce the effectiveness of an HIV vaccine. We hypothesized that behavioral risk compensation after vaccination may accelerate the transmission of vaccine resistant strains, increasing the rate of viral adaptation and leading to a more rapid decline in vaccine effectiveness. To test our hypothesis, we modeled: (a) the impact of risk compensation on rates of HIV adaptation via strain replacement in response to a partially effective vaccine; and (b) the combined impact of risk compensation and viral adaptation on vaccine-mediated epidemic control. We used an agent-based epidemic model that was calibrated to HIV-1 trends in South Africa, and includes demographics, sexual network structure and behavior, and within-host disease dynamics. Our model predicts that risk compensation can increase the rate of HIV viral adaptation in response to a vaccine. In combination, risk compensation and viral adaptation can, under certain scenarios, reverse initial declines in prevalence due to vaccination, and result in HIV prevalence at 15 years equal to or greater than prevalence without a vaccine.}, } @article {pmid33758263, year = {2021}, author = {Lobaton, J and Andrew, R and Duitama, J and Kirkland, L and Macfadyen, S and Rader, R}, title = {Using RNA-seq to characterize pollen-stigma interactions for pollination studies.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {6635}, pmid = {33758263}, issn = {2045-2322}, mesh = {Computational Biology/methods ; Flowers/*genetics ; Gene Expression Profiling ; Gene Expression Regulation, Plant ; High-Throughput Nucleotide Sequencing ; Phylogeny ; *Plant Physiological Phenomena ; Pollen/*genetics ; Pollination/*physiology ; Polymorphism, Single Nucleotide ; Reproduction ; }, abstract = {Insects are essential for the reproduction of pollinator-dependent crops and contribute to the pollination of 87% of wild plants and 75% of the world's food crops. Understanding pollen flow dynamics between plants and pollinators is thus essential to manage and conserve wild plants and ensure yields are maximized in food crops. However, the determination of pollen transfer in the field is complex and laborious. We developed a field experiment in a pollinator-dependent crop and used high throughput RNA sequencing (RNA-seq) to quantify pollen flow by measuring changes in gene expression between pollination treatments across different apple (Malus domestica Borkh.) cultivars. We tested three potential molecular indicators of successful pollination and validated these results with field data by observing single and multiple visits by honey bees (Apis mellifera) to apple flowers and measured fruit set in a commercial apple orchard. The first indicator of successful outcrossing was revealed via differential gene expression in the cross-pollination treatments after 6 h. The second indicator of successful outcrossing was revealed by the expression of specific genes related to pollen tube formation and defense response at three different time intervals in the stigma and the style following cross-pollination (i.e. after 6, 24, and 48 h). Finally, genotyping variants specific to donor pollen could be detected in cross-pollination treatments, providing a third indicator of successful outcrossing. Field data indicated that one or five flower visits by honey bees were insufficient and at least 10 honey bee flower visits were required to achieve a 25% probability of fruit set under orchard conditions. By combining the genotyping data, the differential expression analysis, and the traditional fruit set field experiments, it was possible to evaluate the pollination effectiveness of honey bee visits under orchards conditions. This is the first time that pollen-stigma-style mRNA expression analysis has been conducted after a pollinator visit (honey bee) to a plant (in vivo apple flowers). This study provides evidence that mRNA sequencing can be used to address complex questions related to stigma-pollen interactions over time in pollination ecology.}, } @article {pmid33758194, year = {2021}, author = {Monnet, AC and Cilleros, K and Médail, F and Albassatneh, MC and Arroyo, J and Bacchetta, G and Bagnoli, F and Barina, Z and Cartereau, M and Casajus, N and Dimopoulos, P and Domina, G and Doxa, A and Escudero, M and Fady, B and Hampe, A and Matevski, V and Misfud, S and Nikolic, T and Pavon, D and Roig, A and Barea, ES and Spanu, I and Strid, A and Vendramin, GG and Leriche, A}, title = {WOODIV, a database of occurrences, functional traits, and phylogenetic data for all Euro-Mediterranean trees.}, journal = {Scientific data}, volume = {8}, number = {1}, pages = {89}, pmid = {33758194}, issn = {2052-4463}, mesh = {*Databases, Factual ; Ecosystem ; *Forests ; Mediterranean Region ; Phylogeny ; *Trees ; }, abstract = {Trees play a key role in the structure and function of many ecosystems worldwide. In the Mediterranean Basin, forests cover approximately 22% of the total land area hosting a large number of endemics (46 species). Despite its particularities and vulnerability, the biodiversity of Mediterranean trees is not well known at the taxonomic, spatial, functional, and genetic levels required for conservation applications. The WOODIV database fills this gap by providing reliable occurrences, four functional traits (plant height, seed mass, wood density, and specific leaf area), and sequences from three DNA-regions (rbcL, matK, and trnH-psbA), together with modelled occurrences and a phylogeny for all 210 Euro-Mediterranean tree species. We compiled, homogenized, and verified occurrence data from sparse datasets and collated them on an INSPIRE-compliant 10 × 10 km grid. We also gathered functional trait and genetic data, filling existing gaps where possible. The WOODIV database can benefit macroecological studies in the fields of conservation, biogeography, and community ecology.}, } @article {pmid33758189, year = {2021}, author = {Compagnoni, A and Levin, S and Childs, DZ and Harpole, S and Paniw, M and Römer, G and Burns, JH and Che-Castaldo, J and Rüger, N and Kunstler, G and Bennett, JM and Archer, CR and Jones, OR and Salguero-Gómez, R and Knight, TM}, title = {Herbaceous perennial plants with short generation time have stronger responses to climate anomalies than those with longer generation time.}, journal = {Nature communications}, volume = {12}, number = {1}, pages = {1824}, pmid = {33758189}, issn = {2041-1723}, mesh = {Biological Variation, Population/physiology ; Climate ; *Climate Change ; Databases, Factual ; Ecosystem ; Models, Statistical ; Plant Development/*physiology ; Plants/*adverse effects ; Population Dynamics/*statistics & numerical data ; Rain ; Regression Analysis ; Temperature ; }, abstract = {There is an urgent need to synthesize the state of our knowledge on plant responses to climate. The availability of open-access data provide opportunities to examine quantitative generalizations regarding which biomes and species are most responsive to climate drivers. Here, we synthesize time series of structured population models from 162 populations of 62 plants, mostly herbaceous species from temperate biomes, to link plant population growth rates (λ) to precipitation and temperature drivers. We expect: (1) more pronounced demographic responses to precipitation than temperature, especially in arid biomes; and (2) a higher climate sensitivity in short-lived rather than long-lived species. We find that precipitation anomalies have a nearly three-fold larger effect on λ than temperature. Species with shorter generation time have much stronger absolute responses to climate anomalies. We conclude that key species-level traits can predict plant population responses to climate, and discuss the relevance of this generalization for conservation planning.}, } @article {pmid33750380, year = {2021}, author = {Olafson, PU and Aksoy, S and Attardo, GM and Buckmeier, G and Chen, X and Coates, CJ and Davis, M and Dykema, J and Emrich, SJ and Friedrich, M and Holmes, CJ and Ioannidis, P and Jansen, EN and Jennings, EC and Lawson, D and Martinson, EO and Maslen, GL and Meisel, RP and Murphy, TD and Nayduch, D and Nelson, DR and Oyen, KJ and Raszick, TJ and Ribeiro, JMC and Robertson, HM and Rosendale, AJ and Sackton, TB and Saelao, P and Swiger, SL and Sze, SH and Tarone, AM and Taylor, DB and Warren, WC and Waterhouse, RM and Weirauch, MT and Werren, JH and Wilson, RK and Zdobnov, EM and Benoit, JB}, title = {The genome of the stable fly, Stomoxys calcitrans, reveals potential mechanisms underlying reproduction, host interactions, and novel targets for pest control.}, journal = {BMC biology}, volume = {19}, number = {1}, pages = {41}, pmid = {33750380}, issn = {1741-7007}, support = {53553//CpG/ ; DEB-1654417//National Science Foundation (US)/ ; R01 AI148551/AI/NIAID NIH HHS/United States ; PP00P3_170664/SNSF_/Swiss National Science Foundation/Switzerland ; 3094-32000-041-D//Agricultural Research Service/ ; 5U54HG00307907//NIH-NHGRI/ ; 1950078//National Science Foundation (US)/ ; 2018-67013-28495//U.S. Department of Agriculture/ ; 1257053//National Science Foundation/ ; }, mesh = {Animals ; *Genome, Insect ; Host-Parasite Interactions/*genetics ; *Insect Control ; Muscidae/*genetics ; Reproduction/genetics ; }, abstract = {BACKGROUND: The stable fly, Stomoxys calcitrans, is a major blood-feeding pest of livestock that has near worldwide distribution, causing an annual cost of over $2 billion for control and product loss in the USA alone. Control of these flies has been limited to increased sanitary management practices and insecticide application for suppressing larval stages. Few genetic and molecular resources are available to help in developing novel methods for controlling stable flies.

RESULTS: This study examines stable fly biology by utilizing a combination of high-quality genome sequencing and RNA-Seq analyses targeting multiple developmental stages and tissues. In conjunction, 1600 genes were manually curated to characterize genetic features related to stable fly reproduction, vector host interactions, host-microbe dynamics, and putative targets for control. Most notable was characterization of genes associated with reproduction and identification of expanded gene families with functional associations to vision, chemosensation, immunity, and metabolic detoxification pathways.

CONCLUSIONS: The combined sequencing, assembly, and curation of the male stable fly genome followed by RNA-Seq and downstream analyses provide insights necessary to understand the biology of this important pest. These resources and new data will provide the groundwork for expanding the tools available to control stable fly infestations. The close relationship of Stomoxys to other blood-feeding (horn flies and Glossina) and non-blood-feeding flies (house flies, medflies, Drosophila) will facilitate understanding of the evolutionary processes associated with development of blood feeding among the Cyclorrhapha.}, } @article {pmid33750296, year = {2021}, author = {Miller, EF and Manica, A}, title = {mtDNAcombine: tools to combine sequences from multiple studies.}, journal = {BMC bioinformatics}, volume = {22}, number = {1}, pages = {115}, pmid = {33750296}, issn = {1471-2105}, support = {BB/M011194/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Bayes Theorem ; *DNA, Mitochondrial/genetics ; *Databases, Nucleic Acid ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: Today an unprecedented amount of genetic sequence data is stored in publicly available repositories. For decades now, mitochondrial DNA (mtDNA) has been the workhorse of genetic studies, and as a result, there is a large volume of mtDNA data available in these repositories for a wide range of species. Indeed, whilst whole genome sequencing is an exciting prospect for the future, for most non-model organisms' classical markers such as mtDNA remain widely used. By compiling existing data from multiple original studies, it is possible to build powerful new datasets capable of exploring many questions in ecology, evolution and conservation biology. One key question that these data can help inform is what happened in a species' demographic past. However, compiling data in this manner is not trivial, there are many complexities associated with data extraction, data quality and data handling.

RESULTS: Here we present the mtDNAcombine package, a collection of tools developed to manage some of the major decisions associated with handling multi-study sequence data with a particular focus on preparing sequence data for Bayesian skyline plot demographic reconstructions.

CONCLUSIONS: There is now more genetic information available than ever before and large meta-data sets offer great opportunities to explore new and exciting avenues of research. However, compiling multi-study datasets still remains a technically challenging prospect. The mtDNAcombine package provides a pipeline to streamline the process of downloading, curating, and analysing sequence data, guiding the process of compiling data sets from the online database GenBank.}, } @article {pmid33749027, year = {2021}, author = {Correia, RA and Ladle, R and Jarić, I and Malhado, ACM and Mittermeier, JC and Roll, U and Soriano-Redondo, A and Veríssimo, D and Fink, C and Hausmann, A and Guedes-Santos, J and Vardi, R and Di Minin, E}, title = {Digital data sources and methods for conservation culturomics.}, journal = {Conservation biology : the journal of the Society for Conservation Biology}, volume = {35}, number = {2}, pages = {398-411}, doi = {10.1111/cobi.13706}, pmid = {33749027}, issn = {1523-1739}, mesh = {*Biodiversity ; *Conservation of Natural Resources ; Humans ; Information Storage and Retrieval ; }, abstract = {Ongoing loss of biological diversity is primarily the result of unsustainable human behavior. Thus, the long-term success of biodiversity conservation depends on a thorough understanding of human-nature interactions. Such interactions are ubiquitous but vary greatly in time and space and are difficult to monitor efficiently at large spatial scales. However, the Information Age also provides new opportunities to better understand human-nature interactions because many aspects of daily life are recorded in a variety of digital formats. The emerging field of conservation culturomics aims to take advantage of digital data sources and methods to study human-nature interactions and thus to provide new tools for studying conservation at relevant temporal and spatial scales. Nevertheless, technical challenges associated with the identification, access, and analysis of relevant data hamper the wider adoption of culturomics methods. To help overcome these barriers, we propose a conservation culturomics research framework that addresses data acquisition, analysis, and inherent biases. The main sources of culturomic data include web pages, social media, and other digital platforms from which metrics of content and engagement can be obtained. Obtaining raw data from these platforms is usually desirable but requires careful consideration of how to access, store, and prepare the data for analysis. Methods for data analysis include network approaches to explore connections between topics, time-series analysis for temporal data, and spatial modeling to highlight spatial patterns. Outstanding challenges associated with culturomics research include issues of interdisciplinarity, ethics, data biases, and validation. The practical guidance we offer will help conservation researchers and practitioners identify and obtain the necessary data and carry out appropriate analyses for their specific questions, thus facilitating the wider adoption of culturomics approaches for conservation applications.}, } @article {pmid33746985, year = {2021}, author = {Sung, MH and Shen, Y and Handel, A and Bahl, J and Ross, TM}, title = {Longitudinal Assessment of Immune Responses to Repeated Annual Influenza Vaccination in a Human Cohort of Adults and Teenagers.}, journal = {Frontiers in immunology}, volume = {12}, number = {}, pages = {642791}, pmid = {33746985}, issn = {1664-3224}, support = {75N93019C00052/AI/NIAID NIH HHS/United States ; U01 AI150747/AI/NIAID NIH HHS/United States ; }, mesh = {Adolescent ; Adult ; Age Factors ; Antibodies, Viral/*blood ; Body Mass Index ; Cohort Studies ; Female ; Hemagglutination Inhibition Tests ; Humans ; Influenza Vaccines/*immunology ; Longitudinal Studies ; Male ; Middle Aged ; *Vaccination ; Young Adult ; }, abstract = {Background: The overall performance of a multiple component vaccine assessed by the vaccine-elicited immune responses across various strains in a repeated vaccination setting has not been well-studied, and the comparison between adults and teenagers is yet to be made. Methods: A human cohort study was conducted at the University of Georgia, with 140 subjects (86 adults and 54 teenagers) repeatedly vaccinated in the 2017/2018 and 2018/2019 influenza seasons. Host information was prospectively collected, and serum samples were collected before and after vaccination in each season. The association between host factors and repeated measures of hemagglutination inhibition (HAI) composite scores was assessed by generalized linear models with generalized estimating equations. Results: The mean HAI composite scores for the entire sample (t = 4.26, df = 139, p < 0.001) and the teenager group (t = 6.44, df = 53, p < 0.001) declined in the second season, while the changes in the adults were not statistically significant (t = -1.14, df = 85, p = 0.26). A mixture pattern of changes in both directions was observed in the adults when stratified by prior vaccination. In addition, the regression analysis suggested an interactive effect of age and BMI on the HAI composite scores in the overall population (beta = 0.005; 95% CI, 0.0008-0.01) and the adults (beta = 0.005; 95% CI, 0.0005-0.01). Conclusions: Our study found distinct vaccine-elicited immune responses between adults and teenagers when both were repeatedly vaccinated in consecutive years. An interactive effect of age and BMI on the HAI composite scores were identified in the overall population and the adults.}, } @article {pmid33744433, year = {2021}, author = {Guo, Z and Fu, Y and Huang, C and Zheng, C and Wu, Z and Chen, X and Gao, S and Ma, Y and Shahen, M and Li, Y and Tu, P and Zhu, J and Wang, Z and Xiao, W and Wang, Y}, title = {NOGEA: A Network-oriented Gene Entropy Approach for Dissecting Disease Comorbidity and Drug Repositioning.}, journal = {Genomics, proteomics & bioinformatics}, volume = {19}, number = {4}, pages = {549-564}, pmid = {33744433}, issn = {2210-3244}, mesh = {Comorbidity ; Computational Biology/methods ; *Drug Repositioning/methods ; Entropy ; *Gene Regulatory Networks ; Humans ; Reproducibility of Results ; }, abstract = {Rapid development of high-throughput technologies has permitted the identification of an increasing number of disease-associated genes (DAGs), which are important for understanding disease initiation and developing precision therapeutics. However, DAGs often contain large amounts of redundant or false positive information, leading to difficulties in quantifying and prioritizing potential relationships between these DAGs and human diseases. In this study, a network-oriented gene entropy approach (NOGEA) is proposed for accurately inferring master genes that contribute to specific diseases by quantitatively calculating their perturbation abilities on directed disease-specific gene networks. In addition, we confirmed that the master genes identified by NOGEA have a high reliability for predicting disease-specific initiation events and progression risk. Master genes may also be used to extract the underlying information of different diseases, thus revealing mechanisms of disease comorbidity. More importantly, approved therapeutic targets are topologically localized in a small neighborhood of master genes in the interactome network, which provides a new way for predicting drug-disease associations. Through this method, 11 old drugs were newly identified and predicted to be effective for treating pancreatic cancer and then validated by in vitro experiments. Collectively, the NOGEA was useful for identifying master genes that control disease initiation and co-occurrence, thus providing a valuable strategy for drug efficacy screening and repositioning. NOGEA codes are publicly available at https://github.com/guozihuaa/NOGEA.}, } @article {pmid33744235, year = {2021}, author = {Hill, EB and Kennedy, AJ and Roberts, KM and Riedl, KM and Grainger, EM and Clinton, SK}, title = {Considerations for Use of the Phenol-Explorer Database to Estimate Dietary (Poly)phenol Intake.}, journal = {Journal of the Academy of Nutrition and Dietetics}, volume = {121}, number = {5}, pages = {833-834}, doi = {10.1016/j.jand.2021.02.010}, pmid = {33744235}, issn = {2212-2672}, support = {TL1 TR002735/TR/NCATS NIH HHS/United States ; }, mesh = {Databases, Factual ; Diet ; Humans ; *Phenol ; *Phenols ; }, } @article {pmid33742810, year = {2021}, author = {Li, J and Zou, SZ and Zhao, Y and Zhao, RK and Dang, ZW and Pan, MQ and Zhu, DN and Zhou, CS}, title = {[Major Ionic Characteristics and Factors of Karst Groundwater at Huixian Karst Wetland, China].}, journal = {Huan jing ke xue= Huanjing kexue}, volume = {42}, number = {4}, pages = {1750-1760}, doi = {10.13227/j.hjkx.202009027}, pmid = {33742810}, issn = {0250-3301}, abstract = {To investigate the major ionic chemical characteristics and seasonal variations, 27 groundwater samples were collected from the wet season, flat season, and dry season during 2018-2019 in the Huixian Karst wetland, which is the largest low-altitude karst wetland in China. The single pollution standard index was applied to evaluate the groundwater pollution during different periods, and the major ionic factors of the karst groundwater were analyzed using the statistical analysis method, Gibbs diagram, and ion ratio. The results revealed that the groundwater samples were a weakly alkaline fresh water that were rich in Ca[2+] and HCO3[-]. The average concentrations of the primary ions followed the order of flat season > wet season > dry season; meanwhile, the water quality in the dry season was better than that in the wet and flat seasons. The K[+] and NO3[-] in the karst groundwater were mostly affected by the spatial distributions of the aquifers, and the Mg[2+], SO4[2-], NO2[-], NH4[+], and TDS were related to the space-season scale. Na[+], Ca[2+], HCO3[-], and Cl[-] were relatively stable ions in the karst groundwater. The hydrochemical characteristics were primarily determined by carbonate rock dissolution and were found to be the HCO3-Ca type, which accounted for 77.78%, 77.78%, and 88.89% in the wet season, flat season, and dry season, respectively. The karst groundwater was predominantly polluted by SO4[2-], NO3[-], and NO2[-]; particularly, NO3[-] exhibited serious pollution points, and SO4[2-] had heavy pollution points in the wet and flat seasons. The chemical composition of the karst groundwater was controlled mostly by water-rock interactions. Ca[2+] and HCO3[-] primarily came from calcite dissolution, and the high concentrations of Mg[2+] and SO4[2-] in a few number of points were controlled by dolomite, dolomitic limestone, and pyrite. K[+], Na[+], SO4[2-], NO3[-], and Cl[-] partly came from atmospheric precipitation, and Na[+] and Cl[-] partly came from human activities; K[+] was related to potash fertilizer, and the main source of NO3[-] was chemical fertilizer.}, } @article {pmid33742448, year = {2021}, author = {Soria, CD and Pacifici, M and Di Marco, M and Stephen, SM and Rondinini, C}, title = {COMBINE: a coalesced mammal database of intrinsic and extrinsic traits.}, journal = {Ecology}, volume = {102}, number = {6}, pages = {e03344}, doi = {10.1002/ecy.3344}, pmid = {33742448}, issn = {1939-9170}, support = {766417//H2020 Marie Skłodowska-Curie Actions/ ; }, mesh = {Animals ; Biodiversity ; *Data Management ; Ecosystem ; Female ; *Mammals ; Phenotype ; }, abstract = {The use of species' traits in macroecological analyses has gained popularity in the last decade, becoming an important tool to understand global biodiversity patterns. Currently, trait data can be found across a wide variety of data sets included in websites, articles, and books, each one with its own taxonomic classification, set of traits, and data management methodology. Mammals, in particular, are among the most studied taxa, with large sources of trait information readily available. To facilitate the use of these data, we did an extensive review of published mammal trait data sources between 1999 and May 2020 and produced COMBINE: a COalesced Mammal dataBase of INtrinsic and Extrinsic traits. Our aim was to create a taxonomically integrated database of mammal traits that maximized trait number and coverage without compromising data quality. COMBINE contains information on 54 traits for 6,234 extant and recently extinct mammal species, including information on morphology, reproduction, diet, biogeography, life habit, phenology, behavior, home range, and density. Additionally, we calculated other relevant traits such as habitat and altitudinal breadths for all species and dispersal for terrestrial non-volant species. All data are compatible with the taxonomies of the IUCN Red List v. 2020-2 and PHYLACINE v. 1.2. Missing data were adequately flagged and imputed for non-biogeographical traits with 20% or more data available. We obtained full data sets for 21 traits such as female maturity, litter size, maximum longevity, trophic level, and dispersal, providing imputation performance statistics for all. This data set will be especially useful for those interested in including species' traits in large-scale ecological and conservation analyses. There are no copyright or proprietary restrictions; we request citation of this publication and all relevant underlying data sources (found in Data S1: trait_data_sources.csv), upon using these data.}, } @article {pmid33742230, year = {2022}, author = {Tipton, L and Zahn, GL and Darcy, JL and Amend, AS and Hynson, NA}, title = {Hawaiian Fungal Amplicon Sequence Variants Reveal Otherwise Hidden Biogeography.}, journal = {Microbial ecology}, volume = {83}, number = {1}, pages = {48-57}, pmid = {33742230}, issn = {1432-184X}, mesh = {*Ecosystem ; *Fungi/genetics ; Hawaii ; Reproducibility of Results ; Sequence Analysis, DNA ; }, abstract = {To study biogeography and other ecological patterns of microorganisms, including fungi, scientists have been using operational taxonomic units (OTUs) as representations of species or species hypotheses. However, when defined by 97% sequence similarity cutoff at an accepted barcode locus such as 16S in bacteria or ITS in fungi, these OTUs can obscure biogeographic patterns, mask taxonomic diversity, and hinder meta-analyses. Amplicon sequence variants (ASVs) have been proposed to alleviate all of these issues and have been shown to do so in bacteria. Analyzing ASVs is just emerging as a common practice among fungal studies, and it is unclear whether the benefits found in bacterial studies of using such an approach carryover to fungi. Here, we conducted a meta-analysis of Hawaiian fungi by analyzing ITS1 amplicon sequencing data as ASVs and exploring ecological patterns. These surveys spanned three island groups and five ecosystems combined into the first comprehensive Hawaiian Mycobiome ASV Database. Our results show that ASVs can be used to combine fungal ITS surveys, increase reproducibility, and maintain the broad ecological patterns observed with OTUs, including diversity orderings. Additionally, the ASVs that comprise some of the most common OTUs in our database reveals some island specialists, indicating that traditional OTU clustering can obscure important biogeographic patterns. We recommend that future fungal studies, especially those aimed at assessing biogeography, analyze ASVs rather than OTUs. We conclude that similar to bacterial studies, ASVs improve reproducibility and data sharing for fungal studies.}, } @article {pmid33741938, year = {2021}, author = {Bozek, K and Hebert, L and Portugal, Y and Mikheyev, AS and Stephens, GJ}, title = {Markerless tracking of an entire honey bee colony.}, journal = {Nature communications}, volume = {12}, number = {1}, pages = {1733}, pmid = {33741938}, issn = {2041-1723}, mesh = {Animals ; Bees/*physiology ; Behavior, Animal/*physiology ; Computational Biology ; Neural Networks, Computer ; }, abstract = {From cells in tissue, to bird flocks, to human crowds, living systems display a stunning variety of collective behaviors. Yet quantifying such phenomena first requires tracking a significant fraction of the group members in natural conditions, a substantial and ongoing challenge. We present a comprehensive, computational method for tracking an entire colony of the honey bee Apis mellifera using high-resolution video on a natural honeycomb background. We adapt a convolutional neural network (CNN) segmentation architecture to automatically identify bee and brood cell positions, body orientations and within-cell states. We achieve high accuracy (~10% body width error in position, ~10° error in orientation, and true positive rate > 90%) and demonstrate months-long monitoring of sociometric colony fluctuations. These fluctuations include ~24 h cycles in the counted detections, negative correlation between bee and brood, and nightly enhancement of bees inside comb cells. We combine detected positions with visual features of organism-centered images to track individuals over time and through challenging occluding events, recovering ~79% of bee trajectories from five observation hives over 5 min timespans. The trajectories reveal important individual behaviors, including waggle dances and crawling inside comb cells. Our results provide opportunities for the quantitative study of collective bee behavior and for advancing tracking techniques of crowded systems.}, } @article {pmid33741909, year = {2021}, author = {Glass, DS and Jin, X and Riedel-Kruse, IH}, title = {Nonlinear delay differential equations and their application to modeling biological network motifs.}, journal = {Nature communications}, volume = {12}, number = {1}, pages = {1788}, pmid = {33741909}, issn = {2041-1723}, mesh = {*Algorithms ; Animals ; Computational Biology/*methods ; Feedback, Physiological ; Gene Expression Regulation ; *Gene Regulatory Networks ; Humans ; *Models, Genetic ; *Nonlinear Dynamics ; Signal Transduction/genetics ; }, abstract = {Biological regulatory systems, such as cell signaling networks, nervous systems and ecological webs, consist of complex dynamical interactions among many components. Network motif models focus on small sub-networks to provide quantitative insight into overall behavior. However, such models often overlook time delays either inherent to biological processes or associated with multi-step interactions. Here we systematically examine explicit-delay versions of the most common network motifs via delay differential equation (DDE) models, both analytically and numerically. We find many broadly applicable results, including parameter reduction versus canonical ordinary differential equation (ODE) models, analytical relations for converting between ODE and DDE models, criteria for when delays may be ignored, a complete phase space for autoregulation, universal behaviors of feedforward loops, a unified Hill-function logic framework, and conditions for oscillations and chaos. We conclude that explicit-delay modeling simplifies the phenomenology of many biological networks and may aid in discovering new functional motifs.}, } @article {pmid33737402, year = {2021}, author = {Pekar, J and Worobey, M and Moshiri, N and Scheffler, K and Wertheim, JO}, title = {Timing the SARS-CoV-2 index case in Hubei province.}, journal = {Science (New York, N.Y.)}, volume = {372}, number = {6540}, pages = {412-417}, pmid = {33737402}, issn = {1095-9203}, support = {R01 AI135992/AI/NIAID NIH HHS/United States ; R01 AI136056/AI/NIAID NIH HHS/United States ; T15 LM011271/LM/NLM NIH HHS/United States ; }, mesh = {Animals ; COVID-19/*epidemiology/transmission/*virology ; China/epidemiology ; Computer Simulation ; Evolution, Molecular ; Genetic Fitness ; *Genome, Viral ; Humans ; Models, Theoretical ; *Pandemics ; Phylogeny ; Retrospective Studies ; SARS-CoV-2/*genetics/*physiology ; Viral Zoonoses ; }, abstract = {Understanding when severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged is critical to evaluating our current approach to monitoring novel zoonotic pathogens and understanding the failure of early containment and mitigation efforts for COVID-19. We used a coalescent framework to combine retrospective molecular clock inference with forward epidemiological simulations to determine how long SARS-CoV-2 could have circulated before the time of the most recent common ancestor of all sequenced SARS-CoV-2 genomes. Our results define the period between mid-October and mid-November 2019 as the plausible interval when the first case of SARS-CoV-2 emerged in Hubei province, China. By characterizing the likely dynamics of the virus before it was discovered, we show that more than two-thirds of SARS-CoV-2-like zoonotic events would be self-limited, dying out without igniting a pandemic. Our findings highlight the shortcomings of zoonosis surveillance approaches for detecting highly contagious pathogens with moderate mortality rates.}, } @article {pmid33735173, year = {2021}, author = {Nev, OA and Lindsay, RJ and Jepson, A and Butt, L and Beardmore, RE and Gudelj, I}, title = {Predicting microbial growth dynamics in response to nutrient availability.}, journal = {PLoS computational biology}, volume = {17}, number = {3}, pages = {e1008817}, pmid = {33735173}, issn = {1553-7358}, mesh = {Biotechnology ; *Candida/cytology/growth & development/physiology ; Cell Proliferation/physiology ; Computational Biology ; Ecology ; *Enterobacteriaceae/cytology/growth & development/physiology ; *Models, Biological ; *Saccharomyces cerevisiae/cytology/growth & development/physiology ; }, abstract = {Developing mathematical models to accurately predict microbial growth dynamics remains a key challenge in ecology, evolution, biotechnology, and public health. To reproduce and grow, microbes need to take up essential nutrients from the environment, and mathematical models classically assume that the nutrient uptake rate is a saturating function of the nutrient concentration. In nature, microbes experience different levels of nutrient availability at all environmental scales, yet parameters shaping the nutrient uptake function are commonly estimated for a single initial nutrient concentration. This hampers the models from accurately capturing microbial dynamics when the environmental conditions change. To address this problem, we conduct growth experiments for a range of micro-organisms, including human fungal pathogens, baker's yeast, and common coliform bacteria, and uncover the following patterns. We observed that the maximal nutrient uptake rate and biomass yield were both decreasing functions of initial nutrient concentration. While a functional form for the relationship between biomass yield and initial nutrient concentration has been previously derived from first metabolic principles, here we also derive the form of the relationship between maximal nutrient uptake rate and initial nutrient concentration. Incorporating these two functions into a model of microbial growth allows for variable growth parameters and enables us to substantially improve predictions for microbial dynamics in a range of initial nutrient concentrations, compared to keeping growth parameters fixed.}, } @article {pmid33733497, year = {2021}, author = {Kanga, S and Meraj, G and Sudhanshu, and Farooq, M and Nathawat, MS and Singh, SK}, title = {Analyzing the Risk to COVID-19 Infection using Remote Sensing and GIS.}, journal = {Risk analysis : an official publication of the Society for Risk Analysis}, volume = {41}, number = {5}, pages = {801-813}, pmid = {33733497}, issn = {1539-6924}, mesh = {COVID-19/*epidemiology/virology ; *Geographic Information Systems ; Humans ; India/epidemiology ; Pandemics ; *Remote Sensing Technology ; Risk Assessment ; SARS-CoV-2/isolation & purification ; }, abstract = {Globally, the COVID-19 pandemic has become a threat to humans and to the socioeconomic systems they have developed since the industrial revolution. Hence, governments and stakeholders call for strategies to help restore normalcy while dealing with this pandemic effectively. Since till now, the disease is yet to have a cure; therefore, only risk-based decision making can help governments achieve a sustainable solution in the long term. To help the decisionmakers explore viable actions, we propose a risk-based assessment framework for analyzing COVID-19 risk to areas, using integrated hazard and vulnerability components associated with this pandemic for effective risk mitigation. The study is carried on a region administrated by Jaipur municipal corporation (JMC), India. Based on the current understanding of this disease, we hypothesized different COVID-19 risk indices (C19Ri) of the wards of JMC such as proximity to hotspots, total population, population density, availability of clean water, and associated land use/land cover, are related with COVID-19 contagion and calculated them in a GIS-based multicriteria risk reduction method. The results showed disparateness in COVID-19 risk areas with a higher risk in north-eastern and south-eastern zone wards within the boundary of JMC. We proposed prioritizing wards under higher risk zones for intelligent decision making regarding COVID-19 risk reduction through appropriate management of resources-related policy consequences. This study aims to serve as a baseline study to be replicated in other parts of the country or world to eradicate the threat of COVID-19 effectively.}, } @article {pmid33731213, year = {2021}, author = {Wang, N and Guo, L and Shewade, HD and Thekkur, P and Zhang, H and Yuan, YL and Wang, XM and Wang, XL and Sun, MM and Huang, F and Zhao, YL}, title = {Effect of using electronic medication monitors on tuberculosis treatment outcomes in China: a longitudinal ecological study.}, journal = {Infectious diseases of poverty}, volume = {10}, number = {1}, pages = {29}, pmid = {33731213}, issn = {2049-9957}, support = {OPP1137180//China-Gates Foundation TB Project/ ; }, mesh = {Aged ; Antitubercular Agents/*therapeutic use ; China ; Electronics ; Female ; Humans ; Longitudinal Studies ; Medication Adherence/psychology/*statistics & numerical data ; Reminder Systems ; Treatment Outcome ; Tuberculosis, Pulmonary/*drug therapy ; }, abstract = {BACKGROUND: In China, an indigenously developed electronic medication monitor (EMM) was designed and used in 138 counties from three provinces. Previous studies showed positive results on accuracy, effectiveness, acceptability, and feasibility, but also found some ineffective implementations. In this paper, we assessed the effect of implementation of EMMs on treatment outcomes.

METHODS: The longitudinal ecological method was used at the county level with aggregate secondary programmatic data. All the notified TB cases in 138 counties were involved in this study from April 2017 to June 2019, and rifampicin-resistant cases were excluded. We fitted a multilevel model to assess the relative change in the quarterly treatment success rate with increasing quarterly EMM coverage rate, in which a mixed effects maximum likelihood regression using random intercept model was applied, by adjusting for seasonal trends, population size, sociodemographic and clinical characteristics, and clustering within counties.

RESULTS: Among all 69 678 notified TB cases, the treatment success rate was slightly increased from 93.5% [95% confidence interval (CI): 93.0-94.0] in second quarter of 2018 to 94.9% (95% CI: 94.4-95.4) in second quarter of 2019 after implementing EMMs. There was a statistically significant effect between quarterly EMM coverage and treatment success rate after adjusting for potential confounders (P = 0.0036), increasing 10% of EMM coverage rate will lead to 0.2% treatment success rate augment. Besides, an increase of 10% of elderly or bacteriologically confirmed TB will lead to a decrease of 0.4% and 0.9% of the treatment success rate.

CONCLUSIONS: Under programmatic settings, we found a statistically significant effect between increasing coverage of EMM and treatment success rate at the county level. More prospective studies are needed to confirm the effect of using EMM on TB treatment outcomes. We suggest performing operational research on EMMs that provides real-time data under programmatic conditions in the future.}, } @article {pmid33730287, year = {2021}, author = {Saina, JK and Li, ZZ and Mekbib, Y and Gichira, AW and Liao, YY}, title = {Transcriptome sequencing and microsatellite marker discovery in Ailanthus altissima (Mill.) Swingle (Simaroubaceae).}, journal = {Molecular biology reports}, volume = {48}, number = {3}, pages = {2007-2023}, pmid = {33730287}, issn = {1573-4978}, support = {Grant No.31500457//National Natural Scientific Foundation of China/ ; }, mesh = {Ailanthus/*genetics ; Chloroplasts/genetics ; Databases, Genetic ; Expressed Sequence Tags ; Gene Expression Regulation, Plant ; Gene Ontology ; Genetic Loci ; Genetics, Population ; Haplotypes/genetics ; Microsatellite Repeats/*genetics ; Molecular Sequence Annotation ; Phylogeny ; Polymorphism, Genetic ; *Sequence Analysis, RNA ; Transcriptome/*genetics ; }, abstract = {Ailanthus altissima Swingle, is a tree species native to East Asia and has a great potential in decorative, bioenergy and industrial applications in many countries. To date, despite its commercial importance, the genomic and genetic resources available for this species are still insufficient. In this study, we characterized the transcriptome of A. altissima and developed thirteen EST-SSRs (expressed sequence tag-simple sequence repeats) based on Illumina paired-end RNA sequencing (RNA-seq). Besides, we developed ten polymorphic chloroplast microsatellite (cpSSR) markers using the available chloroplast genome of A. altissima. The transcriptome data produced 87,797 unigenes, of which 64,891 (73.91%) unigenes were successfully annotated in at least one protein database. For cpSSR markers the number of detected alleles (N) per marker varied from three at cpSSR12 to twelve at cpSSR8, the unbiased haploid diversity indices (uh) varied from 0.111 to 0.485, and haploid diversity indices (h) ranged from 0.101 to 0.444 with an average unbiased haploid diversity index (uh) of 0.274. Overall, a total of 65 different cpSSR alleles were identified at the ten loci among 165 individuals of A. altissima. The allele number per locus for EST-SSRs varied from 2.143 to 9.357, and the values of observed and expected heterozygosity ranged from 0.312 to 1.000 and 0.505 to 0.826, respectively. The molecular markers developed in this study will facilitate future genetic diversity, population structure, long distance-gene transfer and pollen-based gene flow analyses of A. altissima populations from its known distribution ranges in China focusing on planted and natural forest stands.}, } @article {pmid33730196, year = {2021}, author = {Ghennam, K and Attou, F and Abdoun, F}, title = {Impact of atmospheric pollution on asthma and bronchitis based on lichen biomonitoring using IAP, IHI and GIS in Algiers Bay (Algeria).}, journal = {Environmental monitoring and assessment}, volume = {193}, number = {4}, pages = {198}, pmid = {33730196}, issn = {1573-2959}, mesh = {*Air Pollutants/analysis ; *Air Pollution/analysis ; Algeria ; *Asthma/epidemiology ; Bays ; Biological Monitoring ; *Bronchitis ; Cities ; Environmental Monitoring ; Geographic Information Systems ; Humans ; *Lichens ; }, abstract = {We investigated the association between air pollution and asthma and bronchitis hospital admissions in Algiers city (Algeria). In addition, we used geographic information systems (GIS) and statistical methods to evaluate their correlation with the atmospheric pollution estimated by the lichen biomonitoring method of the index of atmospheric purity (IAP), the index of human impact (IHI) and environmental parameters. Thus, we georeferenced 976 local patients (including 771 patients with asthma and 205 patients with bronchitis). Then, we compared the patients to the spatial distribution of IAP in thirty-five areas (communities). The results revealed a significant difference in the mean spatial variation in the diseases among those areas. In fact, maps and generalized linear models (GLMs) revealed a significant negative correlation between IAP and diseases. Therefore, redundancy analysis (RDA) and Monte Carlo tests described a significant effect of IAP, urbanization and the number of roads on the distribution of diseases. We hope our findings contribute to enriching the literature on health research with a low-cost method of monitoring outdoor air pollution.}, } @article {pmid33727612, year = {2021}, author = {Matriano, DM and Alegado, RA and Conaco, C}, title = {Detection of horizontal gene transfer in the genome of the choanoflagellate Salpingoeca rosetta.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {5993}, pmid = {33727612}, issn = {2045-2322}, mesh = {Choanoflagellata/classification/*genetics ; Computational Biology/methods ; Evolution, Molecular ; *Gene Transfer, Horizontal ; *Genome ; Genomics/methods ; Molecular Sequence Annotation ; Phylogeny ; }, abstract = {Horizontal gene transfer (HGT), the movement of heritable materials between distantly related organisms, is crucial in eukaryotic evolution. However, the scale of HGT in choanoflagellates, the closest unicellular relatives of metazoans, and its possible roles in the evolution of animal multicellularity remains unexplored. We identified at least 175 candidate HGTs in the genome of the colonial choanoflagellate Salpingoeca rosetta using sequence-based tests. The majority of these were orthologous to genes in bacterial and microalgal lineages, yet displayed genomic features consistent with the rest of the S. rosetta genome-evidence of ancient acquisition events. Putative functions include enzymes involved in amino acid and carbohydrate metabolism, cell signaling, and the synthesis of extracellular matrix components. Functions of candidate HGTs may have contributed to the ability of choanoflagellates to assimilate novel metabolites, thereby supporting adaptation, survival in diverse ecological niches, and response to external cues that are possibly critical in the evolution of multicellularity in choanoflagellates.}, } @article {pmid33726598, year = {2021}, author = {Sugasawa, S and Webb, B and Healy, SD}, title = {Object manipulation without hands.}, journal = {Proceedings. Biological sciences}, volume = {288}, number = {1947}, pages = {20203184}, pmid = {33726598}, issn = {1471-2954}, support = {/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; *Hand ; Hand Strength ; *Robotics ; }, abstract = {Our current understanding of manipulation is based on primate hands, resulting in a detailed but narrow perspective of ways to handle objects. Although most other animals lack hands, they are still capable of flexible manipulation of diverse objects, including food and nest materials, and depend on dexterity in object handling to survive and reproduce. Birds, for instance, use their bills and feet to forage and build nests, while insects carry food and construct nests with their mandibles and legs. Bird bills and insect mandibles are much simpler than a primate hand, resembling simple robotic grippers. A better understanding of manipulation in these and other species would provide a broader comparative perspective on the origins of dexterity. Here we contrast data from primates, birds and insects, describing how they sense and grasp objects, and the neural architectures that control manipulation. Finally, we outline techniques for collecting comparable manipulation data from animals with diverse morphologies and describe the practical applications of studying manipulation in a wide range of species, including providing inspiration for novel designs of robotic manipulators.}, } @article {pmid33724239, year = {2021}, author = {Kerfeld, CI and Hurvitz, PM and Bjornson, KF}, title = {Physical Activity Measurement in Children Who Use Mobility Assistive Devices: Accelerometry and Global Positioning System.}, journal = {Pediatric physical therapy : the official publication of the Section on Pediatrics of the American Physical Therapy Association}, volume = {33}, number = {2}, pages = {92-99}, doi = {10.1097/PEP.0000000000000786}, pmid = {33724239}, issn = {1538-005X}, mesh = {Accelerometry ; *Cerebral Palsy ; Child ; Exercise ; Geographic Information Systems ; Humans ; *Self-Help Devices ; }, abstract = {PURPOSE: To explore the usefulness of combining accelerometry, global positioning systems, and geographic information systems, to describe the time spent in different locations and physical activity (PA) duration/count levels by location for 4 children with cerebral palsy (CP) who use assistive devices (AD).

METHODS: A descriptive multiple-case study.

RESULTS: Combining the 3 instruments was useful in describing and differentiating duration by location, and amount and location of PA across differing functional levels and AD. For example, the child classified with a Gross Motor Function Classification System (GMFCS) level II exhibited large amounts of PA in community settings. In contrast, the child classified with a GMFCS level V had small amounts of PA and spent most measured time at home.

CONCLUSIONS: Combined accelerometry, global positioning system, and geographic information system have potential to capture time spent and amount/intensity of PA relative to locations within daily environments for children with CP who use AD.}, } @article {pmid33716147, year = {2021}, author = {Pan, TL and Bai, YM and Cheng, CM and Tsai, SJ and Tsai, CF and Su, TP and Li, CT and Lin, WC and Chen, TJ and Liang, CS and Chen, MH}, title = {Atopic dermatitis and dementia risk: A nationwide longitudinal study.}, journal = {Annals of allergy, asthma & immunology : official publication of the American College of Allergy, Asthma, & Immunology}, volume = {127}, number = {2}, pages = {200-205}, doi = {10.1016/j.anai.2021.03.001}, pmid = {33716147}, issn = {1534-4436}, mesh = {Alzheimer Disease/*epidemiology ; Comorbidity ; Databases, Factual ; Dermatitis, Atopic/*epidemiology ; Female ; Humans ; Male ; Middle Aged ; Risk ; Risk Factors ; Taiwan/epidemiology ; }, abstract = {BACKGROUND: Retrospective studies have suggested that patients with dementia have higher prevalence of atopic dermatitis (AD) than those without dementia. However, the temporal association of AD with subsequent dementia remains unknown.

OBJECTIVE: To assess the temporal association of AD with subsequent dementia.

METHODS: We included data of patients with AD aged 45 years and older (n = 1059) and 1:10 age, sex, residence, income, and dementia-related comorbidity-matched controls (n = 10,590) from the Taiwan National Health Insurance Research Database and reviewed their subsequent dementia development from the enrollment date to the end of 2013.

RESULTS: After adjustments for dementia-related comorbidities, patients with AD were found to be more likely to develop any dementia (hazard ratio [HR], 2.02; 95% confidence interval [CI], 1.24-3.29), particularly Alzheimer's disease (HR, 3.74; 95% CI, 1.17-11.97), during the follow-up period than those in the control group. Moderate-to-severe AD was associated with a high subsequent dementia risk (HR, 4.64; 95% CI, 2.58-8.33). Sensitivity analyses with the exclusion of the first 3 (HR, 2.20; 95% CI, 1.28-3.80) or 5 (HR, 2.05; 95% CI, 1.08-3.89) years of observation revealed consistent findings.

CONCLUSION: AD may be an independent risk factor for new-onset dementia. Clinicians may monitor the trajectory of neurocognitive function among elderly patients with AD. Additional studies elucidating the pathomechanisms between AD and subsequent dementia are warranted.}, } @article {pmid33713799, year = {2021}, author = {Peng, J and Rajeevan, H and Kubatko, L and RoyChoudhury, A}, title = {A fast likelihood approach for estimation of large phylogenies from continuous trait data.}, journal = {Molecular phylogenetics and evolution}, volume = {161}, number = {}, pages = {107142}, doi = {10.1016/j.ympev.2021.107142}, pmid = {33713799}, issn = {1095-9513}, mesh = {Bayes Theorem ; Gene Frequency ; Humans ; *Likelihood Functions ; Phenotype ; *Phylogeny ; Reproducibility of Results ; Research Design ; }, abstract = {Despite the recent availability of large-scale genomic data for many individuals, few methods for phylogenetic inference are both computationally efficient and highly accurate for trees with hundreds of taxa. Model-based methods such as those developed in the maximum likelihood and Bayesian frameworks are especially time-consuming, as they involve both computationally intensive calculations on fixed phylogenies and searches through the space of possible phylogenies, and they are known to scale poorly with the addition of taxa. Here, we propose a fast approximation to the maximum likelihood estimator that directly uses continuous trait data, such as allele frequency data. The approximation works by first computing the maximum likelihood estimates of some internal branch lengths, and then inferring the tree-topology using these estimates. Our approach is more computationally efficient than existing methods for such data while still achieving comparable accuracy. This method is innovative in its use of the mathematical properties of tree-topologies for inference, and thus serves as a useful addition to the collection of methods available for estimating phylogenies from continuous trait data.}, } @article {pmid33713720, year = {2021}, author = {Nam, S and Griggs, S and Ash, GI and Dunton, GF and Huang, S and Batten, J and Parekh, N and Whittemore, R}, title = {Ecological momentary assessment for health behaviors and contextual factors in persons with diabetes: A systematic review.}, journal = {Diabetes research and clinical practice}, volume = {174}, number = {}, pages = {108745}, doi = {10.1016/j.diabres.2021.108745}, pmid = {33713720}, issn = {1872-8227}, mesh = {Diabetes Mellitus, Type 1/psychology/*therapy ; Diabetes Mellitus, Type 2/psychology/*therapy ; Eating ; Ecological Momentary Assessment/*statistics & numerical data ; Feeding Behavior ; *Health Behavior ; Humans ; Insulin/administration & dosage ; *Self Care ; }, abstract = {AIM: The objective of this systematic review was to summarize the ecological momentary assessment (EMA) methodology and associations between EMA-measured psychosocial, contextual factors and diabetes self-management.

METHODS: The inclusion criteria were: research of EMA and diabetes self-management behaviors such as glucose checks, administration of insulin and eating-and dietary intake behaviors among persons with diabetes. A comprehensive search of several databases was conducted across all dates until July 2020.

RESULTS: A modified Checklist for Reporting EMA Studies was used to assess the quality of studies. Among the ten included studies, participants were predominantly White adolescents with type 1 diabetes (T1D) and type 2 diabetes was studied in two studies. Time-varying, psychosocial contexts such as negative affect or negative social interaction were associated with missed insulin injection and poor adherence to glucose check. More preceding psychological stress was associated with more calorie intake from snacks or binge eating behaviors. Mornings were the most challenging time of day for adherence to diabetes self-management among adolescents with T1D. Intentional insulin withholding was more common in the afternoon in adults with T1D.

CONCLUSIONS: EMA has potential clinical utility in the assessment of diabetes self-management and in the development of timely and individualized diabetes interventions.}, } @article {pmid33712909, year = {2021}, author = {Yücesoy, H and Dönmez, A and Atmaca-Aydın, E and Yentür, SP and Saruhan-Direskeneli, G and Ankaralı, H and Erdoğan, N and Karagülle, MZ}, title = {Effects of balneological outpatient treatment on clinical parameters and serum cytokine levels in patients with chronic low back pain: a single-blind randomized controlled trial.}, journal = {International journal of biometeorology}, volume = {65}, number = {8}, pages = {1367-1376}, pmid = {33712909}, issn = {1432-1254}, support = {TTU-2018-31745//Bilimsel Araştirma Projeleri Birimi, Istanbul Üniversitesi/ ; }, mesh = {*Chronic Pain/therapy ; Cytokines ; Humans ; *Low Back Pain/therapy ; Outpatients ; Single-Blind Method ; Treatment Outcome ; }, abstract = {This study aimed to investigate the effects of balneological outpatient treatment (hydrotherapy and peloidotherapy) on clinical status and serum cytokine levels in patients with chronic low back pain (CLBP). Seventy-four patients with CLBP who accepted to participate to the study were randomly divided into two groups. The study group was given ten sessions (in 2 weeks) of hydrotherapy, peloidotherapy, and home exercise, while the control group was given only home exercise. All patients were assessed before and at the end of therapy, at the 1st and 3rd months. The primary outcomes were pain intensity on the visual analog scale (VAS) (VAS-pain, VAS-rest, VAS-exercise) and Oswestry Disability Index (ODI). The secondary outcome measures included patient's and physician's global assessment (VAS-PGA), (VAS-DGA), finger-to-floor distance (FFD), modified Schober test, Short Form-36 (SF-36), and the use of analgesic drug. Venous blood samples were drawn from all patients before/1st day and after therapy/12th day to measure serum interleukin (IL)-6 and IL-10 levels. Significant improvement was observed in the study group in VAS-pain, VAS-rest, VAS-exercise, VAS-PGA, VAS-DGA, ODI, and SF-36 parameters after treatment and improvement maintained for 3 months. In the control group, significant improvement was observed in VAS-pain, VAS-exercise, VAS-PGA, VAS-DGA, and ODI scores on the 12th day and continued for 3 months. Decrease in pain, pain during rest and exercise, modified Schober test, VAS-PGA, VAS-DGA, ODI scores, and the increase in SF-36 pain and general health scores showed superiority in favor of the study group in all evaluations. There was a significant increase in IL-10 values from baseline at the end of treatment in the study group. The use of non-steroidal anti-inflammatory drug (NSAID) was significantly lower in the study group compared with the use of NSAID in the control group in the 3rd month. Balneological outpatient treatment improved clinical status in CLBP patients. Although no significant correlation was clearly determined between IL-10 levels and pain score, this effect might be related to the observed increase in the anti-inflammatory cytokine IL-10 levels that was observed only in the study group.}, } @article {pmid33710086, year = {2021}, author = {Hossain, R and Dai, JH and Jamani, S and Ma, Z and Dvorani, E and Graves, E and Burcul, I and Strobel, S}, title = {Hard-to-Reach Populations and Administrative Health Data: A Serial Cross-sectional Study and Application of Data to Improve Interventions for People Experiencing Homelessness.}, journal = {Medical care}, volume = {59}, number = {Suppl 2}, pages = {S139-S145}, doi = {10.1097/MLR.0000000000001481}, pmid = {33710086}, issn = {1537-1948}, mesh = {Cross-Sectional Studies ; Delivery of Health Care/*standards ; Female ; Health Services Accessibility ; *Ill-Housed Persons ; Humans ; Male ; *Medical Informatics ; Ontario ; *Quality Improvement ; }, abstract = {BACKGROUND: Intervention studies with vulnerable groups in the emergency department (ED) suffer from lower quality and an absence of administrative health data. We used administrative health data to identify and describe people experiencing homelessness who access EDs, characterize patterns of ED use relative to the general population, and apply findings to inform the design of a peer support program.

METHODS: We conducted a serial cross-sectional study using administrative health data to examine ED use by people experiencing homelessness and nonhomeless individuals in the Niagara region of Ontario, Canada from April 1, 2010 to March 31, 2018. Outcomes included number of visits; unique patients; group proportions of Canadian Triage and Acuity Scale (CTAS) scores; time spent in emergency; and time to see an MD. Descriptive statistics were generated with t tests for point estimates and a Mann-Whitney U test for distributional measures.

RESULTS: We included 1,486,699 ED visits. The number of unique people experiencing homelessness ranged from 91 in 2010 to 344 in 2017, trending higher over the study period compared with nonhomeless patients. Rate of visits increased from 1.7 to 2.8 per person. People experiencing homelessness presented later with higher overall acuity compared with the general population. Time in the ED and time to see an MD were greater among people experiencing homelessness.

CONCLUSIONS: People experiencing homelessness demonstrate increasing visits, worse health, and longer time in the ED when compared with the general population, which may be a burden on both patients and the health care system.}, } @article {pmid33705403, year = {2021}, author = {Li, P and Chen, C and Li, P and Dong, Y}, title = {A comprehensive examination of the lysine acetylation targets in paper mulberry based on proteomics analyses.}, journal = {PloS one}, volume = {16}, number = {3}, pages = {e0240947}, pmid = {33705403}, issn = {1932-6203}, mesh = {Acetylation ; Amino Acid Motifs ; Chromatography, High Pressure Liquid ; Gene Ontology ; HSP70 Heat-Shock Proteins/metabolism ; Lysine/*metabolism ; Morus/*metabolism ; Nanotechnology ; Phenylalanine Ammonia-Lyase/metabolism ; Proteomics/*methods ; Tandem Mass Spectrometry ; }, abstract = {Rocky desertification is a bottleneck that reduces ecological and environmental security in karst areas. Paper mulberry, a unique deciduous tree, shows good performance in rocky desertification areas. Its resistance mechanisms are therefore of high interest. In this study, a lysine acetylation proteomics analysis of paper mulberry seedling leaves was conducted in combination with the purification of acetylated protein by high-precision nano LC-MS/MS. We identified a total of 7130 acetylation sites in 3179 proteins. Analysis of the modified sites showed a predominance of nine motifs. Six positively charged residues: lysine (K), arginine (R), and histidine (H), serine (S), threonine (T), and tyrosine (Y) occurred most frequently at the +1 position, phenylalanine (F) was both detected both upstream and downstream of the acetylated lysines; and the sequence logos showed a strong preference for lysine and arginine around acetylated lysines. Functional annotation revealed that the identified enzymes were mainly involved in translation, transcription, ribosomal structure and biological processes, showing that lysine acetylation can regulate various aspects of primary carbon and nitrogen metabolism and secondary metabolism. Acetylated proteins were enriched in the chloroplast, cytoplasm, and nucleus, and many stress response-related proteins were also discovered to be acetylated, including PAL, HSP70, and ERF. HSP70, an important protein involved in plant abiotic and disease stress responses, was identified in paper mulberry, although it is rarely found in woody plants. This may be further examined in research in other plants and could explain the good adaptation of paper mulberry to the karst environment. However, these hypotheses require further verification. Our data can provide a new starting point for the further analysis of the acetylation function in paper mulberry and other plants.}, } @article {pmid33705400, year = {2021}, author = {Asaaga, FA and Rahman, M and Kalegowda, SD and Mathapati, J and Savanur, I and Srinivas, PN and Seshadri, T and Narayanswamy, D and Kiran, SK and Oommen, MA and Young, JC and Purse, BV}, title = {'None of my ancestors ever discussed this disease before!' How disease information shapes adaptive capacity of marginalised rural populations in India.}, journal = {PLoS neglected tropical diseases}, volume = {15}, number = {3}, pages = {e0009265}, pmid = {33705400}, issn = {1935-2735}, support = {MR/T029846/1/MRC_/Medical Research Council/United Kingdom ; MR/P024335/2/MRC_/Medical Research Council/United Kingdom ; MR/ P024335/1/MRC_/Medical Research Council/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; IA/CPHI/16/1/502648/WTDBT_/DBT-Wellcome Trust India Alliance/India ; MR/P024335/1/MRC_/Medical Research Council/United Kingdom ; /BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Adaptation, Psychological ; Adolescent ; Adult ; Aged ; Animals ; Disease Outbreaks ; Disease Susceptibility ; Family Characteristics ; Female ; Humans ; India/epidemiology ; Information Services ; Kyasanur Forest Disease/*epidemiology/prevention & control ; Male ; Middle Aged ; Rural Population ; Vaccination ; Young Adult ; Zoonoses/epidemiology ; }, abstract = {Smallholder farmer and tribal communities are often characterised as marginalised and highly vulnerable to emerging zoonotic diseases due to their relatively poor access to healthcare, worse-off health outcomes, proximity to sources of disease risks, and their social and livelihood organisation. Yet, access to relevant and timely disease information that could strengthen their adaptive capacity remain challenging and poorly characterised in the empirical literature. This paper addresses this gap by exploring the role of disease information in shaping the adaptive capacity of smallholder farmer and tribal groups to Kyasanur Forest Disease (KFD), a tick-borne viral haemorrhagic fever. We carried out household surveys (n = 229) and in-depth interviews (n = 25) in two affected districts-Shimoga and Wayanad-in the Western Ghats region. Our findings suggest that, despite the generally limited awareness about KFD, access to disease information improved households' propensity to implement adaptation strategies relative to households that had no access to it. Of the variety of adaptation strategies implemented, vaccination, avoiding forest visits, wearing of protective clothing and footwear, application of dimethyl phthalate (DMP) oil and income diversification were identified by respondents as important adaptive measures during the outbreak seasons. Even so, we identified significant differences between individuals in exposure to disease information and its contribution to substantive adaptive action. Households reported several barriers to implement adaptation strategies including, lack of disease information, low efficacy of existing vaccine, distrust, religio-cultural sentiments, and livelihood concerns. We also found that informal information sharing presented a promising avenue from a health extension perspective albeit with trade-offs with potential distortion of the messages through misinformation and/or reporting bias. Altogether, our findings stress the importance of contextualising disease information and implementing interventions in a participatory way that sufficiently addresses the social determinants of health in order to bolster households' adaptive capacity to KFD and other neglected endemic zoonoses.}, } @article {pmid33692181, year = {2021}, author = {Sigfrid, L and Cevik, M and Jesudason, E and Lim, WS and Rello, J and Amuasi, J and Bozza, F and Palmieri, C and Munblit, D and Holter, JC and Kildal, AB and Reyes, LF and Russell, CD and Ho, A and Turtle, L and Drake, TM and Beltrame, A and Hann, K and Bangura, IR and Fowler, R and Lakoh, S and Berry, C and Lowe, DJ and McPeake, J and Hashmi, M and Dyrhol-Riise, AM and Donohue, C and Plotkin, D and Hardwick, H and Elkheir, N and Lone, NI and Docherty, A and Harrison, E and Baille, JK and Carson, G and Semple, MG and Scott, JT}, title = {What is the recovery rate and risk of long-term consequences following a diagnosis of COVID-19? A harmonised, global longitudinal observational study protocol.}, journal = {BMJ open}, volume = {11}, number = {3}, pages = {e043887}, pmid = {33692181}, issn = {2044-6055}, support = {MC_PC_19026/MRC_/Medical Research Council/United Kingdom ; MC_PC_19059/MRC_/Medical Research Council/United Kingdom ; MC_UU_12014/8/MRC_/Medical Research Council/United Kingdom ; MC_UU_12014/9/MRC_/Medical Research Council/United Kingdom ; }, mesh = {COVID-19/*diagnosis/*psychology ; Colombia ; Ghana ; Humans ; Italy ; Longitudinal Studies ; Norway ; Prospective Studies ; Risk Factors ; Russia ; South Africa ; United Kingdom ; }, abstract = {INTRODUCTION: Very little is known about possible clinical sequelae that may persist after resolution of acute COVID-19. A recent longitudinal cohort from Italy including 143 patients followed up after hospitalisation with COVID-19 reported that 87% had at least one ongoing symptom at 60-day follow-up. Early indications suggest that patients with COVID-19 may need even more psychological support than typical intensive care unit patients. The assessment of risk factors for longer term consequences requires a longitudinal study linked to data on pre-existing conditions and care received during the acute phase of illness. The primary aim of this study is to characterise physical and psychosocial sequelae in patients post-COVID-19 hospital discharge.

METHODS AND ANALYSIS: This is an international open-access prospective, observational multisite study. This protocol is linked with the International Severe Acute Respiratory and emerging Infection Consortium (ISARIC) and the WHO's Clinical Characterisation Protocol, which includes patients with suspected or confirmed COVID-19 during hospitalisation. This protocol will follow-up a subset of patients with confirmed COVID-19 using standardised surveys to measure longer term physical and psychosocial sequelae. The data will be linked with the acute phase data. Statistical analyses will be undertaken to characterise groups most likely to be affected by sequelae of COVID-19. The open-access follow-up survey can be used as a data collection tool by other follow-up studies, to facilitate data harmonisation and to identify subsets of patients for further in-depth follow-up. The outcomes of this study will inform strategies to prevent long-term consequences; inform clinical management, interventional studies, rehabilitation and public health management to reduce overall morbidity; and improve long-term outcomes of COVID-19.

ETHICS AND DISSEMINATION: The protocol and survey are open access to enable low-resourced sites to join the study to facilitate global standardised, longitudinal data collection. Ethical approval has been given by sites in Colombia, Ghana, Italy, Norway, Russia, the UK and South Africa. New sites are welcome to join this collaborative study at any time. Sites interested in adopting the protocol as it is or in an adapted version are responsible for ensuring that local sponsorship and ethical approvals in place as appropriate. The tools are available on the ISARIC website (www.isaric.org). PROTOCOL REGISTRATION NUMBER: osf.io/c5rw3/ PROTOCOL VERSION: 3 August 2020 EUROQOL ID: 37035.}, } @article {pmid33692097, year = {2021}, author = {Thwaites, RS and Sanchez Sevilla Uruchurtu, A and Siggins, MK and Liew, F and Russell, CD and Moore, SC and Fairfield, C and Carter, E and Abrams, S and Short, CE and Thaventhiran, T and Bergstrom, E and Gardener, Z and Ascough, S and Chiu, C and Docherty, AB and Hunt, D and Crow, YJ and Solomon, T and Taylor, GP and Turtle, L and Harrison, EM and Dunning, J and Semple, MG and Baillie, JK and Openshaw, PJ and , }, title = {Inflammatory profiles across the spectrum of disease reveal a distinct role for GM-CSF in severe COVID-19.}, journal = {Science immunology}, volume = {6}, number = {57}, pages = {}, pmid = {33692097}, issn = {2470-9468}, support = {MR/T50256X/1/MRC_/Medical Research Council/United Kingdom ; MC_PC_20060/MRC_/Medical Research Council/United Kingdom ; MRF_MRF-159-0001-ELP-HUNT/MRF/MRF/United Kingdom ; MC_PC_19059/MRC_/Medical Research Council/United Kingdom ; MR/P502091/1/MRC_/Medical Research Council/United Kingdom ; MC_PC_19078/MRC_/Medical Research Council/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; 215091/Z/18/Z/WT_/Wellcome Trust/United Kingdom ; G0701652/MRC_/Medical Research Council/United Kingdom ; MR/V028448/1/MRC_/Medical Research Council/United Kingdom ; MR/S032304/1/MRC_/Medical Research Council/United Kingdom ; MR/R502121/1/MRC_/Medical Research Council/United Kingdom ; 205228/Z/16/Z/WT_/Wellcome Trust/United Kingdom ; MC_PC_19025/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Adult ; Aged ; COVID-19/*blood/immunology ; Cytokines/*blood/immunology ; Female ; Humans ; Inflammation/blood/immunology ; Influenza A Virus, H1N1 Subtype ; Influenza, Human/blood/immunology ; Male ; Middle Aged ; SARS-CoV-2 ; Severity of Illness Index ; }, abstract = {While it is now widely accepted that host inflammatory responses contribute to lung injury, the pathways that drive severity and distinguish coronavirus disease 2019 (COVID-19) from other viral lung diseases remain poorly characterized. We analyzed plasma samples from 471 hospitalized patients recruited through the prospective multicenter ISARIC4C study and 39 outpatients with mild disease, enabling extensive characterization of responses across a full spectrum of COVID-19 severity. Progressive elevation of levels of numerous inflammatory cytokines and chemokines (including IL-6, CXCL10, and GM-CSF) were associated with severity and accompanied by elevated markers of endothelial injury and thrombosis. Principal component and network analyses demonstrated central roles for IL-6 and GM-CSF in COVID-19 pathogenesis. Comparing these profiles to archived samples from patients with fatal influenza, IL-6 was equally elevated in both conditions whereas GM-CSF was prominent only in COVID-19. These findings further identify the key inflammatory, thrombotic, and vascular factors that characterize and distinguish severe and fatal COVID-19.}, } @article {pmid33691092, year = {2021}, author = {Durvasula, A and Lohmueller, KE}, title = {Negative selection on complex traits limits phenotype prediction accuracy between populations.}, journal = {American journal of human genetics}, volume = {108}, number = {4}, pages = {620-631}, pmid = {33691092}, issn = {1537-6605}, support = {R35 GM119856/GM/NIGMS NIH HHS/United States ; }, mesh = {Africa/ethnology ; Computer Simulation ; Datasets as Topic ; Europe/ethnology ; *Genetic Predisposition to Disease ; Genetic Variation/genetics ; *Genetics, Population ; Humans ; *Models, Genetic ; Multifactorial Inheritance/*genetics ; *Phenotype ; Population Growth ; Selection, Genetic/*genetics ; United Kingdom ; }, abstract = {Phenotype prediction is a key goal for medical genetics. Unfortunately, most genome-wide association studies are done in European populations, which reduces the accuracy of predictions via polygenic scores in non-European populations. Here, we use population genetic models to show that human demographic history and negative selection on complex traits can result in population-specific genetic architectures. For traits where alleles with the largest effect on the trait are under the strongest negative selection, approximately half of the heritability can be accounted for by variants in Europe that are absent from Africa, leading to poor performance in phenotype prediction across these populations. Further, under such a model, individuals in the tails of the genetic risk distribution may not be identified via polygenic scores generated in another population. We empirically test these predictions by building a model to stratify heritability between European-specific and shared variants and applied it to 37 traits and diseases in the UK Biobank. Across these phenotypes, ∼30% of the heritability comes from European-specific variants. We conclude that genetic association studies need to include more diverse populations to enable the utility of phenotype prediction in all populations.}, } @article {pmid33683369, year = {2021}, author = {Hu, J and Wuitchik, SJS and Barry, TN and Jamniczky, HA and Rogers, SM and Barrett, RDH}, title = {Heritability of DNA methylation in threespine stickleback (Gasterosteus aculeatus).}, journal = {Genetics}, volume = {217}, number = {1}, pages = {1-15}, pmid = {33683369}, issn = {1943-2631}, mesh = {Animals ; CpG Islands ; *DNA Methylation ; Ecotype ; Epigenome ; Hybridization, Genetic ; *Polymorphism, Genetic ; *Quantitative Trait Loci ; Quantitative Trait, Heritable ; Smegmamorpha/*genetics ; }, abstract = {Epigenetic mechanisms underlying phenotypic change are hypothesized to contribute to population persistence and adaptation in the face of environmental change. To date, few studies have explored the heritability of intergenerationally stable methylation levels in natural populations, and little is known about the relative contribution of cis- and trans-regulatory changes to methylation variation. Here, we explore the heritability of DNA methylation, and conduct methylation quantitative trait loci (meQTLs) analysis to investigate the genetic architecture underlying methylation variation between marine and freshwater ecotypes of threespine stickleback (Gasterosteus aculeatus). We quantitatively measured genome-wide DNA methylation in fin tissue using reduced representation bisulfite sequencing of F1 and F2 crosses, and their marine and freshwater source populations. We identified cytosines (CpG sites) that exhibited stable methylation levels across generations. We found that additive genetic variance explained an average of 24-35% of the methylation variance, with a number of CpG sites possibly autonomous from genetic control. We also detected both cis- and trans-meQTLs, with only trans-meQTLs overlapping with previously identified genomic regions of high differentiation between marine and freshwater ecotypes. Finally, we identified the genetic architecture underlying two key CpG sites that were differentially methylated between ecotypes. These findings demonstrate a potential role for DNA methylation in facilitating adaptation to divergent environments and improve our understanding of the heritable basis of population epigenomic variation.}, } @article {pmid33681953, year = {2021}, author = {Santos, FGTD and Mezzavila, VAM and Rodrigues, TFCDS and Cardoso, LCB and Silva, MD and Oliveira, RR and Radovanovic, CAT}, title = {Trend of transplants and organ and tissue donations in Brazil: a time series analysis.}, journal = {Revista brasileira de enfermagem}, volume = {74}, number = {1}, pages = {e20200058}, doi = {10.1590/0034-7167-2020-0058}, pmid = {33681953}, issn = {1984-0446}, mesh = {Brazil/epidemiology ; Databases as Topic ; Humans ; Research Design ; Tissue Donors/*statistics & numerical data ; Tissue and Organ Procurement/statistics & numerical data/*trends ; Transplants/*statistics & numerical data ; }, abstract = {OBJECTIVES: to indentify the time trend of rates of organs and tissues effective donors, of reports and types of transplanted organs per million people of the Brazilian population.

METHODS: ecological study, of time series, about reports of organ donations and on transplants. The data were provided by the Registro Brasileiro de Transplantes and analyzed using polynomial regression.

RESULTS: an increasing trend was found for potential donors and effective donors, with an average increase of 2.33 and 0.92 per year, respectively. The South Region had the highest rate of potential donors (83.8) and effective donors (34.1) and the North Region, the lowest rate (20.2 and 3.9). The family refusal was the main obstacle to accomplish the donation.

CONCLUSIONS: the results show an increasing trend of potential donors and effective donors throughout Brazil, with emphasis on the southern region of the country. Among the main reasons for non-donation, it is worth emphasizing family refusal and medical contraindication prescription.}, } @article {pmid33679388, year = {2020}, author = {Mattalia, G and Stryamets, N and Grygorovych, A and Pieroni, A and Sõukand, R}, title = {Borders as Crossroads: The Diverging Routes of Herbal Knowledge of Romanians Living on the Romanian and Ukrainian Sides of Bukovina.}, journal = {Frontiers in pharmacology}, volume = {11}, number = {}, pages = {598390}, pmid = {33679388}, issn = {1663-9812}, support = {714874/ERC_/European Research Council/International ; }, abstract = {Cross-border and cross-cultural ethnomedicine are novel ways to address the evolution of local ecological knowledge. As is widely acknowledged, ethnomedicinal knowledge is not static, but evolves according to several factors, including changes in ecological availability and socioeconomic conditions, and yet the effect of the political context on medicinal knowledge remains largely underexplored. Bukovina, a small region of Eastern Europe that has been divided by a border since the 1940s and is currently part of both Romania and Ukraine, represents a unique case study in which to address the impact of political contexts on ethnomedicinal knowledge. The aim of this study was to compare plant-based medicinal uses among Romanians living on the two sides of the Romanian-Ukrainian border. In addition, we performed cross-cultural and cross-border analysis with published data on the ethnomedicine of the neighboring ethnolinguistic group of Hutsuls. We conducted 59 semistructured interviews with conveniently selected Romanians living in both Romanian and Ukrainian Bukovina. We elicited preparations for treating different ailments and disorders by naming each part of the body. We also asked about the sources of this medicinal knowledge. We documented the medicinal use of 108 plant taxa belonging to 45 families. Fifty-four taxa were common to both Romanian communities; 20 were only found among Romanians living in Romania and 34 only among Romanians living in Ukraine. However, the number of recorded uses was higher among Romanians living in Romania, revealing that they make consistent use of local medicinal plants, and Romanians living in Ukrainian Bukovina use more taxa but less consistently. Comparison with the data published in our study on neighboring Hutsuls shows that medicinal knowledge is more homogeneous among Hutsuls and Romanians living in Ukraine, yet many similar uses were found among Romanian communities across the border. We argue that the 50 years during which Ukrainian Bukovina was part of the USSR resulted in the integration of standard pan-Soviet elements as evidenced by several plant uses common among the groups living in Ukraine yet not among Hutsuls and Romanians living in Romania.}, } @article {pmid33679174, year = {2021}, author = {Anton, V and Germishuys, J and Bergström, P and Lindegarth, M and Obst, M}, title = {An open-source, citizen science and machine learning approach to analyse subsea movies.}, journal = {Biodiversity data journal}, volume = {9}, number = {}, pages = {e60548}, pmid = {33679174}, issn = {1314-2828}, abstract = {BACKGROUND: The increasing access to autonomously-operated technologies offer vast opportunities to sample large volumes of biological data. However, these technologies also impose novel demands on ecologists who need to apply tools for data management and processing that are efficient, publicly available and easy to use. Such tools are starting to be developed for a wider community and here we present an approach to combine essential analytical functions for analysing large volumes of image data in marine ecological research.

NEW INFORMATION: This paper describes the Koster Seafloor Observatory, an open-source approach to analysing large amounts of subsea movie data for marine ecological research. The approach incorporates three distinct modules to: manage and archive the subsea movies, involve citizen scientists to accurately classify the footage and, finally, train and test machine learning algorithms for detection of biological objects. This modular approach is based on open-source code and allows researchers to customise and further develop the presented functionalities to various types of data and questions related to analysis of marine imagery. We tested our approach for monitoring cold water corals in a Marine Protected Area in Sweden using videos from remotely-operated vehicles (ROVs). Our study resulted in a machine learning model with an adequate performance, which was entirely trained with classifications provided by citizen scientists. We illustrate the application of machine learning models for automated inventories and monitoring of cold water corals. Our approach shows how citizen science can be used to effectively extract occurrence and abundance data for key ecological species and habitats from underwater footage. We conclude that the combination of open-source tools, citizen science systems, machine learning and high performance computational resources are key to successfully analyse large amounts of underwater imagery in the future.}, } @article {pmid33677572, year = {2021}, author = {Dion, MB and Plante, PL and Zufferey, E and Shah, SA and Corbeil, J and Moineau, S}, title = {Streamlining CRISPR spacer-based bacterial host predictions to decipher the viral dark matter.}, journal = {Nucleic acids research}, volume = {49}, number = {6}, pages = {3127-3138}, pmid = {33677572}, issn = {1362-4962}, mesh = {*Bacteriophages ; *Clustered Regularly Interspaced Short Palindromic Repeats ; *Databases, Nucleic Acid ; Gastrointestinal Tract/microbiology ; *Genome, Bacterial ; Internet ; Metagenomics/*methods ; Software ; }, abstract = {Thousands of new phages have recently been discovered thanks to viral metagenomics. These phages are extremely diverse and their genome sequences often do not resemble any known phages. To appreciate their ecological impact, it is important to determine their bacterial hosts. CRISPR spacers can be used to predict hosts of unknown phages, as spacers represent biological records of past phage-bacteria interactions. However, no guidelines have been established to standardize host prediction based on CRISPR spacers. Additionally, there are no tools that use spacers to perform host predictions on large viral datasets. Here, we developed a set of tools that includes all the necessary steps for predicting the hosts of uncharacterized phages. We created a database of >11 million spacers and a program to execute host predictions on large viral datasets. Our host prediction approach uses biological criteria inspired by how CRISPR-Cas naturally work as adaptive immune systems, which make the results easy to interpret. We evaluated the performance using 9484 phages with known hosts and obtained a recall of 49% and a precision of 69%. We also found that this host prediction method yielded higher performance for phages that infect gut-associated bacteria, suggesting it is well suited for gut-virome characterization.}, } @article {pmid33677570, year = {2021}, author = {Brose, J and Lau, KH and Dang, TTT and Hamilton, JP and Martins, LDV and Hamberger, B and Hamberger, B and Jiang, J and O'Connor, SE and Buell, CR}, title = {The Mitragyna speciosa (Kratom) Genome: a resource for data-mining potent pharmaceuticals that impact human health.}, journal = {G3 (Bethesda, Md.)}, volume = {11}, number = {4}, pages = {}, pmid = {33677570}, issn = {2160-1836}, mesh = {Data Mining ; Humans ; *Mitragyna/genetics ; Plant Extracts ; *Secologanin Tryptamine Alkaloids ; }, abstract = {Mitragyna speciosa (kratom) produces numerous compounds with pharmaceutical properties including the production of bioactive monoterpene indole and oxindole alkaloids. Using a linked-read approach, a 1,122,519,462 bp draft assembly of M. speciosa "Rifat" was generated with an N50 scaffold size of 1,020,971 bp and an N50 contig size of 70,448 bp that encodes 55,746 genes. Chromosome counting revealed that "Rifat" is a tetraploid with a base chromosome number of 11, which was further corroborated by orthology and syntenic analysis of the genome. Analysis of genes and clusters involved in specialized metabolism revealed genes putatively involved in alkaloid biosynthesis. Access to the genome of M. speciosa will facilitate an improved understanding of alkaloid biosynthesis and accelerate the production of bioactive alkaloids in heterologous hosts.}, } @article {pmid33676593, year = {2021}, author = {Bloom, CI and Drake, TM and Docherty, AB and Lipworth, BJ and Johnston, SL and Nguyen-Van-Tam, JS and Carson, G and Dunning, J and Harrison, EM and Baillie, JK and Semple, MG and Cullinan, P and Openshaw, PJM and , }, title = {Risk of adverse outcomes in patients with underlying respiratory conditions admitted to hospital with COVID-19: a national, multicentre prospective cohort study using the ISARIC WHO Clinical Characterisation Protocol UK.}, journal = {The Lancet. Respiratory medicine}, volume = {9}, number = {7}, pages = {699-711}, pmid = {33676593}, issn = {2213-2619}, support = {G0701652/MRC_/Medical Research Council/United Kingdom ; MR/T031565/1/MRC_/Medical Research Council/United Kingdom ; MC_PC_19059/MRC_/Medical Research Council/United Kingdom ; MR/S032304/1/MRC_/Medical Research Council/United Kingdom ; MC_PC_19025/MRC_/Medical Research Council/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; MR/S019669/1/MRC_/Medical Research Council/United Kingdom ; MC_PC_15001/MRC_/Medical Research Council/United Kingdom ; 109965/Z/15/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Adolescent ; Adult ; Asthma/*complications/*mortality ; COVID-19/*complications/*mortality ; Clinical Protocols ; Cohort Studies ; Female ; Hospital Mortality ; Hospitalization ; Humans ; Male ; Middle Aged ; Prospective Studies ; Pulmonary Disease, Chronic Obstructive/*complications/*mortality ; Risk Assessment ; United Kingdom ; World Health Organization ; Young Adult ; }, abstract = {BACKGROUND: Studies of patients admitted to hospital with COVID-19 have found varying mortality outcomes associated with underlying respiratory conditions and inhaled corticosteroid use. Using data from a national, multicentre, prospective cohort, we aimed to characterise people with COVID-19 admitted to hospital with underlying respiratory disease, assess the level of care received, measure in-hospital mortality, and examine the effect of inhaled corticosteroid use.

METHODS: We analysed data from the International Severe Acute Respiratory and emerging Infection Consortium (ISARIC) WHO Clinical Characterisation Protocol UK (CCP-UK) study. All patients admitted to hospital with COVID-19 across England, Scotland, and Wales between Jan 17 and Aug 3, 2020, were eligible for inclusion in this analysis. Patients with asthma, chronic pulmonary disease, or both, were identified and stratified by age (<16 years, 16-49 years, and ≥50 years). In-hospital mortality was measured by use of multilevel Cox proportional hazards, adjusting for demographics, comorbidities, and medications (inhaled corticosteroids, short-acting β-agonists [SABAs], and long-acting β-agonists [LABAs]). Patients with asthma who were taking an inhaled corticosteroid plus LABA plus another maintenance asthma medication were considered to have severe asthma.

FINDINGS: 75 463 patients from 258 participating health-care facilities were included in this analysis: 860 patients younger than 16 years (74 [8·6%] with asthma), 8950 patients aged 16-49 years (1867 [20·9%] with asthma), and 65 653 patients aged 50 years and older (5918 [9·0%] with asthma, 10 266 [15·6%] with chronic pulmonary disease, and 2071 [3·2%] with both asthma and chronic pulmonary disease). Patients with asthma were significantly more likely than those without asthma to receive critical care (patients aged 16-49 years: adjusted odds ratio [OR] 1·20 [95% CI 1·05-1·37]; p=0·0080; patients aged ≥50 years: adjusted OR 1·17 [1·08-1·27]; p<0·0001), and patients aged 50 years and older with chronic pulmonary disease (with or without asthma) were significantly less likely than those without a respiratory condition to receive critical care (adjusted OR 0·66 [0·60-0·72] for those without asthma and 0·74 [0·62-0·87] for those with asthma; p<0·0001 for both). In patients aged 16-49 years, only those with severe asthma had a significant increase in mortality compared to those with no asthma (adjusted hazard ratio [HR] 1·17 [95% CI 0·73-1·86] for those on no asthma therapy, 0·99 [0·61-1·58] for those on SABAs only, 0·94 [0·62-1·43] for those on inhaled corticosteroids only, 1·02 [0·67-1·54] for those on inhaled corticosteroids plus LABAs, and 1·96 [1·25-3·08] for those with severe asthma). Among patients aged 50 years and older, those with chronic pulmonary disease had a significantly increased mortality risk, regardless of inhaled corticosteroid use, compared to patients without an underlying respiratory condition (adjusted HR 1·16 [95% CI 1·12-1·22] for those not on inhaled corticosteroids, and 1·10 [1·04-1·16] for those on inhaled corticosteroids; p<0·0001). Patients aged 50 years and older with severe asthma also had an increased mortality risk compared to those not on asthma therapy (adjusted HR 1·24 [95% CI 1·04-1·49]). In patients aged 50 years and older, inhaled corticosteroid use within 2 weeks of hospital admission was associated with decreased mortality in those with asthma, compared to those without an underlying respiratory condition (adjusted HR 0·86 [95% CI 0·80-0·92]).

INTERPRETATION: Underlying respiratory conditions are common in patients admitted to hospital with COVID-19. Regardless of the severity of symptoms at admission and comorbidities, patients with asthma were more likely, and those with chronic pulmonary disease less likely, to receive critical care than patients without an underlying respiratory condition. In patients aged 16 years and older, severe asthma was associated with increased mortality compared to non-severe asthma. In patients aged 50 years and older, inhaled corticosteroid use in those with asthma was associated with lower mortality than in patients without an underlying respiratory condition; patients with chronic pulmonary disease had significantly increased mortality compared to those with no underlying respiratory condition, regardless of inhaled corticosteroid use. Our results suggest that the use of inhaled corticosteroids, within 2 weeks of admission, improves survival for patients aged 50 years and older with asthma, but not for those with chronic pulmonary disease.

FUNDING: National Institute for Health Research, Medical Research Council, NIHR Health Protection Research Units in Emerging and Zoonotic Infections at the University of Liverpool and in Respiratory Infections at Imperial College London in partnership with Public Health England.}, } @article {pmid33672968, year = {2021}, author = {Sun, H and Hu, L and Shou, W and Wang, J}, title = {Self-Organized Crowd Dynamics: Research on Earthquake Emergency Response Patterns of Drill-Trained Individuals Based on GIS and Multi-Agent Systems Methodology.}, journal = {Sensors (Basel, Switzerland)}, volume = {21}, number = {4}, pages = {}, pmid = {33672968}, issn = {1424-8220}, support = {41906185//National Natural Science Foundation of China/ ; }, mesh = {China ; Crowding ; *Disaster Planning ; *Earthquakes ; Emergencies ; *Geographic Information Systems ; Humans ; }, abstract = {Predicting evacuation patterns is useful in emergency management situations such as an earthquake. To find out how pre-trained individuals interact with one another to achieve their own goal to reach the exit as fast as possible firstly, we investigated urban people's evacuation behavior under earthquake disaster coditions, established crowd response rules in emergencies, and described the drill strategy and exit familiarity quantitatively through a cellular automata model. By setting different exit familiarity ratios, simulation experiments under different strategies were conducted to predict people's reactions before an emergency. The corresponding simulation results indicated that the evacuees' training level could affect a multi-exit zone's evacuation pattern and clearance time. Their exit choice preferences may disrupt the exit options' balance, leading to congestion in some of the exits. Secondly, due to people's rejection of long distances, congestion, and unfamiliar exits, some people would hesitant about the evacuation direction during the evacuation process. This hesitation would also significantly reduce the overall evacuation efficiency. Finally, taking a community in Zhuhai City, China, as an example, put forward the best urban evacuation drill strategy. The quantitative relation between exit familiar level and evacuation efficiency was obtained. The final results showed that the optimized evacuation plan could improve evacuation's overall efficiency through the self-organization effect. These studies may have some impact on predicting crowd behavior during evacuation and designing the evacuation plan.}, } @article {pmid33667773, year = {2021}, author = {Lippold, H and Zedek, L}, title = {Metal dissociation from humic colloids: Kinetics with time-dependent rate constants.}, journal = {Chemosphere}, volume = {275}, number = {}, pages = {130045}, doi = {10.1016/j.chemosphere.2021.130045}, pmid = {33667773}, issn = {1879-1298}, mesh = {*Colloids ; Dissociative Disorders ; Humans ; *Humic Substances/analysis ; Kinetics ; Metals ; }, abstract = {The mobility of contaminant metals in aqueous subsurface environments is largely controlled by their interaction with humic substances as colloidal constituents of Dissolved Organic Matter. Transport models for predicting carrier-bound migration are based on a competitive partitioning process between solid surface and colloids. However, it has been observed that dissociation of multivalent metals from humic complexes is a slow kinetic process, which is even more impeded with increasing time of contact. Based on findings obtained in isotope exchange experiments, the convoluted time dependence of dissociation was fully described by a complex two-site approach, integrating rate "constants" that are in turn time-dependent. Thus, this study presents the treatment of a particular phenomenon: kinetics within kinetics. The analysis showed that the inertization process does not lead to irreversible binding. Consequently, thermodynamic concepts using equilibrium constants remain applicable in speciation and transport modeling if long time frames are appropriate.}, } @article {pmid33664263, year = {2021}, author = {Warren, WC and Boggs, TE and Borowsky, R and Carlson, BM and Ferrufino, E and Gross, JB and Hillier, L and Hu, Z and Keene, AC and Kenzior, A and Kowalko, JE and Tomlinson, C and Kremitzki, M and Lemieux, ME and Graves-Lindsay, T and McGaugh, SE and Miller, JT and Mommersteeg, MTM and Moran, RL and Peuß, R and Rice, ES and Riddle, MR and Sifuentes-Romero, I and Stanhope, BA and Tabin, CJ and Thakur, S and Yamamoto, Y and Rohner, N}, title = {A chromosome-level genome of Astyanax mexicanus surface fish for comparing population-specific genetic differences contributing to trait evolution.}, journal = {Nature communications}, volume = {12}, number = {1}, pages = {1447}, pmid = {33664263}, issn = {2041-1723}, support = {PG/15/111/31939/BHF_/British Heart Foundation/United Kingdom ; DP2 AG071466/AG/NIA NIH HHS/United States ; BB/C517041/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; R15 HD099022/HD/NICHD NIH HHS/United States ; R01 DE025033/DE/NIDCR NIH HHS/United States ; R01 GM127872/GM/NIGMS NIH HHS/United States ; R24 OD011198/OD/NIH HHS/United States ; }, mesh = {Adaptation, Physiological/*genetics ; Animals ; Biological Evolution ; Caves ; Characidae/*embryology/*genetics ; Chromosome Mapping ; Evolution, Molecular ; Eye/*embryology ; Gene Editing ; Genome/genetics ; Homeodomain Proteins/genetics ; Mitogen-Activated Protein Kinase Phosphatases/genetics ; Multifactorial Inheritance/*genetics ; Quantitative Trait Loci/genetics ; }, abstract = {Identifying the genetic factors that underlie complex traits is central to understanding the mechanistic underpinnings of evolution. Cave-dwelling Astyanax mexicanus populations are well adapted to subterranean life and many populations appear to have evolved troglomorphic traits independently, while the surface-dwelling populations can be used as a proxy for the ancestral form. Here we present a high-resolution, chromosome-level surface fish genome, enabling the first genome-wide comparison between surface fish and cavefish populations. Using this resource, we performed quantitative trait locus (QTL) mapping analyses and found new candidate genes for eye loss such as dusp26. We used CRISPR gene editing in A. mexicanus to confirm the essential role of a gene within an eye size QTL, rx3, in eye formation. We also generated the first genome-wide evaluation of deletion variability across cavefish populations to gain insight into this potential source of cave adaptation. The surface fish genome reference now provides a more complete resource for comparative, functional and genetic studies of drastic trait differences within a species.}, } @article {pmid33662045, year = {2021}, author = {Becerra, MB and Rodriquez, EJ and Avina, RM and Becerra, BJ}, title = {Experiences of violence and mental health outcomes among Asian American transgender adults in the United States.}, journal = {PloS one}, volume = {16}, number = {3}, pages = {e0247812}, pmid = {33662045}, issn = {1932-6203}, mesh = {Adolescent ; Adult ; Asian People/*genetics ; Databases, Factual ; Female ; Health Surveys/*methods ; Humans ; Male ; Mental Disorders/pathology/*psychology ; Outcome Assessment, Health Care/*methods ; Prevalence ; Risk Factors ; Suicidal Ideation ; Transgender Persons/*psychology/statistics & numerical data ; United States ; Violence/*statistics & numerical data ; Young Adult ; }, abstract = {PURPOSE: We addressed prevalence and factors associated with mental health outcomes (suicidal behavior and psychological distress) among Asian Americans (AA), who identify as transgender, a key group among sexual and gender minorities that is overlooked and understudied.

METHODS: We used data from 2015 United States Transgender Survey during 2019-2020 with our population as census defined AA. Outcomes included suicidal ideation, suicidal thoughts, and serious psychological distress (SPD). Independent variables included any abuse, partner abuse, bathroom-related abuse, and additional covariates. Adjusted odds ratio and 95% confidence interval (aOR; 95% CI) for each outcome are adjusted for age, marital status, citizenship status, education level, employment status, as well as poverty status.

RESULTS: Nearly 67% reported experiencing any abuse, 52% reported abuse from romantic/sexual partner(s), while 29% reported harassment/abuse when trying to use bathrooms. Moreover, 82% reported suicidal thoughts, 40% reported suicidal attempts, and 39% had SPD. Results demonstrated that any abuse/violence had higher odds of suicidal thoughts (adjusted odds ratio [aOR] = 2.67, 95% confidence interval (CI):[1.98-3.58], suicidal attempts (aOR = 2.83, 95% CI:[2.18-3.68]), and SPD (aOR = 1.56, 95% CI:[1.20, 2.04]). Abuse from romantic/sexual partners had higher odds of suicidal thoughts (aOR = 2.47, 95% CI:[1.76-3.47]), suicidal attempts (aOR = 2.17, 95% CI:[1.68-2.80]), and SPD (aOR = 2.72, 95% CI:[2.03-3.63]). Experience of harassment/abuse during bathroom use had increased odds of suicidal attempts (aOR = 1.81, 95% CI:[1.41-2.31]).

CONCLUSION: Exposure to violence is common among AA transgender individuals and related to negative mental health outcomes. Initiatives to reduce exposure to abuse and providing resources for trauma-informed care are imperative to improve health outcomes.}, } @article {pmid33662005, year = {2021}, author = {Jansson, S and Malmqvist, E and Mlacha, Y and Ignell, R and Okumu, F and Killeen, G and Kirkeby, C and Brydegaard, M}, title = {Real-time dispersal of malaria vectors in rural Africa monitored with lidar.}, journal = {PloS one}, volume = {16}, number = {3}, pages = {e0247803}, pmid = {33662005}, issn = {1932-6203}, mesh = {Africa/epidemiology ; Animals ; Anopheles/*physiology ; Environmental Monitoring/*methods ; Female ; Geographic Information Systems/*standards ; Malaria/*diagnosis/epidemiology/prevention & control/transmission ; Male ; Mosquito Vectors/*parasitology ; Rural Population/*statistics & numerical data ; }, abstract = {Lack of tools for detailed, real-time observation of mosquito behavior with high spatio-temporal resolution limits progress towards improved malaria vector control. We deployed a high-resolution entomological lidar to monitor a half-kilometer static transect positioned over rice fields outside a Tanzanian village. A quarter of a million in situ insect observations were classified, and several insect taxa were identified based on their modulation signatures. We observed distinct range distributions of male and female mosquitoes in relation to the village periphery, and spatio-temporal behavioral features, such as swarming. Furthermore, we observed that the spatial distributions of males and females change independently of each other during the day, and were able to estimate the daily dispersal of mosquitoes towards and away from the village. The findings of this study demonstrate how lidar-based monitoring could dramatically improve our understanding of malaria vector ecology and control options.}, } @article {pmid33661897, year = {2021}, author = {Rodriguez de Rivera, O and McCrea, R}, title = {Removal modelling in ecology: A systematic review.}, journal = {PloS one}, volume = {16}, number = {3}, pages = {e0229965}, pmid = {33661897}, issn = {1932-6203}, mesh = {Animals ; *Biomass ; Conservation of Natural Resources/*methods ; Data Interpretation, Statistical ; *Models, Statistical ; Population Density ; }, abstract = {Removal models were proposed over 80 years ago as a tool to estimate unknown population size. More recently, they are used as an effective tool for management actions for the control of non desirable species, or for the evaluation of translocation management actions. Although the models have evolved over time, in essence, the protocol for data collection has remained similar: at each sampling occasion attempts are made to capture and remove individuals from the study area. Within this paper we review the literature of removal modelling and highlight the methodological developments for the analysis of removal data, in order to provide a unified resource for ecologists wishing to implement these approaches. Models for removal data have developed to better accommodate important features of the data and we discuss the shift in the required assumptions for the implementation of the models. The relative simplicity of this type of data and associated models mean that the method remains attractive and we discuss the potential future role of this technique.}, } @article {pmid33658582, year = {2021}, author = {Scieuzo, C and Salvia, R and Franco, A and Pezzi, M and Cozzolino, F and Chicca, M and Scapoli, C and Vogel, H and Monti, M and Ferracini, C and Pucci, P and Alma, A and Falabella, P}, title = {An integrated transcriptomic and proteomic approach to identify the main Torymus sinensis venom components.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {5032}, pmid = {33658582}, issn = {2045-2322}, mesh = {Animals ; Deoxyribonucleases/classification/*genetics/isolation & purification/metabolism ; Esterases/classification/*genetics/isolation & purification/metabolism ; Gene Ontology ; Insect Proteins/classification/*genetics/isolation & purification/metabolism ; Molecular Sequence Annotation ; Oviposition/physiology ; Peptide Hydrolases/classification/*genetics/isolation & purification/metabolism ; Phosphoric Monoester Hydrolases/classification/*genetics/isolation & purification/metabolism ; Protease Inhibitors/classification/isolation & purification/metabolism ; Proteome/classification/*genetics/isolation & purification/metabolism ; RNA, Messenger/genetics/metabolism ; Transcriptome ; Wasp Venoms/*chemistry/toxicity ; Wasps/chemistry/pathogenicity/physiology ; }, abstract = {During oviposition, ectoparasitoid wasps not only inject their eggs but also a complex mixture of proteins and peptides (venom) in order to regulate the host physiology to benefit their progeny. Although several endoparasitoid venom proteins have been identified, little is known about the components of ectoparasitoid venom. To characterize the protein composition of Torymus sinensis Kamijo (Hymenoptera: Torymidae) venom, we used an integrated transcriptomic and proteomic approach and identified 143 venom proteins. Moreover, focusing on venom gland transcriptome, we selected additional 52 transcripts encoding putative venom proteins. As in other parasitoid venoms, hydrolases, including proteases, phosphatases, esterases, and nucleases, constitute the most abundant families in T. sinensis venom, followed by protease inhibitors. These proteins are potentially involved in the complex parasitic syndrome, with different effects on the immune system, physiological processes and development of the host, and contribute to provide nutrients to the parasitoid progeny. Although additional in vivo studies are needed, initial findings offer important information about venom factors and their putative host effects, which are essential to ensure the success of parasitism.}, } @article {pmid33657095, year = {2021}, author = {Basinski, AJ and Fichet-Calvet, E and Sjodin, AR and Varrelman, TJ and Remien, CH and Layman, NC and Bird, BH and Wolking, DJ and Monagin, C and Ghersi, BM and Barry, PA and Jarvis, MA and Gessler, PE and Nuismer, SL}, title = {Bridging the gap: Using reservoir ecology and human serosurveys to estimate Lassa virus spillover in West Africa.}, journal = {PLoS computational biology}, volume = {17}, number = {3}, pages = {e1008811}, pmid = {33657095}, issn = {1553-7358}, support = {R01 GM122079/GM/NIGMS NIH HHS/United States ; }, mesh = {Africa, Western ; Animals ; Animals, Wild/virology ; Computational Biology ; Disease Reservoirs/*virology ; Ecology ; Humans ; *Lassa Fever/epidemiology/transmission/veterinary/virology ; *Lassa virus ; Machine Learning ; *Models, Biological ; Models, Statistical ; Risk ; Rodentia/virology ; }, abstract = {Forecasting the risk of pathogen spillover from reservoir populations of wild or domestic animals is essential for the effective deployment of interventions such as wildlife vaccination or culling. Due to the sporadic nature of spillover events and limited availability of data, developing and validating robust, spatially explicit, predictions is challenging. Recent efforts have begun to make progress in this direction by capitalizing on machine learning methodologies. An important weakness of existing approaches, however, is that they generally rely on combining human and reservoir infection data during the training process and thus conflate risk attributable to the prevalence of the pathogen in the reservoir population with the risk attributed to the realized rate of spillover into the human population. Because effective planning of interventions requires that these components of risk be disentangled, we developed a multi-layer machine learning framework that separates these processes. Our approach begins by training models to predict the geographic range of the primary reservoir and the subset of this range in which the pathogen occurs. The spillover risk predicted by the product of these reservoir specific models is then fit to data on realized patterns of historical spillover into the human population. The result is a geographically specific spillover risk forecast that can be easily decomposed and used to guide effective intervention. Applying our method to Lassa virus, a zoonotic pathogen that regularly spills over into the human population across West Africa, results in a model that explains a modest but statistically significant portion of geographic variation in historical patterns of spillover. When combined with a mechanistic mathematical model of infection dynamics, our spillover risk model predicts that 897,700 humans are infected by Lassa virus each year across West Africa, with Nigeria accounting for more than half of these human infections.}, } @article {pmid33654452, year = {2021}, author = {Kim, HW and Yoon, S and Kim, M and Shin, M and Yoon, H and Kim, K}, title = {EcoBank: A flexible database platform for sharing ecological data.}, journal = {Biodiversity data journal}, volume = {9}, number = {}, pages = {e61866}, pmid = {33654452}, issn = {1314-2828}, abstract = {BACKGROUND: Environmental crisis challenges the human race harder than ever before. Ecologists have produced a massive amount of data to cope with the crisis. Accordingly, many national scale ecological database systems have been developed worldwide to manage and analyse these datasets. However, in Korea, ecological datasets produced by different research institutes for different purposes have not been integrated or serviced due to poorly designed information infrastructure. To address this obstacle, we present EcoBank (www.nie-ecobank.kr), an open, web-based ecological database platform designed to play an important role in ecosystem analysis, not only in Korea, but also worldwide.

NEW INFORMATION: The architecture of EcoBank comprises core technologies of WebGIS, Application Programming Interface (API), responsive web and open-source software (OSS). Comprehensive ecological datasets from three different sources, including the National Institute of Ecology (NIE) in Korea, related national and international platforms and repositories, enter the three conceptual modules in EcoBank: data management, analysis and service. Diverse potential stakeholders of EcoBank can be classified into three groups: researchers, policy-makers and public users. EcoBank aims to expand its horizons through mutual communication amongst these stakeholders. We opened and launched the EcoBank service in December 2019 and have now begun to broaden its network by linking it to other data platforms and repositories over the globe to find possible solutions to ecological issues in Korea.}, } @article {pmid33651464, year = {2021}, author = {Meng, L and Zhou, Y and Gu, L and Richardson, AD and Peñuelas, J and Fu, Y and Wang, Y and Asrar, GR and De Boeck, HJ and Mao, J and Zhang, Y and Wang, Z}, title = {Photoperiod decelerates the advance of spring phenology of six deciduous tree species under climate warming.}, journal = {Global change biology}, volume = {27}, number = {12}, pages = {2914-2927}, doi = {10.1111/gcb.15575}, pmid = {33651464}, issn = {1365-2486}, support = {//College of Liberal Arts and Science/ ; EF-1702697//NSF/ ; DE-AC05-1008 00OR22725//US Department of Energy/ ; 80NSSC19K1356/NASA/NASA/United States ; ERC-SyG-2013-610028/ERC_/European Research Council/International ; }, mesh = {Climate Change ; Ecosystem ; Europe ; *Photoperiod ; Plant Leaves ; Seasons ; Temperature ; *Trees ; }, abstract = {Vegetation phenology in spring has substantially advanced under climate warming, consequently shifting the seasonality of ecosystem process and altering biosphere-atmosphere feedbacks. However, whether and to what extent photoperiod (i.e., daylength) affects the phenological advancement is unclear, leading to large uncertainties in projecting future phenological changes. Here we examined the photoperiod effect on spring phenology at a regional scale using in situ observation of six deciduous tree species from the Pan European Phenological Network during 1980-2016. We disentangled the photoperiod effect from the temperature effect (i.e., forcing and chilling) by utilizing the unique topography of the northern Alps of Europe (i.e., varying daylength but uniform temperature distribution across latitudes) and examining phenological changes across latitudes. We found prominent photoperiod-induced shifts in spring leaf-out across latitudes (up to 1.7 days per latitudinal degree). Photoperiod regulates spring phenology by delaying early leaf-out and advancing late leaf-out caused by temperature variations. Based on these findings, we proposed two phenological models that consider the photoperiod effect through different mechanisms and compared them with a chilling model. We found that photoperiod regulation would slow down the advance in spring leaf-out under projected climate warming and thus mitigate the increasing frost risk in spring that deciduous forests will face in the future. Our findings identify photoperiod as a critical but understudied factor influencing spring phenology, suggesting that the responses of terrestrial ecosystem processes to climate warming are likely to be overestimated without adequately considering the photoperiod effect.}, } @article {pmid33651293, year = {2021}, author = {Zhong, QQ and Shen, L and Zhao, YQ and Hao, YC and Meng, LC and Liu, YJ and Xu, X and Shang, YN and Gao, BY and Yue, QY}, title = {Preferential capture of phosphate by an Enteromorpha prolifera-based biopolymer encapsulating hydrous zirconium oxide nanoparticles.}, journal = {Environmental science and pollution research international}, volume = {28}, number = {26}, pages = {34584-34597}, pmid = {33651293}, issn = {1614-7499}, support = {18130234a//Tangshan Science and Technology Research and Development Program/ ; Z2018017//Science and Technology Project of Hebei Education Department/ ; 51602344//National Natural Science Foundation of China (CN)/ ; BK20160241//Natural Science Foundation of Jiangsu Province (BK20160241)/ ; }, mesh = {Adsorption ; Biopolymers ; Hydrogen-Ion Concentration ; Kinetics ; *Nanoparticles ; Phosphates ; *Water Pollutants, Chemical/analysis ; Zirconium ; }, abstract = {Preferential removal of phosphate from aqueous was conducted by a novel biomass-based nanocomposite (EP-N[+]-Zr) with encapsulated hydrous zirconium oxide, and the biopolymer EP-N[+]-Zr features were described. EP-N[+]-Zr exhibited high selective sequestration toward phosphate when humic acid or other competing anions (Cl[-], SO4[2-], NO3[-], ClO4[-]) coexisted at relatively high levels. Such excellent performance of EP-N[+]-Zr was attributed to its specific two site structures; the embedded HZO nanoparticles and quaternary ammonia groups [N[+](CH2CH3)3Cl[-]] bonded inside the biomass-Enteromorpha prolifera, which facilitated preferable capture towards phosphate through specific affinity and nonspecific preconcentration of phosphate ions on the basis of the ion exchange, respectively. The maximum adsorption capacity of phosphate (20 °C) as calculated by Langmuir model was 88.5 mg(P)/g. Regeneration tests showed that EP-N[+]-Zr could be recycled at least five times without noticeable capacity losses using binary NaOH-NaCl as eluent.}, } @article {pmid33650373, year = {2021}, author = {Chen, F and Li, HB}, title = {Spatial-temporal variations of soil erosion in Southern Yunnan Mountainous Area using GIS and RUSLE: A case study in Yuanyang County, Yunnan Province, China.}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {32}, number = {2}, pages = {629-637}, doi = {10.13287/j.1001-9332.202102.018}, pmid = {33650373}, issn = {1001-9332}, mesh = {China ; Conservation of Natural Resources ; *Environmental Monitoring ; *Geographic Information Systems ; Humans ; Models, Theoretical ; Soil ; Soil Erosion ; }, abstract = {It is of great significance to understand the spatial-temporal change of soil erosion in the Southern Yunnan Mountainous Area, especially for soil and water conservation planning and ecolo-gical protection in the world cultural heritage area. Based on the RUSLE model and GIS/RS space information technology, we examined the spatial-temporal variation of soil erosion and its relationship with environmental factors in Yuanyang County from 2005 to 2015. The results showed that, during the study period, the spatial differentiation of soil erosion in Yuanyang County was substantial. The soil erosion area was concentrated on the southeast and southwest region. Erosion widely distributed among both sides of Tengtiao River. Extreme and severe erosion presented a point distribution pattern. The average soil erosion modulus was 11.06 t·hm[-2]·a[-1] from 2005 to 2015. The erosion level was basically slight and mild, accounting 80% of the total. Mild and moderate erosion contributed nearly 50% of total annual soil erosion, which was the key level of soil erosion control. During the study period, soil erosion had been slowed down with the improvement of forest cover. The terrain was complicated and changeable in Yuanyang County, and soil erosion distribution had a prominent correlation with altitude and slope. The formation of this distribution pattern was driven by numerous natural and human factors. The key area of soil and water protective governance were below 500 m, above 1500 m and slope located at 25°-45°.}, } @article {pmid33648559, year = {2021}, author = {Plichta, DR and Somani, J and Pichaud, M and Wallace, ZS and Fernandes, AD and Perugino, CA and Lähdesmäki, H and Stone, JH and Vlamakis, H and Chung, DC and Khanna, D and Pillai, S and Xavier, RJ}, title = {Congruent microbiome signatures in fibrosis-prone autoimmune diseases: IgG4-related disease and systemic sclerosis.}, journal = {Genome medicine}, volume = {13}, number = {1}, pages = {35}, pmid = {33648559}, issn = {1756-994X}, support = {UM1 AI144295/NH/NIH HHS/United States ; U19 AI110495/AI/NIAID NIH HHS/United States ; P30 DK043351/DK/NIDDK NIH HHS/United States ; UM1 AI110557/AI/NIAID NIH HHS/United States ; K24 AR063120/NH/NIH HHS/United States ; UM1 AI144295/AI/NIAID NIH HHS/United States ; K24 AR063120/AR/NIAMS NIH HHS/United States ; }, mesh = {Bacteroidetes/physiology ; Case-Control Studies ; Cohort Studies ; Extracellular Matrix/metabolism ; Fibrosis ; Firmicutes/physiology ; *Gastrointestinal Microbiome ; Humans ; Immunoglobulin G4-Related Disease/*microbiology ; Scleroderma, Systemic/*microbiology ; Signal Transduction ; Species Specificity ; }, abstract = {BACKGROUND: Immunoglobulin G4-related disease (IgG4-RD) and systemic sclerosis (SSc) are rare autoimmune diseases characterized by the presence of CD4+ cytotoxic T cells in the blood as well as inflammation and fibrosis in various organs, but they have no established etiologies. Similar to other autoimmune diseases, the gut microbiome might encode disease-triggering or disease-sustaining factors.

METHODS: The gut microbiomes from IgG4-RD and SSc patients as well as healthy individuals with no recent antibiotic treatment were studied by metagenomic sequencing of stool DNA. De novo assembly-based taxonomic and functional characterization, followed by association and accessory gene set enrichment analysis, were applied to describe microbiome changes associated with both diseases.

RESULTS: Microbiomes of IgG4-RD and SSc patients distinctly separated from those of healthy controls: numerous opportunistic pathogenic Clostridium and typically oral Streptococcus species were significantly overabundant, while Alistipes, Bacteroides, and butyrate-producing species were depleted in the two diseases compared to healthy controls. Accessory gene content analysis in these species revealed an enrichment of Th17-activating Eggerthella lenta strains in IgG4-RD and SSc and a preferential colonization of a homocysteine-producing strain of Clostridium bolteae in SSc. Overabundance of the classical mevalonate pathway, hydroxyproline dehydratase, and fibronectin-binding protein in disease microbiomes reflects potential functional differences in host immune recognition and extracellular matrix utilization associated with fibrosis. Strikingly, the majority of species that were differentially abundant in IgG4-RD and SSc compared to controls showed the same directionality in both diseases. Compared with multiple sclerosis and rheumatoid arthritis, the gut microbiomes of IgG4-RD and SSc showed similar signatures; in contrast, the most differentially abundant taxa were not the facultative anaerobes consistently identified in inflammatory bowel diseases, suggesting the microbial signatures of IgG4-RD and SSc do not result from mucosal inflammation and decreased anaerobism.

CONCLUSIONS: These results provide an initial characterization of gut microbiome ecology in fibrosis-prone IgG4-RD and SSc and reveal microbial functions that offer insights into the pathophysiology of these rare diseases.}, } @article {pmid33648321, year = {2021}, author = {Rand, DM and Ragavendran, A}, title = {COBRE for Computational Biology of Human Disease at Brown University: Progress and Prospects.}, journal = {Rhode Island medical journal (2013)}, volume = {104}, number = {2}, pages = {54-59}, pmid = {33648321}, issn = {2327-2228}, support = {P20 GM109035/GM/NIGMS NIH HHS/United States ; }, mesh = {*Biomedical Research ; *Computational Biology/education ; Humans ; Rhode Island ; Universities ; }, abstract = {We provide a program update on the COBRE Center for the Computational Biology of Human Disease (CBHD) at Brown University and affiliated hospitals. High throughput data from multiple 'omics-level' technologies are fundamental factors in identifying and treating human disease. The acquisition of these data is now straightforward, but the efficient and creative interpretation of these data remains a serious impediment to progress for faculty at all levels in both the basic and translational aspects of biomedical science. The CBHD COBRE seeks to build close collaboration between laboratory scientists working with model systems and data scientists working with computational and bioinformatics tools that can accelerate human disease research implementation. We describe the accomplishments of junior faculty Project Leaders (9) and Pilots Project leaders (8) and the objectives of the CBHD COBRE's core facility: The Computational Biology Core (CBC). To extend the CBHD COBRE's reach in the future, we encourage one and all to visit the CBHD COBRE and bring your data sets and questions. Only by engaging with new people and challenges can the program grow to serve the broader biomedical research community in the State of Rhode Island.}, } @article {pmid33647008, year = {2021}, author = {Czuppon, P and Débarre, F and Gonçalves, A and Tenaillon, O and Perelson, AS and Guedj, J and Blanquart, F}, title = {Success of prophylactic antiviral therapy for SARS-CoV-2: Predicted critical efficacies and impact of different drug-specific mechanisms of action.}, journal = {PLoS computational biology}, volume = {17}, number = {3}, pages = {e1008752}, pmid = {33647008}, issn = {1553-7358}, support = {R01 AI028433/AI/NIAID NIH HHS/United States ; R01 OD011095/OD/NIH HHS/United States ; }, mesh = {Antiviral Agents/administration & dosage/*therapeutic use ; Basic Reproduction Number/statistics & numerical data ; COVID-19/*prevention & control/transmission/virology ; Computational Biology ; Drug Repositioning ; Drug Therapy, Combination ; Host Microbial Interactions/drug effects/immunology ; Humans ; Models, Biological ; Pandemics/prevention & control ; Primary Prevention/methods ; Risk Factors ; *SARS-CoV-2/drug effects/pathogenicity/physiology ; Stochastic Processes ; Time Factors ; Treatment Outcome ; Viral Load/drug effects ; Virus Internalization/drug effects ; Virus Replication/drug effects ; *COVID-19 Drug Treatment ; }, abstract = {Repurposed drugs that are safe and immediately available constitute a first line of defense against new viral infections. Despite limited antiviral activity against SARS-CoV-2, several drugs are being tested as medication or as prophylaxis to prevent infection. Using a stochastic model of early phase infection, we evaluate the success of prophylactic treatment with different drug types to prevent viral infection. We find that there exists a critical efficacy that a treatment must reach in order to block viral establishment. Treatment by a combination of drugs reduces the critical efficacy, most effectively by the combination of a drug blocking viral entry into cells and a drug increasing viral clearance. Below the critical efficacy, the risk of infection can nonetheless be reduced. Drugs blocking viral entry into cells or enhancing viral clearance reduce the risk of infection more than drugs that reduce viral production in infected cells. The larger the initial inoculum of infectious virus, the less likely is prevention of an infection. In our model, we find that as long as the viral inoculum is smaller than 10 infectious virus particles, viral infection can be prevented almost certainly with drugs of 90% efficacy (or more). Even when a viral infection cannot be prevented, antivirals delay the time to detectable viral loads. The largest delay of viral infection is achieved by drugs reducing viral production in infected cells. A delay of virus infection flattens the within-host viral dynamic curve, possibly reducing transmission and symptom severity. Thus, antiviral prophylaxis, even with reduced efficacy, could be efficiently used to prevent or alleviate infection in people at high risk.}, } @article {pmid33646334, year = {2021}, author = {Lin, PC and Peng, CY and Pan, CH and Lee, JY and Hsieh, TJ and Chuang, YS and Turesky, RJ and Wu, CF and Wu, MT}, title = {Risk of two common glandular cell-type cancers (breast and colorectal cancers) in Chinese occupational chefs: a nationwide ecological study in Taiwan.}, journal = {International archives of occupational and environmental health}, volume = {94}, number = {6}, pages = {1363-1373}, pmid = {33646334}, issn = {1432-1246}, mesh = {Adolescent ; Adult ; Air Pollutants ; Breast Neoplasms/*epidemiology ; Colorectal Neoplasms/*epidemiology ; *Cooking ; Databases, Factual ; Female ; Humans ; Male ; Middle Aged ; Oils ; Registries ; Risk ; Smoke ; Taiwan/epidemiology ; Young Adult ; }, abstract = {OBJECTIVES: Cooking oil fumes (COFs) contain many carcinogens. We investigated the association between COFs and incidence risk of colorectal cancer and female breast in chefs.

METHODS: We identified Chinese food chefs and non-Chinese food chefs from Taiwan's national database of certified chefs in 1984-2007. In total, 379,275 overall and 259,450 females had not been diagnosed as having any cancer before chef certification. We followed these chefs in Taiwan's Cancer Registry Database (1979-2010) and Taiwan's National Death Statistics Database (1985-2011) for newly diagnosed colorectal cancer and female breast cancer.

RESULTS: A total of 4,218,135 and 2,873,515 person-years were included in our analysis of colorectal cancer and female breast cancer incidence, respectively. Compared to non-Chinese food chefs, the Chinese food chefs had an adjusted IRR for colorectal cancer of 1.65 (95% CI  1.17-2.33). The risk of colorectal cancer was even higher among female Chinese food chefs certified for more than 5 years (adjusted incident rate ratio (IRR) = 2.39, 95% CI   1.38-4.12). For female breast cancer, the risk was also significant (adjusted IRR = 1.40, 95% CI 1.10-1.78) and the risks were even higher in female Chinese food chefs certified for more than 5 years (adjusted IRR = 1.74, 95% CI 1.37-2.22).

CONCLUSIONS: This study found that Chinese food chefs had an increased risk of colorectal cancer and female breast cancer, particularly female chefs who had worked for more than 5 years. Future human and animal studies are necessary to re-confirm these findings.}, } @article {pmid33646317, year = {2021}, author = {Yang, YY and Zhang, JX and Xiao, X and Du, M and Luan, HJ and Yu, QX and Liang, Y}, title = {Speciation and Potential Ecological Risk of Heavy Metals in Soils from Overlapped Areas of Farmland and Coal Resources in Northern Xuzhou, China.}, journal = {Bulletin of environmental contamination and toxicology}, volume = {107}, number = {6}, pages = {1053-1058}, pmid = {33646317}, issn = {1432-0800}, support = {2017XKZD13//the Fundamental Research.Funds for the Central Universities of China/ ; }, mesh = {China ; Coal ; Environmental Monitoring ; Farms ; *Metals, Heavy/analysis ; Risk Assessment ; Soil ; *Soil Pollutants/analysis ; }, abstract = {Contamination caused by heavy metals (HMs) in soil of overlapped area of farmland and coal resources (OAFCR) has impact on crops. The concentrations and speciation of As, Cd, Cr, Cu, Pb and Zn were investigated in topsoil of an OAFCR in Xuzhou, China. The results showed that mean concentrations of all six metals were higher than the background values of Xuzhou city and Cd was moderate accumulated with the maximum Igeo equalled to 2.13. Cd showed moderate contamination level (IPi = 1.75) and potential ecological risk (Er = 44.06). Most of the total Cr, Cu, Ni, Pb, and Zn were presented in the residual forms (above 60%), and the percentages of reducible, oxidisable and residual forms of Pb were 23%, 21% and 43% respectively. Pb and Cd reflected a moderate degree of potential ecological risk and a considerable migration risk and ecotoxicity.}, } @article {pmid33639712, year = {2021}, author = {Lei, J and Booth, DT and Rusli, MU and Zhang, Z}, title = {Spatial Ecology of Asian Water Monitors Adjacent to a Sea Turtle Nesting Beach.}, journal = {Zoological science}, volume = {38}, number = {1}, pages = {1-7}, doi = {10.2108/zs200071}, pmid = {33639712}, issn = {0289-0003}, mesh = {*Animal Distribution ; Animals ; *Ecosystem ; Female ; Geographic Information Systems ; Homing Behavior ; Lizards/*physiology ; Malaysia ; Male ; Nesting Behavior ; Predatory Behavior ; Turtles ; }, abstract = {Nest predation is the main cause of hatching failure for many turtle populations. For green turtles (Chelonia mydas) nesting at Chagar Hutang in Redang Island, Malaysia, Asian water monitors (Varanus salvator) are a potential nest predator. However, no studies have documented the space use of this species in coastal habitat adjacent to a sea turtle nesting beach to assess its potential impact on turtle nests. Here, we used Global Positioning System (GPS) data loggers to quantify space use of Asian water monitors in order to establish the extent to which they use sea turtle nesting areas. Asian water monitors had a diurnal activity pattern and spent most of their time in rain forest habitat behind the sea turtle nesting beach. The home range occupied by Asian water monitors varied between 0.015 and 0.198 km[2] calculated by the Kernel Brownian Bridge method. The space use patterns of individual Asian water monitors varied between individuals. Two males had relatively small home ranges, whereas one male and the female had a relatively large home range. Because tracked Asian water monitors in this study rarely visited the sea turtle nesting areas, it is probable that only a few individuals are responsible for opening nests.}, } @article {pmid33638015, year = {2021}, author = {Anand, V and Oinam, B and Singh, IH}, title = {Predicting the current and future potential spatial distribution of endangered Rucervus eldii eldii (Sangai) using MaxEnt model.}, journal = {Environmental monitoring and assessment}, volume = {193}, number = {3}, pages = {147}, pmid = {33638015}, issn = {1573-2959}, mesh = {Animals ; *Climate Change ; Ecosystem ; *Environmental Monitoring ; Geographic Information Systems ; Parks, Recreational ; }, abstract = {Ecological factors that control the species distribution patterns at various spatiotemporal scales will get affected by climate change. To combat the situation, in the past few decades geographical information system (GIS) and remote sensing have been widely used by the researchers in the field of wildlife and habitat suitability modeling. The main objective of this study is to map and predict the current and future habitat suitability potential of Rucervus eldii eldii in Keibul Lamjao National Park (KLNP) using MaxEnt. Presence location data of the species, topographic factors, and bio-climatic variables were used as input in the MaxEnt software to map current habitat suitability potential. To map the habitat suitability potential for future, two representative concentration pathway (RCP) scenarios RCP 2.6 and RCP 8.5 for the years 2050 and 2070 were used. The model returned an average AUC value of 0.944 which indicates the model to be sensitive and descriptive. Isothermality and precipitation in the wettest quarter were found to be two most significant variables. The suitable range of precipitation in the wettest quarter for Rucervus eldii eldii varies from 1365 to 1410 mm with an optimal value of 1405 mm and isothermality from 46.43 to 46.6% with an optimal value of 46.5%. Current habitat suitability results of the model show 0.45 km[2] of the area under no potential, 29.25 km[2] of the area under least potential, 8.29 km[2] of the area under moderate potential, 9.21 km[2] of the area under good potential, and 8.82 km[2] of the area under high potential. Both RCPs for the years 2050 and 2070 show the decreasing trend in the area under high suitability potential and increasing trend under no suitability potential. The results of this study can provide aid in the management and protection of Rucervus eldii eldii.}, } @article {pmid33637740, year = {2021}, author = {Goyal, A and Wang, T and Dubinkina, V and Maslov, S}, title = {Ecology-guided prediction of cross-feeding interactions in the human gut microbiome.}, journal = {Nature communications}, volume = {12}, number = {1}, pages = {1335}, pmid = {33637740}, issn = {2041-1723}, mesh = {Algorithms ; Computational Biology/methods ; *Ecology ; Gastrointestinal Microbiome/*genetics/*physiology ; Humans ; Intestines/*microbiology ; Machine Learning ; Metabolome ; Metabolomics ; Metagenomics ; Models, Biological ; }, abstract = {Understanding a complex microbial ecosystem such as the human gut microbiome requires information about both microbial species and the metabolites they produce and secrete. These metabolites are exchanged via a large network of cross-feeding interactions, and are crucial for predicting the functional state of the microbiome. However, till date, we only have information for a part of this network, limited by experimental throughput. Here, we propose an ecology-based computational method, GutCP, using which we predict hundreds of new experimentally untested cross-feeding interactions in the human gut microbiome. GutCP utilizes a mechanistic model of the gut microbiome with the explicit exchange of metabolites and their effects on the growth of microbial species. To build GutCP, we combine metagenomic and metabolomic measurements from the gut microbiome with optimization techniques from machine learning. Close to 65% of the cross-feeding interactions predicted by GutCP are supported by evidence from genome annotations, which we provide for experimental testing. Our method has the potential to greatly improve existing models of the human gut microbiome, as well as our ability to predict the metabolic profile of the gut.}, } @article {pmid33636795, year = {2021}, author = {Aigle, A and Colin, Y and Bouchali, R and Bourgeois, E and Marti, R and Ribun, S and Marjolet, L and Pozzi, ACM and Misery, B and Colinon, C and Bernardin-Souibgui, C and Wiest, L and Blaha, D and Galia, W and Cournoyer, B}, title = {Spatio-temporal variations in chemical pollutants found among urban deposits match changes in thiopurine S-methyltransferase-harboring bacteria tracked by the tpm metabarcoding approach.}, journal = {The Science of the total environment}, volume = {767}, number = {}, pages = {145425}, doi = {10.1016/j.scitotenv.2021.145425}, pmid = {33636795}, issn = {1879-1026}, mesh = {*Bacteria/enzymology/genetics ; DNA Barcoding, Taxonomic ; Environmental Monitoring ; Geologic Sediments ; Methyltransferases ; Spatio-Temporal Analysis ; *Water Pollutants, Chemical/analysis ; }, abstract = {The bTPMT (bacterial thiopurine S-methyltransferase), encoded by the tpm gene, can detoxify metalloid-containing oxyanions and xenobiotics. The hypothesis of significant relationships between tpm distribution patterns and chemical pollutants found in urban deposits was investigated. The tpm gene was found conserved among eight bacterial phyla with no sign of horizontal gene transfers but a predominance among gammaproteobacteria. A DNA metabarcoding approach was designed for tracking tpm-harboring bacteria among polluted urban deposits and sediments recovered for more than six years in a detention basin (DB). This DB recovers runoff waters and sediments from a zone of high commercial activities. The PCR products from DB samples led to more than 540,000 tpm reads after DADA2 or MOTHUR bio-informatic manipulations that were allocated to more than 88 and less than 634 sequence variants per sample. The tpm community patterns were significantly different between the recent urban deposits and those that had accumulated for more than 2 years in the DB, and between those of the DB surface and the DB settling pit. These groups of samples had distinct mixture of priority pollutants. Significant relationships between tpm ordination patterns, sediment accumulation time periods and location, and concentrations in PAH, chlorpyrifos, and 4-nonylphenols (NP) were observed. These correlations matched the higher occurrences of, among others, Aeromonas, Pseudomonas, and Xanthomonas tpm-harboring bacteria in recent urban DB deposits more contaminated with chrysene and alkylphenol ethoxylates. Highly significant drops in tpm reads allocated to Aeromonas species were recorded in the oldest DB sediments accumulating naphthalene and metallic pollutants. Degraders of urban pollutants such as P. aeruginosa and P. putida showed conserved distribution patterns over time but P. syringae phytopathogens were more abundant in the oldest sediments. TPMT-harboring bacteria can be used to assess the incidence of high risk priority pollutants on environmental systems.}, } @article {pmid33634334, year = {2021}, author = {Srivastava, A and Mishra, S and Verma, D}, title = {Characterization of Oral Bacterial Composition of Adult Smokeless Tobacco Users from Healthy Indians Using 16S rDNA Analysis.}, journal = {Microbial ecology}, volume = {82}, number = {4}, pages = {1061-1073}, pmid = {33634334}, issn = {1432-184X}, support = {SB/YS/LS-102/2014//Science and Engineering Research Board/ ; F 30-442/2018/BSR//University Grants Commission/ ; }, mesh = {Adult ; Bacteria/genetics ; DNA, Ribosomal/genetics ; Humans ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; *Tobacco, Smokeless ; }, abstract = {The present investigation is aiming to report the oral bacterial composition of smokeless tobacco (SLT) users and to determine the influence of SLT products on the healthy Indian population. With the aid of the V3 hypervariable region of the 16S rRNA gene, a total of 8,080,889 high-quality reads were clustered into 15 phyla and 180 genera in the oral cavity of the SLT users. Comparative analysis revealed a more diverse microbiome where two phyla and sixteen genera were significantly different among the SLT users as compared to the control group (p-value < 0.05). The prevalence of Fusobacteria-, Porphyromonas-, Desulfobulbus-, Enterococcus-, and Parvimonas-like genera among SLT users indicates altered bacterial communities among SLT users. Besides, the depletion of health-compatible bacteria such as Lactobacillus and Haemophilus also suggests poor oral health. Here, the majority of the altered genera belong to Gram-negative anaerobes that have been reported for assisting biofilm formation that leads in the progression of several oral diseases. The PICRUSt analysis further supports the hypothesis where a significant increase in the count of the genes involved in the metabolism of nitrogen, amino acids, and nicotinate/nicotinamide was observed among tobacco chewers. Moreover, this study has a high significance in Indian prospects where the SLT consumers are prevalent but we are deficient in information on their oral microbiome.}, } @article {pmid33633171, year = {2021}, author = {de Jager, D and Glanzmann, B and Möller, M and Hoal, E and van Helden, P and Harper, C and Bloomer, P}, title = {High diversity, inbreeding and a dynamic Pleistocene demographic history revealed by African buffalo genomes.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {4540}, pmid = {33633171}, issn = {2045-2322}, mesh = {Africa, Southern ; Animals ; Biological Evolution ; Buffaloes/*genetics ; Computational Biology/methods ; Databases, Genetic ; *Genetic Variation ; Genetics, Population ; *Genome ; Genome-Wide Association Study ; *Genomics/methods ; *Inbreeding ; Phylogeny ; }, abstract = {Genomes retain records of demographic changes and evolutionary forces that shape species and populations. Remnant populations of African buffalo (Syncerus caffer) in South Africa, with varied histories, provide an opportunity to investigate signatures left in their genomes by past events, both recent and ancient. Here, we produce 40 low coverage (7.14×) genome sequences of Cape buffalo (S. c. caffer) from four protected areas in South Africa. Genome-wide heterozygosity was the highest for any mammal for which these data are available, while differences in individual inbreeding coefficients reflected the severity of historical bottlenecks and current census sizes in each population. PSMC analysis revealed multiple changes in Ne between approximately one million and 20 thousand years ago, corresponding to paleoclimatic changes and Cape buffalo colonisation of southern Africa. The results of this study have implications for buffalo management and conservation, particularly in the context of the predicted increase in aridity and temperature in southern Africa over the next century as a result of climate change.}, } @article {pmid33630346, year = {2021}, author = {Hovel, KA and Duffy, JE and Stachowicz, JJ and Reynolds, P and Boström, C and Boyer, KE and Cimon, S and Cusson, M and Fodrie, FJ and Gagnon, K and Hereu, CM and Hori, M and Jorgensen, P and Kruschel, C and Lee, KS and Nakaoka, M and O'Connor, NE and Rossi, F and Ruesink, J and Tomas, F and Ziegler, S}, title = {Joint effects of patch edges and habitat degradation on faunal predation risk in a widespread marine foundation species.}, journal = {Ecology}, volume = {102}, number = {5}, pages = {e03316}, doi = {10.1002/ecy.3316}, pmid = {33630346}, issn = {1939-9170}, mesh = {Animals ; Biodiversity ; Ecosystem ; Humans ; Pacific Ocean ; *Predatory Behavior ; *Zosteraceae ; }, abstract = {Human activities degrade and fragment coastal marine habitats, reducing their structural complexity and making habitat edges a prevalent seascape feature. Though habitat edges frequently are implicated in reduced faunal survival and biodiversity, results of experiments on edge effects have been inconsistent, calling for a mechanistic approach to the study of edges that explicitly includes indirect and interactive effects of habitat alteration at multiple scales across biogeographic gradients. We used an experimental network spanning 17 eelgrass (Zostera marina) sites across the Atlantic and Pacific oceans and the Mediterranean Sea to determine (1) if eelgrass edges consistently increase faunal predation risk, (2) whether edge effects on predation risk are altered by habitat degradation (shoot thinning), and (3) whether variation in the strength of edge effects among sites can be explained by biogeographical variability in covarying eelgrass habitat features. Contrary to expectations, at most sites, predation risk for tethered crustaceans (crabs or shrimps) was lower along patch edges than in patch interiors, regardless of the extent of habitat degradation. However, the extent to which edges reduced predation risk, compared to the patch interior, was correlated with the extent to which edges supported higher eelgrass structural complexity and prey biomass compared to patch interiors. This suggests an indirect component to edge effects in which the impact of edge proximity on predation risk is mediated by the effect of edges on other key biotic factors. Our results suggest that studies on edge effects should consider structural characteristics of patch edges, which may vary geographically, and multiple ways that humans degrade habitats.}, } @article {pmid33629367, year = {2021}, author = {Noghrehchi, F and Stoklosa, J and Penev, S and Warton, DI}, title = {Selecting the model for multiple imputation of missing data: Just use an IC!.}, journal = {Statistics in medicine}, volume = {40}, number = {10}, pages = {2467-2497}, pmid = {33629367}, issn = {1097-0258}, mesh = {*Algorithms ; Bayes Theorem ; Bias ; Computer Simulation ; Humans ; Likelihood Functions ; }, abstract = {Multiple imputation and maximum likelihood estimation (via the expectation-maximization algorithm) are two well-known methods readily used for analyzing data with missing values. While these two methods are often considered as being distinct from one another, multiple imputation (when using improper imputation) is actually equivalent to a stochastic expectation-maximization approximation to the likelihood. In this article, we exploit this key result to show that familiar likelihood-based approaches to model selection, such as Akaike's information criterion (AIC) and the Bayesian information criterion (BIC), can be used to choose the imputation model that best fits the observed data. Poor choice of imputation model is known to bias inference, and while sensitivity analysis has often been used to explore the implications of different imputation models, we show that the data can be used to choose an appropriate imputation model via conventional model selection tools. We show that BIC can be consistent for selecting the correct imputation model in the presence of missing data. We verify these results empirically through simulation studies, and demonstrate their practicality on two classical missing data examples. An interesting result we saw in simulations was that not only can parameter estimates be biased by misspecifying the imputation model, but also by overfitting the imputation model. This emphasizes the importance of using model selection not just to choose the appropriate type of imputation model, but also to decide on the appropriate level of imputation model complexity.}, } @article {pmid33622985, year = {2020}, author = {Wei, L and Shao, W and Ma, L and Lin, Z}, title = {Genomewide analysis of microsatellite markers based on sequenced database in two anuran species.}, journal = {Journal of genetics}, volume = {99}, number = {}, pages = {}, pmid = {33622985}, issn = {0973-7731}, mesh = {Animals ; Anura/classification/*genetics ; *Databases, Genetic ; *Genome ; *Microsatellite Repeats ; Whole Genome Sequencing/*methods ; Xenopus laevis/*genetics ; }, abstract = {Eukaryotic and prokaryotic cell genomes exhibit multiple microsatellites. In this study, we characterized microsatellites in genomes and genes of Nanorana parkeri and Xenopus laevis. This characterization was used for gene ontology (GO) analysis of coding sequences (CDS). Compared to the genome of N. parkeri, the genome of X. laevis is larger and contains more number of microsatellites, but the diversity of both species are similar. Trinucleotide repeats in the genome of N. parkeri and dinucleotide and tetranucleotide repeats inthe genome of X. laevis were the most diverse. In both the species, diversity of microsatellites was highest in intergenic regions, followed by intron and exon regions, and lowest in coding regions. Microsatellites in CDS are thus subject to higher selective pressure. Many microsatellites are concentrated upstream and downstream of genes in both species, suggesting suppression of repeats in the middle of protein-CDS. Repeats are enriched in regions near gene termini purely due to the biophysical constraints of protein structure. In GO analysis, two and five unique GO terms, only found in N. parkeri and X. laevis, respectively, indicate advantageous mutations during species evolution. Biological process, cellular component and molecular function ontology reflected in the GO analysis predicted that the microsatellites located in CDS can alter protein function and may provide a molecular basis for species adaptation to new and changing environments.}, } @article {pmid33619299, year = {2021}, author = {Fonseca Dos Reis, E and Viney, M and Masuda, N}, title = {Network analysis of the immune state of mice.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {4306}, pmid = {33619299}, issn = {2045-2322}, mesh = {Animals ; *Biomarkers ; Computational Biology/methods ; Immune System/*physiology ; *Immunity ; Mice ; *Models, Biological ; Neural Networks, Computer ; }, abstract = {The mammalian immune system protects individuals from infection and disease. It is a complex system of interacting cells and molecules, which has been studied extensively to investigate its detailed function, principally using laboratory mice. Despite the complexity of the immune system, it is often analysed using a restricted set of immunological parameters. Here we have sought to generate a system-wide view of the murine immune response, which we have done by undertaking a network analysis of 120 immune measures. To date, there has only been limited network analyses of the immune system. Our network analysis identified a relatively low number of communities of immune measure nodes. Some of these communities recapitulate the well-known T helper 1 vs. T helper 2 cytokine polarisation (where ordination analyses failed to do so), which validates the utility of our approach. Other communities we detected show apparently novel juxtapositions of immune nodes. We suggest that the structure of these other communities might represent functional immunological units, which may require further empirical investigation. These results show the utility of network analysis in understanding the functioning of the mammalian immune system.}, } @article {pmid33618298, year = {2021}, author = {Wang, Z and Zhang, F and Zhang, X and Chan, NW and Kung, HT and Ariken, M and Zhou, X and Wang, Y}, title = {Regional suitability prediction of soil salinization based on remote-sensing derivatives and optimal spectral index.}, journal = {The Science of the total environment}, volume = {775}, number = {}, pages = {145807}, doi = {10.1016/j.scitotenv.2021.145807}, pmid = {33618298}, issn = {1879-1026}, abstract = {Soil salinization is an extremely serious land degradation problem in arid and semi-arid regions that hinders the sustainable development of agriculture and food security. Information and research on soil salinity using remote sensing (RS) technology provide a quick and accurate assessment and solutions to address this problem. This study aims to compare the capabilities of Landsat-8 OLI and Sentinel-2A MSI in RS prediction and exploration of the potential application of derivatives to RS prediction of salinized soils. It explores the ability of derivatives to be used in the Landsat-8 OLI and Sentinel-2A MSI multispectral data, and it was used as a data source as well as to address the adaptability of salinity prediction on a regional scale. The two-dimensional (2D) and three-dimensional (3D) optimal spectral indices are used to screen the bands that are most sensitive to soil salinity (0-10 cm), and RS data and topographic factors are combined with machine learning to construct a comprehensive soil salinity estimation model based on gray correlation analysis. The results are as follows: (1) The optimal spectral index (2D, 3D) can effectively consider possible combinations of the bands between the interaction effects and responding to sensitive bands of soil properties to circumvent the problem of applicability of spectral indices in different regions; (2) Both the Landsat-8 OLI and Sentinel-2A MSI multispectral RS data sources, after the first-order derivative techniques are all processed, show improvements in the prediction accuracy of the model; (3) The best performance/accuracy of the predictive model is for sentinel data under first-order derivatives. This study compared the capabilities of Landsat-8 OLI and Sentinel-2A MSI in RS prediction in finding the potential application of derivatives to RS prediction of salinized soils, with the results providing some theoretical basis and technical guidance for salinized soil prediction and environmental management planning.}, } @article {pmid33606979, year = {2021}, author = {Camarillo-Guerrero, LF and Almeida, A and Rangel-Pineros, G and Finn, RD and Lawley, TD}, title = {Massive expansion of human gut bacteriophage diversity.}, journal = {Cell}, volume = {184}, number = {4}, pages = {1098-1109.e9}, pmid = {33606979}, issn = {1097-4172}, support = {/WT_/Wellcome Trust/United Kingdom ; 098051/WT_/Wellcome Trust/United Kingdom ; BB/P027849/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Bacteriophages/*genetics ; *Biodiversity ; Databases, Nucleic Acid ; *Gastrointestinal Microbiome ; Host Specificity ; Humans ; Phylogeography ; }, abstract = {Bacteriophages drive evolutionary change in bacterial communities by creating gene flow networks that fuel ecological adaptions. However, the extent of viral diversity and its prevalence in the human gut remains largely unknown. Here, we introduce the Gut Phage Database, a collection of ∼142,000 non-redundant viral genomes (>10 kb) obtained by mining a dataset of 28,060 globally distributed human gut metagenomes and 2,898 reference genomes of cultured gut bacteria. Host assignment revealed that viral diversity is highest in the Firmicutes phyla and that ∼36% of viral clusters (VCs) are not restricted to a single species, creating gene flow networks across phylogenetically distinct bacterial species. Epidemiological analysis uncovered 280 globally distributed VCs found in at least 5 continents and a highly prevalent phage clade with features reminiscent of p-crAssphage. This high-quality, large-scale catalog of phage genomes will improve future virome studies and enable ecological and evolutionary analysis of human gut bacteriophages.}, } @article {pmid33605211, year = {2021}, author = {Weinstein, BG and Marconi, S and Bohlman, SA and Zare, A and Singh, A and Graves, SJ and White, EP}, title = {A remote sensing derived data set of 100 million individual tree crowns for the National Ecological Observatory Network.}, journal = {eLife}, volume = {10}, number = {}, pages = {}, pmid = {33605211}, issn = {2050-084X}, mesh = {*Deep Learning ; Ecology/*methods ; *Remote Sensing Technology ; *Trees ; United States ; }, abstract = {Forests provide biodiversity, ecosystem, and economic services. Information on individual trees is important for understanding forest ecosystems but obtaining individual-level data at broad scales is challenging due to the costs and logistics of data collection. While advances in remote sensing techniques allow surveys of individual trees at unprecedented extents, there remain technical challenges in turning sensor data into tangible information. Using deep learning methods, we produced an open-source data set of individual-level crown estimates for 100 million trees at 37 sites across the United States surveyed by the National Ecological Observatory Network's Airborne Observation Platform. Each canopy tree crown is represented by a rectangular bounding box and includes information on the height, crown area, and spatial location of the tree. These data have the potential to drive significant expansion of individual-level research on trees by facilitating both regional analyses and cross-region comparisons encompassing forest types from most of the United States.}, } @article {pmid33604424, year = {2021}, author = {Barton, MA and Simha, P and Magri, ME and Dutta, S and Kabir, H and Selvakumar, A and Zhou, X and Lv, Y and Martin, T and Kizos, T and Triantafyllou, E and Kataki, R and Gerchman, Y and Herscu-Kluska, R and Alrousan, D and Dalahmeh, S and Goh, EG and Elenciuc, D and Głowacka, A and Korculanin, L and Tzeng, RV and Ray, SS and Ganesapillai, M and Niwagaba, C and Prouty, C and Mihelcic, JR and Vinnerås, B}, title = {Attitudes of food consumers at universities towards recycling human urine as crop fertiliser: A multinational survey dataset.}, journal = {Data in brief}, volume = {35}, number = {}, pages = {106794}, pmid = {33604424}, issn = {2352-3409}, abstract = {We present here a data set generated from a multinational survey on opinions of university community members on the prospect of consuming food grown with human urine as fertiliser and about their urine recycling perceptions in general. The data set comprises answers from 3,763 university community members (students, faculty/researchers, and staff) from 20 universities in 16 countries and includes demographic variables (age bracket, gender, type of settlement of origin, academic discipline, and role in the university). Questions were designed based on Ajzen's theory of planned behaviour to elicit information about three components of behavioural intention-attitudes, subjective norms, and perceived behavioural control. Survey questions covered perceived risks and benefits (attitudes), perceptions of colleagues (injunctive social norm) and willingness to consume food grown with cow urine/faeces (descriptive social norm), and willingness to pay a price premium for food grown with human urine as fertiliser (perceived behavioural control). We also included a question about acceptable urine recycling and disposal options and assessed general environmental outlook via the 15-item revised New Ecological Paradigm (NEP) scale. Data were collected through a standardised survey instrument translated into the relevant languages and then administered via an online form. Invitations to the survey were sent by email to university mailing lists or to a systematic sample of the university directory. Only a few studies on attitudes towards using human urine as fertiliser have been conducted previously. The data described here, which we analysed in "Willingness among food consumers at universities to recycle human urine as crop fertiliser: Evidence from a multinational survey" [1], may be used to further understand potential barriers to acceptance of new sanitation systems based on wastewater source separation and urine recycling and can help inform the design of future sociological studies.}, } @article {pmid33603119, year = {2021}, author = {Crozier, LG and Burke, BJ and Chasco, BE and Widener, DL and Zabel, RW}, title = {Climate change threatens Chinook salmon throughout their life cycle.}, journal = {Communications biology}, volume = {4}, number = {1}, pages = {222}, pmid = {33603119}, issn = {2399-3642}, mesh = {Animal Migration ; Animals ; *Climate Change ; Computer Simulation ; Databases, Factual ; *Endangered Species ; *Life Cycle Stages ; Models, Theoretical ; Population Dynamics ; Salmon/*growth & development ; }, abstract = {Widespread declines in Atlantic and Pacific salmon (Salmo salar and Oncorhynchus spp.) have tracked recent climate changes, but managers still lack quantitative projections of the viability of any individual population in response to future climate change. To address this gap, we assembled a vast database of survival and other data for eight wild populations of threatened Chinook salmon (O. tshawytscha). For each population, we evaluated climate impacts at all life stages and modeled future trajectories forced by global climate model projections. Populations rapidly declined in response to increasing sea surface temperatures and other factors across diverse model assumptions and climate scenarios. Strong density dependence limited the number of salmon that survived early life stages, suggesting a potentially efficacious target for conservation effort. Other solutions require a better understanding of the factors that limit survival at sea. We conclude that dramatic increases in smolt survival are needed to overcome the negative impacts of climate change for this threatened species.}, } @article {pmid33602043, year = {2021}, author = {Shaw, E and Walpole, S and McLean, M and Alvarez-Nieto, C and Barna, S and Bazin, K and Behrens, G and Chase, H and Duane, B and El Omrani, O and Elf, M and Faerron Guzmán, CA and Falceto de Barros, E and Gibbs, TJ and Groome, J and Hackett, F and Harden, J and Hothersall, EJ and Hourihane, M and Huss, NM and Ikiugu, M and Joury, E and Leedham-Green, K and MacKenzie-Shalders, K and Madden, DL and McKimm, J and Nayna Schwerdtle, P and Peters, S and Redvers, N and Sheffield, P and Singleton, J and Tun, S and Woollard, R}, title = {AMEE Consensus Statement: Planetary health and education for sustainable healthcare.}, journal = {Medical teacher}, volume = {43}, number = {3}, pages = {272-286}, doi = {10.1080/0142159X.2020.1860207}, pmid = {33602043}, issn = {1466-187X}, mesh = {Curriculum ; Delivery of Health Care ; *Education, Medical ; Europe ; Humans ; *Planets ; }, abstract = {The purpose of this Consensus Statement is to provide a global, collaborative, representative and inclusive vision for educating an interprofessional healthcare workforce that can deliver sustainable healthcare and promote planetary health. It is intended to inform national and global accreditation standards, planning and action at the institutional level as well as highlight the role of individuals in transforming health professions education. Many countries have agreed to 'rapid, far-reaching and unprecedented changes' to reduce greenhouse gas emissions by 45% within 10 years and achieve carbon neutrality by 2050, including in healthcare. Currently, however, health professions graduates are not prepared for their roles in achieving these changes. Thus, to reduce emissions and meet the 2030 Sustainable Development Goals (SDGs), health professions education must equip undergraduates, and those already qualified, with the knowledge, skills, values, competence and confidence they need to sustainably promote the health, human rights and well-being of current and future generations, while protecting the health of the planet.The current imperative for action on environmental issues such as climate change requires health professionals to mobilize politically as they have before, becoming strong advocates for major environmental, social and economic change. A truly ethical relationship with people and the planet that we inhabit so precariously, and to guarantee a future for the generations which follow, demands nothing less of all health professionals.This Consensus Statement outlines the changes required in health professions education, approaches to achieve these changes and a timeline for action linked to the internationally agreed SDGs. It represents the collective vision of health professionals, educators and students from various health professions, geographic locations and cultures. 'Consensus' implies broad agreement amongst all individuals engaged in discussion on a specific issue, which in this instance, is agreement by all signatories of this Statement developed under the auspices of the Association for Medical Education in Europe (AMEE).To ensure a shared understanding and to accurately convey information, we outline key terms in a glossary which accompanies this Consensus Statement (Supplementary Appendix 1). We acknowledge, however, that terms evolve and that different terms resonate variably depending on factors such as setting and audience. We define education for sustainable healthcare as the process of equipping current and future health professionals with the knowledge, values, confidence and capacity to provide environmentally sustainable services through health professions education. We define a health professional as a person who has gained a professional qualification for work in the health system, whether in healthcare delivery, public health or a management or supporting role and education as 'the system comprising structures, curricula, faculty and activities contributing to a learning process'. This Statement is relevant to the full continuum of training - from undergraduate to postgraduate and continuing professional development.}, } @article {pmid33598385, year = {2021}, author = {de Carvalho Dutra, A and Silva, LL and Pedroso, RB and Tchuisseu, YP and da Silva, MT and Bergamini, M and Scheidt, JFHC and Iora, PH and do Lago Franco, R and Staton, CA and Vissoci, JRN and Nihei, OK and de Andrade, L}, title = {The Impact of Socioeconomic Factors, Coverage and Access to Health on Heart Ischemic Disease Mortality in a Brazilian Southern State: A Geospatial Analysis.}, journal = {Global heart}, volume = {16}, number = {1}, pages = {5}, pmid = {33598385}, issn = {2211-8179}, mesh = {Brazil/epidemiology ; Cities ; Humans ; *Myocardial Ischemia ; Socioeconomic Factors ; Spatial Analysis ; }, abstract = {BACKGROUND: No other disease has killed more than ischemic heart disease (IHD) for the past few years globally. Despite the advances in cardiology, the response time for starting treatment still leads patients to death because of the lack of healthcare coverage and access to referral centers.

OBJECTIVES: To analyze the spatial disparities related to IHD mortality in the Parana state, Brazil.

METHODS: An ecological study using secondary data from Brazilian Health Informatics Department between 2013-2017 was performed to verify the IHD mortality. An spatial analysis was performed using the Global Moran and Local Indicators of Spatial Association (LISA) to verify the spatial dependency of IHD mortality. Lastly, multivariate spatial regression models were also developed using Ordinary Least Squares and Geographically Weighted Regression (GWR) to identify socioeconomic indicators (aging, income, and illiteracy rates), exam coverage (catheterization, angioplasty, and revascularization rates), and access to health (access index to cardiologists and chemical reperfusion centers) significantly correlated with IHD mortality. The chosen model was based on p < 0.05, highest adjusted R[2] and lowest Akaike Information Criterion.

RESULTS: A total of 22,920 individuals died from IHD between 2013-2017. The spatial analysis confirmed a positive spatial autocorrelation global between IDH mortality rates (Moran's I: 0.633, p < 0.01). The LISA analysis identified six high-high pattern clusters composed by 66 municipalities (16.5%). GWR presented the best model (Adjusted R[2]: 0.72) showing that accessibility to cardiologists and chemical reperfusion centers, and revascularization and angioplasty rates differentially affect the IHD mortality rates geographically. Aging and illiteracy rate presented positive correlation with IHD mortality rate, while income ratio presented negative correlation (p < 0.05).

CONCLUSION: Regions of vulnerability were unveiled by the spatial analysis where sociodemographic, exam coverage and accessibility to health variables impacted differently the IHD mortality rates in Paraná state, Brazil.

HIGHLIGHTS: The increase in ischemic heart disease mortality rates is related to geographical disparities.The IHD mortality is differentially associated to socioeconomic factors, exam coverage, and access to health.Higher accessibility to chemical reperfusion centers did not necessarily improve patient outcomes in some regions of the state.Clusters of high mortality rate are placed in regions with low amount of cardiologists, income and schooling.}, } @article {pmid33592536, year = {2021}, author = {Taş, N and de Jong, AE and Li, Y and Trubl, G and Xue, Y and Dove, NC}, title = {Metagenomic tools in microbial ecology research.}, journal = {Current opinion in biotechnology}, volume = {67}, number = {}, pages = {184-191}, doi = {10.1016/j.copbio.2021.01.019}, pmid = {33592536}, issn = {1879-0429}, mesh = {Ecology ; High-Throughput Nucleotide Sequencing ; Metagenome/genetics ; *Metagenomics ; *Microbiota/genetics ; Sequence Analysis, DNA ; }, abstract = {Ability to directly sequence DNA from the environment permanently changed microbial ecology. Here, we review the new insights to microbial life gleaned from the applications of metagenomics, as well as the extensive set of analytical tools that facilitate exploration of diversity and function of complex microbial communities. While metagenomics is shaping our understanding of microbial functions in ecosystems via gene-centric and genome-centric methods, annotating functions, metagenome assembly and binning in heterogeneous samples remains challenging. Development of new analysis and sequencing platforms generating high-throughput long-read sequences and functional screening opportunities will aid in harnessing metagenomes to increase our understanding of microbial taxonomy, function, ecology, and evolution in the environment.}, } @article {pmid33592451, year = {2021}, author = {Boori, MS and Choudhary, K and Paringer, R and Kupriyanov, A}, title = {Spatiotemporal ecological vulnerability analysis with statistical correlation based on satellite remote sensing in Samara, Russia.}, journal = {Journal of environmental management}, volume = {285}, number = {}, pages = {112138}, doi = {10.1016/j.jenvman.2021.112138}, pmid = {33592451}, issn = {1095-8630}, mesh = {China ; Cities ; *Ecosystem ; Environmental Monitoring ; Humans ; *Remote Sensing Technology ; Russia ; }, abstract = {In the present global situation, when everywhere ecology is degraded due to the extreme exhaustion of natural resources. Therefore spatiotemporal ecological vulnerability analysis is necessary for the current situation for sustainable development with protection of fragile eco-environment. Remote sensing is a unique tool to provide complete and continuous land surface information at different scales, which can use for eco-environment analysis. A methodology constructed on the principal component analysis (PCA) to identify satellite remote sensing ecological index (RSEI) for ecological vulnerability analysis and distribution based on four land surface parameters (dryness, greenness, temperature and moisture) by using Landsat TM/ETM+/OLI/TIRS data in the Samara region Russia. The results were verified by the following four methods: location-based, categorization-based, correlation-based and city center to outwards distance-based comparisons. Results indicate that ecological condition was improved from 2010 to 2015 as RSEI increased from 0.79 to 0.98 and from 2015 to 2020 the ecological condition was degraded as RSEI decreased from 0.98 to 0.82 but overall it was improved in this decade. RSEI distribution curve shows moderate to good and excellent ecological conditions and degraded ecological condition was basically characterized by high human interference and socioeconomic activities in the study area. Such a technique is a baseline for highly accurate ecological conditions mapping, monitoring and can use for decision making, management and sustainable development.}, } @article {pmid33592242, year = {2021}, author = {Battel, L and Cunegatto, F and Viduani, A and Fisher, HL and Kohrt, BA and Mondelli, V and Swartz, JR and Kieling, C}, title = {Mind the brain gap: The worldwide distribution of neuroimaging research on adolescent depression.}, journal = {NeuroImage}, volume = {231}, number = {}, pages = {117865}, pmid = {33592242}, issn = {1095-9572}, support = {MC_PC_MR/R019460/1/MRC_/Medical Research Council/United Kingdom ; R21 MH124072/MH/NIMH NIH HHS/United States ; /DH_/Department of Health/United Kingdom ; }, mesh = {Adolescent ; Adolescent Behavior ; Biomedical Research/economics/*methods/trends ; Brain/*diagnostic imaging ; Databases, Factual/economics/trends ; Depression/*diagnostic imaging/economics/epidemiology ; *Developing Countries/economics ; *Global Health/economics/trends ; Humans ; Neuroimaging/economics/*methods/trends ; Risk Factors ; }, abstract = {Adolescents comprise one fourth of the world's population, with about 90% of them living in low- and middle-income countries (LMICs). The incidence of depression markedly increases during adolescence, making the disorder a leading cause of disease-related disability in this age group. However, most research on adolescent depression has been performed in high-income countries (HICs). To ascertain the extent to which this disparity operates in neuroimaging research, a systematic review of the literature was performed. A total of 148 studies were identified, with neuroimaging data available for 4,729 adolescents with depression. When stratified by income group, 122 (82%) studies originated from HICs, while 26 (18%) were conducted in LMICs, for a total of 3,705 and 1,024 adolescents with depression respectively. A positive Spearman rank correlation was observed between country per capita income and sample size (rs=0.673, p = 0.023). Our results support the previous reports showing a large disparity between the number of studies and the adolescent population per world region. Future research comparing neuroimaging findings across populations from HICs and LMICs may provide unique insights to enhance our understanding of the neurobiological processes underlying the development of depression.}, } @article {pmid33591316, year = {2021}, author = {Chao, KH and Barton, K and Palmer, S and Lanfear, R}, title = {sangeranalyseR: Simple and Interactive Processing of Sanger Sequencing Data in R.}, journal = {Genome biology and evolution}, volume = {13}, number = {3}, pages = {}, pmid = {33591316}, issn = {1759-6653}, mesh = {Computational Biology/*methods ; DNA ; Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA/*methods ; *Software ; User-Computer Interface ; Web Browser ; }, abstract = {sangeranalyseR is feature-rich, free, and open-source R package for processing Sanger sequencing data. It allows users to go from loading reads to saving aligned contigs in a few lines of R code by using sensible defaults for most actions. It also provides complete flexibility for determining how individual reads and contigs are processed, both at the command-line in R and via interactive Shiny applications. sangeranalyseR provides a wide range of options for all steps in Sanger processing pipelines including trimming reads, detecting secondary peaks, viewing chromatograms, detecting indels and stop codons, aligning contigs, estimating phylogenetic trees, and more. Input data can be in either ABIF or FASTA format. sangeranalyseR comes with extensive online documentation and outputs aligned and unaligned reads and contigs in FASTA format, along with detailed interactive HTML reports. sangeranalyseR supports the use of colorblind-friendly palettes for viewing alignments and chromatograms. It is released under an MIT licence and available for all platforms on Bioconductor (https://bioconductor.org/packages/sangeranalyseR, last accessed February 22, 2021) and on Github (https://github.com/roblanf/sangeranalyseR, last accessed February 22, 2021).}, } @article {pmid33591270, year = {2021}, author = {Turnšek, J and Brunson, JK and Viedma, MDPM and Deerinck, TJ and Horák, A and Oborník, M and Bielinski, VA and Allen, AE}, title = {Proximity proteomics in a marine diatom reveals a putative cell surface-to-chloroplast iron trafficking pathway.}, journal = {eLife}, volume = {10}, number = {}, pages = {}, pmid = {33591270}, issn = {2050-084X}, support = {F31 ES030613/ES/NIEHS NIH HHS/United States ; R24 GM137200/GM/NIGMS NIH HHS/United States ; 1F31ES030613-01/NH/NIH HHS/United States ; }, mesh = {Biological Transport ; Cell Membrane/metabolism ; Chloroplasts/metabolism ; Diatoms/genetics/*metabolism ; Iron/*metabolism ; Multigene Family ; Proteomics/methods ; Transferrin/*metabolism ; }, abstract = {Iron is a biochemically critical metal cofactor in enzymes involved in photosynthesis, cellular respiration, nitrate assimilation, nitrogen fixation, and reactive oxygen species defense. Marine microeukaryotes have evolved a phytotransferrin-based iron uptake system to cope with iron scarcity, a major factor limiting primary productivity in the global ocean. Diatom phytotransferrin is endocytosed; however, proteins downstream of this environmentally ubiquitous iron receptor are unknown. We applied engineered ascorbate peroxidase APEX2-based subcellular proteomics to catalog proximal proteins of phytotransferrin in the model marine diatom Phaeodactylum tricornutum. Proteins encoded by poorly characterized iron-sensitive genes were identified including three that are expressed from a chromosomal gene cluster. Two of them showed unambiguous colocalization with phytotransferrin adjacent to the chloroplast. Further phylogenetic, domain, and biochemical analyses suggest their involvement in intracellular iron processing. Proximity proteomics holds enormous potential to glean new insights into iron acquisition pathways and beyond in these evolutionarily, ecologically, and biotechnologically important microalgae.}, } @article {pmid33590960, year = {2021}, author = {Feron, R and Pan, Q and Wen, M and Imarazene, B and Jouanno, E and Anderson, J and Herpin, A and Journot, L and Parrinello, H and Klopp, C and Kottler, VA and Roco, AS and Du, K and Kneitz, S and Adolfi, M and Wilson, CA and McCluskey, B and Amores, A and Desvignes, T and Goetz, FW and Takanashi, A and Kawaguchi, M and Detrich, HW and Oliveira, MA and Nóbrega, RH and Sakamoto, T and Nakamoto, M and Wargelius, A and Karlsen, Ø and Wang, Z and Stöck, M and Waterhouse, RM and Braasch, I and Postlethwait, JH and Schartl, M and Guiguen, Y}, title = {RADSex: A computational workflow to study sex determination using restriction site-associated DNA sequencing data.}, journal = {Molecular ecology resources}, volume = {21}, number = {5}, pages = {1715-1731}, pmid = {33590960}, issn = {1755-0998}, support = {R35 GM139635/GM/NIGMS NIH HHS/United States ; PLR-1444167//National Science Foundation (USA) Office of Polar Programs/ ; PP00P3_170664//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; R01 GM085318/GM/NIGMS NIH HHS/United States ; R01GM085318//National Institute of Health (USA)/ ; SCHA 408/10-1//Agence Nationale de la Recherche/ ; R35GM139635//National Institute of Health (USA)/ ; PLR-1247510//National Science Foundation (USA) Office of Polar Programs/ ; ANR-10-INBS-09//Agence Nationale de la Recherche/ ; OPP-1543383//National Science Foundation (USA) Office of Polar Programs/ ; SCHA 408/10-1//Deutsche Forschungsgemeinschaft/ ; }, mesh = {Animals ; *Computational Biology ; DNA ; Female ; Fishes/*genetics ; Male ; Sequence Analysis, DNA ; *Sex Chromosomes ; *Sex Determination Analysis ; Software ; Workflow ; }, abstract = {The study of sex determination and sex chromosome organization in nonmodel species has long been technically challenging, but new sequencing methodologies now enable precise and high-throughput identification of sex-specific genomic sequences. In particular, restriction site-associated DNA sequencing (RAD-Seq) is being extensively applied to explore sex determination systems in many plant and animal species. However, software specifically designed to search for and visualize sex-biased markers using RAD-Seq data is lacking. Here, we present RADSex, a computational analysis workflow designed to study the genetic basis of sex determination using RAD-Seq data. RADSex is simple to use, requires few computational resources, makes no prior assumptions about the type of sex-determination system or structure of the sex locus, and offers convenient visualization through a dedicated R package. To demonstrate the functionality of RADSex, we re-analysed a published data set of Japanese medaka, Oryzias latipes, where we uncovered a previously unknown Y chromosome polymorphism. We then used RADSex to analyse new RAD-Seq data sets from 15 fish species spanning multiple taxonomic orders. We identified the sex determination system and sex-specific markers in six of these species, five of which had no known sex-markers prior to this study. We show that RADSex greatly facilitates the study of sex determination systems in nonmodel species thanks to its speed of analyses, low resource usage, ease of application and visualization options. Furthermore, our analysis of new data sets from 15 species provides new insights on sex determination in fish.}, } @article {pmid33590697, year = {2021}, author = {Macher, TH and Beermann, AJ and Leese, F}, title = {TaxonTableTools: A comprehensive, platform-independent graphical user interface software to explore and visualise DNA metabarcoding data.}, journal = {Molecular ecology resources}, volume = {21}, number = {5}, pages = {1705-1714}, doi = {10.1111/1755-0998.13358}, pmid = {33590697}, issn = {1755-0998}, support = {FKZ 3719 24 2040//German Federal Environmental Agency/ ; //UNIVERSITAET DUISBURG-ESSEN/ ; }, mesh = {Biodiversity ; *Computational Biology ; DNA ; *DNA Barcoding, Taxonomic ; Data Visualization ; *Software ; }, abstract = {DNA metabarcoding is increasingly used as a tool to assess biodiversity in research and environmental management. Powerful analysis software exists to process raw data. However, the translation of sequence read data into biological information and downstream analyses may be difficult for end users with limited expertise in bioinformatics. Thus, there is a growing need for easy-to-use, graphical user interface (GUI) software to analyse and visualise DNA metabarcoding data. Here, we present TaxonTableTools (TTT), a new platform-independent GUI that aims to fill this gap by providing simple, reproducible analysis and visualisation workflows. At its base, TTT uses a "TaXon table", which is a data format that can be generated easily within TTT from two input files: a read table and a taxonomy table obtained using various published metabarcoding pipelines. TTT analysis and visualisation modules include Venn diagrams to compare taxon overlap among replicates, samples, or analysis methods. TTT analyses and visualises basic statistics, such as read proportion per taxon, as well as more sophisticated visualisations, such as interactive Krona charts for taxonomic data exploration. Various ecological analyses can be produced directly, including alpha or beta diversity estimates, and rarefaction analysis ordination plots. Metabarcoding data can be converted into formats required for traditional, taxonomy-based analyses performed by regulatory bioassessment programs. In addition, TTT is able to produce html-based interactive graphics that can be analysed in any web browser. The software comes with a manual and tutorial, is free and publicly available through GitHub (https://github.com/TillMacher/TaxonTableTools) or the Python package index (https://pypi.org/project/taxontabletools/).}, } @article {pmid33589842, year = {2021}, author = {Schorn, MA and Verhoeven, S and Ridder, L and Huber, F and Acharya, DD and Aksenov, AA and Aleti, G and Moghaddam, JA and Aron, AT and Aziz, S and Bauermeister, A and Bauman, KD and Baunach, M and Beemelmanns, C and Beman, JM and Berlanga-Clavero, MV and Blacutt, AA and Bode, HB and Boullie, A and Brejnrod, A and Bugni, TS and Calteau, A and Cao, L and Carrión, VJ and Castelo-Branco, R and Chanana, S and Chase, AB and Chevrette, MG and Costa-Lotufo, LV and Crawford, JM and Currie, CR and Cuypers, B and Dang, T and de Rond, T and Demko, AM and Dittmann, E and Du, C and Drozd, C and Dujardin, JC and Dutton, RJ and Edlund, A and Fewer, DP and Garg, N and Gauglitz, JM and Gentry, EC and Gerwick, L and Glukhov, E and Gross, H and Gugger, M and Guillén Matus, DG and Helfrich, EJN and Hempel, BF and Hur, JS and Iorio, M and Jensen, PR and Kang, KB and Kaysser, L and Kelleher, NL and Kim, CS and Kim, KH and Koester, I and König, GM and Leao, T and Lee, SR and Lee, YY and Li, X and Little, JC and Maloney, KN and Männle, D and Martin H, C and McAvoy, AC and Metcalf, WW and Mohimani, H and Molina-Santiago, C and Moore, BS and Mullowney, MW and Muskat, M and Nothias, LF and O'Neill, EC and Parkinson, EI and Petras, D and Piel, J and Pierce, EC and Pires, K and Reher, R and Romero, D and Roper, MC and Rust, M and Saad, H and Saenz, C and Sanchez, LM and Sørensen, SJ and Sosio, M and Süssmuth, RD and Sweeney, D and Tahlan, K and Thomson, RJ and Tobias, NJ and Trindade-Silva, AE and van Wezel, GP and Wang, M and Weldon, KC and Zhang, F and Ziemert, N and Duncan, KR and Crüsemann, M and Rogers, S and Dorrestein, PC and Medema, MH and van der Hooft, JJJ}, title = {A community resource for paired genomic and metabolomic data mining.}, journal = {Nature chemical biology}, volume = {17}, number = {4}, pages = {363-368}, pmid = {33589842}, issn = {1552-4469}, support = {R01 GM118815/GM/NIGMS NIH HHS/United States ; UL1 TR001863/TR/NCATS NIH HHS/United States ; R35 GM138002/GM/NIGMS NIH HHS/United States ; R01 AT009143/AT/NCCIH NIH HHS/United States ; U19 AI142720/AI/NIAID NIH HHS/United States ; DP2 AT010401/AT/NCCIH NIH HHS/United States ; F32 CA221327/CA/NCI NIH HHS/United States ; U01 GM110706/GM/NIGMS NIH HHS/United States ; }, mesh = {Data Mining/*methods ; Databases, Factual ; Genomics/*methods ; Metabolomics/*methods ; }, abstract = {Genomics and metabolomics are widely used to explore specialized metabolite diversity. The Paired Omics Data Platform is a community initiative to systematically document links between metabolome and (meta)genome data, aiding identification of natural product biosynthetic origins and metabolite structures.}, } @article {pmid33586683, year = {2021}, author = {Petrosino, JM and Longenecker, JZ and Ramkumar, S and Xu, X and Dorn, LE and Bratasz, A and Yu, L and Maurya, S and Tolstikov, V and Bussberg, V and Janssen, PM and Periasamy, M and Kiebish, MA and Duester, G and von Lintig, J and Ziouzenkova, O and Accornero, F}, title = {Paracardial fat remodeling affects systemic metabolism through alcohol dehydrogenase 1.}, journal = {The Journal of clinical investigation}, volume = {131}, number = {4}, pages = {}, pmid = {33586683}, issn = {1558-8238}, support = {K99 HL121284/HL/NHLBI NIH HHS/United States ; P30 EY011373/EY/NEI NIH HHS/United States ; R00 HL121284/HL/NHLBI NIH HHS/United States ; R01 HL113084/HL/NHLBI NIH HHS/United States ; F31 AR073638/AR/NIAMS NIH HHS/United States ; R01 EY028121/EY/NEI NIH HHS/United States ; R01 HL154001/HL/NHLBI NIH HHS/United States ; P30 CA016058/CA/NCI NIH HHS/United States ; T32 GM068412/GM/NIGMS NIH HHS/United States ; R01 HL136951/HL/NHLBI NIH HHS/United States ; }, mesh = {Adipose Tissue/*enzymology/pathology ; Alcohol Dehydrogenase/deficiency/*metabolism ; Animals ; Cell Nucleus/genetics/metabolism ; Metabolomics ; Mice ; Mice, Knockout ; Mitochondria, Heart/genetics/*metabolism/pathology ; Obesity/*enzymology/genetics/pathology ; Pericardium/*enzymology/pathology ; Peroxisome Proliferator-Activated Receptor Gamma Coactivator 1-alpha/genetics/metabolism ; Retinaldehyde/metabolism ; Signal Transduction/genetics ; }, abstract = {The relationship between adiposity and metabolic health is well established. However, very little is known about the fat depot, known as paracardial fat (pCF), located superior to and surrounding the heart. Here, we show that pCF remodels with aging and a high-fat diet and that the size and function of this depot are controlled by alcohol dehydrogenase 1 (ADH1), an enzyme that oxidizes retinol into retinaldehyde. Elderly individuals and individuals with obesity have low ADH1 expression in pCF, and in mice, genetic ablation of Adh1 is sufficient to drive pCF accumulation, dysfunction, and global impairments in metabolic flexibility. Metabolomics analysis revealed that pCF controlled the levels of circulating metabolites affecting fatty acid biosynthesis. Also, surgical removal of the pCF depot was sufficient to rescue the impairments in cardiometabolic flexibility and fitness observed in Adh1-deficient mice. Furthermore, treatment with retinaldehyde prevented pCF remodeling in these animals. Mechanistically, we found that the ADH1/retinaldehyde pathway works by driving PGC-1α nuclear translocation and promoting mitochondrial fusion and biogenesis in the pCF depot. Together, these data demonstrate that pCF is a critical regulator of cardiometabolic fitness and that retinaldehyde and its generating enzyme ADH1 act as critical regulators of adipocyte remodeling in the pCF depot.}, } @article {pmid33586292, year = {2021}, author = {Uengwetwanit, T and Pootakham, W and Nookaew, I and Sonthirod, C and Angthong, P and Sittikankaew, K and Rungrassamee, W and Arayamethakorn, S and Wongsurawat, T and Jenjaroenpun, P and Sangsrakru, D and Leelatanawit, R and Khudet, J and Koehorst, JJ and Schaap, PJ and Martins Dos Santos, V and Tangy, F and Karoonuthaisiri, N}, title = {A chromosome-level assembly of the black tiger shrimp (Penaeus monodon) genome facilitates the identification of growth-associated genes.}, journal = {Molecular ecology resources}, volume = {21}, number = {5}, pages = {1620-1640}, pmid = {33586292}, issn = {1755-0998}, support = {P20 GM125503/GM/NIGMS NIH HHS/United States ; P20GM125503//National Institute of General Medical Sciences of the National Institutes of Health/ ; 734486//European Union's Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant/ ; P1651718//National Center for Genetic Engineering and Biotechnology/ ; P1950419//TDG Food and Feed program, National Science and Technology Development Agency/ ; }, mesh = {Animals ; Aquaculture ; Chromosomes ; *Genome ; *Penaeidae/genetics/growth & development ; Transcriptome ; }, abstract = {To salvage marine ecosystems from fishery overexploitation, sustainable and efficient aquaculture must be emphasized. The knowledge obtained from available genome sequence of marine organisms has accelerated marine aquaculture in many cases. The black tiger shrimp (Penaeus monodon) is one of the most prominent cultured penaeid shrimps (Crustacean) with an average annual global production of half a million tons in the last decade. However, its currently available genome assemblies lack the contiguity and completeness required for accurate genome annotation due to the highly repetitive nature of the genome and technical difficulty in extracting high-quality, high-molecular weight DNA. Here, we report the first chromosome-level whole-genome assembly of P. monodon. The combination of long-read Pacific Biosciences (PacBio) and long-range Chicago and Hi-C technologies enabled a successful assembly of this first high-quality genome sequence. The final assembly covered 2.39 Gb (92.3% of the estimated genome size) and contained 44 pseudomolecules, corresponding to the haploid chromosome number. Repetitive elements occupied a substantial portion of the assembly (62.5%), the highest of the figures reported among crustacean species. The availability of this high-quality genome assembly enabled the identification of genes associated with rapid growth in the black tiger shrimp through the comparison of hepatopancreas transcriptome of slow-growing and fast-growing shrimps. The results highlighted several growth-associated genes. Our high-quality genome assembly provides an invaluable resource for genetic improvement and breeding penaeid shrimp in aquaculture. The availability of P. monodon genome enables analyses of ecological impact, environment adaptation and evolution, as well as the role of the genome to protect the ecological resources by promoting sustainable shrimp farming.}, } @article {pmid35530077, year = {2019}, author = {Wang, J and Sui, M and Ma, Z and Li, H and Yuan, B}, title = {Antibacterial performance of polymer quaternary ammonium salt-capped silver nanoparticles on Bacillus subtilis in water.}, journal = {RSC advances}, volume = {9}, number = {44}, pages = {25667-25676}, pmid = {35530077}, issn = {2046-2069}, abstract = {In this study, we prepared polymer quaternary ammonium salt-capped silver nanoparticles (PQAS-AgNPs) and investigated their antimicrobial activities. The antimicrobial effectiveness of PQAS-AgNPs on Bacillus subtilis (B. subtilis), and the effect of dose, pH, chloride ion and humic acid (HA) were studied. It was found that PQAS-AgNPs revealed excellent antimicrobial activity to B. subtilis, compared with polyvinylpyrrolidone-capped silver nanoparticles (PVP-AgNPs), which was the reference antimicrobial material. The positive surface, the antimicrobial activity of PQAS, and the synergistic antibacterial effect between PQAS and AgNPs contributed to the significant antibacterial superiority of PQAS-AgNPs. This study demonstrated that the impact of the dose of the material was positive and the microbiocidal efficacy of PQAS-AgNPs was stronger at lower pH. In addition, the antibacterial performance of PQAS-AgNPs decreased in the presence of Cl[-] and HA. Finally, in combination with the results of FCM and adenosine triphosphate (ATP) content, it was found that PQAS-AgNPs destroyed the respiratory chain of bacterial cells, reduced the synthesis of ATP, and destroyed the cell wall and cell membrane function.}, } @article {pmid33869336, year = {2019}, author = {Tziraki-Segal, C and De Luca, V and Santana, S and Romano, R and Tramontano, G and Scattola, P and Celata, C and Gelmi, G and Ponce Márquez, S and Lopez-Samaniego, L and Zavagli, V and Halkoaho, A and Grimes, C and Tomás, MT and Fernandes, B and Calzà, L and Speranza, P and Coppola, L and Jager-Wittenaar, H and O'Caoimh, R and Pietilä, AM and Carriazo, AM and Apostolo, J and Iaccarino, G and Liotta, G and Tramontano, D and Molloy, W and Triassi, M and Viggiani, V and Illario, M}, title = {Creating a Culture of Health in Planning and Implementing Innovative Strategies Addressing Non-communicable Chronic Diseases.}, journal = {Frontiers in sociology}, volume = {4}, number = {}, pages = {9}, pmid = {33869336}, issn = {2297-7775}, abstract = {Ongoing demographic changes are challenging health systems worldwide especially in relation to increasing longevity and the resultant rise of non-communicable diseases (NCDs). To meet these challenges, a paradigm shift to a more proactive approach to health promotion, and maintenance is needed. This new paradigm focuses on creating and implementing an ecological model of Culture of Health. The conceptualization of the Culture of Health is defined as one where good health and well-being flourish across geographic, demographic, and social sectors; fostering healthy equitable communities where citizens have the opportunity to make choices and be co-producers of healthy lifestyles. Based on Antonovsky's Salutogenesis model which asserts that the experience of health moves along a continuum across the lifespan, we will identify the key drivers for achieving a Culture of Health. These include mindset/expectations, sense of community, and civic engagement. The present article discusses these drivers and identifies areas where policy and research actions are needed to advance positive change on population health and well-being. We highlight empirical evidence of drivers within the EU guided by the activities within the thematic Action Groups of the European Innovation Partnership on Active and Healthy Aging (EIP on AHA), focusing on Lifespan Health Promotion and Prevention of Age-Related Frailty and Disease (A3 Action Group). We will specifically focus on the effect of Culture on Health, highlighting cross-cutting drivers across domains such as innovations at the individual and community level, and in synergies with business, policy, and research entities. We will present examples of drivers for creating a Culture of Health, the barriers, the remaining gaps, and areas of future research to achieve an inclusive and sustainable asset-based community.}, } @article {pmid34306605, year = {2018}, author = {Rossetti, BJ and Dynes, T and Brosi, B and de Roode, JC and Kong, J}, title = {GRAPHITE: A Graphical Environment for Scalable in situ Video Tracking of Moving Insects.}, journal = {Methods in ecology and evolution}, volume = {9}, number = {4}, pages = {956-964}, pmid = {34306605}, issn = {2041-210X}, support = {R01 GM109501/GM/NIGMS NIH HHS/United States ; }, abstract = {1. Methods for measuring animal movement are critical for understanding numerous ecological and evolutionary processes. However, few methods are available for small organisms, and even fewer methods offer consistent individual-level resolution while remaining affordable, scalable and operable in the field. 2. We describe a low-cost animal movement tracking method with a user-friendly graphical interface, called GRAPHITE. Our automated software can quantify motions of insects by offline video analysis of inexpensive and lightweight human-readable tags attached to individual insects. The integrated graphical editor provides a full-featured environment for users to review the generated tracking data and make individual- or group-level edits. 3. GRAPHITE is a novel video analysis and graphical editing software (MATLAB v.9.0.0+) that identifies tags in image frames with a minimal false negative rate, links sequences of corresponding tags into "tracks" for each individual insect, infers the tag identifier, and provides a user-friendly graphical environment for editing tracking data. Users can either batch process raw video data using the full analysis pipeline or execute GRAPHITE modules independently for a tailored analysis. 4. We demonstrate the efficacy of the developed software with a specific application to the movement of honey bees at the entrance of hives. However, this system can be easily modified to track individually marked insects of 3 mm and larger. A notable advantage of this method is its ability to provide easy access to individual-level tracking data using human-readable tags.}, } @article {pmid35620776, year = {2018}, author = {Jones, CA and Wassel, A and Mierse, W and Sills, ES}, title = {The 500-year Cultural & Economic Trajectory of Tobacco: A Circle Complete.}, journal = {Journal of health economics and outcomes research}, volume = {5}, number = {2}, pages = {175-182}, doi = {10.36469/9809}, pmid = {35620776}, issn = {2327-2236}, abstract = {Who smokes, and why do they do it? What factors discourage and otherwise reward or incentivize smoking? Tobacco use has been accompanied by controversy from the moment of its entry into European culture, and conflicting opinions regarding its potentially adverse influence on health have coexisted for hundreds of years. Its use in all forms represents the world's single greatest cause of preventable disease and death. Tobacco was introduced to Europe by Christopher Columbus, who in October 1492 discovered the crop in Cuba. While the next four centuries would see tobacco as the most highly traded economic commodity, by 1900, the now familiar cigarette remained obscure and accounted for only 2% of total tobacco sales. Global tobacco consumption rose sharply after 1914 and became especially prevalent following World War II, particularly among men. Indeed, overall tobacco sales increased by more than 60% by the mid-20th century, and cigarettes were a critical driver of this growth. Cigarettes dominated the tobacco market by 1950, by then accounting for more than 80% of all tobacco purchases. In the absence of clinical and scientific evidence against tobacco, moral and religious arguments dominated opposition voices against tobacco consumption in the 1800s. However, by the mid-20th century, advancements in medical research supported enhanced government and voluntary actions against tobacco advertising and also raised awareness of the dangers associated with passive tobacco smoke exposure. Solid epidemiological work connecting tobacco use with "the shortening of life span" began to appear in the medical literature in the 1950s, linking smoking with lung cancer and related conditions. In subsequent years, these developments led to significant curtailment of tobacco use. This monograph explores aspects of the intersection of tobacco with themes of behavioral incentives, religion, culture, literature, economics, and government over the past five centuries.}, } @article {pmid34722870, year = {2017}, author = {Rougier, NP and Hinsen, K and Alexandre, F and Arildsen, T and Barba, LA and Benureau, FCY and Brown, CT and de Buyl, P and Caglayan, O and Davison, AP and Delsuc, MA and Detorakis, G and Diem, AK and Drix, D and Enel, P and Girard, B and Guest, O and Hall, MG and Henriques, RN and Hinaut, X and Jaron, KS and Khamassi, M and Klein, A and Manninen, T and Marchesi, P and McGlinn, D and Metzner, C and Petchey, O and Plesser, HE and Poisot, T and Ram, K and Ram, Y and Roesch, E and Rossant, C and Rostami, V and Shifman, A and Stachelek, J and Stimberg, M and Stollmeier, F and Vaggi, F and Viejo, G and Vitay, J and Vostinar, AE and Yurchak, R and Zito, T}, title = {Sustainable computational science: the ReScience initiative.}, journal = {PeerJ. Computer science}, volume = {3}, number = {}, pages = {e142}, pmid = {34722870}, issn = {2376-5992}, abstract = {Computer science offers a large set of tools for prototyping, writing, running, testing, validating, sharing and reproducing results; however, computational science lags behind. In the best case, authors may provide their source code as a compressed archive and they may feel confident their research is reproducible. But this is not exactly true. James Buckheit and David Donoho proposed more than two decades ago that an article about computational results is advertising, not scholarship. The actual scholarship is the full software environment, code, and data that produced the result. This implies new workflows, in particular in peer-reviews. Existing journals have been slow to adapt: source codes are rarely requested and are hardly ever actually executed to check that they produce the results advertised in the article. ReScience is a peer-reviewed journal that targets computational research and encourages the explicit replication of already published research, promoting new and open-source implementations in order to ensure that the original research can be replicated from its description. To achieve this goal, the whole publishing chain is radically different from other traditional scientific journals. ReScience resides on GitHub where each new implementation of a computational study is made available together with comments, explanations, and software tests.}, } @article {pmid33585386, year = {2020}, author = {Litaker, JR and Tamez, N and Durkalski, W and Taylor, R}, title = {Using Health Insurance Network Provider Data and Public Data Sets to Identify SARS-CoV-2 Vaccinators in the USA.}, journal = {Frontiers in public health}, volume = {8}, number = {}, pages = {616140}, pmid = {33585386}, issn = {2296-2565}, mesh = {COVID-19/immunology/*prevention & control ; *COVID-19 Vaccines/supply & distribution ; *Datasets as Topic ; Health Personnel/statistics & numerical data ; Humans ; Immunity, Herd ; Influenza A Virus, H1N1 Subtype ; Influenza Vaccines ; *Insurance Carriers/statistics & numerical data ; *Insurance, Health ; Mass Vaccination/*organization & administration ; Pharmacies/statistics & numerical data ; Primary Health Care/statistics & numerical data ; Texas ; Vaccination Coverage/statistics & numerical data ; }, abstract = {Objective: Mass vaccination planning is occurring at all levels of government in advance of regulatory approval and manufacture of a SARS-CoV-2 vaccine for distribution sometime in 2021. We outline a methodology in which both health insurance provider network data and publicly available data sources can be used to identify and plan for SARS-CoV-2 vaccinator capacity at the county level. Methods: Sendero Health Plans, Inc. provider network data, Texas State Board of Pharmacy data, US Census Bureau data, and H1N1 monovalent vaccine data were utilized to identify providers with demonstrated capacity to vaccinate the population in Travis County, Texas to achieve an estimated SARS-CoV-2 herd immunity target of 67%. Results: Within the Sendero network, 2,356 non-pharmacy providers were identified with 788 (33.4%) practicing in primary care and 1,569 (66.6%) practicing as specialists. Of the total, 686 (29.1%) provided at least one immunization between January 1, 2019 and September 30, 2020. There are 300 pharmacies with active licenses in Travis County with 161 (53.7%) classified as community pharmacies. We estimate that 1,707,098 doses of a 2-dose SARS-CoV-2 vaccine series will need to be administered within Travis County, Texas to achieve the estimated 67% herd immunity threshold to disrupt person-to-person transmission of the SARS-CoV-2 virus based on 2020 census data. Conclusion: A community-based health insurance plan can use data from its provider network and public data sources to support the CDC call to action to identify SARS-CoV-2 vaccinators in the community, including physicians, nurse practitioners, physician assistants, and pharmacies in order to provide macro level estimates of SARS-CoV-2 administration and throughput.}, } @article {pmid33585383, year = {2020}, author = {Pansini, R and Fornacca, D}, title = {COVID-19 Higher Mortality in Chinese Regions With Chronic Exposure to Lower Air Quality.}, journal = {Frontiers in public health}, volume = {8}, number = {}, pages = {597753}, pmid = {33585383}, issn = {2296-2565}, mesh = {Air Pollutants/analysis ; Air Pollution/*adverse effects/analysis ; COVID-19/epidemiology/*mortality ; China/epidemiology ; Datasets as Topic ; Humans ; }, abstract = {We investigated the geographical character of the COVID-19 infection in China and correlated it with satellite- and ground-based measurements of air quality. Controlling for population density, we found more viral infections in those prefectures (U.S. county equivalent) afflicted by high Carbon Monoxide, Formaldehyde, PM 2.5, and Nitrogen Dioxide values. Higher mortality was also correlated with relatively poor air quality. When summarizing the results at a greater administrative level, we found that the 10 provinces (U.S. state equivalent) with the highest rate of mortality by COVID-19, were often the most polluted but not the most densely populated. Air pollution appears to be a risk factor for the incidence of this disease, despite the conventionally apprehended influence of human mobility on disease dynamics from the site of first appearance, Wuhan. The raw correlations reported here should be interpreted in a broader context, accounting for the growing evidence reported by several other studies. These findings warn communities and policymakers on the implications of long-term air pollution exposure as an ecological, multi-scale public health issue.}, } @article {pmid33582457, year = {2021}, author = {Liang, X and Martyniuk, CJ and Simmons, DBD}, title = {Current topics in omics, ecotoxicology, and environmental science.}, journal = {Comparative biochemistry and physiology. Part D, Genomics & proteomics}, volume = {38}, number = {}, pages = {100782}, doi = {10.1016/j.cbd.2020.100782}, pmid = {33582457}, issn = {1878-0407}, mesh = {Animals ; *Computational Biology ; *Ecotoxicology ; *Environmental Science ; Humans ; Metabolomics ; Proteomics ; Transcriptome ; }, } @article {pmid33582215, year = {2021}, author = {Parsa, S and Mogharab, V and Ebrahimi, M and Ahmadi, SR and Shahi, B and Mehramiz, NJ and Foroughian, M and Zarenezhad, M and Kalani, N and Abdi, MH and Javdani, F and Keshavarz, P and Hatami, N}, title = {COVID-19 as a worldwide selective event and bitter taste receptor polymorphisms: An ecological correlational study.}, journal = {International journal of biological macromolecules}, volume = {177}, number = {}, pages = {204-210}, pmid = {33582215}, issn = {1879-0003}, mesh = {Alleles ; COVID-19/*genetics/*mortality ; Correlation of Data ; Databases, Factual ; Genetic Association Studies ; Genetic Predisposition to Disease ; Genotype ; Humans ; *Polymorphism, Single Nucleotide ; Receptors, G-Protein-Coupled/*genetics ; Taste/*genetics ; }, abstract = {BACKGROUND: Given the observed olfactory and gustatory dysfunctions in patients with COVID-19 and recent findings on taste receptors possible important activities in the immune system, we elected to estimate the correlation between COVID-19 mortality and polymorphism of a particular type of bitter taste receptor gene called TAS2R38, in a worldwide epidemiological point of view.

METHODS: Pooled rate of each of the rs713598, rs1726866, rs10246939, and PAV/AVI polymorphisms of the TAS2R38 gene was obtained in different countries using a systematic review methodology and its relationship with the mortality of COVID-19. Data were analyzed by the comprehensive meta-analysis software and SPSS.

RESULTS: There was only a significant reverse Pearson correlation in death counts and PAV/AVI ratio, p = 0.047, r = -0.503. Also, a significant reverse correlation of PAV/AVI ratio and death rate was seen, r = -0.572 p = 0.021. rs10246939 ratio had a significant positive correlation with death rate, r = 0.851 p = 0.031. Further analysis was not significant. Our results showed that the higher presence of PAV allele than AVI, and a higher rate of G allele than A in rs10246939 polymorphism in a country, could be associated with lower COVID-19 mortality. While assessing all three polymorphisms showed a huge diversity worldwide.

CONCLUSION: Due to extraoral activities of bitter taste receptor genes, especially in mucosal immunity, this gene seems to be a good candidate for future studies on COVID-19 pathophysiology. Also, the high worldwide diversity of TAS2R38 genes polymorphism and its possible assassination with mortality raises concerns about the efficiency of vaccine projects in different ethnicities.}, } @article {pmid33581496, year = {2021}, author = {Singh, VK and Kumar, D and Singh, SK and Pham, QB and Linh, NTT and Mohammed, S and Anh, DT}, title = {Development of fuzzy analytic hierarchy process based water quality model of Upper Ganga river basin, India.}, journal = {Journal of environmental management}, volume = {284}, number = {}, pages = {111985}, doi = {10.1016/j.jenvman.2021.111985}, pmid = {33581496}, issn = {1095-8630}, mesh = {Analytic Hierarchy Process ; Environmental Monitoring ; India ; *Rivers ; *Water Pollutants, Chemical/analysis ; Water Quality ; }, abstract = {The ecological sustainability of rivers is in question due to severe pollution and lack of stringent regulations. Long term (1990-2016) water quality data of five stations namely Haridwar, Bareilly, Kanpur, Prayagraj and Varanasi of Upper Ganga river, India was considered for analysis using fuzzy analytical process (FAHP) based water quality index (WQI) to assess surface water quality. The value of water physical, biological and chemical parameters of temporal resolution (monthly, seasonal and yearly) indicate that value of electrical conductivity (EC), total dissolved solids (TDS), biological oxygen demand (BOD), chemical oxygen demand (COD), total alkalinity (Mg CaCO3), total hardness (Mg CaCO3), calcium (Ca), magnesium (Mg), sodium (Na), chlorine (Cl) and bicarbonate (HCO3) were observed very high compared to recommended value of Bureau of Indian Standards (BIS) and World Health Organization (WHO) at Kanpur, Prayagraj and Varanasi stations. However, low value of parameters is observed at Haridwar and Bareilly stations. Also, the high deviation was observed in water quality parameters during 1990-2010 whereas the deviation of parameters is decreased in 2011-2016. It is observed from the piper diagram that magnesium and bicarbonate at Haridwar, sodium, potassium and bicarbonate in Bareilly, Kanpur, Prayagraj and Varanasi stations are dominant during monthly and seasonal periods. The fuzzy based WQI value indicate that water quality is excellent to poor at Haridwar, while poor to unsuitable in Bareilly, Kanpur, Prayagraj and Varanasi during monthly and seasonal periods. The water quality ranges from poor to unsuitable during the 1990-2010 period and good to very poor during the 2011-2016 period at Bareilly, Kanpur, Prayagraj and Varanasi stations. Whereas very good to good during 1990-2010 and excellent to good during 2011-2016 at Haridwar. It was also determined that water quality parameters (Ca, Na+K, SO4, Hardness, Cl and Mg) and WQI values were increased with length of the stream. It indicates that drain discharge, urban growth, urban functions, ecological footprints and crop area increment were key sources of pollution.}, } @article {pmid33577568, year = {2021}, author = {Titus, M and Hagstrom, G and Watson, JR}, title = {Unsupervised manifold learning of collective behavior.}, journal = {PLoS computational biology}, volume = {17}, number = {2}, pages = {e1007811}, pmid = {33577568}, issn = {1553-7358}, mesh = {Animals ; *Behavior ; *Behavior, Animal ; Computational Biology ; Ecosystem ; Fishes/physiology ; Humans ; Models, Biological ; Models, Psychological ; Social Behavior ; Synthetic Biology ; *Systems Analysis ; Systems Biology ; *Unsupervised Machine Learning ; }, abstract = {Collective behavior is an emergent property of numerous complex systems, from financial markets to cancer cells to predator-prey ecological systems. Characterizing modes of collective behavior is often done through human observation, training generative models, or other supervised learning techniques. Each of these cases requires knowledge of and a method for characterizing the macro-state(s) of the system. This presents a challenge for studying novel systems where there may be little prior knowledge. Here, we present a new unsupervised method of detecting emergent behavior in complex systems, and discerning between distinct collective behaviors. We require only metrics, d(1), d(2), defined on the set of agents, X, which measure agents' nearness in variables of interest. We apply the method of diffusion maps to the systems (X, d(i)) to recover efficient embeddings of their interaction networks. Comparing these geometries, we formulate a measure of similarity between two networks, called the map alignment statistic (MAS). A large MAS is evidence that the two networks are codetermined in some fashion, indicating an emergent relationship between the metrics d(1) and d(2). Additionally, the form of the macro-scale organization is encoded in the covariances among the two sets of diffusion map components. Using these covariances we discern between different modes of collective behavior in a data-driven, unsupervised manner. This method is demonstrated on a synthetic flocking model as well as empirical fish schooling data. We show that our state classification subdivides the known behaviors of the school in a meaningful manner, leading to a finer description of the system's behavior.}, } @article {pmid33570780, year = {2021}, author = {Roumeliotis, S and Abd ElHafeez, S and Jager, KJ and Dekker, FW and Stel, VS and Pitino, A and Zoccali, C and Tripepi, G}, title = {Be careful with ecological associations.}, journal = {Nephrology (Carlton, Vic.)}, volume = {26}, number = {6}, pages = {501-505}, doi = {10.1111/nep.13861}, pmid = {33570780}, issn = {1440-1797}, mesh = {*Bias ; Humans ; Observational Studies as Topic/*statistics & numerical data ; *Public Health ; *Research ; Research Design/*statistics & numerical data ; }, abstract = {Ecological studies are observational studies commonly used in public health research. The main characteristic of this study design is that the statistical analysis is based on pooled (i.e., aggregated) rather than on individual data. Thus, patient-level information such as age, gender, income and disease condition are not considered as individual characteristics but as mean values or frequencies, calculated at country or community level. Ecological studies can be used to compare the aggregated prevalence and incidence data of a given condition across different geographical areas, to assess time-related trends of the frequency of a pre-defined disease/condition, to identify factors explaining changes in health indicators over time in specific populations, to discriminate genetic from environmental causes of geographical variation in disease, or to investigate the relationship between a population-level exposure and a specific disease or condition. The major pitfall in ecological studies is the ecological fallacy, a bias which occurs when conclusions about individuals are erroneously deduced from results about the group to which those individuals belong. In this paper, by using a series of examples, we provide a general explanation of the ecological studies and provide some useful elements to recognize or suspect ecological fallacy in this type of studies.}, } @article {pmid33569710, year = {2021}, author = {Souza, C and Garrido, MV and Saraiva, M and Carmo, JC}, title = {RealPic: Picture norms of real-world common items.}, journal = {Behavior research methods}, volume = {53}, number = {4}, pages = {1746-1761}, pmid = {33569710}, issn = {1554-3528}, mesh = {Databases, Factual ; Humans ; *Semantics ; }, abstract = {Pictures are often used as stimuli in several fields, such as psychology and neuroscience. However, co-occurring image-related properties might impact their processing, emphasizing the importance of validating such materials to guarantee the quality of research and professional practices. This is particularly relevant for pictures of common items because of their wide applicability potential. Normative studies have already been conducted to create and validate such pictures, yet most of them focused on stimulus without naturalistic elements (e.g., line drawings). Norms for real-world pictures of common items are rare, and their normative examination does not always simultaneously assess affective, semantic and perceptive dimensions, namely in the Portuguese context. Real-world pictures constitute pictorial representations of the world with realistic details (e.g., natural color or position), thus improving their ecological validity and their suitability for empirical studies or intervention purposes. Consequently, the establishment of norms for real-world pictures is mandatory for exploring their ecological richness and to uncover their impact across several relevant dimensions. In this study, we established norms for 596 real-world pictures of common items (e.g., tomato, drum) selected from existing databases and distributed into 12 categories. The pictures were evaluated on nine dimensions by a Portuguese sample. The results present the norms by item, by dimension and their correlations as well as cross-cultural analyses. RealPic is a culturally based dataset that offers systematic and flexible standards and is suitable for selecting stimuli while controlling for confounding effects in empirical tasks and interventional applications.}, } @article {pmid33567706, year = {2021}, author = {Belichenko, O and Kolosova, V and Melnikov, D and Kalle, R and Sõukand, R}, title = {Language of Administration as a Border: Wild Food Plants Used by Setos and Russians in Pechorsky District of Pskov Oblast, NW Russia.}, journal = {Foods (Basel, Switzerland)}, volume = {10}, number = {2}, pages = {}, pmid = {33567706}, issn = {2304-8158}, support = {714874/ERC_/European Research Council/International ; }, abstract = {Socio-economic changes impact local ethnobotanical knowledge as much as the ecological ones. During an ethnobotanical field study in 2018-2019, we interviewed 25 Setos and 38 Russians in the Pechorsky District of Pskov Oblast to document changes in wild plant use within the last 70 years according to the current and remembered practices. Of the 71 botanical taxa reported, the most popular were Vaccinium vitis-idaea, Vaccinium oxycoccos, Vaccinium myrtillus, Betula spp., and Rumex acetosa. The obtained data was compared with that of 37 Setos and 35 Estonians interviewed at the same time on the other side of the border. Our data revealed a substantial level of homogeneity within the plants used by three or more people with 30 of 56 plants overlapping across all four groups. However, Seto groups are ethnobotanically closer to the dominant ethnic groups immediately surrounding them than they are to Setos across the border. Further study of minor ethnic groups in a post-Soviet context is needed, paying attention to knowledge transmission patterns.}, } @article {pmid33565675, year = {2021}, author = {Singh, J and Kumar, V and Kumar, P and Kumar, P and Yadav, KK and Cabral-Pinto, MMS and Kamyab, H and Chelliapan, S}, title = {An experimental investigation on phytoremediation performance of water lettuce (Pistia stratiotes L.) for pollutants removal from paper mill effluent.}, journal = {Water environment research : a research publication of the Water Environment Federation}, volume = {93}, number = {9}, pages = {1543-1553}, doi = {10.1002/wer.1536}, pmid = {33565675}, issn = {1554-7531}, support = {F1-17.1/2015-16/RGNF-2015-17-SC-UTT-5597//University Grants Commission/ ; }, mesh = {*Araceae ; Biodegradation, Environmental ; Biological Oxygen Demand Analysis ; *Environmental Pollutants ; *Water Pollutants, Chemical/analysis ; }, abstract = {The present study describes the phytoremediation performance of water lettuce (Pistia stratiotes L.) for physicochemical pollutants elimination from paper mill effluent (PME). For this, pot (glass aquarium) experiments were conducted using 0% (BWW: borewell water), 25%, 50%, 75%, and 100% treatments of PME under natural day/light regime. Results of the experiments showed that the highest removal of pH (10.75%), electrical conductivity (EC: 63.82%), total dissolved solids (TDS: 71.20%) biological oxygen demand (BOD: 85.03%), chemical oxygen demand (COD: 80.46%), total Kjeldahl's nitrogen (TKN: 93.03%), phosphorus (P: 85.56%), sodium (Na: 91.89%), potassium (K: 84.04%), calcium (Ca: 84.75%), and magnesium (Mg: 83.62%), most probable number (MPN: 77.63%), and standard plate count (SPC: 74.43%) was noted in 75% treatment of PME after treatment by P. stratiotes. PCA showed the best vector length for TKN, Na, and Ca. The maximum plant growth parameters including, total fresh biomass (81.30 ± 0.28 g), chlorophyll content (3.67 ± 0.05 mg g[-1] f.wt), and relative growth rate (0.0051 gg[-1] d[-1]) was also measured in 75% PME treatment after phytoremediation experiments. The findings of this study make useful insight into the biological management of PME through plant-based pollutant eradication while leftover biomass may be used as a feedstock for low-cost bioenergy production. PRACTITIONER POINTS: Biological treatment of paper mill effluent using water lettuce is presented. Best reduction of physicochemical and microbiological pollutants was attained in 75% treatment. Maximum production of chlorophyll, plant biomass, and highest growth rate was also observed in 75% treatment.}, } @article {pmid33564871, year = {2021}, author = {Hagedoorn, NN and Wagenaar, JHL and Nieboer, D and Bath, D and Von Both, U and Carrol, ED and Eleftheriou, I and Emonts, M and Van Der Flier, M and De Groot, R and Herberg, J and Kohlmaier, B and Levin, M and Lim, E and Maconochie, I and Martinon-Torres, F and Nijman, R and Pokorn, M and Rivero Calle, I and Tsolia, M and Yeung, S and Zavadska, D and Zenz, W and Vermont, CL and Oostenbrink, R and Moll, HA and , }, title = {Impact of a clinical decision rule on antibiotic prescription for children with suspected lower respiratory tract infections presenting to European emergency departments: a simulation study based on routine data.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {76}, number = {5}, pages = {1349-1357}, doi = {10.1093/jac/dkab023}, pmid = {33564871}, issn = {1460-2091}, support = {/DH_/Department of Health/United Kingdom ; }, mesh = {*Anti-Bacterial Agents/therapeutic use ; Child ; Clinical Decision Rules ; Emergency Service, Hospital ; Europe ; Humans ; Netherlands ; *Respiratory Tract Infections/drug therapy ; Retrospective Studies ; }, abstract = {BACKGROUND: Discriminating viral from bacterial lower respiratory tract infections (LRTIs) in children is challenging thus commonly resulting in antibiotic overuse. The Feverkidstool, a validated clinical decision rule including clinical symptoms and C-reactive protein, safely reduced antibiotic use in children at low/intermediate risk for bacterial LRTIs in a multicentre trial at emergency departments (EDs) in the Netherlands.

OBJECTIVES: Using routine data from an observational study, we simulated the impact of the Feverkidstool on antibiotic prescriptions compared with observed antibiotic prescriptions in children with suspected LRTIs at 12 EDs in eight European countries.

METHODS: We selected febrile children aged 1 month to 5 years with respiratory symptoms and excluded upper respiratory tract infections. Using the Feverkidstool, we calculated individual risks for bacterial LRTI retrospectively. We simulated antibiotic prescription rates under different scenarios: (1) applying effect estimates on antibiotic prescription from the trial; and (2) varying both usage (50%-100%) and compliance (70%-100%) with the Feverkidstool's advice to withhold antibiotics in children at low/intermediate risk for bacterial LRTI (≤10%).

RESULTS: Of 4938 children, 4209 (85.2%) were at low/intermediate risk for bacterial LRTI. Applying effect estimates from the trial, the Feverkidstool reduced antibiotic prescription from 33.5% to 24.1% [pooled risk difference: 9.4% (95% CI: 5.7%-13.1%)]. Simulating 50%-100% usage with 90% compliance resulted in risk differences ranging from 8.3% to 15.8%. Our simulations suggest that antibiotic prescriptions would be reduced in EDs with high baseline antibiotic prescription rates or predominantly (>85%) low/intermediate-risk children.

CONCLUSIONS: Implementation of the Feverkidstool could reduce antibiotic prescriptions in children with suspected LRTIs in European EDs.}, } @article {pmid33563718, year = {2021}, author = {Chakraborty, M and Chang, CH and Khost, DE and Vedanayagam, J and Adrion, JR and Liao, Y and Montooth, KL and Meiklejohn, CD and Larracuente, AM and Emerson, JJ}, title = {Evolution of genome structure in the Drosophila simulans species complex.}, journal = {Genome research}, volume = {31}, number = {3}, pages = {380-396}, pmid = {33563718}, issn = {1549-5469}, support = {S10 OD021718/OD/NIH HHS/United States ; K99 GM129411/GM/NIGMS NIH HHS/United States ; S10 RR025496/RR/NCRR NIH HHS/United States ; P30 CA008748/CA/NCI NIH HHS/United States ; R35 GM119515/GM/NIGMS NIH HHS/United States ; S10 OD010794/OD/NIH HHS/United States ; P30 CA062203/CA/NCI NIH HHS/United States ; R01 GM123303/GM/NIGMS NIH HHS/United States ; R01 GM123194/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; DNA Copy Number Variations/genetics ; DNA Transposable Elements/genetics ; DNA, Satellite/genetics ; Drosophila melanogaster/genetics ; Drosophila simulans/*classification/*genetics ; *Evolution, Molecular ; Female ; Genome, Insect/*genetics ; Male ; }, abstract = {The rapid evolution of repetitive DNA sequences, including satellite DNA, tandem duplications, and transposable elements, underlies phenotypic evolution and contributes to hybrid incompatibilities between species. However, repetitive genomic regions are fragmented and misassembled in most contemporary genome assemblies. We generated highly contiguous de novo reference genomes for the Drosophila simulans species complex (D. simulans, D. mauritiana, and D. sechellia), which speciated ∼250,000 yr ago. Our assemblies are comparable in contiguity and accuracy to the current D. melanogaster genome, allowing us to directly compare repetitive sequences between these four species. We find that at least 15% of the D. simulans complex species genomes fail to align uniquely to D. melanogaster owing to structural divergence-twice the number of single-nucleotide substitutions. We also find rapid turnover of satellite DNA and extensive structural divergence in heterochromatic regions, whereas the euchromatic gene content is mostly conserved. Despite the overall preservation of gene synteny, euchromatin in each species has been shaped by clade- and species-specific inversions, transposable elements, expansions and contractions of satellite and tRNA tandem arrays, and gene duplications. We also find rapid divergence among Y-linked genes, including copy number variation and recent gene duplications from autosomes. Our assemblies provide a valuable resource for studying genome evolution and its consequences for phenotypic evolution in these genetic model species.}, } @article {pmid33563315, year = {2021}, author = {Wu, G and Zhao, N and Zhang, C and Lam, YY and Zhao, L}, title = {Guild-based analysis for understanding gut microbiome in human health and diseases.}, journal = {Genome medicine}, volume = {13}, number = {1}, pages = {22}, pmid = {33563315}, issn = {1756-994X}, mesh = {Databases, Genetic ; *Disease ; Female ; *Gastrointestinal Microbiome/genetics ; *Health ; Humans ; Metagenomics ; Obesity/genetics ; Phylogeny ; Polycystic Ovary Syndrome/microbiology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {To demonstrate the causative role of gut microbiome in human health and diseases, we first need to identify, via next-generation sequencing, potentially important functional members associated with specific health outcomes and disease phenotypes. However, due to the strain-level genetic complexity of the gut microbiota, microbiome datasets are highly dimensional and highly sparse in nature, making it challenging to identify putative causative agents of a particular disease phenotype. Members of an ecosystem seldomly live independently from each other. Instead, they develop local interactions and form inter-member organizations to influence the ecosystem's higher-level patterns and functions. In the ecological study of macro-organisms, members are defined as belonging to the same "guild" if they exploit the same class of resources in a similar way or work together as a coherent functional group. Translating the concept of "guild" to the study of gut microbiota, we redefine guild as a group of bacteria that show consistent co-abundant behavior and likely to work together to contribute to the same ecological function. In this opinion article, we discuss how to use guilds as the aggregation unit to reduce dimensionality and sparsity in microbiome-wide association studies for identifying candidate gut bacteria that may causatively contribute to human health and diseases.}, } @article {pmid33550152, year = {2021}, author = {Mendy, A and Wu, X and Keller, JL and Fassler, CS and Apewokin, S and Mersha, TB and Xie, C and Pinney, SM}, title = {Long-term exposure to fine particulate matter and hospitalization in COVID-19 patients.}, journal = {Respiratory medicine}, volume = {178}, number = {}, pages = {106313}, pmid = {33550152}, issn = {1532-3064}, support = {K08 CA237735/CA/NCI NIH HHS/United States ; }, mesh = {Adult ; Air Pollutants/*adverse effects ; Air Pollution/*adverse effects ; Asthma/epidemiology ; COVID-19/*epidemiology ; Environmental Exposure/*adverse effects ; Female ; Hospitalization/*statistics & numerical data ; Humans ; Logistic Models ; Male ; Middle Aged ; Odds Ratio ; Particulate Matter/*adverse effects ; Pulmonary Disease, Chronic Obstructive/epidemiology ; Socioeconomic Factors ; Time Factors ; }, abstract = {BACKGROUND: Ecological evidence suggests that exposure to air pollution affects coronavirus disease 2019 (COVID-19) outcomes. However, no individual-level study has confirmed the association to date.

METHODS: We identified COVID-19 patients diagnosed at the University of Cincinnati hospitals and clinics and estimated particulate matter ≤2.5 μm (PM2.5) exposure over a 10-year period (2008-2017) at their residential zip codes. We used logistic regression to evaluate the association between PM2.5 exposure and hospitalizations for COVID-19, adjusting for socioeconomic characteristics and comorbidities.

RESULTS: Among the 1128 patients included in our study, the mean (standard deviation) PM2.5 was 11.34 (0.70) μg/m[3] for the 10-year average exposure and 13.83 (1.03) μg/m[3] for the 10-year maximal exposures. The association between long-term PM2.5 exposure and hospitalization for COVID-19 was contingent upon having pre-existing asthma or chronic obstructive pulmonary (COPD) (Pinteraction = 0.030 for average PM2.5 and Pinteraction = 0.001 for maximal PM2.5). In COVID-19 patients with asthma or COPD, the odds of hospitalization were 62% higher with 1 μg/m[3] increment in 10-year average PM2.5 (odds ratio [OR]: 1.62, 95% confidence interval [CI]: 1.00-2.64) and 65% higher with 1 μg/m[3] increase in 10-year maximal PM2.5 levels (OR: 1.65, 95% CI: 1.16-2.35). However, among COVID-19 patients without asthma or COPD, PM2.5 exposure was not associated with higher hospitalizations (OR: 0.84, 95% CI: 0.65-1.09 for average PM2.5 and OR: 0.78, 95% CI: 0.65-0.95 for maximal PM2.5).

CONCLUSIONS: Long-term exposure to PM2.5 is associated with higher odds of hospitalization in COVID-19 patients with pre-existing asthma or COPD.}, } @article {pmid33546593, year = {2021}, author = {Wang, J and Mu, W and Yang, T and Song, Y and Hou, YG and Wang, Y and Gao, Z and Liu, X and Liu, H and Zhao, H}, title = {Targeted enrichment of novel chloroplast-based probes reveals a large-scale phylogeny of 412 bamboos.}, journal = {BMC plant biology}, volume = {21}, number = {1}, pages = {76}, pmid = {33546593}, issn = {1471-2229}, support = {2015BAD04B01//National Science and Technology Program during the Twelfth Five-year Plan Period (CN)/ ; 2015BAD04B03//National Science and Technology Program during the Twelfth Five-year Plan Period/ ; }, mesh = {Chloroplasts/*metabolism ; DNA Probes/*metabolism ; Databases, Genetic ; Genome, Plant ; *Phylogeny ; Poaceae/*classification/genetics ; Species Specificity ; }, abstract = {BACKGROUND: The subfamily Bambusoideae belongs to the grass family Poaceae and has significant roles in culture, economy, and ecology. However, the phylogenetic relationships based on large-scale chloroplast genomes (CpGenomes) were elusive. Moreover, most of the chloroplast DNA sequencing methods cannot meet the requirements of large-scale CpGenome sequencing, which greatly limits and impedes the in-depth research of plant genetics and evolution.

RESULTS: To develop a set of bamboo probes, we used 99 high-quality CpGenomes with 6 bamboo CpGenomes as representative species for the probe design, and assembled 15 M unique sequences as the final pan-chloroplast genome. A total of 180,519 probes for chloroplast DNA fragments were designed and synthesized by a novel hybridization-based targeted enrichment approach. Another 468 CpGenomes were selected as test data to verify the quality of the newly synthesized probes and the efficiency of the probes for chloroplast capture. We then successfully applied the probes to synthesize, enrich, and assemble 358 non-redundant CpGenomes of woody bamboo in China. Evaluation analysis showed the probes may be applicable to chloroplasts in Magnoliales, Pinales, Poales et al. Moreover, we reconstructed a phylogenetic tree of 412 bamboos (358 in-house and 54 published), supporting a non-monophyletic lineage of the genus Phyllostachys. Additionally, we shared our data by uploading a dataset of bamboo CpGenome into CNGB (https://db.cngb.org/search/project/CNP0000502/) to enrich resources and promote the development of bamboo phylogenetics.

CONCLUSIONS: The development of the CpGenome enrichment pipeline and its performance on bamboos recommended an inexpensive, high-throughput, time-saving and efficient CpGenome sequencing strategy, which can be applied to facilitate the phylogenetics analysis of most green plants.}, } @article {pmid33544674, year = {2021}, author = {Garrison, L and Muller, J and Schreiber, S and Oeltze-Jafra, S and Hauser, H and Bruckner, S}, title = {DimLift: Interactive Hierarchical Data Exploration Through Dimensional Bundling.}, journal = {IEEE transactions on visualization and computer graphics}, volume = {27}, number = {6}, pages = {2908-2922}, doi = {10.1109/TVCG.2021.3057519}, pmid = {33544674}, issn = {1941-0506}, mesh = {Algorithms ; *Computer Graphics ; Data Interpretation, Statistical ; Data Science/*methods ; *Data Visualization ; Databases, Factual ; Humans ; Medical Informatics Applications ; }, abstract = {The identification of interesting patterns and relationships is essential to exploratory data analysis. This becomes increasingly difficult in high dimensional datasets. While dimensionality reduction techniques can be utilized to reduce the analysis space, these may unintentionally bury key dimensions within a larger grouping and obfuscate meaningful patterns. With this work we introduce DimLift, a novel visual analysis method for creating and interacting with dimensional bundles. Generated through an iterative dimensionality reduction or user-driven approach, dimensional bundles are expressive groups of dimensions that contribute similarly to the variance of a dataset. Interactive exploration and reconstruction methods via a layered parallel coordinates plot allow users to lift interesting and subtle relationships to the surface, even in complex scenarios of missing and mixed data types. We exemplify the power of this technique in an expert case study on clinical cohort data alongside two additional case examples from nutrition and ecology.}, } @article {pmid33536526, year = {2021}, author = {Li, D and Yin, N and Xu, R and Wang, L and Zhang, Z and Li, K}, title = {Sludge amendment accelerating reclamation process of reconstructed mining substrates.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {2905}, pmid = {33536526}, issn = {2045-2322}, abstract = {We constructed a mining soil restoration system combining plant, complex substrate and microbe. Sludge was added to reconstructed mine substrates (RMS) to accelerate the reclamation process. The effect of sludge on plant growth, microbial activity, soil aggregate stability, and aggregation-associated soil characteristics was monitored during 10 years of reclamation. Results show that the height and total biomass of ryegrass increases with reclamation time. Sludge amendment increases the aggregate binding agent content and soil aggregate stability. Soil organic carbon (SOC) and light-fraction SOC (LFOC) in the RMS increase by 151% and 247% compared with those of the control, respectively. A similar trend was observed for the glomalin-related soil protein (GRSP). Stable soil aggregate indexes increase until the seventh year. In short, the variables of RMS determined after 3-7 years insignificantly differ from those of the untreated sample in the tenth-year. Furthermore, significant positive correlations between the GRSP and SOC and GRSP and soil structure-related variables were observed in RMS. Biological stimulation of the SOC and GRSP accelerates the recovery of the soil structure and ecosystem function. Consequently, the plant-complex substrate-microbe ecological restoration system can be used as an effective tool in early mining soil reclamation.}, } @article {pmid33532534, year = {2021}, author = {Eze, PU and Ezenkwu, CP and Etteh, CC}, title = {Community informatics for sustainable management of pandemics in developing countries: A case study of COVID-19 in Nigeria.}, journal = {Ethics, medicine, and public health}, volume = {16}, number = {}, pages = {100632}, pmid = {33532534}, issn = {2352-5525}, abstract = {Although a significant number of the human population in developing countries live in urban communities, majority of the population lives in rural areas. Developing countries, especially in their rural areas, suffer from a lack of healthcare facilities, poverty and high rate of illiteracy. Motivated by the huge socio-economic gap between the developed and the developing worlds, there have been several studies into the COVID-19 pandemic management in developing countries. However, none of these research works emphasised the health cultural beliefs of any developing economy as a basis for their recommendations. Specifically, this paper discusses the pandemic situation in Nigeria with emphasis on the prevalent health cultural beliefs of the citizens of the country, especially those living in rural communities. This is important because each local community defines a socio-ecological cluster of people who are more tightly knitted together in terms of language, relationship, culture, religion, social amenities, business, leadership and so on. As such, there is a need to prepare the socio-ecological units to be more resistant to the spread of the virus; a weaker social-ecological unit will entail a higher risk of community transmissions. With respect to the peculiarity of each local community, this paper recommends strategies for controlling and managing the pandemic in Nigeria using community informatics or grass-root computing. We argue that community informatics can empower and support policy makers and governments of developing countries such as Nigeria in combating and effectively managing a pandemic.}, } @article {pmid33531401, year = {2021}, author = {Crossette, E and Gumm, J and Langenfeld, K and Raskin, L and Duhaime, M and Wigginton, K}, title = {Metagenomic Quantification of Genes with Internal Standards.}, journal = {mBio}, volume = {12}, number = {1}, pages = {}, pmid = {33531401}, issn = {2150-7511}, mesh = {Databases, Nucleic Acid ; Drug Resistance, Microbial/*genetics ; Gene Dosage ; *Metagenomics ; Polymerase Chain Reaction ; Tetracycline Resistance/genetics ; }, abstract = {We demonstrate that an assembly-independent and spike-in facilitated metagenomic quantification approach can be used to screen and quantify over 2,000 genes simultaneously, while delivering absolute gene concentrations comparable to those for quantitative PCR (qPCR). DNA extracted from dairy manure slurry, digestate, and compost was spiked with genomic DNA from a marine bacterium and sequenced using the Illumina HiSeq4000. We compared gene copy concentrations, in gene copies per mass of sample, of five antimicrobial resistance genes (ARGs) generated with (i) our quantitative metagenomic approach, (ii) targeted qPCR, and (iii) a hybrid quantification approach involving metagenomics and qPCR-based 16S rRNA gene quantification. Although qPCR achieved lower quantification limits, the metagenomic method avoided biases caused by primer specificity inherent to qPCR-based methods and was able to detect orders of magnitude more genes than is possible with qPCR assays. We used the approach to simultaneously quantify ARGs in the Comprehensive Antimicrobial Resistance Database (CARD). We observed that the total abundance of tetracycline resistance genes was consistent across different stages of manure treatment on three farms, but different samples were dominated by different tetracycline resistance gene families.IMPORTANCE qPCR and metagenomics are central molecular techniques that have offered insights into biological processes for decades, from monitoring spatial and temporal gene dynamics to tracking ARGs or pathogens. Still needed is a tool that can quantify thousands of relevant genes in a sample as gene copies per sample mass or volume. We compare a quantitative metagenomic approach with traditional qPCR approaches in the quantification of ARG targets in dairy manure samples. By leveraging the benefits of nontargeted community genomics, we demonstrate high-throughput absolute gene quantification of all known ARG sequences in environmental samples.}, } @article {pmid33530360, year = {2021}, author = {Daniotti, S and Re, I}, title = {Marine Biotechnology: Challenges and Development Market Trends for the Enhancement of Biotic Resources in Industrial Pharmaceutical and Food Applications. A Statistical Analysis of Scientific Literature and Business Models.}, journal = {Marine drugs}, volume = {19}, number = {2}, pages = {}, pmid = {33530360}, issn = {1660-3397}, mesh = {Animals ; Biotechnology/*methods/trends ; Computational Biology/methods/trends ; Drug Industry/*methods/trends ; Food Technology/*methods/trends ; Humans ; Marine Biology/*methods/trends ; Marketing/*methods/trends ; Pharmaceutical Preparations/analysis/chemistry ; }, abstract = {Biotechnology is an essential tool for the sustainable exploitation of marine resources, although the full development of their potential is complicated by a series of cognitive and technological limitations. Thanks to an innovative systematic approach that combines the meta-analysis of 620 articles produced worldwide with 29 high TRL (Technology Readiness Level) European funded projects, the study provides an assessment of the growth prospects of blue biotechnologies, with a focus on pharmaceutical and food applications, and the most promising technologies to overcome the main challenges in the commercialization of marine products. The results show a positive development trend, with publications more than doubled from 2010 (36) to 2019 (70). Biochemical and molecular characterization, with 150 studies, is the most widely used technology. However, the emerging technologies in basic research are omics technologies, pharmacological analysis and bioinformatics, which have doubled the number of publications in the last five years. On the other hand, technologies for optimizing the conditions of cultivation, harvesting and extraction are central to most business models with immediate commercial exploitation (65% of high-TRL selected projects), especially in food and nutraceutical applications. This research offers a starting point for future research to overcome all those obstacles that restrict the marketing of products derived from organisms.}, } @article {pmid33529881, year = {2021}, author = {Lee, JH}, title = {Setting the governance of a participatory ecosystem service assessment based on text mining the language of stakeholders' opinions.}, journal = {Journal of environmental management}, volume = {284}, number = {}, pages = {112003}, doi = {10.1016/j.jenvman.2021.112003}, pmid = {33529881}, issn = {1095-8630}, mesh = {*Attitude ; Data Mining ; *Ecosystem ; Organizations ; Public Opinion ; }, abstract = {The resident participatory ecosystem service assessment is a method for determining local situations through the ecological knowledge of residents who most closely experience changes in local ecosystems. This is an opportunity for residents to synthesize their environmental knowledge. It provides valuable research material for researchers, can be utilized as a pathway for civil servants to reflect residents' opinions on policy, and can help environmental organizations instill environmental awareness and develop environmental public opinions in residents. Despite the participation of various stakeholders in resident participatory ecosystem service assessment, discussions concerning their roles and the nature of cooperation have largely not borne fruit. This study ascertained opinions on the development of the resident participatory ecosystem service assessment from local residents, local universities and research institutes, and relevant civil servants who participated as stakeholders in environmental organizations in this assessment. Upon organizing the stakeholders' interests through text mining based on the Q methodology, results indicated that research groups were interested in utilizing research evaluation techniques of a participatory ecosystem services assessment. In contrast, environmental organizations and civil servants were interested in utilizing the assessment results for political application. These two groups agreed that it is important to periodically map and utilize the research results of resident participatory ecosystem service assessment. The South Korean case featured in this study indicated that research teams will have to do their utmost in technique development, as will civil servants and environmental organizations, in creating measures for policy application. All of these groups should first attempt to map the results of resident participation, thereby creating resources for research and policy application, and make advances toward governance for robust resident participatory ecosystem service assessment.}, } @article {pmid33529447, year = {2021}, author = {Miantezila Basilua, J and Mesia Kahunu, G and Pochart, P and Tona Lutete, G}, title = {Overview of HIV treatment failure in Africa using the WHO Pharmacovigilance data.}, journal = {Tropical medicine & international health : TM & IH}, volume = {26}, number = {5}, pages = {530-534}, doi = {10.1111/tmi.13556}, pmid = {33529447}, issn = {1365-3156}, mesh = {Adolescent ; Africa ; Anti-Retroviral Agents/*therapeutic use ; Child ; Child, Preschool ; Databases, Factual ; Female ; HIV Infections/*drug therapy ; Humans ; Infant ; Male ; *Pharmacovigilance ; Retrospective Studies ; Treatment Failure ; World Health Organization ; }, abstract = {OBJECTIVE: To characterise the factors associated with HIV treatment failure (HIVTF) from reported pharmacovigilance data in Africa.

MATERIALS AND METHODS: This is an observational pharmacovigilance analysis of the safety data of HIVTF available in the WHO International Pharmacovigilance database 'VigiBase[®] '. We used the Standardised MedDRA Queries (SMQ) to identify all the terms corresponding to HIVTF. To identify all relevant molecules and classes of antiretroviral therapy, we used the anatomic, therapeutic, and chemical classification. We presented results as a percentage or an adjusted Reporting Odds Ratio (aROR) with a 95% confidence interval (95% CI).

RESULTS: HIVTF was more reported in Africa compared with the rest of the world with 19.1% (18.1%-20.1%) corresponding to 1206 of all 6304 HIVTF reports. Among all the 37 WHO country members in Africa, South Africa was the main source of origin for these HIVTF reports with 86.8% (84.9%-88.7%). Compared to adults, children and adolescents were the most population groups affected by HIVTF, aROR = 2.7, (95% CI) 1.7-4.2 and aROR = 7.9, (95% CI) 4.5-13.9, respectively.

CONCLUSION: South Africa was the leading country of the reporting of HIVTF in Africa. The proportion of HIVTF was higher in both HIV-infected children and adolescents than in adults. There is a need for the improvement of medical care for children and adolescents with HIV infection in Africa.}, } @article {pmid33529267, year = {2021}, author = {Ichikawa, J and Fujii, K and Nagai, T and Omori, T and Oka, N}, title = {Quantitative analysis of spontaneous sociality in children's group behavior during nursery activity.}, journal = {PloS one}, volume = {16}, number = {2}, pages = {e0246041}, pmid = {33529267}, issn = {1932-6203}, mesh = {Child ; Child Behavior/*psychology ; Child, Preschool ; Female ; Group Processes ; Humans ; Male ; Movement ; *Social Behavior ; }, abstract = {Sociality is the tendency to spontaneously interact with others to establish and maintain relationships. Some approaches, including questionnaires, tests, controlled experiments, and qualitative field research, cannot capture complex social interactions, such as in children during nursery activities, because of problems with ecological validity and the labor cost of analysis. Here, we introduced a new methodology for the quantitative analysis of spontaneous social movement and investigated children's group behavior using position data. We periodically visited a nursery and recorded videos of eurhythmics, in which children move in tune with music, in different classes. The results revealed that children in the six-year-old class approached others in a short period of time (within one second) and established group behavior like that in a game of tag. It can be interpreted that such social behavior may include actions related to the cognition of anticipating others' behaviors in a complex situation. Although only a small amount of data could be acquired, this study suggests one of the characteristics of social behaviors in the classroom considering an ecological approach.}, } @article {pmid33528535, year = {2021}, author = {Khatana, SAM and Venkataramani, AS and Nathan, AS and Dayoub, EJ and Eberly, LA and Kazi, DS and Yeh, RW and Mitra, N and Subramanian, SV and Groeneveld, PW}, title = {Association Between County-Level Change in Economic Prosperity and Change in Cardiovascular Mortality Among Middle-aged US Adults.}, journal = {JAMA}, volume = {325}, number = {5}, pages = {445-453}, pmid = {33528535}, issn = {1538-3598}, support = {K23 HL153772/HL/NHLBI NIH HHS/United States ; T32 HL007843/HL/NHLBI NIH HHS/United States ; }, mesh = {Adult ; Cardiovascular Diseases/*mortality ; Employment/economics/statistics & numerical data/*trends ; Female ; Humans ; Income/*trends ; Linear Models ; Male ; Middle Aged ; Mortality/trends ; Retrospective Studies ; United States/epidemiology ; }, abstract = {IMPORTANCE: After a decline in cardiovascular mortality for nonelderly US adults, recent stagnation has occurred alongside rising income inequality. Whether this is associated with underlying economic trends is unclear.

OBJECTIVE: To assess the association between changes in economic prosperity and trends in cardiovascular mortality in middle-aged US adults.

Retrospective analysis of the association between change in 7 markers of economic prosperity in 3123 US counties and county-level cardiovascular mortality among 40- to 64-year-old adults (102 660 852 individuals in 2010).

EXPOSURES: Mean rank for change in 7 markers of economic prosperity between 2 time periods (baseline: 2007-2011 and follow-up: 2012-2016). A higher mean rank indicates a greater relative increase or lower relative decrease in prosperity (range, 5 to 92; mean [SD], 50 [14]).

MAIN OUTCOMES AND MEASURES: Mean annual percentage change (APC) in age-adjusted cardiovascular mortality rates. Generalized linear mixed-effects models were used to estimate the additional APC associated with a change in prosperity.

RESULTS: Among 102 660 852 residents aged 40 to 64 years living in these counties in 2010 (51% women), 979 228 cardiovascular deaths occurred between 2010 and 2017. Age-adjusted cardiovascular mortality rates did not change significantly between 2010 and 2017 in counties in the lowest tertile for change in economic prosperity (mean [SD], 114.1 [47.9] to 116.1 [52.7] deaths per 100 000 individuals; APC, 0.2% [95% CI, -0.3% to 0.7%]). Mortality decreased significantly in the intermediate tertile (mean [SD], 104.7 [38.8] to 101.9 [41.5] deaths per 100 000 individuals; APC, -0.4% [95% CI, -0.8% to -0.1%]) and highest tertile for change in prosperity (100.0 [37.9] to 95.1 [39.1] deaths per 100 000 individuals; APC, -0.5% [95% CI, -0.9% to -0.1%]). After accounting for baseline prosperity and demographic and health care-related variables, a 10-point higher mean rank for change in economic prosperity was associated with 0.4% (95% CI, 0.2% to 0.6%) additional decrease in mortality per year.

CONCLUSIONS AND RELEVANCE: In this retrospective study of US county-level mortality data from 2010 to 2017, a relative increase in county-level economic prosperity was significantly associated with a small relative decrease in cardiovascular mortality among middle-aged adults. Individual-level inferences are limited by the ecological nature of the study.}, } @article {pmid33526659, year = {2021}, author = {Che, Y and Yang, Y and Xu, X and Břinda, K and Polz, MF and Hanage, WP and Zhang, T}, title = {Conjugative plasmids interact with insertion sequences to shape the horizontal transfer of antimicrobial resistance genes.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {118}, number = {6}, pages = {}, pmid = {33526659}, issn = {1091-6490}, mesh = {Chromosomes, Bacterial/genetics ; *Conjugation, Genetic ; Drug Resistance, Bacterial/*genetics ; Gene Transfer, Horizontal/*genetics ; *Genes, Bacterial ; Mosaicism ; Mutagenesis, Insertional/*genetics ; Phylogeny ; Plasmids/*genetics ; Synteny/genetics ; }, abstract = {It is well established that plasmids play an important role in the dissemination of antimicrobial resistance (AMR) genes; however, little is known about the role of the underlying interactions between different plasmid categories and other mobile genetic elements (MGEs) in shaping the promiscuous spread of AMR genes. Here, we developed a tool designed for plasmid classification, AMR gene annotation, and plasmid visualization and found that most plasmid-borne AMR genes, including those localized on class 1 integrons, are enriched in conjugative plasmids. Notably, we report the discovery and characterization of a massive insertion sequence (IS)-associated AMR gene transfer network (245 combinations covering 59 AMR gene subtypes and 53 ISs) linking conjugative plasmids and phylogenetically distant pathogens, suggesting a general evolutionary mechanism for the horizontal transfer of AMR genes mediated by the interaction between conjugative plasmids and ISs. Moreover, our experimental results confirmed the importance of the observed interactions in aiding the horizontal transfer and expanding the genetic range of AMR genes within complex microbial communities.}, } @article {pmid33514746, year = {2021}, author = {Li, H and Yang, X and Zhang, Y and Gao, Z and Liang, Y and Chen, J and Shi, T}, title = {Nelumbo genome database, an integrative resource for gene expression and variants of Nelumbo nucifera.}, journal = {Scientific data}, volume = {8}, number = {1}, pages = {38}, pmid = {33514746}, issn = {2052-4463}, support = {31870208//National Natural Science Foundation of China (National Science Foundation of China)/ ; 31570220//National Natural Science Foundation of China (National Science Foundation of China)/ ; 31471899//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {*Databases, Genetic ; Gene Expression ; *Genome, Plant ; Genomics ; Nelumbo/*genetics ; }, abstract = {Sacred lotus (Nelumbo nucifera, or lotus) is one of the most widely grown aquatic plant species with important uses, such as in water gardening and in vegetable and herbal medicine. A public genomic database of lotus would facilitate studies of lotus and other aquatic plant species. Here, we constructed an integrative database: the Nelumbo Genome Database (NGD, http://nelumbo.biocloud.net). This database is a collection of the most updated lotus genome assembly and contains information on both gene expression in different tissues and coexpression networks. In the NGD, we also integrated genetic variants and key traits from our 62 newly sequenced lotus cultivars and 26 previously reported cultivars, which are valuable for lotus germplasm studies. As applications including BLAST, BLAT, Primer, Annotation Search, Variant and Trait Search are deployed, users can perform sequence analyses and gene searches via the NGD. Overall, the valuable genomic resources provided in the NGD will facilitate future studies on population genetics and molecular breeding of lotus.}, } @article {pmid33511362, year = {2021}, author = {Blair, GS and Bassett, R and Bastin, L and Beevers, L and Borrajo, MI and Brown, M and Dance, SL and Dionescu, A and Edwards, L and Ferrario, MA and Fraser, R and Fraser, H and Gardner, S and Henrys, P and Hey, T and Homann, S and Huijbers, C and Hutchison, J and Jonathan, P and Lamb, R and Laurie, S and Leeson, A and Leslie, D and McMillan, M and Nundloll, V and Oyebamiji, O and Phillipson, J and Pope, V and Prudden, R and Reis, S and Salama, M and Samreen, F and Sejdinovic, D and Simm, W and Street, R and Thornton, L and Towe, R and Hey, JV and Vieno, M and Waller, J and Watkins, J}, title = {The Role of Digital Technologies in Responding to the Grand Challenges of the Natural Environment: The Windermere Accord.}, journal = {Patterns (New York, N.Y.)}, volume = {2}, number = {1}, pages = {100156}, pmid = {33511362}, issn = {2666-3899}, abstract = {Digital technology is having a major impact on many areas of society, and there is equal opportunity for impact on science. This is particularly true in the environmental sciences as we seek to understand the complexities of the natural environment under climate change. This perspective presents the outcomes of a summit in this area, a unique cross-disciplinary gathering bringing together environmental scientists, data scientists, computer scientists, social scientists, and representatives of the creative arts. The key output of this workshop is an agreed vision in the form of a framework and associated roadmap, captured in the Windermere Accord. This accord envisions a new kind of environmental science underpinned by unprecedented amounts of data, with technological advances leading to breakthroughs in taming uncertainty and complexity, and also supporting openness, transparency, and reproducibility in science. The perspective also includes a call to build an international community working in this important area.}, } @article {pmid33508672, year = {2021}, author = {Zhang, B and Zheng, T and Zheng, X and Walther, M}, title = {Utilization of pit lake on the cleaning process of residual saltwater in unconfined coastal aquifers.}, journal = {The Science of the total environment}, volume = {770}, number = {}, pages = {144670}, doi = {10.1016/j.scitotenv.2020.144670}, pmid = {33508672}, issn = {1879-1026}, abstract = {Subsurface dams are widely used to prevent saltwater intrusion. Once a subsurface dam is established, a large amount of residual saltwater (RSW) may trap behind the dam and negatively affect the groundwater exploitation over the long term. Based on monitoring hydrological information and field-scale numerical models, we proposed three kinds of RSW clean-up strategy coupling the applications of a pit lake and wells in a coastal aquifer. We firstly investigated the spontaneous natural removal of RSW in an actual coastal aquifer affected by a pit lake, assessed the impact of pit lake drainage on the removal of RSW, and designed a feasible strategy for reducing residual saltwater utilizing both pit lake and wells. Our results indicated that RSW remediation is a slow process under natural conditions. The area of the RSW decreased from 15.17 to 11.62 km[2] after 20 years, and the Cl[-] concentration of RSW around the pit lake increased to 1750 mg/L. The RSW cleaning efficiency can be significantly enhanced by the pit lake drainage process. With the pit lake drainage rate of 1.6E5 m[3]/d, the area of the RSW decreased by 10.14 km[2] in five years being 17-times larger than that of the natural restoration scheme (0.58 km[2]). With the combined well-lake drainage system, the total residual saltwater area decreased by more than 90% within five years, and the Cl[-] concentration of RSW almost reached WHO standards for drinking-water quality (250 mg/L). RSW upstream the subsurface dam was thoroughly cleaned up adopting the well-lake drainage strategy. Therefore, a well-lake drainage strategy can be strongly recommended for removing the RSW in coastal aquifers.}, } @article {pmid33504823, year = {2021}, author = {Grantz, KH and Cummings, DAT and Zimmer, S and Vukotich, C and Galloway, D and Schweizer, ML and Guclu, H and Cousins, J and Lingle, C and Yearwood, GMH and Li, K and Calderone, P and Noble, E and Gao, H and Rainey, J and Uzicanin, A and Read, JM}, title = {Age-specific social mixing of school-aged children in a US setting using proximity detecting sensors and contact surveys.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {2319}, pmid = {33504823}, issn = {2045-2322}, support = {U01 CK000179/CK/NCEZID CDC HHS/United States ; U54 GM088491/GM/NIGMS NIH HHS/United States ; }, mesh = {Adolescent ; Child ; Child, Preschool ; Contact Tracing/statistics & numerical data ; Ecology ; Female ; Humans ; Male ; Surveys and Questionnaires ; Virus Diseases/*epidemiology ; }, abstract = {Comparisons of the utility and accuracy of methods for measuring social interactions relevant to disease transmission are rare. To increase the evidence base supporting specific methods to measure social interaction, we compared data from self-reported contact surveys and wearable proximity sensors from a cohort of schoolchildren in the Pittsburgh metropolitan area. Although the number and type of contacts recorded by each participant differed between the two methods, we found good correspondence between the two methods in aggregate measures of age-specific interactions. Fewer, but longer, contacts were reported in surveys, relative to the generally short proximal interactions captured by wearable sensors. When adjusted for expectations of proportionate mixing, though, the two methods produced highly similar, assortative age-mixing matrices. These aggregate mixing matrices, when used in simulation, resulted in similar estimates of risk of infection by age. While proximity sensors and survey methods may not be interchangeable for capturing individual contacts, they can generate highly correlated data on age-specific mixing patterns relevant to the dynamics of respiratory virus transmission.}, } @article {pmid33500774, year = {2020}, author = {Bolyen, E and Dillon, MR and Bokulich, NA and Ladner, JT and Larsen, BB and Hepp, CM and Lemmer, D and Sahl, JW and Sanchez, A and Holdgraf, C and Sewell, C and Choudhury, AG and Stachurski, J and McKay, M and Simard, A and Engelthaler, DM and Worobey, M and Keim, P and Caporaso, JG}, title = {Reproducibly sampling SARS-CoV-2 genomes across time, geography, and viral diversity.}, journal = {F1000Research}, volume = {9}, number = {}, pages = {657}, pmid = {33500774}, issn = {2046-1402}, mesh = {COVID-19 ; Computational Biology ; *Genome, Viral ; Geography ; Humans ; Pandemics ; *Phylogeny ; Retrospective Studies ; SARS-CoV-2/*genetics ; Software ; }, abstract = {The COVID-19 pandemic has led to a rapid accumulation of SARS-CoV-2 genomes, enabling genomic epidemiology on local and global scales. Collections of genomes from resources such as GISAID must be subsampled to enable computationally feasible phylogenetic and other analyses. We present genome-sampler, a software package that supports sampling collections of viral genomes across multiple axes including time of genome isolation, location of genome isolation, and viral diversity. The software is modular in design so that these or future sampling approaches can be applied independently and combined (or replaced with a random sampling approach) to facilitate custom workflows and benchmarking. genome-sampler is written as a QIIME 2 plugin, ensuring that its application is fully reproducible through QIIME 2's unique retrospective data provenance tracking system. genome-sampler can be installed in a conda environment on macOS or Linux systems. A complete default pipeline is available through a Snakemake workflow, so subsampling can be achieved using a single command. genome-sampler is open source, free for all to use, and available at https://caporasolab.us/genome-sampler. We hope that this will facilitate SARS-CoV-2 research and support evaluation of viral genome sampling approaches for genomic epidemiology.}, } @article {pmid33501213, year = {2020}, author = {Chiba, N and Suzuki, R and Arita, T}, title = {Evolution of Complex Niche-Constructing Behaviors and Ecological Inheritance of Adaptive Structures in a Physically Grounded Environment.}, journal = {Frontiers in robotics and AI}, volume = {7}, number = {}, pages = {45}, pmid = {33501213}, issn = {2296-9144}, abstract = {Niche construction is a process in which organisms modify the selection pressures on themselves and others through their ecological activities, and ecological inheritance is the consequence of niche construction inherited through generations. However, it is still unclear how such mutual interactions between robots or embodied agents and their physical environments can yield complex and divergent evolutionary processes or an open-ended evolution. Our purpose is to clarify what kind of complex and various niche-constructing behaviors evolve in a physically grounded environment under various conditions of ecological inheritance of constructed structures and spatial relationships. We focus on a predator-prey relationship, and constructed an evolutionary model in which a prey creature has to avoid predation through the construction of a structure composed of objects in a 2D physically simulated environment supported by a physics engine. We used a deep auto-encoder to extract the defining feature of adaptive structures automatically. The results in the case of no ecological inheritance revealed that the number of available resources can affect the diversity of emerging adaptive structures. Also, in the case with ecological inheritance, it was found that combinations of two types of ecological inheritance, which are the inheritance of adaptive structures and birthplace, can have strong effects on the diversity of emerging structures and the adaptivity of the population. We expect that findings in evolutionary simulations of niche-constructing behavior might contribute to evolutionary design of robotic builders or robot fabrication, especially when we assume physically simulated environments.}, } @article {pmid33500495, year = {2021}, author = {Lazzerini, N and Balter, V and Coulon, A and Tacail, T and Marchina, C and Lemoine, M and Bayarkhuu, N and Turbat, T and Lepetz, S and Zazzo, A}, title = {Monthly mobility inferred from isoscapes and laser ablation strontium isotope ratios in caprine tooth enamel.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {2277}, pmid = {33500495}, issn = {2045-2322}, mesh = {Animal Migration/*physiology ; Animals ; Biological Availability ; Dental Enamel/*chemistry ; Geographic Information Systems ; Geography ; Goats/*metabolism ; *Laser Therapy ; Mongolia ; Strontium Isotopes/*analysis ; Time Factors ; }, abstract = {Strontium isotopic analysis of sequentially formed tissues, such as tooth enamel, is commonly used to study provenance and mobility of humans and animals. However, the potential of [87]Sr/[86]Sr in tooth enamel to track high-frequency movements has not yet been established, in part due to the lack of data on modern animals of known movement and predictive model of isotope variation across the landscape. To tackle this issue, we measured the [87]Sr/[86]Sr in plant samples taken from a 2000 km[2] area in the Altai Mountains (Mongolia), and the [87]Sr/[86]Sr in tooth enamel of domestic caprines whose mobility was monitored using GPS tracking. We show that high-resolution, sequential profiles of strontium isotope composition of tooth enamel reliably reflect the high-frequency mobility of domestic livestock and that short-term residency of about 45 days can be resolved. This offers new perspectives in various disciplines, including forensics, ecology, palaeoanthropology, and bioarchaeology.}, } @article {pmid33500478, year = {2021}, author = {Ivanov, V and Marusik, Y and Pétillon, J and Mutanen, M}, title = {Relevance of ddRADseq method for species and population delimitation of closely related and widely distributed wolf spiders (Araneae, Lycosidae).}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {2177}, pmid = {33500478}, issn = {2045-2322}, mesh = {Animals ; Databases, Genetic ; Electron Transport Complex IV/genetics ; Haplotypes/genetics ; Likelihood Functions ; *Phylogeny ; Principal Component Analysis ; *Restriction Mapping ; Sequence Analysis, DNA/*methods ; Species Specificity ; Spiders/*genetics ; }, abstract = {Although species delimitation is often controversial, emerging DNA-based and classical morphology-based methods are rarely compared using large-scale samplings, even less in the case of widely distributed species that have distant, allopatric populations. In the current study, we examined species boundaries within two wolf spider species of the genus Pardosa (Araneae, Lycosidae), P. riparia and P. palustris. Wolf spiders constitute an excellent model for testing the relevance of traditional vs. modern methods in species and population delimitation because several closely related species are distributed over cross-continental geographic ranges. Allopatric populations of the two Pardosa species were sampled across Europe to Far East Russia (latitudinal range > 150°) and several dozen individuals were studied using morphological characters (morphometry of three measures for both sexes, plus five in males only and two in females only), DNA barcoding (COI sequencing) and double-digest restriction site associated DNA sequencing (ddRADseq). The results obtained allow for changing the taxonomic status of two Far East Russian populations to subspecies and ddRADseq proved to be a powerful tool for taxonomic research despite scarce sampling and inherent subjectivity of species delimitation in allopatry. Overall, this study pleads for both multi-criteria and more population-based studies in taxonomy.}, } @article {pmid33500403, year = {2021}, author = {Fellows Yates, JA and Andrades Valtueña, A and Vågene, ÅJ and Cribdon, B and Velsko, IM and Borry, M and Bravo-Lopez, MJ and Fernandez-Guerra, A and Green, EJ and Ramachandran, SL and Heintzman, PD and Spyrou, MA and Hübner, A and Gancz, AS and Hider, J and Allshouse, AF and Zaro, V and Warinner, C}, title = {Community-curated and standardised metadata of published ancient metagenomic samples with AncientMetagenomeDir.}, journal = {Scientific data}, volume = {8}, number = {1}, pages = {31}, pmid = {33500403}, issn = {2052-4463}, support = {208934/Z/17/Z//Wellcome Trust (Wellcome)/International ; EXC 2051-Project-ID 390713860//Deutsche Forschungsgemeinschaft (German Research Foundation)/International ; T32 GM007197/GM/NIGMS NIH HHS/United States ; DGE1255832//National Science Foundation (NSF)/International ; ERC-2014-ADG 670518//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/International ; IA201219 PAPIIT-DGAPA- UNAM//Universidad Nacional Autónoma de México (National Autonomous University of Mexico)/International ; AH/N005015/1//RCUK | Arts and Humanities Research Council (AHRC)/International ; }, mesh = {*Databases, Genetic ; Humans ; Metadata ; *Metagenome ; *Metagenomics ; Publications ; }, abstract = {Ancient DNA and RNA are valuable data sources for a wide range of disciplines. Within the field of ancient metagenomics, the number of published genetic datasets has risen dramatically in recent years, and tracking this data for reuse is particularly important for large-scale ecological and evolutionary studies of individual taxa and communities of both microbes and eukaryotes. AncientMetagenomeDir (archived at https://doi.org/10.5281/zenodo.3980833) is a collection of annotated metagenomic sample lists derived from published studies that provide basic, standardised metadata and accession numbers to allow rapid data retrieval from online repositories. These tables are community-curated and span multiple sub-disciplines to ensure adequate breadth and consensus in metadata definitions, as well as longevity of the database. Internal guidelines and automated checks facilitate compatibility with established sequence-read archives and term-ontologies, and ensure consistency and interoperability for future meta-analyses. This collection will also assist in standardising metadata reporting for future ancient metagenomic studies.}, } @article {pmid33500285, year = {2021}, author = {Heyerdahl, LW and Vray, M and Leger, V and Le Fouler, L and Antouly, J and Troit, V and Giles-Vernick, T}, title = {Evaluating the motivation of Red Cross Health volunteers in the COVID-19 pandemic: a mixed-methods study protocol.}, journal = {BMJ open}, volume = {11}, number = {1}, pages = {e042579}, pmid = {33500285}, issn = {2044-6055}, mesh = {Adult ; COVID-19/epidemiology/therapy ; Community Health Services/*organization & administration ; France ; Humans ; *Motivation ; Public Health ; Qualitative Research ; *Red Cross ; Research Design ; Social Media ; Volunteers/*psychology ; }, abstract = {INTRODUCTION: Voluntary organisations provide essential support to vulnerable populations and front-line health responders to the COVID-19 pandemic. The French Red Cross (FRC) is prominent among organisations offering health and support services in the current crisis. Comprised primarily of lay volunteers and some trained health workers, FRC volunteers in the Paris (France) region have faced challenges in adapting to pandemic conditions, working with sick and vulnerable populations, managing limited resources and coping with high demand for their services. Existing studies of volunteers focus on individual, social and organisational determinants of motivation, but attend less to contextual ones. Public health incertitude about the COVID-19 pandemic is an important feature of this pandemic. Whether and how uncertainty interacts with volunteer understandings and experiences of their work and organisational relations to contribute to Red Cross worker motivation is the focus of this investigation.

METHODS AND ANALYSIS: This mixed-methods study will investigate volunteer motivation using ethnographic methods and social network listening. Semi-structured interviews and observations will illuminate FRC volunteer work relations, experiences and concerns during the pandemic. A questionnaire targeting a sample of Paris region volunteers will allow quantification of motivation. These findings will iteratively shape and be influenced by a social media (Twitter) analysis of biomedical and public health uncertainties and debates around COVID-19. These tweets provide insight into a French lay public's interpretations of these debates. We evaluate whether and how socio-political conditions and discourses concerning COVID-19 interact with volunteer experiences, working conditions and organisational relations to influence volunteer motivation. Data collection began on 15 June 2020 and will continue until 15 April 2021.

ETHICS AND DISSEMINATION: The protocol has received ethical approval from the Institut Pasteur Institutional Review Board (no 2020-03). We will disseminate findings through peer-reviewed articles, conference presentations and recommendations to the FRC.}, } @article {pmid33499858, year = {2021}, author = {Torres-Roman, JS and Ronceros-Cardenas, L and Valcarcel, B and Arce-Huamani, MA and Bazalar-Palacios, J and Ybaseta-Medina, J and La Vecchia, C and Alvarez, CS}, title = {Cervical cancer mortality in Peru: regional trend analysis from 2008-2017.}, journal = {BMC public health}, volume = {21}, number = {1}, pages = {219}, pmid = {33499858}, issn = {1471-2458}, mesh = {Aged, 80 and over ; Cluster Analysis ; Databases, Factual ; Female ; Humans ; Mortality ; Peru/epidemiology ; Spatial Analysis ; *Uterine Cervical Neoplasms ; }, abstract = {BACKGROUND: Cervical cancer is the third leading cause of cancer-related death among Latin American women. Peru has the sixth highest mortality rate for cervical cancer in the region with regional variations. We aimed to determine overall and regional cervical cancer mortality rates and trends in Peru between 2008 and 2017.

METHODS: We performed an ecological study on the number of deaths by cervical cancer in Peru. Deaths were extracted from the Peruvian Ministry of Health mortality database. Age-standardized mortality rates (ASMR) were estimated per 100,000 women-years using the world standard Segi population. We computed mortality trends using the Joinpoint regression program, estimating the annual percent change (APC). For spatial analysis, GeoDA software was used.

RESULTS: Peru showed downward trends in the last decade (from 11.62 in 2008 to 9.69 in 2017 (APC = - 2.2, 95% CI: - 4.3, - 0.1, p < 0.05). According to regional-specific analysis, the highest ASMR was in the rainforest region, although this declined from 34.16 in 2008 to 17.98 in 2017 (APC = - 4.3, 95% CI: - 7.2, - 1.3, p < 0.01). Concerning spatial analysis and clustering, the mortality rates from 2008 to 2017 showed a positive spatial autocorrelation and significant clustering (Moran's I: 0.35, p < 0.001) predominantly in the neighboring North-East departments (Loreto, Ucayali, and San Martin).

CONCLUSIONS: Although mortality trends in the entire population are decreasing, mortality rates remain very high, mainly in the rainforest region. Our results encourage a need for further development and improvement of the current health care delivery system in Peru.}, } @article {pmid33499782, year = {2021}, author = {Laubach, ZM and Murray, EJ and Hoke, KL and Safran, RJ and Perng, W}, title = {A biologist's guide to model selection and causal inference.}, journal = {Proceedings. Biological sciences}, volume = {288}, number = {1943}, pages = {20202815}, pmid = {33499782}, issn = {1471-2954}, support = {KL2 TR002534/TR/NCATS NIH HHS/United States ; }, mesh = {Causality ; *Confounding Factors, Epidemiologic ; Data Interpretation, Statistical ; Humans ; }, abstract = {A goal of many research programmes in biology is to extract meaningful insights from large, complex datasets. Researchers in ecology, evolution and behavior (EEB) often grapple with long-term, observational datasets from which they construct models to test causal hypotheses about biological processes. Similarly, epidemiologists analyse large, complex observational datasets to understand the distribution and determinants of human health. A key difference in the analytical workflows for these two distinct areas of biology is the delineation of data analysis tasks and explicit use of causal directed acyclic graphs (DAGs), widely adopted by epidemiologists. Here, we review the most recent causal inference literature and describe an analytical workflow that has direct applications for EEB. We start this commentary by defining four distinct analytical tasks (description, prediction, association, causal inference). The remainder of the text is dedicated to causal inference, specifically focusing on the use of DAGs to inform the modelling strategy. Given the increasing interest in causal inference and misperceptions regarding this task, we seek to facilitate an exchange of ideas between disciplinary silos and provide an analytical framework that is particularly relevant for making causal inference from observational data.}, } @article {pmid33498597, year = {2021}, author = {Bester, R and Cook, G and Maree, HJ}, title = {Citrus Tristeza Virus Genotype Detection Using High-Throughput Sequencing.}, journal = {Viruses}, volume = {13}, number = {2}, pages = {}, pmid = {33498597}, issn = {1999-4915}, mesh = {Citrus/*virology ; Closterovirus/*genetics ; Computational Biology ; Genetic Variation ; *Genome, Viral ; Genotype ; High-Throughput Nucleotide Sequencing ; Phylogeny ; Plant Diseases/virology ; RNA, Viral/genetics ; }, abstract = {The application of high-throughput sequencing (HTS) has successfully been used for virus discovery to resolve disease etiology in many agricultural crops. The greatest advantage of HTS is that it can provide a complete viral status of a plant, including information on mixed infections of viral species or virus variants. This provides insight into the virus population structure, ecology, or evolution and can be used to differentiate among virus variants that may contribute differently toward disease etiology. In this study, the use of HTS for citrus tristeza virus (CTV) genotype detection was evaluated. A bioinformatic pipeline for CTV genotype detection was constructed and evaluated using simulated and real data sets to determine the parameters to discriminate between false positive read mappings and true genotype-specific genome coverage. A 50% genome coverage cut-off was identified for non-target read mappings. HTS with the associated bioinformatic pipeline was validated and proposed as a CTV genotyping assay.}, } @article {pmid33497378, year = {2021}, author = {Vörös, D and Könnyű, B and Czárán, T}, title = {Catalytic promiscuity in the RNA World may have aided the evolution of prebiotic metabolism.}, journal = {PLoS computational biology}, volume = {17}, number = {1}, pages = {e1008634}, pmid = {33497378}, issn = {1553-7358}, mesh = {Computational Biology ; Computer Simulation ; *Evolution, Chemical ; Models, Biological ; RNA, Catalytic/chemistry/*metabolism ; Substrate Specificity/physiology ; }, abstract = {The Metabolically Coupled Replicator System (MCRS) model of early chemical evolution offers a plausible and efficient mechanism for the self-assembly and the maintenance of prebiotic RNA replicator communities, the likely predecessors of all life forms on Earth. The MCRS can keep different replicator species together due to their mandatory metabolic cooperation and limited mobility on mineral surfaces, catalysing reaction steps of a coherent reaction network that produces their own monomers from externally supplied compounds. The complexity of the MCRS chemical engine can be increased by assuming that each replicator species may catalyse more than a single reaction of metabolism, with different catalytic activities of the same RNA sequence being in a trade-off relation: one catalytic activity of a promiscuous ribozyme can increase only at the expense of the others on the same RNA strand. Using extensive spatially explicit computer simulations we have studied the possibility and the conditions of evolving ribozyme promiscuity in an initial community of single-activity replicators attached to a 2D surface, assuming an additional trade-off between replicability and catalytic activity. We conclude that our promiscuous replicators evolve under weak catalytic trade-off, relatively strong activity/replicability trade-off and low surface mobility of the replicators and the metabolites they produce, whereas catalytic specialists benefit from very strong catalytic trade-off, weak activity/replicability trade-off and high mobility. We argue that the combination of conditions for evolving promiscuity are more probable to occur for surface-bound RNA replicators, suggesting that catalytic promiscuity may have been a significant factor in the diversification of prebiotic metabolic reaction networks.}, } @article {pmid33493157, year = {2021}, author = {Wieters, B and Steige, KA and He, F and Koch, EM and Ramos-Onsins, SE and Gu, H and Guo, YL and Sunyaev, S and de Meaux, J}, title = {Polygenic adaptation of rosette growth in Arabidopsis thaliana.}, journal = {PLoS genetics}, volume = {17}, number = {1}, pages = {e1008748}, pmid = {33493157}, issn = {1553-7404}, support = {R01 MH101244/MH/NIMH NIH HHS/United States ; R35 GM127131/GM/NIGMS NIH HHS/United States ; }, mesh = {Acclimatization/genetics ; Adaptation, Physiological/*genetics ; Arabidopsis/*genetics/growth & development ; China ; Europe ; Genetic Variation/genetics ; Genetics, Population ; Genotype ; Multifactorial Inheritance/*genetics ; Phenotype ; Plant Development/genetics ; *Selection, Genetic ; }, abstract = {The rate at which plants grow is a major functional trait in plant ecology. However, little is known about its evolution in natural populations. Here, we investigate evolutionary and environmental factors shaping variation in the growth rate of Arabidopsis thaliana. We used plant diameter as a proxy to monitor plant growth over time in environments that mimicked latitudinal differences in the intensity of natural light radiation, across a set of 278 genotypes sampled within four broad regions, including an outgroup set of genotypes from China. A field experiment conducted under natural conditions confirmed the ecological relevance of the observed variation. All genotypes markedly expanded their rosette diameter when the light supply was decreased, demonstrating that environmental plasticity is a predominant source of variation to adapt plant size to prevailing light conditions. Yet, we detected significant levels of genetic variation both in growth rate and growth plasticity. Genome-wide association studies revealed that only 2 single nucleotide polymorphisms associate with genetic variation for growth above Bonferroni confidence levels. However, marginally associated variants were significantly enriched among genes with an annotated role in growth and stress reactions. Polygenic scores computed from marginally associated variants confirmed the polygenic basis of growth variation. For both light regimes, phenotypic divergence between the most distantly related population (China) and the various regions in Europe is smaller than the variation observed within Europe, indicating that the evolution of growth rate is likely to be constrained by stabilizing selection. We observed that Spanish genotypes, however, reach a significantly larger size than Northern European genotypes. Tests of adaptive divergence and analysis of the individual burden of deleterious mutations reveal that adaptive processes have played a more important role in shaping regional differences in rosette growth than maladaptive evolution.}, } @article {pmid33491551, year = {2021}, author = {Villaveces, A and Sanhueza, A and Henríquez Roldán, CF and Escamilla-Cejudo, JA and Rodrigues, EMS}, title = {Transport modes and road traffic mortality in the Americas: Deaths among pedestrian and motorcycle users through the lifespan.}, journal = {International journal of injury control and safety promotion}, volume = {28}, number = {1}, pages = {103-112}, doi = {10.1080/17457300.2020.1858112}, pmid = {33491551}, issn = {1745-7319}, mesh = {Accidents, Traffic/*mortality ; Adolescent ; Adult ; Aged ; Americas/epidemiology ; Databases, Factual ; Female ; Humans ; *Longevity ; Male ; Middle Aged ; *Motorcycles ; *Pedestrians ; Transportation/*methods ; Young Adult ; }, abstract = {In the Americas, almost half of road traffic deaths occur among motorcycle users and pedestrians (23% and 22%, respectively). Recent individual country trends show that nations are experiencing changes in deaths depending on the mode of transport used. While national trends are useful, analyses of disaggregated data by sex and age may provide more information about the impact of traffic crashes at different stages of the life course. Methods: We used mortality data from all land transport modes reported to PAHO/WHO (2000-2015) and included them in an ecological study to quantify temporal trends and estimate the association between mortality by mode, age group, sex, and selected socio-economic indicators. Results: Motorcycle and pedestrian mortality rates remain extremely high. Males younger less than 45 years have a higher burden of motorcycle-related mortality while older persons tend to die more as pedestrians. Discussion: Policies differentially aimed at addressing deaths by mode of transport and age are necessary because active living improves wellbeing especially among older individuals. For this to occur, safe environments must be created or maintained.}, } @article {pmid33486197, year = {2021}, author = {Zhu, L and Zhao, Z and Wang, Y and Huang, Q and Sun, Y and Bi, D}, title = {Weighting of toilet assessment scheme in China implementing analytic hierarchy process.}, journal = {Journal of environmental management}, volume = {283}, number = {}, pages = {111992}, doi = {10.1016/j.jenvman.2021.111992}, pmid = {33486197}, issn = {1095-8630}, mesh = {Analytic Hierarchy Process ; *Bathroom Equipment ; China ; Humans ; Public Health ; Sanitation ; Toilet Facilities ; }, abstract = {Advancing toilet technologies to address public health and sanitation issues are a concern of governments and organizations. This article mainly studies the assessment methods for the public toilets and some rural toilets considering from design to demolition to assist for the innovation of toilet technologies. The Analytic Hierarchy Process (AHP) and Life Cycle Assessment (LCA) methods were adopted to identify the assessment indicators and rank the weight. The outcome of Toilet Assessment Scheme (TAS), which includes a set of weightings and a classification system for the selected assessment indicators and sub-indicators. The weight calculation result showed that water resources, ecology, and indoor environmental quality are relatively high, which indicates that saving water, protecting the environment and optimizing the toilet environment should be given priority at the current stage. The individual questionnaire experts from the perspective of gender, profession, and generation, have different emphases on the evaluation scheme. This study can improve the comprehensiveness of toilet evaluation under the distinct background conditions, and will play a relevant role in the promotion of new toilet technology. The TAS can accelerate the toilet revolution in areas where toilets are scarce, and thus will improve the sanitary and health conditions of these populations.}, } @article {pmid33485466, year = {2021}, author = {Cai, L and Arnold, BJ and Xi, Z and Khost, DE and Patel, N and Hartmann, CB and Manickam, S and Sasirat, S and Nikolov, LA and Mathews, S and Sackton, TB and Davis, CC}, title = {Deeply Altered Genome Architecture in the Endoparasitic Flowering Plant Sapria himalayana Griff. (Rafflesiaceae).}, journal = {Current biology : CB}, volume = {31}, number = {5}, pages = {1002-1011.e9}, doi = {10.1016/j.cub.2020.12.045}, pmid = {33485466}, issn = {1879-0445}, mesh = {Gene Transfer, Horizontal ; Genome, Plant/*genetics ; Magnoliopsida/*genetics ; Phylogeny ; Symbiosis/*genetics ; }, abstract = {Despite more than 2,000-fold variation in genome size, key features of genome architecture are largely conserved across angiosperms. Parasitic plants have elucidated the many ways in which genomes can be modified, yet we still lack comprehensive genome data for species that represent the most extreme form of parasitism. Here, we present the highly modified genome of the iconic endophytic parasite Sapria himalayana Griff. (Rafflesiaceae), which lacks a typical plant body. First, 44% of the genes conserved in eurosids are lost in Sapria, dwarfing previously reported levels of gene loss in vascular plants. These losses demonstrate remarkable functional convergence with other parasitic plants, suggesting a common genetic roadmap underlying the evolution of plant parasitism. Second, we identified extreme disparity in intron size among retained genes. This includes a category of genes with introns longer than any so far observed in angiosperms, nearing 100 kb in some cases, and a second category of genes with exceptionally short or absent introns. Finally, at least 1.2% of the Sapria genome, including both genic and intergenic content, is inferred to be derived from host-to-parasite horizontal gene transfers (HGTs) and includes genes potentially adaptive for parasitism. Focused phylogenomic reconstruction of HGTs reveals a hidden history of former host-parasite associations involving close relatives of Sapria's modern hosts in the grapevine family. Our findings offer a unique perspective into how deeply angiosperm genomes can be altered to fit an extreme form of plant parasitism and demonstrate the value of HGTs as DNA fossils to investigate extinct symbioses.}, } @article {pmid33485207, year = {2021}, author = {Kang, A and Ren, L and Hua, C and Song, H and Dong, M and Fang, Z and Zhu, M}, title = {Environmental management strategy in response to COVID-19 in China: Based on text mining of government open information.}, journal = {The Science of the total environment}, volume = {769}, number = {}, pages = {145158}, pmid = {33485207}, issn = {1879-1026}, mesh = {*COVID-19 ; China/epidemiology ; Conservation of Natural Resources ; Data Mining ; Government ; Humans ; *Pandemics ; Retrospective Studies ; SARS-CoV-2 ; }, abstract = {Coronavirus disease 2019 (COVID-19) is a global pandemic and a major health emergency. In the process of fighting against COVID-19, the China Ministry of Ecology and Environment (MEE) responded quickly and set up a working group as soon as possible. This article uses text mining to retrospectively analyze the government's public information on the website of MEE during the epidemic, sort out the timeline of MEE's response to COVID-19. We find that MEE's work during the COVID-19 pandemic is focused on medical waste and wastewater treatment, environment emergency monitoring, pollution prevention, and other environmental management for supporting economic recovery. It drafted three main medical waste management plans, an emergency environmental monitoring plan, and formulated "two lists" - a Positive checklist for Environmental impact assessment (EIA) approval and a positive checklist for supervision and enforcement, to promote the resumption of work and production. 2020 is the final year of China's "three years of fighting pollution prevention and control". In the case of the sudden COVID-19 epidemic, the Chinese environment department has ensured that the quality of the ecological environment has not been affected by the epidemic prevention and control while ensuring the smooth progress of the fight against pollution. China's medical waste disposal capacity has also been greatly improved during this epidemic. The review of China's environmental management strategy in response to COVID-19 can provide a reference for countries in the world that are still in the critical period of epidemic control; it can provide action guidelines for the ecological environment system to respond to sudden pandemic events in the future.}, } @article {pmid33484722, year = {2021}, author = {Barnett-Itzhaki, Z and Levi, A}, title = {Effects of chronic exposure to ambient air pollutants on COVID-19 morbidity and mortality - A lesson from OECD countries.}, journal = {Environmental research}, volume = {195}, number = {}, pages = {110723}, pmid = {33484722}, issn = {1096-0953}, mesh = {*Air Pollutants/analysis/toxicity ; *Air Pollution/adverse effects/analysis ; *COVID-19 ; Environmental Exposure/analysis ; Humans ; Morbidity ; Organisation for Economic Co-Operation and Development ; Particulate Matter/analysis/toxicity ; SARS-CoV-2 ; }, abstract = {BACKGROUND: Exposure to ambient air pollution is related to 4.2 million premature deaths per year worldwide and is associated with a variety of adverse health outcomes, such as respiratory and cardiovascular morbidity. Furthermore, exposure to air pollution can increase human sensitivity to respiratory pathogens via damage to the respiratory tract or via airborne transmission on the surface of particulate matter, and might be an additional factor influencing COVID-19 morbidity and mortality rates. The aim of this study was to examine the association between populations' exposure to air pollution and the morbidity and mortality rates from COVID-19.

METHODS: We examined the association between population-weighted long-term exposure to PM2.5 and NOx, and the morbidity and mortality over time following the detection of the first COVID-19 positive case in 36 OECD countries. Pearson and Spearman correlations between daily COVID-19 morbidity and mortality (Jan-Jun 2020) on the 10[th], 20[th], 40[th], 60[th] and 80[th] days since first confirmed case in the country, and demographic, health, economic, and environmental data were calculated. Multivariate linear regression were used to examine the associations between demographic, health, economic and air pollution features and the rate of confirmed cases and deaths on the 60[th] and 80[th] days following the first confirmed case.

RESULTS: PM2.5 concentrations in 2015-2017 were positively correlated with COVID-19 morbidity and mortality on the 10[th], 20[th], 40[th] and 60[th] days since the first confirmed case in all countries. NOx concentrations in 2015-2017 and country's density (population/Km[2]) were positively correlated with COVID-19 morbidity and mortality on the 60[th] day. All multivariate linear regressions consisting PM2.5 concentrations models were statistically significant. Our models also emphasize the importance of the relative number of hospital beds in decreasing the morbidity and mortality of COVID-19.

CONCLUSIONS: The adverse health outcomes stemming from long-term exposure to various air pollutants has long been known to the scientific community. According to our results and previously published studies, it appears that long-term exposure to air pollutants concentrations exceeding WHO guidelines, such as PM2.5 and NOx, might exacerbate morbidity and mortality rates from COVID-19. These results should raise a red flag globally among decision makers about the urgent need to reduce air pollution and its harmful effects.}, } @article {pmid33484583, year = {2021}, author = {Zu, P and Koch, H and Schwery, O and Pironon, S and Phillips, C and Ondo, I and Farrell, IW and Nes, WD and Moore, E and Wright, GA and Farman, DI and Stevenson, PC}, title = {Pollen sterols are associated with phylogeny and environment but not with pollinator guilds.}, journal = {The New phytologist}, volume = {230}, number = {3}, pages = {1169-1184}, pmid = {33484583}, issn = {1469-8137}, support = {BB/M011224/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/P005276/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/S004653/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/P007449/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; Insecta ; Phylogeny ; *Phytosterols ; Pollen ; *Sterols ; }, abstract = {Phytosterols are primary plant metabolites that have fundamental structural and regulatory functions. They are also essential nutrients for phytophagous insects, including pollinators, that cannot synthesize sterols. Despite the well-described composition and diversity in vegetative plant tissues, few studies have examined phytosterol diversity in pollen. We quantified 25 pollen phytosterols in 122 plant species (105 genera, 51 families) to determine their composition and diversity across plant taxa. We searched literature and databases for plant phylogeny, environmental conditions, and pollinator guilds of the species to examine the relationships with pollen sterols. 24-methylenecholesterol, sitosterol and isofucosterol were the most common and abundant pollen sterols. We found phylogenetic clustering of twelve individual sterols, total sterol content and sterol diversity, and of sterol groupings that reflect their underlying biosynthesis pathway (C-24 alkylation, ring B desaturation). Plants originating in tropical-like climates (higher mean annual temperature, lower temperature seasonality, higher precipitation in wettest quarter) were more likely to record higher pollen sterol content. However, pollen sterol composition and content showed no clear relationship with pollinator guilds. Our study is the first to show that pollen sterol diversity is phylogenetically clustered and that pollen sterol content may adapt to environmental conditions.}, } @article {pmid33480994, year = {2021}, author = {Takou, M and Hämälä, T and Koch, EM and Steige, KA and Dittberner, H and Yant, L and Genete, M and Sunyaev, S and Castric, V and Vekemans, X and Savolainen, O and Meaux, J}, title = {Maintenance of Adaptive Dynamics and No Detectable Load in a Range-Edge Outcrossing Plant Population.}, journal = {Molecular biology and evolution}, volume = {38}, number = {5}, pages = {1820-1836}, pmid = {33480994}, issn = {1537-1719}, mesh = {Arabidopsis/*genetics ; Gene Flow ; Genes, Recessive ; Genetic Fitness ; *Genetic Load ; Genome, Plant ; *Plant Dispersal ; Population Dynamics ; Selection, Genetic ; }, abstract = {During range expansion, edge populations are expected to face increased genetic drift, which in turn can alter and potentially compromise adaptive dynamics, preventing the removal of deleterious mutations and slowing down adaptation. Here, we contrast populations of the European subspecies Arabidopsis lyrata ssp. petraea, which expanded its Northern range after the last glaciation. We document a sharp decline in effective population size in the range-edge population and observe that nonsynonymous variants segregate at higher frequencies. We detect a 4.9% excess of derived nonsynonymous variants per individual in the range-edge population, suggesting an increase of the genomic burden of deleterious mutations. Inference of the fitness effects of mutations and modeling of allele frequencies under the explicit demographic history of each population predicts a depletion of rare deleterious variants in the range-edge population, but an enrichment for fixed ones, consistent with the bottleneck effect. However, the demographic history of the range-edge population predicts a small net decrease in per-individual fitness. Consistent with this prediction, the range-edge population is not impaired in its growth and survival measured in a common garden experiment. We further observe that the allelic diversity at the self-incompatibility locus, which ensures strict outcrossing and evolves under negative frequency-dependent selection, has remained unchanged. Genomic footprints indicative of selective sweeps are broader in the Northern population but not less frequent. We conclude that the outcrossing species A. lyrata ssp. petraea shows a strong resilience to the effect of range expansion.}, } @article {pmid33480058, year = {2021}, author = {Marconi, S and Graves, SJ and Weinstein, BG and Bohlman, S and White, EP}, title = {Estimating individual-level plant traits at scale.}, journal = {Ecological applications : a publication of the Ecological Society of America}, volume = {31}, number = {4}, pages = {e02300}, doi = {10.1002/eap.2300}, pmid = {33480058}, issn = {1051-0761}, support = {GBMF4563//Gordon and Betty Moore Foundation's Data-Driven Discovery Initiative/ ; 1926542//National Science Foundation/ ; DEB-1442280//NSF Dimension of Biodiversity program/ ; FLA-FOR-005470//USDA/NIFA McIntire-Stennis program/ ; //University of Florida Biodiversity Institute (UFBI)/ ; //Informatics Institute (UFII) Graduate Fellowship/ ; }, mesh = {*Ecosystem ; *Forests ; Humans ; Plant Leaves ; Plants ; Trees ; }, abstract = {Functional ecology has increasingly focused on describing ecological communities based on their traits (measurable features affecting individuals' fitness and performance). Analyzing trait distributions within and among forests could significantly improve understanding of community composition and ecosystem function. Historically, data on trait distributions are generated by (1) collecting a small number of leaves from a small number of trees, which suffers from limited sampling but produces information at the fundamental ecological unit (the individual), or (2) using remote-sensing images to infer traits, producing information continuously across large regions, but as plots (containing multiple trees of different species) or pixels, not individuals. Remote-sensing methods that identify individual trees and estimate their traits would provide the benefits of both approaches, producing continuous large-scale data linked to biological individuals. We used data from the National Ecological Observatory Network (NEON) to develop a method to scale up functional traits from 160 trees to the millions of trees within the spatial extent of two NEON sites. The pipeline consists of three stages: (1) image segmentation, to identify individual trees and estimate structural traits; (2) an ensemble of models to infer leaf mass area (LMA), nitrogen, carbon, and phosphorus content using hyperspectral signatures, and DBH from allometry; and (3) predictions for segmented crowns for the full remote-sensing footprint at the NEON sites. The R[2] values on held-out test data ranged from 0.41 to 0.75 on held-out test data. The ensemble approach performed better than single partial least-squares models. Carbon performed poorly compared to other traits (R[2] of 0.41). The crown segmentation step contributed the most uncertainty in the pipeline, due to over-segmentation. The pipeline produced good estimates of DBH (R[2] of 0.62 on held-out data). Trait predictions for crowns performed significantly better than comparable predictions on pixels, resulting in improvement of R[2] on test data of between 0.07 and 0.26. We used the pipeline to produce individual-level trait data for ~5 million individual crowns, covering a total extent of ~360 km[2] . This large data set allows testing ecological questions on landscape scales, revealing that foliar traits are correlated with structural traits and environmental conditions.}, } @article {pmid33479183, year = {2021}, author = {Grunert, K and Holden, H and Jakobsen, ER and Stenseth, NC}, title = {Evolutionarily stable strategies in stable and periodically fluctuating populations: The Rosenzweig-MacArthur predator-prey model.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {118}, number = {4}, pages = {}, pmid = {33479183}, issn = {1091-6490}, mesh = {*Adaptation, Physiological ; Animals ; Biological Evolution ; Computational Biology ; Computer Simulation ; Ecosystem ; *Food Chain ; *Models, Biological ; Population Dynamics ; Predatory Behavior/*physiology ; }, abstract = {An evolutionarily stable strategy (ESS) is an evolutionary strategy that, if adapted by a population, cannot be invaded by any deviating (mutant) strategy. The concept of ESS has been extensively studied and widely applied in ecology and evolutionary biology [M. Smith, On Evolution (1972)] but typically on the assumption that the system is ecologically stable. With reference to a Rosenzweig-MacArthur predator-prey model [M. Rosenzweig, R. MacArthur, Am. Nat. 97, 209-223 (1963)], we derive the mathematical conditions for the existence of an ESS when the ecological dynamics have asymptotically stable limit points as well as limit cycles. By extending the framework of Reed and Stenseth [J. Reed, N. C. Stenseth, J. Theoret. Biol. 108, 491-508 (1984)], we find that ESSs occur at values of the evolutionary strategies that are local optima of certain functions of the model parameters. These functions are identified and shown to have a similar form for both stable and fluctuating populations. We illustrate these results with a concrete example.}, } @article {pmid33478122, year = {2021}, author = {Nagakura, Y and Kato, H and Asano, S and Jinno, Y and Tanei, S}, title = {The Significant Association between Health Examination Results and Population Health: A Cross-Sectional Ecological Study Using a Nation-Wide Health Checkup Database in Japan.}, journal = {International journal of environmental research and public health}, volume = {18}, number = {2}, pages = {}, pmid = {33478122}, issn = {1660-4601}, mesh = {Cross-Sectional Studies ; Databases, Factual ; Japan/epidemiology ; *Life Expectancy ; *Population Health ; }, abstract = {In Japan, population health with life expectancy (LE) and healthy life expectancy (HALE) as indicators varies across the 47 prefectures (administrative regions). This study investigates how health examination results, including attitude toward improving life habits, are associated with population health. The association between health checkup variables and summary population health outcomes (i.e., life expectancy and healthy life expectancy) was investigated using a cross-sectional ecological design with prefectures as the unit of analysis. The medical records, aggregated by prefecture, gender, and age in the National Database of Health Insurance Claims and Specific Health Checkups of Japan (NDB) Open Data Japan, were used as health checkup variables. Body weight, blood pressure, liver enzymes, drinking habits, smoking habits, diabetes, serum lipids, and answers to questions regarding attitude toward improving health habits were significantly correlated to population health outcomes. Multiple regression analysis also revealed significant influence of these variables on population health. This study highlights that health examination results, including attitude toward improving health habits, are positively associated with population health. Consequently, implementing measures to improve health habits in response to the examination results could help the population maintain a healthy life.}, } @article {pmid33473136, year = {2021}, author = {Grantham, HS and Duncan, A and Evans, TD and Jones, KR and Beyer, HL and Schuster, R and Walston, J and Ray, JC and Robinson, JG and Callow, M and Clements, T and Costa, HM and DeGemmis, A and Elsen, PR and Ervin, J and Franco, P and Goldman, E and Goetz, S and Hansen, A and Hofsvang, E and Jantz, P and Jupiter, S and Kang, A and Langhammer, P and Laurance, WF and Lieberman, S and Linkie, M and Malhi, Y and Maxwell, S and Mendez, M and Mittermeier, R and Murray, NJ and Possingham, H and Radachowsky, J and Saatchi, S and Samper, C and Silverman, J and Shapiro, A and Strassburg, B and Stevens, T and Stokes, E and Taylor, R and Tear, T and Tizard, R and Venter, O and Visconti, P and Wang, S and Watson, JEM}, title = {Author Correction: Anthropogenic modification of forests means only 40% of remaining forests have high ecosystem integrity.}, journal = {Nature communications}, volume = {12}, number = {1}, pages = {592}, doi = {10.1038/s41467-021-20999-7}, pmid = {33473136}, issn = {2041-1723}, } @article {pmid33473131, year = {2021}, author = {Morii, Y and Kitazawa, M and Squires, TE and Watanabe, M and Watanabe, Y and Saito, T and Yamazaki, D and Uchida, A and Machida, Y}, title = {A complete dietary review of Japanese birds with special focus on molluscs.}, journal = {Scientific data}, volume = {8}, number = {1}, pages = {19}, pmid = {33473131}, issn = {2052-4463}, mesh = {Animals ; *Birds ; Databases, Factual ; *Diet ; Japan ; Mollusca ; }, abstract = {Birds often hold important positions in the food webs of ecosystems. As a result, interactions between birds and their prey have attracted attention not only in ecology, but also in fields like agriculture and conservation. Avian food resources are well researched in Japan, however there is no database critically reviewing molluscs as a food resource for birds. Here, we present a new database reviewing dietary information for all Japanese bird species. In addition to addressing general diet categories and specific food habits for each bird, we include detailed data on the molluscan prey observed for all species that consume them. The information within this database was collected through intense literary review to provide a complete look at bird species historically present around the country. We also include new information on snail species found in the upper digestive tract of harvested wild birds. This database is publicly available in the Zenodo repository. The information should aid research around the Japanese archipelago, especially projects involving birds or molluscs.}, } @article {pmid33471991, year = {2021}, author = {, and Dorling, L and Carvalho, S and Allen, J and González-Neira, A and Luccarini, C and Wahlström, C and Pooley, KA and Parsons, MT and Fortuno, C and Wang, Q and Bolla, MK and Dennis, J and Keeman, R and Alonso, MR and Álvarez, N and Herraez, B and Fernandez, V and Núñez-Torres, R and Osorio, A and Valcich, J and Li, M and Törngren, T and Harrington, PA and Baynes, C and Conroy, DM and Decker, B and Fachal, L and Mavaddat, N and Ahearn, T and Aittomäki, K and Antonenkova, NN and Arnold, N and Arveux, P and Ausems, MGEM and Auvinen, P and Becher, H and Beckmann, MW and Behrens, S and Bermisheva, M and Białkowska, K and Blomqvist, C and Bogdanova, NV and Bogdanova-Markov, N and Bojesen, SE and Bonanni, B and Børresen-Dale, AL and Brauch, H and Bremer, M and Briceno, I and Brüning, T and Burwinkel, B and Cameron, DA and Camp, NJ and Campbell, A and Carracedo, A and Castelao, JE and Cessna, MH and Chanock, SJ and Christiansen, H and Collée, JM and Cordina-Duverger, E and Cornelissen, S and Czene, K and Dörk, T and Ekici, AB and Engel, C and Eriksson, M and Fasching, PA and Figueroa, J and Flyger, H and Försti, A and Gabrielson, M and Gago-Dominguez, M and Georgoulias, V and Gil, F and Giles, GG and Glendon, G and Garcia, EBG and Alnæs, GIG and Guénel, P and Hadjisavvas, A and Haeberle, L and Hahnen, E and Hall, P and Hamann, U and Harkness, EF and Hartikainen, JM and Hartman, M and He, W and Heemskerk-Gerritsen, BAM and Hillemanns, P and Hogervorst, FBL and Hollestelle, A and Ho, WK and Hooning, MJ and Howell, A and Humphreys, K and Idris, F and Jakubowska, A and Jung, A and Kapoor, PM and Kerin, MJ and Khusnutdinova, E and Kim, SW and Ko, YD and Kosma, VM and Kristensen, VN and Kyriacou, K and Lakeman, IMM and Lee, JW and Lee, MH and Li, J and Lindblom, A and Lo, WY and Loizidou, MA and Lophatananon, A and Lubiński, J and MacInnis, RJ and Madsen, MJ and Mannermaa, A and Manoochehri, M and Manoukian, S and Margolin, S and Martinez, ME and Maurer, T and Mavroudis, D and McLean, C and Meindl, A and Mensenkamp, AR and Michailidou, K and Miller, N and Mohd Taib, NA and Muir, K and Mulligan, AM and Nevanlinna, H and Newman, WG and Nordestgaard, BG and Ng, PS and Oosterwijk, JC and Park, SK and Park-Simon, TW and Perez, JIA and Peterlongo, P and Porteous, DJ and Prajzendanc, K and Prokofyeva, D and Radice, P and Rashid, MU and Rhenius, V and Rookus, MA and Rüdiger, T and Saloustros, E and Sawyer, EJ and Schmutzler, RK and Schneeweiss, A and Schürmann, P and Shah, M and Sohn, C and Southey, MC and Surowy, H and Suvanto, M and Thanasitthichai, S and Tomlinson, I and Torres, D and Truong, T and Tzardi, M and Valova, Y and van Asperen, CJ and Van Dam, RM and van den Ouweland, AMW and van der Kolk, LE and van Veen, EM and Wendt, C and Williams, JA and Yang, XR and Yoon, SY and Zamora, MP and Evans, DG and de la Hoya, M and Simard, J and Antoniou, AC and Borg, Å and Andrulis, IL and Chang-Claude, J and García-Closas, M and Chenevix-Trench, G and Milne, RL and Pharoah, PDP and Schmidt, MK and Spurdle, AB and Vreeswijk, MPG and Benitez, J and Dunning, AM and Kvist, A and Teo, SH and Devilee, P and Easton, DF}, title = {Breast Cancer Risk Genes - Association Analysis in More than 113,000 Women.}, journal = {The New England journal of medicine}, volume = {384}, number = {5}, pages = {428-439}, pmid = {33471991}, issn = {1533-4406}, support = {16563/CRUK_/Cancer Research UK/United Kingdom ; 203477/Z/16/Z/WT_/Wellcome Trust/United Kingdom ; 20861/CRUK_/Cancer Research UK/United Kingdom ; 23382/CRUK_/Cancer Research UK/United Kingdom ; 16561/CRUK_/Cancer Research UK/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; MR/P012930/1/MRC_/Medical Research Council/United Kingdom ; A16563/CRUK_/Cancer Research UK/United Kingdom ; 203477/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Adolescent ; Adult ; Age Factors ; Aged ; Aged, 80 and over ; Breast Neoplasms/*genetics ; Female ; Genetic Predisposition to Disease/*genetics ; *Genetic Variation ; Humans ; Logistic Models ; Middle Aged ; *Mutation, Missense ; Odds Ratio ; Risk ; Sequence Analysis, DNA ; Young Adult ; }, abstract = {BACKGROUND: Genetic testing for breast cancer susceptibility is widely used, but for many genes, evidence of an association with breast cancer is weak, underlying risk estimates are imprecise, and reliable subtype-specific risk estimates are lacking.

METHODS: We used a panel of 34 putative susceptibility genes to perform sequencing on samples from 60,466 women with breast cancer and 53,461 controls. In separate analyses for protein-truncating variants and rare missense variants in these genes, we estimated odds ratios for breast cancer overall and tumor subtypes. We evaluated missense-variant associations according to domain and classification of pathogenicity.

RESULTS: Protein-truncating variants in 5 genes (ATM, BRCA1, BRCA2, CHEK2, and PALB2) were associated with a risk of breast cancer overall with a P value of less than 0.0001. Protein-truncating variants in 4 other genes (BARD1, RAD51C, RAD51D, and TP53) were associated with a risk of breast cancer overall with a P value of less than 0.05 and a Bayesian false-discovery probability of less than 0.05. For protein-truncating variants in 19 of the remaining 25 genes, the upper limit of the 95% confidence interval of the odds ratio for breast cancer overall was less than 2.0. For protein-truncating variants in ATM and CHEK2, odds ratios were higher for estrogen receptor (ER)-positive disease than for ER-negative disease; for protein-truncating variants in BARD1, BRCA1, BRCA2, PALB2, RAD51C, and RAD51D, odds ratios were higher for ER-negative disease than for ER-positive disease. Rare missense variants (in aggregate) in ATM, CHEK2, and TP53 were associated with a risk of breast cancer overall with a P value of less than 0.001. For BRCA1, BRCA2, and TP53, missense variants (in aggregate) that would be classified as pathogenic according to standard criteria were associated with a risk of breast cancer overall, with the risk being similar to that of protein-truncating variants.

CONCLUSIONS: The results of this study define the genes that are most clinically useful for inclusion on panels for the prediction of breast cancer risk, as well as provide estimates of the risks associated with protein-truncating variants, to guide genetic counseling. (Funded by European Union Horizon 2020 programs and others.).}, } @article {pmid33470199, year = {2020}, author = {Lv, W and Lei, Y and Deng, Y and Sun, N and Liu, X and Yang, L and He, S}, title = {Accelerated evolution and positive selection of rhodopsin in Tibetan loaches living in high altitude.}, journal = {International journal of biological macromolecules}, volume = {165}, number = {Pt B}, pages = {2598-2606}, doi = {10.1016/j.ijbiomac.2020.10.151}, pmid = {33470199}, issn = {1879-0003}, mesh = {Adaptation, Biological ; Altitude ; Amino Acid Substitution ; Animals ; Cold Temperature ; Computational Biology ; Cypriniformes/*genetics ; *Evolution, Molecular ; Fish Proteins/chemistry/*genetics/physiology ; Models, Molecular ; Phylogeny ; Rhodopsin/chemistry/*genetics/physiology ; *Selection, Genetic ; Sequence Alignment ; Tibet ; }, abstract = {Rhodopsin (RH1), the temperature-sensitive visual pigment, attained cold adaptation by functional trade-offs between protein stability and activity. Recent studies suggested convergent selection pressures drove cold adaptation of rhodopsin in high altitude catfishes through nonparallel molecular mechanisms. Here, we tested whether the similar shift occurred in RH1 of Tibetan loaches on the Qinghai-Tibet Plateau (QTP) by investigating the molecular evolution and potential effect on function of RH1. We sequenced RH1 from 27 Triplophysa species, and four lowland loaches and combined these data with published sequences. Tests using a series of models of molecular evolution resulted in strong evidence for accelerated evolution and positive selection in Triplophysa RH1. Three positively selected sites were near key functional domains modulating nonspectral properties of rhodopsin, substitutions of which were likely to compensate for cold-induced decrease in rhodopsin kinetics in cold environments. Moreover, although accelerated evolutionary rates in Tibetan loaches was convergent with those in high altitude catfishes, the sites under positive selection were nonoverlapping. Our findings provide evidence for convergent shift in selection pressures of RH1 in high altitude fish during the ecological transition to cold environment of the QTP.}, } @article {pmid33469716, year = {2021}, author = {Cumer, T and Pouchon, C and Boyer, F and Yannic, G and Rioux, D and Bonin, A and Capblancq, T}, title = {Double-digest RAD-sequencing: do pre- and post-sequencing protocol parameters impact biological results?.}, journal = {Molecular genetics and genomics : MGG}, volume = {296}, number = {2}, pages = {457-471}, pmid = {33469716}, issn = {1617-4623}, support = {ANR-15-CE02-0004//ANR project APPATS/ ; ANR10 LABX56//Labex OSUG@2020/ ; CPER0713 CIRA//Auvergne-Rhône-Alpes region/ ; }, mesh = {Alleles ; Animals ; Butterflies/*genetics ; Computational Biology/methods ; DNA Restriction Enzymes/metabolism ; Fagus/*genetics ; Genetics, Population ; High-Throughput Nucleotide Sequencing/*methods ; Polymorphism, Single Nucleotide ; Reproducibility of Results ; Sequence Analysis, DNA/*methods ; }, abstract = {Next-generation sequencing technologies have opened a new era of research in population genetics. Following these new sequencing opportunities, the use of restriction enzyme-based genotyping techniques, such as restriction site-associated DNA sequencing (RAD-seq) or double-digest RAD-sequencing (ddRAD-seq), has dramatically increased in the last decade. From DNA sampling to SNP calling, the laboratory and bioinformatic parameters of enzyme-based techniques have been investigated in the literature. However, the impact of those parameters on downstream analyses and biological results remains less documented. In this study, we investigated the effects of sevral pre- and post-sequencing settings on ddRAD-seq results for two biological systems: a complex of butterfly species (Coenonympha sp.) and several populations of common beech (Fagus sylvatica). Our results suggest that pre-sequencing parameters (i.e., DNA quantity, number of PCR cycles during library preparation) have a significant impact on the number of recovered reads and SNPs, on the number of unique alleles and on individual heterozygosity. In the same way, we found that post-sequencing settings (i.e., clustering and minimum coverage thresholds) influenced loci reconstruction (e.g., number of loci, mean coverage) and SNP calling (e.g., number of SNPs; heterozygosity) but had only a marginal impact on downstream analyses (e.g., measure of genetic differentiation, estimation of individual admixture, and demographic inferences). In addition, replication analyses confirmed the reproducibility of the ddRAD-seq procedure. Overall, this study assesses the degree of sensitivity of ddRAD-seq data to pre- and post-sequencing protocols, and illustrates its robustness when studying population genetics.}, } @article {pmid33468057, year = {2021}, author = {Weißbach, S and Sys, S and Hewel, C and Todorov, H and Schweiger, S and Winter, J and Pfenninger, M and Torkamani, A and Evans, D and Burger, J and Everschor-Sitte, K and May-Simera, HL and Gerber, S}, title = {Reliability of genomic variants across different next-generation sequencing platforms and bioinformatic processing pipelines.}, journal = {BMC genomics}, volume = {22}, number = {1}, pages = {62}, pmid = {33468057}, issn = {1471-2164}, support = {U01 HG006476/HG/NHGRI NIH HHS/United States ; Resilience, Adaptation and Longevity//ReALity/ ; Mainz Institute of Multiscale Modeling//M3odel/ ; R01 HG010881/HG/NHGRI NIH HHS/United States ; Emergent AI Center//Carl-Zeiss-Stiftung/ ; }, mesh = {*Computational Biology ; Cross-Sectional Studies ; Genomics ; *High-Throughput Nucleotide Sequencing ; Humans ; Polymorphism, Single Nucleotide ; Reproducibility of Results ; }, abstract = {BACKGROUND: Next Generation Sequencing (NGS) is the fundament of various studies, providing insights into questions from biology and medicine. Nevertheless, integrating data from different experimental backgrounds can introduce strong biases. In order to methodically investigate the magnitude of systematic errors in single nucleotide variant calls, we performed a cross-sectional observational study on a genomic cohort of 99 subjects each sequenced via (i) Illumina HiSeq X, (ii) Illumina HiSeq, and (iii) Complete Genomics and processed with the respective bioinformatic pipeline. We also repeated variant calling for the Illumina cohorts with GATK, which allowed us to investigate the effect of the bioinformatics analysis strategy separately from the sequencing platform's impact.

RESULTS: The number of detected variants/variant classes per individual was highly dependent on the experimental setup. We observed a statistically significant overrepresentation of variants uniquely called by a single setup, indicating potential systematic biases. Insertion/deletion polymorphisms (indels) were associated with decreased concordance compared to single nucleotide polymorphisms (SNPs). The discrepancies in indel absolute numbers were particularly prominent in introns, Alu elements, simple repeats, and regions with medium GC content. Notably, reprocessing sequencing data following the best practice recommendations of GATK considerably improved concordance between the respective setups.

CONCLUSION: We provide empirical evidence of systematic heterogeneity in variant calls between alternative experimental and data analysis setups. Furthermore, our results demonstrate the benefit of reprocessing genomic data with harmonized pipelines when integrating data from different studies.}, } @article {pmid33467216, year = {2021}, author = {Kedves, O and Shahab, D and Champramary, S and Chen, L and Indic, B and Bóka, B and Nagy, VD and Vágvölgyi, C and Kredics, L and Sipos, G}, title = {Epidemiology, Biotic Interactions and Biological Control of Armillarioids in the Northern Hemisphere.}, journal = {Pathogens (Basel, Switzerland)}, volume = {10}, number = {1}, pages = {}, pmid = {33467216}, issn = {2076-0817}, support = {GINOP-2.3.2-15-2016-00052//Széchenyi 2020 Programme/ ; }, abstract = {Armillarioids, including the genera Armillaria, Desarmillaria and Guyanagaster, represent white-rot specific fungal saprotrophs with soilborne pathogenic potentials on woody hosts. They propagate in the soil by root-like rhizomorphs, connecting between susceptible root sections of their hosts, and often forming extended colonies in native forests. Pathogenic abilities of Armillaria and Desarmillaria genets can readily manifest in compromised hosts, or hosts with full vigour can be invaded by virulent mycelia when exposed to a larger number of newly formed genets. Armillaria root rot-related symptoms are indicators of ecological imbalances in native forests and plantations at the rhizosphere levels, often related to abiotic environmental threats, and most likely unfavourable changes in the microbiome compositions in the interactive zone of the roots. The less-studied biotic impacts that contribute to armillarioid host infection include fungi and insects, as well as forest conditions. On the other hand, negative biotic impactors, like bacterial communities, antagonistic fungi, nematodes and plant-derived substances may find applications in the environment-friendly, biological control of armillarioid root diseases, which can be used instead of, or in combination with the classical, but frequently problematic silvicultural and chemical control measures.}, } @article {pmid33466575, year = {2021}, author = {Guo, S and Wang, Y and Huang, J and Dong, J and Zhang, J}, title = {Decoupling and Decomposition Analysis of Land Natural Capital Utilization and Economic Growth: A Case Study in Ningxia Hui Autonomous Region, China.}, journal = {International journal of environmental research and public health}, volume = {18}, number = {2}, pages = {}, pmid = {33466575}, issn = {1660-4601}, mesh = {Agriculture ; China ; Conservation of Natural Resources ; *Economic Development ; Forests ; *Industry ; }, abstract = {In order to reduce the depletion of land natural capital and develop economy simultaneously, it is necessary to study how to achieve the strong decoupling relationship between them. However, so far such studies have been relatively limited. Thus, taking the case of Ningxia Hui Autonomous Region, China, this paper firstly analyzes the state of land natural capital utilization in 1999-2017 by using improved ecological footprint. Then, decoupling state is quantified by Tapio decoupling model. Last, major driving factors on the decoupling relationship are explored with combination of LMDI decomposition and Kaya identity equation. Results showed that: (1) Both natural capital flows and stock depletion of cultivated land decrease obviously during the transition to corn-based intensive ecological agriculture. Grassland and water are the most unsustainable development sectors among all land types with their stock depletion intensified. Forest land and construction land could basically meet the consumer demand, but the flow occupancy of construction land is the fastest-growing segment. (2) Decoupling relationship is in an alternating state between weak decoupling and strong decoupling in 1999-2017. Wherein, the cultivated land and forest land showed a preferred decoupling state, followed by grassland, while the water and construction land showed the unfavorable expansive negative decoupling and weak decoupling. (3) Decomposition results show that intensity effect is the major factor that promotes the decoupling while economic effect inhibits the decoupling, but this negative impact is weakening in the process of industrial transformation. The other three factors affect less on the decoupling. This study has a certain reference value to construct an ecological civilization in eco-fragile regions and formulate relevant policies on the increase of land natural capital efficiency.}, } @article {pmid33465070, year = {2021}, author = {Janulevicius, A and van Doorn, GS}, title = {Selection for rapid uptake of scarce or fluctuating resource explains vulnerability of glycolysis to imbalance.}, journal = {PLoS computational biology}, volume = {17}, number = {1}, pages = {e1008547}, pmid = {33465070}, issn = {1553-7358}, mesh = {Adenosine Triphosphate/metabolism ; Bioreactors ; Computational Biology ; Glucose/*metabolism ; Glycolysis/*physiology ; *Models, Biological ; Pyruvic Acid/metabolism ; Saccharomyces cerevisiae/cytology/metabolism ; }, abstract = {Glycolysis is a conserved central pathway in energy metabolism that converts glucose to pyruvate with net production of two ATP molecules. Because ATP is produced only in the lower part of glycolysis (LG), preceded by an initial investment of ATP in the upper glycolysis (UG), achieving robust start-up of the pathway upon activation presents a challenge: a sudden increase in glucose concentration can throw a cell into a self-sustaining imbalanced state in which UG outpaces LG, glycolytic intermediates accumulate and the cell is unable to maintain high ATP concentration needed to support cellular functions. Such metabolic imbalance can result in "substrate-accelerated death", a phenomenon observed in prokaryotes and eukaryotes when cells are exposed to an excess of substrate that previously limited growth. Here, we address why evolution has apparently not eliminated such a costly vulnerability and propose that it is a manifestation of an evolutionary trade-off, whereby the glycolysis pathway is adapted to quickly secure scarce or fluctuating resource at the expense of vulnerability in an environment with ample resource. To corroborate this idea, we perform individual-based eco-evolutionary simulations of a simplified yeast glycolysis pathway consisting of UG, LG, phosphate transport between a vacuole and a cytosol, and a general ATP demand reaction. The pathway is evolved in constant or fluctuating resource environments by allowing mutations that affect the (maximum) reaction rate constants, reflecting changing expression levels of different glycolytic enzymes. We demonstrate that under limited constant resource, populations evolve to a genotype that exhibits balanced dynamics in the environment it evolved in, but strongly imbalanced dynamics under ample resource conditions. Furthermore, when resource availability is fluctuating, imbalanced dynamics confers a fitness advantage over balanced dynamics: when glucose is abundant, imbalanced pathways can quickly accumulate the glycolytic intermediate FBP as intracellular storage that is used during periods of starvation to maintain high ATP concentration needed for growth. Our model further predicts that in fluctuating environments, competition for glucose can result in stable coexistence of balanced and imbalanced cells, as well as repeated cycles of population crashes and recoveries that depend on such polymorphism. Overall, we demonstrate the importance of ecological and evolutionary arguments for understanding seemingly maladaptive aspects of cellular metabolism.}, } @article {pmid33465065, year = {2021}, author = {Schaber, KL and Perkins, TA and Lloyd, AL and Waller, LA and Kitron, U and Paz-Soldan, VA and Elder, JP and Rothman, AL and Civitello, DJ and Elson, WH and Morrison, AC and Scott, TW and Vazquez-Prokopec, GM}, title = {Disease-driven reduction in human mobility influences human-mosquito contacts and dengue transmission dynamics.}, journal = {PLoS computational biology}, volume = {17}, number = {1}, pages = {e1008627}, pmid = {33465065}, issn = {1553-7358}, support = {P01 AI098670/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Computational Biology ; Dengue/*epidemiology/prevention & control/*transmission/virology ; Dengue Virus ; Disease Outbreaks/*statistics & numerical data ; Female ; Humans ; Models, Statistical ; *Mosquito Vectors/physiology/virology ; Population Dynamics ; }, abstract = {Heterogeneous exposure to mosquitoes determines an individual's contribution to vector-borne pathogen transmission. Particularly for dengue virus (DENV), there is a major difficulty in quantifying human-vector contacts due to the unknown coupled effect of key heterogeneities. To test the hypothesis that the reduction of human out-of-home mobility due to dengue illness will significantly influence population-level dynamics and the structure of DENV transmission chains, we extended an existing modeling framework to include social structure, disease-driven mobility reductions, and heterogeneous transmissibility from different infectious groups. Compared to a baseline model, naïve to human pre-symptomatic infectiousness and disease-driven mobility changes, a model including both parameters predicted an increase of 37% in the probability of a DENV outbreak occurring; a model including mobility change alone predicted a 15.5% increase compared to the baseline model. At the individual level, models including mobility change led to a reduction of the importance of out-of-home onward transmission (R, the fraction of secondary cases predicted to be generated by an individual) by symptomatic individuals (up to -62%) at the expense of an increase in the relevance of their home (up to +40%). An individual's positive contribution to R could be predicted by a GAM including a non-linear interaction between an individual's biting suitability and the number of mosquitoes in their home (>10 mosquitoes and 0.6 individual attractiveness significantly increased R). We conclude that the complex fabric of social relationships and differential behavioral response to dengue illness cause the fraction of symptomatic DENV infections to concentrate transmission in specific locations, whereas asymptomatic carriers (including individuals in their pre-symptomatic period) move the virus throughout the landscape. Our findings point to the difficulty of focusing vector control interventions reactively on the home of symptomatic individuals, as this approach will fail to contain virus propagation by visitors to their house and asymptomatic carriers.}, } @article {pmid33464571, year = {2021}, author = {Diez, JM and Boone, R and Bohner, T and Godoy, O}, title = {Frequency-dependent tree growth depends on climate.}, journal = {Ecology}, volume = {102}, number = {4}, pages = {e03284}, doi = {10.1002/ecy.3284}, pmid = {33464571}, issn = {1939-9170}, mesh = {Climate Change ; *Pinus ; *Trees ; }, abstract = {Climate and competition interact to affect species' performance, such as growth and survival, and help determine species distributions and coexistence. However, it is unclear how climatic conditions modulate frequency-dependent performance, that is, how performance changes as a species becomes locally rare or common. This is critical because declines in performance as a species becomes more common (negative frequency dependence) is a signature of niche differences among species that stabilize coexistence, whereas positive frequency dependence leads to priority effects and hampers species coexistence. Here, we used dendrochronology and hierarchical models to test whether frequency-dependent growth of sugar pine (Pinus lambertiana) depends on climatic conditions. We found that growth rates were strongly dependent on annual precipitation, but no frequency dependence was evident across all years. However, there was a strong interaction between precipitation and frequency dependence, revealing stabilizing niche differences in dry years but positive frequency dependence in wet years. These differences emerged because of precipitation-driven changes in the direction and strength of both con- and heterospecific competition. Overall, these results show how stabilizing and destabilizing effects can be temporally dynamic for long-lived species and interact with climate variation.}, } @article {pmid33462369, year = {2021}, author = {Khataee, H and Scheuring, I and Czirok, A and Neufeld, Z}, title = {Effects of social distancing on the spreading of COVID-19 inferred from mobile phone data.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {1661}, pmid = {33462369}, issn = {2045-2322}, mesh = {COVID-19/epidemiology/pathology/*transmission/virology ; Cell Phone ; Europe/epidemiology ; Geographic Information Systems ; Humans ; Pandemics ; *Physical Distancing ; Quarantine ; SARS-CoV-2/isolation & purification ; Travel/statistics & numerical data ; }, abstract = {A better understanding of how the COVID-19 pandemic responds to social distancing efforts is required for the control of future outbreaks and to calibrate partial lock-downs. We present quantitative relationships between key parameters characterizing the COVID-19 epidemiology and social distancing efforts of nine selected European countries. Epidemiological parameters were extracted from the number of daily deaths data, while mitigation efforts are estimated from mobile phone tracking data. The decrease of the basic reproductive number ([Formula: see text]) as well as the duration of the initial exponential expansion phase of the epidemic strongly correlates with the magnitude of mobility reduction. Utilizing these relationships we decipher the relative impact of the timing and the extent of social distancing on the total death burden of the pandemic.}, } @article {pmid33462272, year = {2021}, author = {Jacobson, DK and Honap, TP and Ozga, AT and Meda, N and Kagoné, TS and Carabin, H and Spicer, P and Tito, RY and Obregon-Tito, AJ and Reyes, LM and Troncoso-Corzo, L and Guija-Poma, E and Sankaranarayanan, K and Lewis, CM}, title = {Analysis of global human gut metagenomes shows that metabolic resilience potential for short-chain fatty acid production is strongly influenced by lifestyle.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {1724}, pmid = {33462272}, issn = {2045-2322}, support = {R01 GM089886/GM/NIGMS NIH HHS/United States ; U54 GM104938/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacteria/classification/*genetics ; Computational Biology/methods ; Developed Countries ; Fatty Acids, Volatile/*analysis ; Feces/*microbiology ; Gastrointestinal Microbiome/*genetics ; Humans ; *Life Style ; Metagenome ; Phylogeny ; }, abstract = {High taxonomic diversity in non-industrial human gut microbiomes is often interpreted as beneficial; however, it is unclear if taxonomic diversity engenders ecological resilience (i.e. community stability and metabolic continuity). We estimate resilience through genus and species-level richness, phylogenetic diversity, and evenness in short-chain fatty acid (SCFA) production among a global gut metagenome panel of 12 populations (n = 451) representing industrial and non-industrial lifestyles, including novel metagenomic data from Burkina Faso (n = 90). We observe significantly higher genus-level resilience in non-industrial populations, while SCFA production in industrial populations is driven by a few phylogenetically closely related species (belonging to Bacteroides and Clostridium), meaning industrial microbiomes have low resilience potential. Additionally, database bias obfuscates resilience estimates, as we were 2-5 times more likely to identify SCFA-encoding species in industrial microbiomes compared to non-industrial. Overall, we find high phylogenetic diversity, richness, and evenness of bacteria encoding SCFAs in non-industrial gut microbiomes, signaling high potential for resilience in SCFA production, despite database biases that limit metagenomic analysis of non-industrial populations.}, } @article {pmid33461660, year = {2021}, author = {Urban, L and Holzer, A and Baronas, JJ and Hall, MB and Braeuninger-Weimer, P and Scherm, MJ and Kunz, DJ and Perera, SN and Martin-Herranz, DE and Tipper, ET and Salter, SJ and Stammnitz, MR}, title = {Freshwater monitoring by nanopore sequencing.}, journal = {eLife}, volume = {10}, number = {}, pages = {}, pmid = {33461660}, issn = {2050-084X}, support = {OpenPlant Fund (BBSRC BB/L014130/1)/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; Graduate Student Fellowship (203828/Z/16/A, 203828/Z/16/Z)/WT_/Wellcome Trust/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; Graduate Student Fellowship (102453/Z/13/Z)/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Bacteria/classification/genetics ; Base Sequence ; Cluster Analysis ; Computational Biology/methods ; Environmental Monitoring/methods ; Fresh Water/*microbiology ; Geography ; Metagenome/*genetics ; Metagenomics/*methods ; Microbiota/*genetics ; Nanopore Sequencing/*methods ; RNA, Ribosomal, 16S/genetics ; Rivers/microbiology ; Sequence Homology, Nucleic Acid ; Species Specificity ; United Kingdom ; *Water Microbiology ; }, abstract = {While traditional microbiological freshwater tests focus on the detection of specific bacterial indicator species, including pathogens, direct tracing of all aquatic DNA through metagenomics poses a profound alternative. Yet, in situ metagenomic water surveys face substantial challenges in cost and logistics. Here, we present a simple, fast, cost-effective and remotely accessible freshwater diagnostics workflow centred around the portable nanopore sequencing technology. Using defined compositions and spatiotemporal microbiota from surface water of an example river in Cambridge (UK), we provide optimised experimental and bioinformatics guidelines, including a benchmark with twelve taxonomic classification tools for nanopore sequences. We find that nanopore metagenomics can depict the hydrological core microbiome and fine temporal gradients in line with complementary physicochemical measurements. In a public health context, these data feature relevant sewage signals and pathogen maps at species level resolution. We anticipate that this framework will gather momentum for new environmental monitoring initiatives using portable devices.}, } @article {pmid33461273, year = {2021}, author = {Almeida, ÂS and Ribeiro, CJN and Carlini, CC and Santos, RS and Dos Santos, AD and Tavares, DS and De Araújo, KCGM and Moura, TR and Santos, PLD}, title = {Spatial and spatiotemporal dynamics of visceral leishmaniasis in an endemic North-eastern region of Brazil.}, journal = {Geospatial health}, volume = {15}, number = {2}, pages = {}, doi = {10.4081/gh.2020.885}, pmid = {33461273}, issn = {1970-7096}, mesh = {Adult ; Aged ; Aged, 80 and over ; Animals ; Bayes Theorem ; Brazil/epidemiology ; Environment ; Geographic Information Systems ; Humans ; Insect Vectors/*parasitology ; Leishmaniasis, Visceral/*epidemiology/parasitology ; Middle Aged ; Sex Distribution ; Spatial Analysis ; Spatio-Temporal Analysis ; Urban Population/*statistics & numerical data ; }, abstract = {Visceral Leishmaniasis (VL) is a neglected disease with increasing incidence in Brazil, particularly in the North-eastern. The aim of this study was to analyze the spatial and spatiotemporal dynamics of VL in an endemic region of North-eastern Brazil, between 2009 and 2017. Using spatial analysis techniques, an ecological and time series study was made regarding VL cases in Sergipe filed as notifiable disease events. With data from the Brazilian Institute of Geography and Statistics (Instituto Brasileiro de Geografia e Estatística, IBGE), a digital population and cartographic baseline was established. Segmented linear regression was used to examine the temporal trends. The statistical analysis methods of Global and Local Moran' I, local Bayesian empirical methodology and spatial-temporal scanning were used to produce thematic maps. High instances were found among adults, males, urban residents, non-Whites and persons with low levels of education. A decrease in the recovery rate and an increase in the proportion of urban cases and lethality was found. A heterogeneous VL distribution with spatiotemporal agglomeration on the seaside of the state was seen in Sergipe. To better manage the disease, new research is encouraged together with development of public health strategies. Further, improving health care networks, especially primary care, is suggested as this approach has a key role in health promotion, prevention and monitoring of the most prevalent diseases.}, } @article {pmid33460891, year = {2021}, author = {Gujre, N and Rangan, L and Mitra, S}, title = {Occurrence, geochemical fraction, ecological and health risk assessment of cadmium, copper and nickel in soils contaminated with municipal solid wastes.}, journal = {Chemosphere}, volume = {271}, number = {}, pages = {129573}, doi = {10.1016/j.chemosphere.2021.129573}, pmid = {33460891}, issn = {1879-1298}, mesh = {Adult ; Cadmium/analysis ; Child ; Copper/analysis ; Environmental Monitoring ; Humans ; India ; *Metals, Heavy/analysis ; Nickel/analysis ; Risk Assessment ; Soil ; *Soil Pollutants/analysis ; Solid Waste ; }, abstract = {Unscientific municipal solid waste (MSW) dumping provokes heavy metal (HM) associated ecological and human health hazards through heightened bioavailability and bioaccumulation. In this study, we focused on three important HMs Cadmium (Cd), Copper (Cu) and Nickel (Ni) and their geochemical fractions, to enable clutter free data management, analysis and interpretation. Stratified random soil sampling was carried out from twenty different locations around a Ramsar site (Deepor Beel) in Guwahati, India. The spatial concentration profiles of Cd, Cu and Ni were determined by data elicited from geochemical fractionation and the Geographic Information System (GIS). Ecological and health risks indices were used to evaluate the severity of soil pollution and assess the level of health risks. All the three HMs thus evaluated, conformed to the potential bioavailable category. Cd (54.59%) was associated mostly with the carbonate bound fraction (F3), while 25.53% of Cu and 40.60% Ni were associated with the exchangeable fraction (F2). Significant contamination levels and higher ecological risks posed by these metals were in the order Cd > Ni > Cu. Children were found to be more vulnerable towards Cd associated health risks whereas, Ni posed threats to both adults and children. Cu posed no risk to human health. Geochemical fractionation and different indices played a critical role in the integrated assessment of soil pollution, ecological and health risk assessment, and provided an empirical basis for the sustainable future planning and comprehensive adaptive management practices for MSW.}, } @article {pmid33460060, year = {2020}, author = {Pinkert, S and Friess, N and Zeuss, D and Gossner, MM and Brandl, R and Brunzel, S}, title = {Mobility costs and energy uptake mediate the effects of morphological traits on species' distribution and abundance.}, journal = {Ecology}, volume = {101}, number = {10}, pages = {e03121}, doi = {10.1002/ecy.3121}, pmid = {33460060}, issn = {1939-9170}, support = {//Stifterverband/ ; //Google/ ; //Federal Office for the Environment/ ; }, mesh = {Animals ; Biological Evolution ; Body Size ; *Butterflies ; *Energy Metabolism ; Population Dynamics ; }, abstract = {Individuals of large or dark-colored ectothermic species often have a higher reproduction and activity than small or light-colored ones. However, investments into body size or darker colors should negatively affect the fitness of individuals as they increase their growth and maintenance costs. Thus, it is unlikely that morphological traits directly affect species' distribution and abundance. Yet, this simplification is frequently made in trait-based ecological analyses. Here, we integrated the energy allocation strategies of species into an ecophysiological framework to explore the mechanisms that link species' morphological traits and population dynamics. We hypothesized that the effects of morphological traits on species' distribution and abundance are not direct but mediated by components of the energy budget and that species can allocate more energy towards dispersal and reproduction if they compensate their energetic costs by reducing mobility costs or increasing energy uptake. To classify species' energy allocation strategies, we used easily measured proxies for the mobility costs and energy uptake of butterflies that can be also applied to other taxa. We demonstrated that contrasting effects of morphological traits on distribution and abundance of butterfly species offset each other when species' energy allocation strategies are not taken into account. Larger and darker butterfly species had wider distributions and were more abundant if they compensated the investment into body size and color darkness (i.e., melanin) by reducing their mobility costs or increasing energy uptake. Adults of darker species were more mobile and foraged less compared to lighter colored ones, if an investment into melanin was indirectly compensated via a size-dependent reduction of mobility costs or increase of energy uptake. Our results indicate that differences in the energy allocations strategies of species account for a considerable part of the variation in species' distribution and abundance that is left unexplained by morphological traits alone and ignoring these differences can lead to false mechanistic conclusions. Therefore, our findings highlight the potential of integrating proxies for species' energy allocation strategies into trait-based models not only for understanding the physiological mechanisms underlying variation in species' distribution and abundance, but also for improving predictions of the population dynamics of species.}, } @article {pmid33459584, year = {2021}, author = {Jones, C and Webster, G and Mullins, AJ and Jenner, M and Bull, MJ and Dashti, Y and Spilker, T and Parkhill, J and Connor, TR and LiPuma, JJ and Challis, GL and Mahenthiralingam, E}, title = {Kill and cure: genomic phylogeny and bioactivity of Burkholderia gladioli bacteria capable of pathogenic and beneficial lifestyles.}, journal = {Microbial genomics}, volume = {7}, number = {1}, pages = {}, pmid = {33459584}, issn = {2057-5858}, support = {BB/S008020/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; MR/L015080/1/MRC_/Medical Research Council/United Kingdom ; BB/R012121/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/L021692/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/M017982/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/L023342/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; MR/T030062/1/MRC_/Medical Research Council/United Kingdom ; BB/S007652/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Biosynthetic Pathways ; Bongkrekic Acid/metabolism ; Burkholderia gladioli/*classification/genetics/pathogenicity/physiology ; Cystic Fibrosis/*microbiology ; Food Microbiology ; High-Throughput Nucleotide Sequencing ; Humans ; Phylogeny ; Plant Diseases/*microbiology ; Trimethoprim/pharmacology ; Whole Genome Sequencing/*methods ; }, abstract = {Burkholderia gladioli is a bacterium with a broad ecology spanning disease in humans, animals and plants, but also encompassing multiple beneficial interactions. It is a plant pathogen, a toxin-producing food-poisoning agent, and causes lung infections in people with cystic fibrosis (CF). Contrasting beneficial traits include antifungal production exploited by insects to protect their eggs, plant protective abilities and antibiotic biosynthesis. We explored the genomic diversity and specialized metabolic potential of 206 B. gladioli strains, phylogenomically defining 5 clades. Historical disease pathovars (pv.) B. gladioli pv. allicola and B. gladioli pv. cocovenenans were distinct, while B. gladioli pv. gladioli and B. gladioli pv. agaricicola were indistinguishable; soft-rot disease and CF infection were conserved across all pathovars. Biosynthetic gene clusters (BGCs) for toxoflavin, caryoynencin and enacyloxin were dispersed across B. gladioli, but bongkrekic acid and gladiolin production were clade-specific. Strikingly, 13 % of CF infection strains characterized were bongkrekic acid-positive, uniquely linking this food-poisoning toxin to this aspect of B. gladioli disease. Mapping the population biology and metabolite production of B. gladioli has shed light on its diverse ecology, and by demonstrating that the antibiotic trimethoprim suppresses bongkrekic acid production, a potential therapeutic strategy to minimize poisoning risk in CF has been identified.}, } @article {pmid33455490, year = {2022}, author = {Kuniyoshi, Y and Tokutake, H and Takahashi, N and Kamura, A and Yasuda, S and Tashiro, M}, title = {Regional variation in the development of neonatal hyperbilirubinemia and relation with sunshine duration in Japan: an ecological study.}, journal = {The journal of maternal-fetal & neonatal medicine : the official journal of the European Association of Perinatal Medicine, the Federation of Asia and Oceania Perinatal Societies, the International Society of Perinatal Obstetricians}, volume = {35}, number = {25}, pages = {4946-4951}, doi = {10.1080/14767058.2021.1873270}, pmid = {33455490}, issn = {1476-4954}, mesh = {Infant, Newborn ; Humans ; Japan/epidemiology ; *Hyperbilirubinemia, Neonatal/epidemiology ; Insurance, Health ; Databases, Factual ; Time Factors ; }, abstract = {BACKGROUND: Few studies have investigated the regional variations in the development of neonatal hyperbilirubinemia. This study aimed to investigate regional variations in medical costs for neonatal hyperbilirubinemia and the correlations between sunshine duration and medical care costs for neonatal hyperbilirubinemia in an ecological study, using the National Database of Japan.

METHODS: We obtained data on the annual medical costs for neonatal hyperbilirubinemia, annual live births, and annual sunshine duration in each prefecture from the National Database of Health Insurance Claims and Specific Health Checkups of Japan (NDB) Open Data, Vital Statistics in Japan, and System of Social and Demographic Statistics Prefectural Data Basic Data from 2014 to 2017. We created choropleth maps showing the regional variations (quartiles) in the annual medical costs for neonatal hyperbilirubinemia per 10 live births and the annual sunshine duration in each prefecture. We used Pearson's correlation coefficients to evaluate the associations between the annual sunshine duration and annual medical care costs for neonatal hyperbilirubinemia per 10 live births in each prefecture.

RESULTS: The Tohoku region (on the Sea of Japan side) and the Hokuriku region were likely to have higher medical care costs for neonatal hyperbilirubinemia and shorter sunshine duration than the rest of the country. There were weak and negative correlations between the annual sunshine duration and the annual medical care costs for neonatal hyperbilirubinemia. The correlation coefficients ranged from -0.086 to -0.33.

CONCLUSION: There could be regional variations in the medical care costs for neonatal hyperbilirubinemia in Japan. Short sunshine duration could be a prognostic factor for the development of neonatal hyperbilirubinemia.}, } @article {pmid33444539, year = {2021}, author = {Gupta, RK and Harrison, EM and Ho, A and Docherty, AB and Knight, SR and van Smeden, M and Abubakar, I and Lipman, M and Quartagno, M and Pius, R and Buchan, I and Carson, G and Drake, TM and Dunning, J and Fairfield, CJ and Gamble, C and Green, CA and Halpin, S and Hardwick, HE and Holden, KA and Horby, PW and Jackson, C and Mclean, KA and Merson, L and Nguyen-Van-Tam, JS and Norman, L and Olliaro, PL and Pritchard, MG and Russell, CD and Scott-Brown, J and Shaw, CA and Sheikh, A and Solomon, T and Sudlow, C and Swann, OV and Turtle, L and Openshaw, PJM and Baillie, JK and Semple, MG and Noursadeghi, M and , }, title = {Development and validation of the ISARIC 4C Deterioration model for adults hospitalised with COVID-19: a prospective cohort study.}, journal = {The Lancet. Respiratory medicine}, volume = {9}, number = {4}, pages = {349-359}, pmid = {33444539}, issn = {2213-2619}, support = {G0701652/MRC_/Medical Research Council/United Kingdom ; MC_PC_19059/MRC_/Medical Research Council/United Kingdom ; IS-HPU-1112-10117/DH_/Department of Health/United Kingdom ; MC_UU_12014/9/MRC_/Medical Research Council/United Kingdom ; MC_PC_19025/MRC_/Medical Research Council/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; MC_PC_15001/MRC_/Medical Research Council/United Kingdom ; 109965/Z/15/Z/WT_/Wellcome Trust/United Kingdom ; MC_PC_19026/MRC_/Medical Research Council/United Kingdom ; DRF-2018-11-ST2-004/DH_/Department of Health/United Kingdom ; MC_UU_00004/07/MRC_/Medical Research Council/United Kingdom ; MR/V033441/1/MRC_/Medical Research Council/United Kingdom ; MR/S032304/1/MRC_/Medical Research Council/United Kingdom ; MC_UU_12023/21/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Aged ; Aged, 80 and over ; COVID-19/*diagnosis/mortality/therapy ; *Clinical Decision Rules ; Clinical Decision-Making/*methods ; *Clinical Deterioration ; Critical Care/statistics & numerical data ; Female ; Hospital Mortality ; Humans ; Intensive Care Units/statistics & numerical data ; Logistic Models ; Male ; Middle Aged ; Patient Admission/statistics & numerical data ; Prognosis ; Prospective Studies ; Reproducibility of Results ; Respiration, Artificial/statistics & numerical data ; SARS-CoV-2/isolation & purification ; Severity of Illness Index ; United Kingdom/epidemiology ; }, abstract = {BACKGROUND: Prognostic models to predict the risk of clinical deterioration in acute COVID-19 cases are urgently required to inform clinical management decisions.

METHODS: We developed and validated a multivariable logistic regression model for in-hospital clinical deterioration (defined as any requirement of ventilatory support or critical care, or death) among consecutively hospitalised adults with highly suspected or confirmed COVID-19 who were prospectively recruited to the International Severe Acute Respiratory and Emerging Infections Consortium Coronavirus Clinical Characterisation Consortium (ISARIC4C) study across 260 hospitals in England, Scotland, and Wales. Candidate predictors that were specified a priori were considered for inclusion in the model on the basis of previous prognostic scores and emerging literature describing routinely measured biomarkers associated with COVID-19 prognosis. We used internal-external cross-validation to evaluate discrimination, calibration, and clinical utility across eight National Health Service (NHS) regions in the development cohort. We further validated the final model in held-out data from an additional NHS region (London).

FINDINGS: 74 944 participants (recruited between Feb 6 and Aug 26, 2020) were included, of whom 31 924 (43·2%) of 73 948 with available outcomes met the composite clinical deterioration outcome. In internal-external cross-validation in the development cohort of 66 705 participants, the selected model (comprising 11 predictors routinely measured at the point of hospital admission) showed consistent discrimination, calibration, and clinical utility across all eight NHS regions. In held-out data from London (n=8239), the model showed a similarly consistent performance (C-statistic 0·77 [95% CI 0·76 to 0·78]; calibration-in-the-large 0·00 [-0·05 to 0·05]); calibration slope 0·96 [0·91 to 1·01]), and greater net benefit than any other reproducible prognostic model.

INTERPRETATION: The 4C Deterioration model has strong potential for clinical utility and generalisability to predict clinical deterioration and inform decision making among adults hospitalised with COVID-19.

FUNDING: National Institute for Health Research (NIHR), UK Medical Research Council, Wellcome Trust, Department for International Development, Bill & Melinda Gates Foundation, EU Platform for European Preparedness Against (Re-)emerging Epidemics, NIHR Health Protection Research Unit (HPRU) in Emerging and Zoonotic Infections at University of Liverpool, NIHR HPRU in Respiratory Infections at Imperial College London.}, } @article {pmid33443039, year = {2020}, author = {Goulard, R and Buehlmann, C and Niven, JE and Graham, P and Webb, B}, title = {A motion compensation treadmill for untethered wood ants (Formica rufa): evidence for transfer of orientation memories from free-walking training.}, journal = {The Journal of experimental biology}, volume = {223}, number = {Pt 24}, pages = {}, pmid = {33443039}, issn = {1477-9145}, support = {BB/R005036/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; *Ants ; Memory ; Orientation ; Orientation, Spatial ; Walking ; }, abstract = {The natural scale of insect navigation during foraging makes it challenging to study under controlled conditions. Virtual reality and trackball setups have offered experimental control over visual environments while studying tethered insects, but potential limitations and confounds introduced by tethering motivates the development of alternative untethered solutions. In this paper, we validate the use of a motion compensator (or 'treadmill') to study visually driven behaviour of freely moving wood ants (Formica rufa). We show how this setup allows naturalistic walking behaviour and preserves foraging motivation over long time frames. Furthermore, we show that ants are able to transfer associative and navigational memories from classical maze and arena contexts to our treadmill. Thus, we demonstrate the possibility to study navigational behaviour over ecologically relevant durations (and virtual distances) in precisely controlled environments, bridging the gap between natural and highly controlled laboratory experiments.}, } @article {pmid33441598, year = {2021}, author = {Kiang, MV and Santillana, M and Chen, JT and Onnela, JP and Krieger, N and Engø-Monsen, K and Ekapirat, N and Areechokchai, D and Prempree, P and Maude, RJ and Buckee, CO}, title = {Incorporating human mobility data improves forecasts of Dengue fever in Thailand.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {923}, pmid = {33441598}, issn = {2045-2322}, support = {K99 DA051534/DA/NIDA NIH HHS/United States ; R01 GM130668/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Dengue/*epidemiology ; Disease Outbreaks ; Epidemics ; Forecasting/*methods ; Humans ; Incidence ; Models, Statistical ; Mosquito Vectors ; Population Dynamics/*trends ; Thailand/epidemiology ; Travel ; }, abstract = {Over 390 million people worldwide are infected with dengue fever each year. In the absence of an effective vaccine for general use, national control programs must rely on hospital readiness and targeted vector control to prepare for epidemics, so accurate forecasting remains an important goal. Many dengue forecasting approaches have used environmental data linked to mosquito ecology to predict when epidemics will occur, but these have had mixed results. Conversely, human mobility, an important driver in the spatial spread of infection, is often ignored. Here we compare time-series forecasts of dengue fever in Thailand, integrating epidemiological data with mobility models generated from mobile phone data. We show that geographically-distant provinces strongly connected by human travel have more highly correlated dengue incidence than weakly connected provinces of the same distance, and that incorporating mobility data improves traditional time-series forecasting approaches. Notably, no single model or class of model always outperformed others. We propose an adaptive, mosaic forecasting approach for early warning systems.}, } @article {pmid33439135, year = {2021}, author = {Mardini, MT and Nerella, S and Kheirkhahan, M and Ranka, S and Fillingim, RB and Hu, Y and Corbett, DB and Cenko, E and Weber, E and Rashidi, P and Manini, TM}, title = {The Temporal Relationship Between Ecological Pain and Life-Space Mobility in Older Adults With Knee Osteoarthritis: A Smartwatch-Based Demonstration Study.}, journal = {JMIR mHealth and uHealth}, volume = {9}, number = {1}, pages = {e19609}, pmid = {33439135}, issn = {2291-5222}, support = {UL1 TR001427/TR/NCATS NIH HHS/United States ; P30 AG028740/AG/NIA NIH HHS/United States ; R21 AG059207/AG/NIA NIH HHS/United States ; }, mesh = {Aged ; Ecological Momentary Assessment ; Female ; Humans ; Male ; *Osteoarthritis, Knee ; Pain ; Surveys and Questionnaires ; }, abstract = {BACKGROUND: Older adults who experience pain are more likely to reduce their community and life-space mobility (ie, the usual range of places in an environment in which a person engages). However, there is significant day-to-day variability in pain experiences that offer unique insights into the consequences on life-space mobility, which are not well understood. This variability is complex and cannot be captured with traditional recall-based pain surveys. As a solution, ecological momentary assessments record repeated pain experiences throughout the day in the natural environment.

OBJECTIVE: The aim of this study was to examine the temporal association between ecological momentary assessments of pain and GPS metrics in older adults with symptomatic knee osteoarthritis by using a smartwatch platform called Real-time Online Assessment and Mobility Monitor.

METHODS: Participants (n=19, mean 73.1 years, SD 4.8; female: 13/19, 68%; male: 6/19, 32%) wore a smartwatch for a mean period of 13.16 days (SD 2.94). Participants were prompted in their natural environment about their pain intensity (range 0-10) at random time windows in the morning, afternoon, and evening. GPS coordinates were collected at 15-minute intervals and aggregated each day into excursion, ellipsoid, clustering, and trip frequency features. Pain intensity ratings were averaged across time windows for each day. A random effects model was used to investigate the within and between-person effects.

RESULTS: The daily mean pain intensities reported by participants ranged between 0 and 8 with 40% reporting intensities ≥2. The within-person associations between pain intensity and GPS features were more likely to be statistically significant than those observed between persons. Within-person pain intensity was significantly associated with excursion size, and others (excursion span, total distance, and ellipse major axis) showed a statistical trend (excursion span: P=.08; total distance: P=.07; ellipse major axis: P=.07). Each point increase in the mean pain intensity was associated with a 3.06 km decrease in excursion size, 2.89 km decrease in excursion span, 5.71 km decrease total distance travelled per day, 31.4 km[2] decrease in ellipse area, 0.47 km decrease ellipse minor axis, and 3.64 km decrease in ellipse major axis. While not statistically significant, the point estimates for number of clusters (P=.73), frequency of trips (P=.81), and homestay (P=.15) were positively associated with pain intensity, and entropy (P=.99) was negatively associated with pain intensity.

CONCLUSIONS: In this demonstration study, higher intensity knee pain in older adults was associated with lower life-space mobility. Results demonstrate that a custom-designed smartwatch platform is effective at simultaneously collecting rich information about ecological pain and life-space mobility. Such smart tools are expected to be important for remote health interventions that harness the variability in pain symptoms while understanding their impact on life-space mobility.}, } @article {pmid33436802, year = {2021}, author = {Dong, Z and Yang, S and Lee, BH}, title = {Bioinformatic mapping of a more precise Aspergillus niger degradome.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {693}, pmid = {33436802}, issn = {2045-2322}, mesh = {Aspergillus niger/genetics/*metabolism ; Catalytic Domain ; Computational Biology/*methods ; Fungal Proteins/classification/genetics/*metabolism ; *Genome, Fungal ; Peptide Hydrolases/classification/genetics/*metabolism ; *Proteolysis ; Whole Genome Sequencing ; }, abstract = {Aspergillus niger has the ability to produce a large variety of proteases, which are of particular importance for protein digestion, intracellular protein turnover, cell signaling, flavour development, extracellular matrix remodeling and microbial defense. However, the A. niger degradome (the full repertoire of peptidases encoded by the A. niger genome) available is not accurate and comprehensive. Herein, we have utilized annotations of A. niger proteases in AspGD, JGI, and version 12.2 MEROPS database to compile an index of at least 232 putative proteases that are distributed into the 71 families/subfamilies and 26 clans of the 6 known catalytic classes, which represents ~ 1.64% of the 14,165 putative A. niger protein content. The composition of the A. niger degradome comprises ~ 7.3% aspartic, ~ 2.2% glutamic, ~ 6.0% threonine, ~ 17.7% cysteine, ~ 31.0% serine, and ~ 35.8% metallopeptidases. One hundred and two proteases have been reassigned into the above six classes, while the active sites and/or metal-binding residues of 110 proteases were recharacterized. The probable physiological functions and active site architectures of these peptidases were also investigated. This work provides a more precise overview of the complete degradome of A. niger, which will no doubt constitute a valuable resource and starting point for further experimental studies on the biochemical characterization and physiological roles of these proteases.}, } @article {pmid33436710, year = {2021}, author = {Miller, BS and , and Balcazar, N and Nieukirk, S and Leroy, EC and Aulich, M and Shabangu, FW and Dziak, RP and Lee, WS and Hong, JK}, title = {An open access dataset for developing automated detectors of Antarctic baleen whale sounds and performance evaluation of two commonly used detectors.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {806}, pmid = {33436710}, issn = {2045-2322}, mesh = {Access to Information ; Acoustics/*instrumentation ; Animals ; Antarctic Regions ; Balaenoptera/*physiology ; Datasets as Topic ; Signal Processing, Computer-Assisted/*instrumentation ; Sound Spectrography/*instrumentation/methods ; Species Specificity ; Vocalization, Animal/*physiology ; }, abstract = {Since 2001, hundreds of thousands of hours of underwater acoustic recordings have been made throughout the Southern Ocean south of 60° S. Detailed analysis of the occurrence of marine mammal sounds in these circumpolar recordings could provide novel insights into their ecology, but manual inspection of the entirety of all recordings would be prohibitively time consuming and expensive. Automated signal processing methods have now developed to the point that they can be applied to these data in a cost-effective manner. However training and evaluating the efficacy of these automated signal processing methods still requires a representative annotated library of sounds to identify the true presence and absence of different sound types. This work presents such a library of annotated recordings for the purpose of training and evaluating automated detectors of Antarctic blue and fin whale calls. Creation of the library has focused on the annotation of a representative sample of recordings to ensure that automated algorithms can be developed and tested across a broad range of instruments, locations, environmental conditions, and years. To demonstrate the utility of the library, we characterise the performance of two automated detection algorithms that have been commonly used to detect stereotyped calls of blue and fin whales. The availability of this library will facilitate development of improved detectors for the acoustic presence of Southern Ocean blue and fin whales. It can also be expanded upon to facilitate standardization of subsequent analysis of spatiotemporal trends in call-density of these circumpolar species.}, } @article {pmid33433310, year = {2021}, author = {Schniete, JK and Selem-Mojica, N and Birke, AS and Cruz-Morales, P and Hunter, IS and Barona-Gomez, F and Hoskisson, PA}, title = {ActDES - a curated Actinobacterial Database for Evolutionary Studies.}, journal = {Microbial genomics}, volume = {7}, number = {1}, pages = {}, pmid = {33433310}, issn = {2057-5858}, support = {BB/N023544/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/T001038/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Actinobacteria/classification/*genetics ; Base Composition ; Data Curation ; Databases, Genetic ; Evolution, Molecular ; Genome, Bacterial ; Molecular Sequence Annotation ; Phylogeny ; }, abstract = {Actinobacteria is a large and diverse phylum of bacteria that contains medically and ecologically relevant organisms. Many members are valuable sources of bioactive natural products and chemical precursors that are exploited in the clinic and made using the enzyme pathways encoded in their complex genomes. Whilst the number of sequenced genomes has increased rapidly in the last 20 years, the large size, complexity and high G+C content of many actinobacterial genomes means that the sequences remain incomplete and consist of large numbers of contigs with poor annotation, which hinders large-scale comparative genomic and evolutionary studies. To enable greater understanding and exploitation of actinobacterial genomes, specialized genomic databases must be linked to high-quality genome sequences. Here, we provide a curated database of 612 high-quality actinobacterial genomes from 80 genera, chosen to represent a broad phylogenetic group with equivalent genome re-annotation. Utilizing this database will provide researchers with a framework for evolutionary and metabolic studies, to enable a foundation for genome and metabolic engineering, to facilitate discovery of novel bioactive therapeutics and studies on gene family evolution. This article contains data hosted by Microreact.}, } @article {pmid33431818, year = {2021}, author = {Henson, P and D'Mello, R and Vaidyam, A and Keshavan, M and Torous, J}, title = {Anomaly detection to predict relapse risk in schizophrenia.}, journal = {Translational psychiatry}, volume = {11}, number = {1}, pages = {28}, pmid = {33431818}, issn = {2158-3188}, support = {K23MH116130-03//U.S. Department of Health & Human Services | NIH | National Institute of Mental Health (NIMH)/International ; }, mesh = {Accelerometry/methods/psychology ; Adult ; Boston ; Ecological Momentary Assessment/statistics & numerical data ; Female ; Health Surveys/*methods ; Humans ; Longitudinal Studies ; Male ; Mobile Applications ; Movement ; Phenotype ; Recurrence ; Reproducibility of Results ; Risk Assessment ; Schizophrenia/*diagnosis/physiopathology ; Screen Time ; Sensitivity and Specificity ; Sleep ; Smartphone ; Social Behavior ; Telemedicine/*methods ; }, abstract = {The integration of technology in clinical care is growing rapidly and has become especially relevant during the global COVID-19 pandemic. Smartphone-based digital phenotyping, or the use of integrated sensors to identify patterns in behavior and symptomatology, has shown potential in detecting subtle moment-to-moment changes. These changes, often referred to as anomalies, represent significant deviations from an individual's baseline, may be useful in informing the risk of relapse in serious mental illness. Our investigation of smartphone-based anomaly detection resulted in 89% sensitivity and 75% specificity for predicting relapse in schizophrenia. These results demonstrate the potential of longitudinal collection of real-time behavior and symptomatology via smartphones and the clinical utility of individualized analysis. Future studies are necessary to explore how specificity can be improved, just-in-time adaptive interventions utilized, and clinical integration achieved.}, } @article {pmid33430148, year = {2021}, author = {Stryamets, N and Mattalia, G and Pieroni, A and Khomyn, I and Sõukand, R}, title = {Dining Tables Divided by a Border: The Effect of Socio-Political Scenarios on Local Ecological Knowledge of Romanians Living in Ukrainian and Romanian Bukovina.}, journal = {Foods (Basel, Switzerland)}, volume = {10}, number = {1}, pages = {}, pmid = {33430148}, issn = {2304-8158}, support = {714874/ERC_/European Research Council/International ; }, abstract = {Local cuisine is an important reservoir of local ecological knowledge shaped by a variety of socio-cultural, economic, and ecological factors. The aim was to document and compare the current use of wild and semi-cultivated plant food taxa by Romanians living in Romania and Ukraine. These two groups share similar ecological conditions and historically belonged to the same province, but were divided in the 1940s by the creation of a state border. We conducted 60 semi-structured interviews with rural residents. The contemporary use of 46 taxa (plus 5 cultivated taxa with uncommon uses), belonging to 20 families, for food consumption were recorded. Romanians in Romanian Bukovina used 27 taxa belonging to 15 families, while in Ukraine they used 40 taxa belonging to 18 families. Jams, sarmale, homemade beer, and the homemade alcoholic drink "socată" are used more by Romanians in Southern Bukovina, while tea, soups, and birch sap are used more in Northern Bukovina. We discuss the strong influence of socio-political scenarios on the use of wild food plants. Cross-ethnic marriages, as well as markets and women's networks, i.e., "neighbors do so", may have had a great impact on changes in wild food use. In addition, rapid changes in lifestyle (open work market and social migration) are other explanations for the abandonment of wild edible plants.}, } @article {pmid33423323, year = {2021}, author = {Huang, Y and Wang, R and Gao, T and Wu, T and Zhang, Q and Shi, Y and Ding, S and Zhao, Z}, title = {Transcriptome analysis of immune response against Siniperca chuatsi rhabdovirus infection in mandarin fish Siniperca chuatsi.}, journal = {Journal of fish diseases}, volume = {44}, number = {6}, pages = {675-687}, doi = {10.1111/jfd.13329}, pmid = {33423323}, issn = {1365-2761}, support = {CX[18]2012//Jiangsu Agriculture Science and Technology Independent Innovation Fund/ ; CX[19]2033//Jiangsu Agriculture Science and Technology Independent Innovation Fund/ ; 2018YFD0900302-2//National Key Research and Development Program of China/ ; BE2018398//Science and Technology Planning Project of Jiangsu Province/ ; 32002423//National Natural Science Foundation of China/ ; B200202142//Fundamental Research Funds for the Central Universities/ ; BK20180501//Natural Science Foundation of Jiangsu Province/ ; 2019M651666//China Postdoctoral Science Foundation/ ; }, mesh = {Adaptive Immunity/*genetics ; Animals ; Apoptosis ; Fish Diseases/*immunology/virology ; Fish Proteins/genetics/*immunology ; Gene Expression Profiling ; Gene Expression Regulation/*immunology ; Gene Ontology ; Immunity, Innate/*genetics ; Perciformes/*genetics/*immunology ; Rhabdoviridae/physiology ; Rhabdoviridae Infections/immunology/veterinary/virology ; Transcriptome/*immunology ; }, abstract = {As one of the piscine rhabdoviruses, Siniperca chuatsi rhabdovirus (SCRV) has caused considerable losses to mandarin fish aquaculture industry. RNA-seq, as efficient transcriptome research method, has been widely used to study the immune response of fish to pathogens. This study reported the effect of SCRV infection at 0, 24 and 60 hr on S. chuatsi at the transcriptome level. A total of 61,527 unigenes with high quality were obtained, and 3,095, 1,854 and 227 differentially expressed genes (DEGs) were labelled between the Sc24 and Sc0 groups, the Sc60 and Sc0 groups and the Sc60 and Sc24 groups, respectively. Genes involved in innate and adaptive immunity were highlighted. In Gene Ontology analysis, the DEGs that participated in immune response, innate immune response and the regulation of apoptotic process were identified as enriched classes. Kyoto Encyclopedia of Genes and Genomes pathway results indicated that most DEGs caused by SCRV infection were identified in the immune system (retinoic acid-inducible gene-I-like receptor/Toll-like receptor/nucleotide-binding oligomerization domain-like receptor/C-type lectin receptor signalling pathway), cellular processes, cell growth and death (p53 signalling pathway, cellular senescence, apoptosis and phagosome), and metabolism. Quantitative real-time PCR was used to further verify the expression levels of 15 immune-related DEGs. The transcriptome database obtained in this study provided further in-depth insight into the immune response of S. chuatsi against SCRV.}, } @article {pmid33421855, year = {2021}, author = {Sajatovic, M and Wilson, B and Shegog, R and B S Briggs, F and Escoffery, C and Jobst, BC and Johnson, EK and Fraser, RT and Quarells, RC and Spruill, TM}, title = {The Managing Epilepsy Well (MEW) network database: Lessons learned in refining and implementing an integrated data tool in service of a national U.S. Research Collaborative.}, journal = {Epilepsy & behavior : E&B}, volume = {115}, number = {}, pages = {107650}, doi = {10.1016/j.yebeh.2020.107650}, pmid = {33421855}, issn = {1525-5069}, support = {U48 DP005013/DP/NCCDPHP CDC HHS/United States ; U48 DP005042/DP/NCCDPHP CDC HHS/United States ; U48 DP006377/DP/NCCDPHP CDC HHS/United States ; U48 DP005008/DP/NCCDPHP CDC HHS/United States ; U48 DP006389/DP/NCCDPHP CDC HHS/United States ; U48 DP006413/DP/NCCDPHP CDC HHS/United States ; }, mesh = {Adult ; Anticonvulsants ; Common Data Elements ; *Epilepsy/therapy ; Female ; Humans ; Male ; Quality of Life ; Seizures ; *Self-Management ; }, abstract = {Epilepsy self-management (ESM) is the summative set of behaviors that people with epilepsy use to cope with seizures and optimize health. This report describes the implementation and evolution of the Managing Epilepsy Well Network Database (MEW DB), an integrated data resource intended to advance knowledge on ESM. The MEW DB utilizes a three-tiered (Tier 1-3) system of data organization, with tiers of data generally increasing in ascending complexity or collection burden. A MEW DB Steering Committee (SC) establishes consensus on planned analyses using a standardized new analysis request template. The data management structure facilitates harmonization and integration of additional data, or to update the database as new data become available. The current MEW DB comprises 1,563 people with epilepsy. Mean age was 39.9 years, 64.9% women (N = 1006), 12.8% African American (N = 170), 22.2% Hispanic (N = 306). On average, individuals have lived with epilepsy since their early 20s and are prescribed between 1 and 2 antiepileptic drugs. The MEW DB spans multiple socio-ecological levels to provide a robust multi-tiered framework for studying ESM. A total of 41 common data elements have been identified through iterative consensus. This integrated database takes advantage of an extensive collective background of archival evidence in ESM and brings together engaged investigators to build a dataset that represents diverse types of individuals with epilepsy, targets health domains important to ESM, and facilitates analyses that would not be possible with sites operating independently. Overall, the MEW DB serves the greater mission of this research collaborative and has potential to advance ESM research.}, } @article {pmid33421615, year = {2021}, author = {Mikula, O and Nicolas, V and Šumbera, R and Konečný, A and Denys, C and Verheyen, E and Bryjová, A and Lemmon, AR and Moriarty Lemmon, E and Bryja, J}, title = {Nuclear phylogenomics, but not mitogenomics, resolves the most successful Late Miocene radiation of African mammals (Rodentia: Muridae: Arvicanthini).}, journal = {Molecular phylogenetics and evolution}, volume = {157}, number = {}, pages = {107069}, doi = {10.1016/j.ympev.2021.107069}, pmid = {33421615}, issn = {1095-9513}, mesh = {Africa South of the Sahara ; Animals ; Bayes Theorem ; Cell Nucleus/*genetics ; DNA, Mitochondrial/genetics ; Databases as Topic ; Genetic Loci ; *Genome, Mitochondrial ; Murinae/*classification/*genetics ; Phylogeny ; Species Specificity ; }, abstract = {The tribe Arvicanthini (Muridae: Murinae) is a highly diversified group of rodents (ca. 100 species) and with 18 African genera (plus one Asiatic) represents probably the most successful adaptive radiation of extant mammals in Africa. They colonized a broad spectrum of habitats (from rainforests to semi-deserts) in whole sub-Saharan Africa and their members often belong to most abundant parts of mammal communities. Despite intensive efforts, the phylogenetic relationships among major lineages (i.e. genera) remained obscured, which was likely caused by the intensive radiation of the group, dated to the Late Miocene. Here we used genomic scale data (377 nuclear loci; 581,030 bp) and produced the first fully resolved species tree containing all currently delimited genera of the tribe. Mitogenomes were also extracted, and while the results were largely congruent, there was less resolution at basal nodes of the mitochondrial phylogeny. Results of a fossil-based divergence dating analysis suggest that the African radiation started early after the colonization of Africa by a single arvicanthine ancestor from Asia during the Messinian stage (ca. 7 Ma), and was likely linked with a fragmentation of the pan-African Miocene forest. Some lineages remained in the rain forest, while many others successfully colonized broad spectrum of new open habitats (e.g. savannas, wetlands or montane moorlands) that appeared at the beginning of Pliocene. One lineage even evolved partially arboricolous life style in savanna woodlands, which allowed them to re-colonize equatorial forests. We also discuss delimitation of genera in Arvicanthini and propose corresponding taxonomic changes.}, } @article {pmid33421422, year = {2021}, author = {Hassine, TB and Ali, MB and Ghodhbane, I and Said, ZB and Hammami, S}, title = {Rabies in Tunisia: A spatio-temporal analysis in the region of CapBon-Nabeul.}, journal = {Acta tropica}, volume = {216}, number = {}, pages = {105822}, doi = {10.1016/j.actatropica.2021.105822}, pmid = {33421422}, issn = {1873-6254}, mesh = {Animals ; Disease Reservoirs/veterinary/virology ; Dog Diseases/*epidemiology ; Dogs/virology ; Geographic Information Systems ; Population Dynamics ; Rabies/*epidemiology/*veterinary ; *Seasons ; *Spatio-Temporal Analysis ; Tunisia/epidemiology ; }, abstract = {Human rabies is a significant public health concern in Tunisia. However, the spatiotemporal spread pattern of rabies in dogs, the major reservoir and vector, and its determinants are poorly understood. We collected geographic locations and timeline of reported animal rabies cases in the region of CapBon (study area), for the years 2015-2019 and integrated them in Geographical Information System (GIS) approach to explore the spatio-temporal pattern of dog rabies. The results show that roads and irrigated areas can act as ecological corridors to viral spread. Our study showed that there was a significant seasonal variation in the number of cases of rabies recorded, with a strong peak in spring and lower peak in winter and summer. These findings may play a role in updating and directing public health policy, as well as providing opportunities for authorities to explore control options in time and space. A better knowledge of the ecology and dog population dynamics is still necessary and important to achieve an effective rabies control.}, } @article {pmid33419455, year = {2021}, author = {Mehta, TK and Koch, C and Nash, W and Knaack, SA and Sudhakar, P and Olbei, M and Bastkowski, S and Penso-Dolfin, L and Korcsmaros, T and Haerty, W and Roy, S and Di-Palma, F}, title = {Evolution of regulatory networks associated with traits under selection in cichlids.}, journal = {Genome biology}, volume = {22}, number = {1}, pages = {25}, pmid = {33419455}, issn = {1474-760X}, support = {BB/J004669/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/T/000PR9817/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/CSP17270/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/J004529/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/P016774/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/M011216/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; Cichlids/*genetics/*metabolism ; DNA-Binding Proteins ; *Evolution, Molecular ; *Gene Regulatory Networks ; Genome ; Genotype ; Lakes ; Opsins/genetics/metabolism ; *Phenotype ; Phylogeny ; Transcription Factors ; }, abstract = {BACKGROUND: Seminal studies of vertebrate protein evolution speculated that gene regulatory changes can drive anatomical innovations. However, very little is known about gene regulatory network (GRN) evolution associated with phenotypic effect across ecologically diverse species. Here we use a novel approach for comparative GRN analysis in vertebrate species to study GRN evolution in representative species of the most striking examples of adaptive radiations, the East African cichlids. We previously demonstrated how the explosive phenotypic diversification of East African cichlids can be attributed to diverse molecular mechanisms, including accelerated regulatory sequence evolution and gene expression divergence.

RESULTS: To investigate these mechanisms across species at a genome-wide scale, we develop a novel computational pipeline that predicts regulators for co-extant and ancestral co-expression modules along a phylogeny, and candidate regulatory regions associated with traits under selection in cichlids. As a case study, we apply our approach to a well-studied adaptive trait-the visual system-for which we report striking cases of network rewiring for visual opsin genes, identify discrete regulatory variants, and investigate their association with cichlid visual system evolution. In regulatory regions of visual opsin genes, in vitro assays confirm that transcription factor binding site mutations disrupt regulatory edges across species and segregate according to lake species phylogeny and ecology, suggesting GRN rewiring in radiating cichlids.

CONCLUSIONS: Our approach reveals numerous novel potential candidate regulators and regulatory regions across cichlid genomes, including some novel and some previously reported associations to known adaptive evolutionary traits.}, } @article {pmid33418911, year = {2021}, author = {Leão, T and Wang, M and Moss, N and da Silva, R and Sanders, J and Nurk, S and Gurevich, A and Humphrey, G and Reher, R and Zhu, Q and Belda-Ferre, P and Glukhov, E and Whitner, S and Alexander, KL and Rex, R and Pevzner, P and Dorrestein, PC and Knight, R and Bandeira, N and Gerwick, WH and Gerwick, L}, title = {A Multi-Omics Characterization of the Natural Product Potential of Tropical Filamentous Marine Cyanobacteria.}, journal = {Marine drugs}, volume = {19}, number = {1}, pages = {}, pmid = {33418911}, issn = {1660-3397}, support = {GM107550/NH/NIH HHS/United States ; GM118815//National Institute of Health/ ; 13425-13-7//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; T32 GM067550/NH/NIH HHS/United States ; 19-16-00049//Russian Science Foundation/ ; }, mesh = {Biological Products/*pharmacology ; Chromatography, High Pressure Liquid ; Cyanobacteria/*chemistry/genetics ; Genome, Bacterial ; Genomics ; Marine Biology ; Mass Spectrometry ; Metabolomics ; Multigene Family ; Phylogeny ; Tropical Climate ; }, abstract = {Microbial natural products are important for the understanding of microbial interactions, chemical defense and communication, and have also served as an inspirational source for numerous pharmaceutical drugs. Tropical marine cyanobacteria have been highlighted as a great source of new natural products, however, few reports have appeared wherein a multi-omics approach has been used to study their natural products potential (i.e., reports are often focused on an individual natural product and its biosynthesis). This study focuses on describing the natural product genetic potential as well as the expressed natural product molecules in benthic tropical cyanobacteria. We collected from several sites around the world and sequenced the genomes of 24 tropical filamentous marine cyanobacteria. The informatics program antiSMASH was used to annotate the major classes of gene clusters. BiG-SCAPE phylum-wide analysis revealed the most promising strains for natural product discovery among these cyanobacteria. LCMS/MS-based metabolomics highlighted the most abundant molecules and molecular classes among 10 of these marine cyanobacterial samples. We observed that despite many genes encoding for peptidic natural products, peptides were not as abundant as lipids and lipopeptides in the chemical extracts. Our results highlight a number of highly interesting biosynthetic gene clusters for genome mining among these cyanobacterial samples.}, } @article {pmid33418146, year = {2021}, author = {Tomazatos, A and von Possel, R and Pekarek, N and Holm, T and Rieger, T and Baum, H and Bialonski, A and Maranda, I and Erdelyi-Molnár, I and Spînu, M and Lühken, R and Jansen, S and Emmerich, P and Schmidt-Chanasit, J and Cadar, D}, title = {Discovery and genetic characterization of a novel orthonairovirus in Ixodes ricinus ticks from Danube Delta.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {88}, number = {}, pages = {104704}, doi = {10.1016/j.meegid.2021.104704}, pmid = {33418146}, issn = {1567-7257}, mesh = {A549 Cells ; Animals ; Antibodies, Viral ; Arthropod Vectors/*virology ; Birds ; Cattle ; Cell Line ; Chlorocebus aethiops ; Dogs ; Genome, Viral ; High-Throughput Nucleotide Sequencing ; Host Microbial Interactions ; Humans ; Ixodes/*virology ; Madin Darby Canine Kidney Cells ; Mice ; Mice, Inbred C57BL ; Nucleoproteins/genetics/metabolism ; Phylogeny ; Serologic Tests ; Tick-Borne Diseases/virology ; Vero Cells ; Viral Proteins/genetics/metabolism ; Virus Diseases/virology ; Viruses/*classification/*genetics/immunology/*metabolism ; }, abstract = {Different arthropod species are vectors of a wide array of arboviruses (arthropod-borne viruses) and have likely been central to viral evolution. To better understand the extent of arthropod-borne pathogens, as well as their origin and evolutionary history, it is crucial to uncover the full range of microbial agents, including viruses associated with arthropods. In this study, a collection of ticks obtained in 2016 directly from mammal and bird hosts from several rural and natural sites of Danube Delta was subjected to transcriptome sequencing and amplification assays. Vector surveillance revealed the presence of a novel orthonairovirus species, designated Sulina virus, in Ixodes ricinus ticks. Phylogenetic clustering of each viral protein consistently placed the new virus in the Orthonairovirus genus as a new genogroup closely related to Tamdy orthonairovirus, a genogroup comprising both pathogenic and tick-associated orthonairoviruses. The serological testing of engorged ticks and blood of infected hosts, along with the inoculation of vertebrate cells and mice found no specific antibodies or viral replication, suggesting that Sulina virus is an orthonairovirus associated with the virome of Ixodes ricinus. Finally, the characterization of a novel orthonairovirus identified using high throughput sequencing will advance our knowledge of interactions between viruses and tick vectors, expanding our perspective on fundamental questions regarding orthonairovirus evolution, diversity, ecology and potential of emergence as pathogens.}, } @article {pmid33412560, year = {2021}, author = {Ursell, T}, title = {Structured environments foster competitor coexistence by manipulating interspecies interfaces.}, journal = {PLoS computational biology}, volume = {17}, number = {1}, pages = {e1007762}, pmid = {33412560}, issn = {1553-7358}, mesh = {Animals ; Computational Biology ; *Computer Simulation ; *Ecosystem ; *Microbial Consortia ; *Microbial Interactions ; *Models, Biological ; }, abstract = {Natural environments, like soils or the mammalian gut, frequently contain microbial consortia competing within a niche, wherein many species contain genetically encoded mechanisms of interspecies competition. Recent computational work suggests that physical structures in the environment can stabilize local competition between species that would otherwise be subject to competitive exclusion under isotropic conditions. Here we employ Lotka-Volterra models to show that interfacial competition localizes to physical structures, stabilizing competitive ecological networks of many species, even with significant differences in the strength of competitive interactions between species. Within a limited range of parameter space, we show that for stable communities the length-scale of physical structure inversely correlates with the width of the distribution of competitive fitness, such that physical environments with finer structure can sustain a broader spectrum of interspecific competition. These results highlight the potentially stabilizing effects of physical structure on microbial communities and lay groundwork for engineering structures that stabilize and/or select for diverse communities of ecological, medical, or industrial utility.}, } @article {pmid33412253, year = {2021}, author = {Shi, X and Guan, K and Peng, X and Xu, B and Zhou, X and Wang, S and Xu, S and Zheng, M and Huang, J and Wan, X and Guan, W and Su, KP and Ye, M and Gao, X and Yin, Z and Li, X}, title = {Ghrelin modulates dopaminergic neuron formation and attention deficit hyperactivity disorder-like behaviors: From animals to human models.}, journal = {Brain, behavior, and immunity}, volume = {94}, number = {}, pages = {327-337}, doi = {10.1016/j.bbi.2020.12.029}, pmid = {33412253}, issn = {1090-2139}, mesh = {Animals ; *Attention Deficit Disorder with Hyperactivity/genetics ; Child ; Dopaminergic Neurons ; Ghrelin ; Humans ; Impulsive Behavior ; Zebrafish ; }, abstract = {Attention deficit hyperactivity disorder (ADHD) is one of the most prevalent psychiatric disorders in children. The orexigenic hormone ghrelin is important in neuroprotection and neurodevelopment, which may play an important role in psychopathogenesis of ADHD. This study aimed to systematically investigate the genomic and pharmacological manipulations of ghrelin functioning in ADHD-like symptoms in zebrafish models and validated the effects of ghrelin polymorphisms in human subjects with ADHD. We firstly generated ghrelin[Δ/Δ] zebrafish mutant, which displayed hyperactive, attention deficit-like and impulsive-like behaviors, as well as endophenotypes, mimicking human ADHD. Ghrelin[Δ/Δ] zebrafish exhibited downregulated expression levels of wnt1, wnt3a, wnt5a that are critical for dopaminergic neuron development to possibly regulate their number and spatial organization. Pharmacological blockade of wnt signaling with XAV939 induced a reduced moving activity and less dopaminergic neurons; whereas, wnt agonist SB415286 rescued hyperactivity and dopaminergic neuron loss in ghrelin[Δ/Δ] zebrafish. In addition, we further identified and validated a SNP, rs696217, on orexigenic hormone preproghrelin/ghrelin (T408T, Met72Met) to be associated with a higher risk of ADHD in a case-controlled association study with 248 subjects with ADHD and 208 subjects of healthy controls. Together, our results reveal a novel endogenous role for orexigenic hormone ghrelin in ADHD, which provides insights into genetic regulation and drug screens for the identification of novel treatments of ADHD.}, } @article {pmid33410920, year = {2021}, author = {Huang, X and Zhang, H and Guo, R and Wang, Q and Liu, X and Kuang, W and Song, H and Liao, J and Huang, Y and Wang, Z}, title = {Systematic identification and characterization of circular RNAs involved in flag leaf senescence of rice.}, journal = {Planta}, volume = {253}, number = {2}, pages = {26}, pmid = {33410920}, issn = {1432-2048}, support = {JXXTCX201701-04//Jiangxi Special Fund for Agro-scientific Research in the Collaborative Innovation/ ; 31760380//National Natural Science Foundation of China/ ; 20181BAB214011//Jiangxi Provincial Department of Science and Technology/ ; GJJ170247//Education Department of Jiangxi Province/ ; }, mesh = {*Aging/genetics ; Gene Ontology ; MicroRNAs/metabolism ; *Oryza/genetics ; *Plant Leaves/genetics ; *RNA, Circular/genetics/metabolism ; RNA, Messenger/metabolism ; }, abstract = {Circular RNAs (circRNAs) identification, expression profiles, and construction of circRNA-parental gene relationships and circRNA-miRNA-mRNA ceRNA networks indicate that circRNAs are involved in flag leaf senescence of rice. Circular RNAs (circRNAs) are a class of 3'-5' head-to-tail covalently closed non-coding RNAs which have been proved to play important roles in various biological processes. However, no systematic identification of circRNAs associated with leaf senescence in rice has been studied. In this study, a genome-wide high-throughput sequencing analysis was performed using rice flag leaves developing from normal to senescence. Here, a total of 6612 circRNAs were identified, among which, 113 circRNAs were differentially expressed (DE) during the leaf senescence process. Moreover, 4601 (69.59%) circRNAs were derived from the exons or introns of their parental genes, while 2110 (71%) of the parental genes produced only one circRNA. The sequence alignment analysis showed that hundreds of rice circRNAs were conserved among different plant species. Gene Ontology (GO) enrichment analysis revealed that parental genes of DE circRNAs were enriched in many biological processes closely related to leaf senescence. Through weighted gene co-expression network analysis (WGCNA), six continuously down-expressed circRNAs, 18 continuously up-expressed circRNAs and 15 turn-point high-expressed circRNAs were considered to be highly associated with leaf senescence. Additionally, a total of 17 senescence-associated circRNAs were predicted to have parental genes, in which, regulations of three circRNAs to their parental genes were validated by qRT-PCR. The competing endogenous RNA (ceRNA) networks were also constructed. And a total of 11 senescence-associated circRNAs were predicted to act as miRNA sponges to regulate mRNAs, in which, regulation of two circRNAs to eight mRNAs was validated by qRT-PCR. It is discussed that senescence-associated circRNAs were involved in flag leaf senescence probably through mediating their parental genes and ceRNA networks, to participate in several well-studied senescence-associated processes, mainly including the processes of transcription, translation, and posttranslational modification (especially protein glycosylation), oxidation-reduction process, involvement of senescence-associated genes, hormone signaling pathway, proteolysis, and DNA damage repair. This study not only showed the systematic identification of circRNAs involved in leaf senescence of rice, but also laid a foundation for functional research on candidate circRNAs.}, } @article {pmid33408411, year = {2021}, author = {Zhou, Y and Shearwin-Whyatt, L and Li, J and Song, Z and Hayakawa, T and Stevens, D and Fenelon, JC and Peel, E and Cheng, Y and Pajpach, F and Bradley, N and Suzuki, H and Nikaido, M and Damas, J and Daish, T and Perry, T and Zhu, Z and Geng, Y and Rhie, A and Sims, Y and Wood, J and Haase, B and Mountcastle, J and Fedrigo, O and Li, Q and Yang, H and Wang, J and Johnston, SD and Phillippy, AM and Howe, K and Jarvis, ED and Ryder, OA and Kaessmann, H and Donnelly, P and Korlach, J and Lewin, HA and Graves, J and Belov, K and Renfree, MB and Grutzner, F and Zhou, Q and Zhang, G}, title = {Platypus and echidna genomes reveal mammalian biology and evolution.}, journal = {Nature}, volume = {592}, number = {7856}, pages = {756-762}, pmid = {33408411}, issn = {1476-4687}, support = {615253/ERC_/European Research Council/International ; 677696/ERC_/European Research Council/International ; /HHMI/Howard Hughes Medical Institute/United States ; }, mesh = {Animals ; *Biological Evolution ; Female ; *Genome ; Male ; Mammals/genetics ; Phylogeny ; Platypus/*genetics ; Sex Chromosomes/genetics ; Tachyglossidae/*genetics ; }, abstract = {Egg-laying mammals (monotremes) are the only extant mammalian outgroup to therians (marsupial and eutherian animals) and provide key insights into mammalian evolution[1,2]. Here we generate and analyse reference genomes of the platypus (Ornithorhynchus anatinus) and echidna (Tachyglossus aculeatus), which represent the only two extant monotreme lineages. The nearly complete platypus genome assembly has anchored almost the entire genome onto chromosomes, markedly improving the genome continuity and gene annotation. Together with our echidna sequence, the genomes of the two species allow us to detect the ancestral and lineage-specific genomic changes that shape both monotreme and mammalian evolution. We provide evidence that the monotreme sex chromosome complex originated from an ancestral chromosome ring configuration. The formation of such a unique chromosome complex may have been facilitated by the unusually extensive interactions between the multi-X and multi-Y chromosomes that are shared by the autosomal homologues in humans. Further comparative genomic analyses unravel marked differences between monotremes and therians in haptoglobin genes, lactation genes and chemosensory receptor genes for smell and taste that underlie the ecological adaptation of monotremes.}, } @article {pmid33400719, year = {2021}, author = {Porter, WT and Barrand, ZA and Wachara, J and DaVall, K and Mihaljevic, JR and Pearson, T and Salkeld, DJ and Nieto, NC}, title = {Predicting the current and future distribution of the western black-legged tick, Ixodes pacificus, across the Western US using citizen science collections.}, journal = {PloS one}, volume = {16}, number = {1}, pages = {e0244754}, pmid = {33400719}, issn = {1932-6203}, mesh = {*Animal Distribution ; Animals ; Arthropod Vectors/growth & development/physiology ; California ; *Citizen Science ; Climate ; Climate Change ; Humans ; Ixodes/growth & development/*physiology ; Lyme Disease/transmission ; Northwestern United States ; Seasons ; Tick Infestations/parasitology ; }, abstract = {In the twenty-first century, ticks and tick-borne diseases have expanded their ranges and impact across the US. With this spread, it has become vital to monitor vector and disease distributions, as these shifts have public health implications. Typically, tick-borne disease surveillance (e.g., Lyme disease) is passive and relies on case reports, while disease risk is calculated using active surveillance, where researchers collect ticks from the environment. Case reports provide the basis for estimating the number of cases; however, they provide minimal information on vector population or pathogen dynamics. Active surveillance monitors ticks and sylvatic pathogens at local scales, but it is resource-intensive. As a result, data are often sparse and aggregated across time and space to increase statistical power to model or identify range changes. Engaging public participation in surveillance efforts allows spatially and temporally diverse samples to be collected with minimal effort. These citizen-driven tick collections have the potential to provide a powerful tool for tracking vector and pathogen changes. We used MaxEnt species distribution models to predict the current and future distribution of Ixodes pacificus across the Western US through the use of a nationwide citizen science tick collection program. Here, we present niche models produced through citizen science tick collections over two years. Despite obvious limitations with citizen science collections, the models are consistent with previously-predicted species ranges in California that utilized more than thirty years of traditional surveillance data. Additionally, citizen science allows for an expanded understanding of I. pacificus distribution in Oregon and Washington. With the potential for rapid environmental changes instigated by a burgeoning human population and rapid climate change, the development of tools, concepts, and methodologies that provide rapid, current, and accurate assessment of important ecological qualities will be invaluable for monitoring and predicting disease across time and space.}, } @article {pmid33397434, year = {2021}, author = {Della Coletta, R and Qiu, Y and Ou, S and Hufford, MB and Hirsch, CN}, title = {How the pan-genome is changing crop genomics and improvement.}, journal = {Genome biology}, volume = {22}, number = {1}, pages = {3}, pmid = {33397434}, issn = {1474-760X}, mesh = {Computational Biology ; Crops, Agricultural/*genetics ; DNA Transposable Elements ; Genetic Variation ; *Genome, Plant ; Genomics/*methods ; }, abstract = {Crop genomics has seen dramatic advances in recent years due to improvements in sequencing technology, assembly methods, and computational resources. These advances have led to the development of new tools to facilitate crop improvement. The study of structural variation within species and the characterization of the pan-genome has revealed extensive genome content variation among individuals within a species that is paradigm shifting to crop genomics and improvement. Here, we review advances in crop genomics and how utilization of these tools is shifting in light of pan-genomes that are becoming available for many crop species.}, } @article {pmid33395940, year = {2021}, author = {Dorne, JLCM and Richardson, J and Livaniou, A and Carnesecchi, E and Ceriani, L and Baldin, R and Kovarich, S and Pavan, M and Saouter, E and Biganzoli, F and Pasinato, L and Zare Jeddi, M and Robinson, TP and Kass, GEN and Liem, AKD and Toropov, AA and Toropova, AP and Yang, C and Tarkhov, A and Georgiadis, N and Di Nicola, MR and Mostrag, A and Verhagen, H and Roncaglioni, A and Benfenati, E and Bassan, A}, title = {EFSA's OpenFoodTox: An open source toxicological database on chemicals in food and feed and its future developments.}, journal = {Environment international}, volume = {146}, number = {}, pages = {106293}, doi = {10.1016/j.envint.2020.106293}, pmid = {33395940}, issn = {1873-6750}, mesh = {Animals ; Databases, Factual ; *Food ; *Food Safety ; Humans ; Quantitative Structure-Activity Relationship ; Risk Assessment ; }, abstract = {Since its creation in 2002, the European Food Safety Authority (EFSA) has produced risk assessments for over 5000 substances in >2000 Scientific Opinions, Statements and Conclusions through the work of its Scientific Panels, Units and Scientific Committee. OpenFoodTox is an open source toxicological database, available both for download and data visualisation which provides data for all substances evaluated by EFSA including substance characterisation, links to EFSA's outputs, applicable legislations regulations, and a summary of hazard identification and hazard characterisation data for human health, animal health and ecological assessments. The database has been structured using OECD harmonised templates for reporting chemical test summaries (OHTs) to facilitate data sharing with stakeholders with an interest in chemical risk assessment, such as sister agencies, international scientific advisory bodies, and others. This manuscript provides a description of OpenFoodTox including data model, content and tools to download and search the database. Examples of applications of OpenFoodTox in chemical risk assessment are discussed including new quantitative structure-activity relationship (QSAR) models, integration into tools (OECD QSAR Toolbox and AMBIT-2.0), assessment of environmental footprints and testing of threshold of toxicological concern (TTC) values for food related compounds. Finally, future developments for OpenFoodTox 2.0 include the integration of new properties, such as physico-chemical properties, exposure data, toxicokinetic information; and the future integration within in silico modelling platforms such as QSAR models and physiologically-based kinetic models. Such structured in vivo, in vitro and in silico hazard data provide different lines of evidence which can be assembled, weighed and integrated using harmonised Weight of Evidence approaches to support the use of New Approach Methodologies (NAMs) in chemical risk assessment and the reduction of animal testing.}, } @article {pmid33392900, year = {2021}, author = {Keshavarzi, A and Kumar, V and Ertunç, G and Brevik, EC}, title = {Ecological risk assessment and source apportionment of heavy metals contamination: an appraisal based on the Tellus soil survey.}, journal = {Environmental geochemistry and health}, volume = {43}, number = {5}, pages = {2121-2142}, pmid = {33392900}, issn = {1573-2983}, mesh = {Agriculture ; Cities ; Databases, Factual ; Ecology ; Environmental Monitoring/methods ; Environmental Pollution/analysis ; Humans ; Ireland ; Metals, Heavy/*analysis/toxicity ; Multivariate Analysis ; Risk Assessment ; Soil/chemistry ; Soil Pollutants/*analysis ; Surveys and Questionnaires ; }, abstract = {It is imperative to comprehend the level and spatial distribution of soil pollution with heavy metals to find sustainable management approaches for affected soils. Selected heavy metals (Mn, Zn, Pb, Cu, Cr, Ni, As, Co, and Cd) and physiochemical parameters were appraised for 620 samples from industrial, agricultural and urban sites in Northern Ireland using the Tellus database. The findings of this study showed that among the analyzed heavy metals, Mn content was the highest and Cd content the lowest. Pearson's correlation analysis revealed that heavy metals were highly correlated with each other, signifying similar sources for the heavy metals. Mixed factors (anthropogenic and lithogenic) were responsible for the contribution of heavy metals as revealed by multivariate statistical analysis. The results of contamination factor and enrichment factor analyses suggest that As, Cd, and Pb showed very high risk for pollution in the study area. The geoaccumulation index revealed that with the exception of Cd, all analyzed heavy metals showed severe accumulation in the soils. The potential and modified ecological risk indices inferred that Cd, As, and Pb represented ecological threats in the soils of Northern Ireland. The findings of this study will aid in forming approaches to decrease the risks associated with heavy metals in industrial, urban and agricultural soils, and help create guidelines to protect the environment from long-term accumulation of heavy metals.}, } @article {pmid33391680, year = {2020}, author = {Módra, G and Maák, I and Lőrincz, Á and Juhász, O and Kiss, PJ and Lőrinczi, G}, title = {Protective behavior or 'true' tool use? Scrutinizing the tool use behavior of ants.}, journal = {Ecology and evolution}, volume = {10}, number = {24}, pages = {13787-13795}, pmid = {33391680}, issn = {2045-7758}, abstract = {In the genus Aphaenogaster, workers use tools to transport liquid food to the colony. During this behavior, ants place or drop various kinds of debris into liquids or soft food, and then, they carry the food-soaked tools back to the nest. According to some authors, this behavior is not "true" tool use because it represents two separate processes: a defense response to cover the dangerous liquid and a transport of food. Here, we investigated the debris dropping and retrieving behavior of the ant Aphaenogaster subterranea to establish which of the two hypotheses is more probable by conducting manipulative experiments. We tested the responses of eight colonies (a) to liquid food (honey-water) and nonfood liquids (water) in different distances from the nest and (b) to nonthreatening liquids previously covered or presented as small droplets. We also tested whether the nutritional condition of colonies (i.e., starved or satiated) would affect the intensity and rate of debris dropping. Our results were consistent with the tool-using behavior hypothesis. Firstly, ants clearly differentiated between honey-water and water, and they directed more of their foraging effort toward liquids farther from the nest. Secondly, ants performed object dropping even into liquids that did not pose the danger of drowning or becoming entangled. Lastly, the nutritional condition of colonies had a significant effect on the intensity and rate of object dropping, but in the opposite direction than we expected. Our results suggest that the foraging behavior of A. subterranea is more complex than that predicted by the two-component behavior hypothesis and deserves to be considered as "true" tool use.}, } @article {pmid33388087, year = {2021}, author = {Mang'era, CM and Khamis, FM and Awuoche, EO and Hassanali, A and Ombura, FLO and Mireji, PO}, title = {Transcriptomic response of Anopheles gambiae sensu stricto mosquito larvae to Curry tree (Murraya koenigii) phytochemicals.}, journal = {Parasites & vectors}, volume = {14}, number = {1}, pages = {1}, pmid = {33388087}, issn = {1756-3305}, support = {02691//Grand Challenges Canada/ ; }, mesh = {Animals ; Anopheles/*drug effects/*genetics ; Computational Biology ; Female ; *Gene Expression Profiling ; Insecticides/pharmacology ; Larva/*drug effects/genetics ; Metabolic Networks and Pathways/drug effects ; Mosquito Vectors/drug effects ; Murraya/*chemistry ; Phytochemicals/chemistry/*pharmacology ; Plant Leaves/chemistry ; }, abstract = {BACKGROUND: Insect growth regulators (IGRs) can control insect vector populations by disrupting growth and development in juvenile stages of the vectors. We previously identified and described the curry tree (Murraya koenigii (L.) Spreng) phytochemical leaf extract composition (neplanocin A, 3-(1-naphthyl)-L-alanine, lumiflavine, terezine C, agelaspongin and murrayazolinol), which disrupted growth and development in Anopheles gambiae sensu stricto mosquito larvae by inducing morphogenetic abnormalities, reducing locomotion and delaying pupation in the mosquito. Here, we attempted to establish the transcriptional process in the larvae that underpins these phenotypes in the mosquito.

METHODS: We first exposed third-fourth instar larvae of the mosquito to the leaf extract and consequently the inherent phytochemicals (and corresponding non-exposed controls) in two independent biological replicates. We collected the larvae for our experiments sampled 24 h before peak pupation, which was 7 and 18 days post-exposure for controls and exposed larvae, respectively. The differences in duration to peak pupation were due to extract-induced growth delay in the larvae. The two study groups (exposed vs control) were consequently not age-matched. We then sequentially (i) isolated RNA (whole larvae) from each replicate treatment, (ii) sequenced the RNA on Illumina HiSeq platform, (iii) performed differential bioinformatics analyses between libraries (exposed vs control) and (iv) independently validated the transcriptome expression profiles through RT-qPCR.

RESULTS: Our analyses revealed significant induction of transcripts predominantly associated with hard cuticular proteins, juvenile hormone esterases, immunity and detoxification in the larvae samples exposed to the extract relative to the non-exposed control samples. Our analysis also revealed alteration of pathways functionally associated with putrescine metabolism and structural constituents of the cuticle in the extract-exposed larvae relative to the non-exposed control, putatively linked to the exoskeleton and immune response in the larvae. The extract-exposed larvae also appeared to have suppressed pathways functionally associated with molting, cell division and growth in the larvae. However, given the age mismatch between the extract-exposed and non-exposed larvae, we can attribute the modulation of innate immune, detoxification, cuticular and associated transcripts and pathways we observed to effects of age differences among the larvae samples (exposed vs control) and to exposures of the larvae to the extract.

CONCLUSIONS: The exposure treatment appears to disrupt cuticular development, immune response and oxidative stress pathways in Anopheles gambiae s.s larvae. These pathways can potentially be targeted in development of more efficacious curry tree phytochemical-based IGRs against An. gambiae s.s mosquito larvae.}, } @article {pmid33380617, year = {2020}, author = {Tomanic, M and Soldatovic, I and Jovanovic, A and Vukasinovic, D and Maksimovic, M}, title = {Translation, adaptation and validation of the youth attitude to noise scale (YANS) questionnaire into serbian language.}, journal = {Noise & health}, volume = {22}, number = {105}, pages = {56-61}, pmid = {33380617}, issn = {1998-4030}, mesh = {Adolescent ; *Attitude ; Factor Analysis, Statistical ; Female ; Humans ; Language ; Male ; *Noise ; Psychiatric Status Rating Scales/*standards ; Psychometrics ; Reproducibility of Results ; Schools ; Serbia ; Students/*psychology ; Surveys and Questionnaires/*standards ; Translations ; }, abstract = {CONTEXT: Several language variations of YANS have been published. There is a rationale in grouping languages where one variation is usable for several countries. The people of four ex-Yugoslavian countries do speak practically one language whatever its present name.

AIM: To make a Serbian version of YANS which would be usable in Serbia, Croatia, Bosnia and Herzegovina and Montenegro.

SETTINGS AND DESIGN: Translation and test-retest survey in a secondary school.

MATERIAL AND METHODS: The translation process was performed according to the relevant guidelines through a standard procedure: English-Serbian-English-Consensus (people fluent in English)-Pilot assessment (20 students). The survey was performed in a Belgrade high school. Test YANS was completed by 244 students (response rate 98,8%, males 44%). Retest YANS was carried out among 60 randomly chosen students from the primary sample (response rate 96.7%, males 58%). In the statistical analysis we used the Olsen's model of classification as well as previous validation of YANS. A reliability measure for analyzing survey items was Cronbach's alpha. Determination of the mean differences between test and retest with respect to normal distribution of data was performed with the Student's paired t-test.

RESULTS: Factor analysis between items grouped into four factors showed no significant association, except for a weak but negative one between two specific factors. The internal reliability (Cronbach's alpha) was 0.721 and assessed as acceptable. The test-retest comparison did not reveal any significant differences. Mean overall YANS score was 2.76, which is higher than on testing in Sweden, very similar to the Brazilian one, and lower than in Belgium and China.

CONCLUSION: Serbian version of YANS is a valid and reliable research instrument. It may also be used in Croatia, Bosnia and Herzegovina and Montenegro.}, } @article {pmid33378381, year = {2020}, author = {Laso-Jadart, R and Ambroise, C and Peterlongo, P and Madoui, MA}, title = {metaVaR: Introducing metavariant species models for reference-free metagenomic-based population genomics.}, journal = {PloS one}, volume = {15}, number = {12}, pages = {e0244637}, pmid = {33378381}, issn = {1932-6203}, mesh = {Cluster Analysis ; Computational Biology/*methods ; *Genetic Variation ; Genetics, Population ; Metagenomics/*methods ; Models, Genetic ; Selection, Genetic ; Software ; }, abstract = {The availability of large metagenomic data offers great opportunities for the population genomic analysis of uncultured organisms, which represent a large part of the unexplored biosphere and play a key ecological role. However, the majority of these organisms lack a reference genome or transcriptome, which constitutes a technical obstacle for classical population genomic analyses. We introduce the metavariant species (MVS) model, in which a species is represented only by intra-species nucleotide polymorphism. We designed a method combining reference-free variant calling, multiple density-based clustering and maximum-weighted independent set algorithms to cluster intra-species variants into MVSs directly from multisample metagenomic raw reads without a reference genome or read assembly. The frequencies of the MVS variants are then used to compute population genomic statistics such as FST, in order to estimate genomic differentiation between populations and to identify loci under natural selection. The MVS construction was tested on simulated and real metagenomic data. MVSs showed the required quality for robust population genomics and allowed an accurate estimation of genomic differentiation (ΔFST < 0.0001 and <0.03 on simulated and real data respectively). Loci predicted under natural selection on real data were all detected by MVSs. MVSs represent a new paradigm that may simplify and enhance holistic approaches for population genomics and the evolution of microorganisms.}, } @article {pmid33376754, year = {2020}, author = {McKay, B and Ebell, M and Billings, WZ and Dale, AP and Shen, Y and Handel, A}, title = {Associations Between Relative Viral Load at Diagnosis and Influenza A Symptoms and Recovery.}, journal = {Open forum infectious diseases}, volume = {7}, number = {11}, pages = {ofaa494}, pmid = {33376754}, issn = {2328-8957}, support = {U19 AI117891/AI/NIAID NIH HHS/United States ; U54 GM111274/GM/NIGMS NIH HHS/United States ; }, abstract = {BACKGROUND: Rapid point-of-care polymerase chain reaction (PCR) diagnostic tests generally provide a qualitative result of positive or negative only. Additional information about the relative viral load could be calculated. Such quantitative information might be useful for making treatment decisions.

METHODS: We enrolled students at a university health center who presented with cough and 1 additional flu-like symptom from December 2016 to February 2017. Data were collected before, during, and 5 days after the clinic visit. All those enrolled in the study received a point-of-care PCR test (cobas Liat). For those patients that tested positive for influenza A, we investigated correlations between the relative viral load and measures of disease severity and recovery.

RESULTS: One hundred thirty-five students tested positive for influenza A. We found a positive correlation between viral load and body temperature. Time since symptom onset seemed to have a negative correlation but was not statistically significant. We did not find any correlations between viral load and overall symptom severity or outcomes related to recovery.

CONCLUSIONS: Although we found a correlation between relative viral load and body temperature, for our study population of young, overall healthy adults, we did not find that relative viral load provided additional information that could help in determining treatment and disease outcomes. It could be that viral load does provide useful additional information for other groups of patients, such as young children or older adults. Further studies on those populations are warranted.}, } @article {pmid33374586, year = {2020}, author = {Ghafar, A and Koehler, AV and Hall, RS and Gauci, CG and Gasser, RB and Jabbar, A}, title = {Targeted Next-Generation Sequencing and Informatics as an Effective Tool to Establish the Composition of Bovine Piroplasm Populations in Endemic Regions.}, journal = {Microorganisms}, volume = {9}, number = {1}, pages = {}, pmid = {33374586}, issn = {2076-2607}, abstract = {Protists of the genera Babesia and Theileria (piroplasms) cause some of the most prevalent and debilitating diseases for bovines worldwide. In this study, we established and used a next-generation sequencing-informatic approach to explore the composition of Babesia and Theileria populations in cattle and water buffalo in a country (Pakistan) endemic for these pathogens. We collected individual blood samples from cattle (n = 212) and water buffalo (n = 154), extracted genomic DNAs, PCR-amplified the V4 hypervariable region of 18S small subunit rRNA gene from piroplasms, sequenced amplicons using Illumina technology, and then analysed data using bioinformatic platforms. The results revealed piroplasms in 68.9% (252/366) samples, with overall occurrence being markedly higher in cattle (85.8%) than in water buffaloes (45.5%). Babesia (B.) occultans and Theileria (T.) lestoquardi-like species were recorded for the first time in Pakistan, and, overall, T. annulata was most commonly detected (65.8%) followed by B. bovis (7.1%), B. bigemina (4.4%), and T. orientalis (0.5%), with the genetic variability within B. bovis being pronounced. The occurrence and composition of piroplasm species varied markedly across different agro-ecological zones. The high detection of T. annulata in asymptomatic animals suggested a relatively high level of endemic stability of tropical theileriosis in the bovine population.}, } @article {pmid33372367, year = {2021}, author = {Lemm, JU and Venohr, M and Globevnik, L and Stefanidis, K and Panagopoulos, Y and van Gils, J and Posthuma, L and Kristensen, P and Feld, CK and Mahnkopf, J and Hering, D and Birk, S}, title = {Multiple stressors determine river ecological status at the European scale: Towards an integrated understanding of river status deterioration.}, journal = {Global change biology}, volume = {27}, number = {9}, pages = {1962-1975}, doi = {10.1111/gcb.15504}, pmid = {33372367}, issn = {1365-2486}, support = {//European Commission: FP7 Environment/ ; //Dutch 'Water Quality Knowledge Impulse' project/ ; }, mesh = {Ecosystem ; *Environmental Monitoring ; Hydrology ; *Rivers ; Water Quality ; }, abstract = {The biota of European rivers are affected by a wide range of stressors impairing water quality and hydro-morphology. Only about 40% of Europe's rivers reach 'good ecological status', a target set by the European Water Framework Directive (WFD) and indicated by the biota. It is yet unknown how the different stressors in concert impact ecological status and how the relationship between stressors and status differs between river types. We linked the intensity of seven stressors to recently measured ecological status data for more than 50,000 sub-catchment units (covering almost 80% of Europe's surface area), which were distributed among 12 broad river types. Stressor data were either derived from remote sensing data (extent of urban and agricultural land use in the riparian zone) or modelled (alteration of mean annual flow and of base flow, total phosphorous load, total nitrogen load and mixture toxic pressure, a composite metric for toxic substances), while data on ecological status were taken from national statutory reporting of the second WFD River Basin Management Plans for the years 2010-2015. We used Boosted Regression Trees to link ecological status to stressor intensities. The stressors explained on average 61% of deviance in ecological status for the 12 individual river types, with all seven stressors contributing considerably to this explanation. On average, 39.4% of the deviance was explained by altered hydro-morphology (morphology: 23.2%; hydrology: 16.2%), 34.4% by nutrient enrichment and 26.2% by toxic substances. More than half of the total deviance was explained by stressor interaction, with nutrient enrichment and toxic substances interacting most frequently and strongly. Our results underline that the biota of all European river types are determined by co-occurring and interacting multiple stressors, lending support to the conclusion that fundamental management strategies at the catchment scale are required to reach the ambitious objective of good ecological status of surface waters.}, } @article {pmid33371887, year = {2020}, author = {Ha, MJ and Kim, J and Galloway-Peña, J and Do, KA and Peterson, CB}, title = {Compositional zero-inflated network estimation for microbiome data.}, journal = {BMC bioinformatics}, volume = {21}, number = {Suppl 21}, pages = {581}, pmid = {33371887}, issn = {1471-2105}, support = {5R21CA220299-02/CA/NCI NIH HHS/United States ; P30CA016672/CA/NCI NIH HHS/United States ; K01 AI143881/AI/NIAID NIH HHS/United States ; UL1 TR003167/TR/NCATS NIH HHS/United States ; R21 CA220299/CA/NCI NIH HHS/United States ; }, mesh = {Computational Biology/*methods ; Humans ; Leukemia/microbiology ; *Microbiota ; }, abstract = {BACKGROUND: The estimation of microbial networks can provide important insight into the ecological relationships among the organisms that comprise the microbiome. However, there are a number of critical statistical challenges in the inference of such networks from high-throughput data. Since the abundances in each sample are constrained to have a fixed sum and there is incomplete overlap in microbial populations across subjects, the data are both compositional and zero-inflated.

RESULTS: We propose the COmpositional Zero-Inflated Network Estimation (COZINE) method for inference of microbial networks which addresses these critical aspects of the data while maintaining computational scalability. COZINE relies on the multivariate Hurdle model to infer a sparse set of conditional dependencies which reflect not only relationships among the continuous values, but also among binary indicators of presence or absence and between the binary and continuous representations of the data. Our simulation results show that the proposed method is better able to capture various types of microbial relationships than existing approaches. We demonstrate the utility of the method with an application to understanding the oral microbiome network in a cohort of leukemic patients.

CONCLUSIONS: Our proposed method addresses important challenges in microbiome network estimation, and can be effectively applied to discover various types of dependence relationships in microbial communities. The procedure we have developed, which we refer to as COZINE, is available online at https://github.com/MinJinHa/COZINE .}, } @article {pmid33370386, year = {2020}, author = {Ye, X and Yang, Z and Jiang, Y and Yu, L and Guo, R and Meng, Y and Shao, C}, title = {sRNATargetDigger: A bioinformatics software for bidirectional identification of sRNA-target pairs with co-regulatory sRNAs information.}, journal = {PloS one}, volume = {15}, number = {12}, pages = {e0244480}, pmid = {33370386}, issn = {1932-6203}, mesh = {Arabidopsis/genetics ; Computational Biology/*methods ; Data Mining/*methods ; Datasets as Topic ; Gene Expression Regulation, Plant ; *Gene Regulatory Networks ; High-Throughput Nucleotide Sequencing ; RNA Stability/genetics ; RNA, Small Untranslated/genetics/*metabolism ; *Software ; }, abstract = {Identification of the target genes of microRNAs (miRNAs), trans-acting small interfering RNAs (ta-siRNAs), and small interfering RNAs (siRNAs) is an important step for understanding their regulatory roles in plants. In recent years, many bioinformatics software packages based on small RNA (sRNA) high-throughput sequencing (HTS) and degradome sequencing data analysis have provided strong technical support for large-scale mining of sRNA-target pairs. However, sRNA-target regulation is achieved using a complex network of interactions since one transcript might be co-regulated by multiple sRNAs and one sRNA may also affect multiple targets. Currently used mining software can realize the mining of multiple unknown targets using known sRNA, but it cannot rule out the possibility of co-regulation of the same target by other unknown sRNAs. Hence, the obtained regulatory network may be incomplete. We have developed a new mining software, sRNATargetDigger, that includes two function modules, "Forward Digger" and "Reverse Digger", which can identify regulatory sRNA-target pairs bidirectionally. Moreover, it has the ability to identify unknown sRNAs co-regulating the same target, in order to obtain a more authentic and reliable sRNA-target regulatory network. Upon re-examination of the published sRNA-target pairs in Arabidopsis thaliana, sRNATargetDigger found 170 novel co-regulatory sRNA-target pairs. This software can be downloaded from http://www.bioinfolab.cn/sRNATD.html.}, } @article {pmid33367263, year = {2020}, author = {Cruzan, MB and Hendrickson, EC}, title = {Landscape Genetics of Plants: Challenges and Opportunities.}, journal = {Plant communications}, volume = {1}, number = {6}, pages = {100100}, pmid = {33367263}, issn = {2590-3462}, mesh = {*Ecosystem ; *Gene Flow ; Genetics, Population/*instrumentation ; Geographic Information Systems/*instrumentation ; Plant Dispersal/*genetics ; Plants/*genetics ; }, abstract = {Dispersal is one of the most important but least understood processes in plant ecology and evolutionary biology. Dispersal of seeds maintains and establishes populations, and pollen and seed dispersal are responsible for gene flow within and among populations. Traditional views of dispersal and gene flow assume models that are governed solely by geographic distance and do not account for variation in dispersal vector behavior in response to heterogenous landscapes. Landscape genetics integrates population genetics with Geographic Information Systems (GIS) to evaluate the effects of landscape features on gene flow patterns (effective dispersal). Surprisingly, relatively few landscape genetic studies have been conducted on plants. Plants present advantages because their populations are stationary, allowing more reliable estimates of the effects of landscape features on effective dispersal rates. On the other hand, plant dispersal is intrinsically complex because it depends on the habitat preferences of the plant and its pollen and seed dispersal vectors. We discuss strategies to assess the separate contributions of pollen and seed movement to effective dispersal and to delineate the effects of plant habitat quality from those of landscape features that affect vector behavior. Preliminary analyses of seed dispersal for three species indicate that isolation by landscape resistance is a better predictor of the rates and patterns of dispersal than geographic distance. Rates of effective dispersal are lower in areas of high plant habitat quality, which may be due to the effects of the shape of the dispersal kernel or to movement behaviors of biotic vectors. Landscape genetic studies in plants have the potential to provide novel insights into the process of gene flow among populations and to improve our understanding of the behavior of biotic and abiotic dispersal vectors in response to heterogeneous landscapes.}, } @article {pmid33365126, year = {2020}, author = {Allen, DC and Datry, T and Boersma, KS and Bogan, MT and Boulton, AJ and Bruno, D and Busch, MH and Costigan, KH and Dodds, WK and Fritz, KM and Godsey, SE and Jones, JB and Kaletova, T and Kampf, SK and Mims, MC and Neeson, TM and Olden, JD and Pastor, AV and Poff, NL and Ruddell, BL and Ruhi, A and Singer, G and Vezza, P and Ward, AS and Zimmer, M}, title = {River ecosystem conceptual models and non-perennial rivers: A critical review.}, journal = {WIREs. Water}, volume = {7}, number = {5}, pages = {}, pmid = {33365126}, issn = {2049-1948}, support = {EPA999999/ImEPA/Intramural EPA/United States ; }, abstract = {Conceptual models underpin river ecosystem research. However, current models focus on continuously flowing rivers and few explicitly address characteristics such as flow cessation and drying. The applicability of existing conceptual models to nonperennial rivers that cease to flow (intermittent rivers and ephemeral streams, IRES) has not been evaluated. We reviewed 18 models, finding that they collectively describe main drivers of biogeochemical and ecological patterns and processes longitudinally (upstream-downstream), laterally (channel-riparian-floodplain), vertically (surface water-groundwater), and temporally across local and landscape scales. However, perennial rivers are longitudinally continuous while IRES are longitudinally discontinuous. Whereas perennial rivers have bidirectional lateral connections between aquatic and terrestrial ecosystems, in IRES, this connection is unidirectional for much of the time, from terrestrial-to-aquatic only. Vertical connectivity between surface and subsurface water occurs bidirectionally and is temporally consistent in perennial rivers. However, in IRES, this exchange is temporally variable, and can become unidirectional during drying or rewetting phases. Finally, drying adds another dimension of flow variation to be considered across temporal and spatial scales in IRES, much as flooding is considered as a temporally and spatially dynamic process in perennial rivers. Here, we focus on ways in which existing models could be modified to accommodate drying as a fundamental process that can alter these patterns and processes across spatial and temporal dimensions in streams. This perspective is needed to support river science and management in our era of rapid global change, including increasing duration, frequency, and occurrence of drying.}, } @article {pmid33363575, year = {2020}, author = {Chakraborty, A and Viswanath, A and Malipatil, R and Rathore, A and Thirunavukkarasu, N}, title = {Structural and Functional Characteristics of miRNAs in Five Strategic Millet Species and Their Utility in Drought Tolerance.}, journal = {Frontiers in genetics}, volume = {11}, number = {}, pages = {608421}, pmid = {33363575}, issn = {1664-8021}, abstract = {Millets are the strategic food crops in arid and drought-prone ecologies. Millets, by virtue of nature, are very well-adapted to drought conditions and able to produce sustainable yield. Millets have important nutrients that can help prevent micro-nutrient malnutrition. As a result of the adverse effect of climate change and widespread malnutrition, millets have attained a strategic position to sustain food and nutritional security. Although millets can adapt well to the drought ecologies where other cereals fail completely, the yield level is very low under stress. There is a tremendous opportunity to increase the genetic potential of millet crops in dry lands when the genetics of the drought-tolerance mechanism is fully explained. MicroRNAs (miRNAs) are the class of small RNAs that control trait expression. They are part of the gene regulation but little studied in millets. In the present study, novel miRNAs and gene targets were identified from the genomic resources of pearl millet, sorghum, foxtail millet, finger millet, and proso millet through in silico approaches. A total of 1,002 miRNAs from 280 families regulating 23,158 targets were identified using different filtration criteria in five millet species. The unique as well as conserved structural features and functional characteristics of miRNA across millets were explained. About 84 miRNAs were conserved across millets in different species combinations, which explained the evolutionary relationship of the millets. Further, 215 miRNAs controlling 155 unique major drought-responsive genes, transcription factors, and protein families revealed the genetics of drought tolerance that are accumulated in the millet genomes. The miRNAs regulating the drought stress through specific targets or multiple targets showed through a network analysis. The identified genes regulated by miRNA genes could be useful in developing functional markers and used for yield improvement under drought in millets as well as in other crops.}, } @article {pmid33360552, year = {2021}, author = {Ngo, PT and Pham, TD and Hoang, ND and Tran, DA and Amiri, M and Le, TT and Hoa, PV and Bui, PV and Nhu, VH and Bui, DT}, title = {A new hybrid equilibrium optimized SysFor based geospatial data mining for tropical storm-induced flash flood susceptible mapping.}, journal = {Journal of environmental management}, volume = {280}, number = {}, pages = {111858}, doi = {10.1016/j.jenvman.2020.111858}, pmid = {33360552}, issn = {1095-8630}, mesh = {*Cyclonic Storms ; Data Mining ; *Floods ; Rivers ; Vietnam ; }, abstract = {Flash flood is one of the most dangerous hydrologic and natural phenomena and is considered as the top ranking of such events among various natural disasters due to their fast onset characteristics and the proportion of individual fatalities. Mapping the probability of flash flood events remains challenges because of its complexity and rapid onset of precipitation. Thus, this study aims to propose a state-of-the-art data mining approach based on a hybrid equilibrium optimized SysFor, namely, the HE-SysFor model, for spatial prediction of flash floods. A tropical storm region located in the Northwest areas of Vietnam is selected as a case study. For this purpose, 1866 flash-flooded locations and ten indicators were used. The results show that the proposed HE-SysFor model yielded the highest predictive performance (total accuracy = 93.8%, Kappa index = 0.875, F1-score = 0.939, and AUC = 0.975) and produced the better performance than those of the C4.5 decision tree (C4.5), the radial basis function-based support vector machine (SVM-RBF), the logistic regression (LReg), and deep learning neural network (DeepLNN) models in both the training and the testing phases. Among the ten indicators, elevation, slope, and land cover are the most important. It is concluded that the proposed model provides an alternative tool and may help for effectively monitoring flash floods in tropical areas and robust policies for decision making in mitigating the flash flood impacts.}, } @article {pmid33360234, year = {2021}, author = {Müller, AK and Markert, N and Leser, K and Kämpfer, D and Schiwy, S and Riegraf, C and Buchinger, S and Gan, L and Abdallah, AT and Denecke, B and Segner, H and Brinkmann, M and Crawford, SE and Hollert, H}, title = {Bioavailability and impacts of estrogenic compounds from suspended sediment on rainbow trout (Oncorhynchus mykiss).}, journal = {Aquatic toxicology (Amsterdam, Netherlands)}, volume = {231}, number = {}, pages = {105719}, doi = {10.1016/j.aquatox.2020.105719}, pmid = {33360234}, issn = {1879-1514}, mesh = {Animals ; Biological Availability ; Environmental Exposure ; Estrogens/*toxicity ; Female ; Gene Ontology ; Geologic Sediments/*chemistry ; Liver/drug effects/metabolism ; Male ; Oncorhynchus mykiss/*metabolism ; Vitellogenins/metabolism ; Water Pollutants, Chemical/toxicity ; }, abstract = {Numerous environmental pollutants have the potential to accumulate in sediments, and among them are endocrine-disrupting chemicals (EDCs). It is well documented that water-borne exposure concentrations of some potent EDCs, more specifically estrogenic- active compounds (ECs), can impair the reproduction of fish. In contrast, little is known about the bioavailability and effects of sediment-associated ECs on fish. Particularly, when sediments are disturbed, e.g., during flood events, chemicals may be released from the sediment and become bioavailable. The main objectives of this study were to evaluate a) whether ECs from the sediment become bioavailable to fish when the sediment is suspended, and b) whether such exposure leads to endocrine responses in fish. Juvenile rainbow trout (Oncorhynchus mykiss) were exposed over 21 days to constantly suspended sediments in the following treatments: i) a contaminated sediment from the Luppe River, representing a "hotspot" for EC accumulation, ii) a reference sediment (exhibiting only background contamination), iii) three dilutions, 2-, 4- and 8-fold of Luppe sediment diluted with the reference sediment, and iv) a water-only control. Measured estrogenic activity using in vitro bioassays as well as target analysis of nonylphenol and estrone via LC-MS/MS in sediment, water, fish plasma, as well as bile samples, confirmed that ECs became bioavailable from the sediment during suspension. ECs were dissolved in the water phase, as indicated by passive samplers, and were readily taken up by the exposed trout. An estrogenic response of fish to Luppe sediment was indicated by increased abundance of transcripts of typical estrogen responsive genes, i.e. vitelline envelope protein α in the liver and vitellogenin induction in the skin mucus. Altered gene expression profiles of trout in response to suspended sediment from the Luppe River suggest that in addition to ECs a number of other contaminants such as dioxins, polychlorinated biphenyls (PCBs) and heavy metals were remobilized during suspension. The results of the present study demonstrated that sediments not only function as a sink for ECs but can turn into a significant source of pollution when sediments are resuspended as during flood-events. This highlights the need for sediment quality criteria considering bioavailability sediment-bound contaminants in context of flood events.}, } @article {pmid33351797, year = {2020}, author = {Kloosterman, AM and Cimermancic, P and Elsayed, SS and Du, C and Hadjithomas, M and Donia, MS and Fischbach, MA and van Wezel, GP and Medema, MH}, title = {Expansion of RiPP biosynthetic space through integration of pan-genomics and machine learning uncovers a novel class of lanthipeptides.}, journal = {PLoS biology}, volume = {18}, number = {12}, pages = {e3001026}, pmid = {33351797}, issn = {1545-7885}, mesh = {Algorithms ; Bacteriocins/*genetics/metabolism ; Biological Products/analysis/metabolism ; Computational Biology/methods ; Genome/genetics ; Genomics/*methods ; Machine Learning ; Multigene Family/genetics ; Peptides/genetics ; Protein Processing, Post-Translational/*genetics/physiology ; Ribosomes/metabolism ; }, abstract = {Microbial natural products constitute a wide variety of chemical compounds, many which can have antibiotic, antiviral, or anticancer properties that make them interesting for clinical purposes. Natural product classes include polyketides (PKs), nonribosomal peptides (NRPs), and ribosomally synthesized and post-translationally modified peptides (RiPPs). While variants of biosynthetic gene clusters (BGCs) for known classes of natural products are easy to identify in genome sequences, BGCs for new compound classes escape attention. In particular, evidence is accumulating that for RiPPs, subclasses known thus far may only represent the tip of an iceberg. Here, we present decRiPPter (Data-driven Exploratory Class-independent RiPP TrackER), a RiPP genome mining algorithm aimed at the discovery of novel RiPP classes. DecRiPPter combines a Support Vector Machine (SVM) that identifies candidate RiPP precursors with pan-genomic analyses to identify which of these are encoded within operon-like structures that are part of the accessory genome of a genus. Subsequently, it prioritizes such regions based on the presence of new enzymology and based on patterns of gene cluster and precursor peptide conservation across species. We then applied decRiPPter to mine 1,295 Streptomyces genomes, which led to the identification of 42 new candidate RiPP families that could not be found by existing programs. One of these was studied further and elucidated as a representative of a novel subfamily of lanthipeptides, which we designate class V. The 2D structure of the new RiPP, which we name pristinin A3 (1), was solved using nuclear magnetic resonance (NMR), tandem mass spectrometry (MS/MS) data, and chemical labeling. Two previously unidentified modifying enzymes are proposed to create the hallmark lanthionine bridges. Taken together, our work highlights how novel natural product families can be discovered by methods going beyond sequence similarity searches to integrate multiple pathway discovery criteria.}, } @article {pmid33351289, year = {2021}, author = {Gargiulo, R and Kull, T and Fay, MF}, title = {Effective double-digest RAD sequencing and genotyping despite large genome size.}, journal = {Molecular ecology resources}, volume = {21}, number = {4}, pages = {1037-1055}, doi = {10.1111/1755-0998.13314}, pmid = {33351289}, issn = {1755-0998}, support = {//Kew Pilot Study Fund 2018/ ; IUT 21-1//Estonian Ministry of Education and Research/ ; SR18/1418//British Ecological Society/ ; }, mesh = {Computational Biology ; *Genome Size ; Genotype ; *Orchidaceae/genetics ; Reproducibility of Results ; Sequence Analysis ; *Sequence Analysis, DNA ; Workflow ; }, abstract = {Obtaining informative data is the ambition of any genomic project, but in nonmodel species with very large genomes, pursuing such a goal requires surmounting a series of analytical challenges. Double-digest RAD sequencing is routinely used in nonmodel organisms and offers some control over the volume of data obtained. However, the volume of data recovered is not always an indication of the reliability of data sets, and quality checks are necessary to ensure that true and artefactual information is set apart. In the present study, we aim to fill the gap existing between the known applicability of RAD sequencing methods in plants with large genomes and the use of the retrieved loci for population genetic inference. By analysing two populations of Cypripedium calceolus, a nonmodel orchid species with a large genome size (1C ~ 31.6 Gbp), we provide a complete workflow from library preparation to bioinformatic filtering and inference of genetic diversity and differentiation. We show how filtering strategies to dismiss potentially misleading data need to be explored and adapted to data set-specific features. Moreover, we suggest that the occurrence of organellar sequences in libraries should not be neglected when planning the experiment and analysing the results. Finally, we explain how, in the absence of prior information about the genome of the species, seeking high standards of quality during library preparation and sequencing can provide an insurance against unpredicted technical or biological constraints.}, } @article {pmid33350960, year = {2020}, author = {Luo, Y and Oh, CY and Jean, BS and Choe, EK}, title = {Interrelationships Between Patients' Data Tracking Practices, Data Sharing Practices, and Health Literacy: Onsite Survey Study.}, journal = {Journal of medical Internet research}, volume = {22}, number = {12}, pages = {e18937}, pmid = {33350960}, issn = {1438-8871}, mesh = {Adolescent ; Adult ; Female ; Health Literacy/*methods ; Humans ; Information Dissemination/*methods ; Male ; Retrospective Studies ; Surveys and Questionnaires ; Young Adult ; }, abstract = {BACKGROUND: Although the use of patient-generated data (PGD) in the optimization of patient care shows great promise, little is known about whether patients who track their PGD necessarily share the data with their clinicians. Meanwhile, health literacy-an important construct that captures an individual's ability to manage their health and to engage with their health care providers-has often been neglected in prior studies focused on PGD tracking and sharing. To leverage the full potential of PGD, it is necessary to bridge the gap between patients' data tracking and data sharing practices by first understanding the interrelationships between these practices and the factors contributing to these practices.

OBJECTIVE: This study aims to systematically examine the interrelationships between PGD tracking practices, data sharing practices, and health literacy among individual patients.

METHODS: We surveyed 109 patients at the time they met with a clinician at a university health center, unlike prior research that often examined patients' retrospective experience after some time had passed since their clinic visit. The survey consisted of 39 questions asking patients about their PGD tracking and sharing practices based on their current clinical encounter. The survey also contained questions related to the participants' health literacy. All the participants completed the survey on a tablet device. The onsite survey study enabled us to collect ecologically valid data based on patients' immediate experiences situated within their clinic visit.

RESULTS: We found no evidence that tracking PGD was related to self-reports of having sufficient information to manage one's health; however, the number of data types participants tracked positively related to their self-assessed ability to actively engage with health care providers. Participants' data tracking practices and their health literacy did not relate to their data sharing practices; however, their ability to engage with health care providers positively related to their willingness to share their data with clinicians in the future. Participants reported several benefits of, and barriers to, sharing their PGD with clinicians.

CONCLUSIONS: Although tracking PGD could help patients better engage with health care providers, it may not provide patients with sufficient information to manage their health. The gaps between tracking and sharing PGD with health care providers call for efforts to inform patients of how their data relate to their health and to facilitate efficient clinician-patient communication. To realize the full potential of PGD and to promote individuals' health literacy, empowering patients to effectively track and share their PGD is important-both technologies and health care providers can play important roles.}, } @article {pmid33347737, year = {2021}, author = {Romanelli, JP and Meli, P and Naves, RP and Alves, MC and Rodrigues, RR}, title = {Reliability of evidence-review methods in restoration ecology.}, journal = {Conservation biology : the journal of the Society for Conservation Biology}, volume = {35}, number = {1}, pages = {142-154}, doi = {10.1111/cobi.13661}, pmid = {33347737}, issn = {1523-1739}, mesh = {*Conservation of Natural Resources ; Ecology ; Reproducibility of Results ; *Research Design ; }, abstract = {In restoration science, evidence reviews play a crucial role in summarizing research findings in practice and policy. However, if unreliable or inappropriate methods are used to review evidence, decisions based on these reviews may not accurately reflect the available evidence base. To assess the current value of restoration reviews, we examined a sample of meta-analyses and narrative syntheses (n = 91) with the Collaboration for Environmental Evidence Synthesis Assessment Tool (CEESAT), which uses detailed criteria to assesses the method of policy-relevant evidence synthesis according to elements important for objectivity, transparency, and comprehensiveness. Overall, reviews scored low based on this standard: median score 16 out of 39, modal score 15, and mean 16.6. Meta-analyses scored higher than narrative syntheses (median 17 vs. 5, respectively), although there were some outlier narrative syntheses that had high scores, suggesting that quantitative synthesis does not solely reflect the reliability of a review. In general, criteria spanning the more fundamental review stages (i.e., searching for studies and including studies) received low scores for both synthesis types. Conversely, criteria comprising the later stages of the review (i.e., critical appraisal, data extraction, and data synthesis) were generally well described in meta-analyses; thus, these criteria achieved the highest individual CEESAT scores. We argue that restoration ecology is well positioned to advance so-called evidence-based restoration, but review authors should elucidate their conceptual understanding of evidence syntheses and recognize that conducting reliable reviews demands the same methodological rigor and reporting standards used in primary research. Given the potential of evidence reviews to inform management, policy, and research, it is of vital importance that the overall methodological reliability of restoration reviews be improved.}, } @article {pmid33345776, year = {2020}, author = {Gaimann, MU and Nguyen, M and Desponds, J and Mayer, A}, title = {Early life imprints the hierarchy of T cell clone sizes.}, journal = {eLife}, volume = {9}, number = {}, pages = {}, pmid = {33345776}, issn = {2050-084X}, support = {SFARI/597491-RWC//Simons Foundation/ ; 17764421//National Science Foundation/ ; 1764421//National Science Foundation/ ; }, mesh = {Adolescent ; Adult ; Aged ; Aged, 80 and over ; Aging ; Cell Proliferation ; Child ; *Clone Cells ; Computer Simulation ; Databases, Factual ; Humans ; Immunologic Memory ; Middle Aged ; *Models, Biological ; Stochastic Processes ; T-Lymphocytes/*classification/physiology ; Young Adult ; }, abstract = {The adaptive immune system responds to pathogens by selecting clones of cells with specific receptors. While clonal selection in response to particular antigens has been studied in detail, it is unknown how a lifetime of exposures to many antigens collectively shape the immune repertoire. Here, using mathematical modeling and statistical analyses of T cell receptor sequencing data, we develop a quantitative theory of human T cell dynamics compatible with the statistical laws of repertoire organization. We find that clonal expansions during a perinatal time window leave a long-lasting imprint on the human T cell repertoire, which is only slowly reshaped by fluctuating clonal selection during adult life. Our work provides a mechanism for how early clonal dynamics imprint the hierarchy of T cell clone sizes with implications for pathogen defense and autoimmunity.}, } @article {pmid33342606, year = {2021}, author = {Wang, X and Yao, J and Sun, YC and Wood, TK}, title = {Type VII Toxin/Antitoxin Classification System for Antitoxins that Enzymatically Neutralize Toxins.}, journal = {Trends in microbiology}, volume = {29}, number = {5}, pages = {388-393}, doi = {10.1016/j.tim.2020.12.001}, pmid = {33342606}, issn = {1878-4380}, mesh = {Antitoxins/analysis/*classification/*metabolism ; Bacteria/*metabolism ; Bacterial Toxins/*metabolism ; Computational Biology/methods ; Immunologic Factors ; *Toxin-Antitoxin Systems ; }, abstract = {Toxin/antitoxin (TA) systems are present in nearly all bacterial and archaeal strains and consist of a toxin that reduces growth and an antitoxin that masks toxin activity. Currently there are six primary classes for TA systems based on the nature of the antitoxin and the way that the antitoxin inactivates the toxin. Here we show that there now are at least three additional and distinct TA systems in which the antitoxin is an enzyme and the cognate toxin is the direct target of the antitoxin: Hha/TomB (antitoxin oxidizes Cys18 of the toxin), TglT/TakA (antitoxin phosphorylates Ser78 of the toxin), and HepT/MntA (antitoxin adds three AMPs to Tyr104 of the toxin). Thus, we suggest the type VII TA system should be used to designate those TA systems in which the enzyme antitoxin chemically modifies the toxin post-translationally to neutralize it. Defining the type VII TA system using this specific criterion will aid researchers in classifying newly discovered TA systems as well as refine the framework for recognizing the diverse biochemical functions in TA systems.}, } @article {pmid33341900, year = {2021}, author = {Goswami, P and Bartas, M and Lexa, M and Bohálová, N and Volná, A and Červeň, J and Červeňová, V and Pečinka, P and Špunda, V and Fojta, M and Brázda, V}, title = {SARS-CoV-2 hot-spot mutations are significantly enriched within inverted repeats and CpG island loci.}, journal = {Briefings in bioinformatics}, volume = {22}, number = {2}, pages = {1338-1345}, pmid = {33341900}, issn = {1477-4054}, mesh = {COVID-19/*virology ; *CpG Islands ; DNA Methylation ; Genome, Viral ; Humans ; *Mutation ; Protein Binding ; SARS-CoV-2/*genetics ; }, abstract = {SARS-CoV-2 is an intensively investigated virus from the order Nidovirales (Coronaviridae family) that causes COVID-19 disease in humans. Through enormous scientific effort, thousands of viral strains have been sequenced to date, thereby creating a strong background for deep bioinformatics studies of the SARS-CoV-2 genome. In this study, we inspected high-frequency mutations of SARS-CoV-2 and carried out systematic analyses of their overlay with inverted repeat (IR) loci and CpG islands. The main conclusion of our study is that SARS-CoV-2 hot-spot mutations are significantly enriched within both IRs and CpG island loci. This points to their role in genomic instability and may predict further mutational drive of the SARS-CoV-2 genome. Moreover, CpG islands are strongly enriched upstream from viral ORFs and thus could play important roles in transcription and the viral life cycle. We hypothesize that hypermethylation of these loci will decrease the transcription of viral ORFs and could therefore limit the progression of the disease.}, } @article {pmid33341760, year = {2020}, author = {Sit, M and Demiray, BZ and Xiang, Z and Ewing, GJ and Sermet, Y and Demir, I}, title = {A comprehensive review of deep learning applications in hydrology and water resources.}, journal = {Water science and technology : a journal of the International Association on Water Pollution Research}, volume = {82}, number = {12}, pages = {2635-2670}, doi = {10.2166/wst.2020.369}, pmid = {33341760}, issn = {0273-1223}, mesh = {Climate Change ; *Deep Learning ; Hydrology ; *Water Resources ; }, abstract = {The global volume of digital data is expected to reach 175 zettabytes by 2025. The volume, variety and velocity of water-related data are increasing due to large-scale sensor networks and increased attention to topics such as disaster response, water resources management, and climate change. Combined with the growing availability of computational resources and popularity of deep learning, these data are transformed into actionable and practical knowledge, revolutionizing the water industry. In this article, a systematic review of literature is conducted to identify existing research that incorporates deep learning methods in the water sector, with regard to monitoring, management, governance and communication of water resources. The study provides a comprehensive review of state-of-the-art deep learning approaches used in the water industry for generation, prediction, enhancement, and classification tasks, and serves as a guide for how to utilize available deep learning methods for future water resources challenges. Key issues and challenges in the application of these techniques in the water domain are discussed, including the ethics of these technologies for decision-making in water resources management and governance. Finally, we provide recommendations and future directions for the application of deep learning models in hydrology and water resources.}, } @article {pmid33339232, year = {2020}, author = {Dupin, J and Raimondeau, P and Hong-Wa, C and Manzi, S and Gaudeul, M and Besnard, G}, title = {Resolving the Phylogeny of the Olive Family (Oleaceae): Confronting Information from Organellar and Nuclear Genomes.}, journal = {Genes}, volume = {11}, number = {12}, pages = {}, pmid = {33339232}, issn = {2073-4425}, mesh = {Cell Nucleus/genetics ; DNA, Chloroplast/genetics ; DNA, Mitochondrial/genetics ; DNA, Plant/genetics ; DNA, Ribosomal/genetics ; Datasets as Topic ; Evolution, Molecular ; Genes, Plant ; Genetic Variation ; *Genome, Plant ; Likelihood Functions ; Multigene Family ; Oleaceae/classification/*genetics ; Phylogeny ; Phytochrome/genetics ; Plant Proteins/genetics ; Plastids/*genetics ; Polyploidy ; Species Specificity ; }, abstract = {The olive family, Oleaceae, is a group of woody plants comprising 28 genera and ca. 700 species, distributed on all continents (except Antarctica) in both temperate and tropical environments. It includes several genera of major economic and ecological importance such as olives, ash trees, jasmines, forsythias, osmanthuses, privets and lilacs. The natural history of the group is not completely understood yet, but its diversification seems to be associated with polyploidisation events and the evolution of various reproductive and dispersal strategies. In addition, some taxonomical issues still need to be resolved, particularly in the paleopolyploid tribe Oleeae. Reconstructing a robust phylogenetic hypothesis is thus an important step toward a better comprehension of Oleaceae's diversity. Here, we reconstructed phylogenies of the olive family using 80 plastid coding sequences, 37 mitochondrial genes, the complete nuclear ribosomal cluster and a small multigene family encoding phytochromes (phyB and phyE) of 61 representative species. Tribes and subtribes were strongly supported by all phylogenetic reconstructions, while a few Oleeae genera are still polyphyletic (Chionanthus, Olea, Osmanthus, Nestegis) or paraphyletic (Schrebera, Syringa). Some phylogenetic relationships among tribes remain poorly resolved with conflicts between topologies reconstructed from different genomic regions. The use of nuclear data remains an important challenge especially in a group with ploidy changes (both paleo- and neo-polyploids). This work provides new genomic datasets that will assist the study of the biogeography and taxonomy of the whole Oleaceae.}, } @article {pmid33338173, year = {2020}, author = {Lima, SVMA and Cruz, LZ and Araújo, DDC and Santos, ADD and Queiroz, AAFLN and Araújo, KCGM and Mendes, IAC}, title = {Quality of tuberculosis information systems after record linkage.}, journal = {Revista brasileira de enfermagem}, volume = {73}, number = {suppl 5}, pages = {e20200536}, doi = {10.1590/0034-7167-2020-0536}, pmid = {33338173}, issn = {1984-0446}, mesh = {Brazil/epidemiology ; Humans ; Incidence ; Information Systems ; Male ; *Tuberculosis/epidemiology ; }, abstract = {OBJECTIVE: to analyze the quality of a tuberculosis notification information system after record linkage and spatial and temporal distribution of tuberculosis in a Brazilian state.

METHOD: an ecological study carried between 2006 and 2016 in Sergipe, Brazil. A deterministic linkage was performed with Notifiable Diseases Information System and Mortality Information System, recording 7,873 cases and 483 deaths. The temporal trend of tuberculosis incidence was calculated.

RESULTS: there was an increase among men (2.75%), > 60 years (6.29%), higher education (4.34%) and indigenous (4.76%). A total of 190 new cases (2.9%) was found. There was an increasing trend in tuberculosis incidence with a concentration of deaths in the metropolitan region.

CONCLUSION: the quality of the information system showed fragility in identifying cases and deaths in Sergipe. Temporal distribution showed an increasing trend in tuberculosis incidence, and spatial distribution identified higher incidences in southeastern Brazil.}, } @article {pmid33334059, year = {2020}, author = {Fofanov, MV and Prokopov, DY and Kuhl, H and Schartl, M and Trifonov, VA}, title = {Evolution of MicroRNA Biogenesis Genes in the Sterlet (Acipenser ruthenus) and Other Polyploid Vertebrates.}, journal = {International journal of molecular sciences}, volume = {21}, number = {24}, pages = {}, pmid = {33334059}, issn = {1422-0067}, support = {Project No. 18-44-04007//the Russian Science Foundation/ ; 2816ERA04G//German Federal Ministry of Food and Agriculture through the Federal Office for Agriculture and Food/ ; 408/14-1//DFG SCHA/ ; }, mesh = {Alleles ; Amino Acid Sequence ; Animals ; Base Sequence ; Computational Biology/methods ; Fishes/classification/*genetics ; Gene Expression Profiling ; MicroRNAs/*genetics ; Phylogeny ; *Polyploidy ; Vertebrates/*genetics ; }, abstract = {MicroRNAs play a crucial role in eukaryotic gene regulation. For a long time, only little was known about microRNA-based gene regulatory mechanisms in polyploid animal genomes due to difficulties of polyploid genome assembly. However, in recent years, several polyploid genomes of fish, amphibian, and even invertebrate species have been sequenced and assembled. Here we investigated several key microRNA-associated genes in the recently sequenced sterlet (Acipenser ruthenus) genome, whose lineage has undergone a whole genome duplication around 180 MYA. We show that two paralogs of drosha, dgcr8, xpo1, and xpo5 as well as most ago genes have been retained after the acipenserid-specific whole genome duplication, while ago1 and ago3 genes have lost one paralog. While most diploid vertebrates possess only a single copy of dicer1, we strikingly found four paralogs of this gene in the sterlet genome, derived from a tandem segmental duplication that occurred prior to the last whole genome duplication. ago1,3,4 and exportins1,5 look to be prone to additional segment duplications producing up to four-five paralog copies in ray-finned fishes. We demonstrate for the first time exon microsatellite amplification in the acipenserid drosha2 gene, resulting in a highly variable protein product, which may indicate sub- or neofunctionalization. Paralogous copies of most microRNA metabolism genes exhibit different expression profiles in various tissues and remain functional despite the rediploidization process. Subfunctionalization of microRNA processing gene paralogs may be beneficial for different pathways of microRNA metabolism. Genetic variability of microRNA processing genes may represent a substrate for natural selection, and, by increasing genetic plasticity, could facilitate adaptations to changing environments.}, } @article {pmid33333300, year = {2021}, author = {Barbosa, J and De Schamphelaere, K and Janssen, C and Asselman, J}, title = {Prioritization of contaminants and biological process targets in the North Sea using toxicity data from ToxCast.}, journal = {The Science of the total environment}, volume = {758}, number = {}, pages = {144157}, doi = {10.1016/j.scitotenv.2020.144157}, pmid = {33333300}, issn = {1879-1026}, mesh = {Animals ; *Biological Assay ; *Biological Phenomena ; Databases, Factual ; North Sea ; }, abstract = {The increasing number of chemicals detected in the marine environment underlines the need for appropriate prioritization strategies prior to further testing and potential inclusion into monitoring programs. Here, a prioritization strategy is proposed for chemicals detected in the North Sea over the last decade, through the development of a Concern Index (CI) using exposure and toxicity data obtained from peer-review publications and the ToxCast database, respectively. A total of 158 chemicals were ranked and the most sensitive tested assay endpoints were identified. Additionally, similar analysis was performed for the classes of chemicals and Biological Process Targets (BPTs). By first ranking chemicals currently acknowledged for their high toxicity to the aquatic environment, i.e. naphthalene, salicylic acid and simazine, the obtained results not only reinforce the risk posed by these but also promote a confident extrapolation from mammalian in vitro toxicity data to fish. Furthermore, genes targeted by the most sensitive assays, related to basic cell maintenance processes and immune defense, are highly evolutionarily conserved across species. The identification of these assays further reinforces the importance of a shift from traditional toxicity endpoints to lower levels of biological organization, allowing the detection of adverse effects at lower concentrations.}, } @article {pmid33333253, year = {2021}, author = {Cheng, W and Pan, A and Rathbun, SL and Ge, Y and Xiao, Q and Martinez, L and Ling, F and Liu, S and Wang, X and Yu, Z and Ebell, MH and Li, C and Handel, A and Chen, E and Shen, Y}, title = {Effectiveness of neuraminidase inhibitors to prevent mortality in patients with laboratory-confirmed avian influenza A H7N9.}, journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases}, volume = {103}, number = {}, pages = {573-578}, doi = {10.1016/j.ijid.2020.12.028}, pmid = {33333253}, issn = {1878-3511}, mesh = {Adult ; Aged ; Antiviral Agents/*therapeutic use ; Female ; Humans ; *Influenza A Virus, H7N9 Subtype ; Influenza, Human/*drug therapy/mortality/*virology ; Laboratories ; Male ; Middle Aged ; Neuraminidase/*antagonists & inhibitors ; }, abstract = {OBJECTIVES: Avian influenza virus A(H7N9) remains a threat to humans and has great potential to cause a pandemic in the foreseeable future. Antiviral treatment with neuraminidase inhibitors has been recommended to treat patients with H7N9 infection as early as possible, although evidence-based research on their effectiveness for H7N9 infection is lacking.

METHODS: Data from all laboratory-confirmed cases of H7N9 infection in Zhejiang Province between 2013 and 2017 were retrieved, and time-dependent survival models were used to evaluate the effectiveness of treatment with neuraminidase inhibitors to reduce the risk of mortality.

RESULTS: The final optimal model found no significant association (odds ratio 1.29, 95% confidence interval 0.78-2.15) between time to treatment with neuraminidase inhibitors and survival after controlling for age and white blood cell count. Sensitivity analyses with multiple imputation for missing data concurred with the primary analysis.

CONCLUSIONS: No association was found between treatment with neuraminidase inhibitors and survival in patients with H7N9 infection using various adjusted models and sensitivity analyses of missing data imputations.}, } @article {pmid33332530, year = {2021}, author = {Liu, C and Cui, Y and Li, X and Yao, M}, title = {microeco: an R package for data mining in microbial community ecology.}, journal = {FEMS microbiology ecology}, volume = {97}, number = {2}, pages = {}, doi = {10.1093/femsec/fiaa255}, pmid = {33332530}, issn = {1574-6941}, mesh = {Computational Biology ; Data Mining ; Ecology ; *Microbiota ; *Software ; }, abstract = {A large amount of sequencing data is produced in microbial community ecology studies using the high-throughput sequencing technique, especially amplicon-sequencing-based community data. After conducting the initial bioinformatic analysis of amplicon sequencing data, performing the subsequent statistics and data mining based on the operational taxonomic unit and taxonomic assignment tables is still complicated and time-consuming. To address this problem, we present an integrated R package-'microeco' as an analysis pipeline for treating microbial community and environmental data. This package was developed based on the R6 class system and combines a series of commonly used and advanced approaches in microbial community ecology research. The package includes classes for data preprocessing, taxa abundance plotting, venn diagram, alpha diversity analysis, beta diversity analysis, differential abundance test and indicator taxon analysis, environmental data analysis, null model analysis, network analysis and functional analysis. Each class is designed to provide a set of approaches that can be easily accessible to users. Compared with other R packages in the microbial ecology field, the microeco package is fast, flexible and modularized to use and provides powerful and convenient tools for researchers. The microeco package can be installed from CRAN (The Comprehensive R Archive Network) or github (https://github.com/ChiLiubio/microeco).}, } @article {pmid33331551, year = {2020}, author = {Matos, CA and Osorio-de-Castro, CGS and Coimbra, CEA and Silva, MJSD}, title = {[Profile of antineoplastic medication among indigenous people treated in the Brazilian Unified National Health System].}, journal = {Cadernos de saude publica}, volume = {36}, number = {12}, pages = {e00100520}, doi = {10.1590/0102-311X00100520}, pmid = {33331551}, issn = {1678-4464}, mesh = {*Antineoplastic Agents/therapeutic use ; Brazil/epidemiology ; Humans ; Indians, South American ; Indigenous Peoples ; *Population Groups ; }, abstract = {Brazil has an estimated 900,000 indigenous people (0.4% of the country's population), belonging to more than 300 different ethnic groups. However, information is scarce on cancer epidemiology and the antineoplastic drugs used in treatment of these individuals. The study's objectives are to identify the antineoplastic drugs used and to describe the profile of use of these drugs in the indigenous population treated in Brazil, as well as to describe the patients' epidemiological profile. An ecological study was performed involving outpatient chemotherapy care from January 2014 to December 2018 throughout Brazil. The data source was the Outpatient Information System of the Brazilian Health Informatics Department, considering only Authorizations for High-Complexity Chemotherapy Procedures. We identified 2,425 authorizations for chemotherapy procedures for treatment of indigenous patients. Of these, 2,292 authorizations for a total of 210 individuals were analyzed. We found an increase in the number of authorizations and of indigenous persons receiving chemotherapy over the period, with a higher concentration of individuals living in and receiving treatment in the South of Brazil, plus a wide diversity in the types of diagnosed tumors (n = 63) and of treatment regimen used during the treatment (n = 107). The current study provided a new overview of the epidemiological profile of indigenous patients receiving chemotherapy in the Brazilian Unified National Health System. The findings help fill a current knowledge gap on indigenous people's health in Brazil.}, } @article {pmid33328667, year = {2020}, author = {Belletti, B and Garcia de Leaniz, C and Jones, J and Bizzi, S and Börger, L and Segura, G and Castelletti, A and van de Bund, W and Aarestrup, K and Barry, J and Belka, K and Berkhuysen, A and Birnie-Gauvin, K and Bussettini, M and Carolli, M and Consuegra, S and Dopico, E and Feierfeil, T and Fernández, S and Fernandez Garrido, P and Garcia-Vazquez, E and Garrido, S and Giannico, G and Gough, P and Jepsen, N and Jones, PE and Kemp, P and Kerr, J and King, J and Łapińska, M and Lázaro, G and Lucas, MC and Marcello, L and Martin, P and McGinnity, P and O'Hanley, J and Olivo Del Amo, R and Parasiewicz, P and Pusch, M and Rincon, G and Rodriguez, C and Royte, J and Schneider, CT and Tummers, JS and Vallesi, S and Vowles, A and Verspoor, E and Wanningen, H and Wantzen, KM and Wildman, L and Zalewski, M}, title = {More than one million barriers fragment Europe's rivers.}, journal = {Nature}, volume = {588}, number = {7838}, pages = {436-441}, pmid = {33328667}, issn = {1476-4687}, mesh = {Agriculture/statistics & numerical data ; Altitude ; Biodiversity ; Datasets as Topic ; *Ecosystem ; Environmental Restoration and Remediation/methods/trends ; Europe ; Human Activities ; Humans ; Logistic Models ; Machine Learning ; Population Density ; Power Plants/supply & distribution ; *Rivers ; }, abstract = {Rivers support some of Earth's richest biodiversity[1] and provide essential ecosystem services to society[2], but they are often fragmented by barriers to free flow[3]. In Europe, attempts to quantify river connectivity have been hampered by the absence of a harmonized barrier database. Here we show that there are at least 1.2 million instream barriers in 36 European countries (with a mean density of 0.74 barriers per kilometre), 68 per cent of which are structures less than two metres in height that are often overlooked. Standardized walkover surveys along 2,715 kilometres of stream length for 147 rivers indicate that existing records underestimate barrier numbers by about 61 per cent. The highest barrier densities occur in the heavily modified rivers of central Europe and the lowest barrier densities occur in the most remote, sparsely populated alpine areas. Across Europe, the main predictors of barrier density are agricultural pressure, density of river-road crossings, extent of surface water and elevation. Relatively unfragmented rivers are still found in the Balkans, the Baltic states and parts of Scandinavia and southern Europe, but these require urgent protection from proposed dam developments. Our findings could inform the implementation of the EU Biodiversity Strategy, which aims to reconnect 25,000 kilometres of Europe's rivers by 2030, but achieving this will require a paradigm shift in river restoration that recognizes the widespread impacts caused by small barriers.}, } @article {pmid33328476, year = {2020}, author = {Flati, T and Gioiosa, S and Chillemi, G and Mele, A and Oliverio, A and Mannironi, C and Rinaldi, A and Castrignanò, T}, title = {A gene expression atlas for different kinds of stress in the mouse brain.}, journal = {Scientific data}, volume = {7}, number = {1}, pages = {437}, pmid = {33328476}, issn = {2052-4463}, mesh = {Animals ; Brain/*physiology ; Computational Biology ; Data Mining ; Datasets as Topic ; Female ; *Gene Expression ; Male ; Mice ; *Stress, Physiological ; *Stress, Psychological ; *Transcriptome ; }, abstract = {Stressful experiences are part of everyday life and animals have evolved physiological and behavioral responses aimed at coping with stress and maintaining homeostasis. However, repeated or intense stress can induce maladaptive reactions leading to behavioral disorders. Adaptations in the brain, mediated by changes in gene expression, have a crucial role in the stress response. Recent years have seen a tremendous increase in studies on the transcriptional effects of stress. The input raw data are freely available from public repositories and represent a wealth of information for further global and integrative retrospective analyses. We downloaded from the Sequence Read Archive 751 samples (SRA-experiments), from 18 independent BioProjects studying the effects of different stressors on the brain transcriptome in mice. We performed a massive bioinformatics re-analysis applying a single, standardized pipeline for computing differential gene expression. This data mining allowed the identification of novel candidate stress-related genes and specific signatures associated with different stress conditions. The large amount of computational results produced was systematized in the interactive "Stress Mice Portal".}, } @article {pmid33327629, year = {2020}, author = {Mead, HL and Hamm, PS and Shaffer, IN and Teixeira, MM and Wendel, CS and Wiederhold, NP and Thompson, GR and Muñiz-Salazar, R and Castañón-Olivares, LR and Keim, P and Plude, C and Terriquez, J and Galgiani, JN and Orbach, MJ and Barker, BM}, title = {Differential Thermotolerance Adaptation between Species of Coccidioides.}, journal = {Journal of fungi (Basel, Switzerland)}, volume = {6}, number = {4}, pages = {}, pmid = {33327629}, issn = {2309-608X}, support = {PH//University of New Mexico (UNM) Graduate and Professional Student Association High Priority GrantUniversity of New Mexico (UNM) Graduate and Professional Student Association High Priority Grant/ ; PO 1AI061310-01/NH/NIH HHS/United States ; HLM//Grants in Community, Culture, and Environment by The Center for Ecosystem Science and Society and the McAllister Program in Community, Culture, and Environment at Northern Arizona University/ ; 1978//Flinn Foundation of Arizona/ ; U19 AI166058/AI/NIAID NIH HHS/United States ; 6017//ADCRC/ ; DGE 0114420//NSF/ ; 16-162415//Arizona Department of Health Services/ ; }, abstract = {Coccidioidomycosis, or Valley fever, is caused by two species of dimorphic fungi. Based on molecular phylogenetic evidence, the genus Coccidioides contains two reciprocally monophyletic species: C. immitis and C. posadasii. However, phenotypic variation between species has not been deeply investigated. We therefore explored differences in growth rate under various conditions. A collection of 39 C. posadasii and 46 C. immitis isolates, representing the full geographical range of the two species, was screened for mycelial growth rate at 37 °C and 28 °C on solid media. The radial growth rate was measured for 16 days on yeast extract agar. A linear mixed effect model was used to compare the growth rate of C. posadasii and C. immitis at 37 °C and 28 °C, respectively. C. posadasii grew significantly faster at 37 °C, when compared to C. immitis; whereas both species had similar growth rates at 28 °C. These results indicate thermotolerance differs between these two species. As the ecological niche has not been well-described for Coccidioides spp., and disease variability between species has not been shown, the evolutionary pressure underlying the adaptation is unclear. However, this research reveals the first significant phenotypic difference between the two species that directly applies to ecological research.}, } @article {pmid33327560, year = {2020}, author = {Um, HJ and Ko, JW and Won, SB and Kwon, YH}, title = {Effects of Dietary Vitamin B6 Restriction on Hepatic Gene Expression Profile of Non-Obese and Obese Mice.}, journal = {Nutrients}, volume = {12}, number = {12}, pages = {}, pmid = {33327560}, issn = {2072-6643}, support = {NRF-2017R1A2B4011432//National Research Foundation of Korea/ ; }, mesh = {Animals ; Diet, Fat-Restricted ; Diet, High-Fat ; Dietary Fats/metabolism ; Down-Regulation/drug effects ; Gene Ontology ; Liver/metabolism ; Male ; Mice ; Mice, Inbred C57BL ; Mice, Obese ; Obesity/complications/*metabolism ; Signal Transduction/*drug effects ; Transcriptome/*drug effects ; Up-Regulation/drug effects ; Vitamin B 6/*pharmacology ; Vitamin B 6 Deficiency/complications/*metabolism ; }, abstract = {Although vitamin B6 is contained in various foods, its deficiency is one of the most common micronutrient deficiencies worldwide. Furthermore, patients with obesity and cardiovascular disease are more likely to have suboptimal vitamin B6 status than healthy people. Therefore, we investigated the effects of dietary vitamin B6 restriction on hepatic gene expression and function in obese mice. C57BL/6J male mice were fed a low-fat (LF) or high-fat (HF) diet in combination with sufficient (7 mg pyridoxine/kg diet) or insufficient (1 mg) amounts of vitamin B6 for 16 weeks. Analysis of microarray data revealed that expressions of 4000 genes were significantly altered by the experimental diets (LF7, LF1, HF7, and HF1). The effects of dietary fat content on gene expressions were markedly greater than vitamin B6 content. Only three differentially expressed genes (DEGs) were overlapped between the LF1/LF7 and HF1/HF7 comparison. In the LF1/LF7 comparison, 54 upregulated DEGs were enriched in gene ontology (GO) terms associated with the sterol metabolic process and 54 downregulated DEGs were enriched in GO terms associated with immune response. In HF1/HF7 comparison, 26 upregulated DEGs were enriched in GO terms associated with amino acid catabolic process. High-fat consumption downregulated gene expressions associated with vitamin B6-dependent pathways. In conclusion, our data suggest that obesity may differentially regulate vitamin B6-associated metabolic pathways in the body.}, } @article {pmid33326609, year = {2021}, author = {Zhu, J and Smith-Warner, SA and Yu, D and Zhang, X and Blot, WJ and Xiang, YB and Sinha, R and Park, Y and Tsugane, S and White, E and Koh, WP and Park, SK and Sawada, N and Kanemura, S and Sugawara, Y and Tsuji, I and Robien, K and Tomata, Y and Yoo, KY and Kim, J and Yuan, JM and Gao, YT and Rothman, N and Lazovich, D and Abe, SK and Rahman, MS and Loftfield, E and Takata, Y and Li, X and Lee, JE and Saito, E and Freedman, ND and Inoue, M and Lan, Q and Willett, WC and Zheng, W and Shu, XO}, title = {Associations of coffee and tea consumption with lung cancer risk.}, journal = {International journal of cancer}, volume = {148}, number = {10}, pages = {2457-2470}, pmid = {33326609}, issn = {1097-0215}, support = {R03 CA183021/NH/NIH HHS/United States ; R01 CA082729/CA/NCI NIH HHS/United States ; R03 CA183021/CA/NCI NIH HHS/United States ; UM1 CA182910/CA/NCI NIH HHS/United States ; P30 DK056341/DK/NIDDK NIH HHS/United States ; UM1 CA173640/CA/NCI NIH HHS/United States ; R03 CA183021/NH/NIH HHS/United States ; }, abstract = {Associations of coffee and tea consumption with lung cancer risk have been inconsistent, and most lung cancer cases investigated were smokers. Included in this study were over 1.1 million participants from 17 prospective cohorts. Cox regression analyses were conducted to estimate hazard ratios (HRs) and 95% confidence intervals (CIs). Potential effect modifications by sex, smoking, race, cancer subtype and coffee type were assessed. After a median 8.6 years of follow-up, 20 280 incident lung cancer cases were identified. Compared with noncoffee and nontea consumption, HRs (95% CIs) associated with exclusive coffee drinkers (≥2 cups/d) among current, former and never smokers were 1.30 (1.15-1.47), 1.49 (1.27-1.74) and 1.35 (1.15-1.58), respectively. Corresponding HRs for exclusive tea drinkers (≥2 cups/d) were 1.16 (1.02-1.32), 1.10 (0.92-1.32) and 1.37 (1.17-1.61). In general, the coffee and tea associations did not differ significantly by sex, race or histologic subtype. Our findings suggest that higher consumption of coffee or tea is associated with increased lung cancer risk. However, these findings should not be assumed to be causal because of the likelihood of residual confounding by smoking, including passive smoking, and change of coffee and tea consumption after study enrolment.}, } @article {pmid33322568, year = {2020}, author = {Lynch, I and Afantitis, A and Exner, T and Himly, M and Lobaskin, V and Doganis, P and Maier, D and Sanabria, N and Papadiamantis, AG and Rybinska-Fryca, A and Gromelski, M and Puzyn, T and Willighagen, E and Johnston, BD and Gulumian, M and Matzke, M and Green Etxabe, A and Bossa, N and Serra, A and Liampa, I and Harper, S and Tämm, K and Jensen, AC and Kohonen, P and Slater, L and Tsoumanis, A and Greco, D and Winkler, DA and Sarimveis, H and Melagraki, G}, title = {Can an InChI for Nano Address the Need for a Simplified Representation of Complex Nanomaterials across Experimental and Nanoinformatics Studies?.}, journal = {Nanomaterials (Basel, Switzerland)}, volume = {10}, number = {12}, pages = {}, pmid = {33322568}, issn = {2079-4991}, support = {731032 (NanoCommons)//Horizon 2020 Framework Programme/ ; 814572 (NanoAolveIT)//Horizon 2020 Framework Programme/ ; }, abstract = {Chemoinformatics has developed efficient ways of representing chemical structures for small molecules as simple text strings, simplified molecular-input line-entry system (SMILES) and the IUPAC International Chemical Identifier (InChI), which are machine-readable. In particular, InChIs have been extended to encode formalized representations of mixtures and reactions, and work is ongoing to represent polymers and other macromolecules in this way. The next frontier is encoding the multi-component structures of nanomaterials (NMs) in a machine-readable format to enable linking of datasets for nanoinformatics and regulatory applications. A workshop organized by the H2020 research infrastructure NanoCommons and the nanoinformatics project NanoSolveIT analyzed issues involved in developing an InChI for NMs (NInChI). The layers needed to capture NM structures include but are not limited to: core composition (possibly multi-layered); surface topography; surface coatings or functionalization; doping with other chemicals; and representation of impurities. NM distributions (size, shape, composition, surface properties, etc.), types of chemical linkages connecting surface functionalization and coating molecules to the core, and various crystallographic forms exhibited by NMs also need to be considered. Six case studies were conducted to elucidate requirements for unambiguous description of NMs. The suggested NInChI layers are intended to stimulate further analysis that will lead to the first version of a "nano" extension to the InChI standard.}, } @article {pmid33320930, year = {2021}, author = {Du, W and Li, G and Ho, N and Jenkins, L and Hockaday, D and Tan, J and Cao, H}, title = {CyanoPATH: a knowledgebase of genome-scale functional repertoire for toxic cyanobacterial blooms.}, journal = {Briefings in bioinformatics}, volume = {22}, number = {4}, pages = {}, doi = {10.1093/bib/bbaa375}, pmid = {33320930}, issn = {1477-4054}, mesh = {*Cyanobacteria/genetics/metabolism ; *Databases, Genetic ; *Genome, Bacterial ; *Harmful Algal Bloom ; *Knowledge Bases ; }, abstract = {CyanoPATH is a database that curates and analyzes the common genomic functional repertoire for cyanobacteria harmful algal blooms (CyanoHABs) in eutrophic waters. Based on the literature of empirical studies and genome/protein databases, it summarizes four types of information: common biological functions (pathways) driving CyanoHABs, customized pathway maps, classification of blooming type based on databases and the genomes of cyanobacteria. A total of 19 pathways are reconstructed, which are involved in the utilization of macronutrients (e.g. carbon, nitrogen, phosphorus and sulfur), micronutrients (e.g. zinc, magnesium, iron, etc.) and other resources (e.g. light and vitamins) and in stress resistance (e.g. lead and copper). These pathways, comprised of both transport and biochemical reactions, are reconstructed with proteins from NCBI and reactions from KEGG and visualized with self-created transport/reaction maps. The pathways are hierarchical and consist of subpathways, protein/enzyme complexes and constituent proteins. New cyanobacterial genomes can be annotated and visualized for these pathways and compared with existing species. This set of genomic functional repertoire is useful in analyzing aquatic metagenomes and metatranscriptomes in CyanoHAB research. Most importantly, it establishes a link between genome and ecology. All these reference proteins, pathways and maps and genomes are free to download at http://www.csbg-jlu.info/CyanoPATH.}, } @article {pmid33315871, year = {2020}, author = {Fisher, M and Nyabaro, V and Mendum, R and Osiru, M}, title = {Making it to the PhD: Gender and student performance in sub-Saharan Africa.}, journal = {PloS one}, volume = {15}, number = {12}, pages = {e0241915}, pmid = {33315871}, issn = {1932-6203}, mesh = {Academic Performance/statistics & numerical data ; Adult ; Africa South of the Sahara ; Computer Simulation ; Datasets as Topic ; Education, Graduate/organization & administration/*statistics & numerical data ; *Educational Status ; Female ; Humans ; Male ; Models, Theoretical ; *Organizational Policy ; Publications/statistics & numerical data ; Qualitative Research ; Sexism/*prevention & control/statistics & numerical data ; Students/*statistics & numerical data ; Surveys and Questionnaires/statistics & numerical data ; Universities/organization & administration/statistics & numerical data ; }, abstract = {Women's underrepresentation in science, technology, engineering, and mathematics (STEM) impedes progress in solving Africa's complex development problems. As in other regions, women's participation in STEM drops progressively moving up the education and career ladder, with women currently constituting 30% of Africa's STEM researchers. This study elucidates gender-based differences in PhD performance using new survey data from 227 alumni of STEM PhD programs in 17 African countries. We find that, compared to their male counterparts, sampled women had about one less paper accepted for publication during their doctoral studies and took about half a year longer to finish their PhD training. Negative binomial regression models provide insights on the observed differences in women's and men's PhD performance. Results indicate that the correlates of publication productivity and time to PhD completion are very similar for women and men, but some gender-based differences are observed. For publication output, we find that good supervision had a stronger impact for men than women; and getting married during the PhD reduced women's publication productivity but increased that of men. Becoming a parent during the PhD training was a key reason that women took longer to complete the PhD, according to our results. Findings suggest that having a female supervisor, attending an institution with gender policies in place, and pursuing the PhD in a department where sexual harassment by faculty was perceived as uncommon were enabling factors for women's timely completion of their doctoral studies. Two priority interventions emerge from this study: (1) family-friendly policies and facilities that are supportive of women's roles as wives and mothers and (2) fostering broader linkages and networks for women in STEM, including ensuring mentoring and supervisory support that is tailored to their specific needs and circumstances.}, } @article {pmid33314612, year = {2021}, author = {De-Kayne, R and Frei, D and Greenway, R and Mendes, SL and Retel, C and Feulner, PGD}, title = {Sequencing platform shifts provide opportunities but pose challenges for combining genomic data sets.}, journal = {Molecular ecology resources}, volume = {21}, number = {3}, pages = {653-660}, doi = {10.1111/1755-0998.13309}, pmid = {33314612}, issn = {1755-0998}, support = {31003A_163446//SNSF/ ; //European Regional Development Fund/ ; //Swiss Federal Office for the Environment and Eawag/ ; SFRH/BD/145153/2019//Portuguese National Science Foundation/ ; }, mesh = {*Computational Biology/trends ; *Genomics/trends ; *High-Throughput Nucleotide Sequencing ; Reproducibility of Results ; *Sequence Analysis, DNA ; }, abstract = {Technological advances in DNA sequencing over the last decade now permit the production and curation of large genomic data sets in an increasing number of nonmodel species. Additionally, these new data provide the opportunity for combining data sets, resulting in larger studies with a broader taxonomic range. Whilst the development of new sequencing platforms has been beneficial, resulting in a higher throughput of data at a lower per-base cost, shifts in sequencing technology can also pose challenges for those wishing to combine new sequencing data with data sequenced on older platforms. Here, we outline the types of studies where the use of curated data might be beneficial, and highlight potential biases that might be introduced by combining data from different sequencing platforms. As an example of the challenges associated with combining data across sequencing platforms, we focus on the impact of the shift in Illumina's base calling technology from a four-channel system to a two-channel system. We caution that when data are combined from these two systems, erroneous guanine base calls that result from the two-channel chemistry can make their way through a bioinformatic pipeline, eventually leading to inaccurate and potentially misleading conclusions. We also suggest solutions for dealing with such potential artefacts, which make samples sequenced on different sequencing platforms appear more differentiated from one another than they really are. Finally, we stress the importance of archiving tissue samples and the associated sequences for the continued reproducibility and reusability of sequencing data in the face of ever-changing sequencing platform technology.}, } @article {pmid33313542, year = {2020}, author = {Wu, S and Wen, W and Wang, Y and Fan, J and Wang, C and Gou, W and Guo, X}, title = {MVS-Pheno: A Portable and Low-Cost Phenotyping Platform for Maize Shoots Using Multiview Stereo 3D Reconstruction.}, journal = {Plant phenomics (Washington, D.C.)}, volume = {2020}, number = {}, pages = {1848437}, pmid = {33313542}, issn = {2643-6515}, abstract = {Plant phenotyping technologies play important roles in plant research and agriculture. Detailed phenotypes of individual plants can guide the optimization of shoot architecture for plant breeding and are useful to analyze the morphological differences in response to environments for crop cultivation. Accordingly, high-throughput phenotyping technologies for individual plants grown in field conditions are urgently needed, and MVS-Pheno, a portable and low-cost phenotyping platform for individual plants, was developed. The platform is composed of four major components: a semiautomatic multiview stereo (MVS) image acquisition device, a data acquisition console, data processing and phenotype extraction software for maize shoots, and a data management system. The platform's device is detachable and adjustable according to the size of the target shoot. Image sequences for each maize shoot can be captured within 60-120 seconds, yielding 3D point clouds of shoots are reconstructed using MVS-based commercial software, and the phenotypic traits at the organ and individual plant levels are then extracted by the software. The correlation coefficient (R [2]) between the extracted and manually measured plant height, leaf width, and leaf area values are 0.99, 0.87, and 0.93, respectively. A data management system has also been developed to store and manage the acquired raw data, reconstructed point clouds, agronomic information, and resulting phenotypic traits. The platform offers an optional solution for high-throughput phenotyping of field-grown plants, which is especially useful for large populations or experiments across many different ecological regions.}, } @article {pmid33312689, year = {2020}, author = {van der Bijl, W and Zeuss, D and Chazot, N and Tunström, K and Wahlberg, N and Wiklund, C and Fitzpatrick, JL and Wheat, CW}, title = {Butterfly dichromatism primarily evolved via Darwin's, not Wallace's, model.}, journal = {Evolution letters}, volume = {4}, number = {6}, pages = {545-555}, pmid = {33312689}, issn = {2056-3744}, abstract = {Sexual dimorphism is typically thought to result from sexual selection for elaborated male traits, as proposed by Darwin. However, natural selection could reduce expression of elaborated traits in females, as proposed by Wallace. Darwin and Wallace debated the origins of dichromatism in birds and butterflies, and although evidence in birds is roughly equal, if not in favor of Wallace's model, butterflies lack a similar scale of study. Here, we present a large-scale comparative phylogenetic analysis of the evolution of butterfly coloration, using all European non-hesperiid butterfly species (n = 369). We modeled evolutionary changes in coloration for each species and sex along their phylogeny, thereby estimating the rate and direction of evolution in three-dimensional color space using a novel implementation of phylogenetic ridge regression. We show that male coloration evolved faster than female coloration, especially in strongly dichromatic clades, with male contribution to changes in dichromatism roughly twice that of females. These patterns are consistent with a classic Darwinian model of dichromatism via sexual selection on male coloration, suggesting this model was the dominant driver of dichromatism in European butterflies.}, } @article {pmid33308363, year = {2020}, author = {Herpertz, SC and Matzke, B and Hillmann, K and Neukel, C and Mancke, F and Jaentsch, B and Schwenger, U and Honecker, H and Bullenkamp, R and Steinmann, S and Krauch, M and Bauer, S and Borzikowsky, C and Bertsch, K and Dempfle, A}, title = {A mechanism-based group-psychotherapy approach to aggressive behaviour in borderline personality disorder: findings from a cluster-randomised controlled trial.}, journal = {BJPsych open}, volume = {7}, number = {1}, pages = {e17}, pmid = {33308363}, issn = {2056-4724}, abstract = {BACKGROUND: Aggressive behaviour is a prevalent and harmful phenomenon in patients with borderline personality disorder (BPD). However, no short-term, low-cost programme exists that specifically focuses on aggression.

AIMS: Attuning therapy modules to pathogenetic mechanisms that underlie reactive aggression in BPD, we composed a 6 week mechanism-based anti-aggression psychotherapy (MAAP) approach for the group setting, which we tested against a non-specific supportive psychotherapy (NSSP).

METHOD: A cluster-randomised two-arm parallel-group phase II trial of N = 59 patients with BPD and overt aggressive behaviour was performed (German Registry for Clinical Trials, DRKS00009445). The primary outcome was the externally directed overt aggression score of the Modified Overt Aggression Scale (M-OAS) post-treatment (adjusted for pre-treatment overt aggression). Secondary outcomes were M-OAS irritability, M-OAS response rate and ecological momentary assessment of anger post-treatment and at 6 month follow-up, as well as M-OAS overt aggression score at follow-up.

RESULTS: Although no significant difference in M-OAS overt aggression between treatments was found post-treatment (adjusted difference in mean 3.49 (95% CI -5.32 to 12.31, P = 0.22), the MAAP group showed a clinically relevant decrease in aggressive behaviour of 65% on average (versus 33% in the NSSP group), with particularly strong improvement among those with the highest baseline aggression. Most notably, significant differences in reduction in overt aggression between MAAP and NSSP were found at follow-up.

CONCLUSIONS: Patients with BPD and aggressive behaviour benefited from a short group psychotherapy, with improvements particularly visible at 6 month follow-up. Further studies are required to show whether these effects are specific to MAAP.}, } @article {pmid33307546, year = {2021}, author = {Pairo-Castineira, E and Clohisey, S and Klaric, L and Bretherick, AD and Rawlik, K and Pasko, D and Walker, S and Parkinson, N and Fourman, MH and Russell, CD and Furniss, J and Richmond, A and Gountouna, E and Wrobel, N and Harrison, D and Wang, B and Wu, Y and Meynert, A and Griffiths, F and Oosthuyzen, W and Kousathanas, A and Moutsianas, L and Yang, Z and Zhai, R and Zheng, C and Grimes, G and Beale, R and Millar, J and Shih, B and Keating, S and Zechner, M and Haley, C and Porteous, DJ and Hayward, C and Yang, J and Knight, J and Summers, C and Shankar-Hari, M and Klenerman, P and Turtle, L and Ho, A and Moore, SC and Hinds, C and Horby, P and Nichol, A and Maslove, D and Ling, L and McAuley, D and Montgomery, H and Walsh, T and Pereira, AC and Renieri, A and , and , and , and , and , and , and Shen, X and Ponting, CP and Fawkes, A and Tenesa, A and Caulfield, M and Scott, R and Rowan, K and Murphy, L and Openshaw, PJM and Semple, MG and Law, A and Vitart, V and Wilson, JF and Baillie, JK}, title = {Genetic mechanisms of critical illness in COVID-19.}, journal = {Nature}, volume = {591}, number = {7848}, pages = {92-98}, pmid = {33307546}, issn = {1476-4687}, support = {MR/K01417X/1/MRC_/Medical Research Council/United Kingdom ; MR/M00869X/2/MRC_/Medical Research Council/United Kingdom ; MC_PC_19056/MRC_/Medical Research Council/United Kingdom ; 104036/Z/14/Z/WT_/Wellcome Trust/United Kingdom ; G1001253/MRC_/Medical Research Council/United Kingdom ; MR/L501542/1/MRC_/Medical Research Council/United Kingdom ; MR/R026408/1/MRC_/Medical Research Council/United Kingdom ; MR/N02995X/1/MRC_/Medical Research Council/United Kingdom ; MC_PC_20004/MRC_/Medical Research Council/United Kingdom ; MR/S006753/1/MRC_/Medical Research Council/United Kingdom ; 216767/Z/19/Z/WT_/Wellcome Trust/United Kingdom ; G0701075/MRC_/Medical Research Council/United Kingdom ; G0901254/MRC_/Medical Research Council/United Kingdom ; MC_PC_19026/MRC_/Medical Research Council/United Kingdom ; MC_EX_MR/M009203/1/MRC_/Medical Research Council/United Kingdom ; G-0907/PUK_/Parkinson's UK/United Kingdom ; 205228/Z/16/Z/WT_/Wellcome Trust/United Kingdom ; 103258/Z/13/A/WT_/Wellcome Trust/United Kingdom ; MC_PC_19059/MRC_/Medical Research Council/United Kingdom ; MC_UU_00007/15/MRC_/Medical Research Council/United Kingdom ; MC_UU_12008/1/MRC_/Medical Research Council/United Kingdom ; G-1307/PUK_/Parkinson's UK/United Kingdom ; MC_UU_12014/9/MRC_/Medical Research Council/United Kingdom ; MR/S032304/1/MRC_/Medical Research Council/United Kingdom ; MR/M009203/1/MRC_/Medical Research Council/United Kingdom ; MR/J004758/1/MRC_/Medical Research Council/United Kingdom ; MC_UU_00007/10/MRC_/Medical Research Council/United Kingdom ; MR/P015514/1/MRC_/Medical Research Council/United Kingdom ; MC_PC_19025/MRC_/Medical Research Council/United Kingdom ; MR/R026408/1/WT_/Wellcome Trust/United Kingdom ; 215091/Z/18/Z/WT_/Wellcome Trust/United Kingdom ; 109965/Z/15/Z/WT_/Wellcome Trust/United Kingdom ; MC_PC_14089/MRC_/Medical Research Council/United Kingdom ; }, mesh = {2',5'-Oligoadenylate Synthetase/genetics ; COVID-19/*genetics/pathology/*physiopathology ; Chromosomes, Human, Pair 12/genetics ; Chromosomes, Human, Pair 19/genetics ; Chromosomes, Human, Pair 21/genetics ; Critical Care ; *Critical Illness ; Dipeptidyl-Peptidases and Tripeptidyl-Peptidases/genetics ; Drug Repositioning ; Female ; Genome-Wide Association Study ; Humans ; Inflammation/genetics/pathology/physiopathology ; Lung/pathology/physiopathology/virology ; Male ; Multigene Family/genetics ; Receptor, Interferon alpha-beta/genetics ; Receptors, CCR2/genetics ; TYK2 Kinase/genetics ; United Kingdom ; }, abstract = {Host-mediated lung inflammation is present[1], and drives mortality[2], in the critical illness caused by coronavirus disease 2019 (COVID-19). Host genetic variants associated with critical illness may identify mechanistic targets for therapeutic development[3]. Here we report the results of the GenOMICC (Genetics Of Mortality In Critical Care) genome-wide association study in 2,244 critically ill patients with COVID-19 from 208 UK intensive care units. We have identified and replicated the following new genome-wide significant associations: on chromosome 12q24.13 (rs10735079, P = 1.65 × 10[-8]) in a gene cluster that encodes antiviral restriction enzyme activators (OAS1, OAS2 and OAS3); on chromosome 19p13.2 (rs74956615, P = 2.3 × 10[-8]) near the gene that encodes tyrosine kinase 2 (TYK2); on chromosome 19p13.3 (rs2109069, P = 3.98 × 10[-12]) within the gene that encodes dipeptidyl peptidase 9 (DPP9); and on chromosome 21q22.1 (rs2236757, P = 4.99 × 10[-8]) in the interferon receptor gene IFNAR2. We identified potential targets for repurposing of licensed medications: using Mendelian randomization, we found evidence that low expression of IFNAR2, or high expression of TYK2, are associated with life-threatening disease; and transcriptome-wide association in lung tissue revealed that high expression of the monocyte-macrophage chemotactic receptor CCR2 is associated with severe COVID-19. Our results identify robust genetic signals relating to key host antiviral defence mechanisms and mediators of inflammatory organ damage in COVID-19. Both mechanisms may be amenable to targeted treatment with existing drugs. However, large-scale randomized clinical trials will be essential before any change to clinical practice.}, } @article {pmid33306534, year = {2021}, author = {Hunt, CW and Chaturvedi, R and Brown, L and Stafford, C and Cauley, CE and Goldstone, RN and Francone, TD and Kunitake, H and Bordeianou, L and Ricciardi, R}, title = {Diverticular Disease Epidemiology: Rising Rates of Diverticular Disease Mortality Across Developing Nations.}, journal = {Diseases of the colon and rectum}, volume = {64}, number = {1}, pages = {81-90}, pmid = {33306534}, issn = {1530-0358}, mesh = {Adult ; Aged ; Aged, 80 and over ; Cost of Illness ; Databases, Factual ; Developed Countries/statistics & numerical data ; Developing Countries/economics/*statistics & numerical data ; Diet/statistics & numerical data ; Diverticular Diseases/economics/*mortality ; Female ; Global Health/economics/statistics & numerical data ; Health Expenditures/statistics & numerical data ; *Health Status Disparities ; Humans ; Male ; Middle Aged ; Overweight/economics/epidemiology ; World Health Organization ; }, abstract = {BACKGROUND: The incidence of diverticular disease is growing in the Western world. However, the global burden of disease is unknown in the developing world.

OBJECTIVE: This study aimed to determine the global burden of diverticular disease as measured by disease-specific mortality while identifying indicators of rising disease rates.

DESIGN: We undertook an ecological analysis based on data from the World Health Organization Mortality Database. Then, we analyzed global age-adjusted mortality rates from diverticular disease and compared them to national rates of overweight adults, health expenditures, and dietary composition.

SETTINGS: National vital statistics data were collected.

PATIENTS: Diverticular disease deaths from January 1, 1994 through December 31, 2016 were evaluated.

MAIN OUTCOME MEASURES: The primary outcome measured was the national age-adjusted mortality rate.

RESULTS: The average age-adjusted mortality rate for diverticular disease was 0.51 ± 0.31/100,000 with a range of 0.11 to 1.75/100,000. During the study period, we noted that 57% of nations had increasing diverticular disease mortality rates, whereas only 7% had decreasing rates. More developed nations (40%) than developing nations (24%) were categorized as having high diverticular disease mortality burden over the time period of the study, and developed nations had higher percentages of overweight adults (58.9 ± 3.1%) than developing nations (50.6 ± 6.7%; p < 0.0001). However, developing nations revealed more rapid increases in diverticular disease mortality (0.027 ± 0.024/100,000 per year) than developed nations (0.005 ± 0.025/100,000 per year; p = 0.001), as well as faster expanding proportions of overweight adults (0.76 ± 0.12% per year) than in already developed nations (0.53 ± 0.10% per year; p<0.0001).

LIMITATIONS: Ecological studies cannot define cause and effect.

CONCLUSIONS: There is considerable variability in diverticular disease mortality across the globe. Developing nations were characterized by rapid increases in diverticular disease mortality and expanding percentages of overweight adults. Public health interventions in developing nations are needed to alter mortality rates from diverticular disease. See Video Abstract at http://links.lww.com/DCR/B397. EPIDEMIOLOGÍA DE LA ENFERMEDAD DIVERTICULAR: TASAS CRECIENTES DE MORTALIDAD POR ENFERMEDAD DIVERTICULAR EN LOS PAÍSES EN DESARROLLO: La incidencia de la enfermedad diverticular está creciendo en el mundo occidental. Sin embargo, la carga mundial de la enfermedad es desconocida en el mundo en desarrollo.Determinar la carga global de la enfermedad diverticular medida por la mortalidad específica de la enfermedad mientras se identifican los indicadores de aumento de las tasas de enfermedad.Realizamos un análisis ecológico basado en datos de la Base de datos de mortalidad de la Organización Mundial de la Salud. Luego, analizamos las tasas globales de mortalidad ajustadas por edad por enfermedad diverticular y las comparamos con las tasas nacionales de adultos con sobrepeso, gastos de salud y composición dietética.Datos nacionales de estadísticas vitales.Muertes por enfermedades diverticulares desde el 1 de enero de 1994 hasta el 31 de diciembre de 2016.Tasa nacional de mortalidad ajustada por edad.La tasa promedio de mortalidad ajustada por edad para la enfermedad diverticular fue de 0,51 ± 0,31 / 100,000 con un rango de 0,11 a 1,75 / 100,000. Durante el período de estudio, notamos que el 57% de las naciones tenían tasas crecientes de mortalidad por enfermedades diverticulares, mientras que solo el 7% tenían tasas decrecientes. Las naciones más desarrolladas (40%) que las naciones en desarrollo (24%) se clasificaron como que tienen una alta carga de mortalidad por enfermedad diverticular durante el período de tiempo del estudio, y las naciones desarrolladas tuvieron porcentajes más altos de adultos con sobrepeso (58.9 ± 3.1%) que las naciones en desarrollo (50,6 ± 6,7%) (p <0,0001). Sin embargo, las naciones en desarrollo revelaron aumentos más rápidos en la mortalidad por enfermedades diverticulares (0.027 ± 0.024 / 100,000 por año) que las naciones desarrolladas (0.005 ± 0.025 / 100,000 por año) (p = 0.001), así como proporciones de adultos con sobrepeso en expansión más rápida (0.76 ± 0.12% por año) que en las naciones ya desarrolladas (0.53 ± 0.10% por año) (p <0.0001).Los estudios ecológicos no pueden definir causa y efecto.Existe una considerable variabilidad en la mortalidad por enfermedad diverticular en todo el mundo. Los países en desarrollo se caracterizaron por un rápido aumento en la mortalidad por enfermedades diverticulares y porcentajes crecientes de adultos con sobrepeso. Se necesitan intervenciones de salud pública en los países en desarrollo para alterar las tasas de mortalidad por enfermedad diverticular. Consulte Video Resumen en http://links.lww.com/DCR/B397.}, } @article {pmid33305441, year = {2021}, author = {Pegoraro, EF and Mauritz, ME and Ogle, K and Ebert, CH and Schuur, EAG}, title = {Lower soil moisture and deep soil temperatures in thermokarst features increase old soil carbon loss after 10 years of experimental permafrost warming.}, journal = {Global change biology}, volume = {27}, number = {6}, pages = {1293-1308}, doi = {10.1111/gcb.15481}, pmid = {33305441}, issn = {1365-2486}, support = {//National Parks Inventory and Monitoring Program/ ; DE-SC0006982//U.S. Department of Energy/ ; DE-SC0014085//U.S. Department of Energy/ ; 1026415//National Science Foundation/ ; 0747195//National Science Foundation/ ; //The Scientific Research Society/ ; }, mesh = {Bayes Theorem ; Carbon ; Ecosystem ; *Permafrost ; Soil ; Temperature ; }, abstract = {Almost half of the global terrestrial soil carbon (C) is stored in the northern circumpolar permafrost region, where air temperatures are increasing two times faster than the global average. As climate warms, permafrost thaws and soil organic matter becomes vulnerable to greater microbial decomposition. Long-term soil warming of ice-rich permafrost can result in thermokarst formation that creates variability in environmental conditions. Consequently, plant and microbial proportional contributions to ecosystem respiration may change in response to long-term soil warming. Natural abundance δ[13] C and Δ[14] C of aboveground and belowground plant material, and of young and old soil respiration were used to inform a mixing model to partition the contribution of each source to ecosystem respiration fluxes. We employed a hierarchical Bayesian approach that incorporated gross primary productivity and environmental drivers to constrain source contributions. We found that long-term experimental permafrost warming introduced a soil hydrology component that interacted with temperature to affect old soil C respiration. Old soil C loss was suppressed in plots with warmer deep soil temperatures because they tended to be wetter. When soil volumetric water content significantly decreased in 2018 relative to 2016 and 2017, the dominant respiration sources shifted from plant aboveground and young soil respiration to old soil respiration. The proportion of ecosystem respiration from old soil C accounted for up to 39% of ecosystem respiration and represented a 30-fold increase compared to the wet-year average. Our findings show that thermokarst formation may act to moderate microbial decomposition of old soil C when soil is highly saturated. However, when soil moisture decreases, a higher proportion of old soil C is vulnerable to decomposition and can become a large flux to the atmosphere. As permafrost systems continue to change with climate, we must understand the thresholds that may propel these systems from a C sink to a source.}, } @article {pmid33302865, year = {2020}, author = {Leal, BSS and Brandão, MM and Palma-Silva, C and Pinheiro, F}, title = {Differential gene expression reveals mechanisms related to habitat divergence between hybridizing orchids from the Neotropical coastal plains.}, journal = {BMC plant biology}, volume = {20}, number = {1}, pages = {554}, pmid = {33302865}, issn = {1471-2229}, support = {16/22785-8//FAPESP/ ; 18/18967-9//FAPESP/ ; 305398/2019-9//CNPq/ ; }, mesh = {Adaptation, Physiological/genetics ; Brazil ; *Ecosystem ; Gene Expression Profiling/*methods ; *Gene Expression Regulation, Plant ; Gene Ontology ; Gene-Environment Interaction ; Genetic Speciation ; Geography ; Hybridization, Genetic ; Orchidaceae/classification/*genetics ; Principal Component Analysis ; Species Specificity ; *Tropical Climate ; *Wetlands ; }, abstract = {BACKGROUND: Closely related hybridizing species are ideal systems for identifying genomic regions underlying adaptive divergence. Although gene expression plays a central role in determining ecologically-based phenotypic differences, few studies have inferred the role of gene expression for adaptive divergence in Neotropical systems. In this study, we conduct genome-wide expression analysis alongside soil elemental analysis in sympatric and allopatric populations of Epidendrum fulgens and E. puniceoluteum (Orchidaceae), which occur in contrasting adjacent habitats in the Neotropical coastal plains.

RESULTS: These species were highly differentiated by their gene expression profiles, as determined by 18-21% of transcripts. Gene ontology (GO) terms associated with reproductive processes were enriched according to comparisons between species in both allopatric and sympatric populations. Species showed differential expression in genes linked to salt and waterlogging tolerance according to comparisons between species in sympatry, and biological processes related to environmental stimulus appeared as representative among those transcripts associated with edaphic characteristics in each sympatric zone. Hybrids, in their turn, were well differentiated from E. fulgens, but exhibited a similar gene expression profile to flooding-tolerant E. puniceolutem. When compared with parental species, hybrids showed no transcripts with additive pattern of expression and increased expression for almost all transgressive transcripts.

CONCLUSIONS: This study sheds light on general mechanisms promoting ecological differentiation and assortative mating, and suggests candidate genes, such as those encoding catalase and calcium-dependent protein kinase, underling adaptation to harsh edaphic conditions in the Neotropical coastal plains. Moreover, it demonstrates that differential gene expression plays a central role in determining ecologically-based phenotypic differences among co-occurring species and their hybrids.}, } @article {pmid33301457, year = {2020}, author = {Gostic, KM and McGough, L and Baskerville, EB and Abbott, S and Joshi, K and Tedijanto, C and Kahn, R and Niehus, R and Hay, JA and De Salazar, PM and Hellewell, J and Meakin, S and Munday, JD and Bosse, NI and Sherrat, K and Thompson, RN and White, LF and Huisman, JS and Scire, J and Bonhoeffer, S and Stadler, T and Wallinga, J and Funk, S and Lipsitch, M and Cobey, S}, title = {Practical considerations for measuring the effective reproductive number, Rt.}, journal = {PLoS computational biology}, volume = {16}, number = {12}, pages = {e1008409}, pmid = {33301457}, issn = {1553-7358}, support = {R01 GM122876/GM/NIGMS NIH HHS/United States ; T32 AI007535/AI/NIAID NIH HHS/United States ; 210758/Z/18/Z/WT_/Wellcome Trust/United Kingdom ; U54 GM088558/GM/NIGMS NIH HHS/United States ; /WT_/Wellcome Trust/United Kingdom ; F32 GM134721/GM/NIGMS NIH HHS/United States ; HHSN272201400005C/AI/NIAID NIH HHS/United States ; }, mesh = {*Basic Reproduction Number ; *COVID-19/epidemiology/transmission ; Computational Biology ; Humans ; Models, Statistical ; SARS-CoV-2 ; }, abstract = {Estimation of the effective reproductive number Rt is important for detecting changes in disease transmission over time. During the Coronavirus Disease 2019 (COVID-19) pandemic, policy makers and public health officials are using Rt to assess the effectiveness of interventions and to inform policy. However, estimation of Rt from available data presents several challenges, with critical implications for the interpretation of the course of the pandemic. The purpose of this document is to summarize these challenges, illustrate them with examples from synthetic data, and, where possible, make recommendations. For near real-time estimation of Rt, we recommend the approach of Cori and colleagues, which uses data from before time t and empirical estimates of the distribution of time between infections. Methods that require data from after time t, such as Wallinga and Teunis, are conceptually and methodologically less suited for near real-time estimation, but may be appropriate for retrospective analyses of how individuals infected at different time points contributed to the spread. We advise caution when using methods derived from the approach of Bettencourt and Ribeiro, as the resulting Rt estimates may be biased if the underlying structural assumptions are not met. Two key challenges common to all approaches are accurate specification of the generation interval and reconstruction of the time series of new infections from observations occurring long after the moment of transmission. Naive approaches for dealing with observation delays, such as subtracting delays sampled from a distribution, can introduce bias. We provide suggestions for how to mitigate this and other technical challenges and highlight open problems in Rt estimation.}, } @article {pmid33300727, year = {2020}, author = {Liang, YY and Zhao, YD}, title = {[Construction and optimization of ecological network in Xi'an based on landscape analysis].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {31}, number = {11}, pages = {3767-3776}, doi = {10.13287/j.1001-9332.202011.019}, pmid = {33300727}, issn = {1001-9332}, mesh = {Cities ; City Planning ; *Conservation of Natural Resources ; *Ecosystem ; Urbanization ; }, abstract = {Ecological network can connect fragmented habitat patches to increase the connectivity among landscapes, which plays an important role to landscapes and ecological problems caused by urbanization. In this study, the ecological networks of Xi'an City were constructed using landscape pattern index and morphological spatial pattern analysis to reveal landscape pattern features. The performance of the network was evaluated with the gravity model to provide an optimization strategy. The landscape richness index was relatively high, with significant differences of landscape patterns between north and south parts. The ecological sources were predominated in the south and east areas, while a higher comprehensive resistance with low connectivity was found in the north and central areas. The ecological corridors were unevenly distributed, with the radiation channels derived from hydrological analysis providing a supplementary role. Furthermore, ecological networks could be optimized by introducing other ecological sources, supplementing stepping stones, and repairing fracture points, to reduce the problems of uneven distribution of ecological sources, the excessively long ecological corridors in local regions, and the obstruction of road networks. Our optimization method provided an optional way to assist urban planning of Xi'an City.}, } @article {pmid33299887, year = {2020}, author = {Zhu, M and Li, Y and Ding, C and Wang, J and Ma, Y and Li, Z and Zhang, X and Wang, P}, title = {Proteomic Profiling Change and Its Implies in the Early Mycosis Fungoides (MF) Using Isobaric Tags for Relative and Absolute Quantification (iTRAQ).}, journal = {BioMed research international}, volume = {2020}, number = {}, pages = {9237381}, pmid = {33299887}, issn = {2314-6141}, mesh = {Adult ; Biomarkers/metabolism ; Early Detection of Cancer ; Female ; Gene Expression Profiling ; *Gene Expression Regulation ; Gene Ontology ; Genetic Markers ; Humans ; Isotope Labeling ; Male ; Middle Aged ; Mycosis Fungoides/*diagnosis/*metabolism ; Neoplasms/metabolism ; Peptides/chemistry ; *Proteome ; Signal Transduction/genetics ; Skin Neoplasms/diagnosis/metabolism ; }, abstract = {PURPOSE: Mycosis fungoides (MF) is the most common T-cell lymphoma, with indolent biologic behavior in the early stage and features of invasive in the tumor stage. The diagnosis of MF is still ambiguous and difficult. We focused on the proteomic profiling change in the pathogenesis of early MF and identified candidate biomarkers for early diagnosis.

METHODS: We collected peripheral blood samples of MF patients and healthy individuals (HI) performed proteomic profiling analysis using isobaric tags for relative and absolute quantification (iTRAQ) platform. Differently expressed proteins (DEPs) were filtered, and involved biological functions were analyzed through Gene Ontology (GO) and Ingenuity Pathway Analysis (IPA) software.

RESULTS: We identified 78 DEPs including fifty proteins were upregulated and 28 proteins were downregulated in the MF group with HI as a control. Total DEPs were analyzed according to the biological regulation and metabolic process through GO analysis. The pathways of LXR/RXR activation and FXR/RXR activation were significantly activated, in which APOH, CLU, and ITIH4 were involved. The top annotated disease and function network was (Cancer, Organismal Injury and Abnormalities, Reproductive System Disease), with a key node CLU. These DEPs were involved in cancer, including thyroid carcinoma, head and neck carcinoma, and cancer of secretory structure, in which CLU, GNAS, and PKM played an indirect role in the occurrence and development of cancer. Relevant causal network was IL12 (family), which is related to GNAS, PKM, and other DEPs.

CONCLUSION: Proteomic profiling of early-stage MF provided candidate protein biomarkers such as CLU, GNAS, and PKM, which benefit the early diagnosis and understanding of the mechanism of MF development. Besides, lipid metabolism may be one of the pathogenesis of MF, and IL12 was a potential marker for the diagnosis and treatment of early MF.}, } @article {pmid33299390, year = {2020}, author = {Hamadeh, RR and Lee, J and Abu-Rmeileh, NME and Darawad, M and Mostafa, A and Kheirallah, KA and Yusufali, A and Thomas, J and Salama, M and Nakkash, R and Salloum, RG}, title = {Gender differences in waterpipe tobacco smoking among university students in four Eastern Mediterranean countries.}, journal = {Tobacco induced diseases}, volume = {18}, number = {}, pages = {100}, pmid = {33299390}, issn = {1617-9625}, abstract = {INTRODUCTION: Males have a higher prevalence of waterpipe tobacco smoking (WTS) than females in most Eastern Mediterranean Region (EMR) countries, with a smaller gender gap than that of cigarette smoking. The objective of this study was to determine gender differences among university students with respect to WTS initiation, smoking behavior, tobacco flavors, and expenditure on WTS, in four EMR countries.

METHODS: A cross-sectional online survey was conducted based on convenient samples of ever waterpipe smokers among university students in four EMR countries (Egypt, Jordan, Occupied Palestinian Territories, and the United Arab Emirates) in 2016. The total samples included 2470 participants. Study participants were invited through flyers, university portals, emails and Facebook, followed by emails with links to the internet survey.

RESULTS: Females (80.4%) were more likely than males (66.4%, p<0.001) to be in the younger age group (18-22 years) and they were less likely to be current waterpipe smokers (females, 60.0%; males 69.5%, p<0.001). Two-thirds of students across both genders smoked their first waterpipe at the age of 15-19 years, with more females starting with family members. Over one-third of males and 14.9% of the females usually smoked ≥10 heads (p<0.001). About half (46.6%) of females smoked for less than half an hour compared to 30.5% of males (p<0.001). Only 1% of females smoked non-flavored tobacco compared to 11% of males (p<0.001). There was a significant (p=0.05) positive correlation (r=0.808) with respect to tobacco flavor usually smoked between males and females with apple/double apple being the most popular.

CONCLUSIONS: There were gender differences in WTS in several aspects. The study has implications for educational establishments, tobacco control and women civil society groups, as well as policymakers.}, } @article {pmid33299196, year = {2020}, author = {Egli, L and Schröter, M and Scherber, C and Tscharntke, T and Seppelt, R}, title = {Crop asynchrony stabilizes food production.}, journal = {Nature}, volume = {588}, number = {7837}, pages = {E7-E12}, pmid = {33299196}, issn = {1476-4687}, mesh = {*Biodiversity ; Crop Production/*methods ; Crops, Agricultural/classification/*growth & development ; Datasets as Topic ; *Food Supply ; Humans ; Time Factors ; }, } @article {pmid33298108, year = {2020}, author = {Pieroni, A and Vandebroek, I and Prakofjewa, J and Bussmann, RW and Paniagua-Zambrana, NY and Maroyi, A and Torri, L and Zocchi, DM and Dam, ATK and Khan, SM and Ahmad, H and Yeşil, Y and Huish, R and Pardo-de-Santayana, M and Mocan, A and Hu, X and Boscolo, O and Sõukand, R}, title = {Taming the pandemic? The importance of homemade plant-based foods and beverages as community responses to COVID-19.}, journal = {Journal of ethnobiology and ethnomedicine}, volume = {16}, number = {1}, pages = {75}, pmid = {33298108}, issn = {1746-4269}, mesh = {Beverages/supply & distribution ; Bolivia ; Brazil ; COVID-19/epidemiology/prevention & control/*therapy ; Cambodia ; China ; Food ; Global Health ; Humans ; Italy ; Jamaica ; Lithuania ; New York City ; Pakistan ; Phytotherapy/*methods ; *Plants, Medicinal ; Poland ; Romania ; Rural Population ; South Africa ; Spain ; Turkey ; Urban Population ; }, abstract = {Household responses to COVID-19 in different corners of the world represent the primary health care that communities have relied on for preventing and mitigating symptoms. During a very complex and confusing time, in which public health services in multiple countries have been completely overwhelmed, and in some cases even collapsed, these first-line household responses have been quintessential for building physical, mental, and social resilience, and for improving individual and community health. This editorial discusses the outcomes of a rapid-response preliminary survey during the first phase of the pandemic among social and community contacts in five metropolises heavily affected by the COVID-19 health crisis (Wuhan, Milan, Madrid, New York, and Rio de Janeiro), and in twelve rural areas or countries initially less affected by the pandemic (Appalachia, Jamaica, Bolivia, Romania, Belarus, Lithuania, Poland, Georgia, Turkey, Pakistan, Cambodia, and South Africa). We summarized our perspectives as 17 case studies, observing that people have relied primarily on teas and spices ("food-medicines") and that there exist clear international plant favorites, popularized by various new media. Urban diasporas and rural households seem to have repurposed homemade plant-based remedies that they use in normal times for treating the flu and other respiratory symptoms or that they simply consider healthy foods. The most remarkable shift in many areas has been the increased consumption of ginger and garlic, followed by onion, turmeric, and lemon. Our preliminary inventory of food medicines serves as a baseline for future systematic ethnobotanical studies and aims to inspire in-depth research on how use patterns of plant-based foods and beverages, both "traditional" and "new", are changing during and after the COVID-19 pandemic. Our reflections in this editorial call attention to the importance of ethnobiology, ethnomedicine, and ethnogastronomy research into domestic health care strategies for improving community health.}, } @article {pmid33297265, year = {2021}, author = {Hossain Bhuiyan, MA and Chandra Karmaker, S and Bodrud-Doza, M and Rakib, MA and Saha, BB}, title = {Enrichment, sources and ecological risk mapping of heavy metals in agricultural soils of dhaka district employing SOM, PMF and GIS methods.}, journal = {Chemosphere}, volume = {263}, number = {}, pages = {128339}, doi = {10.1016/j.chemosphere.2020.128339}, pmid = {33297265}, issn = {1879-1298}, mesh = {Agriculture ; Bangladesh ; China ; Environmental Monitoring ; Geographic Information Systems ; *Metals, Heavy/analysis ; Risk Assessment ; Soil ; *Soil Pollutants/analysis ; }, abstract = {Rapid urbanization and industrial growth have triggered heavy metal contamination in agricultural soil in Dhaka, which is a serious concern for ecological risk and public health issues. In this study, fifty-four soil samples from agricultural lands of Dhaka had been analyzed for assessing accumulation, spatial enrichment, ecological risk and sources apportionment of heavy metals using a combined approach of self-organizing map (SOM), positive matrix factorization (PMF), geographical information system (GIS), and enrichment factor (EF). The results of the enrichment factor, geoaccumulation index and contamination factor index showed that more than 90% of the soil samples were polluted by higher levels of Cr and Cd. The mean pollution load index (PLI) results demonstrated that about 73% of soil samples were moderately polluted by heavy metals. Based on SOM and PMF analysis, four potential sources of heavy metals were found in this study area: (i) agrochemical and sewage irrigation (Cd-As); (ii) combined effect of agriculture, industrial and natural sources (Mn, Co, Ni and Zn); (iii) atmospheric deposition and industrial emission (As-Pb); (iv) chemical and leather tanning industries (Cr). The ecological risk index demonstrated that in terms of Cd content, about 75% of soil samples were moderate to high risk, and 20% were moderate to considerable ecological risk, which was the serious environmental, ecological, and public health concern. The spatial projection of ecological risk values showed that the southern part of Dhaka (Keraniganj Upazila) is a high ecological risk in terms of heavy metal pollution. These risk maps in agricultural soils may play a vital role in reducing pollution sources; so that zonal pollution control, as well as ecological protection, may be achieved in this resource-based agricultural land.}, } @article {pmid33297197, year = {2021}, author = {Wojnarowska, M and Ilba, M and Szakiel, J and Turek, P and Sołtysik, M}, title = {Identifying the location of odour nuisance emitters using spatial GIS analyses.}, journal = {Chemosphere}, volume = {263}, number = {}, pages = {128252}, doi = {10.1016/j.chemosphere.2020.128252}, pmid = {33297197}, issn = {1879-1298}, mesh = {*Geographic Information Systems ; *Odorants ; Spatial Analysis ; }, abstract = {The primary objective of the article was to establish the location of odour emitters with the use of spatial GIS analyses. The odour emitter location analysis based on measurements was carried out using QGIS software tools. The algorithm of the procedure was developed by analysing vector elements, including simulated odour streaks (in the form of wedge buffer surfaces) and a regular grid of points needed to determine the presence of a given buffer in a given location. Statistical analysis was performed in ArcGIS software. The detailed aim of the conducted study was to analyse the nuisance of odours from the measurement data on the basis of IDW interpolation and the arrangement of buildings. An innovative element of the developed analysis is the application of the inversed method of fragrance streak propagation. Identifying a streak from the measuring point towards the blowing wind is very likely to determine the approximate location of the odour emitter measured. The described method should provide better results at the location of emitters than the above mentioned methods using interpolation, because of taking into account wind direction and speed. In addition, it is a method that can be applied over a large open area where methods based on simulation and particle propagation would not be efficient or highly impossible to apply due to extensive and complex analysis. It was necessary to conduct field studies in order to meet the main goal, which resulted in sensory evaluation of the intensity of odour nuisance in an urbanised area. Odour concentration tests using field olfactometry with NasalRanger olfactometer were taken.}, } @article {pmid33295865, year = {2020}, author = {Lefoulon, E and Clark, T and Guerrero, R and Cañizales, I and Cardenas-Callirgos, JM and Junker, K and Vallarino-Lhermitte, N and Makepeace, BL and Darby, AC and Foster, JM and Martin, C and Slatko, BE}, title = {Diminutive, degraded but dissimilar: Wolbachia genomes from filarial nematodes do not conform to a single paradigm.}, journal = {Microbial genomics}, volume = {6}, number = {12}, pages = {}, pmid = {33295865}, issn = {2057-5858}, mesh = {Animals ; Databases, Genetic ; Evolution, Molecular ; Filarioidea/*microbiology ; Genome Size ; Genome, Bacterial ; Genomics ; Molecular Sequence Annotation ; Phylogeny ; Sequence Analysis, DNA/*methods ; Wolbachia/*classification/genetics/isolation & purification ; }, abstract = {Wolbachia are alpha-proteobacteria symbionts infecting a large range of arthropod species and two different families of nematodes. Interestingly, these endosymbionts are able to induce diverse phenotypes in their hosts: they are reproductive parasites within many arthropods, nutritional mutualists within some insects and obligate mutualists within their filarial nematode hosts. Defining Wolbachia 'species' is controversial and so they are commonly classified into 17 different phylogenetic lineages, termed supergroups, named A-F, H-Q and S. However, available genomic data remain limited and not representative of the full Wolbachia diversity; indeed, of the 24 complete genomes and 55 draft genomes of Wolbachia available to date, 84 % belong to supergroups A and B, exclusively composed of Wolbachia from arthropods. For the current study, we took advantage of a recently developed DNA-enrichment method to produce four complete genomes and two draft genomes of Wolbachia from filarial nematodes. Two complete genomes, wCtub and wDcau, are the smallest Wolbachia genomes sequenced to date (863 988 bp and 863 427 bp, respectively), as well as the first genomes representing supergroup J. These genomes confirm the validity of this supergroup, a controversial clade due to weaknesses of the multilocus sequence typing approach. We also produced the first draft Wolbachia genome from a supergroup F filarial nematode representative (wMhie), two genomes from supergroup D (wLsig and wLbra) and the complete genome of wDimm from supergroup C. Our new data confirm the paradigm of smaller Wolbachia genomes from filarial nematodes containing low levels of transposable elements and the absence of intact bacteriophage sequences, unlike many Wolbachia from arthropods, where both are more abundant. However, we observe differences among the Wolbachia genomes from filarial nematodes: no global co-evolutionary pattern, strong synteny between supergroup C and supergroup J Wolbachia, and more transposable elements observed in supergroup D Wolbachia compared to the other supergroups. Metabolic pathway analysis indicates several highly conserved pathways (haem and nucleotide biosynthesis, for example) as opposed to more variable pathways, such as vitamin B biosynthesis, which might be specific to certain host-symbiont associations. Overall, there appears to be no single Wolbachia-filarial nematode pattern of co-evolution or symbiotic relationship.}, } @article {pmid33293507, year = {2020}, author = {Grantham, HS and Duncan, A and Evans, TD and Jones, KR and Beyer, HL and Schuster, R and Walston, J and Ray, JC and Robinson, JG and Callow, M and Clements, T and Costa, HM and DeGemmis, A and Elsen, PR and Ervin, J and Franco, P and Goldman, E and Goetz, S and Hansen, A and Hofsvang, E and Jantz, P and Jupiter, S and Kang, A and Langhammer, P and Laurance, WF and Lieberman, S and Linkie, M and Malhi, Y and Maxwell, S and Mendez, M and Mittermeier, R and Murray, NJ and Possingham, H and Radachowsky, J and Saatchi, S and Samper, C and Silverman, J and Shapiro, A and Strassburg, B and Stevens, T and Stokes, E and Taylor, R and Tear, T and Tizard, R and Venter, O and Visconti, P and Wang, S and Watson, JEM}, title = {Anthropogenic modification of forests means only 40% of remaining forests have high ecosystem integrity.}, journal = {Nature communications}, volume = {11}, number = {1}, pages = {5978}, pmid = {33293507}, issn = {2041-1723}, mesh = {Africa, Central ; *Biodiversity ; Canada ; Climate Change ; Conservation of Natural Resources/legislation & jurisprudence/*statistics & numerical data ; *Environmental Policy ; *Forests ; New Guinea ; Russia ; }, abstract = {Many global environmental agendas, including halting biodiversity loss, reversing land degradation, and limiting climate change, depend upon retaining forests with high ecological integrity, yet the scale and degree of forest modification remain poorly quantified and mapped. By integrating data on observed and inferred human pressures and an index of lost connectivity, we generate a globally consistent, continuous index of forest condition as determined by the degree of anthropogenic modification. Globally, only 17.4 million km[2] of forest (40.5%) has high landscape-level integrity (mostly found in Canada, Russia, the Amazon, Central Africa, and New Guinea) and only 27% of this area is found in nationally designated protected areas. Of the forest inside protected areas, only 56% has high landscape-level integrity. Ambitious policies that prioritize the retention of forest integrity, especially in the most intact areas, are now urgently needed alongside current efforts aimed at halting deforestation and restoring the integrity of forests globally.}, } @article {pmid33293248, year = {2021}, author = {Kamalyan, L and Yang, JA and Pope, CN and Paolillo, EW and Campbell, LM and Tang, B and Marquine, MJ and Depp, CA and Moore, RC}, title = {Increased Social Interactions Reduce the Association Between Constricted Life-Space and Lower Daily Happiness in Older Adults With and Without HIV: A GPS and Ecological Momentary Assessment Study.}, journal = {The American journal of geriatric psychiatry : official journal of the American Association for Geriatric Psychiatry}, volume = {29}, number = {8}, pages = {867-879}, pmid = {33293248}, issn = {1545-7214}, support = {R21 MH116104/MH/NIMH NIH HHS/United States ; T32 DA031098/DA/NIDA NIH HHS/United States ; T32 AA013525/AA/NIAAA NIH HHS/United States ; K23 MH107260/MH/NIMH NIH HHS/United States ; L30 MH104725/MH/NIMH NIH HHS/United States ; R01 AG062387/AG/NIA NIH HHS/United States ; P30 MH062512/MH/NIMH NIH HHS/United States ; F31 AG067869/AG/NIA NIH HHS/United States ; R25 MH108389/MH/NIMH NIH HHS/United States ; F31 AA027198/AA/NIAAA NIH HHS/United States ; }, mesh = {Aged ; Aged, 80 and over ; *Ecological Momentary Assessment ; Geographic Information Systems ; *HIV Infections ; Happiness ; Humans ; Social Interaction ; }, abstract = {OBJECTIVE: Older persons with human immunodeficiency virus (HIV) (PWH) are particularly susceptible to life-space restrictions. The aims of this study included: 1) using global positioning system (GPS) derived indicators as an assessment of time spent at home among older adults with and without HIV; 2) using ecological momentary assessment (EMA) to examine real-time relationships between life-space, mood (happiness, sadness, anxious), fatigue, and pain; and 3) determining if number of daily social interactions moderated the effect of life-space on mood.

METHODS: Eighty-eight older adults (PWH n = 54, HIV-negative n = 34) completed smartphone-based EMA surveys assessing mood, fatigue, pain, and social interactions four times per day for two weeks. Participants' smartphones were GPS enabled throughout the study. Mixed-effects regression models analyzed concurrent and lagged associations among life-space and behavioral indicators of health.

RESULTS: PWH spent more of their time at home (79% versus 70%, z = -2.08; p = 0.04) and reported lower mean happiness (3.2 versus 3.7; z = 2.63; p = 0.007) compared to HIV-negative participants. Controlling for covariates, more daily social interactions were associated with higher ratings of real-time happiness (b = 0.12; t = 5.61; df = 1087.9; p< 0.001). Similar findings were seen in lagged analyses: prior day social interactions (b = 0.15; t = 7.3; df = 1024.9; p < 0.0001) and HIV status (b = -0.48; t = -2.56; df = 1026.8; p = 0.01) attenuated the effect of prior day time spent at home on happiness.

CONCLUSION: Accounting for engagement in social interactions reduced the significant effect of time spent at home and lower happiness. Interventions targeting social isolation within the context of constricted life-space may be beneficial for increasing positive mood in older adults, and especially relevant to older PWH.}, } @article {pmid33291220, year = {2020}, author = {Hufsky, F and Beerenwinkel, N and Meyer, IM and Roux, S and Cook, GM and Kinsella, CM and Lamkiewicz, K and Marquet, M and Nieuwenhuijse, DF and Olendraite, I and Paraskevopoulou, S and Young, F and Dijkman, R and Ibrahim, B and Kelly, J and Le Mercier, P and Marz, M and Ramette, A and Thiel, V}, title = {The International Virus Bioinformatics Meeting 2020.}, journal = {Viruses}, volume = {12}, number = {12}, pages = {}, pmid = {33291220}, issn = {1999-4915}, mesh = {COVID-19 ; *Computational Biology ; Congresses as Topic ; Evolution, Molecular ; Genome, Viral ; Humans ; Metagenomics ; RNA Viruses/*genetics/pathogenicity ; *Virology ; }, abstract = {The International Virus Bioinformatics Meeting 2020 was originally planned to take place in Bern, Switzerland, in March 2020. However, the COVID-19 pandemic put a spoke in the wheel of almost all conferences to be held in 2020. After moving the conference to 8-9 October 2020, we got hit by the second wave and finally decided at short notice to go fully online. On the other hand, the pandemic has made us even more aware of the importance of accelerating research in viral bioinformatics. Advances in bioinformatics have led to improved approaches to investigate viral infections and outbreaks. The International Virus Bioinformatics Meeting 2020 has attracted approximately 120 experts in virology and bioinformatics from all over the world to join the two-day virtual meeting. Despite concerns being raised that virtual meetings lack possibilities for face-to-face discussion, the participants from this small community created a highly interactive scientific environment, engaging in lively and inspiring discussions and suggesting new research directions and questions. The meeting featured five invited and twelve contributed talks, on the four main topics: (1) proteome and RNAome of RNA viruses, (2) viral metagenomics and ecology, (3) virus evolution and classification and (4) viral infections and immunology. Further, the meeting featured 20 oral poster presentations, all of which focused on specific areas of virus bioinformatics. This report summarizes the main research findings and highlights presented at the meeting.}, } @article {pmid33290786, year = {2021}, author = {Chen, Z and Boon, SS and Wang, MH and Chan, RWY and Chan, PKS}, title = {Genomic and evolutionary comparison between SARS-CoV-2 and other human coronaviruses.}, journal = {Journal of virological methods}, volume = {289}, number = {}, pages = {114032}, pmid = {33290786}, issn = {1879-0984}, mesh = {Animals ; Betacoronavirus/*genetics ; Computational Biology ; Coronavirus Infections/*virology ; Databases, Genetic ; *Evolution, Molecular ; *Genome, Viral ; Humans ; Phylogeny ; SARS-CoV-2/*genetics ; }, abstract = {Three highly pathogenic human coronaviruses can cause severe acute respiratory syndrome (SARS-CoV, SARS-CoV-2 and MERS-CoV). Although phylogenetic analyses have indicated ancient origin of human coronaviruses from animal relatives, their evolutionary history remains to be established. Using phylogenetics and "high order genomic structures" including trimer spectrums, codon usage and dinucleotide suppression, we observed distinct clustering of all human coronaviruses that formed phylogenetic clades with their closest animal relatives, indicating they have encompassed long evolutionary histories within specific ecological niches before jumping species barrier to infect humans. The close relationships between SARS-CoV and SARS-CoV-2 imply similar evolutionary origin. However, a lower Effective Codon Number (ENC) pattern and CpG dinucleotide suppression in SARS-CoV-2 genomes compared to SARS-CoV and MERS-CoV may imply a better host fitness, and thus their success in sustaining a pandemic. Characterization of coronavirus heterogeneity via complementary approaches enriches our understanding on the evolution and virus-host interaction of these emerging human pathogens while the underlying mechanistic basis in pathogenicity warrants further investigation.}, } @article {pmid33289563, year = {2020}, author = {Chachulski, L and Windshügel, B}, title = {LEADS-FRAG: A Benchmark Data Set for Assessment of Fragment Docking Performance.}, journal = {Journal of chemical information and modeling}, volume = {60}, number = {12}, pages = {6544-6554}, doi = {10.1021/acs.jcim.0c00693}, pmid = {33289563}, issn = {1549-960X}, mesh = {*Benchmarking ; Ligands ; Molecular Docking Simulation ; Protein Binding ; *Software ; }, abstract = {Fragment-based drug design is a popular approach in drug discovery, which makes use of computational methods such as molecular docking. To assess fragment placement performance of molecular docking programs, we constructed LEADS-FRAG, a benchmark data set containing 93 high-quality protein-fragment complexes that were selected from the Protein Data Bank using a rational and unbiased process. The data set contains fully prepared protein and fragment structures and is publicly available. Moreover, we used LEADS-FRAG for evaluating the small-molecule docking programs AutoDock, AutoDock Vina, FlexX, and GOLD for their fragment docking performance. GOLD in combination with the scoring function ChemPLP and AutoDock Vina performed best and generated near-native conformations (root mean square deviation <1.5 Å) for more than 50% of the data set considering the top-ranked docking pose. Taking into account all docking poses, the tested programs generated near-native conformations for up to 86% of the fragments in LEADS-FRAG. By rescoring all docking poses with the GOLD scoring functions and the Protein-Ligand Informatics force field, the number of near-native conformations increased up to 40% with respect to the top-rescored poses. Our results show that conventional small-molecule docking programs achieve a satisfactory fragment docking performance when utilizing rescoring.}, } @article {pmid33288699, year = {2020}, author = {Duda, MP and Allen-Mahé, S and Barbraud, C and Blais, JM and Boudreau, A and Bryant, R and Delord, K and Grooms, C and Kimpe, LE and Letournel, B and Lim, JE and Lormée, H and Michelutti, N and Robertson, GJ and Urtizbéréa, F and Wilhelm, SI and Smol, JP}, title = {Linking 19th century European settlement to the disruption of a seabird's natural population dynamics.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {117}, number = {51}, pages = {32484-32492}, pmid = {33288699}, issn = {1091-6490}, mesh = {Animals ; Atlantic Ocean ; *Birds ; Carbon Isotopes/analysis ; Conservation of Natural Resources ; Diatoms ; Ecosystem ; Environmental Monitoring ; Eutrophication ; France ; Geographic Information Systems ; Geologic Sediments/*analysis ; Humans ; Interferon-Induced Helicase, IFIH1/analysis ; Islands ; Nitrogen Isotopes/analysis ; Ponds ; Population Dynamics ; Zinc/analysis ; }, abstract = {Recent estimates indicate that ∼70% of the world's seabird populations have declined since the 1950s due to human activities. However, for almost all bird populations, there is insufficient long-term monitoring to understand baseline (i.e., preindustrial) conditions, which are required to distinguish natural versus anthropogenically driven changes. Here, we address this lack of long-term monitoring data with multiproxy paleolimnological approaches to examine the long-term population dynamics of a major colony of Leach's Storm-petrel (Hydrobates leucorhous) on Grand Colombier Island in the St. Pierre and Miquelon archipelago-an overseas French territory in the northwest Atlantic Ocean. By reconstructing the last ∼5,800 y of storm-petrel dynamics, we demonstrate that this colony underwent substantial natural fluctuations until the start of the 19th century, when population cycles were disrupted, coinciding with the establishment and expansion of a European settlement. Our paleoenvironmental data, coupled with on-the-ground population surveys, indicate that the current colony is only ∼16% of the potential carrying capacity, reinforcing concerning trends of globally declining seabird populations. As seabirds are sentinel species of marine ecosystem health, such declines provide a call to action for global conservation. In response, we emphasize the need for enlarged protected areas and the rehabilitation of disturbed islands to protect ecologically critical seabird populations. Furthermore, long-term data, such as those provided by paleoecological approaches, are required to better understand shifting baselines in conservation to truly recognize current rates of ecological loss.}, } @article {pmid33287164, year = {2020}, author = {Marques, I and Fernandes, I and David, PHC and Paulo, OS and Goulao, LF and Fortunato, AS and Lidon, FC and DaMatta, FM and Ramalho, JC and Ribeiro-Barros, AI}, title = {Transcriptomic Leaf Profiling Reveals Differential Responses of the Two Most Traded Coffee Species to Elevated [CO2].}, journal = {International journal of molecular sciences}, volume = {21}, number = {23}, pages = {}, pmid = {33287164}, issn = {1422-0067}, support = {727934//BreedCAFS/ ; PTDC/ASP-AGR/31257/2017//Fundação para a Ciência e a Tecnologia/ ; UIDB/00239/2020//Research unit CEF/ ; UIDP/04035/2020//Research unit GeoBioTec/ ; UID/AGR/04129/2020//Research unit LEAF/ ; UIDB/04551/2020//Research Unit Green-IT/ ; CRA-RED-00053-16//Conselho Nacional de Desenvolvimento Científico e Tecnológico, Brazil (CNPq), and the Fundação de Amparo à Pesquisa do Estado de Minas Gerais, Brazil/ ; }, mesh = {Air Pressure ; Carbon Dioxide/*metabolism ; Coffea/*genetics/*metabolism ; Computational Biology/methods ; Gene Expression Profiling ; *Gene Expression Regulation, Plant ; Gene Ontology ; Genotype ; Molecular Sequence Annotation ; *Transcriptome ; }, abstract = {As atmospheric [CO2] continues to rise to unprecedented levels, understanding its impact on plants is imperative to improve crop performance and sustainability under future climate conditions. In this context, transcriptional changes promoted by elevated CO2 (eCO2) were studied in genotypes from the two major traded coffee species: the allopolyploid Coffea arabica (Icatu) and its diploid parent, C. canephora (CL153). While Icatu expressed more genes than CL153, a higher number of differentially expressed genes were found in CL153 as a response to eCO2. Although many genes were found to be commonly expressed by the two genotypes under eCO2, unique genes and pathways differed between them, with CL153 showing more enriched GO terms and metabolic pathways than Icatu. Divergent functional categories and significantly enriched pathways were found in these genotypes, which altogether supports contrasting responses to eCO2. A considerable number of genes linked to coffee physiological and biochemical responses were found to be affected by eCO2 with the significant upregulation of photosynthetic, antioxidant, and lipidic genes. This supports the absence of photosynthesis down-regulation and, therefore, the maintenance of increased photosynthetic potential promoted by eCO2 in these coffee genotypes.}, } @article {pmid33275956, year = {2021}, author = {Piovani, D and Christodoulou, MN and Hadjidemetriou, A and Pantavou, K and Zaza, P and Bagos, PG and Bonovas, S and Nikolopoulos, GK}, title = {Effect of early application of social distancing interventions on COVID-19 mortality over the first pandemic wave: An analysis of longitudinal data from 37 countries.}, journal = {The Journal of infection}, volume = {82}, number = {1}, pages = {133-142}, pmid = {33275956}, issn = {1532-2742}, mesh = {Adolescent ; Adult ; Aged ; COVID-19/mortality/*prevention & control/transmission ; *Crowding ; Humans ; Longitudinal Studies ; Middle Aged ; Organisation for Economic Co-Operation and Development/statistics & numerical data ; *Physical Distancing ; *Policy Making ; SARS-CoV-2 ; Young Adult ; }, abstract = {OBJECTIVES: To estimate the effect of early application of social distancing interventions on Covid-19 cumulative mortality during the first pandemic wave.

METHODS: Ecological longitudinal study using multivariable negative binomial regression for panel data. Daily numbers of Covid-19 cases and deaths, and data on social distancing interventions, for the 37 member countries of the Organization for Economic Cooperation and Development (OECD) were analysed.

RESULTS: Covid-19 cumulative mortality over the first pandemic wave varied widely across countries (range, 4.16 to 855 deaths per million population). On average, one-day delay in application of mass gatherings ban was associated with an adjusted increase in Covid-19 cumulative mortality by 6.97% (95% CI, 3.45 to 10.5), whilst a one-day delay in school closures was associated with an increase of 4.37% (95% CI, 1.58 to 7.17) over the study period. We estimated that if each country had enacted both interventions one week earlier, Covid-19 cumulative mortality could have been reduced by an average of 44.1% (95% CI, 20.2 to 67.9).

CONCLUSIONS: Early application of mass gatherings ban and school closures in outbreak epicentres was associated with an important reduction in Covid-19 cumulative mortality during the first pandemic wave. These findings may support policy decision making.}, } @article {pmid33271881, year = {2020}, author = {Smolikova, G and Gorbach, D and Lukasheva, E and Mavropolo-Stolyarenko, G and Bilova, T and Soboleva, A and Tsarev, A and Romanovskaya, E and Podolskaya, E and Zhukov, V and Tikhonovich, I and Medvedev, S and Hoehenwarter, W and Frolov, A}, title = {Bringing New Methods to the Seed Proteomics Platform: Challenges and Perspectives.}, journal = {International journal of molecular sciences}, volume = {21}, number = {23}, pages = {}, pmid = {33271881}, issn = {1422-0067}, support = {FR3117/2-3//Deutsche Forschungsgemeinschaft/ ; 20-16-00086//Russian Science Foundation/ ; }, mesh = {Chromatography, Liquid ; Computational Biology/methods ; Humans ; Mass Spectrometry ; Plant Proteins/*metabolism ; Protein Processing, Post-Translational ; *Proteome ; *Proteomics/methods ; Seeds/*metabolism ; Workflow ; }, abstract = {For centuries, crop plants have represented the basis of the daily human diet. Among them, cereals and legumes, accumulating oils, proteins, and carbohydrates in their seeds, distinctly dominate modern agriculture, thus play an essential role in food industry and fuel production. Therefore, seeds of crop plants are intensively studied by food chemists, biologists, biochemists, and nutritional physiologists. Accordingly, seed development and germination as well as age- and stress-related alterations in seed vigor, longevity, nutritional value, and safety can be addressed by a broad panel of analytical, biochemical, and physiological methods. Currently, functional genomics is one of the most powerful tools, giving direct access to characteristic metabolic changes accompanying plant development, senescence, and response to biotic or abiotic stress. Among individual post-genomic methodological platforms, proteomics represents one of the most effective ones, giving access to cellular metabolism at the level of proteins. During the recent decades, multiple methodological advances were introduced in different branches of life science, although only some of them were established in seed proteomics so far. Therefore, here we discuss main methodological approaches already employed in seed proteomics, as well as those still waiting for implementation in this field of plant research, with a special emphasis on sample preparation, data acquisition, processing, and post-processing. Thereby, the overall goal of this review is to bring new methodologies emerging in different areas of proteomics research (clinical, food, ecological, microbial, and plant proteomics) to the broad society of seed biologists.}, } @article {pmid33270882, year = {2021}, author = {Yuan, L and Song, X and Zhang, L and Yu, Y and Liang, Z and Lei, Y and Ruan, J and Tan, B and Liu, J and Li, C}, title = {The transcriptional repressors VAL1 and VAL2 recruit PRC2 for genome-wide Polycomb silencing in Arabidopsis.}, journal = {Nucleic acids research}, volume = {49}, number = {1}, pages = {98-113}, pmid = {33270882}, issn = {1362-4962}, mesh = {Arabidopsis/*genetics/metabolism ; Arabidopsis Proteins/genetics/*metabolism ; Epigenetic Repression ; *Gene Expression Regulation, Plant ; Gene Ontology ; *Gene Silencing ; Histones/metabolism ; Homeodomain Proteins/genetics/metabolism ; Polycomb Repressive Complex 2/genetics/*metabolism ; Protein Binding ; Protein Interaction Mapping ; Repressor Proteins/deficiency/genetics/*metabolism ; Response Elements/genetics ; Transcription Factors/genetics/metabolism ; Transcription, Genetic ; }, abstract = {The Polycomb repressive complex 2 (PRC2) catalyzes histone H3 Lys27 trimethylation (H3K27me3) to repress gene transcription in multicellular eukaryotes. Despite its importance in gene silencing and cellular differentiation, how PRC2 is recruited to target loci is still not fully understood. Here, we report genome-wide evidence for the recruitment of PRC2 by the transcriptional repressors VIVIPAROUS1/ABI3-LIKE1 (VAL1) and VAL2 in Arabidopsis thaliana. We show that the val1 val2 double mutant possesses somatic embryonic phenotypes and a transcriptome strikingly similar to those of the swn clf double mutant, which lacks the PRC2 catalytic subunits SWINGER (SWN) and CURLY LEAF (CLF). We further show that VAL1 and VAL2 physically interact with SWN and CLF in vivo. Genome-wide binding profiling demonstrated that they colocalize with SWN and CLF at PRC2 target loci. Loss of VAL1/2 significantly reduces SWN and CLF enrichment at PRC2 target loci and leads to a genome-wide redistribution of H3K27me3 that strongly affects transcription. Finally, we provide evidence that the VAL1/VAL2-RY regulatory system is largely independent of previously identified modules for Polycomb silencing in plants. Together, our work demonstrates an extensive genome-wide interaction between VAL1/2 and PRC2 and provides mechanistic insights into the establishment of Polycomb silencing in plants.}, } @article {pmid33270722, year = {2020}, author = {Lin, YP and Schmeller, DS and Ding, TS and Wang, YC and Lien, WY and Henle, K and Klenke, RA}, title = {A GIS-based policy support tool to determine national responsibilities and priorities for biodiversity conservation.}, journal = {PloS one}, volume = {15}, number = {12}, pages = {e0243135}, pmid = {33270722}, issn = {1932-6203}, mesh = {Animals ; Asia ; *Biodiversity ; *Conservation of Natural Resources ; Ecological Parameter Monitoring ; Ecosystem ; Europe ; *Geographic Information Systems ; }, abstract = {Efficient biodiversity conservation requires that limited resources be allocated in accordance with national responsibilities and priorities. Without appropriate computational tools, the process of determining these national responsibilities and conservation priorities is time intensive when considering many species across geographic scales. Here, we have developed a computational tool as a module for the ArcGIS geographic information system. The ArcGIS National Responsibility Assessment Tool (NRA-Tool) can be used to create hierarchical lists of national responsibilities and priorities for global species conservation. Our tool will allow conservationists to prioritize conservation efforts and to focus limited resources on relevant species and regions. We showcase our tool with data on 258 bird species and various biophysical regions, including Environmental Zones in 58 Asian countries and regions. Our tool provides a decision support system for conservation policy with attractive and easily interpretable visual outputs illustrating national responsibilities and priorities for species conservation. The graphical output allows for smooth integration into assessment reports, such as the European Article 17 report, the Living Planet Index report, or similar regional and global reports.}, } @article {pmid33269353, year = {2020}, author = {Pekar, J and Worobey, M and Moshiri, N and Scheffler, K and Wertheim, JO}, title = {Timing the SARS-CoV-2 Index Case in Hubei Province.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {33269353}, issn = {2692-8205}, support = {R01 AI135992/AI/NIAID NIH HHS/United States ; R01 AI136056/AI/NIAID NIH HHS/United States ; T15 LM011271/LM/NLM NIH HHS/United States ; }, abstract = {Understanding when SARS-CoV-2 emerged is critical to evaluating our current approach to monitoring novel zoonotic pathogens and understanding the failure of early containment and mitigation efforts for COVID-19. We employed a coalescent framework to combine retrospective molecular clock inference with forward epidemiological simulations to determine how long SARS-CoV-2 could have circulated prior to the time of the most recent common ancestor. Our results define the period between mid-October and mid-November 2019 as the plausible interval when the first case of SARS-CoV-2 emerged in Hubei province. By characterizing the likely dynamics of the virus before it was discovered, we show that over two-thirds of SARS-CoV-2-like zoonotic events would be self-limited, dying out without igniting a pandemic. Our findings highlight the shortcomings of zoonosis surveillance approaches for detecting highly contagious pathogens with moderate mortality rates.}, } @article {pmid33268804, year = {2020}, author = {Grujic, O and Phung, TN and Kwon, SB and Arneson, A and Lee, Y and Lohmueller, KE and Ernst, J}, title = {Identification and characterization of constrained non-exonic bases lacking predictive epigenomic and transcription factor binding annotations.}, journal = {Nature communications}, volume = {11}, number = {1}, pages = {6168}, pmid = {33268804}, issn = {2041-1723}, support = {UH3 NS104095/NS/NINDS NIH HHS/United States ; T32 CA201160/CA/NCI NIH HHS/United States ; R01 ES024995/ES/NIEHS NIH HHS/United States ; UG3 NS104095/NS/NINDS NIH HHS/United States ; DP1 DA044371/DA/NIDA NIH HHS/United States ; U01 HG007912/HG/NHGRI NIH HHS/United States ; U01 MH105578/MH/NIMH NIH HHS/United States ; R35 GM119856/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Base Sequence ; Epigenesis, Genetic ; Evolution, Molecular ; Exons ; Gene Ontology ; *Genome ; Humans ; *Introns ; Invertebrates/*genetics ; Molecular Sequence Annotation ; Protein Binding ; Sequence Alignment ; Sequence Homology, Nucleic Acid ; Transcription Factors/genetics/*metabolism ; Vertebrates/*genetics ; }, abstract = {Annotations of evolutionary sequence constraint based on multi-species genome alignments and genome-wide maps of epigenomic marks and transcription factor binding provide important complementary information for understanding the human genome and genetic variation. Here we developed the Constrained Non-Exonic Predictor (CNEP) to quantify the evidence of each base in the genome being in an evolutionarily constrained non-exonic element from an input of over 60,000 epigenomic and transcription factor binding features. We find that the CNEP score outperforms baseline and related existing scores at predicting evolutionarily constrained non-exonic bases from such data. However, a subset of them are still not well predicted by CNEP. We developed a complementary Conservation Signature Score by CNEP (CSS-CNEP) that is predictive of those bases. We further characterize the nature of constrained non-exonic bases with low CNEP scores using additional types of information. CNEP and CSS-CNEP are resources for analyzing constrained non-exonic bases in the genome.}, } @article {pmid33266327, year = {2020}, author = {Kõljalg, U and Nilsson, HR and Schigel, D and Tedersoo, L and Larsson, KH and May, TW and Taylor, AFS and Jeppesen, TS and Frøslev, TG and Lindahl, BD and Põldmaa, K and Saar, I and Suija, A and Savchenko, A and Yatsiuk, I and Adojaan, K and Ivanov, F and Piirmann, T and Pöhönen, R and Zirk, A and Abarenkov, K}, title = {The Taxon Hypothesis Paradigm-On the Unambiguous Detection and Communication of Taxa.}, journal = {Microorganisms}, volume = {8}, number = {12}, pages = {}, pmid = {33266327}, issn = {2076-2607}, abstract = {Here, we describe the taxon hypothesis (TH) paradigm, which covers the construction, identification, and communication of taxa as datasets. Defining taxa as datasets of individuals and their traits will make taxon identification and most importantly communication of taxa precise and reproducible. This will allow datasets with standardized and atomized traits to be used digitally in identification pipelines and communicated through persistent identifiers. Such datasets are particularly useful in the context of formally undescribed or even physically undiscovered species if data such as sequences from samples of environmental DNA (eDNA) are available. Implementing the TH paradigm will to some extent remove the impediment to hastily discover and formally describe all extant species in that the TH paradigm allows discovery and communication of new species and other taxa also in the absence of formal descriptions. The TH datasets can be connected to a taxonomic backbone providing access to the vast information associated with the tree of life. In parallel to the description of the TH paradigm, we demonstrate how it is implemented in the UNITE digital taxon communication system. UNITE TH datasets include rich data on individuals and their rDNA ITS sequences. These datasets are equipped with digital object identifiers (DOI) that serve to fix their identity in our communication. All datasets are also connected to a GBIF taxonomic backbone. Researchers processing their eDNA samples using UNITE datasets will, thus, be able to publish their findings as taxon occurrences in the GBIF data portal. UNITE species hypothesis (species level THs) datasets are increasingly utilized in taxon identification pipelines and even formally undescribed species can be identified and communicated by using UNITE. The TH paradigm seeks to achieve unambiguous, unique, and traceable communication of taxa and their properties at any level of the tree of life. It offers a rapid way to discover and communicate undescribed species in identification pipelines and data portals before they are lost to the sixth mass extinction.}, } @article {pmid33263699, year = {2020}, author = {Barbosa, CC and Bonfim, CVD and Brito, CMG and Souza, WV and Melo, MFO and Medeiros, ZM}, title = {Spatial analysis of epidemiological and quality indicators of health services for leprosy in hyperendemic areas in Northeastern Brazil.}, journal = {Revista do Instituto de Medicina Tropical de Sao Paulo}, volume = {62}, number = {}, pages = {e93}, pmid = {33263699}, issn = {1678-9946}, mesh = {Adolescent ; Adult ; Aged ; Bayes Theorem ; Brazil/epidemiology ; Endemic Diseases/*statistics & numerical data ; Female ; Health Information Systems ; Health Services/*statistics & numerical data ; Humans ; Leprosy/*epidemiology ; Male ; Middle Aged ; Population Surveillance ; *Quality Indicators, Health Care ; Spatial Analysis ; Young Adult ; }, abstract = {Leprosy is a public health problem due to the physical disabilities and deformities it causes. This study aimed to describe new leprosy cases using an operational classification and analyzing spatial patterns by means of epidemiological and quality indicators of health services in Pernambuco State, Brazil, between 2005 and 2014. This was an ecological study performed in 184 municipalities grouped into 12 health regions units for analysis. To analyze spatial patterns, the Bayesian local empirical method and Moran's spatial autocorrelation indicator were applied and box and Moran maps were used. Individuals aged ≥15 years old, grade zero physical disability and complete remission as the treatment outcome were predominant in both paucibacillary and multibacillary cases, the only difference was the predominance of females (n=9,286; 63.00%) and males (n=8,564; 60.70%), respectively. These variables were correlated (p<0.05) with the operational classification. The overall detection rate showed three high-priority areas; the indicator rate of grade 2 physical disability revealed clusters in regions IV, V, and VI; and the indicator rate of cases with some degree of disability showed precarious municipalities in seven health regions. Pernambuco maintains an active chain of transmission and ongoing endemicity of leprosy. Therefore, spatial analysis methods allow the identification of priority areas for intervention, thereby supporting the disease elimination strategy.}, } @article {pmid33263214, year = {2021}, author = {Hassell, JM and Bettridge, JM and Ward, MJ and Ogendo, A and Imboma, T and Muloi, D and Fava, F and Robinson, TP and Begon, M and Fèvre, EM}, title = {Socio-ecological drivers of vertebrate biodiversity and human-animal interfaces across an urban landscape.}, journal = {Global change biology}, volume = {27}, number = {4}, pages = {781-792}, pmid = {33263214}, issn = {1365-2486}, support = {G1100783/1//Natural Environment Research Council/ ; WT103953MA/WT_/Wellcome Trust/United Kingdom ; G1100783/MRC_/Medical Research Council/United Kingdom ; //Biotechnology and Biological Science Research Council/ ; MR/R015090/1/MRC_/Medical Research Council/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; NA//CGIAR Research Program on Agriculture for Nutrition and Health/ ; //Economic and Social Research Council/ ; }, mesh = {Animals ; *Biodiversity ; Cities ; Conservation of Natural Resources ; *Ecosystem ; Europe ; Humans ; Kenya ; North America ; Urbanization ; Vertebrates ; }, abstract = {Urbanization can have profound impacts on the distributional ecology of wildlife and livestock, with implications for biodiversity conservation, ecosystem services and human health. A wealth of studies have assessed biotic responses to urbanization in North America and Europe, but there is little empirical evidence that directly links human activities to urban biodiversity in the tropics. Results from a large-scale field study conducted in Nairobi, Kenya, are used to explore the impact of human activities on the biodiversity of wildlife and livestock with which humans co-exist across the city. The structure of sympatric wildlife, livestock and human populations are characterized using unsupervised machine learning, and statistical modelling is used to relate compositional variation in these communities to socio-ecological drivers occurring across the city. By characterizing landscape-scale drivers acting on these interfaces, we demonstrate that socioeconomics, elevation and subsequent changes in habitat have measurable impacts upon the diversity, density and species assemblage of wildlife, livestock and humans. Restructuring of wildlife and livestock assemblages (both in terms of species diversity and composition) has important implications for the emergence of novel diseases at urban interfaces, and we therefore use our results to generate a set of testable hypotheses that explore the influence of urban change on microbial communities. These results provide novel insight into the impact of urbanization on biodiversity in the tropics. An understanding of associations between urban processes and the structure of human and animal populations is required to link urban development to conservation efforts and risks posed by disease emergence to human health, ultimately informing sustainable urban development policy.}, } @article {pmid33262330, year = {2020}, author = {Jiang, S and Zhou, D and Wang, YY and Jia, P and Wan, C and Li, X and He, G and Cao, D and Jiang, X and Kendler, KS and Tsuang, M and Mize, T and Wu, JS and Lu, Y and He, L and Chen, J and Zhao, Z and Chen, X}, title = {Retraction Note: Identification of de novo mutations in prenatal neurodevelopment-associated genes in schizophrenia in two Han Chinese patient-sibling family-based cohorts.}, journal = {Translational psychiatry}, volume = {10}, number = {1}, pages = {417}, pmid = {33262330}, issn = {2158-3188}, abstract = {This article has been retracted. Please see the Retraction Notice for more detail: https://doi.org/10.1038/s41398-020-00987-z.}, } @article {pmid33260097, year = {2021}, author = {Fridman, M and Krasko, O and Levin, L and Veyalkin, I and Lam, AK}, title = {Second primary malignancies in patients with papillary thyroid carcinoma after effect of post-chernobyl irradiation: A risk analysis of more than two decades of observations.}, journal = {Cancer epidemiology}, volume = {70}, number = {}, pages = {101860}, doi = {10.1016/j.canep.2020.101860}, pmid = {33260097}, issn = {1877-783X}, mesh = {Adolescent ; *Chernobyl Nuclear Accident ; Child ; Female ; Humans ; Male ; Neoplasms, Radiation-Induced/*etiology ; Neoplasms, Second Primary/*etiology ; Risk Assessment ; Thyroid Cancer, Papillary/*complications ; Time Factors ; }, abstract = {BACKGROUND: Second primary malignancy in patients with papillary thyroid carcinoma after Chernobyl accident is an emerging problem. The aims of the study are to investigate the rates and distribution of second primary malignant tumours in Belarus survivors of post-Chernobyl papillary thyroid carcinoma and the cumulative rate of developing a second primary malignancy in a group of patients with metachronous second primaries.

METHODS: Patients aged 18 or younger at the time of Chernobyl accident who were diagnosed with papillary thyroid carcinoma after 1986 were identified from the Belarus Cancer Registry. The clinical and demographic of these patients were analysed to correlate with the factors for the development of secondary primary cancer.

RESULTS: Secondary primary cancer was detected in 1.8 % (119 of 6559) of the patients with papillary thyroid carcinoma. The cumulative incidence tended to rise with increasing age of the cohort and varied depending on the sex of patients. In female patients, breast carcinoma and genital tract carcinomas prevailed, in men patients - lymphoma/ leukaemia and the alimentary tract malignancies predominated. A significant excess risk was revealed for breast carcinoma in females, colon carcinoma in males, and the urinary system carcinomas in males (absolute excess risk [AER] = 3.23, 3.01 and 2.17 correspondingly). Overall, our results pointed to the increased risk of new solid primaries in females, males and both genders (AER = 3.31, 7.19, 4.28 correspondingly) as well as increase risk of lymphoid/hematopoietic malignancies in females and both genders (AER = 1.24) and leukaemia in male patients (AER = 1.45).

CONCLUSION: Patients with papillary thyroid carcinoma after Chernobyl accident are at risk of secondary primary malignancy. Awareness and screening of secondary cancer is needed for patients with papillary thyroid carcinoma after Chernobyl accident.}, } @article {pmid33257553, year = {2020}, author = {de Villemereuil, P and Charmantier, A and Arlt, D and Bize, P and Brekke, P and Brouwer, L and Cockburn, A and Côté, SD and Dobson, FS and Evans, SR and Festa-Bianchet, M and Gamelon, M and Hamel, S and Hegelbach, J and Jerstad, K and Kempenaers, B and Kruuk, LEB and Kumpula, J and Kvalnes, T and McAdam, AG and McFarlane, SE and Morrissey, MB and Pärt, T and Pemberton, JM and Qvarnström, A and Røstad, OW and Schroeder, J and Senar, JC and Sheldon, BC and van de Pol, M and Visser, ME and Wheelwright, NT and Tufto, J and Chevin, LM}, title = {Fluctuating optimum and temporally variable selection on breeding date in birds and mammals.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {117}, number = {50}, pages = {31969-31978}, pmid = {33257553}, issn = {1091-6490}, support = {678140/ERC_/European Research Council/International ; BB/L006081/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; Biological Evolution ; Birds/*physiology ; Datasets as Topic ; Genetic Fitness ; Mammals/*physiology ; *Models, Genetic ; Reproduction/*genetics ; Selection, Genetic/*physiology ; Time Factors ; }, abstract = {Temporal variation in natural selection is predicted to strongly impact the evolution and demography of natural populations, with consequences for the rate of adaptation, evolution of plasticity, and extinction risk. Most of the theory underlying these predictions assumes a moving optimum phenotype, with predictions expressed in terms of the temporal variance and autocorrelation of this optimum. However, empirical studies seldom estimate patterns of fluctuations of an optimum phenotype, precluding further progress in connecting theory with observations. To bridge this gap, we assess the evidence for temporal variation in selection on breeding date by modeling a fitness function with a fluctuating optimum, across 39 populations of 21 wild animals, one of the largest compilations of long-term datasets with individual measurements of trait and fitness components. We find compelling evidence for fluctuations in the fitness function, causing temporal variation in the magnitude, but not the direction of selection. However, fluctuations of the optimum phenotype need not directly translate into variation in selection gradients, because their impact can be buffered by partial tracking of the optimum by the mean phenotype. Analyzing individuals that reproduce in consecutive years, we find that plastic changes track movements of the optimum phenotype across years, especially in bird species, reducing temporal variation in directional selection. This suggests that phenological plasticity has evolved to cope with fluctuations in the optimum, despite their currently modest contribution to variation in selection.}, } @article {pmid33248190, year = {2021}, author = {Chmurzynska, A and Mlodzik-Czyzewska, MA and Malinowska, AM and Radziejewska, A and Mikołajczyk-Stecyna, J and Bulczak, E and Wiebe, DJ}, title = {Greater self-reported preference for fat taste and lower fat restraint are associated with more frequent intake of high-fat food.}, journal = {Appetite}, volume = {159}, number = {}, pages = {105053}, doi = {10.1016/j.appet.2020.105053}, pmid = {33248190}, issn = {1095-8304}, mesh = {Dietary Fats ; Energy Intake ; *Food Preferences ; Humans ; Poland ; Self Report ; *Taste ; }, abstract = {The determinants of the intake of high-fat products are not well recognized, but fat preference may be one of them. The aim of this study was thus to determine whether intake of different types of high-fat food is associated with fat preference in people with normal and increased body weight. Participants aged 20-40 years [n = 421] were enrolled in Poznań, Poland in 2016-2018. Fat preference was measured using the Fat Preference Questionnaire. Self-reported preference for fat taste (TASTE) and fat restraint (DIFF) scores were calculated. The frequency of consuming high-fat food was measured with an application for mobile devices using ecological momentary assessment. TASTE was positively associated with calorie intake and total frequency of eating high-fat food in both the normal weight and the overweight/obese groups. Overweight and obese people had lower DIFF (p < 0.001) than normal weight people. DIFF was negatively associated with total calorie intake and total intake of high-fat food, but only in normal weight people (β = -0.16, p < 0.01 and β = -0.26, p < 0.001, respectively). DIFF was negatively associated with the frequency of eating sweet (β = -0.33, p < 0.000) and meat high-fat food (β = -0.25, p < 0.001) in the normal weight group. The frequency of consumption of high-fat food and calorie intake are positively associated with self-reported preference for fat taste. In normal weight subjects fat restraint is negatively associated with calorie intake and total frequency of high-fat food intake, as well as with intake of different types of fatty food. Fat preference measures are thus associated with high-fat food intake, but these associations differ by body weight status.}, } @article {pmid33242236, year = {2020}, author = {Esken, J and Goris, T and Gadkari, J and Bischler, T and Förstner, KU and Sharma, CM and Diekert, G and Schubert, T}, title = {Tetrachloroethene respiration in Sulfurospirillum species is regulated by a two-component system as unraveled by comparative genomics, transcriptomics, and regulator binding studies.}, journal = {MicrobiologyOpen}, volume = {9}, number = {12}, pages = {e1138}, pmid = {33242236}, issn = {2045-8827}, mesh = {Base Sequence ; Campylobacteraceae/*genetics/*metabolism ; Computational Biology/methods ; Electrophoretic Mobility Shift Assay ; Genome, Bacterial/genetics ; Genomics/methods ; Oxidoreductases/*genetics ; Promoter Regions, Genetic/genetics ; Sequence Alignment ; Tetrachloroethylene/*metabolism ; Transcriptome/genetics ; }, abstract = {Energy conservation via organohalide respiration (OHR) in dehalogenating Sulfurospirillum species is an inducible process. However, the gene products involved in tetrachloroethene (PCE) sensing and signal transduction have not been unambiguously identified. Here, genome sequencing of Sulfurospirillum strains defective in PCE respiration and comparative genomics, which included the PCE-respiring representatives of the genus, uncovered the genetic inactivation of a two-component system (TCS) in the OHR gene region of the natural mutants. The assumption that the TCS gene products serve as a PCE sensor that initiates gene transcription was supported by the constitutive low-level expression of the TCS operon in fumarate-adapted cells of Sulfurospirillum multivorans. Via RNA sequencing, eight transcriptional units were identified in the OHR gene region, which includes the TCS operon, the PCE reductive dehalogenase operon, the gene cluster for norcobamide biosynthesis, and putative accessory genes with unknown functions. The OmpR-family response regulator (RR) encoded in the TCS operon was functionally characterized by promoter-binding assays. The RR bound a cis-regulatory element that contained a consensus sequence of a direct repeat (CTATW) separated by 17 bp. Its location either overlapping the -35 box or 50 bp further upstream indicated different regulatory mechanisms. Sequence variations in the regulator binding sites identified in the OHR gene region were in accordance with differences in the transcript levels of the respective gene clusters forming the PCE regulon. The results indicate the presence of a fine-tuned regulatory network controlling PCE metabolism in dehalogenating Sulfurospirillum species, a group of metabolically versatile organohalide-respiring bacteria.}, } @article {pmid33232313, year = {2020}, author = {Thessen, AE and Walls, RL and Vogt, L and Singer, J and Warren, R and Buttigieg, PL and Balhoff, JP and Mungall, CJ and McGuinness, DL and Stucky, BJ and Yoder, MJ and Haendel, MA}, title = {Transforming the study of organisms: Phenomic data models and knowledge bases.}, journal = {PLoS computational biology}, volume = {16}, number = {11}, pages = {e1008376}, pmid = {33232313}, issn = {1553-7358}, support = {R24 OD011883/OD/NIH HHS/United States ; RM1 HG010860/HG/NHGRI NIH HHS/United States ; U13 CA221044/CA/NCI NIH HHS/United States ; U2C ES026555/ES/NIEHS NIH HHS/United States ; }, mesh = {Animals ; Classification ; Computational Biology ; *Databases, Genetic ; Ecosystem ; Gene-Environment Interaction ; Humans ; *Knowledge Bases ; Models, Biological ; Models, Genetic ; Models, Statistical ; *Phenomics ; Phenotype ; Semantics ; }, abstract = {The rapidly decreasing cost of gene sequencing has resulted in a deluge of genomic data from across the tree of life; however, outside a few model organism databases, genomic data are limited in their scientific impact because they are not accompanied by computable phenomic data. The majority of phenomic data are contained in countless small, heterogeneous phenotypic data sets that are very difficult or impossible to integrate at scale because of variable formats, lack of digitization, and linguistic problems. One powerful solution is to represent phenotypic data using data models with precise, computable semantics, but adoption of semantic standards for representing phenotypic data has been slow, especially in biodiversity and ecology. Some phenotypic and trait data are available in a semantic language from knowledge bases, but these are often not interoperable. In this review, we will compare and contrast existing ontology and data models, focusing on nonhuman phenotypes and traits. We discuss barriers to integration of phenotypic data and make recommendations for developing an operationally useful, semantically interoperable phenotypic data ecosystem.}, } @article {pmid33230292, year = {2021}, author = {Dührkop, K and Nothias, LF and Fleischauer, M and Reher, R and Ludwig, M and Hoffmann, MA and Petras, D and Gerwick, WH and Rousu, J and Dorrestein, PC and Böcker, S}, title = {Systematic classification of unknown metabolites using high-resolution fragmentation mass spectra.}, journal = {Nature biotechnology}, volume = {39}, number = {4}, pages = {462-471}, pmid = {33230292}, issn = {1546-1696}, support = {R01 GM107550/GM/NIGMS NIH HHS/United States ; P41 GM103484/GM/NIGMS NIH HHS/United States ; R03 CA211211/CA/NCI NIH HHS/United States ; }, mesh = {Animals ; Aquatic Organisms/*chemistry ; Biological Products/*analysis ; Chromatography, Liquid ; Computational Biology/*methods ; Euphorbia/*chemistry ; Gastrointestinal Microbiome ; Metabolomics/*methods ; Mice ; Neural Networks, Computer ; Tandem Mass Spectrometry ; }, abstract = {Metabolomics using nontargeted tandem mass spectrometry can detect thousands of molecules in a biological sample. However, structural molecule annotation is limited to structures present in libraries or databases, restricting analysis and interpretation of experimental data. Here we describe CANOPUS (class assignment and ontology prediction using mass spectrometry), a computational tool for systematic compound class annotation. CANOPUS uses a deep neural network to predict 2,497 compound classes from fragmentation spectra, including all biologically relevant classes. CANOPUS explicitly targets compounds for which neither spectral nor structural reference data are available and predicts classes lacking tandem mass spectrometry training data. In evaluation using reference data, CANOPUS reached very high prediction performance (average accuracy of 99.7% in cross-validation) and outperformed four baseline methods. We demonstrate the broad utility of CANOPUS by investigating the effect of microbial colonization in the mouse digestive system, through analysis of the chemodiversity of different Euphorbia plants and regarding the discovery of a marine natural product, revealing biological insights at the compound class level.}, } @article {pmid33230180, year = {2020}, author = {Nand, M and Maiti, P and Joshi, T and Chandra, S and Pande, V and Kuniyal, JC and Ramakrishnan, MA}, title = {Virtual screening of anti-HIV1 compounds against SARS-CoV-2: machine learning modeling, chemoinformatics and molecular dynamics simulation based analysis.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {20397}, pmid = {33230180}, issn = {2045-2322}, mesh = {Anti-HIV Agents/*pharmacology ; Antiviral Agents/*pharmacology ; COVID-19/virology ; Cheminformatics/*methods ; Coronavirus 3C Proteases/antagonists & inhibitors ; *Deep Learning ; Drug Evaluation, Preclinical/methods ; Drug Repositioning/*methods ; HIV-1/*drug effects ; Humans ; Infectious bronchitis virus/drug effects ; Molecular Docking Simulation ; *Molecular Dynamics Simulation ; Protease Inhibitors/*pharmacology ; SARS-CoV-2/*drug effects/enzymology ; *COVID-19 Drug Treatment ; }, abstract = {COVID-19 caused by the SARS-CoV-2 is a current global challenge and urgent discovery of potential drugs to combat this pandemic is a need of the hour. 3-chymotrypsin-like cysteine protease (3CLpro) enzyme is the vital molecular target against the SARS-CoV-2. Therefore, in the present study, 1528 anti-HIV1compounds were screened by sequence alignment between 3CLpro of SARS-CoV-2 and avian infectious bronchitis virus (avian coronavirus) followed by machine learning predictive model, drug-likeness screening and molecular docking, which resulted in 41 screened compounds. These 41 compounds were re-screened by deep learning model constructed considering the IC50 values of known inhibitors which resulted in 22 hit compounds. Further, screening was done by structural activity relationship mapping which resulted in two structural clefts. Thereafter, functional group analysis was also done, where cluster 2 showed the presence of several essential functional groups having pharmacological importance. In the final stage, Cluster 2 compounds were re-docked with four different PDB structures of 3CLpro, and their depth interaction profile was analyzed followed by molecular dynamics simulation at 100 ns. Conclusively, 2 out of 1528 compounds were screened as potential hits against 3CLpro which could be further treated as an excellent drug against SARS-CoV-2.}, } @article {pmid33226631, year = {2021}, author = {McLean, BS and Guralnick, RP}, title = {Digital biodiversity data sets reveal breeding phenology and its drivers in a widespread North American mammal.}, journal = {Ecology}, volume = {102}, number = {3}, pages = {e03258}, doi = {10.1002/ecy.3258}, pmid = {33226631}, issn = {1939-9170}, mesh = {Animals ; Biodiversity ; *Climate Change ; *Ecosystem ; Female ; Mammals ; Mice ; Reproduction ; Seasons ; United States ; }, abstract = {Shifts in reproductive timing are among the most commonly documented responses of organisms to global climate change. However, our knowledge of these responses is biased towards taxa that are easily observable and abundant in existing biodiversity data sets. Mammals are common subjects in reproductive biology, but mammalian phenology and its drivers in the wild remain poorly understood because many species are small, secretive, or too labor-intensive to monitor. We took an informatics-based approach to reconstructing breeding phenology in the widespread North American deer mouse (Peromyscus maniculatus) using individual-level reproductive observations from digitized museum specimens and field censuses spanning >100 yr and >45 degrees of latitude. We reconstructed female phenology in different regions and tested the importance of three environmental variables (photoperiod, temperature, precipitation) as breeding cues. Photoperiod and temperature were strong positive and negative breeding cues, respectively, whereas precipitation was not a significant predictor of breeding phenology. However, phenologies and the use of environmental cues varied substantially among regions, and we found evidence that these cueing repertoires are tuned to ecosystem-specific limiting conditions. Our results reiterate the importance of ecological context in optimizing reproduction and demonstrate how harmonization across biodiversity data resources allows new insight into phenology and its drivers in wild mammals.}, } @article {pmid33226083, year = {2021}, author = {Gornik, SG and Bergheim, BG and Morel, B and Stamatakis, A and Foulkes, NS and Guse, A}, title = {Photoreceptor Diversification Accompanies the Evolution of Anthozoa.}, journal = {Molecular biology and evolution}, volume = {38}, number = {5}, pages = {1744-1760}, pmid = {33226083}, issn = {1537-1719}, mesh = {Animals ; Anthozoa/*genetics/metabolism ; *Biological Evolution ; Cryptochromes/*genetics/metabolism ; Opsins/*genetics/metabolism ; Photoreceptor Cells, Invertebrate/*metabolism ; }, abstract = {Anthozoan corals are an ecologically important group of cnidarians, which power the productivity of reef ecosystems. They are sessile, inhabit shallow, tropical oceans and are highly dependent on sun- and moonlight to regulate sexual reproduction, phototaxis, and photosymbiosis. However, their exposure to high levels of sunlight also imposes an increased risk of UV-induced DNA damage. How have these challenging photic environments influenced photoreceptor evolution and function in these animals? To address this question, we initially screened the cnidarian photoreceptor repertoire for Anthozoa-specific signatures by a broad-scale evolutionary analysis. We compared transcriptomic data of more than 36 cnidarian species and revealed a more diverse photoreceptor repertoire in the anthozoan subphylum than in the subphylum Medusozoa. We classified the three principle opsin classes into distinct subtypes and showed that Anthozoa retained all three classes, which diversified into at least six subtypes. In contrast, in Medusozoa, only one class with a single subtype persists. Similarly, in Anthozoa, we documented three photolyase classes and two cryptochrome (CRY) classes, whereas CRYs are entirely absent in Medusozoa. Interestingly, we also identified one anthozoan CRY class, which exhibited unique tandem duplications of the core functional domains. We next explored the functionality of anthozoan photoreceptors in the model species Exaiptasia diaphana (Aiptasia), which recapitulates key photo-behaviors of corals. We show that the diverse opsin genes are differentially expressed in important life stages common to reef-building corals and Aiptasia and that CRY expression is light regulated. We thereby provide important clues linking coral evolution with photoreceptor diversification.}, } @article {pmid33223970, year = {2020}, author = {Mohd, MH and Rahman, MAA and Nazri, MN and Tan, CH and Mohamad, Y and Lim, CS and Mustapa, B and Shaari, H and Hii, YS and Kim, DK}, title = {Reefing Viability Index for Rigs-to-Reefs (R2R) in Malaysia.}, journal = {TheScientificWorldJournal}, volume = {2020}, number = {}, pages = {4695894}, pmid = {33223970}, issn = {1537-744X}, mesh = {*Coral Reefs ; *Ecosystem ; Humans ; Malaysia/epidemiology ; Marine Biology/*methods/trends ; Oceans and Seas/epidemiology ; *Oil and Gas Fields ; Oil and Gas Industry/methods/trends ; Petroleum Pollution/*prevention & control ; }, abstract = {Decommissioning of the offshore platform as an artificial reef, known as Rigs-to-Reefs (R2R), has become a sustainable approach for oil companies. The platform was reused to serve the underwater ecosystem as an artificial reef for a new marine ecosystem which helps to tackle food security issue. This paper presents the findings of the formulation of the reefing viability index to recognize an offshore region that can be used for R2R projects within the South China Sea. The combined effects of spatial data, numerical modelling, and geographic system (GIS) are proposed to study the relationship of spawning ground coral reefs, diversity, and planula larvae in the process of colonization to establish a map of the reef potential environment. Coral connectivity and spawning behaviour were studied to determine the possible source of coral seedling released during the spawning season, twice a year. A geographic reef viability index was established consisting of seven parameters which are coral larval density, pelagic larval length, sea currents, temperature, chlorophyll-a, depth, and substrate availability. The ocean hydrodynamic model was designed to resemble the pattern of larval scattering. By using the simulations and rankings, there were 95 (21%) sites which could probably be used for in situ reefing, whereas 358 (79%) sites were likely ideal for ex situ reefing. Validation of the viability index was carried out using media footage assessment of remotely operated vehicle (ROV).}, } @article {pmid33219693, year = {2021}, author = {Lan, Y and Sun, R and Ouyang, J and Ding, W and Kim, MJ and Wu, J and Li, Y and Shi, T}, title = {AtMAD: Arabidopsis thaliana multi-omics association database.}, journal = {Nucleic acids research}, volume = {49}, number = {D1}, pages = {D1445-D1451}, pmid = {33219693}, issn = {1362-4962}, mesh = {Arabidopsis/*genetics/metabolism ; Computational Biology/*methods ; Data Mining ; *Databases, Genetic ; Gene Regulatory Networks ; Gene-Environment Interaction ; *Genetic Association Studies ; *Genome, Plant ; Genome-Wide Association Study ; Genotype ; Internet ; Metabolome ; Molecular Sequence Annotation ; Phenotype ; Software ; Transcriptome ; }, abstract = {Integration analysis of multi-omics data provides a comprehensive landscape for understanding biological systems and mechanisms. The abundance of high-quality multi-omics data (genomics, transcriptomics, methylomics and phenomics) for the model organism Arabidopsis thaliana enables scientists to study the genetic mechanism of many biological processes. However, no resource is available to provide comprehensive and systematic multi-omics associations for Arabidopsis. Here, we developed an Arabidopsis thaliana Multi-omics Association Database (AtMAD, http://www.megabionet.org/atmad), a public repository for large-scale measurements of associations between genome, transcriptome, methylome, pathway and phenotype in Arabidopsis, designed for facilitating identification of eQTL, emQTL, Pathway-mQTL, Phenotype-pathway, GWAS, TWAS and EWAS. Candidate variants/methylations/genes were identified in AtMAD for specific phenotypes or biological processes, many of them are supported by experimental evidence. Based on the multi-omics association strategy, we have identified 11 796 cis-eQTLs and 10 119 trans-eQTLs. Among them, 68 837 environment-eQTL associations and 149 622 GWAS-eQTL associations were identified and stored in AtMAD. For expression-methylation quantitative trait loci (emQTL), we identified 265 776 emQTLs and 122 344 pathway-mQTLs. For TWAS and EWAS, we obtained 62 754 significant phenotype-gene associations and 3 993 379 significant phenotype-methylation associations, respectively. Overall, the multi-omics associated network in AtMAD will provide new insights into exploring biological mechanisms of plants at multi-omics levels.}, } @article {pmid33219271, year = {2020}, author = {Serra, V and Gammuto, L and Nitla, V and Castelli, M and Lanzoni, O and Sassera, D and Bandi, C and Sandeep, BV and Verni, F and Modeo, L and Petroni, G}, title = {Morphology, ultrastructure, genomics, and phylogeny of Euplotes vanleeuwenhoeki sp. nov. and its ultra-reduced endosymbiont "Candidatus Pinguicoccus supinus" sp. nov.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {20311}, pmid = {33219271}, issn = {2045-2322}, mesh = {Computational Biology ; DNA, Bacterial/isolation & purification ; Euplotes/*classification/genetics/microbiology/ultrastructure ; Genome, Bacterial ; Genome, Mitochondrial ; Microscopy, Electron, Scanning ; Microscopy, Electron, Transmission ; Phylogeny ; Symbiosis/*genetics ; *Terminology as Topic ; Verrucomicrobia/*genetics/isolation & purification ; }, abstract = {Taxonomy is the science of defining and naming groups of biological organisms based on shared characteristics and, more recently, on evolutionary relationships. With the birth of novel genomics/bioinformatics techniques and the increasing interest in microbiome studies, a further advance of taxonomic discipline appears not only possible but highly desirable. The present work proposes a new approach to modern taxonomy, consisting in the inclusion of novel descriptors in the organism characterization: (1) the presence of associated microorganisms (e.g.: symbionts, microbiome), (2) the mitochondrial genome of the host, (3) the symbiont genome. This approach aims to provide a deeper comprehension of the evolutionary/ecological dimensions of organisms since their very first description. Particularly interesting, are those complexes formed by the host plus associated microorganisms, that in the present study we refer to as "holobionts". We illustrate this approach through the description of the ciliate Euplotes vanleeuwenhoeki sp. nov. and its bacterial endosymbiont "Candidatus Pinguicoccus supinus" gen. nov., sp. nov. The endosymbiont possesses an extremely reduced genome (~ 163 kbp); intriguingly, this suggests a high integration between host and symbiont.}, } @article {pmid33213531, year = {2021}, author = {Bommarito, C and Thieltges, DW and Pansch, C and Barboza, FR and Pranovi, F and Wahl, M}, title = {Effects of first intermediate host density, host size and salinity on trematode infections in mussels of the south-western Baltic Sea.}, journal = {Parasitology}, volume = {148}, number = {4}, pages = {486-494}, pmid = {33213531}, issn = {1469-8161}, mesh = {Animals ; Baltic States ; Bivalvia/anatomy & histology/growth & development/*parasitology ; North Sea ; Salinity ; Trematoda/*growth & development ; Vinca/growth & development/parasitology ; }, abstract = {Trematode prevalence and abundance in hosts are known to be affected by biotic drivers as well as by abiotic drivers. In this study, we used the unique salinity gradient found in the south-western Baltic Sea to: (i) investigate patterns of trematode infections in the first intermediate host, the periwinkle Littorina littorea and in the downstream host, the mussel Mytilus edulis, along a regional salinity gradient (from 13 to 22) and (ii) evaluate the effects of first intermediate host (periwinkle) density, host size and salinity on trematode infections in mussels. Two species dominated the trematode community, Renicola roscovita and Himasthla elongata. Salinity, mussel size and density of infected periwinkles were significantly correlated with R. roscovita, and salinity and density correlated with H. elongata abundance. These results suggest that salinity, first intermediate host density and host size play an important role in determining infection levels in mussels, with salinity being the main major driver. Under expected global change scenarios, the predicted freshening of the Baltic Sea might lead to reduced trematode transmission, which may be further enhanced by a potential decrease in periwinkle density and mussel size.}, } @article {pmid33208397, year = {2021}, author = {Hagedoorn, NN and Borensztajn, D and Nijman, RG and Nieboer, D and Herberg, JA and Balode, A and von Both, U and Carrol, E and Eleftheriou, I and Emonts, M and van der Flier, M and de Groot, R and Kohlmaier, B and Lim, E and Maconochie, I and Martinón-Torres, F and Pokorn, M and Strle, F and Tsolia, M and Zavadska, D and Zenz, W and Levin, M and Vermont, C and Moll, HA}, title = {Development and validation of a prediction model for invasive bacterial infections in febrile children at European Emergency Departments: MOFICHE, a prospective observational study.}, journal = {Archives of disease in childhood}, volume = {106}, number = {7}, pages = {641-647}, pmid = {33208397}, issn = {1468-2044}, mesh = {Anti-Bacterial Agents/therapeutic use ; Bacteremia/diagnosis/epidemiology/microbiology ; Bacterial Infections/*diagnosis/epidemiology/metabolism ; Biomarkers/*analysis ; C-Reactive Protein/metabolism ; Child ; Child, Preschool ; Clinical Decision Rules ; Emergency Service, Hospital/*statistics & numerical data ; Europe/epidemiology ; Female ; Fever/*microbiology ; Humans ; Inappropriate Prescribing/*prevention & control ; Infant ; Male ; Meningitis/diagnosis/epidemiology/microbiology ; Prospective Studies ; Sensitivity and Specificity ; }, abstract = {OBJECTIVES: To develop and cross-validate a multivariable clinical prediction model to identify invasive bacterial infections (IBI) and to identify patient groups who might benefit from new biomarkers.

DESIGN: Prospective observational study.

SETTING: 12 emergency departments (EDs) in 8 European countries.

PATIENTS: Febrile children aged 0-18 years.

MAIN OUTCOME MEASURES: IBI, defined as bacteraemia, meningitis and bone/joint infection. We derived and cross-validated a model for IBI using variables from the Feverkidstool (clinical symptoms, C reactive protein), neurological signs, non-blanching rash and comorbidity. We assessed discrimination (area under the receiver operating curve) and diagnostic performance at different risk thresholds for IBI: sensitivity, specificity, negative and positive likelihood ratios (LRs).

RESULTS: Of 16 268 patients, 135 (0.8%) had an IBI. The discriminative ability of the model was 0.84 (95% CI 0.81 to 0.88) and 0.78 (95% CI 0.74 to 0.82) in pooled cross-validations. The model performed well for the rule-out threshold of 0.1% (sensitivity 0.97 (95% CI 0.93 to 0.99), negative LR 0.1 (95% CI 0.0 to 0.2) and for the rule-in threshold of 2.0% (specificity 0.94 (95% CI 0.94 to 0.95), positive LR 8.4 (95% CI 6.9 to 10.0)). The intermediate thresholds of 0.1%-2.0% performed poorly (ranges: sensitivity 0.59-0.93, negative LR 0.14-0.57, specificity 0.52-0.88, positive LR 1.9-4.8) and comprised 9784 patients (60%).

CONCLUSIONS: The rule-out threshold of this model has potential to reduce antibiotic treatment while the rule-in threshold could be used to target treatment in febrile children at the ED. In more than half of patients at intermediate risk, sensitive biomarkers could improve identification of IBI and potentially reduce unnecessary antibiotic prescriptions.}, } @article {pmid33208098, year = {2020}, author = {Wu, X and Li, X and Wang, W and Shan, Y and Wang, C and Zhu, M and La, Q and Zhong, Y and Xu, Y and Nan, P and Li, X}, title = {Integrated metabolomics and transcriptomics study of traditional herb Astragalus membranaceus Bge. var. mongolicus (Bge.) Hsiao reveals global metabolic profile and novel phytochemical ingredients.}, journal = {BMC genomics}, volume = {21}, number = {Suppl 10}, pages = {697}, pmid = {33208098}, issn = {1471-2164}, mesh = {*Astragalus propinquus/genetics ; Computational Biology ; Humans ; *Metabolome ; Metabolomics ; Phytochemicals ; Transcriptome ; }, abstract = {BACKGROUND: Astragalus membranaceus Bge. var. mongolicus (Bge.) Hsiao is one of the most common herbs widely used in South and East Asia, to enhance people's health and reinforce vital energy. Despite its prevalence, however, the knowledge about phytochemical compositions and metabolite biosynthesis in Astragalus membranaceus Bge. var. mongolicus (Bge.) Hsiao is very limited.

RESULTS: An integrated metabolomics and transcriptomics analysis using state-of-the-art UPLC-Q-Orbitrap mass spectrometer and advanced bioinformatics pipeline were conducted to study global metabolic profiles and phytochemical ingredients/biosynthesis in Astragalus membranaceus Bge. var. mongolicus (Bge.) Hsiao. A total of 5435 metabolites were detected, from which 2190 were annotated, representing an order of magnitude increase over previously known. Metabolic profiling of Astragalus membranaceus Bge. var. mongolicus (Bge.) Hsiao tissues found contents and synthetic enzymes for phytochemicals were significantly higher in leaf and stem in general, whereas the contents of the main bioactive ingredients were significantly enriched in root, underlying the value of root in herbal remedies. Using integrated metabolomics and transcriptomics data, we illustrated the complete pathways of phenylpropanoid biosynthesis, flavonoid biosynthesis, and isoflavonoid biosynthesis, in which some were first reported in the herb. More importantly, we discovered novel flavonoid derivatives using informatics method for neutral loss scan, in addition to inferring their likely synthesis pathways in Astragalus membranaceus Bge. var. mongolicus (Bge.) Hsiao.

CONCLUSIONS: The current study represents the most comprehensive metabolomics and transcriptomics analysis on traditional herb Astragalus membranaceus Bge. var. mongolicus (Bge.) Hsiao. We demonstrated our integrated metabolomics and transcriptomics approach offers great potentials in discovering novel metabolite structure and associated synthesis pathways. This study provides novel insights into the phytochemical ingredients, metabolite biosynthesis, and complex metabolic network in herbs, highlighting the rich natural resource and nutritional value of traditional herbal plants.}, } @article {pmid33206700, year = {2020}, author = {Maitland, VC and Robinson, CV and Porter, TM and Hajibabaei, M}, title = {Freshwater diatom biomonitoring through benthic kick-net metabarcoding.}, journal = {PloS one}, volume = {15}, number = {11}, pages = {e0242143}, pmid = {33206700}, issn = {1932-6203}, mesh = {Animals ; Biodiversity ; Biofilms ; Biological Monitoring ; Computational Biology ; DNA/analysis ; *DNA Barcoding, Taxonomic ; Diatoms/*genetics/physiology ; Ecosystem ; Environmental Monitoring/*methods ; Fresh Water ; High-Throughput Nucleotide Sequencing ; Invertebrates ; Periphyton/*genetics/physiology ; Rivers ; Water Quality ; }, abstract = {Biomonitoring is an essential tool for assessing ecological conditions and informing management strategies. The application of DNA metabarcoding and high throughput sequencing has improved data quantity and resolution for biomonitoring of taxa such as macroinvertebrates, yet, there remains the need to optimise these methods for other taxonomic groups. Diatoms have a longstanding history in freshwater biomonitoring as bioindicators of water quality status. However, multi-substrate periphyton collection, a common diatom sampling practice, is time-consuming and thus costly in terms of labour. This study examined whether the benthic kick-net technique used for macroinvertebrate biomonitoring could be applied to bulk-sample diatoms for metabarcoding. To test this approach, we collected samples using both conventional multi-substrate microhabitat periphyton collections and bulk-tissue kick-net methodologies in parallel from replicated sites with different habitat status (good/fair). We found there was no significant difference in community assemblages between conventional periphyton collection and kick-net methodologies or site status, but there was significant difference between diatom communities depending on site (P = 0.042). These results show the diatom taxonomic coverage achieved through DNA metabarcoding of kick-net is suitable for ecological biomonitoring applications. The shift to a more robust sampling approach and capturing diatoms as well as macroinvertebrates in a single sampling event has the potential to significantly improve efficiency of biomonitoring programmes that currently only use the kick-net technique to sample macroinvertebrates.}, } @article {pmid33206635, year = {2020}, author = {Turakhia, Y and De Maio, N and Thornlow, B and Gozashti, L and Lanfear, R and Walker, CR and Hinrichs, AS and Fernandes, JD and Borges, R and Slodkowicz, G and Weilguny, L and Haussler, D and Goldman, N and Corbett-Detig, R}, title = {Stability of SARS-CoV-2 phylogenies.}, journal = {PLoS genetics}, volume = {16}, number = {11}, pages = {e1009175}, pmid = {33206635}, issn = {1553-7404}, support = {5U41HG002371-19/NH/NIH HHS/United States ; U41 HG002371/HG/NHGRI NIH HHS/United States ; R35 GM128932/GM/NIGMS NIH HHS/United States ; MC_U105185859/MRC_/Medical Research Council/United Kingdom ; F31 HG010584/HG/NHGRI NIH HHS/United States ; }, mesh = {Algorithms ; COVID-19 ; Computational Biology ; Evolution, Molecular ; Genome, Viral/*genetics ; Humans ; *Phylogeny ; RNA, Viral/genetics ; SARS-CoV-2/*genetics ; Sequence Alignment ; Whole Genome Sequencing ; }, abstract = {The SARS-CoV-2 pandemic has led to unprecedented, nearly real-time genetic tracing due to the rapid community sequencing response. Researchers immediately leveraged these data to infer the evolutionary relationships among viral samples and to study key biological questions, including whether host viral genome editing and recombination are features of SARS-CoV-2 evolution. This global sequencing effort is inherently decentralized and must rely on data collected by many labs using a wide variety of molecular and bioinformatic techniques. There is thus a strong possibility that systematic errors associated with lab-or protocol-specific practices affect some sequences in the repositories. We find that some recurrent mutations in reported SARS-CoV-2 genome sequences have been observed predominantly or exclusively by single labs, co-localize with commonly used primer binding sites and are more likely to affect the protein-coding sequences than other similarly recurrent mutations. We show that their inclusion can affect phylogenetic inference on scales relevant to local lineage tracing, and make it appear as though there has been an excess of recurrent mutation or recombination among viral lineages. We suggest how samples can be screened and problematic variants removed, and we plan to regularly inform the scientific community with our updated results as more SARS-CoV-2 genome sequences are shared (https://virological.org/t/issues-with-sars-cov-2-sequencing-data/473 and https://virological.org/t/masking-strategies-for-sars-cov-2-alignments/480). We also develop tools for comparing and visualizing differences among very large phylogenies and we show that consistent clade- and tree-based comparisons can be made between phylogenies produced by different groups. These will facilitate evolutionary inferences and comparisons among phylogenies produced for a wide array of purposes. Building on the SARS-CoV-2 Genome Browser at UCSC, we present a toolkit to compare, analyze and combine SARS-CoV-2 phylogenies, find and remove potential sequencing errors and establish a widely shared, stable clade structure for a more accurate scientific inference and discourse.}, } @article {pmid33205462, year = {2021}, author = {Culina, A and Adriaensen, F and Bailey, LD and Burgess, MD and Charmantier, A and Cole, EF and Eeva, T and Matthysen, E and Nater, CR and Sheldon, BC and Saether, BE and Vriend, SJG and Zajkova, Z and Adamík, P and Aplin, LM and Angulo, E and Artemyev, A and Barba, E and Barišić, S and Belda, E and Bilgin, CC and Bleu, J and Both, C and Bouwhuis, S and Branston, CJ and Broggi, J and Burke, T and Bushuev, A and Camacho, C and Campobello, D and Canal, D and Cantarero, A and Caro, SP and Cauchoix, M and Chaine, A and Cichoń, M and Ćiković, D and Cusimano, CA and Deimel, C and Dhondt, AA and Dingemanse, NJ and Doligez, B and Dominoni, DM and Doutrelant, C and Drobniak, SM and Dubiec, A and Eens, M and Einar Erikstad, K and Espín, S and Farine, DR and Figuerola, J and Kavak Gülbeyaz, P and Grégoire, A and Hartley, IR and Hau, M and Hegyi, G and Hille, S and Hinde, CA and Holtmann, B and Ilyina, T and Isaksson, C and Iserbyt, A and Ivankina, E and Kania, W and Kempenaers, B and Kerimov, A and Komdeur, J and Korsten, P and Král, M and Krist, M and Lambrechts, M and Lara, CE and Leivits, A and Liker, A and Lodjak, J and Mägi, M and Mainwaring, MC and Mänd, R and Massa, B and Massemin, S and Martínez-Padilla, J and Mazgajski, TD and Mennerat, A and Moreno, J and Mouchet, A and Nakagawa, S and Nilsson, JÅ and Nilsson, JF and Cláudia Norte, A and van Oers, K and Orell, M and Potti, J and Quinn, JL and Réale, D and Kristin Reiertsen, T and Rosivall, B and Russell, AF and Rytkönen, S and Sánchez-Virosta, P and Santos, ESA and Schroeder, J and Senar, JC and Seress, G and Slagsvold, T and Szulkin, M and Teplitsky, C and Tilgar, V and Tolstoguzov, A and Török, J and Valcu, M and Vatka, E and Verhulst, S and Watson, H and Yuta, T and Zamora-Marín, JM and Visser, ME}, title = {Connecting the data landscape of long-term ecological studies: The SPI-Birds data hub.}, journal = {The Journal of animal ecology}, volume = {90}, number = {9}, pages = {2147-2160}, pmid = {33205462}, issn = {1365-2656}, mesh = {Animals ; *Birds ; Databases, Factual ; *Metadata ; }, abstract = {The integration and synthesis of the data in different areas of science is drastically slowed and hindered by a lack of standards and networking programmes. Long-term studies of individually marked animals are not an exception. These studies are especially important as instrumental for understanding evolutionary and ecological processes in the wild. Furthermore, their number and global distribution provides a unique opportunity to assess the generality of patterns and to address broad-scale global issues (e.g. climate change). To solve data integration issues and enable a new scale of ecological and evolutionary research based on long-term studies of birds, we have created the SPI-Birds Network and Database (www.spibirds.org)-a large-scale initiative that connects data from, and researchers working on, studies of wild populations of individually recognizable (usually ringed) birds. Within year and a half since the establishment, SPI-Birds has recruited over 120 members, and currently hosts data on almost 1.5 million individual birds collected in 80 populations over 2,000 cumulative years, and counting. SPI-Birds acts as a data hub and a catalogue of studied populations. It prevents data loss, secures easy data finding, use and integration and thus facilitates collaboration and synthesis. We provide community-derived data and meta-data standards and improve data integrity guided by the principles of Findable, Accessible, Interoperable and Reusable (FAIR), and aligned with the existing metadata languages (e.g. ecological meta-data language). The encouraging community involvement stems from SPI-Bird's decentralized approach: research groups retain full control over data use and their way of data management, while SPI-Birds creates tailored pipelines to convert each unique data format into a standard format. We outline the lessons learned, so that other communities (e.g. those working on other taxa) can adapt our successful model. Creating community-specific hubs (such as ours, COMADRE for animal demography, etc.) will aid much-needed large-scale ecological data integration.}, } @article {pmid33205140, year = {2020}, author = {August, TA and Pescott, OL and Joly, A and Bonnet, P}, title = {AI Naturalists Might Hold the Key to Unlocking Biodiversity Data in Social Media Imagery.}, journal = {Patterns (New York, N.Y.)}, volume = {1}, number = {7}, pages = {100116}, pmid = {33205140}, issn = {2666-3899}, abstract = {The increasing availability of digital images, coupled with sophisticated artificial intelligence (AI) techniques for image classification, presents an exciting opportunity for biodiversity researchers to create new datasets of species observations. We investigated whether an AI plant species classifier could extract previously unexploited biodiversity data from social media photos (Flickr). We found over 60,000 geolocated images tagged with the keyword "flower" across an urban and rural location in the UK and classified these using AI, reviewing these identifications and assessing the representativeness of images. Images were predominantly biodiversity focused, showing single species. Non-native garden plants dominated, particularly in the urban setting. The AI classifier performed best when photos were focused on single native species in wild situations but also performed well at higher taxonomic levels (genus and family), even when images substantially deviated from this. We present a checklist of questions that should be considered when undertaking a similar analysis.}, } @article {pmid33201333, year = {2020}, author = {Castro Monzon, F and Rödel, MO and Jeschke, JM}, title = {Tracking Batrachochytrium dendrobatidis Infection Across the Globe.}, journal = {EcoHealth}, volume = {17}, number = {3}, pages = {270-279}, pmid = {33201333}, issn = {1612-9210}, mesh = {Amphibians/microbiology ; Animals ; Chytridiomycota/*pathogenicity ; Communicable Diseases, Emerging/*epidemiology ; Databases as Topic ; *Internationality ; }, abstract = {Infection records of Batrachochytrium dendrobatidis (Bd), a pathogen that has devastated amphibian populations worldwide, have rapidly increased since the pathogen's discovery. Dealing with so many records makes it difficult to (a) know where, when and in which species infections have been detected, (b) understand how widespread and pervasive Bd is and (c) prioritize study and management areas. We conducted a systematic review of papers and compiled a database with Bd infection records. Our dataset covers 71 amphibian families and 119 countries. The data revealed how widespread and adaptable Bd is, being able to infect over 50% of all tested amphibian species, with over 1000 confirmed host species and being present in 86 countries. The distribution of infected species is uneven among and within countries. Areas where the distributions of many infected species overlap are readily visible; these are regions where Bd likely develops well. Conversely, areas where the distributions of species that tested negative overlap, such as the Atlantic Coast in the USA, suggest the presence of Bd refuges. Finally, we report how the number of tested and infected species has changed through time, and provide a list of oldest detection records per country.}, } @article {pmid33201177, year = {2021}, author = {Sarmah, DT and Bairagi, N and Chatterjee, S}, title = {Tracing the footsteps of autophagy in computational biology.}, journal = {Briefings in bioinformatics}, volume = {22}, number = {4}, pages = {}, pmid = {33201177}, issn = {1477-4054}, mesh = {*Autophagy ; *Computational Biology ; Humans ; *Models, Biological ; Neoplasms/*metabolism ; *Signal Transduction ; }, abstract = {Autophagy plays a crucial role in maintaining cellular homeostasis through the degradation of unwanted materials like damaged mitochondria and misfolded proteins. However, the contribution of autophagy toward a healthy cell environment is not only limited to the cleaning process. It also assists in protein synthesis when the system lacks the amino acids' inflow from the extracellular environment due to diet consumptions. Reduction in the autophagy process is associated with diseases like cancer, diabetes, non-alcoholic steatohepatitis, etc., while uncontrolled autophagy may facilitate cell death. We need a better understanding of the autophagy processes and their regulatory mechanisms at various levels (molecules, cells, tissues). This demands a thorough understanding of the system with the help of mathematical and computational tools. The present review illuminates how systems biology approaches are being used for the study of the autophagy process. A comprehensive insight is provided on the application of computational methods involving mathematical modeling and network analysis in the autophagy process. Various mathematical models based on the system of differential equations for studying autophagy are covered here. We have also highlighted the significance of network analysis and machine learning in capturing the core regulatory machinery governing the autophagy process. We explored the available autophagic databases and related resources along with their attributes that are useful in investigating autophagy through computational methods. We conclude the article addressing the potential future perspective in this area, which might provide a more in-depth insight into the dynamics of autophagy.}, } @article {pmid33199911, year = {2021}, author = {Tripathi, A and Vázquez-Baeza, Y and Gauglitz, JM and Wang, M and Dührkop, K and Nothias-Esposito, M and Acharya, DD and Ernst, M and van der Hooft, JJJ and Zhu, Q and McDonald, D and Brejnrod, AD and Gonzalez, A and Handelsman, J and Fleischauer, M and Ludwig, M and Böcker, S and Nothias, LF and Knight, R and Dorrestein, PC}, title = {Chemically informed analyses of metabolomics mass spectrometry data with Qemistree.}, journal = {Nature chemical biology}, volume = {17}, number = {2}, pages = {146-151}, pmid = {33199911}, issn = {1552-4469}, support = {R01 GM107550/GM/NIGMS NIH HHS/United States ; P41 GM103484/GM/NIGMS NIH HHS/United States ; DP1 AT010885/AT/NCCIH NIH HHS/United States ; R03 CA211211/CA/NCI NIH HHS/United States ; U19 AG063744/AG/NIA NIH HHS/United States ; P30 DK120515/DK/NIDDK NIH HHS/United States ; }, mesh = {Algorithms ; Cluster Analysis ; DNA/chemistry ; DNA Fingerprinting ; Databases, Factual ; Ecology ; Food Analysis ; Mass Spectrometry/*methods ; *Metabolomics ; Microbiota ; Multivariate Analysis ; Software ; Tandem Mass Spectrometry ; Workflow ; }, abstract = {Untargeted mass spectrometry is employed to detect small molecules in complex biospecimens, generating data that are difficult to interpret. We developed Qemistree, a data exploration strategy based on the hierarchical organization of molecular fingerprints predicted from fragmentation spectra. Qemistree allows mass spectrometry data to be represented in the context of sample metadata and chemical ontologies. By expressing molecular relationships as a tree, we can apply ecological tools that are designed to analyze and visualize the relatedness of DNA sequences to metabolomics data. Here we demonstrate the use of tree-guided data exploration tools to compare metabolomics samples across different experimental conditions such as chromatographic shifts. Additionally, we leverage a tree representation to visualize chemical diversity in a heterogeneous collection of samples. The Qemistree software pipeline is freely available to the microbiome and metabolomics communities in the form of a QIIME2 plugin, and a global natural products social molecular networking workflow.}, } @article {pmid33199816, year = {2020}, author = {Mawla, I and Schrepf, A and Ichesco, E and Harte, SE and Klumpp, DJ and Griffith, JW and Strachan, E and Yang, CC and Lai, H and Andriole, G and Magnotta, VA and Kreder, K and Clauw, DJ and Harris, RE and Clemens, JQ and Landis, JR and Mullins, C and Rodriguez, LV and Mayer, EA and Kutch, JJ}, title = {Natural bladder filling alters resting brain function at multiple spatial scales: a proof-of-concept MAPP Network Neuroimaging Study.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {19901}, pmid = {33199816}, issn = {2045-2322}, support = {DK082316/DK/NIDDK NIH HHS/United States ; DK082344/DK/NIDDK NIH HHS/United States ; U01 DK082344/DK/NIDDK NIH HHS/United States ; DK082370/DK/NIDDK NIH HHS/United States ; R01 DK110669/DK/NIDDK NIH HHS/United States ; U01 DK082325/DK/NIDDK NIH HHS/United States ; DK082342/DK/NIDDK NIH HHS/United States ; U01 DK082370/DK/NIDDK NIH HHS/United States ; DK082345/DK/NIDDK NIH HHS/United States ; DK082325/DK/NIDDK NIH HHS/United States ; R01 DK121724/DK/NIDDK NIH HHS/United States ; DK082315/DK/NIDDK NIH HHS/United States ; }, mesh = {Adult ; Brain/*physiology ; Chronic Pain/physiopathology ; Cystitis, Interstitial/*physiopathology ; Female ; Humans ; Magnetic Resonance Imaging/*methods ; Male ; *Nervous System Physiological Phenomena ; Neuroimaging/*methods ; Pelvic Pain/physiopathology ; Proof of Concept Study ; Rest ; Urinary Bladder/*physiology ; Urination ; *Urodynamics ; }, abstract = {Neural circuitry regulating urine storage in humans has been largely inferred from fMRI during urodynamic studies driven by catheter infusion of fluid into the bladder. However, urodynamic testing may be confounded by artificially filling the bladder repeatedly at a high rate and examining associated time-locked changes in fMRI signals. Here we describe and test a more ecologically-valid paradigm to study the brain response to bladder filling by (1) filling the bladder naturally with oral water ingestion, (2) examining resting state fMRI (rs-fMRI) which is more natural since it is not linked with a specific stimulus, and (3) relating rs-fMRI measures to self-report (urinary urge) and physiologic measures (voided volume). To establish appropriate controls and analyses for future clinical studies, here we analyze data collected from healthy individuals (N = 62) as part of the Multidisciplinary Approach to the Study of Chronic Pelvic Pain (MAPP) Research Network. Participants orally ingested approximately 350 mL of water, and had a 10 min "fuller bladder" rs-fMRI scan approximately 1 h later. A second 10 min "empty bladder" rs-fMRI scan was conducted immediately following micturition. We examined multiple spatial scales of brain function, including local activity, circuits, and networks. We found changes in brain function distributed across micturition loci (e.g., subregions of the salience, sensorimotor, and default networks) that were significantly related to the stimulus (volume) and response (urinary urge). Based on our results, this paradigm can be applied in the future to study the neurobiological underpinnings of urologic conditions.}, } @article {pmid33199593, year = {2020}, author = {Senior, AM and Nakagawa, S and Raubenheimer, D and Simpson, SJ}, title = {Global associations between macronutrient supply and age-specific mortality.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {117}, number = {48}, pages = {30824-30835}, pmid = {33199593}, issn = {1091-6490}, mesh = {Age Factors ; Algorithms ; Databases, Factual ; Diet ; Dietary Supplements ; Energy Intake ; Female ; Geography ; Global Health ; Humans ; *Longevity ; Male ; Models, Theoretical ; *Nutrients/supply & distribution ; Nutrition Surveys ; *Nutritional Status ; Public Health Surveillance ; Socioeconomic Factors ; }, abstract = {Animal experiments have demonstrated that energy intake and the balance of macronutrients determine life span and patterns of age-specific mortality (ASM). Similar effects have also been detected in epidemiological studies in humans. Using global supply data and 1,879 life tables from 103 countries, we test for these effects at a macrolevel: between the nutrient supplies of nations and their patterns of ASM. We find that macronutrient supplies are strong predictors of ASM even after correction for time and economic factors. Globally, signatures of undernutrition are evident in the effects of low supply on life expectancy at birth and high mortality across ages, even as recently as 2016. However, in wealthy countries, the effects of overnutrition are prominent, where high supplies particularly from fats and carbohydrates are predicted to lead to high levels of mortality. Energy supplied at around 3,500 kcal/cap/d minimized mortality across ages. However, we show that the macronutrient composition of energy supply that minimizes mortality varies with age. In early life, 40 to 45% energy from each of fat and carbohydrate and 16% from protein minimizes mortality. In later life, replacing fat with carbohydrates to around 65% of total energy and reducing protein to 11% is associated with the lowest level of mortality. These results, particularly those regarding fats, accord both with experimental data from animals and within-country epidemiological studies on the association between macronutrient intake and risk of age-related chronic diseases.}, } @article {pmid33198888, year = {2020}, author = {Zajitschek, SR and Zajitschek, F and Bonduriansky, R and Brooks, RC and Cornwell, W and Falster, DS and Lagisz, M and Mason, J and Senior, AM and Noble, DW and Nakagawa, S}, title = {Sexual dimorphism in trait variability and its eco-evolutionary and statistical implications.}, journal = {eLife}, volume = {9}, number = {}, pages = {}, pmid = {33198888}, issn = {2050-084X}, support = {DP180100818//Australian Research Council/International ; UM1 HG006370/HG/NHGRI NIH HHS/United States ; DE180101520//Australian Research Council Fellowship/International ; FT160100113//Australian Research Council/International ; }, mesh = {Animals ; *Biological Evolution ; Databases, Factual ; *Ecosystem ; Female ; Male ; Mice ; *Sex Characteristics ; }, abstract = {Biomedical and clinical sciences are experiencing a renewed interest in the fact that males and females differ in many anatomic, physiological, and behavioural traits. Sex differences in trait variability, however, are yet to receive similar recognition. In medical science, mammalian females are assumed to have higher trait variability due to estrous cycles (the 'estrus-mediated variability hypothesis'); historically in biomedical research, females have been excluded for this reason. Contrastingly, evolutionary theory and associated data support the 'greater male variability hypothesis'. Here, we test these competing hypotheses in 218 traits measured in >26,900 mice, using meta-analysis methods. Neither hypothesis could universally explain patterns in trait variability. Sex bias in variability was trait-dependent. While greater male variability was found in morphological traits, females were much more variable in immunological traits. Sex-specific variability has eco-evolutionary ramifications, including sex-dependent responses to climate change, as well as statistical implications including power analysis considering sex difference in variance.}, } @article {pmid33198778, year = {2020}, author = {Rotenberg, D and Baumann, AA and Ben-Mahmoud, S and Christiaens, O and Dermauw, W and Ioannidis, P and Jacobs, CGC and Vargas Jentzsch, IM and Oliver, JE and Poelchau, MF and Rajarapu, SP and Schneweis, DJ and Snoeck, S and Taning, CNT and Wei, D and Widana Gamage, SMK and Hughes, DST and Murali, SC and Bailey, ST and Bejerman, NE and Holmes, CJ and Jennings, EC and Rosendale, AJ and Rosselot, A and Hervey, K and Schneweis, BA and Cheng, S and Childers, C and Simão, FA and Dietzgen, RG and Chao, H and Dinh, H and Doddapaneni, HV and Dugan, S and Han, Y and Lee, SL and Muzny, DM and Qu, J and Worley, KC and Benoit, JB and Friedrich, M and Jones, JW and Panfilio, KA and Park, Y and Robertson, HM and Smagghe, G and Ullman, DE and van der Zee, M and Van Leeuwen, T and Veenstra, JA and Waterhouse, RM and Weirauch, MT and Werren, JH and Whitfield, AE and Zdobnov, EM and Gibbs, RA and Richards, S}, title = {Correction to: Genome-enabled insights into the biology of thrips as crop pests.}, journal = {BMC biology}, volume = {18}, number = {1}, pages = {169}, pmid = {33198778}, issn = {1741-7007}, abstract = {An amendment to this paper has been published and can be accessed via the original article.}, } @article {pmid33198651, year = {2020}, author = {Welzel, M and Lange, A and Heider, D and Schwarz, M and Freisleben, B and Jensen, M and Boenigk, J and Beisser, D}, title = {Natrix: a Snakemake-based workflow for processing, clustering, and taxonomically assigning amplicon sequencing reads.}, journal = {BMC bioinformatics}, volume = {21}, number = {1}, pages = {526}, pmid = {33198651}, issn = {1471-2105}, support = {BO 3245/19-1//Deutsche Forschungsgemeinschaft/ ; HMWK LOEWE, MOSLA research cluster//Hessisches Ministerium fr Wissenschaft und Kunst/ ; }, mesh = {Cluster Analysis ; DNA, Environmental/genetics/isolation & purification ; Data Analysis ; Databases, Genetic ; Floods ; *High-Throughput Nucleotide Sequencing ; Microbiota/genetics ; Reproducibility of Results ; *Software ; *Workflow ; }, abstract = {BACKGROUND: Sequencing of marker genes amplified from environmental samples, known as amplicon sequencing, allows us to resolve some of the hidden diversity and elucidate evolutionary relationships and ecological processes among complex microbial communities. The analysis of large numbers of samples at high sequencing depths generated by high throughput sequencing technologies requires efficient, flexible, and reproducible bioinformatics pipelines. Only a few existing workflows can be run in a user-friendly, scalable, and reproducible manner on different computing devices using an efficient workflow management system.

RESULTS: We present Natrix, an open-source bioinformatics workflow for preprocessing raw amplicon sequencing data. The workflow contains all analysis steps from quality assessment, read assembly, dereplication, chimera detection, split-sample merging, sequence representative assignment (OTUs or ASVs) to the taxonomic assignment of sequence representatives. The workflow is written using Snakemake, a workflow management engine for developing data analysis workflows. In addition, Conda is used for version control. Thus, Snakemake ensures reproducibility and Conda offers version control of the utilized programs. The encapsulation of rules and their dependencies support hassle-free sharing of rules between workflows and easy adaptation and extension of existing workflows. Natrix is freely available on GitHub (https://github.com/MW55/Natrix) or as a Docker container on DockerHub (https://hub.docker.com/r/mw55/natrix).

CONCLUSION: Natrix is a user-friendly and highly extensible workflow for processing Illumina amplicon data.}, } @article {pmid33196910, year = {2020}, author = {Otte, FW and Rothwell, M and Woods, C and Davids, K}, title = {Specialist Coaching Integrated into a Department of Methodology in Team Sports Organisations.}, journal = {Sports medicine - open}, volume = {6}, number = {1}, pages = {55}, pmid = {33196910}, issn = {2199-1170}, abstract = {With increasing resources in sports organisations being allocated to the development and preparation of individual athletes and sub-groups with specialist performance roles, the work of coaches, specialist (role) coaches and support staff needs to be functionally and coherently integrated. This integration of sport science support and coaching can be administered by staff in a Department of Methodology (DoM). Particularly, in this paper, we propose how specialist coaching can be situated in a DoM, presenting a model advocating effective functioning in high-performance team sports organisations. Using principles of ecological dynamics, we provide a rationale for a functional methodology for the design of practice tasks in a DoM that views learners as wayfinders, self-regulating their way through competitive performance environments. This rationale for athlete self-regulation in practice could improve athlete performance by enhancing problem solving, engagement with constraints of learning designs and supporting better attunement to contextual information abundant in a competitive environment. Finally, by introducing this unified and multidisciplinary DoM, specialist coaches, team coaches and sport science support staff, within the organisational structure, can collaboratively debate and co-design individualised athlete training programmes to enrich skill adaptability and performance functionality. To underline these contentions, three high-performance sport case studies from Australian Football: goalkeeping in Association Football and Rugby League are presented.}, } @article {pmid33193120, year = {2020}, author = {Rosen, GL and Hammrich, P}, title = {Teaching Microbiome Analysis: From Design to Computation Through Inquiry.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {528051}, pmid = {33193120}, issn = {1664-302X}, abstract = {In this article, we present our three-class course sequence to educate students about microbiome analysis and metagenomics through experiential learning by taking them from inquiry to analysis of the microbiome: Molecular Ecology Lab, Bioinformatics, and Computational Microbiome Analysis. Students developed hypotheses, designed lab experiments, sequenced the DNA from microbiomes, learned basic python/R scripting, became proficient in at least one microbiome analysis software, and were able to analyze data generated from the microbiome experiments. While over 150 students (graduate and undergraduate) were impacted by the development of the series of courses, our assessment was only on undergraduate learning, where 45 students enrolled in at least one of the three courses and 4 students took all three. Students gained skills in bioinformatics through the courses, and several positive comments were received through surveys and private correspondence. Through a summative assessment, general trends show that students became more proficient in comparative genomic techniques and had positive attitudes toward their abilities to bridge biology and bioinformatics. While most students took individual or 2 of the courses, we show that pre- and post-surveys of these individual classes still showed progress toward learning objectives. It is expected that students trained will enter the workforce with skills needed to innovate in the biotechnology, health, and environmental industries. Students are trained to maximize impact and tackle real world problems in biology and medicine with their learned knowledge of data science and machine learning. The course materials for the new microbiome analysis course are available on Github: https://github.com/EESI/Comp_Metagenomics_resources.}, } @article {pmid33188214, year = {2020}, author = {Finch, G and Nandyal, S and Perretta, C and Davies, B and Rosendale, AJ and Holmes, CJ and Gantz, JD and Spacht, DE and Bailey, ST and Chen, X and Oyen, K and Didion, EM and Chakraborty, S and Lee, RE and Denlinger, DL and Matter, SF and Attardo, GM and Weirauch, MT and Benoit, JB}, title = {Multi-level analysis of reproduction in an Antarctic midge identifies female and male accessory gland products that are altered by larval stress and impact progeny viability.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {19791}, pmid = {33188214}, issn = {2045-2322}, mesh = {Animals ; Female ; Insect Proteins/chemistry/metabolism ; Larva/metabolism ; Male ; Proteomics/*methods ; RNA-Seq/methods ; }, abstract = {The Antarctic midge, Belgica antarctica, is a wingless, non-biting midge endemic to Antarctica. Larval development requires at least 2 years, but adults live only 2 weeks. The nonfeeding adults mate in swarms and females die shortly after oviposition. Eggs are suspended in a gel of unknown composition that is expressed from the female accessory gland. This project characterizes molecular mechanisms underlying reproduction in this midge by examining differential gene expression in whole males, females, and larvae, as well as in male and female accessory glands. Functional studies were used to assess the role of the gel encasing the eggs, as well as the impact of stress on reproductive biology. RNA-seq analyses revealed sex- and development-specific gene sets along with those associated with the accessory glands. Proteomic analyses were used to define the composition of the egg-containing gel, which is generated during multiple developmental stages and derived from both the accessory gland and other female organs. Functional studies indicate the gel provides a larval food source as well as a buffer for thermal and dehydration stress. All of these function are critical to juvenile survival. Larval dehydration stress directly reduces production of storage proteins and key accessory gland components, a feature that impacts adult reproductive success. Modeling reveals that bouts of dehydration may have a significant impact on population growth. This work lays a foundation for further examination of reproduction in midges and provides new information related to general reproduction in dipterans. A key aspect of this work is that reproduction and stress dynamics, currently understudied in polar organisms, are likely to prove critical in determining how climate change will alter their survivability.}, } @article {pmid33185245, year = {2020}, author = {Rao, RT and Sharma, S and Sivakumar, N and Jayakumar, K}, title = {Genomic islands and the evolution of livestock-associated Staphylococcus aureus genomes.}, journal = {Bioscience reports}, volume = {40}, number = {11}, pages = {}, pmid = {33185245}, issn = {1573-4935}, mesh = {Animals ; Computational Biology ; Databases, Genetic ; *Evolution, Molecular ; Gene Expression Regulation, Bacterial ; *Gene Transfer, Horizontal ; *Genome, Bacterial ; *Genomic Islands ; Livestock/*microbiology ; Staphylococcal Infections/genetics/microbiology/*veterinary ; Staphylococcus aureus/*genetics/isolation & purification/pathogenicity ; Virulence ; }, abstract = {BACKGROUND: Genomic Islands (GIs) are commonly believed to be relics of horizontal transfer and associated with specific metabolic capacities, including virulence of the strain. Horizontal gene transfer (HGT) plays a vital role in the acquisition of GIs and the evolution and adaptation of bacterial genomes.

OBJECTIVE: The present study was designed to predict the GIs and role of HGT in evolution of livestock-associated Staphylococcus aureus (LA-SA).

METHODS: GIs were predicted with two methods namely, Ensemble algorithm for Genomic Island Detection (EGID) tool, and Seq word Sniffer script. Functional characterization of GI elements was performed with clustering of orthologs. The putative donor predictions of GIs was done with the aid of the pre_GI database.

RESULTS: The present study predicted a pan of 46 GIs across the LA-SA genomes. Functional characterization of GI sequences revealed few unique results like the presence of metabolic operons like leuABCD and folPK genes in GIs and showed the importance of GIs in the adaptation to the host niche. The developed framework for GI donor prediction results revealed Rickettsia and Mycoplasma as the major donors of GI elements.

CONCLUSIONS: The role of GIs during the evolutionary race of LA-SA could be concluded from the present study. Niche adaptation of LA-SA enhanced presumably due to these GIs. Future studies could focus on the evolutionary relationships between Rickettsia and Mycoplasma sp. with S. aureus and also the evolution of Leucine/Isoleucine mosaic operon (leuABCD).}, } @article {pmid33184337, year = {2020}, author = {Hu, Y and Xing, P and Yang, F and Feng, G and Yang, G and Zhang, Z}, title = {A birdstrike risk assessment model and its application at Ordos Airport, China.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {19627}, pmid = {33184337}, issn = {2045-2322}, mesh = {Accidents, Aviation/*prevention & control/*statistics & numerical data ; Airports/*statistics & numerical data ; Animals ; Behavior, Animal/*physiology ; *Birds/classification ; China ; Databases as Topic ; Flight, Animal/*physiology ; *Models, Statistical ; Risk ; Risk Assessment/*methods ; Risk Management ; Safety ; }, abstract = {Birdstrikes are an important threat to aviation safety. A standardized, scientific process for assessing birdstrike risk could prevent accidents, thereby improving the flight safety and reducing economic losses. However, China currently lacks a unified birdstrike risk assessment system. Here, we propose and validate a new model for assessing birdstrike risk in order to fill that need. The model consists of two elements. First, empirical data are collected on the occurrence of birds at the airport and in a surrounding 8 km buffer. Second, each species is evaluated with a risk assessment matrix that takes into account the number of birds, weight, flight altitude, a tendency to cluster, and range of activity. These five factors allow each species to be divided into one of three risk levels: high danger (level 3), moderate danger (level 2) and low danger (level 1). We propose corresponding birdstrike prevention measures for each level. We apply this method to the civil aviation airport in Ordos, China. We found that 20 of the 118 species of birds in and around the airport were high danger birds (level 3). To validate this process, we compared these species with records of birdstrike accidents in a database maintained by the Civil Aviation Administration of China (CAAC) for 2007-2016. We found that 42% of the species we identified as high risk had been involved in at least one birdstrike accident, and that the remaining 58% belonged to families that appeared in the database. The high degree of overlap gives us high confidence in the practicality of our risk assessment model, which is based on the risk management concept of ISO 31000. Critically, this new model and method for predicting bird strike risk can be replicated at other airports around the world, even where no extensive records have been kept of past birdstrikes.}, } @article {pmid33184309, year = {2020}, author = {García-Jiménez, R and Margalida, A and Pérez-García, JM}, title = {Influence of individual biological traits on GPS fix-loss errors in wild bird tracking.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {19621}, pmid = {33184309}, issn = {2045-2322}, mesh = {*Animal Migration ; Animals ; Animals, Wild/*physiology ; Birds/*physiology ; Breeding ; Ecosystem ; Female ; France ; *Geographic Information Systems ; Humans ; Male ; Spain ; Telemetry ; Territoriality ; }, abstract = {In recent decades, global positioning system (GPS) location data and satellite telemetry systems for data transmission have become fundamental in the study of basic ecological traits in wildlife biology. Evaluating GPS location errors is essential in assessing detailed information about the behaviour of an animal species such as migration, habitat selection, species distribution or foraging strategy. While many studies of the influence of environmental and technical factors on the fix errors of solar-powered GPS transmitters have been published, few studies have focussed on the performance of GPS systems in relation to a species' biological traits. Here, we evaluate the possible effects of the biological traits of a large raptor on the frequency of lost fixes-the fix-loss rate (FLR). We analysed 95,686 records obtained from 20 Bearded Vultures Gypaetus barbatus tracked with 17 solar-powered satellite transmitters in the Pyrenees (Spain, France and Andorra), between 2006 and 2019 to evaluate the influence of biological, technical, and environmental factors on the fix-loss rate of transmitters. We show that combined effects of technical factors and the biological traits of birds explained 23% of the deviance observed. As expected, the transmitter usage time significantly increased errors in the fix-loss rate, although the flight activity of birds revealed an unexpected trade-off: the greater the proportion of fixes recorded from perched birds, the lower the FLR. This finding seems related with the fact that territorial and breeding birds spend significantly more time flying than non-territorial individuals. The fix success rate is apparently due to the interactions between a complex of factors. Non-territorial adults and subadults, males, and breeding individuals showed a significantly lower FLR than juveniles-immatures females, territorial birds or non-breeding individuals. Animal telemetry tracking studies should include error analyses before reaching any ecological conclusions or hypotheses about spatial distribution.}, } @article {pmid33183408, year = {2020}, author = {McGough, SF and MacFadden, DR and Hattab, MW and Mølbak, K and Santillana, M}, title = {Rates of increase of antibiotic resistance and ambient temperature in Europe: a cross-national analysis of 28 countries between 2000 and 2016.}, journal = {Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin}, volume = {25}, number = {45}, pages = {}, pmid = {33183408}, issn = {1560-7917}, support = {R01 GM130668/GM/NIGMS NIH HHS/United States ; }, mesh = {Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Bacterial/drug effects ; Europe ; Humans ; *Temperature ; }, abstract = {BackgroundThe rapid increase of bacterial antibiotic resistance could soon render our most effective method to address infections obsolete. Factors influencing pathogen resistance prevalence in human populations remain poorly described, though temperature is known to contribute to mechanisms of spread.AimTo quantify the role of temperature, spatially and temporally, as a mechanistic modulator of transmission of antibiotic resistant microbes.MethodsAn ecologic analysis was performed on country-level antibiotic resistance prevalence in three common bacterial pathogens across 28 European countries, collectively representing over 4 million tested isolates. Associations of minimum temperature and other predictors with change in antibiotic resistance rates over 17 years (2000-2016) were evaluated with multivariable models. The effects of predictors on the antibiotic resistance rate change across geographies were quantified.ResultsDuring 2000-2016, for Escherichia coli and Klebsiella pneumoniae, European countries with 10°C warmer ambient minimum temperatures compared to others, experienced more rapid resistance increases across all antibiotic classes. Increases ranged between 0.33%/year (95% CI: 0.2 to 0.5) and 1.2%/year (95% CI: 0.4 to 1.9), even after accounting for recognised resistance drivers including antibiotic consumption and population density. For Staphylococcus aureus a decreasing relationship of -0.4%/year (95% CI: -0.7 to 0.0) was found for meticillin resistance, reflecting widespread declines in meticillin-resistant S. aureus across Europe over the study period.ConclusionWe found evidence of a long-term effect of ambient minimum temperature on antibiotic resistance rate increases in Europe. Ambient temperature might considerably influence antibiotic resistance growth rates, and explain geographic differences observed in cross-sectional studies. Rising temperatures globally may hasten resistance spread, complicating mitigation efforts.}, } @article {pmid33183267, year = {2020}, author = {Khazaei, Z and Goodarzi, E and Borhaninejad, V and Iranmanesh, F and Mirshekarpour, H and Mirzaei, B and Naemi, H and Bechashk, SM and Darvishi, I and Ershad Sarabi, R and Naghibzadeh-Tahami, A}, title = {The association between incidence and mortality of brain cancer and human development index (HDI): an ecological study.}, journal = {BMC public health}, volume = {20}, number = {1}, pages = {1696}, pmid = {33183267}, issn = {1471-2458}, mesh = {*Brain Neoplasms/epidemiology/mortality ; *Developing Countries ; Female ; Global Health ; Humans ; Incidence ; Male ; Socioeconomic Factors ; }, abstract = {BACKGROUND: Brain cancer is a rare and deadly malignancy with a low survival rate. The present study aims to evaluate the epidemiology of brain cancer and its relationship with the human development index (HDI) worldwide.

METHODS: This is an ecological study. The data on cancer incidence and cancer mortality was extracted from the World Bank for Cancer in 2018 (GLOBOCAN 2018). The incidence, mortality rate, and brain cancer distribution maps were drawn for different countries. We used correlation and regression tests to examine the association of incidence and mortality rates of brain cancer with HDI. The statistical analysis was carried out by Stata-14 and a significance level of 0.05 was considered.

RESULTS: According to the results of Global Cancer Registry in 2018, there were 18,078,957 registered cases of cancer in both sexes, of which 29,681 were related to brain cancer. The highest incidence (102,260 cases, 34.4%) and mortality (77,815 cases, 32.3%) belonged to very high HDI regions. Results showed that incidence (r = 0.690, P < 0.0001) and mortality rates (r = 0.629, P < 0.001) of brain cancer are significantly correlated with HDI. We also observed a positive correlation between brain cancer incidence and Gross National Income (GNI) (r = 0.346, P < 0.001), Mean Years of Schooling (MYS) (r = 0.64, P < 0.001), TABLE (LEB) (r = 0.66, P < 0.001) and Expected Years of Schooling (EYS) (r = 0.667, P < 0.001). Results also revealed that mortality rate was significantly correlated with GNI (r = 0.28, P < 0.01), MYS (r = 0.591, P < 0.01), LEB (r = 0.624, P < 0.01), and EYS (r = 0.605, P < 0.01).

CONCLUSION: The results of the study showed that the incidence and mortality of brain cancer in countries with higher HDI levels is higher than countries with lower HDI levels, so attention to risk factors and action to reduce it in countries with higher HDI levels in controlling this cancer in this Countries are effective.}, } @article {pmid33182777, year = {2020}, author = {Novotný, J and Strnadová, K and Dvořánková, B and Kocourková, Š and Jakša, R and Dundr, P and Pačes, V and Smetana, K and Kolář, M and Lacina, L}, title = {Single-Cell RNA Sequencing Unravels Heterogeneity of the Stromal Niche in Cutaneous Melanoma Heterogeneous Spheroids.}, journal = {Cancers}, volume = {12}, number = {11}, pages = {}, pmid = {33182777}, issn = {2072-6694}, support = {"Center for Tumor Ecology - Research of the Cancer Microenvironment Supporting Cancer Growth and Spread" CZ.02.1.01/0.0/0.0/16_019/0000785//Operational Programme Research, Development and Education/ ; CZ.1.05/2.1.00/19.0400//Research and Development for Innovations Operational Program co-financed by the European Regional Development Fund and the state budget of the Czech Republic)/ ; Progress programme Q28//Charles University/ ; 19-05048S.//Czech Science Foundation/ ; MEYS Grant No: LM2018131//ELIXIR CZ research infrastructure project/ ; }, abstract = {Heterogeneous spheroids have recently acquired a prominent position in melanoma research because they incorporate microenvironmental cues relevant for melanoma. In this study, we focused on the analysis of microenvironmental factors introduced in melanoma heterogeneous spheroids by different dermal fibroblasts. We aimed to map the fibroblast diversity resulting from previously acquired damage caused by exposure to extrinsic and intrinsic stimuli. To construct heterogeneous melanoma spheroids, we used normal dermal fibroblasts from the sun-protected skin of a juvenile donor. We compared them to the fibroblasts from the sun-exposed photodamaged skin of an adult donor. Further, we analysed the spheroids by single-cell RNA sequencing. To validate transcriptional data, we also compared the immunohistochemical analysis of heterogeneous spheroids to melanoma biopsies. We have distinguished three functional clusters in primary human fibroblasts from melanoma spheroids. These clusters differed in the expression of (a) extracellular matrix-related genes, (b) pro-inflammatory factors, and (c) TGFβ signalling superfamily. We observed a broader deregulation of gene transcription in previously photodamaged cells. We have confirmed that pro-inflammatory cytokine IL-6 significantly enhances melanoma invasion to the extracellular matrix in our model. This supports the opinion that the aspects of ageing are essential for reliable melanoma 3D modelling in vitro.}, } @article {pmid33181932, year = {2020}, author = {Taillardat, P and Marchand, C and Friess, DA and Widory, D and David, F and Ohte, N and Nakamura, T and Van Vinh, T and Thanh-Nho, N and Ziegler, AD}, title = {Respective contribution of urban wastewater and mangroves on nutrient dynamics in a tropical estuary during the monsoon season.}, journal = {Marine pollution bulletin}, volume = {160}, number = {}, pages = {111652}, doi = {10.1016/j.marpolbul.2020.111652}, pmid = {33181932}, issn = {1879-3363}, mesh = {Environmental Monitoring ; *Estuaries ; Nutrients ; Rivers ; Seasons ; Vietnam ; *Wastewater ; }, abstract = {Estuaries of Southeast Asia are increasingly impacted by land-cover changes and pollution. Here, our research objectives were to (1) determine the origins of nutrient loads along the Can Gio estuary (Vietnam) and (2) identify the processes that affect the nutrient pools during the monsoon. We constructed four 24-h time-series along the salinity gradient measuring nutrient concentrations and stable isotopes values. In the upper estuary, urban effluents from Ho Chi Minh City were the main input of nutrients, leading to dissolved oxygen saturation <20%. In the lower estuary, ammonium and nitrite concentration peaks were explained by mangrove export. No contribution from aquaculture was detected, as it represents <0.01% of the total river discharge. Along the salinity gradient, nutrient inputs were rapidly consumed, potentially by phytoplankton while nitrate dual-stable isotopes indicated that nitrification occurred. Thus, even in a large and productive estuary, urban wastewater can affect nutrient dynamics with potentially important ecological risks.}, } @article {pmid33181821, year = {2020}, author = {Reyserhove, L and Desmet, P and Oldoni, D and Adriaens, T and Strubbe, D and Davis, AJS and Vanderhoeven, S and Verloove, F and Groom, Q}, title = {A checklist recipe: making species data open and FAIR.}, journal = {Database : the journal of biological databases and curation}, volume = {2020}, number = {}, pages = {}, pmid = {33181821}, issn = {1758-0463}, mesh = {*Biodiversity ; *Checklist ; Plants ; Registries ; Workflow ; }, abstract = {Species checklists are a crucial source of information for research and policy. Unfortunately, many traditional species checklists vary wildly in their content, format, availability and maintenance. The fact that these are not open, findable, accessible, interoperable and reusable (FAIR) severely hampers fast and efficient information flow to policy and decision-making that are required to tackle the current biodiversity crisis. Here, we propose a reproducible, semi-automated workflow to transform traditional checklist data into a FAIR and open species registry. We showcase our workflow by applying it to the publication of the Manual of Alien Plants, a species checklist specifically developed for the Tracking Invasive Alien Species (TrIAS) project. Our approach combines source data management, reproducible data transformation to Darwin Core using R, version control, data documentation and publication to the Global Biodiversity Information Facility (GBIF). This checklist publication workflow is openly available for data holders and applicable to species registries varying in thematic, taxonomic or geographical scope and could serve as an important tool to open up research and strengthen environmental decision-making.}, } @article {pmid33179728, year = {2021}, author = {Rafiepour, M and Ebrahimie, E and Vahidi, MF and Salekdeh, GH and Niazi, A and Dadpasand, M and Liang, D and Si, J and Ding, X and Han, J and Zhang, Y and Qanbari, S}, title = {Whole-Genome Resequencing Reveals Adaptation Prior to the Divergence of Buffalo Subspecies.}, journal = {Genome biology and evolution}, volume = {13}, number = {1}, pages = {}, pmid = {33179728}, issn = {1759-6653}, mesh = {*Adaptation, Biological ; Animals ; Buffaloes/*genetics ; Cattle ; Computational Biology ; Female ; Genetic Variation ; *Genome ; Genomics ; Iran ; Male ; Polymorphism, Single Nucleotide ; }, abstract = {The application of high-throughput genotyping or sequencing data helps us to understand the genomic response to natural and artificial selection. In this study, we scanned the genomes of five indigenous buffalo populations belong to three recognized breeds, adapted to different geographical and agro-ecological zones in Iran, to unravel the extent of genomic diversity and to localize genomic regions and genes underwent past selection. A total of 46 river buffalo whole genomes, from West and East Azerbaijan, Gilan, Mazandaran, and Khuzestan provinces, were resequenced. Our sequencing data reached to a coverage above 99% of the river buffalo reference genome and an average read depth around 9.2× per sample. We identified 20.55 million SNPs, including 63,097 missense, 707 stop-gain, and 159 stop-loss mutations that might have functional consequences. Genomic diversity analyses showed modest structuring among Iranian buffalo populations following frequent gene flow or admixture in the recent past. Evidence of positive selection was investigated using both differentiation (Fst) and fixation (Pi) metrics. Analysis of fixation revealed three genomic regions in all three breeds with aberrant polymorphism contents on BBU2, 20, and 21. Fixation signal on BBU2 overlapped with the OCA2-HERC2 genes, suggestive of adaptation to UV exposure through pigmentation mechanism. Further validation using resequencing data from other five bovine species as well as the Axiom Buffalo Genotyping Array 90K data of river and swamp buffaloes indicated that these fixation signals persisted across river and swamp buffaloes and extended to taurine cattle, implying an ancient evolutionary event occurred before the speciation of buffalo and taurine cattle. These results contributed to our understanding of major genetic switches that took place during the evolution of modern buffaloes.}, } @article {pmid33177945, year = {2020}, author = {Santos, J and Rupino da Cunha, P and Sales, F}, title = {A strategy to digitise natural history collections with limited resources.}, journal = {Biodiversity data journal}, volume = {8}, number = {}, pages = {e55959}, pmid = {33177945}, issn = {1314-2828}, abstract = {The present work is a contribution towards accelerating the digitisation process of natural history collections, usually a slow process. A two-stage process was developed at the herbarium of the University of Coimbra: (i) a new workflow was established to automatically create records in the herbarium master database with minimum information, while capturing digital images; (ii) these records are then used to populate a web-based crowdsourcing platform where citizens are involved in the transcription of specimen labels from the digital images. This approach simplifies and accelerates databasing, reduces specimen manipulation and promotes the involvement of citizens in the scientific goals of the herbarium. The novel features of this process are: (i) the validation method of the crowdsourcing contribution that ensures quality control, enabling the data to integrate the master database directly and (ii) the field-by-field integration in the master database enables immediate corrections to any record in the catalogue.}, } @article {pmid33177665, year = {2020}, author = {Feng, S and Stiller, J and Deng, Y and Armstrong, J and Fang, Q and Reeve, AH and Xie, D and Chen, G and Guo, C and Faircloth, BC and Petersen, B and Wang, Z and Zhou, Q and Diekhans, M and Chen, W and Andreu-Sánchez, S and Margaryan, A and Howard, JT and Parent, C and Pacheco, G and Sinding, MS and Puetz, L and Cavill, E and Ribeiro, ÂM and Eckhart, L and Fjeldså, J and Hosner, PA and Brumfield, RT and Christidis, L and Bertelsen, MF and Sicheritz-Ponten, T and Tietze, DT and Robertson, BC and Song, G and Borgia, G and Claramunt, S and Lovette, IJ and Cowen, SJ and Njoroge, P and Dumbacher, JP and Ryder, OA and Fuchs, J and Bunce, M and Burt, DW and Cracraft, J and Meng, G and Hackett, SJ and Ryan, PG and Jønsson, KA and Jamieson, IG and da Fonseca, RR and Braun, EL and Houde, P and Mirarab, S and Suh, A and Hansson, B and Ponnikas, S and Sigeman, H and Stervander, M and Frandsen, PB and van der Zwan, H and van der Sluis, R and Visser, C and Balakrishnan, CN and Clark, AG and Fitzpatrick, JW and Bowman, R and Chen, N and Cloutier, A and Sackton, TB and Edwards, SV and Foote, DJ and Shakya, SB and Sheldon, FH and Vignal, A and Soares, AER and Shapiro, B and González-Solís, J and Ferrer-Obiol, J and Rozas, J and Riutort, M and Tigano, A and Friesen, V and Dalén, L and Urrutia, AO and Székely, T and Liu, Y and Campana, MG and Corvelo, A and Fleischer, RC and Rutherford, KM and Gemmell, NJ and Dussex, N and Mouritsen, H and Thiele, N and Delmore, K and Liedvogel, M and Franke, A and Hoeppner, MP and Krone, O and Fudickar, AM and Milá, B and Ketterson, ED and Fidler, AE and Friis, G and Parody-Merino, ÁM and Battley, PF and Cox, MP and Lima, NCB and Prosdocimi, F and Parchman, TL and Schlinger, BA and Loiselle, BA and Blake, JG and Lim, HC and Day, LB and Fuxjager, MJ and Baldwin, MW and Braun, MJ and Wirthlin, M and Dikow, RB and Ryder, TB and Camenisch, G and Keller, LF and DaCosta, JM and Hauber, ME and Louder, MIM and Witt, CC and McGuire, JA and Mudge, J and Megna, LC and Carling, MD and Wang, B and Taylor, SA and Del-Rio, G and Aleixo, A and Vasconcelos, ATR and Mello, CV and Weir, JT and Haussler, D and Li, Q and Yang, H and Wang, J and Lei, F and Rahbek, C and Gilbert, MTP and Graves, GR and Jarvis, ED and Paten, B and Zhang, G}, title = {Dense sampling of bird diversity increases power of comparative genomics.}, journal = {Nature}, volume = {587}, number = {7833}, pages = {252-257}, pmid = {33177665}, issn = {1476-4687}, support = {U01 HL137183/HL/NHLBI NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; T32 HG008345/HG/NHGRI NIH HHS/United States ; R01 HG010053/HG/NHGRI NIH HHS/United States ; R01 HG010485/HG/NHGRI NIH HHS/United States ; U54 HG007990/HG/NHGRI NIH HHS/United States ; R35 GM133412/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Birds/*classification/*genetics ; Chickens/genetics ; Conservation of Natural Resources ; Datasets as Topic ; Finches/genetics ; Genome/*genetics ; Genomics/*methods/*standards ; Humans ; *Phylogeny ; Selection, Genetic/genetics ; Synteny/genetics ; }, abstract = {Whole-genome sequencing projects are increasingly populating the tree of life and characterizing biodiversity[1-4]. Sparse taxon sampling has previously been proposed to confound phylogenetic inference[5], and captures only a fraction of the genomic diversity. Here we report a substantial step towards the dense representation of avian phylogenetic and molecular diversity, by analysing 363 genomes from 92.4% of bird families-including 267 newly sequenced genomes produced for phase II of the Bird 10,000 Genomes (B10K) Project. We use this comparative genome dataset in combination with a pipeline that leverages a reference-free whole-genome alignment to identify orthologous regions in greater numbers than has previously been possible and to recognize genomic novelties in particular bird lineages. The densely sampled alignment provides a single-base-pair map of selection, has more than doubled the fraction of bases that are confidently predicted to be under conservation and reveals extensive patterns of weak selection in predominantly non-coding DNA. Our results demonstrate that increasing the diversity of genomes used in comparative studies can reveal more shared and lineage-specific variation, and improve the investigation of genomic characteristics. We anticipate that this genomic resource will offer new perspectives on evolutionary processes in cross-species comparative analyses and assist in efforts to conserve species.}, } @article {pmid33176069, year = {2021}, author = {Garcia, CB and Chapman, IF and Chen, SH and Lazear, E and Lentz, TB and Williams, C and Dums, JT and Goller, CC and Robertson, SD}, title = {Integrating research into a molecular cloning course to address the evolving biotechnology landscape.}, journal = {Biochemistry and molecular biology education : a bimonthly publication of the International Union of Biochemistry and Molecular Biology}, volume = {49}, number = {1}, pages = {115-128}, doi = {10.1002/bmb.21402}, pmid = {33176069}, issn = {1539-3429}, mesh = {Animals ; Biotechnology/*education ; Calcium/metabolism ; Cloning, Molecular ; Curriculum ; Fluorescent Dyes/chemistry ; Humans ; Proteins/analysis ; *Research ; Students ; }, abstract = {The rapid development of molecular biotechnology presents a curricular challenge for educators trying to provide students with relevant coursework. A comprehensive biology education should also include opportunities for students to develop intellectual and technical skills through authentic research experiences. Integrating relevant and interesting research projects into their classes, however, can be a challenging task for instructors. To address these varied demands, we redesigned our existing molecular cloning course to incorporate an independent research project assessing calcium signaling. In the revised course, students use traditional and recombination-based cloning strategies to generate bacterial and mammalian expression vectors encoding CaMPARI, a novel fluorescent calcium indicator. Bacterially-expressed CaMPARI is used in protein quantification and purification assays. Students must also design their own research project evaluating the effect of chemotherapeutic agents on calcium signaling in a mammalian system. Revised and novel labs were designed to be modular, facilitating their integration into the course over 2 years. End-of-semester student evaluations were compared between years revealing a significant difference in students' perception of the course's difficulty between years. This change in attitude highlights potential pedagogical considerations that must be examined when introducing new material and activities into existing courses. Since calcium signaling is important for cellular process across diverse species, instructors may be able to develop research projects within their respective areas of interest. Integration of authentic research experiences into the curriculum is challenging; however, the framework described here provides a versatile structure that can be adapted to merge diverse instructor interests with evolving educational needs.}, } @article {pmid33171740, year = {2020}, author = {Sommers, P and Porazinska, DL and Darcy, JL and Gendron, EMS and Vimercati, L and Solon, AJ and Schmidt, SK}, title = {Microbial Species-Area Relationships in Antarctic Cryoconite Holes Depend on Productivity.}, journal = {Microorganisms}, volume = {8}, number = {11}, pages = {}, pmid = {33171740}, issn = {2076-2607}, support = {1443578//National Science Foundation/ ; }, abstract = {The island species-area relationship (ISAR) is a positive association between the number of species and the area of an isolated, island-like habitat. ISARs are ubiquitous across domains of life, yet the processes generating ISARs remain poorly understood, particularly for microbes. Larger and more productive islands are hypothesized to have more species because they support larger populations of each species and thus reduce the probability of stochastic extinctions in small population sizes. Here, we disentangled the effects of "island" size and productivity on the ISAR of Antarctic cryoconite holes. We compared the species richness of bacteria and microbial eukaryotes on two glaciers that differ in their productivity across varying hole sizes. We found that cryoconite holes on the more productive Canada Glacier gained more species with increasing hole area than holes on the less productive Taylor Glacier. Within each glacier, neither productivity nor community evenness explained additional variation in the ISAR. Our results are, therefore, consistent with productivity shaping microbial ISARs at broad scales. More comparisons of microbial ISARs across environments with limited confounding factors, such as cryoconite holes, and experimental manipulations within these systems will further contribute to our understanding of the processes shaping microbial biogeography.}, } @article {pmid33168070, year = {2020}, author = {Nesterenko, MA and Starunov, VV and Shchenkov, SV and Maslova, AR and Denisova, SA and Granovich, AI and Dobrovolskij, AA and Khalturin, KV}, title = {Molecular signatures of the rediae, cercariae and adult stages in the complex life cycles of parasitic flatworms (Digenea: Psilostomatidae).}, journal = {Parasites & vectors}, volume = {13}, number = {1}, pages = {559}, pmid = {33168070}, issn = {1756-3305}, support = {МК-2105.2017.4//Council on grants of the President of the Russian Federation/ ; 19-34-90111//RFBR/ ; }, mesh = {Animals ; Cercaria/genetics ; Computational Biology ; Gene Ontology ; *Life Cycle Stages ; Snails/parasitology ; *Transcriptome ; Trematoda/*genetics/*growth & development ; }, abstract = {BACKGROUND: Parasitic flatworms (Trematoda: Digenea) represent one of the most remarkable examples of drastic morphological diversity among the stages within a life cycle. Which genes are responsible for extreme differences in anatomy, physiology, behavior, and ecology among the stages? Here we report a comparative transcriptomic analysis of parthenogenetic and amphimictic generations in two evolutionary informative species of Digenea belonging to the family Psilostomatidae.

METHODS: In this study the transcriptomes of rediae, cercariae and adult worm stages of Psilotrema simillimum and Sphaeridiotrema pseudoglobulus, were sequenced and analyzed. High-quality transcriptomes were generated, and the reference sets of protein-coding genes were used for differential expression analysis in order to identify stage-specific genes. Comparative analysis of gene sets, their expression dynamics and Gene Ontology enrichment analysis were performed for three life stages within each species and between the two species.

RESULTS: Reference transcriptomes for P. simillimum and S. pseudoglobulus include 21,433 and 46,424 sequences, respectively. Among 14,051 orthologous groups (OGs), 1354 are common and specific for two analyzed psilostomatid species, whereas 13 and 43 OGs were unique for P. simillimum and S. pseudoglobulus, respectively. In contrast to P. simillimum, where more than 60% of analyzed genes were active in the redia, cercaria and adult worm stages, in S. pseudoglobulus less than 40% of genes had such a ubiquitous expression pattern. In general, 7805 (36.41%) and 30,622 (65.96%) of genes were preferentially expressed in one of the analyzed stages of P. simillimum and S. pseudoglobulus, respectively. In both species 12 clusters of co-expressed genes were identified, and more than a half of the genes belonging to the reference sets were included into these clusters. Functional specialization of the life cycle stages was clearly supported by Gene Ontology enrichment analysis.

CONCLUSIONS: During the life cycles of the two species studied, most of the genes change their expression levels considerably, consequently the molecular signature of a stage is not only a unique set of expressed genes, but also the specific levels of their expression. Our results indicate unexpectedly high level of plasticity in gene regulation between closely related species. Transcriptomes of P. simillimum and S. pseudoglobulus provide high quality reference resource for future evolutionary studies and comparative analyses.}, } @article {pmid33166079, year = {2021}, author = {Nie, Y and Wu, XL}, title = {Getting back to the nature of the microbial world: from the description and inductive reasoning to deductive study after 'meta-omics'.}, journal = {Microbial biotechnology}, volume = {14}, number = {1}, pages = {22-25}, pmid = {33166079}, issn = {1751-7915}, mesh = {Databases, Factual ; *Microbiota ; }, abstract = {'Omics' studies have by now deposited massive amounts of data into the databases, and it is now time to return to the question as to what can we actually learn from them. Increased application of the deductive approach in synthetic microbial ecology and synthetic microbiome research will undoubtedly provide exciting new opportunities for advancing our understanding of microbial ecology.}, } @article {pmid33164845, year = {2021}, author = {Green Etxabe, A and Pini, JM and Short, S and Cunha, L and Kille, P and Watson, GJ}, title = {Identifying conserved polychaete molecular markers of metal exposure: Comparative analyses using the Alitta virens (Annelida, Lophotrochozoa) transcriptome.}, journal = {Comparative biochemistry and physiology. Toxicology & pharmacology : CBP}, volume = {240}, number = {}, pages = {108913}, doi = {10.1016/j.cbpc.2020.108913}, pmid = {33164845}, issn = {1532-0456}, mesh = {Animals ; Annelida/*genetics ; Biomarkers/*analysis ; Copper/toxicity ; Gene Expression Profiling/methods ; Gene Ontology ; Metals/*toxicity ; Polychaeta/classification/*genetics ; RNA-Seq/methods ; Reverse Transcriptase Polymerase Chain Reaction ; Species Specificity ; Transcriptome/*drug effects ; Water Pollutants, Chemical/toxicity ; Zinc/toxicity ; }, abstract = {Polychaetes are vital for evaluating the effects of toxic metals in marine systems, and sensitive molecular biomarkers should be integral to monitoring efforts. However, the few polychaete markers that exist are inconsistent, even within the same species, failing to identify gene expression changes in metal-exposed animals incurring clear metabolic costs. Comparing previously characterised polychaete metal-responsive genes with those of another carefully selected species could identify biomarkers applicable across polychaetes. The ragworm Alitta virens (Sars, 1835) is particularly suited for such comparisons due to its dominance of fully saline coastal areas, widespread distribution, large biomass, and its phylogenetic position relative to other polychaete 'omic' resources. A transcriptome atlas for A. virens was generated and an RNASeq-qPCR screening approach was used to characterise the response to chronic exposures of environmentally relevant concentrations of copper and zinc in controlled mesocosms. Genes presenting dramatic expression changes in A. virens were compared with known metal-responsive genes in other polychaetes to identify new possible biomarkers and assess those currently used. This revealed some current markers should probably be abandoned (e.g. Atox1), while others, such as GST-Omega, should be used with caution, as different polychaete species appear to upregulate distinct GST-Omega orthologues. In addition, the comparisons give some indication of genes that are induced by metal exposure across phylogenetically divergent polychaetes, including a suite of haemoglobin subunits and linker chains that could play conserved roles in metal-stress response. Although such newly identified markers need further characterisation, they offer alternatives to current markers that are plainly insufficient.}, } @article {pmid33161547, year = {2021}, author = {Birt, HWG and Dennis, PG}, title = {Inference and Analysis of SPIEC-EASI Microbiome Networks.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2232}, number = {}, pages = {155-171}, doi = {10.1007/978-1-0716-1040-4_14}, pmid = {33161547}, issn = {1940-6029}, mesh = {Algorithms ; Computational Biology/*methods ; Humans ; Microbiota/*genetics ; RNA, Ribosomal, 16S/*genetics ; *Software ; }, abstract = {Network analysis facilitates examination of the interactions between different populations in a community. It can provide a range of metrics describing the social characteristics of each population and emergent structural properties of the community, which may be used to address novel ecological questions. Using a publicly available dataset, this chapter provides point-by-point code and instructions to infer and analyze a SPIEC-EASI (SParse InversE Covariance Estimation for Ecological Association Inference) network using free, open source software (R and Gephi).}, } @article {pmid33161151, year = {2021}, author = {Mai, Y and Peng, S and Li, H and Gao, Y and Lai, Z}, title = {NOD-like receptor signaling pathway activation: A potential mechanism underlying negative effects of benzo(α)pyrene on zebrafish.}, journal = {Comparative biochemistry and physiology. Toxicology & pharmacology : CBP}, volume = {240}, number = {}, pages = {108935}, doi = {10.1016/j.cbpc.2020.108935}, pmid = {33161151}, issn = {1532-0456}, mesh = {Animals ; Benzo(a)pyrene/*toxicity ; Gene Expression Profiling/methods ; Gene Ontology ; Liver/drug effects/metabolism ; NLR Proteins/*genetics/metabolism ; Oxidative Stress/drug effects ; RNA-Seq/methods ; Reverse Transcriptase Polymerase Chain Reaction ; Signal Transduction/*genetics ; Time Factors ; Transcriptome/*drug effects ; Water Pollutants, Chemical/toxicity ; Zebrafish/*genetics/metabolism ; Zebrafish Proteins/*genetics/metabolism ; }, abstract = {Benzo(α)pyrene (BaP) is one of typical polycyclic aromatic hydrocarbons (PAHs) in aquatic environments and has been shown to cause toxic effects to aquatic animals. Although the negative effects of BaP have been investigated, the potential toxic mechanisms remain uncharacterized. To explore the potential mechanisms mediating the toxic effects of BaP, zebrafish (Danio rerio) were exposed to BaP for 15 days and the toxic effects of BaP in zebrafish liver were investigated using physiological and transcriptomic analyses. After 15-day BaP exposure, zebrafish liver exhibited abnormalities including increased cytoplasmic vacuolation, inflammatory cell infiltration, swelled nuclei and irregular pigmentation. BaP exposure also induced oxidative stress to the liver of zebrafish. Transcriptomic profiles revealed 5129 differentially expressed genes (DEGs) after 15-days of BaP exposure, and the vast majority of DEGs were up-regulated under BaP treatment. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses suggest that genes related to immune response were significantly dysregulated. Furthermore, the nucleotide-binding, oligomerization domain (NOD)-like receptor signaling pathway was significantly enriched and most of the genes in this pathway exhibited enhanced expression after BaP exposure. These results partially explained the mechanisms underlying the toxic effects of BaP on zebrafish liver. In conclusion, BaP has the potential to induce physiological responses in zebrafish liver through altering associated genes.}, } @article {pmid33159676, year = {2020}, author = {Wang, L and Liang, J and Shang, Q and Sa, W and Wang, L}, title = {The complete plastome of Sorbaria kirilowii: genome structure, comparative analysis, and phylogenetic implications.}, journal = {Molecular biology reports}, volume = {47}, number = {12}, pages = {9677-9687}, doi = {10.1007/s11033-020-05976-5}, pmid = {33159676}, issn = {1573-4978}, support = {2019-ZJ-962Q//Natural Science Foundation of Qinghai/ ; 2019-NK-106//Natural Science Foundation of Qinghai/ ; 2018-ZJ-963Q//Natural Science Foundation of Qinghai/ ; 2017-NK-151//Natural Science Foundation of Qinghai/ ; 2016-ZJ-Y01//Natural Science Foundation of Qinghai/ ; }, mesh = {Chloroplasts/*genetics ; DNA, Intergenic/chemistry/genetics ; DNA, Plant/chemistry/*genetics ; Gene Ontology ; *Genes, Plant ; Genetic Variation ; Genome Size ; *Genome, Chloroplast ; Molecular Sequence Annotation ; Phylogeny ; Plant Leaves/genetics ; Rosaceae/classification/*genetics ; }, abstract = {Sorbaria kirilowii is a deciduous perennial admired for its showy white blossoms. Though of importance for horticultural purposes, the plastomic study concerning this species is still lacking. Here, the plastome of S. kirilowii was de novo assembled using the high-throughput sequencing data. The complete plastome assembly of S. kirilowii was 160,810 bp in length, with a GC content of 36.03%. It featured a typical quadripartite structure, containing a pair of inverted repeats (IRs; 26,338 bp) separated by a large single-copy (LSC; 88,762 bp) and a small single-copy (SSC, 19,372 bp). In total, 132 genes were annotated in the plastome, including 87 protein-coding genes, 8 rRNA genes, and 37 tRNA genes. Furthermore, 63 SSRs, most of which were AT-rich, were identified in the cp genome of S. kirilowii. 71.7% of the cpSSRs were shown to be located in the intergenic regions. In addition, 49 repeats of varying sizes and types were also identified in the plastome. Through comparison, eight divergence hotspots were identified between the plastome of S. kirilowii and S. sorbifolia var. stellipila. These variable regions could potentially be developed into molecular markers for species delimitation or phylogenetics in future studies. We re-investigated the relationship among 17 Rosaceae species using the plastomic sequences, and S. kirilowii was shown to be a sister to S. sorbifolia var. stellipila. Overall, this study provides plastomic resources which could facilitate marker development and phylogenomics of Rosaceae.}, } @article {pmid33158406, year = {2022}, author = {Deogan, C and Abrahamsson, K and Mannheimer, L and Björkenstam, C}, title = {Having a child without wanting to? Estimates and contributing factors from a population-based survey in Sweden.}, journal = {Scandinavian journal of public health}, volume = {50}, number = {2}, pages = {215-222}, pmid = {33158406}, issn = {1651-1905}, mesh = {*Abortion, Induced ; Adolescent ; Adult ; Aged ; Aged, 80 and over ; Child ; Female ; Humans ; Male ; Middle Aged ; Pregnancy ; Pregnancy, Unplanned ; *Pregnancy, Unwanted ; Prevalence ; Sweden ; Young Adult ; }, abstract = {AIMS: The aims of the current study were to identify the prevalence of unwanted childbirth (UC), to explore the association with sociodemographic factors and to identify possible contributing factors such as psychosomatic health, contraceptive use, experiences of induced abortion and sexual violence.

METHODS: We used Swedish data from the randomised population-based study SRHR2017 on sexual and reproductive health and rights (SRHR), based on self-administered surveys, linked to nationwide registers. The national sample consisted of 14,537 women and men aged between 16 and 84 years. With logistic regression, we examined differences in self-reported experience of UC, stratified by sex, in relation to socio-economic factors, as well as several possible contributing factors.

RESULTS: Despite advances in SRHR and fertility control, 6% of women and men in Sweden reported UC. This experience tends to be unevenly distributed in the population according to age, country of birth and, to some extent, income and educational attainment. Previous experience of induced abortion, sexual violence and threat from a partner were significantly associated with UC, whereas self-reported good health was protective.

CONCLUSIONS: Mechanisms behind unintended, unplanned, unwanted or mistimed pregnancies are complex. Current results focus on the role of individual factors and personal experiences. In addition, in line with previous understanding, there is a need for adopting a broader socio-ecological perspective on fertility intentions.}, } @article {pmid33158212, year = {2020}, author = {Turnbull, OMH and Ortiz-Baez, AS and Eden, JS and Shi, M and Williamson, JE and Gaston, TF and Zhang, YZ and Holmes, EC and Geoghegan, JL}, title = {Meta-Transcriptomic Identification of Divergent Amnoonviridae in Fish.}, journal = {Viruses}, volume = {12}, number = {11}, pages = {}, pmid = {33158212}, issn = {1999-4915}, mesh = {Animals ; Australia ; China ; Computational Biology ; Data Mining ; Fish Diseases/*virology ; Host Specificity ; Orthomyxoviridae/*classification/isolation & purification ; Orthomyxoviridae Infections/*veterinary ; Phylogeny ; Sequence Analysis, RNA ; Tilapia/*virology ; *Transcriptome ; }, abstract = {Tilapia lake virus (TiLV) has caused mass mortalities in farmed and wild tilapia with serious economic and ecological consequences. Until recently, this virus was the sole member of the Amnoonviridae, a family within the order Articulavirales comprising segmented negative-sense RNA viruses. We sought to identify additional viruses within the Amnoonviridae through total RNA sequencing (meta-transcriptomics) and data mining of published transcriptomes. Accordingly, we sampled marine fish species from both Australia and China and discovered several segments of two new viruses within the Amnoonviridae, tentatively called Flavolineata virus and Piscibus virus, respectively. In addition, by mining vertebrate transcriptome data, we identified nine additional virus transcripts matching to multiple genomic segments of TiLV in both marine and freshwater fish. These new viruses retained sequence conservation with the distantly related Orthomyxoviridae in the RdRp subunit PB1, but formed a distinct and diverse phylogenetic group. These data suggest that the Amnoonviridae have a broad host range within fish and that greater animal sampling will identify additional divergent members of the Articulavirales.}, } @article {pmid33154745, year = {2020}, author = {Guslund, NC and Solbakken, MH and Brieuc, MSO and Jentoft, S and Jakobsen, KS and Qiao, SW}, title = {Single-Cell Transcriptome Profiling of Immune Cell Repertoire of the Atlantic Cod Which Naturally Lacks the Major Histocompatibility Class II System.}, journal = {Frontiers in immunology}, volume = {11}, number = {}, pages = {559555}, pmid = {33154745}, issn = {1664-3224}, mesh = {Animals ; Computational Biology ; Fish Proteins/*genetics ; Gadus morhua/*genetics ; *Gene Expression Profiling/methods ; Histocompatibility Antigens Class II/*genetics/immunology ; Leukocytes/immunology/metabolism ; *Single-Cell Analysis/methods ; *Transcriptome ; }, abstract = {The Atlantic cod's unusual immune system, entirely lacking the Major Histocompatibility class II pathway, has prompted intriguing questions about what mechanisms are used to combat bacterial infections and how immunological memory is generated. By single-cell RNA sequencing we here report an in-depth characterisation of cell types found in immune tissues, the spleen and peripheral blood leukocytes of Atlantic cod. Unbiased transcriptional clustering revealed eleven distinct immune cell signatures. Resolution at the single cell level enabled characterisation of the major cell subsets including the cytotoxic T cells, B cells, erythrocytes, thrombocytes, neutrophils, and macrophages. Additionally, to our knowledge we are the first to uncover cell subsets in Atlantic cod which may represent dendritic cells, natural killer-like cells, and a population of cytotoxic cells expressing GATA-3, a master transcription factor of T helper 2 cells. We further identify putative gene markers for each cluster and describe the relative proportions of each cell type in the spleen and peripheral blood leukocytes. Of the major haematopoietic cell populations, the lymphocytes make up 55 and 68% of the spleen and peripheral blood leukocytes respectively, while the myeloid cells make up 45 and 32%. By single-cell analysis, this study provides the most detailed molecular and cellular characterisation of the immune system of the Atlantic cod so far.}, } @article {pmid33149150, year = {2020}, author = {Lösel, PD and van de Kamp, T and Jayme, A and Ershov, A and Faragó, T and Pichler, O and Tan Jerome, N and Aadepu, N and Bremer, S and Chilingaryan, SA and Heethoff, M and Kopmann, A and Odar, J and Schmelzle, S and Zuber, M and Wittbrodt, J and Baumbach, T and Heuveline, V}, title = {Introducing Biomedisa as an open-source online platform for biomedical image segmentation.}, journal = {Nature communications}, volume = {11}, number = {1}, pages = {5577}, pmid = {33149150}, issn = {2041-1723}, mesh = {Algorithms ; Animals ; Datasets as Topic ; Heart/diagnostic imaging ; Humans ; Image Processing, Computer-Assisted/*methods ; Imaging, Three-Dimensional/*methods ; Mice ; Neural Networks, Computer ; Oryzias ; Software ; Tomography, X-Ray Computed ; Tooth/diagnostic imaging ; Uncertainty ; Weevils ; }, abstract = {We present Biomedisa, a free and easy-to-use open-source online platform developed for semi-automatic segmentation of large volumetric images. The segmentation is based on a smart interpolation of sparsely pre-segmented slices taking into account the complete underlying image data. Biomedisa is particularly valuable when little a priori knowledge is available, e.g. for the dense annotation of the training data for a deep neural network. The platform is accessible through a web browser and requires no complex and tedious configuration of software and model parameters, thus addressing the needs of scientists without substantial computational expertise. We demonstrate that Biomedisa can drastically reduce both the time and human effort required to segment large images. It achieves a significant improvement over the conventional approach of densely pre-segmented slices with subsequent morphological interpolation as well as compared to segmentation tools that also consider the underlying image data. Biomedisa can be used for different 3D imaging modalities and various biomedical applications.}, } @article {pmid33148684, year = {2021}, author = {Fernandes, A and Van Lenthe, FJ and Vallée, J and Sueur, C and Chaix, B}, title = {Linking physical and social environments with mental health in old age: a multisensor approach for continuous real-life ecological and emotional assessment.}, journal = {Journal of epidemiology and community health}, volume = {75}, number = {5}, pages = {477-483}, pmid = {33148684}, issn = {1470-2738}, mesh = {Aged ; Built Environment ; Cities ; Geographic Information Systems ; Humans ; *Mental Health ; *Social Environment ; }, abstract = {BACKGROUND: Urban stress is mentioned as a plausible mechanism leading to chronic stress, which is a risk factor of depression. Yet, an accurate assessment of urban stressors in environmental epidemiology requires new methods. This article discusses methods for the sensor-based continuous assesment of geographic environments, stress and depressive symptoms in older age. We report protocols of the promoting mental well-being and healthy ageing in cities (MINDMAP) and Healthy Aging and Networks in Cities (HANC) studies nested in the RECORD Cohort as a background for a broad discussion about the theoretical foundation and monitoring tools of mobile sensing research in older age. Specifically, these studies allow one to compare how older people with and without depression perceive, navigate and use their environment; and how the built environments, networks of social contacts, and spatial mobility patterns influence the mental health of older people.

METHODS: Our research protocol combines (1) Global Positioning System (GPS) and accelerometer tracking and a GPS-based mobility survey to assess participants' mobility patterns, activity patterns and environmental exposures; (2) proximity detection to assess whether household members are close to each other; (3) ecological momentary assessment to track momentary mood and stress and environmental perceptions; and (4) electrodermal activity for the tentative prediction of stress. Data will be compared within individuals (at different times) and between persons with and without depressive symptoms.

CONCLUSION: The development of mobile sensing and survey technologies opens an avenue to improve understanding of the role of momentary stressors and resourcing features of residential and non-residential environments for older populations' mental health. However, validation, privacy and ethical aspects are important issues to consider.}, } @article {pmid33147630, year = {2021}, author = {Peltier, DMP and Guo, J and Nguyen, P and Bangs, M and Gear, L and Wilson, M and Jefferys, S and Samuels-Crow, K and Yocom, LL and Liu, Y and Fell, MK and Auty, D and Schwalm, C and Anderegg, WRL and Koch, GW and Litvak, ME and Ogle, K}, title = {Temporal controls on crown nonstructural carbohydrates in southwestern US tree species.}, journal = {Tree physiology}, volume = {41}, number = {3}, pages = {388-402}, doi = {10.1093/treephys/tpaa149}, pmid = {33147630}, issn = {1758-4469}, mesh = {Carbohydrate Metabolism ; Carbohydrates ; Carbon ; Ecosystem ; *Pinus ; Plant Leaves ; *Trees ; }, abstract = {In trees, large uncertainties remain in how nonstructural carbohydrates (NSCs) respond to variation in water availability in natural, intact ecosystems. Variation in NSC pools reflects temporal fluctuations in supply and demand, as well as physiological coordination across tree organs in ways that differ across species and NSC fractions (e.g., soluble sugars vs starch). Using landscape-scale crown (leaves and twigs) NSC concentration measurements in three foundation tree species (Populus tremuloides, Pinus edulis, Juniperus osteosperma), we evaluated in situ, seasonal variation in NSC responses to moisture stress on three timescales: short-term (via predawn water potential), seasonal (via leaf δ13C) and annual (via current year's ring width index). Crown NSC responses to moisture stress appeared to depend on hydraulic strategy, where J. osteosperma appears to regulate osmotic potentials (via higher sugar concentrations), P. edulis NSC responses suggest respiratory depletion and P. tremuloides responses were consistent with direct sink limitations. We also show that overly simplistic models can mask seasonal and tissue variation in NSC responses, as well as strong interactions among moisture stress at different timescales. In general, our results suggest large seasonal variation in crown NSC concentrations reflecting the multiple cofunctions of NSCs in plant tissues, including storage, growth and osmotic regulation of hydraulically vulnerable leaves. We emphasize that crown NSC pool size cannot be viewed as a simple physiological metric of stress; in situ NSC dynamics are complex, varying temporally, across species, among NSC fractions and among tissue types.}, } @article {pmid33147272, year = {2020}, author = {Altamiranda-Saavedra, M and Osorio-Olvera, L and Yáñez-Arenas, C and Marín-Ortiz, JC and Parra-Henao, G}, title = {Geographic abundance patterns explained by niche centrality hypothesis in two Chagas disease vectors in Latin America.}, journal = {PloS one}, volume = {15}, number = {11}, pages = {e0241710}, pmid = {33147272}, issn = {1932-6203}, mesh = {Algorithms ; Animals ; Chagas Disease/epidemiology/parasitology/*pathology/transmission ; Databases, Factual ; *Ecosystem ; Humans ; Insect Vectors ; Models, Theoretical ; Population Density ; Rhodnius/*parasitology ; South America/epidemiology ; Triatoma/*parasitology ; }, abstract = {Ecoepidemiological scenarios for Chagas disease transmission are complex, so vector control measures to decrease human-vector contact and prevent infection transmission are difficult to implement in all geographic contexts. This study assessed the geographic abundance patterns of two vector species of Chagas disease: Triatoma maculata (Erichson, 1848) and Rhodnius pallescens (Barber, 1932) in Latin America. We modeled their potential distribution using the maximum entropy algorithm implemented in Maxent and calculated distances to their niche centroid by fitting a minimum-volume ellipsoid. In addition, to determine which method would accurately explain geographic abundance patterns, we compared the correlation between population abundance and the distance to the ecological niche centroid (DNC) and between population abundance and Maxent environmental suitability. The potential distribution estimated for T. maculata showed that environmental suitability covers a large area, from Panama to Northern Brazil. R. pallescens showed a more restricted potential distribution, with environmental suitability covering mostly the coastal zone of Costa Rica and some areas in Nicaragua, Honduras, Belize and the Yucatán Peninsula in Mexico, northern Colombia, Acre, and Rondônia states in Brazil, as well as a small region of the western Brazilian Amazon. We found a negative slope in the relationship between population abundance and the DNC in both species. R. pallecens has a more extensive potential latitudinal range than previously reported, and the distribution model for T. maculata corroborates previous studies. In addition, population abundance increases according to the niche centroid proximity, indicating that population abundance is limited by the set of scenopoetic variables at coarser scales (non-interactive variables) used to determine the ecological niche. These findings might be used by public health agencies in Latin America to implement actions and support programs for disease prevention and vector control, identifying areas in which to expand entomological surveillance and maintain chemical control, in order to decrease human-vector contact.}, } @article {pmid33143227, year = {2020}, author = {Petrushin, I and Belikov, S and Chernogor, L}, title = {Cooperative Interaction of Janthinobacterium sp. SLB01 and Flavobacterium sp. SLB02 in the Diseased Sponge Lubomirskia baicalensis.}, journal = {International journal of molecular sciences}, volume = {21}, number = {21}, pages = {}, pmid = {33143227}, issn = {1422-0067}, support = {19-14-00088//Russian Science Foundation/ ; 0345-2019-0002 (AAAA-A16-116122110066-1)//Siberian Branch, Russian Academy of Sciences/ ; }, mesh = {Animals ; Cooperative Behavior ; *Ecosystem ; Flavobacterium/*physiology ; Lakes ; Oxalobacteraceae/*physiology ; Phylogeny ; Porifera/*metabolism/*microbiology ; *Symbiosis ; }, abstract = {Endemic freshwater sponges (demosponges, Lubomirskiidae) dominate in Lake Baikal, Central Siberia, Russia. These sponges are multicellular filter-feeding animals that represent a complex consortium of many species of eukaryotes and prokaryotes. In recent years, mass disease and death of Lubomirskia baicalensis has been a significant problem in Lake Baikal. The etiology and ecology of these events remain unknown. Bacteria from the families Flavobacteriaceae and Oxalobacteraceae dominate the microbiomes of diseased sponges. Both species are opportunistic pathogens common in freshwater ecosystems. The aim of our study was to analyze the genomes of strains Janthinobacterium sp. SLB01 and Flavobacterium sp. SLB02, isolated from diseased sponges to identify the reasons for their joint dominance. Janthinobacterium sp. SLB01 attacks other cells using a type VI secretion system and suppresses gram-positive bacteria with violacein, and regulates its own activity via quorum sensing. It produces floc and strong biofilm by exopolysaccharide biosynthesis and PEP-CTERM/XrtA protein expression. Flavobacterium sp. SLB02 utilizes the fragments of cell walls produced by polysaccharides. These two strains have a marked difference in carbohydrate acquisition. We described a possible means of joint occupation of the ecological niche in the freshwater sponge microbial community. This study expands the understanding of the symbiotic relationship of microorganisms with freshwater Baikal sponges.}, } @article {pmid33142319, year = {2021}, author = {Wu, X and Liu, T and Ye, C and Ye, W and Ji, G}, title = {scAPAtrap: identification and quantification of alternative polyadenylation sites from single-cell RNA-seq data.}, journal = {Briefings in bioinformatics}, volume = {22}, number = {4}, pages = {}, doi = {10.1093/bib/bbaa273}, pmid = {33142319}, issn = {1477-4054}, mesh = {*Databases, Nucleic Acid ; *Genome ; Molecular Sequence Annotation ; *RNA 3' Polyadenylation Signals ; *RNA-Seq ; *Single-Cell Analysis ; *Software ; }, abstract = {Alternative polyadenylation (APA) generates diverse mRNA isoforms, which contributes to transcriptome diversity and gene expression regulation by affecting mRNA stability, translation and localization in cells. The rapid development of 3' tag-based single-cell RNA-sequencing (scRNA-seq) technologies, such as CEL-seq and 10x Genomics, has led to the emergence of computational methods for identifying APA sites and profiling APA dynamics at single-cell resolution. However, existing methods fail to detect the precise location of poly(A) sites or sites with low read coverage. Moreover, they rely on priori genome annotation and can only detect poly(A) sites located within or near annotated genes. Here we proposed a tool called scAPAtrap for detecting poly(A) sites at the whole genome level in individual cells from 3' tag-based scRNA-seq data. scAPAtrap incorporates peak identification and poly(A) read anchoring, enabling the identification of the precise location of poly(A) sites, even for sites with low read coverage. Moreover, scAPAtrap can identify poly(A) sites without using priori genome annotation, which helps locate novel poly(A) sites in previously overlooked regions and improve genome annotation. We compared scAPAtrap with two latest methods, scAPA and Sierra, using scRNA-seq data from different experimental technologies and species. Results show that scAPAtrap identified poly(A) sites with higher accuracy and sensitivity than competing methods and could be used to explore APA dynamics among cell types or the heterogeneous APA isoform expression in individual cells. scAPAtrap is available at https://github.com/BMILAB/scAPAtrap.}, } @article {pmid33139555, year = {2020}, author = {Chen, D and Zhang, Q and Tang, W and Huang, Z and Wang, G and Wang, Y and Shi, J and Xu, H and Lin, L and Li, Z and Chi, W and Huang, L and Xia, J and Zhang, X and Guo, L and Wang, Y and Ma, P and Tang, J and Zhou, G and Liu, M and Liu, F and Hua, X and Wang, B and Shen, Q and Jiang, Q and Lin, J and Chen, X and Wang, H and Dou, M and Liu, L and Pan, H and Qi, Y and Wu, B and Fang, J and Zhou, Y and Cen, W and He, W and Zhang, Q and Xue, T and Lin, G and Zhang, W and Liu, Z and Qu, L and Wang, A and Ye, Q and Chen, J and Zhang, Y and Ming, R and Van Montagu, M and Tang, H and Van de Peer, Y and Chen, Y and Zhang, J}, title = {The evolutionary origin and domestication history of goldfish (Carassius auratus).}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {117}, number = {47}, pages = {29775-29785}, pmid = {33139555}, issn = {1091-6490}, mesh = {Animals ; Contig Mapping ; Datasets as Topic ; *Domestication ; *Evolution, Molecular ; Female ; Fish Proteins/genetics ; Genetic Variation ; Genome/genetics ; Genomics ; Goldfish/*genetics ; Hybridization, Genetic ; Male ; Models, Animal ; Phylogeny ; Protein-Tyrosine Kinases/genetics ; Selective Breeding/*genetics ; }, abstract = {Goldfish have been subjected to over 1,000 y of intensive domestication and selective breeding. In this report, we describe a high-quality goldfish genome (2n = 100), anchoring 95.75% of contigs into 50 pseudochromosomes. Comparative genomics enabled us to disentangle the two subgenomes that resulted from an ancient hybridization event. Resequencing 185 representative goldfish variants and 16 wild crucian carp revealed the origin of goldfish and identified genomic regions that have been shaped by selective sweeps linked to its domestication. Our comprehensive collection of goldfish varieties enabled us to associate genetic variations with a number of well-known anatomical features, including features that distinguish traditional goldfish clades. Additionally, we identified a tyrosine-protein kinase receptor as a candidate causal gene for the first well-known case of Mendelian inheritance in goldfish-the transparent mutant. The goldfish genome and diversity data offer unique resources to make goldfish a promising model for functional genomics, as well as domestication.}, } @article {pmid33137183, year = {2021}, author = {Roux, S and Páez-Espino, D and Chen, IA and Palaniappan, K and Ratner, A and Chu, K and Reddy, TBK and Nayfach, S and Schulz, F and Call, L and Neches, RY and Woyke, T and Ivanova, NN and Eloe-Fadrosh, EA and Kyrpides, NC}, title = {IMG/VR v3: an integrated ecological and evolutionary framework for interrogating genomes of uncultivated viruses.}, journal = {Nucleic acids research}, volume = {49}, number = {D1}, pages = {D764-D775}, pmid = {33137183}, issn = {1362-4962}, mesh = {Base Sequence ; Cluster Analysis ; *Databases, Genetic ; *Ecosystem ; *Evolution, Molecular ; *Genome, Viral ; Geography ; Molecular Sequence Annotation ; Sequence Homology, Nucleic Acid ; User-Computer Interface ; Viruses/*genetics ; }, abstract = {Viruses are integral components of all ecosystems and microbiomes on Earth. Through pervasive infections of their cellular hosts, viruses can reshape microbial community structure and drive global nutrient cycling. Over the past decade, viral sequences identified from genomes and metagenomes have provided an unprecedented view of viral genome diversity in nature. Since 2016, the IMG/VR database has provided access to the largest collection of viral sequences obtained from (meta)genomes. Here, we present the third version of IMG/VR, composed of 18 373 cultivated and 2 314 329 uncultivated viral genomes (UViGs), nearly tripling the total number of sequences compared to the previous version. These clustered into 935 362 viral Operational Taxonomic Units (vOTUs), including 188 930 with two or more members. UViGs in IMG/VR are now reported as single viral contigs, integrated proviruses or genome bins, and are annotated with a new standardized pipeline including genome quality estimation using CheckV, taxonomic classification reflecting the latest ICTV update, and expanded host taxonomy prediction. The new IMG/VR interface enables users to efficiently browse, search, and select UViGs based on genome features and/or sequence similarity. IMG/VR v3 is available at https://img.jgi.doe.gov/vr, and the underlying data are available to download at https://genome.jgi.doe.gov/portal/IMG_VR.}, } @article {pmid33137114, year = {2020}, author = {Zapién-Campos, R and Sieber, M and Traulsen, A}, title = {Stochastic colonization of hosts with a finite lifespan can drive individual host microbes out of equilibrium.}, journal = {PLoS computational biology}, volume = {16}, number = {11}, pages = {e1008392}, pmid = {33137114}, issn = {1553-7358}, mesh = {Animals ; Caenorhabditis elegans/growth & development/microbiology ; Computational Biology ; Computer Simulation ; Drosophila melanogaster/growth & development/microbiology ; Gastrointestinal Microbiome/physiology ; Host Microbial Interactions/*physiology ; Humans ; Longevity/*physiology ; Mathematical Concepts ; Microbiota/physiology ; *Models, Biological ; Stochastic Processes ; Zebrafish/growth & development/microbiology ; }, abstract = {Macroorganisms are inhabited by microbial communities that often change through the lifespan of an individual. One of the factors contributing to this change is colonization from the environment. The colonization of initially microbe-free hosts is particularly interesting, as their microbiome depends entirely on microbes of external origin. We present a mathematical model of this process with a particular emphasis on the effect of ecological drift and a finite host lifespan. Our results indicate the host lifespan becomes especially relevant for short-living organisms (e.g. Caenorhabditis elegans, Drosophila melanogaster, and Danio rerio). In this case, alternative microbiome states (often called enterotypes), the coexistence of microbe-free and colonized hosts, and a reduced probability of colonization can be observed in our model. These results unify multiple reported observations around colonization and suggest that no selective or deterministic drivers are necessary to explain them.}, } @article {pmid33135271, year = {2021}, author = {Yamaguchi, K and Koyanagi, M and Kuraku, S}, title = {Visual and nonvisual opsin genes of sharks and other nonosteichthyan vertebrates: Genomic exploration of underwater photoreception.}, journal = {Journal of evolutionary biology}, volume = {34}, number = {6}, pages = {968-976}, doi = {10.1111/jeb.13730}, pmid = {33135271}, issn = {1420-9101}, mesh = {Adaptation, Biological ; Animals ; Ecosystem ; Genome ; Opsins/*genetics ; Sharks/*genetics ; Vision, Ocular/*genetics ; }, abstract = {Vision of sharks embraces various biological and ecological themes ranging from predation and adaptation to deep-sea life. However, behavioural and genetic studies have been limited by their elusive lifestyles, repeatedly reported declines of wild populations, and their unique life-history traits including low fecundity and enhanced longevity. Sharks have also not been actively studied on the cellular and molecular levels, because of additional difficulties in cell culture, tissue collection and genome sequencing. A recent study circumvented some of these obstacles by means of genome informatics thereby portrayed the variation of visual opsin gene repertoires among elasmobranchs (sharks and rays) and spectral shifts of the rhodopsin pigment. Comprehensive surveys in whole-genome sequences are also revealing the repertoires of nonvisual opsins with unknown functions. This review is aimed to summarize existing studies on shark opsins with an emphasis on genomic investigation of gene repertoires and to provide insights into the better understanding of underwater ecology of marine megafauna with in vitro experimentation.}, } @article {pmid33133210, year = {2020}, author = {Chen, C and ValizadehAslani, T and Rosen, GL and Anderson, LM and Jungquist, CR}, title = {Healthcare Shift Workers' Temporal Habits for Eating, Sleeping, and Light Exposure: A Multi-Instrument Pilot Study.}, journal = {Journal of circadian rhythms}, volume = {18}, number = {}, pages = {6}, pmid = {33133210}, issn = {1740-3391}, abstract = {BACKGROUND: Circadian misalignment can impair healthcare shift workers' physical and mental health, resulting in sleep deprivation, obesity, and chronic disease. This multidisciplinary research team assessed eating patterns and sleep/physical activity of healthcare workers on three different shifts (day, night, and rotating-shift). To date, no study of real-world shift workers' daily eating and sleep has utilized a largely-objective measurement.

METHOD: During this fourteen-day observational study, participants wore two devices (Actiwatch and Bite Technologies counter) to measure physical activity, sleep, light exposure, and eating time. Participants also reported food intake via food diaries on personal mobile devices.

RESULTS: In fourteen (5 day-, 5 night-, and 4 rotating-shift) participants, no baseline difference in BMI was observed. Overall, rotating-shift workers consumed fewer calories and had less activity and sleep than day- and night-shift workers. For eating patterns, compared to night- and rotating-shift, day-shift workers ate more frequently during work days. Night workers, however, consumed more calories at work relative to day and rotating workers. For physical activity and sleep, night-shift workers had the highest activity and least sleep on work days.

CONCLUSION: This pilot study utilized primarily objective measurement to examine shift workers' habits outside the laboratory. Although no association between BMI and eating patterns/activity/sleep was observed across groups, a small, homogeneous sample may have influenced this. Overall, shift work was associated with 1) increased calorie intake and higher-fat and -carbohydrate diets and 2) sleep deprivation. A larger, more diverse sample can participate in future studies that objectively measure shift workers' real-world habits.}, } @article {pmid33129268, year = {2020}, author = {Djemiel, C and Dequiedt, S and Karimi, B and Cottin, A and Girier, T and El Djoudi, Y and Wincker, P and Lelièvre, M and Mondy, S and Chemidlin Prévost-Bouré, N and Maron, PA and Ranjard, L and Terrat, S}, title = {BIOCOM-PIPE: a new user-friendly metabarcoding pipeline for the characterization of microbial diversity from 16S, 18S and 23S rRNA gene amplicons.}, journal = {BMC bioinformatics}, volume = {21}, number = {1}, pages = {492}, pmid = {33129268}, issn = {1471-2105}, mesh = {Archaea/*genetics ; Bacteria/*genetics ; *Biodiversity ; Cluster Analysis ; Computational Biology/*methods ; Computer Simulation ; *DNA Barcoding, Taxonomic ; Databases, Genetic ; Fungi/*genetics ; *Genes, rRNA ; Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 23S/genetics ; *Software ; Soil Microbiology ; }, abstract = {BACKGROUND: The ability to compare samples or studies easily using metabarcoding so as to better interpret microbial ecology results is an upcoming challenge. A growing number of metabarcoding pipelines are available, each with its own benefits and limitations. However, very few have been developed to offer the opportunity to characterize various microbial communities (e.g., archaea, bacteria, fungi, photosynthetic microeukaryotes) with the same tool.

RESULTS: BIOCOM-PIPE is a flexible and independent suite of tools for processing data from high-throughput sequencing technologies, Roche 454 and Illumina platforms, and focused on the diversity of archaeal, bacterial, fungal, and photosynthetic microeukaryote amplicons. Various original methods were implemented in BIOCOM-PIPE to (1) remove chimeras based on read abundance, (2) align sequences with structure-based alignments of RNA homologs using covariance models, and (3) a post-clustering tool (ReClustOR) to improve OTUs consistency based on a reference OTU database. The comparison with two other pipelines (FROGS and mothur) and Amplicon Sequence Variant definition highlighted that BIOCOM-PIPE was better at discriminating land use groups.

CONCLUSIONS: The BIOCOM-PIPE pipeline makes it possible to analyze 16S, 18S and 23S rRNA genes in the same packaged tool. The new post-clustering approach defines a biological database from previously analyzed samples and performs post-clustering of reads with this reference database by using open-reference clustering. This makes it easier to compare projects from various sequencing runs, and increased the congruence among results. For all users, the pipeline was developed to allow for adding or modifying the components, the databases and the bioinformatics tools easily, giving high modularity for each analysis.}, } @article {pmid33127951, year = {2020}, author = {Korpela, J and Suzuki, H and Matsumoto, S and Mizutani, Y and Samejima, M and Maekawa, T and Nakai, J and Yoda, K}, title = {Machine learning enables improved runtime and precision for bio-loggers on seabirds.}, journal = {Communications biology}, volume = {3}, number = {1}, pages = {633}, pmid = {33127951}, issn = {2399-3642}, mesh = {Animals ; Behavior, Animal ; *Birds ; Environmental Monitoring/*methods ; Geographic Information Systems ; *Machine Learning ; Monitoring, Physiologic/instrumentation ; Video Recording ; }, abstract = {Unravelling the secrets of wild animals is one of the biggest challenges in ecology, with bio-logging (i.e., the use of animal-borne loggers or bio-loggers) playing a pivotal role in tackling this challenge. Bio-logging allows us to observe many aspects of animals' lives, including their behaviours, physiology, social interactions, and external environment. However, bio-loggers have short runtimes when collecting data from resource-intensive (high-cost) sensors. This study proposes using AI on board video-loggers in order to use low-cost sensors (e.g., accelerometers) to automatically detect and record complex target behaviours that are of interest, reserving their devices' limited resources for just those moments. We demonstrate our method on bio-loggers attached to seabirds including gulls and shearwaters, where it captured target videos with 15 times the precision of a baseline periodic-sampling method. Our work will provide motivation for more widespread adoption of AI in bio-loggers, helping us to shed light onto until now hidden aspects of animals' lives.}, } @article {pmid33126516, year = {2020}, author = {ValizadehAslani, T and Zhao, Z and Sokhansanj, BA and Rosen, GL}, title = {Amino Acid k-mer Feature Extraction for Quantitative Antimicrobial Resistance (AMR) Prediction by Machine Learning and Model Interpretation for Biological Insights.}, journal = {Biology}, volume = {9}, number = {11}, pages = {}, pmid = {33126516}, issn = {2079-7737}, support = {1650431//National Science Foundation/ ; }, abstract = {Machine learning algorithms can learn mechanisms of antimicrobial resistance from the data of DNA sequence without any a priori information. Interpreting a trained machine learning algorithm can be exploited for validating the model and obtaining new information about resistance mechanisms. Different feature extraction methods, such as SNP calling and counting nucleotide k-mers have been proposed for presenting DNA sequences to the model. However, there are trade-offs between interpretability, computational complexity and accuracy for different feature extraction methods. In this study, we have proposed a new feature extraction method, counting amino acid k-mers or oligopeptides, which provides easier model interpretation compared to counting nucleotide k-mers and reaches the same or even better accuracy in comparison with different methods. Additionally, we have trained machine learning algorithms using different feature extraction methods and compared the results in terms of accuracy, model interpretability and computational complexity. We have built a new feature selection pipeline for extraction of important features so that new AMR determinants can be discovered by analyzing these features. This pipeline allows the construction of models that only use a small number of features and can predict resistance accurately.}, } @article {pmid33125392, year = {2020}, author = {Sala, C and Giampieri, E and Vitali, S and Garagnani, P and Remondini, D and Bazzani, A and Franceschi, C and Castellani, GC}, title = {Gut microbiota ecology: Biodiversity estimated from hybrid neutral-niche model increases with health status and aging.}, journal = {PloS one}, volume = {15}, number = {10}, pages = {e0237207}, pmid = {33125392}, issn = {1932-6203}, mesh = {Adolescent ; Adult ; Aged ; Aged, 80 and over ; *Aging/genetics/physiology ; Biodiversity ; Child ; Child, Preschool ; Databases, Nucleic Acid ; Female ; *Gastrointestinal Microbiome/genetics/physiology ; Health Status ; Healthy Aging/genetics/physiology ; Humans ; Infant ; Infant, Newborn ; Male ; Metagenome ; Middle Aged ; *Models, Biological ; RNA, Ribosomal, 16S/genetics ; Young Adult ; }, abstract = {In this work we propose an index to estimate the gut microbiota biodiversity using a modeling approach with the aim of describing its relationship with health and aging. The gut microbiota, a complex ecosystem that links nutrition and metabolism, has a pervasive effect on all body organs and systems, undergoes profound changes with age and life-style, and substantially contributes to the pathogenesis of age-related diseases. For these reasons, the gut microbiota is a suitable candidate for assessing and quantifying healthy aging, i.e. the capability of individuals to reach an advanced age, avoiding or postponing major age-related diseases. The importance of the gut microbiota in health and aging has been proven to be related not only to its taxonomic composition, but also to its ecological properties, namely its biodiversity. Following an ecological approach, here we intended to characterize the relationship between the gut microbiota biodiversity and healthy aging through the development a parsimonious model of gut microbiota from which biodiversity can be estimated. We analysed publicly available metagenomic data relative to subjects of different ages, countries, nutritional habits and health status and we showed that a hybrid niche-neutral model well describes the observed patterns of bacterial relative abundance. Moreover, starting from such ecological modeling, we derived an estimate of the gut microbiota biodiversity that is consistent with classical indices, while having a higher statistical power. This allowed us to unveil an increase of the gut microbiota biodiversity during aging and to provide a good predictor of health status in old age, dependent on life-style and aging disorders.}, } @article {pmid33125079, year = {2021}, author = {Garczarek, L and Guyet, U and Doré, H and Farrant, GK and Hoebeke, M and Brillet-Guéguen, L and Bisch, A and Ferrieux, M and Siltanen, J and Corre, E and Le Corguillé, G and Ratin, M and Pitt, FD and Ostrowski, M and Conan, M and Siegel, A and Labadie, K and Aury, JM and Wincker, P and Scanlan, DJ and Partensky, F}, title = {Cyanorak v2.1: a scalable information system dedicated to the visualization and expert curation of marine and brackish picocyanobacteria genomes.}, journal = {Nucleic acids research}, volume = {49}, number = {D1}, pages = {D667-D676}, pmid = {33125079}, issn = {1362-4962}, mesh = {Aquatic Organisms/*genetics ; Bacterial Proteins/genetics ; Cyanobacteria/*genetics ; *Data Curation ; *Databases, Genetic ; *Genome, Bacterial ; Geography ; *Information Systems ; Likelihood Functions ; Phylogeny ; User-Computer Interface ; }, abstract = {Cyanorak v2.1 (http://www.sb-roscoff.fr/cyanorak) is an information system dedicated to visualizing, comparing and curating the genomes of Prochlorococcus, Synechococcus and Cyanobium, the most abundant photosynthetic microorganisms on Earth. The database encompasses sequences from 97 genomes, covering most of the wide genetic diversity known so far within these groups, and which were split into 25,834 clusters of likely orthologous groups (CLOGs). The user interface gives access to genomic characteristics, accession numbers as well as an interactive map showing strain isolation sites. The main entry to the database is through search for a term (gene name, product, etc.), resulting in a list of CLOGs and individual genes. Each CLOG benefits from a rich functional annotation including EggNOG, EC/K numbers, GO terms, TIGR Roles, custom-designed Cyanorak Roles as well as several protein motif predictions. Cyanorak also displays a phyletic profile, indicating the genotype and pigment type for each CLOG, and a genome viewer (Jbrowse) to visualize additional data on each genome such as predicted operons, genomic islands or transcriptomic data, when available. This information system also includes a BLAST search tool, comparative genomic context as well as various data export options. Altogether, Cyanorak v2.1 constitutes an invaluable, scalable tool for comparative genomics of ecologically relevant marine microorganisms.}, } @article {pmid33123928, year = {2021}, author = {Lin, Z and Yuan, T and Zhou, L and Cheng, S and Qu, X and Lu, P and Feng, Q}, title = {Impact factors of the accumulation, migration and spread of antibiotic resistance in the environment.}, journal = {Environmental geochemistry and health}, volume = {43}, number = {5}, pages = {1741-1758}, doi = {10.1007/s10653-020-00759-0}, pmid = {33123928}, issn = {1573-2983}, support = {2019B003//Jiangsu Key Laboratory of Coal-based Greenhouse Gas Control and Utilization/ ; }, mesh = {Anti-Bacterial Agents/pharmacology ; Bacteria/genetics ; Biodiversity ; Drug Resistance, Bacterial ; *Drug Resistance, Microbial/drug effects/genetics ; Environmental Pollutants ; *Gene Transfer, Horizontal ; Metals, Heavy/pharmacology ; Microbiota ; }, abstract = {Antibiotic resistance is a great concern, which leads to global public health risks and ecological and environmental risks. The presence of antibiotic-resistant genes and antibiotic-resistant bacteria in the environment exacerbates the risk of spreading antibiotic resistance. Among them, horizontal gene transfer is an important mode in the spread of antibiotic resistance genes, and it is one of the reasons that the antibiotic resistance pollution has become increasingly serious. At the same time, free antibiotic resistance genes and resistance gene host bacterial also exist in the natural environment. They can not only affect horizontal gene transfer, but can also migrate and aggregate among environmental media in many ways and then continue to affect the proliferate and transfer of antibiotic resistance genes. All this shows the seriousness of antibiotic resistance pollution. Therefore, in this review, we reveal the sensitive factors affecting the distribution and spread of antibiotic resistance through three aspects: the influencing factors of horizontal gene transfer, the host bacteria of resistance genes and the migration of antibiotic resistance between environmental media. This review reveals the huge role of environmental migration in the spread of antibiotic resistance, and the environmental behavior of antibiotic resistance deserves wider attention. Meanwhile, extracellular antibiotic resistance genes and intracellular antibiotic resistance genes play different roles, so they should be studied separately.}, } @article {pmid33122629, year = {2020}, author = {Cai, W and Snyder, J and Hastings, A and D'Souza, RM}, title = {Mutualistic networks emerging from adaptive niche-based interactions.}, journal = {Nature communications}, volume = {11}, number = {1}, pages = {5470}, pmid = {33122629}, issn = {2041-1723}, mesh = {Animals ; Biological Evolution ; Computational Biology ; Ecology/*methods ; Ecosystem ; *Food Chain ; *Models, Theoretical ; *Symbiosis ; }, abstract = {Mutualistic networks are vital ecological and social systems shaped by adaptation and evolution. They involve bipartite cooperation via the exchange of goods or services between actors of different types. Empirical observations of mutualistic networks across genres and geographic conditions reveal correlated nested and modular patterns. Yet, the underlying mechanism for the network assembly remains unclear. We propose a niche-based adaptive mechanism where both nestedness and modularity emerge simultaneously as complementary facets of an optimal niche structure. Key dynamical properties are revealed at different timescales. Foremost, mutualism can either enhance or reduce the network stability, depending on competition intensity. Moreover, structural adaptations are asymmetric, exhibiting strong hysteresis in response to environmental change. Finally, at the evolutionary timescale we show that the adaptive mechanism plays a crucial role in preserving the distinctive patterns of mutualism under species invasions and extinctions.}, } @article {pmid33118171, year = {2021}, author = {Seyednasrollah, B and Bowling, DR and Cheng, R and Logan, BA and Magney, TS and Frankenberg, C and Yang, JC and Young, AM and Hufkens, K and Arain, MA and Black, TA and Blanken, PD and Bracho, R and Jassal, R and Hollinger, DY and Law, BE and Nesic, Z and Richardson, AD}, title = {Seasonal variation in the canopy color of temperate evergreen conifer forests.}, journal = {The New phytologist}, volume = {229}, number = {5}, pages = {2586-2600}, pmid = {33118171}, issn = {1469-8137}, support = {80NSSC19M0130/ImNASA/Intramural NASA/United States ; 80NSSC20K0010/ImNASA/Intramural NASA/United States ; }, mesh = {Climate ; Forests ; North America ; Photosynthesis ; Plant Leaves ; Seasons ; *Tracheophyta ; }, abstract = {Evergreen conifer forests are the most prevalent land cover type in North America. Seasonal changes in the color of evergreen forest canopies have been documented with near-surface remote sensing, but the physiological mechanisms underlying these changes, and the implications for photosynthetic uptake, have not been fully elucidated. Here, we integrate on-the-ground phenological observations, leaf-level physiological measurements, near surface hyperspectral remote sensing and digital camera imagery, tower-based CO2 flux measurements, and a predictive model to simulate seasonal canopy color dynamics. We show that seasonal changes in canopy color occur independently of new leaf production, but track changes in chlorophyll fluorescence, the photochemical reflectance index, and leaf pigmentation. We demonstrate that at winter-dormant sites, seasonal changes in canopy color can be used to predict the onset of canopy-level photosynthesis in spring, and its cessation in autumn. Finally, we parameterize a simple temperature-based model to predict the seasonal cycle of canopy greenness, and we show that the model successfully simulates interannual variation in the timing of changes in canopy color. These results provide mechanistic insight into the factors driving seasonal changes in evergreen canopy color and provide opportunities to monitor and model seasonal variation in photosynthetic activity using color-based vegetation indices.}, } @article {pmid33111499, year = {2020}, author = {Zrimec, J}, title = {Multiple plasmid origin-of-transfer regions might aid the spread of antimicrobial resistance to human pathogens.}, journal = {MicrobiologyOpen}, volume = {9}, number = {12}, pages = {e1129}, pmid = {33111499}, issn = {2045-8827}, mesh = {Algorithms ; Bacteria/drug effects/*genetics ; Conjugation, Genetic/*genetics ; Databases, Genetic ; Drug Resistance, Bacterial/*genetics ; Gene Transfer, Horizontal/*genetics ; Humans ; Nucleic Acid Conformation ; Plasmids/*genetics ; Sequence Alignment ; Transformation, Bacterial/*genetics ; }, abstract = {Antimicrobial resistance poses a great danger to humanity, in part due to the widespread horizontal gene transfer of plasmids via conjugation. Modeling of plasmid transfer is essential to uncovering the fundamentals of resistance transfer and for the development of predictive measures to limit the spread of resistance. However, a major limitation in the current understanding of plasmids is the incomplete characterization of the conjugative DNA transfer mechanisms, which conceals the actual potential for plasmid transfer in nature. Here, we consider that the plasmid-borne origin-of-transfer substrates encode specific DNA structural properties that can facilitate finding these regions in large datasets and develop a DNA structure-based alignment procedure for typing the transfer substrates that outperforms sequence-based approaches. Thousands of putative DNA transfer substrates are identified, showing that plasmid mobility can be twofold higher and span almost twofold more host species than is currently known. Over half of all putative mobile plasmids contain the means for mobilization by conjugation systems belonging to different mobility groups, which can hypothetically link previously confined host ranges across ecological habitats into a robust plasmid transfer network. This hypothetical network is found to facilitate the transfer of antimicrobial resistance from environmental genetic reservoirs to human pathogens, which might be an important driver of the observed rapid resistance development in humans and thus an important point of focus for future prevention measures.}, } @article {pmid33111231, year = {2021}, author = {Kazuva, E and Zhang, J and Tong, Z and Liu, XP and Memon, S and Mhache, E}, title = {GIS- and MCD-based suitability assessment for optimized location of solid waste landfills in Dar es Salaam, Tanzania.}, journal = {Environmental science and pollution research international}, volume = {28}, number = {9}, pages = {11259-11278}, pmid = {33111231}, issn = {1614-7499}, support = {20190303081SF; 20180201033SF//National Science and Technology Development Plan, the projects of Jilin Province, China/ ; }, mesh = {Cities ; Decision Support Techniques ; Geographic Information Systems ; *Refuse Disposal ; *Solid Waste ; Tanzania ; Waste Disposal Facilities ; }, abstract = {Despite recent advancements in waste management technologies, landfills remain the dominant approach for the final disposal of solid waste (SW) around the world. However, landfills are associated with adverse environmental and health-related impacts. This study is primarily applied to Dar es Salaam, a city in the East African region that has failed to follow appropriate approaches for site selection and that the methods used to select the current sites are manually operated. The study used a geographical information system (GIS) combined with multicriteria decision analysis (MCDA) to objectively determine the optimal landfill sites. A comprehensive list of assessment criteria was examined through a computerized site selection procedure based on GIS to analyze the ground that was surveyed and to remotely obtain data. Analytical hierarchy process (AHP)-one of the best MCDA approaches-was used to assign relative weight and evaluate each criterion. Finally, the study computed site suitability indices (SSIs), which aids in the identification of site suitability levels (SSLs) for the entire region. The final suitability map produced by overlaying the criteria map layers showed that a large part of the study area (60.92%) was completely unsuitable for landfill siting. The remaining areas consisted of land with varying suitability level, which were grouped into four classes: very low (30.92%), low (2.05%), moderate (5.65%), and high (0.46). To this end, only the high suitability class (0.46%) was of acceptable suitability levels (ASLs) (SSI ≥ 2.0). From the numerous identified sites with ASL, only three sites were suggested. Due to concerns regarding the lifespan and environment-related risks associated with these suggested sites, there is a need to further study new environmentally friendly techniques, considering the importance of circular economy agenda of waste to resource/energy for sustainable solid waste management.}, } @article {pmid33111101, year = {2020}, author = {Blumstein, M and Richardson, A and Weston, D and Zhang, J and Muchero, W and Hopkins, R}, title = {Protocol for Projecting Allele Frequency Change under Future Climate Change at Adaptive-Associated Loci.}, journal = {STAR protocols}, volume = {1}, number = {2}, pages = {100061}, pmid = {33111101}, issn = {2666-1667}, mesh = {Adaptation, Biological/*genetics ; *Climate Change ; Databases, Genetic ; Gene Frequency/*genetics ; Genetic Loci/genetics ; Genetics, Population/*methods ; Genome, Plant/genetics ; Models, Genetic ; }, abstract = {We describe how to predict population-level allele frequency change at loci associated with locally adapted traits under future climate conditions. Our method can identify populations that are at higher risk of local extinction and those that might be prime targets for conservation intervention. We draw on previously developed community ecology statistical methods and apply them in novel ways to plant genomes. While a powerful diagnostic tool, our method requires a wealth of genomic data for use. For complete details on the use and execution of this protocol, please refer to Blumstein et al. (2020).}, } @article {pmid33109753, year = {2020}, author = {Gruber-Vodicka, HR and Seah, BKB and Pruesse, E}, title = {phyloFlash: Rapid Small-Subunit rRNA Profiling and Targeted Assembly from Metagenomes.}, journal = {mSystems}, volume = {5}, number = {5}, pages = {}, pmid = {33109753}, issn = {2379-5077}, abstract = {The small-subunit rRNA (SSU rRNA) gene is the key marker in molecular ecology for all domains of life, but it is largely absent from metagenome-assembled genomes that often are the only resource available for environmental microbes. Here, we present phyloFlash, a pipeline to overcome this gap with rapid, SSU rRNA-centered taxonomic classification, targeted assembly, and graph-based binning of full metagenomic assemblies. We show that a cleanup of artifacts is pivotal even with a curated reference database. With such a filtered database, the general-purpose mapper BBmap extracts SSU rRNA reads five times faster than the rRNA-specialized tool SortMeRNA with similar sensitivity and higher selectivity on simulated metagenomes. Reference-based targeted assemblers yielded either highly fragmented assemblies or high levels of chimerism, so we employ the general-purpose genomic assembler SPAdes. Our optimized implementation is independent of reference database composition and has satisfactory levels of chimera formation. phyloFlash quickly processes Illumina (meta)genomic data, is straightforward to use, even as part of high-throughput quality control, and has user-friendly output reports. The software is available at https://github.com/HRGV/phyloFlash (GPL3 license) and is documented with an online manual.IMPORTANCE To track organisms across all domains of life, the SSU rRNA gene is the gold standard. Many environmental microbes are known only from high-throughput sequence data, but the SSU rRNA gene, the key to visualization by molecular probes and link to existing literature, is often missing from metagenome-assembled genomes (MAGs). The easy-to-use phyloFlash software suite tackles this gap with rapid, SSU rRNA-centered taxonomic classification, targeted assembly, and graph-based linking to MAGs. Starting from a cleaned reference database, phyloFlash profiles the taxonomic diversity and assembles the sorted SSU rRNA reads. The phyloFlash design is domain agnostic and covers eukaryotes, archaea, and bacteria alike. phyloFlash also provides utilities to visualize multisample comparisons and to integrate the recovered SSU rRNAs in a metagenomics workflow by linking them to MAGs using assembly graph parsing.}, } @article {pmid33109531, year = {2020}, author = {de Mestral, C and Hussain, MA and Austin, PC and Forbes, TL and Sivaswamy, A and Kayssi, A and Salata, K and Wijeysundera, HC and Verma, S and Al-Omran, M}, title = {Regional health care services and rates of lower extremity amputation related to diabetes and peripheral artery disease: an ecological study.}, journal = {CMAJ open}, volume = {8}, number = {4}, pages = {E659-E666}, pmid = {33109531}, issn = {2291-0026}, mesh = {Adult ; Aged ; Aged, 80 and over ; Amputation, Surgical/*statistics & numerical data/trends ; Data Interpretation, Statistical ; Diabetes Mellitus, Type 2/complications ; Diabetic Angiopathies/*surgery ; Ecology ; Female ; Humans ; Leg/blood supply/*surgery ; Male ; Middle Aged ; Ontario ; Patient Acceptance of Health Care/*statistics & numerical data ; Peripheral Arterial Disease/etiology/*surgery ; }, abstract = {BACKGROUND: The care necessary to prevent amputation from diabetes and peripheral artery disease (PAD) remains disjointed in many jurisdictions. To help inform integrated regional care, this study explores the correlation between regional health care services and rates of lower extremity amputation.

METHODS: This ecological study included 14 administrative health regions in Ontario, Canada. All diabetes- or PAD-related major (above ankle) amputations (Apr. 1, 2007, to Mar. 31, 2017) were identified among residents 40 years of age and older. For each region, age-and sex-adjusted amputation rates were calculated as well as per capita counts of key health providers (podiatrists and chiropodists, as well as surgeons) and health care utilization among study patients in the year before the first major amputation (physician visits, publicly funded podiatry visits, emergency department visits, hospital admissions, home care nursing, minor amputation, limb revascularization).

RESULTS: A total of 11 658 patients with major amputation were identified (of whom 79.2% had diabetes and 96.5% had PAD). There was wide regional variation in amputation rates: 2.53 to 11.77 per 100 000 person-quarters. At a regional level, the proportion of study patients who received revascularization showed the strongest negative correlation with amputation rates. The regional proportion of study patients who saw a vascular surgeon showed the strongest negative correlation with amputation rates, relative to other health provider visits. Other measures of health care utilization among patients correlated poorly with regional amputation rates, as did the regional provider counts. The results were similar when we restricted the analysis to diabetes-related amputations.

INTERPRETATION: Amputation rates related to diabetes and PAD vary widely across Ontario. Access to vascular assessment and revascularization must be integrated into regional amputation prevention efforts.}, } @article {pmid33105263, year = {2020}, author = {Rapport, F and Hughes, SE}, title = {Frameworks for Change in Hearing Research: Valuing Qualitative Methods in the Real World.}, journal = {Ear and hearing}, volume = {41 Suppl 1}, number = {}, pages = {91S-98S}, doi = {10.1097/AUD.0000000000000932}, pmid = {33105263}, issn = {1538-4667}, mesh = {*Health Personnel ; *Hearing ; Humans ; Qualitative Research ; }, abstract = {In this article, we examine ecological validity in hearing science from a qualitative methodological perspective. We present an overview of qualitative methods, presenting their key characteristics and contrasting these techniques with quantitative approaches to enquiry. We argue that ecological validity sits at the heart of the qualitative paradigm and seek to clearly emphasize the methodological gap that could be effectively filled by qualitative or mixed methods. In doing so, we discuss qualitative methods that may work particularly well in enhancing ecological validity in hearing science and explore their range of applications in this field. These approaches can be applied to a wide range of hearing health research questions to present a unique understanding of people's experiences of disease and disability, indicating gradations of personal health and illness in nuanced ways. We acknowledge and commend the current expansion of qualitative methods within hearing science and present recommendations for increasing ecological validity, both in the design of future studies and in the context of the wider research cycle. We call on qualitative researchers to strive for transparency, rigor, and trustworthiness and highlight challenges to be overcome if qualitative methods are to contribute to effective, efficient research strategies. To facilitate the transference of high-quality research findings into practice, we stress the need for joined-up working to create a research culture that promotes coproduction of ecologically valid research designs, involving not only hearing researchers but also implementation scientists, hearing healthcare professionals and, most importantly, people with hearing loss for whom these efforts could make a difference.}, } @article {pmid33104797, year = {2021}, author = {Mansi, L and Tangaro, MA and Lo Giudice, C and Flati, T and Kopel, E and Schaffer, AA and Castrignanò, T and Chillemi, G and Pesole, G and Picardi, E}, title = {REDIportal: millions of novel A-to-I RNA editing events from thousands of RNAseq experiments.}, journal = {Nucleic acids research}, volume = {49}, number = {D1}, pages = {D1012-D1019}, pmid = {33104797}, issn = {1362-4962}, mesh = {Base Sequence/genetics ; Computational Biology/*methods ; Data Curation/methods ; Data Mining/methods ; *Databases, Genetic ; Gene Expression Profiling/methods ; *Gene Expression Regulation ; Genomics/methods ; Humans ; Internet ; Proteome/*genetics ; Proteomics/methods ; RNA Editing/*genetics ; Transcriptome/*genetics ; }, abstract = {RNA editing is a relevant epitranscriptome phenomenon able to increase the transcriptome and proteome diversity of eukaryotic organisms. ADAR mediated RNA editing is widespread in humans in which millions of A-to-I changes modify thousands of primary transcripts. RNA editing has pivotal roles in the regulation of gene expression or modulation of the innate immune response or functioning of several neurotransmitter receptors. Massive transcriptome sequencing has fostered the research in this field. Nonetheless, different aspects of the RNA editing biology are still unknown and need to be elucidated. To support the study of A-to-I RNA editing we have updated our REDIportal catalogue raising its content to about 16 millions of events detected in 9642 human RNAseq samples from the GTEx project by using a dedicated pipeline based on the HPC version of the REDItools software. REDIportal now allows searches at sample level, provides overviews of RNA editing profiles per each RNAseq experiment, implements a Gene View module to look at individual events in their genic context and hosts the CLAIRE database. Starting from this novel version, REDIportal will start collecting non-human RNA editing changes for comparative genomics investigations. The database is freely available at http://srv00.recas.ba.infn.it/atlas/index.html.}, } @article {pmid33101223, year = {2020}, author = {Fernández-Juárez, V and Bennasar-Figueras, A and Sureda-Gomila, A and Ramis-Munar, G and Agawin, NSR}, title = {Differential Effects of Varying Concentrations of Phosphorus, Iron, and Nitrogen in N2-Fixing Cyanobacteria.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {541558}, pmid = {33101223}, issn = {1664-302X}, abstract = {Diazotrophs or N2-fixers are one of the most ecologically significant groups in marine ecosystems (pelagic and benthic). Inorganic phosphorus (PO4 [3-]) and iron (Fe) can limit the growth and N2-fixing capacities of cyanobacteria. However, studies investigating co-limitation of these factors are lacking. Here, we added different concentrations of PO4 [3-] and Fe in two cyanobacterial species whose relatives can be found in seagrass habitats: the unicellular Halothece sp. (PCC 7418) and the filamentous Fischerella muscicola (PCC 73103), grown under different nitrate (NO3 [-]) concentrations and under N2 as sole N source, respectively. Their growth, pigment content, N2-fixation rates, oxidative stress responses, and morphological and cellular changes were investigated. Our results show a serial limitation of NO3 [-] and PO4 [3-] (with NO3 [-] as the primary limiting nutrient) for Halothece sp. Simultaneous co-limitation of PO4 [3-] and Fe was found for both species tested, and high levels of Fe (especially when added with high PO4 [3-] levels) inhibited the growth of Halothece sp. Nutrient limitation (PO4 [3-], Fe, and/or NO3 [-]) enhanced oxidative stress responses, morphological changes, and apoptosis. Furthermore, an extensive bio-informatic analysis describing the predicted Pho, Fur, and NtcA regulons (involved in the survival of cells to P, Fe, and N limitation) was made using the complete genome of Halothece sp. as a model, showing the potential of this strain to adapt to different nutrient regimes (P, Fe, or N).}, } @article {pmid33095853, year = {2021}, author = {Geretti, AM and Stockdale, AJ and Kelly, SH and Cevik, M and Collins, S and Waters, L and Villa, G and Docherty, A and Harrison, EM and Turtle, L and Openshaw, PJM and Baillie, JK and Sabin, CA and Semple, MG}, title = {Outcomes of Coronavirus Disease 2019 (COVID-19) Related Hospitalization Among People With Human Immunodeficiency Virus (HIV) in the ISARIC World Health Organization (WHO) Clinical Characterization Protocol (UK): A Prospective Observational Study.}, journal = {Clinical infectious diseases : an official publication of the Infectious Diseases Society of America}, volume = {73}, number = {7}, pages = {e2095-e2106}, pmid = {33095853}, issn = {1537-6591}, support = {205228/Z/16/Z/WT_/Wellcome Trust/United Kingdom ; MC_PC_19059/MRC_/Medical Research Council/United Kingdom ; MC_PC_19025/MRC_/Medical Research Council/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; MC_PC_15001/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Adult ; *COVID-19 ; HIV ; *HIV Infections/complications/epidemiology ; Hospitalization ; Humans ; Middle Aged ; Observational Studies as Topic ; SARS-CoV-2 ; United Kingdom ; World Health Organization ; }, abstract = {BACKGROUND: Evidence is conflicting about how human immunodeficiency virus (HIV) modulates coronavirus disease 2019 (COVID-19). We compared the presentation characteristics and outcomes of adults with and without HIV who were hospitalized with COVID-19 at 207 centers across the United Kingdom and whose data were prospectively captured by the International Severe Acute Respiratory and Emerging Infection Consortium (ISARIC) World Health Organization (WHO) Clinical Characterization Protocol (CCP) study.

METHODS: We used Kaplan-Meier methods and Cox regression to describe the association between HIV status and day-28 mortality, after separate adjustment for sex, ethnicity, age, hospital acquisition of COVID-19 (definite hospital acquisition excluded), presentation date, 10 individual comorbidities, and disease severity at presentation (as defined by hypoxia or oxygen therapy).

RESULTS: Among 47 592 patients, 122 (0.26%) had confirmed HIV infection, and 112/122 (91.8%) had a record of antiretroviral therapy. At presentation, HIV-positive people were younger (median 56 vs 74 years; P < .001) and had fewer comorbidities, more systemic symptoms and higher lymphocyte counts and C-reactive protein levels. The cumulative day-28 mortality was similar in the HIV-positive versus HIV-negative groups (26.7% vs. 32.1%; P = .16), but in those under 60 years of age HIV-positive status was associated with increased mortality (21.3% vs. 9.6%; P < .001 [log-rank test]). Mortality was higher among people with HIV after adjusting for age (adjusted hazard ratio [aHR] 1.47, 95% confidence interval [CI] 1.01-2.14; P = .05), and the association persisted after adjusting for the other variables (aHR 1.69; 95% CI 1.15-2.48; P = .008) and when restricting the analysis to people aged <60 years (aHR 2.87; 95% CI 1.70-4.84; P < .001).

CONCLUSIONS: HIV-positive status was associated with an increased risk of day-28 mortality among patients hospitalized for COVID-19.}, } @article {pmid33095844, year = {2020}, author = {Snell Taylor, S and Coyle, JR and White, EP and Hurlbert, AH}, title = {A simulation study of the use of temporal occupancy for identifying core and transient species.}, journal = {PloS one}, volume = {15}, number = {10}, pages = {e0241198}, pmid = {33095844}, issn = {1932-6203}, mesh = {*Animal Distribution ; Animals ; Computer Simulation ; Ecological Parameter Monitoring/*methods ; *Ecosystem ; *Models, Biological ; Population Dynamics ; Time Factors ; }, abstract = {Transient species, which do not maintain self-sustaining populations in a system where they are observed, are ubiquitous in nature and their presence often impacts the interpretation of ecological patterns and processes. Identifying transient species from temporal occupancy, the proportion of time a species is observed at a given site over a time series, is subject to classification errors as a result of imperfect detection and source-sink dynamics. We use a simulation-based approach to assess how often errors in detection or classification occur in order to validate the use of temporal occupancy as a metric for inferring whether a species is a core or transient member of a community. We found that low detection increases error in the classification of core species, while high habitat heterogeneity and high detection increase error in classification of transient species. These findings confirm that temporal occupancy is a valid metric for inferring whether a species can maintain a self-sustaining population, but imperfect detection, low abundance, and highly heterogeneous landscapes may yield high misclassification rates.}, } @article {pmid33093509, year = {2020}, author = {Perry, BW and Schield, DR and Westfall, AK and Mackessy, SP and Castoe, TA}, title = {Physiological demands and signaling associated with snake venom production and storage illustrated by transcriptional analyses of venom glands.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {18083}, pmid = {33093509}, issn = {2045-2322}, mesh = {Animals ; Biomarkers/*analysis ; Computational Biology/*methods ; Crotalid Venoms/*metabolism ; Crotalus/*genetics/physiology ; *Gene Expression Profiling ; *Gene Expression Regulation ; Salivary Glands/*metabolism ; Signal Transduction ; Time Factors ; }, abstract = {Despite the extensive body of research on snake venom, many facets of snake venom systems, such as the physiology and regulation of the venom gland itself, remain virtually unstudied. Here, we use time series gene expression analyses of the rattlesnake venom gland in comparison with several non-venom tissues to characterize physiological and cellular processes associated with venom production and to highlight key distinctions of venom gland cellular and physiological function. We find consistent evidence for activation of stress response pathways in the venom gland, suggesting that mitigation of cellular stress is a crucial component of venom production. Additionally, we demonstrate evidence for an unappreciated degree of cellular and secretory activity in the steady state venom gland relative to other secretory tissues and identify vacuolar ATPases as the likely mechanisms driving acidification of the venom gland lumen during venom production and storage.}, } @article {pmid33092533, year = {2020}, author = {Ponomarenko, M and Kleshchev, M and Ponomarenko, P and Chadaeva, I and Sharypova, E and Rasskazov, D and Kolmykov, S and Drachkova, I and Vasiliev, G and Gutorova, N and Ignatieva, E and Savinkova, L and Bogomolov, A and Osadchuk, L and Osadchuk, A and Oshchepkov, D}, title = {Disruptive natural selection by male reproductive potential prevents underexpression of protein-coding genes on the human Y chromosome as a self-domestication syndrome.}, journal = {BMC genetics}, volume = {21}, number = {Suppl 1}, pages = {89}, pmid = {33092533}, issn = {1471-2156}, support = {19-15-00075//Russian Science Support Foundation/International ; }, mesh = {Chromosomes, Human, Y/*genetics ; Databases, Genetic ; Domestication ; Humans ; Male ; Polymorphism, Single Nucleotide ; Promoter Regions, Genetic ; Reproduction/*genetics ; *Selection, Genetic ; TATA-Box Binding Protein/genetics ; }, abstract = {BACKGROUND: In population ecology, the concept of reproductive potential denotes the most vital indicator of chances to produce and sustain a healthy descendant until his/her reproductive maturity under the best conditions. This concept links quality of life and longevity of an individual with disease susceptibilities encoded by his/her genome. Female reproductive potential has been investigated deeply, widely, and comprehensively in the past, but the male one has not received an equal amount of attention. Therefore, here we focused on the human Y chromosome and found candidate single-nucleotide polymorphism (SNP) markers of male reproductive potential.

RESULTS: Examining in silico (i.e., using our earlier created Web-service SNP_TATA_Z-tester) all 1206 unannotated SNPs within 70 bp proximal promoters of all 63 Y-linked genes, we found 261 possible male-reproductive-potential SNP markers that can significantly alter the binding affinity of TATA-binding protein (TBP) for these promoters. Among them, there are candidate SNP markers of spermatogenesis disorders (e.g., rs1402972626), pediatric cancer (e.g., rs1483581212) as well as male anxiety damaging family relationships and mother's and children's health (e.g., rs187456378). First of all, we selectively verified in vitro both absolute and relative values of the analyzed TBP-promoter affinity, whose Pearson's coefficients of correlation between predicted and measured values were r = 0.84 (significance p <  0.025) and r = 0.98 (p <  0.025), respectively. Next, we found that there are twofold fewer candidate SNP markers decreasing TBP-promoter affinity relative to those increasing it, whereas in the genome-wide norm, SNP-induced damage to TBP-promoter complexes is fourfold more frequent than SNP-induced improvement (p <  0.05, binomial distribution). This means natural selection against underexpression of these genes. Meanwhile, the numbers of candidate SNP markers of an increase and decrease in male reproductive potential were indistinguishably equal to each other (p <  0.05) as if male self-domestication could have happened, with its experimentally known disruptive natural selection. Because there is still not enough scientific evidence that this could have happened, we discuss the human diseases associated with candidate SNP markers of male reproductive potential that may correspond to domestication-related disorders in pets.

CONCLUSIONS: Overall, our findings seem to support a self-domestication syndrome with disruptive natural selection by male reproductive potential preventing Y-linked underexpression of a protein.}, } @article {pmid33092216, year = {2020}, author = {Macioszek, VK and Gapińska, M and Zmienko, A and Sobczak, M and Skoczowski, A and Oliwa, J and Kononowicz, AK}, title = {Complexity of Brassica oleracea-Alternaria brassicicola Susceptible Interaction Reveals Downregulation of Photosynthesis at Ultrastructural, Transcriptional, and Physiological Levels.}, journal = {Cells}, volume = {9}, number = {10}, pages = {}, pmid = {33092216}, issn = {2073-4409}, mesh = {Alternaria/physiology/*ultrastructure ; Brassica/*genetics/*microbiology/physiology/ultrastructure ; Chlorophyll A/metabolism ; Chloroplasts/metabolism/ultrastructure ; Disease Susceptibility ; *Down-Regulation ; Gene Expression Regulation, Plant ; Gene Ontology ; Host-Pathogen Interactions/*genetics ; Mesophyll Cells/microbiology/ultrastructure ; *Photosynthesis/genetics ; Plant Diseases/*microbiology ; Plant Leaves/microbiology/ultrastructure ; Time Factors ; *Transcription, Genetic ; }, abstract = {Black spot disease, caused by Alternaria brassicicola in Brassica species, is one of the most devastating diseases all over the world, especially since there is no known fully resistant Brassica cultivar. In this study, the visualization of black spot disease development on Brassica oleracea var. capitata f. alba (white cabbage) leaves and subsequent ultrastructural, molecular and physiological investigations were conducted. Inter- and intracellular hyphae growth within leaf tissues led to the loss of host cell integrity and various levels of organelle disintegration. Severe symptoms of chloroplast damage included the degeneration of chloroplast envelope and grana, and the loss of electron denseness by stroma at the advanced stage of infection. Transcriptional profiling of infected leaves revealed that photosynthesis was the most negatively regulated biological process. However, in infected leaves, chlorophyll and carotenoid content did not decrease until 48 hpi, and several chlorophyll a fluorescence parameters, such as photosystem II quantum yield (Fv/Fm), non-photochemical quenching (NPQ), or plant vitality parameter (Rdf) decreased significantly at 24 and 48 hpi compared to control leaves. Our results indicate that the initial stages of interaction between B. oleracea and A. brassicicola are not uniform within an inoculation site and show a complexity of host responses and fungal attempts to overcome host cell defense mechanisms. The downregulation of photosynthesis at the early stage of this susceptible interaction suggests that it may be a part of a host defense strategy, or, alternatively, that chloroplasts are targets for the unknown virulence factor(s) of A. brassicicola. However, the observed decrease of photosynthetic efficiency at the later stages of infection is a result of the fungus-induced necrotic lesion expansion.}, } @article {pmid33092158, year = {2020}, author = {Shtratnikova, VY and Schelkunov, MI and Fokina, VV and Bragin, EY and Lobastova, TG and Shutov, AA and Kazantsev, AV and Donova, MV}, title = {Genome-Wide Transcriptome Profiling Provides Insight on Cholesterol and Lithocholate Degradation Mechanisms in Nocardioides simplex VKM Ac-2033D.}, journal = {Genes}, volume = {11}, number = {10}, pages = {}, pmid = {33092158}, issn = {2073-4425}, mesh = {Actinobacteria/genetics/growth & development/*metabolism ; Bacterial Proteins/genetics/*metabolism ; Cholesterol/*metabolism ; Computational Biology ; Gene Expression Profiling ; *Gene Expression Regulation, Bacterial ; *Genome, Bacterial ; Genome-Wide Association Study ; Lithocholic Acid/*metabolism ; *Transcriptome ; }, abstract = {Steroid microbial degradation plays a significant ecological role for biomass decomposition and removal/detoxification of steroid pollutants. In this study, the initial steps of cholesterol degradation and lithocholate bioconversion by a strain with enhanced 3-ketosteroid dehydrogenase (3-KSD) activity, Nocardioides simplex VKM Ac-2033D, were studied. Biochemical, transcriptomic, and bioinformatic approaches were used. Among the intermediates of sterol sidechain oxidation cholest-5-en-26-oic acid and 3-oxo-cholesta-1,4-dien-26-oic acid were identified as those that have not been earlier reported for N. simplex and related species. The transcriptomic approach revealed candidate genes of cholesterol and lithocholic acid (LCA) catabolism by the strain. A separate set of genes combined in cluster and additional 3-ketosteroid Δ[1]-dehydrogenase and 3-ketosteroid 9α-hydroxylases that might be involved in LCA catabolism were predicted. Bioinformatic calculations based on transcriptomic data showed the existence of a previously unknown transcription factor, which regulates cholate catabolism gene orthologs. The results contribute to the knowledge on diversity of steroid catabolism regulation in actinobacteria and might be used at the engineering of microbial catalysts for ecological and industrial biotechnology.}, } @article {pmid33090846, year = {2020}, author = {Anichini, M and de Heer Kloots, M and Ravignani, A}, title = {Interactive rhythms in the wild, in the brain, and in silico.}, journal = {Canadian journal of experimental psychology = Revue canadienne de psychologie experimentale}, volume = {74}, number = {3}, pages = {170-175}, doi = {10.1037/cep0000224}, pmid = {33090846}, issn = {1878-7290}, support = {//Hanse-Wissenschaftskolleg (Institute for Advanced Study)/ ; //European Union Horizon/ ; }, mesh = {Animals ; Behavior, Animal/*physiology ; Biological Ontologies ; Brain/*physiology ; Computer Simulation ; Humans ; *Interdisciplinary Research/standards ; Models, Biological ; *Neurosciences/standards ; *Periodicity ; *Physiology, Comparative/standards ; *Social Behavior ; }, abstract = {There are some historical divisions in methods, rationales, and purposes between studies on comparative cognition and behavioural ecology. In turn, the interaction between these two branches and studies from mathematics, computation, and neuroscience is not usual. In this short piece, we attempt to build bridges among these disciplines. We present a series of interconnected vignettes meant to illustrate what a more interdisciplinary approach looks like when successful, and its advantages. Concretely, we focus on a recent topic, namely animal rhythms in interaction, studied under different approaches. We showcase 5 research efforts, which we believe successfully link 5 particular scientific areas of rhythm research conceptualised as the following: social neuroscience, detailed rhythmic quantification, ontogeny, computational approaches, and spontaneous interactions. Our suggestions will hopefully spur a "comparative rhythms in interaction" field, which can integrate and capitalize on knowledge from zoology, comparative psychology, neuroscience, and computation. (PsycInfo Database Record (c) 2020 APA, all rights reserved).}, } @article {pmid33090204, year = {2021}, author = {Del Vecchio, S and Mattana, E and Ulian, T and Buffa, G}, title = {Functional seed traits and germination patterns predict species coexistence in Northeast Mediterranean foredune communities.}, journal = {Annals of botany}, volume = {127}, number = {3}, pages = {361-370}, pmid = {33090204}, issn = {1095-8290}, mesh = {*Ecosystem ; *Germination ; Italy ; Seeds ; Temperature ; }, abstract = {BACKGROUND AND AIMS: The structure of plant communities, which is based on species abundance ratios, is closely linked to ecosystem functionality. Seed germination niche plays a major role in shaping plant communities, although it has often been neglected when explaining species coexistence. The aim of this work is to link the seed germination niche to community ecology, investigating how functional seed traits contribute to species coexistence.

METHODS: Species selection was based on a database of 504 vegetation surveys from the Veneto coast (Italy). Through cluster analysis we identified the foredune community and selected all of its 19 plant species. By using the 'Phi coefficient' and frequency values, species were pooled in different categories (foundation species, accidental species of the semi-fixed dune and aliens), then the 19 species were grouped according to their germination responses to temperature and photoperiod through cluster analyses. For each germination cluster, we investigated germination trends against temperature and photoperiod by using generalized linear mixed models.

KEY RESULTS: We identified four germination strategies: (1) high germination under all tested conditions ('high-germinating'); (2) high germination at warm temperatures in the dark ('dark warm-cued'); (3) high germination at warm temperatures in the light ('light warm-cued'); and (4) low germination, regardless of conditions ('low-germinating'). Foredune foundation species showed a narrow germination niche, being 'low-germinating' or 'dark warm-cued'. Annual species of semi-fixed dunes were 'high-germinating', while alien species were the only members of the 'light warm-cued' cluster.

CONCLUSIONS: Our research suggests that different categories of species have dissimilar seed germination niches, which contributes to explaining their coexistence. Climatic events, such as rising temperature, could alter germination patterns, favouring seed regeneration of certain categories (i.e. alien and semi-fixed dune species) at the expense of others (i.e. foundation species, pivotal to ecosystem functioning), and hence potentially altering the plant community structure.}, } @article {pmid33087857, year = {2020}, author = {Maák, I and Tóth, E and Lenda, M and Lőrinczi, G and Kiss, A and Juhász, O and Czechowski, W and Torma, A}, title = {Behaviours indicating cannibalistic necrophagy in ants are modulated by the perception of pathogen infection level.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {17906}, pmid = {33087857}, issn = {2045-2322}, mesh = {Adaptation, Psychological/physiology ; Animals ; Ants/*physiology ; Behavior, Animal/*physiology ; *Cadaver ; Cannibalism ; Health Behavior ; Perception/*physiology ; *Social Behavior ; Starvation/psychology ; }, abstract = {Cannibalistic necrophagy is rarely observed in social hymenopterans, although a lack of food could easily favour such behaviour. One of the main supposed reasons for the rarity of necrophagy is that eating of nestmate corpses carries the risk of rapid spread of pathogens or parasites. Here we present an experimental laboratory study on behaviour indicating consumption of nestmate corpses in the ant Formica polyctena. We examined whether starvation and the fungal infection level of the corpses affects the occurrence of cannibalistic necrophagy. Our results showed that the ants distinguished between corpses of different types and with different levels of infection risk, adjusting their behaviour accordingly. The frequency of behaviours indicating cannibalistic necrophagy increased during starvation, although these behaviours seem to be fairly common in F. polyctena even in the presence of other food sources. The occurrence and significance of cannibalistic necrophagy deserve further research because, in addition to providing additional food, it may be part of the hygienic behaviour repertoire. The ability to detect infections and handle pathogens are important behavioural adaptations for social insects, crucial for the fitness of both individual workers and the entire colony.}, } @article {pmid33084948, year = {2021}, author = {Verma, D and Srivastava, A and Garg, PK and Akhter, Y and Dubey, AK and Mishra, S and Deo, SVS}, title = {Taxonomic profiling and functional characterization of the healthy human oral bacterial microbiome from the north Indian urban sub-population.}, journal = {Archives of microbiology}, volume = {203}, number = {3}, pages = {927-939}, pmid = {33084948}, issn = {1432-072X}, support = {SB/YS/LS-102/2014//Science and Engineering Research Board/ ; }, mesh = {Adolescent ; Adult ; Bacteria/*classification/*genetics/isolation & purification ; Female ; High-Throughput Nucleotide Sequencing ; Humans ; India ; Male ; Metagenome ; Microbiota/*genetics ; Middle Aged ; Mouth/*microbiology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Poor oral health has broad consequences that can be seen at personal as well as societal levels, especially in developing countries like India. We have limited information on the healthy oral cavity's inhabitant microorganisms that play a crucial role in overall oral health. In a comprehensive culture-independent approach, the bacterial composition of healthy human oral cavities was determined from a sub-population of northern India. During this study, 20 mouthwash-derived metagenomes were explored for identifying bacterial diversity using the 16S rRNA hypervariable V3 region with the MiSeq Illumina platform. On the taxonomy assignment of operational taxonomic units (OTUs), 20 assigned phyla and 162 genera were recovered among the participants. The mean relative abundance revealed that Streptococcus was the dominant genera among the participants. However, at inter-individual analysis, Neisseria and Haemophilus exhibited first-order dominance among five and three healthy individuals, respectively. Correlation studies indicate that Streptococcus shares a strong relationship with Rothia, Corynebacterium, Prevotella, and Veillonella, whereas it was negatively correlated with Neisseria, Aggregatibacter, Porphyromonas, and Fusobacteria like Gram-negative bacteria. Bacterial diversity showed insignificant differences at the level of age and gender within and between the participants. The results support several of the major findings of previous reports on the healthy oral microbiome of the Indian population, however, the present investigation further illustrates that demographic region leaves an impact on overall bacterial composition. The study will assist in a better understanding of the oral microbiome from region-specific Indian population that was otherwise highly under-represented.}, } @article {pmid33084878, year = {2020}, author = {Parca, L and Truglio, M and Biagini, T and Castellana, S and Petrizzelli, F and Capocefalo, D and Jordán, F and Carella, M and Mazza, T}, title = {Pyntacle: a parallel computing-enabled framework for large-scale network biology analysis.}, journal = {GigaScience}, volume = {9}, number = {10}, pages = {}, pmid = {33084878}, issn = {2047-217X}, mesh = {*Algorithms ; *Computational Biology ; Proteins ; Transcriptome ; }, abstract = {BACKGROUND: Some natural systems are big in size, complex, and often characterized by convoluted mechanisms of interaction, such as epistasis, pleiotropy, and trophism, which cannot be immediately ascribed to individual natural events or biological entities but that are often derived from group effects. However, the determination of important groups of entities, such as genes or proteins, in complex systems is considered a computationally hard task.

RESULTS: We present Pyntacle, a high-performance framework designed to exploit parallel computing and graph theory to efficiently identify critical groups in big networks and in scenarios that cannot be tackled with traditional network analysis approaches.

CONCLUSIONS: We showcase potential applications of Pyntacle with transcriptomics and structural biology data, thereby highlighting the outstanding improvement in terms of computational resources over existing tools.}, } @article {pmid33084116, year = {2020}, author = {Lu, L and Xu, X and Du, X and Zeng, T and Yang, T and Chen, Y and Tao, Z and Zhong, S and Wen, J and Zhou, C}, title = {Transcriptome analyses to reveal the dynamic change mechanism of pigeon magnum during one egg-laying cycle.}, journal = {Molecular reproduction and development}, volume = {87}, number = {11}, pages = {1141-1151}, doi = {10.1002/mrd.23428}, pmid = {33084116}, issn = {1098-2795}, mesh = {Animals ; Apoptosis ; Columbidae/genetics/*physiology ; Egg Proteins/*biosynthesis/genetics ; Female ; *Gene Expression Regulation ; *Gene Expression Regulation, Developmental ; Gene Ontology ; Mucous Membrane/metabolism/ultrastructure ; Oviducts/*metabolism ; Oviposition/*physiology ; Ovulation/physiology ; Periodicity ; Protein Transport ; RNA, Messenger/biosynthesis/genetics ; *Transcriptome ; }, abstract = {We analyzed the transcriptome of pigeon magnum in three stages (C1: pre-ovulation, C2: post-ovulation, C3: 5-6 days after ovulation) to elucidate the molecular and cellular events associated with morphological changes during the laying cycle. We observed that C1 was highly developed, apoptosis rate was highest in C2, and C3 attained the smallest size. Through RNA-sequencing, we obtained 54,764,938 (97.2%) high-quality clean reads that aligned to 20,767 genes. Gene expression profile analysis showed the greatest difference between C1 and C3; 3966 differentially expressed genes (DEGs) were identified, of which 2250 genes were upregulated and 1716 genes were downregulated in C1. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses revealed that protein processing and transport activities were prominent in C1, and upregulated genes included those related to signal recognition particle (SRP), signal recognition particle receptor (SRPR), translocon, GRP78, RRBP1, TRAP, TRAM1, and OST. Egg white protein-related gene expression was highest, with OVALY being the most highly expressed. In C2, apoptosis-related gene expression was higher than in C1, and fatty acid metabolism was active, which may be correlated with magnum tissue regression. Collagen- and laminin-related gene expression was prominent in C1 and C3, indicating roles in egg white protein generation and magnum reconstruction. PR gene expression was highest and exhibited drastic change in the three groups, indicating that PR and its regulation may be involved in changes in magnum morphology and function. Through the identification and functional analysis of DEGs and other crucial genes, this may contribute to understand the egg white protein production, magnum tissue regression, and magnum regeneration mechanisms.}, } @article {pmid33082360, year = {2020}, author = {Tessler, M and Gaffney, JP and Oliveira, AG and Guarnaccia, A and Dobi, KC and Gujarati, NA and Galbraith, M and Mirza, JD and Sparks, JS and Pieribone, VA and Wood, RJ and Gruber, DF}, title = {A putative chordate luciferase from a cosmopolitan tunicate indicates convergent bioluminescence evolution across phyla.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {17724}, pmid = {33082360}, issn = {2045-2322}, mesh = {Animals ; Biological Evolution ; Chordata ; Computational Biology ; Evolution, Molecular ; Gene Expression Profiling ; Imidazoles ; Luciferases/*genetics ; Luminescence ; Luminescent Measurements ; Models, Molecular ; Phylogeny ; Pyrazines ; Sequence Alignment ; Sequence Analysis, DNA ; Species Specificity ; *Urochordata ; }, abstract = {Pyrosomes are tunicates in the phylum Chordata, which also contains vertebrates. Their gigantic blooms play important ecological and biogeochemical roles in oceans. Pyrosoma, meaning "fire-body", derives from their brilliant bioluminescence. The biochemistry of this light production is unknown, but has been hypothesized to be bacterial in origin. We found that mixing coelenterazine-a eukaryote-specific luciferin-with Pyrosoma atlanticum homogenate produced light. To identify the bioluminescent machinery, we sequenced P. atlanticum transcriptomes and found a sequence match to a cnidarian luciferase (RLuc). We expressed this novel luciferase (PyroLuc) and, combined with coelenterazine, it produced light. A similar gene was recently predicted from a bioluminescent brittle star, indicating that RLuc-like luciferases may have evolved convergently from homologous dehalogenases across phyla (Cnidaria, Echinodermata, and Chordata). This report indicates that a widespread gene may be able to functionally converge, resulting in bioluminescence across animal phyla, and describes and characterizes the first putative chordate luciferase.}, } @article {pmid33082154, year = {2020}, author = {Clift, AK and Coupland, CAC and Keogh, RH and Diaz-Ordaz, K and Williamson, E and Harrison, EM and Hayward, A and Hemingway, H and Horby, P and Mehta, N and Benger, J and Khunti, K and Spiegelhalter, D and Sheikh, A and Valabhji, J and Lyons, RA and Robson, J and Semple, MG and Kee, F and Johnson, P and Jebb, S and Williams, T and Hippisley-Cox, J}, title = {Living risk prediction algorithm (QCOVID) for risk of hospital admission and mortality from coronavirus 19 in adults: national derivation and validation cohort study.}, journal = {BMJ (Clinical research ed.)}, volume = {371}, number = {}, pages = {m3731}, pmid = {33082154}, issn = {1756-1833}, support = {MR/M501633/2/MRC_/Medical Research Council/United Kingdom ; MR/K006584/1/MRC_/Medical Research Council/United Kingdom ; MC_PC_20029/MRC_/Medical Research Council/United Kingdom ; RP-PG-0407-10314/DH_/Department of Health/United Kingdom ; MR/S017968/1/MRC_/Medical Research Council/United Kingdom ; G0902393/MRC_/Medical Research Council/United Kingdom ; MC_PC_19004/MRC_/Medical Research Council/United Kingdom ; MC_PC_19075/MRC_/Medical Research Council/United Kingdom ; 05/40/04/DH_/Department of Health/United Kingdom ; MC_PC_13041/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Adult ; Aged, 80 and over ; *Algorithms ; Betacoronavirus/isolation & purification ; COVID-19 ; *Clinical Decision Rules ; Cohort Studies ; *Coronavirus Infections/mortality/therapy ; Databases, Factual/statistics & numerical data ; England/epidemiology ; Female ; Hospitalization/*statistics & numerical data ; Humans ; Male ; *Mortality ; *Pandemics ; *Pneumonia, Viral/mortality/therapy ; Prognosis ; Reproducibility of Results ; *Risk Assessment/methods/standards ; SARS-CoV-2 ; }, abstract = {OBJECTIVE: To derive and validate a risk prediction algorithm to estimate hospital admission and mortality outcomes from coronavirus disease 2019 (covid-19) in adults.

DESIGN: Population based cohort study.

SETTING AND PARTICIPANTS: QResearch database, comprising 1205 general practices in England with linkage to covid-19 test results, Hospital Episode Statistics, and death registry data. 6.08 million adults aged 19-100 years were included in the derivation dataset and 2.17 million in the validation dataset. The derivation and first validation cohort period was 24 January 2020 to 30 April 2020. The second temporal validation cohort covered the period 1 May 2020 to 30 June 2020.

MAIN OUTCOME MEASURES: The primary outcome was time to death from covid-19, defined as death due to confirmed or suspected covid-19 as per the death certification or death occurring in a person with confirmed severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in the period 24 January to 30 April 2020. The secondary outcome was time to hospital admission with confirmed SARS-CoV-2 infection. Models were fitted in the derivation cohort to derive risk equations using a range of predictor variables. Performance, including measures of discrimination and calibration, was evaluated in each validation time period.

RESULTS: 4384 deaths from covid-19 occurred in the derivation cohort during follow-up and 1722 in the first validation cohort period and 621 in the second validation cohort period. The final risk algorithms included age, ethnicity, deprivation, body mass index, and a range of comorbidities. The algorithm had good calibration in the first validation cohort. For deaths from covid-19 in men, it explained 73.1% (95% confidence interval 71.9% to 74.3%) of the variation in time to death (R[2]); the D statistic was 3.37 (95% confidence interval 3.27 to 3.47), and Harrell's C was 0.928 (0.919 to 0.938). Similar results were obtained for women, for both outcomes, and in both time periods. In the top 5% of patients with the highest predicted risks of death, the sensitivity for identifying deaths within 97 days was 75.7%. People in the top 20% of predicted risk of death accounted for 94% of all deaths from covid-19.

CONCLUSION: The QCOVID population based risk algorithm performed well, showing very high levels of discrimination for deaths and hospital admissions due to covid-19. The absolute risks presented, however, will change over time in line with the prevailing SARS-C0V-2 infection rate and the extent of social distancing measures in place, so they should be interpreted with caution. The model can be recalibrated for different time periods, however, and has the potential to be dynamically updated as the pandemic evolves.}, } @article {pmid33081761, year = {2020}, author = {Nie, D and Gui, J and Zhao, N and Lin, Y and Tang, H and Cai, F and Shen, G and Liu, J and Zhang, E and Chen, M}, title = {Haematological and serum biochemical reference values in Chinese water deer (Hydropotes inermis): a preliminary study.}, journal = {BMC veterinary research}, volume = {16}, number = {1}, pages = {395}, pmid = {33081761}, issn = {1746-6148}, support = {No.31401985//National Natural Science Foundation of China/ ; No. 31872250//National Natural Science Foundation of China/ ; No. LKT2020015//research project on Bureau of Ecology and Environment of Pudong New Area, Shanghai/ ; }, mesh = {Animals ; Blood Chemical Analysis/*veterinary ; Databases, Factual ; Deer/*blood ; Female ; Hematologic Tests/*veterinary ; Male ; Reference Values ; }, abstract = {BACKGROUND: A selection of haematological and serum biochemical profile was first presented from the 81 samples of Chinese water deer (Hydropotes inermis). The deer health assessment database was initially established, especially in relation to determining potential effects associated with diseases diagnosis.

RESULTS: Blood samples were analyzed for different haematological parameters viz. white blood cells (WBC), red blood cells (RBC), haemoglobin (HGB), packed-cell volume (PCV), platelet count (PLT), mean corpuscular haemoglobin (MCH), mean corpuscular haemoglobin concentration (MCHC), mean corpuscular volume (MCV), mean red blood cells distribution width coefficient of variation (RDW) and different hematological parameters viz. total protein (TP), albumin (ALB), globulin (GLB), albumin to globulin ratio (A/G), total bilirubin (TBIL), alkaline phosphatase (ALP), γ-glutamyl transferase (GGT), alanine aminotransferase (ALT), aspartate aminotransferase (AST), AST/ALT, creatinine, urea (BUN), uric acid, total cholesterol (TC), triglyceride, creatine kinase (CK), lactate dehydrogenase (LDH) and cortisol. The adult females had higher values than adult males in albumin, mean corpuscular volume, packed-cell volume, and hemoglobin content values. The deer from Shanghai had higher urea nitrogen values than those from Zhoushan.

CONCLUSION: To our knowledge this is the first report about the haematological and serum biochemical parameters in Chinese water deer. We had initially established a profile of Chinese water deer on haematological and serum biochemical parameters based on 81 samples we had collected. The findings can serve as a primary reference for health monitoring and disease prevention in this species.}, } @article {pmid33077803, year = {2020}, author = {Sauer, FG and Jaworski, L and Erdbeer, L and Heitmann, A and Schmidt-Chanasit, J and Kiel, E and Lühken, R}, title = {Geometric morphometric wing analysis represents a robust tool to identify female mosquitoes (Diptera: Culicidae) in Germany.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {17613}, pmid = {33077803}, issn = {2045-2322}, mesh = {Aedes/anatomy & histology/genetics ; Animals ; Culicidae/*anatomy & histology/genetics ; DNA Barcoding, Taxonomic ; Electron Transport Complex IV/genetics ; Female ; Germany ; Wings, Animal/*anatomy & histology ; }, abstract = {Accurate species identification is the prerequisite to assess the relevance of mosquito specimens, but is often hindered by missing or damaged morphological features. The present study analyses the applicability of wing geometric morphometrics as a low-cost and practical alternative to identify native mosquitoes in Germany. Wing pictures were collected for 502 female mosquitoes of five genera and 19 species from 80 sampling sites. The reliable species identification based on interspecific wing geometry of 18 landmarks per specimen was tested. Leave-one-out cross validation revealed an overall accuracy of 99% for the genus and 90% for the species identification. Misidentifications were mainly due to three pairings of Aedes species: Aedes annulipes vs. Aedes cantans, Aedes cinereus vs. Aedes rossicus and Aedes communis vs. Aedes punctor. Cytochrome oxidase subunit I (COI) gene region was sequenced to validate the morphological and morphometric identification. Similar to the results of the morphometric analysis, the same problematic three Aedes-pairs clustered, but most other species could be well separated. Overall, our study underpins that morphometric wing analysis is a robust tool for reliable mosquito identification, which reach the accuracy of COI barcoding.}, } @article {pmid33077707, year = {2020}, author = {Herold, M and Martínez Arbas, S and Narayanasamy, S and Sheik, AR and Kleine-Borgmann, LAK and Lebrun, LA and Kunath, BJ and Roume, H and Bessarab, I and Williams, RBH and Gillece, JD and Schupp, JM and Keim, PS and Jäger, C and Hoopmann, MR and Moritz, RL and Ye, Y and Li, S and Tang, H and Heintz-Buschart, A and May, P and Muller, EEL and Laczny, CC and Wilmes, P}, title = {Integration of time-series meta-omics data reveals how microbial ecosystems respond to disturbance.}, journal = {Nature communications}, volume = {11}, number = {1}, pages = {5281}, pmid = {33077707}, issn = {2041-1723}, support = {R01 AI108888/AI/NIAID NIH HHS/United States ; R01 AI143254/AI/NIAID NIH HHS/United States ; }, mesh = {Bacteria/classification/*genetics/isolation & purification/*metabolism ; Bioreactors/microbiology ; Ecosystem ; Metabolomics ; Metagenome ; Metagenomics ; *Microbiota ; Proteomics ; Time Factors ; Wastewater/*microbiology ; }, abstract = {The development of reliable, mixed-culture biotechnological processes hinges on understanding how microbial ecosystems respond to disturbances. Here we reveal extensive phenotypic plasticity and niche complementarity in oleaginous microbial populations from a biological wastewater treatment plant. We perform meta-omics analyses (metagenomics, metatranscriptomics, metaproteomics and metabolomics) on in situ samples over 14 months at weekly intervals. Based on 1,364 de novo metagenome-assembled genomes, we uncover four distinct fundamental niche types. Throughout the time-series, we observe a major, transient shift in community structure, coinciding with substrate availability changes. Functional omics data reveals extensive variation in gene expression and substrate usage amongst community members. Ex situ bioreactor experiments confirm that responses occur within five hours of a pulse disturbance, demonstrating rapid adaptation by specific populations. Our results show that community resistance and resilience are a function of phenotypic plasticity and niche complementarity, and set the foundation for future ecological engineering efforts.}, } @article {pmid33076987, year = {2020}, author = {Longbottom, J and Caminade, C and Gibson, HS and Weiss, DJ and Torr, S and Lord, JS}, title = {Modelling the impact of climate change on the distribution and abundance of tsetse in Northern Zimbabwe.}, journal = {Parasites & vectors}, volume = {13}, number = {1}, pages = {526}, pmid = {33076987}, issn = {1756-3305}, support = {BB/P006159/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/S01375X/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; 1964851/MRC_/Medical Research Council/United Kingdom ; BB/P005888/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/L019035/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; *Climate Change ; Female ; Humans ; Insect Vectors/parasitology ; Population Dynamics ; Temperature ; Trypanosoma brucei gambiense/*physiology ; Trypanosomiasis, African/*epidemiology/parasitology ; Tsetse Flies/parasitology/*physiology ; Vector Borne Diseases/*epidemiology/parasitology ; Weather ; Zimbabwe/epidemiology ; }, abstract = {BACKGROUND: Climate change is predicted to impact the transmission dynamics of vector-borne diseases. Tsetse flies (Glossina) transmit species of Trypanosoma that cause human and animal African trypanosomiasis. A previous modelling study showed that temperature increases between 1990 and 2017 can explain the observed decline in abundance of tsetse at a single site in the Mana Pools National Park of Zimbabwe. Here, we apply a mechanistic model of tsetse population dynamics to predict how increases in temperature may have changed the distribution and relative abundance of Glossina pallidipes across northern Zimbabwe.

METHODS: Local weather station temperature measurements were previously used to fit the mechanistic model to longitudinal G. pallidipes catch data. To extend the use of the model, we converted MODIS land surface temperature to air temperature, compared the converted temperatures with available weather station data to confirm they aligned, and then re-fitted the mechanistic model using G. pallidipes catch data and air temperature estimates. We projected this fitted model across northern Zimbabwe, using simulations at a 1 km × 1 km spatial resolution, between 2000 to 2016.

RESULTS: We produced estimates of relative changes in G. pallidipes mortality, larviposition, emergence rates and abundance, for northern Zimbabwe. Our model predicts decreasing tsetse populations within low elevation areas in response to increasing temperature trends during 2000-2016. Conversely, we show that high elevation areas (> 1000 m above sea level), previously considered too cold to sustain tsetse, may now be climatically suitable.

CONCLUSIONS: To our knowledge, the results of this research represent the first regional-scale assessment of temperature related tsetse population dynamics, and the first high spatial-resolution estimates of this metric for northern Zimbabwe. Our results suggest that tsetse abundance may have declined across much of the Zambezi Valley in response to changing climatic conditions during the study period. Future research including empirical studies is planned to improve model accuracy and validate predictions for other field sites in Zimbabwe.}, } @article {pmid33075615, year = {2020}, author = {Yang, L and Chen, Y and Shi, L and Yu, J and Yao, J and Sun, J and Zhao, L and Sun, J}, title = {Enhanced Cd accumulation by Graphene oxide (GO) under Cd stress in duckweed.}, journal = {Aquatic toxicology (Amsterdam, Netherlands)}, volume = {229}, number = {}, pages = {105579}, doi = {10.1016/j.aquatox.2020.105579}, pmid = {33075615}, issn = {1879-1514}, mesh = {Absorption, Physiological/drug effects ; Araceae/drug effects/growth & development/*metabolism/ultrastructure ; Autophagy/drug effects/genetics ; Biodegradation, Environmental/drug effects ; Cadmium/*metabolism ; Cell Membrane Permeability/drug effects ; Gene Expression Regulation, Plant/drug effects ; Gene Ontology ; Graphite/*toxicity ; Phagosomes/drug effects/metabolism ; Phenotype ; Plant Proteins/genetics/metabolism ; Plant Roots/drug effects/metabolism/ultrastructure ; *Stress, Physiological/drug effects ; Water Pollutants, Chemical/toxicity ; }, abstract = {Effective phytoremediation by aquatic plant such as duckweed could be applied to solve Cd pollution. In the present study, the impact of Graphene oxide (GO) on the accumulation of Cd in duckweed has been studied. The response of duckweed was also investigated, concluding growth, Cd[2+] flux, and gene expression response. Results showed that GO promoted the accumulation of Cd in duckweed. After 6 h of Cd enrichment in duckweed, Cd content was about 1.4 times that of the control group at fronds and 1.25 times that of the control group at roots, meanwhile, Cd content in the water system was 0.67 times that of the control group. The Cd[2+] influx increased significantly. 4471 genes were up-regulated and 3230 genes were down-regulated significantly as duckweed treated with GO under Cd treatment. Moreover, phagosome pathway was downregulated, some key proteins: Stx7, Rab7 and Tubastatin B (TUBB) were significantly downregulated with GO addition under Cd stress. Scanning electron microscope (SEM) observation showed that GO and Cd were attached on the cell surface of duckweed as white crystal. GO could be applied in phytoremediation by duckweed of Cd in aquatic system.}, } @article {pmid33075563, year = {2021}, author = {Zhang, L and Zhang, Z and Li, C and Zhu, T and Gao, J and Zhou, H and Zheng, Y and Chang, Q and Wang, M and Wu, J and Ran, L and Wu, Y and Miao, H and Zou, X and Liang, B}, title = {S100A11 Promotes Liver Steatosis via FOXO1-Mediated Autophagy and Lipogenesis.}, journal = {Cellular and molecular gastroenterology and hepatology}, volume = {11}, number = {3}, pages = {697-724}, pmid = {33075563}, issn = {2352-345X}, mesh = {Animals ; Autophagy/genetics ; Cell Line, Tumor ; Datasets as Topic ; Diet, High-Fat/adverse effects ; Disease Models, Animal ; Forkhead Box Protein O1/*metabolism ; Hepatocytes ; Humans ; Lipogenesis/genetics ; Liver/pathology ; Mice ; Mice, Transgenic ; Non-alcoholic Fatty Liver Disease/*genetics/pathology ; S100 Proteins/genetics/*metabolism ; Tupaiidae ; Up-Regulation ; }, abstract = {BACKGROUND & AIMS: Nonalcoholic fatty liver disease (NAFLD) is becoming a severe liver disorder worldwide. Autophagy plays a critical role in liver steatosis. However, the role of autophagy in NAFLD remains exclusive and under debate. In this study, we investigated the role of S100 calcium binding protein A11 (S100A11) in the pathogenesis of hepatic steatosis.

METHODS: We performed liver proteomics in a well-established tree shrew model of NAFLD. The expression of S100A11 in different models of NAFLD was detected by Western blot and/or quantitative polymerase chain reaction. Liver S100A11 overexpression mice were generated by injecting a recombinant adenovirus gene transfer vector through the tail vein and then induced by a high-fat and high-cholesterol diet. Cell lines with S100a11 stable overexpression were established with a recombinant lentiviral vector. The lipid content was measured with either Bodipy staining, Oil Red O staining, gas chromatography, or a triglyceride kit. The autophagy and lipogenesis were detected in vitro and in vivo by Western blot and quantitative polymerase chain reaction. The functions of Sirtuin 1, histone deacetylase 6 (HDAC6), and FOXO1 were inhibited by specific inhibitors. The interactions between related proteins were analyzed by a co-immunoprecipitation assay and immunofluorescence analysis.

RESULTS: The expression of S100A11 was up-regulated significantly in a time-dependent manner in the tree shrew model of NAFLD. S100A11 expression was induced consistently in oleic acid-treated liver cells as well as the livers of mice fed a high-fat diet and NAFLD patients. Both in vitro and in vivo overexpression of S100A11 could induce hepatic lipid accumulation. Mechanistically, overexpression of S100A11 activated an autophagy and lipogenesis process through up-regulation and acetylation of the transcriptional factor FOXO1, consequently promoting lipogenesis and lipid accumulation in vitro and in vivo. Inhibition of HDAC6, a deacetylase of FOXO1, showed similar phenotypes to S100A11 overexpression in Hepa 1-6 cells. S100A11 interacted with HDAC6 to inhibit its activity, leading to the release and activation of FOXO1. Under S100A11 overexpression, the inhibition of FOXO1 and autophagy could alleviate the activated autophagy as well as up-regulated lipogenic genes. Both FOXO1 and autophagy inhibition and Dgat2 deletion could reduce liver cell lipid accumulation significantly.

CONCLUSIONS: A high-fat diet promotes liver S100A11 expression, which may interact with HDAC6 to block its binding to FOXO1, releasing or increasing the acetylation of FOXO1, thus activating autophagy and lipogenesis, and accelerating lipid accumulation and liver steatosis. These findings indicate a completely novel S100A11-HDAC6-FOXO1 axis in the regulation of autophagy and liver steatosis, providing potential possibilities for the treatment of NAFLD.}, } @article {pmid33070780, year = {2020}, author = {Rotenberg, D and Baumann, AA and Ben-Mahmoud, S and Christiaens, O and Dermauw, W and Ioannidis, P and Jacobs, CGC and Vargas Jentzsch, IM and Oliver, JE and Poelchau, MF and Rajarapu, SP and Schneweis, DJ and Snoeck, S and Taning, CNT and Wei, D and Widana Gamage, SMK and Hughes, DST and Murali, SC and Bailey, ST and Bejerman, NE and Holmes, CJ and Jennings, EC and Rosendale, AJ and Rosselot, A and Hervey, K and Schneweis, BA and Cheng, S and Childers, C and Simão, FA and Dietzgen, RG and Chao, H and Dinh, H and Doddapaneni, HV and Dugan, S and Han, Y and Lee, SL and Muzny, DM and Qu, J and Worley, KC and Benoit, JB and Friedrich, M and Jones, JW and Panfilio, KA and Park, Y and Robertson, HM and Smagghe, G and Ullman, DE and van der Zee, M and Van Leeuwen, T and Veenstra, JA and Waterhouse, RM and Weirauch, MT and Werren, JH and Whitfield, AE and Zdobnov, EM and Gibbs, RA and Richards, S}, title = {Genome-enabled insights into the biology of thrips as crop pests.}, journal = {BMC biology}, volume = {18}, number = {1}, pages = {142}, pmid = {33070780}, issn = {1741-7007}, support = {U54 HG003273/HG/NHGRI NIH HHS/United States ; }, mesh = {Animals ; Crops, Agricultural ; Feeding Behavior ; Food Chain ; *Genome, Insect ; Immunity, Innate/genetics ; *Life History Traits ; Perception ; Phylogeny ; Reproduction/genetics ; Thysanoptera/genetics/immunology/*physiology ; *Transcriptome ; }, abstract = {BACKGROUND: The western flower thrips, Frankliniella occidentalis (Pergande), is a globally invasive pest and plant virus vector on a wide array of food, fiber, and ornamental crops. The underlying genetic mechanisms of the processes governing thrips pest and vector biology, feeding behaviors, ecology, and insecticide resistance are largely unknown. To address this gap, we present the F. occidentalis draft genome assembly and official gene set.

RESULTS: We report on the first genome sequence for any member of the insect order Thysanoptera. Benchmarking Universal Single-Copy Ortholog (BUSCO) assessments of the genome assembly (size = 415.8 Mb, scaffold N50 = 948.9 kb) revealed a relatively complete and well-annotated assembly in comparison to other insect genomes. The genome is unusually GC-rich (50%) compared to other insect genomes to date. The official gene set (OGS v1.0) contains 16,859 genes, of which ~ 10% were manually verified and corrected by our consortium. We focused on manual annotation, phylogenetic, and expression evidence analyses for gene sets centered on primary themes in the life histories and activities of plant-colonizing insects. Highlights include the following: (1) divergent clades and large expansions in genes associated with environmental sensing (chemosensory receptors) and detoxification (CYP4, CYP6, and CCE enzymes) of substances encountered in agricultural environments; (2) a comprehensive set of salivary gland genes supported by enriched expression; (3) apparent absence of members of the IMD innate immune defense pathway; and (4) developmental- and sex-specific expression analyses of genes associated with progression from larvae to adulthood through neometaboly, a distinct form of maturation differing from either incomplete or complete metamorphosis in the Insecta.

CONCLUSIONS: Analysis of the F. occidentalis genome offers insights into the polyphagous behavior of this insect pest that finds, colonizes, and survives on a widely diverse array of plants. The genomic resources presented here enable a more complete analysis of insect evolution and biology, providing a missing taxon for contemporary insect genomics-based analyses. Our study also offers a genomic benchmark for molecular and evolutionary investigations of other Thysanoptera species.}, } @article {pmid33068828, year = {2020}, author = {Nischwitz, V and Gottselig, N and Braun, M}, title = {Preparative field flow fractionation for complex environmental samples: online detection by inductively coupled plasma mass spectrometry and offline detection by gas chromatography with flame ionization.}, journal = {Journal of chromatography. A}, volume = {1632}, number = {}, pages = {461581}, doi = {10.1016/j.chroma.2020.461581}, pmid = {33068828}, issn = {1873-3778}, mesh = {Environmental Pollutants/*analysis ; *Flame Ionization ; Fractionation, Field Flow/*methods ; Gas Chromatography-Mass Spectrometry/*methods ; Nanoparticles/chemistry ; *Online Systems ; Particle Size ; Particulate Matter/analysis ; Phosphorus/analysis ; Reproducibility of Results ; Soil/chemistry ; Zea mays/chemistry ; }, abstract = {Asymmetric flow field flow fractionation (AF4) in particular online with elemental detection via inductively coupled plasma mass spectrometry (ICP-MS) has been developed as powerful and flexible separation technique for suspensions of nano- and micro-particles covering a broad range of applications including environmental water samples and soil extracts. However, for challenging applications, such as particulate phosphorus determination in non-contaminated water samples at levels close to the limit of detection the throughput of the analytical field flow fractionation (FFF) is not sufficient. The same holds true for more specific identification and quantification of black carbon (BC) which needs a subsequent complex multi-step analysis using the well-established benzene polycarboxylic acids (BPCA) method. To overcome these limitations, the performance of a commercially available preparative AF4 channel, which has rarely been applied, yet, was investigated in this study. Using the example of an extract from charcoal spiked soil, method development for the preparative channel was performed and the results from six replicate fractionations with multi-element online detection by ICP-MS were compared to the results from the analytical channel for the same extracts. A similar fractionation pattern was achieved and the quantitative results agreed well for most of the particulate fractions (ratio 1.7 with standard deviation (SD) 0.2 for fraction 1, ratio 0.81 with SD 0.14 for fraction 2 and ratio 1.1 with SD 0.2 for fraction 3). Relative standard deviations were in the range of 9% to 18% for the preparative channel and between 3% and 17% for the analytical channel. Transferability of the separation parameters between both channels is discussed as well as the operational challenges of the preparative channel. As proof of principle, preparative fractionation of an extract from charcoal spiked soil was performed with fraction collection and subsequent quantification of BC via the BPCA method including derivatization, cation exchange pre-cleaning and finally gas chromatographic separation and quantification via flame ionization detection. The results indicated the majority of detected BC in the often so-called dissolved fraction was bound to nanoparticles (48%) and colloids (27%). Only 25% was detected in the cross flow (truly dissolved fraction). This successful example opens new possibilities for hyphenation of FFF separation with multiple detection techniques for improved characterization of particulate matter in challenging applications.}, } @article {pmid33064783, year = {2020}, author = {Tirados, I and Hope, A and Selby, R and Mpembele, F and Miaka, EM and Boelaert, M and Lehane, MJ and Torr, SJ and Stanton, MC}, title = {Impact of tiny targets on Glossina fuscipes quanzensis, the primary vector of human African trypanosomiasis in the Democratic Republic of the Congo.}, journal = {PLoS neglected tropical diseases}, volume = {14}, number = {10}, pages = {e0008270}, pmid = {33064783}, issn = {1935-2735}, mesh = {Animals ; Democratic Republic of the Congo ; Ecosystem ; Insect Control/instrumentation/*methods ; *Insect Vectors ; Insecticides ; Nitriles ; Pyrethrins ; Trypanosomiasis, African/*prevention & control ; *Tsetse Flies ; }, abstract = {Over the past 20 years there has been a >95% reduction in the number of Gambian Human African trypanosomiasis (g-HAT) cases reported globally, largely as a result of large-scale active screening and treatment programmes. There are however still foci where the disease persists, particularly in parts of the Democratic Republic of the Congo (DRC). Additional control efforts such as tsetse control using Tiny Targets may therefore be required to achieve g-HAT elimination goals. The purpose of this study was to evaluate the impact of Tiny Targets within DRC. In 2015-2017, pre- and post-intervention tsetse abundance data were collected from 1,234 locations across three neighbouring Health Zones (Yasa Bonga, Mosango, Masi Manimba). Remotely sensed dry season data were combined with pre-intervention tsetse presence/absence data from 332 locations within a species distribution modelling framework to produce a habitat suitability map. The impact of Tiny Targets on the tsetse population was then evaluated by fitting a generalised linear mixed model to the relative fly abundance data collected from 889 post-intervention monitoring sites within Yasa Bonga, with habitat suitability, proximity to the intervention and intervention duration as covariates. Immediately following the introduction of the intervention, we observe a dramatic reduction in fly catches by > 85% (pre-intervention: 0.78 flies/trap/day, 95% CI 0.676-0.900; 3 month post-intervention: 0.11 flies/trap/day, 95% CI 0.070-0.153) which is sustained throughout the study period. Declines in catches were negatively associated with proximity to Tiny Targets, and while habitat suitability is positively associated with abundance its influence is reduced in the presence of the intervention. This study adds to the body of evidence demonstrating the impact of Tiny Targets on tsetse across a range of ecological settings, and further characterises the factors which modify its impact. The habitat suitability maps have the potential to guide the expansion of tsetse control activities in this area.}, } @article {pmid33063404, year = {2021}, author = {Sallinger, E and Robeson, MS and Haselkorn, TS}, title = {Characterization of the bacterial microbiomes of social amoebae and exploration of the roles of host and environment on microbiome composition.}, journal = {Environmental microbiology}, volume = {23}, number = {1}, pages = {126-142}, doi = {10.1111/1462-2920.15279}, pmid = {33063404}, issn = {1462-2920}, support = {1726009//National Science Foundation (NSF)/ ; //College of Natural Sciences/ ; //University of Central Arkansas/ ; }, mesh = {Amoeba/*microbiology/physiology ; Bacteria/classification/genetics/*isolation & purification ; Bacterial Physiological Phenomena ; *Host Specificity ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Soil/chemistry ; *Soil Microbiology ; Symbiosis ; }, abstract = {As predators of bacteria, amoebae select for traits that allow bacteria to become symbionts by surviving phagocytosis and exploiting the eukaryotic intracellular environment. Soil-dwelling social amoebae can help us answer questions about the natural ecology of these amoeba-bacteria symbioses along the pathogen-mutualist spectrum. Our objective was to characterize the natural bacterial microbiome of phylogenetically and morphologically diverse social amoeba species using next-generation sequencing of 16S rRNA amplicons directly from amoeba fruiting bodies. We found six phyla of amoeba-associated bacteria: Proteobacteria, Bacteroidetes, Actinobacteria, Chlamydiae, Firmicutes, and Acidobacteria. The most common associates of amoebae were classified to order Chlamydiales and genus Burkholderia-Caballeronia-Paraburkholderia. These bacteria were present in multiple amoeba species across multiple locations. While there was substantial intraspecific variation, there was some evidence for host specificity and differentially abundant taxa between different amoeba hosts. Amoebae microbiomes were distinct from the microbiomes of their soil habitat, and soil pH affected amoeba microbiome diversity. Alpha-diversity was unsurprisingly lower in amoebae samples compared with soil, but beta-diversity between amoebae samples was higher than between soil samples. Further exploration of social amoebae microbiomes may help us understand the roles of bacteria, host, and environment on symbiotic interactions and microbiome formation in basal eukaryotic organisms.}, } @article {pmid33060594, year = {2020}, author = {Middleton-Welling, J and Dapporto, L and García-Barros, E and Wiemers, M and Nowicki, P and Plazio, E and Bonelli, S and Zaccagno, M and Šašić, M and Liparova, J and Schweiger, O and Harpke, A and Musche, M and Settele, J and Schmucki, R and Shreeve, T}, title = {A new comprehensive trait database of European and Maghreb butterflies, Papilionoidea.}, journal = {Scientific data}, volume = {7}, number = {1}, pages = {351}, pmid = {33060594}, issn = {2052-4463}, mesh = {Africa, Northern ; Animals ; Biological Evolution ; Butterflies/*classification ; Conservation of Natural Resources ; Databases, Factual ; Ecology ; Europe ; Phylogeny ; }, abstract = {Trait-based analyses explaining the different responses of species and communities to environmental changes are increasing in frequency. European butterflies are an indicator group that responds rapidly to environmental changes with extensive citizen science contributions to documenting changes of abundance and distribution. Species traits have been used to explain long- and short-term responses to climate, land-use and vegetation changes. Studies are often characterised by limited trait sets being used, with risks that the relative roles of different traits are not fully explored. Butterfly trait information is dispersed amongst various sources and descriptions sometimes differ between sources. We have therefore drawn together multiple information sets to provide a comprehensive trait database covering 542 taxa and 25 traits described by 217 variables and sub-states of the butterflies of Europe and Maghreb (northwest Africa) which should serve for improved trait-based ecological, conservation-related, phylogeographic and evolutionary studies of this group of insects. We provide this data in two forms; the basic data and as processed continuous and multinomial data, to enhance its potential usage.}, } @article {pmid33057099, year = {2020}, author = {Ten Thij, M and Bathina, K and Rutter, LA and Lorenzo-Luaces, L and van de Leemput, IA and Scheffer, M and Bollen, J}, title = {Depression alters the circadian pattern of online activity.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {17272}, pmid = {33057099}, issn = {2045-2322}, mesh = {Adolescent ; Adult ; Affect ; *Circadian Rhythm ; Cohort Studies ; Depression/*physiopathology/psychology ; Female ; Humans ; Male ; Middle Aged ; Sleep ; Social Media/*statistics & numerical data ; Wakefulness ; Young Adult ; }, abstract = {Human sleep/wake cycles follow a stable circadian rhythm associated with hormonal, emotional, and cognitive changes. Changes of this cycle are implicated in many mental health concerns. In fact, the bidirectional relation between major depressive disorder and sleep has been well-documented. Despite a clear link between sleep disturbances and subsequent disturbances in mood, it is difficult to determine from self-reported data which specific changes of the sleep/wake cycle play the most important role in this association. Here we observe marked changes of activity cycles in millions of twitter posts of 688 subjects who explicitly stated in unequivocal terms that they had received a (clinical) diagnosis of depression as compared to the activity cycles of a large control group (n = 8791). Rather than a phase-shift, as reported in other work, we find significant changes of activity levels in the evening and before dawn. Compared to the control group, depressed subjects were significantly more active from 7 PM to midnight and less active from 3 to 6 AM. Content analysis of tweets revealed a steady rise in rumination and emotional content from midnight to dawn among depressed individuals. These results suggest that diagnosis and treatment of depression may focus on modifying the timing of activity, reducing rumination, and decreasing social media use at specific hours of the day.}, } @article {pmid33055958, year = {2020}, author = {Servino, LM and Schwertner, CF}, title = {Electronic identification key and data base to the genus Chinavia (Heteroptera: Pentatomidae) with morphological and distributional data.}, journal = {Zootaxa}, volume = {4809}, number = {1}, pages = {zootaxa.4809.1.13}, doi = {10.11646/zootaxa.4809.1.13}, pmid = {33055958}, issn = {1175-5334}, mesh = {Animals ; Data Management ; *Heteroptera ; }, abstract = {The genus Chinavia Orian has a great diversity of species, being distributed in the Nearctic, Neotropical and Afrotropical regions (Rolston 1983; Schwertner Grazia 2007, Grazia Schwertner 2017). The genus is included in the subfamily Pentatominae, tribe Nezarini, whose individuals retain their green coloration after death, average size between 9 and 19 mm, and considered polyphagous (Rolston 1983; Schwertner et al. 2002; Rider 2020). Some species of Chinavia are recorded as important crop pests in different countries (e.g. Matesco et al. 2007; Herbert Toews 2012), and those species are better known regarding distribution, ecology and other biological aspects. However, the great majority of species is known only for the adult morphology, and there are still problems concerning the correct identification of the species due to their wide distribution.}, } @article {pmid33053371, year = {2021}, author = {Lasso, G and Honig, B and Shapira, SD}, title = {A Sweep of Earth's Virome Reveals Host-Guided Viral Protein Structural Mimicry and Points to Determinants of Human Disease.}, journal = {Cell systems}, volume = {12}, number = {1}, pages = {82-91.e3}, pmid = {33053371}, issn = {2405-4720}, support = {U54 CA209997/CA/NCI NIH HHS/United States ; R01 GM030518/GM/NIGMS NIH HHS/United States ; S10 OD012351/OD/NIH HHS/United States ; R01 GM109018/GM/NIGMS NIH HHS/United States ; S10 OD021764/OD/NIH HHS/United States ; }, mesh = {Animals ; Coronavirus/chemistry/*genetics ; Culicidae ; Databases, Genetic ; Host-Pathogen Interactions/*genetics ; Humans ; Molecular Mimicry/*genetics ; Protein Structure, Secondary ; Viral Proteins/chemistry/*genetics ; Virome/*genetics ; Virus Diseases/epidemiology/*genetics ; Viruses/chemistry/genetics ; }, abstract = {Viruses deploy genetically encoded strategies to coopt host machinery and support viral replicative cycles. Here, we use protein structure similarity to scan for molecular mimicry, manifested by structural similarity between viral and endogenous host proteins, across thousands of cataloged viruses and hosts spanning broad ecological niches and taxonomic range, including bacteria, plants and fungi, invertebrates, and vertebrates. This survey identified over 6,000,000 instances of structural mimicry; more than 70% of viral mimics cannot be discerned through protein sequence alone. We demonstrate that the manner and degree to which viruses exploit molecular mimicry varies by genome size and nucleic acid type and identify 158 human proteins that are mimicked by coronaviruses, providing clues about cellular processes driving pathogenesis. Our observations point to molecular mimicry as a pervasive strategy employed by viruses and indicate that the protein structure space used by a given virus is dictated by the host proteome. A record of this paper's transparent peer review process is included in the Supplemental Information.}, } @article {pmid33052473, year = {2020}, author = {Yang, L and Lei, L and Liu, H and Wang, J and Zheng, H and Zou, D}, title = {Whole-genome mining of abiotic stress gene loci in rice.}, journal = {Planta}, volume = {252}, number = {5}, pages = {85}, doi = {10.1007/s00425-020-03488-x}, pmid = {33052473}, issn = {1432-2048}, support = {2019M651249//China Postdoctoral Foundation/ ; 2018YFD0300105-1//The integration and demonstration of full mechanized high yield and efficiency technology system of japonica rice in semi-humid region of Heilongjiang Province, China/ ; }, mesh = {*Data Mining ; Genome-Wide Association Study ; *Oryza/genetics ; Quantitative Trait Loci/genetics ; *Stress, Physiological/genetics ; }, abstract = {We projected meta-QTL (MQTL) for drought, salinity, cold state, and high metal ion tolerance in rice using a meta-analysis based on high-density consensus maps. In addition, a genome-wide association analysis was used to validate the results of the meta-analysis, and four new chromosome intervals for mining abiotic stress candidate genes were obtained. Drought, severe cold, high salinity, and high metallic ion concentrations severely restrict rice production. Consequently, the breeding of abiotic stress-tolerant variety is being paid increasingly more attention. This study aimed to identify meta-quantitative trait loci (MQTL) for abiotic stress tolerance in rice, as well as the molecular markers and potential candidate genes of the MQTL regions. We summarized 2785 rice QTL and conducted a meta-analysis of 159 studies. We found 82 drought tolerance (DT), 70 cold tolerance (CT), 70 salt tolerance (ST), and 51 heavy metal ion tolerance (IT) meta-QTL, as well as 20 DT, 11 CT, 22 ST, and 5 IT candidate genes in the MQTL interval. Thirty-one multiple-tolerance related MQTL regions, which were highly enriched, were also detected, and 13 candidate genes related to multiple-tolerance were obtained. In addition, the correlation between DT, CT, and ST was significant in the rice genome. Four candidate genes and four MM-QTL regions were detected simultaneously by GWAS and meta-analysis. The four candidate genes showed distinct genetic differentiation and substantial genetic distance between indica and japonica rice, and the four MM-QTL are potential intervals for mining abiotic stress-related candidate genes. The candidate genes identified in this study will not only be useful for marker-assisted selection and pyramiding but will also accelerate the fine mapping and cloning of the candidate genes associated with abiotic stress-tolerance mechanisms in rice.}, } @article {pmid33051510, year = {2020}, author = {Pimsler, ML and Oyen, KJ and Herndon, JD and Jackson, JM and Strange, JP and Dillon, ME and Lozier, JD}, title = {Biogeographic parallels in thermal tolerance and gene expression variation under temperature stress in a widespread bumble bee.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {17063}, pmid = {33051510}, issn = {2045-2322}, mesh = {Acclimatization/genetics/physiology ; Animals ; Bees/*genetics/*physiology ; California ; Climate Change ; Female ; Gene Expression ; Gene Ontology ; Genes, Insect ; Heat-Shock Response/genetics/physiology ; Oregon ; Phylogeography ; Stress, Physiological/genetics/physiology ; Temperature ; }, abstract = {Global temperature changes have emphasized the need to understand how species adapt to thermal stress across their ranges. Genetic mechanisms may contribute to variation in thermal tolerance, providing evidence for how organisms adapt to local environments. We determine physiological thermal limits and characterize genome-wide transcriptional changes at these limits in bumble bees using laboratory-reared Bombus vosnesenskii workers. We analyze bees reared from latitudinal (35.7-45.7°N) and altitudinal (7-2154 m) extremes of the species' range to correlate thermal tolerance and gene expression among populations from different climates. We find that critical thermal minima (CTMIN) exhibit strong associations with local minimums at the location of queen origin, while critical thermal maximum (CTMAX) was invariant among populations. Concordant patterns are apparent in gene expression data, with regional differentiation following cold exposure, and expression shifts invariant among populations under high temperatures. Furthermore, we identify several modules of co-expressed genes that tightly correlate with critical thermal limits and temperature at the region of origin. Our results reveal that local adaptation in thermal limits and gene expression may facilitate cold tolerance across a species range, whereas high temperature responses are likely constrained, both of which may have implications for climate change responses of bumble bees.}, } @article {pmid33051448, year = {2020}, author = {Aliko, S and Huang, J and Gheorghiu, F and Meliss, S and Skipper, JI}, title = {A naturalistic neuroimaging database for understanding the brain using ecological stimuli.}, journal = {Scientific data}, volume = {7}, number = {1}, pages = {347}, pmid = {33051448}, issn = {2052-4463}, support = {EP/M026965/1//RCUK | Engineering and Physical Sciences Research Council (EPSRC)/International ; }, mesh = {Brain/*physiology ; *Brain Mapping ; Databases, Factual ; Humans ; *Magnetic Resonance Imaging ; }, abstract = {Neuroimaging has advanced our understanding of human psychology using reductionist stimuli that often do not resemble information the brain naturally encounters. It has improved our understanding of the network organization of the brain mostly through analyses of 'resting-state' data for which the functions of networks cannot be verifiably labelled. We make a 'Naturalistic Neuroimaging Database' (NNDb v1.0) publically available to allow for a more complete understanding of the brain under more ecological conditions during which networks can be labelled. Eighty-six participants underwent behavioural testing and watched one of 10 full-length movies while functional magnetic resonance imaging was acquired. Resulting timeseries data are shown to be of high quality, with good signal-to-noise ratio, few outliers and low movement. Data-driven functional analyses provide further evidence of data quality. They also demonstrate accurate timeseries/movie alignment and how movie annotations might be used to label networks. The NNDb can be used to answer questions previously unaddressed with standard neuroimaging approaches, progressing our knowledge of how the brain works in the real world.}, } @article {pmid33051443, year = {2020}, author = {Boakes, EH and Fuller, RA and Mace, GM and Ding, C and Ang, TT and Auffret, AG and Clark, NE and Dunn, J and Gilbert, J and Golovnyuk, V and Gupta, G and Irlich, U and Joachim, E and O' Connor, K and Potapov, E and Potapov, R and Schleicher, J and Stebbing, S and Townshend, T and McGowan, PJK}, title = {GalliForm, a database of Galliformes occurrence records from the Indo-Malay and Palaearctic, 1800-2008.}, journal = {Scientific data}, volume = {7}, number = {1}, pages = {344}, pmid = {33051443}, issn = {2052-4463}, support = {F/07/08/AK//Leverhulme Trust/International ; F/07/08/AK//Leverhulme Trust/International ; }, mesh = {*Animal Distribution ; Animals ; Asia ; Biodiversity ; *Databases, Factual ; Europe ; *Galliformes ; Geographic Mapping ; }, abstract = {Historical as well as current species distribution data are needed to track changes in biodiversity. Species distribution data are found in a variety of sources, each of which has its own distinct bias toward certain taxa, time periods or places. We present GalliForm, a database that comprises 186687 galliform occurrence records linked to 118907 localities in Europe and Asia. Records were derived from museums, peer-reviewed and grey literature, unpublished field notes, diaries and correspondence, banding records, atlas records and online birding trip reports. We describe data collection processes, georeferencing methods and quality-control procedures. This database has underpinned several peer-reviewed studies, investigating spatial and temporal bias in biodiversity data, species' geographic range changes and local extirpation patterns. In our rapidly changing world, an understanding of long-term change in species' distributions is key to predicting future impacts of threatening processes such as land use change, over-exploitation of species and climate change. This database, its historical aspect in particular, provides a valuable source of information for further studies in macroecology and biodiversity conservation.}, } @article {pmid33048938, year = {2020}, author = {Doussot, C and Bertrand, OJN and Egelhaaf, M}, title = {Visually guided homing of bumblebees in ambiguous situations: A behavioural and modelling study.}, journal = {PLoS computational biology}, volume = {16}, number = {10}, pages = {e1008272}, pmid = {33048938}, issn = {1553-7358}, mesh = {Animals ; Bees ; Computational Biology ; Cues ; Flight, Animal ; Homing Behavior/*physiology ; *Models, Biological ; Spatial Learning/*physiology ; Spatial Navigation/*physiology ; Visual Fields/*physiology ; }, abstract = {Returning home is a crucial task accomplished daily by many animals, including humans. Because of their tiny brains, insects, like bees or ants, are good study models for efficient navigation strategies. Bees and ants are known to rely mainly on learned visual information about the nest surroundings to pinpoint their barely visible nest-entrance. During the return, when the actual sight of the insect matches the learned information, the insect is easily guided home. Occasionally, modifications to the visual environment may take place while the insect is on a foraging trip. Here, we addressed the ecologically relevant question of how bumblebees' homing is affected by such a situation. In an artificial setting, we habituated bees to be guided to their nest by two constellations of visual cues. After habituation, these cues were displaced during foraging trips into a conflict situation. We recorded bumblebees' return flights in such circumstances and investigated where they search for their nest entrance following the degree of displacement between the two visually relevant cues. Bumblebees mostly searched at the fictive nest location as indicated by either cue constellation, but never at a compromise location between them. We compared these experimental results to the predictions of different types of homing models. We found that models guiding an agent by a single holistic view of the nest surroundings could not account for the bumblebees' search behaviour in cue-conflict situations. Instead, homing models relying on multiple views were sufficient. We could further show that homing models required fewer views and got more robust to height changes if optic flow-based spatial information was encoded and learned, rather than just brightness information.}, } @article {pmid33045770, year = {2020}, author = {Shin, J and Lee, SG and Park, EC and Nam, JY}, title = {Socioeconomic Status and Successful Delivery after an Infertility Diagnosis: a Nationwide Health Insurance Cohort Study in Korea Conducted from 2005 to 2013.}, journal = {Journal of Korean medical science}, volume = {35}, number = {39}, pages = {e341}, pmid = {33045770}, issn = {1598-6357}, mesh = {Adult ; Cohort Studies ; Databases, Factual ; Female ; Healthcare Disparities ; Humans ; Income ; Infertility, Female/*diagnosis ; Pregnancy ; Proportional Hazards Models ; Republic of Korea ; Retrospective Studies ; *Social Class ; Young Adult ; }, abstract = {BACKGROUND: The global disease burden of infertility is rising and accessibility to infertility treatments and assisted reproduction is a challenging issue. Therefore, we investigated characteristics of successful delivery after an infertility diagnosis among infertile women.

METHODS: We designed a retrospective cohort study with the main outcome measure of a delivery medical record after the initial diagnosis of infertility. A total of 10,108 women patients who were diagnosed with infertility between 2005 to 2013 in the National Health Insurance Cooperation Cohort Database of Korea were enrolled. The adjusted hazard ratios (HRs) and 95% confidence intervals (CIs) for subsequent delivery were estimated by applying a Cox proportional-hazard regression model.

RESULTS: Approximately 55% of infertile women who reported infertility had a delivery eventually. Infertile women who are aged between 30 to 39 (HR, 0.80; 95% CI, 0.75-0.84), in low income level (HR, 0.77; 95% CI, 0.71-0.84), or diagnosed with diabetes (HR, 0.76; 95% CI, 0.60-0.96) were less likely to report a delivery.

CONCLUSION: These findings highlight demographic, socioeconomic, and medical characteristics of reporting a consequent delivery. Although many previous articles reported an association between socioeconomic status and receiving medical evaluation, there were few studies regarding successful delivery after an infertility diagnosis across socioeconomic status. Thus, the maintaining of support for low socioeconomic status infertile women and their family should be considered after the infertility diagnosis in aspects of financial and social approaches.}, } @article {pmid33044975, year = {2020}, author = {Ramos-Arredondo, RI and Carvajal-Gámez, BE and Gendron, D and Gallegos-Funes, FJ and Mújica-Vargas, D and Rosas-Fernández, JB}, title = {PhotoId-Whale: Blue whale dorsal fin classification for mobile devices.}, journal = {PloS one}, volume = {15}, number = {10}, pages = {e0237570}, pmid = {33044975}, issn = {1932-6203}, mesh = {Algorithms ; Animal Fins/*anatomy & histology ; Animals ; Balaenoptera/*anatomy & histology ; Databases, Factual ; Image Processing, Computer-Assisted/methods/statistics & numerical data ; *Mobile Applications ; Pattern Recognition, Automated/methods/statistics & numerical data ; Photography/*methods/statistics & numerical data ; }, abstract = {Photo-identification (photo-id) is a method used in field studies by biologists to monitor animals according to their density, movement patterns and behavior, with the aim of predicting and preventing ecological risks. However, these methods can introduce subjectivity when manually classifying an individual animal, creating uncertainty or inaccuracy in the data as a result of the human criteria involved. One of the main objectives in photo-id is to implement an automated mechanism that is free of biases, portable, and easy to use. The main aim of this work is to develop an autonomous and portable photo-id system through the optimization of image classification algorithms that have high statistical dependence, with the goal of classifying dorsal fin images of the blue whale through offline information processing on a mobile platform. The new proposed methodology is based on the Scale Invariant Feature Transform (SIFT) that, in conjunction with statistical discriminators such as the variance and the standard deviation, fits the extracted data and selects the closest pixels that comprise the edges of the dorsal fin of the blue whale. In this way, we ensure the elimination of the most common external factors that could affect the quality of the image, thus avoiding the elimination of relevant sections of the dorsal fin. The photo-id method presented in this work has been developed using blue whale images collected off the coast of Baja California Sur. The results shown have qualitatively and quantitatively validated the method in terms of its sensitivity, specificity and accuracy on the Jetson Tegra TK1 mobile platform. The solution optimizes classic SIFT, balancing the results obtained with the computational cost, provides a more economical form of processing and obtains a portable system that could be beneficial for field studies through mobile platforms, making it available to scientists, government and the general public.}, } @article {pmid33043370, year = {2020}, author = {Barnett, I and Torous, J and Reeder, HT and Baker, J and Onnela, JP}, title = {Determining sample size and length of follow-up for smartphone-based digital phenotyping studies.}, journal = {Journal of the American Medical Informatics Association : JAMIA}, volume = {27}, number = {12}, pages = {1844-1849}, pmid = {33043370}, issn = {1527-974X}, support = {U01 MH116925/MH/NIMH NIH HHS/United States ; K23 MH116130/MH/NIMH NIH HHS/United States ; DP2 MH103909/MH/NIMH NIH HHS/United States ; R01 MH116884/MH/NIMH NIH HHS/United States ; }, mesh = {*Ecological Momentary Assessment ; Humans ; *Longitudinal Studies ; Models, Statistical ; Research Design ; *Sample Size ; *Smartphone ; *Telemedicine ; }, abstract = {OBJECTIVE: Studies that use patient smartphones to collect ecological momentary assessment and sensor data, an approach frequently referred to as digital phenotyping, have increased in popularity in recent years. There is a lack of formal guidelines for the design of new digital phenotyping studies so that they are powered to detect both population-level longitudinal associations as well as individual-level change points in multivariate time series. In particular, determining the appropriate balance of sample size relative to the targeted duration of follow-up is a challenge.

MATERIALS AND METHODS: We used data from 2 prior smartphone-based digital phenotyping studies to provide reasonable ranges of effect size and parameters. We considered likelihood ratio tests for generalized linear mixed models as well as for change point detection of individual-level multivariate time series.

RESULTS: We propose a joint procedure for sequentially calculating first an appropriate length of follow-up and then a necessary minimum sample size required to provide adequate power. In addition, we developed an accompanying accessible sample size and power calculator.

DISCUSSION: The 2-parameter problem of identifying both an appropriate sample size and duration of follow-up for a longitudinal study requires the simultaneous consideration of 2 analysis methods during study design.

CONCLUSION: The temporally dense longitudinal data collected by digital phenotyping studies may warrant a variety of applicable analysis choices. Our use of generalized linear mixed models as well as change point detection to guide sample size and study duration calculations provide a tool to effectively power new digital phenotyping studies.}, } @article {pmid33043240, year = {2020}, author = {Schuch, S and Bock, O and Freitag, K and Moretti, L}, title = {Cognitive Multitasking: Inhibition in Task Switching Depends on Stimulus Complexity.}, journal = {Journal of cognition}, volume = {3}, number = {1}, pages = {30}, pmid = {33043240}, issn = {2514-4820}, abstract = {We report a series of three experiments investigating inhibition in task switching, using N-2 repetition costs as an empirical marker. The experiments were structurally identical, employing a standard experimental paradigm where participants switch between three different categorization tasks. The experiments differed with respect to the stimulus material. According to prominent theories of cognitive control, N-2 repetition costs should be observed in all three experiments. To our surprise, this is not what we observed: N-2 repetition costs did not occur in Experiment 1, where we used static pictures from a driving simulator environment showing an oncoming car, embedded in a car-driving scene. In contrast, we observed robust N-2 repetition costs in Experiment 2, where we used static pictures of faces, and in Experiment 3, where the identical car stimuli from Experiment 1 were used, but without the surrounding visual scene. These results suggest that N-2 repetition costs depend on the complexity of the stimulus material. We discuss two aspects of complexity: 1) When the relevant stimulus feature is embedded in a complex visual scene, task-irrelevant features in that scene might trigger additional task sets, and thus induce additional task switches, attenuating N-2 repetition costs among the instructed task sets. 2) The presence of distractors might lead to additional covert or overt shifts of spatial attention, which in turn might reduce the size of N-2 repetition costs. On a more general level, the results illustrate the difficulty of transferring laboratory tasks to settings that bear more similarity to everyday life situations.}, } @article {pmid33039932, year = {2021}, author = {Zhang, X and Gu, X and Wang, L and Zhou, Y and Huang, Z and Xu, C and Cheng, C}, title = {Spatiotemporal variations in the incidence of bacillary dysentery and long-term effects associated with meteorological and socioeconomic factors in China from 2013 to 2017.}, journal = {The Science of the total environment}, volume = {755}, number = {Pt 2}, pages = {142626}, doi = {10.1016/j.scitotenv.2020.142626}, pmid = {33039932}, issn = {1879-1026}, mesh = {Bayes Theorem ; Beijing ; China/epidemiology ; *Dysentery, Bacillary/epidemiology ; Humans ; Incidence ; Meteorological Concepts ; Socioeconomic Factors ; }, abstract = {Bacillary dysentery is a global public health problem that exhibits manifest spatiotemporal heterogeneity. However, long-term variations and regional determinant factors remain unclear. In this study, the Bayesian space-time hierarchy model was used to identify the long-term spatiotemporal heterogeneity of the incidence of bacillary dysentery and quantify the associations of meteorological factors with the incidence of bacillary dysentery in northern and southern China from 2013 to 2017. GeoDetector was used to quantify the determinant powers of socioeconomic factors in the two regions. The results showed that the incidence of bacillary dysentery peaked in summer (June to August), indicating temporal seasonality. Geographically, the hot spots (high-risk areas) were distributed in northwestern China (Xinjiang, Gansu, and Ningxia) and northern China (including Beijing, Tianjin, and Hebei), whereas the cold spots (low-risk areas) were concentrated in southeastern China (Jiangsu, Zhejiang, Fujian, and Guangdong). Moreover, significant regional differences were found among the meteorological and socioeconomic factors. Average temperature was the dominant meteorological factor in both northern and southern China. In northern and southern China, a 1 °C increase in the average temperature led to an increase of 1.01% and 4.26% in bacillary dysentery risk, respectively. The dominant socioeconomic factors in northern and southern China were per capita gross domestic product and the number of health technicians, with q statistic values of 0.81 and 0.49, respectively. These findings suggest that hot, moist, and overcrowded environments or poor health conditions increase the risk of bacillary dysentery. This study provides suggestions and serves as a basis for surveillance efforts. Further, the suggestions may aid in the control of bacillary dysentery and in the implementation of disease prevention policies.}, } @article {pmid33037820, year = {2021}, author = {Bastian, FB and Roux, J and Niknejad, A and Comte, A and Fonseca Costa, SS and de Farias, TM and Moretti, S and Parmentier, G and de Laval, VR and Rosikiewicz, M and Wollbrett, J and Echchiki, A and Escoriza, A and Gharib, WH and Gonzales-Porta, M and Jarosz, Y and Laurenczy, B and Moret, P and Person, E and Roelli, P and Sanjeev, K and Seppey, M and Robinson-Rechavi, M}, title = {The Bgee suite: integrated curated expression atlas and comparative transcriptomics in animals.}, journal = {Nucleic acids research}, volume = {49}, number = {D1}, pages = {D831-D847}, pmid = {33037820}, issn = {1362-4962}, support = {U01 CA215010/CA/NCI NIH HHS/United States ; }, mesh = {Animals ; *Data Curation ; *Databases, Genetic ; Gene Expression Regulation ; Molecular Sequence Annotation ; Transcriptome/*genetics ; User-Computer Interface ; }, abstract = {Bgee is a database to retrieve and compare gene expression patterns in multiple animal species, produced by integrating multiple data types (RNA-Seq, Affymetrix, in situ hybridization, and EST data). It is based exclusively on curated healthy wild-type expression data (e.g., no gene knock-out, no treatment, no disease), to provide a comparable reference of normal gene expression. Curation includes very large datasets such as GTEx (re-annotation of samples as 'healthy' or not) as well as many small ones. Data are integrated and made comparable between species thanks to consistent data annotation and processing, and to calls of presence/absence of expression, along with expression scores. As a result, Bgee is capable of detecting the conditions of expression of any single gene, accommodating any data type and species. Bgee provides several tools for analyses, allowing, e.g., automated comparisons of gene expression patterns within and between species, retrieval of the prefered conditions of expression of any gene, or enrichment analyses of conditions with expression of sets of genes. Bgee release 14.1 includes 29 animal species, and is available at https://bgee.org/ and through its Bioconductor R package BgeeDB.}, } @article {pmid33037786, year = {2021}, author = {Bensch, S and Inumaru, M and Sato, Y and Lee Cruz, L and Cunningham, AA and Goodman, SJ and Levin, II and Parker, PG and Casanueva, P and Hernández, MA and Moreno-Rueda, G and Rojo, MA}, title = {Contaminations contaminate common databases.}, journal = {Molecular ecology resources}, volume = {21}, number = {2}, pages = {355-362}, pmid = {33037786}, issn = {1755-0998}, support = {2017-03937//Swedish Research Council/ ; }, mesh = {Animals ; *Bird Diseases/parasitology ; Birds/*parasitology ; DNA, Protozoan ; *Databases, Genetic ; *Haemosporida/genetics ; Phylogeny ; Polymerase Chain Reaction ; }, abstract = {The polymerase chain reaction (PCR) is a very powerful method to detect and identify pathogens. The high sensitivity of the method, however, comes with a cost; any of the millions of artificial DNA copies generated by PCR can serve as a template in a following experiment. If not identified as contaminations, these may result in erroneous conclusions on the occurrence of the pathogen, thereby inflating estimates of host range and geographic distribution. In the present paper, we evaluate whether several published records of avian haemosporidian parasites, in either unusual host species or geographical regions, might stem from PCR contaminations rather than novel biological findings. The detailed descriptions of these cases are shedding light upon the steps in the work process that might lead to PCR contaminations. By increasing the awareness of this problem, it will aid in developing procedures that keep these to a minimum. The examples in the present paper are from haemosporidians of birds, however the problem of contaminations and suggested actions should apply generally to all kinds of PCR-based identifications, not just of parasites and pathogens.}, } @article {pmid33035767, year = {2020}, author = {Liao, Y and Jiang, X and Xiao, Y and Li, M}, title = {Exposure of microalgae Euglena gracilis to polystyrene microbeads and cadmium: Perspective from the physiological and transcriptional responses.}, journal = {Aquatic toxicology (Amsterdam, Netherlands)}, volume = {228}, number = {}, pages = {105650}, doi = {10.1016/j.aquatox.2020.105650}, pmid = {33035767}, issn = {1879-1514}, mesh = {Aquatic Organisms/drug effects/genetics/growth & development ; Cadmium/*toxicity ; *Environmental Exposure ; Euglena gracilis/drug effects/*genetics/*physiology/ultrastructure ; Gene Expression Profiling ; Gene Ontology ; Microalgae/drug effects/*genetics/physiology/ultrastructure ; *Microspheres ; Oxidative Stress/drug effects ; Photosynthesis/drug effects ; Pigments, Biological/metabolism ; Polystyrenes/*toxicity ; Transcription, Genetic/*drug effects ; Water Pollutants, Chemical/toxicity ; }, abstract = {Micro(nano)plastics (MPs/NPs) are already present as contaminants in the natural environment globally and have been shown to be difficult to degrade, resulting in the potential for ecological damage and public health concerns. However, the adverse effects of exposure to MPs/NPs by aquatic organisms, especially freshwater microalgae, remains unclear. In the present study, the growth, physiology and transcriptome of the freshwater microalgae Euglena gracilis were comprehensively analyzed following exposure to 1 mg/L of polystyrene (PS) microbeads (5 μm PS-MPs and 100 nm PS-NPs), 0.5 mg/L cadmium (Cd), or a mixture of PS microbeads and Cd for 96 h. Results showed that the toxicity of PS-MPs to microalgae was greater than PS-NPs, inducing increased growth inhibition, oxidative damage and decreased photosynthesis pigment concentrations. PS-MPs alone or in combination with Cd caused cavitation within microalgal cells, as well as increasing the number and volume of vacuoles. The combined exposure toxicity test showed that a combination of Cd + PS-NPs was more toxic than Cd + PS-MPs, which may be explained by the transcriptomic analysis results. Differentially expressed genes (DEGs) in the Cd + PS-NPs group were mainly enriched in metabolism-related pathways, suggesting that algal metabolism was hindered, resulting in aggravation of toxicity. The reduced toxicity induced by Cd + PS-MPs may indicate a response to resist external stress processes. In addition, no adsorption of 0.5 mg/L Cd to 1 mg/L PS microbeads was observed, suggesting that adsorption of MPs/NPs and Cd was not the key factor determining the combined toxicity effects in this study.}, } @article {pmid33033455, year = {2020}, author = {Maksimovic, M and Vlajinac, H and Radak, D and Marinkovic, J and Maksimovic, J and Jorga, J}, title = {Association of overweight and obesity with cardiovascular risk factors in patients with atherosclerotic diseases.}, journal = {Journal of medical biochemistry}, volume = {39}, number = {2}, pages = {215-223}, pmid = {33033455}, issn = {1452-8258}, abstract = {BACKGROUND: The aim of this study was to compare demographic, clinical and biochemical characteristics, including inflammatory markers, according to the nutritional status of patients with verified atherosclerotic disease.

METHODS: This cross-sectional study involved 1045 consecutive patients with verified carotid disease or peripheral arterial disease (PAD). Anthropometric parameters and data on cardiovascular risk factors and therapy for hypertension and hyperlipidemia were collected for all participants.

RESULTS: Carotid disease was positively and PAD was negatively associated with body mass index (BMI). Negative association between obesity and PAD was significant only in former smokers, not in current smokers or in patients who never smoked. Overweight and general obesity were significantly related to metabolic syndrome (p < 0.001), lower values of high - density lipoprotein cholesterol (p < 0.001), increased triglycerides (p < 0.001), hyperglycemia (p < 0.001), self-reported diabetes (p < 0.001), hypertension (p < 0.001), high serum uric acid (p < 0.001), increased high sensitivity C-reactive protein (p = 0.020) and former smoking (p = 0.005) after adjustment for age, gender and type of disease. Antihypertensive therapy seems to be less effective in patients who are overweight and obese.

CONCLUSIONS: In conclusion, overweight and general obesity were significantly related to several cardiovascular risk factors.}, } @article {pmid33033298, year = {2020}, author = {Gulyaeva, M and Huettmann, F and Shestopalov, A and Okamatsu, M and Matsuno, K and Chu, DH and Sakoda, Y and Glushchenko, A and Milton, E and Bortz, E}, title = {Data mining and model-predicting a global disease reservoir for low-pathogenic Avian Influenza (A) in the wider pacific rim using big data sets.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {16817}, pmid = {33033298}, issn = {2045-2322}, mesh = {Animals ; Birds/*virology ; Chickens/virology ; *Data Mining/methods ; Datasets as Topic ; *Disease Reservoirs/statistics & numerical data/virology ; Ducks/virology ; Forecasting ; Influenza in Birds/*epidemiology/virology ; Models, Statistical ; Orthomyxoviridae/pathogenicity ; Pacific Ocean ; Prevalence ; }, abstract = {Avian Influenza (AI) is a complex but still poorly understood disease; specifically when it comes to reservoirs, co-infections, connectedness and wider landscape perspectives. Low pathogenic (Low-path LP) AI in chickens caused by less virulent strains of AI viruses (AIVs)-when compared with highly pathogenic AIVs (HPAIVs)-are not even well-described yet or known how they contribute to wider AI and immune system issues. Co-circulation of LPAIVs with HPAIVs suggests their interactions in their ecological aspects. Here we show for the Pacific Rim an international approach how to data mine and model-predict LP AI and its ecological niche with machine learning and open access data sets and geographic information systems (GIS) on a 5 km pixel size for best-possible inference. This is based on the best-available data on the issue (~ 40,827 records of lab-analyzed field data from Japan, Russia, Vietnam, Mongolia, Alaska and Influenza Research Database (IRD) and U.S. Department of Agriculture (USDA) database sets, as well as 19 GIS data layers). We sampled 157 hosts and 110 low-path AIVs with 32 species as drivers. The prevalence across low-path AIV subtypes is dominated by Muscovy ducks, Mallards, Whistling Swans and gulls also emphasizing industrial impacts for the human-dominated wildlife contact zone. This investigation sets a good precedent for the study of reservoirs, big data mining, predictions and subsequent outbreaks of HPAI and other pandemics.}, } @article {pmid33033280, year = {2020}, author = {Zelenka, J and Kasanický, T and Budinská, I and Kaňuch, P}, title = {An agent-based algorithm resembles behaviour of tree-dwelling bats under fission-fusion dynamics.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {16793}, pmid = {33033280}, issn = {2045-2322}, mesh = {Algorithms ; Animals ; Behavior, Animal/*physiology ; *Computer Simulation ; *Ecosystem ; *Social Behavior ; Trees ; }, abstract = {Utilization of computational approach in the study of social behaviour of animals is increasing and we attempted such an approach in our study of tree-dwelling bats. These bats live in highly dynamic fission-fusion societies that share multiple roosts in a common home range. The key behavioural component associated with complex and non-centralized decision-making processes in roost switching is swarming around potential locations in order to recruit members to the new roost. To understand roost switching dynamics of bat groups in their natural environment, we employed a computational model, the SkyBat, which is based on swarm algorithm, to model this process. In a simulated environment of this agent-based model, we replicated natural fission-fusion dynamics of the Leisler's bat, Nyctalus leisleri, groups according to predefined species and habitat parameters. Spatiotemporal patterns of swarming activity of agents were similar to bats. The number of simulated groups formed prior to sunrise, the mean number of individuals in groups and the roost height did not differ significantly from data on a local population of bats collected in the field. Thus, the swarm algorithm gave a basic framework of roost-switching, suggesting possible applications in the study of bat behaviour in rapidly changing environments as well as in the field of computer science.}, } @article {pmid33033218, year = {2020}, author = {Pandolfi, JM and Staples, TL and Kiessling, W}, title = {Increased extinction in the emergence of novel ecological communities.}, journal = {Science (New York, N.Y.)}, volume = {370}, number = {6513}, pages = {220-222}, doi = {10.1126/science.abb3996}, pmid = {33033218}, issn = {1095-9203}, mesh = {*Biodiversity ; Datasets as Topic ; *Extinction, Biological ; Genetic Speciation ; Introduced Species ; *Plankton ; Probability ; }, abstract = {Environmental change is transforming ecological assemblages into new configurations, resulting in novel communities. We developed a robust methodology to detect novel communities, examine patterns of emergence, and quantify probabilities of local demographic turnover in transitions to and from novel communities. Using a global dataset of Cenozoic marine plankton communities, we found that the probability of local extinction, origination, and emigration during transitions to a novel community increased two to four times that of background community changes. Although rare, novel communities were five times more likely than chance to shift into another novel state. For marine plankton communities at a 100,000-year time grain, novel communities were sensitive to further extinctions and substantial community change.}, } @article {pmid33033216, year = {2020}, author = {M Real, F and Haas, SA and Franchini, P and Xiong, P and Simakov, O and Kuhl, H and Schöpflin, R and Heller, D and Moeinzadeh, MH and Heinrich, V and Krannich, T and Bressin, A and Hartmann, MF and Wudy, SA and Dechmann, DKN and Hurtado, A and Barrionuevo, FJ and Schindler, M and Harabula, I and Osterwalder, M and Hiller, M and Wittler, L and Visel, A and Timmermann, B and Meyer, A and Vingron, M and Jiménez, R and Mundlos, S and Lupiáñez, DG}, title = {The mole genome reveals regulatory rearrangements associated with adaptive intersexuality.}, journal = {Science (New York, N.Y.)}, volume = {370}, number = {6513}, pages = {208-214}, pmid = {33033216}, issn = {1095-9203}, support = {R01 HG003988/HG/NHGRI NIH HHS/United States ; }, mesh = {Adaptation, Physiological/*genetics ; Animals ; Chromosome Inversion ; Datasets as Topic ; Female ; Fibroblast Growth Factor 9/*genetics ; Gene Expression Regulation ; Genome ; Mice ; Mice, Transgenic ; Moles/*genetics ; *Regulatory Elements, Transcriptional ; Sex Differentiation/*genetics ; Steroid 17-alpha-Hydroxylase/*genetics ; Tandem Repeat Sequences ; Testosterone/blood/genetics ; }, abstract = {Linking genomic variation to phenotypical traits remains a major challenge in evolutionary genetics. In this study, we use phylogenomic strategies to investigate a distinctive trait among mammals: the development of masculinizing ovotestes in female moles. By combining a chromosome-scale genome assembly of the Iberian mole, Talpa occidentalis, with transcriptomic, epigenetic, and chromatin interaction datasets, we identify rearrangements altering the regulatory landscape of genes with distinct gonadal expression patterns. These include a tandem triplication involving CYP17A1, a gene controlling androgen synthesis, and an intrachromosomal inversion involving the pro-testicular growth factor gene FGF9, which is heterochronically expressed in mole ovotestes. Transgenic mice with a knock-in mole CYP17A1 enhancer or overexpressing FGF9 showed phenotypes recapitulating mole sexual features. Our results highlight how integrative genomic approaches can reveal the phenotypic impact of noncoding sequence changes.}, } @article {pmid33032576, year = {2020}, author = {Diller, M and Johnson, E and Hicks, A and Hogan, WR}, title = {A realism-based approach to an ontological representation of symbiotic interactions.}, journal = {BMC medical informatics and decision making}, volume = {20}, number = {1}, pages = {258}, pmid = {33032576}, issn = {1472-6947}, support = {UL1 TR001427/TR/NCATS NIH HHS/United States ; U24 GM110707/GM/NIGMS NIH HHS/United States ; R01 GM101151/GM/NIGMS NIH HHS/United States ; }, mesh = {*Biological Ontologies ; Humans ; *Symbiosis ; }, abstract = {BACKGROUND: The symbiotic interactions that occur between humans and organisms in our environment have a tremendous impact on our health. Recently, there has been a surge in interest in understanding the complex relationships between the microbiome and human health and host immunity against microbial pathogens, among other things. To collect and manage data about these interactions and their complexity, scientists will need ontologies that represent symbiotic interactions as they occur in reality.

METHODS: We began with two papers that reviewed the usage of 'symbiosis' and related terms in the biology and ecology literature and prominent textbooks. We then analyzed several prominent standard terminologies and ontologies that contain representations of symbiotic interactions, to determine if they appropriately defined 'symbiosis' and related terms according to current scientific usage as identified by the review papers. In the process, we identified several subtypes of symbiotic interactions, as well as the characteristics that differentiate them, which we used to propose textual and axiomatic definitions for each subtype of interaction. To both illustrate how to use the ontological representations and definitions we created and provide additional quality assurance on key definitions, we carried out a referent tracking analysis and representation of three scenarios involving symbiotic interactions among organisms.

RESULTS: We found one definition of 'symbiosis' in an existing ontology that was consistent with the vast preponderance of scientific usage in biology and ecology. However, that ontology changed its definition during the course of our work, and discussions are ongoing. We present a new definition that we have proposed. We also define 34 subtypes of symbiosis. Our referent tracking analysis showed that it is necessary to define symbiotic interactions at the level of the individual, rather than at the species level, due to the complex nature in which organisms can go from participating in one type of symbiosis with one organism to participating in another type of symbiosis with a different organism.

CONCLUSION: As a result of our efforts here, we have developed a robust representation of symbiotic interactions using a realism-based approach, which fills a gap in existing biomedical ontologies.}, } @article {pmid33031625, year = {2020}, author = {Riginos, C and Crandall, ED and Liggins, L and Gaither, MR and Ewing, RB and Meyer, C and Andrews, KR and Euclide, PT and Titus, BM and Therkildsen, NO and Salces-Castellano, A and Stewart, LC and Toonen, RJ and Deck, J}, title = {Building a global genomics observatory: Using GEOME (the Genomic Observatories Metadatabase) to expedite and improve deposition and retrieval of genetic data and metadata for biodiversity research.}, journal = {Molecular ecology resources}, volume = {20}, number = {6}, pages = {1458-1469}, doi = {10.1111/1755-0998.13269}, pmid = {33031625}, issn = {1755-0998}, support = {DEB-1457848//Division of Environmental Biology/ ; OISE-1243541//Division of Environmental Biology/ ; }, mesh = {*Biodiversity ; *Databases, Nucleic Acid ; Ecology ; *Genomics ; Information Storage and Retrieval ; *Metadata ; *Research ; Workflow ; }, abstract = {Genetic data represent a relatively new frontier for our understanding of global biodiversity. Ideally, such data should include both organismal DNA-based genotypes and the ecological context where the organisms were sampled. Yet most tools and standards for data deposition focus exclusively either on genetic or ecological attributes. The Genomic Observatories Metadatabase (GEOME: geome-db.org) provides an intuitive solution for maintaining links between genetic data sets stored by the International Nucleotide Sequence Database Collaboration (INSDC) and their associated ecological metadata. GEOME facilitates the deposition of raw genetic data to INSDCs sequence read archive (SRA) while maintaining persistent links to standards-compliant ecological metadata held in the GEOME database. This approach facilitates findable, accessible, interoperable and reusable data archival practices. Moreover, GEOME enables data management solutions for large collaborative groups and expedites batch retrieval of genetic data from the SRA. The article that follows describes how GEOME can enable genuinely open data workflows for researchers in the field of molecular ecology.}, } @article {pmid33031489, year = {2021}, author = {Miyazawa, H and Osigus, HJ and Rolfes, S and Kamm, K and Schierwater, B and Nakano, H}, title = {Mitochondrial Genome Evolution of Placozoans: Gene Rearrangements and Repeat Expansions.}, journal = {Genome biology and evolution}, volume = {13}, number = {1}, pages = {}, pmid = {33031489}, issn = {1759-6653}, mesh = {Animals ; DNA, Mitochondrial/genetics ; *Evolution, Molecular ; Exons ; Gene Order ; *Gene Rearrangement ; *Genome, Mitochondrial ; Haplotypes ; Introns ; Mitochondria/*genetics ; Phylogeny ; Placozoa/*genetics ; RNA, Ribosomal ; RNA, Ribosomal, 16S ; RNA, Transfer ; }, abstract = {Placozoans, nonbilaterian animals with the simplest known metazoan bauplan, are currently classified into 20 haplotypes belonging to three genera, Polyplacotoma, Trichoplax, and Hoilungia. The latter two comprise two and five clades, respectively. In Trichoplax and Hoilungia, previous studies on six haplotypes belonging to four different clades have shown that their mtDNAs are circular chromosomes of 32-43 kb in size, which encode 12 protein-coding genes, 24 tRNAs, and two rRNAs. These mitochondrial genomes (mitogenomes) also show unique features rarely seen in other metazoans, including open reading frames (ORFs) of unknown function, and group I and II introns. Here, we report seven new mitogenomes, covering the five previously described haplotypes H2, H17, H19, H9, and H11, as well as two new haplotypes, H23 (clade III) and H24 (clade VII). The overall gene content is shared between all placozoan mitochondrial genomes, but genome sizes, gene orders, and several exon-intron boundaries vary among clades. Phylogenomic analyses strongly support a tree topology different from previous 16S rRNA analyses, with clade VI as the sister group to all other Hoilungia clades. We found small inverted repeats in all 13 mitochondrial genomes of the Trichoplax and Hoilungia genera and evaluated their distribution patterns among haplotypes. Because Polyplacotoma mediterranea (H0), the sister to the remaining haplotypes, has a small mitochondrial genome with few small inverted repeats and ORFs, we hypothesized that the proliferation of inverted repeats and ORFs substantially contributed to the observed increase in the size and GC content of the Trichoplax and Hoilungia mitochondrial genomes.}, } @article {pmid33031471, year = {2020}, author = {Galen, SC and Borner, J and Perkins, SL and Weckstein, JD}, title = {Phylogenomics from transcriptomic "bycatch" clarify the origins and diversity of avian trypanosomes in North America.}, journal = {PloS one}, volume = {15}, number = {10}, pages = {e0240062}, pmid = {33031471}, issn = {1932-6203}, mesh = {Animals ; Bayes Theorem ; Biological Evolution ; Birds/*genetics/parasitology ; Contig Mapping ; DNA Barcoding, Taxonomic ; DNA, Protozoan/chemistry/metabolism ; Databases, Factual ; Haplotypes ; Humans ; North America ; Phylogeny ; RNA, Ribosomal, 18S/chemistry/classification/metabolism ; *Transcriptome ; Trypanosoma/classification/*genetics/pathogenicity ; Trypanosoma cruzi/classification ; }, abstract = {The eukaryotic blood parasite genus Trypanosoma includes several important pathogens of humans and livestock, but has been understudied in wildlife broadly. The trypanosomes that infect birds are in particular need of increased attention, as these parasites are abundant and globally distributed, yet few studies have addressed their evolutionary origins and diversity using modern molecular and analytical approaches. Of specific interest are the deep evolutionary relationships of the avian trypanosomes relative to the trypanosome species that are pathogenic in humans, as well as their species level diversity in regions where they have been understudied such as North America. Here, we address these unresolved areas of study using phylogenomic data for two species of avian trypanosomes that were isolated as "bycatch" from host transcriptome assemblies, as well as a large 18S DNA barcode sequence dataset that includes 143 novel avian Trypanosoma 18S sequences from North America. Using a phylogenomic approach, we find that the avian trypanosomes are nested within a clade of primarily mammalian trypanosomes that includes the human pathogen Trypanosoma cruzi, and are paraphyletic with respect to the ruminant trypanosome Trypanosoma theileri. DNA barcode sequences showed that T. avium and an unidentified small, non-striated trypanosome that was morphologically similar to T. everetti are each represented by highly abundant and divergent 18S haplotypes in North America. Community-level sampling revealed that additional species-level Trypanosoma lineages exist in this region. We compared the newly sequenced DNA barcodes from North America to a global database, and found that avian Trypanosoma 18S haplotypes generally exhibited a marked lack of host specificity with at least one T. avium haplotype having an intercontinental distribution. This highly abundant T. avium haplotype appears to have a remarkably high dispersal ability and cosmopolitan capacity to evade avian host immune defenses, which warrant further study.}, } @article {pmid33031367, year = {2020}, author = {Kamiya, T and Greischar, MA and Schneider, DS and Mideo, N}, title = {Uncovering drivers of dose-dependence and individual variation in malaria infection outcomes.}, journal = {PLoS computational biology}, volume = {16}, number = {10}, pages = {e1008211}, pmid = {33031367}, issn = {1553-7358}, mesh = {Anemia/complications ; Animals ; Bayes Theorem ; Computational Biology ; Female ; *Host-Parasite Interactions ; *Malaria/complications/immunology/parasitology/physiopathology ; Mice ; Mice, Inbred C57BL ; Parasite Load ; Plasmodium chabaudi/pathogenicity/physiology ; }, abstract = {To understand why some hosts get sicker than others from the same type of infection, it is essential to explain how key processes, such as host responses to infection and parasite growth, are influenced by various biotic and abiotic factors. In many disease systems, the initial infection dose impacts host morbidity and mortality. To explore drivers of dose-dependence and individual variation in infection outcomes, we devised a mathematical model of malaria infection that allowed host and parasite traits to be linear functions (reaction norms) of the initial dose. We fitted the model, using a hierarchical Bayesian approach, to experimental time-series data of acute Plasmodium chabaudi infection across doses spanning seven orders of magnitude. We found evidence for both dose-dependent facilitation and debilitation of host responses. Most importantly, increasing dose reduced the strength of activation of indiscriminate host clearance of red blood cells while increasing the half-life of that response, leading to the maximal response at an intermediate dose. We also explored the causes of diverse infection outcomes across replicate mice receiving the same dose. Besides random noise in the injected dose, we found variation in peak parasite load was due to unobserved individual variation in host responses to clear infected cells. Individual variation in anaemia was likely driven by random variation in parasite burst size, which is linked to the rate of host cells lost to malaria infection. General host vigour in the absence of infection was also correlated with host health during malaria infection. Our work demonstrates that the reaction norm approach provides a useful quantitative framework for examining the impact of a continuous external factor on within-host infection processes.}, } @article {pmid33031193, year = {2020}, author = {Chen, C and Stock, C and Hoffmeister, M and Brenner, H}, title = {Self-Reported Lower Gastrointestinal Endoscopy Use and Changes in Colorectal Cancer Mortality Rates in European Countries.}, journal = {Clinical and translational gastroenterology}, volume = {11}, number = {10}, pages = {e00243}, pmid = {33031193}, issn = {2155-384X}, mesh = {Colonoscopy/*statistics & numerical data ; Colorectal Neoplasms/diagnosis/*mortality ; Early Detection of Cancer/methods/*statistics & numerical data ; Europe/epidemiology ; Female ; Humans ; Male ; Middle Aged ; Patient Acceptance of Health Care/*statistics & numerical data ; Self Report/statistics & numerical data ; }, abstract = {INTRODUCTION: To quantify the association of self-reported lower gastrointestinal endoscopy use measured in 2004/05 with colorectal cancer (CRC) mortality changes over 2004-2015 in Europe.

METHODS: An ecological analysis was performed using endoscopy utilization data from the Survey of Health, Aging, and Retirement in 11 European countries in 2004/05 and CRC mortality data from the World Health Organization Mortality Database over 2004-2015. Mortality trends were compared through annual mortality changes from joinpoint regression models. Cross-national variations in mortality trends with respect to endoscopy use were tested for statistical significance by negative binomial regression models.

RESULTS: The proportion of respondents who reported having had an endoscopy within 10 years varied widely across countries, from 6.1% to 25.1%. Large disparities in CRC mortality trends were also observed, with annual mortality change ranging from a decline of 3.3% to an increase of 0.9% for men and from a decline of 3.3% to a decline of 0.6% for women. Endoscopy uptake was negatively associated with the magnitude of annual mortality change over 2004-2015 (rate ratio for a 10-year mortality change per 10% higher endoscopy use, 0.88; 95% confidence interval, 0.82-0.94).

DISCUSSION: This analysis provides quantitative evidence on the contributions of endoscopy use to CRC mortality declines in European countries over the past decade. A considerable fraction of protection is likely to be delivered through endoscopic removal of adenomas and sessile serrated lesions. With many European countries having recently implemented CRC screening programs, an increase in endoscopy use and a subsequent reduction in CRC mortality would be expected.}, } @article {pmid33030635, year = {2020}, author = {Asefi, H and Zhang, Y and Lim, S and Maghrebi, M and Shahparvari, S}, title = {A multi-criteria decision support framework for municipal solid waste landfill siting: a case study of New South Wales (Australia).}, journal = {Environmental monitoring and assessment}, volume = {192}, number = {11}, pages = {682}, doi = {10.1007/s10661-020-08565-y}, pmid = {33030635}, issn = {1573-2959}, mesh = {Australia ; *Decision Support Techniques ; Environmental Monitoring ; New South Wales ; *Solid Waste ; Waste Disposal Facilities ; }, abstract = {Sanitary waste disposal and site selection for establishing landfills are challenging problems for environmental planners. This paper aims to take environmental, socio-economic, geological, geomorphological, hydrological and ecological factors into consideration to provide a decision support framework for landfill siting. Analytical hierarchy process (AHP) and Decision Making Trial and Evaluation Laboratory (DEMATEL) are coupled to develop an efficient multi-criteria decision-making method to be utilized in a Geographic Information System (GIS) environment for evaluating the suitability for landfill siting. As the first attempt to employ DEMATEL effectively in a landfill site selection problem, the proposed method is tested with landfill siting scenarios in New South Wales (NSW), Australia. Regional analysis is also performed to identify the potentially most suitable statistical divisions for landfill siting in NSW. The top two ranked zones covering 0.7% and 22% of the study area, respectively, are considered as the optimal areas for establishing landfills, while the bottom two ranked zones are not recommended for further consideration. Further detailed analysis is also conducted on the existing landfills, which shows that 1.0% and 37.0% of them are ranks 1 and 2, respectively. The scenario-based analysis implies that, among the contributing factors; geological and economic factors are highly important.}, } @article {pmid33028186, year = {2020}, author = {Fernando, PC and Mabee, PM and Zeng, E}, title = {Integration of anatomy ontology data with protein-protein interaction networks improves the candidate gene prediction accuracy for anatomical entities.}, journal = {BMC bioinformatics}, volume = {21}, number = {1}, pages = {442}, pmid = {33028186}, issn = {1471-2105}, support = {DBI-1062542//National Science Foundation/ ; NSF 0956049//National Science Foundation/ ; EPSCoR grant IIA-1355423//National Science Foundation/ ; OAC-1626516//National Science Foundation/ ; }, mesh = {Animals ; Area Under Curve ; Databases, Protein ; Gene Regulatory Networks ; Mice ; Phenotype ; Protein Interaction Mapping/*methods ; *Protein Interaction Maps ; ROC Curve ; User-Computer Interface ; Zebrafish/metabolism ; }, abstract = {BACKGROUND: Identification of genes responsible for anatomical entities is a major requirement in many fields including developmental biology, medicine, and agriculture. Current wet lab techniques used for this purpose, such as gene knockout, are high in resource and time consumption. Protein-protein interaction (PPI) networks are frequently used to predict disease genes for humans and gene candidates for molecular functions, but they are rarely used to predict genes for anatomical entities. Moreover, PPI networks suffer from network quality issues, which can be a limitation for their usage in predicting candidate genes. Therefore, we developed an integrative framework to improve the candidate gene prediction accuracy for anatomical entities by combining existing experimental knowledge about gene-anatomical entity relationships with PPI networks using anatomy ontology annotations. We hypothesized that this integration improves the quality of the PPI networks by reducing the number of false positive and false negative interactions and is better optimized to predict candidate genes for anatomical entities. We used existing Uberon anatomical entity annotations for zebrafish and mouse genes to construct gene networks by calculating semantic similarity between the genes. These anatomy-based gene networks were semantic networks, as they were constructed based on the anatomy ontology annotations that were obtained from the experimental data in the literature. We integrated these anatomy-based gene networks with mouse and zebrafish PPI networks retrieved from the STRING database and compared the performance of their network-based candidate gene predictions.

RESULTS: According to evaluations of candidate gene prediction performance tested under four different semantic similarity calculation methods (Lin, Resnik, Schlicker, and Wang), the integrated networks, which were semantically improved PPI networks, showed better performances by having higher area under the curve values for receiver operating characteristic and precision-recall curves than PPI networks for both zebrafish and mouse.

CONCLUSION: Integration of existing experimental knowledge about gene-anatomical entity relationships with PPI networks via anatomy ontology improved the candidate gene prediction accuracy and optimized them for predicting candidate genes for anatomical entities.}, } @article {pmid33025098, year = {2021}, author = {Castillo, A and Galtés, I and Crespo, S and Jordana, X}, title = {Technical note: preliminary insight into a new method for age-at-death estimation from the pubic symphysis.}, journal = {International journal of legal medicine}, volume = {135}, number = {3}, pages = {929-937}, pmid = {33025098}, issn = {1437-1596}, mesh = {Adult ; Age Determination by Skeleton/*methods ; Aged ; Aged, 80 and over ; Datasets as Topic ; Decision Trees ; Female ; Forensic Anthropology/*methods ; Humans ; Machine Learning ; Male ; Middle Aged ; Pubic Symphysis/*anatomy & histology/*physiology ; Spain ; }, abstract = {Age-at-death estimation methods are important in forensic anthropology. However, age assessment is problematic due to inter-individual variation. The subjectivity of visual scoring systems can affect the accuracy and reliability of methods as well. One of the most studied skeletal regions for age assessment is the pubic symphysis. Few studies on Spanish pubic symphysis collections have been conducted, making further research necessary as well as the sampling of more forensic skeletal collections. This study is a preliminary development of an age-at-death estimation method from the pubic symphysis based on a new simple scoring system. A documented late twentieth century skeletal collection (N = 29) and a twenty-first century forensic collection (N = 76) are used. Sixteen traits are evaluated, and a new trait (microgrooves) is described and evaluated for the first time in this study. All traits are scored in a binary manner (present or absent), thus reducing ambiguity and subjectivity. Several data sets are constructed based on different age intervals. Machine learning methods are employed to evaluate the scoring system's performance. The results show that microgrooves, macroporosity, beveling, lower extremity, ventral and dorsal margin decomposition, and lipping are the best preforming traits. The new microgroove trait proves to be a good age predictor. Reliable classification results are obtained for three age intervals (≤ 29, 30-69, ≥ 70). Older individuals are reliably classified with two age intervals (< 80, ≥ 80). The combination of binary attributes and machine learning algorithms is a promising tool for gaining objectivity in age-at-death assessment.}, } @article {pmid33024311, year = {2020}, author = {Martínez Martínez, J and Martinez-Hernandez, F and Martinez-Garcia, M}, title = {Single-virus genomics and beyond.}, journal = {Nature reviews. Microbiology}, volume = {18}, number = {12}, pages = {705-716}, pmid = {33024311}, issn = {1740-1534}, mesh = {Animals ; Aquatic Organisms ; Carbon Cycle ; Cell Culture Techniques ; Computational Biology/instrumentation/*methods ; Genetic Variation ; *Genome, Viral ; Humans ; *Metagenome ; Metagenomics/instrumentation/*methods ; Optical Tweezers ; Virion/*genetics/metabolism/ultrastructure ; Viruses/classification/*genetics/metabolism/ultrastructure ; }, abstract = {Viruses are extremely diverse and modulate important biological and ecological processes globally. However, much of viral diversity remains uncultured and yet to be discovered. Several powerful culture-independent tools, in particular metagenomics, have substantially advanced virus discovery. Among those tools is single-virus genomics, which yields sequenced reference genomes from individual sorted virus particles without the need for cultivation. This new method complements virus culturing and metagenomic approaches and its advantages include targeted investigation of specific virus groups and investigation of genomic microdiversity within viral populations. In this Review, we provide a brief history of single-virus genomics, outline how this emergent method has facilitated advances in virus ecology and discuss its current limitations and future potential. Finally, we address how this method may synergistically intersect with other single-virus and single-cell approaches.}, } @article {pmid33024126, year = {2020}, author = {Graham, C and Pakhomov, EA and Hunt, BPV}, title = {A salmon diet database for the North Pacific Ocean.}, journal = {Scientific data}, volume = {7}, number = {1}, pages = {332}, pmid = {33024126}, issn = {2052-4463}, mesh = {Animals ; Databases, Factual ; Diet/*veterinary ; Pacific Ocean ; *Salmon ; }, abstract = {The North Pacific Marine Salmon Diet Database is an open-access relational database built to centralize and make accessible salmon diet data through a standardized database structure. The initial data contribution contains 21,862 observations of salmon diet, and associated salmon biological parameters, prey biological parameters, and environmental data from the North Pacific Ocean. The data come from 907 unique spatial areas and mostly fall within two time periods, 1959-1969 and 1987-1997, during which there are more data available compared to other time periods. Data were extracted from 62 sources identified through a systematic literature review, targeting peer-reviewed and gray literature. The purpose of this database is to consolidate data into a common format to address gaps in our ecological understanding of the North Pacific Ocean, particularly with respect to salmon. This database can be used to address a variety of questions regarding salmon foraging, productivity, and marine survival. The North Pacific Marine Salmon Diet Database will continue to grow in the future as more data are digitized and become available.}, } @article {pmid33022194, year = {2020}, author = {Loxley, GM and Hooks, DO and Antonopoulos, A and Dell, A and Haslam, SM and Linklater, WL and Hurst, JL and Beynon, RJ}, title = {Vulpeculin: a novel and abundant lipocalin in the urine of the common brushtail possum, Trichosurus vulpecula.}, journal = {Open biology}, volume = {10}, number = {10}, pages = {200218}, pmid = {33022194}, issn = {2046-2441}, mesh = {Animals ; Biomarkers/urine ; Chromatography, Liquid ; Computational Biology/methods ; Databases, Chemical ; Databases, Genetic ; Gene Expression ; Lipocalins/*pharmacokinetics/*urine ; Mass Spectrometry/methods ; Phylogeny ; Polysaccharides ; Proteins/chemistry ; Proteinuria ; Trichosurus/*urine ; }, abstract = {Lipocalins are a family of secreted proteins. They are capable of binding small lipophilic compounds and have been extensively studied for their role in chemosignalling in rodent urine. Urine of the common brushtail possum (Trichosurus vulpecula) contains a prominent glycoprotein of 20 kDa, expressed in both sexes. We have isolated this protein and determined its primary sequence by mass spectrometry, including the use of metabolic labelling to resolve the leucine/isoleucine isobaric ambiguity. The protein sequence was identified as a lipocalin, and phylogenetic analysis grouped the protein with other marsupial lipocalin sequences in a phylogenetic clade distinct from established cross-species lipocalin sub-families. The pattern of expression in possum urine and the similarity in sequence and structure to other lipocalins suggests this protein may have a role in brushtail possum chemosignalling.}, } @article {pmid33020914, year = {2021}, author = {Smith, JE and Pinter-Wollman, N}, title = {Observing the unwatchable: Integrating automated sensing, naturalistic observations and animal social network analysis in the age of big data.}, journal = {The Journal of animal ecology}, volume = {90}, number = {1}, pages = {62-75}, doi = {10.1111/1365-2656.13362}, pmid = {33020914}, issn = {1365-2656}, mesh = {Animals ; *Big Data ; Female ; Social Behavior ; *Social Network Analysis ; }, abstract = {In the 4.5 decades since Altmann (1974) published her seminal paper on the methods for the observational study of behaviour, automated detection and analysis of social interaction networks have fundamentally transformed the ways that ecologists study social behaviour. Methodological developments for collecting data remotely on social behaviour involve indirect inference of associations, direct recordings of interactions and machine vision. These recent technological advances are improving the scale and resolution with which we can dissect interactions among animals. They are also revealing new intricacies of animal social interactions at spatial and temporal resolutions as well as in ecological contexts that have been hidden from humans, making the unwatchable seeable. We first outline how these technological applications are permitting researchers to collect exquisitely detailed information with little observer bias. We further recognize new emerging challenges from these new reality-mining approaches. While technological advances in automating data collection and its analysis are moving at an unprecedented rate, we urge ecologists to thoughtfully combine these new tools with classic behavioural and ecological monitoring methods to place our understanding of animal social networks within fundamental biological contexts.}, } @article {pmid33012235, year = {2020}, author = {Ferrari, G and Neukamm, J and Baalsrud, HT and Breidenstein, AM and Ravinet, M and Phillips, C and Rühli, F and Bouwman, A and Schuenemann, VJ}, title = {Variola virus genome sequenced from an eighteenth-century museum specimen supports the recent origin of smallpox.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {375}, number = {1812}, pages = {20190572}, pmid = {33012235}, issn = {1471-2970}, mesh = {Animals ; England ; *Evolution, Molecular ; *Genome, Viral ; History, 18th Century ; Humans ; Infant ; Museums ; Phylogeny ; Smallpox/*history ; Variola virus/*genetics ; }, abstract = {Smallpox, caused by the variola virus (VARV), was a highly virulent disease with high mortality rates causing a major threat for global human health until its successful eradication in 1980. Despite previously published historic and modern VARV genomes, its past dissemination and diversity remain debated. To understand the evolutionary history of VARV with respect to historic and modern VARV genetic variation in Europe, we sequenced a VARV genome from a well-described eighteenth-century case from England (specimen P328). In our phylogenetic analysis, the new genome falls between the modern strains and another historic strain from Lithuania, supporting previous claims of larger diversity in early modern Europe compared to the twentieth century. Our analyses also resolve a previous controversy regarding the common ancestor between modern and historic strains by confirming a later date around the seventeenth century. Overall, our results point to the benefit of historic genomes for better resolution of past VARV diversity and highlight the value of such historic genomes from around the world to further understand the evolutionary history of smallpox as well as related diseases. This article is part of the theme issue 'Insights into health and disease from ancient biomolecules'.}, } @article {pmid33011421, year = {2021}, author = {Sannigrahi, S and Pilla, F and Zhang, Q and Chakraborti, S and Wang, Y and Basu, B and Basu, AS and Joshi, PK and Keesstra, S and Roy, PS and Sutton, PC and Bhatt, S and Rahmat, S and Jha, S and Singh, LK}, title = {Examining the effects of green revolution led agricultural expansion on net ecosystem service values in India using multiple valuation approaches.}, journal = {Journal of environmental management}, volume = {277}, number = {}, pages = {111381}, doi = {10.1016/j.jenvman.2020.111381}, pmid = {33011421}, issn = {1095-8630}, mesh = {Agriculture ; Biodiversity ; *Conservation of Natural Resources ; *Ecosystem ; Humans ; India ; }, abstract = {Ecosystem Services (ESs) are bundles of natural processes and functions that are essential for human well-being, subsistence, and livelihoods. The 'Green Revolution' (GR) has substantial impact on the agricultural landscape and ESs in India. However, the effects of GR on ESs have not been adequately documented and analyzed. This leads to the main hypothesis of this work - 'the incremental trend of ESs in India is mainly prompted by GR led agricultural innovations that took place during 1960 - 1970'. The analysis was carried out through five successive steps. First, the spatiotemporal Ecosystem Service Values (ESVs) in Billion US$ for 1985, 1995, and 2005 were estimated using several value transfer approaches. Second, the sensitivity and elasticity of different ESs to land conversion were carried out using coefficient of sensitivity and coefficient of elasticity. Third, the Geographically Weighted Regression model was performed using five explanatory factors, i.e., total crop area, crop production, crop yield, net irrigated area, and cropping intensity, to explore the cumulative and individual effects of these driving factors on ESVs. Fourth, Multi-Layer Perceptron based Artificial Neural Network was employed to estimate the normalized importance of these explanatory factors. Fifth, simple and multiple linear regression modeling was done to assess the linear associations between the driving factors and the ESs. During the observation periods, cropland, forestland and water bodies contributed to 80%-90% of ESVs, followed by grassland, mangrove, wetland and urban built-up. In all three evaluation years, the highest estimated ESVs among the nine ES categories was provided by water regulation, followed by soil formation and soil-water retention, biodiversity maintenance, waste treatment, climate regulation, and greenhouse gas regulation. Among the five explanatory factors, total crop area, crop production, and net irrigated area showed strong positive associations with ESVs, while cropping intensity exhibited a negative association. Therefore, the study reveals a strong association between GR led agricultural expansion and ESVs in India. This study suggests that there should be an urgent need for formulation of rigorous ecosystem management strategies and policies to preserve ecological integrity and flow of uninterrupted ESs and to sustain human well-being.}, } @article {pmid33007173, year = {2020}, author = {Drake, TM and Docherty, AB and Harrison, EM and Quint, JK and Adamali, H and Agnew, S and Babu, S and Barber, CM and Barratt, S and Bendstrup, E and Bianchi, S and Villegas, DC and Chaudhuri, N and Chua, F and Coker, R and Chang, W and Crawshaw, A and Crowley, LE and Dosanjh, D and Fiddler, CA and Forrest, IA and George, PM and Gibbons, MA and Groom, K and Haney, S and Hart, SP and Heiden, E and Henry, M and Ho, LP and Hoyles, RK and Hutchinson, J and Hurley, K and Jones, M and Jones, S and Kokosi, M and Kreuter, M and MacKay, LS and Mahendran, S and Margaritopoulos, G and Molina-Molina, M and Molyneaux, PL and O'Brien, A and O'Reilly, K and Packham, A and Parfrey, H and Poletti, V and Porter, JC and Renzoni, E and Rivera-Ortega, P and Russell, AM and Saini, G and Spencer, LG and Stella, GM and Stone, H and Sturney, S and Thickett, D and Thillai, M and Wallis, T and Ward, K and Wells, AU and West, A and Wickremasinghe, M and Woodhead, F and Hearson, G and Howard, L and Baillie, JK and Openshaw, PJM and Semple, MG and Stewart, I and Jenkins, RG and , }, title = {Outcome of Hospitalization for COVID-19 in Patients with Interstitial Lung Disease. An International Multicenter Study.}, journal = {American journal of respiratory and critical care medicine}, volume = {202}, number = {12}, pages = {1656-1665}, pmid = {33007173}, issn = {1535-4970}, support = {G0701652/MRC_/Medical Research Council/United Kingdom ; RP-2016-07-012/DH_/Department of Health/United Kingdom ; MC_PC_19059/MRC_/Medical Research Council/United Kingdom ; IS-HPU-1112-10117/DH_/Department of Health/United Kingdom ; MR/V033441/1/MRC_/Medical Research Council/United Kingdom ; MR/S002782/1/MRC_/Medical Research Council/United Kingdom ; MR/S032304/1/MRC_/Medical Research Council/United Kingdom ; MC_PC_19025/MRC_/Medical Research Council/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; MR/S019669/1/MRC_/Medical Research Council/United Kingdom ; FS/18/13/33281/BHF_/British Heart Foundation/United Kingdom ; 109965/Z/15/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Aged ; Aged, 80 and over ; COVID-19/*epidemiology ; Comorbidity ; Disease Progression ; Europe/epidemiology ; Female ; Hospitalization/*statistics & numerical data ; Humans ; Lung Diseases, Interstitial/diagnosis/*epidemiology/therapy ; Male ; Middle Aged ; Retrospective Studies ; SARS-CoV-2 ; Tomography, X-Ray Computed ; }, abstract = {Rationale: The impact of coronavirus disease (COVID-19) on patients with interstitial lung disease (ILD) has not been established.Objectives: To assess outcomes in patients with ILD hospitalized for COVID-19 versus those without ILD in a contemporaneous age-, sex-, and comorbidity-matched population.Methods: An international multicenter audit of patients with a prior diagnosis of ILD admitted to the hospital with COVID-19 between March 1 and May 1, 2020, was undertaken and compared with patients without ILD, obtained from the ISARIC4C (International Severe Acute Respiratory and Emerging Infection Consortium Coronavirus Clinical Characterisation Consortium) cohort, admitted with COVID-19 over the same period. The primary outcome was survival. Secondary analysis distinguished idiopathic pulmonary fibrosis from non-idiopathic pulmonary fibrosis ILD and used lung function to determine the greatest risks of death.Measurements and Main Results: Data from 349 patients with ILD across Europe were included, of whom 161 were admitted to the hospital with laboratory or clinical evidence of COVID-19 and eligible for propensity score matching. Overall mortality was 49% (79/161) in patients with ILD with COVID-19. After matching, patients with ILD with COVID-19 had significantly poorer survival (hazard ratio [HR], 1.60; confidence interval, 1.17-2.18; P = 0.003) than age-, sex-, and comorbidity-matched controls without ILD. Patients with an FVC of <80% had an increased risk of death versus patients with FVC ≥80% (HR, 1.72; 1.05-2.83). Furthermore, obese patients with ILD had an elevated risk of death (HR, 2.27; 1.39-3.71).Conclusions: Patients with ILD are at increased risk of death from COVID-19, particularly those with poor lung function and obesity. Stringent precautions should be taken to avoid COVID-19 in patients with ILD.}, } @article {pmid33004393, year = {2020}, author = {Hasan, MM and Tasnim, F and Tariqujjaman, M and Ahmed, S and Cleary, A and Mamun, A}, title = {Examining the prevalence, correlates and inequalities of undiagnosed hypertension in Nepal: a population-based cross-sectional study.}, journal = {BMJ open}, volume = {10}, number = {10}, pages = {e037592}, pmid = {33004393}, issn = {2044-6055}, mesh = {Adult ; Blood Pressure ; Cross-Sectional Studies ; Female ; Humans ; *Hypertension/diagnosis/epidemiology ; Male ; Nepal/epidemiology ; Prevalence ; Risk Factors ; }, abstract = {OBJECTIVE: To examine the prevalence, correlates and sociodemographic inequalities of undiagnosed hypertension in Nepal.

DESIGN: This study used cross-sectional 2016 Nepal Demographic and Health Survey (NDHS) data. Undiagnosed patients with hypertension were defined as an NDHS respondent who was diagnosed as hypertensive (systolic blood pressure ≥140 mmHg and/or diastolic blood pressure ≥90 mmHg) during the survey, but never took any prescribed anti-hypertensive medicine to lower/control blood pressure and was never identified as having hypertension by a health professional prior the survey. Multiple binary logistic regression analysis was performed, and Concentration Index was measured.

SETTING: Nepal.

PARTICIPANTS: Adult patients with hypertension.

RESULTS: Among 3334 patients with hypertension, 50.4% remained undiagnosed during the survey in Nepal. Adjusted model reveals that patients who were male, belonged to households other than the highest wealth quintile, and lived in province 4 and province 5 were at higher risk of remaining undiagnosed for hypertension. Patients who were ≥65 years of age and were overweight/obese were at lower risk of remaining undiagnosed for hypertension. The poor-rich gap was 24.6 percentage points (Q1=64.1% vs Q5=39.6%) and poor:rich ratio was 1.6 (Q1/Q5=1.6) in the prevalence of undiagnosed hypertension. Undiagnosed hypertension was disproportionately higher among lower socioeconomic status groups (Concentration Index, C=-0.18). Inequalities in the prevalence of undiagnosed hypertension further varied across other geographic locations, including place of residence, ecological zones and administrative provinces.

CONCLUSIONS: Undiagnosed hypertension was highly prevalent in Nepal and there were substantial inequalities by sociodemographics and subnational levels. Increasing awareness, strengthening routine screening to diagnose hypertension at primary health service facilities and enactment of social health insurance policy may help Nepal to prevent and control this burden.}, } @article {pmid33004007, year = {2020}, author = {Hufnagel, DE and Hufford, MB and Seetharam, AS}, title = {SequelTools: a suite of tools for working with PacBio Sequel raw sequence data.}, journal = {BMC bioinformatics}, volume = {21}, number = {1}, pages = {429}, pmid = {33004007}, issn = {1471-2105}, support = {Grant number IOS-1744001//National Science Foundation (US)/ ; }, mesh = {Arabidopsis/genetics ; Benchmarking ; High-Throughput Nucleotide Sequencing/*methods/standards ; Quality Control ; *Software ; }, abstract = {BACKGROUND: PacBio sequencing is an incredibly valuable third-generation DNA sequencing method due to very long read lengths, ability to detect methylated bases, and its real-time sequencing methodology. Yet, hitherto no tool was available for analyzing the quality of, subsampling, and filtering PacBio data.

RESULTS: Here we present SequelTools, a command-line program containing three tools: Quality Control, Read Subsampling, and Read Filtering. The Quality Control tool quickly processes PacBio Sequel raw sequence data from multiple SMRTcells producing multiple statistics and publication-quality plots describing the quality of the data including N50, read length and count statistics, PSR, and ZOR. The Read Subsampling tool allows the user to subsample reads by one or more of the following criteria: longest subreads per CLR or random CLR selection. The Read Filtering tool provides options for normalizing data by filtering out certain low-quality scraps reads and/or by minimum CLR length. SequelTools is implemented in bash, R, and Python using only standard libraries and packages and is platform independent.

CONCLUSIONS: SequelTools is a program that provides the only free, fast, and easy-to-use quality control tool, and the only program providing this kind of read subsampling and read filtering for PacBio Sequel raw sequence data, and is available at https://github.com/ISUgenomics/SequelTools .}, } @article {pmid32999287, year = {2020}, author = {Grantz, KH and Meredith, HR and Cummings, DAT and Metcalf, CJE and Grenfell, BT and Giles, JR and Mehta, S and Solomon, S and Labrique, A and Kishore, N and Buckee, CO and Wesolowski, A}, title = {The use of mobile phone data to inform analysis of COVID-19 pandemic epidemiology.}, journal = {Nature communications}, volume = {11}, number = {1}, pages = {4961}, pmid = {32999287}, issn = {2041-1723}, support = {DP2 DA040244/DA/NIDA NIH HHS/United States ; DP2 LM013102/LM/NLM NIH HHS/United States ; R35 GM124715/GM/NIGMS NIH HHS/United States ; }, mesh = {Behavior ; Betacoronavirus ; COVID-19 ; *Cell Phone ; Coronavirus Infections/*epidemiology/prevention & control/transmission ; Databases, Factual ; Decision Making ; Humans ; Infection Control/methods ; *Mobile Applications ; *Pandemics ; Pneumonia, Viral/*epidemiology/prevention & control/transmission ; Public Health ; Risk Factors ; SARS-CoV-2 ; }, abstract = {The ongoing coronavirus disease 2019 (COVID-19) pandemic has heightened discussion of the use of mobile phone data in outbreak response. Mobile phone data have been proposed to monitor effectiveness of non-pharmaceutical interventions, to assess potential drivers of spatiotemporal spread, and to support contact tracing efforts. While these data may be an important part of COVID-19 response, their use must be considered alongside a careful understanding of the behaviors and populations they capture. Here, we review the different applications for mobile phone data in guiding and evaluating COVID-19 response, the relevance of these applications for infectious disease transmission and control, and potential sources and implications of selection bias in mobile phone data. We also discuss best practices and potential pitfalls for directly integrating the collection, analysis, and interpretation of these data into public health decision making.}, } @article {pmid32999073, year = {2020}, author = {Bawa, KS and Nawn, N and Chellam, R and Krishnaswamy, J and Mathur, V and Olsson, SB and Pandit, N and Rajagopal, P and Sankaran, M and Shaanker, RU and Shankar, D and Ramakrishnan, U and Vanak, AT and Quader, S}, title = {Opinion: Envisioning a biodiversity science for sustaining human well-being.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {117}, number = {42}, pages = {25951-25955}, pmid = {32999073}, issn = {1091-6490}, mesh = {*Biodiversity ; Conservation of Natural Resources/methods/*trends ; *Decision Making ; *Environmental Health ; *Global Health ; *Health Planning ; Humans ; }, } @article {pmid32996237, year = {2021}, author = {Barbera, P and Czech, L and Lutteropp, S and Stamatakis, A}, title = {SCRAPP: A tool to assess the diversity of microbial samples from phylogenetic placements.}, journal = {Molecular ecology resources}, volume = {21}, number = {1}, pages = {340-349}, pmid = {32996237}, issn = {1755-0998}, support = {//Klaus Tschira Stiftung/ ; }, mesh = {*Algorithms ; *Microbiota ; *Phylogeny ; Sequence Analysis, DNA ; *Software ; }, abstract = {Microbial ecology research is currently driven by the continuously decreasing cost of DNA sequencing and the improving accuracy of data analysis methods. One such analysis method is phylogenetic placement, which establishes the phylogenetic identity of the anonymous environmental sequences in a sample by means of a given phylogenetic reference tree. However, assessing the diversity of a sample remains challenging, as traditional methods do not scale well with the increasing data volumes and/or do not leverage the phylogenetic placement information. Here, we present scrapp, a highly parallel and scalable tool that uses a molecular species delimitation algorithm to quantify the diversity distribution over the reference phylogeny for a given phylogenetic placement of the sample. scrapp employs a novel approach to cluster phylogenetic placements, called placement space clustering, to efficiently perform dimensionality reduction, so as to scale on large data volumes. Furthermore, it uses the phylogeny-aware molecular species delimitation method mPTP to quantify diversity. We evaluated scrapp using both, simulated and empirical data sets. We use simulated data to verify our approach. Tests on an empirical data set show that scrapp-derived metrics can classify samples by their diversity-correlated features equally well or better than existing, commonly used approaches. scrapp is available at https://github.com/pbdas/scrapp.}, } @article {pmid32994391, year = {2020}, author = {Lim, JY and Svenning, JC and Göldel, B and Faurby, S and Kissling, WD}, title = {Frugivore-fruit size relationships between palms and mammals reveal past and future defaunation impacts.}, journal = {Nature communications}, volume = {11}, number = {1}, pages = {4904}, pmid = {32994391}, issn = {2041-1723}, mesh = {Animals ; Arecaceae/anatomy & histology/*physiology ; *Biological Coevolution ; Body Size/genetics ; *Conservation of Natural Resources ; Datasets as Topic ; Extinction, Biological ; Fruit/*anatomy & histology/genetics ; Herbivory/physiology ; Mammals/anatomy & histology/*physiology ; Organ Size/genetics ; Quantitative Trait Loci ; Seed Dispersal/physiology ; }, abstract = {Mammalian frugivores are critical seed dispersers, but many are under threat of extinction. Futhermore, the impact of past and future defaunation on plant assemblages has yet to be quantified at the global scale. Here, we integrate palm and mammalian frugivore trait and occurrence data and reveal a global positive relationship between fruit size and frugivore body size. Global variation in fruit size is better explained by present-day frugivore assemblages than by Late Pleistocene assemblages, suggesting ecological and evolutionary reorganization after end-Pleistocene extinctions, except in the Neotropics, where some large-fruited palm species may have outlived their main seed dispersers by thousands of years. Our simulations of frugivore extinction over the next 100 years suggest that the impact of defaunation will be highest in the Old World tropics, and an up to 4% assemblage-level decrease in fruit size would be required to maintain the global body size-fruit size relationship. Overall, our results suggest that while some palm species may be able to keep pace with future defaunation through evolutionary changes in fruit size, large-fruited species may be especially vulnerable to continued defaunation.}, } @article {pmid32994275, year = {2020}, author = {Fan, H and Zhang, Y and Zhang, J and Yao, Q and Song, Y and Shen, Q and Lin, J and Gao, Y and Wang, X and Zhang, L and Zhang, Y and Liu, P and Zhao, J and Cui, Q and Li, JZ and Chang, Y}, title = {Cold-Inducible Klf9 Regulates Thermogenesis of Brown and Beige Fat.}, journal = {Diabetes}, volume = {69}, number = {12}, pages = {2603-2618}, doi = {10.2337/db19-1153}, pmid = {32994275}, issn = {1939-327X}, mesh = {Adipose Tissue, Beige/*physiology ; Adipose Tissue, Brown/*physiology ; Adrenergic beta-3 Receptor Agonists/metabolism ; Animals ; Blood Glucose ; *Cold Temperature ; Energy Metabolism ; Gene Expression Regulation/physiology ; Glucose/metabolism ; Kruppel-Like Transcription Factors/genetics/*metabolism ; Lipid Metabolism ; Male ; Mice ; Mice, Transgenic ; Oxygen Consumption ; Thermogenesis/*physiology ; }, abstract = {Promoting development and function of brown and beige fat may represent an attractive treatment of obesity. In the current study, we show that fat Klf9 expression is markedly induced by cold exposure and a β-adrenergic agonist. Moreover, Klf9 expression levels in human white adipose tissue (WAT) are inversely correlated with adiposity, and Klf9 overexpression in primary fat cells stimulates cellular thermogenesis, which is Ucp1 dependent. Fat-specific Klf9 transgenic mice gain less weight and have smaller fat pads due to increased thermogenesis of brown and beige fat. Moreover, Klf9 transgenic mice displayed lower fasting blood glucose levels and improved glucose tolerance and insulin sensitivity under the high-fat diet condition. Conversely, Klf9 mutation in brown adipocytes reduces the expression of thermogenic genes, causing a reduction in cellular respiration. Klf9-mutant mice exhibited obesity and cold sensitivity due to impairments in the thermogenic function of fat. Finally, fat Klf9 deletion inhibits the β3 agonist-mediated induction of WAT browning and brown adipose tissue thermogenesis. Mechanistically, cold-inducible Klf9 stimulates expression of Pgc1α, a master regulator of fat thermogenesis, by a direct binding to its gene promoter region, subsequently promoting energy expenditure. The current study reveals a critical role for KLF9 in mediating thermogenesis of brown and beige fat.}, } @article {pmid32991214, year = {2020}, author = {Beckman, RA and Kareva, I and Adler, FR}, title = {How Should Cancer Models Be Constructed?.}, journal = {Cancer control : journal of the Moffitt Cancer Center}, volume = {27}, number = {1}, pages = {1073274820962008}, pmid = {32991214}, issn = {1526-2359}, support = {U54 CA209978/CA/NCI NIH HHS/United States ; }, mesh = {*Biological Evolution ; *Game Theory ; Humans ; *Models, Biological ; Neoplasms/genetics/*metabolism/*pathology ; Population Dynamics ; Tumor Microenvironment ; }, abstract = {Choosing and optimizing treatment strategies for cancer requires capturing its complex dynamics sufficiently well for understanding but without being overwhelmed. Mathematical models are essential to achieve this understanding, and we discuss the challenge of choosing the right level of complexity to address the full range of tumor complexity from growth, the generation of tumor heterogeneity, and interactions within tumors and with treatments and the tumor microenvironment. We discuss the differences between conceptual and descriptive models, and compare the use of predator-prey models, evolutionary game theory, and dynamic precision medicine approaches in the face of uncertainty about mechanisms and parameter values. Although there is of course no one-size-fits-all approach, we conclude that broad and flexible thinking about cancer, based on combined modeling approaches, will play a key role in finding creative and improved treatments.}, } @article {pmid32989148, year = {2020}, author = {Li, R and Chen, B and Zhang, T and Ren, Z and Song, Y and Xiao, Y and Hou, L and Cai, J and Xu, B and Li, M and Chan, KKY and Tu, Y and Yang, M and Yang, J and Liu, Z and Shen, C and Wang, C and Xu, L and Liu, Q and Bao, S and Zhang, J and Bi, Y and Bai, Y and Deng, K and Zhang, W and Huang, W and Whittington, JD and Stenseth, NC and Guan, D and Gong, P and Xu, B}, title = {Global COVID-19 pandemic demands joint interventions for the suppression of future waves.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {117}, number = {42}, pages = {26151-26157}, pmid = {32989148}, issn = {1091-6490}, support = {MC_PC_19012/MRC_/Medical Research Council/United Kingdom ; MR/R015600/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Betacoronavirus ; COVID-19 ; Climate ; Communicable Disease Control/*methods ; Communicable Diseases, Emerging/epidemiology/*prevention & control/transmission ; Coronavirus Infections/epidemiology/*prevention & control/transmission ; Disease Transmission, Infectious/*prevention & control ; Forecasting ; Global Health/*trends ; Humans ; International Cooperation ; Models, Theoretical ; Pandemics/*prevention & control ; Pneumonia, Viral/epidemiology/*prevention & control/transmission ; SARS-CoV-2 ; Travel ; }, abstract = {Emerging evidence suggests a resurgence of COVID-19 in the coming years. It is thus critical to optimize emergency response planning from a broad, integrated perspective. We developed a mathematical model incorporating climate-driven variation in community transmissions and movement-modulated spatial diffusions of COVID-19 into various intervention scenarios. We find that an intensive 8-wk intervention targeting the reduction of local transmissibility and international travel is efficient and effective. Practically, we suggest a tiered implementation of this strategy where interventions are first implemented at locations in what we call the Global Intervention Hub, followed by timely interventions in secondary high-risk locations. We argue that thinking globally, categorizing locations in a hub-and-spoke intervention network, and acting locally, applying interventions at high-risk areas, is a functional strategy to avert the tremendous burden that would otherwise be placed on public health and society.}, } @article {pmid32987143, year = {2020}, author = {Glowacki, L}, title = {The emergence of locally adaptive institutions: Insights from traditional social structures of East African pastoralists.}, journal = {Bio Systems}, volume = {198}, number = {}, pages = {104257}, doi = {10.1016/j.biosystems.2020.104257}, pmid = {32987143}, issn = {1872-8324}, mesh = {*Adaptation, Psychological ; Africa, Eastern ; Animal Husbandry/methods ; *Community Networks ; *Community-Institutional Relations ; Farmers/*psychology/statistics & numerical data ; Female ; Humans ; Male ; Models, Theoretical ; Problem Solving ; *Resilience, Psychological ; Social Behavior ; Social Conditions ; Social Environment ; }, abstract = {Humans inhabit the widest range of ecological and social niches of any mammal. Yet each ecological and social environment presents a set of challenges that we must solve in order to successfully inhabit it. We are able to do so by building institutions that can flexibly respond to changing circumstances. Institutions that solve adaptive challenges necessary for human sociality, such as how to resolve conflicts, find mates, and extract and distribute resources, are termed locally adaptive institutions. The design of locally adaptive institutions promotes coordination and cooperation among unrelated individuals, reflecting the constraints of the particular ecological and social challenges to which they are responsive. Institutions generally are enabled by a suite of social and psychological mechanisms, including norm compliance, self-interested design, selective imitation, and cultural group selection among others. The development of locally adaptive institutions are likely to be especially shaped by self-interested design in which agents are sensitive to the payoffs from various norms and choose to enforce and follow those which they anticipate to be most beneficial to themselves. Exogenous shocks, including the advent of material and cultural technologies, population pressures, or even group conflict can contribute to the modification of existing social institutions and the development of new social structures. Using several case examples from traditional east African pastoralist societies, I illustrate how ecological and social pressures shape the development of social norms that underlie locally adaptive social institutions and facilitate continued cooperation in the face of change at scales ranging from local to global.}, } @article {pmid32986829, year = {2021}, author = {Lyu, C and Chen, T and Qiang, B and Liu, N and Wang, H and Zhang, L and Liu, Z}, title = {CMNPD: a comprehensive marine natural products database towards facilitating drug discovery from the ocean.}, journal = {Nucleic acids research}, volume = {49}, number = {D1}, pages = {D509-D515}, pmid = {32986829}, issn = {1362-4962}, mesh = {Aquatic Organisms/*chemistry ; Biological Products/*chemistry ; *Databases, Factual ; *Drug Discovery ; *Oceans and Seas ; Phylogeny ; Search Engine ; User-Computer Interface ; }, abstract = {Marine organisms are expected to be an important source of inspiration for drug discovery after terrestrial plants and microorganisms. Despite the remarkable progress in the field of marine natural products (MNPs) chemistry, there are only a few open access databases dedicated to MNPs research. To meet the growing demand for mining and sharing for MNPs-related data resources, we developed CMNPD, a comprehensive marine natural products database based on manually curated data. CMNPD currently contains more than 31 000 chemical entities with various physicochemical and pharmacokinetic properties, standardized biological activity data, systematic taxonomy and geographical distribution of source organisms, and detailed literature citations. It is an integrated platform for structure dereplication (assessment of novelty) of (marine) natural products, discovery of lead compounds, data mining of structure-activity relationships and investigation of chemical ecology. Access is available through a user-friendly web interface at https://www.cmnpd.org. We are committed to providing a free data sharing platform for not only professional MNPs researchers but also the broader scientific community to facilitate drug discovery from the ocean.}, } @article {pmid32986700, year = {2020}, author = {Shan, Y and Wang, X and Wang, Z and Liang, L and Li, J and Sun, J}, title = {The pattern and mechanism of air pollution in developed coastal areas of China: From the perspective of urban agglomeration.}, journal = {PloS one}, volume = {15}, number = {9}, pages = {e0237863}, pmid = {32986700}, issn = {1932-6203}, mesh = {Air Pollutants/analysis ; Air Pollution/*analysis ; Algorithms ; China ; *Ecosystem ; Factor Analysis, Statistical ; *Geographic Information Systems ; Gross Domestic Product ; Models, Theoretical ; Particle Size ; Particulate Matter/analysis ; Time Factors ; *Urbanization ; }, abstract = {The green development of coastal urban agglomerations, which are strategic core areas of national economic growth in China, has become a major focus of both academics and government agencies. In this paper, China's coastal urban agglomeration is taken as the research area, aiming at the serious air pollution problem of coastal urban agglomeration, geographic information system (ArcGIS10.2) spatial analysis and the spatial Dubin model were applied to National Aeronautics and Space Administration atmospheric remote sensing image inversion fine particulate matter (PM2.5) data from 2010-2016 to reveal the temporal and spatial evolution characteristics and Influence mechanism of PM2.5 in China's coastal urban agglomerations, with a view to providing a reference value for coordinating air pollution in the coastal cities of the world. From 2010-2016, the PM2.5 concentration in China's coastal urban agglomerations decreased as a whole, and large spatial differences in PM2.5 concentration were observed in China's coastal urban agglomerations; the core high-pollution areas were the Beijing-Tianjin-Hebei, Shandong Peninsula, and Yangtze River Delta urban agglomerations. Large spatial differences in PM2.5 concentration were also observed within individual urban agglomerations, with higher PM2.5 concentrations found in the northern parts of the urban agglomerations. Significant spatial autocorrelation and spatial heterogeneity were observed among PM2.5-polluted cities in China's coastal urban agglomerations. The northern coastal urban agglomerations formed a relatively stable and continuous high-pollution zone. The spatial Dubin model was used to analyze the driving factors of PM2.5 pollution in coastal urban agglomerations. Together, meteorological, socioeconomic, pollution source, and ecological factors affected the spatial characteristics of PM2.5 pollution during the study period, and the overall effect was a mixed effect with significant spatial variation. Among them, meteorological factors were the greatest driver of PM2.5 pollution. In the short term, the rapid increase in population density, industrial emissions, industrial energy consumption, and total traffic emissions were the important driving factors of PM2.5 pollution in the coastal urban agglomerations of China.}, } @article {pmid32986250, year = {2021}, author = {Romero-López, JP and Carnalla-Cortés, M and Pacheco-Olvera, DL and Ocampo-Godínez, JM and Oliva-Ramírez, J and Moreno-Manjón, J and Bernal-Alferes, B and López-Olmedo, N and García-Latorre, E and Domínguez-López, ML and Reyes-Sandoval, A and Jiménez-Zamudio, L}, title = {A bioinformatic prediction of antigen presentation from SARS-CoV-2 spike protein revealed a theoretical correlation of HLA-DRB1*01 with COVID-19 fatality in Mexican population: An ecological approach.}, journal = {Journal of medical virology}, volume = {93}, number = {4}, pages = {2029-2038}, pmid = {32986250}, issn = {1096-9071}, mesh = {*Antigen Presentation ; *COVID-19/immunology/mortality ; Computational Biology ; Epitopes, T-Lymphocyte/immunology ; Genetic Variation ; HLA-DRB1 Chains/*immunology ; Hospitalization ; Humans ; Mexico ; Protein Structure, Tertiary ; SARS-CoV-2/immunology ; Spike Glycoprotein, Coronavirus/*immunology ; }, abstract = {SARS-CoV-2 infection is causing a pandemic disease that is reflected in challenging public health problems worldwide. Human leukocyte antigen (HLA)-based epitope prediction and its association with disease outcomes provide an important base for treatment design. A bioinformatic prediction of T cell epitopes and their restricted HLA Class I and II alleles was performed to obtain immunogenic epitopes and HLA alleles from the spike protein of the severe acute respiratory syndrome coronavirus 2 virus. Also, a correlation with the predicted fatality rate of hospitalized patients in 28 states of Mexico was done. Here, we describe a set of 10 highly immunogenic epitopes, together with different HLA alleles that can efficiently present these epitopes to T cells. Most of these epitopes are located within the S1 subunit of the spike protein, suggesting that this area is highly immunogenic. A statistical negative correlation was found between the frequency of HLA-DRB1*01 and the fatality rate in hospitalized patients in Mexico.}, } @article {pmid32977729, year = {2021}, author = {Fornasier-Santos, C and Millet, GP and Stridgeon, P and Brocherie, F and Girard, O and Nottin, S}, title = {How does playing position affect fatigue-induced changes in high-intensity locomotor and micro-movements patterns during professional rugby union games?.}, journal = {European journal of sport science}, volume = {21}, number = {10}, pages = {1364-1374}, doi = {10.1080/17461391.2020.1829715}, pmid = {32977729}, issn = {1536-7290}, mesh = {Acceleration ; Adult ; Athletic Performance/*physiology ; Football/*physiology ; Geographic Information Systems ; Humans ; Male ; Micro-Electrical-Mechanical Systems ; *Muscle Fatigue ; Running/physiology ; }, abstract = {AbstractWe questioned whether changes in high-intensity locomotor and micro-movements patterns between the first and second part of each half depend on playing position in the 2014-2015 European rugby union championship winning team. Thirty-three rugby players were grouped according to five playing positions. Players were equipped with micro-electromechanical system including a GPS sampling at 10 Hz and high temporal resolution micro-sensors during 17 Top14 and 7 European games. High-speed movements (HSM), high-intensity accelerations (HIA), repeated high-intensity efforts (RHIE), and high-intensity micro-movements (HIMM) were subsequently compared between four 20-min game periods. No significant group × time interactions were observed for any locomotor variables (p > 0.283). Irrespectively of playing position, the number of HSM (p = 0.019), decreased from 0-20 min to 60-80 min as well as from 40-60 to 60-80 min (p < 0.001) with HIA (p = 0.020) and RHIE (p < 0.001). Significant group × time interaction was found for HIMM (p = 0.03) with a significant decrease observed in back row forwards from 0-20 to 60-80 min periods (-17.5%; ES = 0.6; p = 0.031). In elite rugby union, fatigue-induced changes during the last 20 min are independent from playing positions in high-intensity locomotor patterns in contrary to HIMM. Training drills that include specific RHIE (high-speed and HIA efforts) may be useful to postpone match-related fatigue.}, } @article {pmid32975240, year = {2020}, author = {Arranz Izquierdo, J and Boronat Moreiro, MA and Zaforteza Dezcallar, M and Ripoll Amengual, J and Roca Casas, A and Carandell Jäger, E and Ballester Camps, A and Llobera Cánaves, J}, title = {[Evolution of the outpatient antibiotic prescription between 2012 and 2018. Characteristics of the ABPresclín platform created for the analysis of antibiotic prescription in the health service of the Balearic Islands.].}, journal = {Revista espanola de salud publica}, volume = {94}, number = {}, pages = {}, pmid = {32975240}, issn = {2173-9110}, mesh = {Adult ; Aged, 80 and over ; Anti-Bacterial Agents/*therapeutic use ; Databases, Factual ; Drug Prescriptions ; Female ; Geography ; *Health Services ; Health Services Research ; Humans ; Male ; Middle Aged ; *Outpatients ; *Practice Patterns, Physicians' ; Prescriptions ; Primary Health Care/organization & administration ; Respiratory Tract Infections/*drug therapy/epidemiology ; Spain ; }, abstract = {OBJECTIVE: One of the fist lines of action of the National Plan against Antibiotic Resistance (PRAN) is to monitor the use of antibiotics as a fundamental basis for the fight against resistance. In order to know the antibiotic prescription habits, we pretended to describe the outpatient prescription of systemic antibiotics in the Balearic Islands through exploitation of ABPresclín database.

METHODS: It was an ecological descriptive study of the electronic outpatient prescriptions of systemic antibiotics of the Health Service of the Balearic Islands from 2012 to 2018. Combining the prescription with population information data by year and geographical area, prescription rates were obtained per 1,000 person, distributed by professional, health centres, geographical areas: distribution per patient characteristics, type of antibiotics and associated diagnoses.

RESULTS: 3,517,101 prescriptions are analyzed with an average prescription period (TPp) per 1,000 person-years of 472.1. A quarter of the population received at least one prescription of antibiotics. TPp was higher in over 80 years (899.0) and in women (553.4). 68.9% of the prescription was made in primary care (AP) and 17.9% in out-of-hours settings. TPp in AP was 333.1, varying from 192.3 to 527.0, according to basic health areas. The TPp of the most commonly used antibiotics was: amoxicillin/clavulanic (143), amoxicillin (95.9), azithromycin (54.5), fosfomycin (41.5) and ciprofloxacin (29.7). The main associated diagnoses were: lower respiratory infections (16.5%), urinary infections (15%), non-infectious (15%), tonsillitis (14.3%) and upper respiratory infections (13%).

CONCLUSIONS: Balearic Islands have a relatively low antibiotic prescription rate with a marked variability between prescribers. Amoxicillin/clavulanic was the most prescribed antibiotic, with an increase in azithromycin. Respiratory infections were the main reason for prescription. ABPresclín is useful to promote better use of antibiotics.}, } @article {pmid32972990, year = {2020}, author = {Bush, ER and Whytock, RC and Bahaa-El-Din, L and Bourgeois, S and Bunnefeld, N and Cardoso, AW and Dikangadissi, JT and Dimbonda, P and Dimoto, E and Edzang Ndong, J and Jeffery, KJ and Lehmann, D and Makaga, L and Momboua, B and Momont, LRW and Tutin, CEG and White, LJT and Whittaker, A and Abernethy, K}, title = {Long-term collapse in fruit availability threatens Central African forest megafauna.}, journal = {Science (New York, N.Y.)}, volume = {370}, number = {6521}, pages = {1219-1222}, doi = {10.1126/science.abc7791}, pmid = {32972990}, issn = {1095-9203}, support = {679651/ERC_/European Research Council/International ; }, mesh = {Africa, Central ; Animals ; Datasets as Topic ; *Elephants ; *Famine ; Forests ; Fruit/*growth & development ; Gabon ; Parks, Recreational ; Reproduction ; Trees/growth & development ; }, abstract = {Afrotropical forests host much of the world's remaining megafauna, although these animals are confined to areas where direct human influences are low. We used a rare long-term dataset of tree reproduction and a photographic database of forest elephants to assess food availability and body condition of an emblematic megafauna species at Lopé National Park, Gabon. Our analysis reveals an 81% decline in fruiting over a 32-year period (1986-2018) and an 11% decline in body condition of fruit-dependent forest elephants from 2008 to 2018. Fruit famine in one of the last strongholds for African forest elephants should raise concern about the ability of this species and other fruit-dependent megafauna to persist in the long term, with potential consequences for broader ecosystem and biosphere functioning.}, } @article {pmid32972085, year = {2020}, author = {Medo, A and Nishizawa, H and Yokoyama, A and Kume, M and Mitsunaga, Y and Arai, N and Yamane, H and Ikeya, K and Viputhanumas, T and Mitamura, H}, title = {Gut Morphometry Represents Diet Preference to Indigestible Materials in the Largest Freshwater Fish, Mekong Giant Catfish (Pangasianodon gigas).}, journal = {Zoological science}, volume = {37}, number = {5}, pages = {444-449}, doi = {10.2108/zs200047}, pmid = {32972085}, issn = {0289-0003}, mesh = {Animals ; Catfishes/*anatomy & histology/physiology ; Diet/*veterinary ; Digestion/*physiology ; Gastrointestinal Tract/*anatomy & histology ; Species Specificity ; }, abstract = {The Mekong giant catfish Pangasianodon gigas is one of the largest freshwater fish, measuring up to 3 m in total length. This study was designed to determine the feeding habits of P. gigas to better understand how the fish achieve their large body size. We compared the relationship between gut length (GL) and total length (TL) among related species in superfamily Bagroidea, order Siluriformes (Pangasianodon hypophthalmus and Hemibagrus nemurus) in the Kaeng Krachan reservoir, Thailand. The mean relative gut length (RGL = GL / TL) of P. gigas was 3.50, showing that they have relatively long guts, with values more similar to those of omnivorous P. hypophthalmus (RGL = 3.70) than to those of carnivorous H. nemurus (RGL = 0.92). In the allometric relationship (i.e., log10 GL = log10 a + b log10 TL), the slope close to 1 for P. gigas (b = 1.07) has been widely observed in carnivores, while P. gigas has a greater intercept of the linear equation than P. hypophthalmus and H. nemurus, resulting in a similar GL of P. gigas to omnivorous P. hypophthalmus at approximately 35 cm in TL. Moreover, GL of P. gigas at 150 to 250 cm in TL showed great variations (RGL = 1.35-6.32). The variation in RGL for P. gigas seemed to result from a poor nutritional state. In conclusion, P. gigas is suggested to feed on indigestible materials such as plants, algae, and sediments, and potentially experience fasting in a reservoir.}, } @article {pmid32970758, year = {2020}, author = {Lötsch, J and Ultsch, A}, title = {A non-parametric effect-size measure capturing changes in central tendency and data distribution shape.}, journal = {PloS one}, volume = {15}, number = {9}, pages = {e0239623}, pmid = {32970758}, issn = {1932-6203}, mesh = {*Artificial Intelligence ; Behavioral Research/*methods ; Biostatistics/*methods ; Data Interpretation, Statistical ; Humans ; }, abstract = {MOTIVATION: Calculating the magnitude of treatment effects or of differences between two groups is a common task in quantitative science. Standard effect size measures based on differences, such as the commonly used Cohen's, fail to capture the treatment-related effects on the data if the effects were not reflected by the central tendency. The present work aims at (i) developing a non-parametric alternative to Cohen's d, which (ii) circumvents some of its numerical limitations and (iii) involves obvious changes in the data that do not affect the group means and are therefore not captured by Cohen's d.

RESULTS: We propose "Impact" as a novel non-parametric measure of effect size obtained as the sum of two separate components and includes (i) a difference-based effect size measure implemented as the change in the central tendency of the group-specific data normalized to pooled variability and (ii) a data distribution shape-based effect size measure implemented as the difference in probability density of the group-specific data. Results obtained on artificial and empirical data showed that "Impact"is superior to Cohen's d by its additional second component in detecting clearly visible effects not reflected in central tendencies. The proposed effect size measure is invariant to the scaling of the data, reflects changes in the central tendency in cases where differences in the shape of probability distributions between subgroups are negligible, but captures changes in probability distributions as effects and is numerically stable even if the variances of the data set or its subgroups disappear.

CONCLUSIONS: The proposed effect size measure shares the ability to observe such an effect with machine learning algorithms. Therefore, the proposed effect size measure is particularly well suited for data science and artificial intelligence-based knowledge discovery from big and heterogeneous data.}, } @article {pmid32970744, year = {2020}, author = {Gut, U}, title = {Assessing site signal preservation in reference chronologies for dendro-provenancing.}, journal = {PloS one}, volume = {15}, number = {9}, pages = {e0239425}, pmid = {32970744}, issn = {1932-6203}, mesh = {Algorithms ; Databases, Factual ; Norway ; Picea/*growth & development/physiology ; Switzerland ; Time Factors ; }, abstract = {Regional differences in tree growth can be used to approximate the geographical provenance of ring-width series ('dendro-provenancing'). This method relies on cross-dated ring-width series (reference chronologies) that are thought to represent the radial growth signal of trees in a given region. Reference chronologies are often established from ring-width series of living tree populations. Frequently, they are too short to allow for investigating the provenance of historical wood. Thus, references are extended by ring-width series from buildings and art-historical objects that exhibit best matching growth patterns with the living tree references. Yet, series from other provenances may erroneously be included. Thereby the local or regional growth signal of the references is progressively contaminated, but this has received little attention to date. I investigate this contamination risk using a simulation approach that allows for generating pseudo site chronologies that preserve the relevant statistical properties of the real site chronologies. While the exact provenance of historical wood is unknown, for simulated ring-width series the provenance is unambiguous. Hence, pseudo reference chronologies may be established while monitoring the signal mixture. Specifically, 15 site chronologies of Norway spruce (Picea abies (L.) H. Karst.) from northeastern Switzerland were used to generate 15 pseudo site growth signals that span 1000 years. The simulation demonstrates that quasi uncontaminated references can be established in ideal circumstances for the study area. However, the thresholds for the similarity in between-series correlation must be very high. Even then, contaminated pseudo references occurred in rare cases during the simulation. Yet, elevation-specific pseudo references were established with lower thresholds. Simulation currently offers the only approach for assessing the contamination risk of reference chronologies, and it allows for elucidating the conditions under which acceptable levels of contamination can be guaranteed. Therefore, the present approach paves the way towards a practical simulation tool for dendro-provenancing.}, } @article {pmid32969495, year = {2020}, author = {Wheatley, R and Pavlic, TP and Levy, O and Wilson, RS}, title = {Habitat features and performance interact to determine the outcomes of terrestrial predator-prey pursuits.}, journal = {The Journal of animal ecology}, volume = {89}, number = {12}, pages = {2958-2971}, doi = {10.1111/1365-2656.13353}, pmid = {32969495}, issn = {1365-2656}, mesh = {Animals ; *Ecosystem ; *Predatory Behavior ; }, abstract = {Animals are responsive to predation risk, often seeking safer habitats at the cost of foraging rewards. Although previous research has examined how habitat features affect detection by predators, little is known about how the interaction of habitat features, sensory cues and physical performance capabilities affect prey escape performance once detected. To investigate how specific habitat features affect predation risk, we developed an individual-based model of terrestrial predator-prey pursuits in habitats with programmable features. We ran simulations varying the relative performance capabilities of predator and prey as well as the availability and abundance of refuges and obstacles in the habitat. Prey were more likely to avoid detection in complex habitats containing a higher abundance of obstacles; however, if detected, prey escape probability was dependent on both the abundance of refuges and obstacles and the predator's relative performance capabilities. Our model accurately predicted the relative escape success for impala escaping from cheetah in open savanna versus acacia thicket habitat, though escape success was consistently underestimated. Our model provides a mechanistic explanation for the differential effects of habitat on survival for different predator-prey pairs. Its flexible nature means that our model can be refined to simulate specific systems and could have applications towards management programmes for species threatened by habitat loss and predation.}, } @article {pmid32966309, year = {2020}, author = {Walters, KE and Martiny, JBH}, title = {Alpha-, beta-, and gamma-diversity of bacteria varies across habitats.}, journal = {PloS one}, volume = {15}, number = {9}, pages = {e0233872}, pmid = {32966309}, issn = {1932-6203}, mesh = {Bacteria/*classification ; Databases, Genetic ; *Ecosystem ; Microbiota ; RNA, Ribosomal, 16S/genetics ; *Soil Microbiology ; }, abstract = {Bacteria are essential parts of ecosystems and are the most diverse organisms on the planet. Yet, we still do not know which habitats support the highest diversity of bacteria across multiple scales. We analyzed alpha-, beta-, and gamma-diversity of bacterial assemblages using 11,680 samples compiled by the Earth Microbiome Project. We found that soils contained the highest bacterial richness within a single sample (alpha-diversity), but sediment assemblages displayed the highest gamma-diversity. Sediment, biofilms/mats, and inland water exhibited the most variation in community composition among geographic locations (beta-diversity). Within soils, agricultural lands, hot deserts, grasslands, and shrublands contained the highest richness, while forests, cold deserts, and tundra biomes consistently harbored fewer bacterial species. Surprisingly, agricultural soils encompassed similar levels of beta-diversity as other soil biomes. These patterns were robust to the alpha- and beta- diversity metrics used and the taxonomic binning approach. Overall, the results support the idea that spatial environmental heterogeneity is an important driver of bacterial diversity.}, } @article {pmid32963240, year = {2020}, author = {Berner, LT and Massey, R and Jantz, P and Forbes, BC and Macias-Fauria, M and Myers-Smith, I and Kumpula, T and Gauthier, G and Andreu-Hayles, L and Gaglioti, BV and Burns, P and Zetterberg, P and D'Arrigo, R and Goetz, SJ}, title = {Summer warming explains widespread but not uniform greening in the Arctic tundra biome.}, journal = {Nature communications}, volume = {11}, number = {1}, pages = {4621}, pmid = {32963240}, issn = {2041-1723}, mesh = {Arctic Regions ; Climate Change ; *Ecosystem ; Environmental Monitoring ; Plant Development ; Plants ; *Seasons ; Soil ; Temperature ; *Tundra ; }, abstract = {Arctic warming can influence tundra ecosystem function with consequences for climate feedbacks, wildlife and human communities. Yet ecological change across the Arctic tundra biome remains poorly quantified due to field measurement limitations and reliance on coarse-resolution satellite data. Here, we assess decadal changes in Arctic tundra greenness using time series from the 30 m resolution Landsat satellites. From 1985 to 2016 tundra greenness increased (greening) at ~37.3% of sampling sites and decreased (browning) at ~4.7% of sampling sites. Greening occurred most often at warm sampling sites with increased summer air temperature, soil temperature, and soil moisture, while browning occurred most often at cold sampling sites that cooled and dried. Tundra greenness was positively correlated with graminoid, shrub, and ecosystem productivity measured at field sites. Our results support the hypothesis that summer warming stimulated plant productivity across much, but not all, of the Arctic tundra biome during recent decades.}, } @article {pmid32963001, year = {2020}, author = {Dueholm, MS and Andersen, KS and McIlroy, SJ and Kristensen, JM and Yashiro, E and Karst, SM and Albertsen, M and Nielsen, PH}, title = {Generation of Comprehensive Ecosystem-Specific Reference Databases with Species-Level Resolution by High-Throughput Full-Length 16S rRNA Gene Sequencing and Automated Taxonomy Assignment (AutoTax).}, journal = {mBio}, volume = {11}, number = {5}, pages = {}, pmid = {32963001}, issn = {2150-7511}, mesh = {Automation, Laboratory ; Bacteria/*classification ; DNA Primers ; *Databases, Nucleic Acid ; *Ecosystem ; *High-Throughput Nucleotide Sequencing ; Microbiota/*genetics ; Phylogeny ; RNA, Ribosomal, 16S/*genetics ; Reference Values ; Sequence Analysis, DNA ; Wastewater/microbiology ; }, abstract = {High-throughput 16S rRNA gene amplicon sequencing is an essential method for studying the diversity and dynamics of microbial communities. However, this method is presently hampered by the lack of high-identity reference sequences for many environmental microbes in the public 16S rRNA gene reference databases and by the absence of a systematic and comprehensive taxonomy for the uncultured majority. Here, we demonstrate how high-throughput synthetic long-read sequencing can be applied to create ecosystem-specific full-length 16S rRNA gene amplicon sequence variant (FL-ASV) resolved reference databases that include high-identity references (>98.7% identity) for nearly all abundant bacteria (>0.01% relative abundance) using Danish wastewater treatment systems and anaerobic digesters as an example. In addition, we introduce a novel sequence identity-based approach for automated taxonomy assignment (AutoTax) that provides a complete seven-rank taxonomy for all reference sequences, using the SILVA taxonomy as a backbone, with stable placeholder names for unclassified taxa. The FL-ASVs are perfectly suited for the evaluation of taxonomic resolution and bias associated with primers commonly used for amplicon sequencing, allowing researchers to choose those that are ideal for their ecosystem. Reference databases processed with AutoTax greatly improves the classification of short-read 16S rRNA ASVs at the genus- and species-level, compared with the commonly used universal reference databases. Importantly, the placeholder names provide a way to explore the unclassified environmental taxa at different taxonomic ranks, which in combination with in situ analyses can be used to uncover their ecological roles.}, } @article {pmid32960879, year = {2020}, author = {Makori, DM and Abdel-Rahman, EM and Landmann, T and Mutanga, O and Odindi, J and Nguku, E and Tonnang, HE and Raina, S}, title = {Suitability of resampled multispectral datasets for mapping flowering plants in the Kenyan savannah.}, journal = {PloS one}, volume = {15}, number = {9}, pages = {e0232313}, pmid = {32960879}, issn = {1932-6203}, mesh = {Animals ; Beekeeping/*methods ; Bees/physiology ; Datasets as Topic ; Environmental Monitoring/*methods ; Grassland ; Kenya ; Machine Learning ; Magnoliopsida/*growth & development ; Photography ; Pollination ; }, abstract = {Pollination services and honeybee health in general are important in the African savannahs particularly to farmers who often rely on honeybee products as a supplementary source of income. Therefore, it is imperative to understand the floral cycle, abundance and spatial distribution of melliferous plants in the African savannah landscapes. Furthermore, placement of apiaries in the landscapes could benefit from information on spatiotemporal patterns of flowering plants, by optimising honeybees' foraging behaviours, which could improve apiary productivity. This study sought to assess the suitability of simulated multispectral data for mapping melliferous (flowering) plants in the African savannahs. Bi-temporal AISA Eagle hyperspectral images, resampled to four sensors (i.e. WorldView-2, RapidEye, Spot-6 and Sentinel-2) spatial and spectral resolutions, and a 10-cm ultra-high spatial resolution aerial imagery coinciding with onset and peak flowering periods were used in this study. Ground reference data was collected at the time of imagery capture. The advanced machine learning random forest (RF) classifier was used to map the flowering plants at a landscape scale and a classification accuracy validated using 30% independent test samples. The results showed that 93.33%, 69.43%, 67.52% and 82.18% accuracies could be achieved using WorldView-2, RapidEye, Spot-6 and Sentinel-2 data sets respectively, at the peak flowering period. Our study provides a basis for the development of operational and cost-effective approaches for mapping flowering plants in an African semiarid agroecological landscape. Specifically, such mapping approaches are valuable in providing timely and reliable advisory tools for guiding the implementation of beekeeping systems at a landscape scale.}, } @article {pmid32960186, year = {2020}, author = {Swann, OV and Holden, KA and Turtle, L and Pollock, L and Fairfield, CJ and Drake, TM and Seth, S and Egan, C and Hardwick, HE and Halpin, S and Girvan, M and Donohue, C and Pritchard, M and Patel, LB and Ladhani, S and Sigfrid, L and Sinha, IP and Olliaro, PL and Nguyen-Van-Tam, JS and Horby, PW and Merson, L and Carson, G and Dunning, J and Openshaw, PJM and Baillie, JK and Harrison, EM and Docherty, AB and Semple, MG and , }, title = {Clinical characteristics of children and young people admitted to hospital with covid-19 in United Kingdom: prospective multicentre observational cohort study.}, journal = {BMJ (Clinical research ed.)}, volume = {370}, number = {}, pages = {m3249}, pmid = {32960186}, issn = {1756-1833}, support = {MC_PC_19059/MRC_/Medical Research Council/United Kingdom ; IS-HPU-1112-10117/DH_/Department of Health/United Kingdom ; MR/V033441/1/MRC_/Medical Research Council/United Kingdom ; MR/S032304/1/MRC_/Medical Research Council/United Kingdom ; MC_PC_19025/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Adolescent ; Age Factors ; *Betacoronavirus ; COVID-19 ; Child ; Child, Preschool ; Cohort Studies ; Coronavirus Infections/complications/*epidemiology/therapy ; Critical Care ; Female ; Hospital Mortality ; Hospitalization/*statistics & numerical data ; Humans ; Infant ; Infant, Newborn ; Male ; Pandemics ; Pneumonia, Viral/complications/*epidemiology/therapy ; Respiration, Artificial ; SARS-CoV-2 ; Systemic Inflammatory Response Syndrome/diagnosis/*epidemiology/therapy ; United Kingdom ; Young Adult ; }, abstract = {OBJECTIVE: To characterise the clinical features of children and young people admitted to hospital with laboratory confirmed severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in the UK and explore factors associated with admission to critical care, mortality, and development of multisystem inflammatory syndrome in children and adolescents temporarily related to coronavirus disease 2019 (covid-19) (MIS-C).

DESIGN: Prospective observational cohort study with rapid data gathering and near real time analysis.

SETTING: 260 hospitals in England, Wales, and Scotland between 17 January and 3 July 2020, with a minimum follow-up time of two weeks (to 17 July 2020).

PARTICIPANTS: 651 children and young people aged less than 19 years admitted to 138 hospitals and enrolled into the International Severe Acute Respiratory and emergency Infections Consortium (ISARIC) WHO Clinical Characterisation Protocol UK study with laboratory confirmed SARS-CoV-2.

MAIN OUTCOME MEASURES: Admission to critical care (high dependency or intensive care), in-hospital mortality, or meeting the WHO preliminary case definition for MIS-C.

RESULTS: Median age was 4.6 (interquartile range 0.3-13.7) years, 35% (225/651) were under 12 months old, and 56% (367/650) were male. 57% (330/576) were white, 12% (67/576) South Asian, and 10% (56/576) black. 42% (276/651) had at least one recorded comorbidity. A systemic mucocutaneous-enteric cluster of symptoms was identified, which encompassed the symptoms for the WHO MIS-C criteria. 18% (116/632) of children were admitted to critical care. On multivariable analysis, this was associated with age under 1 month (odds ratio 3.21, 95% confidence interval 1.36 to 7.66; P=0.008), age 10-14 years (3.23, 1.55 to 6.99; P=0.002), and black ethnicity (2.82, 1.41 to 5.57; P=0.003). Six (1%) of 627 patients died in hospital, all of whom had profound comorbidity. 11% (52/456) met the WHO MIS-C criteria, with the first patient developing symptoms in mid-March. Children meeting MIS-C criteria were older (median age 10.7 (8.3-14.1) v 1.6 (0.2-12.9) years; P<0.001) and more likely to be of non-white ethnicity (64% (29/45) v 42% (148/355); P=0.004). Children with MIS-C were five times more likely to be admitted to critical care (73% (38/52) v 15% (62/404); P<0.001). In addition to the WHO criteria, children with MIS-C were more likely to present with fatigue (51% (24/47) v 28% (86/302); P=0.004), headache (34% (16/47) v 10% (26/263); P<0.001), myalgia (34% (15/44) v 8% (21/270); P<0.001), sore throat (30% (14/47) v (12% (34/284); P=0.003), and lymphadenopathy (20% (9/46) v 3% (10/318); P<0.001) and to have a platelet count of less than 150 × 10[9]/L (32% (16/50) v 11% (38/348); P<0.001) than children who did not have MIS-C. No deaths occurred in the MIS-C group.

CONCLUSIONS: Children and young people have less severe acute covid-19 than adults. A systemic mucocutaneous-enteric symptom cluster was also identified in acute cases that shares features with MIS-C. This study provides additional evidence for refining the WHO MIS-C preliminary case definition. Children meeting the MIS-C criteria have different demographic and clinical features depending on whether they have acute SARS-CoV-2 infection (polymerase chain reaction positive) or are post-acute (antibody positive).

STUDY REGISTRATION: ISRCTN66726260.}, } @article {pmid32957925, year = {2020}, author = {Zhao, Z and Cristian, A and Rosen, G}, title = {Keeping up with the genomes: efficient learning of our increasing knowledge of the tree of life.}, journal = {BMC bioinformatics}, volume = {21}, number = {1}, pages = {412}, pmid = {32957925}, issn = {1471-2105}, mesh = {Algorithms ; Bacteria/genetics ; Bayes Theorem ; Gastrointestinal Microbiome/*genetics ; *Genome, Bacterial ; Humans ; *Machine Learning ; Metagenome ; Metagenomics/*methods ; Sequence Analysis, DNA/methods ; }, abstract = {BACKGROUND: It is a computational challenge for current metagenomic classifiers to keep up with the pace of training data generated from genome sequencing projects, such as the exponentially-growing NCBI RefSeq bacterial genome database. When new reference sequences are added to training data, statically trained classifiers must be rerun on all data, resulting in a highly inefficient process. The rich literature of "incremental learning" addresses the need to update an existing classifier to accommodate new data without sacrificing much accuracy compared to retraining the classifier with all data.

RESULTS: We demonstrate how classification improves over time by incrementally training a classifier on progressive RefSeq snapshots and testing it on: (a) all known current genomes (as a ground truth set) and (b) a real experimental metagenomic gut sample. We demonstrate that as a classifier model's knowledge of genomes grows, classification accuracy increases. The proof-of-concept naïve Bayes implementation, when updated yearly, now runs in 1/4[th] of the non-incremental time with no accuracy loss.

CONCLUSIONS: It is evident that classification improves by having the most current knowledge at its disposal. Therefore, it is of utmost importance to make classifiers computationally tractable to keep up with the data deluge. The incremental learning classifier can be efficiently updated without the cost of reprocessing nor the access to the existing database and therefore save storage as well as computation resources.}, } @article {pmid32957527, year = {2020}, author = {Juhász, O and Fürjes-Mikó, Á and Tenyér, A and Somogyi, AÁ and Aguilon, DJ and Kiss, PJ and Bátori, Z and Maák, I}, title = {Consequences of Climate Change-Induced Habitat Conversions on Red Wood Ants in a Central European Mountain: A Case Study.}, journal = {Animals : an open access journal from MDPI}, volume = {10}, number = {9}, pages = {}, pmid = {32957527}, issn = {2076-2615}, support = {2017-01-X-NZ8-01042//Fundacja na rzecz Nauki Polskiej/ ; NKFIH K 124796//Országos Tudományos Kutatási Alapprogramok/ ; }, abstract = {The consequences of anthropogenic climate change are one of the major concerns of conservation biology. A cascade of negative effects is expected to affect various ecosystems, one of which is Central European coniferous forests and their unique biota. These coniferous forests are the primary habitat of many forest specialist species such as red wood ants. Climate change-induced rising of temperature allows trees to skip winter hibernation, making them more vulnerable to storms that cause wind felling, and in turn, promotes bark beetle infestations that results in unscheduled clear-cuttings. Red wood ants can also be exposed to such habitat changes. We investigated the effects of bark beetle-induced clear-cutting and the absence of coniferous trees on colonies of Formica polyctena, including a mixed-coniferous forest as a reference. Our aim was to investigate how these habitat features affect the nest characteristics and nesting habits of F. polyctena. Our results indicate that, in the absence of conifers, F. polyctena tend to use different alternatives for nest material, colony structure, and food sources. However, the vitality of F. polyctena colonies significantly decreased (smaller nest mound volumes). Our study highlights the ecological flexibility of this forest specialist and its potential to survive under extreme conditions.}, } @article {pmid32951075, year = {2020}, author = {Robeva, RS and Jungck, JR and Gross, LJ}, title = {Changing the Nature of Quantitative Biology Education: Data Science as a Driver.}, journal = {Bulletin of mathematical biology}, volume = {82}, number = {10}, pages = {127}, doi = {10.1007/s11538-020-00785-0}, pmid = {32951075}, issn = {1522-9602}, mesh = {*Computational Biology/education/trends ; Curriculum/trends ; *Data Science ; Humans ; }, abstract = {We live in a data-rich world with rapidly growing databases with zettabytes of data. Innovation, computation, and technological advances have now tremendously accelerated the pace of discovery, providing driverless cars, robotic devices, expert healthcare systems, precision medicine, and automated discovery to mention a few. Even though the definition of the term data science continues to evolve, the sweeping impact it has already produced on society is undeniable. We are at a point when new discoveries through data science have enormous potential to advance progress but also to be used maliciously, with harmful ethical and social consequences. Perhaps nowhere is this more clearly exemplified than in the biological and medical sciences. The confluence of (1) machine learning, (2) mathematical modeling, (3) computation/simulation, and (4) big data have moved us from the sequencing of genomes to gene editing and individualized medicine; yet, unsettled policies regarding data privacy and ethical norms could potentially open doors for serious negative repercussions. The data science revolution has amplified the urgent need for a paradigm shift in undergraduate biology education. It has reaffirmed that data science education interacts and enhances mathematical education in advancing quantitative conceptual and skill development for the new generation of biologists. These connections encourage us to strive to cultivate a broadly skilled workforce of technologically savvy problem-solvers, skilled at handling the unique challenges pertaining to biological data, and capable of collaborating across various disciplines in the sciences, the humanities, and the social sciences. To accomplish this, we suggest development of open curricula that extend beyond the job certification rhetoric and combine data acumen with modeling, experimental, and computational methods through engaging projects, while also providing awareness and deep exploration of their societal implications. This process would benefit from embracing the pedagogy of experiential learning and involve students in open-ended explorations derived from authentic inquiries and ongoing research. On this foundation, we encourage development of flexible data science initiatives for the education of life science undergraduates within and across existing models.}, } @article {pmid32948072, year = {2020}, author = {Song, Y and Chen, P and Liu, P and Bu, C and Zhang, D}, title = {High-Temperature-Responsive Poplar lncRNAs Modulate Target Gene Expression via RNA Interference and Act as RNA Scaffolds to Enhance Heat Tolerance.}, journal = {International journal of molecular sciences}, volume = {21}, number = {18}, pages = {}, pmid = {32948072}, issn = {1422-0067}, support = {2017ZY04//the Fundamental Research Funds for the Central Universities/ ; 31400553, 31670333 and 31770707//the Project of the National Natural Science Foundation of China/ ; B20050//the 111 Project/ ; }, mesh = {Adaptation, Physiological/genetics ; Arabidopsis ; Base Sequence ; Calcium Signaling ; DNA Damage ; DNA, Plant/genetics ; Gene Expression Regulation, Plant/*genetics ; Gene Ontology ; Genes, Plant ; Hot Temperature ; Nanostructures ; Nucleic Acid Conformation ; Nucleotide Motifs ; Photosynthesis ; Plant Proteins/biosynthesis/genetics ; Plants, Genetically Modified ; Populus/*genetics/physiology ; Promoter Regions, Genetic/genetics ; *RNA Interference ; RNA, Long Noncoding/*genetics ; RNA, Plant/*genetics ; RNA, Small Interfering/genetics/pharmacology ; Recombinant Proteins/metabolism ; Stress, Physiological/genetics ; Transcription, Genetic ; }, abstract = {High-temperature stress is a threat to plant development and survival. Long noncoding RNAs (lncRNAs) participate in plant stress responses, but their functions in the complex stress response network remain unknown. Poplar contributes to terrestrial ecological stability. In this study, we identified 204 high-temperature-responsive lncRNAs in an abiotic stress-tolerant poplar (Populus simonii) species using strand-specific RNA sequencing (ssRNA-seq). Mimicking overexpressed and repressed candidate lncRNAs in poplar was used to illuminate their regulation pattern on targets using nano sheet mediation. These lncRNAs were predicted to target 185 genes, of which 100 were cis genes and 119 were trans genes. Gene Ontology enrichment analysis showed that anatomical structure morphogenesis and response to stress and signaling were significantly enriched. Among heat-responsive LncRNAs, TCONS_00202587 binds to upstream sequences via its secondary structure and interferes with target gene transcription. TCONS_00260893 enhances calcium influx in response to high-temperature treatment by interfering with a specific variant/isoform of the target gene. Heterogeneous expression of these two lncRNA targets promoted photosynthetic protection and recovery, inhibited membrane peroxidation, and suppressed DNA damage in Arabidopsis under heat stress. These results showed that lncRNAs can regulate their target genes by acting as potential RNA scaffolds or through the RNA interference pathway.}, } @article {pmid32947762, year = {2020}, author = {Gao, C and Feng, Y and Tong, X and Jin, Y and Liu, S and Wu, P and Ye, Z and Gu, C}, title = {Modeling urban encroachment on ecological land using cellular automata and cross-entropy optimization rules.}, journal = {The Science of the total environment}, volume = {744}, number = {}, pages = {140996}, doi = {10.1016/j.scitotenv.2020.140996}, pmid = {32947762}, issn = {1879-1026}, mesh = {Algorithms ; China ; *Conservation of Natural Resources ; Entropy ; Forests ; *Urban Renewal ; }, abstract = {Rapid urban expansion often leads to substantial encroachment on ecological lands and destruction of natural environments. We developed a new cellular automata model (named CACEO) that uses cross-entropy optimization (CEO) to reproduce and project urban expansion into coastal areas and to assess urban encroachment on ecological lands. The CEO algorithm automatically searches for the near-optimal CA parameters and is capable of objectively parameterizing CA models to predict multi-objective scenarios. We calibrated CACEO by simulating urban expansion at Wenzhou from 1995 to 2005, validated the model from 2005 to 2015 using real data, and then predicted urban expansion for 2025 and 2035. End-state overall accuracies were 93.8% for 2005 and 94.4% for 2015, while figure-of-merit metrics were 27.9% for 2005 and 19.1% for 2015. We predicted four different scenarios to year 2025 and 2035: (1) a business-as-usual (BAU)-scenario using benchmark settings; (2) a District-scenario based on a district-oriented urban development strategy; (3) a Road-scenario based on a road network-oriented urban development strategy; and (4) a Coast-scenario based on a coast-oriented urban development strategy. Each scenario predicts a substantially different pattern of urban encroachment on ecological land and significant loss of farmland, forest, wetland and grassland. These scenarios should be useful in adjusting urban development strategies at Wenzhou and elsewhere.}, } @article {pmid32941419, year = {2020}, author = {Zhao, Z and Sokhansanj, BA and Malhotra, C and Zheng, K and Rosen, GL}, title = {Genetic grouping of SARS-CoV-2 coronavirus sequences using informative subtype markers for pandemic spread visualization.}, journal = {PLoS computational biology}, volume = {16}, number = {9}, pages = {e1008269}, pmid = {32941419}, issn = {1553-7358}, mesh = {Betacoronavirus/*classification/*genetics ; COVID-19 ; *Coronavirus Infections/epidemiology/transmission/virology ; Evolution, Molecular ; Genetic Markers/genetics ; Genome, Viral/genetics ; Genomics/*methods ; Humans ; Mutation/genetics ; *Pandemics ; Phylogeny ; *Pneumonia, Viral/epidemiology/transmission/virology ; RNA, Viral/genetics ; SARS-CoV-2 ; Sequence Alignment ; Sequence Analysis, RNA ; Spatio-Temporal Analysis ; }, abstract = {We propose an efficient framework for genetic subtyping of SARS-CoV-2, the novel coronavirus that causes the COVID-19 pandemic. Efficient viral subtyping enables visualization and modeling of the geographic distribution and temporal dynamics of disease spread. Subtyping thereby advances the development of effective containment strategies and, potentially, therapeutic and vaccine strategies. However, identifying viral subtypes in real-time is challenging: SARS-CoV-2 is a novel virus, and the pandemic is rapidly expanding. Viral subtypes may be difficult to detect due to rapid evolution; founder effects are more significant than selection pressure; and the clustering threshold for subtyping is not standardized. We propose to identify mutational signatures of available SARS-CoV-2 sequences using a population-based approach: an entropy measure followed by frequency analysis. These signatures, Informative Subtype Markers (ISMs), define a compact set of nucleotide sites that characterize the most variable (and thus most informative) positions in the viral genomes sequenced from different individuals. Through ISM compression, we find that certain distant nucleotide variants covary, including non-coding and ORF1ab sites covarying with the D614G spike protein mutation which has become increasingly prevalent as the pandemic has spread. ISMs are also useful for downstream analyses, such as spatiotemporal visualization of viral dynamics. By analyzing sequence data available in the GISAID database, we validate the utility of ISM-based subtyping by comparing spatiotemporal analyses using ISMs to epidemiological studies of viral transmission in Asia, Europe, and the United States. In addition, we show the relationship of ISMs to phylogenetic reconstructions of SARS-CoV-2 evolution, and therefore, ISMs can play an important complementary role to phylogenetic tree-based analysis, such as is done in the Nextstrain project. The developed pipeline dynamically generates ISMs for newly added SARS-CoV-2 sequences and updates the visualization of pandemic spatiotemporal dynamics, and is available on Github at https://github.com/EESI/ISM (Jupyter notebook), https://github.com/EESI/ncov_ism (command line tool) and via an interactive website at https://covid19-ism.coe.drexel.edu/.}, } @article {pmid32939625, year = {2021}, author = {Thomas, AL and Evans, LM and Nelsen, MD and Chesler, EJ and Powers, MS and Booher, WC and Lowry, CA and DeFries, JC and Ehringer, MA}, title = {Whole-Genome Sequencing of Inbred Mouse Strains Selected for High and Low Open-Field Activity.}, journal = {Behavior genetics}, volume = {51}, number = {1}, pages = {68-81}, pmid = {32939625}, issn = {1573-3297}, support = {R21 MH116263/MH/NIMH NIH HHS/United States ; R01 AA018776/AA/NIAAA NIH HHS/United States ; R01 MH100141/MH/NIMH NIH HHS/United States ; }, mesh = {Animals ; Anxiety/*genetics ; Anxiety Disorders/genetics ; Chromosome Mapping/methods ; Computational Biology/methods ; Disease Models, Animal ; Genomics/methods ; Genotype ; Humans ; Mice ; Mice, Inbred BALB C/genetics ; Mice, Inbred C57BL/genetics ; Mice, Inbred Strains/*genetics ; Open Field Test/*physiology ; Phenotype ; Polymorphism, Single Nucleotide/genetics ; Quantitative Trait Loci/genetics ; Rats ; Exome Sequencing/methods ; }, abstract = {We conducted whole-genome sequencing of four inbred mouse strains initially selected for high (H1, H2) or low (L1, L2) open-field activity (OFA), and then examined strain distribution patterns for all DNA variants that differed between their BALB/cJ and C57BL/6J parental strains. Next, we assessed genome-wide sharing (3,678,826 variants) both between and within the High and Low Activity strains. Results suggested that about 10% of these DNA variants may be associated with OFA, and clearly demonstrated its polygenic nature. Finally, we conducted bioinformatic analyses of functional genomics data from mouse, rat, and human to refine previously identified quantitative trait loci (QTL) for anxiety-related measures. This combination of sequence analysis and genomic-data integration facilitated refinement of previously intractable QTL findings, and identified possible genes for functional follow-up studies.}, } @article {pmid32938501, year = {2020}, author = {Zhang, Z and Wang, J and Wang, J and Wang, J and Li, Y}, title = {Estimate of the sequenced proportion of the global prokaryotic genome.}, journal = {Microbiome}, volume = {8}, number = {1}, pages = {134}, pmid = {32938501}, issn = {2049-2618}, mesh = {Archaea/classification/genetics/isolation & purification ; Bacteria/classification/genetics/isolation & purification ; Databases, Genetic ; *Earth, Planet ; Genome/*genetics ; Genomics/*statistics & numerical data ; Microbiota/*genetics ; Prokaryotic Cells/*classification/*metabolism ; Sequence Alignment ; Sequence Analysis/*statistics & numerical data ; }, abstract = {BACKGROUND: Sequencing prokaryotic genomes has revolutionized our understanding of the many roles played by microorganisms. However, the cell and taxon proportions of genome-sequenced bacteria or archaea on earth remain unknown. This study aimed to explore this basic question using large-scale alignment between the sequences released by the Earth Microbiome Project and 155,810 prokaryotic genomes from public databases.

RESULTS: Our results showed that the median proportions of the genome-sequenced cells and taxa (at 100% identities in the 16S-V4 region) in different biomes reached 38.1% (16.4-86.3%) and 18.8% (9.1-52.6%), respectively. The sequenced proportions of the prokaryotic genomes in biomes were significantly negatively correlated with the alpha diversity indices, and the proportions sequenced in host-associated biomes were significantly higher than those in free-living biomes. Due to a set of cosmopolitan OTUs that are found in multiple samples and preferentially sequenced, only 2.1% of the global prokaryotic taxa are represented by sequenced genomes. Most of the biomes were occupied by a few predominant taxa with a high relative abundance and much higher genome-sequenced proportions than numerous rare taxa.

CONCLUSIONS: These results reveal the current situation of prokaryotic genome sequencing for earth biomes, provide a more reasonable and efficient exploration of prokaryotic genomes, and promote our understanding of microbial ecological functions. Video Abstract.}, } @article {pmid32933777, year = {2020}, author = {Laubmeier, AN and Cazelles, B and Cuddington, K and Erickson, KD and Fortin, MJ and Ogle, K and Wikle, CK and Zhu, K and Zipkin, EF}, title = {Ecological Dynamics: Integrating Empirical, Statistical, and Analytical Methods.}, journal = {Trends in ecology & evolution}, volume = {35}, number = {12}, pages = {1090-1099}, doi = {10.1016/j.tree.2020.08.006}, pmid = {32933777}, issn = {1872-8383}, mesh = {Animals ; Bayes Theorem ; Ecosystem ; *Models, Biological ; *Models, Statistical ; Population Dynamics ; Predatory Behavior ; Uncertainty ; }, abstract = {Understanding ecological processes and predicting long-term dynamics are ongoing challenges in ecology. To address these challenges, we suggest an approach combining mathematical analyses and Bayesian hierarchical statistical modeling with diverse data sources. Novel mathematical analysis of ecological dynamics permits a process-based understanding of conditions under which systems approach equilibrium, experience large oscillations, or persist in transient states. This understanding is improved by combining ecological models with empirical observations from a variety of sources. Bayesian hierarchical models explicitly couple process-based models and data, yielding probabilistic quantification of model parameters, system characteristics, and associated uncertainties. We outline relevant tools from dynamical analysis and hierarchical modeling and argue for their integration, demonstrating the value of this synthetic approach through a simple predator-prey example.}, } @article {pmid32926367, year = {2021}, author = {Ferrall-Fairbanks, MC and Altrock, PM}, title = {Investigating Inter- and Intrasample Diversity of Single-Cell RNA Sequencing Datasets.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2194}, number = {}, pages = {177-186}, doi = {10.1007/978-1-0716-0849-4_10}, pmid = {32926367}, issn = {1940-6029}, mesh = {Computational Biology/*methods ; Data Interpretation, Statistical ; Disease Progression ; Gene Expression Profiling/*methods ; *Genetic Heterogeneity ; Humans ; Neoplasms/*genetics ; Quality Control ; Sequence Analysis, RNA/*methods ; Single-Cell Analysis/*methods ; Software ; }, abstract = {Tumor heterogeneity can arise from a variety of extrinsic and intrinsic sources and drives unfavorable outcomes. With recent technological advances, single-cell RNA sequencing has become a way for researchers to easily assay tumor heterogeneity at the transcriptomic level with high resolution. However, ongoing research focuses on different ways to analyze this big data and how to compare across multiple different samples. In this chapter, we provide a practical guide to calculate inter- and intrasample diversity metrics from single-cell RNA sequencing datasets. These measures of diversity are adapted from commonly used metrics in statistics and ecology to quantify and compare sample heterogeneity at single-cell resolution.}, } @article {pmid32925930, year = {2020}, author = {Martínez, N and Matute, H and Goikoetxea, E}, title = {PicPsy: A new bank of 106 photographs and line drawings with written naming norms for Spanish-speaking children and adults.}, journal = {PloS one}, volume = {15}, number = {9}, pages = {e0238976}, pmid = {32925930}, issn = {1932-6203}, mesh = {Adolescent ; Child ; Child, Preschool ; Databases, Factual ; Female ; Form Perception/physiology ; Humans ; Language ; Language Development ; Male ; *Names ; Pattern Recognition, Visual/*classification/physiology ; Recognition, Psychology ; Translations ; Visual Perception/physiology ; Writing ; }, abstract = {The use of pictures as experimental stimuli is a frequent practice in psychological and educational research. In addition, picture-naming task allows the study of different cognitive processes such as perception, attention, memory and language. Line drawings have been widely used in research to date but it has begun to be highlighted the need for more ecological stimuli such as photographs. However, normative data of a photographic set has not been published yet for use with children. We present PicPsy, a new standardized bank of photographs and matched line drawing. We collected written picture-naming norms for name agreement, unknown responses, alternative names, familiarity and visual complexity. A total of 118 native Spanish-speaking children in grades 3-4 participated in the study. For comparison purposes, 89 adults were also included in the study. Child and adult performance was highly correlated, but we found significant age group differences in all variables examined except for visual complexity. Researchers and teachers could benefit from using the new standardized bank reported here which is published under public domain license. The data and materials for this research are available at the Open Science Framework, https://osf.io/nyf3t/.}, } @article {pmid32924382, year = {2020}, author = {Yasir, M and Hui, S and Binghu, H and Rahman, SU}, title = {Coastline extraction and land use change analysis using remote sensing (RS) and geographic information system (GIS) technology - A review of the literature.}, journal = {Reviews on environmental health}, volume = {35}, number = {4}, pages = {453-460}, doi = {10.1515/reveh-2019-0103}, pmid = {32924382}, issn = {2191-0308}, mesh = {*Aquaculture ; China ; Environmental Monitoring/*methods ; Geographic Information Systems/*statistics & numerical data ; Remote Sensing Technology/*methods ; }, abstract = {Coastlines mapping techniques or the coastline automated analyses have been sought after. In practice, various sorts of seacoasts, for example, biological, silty, arenaceous, artificial, and bedrock coasts, have their own attributes, which force various degrees of intricacy on coastline mapping. As an extraordinary kind of complex artificial coast, aquaculture coast is shaped by the farming of aquatic organisms on silt tidal flats. With the rapid growth of coastal aquaculture in recent years, aquaculture coasts have increased in some developing countries. It has been estimated that aquaculture coasts constitute about 30% of all coastlines in mainland China. In order to identify, monitor, model, and manage the vast expanse of coastal aquaculture, effective methods of extracting aquaculture coastlines from remotely sensed imagery are desired. Secondly, with the rapid economic development in coastal areas, the development of coastal zone resources is also increasing day by day, which benefits the development of island coastal zone. Using oneself has become an important link in the development of marine economy. Due to the limited coastal resources and low environmental carrying capacity, the overexploitation and utilization of coastal resources will lead to a series of problems, such as coastal erosion, coastal migration and accumulation, island area reduction, etc., Both man-made activities and natural factors will lead to coastline changes, which will lead to corresponding changes in coastal ecological environment, thus affecting the coordinated development of coastal economy and the survival of coastal residents. Therefore, efficient, accurate and timely acquisition of coastline information and research on the spatial-temporal changes of coastline are of great significance to the protection of the living environment of coastal residents, the effective development of island and coastal resources, the coordination of sustainable economic development in coastal areas and the mitigation of marine disasters. This paper presents a review of those papers reporting coastline extraction and land use and land cover (LULC) change analysis using remote sensing (RS) and geographic information system (GIS) technology.}, } @article {pmid32916808, year = {2020}, author = {Guo, Y and Yin, G and Sun, H and Wang, H and Chen, S and Senthilnath, J and Wang, J and Fu, Y}, title = {Scaling Effects on Chlorophyll Content Estimations with RGB Camera Mounted on a UAV Platform Using Machine-Learning Methods.}, journal = {Sensors (Basel, Switzerland)}, volume = {20}, number = {18}, pages = {}, pmid = {32916808}, issn = {1424-8220}, support = {Grant No. 31770516//the General Program of National Nature Science Foundation of China/ ; 2017YFA06036001//the National Key Research and Development Program of China/ ; 2018EYT05//111 Project (B18006) and Fundamental Research Funds for the Central Universities/ ; }, mesh = {Agriculture ; Chlorophyll/*analysis ; *Machine Learning ; Plant Leaves/*chemistry ; *Remote Sensing Technology ; Zea mays/*chemistry ; }, abstract = {Timely monitoring and precise estimation of the leaf chlorophyll contents of maize are crucial for agricultural practices. The scale effects are very important as the calculated vegetation index (VI) were crucial for the quantitative remote sensing. In this study, the scale effects were investigated by analyzing the linear relationships between VI calculated from red-green-blue (RGB) images from unmanned aerial vehicles (UAV) and ground leaf chlorophyll contents of maize measured using SPAD-502. The scale impacts were assessed by applying different flight altitudes and the highest coefficient of determination (R[2]) can reach 0.85. We found that the VI from images acquired from flight altitude of 50 m was better to estimate the leaf chlorophyll contents using the DJI UAV platform with this specific camera (5472 × 3648 pixels). Moreover, three machine-learning (ML) methods including backpropagation neural network (BP), support vector machine (SVM), and random forest (RF) were applied for the grid-based chlorophyll content estimation based on the common VI. The average values of the root mean square error (RMSE) of chlorophyll content estimations using ML methods were 3.85, 3.11, and 2.90 for BP, SVM, and RF, respectively. Similarly, the mean absolute error (MAE) were 2.947, 2.460, and 2.389, for BP, SVM, and RF, respectively. Thus, the ML methods had relative high precision in chlorophyll content estimations using VI; in particular, the RF performed better than BP and SVM. Our findings suggest that the integrated ML methods with RGB images of this camera acquired at a flight altitude of 50 m (spatial resolution 0.018 m) can be perfectly applied for estimations of leaf chlorophyll content in agriculture.}, } @article {pmid32915913, year = {2020}, author = {Zhao, J and Zou, W and Hu, T}, title = {Novel genes associated with folic acid-mediated metabolism in mouse: A bioinformatics study.}, journal = {PloS one}, volume = {15}, number = {9}, pages = {e0238940}, pmid = {32915913}, issn = {1932-6203}, mesh = {Animals ; Computational Biology ; Databases, Genetic ; Female ; Folic Acid/*genetics/*metabolism ; Gene Expression Profiling ; *Gene Regulatory Networks ; Homocysteine/genetics/metabolism ; Kidney/metabolism ; Male ; Mice ; MicroRNAs/genetics ; Protein Interaction Maps ; Tetratricopeptide Repeat/genetics ; }, abstract = {Folic acid plays an essential role in the central nervous system and cancer. This study aimed to screen genes related to folic acid metabolism. Datasets (GSE80587, GSE65267 and GSE116299) correlated to folic acid were screened in the Gene Expression Omnibus. Weighed gene co-expression network analysis was performed to identify modules associated with sample traits of folic acid and organs (brain, prostate and kidney). Functional enrichment analysis was performed for the eigengenes in modules that were significantly correlated with sample traits. Accordingly, the hub genes and key nodes in the modules were identified using the protein interaction network. A total of 17,252 genes in three datasets were identified. One module, which included 97 genes that were highly correlated with sample traits (including folic acid treatment [cor = -0.57, P = 3e-04] and kidney [cor = -0.68, p = 4e-06]), was screened out. Hub genes, including tetratricopeptide repeat protein 38 (Ttc38) and miR-185, as well as those (including Sema3A, Insl3, Dll1, Msh4 and Snai1) associated with "neuropilin binding", "regulation of reproductive process" and "vitamin D metabolic process", were identified. Genes, including Ttc38, Sema3A, Insl3, Dll1, Msh4 and Snai1, were the novel factors that may be associated with the development of the kidneys and related to folic acid treatment.}, } @article {pmid32915483, year = {2021}, author = {Possantti, I and Silva, T}, title = {Technological Hazard Vulnerability: A GIS-Based Approach for Supporting Environmental Zoning.}, journal = {Integrated environmental assessment and management}, volume = {17}, number = {2}, pages = {445-454}, doi = {10.1002/ieam.4339}, pmid = {32915483}, issn = {1551-3793}, support = {//Codex Remote-Acquaplan-GITEC Brasil-GITEC GmbH Consortium/ ; }, mesh = {Brazil ; Environmental Monitoring ; *Geographic Information Systems ; Lakes ; *Water Quality ; }, abstract = {Technological hazard assessments are extremely rare in Brazil, despite their importance for planning. Aquatic systems are of particular concern, since they are the endpoint of every process occurring in the watershed, including technological disasters. Thus, our goal is to map the technological hazard vulnerability in lagoon systems though a geographic information systems (GIS) model. The technological hazard vulnerability model consists of the spatial overlapping of technological pressure and fragility, having environmental systems as spatial units. The methodology was applied to the lagoon systems of the Rio Grande do Sul State, Southern Brazil, as a case study. The very high vulnerability of the Northern Guaíba Lake is due to the high concentration of technological infrastructures combined with high fragilities of wetland systems. In the Patos Lagoon Estuary, highly vulnerable systems consist mostly in shallow waters. The Mirim Lagoon was less vulnerable compared to other systems, due to a much smaller occurrence of elements of technological pressure. The proposed methodology allowed for the identification of environmental systems particularly vulnerable to technological hazards, where management efforts must be more intense. The results were used for the Ecological-Economic Zoning of the Rio Grande do Sul, as well as to revise the water quality framework of the Patos Lagoon estuary, currently underway. Integr Environ Assess Manag 2021;17:445-454. © 2020 SETAC.}, } @article {pmid32913322, year = {2020}, author = {Pârvulescu, L and Iorgu, EI and Zaharia, C and Ion, MC and Satmari, A and Krapal, AM and Popa, OP and Miok, K and Petrescu, I and Popa, LO}, title = {The future of endangered crayfish in light of protected areas and habitat fragmentation.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {14870}, pmid = {32913322}, issn = {2045-2322}, mesh = {Animals ; Astacoidea/*classification/*genetics ; Conservation of Natural Resources/*methods ; *Ecosystem ; *Endangered Species ; Genetics, Population ; Geography ; Rivers ; Species Specificity ; }, abstract = {The long-term survival of a species requires, among other things, gene flow between populations. Approaches for the evaluation of fragmentation in the frame of freshwater habitats consider only a small amount of the information that combined demography and geography are currently able to provide. This study addresses two species of Austropotamobius crayfish in the light of population genetics, spatial ecology and protected areas of the Carpathians. Advancing the classical approaches, we defined ecological distances upon the rasterised river network as a surrogate of habitat resistance to migration, quantifying the deviations from the species´ suitability range for a set of relevant geospatial variables in each cell of the network. Molecular analyses revealed the populations of the two Austropotamobius crayfish species are clearly distinct, lacking hybridisation. Comparing pairs of populations, we found, in some cases, a strong disagreement regarding genetic and ecological distances, potentially due to human-mediated translocations or the geophysical phenomena of regressive erosion, which may have led to unexpected colonisation routes. Protected areas were found to offer appropriate local habitat conditions but failed to ensure connectivity. The methodology applied in this study allowed us to quantify the contribution of each geospatial (environmental) variable to the overall effect of fragmentation, and we found that water quality was the most important variable. A multilevel approach proved to reveal a better understanding of drivers behind the distribution patterns, which can lead to more adequate conservation measures.}, } @article {pmid32912998, year = {2020}, author = {Worobey, M and Pekar, J and Larsen, BB and Nelson, MI and Hill, V and Joy, JB and Rambaut, A and Suchard, MA and Wertheim, JO and Lemey, P}, title = {The emergence of SARS-CoV-2 in Europe and North America.}, journal = {Science (New York, N.Y.)}, volume = {370}, number = {6516}, pages = {564-570}, pmid = {32912998}, issn = {1095-9203}, support = {U19 AI135995/AI/NIAID NIH HHS/United States ; BB/M010996/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; R01 AI136056/AI/NIAID NIH HHS/United States ; T15 LM011271/LM/NLM NIH HHS/United States ; /WT_/Wellcome Trust/United Kingdom ; K01 AI110181/AI/NIAID NIH HHS/United States ; R01 AI135992/AI/NIAID NIH HHS/United States ; }, mesh = {Air Travel ; Betacoronavirus/*genetics ; COVID-19 ; China/epidemiology ; Computer Simulation ; Contact Tracing ; Coronavirus Infections/*epidemiology/prevention & control/*transmission ; Evolution, Molecular ; Genome, Viral ; Germany/epidemiology ; Humans ; Italy/epidemiology ; Mass Screening ; Mutation ; Pandemics/prevention & control ; *Phylogeny ; Pneumonia, Viral/*epidemiology/prevention & control/*transmission ; SARS-CoV-2 ; Washington/epidemiology ; }, abstract = {Accurate understanding of the global spread of emerging viruses is critical for public health responses and for anticipating and preventing future outbreaks. Here we elucidate when, where, and how the earliest sustained severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission networks became established in Europe and North America. Our results suggest that rapid early interventions successfully prevented early introductions of the virus from taking hold in Germany and the United States. Other, later introductions of the virus from China to both Italy and Washington state, United States, founded the earliest sustained European and North America transmission networks. Our analyses demonstrate the effectiveness of public health measures in preventing onward transmission and show that intensive testing and contact tracing could have prevented SARS-CoV-2 outbreaks from becoming established in these regions.}, } @article {pmid32912585, year = {2021}, author = {Zago, M and Bardelli, T and Rossetti, L and Nazzicari, N and Carminati, D and Galli, A and Giraffa, G}, title = {Evaluation of bacterial communities of Grana Padano cheese by DNA metabarcoding and DNA fingerprinting analysis.}, journal = {Food microbiology}, volume = {93}, number = {}, pages = {103613}, doi = {10.1016/j.fm.2020.103613}, pmid = {32912585}, issn = {1095-9998}, mesh = {Bacteria/classification/genetics ; Biodiversity ; Cheese/*microbiology ; Computational Biology ; DNA Barcoding, Taxonomic/*methods ; DNA Fingerprinting/*methods ; DNA, Bacterial/genetics ; *Food Microbiology ; Genotyping Techniques ; Lactobacillus/genetics ; Microbiota/*genetics ; Random Amplified Polymorphic DNA Technique ; Streptococcus thermophilus/genetics ; Thylakoids ; }, abstract = {The composition of the bacterial community of Grana Padano (GP) cheese was evaluated by an amplicon-based metagenomic approach (DNA metabarcoding) and RAPD-PCR fingerprinting. One hundred eighteen cheeses, which included 118 dairies located in the production area of GP, were collected. Two hundred fifty-four OTUs were detected, of which 82 were further discriminated between dominant (32 OTUs; > 1% total reads) and subdominant (50 OTUs; between 0.1% and 1% total reads) taxa. Lactobacillus (L.) delbrueckii, Lacticaseibacillus (Lact.) rhamnosus, Lact. casei, Limosilactobacillus fermentum, Lactococcus (Lc.) raffinolactis, L. helveticus, Streptococcus thermophilus, and Lc. lactis were the major dominant taxa ('core microbiota'). The origin of samples significantly impacted on both richness, evenness, and the relative abundance of bacterial species, with peculiar pattern distribution among the five GP production regions. A differential analysis allowed to find bacterial species significantly associated with specific region pairings. The analysis of pattern similarity among RAPD-PCR profiles highlighted the presence of a 'core' community banding pattern present in all the GP samples, which was strictly associated with the core microbiota highlighted by DNA metabarcoding. A trend to group samples according to the five production regions was also observed. This study widened our knowledge on the bacterial composition and ecology of Grana Padano cheese.}, } @article {pmid32912216, year = {2020}, author = {Akulova, VS and Sharov, VV and Aksyonova, AI and Putintseva, YA and Oreshkova, NV and Feranchuk, SI and Kuzmin, DA and Pavlov, IN and Litovka, YA and Krutovsky, KV}, title = {De novo sequencing, assembly and functional annotation of Armillaria borealis genome.}, journal = {BMC genomics}, volume = {21}, number = {Suppl 7}, pages = {534}, pmid = {32912216}, issn = {1471-2164}, support = {14.Y26.31.0004//Government of Russian Federation/ ; 0287-2019-0002//Federal Research Center "Krasnoyarsk Scientific Center"/ ; 0356-2016-0704//Federal Research Center "Krasnoyarsk Scientific Center"/ ; 0356-2019-0024//Federal Research Center "Krasnoyarsk Scientific Center"/ ; }, mesh = {*Armillaria/genetics ; *Basidiomycota ; Plants ; Siberia ; }, abstract = {BACKGROUND: Massive forest decline has been observed almost everywhere as a result of negative anthropogenic and climatic effects, which can interact with pests, fungi and other phytopathogens and aggravate their effects. Climatic changes can weaken trees and make fungi, such as Armillaria more destructive. Armillaria borealis (Marxm. & Korhonen) is a fungus from the Physalacriaceae family (Basidiomycota) widely distributed in Eurasia, including Siberia and the Far East. Species from this genus cause the root white rot disease that weakens and often kills woody plants. However, little is known about ecological behavior and genetics of A. borealis. According to field research data, A. borealis is less pathogenic than A. ostoyae, and its aggressive behavior is quite rare. Mainly A. borealis behaves as a secondary pathogen killing trees already weakened by other factors. However, changing environment might cause unpredictable effects in fungus behavior.

RESULTS: The de novo genome assembly and annotation were performed for the A. borealis species for the first time and presented in this study. The A. borealis genome assembly contained ~ 68 Mbp and was comparable with ~ 60 and ~ 79.5 Mbp for the A. ostoyae and A. mellea genomes, respectively. The N50 for contigs equaled 50,544 bp. Functional annotation analysis revealed 21,969 protein coding genes and provided data for further comparative analysis. Repetitive sequences were also identified. The main focus for further study and comparative analysis will be on the enzymes and regulatory factors associated with pathogenicity.

CONCLUSIONS: Pathogenic fungi such as Armillaria are currently one of the main problems in forest conservation. A comprehensive study of these species and their pathogenicity is of great importance and needs good genomic resources. The assembled genome of A. borealis presented in this study is of sufficiently good quality for further detailed comparative study on the composition of enzymes in other Armillaria species. There is also a fundamental problem with the identification and classification of species of the Armillaria genus, where the study of repetitive sequences in the genomes of basidiomycetes and their comparative analysis will help us identify more accurately taxonomy of these species and reveal their evolutionary relationships.}, } @article {pmid32907897, year = {2020}, author = {Grigoroglou, C and Munford, L and Webb, R and Kapur, N and Doran, T and Ashcroft, D and Kontopantelis, E}, title = {Impact of a national primary care pay-for-performance scheme on ambulatory care sensitive hospital admissions: a small-area analysis in England.}, journal = {BMJ open}, volume = {10}, number = {9}, pages = {e036046}, pmid = {32907897}, issn = {2044-6055}, support = {MR/N015126/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {*Ambulatory Care ; England ; Hospitalization ; Hospitals ; Humans ; Primary Health Care ; *Reimbursement, Incentive ; Small-Area Analysis ; }, abstract = {OBJECTIVE: We aimed to spatially describe hospital admissions for ambulatory care sensitive conditions (ACSC) in England at small-area geographical level and assess whether recorded practice performance under one of the world's largest primary care pay-for-performance schemes led to reductions in these potentially avoidable hospitalisations for chronic conditions incentivised in the scheme.

SETTING: We obtained numbers of ACSC hospital admissions from the Hospital Episode Statistics database and information on recorded practice performance from the Quality and Outcomes Framework (QOF) administrative dataset for 2015/2016. We fitted three sets of negative binomial models to examine ecological associations between incentivised ACSC admissions, general practice performance, deprivation, urbanity and other sociodemographic characteristics.

RESULTS: Hospital admissions for QOF incentivised ACSCs varied within and between regions, with clusters of high numbers of hospital admissions for incentivised ACSCs identified across England. Our models indicated a very small effect of the QOF on reducing admissions for incentivised ACSCs (0.993, 95% CI 0.990 to 0.995), however, other factors, such as deprivation (1.021, 95% CI 1.020 to 1.021) and urbanicity (0.875, 95% CI 0.862 to 0.887), were far more important in explaining variations in admissions for ACSCs. People in deprived areas had a higher risk of being admitted in hospital for an incentivised ACSC condition.

CONCLUSION: Spatial analysis based on routinely collected data can be used to identify areas with high rates of potentially avoidable hospital admissions, providing valuable information for targeting resources and evaluating public health interventions. Our findings suggest that the QOF had a very small effect on reducing avoidable hospitalisation for incentivised conditions. Material deprivation and urbanicity were the strongest predictors of the variation in ACSC rates for all QOF incentivised conditions across England.}, } @article {pmid32907855, year = {2020}, author = {Knight, SR and Ho, A and Pius, R and Buchan, I and Carson, G and Drake, TM and Dunning, J and Fairfield, CJ and Gamble, C and Green, CA and Gupta, R and Halpin, S and Hardwick, HE and Holden, KA and Horby, PW and Jackson, C and Mclean, KA and Merson, L and Nguyen-Van-Tam, JS and Norman, L and Noursadeghi, M and Olliaro, PL and Pritchard, MG and Russell, CD and Shaw, CA and Sheikh, A and Solomon, T and Sudlow, C and Swann, OV and Turtle, LC and Openshaw, PJ and Baillie, JK and Semple, MG and Docherty, AB and Harrison, EM and , }, title = {Risk stratification of patients admitted to hospital with covid-19 using the ISARIC WHO Clinical Characterisation Protocol: development and validation of the 4C Mortality Score.}, journal = {BMJ (Clinical research ed.)}, volume = {370}, number = {}, pages = {m3339}, pmid = {32907855}, issn = {1756-1833}, support = {MC_PC_19059/MRC_/Medical Research Council/United Kingdom ; MC_UU_12014/9/MRC_/Medical Research Council/United Kingdom ; MR/V033441/1/MRC_/Medical Research Council/United Kingdom ; MR/R005982/1/MRC_/Medical Research Council/United Kingdom ; MR/S032304/1/MRC_/Medical Research Council/United Kingdom ; MC_PC_19025/MRC_/Medical Research Council/United Kingdom ; MC_PC_15001/MRC_/Medical Research Council/United Kingdom ; RP-2016-07-012/DH_/Department of Health/United Kingdom ; 207511/WT_/Wellcome Trust/United Kingdom ; 215091/WT_/Wellcome Trust/United Kingdom ; MC_PC_19026/MRC_/Medical Research Council/United Kingdom ; DRF-2018-11-ST2-004/DH_/Department of Health/United Kingdom ; 205228/WT_/Wellcome Trust/United Kingdom ; IS-HPU-1112-10117/DH_/Department of Health/United Kingdom ; }, mesh = {Aged ; Aged, 80 and over ; *Betacoronavirus ; COVID-19 ; Clinical Protocols ; Cohort Studies ; Coronavirus Infections/*diagnosis/*mortality ; Female ; Hospital Mortality ; *Hospitalization ; Humans ; Male ; Middle Aged ; Pandemics ; Pneumonia, Viral/*diagnosis/*mortality ; Predictive Value of Tests ; ROC Curve ; Risk Assessment ; SARS-CoV-2 ; Survival Rate ; United Kingdom ; }, abstract = {OBJECTIVE: To develop and validate a pragmatic risk score to predict mortality in patients admitted to hospital with coronavirus disease 2019 (covid-19).

DESIGN: Prospective observational cohort study.

SETTING: International Severe Acute Respiratory and emerging Infections Consortium (ISARIC) World Health Organization (WHO) Clinical Characterisation Protocol UK (CCP-UK) study (performed by the ISARIC Coronavirus Clinical Characterisation Consortium-ISARIC-4C) in 260 hospitals across England, Scotland, and Wales. Model training was performed on a cohort of patients recruited between 6 February and 20 May 2020, with validation conducted on a second cohort of patients recruited after model development between 21 May and 29 June 2020. PARTICIPANTS: Adults (age ≥18 years) admitted to hospital with covid-19 at least four weeks before final data extraction.

MAIN OUTCOME MEASURE: In-hospital mortality.

RESULTS: 35 463 patients were included in the derivation dataset (mortality rate 32.2%) and 22 361 in the validation dataset (mortality rate 30.1%). The final 4C Mortality Score included eight variables readily available at initial hospital assessment: age, sex, number of comorbidities, respiratory rate, peripheral oxygen saturation, level of consciousness, urea level, and C reactive protein (score range 0-21 points). The 4C Score showed high discrimination for mortality (derivation cohort: area under the receiver operating characteristic curve 0.79, 95% confidence interval 0.78 to 0.79; validation cohort: 0.77, 0.76 to 0.77) with excellent calibration (validation: calibration-in-the-large=0, slope=1.0). Patients with a score of at least 15 (n=4158, 19%) had a 62% mortality (positive predictive value 62%) compared with 1% mortality for those with a score of 3 or less (n=1650, 7%; negative predictive value 99%). Discriminatory performance was higher than 15 pre-existing risk stratification scores (area under the receiver operating characteristic curve range 0.61-0.76), with scores developed in other covid-19 cohorts often performing poorly (range 0.63-0.73).

CONCLUSIONS: An easy-to-use risk stratification score has been developed and validated based on commonly available parameters at hospital presentation. The 4C Mortality Score outperformed existing scores, showed utility to directly inform clinical decision making, and can be used to stratify patients admitted to hospital with covid-19 into different management groups. The score should be further validated to determine its applicability in other populations.

STUDY REGISTRATION: ISRCTN66726260.}, } @article {pmid32905909, year = {2020}, author = {Corami, F and Rosso, B and Roman, M and Picone, M and Gambaro, A and Barbante, C}, title = {Evidence of small microplastics (<100 μm) ingestion by Pacific oysters (Crassostrea gigas): A novel method of extraction, purification, and analysis using Micro-FTIR.}, journal = {Marine pollution bulletin}, volume = {160}, number = {}, pages = {111606}, doi = {10.1016/j.marpolbul.2020.111606}, pmid = {32905909}, issn = {1879-3363}, mesh = {Animals ; *Crassostrea ; Microplastics ; Plastics ; Spectroscopy, Fourier Transform Infrared ; *Water Pollutants, Chemical/analysis ; }, abstract = {Microplastics (MPs) are present in fresh, brackish, or marine waters. Micro- and macroinvertebrates can mistake MPs or small microplastics (SMPs, <100 μm) to be food particles and easily ingest them according to the size of their mouthparts. SMPs may then block the passage of food through the intestinal tract (i.e. hepatopancreas), accumulate within the organism, and enter the food web. Pacific oysters (Crassostrea gigas) are allochthonous filter-feeding bivalve mollusks, which have been introduced in coastal seas around the world in both natural banks and farms. Considering their economic and ecological value, these bivalves have been chosen as a model to study the ingestion of SMPs. A novel method for the extraction and purification of SMPs in bivalves was developed. Quantification and simultaneous polymer identification of SMPs using Micro-FTIR (Fourier Transform Infrared Spectroscopy) were performed, with a limit of detection for the particle size of 5 μm.}, } @article {pmid32904806, year = {2020}, author = {Henkhaus, N and Bartlett, M and Gang, D and Grumet, R and Jordon-Thaden, I and Lorence, A and Lyons, E and Miller, S and Murray, S and Nelson, A and Specht, C and Tyler, B and Wentworth, T and Ackerly, D and Baltensperger, D and Benfey, P and Birchler, J and Chellamma, S and Crowder, R and Donoghue, M and Dundore-Arias, JP and Fletcher, J and Fraser, V and Gillespie, K and Guralnick, L and Haswell, E and Hunter, M and Kaeppler, S and Kepinski, S and Li, FW and Mackenzie, S and McDade, L and Min, Y and Nemhauser, J and Pearson, B and Petracek, P and Rogers, K and Sakai, A and Sickler, D and Taylor, C and Wayne, L and Wendroth, O and Zapata, F and Stern, D}, title = {Plant science decadal vision 2020-2030: Reimagining the potential of plants for a healthy and sustainable future.}, journal = {Plant direct}, volume = {4}, number = {8}, pages = {e00252}, pmid = {32904806}, issn = {2475-4455}, abstract = {Plants, and the biological systems around them, are key to the future health of the planet and its inhabitants. The Plant Science Decadal Vision 2020-2030 frames our ability to perform vital and far-reaching research in plant systems sciences, essential to how we value participants and apply emerging technologies. We outline a comprehensive vision for addressing some of our most pressing global problems through discovery, practical applications, and education. The Decadal Vision was developed by the participants at the Plant Summit 2019, a community event organized by the Plant Science Research Network. The Decadal Vision describes a holistic vision for the next decade of plant science that blends recommendations for research, people, and technology. Going beyond discoveries and applications, we, the plant science community, must implement bold, innovative changes to research cultures and training paradigms in this era of automation, virtualization, and the looming shadow of climate change. Our vision and hopes for the next decade are encapsulated in the phrase reimagining the potential of plants for a healthy and sustainable future. The Decadal Vision recognizes the vital intersection of human and scientific elements and demands an integrated implementation of strategies for research (Goals 1-4), people (Goals 5 and 6), and technology (Goals 7 and 8). This report is intended to help inspire and guide the research community, scientific societies, federal funding agencies, private philanthropies, corporations, educators, entrepreneurs, and early career researchers over the next 10 years. The research encompass experimental and computational approaches to understanding and predicting ecosystem behavior; novel production systems for food, feed, and fiber with greater crop diversity, efficiency, productivity, and resilience that improve ecosystem health; approaches to realize the potential for advances in nutrition, discovery and engineering of plant-based medicines, and "green infrastructure." Launching the Transparent Plant will use experimental and computational approaches to break down the phytobiome into a "parts store" that supports tinkering and supports query, prediction, and rapid-response problem solving. Equity, diversity, and inclusion are indispensable cornerstones of realizing our vision. We make recommendations around funding and systems that support customized professional development. Plant systems are frequently taken for granted therefore we make recommendations to improve plant awareness and community science programs to increase understanding of scientific research. We prioritize emerging technologies, focusing on non-invasive imaging, sensors, and plug-and-play portable lab technologies, coupled with enabling computational advances. Plant systems science will benefit from data management and future advances in automation, machine learning, natural language processing, and artificial intelligence-assisted data integration, pattern identification, and decision making. Implementation of this vision will transform plant systems science and ripple outwards through society and across the globe. Beyond deepening our biological understanding, we envision entirely new applications. We further anticipate a wave of diversification of plant systems practitioners while stimulating community engagement, underpinning increasing entrepreneurship. This surge of engagement and knowledge will help satisfy and stoke people's natural curiosity about the future, and their desire to prepare for it, as they seek fuller information about food, health, climate and ecological systems.}, } @article {pmid32901704, year = {2020}, author = {Jaen-Varas, DC and Mari, JJ and Asevedo, E and Borschmann, R and Diniz, E and Ziebold, C and Gadelha, A}, title = {A 10-year ecological study of the methods of suicide used by Brazilian adolescents.}, journal = {Cadernos de saude publica}, volume = {36}, number = {8}, pages = {e00104619}, doi = {10.1590/0102-311X00104619}, pmid = {32901704}, issn = {1678-4464}, mesh = {Adolescent ; Adult ; Brazil/epidemiology ; Child ; Female ; Humans ; Male ; Odds Ratio ; Research Design ; Suicidal Ideation ; *Suicide ; Young Adult ; }, abstract = {Suicide among adolescents has become a major public health problem worldwide. Our study sought to describe the most commonly used methods of suicide among adolescents aged 10 to 19 years in Brazil between 2006 and 2015. Complete data were obtained from the Brazilian Health Informatics Department (DATASUS) and coded into seven categories of suicide methods. The following statistical analyzes were performed: chi-square (χ2) tests to examine the association between the frequency of each suicide method and the year; odds ratios (OR) and 95% confidence intervals (95%CI) compared the relative chances of each suicide method occurring between boys and girls. In total, 8,026 suicides among Brazilian adolescents were registered over the analyzed period. The most commonly used method of suicide by both sexes was hanging (2015 = 70.3%), and the most significant increase was observed in girls (2015 = 65.82%). The proportional use of arms (2006 = 14.2%; 2015 = 9.1%) and poisoning (2006 = 13.3%; 2015 = 9.2%) decreased over the period. The increase in hanging is worrisome, mostly due to difficulties to impose access barriers and to its high lethality. In such context, a comprehensive understanding of suicide behaviors among adolescents in Brazil should be drawn to inform general prevention measures and, more specifically, the reasons for the increase in hanging need to be further investigated.}, } @article {pmid32899582, year = {2020}, author = {Guo, Y and Wang, H and Wu, Z and Wang, S and Sun, H and Senthilnath, J and Wang, J and Robin Bryant, C and Fu, Y}, title = {Modified Red Blue Vegetation Index for Chlorophyll Estimation and Yield Prediction of Maize from Visible Images Captured by UAV.}, journal = {Sensors (Basel, Switzerland)}, volume = {20}, number = {18}, pages = {}, pmid = {32899582}, issn = {1424-8220}, support = {Grant No. 31770516//the General Program of National Nature Science Foundation of China/ ; 2017YFA06036001//the National Key Research and Development Program of China/ ; 2018EYT05//the 111 Project (B18006) and Fundamental Research Funds for the Central Universities/ ; }, abstract = {The vegetation index (VI) has been successfully used to monitor the growth and to predict the yield of agricultural crops. In this paper, a long-term observation was conducted for the yield prediction of maize using an unmanned aerial vehicle (UAV) and estimations of chlorophyll contents using SPAD-502. A new vegetation index termed as modified red blue VI (MRBVI) was developed to monitor the growth and to predict the yields of maize by establishing relationships between MRBVI- and SPAD-502-based chlorophyll contents. The coefficients of determination (R[2]s) were 0.462 and 0.570 in chlorophyll contents' estimations and yield predictions using MRBVI, and the results were relatively better than the results from the seven other commonly used VI approaches. All VIs during the different growth stages of maize were calculated and compared with the measured values of chlorophyll contents directly, and the relative error (RE) of MRBVI is the lowest at 0.355. Further, machine learning (ML) methods such as the backpropagation neural network model (BP), support vector machine (SVM), random forest (RF), and extreme learning machine (ELM) were adopted for predicting the yields of maize. All VIs calculated for each image captured during important phenological stages of maize were set as independent variables and the corresponding yields of each plot were defined as dependent variables. The ML models used the leave one out method (LOO), where the root mean square errors (RMSEs) were 2.157, 1.099, 1.146, and 1.698 (g/hundred grain weight) for BP, SVM, RF, and ELM. The mean absolute errors (MAEs) were 1.739, 0.886, 0.925, and 1.356 (g/hundred grain weight) for BP, SVM, RF, and ELM, respectively. Thus, the SVM method performed better in predicting the yields of maize than the other ML methods. Therefore, it is strongly suggested that the MRBVI calculated from images acquired at different growth stages integrated with advanced ML methods should be used for agricultural- and ecological-related chlorophyll estimation and yield predictions.}, } @article {pmid32893553, year = {2020}, author = {Li, M and Zhang, XB and Jing, ZX and Yu, FL and Huang, S and Wang, J and Kang, LP and Wang, L}, title = {[Comparative study on distribution of Callicarpa nudiflora by different regionalization methods].}, journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica}, volume = {45}, number = {15}, pages = {3642-3650}, doi = {10.19540/j.cnki.cjcmm.20200527.101}, pmid = {32893553}, issn = {1001-5302}, mesh = {*Callicarpa ; China ; Data Collection ; Information Storage and Retrieval ; Vietnam ; }, abstract = {This article is based on basic data such as field surveys and literature surveys, contrasting and analyzing the distribution of Callicarpa nudiflora by different zoning methods, different data sources, and different spatial scales. The results showed that there were certain differences in the distribution results obtained by using different methods, such as qualitative description, similar ecological environment, and niche model, to divide the distribution of the C. nudiflora, but all of them could reflect the distribution of C. nudiflora to different degrees. Among them, the qualitative description division method has certain advantages in macro guidance in a large scale. The distribution range obtained by the ecological environment similar division method is wider than that obtained by applying the qualitative description method and the niche model method. The results of the zoning of the distribution of the C. nudiflora obtained from different data sources were different. The number and representativeness of the survey data have an impact on the zoning results. Through the analysis of the distribution of different spatial scales, the ecological factors and contribution rates that affect the distribution of C. nudiflora are different in China and in the world. The comprehensive multi-source data analysis showed that C. nudiflora mainly distributed in southern coastal provinces such as Hainan, Guangdong, Guangxi and Fujian in China, and also in Jiangxi, Guizhou, Yunnan, Sichuan, Chongqing, Hunan, Gansu, Taiwan and other provinces. Globally, C. nudiflora are suitable for distribution in Southeast Asia, such as China, Vietnam, Laos, Myanmar, India, etc. There are also potential distribution areas in the southern United States and Mexico.}, } @article {pmid32893552, year = {2020}, author = {Fan, JY and Ding, R and Zhao, MM and Wang, M and Gu, R and Zhong, SH}, title = {[Geological distribution of exudation and storage area of Tibetan medicine Zha-xun in Sichuan province based on GIS].}, journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica}, volume = {45}, number = {15}, pages = {3631-3641}, doi = {10.19540/j.cnki.cjcmm.20200527.103}, pmid = {32893552}, issn = {1001-5302}, mesh = {China ; *Geographic Information Systems ; Geology ; *Medicine, Tibetan Traditional ; Medicine, Traditional ; Temperature ; }, abstract = {Zha-xun is widely used in Tibetan medicine and is also an international traditional medicine. This study believes that the black organic matter constituting Zha-xun is mainly stored in the rocks. The exudation points of Zha-xun mostly distribute on the cliffs of high mountains, which makes it difficult to evaluate its resource distribution and storage area. This paper was aimed at the exudation environment of Tibetan medicine Zha-xun in Sichuan province and 6 ecological environmental factors of the Zha-xun were determined via the field investigation. Combining with these 6 factors as well as the GIS data of Sichuan province, ArcGIS software was used to extract ideal environmental factors which are suitable for exudation of Zha-xun, including geology types, geomorphological types, altitude, slope, vegetation types, and mean annual temperature. The spatial overlay analyses on the extracted environmental factors were carried out to predict the distribution area of Zha-xun in Sichuan province. Afterwards, field investigation was conducted to verify the prediction. The prediction showed that the exudation spots of Zha-xun in Sichuan province mainly located in 29 counties including 12 in Aba Prefecture, 15 in Ganzi Prefecture, and Muli County and Dechang County in Liangshan Prefecture. The deposit areas of Zha-xun were located in the Triassic, Devonian and Silurian strata and were basically distributed in 9 basins, including Dingqu River, Yalong River, Xianshui River, Dadu River, Suomo River, Minjiang River and Baishui River, characterized by a fragmented patch-like distribution along the mountain ranges, and the exudation spots of Zha-xun were mainly scattered among the rain-free cliffs' concavities of river valleys at a certain altitude. The prediction was consistent with the field investigation results, which suggested that it is possible and feasible to predict distribution of Zha-xun resources based on GIS-analysis. The study may provide a scientific basis for comprehensive investigations into Zha-xun's distribution and formation mechanism, thus promoting rational development and utilization of Zha-xun resources.}, } @article {pmid32891993, year = {2021}, author = {Li, K and Xu, T and Xi, J and Jia, H and Gao, Z and Sun, Z and Yin, D and Leng, L}, title = {Multi-factor analysis of algal blooms in gate-controlled urban water bodies by data mining.}, journal = {The Science of the total environment}, volume = {753}, number = {}, pages = {141821}, doi = {10.1016/j.scitotenv.2020.141821}, pmid = {32891993}, issn = {1879-1026}, mesh = {China ; Cities ; Data Mining ; *Environmental Monitoring ; *Eutrophication ; Factor Analysis, Statistical ; Humans ; Lakes ; Phosphorus/analysis ; }, abstract = {Intense human disturbance has made algal bloom a prominent environmental problem in gate-controlled urban water bodies. Urban water bodies present the characteristics of natural rivers and lakes simultaneously, whose algal blooms may manifest multi-factor interactions. Hence, effective regulation strategies require a multi-factor analysis to understand local blooming mechanisms. This study designed a holistic multi-factor analysis framework by integrating five data mining techniques. First, the Kolmogorov-Smirnov test was conducted to screen out the possible explanatory variables. Then, correlation analyses and principal component analyses were performed to identify variable collinearity and mutual causality, respectively. After collinearity and mutual causality were treated prudently by using orthogonalization and instrumental variables, multilinear regression can be properly conducted to quantify factor contributions to algae growth. Lastly, a decision tree was used innovatively to depict the limiting threshold curves of each driving factor that restricts algae growth under different circumstances. The driving factors, their contributions, and the limiting threshold curves compose the complete blooming mechanisms, thus providing a clear direction for the targeted regulation task. A typical case study was performed in Suzhou, a Chinese city with an intricate gate-controlled river network. Results confirmed that climatic factors (i.e., water temperature and solar radiation), hydrodynamic factors (i.e., flow velocity), nutrients (i.e., phosphorus and nitrogen), and external loadings contributed 49.3%, 21.7%, 21.3%, and 7.7%, respectively, to algae growth. These results indicate that a joint regulation strategy is urgently required. Future studies can focus on coupling the revealed mechanisms with an ecological model to provide a comprehensive toolkit for the optimization of an adaptive joint regulation plan under the background of global warming.}, } @article {pmid32891983, year = {2020}, author = {Schwarz, JN}, title = {Dynamic partitioning of tropical Indian Ocean surface waters using ocean colour data - management and modelling applications.}, journal = {Journal of environmental management}, volume = {276}, number = {}, pages = {111308}, doi = {10.1016/j.jenvman.2020.111308}, pmid = {32891983}, issn = {1095-8630}, mesh = {*Chlorophyll/analysis ; Color ; Indian Ocean ; Temperature ; *Wind ; }, abstract = {Over the past few decades, partitioning of the surface ocean into ecologically-meaningful spatial domains has been approached using a range of data types, with the aim of improving our understanding of open ocean processes, supporting marine management decisions and constraining coupled ocean-biogeochemical models. The simplest partitioning method, which could provide low-latency information for managers at low cost, remains a purely optical classification based on ocean colour remote sensing. The question is whether such a simple approach has value. Here, the efficacy of optical classifications in constraining physical variables that modulate the epipelagic environment is tested for the tropical Indian Ocean, with a focus on the Chagos marine protected area (MPA). Using remote sensing data, it was found that optical classes corresponded to distinctive ranges of wind speed, wind stress curl, sea surface temperature, sea surface slope, sea surface height anomaly and geostrophic currents (Kruskal-Wallis and post-hoc Tukey honestly significantly different tests, α = 0.01). Between-class differences were significant for a set of sub-domains that resolved zonal and meridional gradients across the MPA and Seychelles-Chagos Thermocline Ridge, whereas between-domain differences were only significant for the north-south gradient (PERMANOVA, α = 0.01). A preliminary test of between-class differences in surface CO2 concentrations from the Orbiting Carbon Observatory-2 demonstrated a small decrease in mean pCO2 with increasing chlorophyll (chl), from 418 to 398 ppm. Simple optical class maps therefore provide an overview of growth conditions, the spatial distribution of resources - from which habitat fragmentation metrics can be calculated, and carbon sequestration potential. Within the 17 year study period, biotic variables were found to have decreased at up to 0.025%a[-1] for all optical classes, which is slower than reported elsewhere (Mann-Kendall-Sen regression, α = 0.01). Within the MPA, positive Indian Ocean Dipole conditions and negative Southern Oscillation Indices were weakly associated with decreasing chl, fluorescence line height (FLH), eddy kinetic energy, easterly wind stress and wind stress curl, and with increasing FLH/chl, sea surface temperature, SSH gradients and northerly wind stress, consistent with reduced surface mixing and increased stratification. The optical partitioning scheme described here can be applied in Google Earth Engine to support management decisions at daily or monthly scales, and potential applications are discussed.}, } @article {pmid32887735, year = {2020}, author = {Ladner, JT and Larsen, BB and Bowers, JR and Hepp, CM and Bolyen, E and Folkerts, M and Sheridan, K and Pfeiffer, A and Yaglom, H and Lemmer, D and Sahl, JW and Kaelin, EA and Maqsood, R and Bokulich, NA and Quirk, G and Watts, TD and Komatsu, KK and Waddell, V and Lim, ES and Caporaso, JG and Engelthaler, DM and Worobey, M and Keim, P}, title = {An Early Pandemic Analysis of SARS-CoV-2 Population Structure and Dynamics in Arizona.}, journal = {mBio}, volume = {11}, number = {5}, pages = {}, pmid = {32887735}, issn = {2150-7511}, support = {R00 DK107923/DK/NIDDK NIH HHS/United States ; }, mesh = {Arizona/epidemiology ; Betacoronavirus/classification/*genetics/isolation & purification ; COVID-19 ; Coronavirus Infections/*epidemiology/*transmission/virology ; Evolution, Molecular ; Genome, Viral/genetics ; Humans ; Incidence ; Mutation ; Pandemics ; Phylogeny ; Pneumonia, Viral/*epidemiology/*transmission/virology ; SARS-CoV-2 ; Viral Proteins/genetics ; }, abstract = {In December of 2019, a novel coronavirus, SARS-CoV-2, emerged in the city of Wuhan, China, causing severe morbidity and mortality. Since then, the virus has swept across the globe, causing millions of confirmed infections and hundreds of thousands of deaths. To better understand the nature of the pandemic and the introduction and spread of the virus in Arizona, we sequenced viral genomes from clinical samples tested at the TGen North Clinical Laboratory, the Arizona Department of Health Services, and those collected as part of community surveillance projects at Arizona State University and the University of Arizona. Phylogenetic analysis of 84 genomes from across Arizona revealed a minimum of 11 distinct introductions inferred to have occurred during February and March. We show that >80% of our sequences descend from strains that were initially circulating widely in Europe but have since dominated the outbreak in the United States. In addition, we show that the first reported case of community transmission in Arizona descended from the Washington state outbreak that was discovered in late February. Notably, none of the observed transmission clusters are epidemiologically linked to the original travel-related case in the state, suggesting successful early isolation and quarantine. Finally, we use molecular clock analyses to demonstrate a lack of identifiable, widespread cryptic transmission in Arizona prior to the middle of February 2020.IMPORTANCE As the COVID-19 pandemic swept across the United States, there was great differential impact on local and regional communities. One of the earliest and hardest hit regions was in New York, while at the same time Arizona (for example) had low incidence. That situation has changed dramatically, with Arizona now having the highest rate of disease increase in the country. Understanding the roots of the pandemic during the initial months is essential as the pandemic continues and reaches new heights. Genomic analysis and phylogenetic modeling of SARS-COV-2 in Arizona can help to reconstruct population composition and predict the earliest undetected introductions. This foundational work represents the basis for future analysis and understanding as the pandemic continues.}, } @article {pmid32886993, year = {2020}, author = {Harnisz, M and Kiedrzyńska, E and Kiedrzyński, M and Korzeniewska, E and Czatzkowska, M and Koniuszewska, I and Jóźwik, A and Szklarek, S and Niestępski, S and Zalewski, M}, title = {The impact of WWTP size and sampling season on the prevalence of antibiotic resistance genes in wastewater and the river system.}, journal = {The Science of the total environment}, volume = {741}, number = {}, pages = {140466}, doi = {10.1016/j.scitotenv.2020.140466}, pmid = {32886993}, issn = {1879-1026}, mesh = {Anti-Bacterial Agents ; Drug Resistance, Microbial ; Genes, Bacterial ; Prevalence ; RNA, Ribosomal, 16S ; *Rivers ; Seasons ; Wastewater/*analysis ; }, abstract = {There is a growing concern about the fate of antibiotic resistance genes (ARGs) during wastewater treatment and their potential impacts on the receiving water bodies. We hypothesised that the quantity of ARGs in effluents may be related to the size of wastewater treatment plants (WWTPs) and sampling season. To date, only several attempts have been made to investigate the impact of the above factors at the catchment scale. Therefore, the goal of the present study was to explore possible differences in the quantity of ARGs in treated wastewater from small, medium-sized and large WWTPs in the catchment of the Pilica River (9258 km[2]). The impact of treated wastewater on the concentration of ARGs was also determined along the river continuum from upland to lowland segments to the point of confluence with the Vistula (342 km). Treated effluent was sampled in 17 WWTPs, and river water was sampled in 7 sampling sites in four seasons. The concentrations of blaTEM, tet(A), ermF, sul1 and aac(6')-Ib-cr genes, the integrase gene intI1 and the 16S rRNA gene were analysed by quantitative PCR. The physical and chemical parameters and nutrient concentrations (23 various parameters) in the analysed samples were determined. The highest absolute concentrations of the studied genes were noted in effluent samples from small WWTPs (p < 0.01). The concentration of ARGs (gene copies/mL) peaked in winter and spring samples (p < 0.04). The results of statistical analyses indicate that in small WWTPs, the absolute concentration of ARGs can be predicted based on the biochemical oxygen demand, in routine water analyses. However, none of the studied parameters supported predictions of ARG abundance in medium-sized and large WWTPs or in river water.}, } @article {pmid32885451, year = {2021}, author = {Richardson, AD and Aubrecht, DM and Basler, D and Hufkens, K and Muir, CD and Hanssen, L}, title = {Developmental changes in the reflectance spectra of temperate deciduous tree leaves and implications for thermal emissivity and leaf temperature.}, journal = {The New phytologist}, volume = {229}, number = {2}, pages = {791-804}, pmid = {32885451}, issn = {1469-8137}, mesh = {*Plant Leaves ; Seasons ; Spectrum Analysis ; Temperature ; *Trees ; }, abstract = {Leaf optical properties impact leaf energy balance and thus leaf temperature. The effect of leaf development on mid-infrared (MIR) reflectance, and hence thermal emissivity, has not been investigated in detail. We measured a suite of morphological characteristics, as well as directional-hemispherical reflectance from ultraviolet to thermal infrared wavelengths (250 nm to 20 µm) of leaves from five temperate deciduous tree species over the 8 wk following spring leaf emergence. By contrast to reflectance at shorter wavelengths, the shape and magnitude of MIR reflectance spectra changed markedly with development. MIR spectral differences among species became more pronounced and unique as leaves matured. Comparison of reflectance spectra of intact vs dried and ground leaves points to cuticular development - and not internal structural or biochemical changes - as the main driving factor. Accompanying the observed spectral changes was a drop in thermal emissivity from about 0.99 to 0.95 over the 8 wk following leaf emergence. Emissivity changes were not large enough to substantially influence leaf temperature, but they could potentially lead to a bias in radiometrically measured temperatures of up to 3 K. Our results also pointed to the potential for using MIR spectroscopy to better understand species-level differences in cuticular development and composition.}, } @article {pmid32883435, year = {2020}, author = {Therkildsen, NO and Baumann, H}, title = {A comprehensive non-redundant reference transcriptome for the Atlantic silverside Menidia menidia.}, journal = {Marine genomics}, volume = {53}, number = {}, pages = {100738}, doi = {10.1016/j.margen.2019.100738}, pmid = {32883435}, issn = {1876-7478}, mesh = {Animals ; Fishes/*genetics ; Gene Expression Profiling ; Gene Ontology ; *Genome ; *Transcriptome ; }, abstract = {The Atlantic silverside (Menidia menidia) has been the focus of extensive research efforts in ecology, evolutionary biology, and physiology over the past three decades, but lack of genomic resources has so far hindered examination of the molecular basis underlying the remarkable patterns of phenotypic variation described in this species. We here present the first reference transcriptome for M. menidia. We sought to capture a single representative sequence from as many genes as possible by first using a combination of Trinity and the CLC Genomics Workbench to de novo assemble contigs based on RNA-seq data from multiple individuals, tissue types, and life stages. To reduce redundancy, we passed the combined raw assemblies through a stringent filtering pipeline based both on sequence similarity to related species and computational predictions of transcript quality, condensing an initial set of >480,000 contigs to a final set of 20,998 representative contigs, amounting to a total length of 53.3 Mb. In this final assembly, 91% of the contigs were functionally annotated with putative gene function and gene ontology (GO) terms and/or InterProScan identifiers. The assembly contains complete or nearly complete copies of >95% of 248 highly conserved core genes present in low copy number across higher eukaryotes, and partial copies of another 3.8%, suggesting that our assembly provides relatively comprehensive coverage of the M. menidia transcriptome. The assembly provided here will be an important resource for future research.}, } @article {pmid32882617, year = {2020}, author = {Li, H and Jia, S and Tang, Y and Jiang, Y and Yang, S and Zhang, J and Yan, B and Wang, Y and Guo, J and Zhao, S and Yang, Q and Shao, R}, title = {A transcriptomic analysis reveals the adaptability of the growth and physiology of immature tassel to long-term soil water deficit in Zea mays L.}, journal = {Plant physiology and biochemistry : PPB}, volume = {155}, number = {}, pages = {756-768}, doi = {10.1016/j.plaphy.2020.08.027}, pmid = {32882617}, issn = {1873-2690}, mesh = {*Droughts ; Gene Expression Regulation, Plant ; Gene Ontology ; Inflorescence/*growth & development ; Soil ; *Stress, Physiological ; *Transcriptome ; Water ; Zea mays/genetics/*physiology ; }, abstract = {Drought is a key threat to maize growth and yield. Understanding the mechanism of immature tassel (IT) response to long term drought is of paramount importance. Here, the maize inbred line PH6WC was tested under well-watered (CK) and two water deficit treatments (WD1 and WD2). The final IT length in the WD1 and WD2 treatments decreased by nearly 6.2% and 21.2% compared to the CK, respectively, and the average accumulation rate IT dry matter was 1.5-fold and 1.8-fold slower, respectively. Furthermore, RNA sequencing analysis was conducted on the IT sampled at 30 days after the WD treatments. In total, the cellular component in gene ontology (GO) analysis suggested that the differentially expressed genes were significantly enriched in three common terms (apoplast, plant-type cell wall, and anchored component of membrane) among the CK vs WD1, CK vs WD2, and WD1 vs WD2 comparisons. Next, a co-expression network analysis identified 44 modules that contained global expression genes. Finally, by combining the GO analysis with modules, nine genes involved in carbohydrate metabolism and the antioxidant system were screened out, and the six corresponding physiological parameters were all significantly increased under the WD treatments. These results showed that, although the IT length and dry matter decreased, the IT enhanced the adaptation to drought by regulating their own genetic and physiological changes.}, } @article {pmid32882595, year = {2020}, author = {Papinutto, M and Lao, J and Lalanne, D and Caldara, R}, title = {Watchers do not follow the eye movements of Walkers.}, journal = {Vision research}, volume = {176}, number = {}, pages = {130-140}, doi = {10.1016/j.visres.2020.08.001}, pmid = {32882595}, issn = {1878-5646}, mesh = {Adaptation, Physiological ; *Eye Movements ; *Fixation, Ocular ; Humans ; Saccades ; }, abstract = {Eye movements are a functional signature of how the visual system effectively decodes and adapts to the environment. However, scientific knowledge in eye movements mostly arises from studies conducted in laboratories, with well-controlled stimuli presented in constrained unnatural settings. Only a few studies have attempted to directly compare and assess whether eye movement data acquired in the real world generalize with those in laboratory settings, with same visual inputs. However, none of these studies controlled for both the auditory signals typical of real-world settings and the top-down task effects across conditions, leaving this question unresolved. To minimize this inherent gap across conditions, we compared the eye movements recorded from observers during ecological spatial navigation in the wild (the Walkers) with those recorded in laboratory (the Watchers) on the same visual and auditory inputs, with both groups performing the very same active cognitive task. We derived robust data-driven statistical saliency and motion maps. The Walkers and Watchers differed in terms of eye movement characteristics: fixation number and duration, saccade amplitude. The Watchers relied significantly more on saliency and motion than the Walkers. Interestingly, both groups exhibited similar fixation patterns towards social agents and objects. Altogether, our data show that eye movements patterns obtained in laboratory do not fully generalize to real world, even when task and auditory information is controlled. These observations invite to caution when generalizing the eye movements obtained in laboratory with those of ecological spatial navigation.}, } @article {pmid32879395, year = {2020}, author = {Richard, JC and Leis, E and Dunn, CD and Agbalog, R and Waller, D and Knowles, S and Putnam, J and Goldberg, TL}, title = {Mass mortality in freshwater mussels (Actinonaias pectorosa) in the Clinch River, USA, linked to a novel densovirus.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {14498}, pmid = {32879395}, issn = {2045-2322}, mesh = {Animals ; Biodiversity ; Computational Biology ; Densovirus/*pathogenicity ; Ecosystem ; Environmental Monitoring ; Genome ; Genomics ; Open Reading Frames ; Parvoviridae Infections/mortality/*veterinary ; Phylogeny ; Rivers ; Tennessee ; Unionidae/*virology ; Viral Load ; Virginia ; }, abstract = {Freshwater mussels (order Unionida) are among the world's most biodiverse but imperiled taxa. Recent unionid mass mortality events around the world threaten ecosystem services such as water filtration, nutrient cycling, habitat stabilization, and food web enhancement, but causes have remained elusive. To examine potential infectious causes of these declines, we studied mussels in Clinch River, Virginia and Tennessee, USA, where the endemic and once-predominant pheasantshell (Actinonaias pectorosa) has suffered precipitous declines since approximately 2016. Using metagenomics, we identified 17 novel viruses in Clinch River pheasantshells. However, only one virus, a novel densovirus (Parvoviridae; Densovirinae), was epidemiologically linked to morbidity. Clinch densovirus 1 was 11.2 times more likely to be found in cases (moribund mussels) than controls (apparently healthy mussels from the same or matched sites), and cases had 2.7 (log10) times higher viral loads than controls. Densoviruses cause lethal epidemic disease in invertebrates, including shrimp, cockroaches, crickets, moths, crayfish, and sea stars. Viral infection warrants consideration as a factor in unionid mass mortality events either as a direct cause, an indirect consequence of physiological compromise, or a factor interacting with other biological and ecological stressors to precipitate mortality.}, } @article {pmid32873781, year = {2020}, author = {Jiang, S and Zhou, D and Wang, YY and Jia, P and Wan, C and Li, X and He, G and Cao, D and Jiang, X and Kendler, KS and Tsuang, M and Mize, T and Wu, JS and Lu, Y and He, L and Chen, J and Zhao, Z and Chen, X}, title = {Identification of de novo mutations in prenatal neurodevelopment-associated genes in schizophrenia in two Han Chinese patient-sibling family-based cohorts.}, journal = {Translational psychiatry}, volume = {10}, number = {1}, pages = {307}, pmid = {32873781}, issn = {2158-3188}, support = {R01 LM012806/LM/NLM NIH HHS/United States ; R01 MH085560/MH/NIMH NIH HHS/United States ; R01 MH101054/MH/NIMH NIH HHS/United States ; }, mesh = {China ; Connexins/genetics ; Genetic Predisposition to Disease ; Genome-Wide Association Study ; Humans ; Mutation ; *Schizophrenia/genetics ; Siblings ; }, abstract = {Schizophrenia (SCZ) is a severe psychiatric disorder with a strong genetic component. High heritability of SCZ suggests a major role for transmitted genetic variants. Furthermore, SCZ is also associated with a marked reduction in fecundity, leading to the hypothesis that alleles with large effects on risk might often occur de novo. In this study, we conducted whole-genome sequencing for 23 families from two cohorts with unaffected siblings and parents. Two nonsense de novo mutations (DNMs) in GJC1 and HIST1H2AD were identified in SCZ patients. Ten genes (DPYSL2, NBPF1, SDK1, ZNF595, ZNF718, GCNT2, SNX9, AACS, KCNQ1, and MSI2) were found to carry more DNMs in SCZ patients than their unaffected siblings by burden test. Expression analyses indicated that these DNM implicated genes showed significantly higher expression in prefrontal cortex in prenatal stage. The DNM in the GJC1 gene is highly likely a loss function mutation (pLI = 0.94), leading to the dysregulation of ion channel in the glutamatergic excitatory neurons. Analysis of rare variants in independent exome sequencing dataset indicates that GJC1 has significantly more rare variants in SCZ patients than in unaffected controls. Data from genome-wide association studies suggested that common variants in the GJC1 gene may be associated with SCZ and SCZ-related traits. Genes co-expressed with GJC1 are involved in SCZ, SCZ-associated pathways, and drug targets. These evidences suggest that GJC1 may be a risk gene for SCZ and its function may be involved in prenatal and early neurodevelopment, a vulnerable period for developmental disorders such as SCZ.}, } @article {pmid32871096, year = {2020}, author = {Eyre, MT and Carvalho-Pereira, TSA and Souza, FN and Khalil, H and Hacker, KP and Serrano, S and Taylor, JP and Reis, MG and Ko, AI and Begon, M and Diggle, PJ and Costa, F and Giorgi, E}, title = {A multivariate geostatistical framework for combining multiple indices of abundance for disease vectors and reservoirs: a case study of rattiness in a low-income urban Brazilian community.}, journal = {Journal of the Royal Society, Interface}, volume = {17}, number = {170}, pages = {20200398}, pmid = {32871096}, issn = {1742-5662}, support = {MR/T029781/1/MRC_/Medical Research Council/United Kingdom ; UL1 TR001863/TR/NCATS NIH HHS/United States ; F31 AI114245/AI/NIAID NIH HHS/United States ; 102330/Z/13/Z/WT_/Wellcome Trust/United Kingdom ; R01 TW009504/TW/FIC NIH HHS/United States ; /WT_/Wellcome Trust/United Kingdom ; U01 AI088752/AI/NIAID NIH HHS/United States ; 218987/Z/19/Z/WT_/Wellcome Trust/United Kingdom ; R25 TW009338/TW/FIC NIH HHS/United States ; MR/P024084/1/MRC_/Medical Research Council/United Kingdom ; R01 AI052473/AI/NIAID NIH HHS/United States ; 1964635/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Animals ; Brazil/epidemiology ; Disease Reservoirs ; *Insect Vectors ; Rats ; *Zoonoses ; }, abstract = {A key requirement in studies of endemic vector-borne or zoonotic disease is an estimate of the spatial variation in vector or reservoir host abundance. For many vector species, multiple indices of abundance are available, but current approaches to choosing between or combining these indices do not fully exploit the potential inferential benefits that might accrue from modelling their joint spatial distribution. Here, we develop a class of multivariate generalized linear geostatistical models for multiple indices of abundance. We illustrate this novel methodology with a case study on Norway rats in a low-income urban Brazilian community, where rat abundance is a likely risk factor for human leptospirosis. We combine three indices of rat abundance to draw predictive inferences on a spatially continuous latent process, rattiness, that acts as a proxy for abundance. We show how to explore the association between rattiness and spatially varying environmental factors, evaluate the relative importance of each of the three contributing indices and assess the presence of residual, unexplained spatial variation, and identify rattiness hotspots. The proposed methodology is applicable more generally as a tool for understanding the role of vector or reservoir host abundance in predicting spatial variation in the risk of human disease.}, } @article {pmid32870907, year = {2020}, author = {Vergara, D and Gaudino, R and Blank, T and Keegan, B}, title = {Modeling cannabinoids from a large-scale sample of Cannabis sativa chemotypes.}, journal = {PloS one}, volume = {15}, number = {9}, pages = {e0236878}, pmid = {32870907}, issn = {1932-6203}, mesh = {Cannabinoids/*analysis ; Cannabis/*chemistry/classification ; Databases, Chemical ; Plant Extracts/*chemistry ; }, abstract = {The widespread legalization of Cannabis has opened the industry to using contemporary analytical techniques for chemotype analysis. Chemotypic data has been collected on a large variety of oil profiles inherent to the cultivars that are commercially available. The unknown gene regulation and pharmacokinetics of dozens of cannabinoids offer opportunities of high interest in pharmacology research. Retailers in many medical and recreational jurisdictions are typically required to report chemical concentrations of at least some cannabinoids. Commercial cannabis laboratories have collected large chemotype datasets of diverse Cannabis cultivars. In this work a data set of 17,600 cultivars tested by Steep Hill Inc., is examined using machine learning techniques to interpolate missing chemotype observations and cluster cultivars into groups based on chemotype similarity. The results indicate cultivars cluster based on their chemotypes, and that some imputation methods work better than others at grouping these cultivars based on chemotypic identity. Due to the missing data and to the low signal to noise ratio for some less common cannabinoids, their behavior could not be accurately predicted. These findings have implications for characterizing complex interactions in cannabinoid biosynthesis and improving phenotypical classification of Cannabis cultivars.}, } @article {pmid32870399, year = {2020}, author = {Hinkelman, J and Vršanský, P and Garcia, T and Tejedor, A and Bertner, P and Sorokin, A and Gallice, GR and Koubová, I and Nagy, Š and Vidlička, Ľ}, title = {Neotropical Melyroidea group cockroaches reveal various degrees of (eu)sociality.}, journal = {Die Naturwissenschaften}, volume = {107}, number = {5}, pages = {39}, doi = {10.1007/s00114-020-01694-x}, pmid = {32870399}, issn = {1432-1904}, support = {APVV0436-12//Agentúra na Podporu Výskumu a Vývoja/ ; VEGA 2/0042/18//Vedecká Grantová Agentúra MŠVVaŠ SR a SAV/ ; VEGA 2/0139/17//Vedecká Grantová Agentúra MŠVVaŠ SR a SAV/ ; AMBA//United Nations Educational, Scientific and Cultural Organization/ ; }, mesh = {Animals ; Cockroaches/*physiology ; Ecuador ; Female ; Peru ; Phylogeny ; *Social Behavior ; Tropical Climate ; }, abstract = {Eusociality in its various degrees represents an animal social system characterised by cooperative brood care, differentiation into castes and generational overlap. The fossil record indicates that eusociality is likely to have originated in hymenopterans and blattodeans during the Cretaceous. In this study, we present findings from surveys in Peruvian (Villa Carmen) and Ecuadorian (Rio Bigal, El Reventador) cloud forests revealing the first extant cockroach species living in complex, structured groups (n = 90-200 individuals, ˃ 20 adults). We observed and described behaviours that suggest the existence of cooperative care, nest guarding, nest chamber preparation within hardwood Casearia sp. (Salicaceae) and bamboo (Bambusoideae), multiple overlapping generations ('different stages of' instars), colony translocation, possibly a sole reproductive female (1.25 times larger white 'queen', but no potential 'king' observed), and morphologically diversified immature stages. In order to define the lineage where this type of sociality originated and occurs, the forms of Melyroidea magnifica Shelford, 1912, M. ecuadoriana sp. n., M. mimetica Shelford, 1912 and an undescribed species from Peru are also described in a separate section of this study. Blattoid morphological characteristics such as typical styli suggest categorisation within distinct Oulopterygidae (Rehn, 1951), outside Corydiidae Saussure 1864. Transitional advanced sociality or semisociality in related Aclavoidea socialis gen. et sp. n. is documented in a rotting stump (n = 80 individuals, few adults). Close phylogenetic relation between the genera, conserved morphology of numerous characters and their diverse feeding strategies generally lacking specialisation suggests a rather recent origin of a social way of life in this group. Eusociality in invertebrates and vertebrates can thus originate in various phylogenetical and ecological trajectories including predation, parasitism, care for herbs and the new one, documented through diet shift from detritivory to fungivory and algaevory. Interdisciplinary approaches reveal the low degree of knowledge of rainforest ecosystems, with fundamental groups remaining still systematically and also behaviourally undescribed.}, } @article {pmid32870239, year = {2020}, author = {Shen, Y and Li, C and Dong, H and Wang, Z and Martinez, L and Sun, Z and Handel, A and Chen, Z and Chen, E and Ebell, MH and Wang, F and Yi, B and Wang, H and Wang, X and Wang, A and Chen, B and Qi, Y and Liang, L and Li, Y and Ling, F and Chen, J and Xu, G}, title = {Community Outbreak Investigation of SARS-CoV-2 Transmission Among Bus Riders in Eastern China.}, journal = {JAMA internal medicine}, volume = {180}, number = {12}, pages = {1665-1671}, pmid = {32870239}, issn = {2168-6114}, mesh = {Air Pollution ; *COVID-19/diagnosis/epidemiology/prevention & control/transmission ; China/epidemiology ; Cohort Studies ; Communicable Disease Control/*methods ; *Community-Acquired Infections/diagnosis/epidemiology/prevention & control/transmission ; Disease Transmission, Infectious/prevention & control/statistics & numerical data ; Female ; Humans ; Male ; Middle Aged ; Motor Vehicles/*statistics & numerical data ; Risk Assessment ; *SARS-CoV-2/isolation & purification/pathogenicity ; Transportation/*methods ; }, abstract = {IMPORTANCE: Evidence of whether severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus that causes coronavirus disease 2019 (COVID-19), can be transmitted as an aerosol (ie, airborne) has substantial public health implications.

OBJECTIVE: To investigate potential transmission routes of SARS-CoV-2 infection with epidemiologic evidence from a COVID-19 outbreak.

This cohort study examined a community COVID-19 outbreak in Zhejiang province. On January 19, 2020, 128 individuals took 2 buses (60 [46.9%] from bus 1 and 68 [53.1%] from bus 2) on a 100-minute round trip to attend a 150-minute worship event. The source patient was a passenger on bus 2. We compared risks of SARS-CoV-2 infection among at-risk individuals taking bus 1 (n = 60) and bus 2 (n = 67 [source patient excluded]) and among all other individuals (n = 172) attending the worship event. We also divided seats on the exposed bus into high-risk and low-risk zones according to the distance from the source patient and compared COVID-19 risks in each zone. In both buses, central air conditioners were in indoor recirculation mode.

MAIN OUTCOMES AND MEASURES: SARS-CoV-2 infection was confirmed by reverse transcription polymerase chain reaction or by viral genome sequencing results. Attack rates for SARS-CoV-2 infection were calculated for different groups, and the spatial distribution of individuals who developed infection on bus 2 was obtained.

RESULTS: Of the 128 participants, 15 (11.7%) were men, 113 (88.3%) were women, and the mean age was 58.6 years. On bus 2, 24 of the 68 individuals (35.3% [including the index patient]) received a diagnosis of COVID-19 after the event. Meanwhile, none of the 60 individuals in bus 1 were infected. Among the other 172 individuals at the worship event, 7 (4.1%) subsequently received a COVID-19 diagnosis. Individuals in bus 2 had a 34.3% (95% CI, 24.1%-46.3%) higher risk of getting COVID-19 compared with those in bus 1 and were 11.4 (95% CI, 5.1-25.4) times more likely to have COVID-19 compared with all other individuals attending the worship event. Within bus 2, individuals in high-risk zones had moderately, but nonsignificantly, higher risk for COVID-19 compared with those in the low-risk zones. The absence of a significantly increased risk in the part of the bus closer to the index case suggested that airborne spread of the virus may at least partially explain the markedly high attack rate observed.

CONCLUSIONS AND RELEVANCE: In this cohort study and case investigation of a community outbreak of COVID-19 in Zhejiang province, individuals who rode a bus to a worship event with a patient with COVID-19 had a higher risk of SARS-CoV-2 infection than individuals who rode another bus to the same event. Airborne spread of SARS-CoV-2 seems likely to have contributed to the high attack rate in the exposed bus. Future efforts at prevention and control must consider the potential for airborne spread of the virus.}, } @article {pmid32869468, year = {2021}, author = {Jia, P and Dai, S and Rohli, KE and Rohli, RV and Ma, Y and Yu, C and Pan, X and Zhou, W}, title = {Natural environment and childhood obesity: A systematic review.}, journal = {Obesity reviews : an official journal of the International Association for the Study of Obesity}, volume = {22 Suppl 1}, number = {Suppl 1}, pages = {e13097}, pmid = {32869468}, issn = {1467-789X}, support = {T32 GM008629/GM/NIGMS NIH HHS/United States ; T32 GM145441/GM/NIGMS NIH HHS/United States ; }, mesh = {*Air Pollution ; Child ; Cross-Sectional Studies ; Exercise ; Humans ; Longitudinal Studies ; *Pediatric Obesity/epidemiology/etiology ; }, abstract = {The associations between built and food environments and childhood obesity have been studied extensively. However, the association between the natural environment and childhood obesity has received too little scholarly attention. This study reviewed the literature published before 1 January 2019, which described associations between a full range of natural environmental factors (e.g., rainfall, temperature, sunlight, natural disasters, flood and drought) and weight-related behaviours and childhood obesity. Five cross-sectional studies and one longitudinal study were identified. Measures of natural environmental factors varied across six included studies, falling into five broad categories: weather conditions, altitude, natural disaster risk, air quality and day length. It was found that temperature was a significant weather indicator in most included studies and was associated with a reduction of daily physical activity. Children living in high-altitude areas were more likely to be shorter and heavier than their counterparts in low-altitude areas. Findings of this study will contribute to helping multiple stakeholders, including policy makers and urban planners, and formulate health policies and interventions to mitigate the detrimental impact of the natural environment on childhood obesity. More longitudinal studies should be designed to confirm these effects and explore the potential health effects of more natural environmental factors.}, } @article {pmid32859925, year = {2020}, author = {Jurburg, SD and Konzack, M and Eisenhauer, N and Heintz-Buschart, A}, title = {The archives are half-empty: an assessment of the availability of microbial community sequencing data.}, journal = {Communications biology}, volume = {3}, number = {1}, pages = {474}, pmid = {32859925}, issn = {2399-3642}, mesh = {Databases, Nucleic Acid ; *Environmental Microbiology ; High-Throughput Nucleotide Sequencing ; *Metagenome ; *Metagenomics/methods ; *Microbiota/genetics ; RNA, Ribosomal, 16S ; Sequence Analysis, DNA ; }, abstract = {As DNA sequencing has become more popular, the public genetic repositories where sequences are archived have experienced explosive growth. These repositories now hold invaluable collections of sequences, e.g., for microbial ecology, but whether these data are reusable has not been evaluated. We assessed the availability and state of 16S rRNA gene amplicon sequences archived in public genetic repositories (SRA, EBI, and DDJ). We screened 26,927 publications in 17 microbiology journals, identifying 2015 16S rRNA gene sequencing studies. Of these, 7.2% had not made their data public at the time of analysis. Among a subset of 635 studies sequencing the same gene region, 40.3% contained data which was not available or not reusable, and an additional 25.5% contained faults in data formatting or data labeling, creating obstacles for data reuse. Our study reveals gaps in data availability, identifies major contributors to data loss, and offers suggestions for improving data archiving practices.}, } @article {pmid32859198, year = {2020}, author = {Neukamm, J and Pfrengle, S and Molak, M and Seitz, A and Francken, M and Eppenberger, P and Avanzi, C and Reiter, E and Urban, C and Welte, B and Stockhammer, PW and Teßmann, B and Herbig, A and Harvati, K and Nieselt, K and Krause, J and Schuenemann, VJ}, title = {2000-year-old pathogen genomes reconstructed from metagenomic analysis of Egyptian mummified individuals.}, journal = {BMC biology}, volume = {18}, number = {1}, pages = {108}, pmid = {32859198}, issn = {1741-7007}, support = {845479//the European Union's Horizon 2020 research and innovation program under the Marie Sklodowska-Curie/International ; ALTF 1086-2018//European Molecular Biology Organization (EMBO) long-term fellowship/International ; }, mesh = {DNA, Ancient/analysis ; Egypt ; *Genome, Bacterial ; *Genome, Viral ; Hepatitis B virus/*genetics ; Humans ; Metagenomics ; Microbiota ; Mummies/*microbiology/virology ; Mycobacterium leprae/*genetics ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: Recent advances in sequencing have facilitated large-scale analyses of the metagenomic composition of different samples, including the environmental microbiome of air, water, and soil, as well as the microbiome of living humans and other animals. Analyses of the microbiome of ancient human samples may provide insights into human health and disease, as well as pathogen evolution, but the field is still in its very early stages and considered highly challenging.

RESULTS: The metagenomic and pathogen content of Egyptian mummified individuals from different time periods was investigated via genetic analysis of the microbial composition of various tissues. The analysis of the dental calculus' microbiome identified Red Complex bacteria, which are correlated with periodontal diseases. From bone and soft tissue, genomes of two ancient pathogens, a 2200-year-old Mycobacterium leprae strain and a 2000-year-old human hepatitis B virus, were successfully reconstructed.

CONCLUSIONS: The results show the reliability of metagenomic studies on Egyptian mummified individuals and the potential to use them as a source for the extraction of ancient pathogen DNA.}, } @article {pmid32856310, year = {2020}, author = {Nam, S and Dunton, GF and Ordway, MR and Ash, GI and Jeon, S and Vlahov, D and Whittemore, R and Nelson, LE and Sinha, R and Nunez-Smith, M and Granger, DA}, title = {Feasibility and acceptability of intensive, real-time biobehavioral data collection using ecological momentary assessment, salivary biomarkers, and accelerometers among middle-aged African Americans.}, journal = {Research in nursing & health}, volume = {43}, number = {5}, pages = {453-464}, pmid = {32856310}, issn = {1098-240X}, support = {K23 NR016277/NR/NINR NIH HHS/United States ; }, mesh = {Accelerometry/*statistics & numerical data ; Black or African American/*psychology/statistics & numerical data ; Biobehavioral Sciences/*methods/statistics & numerical data ; Biomarkers/*chemistry ; Ecological Momentary Assessment/*statistics & numerical data ; Feasibility Studies ; Female ; Humans ; Male ; Middle Aged ; Racism/*psychology/statistics & numerical data ; Saliva/*chemistry ; Surveys and Questionnaires ; }, abstract = {Perceived racial discrimination is linked to unhealthy behaviors and stress-related morbidities. A compelling body of research indicates that perceived racial discrimination may contribute to health disparities among African Americans (AAs). The purposes of this study were to describe the study protocol including data collection procedures and study measures and to evaluate the feasibility and acceptability of intensive biobehavioral data collection using ecological momentary assessment (EMA), salivary biomarkers, and accelerometers over 7 days among middle-aged AAs with a goal of understanding the relationships between perceived racial discrimination and biobehavioral responses to stress. Twelve AA men and women participated in the feasibility/acceptability study. They completed surveys, anthropometrics, and received in-person training in EMA and saliva sample collection at baseline. Participants were asked to respond to the random prompt text message-based EMA five times a day, wear an accelerometer daily for 7 days, and to self-collect saliva samples four times a day for 4 consecutive days. The EMA surveys included perceived racial discrimination, affective states, lifestyle behaviors, and social and physical contexts. The mean EMA response rate was 82.8%. All participants collected saliva samples four times a day for 4 consecutive days. About 83% of participants wore the accelerometer on the hip 6 out of 7 days. Despite the perception that the intensive nature of assessments would result in high participant burden, the acceptability of the study procedures was uniformly favorable.}, } @article {pmid32853270, year = {2020}, author = {Xu, J and Yin, P and Hu, W and Fu, L and Zhao, H}, title = {Assessing the ecological regime and spatial spillover effects of a reclaimed mining subsided lake: A case study of the Pan'an Lake wetland in Xuzhou.}, journal = {PloS one}, volume = {15}, number = {8}, pages = {e0238243}, pmid = {32853270}, issn = {1932-6203}, mesh = {China ; Coal Mining/*methods ; Conservation of Natural Resources/*methods ; Ecology/methods ; Ecosystem ; Environmental Monitoring/methods ; Lakes ; Wetlands ; }, abstract = {In the North China Plain, coal mining subsided lakes are surface water bodies that form after the conclusion of coal mining. In China, mining subsided lakes are often transformed into artificial wetland parks for ecological restoration. While many studies have focused on evaluating coal mining subsidence lake ecosystem service value and water pollution, little attention has been paid to changes in ecological regimes and ecological spillover effects before and after the reclamation of mining areas. This paper examines the Pan'an Lake artificial wetland in Jiawang District, Xuzhou, as a case study. Changes in the ecological regime of the mining subsidence area before and after land reclamation and corresponding spatial spillover effect on land prices are assessed based on remote sensing, GIS raster calculations and geostatistical methods. The results show that the ecosystem service value and ecological storage capacity changed significantly after the mining subsided lake was transformed into an artificial wetland and the wetland ecosystem has been developing well with significantly positive spillover effects on surrounding land prices. From 2008 to 2017, service functions of the artificial wetland ecosystem of Pan'an Lake increased by 81.95%, and the system's ecological storage capacity increased from RMB 6,754 yuan/hm2 in 2008 to RMB 12,289 yuan/hm2 in 2017. The average impact of the Pan'an Lake artificial wetland on the spillover effects of surrounding residential land prices was measured at RMB 195.18 yuan/m2, and the total spillover value of planned residential land in the study area was measured at RMB 805,422,100 yuan. The present study can serve as a useful guide for evaluating the economic feasibility of land reclamation planning and ecological restoration in mining subsidence areas.}, } @article {pmid32848201, year = {2020}, author = {Grimes, DR and Jansen, M and Macauley, RJ and Scott, JG and Basanta, D}, title = {Evidence for hypoxia increasing the tempo of evolution in glioblastoma.}, journal = {British journal of cancer}, volume = {123}, number = {10}, pages = {1562-1569}, pmid = {32848201}, issn = {1532-1827}, support = {K12 CA076917/CA/NCI NIH HHS/United States ; P30 CA043703/CA/NCI NIH HHS/United States ; P30 CA076292/CA/NCI NIH HHS/United States ; A19834/CRUK_/Cancer Research UK/United Kingdom ; U01 CA202958/CA/NCI NIH HHS/United States ; /WT_/Wellcome Trust/United Kingdom ; }, mesh = {Algorithms ; Brain Neoplasms/*genetics/metabolism/*pathology ; Cell Hypoxia/physiology ; Cell Line, Tumor ; Cell Proliferation/genetics ; Clonal Evolution/*physiology ; Computational Biology/methods ; Disease Progression ; Glioblastoma/*genetics/metabolism/*pathology ; High-Throughput Nucleotide Sequencing/methods/statistics & numerical data ; Humans ; Image Processing, Computer-Assisted/methods/statistics & numerical data ; Models, Theoretical ; Neoplasm Metastasis ; Neoplastic Stem Cells/metabolism/pathology ; Oxygen/metabolism ; Time Factors ; Tumor Hypoxia/*physiology ; }, abstract = {BACKGROUND: Tumour hypoxia is associated with metastatic disease, and while there have been many mechanisms proposed for why tumour hypoxia is associated with metastatic disease, it remains unclear whether one precise mechanism is the key reason or several in concert. Somatic evolution drives cancer progression and treatment resistance, fuelled not only by genetic and epigenetic mutation but also by selection from interactions between tumour cells, normal cells and physical micro-environment. Ecological habitats influence evolutionary dynamics, but the impact on tempo of evolution is less clear.

METHODS: We explored this complex dialogue with a combined clinical-theoretical approach by simulating a proliferative hierarchy under heterogeneous oxygen availability with an agent-based model. Predictions were compared against histology samples taken from glioblastoma patients, stained to elucidate areas of necrosis and TP53 expression heterogeneity.

RESULTS: Results indicate that cell division in hypoxic environments is effectively upregulated, with low-oxygen niches providing avenues for tumour cells to spread. Analysis of human data indicates that cell division is not decreased under hypoxia, consistent with our results.

CONCLUSIONS: Our results suggest that hypoxia could be a crucible that effectively warps evolutionary velocity, making key mutations more likely. Thus, key tumour ecological niches such as hypoxic regions may alter the evolutionary tempo, driving mutations fuelling tumour heterogeneity.}, } @article {pmid32847630, year = {2020}, author = {Palatini, U and Masri, RA and Cosme, LV and Koren, S and Thibaud-Nissen, F and Biedler, JK and Krsticevic, F and Johnston, JS and Halbach, R and Crawford, JE and Antoshechkin, I and Failloux, AB and Pischedda, E and Marconcini, M and Ghurye, J and Rhie, A and Sharma, A and Karagodin, DA and Jenrette, J and Gamez, S and Miesen, P and Masterson, P and Caccone, A and Sharakhova, MV and Tu, Z and Papathanos, PA and Van Rij, RP and Akbari, OS and Powell, J and Phillippy, AM and Bonizzoni, M}, title = {Improved reference genome of the arboviral vector Aedes albopictus.}, journal = {Genome biology}, volume = {21}, number = {1}, pages = {215}, pmid = {32847630}, issn = {1474-760X}, support = {R01 AI151004/AI/NIAID NIH HHS/United States ; R21 AI135258/AI/NIAID NIH HHS/United States ; 1R01AI151004-01//Foundation for the National Institutes of Health/International ; R01AI32409//Foundation for the National Institutes of Health/International ; 1DP2AI152071-01//Foundation for the National Institutes of Health/International ; R21AI135258//Foundation for the National Institutes of Health/International ; DP2 AI152071/AI/NIAID NIH HHS/United States ; }, mesh = {Aedes/*genetics/immunology/virology ; Animals ; Arboviruses/*genetics ; Chromosome Mapping ; Chromosomes ; *Genome ; Genome Size ; Immunity ; Insect Vectors ; Mosquito Vectors/*genetics/immunology/virology ; RNA, Small Interfering/genetics ; Transcriptome ; }, abstract = {BACKGROUND: The Asian tiger mosquito Aedes albopictus is globally expanding and has become the main vector for human arboviruses in Europe. With limited antiviral drugs and vaccines available, vector control is the primary approach to prevent mosquito-borne diseases. A reliable and accurate DNA sequence of the Ae. albopictus genome is essential to develop new approaches that involve genetic manipulation of mosquitoes.

RESULTS: We use long-read sequencing methods and modern scaffolding techniques (PacBio, 10X, and Hi-C) to produce AalbF2, a dramatically improved assembly of the Ae. albopictus genome. AalbF2 reveals widespread viral insertions, novel microRNAs and piRNA clusters, the sex-determining locus, and new immunity genes, and enables genome-wide studies of geographically diverse Ae. albopictus populations and analyses of the developmental and stage-dependent network of expression data. Additionally, we build the first physical map for this species with 75% of the assembled genome anchored to the chromosomes.

CONCLUSION: The AalbF2 genome assembly represents the most up-to-date collective knowledge of the Ae. albopictus genome. These resources represent a foundation to improve understanding of the adaptation potential and the epidemiological relevance of this species and foster the development of innovative control measures.}, } @article {pmid32846918, year = {2020}, author = {Zhang, Z and Zhan, W and He, Z and Zou, Y}, title = {Application of Spatio-Temporal Context and Convolution Neural Network (CNN) in Grooming Behavior of Bactrocera minax (Diptera: Trypetidae) Detection and Statistics.}, journal = {Insects}, volume = {11}, number = {9}, pages = {}, pmid = {32846918}, issn = {2075-4450}, support = {31972274//National Natural Science Foundation of China/ ; 31772206//National Natural Science Foundation of China/ ; }, abstract = {Statistical analysis and research on insect grooming behavior can find more effective methods for pest control. Traditional manual insect grooming behavior statistical methods are time-consuming, labor-intensive, and error-prone. Based on computer vision technology, this paper uses spatio-temporal context to extract video features, uses self-built Convolution Neural Network (CNN) to train the detection model, and proposes a simple and effective Bactrocera minax grooming behavior detection method, which automatically detects the grooming behaviors of the flies and analysis results by a computer program. Applying the method training detection model proposed in this paper, the videos of 22 adult flies with a total of 1320 min of grooming behavior were detected and analyzed, and the total detection accuracy was over 95%, the standard error of the accuracy of the behavior detection of each adult flies was less than 3%, and the difference was less than 15% when compared with the results of manual observation. The experimental results show that the method in this paper greatly reduces the time of manual observation and at the same time ensures the accuracy of insect behavior detection and analysis, which proposes a new informatization analysis method for the behavior statistics of Bactrocera minax and also provides a new idea for related insect behavior identification research.}, } @article {pmid32841884, year = {2020}, author = {Toropov, AA and Toropova, AP and Benfenati, E}, title = {QSAR model for pesticides toxicity to Rainbow Trout based on "ideal correlations".}, journal = {Aquatic toxicology (Amsterdam, Netherlands)}, volume = {227}, number = {}, pages = {105589}, doi = {10.1016/j.aquatox.2020.105589}, pmid = {32841884}, issn = {1879-1514}, mesh = {Animals ; Databases, Factual ; *Models, Theoretical ; Monte Carlo Method ; *Oncorhynchus mykiss ; Pesticides/chemistry/*toxicity ; Quantitative Structure-Activity Relationship ; Water Pollutants, Chemical/chemistry/*toxicity ; }, abstract = {Pesticides have an impact on the aquatic environment, with ecological effects. The regulation of this impact is of key importance. One of the components of the planning of agricultural and industrial activities is the development of databases and models in order to identify substances that may cause damage. In this study, a quantitative structure-activity relationship (QSAR) approach was established for the prediction of acute toxicity toward rainbow trout of various pesticides. The so-called index of ideality of correlation is the main component of this approach. The validation of this approach has been carried out with three random splits into the training and validation sets. The range of statistical quality of models obtained here for the validation set is R[2] = [0.81-0.86] and RMSE = [0.55-0.65].}, } @article {pmid32841269, year = {2020}, author = {Zhang, J and Yao, Y and Suo, N}, title = {Automatic classification of fine-scale mountain vegetation based on mountain altitudinal belt.}, journal = {PloS one}, volume = {15}, number = {8}, pages = {e0238165}, pmid = {32841269}, issn = {1932-6203}, mesh = {Algorithms ; *Altitude ; China ; Cluster Analysis ; Databases, Factual ; *Ecosystem ; Environmental Monitoring/statistics & numerical data ; Image Processing, Computer-Assisted ; Neural Networks, Computer ; Plants/*classification ; Remote Sensing Technology/statistics & numerical data ; *Satellite Imagery/statistics & numerical data ; }, abstract = {Vegetation mapping is of considerable significance to both geoscience and mountain ecology, and the improved resolution of remote sensing images makes it possible to map vegetation at a finer scale. While the automatic classification of vegetation has gradually become a research hotspot, real-time and rapid collection of samples has become a bottleneck. How to achieve fine-scale classification and automatic sample selection at the same time needs further study. Stratified sampling based on appropriate prior knowledge is an effective sampling method for geospatial objects. Therefore, based on the idea of stratified sampling, this paper used the following three steps to realize the automatic selection of representative samples and classification of fine-scale mountain vegetation: 1) using Mountain Altitudinal Belt (MAB) distribution information to stratify the study area into multiple vegetation belts; 2) selecting and correcting samples through iterative clustering at each belt automatically; 3) using RF (Random Forest) classifier with strong robustness to achieve automatic classification. The average sample accuracy of nine vegetation formations was 0.933, and the total accuracy of the classification result was 92.2%, with the kappa coefficient of 0.910. The results showed that this method could automatically select high-quality samples and obtain a high-accuracy vegetation map. Compared with the traditional vegetation mapping method, this method greatly improved the efficiency, which is of great significance for the fine-scale mountain vegetation mapping in large-scale areas.}, } @article {pmid32841247, year = {2020}, author = {Lachica, ZPT and Peralta, JM and Diamante, EO and Murao, LAE and Mata, MAE and Alviola Iv, PA}, title = {A cointegration analysis of rabies cases and weather components in Davao City, Philippines from 2006 to 2017.}, journal = {PloS one}, volume = {15}, number = {8}, pages = {e0236278}, pmid = {32841247}, issn = {1932-6203}, mesh = {Animals ; Causality ; Cities/statistics & numerical data ; Datasets as Topic ; Disease Reservoirs/*virology ; Dogs/*virology ; Ecological Parameter Monitoring/*statistics & numerical data ; Forecasting/methods ; Humans ; Incidence ; Models, Statistical ; Philippines/epidemiology ; Rabies/*epidemiology/prevention & control/virology ; Rabies virus ; Spatio-Temporal Analysis ; *Weather ; }, abstract = {Rabies is a lethal viral disease and dogs are the major disease reservoir in the Philippines. Spatio-temporal variations in environmental factors are known to affect disease dynamics. Some rabies-affected countries considered investigating the role of weather components in driving rabies cases and it has helped them to strategize their control efforts. In this study, cointegration analysis was conducted between the monthly reported rabies cases and the weather components, such as temperature and precipitation, to verify the effect of weather components on rabies incidence in Davao City, Philippines. With the Engle-Granger cointegration tests, we found that rabies cases are cointegrated into each of the weather components. It was further validated, using the Granger causality test, that each weather component predicts the rabies cases and not vice versa. Moreover, we performed the Johansen cointegration test to show that the weather components simultaneously affect the number of rabies cases, which allowed us to estimate a vector-error correction model for rabies incidence as a function of temperature and precipitation. Our analyses showed that canine rabies in Davao City was weather-sensitive, which implies that rabies incidence could be projected using established long-run relationship among reported rabies cases, temperature, and precipitation. This study also provides empirical evidence that can guide local health officials in formulating preventive strategies for rabies control and eradication based on weather patterns.}, } @article {pmid32840629, year = {2020}, author = {Natsch, A and Haupt, T and Wareing, B and Landsiedel, R and Kolle, SN}, title = {Predictivity of the kinetic direct peptide reactivity assay (kDPRA) for sensitizer potency assessment and GHS subclassification.}, journal = {ALTEX}, volume = {37}, number = {4}, pages = {652-664}, doi = {10.14573/altex.2004292}, pmid = {32840629}, issn = {1868-8551}, mesh = {Animal Testing Alternatives ; Animals ; Databases, Factual ; *Hazardous Substances ; Humans ; Peptides/*toxicity ; ROC Curve ; Skin Diseases/*chemically induced ; }, abstract = {Several in vitro OECD test guidelines address key events 1-3 of the adverse outcome pathway for skin sensitization, but none are validated for sensitizer potency assessment. The reaction of sensitizing molecules with skin proteins is the molecular initiating event and appears to be rate-limiting, as chemical reactivity strongly correlates with sensitizer potency. The kinetic direct peptide reactivity assay (kDPRA), a modification of the DPRA (OECD TG 442C), allows derivation of rate constants of the depletion of the cysteine-containing model peptide upon reaction with the test item. Its reproducibility was demonstrated in an inter-laboratory study. Here, we present a database of rate constants, expressed as log kmax, for 180 chemicals to define the prediction threshold to identify strong sensitizers (classified as GHS 1A). A threshold of log kmax -2 offers a balanced accuracy of 85% for predicting GHS 1A sensitizers according to the local lymph node assay. The kDPRA is proposed as a stand-alone assay for identification of GHS 1A sensitizers among chemicals identified as sensitizers by other tests or defined approaches. It may also be used for the prediction of sensitizer potency on a continuous scale, ideally in combination with continuous parameters from other in vitro assays. We show how the rate constant could be combined with read-outs of other in vitro assays in a defined approach. A decision model based on log kmax alone has, however, a high predictivity and can be used as stand-alone model for identification of GHS 1A sensitizers among chemicals predicted as sensitizers.}, } @article {pmid32839955, year = {2021}, author = {Ponciano-Rodríguez, G and Gaso, MI and Armienta, MA and Trueta, C and Morales, I and Alfaro, R and Segovia, N}, title = {Indoor radon exposure and excess of lung cancer mortality: the case of Mexico-an ecological study.}, journal = {Environmental geochemistry and health}, volume = {43}, number = {1}, pages = {221-234}, pmid = {32839955}, issn = {1573-2983}, mesh = {Air Pollutants, Radioactive/*adverse effects ; Air Pollution, Indoor/*adverse effects ; Humans ; Lung Neoplasms/*mortality ; Mexico/epidemiology ; Risk Assessment ; }, abstract = {Radon is a radioactive gas that can migrate from soils and rocks and accumulate in indoor areas such as dwellings and buildings. Many studies have shown a strong association between the exposure to radon, and its decay products, and lung cancer (LC), particularly in miners. In Mexico, according to published surveys, there is evidence of radon exposure in large groups of the population, nevertheless, only few attention has been paid to its association as a risk factor for LC. The aim of this ecological study is to evaluate the excess risk of lung cancer mortality in Mexico due to indoor radon exposure. Mean radon levels per state of the Country were obtained from different publications and lung cancer mortality was obtained from the National Institute of Statistics, Geography and Informatics for the period 2001-2013. A model proposed by the International Commission on Radiological Protection to estimate the annual excess risk of LC mortality (per 10[5] inhabitants) per dose unit of radon was used. The average indoor radon concentrations found rank from 51 to 1863 Bq m[-3], the higher average dose exposure found was 3.13 mSv year[-1] in the north of the country (Chihuahua) and the mortality excess of LC cases found in the country was 10 ± 1.5 (range 1-235 deaths) per 10[5] inhabitants. The highest values were found mainly in the Northern part of the country, where numerous uranium deposits are found, followed by Mexico City, the most crowded and most air polluted area in the country. A positive correlation (r = 0.98 p < 0.0001) was found between the excess of LC cases and the dose of radon exposure. Although the excess risk of LC mortality associated with indoor radon found in this study was relatively low, further studies are needed in order to accurately establish its magnitude in the country.}, } @article {pmid32838759, year = {2020}, author = {Castrignanò, T and Gioiosa, S and Flati, T and Cestari, M and Picardi, E and Chiara, M and Fratelli, M and Amente, S and Cirilli, M and Tangaro, MA and Chillemi, G and Pesole, G and Zambelli, F}, title = {ELIXIR-IT HPC@CINECA: high performance computing resources for the bioinformatics community.}, journal = {BMC bioinformatics}, volume = {21}, number = {Suppl 10}, pages = {352}, pmid = {32838759}, issn = {1471-2105}, mesh = {Algorithms ; Animals ; Cell Line ; *Computational Biology ; *Computing Methodologies ; Databases, Genetic ; Gene Fusion ; Genome ; Humans ; Prunus persica/genetics ; RNA Editing ; *Software ; Swallows/genetics ; }, abstract = {BACKGROUND: The advent of Next Generation Sequencing (NGS) technologies and the concomitant reduction in sequencing costs allows unprecedented high throughput profiling of biological systems in a cost-efficient manner. Modern biological experiments are increasingly becoming both data and computationally intensive and the wealth of publicly available biological data is introducing bioinformatics into the "Big Data" era. For these reasons, the effective application of High Performance Computing (HPC) architectures is becoming progressively more recognized also by bioinformaticians. Here we describe HPC resources provisioning pilot programs dedicated to bioinformaticians, run by the Italian Node of ELIXIR (ELIXIR-IT) in collaboration with CINECA, the main Italian supercomputing center.

RESULTS: Starting from April 2016, CINECA and ELIXIR-IT launched the pilot Call "ELIXIR-IT HPC@CINECA", offering streamlined access to HPC resources for bioinformatics. Resources are made available either through web front-ends to dedicated workflows developed at CINECA or by providing direct access to the High Performance Computing systems through a standard command-line interface tailored for bioinformatics data analysis. This allows to offer to the biomedical research community a production scale environment, continuously updated with the latest available versions of publicly available reference datasets and bioinformatic tools. Currently, 63 research projects have gained access to the HPC@CINECA program, for a total handout of ~ 8 Millions of CPU/hours and, for data storage, ~ 100 TB of permanent and ~ 300 TB of temporary space.

CONCLUSIONS: Three years after the beginning of the ELIXIR-IT HPC@CINECA program, we can appreciate its impact over the Italian bioinformatics community and draw some considerations. Several Italian researchers who applied to the program have gained access to one of the top-ranking public scientific supercomputing facilities in Europe. Those investigators had the opportunity to sensibly reduce computational turnaround times in their research projects and to process massive amounts of data, pursuing research approaches that would have been otherwise difficult or impossible to undertake. Moreover, by taking advantage of the wealth of documentation and training material provided by CINECA, participants had the opportunity to improve their skills in the usage of HPC systems and be better positioned to apply to similar EU programs of greater scale, such as PRACE. To illustrate the effective usage and impact of the resources awarded by the program - in different research applications - we report five successful use cases, which have already published their findings in peer-reviewed journals.}, } @article {pmid32838733, year = {2020}, author = {Liguori, L and Monticelli, M and Allocca, M and Cubellis, MV and Hay Mele, B}, title = {Bioinformatics tools for marine biotechnology: a practical tutorial with a metagenomic approach.}, journal = {BMC bioinformatics}, volume = {21}, number = {Suppl 10}, pages = {348}, pmid = {32838733}, issn = {1471-2105}, mesh = {Amino Acid Sequence ; Bacterial Proteins/chemistry ; Base Sequence ; Biotechnology/*education ; Computational Biology/*education ; Databases, Factual ; Databases, Protein ; Goals ; Humans ; Learning ; Marine Biology/*education ; *Metagenomics ; User-Computer Interface ; }, abstract = {BACKGROUND: Bioinformatics has pervaded all fields of biology and has become an indispensable tool for almost all research projects. Although teaching bioinformatics has been incorporated in all traditional life science curricula, practical hands-on experiences in tight combination with wet-lab experiments are needed to motivate students.

RESULTS: We present a tutorial that starts from a practical problem: finding novel enzymes from marine environments. First, we introduce the idea of metagenomics, a recent approach that extends biotechnology to non-culturable microbes. We presuppose that a probe for the screening of metagenomic cosmid library is needed. The students start from the chemical structure of the substrate that should be acted on by the novel enzyme and end with the sequence of the probe. To attain their goal, they discover databases such as BRENDA and programs such as BLAST and Clustal Omega. Students' answers to a satisfaction questionnaire show that a multistep tutorial integrated into a research wet-lab project is preferable to conventional lectures illustrating bioinformatics tools.

CONCLUSION: Experimental biologists can better operate basic bioinformatics if a problem-solving approach is chosen.}, } @article {pmid32838290, year = {2020}, author = {Bhayani, S and Sengupta, R and Markossian, T and Tootooni, S and Luke, A and Shoham, D and Cooper, R and Kramer, H}, title = {Dialysis, COVID-19, Poverty, and Race in Greater Chicago: An Ecological Analysis.}, journal = {Kidney medicine}, volume = {2}, number = {5}, pages = {552-558.e1}, pmid = {32838290}, issn = {2590-0595}, support = {T35 HL120835/HL/NHLBI NIH HHS/United States ; }, abstract = {RATIONALE & OBJECTIVE: Persons with end-stage kidney disease receiving in-center maintenance hemodialysis may be at high risk for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) exposure and severe outcomes with coronavirus disease 2019 (COVID-19). The objective of this study was to examine the correlation of SARS-CoV-2 positivity rate per capita and COVID-19-associated deaths with number of dialysis stations and demographics of residents within zip codes in Cook County, IL.

STUDY DESIGN: Ecological analysis.

SETTING & PARTICIPANTS: Data for SARS-CoV-2 test results and COVID-19-associated deaths during January 21 to June 15, 2020, among the 5,232,412 residents living within the 163 zip codes in Cook County, IL, were merged with demographic and income data from the US Census Bureau. The total number of positive test results in this population was 84,353 and total number of deaths was 4,007.

ASSESSMENTS: Number of dialysis stations and stations per capita within a zip code were calculated. SARS-CoV-2-positive test results per capita were calculated as number of positive test results divided by the zip code population. COVID-19-associated deaths per capita were calculated as COVID-19 deaths among residents for a given zip code divided by the zip code population.

ANALYTIC APPROACH: Spearman rank correlation coefficients were calculated to examine the correlation of SARS-CoV-2-positive tests per capita and COVID-19-associated deaths per capita with dialysis stations, demographics, and household poverty. To account for multiple testing, statistical significance was considered as P < 0.005.

RESULTS: Among the 163 Cook County zip codes, there were 2,501 dialysis stations. Positive test results per capita were significantly associated with number of dialysis stations (r = 0.25; 95% CI, 0.19 to 0.29; P < 0.005) but not with dialysis stations per capita (r = 0.02; 95% CI, -0.03 to 0.08; P = 0.7). Positive test results per capita also correlated significantly with number of households living in poverty (r = 0.57; 95% CI, 0.53-0.6; P < 0.005) and percentage of residents reporting Black race (r = 0.28; 95% CI, 0.23-0.33; P < 0.005) and Hispanic ethnicity (r = 0.68; 95% CI, 0.65-0.7; P < 0.001;). COVID-19-associated deaths per capita correlated significantly with the percentage of residents reporting Black race (r = 0.24; 95% CI, 0.19-0.29; P < 0.005) and with percentage of households living in poverty (r = 0.34; 95% CI, 0.29-0.38; P < 0.005). The association between the number of COVID-19-associated deaths per capita and total number of dialysis stations (r = 0.20; 95% CI, 0.14-0.25; P = 0.01) did not achieve a priori significance, whereas the association with dialysis stations per capita (r = 0.12; 95% CI, 0.07-0.17; P = 0.01) was not significant.

LIMITATIONS: Analysis is at the zip code level and not at the person level.

CONCLUSIONS: The number of dialysis stations within a zip code correlates with the SARS-CoV-2 positivity rate per capita in Cook County, IL, and this correlation may be driven by population density and the demographics of the residents. These findings highlight the high risk of SARS-CoV-2 exposure for patients with end-stage kidney disease living in poor urban areas.}, } @article {pmid32830865, year = {2020}, author = {Mabry, ME and Brose, JM and Blischak, PD and Sutherland, B and Dismukes, WT and Bottoms, CA and Edger, PP and Washburn, JD and An, H and Hall, JC and McKain, MR and Al-Shehbaz, I and Barker, MS and Schranz, ME and Conant, GC and Pires, JC}, title = {Phylogeny and multiple independent whole-genome duplication events in the Brassicales.}, journal = {American journal of botany}, volume = {107}, number = {8}, pages = {1148-1164}, pmid = {32830865}, issn = {1537-2197}, support = {K12 GM000708/GM/NIGMS NIH HHS/United States ; K12GM000708/GF/NIH HHS/United States ; }, mesh = {Evolution, Molecular ; *Gene Duplication ; Genome ; Genome, Plant/genetics ; Humans ; Magnoliopsida/*genetics ; Phylogeny ; Polyploidy ; }, abstract = {PREMISE: Whole-genome duplications (WGDs) are prevalent throughout the evolutionary history of plants. For example, dozens of WGDs have been phylogenetically localized across the order Brassicales, specifically, within the family Brassicaceae. A WGD event has also been identified in the Cleomaceae, the sister family to Brassicaceae, yet its placement, as well as that of WGDs in other families in the order, remains unclear.

METHODS: Phylo-transcriptomic data were generated and used to infer a nuclear phylogeny for 74 Brassicales taxa. Genome survey sequencing was also performed on 66 of those taxa to infer a chloroplast phylogeny. These phylogenies were used to assess and confirm relationships among the major families of the Brassicales and within Brassicaceae. Multiple WGD inference methods were then used to assess the placement of WGDs on the nuclear phylogeny.

RESULTS: Well-supported chloroplast and nuclear phylogenies for the Brassicales and the putative placement of the Cleomaceae-specific WGD event Th-ɑ are presented. This work also provides evidence for previously hypothesized WGDs, including a well-supported event shared by at least two members of the Resedaceae family, and a possible event within the Capparaceae.

CONCLUSIONS: Phylogenetics and the placement of WGDs within highly polyploid lineages continues to be a major challenge. This study adds to the conversation on WGD inference difficulties by demonstrating that sampling is especially important for WGD identification and phylogenetic placement. Given its economic importance and genomic resources, the Brassicales continues to be an ideal group for assessing WGD inference methods.}, } @article {pmid32827030, year = {2021}, author = {Turner, AM and Taylor, JO and Hartzler, AL and Osterhage, KP and Bosold, AL and Painter, IS and Demiris, G}, title = {Personal health information management among healthy older adults: Varying needs and approaches.}, journal = {Journal of the American Medical Informatics Association : JAMIA}, volume = {28}, number = {2}, pages = {322-333}, pmid = {32827030}, issn = {1527-974X}, support = {R01 HS022106/HS/AHRQ HHS/United States ; }, mesh = {Aged ; Aged, 80 and over ; Electronic Health Records ; Emergencies ; Female ; *Health Information Management/organization & administration ; *Health Records, Personal ; Humans ; Interviews as Topic ; Male ; Medical Informatics ; Middle Aged ; Surveys and Questionnaires ; }, abstract = {OBJECTIVE: With age, older adults experience a greater number of chronic diseases and medical visits, and an increased need to manage their health information. Technological advances in consumer health information technologies (HITs) help patients gather, track, and organize their health information within and outside of clinical settings. However, HITs have not focused on the needs of older adults and their caregivers. The goal of the SOARING (Studying Older Adults and Researching their Information Needs and Goals) Project was to understand older adult personal health information management (PHIM) needs and practices to inform the design of HITs that support older adults.

MATERIALS AND METHODS: Drawing on the Work System Model, we took an ecological approach to investigate PHIM needs and practices of older adults in different residential settings. We conducted in-depth interviews and surveys with adults 60 years of age and older.

RESULTS: We performed on-site in-person interview sessions with 88 generally healthy older adults in various settings including independent housing, retirement communities, assisted living, and homelessness. Our analysis revealed 5 key PHIM activities that older adults engage in: seeking, tracking, organizing, sharing health information, and emergency planning. We identified 3 major themes influencing older adults' practice of PHIM: (1) older adults are most concerned with maintaining health and preventing illness, (2) older adults frequently involve others in PHIM activities, and (3) older adults' approach to PHIM is situational and context-dependent.

DISCUSSION: Older adults' approaches to PHIM are dynamic and sensitive to changes in health, social networks, personal habits, motivations, and goals.

CONCLUSIONS: PHIM tools that meet the needs of older adults should accommodate the dynamic nature of aging and variations in individual, organizational, and social contexts.}, } @article {pmid32822610, year = {2020}, author = {Goldshtein, A and Handel, M and Eitan, O and Bonstein, A and Shaler, T and Collet, S and Greif, S and Medellín, RA and Emek, Y and Korman, A and Yovel, Y}, title = {Reinforcement Learning Enables Resource Partitioning in Foraging Bats.}, journal = {Current biology : CB}, volume = {30}, number = {20}, pages = {4096-4102.e6}, pmid = {32822610}, issn = {1879-0445}, support = {648032/ERC_/European Research Council/International ; }, mesh = {Animals ; Behavior, Animal/*physiology ; Chiroptera/*physiology ; Feeding Behavior/*physiology ; Female ; Flight, Animal/*physiology ; Geographic Information Systems ; Lactation ; Movement/physiology ; Wearable Electronic Devices ; }, abstract = {Every evening, from late spring to mid-summer, tens of thousands of hungry lactating female lesser long-nosed bats (Leptonycteris yerbabuenae) emerge from their roost and navigate over the Sonoran Desert, seeking for nectar and pollen [1, 2]. The bats roost in a huge maternal colony that is far from the foraging grounds but allows their pups to thermoregulate [3] while the mothers are foraging. Thus, the mothers have to fly tens of kilometers to the foraging sites-fields with thousands of Saguaro cacti [4, 5]. Once at the field, they must compete with many other bats over the same flowering cacti. Several solutions have been suggested for this classical foraging task of exploiting a resource composed of many renewable food sources whose locations are fixed. Some animals randomly visit the food sources [6], and some actively defend a restricted foraging territory [7-11] or use simple forms of learning, such as "win-stay lose-switch" strategy [12]. Many species have been suggested to follow a trapline, that is, to revisit the food sources in a repeating ordered manner [13-22]. We thus hypothesized that lesser long-nosed bats would visit cacti in a sequenced manner. Using miniature GPS devices, aerial imaging, and video recordings, we tracked the full movement of the bats and all of their visits to their natural food sources. Based on real data and evolutionary simulations, we argue that the bats use a reinforcement learning strategy that requires minimal memory to create small, non-overlapping cacti-cores and exploit nectar efficiently, without social communication.}, } @article {pmid32819980, year = {2020}, author = {Berra, TZ and Assis, IS and Arroyo, LH and Arcoverde, MAM and Alves, JD and Campoy, LT and Alves, LS and Crispim, JA and Bruce, ATI and Alves, YM and Lima Dos Santos, F and da Costa Uchôa, SA and Fiorati, RC and Lapão, L and Arcêncio, RA}, title = {Social determinants of deaths from pneumonia and tuberculosis in children in Brazil: an ecological study.}, journal = {BMJ open}, volume = {10}, number = {8}, pages = {e034074}, pmid = {32819980}, issn = {2044-6055}, mesh = {Brazil/epidemiology ; Child ; Child, Preschool ; Humans ; Incidence ; *Pneumonia/epidemiology ; Social Determinants of Health ; *Tuberculosis/epidemiology ; *Tuberculosis, Pulmonary/epidemiology ; }, abstract = {OBJECTIVE: To identify the risk areas of deaths due to unspecified pneumonia and tuberculosis (TB) in children, and to identify if there is a relationship between these events with higher TB incidence and social determinants.

METHODS: Ecological study carried out in Brazil. All cases of TB or unspecified pneumonia deaths in children under 5 years of age reported between 2006 and 2016 were included and collected through Department of Informatics of the Unified Health System (Brazil's electronic database). The Spatial Scan Statistics was used to identify areas at higher risk of dying from this event. The spatial association was verified through the Getis-Ord techniques. The Bivariate Moran Global Index was used to verify the spatial autocorrelation between the two events. To identify the association of TB and pneumonia deaths with endemic areas of pulmonary TB and social determinants, four explanatory statistical models were identified.

RESULTS: A total of 21 391 cases of pneumonia and 238 cases of TB were identified. Spatial scanning analysis enabled the detection of four clusters of risk for TB (relative risk, RR, between 3.30 and 18.18) and 22 clusters for pneumonia (RR between 1.38 and 5.24). The spatial association of the events was confirmed (z-score 3.74 and 64.34) and spatial autocorrelation between events (Moran Index:0.031 (p=0.001)). The zero-inflated negative binomial distribution was chosen, and an association for both events was identified with the TB incidence rate (OR 5.3, 95% CI 2.85 to 9.84; OR 6.63, 95% CI 5.62 to 7.81), with the Gini Index (OR 1.78, 95% CI 1.12 to 2.82; OR 4.22, 95% CI 3.63 to4.92). Primary care coverage showed an inverse association for both events (OR 0.10, 95% CI 0.67 to 0.17; OR 0.18, 95% CI 0.15 to 0.21) for pneumonia). Finally, a family that benefited from the Bolsa Família Programme had an inverse association for deaths from pneumonia (OR 0.81, 95% CI 0.52 to 1.25).

CONCLUSIONS: The results do not just contribute to reduce mortality in children, but mainly contribute to prevent premature deaths through identification of critical areas in Brazil, which is crucial to qualify health surveillance services.}, } @article {pmid32818149, year = {2020}, author = {Kaplan, F and Shapiro-Ilan, D and Schiller, KC}, title = {Dynamics of entomopathogenic nematode foraging and infectivity in microgravity.}, journal = {NPJ microgravity}, volume = {6}, number = {}, pages = {20}, pmid = {32818149}, issn = {2373-8065}, abstract = {Microgravity is a unique environment to elucidate host-parasite biology. Entomopathogenic nematodes (EPNs), model parasites, kill host insects with mutualistic bacteria and provide environmentally friendly pest control. It is unknown how microgravity affects a multistep insect invasion by parasites with mutualistic bacteria. EPNs respond directionally to electromagnetic cues and their sinusoidal locomotion is affected by various physical factors. Therefore, we expected microgravity to impact EPN functionality. Microgravity experiments during space flight on the International Space Station (ISS) indicated that EPNs successfully emerged from consumed insect host cadavers, moved through soil, found and infected bait insects in a manner equivalent to Earth controls. However, nematodes that developed entirely in space, from the egg stage, died upon return to Earth, unlike controls in microgravity and on Earth. This agricultural biocontrol experiment in space gives insight to long-term space flight for symbiotic organisms, parasite biology, and the potential for sustainable crop protection in space.}, } @article {pmid32816076, year = {2020}, author = {Yilmaz, FC and Zengin, M and Tekin Cure, C}, title = {Determination of ecologically sensitive areas in Denizli province using geographic information systems (GIS) and analytical hierarchy process (AHP).}, journal = {Environmental monitoring and assessment}, volume = {192}, number = {9}, pages = {589}, doi = {10.1007/s10661-020-08514-9}, pmid = {32816076}, issn = {1573-2959}, mesh = {*Ecosystem ; Environmental Monitoring ; *Geographic Information Systems ; }, abstract = {Ecological sensitivity is defined as the ecosystem's reaction to environmental change caused by internal and external factors. The degree of ecological sensitivity varies in spatial dimension depending on the natural and cultural features. Ecological sensitivity analysis is based on basis of mapping these differences. As a result of the analysis, an important data that can be a base for spatial plans at different scales is provided. In accordance with this aim, Denizli province was selected for the study area in this research. The factors affecting sensitivity were determined by the literature survey, which was conducted by considering the characteristics of the study area. In this context, elevation, slope, aspect, the proximity to water surface, land cover, and vegetation coverage were evaluated as natural factors, and the proximity to primary traffic roads and residential areas as cultural factors. Each factor was spatially grouped by means of geographic information systems (GIS) according to the degree of impact on ecological sensitivity. Scale 1 (lowest ecological sensitivity) to 5 (highest ecological sensitivity) was used for the spatial grouping. A analytical hierarchy process (AHP) was applied to weight the factors. The overlay method was used in line with the weighted scores in order to determine the composite ecological sensitivity. As a result of the study, the area of 286.26 sq km (2.37%) as highly and more sensitive, 5267.47 sq km (43.50%) as moderately sensitive, and 6554.56 sq km (54.13%) as mildly and less sensitive was determined. In line with the results, suggestions for protection-utilization balance were developed.}, } @article {pmid32815545, year = {2020}, author = {Harjes, J and Link, A and Weibulat, T and Triebel, D and Rambold, G}, title = {FAIR digital objects in environmental and life sciences should comprise workflow operation design data and method information for repeatability of study setups and reproducibility of results.}, journal = {Database : the journal of biological databases and curation}, volume = {2020}, number = {}, pages = {}, pmid = {32815545}, issn = {1758-0463}, mesh = {Computational Biology ; *Databases, Factual ; *Information Dissemination ; Reproducibility of Results ; *Research Design ; *Software ; Workflow ; }, abstract = {Repeatability of study setups and reproducibility of research results by underlying data are major requirements in science. Until now, abstract models for describing the structural logic of studies in environmental sciences are lacking and tools for data management are insufficient. Mandatory for repeatability and reproducibility is the use of sophisticated data management solutions going beyond data file sharing. Particularly, it implies maintenance of coherent data along workflows. Design data concern elements from elementary domains of operations being transformation, measurement and transaction. Operation design elements and method information are specified for each consecutive workflow segment from field to laboratory campaigns. The strict linkage of operation design element values, operation values and objects is essential. For enabling coherence of corresponding objects along consecutive workflow segments, the assignment of unique identifiers and the specification of their relations are mandatory. The abstract model presented here addresses these aspects, and the software DiversityDescriptions (DWB-DD) facilitates the management of thusly connected digital data objects and structures. DWB-DD allows for an individual specification of operation design elements and their linking to objects. Two workflow design use cases, one for DNA barcoding and another for cultivation of fungal isolates, are given. To publish those structured data, standard schema mapping and XML-provision of digital objects are essential. Schemas useful for this mapping include the Ecological Markup Language, the Schema for Meta-omics Data of Collection Objects and the Standard for Structured Descriptive Data. Data pipelines with DWB-DD include the mapping and conversion between schemas and functions for data publishing and archiving according to the Open Archival Information System standard. The setting allows for repeatability of study setups, reproducibility of study results and for supporting work groups to structure and maintain their data from the beginning of a study. The theory of 'FAIR++' digital objects is introduced.}, } @article {pmid32815317, year = {2020}, author = {Nascimento Lemos, L and Manoharan, L and William Mendes, L and Monteiro Venturini, A and Satler Pylro, V and Tsai, SM}, title = {Metagenome assembled-genomes reveal similar functional profiles of CPR/Patescibacteria phyla in soils.}, journal = {Environmental microbiology reports}, volume = {12}, number = {6}, pages = {651-655}, doi = {10.1111/1758-2229.12880}, pmid = {32815317}, issn = {1758-2229}, support = {//Brazilian Microbiome Project/International ; 140032/2015-0//Conselho Nacional de Desenvolvimento Científico e Tecnológico/International ; 161931/2015-4//Conselho Nacional de Desenvolvimento Científico e Tecnológico/International ; Finance Code 001//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/International ; 2014/50320-4//Fundação de Amparo à Pesquisa do Estado de São Paulo/International ; 2015/13546-7//Fundação de Amparo à Pesquisa do Estado de São Paulo/International ; 2016/18215-1//Fundação de Amparo à Pesquisa do Estado de São Paulo/International ; 2017/09643-2//Fundação de Amparo à Pesquisa do Estado de São Paulo/International ; 2017/24037-1//Fundação de Amparo à Pesquisa do Estado de São Paulo/International ; //Coordination for the Improvement of Higher Education Personnel/International ; //National Council for Scientific and Technological Development/International ; //São Paulo Research Foundation/International ; }, mesh = {Bacteria/classification/*genetics/isolation & purification ; Databases, Genetic ; Genome Size ; *Genome, Bacterial ; Metagenome ; Microbiota ; Phylogeny ; *Soil Microbiology ; }, abstract = {Soil microbiome is one of the most heterogeneous biological systems. State-of-the-art molecular approaches such as those based on single-amplified genomes (SAGs) and metagenome assembled-genomes (MAGs) are now improving our capacity for disentailing soil microbial-mediated processes. Here, we analysed publicly available datasets of soil microbial genomes and MAG's reconstructed from the Amazon's tropical soil (primary forest and pasture) and active layer of permafrost, aiming to evaluate their genome size. Our results suggest that the Candidate Phyla Radiation (CPR)/Patescibacteria phyla have genomes with an average size fourfold smaller than the mean identified in the RefSoil database, which lacks any representative of this phylum. Also, by analysing the potential metabolism of 888 soil microbial genomes, we show that CPR/Patescibacteria representatives share similar functional profiles, but different from other microbial phyla and are frequently neglected in the soil microbial surveys. Finally, we argue that the use of MAGs may be a better choice over SAGs to expand the soil microbial databases, like RefSoil.}, } @article {pmid32813714, year = {2020}, author = {Kinkar, L and Korhonen, PK and Wang, D and Zhu, XQ and Chelomina, GN and Wang, T and Hall, RS and Koehler, AV and Harliwong, I and Yang, B and Fink, JL and Young, ND and Gasser, RB}, title = {Marked mitochondrial genetic variation in individuals and populations of the carcinogenic liver fluke Clonorchis sinensis.}, journal = {PLoS neglected tropical diseases}, volume = {14}, number = {8}, pages = {e0008480}, pmid = {32813714}, issn = {1935-2735}, mesh = {Animals ; China/epidemiology ; Clonorchiasis/epidemiology/*parasitology ; Clonorchis sinensis/*genetics ; DNA, Mitochondrial/*genetics ; *Genetic Variation ; Haploidy ; Host-Parasite Interactions ; Humans ; Phylogeny ; Russia/epidemiology ; }, abstract = {Clonorchiasis is a neglected tropical disease caused by the Chinese liver fluke, Clonorchis sinensis, and is often associated with a malignant form of bile duct cancer (cholangiocarcinoma). Although some aspects of the epidemiology of clonorchiasis are understood, little is known about the genetics of C. sinensis populations. Here, we conducted a comprehensive genetic exploration of C. sinensis from endemic geographic regions using complete mitochondrial protein gene sets. Genomic DNA samples from C. sinensis individuals (n = 183) collected from cats and dogs in China (provinces of Guangdong, Guangxi, Hunan, Heilongjiang and Jilin) as well as from rats infected with metacercariae from cyprinid fish from the Russian Far East (Primorsky Krai region) were deep sequenced using the BGISEQ-500 platform. Informatic analyses of mitochondrial protein gene data sets revealed marked genetic variation within C. sinensis; significant variation was identified within and among individual worms from distinct geographical locations. No clear affiliation with a particular location or host species was evident, suggesting a high rate of dispersal of the parasite across endemic regions. The present work provides a foundation for future biological, epidemiological and ecological studies using mitochondrial protein gene data sets, which could aid in elucidating associations between particular C. sinensis genotypes/haplotypes and the pathogenesis or severity of clonorchiasis and its complications (including cholangiocarcinoma) in humans.}, } @article {pmid32811988, year = {2020}, author = {Gemmell, NJ and Rutherford, K and Prost, S and Tollis, M and Winter, D and Macey, JR and Adelson, DL and Suh, A and Bertozzi, T and Grau, JH and Organ, C and Gardner, PP and Muffato, M and Patricio, M and Billis, K and Martin, FJ and Flicek, P and Petersen, B and Kang, L and Michalak, P and Buckley, TR and Wilson, M and Cheng, Y and Miller, H and Schott, RK and Jordan, MD and Newcomb, RD and Arroyo, JI and Valenzuela, N and Hore, TA and Renart, J and Peona, V and Peart, CR and Warmuth, VM and Zeng, L and Kortschak, RD and Raison, JM and Zapata, VV and Wu, Z and Santesmasses, D and Mariotti, M and Guigó, R and Rupp, SM and Twort, VG and Dussex, N and Taylor, H and Abe, H and Bond, DM and Paterson, JM and Mulcahy, DG and Gonzalez, VL and Barbieri, CG and DeMeo, DP and Pabinger, S and Van Stijn, T and Clarke, S and Ryder, O and Edwards, SV and Salzberg, SL and Anderson, L and Nelson, N and Stone, C and , }, title = {Publisher Correction: The tuatara genome reveals ancient features of amniote evolution.}, journal = {Nature}, volume = {585}, number = {7823}, pages = {E3}, doi = {10.1038/s41586-020-2661-6}, pmid = {32811988}, issn = {1476-4687}, abstract = {An amendment to this paper has been published and can be accessed via a link at the top of the paper.}, } @article {pmid32807955, year = {2020}, author = {Jarmusch, AK and Wang, M and Aceves, CM and Advani, RS and Aguirre, S and Aksenov, AA and Aleti, G and Aron, AT and Bauermeister, A and Bolleddu, S and Bouslimani, A and Caraballo Rodriguez, AM and Chaar, R and Coras, R and Elijah, EO and Ernst, M and Gauglitz, JM and Gentry, EC and Husband, M and Jarmusch, SA and Jones, KL and Kamenik, Z and Le Gouellec, A and Lu, A and McCall, LI and McPhail, KL and Meehan, MJ and Melnik, AV and Menezes, RC and Montoya Giraldo, YA and Nguyen, NH and Nothias, LF and Nothias-Esposito, M and Panitchpakdi, M and Petras, D and Quinn, RA and Sikora, N and van der Hooft, JJJ and Vargas, F and Vrbanac, A and Weldon, KC and Knight, R and Bandeira, N and Dorrestein, PC}, title = {ReDU: a framework to find and reanalyze public mass spectrometry data.}, journal = {Nature methods}, volume = {17}, number = {9}, pages = {901-904}, pmid = {32807955}, issn = {1548-7105}, support = {P41 GM103484/GM/NIGMS NIH HHS/United States ; T32 AR064194/AR/NIAMS NIH HHS/United States ; R03 CA211211/CA/NCI NIH HHS/United States ; R01 GM107550/GM/NIGMS NIH HHS/United States ; R01 LM013115/LM/NLM NIH HHS/United States ; }, mesh = {*Databases, Chemical ; *Mass Spectrometry ; Metabolomics/*methods ; Metadata ; Models, Chemical ; *Software ; }, abstract = {We present ReDU (https://redu.ucsd.edu/), a system for metadata capture of public mass spectrometry-based metabolomics data, with validated controlled vocabularies. Systematic capture of knowledge enables the reanalysis of public data and/or co-analysis of one's own data. ReDU enables multiple types of analyses, including finding chemicals and associated metadata, comparing the shared and different chemicals between groups of samples, and metadata-filtered, repository-scale molecular networking.}, } @article {pmid32807484, year = {2020}, author = {Azarpazhooh, MR and Morovatdar, N and Avan, A and Phan, TG and Divani, AA and Yassi, N and Stranges, S and Silver, B and Biller, J and Tokazebani Belasi, M and Kazemi Neya, S and Khorram, B and Frydman, A and Nilanont, Y and Onorati, E and Di Napoli, M}, title = {COVID-19 Pandemic and Burden of Non-Communicable Diseases: An Ecological Study on Data of 185 Countries.}, journal = {Journal of stroke and cerebrovascular diseases : the official journal of National Stroke Association}, volume = {29}, number = {9}, pages = {105089}, pmid = {32807484}, issn = {1532-8511}, mesh = {Age Factors ; Aged ; Aged, 80 and over ; Betacoronavirus/pathogenicity ; COVID-19 ; Cause of Death ; Coronavirus Infections/*epidemiology/mortality/prevention & control/virology ; Cost of Illness ; Databases, Factual ; Female ; *Global Health ; Health Services Needs and Demand ; Health Status Disparities ; Healthcare Disparities ; Host-Pathogen Interactions ; Humans ; Incidence ; Infection Control ; Male ; Middle Aged ; Needs Assessment ; Noncommunicable Diseases/*epidemiology/mortality/prevention & control ; Pandemics/prevention & control ; Pneumonia, Viral/*epidemiology/mortality/prevention & control/virology ; Prognosis ; Risk Factors ; SARS-CoV-2 ; Time Factors ; }, abstract = {BACKGROUND: The interaction between coronavirus disease 2019 (COVID-19) and non-communicable diseases may increase the global burden of disease. We assessed the association of COVID-19 with ageing and non-communicable diseases.

METHODS: We extracted data regarding non-communicable disease, particularly cardiovascular disease, deaths, disability-adjusted life years (DALYs), and healthy life expectancy (HALE) from the Global Burden of Disease Study (GBD) 2017. We obtained data of confirmed COVID-19 cases, deaths, and tests from the Our World in Data database as of May 28, 2020. Potential confounders of pandemic outcomes analyzed include institutional lockdown delay, hemispheric geographical location, and number of tourists. We compared all countries according to GBD classification and World Bank income level. We assessed the correlation between independent variables associated with COVID-19 caseload and mortality using Spearman's rank correlation and adjusted mixed model analysis.

FINDINGS: High-income had the highest, and the Southeast Asia, East Asia, and Oceania region had the least cases per million population (3050.60 vs. 63.86). Sub-saharan region has reported the lowest number of COVID-19 mortality (1.9). Median delay to lockdown initiation varied from one day following the first case in Latin America and Caribbean region, to 34 days in Southeast Asia, East Asia, and Oceania. Globally, non-communicable disease DALYs were correlated with COVID-19 cases (r = 0.32, p<0.001) and deaths (r = 0.37, p<0.001). HALE correlated with COVID-19 cases (r = 0.63, p<0.001) and deaths (r = 0.61, p<0.001). HALE was independently associated with COVID-19 case rate and the number of tourists was associated with COVID-19 mortality in the adjusted model.

INTERPRETATION: Preventive measures against COVID-19 should protect the public from the dual burden of communicable and non-communicable diseases, particularly in the elderly. In addition to active COVID-19 surveillance, policymakers should utilize this evidence as a guide for prevention and coordination of health services. This model is timely, as many countries have begun to reduce social isolation.}, } @article {pmid32806747, year = {2020}, author = {Lee, LS and Navarro-Domínguez, BM and Wu, Z and Montiel, EE and Badenhorst, D and Bista, B and Gessler, TB and Valenzuela, N}, title = {Karyotypic Evolution of Sauropsid Vertebrates Illuminated by Optical and Physical Mapping of the Painted Turtle and Slider Turtle Genomes.}, journal = {Genes}, volume = {11}, number = {8}, pages = {}, pmid = {32806747}, issn = {2073-4425}, mesh = {Animals ; Cells, Cultured ; *Chromosome Painting/methods ; Chromosomes, Artificial, Bacterial ; Computational Biology/methods ; Databases, Genetic ; *Evolution, Molecular ; *Genome ; In Situ Hybridization, Fluorescence ; *Karyotype ; Microscopy, Fluorescence ; Phylogeny ; *Physical Chromosome Mapping/methods ; Turtles/classification/*genetics ; }, abstract = {Recent sequencing and software enhancements have advanced our understanding of the evolution of genomic structure and function, especially addressing novel evolutionary biology questions. Yet fragmentary turtle genome assemblies remain a challenge to fully decipher the genetic architecture of adaptive evolution. Here, we use optical mapping to improve the contiguity of the painted turtle (Chrysemys picta) genome assembly and use de novo fluorescent in situ hybridization (FISH) of bacterial artificial chromosome (BAC) clones, BAC-FISH, to physically map the genomes of the painted and slider turtles (Trachemys scripta elegans). Optical mapping increased C. picta's N50 by ~242% compared to the previous assembly. Physical mapping permitted anchoring ~45% of the genome assembly, spanning 5544 genes (including 20 genes related to the sex determination network of turtles and vertebrates). BAC-FISH data revealed assembly errors in C. picta and T. s. elegans assemblies, highlighting the importance of molecular cytogenetic data to complement bioinformatic approaches. We also compared C. picta's anchored scaffolds to the genomes of other chelonians, chicken, lizards, and snake. Results revealed a mostly one-to-one correspondence between chromosomes of painted and slider turtles, and high homology among large syntenic blocks shared with other turtles and sauropsids. Yet, numerous chromosomal rearrangements were also evident across chelonians, between turtles and squamates, and between avian and non-avian reptiles.}, } @article {pmid32806389, year = {2020}, author = {Wiener, MJ and Moreno, S and Jafvert, CT and Nies, LF}, title = {Time series analysis of water use and indirect reuse within a HUC-4 basin (Wabash) over a nine year period.}, journal = {The Science of the total environment}, volume = {738}, number = {}, pages = {140221}, doi = {10.1016/j.scitotenv.2020.140221}, pmid = {32806389}, issn = {1879-1026}, abstract = {Anthropogenic water use and reuse represent major components of the water cycle. In the context of climate change, water reuse and recycling are considered necessary components for an integrated water management approach. Unplanned, or de facto, indirect water reuse occurs in most of the U.S. river systems, however, there is little real-time documentation of it. Despite the fact that there are national and state agencies that systematically collect data on water withdrawals and wastewater discharges, their databases are organized and managed in a way that makes it challenging to use them for water resource management analysis. The ability to combine reported water data to perform large scale analysis about water use and reuse is severely limited. In this paper, we apply a simple but effective methodology to complete a time series watershed-scale analysis of water use and unplanned indirect reuse for the Wabash River Watershed. Results document the occurrence of indirect water reuse, ranging from 3% to 134%, in a water-rich area of the U.S. The time series analysis shows that reported data effectively describe the water use trends through nine years, from 2009 to 2017, clearly reflecting both anthropogenic and natural events in the watershed, such as the retirement of thermoelectric power plants, and the occurrence of an extreme drought in 2012. We demonstrate the feasibility and significance of using available water datasets to perform large scale water use analysis, describe limitations encountered in the process, and highlight areas for improvement in water data management.}, } @article {pmid32804417, year = {2020}, author = {Ederveen, THA and Smits, JPH and Boekhorst, J and Schalkwijk, J and van den Bogaard, EH and Zeeuwen, PLJM}, title = {Skin microbiota in health and disease: From sequencing to biology.}, journal = {The Journal of dermatology}, volume = {47}, number = {10}, pages = {1110-1118}, pmid = {32804417}, issn = {1346-8138}, mesh = {Biology ; Diet ; Humans ; *Microbiota ; *Probiotics ; Skin ; }, abstract = {Microbiota live in a closely regulated interaction with their environment, and vice versa. The presence and absence of microbial entities is greatly influenced by features of the niche in which they thrive. Characteristic of this phenomenon is that different human skin sites harbor niche-specific communities of microbes. Microbial diversity is considerable, and the current challenge lies in determining which microbes and (corresponding) functionality are of importance to a given ecological niche. Furthermore, as there is increasing evidence of microbial involvement in health and disease, the need arises to fundamentally understand microbiome processes for application in health care, nutrition and personal care products (e.g. diet, cosmetics, probiotics). This review provides a current overview of state-of-the-art sequencing-based techniques and corresponding data analysis methodology for profiling of complex microbial communities. Furthermore, we also summarize the existing knowledge regarding cutaneous microbiota and their human host for a wide range of skin diseases.}, } @article {pmid32799353, year = {2020}, author = {Xia, J and Wang, J and Niu, S}, title = {Research challenges and opportunities for using big data in global change biology.}, journal = {Global change biology}, volume = {26}, number = {11}, pages = {6040-6061}, doi = {10.1111/gcb.15317}, pmid = {32799353}, issn = {1365-2486}, support = {31722009//National Natural Science Foundation of China/ ; 2017YFA0604600//National Key R&D Program of China/ ; }, mesh = {*Big Data ; Biology ; Earth, Planet ; *Ecosystem ; Meta-Analysis as Topic ; }, abstract = {Global change biology has been entering a big data era due to the vast increase in availability of both environmental and biological data. Big data refers to large data volume, complex data sets, and multiple data sources. The recent use of such big data is improving our understanding of interactions between biological systems and global environmental changes. In this review, we first explore how big data has been analyzed to identify the general patterns of biological responses to global changes at scales from gene to ecosystem. After that, we investigate how observational networks and space-based big data have facilitated the discovery of emergent mechanisms and phenomena on the regional and global scales. Then, we evaluate the predictions of terrestrial biosphere under global changes by big modeling data. Finally, we introduce some methods to extract knowledge from big data, such as meta-analysis, machine learning, traceability analysis, and data assimilation. The big data has opened new research opportunities, especially for developing new data-driven theories for improving biological predictions in Earth system models, tracing global change impacts across different organismic levels, and constructing cyberinfrastructure tools to accelerate the pace of model-data integrations. These efforts will uncork the bottleneck of using big data to understand biological responses and adaptations to future global changes.}, } @article {pmid32797732, year = {2020}, author = {Burley, SK and Bromberg, Y and Craig, P and Duffy, S and Dutta, S and Hall, BL and Hudson, BP and Jiang, J and D Khare, S and Koeppe, JR and Lubin, JH and Mills, SA and Pikaart, MJ and Roberts, R and Sarma, V and Singh, J and Tischfield, JA and Xie, L and Zardecki, C}, title = {Virtual Boot Camp: COVID-19 evolution and structural biology.}, journal = {Biochemistry and molecular biology education : a bimonthly publication of the International Union of Biochemistry and Molecular Biology}, volume = {48}, number = {5}, pages = {511-513}, pmid = {32797732}, issn = {1539-3429}, support = {P41 RR012408/RR/NCRR NIH HHS/United States ; T32 GM135141/GM/NIGMS NIH HHS/United States ; R01 GM133198/GM/NIGMS NIH HHS/United States ; R01GM133198/NH/NIH HHS/United States ; T32 GM008339/GM/NIGMS NIH HHS/United States ; T32 GM008339/NH/NIH HHS/United States ; }, mesh = {COVID-19/*epidemiology ; Computational Biology/*education ; *Coronavirus 3C Proteases/chemistry/genetics ; *Curriculum ; *Education, Distance ; *Evolution, Molecular ; Humans ; *Pandemics ; *SARS-CoV-2/chemistry/genetics ; }, } @article {pmid32796904, year = {2020}, author = {Frade, PR and Glasl, B and Matthews, SA and Mellin, C and Serrão, EA and Wolfe, K and Mumby, PJ and Webster, NS and Bourne, DG}, title = {Spatial patterns of microbial communities across surface waters of the Great Barrier Reef.}, journal = {Communications biology}, volume = {3}, number = {1}, pages = {442}, pmid = {32796904}, issn = {2399-3642}, mesh = {Animals ; Anthozoa/*microbiology ; Bacteria/growth & development ; *Coral Reefs ; Databases as Topic ; *Microbiota ; *Water Microbiology ; }, abstract = {Microorganisms are fundamental drivers of biogeochemical cycling, though their contribution to coral reef ecosystem functioning is poorly understood. Here, we infer predictors of bacterioplankton community dynamics across surface-waters of the Great Barrier Reef (GBR) through a meta-analysis, combining microbial with environmental data from the eReefs platform. Nutrient dynamics and temperature explained 41.4% of inter-seasonal and cross-shelf variation in bacterial assemblages. Bacterial families OCS155, Cryomorphaceae, Flavobacteriaceae, Synechococcaceae and Rhodobacteraceae dominated inshore reefs and their relative abundances positively correlated with nutrient loads. In contrast, Prochlorococcaceae negatively correlated with nutrients and became increasingly dominant towards outershelf reefs. Cyanobacteria in Prochlorococcaceae and Synechococcaceae families occupy complementary cross-shelf biogeochemical niches; their abundance ratios representing a potential indicator of GBR nutrient levels. One Flavobacteriaceae-affiliated taxa was putatively identified as diagnostic for ecosystem degradation. Establishing microbial observatories along GBR environmental gradients will facilitate robust assessments of microbial contributions to reef health and inform tipping-points in reef condition.}, } @article {pmid32796632, year = {2020}, author = {Ramos, JLS and Figueiredo, FWDS and Zuchelo, LTS and Purcino, FAC and Adami, F and Goncalves, R and Ruiz, CA and Baracat, EC and Soares Junior, JM and Sorpreso, ICE}, title = {Health Services, Socioeconomic Indicators, and Primary Care Coverage in Mortality by Lower Genital Tract and Breast Neoplasias in Brazilian Women during Reproductive and Non-Reproductive Periods.}, journal = {International journal of environmental research and public health}, volume = {17}, number = {16}, pages = {}, pmid = {32796632}, issn = {1660-4601}, mesh = {Brazil/epidemiology ; Breast Neoplasms/*mortality ; Female ; Genital Neoplasms, Female/*mortality ; Genitalia ; Health Services ; Humans ; Primary Health Care/*organization & administration/statistics & numerical data ; Socioeconomic Factors ; }, abstract = {Women's health assistance at the low-complexity level is focused on the most common diseases and can be affected by primary health care coverage, particularly in areas far away from large urban centers. Thus, in this work, we aim to analyze the relationship between socioeconomic status, health care indicators, and primary care coverage in mortality from neoplasms of the lower genital tract and breast in Brazilian women during reproductive and non-reproductive periods. We conducted an ecological study at the Gynecology Discipline, Medicine School, University of São Paulo. Secondary data were collected from women according to reproductive periods and mortality data from the Mortality Information System based on International Classification of Disease-10th edition regarding breast and lower genital tract neoplasms in 2017. The health service and socioeconomic indicators were obtained from the Informatics Department of the Unified Health System and Brazilian Institute of Geography and Statistics. Our results showed that primary care coverage and health service indicators were not associated with mortality from breast cancer and the female lower genital tract, both in reproductive and non-reproductive periods. Sociodemographic indicators were found to be associated with mortality from breast cancer and the female lower genital tract, with income being associated with reproductive period (β = -0.4; 95% CI, -0.8 to -0.03) and educational level in the non-reproductive period (β = 9.7; 95% CI, 1.5 to 18.0).}, } @article {pmid32795814, year = {2020}, author = {Lazzaro, L and Bolpagni, R and Buffa, G and Gentili, R and Lonati, M and Stinca, A and Acosta, ATR and Adorni, M and Aleffi, M and Allegrezza, M and Angiolini, C and Assini, S and Bagella, S and Bonari, G and Bovio, M and Bracco, F and Brundu, G and Caccianiga, M and Carnevali, L and Di Cecco, V and Ceschin, S and Ciaschetti, G and Cogoni, A and Foggi, B and Frattaroli, AR and Genovesi, P and Gigante, D and Lucchese, F and Mainetti, A and Mariotti, M and Minissale, P and Paura, B and Pellizzari, M and Perrino, EV and Pirone, G and Poggio, L and Poldini, L and Poponessi, S and Prisco, I and Prosser, F and Puglisi, M and Rosati, L and Selvaggi, A and Sottovia, L and Spampinato, G and Stanisci, A and Venanzoni, R and Viciani, D and Vidali, M and Villani, M and Lastrucci, L}, title = {Impact of invasive alien plants on native plant communities and Natura 2000 habitats: State of the art, gap analysis and perspectives in Italy.}, journal = {Journal of environmental management}, volume = {274}, number = {}, pages = {111140}, doi = {10.1016/j.jenvman.2020.111140}, pmid = {32795814}, issn = {1095-8630}, mesh = {Biodiversity ; *Ecosystem ; *Introduced Species ; Italy ; Plants ; }, abstract = {Invasive alien plants are a major threat to biodiversity and they contribute to the unfavourable conservation status of habitats of interest to the European Community. In order to favour implementation of European Union Regulation no. 1143/2014 on invasive alien species, the Italian Society of Vegetation Science carried out a large survey led by a task force of 49 contributors with expertise in vegetation across all the Italian administrative regions. The survey summed up the knowledge on impact mechanisms of invasive alien plants in Italy and their outcomes on plant communities and the EU habitats of Community Interest, in accordance with Directive no. 92/43/EEC. The survey covered 241 alien plant species reported as having deleterious ecological impacts. The data collected illustrate the current state of the art, highlight the main gaps in knowledge, and suggest topics to be further investigated. In particular, the survey underlined competition as being the main mechanism of ecological impact on plant communities and Natura 2000 habitats. Of the 241 species, only Ailanthus altissima was found to exert an ecological impact on plant communities and Natura 2000 habitats in all Italian regions; while a further 20 species impact up to ten out of the 20 Italian administrative regions. Our data indicate that 84 out of 132 Natura 2000 Habitats (64%) are subjected to some degree of impact by invasive alien plants. Freshwater habitats and natural and semi-natural grassland formations were impacted by the highest number of alien species, followed by coastal sand dunes and inland dunes, and forests. Although not exhaustive, this research is the first example of nationwide evaluation of the ecological impacts of invasive alien plants on plant communities and Natura 2000 Habitats.}, } @article {pmid32795263, year = {2020}, author = {Puente-Sánchez, F and García-García, N and Tamames, J}, title = {SQMtools: automated processing and visual analysis of 'omics data with R and anvi'o.}, journal = {BMC bioinformatics}, volume = {21}, number = {1}, pages = {358}, pmid = {32795263}, issn = {1471-2105}, support = {CTM2016-80095-C2-1-R//Ministerio de Economía, Industria y Competitividad, Gobierno de España/ ; PID2019-110011RB-C31//Ministerio de Economía, Industria y Competitividad, Gobierno de España/ ; IJC2018-035180-I//Ministerio de Ciencia, Innovación y Universidades/ ; SEV-2013-0347-17-2//Ministerio de Ciencia, Innovación y Universidades/ ; }, mesh = {Computational Biology/*methods ; Contig Mapping ; Databases, Factual ; High-Throughput Nucleotide Sequencing ; Metagenomics ; *Software ; }, abstract = {BACKGROUND: The dramatic decrease in sequencing costs over the last decade has boosted the adoption of high-throughput sequencing applications as a standard tool for the analysis of environmental microbial communities. Nowadays even small research groups can easily obtain raw sequencing data. After that, however, non-specialists are faced with the double challenge of choosing among an ever-increasing array of analysis methodologies, and navigating the vast amounts of results returned by these approaches.

RESULTS: Here we present a workflow that relies on the SqueezeMeta software for the automated processing of raw reads into annotated contigs and reconstructed genomes (bins). A set of custom scripts seamlessly integrates the output into the anvi'o analysis platform, allowing filtering and visual exploration of the results. Furthermore, we provide a software package with utility functions to expose the SqueezeMeta results to the R analysis environment.

CONCLUSIONS: Altogether, our workflow allows non-expert users to go from raw sequencing reads to custom plots with only a few powerful, flexible and well-documented commands.}, } @article {pmid32793786, year = {2020}, author = {Skarlupka, AL and Handel, A and Ross, TM}, title = {Dataset of antigenic distance measures, hemagglutination inhibition, viral lung titers, and weight loss in mice and ferrets when exposed to HA-based vaccination or sub-lethal A(H1) influenza infection.}, journal = {Data in brief}, volume = {32}, number = {}, pages = {106118}, pmid = {32793786}, issn = {2352-3409}, } @article {pmid32788682, year = {2020}, author = {Pan, J and Li, Z and Dai, S and Ding, H and Wang, Q and Li, X and Ding, G and Wang, P and Guan, Y and Liu, W}, title = {Integrative analyses of transcriptomics and metabolomics upon seed germination of foxtail millet in response to salinity.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {13660}, pmid = {32788682}, issn = {2045-2322}, mesh = {Computational Biology ; Gene Expression Profiling ; Gene Expression Regulation, Plant ; Germination ; *Metabolome ; Phylogeny ; Plant Proteins/genetics/*metabolism ; *Salinity ; Salt Tolerance ; Seeds/genetics/*growth & development/metabolism ; Setaria Plant/genetics/*growth & development/metabolism ; *Stress, Physiological ; *Transcriptome ; }, abstract = {Salinity stress has become an expanding threat to food security worldwide. Revealing the mechanisms of salinity tolerance in plants has immense significance. Foxtail millet (Setaria italica L.) has been regarded as a model crop for exploring mechanisms under stress, considering its extreme adaptation abilities to adverse ecologies. In present study, two foxtail millet cultivars of Yugu2 and An04 with contrasting salt tolerance properties were investigated through integrative analyses of transcriptomics and metabolomics. In the transcriptomics results, 8887 and 12,249 DEGs were identified in Yugu2 and An04 in response to salinity, respectively, and 3149 of which were overlapped between two varieties. These salinity-responsive genes indicated that ion transport, redox homeostasis, phytohormone metabolism, signaling and secondary metabolism were enriched in Yugu2 by GO and KEGG analyses. The integrative omics analysis implied that phenylpropanoid, flavonoid and lignin biosynthesis pathways, and lysophospholipids were vital in determining the foxtail millet salinity tolerance. Importantly, the tolerance of Yugu2 attributed to higher efficiencies of ion channel and antioxidant system. All these provide a comprehensive regulatory network of foxtail millet to cope with salinity, and shed some lights on salt tolerance which is relevant for other cereal crops.}, } @article {pmid32788594, year = {2020}, author = {Kaufman, D and McKay, N and Routson, C and Erb, M and Davis, B and Heiri, O and Jaccard, S and Tierney, J and Dätwyler, C and Axford, Y and Brussel, T and Cartapanis, O and Chase, B and Dawson, A and de Vernal, A and Engels, S and Jonkers, L and Marsicek, J and Moffa-Sánchez, P and Morrill, C and Orsi, A and Rehfeld, K and Saunders, K and Sommer, PS and Thomas, E and Tonello, M and Tóth, M and Vachula, R and Andreev, A and Bertrand, S and Biskaborn, B and Bringué, M and Brooks, S and Caniupán, M and Chevalier, M and Cwynar, L and Emile-Geay, J and Fegyveresi, J and Feurdean, A and Finsinger, W and Fortin, MC and Foster, L and Fox, M and Gajewski, K and Grosjean, M and Hausmann, S and Heinrichs, M and Holmes, N and Ilyashuk, B and Ilyashuk, E and Juggins, S and Khider, D and Koinig, K and Langdon, P and Larocque-Tobler, I and Li, J and Lotter, A and Luoto, T and Mackay, A and Magyari, E and Malevich, S and Mark, B and Massaferro, J and Montade, V and Nazarova, L and Novenko, E and Pařil, P and Pearson, E and Peros, M and Pienitz, R and Płóciennik, M and Porinchu, D and Potito, A and Rees, A and Reinemann, S and Roberts, S and Rolland, N and Salonen, S and Self, A and Seppä, H and Shala, S and St-Jacques, JM and Stenni, B and Syrykh, L and Tarrats, P and Taylor, K and van den Bos, V and Velle, G and Wahl, E and Walker, I and Wilmshurst, J and Zhang, E and Zhilich, S}, title = {Publisher Correction: A global database of Holocene paleotemperature records.}, journal = {Scientific data}, volume = {7}, number = {1}, pages = {271}, doi = {10.1038/s41597-020-00611-1}, pmid = {32788594}, issn = {2052-4463}, abstract = {An amendment to this paper has been published and can be accessed via a link at the top of the paper.}, } @article {pmid32781916, year = {2021}, author = {Otte, FW and Millar, SK and Klatt, S}, title = {What do you hear? The effect of stadium noise on football players' passing performances.}, journal = {European journal of sport science}, volume = {21}, number = {7}, pages = {1035-1044}, doi = {10.1080/17461391.2020.1809714}, pmid = {32781916}, issn = {1536-7290}, mesh = {Adolescent ; Adult ; Athletic Performance/*psychology ; Auditory Perception/physiology ; Cues ; Humans ; Male ; *Noise ; *Occupational Exposure ; Physical Conditioning, Human/physiology ; Soccer/*psychology ; Task Performance and Analysis ; Young Adult ; }, abstract = {Stadium noise - created by spectators and fans - plays a critical part in the reality of professional sports. Due to a lack of research on the impact of these auditory cues and multimodal environments on motor performance, it is currently unclear how professional athletes experience and perceive stadium noise and how this potentially affects performance in practice. In order to explore the effect of stadium noise on athletes' performance, this paper presents an experimental design using the unique and standardised football training tool known as the "Footbonaut". Specifically, fifteen skilled German football players engaged in a standardised football-specific technical training programme while subjected to four different auditory training conditions; these included both "positive" and "negative" stadium noise conditions, a "baseline" condition providing auditory guidance, and a "no (auditory) cue" condition. Performance data for passing accuracy and passing time were measured for training in each auditory condition. A repeated measures MANOVA revealed a significant main effect for passing time. Specifically, participants showed faster passing times in the baseline compared to the negative and no auditory cue conditions. Findings are presented and discussed from a constraints-led perspective, allied to principles of ecological dynamics and nonlinear pedagogy. Particularly, the use of representative training experiences (including multimodal sensory and emotional information) appears to underline training to refine expert athletes' adaptive coordination of complex motor actions.}, } @article {pmid32778752, year = {2020}, author = {Hansen, AJ and Burns, P and Ervin, J and Goetz, SJ and Hansen, M and Venter, O and Watson, JEM and Jantz, PA and Virnig, ALS and Barnett, K and Pillay, R and Atkinson, S and Supples, C and Rodríguez-Buritica, S and Armenteras, D}, title = {A policy-driven framework for conserving the best of Earth's remaining moist tropical forests.}, journal = {Nature ecology & evolution}, volume = {4}, number = {10}, pages = {1377-1384}, pmid = {32778752}, issn = {2397-334X}, support = {80NSSC18K0338/ImNASA/Intramural NASA/United States ; }, mesh = {Biodiversity ; *Conservation of Natural Resources ; *Forests ; Humans ; Policy ; }, abstract = {Tropical forests vary in composition, structure and function such that not all forests have similar ecological value. This variability is caused by natural and anthropogenic disturbance regimes, which influence the ability of forests to support biodiversity, store carbon, mediate water yield and facilitate human well-being. While international environmental agreements mandate protecting and restoring forests, only forest extent is typically considered, while forest quality is ignored. Consequently, the locations and loss rates of forests of high ecological value are unknown and coordinated strategies for conserving these forests remain undeveloped. Here, we map locations high in forest structural integrity as a measure of ecological quality on the basis of recently developed fine-resolution maps of three-dimensional forest structure, integrated with human pressure across the global moist tropics. Our analyses reveal that tall forests with closed canopies and low human pressure typical of natural conditions comprise half of the global humid or moist tropical forest estate, largely limited to the Amazon and Congo basins. Most of these forests have no formal protection and, given recent rates of loss, are at substantial risk. With the rapid disappearance of these 'best of the last' forests at stake, we provide a policy-driven framework for their conservation and restoration, and recommend locations to maintain protections, add new protections, mitigate deleterious human impacts and restore forest structure.}, } @article {pmid32778648, year = {2020}, author = {Bennett, JM and Steets, JA and Burns, JH and Burkle, LA and Vamosi, JC and Wolowski, M and Arceo-Gómez, G and Burd, M and Durka, W and Ellis, AG and Freitas, L and Li, J and Rodger, JG and Ştefan, V and Xia, J and Knight, TM and Ashman, TL}, title = {Land use and pollinator dependency drives global patterns of pollen limitation in the Anthropocene.}, journal = {Nature communications}, volume = {11}, number = {1}, pages = {3999}, pmid = {32778648}, issn = {2041-1723}, mesh = {Animals ; Bees ; Databases, Factual ; *Ecology ; Ecosystem ; Phylogeny ; *Plant Physiological Phenomena ; Plants/classification ; *Pollen ; *Pollination ; Urbanization ; }, abstract = {Land use change, by disrupting the co-evolved interactions between plants and their pollinators, could be causing plant reproduction to be limited by pollen supply. Using a phylogenetically controlled meta-analysis on over 2200 experimental studies and more than 1200 wild plants, we ask if land use intensification is causing plant reproduction to be pollen limited at global scales. Here we report that plants reliant on pollinators in urban settings are more pollen limited than similarly pollinator-reliant plants in other landscapes. Plants functionally specialized on bee pollinators are more pollen limited in natural than managed vegetation, but the reverse is true for plants pollinated exclusively by a non-bee functional group or those pollinated by multiple functional groups. Plants ecologically specialized on a single pollinator taxon were extremely pollen limited across land use types. These results suggest that while urbanization intensifies pollen limitation, ecologically and functionally specialized plants are at risk of pollen limitation across land use categories.}, } @article {pmid32771620, year = {2020}, author = {Dyakov, IN and Mavletova, DA and Chernyshova, IN and Snegireva, NA and Gavrilova, MV and Bushkova, KK and Dyachkova, MS and Alekseeva, MG and Danilenko, VN}, title = {FN3 protein fragment containing two type III fibronectin domains from B. longum GT15 binds to human tumor necrosis factor alpha in vitro.}, journal = {Anaerobe}, volume = {65}, number = {}, pages = {102247}, pmid = {32771620}, issn = {1095-8274}, mesh = {Bacterial Proteins/chemistry/*metabolism ; Bifidobacteriales Infections/metabolism/microbiology ; Bifidobacterium/genetics/*metabolism ; Computational Biology/methods ; Cytokines/metabolism ; *Fibronectin Type III Domain ; Fibronectins/chemistry/*metabolism ; Host-Pathogen Interactions ; Humans ; Multigene Family ; Protein Binding ; Recombinant Proteins/genetics/isolation & purification/metabolism ; Tumor Necrosis Factor-alpha/*metabolism ; }, abstract = {Most species of the genus Bifidobacterium contain the gene cluster PFNA, which is presumably involved in the species-specific communication between bacteria and their hosts. The gene cluster PFNA consists of five genes including fn3, which codes for a protein containing two fibronectin type III domains. Each fibronectin domain contains sites similar to cytokine-binding sites of human receptors. Based on this finding we assumed that this protein would bind specifically to human cytokines in vitro. We cloned a fragment of the fn3 gene (1503 bp; 501 aa) containing two fibronectin domains, from the strain B. longum subsp. longum GT15. After cloning the fragment into the expression vector pET16b and expressing it in E. coli, the protein product was purified to a homogenous state for further analysis. Using the immunoferment method, we tested the purified fragment's ability to bind the following human cytokines: IL-1β, IL-6, IL-10, TNFα. We developed a sandwich ELISA system to detect any specific interactions between the purified protein and any of the studied cytokines. We found that the purified protein fragment only binds to TNFα.}, } @article {pmid32770154, year = {2020}, author = {Cichocki, N and Hübschmann, T and Schattenberg, F and Kerckhof, FM and Overmann, J and Müller, S}, title = {Bacterial mock communities as standards for reproducible cytometric microbiome analysis.}, journal = {Nature protocols}, volume = {15}, number = {9}, pages = {2788-2812}, pmid = {32770154}, issn = {1750-2799}, mesh = {Bacteria/*cytology ; Computational Biology ; Cytological Techniques/*standards ; *Microbiota ; Reference Standards ; Reproducibility of Results ; }, abstract = {Flow cytometry has recently established itself as a tool to track short-term dynamics in microbial community assembly and link those dynamics with ecological parameters. However, instrumental configurations of commercial cytometers and variability introduced through differential handling of the cells and instruments frequently cause data set variability at the single-cell level. This is especially pronounced with microorganisms, which are in the lower range of optical resolution. Although alignment beads are valuable to generally minimize instrumental noise and align overall machine settings, an artificial microbial cytometric mock community (mCMC) is mandatory for validating lab workflows and enabling comparison of data between experiments, thus representing a necessary reference standard for the reproducible cytometric characterization of microbial communities, especially in long-term studies. In this study, the mock community consisted of two Gram-positive and two Gram-negative bacterial strains, which can be assembled with respective subsets of cells, including spores, in any selected ratio or concentration. The preparation of the four strains takes a maximum of 5 d, and the stains are storable with either PFA/ethanol fixation at -20 °C or drying at 4 °C for at least 6 months. Starting from this stock, an mCMC can be assembled within 1 h. Fluorescence staining methods are presented and representatively applied with two high-resolution cell sorters and three benchtop flow cytometers. Benchmarked data sets allow the use of bioinformatic evaluation procedures to decode community behavior or convey qualified cell sorting decisions for subsequent high-resolution sequencing or proteomic routines.}, } @article {pmid32768759, year = {2020}, author = {Fang, Y and Zheng, T and Zheng, X and Peng, H and Wang, H and Xin, J and Zhang, B}, title = {Assessment of the hydrodynamics role for groundwater quality using an integration of GIS, water quality index and multivariate statistical techniques.}, journal = {Journal of environmental management}, volume = {273}, number = {}, pages = {111185}, doi = {10.1016/j.jenvman.2020.111185}, pmid = {32768759}, issn = {1095-8630}, mesh = {Environmental Monitoring ; Geographic Information Systems ; *Groundwater ; Hydrodynamics ; Water Pollutants, Chemical/*analysis ; Water Quality ; }, abstract = {To explore the impact of groundwater hydrodynamics on water quality, a cost-effective geospatial model was developed using geographic information system (GIS) technology and the Dupuit assumption. Meanwhile, the groundwater quality in the Dagu River Basin was evaluated based on the water quality index (WQI) and multivariate statistical analyses. In April (dry season) and September (rainy season) 2017, the groundwater level was automatically monitored from 115 wells, and the water quality including 21 hydrochemical parameters was sampled from 37 wells. Results reveal that the WQI values varied from 35.01 to 64.74, with mean values of 51.89 and 47.87 in the rainy and dry seasons. Approximately 80% of the samples exhibited moderate water quality, with no significant difference between the rainy and dry seasons. Nitrate pollution and the integrated water quality in the central and northern regions were generally worse than that in the southern region. The Darcy velocity in the central and northern regions was relatively high with a maximum rate of 0.56 m/d, compared with the southern region. This correlation illustrates the effect of groundwater hydrodynamics on quality. The sowing of greater chemical fertilizers combined with faster groundwater movement is likely responsible for the large-scale nitrate pollution in the central and northern regions. Results also proved the accuracy of the geospatial model with a valid uncertainty. The geospatial model provides a valuable alternative for the spatial analysis of the effect of groundwater hydrodynamics on water quality.}, } @article {pmid32760547, year = {2020}, author = {Carraro, L and Bertuzzo, E and Fronhofer, EA and Furrer, R and Gounand, I and Rinaldo, A and Altermatt, F}, title = {Generation and application of river network analogues for use in ecology and evolution.}, journal = {Ecology and evolution}, volume = {10}, number = {14}, pages = {7537-7550}, pmid = {32760547}, issn = {2045-7758}, abstract = {Several key processes in freshwater ecology are governed by the connectivity inherent to dendritic river networks. These have extensively been analyzed from a geomorphological and hydrological viewpoint, yet structures classically used in ecological modeling have been poorly representative of the structure of real river basins, often failing to capture well-known scaling features of natural rivers. Pioneering work identified optimal channel networks (OCNs) as spanning trees reproducing all scaling features characteristic of natural stream networks worldwide. While OCNs have been used to create landscapes for studies on metapopulations, biodiversity, and epidemiology, their generation has not been generally accessible.Given the increasing interest in dendritic riverine networks by ecologists and evolutionary biologists, we here present a method to generate OCNs and, to facilitate its application, we provide the R-package OCNet. Owing to the stochastic process generating OCNs, multiple network replicas spanning the same surface can be built; this allows performing computational experiments whose results are irrespective of the particular shape of a single river network. The OCN construct also enables the generation of elevational gradients derived from the optimal network configuration, which can constitute three-dimensional landscapes for spatial studies in both terrestrial and freshwater realms. Moreover, the package provides functions that aggregate OCNs into an arbitrary number of nodes, calculate several descriptors of river networks, and draw relevant network features.We describe the main functionalities of the package and its integration with other R-packages commonly used in spatial ecology. Moreover, we exemplify the generation of OCNs and discuss an application to a metapopulation model for an invasive riverine species.In conclusion, OCNet provides a powerful tool to generate realistic river network analogues for various applications. It thereby allows the design of spatially realistic studies in increasingly impacted ecosystems and enhances our knowledge on spatial processes in freshwater ecology in general.}, } @article {pmid32760510, year = {2020}, author = {Webb, TJ and Lines, A and Howarth, LM}, title = {Occupancy-derived thermal affinities reflect known physiological thermal limits of marine species.}, journal = {Ecology and evolution}, volume = {10}, number = {14}, pages = {7050-7061}, pmid = {32760510}, issn = {2045-7758}, abstract = {Predicting how species will respond to increased environmental temperatures is key to understanding the ecological consequences of global change. The physiological tolerances of a species define its thermal limits, while its thermal affinity is a summary of the environmental temperatures at the localities at which it actually occurs. Experimentally derived thermal limits are known to be related to observed latitudinal ranges in marine species, but accurate range maps from which to derive latitudinal ranges are lacking for many marine species. An alternative approach is to combine widely available data on global occurrences with gridded global temperature datasets to derive measures of species-level "thermal affinity"-that is, measures of the central tendency, variation, and upper and lower bounds of the environmental temperatures at the locations at which a species has been recorded to occur. Here, we test the extent to which such occupancy-derived measures of thermal affinity are related to the known thermal limits of marine species using data on 533 marine species from 24 taxonomic classes and with experimentally derived critical upper temperatures spanning 2-44.5°C. We show that thermal affinity estimates are consistently and positively related to the physiological tolerances of marine species, despite gaps and biases in the source data. Our method allows thermal affinity measures to be rapidly and repeatably estimated for many thousands more marine species, substantially expanding the potential to assess vulnerability of marine communities to warming seas.}, } @article {pmid32760314, year = {2020}, author = {Otte, FW and Davids, K and Millar, SK and Klatt, S}, title = {When and How to Provide Feedback and Instructions to Athletes?-How Sport Psychology and Pedagogy Insights Can Improve Coaching Interventions to Enhance Self-Regulation in Training.}, journal = {Frontiers in psychology}, volume = {11}, number = {}, pages = {1444}, pmid = {32760314}, issn = {1664-1078}, abstract = {In specialist sports coaching, the type and manner of augmented information that the coach chooses to use in communicating and training with individual athletes can have a significant impact on skill development and performance. Informed by insights from psychology, pedagogy, and sport science, this position paper presents a practitioner-based approach in response to the overarching question: When, why, and how could coaches provide information to athletes during coaching interventions? In an ecological dynamics rationale, practice is seen as a search for functional performance solutions, and augmented feedback is outlined as instructional constraints to guide athletes' self-regulation of action in practice. Using the exemplar of team sports, we present a Skill Training Communication Model for practical application in the context of the role of a specialist coach, using a constraints-led approach (CLA). Further based on principles of a non-linear pedagogy and using the recently introduced Periodization of Skill Training (PoST) framework, the proposed model aims to support practitioners' understanding of the pedagogical constraints of feedback and instruction during practice. In detail, the PoST framework's three skill development and training stages work to (1) directly impact constraint manipulations in practice designs and (2) indirectly affect coaches' choices of external (coach-induced) information. In turn, these guide practitioners on how and when to apply different verbal instruction methodologies and aim to support the design of effective skill learning environments. Finally, several practical guidelines in regard to sports coaches' feedback and instruction processes are proposed.}, } @article {pmid32760000, year = {2020}, author = {Gemmell, NJ and Rutherford, K and Prost, S and Tollis, M and Winter, D and Macey, JR and Adelson, DL and Suh, A and Bertozzi, T and Grau, JH and Organ, C and Gardner, PP and Muffato, M and Patricio, M and Billis, K and Martin, FJ and Flicek, P and Petersen, B and Kang, L and Michalak, P and Buckley, TR and Wilson, M and Cheng, Y and Miller, H and Schott, RK and Jordan, MD and Newcomb, RD and Arroyo, JI and Valenzuela, N and Hore, TA and Renart, J and Peona, V and Peart, CR and Warmuth, VM and Zeng, L and Kortschak, RD and Raison, JM and Zapata, VV and Wu, Z and Santesmasses, D and Mariotti, M and Guigó, R and Rupp, SM and Twort, VG and Dussex, N and Taylor, H and Abe, H and Bond, DM and Paterson, JM and Mulcahy, DG and Gonzalez, VL and Barbieri, CG and DeMeo, DP and Pabinger, S and Van Stijn, T and Clarke, S and Ryder, O and Edwards, SV and Salzberg, SL and Anderson, L and Nelson, N and Stone, C and , }, title = {The tuatara genome reveals ancient features of amniote evolution.}, journal = {Nature}, volume = {584}, number = {7821}, pages = {403-409}, pmid = {32760000}, issn = {1476-4687}, support = {R35 GM124827/GM/NIGMS NIH HHS/United States ; 108749/WT_/Wellcome Trust/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; R01 HG006677/HG/NHGRI NIH HHS/United States ; WT108749/Z/15/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Animals ; Conservation of Natural Resources/trends ; *Evolution, Molecular ; Female ; Genetics, Population ; Genome/*genetics ; Lizards/genetics ; Male ; Molecular Sequence Annotation ; New Zealand ; *Phylogeny ; Reptiles/*genetics ; Sex Characteristics ; Snakes/genetics ; Synteny ; }, abstract = {The tuatara (Sphenodon punctatus)-the only living member of the reptilian order Rhynchocephalia (Sphenodontia), once widespread across Gondwana[1,2]-is an iconic species that is endemic to New Zealand[2,3]. A key link to the now-extinct stem reptiles (from which dinosaurs, modern reptiles, birds and mammals evolved), the tuatara provides key insights into the ancestral amniotes[2,4]. Here we analyse the genome of the tuatara, which-at approximately 5 Gb-is among the largest of the vertebrate genomes yet assembled. Our analyses of this genome, along with comparisons with other vertebrate genomes, reinforce the uniqueness of the tuatara. Phylogenetic analyses indicate that the tuatara lineage diverged from that of snakes and lizards around 250 million years ago. This lineage also shows moderate rates of molecular evolution, with instances of punctuated evolution. Our genome sequence analysis identifies expansions of proteins, non-protein-coding RNA families and repeat elements, the latter of which show an amalgam of reptilian and mammalian features. The sequencing of the tuatara genome provides a valuable resource for deep comparative analyses of tetrapods, as well as for tuatara biology and conservation. Our study also provides important insights into both the technical challenges and the cultural obligations that are associated with genome sequencing.}, } @article {pmid32758003, year = {2020}, author = {Elsaeed, E and Enany, S and Hanora, A and Fahmy, N}, title = {Comparative Metagenomic Screening of Aromatic Hydrocarbon Degradation and Secondary Metabolite-Producing Genes in the Red Sea, the Suez Canal, and the Mediterranean Sea.}, journal = {Omics : a journal of integrative biology}, volume = {24}, number = {9}, pages = {541-550}, doi = {10.1089/omi.2020.0070}, pmid = {32758003}, issn = {1557-8100}, mesh = {Aquatic Organisms/genetics/metabolism ; Databases, Genetic ; Ecosystem ; Hydrocarbons, Aromatic/*metabolism ; Indian Ocean ; Mediterranean Sea ; *Metagenome ; *Metagenomics/methods/standards ; *Microbiota/genetics ; Seawater ; *Secondary Metabolism ; *Water Microbiology ; Water Pollution ; }, abstract = {Marine and ecosystem pollution due to oil spills can be addressed by identifying the aromatic hydrocarbon (HC)-degrading microorganisms and their responsible genes for biodegradation. Moreover, screening for genes coding for secondary metabolites is invaluable for drug discovery. We report here, the first metagenomic study investigating the shotgun metagenome of the Suez Canal water sampled at Ismailia city concerning its aromatic HC degradation potential in comparison to the seawater sampled at Halayeb city at the Red Sea and Sallum city at the Mediterranean Sea. Moreover, for an in-depth understanding of marine biotechnology applications, we screened for the polyketide synthases (PKSs) and nonribosomal peptide synthetase (NRPS) domains in those three metagenomes. By mapping against functional protein databases, we found that 13, 6, and 3 gene classes from the SEED database; 2, 1, and 3 gene classes from the EgGNOG; and 5, 4, and 2 genes from the InterPro2GO database were identified to be differentially abundant among Halayeb, Ismailia, and Sallum metagenomes, respectively. Also, Halayeb metagenome in the Red Sea reported the highest number of PKS domains showing higher potential in secondary metabolite production in addition to the oil degradation potential.}, } @article {pmid32757488, year = {2021}, author = {Xu, Y and Tandon, R and Ancheta, C and Arroyo, P and Gilbert, JA and Stephens, B and Kelley, ST}, title = {Quantitative profiling of built environment bacterial and fungal communities reveals dynamic material dependent growth patterns and microbial interactions.}, journal = {Indoor air}, volume = {31}, number = {1}, pages = {188-205}, doi = {10.1111/ina.12727}, pmid = {32757488}, issn = {1600-0668}, support = {F32 GM020013/GM/NIGMS NIH HHS/United States ; }, mesh = {Air Pollution, Indoor ; Bacteria ; *Built Environment ; Construction Materials ; *Environmental Microbiology ; Fungi ; Humans ; Humidity ; Microbial Interactions ; Microbiota ; Mycobiome ; Phylogeny ; RNA, Ribosomal, 16S ; }, abstract = {Indoor microbial communities vary in composition and diversity depending on material type, moisture levels, and occupancy. In this study, we integrated bacterial cell counting, fungal biomass estimation, and fluorescence-assisted cell sorting (FACS) with amplicon sequencing of bacterial (16S rRNA) and fungal (ITS) communities to investigate the influence of wetting on medium density fiberboard (MDF) and gypsum wallboard. Surface samples were collected longitudinally from wetted materials maintained at high relative humidity (~95%). Bacterial and fungal growth patterns were strongly time-dependent and material-specific. Fungal growth phenotypes differed between materials: spores dominated MDF surfaces while fungi transitioned from spores to hyphae on gypsum. FACS confirmed that most of the bacterial cells were intact (viable) on both materials over the course of the study. Integrated cell count and biomass data (quantitative profiling) revealed that small changes in relative abundance often resulted from large changes in absolute abundance, while negative correlations in relative abundances were explained by rapid growth of only one group of bacteria or fungi. Comparisons of bacterial-bacterial and fungal-bacterial networks suggested a top-down control of fungi on bacterial growth, possibly via antibiotic production. In conclusion, quantitative profiling provides novel insights into microbial growth dynamics on building materials with potential implications for human health.}, } @article {pmid32756849, year = {2020}, author = {Nascimento, LFC}, title = {CONGENITAL SYPHILIS IN THE PARAÍBA VALLEY USING A SPATIAL APPROACH.}, journal = {Revista paulista de pediatria : orgao oficial da Sociedade de Pediatria de Sao Paulo}, volume = {38}, number = {}, pages = {e2018395}, pmid = {32756849}, issn = {1984-0462}, mesh = {Brazil/epidemiology ; Delivery of Health Care/organization & administration ; Ecosystem ; Female ; Geographic Information Systems/*instrumentation/statistics & numerical data ; Humans ; Incidence ; Infant, Newborn ; Live Birth/epidemiology ; Male ; Patient Care Team/*statistics & numerical data ; Pediatricians/statistics & numerical data ; Pregnancy ; Social Class ; Spatial Analysis ; Syphilis, Congenital/*epidemiology ; Vulnerable Populations/*statistics & numerical data ; }, abstract = {OBJECTIVE: To compare spatial patterns of congenital syphilis (CS) with those of socioeconomic and medical variables in Paraíba Valley, São Paulo, between 2012 and 2016.

METHODS: Ecological and exploratory study developed using spatial analysis tools, with information on CS cases obtained from official data reports. Rates were found for CS cases per 1,000 live births, number of family health teams and pediatricians available in the health system per 100,000 inhabitants, and social vulnerability index values. Thematic maps were constructed with these variables and compared using TerraView 4.2.2 software. Estimated global Moran (IM) indexes were calculated. In order to detect areas with priority attention regarding the incidence of CS, BoxMaps were developed. The Spearman correlation was estimated for the variable values and compared using the Kruskal-Wallis test. P <0.05 was significant.

RESULTS: 144,613 births and 870 CS cases (6.04/1000 live births) occurred during the study period. The average value of CS rates per municipality was 4.0±4.1, (0.0-17.6/1000 live births). Higher CS rates occurred in municipalities of the Upper Vale do Paraíba, contrary to the proportions of pediatricians who were in the far east of the region. The thematic maps of the variables presented a mosaic aspect, which characterized the random distribution of the variables. The IM were not significant. No significant correlation was found between the variables. The BoxMap identified eight municipalities with high CS rates.

CONCLUSIONS: Even though it was not possible to identify a spatial pattern of CS rates, it was shown that eight municipalities deserve the attention of city managers.}, } @article {pmid32756341, year = {2020}, author = {Sierra, MA and Li, Q and Pushalkar, S and Paul, B and Sandoval, TA and Kamer, AR and Corby, P and Guo, Y and Ruff, RR and Alekseyenko, AV and Li, X and Saxena, D}, title = {The Influences of Bioinformatics Tools and Reference Databases in Analyzing the Human Oral Microbial Community.}, journal = {Genes}, volume = {11}, number = {8}, pages = {}, pmid = {32756341}, issn = {2073-4425}, support = {R01 LM012517/LM/NLM NIH HHS/United States ; CA206105/NH/NIH HHS/United States ; DE025992/NH/NIH HHS/United States ; DE027074/NH/NIH HHS/United States ; }, mesh = {Computational Biology/methods/*standards ; DNA Barcoding, Taxonomic/methods/standards ; Databases, Genetic/*standards ; Humans ; *Microbiota ; Mouth/*microbiology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {There is currently no criterion to select appropriate bioinformatics tools and reference databases for analysis of 16S rRNA amplicon data in the human oral microbiome. Our study aims to determine the influence of multiple tools and reference databases on α-diversity measurements and β-diversity comparisons analyzing the human oral microbiome. We compared the results of taxonomical classification by Greengenes, the Human Oral Microbiome Database (HOMD), National Center for Biotechnology Information (NCBI) 16S, SILVA, and the Ribosomal Database Project (RDP) using Quantitative Insights Into Microbial Ecology (QIIME) and the Divisive Amplicon Denoising Algorithm (DADA2). There were 15 phyla present in all of the analyses, four phyla exclusive to certain databases, and different numbers of genera were identified in each database. Common genera found in the oral microbiome, such as Veillonella, Rothia, and Prevotella, are annotated by all databases; however, less common genera, such as Bulleidia and Paludibacter, are only annotated by large databases, such as Greengenes. Our results indicate that using different reference databases in 16S rRNA amplicon data analysis could lead to different taxonomic compositions, especially at genus level. There are a variety of databases available, but there are no defined criteria for data curation and validation of annotations, which can affect the accuracy and reproducibility of results, making it difficult to compare data across studies.}, } @article {pmid32752210, year = {2020}, author = {von Reumont, BM and Lüddecke, T and Timm, T and Lochnit, G and Vilcinskas, A and von Döhren, J and Nilsson, MA}, title = {Proteo-Transcriptomic Analysis Identifies Potential Novel Toxins Secreted by the Predatory, Prey-Piercing Ribbon Worm Amphiporus lactifloreus.}, journal = {Marine drugs}, volume = {18}, number = {8}, pages = {}, pmid = {32752210}, issn = {1660-3397}, support = {LOEWE Center "Translational Biodiversity Genomics"//Hessen State Ministry of Higher Education, Research and the Arts (HMWK)/ ; }, mesh = {Animals ; Databases, Genetic ; *Gene Expression Profiling ; Invertebrates/*genetics/*metabolism ; Marine Toxins/*genetics/*metabolism ; *Proteome ; *Proteomics ; *Transcriptome ; }, abstract = {Nemerteans (ribbon worms) employ toxins to subdue their prey, but research thus far has focused on the small-molecule components of mucus secretions and few protein toxins have been characterized. We carried out a preliminary proteotranscriptomic analysis of putative toxins produced by the hoplonemertean Amphiporus lactifloreus (Hoplonemertea, Amphiporidae). No variants were found of known nemertean-specific toxin proteins (neurotoxins, cytotoxins, parbolysins or nemertides) but several toxin-like transcripts were discovered, expressed strongly in the proboscis, including putative metalloproteinases and sequences resembling sea anemone actitoxins, crown-of-thorn sea star plancitoxins, and multiple classes of inhibitor cystine knot/knottin family proteins. Some of these products were also directly identified in the mucus proteome, supporting their preliminary identification as secreted toxin components. Two new nemertean-typical toxin candidates could be described and were named U-nemertotoxin-1 and U-nemertotoxin-2. Our findings provide insight into the largely overlooked venom system of nemerteans and support a hypothesis in which the nemertean proboscis evolved in several steps from a flesh-melting organ in scavenging nemerteans to a flesh-melting and toxin-secreting venom apparatus in hunting hoplonemerteans.}, } @article {pmid32751145, year = {2020}, author = {Kolosova, V and Belichenko, O and Rodionova, A and Melnikov, D and Sõukand, R}, title = {Foraging in Boreal Forest: Wild Food Plants of the Republic of Karelia, NW Russia.}, journal = {Foods (Basel, Switzerland)}, volume = {9}, number = {8}, pages = {}, pmid = {32751145}, issn = {2304-8158}, support = {714874/ERC_/European Research Council/International ; }, abstract = {While the current consumption of wild food plants in the taiga of the American continent is a relatively well-researched phenomenon, the European taiga area is heavily underrepresented in the scientific literature. The region is important due to its distinctive ecological conditions with restricted seasonal availability of wild plants. During an ethnobotanical field study conducted in 2018-2019, 73 people from ten settlements in the Republic of Karelia were interviewed. In addition, we conducted historical data analysis and ethnographical source analysis. The most widely consumed wild food plants are forest berries (three Vaccinium species, and Rubus chamaemorus), sap-yielding Betula and acidic Rumex. While throughout the lifetime of the interviewees the list of used plants did not change considerably, the ways in which they are processed and stored underwent several stages in function of centrally available goods, people's welfare, technical progress, and ideas about the harm and benefit of various products and technological processes. Differences in the food use of wild plants among different ethnic groups living in the region were on the individual level, while all groups exhibited high variability in the methods of preparation of most used berries. The sustainability of berry use over time has both ecological and economical factors.}, } @article {pmid32750867, year = {2022}, author = {Pursalim, M and Keong, KC}, title = {An Efficient Multiresolution Clustering for Motif Discovery in Complex Networks.}, journal = {IEEE/ACM transactions on computational biology and bioinformatics}, volume = {19}, number = {1}, pages = {284-294}, doi = {10.1109/TCBB.2020.3003018}, pmid = {32750867}, issn = {1557-9964}, mesh = {*Algorithms ; Cluster Analysis ; *Computational Biology ; Genomics ; }, abstract = {Motif discovery and network clustering in complex networks have received a lot of attention in recent years, also they are still challenging tasks in bioinformatics, big data analytics and data mining applications. Motif discovery in big data networks has a lot of important applications in different domains such as engineering, bioinformatics, cheminformatics, genomics, sociology and ecology for revealing hidden frequent structures, functional building blocks, or knowledge discovery. In this paper, a motif localization method based on a novel clustering algorithm in complex networks is presented. In our method, for each complex network, a novel structure so-called Augmented Multiresolution Network (AMN) is generated, then it is adaptively partitioned into several clusters and their corresponding subnets. Then top ranked subnets are chosen to discover network motifs. We show that the proposed method provides an efficient solution for clustering and motif discovery; It speeds up current motif discovery algorithms by pruning non-promising regions of complex networks. Experimental results show our algorithm efficiently deals with complex networks representing large datasets with high-dimensionality such as big scientific data. Our method also provides motivations for future studies in big data and complex networks.}, } @article {pmid32612807, year = {2019}, author = {Sima, AC and Dessimoz, C and Stockinger, K and Zahn-Zabal, M and Mendes de Farias, T}, title = {A hands-on introduction to querying evolutionary relationships across multiple data sources using SPARQL.}, journal = {F1000Research}, volume = {8}, number = {}, pages = {1822}, pmid = {32612807}, issn = {2046-1402}, mesh = {*Biological Evolution ; *Computational Biology ; Databases, Factual ; Genome, Microbial ; *Information Storage and Retrieval ; *Programming Languages ; }, abstract = {The increasing use of Semantic Web technologies in the life sciences, in particular the use of the Resource Description Framework (RDF) and the RDF query language SPARQL, opens the path for novel integrative analyses, combining information from multiple data sources. However, analyzing evolutionary data in RDF is not trivial, due to the steep learning curve required to understand both the data models adopted by different RDF data sources, as well as the equivalent SPARQL constructs required to benefit from this data - in particular, recursive property paths. In this article, we provide a hands-on introduction to querying evolutionary data across several data sources that publish orthology information in RDF, namely: The Orthologous MAtrix (OMA), the European Bioinformatics Institute (EBI) RDF platform, the Database of Orthologous Groups (OrthoDB) and the Microbial Genome Database (MBGD). We present four protocols in increasing order of complexity. In these protocols, we demonstrate through SPARQL queries how to retrieve pairwise orthologs, homologous groups, and hierarchical orthologous groups. Finally, we show how orthology information in different data sources can be compared, through the use of federated SPARQL queries.}, } @article {pmid32747674, year = {2020}, author = {Tu, N and Liang, D and Zhang, P}, title = {Whole-exome sequencing and genome-wide evolutionary analyses identify novel candidate genes associated with infrared perception in pit vipers.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {13033}, pmid = {32747674}, issn = {2045-2322}, mesh = {Amino Acid Substitution/genetics ; Animals ; Brain/metabolism ; Computer Simulation ; Crotalinae/*genetics ; *Evolution, Molecular ; Gene Expression Regulation ; Gene Ontology ; *Genetic Association Studies ; *Genome ; *Infrared Rays ; Open Reading Frames/genetics ; Phylogeny ; Potassium Channels/chemistry/genetics ; Selection, Genetic ; Visual Perception/*genetics ; *Exome Sequencing ; }, abstract = {Pit vipers possess a unique thermal sensory system consisting of facial pits that allow them to detect minute temperature fluctuations within their environments. Biologists have long attempted to elucidate the genetic basis underlying the infrared perception of pit vipers. Early studies have shown that the TRPA1 gene is the thermal sensor associated with infrared detection in pit vipers. However, whether genes other than TRPA1 are also involved in the infrared perception of pit vipers remains unknown. Here, we sequenced the whole exomes of ten snake species and performed genome-wide evolutionary analyses to search for novel candidate genes that might be involved in the infrared perception of pit vipers. We applied both branch-length-comparison and selection-pressure-alteration analyses to identify genes that specifically underwent accelerated evolution in the ancestral lineage of pit vipers. A total of 47 genes were identified. These genes were significantly enriched in the ion transmembrane transporter, stabilization of membrane potential, and temperature gating activity functional categories. The expression levels of these candidate genes in relevant nerve tissues (trigeminal ganglion, dorsal root ganglion, midbrain, and cerebrum) were also investigated in this study. We further chose one of our candidate genes, the potassium channel gene KCNK4, as an example to discuss its possible role in the infrared perception of pit vipers. Our study provides the first genome-wide survey of infrared perception-related genes in pit vipers via comparative evolutionary analyses and reveals valuable candidate genes for future functional studies.}, } @article {pmid32746696, year = {2021}, author = {Baker, BJ and Appler, KE and Gong, X}, title = {New Microbial Biodiversity in Marine Sediments.}, journal = {Annual review of marine science}, volume = {13}, number = {}, pages = {161-175}, doi = {10.1146/annurev-marine-032020-014552}, pmid = {32746696}, issn = {1941-0611}, mesh = {Archaea/*classification/genetics ; Bacteria/*classification/genetics ; Biodiversity ; Datasets as Topic ; Geologic Sediments/*microbiology ; *Metagenome ; Metagenomics ; Microbiota/*genetics ; Phylogeny ; Seawater/*microbiology ; }, abstract = {Microbes in marine sediments represent a large portion of the biosphere, and resolving their ecology is crucial for understanding global ocean processes. Single-gene diversity surveys have revealed several uncultured lineages that are widespread in ocean sediments and whose ecological roles are unknown, and advancements in the computational analysis of increasingly large genomic data sets have made it possible to reconstruct individual genomes from complex microbial communities. Using these metagenomic approaches to characterize sediments is transforming our view of microbial communities on the ocean floor and the biodiversity of the planet. In recent years, marine sediments have been a prominent source of new lineages in the tree of life. The incorporation of these lineages into existing phylogenies has revealed that many belong to distinct phyla, including archaeal phyla that are advancing our understanding of the origins of cellular complexity and eukaryotes. Detailed comparisons of the metabolic potentials of these new lineages have made it clear that uncultured bacteria and archaea are capable of mediating key previously undescribed steps in carbon and nutrient cycling.}, } @article {pmid32745624, year = {2020}, author = {Zhang, T and Guan, P and Liu, W and Zhao, G and Fang, Y and Fu, H and Gui, JF and Li, G and Liu, JX}, title = {Copper stress induces zebrafish central neural system myelin defects via WNT/NOTCH-hoxb5b signaling and pou3f1/fam168a/fam168b DNA methylation.}, journal = {Biochimica et biophysica acta. Gene regulatory mechanisms}, volume = {1863}, number = {10}, pages = {194612}, doi = {10.1016/j.bbagrm.2020.194612}, pmid = {32745624}, issn = {1876-4320}, mesh = {Animals ; Animals, Genetically Modified ; Axons/metabolism ; Copper/adverse effects/*metabolism ; *DNA Methylation ; Embryonic Development/genetics ; Gain of Function Mutation ; Gene Expression Regulation, Developmental ; Loss of Function Mutation ; Myelin Sheath/*genetics/*metabolism ; Receptors, Notch/metabolism ; Signal Transduction ; *Stress, Physiological ; Wnt Proteins/metabolism ; Zebrafish/*genetics/*metabolism ; Zebrafish Proteins/genetics/metabolism ; }, abstract = {Unbalanced copper (Cu) homeostasis is associated with neurological development defects and diseases. However, the molecular mechanisms remain elusive. Here, central neural system (CNS) myelin defects and the down-regulated expression of WNT/NOTCH signaling and its down-stream mediator hoxb5b were observed in Cu[2+] stressed zebrafish larvae. The loss/knockdown-of-function of hoxb5b phenocopied the myelin and axon defects observed in Cu[2+] stressed embryos. Meanwhile, the activation of WNT/NOTCH signaling and ectopic expression of hoxb5b could rescue Cu induced myelin defects. Additionally, fam168b, similar to pou3f1/2, exhibited significant promoter hypermethylation and reduced expression in Cu[2+] stressed embryos. The hypermethylated locus in fam168b promoter acted pivotally in its transcription, and the loss/knockdown of fam168b/pou3f1 also induced myelin defects. This study also demonstrated that fam168b/pou3f1 and hoxb5b axis acted in a seesaw manner during fish embryogenesis: Cu induced the down-regulated expression of the WNT&NOTCH-hoxb5b axis through the function of copper transporter cox17, coupled with the promoter methylation of genes fam168b/pou3f1, and its subsequent down-regulated expression through the function of another transporter atp7b, making joint contributions to myelin defects in embryos.}, } @article {pmid32743975, year = {2021}, author = {Jia, P and Pan, X and Liu, F and He, P and Zhang, W and Liu, L and Zou, Y and Chen, L}, title = {Land use mix in the neighbourhood and childhood obesity.}, journal = {Obesity reviews : an official journal of the International Association for the Study of Obesity}, volume = {22 Suppl 1}, number = {Suppl 1}, pages = {e13098}, pmid = {32743975}, issn = {1467-789X}, mesh = {Child ; Cross-Sectional Studies ; Geographic Information Systems ; Humans ; Longitudinal Studies ; *Pediatric Obesity/epidemiology ; Residence Characteristics ; }, abstract = {Land use mix (LUM) in the neighbourhood is an important aspect for promoting healthier lifestyles and consequently reducing the risk for childhood obesity. However, findings of the association between LUM and childhood obesity remain controversial. A literature search was conducted on Cochrane Library, PubMed and Web of Science for articles published before 1 January 2019. In total, 25 cross-sectional and two longitudinal studies were identified. Among them, Geographic Information Systems were used to measure LUM in 15 studies, and perceived LUM was measured in 12 studies. Generally, most studies revealed an association between a higher LUM and higher PA levels and lower obesity rates, although some studies also reported null or negative associations. The various exposure and outcome assessment have limited the synthesis to obtain pooled estimates. The evidence remains scare on the association between LUM and children's weight status, and more longitudinal studies are needed to examine the independent pathways and causality between LUM and weight-related behaviours/outcomes.}, } @article {pmid32737307, year = {2020}, author = {Uzun, M and Alekseeva, L and Krutkina, M and Koziaeva, V and Grouzdev, D}, title = {Unravelling the diversity of magnetotactic bacteria through analysis of open genomic databases.}, journal = {Scientific data}, volume = {7}, number = {1}, pages = {252}, pmid = {32737307}, issn = {2052-4463}, support = {18-34-01005//Russian Foundation for Basic Research (RFBR)/International ; 18-34-01005//Russian Foundation for Basic Research (RFBR)/International ; }, mesh = {Bacteria/*classification/genetics ; Datasets as Topic ; *Genome, Bacterial ; Genomics ; Iron ; Magnetosomes/*genetics ; Phylogeny ; Sulfides ; }, abstract = {Magnetotactic bacteria (MTB) are prokaryotes that possess genes for the synthesis of membrane-bounded crystals of magnetite or greigite, called magnetosomes. Despite over half a century of studying MTB, only about 60 genomes have been sequenced. Most belong to Proteobacteria, with a minority affiliated with the Nitrospirae, Omnitrophica, Planctomycetes, and Latescibacteria. Due to the scanty information available regarding MTB phylogenetic diversity, little is known about their ecology, evolution and about the magnetosome biomineralization process. This study presents a large-scale search of magnetosome biomineralization genes and reveals 38 new MTB genomes. Several of these genomes were detected in the phyla Elusimicrobia, Candidatus Hydrogenedentes, and Nitrospinae, where magnetotactic representatives have not previously been reported. Analysis of the obtained putative magnetosome biomineralization genes revealed a monophyletic origin capable of putative greigite magnetosome synthesis. The ecological distributions of the reconstructed MTB genomes were also analyzed and several patterns were identified. These data suggest that open databases are an excellent source for obtaining new information of interest.}, } @article {pmid32736102, year = {2020}, author = {Bailet, B and Apothéloz-Perret-Gentil, L and Baričević, A and Chonova, T and Franc, A and Frigerio, JM and Kelly, M and Mora, D and Pfannkuchen, M and Proft, S and Ramon, M and Vasselon, V and Zimmermann, J and Kahlert, M}, title = {Diatom DNA metabarcoding for ecological assessment: Comparison among bioinformatics pipelines used in six European countries reveals the need for standardization.}, journal = {The Science of the total environment}, volume = {745}, number = {}, pages = {140948}, doi = {10.1016/j.scitotenv.2020.140948}, pmid = {32736102}, issn = {1879-1026}, mesh = {Computational Biology ; DNA Barcoding, Taxonomic ; Diatoms/*genetics ; Europe ; Rivers ; }, abstract = {Ecological assessment of lakes and rivers using benthic diatom assemblages currently requires considerable taxonomic expertise to identify species using light microscopy. This traditional approach is also time-consuming. Diatom metabarcoding is a promising alternative and there is increasing interest in using this approach for routine assessment. However, until now, analysis protocols for diatom metabarcoding have been developed and optimised by research groups working in isolation. The diversity of existing bioinformatics methods highlights the need for an assessment of the performance and comparability of results of different methods. The aim of this study was to test the correspondence of outputs from six bioinformatics pipelines currently in use for diatom metabarcoding in different European countries. Raw sequence data from 29 biofilm samples were treated by each of the bioinformatics pipelines, five of them using the same curated reference database. The outputs of the pipelines were compared in terms of sequence unit assemblages, taxonomic assignment, biotic index score and ecological assessment outcomes. The three last components were also compared to outputs from traditional light microscopy, which is currently accepted for ecological assessment of phytobenthos, as required by the Water Framework Directive. We also tested the performance of the pipelines on the two DNA markers (rbcL and 18S-V4) that are currently used by the working groups participating in this study. The sequence unit assemblages produced by different pipelines showed significant differences in terms of assigned and unassigned read numbers and sequence unit numbers. When comparing the taxonomic assignments at genus and species level, correspondence of the taxonomic assemblages between pipelines was weak. Most discrepancies were linked to differential detection or quantification of taxa, despite the use of the same reference database. Subsequent calculation of biotic index scores also showed significant differences between approaches, which were reflected in the final ecological assessment. Use of the rbcL marker always resulted in better correlation among molecular datasets and also in results closer to these generated using traditional microscopy. This study shows that decisions made in pipeline design have implications for the dataset's structure and the taxonomic assemblage, which in turn may affect biotic index calculation and ecological assessment. There is a need to define best-practice bioinformatics parameters in order to ensure the best representation of diatom assemblages. Only the use of similar parameters will ensure the compatibility of data from different working groups. The future of diatom metabarcoding for ecological assessment may also lie in the development of new metrics using, for example, presence/absence instead of relative abundance data.}, } @article {pmid32734159, year = {2020}, author = {Bui, AAT and Hosseini, A and Rocchio, R and Jacobs, N and Ross, MK and Okelo, S and Lurmann, F and Eckel, S and Dzubur, E and Dunton, G and Gilliland, F and Sarrafzadeh, M and Habre, R}, title = {Biomedical REAl-Time Health Evaluation (BREATHE): toward an mHealth informatics platform.}, journal = {JAMIA open}, volume = {3}, number = {2}, pages = {190-200}, pmid = {32734159}, issn = {2574-2531}, support = {U01 EB021980/EB/NIBIB NIH HHS/United States ; U01 EB021983/EB/NIBIB NIH HHS/United States ; U24 EB021996/EB/NIBIB NIH HHS/United States ; U54 EB022002/EB/NIBIB NIH HHS/United States ; }, abstract = {OBJECTIVE: To describe a configurable mobile health (mHealth) framework for integration of physiologic and environmental sensors to be used in studies focusing on the domain of pediatric asthma.

MATERIALS AND METHODS: The Biomedical REAl-Time Health Evaluation (BREATHE) platform connects different sensors and data streams, contextualizing an individual's symptoms and daily activities over time to understand pediatric asthma's presentation and its management. A smartwatch/smartphone combination serves as a hub for personal/wearable sensing devices collecting data on health (eg, heart rate, spirometry, medications), motion, and personal exposures (eg, particulate matter, ozone); securely transmitting information to BREATHE's servers; and interacting with the user (eg, ecological momentary assessments). Server-side integration of electronic health record data and spatiotemporally correlated information (eg, weather, traffic) elaborates on these observations. An initial panel study involving pediatric asthma patients was conducted to assess BREATHE.

RESULTS: Twenty subjects were enrolled, during which BREATHE accrued seven consecutive days of continuous data per individual. The data were used to confirm knowledge about asthma (use of controller inhalers, time-activity behaviors, personal air pollution exposure), and additional analyses provided insights into within-day associations of environmental triggers and asthma exacerbations. Exit surveys focusing on mHealth usability, while positive, noted several translational challenges.

DISCUSSION: Based on these promising results, a longitudinal panel study to evaluate individual microenvironments and exposures is ongoing. Lessons learned thus far reflect the need to address various usability aspects, including convenience and ongoing engagement.

CONCLUSION: BREATHE enables multi-sensor mHealth studies, capturing new types of information alongside an evolving understanding of personal exposomes.}, } @article {pmid32730363, year = {2020}, author = {Mallick, I and Kirtania, P and Szabó, M and Bashir, F and Domonkos, I and Kós, PB and Vass, I}, title = {A simple method to produce Synechocystis PCC6803 biofilm under laboratory conditions for electron microscopic and functional studies.}, journal = {PloS one}, volume = {15}, number = {7}, pages = {e0236842}, pmid = {32730363}, issn = {1932-6203}, mesh = {Biofilms/*growth & development ; Cell Membrane/*metabolism/ultrastructure ; Microscopy, Electron, Scanning/*methods ; Polysaccharides, Bacterial/*metabolism/ultrastructure ; Synechocystis/*growth & development/metabolism/*ultrastructure ; }, abstract = {Cyanobacteria can form biofilms in nature, which have ecological roles and high potential for practical applications. In order to study them we need biofilm models that contain healthy cells and can withstand physical manipulations needed for structural studies. At present, combined studies on the structural and physiological features of axenic cyanobacterial biofilms are limited, mostly due to the shortage of suitable model systems. Here, we present a simple method to establish biofilms using the cyanobacterium Synechocystis PCC6803 under standard laboratory conditions to be directly used for photosynthetic activity measurements and scanning electron microscopy (SEM). We found that glass microfiber filters (GMF) with somewhat coarse surface features provided a suitable skeleton to form Synechocystis PCC6803 biofilms. Being very fragile, untreated GMFs were unable to withstand the processing steps needed for SEM. Therefore, we used polyhydroxybutyrate coating to stabilize the filters. We found that up to five coats resulted in GMF stabilization and made possible to obtain high resolution SEM images of the structure of the surface-attached cells and the extensive exopolysaccharide and pili network, which are essential features of biofilm formation. By using pulse-amplitude modulated variable chlorophyll fluorescence imaging, it was also demonstrated that the biofilms contain photosynthetically active cells. Therefore, the Synechocystis PCC6803 biofilms formed on coated GMFs can be used for both structural and functional investigations. The model presented here is easy to replicate and has a potential for high-throughput studies.}, } @article {pmid32730290, year = {2020}, author = {Carrick, PJ and Forsythe, KJ}, title = {The species composition-ecosystem function relationship: A global meta-analysis using data from intact and recovering ecosystems.}, journal = {PloS one}, volume = {15}, number = {7}, pages = {e0236550}, pmid = {32730290}, issn = {1932-6203}, mesh = {Biodiversity ; Biomass ; Databases, Factual ; *Ecosystem ; Environmental Restoration and Remediation ; Soil/chemistry ; }, abstract = {The idea that biodiversity is necessary in order for ecosystems to function properly has long been used as a basic argument for the conservation of species, and has led to an abundance of research exploring the relationships between species richness and ecosystem function. Here we present a meta-analysis of global ecosystems using the Bray-Curtis index to explore more complex changes in the species composition of natural ecosystems, and their relationship with ecosystem functions. By using data recorded, firstly in reference sites and secondly in recovering sites, captured in restoration ecology studies, we pose the following questions: Firstly, how much variation is there in species composition and in ecosystem function in an intact ecosystem? Secondly, once an ecosystem has become degraded, is there a general relationship between its recovery in species composition and its recovery in ecosystem function? Thirdly, is this relationship the same for all types of ecosystem functions? Data from 21 studies yielded 478 comparisons of mean values for ecosystems. On Average, sites within the same intact natural ecosystems shared only a 48% similarity in species composition but were 69% similar in ecosystem functioning. In recovering ecosystems the relationship between species composition and ecosystem function was weak and saturating (directly accounting for only 2% of the variation). Only two of the six types of ecosystem function examined, biomass and biotic structure, showed a significant relationship with species composition, and the three types that measured soil functions showed no significant relationship. To date, most biodiversity-ecosystem function (BEF) research has been conducted in simplified ecosystems using the simple species richness metric. This study encourages a broader examination of the drivers of ecosystem functions under realistic scenarios of biodiversity change, and highlights the need to properly account for the extensive natural variation.}, } @article {pmid32730245, year = {2020}, author = {D'Andrea, R and Gibbs, T and O'Dwyer, JP}, title = {Emergent neutrality in consumer-resource dynamics.}, journal = {PLoS computational biology}, volume = {16}, number = {7}, pages = {e1008102}, pmid = {32730245}, issn = {1553-7358}, mesh = {*Biodiversity ; Biological Evolution ; Computational Biology ; Computer Simulation ; Ecosystem ; *Models, Biological ; Stochastic Processes ; }, abstract = {Neutral theory assumes all species and individuals in a community are ecologically equivalent. This controversial hypothesis has been tested across many taxonomic groups and environmental contexts, and successfully predicts species abundance distributions across multiple high-diversity communities. However, it has been critiqued for its failure to predict a broader range of community properties, particularly regarding community dynamics from generational to geological timescales. Moreover, it is unclear whether neutrality can ever be a true description of a community given the ubiquity of interspecific differences, which presumably lead to ecological inequivalences. Here we derive analytical predictions for when and why non-neutral communities of consumers and resources may present neutral-like outcomes, which we verify using numerical simulations. Our results, which span both static and dynamical community properties, demonstrate the limitations of summarizing distributions to detect non-neutrality, and provide a potential explanation for the successes of neutral theory as a description of macroecological pattern.}, } @article {pmid32730203, year = {2020}, author = {Valentini, G and Mizumoto, N and Pratt, SC and Pavlic, TP and Walker, SI}, title = {Revealing the structure of information flows discriminates similar animal social behaviors.}, journal = {eLife}, volume = {9}, number = {}, pages = {}, pmid = {32730203}, issn = {2050-084X}, support = {PHY-1505048//National Science Foundation/International ; Overseas Research Fellowship//Japan Society for the Promotion of Science/International ; }, mesh = {*Animal Communication ; Animals ; Ants/*physiology ; Behavior, Animal ; Ethology/*methods ; Isoptera/*physiology ; Social Behavior ; }, abstract = {Behavioral correlations stretching over time are an essential but often neglected aspect of interactions among animals. These correlations pose a challenge to current behavioral-analysis methods that lack effective means to analyze complex series of interactions. Here we show that non-invasive information-theoretic tools can be used to reveal communication protocols that guide complex social interactions by measuring simultaneous flows of different types of information between subjects. We demonstrate this approach by showing that the tandem-running behavior of the ant Temnothorax rugatulus and that of the termites Coptotermes formosanus and Reticulitermes speratus are governed by different communication protocols. Our discovery reconciles the diverse ultimate causes of tandem running across these two taxa with their apparently similar signaling mechanisms. We show that bidirectional flow of information is present only in ants and is consistent with the use of acknowledgement signals to regulate the flow of directional information.}, } @article {pmid32727359, year = {2020}, author = {Mussmann, SM and Douglas, MR and Chafin, TK and Douglas, ME}, title = {ADMIXPIPE: population analyses in ADMIXTURE for non-model organisms.}, journal = {BMC bioinformatics}, volume = {21}, number = {1}, pages = {337}, pmid = {32727359}, issn = {1471-2105}, mesh = {Bayes Theorem ; Computational Biology ; Genome ; *Models, Biological ; Polymorphism, Single Nucleotide ; *Software ; }, abstract = {BACKGROUND: Research on the molecular ecology of non-model organisms, while previously constrained, has now been greatly facilitated by the advent of reduced-representation sequencing protocols. However, tools that allow these large datasets to be efficiently parsed are often lacking, or if indeed available, then limited by the necessity of a comparable reference genome as an adjunct. This, of course, can be difficult when working with non-model organisms. Fortunately, pipelines are currently available that avoid this prerequisite, thus allowing data to be a priori parsed. An oft-used molecular ecology program (i.e., STRUCTURE), for example, is facilitated by such pipelines, yet they are surprisingly absent for a second program that is similarly popular and computationally more efficient (i.e., ADMIXTURE). The two programs differ in that ADMIXTURE employs a maximum-likelihood framework whereas STRUCTURE uses a Bayesian approach, yet both produce similar results. Given these issues, there is an overriding (and recognized) need among researchers in molecular ecology for bioinformatic software that will not only condense output from replicated ADMIXTURE runs, but also infer from these data the optimal number of population clusters (K).

RESULTS: Here we provide such a program (i.e., ADMIXPIPE) that (a) filters SNPs to allow the delineation of population structure in ADMIXTURE, then (b) parses the output for summarization and graphical representation via CLUMPAK. Our benchmarks effectively demonstrate how efficient the pipeline is for processing large, non-model datasets generated via double digest restriction-site associated DNA sequencing (ddRAD). Outputs not only parallel those from STRUCTURE, but also visualize the variation among individual ADMIXTURE runs, so as to facilitate selection of the most appropriate K-value.

CONCLUSIONS: ADMIXPIPE successfully integrates ADMIXTURE analysis with popular variant call format (VCF) filtering software to yield file types readily analyzed by CLUMPAK. Large population genomic datasets derived from non-model organisms are efficiently analyzed via the parallel-processing capabilities of ADMIXTURE. ADMIXPIPE is distributed under the GNU Public License and freely available for Mac OSX and Linux platforms at: https://github.com/stevemussmann/admixturePipeline .}, } @article {pmid32725919, year = {2020}, author = {Pérez-Portela, R and Riesgo, A and Wangensteen, OS and Palacín, C and Turon, X}, title = {Enjoying the warming Mediterranean: Transcriptomic responses to temperature changes of a thermophilous keystone species in benthic communities.}, journal = {Molecular ecology}, volume = {29}, number = {17}, pages = {3299-3315}, doi = {10.1111/mec.15564}, pmid = {32725919}, issn = {1365-294X}, mesh = {Computational Biology ; *Gene Expression Profiling ; Gene Ontology ; Temperature ; *Transcriptome ; }, abstract = {Information about the genomic processes underlying responses to temperature changes is still limited in non-model marine invertebrates. In this sense, transcriptomic analyses can help to identify genes potentially related to thermal responses. We here investigated, via RNA-seq, whole-transcriptomic responses to increased and decreased temperatures in a thermophilous keystone sea urchin, Arbacia lixula, whose populations are increasing in the Mediterranean. This species is a key driver of benthic communities' structure due to its grazing activity. We found a strong response to experimentally induced cold temperature (7°C), with 1,181 differentially expressed transcripts relative to the control condition (13°C), compared to only 179 in the warm (22°C) treatment. A total of 84 (cold treatment) and three (warm treatment) gene ontology terms were linked to the differentially expressed transcripts. At 7°C the expression of genes encoding different heat shock proteins (HSPs) was upregulated, together with apoptotic suppressor genes (e.g., Bcl2), genes involved in the infection response and/or pathogen-recognition (e.g., echinoidin) and ATP-associated genes, while protein biosynthesis and DNA replication pathways were downregulated. At 22°C neither HSPs induction nor activation of the previously mentioned pathways were detected, with the exception of some apoptotic-related activities that were upregulated. Our results suggest a strong transcriptional response associated with low temperatures, and support the idea of low water temperature being a major limitation for A. lixula expansion across deep Mediterranean and northern Atlantic waters.}, } @article {pmid32725754, year = {2021}, author = {Mei, K and Huang, H and Xia, F and Hong, A and Chen, X and Zhang, C and Qiu, G and Chen, G and Wang, Z and Wang, C and Yang, B and Xiao, Q and Jia, P}, title = {State-of-the-art of measures of the obesogenic environment for children.}, journal = {Obesity reviews : an official journal of the International Association for the Study of Obesity}, volume = {22 Suppl 1}, number = {Suppl 1}, pages = {e13093}, pmid = {32725754}, issn = {1467-789X}, support = {SKLURE2018-2-5//State Key Laboratory of Urban and Regional Ecology of China/ ; }, mesh = {Child ; Cross-Sectional Studies ; Exercise ; Food ; Humans ; *Pediatric Obesity/epidemiology/etiology ; *Residence Characteristics ; }, abstract = {Various measures of the obesogenic environment have been proposed and used in childhood obesity research. The variety of measures poses methodological challenges to designing new research because methodological characteristics integral to developing the measures vary across studies. A systematic review has been conducted to examine the associations between different levels of obesogenic environmental measures (objective or perceived) and childhood obesity. The review includes all articles published in the Cochrane Library, PubMed, Web of Science and Scopus by 31 December 2018. A total of 339 associations in 101 studies have been identified from 18 countries, of which 78 are cross-sectional. Overall, null associations are predominant. Among studies with non-null associations, negative relationships between healthy food outlets in residential neighbourhoods and childhood obesity is found in seven studies; positive associations between unhealthy food outlets and childhood obesity are found in eight studies, whereas negative associations are found in three studies. Measures of recreational or physical activity facilities around the participants' home are also negatively correlated to childhood obesity in nine out of 15 studies. Results differ by the types of measurement, environmental indicators and geographic units used to characterize obesogenic environments in residential and school neighbourhoods. To improve the study quality and compare reported findings, a reporting standard for spatial epidemiological research should be adopted.}, } @article {pmid32724218, year = {2020}, author = {Muñoz, ÁG and Chourio, X and Rivière-Cinnamond, A and Diuk-Wasser, MA and Kache, PA and Mordecai, EA and Harrington, L and Thomson, MC}, title = {AeDES: a next-generation monitoring and forecasting system for environmental suitability of Aedes-borne disease transmission.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {12640}, pmid = {32724218}, issn = {2045-2322}, support = {001/WHO_/World Health Organization/International ; R35 GM133439/GM/NIGMS NIH HHS/United States ; U01 CK000509/CK/NCEZID CDC HHS/United States ; 1R35GM133439-01/NH/NIH HHS/United States ; }, mesh = {Aedes/*virology ; Animals ; Betacoronavirus/isolation & purification ; COVID-19 ; Climate ; Coronavirus Infections/pathology/transmission/virology ; Databases, Factual ; Decision Making ; *Epidemiological Monitoring/veterinary ; Humans ; Mosquito Vectors/*virology ; Pandemics ; Pneumonia, Viral/pathology/transmission/virology ; SARS-CoV-2 ; Vector Borne Diseases/epidemiology/*pathology/virology ; }, abstract = {Aedes-borne diseases, such as dengue and chikungunya, are responsible for more than 50 million infections worldwide every year, with an overall increase of 30-fold in the last 50 years, mainly due to city population growth, more frequent travels and ecological changes. In the United States of America, the vast majority of Aedes-borne infections are imported from endemic regions by travelers, who can become new sources of mosquito infection upon their return home if the exposed population is susceptible to the disease, and if suitable environmental conditions for the mosquitoes and the virus are present. Since the susceptibility of the human population can be determined via periodic monitoring campaigns, the environmental suitability for the presence of mosquitoes and viruses becomes one of the most important pieces of information for decision makers in the health sector. We present a next-generation monitoring and forecasting system for [Formula: see text]-borne diseases' environmental suitability (AeDES) of transmission in the conterminous United States and transboundary regions, using calibrated ento-epidemiological models, climate models and temperature observations. After analyzing the seasonal predictive skill of AeDES, we briefly consider the recent Zika epidemic, and the compound effects of the current Central American dengue outbreak happening during the SARS-CoV-2 pandemic, to illustrate how a combination of tailored deterministic and probabilistic forecasts can inform key prevention and control strategies .}, } @article {pmid32722260, year = {2020}, author = {Zhang, Y and Zheng, J}, title = {Bioinformatics of Metalloproteins and Metalloproteomes.}, journal = {Molecules (Basel, Switzerland)}, volume = {25}, number = {15}, pages = {}, pmid = {32722260}, issn = {1420-3049}, support = {31771407//National Natural Science Foundation of China/ ; 2019A1515011938//Guangdong Basic and Applied Basic Research Foundation/ ; JCYJ20180305124023495//Science and Technology Innovation Committee of Shenzhen Municipality/ ; 2019SHIBS0003//Shenzhen-Hong Kong Institute of Brain Science-Shenzhen Fundamental Research Institutions/ ; }, mesh = {Animals ; Binding Sites ; Computational Biology/*methods ; Eukaryota ; Genomics ; Humans ; Metalloproteins/chemistry/*genetics/*metabolism ; Prokaryotic Cells/metabolism ; Proteome/chemistry/genetics/metabolism ; Trace Elements/chemistry ; }, abstract = {Trace metals are inorganic elements that are required for all organisms in very low quantities. They serve as cofactors and activators of metalloproteins involved in a variety of key cellular processes. While substantial effort has been made in experimental characterization of metalloproteins and their functions, the application of bioinformatics in the research of metalloproteins and metalloproteomes is still limited. In the last few years, computational prediction and comparative genomics of metalloprotein genes have arisen, which provide significant insights into their distribution, function, and evolution in nature. This review aims to offer an overview of recent advances in bioinformatic analysis of metalloproteins, mainly focusing on metalloprotein prediction and the use of different metals across the tree of life. We describe current computational approaches for the identification of metalloprotein genes and metal-binding sites/patterns in proteins, and then introduce a set of related databases. Furthermore, we discuss the latest research progress in comparative genomics of several important metals in both prokaryotes and eukaryotes, which demonstrates divergent and dynamic evolutionary patterns of different metalloprotein families and metalloproteomes. Overall, bioinformatic studies of metalloproteins provide a foundation for systematic understanding of trace metal utilization in all three domains of life.}, } @article {pmid32716295, year = {2020}, author = {Abdill, RJ and Adamowicz, EM and Blekhman, R}, title = {International authorship and collaboration across bioRxiv preprints.}, journal = {eLife}, volume = {9}, number = {}, pages = {}, pmid = {32716295}, issn = {2050-084X}, support = {R35 GM128716/GM/NIGMS NIH HHS/United States ; R35-GM128716/NH/NIH HHS/United States ; }, mesh = {*Authorship ; Bibliometrics ; Biomedical Research/trends ; Datasets as Topic ; Internationality ; Online Systems/statistics & numerical data/trends ; *Preprints as Topic/trends ; *Research Personnel ; }, abstract = {Preprints are becoming well established in the life sciences, but relatively little is known about the demographics of the researchers who post preprints and those who do not, or about the collaborations between preprint authors. Here, based on an analysis of 67,885 preprints posted on bioRxiv, we find that some countries, notably the United States and the United Kingdom, are overrepresented on bioRxiv relative to their overall scientific output, while other countries (including China, Russia, and Turkey) show lower levels of bioRxiv adoption. We also describe a set of 'contributor countries' (including Uganda, Croatia and Thailand): researchers from these countries appear almost exclusively as non-senior authors on international collaborations. Lastly, we find multiple journals that publish a disproportionate number of preprints from some countries, a dynamic that almost always benefits manuscripts from the US.}, } @article {pmid32716281, year = {2020}, author = {Memon, A and Rogers, I and Fitzsimmons, SMDD and Carter, B and Strawbridge, R and Hidalgo-Mazzei, D and Young, AH}, title = {Association between naturally occurring lithium in drinking water and suicide rates: systematic review and meta-analysis of ecological studies.}, journal = {The British journal of psychiatry : the journal of mental science}, volume = {217}, number = {6}, pages = {667-678}, doi = {10.1192/bjp.2020.128}, pmid = {32716281}, issn = {1472-1465}, mesh = {*Drinking Water ; Female ; Humans ; Lithium/analysis ; Male ; Prevalence ; *Suicide ; Water Supply ; }, abstract = {BACKGROUND: The prevalence of mental health conditions and national suicide rates are increasing in many countries. Lithium is widely and effectively used in pharmacological doses for the treatment and prevention of manic/depressive episodes, stabilising mood and reducing the risk of suicide. Since the 1990s, several ecological studies have tested the hypothesis that trace doses of naturally occurring lithium in drinking water may have a protective effect against suicide in the general population.

AIMS: To synthesise the global evidence on the association between lithium levels in drinking water and suicide mortality rates.

METHOD: The MEDLINE, Embase, Web of Science and PsycINFO databases were searched to identify eligible ecological studies published between 1 January 1946 and 10 September 2018. Standardised regression coefficients for total (i.e. both genders combined), male and female suicide mortality rates were extracted and pooled using random-effects meta-analysis. The study was registered with PROSPERO (CRD42016041375).

RESULTS: The literature search identified 415 articles; of these, 15 ecological studies were included in the synthesis. The random-effects meta-analysis showed a consistent protective (or inverse) association between lithium levels/concentration in publicly available drinking water and total (pooled β = -0.27, 95% CI -0.47 to -0.08; P = 0.006, I2 = 83.3%), male (pooled β = -0.26, 95% CI -0.56 to 0.03; P = 0.08, I2 = 91.9%) and female (pooled β = -0.13, 95% CI -0.24 to -0.02; P = 0.03, I2 = 28.5%) suicide mortality rates. A similar protective association was observed in the six studies included in the narrative synthesis, and subgroup meta-analyses based on the higher/lower suicide mortality rates and lithium levels/concentration.

CONCLUSIONS: This synthesis of ecological studies, which are subject to the ecological fallacy/bias, supports the hypothesis that there is a protective (or inverse) association between lithium intakes from public drinking water and suicide mortality at the population level. Naturally occurring lithium in drinking water may have the potential to reduce the risk of suicide and may possibly help in mood stabilisation, particularly in populations with relatively high suicide rates and geographical areas with a greater range of lithium concentration in the drinking water. All the available evidence suggests that randomised community trials of lithium supplementation of the water supply might be a means of testing the hypothesis, particularly in communities (or settings) with demonstrated high prevalence of mental health conditions, violent criminal behaviour, chronic substance misuse and risk of suicide.}, } @article {pmid32712871, year = {2020}, author = {Duarte Neto, JMW and Wanderley, MCA and da Silva, TAF and Marques, DAV and da Silva, GR and Gurgel, JF and Oliveira, JP and Porto, ALF}, title = {Bacillus thuringiensis endotoxin production: a systematic review of the past 10 years.}, journal = {World journal of microbiology & biotechnology}, volume = {36}, number = {9}, pages = {128}, doi = {10.1007/s11274-020-02904-4}, pmid = {32712871}, issn = {1573-0972}, support = {152774/2018-1//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 305719/2016-5//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 426192/2018-4//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; BFP//Fundação de Amparo à Ciência e Tecnologia do Estado de Pernambuco/ ; IBPG-0475-5.05/17//Fundação de Amparo à Ciência e Tecnologia do Estado de Pernambuco/ ; SIN-0156-5.01/17//Fundação de Amparo à Ciência e Tecnologia do Estado de Pernambuco/ ; }, mesh = {Animals ; Bacillus thuringiensis/*metabolism ; Bacillus thuringiensis Toxins/analysis/*biosynthesis ; Biological Assay ; Biological Control Agents ; Databases, Factual ; Endotoxins/analysis/*biosynthesis ; Insecticides/pharmacology ; Larva/drug effects ; Pest Control, Biological ; }, abstract = {Bacillus thuringiensis (Bt) is one of the most promising biological control agents used commercially. Its products can contribute to reducing ecological and environmental problems associated with the use of chemical pesticides. Among the limiting factors of using Bt as bioinsecticide are the costs and ensuring its biological activity, which may vary according to the strain and culture conditions. This systematic review aimed to collect state-of-the-art information on the production of Bt endotoxins and to score the methodological feasibility of the data obtained, thus highlighting possible incoherencies. In order to consolidate recent findings and guide future studies, a total of 47 original articles from the last 10 years was analysed, with special attention being given to corroborating data, identifying inconsistencies and suggesting future adjustments so as to increase data reliability. With a maximum score of 8 points, three production parameters were classified on the following scale: preferable (score: 2), adequate (score: 1) and inadequate (score: 0), and another two parameter were classified as adequate (score: 1) or inadequate (score: 0). No article scored more than 6 out of the maximum of 8, thus reflecting the need for more detailed studies regarding Bt endotoxin production. The lack of standardization of methods and units of measurement also have made a comparison of results and an overall analysis difficult. Standards are suggested in the present study. The inclusion of bioassays and quantifying toxin via alkaline dilution are strongly recommended for studies of this nature, along with LC50 expressed in mg/L. Sixteen articles (34%) did not use either of these suggested methods, which indicates the need for further supporting studies. These findings reinforce the need for robust studies in this area, which could include the development of more affordable and effective bioinsecticides, thus increasing their competitiveness against insecticides derived from unsustainable sources.}, } @article {pmid32712867, year = {2020}, author = {Martin, EC and Leue, C and Delespaul, P and Peeters, F and Janssen, AML and Lousberg, R and Erdkamp, A and van de Weijer, S and Widdershoven, J and Blom, H and Bruintjes, T and Zwergal, A and Grill, E and Guinand, N and Perez-Fornos, A and van de Berg, MR and Stultiens, JJA and Kingma, H and van de Berg, R}, title = {Introducing the DizzyQuest: an app-based diary for vestibular disorders.}, journal = {Journal of neurology}, volume = {267}, number = {Suppl 1}, pages = {3-14}, pmid = {32712867}, issn = {1432-1459}, mesh = {Dizziness/diagnosis ; Humans ; *Mobile Applications ; Quality of Life ; Retrospective Studies ; Surveys and Questionnaires ; Vertigo ; *Vestibular Diseases/diagnosis ; }, abstract = {BACKGROUND: Most questionnaires currently used for assessing symptomatology of vestibular disorders are retrospective, inducing recall bias and lowering ecological validity. An app-based diary, administered multiple times in daily life, could increase the accuracy and ecological validity of symptom measurement. The objective of this study was to introduce a new experience sampling method (ESM) based vestibular diary app (DizzyQuest), evaluate response rates, and to provide examples of DizzyQuest outcome measures which can be used in future research.

METHODS: Sixty-three patients diagnosed with a vestibular disorder were included. The DizzyQuest consisted of four questionnaires. The morning- and evening-questionnaires were administered once each day, the within-day-questionnaire 10 times a day using a semi-random time schedule, and the attack questionnaire could be completed after the occurrence of a vertigo or dizziness attack. Data were collected for 4 weeks. Response rates and loss-to-follow-up were determined. Reported symptoms in the within-day-questionnaire were compared within and between patients and subgroups of patients with different vestibular disorders.

RESULTS: Fifty-one patients completed the study period. Average response rates were significantly higher than the desired response rate of > 50% (p < 0.001). The attack-questionnaire was used 159 times. A variety of neuro-otological symptoms and different disease profiles were demonstrated between patients and subgroups of patients with different vestibular disorders.

CONCLUSION: The DizzyQuest is able to capture vestibular symptoms within their psychosocial context in daily life, with little recall bias and high ecological validity. The DizzyQuest reached the desired response rates and showed different disease profiles between subgroups of patients with different vestibular disorders. This is the first time ESM was used to assess daily symptoms and quality of life in vestibular disorders, showing that it might be a useful tool in this population.}, } @article {pmid32707761, year = {2020}, author = {Ye, S and Lu, S and Bai, X and Gu, J}, title = {ResNet-Locust-BN Network-Based Automatic Identification of East Asian Migratory Locust Species and Instars from RGB Images.}, journal = {Insects}, volume = {11}, number = {8}, pages = {}, pmid = {32707761}, issn = {2075-4450}, abstract = {Locusts are agricultural pests found in many parts of the world. Developing efficient and accurate locust information acquisition techniques helps in understanding the relation between locust distribution density and structural changes in locust communities. It also helps in understanding the hydrothermal and vegetation growth conditions that affect locusts in their habitats in various parts of the world as well as in providing rapid and accurate warnings on locust plague outbreak. This study is a preliminary attempt to explore whether the batch normalization-based convolutional neural network (CNN) model can be applied used to perform automatic classification of East Asian migratory locust (AM locust), Oxya chinensis (rice locusts), and cotton locusts. In this paper, we present a way of applying the CNN technique to identify species and instars of locusts using the proposed ResNet-Locust-BN model. This model is based on the ResNet architecture and involves introduction of a BatchNorm function before each convolution layer to improve the network's stability, convergence speed, and classification accuracy. Subsequently, locust image data collected in the field were used as input to train the model. By performing comparison experiments of the activation function, initial learning rate, and batch size, we selected ReLU as the preferred activation function. The initial learning rate and batch size were set to 0.1 and 32, respectively. Experiments performed to evaluate the accuracy of the proposed ResNet-Locust-BN model show that the model can effectively distinguish AM locust from rice locusts (93.60% accuracy) and cotton locusts (97.80% accuracy). The model also performed well in identifying the growth status information of AM locusts (third-instar (77.20% accuracy), fifth-instar (88.40% accuracy), and adult (93.80% accuracy)) with an overall accuracy of 90.16%. This is higher than the accuracy scores obtained by using other typical models: AlexNet (73.68%), GoogLeNet (69.12%), ResNet 18 (67.60%), ResNet 50 (80.84%), and VggNet (81.70%). Further, the model has good robustness and fast convergence rate.}, } @article {pmid32706728, year = {2020}, author = {Elliston, KG and Schüz, B and Albion, T and Ferguson, SG}, title = {Comparison of Geographic Information System and Subjective Assessments of Momentary Food Environments as Predictors of Food Intake: An Ecological Momentary Assessment Study.}, journal = {JMIR mHealth and uHealth}, volume = {8}, number = {7}, pages = {e15948}, pmid = {32706728}, issn = {2291-5222}, mesh = {Adult ; *Eating ; *Ecological Momentary Assessment ; Female ; *Food Supply/statistics & numerical data ; *Geographic Information Systems ; Humans ; Male ; }, abstract = {BACKGROUND: It has been observed that eating is influenced by the presence and availability of food. Being aware of the presence of food in the environment may enable mobile health (mHealth) apps to use geofencing techniques to determine the most appropriate time to proactively deliver interventions. To date, however, studies on eating typically rely on self-reports of environmental contexts, which may not be accurate or feasible for issuing mHealth interventions.

OBJECTIVE: This study aimed to compare the subjective and geographic information system (GIS) assessments of the momentary food environment to explore the feasibility of using GIS data to predict eating behavior and inform geofenced interventions.

METHODS: In total, 72 participants recorded their food intake in real-time for 14 days using an ecological momentary assessment approach. Participants logged their food intake and responded to approximately 5 randomly timed assessments each day. During each assessment, the participants reported the number and type of food outlets nearby. Their electronic diaries simultaneously recorded their GPS coordinates. The GPS data were later overlaid with a GIS map of food outlets to produce an objective count of the number of food outlets within 50 m of the participant.

RESULTS: Correlations between self-reported and GIS counts of food outlets within 50 m were only of a small size (r=0.17; P<.001). Logistic regression analyses revealed that the GIS count significantly predicted eating similar to the self-reported counts (area under the curve for the receiver operating characteristic curve [AUC-ROC] self-report=0.53, SE 0.00 versus AUC-ROC 50 m GIS=0.53, SE 0.00; P=.41). However, there was a significant difference between the GIS-derived and self-reported counts of food outlets and the self-reported type of food outlets (AUC-ROC self-reported outlet type=0.56, SE 0.01; P<.001).

CONCLUSIONS: The subjective food environment appears to predict eating better than objectively measured food environments via GIS. mHealth apps may need to consider the type of food outlets rather than the raw number of outlets in an individual's environment.}, } @article {pmid32706331, year = {2020}, author = {Pérez-Cobas, AE and Gomez-Valero, L and Buchrieser, C}, title = {Metagenomic approaches in microbial ecology: an update on whole-genome and marker gene sequencing analyses.}, journal = {Microbial genomics}, volume = {6}, number = {8}, pages = {}, pmid = {32706331}, issn = {2057-5858}, mesh = {Computational Biology/methods ; Genetic Markers/*genetics ; High-Throughput Nucleotide Sequencing/*methods ; Metagenome ; Metagenomics/*methods ; Microbiota/*genetics ; Software ; Whole Genome Sequencing/*methods ; }, abstract = {Metagenomics and marker gene approaches, coupled with high-throughput sequencing technologies, have revolutionized the field of microbial ecology. Metagenomics is a culture-independent method that allows the identification and characterization of organisms from all kinds of samples. Whole-genome shotgun sequencing analyses the total DNA of a chosen sample to determine the presence of micro-organisms from all domains of life and their genomic content. Importantly, the whole-genome shotgun sequencing approach reveals the genomic diversity present, but can also give insights into the functional potential of the micro-organisms identified. The marker gene approach is based on the sequencing of a specific gene region. It allows one to describe the microbial composition based on the taxonomic groups present in the sample. It is frequently used to analyse the biodiversity of microbial ecosystems. Despite its importance, the analysis of metagenomic sequencing and marker gene data is quite a challenge. Here we review the primary workflows and software used for both approaches and discuss the current challenges in the field.}, } @article {pmid32699823, year = {2020}, author = {Nardoto, GB and Sena-Souza, JP and Kisaka, TB and Costa, FJV and Duarte-Neto, PJ and Ehleringer, J and Martinelli, LA}, title = {Increased in carbon isotope ratios of Brazilian fingernails are correlated with increased in socioeconomic status.}, journal = {NPJ science of food}, volume = {4}, number = {}, pages = {9}, pmid = {32699823}, issn = {2396-8370}, abstract = {High δ [13]C in human tissues in Brazil indicate high consumption of C4-based sources due to the consumption of highly processed food and animal protein. The significant positive correlation between the human developed index (HDI) developed by the United Nations Development Program, and fingernail δ [13]C at the county level proved to be useful as a new proxy in tracking human nutrition. Regions with higher HDI are those with higher consumption of highly processed food.}, } @article {pmid32690705, year = {2020}, author = {Okhovat, M and Nevonen, KA and Davis, BA and Michener, P and Ward, S and Milhaven, M and Harshman, L and Sohota, A and Fernandes, JD and Salama, SR and O'Neill, RJ and Ahituv, N and Veeramah, KR and Carbone, L}, title = {Co-option of the lineage-specific LAVA retrotransposon in the gibbon genome.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {117}, number = {32}, pages = {19328-19338}, pmid = {32690705}, issn = {1091-6490}, support = {F32 GM125388/GM/NIGMS NIH HHS/United States ; P51 OD011092/OD/NIH HHS/United States ; R01 HG010329/HG/NHGRI NIH HHS/United States ; R01 HG010333/HG/NHGRI NIH HHS/United States ; }, mesh = {Animals ; Chromatin/genetics ; Evolution, Molecular ; Gene Expression Regulation ; *Genome ; Hylobates/classification/*genetics ; Mutagenesis, Insertional ; Regulatory Sequences, Nucleic Acid ; *Retroelements ; Species Specificity ; }, abstract = {Co-option of transposable elements (TEs) to become part of existing or new enhancers is an important mechanism for evolution of gene regulation. However, contributions of lineage-specific TE insertions to recent regulatory adaptations remain poorly understood. Gibbons present a suitable model to study these contributions as they have evolved a lineage-specific TE called LAVA (LINE-AluSz-VNTR-AluLIKE), which is still active in the gibbon genome. The LAVA retrotransposon is thought to have played a role in the emergence of the highly rearranged structure of the gibbon genome by disrupting transcription of cell cycle genes. In this study, we investigated whether LAVA may have also contributed to the evolution of gene regulation by adopting enhancer function. We characterized fixed and polymorphic LAVA insertions across multiple gibbons and found 96 LAVA elements overlapping enhancer chromatin states. Moreover, LAVA was enriched in multiple transcription factor binding motifs, was bound by an important transcription factor (PU.1), and was associated with higher levels of gene expression in cis We found gibbon-specific signatures of purifying/positive selection at 27 LAVA insertions. Two of these insertions were fixed in the gibbon lineage and overlapped with enhancer chromatin states, representing putative co-opted LAVA enhancers. These putative enhancers were located within genes encoding SETD2 and RAD9A, two proteins that facilitate accurate repair of DNA double-strand breaks and prevent chromosomal rearrangement mutations. Co-option of LAVA in these genes may have influenced regulation of processes that preserve genome integrity. Our findings highlight the importance of considering lineage-specific TEs in studying evolution of gene regulatory elements.}, } @article {pmid32687148, year = {2020}, author = {Rosa, BA and Choi, YJ and McNulty, SN and Jung, H and Martin, J and Agatsuma, T and Sugiyama, H and Le, TH and Doanh, PN and Maleewong, W and Blair, D and Brindley, PJ and Fischer, PU and Mitreva, M}, title = {Comparative genomics and transcriptomics of 4 Paragonimus species provide insights into lung fluke parasitism and pathogenesis.}, journal = {GigaScience}, volume = {9}, number = {7}, pages = {}, pmid = {32687148}, issn = {2047-217X}, support = {U54 HG003079/HG/NHGRI NIH HHS/United States ; }, mesh = {Animals ; *Computational Biology/methods ; Disease Susceptibility ; *Gene Expression Profiling/methods ; Gene Ontology ; *Genomics/methods ; Host-Parasite Interactions ; Humans ; Molecular Sequence Annotation ; Multigene Family ; Paragonimiasis/*parasitology ; Paragonimus/classification/*genetics ; Phylogeny ; *Transcriptome ; }, abstract = {BACKGROUND: Paragonimus spp. (lung flukes) are among the most injurious foodborne helminths, infecting ∼23 million people and subjecting ∼292 million to infection risk. Paragonimiasis is acquired from infected undercooked crustaceans and primarily affects the lungs but often causes lesions elsewhere including the brain. The disease is easily mistaken for tuberculosis owing to similar pulmonary symptoms, and accordingly, diagnostics are in demand.

RESULTS: We assembled, annotated, and compared draft genomes of 4 prevalent and distinct Paragonimus species: Paragonimus miyazakii, Paragonimus westermani, Paragonimus kellicotti, and Paragonimus heterotremus. Genomes ranged from 697 to 923 Mb, included 12,072-12,853 genes, and were 71.6-90.1% complete according to BUSCO. Orthologous group analysis spanning 21 species (lung, liver, and blood flukes, additional platyhelminths, and hosts) provided insights into lung fluke biology. We identified 256 lung fluke-specific and conserved orthologous groups with consistent transcriptional adult-stage Paragonimus expression profiles and enriched for iron acquisition, immune modulation, and other parasite functions. Previously identified Paragonimus diagnostic antigens were matched to genes, providing an opportunity to optimize and ensure pan-Paragonimus reactivity for diagnostic assays.

CONCLUSIONS: This report provides advances in molecular understanding of Paragonimus and underpins future studies into the biology, evolution, and pathogenesis of Paragonimus and related foodborne flukes. We anticipate that these novel genomic and transcriptomic resources will be invaluable for future lung fluke research.}, } @article {pmid32686007, year = {2020}, author = {Zhu, B and Li, C and Wang, J and Li, J and Li, X}, title = {Elevation rather than season determines the assembly and co-occurrence patterns of soil bacterial communities in forest ecosystems of Mount Gongga.}, journal = {Applied microbiology and biotechnology}, volume = {104}, number = {17}, pages = {7589-7602}, doi = {10.1007/s00253-020-10783-w}, pmid = {32686007}, issn = {1432-0614}, support = {31870473//National Natural Science Foundation of China/ ; 41630751//National Natural Science Foundation of China/ ; XXH13503-03-106//the 13th Five-year Informatization Plan of Chinese Academy of Sciences/ ; Sino BON//China Biodiversity Observation Networks/ ; }, mesh = {China ; *Ecosystem ; Forests ; RNA, Ribosomal, 16S/genetics ; Seasons ; *Soil ; Soil Microbiology ; }, abstract = {Seasonal dynamics of soil microbial communities may influence ecosystem functions and services. However, few observations have been conducted on the dynamics of a bacterial community assembly across seasons in different elevations in mountain forest ecosystems. In this study, the diversity, compositions, community assembly processes, and co-occurrence interactions of soil bacterial communities were investigated using Illumina sequencing of 16S rRNA genes across different seasons during two consecutive years (2016 and 2017) at two elevational sites in Mount Gongga, China. These two sites included an evergreen broad-leaved forest (EBF, 2100 m a.s.l.) and a dark coniferous forest (DCF, 3000 m a.s.l.). The results showed that bacterial diversity and structure varied considerably between the two elevational sites with only limited seasonal variations. Interannuality had a significant effect on the diversity and structure of soil bacterial communities. The bacterial alpha diversity was significantly higher at site EBF(e.g., OTUs richness, 2207 ± 276) than at site DCF(e.g., OTUs richness, 1826 ± 315). Soil pH, temperature, elevation, and water content were identified as important factors shaping soil bacterial communities in the mountain forests. Bacterial community assembly was primarily governed by deterministic processes regardless of elevation and season. Deterministic processes were stronger at site DCF than at EBF. The soil bacterial community at site EBF harbored a more complex and connected network with less resistance to environmental changes. Overall, this study showed that seasonal dynamics of bacterial communities were much weaker than those along elevations, implying that a single-season survey on a bacterial community along an elevational gradient can represent overall changes in the bacterial community. KEY POINTS: • Seasonal dynamics of soil bacterial communities were studied in Mount Gongga. • The bacterial community was mainly affected by elevation rather than season. • Deterministic processes dominated bacterial community assembly. • The bacterial network was more complex but less stable at EBF than at DCF.}, } @article {pmid32681003, year = {2020}, author = {Li, S and Crawford, FW and Gerstein, MB}, title = {Using sigLASSO to optimize cancer mutation signatures jointly with sampling likelihood.}, journal = {Nature communications}, volume = {11}, number = {1}, pages = {3575}, pmid = {32681003}, issn = {2041-1723}, support = {DP2 HD091799/HD/NICHD NIH HHS/United States ; R01 HG008126/HG/NHGRI NIH HHS/United States ; }, mesh = {Computational Biology/*methods ; Genome, Human ; Humans ; *Mutation ; Neoplasms/*genetics ; Probability ; Software ; }, abstract = {Multiple mutational processes drive carcinogenesis, leaving characteristic signatures in tumor genomes. Determining the active signatures from a full repertoire of potential ones helps elucidate mechanisms of cancer development. This involves optimally decomposing the counts of cancer mutations, tabulated according to their trinucleotide context, into a linear combination of known signatures. Here, we develop sigLASSO (a software tool at github.com/gersteinlab/siglasso) to carry out this optimization efficiently. sigLASSO has four key aspects: (1) It jointly optimizes the likelihood of sampling and signature fitting, by explicitly factoring multinomial sampling into the objective function. This is particularly important when mutation counts are low and sampling variance is high (e.g., in exome sequencing). (2) sigLASSO uses L1 regularization to parsimoniously assign signatures, leading to sparse and interpretable solutions. (3) It fine-tunes model complexity, informed by data scale and biological priors. (4) Consequently, sigLASSO can assess model uncertainty and abstain from making assignments in low-confidence contexts.}, } @article {pmid32678108, year = {2020}, author = {Kaufman, D and McKay, N and Routson, C and Erb, M and Davis, B and Heiri, O and Jaccard, S and Tierney, J and Dätwyler, C and Axford, Y and Brussel, T and Cartapanis, O and Chase, B and Dawson, A and de Vernal, A and Engels, S and Jonkers, L and Marsicek, J and Moffa-Sánchez, P and Morrill, C and Orsi, A and Rehfeld, K and Saunders, K and Sommer, PS and Thomas, E and Tonello, M and Tóth, M and Vachula, R and Andreev, A and Bertrand, S and Biskaborn, B and Bringué, M and Brooks, S and Caniupán, M and Chevalier, M and Cwynar, L and Emile-Geay, J and Fegyveresi, J and Feurdean, A and Finsinger, W and Fortin, MC and Foster, L and Fox, M and Gajewski, K and Grosjean, M and Hausmann, S and Heinrichs, M and Holmes, N and Ilyashuk, B and Ilyashuk, E and Juggins, S and Khider, D and Koinig, K and Langdon, P and Larocque-Tobler, I and Li, J and Lotter, A and Luoto, T and Mackay, A and Magyari, E and Malevich, S and Mark, B and Massaferro, J and Montade, V and Nazarova, L and Novenko, E and Pařil, P and Pearson, E and Peros, M and Pienitz, R and Płóciennik, M and Porinchu, D and Potito, A and Rees, A and Reinemann, S and Roberts, S and Rolland, N and Salonen, S and Self, A and Seppä, H and Shala, S and St-Jacques, JM and Stenni, B and Syrykh, L and Tarrats, P and Taylor, K and van den Bos, V and Velle, G and Wahl, E and Walker, I and Wilmshurst, J and Zhang, E and Zhilich, S}, title = {Author Correction: A global database of Holocene paleotemperature records.}, journal = {Scientific data}, volume = {7}, number = {1}, pages = {246}, doi = {10.1038/s41597-020-00584-1}, pmid = {32678108}, issn = {2052-4463}, abstract = {An amendment to this paper has been published and can be accessed via a link at the top of the paper.}, } @article {pmid32677880, year = {2020}, author = {Zhang, Q and Xu, J and Warren, A and Yang, R and Shen, Z and Yi, Z}, title = {Assessing the utility of Hsp90 gene for inferring evolutionary relationships within the ciliate subclass Hypotricha (Protista, Ciliophora).}, journal = {BMC evolutionary biology}, volume = {20}, number = {1}, pages = {86}, pmid = {32677880}, issn = {1471-2148}, support = {31772440//National Natural Science Foundation of China/International ; 31970486//National Natural Science Foundation of China/International ; 31672279//National Natural Science Foundation of China/International ; 2018SDKJ0406-1//Marine S&T Fund of Shandong Province for Pilot National Laboratory for Marine Science and Technology (Qingdao)/International ; GDOE(2019)A23//Guangdong MEPP Fund/International ; }, mesh = {Amino Acid Sequence ; Base Sequence ; Ciliophora/classification/*genetics ; DNA, Ribosomal/genetics ; Databases, Genetic ; Databases, Protein ; *Evolution, Molecular ; HSP90 Heat-Shock Proteins/chemistry/*genetics ; Phylogeny ; }, abstract = {BACKGROUND: Although phylogenomic analyses are increasingly used to reveal evolutionary relationships among ciliates, relatively few nuclear protein-coding gene markers have been tested for their suitability as candidates for inferring phylogenies within this group. In this study, we investigate the utility of the heat-shock protein 90 gene (Hsp90) as a marker for inferring phylogenetic relationships among hypotrich ciliates.

RESULTS: A total of 87 novel Hsp90 gene sequences of 10 hypotrich species were generated. Of these, 85 were distinct sequences. Phylogenetic analyses based on these data showed that: (1) the Hsp90 gene amino acid trees are comparable to the small subunit rDNA tree for recovering phylogenetic relationships at the rank of class, but lack sufficient phylogenetic signal for inferring evolutionary relationships at the genus level; (2) Hsp90 gene paralogs are recent and therefore unlikely to pose a significant problem for recovering hypotrich clades; (3) definitions of some hypotrich orders and families need to be revised as their monophylies are not supported by various gene markers; (4) The order Sporadotrichida is paraphyletic, but the monophyly of the "core" Urostylida is supported; (5) both the subfamily Oxytrichinae and the genus Urosoma seem to be non-monophyletic, but monophyly of Urosoma is not rejected by AU tests.

CONCLUSIONS: Our results for the first time demonstrate that the Hsp90 gene is comparable to SSU rDNA for recovering phylogenetic relationships at the rank of class, and its paralogs are unlikely to pose a significant problem for recovering hypotrich clades. This study shows the value of careful gene marker selection for phylogenomic analyses of ciliates.}, } @article {pmid32677034, year = {2020}, author = {Wang, K and Tomura, R and Chen, W and Kiyooka, M and Ishizaki, H and Aizu, T and Minakuchi, Y and Seki, M and Suzuki, Y and Omotezako, T and Suyama, R and Masunaga, A and Plessy, C and Luscombe, NM and Dantec, C and Lemaire, P and Itoh, T and Toyoda, A and Nishida, H and Onuma, TA}, title = {A genome database for a Japanese population of the larvacean Oikopleura dioica.}, journal = {Development, growth & differentiation}, volume = {62}, number = {6}, pages = {450-461}, doi = {10.1111/dgd.12689}, pmid = {32677034}, issn = {1440-169X}, support = {16H06279//JSPS KAKENHI/ ; 221S0002//MEXT KAKENHI/ ; 24870019//Grants-in-Aid for Scientific Research from the JSPS/ ; 26840079//Grants-in-Aid for Scientific Research from the JSPS/ ; 18K06256//Grants-in-Aid for Scientific Research from the JSPS/ ; 26650079//Grants-in-Aid for Scientific Research from the JSPS/ ; 15H04377//Grants-in-Aid for Scientific Research from the JSPS/ ; 16K14735//Grants-in-Aid for Scientific Research from the JSPS/ ; 17KT0023//Grants-in-Aid for Scientific Research from the JSPS/ ; 19H03234//Grants-in-Aid for Scientific Research from the JSPS/ ; //Inamori Foundation (2015)/ ; //Kato Memorial Research Foundation (2015-2016)/ ; //Sumitomo Foundation (2016-2017)/ ; //Japan Foundation for Applied Enzymology (2017, 2019)/ ; }, mesh = {Animals ; *Databases, Genetic ; Japan ; *Models, Genetic ; Transcriptome ; Urochordata/*genetics ; }, abstract = {The larvacean Oikopleura dioica is a planktonic chordate and is a tunicate that belongs to the closest relatives to vertebrates. Its simple and transparent body, invariant embryonic cell lineages, and short life cycle of 5 days make it a promising model organism for the study of developmental biology. The genome browser OikoBase was established in 2013 using Norwegian O. dioica. However, genome information for other populations is not available, even though many researchers have studied local populations. In the present study, we sequenced using Illumina and PacBio RSII technologies the genome of O. dioica from a southwestern Japanese population that was cultured in our laboratory for 3 years. The genome of Japanese O. dioica was assembled into 576 scaffold sequences with a total length and N50 length of 56.6 and 1.5 Mb, respectively. A total of 18,743 gene models (transcript models) were predicted in the genome assembly, named OSKA2016. In addition, 19,277 non-redundant transcripts were assembled using RNA-seq data. The OSKA2016 has global sequence similarity of only 86.5% when compared with the OikoBase, highlighting the sequence difference between the two far distant O. dioica populations on the globe. The genome assembly, transcript assembly, and transcript models were incorporated into ANISEED (https://www.aniseed.cnrs.fr/) for genome browsing and BLAST searches. Mapping of reads obtained from male- or female-specific genome libraries yielded male-specific scaffolds in the OSKA2016 and revealed that over 2.6 Mb of sequence were included in the male-specific Y-region. The genome and transcriptome resources from two distinct populations will be useful datasets for developmental biology, evolutionary biology, and molecular ecology using this model organism.}, } @article {pmid32671561, year = {2020}, author = {Nautiyal, S and Goswami, M and Nidamanuri, RR and Hoffmann, EM and Buerkert, A}, title = {Structure and composition of field margin vegetation in the rural-urban interface of Bengaluru, India: a case study on an unexplored dimension of agroecosystems.}, journal = {Environmental monitoring and assessment}, volume = {192}, number = {8}, pages = {520}, doi = {10.1007/s10661-020-08428-6}, pmid = {32671561}, issn = {1573-2959}, support = {BT/IN/GERMAN/DFG/14/BVCR/2016//Department of Biotechnology, Ministry of Science and Technology/ ; }, mesh = {Agriculture ; Biodiversity ; *Conservation of Natural Resources ; Ecosystem ; *Environmental Monitoring ; Europe ; Humans ; India ; }, abstract = {Field margin vegetation (FMV) refers to the plant community in the interface between agriculture and natural environments. Substantial work has been carried out on the management of field margins in European countries with the aim of conserving field-level biodiversity and enhancing agronomic benefits. India, instead, is lagging behind in the assessment of FMV and formulating subsequent management strategies for biodiversity conservation at the field boundaries. This study is a first step to better understand the structural and functional dimensions of field margin vegetation along an agricultural transformation gradient near the megacity of Bengaluru, India. Empirical field studies along with the detection of vegetation change using remote sensing and geo-informatics technique were used to record information on field margin vegetation. The phytosociological study, revealed a total of 81 species, comprising 29 species of trees, 21 shrubs and 31 herbs at the field margins of six selected villages of northern Bengaluru. Randomly selected 355 field boundaries were delineated from high-resolution Worldview 3 images for the year 2018 and from Google Earth images for the year 2004-2005. The FMV area was around to 85.40 ha in 2004-2005 but declined to 76.69 ha in 2017-2018. The survey also indicated that local farmers have in-depth ecological knowledge on the importance of FMV in ensuring a sustainable flow of resources within the agricultural landscape. The results demonstrate that rural and transition zones of the study area have higher dominance of planted tree species on the margins, whereas urban zone exhibits comparatively uniform dominance for all species. Our study also highlights the need for conservation of FMV to ensure agroecosystem health as a prerequisite for sustainable socioecological development.}, } @article {pmid32671460, year = {2020}, author = {Villalona, E and Ezray, BD and Laveaga, E and Agrawal, AA and Ali, JG and Hines, HM}, title = {The role of toxic nectar secondary compounds in driving differential bumble bee preferences for milkweed flowers.}, journal = {Oecologia}, volume = {193}, number = {3}, pages = {619-630}, doi = {10.1007/s00442-020-04701-0}, pmid = {32671460}, issn = {1432-1939}, mesh = {Animals ; *Asclepias ; Bees ; Flowers ; *Plant Nectar ; Pollination ; }, abstract = {While morphological differences such as tongue length are often featured as drivers of pollinator floral preferences, differences in chemical detection and tolerance to secondary compounds may also play a role. We sought to better understand the role of secondary compounds in floral preference by examining visitation of milkweed flowers, which can contain toxic cardenolides in their nectar, by bumble bees (Bombus spp.), some of their most abundant and important pollinators. We examine bumble bee species visitation of common milkweed (Asclepias syriaca) compared to other flowers in the field and test whether observed preferences may be influenced by avoidance and tolerance of cardenolides, as measured by the cardenolide ouabain, in the lab. We reveal that common milkweed is visited predominantly by one bumble bee species, Bombus griseocollis, in a ratio much higher than the abundance of this species in the community. We confirmed the presence and toxicity of cardenolides in A. syriaca nectar. Lab experiments revealed that B. griseocollis, compared to the common bumble bees B. impatiens and B. bimaculatus, exhibit greater avoidance of cardenolides, but only at levels that start to induce illness, whereas the other species exhibit either no or reduced avoidance of cardenolides, resulting in illness and mortality in these bees. Toxicity experiments reveal that B. griseocollis also has a substantially higher tolerance for cardenolides than B. impatiens. Together, these results support a potential evolutionary association between B. griseocollis and milkweed that may involve increased ability to both detect and tolerate milkweed cardenolides.}, } @article {pmid32668814, year = {2020}, author = {Matos, A and Domínguez-Pérez, D and Almeida, D and Agüero-Chapin, G and Campos, A and Osório, H and Vasconcelos, V and Antunes, A}, title = {Shotgun Proteomics of Ascidians Tunic Gives New Insights on Host-Microbe Interactions by Revealing Diverse Antimicrobial Peptides.}, journal = {Marine drugs}, volume = {18}, number = {7}, pages = {}, pmid = {32668814}, issn = {1660-3397}, mesh = {Animals ; Chromatography, Liquid ; Databases, Protein ; High-Throughput Screening Assays ; Host-Pathogen Interactions ; Microbiota ; Pore Forming Cytotoxic Proteins/*metabolism ; *Proteome ; *Proteomics ; Spectrometry, Mass, Electrospray Ionization ; Tandem Mass Spectrometry ; Urochordata/*metabolism/microbiology ; }, abstract = {Ascidians are marine invertebrates associated with diverse microbial communities, embedded in their tunic, conferring special ecological and biotechnological relevance to these model organisms used in evolutionary and developmental studies. Next-generation sequencing tools have increased the knowledge of ascidians' associated organisms and their products, but proteomic studies are still scarce. Hence, we explored the tunic of three ascidian species using a shotgun proteomics approach. Proteins extracted from the tunic of Ciona sp., Molgula sp., and Microcosmus sp. were processed using a nano LC-MS/MS system (Ultimate 3000 liquid chromatography system coupled to a Q-Exactive Hybrid Quadrupole-Orbitrap mass spectrometer). Raw data was searched against UniProtKB - the Universal Protein Resource Knowledgebase (Bacteria and Metazoa section) using Proteome Discoverer software. The resulting proteins were merged with a non-redundant Antimicrobial Peptides (AMPs) database and analysed with MaxQuant freeware. Overall, 337 metazoan and 106 bacterial proteins were identified being mainly involved in basal metabolism, cytoskeletal and catalytic functions. 37 AMPs were identified, most of them attributed to eukaryotic origin apart from bacteriocins. These results and the presence of "Biosynthesis of antibiotics" as one of the most highlighted pathways revealed the tunic as a very active tissue in terms of bioactive compounds production, giving insights on the interactions between host and associated organisms. Although the present work constitutes an exploratory study, the approach employed revealed high potential for high-throughput characterization and biodiscovery of the ascidians' tunic and its microbiome.}, } @article {pmid32667066, year = {2020}, author = {Caputo, A and Tomai, M}, title = {A systematic review of psychodynamic theories in community psychology: Discovering the unconscious in community work.}, journal = {Journal of community psychology}, volume = {48}, number = {6}, pages = {2069-2085}, doi = {10.1002/jcop.22407}, pmid = {32667066}, issn = {1520-6629}, mesh = {Concept Formation/physiology ; Countertransference ; Data Management ; Ecosystem ; Emotions/physiology ; Empowerment ; Humans ; Interpersonal Psychotherapy/methods/trends ; Peer Review/*methods ; Projective Techniques/*statistics & numerical data ; Psychoanalysis/*statistics & numerical data/trends ; Psychoanalytic Theory ; Psychology, Social ; Publications/trends ; Residence Characteristics/*statistics & numerical data ; Transference, Psychology ; }, abstract = {The aim of this systematic review is to provide a narrative synthesis of the peer-reviewed literature regarding the role of psychodynamics in community psychology. The authors screened 301 records on the topic, found in major citation databases (Scopus and Web of Science) without time or language restrictions. Ten articles addressing the review question were identified, showing the contributions of interpersonal psychoanalysis, Adlerian psychology, the Tavistock psychodynamic model, and Lacanian psychoanalysis. Several points of synergy between community psychology and psychodynamics were outlined mainly concerning empowerment theory, preventative and ecological perspective, power, and social order. Besides, the view on the community life, the role of emotion, and the conceptualization of the unconscious domain are discussed. Implications for community interventions are highlighted, regarding clients' demands, the role of community practitioners, and the use of transference/countertransference in consultative work. Limitations and future directions are also considered.}, } @article {pmid32666688, year = {2021}, author = {Jia, P and Cao, X and Yang, H and Dai, S and He, P and Huang, G and Wu, T and Wang, Y}, title = {Green space access in the neighbourhood and childhood obesity.}, journal = {Obesity reviews : an official journal of the International Association for the Study of Obesity}, volume = {22 Suppl 1}, number = {Suppl 1}, pages = {e13100}, pmid = {32666688}, issn = {1467-789X}, mesh = {Body Mass Index ; Child ; Cross-Sectional Studies ; Humans ; *Parks, Recreational ; *Pediatric Obesity/epidemiology/prevention & control ; Residence Characteristics ; }, abstract = {Access to green space may influence individual physical activity (PA) and subsequently weight status, as increased exposure to green space could improve health by increasing opportunities and the actual levels of PA. However, whether such associations hold empirically remains inconclusive. This study reviewed articles that analysed the association between access to green space and weight-related behaviours/outcomes among children, published before 1 January 2019. The sample sizes ranged from 108 to 44 278. Four cohorts and 17 cross-sectional studies conducted in nine countries were identified. Overall, evidence showed a positive association between access to green space and PA and a negative association between access to green space and television-watching time, body mass index (BMI) and weight status among children. Distance to the nearest green space, measured by geographic information system (GIS) in 10 studies, was often used to represent access to the nearest green space. It still remains difficult to draw a clear conclusion on the association between access to green space and BMI. Longitudinal studies can directly estimate the strength of the association between exposure and disease, which is needed to determine the causal association between access to green space and weight status.}, } @article {pmid32665548, year = {2020}, author = {Lin, H and Peddada, SD}, title = {Analysis of compositions of microbiomes with bias correction.}, journal = {Nature communications}, volume = {11}, number = {1}, pages = {3514}, pmid = {32665548}, issn = {2041-1723}, mesh = {Computational Biology/*methods ; Ecology ; Humans ; Microbiology ; Microbiota/*genetics ; }, abstract = {Differential abundance (DA) analysis of microbiome data continues to be a challenging problem due to the complexity of the data. In this article we define the notion of "sampling fraction" and demonstrate a major hurdle in performing DA analysis of microbiome data is the bias introduced by differences in the sampling fractions across samples. We introduce a methodology called Analysis of Compositions of Microbiomes with Bias Correction (ANCOM-BC), which estimates the unknown sampling fractions and corrects the bias induced by their differences among samples. The absolute abundance data are modeled using a linear regression framework. This formulation makes a fundamental advancement in the field because, unlike the existing methods, it (a) provides statistically valid test with appropriate p-values, (b) provides confidence intervals for differential abundance of each taxon, (c) controls the False Discovery Rate (FDR), (d) maintains adequate power, and (e) is computationally simple to implement.}, } @article {pmid32663906, year = {2020}, author = {Essl, F and Lenzner, B and Bacher, S and Bailey, S and Capinha, C and Daehler, C and Dullinger, S and Genovesi, P and Hui, C and Hulme, PE and Jeschke, JM and Katsanevakis, S and Kühn, I and Leung, B and Liebhold, A and Liu, C and MacIsaac, HJ and Meyerson, LA and Nuñez, MA and Pauchard, A and Pyšek, P and Rabitsch, W and Richardson, DM and Roy, HE and Ruiz, GM and Russell, JC and Sanders, NJ and Sax, DF and Scalera, R and Seebens, H and Springborn, M and Turbelin, A and van Kleunen, M and von Holle, B and Winter, M and Zenni, RD and Mattsson, BJ and Roura-Pascual, N}, title = {Drivers of future alien species impacts: An expert-based assessment.}, journal = {Global change biology}, volume = {26}, number = {9}, pages = {4880-4893}, pmid = {32663906}, issn = {1365-2486}, support = {I 3757-B29//Austrian Science Fund/ ; I 4011-B32//Austrian Science Fund/ ; //COST/ ; I 4011-B32//BiodivERsA-Belmont Forum Project/ ; PCI2018-092939//BiodivERsA-Belmont Forum Project/ ; CEECIND///Fundação para a Ciência e a Tecnologia/ ; 02037//Fundação para a Ciência e a Tecnologia/ ; /2017//Fundação para a Ciência e a Tecnologia/ ; UIDB///Fundação para a Ciência e a Tecnologia/ ; 00295/2020//Fundação para a Ciência e a Tecnologia/ ; UIDP/00295/2020//Fundação para a Ciência e a Tecnologia/ ; 89967//National Research Foundation/ ; FKZ 01LC1807A//BMBF/ ; 01LC1807B//BMBF/ ; 01LC1807C//BMBF/ ; FKZ 01LC1803A//BMBF/ ; 19-28807X//Czech Science Foundation/ ; RVO 67985939//Czech Academy of Sciences/ ; //Fisheries and Oceans Canada/ ; //Transport Canada/ ; //NSERC/ ; NE///Natural Environment Research Council/ ; R016429/1//Natural Environment Research Council/ ; AFB-170008//CONICYT/ ; //DSI-NRF Centre of Excellence for Invasion Biology/ ; (grant 18576/03)//Oppenheimer Memorial Trust/ ; 1241932//National Science Foundation/ ; 1638702//National Science Foundation/ ; CZ.02.1.01/0.0/0.0/16_019/0000803//OP RDE/ ; 31003A_179491/SNSF_/Swiss National Science Foundation/Switzerland ; 31BD30_184114/SNSF_/Swiss National Science Foundation/Switzerland ; }, mesh = {*Biodiversity ; Climate Change ; Ecosystem ; Forecasting ; Humans ; *Introduced Species ; }, abstract = {Understanding the likely future impacts of biological invasions is crucial yet highly challenging given the multiple relevant environmental, socio-economic and societal contexts and drivers. In the absence of quantitative models, methods based on expert knowledge are the best option for assessing future invasion trajectories. Here, we present an expert assessment of the drivers of potential alien species impacts under contrasting scenarios and socioecological contexts through the mid-21st century. Based on responses from 36 experts in biological invasions, moderate (20%-30%) increases in invasions, compared to the current conditions, are expected to cause major impacts on biodiversity in most socioecological contexts. Three main drivers of biological invasions-transport, climate change and socio-economic change-were predicted to significantly affect future impacts of alien species on biodiversity even under a best-case scenario. Other drivers (e.g. human demography and migration in tropical and subtropical regions) were also of high importance in specific global contexts (e.g. for individual taxonomic groups or biomes). We show that some best-case scenarios can substantially reduce potential future impacts of biological invasions. However, rapid and comprehensive actions are necessary to use this potential and achieve the goals of the Post-2020 Framework of the Convention on Biological Diversity.}, } @article {pmid32661177, year = {2020}, author = {Sinha, S and Jones, BM and Traniello, IM and Bukhari, SA and Halfon, MS and Hofmann, HA and Huang, S and Katz, PS and Keagy, J and Lynch, VJ and Sokolowski, MB and Stubbs, LJ and Tabe-Bordbar, S and Wolfner, MF and Robinson, GE}, title = {Behavior-related gene regulatory networks: A new level of organization in the brain.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {117}, number = {38}, pages = {23270-23279}, pmid = {32661177}, issn = {1091-6490}, support = {R01 GM114341/GM/NIGMS NIH HHS/United States ; R35 GM131819/GM/NIGMS NIH HHS/United States ; U01 NS108637/NS/NINDS NIH HHS/United States ; }, mesh = {Animals ; *Behavior ; Brain/growth & development/*physiology ; Gene Expression Regulation, Developmental ; *Gene Regulatory Networks ; Humans ; }, abstract = {Neuronal networks are the standard heuristic model today for describing brain activity associated with animal behavior. Recent studies have revealed an extensive role for a completely distinct layer of networked activities in the brain-the gene regulatory network (GRN)-that orchestrates expression levels of hundreds to thousands of genes in a behavior-related manner. We examine emerging insights into the relationships between these two types of networks and discuss their interplay in spatial as well as temporal dimensions, across multiple scales of organization. We discuss properties expected of behavior-related GRNs by drawing inspiration from the rich literature on GRNs related to animal development, comparing and contrasting these two broad classes of GRNs as they relate to their respective phenotypic manifestations. Developmental GRNs also represent a third layer of network biology, playing out over a third timescale, which is believed to play a crucial mediatory role between neuronal networks and behavioral GRNs. We end with a special emphasis on social behavior, discuss whether unique GRN organization and cis-regulatory architecture underlies this special class of behavior, and review literature that suggests an affirmative answer.}, } @article {pmid32660426, year = {2020}, author = {Zhang, H and Xu, H and Liu, H and Pan, X and Xu, M and Zhang, G and He, M}, title = {PacBio single molecule long-read sequencing provides insight into the complexity and diversity of the Pinctada fucata martensii transcriptome.}, journal = {BMC genomics}, volume = {21}, number = {1}, pages = {481}, pmid = {32660426}, issn = {1471-2164}, support = {CARS-49//Earmarked Fund for Modern Agro-industry Technology Research System/ ; 2017B0303014052//the Science and Technology Planning Project of Guangdong Province, China/ ; }, mesh = {Alternative Splicing/genetics ; Animals ; Computational Biology ; Gene Expression Profiling/*methods ; High-Throughput Nucleotide Sequencing/*methods ; Open Reading Frames/genetics ; Pinctada/*genetics/growth & development ; RNA, Long Noncoding/genetics/isolation & purification ; RNA-Seq/*methods ; *Transcriptome ; }, abstract = {BACKGROUND: The pearl oyster Pinctada fucata martensii is an economically valuable shellfish for seawater pearl production, and production of pearls depends on its growth. To date, the molecular mechanisms of the growth of this species remain poorly understood. The transcriptome sequencing has been considered to understanding of the complexity of mechanisms of the growth of P. f. martensii. The recently released genome sequences of P. f. martensii, as well as emerging Pacific Bioscience (PacBio) single-molecular sequencing technologies, provide an opportunity to thoroughly investigate these molecular mechanisms.

RESULTS: Herein, the full-length transcriptome was analysed by combining PacBio single-molecule long-read sequencing (PacBio sequencing) and Illumina sequencing. A total of 20.65 Gb of clean data were generated, including 574,561 circular consensus reads, among which 443,944 full-length non-chimeric (FLNC) sequences were identified. Through transcript clustering analysis of FLNC reads, 32,755 consensus isoforms were identified, including 32,095 high-quality consensus sequences. After removing redundant reads, 16,388 transcripts were obtained, and 641 fusion transcripts were derived by performing fusion transcript prediction of consensus sequences. Alternative splicing analysis of the 16,388 transcripts was performed after accounting for redundancy, and 9097 gene loci were detected, including 1607 new gene loci and 14,946 newly discovered transcripts. The original boundary of 11,235 genes on the chromosomes was corrected, 12,025 complete open reading frame sequences and 635 long non-coding RNAs (LncRNAs) were predicted, and functional annotation of 13,482 new transcripts was achieved. Two thousand three hundred eighteen alternative splicing events were detected. A total of 228 differentially expressed transcripts (DETs) were identified between the largest (L) and smallest (S) pearl oysters. Compared with the S, the L showed 99 and 129 significantly up-and down-regulated DETs, respectively. Six of these DETs were further confirmed by quantitative real-time RT-PCR (RT-qPCR) in independent experiment.

CONCLUSIONS: Our results significantly improve existing gene models and genome annotations, optimise the genome structure, and in-depth understanding of the complexity and diversity of the differential growth patterns of P. f. martensii.}, } @article {pmid32659508, year = {2020}, author = {Azarpazhooh, MR and Amiri, A and Morovatdar, N and Steinwender, S and Rezaei Ardani, A and Yassi, N and Biller, J and Stranges, S and Tokazebani Belasi, M and Neya, SK and Khorram, B and Sheikh Andalibi, MS and Arsang-Jang, S and Mokhber, N and Di Napoli, M}, title = {Correlations between COVID-19 and burden of dementia: An ecological study and review of literature.}, journal = {Journal of the neurological sciences}, volume = {416}, number = {}, pages = {117013}, pmid = {32659508}, issn = {1878-5883}, mesh = {Age Distribution ; COVID-19/*epidemiology ; Cause of Death ; Comorbidity ; Databases, Factual ; Dementia/*epidemiology ; Global Burden of Disease ; Humans ; Pandemics ; }, abstract = {INTRODUCTION: Current evidence on the association between COVID-19 and dementia is sparse. This study aims to investigate the associations between COVID-19 caseload and the burden of dementia.

METHODS: We gathered data regarding burden of dementia (disability-adjusted life years [DALYs] per 100,000), life expectancy, and healthy life expectancy (HALE) from the Global Burden of Disease (GBD) 2017 study. We obtained COVID-19 data from Our World in Data database. We analyzed the association of COVID-19 cases and deaths with the burden of dementia using Spearman's rank correlation coefficient.

RESULTS: Globally, we found significant positive (p < .001) correlations between life expectancy (r = 0.60), HALE (r = 0.58), and dementia DALYs (r = 0.46) with COVID-19 caseloads. Likewise, we found similar correlations between life expectancy (r = 0.60), HALE (r = 0.58) and dementia DALYs (r = 0.54) with COVID-19 mortality.

CONCLUSION: Health policymakers should clarify a targeted model of disease surveillance in order to reduce the dual burden of dementia and COVID-19.}, } @article {pmid32658966, year = {2020}, author = {Smith, SA and Walker-Hale, N and Walker, JF}, title = {Intragenic Conflict in Phylogenomic Data Sets.}, journal = {Molecular biology and evolution}, volume = {37}, number = {11}, pages = {3380-3388}, doi = {10.1093/molbev/msaa170}, pmid = {32658966}, issn = {1537-1719}, mesh = {Animals ; Computer Simulation ; *Datasets as Topic ; Insecta/genetics ; Mammals/genetics ; *Models, Genetic ; *Phylogeny ; }, abstract = {Most phylogenetic analyses assume that a single evolutionary history underlies one gene. However, both biological processes and errors can cause intragenic conflict. The extent to which this conflict is present in empirical data sets is not well documented, but if common, could have far-reaching implications for phylogenetic analyses. We examined several large phylogenomic data sets from diverse taxa using a fast and simple method to identify well-supported intragenic conflict. We found conflict to be highly variable between data sets, from 1% to >92% of genes investigated. We analyzed four exemplar genes in detail and analyzed simulated data under several scenarios. Our results suggest that alignment error may be one major source of conflict, but other conflicts remain unexplained and may represent biological signal or other errors. Whether as part of data analysis pipelines or to explore biologically processes, analyses of within-gene phylogenetic signal should become common.}, } @article {pmid32658938, year = {2020}, author = {Yan, W and Zeng, Z and Gong, H and Duan, Y and Zhao, L and Peng, A}, title = {Locomotor activity patterns of takin (Budorcas taxicolor) in a temperate mountain region.}, journal = {PloS one}, volume = {15}, number = {7}, pages = {e0235464}, pmid = {32658938}, issn = {1932-6203}, mesh = {Animals ; China ; Female ; Geographic Information Systems ; Locomotion/*physiology ; Male ; Phylogeny ; Reproduction/*physiology ; Ruminants/*physiology ; Seasons ; }, abstract = {Understanding locomotor activity patterns would reveal key information about an animal's foraging strategy, energy budget and evolutionary adaptation. We studied the locomotor activity patterns of the takin (Budorcas taxicolor) in a temperate mountain region in China using GPS radio-collar technology from 1 July 2014 to 30 June 2015. Our research showed that takin had a bimodal crepuscular locomotor activity pattern, with an especially obvious movement peak at dusk. The takins showed significant seasonal differences in their movement rates, with the lowest movement rate in winter. The animals also showed sexual differences in their movement rates. In spring, the female movement rate was significantly higher than that of males during daytime, while during nighttime the movement rate of males was higher than that of females. The male movement rate was significantly higher than that of females in summer. The movement rate of the takins were correlated to microenvironment temperature and normalized difference vegetation index (NDVI) in each season. These findings suggest that takin could adjust locomotor activity levels adapt to reproductive requirements, temperature variation and forage variability.}, } @article {pmid32658640, year = {2020}, author = {Minenko, V and Viarenich, K and Zhukova, O and Kukhta, T and Podgaiskaya, M and Khrutchinsky, A and Kutsen, S and Bouville, A and Drozdovitch, V}, title = {Activity concentrations of [131]I and other radionuclides in cow's milk in Belarus during the first month following the Chernobyl accident.}, journal = {Journal of environmental radioactivity}, volume = {220-221}, number = {}, pages = {106264}, pmid = {32658640}, issn = {1879-1700}, support = {Z99 CA999999/ImNIH/Intramural NIH HHS/United States ; }, mesh = {Animals ; *Chernobyl Nuclear Accident ; Humans ; Iodine Radioisotopes ; Milk ; *Radiation Monitoring ; Republic of Belarus ; Ukraine ; }, abstract = {The accident at the Chernobyl nuclear power plant (NPP) in Ukraine on April 26, 1986 led to a considerable release of radioactive material resulting in environmental contamination over vast areas of Belarus, Ukraine and western Russian Federation. The major health effect of the Chernobyl accident was an increase in thyroid cancer incidence in people exposed as children and adolescents, so much attention was paid to the thyroid doses resulting from intakes of [131]I. Because cow's milk consumption was the main source of [131]I intake by people, it was important to measure the [131]I activity concentrations in cow's milk to calculate, or to validate, the thyroid doses to the exposed population. Almost 11,000 measurements of total beta-activity in cow's milk were performed using a DP-100 device during the first month after the Chernobyl accident in the most contaminated regions of Belarus. Using an ecological model and calibration coefficients for the DP-100 device the activity concentration of [131]I in cow's milk was derived as well as the activity concentrations of the other radiologically important radionuclides, namely [134]Cs, [137]Cs, [89]Sr and [90]Sr. The activity concentrations of other radionuclides, such as [90]Y, [132]Te, [132]I, [133]I, [136]Cs, [140]Ba, [140]La, [141]Ce and [144]Ce, in cow's milk were also estimated and were shown to be of minor importance. The concentrations of [95]Zr, [95]Nb, [103]Ru and [106]Ru in cow's milk were negligible. The data obtained in this study were validated by comparing derived [131]I and [137]Cs concentrations in cow's milk with gamma-spectrometry measurements performed in milk produced in the same location close to the same date. The results of this study were essential to assess and validate the radiation doses received by the subjects of epidemiological studies related to the health consequences of the Chernobyl accident.}, } @article {pmid32656252, year = {2020}, author = {Adhikari, B and Jun, SR and Kwon, YM and Kiess, AS and Adhikari, P}, title = {Effects of Housing Types on Cecal Microbiota of Two Different Strains of Laying Hens During the Late Production Phase.}, journal = {Frontiers in veterinary science}, volume = {7}, number = {}, pages = {331}, pmid = {32656252}, issn = {2297-1769}, abstract = {Due to animal welfare issues, European Union has banned the use of conventional cages (CC) and non-EU countries including the US are also under constant public pressure to restrict their use in egg production. Very limited information is available on the composition of the microbial community of hens raised in different housing environments. This study was conducted to determine the effects of CC and enriched colony cages (EC) on cecal microbiota of two commercial laying hen strains, Hy-Line W36 (W36) and Hy-Line Brown (HB) during the late production stage (53, 58, 67, and 72 weeks of age). Cecal microbiota was studied by analyzing 16S rRNA gene sequences with Quantitative Insights Into Microbial Ecology (QIIME) 2 ver. 2018.8. Differentially abundant taxa were identified by Linear discriminant analysis Effect Size (LEfSe) analysis (P < 0.05, LDA score > 2.0). At phylum level, Actinobacteria was significantly enriched in W36 at all time points while Synergistetes (53 weeks), Spirochaetes (58 weeks), and Synergistetes and Spirochaetes (67 weeks) were significantly higher in HB. At genus level, Bifidobacterium (at all time points) and butyric acid producing genera such as Butyricicoccus and Subdoligranulum (58 and 72 weeks) were significantly higher in W36 as compared to HB. Moreover, Proteobacteria (72 weeks) and its associated genus Campylobacter (67 and 72 weeks) were significantly enriched in EC as compared to CC. Alpha diversity was significantly higher in HB (at all time points) and in EC (67 weeks) as compared to W36 and CC, respectively. Similarly, there was a significant difference in community structure (beta diversity) between W36 and HB (all time points) as well as between EC and CC (67 weeks). The effect of housing and strains was not only seen at the bacterial composition and structure but also reflected at their functional level. Notably, KEGG metabolic pathways predicted to be involved in carbohydrates degradation and amino acids biosynthesis by PICRUSt analysis were significantly different between W36 and HB housed at CC and EC. In sum, cecal microbiota composition, diversities, and their functional pathways were affected by housing type which further varied between two commercial laying hen strains, HB and W36. This suggests that both housing and genetic strains of laying hens should be considered for selection of the alternative housing systems such as enriched colony cage.}, } @article {pmid32651419, year = {2020}, author = {Pigeon, KE and MacNearney, D and Hebblewhite, M and Musiani, M and Neufeld, L and Cranston, J and Stenhouse, G and Schmiegelow, F and Finnegan, L}, title = {The density of anthropogenic features explains seasonal and behaviour-based functional responses in selection of linear features by a social predator.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {11437}, pmid = {32651419}, issn = {2045-2322}, mesh = {Animals ; Deer/*physiology ; Ecosystem ; *Geographic Information Systems ; Humans ; Predatory Behavior/*physiology ; Seasons ; Wolves/*physiology ; }, abstract = {Anthropogenic linear features facilitate access and travel efficiency for predators, and can influence predator distribution and encounter rates with prey. We used GPS collar data from eight wolf packs and characteristics of seismic lines to investigate whether ease-of-travel or access to areas presumed to be preferred by prey best explained seasonal selection patterns of wolves near seismic lines, and whether the density of anthropogenic features led to functional responses in habitat selection. At a broad scale, wolves showed evidence of habitat-driven functional responses by exhibiting greater selection for areas near low-vegetation height seismic lines in areas with low densities of anthropogenic features. We highlight the importance of considering landscape heterogeneity and habitat characteristics, and the functional response in habitat selection when investigating seasonal behaviour-based selection patterns. Our results support behaviour in line with search for primary prey during summer and fall, and ease-of-travel during spring, while patterns of selection during winter aligned best with ease-of-travel for the less-industrialized foothills landscape, and with search for primary prey in the more-industrialized boreal landscape. These results highlight that time-sensitive restoration actions on anthropogenic features can affect the probability of overlap between predators and threatened prey within different landscapes.}, } @article {pmid32650792, year = {2020}, author = {Mattalia, G and Stryamets, N and Pieroni, A and Sõukand, R}, title = {Knowledge transmission patterns at the border: ethnobotany of Hutsuls living in the Carpathian Mountains of Bukovina (SW Ukraine and NE Romania).}, journal = {Journal of ethnobiology and ethnomedicine}, volume = {16}, number = {1}, pages = {41}, pmid = {32650792}, issn = {1746-4269}, support = {714874/ERC_/European Research Council/International ; }, mesh = {*Cross-Cultural Comparison ; Ethnicity ; *Ethnobotany ; Humans ; Information Dissemination/*methods ; *Knowledge ; Plants, Edible/classification ; Plants, Medicinal/classification ; Romania ; Ukraine ; }, abstract = {BACKGROUND: Cross-border research is a novel and important tool for detecting variability of ecological knowledge. This is especially evident in regions recently divided and annexed to different political regimes. Therefore, we conducted a study among Hutsuls, a cultural and linguistic minority group living in Northern and Southern Bukovina (Ukraine and Romania, respectively). Indeed, in the 1940s, a border was created: Northern Bukovina was annexed by the USSR while Southern Bukovina remained part of the Kingdom of Romania. In this research, we aim to document uses of plants for food and medicinal preparations, discussing the different dynamics of Local Ecological Knowledge (LEK) transmission among Hutsuls living in Ukraine and Romania.

METHODS: Field research was conducted using convenience and snowball sampling techniques to recruit 31 Hutsuls in Ukraine and 30 in Romania for participation in semi-structured interviews regarding the use of plants for medicinal and food preparation purposes and the sources of such knowledge.

RESULTS: The interviews revealed that, despite a common cultural and linguistic background, ethnobotanical knowledge transmission occurs in different ways on each side of the border. Family is a primary source of ethnobotanical knowledge transmission on both sides of the border; however, in Romania, knowledge from other sources is very limited, whereas in Ukraine interviewees reported several other sources including books, magazines, newspapers, the Internet and television. This is especially evident when analysing the wild plants used for medicinal purposes as we found 53 taxa that were common to both, 47 used only in Ukraine and 11 used only in Romania. While Romanian Hutsuls used almost exclusively locally available plants, Ukrainian Hutsuls often reported novel plants such as Aloe vera, Aronia melanocarpa and Elaeagnus rhamnoides. Knowledge related to these plants was transferred by sources of knowledge other than oral transmission among members of the same family. Therefore, this may imply hybridization of the local body of knowledge with foreign elements originating in the Soviet context which has enriched the corpus of ethnobotanical knowledge held by Ukrainian Hutsuls.

CONCLUSIONS: While ethnobotanical knowledge among Romanian Hutsuls is mainly traditional and vertically transmitted, among Ukrainian Hutsuls there is a considerable proportion of LEK that is transmitted from other (written and visual) sources of knowledge. This cross-border research reveals that despite a common cultural background, socio-political scenarios have impacted Hutsul ethnobotanical knowledge and its transmission patterns.}, } @article {pmid32647000, year = {2020}, author = {Toledo, S and Shohami, D and Schiffner, I and Lourie, E and Orchan, Y and Bartan, Y and Nathan, R}, title = {Cognitive map-based navigation in wild bats revealed by a new high-throughput tracking system.}, journal = {Science (New York, N.Y.)}, volume = {369}, number = {6500}, pages = {188-193}, doi = {10.1126/science.aax6904}, pmid = {32647000}, issn = {1095-9203}, mesh = {Animals ; Chiroptera/*physiology ; Cognition ; Datasets as Topic ; Flight, Animal/*physiology ; Orientation, Spatial/*physiology ; Spatial Navigation/*physiology ; }, abstract = {Seven decades of research on the "cognitive map," the allocentric representation of space, have yielded key neurobiological insights, yet field evidence from free-ranging wild animals is still lacking. Using a system capable of tracking dozens of animals simultaneously at high accuracy and resolution, we assembled a large dataset of 172 foraging Egyptian fruit bats comprising >18 million localizations collected over 3449 bat-nights across 4 years. Detailed track analysis, combined with translocation experiments and exhaustive mapping of fruit trees, revealed that wild bats seldom exhibit random search but instead repeatedly forage in goal-directed, long, and straight flights that include frequent shortcuts. Alternative, non-map-based strategies were ruled out by simulations, time-lag embedding, and other trajectory analyses. Our results are consistent with expectations from cognitive map-like navigation and support previous neurobiological evidence from captive bats.}, } @article {pmid32642861, year = {2020}, author = {Hu, Z and Li, R and Xia, X and Yu, C and Fan, X and Zhao, Y}, title = {A method overview in smart aquaculture.}, journal = {Environmental monitoring and assessment}, volume = {192}, number = {8}, pages = {493}, doi = {10.1007/s10661-020-08409-9}, pmid = {32642861}, issn = {1573-2959}, support = {61963012//National Natural Science Foundation of China (CN)/ ; ZDYF2018015//Key Research and Development Project of Hainan Province/ ; 619QN195//Hainan Provincial Department of Science and Technology (CN)/ ; }, mesh = {Agriculture ; Animals ; *Aquaculture ; *Environmental Monitoring ; Fishes ; Water Quality ; }, abstract = {Aquaculture is an important part of agricultural economy. In the past, major farming accidents often occurred due to subjective experience. There are many factors affecting the water quality of aquaculture. Maintaining an ecological environment with good water quality is the most critical link to ensure the production efficiency and quality of aquaculture. With the continuous development of science and technology, intelligence and informatization in aquaculture has become a new trend. Smart aquaculture cannot only realize real-time monitoring, prediction, warning, and risk control of the physical and chemical factors of the aquaculture environment but can also conduct real-time monitoring of the characteristics and behaviors of the fish, which infers the changes of the aquaculture ecological environment. In this paper, the research achievements over past two decades both are summarized from four aspects: water quality factor acquisition and pre-processing, water quality factor prediction, morphological characteristics, and behavioral characteristic recognition of fish and the mechanism between fish behavior and water quality factors. The advantages and disadvantages of existing research routes, algorithm models, and research methods in smart aquaculture are summarized. The work in this paper can provide a well-organized and summative knowledge reference for further study on the dynamic mechanism between the changes of water quality factors and the fish body characteristics and behavior. Meanwhile, the work can also provide valuable reference for promoting the smart, ecological, and efficient development of aquaculture.}, } @article {pmid32636389, year = {2020}, author = {Buetti-Dinh, A and Herold, M and Christel, S and Hajjami, ME and Bellenberg, S and Ilie, O and Wilmes, P and Poetsch, A and Sand, W and Vera, M and Pivkin, IV and Dopson, M}, title = {Systems biology of acidophile biofilms for efficient metal extraction.}, journal = {Scientific data}, volume = {7}, number = {1}, pages = {215}, pmid = {32636389}, issn = {2052-4463}, support = {2014-6545//Vetenskapsrådet (Swedish Research Council)/International ; INTER/SYSAPP/14/05//Fonds National de la Recherche Luxembourg (National Research Fund)/International ; 205321_173020//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/International ; }, mesh = {Acids/chemistry ; Bacteria/*genetics ; Bacterial Proteins/genetics ; Biofilms/*growth & development ; Copper/isolation & purification ; Metals/*isolation & purification ; RNA, Bacterial/genetics ; *Systems Biology ; }, abstract = {Society's demand for metals is ever increasing while stocks of high-grade minerals are being depleted. Biomining, for example of chalcopyrite for copper recovery, is a more sustainable biotechnological process that exploits the capacity of acidophilic microbes to catalyze solid metal sulfide dissolution to soluble metal sulfates. A key early stage in biomining is cell attachment and biofilm formation on the mineral surface that results in elevated mineral oxidation rates. Industrial biomining of chalcopyrite is typically carried out in large scale heaps that suffer from the downsides of slow and poor metal recoveries. In an effort to mitigate these drawbacks, this study investigated planktonic and biofilm cells of acidophilic (optimal growth pH < 3) biomining bacteria. RNA and proteins were extracted, and high throughput "omics" performed from a total of 80 biomining experiments. In addition, micrographs of biofilm formation on the chalcopyrite mineral surface over time were generated from eight separate experiments. The dataset generated in this project will be of great use to microbiologists, biotechnologists, and industrial researchers.}, } @article {pmid32633756, year = {2020}, author = {Tovo, A and Menzel, P and Krogh, A and Cosentino Lagomarsino, M and Suweis, S}, title = {Taxonomic classification method for metagenomics based on core protein families with Core-Kaiju.}, journal = {Nucleic acids research}, volume = {48}, number = {16}, pages = {e93}, pmid = {32633756}, issn = {1362-4962}, mesh = {Bacteria/*classification/genetics ; Computational Biology ; DNA, Bacterial/genetics ; Databases, Protein ; Gastrointestinal Microbiome/*genetics ; Genetic Markers ; Humans ; *Metagenome ; Metagenomics/*methods ; *Phylogeny ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, DNA ; }, abstract = {Characterizing species diversity and composition of bacteria hosted by biota is revolutionizing our understanding of the role of symbiotic interactions in ecosystems. Determining microbiomes diversity implies the assignment of individual reads to taxa by comparison to reference databases. Although computational methods aimed at identifying the microbe(s) taxa are available, it is well known that inferences using different methods can vary widely depending on various biases. In this study, we first apply and compare different bioinformatics methods based on 16S ribosomal RNA gene and shotgun sequencing to three mock communities of bacteria, of which the compositions are known. We show that none of these methods can infer both the true number of taxa and their abundances. We thus propose a novel approach, named Core-Kaiju, which combines the power of shotgun metagenomics data with a more focused marker gene classification method similar to 16S, but based on emergent statistics of core protein domain families. We thus test the proposed method on various mock communities and we show that Core-Kaiju reliably predicts both number of taxa and abundances. Finally, we apply our method on human gut samples, showing how Core-Kaiju may give more accurate ecological characterization and a fresh view on real microbiomes.}, } @article {pmid32632539, year = {2020}, author = {Krebs, A and van Vugt-Lussenburg, BMA and Waldmann, T and Albrecht, W and Boei, J and Ter Braak, B and Brajnik, M and Braunbeck, T and Brecklinghaus, T and Busquet, F and Dinnyes, A and Dokler, J and Dolde, X and Exner, TE and Fisher, C and Fluri, D and Forsby, A and Hengstler, JG and Holzer, AK and Janstova, Z and Jennings, P and Kisitu, J and Kobolak, J and Kumar, M and Limonciel, A and Lundqvist, J and Mihalik, B and Moritz, W and Pallocca, G and Ulloa, APC and Pastor, M and Rovida, C and Sarkans, U and Schimming, JP and Schmidt, BZ and Stöber, R and Strassfeld, T and van de Water, B and Wilmes, A and van der Burg, B and Verfaillie, CM and von Hellfeld, R and Vrieling, H and Vrijenhoek, NG and Leist, M}, title = {The EU-ToxRisk method documentation, data processing and chemical testing pipeline for the regulatory use of new approach methods.}, journal = {Archives of toxicology}, volume = {94}, number = {7}, pages = {2435-2461}, pmid = {32632539}, issn = {1432-0738}, mesh = {Animals ; Cells, Cultured ; *Documentation ; Electronic Data Processing/*legislation & jurisprudence ; Europe ; *Government Regulation ; Humans ; Policy Making ; Reproducibility of Results ; Retrospective Studies ; Risk Assessment ; Terminology as Topic ; *Toxicity Tests ; Toxicology/*legislation & jurisprudence ; Zebrafish/embryology ; }, abstract = {Hazard assessment, based on new approach methods (NAM), requires the use of batteries of assays, where individual tests may be contributed by different laboratories. A unified strategy for such collaborative testing is presented. It details all procedures required to allow test information to be usable for integrated hazard assessment, strategic project decisions and/or for regulatory purposes. The EU-ToxRisk project developed a strategy to provide regulatorily valid data, and exemplified this using a panel of > 20 assays (with > 50 individual endpoints), each exposed to 19 well-known test compounds (e.g. rotenone, colchicine, mercury, paracetamol, rifampicine, paraquat, taxol). Examples of strategy implementation are provided for all aspects required to ensure data validity: (i) documentation of test methods in a publicly accessible database; (ii) deposition of standard operating procedures (SOP) at the European Union DB-ALM repository; (iii) test readiness scoring accoding to defined criteria; (iv) disclosure of the pipeline for data processing; (v) link of uncertainty measures and metadata to the data; (vi) definition of test chemicals, their handling and their behavior in test media; (vii) specification of the test purpose and overall evaluation plans. Moreover, data generation was exemplified by providing results from 25 reporter assays. A complete evaluation of the entire test battery will be described elsewhere. A major learning from the retrospective analysis of this large testing project was the need for thorough definitions of the above strategy aspects, ideally in form of a study pre-registration, to allow adequate interpretation of the data and to ensure overall scientific/toxicological validity.}, } @article {pmid32628683, year = {2020}, author = {Douanne, N and Dong, G and Douanne, M and Olivier, M and Fernandez-Prada, C}, title = {Unravelling the proteomic signature of extracellular vesicles released by drug-resistant Leishmania infantum parasites.}, journal = {PLoS neglected tropical diseases}, volume = {14}, number = {7}, pages = {e0008439}, pmid = {32628683}, issn = {1935-2735}, support = {PJT-159765//CIHR/Canada ; }, mesh = {Antiprotozoal Agents/*pharmacology ; Computational Biology ; *Drug Resistance ; Extracellular Vesicles ; Gene Expression Regulation/*drug effects/physiology ; Leishmania infantum/*drug effects/*metabolism ; Proteome ; Proteomics ; Protozoan Proteins/genetics/metabolism ; }, abstract = {Leishmaniasis constitutes the 9th largest disease burden among all infectious diseases. Control of this disease is based on a short list of chemotherapeutic agents headed by pentavalent antimonials, followed by miltefosine and amphotericin B; drugs that are far from ideal due to host toxicity, elevated cost, limited access, and high rates of drug resistance. Knowing that the composition of extracellular vesicles (EVs) can vary according to the state of their parental cell, we hypothesized that EVs released by drug-resistant Leishmania infantum parasites could contain unique and differently enriched proteins depending on the drug-resistance mechanisms involved in the survival of their parental cell line. To assess this possibility, we studied EV production, size, morphology, and protein content of three well-characterized drug-resistant L. infantum cell lines and a wild-type strain. Our results are the first to demonstrate that drug-resistance mechanisms can induce changes in the morphology, size, and distribution of L. infantum EVs. In addition, we identified L. infantum's core EV proteome. This proteome is highly conserved among strains, with the exception of a handful of proteins that are enriched differently depending on the drug responsible for induction of antimicrobial resistance. Furthermore, we obtained the first snapshot of proteins enriched in EVs released by antimony-, miltefosine- and amphotericin-resistant parasites. These include several virulence factors, transcription factors, as well as proteins encoded by drug-resistance genes. This detailed study of L. infantum EVs sheds new light on the potential roles of EVs in Leishmania biology, particularly with respect to the parasite's survival in stressful conditions. This work outlines a crucial first step towards the discovery of EV-based profiles capable of predicting response to antileishmanial agents.}, } @article {pmid32626610, year = {2020}, author = {Goëau, H and Mora-Fallas, A and Champ, J and Love, NLR and Mazer, SJ and Mata-Montero, E and Joly, A and Bonnet, P}, title = {A new fine-grained method for automated visual analysis of herbarium specimens: A case study for phenological data extraction.}, journal = {Applications in plant sciences}, volume = {8}, number = {6}, pages = {e11368}, pmid = {32626610}, issn = {2168-0450}, abstract = {PREMISE: Herbarium specimens represent an outstanding source of material with which to study plant phenological changes in response to climate change. The fine-scale phenological annotation of such specimens is nevertheless highly time consuming and requires substantial human investment and expertise, which are difficult to rapidly mobilize.

METHODS: We trained and evaluated new deep learning models to automate the detection, segmentation, and classification of four reproductive structures of Streptanthus tortuosus (flower buds, flowers, immature fruits, and mature fruits). We used a training data set of 21 digitized herbarium sheets for which the position and outlines of 1036 reproductive structures were annotated manually. We adjusted the hyperparameters of a mask R-CNN (regional convolutional neural network) to this specific task and evaluated the resulting trained models for their ability to count reproductive structures and estimate their size.

RESULTS: The main outcome of our study is that the performance of detection and segmentation can vary significantly with: (i) the type of annotations used for training, (ii) the type of reproductive structures, and (iii) the size of the reproductive structures. In the case of Streptanthus tortuosus, the method can provide quite accurate estimates (77.9% of cases) of the number of reproductive structures, which is better estimated for flowers than for immature fruits and buds. The size estimation results are also encouraging, showing a difference of only a few millimeters between the predicted and actual sizes of buds and flowers.

DISCUSSION: This method has great potential for automating the analysis of reproductive structures in high-resolution images of herbarium sheets. Deeper investigations regarding the taxonomic scalability of this approach and its potential improvement will be conducted in future work.}, } @article {pmid32621602, year = {2020}, author = {Spoor, S and Wytko, C and Soto, B and Chen, M and Almsaeed, A and Condon, B and Herndon, N and Hough, H and Jung, S and Staton, M and Wegrzyn, J and Main, D and Feltus, FA and Ficklin, SP}, title = {Tripal and Galaxy: supporting reproducible scientific workflows for community biological databases.}, journal = {Database : the journal of biological databases and curation}, volume = {2020}, number = {}, pages = {}, pmid = {32621602}, issn = {1758-0463}, mesh = {Computational Biology ; *Database Management Systems ; *Databases, Genetic ; *Internet ; *Software ; }, abstract = {Online biological databases housing genomics, genetic and breeding data can be constructed using the Tripal toolkit. Tripal is an open-source, internationally developed framework that implements FAIR data principles and is meant to ease the burden of constructing such websites for research communities. Use of a common, open framework improves the sustainability and manageability of such as site. Site developers can create extensions for their site and in turn share those extensions with others. One challenge that community databases often face is the need to provide tools for their users that analyze increasingly larger datasets using multiple software tools strung together in a scientific workflow on complicated computational resources. The Tripal Galaxy module, a 'plug-in' for Tripal, meets this need through integration of Tripal with the Galaxy Project workflow management system. Site developers can create workflows appropriate to the needs of their community using Galaxy and then share those for execution on their Tripal sites via automatically constructed, but configurable, web forms or using an application programming interface to power web-based analytical applications. The Tripal Galaxy module helps reduce duplication of effort by allowing site developers to spend time constructing workflows and building their applications rather than rebuilding infrastructure for job management of multi-step applications.}, } @article {pmid32619482, year = {2020}, author = {Aikens, EO and Mysterud, A and Merkle, JA and Cagnacci, F and Rivrud, IM and Hebblewhite, M and Hurley, MA and Peters, W and Bergen, S and De Groeve, J and Dwinnell, SPH and Gehr, B and Heurich, M and Hewison, AJM and Jarnemo, A and Kjellander, P and Kröschel, M and Licoppe, A and Linnell, JDC and Merrill, EH and Middleton, AD and Morellet, N and Neufeld, L and Ortega, AC and Parker, KL and Pedrotti, L and Proffitt, KM and Saïd, S and Sawyer, H and Scurlock, BM and Signer, J and Stent, P and Šustr, P and Szkorupa, T and Monteith, KL and Kauffman, MJ}, title = {Wave-like Patterns of Plant Phenology Determine Ungulate Movement Tactics.}, journal = {Current biology : CB}, volume = {30}, number = {17}, pages = {3444-3449.e4}, doi = {10.1016/j.cub.2020.06.032}, pmid = {32619482}, issn = {1879-0445}, mesh = {Animal Migration/*physiology ; Animals ; *Climate Change ; Deer/*physiology ; *Ecosystem ; Geographic Information Systems ; Herbivory ; *Plant Development ; *Plant Physiological Phenomena ; Plants/*metabolism ; }, abstract = {Animals exhibit a diversity of movement tactics [1]. Tracking resources that change across space and time is predicted to be a fundamental driver of animal movement [2]. For example, some migratory ungulates (i.e., hooved mammals) closely track the progression of highly nutritious plant green-up, a phenomenon called "green-wave surfing" [3-5]. Yet general principles describing how the dynamic nature of resources determine movement tactics are lacking [6]. We tested an emerging theory that predicts surfing and the existence of migratory behavior will be favored in environments where green-up is fleeting and moves sequentially across large landscapes (i.e., wave-like green-up) [7]. Landscapes exhibiting wave-like patterns of green-up facilitated surfing and explained the existence of migratory behavior across 61 populations of four ungulate species on two continents (n = 1,696 individuals). At the species level, foraging benefits were equivalent between tactics, suggesting that each movement tactic is fine-tuned to local patterns of plant phenology. For decades, ecologists have sought to understand how animals move to select habitat, commonly defining habitat as a set of static patches [8, 9]. Our findings indicate that animal movement tactics emerge as a function of the flux of resources across space and time, underscoring the need to redefine habitat to include its dynamic attributes. As global habitats continue to be modified by anthropogenic disturbance and climate change [10], our synthesis provides a generalizable framework to understand how animal movement will be influenced by altered patterns of resource phenology.}, } @article {pmid32614827, year = {2020}, author = {Ferguson, AW and Muloi, D and Ngatia, DK and Kiongo, W and Kimuyu, DM and Webala, PW and Olum, MO and Muturi, M and Thumbi, SM and Woodroffe, R and Murugi, L and Fèvre, EM and Murray, S and Martins, DJ}, title = {Volunteer based approach to dog vaccination campaigns to eliminate human rabies: Lessons from Laikipia County, Kenya.}, journal = {PLoS neglected tropical diseases}, volume = {14}, number = {7}, pages = {e0008260}, pmid = {32614827}, issn = {1935-2735}, support = {/WT_/Wellcome Trust/United Kingdom ; 110330/Z/15/Z/WT_/Wellcome Trust/United Kingdom ; G1100783/MRC_/Medical Research Council/United Kingdom ; /BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; Community-Institutional Relations ; Costs and Cost Analysis ; Dogs ; Humans ; Kenya ; Mass Vaccination/economics/*veterinary ; Population Density ; Rabies/*prevention & control ; Volunteers ; }, abstract = {BACKGROUND: An estimated 59,000 people die from rabies annually, with 99% of those deaths attributable to bites from domestic dogs (Canis lupus familiaris). This preventable Neglected Tropical Disease has a large impact across continental Africa, especially for rural populations living in close contact with livestock and wildlife. Mass vaccinations of domestic dogs are effective at eliminating rabies but require large amounts of resources, planning, and political will to implement. Grassroots campaigns provide an alternative method to successful implementation of rabies control but remain understudied in their effectiveness to eliminate the disease from larger regions.

We report on the development, implementation, and effectiveness of a grassroots mass dog rabies vaccination campaign in Kenya, the Laikipia Rabies Vaccination Campaign. During 2015-2017, a total of 13,155 domestic dogs were vaccinated against rabies in 17 communities covering approximately 1500 km2. Based on an estimated population size of 34,275 domestic dogs, percent coverages increased across years, from 2% in 2015 to 24% in 2017, with only 3 of 38 community-years of vaccination exceeding the 70% target. The average cost of vaccinating an animal was $3.44 USD with in-kind contributions and $7.44 USD without in-kind contributions.

CONCLUSIONS/SIGNIFICANCE: The evolution of the Laikipia Rabies Vaccination Campaign from a localized volunteer-effort to a large-scale program attempting to eliminate rabies at the landscape scale provides a unique opportunity to examine successes, failures, and challenges facing grassroots campaigns. Success, in the form of vaccinating more dogs across the study area, was relatively straightforward to achieve. However, lack of effective post-vaccination monitoring and education programs, limited funding, and working in diverse community types appeared to hinder achievement of 70% coverage levels. These results indicate that grassroots campaigns will inevitably be faced with a philosophical question regarding the value of local impacts versus their contributions to a larger effort to eliminate rabies at the regional, country, or global scale.}, } @article {pmid32613025, year = {2020}, author = {Shen, Y and Xu, W and Li, C and Handel, A and Martinez, L and Ling, F and Ebell, M and Fu, X and Pan, J and Ren, J and Gu, W and Chen, E}, title = {A Cluster of Novel Coronavirus Disease 2019 Infections Indicating Person-to-Person Transmission Among Casual Contacts From Social Gatherings: An Outbreak Case-Contact Investigation.}, journal = {Open forum infectious diseases}, volume = {7}, number = {6}, pages = {ofaa231}, pmid = {32613025}, issn = {2328-8957}, abstract = {BACKGROUND: Severe acute respiratory syndrome coronavirus 2, the pathogen causing novel coronavirus disease of 2019 (COVID-19), efficiently spreads from person to person in close contact settings. Transmission among casual contacts in settings such as during social gatherings is not well understood.

METHODS: We report several transmission events to both close and casual contacts from a cluster of 7 COVID-19 cases occurring from mid-January to early February 2020. A total of 539 social and family contacts of the index patient's, including members of a 2-day wedding and a family party, were contacted and screened through epidemiologic surveys. The clinical progression of all cases is described.

RESULTS: We estimate the secondary attack rate among close contacts to be 29% (2 of 7) and for the casual contacts to be 0.6% (3 of 473). The incubation period of our case cluster was 4-12 days (median, 7 days).

CONCLUSIONS: Transmission efficiency among close contacts was higher than among casual contacts; however, transmission from second-generation cases may help spread the virus during the incubation period.}, } @article {pmid32610525, year = {2020}, author = {Englefield, B and Starling, M and Wilson, B and Roder, C and McGreevy, P}, title = {The Australian Roadkill Reporting Project-Applying Integrated Professional Research and Citizen Science to Monitor and Mitigate Roadkill in Australia.}, journal = {Animals : an open access journal from MDPI}, volume = {10}, number = {7}, pages = {}, pmid = {32610525}, issn = {2076-2615}, abstract = {Australia has no national roadkill monitoring scheme. To address this gap in knowledge, a roadkill reporting application (app) was developed to allow members of the public to join professional researchers in gathering Australian data. The app is used to photograph roadkill and simultaneously records the GPS location, time and date. These data are uploaded immediately to a website for data management. To illustrate the capacity to facilitate cost-effective mitigation measures the article focuses on two roadkill hotspots-in Queensland and Tasmania. In total, 1609 reports were gathered in the first three months of the project. They include data on mammals (n = 1203, 75%), birds (n = 125, 7.8%), reptiles (n = 79, 4.9%), amphibians (n = 4, 0.025%), unidentified (n = 189, 11.8%) and unserviceable ones (n = 9). A significant finding is variance in the distribution of mammals and birds at different times of day. These findings reflect diurnal variation in the activity levels of different species and underline the need for data on a targeted species to be collected at appropriate times of day. By continuing to facilitate roadkill monitoring, it is anticipated that the data generated by the app will directly increase knowledge of roadkill numbers and hotspots. Indirectly, it will provide value-added information on animal behaviour, disease and population dynamics as well as for species distribution mapping.}, } @article {pmid32609781, year = {2020}, author = {Kembou Nzale, S and Weeks, WB and Ouafik, L and Rouquette, I and Beau-Faller, M and Lemoine, A and Bringuier, PP and Le Coroller Soriano, AG and Barlesi, F and Ventelou, B}, title = {Inequity in access to personalized medicine in France: Evidences from analysis of geo variations in the access to molecular profiling among advanced non-small-cell lung cancer patients: Results from the IFCT Biomarkers France Study.}, journal = {PloS one}, volume = {15}, number = {7}, pages = {e0234387}, pmid = {32609781}, issn = {1932-6203}, mesh = {Adult ; Aged ; Aged, 80 and over ; Biomarkers ; Carcinoma, Non-Small-Cell Lung/genetics ; Databases, Factual ; Female ; France ; Genetic Testing/trends ; Health Services Accessibility/economics/*trends ; Humans ; Lung Neoplasms/genetics ; Male ; Middle Aged ; Precision Medicine/*economics/*trends ; }, abstract = {In this article, we studied geographic variation in the use of personalized genetic testing for advanced non-small cell lung cancer (NSCLC) and we evaluated the relationship between genetic testing rates and local socioeconomic and ecological variables. We used data on all advanced NSCLC patients who had a genetic test between April 2012 and April 2013 in France in the frame of the IFCT Biomarqueurs-France study (n = 15814). We computed four established measures of geographic variation of the sex-adjusted rates of genetic testing utilization at the "départment" (the French territory is divided into 94 administrative units called 'départements') level. We also performed a spatial regression model to determine the relationship between département-level sex-adjusted rates of genetic testing utilization and economic and ecological variables. Our results are the following: (i) Overall, 46.87% lung cancer admission patients obtained genetic testing for NSCLC; département-level utilization rates varied over 3.2-fold. Measures of geographic variation indicated a relatively high degree of geographic variation. (ii) there was a statistically significant relationship between genetic testing rates and per capita supply of general practitioners, radiotherapists and surgeons (negative correlation for the latter); lower genetic testing rates were also associated with higher local poverty rates. French policymakers should pursue effort toward deprived areas to obtain equal access to personalized medicine for advanced NSCLC patients.}, } @article {pmid32608729, year = {2020}, author = {Zhu, LY and Chen, YY and Liu, J and Wang, YW and Wang, CR and Wei, YS and Zhang, YX}, title = {[Spatio-temporal Evolution and Relationship of Water Environment Quality and Phytoplankton Community in Wenyu River].}, journal = {Huan jing ke xue= Huanjing kexue}, volume = {41}, number = {2}, pages = {702-712}, doi = {10.13227/j.hjkx.201906207}, pmid = {32608729}, issn = {0250-3301}, mesh = {Beijing ; China ; Phytoplankton/*classification ; *Rivers ; Seasons ; Spatio-Temporal Analysis ; Water Pollution/*analysis ; *Water Quality ; }, abstract = {The Wenyu River is an important ecological corridor of Beijing. In this study, the spatio-temporal dynamics of water quality and phytoplankton community in the Wenyu River in 2006, 2011, and 2018, as well as their relationship were thoroughly analyzed by historical data analysis and field surveys. Results show that the water quality in the Wenyu River improved significantly from serious pollution owing to pollution containment. The major water pollutant has shifted from ammonia nitrogen (NH4[+]-N) to total nitrogen (TN). Compared with 2011, the average multiple of NH4[+]-N and total nitrogen TN exceeding the national standard were reduced by factors of 0.29-0.33 and 2.77-2.39, respectively, in 2018. The average concentration of NH4[+]-N and TN decreased from 15.52-19.16 mg·L[-1] and 20.21-19.58 mg·L[-1] in 2011 to 1.93-2.66 mg·L[-1] and 5.66-6.79 mg·L[-1] in 2018. Moreover, dissolved oxygen (DO) and NH4[+]-N concentrations in the Wenyu River and its tributaries, the Qinghe River, almost met requirements of their water function zoning target. Corresponding with the water quality improvement, the phytoplankton and community species increased dramatically. Phytoplankton species increased from 6 to 8 phyla, as well as community species. The dominant species changed from Chlorophyta in 2006 to the Cyanophyta in 2011, then to Bacillariophyta in 2018. The Shannon-Wiener diversity index (H') and evenness Pielou index (J) had improved. However, the major dominant species such as Cyclotella and Melosira persisted, and the Wenyu River was still in the eutrophication state in 2018. Statistical analysis results indicated that Cyanophyta, Bacillariophyta, and other algae abundance were significantly correlated with DO, pH, NH4[+]-N, TN, and TP.}, } @article {pmid32602435, year = {2020}, author = {Zhao, X and Thanapongtharm, W and Lawawirojwong, S and Wei, C and Tang, Y and Zhou, Y and Sun, X and Cui, L and Sattabongkot, J and Kaewkungwal, J}, title = {Malaria Risk Map Using Spatial Multi-Criteria Decision Analysis along Yunnan Border During the Pre-elimination Period.}, journal = {The American journal of tropical medicine and hygiene}, volume = {103}, number = {2}, pages = {793-809}, pmid = {32602435}, issn = {1476-1645}, support = {U19 AI089672/AI/NIAID NIH HHS/United States ; }, mesh = {*Agriculture ; *Altitude ; China/epidemiology ; *Climate ; Communicable Diseases, Imported/*epidemiology ; Decision Support Techniques ; Disease Eradication ; *Forests ; *Geographic Mapping ; Health Facilities ; Humans ; Malaria/*epidemiology/prevention & control ; Myanmar/epidemiology ; *Population Density ; Risk ; Rivers ; Spatio-Temporal Analysis ; *Urbanization ; }, abstract = {In moving toward malaria elimination, finer scale malaria risk maps are required to identify hotspots for implementing surveillance-response activities, allocating resources, and preparing health facilities based on the needs and necessities at each specific area. This study aimed to demonstrate the use of multi-criteria decision analysis (MCDA) in conjunction with geographic information systems (GISs) to create a spatial model and risk maps by integrating satellite remote-sensing and malaria surveillance data from 18 counties of Yunnan Province along the China-Myanmar border. The MCDA composite and annual models and risk maps were created from the consensus among the experts who have been working and know situations in the study areas. The experts identified and provided relative factor weights for nine socioeconomic and disease ecology factors as a weighted linear combination model of the following: ([Forest coverage × 0.041] + [Cropland × 0.086] + [Water body × 0.175] + [Elevation × 0.297] + [Human population density × 0.043] + [Imported case × 0.258] + [Distance to road × 0.030] + [Distance to health facility × 0.033] + [Urbanization × 0.036]). The expert-based model had a good prediction capacity with a high area under curve. The study has demonstrated the novel integrated use of spatial MCDA which combines multiple environmental factors in estimating disease risk by using decision rules derived from existing knowledge or hypothesized understanding of the risk factors via diverse quantitative and qualitative criteria using both data-driven and qualitative indicators from the experts. The model and fine MCDA risk map developed in this study could assist in focusing the elimination efforts in the specifically identified locations with high risks.}, } @article {pmid32602052, year = {2021}, author = {Li, M and Zhao, Y and Tian, X and Liu, P and Xie, J and Dong, N and Feng, J and Gao, Y and Fan, Y and Qiu, Y and Tian, F and Yan, X}, title = {Fluoride Exposure and Blood Pressure: a Systematic Review and Meta-Analysis.}, journal = {Biological trace element research}, volume = {199}, number = {3}, pages = {925-934}, pmid = {32602052}, issn = {1559-0720}, support = {201701D211008//the Outstanding Youth Science Foundation of Shanxi Province/ ; 2017-058//Shanxi Scholarship Council of China/ ; BS03201647//the PhD Start-up Fund of Shanxi Medical University/ ; 201801D121312//the Natural Science Foundation of Shanxi/ ; 201901D211327//the Youth Science and Technology Research Foundation of Shanxi Province/ ; }, mesh = {Blood Pressure ; China ; Databases, Factual ; *Fluorides/toxicity ; Humans ; *Hypertension/chemically induced ; }, abstract = {Fluoride exposure may cause changes in blood pressure, but this conclusion is controversial. Therefore, this meta-analysis aims to investigate the potential relationship between fluoride exposure and blood pressure or hypertension. PubMed, Web of Science, China National Knowledge Infrastructure (CNKI), WANFANG MED ONLINE, and Chinese Scientific Journals Full-Text Databases (VIP) were searched; in addition, two related studies were added manually. In total, 7 observational studies were identified, the pooled odds ratios (ORs) for hypertension between high and reference fluoride exposure groups were calculated, and the pooled standardized weighted mean difference (SMD) of systolic blood pressure (SBP) and diastolic blood pressure (DBP) was estimated using an inverse-variance weighted random-effects model; next, sensitivity analysis and subgroup analysis were used to assess potential sources of heterogeneity; furthermore, publication bias was assessed using the Begg and Egger test. In brief, there were no statistical differences between exposure groups and control groups in terms of blood pressure or hypertension when all included studies considered. However, subgroup analysis indicated that blood pressure will rise with the increase of fluoride exposure concentrations in endemic fluorosis areas. The corresponding pooled SMD estimates were 0.31 (95% CI 0.11, 0.51) and 0.27 (95% CI 0.11, 0.43) for SBP and DBP. Funnel plots suggested no asymmetry. Our findings support the possibility of a positive correlation between fluoride exposure and blood pressure in endemic fluorosis areas. Additional evidence is needed to assess the dose-response relationship between fluoride exposure and blood pressure.}, } @article {pmid32601290, year = {2020}, author = {Stratmann, T and van Oevelen, D and Martínez Arbizu, P and Wei, CL and Liao, JX and Cusson, M and Scrosati, RA and Archambault, P and Snelgrove, PVR and Ramey-Balci, PA and Burd, BJ and Kenchington, E and Gilkinson, K and Belley, R and Soetaert, K}, title = {The BenBioDen database, a global database for meio-, macro- and megabenthic biomass and densities.}, journal = {Scientific data}, volume = {7}, number = {1}, pages = {206}, pmid = {32601290}, issn = {2052-4463}, support = {678760//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/International ; NWO-ALW grant 856.18.003//Nederlandse Organisatie voor Wetenschappelijk Onderzoek (Netherlands Organisation for Scientific Research)/International ; 019.182EN.012//Nederlandse Organisatie voor Wetenschappelijk Onderzoek (Netherlands Organisation for Scientific Research)/International ; 864.13.007//Nederlandse Organisatie voor Wetenschappelijk Onderzoek (Netherlands Organisation for Scientific Research)/International ; }, mesh = {Animals ; Aquatic Organisms ; *Biomass ; *Biota ; *Databases, Factual ; Oceans and Seas ; }, abstract = {Benthic fauna refers to all fauna that live in or on the seafloor, which researchers typically divide into size classes meiobenthos (32/64 µm-0.5/1 mm), macrobenthos (250 µm-1 cm), and megabenthos (>1 cm). Benthic fauna play important roles in bioturbation activity, mineralization of organic matter, and in marine food webs. Evaluating their role in these ecosystem functions requires knowledge of their global distribution and biomass. We therefore established the BenBioDen database, the largest open-access database for marine benthic biomass and density data compiled so far. In total, it includes 11,792 georeferenced benthic biomass and 51,559 benthic density records from 384 and 600 studies, respectively. We selected all references following the procedure for systematic reviews and meta-analyses, and report biomass records as grams of wet mass, dry mass, or ash-free dry mass, or carbon per m[2] and as abundance records as individuals per m[2]. This database provides a point of reference for future studies on the distribution and biomass of benthic fauna.}, } @article {pmid32599781, year = {2020}, author = {Avila-Jimenez, ML and Burns, G and He, Z and Zhou, J and Hodson, A and Avila-Jimenez, JL and Pearce, D}, title = {Functional Associations and Resilience in Microbial Communities.}, journal = {Microorganisms}, volume = {8}, number = {6}, pages = {}, pmid = {32599781}, issn = {2076-2607}, abstract = {Microbial communities have inherently high levels of metabolic flexibility and functional redundancy, yet the structure of microbial communities can change rapidly with environmental perturbation. To understand whether such changes observed at the taxonomic level translate into differences at the functional level, we analyzed the structure of taxonomic and functional gene distribution across Arctic and Antarctic locations. Taxonomic diversity (in terms of alpha diversity and species richness) differed significantly with location. However, we found that functional genes distributed evenly across bacterial networks and that this functional distribution was also even across different geographic locations. For example, on average 15% of the functional genes were related to carbon cycling across all bacterial networks, slightly over 21% of the genes were stress-related and only 0.5% of the genes were linked to carbon degradation functions. In such a distribution, each bacterial network includes all of the functional groups distributed following the same proportions. However, the total number of functional genes that is included in each bacterial network differs, with some clusters including many more genes than others. We found that the proportion of times a specific gene must occur to be linked to a specific cluster is 8%, meaning the relationship between the total number of genes in the cluster and the number of genes per function follows a linear pattern: smaller clusters require a gene to appear less frequently to get fixed within the cluster, while larger clusters require higher gene frequencies. We suggest that this mechanism of functional association between equally rare or equally abundant genes could have implications for ecological resilience, as non-dominant genes also associate in fully functioning ecological networks, potentially suggesting that there are always pre-existing functional networks available to exploit new ecological niches (where they can become dominant) as they emerge; for example, in the case of rapid or sudden environmental change. Furthermore, this pattern did not correlate with taxonomic distribution, suggesting that bacteria associate based on functionality and this is independent of its taxonomic position. Our analyses based on ecological networks also showed no clear evidence of recent environmental impact on polar marine microbial communities at the functional level, unless all communities analyzed have changed exactly in the same direction and intensity, which is unlikely given we are comparing areas changing at different rates.}, } @article {pmid32595183, year = {2021}, author = {Murata, S and Takegami, M and Onozuka, D and Nakaoku, Y and Hagihara, A and Nishimura, K}, title = {Incidence and Mortality of Dementia-Related Missing and Their Associated Factors: An Ecological Study in Japan.}, journal = {Journal of epidemiology}, volume = {31}, number = {6}, pages = {361-368}, pmid = {32595183}, issn = {1349-9092}, mesh = {Adult ; Aged ; Aged, 80 and over ; Databases, Factual ; Dementia/*epidemiology/*mortality/psychology ; Female ; Humans ; Incidence ; Japan/epidemiology ; Male ; Middle Aged ; Police ; Risk Factors ; Wandering Behavior ; }, abstract = {BACKGROUND: Dementia-related missing and subsequent deaths are becoming serious problems with increases in people with dementia. However, there are no sufficient studies investigating the incidence rate, the mortality rate, and their risk factors.

METHODS: An ecological study aggregated at the Japanese prefectural level was conducted. Dementia-related missing persons cases and deaths in 2018 were extracted from the statistics of the National Police Agency in Japan. We extracted variables about older adults' characteristics, care, and safety as candidate variables considered to be relevant to dementia-related missing persons cases and deaths. Associations of the candidate variables with the incidence and mortality rates were analyzed using the generalized linear model (family: quasi-poisson, link: log) adjusted for confounding factors (proportion of older adults and gross prefectural product).

RESULTS: The incidence rate and mortality rate per 100,000 person-year was 21.72 and 0.652 in Japan, respectively. One facility increase in the number of nursing care facilities for older adults per 100,000 persons aged 65-years-old or more was associated with a 7.9% (95% confidence interval [CI], 3.3-12.4%) decrease in the incidence rate. One increase in the number of public health nurses per 100,000 persons was associated with a 3.2% (95% CI, 1.6-4.9%) decrease in the incidence rate. A ten percent increase in the proportion of people who live in an urban area was associated with a 20.3% (95% CI, 8.7-33.2%) increase in the incidence rate and a 12.9% (95% CI, 5.6-19.8%) decrease in the mortality rate.

CONCLUSIONS: Identified associated factors may be useful for managing or predicting dementia-related missing persons cases and associated deaths.}, } @article {pmid32592073, year = {2020}, author = {Ribeiro, P and Jordana, X and Scheirs, S and Ortega-Sánchez, M and Rodriguez-Baeza, A and McGlynn, H and Galtés, I}, title = {Distinction between perimortem and postmortem fractures in human cranial bone.}, journal = {International journal of legal medicine}, volume = {134}, number = {5}, pages = {1765-1774}, pmid = {32592073}, issn = {1437-1596}, support = {SGR14-1420//Conselleria d'Educació, Investigació, Cultura i Esport/ ; }, mesh = {Adult ; Aged ; Algorithms ; Decision Trees ; Female ; Forensic Medicine/*methods ; Humans ; Male ; Middle Aged ; Postmortem Changes ; Skull/*injuries ; Skull Fractures/*pathology ; }, abstract = {Timing of cranial trauma is challenging in forensic cases and literature on the subject is scarce. This study analysed the macroscopic fracture patterns of perimortem cranial fractures and compared them to experimentally reproduced cranial fractures on dry human craniums. The results showed nine traits associated with fresh cranial fractures: undulated margin, flake defects, peels with peel defects, fissures, crushed margins, bridge, bone scales and beveling. All the traits appear on the outer table or on the inner table of the cranium. Although not all characteristics must be present at the same time in all cranial fractures, they do define a new perimortem fracture pattern. Statistical analyses showed that six of these traits (undulated margins, flake defects, crushed margins, bone scales, fissures and peels) are distinctly related with perimortem (fresh) bone conditions. Considering the most discriminant perimortem traits, a decision-making algorithm is developed as a probabilistic approach to distinguish peri- from postmortem cranial fractures with an accuracy of 87%. This algorithm allows the forensic practitioner to incorporate more confidence during cranial trauma evaluation.}, } @article {pmid32590046, year = {2020}, author = {Chan, KO and Hutter, CR and Wood, PL and Grismer, LL and Brown, RM}, title = {Larger, unfiltered datasets are more effective at resolving phylogenetic conflict: Introns, exons, and UCEs resolve ambiguities in Golden-backed frogs (Anura: Ranidae; genus Hylarana).}, journal = {Molecular phylogenetics and evolution}, volume = {151}, number = {}, pages = {106899}, doi = {10.1016/j.ympev.2020.106899}, pmid = {32590046}, issn = {1095-9513}, mesh = {Animals ; Anura/*classification/*genetics ; Conserved Sequence/*genetics ; *Databases, Genetic ; Exons/*genetics ; Introns/*genetics ; Likelihood Functions ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Species Specificity ; }, abstract = {Using FrogCap, a recently-developed sequence-capture protocol, we obtained >12,000 highly informative exons, introns, and ultraconserved elements (UCEs), which we used to illustrate variation in evolutionary histories of these classes of markers, and to resolve long-standing systematic problems in Southeast Asian Golden-backed frogs of the genus-complex Hylarana. We also performed a comprehensive suite of analyses to assess the relative performance of different genetic markers, data filtering strategies, tree inference methods, and different measures of branch support. To reduce gene tree estimation error, we filtered the data using different thresholds of taxon completeness (missing data) and parsimony informative sites (PIS). We then estimated species trees using concatenated datasets and Maximum Likelihood (IQ-TREE) in addition to summary (ASTRAL-III), distance-based (ASTRID), and site-based (SVDQuartets) multispecies coalescent methods. Topological congruence and branch support were examined using traditional bootstrap, local posterior probabilities, gene concordance factors, quartet frequencies, and quartet scores. Our results did not yield a single concordant topology. Instead, introns, exons, and UCEs clearly possessed different phylogenetic signals, resulting in conflicting, yet strongly-supported phylogenetic estimates. However, a combined analysis comprising the most informative introns, exons, and UCEs converged on a similar topology across all analyses, with the exception of SVDQuartets. Bootstrap values were consistently high despite high levels of incongruence and high proportions of gene trees supporting conflicting topologies. Although low bootstrap values did indicate low heuristic support, high bootstrap support did not necessarily reflect congruence or support for the correct topology. This study reiterates findings of some previous studies, which demonstrated that traditional bootstrap values can produce positively misleading measures of support in large phylogenomic datasets. We also showed a remarkably strong positive relationship between branch length and topological congruence across all datasets, implying that very short internodes remain a challenge to resolve, even with orders of magnitude more data than ever before. Overall, our results demonstrate that more data from unfiltered or combined datasets produced superior results. Although data filtering reduced gene tree incongruence, decreased amounts of data also biased phylogenetic estimation. A point of diminishing returns was evident, at which higher congruence (from more stringent filtering) at the expense of amount of data led to topological error as assessed by comparison to more complete datasets across different genomic markers. Additionally, we showed that applying a parameter-rich model to a partitioned analysis of concatenated data produces better results compared to unpartitioned, or even partitioned analysis using model selection. Despite some lingering uncertainties, a combined analysis of our genomic data and sequences supplemented from GenBank (on the basis of a few gene regions) revealed highly supported novel systematic arrangements. Based on these new findings, we transfer Amnirana nicobariensis into the genus Indosylvirana; and I. milleti and Hylarana celebensis to the genus Papurana. We also provisionally place H. attigua in the genus Papurana pending verification from positively identified (voucher substantiated) samples.}, } @article {pmid32589224, year = {2021}, author = {Perla, RJ and Provost, SM and Parry, GJ and Little, K and Provost, LP}, title = {Understanding variation in reported covid-19 deaths with a novel Shewhart chart application.}, journal = {International journal for quality in health care : journal of the International Society for Quality in Health Care}, volume = {33}, number = {1}, pages = {}, pmid = {32589224}, issn = {1464-3677}, mesh = {*Audiovisual Aids ; COVID-19/*mortality ; Computer Simulation ; Data Interpretation, Statistical ; *Epidemiologic Methods ; Humans ; Pandemics ; SARS-CoV-2 ; }, abstract = {OBJECTIVE: Motivated by the coronavirus disease 2019 (covid-19) pandemic, we developed a novel Shewhart chart to visualize and learn from variation in reported deaths in an epidemic.

CONTEXT: Without a method to understand if a day-to-day variation in outcomes may be attributed to meaningful signals of change-rather than variability we would expect-care providers, improvement leaders, policy-makers, and the public will struggle to recognize if epidemic conditions are improving.

METHODS: We developed a novel hybrid C-chart and I-chart to detect within a geographic area the start and end of exponential growth in reported deaths. Reported deaths were the unit of analysis owing to erratic reporting of cases from variability in local testing strategies. We used simulation and case studies to assess chart performance and define technical parameters. This approach also applies to other critical measures related to a pandemic when high-quality data are available.

CONCLUSIONS: The hybrid chart detected the start of exponential growth and identified early signals that the growth phase was ending. During a pandemic, timely reliable signals that an epidemic is waxing or waning may have mortal implications. This novel chart offers a practical tool, accessible to system leaders and frontline teams, to visualize and learn from daily reported deaths during an epidemic. Without Shewhart charts and, more broadly, a theory of variation in our epidemiological arsenal, we lack a scientific method for a real-time assessment of local conditions. Shewhart charts should become a standard method for learning from data in the context of a pandemic or epidemic.}, } @article {pmid32587630, year = {2020}, author = {Nematolahi, S and Nazari, S and Shayan, Z and Ayatollahi, SMT and Amanati, A}, title = {Improved Kaplan-Meier Estimator in Survival Analysis Based on Partially Rank-Ordered Set Samples.}, journal = {Computational and mathematical methods in medicine}, volume = {2020}, number = {}, pages = {7827434}, pmid = {32587630}, issn = {1748-6718}, mesh = {Algorithms ; Child ; Computational Biology ; Computer Simulation ; Databases, Factual/statistics & numerical data ; Hematologic Neoplasms/mortality ; Humans ; *Kaplan-Meier Estimate ; Mathematical Concepts ; Models, Statistical ; Probability ; Sampling Studies ; Statistics, Nonparametric ; *Survival Analysis ; }, abstract = {This study presents a novel methodology to investigate the nonparametric estimation of a survival probability under random censoring time using the ranked observations from a Partially Rank-Ordered Set (PROS) sampling design and employs it in a hematological disorder study. The PROS sampling design has numerous applications in medicine, social sciences and ecology where the exact measurement of the sampling units is costly; however, sampling units can be ordered by using judgment ranking or available concomitant information. The general estimation methods are not directly applicable to the case where samples are from rank-based sampling designs, because the sampling units do not meet the identically distributed assumption. We derive asymptotic distribution of a Kaplan-Meier (KM) estimator under PROS sampling design. Finally, we compare the performance of the suggested estimators via several simulation studies and apply the proposed methods to a real data set. The results show that the proposed estimator under rank-based sampling designs outperforms its counterpart in a simple random sample (SRS).}, } @article {pmid32586012, year = {2020}, author = {Zhou, Y and Rodriguez, J and Fisher, N and Catullo, RA}, title = {Ecological Drivers and Sex-Based Variation in Body Size and Shape in the Queensland Fruit Fly, Bactrocera tryoni (Diptera: Tephritidae).}, journal = {Insects}, volume = {11}, number = {6}, pages = {}, pmid = {32586012}, issn = {2075-4450}, abstract = {The Queensland fruit fly (Bactrocera tryoni; Q-fly) is an Australian endemic horticultural pest species, which has caused enormous economic losses. It has the potential to expand its range to currently Q-fly-free areas and poses a serious threat to the Australian horticultural industry. A large number of studies have investigated the correlation between environmental factors and Q-fly development, reproduction, and expansion. However, it is still not clear how Q-fly morphological traits vary with the environment. Our study focused on three morphological traits (body size, wing shape, and fluctuating asymmetry) in Q-fly samples collected from 1955 to 1965. We assessed how these traits vary by sex, and in response to latitude, environmental variables, and geographic distance. First, we found sexual dimorphism in body size and wing shape, but not in fluctuating asymmetry. Females had a larger body size but shorter and wider wings than males, which may be due to reproductive and/or locomotion differences between females and males. Secondly, the body size of Q-flies varied with latitude, which conforms to Bergmann's rule. Finally, we found Q-fly wing shape was more closely related to temperature rather than aridity, and low temperature and high aridity may lead to high asymmetry in Q-fly populations.}, } @article {pmid32585540, year = {2020}, author = {Sørensen, SN and Wigger, H and Zabeo, A and Semenzin, E and Hristozov, D and Nowack, B and Spurgeon, DJ and Baun, A}, title = {Comparison of species sensitivity distribution modeling approaches for environmental risk assessment of nanomaterials - A case study for silver and titanium dioxide representative materials.}, journal = {Aquatic toxicology (Amsterdam, Netherlands)}, volume = {225}, number = {}, pages = {105543}, doi = {10.1016/j.aquatox.2020.105543}, pmid = {32585540}, issn = {1879-1514}, mesh = {Ecosystem ; Fresh Water/chemistry ; Nanostructures/*toxicity ; Reproducibility of Results ; Risk Assessment ; Silver/toxicity ; Titanium/toxicity ; Toxicity Tests/*methods ; Water Pollutants, Chemical/*toxicity ; }, abstract = {Species sensitivity distributions (SSDs) are used in chemical safety assessments to derive predicted-no-effect-concentrations (PNECs) for substances with a sufficient amount of relevant and reliable ecotoxicity data available. For engineered nanomaterials (ENMs), ecotoxicity data are often compromised by poor reproducibility and the lack of nano-specific characterization needed describe an ENM under test exposure conditions. This may influence the outcome of SSD modelling and hence the regulatory decision-making. This study investigates how the outcome of SSD modelling is influenced by: 1) Selecting input data based on the nano-specific "nanoCRED" reliability criteria, 2) Direct SSD modelling avoiding extrapolation of data by including long-term/chronic NOECs only, and 3) Weighting data according to their nano-specific quality, the number of data available for each species, and the trophic level abundance in the ecosystem. Endpoints from freshwater ecotoxicity studies were collected for the representative nanomaterials NM-300 K (silver) and NM-105 (titanium dioxide), evaluated for regulatory reliability and scored according to the level of nano-specific characterization conducted. The compiled datasets are unique in exclusively dealing with representative ENMs showing minimal batch-to-batch variation. The majority of studies were evaluated as regulatory reliable, while the degree of nano-specific characterization varied greatly. The datasets for NM-300 K and NM-105 were used as input to the nano-weighted n-SSWD model, the probabilistic PSSD+, and the conventional SSD Generator by the US EPA. The conventional SSD generally yielded the most conservative, but least precise HC5 values, with 95 % confidence intervals up to 100-fold wider than the other models. The inclusion of regulatory reliable data only, had little effect on the HC5 generated by the conventional SSD and the PSSD+, whereas the n-SSWD estimated different HC5 values based on data segregated according to reliability, especially for NM-105. The n-SSWD weighting of data significantly affected the estimated HC5 values, however in different ways for the sub-datasets of NM-300 K and NM-105. For NM-300 K, the inclusion of NOECs only in the weighted n-SSWD yielded the most conservative HC5 of all datasets and models (a HC5 based on NOECs only could not be estimated for NM-105, due to limited number of data). Overall, the estimated HC5 values of all models are within a relatively limited concentration range of 25-100 ng Ag/L for NM-300 K and 1-15 μgTiO2/L for NM-105.}, } @article {pmid32581278, year = {2020}, author = {Dörge, DD and Cunze, S and Schleifenbaum, H and Zaenker, S and Klimpel, S}, title = {An investigation of hibernating members from the Culex pipiens complex (Diptera, Culicidae) in subterranean habitats of central Germany.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {10276}, pmid = {32581278}, issn = {2045-2322}, mesh = {Animal Distribution ; Animals ; Caves ; Culex/*physiology ; Datasets as Topic ; Female ; Germany ; *Hibernation ; Male ; Mosquito Vectors/*physiology ; Rain ; Seasons ; Spatial Analysis ; Temperature ; }, abstract = {The Culex pipiens complex encompasses five species and subspecies of the genus Culex. Over time, a multitude of morphologically indistinguishable species has been assigned to this complex with several species being classified as important vectors for different diseases. Some species of this complex hibernate in subterranean habitats, and it has been proven that viruses can survive this phase of hibernation. However, studies focusing on the environmental requirements, ecology and spatial and temporal distribution patterns of mosquitos in underground habitats are sparse. Here, we investigate the main environmental factors and dependencies of Culex, considering the number of individuals and survival probabilities in underground habitats during the winter months. Methods. Since the State of Hesse, Germany harbors about 3500 to 4000 subterranean shelters ample availability of subterranean habitats there provides a good opportunity to conduct detailed investigations of the Culex pipiens complex. In this study, we identified a sample of 727 specimens of overwintering females within the Culex pipiens complex from 52 different underground sites collected over a period of 23 years using qPCR. A complete data set of samplings of hibernating mosquitos from 698 subterranean habitats in Central Germany over the same period was available to study the spatial and temporal patterns and the effect of temperature and precipitation conditions on these hibernating populations using a generalized linear model (GLM). Results. Our qPCR-results show, similar to aboveground studies of mosquitos, that Culex pipiens pipiens and Culex torrentium occur sympatrically. On the other hand, Culex pipiens molestus occurred very rarely. The GLM revealed no shifts in species composition over time, but different preferences for subterranean hibernacula, chemical effects on overwintering populations as well as effects of annual and seasonal mean temperature and precipitation during the active phase from March to November. Cx. p. pipiens and Cx. torrentium are the most common species within Hessian caves and other underground habitats during winter. They co-occur with different frequency without any patterns in species composition. Weather conditions influence the number of overwintering mosquitos during the activity phase. Depending on cave parameters, the number of mosquitos decreases during the winter months.}, } @article {pmid32577818, year = {2020}, author = {Li, H and Huang, X and Li, W and Lu, Y and Dai, X and Zhou, Z and Li, Q}, title = {MicroRNA comparison between poplar and larch provides insight into the different mechanism of wood formation.}, journal = {Plant cell reports}, volume = {39}, number = {9}, pages = {1199-1217}, doi = {10.1007/s00299-020-02559-3}, pmid = {32577818}, issn = {1432-203X}, support = {CAFYBB2017ZY001//Fundamental Research Funds of the Chinese Academy of Forestry/ ; }, mesh = {Arabidopsis/genetics ; Base Sequence ; Cellulose/genetics/metabolism ; Conserved Sequence ; Gene Expression Regulation, Plant ; Gene Ontology ; High-Throughput Nucleotide Sequencing ; Larix/*genetics ; Lignin/genetics/metabolism ; MicroRNAs/*genetics ; Phloem/genetics ; Plant Leaves/genetics ; Polysaccharides/genetics/metabolism ; Populus/*genetics ; Reproducibility of Results ; Wood/*genetics/growth & development/metabolism ; Xylem/genetics ; }, abstract = {MiRNA transcriptome analysis of different tissues in poplar and larch suggests variant roles of miRNAs in regulating wood formation between two kinds of phyla. Poplar and larch belong to two different phyla. Both are ecological woody species and major resources for wood-related industrial applications. However, wood properties are different between these two species and the molecular basis is largely unknown. In this study, we performed high-throughput sequencing of microRNAs (miRNAs) in the three tissues, xylem, phloem and leaf of Populus alba × Populus glandulosa and Larix kaempferi. Differentially expressed miRNA (DEmiRNA) analysis identified 85 xylem-specific miRNAs in P. alba × P. glandulosa and 158 xylem-specific miRNAs in L. kaempferi. Among 36 common miRNAs, 12 were conserved between the two species. GO and KEGG analyses of the miRNA target genes showed similar metabolism in two species. Through KEGG and BLASTN, we predicted target genes of xylem differentially expressed (DEmiRNA) in the wood formation-related pathways and located DEmiRNAs in these pathways. A network was built for wood formation-related DEmiRNAs, their target genes and orthologous genes in Arabidopsis thaliana. Comparison of DEmiRNA and target gene annotation between P. alba × P. glandulosa and L. kaempferi suggested the different functions of DEmiRNAs and divergent mechanism in wood formation between two species, providing knowledge to understand wood formation mechanism in gymnosperm and angiosperm woody plants.}, } @article {pmid32575966, year = {2020}, author = {Peixoto, MV and Duque, AM and Santos, AD and Lima, SVAM and Gonçalves, TP and Novais, APS and De Carvalho, S and Voci, SM and De Araujo, KCGM and Nunes, MAP}, title = {Spatial analysis of cerebral palsy in children and adolescents and its association with health vulnerability.}, journal = {Geospatial health}, volume = {15}, number = {1}, pages = {}, doi = {10.4081/gh.2020.817}, pmid = {32575966}, issn = {1970-7096}, mesh = {Brazil/epidemiology ; *Cerebral Palsy/epidemiology ; Child ; Child, Preschool ; Geographic Information Systems ; Humans ; Prevalence ; *Spatial Analysis ; Surveys and Questionnaires ; }, abstract = {Cerebral Palsy (CP) is commonly associated with low socioeconomic status. Use of spatial statistics and a Geographic Information Systems (GIS) are scarce and may contribute to the understanding of CP in a social context. To that end a spatial analysis of CP in children and adolescents was performed to analyze the association of CP with levels of vulnerability in a city (Aracaju, Sergipe) in north-eastern Brazil. In addition, an ecological study was conducted with data obtained from a populationbased survey and secondary data. Exploratory spatial data analysis and linear regression were used. A total of 288 CP cases were identified, with a prevalence of 1.65/1,000 and differences among city neighbourhoods ranging from 0-4/1,000. The mean age of cases studied was 9 years 1 month, with a standard deviation of 5 years 2 months. Most study subjects with cerebral palsy (163) were male (56.4%). The distribution of CP in the study population was not homogeneous throughout the territory. Some areas had clusters, with more cases associated with areas of high vulnerability. Spatial data analysis using GIS was useful to gain an epidemiological understanding of CP distribution that can guide decisionmaking with respect to production, distribution, and regulation of health goods as well as services at the local level.}, } @article {pmid32575443, year = {2020}, author = {Lötsch, J and Kringel, D and Geisslinger, G and Oertel, BG and Resch, E and Malkusch, S}, title = {Machine-Learned Association of Next-Generation Sequencing-Derived Variants in Thermosensitive Ion Channels Genes with Human Thermal Pain Sensitivity Phenotypes.}, journal = {International journal of molecular sciences}, volume = {21}, number = {12}, pages = {}, pmid = {32575443}, issn = {1422-0067}, support = {n/a//Landesoffensive zur Entwicklung wissenschaftlich-ökonomischer Exzellenz (LOEWE)/ ; n/a//Reproducible cleaning of biomedical laboratory data using methods of visualization, error correction and transformation implemented as interactive R-notebooks/ ; }, mesh = {Adult ; Computational Biology/*methods ; Female ; Genetic Association Studies ; Genetic Variation ; High-Throughput Nucleotide Sequencing ; Hot Temperature ; Humans ; Machine Learning ; Male ; Pain/etiology/*genetics ; Pain Threshold ; Phenotype ; TRPM Cation Channels/*genetics ; TRPV Cation Channels/*genetics ; Young Adult ; }, abstract = {Genetic association studies have shown their usefulness in assessing the role of ion channels in human thermal pain perception. We used machine learning to construct a complex phenotype from pain thresholds to thermal stimuli and associate it with the genetic information derived from the next-generation sequencing (NGS) of 15 ion channel genes which are involved in thermal perception, including ASIC1, ASIC2, ASIC3, ASIC4, TRPA1, TRPC1, TRPM2, TRPM3, TRPM4, TRPM5, TRPM8, TRPV1, TRPV2, TRPV3, and TRPV4. Phenotypic information was complete in 82 subjects and NGS genotypes were available in 67 subjects. A network of artificial neurons, implemented as emergent self-organizing maps, discovered two clusters characterized by high or low pain thresholds for heat and cold pain. A total of 1071 variants were discovered in the 15 ion channel genes. After feature selection, 80 genetic variants were retained for an association analysis based on machine learning. The measured performance of machine learning-mediated phenotype assignment based on this genetic information resulted in an area under the receiver operating characteristic curve of 77.2%, justifying a phenotype classification based on the genetic information. A further item categorization finally resulted in 38 genetic variants that contributed most to the phenotype assignment. Most of them (10) belonged to the TRPV3 gene, followed by TRPM3 (6). Therefore, the analysis successfully identified the particular importance of TRPV3 and TRPM3 for an average pain phenotype defined by the sensitivity to moderate thermal stimuli.}, } @article {pmid32572746, year = {2020}, author = {Tseng, ML and Chang, CH and Lin, CR and Wu, KJ and Chen, Q and Xia, L and Xue, B}, title = {Future trends and guidance for the triple bottom line and sustainability: a data driven bibliometric analysis.}, journal = {Environmental science and pollution research international}, volume = {27}, number = {27}, pages = {33543-33567}, pmid = {32572746}, issn = {1614-7499}, mesh = {*Bibliometrics ; Databases, Factual ; *Publications ; }, abstract = {This study conducts a comprehensive literature review of articles on the triple bottom line (TBL) published from January 1997 to September 2018 to provide significant insights and support to guide further discussion. There were three booms in TBL publications, occurring in 2003, 2011, and 2015, and many articles attempt to address the issue of sustainability by employing the TBL. This literature analysis includes 720, 132, and 58 articles from the Web of Science (WOS), Inspec, and Scopus databases, respectively, and reveals the gaps in existing research. To discover the barriers and points of overlap, these articles are categorized into six aspects of the TBL: economic, environmental, social, operations, technology, and engineering. Examining the top 3 journals in terms of published articles on each aspect reveals the research trends and gaps. The findings provide solid evidence confirming the argument that the TBL as currently defined is insufficient to cover the entire concept of sustainability. The social and engineering aspects still require more discussion to support the linkage of the TBL and to reinforce its theoretical basis. Additionally, to discover the gaps in the data sources, theories applied, methods adopted, and types of contributions, this article summarizes 82 highly cited articles covering each aspect. This article offers theoretical insights by identifying the top contributing countries, institutions, authors, keyword networks, and authorship networks to encourage scholars to push the current discussion further forward, and it provides practical insights to bridge the gap between theory and practice for enhancing the efficiency and effectiveness of improvements.}, } @article {pmid32572035, year = {2020}, author = {Cansler, CA and Hood, SM and Varner, JM and van Mantgem, PJ and Agne, MC and Andrus, RA and Ayres, MP and Ayres, BD and Bakker, JD and Battaglia, MA and Bentz, BJ and Breece, CR and Brown, JK and Cluck, DR and Coleman, TW and Corace, RG and Covington, WW and Cram, DS and Cronan, JB and Crouse, JE and Das, AJ and Davis, RS and Dickinson, DM and Fitzgerald, SA and Fulé, PZ and Ganio, LM and Grayson, LM and Halpern, CB and Hanula, JL and Harvey, BJ and Kevin Hiers, J and Huffman, DW and Keifer, M and Keyser, TL and Kobziar, LN and Kolb, TE and Kolden, CA and Kopper, KE and Kreitler, JR and Kreye, JK and Latimer, AM and Lerch, AP and Lombardero, MJ and McDaniel, VL and McHugh, CW and McMillin, JD and Moghaddas, JJ and O'Brien, JJ and Perrakis, DDB and Peterson, DW and Prichard, SJ and Progar, RA and Raffa, KF and Reinhardt, ED and Restaino, JC and Roccaforte, JP and Rogers, BM and Ryan, KC and Safford, HD and Santoro, AE and Shearman, TM and Shumate, AM and Sieg, CH and Smith, SL and Smith, RJ and Stephenson, NL and Stuever, M and Stevens, JT and Stoddard, MT and Thies, WG and Vaillant, NM and Weiss, SA and Westlind, DJ and Woolley, TJ and Wright, MC}, title = {The Fire and Tree Mortality Database, for empirical modeling of individual tree mortality after fire.}, journal = {Scientific data}, volume = {7}, number = {1}, pages = {194}, pmid = {32572035}, issn = {2052-4463}, mesh = {Databases as Topic ; *Fires ; *Forestry ; *Forests ; *Trees ; United States ; }, abstract = {Wildland fires have a multitude of ecological effects in forests, woodlands, and savannas across the globe. A major focus of past research has been on tree mortality from fire, as trees provide a vast range of biological services. We assembled a database of individual-tree records from prescribed fires and wildfires in the United States. The Fire and Tree Mortality (FTM) database includes records from 164,293 individual trees with records of fire injury (crown scorch, bole char, etc.), tree diameter, and either mortality or top-kill up to ten years post-fire. Data span 142 species and 62 genera, from 409 fires occurring from 1981-2016. Additional variables such as insect attack are included when available. The FTM database can be used to evaluate individual fire-caused mortality models for pre-fire planning and post-fire decision support, to develop improved models, and to explore general patterns of individual fire-induced tree death. The database can also be used to identify knowledge gaps that could be addressed in future research.}, } @article {pmid32571915, year = {2020}, author = {Griffiths, JI and Wallet, P and Pflieger, LT and Stenehjem, D and Liu, X and Cosgrove, PA and Leggett, NA and McQuerry, JA and Shrestha, G and Rossetti, M and Sunga, G and Moos, PJ and Adler, FR and Chang, JT and Sharma, S and Bild, AH}, title = {Circulating immune cell phenotype dynamics reflect the strength of tumor-immune cell interactions in patients during immunotherapy.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {117}, number = {27}, pages = {16072-16082}, pmid = {32571915}, issn = {1091-6490}, support = {P30 CA042014/CA/NCI NIH HHS/United States ; U54 CA209978/CA/NCI NIH HHS/United States ; }, mesh = {Cell Communication/*immunology ; Gene Expression Regulation ; Humans ; Immunologic Factors/genetics/immunology ; Immunotherapy/*methods ; Monocytes/immunology ; Neoplasms/*immunology/*therapy ; *Phenotype ; Sequence Analysis, RNA ; Single-Cell Analysis ; T-Lymphocytes/immunology ; Tumor Microenvironment/*immunology ; }, abstract = {The extent to which immune cell phenotypes in the peripheral blood reflect within-tumor immune activity prior to and early in cancer therapy is unclear. To address this question, we studied the population dynamics of tumor and immune cells, and immune phenotypic changes, using clinical tumor and immune cell measurements and single-cell genomic analyses. These samples were serially obtained from a cohort of advanced gastrointestinal cancer patients enrolled in a trial with chemotherapy and immunotherapy. Using an ecological population model, fitted to clinical tumor burden and immune cell abundance data from each patient, we find evidence of a strong tumor-circulating immune cell interaction in responder patients but not in those patients that progress on treatment. Upon initiation of therapy, immune cell abundance increased rapidly in responsive patients, and once the peak level is reached tumor burden decreases, similar to models of predator-prey interactions; these dynamic patterns were absent in nonresponder patients. To interrogate phenotype dynamics of circulating immune cells, we performed single-cell RNA sequencing at serial time points during treatment. These data show that peripheral immune cell phenotypes were linked to the increased strength of patients' tumor-immune cell interaction, including increased cytotoxic differentiation and strong activation of interferon signaling in peripheral T cells in responder patients. Joint modeling of clinical and genomic data highlights the interactions between tumor and immune cell populations and reveals how variation in patient responsiveness can be explained by differences in peripheral immune cell signaling and differentiation soon after the initiation of immunotherapy.}, } @article {pmid32571206, year = {2020}, author = {Paguem, A and Abanda, B and Achukwi, MD and Baskaran, P and Czemmel, S and Renz, A and Eisenbarth, A}, title = {Whole genome characterization of autochthonous Bos taurus brachyceros and introduced Bos indicus indicus cattle breeds in Cameroon regarding their adaptive phenotypic traits and pathogen resistance.}, journal = {BMC genetics}, volume = {21}, number = {1}, pages = {64}, pmid = {32571206}, issn = {1471-2156}, support = {F-2013BS522//Otto Bayer Foundation/International ; B/5864-1//International Foundation for Science (IFS); Stockholm, Sweden/International ; RE 1536/2//German Research Foundation/International ; PSP-no. 4041002616//the joint RiSC program of the State Ministry of Science, Research and Arts Baden-Württemberg and the University of Tübingen/International ; }, mesh = {Animals ; *Breeding ; Cameroon ; Cattle/*genetics ; Cattle Diseases/*genetics/parasitology ; Disease Resistance/*genetics ; Gene Ontology ; Phenotype ; Polymorphism, Single Nucleotide ; Whole Genome Sequencing/veterinary ; }, abstract = {BACKGROUND: African indigenous taurine cattle display unique adaptive traits shaped by husbandry management, regional climate and exposure to endemic pathogens. They are less productive with respect to milk and meat production which has been associated with amongst others, small size, traditional beliefs, husbandry practices, limited feed resources, disease burden and lack of sustained breeding for trait improvement. This resulted in the severe dwindling of their population size rendering them vulnerable to extinction. The Namchi taurine cattle breed is referred to as [Namchi (Doayo)] and shows resistance traits against trypanosome infection and exposure to tick infestation. Nonetheless, the historically later introduced Zebu cattle are the main cattle breeds in Africa today, even though they suffer more from locally prevailing pathogens. By using a whole genome sequencing approach, we sequenced with high depth for the first time the genomes of five cattle breeds from Cameroon in order to provide a valuable genetic resource for future African cattle breeding: the Namchi, an endangered trypano-tolerant taurine breed, the Kapsiki, an indigenous trypano-susceptible taurine breed, and three Zebu (Bos indicus indicus) breeds: Ngaoundere Gudali, White Fulani and Red Fulani.

RESULTS: Approximately 167 Gigabases of raw sequencing data were generated for each breed and mapped to the cattle reference genomes ARS-UCD1.2 and UMD3.1.The coverage was 103 to 140-fold when aligning the reads to ARS-UCD1.2 with an average mapping rate of ~ 99%, and 22 to 30-fold when aligning the reads to UMD3.1 with an average mapping rate of ~ 64%. The single nucleotide polymorphisms (SNPs) obtained from analysis using the genome ARS-UCD1.2 were compared with reference genomes of European Bos taurus Holstein, the Asian Bos indicus Brahman, and the African trypanotolerant N'Dama breeds. A total of ~ 100 million (M) SNPs were identified and 7.7 M of those were breed-specific. An approximately 11.1 M constituted of small insertions and deletions. By using only breed-specific non-synonymous variants we identified genes as genetic signatures and associated Gene Ontology (GO) terms that could explain certain cattle-breed specific phenotypes such as increased tolerance against trypanosome parasites in the Namchi breed and heat tolerance in the Kapsiki breed. Phylogenetic analysis grouped, except for Namchi, the Bos taurus breeds Kapsiki, N'Dama and Holstein together while the B. indicus breeds White and Red Fulani, Gudali and Brahman clustered separately. The deviating result for Namchi indicates a hybrid status of the selected animal with a recent introgression of Zebu genes into its genome.

CONCLUSIONS: The findings provide the first comprehensive set of genome-wide variant data of the most important Cameroonian cattle breeds. The genomic data shall constitute a foundation for breed amelioration whilst exploiting the heritable traits and support conservation efforts for the endangered local cattle breeds.}, } @article {pmid32570064, year = {2020}, author = {Mi, J and Hou, H and Raval, S and Yang, Y and Zhang, S and Hua, Y and Wang, C and Chen, F}, title = {Effect of crop cultivation on the soil carbon stock in mine dumps of the Loess Plateau, China.}, journal = {The Science of the total environment}, volume = {741}, number = {}, pages = {139809}, doi = {10.1016/j.scitotenv.2020.139809}, pmid = {32570064}, issn = {1879-1026}, abstract = {In the ecological restoration of mine dumps, soil carbon stock (SCS) improvement is an important issue. The type of land use and management approach taken can have a great influence on this issue. On the Loess Plateau, different crops have been cultivated on reclaimed land; however, the effect of long-term crop cultivation on SCS is poorly understood. To address this issue, a field investigation of mine dumps was performed at the Kee Open Pit Mine in Shanxi Province, China. Four sites utilizing different land management methods were analyzed: no reclamation (NR), reclamation with no crop cultivation (NC), and reclamation followed by 11 or 27 years crop cultivation (RC-11 and RC-27, respectively). SCS, associated soil properties (total nitrogen (TN), total phosphorus (TP), total potassium (TK), moisture content (MoiC), and pH), plant community (species composition, plant diversity, and traits), and microbial community operational taxonomic units (OTUs) of fungi and bacteria were determined by field investigation and laboratory analysis. Redundancy analysis was used to show the relationship between SCS and other environmental variables. Results varied by soil depth. At the depth range of 0-20 cm, the SCS of RC-11 was significantly greater compared to that in NR and NC, by 14.64- and 2.25-fold, respectively; whereas compared to RC-27, it was higher by 52.78%. At the depth of 20-40 cm, NC has the largest SCS; the SCS of RC-27 was the lowest, which was less compared to that in NC by 43.64%. Redundancy analysis showed a positive relationship between the SCS and TN, TP, MoiC, as well as average plant coverage, while the bacterial OTUs were negatively related with the SCS. This research suggests the potential of mine dumps for crop cultivation, which could improve the SCS of the mining area on the Loess Plateau.}, } @article {pmid32566672, year = {2020}, author = {Wang, C and Zhang, Y and Han, S}, title = {Its2vec: Fungal Species Identification Using Sequence Embedding and Random Forest Classification.}, journal = {BioMed research international}, volume = {2020}, number = {}, pages = {2468789}, pmid = {32566672}, issn = {2314-6141}, mesh = {Algorithms ; Computational Biology/*methods ; DNA Barcoding, Taxonomic/*methods ; *DNA, Fungal/classification/genetics ; *Fungi/classification/genetics ; *Machine Learning ; Software ; }, abstract = {Fungi play essential roles in many ecological processes, and taxonomic classification is fundamental for microbial community characterization and vital for the study and preservation of fungal biodiversity. To cope with massive fungal barcode data, tools that can implement extensive volumes of barcode sequences, especially the internal transcribed spacer (ITS) region, are necessary. However, high variation in the ITS region and computational requirements for processing high-dimensional features remain challenging for existing predictors. In this study, we developed Its2vec, a bioinformatics tool for the classification of fungal ITS barcodes to the species level. An ITS database covering more than 25,000 species in a broad range of fungal taxa was assembled. For dimensionality reduction, a word embedding algorithm was used to represent an ITS sequence as a dense low-dimensional vector. A random forest-based classifier was built for species identification. Benchmarking results showed that our model achieved an accuracy comparable to that of several state-of-the-art predictors, and more importantly, it could implement large datasets and greatly reduce dimensionality. We expect the Its2vec model to be helpful for fungal species identification and, thus, for revealing microbial community structures and in deepening our understanding of their functional mechanisms.}, } @article {pmid32564312, year = {2021}, author = {Akbar, U and Li, QL and Akmal, MA and Shakib, M and Iqbal, W}, title = {Nexus between agro-ecological efficiency and carbon emission transfer: evidence from China.}, journal = {Environmental science and pollution research international}, volume = {28}, number = {15}, pages = {18995-19007}, pmid = {32564312}, issn = {1614-7499}, mesh = {Agriculture ; *Carbon/analysis ; China ; Coal ; Humans ; *Industry ; }, abstract = {The economy of China is growing rapidly. With this overwhelming growth, the country is experiencing a higher level of carbon emissions. Amid this backdrop, China is under immense pressure to reduce carbon emissions up to a sustainable level. This study adapted 31 provincial panel data from 2007 to 2017 using factor analysis system SBM-undesirable model to calculate the agro-ecological output of each province respectively and used a carbon transfer network impact analysis panel to calculate ecological performance impacts. Results show that (1) overall agro-ecological efficiency in China shows an upward trend but regional differences are evident. The efficiency in the eastern region is higher than that in the central and western regions but the extent of informatization in the central region is higher than that in the western region. (2) Informatization will significantly promote agro-ecological efficiency. (3) Changes in agricultural planting structure, agricultural value-added per capita, employment of human capital in the agricultural sector, and agricultural scale management are also important factors affecting agro-ecological growth. (4) China's amount of carbon transfer is growing year by year, and energy-intensive areas and heavy industry bases are undertaking carbon transfer from the eastern coastal regions; (5) Jiangsu, Henan, and Hebei (Hubei) have the highest centers between 2007 and 2012; (6) inter-provincial carbon transmission is concentrated mainly in the metal smelting and rolling processing industries as well as in the coal, heat, and supply industries.}, } @article {pmid32562821, year = {2020}, author = {Bombonato, JR and do Amaral, DT and Silva, GAR and Khan, G and Moraes, EM and da Silva Andrade, SC and Eaton, DAR and Alonso, DP and Ribolla, PEM and Taylor, N and Zappi, D and Franco, FF}, title = {The potential of genome-wide RAD sequences for resolving rapid radiations: a case study in Cactaceae.}, journal = {Molecular phylogenetics and evolution}, volume = {151}, number = {}, pages = {106896}, doi = {10.1016/j.ympev.2020.106896}, pmid = {32562821}, issn = {1095-9513}, mesh = {Base Sequence ; *Biological Evolution ; Cactaceae/*genetics ; Databases, Genetic ; Genetic Loci ; Genetic Speciation ; *Genome, Plant ; Likelihood Functions ; Phylogeny ; Polymorphism, Single Nucleotide/genetics ; Principal Component Analysis ; *Sequence Analysis, DNA ; }, abstract = {The reconstruction of relationships within recently radiated groups is challenging even when massive amounts of sequencing data are available. The use of restriction site-associated DNA sequencing (RAD-Seq) to this end is promising. Here, we assessed the performance of RAD-Seq to infer the species-level phylogeny of the rapidly radiating genus Cereus (Cactaceae). To examine how the amount of genomic data affects resolution in this group, we used datasets and implemented different analyses. We sampled 52 individuals of Cereus, representing 18 of the 25 species currently recognized, plus members of the closely allied genera Cipocereus and Praecereus, and other 11 Cactaceae genera as outgroups. Three scenarios of permissiveness to missing data were carried out in iPyRAD, assembling datasets with 30% (333 loci), 45% (1440 loci), and 70% (6141 loci) of missing data. For each dataset, Maximum Likelihood (ML) trees were generated using two supermatrices, i.e., only SNPs and SNPs plus invariant sites. Accuracy and resolution were improved when the dataset with the highest number of loci was used (6141 loci), despite the high percentage of missing data included (70%). Coalescent trees estimated using SVDQuartets and ASTRAL are similar to those obtained by the ML reconstructions. Overall, we reconstruct a well-supported phylogeny of Cereus, which is resolved as monophyletic and composed of four main clades with high support in their internal relationships. Our findings also provide insights into the impact of missing data for phylogeny reconstruction using RAD loci.}, } @article {pmid32562000, year = {2020}, author = {Baes, R and Lemmens, L and Mignon, K and Carlier, M and Peeters, E}, title = {Defining heat shock response for the thermoacidophilic model crenarchaeon Sulfolobus acidocaldarius.}, journal = {Extremophiles : life under extreme conditions}, volume = {24}, number = {5}, pages = {681-692}, pmid = {32562000}, issn = {1433-4909}, support = {1134419N//Fonds Wetenschappelijk Onderzoek/ ; 1526418N//Fonds Wetenschappelijk Onderzoek/ ; G021118//Fonds Wetenschappelijk Onderzoek/ ; }, mesh = {*Heat-Shock Response ; *Sulfolobus acidocaldarius ; Temperature ; }, abstract = {The crenarchaeon Sulfolobus acidocaldarius, growing optimally at temperatures between 75 and 80 °C, thrives in volcanic hot spring habitats that are typified by large temperature gradients, which impose frequent temperature stresses on the cells. Heat shock response is characterized by an upregulation of heat shock proteins, but similar to most (hyper-)thermophilic archaea, S. acidocaldarius seems to be able to bear supra-optimal temperatures with a restricted repertoire of chaperones. Here, we study the physiological consequences of continuous high-temperature stress and rapid heat shock for S. acidocaldarius. Growth experiments and cell viability assays demonstrate that temperatures of 85 °C and higher result in a decreased growth rate and, when the cells are rapidly subjected to a heat shock, a dynamic increase in mRNA levels of all relevant heat shock proteins and a subset of transcription regulators is observed. When exponentially growing cultures are exposed to a heat shock, the survival tipping point is situated around 90 °C, and the rate of heating determines whether cells are able to cope with this stress or whether the defense mechanism immediately fails, leading to extensive cell death. In conclusion, S. acidocaldarius does not seem to be better equipped to handle sudden supra-optimal temperature stress than mesophilic organisms.}, } @article {pmid32561737, year = {2020}, author = {Moreau, S and Boyd, PW and Strutton, PG}, title = {Remote assessment of the fate of phytoplankton in the Southern Ocean sea-ice zone.}, journal = {Nature communications}, volume = {11}, number = {1}, pages = {3108}, pmid = {32561737}, issn = {2041-1723}, mesh = {Algorithms ; Chlorophyll/analysis/metabolism ; Datasets as Topic ; Ecological Parameter Monitoring/instrumentation/*methods ; Eutrophication ; *Food Chain ; Herbivory ; Ice Cover/*microbiology ; Oceans and Seas ; Phytoplankton/*physiology ; Remote Sensing Technology/instrumentation/methods ; Seasons ; Seawater/*microbiology ; Spatio-Temporal Analysis ; }, abstract = {In the Southern Ocean, large-scale phytoplankton blooms occur in open water and the sea-ice zone (SIZ). These blooms have a range of fates including physical advection, downward carbon export, or grazing. Here, we determine the magnitude, timing and spatial trends of the biogeochemical (export) and ecological (foodwebs) fates of phytoplankton, based on seven BGC-Argo floats spanning three years across the SIZ. We calculate loss terms using the production of chlorophyll-based on nitrate depletion-compared with measured chlorophyll. Export losses are estimated using conspicuous chlorophyll pulses at depth. By subtracting export losses, we calculate grazing-mediated losses. Herbivory accounts for ~90% of the annually-averaged losses (169 mg C m[-2] d[-1]), and phytodetritus POC export comprises ~10%. Furthermore, export and grazing losses each exhibit distinctive seasonality captured by all floats spanning 60°S to 69°S. These similar trends reveal widespread patterns in phytoplankton fate throughout the Southern Ocean SIZ.}, } @article {pmid32561119, year = {2020}, author = {Nyaga, MM and Sabiu, S and Ndze, VN and Dennis, FE and Jere, KC}, title = {Report of the 1st African Enteric Viruses Genome Initiative (AEVGI) Data and Bioinformatics Workshop on whole-genome analysis of some African rotavirus strains held in Bloemfontein, South Africa.}, journal = {Vaccine}, volume = {38}, number = {34}, pages = {5402-5407}, doi = {10.1016/j.vaccine.2020.06.010}, pmid = {32561119}, issn = {1873-2518}, support = {201945/Z/16/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Computational Biology ; Humans ; *Rotavirus/genetics ; *Rotavirus Infections/epidemiology ; *Rotavirus Vaccines ; South Africa/epidemiology ; }, abstract = {The University of the Free State - Next Generation Sequencing (NGS) Unit, Bloemfontein, South Africa, hosted a data and bioinformatics workshop from 19 to 22 June 2018. The workshop was coordinated by the African Enteric Viruses Genome Initiative (AEVGI) with support from the Bill & Melinda Gates Foundation. The event introduced technologies in NGS and data analysis with focus on the rotavirus (RV) genome. The workshop fostered interactions and networking between professionals, scientific experts, technicians and students. The courses provided an overview of RV diarrhoea and its burden in Africa, while highlighting the key resources and methodologies in NGS and advanced bioinformatics in deciphering vaccine impact. It was concluded that, despite the reported significant decline in RV associated-diarrhoea mortality and morbidity in Africa due to RV vaccine impact, the need for continuous surveillance and genomic characterization to better understand the ever-changing dynamics of RV strains is imperative.}, } @article {pmid32560294, year = {2020}, author = {Liu, L and Wang, Z and Su, Y and Wang, T}, title = {Characterization and Analysis of the Full-Length Transcriptomes of Multiple Organs in Pseudotaxus chienii (W.C.Cheng) W.C.Cheng.}, journal = {International journal of molecular sciences}, volume = {21}, number = {12}, pages = {}, pmid = {32560294}, issn = {1422-0067}, support = {31370364//National Natural Science Foundation of China/ ; 31570652//National Natural Science Foundation of China/ ; 31670200//National Natural Science Foundation of China/ ; 31770587//National Natural Science Foundation of China/ ; 31872670//National Natural Science Foundation of China/ ; 2016A030313320//Natural Science Foundation of Guangdong Province/ ; 2017A030313122//Natural Science Foundation of Guangdong Province/ ; 2017A030303007//Science and Technology Planning Project of Guangdong Province/ ; JCYJ20160425165447211//Project of Department of Science and Technology of Shenzhen City, Guangdong, China/ ; JCYJ20170413155402977//Project of Department of Science and Technology of Shenzhen City, Guangdong, China/ ; JCYJ20170818155249053//Project of Department of Science and Technology of Shenzhen City, Guangdong, China/ ; JCYJ20190813172001780//Project of Department of Science and Technology of Shenzhen City, Guangdong, China/ ; 201804010389//Science and Technology Planning Project of Guangzhou City, China/ ; }, mesh = {Biosynthetic Pathways ; Computational Biology/methods ; *Gene Expression Profiling ; *Gene Expression Regulation, Plant ; Genes, Plant ; High-Throughput Nucleotide Sequencing ; Host-Pathogen Interactions ; Molecular Sequence Annotation ; Multigene Family ; Organ Specificity/genetics ; Phylogeny ; Propanols/metabolism ; Taxaceae/*genetics/metabolism ; *Transcriptome ; }, abstract = {Pseudotaxus chienii, a rare tertiary relict species with economic and ecological value, is a representative of the monotypic genus Pseudotaxus that is endemic to China. P. chienii can adapt well to habitat isolation and ecological heterogeneity under a variety of climate and soil conditions, and is able to survive in harsh environments. However, little is known about the molecular and genetic resources of this long-lived conifer. Herein, we sequenced the transcriptomes of four organs of P. chienii using the PacBio Isoform Sequencing and Illumina RNA Sequencing platforms. Based on the PacBio Iso-Seq data, we obtained 44,896, 58,082, 50,485, and 67,638 full-length unigenes from the root, stem, leaf, and strobilus, respectively, with a mean length of 2692 bp, and a mean N50 length of 3010.75 bp. We then comprehensively annotated these unigenes. The number of organ-specific expressed unigenes ranged from 4393 in leaf to 9124 in strobilus, suggesting their special roles in physiological processes, organ development, and adaptability in the different four organs. A total of 16,562 differentially expressed genes (DEGs) were identified among the four organs and clustered into six subclusters. The gene families related to biotic/abiotic factors, including the TPS, CYP450, and HSP families, were characterized. The expression levels of most DEGs in the phenylpropanoid biosynthesis pathway and plant-pathogen interactions were higher in the root than in the three other organs, suggesting that root constitutes the main organ of defensive compound synthesis and accumulation and has a stronger ability to respond to stress. The sequences were analyzed to predict transcription factors, long non-coding RNAs, and alternative splicing events. The expression levels of most DEGs of C2H2, C3H, bHLH, and bZIP families in the root and stem were higher than those in the leaf and strobilus, indicating that these TFs may play a crucial role in the survival of the root and stem. These results comprise the first comprehensive gene expression profiles obtained for different organs of P. chienii. Our findings will facilitate further studies on the functional genomics, adaptive evolution, and phylogeny of P. chienii, and lay the foundation for the development of conservation strategies for this endangered conifer.}, } @article {pmid32558638, year = {2020}, author = {Prudence, SMM and Addington, E and Castaño-Espriu, L and Mark, DR and Pintor-Escobar, L and Russell, AH and McLean, TC}, title = {Advances in actinomycete research: an ActinoBase review of 2019.}, journal = {Microbiology (Reading, England)}, volume = {166}, number = {8}, pages = {683-694}, pmid = {32558638}, issn = {1465-2080}, support = {BB/M011216/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Actinobacteria/genetics/growth & development/metabolism/*physiology ; Animals ; Bacteriological Techniques ; Biological Products/metabolism ; Biomedical Research/instrumentation/organization & administration ; *Databases, Factual ; Environmental Microbiology ; Gene Expression Regulation, Bacterial ; Streptomyces/genetics/growth & development/metabolism/physiology ; Symbiosis ; }, abstract = {The actinomycetes are Gram-positive bacteria belonging to the order Actinomycetales within the phylum Actinobacteria. They include members with significant economic and medical importance, for example filamentous actinomycetes such as Streptomyces species, which have a propensity to produce a plethora of bioactive secondary metabolites and form symbioses with higher organisms, such as plants and insects. Studying these bacteria is challenging, but also fascinating and very rewarding. As a Microbiology Society initiative, members of the actinomycete research community have been developing a Wikipedia-style resource, called ActinoBase, the purpose of which is to aid in the study of these filamentous bacteria. This review will highlight 10 publications from 2019 that have been of special interest to the ActinoBase community, covering 4 major components of actinomycete research: (i) development and regulation; (ii) specialized metabolites; (iii) ecology and host interactions; and (iv) technology and methodology.}, } @article {pmid32556537, year = {2020}, author = {Piross, IS and Siliwal, M and Kumar, RS and Palatitz, P and Solt, S and Borbáth, P and Vili, N and Magonyi, N and Vas, Z and Rózsa, L and Harnos, A and Fehérvári, P}, title = {Sex interacts with age-dependent change in the abundance of lice-infesting Amur Falcons (Falco amurensis).}, journal = {Parasitology research}, volume = {119}, number = {8}, pages = {2579-2585}, pmid = {32556537}, issn = {1432-1955}, support = {GINOP 2.3.2-15- 2016-00057//European Regional Development Fund/ ; }, mesh = {Age Factors ; Amblycera/*physiology ; Animals ; Bird Diseases/*parasitology ; Ecosystem ; Ectoparasitic Infestations/parasitology/veterinary ; Falconiformes/parasitology ; Female ; India ; Lice Infestations/parasitology/*veterinary ; Male ; Phthiraptera ; Wings, Animal/parasitology ; }, abstract = {Sex-biassed and age-biassed parasite infections are common in nature, including ectoparasites-vertebrate host systems. We investigated the effect of Amur Falcons' sex, age and body size on the abundance of their lice at a migratory stopover site, where the falcons' habitat use and behaviour are more homogeneous across sex and age categories than during the breeding season. We sampled Amur Falcons in Nagaland, India at major roosting sites in 2016. We applied generalized linear models (with negative binomial distribution and log-link) to model the abundance of their two most numerous lice (Colpocephalum subzerafae and Degeeriella rufa) using the host age category (juvenile or adult) and wing length, both in interaction with sex, as explanatory variables. The abundance of C. subzerafae was only affected by host age, being nearly four times higher on juveniles than on adults. Juveniles were also more infested with D. rufa than the adults. Additionally, the abundance of the latter species was lower on adult male Falcons as compared to adult females. A juvenile bias in ectoparasite infestations is common in nature, probably due to juveniles being immunologically naïve, more resource-limited and may be inexperienced in body maintenance behaviours like preening and grooming. On the other hand, female-biassed infestations are much rarer than male-biassed infestations. We briefly discuss the possible causes of female-biassed infestations on Amur Falcons reported here, and in the closely related Red-footed Falcon and Lesser Kestrel as reported in the literature.}, } @article {pmid32555932, year = {2020}, author = {Siqueira, PC and Maciel, ELN and Catão, RC and Brioschi, AP and Silva, TCCD and Prado, TND}, title = {Completeness of yellow fever notification forms in the state of Espírito Santo, Brazil, 2017.}, journal = {Epidemiologia e servicos de saude : revista do Sistema Unico de Saude do Brasil}, volume = {29}, number = {3}, pages = {e2019402}, doi = {10.5123/s1679-49742020000300014}, pmid = {32555932}, issn = {2237-9622}, mesh = {Brazil/epidemiology ; Cities/epidemiology ; *Disease Notification/standards ; Humans ; *Information Systems/standards ; *Yellow Fever/epidemiology ; }, abstract = {Objective to describe the completeness of data on yellow fever notification forms in the municipalities of the state of Espírito Santo, Brazil, in 2017. Methods this is a descriptive ecological study with data from the Notifiable Health Conditions Information System (SINAN); form completeness was categorized as poor (<70.0%), regular (70-89.9%) or excellent (≥90.0%); thematic maps were prepared. Results 53.1% of the municipalities had poor or regular classification for many notification form variables, especially case Final Classification (57.1%), Confirmation/Dismissal Criterion (63.2%) and Closure Date (26.5%), which are required fields. Conclusion completeness was poor or regular for several variables, pointing to the need for a systematic assessment of information on yellow fever held on SINAN.}, } @article {pmid32555361, year = {2020}, author = {Shah, S and Chen, Y and Bhattacharya, D and Chan, CX}, title = {Sex in Symbiodiniaceae dinoflagellates: genomic evidence for independent loss of the canonical synaptonemal complex.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {9792}, pmid = {32555361}, issn = {2045-2322}, mesh = {*Biological Evolution ; Codon Usage ; Datasets as Topic ; Dinoflagellida/genetics/*physiology ; Gene Expression Profiling ; Genome, Protozoan ; Meiosis/genetics ; Selection, Genetic ; Sex ; Synaptonemal Complex/*genetics ; }, abstract = {Dinoflagellates of the Symbiodiniaceae family encompass diverse symbionts that are critical to corals and other species living in coral reefs. It is well known that sexual reproduction enhances adaptive evolution in changing environments. Although genes related to meiotic functions were reported in Symbiodiniaceae, cytological evidence of meiosis and fertilisation are however yet to be observed in these taxa. Using transcriptome and genome data from 21 Symbiodiniaceae isolates, we studied genes that encode proteins associated with distinct stages of meiosis and syngamy. We report the absence of genes that encode main components of the synaptonemal complex (SC), a protein structure that mediates homologous chromosomal pairing and class I crossovers. This result suggests an independent loss of canonical SCs in the alveolates, that also includes the SC-lacking ciliates. We hypothesise that this loss was due in part to permanently condensed chromosomes and repeat-rich sequences in Symbiodiniaceae (and other dinoflagellates) which favoured the SC-independent class II crossover pathway. Our results reveal novel insights into evolution of the meiotic molecular machinery in the ecologically important Symbiodiniaceae and in other eukaryotes.}, } @article {pmid32554569, year = {2020}, author = {Anderegg, WRL and Trugman, AT and Badgley, G and Anderson, CM and Bartuska, A and Ciais, P and Cullenward, D and Field, CB and Freeman, J and Goetz, SJ and Hicke, JA and Huntzinger, D and Jackson, RB and Nickerson, J and Pacala, S and Randerson, JT}, title = {Climate-driven risks to the climate mitigation potential of forests.}, journal = {Science (New York, N.Y.)}, volume = {368}, number = {6497}, pages = {}, doi = {10.1126/science.aaz7005}, pmid = {32554569}, issn = {1095-9203}, mesh = {Carbon Sequestration ; *Climate Change ; Droughts ; Fires ; *Forests ; Policy Making ; }, abstract = {Forests have considerable potential to help mitigate human-caused climate change and provide society with many cobenefits. However, climate-driven risks may fundamentally compromise forest carbon sinks in the 21st century. Here, we synthesize the current understanding of climate-driven risks to forest stability from fire, drought, biotic agents, and other disturbances. We review how efforts to use forests as natural climate solutions presently consider and could more fully embrace current scientific knowledge to account for these climate-driven risks. Recent advances in vegetation physiology, disturbance ecology, mechanistic vegetation modeling, large-scale ecological observation networks, and remote sensing are improving current estimates and forecasts of the risks to forest stability. A more holistic understanding and quantification of such risks will help policy-makers and other stakeholders effectively use forests as natural climate solutions.}, } @article {pmid32552524, year = {2020}, author = {Lyu, G and Li, D and Li, S}, title = {Bioinformatics analysis of BBX family genes and its response to UV-B in Arabidopsis thaliana.}, journal = {Plant signaling & behavior}, volume = {15}, number = {9}, pages = {1782647}, pmid = {32552524}, issn = {1559-2324}, mesh = {Abscisic Acid/pharmacology ; Acetates/pharmacology ; Arabidopsis/genetics/*metabolism/*radiation effects ; Arabidopsis Proteins/genetics/*metabolism ; Computational Biology/*methods ; Cyclopentanes/pharmacology ; Gene Expression Regulation, Plant/genetics/physiology ; Gibberellins/pharmacology ; Light ; Oxylipins/pharmacology ; *Ultraviolet Rays ; }, abstract = {The B-box proteins (BBXs) are a family of zinc finger proteins containing one/two B-box domain(s), which play important roles in plant growth and development. Though the Arabidopsis thaliana BBX family genes have been identified and named, no systematic study has taken on BBX family genes involved in the regulation of UV-B induced photomorphogenesis in Arabidopsis thaliana. In our previous report, BBX24/STO was demonstrated to be a negative regulator in UV-B signaling pathway in Arabidopsis. In the present study, the total 32 BBX family genes from Arabidopsis were analyzed, including their structures, conserved domains, phylogenetic relationships, promoter cis-regulatory elements, expression patterns under UV-B radiation. The expression profile of GEO Datasets (GSE117199) related to UV-B in NCBI database was analyzed. qRT-PCR was used to validate the expression profile of several BBX genes in Arabidopsis treated with UV-B. The promoters of AtBBXs contained cis-acting elements that respond to light and hormones, including ethylene, auxin (IAA), abscisic acid (ABA), gibberellin (GA) and methyl jasmonate (MeJA). BBX24 and BBX25 were collinear blocks, suggesting that BBX25 may also be involved in UV-B signal transduction. Expression profile analysis and qRT-PCR validation showed that UV-B induced up-regulation of BBX1, BBX7, BBX20, BBX25 and BBX32, suggesting that AtBBXs were mainly involved in UV-B photomorphogenesis. It is predicted that BBX1, BBX7, BBX20 and BBX25 may be new members in response to UV-B signaling.}, } @article {pmid32549034, year = {2020}, author = {Duarte, ME and Vigil-Hayes, M and Littletree, S and Belarde-Lewis, M}, title = {"Of Course, Data Can Never Fully Represent Reality": Assessing the Relationship between "Indigenous Data" and "Indigenous Knowledge," "Traditional Ecological Knowledge," and "Traditional Knowledge".}, journal = {Human biology}, volume = {91}, number = {3}, pages = {163-178}, doi = {10.13110/humanbiology.91.3.03}, pmid = {32549034}, issn = {1534-6617}, mesh = {Ecology ; Humans ; Knowledge ; *Population Groups ; }, abstract = {Multiple terms describe Indigenous peoples' creative expressions, including "Indigenous knowledge" (IK), "traditional ecological knowledge" (TEK), "traditional knowledge" (TK), and increasingly, "Indigenous data" (ID). Variation in terms contributes to disciplinary divides, challenges in organizing and finding prior studies about Indigenous peoples' creative expressions, and intellectually divergent chains of reference. The authors applied a decolonial, digital, feminist, ethics-of-care approach to citation analysis of records about Indigenous peoples knowledge and data, including network analyses of author-generated keywords and research areas, and content analysis of peer-reviewed studies about ID. Results reveal ambiguous uses of the term "Indigenous data"; the influence of ecology and environmental studies in research areas and topics associated with IK, TEK, and TK; and the influence of public administration and governance studies in research areas and topics associated with ID studies. Researchers of ID would benefit from applying a more nuanced and robust vocabulary, one informed by studies of IK, TEK, and TK. Researchers of TEK and TK would benefit from the more people-centered approaches of IK. Researchers and systems designers who work with data sets can practice relational accountability by centering the Indigenous peoples from whom observations are sourced, combining narrative methodologies with computational methods to sustain the holism favored by Indigenous science and the relationality of Indigenous peoples.}, } @article {pmid32549033, year = {2020}, author = {Tsosie, KS and Claw, KG}, title = {Indigenizing Science and Reasserting Indigeneity in Research.}, journal = {Human biology}, volume = {91}, number = {3}, pages = {137-140}, doi = {10.13110/humanbiology.91.3.02}, pmid = {32549033}, issn = {1534-6617}, mesh = {Humans ; *Indians, North American ; Research ; }, } @article {pmid32545778, year = {2020}, author = {Hu, S and Chen, L and Li, L and Zhang, T and Yuan, L and Cheng, L and Wang, J and Wen, M}, title = {Simulation of Land Use Change and Ecosystem Service Value Dynamics under Ecological Constraints in Anhui Province, China.}, journal = {International journal of environmental research and public health}, volume = {17}, number = {12}, pages = {}, pmid = {32545778}, issn = {1660-4601}, mesh = {China ; *Conservation of Natural Resources ; *Ecosystem ; Forecasting ; Sustainable Development ; }, abstract = {Land use change has a significant impact on the structure and function of ecosystems, and the transformation of ecosystems affects the mode and efficiency of land use, which reflects a mutual interaction relationship. The prediction and simulation of future land use change can enhance the foresight of land use planning, which is of great significance to regional sustainable development. In this study, future land use changes are characterized under an ecological optimization scenario based on the grey prediction (1,1) model (GM) and a future land use simulation (FLUS) model. In addition, the ecosystem service value (ESV) of Anhui Province from 1995 to 2030 were estimated based on the revised estimation model. The results indicate the following details: (1) the FLUS model was used to simulate the land use layout of Anhui Province in 2018, where the overall accuracy of the simulation results is high, indicating that the FLUS model is applicable for simulating future land use change; (2) the spatial layout of land use types in Anhui Province is stable and the cultivated land has the highest proportion. The most significant characteristic of future land use change is that the area of cultivated land continues to decrease while the area of built-up land continues to expand; and (3) the ESV of Anhui Province is predicted to increase in the future. The regulating service is the largest ESV contributor, and water area is the land use type with the highest proportion of ESV. These findings provide reference for the formulation of sustainable development policies of the regional ecological environment.}, } @article {pmid32545455, year = {2020}, author = {Klimina, KM and Voroshilova, VN and Poluektova, EU and Veselovsky, VA and Yunes, RA and Kovtun, AS and Kudryavtseva, AV and Kasianov, AS and Danilenko, VN}, title = {Toxin-Antitoxin Systems: A Tool for Taxonomic Analysis of Human Intestinal Microbiota.}, journal = {Toxins}, volume = {12}, number = {6}, pages = {}, pmid = {32545455}, issn = {2072-6651}, support = {18-34-00011//Russian Foundation for Basic Research/International ; 19-74-00146//Russian Science Foundation/International ; }, mesh = {Bacteria/classification/*genetics ; Databases, Genetic ; Feces/microbiology ; *Gastrointestinal Microbiome ; Gene Expression Profiling ; Humans ; Intestines/*microbiology ; *Metagenome ; *Metagenomics ; Ribotyping ; Toxin-Antitoxin Systems/*genetics ; }, abstract = {The human gastrointestinal microbiota (HGM) is known for its rich diversity of bacterial species and strains. Yet many studies stop at characterizing the HGM at the family level. This is mainly due to lack of adequate methods for a high-resolution profiling of the HGM. One way to characterize the strain diversity of the HGM is to look for strain-specific functional markers. Here, we propose using type II toxin-antitoxin systems (TAS). To identify TAS systems in the HGM, we previously developed the software TAGMA. This software was designed to detect the TAS systems, MazEF and RelBE, in lactobacilli and bifidobacteria. In this study, we updated the gene catalog created previously and used it to test our software anew on 1346 strains of bacteria, which belonged to 489 species and 49 genera. We also sequenced the genomes of 20 fecal samples and analyzed the results with TAGMA. Although some differences were detected at the strain level, the results showed no particular difference in the bacterial species between our method and other classic analysis software. These results support the use of the updated catalog of genes encoding type II TAS as a useful tool for computer-assisted species and strain characterization of the HGM.}, } @article {pmid32544441, year = {2020}, author = {Weissman, JL and Stoltzfus, A and Westra, ER and Johnson, PLF}, title = {Avoidance of Self during CRISPR Immunization.}, journal = {Trends in microbiology}, volume = {28}, number = {7}, pages = {543-553}, doi = {10.1016/j.tim.2020.02.005}, pmid = {32544441}, issn = {1878-4380}, mesh = {Bacteria/genetics/*virology ; Bacterial Physiological Phenomena/*immunology ; Bacteriophages/*genetics ; CRISPR-Cas Systems/*genetics ; Clustered Regularly Interspaced Short Palindromic Repeats/*genetics ; Immunity, Innate/physiology ; }, abstract = {The battle between microbes and their viruses is ancient and ongoing. Clustered regularly interspaced short palindromic repeat (CRISPR) immunity, the first and, to date, only form of adaptive immunity found in prokaryotes, represents a flexible mechanism to recall past infections while also adapting to a changing pathogenic environment. Critical to the role of CRISPR as an adaptive immune mechanism is its capacity for self versus non-self recognition when acquiring novel immune memories. Yet, CRISPR systems vary widely in both how and to what degree they can distinguish foreign from self-derived genetic material. We document known and hypothesized mechanisms that bias the acquisition of immune memory towards non-self targets. We demonstrate that diversity is the rule, with many widespread but no universal mechanisms for self versus non-self recognition.}, } @article {pmid32543763, year = {2020}, author = {Zhang, CH and Schwartz, GG}, title = {Spatial Disparities in Coronavirus Incidence and Mortality in the United States: An Ecological Analysis as of May 2020.}, journal = {The Journal of rural health : official journal of the American Rural Health Association and the National Rural Health Care Association}, volume = {36}, number = {3}, pages = {433-445}, pmid = {32543763}, issn = {1748-0361}, mesh = {Age Factors ; Betacoronavirus ; COVID-19 ; Coronavirus Infections/*epidemiology/mortality ; Geographic Information Systems ; Humans ; New York City/epidemiology ; Pandemics ; Pneumonia, Viral/*epidemiology/mortality ; Residence Characteristics/*statistics & numerical data ; Risk Factors ; SARS-CoV-2 ; Socioeconomic Factors ; Spatial Analysis ; United States/epidemiology ; }, abstract = {PURPOSE: This ecological analysis investigates the spatial patterns of the COVID-19 epidemic in the United States in relation to socioeconomic variables that characterize US counties.

METHODS: Data on confirmed cases and deaths from COVID-19 for 2,814 US counties were obtained from Johns Hopkins University. We used Geographic Information Systems (GIS) to map the spatial aspects of this pandemic and investigate the disparities between metropolitan and nonmetropolitan communities. Multiple regression models were used to explore the contextual risk factors of infections and death across US counties. We included population density, percent of population aged 65+, percent population in poverty, percent minority population, and percent of the uninsured as independent variables. A state-level measure of the percent of the population that has been tested for COVID-19 was used to control for the impact of testing.

FINDINGS: The impact of COVID-19 in the United States has been extremely uneven. Although densely populated large cities and their surrounding metropolitan areas are hotspots of the pandemic, it is counterintuitive that incidence and mortality rates in some small cities and nonmetropolitan counties approximate those in epicenters such as New York City. Regression analyses support the hypotheses of positive correlations between COVID-19 incidence and mortality rates and socioeconomic factors including population density, proportions of elderly residents, poverty, and percent population tested.

CONCLUSIONS: Knowledge about the spatial aspects of the COVID-19 epidemic and its socioeconomic correlates can inform first responders and government efforts. Directives for social distancing and to "shelter-in-place" should continue to stem the spread of COVID-19.}, } @article {pmid32543366, year = {2020}, author = {Hall, RJ and Thorpe, S and Thomas, GH and Wood, AJ}, title = {Simulating the evolutionary trajectories of metabolic pathways for insect symbionts in the genus Sodalis.}, journal = {Microbial genomics}, volume = {6}, number = {7}, pages = {}, pmid = {32543366}, issn = {2057-5858}, support = {/WT_/Wellcome Trust/United Kingdom ; BB/M011151/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; WT095024MA/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Adaptation, Physiological ; Algorithms ; Animals ; Bacterial Proteins/genetics ; Computational Biology/*methods ; Enterobacteriaceae/*physiology ; Evolution, Molecular ; Metabolic Networks and Pathways ; Models, Theoretical ; Mutation ; Symbiosis ; Tsetse Flies/*microbiology ; }, abstract = {Insect-bacterial symbioses are ubiquitous, but there is still much to uncover about how these relationships establish, persist and evolve. The tsetse endosymbiont Sodalis glossinidius displays intriguing metabolic adaptations to its microenvironment, but the process by which this relationship evolved remains to be elucidated. The recent chance discovery of the free-living species of the genus Sodalis, Sodalis praecaptivus, provides a serendipitous starting point from which to investigate the evolution of this symbiosis. Here, we present a flux balance model for S. praecaptivus and empirically verify its predictions. Metabolic modelling is used in combination with a multi-objective evolutionary algorithm to explore the trajectories that S. glossinidius may have undertaken from this starting point after becoming internalized. The order in which key genes are lost is shown to influence the evolved populations, providing possible targets for future in vitro genetic manipulation. This method provides a detailed perspective on possible evolutionary trajectories for S. glossinidius in this fundamental process of evolutionary and ecological change.}, } @article {pmid32543353, year = {2020}, author = {Gong, YN and Tsao, KC and Hsiao, MJ and Huang, CG and Huang, PN and Huang, PW and Lee, KM and Liu, YC and Yang, SL and Kuo, RL and Chen, KF and Liu, YC and Huang, SY and Huang, HI and Liu, MT and Yang, JR and Chiu, CH and Yang, CT and Chen, GW and Shih, SR}, title = {SARS-CoV-2 genomic surveillance in Taiwan revealed novel ORF8-deletion mutant and clade possibly associated with infections in Middle East.}, journal = {Emerging microbes & infections}, volume = {9}, number = {1}, pages = {1457-1466}, pmid = {32543353}, issn = {2222-1751}, support = {HHSN272201400007C/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Betacoronavirus/classification/*genetics/isolation & purification ; COVID-19 ; Cell Line ; Chlorocebus aethiops ; Coronavirus Infections/*virology ; *Genome, Viral ; Haemophilus parainfluenzae/isolation & purification ; Humans ; Middle East ; Open Reading Frames ; Pandemics ; Phylogeny ; Pneumonia, Viral/*virology ; RNA, Viral ; SARS-CoV-2 ; Sequence Deletion ; Taiwan ; Travel ; Vero Cells ; Virus Cultivation ; Whole Genome Sequencing ; }, abstract = {Taiwan experienced two waves of imported infections with Coronavirus Disease 2019 (COVID-19). This study aimed at investigating the genomic variation of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in Taiwan and compared their evolutionary trajectories with the global strains. We performed culture and full-genome sequencing of SARS-CoV-2 strains followed by phylogenetic analysis. A 382-nucleotides deletion in open reading frame 8 (ORF8) was found in a Taiwanese strain isolated from a patient on February 4, 2020 who had a travel history to Wuhan. Patients in the first wave also included several sporadic, local transmission cases. Genomes of 5 strains sequenced from clustered infections were classified into a new clade with ORF1ab-V378I mutation, in addition to 3 dominant clades ORF8-L84S, ORF3a-G251V and S-D614G. This highlighted clade also included some strains isolated from patients who had a travel history to Turkey and Iran. The second wave mostly resulted from patients who had a travel history to Europe and Americas. All Taiwanese viruses were classified into various clades. Genomic surveillance of SARS-CoV-2 in Taiwan revealed a new ORF8-deletion mutant and a virus clade that may be associated with infections in the Middle East, which contributed to a better understanding of the global SARS-CoV-2 transmission dynamics.}, } @article {pmid32542422, year = {2020}, author = {Vortkamp, I and Schreiber, SJ and Hastings, A and Hilker, FM}, title = {Multiple Attractors and Long Transients in Spatially Structured Populations with an Allee Effect.}, journal = {Bulletin of mathematical biology}, volume = {82}, number = {6}, pages = {82}, pmid = {32542422}, issn = {1522-9602}, support = {DMS-1817124//National Science Foundation/International ; DMS-1716803//National Science Foundation/International ; }, mesh = {Animals ; Computational Biology ; Ecosystem ; Extinction, Biological ; Fractals ; Mathematical Concepts ; *Models, Biological ; Nonlinear Dynamics ; Population Density ; Population Dynamics/*statistics & numerical data ; }, abstract = {We present a discrete-time model of a spatially structured population and explore the effects of coupling when the local dynamics contain a strong Allee effect and overcompensation. While an isolated population can exhibit only bistability and essential extinction, a spatially structured population can exhibit numerous coexisting attractors. We identify mechanisms and parameter ranges that can protect the spatially structured population from essential extinction, whereas it is inevitable in the local system. In the case of weak coupling, a state where one subpopulation density lies above and the other one below the Allee threshold can prevent essential extinction. Strong coupling, on the other hand, enables both populations to persist above the Allee threshold when dynamics are (approximately) out of phase. In both cases, attractors have fractal basin boundaries. Outside of these parameter ranges, dispersal was not found to prevent essential extinction. We also demonstrate how spatial structure can lead to long transients of persistence before the population goes extinct.}, } @article {pmid32542364, year = {2020}, author = {Zhou, C and Xu, Q and He, S and Ye, W and Cao, R and Wang, P and Ling, Y and Yan, X and Wang, Q and Zhang, G}, title = {GTDB: an integrated resource for glycosyltransferase sequences and annotations.}, journal = {Database : the journal of biological databases and curation}, volume = {2020}, number = {}, pages = {}, pmid = {32542364}, issn = {1758-0463}, mesh = {Amino Acid Sequence ; *Databases, Protein ; Gene Ontology ; *Glycosyltransferases ; Molecular Docking Simulation ; Molecular Sequence Annotation ; Software ; User-Computer Interface ; }, abstract = {Glycosyltransferases (GTs), a large class of carbohydrate-active enzymes, adds glycosyl moieties to various substrates to generate multiple bioactive compounds, including natural products with pharmaceutical or agrochemical values. Here, we first collected comprehensive information on GTs, including amino acid sequences, coding region sequences, available tertiary structures, protein classification families, catalytic reactions and metabolic pathways. Then, we developed sequence search and molecular docking processes for GTs, resulting in a GTs database (GTDB). In the present study, 520 179 GTs from approximately 21 647 species that involved in 394 kinds of different reactions were deposited in GTDB. GTDB has the following useful features: (i) text search is provided for retrieving the complete details of a query by combining multiple identifiers and data sources; (ii) a convenient browser allows users to browse data by different classifications and download data in batches; (iii) BLAST is offered for searching against pre-defined sequences, which can facilitate the annotation of the biological functions of query GTs; and lastly, (iv) GTdock using AutoDock Vina performs docking simulations of several GTs with the same single acceptor and displays the results based on 3Dmol.js allowing easy view of models.}, } @article {pmid32542026, year = {2020}, author = {Cheng, W and Ramachandran, S and Crawford, L}, title = {Estimation of non-null SNP effect size distributions enables the detection of enriched genes underlying complex traits.}, journal = {PLoS genetics}, volume = {16}, number = {6}, pages = {e1008855}, pmid = {32542026}, issn = {1553-7404}, support = {MC_QA137853/MRC_/Medical Research Council/United Kingdom ; P20 GM103645/GM/NIGMS NIH HHS/United States ; MC_PC_17228/MRC_/Medical Research Council/United Kingdom ; R01 GM118652/GM/NIGMS NIH HHS/United States ; U10 CA180794/CA/NCI NIH HHS/United States ; P20 GM109035/GM/NIGMS NIH HHS/United States ; }, mesh = {Data Interpretation, Statistical ; Databases, Genetic/statistics & numerical data ; Genome-Wide Association Study/*statistics & numerical data ; Humans ; *Models, Genetic ; Multifactorial Inheritance/*genetics ; *Polymorphism, Single Nucleotide ; Quantitative Trait Loci/*genetics ; United Kingdom ; White People/genetics ; }, abstract = {Traditional univariate genome-wide association studies generate false positives and negatives due to difficulties distinguishing associated variants from variants with spurious nonzero effects that do not directly influence the trait. Recent efforts have been directed at identifying genes or signaling pathways enriched for mutations in quantitative traits or case-control studies, but these can be computationally costly and hampered by strict model assumptions. Here, we present gene-ε, a new approach for identifying statistical associations between sets of variants and quantitative traits. Our key insight is that enrichment studies on the gene-level are improved when we reformulate the genome-wide SNP-level null hypothesis to identify spurious small-to-intermediate SNP effects and classify them as non-causal. gene-ε efficiently identifies enriched genes under a variety of simulated genetic architectures, achieving greater than a 90% true positive rate at 1% false positive rate for polygenic traits. Lastly, we apply gene-ε to summary statistics derived from six quantitative traits using European-ancestry individuals in the UK Biobank, and identify enriched genes that are in biologically relevant pathways.}, } @article {pmid32541861, year = {2020}, author = {Kaufman, D and McKay, N and Routson, C and Erb, M and Davis, B and Heiri, O and Jaccard, S and Tierney, J and Dätwyler, C and Axford, Y and Brussel, T and Cartapanis, O and Chase, B and Dawson, A and de Vernal, A and Engels, S and Jonkers, L and Marsicek, J and Moffa-Sánchez, P and Morrill, C and Orsi, A and Rehfeld, K and Saunders, K and Sommer, PS and Thomas, E and Tonello, M and Tóth, M and Vachula, R and Andreev, A and Bertrand, S and Biskaborn, B and Bringué, M and Brooks, S and Caniupán, M and Chevalier, M and Cwynar, L and Emile-Geay, J and Fegyveresi, J and Feurdean, A and Finsinger, W and Fortin, MC and Foster, L and Fox, M and Gajewski, K and Grosjean, M and Hausmann, S and Heinrichs, M and Holmes, N and Ilyashuk, B and Ilyashuk, E and Juggins, S and Khider, D and Koinig, K and Langdon, P and Larocque-Tobler, I and Li, J and Lotter, A and Luoto, T and Mackay, A and Magyari, E and Malevich, S and Mark, B and Massaferro, J and Montade, V and Nazarova, L and Novenko, E and Pařil, P and Pearson, E and Peros, M and Pienitz, R and Płóciennik, M and Porinchu, D and Potito, A and Rees, A and Reinemann, S and Roberts, S and Rolland, N and Salonen, S and Self, A and Seppä, H and Shala, S and St-Jacques, JM and Stenni, B and Syrykh, L and Tarrats, P and Taylor, K and van den Bos, V and Velle, G and Wahl, E and Walker, I and Wilmshurst, J and Zhang, E and Zhilich, S}, title = {Publisher Correction: A global database of Holocene paleotemperature records.}, journal = {Scientific data}, volume = {7}, number = {1}, pages = {183}, doi = {10.1038/s41597-020-0515-6}, pmid = {32541861}, issn = {2052-4463}, abstract = {An amendment to this paper has been published and can be accessed via a link at the top of the paper.}, } @article {pmid32541802, year = {2020}, author = {Birk, S and Chapman, D and Carvalho, L and Spears, BM and Andersen, HE and Argillier, C and Auer, S and Baattrup-Pedersen, A and Banin, L and Beklioğlu, M and Bondar-Kunze, E and Borja, A and Branco, P and Bucak, T and Buijse, AD and Cardoso, AC and Couture, RM and Cremona, F and de Zwart, D and Feld, CK and Ferreira, MT and Feuchtmayr, H and Gessner, MO and Gieswein, A and Globevnik, L and Graeber, D and Graf, W and Gutiérrez-Cánovas, C and Hanganu, J and Işkın, U and Järvinen, M and Jeppesen, E and Kotamäki, N and Kuijper, M and Lemm, JU and Lu, S and Solheim, AL and Mischke, U and Moe, SJ and Nõges, P and Nõges, T and Ormerod, SJ and Panagopoulos, Y and Phillips, G and Posthuma, L and Pouso, S and Prudhomme, C and Rankinen, K and Rasmussen, JJ and Richardson, J and Sagouis, A and Santos, JM and Schäfer, RB and Schinegger, R and Schmutz, S and Schneider, SC and Schülting, L and Segurado, P and Stefanidis, K and Sures, B and Thackeray, SJ and Turunen, J and Uyarra, MC and Venohr, M and von der Ohe, PC and Willby, N and Hering, D}, title = {Impacts of multiple stressors on freshwater biota across spatial scales and ecosystems.}, journal = {Nature ecology & evolution}, volume = {4}, number = {8}, pages = {1060-1068}, pmid = {32541802}, issn = {2397-334X}, mesh = {Biota ; *Ecosystem ; Europe ; *Fresh Water ; Rivers ; }, abstract = {Climate and land-use change drive a suite of stressors that shape ecosystems and interact to yield complex ecological responses (that is, additive, antagonistic and synergistic effects). We know little about the spatial scales relevant for the outcomes of such interactions and little about effect sizes. These knowledge gaps need to be filled to underpin future land management decisions or climate mitigation interventions for protecting and restoring freshwater ecosystems. This study combines data across scales from 33 mesocosm experiments with those from 14 river basins and 22 cross-basin studies in Europe, producing 174 combinations of paired-stressor effects on a biological response variable. Generalized linear models showed that only one of the two stressors had a significant effect in 39% of the analysed cases, 28% of the paired-stressor combinations resulted in additive effects and 33% resulted in interactive (antagonistic, synergistic, opposing or reversal) effects. For lakes, the frequencies of additive and interactive effects were similar for all spatial scales addressed, while for rivers these frequencies increased with scale. Nutrient enrichment was the overriding stressor for lakes, with effects generally exceeding those of secondary stressors. For rivers, the effects of nutrient enrichment were dependent on the specific stressor combination and biological response variable. These results vindicate the traditional focus of lake restoration and management on nutrient stress, while highlighting that river management requires more bespoke management solutions.}, } @article {pmid32535899, year = {2020}, author = {Hakkenberg, CR and Peet, RK and Wentworth, TR and Zhu, K and Schafale, MP}, title = {Tree canopy cover constrains the fertility-diversity relationship in plant communities of the southeastern United States.}, journal = {Ecology}, volume = {101}, number = {10}, pages = {e03119}, doi = {10.1002/ecy.3119}, pmid = {32535899}, issn = {1939-9170}, mesh = {Biodiversity ; *Forests ; Humans ; Plants ; Southeastern United States ; *Trees ; }, abstract = {The goal of elucidating the primary mechanisms constraining the assembly and distribution of biodiversity remains among the central unresolved challenges facing the field of ecology. Simulation studies and experimental manipulations have focused on how patterns in community assembly result from bivariate relationships along productivity or environmental gradients. However, the joint influence of multiple resource gradients on the distribution of species richness in natural communities remains understudied. Using data from a large network of multiscale vegetation plots across forests and woodlands of the southeastern United States, we find significant evidence for the scale-dependent, joint constraints of forest structure and soil resources on the distribution of vascular plant species richness. In addition to their significant partial effects on species richness, understory light levels and soil fertility positively interact, suggesting a trade-off between the two limiting resources with species richness peaking both in high-light, low-fertility conditions as well as low-light, high-fertility settings. This finding provides a novel perspective on the biodiversity-productivity relationship that suggests a transition in limiting resources from soil nutrients to light availability when enhanced productivity results in reduced light resources for subordinate individuals. Results likewise have meaningful implications for our understanding of scale-dependent community assembly processes as size-asymmetric competition replaces environmental filtering as the primary assembly mechanism structuring temperate forest communities along an increasing soil fertility gradient.}, } @article {pmid32535165, year = {2021}, author = {Hernandez-Beltran, JCR and Rodríguez-Beltrán, J and Millán, AS and Peña-Miller, R and Fuentes-Hernández, A}, title = {Quantifying plasmid dynamics using single-cell microfluidics and image bioinformatics.}, journal = {Plasmid}, volume = {113}, number = {}, pages = {102517}, doi = {10.1016/j.plasmid.2020.102517}, pmid = {32535165}, issn = {1095-9890}, mesh = {Bacteria ; *Computational Biology ; *Microfluidics ; Plasmids/genetics ; beta-Lactam Resistance ; }, abstract = {Multicopy plasmids play an important role in bacterial ecology and evolution by accelerating the rate of adaptation and providing a platform for rapid gene amplification and evolutionary rescue. Despite the relevance of plasmids in bacterial evolutionary dynamics, evaluating the population-level consequences of randomly segregating and replicating plasmids in individual cells remains a challenging problem, both in theory and experimentally. In recent years, technological advances in fluorescence microscopy and microfluidics have allowed studying temporal changes in gene expression by quantifying the fluorescent intensity of individual cells under controlled environmental conditions. In this paper, we will describe the manufacture, experimental setup, and data analysis pipeline of different microfluidic systems that can be used to study plasmid dynamics, both in single-cells and in populations. To illustrate the benefits and limitations of microfluidics to study multicopy plasmid dynamics, we will use an experimental model system consisting on Escherichia coli K12 carrying non-conjugative, multicopy plasmids (19 copies per cell, in average) encoding different fluorescent markers and β-lactam resistance genes. First, we will use an image-based flow cytometer to estimate changes in the allele distribution of a heterogeneous population under different selection regimes. Then we will use a mothermachine microfluidic device to obtain time-series of fluorescent intensity of individual cells to argue that plasmid segregation and replication dynamics are inherently stochastic processes. Finally, using a microchemostat, we track thousands of cells in time to reconstruct bacterial lineages and evaluate the allele frequency distributions that emerge in response to a range of selective pressures.}, } @article {pmid32533355, year = {2020}, author = {Fadai, NT and Simpson, MJ}, title = {Population Dynamics with Threshold Effects Give Rise to a Diverse Family of Allee Effects.}, journal = {Bulletin of mathematical biology}, volume = {82}, number = {6}, pages = {74}, pmid = {32533355}, issn = {1522-9602}, support = {DP170100474//Australian Research Council/International ; }, mesh = {Animals ; Cell Biology/statistics & numerical data ; Computational Biology ; Computer Simulation ; Ecology/statistics & numerical data ; Ecosystem ; Humans ; Logistic Models ; Mathematical Concepts ; *Models, Biological ; Population Dynamics/*statistics & numerical data ; Population Growth ; Stochastic Processes ; Systems Analysis ; }, abstract = {The Allee effect describes populations that deviate from logistic growth models and arises in applications including ecology and cell biology. A common justification for incorporating Allee effects into population models is that the population in question has altered growth mechanisms at some critical density, often referred to as a threshold effect. Despite the ubiquitous nature of threshold effects arising in various biological applications, the explicit link between local threshold effects and global Allee effects has not been considered. In this work, we examine a continuum population model that incorporates threshold effects in the local growth mechanisms. We show that this model gives rise to a diverse family of Allee effects, and we provide a comprehensive analysis of which choices of local growth mechanisms give rise to specific Allee effects. Calibrating this model to a recent set of experimental data describing the growth of a population of cancer cells provides an interpretation of the threshold population density and growth mechanisms associated with the population.}, } @article {pmid32532234, year = {2020}, author = {Bell, GJ and Loop, MS and Mvalo, T and Juliano, JJ and Mofolo, I and Kamthunzi, P and Tegha, G and Lievens, M and Bailey, J and Emch, M and Hoffman, I}, title = {Environmental modifiers of RTS,S/AS01 malaria vaccine efficacy in Lilongwe, Malawi.}, journal = {BMC public health}, volume = {20}, number = {1}, pages = {910}, pmid = {32532234}, issn = {1471-2458}, support = {R01 AI137410/AI/NIAID NIH HHS/United States ; 1R01-AI137410-01/NH/NIH HHS/United States ; }, mesh = {Child ; Environment ; Female ; Geographic Information Systems ; Humans ; Infant ; Malaria Vaccines/*immunology ; Malaria, Falciparum/*epidemiology/prevention & control ; Malawi/epidemiology ; Male ; Plasmodium falciparum/*immunology ; Spatial Analysis ; Surveys and Questionnaires ; Vaccination ; }, abstract = {BACKGROUND: RTS,S/AS01 is the first vaccine against malaria to undergo pilot implementation, beginning in 2019 and vaccinating 360,000 children per year in Malawi, Ghana, and Kenya. The four-dose vaccine is given as a primary three-dose series with a fourth dose given approximately 18 months later. The efficacy of RTS,S/AS01 was variable among the 11 sites participating in the 2009-2014 phase III trial (MALARIA-055, NCT00866619), possibly due to differences in transmission intensity. However, a within-site examination of environmental factors related to transmission intensity and their impact on vaccine efficacy has yet to be conducted.

METHODS: We implemented the phase III RTS,S/AS01 trial at the Malawi site, which enrolled 1578 infants (6-12 weeks) and children (5-17 months) living in the Lilongwe District in Central Malawi and followed them for 3 years between 2009 and 2014. A global positioning system survey and an ecological questionnaire were conducted to collect participant household locations and characteristics, while additional data on background malaria prevalence were obtained from a concurrent Malaria Transmission Intensity (MTI) survey. Negative binomial regression models were used to assess whether the efficacy of the vaccine varied by estimated background malaria prevalence, household roof type, or amount of nearby vegetation.

RESULTS: Vaccine efficacy did not significantly vary by estimated malaria prevalence or by roof type. However, increased vegetation cover was associated with an increase in the efficacy of the three-dose primary RTS,S/AS01 series in the 18 months before the fourth dose and a decrease in the efficacy of the primary vaccine series in the second 18 months following, if the fourth dose was not given. Vegetation cover did not alter the efficacy of the fourth dose in a statistically or practically significant manner.

CONCLUSIONS: Vegetation coverage in this study site might be a proxy for nearness to rivers or branching, shallow wetlands called "dambos" which could serve as breeding sites for mosquitoes. We observed statistically significant modification of the efficacy of RTS,S/AS01 by forest cover, suggesting that initial vaccine efficacy and the importance of the fourth dose varies based on ecological context.

TRIAL REGISTRATION: Efficacy of GSK Biologicals' Candidate Malaria Vaccine (257049) Against Malaria Disease Caused by P. falciparum Infection in Infants and Children in Africa. NCT00866619 prospectively registered 20 March 2009.}, } @article {pmid32527044, year = {2020}, author = {Sardans, J and Gargallo-Garriga, A and Urban, O and Klem, K and Walker, TWN and Holub, P and Janssens, IA and Peñuelas, J}, title = {Ecometabolomics for a Better Understanding of Plant Responses and Acclimation to Abiotic Factors Linked to Global Change.}, journal = {Metabolites}, volume = {10}, number = {6}, pages = {}, pmid = {32527044}, issn = {2218-1989}, support = {CGL2016-79835-P//Ministerio de Economía, Industria y Competitividad, Gobierno de España/ ; ERC-SyG-2013-610028 IMBALANCE-P,//European Research Consortium for Informatics and Mathematics/ ; }, abstract = {The number of ecometabolomic studies, which use metabolomic analyses to disentangle organisms' metabolic responses and acclimation to a changing environment, has grown exponentially in recent years. Here, we review the results and conclusions of ecometabolomic studies on the impacts of four main drivers of global change (increasing frequencies of drought episodes, heat stress, increasing atmospheric carbon dioxide (CO2) concentrations and increasing nitrogen (N) loads) on plant metabolism. Ecometabolomic studies of drought effects confirmed findings of previous target studies, in which most changes in metabolism are characterized by increased concentrations of soluble sugars and carbohydrate derivatives and frequently also by elevated concentrations of free amino acids. Secondary metabolites, especially flavonoids and terpenes, also commonly exhibited increased concentrations when drought intensified. Under heat and increasing N loads, soluble amino acids derived from glutamate and glutamine were the most responsive metabolites. Foliar metabolic responses to elevated atmospheric CO2 concentrations were dominated by greater production of monosaccharides and associated synthesis of secondary metabolites, such as terpenes, rather than secondary metabolites synthesized along longer sugar pathways involving N-rich precursor molecules, such as those formed from cyclic amino acids and along the shikimate pathway. We suggest that breeding for crop genotypes tolerant to drought and heat stress should be based on their capacity to increase the concentrations of C-rich compounds more than the concentrations of smaller N-rich molecules, such as amino acids. This could facilitate rapid and efficient stress response by reducing protein catabolism without compromising enzymatic capacity or increasing the requirement for re-transcription and de novo biosynthesis of proteins.}, } @article {pmid32526299, year = {2020}, author = {Ren, L and Zhang, X and Li, Y and Shang, Y and Chen, S and Wang, S and Qu, Y and Cai, J and Guo, Y}, title = {Comparative analysis of mitochondrial genomes among the subfamily Sarcophaginae (Diptera: Sarcophagidae) and phylogenetic implications.}, journal = {International journal of biological macromolecules}, volume = {161}, number = {}, pages = {214-222}, doi = {10.1016/j.ijbiomac.2020.06.043}, pmid = {32526299}, issn = {1879-0003}, mesh = {Animals ; Computational Biology ; Diptera/classification/genetics ; *Genome, Mitochondrial ; *Genomics/methods ; *Phylogeny ; Sarcophagidae/*classification/*genetics ; }, abstract = {The subfamily Sarcophaginae is extremely diverse in morphology, habit and geographical distribution, and usually considered to be of significant ecological, medical, and forensic significance. In the present study, 18 mitochondrial genomes (mitogenomes) of sarcophagid flies were first obtained. The rearrangement and orientation of genes were identical with that of ancestral insects. The degrees of compositional heterogeneity in the datasets were extremely low. Furthermore, 13 protein-coding genes were evolving under purifying selection. The phylogenic relationship of the genus-group taxa Boettcheria + (Sarcophaga + (Peckia + (Ravinia + Oxysarcodexia))) was strongly supported. Four subgenera were recovered as monophyletic (Liopygia, Liosarcophaga, Pierretia, Heteronychia) in addition to Parasarcophaga as polyphyletic. The sister-relationships between S. dux and S. aegyptiaca, S. pingi and S. kawayuensis were recovered, respectively. Moreover, the molecular phylogenetic relationships among the subgenera Helicophagella, Kozlovea, Kramerea, Pandelleisca, Phallocheira, Pseudothyrsocnema, Sinonipponia and Seniorwhitea were rarely put forward prior to this study. This study provides insight into the population genetics, molecular biology, and phylogeny for the subfamily Sarcophaginae, especially for the subgeneric classification of Sarcophaga. However, compared with the enormous species diversity of flesh flies, the available mitogenomes are still limited for recovering the phylogeny of Sarcophaginae.}, } @article {pmid32524177, year = {2020}, author = {Dekaboruah, E and Suryavanshi, MV and Chettri, D and Verma, AK}, title = {Human microbiome: an academic update on human body site specific surveillance and its possible role.}, journal = {Archives of microbiology}, volume = {202}, number = {8}, pages = {2147-2167}, pmid = {32524177}, issn = {1432-072X}, mesh = {Computational Biology/*trends ; Disease ; *Human Body ; Humans ; Microbiota/*physiology ; }, abstract = {Human body is inhabited by vast number of microorganisms which form a complex ecological community and influence the human physiology, in the aspect of both health and diseases. These microbes show a relationship with the human immune system based on coevolution and, therefore, have a tremendous potential to contribute to the metabolic function, protection against the pathogen and in providing nutrients and energy. However, of these microbes, many carry out some functions that play a crucial role in the host physiology and may even cause diseases. The introduction of new molecular technologies such as transcriptomics, metagenomics and metabolomics has contributed to the upliftment on the findings of the microbiome linked to the humans in the recent past. These rapidly developing technologies are boosting our capacity to understand about the human body-associated microbiome and its association with the human health. The highlights of this review are inclusion of how to derive microbiome data and the interaction between human and associated microbiome to provide an insight on the role played by the microbiome in biological processes of the human body as well as the development of major human diseases.}, } @article {pmid32522348, year = {2020}, author = {Ball, N and Madden, J and Paini, A and Mathea, M and Palmer, AD and Sperber, S and Hartung, T and van Ravenzwaay, B}, title = {Key read across framework components and biology based improvements.}, journal = {Mutation research. Genetic toxicology and environmental mutagenesis}, volume = {853}, number = {}, pages = {503172}, doi = {10.1016/j.mrgentox.2020.503172}, pmid = {32522348}, issn = {1879-3592}, mesh = {Algorithms ; Animals ; Databases, Factual ; Hazardous Substances/*chemistry ; Humans ; Metabolomics/methods ; Mutagens/*chemistry ; Risk Assessment ; }, abstract = {At the 2019 annual meeting of the European Environmental Mutagen and Genomics Society a workshop session related to the use of read across concepts in toxicology was held. The goal of this session was to provide the audience an overview of general read-across concepts. From ECHA's read across assessment framework, the starting point is chemical similarity. There are several approaches and algorithms available for calculating chemical similarity based on molecular descriptors, distance/similarity measures and weighting schemata for specific endpoints. Therefore, algorithms that adapt themselves to the data (endpoint/s) and provide a good ability to distinguish between structural similar and not similar molecules regarding specific endpoints are needed and their use discussed. Toxico-dynamic end points are usually in the focus of read across cases. However, without appropriate attention to kinetics and metabolism such cases are unlikely to be successful. To further enhance the quality of read across cases new approach methods can be very useful. Examples based on a biological approach using plasma metabolomics in rats are given. Finally, with the availability of large data sets of structure activity relationships, in silico tools have been developed which provide hitherto undiscovered information. Automated process is now able to assess the chemical - activity space around the molecule target substance and examples are given demonstrating a high predictivity for certain endpoints of toxicity. Thus, this session provides not only current state of the art criteria for good read across, but also indicates how read-across can be further developed in the near future.}, } @article {pmid32521446, year = {2020}, author = {Zhang, Z and Ding, J and Zhu, C and Wang, J}, title = {Combination of efficient signal pre-processing and optimal band combination algorithm to predict soil organic matter through visible and near-infrared spectra.}, journal = {Spectrochimica acta. Part A, Molecular and biomolecular spectroscopy}, volume = {240}, number = {}, pages = {118553}, doi = {10.1016/j.saa.2020.118553}, pmid = {32521446}, issn = {1873-3557}, abstract = {Visible and near-infrared (Vis-NIR) spectroscopy is a promising alternative to replace soil physicochemical Analysis to quickly and effectively determine the content of soil organic matter (SOM). However, choosing appropriate pre-processing methods and effective data mining techniques is the essential step in Vis-NIR to improve the quality of spectral data and the accuracy of the model prediction. In this study, nine spectral pre-processing methods and optimal band combination algorithms were introduced to process the spectra and select sensitive spectral parameters. The purpose of this study is to determine the effective pre-processing method and explore the prediction potential of the optimal band combination algorithm. Two hundred thirty-three soil samples were gathered from northwestern Xinjiang, China, and the soil properties and reflectance spectra were measured in the laboratory. The spectra were subjected to nine pre-processing methods, e.g., Savitzky-Golay (SG) smoothing, discrete wavelet transformation (DWT), First (FD) and second (SD) derivatives, multiplicative scatter correction (MSC), standard normal variate and detrend (SNV-DT), continuum removal (CR), correction by the maximum reflectance (CMR) and pseudo-absorbance values and detrend (Abs-DT). The results indicate, the SG proved to be the most effective pre-processing method for SOM in saline soil. The Abs-DT, FD, SD, SNV-DT, MSC, CR, DWT, and CMR led to degrading the prediction performance. Furthermore, the use of SG before further processing can improve the prediction effect, although it is not obvious. The optimal band combination algorithm can derive spectral parameters that have a good correlation with SOM content. Prediction accuracy (RPIQ was 3.058 and 3.045 in independent and cross-validation respectively) and model complexity (latent variables were both 4) from spectral parameter combination were both better than that from full-spectrum data. In summary, the combination of SG and the optimal band combination algorithm can improve the prediction accuracy of SOM in saline soil.}, } @article {pmid32520945, year = {2020}, author = {Cardiec, F and Bertrand, S and Witt, MJ and Metcalfe, K and Godley, BJ and McClellan, C and Vilela, R and Parnell, RJ and le Loc'h, F}, title = {"Too Big To Ignore": A feasibility analysis of detecting fishing events in Gabonese small-scale fisheries.}, journal = {PloS one}, volume = {15}, number = {6}, pages = {e0234091}, pmid = {32520945}, issn = {1932-6203}, mesh = {Feasibility Studies ; *Fisheries ; Food Supply ; Gabon ; Geographic Information Systems ; Humans ; Markov Chains ; }, abstract = {In many developing countries, small-scale fisheries provide employment and important food security for local populations. To support resource management, the description of the spatiotemporal extent of fisheries is necessary, but often poorly understood due to the diffuse nature of effort, operated from numerous small wooden vessels. Here, in Gabon, Central Africa, we applied Hidden Markov Models to detect fishing patterns in seven different fisheries (with different gears) from GPS data. Models were compared to information collected by on-board observers (7 trips) and, at a larger scale, to a visual interpretation method (99 trips). Models utilizing different sampling resolutions of GPS acquisition were also tested. Model prediction accuracy was high with GPS data sampling rates up to three minutes apart. The minor loss of accuracy linked to model classification is largely compensated by the savings in time required for analysis, especially in a context of nations or organizations with limited resources. This method could be applied to larger datasets at a national or international scale to identify and more adequately manage fishing effort.}, } @article {pmid32520290, year = {2020}, author = {Pedrosa, NL and Albuquerque, NLS}, title = {Spatial Analysis of COVID-19 cases and intensive care beds in the State of Ceará, Brazil.}, journal = {Ciencia & saude coletiva}, volume = {25}, number = {suppl 1}, pages = {2461-2468}, doi = {10.1590/1413-81232020256.1.10952020}, pmid = {32520290}, issn = {1678-4561}, mesh = {Bayes Theorem ; *Betacoronavirus ; Brazil/epidemiology ; COVID-19 ; Coronavirus Infections/*epidemiology/transmission ; Geographic Information Systems ; *Geographic Mapping ; Hospital Bed Capacity/*statistics & numerical data ; Humans ; Intensive Care Units/*supply & distribution ; *Pandemics ; Pneumonia, Viral/*epidemiology/transmission ; SARS-CoV-2 ; }, abstract = {The geographical distribution of COVID-19 through Geographic Information Systems resources is hardly explored. We aimed to analyze the distribution of COVID-19 cases and the exclusive intensive care beds in the state of Ceará, Brazil. This is an ecological study with the geographic distribution of the case detection coefficient in 184 municipalities. Maps of crude and estimated values (global and local Bayesian method) were developed, calculating the Moran index and using BoxMap and MoranMap. Intensive care beds were distributed through geolocalized points. In total, 3,000 cases and 459 beds were studied. The highest rates were found in the capital Fortaleza, the Metropolitan Region (MR), and the south of this region. A positive spatial autocorrelation has been identified in the local Bayesian rate (I = 0.66). The distribution of beds superimposed on the BoxMap shows clusters with a High-High pattern of number of beds (capital, MR, northwestern part). However, a similar pattern is found in the far east or transition areas with insufficient beds. The MoranMap shows clusters statistically significant in the state. COVID-19 interiorization in Ceará requires contingency measures geared to the distribution of specific intensive care beds for COVID-19 cases in order to meet the demand.}, } @article {pmid32518318, year = {2020}, author = {Wang, E and Zhang, D and Braun, MS and Hotz-Wagenblatt, A and Pärt, T and Arlt, D and Schmaljohann, H and Bairlein, F and Lei, F and Wink, M}, title = {Can Mitogenomes of the Northern Wheatear (Oenanthe oenanthe) Reconstruct Its Phylogeography and Reveal the Origin of Migrant Birds?.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {9290}, pmid = {32518318}, issn = {2045-2322}, mesh = {Animal Migration ; Evolution, Molecular ; *Genetic Speciation ; Genome, Mitochondrial/*genetics ; Germany ; Greece ; Haplotypes/genetics ; High-Throughput Nucleotide Sequencing ; Mitochondria/genetics ; Phylogeny ; Songbirds/*classification/*genetics ; }, abstract = {The Northern Wheatear (Oenanthe oenanthe, including the nominate and the two subspecies O. o. leucorhoa and O. o. libanotica) and the Seebohm's Wheatear (Oenanthe seebohmi) are today regarded as two distinct species. Before, all four taxa were regarded as four subspecies of the Northern Wheatear. Their classification has exclusively been based on ecological and morphological traits, while their molecular characterization is still missing. With this study, we used next-generation sequencing to assemble 117 complete mitochondrial genomes covering O. o. oenanthe, O. o. leucorhoa and O. seebohmi. We compared the resolution power of each individual mitochondrial marker and concatenated marker sets to reconstruct the phylogeny and estimate speciation times of three taxa. Moreover, we tried to identify the origin of migratory wheatears caught on Helgoland (Germany) and on Crete (Greece). Mitogenome analysis revealed two different ancient lineages that separated around 400,000 years ago. Both lineages consisted of a mix of subspecies and species. The phylogenetic trees, as well as haplotype networks are incongruent with the present morphology-based classification. Mitogenome could not distinguish these presumed species. The genetic panmixia among present populations and taxa might be the consequence of mitochondrial introgression between ancient wheatear populations.}, } @article {pmid32516876, year = {2020}, author = {Heinrich, F and Wutke, M and Das, PP and Kamp, M and Gültas, M and Link, W and Schmitt, AO}, title = {Identification of Regulatory SNPs Associated with Vicine and Convicine Content of Vicia faba Based on Genotyping by Sequencing Data Using Deep Learning.}, journal = {Genes}, volume = {11}, number = {6}, pages = {}, pmid = {32516876}, issn = {2073-4425}, mesh = {Deep Learning ; Genotype ; Glucosides/*genetics ; Polymorphism, Single Nucleotide/genetics ; Pyrimidinones ; Regulatory Sequences, Nucleic Acid/*genetics ; Seeds/genetics ; Synteny/genetics ; Transcription Factors/genetics ; Uridine/*analogs & derivatives/genetics ; Vicia faba/*genetics ; }, abstract = {Faba bean (Vicia faba) is a grain legume, which is globally grown for both human consumption as well as feed for livestock. Despite its agro-ecological importance the usage of Vicia faba is severely hampered by its anti-nutritive seed-compounds vicine and convicine (V+C). The genes responsible for a low V+C content have not yet been identified. In this study, we aim to computationally identify regulatory SNPs (rSNPs), i.e., SNPs in promoter regions of genes that are deemed to govern the V+C content of Vicia faba. For this purpose we first trained a deep learning model with the gene annotations of seven related species of the Leguminosae family. Applying our model, we predicted putative promoters in a partial genome of Vicia faba that we assembled from genotyping-by-sequencing (GBS) data. Exploiting the synteny between Medicago truncatula and Vicia faba, we identified two rSNPs which are statistically significantly associated with V+C content. In particular, the allele substitutions regarding these rSNPs result in dramatic changes of the binding sites of the transcription factors (TFs) MYB4, MYB61, and SQUA. The knowledge about TFs and their rSNPs may enhance our understanding of the regulatory programs controlling V+C content of Vicia faba and could provide new hypotheses for future breeding programs.}, } @article {pmid32512838, year = {2020}, author = {Juhász, O and Bátori, Z and Trigos-Peral, G and Lőrinczi, G and Módra, G and Bóni, I and Kiss, PJ and Aguilon, DJ and Tenyér, A and Maák, I}, title = {Large- and Small-Scale Environmental Factors Drive Distributions of Ant Mound Size Across a Latitudinal Gradient.}, journal = {Insects}, volume = {11}, number = {6}, pages = {}, pmid = {32512838}, issn = {2075-4450}, support = {2017-01-X-NZ8-01042//Polish National Science Center, Miniatura/ ; NKFIH K 124796//Hungarian Scientific Research Fund/ ; 4724//SZTE Open Access/ ; }, abstract = {Red wood ants are keystone species of forest ecosystems in Europe. Environmental factors and habitat characteristics affect the size of their nest mounds, an important trait being in concordance with a colony's well-being and impact on its surroundings. In this study, we investigated the effect of large-scale (latitude and altitude) and small-scale environmental factors (e.g., characteristics of the forest) on the size of nest mounds of Formica polyctena in Central Europe. We predicted that the change in nest size is in accordance with Bergmann's rule that states that the body size of endotherm animals increases with the higher latitude and/or altitude. We found that the size of nests increased along the latitudinal gradient in accordance with Bergmann's rule. The irradiation was the most important factor responsible for the changes in nest size, but temperature and local factors, like the perimeter of the trees and their distance from the nest, were also involved. Considering our results, we can better understand the long-term effects and consequences of the fast-changing environmental factors on this ecologically important group. This knowledge can contribute to the planning of forest management tactics in concordance with the assurance of the long-term survival of red wood ants.}, } @article {pmid32512417, year = {2020}, author = {Zhang, S and Khan, WA and Su, L and Zhang, X and Li, C and Qin, W and Zhao, Y}, title = {Predicting oxidative stress induced by organic chemicals by using quantitative Structure-Activity relationship methods.}, journal = {Ecotoxicology and environmental safety}, volume = {201}, number = {}, pages = {110817}, doi = {10.1016/j.ecoenv.2020.110817}, pmid = {32512417}, issn = {1090-2414}, mesh = {Algorithms ; Antioxidant Response Elements/genetics ; Biological Assay ; Databases, Factual ; Genes, Reporter ; Humans ; Logistic Models ; *Organic Chemicals/chemistry/toxicity ; Oxidative Stress/*drug effects/genetics ; Quantitative Structure-Activity Relationship ; beta-Lactamases/genetics ; }, abstract = {Cellular exposure to xenobiotic human-made products will lead to oxidative stress that gives rise to DNA damage, as well as chemical or mechanical damage. Distinguishing the chemicals that will induce oxidative stress and predicting their toxicity is necessary. In the present study, 4270 compounds in the ARE-bla assay were investigated to predict active and inactive compounds by using simple algorithms, namely, recursive partitioning (RP) and binomial logistic regression, and to develop the quantitative structure-activity relationship (QSAR) models of chemicals that activate the ARE pathway to induce oxidative stress and exert toxic effects on cells. A decision tree based on scaffold-based fragments obtained through RP analysis showed the best identification accuracy. However, the overall identification accuracy of this model for active compounds was unsatisfactory due to limited fragments. Furthermore, a binomial logistic regression model was developed from 638 active compounds and 3632 inactive chemicals. The model with a cutoff of 0.15 could predict chemicals that were active or inactive with the prediction accuracy of 69.1%. Its area under the receiver operating characteristic (ROC) curve metric (AUROC) was 0.762, which indicated the acceptable predictive ability of this model. The parameters nBM (number of multiple bonds) and H% (percentage of H atom) played dominant roles in the prediction of the activity (inactive or active) of chemicals. A global QSAR model was developed to predict the toxicity of active chemicals. However, the model displayed an unsatisfactory result with R[2] = 0.316 and R[2]ext = 0.090. Active chemicals were then classified on the basis of structure. A total of 79 compounds with carbon chains could be predicted with acceptable performance by using a QSAR model with six descriptors (R[2] = 0.722, R[2]ext = 0.798, Q[2]Loo = 0.654, Q[2]Boot = 0.755, Q[2]ext = 0.721). The simple models established here contribute to efforts on identification compounds inducing oxidative stress and provide the scientific basis for risk assessment to organisms in the environment.}, } @article {pmid32512194, year = {2020}, author = {Pirani, RM and Peloso, PLV and Prado, JR and Polo, ÉM and Knowles, LL and Ron, SR and Rodrigues, MT and Sturaro, MJ and Werneck, FP}, title = {Diversification history of clown tree frogs in Neotropical rainforests (Anura, Hylidae, Dendropsophus leucophyllatus group).}, journal = {Molecular phylogenetics and evolution}, volume = {150}, number = {}, pages = {106877}, doi = {10.1016/j.ympev.2020.106877}, pmid = {32512194}, issn = {1095-9513}, mesh = {Animals ; Anura/*classification/genetics ; Biodiversity ; Databases, Genetic ; Phylogeny ; Rainforest ; South America ; Species Specificity ; }, abstract = {General consensus emphasizes that no single biological process can explain the patterns of species' distributions and diversification in the Neotropics. Instead, the interplay of several processes across space and time must be taken into account. Here we investigated the phylogenetic relationships and biogeographic history of tree frogs in the Dendropsophus leucophyllatus species group (Amphibia: Hylidae), which is distributed across Amazonia and the Atlantic rainforests. Using Next Generation Sequencing (NGS) and double digest restriction-site associated DNA (ddRADseq), we inferred phylogenetic relationships, species limits, and temporal and geographic patterns of diversification relative to the history of these biomes. Our results indicate that the D. leucophyllatus species group includes at least 14 independent lineages, which are currently arranged into ten described species. Therefore, a significant portion of species in the group are still unnamed. Different processes were associated to the group diversification history. For instance, the Andes uplift likely caused allopatric speciation for Cis-Andean species, whereas it may also be responsible for changes in the Amazonian landscape triggering parapatric speciation by local adaptation to ecological factors. Meanwhile, Atlantic Forest ancestors unable to cross the dry diagonal biomes after rainforest's retraction, evolved in isolation into different species. Diversification in the group began in the early Miocene, when connections between Atlantic Forest and the Andes (Pacific Dominion) by way of a south corridor were possible. The historical scenario in Amazonia, characterized by several speciation events and habitat heterogeneity, helped promoting diversification, resulting in the highest species diversity for the group. This marked species diversification did not happen in Atlantic Forest, where speciation is very recent (late Pliocene and Pleistocene), despite its remarkable climatic heterogeneity.}, } @article {pmid32511416, year = {2020}, author = {Worobey, M and Pekar, J and Larsen, BB and Nelson, MI and Hill, V and Joy, JB and Rambaut, A and Suchard, MA and Wertheim, JO and Lemey, P}, title = {The emergence of SARS-CoV-2 in Europe and the US.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {32511416}, issn = {2692-8205}, support = {U19 AI135995/AI/NIAID NIH HHS/United States ; R01 AI136056/AI/NIAID NIH HHS/United States ; T15 LM011271/LM/NLM NIH HHS/United States ; /WT_/Wellcome Trust/United Kingdom ; K01 AI110181/AI/NIAID NIH HHS/United States ; R01 AI135992/AI/NIAID NIH HHS/United States ; }, abstract = {Accurate understanding of the global spread of emerging viruses is critically important for public health response and for anticipating and preventing future outbreaks. Here, we elucidate when, where and how the earliest sustained SARS-CoV-2 transmission networks became established in Europe and the United States (US). Our results refute prior findings erroneously linking cases in January 2020 with outbreaks that occurred weeks later. Instead, rapid interventions successfully prevented onward transmission of those early cases in Germany and Washington State. Other, later introductions of the virus from China to both Italy and Washington State founded the earliest sustained European and US transmission networks. Our analyses reveal an extended period of missed opportunity when intensive testing and contact tracing could have prevented SARS-CoV-2 from becoming established in the US and Europe.}, } @article {pmid32510727, year = {2020}, author = {Sannino, C and Borruso, L and Mezzasoma, A and Battistel, D and Zucconi, L and Selbmann, L and Azzaro, M and Onofri, S and Turchetti, B and Buzzini, P and Guglielmin, M}, title = {Intra- and inter-cores fungal diversity suggests interconnection of different habitats in an Antarctic frozen lake (Boulder Clay, Northern Victoria Land).}, journal = {Environmental microbiology}, volume = {22}, number = {8}, pages = {3463-3477}, doi = {10.1111/1462-2920.15117}, pmid = {32510727}, issn = {1462-2920}, mesh = {Antarctic Regions ; Clay ; Ecosystem ; Fungi/*classification/genetics ; Ice Cover/chemistry/*microbiology ; Lakes/chemistry/microbiology ; Mycobiome ; Organic Chemicals/analysis ; Permafrost/chemistry/*microbiology ; Salinity ; Salts/analysis ; }, abstract = {A perennially frozen lake at Boulder Clay site (Victoria Land, Antarctica), characterized by the presence of frost mounds, have been selected as an in situ model for ecological studies. Different samples of permafrost, glacier ice and brines have been studied as a unique habitat system. An additional sample of brines (collected in another frozen lake close to the previous one) was also considered. Alpha- and beta-diversity of fungal communities showed both intra- and inter-cores significant (p < 0.05) differences, which suggest the presence of interconnection among the habitats. Therefore, the layers of frost mound and the deep glacier could be interconnected while the brines could probably be considered as an open habitat system not interconnected with each other. Moreover, the absence of similarity between the lake ice and the underlying permafrost suggested that the lake is perennially frozen based. The predominance of positive significant (p < 0.05) co-occurrences among some fungal taxa allowed to postulate the existence of an ecological equilibrium in the habitats systems. The positive significant (p < 0.05) correlation between salt concentration, total organic carbon and pH, and some fungal taxa suggests that a few abiotic parameters could drive fungal diversity inside these ecological niches.}, } @article {pmid32509768, year = {2020}, author = {Emamalipour, M and Seidi, K and Zununi Vahed, S and Jahanban-Esfahlan, A and Jaymand, M and Majdi, H and Amoozgar, Z and Chitkushev, LT and Javaheri, T and Jahanban-Esfahlan, R and Zare, P}, title = {Horizontal Gene Transfer: From Evolutionary Flexibility to Disease Progression.}, journal = {Frontiers in cell and developmental biology}, volume = {8}, number = {}, pages = {229}, pmid = {32509768}, issn = {2296-634X}, abstract = {Flexibility in the exchange of genetic material takes place between different organisms of the same or different species. This phenomenon is known to play a key role in the genetic, physiological, and ecological performance of the host. Exchange of genetic materials can cause both beneficial and/or adverse biological consequences. Horizontal gene transfer (HGT) or lateral gene transfer (LGT) as a general mechanism leads to biodiversity and biological innovations in nature. HGT mediators are one of the genetic engineering tools used for selective introduction of desired changes in the genome for gene/cell therapy purposes. HGT, however, is crucial in development, emergence, and recurrence of various human-related diseases, such as cancer, genetic-, metabolic-, and neurodegenerative disorders and can negatively affect the therapeutic outcome by promoting resistant forms or disrupting the performance of genome editing toolkits. Because of the importance of HGT and its vital physio- and pathological roles, here the variety of HGT mechanisms are reviewed, ranging from extracellular vesicles (EVs) and nanotubes in prokaryotes to cell-free DNA and apoptotic bodies in eukaryotes. Next, we argue that HGT plays a role both in the development of useful features and in pathological states associated with emerging and recurrent forms of the disease. A better understanding of the different HGT mediators and their genome-altering effects/potentials may pave the way for the development of more effective therapeutic and diagnostic regimes.}, } @article {pmid32508508, year = {2020}, author = {Tsai, PY and Ko, CJ and Hsieh, C and Su, YT and Lu, YJ and Lin, RS and Tuanmu, MN}, title = {A trait dataset for Taiwan's breeding birds.}, journal = {Biodiversity data journal}, volume = {8}, number = {}, pages = {e49735}, pmid = {32508508}, issn = {1314-2828}, abstract = {BACKGROUND: Species traits affect how a species interacts with the environment and other species and thus determine the role of the species in an ecosystem. They affect not only population dynamics of a species across space and over time, but also community structure and function through their key role in the community assembly processes. Information on species traits is also highly relevant for conservation planning as they determine the adaptive ability of a species in the face of environmental changes. However, information on species traits is usually scarce and sparsely distributed amongst diverse types of literature and sources. Difficulty in accessing comprehensive information on species traits has formed an essential knowledge gap, limiting our understanding of biodiversity patterns and ecosystem functioning and preventing effective conservation. Even for birds, a well-studied taxon, comprehensive trait information is still unavailable or distributed across different sources for many species.

NEW INFORMATION: In this study, we compiled information from a variety of sources on 23 traits for all breeding birds, including 157 resident and 14 summer visiting species, in Taiwan and surrounding islands. The 23 traits include those related to the movement patterns, morphology, geographic distributions, activity patterns, feeding behaviour, habitat use, and breeding behaviour and strategies of the species. The trait information was obtained, not only from published literature and datasets, but also from unpublished banding records and specimen measurements. The dataset also contains derived traits, including the elevation and temperature boundaries of species distribution ranges in Taiwan. In addition, structured information on nest characters, which is seldom compiled in trait datasets, has been made available, for the first time, for the breeding birds in Taiwan. Therefore, the most comprehensive trait dataset to date on breeding birds in Taiwan will allow trait-based research and applications in diverse topics and thus enhance our understanding of the patterns and dynamics of breeding bird diversity and its functions in Taiwan.}, } @article {pmid32504432, year = {2020}, author = {Sarker, KK and Bristy, MS and Alam, N and Baki, MA and Shojib, FH and Quraishi, SB and Khan, MF}, title = {Ecological risk and source apportionment of heavy metals in surface water and sediments on Saint Martin's Island in the Bay of Bengal.}, journal = {Environmental science and pollution research international}, volume = {27}, number = {25}, pages = {31827-31840}, doi = {10.1007/s11356-020-09384-x}, pmid = {32504432}, issn = {1614-7499}, mesh = {Bays ; China ; Environmental Monitoring ; Geologic Sediments ; Islands ; Metals, Heavy/*analysis ; Risk Assessment ; Rivers ; Water ; Water Pollutants, Chemical/*analysis ; }, abstract = {The study aimed to determine eight hazardous heavy metals in surface water and sediment samples collected from the Naf River, Shah Porir Dwip (estuary), and mostly around Saint Martin's Island in the Bay of Bengal. The results of heavy metals in water samples were ranged as Pb 14.7-313.0, Cd 33.0-70.0, Cr < 11.0-37.0, Cu 38.0-57.0, Zn 26.8-69.2, Ni 102.0-285.0, and Hg 0.3-1.6 μg L[-1]. The concentrations of metals in sediment samples were ranged as Pb < 10.0-37.5, Cd 0.2-1.0, Cr < 5.0-30.1, Cu < 3.0-30.9, Zn 24.1-88.0, Ni < 4.0-48.3, As 0.1-7.3, and Hg < 0.01-0.08 mg kg[-1] dw. Ni and Cr were strongly correlated, suggesting that this pair of metals might diffuse from a common origin. The contamination factor (C[i]f) demonstrated that sediment samples were mostly contaminated by Cd and slightly contaminated by Pb and Zn. The geoaccumulation index (Igeo) revealed considerable values for Cd on Saint Martin's Island. Cd as a single regulator posed moderate to considerable risk frequently among the sampling stations. Pollution load index (PLI) values remained below 1 (< 1), which indicated a decrease from baseline pollution value among all stations. However, potential ecological risk (PER) was graded for two stations (St1 and St13) with a moderate-risk zone due to the Cd contribution. However, shipping emission and lithogenic sources were the most predominant for heavy metals in the sediment, which were determined by applying the principal component analysis-absolute principal component score (PCA-APCS). Graphical abstract.}, } @article {pmid32504167, year = {2020}, author = {Figueiroa, AC and de Lima, AS and Scherer, MEG and Bonetti, J}, title = {How to choose the best category for a protected area? A multicriteria analysis method based on ecosystem services conservation.}, journal = {Environmental monitoring and assessment}, volume = {192}, number = {7}, pages = {416}, doi = {10.1007/s10661-020-08333-y}, pmid = {32504167}, issn = {1573-2959}, mesh = {Biodiversity ; Brazil ; *Conservation of Natural Resources/methods ; Data Interpretation, Statistical ; *Ecosystem ; Environmental Monitoring ; }, abstract = {This study proposes a novel methodology to define protected area (PA) categories based on the analysis of how much a PA can protect important ecosystem services (ESs). PA are important tools to minimize the continuing global biodiversity conservation crisis. However, the contribution of PA to conservation is variable, mainly due to the diverse management categories with which they can be associated. In order to support the assignment of a PA to a management category, a multicriteria analysis (MCA) strategy was developed. Essentially, it consisted of the application of an analytic hierarchy process (AHP) and its association to management categories that could support the conservation of the most significant ESs. To test the methodology, the framework was applied to the Carijós Ecological Station (ESEC Carijós), Santa Catarina, Brazil, and its surrounding area of influence. Using the IUCN list of categories for the case study, it was found that IUCN Ia and IV could be the most efficient measures to protect important ESs at ESEC Carijós. Although the methodology was applied to a particular case, it could be employed worldwide, establishing the best category to be assigned to an existing or proposed potential PA.}, } @article {pmid32503078, year = {2020}, author = {Guzmán-Rangel, G and Torres Díaz, AN and Pavón Meza, EL and Oorts, K and Smolders, E}, title = {Validating the Use of a Toxicity Database for Prediction of Plant Cover and Biodiversity in Multi-Metal Mining-Impacted Soils.}, journal = {Environmental toxicology and chemistry}, volume = {39}, number = {9}, pages = {1826-1838}, doi = {10.1002/etc.4795}, pmid = {32503078}, issn = {1552-8618}, support = {359484//Consejo Nacional de Ciencia y Tecnología/International ; }, mesh = {Arsenic/analysis ; *Biodiversity ; *Databases as Topic ; Metals/*analysis ; Mexico ; *Mining ; *Plants/drug effects ; Risk Assessment ; Soil/*chemistry ; Soil Pollutants/toxicity ; }, abstract = {The validity of soil toxicity databases for predicting ecological impacts in the field is rarely explored. The present study was set up to test whether laboratory toxicity data and the combined concepts of metal availability and mixture toxicity can predict ecological impact in mining-affected soils. Metal and As contamination gradients were sampled approximately 5 different mines in Mexico where plant cover and abundances exhibited clear dose-related responses. Soils were analyzed for total and isotopically exchangeable (labile) concentrations of Ni, Cu, Cd, Pb, and As and for soil properties affecting the availability of these elements. Six different indices of toxic doses were compared to evaluate their accuracy in describing the field response expressed as relative abundance and cover. Each index was based on a different method to calculate the sum of toxic units (Σ TUs) in soil, with 1 toxic unit equal to the concentration of the element in soil yielding 50% adverse effect on plants with median sensitivity as recorded in a recent database of salt-spiked soils. Toxic concentrations in the mine-impacted soils were dominated by Zn and As. In the field, 50% reduced cover or abundance was found at 10 to 13 Σ TUs if these were based on total soil concentrations and thresholds derived from freshly spiked soils, indicating a largely overestimated toxic effect. If thresholds were corrected for differences in availability among freshly spiked soils and spiked and laboratory-aged soils, the overestimation of field toxicity was 5- to 6-fold, irrespective of the consideration of soil properties. Finally, the Σ TU calculated only with labile metals and As overestimated the field toxicity by factors 1.1 to 1.6 (95% confidence interval 1-7; i.e., rather accurate and indicating some Zn-As antagonism as confirmed in experimental studies). That latter index of dose yielded a bell-shaped response on species richness peaking at approximately 1.6 Σ TU. Overall, the present study shows that the current toxicity databases of metals can predict the impact of metal contamination on plant communities within factor 2, expressing the dose as soil-labile concentrations and using the concentration addition concept in these mixed polluted environments. Environ Toxicol Chem 2020;39:1826-1838. © 2020 SETAC.}, } @article {pmid32502238, year = {2020}, author = {Morel, B and Kozlov, AM and Stamatakis, A and Szöllősi, GJ}, title = {GeneRax: A Tool for Species-Tree-Aware Maximum Likelihood-Based Gene Family Tree Inference under Gene Duplication, Transfer, and Loss.}, journal = {Molecular biology and evolution}, volume = {37}, number = {9}, pages = {2763-2774}, pmid = {32502238}, issn = {1537-1719}, support = {714774/ERC_/European Research Council/International ; }, mesh = {Cyanobacteria/genetics ; Gene Deletion ; *Gene Duplication ; Gene Transfer, Horizontal ; *Genetic Techniques ; *Phylogeny ; *Software ; }, abstract = {Inferring phylogenetic trees for individual homologous gene families is difficult because alignments are often too short, and thus contain insufficient signal, while substitution models inevitably fail to capture the complexity of the evolutionary processes. To overcome these challenges, species-tree-aware methods also leverage information from a putative species tree. However, only few methods are available that implement a full likelihood framework or account for horizontal gene transfers. Furthermore, these methods often require expensive data preprocessing (e.g., computing bootstrap trees) and rely on approximations and heuristics that limit the degree of tree space exploration. Here, we present GeneRax, the first maximum likelihood species-tree-aware phylogenetic inference software. It simultaneously accounts for substitutions at the sequence level as well as gene level events, such as duplication, transfer, and loss relying on established maximum likelihood optimization algorithms. GeneRax can infer rooted phylogenetic trees for multiple gene families, directly from the per-gene sequence alignments and a rooted, yet undated, species tree. We show that compared with competing tools, on simulated data GeneRax infers trees that are the closest to the true tree in 90% of the simulations in terms of relative Robinson-Foulds distance. On empirical data sets, GeneRax is the fastest among all tested methods when starting from aligned sequences, and it infers trees with the highest likelihood score, based on our model. GeneRax completed tree inferences and reconciliations for 1,099 Cyanobacteria families in 8 min on 512 CPU cores. Thus, its parallelization scheme enables large-scale analyses. GeneRax is available under GNU GPL at https://github.com/BenoitMorel/GeneRax (last accessed June 17, 2020).}, } @article {pmid32498187, year = {2020}, author = {Yu, J and Li, F and Wang, Y and Lin, Y and Peng, Z and Cheng, K}, title = {Spatiotemporal evolution of tropical forest degradation and its impact on ecological sensitivity: A case study in Jinghong, Xishuangbanna, China.}, journal = {The Science of the total environment}, volume = {727}, number = {}, pages = {138678}, doi = {10.1016/j.scitotenv.2020.138678}, pmid = {32498187}, issn = {1879-1026}, mesh = {Agriculture ; China ; *Conservation of Natural Resources ; *Forests ; Humans ; }, abstract = {Due to rapid urbanization and a growing population, the tropical forest in southwestern China has experienced a dramatic shrinkage, which threatens its biodiversity and imposes limitations to sustainable development. Spatiotemporal change analysis and ecological sensitivity assessment are the important prerequisites for investigating the relationship between eco-environmental quality and human activities. In this study, the tropical forest and other land cover types in Jinghong, China were firstly classified by a machine learning classification algorithm (support vector machine, SVM) with 7 pairs of remote sensing (RS) data (from 1989 to 2018). Then the spatiotemporal change patterns were analyzed. The ecological sensitivity was evaluated based on an index system method (ISM) in which a weighted combination of eleven indicators were produced using an analytic hierarchy process (AHP) method and GIS. Meanwhile four individual sensitivity indicators, including biodiversity sensitivity (BS), water resources sensitivity (WRS), geological hazard sensitivity (GHS) and soil erosion sensitivity (SES) were assessed respectively to create a multi-perspective understanding of the entire ecological sensitivity. The results suggest that the tropical forest experienced a continual decrease from 5631.78 km[2] in 1999 to 4216.23 km[2] in 2018 with an average change rate of -1.49%. The decreased area was mainly encroached on by human settlements and agriculture, particularly in the south of Jinghong. Furthermore, it could be seen that urbanization is the key driver for the changes to ecological sensitivity with both positive and negative impacts. In Jinghong, the region covered by a tropical forest has a relatively higher comprehensive ecological sensitivity (CES) than that of an urban area. This work shows RS and GIS to be powerful tools providing profound insights to researchers with regard to the spatiotemporal evolution of tropical forests and ecological sensitivity. The results are significant for improving policies in order to keep a sustainable balance in regional ecosystem management.}, } @article {pmid32497965, year = {2020}, author = {Schwabe, R and Senges, CHR and Bandow, JE and Heine, T and Lehmann, H and Wiche, O and Schlömann, M and Levicán, G and Tischler, D}, title = {Cultivation dependent formation of siderophores by Gordonia rubripertincta CWB2.}, journal = {Microbiological research}, volume = {238}, number = {}, pages = {126481}, doi = {10.1016/j.micres.2020.126481}, pmid = {32497965}, issn = {1618-0623}, mesh = {Actinobacteria/genetics/*metabolism ; Chelating Agents/metabolism ; Chromatography, Liquid ; Culture Media ; Deferoxamine/metabolism ; Gene Expression Regulation, Bacterial ; Genome, Bacterial ; Iron/*metabolism ; Mass Spectrometry ; Siderophores/*metabolism ; Transcriptome ; }, abstract = {Herein we demonstrate cultivation-dependent siderophore production by the actinomycete Gordonia rubripertincta CWB2. The strain produces mostly citrate, but also desferrioxamine E (DFOE) and new hydroxamate-type siderophores. The production of hydroxamate-like siderophores is influenced by cultivation conditions, for example available carbon sources or presence of metals, such as the rare earth erbium or the heavy metal lead. By cultivation with succinate and extraction with an adsorbing resin (XAD) we purified the G. rubripertincta CWB2 siderophores (yield up to 178 mg L[-1]). The respective workflow comprises genome mining, cultivation, and overproduction strategies, a rapid screening procedure, as well as traditional structure enrichment and structure elucidation methods. This combination of methods allows the discovery of new natural products with metal complexation capacity, also for lanthanides of commercial value. G. rubripertincta CWB2 carries a desferrioxamine-like biosynthetic gene cluster. Its transcription was proven by a transcriptomic approach comparing expression levels of the selected gene cluster during cultivation in iron-depleted and repleted media. Further investigation of the siderophores of this desferrioxamine producing Actinobacterium could lead to new structures.}, } @article {pmid32495495, year = {2020}, author = {Rodriguez-R, LM and Tsementzi, D and Luo, C and Konstantinidis, KT}, title = {Iterative subtractive binning of freshwater chronoseries metagenomes identifies over 400 novel species and their ecologic preferences.}, journal = {Environmental microbiology}, volume = {22}, number = {8}, pages = {3394-3412}, doi = {10.1111/1462-2920.15112}, pmid = {32495495}, issn = {1462-2920}, support = {1241046//National Science Foundation/International ; 1759831//National Science Foundation/International ; }, mesh = {Chloroflexi/*classification/genetics/*isolation & purification ; Databases, Genetic ; Genome, Bacterial/*genetics ; Lakes/*microbiology ; Metagenome/genetics ; Metagenomics ; Microbiota/genetics ; }, abstract = {Recent advances in sequencing technology and bioinformatic pipelines have allowed unprecedented access to the genomes of yet-uncultivated microorganisms from diverse environments. However, the catalogue of freshwater genomes remains limited, and most genome recovery attempts in freshwater ecosystems have only targeted specific taxa. Here, we present a genome recovery pipeline incorporating iterative subtractive binning, and apply it to a time series of 100 metagenomic datasets from seven connected lakes and estuaries along the Chattahoochee River (Southeastern USA). Our set of metagenome-assembled genomes (MAGs) represents >400 yet-unnamed genomospecies, substantially increasing the number of high-quality MAGs from freshwater lakes. We propose names for two novel species: 'Candidatus Elulimicrobium humile' ('Ca. Elulimicrobiota', 'Patescibacteria') and 'Candidatus Aquidulcis frankliniae' ('Chloroflexi'). Collectively, our MAGs represented about half of the total microbial community at any sampling point. To evaluate the prevalence of these genomospecies in the chronoseries, we introduce methodologies to estimate relative abundance and habitat preference that control for uneven genome quality and sample representation. We demonstrate high degrees of habitat-specialization and endemicity for most genomospecies in the Chattahoochee lakes. Wider ecological ranges characterized smaller genomes with higher coding densities, indicating an overall advantage of smaller, more compact genomes for cosmopolitan distributions.}, } @article {pmid32492285, year = {2020}, author = {Ackiss, AS and Balao, F}, title = {Diving in uncharted waters: An updated genetics toolkit highlights the challenges of polyploidy in landscape genomics analyses.}, journal = {Molecular ecology resources}, volume = {20}, number = {4}, pages = {841-843}, doi = {10.1111/1755-0998.13203}, pmid = {32492285}, issn = {1755-0998}, mesh = {Animals ; Computational Biology/methods ; Ecology/methods ; Genome/*genetics ; Genomics/*methods ; Humans ; Polyploidy ; Software ; }, abstract = {As molecular ecologists, we have by necessity become adept at working across computational platforms. A diverse community of scientists has developed a broad array of analytical resources spanning command line to graphical user interface across Linux, Mac, and Windows environments and a dizzying array of program-specific input formats. In light of this, we often explore our data like free divers - filling our lungs with air and descending for a short period of time into one part of our data set before resurfacing, reformatting, and preparing for our next analysis. In this issue of Molecular Ecology Resources, Meirmans (2020) presents an updated version of GenoDive, a program with a toolkit that provides users with the opportunity to stay a while and delve deeper into the diverse portfolio of information provided by a genomic data set. The comprehensive nature of GenoDive coupled with its unique capability to handle both diploid and polyploid data also provides an opportunity to reflect on the unevenness of resources available for the analysis of polyploid versus diploid data. Since new updates include the addition of plug-ins for genotype-environment association analyses, we limit the observations presented here to the common tools used for landscape genomics analyses.}, } @article {pmid32492276, year = {2020}, author = {Sauer, FG and Jaworski, L and Lühken, R and Kiel, E}, title = {Impacts of sampling rhythm and exposition on the effectiveness of artificial resting shelters for mosquito collection in northern Germany.}, journal = {Journal of vector ecology : journal of the Society for Vector Ecology}, volume = {45}, number = {1}, pages = {142-146}, doi = {10.1111/jvec.12383}, pmid = {32492276}, issn = {1948-7134}, mesh = {Animals ; Culicidae ; Germany ; Mosquito Control/*methods ; Mosquito Vectors ; }, } @article {pmid32492136, year = {2020}, author = {Westerman, EL and Bowman, SEJ and Davidson, B and Davis, MC and Larson, ER and Sanford, CPJ}, title = {Deploying Big Data to Crack the Genotype to Phenotype Code.}, journal = {Integrative and comparative biology}, volume = {60}, number = {2}, pages = {385-396}, doi = {10.1093/icb/icaa055}, pmid = {32492136}, issn = {1557-7023}, mesh = {*Big Data ; Computational Biology/*methods ; *Genetic Code ; *Genotype ; *Phenotype ; }, abstract = {Mechanistically connecting genotypes to phenotypes is a longstanding and central mission of biology. Deciphering these connections will unite questions and datasets across all scales from molecules to ecosystems. Although high-throughput sequencing has provided a rich platform on which to launch this effort, tools for deciphering mechanisms further along the genome to phenome pipeline remain limited. Machine learning approaches and other emerging computational tools hold the promise of augmenting human efforts to overcome these obstacles. This vision paper is the result of a Reintegrating Biology Workshop, bringing together the perspectives of integrative and comparative biologists to survey challenges and opportunities in cracking the genotype to phenotype code and thereby generating predictive frameworks across biological scales. Key recommendations include promoting the development of minimum "best practices" for the experimental design and collection of data; fostering sustained and long-term data repositories; promoting programs that recruit, train, and retain a diversity of talent; and providing funding to effectively support these highly cross-disciplinary efforts. We follow this discussion by highlighting a few specific transformative research opportunities that will be advanced by these efforts.}, } @article {pmid32490092, year = {2020}, author = {Schwabe, R and Senges, CHR and Bandow, JE and Heine, T and Lehmann, H and Wiche, O and Schlömann, M and Levicán, G and Tischler, D}, title = {Data on metal-chelating, -immobilisation and biosorption properties by Gordonia rubripertincta CWB2 in dependency on rare earth adaptation.}, journal = {Data in brief}, volume = {31}, number = {}, pages = {105739}, pmid = {32490092}, issn = {2352-3409}, abstract = {Recent studies have shown that the metal adaptation of Actinobacteria offers a rich source of metal inducible environmentally relevant bio-compounds and molecules. These interact through biosorption towards the unique cell walls or via metal chelating activity of metallophors with trace elements, heavy metals and even with lanthanides to overcome limitations and toxic concentrations. Herein, the purpose is to investigate the adaptation potential of Gordonia rubripertincta CWB2 in dependence of the rare earths and to determine if we can utilize promising metallophore metal affinities for metal separation from aquatic solutions. For details on data interpretation and applicability of siderophores we refer to the related article entitled "Cultivation dependent formation of siderophores by Gordonia rubripertincta CWB2" [1]. The respective workflow comprises a metal adaptation method to demonstrate effects on bacterial growth, pH, metallophore production, and metabolic change. All this was evaluated by LC-MS/MS and effects on biosorption of rare earths was verified by ICP-MS. Furthermore, we were able to carry out batch metal adsorption and desorption studies of metallophores entrapped in inorganic polymers of tetramethoxysilane (TMOS) to determine metal chelating capacities and selective enrichment effects from model solutions. The adaptation potential of strain CWB2 at increased erbium and manganese concentrations was verified by increased chelating activity on agar plates, in liquid assays and demonstrated by the successful enrichment of erbium by metallophore-functionalized TMOS-polymers from an aquatic model solution. Furthermore, the number of detected compounds in dependency of rare earths differ in spectral counts and diversity compared to the wild type. Finally, the biosorption of rare earths for the selected adaptation was increased significantly up to 2-fold compared to the wild-type. Overall a holistic approach to metal stress was utilised, integrating a bacterial erbium adaptation, metal chelating, biosorption of lanthanides and immobilization as well as enrichment of metals using metallophore functionalized inorganic TMOS polymers for separation of metals from aquatic model solutions.}, } @article {pmid32488508, year = {2020}, author = {Sajjad, W and Din, G and Rafiq, M and Iqbal, A and Khan, S and Zada, S and Ali, B and Kang, S}, title = {Pigment production by cold-adapted bacteria and fungi: colorful tale of cryosphere with wide range applications.}, journal = {Extremophiles : life under extreme conditions}, volume = {24}, number = {4}, pages = {447-473}, pmid = {32488508}, issn = {1433-4909}, mesh = {Bacteria ; Fungi ; Pigments, Biological/*metabolism ; Ultraviolet Rays ; }, abstract = {Pigments are an essential part of everyday life on Earth with rapidly growing industrial and biomedical applications. Synthetic pigments account for a major portion of these pigments that in turn have deleterious effects on public health and environment. Such drawbacks of synthetic pigments have shifted the trend to use natural pigments that are considered as the best alternative to synthetic pigments due to their significant properties. Natural pigments from microorganisms are of great interest due to their broader applications in the pharmaceutical, food, and textile industry with increasing demand among the consumers opting for natural pigments. To fulfill the market demand of natural pigments new sources should be explored. Cold-adapted bacteria and fungi in the cryosphere produce a variety of pigments as a protective strategy against ecological stresses such as low temperature, oxidative stresses, and ultraviolet radiation making them a potential source for natural pigment production. This review highlights the protective strategies and pigment production by cold-adapted bacteria and fungi, their industrial and biomedical applications, condition optimization for maximum pigment extraction as well as the challenges facing in the exploitation of cryospheric microorganisms for pigment extraction that hopefully will provide valuable information, direction, and progress in forthcoming studies.}, } @article {pmid32488082, year = {2020}, author = {Mohl, JE and Fetcher, N and Stunz, E and Tang, J and Moody, ML}, title = {Comparative transcriptomics of an arctic foundation species, tussock cottongrass (Eriophorum vaginatum), during an extreme heat event.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {8990}, pmid = {32488082}, issn = {2045-2322}, mesh = {Alaska ; Arctic Regions ; Cyperaceae/genetics/*physiology ; Ecotype ; Extreme Heat ; Gene Expression Profiling ; *Gene Expression Regulation, Plant ; Gene Ontology ; Temperature ; }, abstract = {Tussock cottongrass (Eriophorum vaginatum) is a foundation species for much of the arctic moist acidic tundra, which is currently experiencing extreme effects of climate change. The Arctic is facing higher summer temperatures and extreme weather events are becoming more common. We used Illumina RNA-Seq to analyse cDNA libraries for differential expression of genes from leaves of ecologically well-characterized ecotypes of tussock cottongrass found along a latitudinal gradient in the Alaskan Arctic and transplanted into a common garden. Plant sampling was performed on a typical summer day and during an extreme heat event. We obtained a de novo assembly that contained 423,353 unigenes. There were 363 unigenes up-regulated and 1,117 down-regulated among all ecotypes examined during the extreme heat event. Of these, 26 HSP unigenes had >log2-fold up-regulation. Several TFs associated with heat stress in previous studies were identified that had >log2-fold up- or down-regulation during the extreme heat event (e.g., DREB, NAC). There was consistent variation in DEGs among ecotypes, but not specifically related to whether plants originated from taiga or tundra ecosystems. As the climate changes it is essential to determine ecotypic diversity at the genomic level, especially for widespread species that impact ecosystem function.}, } @article {pmid32480144, year = {2020}, author = {Carnesecchi, E and Toma, C and Roncaglioni, A and Kramer, N and Benfenati, E and Dorne, JLCM}, title = {Integrating QSAR models predicting acute contact toxicity and mode of action profiling in honey bees (A. mellifera): Data curation using open source databases, performance testing and validation.}, journal = {The Science of the total environment}, volume = {735}, number = {}, pages = {139243}, doi = {10.1016/j.scitotenv.2020.139243}, pmid = {32480144}, issn = {1879-1026}, mesh = {Animals ; Bees ; *Data Curation ; Ecosystem ; *Pesticides ; Quantitative Structure-Activity Relationship ; Reproducibility of Results ; }, abstract = {Honey bees (Apis mellifera) provide key ecosystem services as pollinators bridging agriculture, the food chain and ecological communities, thereby ensuring food production and security. Ecological risk assessment of single Plant Protection Products (PPPs) requires an understanding of the exposure and toxicity. In silico tools such as QSAR models can play a major role for the prediction of structural, physico-chemical and pharmacokinetic properties of chemicals as well as toxicity of single and multiple chemicals. Here, the first integrative honey bee QSAR model has been developed for PPPs using EFSA's OpenFoodTox, US-EPA ECOTOX and Pesticide Properties DataBase i) to predict acute contact toxicity (LD50) and ii) to profile the Mode of Action (MoA) of pesticides active substances. Three different classification-based and four regression-based models were developed and tested for their performance, thus identifying two models providing the most reliable predictions based on k-NN algorithm. The two-category QSAR model (toxic/non-toxic; n = 411) was validated using sensitivity (=0.93), specificity (=0.85), balanced accuracy (=0.90), and Matthews correlation coefficient (MCC = 0.78) as statistical parameters. The regression-based model (n = 113) was validated for its reliability and robustness (R[2] = 0.74; MAE = 0.52). Current study proposes the MoA profiling for 113 pesticides active substances and the first harmonised MoA classification scheme for acute contact toxicity in honey bees, including LD50s data points from three different databases. The classification allows to further define MoAs and the target site of PPPs active substances, thus enabling regulators and scientists to refine chemical grouping and toxicity extrapolations for single chemicals and component-based mixture risk assessment of multiple chemicals. Relevant future perspectives are briefly addressed to integrate MoA, adverse outcome pathways (AOPs) and toxicokinetic information for the refinement of single-chemical/combined toxicity predictions and risk estimates at different levels of biological organization in the bee health context.}, } @article {pmid32479932, year = {2020}, author = {Jung, DH and Seo, DH and Kim, YJ and Chung, WH and Nam, YD and Park, CS}, title = {The presence of resistant starch-degrading amylases in Bifidobacterium adolescentis of the human gut.}, journal = {International journal of biological macromolecules}, volume = {161}, number = {}, pages = {389-397}, doi = {10.1016/j.ijbiomac.2020.05.235}, pmid = {32479932}, issn = {1879-0003}, mesh = {Amino Acid Sequence ; Amylases/chemistry/*metabolism ; Bifidobacterium/classification/enzymology/genetics ; Bifidobacterium adolescentis/classification/*enzymology/genetics ; Computational Biology/methods ; *Gastrointestinal Microbiome ; Genome, Bacterial ; Humans ; Hydrolysis ; Phylogeny ; Resistant Starch/*metabolism ; }, abstract = {Resistant starch (RS) is a complex prebiotic carbohydrate beneficial to the human gut. In the present study, four genes encoding for putative amylolytic enzymes, likely to be responsible for RS-degradation, were identified in the genome of Bifidobacterium adolescentis P2P3 by comparative genomic analysis. Our results showed that only three enzymes (RSD1, RSD2, and RSD3) exhibited non-gelatinized high amylose corn starch (HACS)-degrading activity in addition to typical α-amylase activity. These three RS-degrading enzymes (RSD) were composed of multiple domains, including signal peptide, catalytic domain, carbohydrate binding domains, and putative cell wall-anchoring domains. Typical catalytic domains were conserved by exhibiting seven typical conserved regions (I-VII) found mostly in α-amylases. Analysis of enzymatic activity revealed that RSD2 displayed stronger activity toward HACS-granules than RSD1 and RSD3. Comparative genomics in combination with enzymatic experiments confirmed that RSDs might be the key enzymes used by RS-degrading bifidobacteria to degrade RS in a particular ecological niche, such as the human gut.}, } @article {pmid32471519, year = {2020}, author = {Jia, J and Jin, J and Chen, Q and Yuan, Z and Li, H and Bian, J and Gui, L}, title = {Eukaryotic expression, Co-IP and MS identify BMPR-1B protein-protein interaction network.}, journal = {Biological research}, volume = {53}, number = {1}, pages = {24}, pmid = {32471519}, issn = {0717-6287}, support = {31660662//National Natural Science Foundation of China/ ; 2020-ZJ-735//National Natural Science Foundation of China/ ; 2019-zz-02//Key of laboratory of Plateau Ecology and Agriculture(Qinghai University)/ ; }, mesh = {Animals ; Bone Morphogenetic Protein Receptors, Type I/*genetics/metabolism ; Computational Biology ; Eukaryota/*genetics/metabolism ; Female ; Genotype ; Mass Spectrometry ; Mutation ; Ovary/*metabolism ; Polymerase Chain Reaction ; Polymorphism, Restriction Fragment Length ; Protein Interaction Maps/*genetics ; Sheep ; Signal Transduction ; }, abstract = {BACKGROUND: BMPR-1B is part of the transforming growth factor β super family and plays a pivotal role in ewe litter size. Functional loss of exon-8 mutations in the BMPR-1B gene (namely the FecB gene) can increase both the ewe ovulation rate and litter size.

RESULTS: This study constructed a eukaryotic expression system, prepared a monoclonal antibody, and characterized BMPR-1B/FecB protein-protein interactions (PPIs). Using Co-immunoprecipitation coupled to mass spectrometry (Co-IP/MS), 23 proteins were identified that specifically interact with FecB in ovary extracts of ewes. Bioinformatics analysis of selected PPIs demonstrated that FecB associated with several other BMPs, primarily via signal transduction in the ovary. FecB and its associated interaction proteins enriched the reproduction process via BMP2 and BMP4 pathways. Signal transduction was identified via Smads proteins and TGF-beta signaling pathway by analyzing the biological processes and pathways. Moreover, other target proteins (GDF5, GDF9, RhoD, and HSP 10) that interact with FecB and that are related to ovulation and litter size in ewes were identified.

CONCLUSIONS: In summary, this research identified a novel pathway and insight to explore the PPi network of BMPR-1B.}, } @article {pmid32469868, year = {2020}, author = {Huber, CD and Kim, BY and Lohmueller, KE}, title = {Population genetic models of GERP scores suggest pervasive turnover of constrained sites across mammalian evolution.}, journal = {PLoS genetics}, volume = {16}, number = {5}, pages = {e1008827}, pmid = {32469868}, issn = {1553-7404}, support = {R35 GM119856/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Computational Biology/*methods ; Conserved Sequence ; Evolution, Molecular ; Genetics, Population ; Genome, Human ; Humans ; Mammals/*genetics ; Models, Genetic ; *Mutation ; Selection, Genetic ; Sequence Alignment ; }, abstract = {Comparative genomic approaches have been used to identify sites where mutations are under purifying selection and of functional consequence by searching for sequences that are conserved across distantly related species. However, the performance of these approaches has not been rigorously evaluated under population genetic models. Further, short-lived functional elements may not leave a footprint of sequence conservation across many species. We use simulations to study how one measure of conservation, the Genomic Evolutionary Rate Profiling (GERP) score, relates to the strength of selection (Nes). We show that the GERP score is related to the strength of purifying selection. However, changes in selection coefficients or functional elements over time (i.e. functional turnover) can strongly affect the GERP distribution, leading to unexpected relationships between GERP and Nes. Further, we show that for functional elements that have a high turnover rate, adding more species to the analysis does not necessarily increase statistical power. Finally, we use the distribution of GERP scores across the human genome to compare models with and without turnover of sites where mutations are under purifying selection. We show that mutations in 4.51% of the noncoding human genome are under purifying selection and that most of this sequence has likely experienced changes in selection coefficients throughout mammalian evolution. Our work reveals limitations to using comparative genomic approaches to identify deleterious mutations. Commonly used GERP score thresholds miss over half of the noncoding sites in the human genome where mutations are under purifying selection.}, } @article {pmid32467364, year = {2020}, author = {McDowell, NG and Allen, CD and Anderson-Teixeira, K and Aukema, BH and Bond-Lamberty, B and Chini, L and Clark, JS and Dietze, M and Grossiord, C and Hanbury-Brown, A and Hurtt, GC and Jackson, RB and Johnson, DJ and Kueppers, L and Lichstein, JW and Ogle, K and Poulter, B and Pugh, TAM and Seidl, R and Turner, MG and Uriarte, M and Walker, AP and Xu, C}, title = {Pervasive shifts in forest dynamics in a changing world.}, journal = {Science (New York, N.Y.)}, volume = {368}, number = {6494}, pages = {}, doi = {10.1126/science.aaz9463}, pmid = {32467364}, issn = {1095-9203}, mesh = {*Acclimatization ; *Biomass ; Carbon Dioxide/analysis ; *Climate Change ; *Forests ; Models, Biological ; Trees/*growth & development ; }, abstract = {Forest dynamics arise from the interplay of environmental drivers and disturbances with the demographic processes of recruitment, growth, and mortality, subsequently driving biomass and species composition. However, forest disturbances and subsequent recovery are shifting with global changes in climate and land use, altering these dynamics. Changes in environmental drivers, land use, and disturbance regimes are forcing forests toward younger, shorter stands. Rising carbon dioxide, acclimation, adaptation, and migration can influence these impacts. Recent developments in Earth system models support increasingly realistic simulations of vegetation dynamics. In parallel, emerging remote sensing datasets promise qualitatively new and more abundant data on the underlying processes and consequences for vegetation structure. When combined, these advances hold promise for improving the scientific understanding of changes in vegetation demographics and disturbances.}, } @article {pmid32466445, year = {2020}, author = {Andrejiová, M and Grincova, A and Marasová, D}, title = {Study of the Percentage of Greenhouse Gas Emissions from Aviation in the EU-27 Countries by Applying Multiple-Criteria Statistical Methods.}, journal = {International journal of environmental research and public health}, volume = {17}, number = {11}, pages = {}, pmid = {32466445}, issn = {1660-4601}, mesh = {*Air Pollution ; *Aviation ; Environmental Monitoring ; European Union ; *Greenhouse Gases ; }, abstract = {The transport sector, including air transport, represents an important source of air pollution. The present article deals with the current situation regarding greenhouse gas emissions in the air in 27 European Union (EU-27) member states. Every member state is characterized by selected parameters that determine the unique nature of a particular country (e.g., population, area, life expectancy, gross domestic product (GDP) per capita, etc.). In addition to these parameters, there were also other parameters which were monitored as they characterize the amount of greenhouse gas emissions and the impact of aviation on these emissions. The main purpose of the article is to compare the European Union member states on the basis of 15 examined parameters. The identification of similarities between the EU-27 member states with regard to the selected parameters was carried out by applying principal component analysis (PCA) and hierarchical cluster analysis. The average linkage method was applied to create a dendrogram representing the similarities between the examined member states. The value of the cophenetic correlation coefficient CC = 0.923 confirmed the correct application of the average linkage method. The cluster analysis outputs were five similarity-based homogeneous groups (clusters) into which the 27 member states were divided on the basis of the examined variables.}, } @article {pmid32466208, year = {2020}, author = {Ruiz-Arrondo, I and Oteo, JA and Lucientes, J and Muniesa, A and de Blas, I}, title = {Surveillance of a Pest Through a Public Health Information System: The Case of the Blackfly (Simulium erythrocephalum) in Zaragoza (Spain) during 2009-2015.}, journal = {International journal of environmental research and public health}, volume = {17}, number = {10}, pages = {}, pmid = {32466208}, issn = {1660-4601}, mesh = {Animals ; Europe ; *Health Information Systems ; Humans ; Insect Bites and Stings/*epidemiology ; Longitudinal Studies ; *Simuliidae ; Spain/epidemiology ; }, abstract = {Background: Animals and people in many Spanish regions are increasingly being affected by blackfly bites in the last decade. Because of blackflies, the city of Zaragoza has become in recent years a paradigm of discomfort in Europe, with thousands of citizens affected. The OMI-AP system (Stacks, Barcelona, Spain) implemented by the Government of Aragón, a software that manages the electronic medical history of all patients, has been evaluated in order to document the increase of insect bite recorded by the primary care consultations in Zaragoza after the first outbreak of blackflies occurred in 2011. Methods: An observational, ecological and longitudinal study of insect bites recorded at the primary care consultations was carried out in primary care during the period 2009-2015. Results: The incidence of medical consultations by insect bites in Basic Health Areas (BHA) near to rivers is higher than the furthest BHA. Rural BHA are more affected by insect bites than the urban ones. The increase of medical assistance due to insect bites in Zaragoza since 2011 is correlated with the blackflies bites. Conclusions: This tool was very useful to describe the initial stage of this public health problem. It could be used for guiding public health responses in terms of surveillance and management of this pest.}, } @article {pmid32459184, year = {2020}, author = {Thomas, NWD and Beattie, Z and Marcoe, J and Wright, K and Sharma, N and Mattek, N and Dodge, H and Wild, K and Kaye, J}, title = {An Ecologically Valid, Longitudinal, and Unbiased Assessment of Treatment Efficacy in Alzheimer Disease (the EVALUATE-AD Trial): Proof-of-Concept Study.}, journal = {JMIR research protocols}, volume = {9}, number = {5}, pages = {e17603}, pmid = {32459184}, issn = {1929-0748}, support = {KL2 TR002370/TR/NCATS NIH HHS/United States ; R01 AG043398/AG/NIA NIH HHS/United States ; UL1 TR002369/TR/NCATS NIH HHS/United States ; U2C AG054397/AG/NIA NIH HHS/United States ; R01 AG024059/AG/NIA NIH HHS/United States ; P30 AG008017/AG/NIA NIH HHS/United States ; U01 AG010483/AG/NIA NIH HHS/United States ; R01 AG056102/AG/NIA NIH HHS/United States ; U2C AG057441/AG/NIA NIH HHS/United States ; R01 AG033581/AG/NIA NIH HHS/United States ; P01 AG043362/AG/NIA NIH HHS/United States ; R01 AG051628/AG/NIA NIH HHS/United States ; P30 AG024978/AG/NIA NIH HHS/United States ; P30 AG066518/AG/NIA NIH HHS/United States ; }, abstract = {BACKGROUND: The current clinical trial assessment methodology relies on a combination of self-report measures, cognitive and physical function tests, and biomarkers. This methodology is limited by recall bias and recency effects in self-reporting and by assessments that are brief, episodic, and clinic based. Continuous monitoring of ecologically valid measures of cognition and daily functioning in the community may provide a more sensitive method to detect subtle, progressive changes in patients with cognitive impairment and dementia.

OBJECTIVE: This study aimed to present an alternative trial approach using a home-based sensing and computing system to detect changes related to common treatments employed in Alzheimer disease (AD). This paper introduces an ongoing study that aims to determine the feasibility of capturing sensor-based data at home and to compare the sensor-based outcomes with conventional outcomes. We describe the methodology used in the assessment protocol and present preliminary results of feasibility measures and examples of data related to medication-taking behavior, activity levels, and sleep.

METHODS: The EVALUATE-AD (Ecologically Valid, Ambient, Longitudinal and Unbiased Assessment of Treatment Efficacy in Alzheimer's Disease) trial is a longitudinal naturalistic observational cohort study recruiting 30 patients and 30 spouse coresident care partners. Participants are monitored continuously using a home-based sensing and computing system for up to 24 months. Outcome measures of the automated system are compared with conventional clinical outcome measures in AD. Acceptance of the home system and protocol are assessed by rates of dropout and protocol adherence. After completion of the study monitoring period, a composite model using multiple functional outcome measures will be created that represents a behavioral-activity signature of initiating or discontinuing AD-related medications, such as cholinesterase inhibitors, memantine, or antidepressants.

RESULTS: The home-based sensing and computing system has been well accepted by individuals with cognitive impairment and their care partners. Participants showed good adherence to the completion of a weekly web-based health survey. Daily activity, medication adherence, and total time in bed could be derived from algorithms using data from the sensing and computing system. The mean monitoring time for current participants was 14.6 months. Medication adherence, as measured with an electronic pillbox, was 77% for participants taking AD-related medications.

CONCLUSIONS: Continuous, home-based assessment provides a novel approach to test the impact of new or existing dementia treatments generating objective, clinically meaningful measures related to cognition and everyday functioning. Combining this approach with the current clinical trial methodology may ultimately reduce trial durations, sample size needs, and reliance on a clinic-based assessment.

DERR1-10.2196/17603.}, } @article {pmid32457140, year = {2020}, author = {Drury, JP and Cowen, MC and Grether, GF}, title = {Competition and hybridization drive interspecific territoriality in birds.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {117}, number = {23}, pages = {12923-12930}, pmid = {32457140}, issn = {1091-6490}, mesh = {Adaptation, Biological ; Aggression/*physiology ; Animals ; Behavior, Animal/*physiology ; Datasets as Topic ; Female ; Genetic Speciation ; Hybridization, Genetic/*physiology ; Male ; North America ; Reproduction/physiology ; Seasons ; Songbirds/*physiology ; *Territoriality ; }, abstract = {Costly interactions between species that arise as a by-product of ancestral similarities in communication signals are expected to persist only under specific evolutionary circumstances. Territorial aggression between species, for instance, is widely assumed to persist only when extrinsic barriers prevent niche divergence or selection in sympatry is too weak to overcome gene flow from allopatry. However, recent theoretical and comparative studies have challenged this view. Here we present a large-scale, phylogenetic analysis of the distribution and determinants of interspecific territoriality. We find that interspecific territoriality is widespread in birds and strongly associated with hybridization and resource overlap during the breeding season. Contrary to the view that territoriality only persists between species that rarely breed in the same areas or where niche divergence is constrained by habitat structure, we find that interspecific territoriality is positively associated with breeding habitat overlap and unrelated to habitat structure. Furthermore, our results provide compelling evidence that ancestral similarities in territorial signals are maintained and reinforced by selection when interspecific territoriality is adaptive. The territorial signals linked to interspecific territoriality in birds depend on the evolutionary age of interacting species, plumage at shallow (within-family) timescales, and song at deeper (between-family) timescales. Evidently, territorial interactions between species have persisted and shaped phenotypic diversity on a macroevolutionary timescale.}, } @article {pmid32455431, year = {2020}, author = {Chmurzynska, A and Mlodzik-Czyzewska, MA and Galinski, G and Malinowska, AM and Radziejewska, A and Mikołajczyk-Stecyna, J and Bulczak, E and Wiebe, DJ}, title = {Polymorphism of CD36 Determines Fat Discrimination but Not Intake of High-Fat Food in 20- to 40-Year-Old Adults.}, journal = {The Journal of nutrition}, volume = {150}, number = {8}, pages = {2016-2022}, doi = {10.1093/jn/nxaa136}, pmid = {32455431}, issn = {1541-6100}, mesh = {Adult ; CD36 Antigens/*genetics/*metabolism ; Carbonic Anhydrases/genetics/metabolism ; *Dietary Fats ; Eating/genetics ; Feeding Behavior ; Female ; *Food Analysis ; Genotype ; Humans ; Male ; *Polymorphism, Genetic ; Receptors, G-Protein-Coupled/genetics/metabolism ; Taste/genetics ; Young Adult ; }, abstract = {BACKGROUND: The determinants of the intake of high-fat products are not well understood.

OBJECTIVE: The aim of this study was to examine the relations between fat perception, intake of high-fat food, and body-weight status, taking into account the polymorphism of the genes that encode the proteins involved in oral fat perception.

METHODS: A total of 421 participants aged 20-40 y were enrolled in Poznań, Poland, from 2016 to 2018. An ascending forced-choice triangle procedure was applied to determine fat discrimination ability. Salad dressings with varying concentrations of canola oil were used as stimuli. Genotyping of rs1761667 (CD36) rs1573611 [free fatty acid receptor 1 (FFAR1)], rs17108973 [free fatty acid receptor 4 (FFAR4)], and rs2274333 (CA6) was performed using TaqMan probes. The frequency of consumption of high-fat foods was measured using an application for mobile devices that uses the ecological momentary assessment approach. The associations were analyzed using linear regression or logistic regression, as appropriate.

RESULTS: Individuals with the GG CD36 genotype were twice as likely to be fat discriminators, compared with the A allele carriers (P < 0.05). The mean total consumption of high-fat food was 45.8 (44.6, 47.0) times/wk and was not associated with fat discrimination or body-weight status. Obese and overweight subjects ate healthy high-fat food less frequently than did participants with normal body weight, at 4.53 (3.83, 5.23) versus 6.68 (5.82, 7.55) times/wk, respectively (P < 0.001). Men ate sweet high-fat food and snacks 15% less frequently than did women (P < 0.001 and P < 0.05) but consumed high-fat meat and fast food almost 40% more often than did women (P < 0.001 for both associations).

CONCLUSIONS: In individuals aged 20-40 y, fat discrimination ability is associated with polymorphism of CD36 but not with the choice of high-fat food. The frequency of consumption of different types of high-fat foods varies by sex and body-weight status.}, } @article {pmid32454244, year = {2020}, author = {Zhang, J and Yao, J and Jiang, J and Pan, X and Luo, M and Xia, Y and Fan, Q and Ding, X and Ruan, J and Handel, A and Bahl, J and Chen, W and Zha, L and Fu, T}, title = {Migration interacts with the local transmission of HIV in developed trade areas: A molecular transmission network analysis in China.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {84}, number = {}, pages = {104376}, doi = {10.1016/j.meegid.2020.104376}, pmid = {32454244}, issn = {1567-7257}, mesh = {Adult ; China/epidemiology ; Contact Tracing ; Demography ; Female ; HIV Infections/epidemiology/*transmission/virology ; *HIV-1 ; Humans ; Male ; Molecular Epidemiology ; Retrospective Studies ; Young Adult ; }, abstract = {The HIV-1 epidemic is a remarkable public health concern in China, especially in developed trade areas. We aimed to investigate the interaction of migration with the local transmission network in a typical trade area, Yiwu City, the world's largest commodity distribution center. Based on 390 pol sequences from 413 participants diagnosed between 2014 and 2016, putative transmission clusters and the underlying demographic and behavioral characteristics were analyzed. Recent infection status was determined by HIV-1 limiting antigen avidity enzyme immunoassay to identify active clusters. Multiple subtypes were identified, with a predominance of CRF01_AE (47.4%) and CRF07_BC (40.8%), followed by 9 other subtypes and 8 URFs. Multivariable analyses revealed that individuals in clusters were more likely to be local residents, infected through heterosexual behaviors, and infected with CRF01_AE (P < .05). Of men who have sex with men (MSM), 81% were linked to other MSM, and only 3% were linked to heterosexual women. Of heterosexual women, 67% were linked to heterosexual men, and 11% to MSM. Yiwu residents were more likely to link to locals than that of migrants (43% vs 20%, P < .001). By contrast, local MSM and migrant MSM all had high percentages of linkage to migrant MSM (57% vs 69%, P = .069). Our findings reveal that migration promotes the dissemination and dynamic change of HIV, which are interwoven between locals and migrants. The results highlight the far-reaching influence of migrant MSM on the local HIV transmission network.}, } @article {pmid32450610, year = {2020}, author = {Shepherd, M and Bromley, R and Stevens, M and Morgia, M and Kneebone, A and Hruby, G and Atyeo, J and Eade, T}, title = {Developing knowledge-based planning for gynaecological and rectal cancers: a clinical validation of RapidPlan[™].}, journal = {Journal of medical radiation sciences}, volume = {67}, number = {3}, pages = {217-224}, pmid = {32450610}, issn = {2051-3909}, mesh = {Dose Fractionation, Radiation ; Female ; Genital Neoplasms, Female/*radiotherapy ; Humans ; *Knowledge Bases ; Radiotherapy Planning, Computer-Assisted/*methods ; Radiotherapy, Intensity-Modulated ; Rectal Neoplasms/*radiotherapy ; Reproducibility of Results ; Time Factors ; }, abstract = {INTRODUCTION: To create and clinically validate knowledge-based planning (KBP) models for gynaecologic (GYN) and rectal cancer patients. Assessment of ecologic generalisability and predictive validity of conventional planning versus single calculation KBP was reviewed against practical metrics of planning time (PT) and radiation oncologist plan preference.

METHOD: Study cohorts were 34 and 42 consecutively treated GYN and rectal cancer patients dosimetrically archived within the centre's research databank. For model training, structures and dose distributions from 22 and 32 GYN and rectal volumetric-modulated arc therapy (VMAT) plans were used in RapidPlan™. Prescription doses ranged from 45 to 60Gy in 25 fractions using a simultaneous integrated boost to 2-4 targets and up to 9 organ-at-risk volumes. For model validation, 12 GYN and 10 rectal were independent of the archive and a single pass KBP VMAT plan was created. Each plan was evaluated against the archived treated plan under blinded conditions for radiation oncologist preference using standard dosimetric quality parameters.

RESULTS: All 22 plans generated in the KBP validation cohort met pre-set GYN and rectal cancer dosimetric quality metrics. Fifty per cent of GYN plans and eighty per cent of rectal plans were judged superior to the manually optimised plans. KBP reduced PT considerably for both tumour sites.

CONCLUSION: Single pass KBP for GYN and rectal cancer patients produced clinically acceptable treatment plans which were non-inferior to conventionally optimised plans in 14 of 22 cases. Efficiencies captured by KBP will have predictable impacts on institutional workflows and resource allocation to facilitate adaptive planning.}, } @article {pmid32449778, year = {2020}, author = {Kuhl, H and Li, L and Wuertz, S and Stöck, M and Liang, XF and Klopp, C}, title = {CSA: A high-throughput chromosome-scale assembly pipeline for vertebrate genomes.}, journal = {GigaScience}, volume = {9}, number = {5}, pages = {}, pmid = {32449778}, issn = {2047-217X}, mesh = {Animals ; Chromosomes/*genetics ; Computational Biology/*methods ; Genomics/*methods ; High-Throughput Nucleotide Sequencing ; Sequence Analysis, DNA ; *Software ; Synteny ; Vertebrates/*metabolism ; }, abstract = {BACKGROUND: Easy-to-use and fast bioinformatics pipelines for long-read assembly that go beyond the contig level to generate highly continuous chromosome-scale genomes from raw data remain scarce.

RESULT: Chromosome-Scale Assembler (CSA) is a novel computationally highly efficient bioinformatics pipeline that fills this gap. CSA integrates information from scaffolded assemblies (e.g., Hi-C or 10X Genomics) or even from diverged reference genomes into the assembly process. As CSA performs automated assembly of chromosome-sized scaffolds, we benchmark its performance against state-of-the-art reference genomes, i.e., conventionally built in a laborious fashion using multiple separate assembly tools and manual curation. CSA increases the contig lengths using scaffolding, local re-assembly, and gap closing. On certain datasets, initial contig N50 may be increased up to 4.5-fold. For smaller vertebrate genomes, chromosome-scale assemblies can be achieved within 12 h using low-cost, high-end desktop computers. Mammalian genomes can be processed within 16 h on compute-servers. Using diverged reference genomes for fish, birds, and mammals, we demonstrate that CSA calculates chromosome-scale assemblies from long-read data and genome comparisons alone. Even contig-level draft assemblies of diverged genomes are helpful for reconstructing chromosome-scale sequences. CSA is also capable of assembling ultra-long reads.

CONCLUSIONS: CSA can speed up and simplify chromosome-level assembly and significantly lower costs of large-scale family-level vertebrate genome projects.}, } @article {pmid32445889, year = {2020}, author = {Guo, J and Xu, W and Hu, Y and Huang, J and Zhao, Y and Zhang, L and Huang, CH and Ma, H}, title = {Phylotranscriptomics in Cucurbitaceae Reveal Multiple Whole-Genome Duplications and Key Morphological and Molecular Innovations.}, journal = {Molecular plant}, volume = {13}, number = {8}, pages = {1117-1133}, doi = {10.1016/j.molp.2020.05.011}, pmid = {32445889}, issn = {1752-9867}, mesh = {*Biological Evolution ; Cucurbitaceae/*genetics ; Datasets as Topic ; *Gene Duplication ; *Genome, Plant ; Phylogeny ; Transcriptome/*genetics ; }, abstract = {The ability of climbing plants to grow upward along others to reach the canopy for photosynthesis is hypothesized as a key innovation in flowering plants. Most members of the Cucurbitaceae, a family containing ∼1000 species and many important crops, are climbers and have characteristic tendrils and pepo fruits. Here, we present 127 newly sequenced transcriptomes and genomes along with other datasets for a total of 136 cucurbits representing all tribes to establish a robust Cucurbitaceae phylogeny containing eight highly resolved major clades. We analyzed whole-genome duplication, diversification dynamics, and ancestral morphologies, and found that after early genome duplication event(s), a burst of diversification and morphological innovations in flower, fruit, and root characters occurred under the climate optimum in the Early Eocene. Species radiation during the Mid-Eocene Climatic Optimum also coincided with several morphological changes shared by 80% of cucurbits. We found that the cucurbit-specific tendril identity gene TEN originated from a paleo-polyploidization event at the origin of the family. Our results support the hypothesis that cucurbit diversifications were probably driven by increased genetic diversity following polyploidizations and by trait morphological innovations under paleo-climate upheavals. Our study provides a phylogenetic framework and new insights into morphological and genomic changes underlying the adaptive evolution of Cucurbitaceae.}, } @article {pmid32444882, year = {2020}, author = {Petrini, A and Mesiti, M and Schubach, M and Frasca, M and Danis, D and Re, M and Grossi, G and Cappelletti, L and Castrignanò, T and Robinson, PN and Valentini, G}, title = {parSMURF, a high-performance computing tool for the genome-wide detection of pathogenic variants.}, journal = {GigaScience}, volume = {9}, number = {5}, pages = {}, pmid = {32444882}, issn = {2047-217X}, support = {R24 OD011883/OD/NIH HHS/United States ; }, mesh = {Algorithms ; Computational Biology/*methods ; Databases, Genetic ; *Genetic Predisposition to Disease ; *Genetic Variation ; Genome-Wide Association Study/*methods ; Genomics/methods ; Humans ; Machine Learning ; Reproducibility of Results ; *Software ; }, abstract = {BACKGROUND: Several prediction problems in computational biology and genomic medicine are characterized by both big data as well as a high imbalance between examples to be learned, whereby positive examples can represent a tiny minority with respect to negative examples. For instance, deleterious or pathogenic variants are overwhelmed by the sea of neutral variants in the non-coding regions of the genome: thus, the prediction of deleterious variants is a challenging, highly imbalanced classification problem, and classical prediction tools fail to detect the rare pathogenic examples among the huge amount of neutral variants or undergo severe restrictions in managing big genomic data.

RESULTS: To overcome these limitations we propose parSMURF, a method that adopts a hyper-ensemble approach and oversampling and undersampling techniques to deal with imbalanced data, and parallel computational techniques to both manage big genomic data and substantially speed up the computation. The synergy between Bayesian optimization techniques and the parallel nature of parSMURF enables efficient and user-friendly automatic tuning of the hyper-parameters of the algorithm, and allows specific learning problems in genomic medicine to be easily fit. Moreover, by using MPI parallel and machine learning ensemble techniques, parSMURF can manage big data by partitioning them across the nodes of a high-performance computing cluster. Results with synthetic data and with single-nucleotide variants associated with Mendelian diseases and with genome-wide association study hits in the non-coding regions of the human genome, involhing millions of examples, show that parSMURF achieves state-of-the-art results and an 80-fold speed-up with respect to the sequential version.

CONCLUSIONS: parSMURF is a parallel machine learning tool that can be trained to learn different genomic problems, and its multiple levels of parallelization and high scalability allow us to efficiently fit problems characterized by big and imbalanced genomic data. The C++ OpenMP multi-core version tailored to a single workstation and the C++ MPI/OpenMP hybrid multi-core and multi-node parSMURF version tailored to a High Performance Computing cluster are both available at https://github.com/AnacletoLAB/parSMURF.}, } @article {pmid32443550, year = {2020}, author = {Leskanicova, A and Chovancova, O and Babincak, M and Verboova, L and Benetinova, Z and Macekova, D and Kostolny, J and Smajda, B and Kiskova, T}, title = {Sexual Dimorphism in Energy Metabolism of Wistar Rats Using Data Analysis.}, journal = {Molecules (Basel, Switzerland)}, volume = {25}, number = {10}, pages = {}, pmid = {32443550}, issn = {1420-3049}, support = {1/0658/20//Vedecká Grantová Agentúra MŠVVaŠ SR a SAV/ ; VVGS-UPJS-2019-1071//VVGS/ ; VVGS-PF-2019-1054//VVGS/ ; VVGS-PF-2019-1040//VVGS/ ; 26220220153//Competence Center for Research and Development in the Field of Diagnostics and Therapy of Oncological Diseases - ITMS/ ; 313011D103//Medical University Science Park in Košice (MediPark, Košice - Phase II) ITMS2014+/ ; }, mesh = {Amino Acids/*blood ; Animals ; Biomarkers/*blood ; Carnitine/analogs & derivatives/blood ; Data Analysis ; Discriminant Analysis ; *Energy Metabolism ; Female ; Male ; Metabolome/genetics ; Metabolomics/methods ; Phenylalanine/blood ; Rats ; *Sex Characteristics ; Tyrosine/blood ; }, abstract = {The prevalence of some chronic diseases, such as cancer or neurodegenerative disorders, differs between sexes. Animal models provide an important tool to adopt potential therapies from preclinical studies to humans. Laboratory rats are the most popular animals in toxicology, neurobehavioral, or cancer research. Our study aimed to reveal the basic differences in blood metabolome (amino acids, biogenic amines, and acylcarnitines) of the adult male (n = 10) and female (n = 10) Wistar rats. Partial least square-discrimination analysis (PLS-DA) and a variance im portance in projection (VIP) score was used to identify the key sex-specific metabolites. All groups of metabolites, as the main markers of energy metabolism, showed a significant sex-dependent pattern. The most important features calculated in PLS-DA according to VIP score were free carnitine (C0), tyrosine (Tyr), and acylcarnitine C5-OH. While aromatic amino acids, such as Tyr and phenylalanine (Phe), were significantly elevated in the blood plasma of males, tryptophan (Trp) was found in higher levels in the blood plasma of females. Besides, significant sex-related changes in urea cycle were found. Our study provides an important insight into sex-specific differences in energy metabolism in rats and indicates that further studies should consider sex as the main aspect in design and data interpretation.}, } @article {pmid32441748, year = {2020}, author = {Joshi, J and Beaudoin, GAW and Patterson, JA and García-García, JD and Belisle, CE and Chang, LY and Li, L and Duncan, O and Millar, AH and Hanson, AD}, title = {Bioinformatic and experimental evidence for suicidal and catalytic plant THI4s.}, journal = {The Biochemical journal}, volume = {477}, number = {11}, pages = {2055-2069}, doi = {10.1042/BCJ20200297}, pmid = {32441748}, issn = {1470-8728}, mesh = {*Arabidopsis/enzymology/genetics ; *Arabidopsis Proteins/chemistry/genetics/metabolism ; Catalysis ; Computational Biology ; Escherichia coli/enzymology/genetics ; Genetic Complementation Test ; *Ligases/chemistry/genetics/metabolism ; *Models, Molecular ; *Plants, Genetically Modified/enzymology/genetics ; Protein Domains ; *Thiamine/biosynthesis/genetics ; Thiazoles/*metabolism ; }, abstract = {Like fungi and some prokaryotes, plants use a thiazole synthase (THI4) to make the thiazole precursor of thiamin. Fungal THI4s are suicide enzymes that destroy an essential active-site Cys residue to obtain the sulfur atom needed for thiazole formation. In contrast, certain prokaryotic THI4s have no active-site Cys, use sulfide as sulfur donor, and are truly catalytic. The presence of a conserved active-site Cys in plant THI4s and other indirect evidence implies that they are suicidal. To confirm this, we complemented the Arabidopsistz-1 mutant, which lacks THI4 activity, with a His-tagged Arabidopsis THI4 construct. LC-MS analysis of tryptic peptides of the THI4 extracted from leaves showed that the active-site Cys was predominantly in desulfurated form, consistent with THI4 having a suicide mechanism in planta. Unexpectedly, transcriptome data mining and deep proteome profiling showed that barley, wheat, and oat have both a widely expressed canonical THI4 with an active-site Cys, and a THI4-like paralog (non-Cys THI4) that has no active-site Cys and is the major type of THI4 in developing grains. Transcriptomic evidence also indicated that barley, wheat, and oat grains synthesize thiamin de novo, implying that their non-Cys THI4s synthesize thiazole. Structure modeling supported this inference, as did demonstration that non-Cys THI4s have significant capacity to complement thiazole auxotrophy in Escherichia coli. There is thus a prima facie case that non-Cys cereal THI4s, like their prokaryotic counterparts, are catalytic thiazole synthases. Bioenergetic calculations show that, relative to suicide THI4s, such enzymes could save substantial energy during the grain-filling period.}, } @article {pmid32441459, year = {2020}, author = {Han, BA and O'Regan, SM and Paul Schmidt, J and Drake, JM}, title = {Integrating data mining and transmission theory in the ecology of infectious diseases.}, journal = {Ecology letters}, volume = {23}, number = {8}, pages = {1178-1188}, pmid = {32441459}, issn = {1461-0248}, support = {1717282//Division of Environmental Biology/ ; //NIMBioS/ ; }, mesh = {Animals ; Data Mining ; Disease Outbreaks ; Humans ; Models, Theoretical ; *Rodentia ; Zoonoses/*epidemiology ; }, abstract = {Our understanding of ecological processes is built on patterns inferred from data. Applying modern analytical tools such as machine learning to increasingly high dimensional data offers the potential to expand our perspectives on these processes, shedding new light on complex ecological phenomena such as pathogen transmission in wild populations. Here, we propose a novel approach that combines data mining with theoretical models of disease dynamics. Using rodents as an example, we incorporate statistical differences in the life history features of zoonotic reservoir hosts into pathogen transmission models, enabling us to bound the range of dynamical phenomena associated with hosts, based on their traits. We then test for associations between equilibrium prevalence, a key epidemiological metric and data on human outbreaks of rodent-borne zoonoses, identifying matches between empirical evidence and theoretical predictions of transmission dynamics. We show how this framework can be generalized to other systems through a rubric of disease models and parameters that can be derived from empirical data. By linking life history components directly to their effects on disease dynamics, our mining-modelling approach integrates machine learning and theoretical models to explore mechanisms in the macroecology of pathogen transmission and their consequences for spillover infection to humans.}, } @article {pmid32435576, year = {2020}, author = {Mois, G and Beer, JM}, title = {The Role of Healthcare Robotics in Providing Support to Older Adults: a Socio-ecological Perspective.}, journal = {Current geriatrics reports}, volume = {9}, number = {2}, pages = {82-89}, pmid = {32435576}, issn = {2196-7865}, abstract = {PURPOSE OF REVIEW: In this review, we provide an overview of how healthcare robotics can facilitate healthy aging, with an emphasis on physical, cognitive, and social supports. We next provide a synthesis of future challenges and considerations in the development and application of healthcare robots. We organize these considerations using a socio-ecological perspective and discuss considerations at the individual, care partner, community healthcare, and healthcare policy levels.

RECENT FINDINGS: Older adults are the fastest growing segment of the US population. Age-related changes and challenges can present difficulties, for older adults want to age healthily and maintain independence. Technology, specifically healthcare robots, has potential to provide health supports to older adults. These supports span widely across the physical, cognitive, and social aspects of healthy aging.

SUMMARY: Our review suggests that while healthcare robotics has potential to revolutionize the way in which older adults manage their health, there are many challenges such as clinical effectiveness, technology acceptance, health informatics, and healthcare policy and ethics. Addressing these challenges at all levels of the healthcare system will help ensure that healthcare robotics promote healthy aging and are applied safely, effectively, and reliably.}, } @article {pmid32434565, year = {2020}, author = {Liu, J and Seetharam, AS and Chougule, K and Ou, S and Swentowsky, KW and Gent, JI and Llaca, V and Woodhouse, MR and Manchanda, N and Presting, GG and Kudrna, DA and Alabady, M and Hirsch, CN and Fengler, KA and Ware, D and Michael, TP and Hufford, MB and Dawe, RK}, title = {Gapless assembly of maize chromosomes using long-read technologies.}, journal = {Genome biology}, volume = {21}, number = {1}, pages = {121}, pmid = {32434565}, issn = {1474-760X}, mesh = {*Chromosomes, Plant ; *Genome, Plant ; Genomics/*methods ; Physical Chromosome Mapping/*methods ; Zea mays/*genetics ; }, abstract = {Creating gapless telomere-to-telomere assemblies of complex genomes is one of the ultimate challenges in genomics. We use two independent assemblies and an optical map-based merging pipeline to produce a maize genome (B73-Ab10) composed of 63 contigs and a contig N50 of 162 Mb. This genome includes gapless assemblies of chromosome 3 (236 Mb) and chromosome 9 (162 Mb), and 53 Mb of the Ab10 meiotic drive haplotype. The data also reveal the internal structure of seven centromeres and five heterochromatic knobs, showing that the major tandem repeat arrays (CentC, knob180, and TR-1) are discontinuous and frequently interspersed with retroelements.}, } @article {pmid32431099, year = {2020}, author = {Senior, AM and Viechtbauer, W and Nakagawa, S}, title = {Revisiting and expanding the meta-analysis of variation: The log coefficient of variation ratio.}, journal = {Research synthesis methods}, volume = {11}, number = {4}, pages = {553-567}, doi = {10.1002/jrsm.1423}, pmid = {32431099}, issn = {1759-2887}, support = {DE180101520//Australian Research Council/ ; DP180100818//Australian Research Council/ ; DP180100818//ARC Discovery Grant/ ; DE180101520//Australian Research Council Discovery Early Career Researcher Award/ ; }, mesh = {Algorithms ; Blood Glucose/analysis ; Computer Simulation ; *Data Interpretation, Statistical ; Diet ; Female ; Glycemic Index ; Humans ; Life Style ; *Meta-Analysis as Topic ; Obesity/therapy ; Pregnancy ; Reproducibility of Results ; *Research Design ; }, abstract = {Meta-analyses are often used to estimate the relative average values of a quantitative outcome in two groups (eg, control and experimental groups). However, they may also examine the relative variability (variance) of those groups. For such comparisons, two relatively new effect size statistics, the log-transformed "variability ratio" (the ratio of two standard deviations; lnVR) and the log-transformed "coefficients of variation ratio" (the ratio of two coefficients of variation; lnCVR) are useful. In practice, lnCVR may be of most use because a treatment may affect the mean and the variance simultaneously. We propose new estimators for lnCVR and lnVR, including for when the two groups are dependent (eg, cross-over and pre-test-post-test designs). Through simulation, we evaluated the bias of these estimators and make recommendations accordingly. We use the methods to demonstrate that: (a) lifestyle interventions have a heterogenizing effect on gestational weight gain in obese women and (b) low-glycemic index (GI) diets have a homogenizing effect on glycemic control in diabetics. We also find that the degree to which dependence among samples is accounted for can impact parameters such as τ[2] (ie, the between-study variance) and I[2] (ie, the proportion of the total variability due to between-study variance), and even the overall effect, and associated qualitative interpretations. Meta-analytic comparison of the variability between two groups enables us to ask completely new questions and to gain fresh insights from existing datasets. We encourage researchers to take advantage of these convenient new effect size measures for the meta-analysis of variation.}, } @article {pmid32429383, year = {2020}, author = {Meina, M and Ratajczak, E and Sadowska, M and Rykaczewski, K and Dreszer, J and Bałaj, B and Biedugnis, S and Węgrzyński, W and Krasuski, A}, title = {Heart Rate Variability and Accelerometry as Classification Tools for Monitoring Perceived Stress Levels-A Pilot Study on Firefighters.}, journal = {Sensors (Basel, Switzerland)}, volume = {20}, number = {10}, pages = {}, pmid = {32429383}, issn = {1424-8220}, mesh = {*Accelerometry ; Electrocardiography ; *Firefighters ; *Heart Rate ; Humans ; Pilot Projects ; *Stress, Psychological ; }, abstract = {Chronic stress is the main cause of health problems in high-risk jobs. Wearable sensors can become an ecologically valid method of stress level assessment in real-life applications. We sought to determine a non-invasive technique for objective stress monitoring. Data were collected from firefighters during 24-h shifts using sensor belts equipped with a dry-lead electrocardiograph (ECG) and a three-axial accelerometer. Levels of stress experienced during fire incidents were evaluated via a brief self-assessment questionnaire. Types of physical activity were distinguished basing on accelerometer readings, and heart rate variability (HRV) time series were segmented accordingly into corresponding fragments. Those segments were classified as stress/no-stress conditions. Receiver Operating Characteristic (ROC) analysis showed true positive classification as stress condition for 15% of incidents (while maintaining almost zero False Positive Rate), which parallels the amount of truly stressful incidents reported in the questionnaires. These results show a firm correspondence between the perceived stress level and physiological data. Psychophysiological measurements are reliable indicators of stress even in ecological settings and appear promising for chronic stress monitoring in high-risk jobs, such as firefighting.}, } @article {pmid32428072, year = {2020}, author = {Moreira, RDS}, title = {COVID-19: intensive care units, mechanical ventilators, and latent mortality profiles associated with case-fatality in Brazil.}, journal = {Cadernos de saude publica}, volume = {36}, number = {5}, pages = {e00080020}, doi = {10.1590/0102-311x00080020}, pmid = {32428072}, issn = {1678-4464}, mesh = {*Betacoronavirus ; Brazil/epidemiology ; COVID-19 ; Comorbidity ; Coronavirus Infections/*mortality ; Cross-Sectional Studies ; Humans ; Intensive Care Units/*supply & distribution ; Latent Class Analysis ; *Pandemics ; Pneumonia, Viral/*mortality ; SARS-CoV-2 ; Spatial Analysis ; Ventilators, Mechanical/*supply & distribution ; }, abstract = {In response to the accelerated increase in the number of COVID-19 cases, countries must increase their supply of beds in intensive care units (ICUs). Respiratory diseases, neoplasms, cardiopathies and hypertension, and diabetes are associated with higher COVID-19 case-fatality. The study aimed to identify the regions of Brazil with higher specific mortality rates from these comorbidities and the regions with the greatest shortage of ICU beds and mechanical ventilators. A cross-sectional ecological study was performed in which the units of analysis were the country's Health Regions. Data were obtained from Brazilian Health Informatics Department - DATASUS (National Registry of Healthcare Establishments - 2019, Mortality Information Systems - 2017, and Population Projections - 2017). We calculated the disease group-specific mortality rates for hypertension, neoplasms, diabetes, cardiac diseases, respiratory diseases and the rates of total ICU beds, private ICU beds, ICU beds in the Brazilian Unified National Health System (SUS), and ventilators in the SUS, per 100,000 inhabitants. The mortality profile was determined by latent profiles analysis, and the cluster analysis of ICU beds and ventilators used the spatial scan method. Kernel maps were constructed for the data's visualization. Level of significance was set at 5%. Four latent mortality profiles were observed. The Health Regions with the highest mean mortality rates were located in regions with shortages of ICU beds and ventilators, especially in parts of the Northeast, Southeast, and South of Brazil. The spatial localization of regions with both the highest mortality and shortages of ICU beds/ventilators requires attention by policymakers and public planners to deal efficiently and fairly with the COVID-19 epidemic in Brazil.}, } @article {pmid32422990, year = {2020}, author = {Aili, SR and Touchard, A and Hayward, R and Robinson, SD and Pineda, SS and Lalagüe, H and Mrinalini, and Vetter, I and Undheim, EAB and Kini, RM and Escoubas, P and Padula, MP and Myers, GSA and Nicholson, GM}, title = {An Integrated Proteomic and Transcriptomic Analysis Reveals the Venom Complexity of the Bullet Ant Paraponera clavata.}, journal = {Toxins}, volume = {12}, number = {5}, pages = {}, pmid = {32422990}, issn = {2072-6651}, support = {R-154-000-648-646//Southeast Asian Biodiversity Genomics Center, National University of Singapore/International ; CEBA, ANR-10-LABX-25-01; project EVA//"Investissement d'Avenir" grant from the Agence Nationale de la Recherche/International ; BING (GY0007194)//PO-FEDER 2014-2020, Région Guyane/International ; FORMIC (GY0013708)//PO-FEDER 2014-2020, Région Guyane/International ; DE160101142//Australian Research Council/International ; DP160104025//Australian Research Council/International ; FRIPRO-YRT Fellowship no. 287462//Norwegian Research Council/International ; }, mesh = {Animals ; Ant Venoms/*chemistry/genetics/toxicity ; Ants/genetics/*metabolism ; Calcium/metabolism ; Cells, Cultured ; Chromatography, High Pressure Liquid ; Chromatography, Reverse-Phase ; Databases, Genetic ; Ganglia, Spinal/drug effects/metabolism ; *Gene Expression Profiling ; Insect Proteins/*analysis/genetics/toxicity ; Mice, Inbred C57BL ; Neurotoxins/*analysis/genetics/toxicity ; *Proteome ; *Proteomics ; Tandem Mass Spectrometry ; *Transcriptome ; }, abstract = {A critical hurdle in ant venom proteomic investigations is the lack of databases to comprehensively and specifically identify the sequence and function of venom proteins and peptides. To resolve this, we used venom gland transcriptomics to generate a sequence database that was used to assign the tandem mass spectrometry (MS) fragmentation spectra of venom peptides and proteins to specific transcripts. This was performed alongside a shotgun liquid chromatography-mass spectrometry (LC-MS/MS) analysis of the venom to confirm that these assigned transcripts were expressed as proteins. Through the combined transcriptomic and proteomic investigation of Paraponera clavata venom, we identified four times the number of proteins previously identified using 2D-PAGE alone. In addition to this, by mining the transcriptomic data, we identified several novel peptide sequences for future pharmacological investigations, some of which conform with inhibitor cysteine knot motifs. These types of peptides have the potential to be developed into pharmaceutical or bioinsecticide peptides.}, } @article {pmid32414415, year = {2020}, author = {F Escapa, I and Huang, Y and Chen, T and Lin, M and Kokaras, A and Dewhirst, FE and Lemon, KP}, title = {Construction of habitat-specific training sets to achieve species-level assignment in 16S rRNA gene datasets.}, journal = {Microbiome}, volume = {8}, number = {1}, pages = {65}, pmid = {32414415}, issn = {2049-2618}, support = {R01 AI101018/AI/NIAID NIH HHS/United States ; R01 DE024468/DE/NIDCR NIH HHS/United States ; R01 DE016937/DE/NIDCR NIH HHS/United States ; R01GM117174//National Institute of General Medical Sciences (US)/International ; R01AI101018//Division of Intramural Research, National Institute of Allergy and Infectious Diseases/International ; R37 DE016937/DE/NIDCR NIH HHS/United States ; UL1 TR001102/TR/NCATS NIH HHS/United States ; R01DE024468/DE/NIDCR NIH HHS/United States ; R01 GM117174/GM/NIGMS NIH HHS/United States ; R37DE016937/DE/NIDCR NIH HHS/United States ; }, mesh = {*Bacteria/genetics ; Bayes Theorem ; *Computational Biology/methods ; Gastrointestinal Microbiome/genetics ; Humans ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {BACKGROUND: The low cost of 16S rRNA gene sequencing facilitates population-scale molecular epidemiological studies. Existing computational algorithms can resolve 16S rRNA gene sequences into high-resolution amplicon sequence variants (ASVs), which represent consistent labels comparable across studies. Assigning these ASVs to species-level taxonomy strengthens the ecological and/or clinical relevance of 16S rRNA gene-based microbiota studies and further facilitates data comparison across studies.

RESULTS: To achieve this, we developed a broadly applicable method for constructing high-resolution training sets based on the phylogenic relationships among microbes found in a habitat of interest. When used with the naïve Bayesian Ribosomal Database Project (RDP) Classifier, this training set achieved species/supraspecies-level taxonomic assignment of 16S rRNA gene-derived ASVs. The key steps for generating such a training set are (1) constructing an accurate and comprehensive phylogenetic-based, habitat-specific database; (2) compiling multiple 16S rRNA gene sequences to represent the natural sequence variability of each taxon in the database; (3) trimming the training set to match the sequenced regions, if necessary; and (4) placing species sharing closely related sequences into a training-set-specific supraspecies taxonomic level to preserve subgenus-level resolution. As proof of principle, we developed a V1-V3 region training set for the bacterial microbiota of the human aerodigestive tract using the full-length 16S rRNA gene reference sequences compiled in our expanded Human Oral Microbiome Database (eHOMD). We also overcame technical limitations to successfully use Illumina sequences for the 16S rRNA gene V1-V3 region, the most informative segment for classifying bacteria native to the human aerodigestive tract. Finally, we generated a full-length eHOMD 16S rRNA gene training set, which we used in conjunction with an independent PacBio single molecule, real-time (SMRT)-sequenced sinonasal dataset to validate the representation of species in our training set. This also established the effectiveness of a full-length training set for assigning taxonomy of long-read 16S rRNA gene datasets.

CONCLUSION: Here, we present a systematic approach for constructing a phylogeny-based, high-resolution, habitat-specific training set that permits species/supraspecies-level taxonomic assignment to short- and long-read 16S rRNA gene-derived ASVs. This advancement enhances the ecological and/or clinical relevance of 16S rRNA gene-based microbiota studies. Video Abstract.}, } @article {pmid32409662, year = {2020}, author = {Cooney, CR and Sheard, C and Clark, AD and Healy, SD and Liker, A and Street, SE and Troisi, CA and Thomas, GH and Székely, T and Hemmings, N and Wright, AE}, title = {Ecology and allometry predict the evolution of avian developmental durations.}, journal = {Nature communications}, volume = {11}, number = {1}, pages = {2383}, pmid = {32409662}, issn = {2041-1723}, mesh = {Animals ; Birds/*physiology ; Body Size/physiology ; Datasets as Topic ; Ecology/methods ; Embryo, Nonmammalian ; Embryonic Development/*physiology ; Female ; *Life History Traits ; Male ; *Models, Biological ; Nesting Behavior/physiology ; Time Factors ; }, abstract = {The duration of the developmental period represents a fundamental axis of life-history variation, yet broad insights regarding the drivers of this diversity are currently lacking. Here, we test mechanistic and ecological explanations for the evolution of developmental duration using embryological data and information on incubation and fledging for 3096 avian species. Developmental phases associated primarily with growth are the longest and most variable, consistent with a role for allometric constraint in determining the duration of development. In addition, developmental durations retain a strong imprint of deep evolutionary history and body size differences among species explain less variation than previously thought. Finally, we reveal ecological correlates of developmental durations, including variables associated with the relative safety of the developmental environment and pressures of breeding phenology. Overall, our results provide broad-scale insight into the relative importance of mechanistic, ecological and evolutionary constraints in shaping the diversification of this key life-history trait.}, } @article {pmid32406155, year = {2020}, author = {Cuomo, RE and Cai, M and Shah, N and Li, J and Chen, WH and Obradovich, N and Mackey, TK}, title = {Characterising communities impacted by the 2015 Indiana HIV outbreak: A big data analysis of social media messages associated with HIV and substance abuse.}, journal = {Drug and alcohol review}, volume = {39}, number = {7}, pages = {908-913}, pmid = {32406155}, issn = {1465-3362}, support = {P30 AI036214/AI/NIAID NIH HHS/United States ; UL1 TR001442/TR/NCATS NIH HHS/United States ; }, mesh = {Big Data ; Data Analysis ; Disease Outbreaks ; *HIV Infections/epidemiology ; Humans ; Indiana/epidemiology ; *Opioid-Related Disorders/epidemiology ; Retrospective Studies ; *Social Media ; United States ; }, abstract = {INTRODUCTION AND AIMS: Infoveillance approaches (i.e. surveillance methods using online content) that leverage big data can provide new insights about infectious disease outbreaks and substance use disorder topics. We assessed social media messages about HIV, opioid use and injection drug use in order to understand how unstructured data can prepare public health practitioners for response to future outbreaks.

DESIGN AND METHODS: We conducted an retrospective analysis of Twitter messages during the 2015 HIV Indiana outbreak using machine learning, statistical and geospatial analysis to examine the transition between opioid prescription drug abuse to heroin injection use and finally HIV transmission risk, and to test possible associations with disease burden and demographic variables in Indiana and Marion County. Tweets from October 2014 to June 2015 were compared to disease burden at the county level for Indiana, and classification of census blocks by presence of relevant messages was done at the census block level for Marion County. Marion County was used as it exhibited the highest total count of Tweets.

RESULTS: 257 messages about substance abuse and HIV were significantly related to HIV rates (P < 0.001) and opioid-related hospitalisations (P = 0.037). Using 157 characteristics from the American Community Survey, a linear classifier was computed with an appreciable correlation (r = 0.49) to risk-related social media messages from Marion County.

DISCUSSION AND CONCLUSIONS: Communities appear to communicate online in response to disease burden. Classification produced an accurate equation to model census block risk based on census data, allowing for high-dimensional estimation of risk for blocks with sparse populations.}, } @article {pmid32404305, year = {2020}, author = {Blom, EF and Ten Haaf, K and Arenberg, DA and de Koning, HJ}, title = {Uptake of minimally invasive surgery and stereotactic body radiation therapy for early stage non-small cell lung cancer in the USA: an ecological study of secular trends using the National Cancer Database.}, journal = {BMJ open respiratory research}, volume = {7}, number = {1}, pages = {}, pmid = {32404305}, issn = {2052-4439}, support = {U01 CA199284/CA/NCI NIH HHS/United States ; }, mesh = {Adult ; Aged ; Aged, 80 and over ; Carcinoma, Non-Small-Cell Lung/pathology/*therapy ; Databases, Factual/*statistics & numerical data ; Early Detection of Cancer ; Female ; Humans ; Lung Neoplasms/pathology/*therapy ; Male ; Middle Aged ; Minimally Invasive Surgical Procedures/*methods ; Neoplasm Staging ; Radiosurgery/*methods ; United States ; }, abstract = {BACKGROUND: We aimed to assess the uptake of minimally invasive surgery (MIS) and stereotactic body radiation therapy (SBRT) among early stage (stage IA-IIB) non-small cell lung cancer (NSCLC) cases in the USA, and the rate of conversions from MIS to open surgery.

MATERIALS AND METHODS: Data were obtained from the US National Cancer Database, a nationwide facility-based cancer registry capturing up to 70% of incident cancer cases in the USA. We included cases diagnosed with early stage (clinical stages IA-IIB) NSCLC between 2010 and 2014. In an ecological analysis, we assessed changes in treatment by year of diagnosis. Among surgically treated cases, we assessed the uptake of MIS and whether conversion to open surgery took place. For cases that received thoracic radiotherapy, we assessed the uptake of SBRT.

RESULTS: Among 117 370 selected cases, radiotherapy use increased 3.4 percentage points between 2010 and 2014 (p<0.0001). Surgical treatments decreased 3.5 percentage points (p<0.0001). Rates of non-treatment remained stable (range: 10.0%-10.6% (p=0.4066)). Among surgically treated stage IA cases, uptake of MIS increased from 28.7% (95% CI 27.8% to 29.7%) in 2010 to 48.6% (95% CI 47.6% to 49.6%) in 2014 (p<0.0001), while conversions decreased from 17.0% (95% CI 15.6% to 18.6%) in 2010 to 9.1% (95% CI 8.3% to 10.0%) in 2014 (p<0.0001). MIS uptake among stages IB-IIB was lower and conversion rates were higher, but time trends were similar. Uptake of SBRT among stage IA receiving thoracic radiotherapy increased from 53.4% (95% CI 51.2% to 55.6%) in 2010 to 73.0% (95% CI 71.4% to 74.6%) in 2014 (p<0.0001). SBRT uptake among stage IB increased from 32.5% (95% CI 29.9% to 35.2%) in 2010 to 48.2% (95% CI 45.6% to 50.8%) in 2014 (p<0.0001).

CONCLUSION: Between 2010 and 2014, uptake of MIS and SBRT among early stage NSCLC significantly increased, while the rate of conversions to open surgery significantly decreased. Continuing these trends may contribute to improving patient care, in particular with the expected increase in early stages due to the implementation of lung cancer screening.}, } @article {pmid32401771, year = {2020}, author = {Miranda, L and Freeman, J}, title = {The two types of society: Computationally revealing recurrent social formations and their evolutionary trajectories.}, journal = {PloS one}, volume = {15}, number = {5}, pages = {e0232609}, pmid = {32401771}, issn = {1932-6203}, mesh = {Datasets as Topic ; Humans ; Social Environment ; Social Sciences ; Societies/*classification/*statistics & numerical data ; }, abstract = {Comparative social science has a long history of attempts to classify societies and cultures in terms of shared characteristics. However, only recently has it become feasible to conduct quantitative analysis of large historical datasets to mathematically approach the study of social complexity and classify shared societal characteristics. Such methods have the potential to identify recurrent social formations in human societies and contribute to social evolutionary theory. However, in order to achieve this potential, repeated studies are needed to assess the robustness of results to changing methods and data sets. Using an improved derivative of the Seshat: Global History Databank, we perform a clustering analysis of 271 past societies from sampling points across the globe to study plausible categorizations inherent in the data. Analysis indicates that the best fit to Seshat data is five subclusters existing as part of two clearly delineated superclusters (that is, two broad "types" of society in terms of social-ecological configuration). Our results add weight to the idea that human societies form recurrent social formations by replicating previous studies with different methods and data. Our results also contribute nuance to previously established measures of social complexity, illustrate diverse trajectories of change, and shed further light on the finite bounds of human social diversity.}, } @article {pmid32400224, year = {2020}, author = {Skinner, CM and Nookaew, I and Ewing, LE and Wongsurawat, T and Jenjaroenpun, P and Quick, CM and Yee, EU and Piccolo, BD and ElSohly, M and Walker, LA and Gurley, B and Koturbash, I}, title = {Potential Probiotic or Trigger of Gut Inflammation - The Janus-Faced Nature of Cannabidiol-Rich Cannabis Extract.}, journal = {Journal of dietary supplements}, volume = {17}, number = {5}, pages = {543-560}, pmid = {32400224}, issn = {1939-022X}, support = {P20 GM109005/GM/NIGMS NIH HHS/United States ; P20 GM125503/GM/NIGMS NIH HHS/United States ; UL1 TR000039/TR/NCATS NIH HHS/United States ; KL2 TR000063/TR/NCATS NIH HHS/United States ; T32 GM106999/GM/NIGMS NIH HHS/United States ; }, mesh = {Akkermansia/drug effects ; Animals ; Cannabidiol/*adverse effects ; *Cannabis ; Chemokines/drug effects ; Colitis/*chemically induced ; Colon/metabolism ; Cytokines/drug effects ; Disease Models, Animal ; Gastrointestinal Microbiome/*drug effects ; Intestinal Mucosa/drug effects ; Male ; Mice ; Mice, Inbred C57BL ; Mucin-2/metabolism ; Plant Extracts/*adverse effects ; }, abstract = {Cannabidiol (CBD) is the major non-psychotropic phytocannabinoid present in Cannabis sativa. In 2018, Congress designated certain C. sativa plant material as "hemp," thus removing it from the DEA's list of controlled substances. As a result, CBD-containing hemp extracts and other CBD products are now widely available and heavily marketed, yet their FDA regulatory status is still hotly debated. The goal of this study was to investigate the effects of a cannabidiol-rich cannabis extract (CRCE) on the gut microbiome and associated histomorphological and molecular changes in the mouse gut mucosa. Male C57BL6/J mice were gavaged with either 0, 61.5, 184.5, or 615 mg/kg/bw of CRCE in sesame oil for 2 weeks (Mon-Fri). Substantial CRCE-induced increases in the relative abundance of A. muciniphila, a bacterial species currently accepted as probiotic, was observed in fecal samples at all doses. This was paralleled by decreases in the relative abundance of other gut bacterial species. Coincident with the observed changes in gut ecology were multiple pro-inflammatory responses, including increased expression of cytokines and chemokines-Il1ß, Cxcl1, and Cxcl2 in the colon tissue. Furthermore, dramatic increases in the relative abundance of A. muciniphila significantly decreased expression of Muc2-a gene intimately associated with gut integrity. Taken together, these findings raise concerns about the safety of long-term CBD usage and underline the need for additional well-designed studies into its tolerability and efficacy.}, } @article {pmid32399614, year = {2020}, author = {Greer, ML and Akman, O and Comar, TD and Hrozencik, D and Rubin, JE}, title = {Paying Our Dues: The Role of Professional Societies in the Evolution of Mathematical Biology Education.}, journal = {Bulletin of mathematical biology}, volume = {82}, number = {5}, pages = {59}, pmid = {32399614}, issn = {1522-9602}, mesh = {Awards and Prizes ; Biology/*education ; Computational Biology/*education ; Curriculum ; Humans ; Interdisciplinary Studies ; Mathematics/*education ; Mentoring ; *Societies, Scientific ; Students ; Training Support ; United States ; }, abstract = {Mathematical biology education provides key foundational underpinnings for the scholarly work of mathematical biology. Professional societies support such education efforts via funding, public speaking opportunities, Web presence, publishing, workshops, prizes, opportunities to discuss curriculum design, and support of mentorship and other means of sustained communication among communities of scholars. Such programs have been critical to the broad expansion of the range and visibility of research and educational activities in mathematical biology. We review these efforts, past and present, across multiple societies-the Society for Mathematical Biology (SMB), the Symposium on Biomathematics and Ecology Education and Research (BEER), the Mathematical Association of America (MAA), and the Society for Industrial and Applied Mathematics (SIAM). We then proceed to suggest ways that professional societies can serve as advocates and community builders for mathematical biologists at all levels, noting that education continues throughout a career and also emphasizing the value of educating new generations of students. Our suggestions include collecting and disseminating data related to biomath education; developing and maintaining mentoring systems and research communities; and providing incentives and visibility for educational efforts within mathematical biology.}, } @article {pmid32397301, year = {2020}, author = {Kancherla, V and Pachón, H and Blencowe, H and Martinez, H and Oakley, GP and Berry, RJ}, title = {The Fallacy of Using Administrative Data in Assessing the Effectiveness of Food Fortification. Comment on: "Folic Acid Fortification and Neural Tube Defect Risk: Analysis of the Food Fortification Initiative Dataset. Nutrients 2020, 12, 247".}, journal = {Nutrients}, volume = {12}, number = {5}, pages = {}, pmid = {32397301}, issn = {2072-6643}, mesh = {*Datasets as Topic ; Female ; Folic Acid/*administration & dosage ; *Food, Fortified ; Humans ; Neural Tube Defects/epidemiology/*prevention & control ; Nutritional Physiological Phenomena/*physiology ; Pregnancy ; Prenatal Care ; Prevalence ; Risk ; }, abstract = {Our objective in this comment is to highlight several limitations in an ecological research study that was published in Nutrients by Murphy and Westmark (2020) in January 2020. The study used data from the Food Fortification Initiative (FFI) website, and applying an ecological study design, made an error of "ecologic fallacy" in concluding that "national fortification with folic acid is not associated with a significant decrease in the prevalence of neural tube defects (NTDs) at the population level". We list study limitations that led to their erroneous conclusions, stemming from incorrect considerations regarding NTD prevalence, the average grain availability for a country, the fortification coverage in a country, the population reach of fortified foods within a country, and the absence of the consideration of fortification type (voluntary vs. mandatory), country-specific policies on elective terminations for NTD-affected pregnancies, stillbirth proportions among those with NTDs, and fortification implementation. FFI data are derived from many sources and intended for fortification advocacy, not for hypothesis testing. The flawed study by Murphy & Westmark (2020) in Nutrients promotes a confusing and incorrect message to stakeholders, misguides policy makers, and hinders progress in global NTD prevention through a cost-effective, safe, and effective intervention: the mandatory large-scale folic acid fortification of staple foods.}, } @article {pmid32396806, year = {2020}, author = {Herren, CM}, title = {Disruption of cross-feeding interactions by invading taxa can cause invasional meltdown in microbial communities.}, journal = {Proceedings. Biological sciences}, volume = {287}, number = {1927}, pages = {20192945}, pmid = {32396806}, issn = {1471-2954}, mesh = {Biota ; *Ecosystem ; *Introduced Species ; *Microbiota ; }, abstract = {The strength of biotic interactions within an ecological community affects the susceptibility of the community to invasion by introduced taxa. In microbial communities, cross-feeding is a widespread type of biotic interaction that has the potential to affect community assembly and stability. Yet, there is little understanding of how the presence of cross-feeding within a community affects invasion risk. Here, I develop a metabolite-explicit model where native microbial taxa interact through both cross-feeding and competition for metabolites. I use this model to study how the strength of biotic interactions, especially cross-feeding, influence whether an introduced taxon can join the community. I found that stronger cross-feeding and competition led to much lower invasion risk, as both types of biotic interactions lead to greater metabolite scarcity for the invader. I also evaluated the impact of a successful invader on community composition and structure. The effect of invaders on the native community was greatest at intermediate levels of cross-feeding; at this 'critical' level of cross-feeding, successful invaders generally cause decreased diversity, decreased productivity, greater metabolite availability, and decreased quantities of metabolites exchanged among taxa. Furthermore, these changes resulting from a successful primary invader made communities further susceptible to future invaders. The increase in invasion risk was greatest when the network of metabolite exchange between taxa was minimally redundant. Thus, this model demonstrates a case of invasional meltdown that is mediated by initial invaders disrupting the metabolite exchange networks of the native community.}, } @article {pmid32396798, year = {2020}, author = {McKay, B and Ebell, M and Dale, AP and Shen, Y and Handel, A}, title = {Virulence-mediated infectiousness and activity trade-offs and their impact on transmission potential of influenza patients.}, journal = {Proceedings. Biological sciences}, volume = {287}, number = {1927}, pages = {20200496}, pmid = {32396798}, issn = {1471-2954}, support = {U19 AI117891/AI/NIAID NIH HHS/United States ; }, mesh = {Humans ; Influenza, Human/*transmission ; *Virulence ; }, abstract = {Communicable diseases are often virulent, i.e. they cause morbidity symptoms in those infected. While some symptoms may be transmission-enhancing, other symptoms are likely to reduce transmission potential. For human diseases, the reduction in transmission opportunities is commonly caused by reduced activity. There is limited data regarding the potential impact of virulence on transmission potential. We performed an exploratory data analysis of 324 influenza patients at a university health centre during the 2016/2017 influenza season. We classified symptoms as infectiousness-related or morbidity-related and calculated two scores. The scores were used to explore the relationship between infectiousness, morbidity (virulence), and activity level. We found a decrease in the activity level with increasing morbidity scores. There was no consistent pattern between an activity level and an infectiousness score. We also found a positive correlation between morbidity and infectiousness scores. Overall, we find that increasing virulence leads to increased infectiousness and reduced activity, suggesting a trade-off that can impact overall transmission potential. Our findings indicate that a reduction of systemic symptoms may increase host activity without reducing infectiousness. Therefore, interventions should target both systemic- and infectiousness-related symptoms to reduce overall transmission potential. Our findings can also inform simulation models that investigate the impact of different interventions on transmission.}, } @article {pmid32395585, year = {2020}, author = {Ahmad, NII and Rahim, NAA and Roslan, A and Adrus, M and Ahamad, M and Hassan, M and Lola, MS and Afiq Ramlee, MN and Zahidin, MA and Abdullah, MT}, title = {Data on ectoparasites infestation on small mammals from different habitats in east-coast Peninsular Malaysia.}, journal = {Data in brief}, volume = {30}, number = {}, pages = {105621}, pmid = {32395585}, issn = {2352-3409}, abstract = {This data article presents on the ectoparasites infestation on small mammals in Peninsular Malaysia. The dataset on ectoparasites infestation is important because it raises a major medical concern regarding the spread of potentially zoonotic disease from wildlife to human. Tick and chigger are the primary ectoparasites as reservoirs of vector-borne diseases found on small mammals in Malaysia. These small mammals that are infested with ectoparasites occupy various types of habitats, including human settlements, could be of community health risks as the carriers of potentially zoonotic diseases. Field samplings were conducted from February 2015 to February 2016 in three different ecological habitats of mixed dipterocarp forest, coastal forest and insular forest, in Terengganu, Malaysia. A total of 35 and 22 species of bats and rodents respectively were captured and examined for ectoparasites. Twenty-three species of bats and 16 species of small mammal were recorded as hosts for at least one species of ectoparasites. These findings show that the highest ectoparasite infestation occurred on bat community.}, } @article {pmid32393943, year = {2020}, author = {van der Hooft, JJJ and Mohimani, H and Bauermeister, A and Dorrestein, PC and Duncan, KR and Medema, MH}, title = {Linking genomics and metabolomics to chart specialized metabolic diversity.}, journal = {Chemical Society reviews}, volume = {49}, number = {11}, pages = {3297-3314}, doi = {10.1039/d0cs00162g}, pmid = {32393943}, issn = {1460-4744}, mesh = {Bacteria/*metabolism ; Biological Products/*chemistry ; Biosynthetic Pathways ; Computational Biology ; Computer Simulation ; Data Mining ; Databases, Genetic ; Drug Discovery ; Fungi/*metabolism ; Genomics/*methods ; High-Throughput Screening Assays ; Humans ; Metabolomics/*methods ; Plants/*metabolism ; Secondary Metabolism ; }, abstract = {Microbial and plant specialized metabolites constitute an immense chemical diversity, and play key roles in mediating ecological interactions between organisms. Also referred to as natural products, they have been widely applied in medicine, agriculture, cosmetic and food industries. Traditionally, the main discovery strategies have centered around the use of activity-guided fractionation of metabolite extracts. Increasingly, omics data is being used to complement this, as it has the potential to reduce rediscovery rates, guide experimental work towards the most promising metabolites, and identify enzymatic pathways that enable their biosynthetic production. In recent years, genomic and metabolomic analyses of specialized metabolic diversity have been scaled up to study thousands of samples simultaneously. Here, we survey data analysis technologies that facilitate the effective exploration of large genomic and metabolomic datasets, and discuss various emerging strategies to integrate these two types of omics data in order to further accelerate discovery.}, } @article {pmid32393397, year = {2020}, author = {Koh, H and Zhao, N}, title = {A powerful microbial group association test based on the higher criticism analysis for sparse microbial association signals.}, journal = {Microbiome}, volume = {8}, number = {1}, pages = {63}, pmid = {32393397}, issn = {2049-2618}, support = {P30 AI094189/AI/NIAID NIH HHS/United States ; U24 OD023382/OD/NIH HHS/United States ; }, mesh = {*Computational Biology ; Humans ; *Microbiota ; *Software ; }, abstract = {BACKGROUND: In human microbiome studies, it is crucial to evaluate the association between microbial group (e.g., community or clade) composition and a host phenotype of interest. In response, a number of microbial group association tests have been proposed, which account for the unique features of the microbiome data (e.g., high-dimensionality, compositionality, phylogenetic relationship). These tests generally fall in the class of aggregation tests which amplify the overall group association by combining all the underlying microbial association signals, and, therefore, they are powerful when many microbial species are associated with a given host phenotype (i.e., low sparsity). However, in practice, the microbial association signals can be highly sparse, and this is especially the situation where we have a difficulty to discover the microbial group association.

METHODS: Here, we introduce a powerful microbial group association test for sparse microbial association signals, namely, microbiome higher criticism analysis (MiHC). MiHC is a data-driven omnibus test taken in a search space spanned by tailoring the higher criticism test to incorporate phylogenetic information and/or modulate sparsity levels and including the Simes test for excessively high sparsity levels. Therefore, MiHC robustly adapts to diverse phylogenetic relevance and sparsity levels.

RESULTS: Our simulations show that MiHC maintains a high power at different phylogenetic relevance and sparsity levels with correct type I error controls. We also apply MiHC to four real microbiome datasets to test the association between respiratory tract microbiome and smoking status, the association between the infant's gut microbiome and delivery mode, the association between the gut microbiome and type 1 diabetes status, and the association between the gut microbiome and human immunodeficiency virus status.

CONCLUSIONS: In practice, the true underlying association pattern on the extent of phylogenetic relevance and sparsity is usually unknown. Therefore, MiHC can be a useful analytic tool because of its high adaptivity to diverse phylogenetic relevance and sparsity levels. MiHC can be implemented in the R computing environment using our software package freely available at https://github.com/hk1785/MiHC.}, } @article {pmid32392470, year = {2020}, author = {Kon, T and Omori, Y and Fukuta, K and Wada, H and Watanabe, M and Chen, Z and Iwasaki, M and Mishina, T and Matsuzaki, SS and Yoshihara, D and Arakawa, J and Kawakami, K and Toyoda, A and Burgess, SM and Noguchi, H and Furukawa, T}, title = {The Genetic Basis of Morphological Diversity in Domesticated Goldfish.}, journal = {Current biology : CB}, volume = {30}, number = {12}, pages = {2260-2274.e6}, doi = {10.1016/j.cub.2020.04.034}, pmid = {32392470}, issn = {1879-0445}, mesh = {Animals ; Biological Evolution ; *DNA Transposable Elements ; *Domestication ; *Gene Duplication ; *Genome-Wide Association Study ; Goldfish/anatomy & histology/*genetics ; *Phenotype ; Tetraploidy ; }, abstract = {Although domesticated goldfish strains exhibit highly diversified phenotypes in morphology, the genetic basis underlying these phenotypes is poorly understood. Here, based on analysis of transposable elements in the allotetraploid goldfish genome, we found that its two subgenomes have evolved asymmetrically since a whole-genome duplication event in the ancestor of goldfish and common carp. We conducted whole-genome sequencing of 27 domesticated goldfish strains and wild goldfish. We identified more than 60 million genetic variations and established a population genetic structure of major goldfish strains. Genome-wide association studies and analysis of strain-specific variants revealed genetic loci associated with several goldfish phenotypes, including dorsal fin loss, long-tail, telescope-eye, albinism, and heart-shaped tail. Our results suggest that accumulated mutations in the asymmetrically evolved subgenomes led to generation of diverse phenotypes in the goldfish domestication history. This study is a key resource for understanding the genetic basis of phenotypic diversity among goldfish strains.}, } @article {pmid32391910, year = {2020}, author = {Escamilla Molgora, JM and Sedda, L and Atkinson, PM}, title = {Biospytial: spatial graph-based computing for ecological Big Data.}, journal = {GigaScience}, volume = {9}, number = {5}, pages = {}, pmid = {32391910}, issn = {2047-217X}, mesh = {*Big Data ; *Databases, Factual ; Ecology ; Geography ; Models, Theoretical ; *Software ; }, abstract = {BACKGROUND: The exponential accumulation of environmental and ecological data together with the adoption of open data initiatives bring opportunities and challenges for integrating and synthesising relevant knowledge that need to be addressed, given the ongoing environmental crises.

FINDINGS: Here we present Biospytial, a modular open source knowledge engine designed to import, organise, analyse and visualise big spatial ecological datasets using the power of graph theory. The engine uses a hybrid graph-relational approach to store and access information. A graph data structure uses linkage relationships to build semantic structures represented as complex data structures stored in a graph database, while tabular and geospatial data are stored in an efficient spatial relational database system. We provide an application using information on species occurrences, their taxonomic classification and climatic datasets. We built a knowledge graph of the Tree of Life embedded in an environmental and geographical grid to perform an analysis on threatened species co-occurring with jaguars (Panthera onca).

CONCLUSIONS: The Biospytial approach reduces the complexity of joining datasets using multiple tabular relations, while its scalable design eases the problem of merging datasets from different sources. Its modular design makes it possible to distribute several instances simultaneously, allowing fast and efficient handling of big ecological datasets. The provided example demonstrates the engine's capabilities in performing basic graph manipulation, analysis and visualizations of taxonomic groups co-occurring in space. The example shows potential avenues for performing novel ecological analyses, biodiversity syntheses and species distribution models aided by a network of taxonomic and spatial relationships.}, } @article {pmid32390750, year = {2020}, author = {Moritz, L and Koch, M}, title = {No Tömösváry organ in flat backed millipedes (Diplopoda, Polydesmida).}, journal = {ZooKeys}, volume = {930}, number = {}, pages = {103-115}, pmid = {32390750}, issn = {1313-2989}, abstract = {The Tömösváry organ is a sensory structure of the head in myriapods and some other terrestrial arthropods. Due to its variable shape, size, and position in millipedes (Diplopoda) the Tömösváry organ is commonly used as diagnostic character in taxonomic descriptions and often included in phylogenetic analyses. For the Polydesmida, the largest millipede order, the Tömösváry organ is inconsistently stated as being either absent or present as a pear-shaped pit covered by a membrane or cuticular disc. In order to resolve this inconsistency, we investigated the morphology of the presumable Tömösváry organ in four polydesmidan species based on paraffin-histology, semi-thin sections and micro-computed tomography. Our results unambiguously favor the view that the articulation of the cephalic tentorium with the head capsule was misidentified as the Tömösváry organ in previous studies, and thus that the Tömösváry organ indeed is absent in the Polydesmida. The pear-shaped pit proved to represent the distal roundish expansion of the incisura lateralis, to which - similarly as in julidan millipedes - the tentorial transverse bar is articulated. The absence of the Tömösváry organ in the Polydesmida does not affect the topology of the interrelationships among the millipede orders retrieved in previous cladistic analyses based on morphology. As a character shared by Colobognatha and Juliformia, however, absence of a Tömösváry organ in Polydesmida favors the optimization of its presence in nematophoran millipedes as a reversal. Further studies are needed to clarify whether among chilognathan millipedes a Tömösváry organ really exists in taxa such as Stemmiulida, and whether the Tömösváry organs are homologous across millipedes.}, } @article {pmid32390748, year = {2020}, author = {VandenSpiegel, D and Shelley, RM and Golovatch, SI}, title = {The millipede genus Globanus Attems, 1914, endemic to São Tomé and Príncipe, with the description of a new species (Diplopoda, Spirostreptida, Spirostreptidae).}, journal = {ZooKeys}, volume = {930}, number = {}, pages = {61-74}, pmid = {32390748}, issn = {1313-2989}, abstract = {During a soil zoological expedition to São Tomé and Príncipe in 2010 by the California Academy of Sciences, millipedes of the genus Globanus were collected. Samples of G. marginescaber (Karsch, 1884) and G. integer (Karsch, 1884) were recovered in addition to those containing a new species. Globanus drewesi sp. nov. is described and additional records, illustrations, and descriptive notes are given for the other two species. A key to all three species of the genus is provided, and a distribution map is presented. The monotypic genus Lobogonus Demange, 1971, which includes L. trilobatus Demange, 1971, from Sierra Leone, mainland western Africa, is revalidated and removed from synonymy under Globanus. Lobogonus is illustrated from a type specimen.}, } @article {pmid32387905, year = {2020}, author = {Wang, R and Li, J and Li, J}, title = {Functional and structural analyses for MlrC enzyme of Novosphingobium sp. THN1 in microcystin-biodegradation: Involving optimized heterologous expression, bioinformatics and site-directed mutagenesis.}, journal = {Chemosphere}, volume = {255}, number = {}, pages = {126906}, doi = {10.1016/j.chemosphere.2020.126906}, pmid = {32387905}, issn = {1879-1298}, mesh = {*Biodegradation, Environmental ; Computational Biology ; Microcystins/*metabolism ; Mutagenesis, Site-Directed ; Sphingomonadaceae/metabolism ; }, abstract = {Enzymatic function of MlrC from Novosphingobium sp. THN1 (i.e., THN1-MlrC) towards linearized microcystins (MCs) and structural/physic-chemical properties of MlrC enzyme deserved urgent research, and heterologous expression (HE) optimization for MlrC is yet to be solved. This study achieved HE of THN1-MlrC by rapid-efficiently constructing HE system, and revealed that THN1-MlrC can degrade linearized MC-LR and linearized MC-RR to produce Adda, providing direct evidence for catalytic function of THN-MlrC and its ecological implication in MC-detoxification. Consequently, to maximize THN1-MlrC expression for production and application, induction conditions for HE of THN1-MlrC was optimized as at 0.1 mM of isopropyl-β-D-thiogalactoside and 30 °C for 8 h, which could be widely applicable for heterologous production of other MlrC homologs. Using bioinformatics and site-mutation experiment, THN1-MlrC was evaluated as a cytoplasm-locating hydrophilic protein with theoretical isoelectric point of 5.57, and contained six verified active sites Glu[39], His[133], Asp[167], His[169], His[191] and Asp[332] in two domains of its 3D structure, among which Glu[39], His[133] and Asp[332] were newly-discovered ones here. The Glu[39], His[133], Asp[167], His[169] and His[191] gathered more closely in 3D structure than in amino acid sequence, while they and Asp[332] surrounded protein center to constitute a potential active pocket for mediating linearized MCs degradation. Due to MlrC sequence homology and conservative active sites, structural/physic-chemical characteristics of THN1-MlrC presented in this study provided a helpful reference for other MlrC homologs of diverse bacteria. This study shed novel insights for functional-structural relationships of THN1-MlrC during MC-biodegradation, and was crucial for research and practical applications in MC-decontamination.}, } @article {pmid32386611, year = {2020}, author = {Shahmanesh, M and Harling, G and Coltart, CEM and Bailey, H and King, C and Gibbs, J and Seeley, J and Phillips, A and Sabin, CA and Aldridge, RW and Sonnenberg, P and Hart, G and Rowson, M and Pillay, D and Johnson, AM and Abubakar, I and Field, N}, title = {From the micro to the macro to improve health: microorganism ecology and society in teaching infectious disease epidemiology.}, journal = {The Lancet. Infectious diseases}, volume = {20}, number = {6}, pages = {e142-e147}, pmid = {32386611}, issn = {1474-4457}, support = {082384/Z/07/Z/WT_/Wellcome Trust/United Kingdom ; R01 HL131049/HL/NHLBI NIH HHS/United States ; /WT_/Wellcome Trust/United Kingdom ; NF-SI-0616-10037/DH_/Department of Health/United Kingdom ; R01 MH114560/MH/NIMH NIH HHS/United States ; 210479/Z/18/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Communicable Disease Control/*methods ; Communicable Diseases/*epidemiology ; *Environmental Microbiology ; Humans ; *Microbiota ; Public Health/education ; }, abstract = {Chronic and emerging infectious diseases and antimicrobial resistance remain a substantial global health threat. Microbiota are increasingly recognised to play an important role in health. Infections also have a profound effect beyond health, especially on global and local economies. To maximise health improvements, the field of infectious disease epidemiology needs to derive learning from ecology and traditional epidemiology. New methodologies and tools are transforming understanding of these systems, from a better understanding of socioeconomic, environmental, and cultural drivers of infection, to improved methods to detect microorganisms, describe the immunome, and understand the role of human microbiota. However, exploiting the potential of novel methods to improve global health remains elusive. We argue that to exploit these advances a shift is required in the teaching of infectious disease epidemiology to ensure that students are well versed in a breadth of disciplines, while maintaining core epidemiological skills. We discuss the following key points using a series of teaching vignettes: (1) integrated training in classic and novel techniques is needed to develop future scientists and professionals who can work from the micro (interactions between pathogens, their cohabiting microbiota, and the host at a molecular and cellular level), with the meso (the affected communities), and to the macro (wider contextual drivers of disease); (2) teach students to use a team-science multidisciplinary approach to effectively integrate biological, clinical, epidemiological, and social tools into public health; and (3) develop the intellectual skills to critically engage with emerging technologies and resolve evolving ethical dilemmas. Finally, students should appreciate that the voices of communities affected by infection need to be kept at the heart of their work.}, } @article {pmid32385271, year = {2020}, author = {Ou, S and Liu, J and Chougule, KM and Fungtammasan, A and Seetharam, AS and Stein, JC and Llaca, V and Manchanda, N and Gilbert, AM and Wei, S and Chin, CS and Hufnagel, DE and Pedersen, S and Snodgrass, SJ and Fengler, K and Woodhouse, M and Walenz, BP and Koren, S and Phillippy, AM and Hannigan, BT and Dawe, RK and Hirsch, CN and Hufford, MB and Ware, D}, title = {Effect of sequence depth and length in long-read assembly of the maize inbred NC358.}, journal = {Nature communications}, volume = {11}, number = {1}, pages = {2288}, pmid = {32385271}, issn = {2041-1723}, mesh = {Base Sequence ; DNA Transposable Elements/genetics ; Genome, Plant ; High-Throughput Nucleotide Sequencing/*methods ; *Inbreeding ; Repetitive Sequences, Nucleic Acid/genetics ; Zea mays/*genetics ; }, abstract = {Improvements in long-read data and scaffolding technologies have enabled rapid generation of reference-quality assemblies for complex genomes. Still, an assessment of critical sequence depth and read length is important for allocating limited resources. To this end, we have generated eight assemblies for the complex genome of the maize inbred line NC358 using PacBio datasets ranging from 20 to 75 × genomic depth and with N50 subread lengths of 11-21 kb. Assemblies with ≤30 × depth and N50 subread length of 11 kb are highly fragmented, with even low-copy genic regions showing degradation at 20 × depth. Distinct sequence-quality thresholds are observed for complete assembly of genes, transposable elements, and highly repetitive genomic features such as telomeres, heterochromatic knobs, and centromeres. In addition, we show high-quality optical maps can dramatically improve contiguity in even our most fragmented base assembly. This study provides a useful resource allocation reference to the community as long-read technologies continue to mature.}, } @article {pmid32385111, year = {2020}, author = {Glaub, A and Huptas, C and Neuhaus, K and Ardern, Z}, title = {Recommendations for bacterial ribosome profiling experiments based on bioinformatic evaluation of published data.}, journal = {The Journal of biological chemistry}, volume = {295}, number = {27}, pages = {8999-9011}, pmid = {32385111}, issn = {1083-351X}, mesh = {Bacteria/*genetics ; Computational Biology/methods ; Genetic Profile ; High-Throughput Nucleotide Sequencing/methods ; Molecular Sequence Annotation/methods ; Protein Biosynthesis/genetics ; RNA, Messenger/genetics ; RNA, Ribosomal/metabolism ; Ribosomes/*genetics ; Sequence Analysis, RNA/*methods ; }, abstract = {Ribosome profiling (RIBO-Seq) has improved our understanding of bacterial translation, including finding many unannotated genes. However, protocols for RIBO-Seq and corresponding data analysis are not yet standardized. Here, we analyzed 48 RIBO-Seq samples from nine studies of Escherichia coli K12 grown in lysogeny broth medium and particularly focused on the size-selection step. We show that for conventional expression analysis, a size range between 22 and 30 nucleotides is sufficient to obtain protein-coding fragments, which has the advantage of removing many unwanted rRNA and tRNA reads. More specific analyses may require longer reads and a corresponding improvement in rRNA/tRNA depletion. There is no consensus about the appropriate sequencing depth for RIBO-Seq experiments in prokaryotes, and studies vary significantly in total read number. Our analysis suggests that 20 million reads that are not mapping to rRNA/tRNA are required for global detection of translated annotated genes. We also highlight the influence of drug-induced ribosome stalling, which causes bias at translation start sites. The resulting accumulation of reads at the start site may be especially useful for detecting weakly expressed genes. As different methods suit different questions, it may not be possible to produce a "one-size-fits-all" ribosome profiling data set. Therefore, experiments should be carefully designed in light of the scientific questions of interest. We propose some basic characteristics that should be reported with any new RIBO-Seq data sets. Careful attention to the factors discussed should improve prokaryotic gene detection and the comparability of ribosome profiling data sets.}, } @article {pmid32379759, year = {2020}, author = {Burgio, KR and MacKenzie, CM and Borrelle, SB and Ernest, SKM and Gill, JL and Ingeman, KE and Teffer, A and White, EP}, title = {Ten Simple Rules for a successful remote postdoc.}, journal = {PLoS computational biology}, volume = {16}, number = {5}, pages = {e1007809}, pmid = {32379759}, issn = {1553-7358}, mesh = {Career Choice ; Education, Distance/*methods/trends ; Engineering/education ; Humans ; Mathematics/education ; Preceptorship/*methods ; Research Personnel/*education ; Science/education ; Technology/education ; }, abstract = {Postdocs are a critical transition for early-career researchers. This transient period, between finishing a PhD and finding a permanent position, is when early-career researchers develop independent research programs and establish collaborative relationships that can make a successful career. Traditionally, postdocs physically relocate-sometimes multiple times-for these short-term appointments, which creates challenges that can disproportionately affect members of traditionally underrepresented groups in science, technology, engineering, and mathematics (STEM). However, many research activities involving analytical and quantitative work do not require a physical presence in a lab and can be accomplished remotely. Other fields have embraced remote work, yet many academics have been hesitant to hire remote postdocs. In this article, we present advice to both principal investigators (PIs) and postdocs for successfully navigating a remote position. Using the combined experience of the authors (as either remote postdocs or employers of remote postdocs), we provide a road map to overcome the real (and perceived) obstacles associated with remote work. With planning, communication, and creativity, remote postdocs can be a fully functioning and productive member of a research lab. Further, our rules can be useful for research labs generally and can help foster a more flexible and inclusive environment.}, } @article {pmid32379295, year = {2020}, author = {Frioux, C and Dittami, SM and Siegel, A}, title = {Using automated reasoning to explore the metabolism of unconventional organisms: a first step to explore host-microbial interactions.}, journal = {Biochemical Society transactions}, volume = {48}, number = {3}, pages = {901-913}, doi = {10.1042/BST20190667}, pmid = {32379295}, issn = {1470-8752}, mesh = {Algorithms ; Arabidopsis ; Bacteria/*metabolism ; Computational Biology ; Escherichia coli ; Haemophilus influenzae ; Metabolic Networks and Pathways ; Microbial Interactions ; Models, Biological ; Models, Theoretical ; Pattern Recognition, Automated ; Phenotype ; Seaweed/*microbiology ; Software ; Systems Biology ; }, abstract = {Systems modelled in the context of molecular and cellular biology are difficult to represent with a single calibrated numerical model. Flux optimisation hypotheses have shown tremendous promise to accurately predict bacterial metabolism but they require a precise understanding of metabolic reactions occurring in the considered species. Unfortunately, this information may not be available for more complex organisms or non-cultured microorganisms such as those evidenced in microbiomes with metagenomic techniques. In both cases, flux optimisation techniques may not be applicable to elucidate systems functioning. In this context, we describe how automatic reasoning allows relevant features of an unconventional biological system to be identified despite a lack of data. A particular focus is put on the use of Answer Set Programming, a logic programming paradigm with combinatorial optimisation functionalities. We describe its usage to over-approximate metabolic responses of biological systems and solve gap-filling problems. In this review, we compare steady-states and Boolean abstractions of metabolic models and illustrate their complementarity via applications to the metabolic analysis of macro-algae. Ongoing applications of this formalism explore the emerging field of systems ecology, notably elucidating interactions between a consortium of microbes and a host organism. As the first step in this field, we will illustrate how the reduction in microbiotas according to expected metabolic phenotypes can be addressed with gap-filling problems.}, } @article {pmid32375306, year = {2020}, author = {Kalle, R and Sõukand, R and Pieroni, A}, title = {Devil Is in the Details: Use of Wild Food Plants in Historical Võromaa and Setomaa, Present-Day Estonia.}, journal = {Foods (Basel, Switzerland)}, volume = {9}, number = {5}, pages = {}, pmid = {32375306}, issn = {2304-8158}, support = {714874//Horizon 2020 Framework Programme/ ; }, abstract = {Biodiversity needs to be preserved to ensure food security. Border zones create high but vulnerable biocultural diversity. Through reviewing scattered historical data and documenting the current use of wild food plants among people currently living in historical Setomaa and Võromaa parishes, we aimed to identify cross-cultural differences and diachronic changes as well as the role borders have played on the local use of wild plants. The Seto have still preserved their distinctive features either by consciously opposing others or by maintaining more historical plant uses. People historically living in Setomaa and Võromaa parishes have already associated the eating of wild plants with famine food in the early 20th century, yet it was stressed more now by the Seto than by Estonians. Loss of Pechory as the center of attraction in the region when the border was closed in the early 1990s brought about a decline in the exchange of knowledge as well as commercial activities around wild food plants. National support for businesses in the area today and the popularity of a healthy lifestyle have introduced new wild food plant applications and are helping to preserve local plant-specific uses in the area.}, } @article {pmid32372858, year = {2020}, author = {Nguyen, VD and Nguyen, TH and Tayeen, ASM and Laughinghouse, HD and Sánchez-Reyes, LL and Wiggins, J and Pontelli, E and Mozzherin, D and O'Meara, B and Stoltzfus, A}, title = {Phylotastic: Improving Access to Tree-of-Life Knowledge With Flexible, on-the-Fly Delivery of Trees.}, journal = {Evolutionary bioinformatics online}, volume = {16}, number = {}, pages = {1176934319899384}, pmid = {32372858}, issn = {1176-9343}, abstract = {A comprehensive phylogeny of species, i.e., a tree of life, has potential uses in a variety of contexts, including research, education, and public policy. Yet, accessing the tree of life typically requires special knowledge, complex software, or long periods of training. The Phylotastic project aims make it as easy to get a phylogeny of species as it is to get driving directions from mapping software. In prior work, we presented a design for an open system to validate and manage taxon names, find phylogeny resources, extract subtrees matching a user's taxon list, scale trees to time, and integrate related resources such as species images. Here, we report the implementation of a set of tools that together represent a robust, accessible system for on-the-fly delivery of phylogenetic knowledge. This set of tools includes a web portal to execute several customizable workflows to obtain species phylogenies (scaled by geologic time and decorated with thumbnail images); more than 30 underlying web services (accessible via a common registry); and code toolkits in R and Python (allowing others to develop custom applications using Phylotastic services). The Phylotastic system, accessible via http://www.phylotastic.org, provides a unique resource to access the current state of phylogenetic knowledge, useful for a variety of cases in which a tree extracted quickly from online resources (as distinct from a tree custom-made from character data) is sufficient, as it is for many casual uses of trees identified here.}, } @article {pmid32372518, year = {2020}, author = {Han, G and Son, H}, title = {What influences adolescents to continuously use e-cigarettes?.}, journal = {Public health nursing (Boston, Mass.)}, volume = {37}, number = {4}, pages = {504-509}, doi = {10.1111/phn.12735}, pmid = {32372518}, issn = {1525-1446}, mesh = {Adolescent ; Adolescent Behavior/*psychology ; Databases, Factual ; Female ; Humans ; Male ; Republic of Korea/epidemiology ; Risk Factors ; Socioeconomic Factors ; Vaping/*epidemiology/*psychology ; }, abstract = {OBJECTIVE: The use of e-cigarettes is rapidly increasing in adolescents. Health care providers pay attention to e-cigarette users because of the risk of developing addiction and problematic behavior. Based on ecological perspective, this study investigated factors influencing continued e-cigarette use.

METHODS: We classified 1556 current e-cigarette users into experimental and continued users using the Korean national representative data. Data were analyzed using the chi-square test and logistic regression based on a complex sample analysis.

RESULTS: Among current e-cigarette users, 55.1% were continued users. Adolescents who use e-cigarettes because of the belief that they are less harmful than cigarettes, concealment, easy purchase, and adding various flavors had a high risk of continued use. Continued users were more likely to have a higher weekly allowance, lower rate of living with family, and higher chance of smoking parents and exposure to passive smoking at home.

CONCLUSIONS: Continued e-cigarette use was influenced by interpersonal and environmental factors, such as ease of purchase and addition of flavoring substances. Improving the environment of adolescents can prevent continued use of e-cigarettes.}, } @article {pmid32369604, year = {2020}, author = {Rovida, C and Barton-Maclaren, T and Benfenati, E and Caloni, F and Chandrasekera, PC and Chesné, C and Cronin, MTD and De Knecht, J and Dietrich, DR and Escher, SE and Fitzpatrick, S and Flannery, B and Herzler, M and Hougaard Bennekou, S and Hubesch, B and Kamp, H and Kisitu, J and Kleinstreuer, N and Kovarich, S and Leist, M and Maertens, A and Nugent, K and Pallocca, G and Pastor, M and Patlewicz, G and Pavan, M and Presgrave, O and Smirnova, L and Schwarz, M and Yamada, T and Hartung, T}, title = {Internationalization of read-across as a validated new approach method (NAM) for regulatory toxicology.}, journal = {ALTEX}, volume = {37}, number = {4}, pages = {579-606}, pmid = {32369604}, issn = {1868-8551}, support = {EPA999999/ImEPA/Intramural EPA/United States ; }, mesh = {Animal Testing Alternatives ; Animals ; *Computer Simulation ; Hazardous Substances/*toxicity ; Humans ; Internationality ; *Reproducibility of Results ; *Risk Assessment ; Toxicology/*legislation & jurisprudence/methods ; }, abstract = {Read-across (RAx) translates available information from well-characterized chemicals to a substance for which there is a toxicological data gap. The OECD is working on case studies to probe general applicability of RAx, and several regulations (e.g., EU-REACH) already allow this procedure to be used to waive new in vivo tests. The decision to prepare a review on the state of the art of RAx as a tool for risk assessment for regulatory purposes was taken during a workshop with international experts in Ranco, Italy in July 2018. Three major issues were identified that need optimization to allow a higher regulatory acceptance rate of the RAx procedure: (i) the definition of similarity of source and target, (ii) the translation of biological/toxicological activity of source to target in the RAx procedure, and (iii) how to deal with issues of ADME that may differ between source and target. The use of new approach methodologies (NAM) was discussed as one of the most important innovations to improve the acceptability of RAx. At present, NAM data may be used to confirm chemical and toxicological similarity. In the future, the use of NAM may be broadened to fully characterize the hazard and toxicokinetic properties of RAx compounds. Concerning available guidance, documents on Good Read-Across Practice (GRAP) and on best practices to perform and evaluate the RAx process were identified. Here, in particular, the RAx guidance, being worked out by the European Commission’s H2020 project EU-ToxRisk together with many external partners with regulatory experience, is given.}, } @article {pmid32368648, year = {2020}, author = {Ken, S and Entani, T and Tsusaka, TW and Sasaki, N}, title = {Effect of REDD+ projects on local livelihood assets in Keo Seima and Oddar Meanchey, Cambodia.}, journal = {Heliyon}, volume = {6}, number = {4}, pages = {e03802}, pmid = {32368648}, issn = {2405-8440}, abstract = {Climate-change mitigation projects are expected to improve local livelihoods in targeted areas. Several REDD+ projects aimed at reducing emissions from deforestation and forest degradation, conserving and enhancing forest carbon stocks, and sustainably managing forests have been implemented in Cambodia but few studies have examined the effects on local livelihoods before and during project implementation. Our study applies a sustainable livelihood framework to assess the livelihood assets of local communities in the Oddar Meanchey and Keo Seima REDD+ project sites in Cambodia before and during project implementation. Five capital assets, namely natural, physical, human, financial, and social capital, are assessed and scored on a 1-to-5 Likert scale. Data analysis collected through 252 interviews in Oddar Meanchey and Keo Seima reveals a slight increase in livelihood assets in both sites from project validation to implementation. Generally, the mean scores for local livelihood assets increased from 2.81 ± 0.07 (±is followed by the standard error) and 2.66 ± 0.06 to 3.07 ± 0.09 and 3.06 ± 0.08 in Oddar Meanchey and Keo Seima, respectively. Nevertheless, natural capital assets sharply declined from 3.50 and 3.32 to 2.09 and 2.25, respectively. Respondents mainly blamed illegal logging for the decline, suggesting that strict patrolling and enforcement must be implemented. Furthermore, the scarcity of carbon-credit buyers and the projects' inability to generate carbon-based revenues has led to dissatisfaction among local communities, inducing avoidable illegal activities in pursuit of short-term benefits. A financial mechanism to ensure sufficient and sustained financial support regardless of carbon-market volatility is urgently needed.}, } @article {pmid32368363, year = {2019}, author = {Boyce, HB and Mallick, P}, title = {Geostatistical visualization of ecological interactions in tumors.}, journal = {Proceedings. IEEE International Conference on Bioinformatics and Biomedicine}, volume = {2019}, number = {}, pages = {2741-2749}, pmid = {32368363}, issn = {2156-1125}, support = {T15 LM007033/LM/NLM NIH HHS/United States ; }, abstract = {Recent advances in our understanding of cancer progression have highlighted the roles played by molecular heterogeneity and by the tumor microenvironment in driving drug resistance and metastasis. The coupling of single-cell measurement technologies with algorithms, such as t-sne and SPADE, have enabled deep investigation of tumor heterogeneity. However, such techniques only capture molecular heterogeneity and do not enable the quantification nor visualization of intercellular interactions. They additionally do not allow the visualization of ecological niches that are critical to understanding tumor behavior. Novel computational tools to quantify and visualize spatial patterns in the tumor microenvironment are critically needed. Here, we take a tumor ecology perspective to examine how predation, mutualism, commensalism, and parasitism may impact tumor development and spatial patterning. We additionally quantify local spatial heterogeneity and the emergent global spatial behavior of the models using geostatistics. By visualizing emergent spatial patterns we demonstrate the potential utility of a geostatistical analysis in differentiating amongst cell-cell interactions in the tumor microenvironment. These studies introduce both an ecological framework for characterizing intercellular interactions in cancer and a novel way of quantifying and visualizing spatial patterns in cancer.}, } @article {pmid32367549, year = {2020}, author = {Yuan, C and Hedeker, D and Mermelstein, R and Xie, H}, title = {A tractable method to account for high-dimensional nonignorable missing data in intensive longitudinal data.}, journal = {Statistics in medicine}, volume = {39}, number = {20}, pages = {2589-2605}, pmid = {32367549}, issn = {1097-0258}, support = {P01 CA098262/CA/NCI NIH HHS/United States ; R01 CA178061/CA/NCI NIH HHS/United States ; }, mesh = {Data Interpretation, Statistical ; Humans ; Linear Models ; *Models, Statistical ; }, abstract = {Despite the need for sensitivity analysis to nonignorable missingness in intensive longitudinal data (ILD), such analysis is greatly hindered by novel ILD features, such as large data volume and complex nonmonotonic missing-data patterns. Likelihood of alternative models permitting nonignorable missingness often involves very high-dimensional integrals, causing curse of dimensionality and rendering solutions computationally prohibitive to obtain. We aim to overcome this challenge by developing a computationally feasible method, nonlinear indexes of local sensitivity to nonignorability (NISNI). We use linear mixed effects models for the incomplete outcome and covariates. We use Markov multinomial models to describe complex missing-data patterns and mechanisms in ILD, thereby permitting missingness probabilities to depend directly on missing data. Using a second-order Taylor series to approximate likelihood under nonignorability, we develop formulas and closed-form expressions for NISNI. Our approach permits the outcome and covariates to be missing simultaneously, as is often the case in ILD, and can capture U-shaped impact of nonignorability in the neighborhood of the missing at random model without fitting alternative models or evaluating integrals. We evaluate performance of this method using simulated data and real ILD collected by the ecological momentary assessment method.}, } @article {pmid32365577, year = {2020}, author = {Adamo, M and Chialva, M and Calevo, J and Rose, S and Girlanda, M and Perotto, S and Balestrini, R}, title = {The Dark Side of Orchid Symbiosis: Can Tulasnella calospora Decompose Host Tissues?.}, journal = {International journal of molecular sciences}, volume = {21}, number = {9}, pages = {}, pmid = {32365577}, issn = {1422-0067}, mesh = {*Basidiomycota ; Computational Biology/methods ; Gene Expression Profiling ; Gene Expression Regulation, Plant ; Germination ; Mycorrhizae ; Orchidaceae/*microbiology/*physiology ; Seeds ; *Symbiosis ; }, abstract = {Photosynthetic orchids associate with mycorrhizal fungi that can be mostly ascribed to the "rhizoctonia" species complex. Rhizoctonias' phylogenetic diversity covers a variety of ecological/nutritional strategies that include, beside the symbiosis establishment with host plants, endophytic and pathogenic associations with non-orchid plants or saprotrophic soil colonization. In addition, orchid mycorrhizal fungi (OMF) that establish a symbiotic relationship with an orchid host can later proliferate in browning and rotting orchid tissues. Environmental triggers and molecular mechanisms governing the switch leading to either a saprotrophic or a mycorrhizal behavior in OMF remain unclear. As the sequenced OMF genomes feature a wide range of genes putatively involved in the degradation of plant cell wall (PCW) components, we tested if these transitions may be correlated with a change in the expression of some PCW degrading enzymes. Regulation of several genes encoding PCW degrading enzymes was evaluated during saprotrophic growth of the OMF Tulasnella calospora on different substrates and under successful and unsuccessful mycorrhizal symbioses. Fungal gene expression in planta was investigated in two orchid species, the terrestrial Mediterranean Serapias vomeracea and the epiphytic tropical Cattleya purpurata. Although we only tested a subset of the CAZyme genes identified in the T. calospora genome, and we cannot exclude therefore a role for different CAZyme families or members inside a family, the results showed that the degradative potential of T. calospora is finely regulated during saprotrophic growth and in symbiosis, often with a different regulation in the two orchid species. These data pose novel questions about the role of fungal PCW degrading enzymes in the development of unsuccessful and successful interactions.}, } @article {pmid32365250, year = {2020}, author = {Ogle, K and Barber, JJ}, title = {Ensuring identifiability in hierarchical mixed effects Bayesian models.}, journal = {Ecological applications : a publication of the Ecological Society of America}, volume = {30}, number = {7}, pages = {e02159}, doi = {10.1002/eap.2159}, pmid = {32365250}, issn = {1051-0761}, mesh = {Bayes Theorem ; Markov Chains ; *Models, Statistical ; Monte Carlo Method ; *Software ; }, abstract = {Ecologists are increasingly familiar with Bayesian statistical modeling and its associated Markov chain Monte Carlo (MCMC) methodology to infer about or to discover interesting effects in data. The complexity of ecological data often suggests implementation of (statistical) models with a commensurately rich structure of effects, including crossed or nested (i.e., hierarchical or multi-level) structures of fixed and/or random effects. Yet, our experience suggests that most ecologists are not familiar with subtle but important problems that often arise with such models and with their implementation in popular software. Of foremost consideration for us is the notion of effect identifiability, which generally concerns how well data, models, or implementation approaches inform about, i.e., identify, quantities of interest. In this paper, we focus on implementation pitfalls that potentially misinform subsequent inference, despite otherwise informative data and models. We illustrate the aforementioned issues using random effects regressions on synthetic data. We show how to diagnose identifiability issues and how to remediate these issues with model reparameterization and computational and/or coding practices in popular software, with a focus on JAGS, OpenBUGS, and Stan. We also show how these solutions can be extended to more complex models involving multiple groups of nested, crossed, additive, or multiplicative effects, for models involving random and/or fixed effects. Finally, we provide example code (JAGS/OpenBUGS and Stan) that practitioners can modify and use for their own applications.}, } @article {pmid32365179, year = {2020}, author = {Minh, BQ and Hahn, MW and Lanfear, R}, title = {New Methods to Calculate Concordance Factors for Phylogenomic Datasets.}, journal = {Molecular biology and evolution}, volume = {37}, number = {9}, pages = {2727-2733}, pmid = {32365179}, issn = {1537-1719}, mesh = {*Datasets as Topic ; *Genetic Techniques ; *Phylogeny ; *Software ; }, abstract = {We implement two measures for quantifying genealogical concordance in phylogenomic data sets: the gene concordance factor (gCF) and the novel site concordance factor (sCF). For every branch of a reference tree, gCF is defined as the percentage of "decisive" gene trees containing that branch. This measure is already in wide usage, but here we introduce a package that calculates it while accounting for variable taxon coverage among gene trees. sCF is a new measure defined as the percentage of decisive sites supporting a branch in the reference tree. gCF and sCF complement classical measures of branch support in phylogenetics by providing a full description of underlying disagreement among loci and sites. An easy to use implementation and tutorial is freely available in the IQ-TREE software package (http://www.iqtree.org/doc/Concordance-Factor, last accessed May 13, 2020).}, } @article {pmid32360354, year = {2021}, author = {Van Dyke, N and Yenugadhati, N and Birkett, NJ and Lindsay, J and Turner, MC and Willhite, CC and Krewski, D}, title = {Association between aluminum in drinking water and incident Alzheimer's disease in the Canadian Study of Health and Aging cohort.}, journal = {Neurotoxicology}, volume = {83}, number = {}, pages = {157-165}, doi = {10.1016/j.neuro.2020.04.002}, pmid = {32360354}, issn = {1872-9711}, mesh = {Age Factors ; Aged ; Aluminum Compounds/*adverse effects ; Alzheimer Disease/diagnosis/*epidemiology/genetics ; Apolipoprotein E4/genetics ; Apolipoproteins E/genetics ; Canada/epidemiology ; Drinking Water/*adverse effects ; Female ; Genetic Predisposition to Disease ; Humans ; Incidence ; Longitudinal Studies ; Male ; Prospective Studies ; Risk Assessment ; Risk Factors ; Water Pollutants, Chemical/*adverse effects ; }, abstract = {Epidemiological evidence linking aluminum in drinking water and Alzheimer's disease (AD) has been inconsistent, with previous studies often limited by small sample sizes. The present study addresses this issue using data from the Canadian Study of Health and Aging (CSHA), a prospective cohort of 10,263 subjects followed-up from 1991-1992 through 2001-2002. Participants' residential histories were linked to municipal drinking water sources in 35 Canadian municipalities to obtain ecologic pH, aluminum, fluoride, iron and silica concentrations in drinking water. Cox proportional hazards models were used to examine associations between aluminum and incident AD [Hazard Ratios (HRs), 95% confidence intervals (CIs)], adjusting for age, gender, history of stroke, education, and high blood pressure. A total of 240 incident AD cases were identified during follow-up of 3, 638 subjects derived from the CSHA cohort with complete data on all covariates. With categorical aluminum measurements, there was an increasing, but not statistically significant, exposure-response relationship (HR = 1.34, 95% CI 0.88-2.04, in the highest aluminum exposure category; p = 0.13 for linear trend). Similar results were observed using continuous aluminum measurements (HR=1.21, 95% CI 0.97-1.52, at the interquartile range of 333.8 μg/L; p = 0.09 for linear trend). In a subsample genotyped for ApoE-ε4, there was some evidence of an association between aluminum and AD (p = 0.03 for linear trend). Although a clear association between aluminum in drinking water and AD was not found, the linear trend observed in ApoE-ε4 subsample warrants further examination.}, } @article {pmid32358490, year = {2020}, author = {Hale, KRS and Valdovinos, FS and Martinez, ND}, title = {Mutualism increases diversity, stability, and function of multiplex networks that integrate pollinators into food webs.}, journal = {Nature communications}, volume = {11}, number = {1}, pages = {2182}, pmid = {32358490}, issn = {2041-1723}, mesh = {Animals ; Biodiversity ; Biomass ; Computer Simulation ; Ecological and Environmental Phenomena ; *Food Chain ; Models, Biological ; Plants ; *Pollination ; *Symbiosis ; }, abstract = {Ecosystems are composed of complex networks of many species interacting in different ways. While ecologists have long studied food webs of feeding interactions, recent studies increasingly focus on mutualistic networks including plants that exchange food for reproductive services provided by animals such as pollinators. Here, we synthesize both types of consumer-resource interactions to better understand the controversial effects of mutualism on ecosystems at the species, guild, and whole-community levels. We find that consumer-resource mechanisms underlying plant-pollinator mutualisms can increase persistence, productivity, abundance, and temporal stability of both mutualists and non-mutualists in food webs. These effects strongly increase with floral reward productivity and are qualitatively robust to variation in the prevalence of mutualism and pollinators feeding upon resources in addition to rewards. This work advances the ability of mechanistic network theory to synthesize different types of interactions and illustrates how mutualism can enhance the diversity, stability, and function of complex ecosystems.}, } @article {pmid32357185, year = {2020}, author = {Dertien, JS and Self, S and Ross, BE and Barrett, K and Baldwin, RF}, title = {The relationship between biodiversity and wetland cover varies across regions of the conterminous United States.}, journal = {PloS one}, volume = {15}, number = {5}, pages = {e0232052}, pmid = {32357185}, issn = {1932-6203}, mesh = {Animals ; Bayes Theorem ; *Biodiversity ; Conservation of Natural Resources ; Databases, Factual ; Mammals/physiology ; United States ; *Wetlands ; }, abstract = {Identifying the factors that determine the spatial distribution of biodiversity is a major focus of ecological research. These factors vary with scale from interspecific interactions to global climatic cycles. Wetlands are important biodiversity hotspots and contributors of ecosystem services, but the association between proportional wetland cover and species richness has shown mixed results. It is not well known as to what extent there is a relationship between proportional wetland cover and species richness, especially at the sub-continental scale. We used the National Wetlands Inventory (NWI) to model wetland cover for the conterminous United States and the National Land Cover Database to estimate wetland change between 2001 and 2011. We used a Bayesian spatial Poisson model to estimate a spatially varying coefficient surface describing the effect of proportional wetland cover on the distribution of amphibians, birds, mammals, and reptiles and the cumulative distribution of terrestrial endemic species. Species richness and wetland cover were significantly correlated, and this relationship varied both spatially and by taxonomic group. Rather than a continental-scale association, however, we found that this relationship changed more closely among ecoregions. The species richness of each of the five groups was positively associated with wetland cover in some or all of the Great Plains; additionally, a positive association was found for mammals in the Southeastern Plains and Piedmont of the eastern U.S. Model results indicated negative association especially in the Cold Deserts and Northern Lakes & Forests of Minnesota and Wisconsin, though these varied greatly between groups. Our results highlight the need for wetland conservation initiatives that focus efforts at the level II and III ecoregional scale rather than along political boundaries.}, } @article {pmid32356884, year = {2020}, author = {Hernandez, AM and Jia, P and Kim, HY and Cuadros, DF}, title = {Geographic Variation and Associated Covariates of Diabetes Prevalence in India.}, journal = {JAMA network open}, volume = {3}, number = {5}, pages = {e203865}, pmid = {32356884}, issn = {2574-3805}, mesh = {Adolescent ; Adult ; Cross-Sectional Studies ; Diabetes Mellitus, Type 2/*epidemiology/etiology ; Female ; Humans ; India/epidemiology ; Male ; Middle Aged ; Prevalence ; Socioeconomic Factors ; Spatial Analysis ; Surveys and Questionnaires ; *Tuberculosis, Pulmonary ; Young Adult ; }, abstract = {IMPORTANCE: Diabetes is a severe metabolic disorder affecting human health worldwide, with increasing prevalence in low- and middle-income countries. Gaps in knowledge regarding factors that lead to diabetes and its association with tuberculosis (TB) endemicity at the national scale still exist, mainly because of the lack of large-scale dual testing and appropriate evaluation methods.

OBJECTIVES: To identify locations in India where diabetes prevalence is concentrated, examine the association of diabetes with sociodemographic and behavioral covariates, and uncover where high regional TB endemicity overlaps with diabetes.

This cross-sectional study included 803 164 men aged 15 to 54 years and women aged 15 to 49 years who participated in the Demographic Health Survey (2015-2016), carried out by the India Ministry of Health and Family Welfare using a 2-stage clustered sampling, which included a diabetes estimation component. The survey was conducted from January 2015 to December 2016, and data analysis was conducted from July 2018 to January 2019.

EXPOSURES: Self-reported diabetes status.

MAIN OUTCOMES AND MEASURES: Self-reported diabetes status was used to estimate the association of covariates, including educational level, sex, age, religion, marital status, alcohol use, tobacco use, obesity status, and household socioeconomic level, with diabetes prevalence. Additionally, regional tuberculosis endemicity level, estimated using the India TB report for 2014 from the Revised National TB Program, was included to evaluate the national extent of the spatial overlap of diabetes and TB.

RESULTS: Among 803 164 sampled individuals (691 982 [86.2%] women; mean [SD] age, 30.09 [9.97] years), substantial geographic variation in diabetes prevalence in India was found, with a concentrated burden at the southern coastline (cluster 1, Andhra Pradesh and Telangana: prevalence, 3.01% [1864 of 61 948 individuals]; cluster 2, Tamil Nadup and Kerala: prevalence, 4.32% [3429 of 79 435 individuals]; cluster 3, east Orissa: prevalence, 2.81% [330 of 11 758 individuals]; cluster 4, Goa: prevalence, 4.43% [83 of 1883 individuals]). Having obesity and overweight (odds ratio [OR], 2.44; 95% CI, 2.18-2.73; P < .001; OR, 1.66; 95% CI, 1.52-1.82; P < .001, respectively), smoking tobacco (OR, 3.04; 95% CI, 1.66-5.56; P < .001), and consuming alcohol (OR, 2.01; 95% CI, 1.37-2.95; P < .001) were associated with increased odds of diabetes. Regional TB endemicity and diabetes spatial distributions showed that there is a lack of consistent geographical overlap between these 2 diseases (eg, TB cluster 4: 60 213 TB cases; 186.79 diabetes cases in 20 183.88 individuals; 0.93% diabetes prevalence; TB cluster 8: 47 381 TB cases; 180.53 diabetes cases in 22 449.18 individuals; 0.80% diabetes prevalence; TB cluster 9: 37 620 TB cases, 601.45 diabetes cases in 12 879.36 individuals; 4.67% diabetes prevalence).

CONCLUSIONS AND RELEVANCE: In this study, identifying spatial clusters of diabetes on the basis of a nationally representative survey suggests that India may face different levels of disease severity, and each region might need to implement control strategies that are more appropriate for its unique epidemiologic context.}, } @article {pmid32356756, year = {2020}, author = {Wang, M and Wang, H and Zheng, H and Dewhurst, R and Roehe, R}, title = {A Knowledge-Driven Network-Based Analytical Framework for the Identification of Rumen Metabolites.}, journal = {IEEE transactions on nanobioscience}, volume = {19}, number = {3}, pages = {518-526}, doi = {10.1109/TNB.2020.2991577}, pmid = {32356756}, issn = {1558-2639}, mesh = {Animals ; *Databases, Genetic ; Fatty Acids, Volatile/metabolism ; Gastrointestinal Microbiome/physiology ; Magnetic Resonance Spectroscopy ; Metabolome/*physiology ; Metabolomics ; Rumen/*metabolism ; }, abstract = {Metabolites are the final production of biochemical reactions in the rumen micro-ecological system and are very sensitive to changes in rumen microbes. Nuclear magnetic resonance (NMR) spectroscopy could both identify and quantify the metabolic composition of the ruminal fluid, which reflects the interaction between rumen microbes and diet. The main challenge of untargeted metabolomics is the compound annotation. Based on non-linear and linear associations between microbial gene abundances and integrals derived from NMR spectra, combined with knowledge of enzymatic reaction from the KEGG database, this study developed a knowledge-driven network-based analytical framework for the inference of metabolites. There were 89 potential metabolites inferred from the integral co-occurrence network. The results are supported by dissimilarity network analysis. The coexistence of non-linear and linear associations between microbial gene abundances and spectral integrals was detected. The study successfully found the corresponding integrals for acetate, butyrate and propionate, which are the major volatile fatty acids (VFA) in the rumen. This novel framework could very efficiently infer metabolites to corresponding integrals from NMR spectra.}, } @article {pmid32355024, year = {2020}, author = {Barton, CM and Alberti, M and Ames, D and Atkinson, JA and Bales, J and Burke, E and Chen, M and Diallo, SY and Earn, DJD and Fath, B and Feng, Z and Gibbons, C and Hammond, R and Heffernan, J and Houser, H and Hovmand, PS and Kopainsky, B and Mabry, PL and Mair, C and Meier, P and Niles, R and Nosek, B and Osgood, N and Pierce, S and Polhill, JG and Prosser, L and Robinson, E and Rosenzweig, C and Sankaran, S and Stange, K and Tucker, G}, title = {Call for transparency of COVID-19 models.}, journal = {Science (New York, N.Y.)}, volume = {368}, number = {6490}, pages = {482-483}, doi = {10.1126/science.abb8637}, pmid = {32355024}, issn = {1095-9203}, support = {MC_UU_00022/5/MRC_/Medical Research Council/United Kingdom ; MR/S037578/1/MRC_/Medical Research Council/United Kingdom ; MR/S037578/2/MRC_/Medical Research Council/United Kingdom ; SPHSU20/CSO_/Chief Scientist Office/United Kingdom ; }, mesh = {Betacoronavirus ; COVID-19 ; *Computer Simulation ; Coronavirus Infections/*epidemiology ; Humans ; *Information Dissemination ; Pandemics ; Pneumonia, Viral/*epidemiology ; SARS-CoV-2 ; *Scholarly Communication ; Software ; }, } @article {pmid32349500, year = {2020}, author = {Salehi, A and Molavi Vardanjani, H}, title = {Secular Trends of Global Burden of Violence, 1990-2015: In Spite of Successes, Women and Children Are Highly Affected in Low- and the Middle-Income Countries.}, journal = {Archives of Iranian medicine}, volume = {23}, number = {4Suppl1}, pages = {S1-S5}, doi = {10.34172/aim.2020.s1}, pmid = {32349500}, issn = {1735-3947}, mesh = {Adolescent ; Adult ; Age Distribution ; Aged ; Aged, 80 and over ; Child ; Child, Preschool ; Databases, Factual ; Developing Countries ; Female ; Global Burden of Disease/*statistics & numerical data/*trends ; Humans ; Infant ; Infant, Newborn ; Interrupted Time Series Analysis ; Male ; Middle Aged ; Quality-Adjusted Life Years ; Sex Distribution ; Socioeconomic Factors ; Violence/classification/*statistics & numerical data/*trends ; Young Adult ; }, abstract = {BACKGROUND: Violence is a challenging modern epidemic worldwide. Less evidence is available on the populations most affected by violence in recent decades. The aim of the study was to ecologically investigate temporal trends of the global burden of violence according to gender, age group, and socio-demographic development.

METHODS: Data on the age- and gender-specific rates of country-level disability adjusted life years (DALYs) attributable to different types of violence i.e. interpersonal violence (IV), and collective violence (CV) and legal interventions were retrieved from online database provided by the global burden of diseases project. Countries were categorized according to their socio-demographic index (SDI). Incidence rate ratio (IRR) per one year was estimated according to age groups, genders and SDI categories applying Poisson regression modeling.

RESULTS: The highest decrease of the DALYs attributable to IV was observed for the under-five-years age group and then for 5-14-years in both genders, globally. Considering the CV, estimated IRRs were significant only for the under-five-years age group, which was at 1.30 (95% CI: 1.20, 1.40, per 10 years) for girls and 1.29 (95% CI: 1.21, 1.39, per 10 years) for boys.

CONCLUSION: The rate of DALYs due to IV has been more decreasing among women and children during the recent decades. By the next 10 years, the attributed DALYs to CV would increase up to 120%. Children, adolescents and women are highly affected by CV in countries with middle-low and middle social development in the recent decades.}, } @article {pmid32349427, year = {2020}, author = {Gu, J and Zeng, Z and Wang, Y and Lyu, Y}, title = {Transcriptome Analysis of Carbohydrate Metabolism Genes and Molecular Regulation of Sucrose Transport Gene LoSUT on the Flowering Process of Developing Oriental Hybrid Lily 'Sorbonne' Bulb.}, journal = {International journal of molecular sciences}, volume = {21}, number = {9}, pages = {}, pmid = {32349427}, issn = {1422-0067}, support = {(grant number 31672190,//the China National Natural Science Foundation (grant number 31672190,/ ; }, mesh = {Amino Acid Sequence ; Carbohydrate Metabolism/*genetics ; Computational Biology/methods ; Flowers/*genetics/metabolism ; *Gene Expression Profiling/methods ; *Gene Expression Regulation, Plant ; Gene Regulatory Networks ; High-Throughput Nucleotide Sequencing ; Lilium/*genetics/metabolism ; Membrane Transport Proteins/chemistry/*genetics/metabolism ; Metabolic Networks and Pathways ; Models, Molecular ; Molecular Sequence Annotation ; Phenotype ; Plant Development/genetics ; Plant Proteins/chemistry/*genetics/metabolism ; Protein Conformation ; Structure-Activity Relationship ; *Transcriptome ; }, abstract = {The quality of Lily cut flower was determined by the quality of bulbs. During the process of vernalization and flower bud differentiation, sugar massively accumulated in the bulb, which influenced the bulb development. However, the details of sugar genes' regulation mechanism for these processes were not fully understood. Here, morphological physiology, transcriptomes and gene engineering technology were used to explore this physiological change. Seventy-two genes of 25 kinds of sugar metabolism-related genes were annotated after re-analyzing transcriptome data of Oriental hybrid lily 'Sorbonne' bulbs, which were generated on Hiseq Illumina 2000. The results showed that these genes were closely related to lily bulb vernalization and development. Combining gene expression pattern with gene co-expression network, five genes (Contig5669, Contig13319, Contig7715, Contig1420 and Contig87292) were considered to be the most potential signals, and the sucrose transporter gene (SUT) was the focus of this study. Carbohydrate transport pathway and genes' regulation mechanism were inferred through a physiological and molecular test. SUT seemed to be the sugar sensor that could sense and regulate sugar concentration, which might have effects on other genes, such as FT, LFY and so on. LoSUT2 and LoSUT4 genes were cloned from Oriental hybrid lily 'Sorbonne' by RACE, which was the first time for these genes in Oriental hybrid lily 'Sorbonne'. The physiological properties of these proteins were analyzed such as hydrophobicity and phosphorylation. In addition, secondary and tertiary structures of proteins were predicted, which indicated the two proteins were membrane proteins. Their cellular locations were verified through positioning the experiment of the fluorescent vector. They were highly expressed in cells around phloem, which illustrated the key role of these genes in sugar transport. Furthermore, transient expression assays showed that overexpressed LoSUT2 and LoSUT4 in Arabidopsis thaliana bloomed significantly earlier than the wild type and the expression of FT, SOC1 and LFY were also affected by LoSUT2 and LoSUT4, which indicated that LoSUT2 and LoSUT4 may regulate plants flowering time.}, } @article {pmid32348787, year = {2020}, author = {Connelly, MT and McRae, CJ and Liu, PJ and Traylor-Knowles, N}, title = {Lipopolysaccharide treatment stimulates Pocillopora coral genotype-specific immune responses but does not alter coral-associated bacteria communities.}, journal = {Developmental and comparative immunology}, volume = {109}, number = {}, pages = {103717}, doi = {10.1016/j.dci.2020.103717}, pmid = {32348787}, issn = {1879-0089}, mesh = {Animals ; Anthozoa/genetics/*immunology/microbiology ; Bacteria/classification/genetics ; *Coral Reefs ; Ecosystem ; Gene Expression Regulation/drug effects ; Gene Ontology ; Genotype ; Host Microbial Interactions/genetics ; Immunity/*drug effects/genetics ; Lipopolysaccharides/*pharmacology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Corals are comprised of a coral host and associated microbes whose interactions are mediated by the coral innate immune system. The diversity of immune factors identified in the Pocillopora damicornis genome suggests that immunity is linked to maintaining microbial symbioses while also being able to detect pathogens. However, it is unclear which immune factors respond to specific microbe-associated molecular patterns and how these immune reactions simultaneously affect coral-associated bacteria. To investigate this, fragments of P. damicornis and P. acuta colonies from Taiwan were subjected to lipopolysaccharide (LPS) treatment to stimulate immune responses and measure bacteria community shifts. RNA-seq revealed genotype-specific immune responses to LPS involving the upregulation of immune receptors, transcription factors, and pore-forming toxins. Bacteria 16S sequencing revealed significantly different bacteria communities between coral genotypes but no differences in bacteria communities were caused by LPS. Our findings confirm that Pocillopora corals activate conserved immune factors in response to LPS and identify transcription factors coordinating Pocillopora corals' immune responses. Additionally, the strong effect of coral genotype on gene expression and bacteria communities highlights the importance of coral genotype in the investigation of coral host-microbe interactions.}, } @article {pmid32348631, year = {2020}, author = {Luo, Y and El-Madany, T and Ma, X and Nair, R and Jung, M and Weber, U and Filippa, G and Bucher, SF and Moreno, G and Cremonese, E and Carrara, A and Gonzalez-Cascon, R and Cáceres Escudero, Y and Galvagno, M and Pacheco-Labrador, J and Martín, MP and Perez-Priego, O and Reichstein, M and Richardson, AD and Menzel, A and Römermann, C and Migliavacca, M}, title = {Nutrients and water availability constrain the seasonality of vegetation activity in a Mediterranean ecosystem.}, journal = {Global change biology}, volume = {26}, number = {8}, pages = {4379-4400}, doi = {10.1111/gcb.15138}, pmid = {32348631}, issn = {1365-2486}, support = {IB16185//Regional Government of Extremadura/International ; //Alexander von Humboldt Foundation/International ; }, mesh = {*Ecosystem ; Nutrients ; Plants ; Seasons ; *Water ; }, abstract = {Anthropogenic nitrogen (N) deposition and resulting differences in ecosystem N and phosphorus (P) ratios are expected to impact photosynthetic capacity, that is, maximum gross primary productivity (GPPmax). However, the interplay between N and P availability with other critical resources on seasonal dynamics of ecosystem productivity remains largely unknown. In a Mediterranean tree-grass ecosystem, we established three landscape-level (24 ha) nutrient addition treatments: N addition (NT), N and P addition (NPT), and a control site (CT). We analyzed the response of ecosystem to altered nutrient stoichiometry using eddy covariance fluxes measurements, satellite observations, and digital repeat photography. A set of metrics, including phenological transition dates (PTDs; timing of green-up and dry-down), slopes during green-up and dry-down period, and seasonal amplitude, were extracted from time series of GPPmax and used to represent the seasonality of vegetation activity. The seasonal amplitude of GPPmax was higher for NT and NPT than CT, which was attributed to changes in structure and physiology induced by fertilization. PTDs were mainly driven by rainfall and exhibited no significant differences among treatments during the green-up period. Yet, both fertilized sites senesced earlier during the dry-down period (17-19 days), which was more pronounced in the NT due to larger evapotranspiration and water usage. Fertilization also resulted in a faster increase in GPPmax during the green-up period and a sharper decline in GPPmax during the dry-down period, with less prominent decline response in NPT. Overall, we demonstrated seasonality of vegetation activity was altered after fertilization and the importance of nutrient-water interaction in such water-limited ecosystems. With the projected warming-drying trend, the positive effects of N fertilization induced by N deposition on GPPmax may be counteracted by an earlier and faster dry-down in particular in areas where the N:P ratio increases, with potential impact on the carbon cycle of water-limited ecosystems.}, } @article {pmid32348334, year = {2020}, author = {Chitsaz, N and Marian, R and Chahl, J}, title = {Experimental method for 3D reconstruction of Odonata wings (methodology and dataset).}, journal = {PloS one}, volume = {15}, number = {4}, pages = {e0232193}, pmid = {32348334}, issn = {1932-6203}, mesh = {Animals ; Databases, Factual ; Flight, Animal/physiology ; Image Processing, Computer-Assisted ; Imaging, Three-Dimensional/instrumentation/methods ; Microscopy, Electron, Scanning ; Models, Anatomic ; Museums ; Odonata/*anatomy & histology/classification/physiology ; Photogrammetry/instrumentation ; South Australia ; Wings, Animal/*anatomy & histology/physiology/ultrastructure ; X-Ray Microtomography ; }, abstract = {Insect wings are highly evolved structures with aerodynamic and structural properties that are not fully understood or systematically modeled. Most species in the insect order Odonata have permanently deployed high aspect ratio wings. Odonata have been documented to exhibit extraordinary flight performance and a wide range of interesting flight behaviors that rely on agility and efficiency. The characteristic three-dimensional corrugated structures of these wings have been observed and modeled for a small number of species, with studies showing that corrugations can provide significant aerodynamic and structural advantages. Comprehensive museum collections are the most practical source of Odonata wing, despite the risk of adverse effects caused by dehydration and preservation of specimens. Museum specimens are not to be handled or damaged and are best left undisturbed in their display enclosures. We have undertaken a systematic process of scanning, modeling, and post-processing the wings of over 80 Odonata species using a novel and accurate method and apparatus we developed for this purpose. The method allows the samples to stay inside their glass cases if necessary and is non-destructive. The measurements taken have been validated against micro-computed tomography scanning and against similar-sized objects with measured dimensions. The resulting publicly available dataset will allow aeronautical analysis of Odonata aerodynamics and structures, the study of the evolution of functional structures, and research into insect ecology. The technique is useable for other orders of insects and other fragile samples.}, } @article {pmid32348330, year = {2020}, author = {Piralam, B and Prosperi, C and Thamthitiwat, S and Bunthi, C and Sawatwong, P and Sangwichian, O and Higdon, MM and Watson, NL and Deloria Knoll, M and Paveenkittiporn, W and Chara, C and Hurst, CP and Akarasewi, P and Rhodes, J and Maloney, SA and O'Brien, KL and Baggett, HC}, title = {Pneumococcal colonization prevalence and density among Thai children with severe pneumonia and community controls.}, journal = {PloS one}, volume = {15}, number = {4}, pages = {e0232151}, pmid = {32348330}, issn = {1932-6203}, mesh = {Anti-Bacterial Agents/therapeutic use ; Bacterial Load ; Case-Control Studies ; Child, Preschool ; Humans ; Infant ; Male ; Nasopharynx/microbiology ; Pneumococcal Vaccines/immunology ; Pneumonia, Pneumococcal/*epidemiology/*microbiology/prevention & control ; Polymerase Chain Reaction ; Prevalence ; Serogroup ; Streptococcus pneumoniae/classification/genetics/isolation & purification ; Thailand/epidemiology ; }, abstract = {BACKGROUND: Pneumococcal colonization prevalence and colonization density, which has been associated with invasive disease, can offer insight into local pneumococcal ecology and help inform vaccine policy discussions.

METHODS: The Pneumonia Etiology Research for Child Health Project (PERCH), a multi-country case-control study, evaluated the etiology of hospitalized cases of severe and very severe pneumonia among children aged 1-59 months. The PERCH Thailand site enrolled children during January 2012-February 2014. We determined pneumococcal colonization prevalence and density, and serotype distribution of colonizing isolates.

RESULTS: We enrolled 224 severe/very severe pneumonia cases and 659 community controls in Thailand. Compared to controls, cases had lower colonization prevalence (54.5% vs. 62.5%, p = 0.12) and lower median colonization density (42.1 vs. 210.2 x 103 copies/mL, p <0.0001); 42% of cases had documented antibiotic pretreatment vs. 0.8% of controls. In no sub-group of assessed cases did pneumococcal colonization density exceed the median for controls, including cases with no prior antibiotics (63.9x103 copies/mL), with consolidation on chest x-ray (76.5x103 copies/mL) or with pneumococcus detected in whole blood by PCR (9.3x103 copies/mL). Serotype distribution was similar among cases and controls, and a high percentage of colonizing isolates from cases and controls were serotypes included in PCV10 (70.0% and 61.8%, respectively) and PCV13 (76.7% and 67.9%, respectively).

CONCLUSIONS: Pneumococcal colonization is common among children aged <5 years in Thailand. However, colonization density was not higher among children with severe pneumonia compared to controls. These results can inform discussions about PCV introduction and provide baseline data to monitor PCV impact after introduction in Thailand.}, } @article {pmid32342413, year = {2020}, author = {Mi, Q and Li, X and Zhang, J}, title = {Identification of risks of herdsmen's grassland transfer behavior in Xinjiang and Inner Mongolia and a possible risk prevention mechanism.}, journal = {Environmental science and pollution research international}, volume = {27}, number = {20}, pages = {25029-25041}, doi = {10.1007/s11356-020-08925-8}, pmid = {32342413}, issn = {1614-7499}, support = {2018D01B16//Natural Science Foundation of Xinjiang Province/ ; }, mesh = {China ; *Grassland ; Humans ; *Income ; Male ; }, abstract = {Effective identification of the risks of grassland circulation is an important prerequisite for improving the management of the grassland rental market. In this study, the potential risks in the game among the subjects of grassland transfer are analyzed through the lens of repeated game theory. With the help of interpretive structural modeling, we analyze the relationships and hierarchy among the risk factors in grassland circulation. We find that social, economic, and ecological risks are the main potential risks of grassland circulation, and there are strong correlations among risk factors. A risk hierarchy analysis shows that social risk is at the upper level, economic risk is at the middle level, ecological risk is at the bottom level, and there are cross-layer effects among the various risk levels. Contract risk, social security risk, and wealth gap risk are the core risk factors that trigger the risks associated with grassland transfer. Therefore, the first priority of the pasture manager (i.e., the government) should be to regulate the grassland circulation market and strengthen supervision and punishment of defaulting subjects. Second, a social security system in which the herdsmen and the government are both invested should be established. Third, the government should strengthen the construction of a "rule of law" system instead of "rule of man," to avoid the loss of government credibility caused by rent-seeking.}, } @article {pmid32336044, year = {2021}, author = {Rücker, G and Schwarzer, G}, title = {Beyond the forest plot: The drapery plot.}, journal = {Research synthesis methods}, volume = {12}, number = {1}, pages = {13-19}, doi = {10.1002/jrsm.1410}, pmid = {32336044}, issn = {1759-2887}, support = {RU 1747/1-2//Deutsche Forschungsgemeinschaft/ ; }, mesh = {Animals ; Biomass ; Carbon Dioxide ; Confidence Intervals ; Data Interpretation, Statistical ; Ecology/statistics & numerical data ; Humans ; Lung Neoplasms/mortality ; *Meta-Analysis as Topic ; Plant Development ; Reproducibility of Results ; Smoking/adverse effects ; }, abstract = {In the era of the "reproducibility crisis" and the "P-value controversy" new ways of presentation and interpretation of the results of a meta-analysis are desirable. One suggestion that has been made for single studies almost six decades ago and taken up now and then is the P-value function. For a given outcome, this function assigns a P-value to each possible hypothetical value, given the data. Moreover, the P-value function simultaneously provides two-sided confidence intervals for all possible alpha levels. An application to meta-analysis, while suggested early, has not been widely established. We introduce the drapery plot that presents the P-value function for all individual studies and pooled estimates in a meta-analysis as curves and the prediction range for a single future study. We also present a scaled variant with the test statistic on the y-axis. Both plots visualize the full information of a pairwise meta-analysis. We see a drapery plot as a complementary figure to a forest plot. It may be even an alternative in meta-analyses with many studies where forest plots tend to become very large and complex.}, } @article {pmid32335714, year = {2020}, author = {Tajima, T and Nagata, J and Akiyama, Y and Torigoe, T and Fujimoto, K and Sato, N and Fujino, Y and Shibao, K and Matsuda, S and Hirata, K}, title = {Open colectomy vs. laparoscopic colectomy in Japan: a retrospective study using real-world data from the diagnosis procedure combination database.}, journal = {Surgery today}, volume = {50}, number = {10}, pages = {1255-1261}, doi = {10.1007/s00595-020-02006-6}, pmid = {32335714}, issn = {1436-2813}, mesh = {Aged ; Aged, 80 and over ; Colectomy/economics/*methods/mortality ; Colorectal Neoplasms/economics/mortality/*surgery ; Costs and Cost Analysis ; Databases, Factual ; Endoscopy, Gastrointestinal/economics/*methods/mortality ; Female ; Hospital Mortality ; Humans ; Japan ; Laparoscopy/economics/*methods/mortality ; Length of Stay/statistics & numerical data ; Logistic Models ; Male ; Middle Aged ; Morbidity ; Retrospective Studies ; Safety ; Treatment Outcome ; }, abstract = {PURPOSE: To compare the short-term outcomes of conventional open colectomy with those of laparoscopic colectomy for colon cancer.

METHODS: We retrieved data between January 2014 and March 2016 from the Diagnosis Procedure Combination database. A total of 69,418 patients who underwent colectomy for colon cancer were analyzed from among 15,901,766 cases of colorectal cancer. We applied a multilevel logistic regression model using a 2-level structure of individuals nested from 1065 hospitals.

RESULTS: A total of 22,440 open colectomy and 46,978 laparoscopic colectomy procedures were performed. The in-hospital mortality rate was significantly lower in the laparoscopic group than in the open group (0.28% vs. 0.06%, odds ratio [OR] 0.40, p < 0.001). Similarly, the 30-day postoperative mortality rate (0.14% vs. 0.03%, OR 0.47, p = 0.019) and surgical morbidity rate (43.0% vs. 25.3%, OR 0.47, p < 0.001) were significantly lower in the laparoscopic group than in the open group. The postoperative length of stay was significantly longer in the open group (mean difference - 5.6 days, p < 0.001) than in the open group. The admission cost was significantly greater in the open group than in the laparoscopic group (mean difference - 95,080 yen, p < 0.001).

CONCLUSIONS: Laparoscopic colectomy is safe and effective in the short term.}, } @article {pmid32333771, year = {2020}, author = {Machac, A}, title = {The Dynamics of Bird Diversity in the New World.}, journal = {Systematic biology}, volume = {69}, number = {6}, pages = {1180-1199}, pmid = {32333771}, issn = {1076-836X}, mesh = {Americas ; Animals ; *Biodiversity ; Birds/*classification ; Geographic Information Systems ; *Models, Biological ; }, abstract = {Three prominent explanations have been proposed to explain the dramatic differences in species richness across regions and elevations, (i) time for speciation, (ii) diversification rates, and (iii) ecological limits. But the relative importance of these explanations and, especially, their interplay and possible synthesis remain largely elusive. Integrating diversification analyses, null models, and geographic information systems, I study avian richness across regions and elevations of the New World. My results reveal that even though the three explanations are differentially important (with ecological limits playing the dominant role), each contributes uniquely to the formation of richness gradients. Further, my results reveal the likely interplay between the explanations. They indicate that ecological limits hinder the diversification process, such that the accumulation of species within a region gradually slows down over time. Yet, it does not seem to converge toward a hard ceiling on regional richness. Instead, species-rich regions show suppressed, but continued, diversification, coupled with signatures of possible competition (esp. Neotropical lowlands). Conversely, species-poor, newly-colonized regions show fast diversification and weak to no signs of competition (esp. Nearctic highlands). These results held across five families of birds, across grid cells, biomes, and elevations. Together, my findings begin to illuminate the rich, yet highly consistent, interplay of the mechanisms that together shape richness gradients in the New World, including the most species-rich biodiversity hotspots on the planet, the Andes and the Amazon. [Biogeography; community; competition; macroevolution; phylogenetics; richness gradient.].}, } @article {pmid32331419, year = {2020}, author = {Holbech, H and Matthiessen, P and Hansen, M and Schüürmann, G and Knapen, D and Reuver, M and Flamant, F and Sachs, L and Kloas, W and Hilscherova, K and Leonard, M and Arning, J and Strauss, V and Iguchi, T and Baumann, L}, title = {ERGO: Breaking Down the Wall between Human Health and Environmental Testing of Endocrine Disrupters.}, journal = {International journal of molecular sciences}, volume = {21}, number = {8}, pages = {}, pmid = {32331419}, issn = {1422-0067}, support = {825753//Horizon 2020 Framework Programme/ ; }, mesh = {Animals ; *Biological Assay/methods ; Biomarkers ; Data Warehousing ; Endocrine Disruptors/*adverse effects/*analysis ; Endocrine System/drug effects/metabolism ; *Environmental Monitoring/methods ; Health Impact Assessment ; Health Plan Implementation ; Humans ; Risk Assessment ; Species Specificity ; Workflow ; }, abstract = {ERGO (EndocRine Guideline Optimization) is the acronym of a European Union-funded research and innovation action, that aims to break down the wall between mammalian and non-mammalian vertebrate regulatory testing of endocrine disruptors (EDs), by identifying, developing and aligning thyroid-related biomarkers and endpoints (B/E) for the linkage of effects between vertebrate classes. To achieve this, an adverse outcome pathway (AOP) network covering various modes of thyroid hormone disruption (THD) in multiple vertebrate classes will be developed. The AOP development will be based on existing and new data from in vitro and in vivo experiments with fish, amphibians and mammals, using a battery of different THDs. This will provide the scientifically plausible and evidence-based foundation for the selection of B/E and assays in lower vertebrates, predictive of human health outcomes. These assays will be prioritized for validation at OECD (Organization for Economic Cooperation and Development) level. ERGO will re-think ED testing strategies from in silico methods to in vivo testing and develop, optimize and validate existing in vivo and early life-stage OECD guidelines, as well as new in vitro protocols for THD. This strategy will reduce requirements for animal testing by preventing duplication of testing in mammals and non-mammalian vertebrates and increase the screening capacity to enable more chemicals to be tested for ED properties.}, } @article {pmid32327744, year = {2020}, author = {Strassburg, BBN and Beyer, HL and Crouzeilles, R and Iribarrem, A and Barros, F and de Siqueira, MF and Sánchez-Tapia, A and Balmford, A and Sansevero, JBB and Brancalion, PHS and Broadbent, EN and Chazdon, RL and Filho, AO and Gardner, TA and Gordon, A and Latawiec, A and Loyola, R and Metzger, JP and Mills, M and Possingham, HP and Rodrigues, RR and Scaramuzza, CAM and Scarano, FR and Tambosi, L and Uriarte, M}, title = {Author Correction: Strategic approaches to restoring ecosystems can triple conservation gains and halve costs.}, journal = {Nature ecology & evolution}, volume = {4}, number = {5}, pages = {765}, doi = {10.1038/s41559-020-1211-9}, pmid = {32327744}, issn = {2397-334X}, abstract = {An amendment to this paper has been published and can be accessed via a link at the top of the paper.}, } @article {pmid32327596, year = {2020}, author = {van Klink, R and Bowler, DE and Gongalsky, KB and Swengel, AB and Gentile, A and Chase, JM}, title = {Meta-analysis reveals declines in terrestrial but increases in freshwater insect abundances.}, journal = {Science (New York, N.Y.)}, volume = {368}, number = {6489}, pages = {417-420}, doi = {10.1126/science.aax9931}, pmid = {32327596}, issn = {1095-9203}, mesh = {Animals ; Datasets as Topic ; Europe ; *Extinction, Biological ; *Fresh Water ; *Insecta ; North America ; Population ; }, abstract = {Recent case studies showing substantial declines of insect abundances have raised alarm, but how widespread such patterns are remains unclear. We compiled data from 166 long-term surveys of insect assemblages across 1676 sites to investigate trends in insect abundances over time. Overall, we found considerable variation in trends even among adjacent sites but an average decline of terrestrial insect abundance by ~9% per decade and an increase of freshwater insect abundance by ~11% per decade. Both patterns were largely driven by strong trends in North America and some European regions. We found some associations with potential drivers (e.g., land-use drivers), and trends in protected areas tended to be weaker. Our findings provide a more nuanced view of spatiotemporal patterns of insect abundance trends than previously suggested.}, } @article {pmid32324730, year = {2020}, author = {Song, C and Saavedra, S}, title = {Telling ecological networks apart by their structure: An environment-dependent approach.}, journal = {PLoS computational biology}, volume = {16}, number = {4}, pages = {e1007787}, pmid = {32324730}, issn = {1553-7358}, mesh = {*Biota ; Computational Biology/*methods ; *Environment ; *Models, Biological ; Symbiosis/physiology ; Temperature ; }, abstract = {The network architecture of an ecological community describes the structure of species interactions established in a given place and time. It has been suggested that this architecture presents unique features for each type of ecological interaction: e.g., nested and modular architectures would correspond to mutualistic and antagonistic interactions, respectively. Recently, Michalska-Smith and Allesina (2019) proposed a computational challenge to test whether it is indeed possible to differentiate ecological interactions based on network architecture. Contrary to the expectation, they found that this differentiation is practically impossible, moving the question to why it is not possible to differentiate ecological interactions based on their network architecture alone. Here, we show that this differentiation becomes possible by adding the local environmental information where the networks were sampled. We show that this can be explained by the fact that environmental conditions are a confounder of ecological interactions and network architecture. That is, the lack of association between network architecture and type of ecological interactions changes by conditioning on the local environmental conditions. Additionally, we find that environmental conditions are linked to the stability of ecological networks, but the direction of this effect depends on the type of interaction network. This suggests that the association between ecological interactions and network architectures exists, but cannot be fully understood without attention to the environmental conditions acting upon them.}, } @article {pmid32321048, year = {2020}, author = {Silva, GDMD and Duarte, EC and Cruz, OG and Garcia, LP}, title = {Identification of micro-regions with under-reported tuberculosis cases in Brazil, 2012-2014.}, journal = {Epidemiologia e servicos de saude : revista do Sistema Unico de Saude do Brasil}, volume = {29}, number = {1}, pages = {e2018485}, doi = {10.5123/S1679-49742020000100025}, pmid = {32321048}, issn = {2237-9622}, mesh = {Brazil/epidemiology ; Cross-Sectional Studies ; Disease Notification/standards/*statistics & numerical data ; Health Information Systems/standards/*statistics & numerical data ; Humans ; Population Surveillance ; Quality Indicators, Health Care ; Sputum/microbiology ; Tuberculosis/diagnosis/*epidemiology ; }, abstract = {OBJECTIVE: to identify Brazilian micro-regions with under-reported tuberculosis cases, from 2012 to 2014.

METHODS: this was an ecological study using data from the Notifiable Health Conditions Information System (SINAN). The indirect estimator of the proportion of notified cases (EIPCN) was calculated as the mean between the proportion of cases that adhered to treatment and the proportion of those who underwent sputum smear microscopy. Negative Binomial Regression was used to investigate evidence of under-reporting in the micro-regions selected through EIPCN.

RESULTS: under-reporting was suspected in 89 (17.5%) micro-regions with EIPCN below 83%. The EIPCN rate ratio in the regression model was 0.996 (95%CI 0.988;1.003) considering all the data and equal to 0.987 (95%CI 0.974;0.999) excluding the 89 micro-regions with suspected under-reporting.

CONCLUSION: evidence of tuberculosis case under-reporting was found in micro-regions where basic indicators of surveillance system quality had poor performance.}, } @article {pmid32320389, year = {2020}, author = {Wu, SL and Sánchez C, HM and Henry, JM and Citron, DT and Zhang, Q and Compton, K and Liang, B and Verma, A and Cummings, DAT and Le Menach, A and Scott, TW and Wilson, AL and Lindsay, SW and Moyes, CL and Hancock, PA and Russell, TL and Burkot, TR and Marshall, JM and Kiware, S and Reiner, RC and Smith, DL}, title = {Vector bionomics and vectorial capacity as emergent properties of mosquito behaviors and ecology.}, journal = {PLoS computational biology}, volume = {16}, number = {4}, pages = {e1007446}, pmid = {32320389}, issn = {1553-7358}, support = {U01 CK000510/CK/NCEZID CDC HHS/United States ; U19 AI089674/AI/NIAID NIH HHS/United States ; }, mesh = {Algorithms ; Animals ; *Behavior, Animal ; Computational Biology ; Computer Simulation ; Culicidae/*physiology ; Disease Vectors ; Ecology ; Ecosystem ; Feeding Behavior ; Female ; Humans ; Malaria/*transmission ; Male ; Models, Theoretical ; Monte Carlo Method ; *Mosquito Vectors ; Oviposition ; Probability ; }, abstract = {Mosquitoes are important vectors for pathogens that infect humans and other vertebrate animals. Some aspects of adult mosquito behavior and mosquito ecology play an important role in determining the capacity of vector populations to transmit pathogens. Here, we re-examine factors affecting the transmission of pathogens by mosquitoes using a new approach. Unlike most previous models, this framework considers the behavioral states and state transitions of adult mosquitoes through a sequence of activity bouts. We developed a new framework for individual-based simulation models called MBITES (Mosquito Bout-based and Individual-based Transmission Ecology Simulator). In MBITES, it is possible to build models that simulate the behavior and ecology of adult mosquitoes in exquisite detail on complex resource landscapes generated by spatial point processes. We also developed an ordinary differential equation model which is the Kolmogorov forward equations for models developed in MBITES under a specific set of simplifying assumptions. While mosquito infection and pathogen development are one possible part of a mosquito's state, that is not our main focus. Using extensive simulation using some models developed in MBITES, we show that vectorial capacity can be understood as an emergent property of simple behavioral algorithms interacting with complex resource landscapes, and that relative density or sparsity of resources and the need to search can have profound consequences for mosquito populations' capacity to transmit pathogens.}, } @article {pmid32319925, year = {2020}, author = {Lekang, K and Lanzén, A and Jonassen, I and Thompson, E and Troedsson, C}, title = {Evaluation of a eukaryote phylogenetic microarray for environmental monitoring of marine sediments.}, journal = {Marine pollution bulletin}, volume = {154}, number = {}, pages = {111102}, doi = {10.1016/j.marpolbul.2020.111102}, pmid = {32319925}, issn = {1879-3363}, mesh = {Biodiversity ; *Ecosystem ; Environmental Monitoring ; *Eukaryota ; Geologic Sediments ; Phylogeny ; }, abstract = {Increased exploitation of resources in sensitive marine ecosystems emphasizes the importance of knowledge regarding ecological impacts. However, current bio-monitoring practices are limited in terms of target-organisms and temporal resolution. Hence, developing new technologies is vital for enhanced ecosystem understanding. In this study, we have applied a prototype version of a phylogenetic microarray to assess the eukaryote community structures of marine sediments from an area with ongoing oil and gas drilling activity. The results were compared with data from both sequencing (metabarcoding) and morphology-based monitoring to evaluate whether microarrays were capable of detecting ecosystem disturbances. A significant correlation between microarray data and chemical pollution indicators, as well as sequencing-based results, was demonstrated, and several potential indicator organisms for pollution-associated parameters were identified, among them a large fraction of microorganisms not covered by traditional morphology-based monitoring. This suggests that microarrays have a potential in future environmental monitoring.}, } @article {pmid32317640, year = {2020}, author = {Laurentino, TG and Moser, D and Roesti, M and Ammann, M and Frey, A and Ronco, F and Kueng, B and Berner, D}, title = {Genomic release-recapture experiment in the wild reveals within-generation polygenic selection in stickleback fish.}, journal = {Nature communications}, volume = {11}, number = {1}, pages = {1928}, pmid = {32317640}, issn = {2041-1723}, mesh = {Adaptation, Physiological/genetics ; Alleles ; Animals ; Computational Biology ; Ecosystem ; Evolution, Molecular ; Female ; Genetics, Population ; *Genome ; Lakes ; Male ; Phenotype ; Polymorphism, Single Nucleotide ; Rivers ; Selection, Genetic ; Smegmamorpha/*genetics/*physiology ; }, abstract = {How rapidly natural selection sorts genome-wide standing genetic variation during adaptation remains largely unstudied experimentally. Here, we present a genomic release-recapture experiment using paired threespine stickleback fish populations adapted to selectively different lake and stream habitats. First, we use pooled whole-genome sequence data from the original populations to identify hundreds of candidate genome regions likely under divergent selection between these habitats. Next, we generate F2 hybrids from the same lake-stream population pair in the laboratory and release thousands of juveniles into a natural stream habitat. Comparing the individuals surviving one year of stream selection to a reference sample of F2 hybrids allows us to detect frequency shifts across the candidate regions toward the genetic variants typical of the stream population-an experimental outcome consistent with polygenic directional selection. Our study reveals that adaptation in nature can be detected as a genome-wide signal over just a single generation.}, } @article {pmid32312246, year = {2020}, author = {Mazamay, S and Bompangue, D and Guégan, JF and Muyembe, JJ and Raoul, F and Broutin, H}, title = {Understanding the spatio-temporal dynamics of meningitis epidemics outside the belt: the case of the Democratic Republic of Congo (DRC).}, journal = {BMC infectious diseases}, volume = {20}, number = {1}, pages = {291}, pmid = {32312246}, issn = {1471-2334}, mesh = {Democratic Republic of the Congo/epidemiology ; *Epidemics ; Epidemiological Monitoring ; Geographic Information Systems ; Haemophilus influenzae/genetics/immunology/isolation & purification ; Humans ; Incidence ; Meningitis, Bacterial/*epidemiology/microbiology ; Neisseria meningitidis/genetics/immunology/isolation & purification ; Seasons ; Streptococcus pneumoniae/genetics/immunology/isolation & purification ; }, abstract = {BACKGROUND: Bacterial meningitis remains a major threat for the population of the meningitis belt. Between 2004 and 2009, in the countries of this belt, more than 200,000 people were infected with a 10% mortality rate. However, for almost 20 years, important meningitis epidemics are also reported outside this belt. Research is still very poorly developed in this part of the word like in the Democratic Republic of Congo (DRC), which experiences recurrent epidemics. This article describes for the first time the spatio-temporal patterns of meningitis cases and epidemics in DRC, in order to provide new insights for surveillance and control measures.

METHODS: Based on weekly suspected cases of meningitis (2000-2012), we used time-series analyses to explore the spatio-temporal dynamics of the disease. We also used both geographic information systems and geostatistics to identify spatial clusters of cases. Both using conventional statistics and the Cleveland's algorithm for decomposition into general trend, seasonal and residuals, we searched for the existence of seasonality.

RESULTS: We observed a low rate of biological confirmation of cases (11%) using soluble antigens search, culture and PCR. The main strains found are Streptococcus pneumoniae, Haemophilus influenzae and Neisseria meningitidis (A and C) serogroups. We identified 8 distinct spatial clusters, located in the northeastern and southeastern part of DRC, and in the capital city province, Kinshasa. A low seasonal trend was observed with higher incidence and attack rate of meningitis during the dry season, with a high heterogeneity in seasonal patterns occurring across the different districts and regions of DRC.

CONCLUSION: Despite challenges related to completeness of data reporting, meningitis dynamics shows weak seasonality in DRC. This tends to suggest that climatic, environmental factors might be less preponderant in shaping seasonal patterns in central Africa. The characterization of 8 distinct clusters of meningitis could be used for a better sentinel meningitis surveillance and optimization of vaccine strategy in DRC. Improving biological monitoring of suspected cases should be a priority for future eco-epidemiological studies to better understand the emergence and spread of meningitis pathogens, and the potential ecological, environmental drivers of this disease.}, } @article {pmid32311614, year = {2020}, author = {Xie, J and Yan, X and Xu, G and Tian, X and Dong, N and Feng, J and Liu, P and Li, M and Zhao, Y and Wei, C and Lyu, Y and Ma, G and Song, G and Wang, T and Yan, X}, title = {ITRAQ-based proteomics reveals the potential mechanism of fluoride-induced myocardial contraction function damage.}, journal = {Ecotoxicology and environmental safety}, volume = {197}, number = {}, pages = {110605}, doi = {10.1016/j.ecoenv.2020.110605}, pmid = {32311614}, issn = {1090-2414}, mesh = {Animals ; Biomarkers/metabolism ; Cardiomyopathies/*chemically induced/metabolism/pathology ; Fluorides/*toxicity ; Gene Ontology ; Male ; Mice ; Myocardial Contraction/*drug effects ; Protein Interaction Mapping ; Proteins/metabolism ; Proteomics/methods ; Rats ; }, abstract = {Fluorosis is a worldwide public health problem, and its adverse effects on the heart have been confirmed by many studies. Abnormal myocardial contractions are often associated with impairment of cardiac function as a cause or consequence. We designed two-part experiments to search for biomarkers and clarify the underlying molecular mechanism of fluoride on myocardial contraction. First, we used Pressure-volume Loop analysis to evaluate changes in myocardial function indexes with multiple fluoride exposure levels in mice (0, 30, 70, and 150 mg/L) exposed for 4 weeks. The results showed that fluoride exposure affects the heart pump function and reduces cardiac contractility. Then, we established a rat model of fluoride exposure (0, 30, 60, and 90 mg/L) for 6 months to carry out proteomic analysis of fluoride-induced myocardial contractile injury. Hematoxylin-eosin (H&E) staining was used to determine the severity of myocardial injury, and myocardial tissue samples were submitted for isobaric tags for relative and absolute quantitation (ITRAQ) analysis. A total of 1607 proteins were successfully identified with 294 differentially expressed proteins (DEPs) in fluoride treated groups. According to Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis, 12 DEPs were confirmed to be involved in pathways related to myocardial contraction. Furthermore, we constructed a protein-protein interaction (PPI) network for these 12 core DEPs to illustrate the role and location of each DEP in the myocardial contraction pathway. The results of this study are helpful for identify a potential mechanism and biomarkers of fluoride-induced myocardial contraction function damage, moreover, which can provide a new insight into the heart toxicity of fluoride in animals at the proteomics level.}, } @article {pmid32302776, year = {2020}, author = {Raynor, B and De la Puente-León, M and Johnson, A and Díaz, EW and Levy, MZ and Recuenco, SE and Castillo-Neyra, R}, title = {Movement patterns of free-roaming dogs on heterogeneous urban landscapes: Implications for rabies control.}, journal = {Preventive veterinary medicine}, volume = {178}, number = {}, pages = {104978}, pmid = {32302776}, issn = {1873-1716}, support = {K01 AI139284/AI/NIAID NIH HHS/United States ; T32 AI070077/AI/NIAID NIH HHS/United States ; }, mesh = {*Animal Distribution ; Animals ; Cities ; Dog Diseases/*prevention & control ; Dogs/*physiology ; *Environment ; Geographic Information Systems ; *Movement ; Peru ; Rabies/prevention & control/*veterinary ; }, abstract = {In 2015, a case of canine rabies in Arequipa, Peru indicated the re-emergence of rabies virus in the city. Despite mass dog vaccination campaigns across the city and reactive ring vaccination and other control activities around positive cases (e.g. elimination of unowned dogs), the outbreak has spread. Here we explore how the urban landscape of Arequipa affects the movement patterns of free-roaming dogs, the main reservoirs of the rabies virus in the area. We tracked 23 free-roaming dogs using Global Positioning System (GPS) collars. We analyzed the spatio-temporal GPS data using the time- local convex hull method. Dog movement patterns varied across local environments. We found that water channels, an urban feature of Arequipa that are dry most of the year, promote movement. Dogs that used the water channels extensively move on average 7 times further (p = 0.002) and 1.2 times more directionally (p = 0.027) than dogs that do not use the water channels at all. They were also 1.3 times faster on average, but this difference was not statistically significant (p = 0.197). Our findings suggest that water channels can be used by dogs as 'highways' to transverse the city and have the potential to spread disease far beyond the radius of control practices. Control efforts should focus on a robust vaccination campaign attuned to the geography of the city, and not limited to small-scale rings surrounding cases.}, } @article {pmid32301987, year = {2020}, author = {Xue, Y and Jonassen, I and Øvreås, L and Taş, N}, title = {Metagenome-assembled genome distribution and key functionality highlight importance of aerobic metabolism in Svalbard permafrost.}, journal = {FEMS microbiology ecology}, volume = {96}, number = {5}, pages = {}, pmid = {32301987}, issn = {1574-6941}, mesh = {Metagenome ; Norway ; *Permafrost ; Soil ; Soil Microbiology ; Svalbard ; }, abstract = {Permafrost underlies a large portion of the land in the Northern Hemisphere. It is proposed to be an extreme habitat and home for cold-adaptive microbial communities. Upon thaw permafrost is predicted to exacerbate increasing global temperature trend, where awakening microbes decompose millennia old carbon stocks. Yet our knowledge on composition, functional potential and variance of permafrost microbiome remains limited. In this study, we conducted a deep comparative metagenomic analysis through a 2 m permafrost core from Svalbard, Norway to determine key permafrost microbiome in this climate sensitive island ecosystem. To do so, we developed comparative metagenomics methods on metagenomic-assembled genomes (MAG). We found that community composition in Svalbard soil horizons shifted markedly with depth: the dominant phylum switched from Acidobacteria and Proteobacteria in top soils (active layer) to Actinobacteria, Bacteroidetes, Chloroflexi and Proteobacteria in permafrost layers. Key metabolic potential propagated through permafrost depths revealed aerobic respiration and soil organic matter decomposition as key metabolic traits. We also found that Svalbard MAGs were enriched in genes involved in regulation of ammonium, sulfur and phosphate. Here, we provide a new perspective on how permafrost microbiome is shaped to acquire resources in competitive and limited resource conditions of deep Svalbard soils.}, } @article {pmid32299848, year = {2020}, author = {Simkin, J and Erickson, AC and Otterstatter, MC and Dummer, TJB and Ogilvie, G}, title = {Current State of Geospatial Methodologic Approaches in Canadian Population Oncology Research.}, journal = {Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology}, volume = {29}, number = {7}, pages = {1294-1303}, doi = {10.1158/1055-9965.EPI-20-0092}, pmid = {32299848}, issn = {1538-7755}, support = {//CIHR/Canada ; }, mesh = {Canada ; Geographic Information Systems/*standards ; Humans ; Medical Oncology/*standards ; Research Design/*standards ; }, abstract = {Geospatial analyses are increasingly used in population oncology. We provide a first review of geospatial analysis in Canadian population oncology research, compare to international peers, and identify future directions. Geospatial-focused peer-reviewed publications from 1992-2020 were compiled using PubMed, MEDLINE, Web of Science, and Google Scholar. Abstracts were screened for data derived from a Canadian cancer registry and use of geographic information systems. Studies were classified by geospatial methodology, geospatial unit, location, cancer site, and study year. Common limitations were documented from article discussion sections. Our search identified 71 publications using data from all provincial and national cancer registries. Thirty-nine percent (N = 28) were published in the most recent 5-year period (2016-2020). Geospatial methodologies included exposure assessment (32.4%), identifying spatial associations (21.1%), proximity analysis (16.9%), cluster detection (15.5%), and descriptive mapping (14.1%). Common limitations included confounding, ecologic fallacy, not accounting for residential mobility, and small case/population sizes. Geospatial analyses are increasingly used in Canadian population oncology; however, efforts are concentrated among a few provinces and common cancer sites, and data are over a decade old. Limitations were similar to those documented internationally, and more work is needed to address them. Organized efforts are needed to identify common challenges, develop leading practices, and identify shared priorities.}, } @article {pmid32298457, year = {2020}, author = {Miralles, A and Bruy, T and Wolcott, K and Scherz, MD and Begerow, D and Beszteri, B and Bonkowski, M and Felden, J and Gemeinholzer, B and Glaw, F and Glöckner, FO and Hawlitschek, O and Kostadinov, I and Nattkemper, TW and Printzen, C and Renz, J and Rybalka, N and Stadler, M and Weibulat, T and Wilke, T and Renner, SS and Vences, M}, title = {Repositories for Taxonomic Data: Where We Are and What is Missing.}, journal = {Systematic biology}, volume = {69}, number = {6}, pages = {1231-1253}, pmid = {32298457}, issn = {1076-836X}, mesh = {Animals ; *Classification ; Databases, Factual/*standards/trends ; }, abstract = {Natural history collections are leading successful large-scale projects of specimen digitization (images, metadata, DNA barcodes), thereby transforming taxonomy into a big data science. Yet, little effort has been directed towards safeguarding and subsequently mobilizing the considerable amount of original data generated during the process of naming 15,000-20,000 species every year. From the perspective of alpha-taxonomists, we provide a review of the properties and diversity of taxonomic data, assess their volume and use, and establish criteria for optimizing data repositories. We surveyed 4113 alpha-taxonomic studies in representative journals for 2002, 2010, and 2018, and found an increasing yet comparatively limited use of molecular data in species diagnosis and description. In 2018, of the 2661 papers published in specialized taxonomic journals, molecular data were widely used in mycology (94%), regularly in vertebrates (53%), but rarely in botany (15%) and entomology (10%). Images play an important role in taxonomic research on all taxa, with photographs used in >80% and drawings in 58% of the surveyed papers. The use of omics (high-throughput) approaches or 3D documentation is still rare. Improved archiving strategies for metabarcoding consensus reads, genome and transcriptome assemblies, and chemical and metabolomic data could help to mobilize the wealth of high-throughput data for alpha-taxonomy. Because long-term-ideally perpetual-data storage is of particular importance for taxonomy, energy footprint reduction via less storage-demanding formats is a priority if their information content suffices for the purpose of taxonomic studies. Whereas taxonomic assignments are quasifacts for most biological disciplines, they remain hypotheses pertaining to evolutionary relatedness of individuals for alpha-taxonomy. For this reason, an improved reuse of taxonomic data, including machine-learning-based species identification and delimitation pipelines, requires a cyberspecimen approach-linking data via unique specimen identifiers, and thereby making them findable, accessible, interoperable, and reusable for taxonomic research. This poses both qualitative challenges to adapt the existing infrastructure of data centers to a specimen-centered concept and quantitative challenges to host and connect an estimated $ \le $2 million images produced per year by alpha-taxonomic studies, plus many millions of images from digitization campaigns. Of the 30,000-40,000 taxonomists globally, many are thought to be nonprofessionals, and capturing the data for online storage and reuse therefore requires low-complexity submission workflows and cost-free repository use. Expert taxonomists are the main stakeholders able to identify and formalize the needs of the discipline; their expertise is needed to implement the envisioned virtual collections of cyberspecimens. [Big data; cyberspecimen; new species; omics; repositories; specimen identifier; taxonomy; taxonomic data.].}, } @article {pmid32297772, year = {2020}, author = {Habibović, M and Gavidia, G and Broers, E and Wetzels, M and Ayoola, I and Ribas, V and Piera-Jimenez, J and Widdershoven, J and Denollet, J}, title = {Type D personality and global positioning system tracked social behavior in patients with cardiovascular disease.}, journal = {Health psychology : official journal of the Division of Health Psychology, American Psychological Association}, volume = {39}, number = {8}, pages = {711-720}, doi = {10.1037/hea0000823}, pmid = {32297772}, issn = {1930-7810}, support = {//European Commission/ ; }, mesh = {Cardiovascular Diseases/*etiology/psychology ; Depression/*psychology ; Female ; Geographic Information Systems/*standards ; Humans ; Male ; Middle Aged ; Risk Factors ; *Social Behavior ; Surveys and Questionnaires ; *Type D Personality ; }, abstract = {OBJECTIVE: Social behavior (e.g., loneliness, isolation) has been indicated as an important risk factor for cardiovascular disease. Recent studies show that Type D personality might be an important predictor of social behavior. Hence, the current exploratory study aims to examine, using ecological assessment, whether Type D personality is associated with a lower likelihood to engage in social encounters in patients with cardiovascular disease.

METHOD: Cardiac patients who participated in the Do CHANGE (Phase 2) trial were included in current analysis. As part of the Do CHANGE intervention, real-life data were collected in the intervention group using the MOVES app, which was installed on patients' mobile phones. For a period of 6 months, Global Positioning System (GPS) data from the participating patients were collected. From the GPS data, 3 target variables were computed: (a) general activity level, (b) social variety, and (c) social opportunity.

RESULTS: A total of 70 patients were included in the analysis. Patients with a Type D personality had lower scores on the "social opportunity" variable compared to non-Type D patients (F = 6.72; p = .01). Type D personality was associated with lower social participation after adjusting for depression and anxiety. No association between Type D personality and general activity or behavioral variety was observed.

CONCLUSIONS: This is the first study to use an ecological measure to assess social behavior of cardiac patients with a Type D personality. Results show that Type D personality might be associated with lower social engagement, which could, in turn, partly explain its association with adverse health outcomes. (PsycInfo Database Record (c) 2020 APA, all rights reserved).}, } @article {pmid32296602, year = {2020}, author = {Chen, W and Ding, J and Wang, J and Zhang, J and Zhang, Z}, title = {Temporal and spatial variability in snow cover over the Xinjiang Uygur Autonomous Region, China, from 2001 to 2015.}, journal = {PeerJ}, volume = {8}, number = {}, pages = {e8861}, pmid = {32296602}, issn = {2167-8359}, abstract = {Xinjiang, China, is a typical arid and semi-arid region of Central Asia that significantly lacks freshwater resources, and the surface runoff in this region is mainly supplied by mountain glacier and snow cover meltwater. Based on the above background and issues of transnational water resources between Xinjiang and Central Asia along the Silk Road Economic Belt, which were highlighted in the major strategy of "The Belt and Road", this study analysed the spatial and temporal variations in snow cover and snow cover days in the Xinjiang region from 2001 to 2015. The study area includes four subregions: Northern Xinjiang, Southern Xinjiang, Eastern Xinjiang and the Ili River Valley. Moderate-resolution Imaging Spectroradiometer (MODIS) 8-day snow cover data were used after removing clouds by combining MOD10A2 and MYD10A2. The results showed that seasonal snow cover occurred from October to April in most regions of Xinjiang and that this snow cover consisted of two processes: snow accumulation and snow ablation. The maximum snow cover occurred in January, whereas the minimum snow cover occurred from July to August. During the seasonal snow cover period, the snowfall rates in Northern Xinjiang and the Ili River Valley were higher, while the other regions had a low snowfall probability. To study the relationship between altitude and snow cover, the normalized snow elevation correlation index (NSACI) was calculated. The NSACI showed a significant correlation between snow cover and elevation in most regions of Xinjiang and was classified into five grades. Snow cover days did not fluctuate obviously from 2001 to 2015, and a decreasing trend was observed in the four subregions except for the Ili River Valley (nonsignificant decreasing trend). We also observed a correlation between snow cover and temperature and found that the correlations between monthly snow cover and monthly temperature in the four subregions were strongly related to the underlying land type and global warming background, which also suggests that the special topography of Xinjiang greatly influences both snow cover and climate change.}, } @article {pmid32296208, year = {2020}, author = {Khan, IA and Arsalan, MH and Mehdi, MR and Kazmi, JH and Seong, JC and Han, D}, title = {Assessment of asthma-prone environment in Karachi, Pakistan using GIS modeling.}, journal = {JPMA. The Journal of the Pakistan Medical Association}, volume = {70}, number = {4}, pages = {636-649}, doi = {10.5455/JPMA.11828}, pmid = {32296208}, issn = {0030-9982}, mesh = {*Asthma/diagnosis/epidemiology/prevention & control ; Cross-Sectional Studies ; Ecological and Environmental Phenomena ; *Environmental Monitoring/methods/statistics & numerical data ; Geographic Information Systems/*statistics & numerical data ; Geographic Mapping ; Humans ; Pakistan/epidemiology ; Public Health ; *Risk Assessment/methods/standards/statistics & numerical data ; Spatial Analysis ; }, abstract = {OBJECTIVE: To determine the association among number of factors influenced by asthma using geographic information system.

METHODS: The cross-sectional study was conducted in Landhi and Korangi towns of Karachi from 2011 to 2013, and comprised ecological mapping and multi-criteria evaluation techniques to discover the relationship of local environmental settings with asthma. Additionally, exacerbating environment and the root causes within the local settings were assessed. Data was gathered using an extended version of the questionnaire developed by the International Union against Tuberculosis and Lung Disease. Data was analysed by using ArcGIS 10.

RESULTS: The findings are very alarming as almost 40% (468,930 estimated pop 1998 census) of the study population lived in high asthma-prone environment, having a very high risk of respiratory disorders, including asthma.

CONCLUSIONS: The integrated environmental effect in the form of respiratory disorders was appraised, focusing on asthma by using multi-criteria analysis.}, } @article {pmid32295655, year = {2020}, author = {Taylor, NG and Stymest, J and Mah, CL}, title = {Validation of a province-wide commercial food store dataset in a heterogeneous predominantly rural food environment.}, journal = {Public health nutrition}, volume = {23}, number = {11}, pages = {1889-1895}, pmid = {32295655}, issn = {1475-2727}, support = {FRN PG1-144782//CIHR/Canada ; }, mesh = {Commerce/*statistics & numerical data ; Databases, Factual ; Datasets as Topic/*standards ; Food Supply/*statistics & numerical data ; Government ; Humans ; Newfoundland and Labrador ; Predictive Value of Tests ; Reproducibility of Results ; Rural Population/*statistics & numerical data ; Sensitivity and Specificity ; *Social Environment ; Urban Population/statistics & numerical data ; }, abstract = {OBJECTIVE: Commercially available business (CAB) datasets for food environments have been investigated for error in large urban contexts and some rural areas, but there is a relative dearth of literature that reports error across regions of variable rurality. The objective of the current study was to assess the validity of a CAB dataset using a government dataset at the provincial scale.

DESIGN: A ground-truthed dataset provided by the government of Newfoundland and Labrador (NL) was used to assess a popular commercial dataset. Concordance, sensitivity, positive-predictive value (PPV) and geocoding errors were calculated. Measures were stratified by store types and rurality to investigate any association between these variables and database accuracy.

SETTING: NL, Canada.

PARTICIPANTS: The current analysis used store-level (ecological) data.

RESULTS: Of 1125 stores, there were 380 stores that existed in both datasets and were considered true-positive stores. The mean positional error between a ground-truthed and test point was 17·72 km. When compared with the provincial dataset of businesses, grocery stores had the greatest agreement, sensitivity = 0·64, PPV = 0·60 and concordance = 0·45. Gas stations had the least agreement, sensitivity = 0·26, PPV = 0·32 and concordance = 0·17. Only 4 % of commercial data points in rural areas matched every criterion examined.

CONCLUSIONS: The commercial dataset exhibits a low level of agreement with the ground-truthed provincial data. Particularly retailers in rural areas or belonging to the gas station category suffered from misclassification and/or geocoding errors. Taken together, the commercial dataset is differentially representative of the ground-truthed reality based on store-type and rurality/urbanity.}, } @article {pmid32295109, year = {2020}, author = {Parry, R and Naccache, F and Ndiaye, EH and Fall, G and Castelli, I and Lühken, R and Medlock, J and Cull, B and Hesson, JC and Montarsi, F and Failloux, AB and Kohl, A and Schnettler, E and Diallo, M and Asgari, S and Dietrich, I and Becker, SC}, title = {Identification and RNAi Profile of a Novel Iflavirus Infecting Senegalese Aedes vexans arabiensis Mosquitoes.}, journal = {Viruses}, volume = {12}, number = {4}, pages = {}, pmid = {32295109}, issn = {1999-4915}, support = {BBS/E/I/00007033/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/I/00007035/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/I/00007033/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; MC_UU_12014/8/MRC_/Medical Research Council/United Kingdom ; MC_UU_12014/8//UK Medical Research Council/International ; }, mesh = {Aedes/*virology ; Animals ; Computational Biology/methods ; Genome, Viral ; Molecular Sequence Annotation ; Mosquito Vectors/virology ; Picornaviridae/*genetics ; *RNA Interference ; RNA, Small Interfering/*genetics ; *RNA, Viral ; Sequence Analysis, RNA ; }, abstract = {The inland floodwater mosquito Aedes vexans (Meigen, 1830) is a competent vector of numerous arthropod-borne viruses such as Rift Valley fever virus (Phenuiviridae) and Zika virus (Flaviviridae). Aedes vexans spp. have widespread Afrotropical distribution and are common European cosmopolitan mosquitoes. We examined the virome of Ae. vexans arabiensis samples from Barkédji village, Senegal, with small RNA sequencing, bioinformatic analysis, and RT-PCR screening. We identified a novel 9494 nt iflavirus (Picornaviridae) designated here as Aedes vexans iflavirus (AvIFV). Annotation of the AvIFV genome reveals a 2782 amino acid polyprotein with iflavirus protein domain architecture and typical iflavirus 5' internal ribosomal entry site and 3' poly-A tail. Aedes vexans iflavirus is most closely related to a partial virus sequence from Venturia canescens (a parasitoid wasp) with 56.77% pairwise amino acid identity. Analysis of AvIFV-derived small RNAs suggests that AvIFV is targeted by the exogenous RNA interference pathway but not the PIWI-interacting RNA response, as ~60% of AvIFV reads corresponded to 21 nt Dicer-2 virus-derived small RNAs and the 24-29 nt AvIFV read population did not exhibit a "ping-pong" signature. The RT-PCR screens of archival and current (circa 2011-2020) Ae. vexans arabiensis laboratory samples and wild-caught mosquitoes from Barkédji suggest that AvIFV is ubiquitous in these mosquitoes. Further, we screened wild-caught European Ae. vexans samples from Germany, the United Kingdom, Italy, and Sweden, all of which tested negative for AvIFV RNA. This report provides insight into the diversity of commensal Aedes viruses and the host RNAi response towards iflaviruses.}, } @article {pmid32293429, year = {2020}, author = {Luo, Z and Ma, Y and Ke, N and Xu, S and Hu, R and Hu, N and Kuang, L}, title = {The association between the supply and utilization of community-based primary care and child health in a context of hospital-oriented healthcare system in urban districts of Guangdong, China: a panel dataset, 2014-2016.}, journal = {BMC health services research}, volume = {20}, number = {1}, pages = {313}, pmid = {32293429}, issn = {1472-6963}, support = {71673311//National Natural Science Foundation of China/ ; }, mesh = {Child Health/*statistics & numerical data ; Child Mortality/trends ; Child, Preschool ; China/epidemiology ; Community Health Services/*statistics & numerical data/*supply & distribution ; Datasets as Topic ; Delivery of Health Care/organization & administration ; Hospitals ; Humans ; Infant ; Infant Mortality/trends ; Patient Acceptance of Health Care/*statistics & numerical data ; Primary Health Care/*statistics & numerical data ; Transients and Migrants/statistics & numerical data ; Urban Population/statistics & numerical data ; }, abstract = {BACKGROUND: Since 2009, the Chinese government has been reforming the healthcare system and has committed to reinforcing increased use of primary care. To date, however, the Chinese healthcare system is still heavily reliant on hospital-based specialty care. Studies consistently show an association between primary care and improved health outcomes, and the same association is also found among the disadvantaged population. Due to the "hukou" system, interprovincial migrants in the urban districts are put in a weak position and become the disadvantaged. Therefore, the aim of this study is to investigate whether greater supply and utilization of primary care was associated with reduced child mortality among the entire population and the interprovincial migrants in urban districts of Guangdong province, China.

METHODS: An ecological study was conducted using a 3-year panel data with repeated measurements within urban districts in Guangdong province from 2014 to 2016, with 178 observations in total. Multilevel linear mixed effects models were applied to explore the associations.

RESULTS: Higher visit proportion to primary care was associated with reductions in the infant mortality rate and the under-five mortality rate in both the entire population and the interprovincial migrants (p < 0.05) in the full models. The association between visit proportion to primary care and reduced neonatal mortality rate was significant among the entire population (p < 0.05) while it was insignificant among the interprovincial migrants (p > 0.05).

CONCLUSIONS: Our ecological study based in urban districts of Guangdong province found consistent associations between higher visit proportion to primary care and improvements in child health among the entire population and the interprovincial migrants, suggesting that China should continue to strengthen and develop the primary care system. The findings from China adds to the previously reported evidence on the association between primary care and improved health, especially that of the disadvantaged.}, } @article {pmid32293258, year = {2020}, author = {Bosshard, L and Peischl, S and Ackermann, M and Excoffier, L}, title = {Dissection of the mutation accumulation process during bacterial range expansions.}, journal = {BMC genomics}, volume = {21}, number = {1}, pages = {253}, pmid = {32293258}, issn = {1471-2164}, support = {310030B-166605//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; }, mesh = {Biological Evolution ; Carrier Proteins/genetics/metabolism ; Computer Simulation ; *Directed Molecular Evolution ; Escherichia coli/*genetics/growth & development ; Gene Ontology ; Genetic Drift ; *Genetic Fitness ; Membrane Proteins/genetics/metabolism ; Models, Genetic ; Mutation ; Mutation Accumulation ; Selection, Genetic ; Silent Mutation ; Whole Genome Sequencing ; }, abstract = {BACKGROUND: Recent experimental work has shown that the evolutionary dynamics of bacteria expanding across space can differ dramatically from what we expect under well-mixed conditions. During spatial expansion, deleterious mutations can accumulate due to inefficient selection on the expansion front, potentially interfering with and modifying adaptive evolutionary processes.

RESULTS: We used whole genome sequencing to follow the genomic evolution of 10 mutator Escherichia coli lines during 39 days (~ 1650 generations) of a spatial expansion, which allowed us to gain a temporal perspective on the interaction of adaptive and non-adaptive evolutionary processes during range expansions. We used elastic net regression to infer the positive or negative effects of mutations on colony growth. The colony size, measured after three day of growth, decreased at the end of the experiment in all 10 lines, and mutations accumulated at a nearly constant rate over the whole experiment. We find evidence that beneficial mutations accumulate primarily at an early stage of the experiment, leading to a non-linear change of colony size over time. Indeed, the rate of colony size expansion remains almost constant at the beginning of the experiment and then decreases after ~ 12 days of evolution. We also find that beneficial mutations are enriched in genes encoding transport proteins, and genes coding for the membrane structure, whereas deleterious mutations show no enrichment for any biological process.

CONCLUSIONS: Our experiment shows that beneficial mutations target specific biological functions mostly involved in inter or extra membrane processes, whereas deleterious mutations are randomly distributed over the whole genome. It thus appears that the interaction between genetic drift and the availability or depletion of beneficial mutations determines the change in fitness of bacterial populations during range expansion.}, } @article {pmid32286335, year = {2020}, author = {Kaufman, D and McKay, N and Routson, C and Erb, M and Davis, B and Heiri, O and Jaccard, S and Tierney, J and Dätwyler, C and Axford, Y and Brussel, T and Cartapanis, O and Chase, B and Dawson, A and de Vernal, A and Engels, S and Jonkers, L and Marsicek, J and Moffa-Sánchez, P and Morrill, C and Orsi, A and Rehfeld, K and Saunders, K and Sommer, PS and Thomas, E and Tonello, M and Tóth, M and Vachula, R and Andreev, A and Bertrand, S and Biskaborn, B and Bringué, M and Brooks, S and Caniupán, M and Chevalier, M and Cwynar, L and Emile-Geay, J and Fegyveresi, J and Feurdean, A and Finsinger, W and Fortin, MC and Foster, L and Fox, M and Gajewski, K and Grosjean, M and Hausmann, S and Heinrichs, M and Holmes, N and Ilyashuk, B and Ilyashuk, E and Juggins, S and Khider, D and Koinig, K and Langdon, P and Larocque-Tobler, I and Li, J and Lotter, A and Luoto, T and Mackay, A and Magyari, E and Malevich, S and Mark, B and Massaferro, J and Montade, V and Nazarova, L and Novenko, E and Pařil, P and Pearson, E and Peros, M and Pienitz, R and Płóciennik, M and Porinchu, D and Potito, A and Rees, A and Reinemann, S and Roberts, S and Rolland, N and Salonen, S and Self, A and Seppä, H and Shala, S and St-Jacques, JM and Stenni, B and Syrykh, L and Tarrats, P and Taylor, K and van den Bos, V and Velle, G and Wahl, E and Walker, I and Wilmshurst, J and Zhang, E and Zhilich, S}, title = {A global database of Holocene paleotemperature records.}, journal = {Scientific data}, volume = {7}, number = {1}, pages = {115}, pmid = {32286335}, issn = {2052-4463}, support = {AGS-1602105//National Science Foundation (NSF)/International ; AGS-1903548//National Science Foundation (NSF)/International ; AGS-1602105//National Science Foundation (NSF)/International ; AGS-1903548//National Science Foundation (NSF)/International ; AGS-1602301//National Science Foundation (NSF)/International ; }, abstract = {A comprehensive database of paleoclimate records is needed to place recent warming into the longer-term context of natural climate variability. We present a global compilation of quality-controlled, published, temperature-sensitive proxy records extending back 12,000 years through the Holocene. Data were compiled from 679 sites where time series cover at least 4000 years, are resolved at sub-millennial scale (median spacing of 400 years or finer) and have at least one age control point every 3000 years, with cut-off values slackened in data-sparse regions. The data derive from lake sediment (51%), marine sediment (31%), peat (11%), glacier ice (3%), and other natural archives. The database contains 1319 records, including 157 from the Southern Hemisphere. The multi-proxy database comprises paleotemperature time series based on ecological assemblages, as well as biophysical and geochemical indicators that reflect mean annual or seasonal temperatures, as encoded in the database. This database can be used to reconstruct the spatiotemporal evolution of Holocene temperature at global to regional scales, and is publicly available in Linked Paleo Data (LiPD) format.}, } @article {pmid32286314, year = {2020}, author = {Assis, J and Fragkopoulou, E and Frade, D and Neiva, J and Oliveira, A and Abecasis, D and Faugeron, S and Serrão, EA}, title = {A fine-tuned global distribution dataset of marine forests.}, journal = {Scientific data}, volume = {7}, number = {1}, pages = {119}, pmid = {32286314}, issn = {2052-4463}, support = {SFRH/BPD/111003/2015//Ministry of Education and Science | Fundação para a Ciência e a Tecnologia (Portuguese Science and Technology Foundation)/International ; DL57/2016/CP1361/CT0035//Ministry of Education and Science | Fundação para a Ciência e a Tecnologia (Portuguese Science and Technology Foundation)/International ; SFRH/BD/144878/2019//Ministry of Education and Science | Fundação para a Ciência e a Tecnologia (Portuguese Science and Technology Foundation)/International ; }, mesh = {Aquatic Organisms/*classification ; Climate ; *Ecosystem ; Phaeophyceae/*classification ; }, abstract = {Species distribution records are a prerequisite to follow climate-induced range shifts across space and time. However, synthesizing information from various sources such as peer-reviewed literature, herbaria, digital repositories and citizen science initiatives is not only costly and time consuming, but also challenging, as data may contain thematic and taxonomic errors and generally lack standardized formats. We address this gap for important marine ecosystem-structuring species of large brown algae and seagrasses. We gathered distribution records from various sources and provide a fine-tuned dataset with ~2.8 million dereplicated records, taxonomically standardized for 682 species, and considering important physiological and biogeographical traits. Specifically, a flagging system was implemented to signal potentially incorrect records reported on land, in regions with limiting light conditions for photosynthesis, and outside the known distribution of species, as inferred from the most recent published literature. We document the procedure and provide a dataset in tabular format based on Darwin Core Standard (DwC), alongside with a set of functions in R language for data management and visualization.}, } @article {pmid32285164, year = {2020}, author = {Khan, SA and Chen, H and Deng, Y and Chen, Y and Zhang, C and Cai, T and Ali, N and Mamadou, G and Xie, D and Guo, B and Varshney, RK and Zhuang, W}, title = {High-density SNP map facilitates fine mapping of QTLs and candidate genes discovery for Aspergillus flavus resistance in peanut (Arachis hypogaea).}, journal = {TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik}, volume = {133}, number = {7}, pages = {2239-2257}, doi = {10.1007/s00122-020-03594-0}, pmid = {32285164}, issn = {1432-2242}, support = {U1705233//National Science Foundation of P.R. China/ ; 31601337//National Science Foundation of P.R. China/ ; 31701463//National Science Foundation of P.R. China/ ; }, mesh = {Aflatoxins/chemistry ; Arachis/*genetics/microbiology ; Aspergillus flavus/*pathogenicity ; Chromosome Mapping ; Computational Biology ; Disease Resistance/*genetics ; Genetic Linkage ; Genetic Markers ; Genotype ; Oligonucleotide Array Sequence Analysis ; Phenotype ; Plant Diseases/*genetics/microbiology ; *Polymorphism, Single Nucleotide ; Quantitative Trait Loci ; }, abstract = {Two novel resistant QTLs mapped and candidate genes identified for Aspergillus flavus resistance in cultivated peanut using SLAF-seq. Aflatoxin contamination in peanuts caused by Aspergillus flavus is a serious food safety issue for human health around the world. Host plant resistance to fungal infection and reduction in aflatoxin are crucial for mitigating this problem. Identification of the resistance-linked markers can be used in marker-assisted breeding for varietal development. Here we report construction of two high-density genetic linkage maps with 1975 SNP loci and 5022 SNP loci, respectively. Two consistent quantitative trait loci (QTL) were identified as qRAF-3-1 and qRAF-14-1, which located on chromosomes A03 and B04, respectively. QTL qRAF-3-1 was mapped within 1.67 cM and had more than 19% phenotypic variance explained (PVE), while qRAF-14-1 was located within 1.34 cM with 5.15% PVE. While comparing with the reference genome, the mapped QTLs, qRAF-3-1 and qRAF-14-1, were located within a physical distance of 1.44 Megabase pair (Mbp) and 2.22 Mbp, harboring 67 and 137 genes, respectively. Among the identified candidate genes, six genes with the same function were found within both QTLs regions. In addition, putative disease resistance RPP13-like protein 1 (RPP13), lipoxygenase (Lox), WRKY transcription factor (WRKY) and cytochrome P450 71B34 genes were also identified. Using microarray analysis, genes responded to A. flavus infection included coding for RPP13, pentatricopeptide repeat-containing-like protein, and Lox which may be possible candidate genes for resistance to A. flavus. The QTLs and candidate genes will further facilitate marker development and validation of genes for deployment in the molecular breeding programs against A. flavus in peanuts.}, } @article {pmid32284567, year = {2020}, author = {Ji, BW and Sheth, RU and Dixit, PD and Tchourine, K and Vitkup, D}, title = {Macroecological dynamics of gut microbiota.}, journal = {Nature microbiology}, volume = {5}, number = {5}, pages = {768-775}, pmid = {32284567}, issn = {2058-5276}, support = {R35 GM131884/GM/NIGMS NIH HHS/United States ; R01 GM079759/GM/NIGMS NIH HHS/United States ; R01 DK118044/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; Bacteria/*classification/genetics ; Biodiversity ; Computer Simulation ; Diet ; Gastrointestinal Microbiome/genetics/*physiology ; Gastrointestinal Tract/*microbiology ; Humans ; Mice ; Microbiota ; Models, Theoretical ; RNA, Ribosomal, 16S ; }, abstract = {The gut microbiota is now widely recognized as a dynamic ecosystem that plays an important role in health and disease. Although current sequencing technologies make it possible to explore how relative abundances of host-associated bacteria change over time, the biological processes governing microbial dynamics remain poorly understood. Therefore, as in other ecological systems, it is important to identify quantitative relationships describing various aspects of gut microbiota dynamics. In the present study, we use multiple high-resolution time series data obtained from humans and mice to demonstrate that, despite their inherent complexity, gut microbiota dynamics can be characterized by several robust scaling relationships. Interestingly, the observed patterns are highly similar to those previously identified across diverse ecological communities and economic systems, including the temporal fluctuations of animal and plant populations and the performance of publicly traded companies. Specifically, we find power-law relationships describing short- and long-term changes in gut microbiota abundances, species residence and return times, and the correlation between the mean and the temporal variance of species abundances. The observed scaling laws are altered in mice receiving different diets and are affected by context-specific perturbations in humans. We use the macroecological relationships to reveal specific bacterial taxa, the dynamics of which are substantially perturbed by dietary and environmental changes. Overall, our results suggest that a quantitative macroecological framework will be important for characterizing and understanding the complex dynamics of diverse microbial communities.}, } @article {pmid32283058, year = {2020}, author = {Shu, T and Zhai, G and Pradhan, A and Olsson, PE and Yin, Z}, title = {Zebrafish cyp17a1 knockout reveals that androgen-mediated signaling is important for male brain sex differentiation.}, journal = {General and comparative endocrinology}, volume = {295}, number = {}, pages = {113490}, doi = {10.1016/j.ygcen.2020.113490}, pmid = {32283058}, issn = {1095-6840}, mesh = {Androgens/*metabolism ; Animals ; Behavior, Animal ; Brain/*physiology ; Female ; Gene Expression Profiling ; Gene Expression Regulation ; *Gene Knockout Techniques ; Gene Ontology ; Male ; *Sex Differentiation/genetics ; *Signal Transduction ; Steroid 17-alpha-Hydroxylase ; Testosterone/analogs & derivatives/metabolism ; Zebrafish/*physiology ; Zebrafish Proteins/*deficiency ; }, abstract = {Brain sex differentiation is a complex process, wherein genes and steroid hormones act to induce specific gender brain differentiation. Testosterone (T) derived from the gonads has been linked to neural circuit modeling in a sex-specific manner. Previously, we have shown that cyp17a1 knockout (KO) zebrafish have low plasma androgen levels, and display compromised male-typical mating behaviors. In this study, we demonstrated that treatment of cyp17a1 KO males with T or 11-ketotestosterone (11-KT) is sufficient to rescue mating impairment by restoring the male-typical secondary sex characters (SSCs) and mating behaviors, confirming an essential role of androgen in maintaining SSCs and mating behaviors. Brain steroid hormone analysis revealed that cyp17a1 KO fish have reduced levels of T and 11-KT. We performed RNA sequencing on brain samples of control and cyp17a1 KO male zebrafish to get insights regarding the impact of cyp17a1 KO on gene expression pattern, and to correlate it with the observed disruption of male-typical mating behaviors. Transcriptome analysis of cyp17a1 KO males showed a differential gene expression when compared to control males. In total, 358 genes were differentially regulated between control males and KO males. Important genes including brain aromatase (cyp19a1b), progesterone receptor (pgr), deiodinase (dio2), and insulin-like growth factor 1 (igf1) that are involved in brain functions, as well as androgen response genes including igf1, frem1a, elovl1a, pax3a, mmp13b, hsc70, ogg1 were regulated. RT-qPCR analysis following rescue of cyp17a1 KO with T and 11-KT further suggested that androgen-mediated signaling is disrupted in the cyp17a1 KO fish. Our results indicated that cyp17a1 KO fish have an incomplete masculinization and altered brain gene expression, which could be due to decreased androgen levels.}, } @article {pmid32282796, year = {2020}, author = {Kuerban, M and Maihemuti, B and Waili, Y and Tuerhong, T}, title = {Ecological risk assessment and source identification of heavy metal pollution in vegetable bases of Urumqi, China, using the positive matrix factorization (PMF) method.}, journal = {PloS one}, volume = {15}, number = {4}, pages = {e0230191}, pmid = {32282796}, issn = {1932-6203}, mesh = {China ; *Environmental Monitoring ; Environmental Pollution/*analysis ; *Geographic Information Systems ; Metals, Heavy/*analysis ; *Models, Biological ; Soil Pollutants/*analysis ; *Vegetables/chemistry/growth & development ; }, abstract = {Heavy metal pollution is a widespread problem and strongly affects human health through the food chain. In this study, the overall pollution situation and source apportionment of heavy metals in soil (Hg, Cd, As, Pb, Ni, Zn, Cu and Cr) were evaluated using various methods including geo-accumulation index (Igeo), potential ecological risk index (RI) and positive matrix factorization combined with Geographical Information System (GIS) to quantify and identify the possible sources to these heavy metals in soils. The results of Igeo showed that this farmland top soil moderate contaminated by Hg, other selected elements with noncontamination level. And the average RI in the top soil was 259.89, indicating a moderate ecological risk, of which Hg and Cd attributed 88.87% of the RI. The results of the PMF model showed that the relative contributions of heavy metals due to atmospheric depositions (18.70%), sewage irrigations (21.17%), soil parent materials (19.11%), industrial and residential coal combustions (17.43%) and agricultural and lithogenic sources (23.59%), respectively. Of these elements, Pb and Cd were came from atmospheric deposition. Cr was attributed to sewage irrigations. As was mainly derived from the soil parent materials. Hg originated from industrial and residential coal combustions, and most of the Cu, Zn and Ni, except for Pb, were predominantly derived from agricultural and lithogenic sources. These results are important in considering management plans to control the aggravation of heavy metal pollution and ultimately to protect soil resources in this region. In addition, this study enhances the understanding of heavy metal contamination occurrence in agroecosystem that helps predicting and limiting the potential of heavy metal exposure to people and ecosystem.}, } @article {pmid32279659, year = {2020}, author = {Arakkal, AT and Barón, AE and Lamb, MM and Fields, SK and Comstock, RD}, title = {Evaluating the effectiveness of traumatic brain injury state laws among high school athletes.}, journal = {Injury epidemiology}, volume = {7}, number = {1}, pages = {12}, pmid = {32279659}, issn = {2197-1714}, support = {R49 CE002106/CE/NCIPC CDC HHS/United States ; R49/CE001172-01/CC/CDC HHS/United States ; R49/CE000674-01/CC/CDC HHS/United States ; R49/CE002106-01/CC/CDC HHS/United States ; R49CE002106/ACL/ACL HHS/United States ; }, abstract = {BACKGROUND: Traumatic brain injury legislation varies across states. A comprehensive nationwide evaluation of state traumatic brain injury laws is vital given growing populations of high school athletes. This study evaluates the effectiveness of traumatic brain injury laws by examining longitudinal trends in incident and recurrent concussion rates and determines if state level variations in legislation's language affected the observed trends.

METHODS: In this retrospective ecological study of a large national sample of US high schools from 2005/06 through 2017/18, piecewise regression models along with a profile likelihood approach were utilized to examine longitudinal trends in incident and recurrent concussion rates.

RESULTS: Overall incident concussion rates increased by an additional 1.85%/standardized month (STDM) (95% confidence interval (CI): 1.14, 2.56%) prior to law passage and decreased by an additional 1.08%/ STDM (95%CI: - 1.43, - 0.72%) after law passage. Similar trends were observed for overall recurrent concussion rates. Among states that specified the category of healthcare provider for return to play clearance, post-law recurrent concussion rates decreased on average by an additional 1.59%/STDM (95%CI: - 3.42, 0.22%) compared to states that did not specify the category of healthcare provider.

CONCLUSIONS: The passage of state level traumatic brain injury laws was associated with an increase in overall incident and recurrent concussion rates prior to law passage and a decrease in rates after law passage. Although not statistically significant, states with traumatic brain injury laws specifying the category of healthcare provider for return to play clearance had a greater rate of decline in post-law recurrent concussion rates compared to states not specifying the category of healthcare provider. The findings suggest that state traumatic brain injury laws may benefit from specifying the category of healthcare provider allowed to provide return to play clearance, if they do not already include such language.}, } @article {pmid32278258, year = {2020}, author = {Wang, RL}, title = {Semantic characterization of adverse outcome pathways.}, journal = {Aquatic toxicology (Amsterdam, Netherlands)}, volume = {222}, number = {}, pages = {105478}, pmid = {32278258}, issn = {1879-1514}, support = {EPA999999/ImEPA/Intramural EPA/United States ; }, mesh = {*Adverse Outcome Pathways ; Animals ; Biological Ontologies ; Biomedical Research/*methods ; Humans ; Phenotype ; Risk Assessment ; *Semantics ; Toxicology/*methods ; }, abstract = {This study was undertaken to systematically assess the utilities and performance of ontology-based semantic analysis in adverse outcome pathway (AOP) research. With an increasing number of AOPs developed by scientific domain experts to organize toxicity information and facilitate chemical risk assessment, there is a pressing need for objective approaches to evaluate the biological coherence and quality of these AOPs. Powered by ontologies covering a wide range of biological domains, abundant phenotypic data annotated ontologically, and some sophisticated knowledge computing tools, semantic analysis has great potential in this area of application. With the events in the AOP-Wiki first annotated into logical definitions and then grouped into phenotypic profiles by individual AOPs, the coherence and quality of AOPs were assessed at several levels: paired key event relationships (KER), all possible event pair combinations within AOPs, and the phenotypic profiles of AOPs, genes, biological pathways, human diseases, and selected chemicals. The semantic similarities were assessed at all these levels based on a unified cross-species vertebrate phenotype ontology encompassing the logical definitions of AOP events as well as many other domain ontologies. A substantial number of KERs and AOPs in the AOP-Wiki were found to be semantically coherent. These same coherent AOPs also mapped to many more genes, pathways, and diseases biologically aligned with the intended chain of events therein leading to their respective adverse outcomes. Significantly, these findings imply that semantic analysis should also have utilities in developing future AOPs by selecting candidate events from either the existing AOP-Wiki events or a broader collection of ontology terms semantically similar to the molecular initiating events or adverse outcomes of interest. In addition, semantic analysis enabled AOP networks to be constructed at the level of phenotypic profiles based on similarities, complementing those based on event sharing by bringing genes, pathways, diseases, and chemicals into the networks too-thus greatly expanding the biological scope and our understanding of AOPs.}, } @article {pmid32277155, year = {2020}, author = {Metegnier, G and Paulino, S and Ramond, P and Siano, R and Sourisseau, M and Destombe, C and Le Gac, M}, title = {Species specific gene expression dynamics during harmful algal blooms.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {6182}, pmid = {32277155}, issn = {2045-2322}, mesh = {Atlantic Ocean ; DNA Barcoding, Taxonomic ; Datasets as Topic ; Dinoflagellida/*genetics ; Gene Expression Profiling ; Gene Expression Regulation ; Harmful Algal Bloom/*physiology ; Ion Channels/genetics ; Ion Transport/genetics ; Microbiota/*genetics ; Photosynthesis/genetics ; Species Specificity ; }, abstract = {Harmful algal blooms are caused by specific members of microbial communities. Understanding the dynamics of these events requires comparing the strategies developed by the problematic species to cope with environmental fluctuations to the ones developed by the other members of the community. During three consecutive years, the meta-transcriptome of micro-eukaryote communities was sequenced during blooms of the toxic dinoflagellate Alexandrium minutum. The dataset was analyzed to investigate species specific gene expression dynamics. Major shifts in gene expression were explained by the succession of different species within the community. Although expression patterns were strongly correlated with fluctuation of the abiotic environment, and more specifically with nutrient concentration, transcripts specifically involved in nutrient uptake and metabolism did not display extensive changes in gene expression. Compared to the other members of the community, A. minutum displayed a very specific expression pattern, with lower expression of photosynthesis transcripts and central metabolism genes (TCA cycle, glucose metabolism, glycolysis…) and contrasting expression pattern of ion transporters across environmental conditions. These results suggest the importance of mixotrophy, cell motility and cell-to-cell interactions during A. minutum blooms.}, } @article {pmid32276612, year = {2020}, author = {da Coelho, RM and Nunes, MAP and Gomes, CVC and Dos Viana, IS and da Silva, ÂM}, title = {Time trends and social security burden of temporary work disability due to chronic venous disease in Brazil.}, journal = {BMC public health}, volume = {20}, number = {1}, pages = {477}, pmid = {32276612}, issn = {1471-2458}, mesh = {Adolescent ; Adult ; Aged ; Brazil/epidemiology ; Chronic Disease ; Databases, Factual ; Disabled Persons/*statistics & numerical data ; Female ; Humans ; Male ; Middle Aged ; Social Security/*economics ; Time Factors ; Vascular Diseases/*economics/*epidemiology ; Young Adult ; }, abstract = {BACKGROUND: Chronic venous disease (CVD) and disability are worldwide problems and have significant socioeconomic implications. This study aims to analyze the time trends and social security burden of temporary work disability due to CVD in Brazil.

METHODS: An ecological time series study using the Brazilian Social Security System database was performed from 2005 to 2014. Data from all benefits granted to workers with temporary disability due to CVD were analyzed. The cases were identified using diagnosis codes I83-I83.9 of the International Classification of Diseases 10th Revision (ICD-10). The time trend analyses were performed by the Joinpoint Regression Model, with sex, age, regions, income, and category of affiliation as variables. Crude and age-standardized rates were calculated.

RESULTS: A total of 429,438 benefits were granted for temporary work disability due to CVD from 2005 to 2014, with a growing trend and an age-standardized annual percent change (APC) of 3.4 (95% CI: 2.6-4.2) (p < 0.05). Social security expense increased 3.5-fold, and the number of days in benefit doubled from 2005 to 2014. In total, 27,017,818 working days were lost. The average duration of benefits was 55.3 days. The majority of workers were women (68.2%) (p < 0.001), between 30 and 59 years old, employed, had a monthly income ≤2 minimum wages (MW) (83.2%), and lived in the regions southeast (53.6%) and south (29.3%). Significantly higher APCs were observed for women than for men (APC: 4.9, 95% CI: 4.0-5.7 versus APC: 1.2, 95% CI: 0.1-2.4). All regions in Brazil had a significant growing trend, except in the north. No significant growth was observed in the age group of 60-69 years. A decreasing trend was observed in workers with monthly incomes above 2 MW (p < 0.05).

CONCLUSIONS: Temporary work disability due to CVD and social security burden showed increasing trends with millions of working days lost, particularly among women and low-income workers. Preventing disability is challenging, and public policies are needed to reduce the social and economic impact of disability. Therefore, measures for promoting health at the workplace should be encouraged.}, } @article {pmid32275714, year = {2020}, author = {Rodríguez-Sánchez, P and van Nes, EH and Scheffer, M}, title = {Climbing Escher's stairs: A way to approximate stability landscapes in multidimensional systems.}, journal = {PLoS computational biology}, volume = {16}, number = {4}, pages = {e1007788}, pmid = {32275714}, issn = {1553-7358}, mesh = {Algorithms ; Computational Biology/*methods ; Ecosystem ; *Models, Biological ; Models, Statistical ; Systems Analysis ; }, abstract = {Stability landscapes are useful for understanding the properties of dynamical systems. These landscapes can be calculated from the system's dynamical equations using the physical concept of scalar potential. Unfortunately, it is well known that for most systems with two or more state variables such potentials do not exist. Here we use an analogy with art to provide an accessible explanation of why this happens and briefly review some of the possible alternatives. Additionally, we introduce a novel and simple computational tool that implements one of those solutions: the decomposition of the differential equations into a gradient term, that has an associated potential, and a non-gradient term, that lacks it. In regions of the state space where the magnitude of the non-gradient term is small compared to the gradient part, we use the gradient term to approximate the potential as quasi-potential. The non-gradient to gradient ratio can be used to estimate the local error introduced by our approximation. Both the algorithm and a ready-to-use implementation in the form of an R package are provided.}, } @article {pmid32271763, year = {2020}, author = {Yunxian, C and Renjie, L and Shuliang, Z and Fenghua, G}, title = {Measuring multi-spatiotemporal scale tourist destination popularity based on text granular computing.}, journal = {PloS one}, volume = {15}, number = {4}, pages = {e0228175}, pmid = {32271763}, issn = {1932-6203}, mesh = {*Data Mining ; Models, Theoretical ; *Spatio-Temporal Analysis ; Time Factors ; }, abstract = {User-generated content (UGC) is an important data source for tourism GIScience research. However, no effective approach exists for identifying hidden spatiotemporal patterns within multi-scale unstructured UGC. Therefore, we developed an algorithm to measure the tourist destination popularity (TDP) based on a multi-spatiotemporal text granular computing model, called TDPMTGC. To accurately granulate the spatial and temporal information of tourism text, tourism text data granules are used to represent landscape objects. These granules are unified objects that possess multiple attributes, such as spatial and temporal dimensions. The multi-spatiotemporal scales are characterized by the multi-hierarchical structure of granular computing, and transformations of granular layers and data granule size are achieved by scale selection in the spatial and temporal dimensions. Therefore, all scales between the spatial and temporal dimension are related, which allows for the comparability of the data granules of all spatial-spatial, temporal-temporal and spatial-temporal layers. This approach achieves a quantitative description and comparison of the popularity value of granules between adjacent scales and cross-scales. Therefore, the TDP with multi-spatiotemporal scales can be deduced and calculated in a systematic framework. We first introduce the conceptual framework of TDPMTGC to construct a quantitative measurement model of TDP at multi-spatiotemporal scales. Then, we present a dataset construction approach to support multi-spatiotemporal scale granular reorganization. Finally, TDPMTGC is derived to describe both the TDP at a single spatial or temporal scale and the patterns and processes of the TDP at multi-spatiotemporal scales. A case study from Jiuzhaigou shows that the TDP derived using TDPMTGC is consistent with the conclusions of existing studies. More importantly, TDPMTGC provides additional detailed characteristics, such as the contributions of different scenic spots in a tourist route or scenic area, the monthly anomalies and daily contributions of TDP in a specific year, the distinct weakening of tourist route scale in tourist cognition, and the daily variations of TDP during in-season and off-season times. This is the first time that a granular computing model has been introduced to tourism GIScience that provides a feasible scheme for reorganizing large-scale unstructured text and constructing public spatiotemporal UGC tourism datasets. TDPMTGC constitutes a new approach for exploring tourist behaviors and the driving mechanisms of tourism patterns and processes.}, } @article {pmid32267904, year = {2020}, author = {Krull, M}, title = {Comparing statistical analyses to estimate thresholds in ecotoxicology.}, journal = {PloS one}, volume = {15}, number = {4}, pages = {e0231149}, pmid = {32267904}, issn = {1932-6203}, mesh = {Bayes Theorem ; Data Interpretation, Statistical ; Datasets as Topic ; Ecotoxicology/*methods ; Likelihood Functions ; Markov Chains ; *Models, Statistical ; Monte Carlo Method ; }, abstract = {Different methods are used in ecotoxicology to estimate thresholds in survival data. This paper uses Monte Carlo simulations to evaluate the accuracy of three methods (maximum likelihood (MLE) and Markov Chain Monte Carlo estimates (Bayesian) of the no-effect concentration (NEC) model and Piecewise regression) in estimating true and apparent thresholds in survival experiments with datasets having different slopes, background mortalities, and experimental designs. Datasets were generated with models that include a threshold parameter (NEC) or not (log-logistic). Accuracy was estimated using root-mean square errors (RMSEs), and RMSE ratios were used to estimate the relative improvement in accuracy by each design and method. All methods had poor performances in shallow and intermediate curves, and accuracy increased with the slope of the curve. The EC5 was generally the most accurate method to estimate true and apparent thresholds, except for steep curves with a true threshold. In that case, the EC5 underestimated the threshold, and MLE and Bayesian estimates were more accurate. In most cases, information criteria weights did not provide strong evidence in support of the true model, suggesting that identifying the true model is a difficult task. Piecewise regression was the only method where the information criteria weights had high support for the threshold model; however, the rate of spurious threshold model selection was also high. Even though thresholds are an attractive concept from a regulatory and practical point of view, threshold estimates, under the experimental conditions evaluated in this work, should be carefully used in survival analysis or when there are any biological reasons to support the existence of a threshold.}, } @article {pmid32267382, year = {2020}, author = {Arroyo, LH and Ramos, ACV and Yamamura, M and Weiller, TH and Crispim, JA and Cartagena-Ramos, D and Fuentealba-Torres, M and Santos, DTD and Palha, PF and Arcêncio, RA}, title = {[Areas with declining vaccination coverage for BCG, poliomyelitis, and MMR in Brazil (2006-2016): maps of regional heterogeneity].}, journal = {Cadernos de saude publica}, volume = {36}, number = {4}, pages = {e00015619}, doi = {10.1590/0102-311X00015619}, pmid = {32267382}, issn = {1678-4464}, mesh = {BCG Vaccine/*administration & dosage ; Brazil ; Female ; Humans ; Immunization Programs ; Infant ; Male ; Measles-Mumps-Rubella Vaccine/*administration & dosage ; Poliomyelitis/*prevention & control ; Vaccination/*statistics & numerical data ; Vaccination Coverage/statistics & numerical data/*trends ; }, abstract = {Immunization is known to be one of the most successful and cost-effective health interventions, resulting in the eradication and control of various diseases in the world. However, Brazil has experienced a worrisome drop in vaccination coverage, associated with the resurgence of various previously controlled or eradicated diseases. This study thus conducted a situational diagnosis weighing Brazil's different regions and time trends in vaccination coverage in order to identify areas with reduction in vaccination coverage for BCG, poliomyelitis, and MMR. This ecological study collected data on the number of children up to one year of age who had been vaccinated with these three vaccines from 2006 to 2016, according to municipality (county). Data were obtained from the Brazilian Health Informatics Department. A spatial scan was performed, analyzing spatial variations in the time trends for vaccination coverage. Downward trends were seen in the number of immunizations in Brazil, with reductions of 0.9%, 1.3%, and 2.7% per year for BCG, poliomyelitis, and MMR, respectively. Significant decreases were also seen in all five major geographic regions with time trends in the reduction of vaccination coverage. The study evidenced an important reduction in vaccination coverage in recent years, with major heterogeneity between municipalities. Thus, focused attention and strategic planning in keeping with each local area's characteristics are necessary to address both the reduction of vaccination coverage and the resurgence of vaccine-preventable diseases in Brazil.}, } @article {pmid32258041, year = {2020}, author = {Ewe, CK and Torres Cleuren, YN and Rothman, JH}, title = {Evolution and Developmental System Drift in the Endoderm Gene Regulatory Network of Caenorhabditis and Other Nematodes.}, journal = {Frontiers in cell and developmental biology}, volume = {8}, number = {}, pages = {170}, pmid = {32258041}, issn = {2296-634X}, support = {R01 HD081266/HD/NICHD NIH HHS/United States ; R01 HD082347/HD/NICHD NIH HHS/United States ; }, abstract = {Developmental gene regulatory networks (GRNs) underpin metazoan embryogenesis and have undergone substantial modification to generate the tremendous variety of animal forms present on Earth today. The nematode Caenorhabditis elegans has been a central model for advancing many important discoveries in fundamental mechanistic biology and, more recently, has provided a strong base from which to explore the evolutionary diversification of GRN architecture and developmental processes in other species. In this short review, we will focus on evolutionary diversification of the GRN for the most ancient of the embryonic germ layers, the endoderm. Early embryogenesis diverges considerably across the phylum Nematoda. Notably, while some species deploy regulative development, more derived species, such as C. elegans, exhibit largely mosaic modes of embryogenesis. Despite the relatively similar morphology of the nematode gut across species, widespread variation has been observed in the signaling inputs that initiate the endoderm GRN, an exemplar of developmental system drift (DSD). We will explore how genetic variation in the endoderm GRN helps to drive DSD at both inter- and intraspecies levels, thereby resulting in a robust developmental system. Comparative studies using divergent nematodes promise to unveil the genetic mechanisms controlling developmental plasticity and provide a paradigm for the principles governing evolutionary modification of an embryonic GRN.}, } @article {pmid32255797, year = {2020}, author = {Purse, BV and Darshan, N and Kasabi, GS and Gerard, F and Samrat, A and George, C and Vanak, AT and Oommen, M and Rahman, M and Burthe, SJ and Young, JC and Srinivas, PN and Schäfer, SM and Henrys, PA and Sandhya, VK and Chanda, MM and Murhekar, MV and Hoti, SL and Kiran, SK}, title = {Predicting disease risk areas through co-production of spatial models: The example of Kyasanur Forest Disease in India's forest landscapes.}, journal = {PLoS neglected tropical diseases}, volume = {14}, number = {4}, pages = {e0008179}, pmid = {32255797}, issn = {1935-2735}, support = {MR/P024335/2/MRC_/Medical Research Council/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; IA/CPHI/16/1/502648/WTDBT_/DBT-Wellcome Trust India Alliance/India ; MR/P024335/1/MRC_/Medical Research Council/United Kingdom ; /BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animal Distribution ; Animals ; Biodiversity ; *Disease Outbreaks ; Disease Susceptibility ; Forests ; Humans ; India/epidemiology ; Kyasanur Forest Disease/*epidemiology ; Population Density ; Risk Factors ; Spatial Regression ; Zoonoses/*epidemiology ; }, abstract = {Zoonotic diseases affect resource-poor tropical communities disproportionately, and are linked to human use and modification of ecosystems. Disentangling the socio-ecological mechanisms by which ecosystem change precipitates impacts of pathogens is critical for predicting disease risk and designing effective intervention strategies. Despite the global "One Health" initiative, predictive models for tropical zoonotic diseases often focus on narrow ranges of risk factors and are rarely scaled to intervention programs and ecosystem use. This study uses a participatory, co-production approach to address this disconnect between science, policy and implementation, by developing more informative disease models for a fatal tick-borne viral haemorrhagic disease, Kyasanur Forest Disease (KFD), that is spreading across degraded forest ecosystems in India. We integrated knowledge across disciplines to identify key risk factors and needs with actors and beneficiaries across the relevant policy sectors, to understand disease patterns and develop decision support tools. Human case locations (2014-2018) and spatial machine learning quantified the relative role of risk factors, including forest cover and loss, host densities and public health access, in driving landscape-scale disease patterns in a long-affected district (Shivamogga, Karnataka State). Models combining forest metrics, livestock densities and elevation accurately predicted spatial patterns in human KFD cases (2014-2018). Consistent with suggestions that KFD is an "ecotonal" disease, landscapes at higher risk for human KFD contained diverse forest-plantation mosaics with high coverage of moist evergreen forest and plantation, high indigenous cattle density, and low coverage of dry deciduous forest. Models predicted new hotspots of outbreaks in 2019, indicating their value for spatial targeting of intervention. Co-production was vital for: gathering outbreak data that reflected locations of exposure in the landscape; better understanding contextual socio-ecological risk factors; and tailoring the spatial grain and outputs to the scale of forest use, and public health interventions. We argue this inter-disciplinary approach to risk prediction is applicable across zoonotic diseases in tropical settings.}, } @article {pmid32250824, year = {2020}, author = {Singh, S and Bhardwaj, A and Verma, VK}, title = {Remote sensing and GIS based analysis of temporal land use/land cover and water quality changes in Harike wetland ecosystem, Punjab, India.}, journal = {Journal of environmental management}, volume = {262}, number = {}, pages = {110355}, doi = {10.1016/j.jenvman.2020.110355}, pmid = {32250824}, issn = {1095-8630}, mesh = {Agriculture ; Conservation of Natural Resources ; *Ecosystem ; Environmental Monitoring ; Geographic Information Systems ; India ; Remote Sensing Technology ; Water Quality ; *Wetlands ; }, abstract = {Wetlands help in maintaining ecological balance in an area, but are shrinking fast all over the world. A study was conducted on the Harike wetland in Punjab state of India to analyze temporal changes in land use/land cover (LULC), water spread area and water pollution by using RS and GIS techniques. The LULC map of Harike wetland ecosystem covering an area of 22213.91 ha was prepared through on-screen visual interpretation of multispectral Resourcesat 2 LISS-IV satellite data (2014 and 2018) having spatial resolution of 5.8 m. Area under agriculture, forest and built up increased and that under waste land, water bodies and wetland decreased during 2014-18. The rate of increase in agricultural land was quite high (18.87 ha/year) during 2006-2014, but reduced to 3.53 ha/year during 2014-2018. The built up land increased comparatively at low rates (0.87 and 0.90 ha/year). Areas under waste land, water bodies and wetland decreased at the rate of 4.32, 1.61 and 13.80 ha/year during 2006-2014 and 2.37, 0.34 and 1.71 ha/year during 2014-2018, respectively. The water spread area of Harike wetland which was 4073 ha and 4166 ha in year 2002 and 2006 reduced to 3918.98 ha and 3910.56 ha in the year 2014 and 2018, respectively. However, wetland ponded area shrinked at a rate of 30.37 ha/year during 2006-2014 and 2.11 ha/year during the period 2014-2018. The area under low and medium turbidity increased by 22.02% and 15.2%, respectively, but decreased by 49% under high turbidity during 2014-18. Wetland water was observed to be rich in macro and micronutrients. The pH, BOD and COD of wetland water increased by 0.51, 9.7 mg/l and 24 mg/l, respectively, during 2002-14 and by 0.03, 2.0 mg/l and 5.92 mg/l, respectively during 2014-18. Interaction between land use, water quality, water inflow, ground water and wetland area has also been studied. Intensive cultivation and declining groundwater levels in the area are negatively affecting the wetland. This necessitates regular monitoring of wetland structural components and water quality along with an urgent plan in place for conservation, rehabilitation and management of Harike wetland ecosystem in participatory mode.}, } @article {pmid32250807, year = {2020}, author = {Alijani, Z and Hosseinali, F and Biswas, A}, title = {Spatio-temporal evolution of agricultural land use change drivers: A case study from Chalous region, Iran.}, journal = {Journal of environmental management}, volume = {262}, number = {}, pages = {110326}, doi = {10.1016/j.jenvman.2020.110326}, pmid = {32250807}, issn = {1095-8630}, mesh = {Agriculture ; *Conservation of Natural Resources ; *Environmental Monitoring ; Geographic Information Systems ; Iran ; }, abstract = {Increasing global population put tremendous pressure on limited land resources and has led to changes in land use. Changing land use patterns are of great importance in environmental studies and critical for land use management decision-making. Thus, it is important to understand the relationship between the pattern of land use/cover change and its drivers in a region to initiate specific planning and management decisions. The objective of this study was to quantify changes in land use from a case study area in Chalous, Iran and identify geophysical characteristics (e.g., slope, elevation and soil) and socio-economic (e.g., population density, tourist industry, accessibility and land price) elements of the changes. This will help assess the impact on the trends in changing land use in the study area and elsewhere with similar conditions. In this study, multi-temporal satellite images, Geographic Information Systems (GIS), and semi-structured interviews were used to evaluate the spatio-temporal dynamics of land use/cover changes over a 20-year period (1996-2016). Supervised classification based on the maximum likelihood algorithm was used to obtain the land use classes with an overall accuracy of 87%, 92% and 93.50%, and kappa coefficients of 82.87%, 88.66% and 89.98% for 1996, 2006 and 2016, respectively. Change detection analysis also showed that agricultural land was reduced by 11.09% and built up areas were increased by 15.89% over the period of 20 years. The comprehensive evaluation of geophysical and socio-economic driving forces and the local characteristics of farmers indicated that economic factor and the tourist industry mainly contributed to the change from agricultural lands to built-up areas. In addition, a lack support from the government and the agricultural ministry also contributed to these conversions. Thus, investigation of the complexity of socio-ecological relationships and interaction with land use change drivers are necessary for sustainable planning and development and policy decisions.}, } @article {pmid32246067, year = {2020}, author = {Djemiel, C and Plassard, D and Terrat, S and Crouzet, O and Sauze, J and Mondy, S and Nowak, V and Wingate, L and Ogée, J and Maron, PA}, title = {µgreen-db: a reference database for the 23S rRNA gene of eukaryotic plastids and cyanobacteria.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {5915}, pmid = {32246067}, issn = {2045-2322}, mesh = {Cyanobacteria/classification/*genetics ; DNA Barcoding, Taxonomic ; DNA, Environmental/*genetics/isolation & purification ; *Databases, Nucleic Acid ; Eukaryota/classification/*genetics ; Photosynthesis ; Plastids/genetics ; RNA, Ribosomal, 23S/*genetics ; Soil/chemistry ; }, abstract = {Studying the ecology of photosynthetic microeukaryotes and prokaryotic cyanobacterial communities requires molecular tools to complement morphological observations. These tools rely on specific genetic markers and require the development of specialised databases to achieve taxonomic assignment. We set up a reference database, called µgreen-db, for the 23S rRNA gene. The sequences were retrieved from generalist (NCBI, SILVA) or Comparative RNA Web (CRW) databases, in addition to a more original approach involving recursive BLAST searches to obtain the best possible sequence recovery. At present, µgreen-db includes 2,326 23S rRNA sequences belonging to both eukaryotes and prokaryotes encompassing 442 unique genera and 736 species of photosynthetic microeukaryotes, cyanobacteria and non-vascular land plants based on the NCBI and AlgaeBase taxonomy. When PR[2]/SILVA taxonomy is used instead, µgreen-db contains 2,217 sequences (399 unique genera and 696 unique species). Using µgreen-db, we were able to assign 96% of the sequences of the V domain of the 23S rRNA gene obtained by metabarcoding after amplification from soil DNA at the genus level, highlighting good coverage of the database. µgreen-db is accessible at http://microgreen-23sdatabase.ea.inra.fr.}, } @article {pmid32245390, year = {2020}, author = {Levy Karin, E and Mirdita, M and Söding, J}, title = {MetaEuk-sensitive, high-throughput gene discovery, and annotation for large-scale eukaryotic metagenomics.}, journal = {Microbiome}, volume = {8}, number = {1}, pages = {48}, pmid = {32245390}, issn = {2049-2618}, mesh = {*Algorithms ; Computational Biology/methods ; Databases, Genetic ; Eukaryota/*genetics ; High-Throughput Screening Assays ; Metagenome ; Metagenomics/instrumentation/*methods ; *Microbiota ; Molecular Sequence Annotation/*methods ; Sequence Analysis, DNA/methods ; }, abstract = {BACKGROUND: Metagenomics is revolutionizing the study of microorganisms and their involvement in biological, biomedical, and geochemical processes, allowing us to investigate by direct sequencing a tremendous diversity of organisms without the need for prior cultivation. Unicellular eukaryotes play essential roles in most microbial communities as chief predators, decomposers, phototrophs, bacterial hosts, symbionts, and parasites to plants and animals. Investigating their roles is therefore of great interest to ecology, biotechnology, human health, and evolution. However, the generally lower sequencing coverage, their more complex gene and genome architectures, and a lack of eukaryote-specific experimental and computational procedures have kept them on the sidelines of metagenomics.

RESULTS: MetaEuk is a toolkit for high-throughput, reference-based discovery, and annotation of protein-coding genes in eukaryotic metagenomic contigs. It performs fast searches with 6-frame-translated fragments covering all possible exons and optimally combines matches into multi-exon proteins. We used a benchmark of seven diverse, annotated genomes to show that MetaEuk is highly sensitive even under conditions of low sequence similarity to the reference database. To demonstrate MetaEuk's power to discover novel eukaryotic proteins in large-scale metagenomic data, we assembled contigs from 912 samples of the Tara Oceans project. MetaEuk predicted >12,000,000 protein-coding genes in 8 days on ten 16-core servers. Most of the discovered proteins are highly diverged from known proteins and originate from very sparsely sampled eukaryotic supergroups.

CONCLUSION: The open-source (GPLv3) MetaEuk software (https://github.com/soedinglab/metaeuk) enables large-scale eukaryotic metagenomics through reference-based, sensitive taxonomic and functional annotation. Video abstract.}, } @article {pmid32237446, year = {2020}, author = {Mu, QR and Jiang, D and He, Y and Geng, L and Ren, GX and Bai, ZF and Zhang, X and Zhang, ZY and Liu, CS}, title = {[Correlation between chemical composition,ecological factors and soil factors of Chinese herbal medicine Daphnes Cortex].}, journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica}, volume = {45}, number = {5}, pages = {1059-1063}, doi = {10.19540/j.cnki.cjcmm.20200105.104}, pmid = {32237446}, issn = {1001-5302}, mesh = {China ; Copper ; Daphne/*chemistry ; Drugs, Chinese Herbal ; Geographic Information Systems ; Hydrogen-Ion Concentration ; Plants, Medicinal/chemistry ; Rain ; Soil/*chemistry ; Sunlight ; Temperature ; }, abstract = {In this paper, the correlation between the chemical constituents of Chinese herbal medicines Daphnes Cortex and the ecological factors and soil factors was studied, which provided a reference for the selection of suitable areas for artificial cultivation of Daphne giraldii and wild tending. The geographic information system(GIS) was applied to obtain the ecological factor information of 23 collection sites of Daphnes Cortex, and the soil factor information was determined by the standard procedure in the soil test standard manual. Combining the information of 93 chemical constituents of Daphnes Cortex in 23 collection sites the correlation between components and ecological factors and soil factors was analyzed by statistical methods. The correlation analysis showed that the longitude, annual average rainfall, annual sunshine intensity, annual average temperature in the ecological factors, soil type, effective copper and pH value were the dominant factors affecting the chemical composition of Daphnes Cortex.}, } @article {pmid32234481, year = {2020}, author = {Tournière, O and Dolan, D and Richards, GS and Sunagar, K and Columbus-Shenkar, YY and Moran, Y and Rentzsch, F}, title = {NvPOU4/Brain3 Functions as a Terminal Selector Gene in the Nervous System of the Cnidarian Nematostella vectensis.}, journal = {Cell reports}, volume = {30}, number = {13}, pages = {4473-4489.e5}, doi = {10.1016/j.celrep.2020.03.031}, pmid = {32234481}, issn = {2211-1247}, mesh = {Animals ; Blastula/metabolism ; Cell Differentiation/genetics ; Cell Proliferation/genetics ; Gene Expression Regulation, Developmental ; Genes, Reporter ; Glutamates/metabolism ; Green Fluorescent Proteins/metabolism ; Nervous System/*metabolism ; Neurons/metabolism ; Receptors, GABA-A/genetics/metabolism ; Sea Anemones/cytology/*genetics ; Transcription Factors/*genetics/metabolism ; Transcriptome/genetics ; Transgenes ; }, abstract = {Terminal selectors are transcription factors that control the morphological, physiological, and molecular features that characterize distinct cell types. Here, we show that, in the sea anemone Nematostella vectensis, NvPOU4 is expressed in post-mitotic cells that give rise to a diverse set of neural cell types, including cnidocytes and NvElav1-expressing neurons. Morphological analyses of NvPOU4 mutants crossed to transgenic reporter lines show that the loss of NvPOU4 does not affect the initial specification of neural cells. Transcriptomes derived from the mutants and from different neural cell populations reveal that NvPOU4 is required for the execution of the terminal differentiation program of these neural cells. These findings suggest that POU4 genes have ancient functions as terminal selectors for morphologically and functionally disparate types of neurons and they provide experimental support for the relevance of terminal selectors for understanding the evolution of cell types.}, } @article {pmid32231370, year = {2020}, author = {Numminen, E and Laine, AL}, title = {The spread of a wild plant pathogen is driven by the road network.}, journal = {PLoS computational biology}, volume = {16}, number = {3}, pages = {e1007703}, pmid = {32231370}, issn = {1553-7358}, mesh = {Ascomycota/*pathogenicity ; Computational Biology ; *Environmental Microbiology ; Geographic Information Systems ; *Models, Biological ; *Models, Statistical ; *Plant Diseases/microbiology/statistics & numerical data ; Transportation ; }, abstract = {Spatial analyses of pathogen occurrence in their natural surroundings entail unique opportunities for assessing in vivo drivers of disease epidemiology. Such studies are however confronted by the complexity of the landscape driving epidemic spread and disease persistence. Since relevant information on how the landscape influences epidemiological dynamics is rarely available, simple spatial models of spread are often used. In the current study we demonstrate both how more complex transmission pathways could be incorpoted to epidemiological analyses and how this can offer novel insights into understanding disease spread across the landscape. Our study is focused on Podosphaera plantaginis, a powdery mildew pathogen that transmits from one host plant to another by wind-dispersed spores. Its host populations often reside next to roads and thus we hypothesize that the road network influences the epidemiology of P. plantaginis. To analyse the impact of roads on the transmission dynamics, we consider a spatial dataset on the presence-absence records on the pathogen collected from a fragmented landscape of host populations. Using both mechanistic transmission modeling and statistical modeling with road-network summary statistics as predictors, we conclude the evident role of the road network in the progression of the epidemics: a phenomena which is manifested both in the enhanced transmission along the roads and in infections typically occurring at the central hub locations of the road network. We also demonstrate how the road network affects the spread of the pathogen using simulations. Jointly our results highlight how human alteration of natural landscapes may increase disease spread.}, } @article {pmid32230763, year = {2020}, author = {Luo, Z and Ma, J and Chen, F and Li, X and Zhang, Q and Yang, Y}, title = {Adaptive Development of Soil Bacterial Communities to Ecological Processes Caused by Mining Activities in the Loess Plateau, China.}, journal = {Microorganisms}, volume = {8}, number = {4}, pages = {}, pmid = {32230763}, issn = {2076-2607}, support = {51974313, 41907405//National Natural Science Foundation of China/ ; BK20180641//Natural Science Foundation of Jiangsu Province/ ; }, abstract = {Microorganisms are the driving force behind the circulation and transformation of the soil substance. The development of soil bacterial communities is critical for ecosystem restoration and evolution. In the Loess Plateau, coal mining activities have aggravated the deterioration of the fragile local ecological environment. The adaptive development of soil bacterial communities in response to different ecological processes caused by coal mining activities was explored through high-throughput sequencing technology and an ecological network analysis of the mining subsidence area of the Daliuta Coal Mine and vegetation rehabilitation area of the Heidaigou Coal Mine in the Loess Plateau. The results showed that while mining subsidence was inhibited, vegetation rehabilitation promoted the soil physicochemical properties. Soil organic matter, available phosphorus and available potassium in the subsidence area decreased significantly (P < 0.05), while soil organic matter, soil water, pH and EC in the vegetation rehabilitation area increased significantly (P < 0.05). The diversity index in the subsidence area decreased by about 20%, while that in the vegetation rehabilitation area increased by 63%. Mining subsidence and vegetation rehabilitation had a distinct influence on the molecular ecological networks of the soil bacteria, which tended to be more complex after the mining subsidence, and the number of connections in the network increased otherwise significantly enhanced interactive relationships. After the vegetation rehabilitation, the number of modules in the ecological network increased, but the contents of modules tended to be simpler. Soil bacterial communities adapted to the changes by changing the relationships between bacteria in response to different ecological processes. This study provides new insights into the monitoring and abatement of the damaged ecological environment in mines.}, } @article {pmid32229555, year = {2020}, author = {Salganik, MJ and Lundberg, I and Kindel, AT and Ahearn, CE and Al-Ghoneim, K and Almaatouq, A and Altschul, DM and Brand, JE and Carnegie, NB and Compton, RJ and Datta, D and Davidson, T and Filippova, A and Gilroy, C and Goode, BJ and Jahani, E and Kashyap, R and Kirchner, A and McKay, S and Morgan, AC and Pentland, A and Polimis, K and Raes, L and Rigobon, DE and Roberts, CV and Stanescu, DM and Suhara, Y and Usmani, A and Wang, EH and Adem, M and Alhajri, A and AlShebli, B and Amin, R and Amos, RB and Argyle, LP and Baer-Bositis, L and Büchi, M and Chung, BR and Eggert, W and Faletto, G and Fan, Z and Freese, J and Gadgil, T and Gagné, J and Gao, Y and Halpern-Manners, A and Hashim, SP and Hausen, S and He, G and Higuera, K and Hogan, B and Horwitz, IM and Hummel, LM and Jain, N and Jin, K and Jurgens, D and Kaminski, P and Karapetyan, A and Kim, EH and Leizman, B and Liu, N and Möser, M and Mack, AE and Mahajan, M and Mandell, N and Marahrens, H and Mercado-Garcia, D and Mocz, V and Mueller-Gastell, K and Musse, A and Niu, Q and Nowak, W and Omidvar, H and Or, A and Ouyang, K and Pinto, KM and Porter, E and Porter, KE and Qian, C and Rauf, T and Sargsyan, A and Schaffner, T and Schnabel, L and Schonfeld, B and Sender, B and Tang, JD and Tsurkov, E and van Loon, A and Varol, O and Wang, X and Wang, Z and Wang, J and Wang, F and Weissman, S and Whitaker, K and Wolters, MK and Woon, WL and Wu, J and Wu, C and Yang, K and Yin, J and Zhao, B and Zhu, C and Brooks-Gunn, J and Engelhardt, BE and Hardt, M and Knox, D and Levy, K and Narayanan, A and Stewart, BM and Watts, DJ and McLanahan, S}, title = {Measuring the predictability of life outcomes with a scientific mass collaboration.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {117}, number = {15}, pages = {8398-8403}, pmid = {32229555}, issn = {1091-6490}, support = {R25 HD074544/HD/NICHD NIH HHS/United States ; R01 HD039135/HD/NICHD NIH HHS/United States ; P2C HD042828/HD/NICHD NIH HHS/United States ; R24 HD047879/HD/NICHD NIH HHS/United States ; T32 HD007545/HD/NICHD NIH HHS/United States ; R01 HD036916/HD/NICHD NIH HHS/United States ; R01 HL133218/HL/NHLBI NIH HHS/United States ; R01 HD040421/HD/NICHD NIH HHS/United States ; P2C HD047879/HD/NICHD NIH HHS/United States ; MC_PC_17209/MRC_/Medical Research Council/United Kingdom ; P2C HD041022/HD/NICHD NIH HHS/United States ; R25 HD072818/HD/NICHD NIH HHS/United States ; }, mesh = {Adolescent ; Child ; Child, Preschool ; Cohort Studies ; Family ; Female ; Humans ; Infant ; Life ; Machine Learning ; Male ; Predictive Value of Tests ; Social Sciences/methods/*standards/statistics & numerical data ; }, abstract = {How predictable are life trajectories? We investigated this question with a scientific mass collaboration using the common task method; 160 teams built predictive models for six life outcomes using data from the Fragile Families and Child Wellbeing Study, a high-quality birth cohort study. Despite using a rich dataset and applying machine-learning methods optimized for prediction, the best predictions were not very accurate and were only slightly better than those from a simple benchmark model. Within each outcome, prediction error was strongly associated with the family being predicted and weakly associated with the technique used to generate the prediction. Overall, these results suggest practical limits to the predictability of life outcomes in some settings and illustrate the value of mass collaborations in the social sciences.}, } @article {pmid32228408, year = {2020}, author = {Valentini, G and Masuda, N and Shaffer, Z and Hanson, JR and Sasaki, T and Walker, SI and Pavlic, TP and Pratt, SC}, title = {Division of labour promotes the spread of information in colony emigrations by the ant Temnothorax rugatulus.}, journal = {Proceedings. Biological sciences}, volume = {287}, number = {1924}, pages = {20192950}, pmid = {32228408}, issn = {1471-2954}, mesh = {Animal Migration ; Animals ; Ants/*physiology ; *Behavior, Animal ; *Social Behavior ; }, abstract = {The fitness of group-living animals often depends on how well members share information needed for collective decision-making. Theoretical studies have shown that collective choices can emerge in a homogeneous group of individuals following identical rules, but real animals show much evidence for heterogeneity in the degree and nature of their contribution to group decisions. In social insects, for example, the transmission and processing of information is influenced by a well-organized division of labour. Studies that accurately quantify how this behavioural heterogeneity affects the spread of information among group members are still lacking. In this paper, we look at nest choices during colony emigrations of the ant Temnothorax rugatulus and quantify the degree of behavioural heterogeneity of workers. Using clustering methods and network analysis, we identify and characterize four behavioural castes of workers-primary, secondary, passive and wandering-covering distinct roles in the spread of information during an emigration. This detailed characterization of the contribution of each worker can improve models of collective decision-making in this species and promises a deeper understanding of behavioural variation at the colony level.}, } @article {pmid32228400, year = {2020}, author = {Adolf, C and Tovar, C and Kühn, N and Behling, H and Berrío, JC and Dominguez-Vázquez, G and Figueroa-Rangel, B and Gonzalez-Carranza, Z and Islebe, GA and Hooghiemstra, H and Neff, H and Olvera-Vargas, M and Whitney, B and Wooller, MJ and Willis, KJ}, title = {Identifying drivers of forest resilience in long-term records from the Neotropics.}, journal = {Biology letters}, volume = {16}, number = {4}, pages = {20200005}, pmid = {32228400}, issn = {1744-957X}, mesh = {Biodiversity ; *Ecosystem ; *Forests ; Mexico ; South America ; Trees ; }, abstract = {Here, we use 30 long-term, high-resolution palaeoecological records from Mexico, Central and South America to address two hypotheses regarding possible drivers of resilience in tropical forests as measured in terms of recovery rates from previous disturbances. First, we hypothesize that faster recovery rates are associated with regions of higher biodiversity, as suggested by the insurance hypothesis. And second, that resilience is due to intrinsic abiotic factors that are location specific, thus regions presently displaying resilience in terms of persistence to current climatic disturbances should also show higher recovery rates in the past. To test these hypotheses, we applied a threshold approach to identify past disturbances to forests within each sequence. We then compared the recovery rates to these events with pollen richness before the event. We also compared recovery rates of each site with a measure of present resilience in the region as demonstrated by measuring global vegetation persistence to climatic perturbations using satellite imagery. Preliminary results indeed show a positive relationship between pre-disturbance taxonomic richness and faster recovery rates. However, there is less evidence to support the concept that resilience is intrinsic to a region; patterns of resilience apparent in ecosystems presently are not necessarily conservative through time.}, } @article {pmid32226594, year = {2020}, author = {Afantitis, A and Melagraki, G and Isigonis, P and Tsoumanis, A and Varsou, DD and Valsami-Jones, E and Papadiamantis, A and Ellis, LA and Sarimveis, H and Doganis, P and Karatzas, P and Tsiros, P and Liampa, I and Lobaskin, V and Greco, D and Serra, A and Kinaret, PAS and Saarimäki, LA and Grafström, R and Kohonen, P and Nymark, P and Willighagen, E and Puzyn, T and Rybinska-Fryca, A and Lyubartsev, A and Alstrup Jensen, K and Brandenburg, JG and Lofts, S and Svendsen, C and Harrison, S and Maier, D and Tamm, K and Jänes, J and Sikk, L and Dusinska, M and Longhin, E and Rundén-Pran, E and Mariussen, E and El Yamani, N and Unger, W and Radnik, J and Tropsha, A and Cohen, Y and Leszczynski, J and Ogilvie Hendren, C and Wiesner, M and Winkler, D and Suzuki, N and Yoon, TH and Choi, JS and Sanabria, N and Gulumian, M and Lynch, I}, title = {NanoSolveIT Project: Driving nanoinformatics research to develop innovative and integrated tools for in silico nanosafety assessment.}, journal = {Computational and structural biotechnology journal}, volume = {18}, number = {}, pages = {583-602}, pmid = {32226594}, issn = {2001-0370}, abstract = {Nanotechnology has enabled the discovery of a multitude of novel materials exhibiting unique physicochemical (PChem) properties compared to their bulk analogues. These properties have led to a rapidly increasing range of commercial applications; this, however, may come at a cost, if an association to long-term health and environmental risks is discovered or even just perceived. Many nanomaterials (NMs) have not yet had their potential adverse biological effects fully assessed, due to costs and time constraints associated with the experimental assessment, frequently involving animals. Here, the available NM libraries are analyzed for their suitability for integration with novel nanoinformatics approaches and for the development of NM specific Integrated Approaches to Testing and Assessment (IATA) for human and environmental risk assessment, all within the NanoSolveIT cloud-platform. These established and well-characterized NM libraries (e.g. NanoMILE, NanoSolutions, NANoREG, NanoFASE, caLIBRAte, NanoTEST and the Nanomaterial Registry (>2000 NMs)) contain physicochemical characterization data as well as data for several relevant biological endpoints, assessed in part using harmonized Organisation for Economic Co-operation and Development (OECD) methods and test guidelines. Integration of such extensive NM information sources with the latest nanoinformatics methods will allow NanoSolveIT to model the relationships between NM structure (morphology), properties and their adverse effects and to predict the effects of other NMs for which less data is available. The project specifically addresses the needs of regulatory agencies and industry to effectively and rapidly evaluate the exposure, NM hazard and risk from nanomaterials and nano-enabled products, enabling implementation of computational 'safe-by-design' approaches to facilitate NM commercialization.}, } @article {pmid32225388, year = {2020}, author = {Wang, Y and Dai, J and Liao, R and Zhou, J and Meng, F and Yao, Y and Chen, H and Tao, Y and Ma, H}, title = {Characterization of physiological states of the suspended marine microalgae using polarized light scattering.}, journal = {Applied optics}, volume = {59}, number = {5}, pages = {1307-1312}, doi = {10.1364/AO.377332}, pmid = {32225388}, issn = {1539-4522}, mesh = {Cell Culture Techniques ; Computer Simulation ; Image Interpretation, Computer-Assisted ; Light ; Microalgae/*physiology ; Microscopy, Polarization/*instrumentation/*methods ; Microspheres ; Models, Biological ; Refractometry ; *Scattering, Radiation ; Seawater ; }, abstract = {Physiological states of marine microalgal cells can influence photosynthesis efficiency, which affects approximately half of global carbon fixation. The detection of the algae physiological profiles is important for marine ecology and economy. In this paper, we propose a polarized light-scattering method to detect sensitive changes in the physiological states of the suspended marine microalgal cells. Our experimental setup is designed to measure the scattered polarization parameters of the cells suspended individually in the seawater. Two species of microalgal cells cultured in the laboratory were measured for several days. Experimental results showed that both species display distinctive changes in their polarized photon scattering features corresponding to changes in their physiological states. The changes are far more prominent than those displayed in unpolarized light scattering. Microscopy observations, simulations for microspheres of different diameters and refractive indices, or different shapes, indicated that the polarization features of the scattered photons are sensitive to the submicrometer microstructures of the cells. This study demonstrates the potential of the polarized light-scattering technique to characterize the physiological states of suspended marine microalgae.}, } @article {pmid32224897, year = {2020}, author = {Novotný, J and Bandúrová, V and Strnad, H and Chovanec, M and Hradilová, M and Šáchová, J and Šteffl, M and Grušanović, J and Kodet, R and Pačes, V and Lacina, L and Smetana, K and Plzák, J and Kolář, M and Vomastek, T}, title = {Analysis of HPV-Positive and HPV-Negative Head and Neck Squamous Cell Carcinomas and Paired Normal Mucosae Reveals Cyclin D1 Deregulation and Compensatory Effect of Cyclin D2.}, journal = {Cancers}, volume = {12}, number = {4}, pages = {}, pmid = {32224897}, issn = {2072-6694}, support = {16-29032A//Agentura Pro Zdravotnický Výzkum České Republiky/International ; 18-11908S//Grantová Agentura České Republiky/International ; Operational Programme Research, Development and Education under the project "Center for Tumor Ecology - Research of the Cancer Microenvironment Supporting Cancer Growth and Spread" (reg. No. CZ.02.1.01/0.0/0.0/16_019/0000785)//Ministerstvo Školství, Mládeže a Tělovýchovy/International ; Research and Development for Innovations Operational Program under project no. CZ.1.05/2.1.00/19.0400//Ministerstvo Školství, Mládeže a Tělovýchovy/International ; }, abstract = {Aberrant regulation of the cell cycle is a typical feature of all forms of cancer. In head and neck squamous cell carcinoma (HNSCC), it is often associated with the overexpression of cyclin D1 (CCND1). However, it remains unclear how CCND1 expression changes between tumor and normal tissues and whether human papillomavirus (HPV) affects differential CCND1 expression. Here, we evaluated the expression of D-type cyclins in a cohort of 94 HNSCC patients of which 82 were subjected to whole genome expression profiling of primary tumors and paired normal mucosa. Comparative analysis of paired samples showed that CCND1 was upregulated in 18% of HNSCC tumors. Counterintuitively, CCND1 was downregulated in 23% of carcinomas, more frequently in HPV-positive samples. There was no correlation between the change in D-type cyclin expression and patient survival. Intriguingly, among the tumors with downregulated CCND1, one-third showed an increase in cyclin D2 (CCND2) expression. On the other hand, one-third of tumors with upregulated CCND1 showed a decrease in CCND2. Collectively, we have shown that CCND1 was frequently downregulated in HNSCC tumors. Furthermore, regardless of the HPV status, our data suggested that a change in CCND1 expression was alleviated by a compensatory change in CCND2 expression.}, } @article {pmid32220321, year = {2020}, author = {Blumstein, M and Richardson, A and Weston, D and Zhang, J and Muchero, W and Hopkins, R}, title = {A New Perspective on Ecological Prediction Reveals Limits to Climate Adaptation in a Temperate Tree Species.}, journal = {Current biology : CB}, volume = {30}, number = {8}, pages = {1447-1453.e4}, doi = {10.1016/j.cub.2020.02.001}, pmid = {32220321}, issn = {1879-0445}, mesh = {*Acclimatization ; British Columbia ; *Carbohydrate Metabolism ; *Climate Change ; Forests ; Oregon ; Populus/*physiology ; Washington ; }, abstract = {Forests absorb a large fraction of anthropogenic CO2 emission, but their ability to continue to act as a sink under climate change depends in part on plant species undergoing rapid adaptation. Yet models of forest response to climate change currently ignore local adaptation as a response mechanism. Thus, considering the evolution of intraspecific trait variation is necessary for reliable, long-term species and climate projections. Here, we combine ecophysiology and predictive climate modeling with analyses of genomic variation to determine whether sugar and starch storage, energy reserves for trees under extreme conditions, have the heritable variation and genetic diversity necessary to evolve in response to climate change within populations of black cottonwood (Populus trichocarpa). Despite current patterns of local adaptation and extensive range-wide heritable variation in storage, we demonstrate that adaptive evolution in response to climate change will be limited by a lack of heritable variation within northern populations and by a need for extreme genetic changes in southern populations. Our method can help design more targeted species management interventions and highlights the power of using genomic tools in ecological prediction to scale from molecular to regional processes to determine the ability of a species to respond to future climates.}, } @article {pmid32219413, year = {2020}, author = {Zhou, N and Bao, J}, title = {FerrDb: a manually curated resource for regulators and markers of ferroptosis and ferroptosis-disease associations.}, journal = {Database : the journal of biological databases and curation}, volume = {2020}, number = {}, pages = {}, pmid = {32219413}, issn = {1758-0463}, mesh = {Apoptosis/genetics ; Biomarkers/*metabolism ; Data Curation/methods ; Data Mining/methods ; *Databases, Factual ; Ferroptosis/*genetics ; *Gene Regulatory Networks ; Genetic Predisposition to Disease/*genetics ; Humans ; Internet ; Iron/metabolism ; Molecular Sequence Annotation/methods ; Neoplasms/genetics/metabolism ; Reactive Oxygen Species/metabolism ; }, abstract = {Ferroptosis is a mode of regulated cell death that depends on iron. Cells die from the toxic accumulation of lipid reactive oxygen species. Ferroptosis is tightly linked to a variety of human diseases, such as cancers and degenerative diseases. The ferroptotic process is complicated and consists of a wide range of metabolites and biomolecules. Although great progress has been achieved, the mechanism of ferroptosis remains enigmatic. We have currently entered an era of extensive knowledge advancement, and thus, it is important to find ways to organize and utilize data efficiently. We have observed a high-quality knowledge base of ferroptosis research is lacking. In this study, we downloaded 784 ferroptosis articles from the PubMed database. Ferroptosis regulators and markers and associated diseases were extracted from these articles and annotated. In summary, 253 regulators (including 108 drivers, 69 suppressors, 35 inducers and 41 inhibitors), 111 markers and 95 ferroptosis-disease associations were found. We then developed FerrDb, the first manually curated database for regulators and markers of ferroptosis and ferroptosis-disease associations. The database has a user-friendly interface, and it will be updated every 6 months to offer long-term service. FerrDb is expected to help researchers acquire insights into ferroptosis. Database URL: http://www.zhounan.org/ferrdb.}, } @article {pmid32219306, year = {2021}, author = {Hu, G and Grover, CE and Arick, MA and Liu, M and Peterson, DG and Wendel, JF}, title = {Homoeologous gene expression and co-expression network analyses and evolutionary inference in allopolyploids.}, journal = {Briefings in bioinformatics}, volume = {22}, number = {2}, pages = {1819-1835}, pmid = {32219306}, issn = {1477-4054}, mesh = {Datasets as Topic ; *Evolution, Molecular ; *Gene Expression Regulation, Plant ; Genes, Plant ; Gossypium/genetics ; *Polyploidy ; RNA, Messenger/genetics ; Sequence Analysis, RNA/methods ; }, abstract = {Polyploidy is a widespread phenomenon throughout eukaryotes. Due to the coexistence of duplicated genomes, polyploids offer unique challenges for estimating gene expression levels, which is essential for understanding the massive and various forms of transcriptomic responses accompanying polyploidy. Although previous studies have explored the bioinformatics of polyploid transcriptomic profiling, the causes and consequences of inaccurate quantification of transcripts from duplicated gene copies have not been addressed. Using transcriptomic data from the cotton genus (Gossypium) as an example, we present an analytical workflow to evaluate a variety of bioinformatic method choices at different stages of RNA-seq analysis, from homoeolog expression quantification to downstream analysis used to infer key phenomena of polyploid expression evolution. In general, EAGLE-RC and GSNAP-PolyCat outperform other quantification pipelines tested, and their derived expression dataset best represents the expected homoeolog expression and co-expression divergence. The performance of co-expression network analysis was less affected by homoeolog quantification than by network construction methods, where weighted networks outperformed binary networks. By examining the extent and consequences of homoeolog read ambiguity, we illuminate the potential artifacts that may affect our understanding of duplicate gene expression, including an overestimation of homoeolog co-regulation and the incorrect inference of subgenome asymmetry in network topology. Taken together, our work points to a set of reasonable practices that we hope are broadly applicable to the evolutionary exploration of polyploids.}, } @article {pmid32219167, year = {2020}, author = {Heckwolf, MJ and Meyer, BS and Häsler, R and Höppner, MP and Eizaguirre, C and Reusch, TBH}, title = {Two different epigenetic information channels in wild three-spined sticklebacks are involved in salinity adaptation.}, journal = {Science advances}, volume = {6}, number = {12}, pages = {eaaz1138}, pmid = {32219167}, issn = {2375-2548}, mesh = {*Acclimatization ; *Adaptation, Biological ; Animals ; Computational Biology/methods ; CpG Islands ; DNA Methylation ; *Epigenesis, Genetic ; Epigenomics/methods ; Gene Expression Regulation ; Gene Ontology ; Genome ; Genomics/methods ; *Salinity ; Smegmamorpha/*physiology ; }, abstract = {Epigenetic inheritance has been proposed to contribute to adaptation and acclimation via two information channels: (i) inducible epigenetic marks that enable transgenerational plasticity and (ii) noninducible epigenetic marks resulting from random epimutations shaped by selection. We studied both postulated channels by sequencing methylomes and genomes of Baltic three-spined sticklebacks (Gasterosteus aculeatus) along a salinity cline. Wild populations differing in salinity tolerance revealed differential methylation (pop-DMS) at genes enriched for osmoregulatory processes. A two-generation experiment demonstrated that 62% of these pop-DMS were noninducible by salinity manipulation, suggesting that they are the result of either direct selection or associated genomic divergence at cis- or trans-regulatory sites. Two-thirds of the remaining inducible pop-DMS increased in similarity to patterns detected in wild populations from corresponding salinities. The level of similarity accentuated over consecutive generations, indicating a mechanism of transgenerational plasticity. While we can attribute natural DNA methylation patterns to the two information channels, their interplay with genomic variation in salinity adaptation is still unresolved.}, } @article {pmid32218481, year = {2020}, author = {Jasinski, SE and Sullivan, RM and Dodson, P}, title = {New Dromaeosaurid Dinosaur (Theropoda, Dromaeosauridae) from New Mexico and Biodiversity of Dromaeosaurids at the end of the Cretaceous.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {5105}, pmid = {32218481}, issn = {2045-2322}, mesh = {Animals ; Behavior, Animal ; Biodiversity ; Biological Evolution ; Datasets as Topic ; *Dinosaurs/anatomy & histology/classification ; Feathers ; Fossils ; New Mexico ; Phylogeny ; }, abstract = {Dromaeosaurids (Theropoda: Dromaeosauridae), a group of dynamic, swift predators, have a sparse fossil record, particularly at the time of their extinction near the Cretaceous-Paleogene boundary. Here we report on a new dromaeosaurid, Dineobellator notohesperus, gen. and sp. nov., consisting of a partial skeleton from the Upper Cretaceous (Maastrichtian) of New Mexico, the first diagnostic dromaeosaurid to be recovered from the latest Cretaceous of the southern United States (southern Laramidia). The holotype includes elements of the skull, axial, and appendicular skeleton. The specimen reveals a host of morphologies that shed light on new behavioral attributes for these feathered dinosaurs. Unique features on its forelimbs suggest greater strength capabilities in flexion than the normal dromaeosaurid condition, in conjunction with a relatively tighter grip strength in the manual claws. Aspects of the caudal vertebrae suggest greater movement near the tail base, aiding in agility and predation. Phylogenetic analysis places Dineobellator within Velociraptorinae. Its phylogenetic position, along with that of other Maastrichtian taxa (Acheroraptor and Dakotaraptor), suggests dromaeosaurids were still diversifying at the end of the Cretaceous. Furthermore, its recovery as a second North American Maastrichtian velociraptorine suggests vicariance of North American velociraptorines after a dispersal event during the Campanian-Maastrichtian from Asia. Features of Dineobellator also imply that dromaeosaurids were active predators that occupied discrete ecological niches while living in the shadow of Tyrannosaurus rex, until the end of the dinosaurs' reign.}, } @article {pmid32216553, year = {2020}, author = {Busse, H and Covic, N and Aakesson, A and Jogo, W}, title = {What Is the Role of Civil Society in Multisectoral Nutrition Governance Systems? A Multicountry Review.}, journal = {Food and nutrition bulletin}, volume = {41}, number = {2}, pages = {244-260}, doi = {10.1177/0379572119877348}, pmid = {32216553}, issn = {1564-8265}, mesh = {*Community Networks ; Developing Countries ; Humans ; Malnutrition/*prevention & control ; *Nutritional Status ; *Public-Private Sector Partnerships ; }, abstract = {BACKGROUND: Solutions to create enabling nutrition environments must come from within communities and involve multiple sectors. As vital actors in community mobilization, rights-based advocacy, and accountable public institutions, civil society organizations (CSOs) can help ensure nutrition programs and policies represent and reach all community members to achieve impact.

OBJECTIVES: To review attributes of civic engagement in multisectoral nutrition governance systems and to provide recommendations to increase CSO participation.

METHODS: We reviewed 7 national case studies of Civil Society Networks involved with the Scaling Up Nutrition movement and characterized 6 functional attributes of CSOs in multisectoral nutrition governance: identify needs of all community members, mobilize and build civic capacity, advocate for political commitments, inform program design and evaluation, ensure accountability mechanisms in public institutions, and report challenges and successes using broad media campaigns.

RESULTS: All studies described government agencies involved with multisectoral nutrition governance systems, at national and subnational levels; however, there was limited evidence of subnational platforms for CSO engagement. Although countries increased investments in public institutions for nutrition, it was unclear whether nutrition service quality improved and none reported corresponding investments in civil society.

CONCLUSION: Our characterization identifies strategies to engage CSOs in multisectoral nutrition governance at multiple ecological levels. We hope future adaptation and application of this characterization will increase community ownership and diverse representation in nutrition governance systems. Both of these are key to enabling national and international entities to address malnutrition's underlying determinants in ways that align with local contexts, values, and systems change processes.}, } @article {pmid32214353, year = {2020}, author = {Sumner-Kalkun, JC and Sjölund, MJ and Arnsdorf, YM and Carnegie, M and Highet, F and Ouvrard, D and Greenslade, AFC and Bell, JR and Sigvald, R and Kenyon, DM}, title = {A diagnostic real-time PCR assay for the rapid identification of the tomato-potato psyllid, Bactericera cockerelli (Šulc, 1909) and development of a psyllid barcoding database.}, journal = {PloS one}, volume = {15}, number = {3}, pages = {e0230741}, pmid = {32214353}, issn = {1932-6203}, support = {BBS/E/C/000J0200/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; Computational Biology ; *DNA Barcoding, Taxonomic ; *Databases, Genetic ; Hemiptera/*classification/*genetics/physiology ; *Solanum lycopersicum ; Real-Time Polymerase Chain Reaction/*methods ; Sequence Analysis, DNA ; Time Factors ; }, abstract = {The accurate and rapid identification of insect pests is an important step in the prevention and control of outbreaks in areas that are otherwise pest free. The potato-tomato psyllid Bactericera cockerelli (Šulc, 1909) is the main vector of 'Candidatus Liberibacter solanacearum' on potato and tomato crops in North America and New Zealand; and is considered a threat for introduction in Europe and other pest-free regions. This study describes the design and validation of the first species-specific TaqMan probe-based real-time PCR assay, targeting the ITS2 gene region of B. cockerelli. The assay detected B. cockerelli genomic DNA from adults, immatures, and eggs, with 100% accuracy. This assay also detected DNA from cloned plasmids containing the ITS2 region of B. cockerelli with 100% accuracy. The assay showed 0% false positives when tested on genomic and cloned DNA from 73 other psyllid species collected from across Europe, New Zealand, Mexico and the USA. This included 8 other species in the Bactericera genus and the main vectors of 'Candidatus Liberibacter solanacearum' worldwide. The limit of detection for this assay at optimum conditions was 0.000001ng DNA (~200 copies) of ITS2 DNA which equates to around a 1:10000 dilution of DNA from one single adult specimen. This assay is the first real-time PCR based method for accurate, robust, sensitive and specific identification of B. cockerelli from all life stages. It can be used as a surveillance and monitoring tool to further study this important crop pest and to aid the prevention of outbreaks, or to prevent their spread after establishment in new areas.}, } @article {pmid32213967, year = {2020}, author = {Zhu, C and Zhang, Z and Wang, H and Wang, J and Yang, S}, title = {Assessing Soil Organic Matter Content in a Coal Mining Area through Spectral Variables of Different Numbers of Dimensions.}, journal = {Sensors (Basel, Switzerland)}, volume = {20}, number = {6}, pages = {}, pmid = {32213967}, issn = {1424-8220}, support = {41861037//National Natural Science Foundation of China/ ; U1603241//National Natural Science Foundation of China/ ; }, abstract = {Soil organic matter (SOM) is a crucial indicator for evaluating soil quality and an important component of soil carbon pools, which play a vital role in terrestrial ecosystems. Rapid, non-destructive and accurate monitoring of SOM content is of great significance for the environmental management and ecological restoration of mining areas. Visible-near-infrared (Vis-NIR) spectroscopy has proven its applicability in estimating SOM over the years. In this study, 168 soil samples were collected from the Zhundong coal field of Xinjiang Province, Northwest China. The SOM content (g kg[-1]) was determined by the potassium dichromate external heating method and the soil reflectance spectra were measured by the spectrometer. Two spectral feature extraction strategies, namely, principal component analysis (PCA) and the optimal band combination algorithm, were introduced to choose spectral variables. Linear models and random forests (RF) were used for predictive models. The coefficient of determination (R[2]), root mean square error (RMSE), and the ratio of the performance to the interquartile distance (RPIQ) were used to evaluate the predictive performance of the model. The results indicated that the variables (2DI and 3DI) derived from the optimal band combination algorithm outperformed the PCA variables (1DV) regardless of whether linear or RF models were used. An inherent gap exists between 2DI and 3DI, and the performance of 2DI is significantly poorer than that of 3DI. The accuracy of the prediction model increases with the increasing number of spectral variable dimensions (in the following order: 1DV < 2DI < 3DI). This study proves that the 3DI is the first choice for the optimal band combination algorithm to derive sensitive parameters related to SOM in the coal mining area. Furthermore, the optimal band combination algorithm can be applied to hyperspectral or multispectral images and to convert the spectral response into image pixels, which may be helpful for a soil property spatial distribution map.}, } @article {pmid32213848, year = {2020}, author = {Martinelli, LA and Nardoto, GB and Perez, MAZ and Junior, GA and Fracassi, FC and Oliveira, JGG and Ottani, IS and Lima, SH and Mazzi, EA and Gomes, TF and Soltangheisi, A and Filho, ALA and Mariano, E and Costa, FJV and Duarte-Neto, PJ and Moreira, MZ and Camargo, PB}, title = {Carbon and Nitrogen Isotope Ratios of Food and Beverage in Brazil.}, journal = {Molecules (Basel, Switzerland)}, volume = {25}, number = {6}, pages = {}, pmid = {32213848}, issn = {1420-3049}, support = {2011/50345-9//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; }, mesh = {Animals ; Beverages/analysis ; Brazil ; Carbon Isotopes/*analysis ; Cattle ; Dairy Products/analysis ; Nitrogen Isotopes/*analysis ; Poultry ; Sheep ; Wine/analysis ; }, abstract = {Several previous studies on targeted food items using carbon and nitrogen stable isotope ratios in Brazil have revealed that many of the items investigated are adulterated; mislabeled or even fraud. Here, we present the first Brazilian isotopic baseline assessment that can be used not only in future forensic cases involving food authenticity, but also in human forensic anthropology studies. The δ[13]C and δ[15]N were determined in 1245 food items and 374 beverages; most of them made in Brazil. The average δ[13]C and δ[15]N of C3 plants were -26.7 ± 1.5‱, and 3.9 ± 3.9‱, respectively, while the average δ[13]C and δ[15]N of C4 plants were -11.5 ± 0.8‱ and 4.6 ± 2.6‱, respectively. The δ[13]C and δ[15]N of plant-based processed foods were -21.8 ± 4.8‱ and 3.9 ± 2.7‱, respectively. The average δ[13]C and δ[15]N of meat, including beef, poultry, pork and lamb were -16.6 ± 4.7‱, and 5.2 ± 2.6‱, respectively, while the δ[13]C and δ[15]N of animal-based processed foods were -17.9 ± 3.3‱ and 3.3 ± 3.5‱, respectively. The average δ[13]C of beverages, including beer and wine was -22.5 ± 3.1‱. We verified that C-C4 constitutes a large proportion of fresh meat, dairy products, as well as animal and plant-based processed foods. The reasons behind this high proportion will be addressed in this study.}, } @article {pmid32213522, year = {2020}, author = {Mandic, S and Hopkins, D and García Bengoechea, E and Moore, A and Sandretto, S and Coppell, K and Ergler, C and Keall, M and Rolleston, A and Kidd, G and Wilson, G and Spence, JC}, title = {Built environment changes and active transport to school among adolescents: BEATS Natural Experiment Study protocol.}, journal = {BMJ open}, volume = {10}, number = {3}, pages = {e034899}, pmid = {32213522}, issn = {2044-6055}, mesh = {Adolescent ; Bicycling/physiology ; Body Weights and Measures ; Built Environment/*statistics & numerical data ; Exercise/*physiology ; Female ; Geographic Information Systems ; Health Behavior ; Humans ; Interinstitutional Relations ; Male ; New Zealand ; *Research Design ; Residence Characteristics ; Safety ; Schools/statistics & numerical data ; Social Support ; Socioeconomic Factors ; Transportation/*methods ; Walking/physiology ; }, abstract = {INTRODUCTION: Natural experiments are considered a priority for examining causal associations between the built environment (BE) and physical activity (PA) because the randomised controlled trial design is rarely feasible. Few natural experiments have examined the effects of walking and cycling infrastructure on PA and active transport in adults, and none have examined the effects of such changes on PA and active transport to school among adolescents. We conducted the Built Environment and Active Transport to School (BEATS) Study in Dunedin city, New Zealand, in 2014-2017. Since 2014, on-road and off-road cycling infrastructure construction has occurred in some Dunedin neighbourhoods, including the neighbourhoods of 6 out of 12 secondary schools. Pedestrian-related infrastructure changes began in 2018. As an extension of the BEATS Study, the BEATS Natural Experiment (BEATS-NE) (2019-2022) will examine the effects of BE changes on adolescents' active transport to school in Dunedin, New Zealand.

METHODS AND ANALYSIS: The BEATS-NE Study will employ contemporary ecological models for active transport that account for individual, social, environmental and policy factors. The published BEATS Study methodology (surveys, accelerometers, mapping, Geographic Information Science analysis and focus groups) and novel methods (environmental scan of school neighbourhoods and participatory mapping) will be used. A core component continues to be the community-based participatory approach with the sustained involvement of key stakeholders to generate locally relevant data, and facilitate knowledge translation into evidence-based policy and planning.

ETHICS AND DISSEMINATION: The BEATS-NE Study has been approved by the University of Otago Ethics Committee (reference: 17/188). The results will be disseminated through scientific publications and symposia, and reports and presentations to stakeholders.

TRIAL REGISTRATION NUMBER: ACTRN12619001335189.}, } @article {pmid32210424, year = {2020}, author = {Ullah, K and Zhang, J}, title = {GIS-based flood hazard mapping using relative frequency ratio method: A case study of Panjkora River Basin, eastern Hindu Kush, Pakistan.}, journal = {PloS one}, volume = {15}, number = {3}, pages = {e0229153}, pmid = {32210424}, issn = {1932-6203}, mesh = {Disaster Planning/methods ; Disasters/prevention & control/*statistics & numerical data ; Environmental Monitoring/*methods ; Floods/prevention & control/*statistics & numerical data ; *Geographic Information Systems ; Humans ; Incidence ; Models, Statistical ; Pakistan ; *Rivers ; }, abstract = {Flood is the most devastating and prevalent disaster among all-natural disasters. Every year, flood claims hundreds of human lives and causes damage to the worldwide economy and environment. Consequently, the identification of flood-vulnerable areas is important for comprehensive flood risk management. The main objective of this study is to delineate flood-prone areas in the Panjkora River Basin (PRB), eastern Hindu Kush, Pakistan. An initial extensive field survey and interpretation of Landsat-7 and Google Earth images identified 154 flood locations that were inundated in 2010 floods. Of the total, 70% of flood locations were randomly used for building a model and 30% were used for validation of the model. Eight flood parameters including slope, elevation, land use, Normalized Difference Vegetation Index (NDVI), topographic wetness index (TWI), drainage density, and rainfall were used to map the flood-prone areas in the study region. The relative frequency ratio was used to determine the correlation between each class of flood parameter and flood occurrences. All of the factors were resampled into a pixel size of 30×30 m and were reclassified through the natural break method. Finally, a final hazard map was prepared and reclassified into five classes, i.e., very low, low, moderate, high, very high susceptibility. The results of the model were found reliable with area under curve values for success and prediction rate of 82.04% and 84.74%, respectively. The findings of this study can play a key role in flood hazard management in the target region; they can be used by the local disaster management authority, researchers, planners, local government, and line agencies dealing with flood risk management.}, } @article {pmid32210056, year = {2020}, author = {Shikov, AE and Malovichko, YV and Skitchenko, RK and Nizhnikov, AA and Antonets, KS}, title = {No More Tears: Mining Sequencing Data for Novel Bt Cry Toxins with CryProcessor.}, journal = {Toxins}, volume = {12}, number = {3}, pages = {}, pmid = {32210056}, issn = {2072-6651}, support = {18-76-00028//Russian Science Foundation/International ; }, mesh = {Algorithms ; Amino Acid Sequence ; Animals ; Bacillus thuringiensis/*metabolism ; Bacillus thuringiensis Toxins/biosynthesis/*chemistry ; Benchmarking ; Biological Control Agents/*chemistry ; Data Mining/*methods ; Endotoxins/biosynthesis/*chemistry ; Hemolysin Proteins/biosynthesis/*chemistry ; Insecta/drug effects ; Markov Chains ; *Pest Control, Biological ; }, abstract = {Bacillus thuringiensis (Bt) is a natural pathogen of insects and some other groups of invertebrates that produces three-domain Cry (3d-Cry) toxins, which are highly host-specific pesticidal proteins. These proteins represent the most commonly used bioinsecticides in the world and are used for commercial purposes on the market of insecticides, being convergent with the paradigm of sustainable growth and ecological development. Emerging resistance to known toxins in pests stresses the need to expand the list of known toxins to broaden the horizons of insecticidal approaches. For this purpose, we have elaborated a fast and user-friendly tool called CryProcessor, which allows productive and precise mining of 3d-Cry toxins. The only existing tool for mining Cry toxins, called a BtToxin_scanner, has significant limitations such as limited query size, lack of accuracy and an outdated database. In order to find a proper solution to these problems, we have developed a robust pipeline, capable of precise 3d-Cry toxin mining. The unique feature of the pipeline is the ability to search for Cry toxins sequences directly on assembly graphs, providing an opportunity to analyze raw sequencing data and overcoming the problem of fragmented assemblies. Moreover, CryProcessor is able to predict precisely the domain layout in arbitrary sequences, allowing the retrieval of sequences of definite domains beyond the bounds of a limited number of toxins presented in CryGetter. Our algorithm has shown efficiency in all its work modes and outperformed its analogues on large amounts of data. Here, we describe its main features and provide information on its benchmarking against existing analogues. CryProcessor is a novel, fast, convenient, open source (https://github.com/lab7arriam/cry_processor), platform-independent, and precise instrument with a console version and elaborated web interface (https://lab7.arriam.ru/tools/cry_processor). Its major merits could make it possible to carry out massive screening for novel 3d-Cry toxins and obtain sequences of specific domains for further comprehensive in silico experiments in constructing artificial toxins.}, } @article {pmid32209348, year = {2020}, author = {Frątczak, M and Vargová, B and Tryjanowski, P and Majláth, I and Jerzak, L and Kurimský, J and Cimbala, R and Jankowiak, Ł and Conka, Z and Majláthová, V}, title = {Infected Ixodes ricinus ticks are attracted by electromagnetic radiation of 900 MHz.}, journal = {Ticks and tick-borne diseases}, volume = {11}, number = {4}, pages = {101416}, doi = {10.1016/j.ttbdis.2020.101416}, pmid = {32209348}, issn = {1877-9603}, mesh = {Animals ; Borrelia burgdorferi Group/*physiology ; *Electromagnetic Fields ; *Electromagnetic Radiation ; Female ; Ixodes/microbiology/physiology/*radiation effects ; Male ; Rickettsia/*physiology ; Taxis Response ; }, abstract = {The electromagnetic field (EMF) is known to influence functions of the nervous, cardiovascular and reproductive systems of many animals, including ticks. The aim of this study was to test the behavior of ticks in the presence of radio-frequency EMF. For testing, 160 adult male and 140 adult female unfed Ixodes ricinus ticks were used. Individuals were exposed to 900 MHz EMF in the Radiation-Shielded Tube (RST). Ticks were attracted to the irradiated area. This effect was significantly stronger for ticks infected with Rickettsia spp., suggesting that pathogens can alter the ticks' response to environmental stimuli. These results lead to the question of whether man-made EMF may have an impact on I. ricinus activity and, as such, be a contributing factor to the ongoing changes in the distribution of the tick and its pathogens currently observed in Europe and elsewhere.}, } @article {pmid32208464, year = {2020}, author = {Ilić Živojinović, J and Backović, D and Belojević, G and Valčić, O and Soldatović, I and Janković, J}, title = {Predictors of burnout among Belgrade veterinary students: A cross-sectional study.}, journal = {PloS one}, volume = {15}, number = {3}, pages = {e0230685}, pmid = {32208464}, issn = {1932-6203}, mesh = {Adult ; *Burnout, Psychological ; Cross-Sectional Studies ; Depersonalization ; Education, Veterinary ; Emotions ; Female ; Health Status ; Humans ; Male ; Odds Ratio ; Personal Satisfaction ; Smoking ; Students, Medical/*psychology ; Surveys and Questionnaires ; Young Adult ; }, abstract = {BACKGROUND: To the best of our knowledge, studies are lacking on burnout among veterinary students in Serbia, and this is the first study trying to address such a problem. Therefore, the aim of this cross-sectional study was to investigate the predictors of burnout among Belgrade veterinary students.

METHODS: Maslach Burnout Inventory (MBI) and anonymous structured questionnaire addressed to personal data, health habits and stressful influence of educational process were applied among 496 respondents from a total of 1113 students from all grades in spring semester 2014 (response rate 44.6%).

RESULTS: The prevalence of burnout was 43.3%. High scores on depersonalization and emotional exhaustion scales of MBI were found among 79.4% and 45.0% students, respectively; low personal accomplishment was reported by 50.5% students. Female students reported higher levels of emotional exhaustion compared to males (p = 0.012). A low score on personal achievement scale of MBI was least frequent among the freshmen and most frequent among sophomores (41.1% and 65.3%, respectively; p = 0.986). There were more students with burnout who considered their health as a worsened vs. pre-study period compared to students with no burnout, both concerning mental (61.4% vs. 38.6%) and physical health (61.1% vs. 38.9%; both p<0.001). There were more smokers among students who suffered from burnout compared to students who did not (52.0% vs. 48.0%; p = 0.013). A multiple regression revealed an independent dose-response effect of perceived stress at exams on the onset of burnout (moderate stress OR = 2.164 and high stress OR = 3.878). Also, students with the moderate and high stressful effect of communication with teaching staff, as well as, those with worse self-perceived physical and mental health had more than two times higher presence of burnout.

CONCLUSIONS: The prevalence of burnout among Belgrade veterinary students is relatively high. Primary prevention should be focused on the revealed predictors of burnout.}, } @article {pmid32205368, year = {2020}, author = {Vorobev, A and Dupouy, M and Carradec, Q and Delmont, TO and Annamalé, A and Wincker, P and Pelletier, E}, title = {Transcriptome reconstruction and functional analysis of eukaryotic marine plankton communities via high-throughput metagenomics and metatranscriptomics.}, journal = {Genome research}, volume = {30}, number = {4}, pages = {647-659}, pmid = {32205368}, issn = {1549-5469}, mesh = {Biodiversity ; Computational Biology/*methods ; Eukaryota/classification/*genetics ; *Gene Expression Profiling/methods ; *Metagenome ; *Metagenomics/methods ; Phylogeny ; Plankton/classification/*genetics ; *Transcriptome ; }, abstract = {Large-scale metagenomic and metatranscriptomic data analyses are often restricted by their gene-centric approach, limiting the ability to understand organismal and community biology. De novo assembly of large and mosaic eukaryotic genomes from complex meta-omics data remains a challenging task, especially in comparison with more straightforward bacterial and archaeal systems. Here, we use a transcriptome reconstruction method based on clustering co-abundant genes across a series of metagenomic samples. We investigated the co-abundance patterns of ∼37 million eukaryotic unigenes across 365 metagenomic samples collected during the Tara Oceans expeditions to assess the diversity and functional profiles of marine plankton. We identified ∼12,000 co-abundant gene groups (CAGs), encompassing ∼7 million unigenes, including 924 metagenomics-based transcriptomes (MGTs, CAGs larger than 500 unigenes). We demonstrated the biological validity of the MGT collection by comparing individual MGTs with available references. We identified several key eukaryotic organisms involved in dimethylsulfoniopropionate (DMSP) biosynthesis and catabolism in different oceanic provinces, thus demonstrating the potential of the MGT collection to provide functional insights on eukaryotic plankton. We established the ability of the MGT approach to capture interspecies associations through the analysis of a nitrogen-fixing haptophyte-cyanobacterial symbiotic association. This MGT collection provides a valuable resource for analyses of eukaryotic plankton in the open ocean by giving access to the genomic content and functional potential of many ecologically relevant eukaryotic species.}, } @article {pmid32204532, year = {2020}, author = {Ma, J and Lu, Y and Chen, F and Li, X and Xiao, D and Wang, H}, title = {Molecular Ecological Network Complexity Drives Stand Resilience of Soil Bacteria to Mining Disturbances among Typical Damaged Ecosystems in China.}, journal = {Microorganisms}, volume = {8}, number = {3}, pages = {}, pmid = {32204532}, issn = {2076-2607}, support = {41907405 and 51974313//National Natural Science Foundation/ ; BK20180641//Natural Science Foundation of Jiangsu Province/ ; }, abstract = {Understanding the interactions of soil microbial species and how they responded to disturbances are essential to ecological restoration and resilience in the semihumid and semiarid damaged mining areas. Information on this, however, remains unobvious and deficiently comprehended. In this study, based on the high throughput sequence and molecular ecology network analysis, we have investigated the bacterial distribution in disturbed mining areas across three provinces in China, and constructed molecular ecological networks to reveal the interactions of soil bacterial communities in diverse locations. Bacterial community diversity and composition were classified measurably between semihumid and semiarid damaged mining sites. Additionally, we distinguished key microbial populations across these mining areas, which belonged to Proteobacteria, Acidobacteria, Actinobacteria, and Chloroflexi. Moreover, the network modules were significantly associated with some environmental factors (e.g., annual average temperature, electrical conductivity value, and available phosphorus value). The study showed that network interactions were completely different across the different mining areas. The keystone species in different mining areas suggested that selected microbial communities, through natural successional processes, were able to resist the corresponding environment. Moreover, the results of trait-based module significances showed that several environmental factors were significantly correlated with some keystone species, such as OTU_8126 (Acidobacteria), OTU_8175 (Burkholderiales), and OTU_129 (Chloroflexi). Our study also implied that the complex network of microbial interaction might drive the stand resilience of soil bacteria in the semihumid and semiarid disturbed mining areas.}, } @article {pmid32203517, year = {2020}, author = {Longbottom, J and Krause, A and Torr, SJ and Stanton, MC}, title = {Quantifying geographic accessibility to improve efficiency of entomological monitoring.}, journal = {PLoS neglected tropical diseases}, volume = {14}, number = {3}, pages = {e0008096}, pmid = {32203517}, issn = {1935-2735}, support = {BB/L019035/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; MR/M014975/1/MRC_/Medical Research Council/United Kingdom ; 1964851/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Animals ; Costs and Cost Analysis ; *Entomology ; Environmental Monitoring/*methods ; *Geographic Information Systems ; Humans ; Insect Vectors ; Livestock ; *Models, Biological ; *Models, Statistical ; Pest Control ; *Remote Sensing Technology ; Trypanosoma ; Trypanosomiasis, African ; Tsetse Flies ; Uganda ; Vector Borne Diseases ; }, abstract = {BACKGROUND: Vector-borne diseases are important causes of mortality and morbidity in humans and livestock, particularly for poorer communities and countries in the tropics. Large-scale programs against these diseases, for example malaria, dengue and African trypanosomiasis, include vector control, and assessing the impact of this intervention requires frequent and extensive monitoring of disease vector abundance. Such monitoring can be expensive, especially in the later stages of a successful program where numbers of vectors and cases are low.

We developed a system that allows the identification of monitoring sites where pre-intervention densities of vectors are predicted to be high, and travel cost to sites is low, highlighting the most efficient locations for longitudinal monitoring. Using remotely sensed imagery and an image classification algorithm, we mapped landscape resistance associated with on- and off-road travel for every gridded location (3m and 0.5m grid cells) within Koboko district, Uganda. We combine the accessibility surface with pre-existing estimates of tsetse abundance and propose a stratified sampling approach to determine the most efficient locations for longitudinal data collection. Our modelled predictions were validated against empirical measurements of travel-time and existing maps of road networks. We applied this approach in northern Uganda where a large-scale vector control program is being implemented to control human African trypanosomiasis, a neglected tropical disease (NTD) caused by trypanosomes transmitted by tsetse flies. Our accessibility surfaces indicate a high performance when compared to empirical data, with remote sensing identifying a further ~70% of roads than existing networks.

CONCLUSIONS/SIGNIFICANCE: By integrating such estimates with predictions of tsetse abundance, we propose a methodology to determine the optimal placement of sentinel monitoring sites for evaluating control programme efficacy, moving from a nuanced, ad-hoc approach incorporating intuition, knowledge of vector ecology and local knowledge of geographic accessibility, to a reproducible, quantifiable one.}, } @article {pmid32203483, year = {2020}, author = {Nakagawa, S and Dunn, AG and Lagisz, M and Bannach-Brown, A and Grames, EM and Sánchez-Tójar, A and O'Dea, RE and Noble, DWA and Westgate, MJ and Arnold, PA and Barrow, S and Bethel, A and Cooper, E and Foo, YZ and Geange, SR and Hennessy, E and Mapanga, W and Mengersen, K and Munera, C and Page, MJ and Welch, V and , and Haddaway, NR}, title = {A new ecosystem for evidence synthesis.}, journal = {Nature ecology & evolution}, volume = {4}, number = {4}, pages = {498-501}, pmid = {32203483}, issn = {2397-334X}, support = {DRF-2018-11-ST2-048/DH_/Department of Health/United Kingdom ; }, mesh = {*Conservation of Natural Resources ; *Ecosystem ; }, } @article {pmid32199317, year = {2020}, author = {Pourghasemi, HR and Gayen, A and Lasaponara, R and Tiefenbacher, JP}, title = {Application of learning vector quantization and different machine learning techniques to assessing forest fire influence factors and spatial modelling.}, journal = {Environmental research}, volume = {184}, number = {}, pages = {109321}, doi = {10.1016/j.envres.2020.109321}, pmid = {32199317}, issn = {1096-0953}, mesh = {Geographic Information Systems ; Iran ; Machine Learning ; Rivers ; *Wildfires ; }, abstract = {This study assesses forest-fire susceptibility (FFS) in Fars Province, Iran using three geographic information system (GIS)-based machine-learning algorithms: boosted regression tree (BRT), general linear model (GLM), and mixture discriminant analysis (MDA). Recently, BRT, GLM, and MDA have become important machine-learning algorithms and their use has been enriched by application to various fields of research. A database of historical FFs identified using Landsat-8 OLI and MODIS satellite images (at 358 locations) and ten influencing factors (elevation, slope, topographical wetness index, aspect, distance from urban areas, annual mean temperature, land use, distance from road, annual mean rainfall, and distance from river) were input into a GIS. The 358 sites were divided into two sets for training (70%) and validation (30%). BRT, GLM, and MDA models were used to analyze the spatial relationships between the factors influencing FFs and the locations of fires to generate an FFS map. The prediction success of each modelled FFS map was determined with the help of the ROC curve, accuracy, overall accuracy, True-skill statistic (TSS), F-measures, corrected classify instances (CCI), and K-fold cross-validation (4-fold). The accuracy results of training and validation dataset in the BRT (AUC = 88.90% and 88.2%) and MDA (AUC = 86.4% and 85.6%) models are more effective than the GLM (AUC = 86.6% and 82.5%) model. Also, the outcome of the 4-fold measure confirmed the results from the other accuracy measures. Therefore, the accuracies of the BRT and MDA models are satisfactory and are suitable for FFS mapping in Fars Province. Finally, the well-accepted neural network application of learning-vector quantization (LVQ) reveals that land use, annual mean rainfall, and slope angle were the most useful determinants of FFS. The resulting FFS maps can enhance the effectiveness of planning and management of forest resources and ecological balances in this province.}, } @article {pmid32197729, year = {2020}, author = {Michel, M and Alberti, C and Carel, JC and Chevreul, K}, title = {Socioeconomic Status of Newborns and Hospital Efficiency: Implications for Hospital Payment Methods.}, journal = {Value in health : the journal of the International Society for Pharmacoeconomics and Outcomes Research}, volume = {23}, number = {3}, pages = {335-342}, doi = {10.1016/j.jval.2019.10.008}, pmid = {32197729}, issn = {1524-4733}, mesh = {Budgets ; Databases, Factual ; Female ; France ; Health Care Rationing/*economics ; Health Services Needs and Demand/economics ; *Hospital Charges ; *Hospital Costs ; Hospitalization/*economics ; Hospitals, Maternity/*economics ; Humans ; Infant, Newborn ; Length of Stay/economics ; Male ; Models, Economic ; Needs Assessment/economics ; Patient Admission/economics ; Patient Discharge/economics ; Pregnancy ; Pregnancy Complications/diagnosis/*economics/*therapy ; Retrospective Studies ; *Social Class ; Time Factors ; }, abstract = {OBJECTIVES: Studies have shown a consistent impact of socioeconomic status at birth for both mother and child; however, no study has looked at its impact on hospital efficiency and financial balance at birth, which could be major if newborns from disadvantaged families have an average length of stay (LOS) longer than other newborns. Our objective was therefore to study the association between socioeconomic status and hospital efficiency and financial balance in that population.

METHODS: A study was carried out using exhaustive national hospital discharge databases. All live births in a maternity hospital located in mainland France between 2012 and 2014 were included. Socioeconomic status was estimated with an ecological indicator and efficiency by variations in patient LOS compared with different mean national LOS. Financial balance was assessed at the admission level through the ratio of production costs and revenues and at the hospital level by the difference in aggregated revenues and production costs for said hospital. Multivariate regression models studied the association between those indicators and socioeconomic status.

RESULTS: A total of 2 149 454 births were included. LOS was shorter than the national means for less disadvantaged patients and longer for the more disadvantaged patients, which increased when adjusted for gestational age, birth weight, and severity. A 1% increase in disadvantaged patients in a hospital's case mix significantly increased the probability that the hospital would be in deficit by 2.6%.

CONCLUSIONS: Reforms should be made to hospital payment methods to take into account patient socioeconomic status so as to improve resource allocation efficiency.}, } @article {pmid32197206, year = {2020}, author = {Yang, G and Zhou, C and Wang, W and Ma, S and Liu, H and Liu, Y and Zhao, Z}, title = {Recycling sustainability of waste paper industry in Beijing City: An analysis based on value chain and GIS model.}, journal = {Waste management (New York, N.Y.)}, volume = {106}, number = {}, pages = {62-70}, doi = {10.1016/j.wasman.2020.03.013}, pmid = {32197206}, issn = {1879-2456}, mesh = {Beijing ; China ; Cities ; Geographic Information Systems ; Recycling ; *Solid Waste ; *Waste Management ; }, abstract = {China established a self-organized and market-driven recycling system, which was dominated by the informal sectors. In recent years, the amount of domestically-recycled waste paper grew slower than expectation in China, which may be resulted from a decline in economic sustainability of current recycling system. For understanding the waste paper recycling system in most cities in China, the economic mechanism remains unclear and the city-level data is extremely insufficient. In this work, an index of recycling sustainability (IRS, benefit divided by cost) is analyzed with a resolution of 1 km[2] grid in Beijing City, by adopting value chain and GIS methodology. Five degrees of IRS are defined, from high-degree (IRS > 1.10) to low-degree (IRS < 0.95). Different stakeholders in the informal waste paper recycling system were interviewed to fill the data gap. Results show that: (1) from 2015 to 2018, the informal recycling of waste paper accounted for approximate 80% in Beijing; (2) the number of informal recyclables distribution sites decreased from 27 to 11, and their average distance to the city-center rose from 27.5 km to 40.9 km; (3) in 2015 and 2018, the grids with high-degree IRS accounted for 99.5% and 89.2%, respectively, indicating a sustainable waste paper recycling industry in Beijing; and (4) according to the scenario analysis, if the operating cost rises by 30%, the grids with low-degree IRS accounts for 98.5%, indicating a nontrivial challenges when the recycling cost keeps increasing in the future. Policy recommendations are put forward for a more sustainable paper waste recycling system in China.}, } @article {pmid32193422, year = {2020}, author = {Jézéquel, C and Tedesco, PA and Bigorne, R and Maldonado-Ocampo, JA and Ortega, H and Hidalgo, M and Martens, K and Torrente-Vilara, G and Zuanon, J and Acosta, A and Agudelo, E and Barrera Maure, S and Bastos, DA and Bogotá Gregory, J and Cabeceira, FG and Canto, ALC and Carvajal-Vallejos, FM and Carvalho, LN and Cella-Ribeiro, A and Covain, R and Donascimiento, C and Dória, CRC and Duarte, C and Ferreira, EJG and Galuch, AV and Giarrizzo, T and Leitão, RP and Lundberg, JG and Maldonado, M and Mojica, JI and Montag, LFA and Ohara, WM and Pires, THS and Pouilly, M and Prada-Pedreros, S and de Queiroz, LJ and Rapp Py-Daniel, L and Ribeiro, FRV and Ríos Herrera, R and Sarmiento, J and Sousa, LM and Stegmann, LF and Valdiviezo-Rivera, J and Villa, F and Yunoki, T and Oberdorff, T}, title = {A database of freshwater fish species of the Amazon Basin.}, journal = {Scientific data}, volume = {7}, number = {1}, pages = {96}, pmid = {32193422}, issn = {2052-4463}, mesh = {Animals ; Biodiversity ; Conservation of Natural Resources ; *Databases, Factual ; *Fishes ; Fresh Water ; Rivers ; South America ; }, abstract = {The Amazon Basin is an unquestionable biodiversity hotspot, containing the highest freshwater biodiversity on earth and facing off a recent increase in anthropogenic threats. The current knowledge on the spatial distribution of the freshwater fish species is greatly deficient in this basin, preventing a comprehensive understanding of this hyper-diverse ecosystem as a whole. Filling this gap was the priority of a transnational collaborative project, i.e. the AmazonFish project - https://www.amazon-fish.com/. Relying on the outputs of this project, we provide the most complete fish species distribution records covering the whole Amazon drainage. The database, including 2,406 validated freshwater native fish species, 232,936 georeferenced records, results from an extensive survey of species distribution including 590 different sources (e.g. published articles, grey literature, online biodiversity databases and scientific collections from museums and universities worldwide) and field expeditions conducted during the project. This database, delivered at both georeferenced localities (21,500 localities) and sub-drainages grains (144 units), represents a highly valuable source of information for further studies on freshwater fish biodiversity, biogeography and conservation.}, } @article {pmid32192173, year = {2020}, author = {Li, X and Lei, S and Liu, F and Wang, W}, title = {Analysis of Plant and Soil Restoration Process and Degree of Refuse Dumps in Open-Pit Coal Mining Areas.}, journal = {International journal of environmental research and public health}, volume = {17}, number = {6}, pages = {}, pmid = {32192173}, issn = {1660-4601}, mesh = {Coal ; *Coal Mining ; *Environmental Restoration and Remediation ; *Garbage ; Plants ; Soil ; *Soil Pollutants ; }, abstract = {Vegetation and soil restoration are the key to ecological reconstruction in the damaged areas of open-pit coal mining areas. Ecological stability is an important indicator of the degree of ecological restoration. In this study, the ecological stability and the process of plant and soil restoration were investigated at different refuse dumps in three coal mines, namely, the Wulanhada (WLHD) coal mine, the Liulingou (LLG) coal mine, and the Jinzhengtai (JZT) coal mine, in Jungar Banner. Results show that organic matter, total N, available N, and available K increased with the increase in restoration age at the two coal mines of WLHD and LLG. In the JZT coal mine, organic matter, total N, and available K firstly increased, and then slightly decreased with the increase in restoration age. The redundancy analysis indicates that most reclaimed mine soil properties (including soil moisture content, organic matter, total N, and available K) are positively correlated with plant species diversity in the three coal mines, while soil pH and soil bulk density showed a negative correlation with plant species diversity. Plant parameters increased with the years since revegetation, except the Pielou index for the WLHD coal mine, and the Pielou and Margalef indexes for the JZT coal mine. The Euclidean distance between the restoration areas and the natural reference areas decreased with the increase in restoration age. Our findings suggest that, in the three coal mines, the change law of ecological stability conformed to the logistic succession model. The same degree of ecological stability in different refuse dumps may correspond to different degrees of vegetation and soil development. This study emphasizes that ecological restoration in mining areas could benefit the structure of the plant community and the recovery of soil properties, which would eventually improve the ecological stability of coal mining areas.}, } @article {pmid32188863, year = {2020}, author = {Ropert-Coudert, Y and Van de Putte, AP and Reisinger, RR and Bornemann, H and Charrassin, JB and Costa, DP and Danis, B and Hückstädt, LA and Jonsen, ID and Lea, MA and Thompson, D and Torres, LG and Trathan, PN and Wotherspoon, S and Ainley, DG and Alderman, R and Andrews-Goff, V and Arthur, B and Ballard, G and Bengtson, J and Bester, MN and Blix, AS and Boehme, L and Bost, CA and Boveng, P and Cleeland, J and Constantine, R and Crawford, RJM and Dalla Rosa, L and Nico de Bruyn, PJ and Delord, K and Descamps, S and Double, M and Emmerson, L and Fedak, M and Friedlaender, A and Gales, N and Goebel, M and Goetz, KT and Guinet, C and Goldsworthy, SD and Harcourt, R and Hinke, JT and Jerosch, K and Kato, A and Kerry, KR and Kirkwood, R and Kooyman, GL and Kovacs, KM and Lawton, K and Lowther, AD and Lydersen, C and Lyver, PO and Makhado, AB and Márquez, MEI and McDonald, BI and McMahon, CR and Muelbert, M and Nachtsheim, D and Nicholls, KW and Nordøy, ES and Olmastroni, S and Phillips, RA and Pistorius, P and Plötz, J and Pütz, K and Ratcliffe, N and Ryan, PG and Santos, M and Southwell, C and Staniland, I and Takahashi, A and Tarroux, A and Trivelpiece, W and Wakefield, E and Weimerskirch, H and Wienecke, B and Xavier, JC and Raymond, B and Hindell, MA}, title = {The retrospective analysis of Antarctic tracking data project.}, journal = {Scientific data}, volume = {7}, number = {1}, pages = {94}, pmid = {32188863}, issn = {2052-4463}, abstract = {The Retrospective Analysis of Antarctic Tracking Data (RAATD) is a Scientific Committee for Antarctic Research project led jointly by the Expert Groups on Birds and Marine Mammals and Antarctic Biodiversity Informatics, and endorsed by the Commission for the Conservation of Antarctic Marine Living Resources. RAATD consolidated tracking data for multiple species of Antarctic meso- and top-predators to identify Areas of Ecological Significance. These datasets and accompanying syntheses provide a greater understanding of fundamental ecosystem processes in the Southern Ocean, support modelling of predator distributions under future climate scenarios and create inputs that can be incorporated into decision making processes by management authorities. In this data paper, we present the compiled tracking data from research groups that have worked in the Antarctic since the 1990s. The data are publicly available through biodiversity.aq and the Ocean Biogeographic Information System. The archive includes tracking data from over 70 contributors across 12 national Antarctic programs, and includes data from 17 predator species, 4060 individual animals, and over 2.9 million observed locations.}, } @article {pmid32188481, year = {2020}, author = {Bozigar, M and Lawson, A and Pearce, J and King, K and Svendsen, E}, title = {A geographic identifier assignment algorithm with Bayesian variable selection to identify neighborhood factors associated with emergency department visit disparities for asthma.}, journal = {International journal of health geographics}, volume = {19}, number = {1}, pages = {9}, pmid = {32188481}, issn = {1476-072X}, support = {F31 HL142124/HL/NHLBI NIH HHS/United States ; }, mesh = {Adolescent ; *Algorithms ; *Asthma/therapy ; Bayes Theorem ; Child ; Child, Preschool ; *Emergency Service, Hospital ; Geographic Information Systems ; Geography ; *Health Status Disparities ; Humans ; *Residence Characteristics ; South Carolina ; Young Adult ; }, abstract = {BACKGROUND: Ecologic health studies often rely on outcomes from health service utilization data that are limited by relatively coarse spatial resolutions and missing geographic information, particularly neighborhood level identifiers. When fine-scale geographic data are missing, the ramifications and strategies for addressing them are not well researched or developed. This study illustrates a novel spatio-temporal framework that combines a geographic identifier assignment (i.e., geographic imputation) algorithm with predictive Bayesian variable selection to identify neighborhood factors associated with disparities in emergency department (ED) visits for asthma.

METHODS: ED visit records with missing fine-scale spatial identifiers (~ 20%) were geocoded using information from known, coarser, misaligned spatial units using an innovative geographic identifier assignment algorithm. We then employed systematic variable selection in a spatio-temporal Bayesian hierarchical model (BHM) predictive framework within the NIMBLE package in R. Our novel methodology is illustrated in an ecologic case study aimed at identifying neighborhood-level predictors of asthma ED visits in South Carolina, United States, from 1999 to 2015. The health outcome was annual ED visit counts in small areas (i.e., census tracts) with primary diagnoses of asthma (ICD9 codes 493.XX) among children ages 5 to 19 years.

RESULTS: We maintained 96% of ED visit records for this analysis. When the algorithm used areal proportions as probabilities for assignment, which addressed differential missingness of census tract identifiers in rural areas, variable selection consistently identified significant neighborhood-level predictors of asthma ED visit risk including pharmacy proximity, average household size, and carbon monoxide interactions. Contrasted with common solutions of removing geographically incomplete records or scaling up analyses, our methodology identified critical differences in parameters estimated, predictors selected, and inferences. We posit that the differences were attributable to improved data resolution, resulting in greater power and less bias. Importantly, without this methodology, we would have inaccurately identified predictors of risk for asthma ED visits, particularly in rural areas.

CONCLUSIONS: Our approach innovatively addressed several issues in ecologic health studies, including missing small-area geographic information, multiple correlated neighborhood covariates, and multiscale unmeasured confounding factors. Our methodology could be widely applied to other small-area studies, useful to a range of researchers throughout the world.}, } @article {pmid32184407, year = {2020}, author = {Beer, C and Zimov, N and Olofsson, J and Porada, P and Zimov, S}, title = {Protection of Permafrost Soils from Thawing by Increasing Herbivore Density.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {4170}, pmid = {32184407}, issn = {2045-2322}, mesh = {Animals ; Atmosphere ; Carbon Cycle ; *Climate Change ; *Ecosystem ; Environmental Monitoring ; Greenhouse Gases ; *Herbivory ; *Permafrost ; *Population Density ; Soil/*chemistry ; }, abstract = {Climate change will cause a substantial future greenhouse gas release from warming and thawing permafrost-affected soils to the atmosphere enabling a positive feedback mechanism. Increasing the population density of big herbivores in northern high-latitude ecosystems will increase snow density and hence decrease the insulation strength of snow during winter. As a consequence, theoretically 80% of current permafrost-affected soils (<10 m) is projected to remain until 2100 even when assuming a strong warming using the Representative Concentration Pathway 8.5. Importantly, permafrost temperature is estimated to remain below -4 °C on average after increasing herbivore population density. Such ecosystem management practices would be therefore theoretically an important additional climate change mitigation strategy. Our results also highlight the importance of new field experiments and observations, and the integration of fauna dynamics into complex Earth System models, in order to reliably project future ecosystem functions and climate.}, } @article {pmid32183712, year = {2020}, author = {Sun, Y and Zhang, Q and Liu, B and Lin, K and Zhang, Z and Pang, E}, title = {CuAS: a database of annotated transcripts generated by alternative splicing in cucumbers.}, journal = {BMC plant biology}, volume = {20}, number = {1}, pages = {119}, pmid = {32183712}, issn = {1471-2229}, support = {Grant No. 31571361//the National Natural Science Foundation of China/ ; }, mesh = {*Alternative Splicing ; Cucumis sativus/*genetics ; *Databases, Genetic ; *Genes, Plant ; *Transcriptome ; }, abstract = {BACKGROUND: Alternative splicing (AS) plays a critical regulatory role in modulating transcriptome and proteome diversity. In particular, it increases the functional diversity of proteins. Recent genome-wide analysis of AS using RNA-Seq has revealed that AS is highly pervasive in plants. Furthermore, it has been suggested that most AS events are subject to tissue-specific regulation.

DESCRIPTION: To reveal the functional characteristics induced by AS and tissue-specific splicing events, a database for exploring these characteristics is needed, especially in plants. To address these goals, we constructed a database of annotated transcripts generated by alternative splicing in cucumbers (CuAS: http://cmb.bnu.edu.cn/alt_iso/index.php) that integrates genomic annotations, isoform-level functions, isoform-level features, and tissue-specific AS events among multiple tissues. CuAS supports a retrieval system that identifies unique IDs (gene ID, isoform ID, UniProt ID, and gene name), chromosomal positions, and gene families, and a browser for visualization of each gene.

CONCLUSION: We believe that CuAS could be helpful for revealing the novel functional characteristics induced by AS and tissue-specific AS events in cucumbers. CuAS is freely available at http://cmb.bnu.edu.cn/alt_iso/index.php.}, } @article {pmid32183482, year = {2020}, author = {Gimenez, JV and Garcia-Unanue, J and Navandar, A and Viejo-Romero, D and Sanchez-Sanchez, J and Gallardo, L and Hernandez-Martin, A and Felipe, JL}, title = {Comparison between Two Different Device Models 18 Hz GPS Used for Time-Motion Analyses in Ecological Testing of Football.}, journal = {International journal of environmental research and public health}, volume = {17}, number = {6}, pages = {}, pmid = {32183482}, issn = {1660-4601}, mesh = {Athletic Performance ; *Football ; Geographic Information Systems ; Humans ; Male ; Motion ; Reproducibility of Results ; Running ; }, abstract = {BACKGROUND: The aim of this study was to compare the validity of two different GPS device models used for time-motion analyses in ecological testing of football.

METHODS: Ten healthy male players from a Spanish university football team participated in this study. The team sport simulation circuit (TSCC) used was based on previous research examining the validity and interunit reliability of different GPS systems. Participants were required to complete eight laps of the TSSC, resulting in a total distance of 1320 m. The GPS units used for the current study were the 18 Hz StatsSport Apex Pro and 18 Hz RealTrack WIMU Pro. Participants were required to wear either of the two GPS units during the test. To establish the construct validity of GPS as a measure of Vmax, timing lights were used as a gold standard.

RESULTS: The results clearly suggest that it is not possible to use the same 18 Hz GPS model or interchange it. The measurement can be considered precise when the noise is at least equal to or lower than the smallest worthwhile change. In this case, all standard deviation in measurement error was higher than the smallest worthwhile change. This is due to an inconsistency in the data processing of each trademark.

CONCLUSIONS: It is important to prevent a club using different GPS trademarks at the same time, since it is not possible to compare in any case any type of result obtained between different trademarks.}, } @article {pmid32182235, year = {2020}, author = {Laloum, D and Robinson-Rechavi, M}, title = {Methods detecting rhythmic gene expression are biologically relevant only for strong signal.}, journal = {PLoS computational biology}, volume = {16}, number = {3}, pages = {e1007666}, pmid = {32182235}, issn = {1553-7358}, mesh = {Animals ; Circadian Rhythm/*genetics ; Computational Biology/*methods ; Databases, Genetic ; Drosophila/genetics ; Gene Expression Profiling/*methods ; Humans ; Mice ; Organ Specificity/genetics ; Reproducibility of Results ; *Software ; Transcriptome/*genetics ; }, abstract = {The nycthemeral transcriptome embodies all genes displaying a rhythmic variation of their mRNAs periodically every 24 hours, including but not restricted to circadian genes. In this study, we show that the nycthemeral rhythmicity at the gene expression level is biologically functional and that this functionality is more conserved between orthologous genes than between random genes. We used this conservation of the rhythmic expression to assess the ability of seven methods (ARSER, Lomb Scargle, RAIN, JTK, empirical-JTK, GeneCycle, and meta2d) to detect rhythmic signal in gene expression. We have contrasted them to a naive method, not based on rhythmic parameters. By taking into account the tissue-specificity of rhythmic gene expression and different species comparisons, we show that no method is strongly favored. The results show that these methods designed for rhythm detection, in addition to having quite similar performances, are consistent only among genes with a strong rhythm signal. Rhythmic genes defined with a standard p-value threshold of 0.01 for instance, could include genes whose rhythmicity is biologically irrelevant. Although these results were dependent on the datasets used and the evolutionary distance between the species compared, we call for caution about the results of studies reporting or using large sets of rhythmic genes. Furthermore, given the analysis of the behaviors of the methods on real and randomized data, we recommend using primarily ARS, empJTK, or GeneCycle, which verify expectations of a classical distribution of p-values. Experimental design should also take into account the circumstances under which the methods seem more efficient, such as giving priority to biological replicates over the number of time-points, or to the number of time-points over the quality of the technique (microarray vs RNAseq). GeneCycle, and to a lesser extent empirical-JTK, might be the most robust method when applied to weakly informative datasets. Finally, our analyzes suggest that rhythmic genes are mainly highly expressed genes.}, } @article {pmid32182187, year = {2020}, author = {Kenyon, C and Manoharan-Basil, SS}, title = {Cultural Drivers of Antibiotic Consumption in High-Income Countries: A Global Ecological Analysis.}, journal = {Microbial drug resistance (Larchmont, N.Y.)}, volume = {26}, number = {9}, pages = {1063-1070}, doi = {10.1089/mdr.2019.0497}, pmid = {32182187}, issn = {1931-8448}, mesh = {Americas ; Anti-Bacterial Agents/*therapeutic use ; Australia ; Avoidance Learning ; Cephalosporins/*therapeutic use ; Cross-Cultural Comparison ; Databases, Factual ; Developed Countries/economics ; Drug Utilization/economics/*statistics & numerical data ; Europe ; Fluoroquinolones/*therapeutic use ; Gross Domestic Product ; *Health Knowledge, Attitudes, Practice ; Humans ; Income/statistics & numerical data ; Japan ; Linear Models ; Macrolides/*therapeutic use ; Uncertainty ; }, abstract = {Background: Previous studies evaluating the cultural and structural factors underpinning the large variations in the consumption of antibiotics in high-income countries have reached different conclusions. Some studies have found that corruption plays a dominant role, whereas other studies have concluded that cultural factors such as the degree of uncertainty avoidance (UA) and performance-orientation versus cooperation-orientation (POCO) are more important. These studies have been limited to Europe, and we, therefore, aimed to expand this analysis to all high-income countries with available data. Methods: Using antibiotic consumption data from the IQVIA MIDAS database, linear regression models were constructed with country-level cephalosporin, fluoroquinolone, and macrolide consumption (defined daily doses/1,000 population/year) as the outcome variables and country-specific scores of UA and POCO (obtained from the Hofstede Index), gross domestic product/capita, world region and markers of effective governance (Control of Corruption and Regulatory Quality extracted from the World Bank data) as the explanatory variables. All data, excluding the Hofstede Indices, used country-level averages for the years 2013 to 2015. Results: Complete data were available for 37 countries from 4 world regions. Consumption of cephalosporins, macrolides, and fluoroquinolones was associated with POCO and UA, but not the markers of effective governance. In the case of macrolide consumption, the association with UA narrowly missed statistical significance. Repeat analyses limited to first European countries and second to non-European countries revealed similar findings. Conclusions: More thought should be given to construct antibiotic stewardship campaigns that are tailored to the local extent of UA and POCO.}, } @article {pmid32181459, year = {2020}, author = {Maroń, AM and Szlapa-Kula, A and Matussek, M and Kruszynski, R and Siwy, M and Janeczek, H and Grzelak, J and Maćkowski, S and Schab-Balcerzak, E and Machura, B}, title = {Photoluminescence enhancement of Re(i) carbonyl complexes bearing D-A and D-π-A ligands.}, journal = {Dalton transactions (Cambridge, England : 2003)}, volume = {49}, number = {14}, pages = {4441-4453}, doi = {10.1039/c9dt04871e}, pmid = {32181459}, issn = {1477-9234}, abstract = {Three Re(i) carbonyl complexes [ReCl(CO)3(Ln)] bearing 2,2'-bipyridine, 2,2':6',2''-terpyridine, and 1,10-phenanthroline functionalized with diphenylamine/or triphenylamine units (L1-L3) were synthesized to explore the impact of highly electron donating units appended to the imine ligand on the thermal and optoelectronic properties of Re(i) systems. Additionally, for comparison, the ligands L1-3 and parent complexes [ReCl(CO)3(bipy)], [ReCl(CO)3(phen)] and [ReCl(CO)3(terpy-κ2N)] were investigated. The thermal stability was evaluated by differential scanning calorimetry. The ground- and excited-state electronic properties of the Re(i) complexes were studied by cyclic voltammetry and differential pulse voltammetry, absorption and emission spectroscopy, as well as using density-functional theory (DFT). The majority of the compounds form amorphous molecular materials with high glass transition temperatures above 100 °C. Compared to the unsubstituted complexes [ReCl(CO)3(bipy)], [ReCl(CO)3(phen)] and [ReCl(CO)3(terpy-κ2N)], the HOMO-LUMO gap of the corresponding Re(i) systems bearing modified imine ligands is reduced, and the decrease in the value of the ΔEH-L is mainly caused by the increase in HOMO energy level. In relation to the parent complexes, all designed Re(i) carbonyls were found to show enhanced photoluminescence, both in solution and in solid state. The investigated ligands and complexes were also preliminarily tested as luminophores in light emitting diodes with the structures ITO/PEDOT:PSS/compound/Al and ITO/PEDOT:PSS/PVK:PBD:compound/Al. The pronounced effect of the ligand chemical structure on electroluminescence ability was clearly visible.}, } @article {pmid32179987, year = {2020}, author = {Piross, IS and Solt, S and Horváth, É and Kotymán, L and Palatitz, P and Bertók, P and Szabó, K and Vili, N and Vas, Z and Rózsa, L and Harnos, A and Fehérvári, P}, title = {Sex-dependent changes in the louse abundance of red-footed falcons (Falco vespertinus).}, journal = {Parasitology research}, volume = {119}, number = {4}, pages = {1327-1335}, pmid = {32179987}, issn = {1432-1955}, mesh = {Animals ; Anoplura/*physiology ; Bird Diseases/parasitology ; Birds/parasitology ; Falconiformes/*parasitology ; Feathers ; Female ; Hungary ; Ischnocera/*physiology ; Lice Infestations/parasitology ; Male ; Phthiraptera/*physiology ; Wings, Animal/anatomy & histology/parasitology ; }, abstract = {Permanent ectoparasites live in stable environments; thus, their population dynamics are mostly adapted to changes in the host life cycle. We aimed to investigate how static and dynamic traits of red-footed falcons interplay with the dynamics of their louse subpopulations during breeding and how they affect the colonisation of new hosts by lice. We sampled red-footed falcon (Falco vespertinus) nestlings (two breeding seasons) and adults (one breeding season) in southern Hungary. The mean abundance of Colpocephalum subzerafae and Degeeriella rufa lice on the nestlings was modelled with generalized linear mixed models using clutch size and host sex in interaction with wing length. For adults, we used wing length and the number of days after laying the first egg, both in interaction with sex. D. rufa abundances increased with the nestlings' wing length. In one year, this trend was steeper on females. In adult birds, both louse species exhibited higher abundances on females at the beginning, but it decreased subsequently through the breeding season. Contrarily, abundances were constantly low on adult males. Apparently, D. rufa postpones transmission until nestlings develop juvenile plumage and choose the more feathered individual among siblings. The sexual difference in the observed abundance could either be caused by the different plumage, or by the females' preference for less parasitized males. Moreover, females likely have more time to preen during the incubation period, lowering their louse burdens. Thus, sex-biased infestation levels likely arise due to parasite preferences in the nestlings and host behavioural processes in the adult falcons.}, } @article {pmid32175321, year = {2020}, author = {Rodriguez-Palacios, A and Mo, KQ and Shah, BU and Msuya, J and Bijedic, N and Deshpande, A and Ilic, S}, title = {Global and Historical Distribution of Clostridioides difficile in the Human Diet (1981-2019): Systematic Review and Meta-Analysis of 21886 Samples Reveal Sources of Heterogeneity, High-Risk Foods, and Unexpected Higher Prevalence Toward the Tropic.}, journal = {Frontiers in medicine}, volume = {7}, number = {}, pages = {9}, pmid = {32175321}, issn = {2296-858X}, abstract = {Clostridioides difficile (CD) is a spore-forming bacterium that causes life-threatening intestinal infections in humans. Although formerly regarded as exclusively nosocomial, there is increasing genomic evidence that person-to-person transmission accounts for only <25% of cases, supporting the culture-based hypothesis that foods may be routine sources of CD-spore ingestion in humans. To synthesize the evidence on the risk of CD exposure via foods, we conducted a systematic review and meta-analysis of studies reporting the culture prevalence of CD in foods between January 1981 and November 2019. Meta-analyses, risk-ratio estimates, and meta-regression were used to estimate weighed-prevalence across studies and food types to identify laboratory and geographical sources of heterogeneity. In total, 21886 food samples were tested for CD between 1981 and 2019 (96.4%, n = 21084, 2007-2019; 232 food-sample-sets; 79 studies; 25 countries). Culture methodology, sample size and type, region, and latitude were sources of heterogeneity (p < 0.05). Although non-strictly-anaerobic methods were reported in some studies, and we confirmed experimentally that improper anaerobiosis of media/sample-handling affects CD recovery in agar (Fisher, p < 0.01), most studies (>72%) employed the same (one-of-six) culture strategy. Because the prevalence was also meta-analytically similar across six culture strategies reported, all studies were integrated using three meta-analytical methods. At the study level (n = 79), the four-decade global cumulative-prevalence of CD in the human diet was 4.1% (95%CI = -3.71, 11.91). At the food-set level (n = 232, mean 12.9 g/sample, similar across regions p > 0.2; 95%CI = 9.7-16.2), the weighted prevalence ranged between 4.5% (95%CI = 3-6%; all studies) and 8% (95%CI = 7-8%; only CD-positive-studies). Risk-ratio ranking and meta-regression showed that milk was the least likely source of CD, while seafood, leafy green vegetables, pork, and poultry carried higher risks (p < 0.05). Across regions, the risk of CD in foods for foodborne exposure reproducibly decreased with Earth latitude (p < 0.001). In conclusion, CD in the human diet is a global non-random-source of foodborne exposure that occurs independently of laboratory culture methods, across regions, and at a variable level depending on food type and latitude. The latitudinal trend (high CD-food-prevalence toward tropic) is unexpectedly inverse to the epidemiological observations of CD-infections in humans (frequent in temperate regions). Findings suggest the plausible hypothesis that ecologically-richer microbiomes in the tropic might protect against intestinal CD colonization/infections despite CD ingestion.}, } @article {pmid32174530, year = {2020}, author = {Parlato, MCM and Valenti, F and Porto, SMC}, title = {Covering plastic films in greenhouses system: A GIS-based model to improve post use suistainable management.}, journal = {Journal of environmental management}, volume = {263}, number = {}, pages = {110389}, doi = {10.1016/j.jenvman.2020.110389}, pmid = {32174530}, issn = {1095-8630}, mesh = {Europe ; *Geographic Information Systems ; Italy ; *Plastics ; Recycling ; }, abstract = {Yearly, in Europe, more than 1 million tonnes of plastic materials are used in agricultural activities. Among the possible applications, plastic films for protected cultivation practices are highly used worldwide because of the significant advantage deriving from the shortening of the growing period. However, in the absence of a correct policy disposal of plastic films, environmental degradation could take place with serious ecological and economic consequences. In this study, a geographical information system (GIS) - based model to locate and quantify the yearly amount of agricultural plastic waste (APW) coming from crop-shelter coverage used in greenhouses system was put forward and was applied in a study area located in southern Italy, highly characterised by protected cultivation practices. Firstly, the areas with the highest density of crop shelters were mapped, then a suitable index to determine APW amount was computed and applied to obtain heat maps related to covering plastic films. Finally, sensitivity analyses were carried out by varying thickness, lifetime, and density of the covering films of the greenhouses, located in the considered samples. The index ranged between 976 kg ha[-1]yr[-1]and, 2484 kg ha[-1]yr[-1]. The results showed that the density of greenhouses and tunnels-greenhouses is still elevated nearby the coastline, highlighting that the guidelines of the territorial plan of the Province of Ragusa concerning the displacement of protected crops from the coast to the internal rural areas were disregarded. Moreover, the GIS-based model results could provide basic information for the analysis of the environmental impact due to transportation of APW. Therefore, these results could offer a suitable tool to improve the correct disposal management of covering plastic films and the related recycle policy.}, } @article {pmid32171258, year = {2020}, author = {Sparks, ME and Bansal, R and Benoit, JB and Blackburn, MB and Chao, H and Chen, M and Cheng, S and Childers, C and Dinh, H and Doddapaneni, HV and Dugan, S and Elpidina, EN and Farrow, DW and Friedrich, M and Gibbs, RA and Hall, B and Han, Y and Hardy, RW and Holmes, CJ and Hughes, DST and Ioannidis, P and Cheatle Jarvela, AM and Johnston, JS and Jones, JW and Kronmiller, BA and Kung, F and Lee, SL and Martynov, AG and Masterson, P and Maumus, F and Munoz-Torres, M and Murali, SC and Murphy, TD and Muzny, DM and Nelson, DR and Oppert, B and Panfilio, KA and Paula, DP and Pick, L and Poelchau, MF and Qu, J and Reding, K and Rhoades, JH and Rhodes, A and Richards, S and Richter, R and Robertson, HM and Rosendale, AJ and Tu, ZJ and Velamuri, AS and Waterhouse, RM and Weirauch, MT and Wells, JT and Werren, JH and Worley, KC and Zdobnov, EM and Gundersen-Rindal, DE}, title = {Brown marmorated stink bug, Halyomorpha halys (Stål), genome: putative underpinnings of polyphagy, insecticide resistance potential and biology of a top worldwide pest.}, journal = {BMC genomics}, volume = {21}, number = {1}, pages = {227}, pmid = {32171258}, issn = {1471-2164}, support = {R01 GM113230/GM/NIGMS NIH HHS/United States ; U54 HG003273/HG/NHGRI NIH HHS/United States ; }, mesh = {Animals ; Ecosystem ; Gene Transfer, Horizontal ; Genome Size ; Heteroptera/classification/*genetics ; Insect Proteins/*genetics ; *Insecticide Resistance ; Introduced Species ; Phylogeny ; Whole Genome Sequencing/*methods ; }, abstract = {BACKGROUND: Halyomorpha halys (Stål), the brown marmorated stink bug, is a highly invasive insect species due in part to its exceptionally high levels of polyphagy. This species is also a nuisance due to overwintering in human-made structures. It has caused significant agricultural losses in recent years along the Atlantic seaboard of North America and in continental Europe. Genomic resources will assist with determining the molecular basis for this species' feeding and habitat traits, defining potential targets for pest management strategies.

RESULTS: Analysis of the 1.15-Gb draft genome assembly has identified a wide variety of genetic elements underpinning the biological characteristics of this formidable pest species, encompassing the roles of sensory functions, digestion, immunity, detoxification and development, all of which likely support H. halys' capacity for invasiveness. Many of the genes identified herein have potential for biomolecular pesticide applications.

CONCLUSIONS: Availability of the H. halys genome sequence will be useful for the development of environmentally friendly biomolecular pesticides to be applied in concert with more traditional, synthetic chemical-based controls.}, } @article {pmid32171122, year = {2020}, author = {Pitombeira de Figueirêdo, L and Athayde, DB and Daam, MA and van Gestel, CAM and Guerra, GDS and Duarte-Neto, PJ and Espíndola, ELG}, title = {Impact of temperature on the toxicity of Kraft 36 EC® (a.s. abamectin) and Score 250 EC® (a.s. difenoconazole) to soil organisms under realistic environmental exposure scenarios.}, journal = {Ecotoxicology and environmental safety}, volume = {194}, number = {}, pages = {110446}, doi = {10.1016/j.ecoenv.2020.110446}, pmid = {32171122}, issn = {1090-2414}, mesh = {Animals ; Arthropods/physiology ; Brazil ; Dioxolanes/*toxicity ; Environmental Exposure ; Fungicides, Industrial ; Insecticides/toxicity ; Ivermectin/*analogs & derivatives/toxicity ; Pesticides/toxicity ; Soil ; Soil Pollutants/*toxicity ; Temperature ; Toxicity Tests ; Triazoles/*toxicity ; }, abstract = {Pesticides can affect all receiving compartments, especially soils, and their fate and effects may be enhanced by temperature, increasing their risk to ecological functions of soils. In Brazil, the most widely used pesticides are the insecticide Kraft 36 EC® (a.s. abamectin) and the fungicide Score 250 EC® (a.s. difenoconazole), which are commonly used in strawberry, often simultaneously as a mixture. The aim of this study was to evaluate the toxicity of realistic environmental applications, single and in mixtures, for both pesticides to the springtail Folsomia candida and the plant species Allium cepa (onion) and Lycopersicum esculentum (tomato). Mesocosms filled with Brazilian natural soil (lattosolo) were dosed with water (control), Kraft (10.8 g a.s/ha), Score (20 g.a.s/ha) and Kraft + Score (10.8 + 20 g a.s./ha). The applications were repeated every 7 days, during 18 days of experiment, and simulating rainfall twice a week. Collembola reproduction tests were conducted with soils from the first (day 1) and last day (day 18) of experiment for each treatment. Plant toxicity tests were carried out in the experimental units. The experiments were run at 23 °C and 33 °C. Kraft, alone and in the binary mixture, showed high toxicity to the springtails in soils from both days 1 and 18, especially at 23 °C where it caused 100% mortality. Score however, was not toxic to the springtails. Plant growth was reduced by Score, but responses varied depending on temperature. This study indicates a high environmental risk of the insecticide Kraft, particularly at lower temperatures (23 °C), and an influence of temperature on pesticide fate and effects.}, } @article {pmid32165619, year = {2020}, author = {Thomas, HJD and Bjorkman, AD and Myers-Smith, IH and Elmendorf, SC and Kattge, J and Diaz, S and Vellend, M and Blok, D and Cornelissen, JHC and Forbes, BC and Henry, GHR and Hollister, RD and Normand, S and Prevéy, JS and Rixen, C and Schaepman-Strub, G and Wilmking, M and Wipf, S and Cornwell, WK and Beck, PSA and Georges, D and Goetz, SJ and Guay, KC and Rüger, N and Soudzilovskaia, NA and Spasojevic, MJ and Alatalo, JM and Alexander, HD and Anadon-Rosell, A and Angers-Blondin, S and Te Beest, M and Berner, LT and Björk, RG and Buchwal, A and Buras, A and Carbognani, M and Christie, KS and Collier, LS and Cooper, EJ and Elberling, B and Eskelinen, A and Frei, ER and Grau, O and Grogan, P and Hallinger, M and Heijmans, MMPD and Hermanutz, L and Hudson, JMG and Johnstone, JF and Hülber, K and Iturrate-Garcia, M and Iversen, CM and Jaroszynska, F and Kaarlejarvi, E and Kulonen, A and Lamarque, LJ and Lantz, TC and Lévesque, E and Little, CJ and Michelsen, A and Milbau, A and Nabe-Nielsen, J and Nielsen, SS and Ninot, JM and Oberbauer, SF and Olofsson, J and Onipchenko, VG and Petraglia, A and Rumpf, SB and Shetti, R and Speed, JDM and Suding, KN and Tape, KD and Tomaselli, M and Trant, AJ and Treier, UA and Tremblay, M and Venn, SE and Vowles, T and Weijers, S and Wookey, PA and Zamin, TJ and Bahn, M and Blonder, B and van Bodegom, PM and Bond-Lamberty, B and Campetella, G and Cerabolini, BEL and Chapin, FS and Craine, JM and Dainese, M and Green, WA and Jansen, S and Kleyer, M and Manning, P and Niinemets, Ü and Onoda, Y and Ozinga, WA and Peñuelas, J and Poschlod, P and Reich, PB and Sandel, B and Schamp, BS and Sheremetiev, SN and de Vries, FT}, title = {Global plant trait relationships extend to the climatic extremes of the tundra biome.}, journal = {Nature communications}, volume = {11}, number = {1}, pages = {1351}, pmid = {32165619}, issn = {2041-1723}, support = {001/WHO_/World Health Organization/International ; }, mesh = {Climate ; Ecosystem ; *Plant Development ; Plants/classification/genetics ; *Tundra ; }, abstract = {The majority of variation in six traits critical to the growth, survival and reproduction of plant species is thought to be organised along just two dimensions, corresponding to strategies of plant size and resource acquisition. However, it is unknown whether global plant trait relationships extend to climatic extremes, and if these interspecific relationships are confounded by trait variation within species. We test whether trait relationships extend to the cold extremes of life on Earth using the largest database of tundra plant traits yet compiled. We show that tundra plants demonstrate remarkably similar resource economic traits, but not size traits, compared to global distributions, and exhibit the same two dimensions of trait variation. Three quarters of trait variation occurs among species, mirroring global estimates of interspecific trait variation. Plant trait relationships are thus generalizable to the edge of global trait-space, informing prediction of plant community change in a warming world.}, } @article {pmid32162068, year = {2020}, author = {Adriaenssens, EM and Sullivan, MB and Knezevic, P and van Zyl, LJ and Sarkar, BL and Dutilh, BE and Alfenas-Zerbini, P and Łobocka, M and Tong, Y and Brister, JR and Moreno Switt, AI and Klumpp, J and Aziz, RK and Barylski, J and Uchiyama, J and Edwards, RA and Kropinski, AM and Petty, NK and Clokie, MRJ and Kushkina, AI and Morozova, VV and Duffy, S and Gillis, A and Rumnieks, J and Kurtböke, İ and Chanishvili, N and Goodridge, L and Wittmann, J and Lavigne, R and Jang, HB and Prangishvili, D and Enault, F and Turner, D and Poranen, MM and Oksanen, HM and Krupovic, M}, title = {Taxonomy of prokaryotic viruses: 2018-2019 update from the ICTV Bacterial and Archaeal Viruses Subcommittee.}, journal = {Archives of virology}, volume = {165}, number = {5}, pages = {1253-1260}, doi = {10.1007/s00705-020-04577-8}, pmid = {32162068}, issn = {1432-8798}, support = {BBS/E/F/000PR10353//UK Biotechnology and Biological Sciences Research Council/ ; Vidi Grant 864.14.004//Netherlands Organization for Scientific Research/ ; MCB-1330800//National Science Foundation/ ; }, mesh = {Archaea/virology ; Archaeal Viruses/*classification ; Bacteria/virology ; Bacteriophages/*classification ; Classification/*methods ; }, abstract = {This article is a summary of the activities of the ICTV's Bacterial and Archaeal Viruses Subcommittee for the years 2018 and 2019. Highlights include the creation of a new order, 10 families, 22 subfamilies, 424 genera and 964 species. Some of our concerns about the ICTV's ability to adjust to and incorporate new DNA- and protein-based taxonomic tools are discussed.}, } @article {pmid32157100, year = {2020}, author = {Kakar, KU and Nawaz, Z and Cui, Z and Cao, P and Jin, J and Shu, Q and Ren, X}, title = {Author Correction: Evolutionary and expression analysis of CAMTA gene family in Nicotiana tabacum yielded insights into their origin, expansion and stress responses.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {4635}, doi = {10.1038/s41598-020-60470-z}, pmid = {32157100}, issn = {2045-2322}, abstract = {An amendment to this paper has been published and can be accessed via a link at the top of the paper.}, } @article {pmid32156798, year = {2020}, author = {Alteio, LV and Schulz, F and Seshadri, R and Varghese, N and Rodriguez-Reillo, W and Ryan, E and Goudeau, D and Eichorst, SA and Malmstrom, RR and Bowers, RM and Katz, LA and Blanchard, JL and Woyke, T}, title = {Complementary Metagenomic Approaches Improve Reconstruction of Microbial Diversity in a Forest Soil.}, journal = {mSystems}, volume = {5}, number = {2}, pages = {}, pmid = {32156798}, issn = {2379-5077}, abstract = {Soil ecosystems harbor diverse microorganisms and yet remain only partially characterized as neither single-cell sequencing nor whole-community sequencing offers a complete picture of these complex communities. Thus, the genetic and metabolic potential of this "uncultivated majority" remains underexplored. To address these challenges, we applied a pooled-cell-sorting-based mini-metagenomics approach and compared the results to bulk metagenomics. Informatic binning of these data produced 200 mini-metagenome assembled genomes (sorted-MAGs) and 29 bulk metagenome assembled genomes (MAGs). The sorted and bulk MAGs increased the known phylogenetic diversity of soil taxa by 7.2% with respect to the Joint Genome Institute IMG/M database and showed clade-specific sequence recruitment patterns across diverse terrestrial soil metagenomes. Additionally, sorted-MAGs expanded the rare biosphere not captured through MAGs from bulk sequences, exemplified through phylogenetic and functional analyses of members of the phylum Bacteroidetes Analysis of 67 Bacteroidetes sorted-MAGs showed conserved patterns of carbon metabolism across four clades. These results indicate that mini-metagenomics enables genome-resolved investigation of predicted metabolism and demonstrates the utility of combining metagenomics methods to tap into the diversity of heterogeneous microbial assemblages.IMPORTANCE Microbial ecologists have historically used cultivation-based approaches as well as amplicon sequencing and shotgun metagenomics to characterize microbial diversity in soil. However, challenges persist in the study of microbial diversity, including the recalcitrance of the majority of microorganisms to laboratory cultivation and limited sequence assembly from highly complex samples. The uncultivated majority thus remains a reservoir of untapped genetic diversity. To address some of the challenges associated with bulk metagenomics as well as low throughput of single-cell genomics, we applied flow cytometry-enabled mini-metagenomics to capture expanded microbial diversity from forest soil and compare it to soil bulk metagenomics. Our resulting data from this pooled-cell sorting approach combined with bulk metagenomics revealed increased phylogenetic diversity through novel soil taxa and rare biosphere members. In-depth analysis of genomes within the highly represented Bacteroidetes phylum provided insights into conserved and clade-specific patterns of carbon metabolism.}, } @article {pmid32152854, year = {2020}, author = {Aripov, T and Blettner, M and Gorbunova, I}, title = {The impact of neighborhood to industrial areas on health in Uzbekistan: an ecological analysis of congenital diseases, infant mortality, and lung cancer.}, journal = {Environmental science and pollution research international}, volume = {27}, number = {14}, pages = {17243-17249}, doi = {10.1007/s11356-020-08190-9}, pmid = {32152854}, issn = {1614-7499}, mesh = {Environmental Exposure/*analysis ; Humans ; Infant ; Infant Mortality ; *Lung Neoplasms ; Prospective Studies ; Uzbekistan ; }, abstract = {After political sovereignty, Uzbekistan's industry is growing fast. However, no investigation was performed so far, to evaluate whether an environmental risk, associated with the industry, is also increasing. Our aim was to investigate whether the distance from factories, as a surrogate measurement for environmental exposure to community, has any influence on some health outcomes in communities of Uzbekistan. For this first investigation, we analyzed prevalence of congenital diseases, infant mortality, and incidence rates of lung cancer, as examples for diseases associated with environmental factors. As crude measurement for the association, we used correlation and regression analysis with the distance to the next factory or plant as explanatory variable. A regression analysis demonstrated an association between the three outcome variables, with the strongest negative correlation (r = - 0.48) and the highest determination power (r[2] = 0.23) for congenital diseases' prevalence. For infant mortality and lung cancer incidence, descriptions and analyses demonstrated lower negative correlation of them with the distance and a lower predictive power of linear models. So, closer distance of the community to specific industrial plants can be considered an indirect factor of higher prevalence of congenital diseases in those communities. Prospective research is needed to further investigate whether the association between birth defects in a neighborhood of industrial plants is causal or due to confounding factors. A policy should consider a degree of known factors distribution in an environment and perform effective prevention of congenital diseases, in close communities.}, } @article {pmid32152534, year = {2020}, author = {Humphreys, AM and Vorontsova, MS and Govaerts, R and Nic Lughadha, E}, title = {Reply to: Regional records improve data quality in determining plant extinction rates.}, journal = {Nature ecology & evolution}, volume = {4}, number = {4}, pages = {515-516}, pmid = {32152534}, issn = {2397-334X}, mesh = {*Data Accuracy ; *Extinction, Biological ; Geography ; Plants ; }, } @article {pmid32151872, year = {2020}, author = {Wan, Y and Jiang, B and Wei, D and Ma, Y}, title = {Ecological criteria for zinc in Chinese soil as affected by soil properties.}, journal = {Ecotoxicology and environmental safety}, volume = {194}, number = {}, pages = {110418}, doi = {10.1016/j.ecoenv.2020.110418}, pmid = {32151872}, issn = {1090-2414}, mesh = {Agriculture ; China ; Databases, Factual ; Ecotoxicology ; Environmental Monitoring/*methods ; Models, Theoretical ; Risk Assessment ; *Soil/chemistry/standards ; Soil Pollutants/*analysis ; Zinc/*analysis ; }, abstract = {The increasing accumulation of zinc (Zn) in agricultural soils has led to the need to assess the potential risk of this element for terrestrial organisms. However, the soil ecological criteria in agricultural soil as a function of soil properties have been sparsely reported. In the present study, we derived the ecological criteria (expressed as predicted no effect concentration (PNEC)) for Zn in soils, based on ecotoxicity data for 19 terrestrial species in Chinese soils, the effect of soil properties on Zn ecotoxicity, differences in species sensitivity, and differences between laboratory and realistic field conditions. First, all ecotoxicity data of Zn for terrestrial organisms in Chinese soils were collected and filtered with given criteria to obtain reliable database. Second, the ecotoxicity data were normalized using Zn ecotoxicity predictive models to eliminate the effect of soil properties on Zn ecotoxicity, and corrected with leaching and aging factors to minimize the differences in Zn ecotoxicity under laboratory and field conditions. Then, species sensitivity distribution (SSD) curves were generated with a Burr Ⅲ function based on corrected ecotoxicity data. The concentration of Zn in soil that provides ecological safety for (100 - x)% of species (HCx), was calculated from the SSD curve and HC5 was used for estimation of PNEC. Finally, we developed the predictive models for HCx by quantifying the relationship between the Zn HCx and soil properties. Results showed that soil pH was the most crucial factor affecting Zn HCx values, with HC5 values varying from 38.3 mg/kg in an acidic soil to 263.3 mg/kg in an alkaline calcareous soil. Both the two-factor (soil pH and OC) and the three-factor (soil pH, OC and CEC) models predicted HCx values well, with determination coefficients (R[2]) of 0.941-0.959 and 0.978-0.982, respectively. This study provides a scientific and reliable basis for the improvement of ecological risk assessment and the establishment of soil environmental quality standards.}, } @article {pmid32151246, year = {2020}, author = {Chen, M and Xu, CY and Wang, X and Ren, CY and Ding, J and Li, L}, title = {Comparative genomics analysis of c-di-GMP metabolism and regulation in Microcystis aeruginosa.}, journal = {BMC genomics}, volume = {21}, number = {1}, pages = {217}, pmid = {32151246}, issn = {1471-2164}, support = {21577081//Natural Science Foundation of China/ ; }, mesh = {Computational Biology ; Cyclic GMP/*metabolism ; Escherichia coli Proteins/genetics/metabolism ; Gene Expression Regulation, Bacterial/*genetics ; Genomics ; Microcystis/classification/genetics/*metabolism ; Phosphorus-Oxygen Lyases/genetics/metabolism ; Phylogeny ; Protein Domains ; Signal Transduction ; }, abstract = {BACKGROUND: Cyanobacteria are of special concern because they proliferate in eutrophic water bodies worldwide and affect water quality. As an ancient photosynthetic microorganism, cyanobacteria can survive in ecologically diverse habitats because of their capacity to rapidly respond to environmental changes through a web of complex signaling networks, including using second messengers to regulate physiology or metabolism. A ubiquitous second messenger, bis-(3',5')-cyclic-dimeric-guanosine monophosphate (c-di-GMP), has been found to regulate essential behaviors in a few cyanobacteria but not Microcystis, which are the most dominant species in cyanobacterial blooms. In this study, comparative genomics analysis was performed to explore the genomic basis of c-di-GMP signaling in Microcystis aeruginosa.

RESULTS: Proteins involved in c-di-GMP metabolism and regulation, such as diguanylate cyclases, phosphodiesterases, and PilZ-containing proteins, were encoded in M. aeruginosa genomes. However, the number of identified protein domains involved in c-di-GMP signaling was not proportional to the size of M. aeruginosa genomes (4.97 Mb in average). Pan-genome analysis showed that genes involved in c-di-GMP metabolism and regulation are conservative in M. aeruginosa strains. Phylogenetic analysis showed good congruence between the two types of phylogenetic trees based on 31 highly conserved protein-coding genes and sensor domain-coding genes. Propensity for gene loss analysis revealed that most of genes involved in c-di-GMP signaling are stable in M. aeruginosa strains. Moreover, bioinformatics and structure analysis of c-di-GMP signal-related GGDEF and EAL domains revealed that they all possess essential conserved amino acid residues that bind the substrate. In addition, it was also found that all selected M. aeruginosa genomes encode PilZ domain containing proteins.

CONCLUSIONS: Comparative genomics analysis of c-di-GMP metabolism and regulation in M. aeruginosa strains helped elucidating the genetic basis of c-di-GMP signaling pathways in M. aeruginosa. Knowledge of c-di-GMP metabolism and relevant signal regulatory processes in cyanobacteria can enhance our understanding of their adaptability to various environments and bloom-forming mechanism.}, } @article {pmid32150554, year = {2020}, author = {Young, NE and Jarnevich, CS and Sofaer, HR and Pearse, I and Sullivan, J and Engelstad, P and Stohlgren, TJ}, title = {A modeling workflow that balances automation and human intervention to inform invasive plant management decisions at multiple spatial scales.}, journal = {PloS one}, volume = {15}, number = {3}, pages = {e0229253}, pmid = {32150554}, issn = {1932-6203}, mesh = {Algorithms ; Apiaceae/*growth & development ; Automation ; Conservation of Natural Resources ; Decision Support Techniques ; Humans ; *Introduced Species ; Models, Statistical ; Pennisetum/*growth & development ; Risk Assessment ; Workflow ; }, abstract = {Predictions of habitat suitability for invasive plant species can guide risk assessments at regional and national scales and inform early detection and rapid-response strategies at local scales. We present a general approach to invasive species modeling and mapping that meets objectives at multiple scales. Our methodology is designed to balance trade-offs between developing highly customized models for few species versus fitting non-specific and generic models for numerous species. We developed a national library of environmental variables known to physiologically limit plant distributions and relied on human input based on natural history knowledge to further narrow the variable set for each species before developing habitat suitability models. To ensure efficiency, we used largely automated modeling approaches and human input only at key junctures. We explore and present uncertainty by using two alternative sources of background samples, including five statistical algorithms, and constructing model ensembles. We demonstrate the use and efficiency of the Software for Assisted Habitat Modeling [SAHM 2.1.2], a package in VisTrails, which performs the majority of the modeling analyses. Our workflow includes solicitation of expert feedback on model outputs such as spatial prediction results and variable response curves, and iterative improvement based on new data availability and directed field validation of initial model results. We highlight the utility of the models for decision-making at regional and local scales with case studies of two plant species that invade natural areas: fountain grass (Pennisetum setaceum) and goutweed (Aegopodium podagraria). By balancing model automation with human intervention, we can efficiently provide land managers with mapped predicted distributions for multiple invasive species to inform decisions across spatial scales.}, } @article {pmid32150536, year = {2020}, author = {Brett, T and Ajelli, M and Liu, QH and Krauland, MG and Grefenstette, JJ and van Panhuis, WG and Vespignani, A and Drake, JM and Rohani, P}, title = {Detecting critical slowing down in high-dimensional epidemiological systems.}, journal = {PLoS computational biology}, volume = {16}, number = {3}, pages = {e1007679}, pmid = {32150536}, issn = {1553-7358}, support = {U01 GM110744/GM/NIGMS NIH HHS/United States ; U54 GM111274/GM/NIGMS NIH HHS/United States ; }, mesh = {*Communicable Diseases, Emerging/epidemiology/transmission ; Computational Biology/methods ; *Epidemics/classification/statistics & numerical data ; *Epidemiological Monitoring ; Humans ; Measles/epidemiology/transmission ; *Models, Biological ; }, abstract = {Despite medical advances, the emergence and re-emergence of infectious diseases continue to pose a public health threat. Low-dimensional epidemiological models predict that epidemic transitions are preceded by the phenomenon of critical slowing down (CSD). This has raised the possibility of anticipating disease (re-)emergence using CSD-based early-warning signals (EWS), which are statistical moments estimated from time series data. For EWS to be useful at detecting future (re-)emergence, CSD needs to be a generic (model-independent) feature of epidemiological dynamics irrespective of system complexity. Currently, it is unclear whether the predictions of CSD-derived from simple, low-dimensional systems-pertain to real systems, which are high-dimensional. To assess the generality of CSD, we carried out a simulation study of a hierarchy of models, with increasing structural complexity and dimensionality, for a measles-like infectious disease. Our five models included: i) a nonseasonal homogeneous Susceptible-Exposed-Infectious-Recovered (SEIR) model, ii) a homogeneous SEIR model with seasonality in transmission, iii) an age-structured SEIR model, iv) a multiplex network-based model (Mplex) and v) an agent-based simulator (FRED). All models were parameterised to have a herd-immunity immunization threshold of around 90% coverage, and underwent a linear decrease in vaccine uptake, from 92% to 70% over 15 years. We found evidence of CSD prior to disease re-emergence in all models. We also evaluated the performance of seven EWS: the autocorrelation, coefficient of variation, index of dispersion, kurtosis, mean, skewness, variance. Performance was scored using the Area Under the ROC Curve (AUC) statistic. The best performing EWS were the mean and variance, with AUC > 0.75 one year before the estimated transition time. These two, along with the autocorrelation and index of dispersion, are promising candidate EWS for detecting disease emergence.}, } @article {pmid32143687, year = {2020}, author = {Pible, O and Allain, F and Jouffret, V and Culotta, K and Miotello, G and Armengaud, J}, title = {Estimating relative biomasses of organisms in microbiota using "phylopeptidomics".}, journal = {Microbiome}, volume = {8}, number = {1}, pages = {30}, pmid = {32143687}, issn = {2049-2618}, mesh = {Bacteria/classification/metabolism ; Bacterial Proteins/*analysis/genetics ; Biomass ; Databases, Protein ; *Microbiota ; *Models, Theoretical ; Peptides/*genetics ; *Phylogeny ; Proteome ; Proteomics/*methods ; Tandem Mass Spectrometry ; }, abstract = {BACKGROUND: There is an important need for the development of fast and robust methods to quantify the diversity and temporal dynamics of microbial communities in complex environmental samples. Because tandem mass spectrometry allows rapid inspection of protein content, metaproteomics is increasingly used for the phenotypic analysis of microbiota across many fields, including biotechnology, environmental ecology, and medicine.

RESULTS: Here, we present a new method for identifying the biomass contribution of any given organism based on a signature describing the number of peptide sequences shared with all other organisms, calculated by mathematical modeling and phylogenetic relationships. This so-called "phylopeptidomics" principle allows for the calculation of the relative ratios of peptide-specified taxa by the linear combination of such signatures applied to an experimental metaproteomic dataset. We illustrate its efficiency using artificial mixtures of two closely related pathogens of clinical interest, and with more complex microbiota models.

CONCLUSIONS: This approach paves the way to a new vision of taxonomic changes and accurate label-free quantitative metaproteomics for fine-tuned functional characterization. Video abstract.}, } @article {pmid32142370, year = {2020}, author = {Dingerdissen, HM and Bastian, F and Vijay-Shanker, K and Robinson-Rechavi, M and Bell, A and Gogate, N and Gupta, S and Holmes, E and Kahsay, R and Keeney, J and Kincaid, H and King, CH and Liu, D and Crichton, DJ and Mazumder, R}, title = {OncoMX: A Knowledgebase for Exploring Cancer Biomarkers in the Context of Related Cancer and Healthy Data.}, journal = {JCO clinical cancer informatics}, volume = {4}, number = {}, pages = {210-220}, pmid = {32142370}, issn = {2473-4276}, support = {U01 CA215010/CA/NCI NIH HHS/United States ; }, mesh = {Animals ; Biological Ontologies ; Biomarkers, Tumor/*analysis ; Computational Biology/*methods ; Data Mining/*methods ; Databases, Genetic/*standards ; Humans ; *Knowledge Bases ; Mice ; Neoplasms/*diagnosis/therapy ; *Software ; User-Computer Interface ; }, abstract = {PURPOSE: The purpose of OncoMX[1] knowledgebase development was to integrate cancer biomarker and relevant data types into a meta-portal, enabling the research of cancer biomarkers side by side with other pertinent multidimensional data types.

METHODS: Cancer mutation, cancer differential expression, cancer expression specificity, healthy gene expression from human and mouse, literature mining for cancer mutation and cancer expression, and biomarker data were integrated, unified by relevant biomedical ontologies, and subjected to rule-based automated quality control before ingestion into the database.

RESULTS: OncoMX provides integrated data encompassing more than 1,000 unique biomarker entries (939 from the Early Detection Research Network [EDRN] and 96 from the US Food and Drug Administration) mapped to 20,576 genes that have either mutation or differential expression in cancer. Sentences reporting mutation or differential expression in cancer were extracted from more than 40,000 publications, and healthy gene expression data with samples mapped to organs are available for both human genes and their mouse orthologs.

CONCLUSION: OncoMX has prioritized user feedback as a means of guiding development priorities. By mapping to and integrating data from several cancer genomics resources, it is hoped that OncoMX will foster a dynamic engagement between bioinformaticians and cancer biomarker researchers. This engagement should culminate in a community resource that substantially improves the ability and efficiency of exploring cancer biomarker data and related multidimensional data.}, } @article {pmid32140907, year = {2020}, author = {Gong, Y and Yang, B and Chen, W}, title = {Systematic genome editing of the genes spanning an entire chromosome by CRISPR/Cas9 in a vertebrate-zebrafish (Danio rerio).}, journal = {Science China. Life sciences}, volume = {63}, number = {7}, pages = {1096-1097}, pmid = {32140907}, issn = {1869-1889}, support = {P30 DK020593/DK/NIDDK NIH HHS/United States ; R01 DK109407/DK/NIDDK NIH HHS/United States ; R01 DK117147/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; Animals, Genetically Modified ; Base Sequence ; CRISPR-Associated Protein 9/*genetics ; CRISPR-Cas Systems/*genetics ; Chromosomes/genetics ; Databases, Genetic ; Gene Editing/*methods ; Genome ; Transcriptome/*genetics ; Zebrafish ; Zebrafish Proteins/genetics ; }, } @article {pmid32140140, year = {2020}, author = {Cullen, CM and Aneja, KK and Beyhan, S and Cho, CE and Woloszynek, S and Convertino, M and McCoy, SJ and Zhang, Y and Anderson, MZ and Alvarez-Ponce, D and Smirnova, E and Karstens, L and Dorrestein, PC and Li, H and Sen Gupta, A and Cheung, K and Powers, JG and Zhao, Z and Rosen, GL}, title = {Emerging Priorities for Microbiome Research.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {136}, pmid = {32140140}, issn = {1664-302X}, abstract = {Microbiome research has increased dramatically in recent years, driven by advances in technology and significant reductions in the cost of analysis. Such research has unlocked a wealth of data, which has yielded tremendous insight into the nature of the microbial communities, including their interactions and effects, both within a host and in an external environment as part of an ecological community. Understanding the role of microbiota, including their dynamic interactions with their hosts and other microbes, can enable the engineering of new diagnostic techniques and interventional strategies that can be used in a diverse spectrum of fields, spanning from ecology and agriculture to medicine and from forensics to exobiology. From June 19-23 in 2017, the NIH and NSF jointly held an Innovation Lab on Quantitative Approaches to Biomedical Data Science Challenges in our Understanding of the Microbiome. This review is inspired by some of the topics that arose as priority areas from this unique, interactive workshop. The goal of this review is to summarize the Innovation Lab's findings by introducing the reader to emerging challenges, exciting potential, and current directions in microbiome research. The review is broken into five key topic areas: (1) interactions between microbes and the human body, (2) evolution and ecology of microbes, including the role played by the environment and microbe-microbe interactions, (3) analytical and mathematical methods currently used in microbiome research, (4) leveraging knowledge of microbial composition and interactions to develop engineering solutions, and (5) interventional approaches and engineered microbiota that may be enabled by selectively altering microbial composition. As such, this review seeks to arm the reader with a broad understanding of the priorities and challenges in microbiome research today and provide inspiration for future investigation and multi-disciplinary collaboration.}, } @article {pmid32138329, year = {2020}, author = {Bojarska, J and Remko, M and Breza, M and Madura, ID and Kaczmarek, K and Zabrocki, J and Wolf, WM}, title = {A Supramolecular Approach to Structure-Based Design with A Focus on Synthons Hierarchy in Ornithine-Derived Ligands: Review, Synthesis, Experimental and in Silico Studies.}, journal = {Molecules (Basel, Switzerland)}, volume = {25}, number = {5}, pages = {}, pmid = {32138329}, issn = {1420-3049}, mesh = {Databases, Factual ; Hydrogen Bonding ; Molecular Conformation ; Molecular Structure ; Ornithine/*chemistry ; }, abstract = {The success of innovative drugs depends on an interdisciplinary and holistic approach to their design and development. The supramolecular architecture of living systems is controlled by non-covalent interactions to a very large extent. The latter are prone to extensive cooperation and like a virtuoso play a symphony of life. Thus, the design of effective ligands should be based on thorough knowledge on the interactions at either a molecular or high topological level. In this work, we emphasize the importance of supramolecular structure and ligand-based design keeping the potential of supramolecular H-bonding synthons in focus. In this respect, the relevance of supramolecular chemistry for advanced therapies is appreciated and undisputable. It has developed tools, such as Hirshfeld surface analysis, using a huge data on supramolecular interactions in over one million structures which are deposited in the Cambridge Structure Database (CSD). In particular, molecular interaction surfaces are useful for identification of macromolecular active sites followed by in silico docking experiments. Ornithine-derived compounds are a new, promising class of multi-targeting ligands for innovative therapeutics and cosmeceuticals. In this work, we present the synthesis together with the molecular and supramolecular structure of a novel ornithine derivative, namely N-α,N-δ)-dibenzoyl-(α)-hydroxymethylornithine, 1. It was investigated by modern experimental and in silico methods in detail. The incorporation of an aromatic system into the ornithine core induces stacking interactions, which are vital in biological processes. In particular, rare C=O[…]π intercontacts have been identified in 1. Supramolecular interactions were analyzed in all structures of ornithine derivatives deposited in the CSD. The influence of substituent was assessed by the Hirshfeld surface analysis. It revealed that the crystal packing is stabilized mainly by H[…]O, O[…]H, C[…]H, Cl (Br, F)[…]H and O[…]O interactions. Additionally, π[…]π, C-H[…]π and N-O[…]π interactions were also observed. All relevant H-bond energies were calculated using the Lippincott and Schroeder H-bond model. A library of synthons is provided. In addition, the large synthons (Long-Range Synthon Aufbau Module) were considered. The DFT optimization either in vacuo or in solutio yields very similar molecular species. The major difference with the relevant crystal structure was related to the conformation of terminal benzoyl C15-C20 ring. Furthermore, in silico prediction of the extensive physicochemical ADME profile (absorption, distribution, metabolism and excretion) related to the drug-likeness and medicinal chemistry friendliness revealed that a novel ornithine derivative 1 has the potential to be a new drug candidate. It has shown good in silico absorption and very low toxicity.}, } @article {pmid32135326, year = {2020}, author = {Wang, K and Xu, Q and Li, T}, title = {Does recent climate warming drive spatiotemporal shifts in functioning of high-elevation hydrological systems?.}, journal = {The Science of the total environment}, volume = {719}, number = {}, pages = {137507}, doi = {10.1016/j.scitotenv.2020.137507}, pmid = {32135326}, issn = {1879-1026}, abstract = {Reference evapotranspiration (ETo) is the basic component of the hydrological cycle. This study systematically analyzed the spatiotemporal variations of ETo in the Three-River Headwaters Region (TRHR) by utilizing the FAO Penman-Monteith equation during the period of 1961-2016, and studied the impact of climatic variables on ETo fluctuation based on sensitivity analysis and contribution analysis. Over the past 56 years, ETo increased in most months and annually in most regions of the TRHR, and the spatial distribution for annual ETo varied apparently. Sensitivity analysis revealed that ETo responded more to changes in maximum temperature and sunshine duration than relative humidity, wind speed, and minimum temperature. The relative importance of climatic variables to ETo was influenced by the ETo sensitivity and the fluctuation of climatic variables. Contribution analysis indicated that the significant temperature increase was mainly responsible for the observed increase in ETo. Besides, spatially distributed analysis showed that the annual TRHR ETo tended to increase from east to west, north to south, and high to low elevation. The analysis also indicated a dominant altitudinal spatial gradient in the sensitivity of ETo to changes in different climatic variables. The physical mechanisms for ETo variations discussed in this study might provide a reference for water resources management and conservation of high-elevation areas.}, } @article {pmid32135309, year = {2020}, author = {Settlecowski, AE and Cuervo, AM and Tello, JG and Harvey, MG and Brumfield, RT and Derryberry, EP}, title = {Investigating the utility of traditional and genomic multi-locus datasets to resolve relationships in Lipaugus and Tijuca (Cotingidae).}, journal = {Molecular phylogenetics and evolution}, volume = {147}, number = {}, pages = {106779}, doi = {10.1016/j.ympev.2020.106779}, pmid = {32135309}, issn = {1095-9513}, support = {P30 CA013330/CA/NCI NIH HHS/United States ; }, mesh = {Animals ; Biological Evolution ; *Databases, Genetic ; *Genetic Loci ; Genetic Speciation ; *Genomics ; Geography ; Passeriformes/*genetics ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {Rapid diversification limits our ability to resolve evolutionary relationships and examine diversification history, as in the case of the Neotropical cotingas. Here we present an analysis with complete taxon sampling for the cotinga genera Lipaugus and Tijuca, which include some of the most range-restricted (e.g., T. condita) and also the most widespread and familiar (e.g., L. vociferans) forest birds in the Neotropics. We used two datasets: (1) Sanger sequencing data sampled from eight loci in 34 individuals across all described taxa and (2) sequence capture data linked to 1,079 ultraconserved elements and conserved exons sampled from one or two individuals per species. Phylogenies estimated from the Sanger sequencing data failed to resolve three nodes, but the sequence capture data produced a well-supported tree. Lipaugus and Tijuca formed a single, highly supported clade, but Tijuca species were not sister and were embedded within Lipaugus. A dated phylogeny confirmed Lipaugus and Tijuca diversified rapidly in the Miocene. Our study provides a detailed evolutionary hypothesis for Lipaugus and Tijuca and demonstrates that increasing genomic sampling can prove instrumental in resolving the evolutionary history of recent radiations.}, } @article {pmid32134018, year = {2020}, author = {Joshua, V and Kaliaperumal, K and Krishnamurthy, KB and Muthusamy, R and Venkatachalam, R and Gowri, KA and Shete, VC and Ramasamy, S and Gupta, N and Murhekar, MV and , }, title = {Exploration of population ecological factors related to the spatial heterogeneity of dengue fever cases diagnosed through a national network of laboratories in India, 2017.}, journal = {The Indian journal of medical research}, volume = {151}, number = {1}, pages = {79-86}, pmid = {32134018}, issn = {0971-5916}, mesh = {Dengue/*diagnosis/*epidemiology/virology ; Dengue Virus/*isolation & purification/pathogenicity ; Disease Outbreaks ; Female ; Humans ; India/epidemiology ; Laboratories ; Male ; Population Density ; *Population Surveillance ; Seasons ; }, abstract = {BACKGROUND & OBJECTIVES: Dengue virus (DENV) transmission is known to be influenced by the environmental conditions. During 2017, the Viral Research and Diagnostic Laboratories (VRDLs) tested 78,744 suspected dengue fever (DF) patients, of whom, 21,260 were laboratory confirmed. The objectives of the study were to evaluate the hypothesis that spatial heterogeneity existed for DF patients and to identify significant determinants of DENV transmission in various districts across the Indian States during 2017.

METHODS: Laboratory confirmed DF cases were analysed from 402 districts spread across the Indian States. The determinants for DF transmission included in the model were population density, proportion of population living in rural areas, proportion o f forest cover area to the total geographical area, proportion of persons not able to read and write and who were aged greater than seven years; the climatic variables considered were minimum, maximum and average temperature, precipitation and cumulative rainfall. The spatial heterogeneity was assessed using spatial regression analysis.

RESULTS: DF cases showed strong spatial dependency, with Moran's I=4.44 (P <0.001). The robust measure for spatial lag (6.55; P=0.01) was found to be the best model fit for the data set. Minimum temperature and cumulative rainfall were significant predictors.

A significant increase in the number of dengue cases has occurred when the minimum temperature was 23.0-25.8°C and the cumulative rainfall 118.14-611.64 mm across the Indian districts. Further in-depth investigations incorporating more number of demographic, ecological and socio-economic factors would be needed for robust conclusions.}, } @article {pmid32133714, year = {2020}, author = {Birer, C and Moreau, CS and Tysklind, N and Zinger, L and Duplais, C}, title = {Disentangling the assembly mechanisms of ant cuticular bacterial communities of two Amazonian ant species sharing a common arboreal nest.}, journal = {Molecular ecology}, volume = {29}, number = {7}, pages = {1372-1385}, doi = {10.1111/mec.15400}, pmid = {32133714}, issn = {1365-294X}, mesh = {Animal Shells/chemistry/microbiology ; Animals ; Ants/classification/*microbiology ; Bacteria/*classification ; DNA Barcoding, Taxonomic ; DNA, Bacterial/genetics ; Environment ; Host Specificity ; Metabolome ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Species Specificity ; Trees ; }, abstract = {Bacteria living on the cuticle of ants are generally studied for their protective role against pathogens, especially in the clade of fungus-growing ants. However, little is known regarding the diversity of cuticular bacteria in other ant host species, as well as the mechanisms leading to the composition of these communities. Here, we used 16S rRNA gene amplicon sequencing to study the influence of host species, species interactions and the pool of bacteria from the environment on the assembly of cuticular bacterial communities on two phylogenetically distant Amazonian ant species that frequently nest together inside the roots system of epiphytic plants, Camponotus femoratus and Crematogaster levior. Our results show that (a) the vast majority of the bacterial community on the cuticle is shared with the nest, suggesting that most bacteria on the cuticle are acquired through environmental acquisition, (b) 5.2% and 2.0% of operational taxonomic units (OTUs) are respectively specific to Ca. femoratus and Cr. levior, probably representing their respective core cuticular bacterial community, and (c) 3.6% of OTUs are shared between the two ant species. Additionally, mass spectrometry metabolomics analysis of metabolites on the cuticle of ants, which excludes the detection of cuticular hydrocarbons produced by the host, were conducted to evaluate correlations among bacterial OTUs and m/z ion mass. Although some positive and negative correlations are found, the cuticular chemical composition was weakly species-specific, suggesting that cuticular bacterial communities are prominently environmentally acquired. Overall, our results suggest the environment is the dominant source of bacteria found on the cuticle of ants.}, } @article {pmid32132605, year = {2020}, author = {Neves, A and Vieira, AR and Sequeira, V and Paiva, RB and Gordo, LS and Paulo, OS}, title = {Highly regional population structure of Spondyliosoma cantharus depicted by nuclear and mitochondrial DNA data.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {4063}, pmid = {32132605}, issn = {2045-2322}, mesh = {Animals ; DNA, Mitochondrial/*genetics ; *Databases, Nucleic Acid ; *Haplotypes ; Phylogeography ; Sea Bream/classification/*genetics ; }, abstract = {Resolution of population structure represents an effective way to define biological stocks and inform efficient fisheries management. In the present study, the phylogeography of the protogynous sparid Spondyliosoma cantharus, in the East Atlantic and Mediterranean Sea, was investigated with nuclear (S7) and mitochondrial (cytochrome b) DNA markers. Significant divergence of four regional genetic groups was observed: North Eastern Atlantic, Mediterranean Sea, Western African Transition (Cape Verde) and Gulf of Guinea (Angola). The two southern populations (Cape Verde and Angola) each comprised reciprocally monophyletic mtDNA lineages, revealed low levels of diversity in Cape Verde and high diversity for Angola despite being represented by only 14 individuals. A complete divergence between North Atlantic and Mediterranean populations was depicted by the mitochondrial marker, but a highly shared nuclear haplotype revealed an incomplete lineage sorting between these regions. Bayesian skyline plots and associated statistics revealed different dynamics among the four regions. Cape Verde showed no expansion and the expansion time estimated for Angola was much older than for the other regions. Mediterranean region seems to have experienced an early population growth but has remained with a stable population size for the last 30000 years while the North Atlantic population has been steadily growing. The lack of genetic structuring within these regions should not be taken as evidence of demographic panmixia in light of potential resolution thresholds and previous evidence of intra-regional phenotypic heterogeneity.}, } @article {pmid32130895, year = {2020}, author = {Shahamatdar, S and He, MX and Reyna, MA and Gusev, A and AlDubayan, SH and Van Allen, EM and Ramachandran, S}, title = {Germline Features Associated with Immune Infiltration in Solid Tumors.}, journal = {Cell reports}, volume = {30}, number = {9}, pages = {2900-2908.e4}, pmid = {32130895}, issn = {2211-1247}, support = {R01 CA227388/CA/NCI NIH HHS/United States ; R01 GM118652/GM/NIGMS NIH HHS/United States ; U01 CA217875/CA/NCI NIH HHS/United States ; U01 CA233100/CA/NCI NIH HHS/United States ; }, mesh = {Autoimmune Diseases/immunology ; DNA Repair/genetics ; Genetic Predisposition to Disease ; Genome-Wide Association Study ; Germ Cells/*metabolism ; Humans ; Leukocytes/metabolism ; Lymphocytes, Tumor-Infiltrating/*immunology ; Multifactorial Inheritance ; Neoplasms/*genetics/*immunology ; Phenotype ; Polymorphism, Single Nucleotide/genetics ; Risk Factors ; T-Lymphocytes, Helper-Inducer/immunology ; Transcription, Genetic ; }, abstract = {The immune composition of the tumor microenvironment influences response and resistance to immunotherapies. While numerous studies have identified somatic correlates of immune infiltration, germline features that associate with immune infiltrates in cancers remain incompletely characterized. We analyze seven million autosomal germline variants in the TCGA cohort and test for association with established immune-related phenotypes that describe the tumor immune microenvironment. We identify one SNP associated with the amount of infiltrating follicular helper T cells; 23 candidate genes, some of which are involved in cytokine-mediated signaling and others containing cancer-risk SNPs; and networks with genes that are part of the DNA repair and transcription elongation pathways. In addition, we find a positive association between polygenic risk for rheumatoid arthritis and amount of infiltrating CD8[+] T cells. Overall, we identify multiple germline genetic features associated with tumor-immune phenotypes and develop a framework for probing inherited features that contribute to differences in immune infiltration.}, } @article {pmid32124068, year = {2020}, author = {Reina-García, J and Toro-Vélez, AF and Peña-Varón, MR and Olaya-Ochoa, J and Figueroa-Casas, A}, title = {Methodological design for the macro-location of a micropollutants monitoring network in tropical rivers: a case study in Cauca River.}, journal = {Environmental monitoring and assessment}, volume = {192}, number = {4}, pages = {205}, pmid = {32124068}, issn = {1573-2959}, mesh = {Colombia ; Environmental Monitoring ; *Geographic Information Systems ; *Rivers ; South America ; *Water Pollutants, Chemical/analysis ; }, abstract = {Establishing scientifically the macro-location of a micropollutants monitoring network in tropical Andean rivers is a complex process, because information gathering is restricted by high-cost of analysis and limited availability of analytical techniques, which lead to inadequate sampling strategies that hinder the representativeness of samples. Thus, this work proposes a methodology for determining the number of representative sampling sections in a micropollutant monitoring network to characterise the ecological risk in tropical Andean torrential rivers. The proposed methodology consists of four stages: identification of the potential sampling units by Spline interpolation; calculation of the number of representative sections for a stratified sampling with an acceptable level of confidence and error; spatial allocation of the potential sampling units into sections by hierarchical cluster analysis; and representation of the spatial distribution of the sampling sections through a geographic information system (GIS). The proposed methodology is dynamic, and therefore, it can be revisited as more data are obtained in the subsequent years; it has the possibility of being applied to other inter-Andean valley rivers that interact with the tropical Andean sloppy mountains and serves as a tool for decision making by environmental authorities regarding the optimisation of the existing monitoring networks in terms of micropollutants to promote sustainable management of water resources. The proposed methodology is applied in the Upper Cauca River Basin (UCRB), which is located in southwest Colombia, South America.}, } @article {pmid32123323, year = {2020}, author = {Chen, F and Wu, P and Deng, S and Zhang, H and Hou, Y and Hu, Z and Zhang, J and Chen, X and Yang, JR}, title = {Dissimilation of synonymous codon usage bias in virus-host coevolution due to translational selection.}, journal = {Nature ecology & evolution}, volume = {4}, number = {4}, pages = {589-600}, pmid = {32123323}, issn = {2397-334X}, support = {R01 GM103232/GM/NIGMS NIH HHS/United States ; }, mesh = {Codon ; *Codon Usage ; RNA, Transfer ; Selection, Genetic ; *Viruses ; }, abstract = {Eighteen of the 20 amino acids are each encoded by more than one synonymous codon. Due to differential transfer RNA supply within the cell, synonymous codons are not used with equal frequency, a phenomenon termed codon usage bias (CUB). Previous studies have demonstrated that CUB of endogenous genes trans-regulates the translational efficiency of other genes. We hypothesized similar effects for CUB of exogenous genes on host translation, and tested it in the case of viral infection, a common form of naturally occurring exogenous gene translation. We analysed public Ribo-Seq datasets from virus-infected yeast and human cells and showed that virus CUB trans-regulated tRNA availability, and therefore the relative decoding time of codons. Manipulative experiments in yeast using 37 synonymous fluorescent proteins confirmed that an exogenous gene with CUB more similar to that of the host would apply decreased translational load on the host per unit of expression, whereas expression of the exogenous gene was elevated. The combination of these two effects was that exogenous genes with CUB overly similar to that of the host severely impeded host translation. Finally, using a manually curated list of viruses and natural and symptomatic hosts, we found that virus CUB tended to be more similar to that of symptomatic hosts than that of natural hosts, supporting a general deleterious effect of excessive CUB similarity between virus and host. Our work revealed repulsion between virus and host CUBs when they are overly similar, a previously unrecognized complexity in the coevolution of virus and host.}, } @article {pmid32122303, year = {2020}, author = {Manchanda, N and Portwood, JL and Woodhouse, MR and Seetharam, AS and Lawrence-Dill, CJ and Andorf, CM and Hufford, MB}, title = {GenomeQC: a quality assessment tool for genome assemblies and gene structure annotations.}, journal = {BMC genomics}, volume = {21}, number = {1}, pages = {193}, pmid = {32122303}, issn = {1471-2164}, support = {Project Number 5030-21000-068-00-D//Agricultural Research Service/ ; 58-5030-8-064//Specific Coorperative Agreement/ ; 58-5030-8-064//Specific Coorperative Agreement/ ; }, mesh = {Chromosome Mapping ; Computational Biology/methods ; Genomics/*methods ; High-Throughput Nucleotide Sequencing ; Humans ; Molecular Sequence Annotation ; Sequence Analysis, DNA ; Software ; }, abstract = {BACKGROUND: Genome assemblies are foundational for understanding the biology of a species. They provide a physical framework for mapping additional sequences, thereby enabling characterization of, for example, genomic diversity and differences in gene expression across individuals and tissue types. Quality metrics for genome assemblies gauge both the completeness and contiguity of an assembly and help provide confidence in downstream biological insights. To compare quality across multiple assemblies, a set of common metrics are typically calculated and then compared to one or more gold standard reference genomes. While several tools exist for calculating individual metrics, applications providing comprehensive evaluations of multiple assembly features are, perhaps surprisingly, lacking. Here, we describe a new toolkit that integrates multiple metrics to characterize both assembly and gene annotation quality in a way that enables comparison across multiple assemblies and assembly types.

RESULTS: Our application, named GenomeQC, is an easy-to-use and interactive web framework that integrates various quantitative measures to characterize genome assemblies and annotations. GenomeQC provides researchers with a comprehensive summary of these statistics and allows for benchmarking against gold standard reference assemblies.

CONCLUSIONS: The GenomeQC web application is implemented in R/Shiny version 1.5.9 and Python 3.6 and is freely available at https://genomeqc.maizegdb.org/ under the GPL license. All source code and a containerized version of the GenomeQC pipeline is available in the GitHub repository https://github.com/HuffordLab/GenomeQC.}, } @article {pmid32114693, year = {2020}, author = {Karthikeyan, S and Rodriguez-R, LM and Heritier-Robbins, P and Hatt, JK and Huettel, M and Kostka, JE and Konstantinidis, KT}, title = {Genome repository of oil systems: An interactive and searchable database that expands the catalogued diversity of crude oil-associated microbes.}, journal = {Environmental microbiology}, volume = {22}, number = {6}, pages = {2094-2106}, doi = {10.1111/1462-2920.14966}, pmid = {32114693}, issn = {1462-2920}, support = {No 321611-00//Gulf of Mexico Research Initiative/International ; //Georgia Institute of Technology/International ; }, mesh = {*Biodegradation, Environmental ; *Databases, Genetic ; Gulf of Mexico ; Hydrocarbons/metabolism ; Metagenome/genetics ; Metagenomics ; Microbiota/genetics ; Oil and Gas Fields/*microbiology ; Petroleum/metabolism/*microbiology ; Petroleum Pollution/*analysis ; }, abstract = {Microbial communities ultimately control the fate of petroleum hydrocarbons (PHCs) that enter the natural environment, but the interactions of microbes with PHCs and the environment are highly complex and poorly understood. Genome-resolved metagenomics can help unravel these complex interactions. However, the lack of a comprehensive database that integrates existing genomic/metagenomic data from oil environments with physicochemical parameters known to regulate the fate of PHCs currently limits data analysis and interpretations. Here, we curated a comprehensive, searchable database that documents microbial populations in natural oil ecosystems and oil spills, along with available underlying physicochemical data, geocoded via geographic information system to reveal their geographic distribution patterns. Analysis of the ~2000 metagenome-assembled genomes (MAGs) available in the database revealed strong ecological niche specialization within habitats. Over 95% of the recovered MAGs represented novel taxa underscoring the limited representation of cultured organisms from oil-contaminated and oil reservoir ecosystems. The majority of MAGs linked to oil-contaminated ecosystems were detectable in non-oiled samples from the Gulf of Mexico but not in comparable samples from elsewhere, indicating that the Gulf is primed for oil biodegradation. The repository should facilitate future work toward a predictive understanding of the microbial taxa and their activities that control the fate of oil spills.}, } @article {pmid32110807, year = {2020}, author = {Raza, SHA and Khan, R and Gui, L and Schreurs, NM and Wang, X and Mei, C and Yang, X and Gong, C and Zan, L}, title = {Bioinformatics analysis and genetic polymorphisms in genomic region of the bovine SH2B2 gene and their associations with molecular breeding for body size traits in qinchuan beef cattle.}, journal = {Bioscience reports}, volume = {40}, number = {3}, pages = {}, pmid = {32110807}, issn = {1573-4935}, mesh = {Adaptor Proteins, Signal Transducing ; Alleles ; Animals ; Body Size/*genetics ; Body Weight/*genetics ; Breeding/methods ; Cattle/*genetics ; Computational Biology ; Gene Frequency/genetics ; Genetic Association Studies ; Genomics ; Genotype ; Haplotypes ; Polymorphism, Single Nucleotide ; Sequence Analysis, DNA ; }, abstract = {The Src homology 2 B 2 (SH2B2) gene regulate energy balance and body weight at least partially by enhancing Janus kinase-2 (JAK2)-mediated cytokine signaling, including leptin and/or GH signaling. Leptin is an adipose hormone that controls body weight. The objective of the present study is to evaluate the association between body measurement traits and SH2B2 gene polymorphisms as responsible mutations. For this purpose, we selected four single-nucleotide polymorphisms (SNPs) in SH2B2 gene, including two in intron 5 (g.20545A>G, and g.20570G>A, one synonymous SNP g.20693T>C, in exon 6 and one in intron 8 (g.24070C>A, and genotyped them in Qinchuan cattle. SNPs in sample populations were in medium polymorphism level (0.250A, g.20693T>C, and g.24070C>A, significantly (P < 0.05) associated with body length (BL) and chest circumference (CC) in Qinchuan cattle. In addition, H4H3 and H5H5 diplotype had highly significantly (P < 0.01) greater body length (BL), rump length (RL), and chest circumference (CC) than H4H2. Our investigation will not only extend the spectrum of genetic variation of bovine SH2B2 gene, but also provide useful information for the marker assisted selection in beef cattle breeding program.}, } @article {pmid32110737, year = {2020}, author = {Lin, ZJ and Jung, J and Goel, S and Skeem, J}, title = {The limits of human predictions of recidivism.}, journal = {Science advances}, volume = {6}, number = {7}, pages = {eaaz0652}, pmid = {32110737}, issn = {2375-2548}, mesh = {Databases as Topic ; Humans ; Likelihood Functions ; Models, Statistical ; *Recidivism ; }, abstract = {Dressel and Farid recently found that laypeople were as accurate as statistical algorithms in predicting whether a defendant would reoffend, casting doubt on the value of risk assessment tools in the criminal justice system. We report the results of a replication and extension of Dressel and Farid's experiment. Under conditions similar to the original study, we found nearly identical results, with humans and algorithms performing comparably. However, algorithms beat humans in the three other datasets we examined. The performance gap between humans and algorithms was particularly pronounced when, in a departure from the original study, participants were not provided with immediate feedback on the accuracy of their responses. Algorithms also outperformed humans when the information provided for predictions included an enriched (versus restricted) set of risk factors. These results suggest that algorithms can outperform human predictions of recidivism in ecologically valid settings.}, } @article {pmid32109701, year = {2020}, author = {Li, K and Yang, B and Wang, L}, title = {Performance evaluation of a biotrickling filter for the removal of gas-phase 1,2-dichlorobenzene: Influence of rhamnolipid and ferric ions.}, journal = {Chemosphere}, volume = {250}, number = {}, pages = {126261}, doi = {10.1016/j.chemosphere.2020.126261}, pmid = {32109701}, issn = {1879-1298}, mesh = {Air Pollutants/analysis/*chemistry ; Biodegradation, Environmental ; Biofilms ; Bioreactors/microbiology ; Chlorobenzenes/*chemistry ; Filtration/methods ; Glycolipids/*chemistry ; Ions ; Iron ; }, abstract = {The aim of this study was to evaluate the influence of rhamnolipid (RL) and ferric ions on the performance of a biotrickling filter (BTF) for the removal of gas-phase 1,2-dichlorobenzene (o-DCB). A comprehensive investigation of microbial growth, pollutant solubility, extracellular polymeric substances (EPS) and enzymatic activity in o-DCB degradation by an isolated strain Bacillus cereus DL-1 with/without RL and Fe[3+] were carried out using batch microcosm experiments. In addition, o-DCB removal performance, biofilm morphology, and microbial community structures in two identical lab-scale biotrickling filters (named BTF1 and BTF2) inoculated with strain DL-1 were studied. The batch microcosm experiments demonstrated that 120 mg L[-1] RL and 4 mg L[-1] Fe[3+] could enhance the biodegradation of o-DCB, which may be due to promotion on bacterial growth, o-DCB solubilization, C12O enzyme activity, and polysaccharide (PS) and protein (PN) in EPS. Fourier transform infrared (FTIR) spectra indicated that the addition of RL with Fe[3+] had notable effects on the functional groups of PS and PN in EPS. The experimental results in BTFs indicate that the removal efficiency of o-DCB decreased from 100% to 56.4% for BTF1, which was not fed with RL and Fe[3+], and from 100% to 80.3% for BTF2, which was fed with RL and Fe[3+], when the inlet loading rate increased from 4.88 to 102 g m[-3] h[-1] at an empty bed residence time of 60 s. In addition, the microbial adhesive strength and the microbial community structure were different among both BTFs, highlighting the positive effects of RL and Fe[3+].}, } @article {pmid32103465, year = {2020}, author = {Cychosz, M and Romeo, R and Soderstrom, M and Scaff, C and Ganek, H and Cristia, A and Casillas, M and de Barbaro, K and Bang, JY and Weisleder, A}, title = {Longform recordings of everyday life: Ethics for best practices.}, journal = {Behavior research methods}, volume = {52}, number = {5}, pages = {1951-1969}, pmid = {32103465}, issn = {1554-3528}, support = {K01 MH111957/MH/NIMH NIH HHS/United States ; T32 MH112510/MH/NIMH NIH HHS/United States ; }, mesh = {Behavioral Research ; *Confidentiality ; Data Collection ; Ethics, Research ; Humans ; Informed Consent ; *Privacy ; *Video Recording ; }, abstract = {Recent advances in large-scale data storage and processing offer unprecedented opportunities for behavioral scientists to collect and analyze naturalistic data, including from underrepresented groups. Audio data, particularly real-world audio recordings, are of particular interest to behavioral scientists because they provide high-fidelity access to subtle aspects of daily life and social interactions. However, these methodological advances pose novel risks to research participants and communities. In this article, we outline the benefits and challenges associated with collecting, analyzing, and sharing multi-hour audio recording data. Guided by the principles of autonomy, privacy, beneficence, and justice, we propose a set of ethical guidelines for the use of longform audio recordings in behavioral research. This article is also accompanied by an Open Science Framework Ethics Repository that includes informed consent resources such as frequent participant concerns and sample consent forms.}, } @article {pmid32102685, year = {2020}, author = {Machulska, A and Eiler, TJ and Grünewald, A and Brück, R and Jahn, K and Niehaves, B and Ullrich, H and Klucken, T}, title = {Promoting smoking abstinence in smokers willing to quit smoking through virtual reality-approach bias retraining: a study protocol for a randomized controlled trial.}, journal = {Trials}, volume = {21}, number = {1}, pages = {227}, pmid = {32102685}, issn = {1745-6215}, support = {005-1706-0006//Ministerium für Kultur und Wissenschaft, Land NRW/ ; }, mesh = {Behavior Therapy/*methods ; Bias ; Humans ; Randomized Controlled Trials as Topic/*methods ; Smokers/psychology ; Smoking Cessation/*methods/psychology ; *Virtual Reality ; }, abstract = {BACKGROUND: Automatic processes to approach smoking-related cues have been repeatedly linked to smoking status, intensity of smoking, and cigarette craving. Moreover, recent findings suggest that targeting those tendencies directly by means of approach bias modification (ABM) has merit in changing maladaptive approach tendencies for drug cues and reducing drug consumption. However, training effects tend to be small. Embedding the training into virtual reality (VR) technology could be a promising way to improve training efficacy. The present protocol describes a randomized controlled trial that aims to assess the efficacy of a newly developed VR-ABM as a means of reducing smoking-related approach biases or nicotine consumption in smokers seeking abstinence.

METHODS: One hundred daily smokers who are motivated to quit smoking will be recruited into the randomized controlled trial. All participants will attend a brief smoking cessation intervention (TAU) and will be randomly assigned either to the experimental (VR-avoidance training) or the placebo-control group (VR-placebo training). During the VR-avoidance training, participants are implicitly instructed to make an avoidance movement in response to smoking-related objects (e.g., cigarettes) and an approach movement in response to alternative objects (e.g., healthy food). During the VR-placebo training, no such contingency between arm movement and item content exists. Trainings are administered in six sessions within two weeks. Training effects on automatic approach tendencies and smoking behavior are measured immediately after training and at a 7-week follow-up.

DISCUSSION: Embedding the training into virtual reality (VR) technology could be a promising new way to improve ecological validity, realism, and immersion and thereby increase ABM training effects. The results of this study can inform future research in the optimization and advancement of treatment for addiction.

TRIAL REGISTRATION: Registered with Current Controlled Trials: study ID ISRCTN16006023. Registered on 28 March 2019.}, } @article {pmid32098186, year = {2020}, author = {Tomazatos, A and Marschang, RE and Maranda, I and Baum, H and Bialonski, A and Spînu, M and Lühken, R and Schmidt-Chanasit, J and Cadar, D}, title = {Letea Virus: Comparative Genomics and Phylogenetic Analysis of a Novel Reassortant Orbivirus Discovered in Grass Snakes (Natrix natrix).}, journal = {Viruses}, volume = {12}, number = {2}, pages = {}, pmid = {32098186}, issn = {1999-4915}, mesh = {Animals ; Arboviruses/genetics ; Colubridae/*virology ; Genetic Variation ; *Genome, Viral ; *Genomics ; Host Specificity ; Orbivirus/*classification/isolation & purification ; *Phylogeny ; Psychodidae/virology ; Reassortant Viruses/classification/*genetics ; Recombination, Genetic ; Romania ; Sequence Analysis, DNA ; Whole Genome Sequencing ; }, abstract = {The discovery and characterization of novel arthropod-borne viruses provide valuable information on their genetic diversity, ecology, evolution and potential to threaten animal or public health. Arbovirus surveillance is not conducted regularly in Romania, being particularly very scarce in the remote and diverse areas like the Danube Delta. Here we describe the detection and genetic characterization of a novel orbivirus (Reoviridae: Orbivirus) designated as Letea virus, which was found in grass snakes (Natrix natrix) during a metagenomic and metatranscriptomic survey conducted between 2014 and 2017. This virus is the first orbivirus discovered in reptiles. Phylogenetic analyses placed Letea virus as a highly divergent species in the Culicoides-/sand fly-borne orbivirus clade. Gene reassortment and intragenic recombination were detected in the majority of the nine Letea virus strains obtained, implying that these mechanisms play important roles in the evolution and diversification of the virus. However, the screening of arthropods, including Culicoides biting midges collected within the same surveillance program, tested negative for Letea virus infection and could not confirm the arthropod vector of the virus. The study provided complete genome sequences for nine Letea virus strains and new information about orbivirus diversity, host range, ecology and evolution. The phylogenetic associations warrant further screening of arthropods, as well as sustained surveillance efforts for elucidation of Letea virus natural cycle and possible implications for animal and human health.}, } @article {pmid32096111, year = {2020}, author = {Wieland, ML and Biggs, BK and Brockman, TA and Johnson, A and Meiers, SJ and Sim, LA and Tolleson, E and Hanza, MM and Weis, JA and Rosenman, JR and Novotny, PJ and Patten, CA and Clark, MM and Millerbernd, J and Sia, IG}, title = {Club Fit: Development of a Physical Activity and Healthy Eating Intervention at a Boys & Girls Club After School Program.}, journal = {The journal of primary prevention}, volume = {41}, number = {2}, pages = {153-170}, pmid = {32096111}, issn = {1573-6547}, support = {UL1TR000135/TR/NCATS NIH HHS/United States ; }, mesh = {Adolescent ; Child ; Community-Based Participatory Research ; *Diet, Healthy ; *Exercise ; Female ; Health Promotion/*methods ; Humans ; Male ; Motivation ; Pilot Projects ; Self Efficacy ; United States ; }, abstract = {Children and adolescents from minority and low income backgrounds face social and environmental challenges to engaging in physical activity and healthy eating to maintain a healthy weight. In this study, we present pilot work to develop and implement a multi-component physical activity and healthy eating intervention at a Boys & Girls Club (BGC) afterschool program. Using a community-based participatory approach, BGC staff and academic researchers developed intervention components informed by formative studies and based on a Social Ecological Theory framework. Components included healthy eating and physical activity policy implementation, staff training, a challenge and self-monitoring program for healthy behaviors, a peer-coaching program for healthy behaviors, and a social marketing campaign. We assessed pilot feasibility through a single group, pre-post study design with measures collected at baseline and 6 months. The sample included 61 children with a mean age of 10.4 years. Mean (SD) body mass index (BMI) percentile was 72.8 (28.9); 47.5% were in the healthy weight range for their age. We found statistically significant improvements of self-efficacy and motivation for physical activity. Self-efficacy and motivation for fruit and vegetable consumption, sugary beverage consumption, and screen time improved but were not statistically different from baseline. We found no improvements of perceived social support, objectively measured physical activity, or self-reported dietary quality. Though BMI did not improve overall, a dose effect was observed such that attendance in Club Fit specific programming was significantly correlated with decreased BMI z scores. Processes and products from this study may be helpful to other communities aiming to address childhood obesity prevention through afterschool programs.}, } @article {pmid32094443, year = {2020}, author = {Sampangi-Ramaiah, MH and Jagadheesh, and Dey, P and Jambagi, S and Vasantha Kumari, MM and Oelmüller, R and Nataraja, KN and Venkataramana Ravishankar, K and Ravikanth, G and Uma Shaanker, R}, title = {An endophyte from salt-adapted Pokkali rice confers salt-tolerance to a salt-sensitive rice variety and targets a unique pattern of genes in its new host.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {3237}, pmid = {32094443}, issn = {2045-2322}, mesh = {Endophytes/drug effects/isolation & purification/*physiology ; Gene Expression Regulation, Plant/drug effects ; Gene Ontology ; *Genes, Plant ; Molecular Sequence Annotation ; Mycelium/drug effects/growth & development ; Oryza/drug effects/*genetics/*microbiology ; Plant Roots/drug effects/growth & development ; Plant Shoots/drug effects/growth & development ; Potassium/metabolism ; Protein Interaction Maps/genetics ; Quality Control ; Reproducibility of Results ; Salinity ; Salt Tolerance/drug effects/*genetics ; Sodium/metabolism ; Sodium Chloride/*pharmacology ; Stress, Physiological/drug effects/genetics ; Transcriptome/genetics ; }, abstract = {Endophytes, both of bacterial and fungal origin, are ubiquitously present in all plants. While their origin and evolution are enigmatic, there is burgeoning literature on their role in promoting growth and stress responses in their hosts. We demonstrate that a salt-tolerant endophyte isolated from salt-adapted Pokkali rice, a Fusarium sp., colonizes the salt-sensitive rice variety IR-64, promotes its growth under salt stress and confers salinity stress tolerance to its host. Physiological parameters, such as assimilation rate and chlorophyll stability index were higher in the colonized plants. Comparative transcriptome analysis revealed 1348 up-regulated and 1078 down-regulated genes in plants colonized by the endophyte. Analysis of the regulated genes by MapMan and interaction network programs showed that they are involved in both abiotic and biotic stress tolerance, and code for proteins involved in signal perception (leucine-rich repeat proteins, receptor-like kinases) and transduction (Ca[2+] and calmodulin-binding proteins), transcription factors, secondary metabolism and oxidative stress scavenging. For nine genes, the data were validated by qPCR analysis in both roots and shoots. Taken together, these results show that salt-adapted Pokkali rice varieties are powerful sources for the identification of novel endophytes, which can be used to confer salinity tolerance to agriculturally important, but salt-sensitive rice varieties.}, } @article {pmid32094358, year = {2020}, author = {Marcus, JH and Posth, C and Ringbauer, H and Lai, L and Skeates, R and Sidore, C and Beckett, J and Furtwängler, A and Olivieri, A and Chiang, CWK and Al-Asadi, H and Dey, K and Joseph, TA and Liu, CC and Der Sarkissian, C and Radzevičiūtė, R and Michel, M and Gradoli, MG and Marongiu, P and Rubino, S and Mazzarello, V and Rovina, D and La Fragola, A and Serra, RM and Bandiera, P and Bianucci, R and Pompianu, E and Murgia, C and Guirguis, M and Orquin, RP and Tuross, N and van Dommelen, P and Haak, W and Reich, D and Schlessinger, D and Cucca, F and Krause, J and Novembre, J}, title = {Genetic history from the Middle Neolithic to present on the Mediterranean island of Sardinia.}, journal = {Nature communications}, volume = {11}, number = {1}, pages = {939}, pmid = {32094358}, issn = {2041-1723}, support = {HHSN271201100005C/DA/NIDA NIH HHS/United States ; R01 GM132383/GM/NIGMS NIH HHS/United States ; R01 HG007089/HG/NHGRI NIH HHS/United States ; T32 GM007197/GM/NIGMS NIH HHS/United States ; }, mesh = {Archaeology/methods ; Body Remains ; Chromosomes, Human, X/genetics ; Chromosomes, Human, Y/genetics ; *DNA, Ancient ; DNA, Mitochondrial/*genetics ; Datasets as Topic ; Female ; Genetics, Population/*history ; History, 15th Century ; History, 16th Century ; History, 17th Century ; History, 18th Century ; History, 19th Century ; History, 20th Century ; History, 21st Century ; History, Ancient ; History, Medieval ; *Human Migration ; Humans ; Italy ; Male ; *Models, Genetic ; Sequence Analysis, DNA ; }, abstract = {The island of Sardinia has been of particular interest to geneticists for decades. The current model for Sardinia's genetic history describes the island as harboring a founder population that was established largely from the Neolithic peoples of southern Europe and remained isolated from later Bronze Age expansions on the mainland. To evaluate this model, we generate genome-wide ancient DNA data for 70 individuals from 21 Sardinian archaeological sites spanning the Middle Neolithic through the Medieval period. The earliest individuals show a strong affinity to western Mediterranean Neolithic populations, followed by an extended period of genetic continuity on the island through the Nuragic period (second millennium BCE). Beginning with individuals from Phoenician/Punic sites (first millennium BCE), we observe spatially-varying signals of admixture with sources principally from the eastern and northern Mediterranean. Overall, our analysis sheds light on the genetic history of Sardinia, revealing how relationships to mainland populations shifted over time.}, } @article {pmid32094260, year = {2020}, author = {Samanta, P and Mandal, RS and Saha, RN and Shaw, S and Ghosh, P and Dutta, S and Ghosh, A and Imamura, D and Morita, M and Ohnishi, M and Ramamurthy, T and Mukhopadhyay, AK}, title = {A Point Mutation in carR Is Involved in the Emergence of Polymyxin B-Sensitive Vibrio cholerae O1 El Tor Biotype by Influencing Gene Transcription.}, journal = {Infection and immunity}, volume = {88}, number = {5}, pages = {}, pmid = {32094260}, issn = {1098-5522}, mesh = {Alleles ; Anti-Bacterial Agents/pharmacology ; Calcium/metabolism ; DNA-Binding Proteins/genetics/metabolism ; Down-Regulation/genetics ; Escherichia coli/genetics ; Point Mutation/*genetics ; Polymorphism, Single Nucleotide/genetics ; Polymyxin B/*pharmacology ; Transcription, Genetic/*genetics ; Vibrio cholerae O1/*drug effects/*genetics/metabolism ; }, abstract = {Antimicrobial peptides play an important role in host defense against Vibrio cholerae Generally, the V. cholerae O1 classical biotype is polymyxin B (PB) sensitive and El Tor is relatively resistant. Detection of classical biotype traits like the production of classical cholera toxin and PB sensitivity in El Tor strains has been reported in recent years, including in the devastating Yemen cholera outbreak during 2016-2018. To investigate the factor(s) responsible for the shift in the trend of sensitivity to PB, we studied the two-component system encoded by carRS, regulating the lipid A modification of El Tor vibrios, and found that only carR contains a single nucleotide polymorphism (SNP) in recently emerged PB-sensitive strains. We designated the two alleles present in PB-resistant and -sensitive strains carR[r] and carR[s] alleles, respectively, and replaced the carR[s] allele of a sensitive strain with the carR[r] allele, using an allelic-exchange approach. The sensitive strain then became resistant. The PB-resistant strain N16961 was made susceptible to PB in a similar fashion. Our in silico CarR protein models suggested that the D89N substitution in the more stable CarR[s] protein brings the two structural domains of CarR closer, constricting the DNA binding cleft. This probably reduces the expression of the carR-regulated almEFG operon, inducing PB susceptibility. Expression of almEFG in PB-sensitive strains was found to be downregulated under natural culturing conditions. In addition, the expression of carR and almEG decreased in all strains with increased concentrations of extracellular Ca[2+] but increased with a rise in pH. The downregulation of almEFG in CarR[s] strains confirmed that the G265A mutation is responsible for the emergence of PB-sensitive El Tor strains.}, } @article {pmid32093752, year = {2020}, author = {Urban, L and Remmele, CW and Dittrich, M and Schwarz, RF and Müller, T}, title = {covRNA: discovering covariate associations in large-scale gene expression data.}, journal = {BMC research notes}, volume = {13}, number = {1}, pages = {92}, pmid = {32093752}, issn = {1756-0500}, support = {124 (Project B2)//Transregio 124 - FungiNet Transregio/ ; }, mesh = {Computational Biology/*methods ; Gene Expression Profiling/*methods ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Multivariate Analysis ; Oligonucleotide Array Sequence Analysis/methods/statistics & numerical data ; Reproducibility of Results ; Sequence Analysis, RNA/*methods ; *Software ; }, abstract = {OBJECTIVE: The biological interpretation of gene expression measurements is a challenging task. While ordination methods are routinely used to identify clusters of samples or co-expressed genes, these methods do not take sample or gene annotations into account. We aim to provide a tool that allows users of all backgrounds to assess and visualize the intrinsic correlation structure of complex annotated gene expression data and discover the covariates that jointly affect expression patterns.

RESULTS: The Bioconductor package covRNA provides a convenient and fast interface for testing and visualizing complex relationships between sample and gene covariates mediated by gene expression data in an entirely unsupervised setting. The relationships between sample and gene covariates are tested by statistical permutation tests and visualized by ordination. The methods are inspired by the fourthcorner and RLQ analyses used in ecological research for the analysis of species abundance data, that we modified to make them suitable for the distributional characteristics of both, RNA-Seq read counts and microarray intensities, and to provide a high-performance parallelized implementation for the analysis of large-scale gene expression data on multi-core computational systems. CovRNA provides additional modules for unsupervised gene filtering and plotting functions to ensure a smooth and coherent analysis workflow.}, } @article {pmid32092852, year = {2020}, author = {Wan, Y and Zhang, M and Hong, A and Zhang, Y and Liu, Y}, title = {Characteristics of Microsatellites Mined from Transcriptome Data and the Development of Novel Markers in Paeonia lactiflora.}, journal = {Genes}, volume = {11}, number = {2}, pages = {}, pmid = {32092852}, issn = {2073-4425}, mesh = {Data Mining ; Databases, Genetic ; Gene Expression Profiling ; *Genetic Markers ; High-Throughput Nucleotide Sequencing ; *Microsatellite Repeats ; Molecular Sequence Annotation ; Paeonia/*genetics/growth & development ; Plant Breeding ; Plant Proteins/genetics ; Quantitative Trait Loci ; Sequence Analysis, RNA/*methods ; }, abstract = {The insufficient number of available simple sequence repeats (SSRs) inhibits genetic research on and molecular breeding of Paeonia lactiflora, a flowering crop with great economic value. The objective of this study was to develop SSRs for P. lactiflora with Illumina RNA sequencing and assess the role of SSRs in gene regulation. The results showed that dinucleotides with AG/CT repeats were the most abundant type of repeat motif in P. lactiflora and were preferentially distributed in untranslated regions. Significant differences in SSR size were observed among motif types and locations. A large number of unigenes containing SSRs participated in catalytic activity, metabolic processes and cellular processes, and 28.16% of all transcription factors and 21.74% of hub genes for inflorescence stem straightness were found to contain SSRs. Successful amplification was achieved with 89.05% of 960 pairs of SSR primers, 55.83% of which were polymorphic, and most of the 46 tested primers had a high level of transferability to the genus Paeonia. Principal component and cluster dendrogram analyses produced results consistent with known genealogical relationships. This study provides a set of SSRs with abundant information for future accession identification, marker-trait association and molecular assisted breeding in P. lactiflora.}, } @article {pmid32092569, year = {2020}, author = {Pinto, ÉSM and Dorn, M and Feltes, BC}, title = {The tale of a versatile enzyme: Alpha-amylase evolution, structure, and potential biotechnological applications for the bioremediation of n-alkanes.}, journal = {Chemosphere}, volume = {250}, number = {}, pages = {126202}, doi = {10.1016/j.chemosphere.2020.126202}, pmid = {32092569}, issn = {1879-1298}, mesh = {Alkanes/chemistry ; *Biodegradation, Environmental ; Biotechnology ; Petroleum/metabolism ; alpha-Amylases ; }, abstract = {As the primary source of a wide range of industrial products, the study of petroleum-derived compounds is of pivotal importance. However, the process of oil extraction and refinement is among the most environmentally hazardous practices, impacting almost all levels of the ecological chain. So far, the most appropriate strategy to overcome such an issue is through bioremediation, which revolves around the employment of different microorganisms to degrade hazardous compounds, generating less environmental impact and lower monetary costs. In this sense, a myriad of organisms and enzymes are considered possible candidates for the bioremediation process. Amidst the potential candidates is α-amylase, an evolutionary conserved starch-degrading enzyme. Notably, α-amylase was not only seen to degrade n-alkanes, a subclass of alkanes considered the most abundant petroleum-derived compounds but also low-density polyethylene, a dangerous pollutant produced from petroleum. Thus, due to its high conservation in both eukaryotic and prokaryotic lineages, in addition to the capability to degrade different types of hazardous compounds, the study of α-amylase becomes a rising interest. Nevertheless, there are no studies that review all biotechnological applications of α-amylase for bioremediation. In this work, we critically review the potential biotechnological applications of α-amylase, focusing on the biodegradation of petroleum-derived compounds. Evolutionary aspects are discussed, as well for all structural information and all features that could impact on the employment of this protein in the biotechnological industry, such as pH, temperature, and medium conditions. New perspectives and critical assessments are conducted regarding the application of α-amylase in the bioremediation of n-alkanes.}, } @article {pmid32091207, year = {2020}, author = {Yang, H and Lou, C and Li, W and Liu, G and Tang, Y}, title = {Computational Approaches to Identify Structural Alerts and Their Applications in Environmental Toxicology and Drug Discovery.}, journal = {Chemical research in toxicology}, volume = {33}, number = {6}, pages = {1312-1322}, doi = {10.1021/acs.chemrestox.0c00006}, pmid = {32091207}, issn = {1520-5010}, mesh = {*Computational Biology ; *Drug Discovery ; *Ecotoxicology ; Humans ; Structure-Activity Relationship ; }, abstract = {Structural alerts are a simple and easy way to identify toxic compounds being widely used in environmental toxicology research and drug discovery. With the emergence of big data techniques in recent years and their applications in chemistry and toxicology, computational approaches have become a promising method to identify structural alerts. In this Review, we describe the recent progress in computational methods for identification of structural alerts and their applications in toxicology. Two major computational approaches, namely frequency analysis and interpretable machine learning models, are reviewed. Recent studies have shown that both approaches are superior to expert systems with respect to predictive capability. Methodologies for defining the applicability domain of such approaches are also reviewed, with their importance stemming from their ability to not only improve the predictive performance of structural alert models but also ensure the confidence of a prediction. In addition to toxicity prediction, structural alerts could be also used to explain quantitative structure-activity relationship models and guide lead optimization in drug discovery. Nevertheless, there are still some challenges to be solved, such as how to address the co-existence of several structural alerts in one molecule, how to directly compare computationally derived structural alerts with expert systems, and how to explore new mechanisms of toxicity.}, } @article {pmid32089532, year = {2020}, author = {Zha, X and Wang, X and Li, J and Gao, F and Zhou, Y}, title = {Complete chloroplast genome of Sophora alopecuroides (Papilionoideae): molecular structures, comparative genome analysis and phylogenetic analysis.}, journal = {Journal of genetics}, volume = {99}, number = {}, pages = {}, pmid = {32089532}, issn = {0973-7731}, mesh = {Computational Biology/methods ; Conserved Sequence ; Genes, Chloroplast ; *Genome, Chloroplast ; *Genomics/methods ; High-Throughput Nucleotide Sequencing ; Microsatellite Repeats ; Molecular Sequence Annotation ; Phenotype ; *Phylogeny ; Repetitive Sequences, Nucleic Acid ; Sophora/*classification/*genetics ; }, abstract = {Sophora alopecuroides belongs to the genus Sophora of the family Papilionoideae. It is mainly distributed in the desert and semidesert areas of northern China, and has high medicinal value and ecological function. Previous studies have reported the chemical composition and ecological functions of S. alopecuroides. However, only a few reports are available on the genomic information of S. alopecuroides, especially the chloroplast genome, which greatly limits the study of the evolutionary relationship between other species of Papilionoideae. Here, we report the complete chloroplast genome of S. alopecuroides. The size of the chloroplast genome is 155,207 bp, and the GC content is 36.44%. The S. alopecuroides chloroplast genome consists of 132 genes, including 83 protein-coding genes, 41 transfer RNA (tRNA) genes,and eight ribosomal RNA (rRNA) genes. Phylogenetic analysis revealed the taxonomic position of S. alopecuroides in Papilionoideae, and the genus Sophora and the genus Ammopiptanthus were highly related. Comparative genomics analysis revealed the gene rearrangement in the evolution of S. alopecuroides. The comparison between S. alopecuroides and the species of the Papilionoideae identified a novel 23 kb inversion between the trnC-GCA and trnF-GAA which occurred before the divergence of Sophora and Ammopiptanthus of Thermopsideae. This study provided an essential data for the understanding of phylogenetic status of S. alopecuroides.}, } @article {pmid32087521, year = {2020}, author = {Booij, SH and Wigman, JTW and Jacobs, N and Thiery, E and Derom, C and Wichers, M and Oravecz, Z}, title = {Cortisol dynamics in depression: Application of a continuous-time process model.}, journal = {Psychoneuroendocrinology}, volume = {115}, number = {}, pages = {104598}, doi = {10.1016/j.psyneuen.2020.104598}, pmid = {32087521}, issn = {1873-3360}, mesh = {Adolescent ; Adult ; Belgium ; Datasets as Topic ; Depression/*metabolism/physiopathology ; Depressive Disorder, Major/*metabolism/physiopathology ; Ecological Momentary Assessment ; Female ; Humans ; Hydrocortisone/*metabolism ; Middle Aged ; Models, Statistical ; Multilevel Analysis ; *Registries ; Saliva/metabolism ; Young Adult ; }, abstract = {BACKGROUND: The temporal dynamics of cortisol may be altered in depression. Optimally studying these dynamics in daily life requires specific analytical methods. We used a continuous-time multilevel process model to study set point (rhythm-corrected mean), variability around this set point, and regulation strength (speed with which cortisol levels regulate back to the set point after any perturbation). We examined the generalizability of the parameters across two data sets with different sampling and assay methods, and the hypothesis that regulation strength, but not set point or variability thereof, would be altered in depressed, compared to non-depressed individuals.

METHODS: The first data set is a general population sample of female twins (n = 523), of which 21 were depressed, with saliva samples collected 10 times a day for 5 days. The second data set consists of pair-matched clinically depressed and non-depressed individuals (n = 30), who collected saliva samples 3 times a day for 30 days. Set point, regulation strength and variability were examined using a Bayesian multilevel Ornstein-Uhlenbeck (OU) process model. They were first compared between samples, and thereafter assessed within samples in relation to depression.

RESULTS: Set point and variability of salivary cortisol were twice as high in the female twin sample, compared to the pair-matched sample. The ratio between set point and variability, as well as regulation strength, which are relative measures and therefore less affected by the specific assay method, were similar across samples. The average regulation strength was high; after an increase in cortisol, cortisol levels would decrease by 63 % after 10 min, and by 95 % after 30 min, but depressed individuals of the pair-matched sample displayed an even faster regulation strength.

CONCLUSIONS: The OU process model recovered similar cortisol dynamics for the relative parameters of the two data sets. The results suggest that regulation strength is increased in depressed individuals. We recommend the presented methodology for future studies and call for replications with more diverse depressed populations.}, } @article {pmid32087246, year = {2020}, author = {Elberri, AI and Galal-Khallaf, A and Gibreel, SE and El-Sakhawy, SF and El-Garawani, I and El-Sayed Hassab ElNabi, S and Mohammed-Geba, K}, title = {DNA and eDNA-based tracking of the North African sharptooth catfish Clarias gariepinus.}, journal = {Molecular and cellular probes}, volume = {51}, number = {}, pages = {101535}, doi = {10.1016/j.mcp.2020.101535}, pmid = {32087246}, issn = {1096-1194}, mesh = {Africa, Northern ; Animals ; Catfishes/*genetics ; DNA/*analysis ; DNA Primers ; Databases, Genetic ; Ecosystem ; Electron Transport Complex IV/*genetics ; Genetics, Population ; Mitochondria/enzymology/*genetics ; Polymerase Chain Reaction ; }, abstract = {The African sharptooth catfish, Clarias gariepinus, contributes much to the River Nile ecosystem by its high omnivorosity, sturdiness, growth rates, and fecundity. It was globally appreciated as a key fluvial aquaculture species. Yet, it is also one of the top world freshwater aliens. Monitoring the genetic diversity of different economically and ecologically important species as well as development of markers that aid their tracing and abundance are fundamental. This is chiefly due to the growing international threats of environmental pollution, reduction, and loss of biodiversity. Herein, the genetic diversity of C. gariepinus along the River Nile in Egypt was assessed through sequencing of the mitochondrial cytochrome oxidase subunit I (COI). Also, a qPCR assay based on C. gariepinus 16srDNA was developed to assess the species abundance through environmental water DNA samples (eDNA). The results showed low genetic diversity of that species in Egypt. Moreover, its populations exhibited high rates of fixation. Testing its eDNA-based marker resulted in an unambiguous quantitative trend in situ, in agreement with reports of local fishermen. These eDNA signals were strong at least 1 Km upstream to the initial sampling areas, even where no C. gariepinus fishing activities are carried out. This possibly indicated a degree of homogenous species-abundance in each of the studied areas. Finally, the results identified a need for better conservation strategies for C. gariepinus, since its low diversity in the Egyptian River Nile may represent a threat against its persistence under the continuously changing environmental conditions. Moreover, using non-invasive sampling methods, e.g. based on aquatic eDNA quantification, can aid much the detection of areas of abundance of C. gariepinus, especially for both the economic importance it contributes and the invasive power it possesses.}, } @article {pmid32086786, year = {2021}, author = {Quintas-Soriano, C and Gibson, DM and Brandt, JS and López-Rodríguez, MD and Cabello, J and Aguilera, PA and Castro, AJ}, title = {An interdisciplinary assessment of private conservation areas in the Western United States.}, journal = {Ambio}, volume = {50}, number = {1}, pages = {150-162}, pmid = {32086786}, issn = {1654-7209}, support = {IIA-1301792//National Science Foundation/ ; }, mesh = {*Conservation of Natural Resources ; *Ecosystem ; United States ; }, abstract = {Conservation easements are the fastest growing private conservation strategy in the United States. However, mechanisms to assess private land conservation as well as their support by the general public are not well understood. This study uses the ecosystem services framework for assessing existing private lands in Idaho and identifies areas for future conservation easements. Using conservation targets of the land trust as a guide for selecting ecosystem services, we (a) mapped the spatial delivery of conservation targets across public and private lands, (b) explored public awareness in terms of social importance and vulnerability, and (c) mapped future priority areas by characterizing conservation bundles. We found that public lands provided the highest levels of conservation targets, and we found no difference in conservation target provision between private areas and conservation easements. The spatial characterization of conservation target bundles identified potential future priority areas for conservation easements, which can guide planning of land trust conservation efforts.}, } @article {pmid32085722, year = {2020}, author = {Khelik, K and Sandve, GK and Nederbragt, AJ and Rognes, T}, title = {NucBreak: location of structural errors in a genome assembly by using paired-end Illumina reads.}, journal = {BMC bioinformatics}, volume = {21}, number = {1}, pages = {66}, pmid = {32085722}, issn = {1471-2105}, support = {Computational Life Science initiative (CLSi)//Universitetet i Oslo/ ; }, mesh = {Genome ; Genomics/*methods ; High-Throughput Nucleotide Sequencing/*methods ; Reproducibility of Results ; Sequence Analysis, DNA/*methods ; Software ; }, abstract = {BACKGROUND: Advances in whole genome sequencing strategies have provided the opportunity for genomic and comparative genomic analysis of a vast variety of organisms. The analysis results are highly dependent on the quality of the genome assemblies used. Assessment of the assembly accuracy may significantly increase the reliability of the analysis results and is therefore of great importance.

RESULTS: Here, we present a new tool called NucBreak aimed at localizing structural errors in assemblies, including insertions, deletions, duplications, inversions, and different inter- and intra-chromosomal rearrangements. The approach taken by existing alternative tools is based on analysing reads that do not map properly to the assembly, for instance discordantly mapped reads, soft-clipped reads and singletons. NucBreak uses an entirely different and unique method to localise the errors. It is based on analysing the alignments of reads that are properly mapped to an assembly and exploit information about the alternative read alignments. It does not annotate detected errors. We have compared NucBreak with other existing assembly accuracy assessment tools, namely Pilon, REAPR, and FRCbam as well as with several structural variant detection tools, including BreakDancer, Lumpy, and Wham, by using both simulated and real datasets.

CONCLUSIONS: The benchmarking results have shown that NucBreak in general predicts assembly errors of different types and sizes with relatively high sensitivity and with lower false discovery rate than the other tools. Such a balance between sensitivity and false discovery rate makes NucBreak a good alternative to the existing assembly accuracy assessment tools and SV detection tools. NucBreak is freely available at https://github.com/uio-bmi/NucBreak under the MPL license.}, } @article {pmid32085426, year = {2020}, author = {Zhu, X and Li, S and Liu, L and Li, S and Luo, Y and Lv, C and Wang, B and Cheng, CHK and Chen, H and Yang, X}, title = {Genome Sequencing and Analysis of Thraustochytriidae sp. SZU445 Provides Novel Insights into the Polyunsaturated Fatty Acid Biosynthesis Pathway.}, journal = {Marine drugs}, volume = {18}, number = {2}, pages = {}, pmid = {32085426}, issn = {1660-3397}, support = {2018YFA0902500//National Key Research and Development Project/ ; 2018A030313139//the Natural Science Foundation of Guangdong Province/ ; SGLH20180622152010394//Joint R&D Project of Shenzhen-Hong Kong Innovation/ ; KQJSCX20180328093806045//Natural Science Foundation of Shenzhen/ ; CKCY2016042710211071//Shenzhen Grant Plan for Science & Technology/ ; 827-000192, 2016100//Shenzhen University Start-up Research Funding/ ; }, mesh = {Algal Proteins/genetics ; Docosahexaenoic Acids ; Fatty Acid Synthases/genetics ; Fatty Acids, Unsaturated/*biosynthesis/*genetics ; Gene Ontology ; Polyketide Synthases/genetics ; Prospective Studies ; Sequence Analysis, DNA ; Stramenopiles/*genetics ; }, abstract = {Thraustochytriidae sp. have broadly gained attention as a prospective resource for the production of omega-3 fatty acids production in significant quantities. In this study, the whole genome of Thraustochytriidae sp. SZU445, which produces high levels of docosapentaenoic acid (DPA) and docosahexaenoic acid (DHA), was sequenced and subjected to protein annotation. The obtained clean reads (63.55 Mb in total) were assembled into 54 contigs and 25 scaffolds, with maximum and minimum lengths of 400 and 0.0054 Mb, respectively. A total of 3513 genes (24.84%) were identified, which could be classified into six pathways and 44 pathway groups, of which 68 genes (1.93%) were involved in lipid metabolism. In the Gene Ontology database, 22,436 genes were annotated as cellular component (8579 genes, 38.24%), molecular function (5236 genes, 23.34%), and biological process (8621 genes, 38.42%). Four enzymes corresponding to the classic fatty acid synthase (FAS) pathway and three enzymes corresponding to the classic polyketide synthase (PKS) pathway were identified in Thraustochytriidae sp. SZU445. Although PKS pathway-associated dehydratase and isomerase enzymes were not detected in Thraustochytriidae sp. SZU445, a putative DHA- and DPA-specific fatty acid pathway was identified.}, } @article {pmid32080143, year = {2020}, author = {Lai, SW and Chang, WC and Lin, CL and Chou, IC and Tsai, FJ and Lai, YJ}, title = {Low ambient temperatures correlate with increased risk of hypoglycemia in patients with type 2 diabetes: An ecological study in Taiwan.}, journal = {Medicine}, volume = {99}, number = {8}, pages = {e19287}, pmid = {32080143}, issn = {1536-5964}, mesh = {Adolescent ; Adult ; Aged ; Aged, 80 and over ; Cold Temperature/*adverse effects ; Databases, Factual ; Diabetes Mellitus, Type 2/*epidemiology ; Emergency Service, Hospital ; Female ; Humans ; Hypoglycemia/*epidemiology ; Incidence ; Male ; Middle Aged ; Retrospective Studies ; Seasons ; Taiwan/epidemiology ; Young Adult ; }, abstract = {Little evidence is available about the relationship between ambient temperatures and hypoglycemia in Taiwan. The purpose of the present paper is to investigate whether there is an association between ambient temperatures and hypoglycemia in patients with type 2 diabetes.An ecological study was conducted to analyze the type 2 diabetes dataset of the Taiwan National Health Insurance Program. Every episode of hypoglycemia diagnosed at emergency department among subjects with type 2 diabetes was identified monthly between 2006 and 2013. Average monthly ambient temperatures in Celsius between 2006 and 2013 were measured according to the database of the Central Weather Bureau in Taiwan.The incidence rates of hypoglycemia were higher during the period of cold ambient temperatures (from December to March) than the period of warm ambient temperatures (from April to November). The peak period of hypoglycemia always occurred in winter months (January and February).Patients with type 2 diabetes in Taiwan are more susceptible to hypoglycemia during the period of cold ambient temperatures, particularly in winter months. Clinicians in Taiwan should remind patients to make a preventive strategy for hypoglycemia during the periods of cold ambient temperatures.}, } @article {pmid32077205, year = {2020}, author = {Zhang, X and Lin, S and Liu, D}, title = {Transcriptomic and physiological responses of Skeletonema costatum to ATP utilization.}, journal = {Environmental microbiology}, volume = {22}, number = {5}, pages = {1861-1869}, doi = {10.1111/1462-2920.14944}, pmid = {32077205}, issn = {1462-2920}, support = {41776116//National Natural Science Foundation of China/International ; 41876127//National Natural Science Foundation of China/International ; 2016YFA0600904//the Ministry of Science and Technology, China/International ; 2016YFE0133700//the Ministry of Science and Technology, China/International ; //Ministry of Science and Technology/International ; //Natural Science Foundation of China/International ; }, mesh = {Adenosine Triphosphate/*metabolism ; Alkaline Phosphatase/genetics ; Computational Biology ; Diatoms/*metabolism ; Dinoflagellida/genetics/metabolism ; Gene Expression Profiling ; Hydrolases/genetics/metabolism ; Phosphorus/*metabolism ; Phytoplankton/metabolism ; Transcriptome ; Up-Regulation ; }, abstract = {The capacity of phytoplankton to utilize dissolved organic phosphorus (DOP) plays an important role in their competition for resources when the availability of dissolved inorganic phosphorus (DIP) is low in the aquatic systems. Here, we explored the physiological and molecular responses of a globally distributed marine diatom, Skeletonema costatum, in utilizing adenosine-5'-triphosphate (ATP) based on incubation experiments under ATP, DIP-replete, and DIP-depleted conditions. The results show that ATP supports the growth of S. costatum as efficiently as DIP. The pathway of S. costatum involved in utilizing ATP is not related to alkaline phosphatase (AP), an important DOP hydrolase, although extracellular hydrolysis is involved. The transcriptome analysis revealed several transcripts related to the hydrolase activity (e.g. NAD+ diphosphatase), which were significantly upregulated in the ATP culture group, indicating their possible involvement in ATP hydrolysis. Meanwhile, ATP-grown S. costatum exhibited downregulation of the genes related to a series of metabolic activities (e.g. purine metabolism), apparently to adapt to ATP condition.}, } @article {pmid32077008, year = {2020}, author = {von Beckerath, O and Paulitschek, AM and Kröger, K and Kowall, B and Santosa, F and Stang, A}, title = {Increasing use of anticoagulants in Germany and its impact on hospitalization rates for genitourinary bleeding.}, journal = {Journal of thrombosis and thrombolysis}, volume = {49}, number = {4}, pages = {533-539}, pmid = {32077008}, issn = {1573-742X}, mesh = {Female ; Humans ; *Anticoagulants/adverse effects ; *Drug Prescriptions/statistics & numerical data ; Germany/epidemiology ; *Hematuria/chemically induced/epidemiology ; Hospitalization/statistics & numerical data ; *Uterine Hemorrhage/chemically induced/epidemiology ; }, abstract = {The aim of the study was to compare nationwide time trends of prescribed oral anticoagulants (OAC) with the time trend of genitourinary bleedings (GUB) in Germany from 2005 through 2016. The annual numbers of hospitalized patients with GUB coded as "hematuria", "excessive, frequent and irregular menstruation", "postmenopausal bleeding" or "abnormal uterine and vaginal bleeding" were extracted from the nationwide hospitalization file by the Federal Bureau of Statistics. Hospitalization rates were age-standardized using the German standard population 2011. Defined daily doses (DDD) of prescribed anticoagulants among outpatients for the same calendar period were extracted from reports of the statutory health insurance drug information system. Based on DDD, drug treatment rates per 100,000 person years (py) were calculated. From 2005 to 2016, annual OAC treatment rates per 100,000 py increased by 135.8% (from 901.4 to 2125.9). Until 2011 direct oral anticoagulants (DOAC) represented less than 0.1% of all OAC, but 49.9% in 2016. In the same period age-standardized rates of hospitalizations for hematuria increased continuously (annual change of 1.03 (95% CI 0.94-1.11) per 100,000 py), that of "postmenopausal" (- 1.93; 95% CI - 2.38 to - 1.49) or "excessive, frequent and irregular menstruation" decreased (- 1.25; 95% CI -1.62 to - 0.87) and that of "abnormal uterine and vaginal haemorrhage" remained almost unchanged. From all cases with hematuria 5.3% received at least 1 red blood cell concentrate (RBC) in 2005 and 8.2% in 2016 whereas all cases with the other three types of bleeding counted for 1.9% in 2005 and 3.8% in 2016. The time trends for GUB in all subgroups changed steadily and showed no effect of the disproportional increase of DAOCs until 2011. Our ecologic nationwide comparison of OAC treatment rates in outpatients and hospitalization rates for GUBs revealed that despite increasing OAC treatment rates from 2011 to 2016 the hospitalization rates for GUB showed steady annual changes unaffected by the increasing prescription rates of DOACs since 2011.}, } @article {pmid32076545, year = {2020}, author = {Brown, JJ and Mihaljevic, JR and Des Marteaux, L and Hrček, J}, title = {Metacommunity theory for transmission of heritable symbionts within insect communities.}, journal = {Ecology and evolution}, volume = {10}, number = {3}, pages = {1703-1721}, pmid = {32076545}, issn = {2045-7758}, abstract = {Microbial organisms are ubiquitous in nature and often form communities closely associated with their host, referred to as the microbiome. The microbiome has strong influence on species interactions, but microbiome studies rarely take interactions between hosts into account, and network interaction studies rarely consider microbiomes. Here, we propose to use metacommunity theory as a framework to unify research on microbiomes and host communities by considering host insects and their microbes as discretely defined "communities of communities" linked by dispersal (transmission) through biotic interactions. We provide an overview of the effects of heritable symbiotic bacteria on their insect hosts and how those effects subsequently influence host interactions, thereby altering the host community. We suggest multiple scenarios for integrating the microbiome into metacommunity ecology and demonstrate ways in which to employ and parameterize models of symbiont transmission to quantitatively assess metacommunity processes in host-associated microbial systems. Successfully incorporating microbiota into community-level studies is a crucial step for understanding the importance of the microbiome to host species and their interactions.}, } @article {pmid32076128, year = {2020}, author = {Darcy, JL and Washburne, AD and Robeson, MS and Prest, T and Schmidt, SK and Lozupone, CA}, title = {A phylogenetic model for the recruitment of species into microbial communities and application to studies of the human microbiome.}, journal = {The ISME journal}, volume = {14}, number = {6}, pages = {1359-1368}, pmid = {32076128}, issn = {1751-7370}, support = {T15 LM009451/LM/NLM NIH HHS/United States ; 5 T15 LM009451-12//U.S. Department of Health & Human Services | NIH | U.S. National Library of Medicine (NLM)/International ; }, mesh = {Bacteria/classification/*genetics/isolation & purification ; Feces/microbiology ; Female ; Gastrointestinal Microbiome ; Humans ; Infant ; Infant, Newborn ; Male ; *Microbiota ; *Phylogeny ; }, abstract = {Understanding when and why new species are recruited into microbial communities is a formidable problem with implications for managing microbial systems, for instance by helping us better understand whether a probiotic or pathogen would be expected to colonize a human microbiome. Much theory in microbial temporal dynamics is focused on how phylogenetic relationships between microbes impact the order in which those microbes are recruited; for example, species that are closely related may competitively exclude each other. However, several recent human microbiome studies have observed closely related bacteria being recruited into microbial communities in short succession, suggesting that microbial community assembly is historically contingent, but competitive exclusion of close relatives may not be important. To address this, we developed a mathematical model that describes the order in which new species are detected in microbial communities over time within a phylogenetic framework. We use our model to test three hypothetical assembly modes: underdispersion (species recruitment is more likely if a close relative was previously detected), overdispersion (recruitment is more likely if a close relative has not been previously detected), and the neutral model (recruitment likelihood is not related to phylogenetic relationships among species). We applied our model to longitudinal human microbiome data, and found that for the individuals we analyzed, the human microbiome generally follows the underdispersion (i.e., nepotism) hypothesis. Exceptions were oral communities and the fecal communities of two infants that had undergone heavy antibiotic treatment. None of the datasets we analyzed showed statistically significant phylogenetic overdispersion.}, } @article {pmid32071193, year = {2020}, author = {Zirin, J and Hu, Y and Liu, L and Yang-Zhou, D and Colbeth, R and Yan, D and Ewen-Campen, B and Tao, R and Vogt, E and VanNest, S and Cavers, C and Villalta, C and Comjean, A and Sun, J and Wang, X and Jia, Y and Zhu, R and Peng, P and Yu, J and Shen, D and Qiu, Y and Ayisi, L and Ragoowansi, H and Fenton, E and Efrem, S and Parks, A and Saito, K and Kondo, S and Perkins, L and Mohr, SE and Ni, J and Perrimon, N}, title = {Large-Scale Transgenic Drosophila Resource Collections for Loss- and Gain-of-Function Studies.}, journal = {Genetics}, volume = {214}, number = {4}, pages = {755-767}, pmid = {32071193}, issn = {1943-2631}, support = {P41 GM132087/GM/NIGMS NIH HHS/United States ; P40 OD018537/OD/NIH HHS/United States ; R24 RR032668/RR/NCRR NIH HHS/United States ; R24 OD021997/OD/NIH HHS/United States ; P30 CA006516/CA/NCI NIH HHS/United States ; R01 GM084947/GM/NIGMS NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; }, mesh = {Animals ; Animals, Genetically Modified/*genetics ; CRISPR-Cas Systems ; *Databases, Genetic ; Drosophila melanogaster/*genetics ; Gain of Function Mutation ; Genetic Engineering/methods ; Loss of Function Mutation ; }, abstract = {The Transgenic RNAi Project (TRiP), a Drosophila melanogaster functional genomics platform at Harvard Medical School, was initiated in 2008 to generate and distribute a genome-scale collection of RNA interference (RNAi) fly stocks. To date, it has generated >15,000 RNAi fly stocks. As this covers most Drosophila genes, we have largely transitioned to development of new resources based on CRISPR technology. Here, we present an update on our libraries of publicly available RNAi and CRISPR fly stocks, and focus on the TRiP-CRISPR overexpression (TRiP-OE) and TRiP-CRISPR knockout (TRiP-KO) collections. TRiP-OE stocks express single guide RNAs targeting upstream of a gene transcription start site. Gene activation is triggered by coexpression of catalytically dead Cas9 fused to an activator domain, either VP64-p65-Rta or Synergistic Activation Mediator. TRiP-KO stocks express one or two single guide RNAs targeting the coding sequence of a gene or genes. Cutting is triggered by coexpression of Cas9, allowing for generation of indels in both germline and somatic tissue. To date, we have generated >5000 TRiP-OE or TRiP-KO stocks for the community. These resources provide versatile, transformative tools for gene activation, gene repression, and genome engineering.}, } @article {pmid32066887, year = {2020}, author = {Gallagher, RV and Falster, DS and Maitner, BS and Salguero-Gómez, R and Vandvik, V and Pearse, WD and Schneider, FD and Kattge, J and Poelen, JH and Madin, JS and Ankenbrand, MJ and Penone, C and Feng, X and Adams, VM and Alroy, J and Andrew, SC and Balk, MA and Bland, LM and Boyle, BL and Bravo-Avila, CH and Brennan, I and Carthey, AJR and Catullo, R and Cavazos, BR and Conde, DA and Chown, SL and Fadrique, B and Gibb, H and Halbritter, AH and Hammock, J and Hogan, JA and Holewa, H and Hope, M and Iversen, CM and Jochum, M and Kearney, M and Keller, A and Mabee, P and Manning, P and McCormack, L and Michaletz, ST and Park, DS and Perez, TM and Pineda-Munoz, S and Ray, CA and Rossetto, M and Sauquet, H and Sparrow, B and Spasojevic, MJ and Telford, RJ and Tobias, JA and Violle, C and Walls, R and Weiss, KCB and Westoby, M and Wright, IJ and Enquist, BJ}, title = {Open Science principles for accelerating trait-based science across the Tree of Life.}, journal = {Nature ecology & evolution}, volume = {4}, number = {3}, pages = {294-303}, pmid = {32066887}, issn = {2397-334X}, mesh = {*Biodiversity ; Biological Evolution ; *Ecology ; Phenotype ; Research ; }, abstract = {Synthesizing trait observations and knowledge across the Tree of Life remains a grand challenge for biodiversity science. Species traits are widely used in ecological and evolutionary science, and new data and methods have proliferated rapidly. Yet accessing and integrating disparate data sources remains a considerable challenge, slowing progress toward a global synthesis to integrate trait data across organisms. Trait science needs a vision for achieving global integration across all organisms. Here, we outline how the adoption of key Open Science principles-open data, open source and open methods-is transforming trait science, increasing transparency, democratizing access and accelerating global synthesis. To enhance widespread adoption of these principles, we introduce the Open Traits Network (OTN), a global, decentralized community welcoming all researchers and institutions pursuing the collaborative goal of standardizing and integrating trait data across organisms. We demonstrate how adherence to Open Science principles is key to the OTN community and outline five activities that can accelerate the synthesis of trait data across the Tree of Life, thereby facilitating rapid advances to address scientific inquiries and environmental issues. Lessons learned along the path to a global synthesis of trait data will provide a framework for addressing similarly complex data science and informatics challenges.}, } @article {pmid32065938, year = {2020}, author = {Douterelo, I and Dutilh, BE and Arkhipova, K and Calero, C and Husband, S}, title = {Microbial diversity, ecological networks and functional traits associated to materials used in drinking water distribution systems.}, journal = {Water research}, volume = {173}, number = {}, pages = {115586}, doi = {10.1016/j.watres.2020.115586}, pmid = {32065938}, issn = {1879-2448}, mesh = {Bacteria ; Biofilms ; *Drinking Water ; Ecology ; Water Microbiology ; Water Quality ; Water Supply ; }, abstract = {Drinking water distribution systems host complex microbial communities as biofilms that interact continuously with delivered water. Understanding the diversity, behavioural and functional characteristics will be a requisite for developing future monitoring strategies and protection against water-borne health risks. To improve understanding, this study investigates mobilisation and accumulation behaviour, microbial community structure and functional variations of biofilms developing on different pipe materials from within an operational network. Samples were collected from four pipes during a repeated flushing operation three months after an initial visit that used hydraulic forces to mobilise regenerating biofilms yet without impacting the upstream network. To minimise confounding factors, test sections were chosen with comparable daily hydraulic regimes, physical dimensions, and all connected straight of a common trunk main and within close proximity, hence similar water chemistry, pressure and age. Taxonomical results showed differences in colonising communities between pipe materials, with several genera, including the bacteria Pseudomonas and the fungi Cladosporium, present in every sample. Diverse bacterial communities dominated compared to more homogeneous fungal, or mycobiome, community distribution. The analysis of bacterial/fungal networks based on relative abundance of operational taxonomic units (OTUs) indicated microbial communities from cast iron pipes were more stable than communities from the non-ferrous pipe materials. Novel analysis of functional traits between all samples were found to be mainly associated to mobile genetic elements that play roles in determining links between cells, including phages, prophages, transposable elements, and plasmids. The use of functional traits can be considered for development in future surveillance methods, capable of delivering network condition information beyond that of limited conventional faecal indicator tests, that will help protect water quality and public health.}, } @article {pmid32060621, year = {2020}, author = {Walter, JM and Coutinho, FH and Leomil, L and Hargreaves, PI and Campeão, ME and Vieira, VV and Silva, BS and Fistarol, GO and Salomon, PS and Sawabe, T and Mino, S and Hosokawa, M and Miyashita, H and Maruyama, F and van Verk, MC and Dutilh, BE and Thompson, CC and Thompson, FL}, title = {Ecogenomics of the Marine Benthic Filamentous Cyanobacterium Adonisia.}, journal = {Microbial ecology}, volume = {80}, number = {2}, pages = {249-265}, doi = {10.1007/s00248-019-01480-x}, pmid = {32060621}, issn = {1432-184X}, support = {BIOCOMP//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; Universal//Conselho Nacional de Desenvolvimento Científico e Tecnológico (BR)/ ; CNE//Fundação Carlos Chagas Filho de Amparo à Pesquisa do Estado do Rio de Janeiro (BR)/ ; }, mesh = {Atlantic Ocean ; Brazil ; Coral Reefs ; Cyanobacteria/genetics/*physiology ; Genome, Bacterial/*physiology ; Phylogeny ; }, abstract = {Turfs are among the major benthic components of reef systems worldwide. The nearly complete genome sequences, basic physiological characteristics, and phylogenomic reconstruction of two phycobiliprotein-rich filamentous cyanobacteria strains isolated from turf assemblages from the Abrolhos Bank (Brazil) are investigated. Both Adonisia turfae CCMR0081[T] (= CBAS 745[T]) and CCMR0082 contain approximately 8 Mbp in genome size and experiments identified that both strains exhibit chromatic acclimation. Whereas CCMR0081[T] exhibits chromatic acclimation type 3 (CA3) regulating both phycocyanin (PC) and phycoerythrin (PE), CCMR0082 strain exhibits chromatic acclimation type 2 (CA2), in correspondence with genes encoding specific photosensors and regulators for PC and PE. Furthermore, a high number and diversity of secondary metabolite synthesis gene clusters were identified in both genomes, and they were able to grow at high temperatures (28 °C, with scant growth at 30 °C). These characteristics provide insights into their widespread distribution in reef systems.}, } @article {pmid32059640, year = {2020}, author = {Soltani, N and Best, T and Grace, D and Nelms, C and Shumaker, K and Romero-Severson, J and Moses, D and Schuster, S and Staton, M and Carlson, J and Gwinn, K}, title = {Transcriptome profiles of Quercus rubra responding to increased O3 stress.}, journal = {BMC genomics}, volume = {21}, number = {1}, pages = {160}, pmid = {32059640}, issn = {1471-2164}, support = {PGRP-OIS-1025974//National Science Foundation/ ; PEN04532 1000326//National Institute of Food and Agriculture/ ; }, mesh = {Biosynthetic Pathways ; Computational Biology/methods ; *Gene Expression Profiling ; Gene Expression Regulation, Plant ; Gene Ontology ; Host-Pathogen Interactions ; Molecular Sequence Annotation ; Ozone/*metabolism ; Quercus/*genetics/*metabolism ; Signal Transduction ; *Stress, Physiological ; *Transcriptome ; }, abstract = {BACKGROUND: Climate plays an essential role in forest health, and climate change may increase forest productivity losses due to abiotic and biotic stress. Increased temperature leads to the increased formation of ozone (O3). Ozone is formed by the interaction of sunlight, molecular oxygen and by the reactions of chemicals commonly found in industrial and automobile emissions such as nitrogen oxides and volatile organic compounds. Although it is well known that productivity of Northern red oak (Quercus rubra) (NRO), an ecologically and economically important species in the forests of eastern North America, is reduced by exposure to O3, limited information is available on its responses to exogenous stimuli at the level of gene expression.

RESULTS: RNA sequencing yielded more than 323 million high-quality raw sequence reads. De novo assembly generated 52,662 unigenes, of which more than 42,000 sequences could be annotated through homology-based searches. A total of 4140 differential expressed genes (DEGs) were detected in response to O3 stress, as compared to their respective controls. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses of the O3-response DEGs revealed perturbation of several biological pathways including energy, lipid, amino acid, carbohydrate and terpenoid metabolism as well as plant-pathogen interaction.

CONCLUSION: This study provides the first reference transcriptome for NRO and initial insights into the genomic responses of NRO to O3. Gene expression profiling reveals altered primary and secondary metabolism of NRO seedlings, including known defense responses such as terpenoid biosynthesis.}, } @article {pmid32055048, year = {2020}, author = {Jia, P and Wang, T and van Vliet, AJH and Skidmore, AK and van Aalst, M}, title = {Worsening of tree-related public health issues under climate change.}, journal = {Nature plants}, volume = {6}, number = {2}, pages = {48}, pmid = {32055048}, issn = {2055-0278}, support = {SKLURE2018-2-5//State Key Laboratory of Urban and Regional Ecology (SKLURE)/International ; }, mesh = {Animals ; *Climate Change ; Forests ; Humans ; *Moths ; Population Dynamics ; *Public Health ; Trees/*physiology ; }, } @article {pmid32053657, year = {2020}, author = {Brumfield, KD and Huq, A and Colwell, RR and Olds, JL and Leddy, MB}, title = {Microbial resolution of whole genome shotgun and 16S amplicon metagenomic sequencing using publicly available NEON data.}, journal = {PloS one}, volume = {15}, number = {2}, pages = {e0228899}, pmid = {32053657}, issn = {1932-6203}, support = {R01 ES030317/ES/NIEHS NIH HHS/United States ; }, mesh = {Archaea/genetics ; Bacteria/genetics ; DNA, Bacterial/genetics ; Databases, Genetic/standards ; High-Throughput Nucleotide Sequencing/methods/*standards ; Metagenome ; Metagenomics/*methods ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA/*methods/standards ; Sequence Analysis, RNA/methods/standards ; Soil ; Whole Genome Sequencing/methods/standards ; }, abstract = {Microorganisms are ubiquitous in the biosphere, playing a crucial role in both biogeochemistry of the planet and human health. However, identifying these microorganisms and defining their function are challenging. Widely used approaches in comparative metagenomics, 16S amplicon sequencing and whole genome shotgun sequencing (WGS), have provided access to DNA sequencing analysis to identify microorganisms and evaluate diversity and abundance in various environments. However, advances in parallel high-throughput DNA sequencing in the past decade have introduced major hurdles, namely standardization of methods, data storage, reproducible interoperability of results, and data sharing. The National Ecological Observatory Network (NEON), established by the National Science Foundation, enables all researchers to address queries on a regional to continental scale around a variety of environmental challenges and provide high-quality, integrated, and standardized data from field sites across the U.S. As the amount of metagenomic data continues to grow, standardized procedures that allow results across projects to be assessed and compared is becoming increasingly important in the field of metagenomics. We demonstrate the feasibility of using publicly available NEON soil metagenomic sequencing datasets in combination with open access Metagenomics Rapid Annotation using the Subsystem Technology (MG-RAST) server to illustrate advantages of WGS compared to 16S amplicon sequencing. Four WGS and four 16S amplicon sequence datasets, from surface soil samples prepared by NEON investigators, were selected for comparison, using standardized protocols collected at the same locations in Colorado between April-July 2014. The dominant bacterial phyla detected across samples agreed between sequencing methodologies. However, WGS yielded greater microbial resolution, increased accuracy, and allowed identification of more genera of bacteria, archaea, viruses, and eukaryota, and putative functional genes that would have gone undetected using 16S amplicon sequencing. NEON open data will be useful for future studies characterizing and quantifying complex ecological processes associated with changing aquatic and terrestrial ecosystems.}, } @article {pmid32052012, year = {2020}, author = {do Nascimento Fernandes de Souza, E and Hawkins, JA}, title = {Ewé: a web-based ethnobotanical database for storing and analysing data.}, journal = {Database : the journal of biological databases and curation}, volume = {2020}, number = {}, pages = {}, pmid = {32052012}, issn = {1758-0463}, mesh = {Brazil ; *Database Management Systems ; *Databases, Factual ; *Ethnobotany ; Fabaceae ; *Internet ; *Plants, Medicinal ; }, abstract = {Ethnobotanical databases serve as repositories of traditional knowledge (TK), either at international or local scales. By documenting plant species with traditional use, and most importantly, the applications and modes of use of such species, ethnobotanical databases play a role in the conservation of TK and also provide access to information that could improve hypothesis generation and testing in ethnobotanical studies. Brazil has a rich medicinal flora and a rich cultural landscape. Nevertheless, cultural change and ecological degradation can lead to loss of TK. Here, we present an online database developed with open-source tools with a capacity to include all medicinal flora of Brazil. We present test data for the Leguminosae comprising a total of 2078 records, referred to here as use reports, including data compiled from literature and herbarium sources. Unlike existing databases, Ewé provides tools for the visualization of large datasets, facilitating hypothesis generation and meta-analyses. The Ewé database is currently available at www.ewedb.com.}, } @article {pmid32047891, year = {2021}, author = {Liu, Z and Ma, A and Mathé, E and Merling, M and Ma, Q and Liu, B}, title = {Network analyses in microbiome based on high-throughput multi-omics data.}, journal = {Briefings in bioinformatics}, volume = {22}, number = {2}, pages = {1639-1655}, pmid = {32047891}, issn = {1477-4054}, support = {UL1 TR002733/TR/NCATS NIH HHS/United States ; }, mesh = {High-Throughput Screening Assays/*methods ; Humans ; Metabolomics/*methods ; Metagenomics/*methods ; *Microbiota ; Proteomics/*methods ; *Transcriptome ; }, abstract = {Together with various hosts and environments, ubiquitous microbes interact closely with each other forming an intertwined system or community. Of interest, shifts of the relationships between microbes and their hosts or environments are associated with critical diseases and ecological changes. While advances in high-throughput Omics technologies offer a great opportunity for understanding the structures and functions of microbiome, it is still challenging to analyse and interpret the omics data. Specifically, the heterogeneity and diversity of microbial communities, compounded with the large size of the datasets, impose a tremendous challenge to mechanistically elucidate the complex communities. Fortunately, network analyses provide an efficient way to tackle this problem, and several network approaches have been proposed to improve this understanding recently. Here, we systemically illustrate these network theories that have been used in biological and biomedical research. Then, we review existing network modelling methods of microbial studies at multiple layers from metagenomics to metabolomics and further to multi-omics. Lastly, we discuss the limitations of present studies and provide a perspective for further directions in support of the understanding of microbial communities.}, } @article {pmid32047153, year = {2020}, author = {Ovaskainen, O and Meyke, E and Lo, C and Tikhonov, G and Delgado, MDM and Roslin, T and Gurarie, E and Abadonova, M and Abduraimov, O and Adrianova, O and Akimova, T and Akkiev, M and Ananin, A and Andreeva, E and Andriychuk, N and Antipin, M and Arzamascev, K and Babina, S and Babushkin, M and Bakin, O and Barabancova, A and Basilskaja, I and Belova, N and Belyaeva, N and Bespalova, T and Bisikalova, E and Bobretsov, A and Bobrov, V and Bobrovskyi, V and Bochkareva, E and Bogdanov, G and Bolshakov, V and Bondarchuk, S and Bukharova, E and Butunina, A and Buyvolov, Y and Buyvolova, A and Bykov, Y and Chakhireva, E and Chashchina, O and Cherenkova, N and Chistjakov, S and Chuhontseva, S and Davydov, EA and Demchenko, V and Diadicheva, E and Dobrolyubov, A and Dostoyevskaya, L and Drovnina, S and Drozdova, Z and Dubanaev, A and Dubrovsky, Y and Elsukov, S and Epova, L and Ermakova, OS and Ermakova, O and Esengeldenova, A and Evstigneev, O and Fedchenko, I and Fedotova, V and Filatova, T and Gashev, S and Gavrilov, A and Gaydysh, I and Golovcov, D and Goncharova, N and Gorbunova, E and Gordeeva, T and Grishchenko, V and Gromyko, L and Hohryakov, V and Hritankov, A and Ignatenko, E and Igosheva, S and Ivanova, U and Ivanova, N and Kalinkin, Y and Kaygorodova, E and Kazansky, F and Kiseleva, D and Knorre, A and Kolpashikov, L and Korobov, E and Korolyova, H and Korotkikh, N and Kosenkov, G and Kossenko, S and Kotlugalyamova, E and Kozlovsky, E and Kozsheechkin, V and Kozurak, A and Kozyr, I and Krasnopevtseva, A and Kruglikov, S and Kuberskaya, O and Kudryavtsev, A and Kulebyakina, E and Kulsha, Y and Kupriyanova, M and Kurbanbagamaev, M and Kutenkov, A and Kutenkova, N and Kuyantseva, N and Kuznetsov, A and Larin, E and Lebedev, P and Litvinov, K and Luzhkova, N and Mahmudov, A and Makovkina, L and Mamontov, V and Mayorova, S and Megalinskaja, I and Meydus, A and Minin, A and Mitrofanov, O and Motruk, M and Myslenkov, A and Nasonova, N and Nemtseva, N and Nesterova, I and Nezdoliy, T and Niroda, T and Novikova, T and Panicheva, D and Pavlov, A and Pavlova, K and Petrenko, P and Podolski, S and Polikarpova, N and Polyanskaya, T and Pospelov, I and Pospelova, E and Prokhorov, I and Prokosheva, I and Puchnina, L and Putrashyk, I and Raiskaya, J and Rozhkov, Y and Rozhkova, O and Rudenko, M and Rybnikova, I and Rykova, S and Sahnevich, M and Samoylov, A and Sanko, V and Sapelnikova, I and Sazonov, S and Selyunina, Z and Shalaeva, K and Shashkov, M and Shcherbakov, A and Shevchyk, V and Shubin, S and Shujskaja, E and Sibgatullin, R and Sikkila, N and Sitnikova, E and Sivkov, A and Skok, N and Skorokhodova, S and Smirnova, E and Sokolova, G and Sopin, V and Spasovski, Y and Stepanov, S and Stratiy, V and Strekalovskaya, V and Sukhov, A and Suleymanova, G and Sultangareeva, L and Teleganova, V and Teplov, V and Teplova, V and Tertitsa, T and Timoshkin, V and Tirski, D and Tolmachev, A and Tomilin, A and Tselishcheva, L and Turgunov, M and Tyukh, Y and Vladimir, V and Vargot, E and Vasin, A and Vasina, A and Vekliuk, A and Vetchinnikova, L and Vinogradov, V and Volodchenkov, N and Voloshina, I and Xoliqov, T and Yablonovska-Grishchenko, E and Yakovlev, V and Yakovleva, M and Yantser, O and Yarema, Y and Zahvatov, A and Zakharov, V and Zelenetskiy, N and Zheltukhin, A and Zubina, T and Kurhinen, J}, title = {Chronicles of nature calendar, a long-term and large-scale multitaxon database on phenology.}, journal = {Scientific data}, volume = {7}, number = {1}, pages = {47}, pmid = {32047153}, issn = {2052-4463}, mesh = {*Biota ; *Climate Change ; *Databases, Factual ; Kyrgyzstan ; Republic of Belarus ; Russia ; Seasons ; Ukraine ; Uzbekistan ; }, abstract = {We present an extensive, large-scale, long-term and multitaxon database on phenological and climatic variation, involving 506,186 observation dates acquired in 471 localities in Russian Federation, Ukraine, Uzbekistan, Belarus and Kyrgyzstan. The data cover the period 1890-2018, with 96% of the data being from 1960 onwards. The database is rich in plants, birds and climatic events, but also includes insects, amphibians, reptiles and fungi. The database includes multiple events per species, such as the onset days of leaf unfolding and leaf fall for plants, and the days for first spring and last autumn occurrences for birds. The data were acquired using standardized methods by permanent staff of national parks and nature reserves (87% of the data) and members of a phenological observation network (13% of the data). The database is valuable for exploring how species respond in their phenology to climate change. Large-scale analyses of spatial variation in phenological response can help to better predict the consequences of species and community responses to climate change.}, } @article {pmid32046265, year = {2020}, author = {Benzarti, E and Sarlet, M and Franssen, M and Desmecht, D and Schmidt-Chanasit, J and Garigliany, MM}, title = {New Insights into the Susceptibility of Immunocompetent Mice to Usutu Virus.}, journal = {Viruses}, volume = {12}, number = {2}, pages = {}, pmid = {32046265}, issn = {1999-4915}, mesh = {Animals ; Belgium ; Birds/virology ; Brain/virology ; Disease Models, Animal ; Disease Susceptibility/*pathology/*virology ; Female ; Flavivirus/classification/*pathogenicity ; Flavivirus Infections/*pathology/virology ; Immunocompetence ; Mice ; Pilot Projects ; RNA, Viral/analysis ; Spinal Cord/virology ; }, abstract = {Usutu virus (USUV) is a mosquito-borne flavivirus that shares many similarities with the closely related West Nile virus (WNV) in terms of ecology and clinical manifestations. Initially distributed in Africa, USUV emerged in Italy in 1996 and managed to co-circulate with WNV in many European countries in a similar mosquito-bird life cycle. The rapid geographic spread of USUV, the seasonal mass mortalities it causes in the European avifauna, and the increasing number of infections with neurological disease both in healthy and immunocompromised humans has stimulated interest in infection studies to delineate USUV pathogenesis. Here, we assessed the pathogenicity of two USUV isolates from a recent Belgian outbreak in immunocompetent mice. The intradermal injection of USUV gave rise to disorientation and paraplegia and was associated with neuronal death in the brain and spinal cord in a single mouse. Intranasal inoculation of USUV could also establish the infection; viral RNA was detected in the brain 15 days post-infection. Overall, this pilot study probes the suitability of this murine model for the study of USUV neuroinvasiveness and the possibility of direct transmission in mammals.}, } @article {pmid32046085, year = {2020}, author = {Chen, L and Wu, Q and He, T and Lan, J and Ding, L and Liu, T and Wu, Q and Pan, Y and Chen, T}, title = {Transcriptomic and Metabolomic Changes Triggered by Fusarium solani in Common Bean (Phaseolus vulgaris L.).}, journal = {Genes}, volume = {11}, number = {2}, pages = {}, pmid = {32046085}, issn = {2073-4425}, mesh = {Arginine/metabolism ; Cell Wall/genetics/metabolism/microbiology ; Chromatography, High Pressure Liquid ; Energy Metabolism ; Fusarium/*pathogenicity ; Gene Expression Regulation, Plant/genetics ; Gene Ontology ; Host Microbial Interactions/*genetics ; Mass Spectrometry ; Metabolomics ; Nitrogen/metabolism ; Phaseolus/genetics/immunology/metabolism/*microbiology ; Plant Diseases/*immunology/microbiology ; Plant Roots/genetics/immunology/metabolism/microbiology ; Proline/metabolism ; RNA-Seq ; Reactive Oxygen Species/metabolism ; Seedlings/genetics/immunology/metabolism/*microbiology ; Signal Transduction/genetics/immunology ; Sugars/metabolism ; Transcriptome/*genetics ; }, abstract = {Common bean (Phaseolus vulgaris L.) is a major legume and is frequently attacked by fungal pathogens, including Fusarium solani f. sp. phaseoli (FSP), which cause Fusarium root rot. FSP substantially reduces common bean yields across the world, including China, but little is known about how common bean plants defend themselves against this fungal pathogen. In the current study, we combined next-generation RNA sequencing and metabolomics techniques to investigate the changes in gene expression and metabolomic processes in common bean infected with FSP. There were 29,722 differentially regulated genes and 300 differentially regulated metabolites between control and infected plants. The combined omics approach revealed that FSP is perceived by PAMP-triggered immunity and effector-triggered immunity. Infected seedlings showed that common bean responded by cell wall modification, ROS generation, and a synergistic hormone-driven defense response. Further analysis showed that FSP induced energy metabolism, nitrogen mobilization, accumulation of sugars, and arginine and proline metabolism. Importantly, metabolic pathways were most significantly enriched, which resulted in increased levels of metabolites that were involved in the plant defense response. A correspondence between the transcript pattern and metabolite profile was observed in the discussed pathways. The combined omics approach enhances our understanding of the less explored pathosystem and will provide clues for the development of common bean cultivars' resistant to FSP.}, } @article {pmid32045413, year = {2020}, author = {Stabach, JA and Cunningham, SA and Connette, G and Mota, JL and Reed, D and Byron, M and Songer, M and Wacher, T and Mertes, K and Brown, JL and Comizzoli, P and Newby, J and Monfort, S and Leimgruber, P}, title = {Short-term effects of GPS collars on the activity, behavior, and adrenal response of scimitar-horned oryx (Oryx dammah).}, journal = {PloS one}, volume = {15}, number = {2}, pages = {e0221843}, pmid = {32045413}, issn = {1932-6203}, mesh = {Africa, Northern ; Animals ; Animals, Wild ; *Antelopes ; Behavior, Animal ; Endangered Species ; *Geographic Information Systems ; Head ; Movement ; Stress, Psychological ; Time Factors ; Wearable Electronic Devices/*adverse effects ; }, abstract = {GPS collars have revolutionized the field of animal ecology, providing detailed information on animal movement and the habitats necessary for species survival. GPS collars also have the potential to cause adverse effects ranging from mild irritation to severe tissue damage, reduced fitness, and death. The impact of GPS collars on the behavior, stress, or activity, however, have rarely been tested on study species prior to release. The objective of our study was to provide a comprehensive assessment of the short-term effects of GPS collars fitted on scimitar-horned oryx (Oryx dammah), an extinct-in-the-wild antelope once widely distributed across Sahelian grasslands in North Africa. We conducted behavioral observations, assessed fecal glucocorticoid metabolites (FGM), and evaluated high-resolution data from tri-axial accelerometers. Using a series of datasets and methodologies, we illustrate clear but short-term effects to animals fitted with GPS collars from two separate manufacturers (Advanced Telemetry Systems-G2110E; Vectronic Aerospace-Vertex Plus). Behavioral observations highlighted a significant increase in the amount of headshaking from pre-treatment levels, returning below baseline levels during the post-treatment period (>3 days post-collaring). Similarly, FGM concentrations increased after GPS collars were fitted on animals but returned to pre-collaring levels within 5 days of collaring. Lastly, tri-axial accelerometers, collecting data at eight positions per second, indicated a > 480 percent increase in the amount of hourly headshaking immediately after collaring. This post-collaring increase in headshaking was estimated to decline in magnitude within 4 hours after GPS collar fitting. These effects constitute a handling and/or habituation response (model dependent), with animals showing short-term responses in activity, behavior, and stress that dissipated within several hours to several days of being fitted with GPS collars. Importantly, none of our analyses indicated any long-term effects that would have more pressing animal welfare concerns.}, } @article {pmid32042412, year = {2020}, author = {Gonçalves, IDSA and Pereira, PF and Silva, MBL and Ladeira, FB and Moreira, TR and Cotta, RMM and da Costa, GD}, title = {Nutritional status coverage trend registered in the SISVAN web in seven municipalities of the Zona Da Mata Mineira, Brazil, from 2008 to 2017, and its association with socio-economic, demographic and organisation of health system variables.}, journal = {Journal of nutritional science}, volume = {9}, number = {}, pages = {e4}, pmid = {32042412}, issn = {2048-6790}, mesh = {Adolescent ; Adult ; Aged ; Aged, 80 and over ; Brazil/epidemiology ; Child ; Child, Preschool ; Female ; Government Programs ; Humans ; Infant ; Infant, Newborn ; Medical Assistance ; Middle Aged ; National Health Programs/statistics & numerical data ; Nutrition Assessment ; *Nutritional Status ; *Organizations ; Pregnancy ; Primary Health Care/statistics & numerical data ; *Public Health/statistics & numerical data ; Public Health Administration ; Regional Health Planning/*organization & administration/statistics & numerical data ; *Socioeconomic Factors ; Young Adult ; }, abstract = {We analysed the coverage trend of the evaluation of the nutritional status of users of public health services registered in the Food and Nutrition Surveillance System (SISVAN) between 2008 and 2017 in seven municipalities and verified the association of the coverage trend with the socio-economic, demographic and organisational aspects of health system variables. It is an ecological time-series study performed with secondary data extracted from health information systems. Descriptive statistics, linear regression model and repeated measures analysis were performed. The coverage of evaluation of nutritional status was low over the period. Five municipalities showed a tendency to increase coverage, although small, while two remained stable. The highest annual variation in coverage increase was concentrated in the group of pregnant women and the lowest in adolescents and older adults. There was a downward trend in follow-ups from the Bolsa Family Programme and a trend towards increased follow-ups from SUS Primary Care (e-SUS AB). SISVAN coverage was positively associated with the proportion of rural population (P ≤ 0·001) and coverage of community health agents (P < 0·001); and negatively associated with total population (P < 0·001), demographic density (P = 0·006) and gross domestic product per capita (P = 0·008). Despite the tendency to increase coverage in some municipalities, SISVAN still presents low coverage of nutritional status assessment, which compromises population monitoring. Knowing the factors that influence the coverage can subsidise the elaboration of strategies for its expansion.}, } @article {pmid32041961, year = {2020}, author = {Manel, S and Guerin, PE and Mouillot, D and Blanchet, S and Velez, L and Albouy, C and Pellissier, L}, title = {Global determinants of freshwater and marine fish genetic diversity.}, journal = {Nature communications}, volume = {11}, number = {1}, pages = {692}, pmid = {32041961}, issn = {2041-1723}, mesh = {Animals ; Aquatic Organisms/classification/genetics ; *Biodiversity ; DNA, Mitochondrial/genetics ; Databases, Genetic ; Environment ; Fishes/classification/*genetics ; *Genetic Variation ; Geography ; }, abstract = {Genetic diversity is estimated to be declining faster than species diversity under escalating threats, but its spatial distribution remains poorly documented at the global scale. Theory predicts that similar processes should foster congruent spatial patterns of genetic and species diversity, but empirical studies are scarce. Using a mined database of 50,588 georeferenced mitochondrial DNA barcode sequences (COI) for 3,815 marine and 1,611 freshwater fish species respectively, we examined the correlation between genetic diversity and species diversity and their global distributions in relation to climate and geography. Genetic diversity showed a clear spatial organisation, but a weak association with species diversity for both marine and freshwater species. We found a predominantly positive relationship between genetic diversity and sea surface temperature for marine species. Genetic diversity of freshwater species varied primarily across the regional basins and was negatively correlated with average river slope. The detection of genetic diversity patterns suggests that conservation measures should consider mismatching spatial signals across multiple facets of biodiversity.}, } @article {pmid32034626, year = {2020}, author = {Aleix-Mata, G and Gutiérrez, J and Ruiz-Ruano, FJ and Lorite, P and Marchal, JA and Sánchez, A}, title = {The complete mitochondrial genome of Talpa aquitania (Talpidae; Insectivora), a mole species endemic to northern Spain and southern France.}, journal = {Molecular biology reports}, volume = {47}, number = {3}, pages = {2397-2403}, pmid = {32034626}, issn = {1573-4978}, mesh = {Animals ; Base Sequence ; Computational Biology/methods ; Eulipotyphla/classification/*genetics ; France ; Genes, Mitochondrial ; *Genome, Mitochondrial ; *Genomics/methods ; Open Reading Frames ; Phylogeny ; Sequence Analysis, DNA ; Spain ; Whole Genome Sequencing ; }, abstract = {The complete mitogenome sequence of Talpa aquitania, a recently described Talpa species, was assembled using whole-genome sequencing data. It varies in length from 16,776 to 16,846 bp, contains 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes, one origin of L-strand replication, and a control region. In the control region, which varied from 1320 to 1390 bp, we identified the extended termination-associated sequence (ETAS-1 and ETAS-2) and the conserved sequence blocks (CSB-1, 2, 3, B, C, D, E, F). In addition, this region includes a 10 bp tandem repeat DNA sequence, with a variable number of repeats that suggest the existence of heteroplasmy. Phylogeny reconstructions based on Maximum Likelihood, Neighbor-joining and Bayesian inference analyses yielded phylogenies with similar topologies demonstrating that T. aquitania and T. occidentalis are sister species.}, } @article {pmid32034435, year = {2020}, author = {Canzler, S and Schor, J and Busch, W and Schubert, K and Rolle-Kampczyk, UE and Seitz, H and Kamp, H and von Bergen, M and Buesen, R and Hackermüller, J}, title = {Prospects and challenges of multi-omics data integration in toxicology.}, journal = {Archives of toxicology}, volume = {94}, number = {2}, pages = {371-388}, pmid = {32034435}, issn = {1432-0738}, support = {Project C5-XomeTox//European Chemical Industry Council/International ; }, mesh = {Animals ; Computational Biology/methods ; Genomics/*methods ; Humans ; Metabolomics/*methods ; Protein Processing, Post-Translational ; Proteomics/*methods ; Single-Cell Analysis ; Tissue Distribution ; Toxicology/*methods ; }, abstract = {Exposure of cells or organisms to chemicals can trigger a series of effects at the regulatory pathway level, which involve changes of levels, interactions, and feedback loops of biomolecules of different types. A single-omics technique, e.g., transcriptomics, will detect biomolecules of one type and thus can only capture changes in a small subset of the biological cascade. Therefore, although applying single-omics analyses can lead to the identification of biomarkers for certain exposures, they cannot provide a systemic understanding of toxicity pathways or adverse outcome pathways. Integration of multiple omics data sets promises a substantial improvement in detecting this pathway response to a toxicant, by an increase of information as such and especially by a systemic understanding. Here, we report the findings of a thorough evaluation of the prospects and challenges of multi-omics data integration in toxicological research. We review the availability of such data, discuss options for experimental design, evaluate methods for integration and analysis of multi-omics data, discuss best practices, and identify knowledge gaps. Re-analyzing published data, we demonstrate that multi-omics data integration can considerably improve the confidence in detecting a pathway response. Finally, we argue that more data need to be generated from studies with a multi-omics-focused design, to define which omics layers contribute most to the identification of a pathway response to a toxicant.}, } @article {pmid32032445, year = {2020}, author = {Lipperman-Kreda, S and Finan, LJ and Kowitt, SD and Grube, JW and Abadi, M and Balassone, A and Kaner, E}, title = {Youth daily exposure to tobacco outlets and cigarette smoking behaviors: does exposure within activity space matter?.}, journal = {Addiction (Abingdon, England)}, volume = {115}, number = {9}, pages = {1728-1735}, pmid = {32032445}, issn = {1360-0443}, support = {P60 AA006282/AA/NIAAA NIH HHS/United States ; }, mesh = {Adolescent ; Adolescent Behavior/*psychology ; California/epidemiology ; Cigarette Smoking/*epidemiology ; Commerce/*statistics & numerical data ; Ecological Momentary Assessment ; Female ; Geographic Information Systems ; Humans ; Male ; Social Environment ; Surveys and Questionnaires ; Tobacco Products/*statistics & numerical data ; Young Adult ; }, abstract = {AIMS: To examine whether daily exposure to tobacco outlets within activity spaces is associated with cigarette smoking and with the number of cigarettes smoked by youth that day.

DESIGN: The study used geographic ecological momentary assessment (GEMA) data that combined daily surveys with ecological momentary assessment of global positioning systems (GPS) using geographic information systems (GIS) to allow for real-time data collection of participants' environments and behaviors.

SETTING: Eight mid-sized California (USA) city areas.

PARTICIPANTS: The analytical sample included 1065 days, which were clustered within 100 smoker and non-smoker participants (aged 16-20 years, 60% female).

MEASUREMENTS: Any cigarette smoking and number of cigarettes smoked on a given day, the number of tobacco outlets within 100 m of activity space polylines each day, the number of minutes participants spent within 100 m of tobacco outlets each day and demographic characteristics (age, sex, race/ethnicity and perceived socio-economic status).

FINDINGS: Controlling for demographic characteristics, the findings of multi-level mixed effects logistic models were inconclusive, whether or not the number of tobacco outlets within 100 m of youths' activity space polylines or the number of minutes spent within 100 m of tobacco outlets were associated with whether the participant smoked cigarettes on a given day [odds ratio (OR) = 1.05, P = 0.24; OR = 0.99, P = 0.81, respectively]. However, in multi-level zero-inflated negative binomial models, the risk of smoking an additional cigarette on a given day increased with each additional tobacco outlet [incidence rate ratio (IRR) = 1.04, P < 0.05] and each additional minute spent within 100 m of tobacco outlets (IRR = 1.01, P < 0.001) each day.

CONCLUSIONS: Among young people in urban California, differences in day-to-day exposure to tobacco outlets within activity spaces does not seem to be significantly associated with whether a person smokes a cigarette on a given day, but higher exposure to tobacco outlets appears to be positively associated with the number of cigarettes smoked on that day.}, } @article {pmid32029788, year = {2020}, author = {Dos Santos, JS and Feltran-Barbieri, R and Fonte, ES and Balmford, A and Maioli, V and Latawiec, A and Strassburg, BBN and Phalan, BT}, title = {Characterising the spatial distribution of opportunities and constraints for land sparing in Brazil.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {1946}, pmid = {32029788}, issn = {2045-2322}, abstract = {Brazil is a megadiversity country with more tropical forest than any other, and is a leading agricultural producer. The technical potential to reconcile these roles by concentrating agriculture on existing farmland and sparing land for nature is well-established, but the spatial overlap of this potential with conservation priorities and institutional constraints remains poorly understood. We mapped conservation priorities, food production potential and socio-economic variables likely to influence the success of land sparing. Pasture occupies 70% of agricultural land but contributes ≤11% of the domestic food supply. Increasing yields on pasture would add little to Brazil's food supply but - if combined with concerted conservation and restoration policies - provides the greatest opportunities for reducing land demand. Our study illustrates a method for identifying municipalities where land-sparing policies are most likely to succeed, and those where further effort is needed to overcome constraints such as land tenure insecurity, lack of access to technical advice, labour constraints, and non-compliance with environmental law.}, } @article {pmid32027685, year = {2020}, author = {Gjesfjeld, E and Silvestro, D and Chang, J and Koch, B and Foster, JG and Alfaro, ME}, title = {A quantitative workflow for modeling diversification in material culture.}, journal = {PloS one}, volume = {15}, number = {2}, pages = {e0227579}, pmid = {32027685}, issn = {1932-6203}, mesh = {*Archaeology ; *Cultural Evolution ; Databases as Topic ; Europe ; *Models, Theoretical ; *Motor Vehicles ; Time Factors ; *Workflow ; }, abstract = {Questions about the evolution of material culture are widespread in the humanities and social sciences. Statistical modeling of long-term changes in material culture is less common due to a lack of appropriate frameworks. Our goal is to close this gap and provide robust statistical methods for examining changes in the diversity of material culture. We provide an open-source and quantitative workflow for estimating rates of origination, extinction, and preservation, as well as identifying key shift points in the diversification histories of material culture. We demonstrate our approach using two distinct kinds of data: age ranges for the production of American car models, and radiocarbon dates associated with archaeological cultures of the European Neolithic. Our approach improves on existing frameworks by disentangling the relative contributions of origination and extinction to diversification. Our method also permits rigorous statistical testing of competing hypotheses to explain changes in diversity. Finally, we stress the value of a flexible approach that can be applied to data in various forms; this flexibility allows scholars to explore commonalities between forms of material culture and ask questions about the general properties of cultural change.}, } @article {pmid32027535, year = {2020}, author = {Dolson, E and Lalejini, A and Jorgensen, S and Ofria, C}, title = {Interpreting the Tape of Life: Ancestry-Based Analyses Provide Insights and Intuition about Evolutionary Dynamics.}, journal = {Artificial life}, volume = {26}, number = {1}, pages = {58-79}, doi = {10.1162/artl_a_00313}, pmid = {32027535}, issn = {1530-9185}, mesh = {*Biodiversity ; *Biological Evolution ; *Computational Biology ; Computer Simulation ; Environment ; Evolution, Molecular ; *Life ; Mutation ; *Phylogeny ; Selection, Genetic ; }, abstract = {Fine-scale evolutionary dynamics can be challenging to tease out when focused on the broad brush strokes of whole populations over long time spans. We propose a suite of diagnostic analysis techniques that operate on lineages and phylogenies in digital evolution experiments, with the aim of improving our capacity to quantitatively explore the nuances of evolutionary histories in digital evolution experiments. We present three types of lineage measurements: lineage length, mutation accumulation, and phenotypic volatility. Additionally, we suggest the adoption of four phylogeny measurements from biology: phylogenetic richness, phylogenetic divergence, phylogenetic regularity, and depth of the most-recent common ancestor. In addition to quantitative metrics, we also discuss several existing data visualizations that are useful for understanding lineages and phylogenies: state sequence visualizations, fitness landscape overlays, phylogenetic trees, and Muller plots. We examine the behavior of these metrics (with the aid of data visualizations) in two well-studied computational contexts: (1) a set of two-dimensional, real-valued optimization problems under a range of mutation rates and selection strengths, and (2) a set of qualitatively different environments in the Avida digital evolution platform. These results confirm our intuition about how these metrics respond to various evolutionary conditions and indicate their broad value.}, } @article {pmid32026745, year = {2020}, author = {Goldstein, SP and Thomas, JG and Foster, GD and Turner-McGrievy, G and Butryn, ML and Herbert, JD and Martin, GJ and Forman, EM}, title = {Refining an algorithm-powered just-in-time adaptive weight control intervention: A randomized controlled trial evaluating model performance and behavioral outcomes.}, journal = {Health informatics journal}, volume = {26}, number = {4}, pages = {2315-2331}, pmid = {32026745}, issn = {1741-2811}, support = {F32 HL143954/HL/NHLBI NIH HHS/United States ; }, mesh = {Algorithms ; Humans ; Obesity/therapy ; Overweight/therapy ; Weight Loss ; *Weight Reduction Programs ; }, abstract = {Suboptimal weight losses are partially attributable to lapses from a prescribed diet. We developed an app (OnTrack) that uses ecological momentary assessment to measure dietary lapses and relevant lapse triggers and provides personalized intervention using machine learning. Initially, tension between user burden and complete data was resolved by presenting a subset of lapse trigger questions per ecological momentary assessment survey. However, this produced substantial missing data, which could reduce algorithm performance. We examined the effect of more questions per ecological momentary assessment survey on algorithm performance, app utilization, and behavioral outcomes. Participants with overweight/obesity (n = 121) used a 10-week mobile weight loss program and were randomized to OnTrack-short (i.e. 8 questions/survey) or OnTrack-long (i.e. 17 questions/survey). Additional questions reduced ecological momentary assessment adherence; however, increased data completeness improved algorithm performance. There were no differences in perceived effectiveness, app utilization, or behavioral outcomes. Minimal differences in utilization and perceived effectiveness likely contributed to similar behavioral outcomes across various conditions.}, } @article {pmid32020500, year = {2020}, author = {Gasparini, S and Del Vecchio, G and Gioiosa, S and Flati, T and Castrignano, T and Legnini, I and Licursi, V and Ricceri, L and Scattoni, ML and Rinaldi, A and Presutti, C and Mannironi, C}, title = {Differential Expression of Hippocampal Circular RNAs in the BTBR Mouse Model for Autism Spectrum Disorder.}, journal = {Molecular neurobiology}, volume = {57}, number = {5}, pages = {2301-2313}, pmid = {32020500}, issn = {1559-1182}, support = {2018-LIFE2020//Regione Lazio/ ; Call HPC@Cineca//ELIXIR-IIB/ ; }, mesh = {Animals ; Autism Spectrum Disorder/genetics/*metabolism ; Brain Chemistry ; *Disease Models, Animal ; Gene Expression Profiling ; Gene Ontology ; Hippocampus/*metabolism ; Humans ; Male ; Mice, Inbred C57BL ; Mice, Inbred Strains/genetics/*metabolism ; Mice, Mutant Strains/genetics/*metabolism ; RNA, Circular/*biosynthesis ; RNA, Messenger/*biosynthesis ; Reverse Transcriptase Polymerase Chain Reaction ; Species Specificity ; }, abstract = {Autism spectrum disorder (ASD) is a heterogeneous neurodevelopmental condition with unknown etiology. Recent experimental evidences suggest the contribution of non-coding RNAs (ncRNAs) in the pathophysiology of ASD. In this work, we aimed to investigate the expression profile of the ncRNA class of circular RNAs (circRNAs) in the hippocampus of the BTBR T + tf/J (BTBR) mouse model and age-matched C57BL/6J (B6) mice. Alongside, we analyzed BTBR hippocampal gene expression profile to evaluate possible correlations between the differential abundance of circular and linear gene products. From RNA sequencing data, we identified circRNAs highly modulated in BTBR mice. Thirteen circRNAs and their corresponding linear isoforms were validated by RT-qPCR analysis. The BTBR-regulated circCdh9 was better characterized in terms of molecular structure and expression, highlighting altered levels not only in the hippocampus, but also in the cerebellum, prefrontal cortex, and amygdala. Finally, gene expression analysis of the BTBR hippocampus pinpointed altered biological and molecular pathways relevant for the ASD phenotype. By comparison of circRNA and gene expression profiles, we identified 6 genes significantly regulated at either circRNA or mRNA gene products, suggesting low overall correlation between circRNA and host gene expression. In conclusion, our results indicate a consistent deregulation of circRNA expression in the hippocampus of BTBR mice. ASD-related circRNAs should be considered in functional studies to identify their contribution to the etiology of the disorder. In addition, as abundant and highly stable molecules, circRNAs represent interesting potential biomarkers for autism.}, } @article {pmid32019918, year = {2020}, author = {Enquist, BJ and Abraham, AJ and Harfoot, MBJ and Malhi, Y and Doughty, CE}, title = {The megabiota are disproportionately important for biosphere functioning.}, journal = {Nature communications}, volume = {11}, number = {1}, pages = {699}, pmid = {32019918}, issn = {2041-1723}, mesh = {Animals ; Biodiversity ; *Biota ; Climate Change ; Conservation of Natural Resources ; Ecosystem ; Humans ; Plants/metabolism ; Population Dynamics ; Trees/growth & development/metabolism ; }, abstract = {A prominent signal of the Anthropocene is the extinction and population reduction of the megabiota-the largest animals and plants on the planet. However, we lack a predictive framework for the sensitivity of megabiota during times of rapid global change and how they impact the functioning of ecosystems and the biosphere. Here, we extend metabolic scaling theory and use global simulation models to demonstrate that (i) megabiota are more prone to extinction due to human land use, hunting, and climate change; (ii) loss of megabiota has a negative impact on ecosystem metabolism and functioning; and (iii) their reduction has and will continue to significantly decrease biosphere functioning. Global simulations show that continued loss of large animals alone could lead to a 44%, 18% and 92% reduction in terrestrial heterotrophic biomass, metabolism, and fertility respectively. Our findings suggest that policies that emphasize the promotion of large trees and animals will have disproportionate impact on biodiversity, ecosystem processes, and climate mitigation.}, } @article {pmid32019442, year = {2020}, author = {Liddell, C and Morgan, ER and Bull, K and Ioannou, CC}, title = {Response to resources and parasites depends on health status in extensively grazed sheep.}, journal = {Proceedings. Biological sciences}, volume = {287}, number = {1920}, pages = {20192905}, pmid = {32019442}, issn = {1471-2954}, support = {BB/S014748/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; Ecology ; Ecosystem ; Geographic Information Systems ; Health Status ; *Host-Parasite Interactions ; Parasites/*physiology ; Sheep/*parasitology ; }, abstract = {A fundamental question in animal ecology is how an individual's internal state and the external environment together shape species distributions across habitats. The increasing availability of biologgers is driving a revolution in answering this question in a wide range of species. In this study, the position of sheep (Ovis aries) from Global Positioning System collars was integrated with remote sensing data, field sampling of parasite distributions, and parasite load and health measures for each tagged individual. This allowed inter-individual variation in habitat use to be examined. Once controlling for a positive relationship between vegetation productivity and tick abundance, healthier individuals spent more of their time at sites with higher vegetation productivity, while less healthy individuals showed a stronger (negative) response to tick abundance. These trends are likely to represent a trade-off in foraging decisions that vary between individuals based on their health status. Given the rarity of studies that explore how animal distributions are affected by health and external factors, we demonstrate the value of integrating biologging technology with remote sensing data, traditional ecological sampling and individual measures of animal health. Our study, using extensively grazed sheep as a model system, opens new possibilities to study free-living grazing systems.}, } @article {pmid32013868, year = {2020}, author = {Zhang, RY and Zou, B and Yan, YW and Jeon, CO and Li, M and Cai, M and Quan, ZX}, title = {Design of targeted primers based on 16S rRNA sequences in meta-transcriptomic datasets and identification of a novel taxonomic group in the Asgard archaea.}, journal = {BMC microbiology}, volume = {20}, number = {1}, pages = {25}, pmid = {32013868}, issn = {1471-2180}, support = {2018YFC0310600//the National Key R&D Program of China/International ; 31870109//National Natural Science Foundation of China/International ; 31170114//National Natural Science Foundation of China/International ; }, mesh = {Archaea/*classification/genetics ; DNA Primers/*genetics ; DNA, Archaeal/genetics ; DNA, Ribosomal/genetics ; Databases, Genetic ; Gene Expression Profiling ; High-Throughput Nucleotide Sequencing ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, RNA/*methods ; }, abstract = {BACKGROUND: Amplification of small subunit (SSU) rRNA genes with universal primers is a common method used to assess microbial populations in various environmental samples. However, owing to limitations in coverage of these universal primers, some microorganisms remain unidentified. The present study aimed to establish a method for amplifying nearly full-length SSU rRNA gene sequences of previously unidentified prokaryotes, using newly designed targeted primers via primer evaluation in meta-transcriptomic datasets.

METHODS: Primer binding regions of universal primer 8F/Arch21F for bacteria or archaea were used for primer evaluation of SSU rRNA sequences in meta-transcriptomic datasets. Furthermore, targeted forward primers were designed based on SSU rRNA reads from unclassified groups unmatched with the universal primer 8F/Arch21F, and these primers were used to amplify nearly full-length special SSU rRNA gene sequences along with universal reverse primer 1492R. Similarity and phylogenetic analysis were used to confirm their novel status.

RESULTS: Using this method, we identified unclassified SSU rRNA sequences that were not matched with universal primer 8F and Arch21F. A new group within the Asgard superphylum was amplified by the newly designed specific primer based on these unclassified SSU rRNA sequences by using mudflat samples.

CONCLUSION: We showed that using specific primers designed based on universal primer evaluation from meta-transcriptomic datasets, identification of novel taxonomic groups from a specific environment is possible.}, } @article {pmid32010196, year = {2019}, author = {Mascarenhas, R and Ruziska, FM and Moreira, EF and Campos, AB and Loiola, M and Reis, K and Trindade-Silva, AE and Barbosa, FAS and Salles, L and Menezes, R and Veiga, R and Coutinho, FH and Dutilh, BE and Guimarães, PR and Assis, APA and Ara, A and Miranda, JGV and Andrade, RFS and Vilela, B and Meirelles, PM}, title = {Integrating Computational Methods to Investigate the Macroecology of Microbiomes.}, journal = {Frontiers in genetics}, volume = {10}, number = {}, pages = {1344}, pmid = {32010196}, issn = {1664-8021}, abstract = {Studies in microbiology have long been mostly restricted to small spatial scales. However, recent technological advances, such as new sequencing methodologies, have ushered an era of large-scale sequencing of environmental DNA data from multiple biomes worldwide. These global datasets can now be used to explore long standing questions of microbial ecology. New methodological approaches and concepts are being developed to study such large-scale patterns in microbial communities, resulting in new perspectives that represent a significant advances for both microbiology and macroecology. Here, we identify and review important conceptual, computational, and methodological challenges and opportunities in microbial macroecology. Specifically, we discuss the challenges of handling and analyzing large amounts of microbiome data to understand taxa distribution and co-occurrence patterns. We also discuss approaches for modeling microbial communities based on environmental data, including information on biological interactions to make full use of available Big Data. Finally, we summarize the methods presented in a general approach aimed to aid microbiologists in addressing fundamental questions in microbial macroecology, including classical propositions (such as "everything is everywhere, but the environment selects") as well as applied ecological problems, such as those posed by human induced global environmental changes.}, } @article {pmid32009143, year = {2020}, author = {Libkind, D and Peris, D and Cubillos, FA and Steenwyk, JL and Opulente, DA and Langdon, QK and Rokas, A and Hittinger, CT}, title = {Into the wild: new yeast genomes from natural environments and new tools for their analysis.}, journal = {FEMS yeast research}, volume = {20}, number = {2}, pages = {}, pmid = {32009143}, issn = {1567-1364}, support = {T32 GM007133/GM/NIGMS NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; }, mesh = {Ascomycota/genetics ; Basidiomycota/genetics ; Chromosome Mapping ; Computational Biology/*methods ; Environment ; *Fermentation ; *Genome, Fungal ; Genomics ; Hanseniaspora/genetics ; High-Throughput Nucleotide Sequencing ; Saccharomyces/*genetics ; Wine/analysis ; Yeasts/classification/*genetics ; }, abstract = {Genomic studies of yeasts from the wild have increased considerably in the past few years. This revolution has been fueled by advances in high-throughput sequencing technologies and a better understanding of yeast ecology and phylogeography, especially for biotechnologically important species. The present review aims to first introduce new bioinformatic tools available for the generation and analysis of yeast genomes. We also assess the accumulated genomic data of wild isolates of industrially relevant species, such as Saccharomyces spp., which provide unique opportunities to further investigate the domestication processes associated with the fermentation industry and opportunistic pathogenesis. The availability of genome sequences of other less conventional yeasts obtained from the wild has also increased substantially, including representatives of the phyla Ascomycota (e.g. Hanseniaspora) and Basidiomycota (e.g. Phaffia). Here, we review salient examples of both fundamental and applied research that demonstrate the importance of continuing to sequence and analyze genomes of wild yeasts.}, } @article {pmid32004558, year = {2020}, author = {Bernard, J and Song, L and Henderson, B and Tasian, GE}, title = {Association Between Daily Water Intake and 24-hour Urine Volume Among Adolescents With Kidney Stones.}, journal = {Urology}, volume = {140}, number = {}, pages = {150-154}, pmid = {32004558}, issn = {1527-9995}, support = {K23 DK106428/DK/NIDDK NIH HHS/United States ; }, mesh = {Adolescent ; Age Factors ; Correlation of Data ; Drinking/*physiology ; Ecological Momentary Assessment/statistics & numerical data ; Female ; Humans ; Male ; Nephrolithiasis/diagnosis/epidemiology/psychology/*urine ; *Risk Reduction Behavior ; Secondary Prevention/*methods ; Sex Factors ; United States/epidemiology ; Urine ; Urine Specimen Collection/methods ; }, abstract = {OBJECTIVE: To determine the association between daily water intake and 24-hour urine volume among adolescents with nephrolithiasis in order to estimate a "fluid prescription," the additional water intake needed to increase urine volume to a target goal.

METHODS: We conducted a secondary analysis of an ecological momentary assessment study that prospectively measured daily water intake of 25 adolescents with nephrolithiasis over 7 days. We identified 24-hour urine volumes obtained for clinical care within 12 months of water intake assessment. A linear regression model was fit to estimate the magnitude of the association between daily water intake and 24-hour urine volume, adjusting for age, sex, race, and daily temperature.

RESULTS: Twenty-two participants completed fifty-seven 24-hour urine collections within 12 months of the study period. Median daily water intake was 1.4 L (IQR 0.67-1.94). Median 24-hour urine volume was 2.01 L (IQR 1.20-2.73). A 1 L increase in daily water intake was associated with a 710 mL increase in 24-hour urine output (95%CI 0.55-0.87). Using the model output, the equation was generated to estimate the additional fluid intake needed fluid prescription (FP) to produce the desired increase in urine output (dUOP): FP = dUOP/0.71.

CONCLUSION: The FP equation (FP = dUOP)/0.71), which reflects the relationship between water intake and urine volume, could be used to help adolescents with nephrolithiasis achieve urine output goals to decrease stone recurrence.}, } @article {pmid31999761, year = {2020}, author = {He, D and Zhang, J and Zhang, X and He, S and Xie, D and Liu, Y and Li, C and Wang, Z and Liu, Y}, title = {Development of SSR markers in Paeonia based on De Novo transcriptomic assemblies.}, journal = {PloS one}, volume = {15}, number = {1}, pages = {e0227794}, pmid = {31999761}, issn = {1932-6203}, mesh = {Gene Expression Profiling ; Gene Expression Regulation, Plant ; Gene Ontology ; Genes, Plant ; Genomics ; *Microsatellite Repeats ; Paeonia/*genetics ; Plant Breeding ; Polymorphism, Genetic ; *Transcriptome ; }, abstract = {Peony is a famous ornamental and medicinal plant in China, and peony hybrid breeding is an important means of germplasm innovation. However, research on the genome of this species is limited, thereby hindering the genetic and breeding research on peony. In the present study, simple sequence repeat (SSR) locus analysis was performed on expressed sequence tags obtained by the transcriptome sequencing of Paeonia using Microsatellite software. Primers with polymorphism were obtained via polymerase chain reaction amplification and electrophoresis. As a result, a total of 86,195 unigenes were obtained by assembling the transcriptome data of Paeonia. Functional annotations were obtained in seven functional databases including 49,172 (Non-Redundant Protein Sequence Database: 57.05%), 38,352 (Nucleotide Sequence Database: 44.49%), 36,477 (Swiss Prot: 42.32%), 38,905 (Clusters of Orthologous Groups for Eukaryotic Complete Genomes: 45.14%), 37,993 (Kyoto Encyclopedia of Genes and Genomes: 44.08%), 26,832 (Gene Ontology: 31.13%) and 37,758 (Pfam: 43.81%) unigenes. Meanwhile, 21,998 SSR loci were distributed in 17,567 unigenes containing SSR sequences, and the SSR distribution frequency was 25.52%, with an average of one SSR sequence per 4.66 kb. Mononucleotide, dinucleotide, and trinucleotide were the main repeat types, accounting for 55.74%, 25.58%, and 13.21% of the total repeat times, respectively. Forty-five pairs of the 100 pairs of primers selected randomly could amplify clear polymorphic bands. The polymorphic primers of these 45 pairs were used to cluster and analyze 16 species of peony. The new SSR molecular markers can be useful for the study of genetic diversity and marker-assisted breeding of peony.}, } @article {pmid31997112, year = {2020}, author = {Zheng, G and Wei, L and Ma, L and Wu, Z and Gu, C and Chen, K}, title = {Comparative analyses of chloroplast genomes from 13 Lagerstroemia (Lythraceae) species: identification of highly divergent regions and inference of phylogenetic relationships.}, journal = {Plant molecular biology}, volume = {102}, number = {6}, pages = {659-676}, pmid = {31997112}, issn = {1573-5028}, support = {LY17C160003//Zhejiang Provincial Natural Science Foundation of China/ ; }, mesh = {Base Sequence ; Chloroplasts/*genetics ; Databases, Nucleic Acid ; Evolution, Molecular ; Genome, Chloroplast/*genetics ; Lagerstroemia/*classification/*genetics ; Molecular Sequence Annotation ; *Phylogeny ; Plant Proteins/genetics ; Plastids ; Sequence Analysis, DNA ; }, abstract = {Seven divergence hotspots as plastid markers for DNA barcoding was selected, and the phylogeny of 13 Lagerstroemia species based on the cp genome data was reconstructed within Myrtales. The Lagerstroemia species used in this study originated in China and have high economic and ecological value. The shared interspecific morphological characteristics and intraspecific morphological variation resulting from hybridization among Lagerstroemia taxa have made resolving their classification problems and phylogenetic relationships difficult. Systematic comparative genomic analysis has been shown to resolve phylogenetic relationships. We sequenced and annotated 6 Lagerstroemia cp genomes (Lagerstroemia excelsa, Lagerstroemia limii, Lagerstroemia siamica, Lagerstroemia tomentosa, Lagerstroemia venusta, and Lagerstroemia calyculata) for the first time and combined them with previously published genomes for Lagerstroemia species. Bioinformatics was used to analyse the 13 cp genomes in terms of gene structure and organization, codon usage, contraction and expansion of inverted repeat regions, repeat structure, divergence hotspots, species pairwise Ka/Ks ratios and phylogenetic relationships. The length varied between 152,049 bp in Lagerstroemia subcostata and 152,521 bp in L. venusta. We selected seven divergence hotspots in the cp genomes that had the potential to act as plastid markers to distinguish Lagerstroemia species. The phylogenetic relationships within Myrtales inferred from the cp genomes of 13 Lagerstroemia species and 27 other Myrtales species were highly supported, which illustrated several novel relationships within Myrtales. Taken together, our results provide comprehensive chloroplast genomic resources, which can be used further for species identification and molecular breeding of Lagerstroemia species.}, } @article {pmid31996500, year = {2020}, author = {Fujimura, R and Azegami, Y and Wei, W and Kakuta, H and Shiratori, Y and Ohte, N and Senoo, K and Otsuka, S and Isobe, K}, title = {Distinct Community Composition of Previously Uncharacterized Denitrifying Bacteria and Fungi across Different Land-Use Types.}, journal = {Microbes and environments}, volume = {35}, number = {1}, pages = {}, pmid = {31996500}, issn = {1347-4405}, mesh = {Bacteria/*classification/genetics/isolation & purification/*metabolism ; *Biodiversity ; Denitrification ; Fungi/*classification/genetics/isolation & purification/*metabolism ; Genes, Bacterial ; Genes, Fungal ; *Microbiota ; Nitrite Reductases/genetics ; Phylogeny ; *Soil Microbiology ; }, abstract = {Recent studies demonstrated that phylogenetically more diverse and abundant bacteria and fungi than previously considered are responsible for denitrification in terrestrial environments. We herein examined the effects of land-use types on the community composition of those denitrifying microbes based on their nitrite reductase gene (nirK and nirS) sequences. These genes can be phylogenetically grouped into several clusters. We used cluster-specific PCR primers to amplify nirK and nirS belonging to each cluster because the most widely used primers only amplify genes belonging to a single cluster. We found that the dominant taxa as well as overall community composition of denitrifying bacteria and fungi, regardless of the cluster they belonged to, differed according to the land-use type. We also identified distinguishing taxa based on individual land-use types, the distribution of which has not previously been characterized, such as denitrifying bacteria or fungi dominant in forest soils, Rhodanobacter having nirK, Penicillium having nirK, and Bradyrhizobium having nirS. These results suggest that land-use management affects the ecological constraints and consequences of denitrification in terrestrial environments through the assembly of distinct communities of denitrifiers.}, } @article {pmid31996368, year = {2020}, author = {Francis-Lyon, PA and Malik, F and Cheng, X and Ghezavati, A and Xin, F and Cai, R}, title = {TRPV6 as a Putative Genomic Susceptibility Locus Influencing Racial Disparities in Cancer.}, journal = {Cancer prevention research (Philadelphia, Pa.)}, volume = {13}, number = {5}, pages = {423-428}, doi = {10.1158/1940-6207.CAPR-19-0351}, pmid = {31996368}, issn = {1940-6215}, mesh = {Black or African American/*genetics ; Calcium/metabolism ; Calcium Channels/*genetics ; *Genetic Predisposition to Disease ; *Health Status Disparities ; *Healthcare Disparities ; Humans ; Neoplasms/ethnology/genetics/*pathology ; Risk Assessment ; TRPV Cation Channels/*genetics ; White People/*genetics ; }, abstract = {It is well established that African Americans exhibit higher incidence, higher mortality, and more aggressive forms of some cancers, including those of breast, prostate, colon, stomach, and cervix. Here we examine the ancestral haplotype of the TRPV6 calcium channel as a putative genomic factor in this racial divide. The minor (ancestral) allele frequency is 60% in people of African ancestry, but between 1% and 11% in all other populations. Research on TRPV6 structure/function, its association with specific cancers, and the evolutionary-ecological conditions that impacted selection of its haplotypes are synthesized to provide evidence for TRPV6 as a germline susceptibility locus in cancer. Recently elucidated mechanisms of TRPV6 channel deactivation are discussed in relation to the location of the allele favored in selection, suggesting a reduced capacity to inactivate the channel in those who have the ancestral haplotype. This could result in an excessively high cellular Ca[2+], which has been implicated in cancer, for those in settings where calcium intake is far higher than in their ancestral environment. A recent report associating increasing calcium intake with a pattern of increase in aggressive prostate cancer in African-American but not European-American men may be related. If TRPV6 is found to be associated with cancer, further research would be warranted to improve risk assessment and examine interventions with the aim of improving cancer outcomes for people of African ancestry.}, } @article {pmid31993260, year = {2020}, author = {Asase, A and Sainge, MN and Radji, RA and Ugbogu, OA and Peterson, AT}, title = {A new model for efficient, need-driven progress in generating primary biodiversity information resources.}, journal = {Applications in plant sciences}, volume = {8}, number = {1}, pages = {e11318}, pmid = {31993260}, issn = {2168-0450}, abstract = {PREMISE: The field of biodiversity informatics has developed rapidly in recent years, with broad availability of large-scale information resources. However, online biodiversity information is biased spatially as a result of slow and uneven capture and digitization of existing data resources. The West African Plants Initiative approach to data capture is a prototype of a novel solution to the problems of the traditional model, in which the institutional "owner" of the specimens is responsible for digital capture of associated data.

METHODS: We developed customized workflows for data capture in formats directly and permanently useful to the "owner" herbarium, and digitized significant numbers of new biodiversity records, adding to the information available for the plants of the region.

RESULTS: In all, 190,953 records of species in 1965 genera and 331 families were captured by mid-2018. These data records covered 16 West African countries, with most of the records (10,000-99,999) from Côte d'Ivoire, Ghana, Togo, Nigeria, and Cameroon, and the fewest data records from Mauritania (<100 records). The West African Plants Initiative has increased available digital accessible knowledge records for West African plants by about 54%. Several of the project institutions have put initial project data online as part of their Global Biodiversity Information Facility data contributions. The average cost of data capture ranged from US$0.50-1.00 per herbarium sheet.

DISCUSSION: Data capture has been cost-effective because it is much less expensive than de novo field collections, allows for development of information resources even for regions in which political situations make contemporary field sampling impossible, and provides a historical baseline against which to compare newer data as they become available. This new paradigm in specimen digitization has considerable promise to accelerate and improve the process of generating high-quality biodiversity information, and can be replicated and applied in many biodiversity-rich, information-poor regions to remedy the present massive gaps in information availability.}, } @article {pmid31992756, year = {2020}, author = {Montoliu-Nerin, M and Sánchez-García, M and Bergin, C and Grabherr, M and Ellis, B and Kutschera, VE and Kierczak, M and Johannesson, H and Rosling, A}, title = {Building de novo reference genome assemblies of complex eukaryotic microorganisms from single nuclei.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {1303}, pmid = {31992756}, issn = {2045-2322}, support = {678792//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; }, mesh = {Algorithms ; Computational Biology/*methods ; Eukaryota/*genetics ; Fungi/genetics ; *Genome ; *Genomics/methods ; Workflow ; }, abstract = {The advent of novel sequencing techniques has unraveled a tremendous diversity on Earth. Genomic data allow us to understand ecology and function of organisms that we would not otherwise know existed. However, major methodological challenges remain, in particular for multicellular organisms with large genomes. Arbuscular mycorrhizal (AM) fungi are important plant symbionts with cryptic and complex multicellular life cycles, thus representing a suitable model system for method development. Here, we report a novel method for large scale, unbiased nuclear sorting, sequencing, and de novo assembling of AM fungal genomes. After comparative analyses of three assembly workflows we discuss how sequence data from single nuclei can best be used for different downstream analyses such as phylogenomics and comparative genomics of single nuclei. Based on analysis of completeness, we conclude that comprehensive de novo genome assemblies can be produced from six to seven nuclei. The method is highly applicable for a broad range of taxa, and will greatly improve our ability to study multicellular eukaryotes with complex life cycles.}, } @article {pmid31992199, year = {2020}, author = {Hui, WK and Zhao, FY and Wang, JY and Chen, XY and Li, JW and Zhong, Y and Li, HY and Zheng, JX and Zhang, LZ and Que, QM and Wu, AM and Gong, W}, title = {De novo transcriptome assembly for the five major organs of Zanthoxylum armatum and the identification of genes involved in terpenoid compound and fatty acid metabolism.}, journal = {BMC genomics}, volume = {21}, number = {1}, pages = {81}, pmid = {31992199}, issn = {1471-2164}, support = {2018YFD1000605//the National Key Research and Development Program of China/ ; 2016NYZ0035//the Forest and Bamboo Breeding Project of Sichuan Province for the Fifth Year Plan/ ; }, mesh = {Biosynthetic Pathways ; Computational Biology/methods ; Fatty Acids/*metabolism ; *Gene Expression Regulation, Plant ; *Lipid Metabolism ; Microsatellite Repeats ; Molecular Sequence Annotation ; Organ Specificity ; Terpenes/*metabolism ; *Transcriptome ; Zanthoxylum/*genetics/*metabolism ; }, abstract = {BACKGROUND: Zanthoxylum armatum (Z. armatum) is a highly economically important tree that presents a special numbing taste. However, the underlying regulatory mechanism of the numbing taste remains poorly understood. Thus, the elucidation of the key genes associated with numbing taste biosynthesis pathways is critical for providing genetic information on Z. armatumand the breeding of high-quality germplasms of this species.

RESULTS: Here, de novo transcriptome assembly was performed for the five major organs of Z. armatum, including the roots, stems, leaf buds, mature leaves and fruits. A total of 111,318 unigenes were generated with an average length of 1014 bp. Additionally, a large number of SSRs were obtained to improve our understanding of the phylogeny and genetics of Z. armatum. The organ-specific unigenes of the five major samples were screened and annotated via GO and KEGG enrichment analysis. A total of 53 and 34 unigenes that were exclusively upregulated in fruit samples were identified as candidate unigenes for terpenoid biosynthesis or fatty acid biosynthesis, elongation and degradation pathways, respectively. Moreover, 40 days after fertilization (Fr4 stage) could be an important period for the accumulation of terpenoid compounds during the fruit development and maturation of Z. armatum. The Fr4 stage could be a key point at which the first few steps of the fatty acid biosynthesis process are promoted, and the catalysis of subsequent reactions could be significantly induced at 62 days after fertilization (Fr6 stage).

CONCLUSIONS: The present study realized de novo transcriptome assembly for the five major organs of Z. armatum. To the best of our knowledge, this study provides the first comprehensive analysis revealing the genes underlying the special numbing taste of Z. armatum. The assembled transcriptome profiles expand the available genetic information on this species and will contribute to gene functional studies, which will aid in the engineering of high-quality cultivars of Z. armatum.}, } @article {pmid31992185, year = {2020}, author = {Zhang, Y and An, D and Li, C and Zhao, Z and Wang, W}, title = {The complete chloroplast genome of greater duckweed (Spirodela polyrhiza 7498) using PacBio long reads: insights into the chloroplast evolution and transcription regulation.}, journal = {BMC genomics}, volume = {21}, number = {1}, pages = {76}, pmid = {31992185}, issn = {1471-2164}, support = {31670366//National Natural Science Foundation of China/ ; }, mesh = {Araceae/*genetics/metabolism ; Chloroplasts/genetics ; Computational Biology ; Evolution, Molecular ; Gene Expression Regulation, Plant ; Genes, Plant ; *Genome, Chloroplast ; *Genomics/methods ; High-Throughput Nucleotide Sequencing ; Introns ; Molecular Sequence Annotation ; Operon ; Photosynthesis/genetics ; RNA Editing ; Reproducibility of Results ; Transcription, Genetic ; }, abstract = {BACKGROUND: Duckweeds (Lemnaceae) are aquatic plants distributed all over the world. The chloroplast genome, as an efficient solar-powered reactor, is an invaluable resource to study biodiversity and to carry foreign genes. The chloroplast genome sequencing has become routine and less expensive with the delivery of high-throughput sequencing technologies, allowing us to deeply investigate genomics and transcriptomics of duckweed organelles.

RESULTS: Here, the complete chloroplast genome of Spirodela polyrhiza 7498 (SpV2) is assembled by PacBio sequencing. The length of 168,956 bp circular genome is composed of a pair of inverted repeats of 31,844 bp, a large single copy of 91,210 bp and a small single copy of 14,058 bp. Compared to the previous version (SpV1) assembled from short reads, the integrity and quality of SpV2 are improved, especially with the retrieval of two repeated fragments in ycf2 gene. There are a number of 107 unique genes, including 78 protein-coding genes, 25 tRNA genes and 4 rRNA genes. With the evidence of full-length cDNAs generated from PacBio isoform sequencing, seven genes (ycf3, clpP, atpF, rpoC1, rpl2, rps12 and ndhA) are detected to contain type-II introns. The ndhA intron has 50% more sequence divergence than the species-barcoding marker of atpF-atpH, showing the potential power to discriminate close species. A number of 37 RNA editing sites are recognized to have cytosine (C) to uracil (U) substitutions, eight of which are newly defined including six from the intergenic regions and two from the coding sequences of rpoC2 and ndhA genes. In addition, nine operon classes are identified using transcriptomic data. It is found that the operons contain multiple subunit genes encoding the same functional complexes comprising of ATP synthase, photosynthesis system, ribosomal proteins, et.al., which could be simultaneously transcribed and coordinately translated in response to the cell stimuli.

CONCLUSIONS: The understanding of the chloroplast genomics and the transcriptomics of S.polyrhiza would greatly facilitate the study of phylogenetic evolution and the application of genetically engineering duckweeds.}, } @article {pmid31989910, year = {2019}, author = {Reddy, UJ and Ramana Reddy, BV and Reddy, BE}, title = {Categorization & Recognition of Lung Tumor Using Machine Learning Representations.}, journal = {Current medical imaging reviews}, volume = {15}, number = {4}, pages = {405-413}, doi = {10.2174/1573405614666180212162727}, pmid = {31989910}, mesh = {Algorithms ; Early Detection of Cancer/methods ; Humans ; Image Interpretation, Computer-Assisted/*methods ; Lung Neoplasms/*diagnostic imaging ; *Machine Learning ; }, abstract = {BACKGROUND: Lung Cancer is the disease spreading around the world nowadays. Early recognition of lung disease is a difficult task as the cells which cause tumor will grow quickly and the majority of these cells are enclosed with each other. From the beginning of the treatment, tumor detection handling systems which are generally utilized for the diagnosis of lung cancer, recognizable proof of hereditary and ecological elements is imperative in creating a novel technique for lung tumor detection. In different cancers, for example, lung cancer, the time calculated is imperative to find the anomaly issue in target images.

METHODS: In this proposed framework, GLCM (Gray Level Co-event Matrix) is utilized for preprocessing of images and to feature extraction procedures to check the condition of the patient whether it is ordinary or irregular. Surface-based elements, for example, GLCM (Gray Level Co-event Matrix) features assume a vital part of remedial image examination which is utilized for the identification of Lung cancer. In the event that lung cancer is effectively distinguished and anticipated in its initial stages, it lessens numerous treatment choices and furthermore, decreases the danger of intrusive surgery and increment survival rate.

RESULTS & CONCLUSION: The proposed method will efficiently identify the position of the tumor in lungs using the probability framework. This will offer a promising outcome for recognition and diagnosis of lung cancer. In this manuscript, GLCM features are used for the prediction of lung tumor and tests are performed for performance analysis in comparison with the histogram and GLCM features, in which GLCM features are accurate in predicting lung tumor even if it takes more time than histogram features. In this manner, early discovery and probability of lung cancer should assume a crucial task in finding a procedure and furthermore, an increment in the survival rate of the patient. This exploration investigates machine learning systems which consider quality articulation, to perceive cancer or to identify lung cancer.}, } @article {pmid31988717, year = {2020}, author = {Glidden, CK and Koehler, AV and Hall, RS and Saeed, MA and Coppo, M and Beechler, BR and Charleston, B and Gasser, RB and Jolles, AE and Jabbar, A}, title = {Elucidating cryptic dynamics of Theileria communities in African buffalo using a high-throughput sequencing informatics approach.}, journal = {Ecology and evolution}, volume = {10}, number = {1}, pages = {70-80}, pmid = {31988717}, issn = {2045-7758}, abstract = {Increasing access to next-generation sequencing (NGS) technologies is revolutionizing the life sciences. In disease ecology, NGS-based methods have the potential to provide higher-resolution data on communities of parasites found in individual hosts as well as host populations.Here, we demonstrate how a novel analytical method, utilizing high-throughput sequencing of PCR amplicons, can be used to explore variation in blood-borne parasite (Theileria-Apicomplexa: Piroplasmida) communities of African buffalo at higher resolutions than has been obtained with conventional molecular tools.Results reveal temporal patterns of synchronized and opposite fluctuations of prevalence and relative abundance of Theileria spp. within the host population, suggesting heterogeneous transmission across taxa. Furthermore, we show that the community composition of Theileria spp. and their subtypes varies considerably between buffalo, with differences in composition reflected in mean and variance of overall parasitemia, thereby showing potential to elucidate previously unexplained contrasts in infection outcomes for host individuals.Importantly, our methods are generalizable as they can be utilized to describe blood-borne parasite communities in any host species. Furthermore, our methodological framework can be adapted to any parasite system given the appropriate genetic marker.The findings of this study demonstrate how a novel NGS-based analytical approach can provide fine-scale, quantitative data, unlocking opportunities for discovery in disease ecology.}, } @article {pmid31985536, year = {2020}, author = {Saunders, GH and Christensen, JH and Gutenberg, J and Pontoppidan, NH and Smith, A and Spanoudakis, G and Bamiou, DE}, title = {Application of Big Data to Support Evidence-Based Public Health Policy Decision-Making for Hearing.}, journal = {Ear and hearing}, volume = {41}, number = {5}, pages = {1057-1063}, pmid = {31985536}, issn = {1538-4667}, mesh = {*Big Data ; Health Policy ; Hearing ; Humans ; *Policy Making ; Prospective Studies ; }, abstract = {Ideally, public health policies are formulated from scientific data; however, policy-specific data are often unavailable. Big data can generate ecologically-valid, high-quality scientific evidence, and therefore has the potential to change how public health policies are formulated. Here, we discuss the use of big data for developing evidence-based hearing health policies, using data collected and analyzed with a research prototype of a data repository known as EVOTION (EVidence-based management of hearing impairments: public health pOlicy-making based on fusing big data analytics and simulaTION), to illustrate our points. Data in the repository consist of audiometric clinical data, prospective real-world data collected from hearing aids and an app, and responses to questionnaires collected for research purposes. To date, we have used the platform and a synthetic dataset to model the estimated risk of noise-induced hearing loss and have shown novel evidence of ways in which external factors influence hearing aid usage patterns. We contend that this research prototype data repository illustrates the value of using big data for policy-making by providing high-quality evidence that could be used to formulate and evaluate the impact of hearing health care policies.}, } @article {pmid31981905, year = {2020}, author = {Li, L and Zhao, Y and Ma, J and Tao, H and Zheng, G and Chen, J and Jiang, W and Lu, Y}, title = {The orphan histidine kinase PdtaS-p regulates both morphological differentiation and antibiotic biosynthesis together with the orphan response regulator PdtaR-p in Streptomyces.}, journal = {Microbiological research}, volume = {233}, number = {}, pages = {126411}, doi = {10.1016/j.micres.2020.126411}, pmid = {31981905}, issn = {1618-0623}, mesh = {Anti-Bacterial Agents/*biosynthesis ; Bacterial Proteins/genetics/*metabolism ; Computational Biology ; Gene Deletion ; Gene Expression Regulation, Bacterial ; Histidine Kinase/genetics/*metabolism ; Mutation ; Phenotype ; RNA Recognition Motif Proteins/genetics ; Streptomyces/*enzymology/genetics ; }, abstract = {In Streptomyces pristinaespiralis, the orphan histidine kinase (HK) PdtaS-p (encoded by SSDG_02492), which belongs to proteins of two-component systems (TCSs), plays an important role in both morphological differentiation and antibiotic biosynthesis. Owing to the isolated genetic organization of pdtaS-p, it is a challenge to identify its cognate response regulator (RR) and hampers the efforts to elucidate the regulation mechanism of PdtaS-p. In this study, based on bioinformatics analysis, we identify the cognate RR PdtaR-p (encoded by SSDG_04087) of PdtaS-p by phenotype similarity of gene deletion mutants as well as in vitro phosphor-transfer assay. We show that the mutants (ΔpdtaR-p and ΔpdtaS-p) exhibit almost the same phenotypical changes, showing a bald phenotype on MS agar and reduced pristinamycin biosynthesis. Further phosphor-transfer assay indicates that the phosphoryl group of HK PdtaS-p can be specifically transferred to RR PdtaR-p. Compared with the majority of RRs that harbor DNA-binding domains, PdtaR-p contains a putative ANTAR RNA-binding domain involved in controlling gene expression at the post-transcription level. Finally, we demonstrate that their ortholog from the model strain Streptomyces coelicolor, PdtaS-c/PdtaR-c, also regulates both morphological differentiation and antibiotics biosynthesis, suggesting that PdtaS-p/PdtaR-p-mediated molecular regulation may be conserved in the genus Streptomyces. To our knowledge, this is the first report describing the functional identification of ANTAR RNA-binding regulators in Streptomyces.}, } @article {pmid31976035, year = {2019}, author = {Monroe-Wise, A and Kinuthia, J and Fuller, S and Dunbar, M and Masuda, D and Opiyo, E and Muchai, B and Chepken, C and Omwenga, E and Oboko, R and Osoti, A and Masys, D and Chung, MH}, title = {Improving Information and Communications Technology (ICT) Knowledge and Skills to Develop Health Research Capacity in Kenya.}, journal = {Online journal of public health informatics}, volume = {11}, number = {3}, pages = {e22}, pmid = {31976035}, issn = {1947-2579}, support = {R25 TW009692/TW/FIC NIH HHS/United States ; }, abstract = {Objectives Information and communication technology (ICT) tools are increasingly important for clinical care and international research. Many technologies would be particularly useful for healthcare workers in resource-limited settings; however, these individuals are the least likely to utilize ICT tools due tolack of knowledge and skills necessary to use them. Our program aimed to train researchers in low-resource settings on using ICT tools and to understand how different didactic modalities build knowledge and skills in this area. Methods We conducted a tiered, blended learning program for researchers in Kenya on three areas of ICT: geographic information systems, data management, and communication tools. Each course included three tiers: online courses, skills workshops, and mentored projects. Concurrently, a training of trainers course was taught to ensure sustainable ongoing training. A mixed qualitative and quantitative survey was conducted at the end of each training to assess knowledge and skill acquisition. Results Course elements that incorporated local examples and hands-on skill building activities were most valuable. Discussion boards were sometimes distracting, depending on multiple factors. Mentored projects were most useful when there were clear expectations, pre-existing projects, and clear timelines. Discussion Training in the use of ICT tools is highly valued among researchers in low-income settings, particularly when it includes hands-on skill-building and local examples. Our students demonstrated acquisition of new skills and felt these skills to be valuable in their workplaces. Conclusions Further training in ICT skills should be considered in other low-resource settings using our program as a foundational model.}, } @article {pmid31975176, year = {2020}, author = {Nolte, AW}, title = {Genomic Access to the Diversity of Fishes.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2090}, number = {}, pages = {397-411}, pmid = {31975176}, issn = {1940-6029}, mesh = {Animals ; Databases, Genetic ; Evolution, Molecular ; Fishes/*genetics ; Genome Size ; Genomics/*methods ; Phylogeny ; }, abstract = {The number of fishes exceeds that of all other vertebrates both in terms of species numbers and in their morphological and phylogenetic diversity. They are an ecologically and economically important group and play an essential role as a resource for humans. This makes the genomic exploration of fishes an important area of research, both from an applied and a basic research perspective. Fish genomes can vary greatly in complexity, which is partially due to differences in size and content of repetitive DNA, a history of genome duplication events and because fishes may be polyploid, all of which complicate the assembly and analysis of genome sequences. However, the advent of modern sequencing techniques now facilitates access to genomic data that permit genome-wide exploration of genetic information even for previously unexplored species. The development of genomic resources for fishes is spearheaded by model organisms that have been subject to genetic analysis and genome sequencing projects for a long time. These offer a great potential for the exploration of new species through the transfer of genomic information in comparative analyses. A growing number of genome sequencing projects and the increasing availability of tools to assemble and access genomic information now move boundaries between model and nonmodel species and promises progress in many interesting but unexplored species that remain to be studied.}, } @article {pmid31975164, year = {2020}, author = {Liu, CC and Shringarpure, S and Lange, K and Novembre, J}, title = {Exploring Population Structure with Admixture Models and Principal Component Analysis.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2090}, number = {}, pages = {67-86}, pmid = {31975164}, issn = {1940-6029}, support = {R01 GM132383/GM/NIGMS NIH HHS/United States ; U01 CA198933/CA/NCI NIH HHS/United States ; }, mesh = {Computational Biology ; Genetics, Population/*methods ; Genome, Human ; Humans ; Models, Genetic ; *Polymorphism, Single Nucleotide ; Principal Component Analysis ; }, abstract = {Population structure is a commonplace feature of genetic variation data, and it has importance in numerous application areas, including evolutionary genetics, conservation genetics, and human genetics. Understanding the structure in a sample is necessary before more sophisticated analyses are undertaken. Here we provide a protocol for running principal component analysis (PCA) and admixture proportion inference-two of the most commonly used approaches in describing population structure. Along with hands-on examples with CEPH-Human Genome Diversity Panel and pragmatic caveats, readers will learn to analyze and visualize population structure on their own data.}, } @article {pmid31972911, year = {2020}, author = {Wang, J and Ding, J and Yu, D and Teng, D and He, B and Chen, X and Ge, X and Zhang, Z and Wang, Y and Yang, X and Shi, T and Su, F}, title = {Machine learning-based detection of soil salinity in an arid desert region, Northwest China: A comparison between Landsat-8 OLI and Sentinel-2 MSI.}, journal = {The Science of the total environment}, volume = {707}, number = {}, pages = {136092}, doi = {10.1016/j.scitotenv.2019.136092}, pmid = {31972911}, issn = {1879-1026}, abstract = {Accurate assessment of soil salinization is considered as one of the most important steps in combating global climate change, especially in arid and semi-arid regions. Multi-spectral remote sensing (RS) data including Landsat series provides the potential for frequent surveys for soil salinization at various scales and resolutions. Additionally, the recently launched Sentinel-2 satellite constellation has temporal revisiting frequency of 5 days, which has been proven to be an ideal approach to assess soil salinity. Yet, studies on detailed comparison in soil salinity tracking between Landsat-8 OLI and Sentinel-2 MSI remain limited. For this purpose, we collected a total of 64 topsoil samples in an arid desert region, the Ebinur Lake Wetland National Nature Reserve (ELWNNR) to compare the monitoring accuracy between Landsat-8 OLI and Sentinel-2 MSI. In this study, the Cubist model was trained using RS-derived covariates (spectral bands, Tasseled Cap transformation-derived wetness (TCW), and satellite salinity indices) and laboratory measured electrical conductivity of 1:5 soil:water extract (EC). The results showed that the measured soil salinity had a significant correlation with surface soil moisture (Pearson's r = 0.75). The introduction of TCW generated satisfactory estimating performance. Compared with OLI dataset, the combination of MSI dataset and Cubist model yielded overall better model performance and accuracy measures (R[2] = 0.912, RMSE = 6.462 dS m[-1], NRMSE = 9.226%, RPD = 3.400 and RPIQ = 6.824, respectively). The differences between Landsat-8 OLI and Sentinel-2 MSI were distinguishable. In conclusion, MSI image with finer spatial resolution performed better than OLI. Combining RS data sets and their derived TCW within a Cubist framework yielded accurate regional salinity map. The increased temporal revisiting frequency and spectral resolution of MSI data are expected to be positive enhancements to the acquisition of high-quality soil salinity information of desert soils.}, } @article {pmid31972373, year = {2020}, author = {Muthye, V and Kandoi, G and Lavrov, DV}, title = {MMPdb and MitoPredictor: Tools for facilitating comparative analysis of animal mitochondrial proteomes.}, journal = {Mitochondrion}, volume = {51}, number = {}, pages = {118-125}, doi = {10.1016/j.mito.2020.01.001}, pmid = {31972373}, issn = {1872-8278}, mesh = {Acanthamoeba castellanii ; Animals ; Caenorhabditis elegans ; *Databases, Protein ; Drosophila melanogaster ; Energy Metabolism/physiology ; Humans ; *Machine Learning ; Mice ; Mitochondria/*metabolism ; Mitochondrial Proteins/*metabolism ; Proteome/genetics ; Saccharomyces cerevisiae ; }, abstract = {Data on experimentally-characterized animal mitochondrial proteomes (mt-proteomes) are limited to a few model organisms and are scattered across multiple databases, impeding a comparative analysis. We developed two resources to address these problems. First, we re-analyzed proteomic data from six species with experimentally characterized mt-proteomes: animals (Homo sapiens, Mus musculus, Caenorhabditis elegans, and Drosophila melanogaster), and outgroups (Acanthamoeba castellanii and Saccharomyces cerevisiae) and created the Metazoan Mitochondrial Proteome Database (MMPdb) to host the results. Second, we developed a novel pipeline, "MitoPredictor" that uses a Random Forest classifier to infer mitochondrial localization of proteins based on orthology, mitochondrial targeting signal prediction, and protein domain analyses. Both tools generate an R Shiny applet that can be used to visualize and interact with the results and can be used on a personal computer. MMPdb is also available online at https://mmpdb.eeob.iastate.edu/.}, } @article {pmid31972020, year = {2020}, author = {Pippel, M and Jebb, D and Patzold, F and Winkler, S and Vogel, H and Myers, G and Hiller, M and Hundsdoerfer, AK}, title = {A highly contiguous genome assembly of the bat hawkmoth Hyles vespertilio (Lepidoptera: Sphingidae).}, journal = {GigaScience}, volume = {9}, number = {1}, pages = {}, pmid = {31972020}, issn = {2047-217X}, mesh = {Animals ; Chiroptera/parasitology ; Computational Biology/methods ; *Genome ; *Genomics/methods ; Molecular Sequence Annotation ; Moths/*genetics ; }, abstract = {BACKGROUND: Adapted to different ecological niches, moth species belonging to the Hyles genus exhibit a spectacular diversity of larval color patterns. These species diverged ∼7.5 million years ago, making this rather young genus an interesting system to study a wide range of questions including the process of speciation, ecological adaptation, and adaptive radiation.

RESULTS: Here we present a high-quality genome assembly of the bat hawkmoth Hyles vespertilio, the first reference genome of a member of the Hyles genus. We generated 51× Pacific Biosciences long reads with an average read length of 8.9 kb. Pacific Biosciences reads longer than 4 kb were assembled into contigs, resulting in a 651.4-Mb assembly consisting of 530 contigs with an N50 value of 7.5 Mb. The circular mitochondrial contig has a length of 15,303 bp. The H. vespertilio genome is very repeat-rich and exhibits a higher repeat content (50.3%) than other Bombycoidea species such as Bombyx mori (45.7%) and Manduca sexta (27.5%). We developed a comprehensive gene annotation workflow to obtain consensus gene models from different evidence including gene projections, protein homology, transcriptome data, and ab initio predictions. The resulting gene annotation is highly complete with 94.5% of BUSCO genes being completely present, which is higher than the BUSCO completeness of the B. mori (92.2%) and M. sexta (90%) annotations.

CONCLUSIONS: Our gene annotation strategy has general applicability to other genomes, and the H. vespertilio genome provides a valuable molecular resource to study a range of questions in this genus, including phylogeny, incomplete lineage sorting, speciation, and hybridization. A genome browser displaying the genome, alignments, and annotations is available at https://genome-public.pks.mpg.de/cgi-bin/hgTracks?db=HLhylVes1.}, } @article {pmid31971962, year = {2020}, author = {Tian, X and Xie, J and Yu, J}, title = {Physiological and transcriptomic responses of Lanzhou Lily (Lilium davidii, var. unicolor) to cold stress.}, journal = {PloS one}, volume = {15}, number = {1}, pages = {e0227921}, pmid = {31971962}, issn = {1932-6203}, mesh = {Cold Temperature/adverse effects ; Gene Expression Regulation, Plant/genetics ; Gene Ontology ; Lilium/*genetics/physiology ; Photosynthesis/genetics/physiology ; Plant Roots/*genetics ; Plants, Medicinal/*genetics/physiology ; RNA-Seq ; Stress, Physiological/genetics ; Transcriptome/*genetics ; }, abstract = {Low temperature induces changes in plants at physiological and molecular levels, thus affecting growth and development. The Lanzhou lily (Lilium davidii, var. unicolor) is an important medicinal plant with high economic value. However, the molecular mechanisms underlying its photosynthetic and antioxidation responses to low temperature still remain poorly understood. This study subjected the Lanzhou lily to the two temperatures of 20°C (control) and 4°C (low temperature) for 24 h. Physiological parameters related to membrane integrity, photosynthesis, antioxidant system, and differentially expressed genes were investigated. Compared with control, low temperature increased the relative electrical conductivity by 43.2%, while it decreased net photosynthesis rate, ratio of variable to maximal fluorescence, and catalase activity by 47.3%, 10.1%, and 11.1%, respectively. In addition, low temperature significantly increased the content of soluble protein, soluble sugar, and proline, as well as the activity of superoxide dismutase and peroxidase. Comparative transcriptome profiling showed that a total of 238,109 differentially expressed genes were detected. Among these, 3,566 were significantly upregulated while 2,982 were significantly downregulated in response to low temperature. Gene Ontology enrichment analysis indicated that in response to low temperature, the mostly significantly enriched differentially expressed genes were mainly involved in phosphorylation, membrane and protein kinase activity, as well as photosynthesis, light harvesting, light reaction, and alpha,alpha-trehalose-phosphate synthase activity. Kyoto Encyclopedia of Genes and Genomes enrichment analysis also indicated that the most significantly enriched pathways involved ribosome biogenesis in eukaryotes, phenylalanine metabolism, circadian rhythm, porphyrin and chlorophyll metabolism, photosynthesis of antenna proteins, photosynthesis, and carbon fixation in photosynthetic organisms. Moreover, the expression patterns of 10 randomly selected differentially expressed genes confirmed the RNA-Seq results. These results expand the understanding of the physiological and molecular mechanisms underlying the response of the Lanzhou lily to low temperature stress.}, } @article {pmid31970906, year = {2020}, author = {Halliday, TM and Rynders, CA and Thomas, E and Bergouignan, A and Pan, Z and Kealey, EH and Cornier, MA and Bessesen, DH}, title = {Appetite-Related Responses to Overfeeding and Longitudinal Weight Change in Obesity-Prone and Obesity-Resistant Adults.}, journal = {Obesity (Silver Spring, Md.)}, volume = {28}, number = {2}, pages = {259-267}, pmid = {31970906}, issn = {1930-739X}, support = {K24 DK002935/DK/NIDDK NIH HHS/United States ; T32 DK007658/DK/NIDDK NIH HHS/United States ; UL 1 RR025780/RR/NCRR NIH HHS/United States ; UL1 RR025780/RR/NCRR NIH HHS/United States ; R00DK100465/DK/NIDDK NIH HHS/United States ; K01 DK113063/DK/NIDDK NIH HHS/United States ; R00 DK100465/DK/NIDDK NIH HHS/United States ; T32 DK07658/DK/NIDDK NIH HHS/United States ; K24 DK02935/DK/NIDDK NIH HHS/United States ; P30 DK048520/DK/NIDDK NIH HHS/United States ; R01 DK062874/DK/NIDDK NIH HHS/United States ; 5 P30 DK048520-21/DK/NIDDK NIH HHS/United States ; RO1 DK62874/DK/NIDDK NIH HHS/United States ; }, mesh = {Adult ; Appetite/*physiology ; Appetite Regulation/*physiology ; Body Weight ; Diet/*methods ; Energy Intake/*physiology ; Female ; Humans ; Male ; Obesity/*physiopathology ; }, abstract = {OBJECTIVE: Appetite responses to 3 days of overfeeding (OF) were examined as correlates of longitudinal weight change in adults classified as obesity prone (OP) or obesity resistant (OR).

METHODS: OP (n = 22) and OR (n = 30) adults consumed a controlled eucaloric and OF diet (140% of energy needs) for 3 days, followed by 3 days of ad libitum feeding. Hunger and satiety were evaluated by visual analog scales. Ghrelin and peptide YY (PYY) levels were measured during a 24-hour inpatient visit on day 3. Body weight and composition were measured annually for 4.0 ± 1.3 years.

RESULTS: Dietary restraint and disinhibition were greater in OP than OR (mean difference: 3.5 ± 1.2 and 3.3 ± 0.9, respectively; P < 0.01) participants, and disinhibition was associated with longitudinal weight change (n = 48; r = 0.35; P = 0.02). Compared with the eucaloric diet, energy intake fell significantly in OR participants following OF (P = 0.03) but not in OP (P = 0.33) participants. Twenty-four-hour PYY area under the curve values increased with OF in OR (P = 0.02) but not in OP (P = 0.17) participants. Furthermore, changes in PYY levels with OF correlated with measured energy intake (r = -0.36; P = 0.01).

CONCLUSIONS: Baseline disinhibition and PYY responses to OF differed between OP and OR adults. Dietary disinhibition was associated with 5-year longitudinal weight gain. Differences in appetite regulation may underlie differences in propensity for weight gain.}, } @article {pmid31965380, year = {2020}, author = {Dore, KM and Hansen, MF and Klegarth, AR and Fichtel, C and Koch, F and Springer, A and Kappeler, P and Parga, JA and Humle, T and Colin, C and Raballand, E and Huang, ZP and Qi, XG and Di Fiore, A and Link, A and Stevenson, PR and Stark, DJ and Tan, N and Gallagher, CA and Anderson, CJ and Campbell, CJ and Kenyon, M and Pebsworth, P and Sprague, D and Jones-Engel, L and Fuentes, A}, title = {Review of GPS collar deployments and performance on nonhuman primates.}, journal = {Primates; journal of primatology}, volume = {61}, number = {3}, pages = {373-387}, pmid = {31965380}, issn = {1610-7365}, support = {PEC 13-249/HX/HSRD VA/United States ; #31622053//National Natural Science Foundation of China (CN)/ ; 0504495//National Science Foundation IGERT GLOBES program/ ; 5189-00135B//Innovationsfonden/ ; R01 AG034513/AG/NIA NIH HHS/United States ; W267-13//National Geographic Society's Waitt Program/ ; PR12-012//Margot Marsh Biodiversity Foundation/ ; 2018TD-017//Department of Science and Technology of Shaanxi Prov. China/ ; BCS 1638822//National Science Foundation/ ; P51 OD010425/CD/ODCDC CDC HHS/United States ; PR14-36//Margot Marsh Biodiversity Foundation/ ; 9234-12//National Geographic Young Explorer's Grant/ ; P51 OD010425/OD/NIH HHS/United States ; P2C HD042828/HD/NICHD NIH HHS/United States ; BCS 1062540//National Science Foundation/ ; #31730104//National Natural Science Foundation of China (CN)/ ; }, mesh = {Animals ; *Ecology/methods ; Geographic Information Systems/*statistics & numerical data ; *Movement ; *Primates ; }, abstract = {Over the past 20 years, GPS collars have emerged as powerful tools for the study of nonhuman primate (hereafter, "primate") movement ecology. As the size and cost of GPS collars have decreased and performance has improved, it is timely to review the use and success of GPS collar deployments on primates to date. Here we compile data on deployments and performance of GPS collars by brand and examine how these relate to characteristics of the primate species and field contexts in which they were deployed. The compiled results of 179 GPS collar deployments across 17 species by 16 research teams show these technologies can provide advantages, particularly in adding to the quality, quantity, and temporal span of data collection. However, aspects of this technology still require substantial improvement in order to make deployment on many primate species pragmatic economically. In particular, current limitations regarding battery lifespan relative to collar weight, the efficacy of remote drop-off mechanisms, and the ability to remotely retrieve data need to be addressed before the technology is likely to be widely adopted. Moreover, despite the increasing utility of GPS collars in the field, they remain substantially more expensive than VHF collars and tracking via handheld GPS units, and cost considerations of GPS collars may limit sample sizes and thereby the strength of inferences. Still, the overall high quality and quantity of data obtained, combined with the reduced need for on-the-ground tracking by field personnel, may help defray the high equipment cost. We argue that primatologists armed with the information in this review have much to gain from the recent, substantial improvements in GPS collar technology.}, } @article {pmid31964679, year = {2020}, author = {Bellenberg, S and Buetti-Dinh, A and Galli, V and Ilie, O and Herold, M and Christel, S and Boretska, M and Pivkin, IV and Wilmes, P and Sand, W and Vera, M and Dopson, M}, title = {Correction for Bellenberg et al., "Automated Microscopic Analysis of Metal Sulfide Colonization by Acidophilic Microorganisms".}, journal = {Applied and environmental microbiology}, volume = {86}, number = {3}, pages = {}, doi = {10.1128/AEM.02702-19}, pmid = {31964679}, issn = {1098-5336}, } @article {pmid31964336, year = {2020}, author = {Buetti-Dinh, A and Herold, M and Christel, S and El Hajjami, M and Delogu, F and Ilie, O and Bellenberg, S and Wilmes, P and Poetsch, A and Sand, W and Vera, M and Pivkin, IV and Friedman, R and Dopson, M}, title = {Reverse engineering directed gene regulatory networks from transcriptomics and proteomics data of biomining bacterial communities with approximate Bayesian computation and steady-state signalling simulations.}, journal = {BMC bioinformatics}, volume = {21}, number = {1}, pages = {23}, pmid = {31964336}, issn = {1471-2105}, support = {031A600A/B//Bundesministerium für Bildung und Forschung/ ; 2014-6545//Vetenskapsrådet/ ; NTER/SYSAPP/14/05//Fonds National de la Recherche Luxembourg/ ; ERASysAPP//SystemsX (CH)/ ; 205321 173020//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; 1161007//Fondecyt/ ; }, mesh = {Algorithms ; Bacteria/genetics ; Bayes Theorem ; Computational Biology/methods ; Computer Simulation ; *Gene Expression Profiling ; *Gene Expression Regulation, Bacterial ; *Gene Regulatory Networks ; *Proteomics ; Signal Transduction ; Systems Biology/methods ; }, abstract = {BACKGROUND: Network inference is an important aim of systems biology. It enables the transformation of OMICs datasets into biological knowledge. It consists of reverse engineering gene regulatory networks from OMICs data, such as RNAseq or mass spectrometry-based proteomics data, through computational methods. This approach allows to identify signalling pathways involved in specific biological functions. The ability to infer causality in gene regulatory networks, in addition to correlation, is crucial for several modelling approaches and allows targeted control in biotechnology applications.

METHODS: We performed simulations according to the approximate Bayesian computation method, where the core model consisted of a steady-state simulation algorithm used to study gene regulatory networks in systems for which a limited level of details is available. The simulations outcome was compared to experimentally measured transcriptomics and proteomics data through approximate Bayesian computation.

RESULTS: The structure of small gene regulatory networks responsible for the regulation of biological functions involved in biomining were inferred from multi OMICs data of mixed bacterial cultures. Several causal inter- and intraspecies interactions were inferred between genes coding for proteins involved in the biomining process, such as heavy metal transport, DNA damage, replication and repair, and membrane biogenesis. The method also provided indications for the role of several uncharacterized proteins by the inferred connection in their network context.

CONCLUSIONS: The combination of fast algorithms with high-performance computing allowed the simulation of a multitude of gene regulatory networks and their comparison to experimentally measured OMICs data through approximate Bayesian computation, enabling the probabilistic inference of causality in gene regulatory networks of a multispecies bacterial system involved in biomining without need of single-cell or multiple perturbation experiments. This information can be used to influence biological functions and control specific processes in biotechnology applications.}, } @article {pmid31959770, year = {2020}, author = {Okuno, S and Aihara, K and Hirata, Y}, title = {Forecasting high-dimensional dynamics exploiting suboptimal embeddings.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {664}, pmid = {31959770}, issn = {2045-2322}, abstract = {Delay embedding-a method for reconstructing dynamical systems by delay coordinates-is widely used to forecast nonlinear time series as a model-free approach. When multivariate time series are observed, several existing frameworks can be applied to yield a single forecast combining multiple forecasts derived from various embeddings. However, the performance of these frameworks is not always satisfactory because they randomly select embeddings or use brute force and do not consider the diversity of the embeddings to combine. Herein, we develop a forecasting framework that overcomes these existing problems. The framework exploits various "suboptimal embeddings" obtained by minimizing the in-sample error via combinatorial optimization. The framework achieves the best results among existing frameworks for sample toy datasets and a real-world flood dataset. We show that the framework is applicable to a wide range of data lengths and dimensions. Therefore, the framework can be applied to various fields such as neuroscience, ecology, finance, fluid dynamics, weather, and disaster prevention.}, } @article {pmid31957792, year = {2020}, author = {Zhu, L and Duval, C and Boissy, P and Montero-Odasso, M and Zou, G and Jog, M and Speechley, M}, title = {Comparing GPS-Based Community Mobility Measures with Self-report Assessments in Older Adults with Parkinson's Disease.}, journal = {The journals of gerontology. Series A, Biological sciences and medical sciences}, volume = {75}, number = {12}, pages = {2361-2370}, pmid = {31957792}, issn = {1758-535X}, support = {200907AMG-208147-AML-CFEB-56596//CIHR/Canada ; }, mesh = {Activities of Daily Living ; Aged ; Female ; *Geographic Information Systems ; Geriatric Assessment/*methods ; Humans ; Male ; Middle Aged ; Mobility Limitation ; Ontario ; Parkinson Disease/*physiopathology ; Quality of Life ; *Self Report ; }, abstract = {BACKGROUND: Real-life community mobility (CM) measures for older adults, especially those with Parkinson's disease (PD), are important tools when helping individuals maintain optimal function and quality of life. This is one of the first studies to compare an objective global positioning system (GPS) sensor and subjective self-report CM measures in an older clinical population.

METHODS: Over 14 days, 54 people in Ontario, Canada with early to mid-stage PD (mean age = 67.5 ± 6.3 years; 47 men; 46 retired) wore a wireless inertial measurement unit with GPS (WIMU-GPS), and completed the Life Space Assessment and mobility diaries. We assessed the convergent validity, reliability and agreement on mobility outcomes using Spearman's correlation, intraclass correlation coefficient, and Bland-Altman analyses, respectively.

RESULTS: Convergent validity was attained by the WIMU-GPS for trip frequency (rs = .69, 95% confidence interval [CI] = 0.52-0.81) and duration outside (rs = .43, 95% CI = 0.18-0.62), but not for life space size (rs = .39, 95% CI = 0.14-0.60). The Life Space Assessment exhibited floor and ceiling effects. Moderate agreements were observed between WIMU-GPS and diary for trip frequency and duration (intraclass correlation coefficients = 0.71, 95% CI = 0.51-0.82; 0.67, 95% CI = 0.42-0.82, respectively). Disagreement was more common among nonretired individuals.

CONCLUSIONS: WIMU-GPS could replace diaries for trip frequency and duration assessments in older adults with PD. Both assessments are best used for retired persons. However, the Life Space Assessment may not reflect actual mobility.}, } @article {pmid31957669, year = {2020}, author = {Fang, TH and Lien, CY}, title = {Mini review of trace metal contamination status in East China Sea sediment.}, journal = {Marine pollution bulletin}, volume = {152}, number = {}, pages = {110874}, doi = {10.1016/j.marpolbul.2019.110874}, pmid = {31957669}, issn = {1879-3363}, mesh = {China ; Environmental Monitoring ; Geologic Sediments ; Metals, Heavy/*analysis ; Risk Assessment ; Water Pollutants, Chemical/*analysis ; }, abstract = {This study reviewed the published papers and employed the guideline values of USEPA (ERL and ERM) and China (MSQ, Class I, II, III) to assess the contamination status of potential toxic metals in East China Sea sediment (ECS). The percentages of metal concentrations exceeding the ERL value follow the sequences: Ni (96%) > As(71%) > Cr(53%) > Cu (19%) > Zn (2.4%) > Hg (0.5%) > Pb (0.4%) > Cd (0%). The similar ranking is also seen for MSQ class I. All metal concentrations were less than the ERM value, except Ni of which value 10.3% exceeded the ERM value. The potentially ecological risk from these sedimentary metals could be reduced because they were mainly present in the residual fraction, which is not available for marine organisms. It seems that the Ni ERL value is too low (20.8. mg kg[-1]), close to the value (18.6 mg kg[-1]) of the upper continental crust, to obey.}, } @article {pmid31953819, year = {2020}, author = {Ludwig, M and Fleischauer, M and Dührkop, K and Hoffmann, MA and Böcker, S}, title = {De Novo Molecular Formula Annotation and Structure Elucidation Using SIRIUS 4.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2104}, number = {}, pages = {185-207}, doi = {10.1007/978-1-0716-0239-3_11}, pmid = {31953819}, issn = {1940-6029}, mesh = {Chromatography, Liquid ; *Computational Biology/methods ; *Databases, Factual ; Humans ; *Metabolomics/methods ; Molecular Structure ; *Software ; Spectrometry, Mass, Electrospray Ionization ; Structure-Activity Relationship ; Tandem Mass Spectrometry ; User-Computer Interface ; Workflow ; }, abstract = {SIRIUS 4 is the best-in-class computational tool for metabolite identification from high-resolution tandem mass spectrometry data. It offers de novo molecular formula annotation with outstanding accuracy. When searching fragmentation spectra in a structure database, it reaches over 70% correct identifications. A predicted fingerprint, which indicates the presence or absence of thousands of molecular properties, helps to deduce information about the compound of interest even if it is not contained in any structure database. Here, we present best practices and describe how to leverage the full potential of SIRIUS 4, how to incorporate it into your own workflow, and how it adds value to the analysis of mass spectrometry data beyond spectral library search.}, } @article {pmid31953430, year = {2020}, author = {Huang, Y and Ciais, P and Goll, DS and Sardans, J and Peñuelas, J and Cresto-Aleina, F and Zhang, H}, title = {The shift of phosphorus transfers in global fisheries and aquaculture.}, journal = {Nature communications}, volume = {11}, number = {1}, pages = {355}, pmid = {31953430}, issn = {2041-1723}, mesh = {Animals ; *Crops, Agricultural ; Databases, Factual ; Ecology ; *Fisheries ; Fishes ; Fresh Water/chemistry ; History, 20th Century ; History, 21st Century ; Humans ; *Phosphorus ; Seafood ; Water Pollutants, Chemical/*analysis/history ; }, abstract = {Global fish production (capture and aquaculture) has increased quickly, which has altered global flows of phosphorus (P). Here we show that in 2016, [Formula: see text] Tg P yr[-1] (mean and interquartile range) was applied in aquaculture to increase fish production; while [Formula: see text] Tg P yr[-1] was removed from aquatic systems by fish harvesting. Between 1950 and 1986, P from fish production went from aquatic towards the land-human systems. This landward P peaked at 0.54 Tg P yr[-1], representing a large but overlooked P flux that might benefit land activities under P scarcity. After 1986, the landward P flux decreased significantly, and became negative around 2004, meaning that humans spend more P to produce fish than harvest P in fish capture. An idealized pathway to return to the balanced anthropogenic P flow would require the mean phosphorus use efficiency (the ratio of harvested to input P) of aquaculture to be increased from a current value of 20% to at least 48% by 2050 - a big challenge.}, } @article {pmid31953418, year = {2020}, author = {Bidder, OR and di Virgilio, A and Hunter, JS and McInturff, A and Gaynor, KM and Smith, AM and Dorcy, J and Rosell, F}, title = {Monitoring canid scent marking in space and time using a biologging and machine learning approach.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {588}, pmid = {31953418}, issn = {2045-2322}, mesh = {Accelerometry/*instrumentation ; Animals ; Behavior, Animal/*physiology ; California ; Dogs ; Female ; Geographic Information Systems ; Machine Learning ; Male ; Smell/*physiology ; Territoriality ; Wireless Technology ; }, abstract = {For canid species, scent marking plays a critical role in territoriality, social dynamics, and reproduction. However, due in part to human dependence on vision as our primary sensory modality, research on olfactory communication is hampered by a lack of tractable methods. In this study, we leverage a powerful biologging approach, using accelerometers in concert with GPS loggers to monitor and describe scent-marking events in time and space. We performed a validation experiment with domestic dogs, monitoring them by video concurrently with the novel biologging approach. We attached an accelerometer to the pelvis of 31 dogs (19 males and 12 females), detecting raised-leg and squat posture urinations by monitoring the change in device orientation. We then deployed this technique to describe the scent marking activity of 3 guardian dogs as they defend livestock from coyote depredation in California, providing an example use-case for the technique. During validation, the algorithm correctly classified 92% of accelerometer readings. High performance was partly due to the conspicuous signatures of archetypal raised-leg postures in the accelerometer data. Accuracy did not vary with the weight, age, and sex of the dogs, resulting in a method that is broadly applicable across canid species' morphologies. We also used models trained on each individual to detect scent marking of others to emulate the use of captive surrogates for model training. We observed no relationship between the similarity in body weight between the dog pairs and the overall accuracy of predictions, although models performed best when trained and tested on the same individual. We discuss how existing methods in the field of movement ecology can be extended to use this exciting new data type. This paper represents an important first step in opening new avenues of research by leveraging the power of modern-technologies and machine-learning to this field.}, } @article {pmid31952628, year = {2020}, author = {Andraka-Christou, B and Nguyen, T and Bradford, DW and Simon, K}, title = {Assessing the impact of drug courts on provider-directed marketing efforts by manufactures of medications for the treatment of opioid use disorder.}, journal = {Journal of substance abuse treatment}, volume = {110}, number = {}, pages = {49-58}, doi = {10.1016/j.jsat.2019.12.004}, pmid = {31952628}, issn = {1873-6483}, mesh = {Adult ; Aged ; *Buprenorphine ; Buprenorphine, Naloxone Drug Combination ; Humans ; Marketing ; Medicare ; *Opioid-Related Disorders/drug therapy ; United States ; }, abstract = {BACKGROUND: Opioid use disorder (OUD) has become an increasingly consequential public health concern, especially in the United States where 47,600 opioid overdose deaths occurred in 2017 (Scholl, Seth, Kariisa, Wilson, & Baldwin, 2019). Medications for OUD (MOUD) are effective for decreasing opioid-related morbidity and mortality, including within the criminal justice system (Hedrich et al., 2012; Medications for Opioid Use Disorder Save Lives, 2019; Moore et al., 2019).While a stronger evidence base exists for agonist MOUD than for antagonist MOUD, a national study of drug courts found that half prohibited agonist MOUD (Matusow et al., 2013).Furthermore, recent media reports suggest that the pharmaceutical manufacturer of an antagonist MOUD has marketed its product towards drug court judges (Goodnough & Zernike, 2017; Harper, 2017). However, no study to date has systematically examined the relationship between MOUD marketing practices and drug courts. This ecological study examines the association at the county level between MOUD manufacturer payments to prescribers and drug court locations.

METHOD: We extracted provider-directed payments from Centers for Medicare and Medicaid Services (CMS)'s Sunshine Act Open Payments data 2014-2017, isolating those records mentioning any MOUD. We compared provider-directed payments for two major MOUDs: buprenorphine and extended-release naltrexone, in counties with and without drug courts.

RESULTS: The presence of any adult drug courts in the county is associated with a 7.86 percentage-point increase in the likelihood of providers in that county receiving any MOUD-related payments (about 22.46% of the sample mean, p<0.001) and with a 10.70% increase in the amount of these payments per 1000 county residents (p<0.001). The association between other forms of drug courts such as juvenile drug courts and Driving-Under-the-Influence courts (DUI) courts are less significant and slightly smaller in magnitude compared to those of adult drug courts. We did not find significant difference between payments by the manufacturer of Vivitrol and manufacturers of Zubsolv, Bunavail, and Suboxone (oral forms of buprenorphine).

CONCLUSIONS: Our results show an ecological association at the county level between MOUD manufacturer payments to prescribers and drug court presence. However, we did not examine a causal association between these variables.}, } @article {pmid31952328, year = {2020}, author = {Li, X and Zhang, Q and Ma, J and Yang, Y and Wang, Y and Fu, C}, title = {Flooding Irrigation Weakens the Molecular Ecological Network Complexity of Soil Microbes During the Process of Dryland-to-Paddy Conversion.}, journal = {International journal of environmental research and public health}, volume = {17}, number = {2}, pages = {}, pmid = {31952328}, issn = {1660-4601}, mesh = {Actinobacteria/classification/growth & development ; Agriculture/*methods ; Bacteria/classification/growth & development ; *Floods ; Fungi/classification/growth & development ; Hydrogen-Ion Concentration ; Microbiota/physiology ; Nitrogen/analysis ; RNA, Ribosomal, 16S/genetics ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {Irrigation has been applied on a large scale for the improvement of grain yield per hectare and production stability. However, the dryland-to-paddy conversion affects the ecological environment of areas of long-term dry farming, especially soil microorganisms. Little attention has been paid to the changes in microbial communities and the interactions between their populations in this process. Therefore, in this paper, the compositions and diversity of soil bacterial and fungal communities were explored through a combination of high-throughput sequencing technology and molecular ecological network methods using bacterial 16S rRNA and fungal ITS. The results showed that: (1) both the abundance and diversity of soil bacteria and fungi decreased in a short time, and the abundance of Actinobacteria, Firmicutes and Olpidiomycota varied greatly. (2) Compared to dry land, the modular structure of interaction networks and interspecific relationships of bacterial and fungal communities in paddy soil were simpler, and the network became more unstable. A cooperative relationship dominated in the molecular ecological network of bacteria, while a competitive relationship was dominant in the network of fungi. Actinobacteria and Firmicutes were the dominant bacterial species in dry land and paddy field, respectively. Ascomycota was dominant in the fungal communities of both dry land and paddy field. (3) The change in soil environmental factors, such as pH, electrical conductivity (EC), organic matter (OM) and available potassium (AK), directly affected the soil microbial community structure, showing a significant correlation (p < 0.05). These environmental factors also influenced the dominant microbial species. Microorganisms are the most important link in the carbon and nitrogen cycles of soil, and a large-scale dryland-to-paddy conversion may reduce the ecological stability of regional soil.}, } @article {pmid31950231, year = {2020}, author = {Schüz, B and Urban, M}, title = {[Unintended consequences and side effects of digital health technology: a public health perspective].}, journal = {Bundesgesundheitsblatt, Gesundheitsforschung, Gesundheitsschutz}, volume = {63}, number = {2}, pages = {192-198}, pmid = {31950231}, issn = {1437-1588}, mesh = {Germany ; *Health Promotion ; Humans ; *Medical Informatics ; *Public Health ; }, abstract = {The discussion of digital health technologies, in particular medical and health apps, is currently dominated by a focus on their potential to reach large parts of the population for the dissemination of evidence-based health promotion and prevention content. However, potentially unintended consequences, side effects, and negative effects of digital health technologies are rarely discussed in public health.In this paper, via a narrative literature review, we propose a perspective on unintended consequences and side-effects of digital health technologies on multiple hierarchical levels of a socio-ecological model of health. Unintended consequences and side-effects of digital health technologies can be identified on an individual level, a level of social relationships, and a health services level.We propose a broader conceptualization of unintended consequences and side-effects of digital health technology together with a more thorough documentation of such effects using multiple levels in a socio-ecological approach. This would build a cumulative evidence base of unintended effects and shift the focus from development-centered discussion of risks and challenges to a comprehensive conception of side effects and undesirable effects of digital health technologies. The proposed division into three effect levels may be helpful here.}, } @article {pmid31945664, year = {2020}, author = {Hash, JB and Oxford, ML and Ward, TM and Fleming, CB and Spieker, SJ}, title = {Sleep Patterns, Problems and Ecology among Toddlers in Families with a Child Protective Services Maltreatment Referral.}, journal = {Journal of pediatric nursing}, volume = {51}, number = {}, pages = {85-91}, pmid = {31945664}, issn = {1532-8449}, support = {U54 HD083091/HD/NICHD NIH HHS/United States ; T32 NR016913/NR/NINR NIH HHS/United States ; P50 HD103524/HD/NICHD NIH HHS/United States ; P30 NR016585/NR/NINR NIH HHS/United States ; R01 HD061362/HD/NICHD NIH HHS/United States ; }, mesh = {*Child Abuse ; *Child Protective Services ; Child, Preschool ; Female ; Humans ; Longitudinal Studies ; Male ; Mothers ; Parents ; Referral and Consultation ; *Sleep/physiology ; Sleep Wake Disorders/epidemiology ; Surveys and Questionnaires ; }, abstract = {PURPOSE: To describe sleep patterns, problems, and ecology among toddlers (13 to 36 months) from families referred to Child Protective Services (CPS) for maltreatment and to compare sleep duration among a subgroup (24- to 36-month-olds) to previously published population-based data.

DESIGN AND METHODS: A secondary analysis of a larger longitudinal study was conducted. Participants included 113 parent-toddler dyads recruited out of CPS offices based on having a recent maltreatment referral. Parents reported about their toddler's sleep at two time points (approximately six months apart).

RESULTS: At the earlier and later time points, respectively, mean sleep duration was 11.03 and 10.90 h (nighttime), 1.36 and 1.36 h (daytime), and 12.47 and 12.28 h (total 24-h). Of the toddlers, 24% and 17% had two or more nighttime awakenings, 34% and 33% had at least a somewhat hard time falling asleep, and 25% and 26% had difficulty sleeping alone. Mean bedtimes were 8:50 pm and 8:58 pm. Nighttime sleeping arrangement/location, nap arrangement/location, and method of falling asleep at night varied. Compared to the population-based data, nighttime sleep duration was 43 min longer and nap duration was 46 min shorter in the CPS sample.

CONCLUSIONS: Symptoms of behavioral sleep problems were common in this sample of toddlers from families referred to CPS for maltreatment. Distribution of sleep, but not total 24-hour sleep, differed significantly between the CPS sample and the population-based data.

PRACTICE IMPLICATIONS: Nurses caring for toddlers from families involved with CPS can play an integral role promoting sleep health and addressing behavioral sleep problems.}, } @article {pmid31943790, year = {2020}, author = {Rachtman, E and Balaban, M and Bafna, V and Mirarab, S}, title = {The impact of contaminants on the accuracy of genome skimming and the effectiveness of exclusion read filters.}, journal = {Molecular ecology resources}, volume = {20}, number = {3}, pages = {}, doi = {10.1111/1755-0998.13135}, pmid = {31943790}, issn = {1755-0998}, support = {IIS-1815485//NSF/ ; }, mesh = {DNA/genetics ; Databases, Genetic ; Genome/*genetics ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Sequence Analysis, DNA/methods ; }, abstract = {The ability to detect the identity of a sample obtained from its environment is a cornerstone of molecular ecological research. Thanks to the falling price of shotgun sequencing, genome skimming, the acquisition of short reads spread across the genome at low coverage, is emerging as an alternative to traditional barcoding. By obtaining far more data across the whole genome, skimming has the promise to increase the precision of sample identification beyond traditional barcoding while keeping the costs manageable. While methods for assembly-free sample identification based on genome skims are now available, little is known about how these methods react to the presence of DNA from organisms other than the target species. In this paper, we show that the accuracy of distances computed between a pair of genome skims based on k-mer similarity can degrade dramatically if the skims include contaminant reads; i.e., any reads originating from other organisms. We establish a theoretical model of the impact of contamination. We then suggest and evaluate a solution to the contamination problem: Query reads in a genome skim against an extensive database of possible contaminants (e.g., all microbial organisms) and filter out any read that matches. We evaluate the effectiveness of this strategy when implemented using Kraken-II, in detailed analyses. Our results show substantial improvements in accuracy as a result of filtering but also point to limitations, including a need for relatively close matches in the contaminant database.}, } @article {pmid31942620, year = {2020}, author = {da Fonseca, RR and Couto, A and Machado, AM and Brejova, B and Albertin, CB and Silva, F and Gardner, P and Baril, T and Hayward, A and Campos, A and Ribeiro, ÂM and Barrio-Hernandez, I and Hoving, HJ and Tafur-Jimenez, R and Chu, C and Frazão, B and Petersen, B and Peñaloza, F and Musacchia, F and Alexander, GC and Osório, H and Winkelmann, I and Simakov, O and Rasmussen, S and Rahman, MZ and Pisani, D and Vinther, J and Jarvis, E and Zhang, G and Strugnell, JM and Castro, LFC and Fedrigo, O and Patricio, M and Li, Q and Rocha, S and Antunes, A and Wu, Y and Ma, B and Sanges, R and Vinar, T and Blagoev, B and Sicheritz-Ponten, T and Nielsen, R and Gilbert, MTP}, title = {A draft genome sequence of the elusive giant squid, Architeuthis dux.}, journal = {GigaScience}, volume = {9}, number = {1}, pages = {}, pmid = {31942620}, issn = {2047-217X}, support = {/WT_/Wellcome Trust/United Kingdom ; BB/M009122/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/N020146/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; WT108749/Z/15/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Animals ; Biological Evolution ; Chromatography, Liquid ; Computational Biology/methods ; DNA Transposable Elements ; Decapodiformes/*genetics ; Gene Expression Profiling ; *Genome ; *Genomics/methods ; Molecular Sequence Annotation ; Multigene Family ; RNA, Untranslated ; Tandem Mass Spectrometry ; Transcriptome ; Whole Genome Sequencing ; }, abstract = {BACKGROUND: The giant squid (Architeuthis dux; Steenstrup, 1857) is an enigmatic giant mollusc with a circumglobal distribution in the deep ocean, except in the high Arctic and Antarctic waters. The elusiveness of the species makes it difficult to study. Thus, having a genome assembled for this deep-sea-dwelling species will allow several pending evolutionary questions to be unlocked.

FINDINGS: We present a draft genome assembly that includes 200 Gb of Illumina reads, 4 Gb of Moleculo synthetic long reads, and 108 Gb of Chicago libraries, with a final size matching the estimated genome size of 2.7 Gb, and a scaffold N50 of 4.8 Mb. We also present an alternative assembly including 27 Gb raw reads generated using the Pacific Biosciences platform. In addition, we sequenced the proteome of the same individual and RNA from 3 different tissue types from 3 other species of squid (Onychoteuthis banksii, Dosidicus gigas, and Sthenoteuthis oualaniensis) to assist genome annotation. We annotated 33,406 protein-coding genes supported by evidence, and the genome completeness estimated by BUSCO reached 92%. Repetitive regions cover 49.17% of the genome.

CONCLUSIONS: This annotated draft genome of A. dux provides a critical resource to investigate the unique traits of this species, including its gigantism and key adaptations to deep-sea environments.}, } @article {pmid31940344, year = {2020}, author = {Bahlai, CA and Zipkin, EF}, title = {The Dynamic Shift Detector: An algorithm to identify changes in parameter values governing populations.}, journal = {PLoS computational biology}, volume = {16}, number = {1}, pages = {e1007542}, pmid = {31940344}, issn = {1553-7358}, mesh = {*Algorithms ; Animals ; Butterflies/physiology ; Coleoptera/physiology ; Computational Biology/*methods ; Ecosystem ; Information Theory ; *Models, Biological ; Models, Statistical ; *Population Dynamics ; }, abstract = {Environmental factors interact with internal rules of population regulation, sometimes perturbing systems to alternate dynamics though changes in parameter values. Yet, pinpointing when such changes occur in naturally fluctuating populations is difficult. An algorithmic approach that can identify the timing and magnitude of parameter shifts would facilitate understanding of abrupt ecological transitions with potential to inform conservation and management of species. The "Dynamic Shift Detector" is an algorithm to identify changes in parameter values governing temporal fluctuations in populations with nonlinear dynamics. The algorithm examines population time series data for the presence, location, and magnitude of parameter shifts. It uses an iterative approach to fitting subsets of time series data, then ranks the fit of break point combinations using model selection, assigning a relative weight to each break. We examined the performance of the Dynamic Shift Detector with simulations and two case studies. Under low environmental/sampling noise, the break point sets selected by the Dynamic Shift Detector contained the true simulated breaks with 70-100% accuracy. The weighting tool generally assigned breaks intentionally placed in simulated data (i.e., true breaks) with weights averaging >0.8 and those due to sampling error (i.e., erroneous breaks) with weights averaging <0.2. In our case study examining an invasion process, the algorithm identified shifts in population cycling associated with variations in resource availability. The shifts identified for the conservation case study highlight a decline process that generally coincided with changing management practices affecting the availability of hostplant resources. When interpreted in the context of species biology, the Dynamic Shift Detector algorithm can aid management decisions and identify critical time periods related to species' dynamics. In an era of rapid global change, such tools can provide key insights into the conditions under which population parameters, and their corresponding dynamics, can shift.}, } @article {pmid31939543, year = {2019}, author = {Carroll, CB and Gomide, M}, title = {[Network analysis of the regulation of gastrointestinal cancer treatment].}, journal = {Cadernos de saude publica}, volume = {36}, number = {1}, pages = {e00041518}, doi = {10.1590/0102-311X00041518}, pmid = {31939543}, issn = {1678-4464}, mesh = {Brazil ; Comprehensive Health Care/*organization & administration ; Delivery of Health Care/*organization & administration ; Gastrointestinal Neoplasms/*therapy ; Government Programs/*organization & administration ; Humans ; Longitudinal Studies ; Social Networking ; }, abstract = {High complexity is a fundamental component of Brazil's National Policy for Cancer Prevention and Control under the Unified National Health System (SUS). The policy mandates guaranteeing comprehensive patient care. Regulation is part of the organizational structure and is responsible for defining treatment flows. In Rio de Janeiro, the Central Regulating Office launched its activities in June 2015, organizing high-complexity outpatient procedures. The current study aims to analyze commuting for treatment by individuals with gastrointestinal tumors in the state of Rio de Janeiro, before and after the implementation of regulation, from the perspective of Social Network Analysis. This ecological study compared the periods before (2013) and after (2016) implementation of the Central Regulating Office. The study drew on secondary data from the Brazilian Health Informatics Department. Two sociograms were designed for the years 2013 and 2016, correlating place of residence with place of hospitalization. This approach allowed identifying some changes in the dynamics of relations between the state's microregions after implementation of the regulation. The microregions with high-complexity oncology establishments displayed an increase in the number of hospitalizations in 2016. The microregion of Rio de Janeiro also maintained degree centrality in the two moments. The use of Social Network Analysis to assess public policies can contribute to health planning and management.}, } @article {pmid31938871, year = {2020}, author = {Petijová, L and Jurčacková, Z and Čellárová, E}, title = {Computational screening of miRNAs and their targets in leaves of Hypericum spp. by transcriptome-mining: a pilot study.}, journal = {Planta}, volume = {251}, number = {2}, pages = {49}, pmid = {31938871}, issn = {1432-2048}, support = {APVV-18-0125//Agentúra na Podporu Výskumu a Vývoja/ ; VEGA 1/0013/19//Vedecká Grantová Agentúra MŠVVaŠ SR a SAV/ ; }, mesh = {*Computational Biology ; Gene Expression Regulation, Plant ; Hypericum/*genetics ; MicroRNAs/chemistry/*genetics/metabolism ; Nucleic Acid Conformation ; Pilot Projects ; Plant Leaves/*genetics ; Transcriptome/*genetics ; }, abstract = {Our work provides a survey of mature miRNAs, their target genes and primary precursors identified by in-silico approach in leaf transcriptomes of five selected Hypericum species. MiRNAs are small non-coding RNA molecules found in animals, terrestrial plants, several algae and molds. As their role lies in the post-transcriptional gene silencing, these tiny molecules regulate many biological processes. Phyto-miRNAs are considered the important regulators of secondary metabolism in medicinal plants. The genus Hypericum comprises many producers of bioactive compounds, mainly unique naphtodianthrones with a great therapeutic potential. The main goal of our work was to identify genetically conserved miRNAs, characterize their primary precursors and target sequences in the leaf transcriptomes of five Hypericum species using in-silico approach. We found 20 sequences of potential Hypericum pri-miRNAs, and predicted and computationally validated their secondary structures. The mature miRNAs were identified by target genes screening analysis. Whereas predicted miRNA profiles differed in less genetically conserved families, the highly conserved miRNAs were found in almost all studied species. Moreover, we detected several novel highly likely miRNA-mRNA interactions, such as mir1171 with predicted regulatory role in the biosynthesis of melatonin in plants. Our work contributes to the knowledge of Hypericum miRNAome and miRNA-mRNA interactions.}, } @article {pmid31938524, year = {2019}, author = {Llanos-Garrido, A and Pérez-Tris, J and Díaz, JA}, title = {The combined use of raw and phylogenetically independent methods of outlier detection uncovers genome-wide dynamics of local adaptation in a lizard.}, journal = {Ecology and evolution}, volume = {9}, number = {24}, pages = {14356-14367}, pmid = {31938524}, issn = {2045-7758}, abstract = {Local adaptation is a dynamic process by which different allele combinations are selected in different populations at different times, and whose genetic signature can be inferred by genome-wide outlier analyses. We combined gene flow estimates with two methods of outlier detection, one of them independent of population coancestry (CIOA) and the other one not (ROA), to identify genetic variants favored when ecology promotes phenotypic convergence. We analyzed genotyping-by-sequencing data from five populations of a lizard distributed over an environmentally heterogeneous range that has been changing since the split of eastern and western lineages ca. 3 mya. Overall, western lizards inhabit forest habitat and are unstriped, whereas eastern ones inhabit shrublands and are striped. However, one population (Lerma) has unstriped phenotype despite its eastern ancestry. The analysis of 73,291 SNPs confirmed the east-west division and identified nonoverlapping sets of outliers (12 identified by ROA and 9 by CIOA). ROA revealed ancestral adaptive variation in the uncovered outliers that were subject to divergent selection and differently fixed for eastern and western populations at the extremes of the environmental gradient. Interestingly, such variation was maintained in Lerma, where we found high levels of heterozygosity for ROA outliers, whereas CIOA uncovered innovative variants that were selected only there. Overall, it seems that both the maintenance of ancestral variation and asymmetric migration have counterbalanced adaptive lineage splitting in our model species. This scenario, which is likely promoted by a changing and heterogeneous environment, could hamper ecological speciation of locally adapted populations despite strong genetic structure between lineages.}, } @article {pmid31938480, year = {2019}, author = {Chesters, D and Beckschäfer, P and Orr, MC and Adamowicz, SJ and Chun, KP and Zhu, CD}, title = {Climatic and vegetational drivers of insect beta diversity at the continental scale.}, journal = {Ecology and evolution}, volume = {9}, number = {24}, pages = {13764-13775}, pmid = {31938480}, issn = {2045-7758}, abstract = {AIM: We construct a framework for mapping pattern and drivers of insect diversity at the continental scale and use it to test whether and which environmental gradients drive insect beta diversity.

LOCATION: Global; North and Central America; Western Europe.

TIME PERIOD: 21st century.

MAJOR TAXA STUDIED: Insects.

METHODS: An informatics system was developed to integrate terrestrial data on insects with environmental parameters. We mined repositories of data for distribution, climatic data were retrieved (WorldClim), and vegetation parameters inferred from remote sensing analysis (MODIS Vegetation Continuous Fields). Beta diversity between sites was calculated and then modeled with two methods, Mantel test with multiple regression and generalized dissimilarity modeling.

RESULTS: Geographic distance was the main driver of insect beta diversity. Independent of geographic distance, bioclimate variables explained more variance in dissimilarity than vegetation variables, although the particular variables found to be significant were more consistent in the latter, particularly, tree cover. Tree cover gradients drove compositional dissimilarity at denser coverages, in both continental case studies. For climate, gradients in temperature parameters were significant in driving beta diversity more so than gradients in precipitation parameters.

MAIN CONCLUSIONS: Although environmental gradients drive insect beta diversity independently of geography, the relative contribution of different climatic and vegetational parameters is not expected to be consistent in different study systems. With further incorporation of additional temporal information and variables, this approach will enable the development of a predictive framework for conserving insect biodiversity at the global scale.}, } @article {pmid31937838, year = {2020}, author = {Li, W and Ma, ZS}, title = {FBA Ecological Guild: Trio of Firmicutes-Bacteroidetes Alliance against Actinobacteria in Human Oral Microbiome.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {287}, pmid = {31937838}, issn = {2045-2322}, mesh = {Actinobacteria/genetics/growth & development/*isolation & purification ; Bacteroidetes/genetics/growth & development/*isolation & purification ; Databases, Factual ; Firmicutes/genetics/growth & development/*isolation & purification ; Humans ; *Microbiota ; Mouth/*microbiology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {In a pioneering study, Zaura et al. (2009) found that majority of oral microbes fall within the five phyla including, Firmicutes, Proteobacteria, Actinobacteria, Bacteroidetes and Fusobacteria. Subsequent studies further identified a set of microbes that were commonly shared among unrelated individuals (i.e., core). However, these existing studies may have not been designed to investigate the interactions among various core species. Here by harnessing the power of ecological network analysis, we identified some important ecological guilds in the form of network clusters. In particular, we found that the strongest cluster is an alliance between Firmicutes and Bacteroidetes against Actinobacteria (FBA-guild). Within the guild, we further identified two sub-guilds, the Actinobacteria-dominant sub-guild (ASG) and Firmicutes-dominant allied with Bacteroidetes sub-guild (FBSG). Furthermore, we identified so-termed guard nodes in both sub-guilds, and their role may be to inhibit the peer sub-guild given they held competitive interactions only with the outside nodes only but held cooperative interactions only with the internal nodes, which we termed civilian nodes given that they only held cooperative interactions. We postulated that FBA-guild might be to do with protection of oral health against some opportunistic pathogens from Corynebacterium and Actinomyces, the two major genera of Actinobacteria (target of FB alliance).}, } @article {pmid31937263, year = {2020}, author = {Herndon, N and Shelton, J and Gerischer, L and Ioannidis, P and Ninova, M and Dönitz, J and Waterhouse, RM and Liang, C and Damm, C and Siemanowski, J and Kitzmann, P and Ulrich, J and Dippel, S and Oberhofer, G and Hu, Y and Schwirz, J and Schacht, M and Lehmann, S and Montino, A and Posnien, N and Gurska, D and Horn, T and Seibert, J and Vargas Jentzsch, IM and Panfilio, KA and Li, J and Wimmer, EA and Stappert, D and Roth, S and Schröder, R and Park, Y and Schoppmeier, M and Chung, HR and Klingler, M and Kittelmann, S and Friedrich, M and Chen, R and Altincicek, B and Vilcinskas, A and Zdobnov, E and Griffiths-Jones, S and Ronshaugen, M and Stanke, M and Brown, SJ and Bucher, G}, title = {Enhanced genome assembly and a new official gene set for Tribolium castaneum.}, journal = {BMC genomics}, volume = {21}, number = {1}, pages = {47}, pmid = {31937263}, issn = {1471-2164}, support = {SFB680//Deutsche Forschungsgemeinschaft/ ; P20 GM103418/GM/NIGMS NIH HHS/United States ; PA2044/1//Deutsche Forschungsgemeinschaft/ ; KL656/7//Deutsche Forschungsgemeinschaft/ ; BU1443/6//Deutsche Forschungsgemeinschaft/ ; WI1797/5//Deutsche Forschungsgemeinschaft/ ; FOR1234//Deutsche Forschungsgemeinschaft/ ; STA1009/10//Deutsche Forschungsgemeinschaft/ ; BU1443/7//Deutsche Forschungsgemeinschaft/ ; PP00P3_170664//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (CH)/ ; Department Herbert Jäckle//Max-Planck-Gesellschaft/ ; SFB 680 / A12//Deutsche Forschungsgemeinschaft/ ; Scho1058/4//Deutsche Forschungsgemeinschaft/ ; }, mesh = {Animals ; Binding Sites ; Computational Biology/methods ; *Genes, Insect ; *Genome, Insect ; *Genomics/methods ; MicroRNAs/genetics ; Molecular Sequence Annotation ; Phylogeny ; RNA Interference ; Reproducibility of Results ; Tribolium/*genetics ; }, abstract = {BACKGROUND: The red flour beetle Tribolium castaneum has emerged as an important model organism for the study of gene function in development and physiology, for ecological and evolutionary genomics, for pest control and a plethora of other topics. RNA interference (RNAi), transgenesis and genome editing are well established and the resources for genome-wide RNAi screening have become available in this model. All these techniques depend on a high quality genome assembly and precise gene models. However, the first version of the genome assembly was generated by Sanger sequencing, and with a small set of RNA sequence data limiting annotation quality.

RESULTS: Here, we present an improved genome assembly (Tcas5.2) and an enhanced genome annotation resulting in a new official gene set (OGS3) for Tribolium castaneum, which significantly increase the quality of the genomic resources. By adding large-distance jumping library DNA sequencing to join scaffolds and fill small gaps, the gaps in the genome assembly were reduced and the N50 increased to 4753kbp. The precision of the gene models was enhanced by the use of a large body of RNA-Seq reads of different life history stages and tissue types, leading to the discovery of 1452 novel gene sequences. We also added new features such as alternative splicing, well defined UTRs and microRNA target predictions. For quality control, 399 gene models were evaluated by manual inspection. The current gene set was submitted to Genbank and accepted as a RefSeq genome by NCBI.

CONCLUSIONS: The new genome assembly (Tcas5.2) and the official gene set (OGS3) provide enhanced genomic resources for genetic work in Tribolium castaneum. The much improved information on transcription start sites supports transgenic and gene editing approaches. Further, novel types of information such as splice variants and microRNA target genes open additional possibilities for analysis.}, } @article {pmid31935215, year = {2020}, author = {Brown, CL and Garner, E and Jospin, G and Coil, DA and Schwake, DO and Eisen, JA and Mukhopadhyay, B and Pruden, AJ}, title = {Whole genome sequence analysis reveals the broad distribution of the RtxA type 1 secretion system and four novel putative type 1 secretion systems throughout the Legionella genus.}, journal = {PloS one}, volume = {15}, number = {1}, pages = {e0223033}, pmid = {31935215}, issn = {1932-6203}, mesh = {ATP-Binding Cassette Transporters/genetics ; Bacterial Proteins/*genetics ; Cell Membrane/genetics ; Computational Biology ; Escherichia coli/genetics ; Genome, Bacterial/genetics ; Hemolysin Proteins/*genetics ; Humans ; Legionella/*genetics/pathogenicity ; Legionella pneumophila/genetics ; Legionellosis/*genetics/microbiology ; Sequence Analysis ; Type I Secretion Systems/*genetics ; Virulence Factors/genetics ; Whole Genome Sequencing ; }, abstract = {Type 1 secretion systems (T1SSs) are broadly distributed among bacteria and translocate effectors with diverse function across the bacterial cell membrane. Legionella pneumophila, the species most commonly associated with Legionellosis, encodes a T1SS at the lssXYZABD locus which is responsible for the secretion of the virulence factor RtxA. Many investigations have failed to detect lssD, the gene encoding the membrane fusion protein of the RtxA T1SS, in non-pneumophila Legionella, which has led to the assumption that this system is a virulence factor exclusively possessed by L. pneumophila. Here we discovered RtxA and its associated T1SS in a novel Legionella taurinensis strain, leading us to question whether this system may be more widespread than previously thought. Through a bioinformatic analysis of publicly available data, we classified and determined the distribution of four T1SSs including the RtxA T1SS and four novel T1SSs among diverse Legionella spp. The ABC transporter of the novel Legionella T1SS Legionella repeat protein secretion system shares structural similarity to those of diverse T1SS families, including the alkaline protease T1SS in Pseudomonas aeruginosa. The Legionella bacteriocin (1-3) secretion systems T1SSs are novel putative bacteriocin transporting T1SSs as their ABC transporters include C-39 peptidase domains in their N-terminal regions, with LB2SS and LB3SS likely constituting a nitrile hydratase leader peptide transport T1SSs. The LB1SS is more closely related to the colicin V T1SS in Escherichia coli. Of 45 Legionella spp. whole genomes examined, 19 (42%) were determined to possess lssB and lssD homologs. Of these 19, only 7 (37%) are known pathogens. There was no difference in the proportions of disease associated and non-disease associated species that possessed the RtxA T1SS (p = 0.4), contrary to the current consensus regarding the RtxA T1SS. These results draw into question the nature of RtxA and its T1SS as a singular virulence factor. Future studies should investigate mechanistic explanations for the association of RtxA with virulence.}, } @article {pmid31931913, year = {2019}, author = {Handel, A and Martinez, L and Sekandi, JN and Bellan, SE and Zhu, L and Chen, C and Liu, Q and Donkor, S and Sutherland, J and Hill, PC and Gilman, RH and Grandjean, L and Whalen, CC}, title = {Evidence for supercoughers in an analysis of six tuberculosis cohorts from China, Peru, The Gambia and Uganda.}, journal = {The international journal of tuberculosis and lung disease : the official journal of the International Union against Tuberculosis and Lung Disease}, volume = {23}, number = {12}, pages = {1286-1292}, doi = {10.5588/ijtld.18.0819}, pmid = {31931913}, issn = {1815-7920}, support = {MC_U190071468/MRC_/Medical Research Council/United Kingdom ; MC_UP_A900_1122/MRC_/Medical Research Council/United Kingdom ; R01 AI093856/AI/NIAID NIH HHS/United States ; 201470/Z/16/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Adolescent ; Adult ; Aged ; Aged, 80 and over ; China/epidemiology ; Cohort Studies ; Cough/etiology/*physiopathology ; Female ; Gambia/epidemiology ; Humans ; Male ; Middle Aged ; Peru/epidemiology ; Tuberculosis, Pulmonary/complications/*epidemiology/transmission ; Uganda/epidemiology ; Young Adult ; }, abstract = {BACKGROUND: It is very difficult to observe tuberculosis (TB) transmission chains and thus, identify superspreaders. We investigate cough duration as a proxy measure of transmission to assess the presence of potential TB superspreaders.DESIGN: We analyzed six studies from China, Peru, The Gambia and Uganda, and determined the distribution of cough duration and compared it with several theoretical distributions. To determine factors associated with cough duration, we used linear regression and boosted regression trees to examine the predictive power of patient, clinical and environmental characteristics.RESULTS: We found within-study heterogeneity in cough duration and strong similarities across studies. Approximately 20% of patients contributed 50% of total cough days, and around 50% of patients contributed 80% of total cough days. The cough duration distribution suggested an initially increasing, and subsequently, decreasing hazard of diagnosis. While some of the exposure variables showed statistically significant associations with cough duration, none of them had a strong effect. Multivariate analyses of different model types did not produce a model that had good predictive power.CONCLUSION: We found consistent evidence for the presence of supercoughers, but no characteristics predictive of such individuals.}, } @article {pmid31925507, year = {2020}, author = {Alhasanat, A and Ou, C}, title = {On the conjecture for the pushed wavefront to the diffusive Lotka-Volterra competition model.}, journal = {Journal of mathematical biology}, volume = {80}, number = {5}, pages = {1413-1422}, pmid = {31925507}, issn = {1432-1416}, mesh = {Animals ; Biodiversity ; Competitive Behavior ; Computational Biology ; Computer Simulation ; *Ecosystem ; Introduced Species ; Logistic Models ; Mathematical Concepts ; *Models, Biological ; Nonlinear Dynamics ; Population Density ; Population Dynamics ; }, abstract = {This paper concerns ecological invasion phenomenon of species based on the diffusive Lotka-Volterra competition model. We investigate the spreading speed (or the minimal wave speed of traveling waves) selection to the model and concentrate on the conjecture raised by Roques et al. (J Math Biol 71(2):465-489, 2015). By using an abstract implicit function theorem in a weighted functional space coupled with a perturbation technique, we not only prove this conjecture, but also show that the fast decay behavior of the first species is necessary and sufficient for the nonlinear speed selection of the whole system. This may lead to further significant results on the answer to the original Hosono's conjecture, a problem that has been outstanding for more than twenty years.}, } @article {pmid31920740, year = {2019}, author = {Verdejo-Garcia, A and Lorenzetti, V and Manning, V and Piercy, H and Bruno, R and Hester, R and Pennington, D and Tolomeo, S and Arunogiri, S and Bates, ME and Bowden-Jones, H and Campanella, S and Daughters, SB and Kouimtsidis, C and Lubman, DI and Meyerhoff, DJ and Ralph, A and Rezapour, T and Tavakoli, H and Zare-Bidoky, M and Zilverstand, A and Steele, D and Moeller, SJ and Paulus, M and Baldacchino, A and Ekhtiari, H}, title = {A Roadmap for Integrating Neuroscience Into Addiction Treatment: A Consensus of the Neuroscience Interest Group of the International Society of Addiction Medicine.}, journal = {Frontiers in psychiatry}, volume = {10}, number = {}, pages = {877}, pmid = {31920740}, issn = {1664-0640}, support = {IK2 CX001510/CX/CSRD VA/United States ; R01 AA023667/AA/NIAAA NIH HHS/United States ; R25 HD045810/HD/NICHD NIH HHS/United States ; R25 MH067127/MH/NIMH NIH HHS/United States ; }, abstract = {Although there is general consensus that altered brain structure and function underpins addictive disorders, clinicians working in addiction treatment rarely incorporate neuroscience-informed approaches into their practice. We recently launched the Neuroscience Interest Group within the International Society of Addiction Medicine (ISAM-NIG) to promote initiatives to bridge this gap. This article summarizes the ISAM-NIG key priorities and strategies to achieve implementation of addiction neuroscience knowledge and tools for the assessment and treatment of substance use disorders. We cover two assessment areas: cognitive assessment and neuroimaging, and two interventional areas: cognitive training/remediation and neuromodulation, where we identify key challenges and proposed solutions. We reason that incorporating cognitive assessment into clinical settings requires the identification of constructs that predict meaningful clinical outcomes. Other requirements are the development of measures that are easily-administered, reliable, and ecologically-valid. Translation of neuroimaging techniques requires the development of diagnostic and prognostic biomarkers and testing the cost-effectiveness of these biomarkers in individualized prediction algorithms for relapse prevention and treatment selection. Integration of cognitive assessments with neuroimaging can provide multilevel targets including neural, cognitive, and behavioral outcomes for neuroscience-informed interventions. Application of neuroscience-informed interventions including cognitive training/remediation and neuromodulation requires clear pathways to design treatments based on multilevel targets, additional evidence from randomized trials and subsequent clinical implementation, including evaluation of cost-effectiveness. We propose to address these challenges by promoting international collaboration between researchers and clinicians, developing harmonized protocols and data management systems, and prioritizing multi-site research that focuses on improving clinical outcomes.}, } @article {pmid31919285, year = {2020}, author = {Krishna, A and Nie, X and Warren, AD and Llorente-Bousquets, JE and Briscoe, AD and Lee, J}, title = {Infrared optical and thermal properties of microstructures in butterfly wings.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {117}, number = {3}, pages = {1566-1572}, pmid = {31919285}, issn = {1091-6490}, mesh = {Animals ; Body Temperature Regulation/*physiology ; Butterflies/*physiology ; Colorado ; Computational Biology ; Ecosystem ; Ecuador ; Florida ; *Infrared Rays ; Mexico ; Models, Biological ; Optical Phenomena ; Spectrum Analysis ; Sunlight ; Temperature ; Wings, Animal/*physiology/ultrastructure ; }, abstract = {While surface microstructures of butterfly wings have been extensively studied for their structural coloration or optical properties within the visible spectrum, their properties in infrared wavelengths with potential ties to thermoregulation are relatively unknown. The midinfrared wavelengths of 7.5 to 14 µm are particularly important for radiative heat transfer in the ambient environment, because of the overlap with the atmospheric transmission window. For instance, a high midinfrared emissivity can facilitate surface cooling, whereas a low midinfrared emissivity can minimize heat loss to surroundings. Here we find that the midinfrared emissivity of butterfly wings from warmer climates such as Archaeoprepona demophoon (Oaxaca, Mexico) and Heliconius sara (Pichincha, Ecuador) is up to 2 times higher than that of butterfly wings from cooler climates such as Celastrina echo (Colorado) and Limenitis arthemis (Florida), using Fourier-transform infrared (FTIR) spectroscopy and infrared thermography. Our optical computations using a unit cell approach reproduce the spectroscopy data and explain how periodic microstructures play a critical role in the midinfrared. The emissivity spectrum governs the temperature of butterfly wings, and we demonstrate that C. echo wings heat up to 8 °C more than A. demophoon wings under the same sunlight in the clear sky of Irvine, CA. Furthermore, our thermal computations show that butterfly wings in their respective habitats can maintain a moderate temperature range through a balance of solar absorption and infrared emission. These findings suggest that the surface microstructures of butterfly wings potentially contribute to thermoregulation and provide an insight into butterflies' survival.}, } @article {pmid31918660, year = {2020}, author = {Nong, W and Chai, ZYH and Jiang, X and Qin, J and Ma, KY and Chan, KM and Chan, TF and Chow, BKC and Kwan, HS and Wong, CKC and Qiu, JW and Hui, JHL and Chu, KH}, title = {A crustacean annotated transcriptome (CAT) database.}, journal = {BMC genomics}, volume = {21}, number = {1}, pages = {32}, pmid = {31918660}, issn = {1471-2164}, support = {Collaborative Research Fund (project no. C4042-14G)//Hong Kong Research Institute of Textiles and Apparel (HK)/ ; }, mesh = {Animals ; Databases, Genetic ; Decapoda/*genetics ; Transcriptome/*genetics ; }, abstract = {BACKGROUND: Decapods are an order of crustaceans which includes shrimps, crabs, lobsters and crayfish. They occur worldwide and are of great scientific interest as well as being of ecological and economic importance in fisheries and aquaculture. However, our knowledge of their biology mainly comes from the group which is most closely related to crustaceans - insects. Here we produce a de novo transcriptome database, crustacean annotated transcriptome (CAT) database, spanning multiple tissues and the life stages of seven crustaceans.

DESCRIPTION: A total of 71 transcriptome assemblies from six decapod species and a stomatopod species, including the coral shrimp Stenopus hispidus, the cherry shrimp Neocaridina davidi, the redclaw crayfish Cherax quadricarinatus, the spiny lobster Panulirus ornatus, the red king crab Paralithodes camtschaticus, the coconut crab Birgus latro, and the zebra mantis shrimp Lysiosquillina maculata, were generated. Differential gene expression analyses within species were generated as a reference and included in a graphical user interface database at http://cat.sls.cuhk.edu.hk/. Users can carry out gene name searches and also access gene sequences based on a sequence query using the BLAST search function.

CONCLUSIONS: The data generated and deposited in this database offers a valuable resource for the further study of these crustaceans, as well as being of use in aquaculture development.}, } @article {pmid31914166, year = {2020}, author = {Joshi, J and Brännström, Å and Dieckmann, U}, title = {Emergence of social inequality in the spatial harvesting of renewable public goods.}, journal = {PLoS computational biology}, volume = {16}, number = {1}, pages = {e1007483}, pmid = {31914166}, issn = {1553-7358}, mesh = {*Biobehavioral Sciences ; Computational Biology ; *Consumer Behavior ; *Ecology ; Humans ; *Socioeconomic Factors ; }, abstract = {Spatially extended ecological public goods, such as forests, grasslands, and fish stocks, are at risk of being overexploited by selfish consumers-a phenomenon widely recognized as the 'tragedy of the commons.' The interplay of spatial and ecological dimensions introduces new features absent in non-spatial ecological contexts, such as consumer mobility, local information availability, and strategy evolution through social learning in neighborhoods. It is unclear how these features interact to influence the harvesting and dispersal strategies of consumers. To answer these questions, we develop and analyze an individual-based, spatially structured, eco-evolutionary model with explicit resource dynamics. We report the following findings. (1) When harvesting efficiency is low, consumers evolve a sedentary consumption strategy, through which the resource is harvested sustainably, but with harvesting rates far below their maximum sustainable value. (2) As harvesting efficiency increases, consumers adopt a mobile 'consume-and-disperse' strategy, which is sustainable, equitable, and gives maximum sustainable yield. (3) A further increase in harvesting efficiency leads to large-scale overexploitation. (4) If costs of dispersal are significant, increased harvesting efficiency also leads to social inequality between frugal sedentary consumers and overexploitative mobile consumers. Whereas overexploitation can occur without social inequality, social inequality always leads to overexploitation. Thus, we identify four conditions that-while being characteristic of technological progress in modern societies-risk social inequality and overexploitation: high harvesting efficiency, moderately low costs of dispersal, high consumer density, and the tendency of consumers to adopt new strategies rapidly. We also show how access to global information-another feature widespread in modern societies-helps mitigate these risks.}, } @article {pmid31911493, year = {2020}, author = {Saw, JHW and Nunoura, T and Hirai, M and Takaki, Y and Parsons, R and Michelsen, M and Longnecker, K and Kujawinski, EB and Stepanauskas, R and Landry, Z and Carlson, CA and Giovannoni, SJ}, title = {Pangenomics Analysis Reveals Diversification of Enzyme Families and Niche Specialization in Globally Abundant SAR202 Bacteria.}, journal = {mBio}, volume = {11}, number = {1}, pages = {}, pmid = {31911493}, issn = {2150-7511}, mesh = {Biodiversity ; Chloroflexi/*enzymology/*genetics ; Computational Biology/methods ; *Genome, Bacterial ; Metabolic Networks and Pathways ; Metabolomics/methods ; *Metagenome ; *Metagenomics ; *Multigene Family ; Phylogeny ; Phylogeography ; }, abstract = {It has been hypothesized that the abundant heterotrophic ocean bacterioplankton in the SAR202 clade of the phylum Chloroflexi evolved specialized metabolisms for the oxidation of organic compounds that are resistant to microbial degradation via common metabolic pathways. Expansions of paralogous enzymes were reported and implicated in hypothetical metabolism involving monooxygenase and dioxygenase enzymes. In the proposed metabolic schemes, the paralogs serve the purpose of diversifying the range of organic molecules that cells can utilize. To further explore SAR202 evolution and metabolism, we reconstructed single amplified genomes and metagenome-assembled genomes from locations around the world that included the deepest ocean trenches. In an analysis of 122 SAR202 genomes that included seven subclades spanning SAR202 diversity, we observed additional evidence of paralog expansions that correlated with evolutionary history, as well as further evidence of metabolic specialization. Consistent with previous reports, families of flavin-dependent monooxygenases were observed mainly in the group III SAR202 genomes, and expansions of dioxygenase enzymes were prevalent in those of group VII. We found that group I SAR202 genomes encode expansions of racemases in the enolase superfamily, which we propose evolved for the degradation of compounds that resist biological oxidation because of chiral complexity. Supporting the conclusion that the paralog expansions indicate metabolic specialization, fragment recruitment and fluorescent in situ hybridization (FISH) with phylogenetic probes showed that SAR202 subclades are indigenous to different ocean depths and geographical regions. Surprisingly, some of the subclades were abundant in surface waters and contained rhodopsin genes, altering our understanding of the ecological role of SAR202 species in stratified water columns.IMPORTANCE The oceans contain an estimated 662 Pg C in the form of dissolved organic matter (DOM). Information about microbial interactions with this vast resource is limited, despite broad recognition that DOM turnover has a major impact on the global carbon cycle. To explain patterns in the genomes of marine bacteria, we propose hypothetical metabolic pathways for the oxidation of organic molecules that are resistant to oxidation via common pathways. The hypothetical schemes we propose suggest new metabolic pathways and classes of compounds that could be important for understanding the distribution of organic carbon throughout the biosphere. These genome-based schemes will remain hypothetical until evidence from experimental cell biology can be gathered to test them. Our findings also fundamentally change our understanding of the ecology of SAR202 bacteria, showing that metabolically diverse variants of these cells occupy niches spanning all depths and are not relegated to the dark ocean.}, } @article {pmid31911491, year = {2020}, author = {Song, SJ and Sanders, JG and Delsuc, F and Metcalf, J and Amato, K and Taylor, MW and Mazel, F and Lutz, HL and Winker, K and Graves, GR and Humphrey, G and Gilbert, JA and Hackett, SJ and White, KP and Skeen, HR and Kurtis, SM and Withrow, J and Braile, T and Miller, M and McCracken, KG and Maley, JM and Ezenwa, VO and Williams, A and Blanton, JM and McKenzie, VJ and Knight, R}, title = {Comparative Analyses of Vertebrate Gut Microbiomes Reveal Convergence between Birds and Bats.}, journal = {mBio}, volume = {11}, number = {1}, pages = {}, pmid = {31911491}, issn = {2150-7511}, mesh = {Animals ; *Biological Evolution ; *Birds ; *Chiroptera ; Computational Biology/methods ; *Gastrointestinal Microbiome ; Metagenome ; Metagenomics/methods ; *Vertebrates ; }, abstract = {Diet and host phylogeny drive the taxonomic and functional contents of the gut microbiome in mammals, yet it is unknown whether these patterns hold across all vertebrate lineages. Here, we assessed gut microbiomes from ∼900 vertebrate species, including 315 mammals and 491 birds, assessing contributions of diet, phylogeny, and physiology to structuring gut microbiomes. In most nonflying mammals, strong correlations exist between microbial community similarity, host diet, and host phylogenetic distance up to the host order level. In birds, by contrast, gut microbiomes are only very weakly correlated to diet or host phylogeny. Furthermore, while most microbes resident in mammalian guts are present in only a restricted taxonomic range of hosts, most microbes recovered from birds show little evidence of host specificity. Notably, among the mammals, bats host especially bird-like gut microbiomes, with little evidence for correlation to host diet or phylogeny. This suggests that host-gut microbiome phylosymbiosis depends on factors convergently absent in birds and bats, potentially associated with physiological adaptations to flight. Our findings expose major variations in the behavior of these important symbioses in endothermic vertebrates and may signal fundamental evolutionary shifts in the cost/benefit framework of the gut microbiome.IMPORTANCE In this comprehensive survey of microbiomes of >900 species, including 315 mammals and 491 birds, we find a striking convergence of the microbiomes of birds and animals that fly. In nonflying mammals, diet and short-term evolutionary relatedness drive the microbiome, and many microbial species are specific to a particular kind of mammal, but flying mammals and birds break this pattern with many microbes shared across different species, with little correlation either with diet or with relatedness of the hosts. This finding suggests that adaptation to flight breaks long-held relationships between hosts and their microbes.}, } @article {pmid31908268, year = {2020}, author = {Edge, MD and Coop, G}, title = {Attacks on genetic privacy via uploads to genealogical databases.}, journal = {eLife}, volume = {9}, number = {}, pages = {}, pmid = {31908268}, issn = {2050-084X}, support = {F32 GM130050/GM/NIGMS NIH HHS/United States ; R01 GM108779/GM/NIGMS NIH HHS/United States ; GM108779/NH/NIH HHS/United States ; GM130050/NH/NIH HHS/United States ; }, mesh = {Data Management/*statistics & numerical data ; Databases, Genetic/*standards ; *Genetic Privacy ; Humans ; }, abstract = {Direct-to-consumer (DTC) genetics services are increasingly popular, with tens of millions of customers. Several DTC genealogy services allow users to upload genetic data to search for relatives, identified as people with genomes that share identical by state (IBS) regions. Here, we describe methods by which an adversary can learn database genotypes by uploading multiple datasets. For example, an adversary who uploads approximately 900 genomes could recover at least one allele at SNP sites across up to 82% of the genome of a median person of European ancestries. In databases that detect IBS segments using unphased genotypes, approximately 100 falsified uploads can reveal enough genetic information to allow genome-wide genetic imputation. We provide a proof-of-concept demonstration in the GEDmatch database, and we suggest countermeasures that will prevent the exploits we describe.}, } @article {pmid31907489, year = {2020}, author = {Suryamohan, K and Krishnankutty, SP and Guillory, J and Jevit, M and Schröder, MS and Wu, M and Kuriakose, B and Mathew, OK and Perumal, RC and Koludarov, I and Goldstein, LD and Senger, K and Dixon, MD and Velayutham, D and Vargas, D and Chaudhuri, S and Muraleedharan, M and Goel, R and Chen, YJ and Ratan, A and Liu, P and Faherty, B and de la Rosa, G and Shibata, H and Baca, M and Sagolla, M and Ziai, J and Wright, GA and Vucic, D and Mohan, S and Antony, A and Stinson, J and Kirkpatrick, DS and Hannoush, RN and Durinck, S and Modrusan, Z and Stawiski, EW and Wiley, K and Raudsepp, T and Kini, RM and Zachariah, A and Seshagiri, S}, title = {The Indian cobra reference genome and transcriptome enables comprehensive identification of venom toxins.}, journal = {Nature genetics}, volume = {52}, number = {1}, pages = {106-117}, pmid = {31907489}, issn = {1546-1718}, mesh = {Amino Acid Sequence ; Animals ; Computational Biology/*methods ; Elapid Venoms/*analysis/*genetics ; Gene Expression Profiling ; *Genome ; India ; Naja naja/*genetics ; Sequence Homology ; *Transcriptome ; }, abstract = {Snakebite envenoming is a serious and neglected tropical disease that kills ~100,000 people annually. High-quality, genome-enabled comprehensive characterization of toxin genes will facilitate development of effective humanized recombinant antivenom. We report a de novo near-chromosomal genome assembly of Naja naja, the Indian cobra, a highly venomous, medically important snake. Our assembly has a scaffold N50 of 223.35 Mb, with 19 scaffolds containing 95% of the genome. Of the 23,248 predicted protein-coding genes, 12,346 venom-gland-expressed genes constitute the 'venom-ome' and this included 139 genes from 33 toxin families. Among the 139 toxin genes were 19 'venom-ome-specific toxins' (VSTs) that showed venom-gland-specific expression, and these probably encode the minimal core venom effector proteins. Synthetic venom reconstituted through recombinant VST expression will aid in the rapid development of safe and effective synthetic antivenom. Additionally, our genome could serve as a reference for snake genomes, support evolutionary studies and enable venom-driven drug discovery.}, } @article {pmid31907310, year = {2020}, author = {Le Provost, G and Badenhausser, I and Le Bagousse-Pinguet, Y and Clough, Y and Henckel, L and Violle, C and Bretagnolle, V and Roncoroni, M and Manning, P and Gross, N}, title = {Land-use history impacts functional diversity across multiple trophic groups.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {117}, number = {3}, pages = {1573-1579}, pmid = {31907310}, issn = {1091-6490}, mesh = {Agriculture ; Animals ; *Biodiversity ; Conservation of Natural Resources ; Databases, Factual ; Ecology ; *Ecosystem ; *Grassland ; Herbivory/classification ; Invertebrates/classification ; Plants/classification ; Population Density ; }, abstract = {Land-use change is a major driver of biodiversity loss worldwide. Although biodiversity often shows a delayed response to land-use change, previous studies have typically focused on a narrow range of current landscape factors and have largely ignored the role of land-use history in shaping plant and animal communities and their functional characteristics. Here, we used a unique database of 220,000 land-use records to investigate how 20-y of land-use changes have affected functional diversity across multiple trophic groups (primary producers, mutualists, herbivores, invertebrate predators, and vertebrate predators) in 75 grassland fields with a broad range of land-use histories. The effects of land-use history on multitrophic trait diversity were as strong as other drivers known to impact biodiversity, e.g., grassland management and current landscape composition. The diversity of animal mobility and resource-acquisition traits was lower in landscapes where much of the land had been historically converted from grassland to crop. In contrast, functional biodiversity was higher in landscapes containing old permanent grasslands, most likely because they offer a stable and high-quality habitat refuge for species with low mobility and specialized feeding niches. Our study shows that grassland-to-crop conversion has long-lasting impacts on the functional biodiversity of agricultural ecosystems. Accordingly, land-use legacy effects must be considered in conservation programs aiming to protect agricultural biodiversity. In particular, the retention of permanent grassland sanctuaries within intensive landscapes may offset ecological debts.}, } @article {pmid31905256, year = {2020}, author = {vonHoldt, BM and DeCandia, AL and Heppenheimer, E and Janowitz-Koch, I and Shi, R and Zhou, H and German, CA and Brzeski, KE and Cassidy, KA and Stahler, DR and Sinsheimer, JS}, title = {Heritability of interpack aggression in a wild pedigreed population of North American grey wolves.}, journal = {Molecular ecology}, volume = {29}, number = {10}, pages = {1764-1775}, pmid = {31905256}, issn = {1365-294X}, support = {R01 HG009120/HG/NHGRI NIH HHS/United States ; R01 GM053275/GM/NIGMS NIH HHS/United States ; }, mesh = {*Aggression ; Animals ; Behavior, Animal ; Pedigree ; Polymorphism, Single Nucleotide ; Reproduction ; United States ; *Wolves/genetics ; Wyoming ; }, abstract = {Aggression is a quantitative trait deeply entwined with individual fitness. Mapping the genomic architecture underlying such traits is complicated by complex inheritance patterns, social structure, pedigree information and gene pleiotropy. Here, we leveraged the pedigree of a reintroduced population of grey wolves (Canis lupus) in Yellowstone National Park, Wyoming, USA, to examine the heritability of and the genetic variation associated with aggression. Since their reintroduction, many ecological and behavioural aspects have been documented, providing unmatched records of aggressive behaviour across multiple generations of a wild population of wolves. Using a linear mixed model, a robust genetic relationship matrix, 12,288 single nucleotide polymorphisms (SNPs) and 111 wolves, we estimated the SNP-based heritability of aggression to be 37% and an additional 14% of the phenotypic variation explained by shared environmental exposures. We identified 598 SNP genotypes from 425 grey wolves to resolve a consensus pedigree that was included in a heritability analysis of 141 individuals with SNP genotype, metadata and aggression data. The pedigree-based heritability estimate for aggression is 14%, and an additional 16% of the phenotypic variation was explained by shared environmental exposures. We find strong effects of breeding status and relative pack size on aggression. Through an integrative approach, these results provide a framework for understanding the genetic architecture of a complex trait that influences individual fitness, with linkages to reproduction, in a social carnivore. Along with a few other studies, we show here the incredible utility of a pedigreed natural population for dissecting a complex, fitness-related behavioural trait.}, } @article {pmid31904811, year = {2020}, author = {Tang, B and Zhang, D and Li, H and Jiang, S and Zhang, H and Xuan, F and Ge, B and Wang, Z and Liu, Y and Sha, Z and Cheng, Y and Jiang, W and Jiang, H and Wang, Z and Wang, K and Li, C and Sun, Y and She, S and Qiu, Q and Wang, W and Li, X and Li, Y and Liu, Q and Ren, Y}, title = {Chromosome-level genome assembly reveals the unique genome evolution of the swimming crab (Portunus trituberculatus).}, journal = {GigaScience}, volume = {9}, number = {1}, pages = {}, pmid = {31904811}, issn = {2047-217X}, mesh = {Animals ; Brachyura/genetics ; *Chromosomes ; Computational Biology/methods ; *Evolution, Molecular ; Gene Expression Profiling ; *Genome ; *Genomics/methods ; Molecular Sequence Annotation ; Multigene Family ; Phylogeny ; Repetitive Sequences, Nucleic Acid ; Transcriptome ; }, abstract = {BACKGROUND: The swimming crab, Portunus trituberculatus, is an important commercial species in China and is widely distributed in the coastal waters of Asia-Pacific countries. Despite increasing interest in swimming crab research, a high-quality chromosome-level genome is still lacking.

FINDINGS: Here, we assembled the first chromosome-level reference genome of P. trituberculatus by combining the short reads, Nanopore long reads, and Hi-C data. The genome assembly size was 1.00 Gb with a contig N50 length of 4.12 Mb. In addition, BUSCO assessment indicated that 94.7% of core eukaryotic genes were present in the genome assembly. Approximately 54.52% of the genome was identified as repetitive sequences, with a total of 16,796 annotated protein-coding genes. In addition, we anchored contigs into chromosomes and identified 50 chromosomes with an N50 length of 21.80 Mb by Hi-C technology.

CONCLUSIONS: We anticipate that this chromosome-level assembly of the P. trituberculatus genome will not only promote study of basic development and evolution but also provide important resources for swimming crab reproduction.}, } @article {pmid31900107, year = {2020}, author = {Walsh, JR and Woodhouse, MR and Andorf, CM and Sen, TZ}, title = {Tissue-specific gene expression and protein abundance patterns are associated with fractionation bias in maize.}, journal = {BMC plant biology}, volume = {20}, number = {1}, pages = {4}, pmid = {31900107}, issn = {1471-2229}, support = {5030-21000-068-00-D//Agricultural Research Service/ ; 2030-21000-024-00-D//Agricultural Research Service/ ; }, mesh = {Chromosome Mapping/methods ; Evolution, Molecular ; Gene Duplication ; Gene Expression/*genetics ; Gene Expression Regulation, Plant/*genetics ; Gene Ontology ; Genes, Plant ; Genome, Plant ; Phylogeny ; Plant Proteins/biosynthesis/genetics ; Pollen/genetics ; Polyploidy ; Zea mays/*genetics ; }, abstract = {BACKGROUND: Maize experienced a whole-genome duplication event approximately 5 to 12 million years ago. Because this event occurred after speciation from sorghum, the pre-duplication subgenomes can be partially reconstructed by mapping syntenic regions to the sorghum chromosomes. During evolution, maize has had uneven gene loss between each ancient subgenome. Fractionation and divergence between these genomes continue today, constantly changing genetic make-up and phenotypes and influencing agronomic traits.

RESULTS: Here we regenerate the subgenome reconstructions for the most recent maize reference genome assembly. Based on both expression and abundance data for homeologous gene pairs across multiple tissues, we observed functional divergence of genes across subgenomes. Although the genes in the larger maize subgenome are often expressing more highly than their homeologs in the smaller subgenome, we observed cases where homeolog expression dominance switches in different tissues. We demonstrate for the first time that protein abundances are higher in the larger subgenome, but they also show tissue-specific dominance, a pattern similar to RNA expression dominance. We also find that pollen expression is uniquely decoupled from protein abundance.

CONCLUSION: Our study shows that the larger subgenome has a greater range of functional assignments and that there is a relative lack of overlap between the subgenomes in terms of gene functions than would be suggested by similar patterns of gene expression and protein abundance. Our study also revealed that some reactions are catalyzed uniquely by the larger and smaller subgenomes. The tissue-specific, nonequivalent expression-level dominance pattern observed here implies a change in regulatory control which favors differentiated selective pressure on the retained duplicates leading to eventual change in gene functions.}, } @article {pmid31899920, year = {2020}, author = {Xu, P and Tang, G and Cui, W and Chen, G and Ma, CL and Zhu, J and Li, P and Shan, L and Liu, Z and Wan, S}, title = {Transcriptional Differences in Peanut (Arachis hypogaea L.) Seeds at the Freshly Harvested, After-ripening and Newly Germinated Seed Stages: Insights into the Regulatory Networks of Seed Dormancy Release and Germination.}, journal = {PloS one}, volume = {15}, number = {1}, pages = {e0219413}, pmid = {31899920}, issn = {1932-6203}, mesh = {Abscisic Acid/metabolism ; Adenosine Triphosphate/biosynthesis ; Arachis/*genetics/growth & development/metabolism ; Brassinosteroids/metabolism ; Citric Acid Cycle/genetics ; *Gene Expression Regulation, Developmental ; *Gene Expression Regulation, Plant ; Gene Ontology ; Gene Regulatory Networks ; Germination/*genetics ; Glycolysis/genetics ; Glycosyltransferases/genetics/metabolism ; Indoleacetic Acids/metabolism ; Molecular Sequence Annotation ; Oxidative Phosphorylation ; Plant Dormancy ; Plant Proteins/*genetics/metabolism ; Quantitative Trait, Heritable ; Seeds/*genetics/growth & development/metabolism ; Signal Transduction ; *Transcriptome ; }, abstract = {Seed dormancy and germination are the two important traits related to plant survival, reproduction and crop yield. To understand the regulatory mechanisms of these traits, it is crucial to clarify which genes or pathways participate in the regulation of these processes. However, little information is available on seed dormancy and germination in peanut. In this study, seeds of the variety Luhua No.14, which undergoes nondeep dormancy, were selected, and their transcriptional changes at three different developmental stages, the freshly harvested seed (FS), the after-ripening seed (DS) and the newly germinated seed (GS) stages, were investigated by comparative transcriptomic analysis. The results showed that genes with increased transcription in the DS vs FS comparison were overrepresented for oxidative phosphorylation, the glycolysis pathway and the tricarboxylic acid (TCA) cycle, suggesting that after a period of dry storage, the intermediates stored in the dry seeds were rapidly mobilized by glycolysis, the TCA cycle, the glyoxylate cycle, etc.; the electron transport chain accompanied by respiration was reactivated to provide ATP for the mobilization of other reserves and for seed germination. In the GS vs DS pairwise comparison, dozens of the upregulated genes were related to plant hormone biosynthesis and signal transduction, including the majority of components involved in the auxin signal pathway, brassinosteroid biosynthesis and signal transduction as well as some GA and ABA signal transduction genes. During seed germination, the expression of some EXPANSIN and XYLOGLUCAN ENDOTRANSGLYCOSYLASE genes was also significantly enhanced. To investigate the effects of different hormones during seed germination, the contents and differential distribution of ABA, GAs, BRs and IAA in the cotyledons, hypocotyls and radicles, and plumules of three seed sections at different developmental stages were also investigated. Combined with previous data in other species, it was suggested that the coordination of multiple hormone signal transduction nets plays a key role in radicle protrusion and seed germination.}, } @article {pmid31899899, year = {2020}, author = {Xu, S and Böttcher, L and Chou, T}, title = {Diversity in biology: definitions, quantification and models.}, journal = {Physical biology}, volume = {17}, number = {3}, pages = {031001}, pmid = {31899899}, issn = {1478-3975}, support = {R01 HL146552/HL/NHLBI NIH HHS/United States ; }, mesh = {Animals ; *Biodiversity ; Data Interpretation, Statistical ; Entropy ; Humans ; *Models, Biological ; }, abstract = {Diversity indices are useful single-number metrics for characterizing a complex distribution of a set of attributes across a population of interest. The utility of these different metrics or sets of metrics depends on the context and application, and whether a predictive mechanistic model exists. In this topical review, we first summarize the relevant mathematical principles underlying heterogeneity in a large population, before outlining the various definitions of 'diversity' and providing examples of scientific topics in which its quantification plays an important role. We then review how diversity has been a ubiquitous concept across multiple fields, including ecology, immunology, cellular barcoding experiments, and socioeconomic studies. Since many of these applications involve sampling of populations, we also review how diversity in small samples is related to the diversity in the entire population. Features that arise in each of these applications are highlighted.}, } @article {pmid31898513, year = {2020}, author = {Waterhouse, RM and Aganezov, S and Anselmetti, Y and Lee, J and Ruzzante, L and Reijnders, MJMF and Feron, R and Bérard, S and George, P and Hahn, MW and Howell, PI and Kamali, M and Koren, S and Lawson, D and Maslen, G and Peery, A and Phillippy, AM and Sharakhova, MV and Tannier, E and Unger, MF and Zhang, SV and Alekseyev, MA and Besansky, NJ and Chauve, C and Emrich, SJ and Sharakhov, IV}, title = {Evolutionary superscaffolding and chromosome anchoring to improve Anopheles genome assemblies.}, journal = {BMC biology}, volume = {18}, number = {1}, pages = {1}, pmid = {31898513}, issn = {1741-7007}, support = {R21 AI099528/AI/NIAID NIH HHS/United States ; R21 AI135298/AI/NIAID NIH HHS/United States ; U24 CA211000/CA/NCI NIH HHS/United States ; R21 AI112734/AI/NIAID NIH HHS/United States ; R01 HG006677/HG/NHGRI NIH HHS/United States ; ZIA HG200398/HG/NHGRI NIH HHS/United States ; }, mesh = {Animals ; Anopheles/*genetics ; *Biological Evolution ; Chromosome Mapping ; *Chromosomes ; Genetic Techniques/*instrumentation ; Genomics/*methods ; *Synteny ; }, abstract = {BACKGROUND: New sequencing technologies have lowered financial barriers to whole genome sequencing, but resulting assemblies are often fragmented and far from 'finished'. Updating multi-scaffold drafts to chromosome-level status can be achieved through experimental mapping or re-sequencing efforts. Avoiding the costs associated with such approaches, comparative genomic analysis of gene order conservation (synteny) to predict scaffold neighbours (adjacencies) offers a potentially useful complementary method for improving draft assemblies.

RESULTS: We evaluated and employed 3 gene synteny-based methods applied to 21 Anopheles mosquito assemblies to produce consensus sets of scaffold adjacencies. For subsets of the assemblies, we integrated these with additional supporting data to confirm and complement the synteny-based adjacencies: 6 with physical mapping data that anchor scaffolds to chromosome locations, 13 with paired-end RNA sequencing (RNAseq) data, and 3 with new assemblies based on re-scaffolding or long-read data. Our combined analyses produced 20 new superscaffolded assemblies with improved contiguities: 7 for which assignments of non-anchored scaffolds to chromosome arms span more than 75% of the assemblies, and a further 7 with chromosome anchoring including an 88% anchored Anopheles arabiensis assembly and, respectively, 73% and 84% anchored assemblies with comprehensively updated cytogenetic photomaps for Anopheles funestus and Anopheles stephensi.

CONCLUSIONS: Experimental data from probe mapping, RNAseq, or long-read technologies, where available, all contribute to successful upgrading of draft assemblies. Our evaluations show that gene synteny-based computational methods represent a valuable alternative or complementary approach. Our improved Anopheles reference assemblies highlight the utility of applying comparative genomics approaches to improve community genomic resources.}, } @article {pmid31898481, year = {2020}, author = {Handel, A}, title = {A software package for immunologists to learn simulation modeling.}, journal = {BMC immunology}, volume = {21}, number = {1}, pages = {1}, pmid = {31898481}, issn = {1471-2172}, support = {U19 AI117891/AI/NIAID NIH HHS/United States ; }, mesh = {Allergy and Immunology/*trends ; Animals ; *Computer Simulation ; Humans ; Immunity ; *Models, Biological ; Programming Languages ; *Software ; }, abstract = {BACKGROUND: As immunology continues to become more quantitative, increasingly sophisticated computational tools are commonly used. One useful toolset are simulation models. Becoming familiar with such models and their uses generally requires writing computer code early in the learning process. This poses a barrier for individuals who do not have prior coding experience.

RESULTS: To help reduce this barrier, I wrote software that teaches the use of mechanistic simulation models to study infection and immune response dynamics, without the need to read or write computer code. The software, called Dynamical Systems Approach to Immune Response Modeling (DSAIRM), is implemented as a freely available package for the R programming language. The target audience are immunologists and other scientists with no or little coding experience. DSAIRM provides a hands-on introduction to simulation models, teaches the basics of those models and what they can be used for. Here, I describe the DSAIRM R package, explain the different ways the package can be used, and provide a few introductory examples.

CONCLUSIONS: Working through DSAIRM will equip individuals with the knowledge needed to critically assess studies using simulation models in the published literature and will help them understand when such a modeling approach might be suitable for their own research. DSAIRM also provides users a potential starting point towards development and use of simulation models in their own research.}, } @article {pmid31896182, year = {2020}, author = {Liu, L and Dong, Y and Kong, M and Zhou, J and Zhao, H and Tang, Z and Zhang, M and Wang, Z}, title = {Insights into the long-term pollution trends and sources contributions in Lake Taihu, China using multi-statistic analyses models.}, journal = {Chemosphere}, volume = {242}, number = {}, pages = {125272}, doi = {10.1016/j.chemosphere.2019.125272}, pmid = {31896182}, issn = {1879-1298}, mesh = {China ; Data Interpretation, Statistical ; Environmental Monitoring/*methods/statistics & numerical data ; Eutrophication ; Factor Analysis, Statistical ; Lakes/*chemistry ; Linear Models ; *Models, Statistical ; Multivariate Analysis ; Principal Component Analysis ; Water Pollutants, Chemical/*analysis ; *Water Quality ; }, abstract = {Eutrophication pollution seriously threatens the sustainable development of Lake Taihu, China. In order to identify the primary parameters of water quality and the potential pollution sources, the water quality dataset of Lake Taihu (2010-2014) was analyzed with the water quality index (WQI) and multivariate statistical analysis methods. Principle component analysis/factor analysis (PCA/FA) and correlation analysis screened out five significant water quality indicators, i.e. potassium permanganate index (CODMn), total nitrogen (TN), total phosphorus (TP), chloride ion (Cl[-]) and dissolved oxygen (DO), to represent the whole datasets and evaluate the water quality with WQI. Since northwestern of Lake Taihu was the most heavily polluted area, the parameters of the water quality were analyzed to further explore the potential sources and their contributions. Five potential pollution sources of northwestern lake were identified, and the contribution rate of each pollution source was calculated by the absolute principal component score-multiple linear regression (APCS-MLR) and positive matrix factorization (PMF) models. In brief, the PMF model was more suitable for pollution source apportionment of the northwestern lake, and the contribution rate was ranked as agricultural non-point source pollution (26.6%) > domestic sewage discharge (23.5%) > industrial wastewater discharge and atmospheric deposition (20.6%) > phytoplankton growth (16.0%) > rainfall or wind disturbance (13.4%). This study might provide useful information for the optimization of water quality management and pollution control strategies of Lake Taihu.}, } @article {pmid31895413, year = {2020}, author = {Wang, W and Das, A and Kainer, D and Schalamun, M and Morales-Suarez, A and Schwessinger, B and Lanfear, R}, title = {The draft nuclear genome assembly of Eucalyptus pauciflora: a pipeline for comparing de novo assemblies.}, journal = {GigaScience}, volume = {9}, number = {1}, pages = {}, pmid = {31895413}, issn = {2047-217X}, mesh = {*Computational Biology/methods ; DNA Contamination ; Eucalyptus/*genetics ; Genome Size ; *Genome, Plant ; *Genomics/methods ; }, abstract = {BACKGROUND: Eucalyptus pauciflora (the snow gum) is a long-lived tree with high economic and ecological importance. Currently, little genomic information for E. pauciflora is available. Here, we sequentially assemble the genome of Eucalyptus pauciflora with different methods, and combine multiple existing and novel approaches to help to select the best genome assembly.

FINDINGS: We generated high coverage of long- (Nanopore, 174×) and short- (Illumina, 228×) read data from a single E. pauciflora individual and compared assemblies from 5 assemblers (Canu, SMARTdenovo, Flye, Marvel, and MaSuRCA) with different read lengths (1 and 35 kb minimum read length). A key component of our approach is to keep a randomly selected collection of ∼10% of both long and short reads separated from the assemblies to use as a validation set for assessing assemblies. Using this validation set along with a range of existing tools, we compared the assemblies in 8 ways: contig N50, BUSCO scores, LAI (long terminal repeat assembly index) scores, assembly ploidy, base-level error rate, CGAL (computing genome assembly likelihoods) scores, structural variation, and genome sequence similarity. Our result showed that MaSuRCA generated the best assembly, which is 594.87 Mb in size, with a contig N50 of 3.23 Mb, and an estimated error rate of ∼0.006 errors per base.

CONCLUSIONS: We report a draft genome of E. pauciflora, which will be a valuable resource for further genomic studies of eucalypts. The approaches for assessing and comparing genomes should help in assessing and choosing among many potential genome assemblies from a single dataset.}, } @article {pmid31895020, year = {2019}, author = {Self, SCW and Liu, Y and Nordone, SK and Yabsley, MJ and Walden, HS and Lund, RB and Bowman, DD and Carpenter, C and McMahan, CS and Gettings, JR}, title = {Canine vector-borne disease: mapping and the accuracy of forecasting using big data from the veterinary community.}, journal = {Animal health research reviews}, volume = {20}, number = {1}, pages = {47-60}, doi = {10.1017/S1466252319000045}, pmid = {31895020}, issn = {1475-2654}, mesh = {Aging ; Animals ; *Big Data ; Dog Diseases/*epidemiology/parasitology/prevention & control ; Dogs ; Humans ; Immunocompromised Host ; Pets ; Risk Factors ; Vector Borne Diseases/epidemiology/*veterinary ; Zoonoses ; }, abstract = {Diagnosis, treatment, and prevention of vector-borne disease (VBD) in pets is one cornerstone of companion animal practices. Veterinarians are facing new challenges associated with the emergence, reemergence, and rising incidence of VBD, including heartworm disease, Lyme disease, anaplasmosis, and ehrlichiosis. Increases in the observed prevalence of these diseases have been attributed to a multitude of factors, including diagnostic tests with improved sensitivity, expanded annual testing practices, climatologic and ecological changes enhancing vector survival and expansion, emergence or recognition of novel pathogens, and increased movement of pets as travel companions. Veterinarians have the additional responsibility of providing information about zoonotic pathogen transmission from pets, especially to vulnerable human populations: the immunocompromised, children, and the elderly. Hindering efforts to protect pets and people is the dynamic and ever-changing nature of VBD prevalence and distribution. To address this deficit in understanding, the Companion Animal Parasite Council (CAPC) began efforts to annually forecast VBD prevalence in 2011. These forecasts provide veterinarians and pet owners with expected disease prevalence in advance of potential changes. This review summarizes the fidelity of VBD forecasts and illustrates the practical use of CAPC pathogen prevalence maps and forecast data in the practice of veterinary medicine and client education.}, } @article {pmid31892236, year = {2019}, author = {Falzon, G and Lawson, C and Cheung, KW and Vernes, K and Ballard, GA and Fleming, PJS and Glen, AS and Milne, H and Mather-Zardain, A and Meek, PD}, title = {ClassifyMe: A Field-Scouting Software for the Identification of Wildlife in Camera Trap Images.}, journal = {Animals : an open access journal from MDPI}, volume = {10}, number = {1}, pages = {}, pmid = {31892236}, issn = {2076-2615}, support = {N/A//Centre for Invasive Species Solutions/ ; }, abstract = {We present ClassifyMe a software tool for the automated identification of animal species from camera trap images. ClassifyMe is intended to be used by ecologists both in the field and in the office. Users can download a pre-trained model specific to their location of interest and then upload the images from a camera trap to a laptop or workstation. ClassifyMe will identify animals and other objects (e.g., vehicles) in images, provide a report file with the most likely species detections, and automatically sort the images into sub-folders corresponding to these species categories. False Triggers (no visible object present) will also be filtered and sorted. Importantly, the ClassifyMe software operates on the user's local machine (own laptop or workstation)-not via internet connection. This allows users access to state-of-the-art camera trap computer vision software in situ, rather than only in the office. The software also incurs minimal cost on the end-user as there is no need for expensive data uploads to cloud services. Furthermore, processing the images locally on the users' end-device allows them data control and resolves privacy issues surrounding transfer and third-party access to users' datasets.}, } @article {pmid31891594, year = {2019}, author = {D'Elia, J and Brandt, J and Burnett, LJ and Haig, SM and Hollenbeck, J and Kirkland, S and Marcot, BG and Punzalan, A and West, CJ and Williams-Claussen, T and Wolstenholme, R and Young, R}, title = {Applying circuit theory and landscape linkage maps to reintroduction planning for California Condors.}, journal = {PloS one}, volume = {14}, number = {12}, pages = {e0226491}, pmid = {31891594}, issn = {1932-6203}, mesh = {Animals ; California ; Conservation of Natural Resources/*methods ; Endangered Species ; Falconiformes/*physiology ; Geographic Information Systems ; Models, Theoretical ; Population Dynamics ; }, abstract = {Conservation practitioners are increasingly looking to species translocations as a tool to recover imperiled taxa. Quantitative predictions of where animals are likely to move when released into new areas would allow managers to better address the social, institutional, and ecological dimensions of conservation translocations. Using >5 million California condor (Gymnogyps californianus) occurrence locations from 75 individuals, we developed and tested circuit-based models to predict condor movement away from release sites. We found that circuit-based models of electrical current were well calibrated to the distribution of condor movement data in southern and central California (continuous Boyce Index = 0.86 and 0.98, respectively). Model calibration was improved in southern California when additional nodes were added to the circuit to account for nesting and feeding areas, where condor movement densities were higher (continuous Boyce Index = 0.95). Circuit-based projections of electrical current around a proposed release site in northern California comported with the condor's historical distribution and revealed that, initially, condor movements would likely be most concentrated in northwestern California and southwest Oregon. Landscape linkage maps, which incorporate information on landscape resistance, complement circuit-based models and aid in the identification of specific avenues for population connectivity or areas where movement between populations may be constrained. We found landscape linkages in the Coast Range and the Sierra Nevada provided the most connectivity to a proposed reintroduction site in northern California. Our methods are applicable to conservation translocations for other species and are flexible, allowing researchers to develop multiple competing hypotheses when there are uncertainties about landscape or social attractants, or uncertainties in the landscape conductance surface.}, } @article {pmid31891589, year = {2019}, author = {de la Sancha, NU and Boyle, SA}, title = {Predictive sampling effort and species-area relationship models for estimating richness in fragmented landscapes.}, journal = {PloS one}, volume = {14}, number = {12}, pages = {e0226529}, pmid = {31891589}, issn = {1932-6203}, mesh = {Animals ; *Biodiversity ; Conservation of Natural Resources/*methods ; Forests ; Geographic Information Systems ; Introduced Species ; Mammals/*physiology ; Models, Theoretical ; Paraguay ; Population Dynamics ; }, abstract = {Loss of habitat, specifically deforestation, is a major driver of biodiversity loss. Species-area relationship (SAR) models traditionally have been used for estimating species richness, species loss as a function of habitat loss, and extrapolation of richness for given areas. Sampling-species relationships (SSRs) are interrelated yet separate drivers for species richness estimates. Traditionally, however, SAR and SSR models have been used independently and not incorporated into a single approach. We developed and compared predictive models that incorporate sampling effort species-area relationships (SESARS) along the entire Atlantic Forest of South America, and then applied the best-fit model to estimate richness in forest remnants of Interior Atlantic Forest of eastern Paraguay. This framework was applied to non-volant small mammal assemblages that reflect different tolerances to forest loss and fragmentation. In order to account for differences in functionality we estimated small mammal richness of 1) the entire non-volant small mammal assemblage, including introduced species; 2) the native species forest assemblage; and 3) the forest-specialist assemblage, with the latter two assemblages being subsets of the entire assemblage. Finally, we geospatially modeled species richness for each of the three assemblages throughout eastern Paraguay to identify remnants with high species richness. We found that multiple regression power-law interaction-term models that only included area and the interactions of area and sampling as predictors, worked best for predicting species richness for the entire assemblage and the native species forest assemblage, while several traditional SAR models (logistic, power, exponential, and ratio) best described forest-specialist richness. Species richness was significantly different between assemblages. We identified obvious remnants with high species richness in eastern Paraguay, and these remnants often were geographically isolated. We also found relatively high predicted species richness (in relation to the entire range of predicted richness values) in several geographically-isolated, medium-size forest remnants that likely have not been considered as possible priority areas for conservation. These findings highlight the importance of using an empirical dataset, created using sources representing diverse sampling efforts, to develop robust predictive models. This approach is particularly important in geographic locations where field sampling is limited yet the geographic area is experiencing rapid and dramatic land cover changes. When combined, area and sampling are powerful modeling predictors for questions of biogeography, ecology, and conservation, especially when addressing habitat loss and fragmentation.}, } @article {pmid31891586, year = {2019}, author = {Howell, KL and Davies, JS and Allcock, AL and Braga-Henriques, A and Buhl-Mortensen, P and Carreiro-Silva, M and Dominguez-Carrió, C and Durden, JM and Foster, NL and Game, CA and Hitchin, B and Horton, T and Hosking, B and Jones, DOB and Mah, C and Laguionie Marchais, C and Menot, L and Morato, T and Pearman, TRR and Piechaud, N and Ross, RE and Ruhl, HA and Saeedi, H and Stefanoudis, PV and Taranto, GH and Thompson, MB and Taylor, JR and Tyler, P and Vad, J and Victorero, L and Vieira, RP and Woodall, LC and Xavier, JR and Wagner, D}, title = {A framework for the development of a global standardised marine taxon reference image database (SMarTaR-ID) to support image-based analyses.}, journal = {PloS one}, volume = {14}, number = {12}, pages = {e0218904}, pmid = {31891586}, issn = {1932-6203}, mesh = {Animals ; Artificial Intelligence ; Biodiversity ; Classification/*methods ; Data Curation/methods/standards ; Databases, Factual ; Ecology ; Ecosystem ; Image Processing, Computer-Assisted/methods/*standards ; Marine Biology/classification/*standards ; }, abstract = {Video and image data are regularly used in the field of benthic ecology to document biodiversity. However, their use is subject to a number of challenges, principally the identification of taxa within the images without associated physical specimens. The challenge of applying traditional taxonomic keys to the identification of fauna from images has led to the development of personal, group, or institution level reference image catalogues of operational taxonomic units (OTUs) or morphospecies. Lack of standardisation among these reference catalogues has led to problems with observer bias and the inability to combine datasets across studies. In addition, lack of a common reference standard is stifling efforts in the application of artificial intelligence to taxon identification. Using the North Atlantic deep sea as a case study, we propose a database structure to facilitate standardisation of morphospecies image catalogues between research groups and support future use in multiple front-end applications. We also propose a framework for coordination of international efforts to develop reference guides for the identification of marine species from images. The proposed structure maps to the Darwin Core standard to allow integration with existing databases. We suggest a management framework where high-level taxonomic groups are curated by a regional team, consisting of both end users and taxonomic experts. We identify a mechanism by which overall quality of data within a common reference guide could be raised over the next decade. Finally, we discuss the role of a common reference standard in advancing marine ecology and supporting sustainable use of this ecosystem.}, } @article {pmid31891233, year = {2020}, author = {Kattge, J and Bönisch, G and Díaz, S and Lavorel, S and Prentice, IC and Leadley, P and Tautenhahn, S and Werner, GDA and Aakala, T and Abedi, M and Acosta, ATR and Adamidis, GC and Adamson, K and Aiba, M and Albert, CH and Alcántara, JM and Alcázar C, C and Aleixo, I and Ali, H and Amiaud, B and Ammer, C and Amoroso, MM and Anand, M and Anderson, C and Anten, N and Antos, J and Apgaua, DMG and Ashman, TL and Asmara, DH and Asner, GP and Aspinwall, M and Atkin, O and Aubin, I and Baastrup-Spohr, L and Bahalkeh, K and Bahn, M and Baker, T and Baker, WJ and Bakker, JP and Baldocchi, D and Baltzer, J and Banerjee, A and Baranger, A and Barlow, J and Barneche, DR and Baruch, Z and Bastianelli, D and Battles, J and Bauerle, W and Bauters, M and Bazzato, E and Beckmann, M and Beeckman, H and Beierkuhnlein, C and Bekker, R and Belfry, G and Belluau, M and Beloiu, M and Benavides, R and Benomar, L and Berdugo-Lattke, ML and Berenguer, E and Bergamin, R and Bergmann, J and Bergmann Carlucci, M and Berner, L and Bernhardt-Römermann, M and Bigler, C and Bjorkman, AD and Blackman, C and Blanco, C and Blonder, B and Blumenthal, D and Bocanegra-González, KT and Boeckx, P and Bohlman, S and Böhning-Gaese, K and Boisvert-Marsh, L and Bond, W and Bond-Lamberty, B and Boom, A and Boonman, CCF and Bordin, K and Boughton, EH and Boukili, V and Bowman, DMJS and Bravo, S and Brendel, MR and Broadley, MR and Brown, KA and Bruelheide, H and Brumnich, F and Bruun, HH and Bruy, D and Buchanan, SW and Bucher, SF and Buchmann, N and Buitenwerf, R and Bunker, DE and Bürger, J and Burrascano, S and Burslem, DFRP and Butterfield, BJ and Byun, C and Marques, M and Scalon, MC and Caccianiga, M and Cadotte, M and Cailleret, M and Camac, J and Camarero, JJ and Campany, C and Campetella, G and Campos, JA and Cano-Arboleda, L and Canullo, R and Carbognani, M and Carvalho, F and Casanoves, F and Castagneyrol, B and Catford, JA and Cavender-Bares, J and Cerabolini, BEL and Cervellini, M and Chacón-Madrigal, E and Chapin, K and Chapin, FS and Chelli, S and Chen, SC and Chen, A and Cherubini, P and Chianucci, F and Choat, B and Chung, KS and Chytrý, M and Ciccarelli, D and Coll, L and Collins, CG and Conti, L and Coomes, D and Cornelissen, JHC and Cornwell, WK and Corona, P and Coyea, M and Craine, J and Craven, D and Cromsigt, JPGM and Csecserits, A and Cufar, K and Cuntz, M and da Silva, AC and Dahlin, KM and Dainese, M and Dalke, I and Dalle Fratte, M and Dang-Le, AT and Danihelka, J and Dannoura, M and Dawson, S and de Beer, AJ and De Frutos, A and De Long, JR and Dechant, B and Delagrange, S and Delpierre, N and Derroire, G and Dias, AS and Diaz-Toribio, MH and Dimitrakopoulos, PG and Dobrowolski, M and Doktor, D and Dřevojan, P and Dong, N and Dransfield, J and Dressler, S and Duarte, L and Ducouret, E and Dullinger, S and Durka, W and Duursma, R and Dymova, O and E-Vojtkó, A and Eckstein, RL and Ejtehadi, H and Elser, J and Emilio, T and Engemann, K and Erfanian, MB and Erfmeier, A and Esquivel-Muelbert, A and Esser, G and Estiarte, M and Domingues, TF and Fagan, WF and Fagúndez, J and Falster, DS and Fan, Y and Fang, J and Farris, E and Fazlioglu, F and Feng, Y and Fernandez-Mendez, F and Ferrara, C and Ferreira, J and Fidelis, A and Finegan, B and Firn, J and Flowers, TJ and Flynn, DFB and Fontana, V and Forey, E and Forgiarini, C and François, L and Frangipani, M and Frank, D and Frenette-Dussault, C and Freschet, GT and Fry, EL and Fyllas, NM and Mazzochini, GG and Gachet, S and Gallagher, R and Ganade, G and Ganga, F and García-Palacios, P and Gargaglione, V and Garnier, E and Garrido, JL and de Gasper, AL and Gea-Izquierdo, G and Gibson, D and Gillison, AN and Giroldo, A and Glasenhardt, MC and Gleason, S and Gliesch, M and Goldberg, E and Göldel, B and Gonzalez-Akre, E and Gonzalez-Andujar, JL and González-Melo, A and González-Robles, A and Graae, BJ and Granda, E and Graves, S and Green, WA and Gregor, T and Gross, N and Guerin, GR and Günther, A and Gutiérrez, AG and Haddock, L and Haines, A and Hall, J and Hambuckers, A and Han, W and Harrison, SP and Hattingh, W and Hawes, JE and He, T and He, P and Heberling, JM and Helm, A and Hempel, S and Hentschel, J and Hérault, B and Hereş, AM and Herz, K and Heuertz, M and Hickler, T and Hietz, P and Higuchi, P and Hipp, AL and Hirons, A and Hock, M and Hogan, JA and Holl, K and Honnay, O and Hornstein, D and Hou, E and Hough-Snee, N and Hovstad, KA and Ichie, T and Igić, B and Illa, E and Isaac, M and Ishihara, M and Ivanov, L and Ivanova, L and Iversen, CM and Izquierdo, J and Jackson, RB and Jackson, B and Jactel, H and Jagodzinski, AM and Jandt, U and Jansen, S and Jenkins, T and Jentsch, A and Jespersen, JRP and Jiang, GF and Johansen, JL and Johnson, D and Jokela, EJ and Joly, CA and Jordan, GJ and Joseph, GS and Junaedi, D and Junker, RR and Justes, E and Kabzems, R and Kane, J and Kaplan, Z and Kattenborn, T and Kavelenova, L and Kearsley, E and Kempel, A and Kenzo, T and Kerkhoff, A and Khalil, MI and Kinlock, NL and Kissling, WD and Kitajima, K and Kitzberger, T and Kjøller, R and Klein, T and Kleyer, M and Klimešová, J and Klipel, J and Kloeppel, B and Klotz, S and Knops, JMH and Kohyama, T and Koike, F and Kollmann, J and Komac, B and Komatsu, K and König, C and Kraft, NJB and Kramer, K and Kreft, H and Kühn, I and Kumarathunge, D and Kuppler, J and Kurokawa, H and Kurosawa, Y and Kuyah, S and Laclau, JP and Lafleur, B and Lallai, E and Lamb, E and Lamprecht, A and Larkin, DJ and Laughlin, D and Le Bagousse-Pinguet, Y and le Maire, G and le Roux, PC and le Roux, E and Lee, T and Lens, F and Lewis, SL and Lhotsky, B and Li, Y and Li, X and Lichstein, JW and Liebergesell, M and Lim, JY and Lin, YS and Linares, JC and Liu, C and Liu, D and Liu, U and Livingstone, S and Llusià, J and Lohbeck, M and López-García, Á and Lopez-Gonzalez, G and Lososová, Z and Louault, F and Lukács, BA and Lukeš, P and Luo, Y and Lussu, M and Ma, S and Maciel Rabelo Pereira, C and Mack, M and Maire, V and Mäkelä, A and Mäkinen, H and Malhado, ACM and Mallik, A and Manning, P and Manzoni, S and Marchetti, Z and Marchino, L and Marcilio-Silva, V and Marcon, E and Marignani, M and Markesteijn, L and Martin, A and Martínez-Garza, C and Martínez-Vilalta, J and Mašková, T and Mason, K and Mason, N and Massad, TJ and Masse, J and Mayrose, I and McCarthy, J and McCormack, ML and McCulloh, K and McFadden, IR and McGill, BJ and McPartland, MY and Medeiros, JS and Medlyn, B and Meerts, P and Mehrabi, Z and Meir, P and Melo, FPL and Mencuccini, M and Meredieu, C and Messier, J and Mészáros, I and Metsaranta, J and Michaletz, ST and Michelaki, C and Migalina, S and Milla, R and Miller, JED and Minden, V and Ming, R and Mokany, K and Moles, AT and Molnár, A and Molofsky, J and Molz, M and Montgomery, RA and Monty, A and Moravcová, L and Moreno-Martínez, A and Moretti, M and Mori, AS and Mori, S and Morris, D and Morrison, J and Mucina, L and Mueller, S and Muir, CD and Müller, SC and Munoz, F and Myers-Smith, IH and Myster, RW and Nagano, M and Naidu, S and Narayanan, A and Natesan, B and Negoita, L and Nelson, AS and Neuschulz, EL and Ni, J and Niedrist, G and Nieto, J and Niinemets, Ü and Nolan, R and Nottebrock, H and Nouvellon, Y and Novakovskiy, A and , and Nystuen, KO and O'Grady, A and O'Hara, K and O'Reilly-Nugent, A and Oakley, S and Oberhuber, W and Ohtsuka, T and Oliveira, R and Öllerer, K and Olson, ME and Onipchenko, V and Onoda, Y and Onstein, RE and Ordonez, JC and Osada, N and Ostonen, I and Ottaviani, G and Otto, S and Overbeck, GE and Ozinga, WA and Pahl, AT and Paine, CET and Pakeman, RJ and Papageorgiou, AC and Parfionova, E and Pärtel, M and Patacca, M and Paula, S and Paule, J and Pauli, H and Pausas, JG and Peco, B and Penuelas, J and Perea, A and Peri, PL and Petisco-Souza, AC and Petraglia, A and Petritan, AM and Phillips, OL and Pierce, S and Pillar, VD and Pisek, J and Pomogaybin, A and Poorter, H and Portsmuth, A and Poschlod, P and Potvin, C and Pounds, D and Powell, AS and Power, SA and Prinzing, A and Puglielli, G and Pyšek, P and Raevel, V and Rammig, A and Ransijn, J and Ray, CA and Reich, PB and Reichstein, M and Reid, DEB and Réjou-Méchain, M and de Dios, VR and Ribeiro, S and Richardson, S and Riibak, K and Rillig, MC and Riviera, F and Robert, EMR and Roberts, S and Robroek, B and Roddy, A and Rodrigues, AV and Rogers, A and Rollinson, E and Rolo, V and Römermann, C and Ronzhina, D and Roscher, C and Rosell, JA and Rosenfield, MF and Rossi, C and Roy, DB and Royer-Tardif, S and Rüger, N and Ruiz-Peinado, R and Rumpf, SB and Rusch, GM and Ryo, M and Sack, L and Saldaña, A and Salgado-Negret, B and Salguero-Gomez, R and Santa-Regina, I and Santacruz-García, AC and Santos, J and Sardans, J and Schamp, B and Scherer-Lorenzen, M and Schleuning, M and Schmid, B and Schmidt, M and Schmitt, S and Schneider, JV and Schowanek, SD and Schrader, J and Schrodt, F and Schuldt, B and Schurr, F and Selaya Garvizu, G and Semchenko, M and Seymour, C and Sfair, JC and Sharpe, JM and Sheppard, CS and Sheremetiev, S and Shiodera, S and Shipley, B and Shovon, TA and Siebenkäs, A and Sierra, C and Silva, V and Silva, M and Sitzia, T and Sjöman, H and Slot, M and Smith, NG and Sodhi, D and Soltis, P and Soltis, D and Somers, B and Sonnier, G and Sørensen, MV and Sosinski, EE and Soudzilovskaia, NA and Souza, AF and Spasojevic, M and Sperandii, MG and Stan, AB and Stegen, J and Steinbauer, K and Stephan, JG and Sterck, F and Stojanovic, DB and Strydom, T and Suarez, ML and Svenning, JC and Svitková, I and Svitok, M and Svoboda, M and Swaine, E and Swenson, N and Tabarelli, M and Takagi, K and Tappeiner, U and Tarifa, R and Tauugourdeau, S and Tavsanoglu, C and Te Beest, M and Tedersoo, L and Thiffault, N and Thom, D and Thomas, E and Thompson, K and Thornton, PE and Thuiller, W and Tichý, L and Tissue, D and Tjoelker, MG and Tng, DYP and Tobias, J and Török, P and Tarin, T and Torres-Ruiz, JM and Tóthmérész, B and Treurnicht, M and Trivellone, V and Trolliet, F and Trotsiuk, V and Tsakalos, JL and Tsiripidis, I and Tysklind, N and Umehara, T and Usoltsev, V and Vadeboncoeur, M and Vaezi, J and Valladares, F and Vamosi, J and van Bodegom, PM and van Breugel, M and Van Cleemput, E and van de Weg, M and van der Merwe, S and van der Plas, F and van der Sande, MT and van Kleunen, M and Van Meerbeek, K and Vanderwel, M and Vanselow, KA and Vårhammar, A and Varone, L and Vasquez Valderrama, MY and Vassilev, K and Vellend, M and Veneklaas, EJ and Verbeeck, H and Verheyen, K and Vibrans, A and Vieira, I and Villacís, J and Violle, C and Vivek, P and Wagner, K and Waldram, M and Waldron, A and Walker, AP and Waller, M and Walther, G and Wang, H and Wang, F and Wang, W and Watkins, H and Watkins, J and Weber, U and Weedon, JT and Wei, L and Weigelt, P and Weiher, E and Wells, AW and Wellstein, C and Wenk, E and Westoby, M and Westwood, A and White, PJ and Whitten, M and Williams, M and Winkler, DE and Winter, K and Womack, C and Wright, IJ and Wright, SJ and Wright, J and Pinho, BX and Ximenes, F and Yamada, T and Yamaji, K and Yanai, R and Yankov, N and Yguel, B and Zanini, KJ and Zanne, AE and Zelený, D and Zhao, YP and Zheng, J and Zheng, J and Ziemińska, K and Zirbel, CR and Zizka, G and Zo-Bi, IC and Zotz, G and Wirth, C}, title = {TRY plant trait database - enhanced coverage and open access.}, journal = {Global change biology}, volume = {26}, number = {1}, pages = {119-188}, doi = {10.1111/gcb.14904}, pmid = {31891233}, issn = {1365-2486}, support = {//International Geosphere-Biosphere Programme (IGBP)/International ; //GIS 'Climat, Environnement et Société' France/International ; //German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig/International ; //AXA Research Fund/International ; //Max Planck Society/International ; //UK Natural Environment Research Council (NERC)/International ; //French Foundation for Biodiversity Research (FRB)/International ; //Max Planck Institute for Biogeochemistry/International ; //International Programme of Biodiversity Science (DIVERSITAS)/International ; P 29142/FWF_/Austrian Science Fund FWF/Austria ; //Future Earth/International ; }, mesh = {*Access to Information ; Biodiversity ; Ecology ; *Ecosystem ; Plants ; }, abstract = {Plant traits-the morphological, anatomical, physiological, biochemical and phenological characteristics of plants-determine how plants respond to environmental factors, affect other trophic levels, and influence ecosystem properties and their benefits and detriments to people. Plant trait data thus represent the basis for a vast area of research spanning from evolutionary biology, community and functional ecology, to biodiversity conservation, ecosystem and landscape management, restoration, biogeography and earth system modelling. Since its foundation in 2007, the TRY database of plant traits has grown continuously. It now provides unprecedented data coverage under an open access data policy and is the main plant trait database used by the research community worldwide. Increasingly, the TRY database also supports new frontiers of trait-based plant research, including the identification of data gaps and the subsequent mobilization or measurement of new data. To support this development, in this article we evaluate the extent of the trait data compiled in TRY and analyse emerging patterns of data coverage and representativeness. Best species coverage is achieved for categorical traits-almost complete coverage for 'plant growth form'. However, most traits relevant for ecology and vegetation modelling are characterized by continuous intraspecific variation and trait-environmental relationships. These traits have to be measured on individual plants in their respective environment. Despite unprecedented data coverage, we observe a humbling lack of completeness and representativeness of these continuous traits in many aspects. We, therefore, conclude that reducing data gaps and biases in the TRY database remains a key challenge and requires a coordinated approach to data mobilization and trait measurements. This can only be achieved in collaboration with other initiatives.}, } @article {pmid31889506, year = {2020}, author = {Walker, JW and Kittur, N and Binder, S and Castleman, JD and Drake, JM and Campbell, CH and King, CH and Colley, DG}, title = {Environmental Predictors of Schistosomiasis Persistent Hotspots following Mass Treatment with Praziquantel.}, journal = {The American journal of tropical medicine and hygiene}, volume = {102}, number = {2}, pages = {328-338}, pmid = {31889506}, issn = {1476-1645}, mesh = {Africa South of the Sahara/epidemiology ; Anthelmintics/*administration & dosage/*therapeutic use ; Child ; Databases, Factual ; Environment ; Humans ; *Mass Drug Administration ; Praziquantel/*administration & dosage/*therapeutic use ; Retrospective Studies ; Schistosomiasis/*drug therapy/epidemiology ; }, abstract = {Schistosomiasis control programs rely heavily on mass drug administration (MDA) campaigns with praziquantel for preventative chemotherapy. Areas where the prevalence and/or intensity of schistosomiasis infection remains high even after several rounds of treatment, termed "persistent hotspots" (PHSs), have been identified in trials of MDA effectiveness conducted by the Schistosomiasis Consortium for Operational Research and Evaluation (SCORE) in Kenya, Mozambique, Tanzania, and Côte d'Ivoire. In this analysis, we apply a previously developed set of criteria to classify the PHS status of 531 study villages from five SCORE trials. We then fit logistic regression models to data from SCORE and publically available georeferenced datasets to evaluate the influence of local environmental and population features, pre-intervention infection burden, and treatment scheduling on PHS status in each trial. The frequency of PHS in individual trials ranged from 35.3% to 71.6% in study villages. Significant relationships between PHS status and MDA frequency, distance to freshwater, rainfall, baseline schistosomiasis burden, elevation, land cover type, and village remoteness were each observed in at least one trial, although the strength and direction of these relationships was not always consistent among study sites. These findings suggest that PHSs are driven in part by environmental conditions that modify the risk and frequency of reinfection.}, } @article {pmid31889116, year = {2019}, author = {Lecaudey, LA and Sturmbauer, C and Singh, P and Ahi, EP}, title = {Molecular mechanisms underlying nuchal hump formation in dolphin cichlid, Cyrtocara moorii.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {20296}, pmid = {31889116}, issn = {2045-2322}, support = {P 29838/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Animals ; *Biological Evolution ; Body Patterning/*genetics ; Cichlids/*anatomy & histology/*genetics ; Computational Biology/methods ; Gene Expression Profiling ; Gene Expression Regulation, Developmental ; High-Throughput Nucleotide Sequencing ; Quantitative Trait, Heritable ; Reproducibility of Results ; Transcriptome ; }, abstract = {East African cichlid fishes represent a model to tackle adaptive changes and their connection to rapid speciation and ecological distinction. In comparison to bony craniofacial tissues, adaptive morphogenesis of soft tissues has been rarely addressed, particularly at the molecular level. The nuchal hump in cichlids fishes is one such soft-tissue and exaggerated trait that is hypothesized to play an innovative role in the adaptive radiation of cichlids fishes. It has also evolved in parallel across lakes in East Africa and Central America. Using gene expression profiling, we identified and validated a set of genes involved in nuchal hump formation in the Lake Malawi dolphin cichlid, Cyrtocara moorii. In particular, we found genes differentially expressed in the nuchal hump, which are involved in controlling cell proliferation (btg3, fosl1a and pdgfrb), cell growth (dlk1), craniofacial morphogenesis (dlx5a, mycn and tcf12), as well as regulators of growth-related signals (dpt, pappa and socs2). This is the first study to identify the set of genes associated with nuchal hump formation in cichlids. Given that the hump is a trait that evolved repeatedly in several African and American cichlid lineages, it would be interesting to see if the molecular pathways and genes triggering hump formation follow a common genetic track or if the trait evolved in parallel, with distinct mechanisms, in other cichlid adaptive radiations and even in other teleost fishes.}, } @article {pmid31888487, year = {2019}, author = {Rittschof, CC and Rubin, BER and Palmer, JH}, title = {The transcriptomic signature of low aggression in honey bees resembles a response to infection.}, journal = {BMC genomics}, volume = {20}, number = {1}, pages = {1029}, pmid = {31888487}, issn = {1471-2164}, support = {Hatch Program: 1012993//National Institute of Food and Agriculture/ ; 2018-67012-28085//National Institute of Food and Agriculture/ ; 549049//Foundation for Food and Agriculture Research/ ; 3489-RDE-019//Kentucky Science and Engineering Foundation/ ; }, mesh = {Animal Diseases/*etiology ; Animals ; Bees/*genetics ; *Behavior, Animal ; Gene Expression Profiling ; Gene Expression Regulation ; Gene Ontology ; Host-Pathogen Interactions/genetics/immunology ; Infections/*veterinary ; Models, Biological ; *Transcriptome ; }, abstract = {BACKGROUND: Behavior reflects an organism's health status. Many organisms display a generalized suite of behaviors that indicate infection or predict infection susceptibility. We apply this concept to honey bee aggression, a behavior that has been associated with positive health outcomes in previous studies. We sequenced the transcriptomes of the brain, fat body, and midgut of adult sibling worker bees who developed as pre-adults in relatively high versus low aggression colonies. Previous studies showed that this pre-adult experience impacts both aggressive behavior and resilience to pesticides. We performed enrichment analyses on differentially expressed genes to determine whether variation in aggression resembles the molecular response to infection. We further assessed whether the transcriptomic signature of aggression in the brain is similar to the neuromolecular response to acute predator threat, exposure to a high-aggression environment as an adult, or adult behavioral maturation.

RESULTS: Across all three tissues assessed, genes that are differentially expressed as a function of aggression significantly overlap with genes whose expression is modulated by a variety of pathogens and parasitic feeding. In the fat body, and to some degree the midgut, our data specifically support the hypothesis that low aggression resembles a diseased or parasitized state. However, we find little evidence of active infection in individuals from the low aggression group. We also find little evidence that the brain molecular signature of aggression is enriched for genes modulated by social cues that induce aggression in adults. However, we do find evidence that genes associated with adult behavioral maturation are enriched in our brain samples.

CONCLUSIONS: Results support the hypothesis that low aggression resembles a molecular state of infection. This pattern is most robust in the peripheral fat body, an immune responsive tissue in the honey bee. We find no evidence of acute infection in bees from the low aggression group, suggesting the physiological state characterizing low aggression may instead predispose bees to negative health outcomes when they are exposed to additional stressors. The similarity of molecular signatures associated with the seemingly disparate traits of aggression and disease suggests that these characteristics may, in fact, be intimately tied.}, } @article {pmid31887177, year = {2019}, author = {Franckowiak, GA and Perdicas, M and Smith, GA}, title = {Spatial ecology of coyotes in the urbanizing landscape of the Cuyahoga Valley, Ohio.}, journal = {PloS one}, volume = {14}, number = {12}, pages = {e0227028}, pmid = {31887177}, issn = {1932-6203}, mesh = {Age Factors ; Animal Migration/*physiology ; Animals ; Coyotes/*physiology ; Female ; Geographic Information Systems ; Homing Behavior/*physiology ; Male ; Ohio ; Photoperiod ; Remote Sensing Technology ; Seasons ; Sex Factors ; *Spatio-Temporal Analysis ; *Urbanization ; }, abstract = {Urban landscapes can present ecological challenges for wildlife species, yet many species survive, and even thrive, near dense human populations. Coyotes (Canis latrans), for example, have expanded their geographic range across North America and, as a result of their adaptability and behavioral flexibility, are now a common occupant of many urban areas in the United States. We investigated the spatial ecology of 27 coyotes fitted with Global Positioning System (GPS) telemetry collars radio-collared in the Cuyahoga Valley, Ohio. Our objectives were to quantify coyote space use, evaluate resource selection, and investigate coyote movement and activity patterns. To measure space use, we estimated home range (95%) and core area (50%) size of coyotes using the adaptive local convex hull (a-LoCoH) method. We found the mean (± SE) home range size of resident coyotes (4.7 ± 1.8 km2) was significantly smaller than ranges of transient coyotes (67.7 ± 89.6 km2). Similarly, mean (± SE) core area size of resident coyotes (0.9 ± 0.6 km2) was significantly smaller than core areas of transient coyotes (11.9 ± 16.7 km2). Home range and core area size of both resident and transient coyotes did not vary by sex, age, or season. For all coyotes, use of natural land cover was significantly greater than use of altered and developed land. When coyotes were using altered and developed land, GPS fixes were most common at night. Coyote movement patterns differed with respect to status, time period, and season; peaking during nighttime hours. A better understanding of coyote space use and movement within anthropogenic landscapes aids management of people, parks, and wildlife by providing the data necessary for research-based management decisions.}, } @article {pmid31882957, year = {2019}, author = {Jiguet, F and Burgess, M and Thorup, K and Conway, G and Arroyo Matos, JL and Barber, L and Black, J and Burton, N and Castelló, J and Clewley, G and Copete, JL and Czajkowski, MA and Dale, S and Davis, T and Dombrovski, V and Drew, M and Elts, J and Gilson, V and Grzegorczyk, E and Henderson, I and Holdsworth, M and Husbands, R and Lorrilliere, R and Marja, R and Minkevicius, S and Moussy, C and Olsson, P and Onrubia, A and Pérez, M and Piacentini, J and Piha, M and Pons, JM and Procházka, P and Raković, M and Robins, H and Seimola, T and Selstam, G and Skierczyński, M and Sondell, J and Thibault, JC and Tøttrup, AP and Walker, J and Hewson, C}, title = {Desert crossing strategies of migrant songbirds vary between and within species.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {20248}, pmid = {31882957}, issn = {2045-2322}, mesh = {Altitude ; Animal Migration/*physiology ; Animals ; Circadian Rhythm/physiology ; *Desert Climate ; *Environment ; Flight, Animal/*physiology ; Geographic Information Systems ; Light ; Seasons ; Songbirds/classification/*physiology ; Species Specificity ; Temperature ; Time Factors ; }, abstract = {Each year, billions of songbirds cross large ecological barriers during their migration. Understanding how they perform this incredible task is crucial to predict how global change may threaten the safety of such journeys. Earlier studies based on radar suggested that most songbirds cross deserts in intermittent flights at high altitude, stopping in the desert during the day, while recent tracking with light loggers suggested diurnal prolongation of nocturnal flights and common non-stop flights for some species. We analyzed light intensity and temperature data obtained from geolocation loggers deployed on 130 individuals of ten migratory songbird species, and show that a large variety of strategies for crossing deserts exists between, but also sometimes within species. Diurnal stopover in the desert is a common strategy in autumn, while most species prolonged some nocturnal flights into the day. Non-stop flights over the desert occurred more frequently in spring than in autumn, and more frequently in foliage gleaners. Temperature recordings suggest that songbirds crossed deserts with flight bouts performed at various altitudes according to species and season, along a gradient ranging from low above ground in autumn to probably >2000 m above ground level, and possibly at higher altitude in spring. High-altitude flights are therefore not the general rule for crossing deserts in migrant songbirds. We conclude that a diversity of migration strategies exists for desert crossing among songbirds, with variations between but also within species.}, } @article {pmid31875022, year = {2019}, author = {Adeyinka, DA and Olakunde, BO and Muhajarine, N}, title = {Evidence of health inequity in child survival: spatial and Bayesian network analyses of stillbirth rates in 194 countries.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {19755}, pmid = {31875022}, issn = {2045-2322}, mesh = {Anemia/*epidemiology ; *Databases, Factual ; Female ; *Healthcare Disparities ; Humans ; Pregnancy ; Pregnancy Complications, Hematologic/*epidemiology ; *Public Health ; Stillbirth/*epidemiology ; }, abstract = {Estimated at 2.6 million annually, stillbirths worldwide have stayed alarmingly high, in contrast to neonatal and under-five mortality rates. It is a neglected public health challenge globally, with less attention to its social determinants. We examined spatial patterns of country-level stillbirth rates and determined the influence of social determinants of health on spatial patterns of stillbirth rates. We also estimated probabilistic relationships between stillbirth rates and significant determinants from the spatial analysis. Using country-level aggregated data from the United Nations databases, it employed ecological spatial analysis and artificial intelligence modeling based on Bayesian network among 194 World Health Organization member countries. From the spatial analysis, thirty-seven countries formed a cluster of high values (hot-spots) for stillbirth and 13 countries formed a cluster of low values (cold-spots). In the multivariate regression, gender inequality and anaemia in pregnancy were significantly associated with spatial patterns of higher stillbirth rates, while higher antenatal care (ANC) coverage and skilled birth attendants during delivery were associated with clusters of lower stillbirth rates. The Bayesian network model suggests strong dependencies between stillbirth rate and gender inequality index, geographic regions and skilled birth attendants during delivery. The Bayesian network predicted that the probability of low stillbirth rate increased from 56% to 100% when the percentage of countries with high skilled birth attendants during delivery increased from 70% to 88%, high ANC coverage increased from 55% to 70%, high prevalence of anaemia in pregnancy decreased from 27% to 11% and high gender inequality index decreased from 43% to 21%. Recognizing the urgency in reducing stillbirths globally, multi-pronged strategies should be designed to promote gender equality and strengthen the reproductive and maternal health services in Africa, Eastern Mediterranean, South Eastern Asia, and other countries with disproportionately high stillbirth rates.}, } @article {pmid31874610, year = {2019}, author = {Chung, NC and Miasojedow, B and Startek, M and Gambin, A}, title = {Jaccard/Tanimoto similarity test and estimation methods for biological presence-absence data.}, journal = {BMC bioinformatics}, volume = {20}, number = {Suppl 15}, pages = {644}, pmid = {31874610}, issn = {1471-2105}, mesh = {Algorithms ; Animals ; Biometry ; Fishes ; Freshwater Biology/*methods ; Probability ; }, abstract = {BACKGROUND: A survey of presences and absences of specific species across multiple biogeographic units (or bioregions) are used in a broad area of biological studies from ecology to microbiology. Using binary presence-absence data, we evaluate species co-occurrences that help elucidate relationships among organisms and environments. To summarize similarity between occurrences of species, we routinely use the Jaccard/Tanimoto coefficient, which is the ratio of their intersection to their union. It is natural, then, to identify statistically significant Jaccard/Tanimoto coefficients, which suggest non-random co-occurrences of species. However, statistical hypothesis testing using this similarity coefficient has been seldom used or studied.

RESULTS: We introduce a hypothesis test for similarity for biological presence-absence data, using the Jaccard/Tanimoto coefficient. Several key improvements are presented including unbiased estimation of expectation and centered Jaccard/Tanimoto coefficients, that account for occurrence probabilities. The exact and asymptotic solutions are derived. To overcome a computational burden due to high-dimensionality, we propose the bootstrap and measurement concentration algorithms to efficiently estimate statistical significance of binary similarity. Comprehensive simulation studies demonstrate that our proposed methods produce accurate p-values and false discovery rates. The proposed estimation methods are orders of magnitude faster than the exact solution, particularly with an increasing dimensionality. We showcase their applications in evaluating co-occurrences of bird species in 28 islands of Vanuatu and fish species in 3347 freshwater habitats in France. The proposed methods are implemented in an open source R package called jaccard (https://cran.r-project.org/package=jaccard).

CONCLUSION: We introduce a suite of statistical methods for the Jaccard/Tanimoto similarity coefficient for binary data, that enable straightforward incorporation of probabilistic measures in analysis for species co-occurrences. Due to their generality, the proposed methods and implementations are applicable to a wide range of binary data arising from genomics, biochemistry, and other areas of science.}, } @article {pmid31873145, year = {2019}, author = {Tarazona, E and Hahn, C and Franch-Gras, L and García-Roger, EM and Carmona, MJ and Gómez, A}, title = {Ecological genomics of adaptation to unpredictability in experimental rotifer populations.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {19646}, pmid = {31873145}, issn = {2045-2322}, mesh = {Acclimatization/*physiology ; Animals ; Databases, Nucleic Acid ; Genetic Association Studies ; *Genome ; *Polymorphism, Single Nucleotide ; Rotifera/*physiology ; *Selection, Genetic ; }, abstract = {Elucidating the genetic basis of phenotypic variation in response to different environments is key to understanding how populations evolve. Facultatively sexual rotifers can develop adaptive responses to fluctuating environments. In a previous evolution experiment, diapause-related traits changed rapidly in response to two selective regimes (predictable vs unpredictable) in laboratory populations of the rotifer Brachionus plicatilis. Here, we investigate the genomic basis of adaptation to environmental unpredictability in these experimental populations. We identified and genotyped genome-wide polymorphisms in 169 clones from both selective regimes after seven cycles of selection using genotyping by sequencing (GBS). Additionally, we used GBS data from the 270 field clones from which the laboratory populations were established. This GBS dataset was used to identify candidate SNPs under selection. A total of 76 SNPs showed divergent selection, three of which are candidates for being under selection in the particular unpredictable fluctuation pattern studied. Most of the remaining SNPs showed strong signals of adaptation to laboratory conditions. Furthermore, a genotype-phenotype association approach revealed five SNPs associated with two key life-history traits in the adaptation to unpredictability. Our results contribute to elucidating the genomic basis for adaptation to unpredictable environments and lay the groundwork for future evolution studies in rotifers.}, } @article {pmid31870407, year = {2019}, author = {Liao, T and Wei, Y and Luo, M and Zhao, GP and Zhou, H}, title = {tmap: an integrative framework based on topological data analysis for population-scale microbiome stratification and association studies.}, journal = {Genome biology}, volume = {20}, number = {1}, pages = {293}, pmid = {31870407}, issn = {1474-760X}, mesh = {Data Mining ; Humans ; *Microbiota ; *Software ; }, abstract = {Untangling the complex variations of microbiome associated with large-scale host phenotypes or environment types challenges the currently available analytic methods. Here, we present tmap, an integrative framework based on topological data analysis for population-scale microbiome stratification and association studies. The performance of tmap in detecting nonlinear patterns is validated by different scenarios of simulation, which clearly demonstrate its superiority over the most commonly used methods. Application of tmap to several population-scale microbiomes extensively demonstrates its strength in revealing microbiome-associated host or environmental features and in understanding the systematic interrelations among their association patterns. tmap is available at https://github.com/GPZ-Bioinfo/tmap.}, } @article {pmid31869356, year = {2019}, author = {Buchner, D and Beermann, AJ and Laini, A and Rolauffs, P and Vitecek, S and Hering, D and Leese, F}, title = {Analysis of 13,312 benthic invertebrate samples from German streams reveals minor deviations in ecological status class between abundance and presence/absence data.}, journal = {PloS one}, volume = {14}, number = {12}, pages = {e0226547}, pmid = {31869356}, issn = {1932-6203}, mesh = {Animals ; Aquatic Organisms/*classification/cytology/genetics/growth & development ; *Biodiversity ; *Biological Evolution ; Databases, Factual/trends ; Ecosystem ; Environmental Monitoring ; Extinction, Biological ; Germany ; Invertebrates/*classification/cytology/genetics/growth & development ; Population Dynamics/trends ; *Rivers ; }, abstract = {Benthic invertebrates are the most commonly used organisms used to assess ecological status as required by the EU Water Framework Directive (WFD). For WFD-compliant assessments, benthic invertebrate communities are sampled, identified and counted. Taxa × abundance matrices are used to calculate indices and the resulting scores are compared to reference values to determine the ecological status class. DNA-based tools, such as DNA metabarcoding, provide a new and precise method for species identification but cannot deliver robust abundance data. To evaluate the applicability of DNA-based tools to ecological status assessment, we evaluated whether the results derived from presence/absence data are comparable to those derived from abundance data. We analysed benthic invertebrate community data obtained from 13,312 WFD assessments of German streams. Broken down to 30 official stream types, we compared assessment results based on abundance and presence/absence data for the assessment modules "organic pollution" (i.e., the saprobic index) and "general degradation" (a multimetric index) as well as their underlying metrics. In 76.6% of cases, the ecological status class did not change after transforming abundance data to presence/absence data. In 12% of cases, the status class was reduced by one (e.g., from good to moderate), and in 11.2% of cases, the class increased by one. In only 0.2% of cases, the status shifted by two classes. Systematic stream type-specific deviations were found and differences between abundance and presence/absence data were most prominent for stream types where abundance information contributed directly to one or several metrics of the general degradation module. For a single stream type, these deviations led to a systematic shift in status from 'good' to 'moderate' (n = 201; with only n = 3 increasing). The systematic decrease in scores was observed, even when considering simulated confidence intervals for abundance data. Our analysis suggests that presence/absence data can yield similar assessment results to those for abundance-based data, despite type-specific deviations. For most metrics, it should be possible to intercalibrate the two data types without substantial efforts. Thus, benthic invertebrate taxon lists generated by standardised DNA-based methods should be further considered as a complementary approach.}, } @article {pmid31869316, year = {2020}, author = {Drozdovitch, V and Minenko, V and Kukhta, T and Trofimik, S and Grakovitch, R and Hatch, M and Cahoon, EK and Veyalkin, I and Polyanskaya, O and Yauseyenka, V and Ostroumova, E and Mabuchi, K and Rozhko, A}, title = {Thyroid Dose Estimates for a Cohort of Belarusian Persons Exposed in Utero and During Early Life to Chernobyl Fallout.}, journal = {Health physics}, volume = {118}, number = {2}, pages = {170-184}, pmid = {31869316}, issn = {1538-5159}, support = {001/WHO_/World Health Organization/International ; Z99 CA999999/ImNIH/Intramural NIH HHS/United States ; }, mesh = {Adolescent ; Cesium Radioisotopes ; *Chernobyl Nuclear Accident ; Cohort Studies ; Female ; Fetus/*radiation effects ; Humans ; Neoplasms, Radiation-Induced/etiology ; Pregnancy ; Radiation Dosage ; Thyroid Gland/*radiation effects ; Thyroid Neoplasms/etiology ; Young Adult ; }, abstract = {Thyroid radiation doses were estimated for a cohort of 2,965 Belarusian persons who were exposed in utero and during early life to fallout from the Chernobyl nuclear power plant accident. Prenatal and postnatal doses to the thyroid due to intake of I, external irradiation from radionuclides deposited on the ground, and ingestion of cesium isotopes (Cs and Cs) were calculated for all cohort members. Dose estimation was based on personal interviews with subjects' mothers; the interviews collected data on subjects' residential history, consumption by mothers during time of pregnancy and breast-feeding, as well as consumption by subjects after birth. Direct instrumental measurements of radioactivity in mothers and the study subjects, if available, were also used for calculation of doses. Intake of I by mothers was found to be the predominant pathway for thyroid exposure for the study subjects. The average thyroid dose due to all exposure pathways was estimated to be 137 mGy (median dose of 25 mGy, maximal dose of 14.8 Gy), including 130 mGy (median dose of 17 mGy, maximal dose of 14.8 Gy) from I intake, 4.9 mGy (median dose of 3.0 mGy, maximal dose of 102 mGy) due to external irradiation, and 2.5 mGy (median dose of 1.7 mGy, maximal dose of 47 mGy) due to ingestion of Cs. The dose estimates will be used to evaluate the radiation-related risk of thyroid cancer and other thyroid diseases in this unique cohort.}, } @article {pmid31868388, year = {2020}, author = {Trull, TJ and Ebner-Priemer, UW}, title = {Ambulatory assessment in psychopathology research: A review of recommended reporting guidelines and current practices.}, journal = {Journal of abnormal psychology}, volume = {129}, number = {1}, pages = {56-63}, doi = {10.1037/abn0000473}, pmid = {31868388}, issn = {1939-1846}, mesh = {Ecological Momentary Assessment ; *Guidelines as Topic ; Humans ; *Mental Disorders ; Psychopathology ; *Research ; }, abstract = {The use of ambulatory assessment (AA; Trull & Ebner-Priemer, 2013) in psychopathology research, which includes experience-sampling methods as well as ecological momentary assessment, has increased dramatically over the last several decades. Previously, methodological and reporting guidelines have been presented to outline best practices and provide input on methodological issues and decisions that are faced when planning and conducting AA studies (e.g., Bolger & Laurenceau, 2013; Mehl & Conner, 2012; Stone & Shiffman, 2002). However, despite the publication of these important resources and guidelines, it remains an open question as to how much uniformity or consistency is evident in the design and reporting of AA studies of psychopathology. To address this, we reviewed the reported practices of published studies using AA in major psychopathology journals (Journal of Abnormal Psychology, Psychological Medicine, Clinical Psychological Science) over the last 7 years (2012-2018). Our review highlights (a) sample selection and size; (b) sampling design; (c) selection and reporting of measures; (d) devices used and software; (e) compliance; (f) participant training, monitoring and remuneration; and (g) data management and analysis. We conclude with recommendations for reporting the features of future AA studies in psychopathology. (PsycINFO Database Record (c) 2019 APA, all rights reserved).}, } @article {pmid31864285, year = {2019}, author = {Wang, L and Abu-Doleh, A and Plank, J and Catalyurek, UV and Firkins, JL and Yu, Z}, title = {The transcriptome of the rumen ciliate Entodinium caudatum reveals some of its metabolic features.}, journal = {BMC genomics}, volume = {20}, number = {1}, pages = {1008}, pmid = {31864285}, issn = {1471-2164}, support = {2012-67015-19437//Department of Agriculture (US)/ ; }, mesh = {Alveolata/cytology/*genetics/*metabolism/physiology ; Animals ; Carbohydrate Metabolism/genetics ; *Gene Expression Profiling ; Intracellular Space/metabolism ; Phagocytosis/genetics ; RNA, Messenger/genetics ; RNA-Seq ; Signal Transduction/genetics ; Symbiosis/genetics ; }, abstract = {BACKGROUND: Rumen ciliates play important roles in rumen function by digesting and fermenting feed and shaping the rumen microbiome. However, they remain poorly understood due to the lack of definitive direct evidence without influence by prokaryotes (including symbionts) in co-cultures or the rumen. In this study, we used RNA-Seq to characterize the transcriptome of Entodinium caudatum, the most predominant and representative rumen ciliate species.

RESULTS: Of a large number of transcripts, > 12,000 were annotated to the curated genes in the NR, UniProt, and GO databases. Numerous CAZymes (including lysozyme and chitinase) and peptidases were represented in the transcriptome. This study revealed the ability of E. caudatum to depolymerize starch, hemicellulose, pectin, and the polysaccharides of the bacterial and fungal cell wall, and to degrade proteins. Many signaling pathways, including the ones that have been shown to function in E. caudatum, were represented by many transcripts. The transcriptome also revealed the expression of the genes involved in symbiosis, detoxification of reactive oxygen species, and the electron-transport chain. Overall, the transcriptomic evidence is consistent with some of the previous premises about E. caudatum. However, the identification of specific genes, such as those encoding lysozyme, peptidases, and other enzymes unique to rumen ciliates might be targeted to develop specific and effective inhibitors to improve nitrogen utilization efficiency by controlling the activity and growth of rumen ciliates. The transcriptomic data will also help the assembly and annotation in future genomic sequencing of E. caudatum.

CONCLUSION: As the first transcriptome of a single species of rumen ciliates ever sequenced, it provides direct evidence for the substrate spectrum, fermentation pathways, ability to respond to various biotic and abiotic stimuli, and other physiological and ecological features of E. caudatum. The presence and expression of the genes involved in the lysis and degradation of microbial cells highlight the dependence of E. caudatum on engulfment of other rumen microbes for its survival and growth. These genes may be explored in future research to develop targeted control of Entodinium species in the rumen. The transcriptome can also facilitate future genomic studies of E. caudatum and other related rumen ciliates.}, } @article {pmid31861946, year = {2019}, author = {Lötsch, J and Ultsch, A}, title = {Current Projection Methods-Induced Biases at Subgroup Detection for Machine-Learning Based Data-Analysis of Biomedical Data.}, journal = {International journal of molecular sciences}, volume = {21}, number = {1}, pages = {}, pmid = {31861946}, issn = {1422-0067}, support = {n/a//Landesoffensive zur Entwicklung wissenschaftlich - ökonomischer Exzellenz (LOEWE)/ ; }, mesh = {Algorithms ; Antigens, CD/analysis ; Computational Biology/*methods ; Datasets as Topic ; Flow Cytometry/*methods ; Humans ; *Machine Learning ; Stochastic Processes ; }, abstract = {Advances in flow cytometry enable the acquisition of large and high-dimensional data sets per patient. Novel computational techniques allow the visualization of structures in these data and, finally, the identification of relevant subgroups. Correct data visualizations and projections from the high-dimensional space to the visualization plane require the correct representation of the structures in the data. This work shows that frequently used techniques are unreliable in this respect. One of the most important methods for data projection in this area is the t-distributed stochastic neighbor embedding (t-SNE). We analyzed its performance on artificial and real biomedical data sets. t-SNE introduced a cluster structure for homogeneously distributed data that did not contain any subgroup structure. In other data sets, t-SNE occasionally suggested the wrong number of subgroups or projected data points belonging to different subgroups, as if belonging to the same subgroup. As an alternative approach, emergent self-organizing maps (ESOM) were used in combination with U-matrix methods. This approach allowed the correct identification of homogeneous data while in sets containing distance or density-based subgroups structures; the number of subgroups and data point assignments were correctly displayed. The results highlight possible pitfalls in the use of a currently widely applied algorithmic technique for the detection of subgroups in high dimensional cytometric data and suggest a robust alternative.}, } @article {pmid31861885, year = {2019}, author = {Ahasan, MS and Subramaniam, K and Campos Krauer, JM and Sayler, KA and Loeb, JC and Goodfriend, OF and Barber, HM and Stephenson, CJ and Popov, VL and Charrel, RN and Wisely, SM and Waltzek, TB and Lednicky, JA}, title = {Three New Orbivirus Species Isolated from Farmed White-Tailed Deer (Odocoileus virginianus) in the United States.}, journal = {Viruses}, volume = {12}, number = {1}, pages = {}, pmid = {31861885}, issn = {1999-4915}, mesh = {Animal Diseases/*epidemiology/*virology ; Animals ; *Animals, Domestic ; Computational Biology/methods ; *Deer ; Genome, Viral ; Genomics/methods ; Geography, Medical ; *Orbivirus/classification/genetics/ultrastructure ; Phylogeny ; Public Health Surveillance ; Reoviridae Infections/*veterinary ; United States/epidemiology ; }, abstract = {We report the detection and gene coding sequences of three novel Orbivirus species found in six dead farmed white-tailed deer in the United States. Phylogenetic analyses indicate that the new orbiviruses are genetically closely related to the Guangxi, Mobuck, Peruvian horse sickness, and Yunnan orbiviruses, which are thought to be solely borne by mosquitos. However, four of the six viruses analyzed in this work were found as co-infecting agents along with a known cervid pathogen, epizootic hemorrhagic disease virus-2 (EHDV-2), raising questions as to whether the new viruses are primary pathogens or secondary pathogens that exacerbate EHDV-2 infections. Moreover, EHDV-2 is known to be a Culicoides-borne virus, raising additional questions as to whether Culicoides species can also serve as vectors for the novel orbiviruses, if mosquitoes can vector EHDV-2, or whether the deer were infected through separate bites by the insects. Our findings expand knowledge of the possible viral pathogens of deer in the United States. Moreover, due to the close genetic relatedness of the three new orbiviruses to viruses that are primary pathogens of cattle and horses, our findings also underscore a crucial need for additional research on the potential role of the three new orbiviruses as pathogens of other animals.}, } @article {pmid31861340, year = {2019}, author = {Bartas, M and Brázda, V and Červeň, J and Pečinka, P}, title = {Characterization of p53 Family Homologs in Evolutionary Remote Branches of Holozoa.}, journal = {International journal of molecular sciences}, volume = {21}, number = {1}, pages = {}, pmid = {31861340}, issn = {1422-0067}, support = {project LO1208 TEWEP//Ministry of Education, Youth and Sports of the Czech Republic in the "National Feasibility Program I"/ ; 18-15548S//The Czech Science Foundation/ ; CZ.1.05/2.1.00/19.0388//EU structural funding Operational Programme Research and Development for innovation/ ; SGS/09/PrF/2019//University of Ostrava/ ; }, mesh = {Amino Acid Sequence ; Databases, Genetic ; Eukaryota/classification/*genetics ; *Evolution, Molecular ; Exons ; Introns ; Models, Molecular ; *Multigene Family ; Phylogeny ; Protein Conformation ; Protein Interaction Domains and Motifs ; *Sequence Homology, Amino Acid ; Tumor Suppressor Protein p53/*chemistry/*genetics/metabolism ; }, abstract = {The p53 family of transcription factors plays key roles in development, genome stability, senescence and tumor development, and p53 is the most important tumor suppressor protein in humans. Although intensively investigated for many years, its initial evolutionary history is not yet fully elucidated. Using bioinformatic and structure prediction methods on current databases containing newly-sequenced genomes and transcriptomes, we present a detailed characterization of p53 family homologs in remote members of the Holozoa group, in the unicellular clades Filasterea, Ichthyosporea and Corallochytrea. Moreover, we show that these newly characterized homologous sequences contain domains that can form structures with high similarity to the human p53 family DNA-binding domain, and some also show similarities to the oligomerization and SAM domains. The presence of these remote homologs demonstrates an ancient origin of the p53 protein family.}, } @article {pmid31856723, year = {2019}, author = {Kim, S and Thapa, I and Zhang, L and Ali, H}, title = {A novel graph theoretical approach for modeling microbiomes and inferring microbial ecological relationships.}, journal = {BMC genomics}, volume = {20}, number = {Suppl 11}, pages = {945}, pmid = {31856723}, issn = {1471-2164}, mesh = {Bacteria/classification/genetics/isolation & purification ; Biomarkers ; Computational Biology/*methods ; Crohn Disease/metabolism/microbiology ; Gastrointestinal Microbiome/genetics ; Humans ; Metabolic Networks and Pathways ; Metagenome ; Microbial Interactions/*physiology ; *Microbiota ; *Models, Biological ; Phenotype ; }, abstract = {BACKGROUND: Microbiomes play vital roles in shaping environments and stabilize them based on their compositions and inter-species relationships among its species. Variations in microbial properties have been reported to have significant impact on their host environment. For example, variants in gut microbiomes have been reported to be associated with several chronic conditions, such as inflammatory disease and irritable bowel syndrome. However, how microbial bacteria contribute to pathogenesis still remains unclear and major research questions in this domain remain unanswered.

METHODS: We propose a split graph model to represent the composition and interactions of a given microbiome. We used metagenomes from Korean populations in this study. The dataset consists of three different types of samples, viz. mucosal tissue and stool from Crohn's disease patients and stool from healthy individuals. We use the split graph model to analyze the impact of microbial compositions on various host phenotypes. Utilizing the graph model, we have developed a pipeline that integrates genomic information and pathway analysis to characterize both critical informative components of inter-bacterial correlations and associations between bacterial taxa and various metabolic pathways.

RESULTS: The obtained results highlight the importance of the microbial communities and their inter-relationships and show how these microbial structures are correlated with Crohn's disease. We show that there are significant positive associations between detected taxonomic biomarkers as well as multiple functional modules in the split graph of mucosal tissue samples from CD patients. Bacteria Moraxellaceae and Pseudomonadaceae were detected as taxonomic biomarkers in CD groups. Higher abundance of these bacteria have been reported in previous study and several metabolic pathways associated with these bacteria were characterized in CD samples.

CONCLUSIONS: The proposed pipeline provides a new way to approach the analysis of complex microbiomes. The results obtained from this study show great potential in unraveling mechansims in complex biological systems to understand how various components in such complex environments are associated with critical biological functions.}, } @article {pmid31854561, year = {2019}, author = {Wang, ZQ and Liu, XX and Yao, ZH and Yao, LG and Chang, Y and Liu, ZC and Cao, LH}, title = {[Endogenous Release of Nitrogen and Phosphorus in the Danjiangkou Reservoir].}, journal = {Huan jing ke xue= Huanjing kexue}, volume = {40}, number = {11}, pages = {4953-4961}, doi = {10.13227/j.hjkx.201812206}, pmid = {31854561}, issn = {0250-3301}, abstract = {In situ sediments were collected at different sites of the Danjiangkou Reservoir using a columnar sediment sampler, and the release rate of N and P at the sediment-water interface was determined through static incubation experiments and the diffusion model of interstitial water molecules. The results showed that there was a significant difference in the release rate for N and P from sediments collected at five sampling sites. The release rates of NH4[+]-N and PO4[3-]-P under static incubation conditions were 13.07-24.88 mg·(m[2]·d)[-1] and 3.06-6.02 mg·(m[2]·d)[-1], whereas those estimated by Fick's Fist Law were 2.67-7.25 mg·(m[2]·d)[-1] and 0.04-0.18 mg·(m[2]·d)[-1], respectively. Overall, the release rates of N and P in the tributaries were 1.48 and 1.57 times higher than that in the reservoir, respectively, and they tended to decrease from the north to the south. The R/F values of NH4[+]-N and PO4[3-]-P were 3.43-4.98 and 29.67-72.88, respectively. The highest release rates of N and P were observed in the Guojiashan tributary for both methods. However, it was found that the release rates of N and P estimated by Fick's Fist Law were significantly lower than those obtained by the simulation method, indicating that the static incubation experiment with intact sediments allowed the release rates of N and P to be closer to the actual situation compared to the interstitial water molecule diffusion model.}, } @article {pmid31852521, year = {2019}, author = {Loh, VHY and Veitch, J and Salmon, J and Cerin, E and Thornton, L and Mavoa, S and Villanueva, K and Timperio, A}, title = {Built environment and physical activity among adolescents: the moderating effects of neighborhood safety and social support.}, journal = {The international journal of behavioral nutrition and physical activity}, volume = {16}, number = {1}, pages = {132}, pmid = {31852521}, issn = {1479-5868}, support = {R01 HL111378/HL/NHLBI NIH HHS/United States ; R01 HL111378/NH/NIH HHS/United States ; }, mesh = {Accelerometry/statistics & numerical data ; Adolescent ; Adolescent Behavior/*psychology ; Australia ; Automobiles/*statistics & numerical data ; *Built Environment ; Crime/psychology/*statistics & numerical data ; Exercise/*psychology ; Family ; Female ; Geographic Information Systems ; Humans ; Male ; Peer Group ; Residence Characteristics ; Self Report ; *Social Support ; Walking/psychology/statistics & numerical data ; }, abstract = {BACKGROUND: Increasing emphasis has been placed on improving physical activity levels through multilevel interventions. This study aims to examine moderating effects of neighborhood safety (crime and traffic) and social support (from parent and sibling/peer) for physical activity in the relationship between the built environment and moderate-to-vigorous physical activity (MVPA) outside school hours among adolescents in Melbourne.

METHODS: Data were from the NEighbourhood Activity in Youth study conducted among adolescents in Melbourne, Australia (n = 358, 15.3 (SD = 1.5) years). MVPA outside school hours was assessed by accelerometer. Built environment features within 1 km and 2 km residential buffers including recreation facilities, park area, and walkability and its components were assessed using Geographic Information Systems. Neighborhood safety, social support for physical activity and sociodemographic information were self-reported by adolescents. Multilevel linear regression models were used to estimate associations.

RESULTS: Support for physical activity from sibling/peer positively moderated the relationship between recreation facilities (1 km), residential density (2 km) and MVPA. Recreation facility (count within 2 km), walkability (1 km and 2 km) and residential density (1 km) had significant positive associations with MVPA outside school hours.

CONCLUSION: The built environment appeared to have stronger facilitating effects on MVPA among adolescents who had favourable support for physical activity from their sibling or peer. Multilevel interventions that target the built environment and social factors are needed to promote MVPA outside school hours among adolescents.}, } @article {pmid31852508, year = {2019}, author = {Manousaki, T and Koutsouveli, V and Lagnel, J and Kollias, S and Tsigenopoulos, CS and Arvanitidis, C and Magoulas, A and Dounas, C and Dailianis, T}, title = {A de novo transcriptome assembly for the bath sponge Spongia officinalis, adjusting for microsymbionts.}, journal = {BMC research notes}, volume = {12}, number = {1}, pages = {813}, pmid = {31852508}, issn = {1756-0500}, support = {MIS: 5001552 - 7834//State Scholarships Foundation (GR)/ ; }, mesh = {Animals ; Aquatic Organisms/genetics/metabolism ; Computational Biology ; Greece ; Microbiota/*genetics ; Phylogeny ; Porifera/*genetics/microbiology ; RNA, Ribosomal/genetics ; RNA-Seq/methods ; Symbiosis/*genetics ; Transcriptome/*genetics ; }, abstract = {OBJECTIVES: We report a transcriptome acquisition for the bath sponge Spongia officinalis, a non-model marine organism that hosts rich symbiotic microbial communities. To this end, a pipeline was developed to efficiently separate between bacterial expressed genes from those of eukaryotic origin. The transcriptome was produced to support the assessment of gene expression and, thus, the response of the sponge, to elevated temperatures, replicating conditions currently occurring in its native habitat.

DATA DESCRIPTION: We describe the assembled transcriptome along with the bioinformatic pipeline used to discriminate between signals of metazoan and prokaryotic origin. The pipeline involves standard read pre-processing steps and incorporates extra analyses to identify and filter prokaryotic reads out of the analysis. The proposed pipeline can be followed to overcome the technical RNASeq problems characteristic for symbiont-rich metazoan organisms with low or non-existent tissue differentiation, such as sponges and cnidarians. At the same time, it can be valuable towards the development of approaches for parallel transcriptomic studies of symbiotic communities and the host.}, } @article {pmid31848272, year = {2019}, author = {Van Goethem, MW and Swenson, TL and Trubl, G and Roux, S and Northen, TR}, title = {Characteristics of Wetting-Induced Bacteriophage Blooms in Biological Soil Crust.}, journal = {mBio}, volume = {10}, number = {6}, pages = {}, pmid = {31848272}, issn = {2150-7511}, mesh = {Bacillus/physiology/virology ; Bacterial Proteins/chemistry/genetics/metabolism ; *Bacteriophages ; Computational Biology/methods ; *Desert Climate ; Ecosystem ; Firmicutes/genetics/metabolism/virology ; Gene Expression Profiling ; Host-Pathogen Interactions ; Metagenome ; Metagenomics/methods ; *Photosynthesis ; Phylogeny ; *Soil Microbiology ; Structure-Activity Relationship ; }, abstract = {Biological soil crusts (biocrusts) are photosynthetic "hot spots" in deserts and cover ∼12% of the Earth's terrestrial surface, and yet they face an uncertain future given expected shifts in rainfall events. Laboratory wetting of biocrust communities is known to cause a bloom of Firmicutes which rapidly become dominant community members within 2 days after emerging from a sporulated state. We hypothesized that their bacteriophages (phages) would respond to such a dramatic increase in their host's abundance. In our experiment, wetting caused Firmicutes to bloom and triggered a significant depletion of cyanobacterial diversity. We used genome-resolved metagenomics to link phage to their hosts and found that the bloom of the genus Bacillus correlated with a dramatic increase in the number of Caudovirales phages targeting these diverse spore-formers (r = 0.762). After 2 days, we observed dramatic reductions in the relative abundances of Bacillus, while the number of Bacillus phages continued to increase, suggestive of a predator-prey relationship. We found predicted auxiliary metabolic genes (AMGs) associated with sporulation in several Caudovirales genomes, suggesting that phages may influence and even benefit from sporulation dynamics in biocrusts. Prophage elements and CRISPR-Cas repeats in Firmicutes metagenome-assembled genomes (MAGs) provide evidence of recent infection events by phages, which were corroborated by mapping viral contigs to their host MAGs. Combined, these findings suggest that the blooming Firmicutes become primary targets for biocrust Caudovirales phages, consistent with the classical "kill-the-winner" hypothesis.IMPORTANCE This work forms part of an overarching research theme studying the effects of a changing climate on biological soil crust (biocrust) in the Southwestern United States. To our knowledge, this study was the first to characterize bacteriophages in biocrust and offers a view into the ecology of phages in response to a laboratory wetting experiment. The phages identified here represent lineages of Caudovirales, and we found that the dynamics of their interactions with their Firmicutes hosts explain the collapse of a bacterial bloom that was induced by wetting. Moreover, we show that phages carried host-altering metabolic genes and found evidence of proviral infection and CRISPR-Cas repeats within host genomes. Our results suggest that phages exert controls on population density by lysing dominant bacterial hosts and that they further impact biocrust by acquiring host genes for sporulation. Future research should explore how dominant these phages are in other biocrust communities and quantify how much the control and lysis of blooming populations contributes to nutrient cycling in biocrusts.}, } @article {pmid31847345, year = {2019}, author = {Tomazatos, A and Jansen, S and Pfister, S and Török, E and Maranda, I and Horváth, C and Keresztes, L and Spînu, M and Tannich, E and Jöst, H and Schmidt-Chanasit, J and Cadar, D and Lühken, R}, title = {Ecology of West Nile Virus in the Danube Delta, Romania: Phylogeography, Xenosurveillance and Mosquito Host-Feeding Patterns.}, journal = {Viruses}, volume = {11}, number = {12}, pages = {}, pmid = {31847345}, issn = {1999-4915}, mesh = {Animals ; Antibodies, Viral/immunology ; *Ecology ; Feeding Behavior ; Genome, Viral ; Humans ; Immunoglobulin G/immunology ; Mosquito Vectors/virology ; Phylogeny ; Phylogeography ; Public Health Surveillance ; RNA, Viral ; Romania/epidemiology ; West Nile Fever/*epidemiology/transmission/*virology ; West Nile virus/*classification/*genetics ; }, abstract = {The ecology of West Nile virus (WNV) in the Danube Delta Biosphere Reserve (Romania) was investigated by combining studies on the virus genetics, phylogeography, xenosurveillance and host-feeding patterns of mosquitoes. Between 2014 and 2016, 655,667 unfed and 3842 engorged mosquito females were collected from four sampling sites. Blood-fed mosquitoes were negative for WNV-RNA, but two pools of unfed Culex pipiens s.l./torrentium collected in 2014 were tested positive. Our results suggest that Romania experienced at least two separate WNV lineage 2 introductions: from Africa into Danube Delta and from Greece into south-eastern Romania in the 1990s and early 2000s, respectively. The genetic diversity of WNV in Romania is primarily shaped by in situ evolution. WNV-specific antibodies were detected for 19 blood-meals from dogs and horses, but not from birds or humans. The hosts of mosquitoes were dominated by non-human mammals (19 species), followed by human and birds (23 species). Thereby, the catholic host-feeding pattern of Culex pipiens s.l./torrentium with a relatively high proportion of birds indicates the species' importance as a potential bridge vector. The low virus prevalence in combination with WNV-specific antibodies indicate continuous, but low activity of WNV in the Danube Delta during the study period.}, } @article {pmid31847283, year = {2019}, author = {Hu, S and Chen, L and Li, L and Wang, B and Yuan, L and Cheng, L and Yu, Z and Zhang, T}, title = {Spatiotemporal Dynamics of Ecosystem Service Value Determined by Land-Use Changes in the Urbanization of Anhui Province, China.}, journal = {International journal of environmental research and public health}, volume = {16}, number = {24}, pages = {}, pmid = {31847283}, issn = {1660-4601}, mesh = {China ; *Conservation of Natural Resources ; *Economic Development ; *Ecosystem ; Environmental Policy ; *Urbanization ; }, abstract = {Urbanization-induced land-use change will lead to variations in the demand and supply of ecosystem services, thus significantly affecting regional ecosystem services. The continuous degradation of ecosystem functions has become a serious problem for humanity to solve. Therefore, quantitative analysis of the corresponding impact of land-use change on ecosystem service value (ESV) is important to socio-economic development and ecological protection. The Anhui province in China has experienced rapid urbanization in recent years, and ecological environmental remediation and protection have become important goals for regional development. In this paper, the province of Anhui has been selected as a case of study, we analyzed the land-use change using Landsat images from 2000, 2005, 2010, and 2015. We then adjusted the equivalent factor of ESV per unit area and estimated the ESV of Anhui province from 2000 to 2015 to analyze the impact of land-use change on ESV. Our results show that (1) paddy field is the main land-use type in Anhui province, the built-up land area has continuously increased, and the water area has continuously decreased; (2) the total ESV of Anhui province decreased from 30,015.58 × 10[7] CNY in 2000 to 29,683.74 × 10[7] CNY in 2015 (the rate of change was -1.11%), and regulating services make the greatest contribution to ESV; and (3) land-use change has led to severe ESV variations, especially for the expansion of water area and built-up land. Our study results provide useful insights for the development of land-use management and environmental protection policies in Anhui province.}, } @article {pmid31846471, year = {2019}, author = {Zeiss, CJ and Shin, D and Vander Wyk, B and Beck, AP and Zatz, N and Sneiderman, CA and Kilicoglu, H}, title = {Menagerie: A text-mining tool to support animal-human translation in neurodegeneration research.}, journal = {PloS one}, volume = {14}, number = {12}, pages = {e0226176}, pmid = {31846471}, issn = {1932-6203}, support = {K24 AG021507/AG/NIA NIH HHS/United States ; P30 AG021342/AG/NIA NIH HHS/United States ; }, mesh = {Animals ; *Biomedical Research ; *Data Mining ; Humans ; *Neurodegenerative Diseases/diagnosis/genetics/therapy ; Outcome Assessment, Health Care ; Translational Research, Biomedical/*methods ; }, abstract = {Discovery studies in animals constitute a cornerstone of biomedical research, but suffer from lack of generalizability to human populations. We propose that large-scale interrogation of these data could reveal patterns of animal use that could narrow the translational divide. We describe a text-mining approach that extracts translationally useful data from PubMed abstracts. These comprise six modules: species, model, genes, interventions/disease modifiers, overall outcome and functional outcome measures. Existing National Library of Medicine natural language processing tools (SemRep, GNormPlus and the Chemical annotator) underpin the program and are further augmented by various rules, term lists, and machine learning models. Evaluation of the program using a 98-abstract test set achieved F1 scores ranging from 0.75-0.95 across all modules, and exceeded F1 scores obtained from comparable baseline programs. Next, the program was applied to a larger 14,481 abstract data set (2008-2017). Expected and previously identified patterns of species and model use for the field were obtained. As previously noted, the majority of studies reported promising outcomes. Longitudinal patterns of intervention type or gene mentions were demonstrated, and patterns of animal model use characteristic of the Parkinson's disease field were confirmed. The primary function of the program is to overcome low external validity of animal model systems by aggregating evidence across a diversity of models that capture different aspects of a multifaceted cellular process. Some aspects of the tool are generalizable, whereas others are field-specific. In the initial version presented here, we demonstrate proof of concept within a single disease area, Parkinson's disease. However, the program can be expanded in modular fashion to support a wider range of neurodegenerative diseases.}, } @article {pmid31846456, year = {2019}, author = {Mittler, JE and Murphy, JT and Stansfield, SE and Peebles, K and Gottlieb, GS and Abernethy, NF and Reid, MC and Goodreau, SM and Herbeck, JT}, title = {Large benefits to youth-focused HIV treatment-as-prevention efforts in generalized heterosexual populations: An agent-based simulation model.}, journal = {PLoS computational biology}, volume = {15}, number = {12}, pages = {e1007561}, pmid = {31846456}, issn = {1553-7358}, support = {R01 AI150467/AI/NIAID NIH HHS/United States ; R01 AI108490/AI/NIAID NIH HHS/United States ; R01 HD068395/HD/NICHD NIH HHS/United States ; R24 HD042828/HD/NICHD NIH HHS/United States ; R21 HD075662/HD/NICHD NIH HHS/United States ; }, mesh = {Adult ; Age Factors ; CD4 Lymphocyte Count ; Computational Biology ; Computer Simulation ; Epidemics/prevention & control ; Female ; HIV Infections/*drug therapy/epidemiology/*prevention & control ; HIV-1 ; Heterosexuality ; Humans ; Male ; Sex Factors ; Software ; Systems Analysis ; Young Adult ; }, abstract = {Predominantly heterosexual HIV-1 epidemics like those in sub-Saharan Africa continue to have high HIV incidence in young people. We used a stochastic, agent-based model for age-disparate networks to test the hypothesis that focusing uptake and retention of ART among youth could enhance the efficiency of treatment as prevention (TasP) campaigns. We used the model to identify strategies that reduce incidence to negligible levels (i.e., < 0.1 cases/100 person-years) 20-25 years after initiation of a targeted TasP campaign. The model was parameterized using behavioral, demographic, and clinical data from published papers and national reports. To keep a focus on the underlying age effects we model a generalized heterosexual population with average risks (i.e., no MSM, no PWIDs, no sex workers) and no entry of HIV+ people from other regions. The model assumes that most people (default 95%, range in variant simulations 60-95%) are "linkable"; i.e., could get linked to effective care given sufficient resources. To simplify the accounting, we assume a rapid jump in the number of people receiving treatment at the start of the TasP campaign, followed by a 2% annual increase that continues until all linkable HIV+ people have been treated. Under historical scenarios of CD4-based targeted ART allocation and current policies of untargeted (random) ART allocation, our model predicts that viral replication would need to be suppressed in 60-85% of infected people at the start of the TasP campaign to drive incidence to negligible levels. Under age-based strategies, by contrast, this percentage dropped by 18-54%, depending on the strength of the epidemic and the age target. For our baseline model, targeting those under age 30 halved the number of people who need to be treated. Age-based targeting also minimized total and time-discounted AIDS deaths over 25 years. Age-based targeting yielded benefits without being highly exclusive; in a model in which 60% of infected people were treated, ~87% and ~58% of those initiating therapy during a campaign targeting those <25 and <30 years, respectively, fell outside the target group. Sensitivity analyses revealed that youth-focused TasP is beneficial due to age-related risk factors (e.g. shorter relationship durations), and an age-specific herd immunity (ASHI) effect that protects uninfected adolescents entering the sexually active population. As testing rates increase in response to UNAIDS 90-90-90 goals, efforts to link all young people to care and treatment could contribute enormously to ending the HIV epidemic.}, } @article {pmid31841854, year = {2020}, author = {D'Amato, D and Gaio, M and Semenzin, E}, title = {A review of LCA assessments of forest-based bioeconomy products and processes under an ecosystem services perspective.}, journal = {The Science of the total environment}, volume = {706}, number = {}, pages = {135859}, doi = {10.1016/j.scitotenv.2019.135859}, pmid = {31841854}, issn = {1879-1026}, mesh = {Conservation of Natural Resources ; *Ecosystem ; Europe ; *Forests ; Humans ; North America ; }, abstract = {The emergence of politically driven bioeconomy strategies worldwide calls for considering the ecological issues associated with bio-based products. Traditionally, life cycle analysis (LCA) approaches are key tools used to assess impacts through product life cycles, but they present limitations regarding the accounting of multiple ecosystem service-related issues, at both the land-use and supply chain levels. Based on a systematic review of empirical articles, this study provides insights on using LCA assessments to account for ecosystem service-related impacts in the context of bioeconomy activities. We address the following research questions: what is the state of the art of the literature performing LCA assessments of forest-based bioeconomy activities, including the temporal distribution, the geographic areas and products/processes at study, and the approaches and methods used? 2. Which impacts and related midpoints are considered by the reviewed studies and what types of ecosystem service- related information do they bear? Out of over 600 articles found through the Scopus search, 155 were deemed relevant for the review. The literature focuses on North-America and Europe. Most of the articles assessed the environmental impact of lower-value biomass uses. Climate change was assessed in over 90% of the studies, while issues related to ozone, eutrophication, human toxicity, resource depletion, acidification, and environmental toxicity were assessed in 40% to 60% of the studies. While the impact categories accounted for in the reviewed LCA studies bear information relevant to certain provisioning and regulating services, several ecosystem services (especially cultural ones) remain unaccounted for. The implications of our study are relevant for professionals working in the ecosystem services, circular bioeconomy, and/or LCA communities.}, } @article {pmid31841568, year = {2019}, author = {Beentjes, KK and Speksnijder, AGCL and Schilthuizen, M and Hoogeveen, M and Pastoor, R and van der Hoorn, BB}, title = {Increased performance of DNA metabarcoding of macroinvertebrates by taxonomic sorting.}, journal = {PloS one}, volume = {14}, number = {12}, pages = {e0226527}, pmid = {31841568}, issn = {1932-6203}, mesh = {Animals ; Annelida/classification/genetics ; Aquatic Organisms/*classification/*genetics ; Biodiversity ; Biota/genetics ; Crustacea/classification/genetics ; DNA/analysis ; DNA Barcoding, Taxonomic/*methods ; Databases, Factual ; Ecological Parameter Monitoring/*methods ; Fresh Water/chemistry ; Invertebrates/*classification/*genetics ; Mollusca/classification/genetics ; Reproducibility of Results ; Water Quality/standards ; }, abstract = {DNA-based identification through the use of metabarcoding has been proposed as the next step in the monitoring of biological communities, such as those assessed under the Water Framework Directive (WFD). Advances have been made in the field of metabarcoding, but challenges remain when using complex samples. Uneven biomass distributions, preferential amplification and reference database deficiencies can all lead to discrepancies between morphological and DNA-based taxa lists. The effects of different taxonomic groups on these issues remain understudied. By metabarcoding WFD monitoring samples, we analyzed six different taxonomic groups of freshwater organisms, both separately and combined. Identifications based on metabarcoding data were compared directly to morphological assessments performed under the WFD. The diversity of taxa for both morphological and DNA-based assessments was similar, although large differences were observed in some samples. The overlap between the two taxon lists was 56.8% on average across all taxa, and was highest for Crustacea, Heteroptera, and Coleoptera, and lowest for Annelida and Mollusca. Taxonomic sorting in six basic groups before DNA extraction and amplification improved taxon recovery by 46.5%. The impact on ecological quality ratio (EQR) scoring was considerable when replacing morphology with DNA-based identifications, but there was a high correlation when only replacing a single taxonomic group with molecular data. Different taxonomic groups provide their own challenges and benefits. Some groups might benefit from a more consistent and robust method of identification. Others present difficulties in molecular processing, due to uneven biomass distributions, large genetic diversity or shortcomings of the reference database. Sorting samples into basic taxonomic groups that require little taxonomic knowledge greatly improves the recovery of taxa with metabarcoding. Current standards for EQR monitoring may not be easily replaced completely with molecular strategies, but the effectiveness of molecular methods opens up the way for a paradigm shift in biomonitoring.}, } @article {pmid31841140, year = {2020}, author = {Phillips, JG and Linscott, TM and Rankin, AM and Kraemer, AC and Shoobs, NF and Parent, CE}, title = {Archipelago-Wide Patterns of Colonization and Speciation Among an Endemic Radiation of Galápagos Land Snails.}, journal = {The Journal of heredity}, volume = {111}, number = {1}, pages = {92-102}, pmid = {31841140}, issn = {1465-7333}, support = {P30 GM103324/GM/NIGMS NIH HHS/United States ; }, mesh = {Animal Distribution ; Animals ; Biodiversity ; Chronology as Topic ; Datasets as Topic ; Ecosystem ; Ecuador ; *Genetic Speciation ; Phylogeny ; Phylogeography ; Sequence Analysis, DNA ; Snails/classification/*genetics ; }, abstract = {Newly arrived species on young or remote islands are likely to encounter less predation and competition than source populations on continental landmasses. The associated ecological release might facilitate divergence and speciation as colonizing lineages fill previously unoccupied niche space. Characterizing the sequence and timing of colonization on islands represents the first step in determining the relative contributions of geographical isolation and ecological factors in lineage diversification. Herein, we use genome-scale data to estimate timing of colonization in Naesiotus snails to the Galápagos islands from mainland South America. We test inter-island patterns of colonization and within-island radiations to understand their contribution to community assembly. Partly contradicting previously published topologies, phylogenetic reconstructions suggest that most Naesiotus species form island-specific clades, with within-island speciation dominating cladogenesis. Galápagos Naesiotus also adhere to the island progression rule, with colonization proceeding from old to young islands and within-island diversification occurring earlier on older islands. Our work provides a framework for evaluating the contribution of colonization and in situ speciation to the diversity of other Galápagos lineages.}, } @article {pmid31840099, year = {2019}, author = {Gui, C and Chen, J and Xie, Q and Mo, X and Zhang, S and Zhang, H and Ma, J and Li, Q and Gu, YC and Ju, J}, title = {CytA, a reductase in the cytorhodin biosynthesis pathway, inactivates anthracycline drugs in Streptomyces.}, journal = {Communications biology}, volume = {2}, number = {}, pages = {454}, pmid = {31840099}, issn = {2399-3642}, mesh = {Anthracyclines/chemistry/*metabolism ; Antibiotics, Antineoplastic/metabolism ; Biocatalysis ; *Biosynthetic Pathways ; Computational Biology/methods ; Gene Silencing ; Glycosylation ; Humans ; *Inactivation, Metabolic ; Molecular Structure ; Multigene Family ; Oxidoreductases/genetics/*metabolism ; Phylogeny ; Streptomyces/enzymology/*metabolism ; }, abstract = {Antibiotic-producing microorganism can develop strategies to deal with self-toxicity. Cytorhodins X and Y, cosmomycins A and B, and iremycin, are produced as final products from a marine-derived Streptomyces sp. SCSIO 1666. These C-7 reduced metabolites show reduced antimicrobial and comparable cytotoxic activities relative to their C-7 glycosylated counterparts. However, the biosynthetic mechanisms and relevant enzymes that drive C-7 reduction in cytorhodin biosynthesis have not yet been characterized. Here we report the discovery and characterization of a reductase, CytA, that mediates C-7 reduction of this anthracycline scaffold; CytA endows the producer Streptomyces sp. SCSIO 1666 with a means of protecting itself from the effects of its anthracycline products. Additionally, we identified cosmomycins C and D as two intermediates involved in cytorhodin biosynthesis and we also broadened the substrate specificity of CytA to clinically used anthracycline drugs.}, } @article {pmid31840098, year = {2019}, author = {Montesinos-Navarro, A and Díaz, G and Torres, P and Caravaca, F and Roldán, A}, title = {Phylogenetic rewiring in mycorrhizal-plant interaction networks increases community stability in naturally fragmented landscapes.}, journal = {Communications biology}, volume = {2}, number = {}, pages = {452}, pmid = {31840098}, issn = {2399-3642}, mesh = {Computational Biology/methods ; Ecosystem ; Microbiota ; Mycorrhizae/*classification/*genetics ; *Phylogeny ; Plants/*classification/*genetics ; Reproducibility of Results ; *Symbiosis ; }, abstract = {Although ecological networks are usually considered a static representation of species' interactions, the interactions can change when the preferred partners are absent (rewiring). In mutualistic networks, rewiring with non-preferred partners can palliate extinction cascades, contributing to communities' stability. In spite of its significance, whether general patterns can shape the rewiring of ecological interactions remains poorly understood. Here, we show a phylogenetic constraint in the rewiring of mycorrhizal networks, so that rewired interactions (i.e., with non-preferred hosts) tend to involve close relatives of preferred hosts. Despite this constraint, rewiring increases the robustness of the fungal community to the simulated loss of their host species. We identify preferred and non-preferred hosts based on the probability that, when the two partners co-occur, they actually interact. Understanding general patterns in the rewiring of interactions can improve our predictions of community responses to interactions' loss, which influences how global changes will affect ecosystem stability.}, } @article {pmid31836897, year = {2019}, author = {Bongaerts, P and Perez-Rosales, G and Radice, VZ and Eyal, G and Gori, A and Gress, E and Hammerman, NM and Hernandez-Agreda, A and Laverick, J and Muir, P and Pinheiro, H and Pyle, RL and Rocha, L and Turner, JA and Booker, R}, title = {Mesophotic.org: a repository for scientific information on mesophotic ecosystems.}, journal = {Database : the journal of biological databases and curation}, volume = {2019}, number = {}, pages = {}, pmid = {31836897}, issn = {1758-0463}, mesh = {*Databases, Factual ; *Ecosystem ; Geography ; Publications ; }, abstract = {Mesophotic coral ecosystems (MCEs) and temperate mesophotic ecosystems (TMEs) occur at depths of roughly 30-150 m depth and are characterized by the presence of photosynthetic organisms despite reduced light availability. Exploration of these ecosystems dates back several decades, but our knowledge remained extremely limited until about a decade ago, when a renewed interest resulted in the establishment of a rapidly growing research community. Here, we present the 'mesophotic.org' database, a comprehensive and curated repository of scientific literature on mesophotic ecosystems. Through both manually curated and automatically extracted metadata, the repository facilitates rapid retrieval of available information about particular topics (e.g. taxa or geographic regions), exploration of spatial/temporal trends in research and identification of knowledge gaps. The repository can be queried to comprehensively obtain available data to address large-scale questions and guide future research directions. Overall, the 'mesophotic.org' repository provides an independent and open-source platform for the ever-growing research community working on MCEs and TMEs to collate and expedite our understanding of the occurrence, composition and functioning of these ecosystems. Database URL: http://mesophotic.org/.}, } @article {pmid31836845, year = {2019}, author = {Smrke, T and Persic, M and Veberic, R and Sircelj, H and Jakopic, J}, title = {Influence of reflective foil on persimmon (Diospyros kaki Thunb.) fruit peel colour and selected bioactive compounds.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {19069}, pmid = {31836845}, issn = {2045-2322}, mesh = {Carotenoids/analysis ; Diospyros/*chemistry ; Fruit/*chemistry ; Light ; Phenols/analysis ; Phytochemicals/*analysis ; *Pigmentation ; Solubility ; }, abstract = {The purpose of this work was to investigate how to overcome the negative effect of anti-hail netting on the photosynthetic photon flux density (PPFD) in persimmon trees and persimmon fruit colour, flesh firmness, total soluble solids (TSS) and individual carotenoid and phenolic compound contents (determined via HPLC-MS) under a hail net with the use of reflective foil. Reflective foil increased the PPFD on the lower side of the fruits, while there was no significant difference on the upper side compared to those of the control group. The CIE colour parameters a* and h° indicated more intense red colouration of the fruits in the foil treatment than those in the control. Among carotenoids, the content of β-carotene increased, and the content of zeaxanthin decreased in fruits in the reflective foil treatment group, while the content of other carotenoids was not affected by the reflective foil. Among individual phenolic compounds in the persimmon peel, greater light intensity significantly influenced all three phenolic compound subgroups: phenolic acids, flavan-3-ols and flavonols. The content of gallic acid in the persimmon flesh increased the most, while other phenolics did not show any significant differences in concentrations between the foil and control groups. This study is the first to examine the influence of reflective foil on bioactive compounds in persimmon fruit. The use of reflective foil in persimmon orchards improves persimmon fruit colour and selected bioactive compound contents.}, } @article {pmid31836825, year = {2019}, author = {Roberts, TP and Kern, FB and Fernando, C and Szathmáry, E and Husbands, P and Philippides, AO and Staras, K}, title = {Encoding Temporal Regularities and Information Copying in Hippocampal Circuits.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {19036}, pmid = {31836825}, issn = {2045-2322}, support = {BB/K019015/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/S00310X/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; Hippocampus/*physiology ; Learning/physiology ; Microelectrodes ; Nerve Net/*physiology ; Periodicity ; Rats ; Time Factors ; }, abstract = {Discriminating, extracting and encoding temporal regularities is a critical requirement in the brain, relevant to sensory-motor processing and learning. However, the cellular mechanisms responsible remain enigmatic; for example, whether such abilities require specific, elaborately organized neural networks or arise from more fundamental, inherent properties of neurons. Here, using multi-electrode array technology, and focusing on interval learning, we demonstrate that sparse reconstituted rat hippocampal neural circuits are intrinsically capable of encoding and storing sub-second-order time intervals for over an hour timescale, represented in changes in the spatial-temporal architecture of firing relationships among populations of neurons. This learning is accompanied by increases in mutual information and transfer entropy, formal measures related to information storage and flow. Moreover, temporal relationships derived from previously trained circuits can act as templates for copying intervals into untrained networks, suggesting the possibility of circuit-to-circuit information transfer. Our findings illustrate that dynamic encoding and stable copying of temporal relationships are fundamental properties of simple in vitro networks, with general significance for understanding elemental principles of information processing, storage and replication.}, } @article {pmid31836780, year = {2019}, author = {Neyens, T and Diggle, PJ and Faes, C and Beenaerts, N and Artois, T and Giorgi, E}, title = {Mapping species richness using opportunistic samples: a case study on ground-floor bryophyte species richness in the Belgian province of Limburg.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {19122}, pmid = {31836780}, issn = {2045-2322}, mesh = {Belgium ; *Biodiversity ; Bryophyta/*genetics/*physiology ; Chromosome Mapping ; Data Collection ; Forests ; Genetic Variation ; Geography ; Models, Statistical ; Normal Distribution ; Observer Variation ; Poisson Distribution ; Proportional Hazards Models ; Species Specificity ; }, abstract = {In species richness studies, citizen-science surveys where participants make individual decisions regarding sampling strategies provide a cost-effective approach to collect a large amount of data. However, it is unclear to what extent the bias inherent to opportunistically collected samples may invalidate our inferences. Here, we compare spatial predictions of forest ground-floor bryophyte species richness in Limburg (Belgium), based on crowd- and expert-sourced data, where the latter are collected by adhering to a rigorous geographical randomisation and data collection protocol. We develop a log-Gaussian Cox process model to analyse the opportunistic sampling process of the crowd-sourced data and assess its sampling bias. We then fit two geostatistical Poisson models to both data-sets and compare the parameter estimates and species richness predictions. We find that the citizens had a higher propensity for locations that were close to their homes and environmentally more valuable. The estimated effects of ecological predictors and spatial species richness predictions differ strongly between the two geostatistical models. Unknown inconsistencies in the sampling process, such as unreported observer's effort, and the lack of a hypothesis-driven study protocol can lead to the occurrence of multiple sources of sampling bias, making it difficult, if not impossible, to provide reliable inferences.}, } @article {pmid31835796, year = {2019}, author = {Li, J and Zhang, J and Li, H and Niu, H and Xu, Q and Jiao, Z and An, J and Jiang, Y and Li, Q and Niu, J}, title = {The Major Factors Causing the Microspore Abortion of Genic Male Sterile Mutant NWMS1 in Wheat (Triticum aestivum L.).}, journal = {International journal of molecular sciences}, volume = {20}, number = {24}, pages = {}, pmid = {31835796}, issn = {1422-0067}, support = {NSFC, 31571646//the National Natural Science foundation of China/ ; No. 182102110147//the Science and Technology Project in Henan Province, China/ ; }, mesh = {Apoptosis/genetics ; Cluster Analysis ; Databases, Genetic ; Gene Expression Regulation, Plant ; Gene Library ; Gene Ontology ; Gene Regulatory Networks ; *Genes, Plant ; Mutation/*genetics ; Plant Infertility/*genetics ; Pollen/*genetics/ultrastructure ; Principal Component Analysis ; Transcriptome/genetics ; Triticum/*genetics/ultrastructure ; }, abstract = {Male sterility is a valuable trait for genetic research and production application of wheat (Triticum aestivum L.). NWMS1, a novel typical genic male sterility mutant, was obtained from Shengnong 1, mutagenized with ethyl methane sulfonate (EMS). Microstructure and ultrastructure observations of the anthers and microspores indicated that the pollen abortion of NWMS1 started at the early uninucleate microspore stage. Pollen grain collapse, plasmolysis, and absent starch grains were the three typical characteristics of the abnormal microspores. The anther transcriptomes of NWMS1 and its wild type Shengnong 1 were compared at the early anther development stage, pollen mother cell meiotic stage, and binucleate microspore stage. Several biological pathways clearly involved in abnormal anther development were identified, including protein processing in endoplasmic reticulum, starch and sucrose metabolism, lipid metabolism, and plant hormone signal transduction. There were 20 key genes involved in the abnormal anther development, screened out by weighted gene co-expression network analysis (WGCNA), including SKP1B, BIP5, KCS11, ADH3, BGLU6, and TIFY10B. The results indicated that the defect in starch and sucrose metabolism was the most important factor causing male sterility in NWMS1. Based on the experimental data, a primary molecular regulation model of abnormal anther and pollen developments in mutant NWMS1 was established. These results laid a solid foundation for further research on the molecular mechanism of wheat male sterility.}, } @article {pmid31835740, year = {2019}, author = {Truchado, DA and Diaz-Piqueras, JM and Gomez-Lucia, E and Doménech, A and Milá, B and Pérez-Tris, J and Schmidt-Chanasit, J and Cadar, D and Benítez, L}, title = {A Novel and Divergent Gyrovirus with Unusual Genomic Features Detected in Wild Passerine Birds from a Remote Rainforest in French Guiana.}, journal = {Viruses}, volume = {11}, number = {12}, pages = {}, pmid = {31835740}, issn = {1999-4915}, mesh = {Animals ; Birds/*virology ; Circoviridae Infections/*veterinary ; Computational Biology/methods ; French Guiana ; *Genome, Viral ; *Genomics/methods ; Gyrovirus/*classification/*genetics ; High-Throughput Nucleotide Sequencing ; Metagenomics ; Phylogeny ; Prevalence ; *Rainforest ; }, abstract = {Sequence-independent amplification techniques have become important tools for virus discovery, metagenomics, and exploration of viral diversity at the global scale, especially in remote areas. Here, we describe the detection and genetic characterization of a novel gyrovirus, named GyV11, present in cloacal, oral, and blood samples from neotropical wild birds in French Guiana. The molecular epidemiology revealed the presence of GyV11 only in passerine birds from three different species at a low prevalence (0.73%). This is the first characterization and prevalence study of a gyrovirus carried out in resident wild bird populations in a remote region, and provides evidence of the fecal-oral route transmission and local circulation of the virus. The molecular phylogeny of gyroviruses reveals the existence of two distinct gyrovirus lineages in which GyV11 is phylogenetically distinct from previously reported gyroviruses. Furthermore, GyV11 is placed basal in the gyrovirus phylogeny, likely owing to its ancestral origin and marked divergence. This study also provides important insights into the ecology, epidemiology, and genomic features of gyroviruses in a remote neotropical rainforest. The pathogenesis of this virus in avian species or whether GyV11 can infect humans and/or chickens needs to be further investigated.}, } @article {pmid31835443, year = {2019}, author = {Kelemen, M and Polishchuk, V and Gavurová, B and Szabo, S and Rozenberg, R and Gera, M and Kozuba, J and Andoga, R and Divoková, A and Blišťan, P}, title = {Correction: Fuzzy Model for Quantitative Assessment of Environmental Start-up Projects in Air Transport.}, journal = {International journal of environmental research and public health}, volume = {16}, number = {24}, pages = {}, pmid = {31835443}, issn = {1660-4601}, abstract = {The authors wish to add the following data corrections to the coauthors listed, because of the updated data for their paper published in the International Journal of Environmental Research and Public Health [...].}, } @article {pmid31834896, year = {2019}, author = {Mair, C and Nickbakhsh, S and Reeve, R and McMenamin, J and Reynolds, A and Gunson, RN and Murcia, PR and Matthews, L}, title = {Estimation of temporal covariances in pathogen dynamics using Bayesian multivariate autoregressive models.}, journal = {PLoS computational biology}, volume = {15}, number = {12}, pages = {e1007492}, pmid = {31834896}, issn = {1553-7358}, support = {MR/S004815/1/MRC_/Medical Research Council/United Kingdom ; BB/L018926/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/M003949/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/L004070/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/R012679/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; MR/R00241X/1/MRC_/Medical Research Council/United Kingdom ; MC_UU_12014/9/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Animals ; Bayes Theorem ; Computational Biology ; Computer Simulation ; Host Microbial Interactions ; *Host-Pathogen Interactions ; Humans ; *Models, Biological ; Multivariate Analysis ; Public Health Informatics ; Respiratory Tract Infections/epidemiology ; Spatio-Temporal Analysis ; Time Factors ; Virus Diseases/epidemiology ; }, abstract = {It is well recognised that animal and plant pathogens form complex ecological communities of interacting organisms within their hosts, and there is growing interest in the health implications of such pathogen interactions. Although community ecology approaches have been used to identify pathogen interactions at the within-host scale, methodologies enabling robust identification of interactions from population-scale data such as that available from health authorities are lacking. To address this gap, we developed a statistical framework that jointly identifies interactions between multiple viruses from contemporaneous non-stationary infection time series. Our conceptual approach is derived from a Bayesian multivariate disease mapping framework. Importantly, our approach captures within- and between-year dependencies in infection risk while controlling for confounding factors such as seasonality, demographics and infection frequencies, allowing genuine pathogen interactions to be distinguished from simple correlations. We validated our framework using a broad range of synthetic data. We then applied it to diagnostic data available for five respiratory viruses co-circulating in a major urban population between 2005 and 2013: adenovirus, human coronavirus, human metapneumovirus, influenza B virus and respiratory syncytial virus. We found positive and negative covariances indicative of epidemiological interactions among specific virus pairs. This statistical framework enables a community ecology perspective to be applied to infectious disease epidemiology with important utility for public health planning and preparedness.}, } @article {pmid31833700, year = {2019}, author = {Yang, AM and Zhu, L and Chen, SH and Jin, H and Xia, XX}, title = {[Geo-informatic spectrum analysis of land use change in the Manas River Basin, China during 1975-2015.].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {30}, number = {11}, pages = {3863-3874}, doi = {10.13287/j.1001-9332.201911.017}, pmid = {31833700}, issn = {1001-9332}, mesh = {China ; Cities ; *Conservation of Natural Resources ; *Rivers ; Spectrum Analysis ; }, abstract = {Geo-informatic spectrum analysis method was used to understand the complex geogra-phical phenomena concisely in graphic language. It is important for the integration research on spatial pattern and temporal process of land use change over multiple temporal and space scales. Based on remote sensing images in 1975, 1990, 1995, 2000, 2005, 2010 and 2015, we built the geo-spectrum of land use/cover change (LUCC) and quantitatively analyzed both the process and rend of LUCC in Manas River Basin. Results showed that the range of land use change in this basin was gradually decreasing, and land use structure tended to be simplistic, then tended to stable in later stage during 1975-1990. At the same period, the area of grassland increased greatly, which was mainly derived from unused land. The area of cultivated land expanded from 1990 to 2015, which mainly converted from unused land, forestland, and grassland. The geo-spectrum of land use change model showed that prophase change type, anaphase change type and continuous change type accounted for 1.3% of the total basin area. The overall characteristics of geo-spectrum unit were dominated by unused land converted to cultivated land, forestland and grassland. The land use change process was relatively stable. The Manas River Basin was covered 61.2% by region with comparatively stable spatial pattern. The most frequent way of land use change was increasingly expanding of cultivated land, which was displayed as: Liumaowan Bay Town of Shawan County and Liuhudi Town of Manas County were the center, then expanded to the two sides and spread to the Gurbantunggut Desert. The construct geo-spectrum of LUCC enriched the LUCC spatial-temporal analysis method system and provided an effective approach for the future research of LUCC under multiple temporal and spatial scales.}, } @article {pmid31833578, year = {2020}, author = {Arvonen, M and Vänni, P and Sarangi, AN and V Tejesvi, M and Vähäsalo, P and Aggarwal, A and Stoll, ML}, title = {Microbial orchestra in juvenile idiopathic arthritis: Sounds of disarray?.}, journal = {Immunological reviews}, volume = {294}, number = {1}, pages = {9-26}, doi = {10.1111/imr.12826}, pmid = {31833578}, issn = {1600-065X}, mesh = {Anti-Bacterial Agents/adverse effects ; Arthritis, Juvenile/immunology/*microbiology ; Child ; Diet ; Dysbiosis/*immunology ; Environmental Exposure/adverse effects ; Humans ; Infant, Newborn ; Microbiota/*immunology ; Risk ; }, abstract = {The role of the microbiota in multiple autoimmune diseases, including juvenile idiopathic arthritis (JIA) has earned substantial attention in the last 10 years. Increasing evidence suggests that the microbiota's link to JIA begins in early childhood, as early life events that influence the nature of the microbiota also appear to influence disease risk. In this review, we discuss these early life events including mode of delivery, infant feeding practice, antibiotics exposure, and other events and their impacts on the microbiota and on disease risk; reported abnormalities of the microbiota in children with JIA; mechanisms by which an altered microbiota at birth and later on in childhood may influence disease risk; and the prospects for therapeutic alteration of the microbiota in children with JIA.}, } @article {pmid31833467, year = {2020}, author = {Kache, PA and Eastwood, G and Collins-Palmer, K and Katz, M and Falco, RC and Bajwa, WI and Armstrong, PM and Andreadis, TG and Diuk-Wasser, MA}, title = {Environmental Determinants of Aedes albopictus Abundance at a Northern Limit of Its Range in the United States.}, journal = {The American journal of tropical medicine and hygiene}, volume = {102}, number = {2}, pages = {436-447}, pmid = {31833467}, issn = {1476-1645}, support = {U01 CK000509/CK/NCEZID CDC HHS/United States ; }, mesh = {Adaptation, Physiological ; Aedes/*physiology ; *Animal Distribution ; Animals ; Connecticut ; Databases, Factual ; *Environment ; New York ; Population Density ; }, abstract = {Aedes albopictus is a vector of arboviruses with high rates of morbidity and mortality. The northern limit of Ae. albopictus in the northeastern United States runs through New York state (NYS) and Connecticut. We present a landscape-level analysis of mosquito abundance measured by daily counts of Ae. albopictus from 338 trap sites in 12 counties during May-September 2017. During the study period, the mean number of Ae. albopictus caught per day of trapping across all sites was 3.21. We constructed four sets of negative binomial generalized linear models to evaluate how trapping methodology, land cover, as well as temperature and precipitation at multiple time intervals influenced Ae. albopictus abundance. Biogents-Sentinel (BGS) traps were 2.78 times as efficient as gravid traps and 1.49 times as efficient as CO2-baited CDC light traps. Greater proportions of low- and medium-intensity development and low proportions of deciduous cover around the trap site were positively associated with increased abundance, as were minimum winter temperature and March precipitation. The cumulative precipitation within a 28-day time window before the date of collection had a nonlinear relationship with abundance, such that greater cumulative precipitation was associated with increased abundance until approximately 70 mm, above which there was a decrease in abundance. We concluded that populations are established in Nassau, Suffolk, and New York City counties in NYS; north of these counties, the species is undergoing population invasion and establishment. We recommend that mosquito surveillance programs monitoring the northward invasion of Ae. albopictus place BGS traps at sites chosen with respect to land cover.}, } @article {pmid31826160, year = {2019}, author = {Sousa, GJB and Garces, TS and Pereira, MLD and Moreira, TMM and Silveira, GMD}, title = {Temporal pattern of tuberculosis cure, mortality, and treatment abandonment in Brazilian capitals.}, journal = {Revista latino-americana de enfermagem}, volume = {27}, number = {}, pages = {e3218}, pmid = {31826160}, issn = {1518-8345}, mesh = {Brazil/epidemiology ; Disease Notification ; Female ; Humans ; Information Systems ; Male ; Residence Characteristics ; Sex Factors ; Time Factors ; Treatment Refusal/*statistics & numerical data ; Tuberculosis/*drug therapy/*mortality ; }, abstract = {OBJECTIVE: to analyze the temporal pattern of tuberculosis cure, mortality, treatment abandonment in Brazilian capitals.

METHOD: this is an ecological study whose data source was the Information System of Notifiable Diseases for Tuberculosis (Sistema de Informação de Agravos de Notificação para Tuberculose). For analysis of temporal evolution, regressions by join points were performed considering the annual percentage variation and the significance of the trend change with 95% confidence interval.

RESULTS: 542,656 cases of tuberculosis were found, with emphasis on a 3% decrease per year in the cure rate for Campo Grande (interval: -5.0 - -0.9) and a 3.5% increase for Rio de Janeiro (interval: 1.9 - 4.7). Regarding abandonment, it decreased 10.9% per year in Rio Branco (interval: -15.8 - -5.7) and increased 12.8% per year in Fortaleza (interval: 7.6 - 18.3). For mortality, a decreasing or stationary tendency was identified, with a greater decrease (7.8%) for Porto Velho (interval:-11.0 - -5.0) and a lower one (2.5%) in Porto Alegre (interval:-4.5 - -0.6).

CONCLUSION: the rates of cure and abandonment are far from the ones recommended by the World Health Organization, showing that Brazilian capitals need interventions aimed at changing this pattern.}, } @article {pmid31826111, year = {2019}, author = {Rodrigues, OMM and Tauil, PL}, title = {Clinical and epidemiological aspects of tuberculosis in the Federal District (Brazil, 2006 to 2015).}, journal = {Revista brasileira de epidemiologia = Brazilian journal of epidemiology}, volume = {22}, number = {}, pages = {e190055}, doi = {10.1590/1980-549720190055}, pmid = {31826111}, issn = {1980-5497}, mesh = {Adolescent ; Adult ; Alcoholism/epidemiology ; Brazil/epidemiology ; Child ; Child, Preschool ; Comorbidity ; Diabetes Mellitus/epidemiology ; Disease Notification ; Epidemiologic Studies ; Female ; Humans ; Incidence ; Infant ; Infant, Newborn ; Information Systems ; Male ; Middle Aged ; Residence Characteristics ; Socioeconomic Factors ; Substance-Related Disorders/epidemiology ; Time Factors ; Tobacco Use Disorder/epidemiology ; Tuberculosis/*mortality ; Young Adult ; }, abstract = {INTRODUCTION: Despite the low incidence rates of tuberculosis (TB) in the Federal District (FD), there are socioeconomic discrepancies allied to intense population growth in recent years, which demonstrates the need to study the trend of the disease in different regions of the FD.

OBJECTIVE: To describe the trend of morbidity and mortality due to TB in the FD from 2006 to 2015.

METHODS: Ecological study, with descriptive and analytical components, historical series type.

RESULTS: There was a decreasing trend in incidence rates (IR) (from 15.1 per 100,000 inhabitants to 11.7 per 100,000 inhabitants, r = -0.50) and in the cure rate (from 86.0% to 74.7, r = -0.91); people experiencing homelessness and incarceration have relative risks from 5 to 16 times higher than the general population; higher IR were found in Paranoá (27.5 per 100,000 inhabitants) and in Estrutural (17.3 per 100,000 inhabitants), areas with poor socioeconomic indicators and demografic explosion during the study period. A higher mean lethality rate was found in Águas Claras (8.5%) and in Lago Sul (7.0%), regions that have a high concentration of homeless and elderly people.

CONCLUSION: TB persists as an important public health problem in the FD, especially in impoverished areas, with significant population growth or a high concentration of elderly or vulnerable populations.}, } @article {pmid31826109, year = {2019}, author = {Menezes, RAM and Pavanitto, DR and Nascimento, LFC}, title = {Spatial distribution of hospitalization rates of children due to pneumonia in the Unified Health System, in the municipalities of the state of São Paulo.}, journal = {Revista brasileira de epidemiologia = Brazilian journal of epidemiology}, volume = {22}, number = {}, pages = {e190053}, doi = {10.1590/1980-549720190053}, pmid = {31826109}, issn = {1980-5497}, mesh = {Brazil/epidemiology ; Child ; Educational Status ; Geographic Information Systems ; Geographic Mapping ; Hospitalization/*statistics & numerical data ; Humans ; Infant ; Infant Mortality ; National Health Programs ; Pneumonia/*mortality ; Residence Characteristics ; *Spatial Analysis ; }, abstract = {OBJECTIVE: To identify spatial patterns in the distribution of hospitalization rates of children with pneumonia in the state of São Paulo, Brazil from 2009 to 2013.

METHODS: This was an exploratory ecological study with data obtained from DATASUS of hospitalizations of children with pneumonia in the municipalities in São Paulo from 2009 to 2013/ Data on maternal education and family income were obtained and rates per thousand children were calculated and inserted in a database of municipalities obtained from IBGE. Thematic, kernel and Moran maps were constructed for the hospitalization rates and the Moran indices were calculated. The TerraView program was used for spatial analysis.

RESULTS: A total of 43,809 children were hospitalized in the study period, with a minimum of zero and a maximum of 69,072. The mean rate per municipality was 11.51 ± 8.62 (SD). The Moran index was 0.21 (p = 0.01). The thematic map showed clusters in the northern, northwestern, midwestern and southwestern regions of the state; the kernel map showed a higher density of rates in the northwestern and midwestern areas, and the Moran map identified 39 municipalities that deserve the attention of municipal and regional managers.

CONCLUSIONS: Geoprocessing identifies regions with higher hospitalization rates for pneumonia and also municipalities that deserve a high intervention priority.}, } @article {pmid31825983, year = {2019}, author = {Xu, M and Cohen, JE}, title = {Analyzing and interpreting spatial and temporal variability of the United States county population distributions using Taylor's law.}, journal = {PloS one}, volume = {14}, number = {12}, pages = {e0226096}, pmid = {31825983}, issn = {1932-6203}, mesh = {Databases, Factual ; Demography ; Ecological and Environmental Phenomena ; Humans ; *Models, Biological ; *Population Density ; Spatio-Temporal Analysis ; United States ; }, abstract = {We study the spatial and temporal variation of the human population in the United States (US) counties from 1790 to 2010, using an ecological scaling pattern called Taylor's law (TL). TL states that the variance of population abundance is a power function of the mean population abundance. Despite extensive studies of TL for non-human populations, testing and interpreting TL using data on human populations are rare. Here we examine three types of TL that quantify the spatial and temporal variation of US county population abundance. Our results show that TL and its quadratic extension describe the mean-variance relationship of county population distribution well. The slope and statistics of TL reveal economic and demographic trends of the county populations. We propose TL as a useful statistical tool for analyzing human population variability. We suggest new ways of using TL to select and make population projections.}, } @article {pmid31824210, year = {2019}, author = {Baker, E and Dupont, S and Smith, VS}, title = {Ecological interactions in the Scratchpads virtual research environment.}, journal = {Biodiversity data journal}, volume = {7}, number = {}, pages = {e47043}, pmid = {31824210}, issn = {1314-2828}, abstract = {BACKGROUND: The Natural History Museum, London has a number of online databases that describe interactions between species, including the HOSTS database of lepidopteran host plants (Robinson et al. 2010) and a database of Dipterocarp Seed Predators. These databases were generally bespoke software, which has increased the technical work necessary to sustain these resources. The decision was taken to migrate these to either the Scratchpads Virtual Research Environment (VRE) (Smith et al. 2011) or to the museum's Data Portal (Scott et al. 2019), depending on the complexity of the existing resource, as both are being sustained by the Informatics Group at the Natural History Museum, London. Resources that can be best represented as a single table were moved to the Data Portal, while those best represented in a relational model were transferred to Scratchpads. In addition, the Phthiraptera.info Scratchpad (Smith and Broom 2019), which already contained ecological interaction data, was migrated to the new system.

NEW INFORMATION: This paper describes the implementation within the Scratchpads VRE of a new ecological interactions module that is capable of handling the needs of these projects, while at the same time is flexible to handle the needs of future projects with different data sources.}, } @article {pmid31823785, year = {2019}, author = {Dadipoor, S and Kok, G and Aghamolaei, T and Ghaffari, M and Heyrani, A and Ghanbarnezhad, A}, title = {Explaining the determinants of hookah consumption among women in southern Iran: a qualitative study.}, journal = {BMC public health}, volume = {19}, number = {1}, pages = {1655}, pmid = {31823785}, issn = {1471-2458}, support = {970266//Hormozgan University of Medical Sciences/ ; }, mesh = {Adolescent ; Adult ; Aged ; Female ; Humans ; Iran/epidemiology ; Middle Aged ; Prevalence ; Qualitative Research ; Risk Factors ; Smoking Water Pipes ; Water Pipe Smoking/*epidemiology ; Young Adult ; }, abstract = {BACKGROUND: The prevalence of hookah consumption has been on the increase in Iran over the past two decades. This rate is higher among women than men in the south of Iran than other geographical areas. The purpose of this study was to explain the determinants of hookah consumption among indigenous women of Bandar Abbas city, southern Iran.

METHODS: This is the first qualitative study with the conventional content analysis approach that has examined the factors affecting the consumption of hookah at all ecological levels in 2018-2019. Participants, with a maximum variation in terms of age, education, occupation, hookah consumption and geographical areas of the city, were selected purposefully to take part in a semi-structured interview. The data were recorded, typed and analyzed according to the framework of the ecological model of health promotion at five levels (intrapersonal, interpersonal, organizational, social and political). The interview continued until data saturation. MAXQDA software version 10 was used for data management.

RESULTS: Interviews were conducted with 56 participants (21 female hookah smokers, 15 female ex- smokers, and 20 experienced experts). A total of eight main categories were extracted from the data including; positive attitude towards hookah consumption, psychosocial needs, sensory charms of hookah, individual factors, family factors, cultural-environmental backgrounds, social-political backgrounds, and economic challenges.

CONCLUSIONS: The results indicated the extensive influence of internal and external factors on the consumption of hookah. In order to successfully reduce the consumption of hookah, it is essential to consider intrapersonal, interpersonal, organizational, social and political factors.}, } @article {pmid31821153, year = {2019}, author = {Ferreri, F and Bourla, A and Peretti, CS and Segawa, T and Jaafari, N and Mouchabac, S}, title = {How New Technologies Can Improve Prediction, Assessment, and Intervention in Obsessive-Compulsive Disorder (e-OCD): Review.}, journal = {JMIR mental health}, volume = {6}, number = {12}, pages = {e11643}, pmid = {31821153}, issn = {2368-7959}, abstract = {BACKGROUND: New technologies are set to profoundly change the way we understand and manage psychiatric disorders, including obsessive-compulsive disorder (OCD). Developments in imaging and biomarkers, along with medical informatics, may well allow for better assessments and interventions in the future. Recent advances in the concept of digital phenotype, which involves using computerized measurement tools to capture the characteristics of a given psychiatric disorder, is one paradigmatic example.

OBJECTIVE: The impact of new technologies on health professionals' practice in OCD care remains to be determined. Recent developments could disrupt not just their clinical practices, but also their beliefs, ethics, and representations, even going so far as to question their professional culture. This study aimed to conduct an extensive review of new technologies in OCD.

METHODS: We conducted the review by looking for titles in the PubMed database up to December 2017 that contained the following terms: [Obsessive] AND [Smartphone] OR [phone] OR [Internet] OR [Device] OR [Wearable] OR [Mobile] OR [Machine learning] OR [Artificial] OR [Biofeedback] OR [Neurofeedback] OR [Momentary] OR [Computerized] OR [Heart rate variability] OR [actigraphy] OR [actimetry] OR [digital] OR [virtual reality] OR [Tele] OR [video].

RESULTS: We analyzed 364 articles, of which 62 were included. Our review was divided into 3 parts: prediction, assessment (including diagnosis, screening, and monitoring), and intervention.

CONCLUSIONS: The review showed that the place of connected objects, machine learning, and remote monitoring has yet to be defined in OCD. Smartphone assessment apps and the Web Screening Questionnaire demonstrated good sensitivity and adequate specificity for detecting OCD symptoms when compared with a full-length structured clinical interview. The ecological momentary assessment procedure may also represent a worthy addition to the current suite of assessment tools. In the field of intervention, CBT supported by smartphone, internet, or computer may not be more effective than that delivered by a qualified practitioner, but it is easy to use, well accepted by patients, reproducible, and cost-effective. Finally, new technologies are enabling the development of new therapies, including biofeedback and virtual reality, which focus on the learning of coping skills. For them to be used, these tools must be properly explained and tailored to individual physician and patient profiles.}, } @article {pmid31819990, year = {2019}, author = {Groom, Q and Dillen, M and Hardy, H and Phillips, S and Willemse, L and Wu, Z}, title = {Improved standardization of transcribed digital specimen data.}, journal = {Database : the journal of biological databases and curation}, volume = {2019}, number = {}, pages = {}, pmid = {31819990}, issn = {1758-0463}, mesh = {*Data Curation ; Databases, Factual/*standards ; Geography ; Museums ; Reference Standards ; Software ; Terminology as Topic ; }, abstract = {There are more than 1.2 billion biological specimens in the world's museums and herbaria. These objects are particularly important forms of biological sample and observation. They underpin biological taxonomy but the data they contain have many other uses in the biological and environmental sciences. Nevertheless, from their conception they are almost entirely documented on paper, either as labels attached to the specimens or in catalogues linked with catalogue numbers. In order to make the best use of these data and to improve the findability of these specimens, these data must be transcribed digitally and made to conform to standards, so that these data are also interoperable and reusable. Through various digitization projects, the authors have experimented with transcription by volunteers, expert technicians, scientists, commercial transcription services and automated systems. We have also been consumers of specimen data for taxonomical, biogeographical and ecological research. In this paper, we draw from our experiences to make specific recommendations to improve transcription data. The paper is split into two sections. We first address issues related to database implementation with relevance to data transcription, namely versioning, annotation, unknown and incomplete data and issues related to language. We then focus on particular data types that are relevant to biological collection specimens, namely nomenclature, dates, geography, collector numbers and uniquely identifying people. We make recommendations to standards organizations, software developers, data scientists and transcribers to improve these data with the specific aim of improving interoperability between collection datasets.}, } @article {pmid31819027, year = {2019}, author = {Hebbar, P and Ravikanth, G and Aravind, NA}, title = {A review on the conservation genetic studies of Indian amphibians and their implications on developing strategies for conservation.}, journal = {Journal of genetics}, volume = {98}, number = {}, pages = {}, pmid = {31819027}, issn = {0973-7731}, mesh = {Amphibians/classification/*genetics ; Animals ; Biodiversity ; *Conservation of Natural Resources ; Databases, Factual ; Genetic Markers ; Genetic Variation ; India ; Phylogeography ; Population Density ; }, abstract = {Amphibians show a very high level of diversity and endemism and are facing global declines from the past few decades. Studies have shown that the molecular tools can be helpful in their conservation efforts. In India, more than 80% of amphibians are endemic and most show a narrow range of distribution. Most of the Indian amphibians lack information on their genetic diversity. In this study, were view the overall trend on amphibian studies in India with the specific focus on conservation genetics. Overall, of the 173 studies, only 14 dealt with the conservation of amphibians through genetic tools and five studies estimated the genetic diversity or gene structure. Here, we discuss the gaps and provide future directions on how genetic studies can be helpful in Indian amphibian conservation.}, } @article {pmid31817465, year = {2019}, author = {Zeng, S and Ma, J and Ren, Y and Liu, GJ and Zhang, Q and Chen, F}, title = {Assessing the Spatial Distribution of Soil PAHs and their Relationship with Anthropogenic Activities at a National Scale.}, journal = {International journal of environmental research and public health}, volume = {16}, number = {24}, pages = {}, pmid = {31817465}, issn = {1660-4601}, mesh = {China ; Coal Mining ; Environmental Monitoring/*methods ; Polycyclic Aromatic Hydrocarbons/*analysis ; Principal Component Analysis ; Risk Assessment ; Soil ; Soil Pollutants/*analysis ; Vehicle Emissions/analysis ; }, abstract = {Soil polycyclic aromatic hydrocarbon (PAH) pollution is a major concern due to its negative impact on soil quality around the world. In China, accurate data on soil PAHs and information on the relationship with anthropogenic activities are limited. In this study, about 30,800 samples from 1833 soil sample sites were reviewed from 306 published reports to build a soil PAHs database. Based on the data obtained, the results demonstrated that 24.11% of surface soils in China are heavily contaminated. Meanwhile, the concentration of soil PAHs varied, in the order of independent mining and industrial areas (IMIA) > urban areas > suburban areas > rural areas, and the spatial distribution in China demonstrated a descending trend from north to south. Moreover, the characteristic ratio and PCA-MLR (principal component analysis-multiple linear regression) analysis demonstrated that coal combustion and vehicular exhaust emissions were the main sources of soil PAH pollution in China. On the other hand, provincial total Σ16PAHs in surface soil were significantly correlated with the per square kilometer GDP (gross domestic product) of industrial land, the per capita GDP, as well as the production and consumption of energy. These results indicate that anthropogenic factors have greatly affected the levels of soil PAHs in China. This study improves our understanding on the status and sources of soil PAH contamination in China, thereby facilitating the implementation of strategies of prevention, control, and remediation of soils.}, } @article {pmid31817220, year = {2019}, author = {Luo, Z and Ma, J and Chen, F and Li, X and Hou, H and Zhang, S}, title = {Cracks Reinforce the Interactions among Soil Bacterial Communities in the Coal Mining Area of Loess Plateau, China.}, journal = {International journal of environmental research and public health}, volume = {16}, number = {24}, pages = {}, pmid = {31817220}, issn = {1660-4601}, mesh = {Bacteria/*isolation & purification ; China ; *Coal Mining ; *Microbiota ; Soil/*chemistry ; *Soil Microbiology ; }, abstract = {Soil microorganisms play a key role in global biogeochemical changes. To understand the interactions among soil bacterial communities and their responses to extreme environments, the soil properties and bacterial community diversity were determined in the post-mining ecosystem of the Loess Plateau, China. The results showed that the soil temperature, pH, organic matter, available phosphorus, and available potassium values were significantly reduced in the post-mining cracks area. However, the richness and uniformity of soil bacterial communities increased by about 50% in the post-mining cracks area. Soil microbial community structure and the network interactions tended to be complex and strengthened in the post-mining cracks area. Moreover, soil nutrient loss caused the differences in soil bacterial community structure compositions in the post-mining cracks area. Furthermore, the relationships between soil physicochemical properties and different modules of the soil bacterial molecular ecological network were changed in a complex manner in the post-mining cracks area. This study provides a theoretical basis for adaptive management and response to cracks in post-mining areas and under other extreme conditions.}, } @article {pmid31810341, year = {2019}, author = {Polishchuk, V and Kelemen, M and Gavurová, B and Varotsos, C and Andoga, R and Gera, M and Christodoulakis, J and Soušek, R and Kozuba, J and Blišťan, P and Szabo, S}, title = {Correction: A Fuzzy Model of Risk Assessment for Environmental Start-Up Projects in the Air Transport Sector. Int. J. Environ. Res. Public Health 2019, 16, 3753.}, journal = {International journal of environmental research and public health}, volume = {16}, number = {23}, pages = {}, pmid = {31810341}, issn = {1660-4601}, abstract = {The authors wish to make the following correction to their paper [...].}, } @article {pmid31808113, year = {2020}, author = {Klatt, S and Ford, PR and Smeeton, NJ}, title = {Attentional and perceptual asymmetries in an immersive decision-making task.}, journal = {Attention, perception & psychophysics}, volume = {82}, number = {4}, pages = {1847-1857}, doi = {10.3758/s13414-019-01935-w}, pmid = {31808113}, issn = {1943-393X}, mesh = {Adult ; Attention/*physiology ; Decision Making/*physiology ; Female ; Functional Laterality/physiology ; Humans ; Male ; Photic Stimulation/methods ; Psychomotor Performance/*physiology ; Recognition, Psychology/physiology ; Soccer/*physiology/*psychology ; Space Perception/*physiology ; Virtual Reality ; Visual Fields/physiology ; Young Adult ; }, abstract = {Pseudoneglect represents the tendency in healthy people to show a slight bias in favour of stimuli appearing in the left visual field. Some studies have shown that this leftward bias can be annulled or reserved towards a rightward bisection bias when lateral attentional biases are assessed in far space. Using an immersive simulated, ecologically valid football task, we investigated whether possible attentional and perceptual asymmetries affect sport-specific decision making. Twenty-seven sport athletes were required to judge different game situations, which involved both perceptual and attentional skills to perceive player configurations in the visual periphery. We did not find any performance differences in accuracy rate between the left and right visual field side for stimuli presented close to the screen centre in an object-detection (perception-based) and feature-recognition (attention-based) task. This result is in line with previous findings showing an absence of a left- or rightward bisection bias in far space. However, accuracy was higher for stimuli being presented at visual angles wide away from the screen centre at the left side compared to the right side of visual field. This finding cannot be explained by literature focusing on pseudoneglect in far space, but rather by previous findings on landmark judgments often showing left bias both in near and in far space. Overall, the current findings provide new perspectives on attentional and perceptual asymmetries in real-world scenarios, and different interpretations of results are discussed.}, } @article {pmid31806560, year = {2020}, author = {DeAngelis, DL}, title = {Mathematical ecologists describe apparently long-stable dynamics that undergo sudden change to a different regime: Comment on "Long transients in ecology: theory and applications by Andrew Morozov et al.".}, journal = {Physics of life reviews}, volume = {32}, number = {}, pages = {44-45}, doi = {10.1016/j.plrev.2019.11.010}, pmid = {31806560}, issn = {1873-1457}, mesh = {Databases, Genetic ; *Ecology ; *Ecosystem ; Humans ; Mathematics ; }, } @article {pmid31804613, year = {2020}, author = {Handel, A and La Gruta, NL and Thomas, PG}, title = {Simulation modelling for immunologists.}, journal = {Nature reviews. Immunology}, volume = {20}, number = {3}, pages = {186-195}, pmid = {31804613}, issn = {1474-1741}, mesh = {Allergy and Immunology ; Computer Simulation ; Humans ; Immunity/*immunology ; Models, Immunological ; }, abstract = {The immune system is inordinately complex with many interacting components determining overall outcomes. Mathematical and computational modelling provides a useful way in which the various contributions of different immunological components can be probed in an integrated manner. Here, we provide an introductory overview and review of mechanistic simulation models. We start out by briefly defining these types of models and contrasting them to other model types that are relevant to the field of immunology. We follow with a few specific examples and then review the different ways one can use such models to answer immunological questions. While our examples focus on immune responses to infection, the overall ideas and descriptions of model uses can be applied to any area of immunology.}, } @article {pmid31800787, year = {2019}, author = {Amann, VR and Santos, LPD and Gigante, DP}, title = {[Association of excess weight and obesity and mortality in Brazilian state capitals and Argentine provinces].}, journal = {Cadernos de saude publica}, volume = {35}, number = {12}, pages = {e00192518}, doi = {10.1590/0102-311X00192518}, pmid = {31800787}, issn = {1678-4464}, mesh = {Adolescent ; Adult ; Argentina/epidemiology ; Body Mass Index ; Brazil/epidemiology ; Female ; Humans ; Male ; Obesity/*mortality ; Overweight/*mortality ; Prevalence ; Risk Factors ; Urban Population ; Weight Gain ; }, abstract = {This study aimed to assess the association between prevalence of excess weight and obesity and overall and disease-specific mortality rates in Brazilian state capitals and Argentine provinces. This was an ecological study with secondary data, where the principal exposures were prevalence rates for excess weight and obesity, estimated with data from Brazil's Vigitel survey (Risk and Protective Factors Surveillance System for Chronic Non-Communicable Diseases Through Telephone Interveiew) in 2014 and Argentina's National Risk Factor Survey in 2013. Overall and specific mortality rates for the year 2015 were obtained from the Brazilian Mortality Information System in the Brazilian Health Informatics Department and the Division of Health Statistics and Information of the Argentine Ministry of Health. Brazilian mortality rates were standardized with the age structure of the Argentine population as the standard. Crude and adjusted linear regressions were used to assess the association between the prevalence rates for excess weight and obesity and the overall and specific mortality rates. After adjusting for potential confounding factors, prevalence of obesity was positively associated with the overall mortality rate both in Brazil (β = 0.18; 95%CI: 0.01; 0.35) and in Argentina (β = 0.06; 95%CI: 0.01; 0.13). There was no association with the specific cardiovascular and cancer mortality rates. We conclude that the Brazilian state capitals and Argentine provinces with the highest prevalence of obesity present higher overall mortality rates, while this association was inconsistent for the specific rates.}, } @article {pmid31800778, year = {2019}, author = {Borges, LF and Souza, ER and Ribeiro, AP and Silva, GWDS and Silva, CMFPD and Santos, JD and Meira, KC}, title = {[Male homicides in two regions of Brazil: analysis of the effect of age, period, and cohort].}, journal = {Cadernos de saude publica}, volume = {35}, number = {12}, pages = {e00008719}, doi = {10.1590/0102-311X00008719}, pmid = {31800778}, issn = {1678-4464}, mesh = {Adolescent ; Adult ; Age Factors ; Aged ; Brazil/epidemiology ; Cohort Effect ; Cohort Studies ; Homicide/*statistics & numerical data ; Humans ; Male ; Middle Aged ; Mortality ; Residence Characteristics ; Risk Factors ; Young Adult ; }, abstract = {The objective was to assess the effect of age, period, and birth cohort on the time trend in mortality from homicides in men in the states of the Northeast and Southeast regions of Brazil from 1980 to 2014. This was an ecological time trend study. PCA models were estimated using estimable functions in inference of the parameters. Mortality and population data were obtained from the Brazilian Health Informatics Department. State-by-state mortality rates from homicide were standardized by the direct method, with the world population as the standard, as proposed by the World Health Organization. The Northeast region recorded 317,711 deaths from homicides and the Southeast 544,640 deaths, corresponding, respectively, corresponding to mean standardized rates of 58.68 and 64.68 deaths per 100,000 men. The highest mean standardized mortality rates were observed in the states of Alagoas (157.74 deaths) and Pernambuco (109.58 deaths). All the states showed an increase in mortality up to the third decade of life, with a progressive reduction in the other age brackets. There was an upward trend in all the states of the Northeast and in Minas Gerais and Espírito Santo in the Southeast, while in the other states there was a downward trend. All the states showed an increase in the risk of death in the younger age brackets, except for the state of São Paulo, which showed the inverse profile. The current study's findings may correlate with the process of discontinuity in the cohort, in which members of wide cohorts found less opportunity for access to employment, income, and education, thus increasing the risk of involvement in crime and death from homicide.}, } @article {pmid31799397, year = {2019}, author = {Stévart, T and Dauby, G and Lowry, PP and Blach-Overgaard, A and Droissart, V and Harris, DJ and Mackinder, BA and Schatz, GE and Sonké, B and Sosef, MSM and Svenning, JC and Wieringa, JJ and Couvreur, TLP}, title = {A third of the tropical African flora is potentially threatened with extinction.}, journal = {Science advances}, volume = {5}, number = {11}, pages = {eaax9444}, pmid = {31799397}, issn = {2375-2548}, mesh = {Africa ; Biodiversity ; Conservation of Natural Resources/methods ; Databases, Factual ; *Endangered Species ; *Extinction, Biological ; Plants ; }, abstract = {Preserving tropical biodiversity is an urgent challenge when faced with the growing needs of countries. Despite their crucial importance for terrestrial ecosystems, most tropical plant species lack extinction risk assessments, limiting our ability to identify conservation priorities. Using a novel approach aligned with IUCN Red List criteria, we conducted a continental-scale preliminary conservation assessment of 22,036 vascular plant species in tropical Africa. Our results underline the high level of extinction risk of the tropical African flora. Thirty-three percent of the species are potentially threatened with extinction, and another third of species are likely rare, potentially becoming threatened in the near future. Four regions are highlighted with a high proportion (>40%) of potentially threatened species: Ethiopia, West Africa, central Tanzania, and southern Democratic Republic of the Congo. Our approach represents a first step toward data-driven conservation assessments applicable at continental scales providing crucial information for sustainable economic development prioritization.}, } @article {pmid31796765, year = {2019}, author = {Romanuk, TN and Binzer, A and Loeuille, N and Carscallen, WMA and Martinez, ND}, title = {Simulated evolution assembles more realistic food webs with more functionally similar species than invasion.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {18242}, pmid = {31796765}, issn = {2045-2322}, abstract = {While natural communities are assembled by both ecological and evolutionary processes, ecological assembly processes have been studied much more and are rarely compared with evolutionary assembly processes. We address these disparities here by comparing community food webs assembled by simulating introductions of species from regional pools of species and from speciation events. Compared to introductions of trophically dissimilar species assumed to be more typical of invasions, introducing species trophically similar to native species assumed to be more typical of sympatric or parapatric speciation events caused fewer extinctions and assembled more empirically realistic networks by introducing more persistent species with higher trophic generality, vulnerability, and enduring similarity to native species. Such events also increased niche overlap and the persistence of both native and introduced species. Contrary to much competition theory, these findings suggest that evolutionary and other processes that more tightly pack ecological niches contribute more to ecosystem structure and function than previously thought.}, } @article {pmid31795456, year = {2019}, author = {Guo, S and Wang, Y}, title = {Ecological Security Assessment Based on Ecological Footprint Approach in Hulunbeir Grassland, China.}, journal = {International journal of environmental research and public health}, volume = {16}, number = {23}, pages = {}, pmid = {31795456}, issn = {1660-4601}, mesh = {China ; Conservation of Natural Resources/methods ; *Grassland ; Industry ; Models, Theoretical ; *Natural Resources ; *Security Measures ; }, abstract = {Hulunbeir grassland, as a crucial ecological barrier and energy supply base in northwest China, suffers from a fragile ecological environment. Therefore, it is crucially important for Hulunbeir grassland to achieve the sustainable development of its social economies and ecological environments through the evaluation of its ecological security. This paper introduces the indexes of the ecological pressure index (EPI), ecological footprint diversity index (EFDI), and ecological coordination coefficient (ECC) based on the ecological footprint model. Furthermore, the Stochastic Impacts by Regression on Population, Affluence, and Technology (STIRPAT) model was applied to analyze the main driving factors of the change of the ecological footprint. The results showed that: The ecological footprint (EF) per capita of Hulunbeir grassland has nearly doubled in 11 years to 11.04 ha/cap in 2016, while the ecological capacity (EC) per capita was rather low and increased slowly, leading to a continuous increase of per capita ecological deficit (ED) (from 5.7113 ha/cap to 11.0937 ha/cap). Within this, the footprint of fossil energy land and grassland contributed the most to the total EF, and forestland and cropland played the major role in EC. The EPI increased from 0.82 in 2006 to 1.25 in 2016, leading the level of ecological security to increase from level 3 (moderately safe) to level 4 (moderately risky). The indexes of the EFDI and ECC both reached a minimum in 2014 and then began to rise, indicating that Hulunbeir steppe's ecological environment, as well as its coordination with economy, was considered to be worse in 2014 but then gradually ameliorated. The STIRPAT model indicated that the main factors driving the EF increase were per capita GDP and the proportion of secondary industry, while the decrease of unit GDP energy consumption played an effective role in curbing the continuous growth of the EF. These findings not only have realistic significance in promoting the coordinated development between economy and natural resource utilization under the constraint of fragile environment, but also provide a scientific reference for similar energy-rich ecologically fragile regions.}, } @article {pmid31791702, year = {2020}, author = {Grebogi, C}, title = {Sudden regime shifts after apparent stasis: Comment on "Long transients in ecology: Theory and applications" by Andrew Morozov et al.}, journal = {Physics of life reviews}, volume = {32}, number = {}, pages = {41-43}, doi = {10.1016/j.plrev.2019.11.009}, pmid = {31791702}, issn = {1873-1457}, mesh = {Databases, Genetic ; *Ecology ; *Ecosystem ; Humans ; }, } @article {pmid31790462, year = {2019}, author = {Larson, JH and Vallazza, JM and Knights, BC}, title = {Estimating the degree to which distance and temperature differences drive changes in fish community composition over time in the upper Mississippi River.}, journal = {PloS one}, volume = {14}, number = {12}, pages = {e0225630}, pmid = {31790462}, issn = {1932-6203}, mesh = {*Animal Migration ; Animals ; *Biota ; Datasets as Topic ; Ecological Parameter Monitoring/*statistics & numerical data ; *Fishes ; Mississippi ; Rivers ; *Temperature ; }, abstract = {Similarity in community composition declines as distance between locations increases, a phenomenon that has been observed in a wide variety of freshwater, marine and terrestrial ecosystems. One driver of the distance-similarity relationship is the presence of environmental gradients that alter the suitability of sites for particular species. Although some environmental gradients, such as geology, do not change on a year-to-year basis, others, such as temperature, vary annually and over longer time periods. Here, we used a 21-year dataset of fish communities in the upper Mississippi River to examine the effect of distance on variation in community composition and to assess whether the effect of distance is primarily due to its effect on thermal regime. Because the Mississippi River is aligned mostly north-to-south, larger distances along the river roughly correspond to larger differences in latitude and therefore thermal regime. As expected, there was a moderate distance-similarity relationship, suggesting greater distance leads to less similarity. The effect of distance appeared to increase slightly over time. Using a subset of data for which air temperature was available, we compared models that incorporated both difference among sites in degree days (a surrogate for thermal regime) and physical distance (river km). Although physical distance presumably incorporates more environmental gradients than just temperature (and other potential mechanisms), temperature alone appears to be more strongly associated with differences in the Mississippi River fish community than distance.}, } @article {pmid31790384, year = {2019}, author = {Barta, T and Kostal, L}, title = {The effect of inhibition on rate code efficiency indicators.}, journal = {PLoS computational biology}, volume = {15}, number = {12}, pages = {e1007545}, pmid = {31790384}, issn = {1553-7358}, mesh = {Action Potentials/physiology ; Adenosine Triphosphate/metabolism ; Animals ; Computational Biology ; Computer Simulation ; Excitatory Postsynaptic Potentials/physiology ; Membrane Potentials/physiology ; *Models, Neurological ; Neural Conduction/physiology ; Neural Inhibition/physiology ; Neurons/*physiology ; Signal-To-Noise Ratio ; Synaptic Transmission/physiology ; }, abstract = {In this paper we investigate the rate coding capabilities of neurons whose input signal are alterations of the base state of balanced inhibitory and excitatory synaptic currents. We consider different regimes of excitation-inhibition relationship and an established conductance-based leaky integrator model with adaptive threshold and parameter sets recreating biologically relevant spiking regimes. We find that given mean post-synaptic firing rate, counter-intuitively, increased ratio of inhibition to excitation generally leads to higher signal to noise ratio (SNR). On the other hand, the inhibitory input significantly reduces the dynamic coding range of the neuron. We quantify the joint effect of SNR and dynamic coding range by computing the metabolic efficiency-the maximal amount of information per one ATP molecule expended (in bits/ATP). Moreover, by calculating the metabolic efficiency we are able to predict the shapes of the post-synaptic firing rate histograms that may be tested on experimental data. Likewise, optimal stimulus input distributions are predicted, however, we show that the optimum can essentially be reached with a broad range of input distributions. Finally, we examine which parameters of the used neuronal model are the most important for the metabolically efficient information transfer.}, } @article {pmid31784436, year = {2019}, author = {Lucas-Thompson, R and Seiter, N and Broderick, PC and Coatsworth, JD and Henry, KL and McKernan, CJ and Smyth, JM}, title = {Moving 2 Mindful (M2M) study protocol: testing a mindfulness group plus ecological momentary intervention to decrease stress and anxiety in adolescents from high-conflict homes with a mixed-method longitudinal design.}, journal = {BMJ open}, volume = {9}, number = {11}, pages = {e030948}, pmid = {31784436}, issn = {2044-6055}, support = {K01 AT009592/AT/NCCIH NIH HHS/United States ; }, mesh = {Adolescent ; Anxiety/*therapy ; Family Conflict/*psychology ; Female ; Humans ; Longitudinal Studies ; Male ; Mindfulness/*methods ; Parents/psychology ; Randomized Controlled Trials as Topic ; Reminder Systems ; Stress, Psychological/*therapy ; Text Messaging ; }, abstract = {INTRODUCTION: Interparental conflict exposure places adolescents at risk for problems with stress and anxiety; existing prevention/intervention strategies focus on reducing interparental conflict. Mindfulness-based programmes may be a promising treatment strategy for this population, but studies have not yet tested whether they are effective in this high-conflict context. In addition, evidence suggests that extensions to traditional treatments, such as delivering components in daily life that are tailored to moments of need, can increase treatment efficacy, particularly when combined with in-person treatments and particularly for adolescents. However, there are no such extensions to mindfulness interventions available. The Moving 2 Mindful study aims to (1) develop an ecological momentary intervention (EMI) supplement to Learning to BREATHE (L2B), an evidence-based mindfulness intervention for adolescents; (2) refine the EMI programme and determine the best delivery plan; (3) examine the feasibility and acceptability of L2B Plus (L2B plus the developed supplement) and (4) examine the potential for L2B Plus to reduce stress and anxiety for adolescents from high-conflict homes.

METHODS AND ANALYSIS: The Moving 2 Mindful study proposes a mixed-methods approach to developing and refining a multimethod adaptive supplement to L2B. Feasibility, acceptability and potential effectiveness will be tested in a sample of 38 families, who will be randomly assigned to receive L2B Plus or an active health and wellness control condition and followed until 3 months postintervention. A range of psychosocial and physiological factors will be assessed at multiple time points. This study is registered with clinicaltrials.gov (ID NCT03869749; pre-results).

ETHICS AND DISSEMINATION: The Institutional Review Board at Colorado State University has approved this study. Findings will be disseminated in scientific journals and conferences, whether they are positive, negative or inconclusive.}, } @article {pmid31784331, year = {2020}, author = {Chaix, B}, title = {How daily environments and situations shape behaviors and health: Momentary studies of mobile sensing and smartphone survey data.}, journal = {Health & place}, volume = {61}, number = {}, pages = {102241}, doi = {10.1016/j.healthplace.2019.102241}, pmid = {31784331}, issn = {1873-2054}, mesh = {*Ecological Momentary Assessment ; Geographic Information Systems ; Humans ; *Mobile Applications ; *Smartphone ; }, } @article {pmid31783517, year = {2019}, author = {Gómez-Silva, B and Vilo-Muñoz, C and Galetović, A and Dong, Q and Castelán-Sánchez, HG and Pérez-Llano, Y and Sánchez-Carbente, MDR and Dávila-Ramos, S and Cortés-López, NG and Martínez-Ávila, L and Dobson, ADW and Batista-García, RA}, title = {Metagenomics of Atacama Lithobiontic Extremophile Life Unveils Highlights on Fungal Communities, Biogeochemical Cycles and Carbohydrate-Active Enzymes.}, journal = {Microorganisms}, volume = {7}, number = {12}, pages = {}, pmid = {31783517}, issn = {2076-2607}, support = {CeBiB FB-0001//Proyecto Basal CONICYT-Chile/ ; SI-5305//Universidad de Antofagasta/ ; Postgraduated fellowships//CONACyT-Mexico/ ; NIH-NCI P30 CA054174//Genome Sequencing Facility, UT Health San Antonio/ ; 1S10OD021805-01//NIH Shared Instrument Grant/ ; Number RP160732//CPRIT Core Facility Award/ ; }, abstract = {Halites, which are typically found in various Atacama locations, are evaporitic rocks that are considered as micro-scaled salterns. Both structural and functional metagenomic analyses of halite nodules were performed. Structural analyses indicated that the halite microbiota is mainly composed of NaCl-adapted microorganisms. In addition, halites appear to harbor a limited diversity of fungal families together with a biodiverse collection of protozoa. Functional analysis indicated that the halite microbiome possesses the capacity to make an extensive contribution to carbon, nitrogen, and sulfur cycles, but possess a limited capacity to fix nitrogen. The halite metagenome also contains a vast repertory of carbohydrate active enzymes (CAZY) with glycosyl transferases being the most abundant class present, followed by glycosyl hydrolases (GH). Amylases were also present in high abundance, with GH also being identified. Thus, the halite microbiota is a potential useful source of novel enzymes that could have biotechnological applicability. This is the first metagenomic report of fungi and protozoa as endolithobionts of halite nodules, as well as the first attempt to describe the repertoire of CAZY in this community. In addition, we present a comprehensive functional metagenomic analysis of the metabolic capacities of the halite microbiota, providing evidence for the first time on the sulfur cycle in Atacama halites.}, } @article {pmid31780345, year = {2020}, author = {Jongeneel, A and Aalbers, G and Bell, I and Fried, EI and Delespaul, P and Riper, H and van der Gaag, M and van den Berg, D}, title = {A time-series network approach to auditory verbal hallucinations: Examining dynamic interactions using experience sampling methodology.}, journal = {Schizophrenia research}, volume = {215}, number = {}, pages = {148-156}, doi = {10.1016/j.schres.2019.10.055}, pmid = {31780345}, issn = {1573-2509}, mesh = {Adult ; Affective Symptoms/*physiopathology ; Data Interpretation, Statistical ; Dissociative Disorders/*physiopathology ; Ecological Momentary Assessment ; Female ; Hallucinations/*physiopathology ; Humans ; Male ; Paranoid Disorders/*physiopathology ; Psychotic Disorders/*physiopathology ; Severity of Illness Index ; Speech Perception/*physiology ; Young Adult ; }, abstract = {BACKGROUND: Identifying variables that influence daily-life fluctuations in auditory verbal hallucinations (AVHs) provides insight into potential mechanisms and targets for intervention. Network analysis, that uses time-series data collected by Experience Sampling Method (ESM), could be used to examine relations between multiple variables over time.

METHODS: 95 daily voice-hearing individuals filled in a short questionnaire ten times a day for six consecutive days at pseudo-random moments. Using multilevel vector auto-regression, relations between voice-hearing and negative affect, positive affect, uncontrollable thoughts, dissociation, and paranoia were analysed in three types of networks: between-subjects (between persons, undirected), contemporaneous (within persons, undirected), and temporal (within persons, directed) networks. Strength centrality was measured to identify the most interconnected variables in the models.

RESULTS: Voice-hearing co-occurred with all variables, while on a 6-day period voice-hearing was only related to uncontrollable thoughts. Voice-hearing was not predicted by any of the factors, but it did predict uncontrollable thoughts and paranoia. All variables showed large autoregressions, i.e. mainly predicted themselves in this severe voice-hearing sample. Uncontrollable thoughts was the most interconnected factor, though relatively uninfluential.

DISCUSSION: Severe voice-hearing might be mainly related to mental state factors on the short-term. Once activated, voice-hearing appears to maintain itself. It is important to assess possible reactivity of AVH to triggers at the start of therapy; if reactive, therapy should focus on the triggering factor. If not reactive, Cognitive Behavioural interventions could be used first to reduce the negative effects of the voices. Limitations are discussed.}, } @article {pmid31777677, year = {2019}, author = {Yang, YS and Ryu, GW and Choi, M}, title = {Factors Associated with Daily Completion Rates in a Smartphone-Based Ecological Momentary Assessment Study.}, journal = {Healthcare informatics research}, volume = {25}, number = {4}, pages = {332-337}, pmid = {31777677}, issn = {2093-3681}, abstract = {OBJECTIVES: Ecological momentary assessment (EMA) methods are known to have validity for capturing momentary changes in variables over time. However, data quality relies on the completion rates, which are influenced by both participants' characteristics and study designs. This study applied an EMA method using a mobile application to assess momentary moods and stress levels in patients with Moyamoya disease to examine variables associated with EMA completion rates.

METHODS: Adults with Moyamoya disease were recruited from a tertiary hospital in Seoul. Patients with cognitive impairment were excluded. The EMA survey was loaded as a mobile application onto the participants' personal smartphones. Notifications were sent at semi-random intervals four times a day for seven consecutive days. Daily completion rates were calculated as the percentage of completed responses per day; overall completion rates were calculated as the proportion of completed responses per total of the 28 scheduled measures in the study and assessed through a descriptive analysis, t-test, ANOVA, and regression analysis, with mixed modeling to identify the point at which the daily completion rate significantly decreased.

RESULTS: A total of 98 participants responded (mean age, 41.00 ± 10.30 years; 69.4% female; 75.5% married). The overall completion rate was 70.66%, with no gender or age differences found. The daily completion rate decreased significantly after day 5 (p = 0.029).

CONCLUSIONS: Obtaining a good completion rate is essential for quality data in EMA methods. Strategic approaches to a study design should be established to encourage participants throughout a study to improve completion rates.}, } @article {pmid31776547, year = {2020}, author = {Wang, Y and LêCao, KA}, title = {Managing batch effects in microbiome data.}, journal = {Briefings in bioinformatics}, volume = {21}, number = {6}, pages = {1954-1970}, doi = {10.1093/bib/bbz105}, pmid = {31776547}, issn = {1477-4054}, mesh = {*Computational Biology ; Data Analysis ; *Microbiota ; }, abstract = {Microbial communities have been increasingly studied in recent years to investigate their role in ecological habitats. However, microbiome studies are difficult to reproduce or replicate as they may suffer from confounding factors that are unavoidable in practice and originate from biological, technical or computational sources. In this review, we define batch effects as unwanted variation introduced by confounding factors that are not related to any factors of interest. Computational and analytical methods are required to remove or account for batch effects. However, inherent microbiome data characteristics (e.g. sparse, compositional and multivariate) challenge the development and application of batch effect adjustment methods to either account or correct for batch effects. We present commonly encountered sources of batch effects that we illustrate in several case studies. We discuss the limitations of current methods, which often have assumptions that are not met due to the peculiarities of microbiome data. We provide practical guidelines for assessing the efficiency of the methods based on visual and numerical outputs and a thorough tutorial to reproduce the analyses conducted in this review.}, } @article {pmid31775812, year = {2019}, author = {Pieroni, A and Zahir, H and Amin, HIM and Sõukand, R}, title = {Where tulips and crocuses are popular food snacks: Kurdish traditional foraging reveals traces of mobile pastoralism in Southern Iraqi Kurdistan.}, journal = {Journal of ethnobiology and ethnomedicine}, volume = {15}, number = {1}, pages = {59}, pmid = {31775812}, issn = {1746-4269}, mesh = {Adult ; Aged ; *Crocus ; Ethnicity ; Ethnobotany ; Female ; Humans ; Iraq ; Male ; Middle Aged ; Plants, Edible/*classification ; Snacks ; *Tulipa ; }, abstract = {BACKGROUND: Iraqi Kurdistan is a special hotspot for bio-cultural diversity and for investigating patterns of traditional wild food plant foraging, considering that this area was the home of the first Neolithic communities and has been, over millennia, a crossroad of different civilizations and cultures. The aim of this ethnobotanical field study was to cross-culturally compare the wild food plants traditionally gathered by Kurdish Muslims and those gathered by the ancient Kurdish Kakai (Yarsan) religious group and to possibly better understand the human ecology behind these practices.

METHODS: Twelve villages were visited and 123 study participants (55 Kakai and 68 Muslim Kurds) were interviewed on the specific topic of the wild food plants they currently gather and consume.

RESULTS: The culinary use of 54 folk wild plant taxa (corresponding to 65 botanical taxa) and two folk wild mushroom taxa were documented. While Kakais and Muslims do share a majority of the quoted food plants and also their uses, among the plant ingredients exclusively and commonly quoted by Muslims non-weedy plants are slightly preponderant. Moreover, more than half of the overall recorded wild food plants are used raw as snacks, i.e. plant parts are consumed on the spot after their gathering and only sometimes do they enter into the domestic arena. Among them, it is worth mentioning the consumption of raw wild crocus corms, also still common in Turkish Kurdistan and that of wild tulip bulbs, which was documented to be popular until the beginning of the twentieth century in the Middle East. Comparison with other ethnobotanical field studies recently conducted among surrounding populations has shown that Kurds tend to gather and consume the largest number of non-weedy wild vegetables.

CONCLUSION: The collected data indicate robust traces of nomadic pastoralism in Kurdish traditional foraging. This finding confirms that studies on wild food plant gathering in the Fertile Crescent and Turco-Arabic-Iranic regions of the Middle East are crucial for understanding the possible evolution of wild food plant gathering through history within the post-Neolithic continuum between pastoralism and horticulturalism.}, } @article {pmid31773859, year = {2020}, author = {Poyarkov, AD and Munkhtsog, B and Korablev, MP and Kuksin, AN and Alexandrov, DY and Chistopolova, MD and Hernandez-Blanco, JA and Munkhtogtokh, O and Karnaukhov, AS and Lkhamsuren, N and Bayaraa, M and Jackson, RM and Maheshwari, A and Rozhnov, VV}, title = {Assurance of the existence of a trans-boundary population of the snow leopard (Panthera uncia) at Tsagaanshuvuut - Tsagan-Shibetu SPA at the Mongolia-Russia border.}, journal = {Integrative zoology}, volume = {15}, number = {3}, pages = {224-231}, doi = {10.1111/1749-4877.12420}, pmid = {31773859}, issn = {1749-4877}, mesh = {Animals ; *Conservation of Natural Resources ; Felidae/genetics/*physiology ; Female ; Genetic Variation ; Geographic Information Systems ; *Homing Behavior ; Mongolia ; Russia ; }, abstract = {The existence of a trans-boundary population of the snow leopard (Panthera uncia) that inhabits the massifs of Tsagaanshuvuut (Mongolia) - Tsagan-Shibetu (Russia) was determined through non-invasive genetic analysis of scat samples and by studying the structure of territory use by a collared female individual. The genetic analysis included species identification of samples through sequencing of a fragment of the cytochrome b gene and individual identification using a panel of 8 microsatellites. The home range of a female snow leopard marked with a satellite Global Positioning System (GPS) collar was represented by the minimum convex polygon method (MCP) 100, the MCP 95 method and the fixed kernel 95 method. The results revealed insignificant genetic differentiation between snow leopards that inhabit both massifs (minimal fixation index [FST ]), and the data testify to the unity of the cross-border group. Moreover, 5 common individuals were identified from Mongolian and Russian territories. This finding clearly shows that their home range includes territories of both countries. In addition, regular movement of a collared snow leopard in Mongolia and Russia confirmed the existence of a cross-border snow leopard group. These data support that trans-boundary conservation is important for snow leopards in both countries. We conclude that it is crucial for Russia to study the northern range of snow leopards in Asia.}, } @article {pmid31773207, year = {2020}, author = {Yang, Z and He, J and Wei, X and Ju, J and Ma, J}, title = {Exploration and genome mining of natural products from marine Streptomyces.}, journal = {Applied microbiology and biotechnology}, volume = {104}, number = {1}, pages = {67-76}, doi = {10.1007/s00253-019-10227-0}, pmid = {31773207}, issn = {1432-0614}, mesh = {Aquatic Organisms/genetics/metabolism ; Biological Products/*isolation & purification ; Biosynthetic Pathways ; Computational Biology ; *Genome, Bacterial ; Multigene Family ; *Secondary Metabolism ; Streptomyces/*genetics/*metabolism ; Whole Genome Sequencing ; }, abstract = {Marine Streptomyces sp. are an important source of bioactive compounds owing to their unique habitats and metabolic pathways. Whole-genome sequencing and bioinformatics analyses have shown that the potential of synthesizing secondary metabolites from marine-derived Streptomyces has been substantially underestimated. Genome mining is an integrated strategy used to discover natural products based on gene cluster sequences and biosynthetic pathways. Its emergence has greatly enhanced the discovery of natural compounds from marine Streptomyces, thereby yielding a large number of bioactive molecules with novel structures and potent activities. In this review, we briefly summarize the current applications of genome mining in marine Streptomyces, such as bioinformatics-based optimization of culture conditions, ribosome engineering, control of regulatory networks, heterologous expression of biosynthetic gene cluster, and combinatorial biosynthesis of natural compounds. Furthermore, we discuss the factors hindering the utilization of marine-derived natural products and conclude with the prospects for this technique.}, } @article {pmid31772182, year = {2019}, author = {Huebner, GM and Mahdavi, A}, title = {A structured open data collection on occupant behaviour in buildings.}, journal = {Scientific data}, volume = {6}, number = {1}, pages = {292}, pmid = {31772182}, issn = {2052-4463}, mesh = {*Conservation of Energy Resources ; *Consumer Behavior ; Datasets as Topic ; *Environment, Controlled ; Housing ; Information Dissemination ; Universities ; }, abstract = {Climate change cannot be addressed without improving the energy efficiency of the buildings in which we live and work. The papers in this collection describe and release a series of datasets that help us understand how occupants influence and experience building energy use, both to aid future research and policy-development, and to spark wider data sharing in this important area.}, } @article {pmid31763752, year = {2020}, author = {Zanne, AE and Abarenkov, K and Afkhami, ME and Aguilar-Trigueros, CA and Bates, S and Bhatnagar, JM and Busby, PE and Christian, N and Cornwell, WK and Crowther, TW and Flores-Moreno, H and Floudas, D and Gazis, R and Hibbett, D and Kennedy, P and Lindner, DL and Maynard, DS and Milo, AM and Nilsson, RH and Powell, J and Schildhauer, M and Schilling, J and Treseder, KK}, title = {Fungal functional ecology: bringing a trait-based approach to plant-associated fungi.}, journal = {Biological reviews of the Cambridge Philosophical Society}, volume = {95}, number = {2}, pages = {409-433}, doi = {10.1111/brv.12570}, pmid = {31763752}, issn = {1469-185X}, mesh = {Animals ; Databases, Factual ; Ecosystem ; Fungi/genetics/*physiology ; Plants/*microbiology ; }, abstract = {Fungi play many essential roles in ecosystems. They facilitate plant access to nutrients and water, serve as decay agents that cycle carbon and nutrients through the soil, water and atmosphere, and are major regulators of macro-organismal populations. Although technological advances are improving the detection and identification of fungi, there still exist key gaps in our ecological knowledge of this kingdom, especially related to function. Trait-based approaches have been instrumental in strengthening our understanding of plant functional ecology and, as such, provide excellent models for deepening our understanding of fungal functional ecology in ways that complement insights gained from traditional and -omics-based techniques. In this review, we synthesize current knowledge of fungal functional ecology, taxonomy and systematics and introduce a novel database of fungal functional traits (Fun[Fun]). Fun[Fun] is built to interface with other databases to explore and predict how fungal functional diversity varies by taxonomy, guild, and other evolutionary or ecological grouping variables. To highlight how a quantitative trait-based approach can provide new insights, we describe multiple targeted examples and end by suggesting next steps in the rapidly growing field of fungal functional ecology.}, } @article {pmid31758057, year = {2019}, author = {Sergio, F and Tavecchia, G and Tanferna, A and Blas, J and Blanco, G and Hiraldo, F}, title = {When and where mortality occurs throughout the annual cycle changes with age in a migratory bird: individual vs population implications.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {17352}, pmid = {31758057}, issn = {2045-2322}, mesh = {Africa, Western ; Age Factors ; Animal Migration/*physiology ; Animals ; Birds/*physiology ; Geographic Information Systems ; Geography ; Longevity/physiology ; Mauritania ; Morocco ; *Mortality ; Population Dynamics ; Raptors/physiology ; Reproduction/physiology ; *Seasons ; Spain ; Time Factors ; }, abstract = {The annual cycle of most animals is structured into discrete stages, such as breeding, migration and dispersal. While there is growing appreciation of the importance of different stages of an organism's annual cycle for its fitness and population dynamics, almost nothing is known about if and how such seasonal effects can change through a species lifespan. Here, we take advantage of the opportunity offered by a long-term satellite/GPS-tracking study and a reliable method of remote death-detection to show that certain stages of both the annual and life cycle of a migratory long-lived raptor, the Black kite Milvus migrans, may represent sensitive bottlenecks for survival. In particular, migratory journeys caused bursts of concentrated-mortality throughout life, but the relative importance of stage-specific survival changed with age. On the other hand, the balance between short-stages of high mortality and long-stages of low mortality made population-growth similarly dependent on all portions of the annual cycle. Our results illustrate how the population dynamics of migratory organisms can be inextricably linked to ecological pressures balanced over multiple stages of the annual cycle and thus multiple areas of the globe, suggesting the frequent need for challenging conservation strategies targeting all portions of a species year-round range.}, } @article {pmid31757998, year = {2019}, author = {Pilot, M and Moura, AE and Okhlopkov, IM and Mamaev, NV and Alagaili, AN and Mohammed, OB and Yavruyan, EG and Manaseryan, NH and Hayrapetyan, V and Kopaliani, N and Tsingarska, E and Krofel, M and Skoglund, P and Bogdanowicz, W}, title = {Global Phylogeographic and Admixture Patterns in Grey Wolves and Genetic Legacy of An Ancient Siberian Lineage.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {17328}, pmid = {31757998}, issn = {2045-2322}, mesh = {Animals ; Arctic Regions ; Databases, Genetic ; Evolution, Molecular ; Gene Flow ; Linkage Disequilibrium ; Phylogeny ; Phylogeography ; Siberia ; Whole Genome Sequencing/*veterinary ; Wolves/*classification/*genetics ; }, abstract = {The evolutionary relationships between extinct and extant lineages provide important insight into species' response to environmental change. The grey wolf is among the few Holarctic large carnivores that survived the Late Pleistocene megafaunal extinctions, responding to that period's profound environmental changes with loss of distinct lineages and phylogeographic shifts, and undergoing domestication. We reconstructed global genome-wide phylogeographic patterns in modern wolves, including previously underrepresented Siberian wolves, and assessed their evolutionary relationships with a previously genotyped wolf from Taimyr, Siberia, dated at 35 Kya. The inferred phylogeographic structure was affected by admixture with dogs, coyotes and golden jackals, stressing the importance of accounting for this process in phylogeographic studies. The Taimyr lineage was distinct from modern Siberian wolves and constituted a sister lineage of modern Eurasian wolves and domestic dogs, with an ambiguous position relative to North American wolves. We detected gene flow from the Taimyr lineage to Arctic dog breeds, but population clustering methods indicated closer similarity of the Taimyr wolf to modern wolves than dogs, implying complex post-divergence relationships among these lineages. Our study shows that introgression from ecologically diverse con-specific and con-generic populations was common in wolves' evolutionary history, and could have facilitated their adaptation to environmental change.}, } @article {pmid31757204, year = {2019}, author = {Patuzzi, I and Baruzzo, G and Losasso, C and Ricci, A and Di Camillo, B}, title = {metaSPARSim: a 16S rRNA gene sequencing count data simulator.}, journal = {BMC bioinformatics}, volume = {20}, number = {Suppl 9}, pages = {416}, pmid = {31757204}, issn = {1471-2105}, support = {-//Università degli Studi di Padova/ ; }, mesh = {Animals ; Computer Simulation ; DNA, Ribosomal/genetics ; Databases, Genetic ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Metagenome ; *Metagenomics ; RNA, Ribosomal, 16S/*genetics ; *Software ; }, abstract = {BACKGROUND: In the last few years, 16S rRNA gene sequencing (16S rDNA-seq) has seen a surprisingly rapid increase in election rate as a methodology to perform microbial community studies. Despite the considerable popularity of this technique, an exiguous number of specific tools are currently available for proper 16S rDNA-seq count data preprocessing and simulation. Indeed, the great majority of tools have been developed adapting methodologies previously used for bulk RNA-seq data, with poor assessment of their applicability in the metagenomics field. For such tools and the few ones specifically developed for 16S rDNA-seq data, performance assessment is challenging, mainly due to the complex nature of the data and the lack of realistic simulation models. In fact, to the best of our knowledge, no software thought for data simulation are available to directly obtain synthetic 16S rDNA-seq count tables that properly model heavy sparsity and compositionality typical of these data.

RESULTS: In this paper we present metaSPARSim, a sparse count matrix simulator intended for usage in development of 16S rDNA-seq metagenomic data processing pipelines. metaSPARSim implements a new generative process that models the sequencing process with a Multivariate Hypergeometric distribution in order to realistically simulate 16S rDNA-seq count table, resembling real experimental data compositionality and sparsity. It provides ready-to-use count matrices and comes with the possibility to reproduce different pre-coded scenarios and to estimate simulation parameters from real experimental data. The tool is made available at http://sysbiobig.dei.unipd.it/?q=Software#metaSPARSimand https://gitlab.com/sysbiobig/metasparsim.

CONCLUSION: metaSPARSim is able to generate count matrices resembling real 16S rDNA-seq data. The availability of count data simulators is extremely valuable both for methods developers, for which a ground truth for tools validation is needed, and for users who want to assess state of the art analysis tools for choosing the most accurate one. Thus, we believe that metaSPARSim is a valuable tool for researchers involved in developing, testing and using robust and reliable data analysis methods in the context of 16S rRNA gene sequencing.}, } @article {pmid31757073, year = {2019}, author = {Yssel, AEJ and Kao, SM and Van de Peer, Y and Sterck, L}, title = {ORCAE-AOCC: A Centralized Portal for the Annotation of African Orphan Crop Genomes.}, journal = {Genes}, volume = {10}, number = {12}, pages = {}, pmid = {31757073}, issn = {2073-4425}, mesh = {*Databases, Genetic ; *Genome, Plant ; *Molecular Sequence Annotation ; }, abstract = {ORCAE (Online Resource for Community Annotation of Eukaryotes) is a public genome annotation curation resource. ORCAE-AOCC is a branch that is dedicated to the genomes published as part of the African Orphan Crops Consortium (AOCC). The motivation behind the development of the ORCAE platform was to create a knowledge-based website where the research-community can make contributions to improve genome annotations. All changes to any given gene-model or gene description are stored, and the entire annotation history can be retrieved. Genomes can either be set to "public" or "restricted" mode; anonymous users can browse public genomes but cannot make any changes. Aside from providing a user-&nbsp;friendly interface to view genome annotations, the platform also includes tools and information (such as gene expression evidence) that enables authorized users to edit and validate genome annotations. The ORCAE-AOCC platform will enable various stakeholders from around the world to coordinate their efforts to annotate and study underutilized crops.}, } @article {pmid31756488, year = {2020}, author = {Zhu, KC and Liu, BS and Guo, HY and Zhang, N and Guo, L and Jiang, SG and Zhang, DC}, title = {Functional analysis of two MyoDs revealed their role in the activation of myomixer expression in yellowfin seabream (Acanthopagrus latus) (Hottuyn, 1782).}, journal = {International journal of biological macromolecules}, volume = {156}, number = {}, pages = {1081-1090}, doi = {10.1016/j.ijbiomac.2019.11.139}, pmid = {31756488}, issn = {1879-0003}, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Binding Sites ; Cloning, Molecular ; Computational Biology ; *Gene Expression Regulation ; Genes, Reporter ; MyoD Protein/*metabolism ; Organ Specificity ; Phylogeny ; Promoter Regions, Genetic ; Protein Binding ; Sea Bream/classification/*genetics/*metabolism ; Sequence Analysis, DNA ; Sequence Deletion ; }, abstract = {Myoblast determination protein (MyoD), a muscle-specific basic helix-loop-helix (bHLH) transcription factor, plays a pivotal role in regulating skeletal muscle growth and development. However, the regulation mechanism of MyoD has not been determined in marine fishes. In the present study, we isolated the MyoD1 (AlMyoD1) and MyoD2 (AlMyoD2) genomic sequences and analyzed the expression patterns in different tissues of yellowfin seabream (Acanthopagrus latus). The open reading frame (ORF) sequences of AlMyoD1 and AlMyoD2 encoded 297 and 271 amino acids possessing three common characteristic domains, respectively, containing a myogenic basic domain, a bHLH domain, and a ser-rich region (helix III). Phylogenetic and genome structure analyses exhibited classic phylogeny and highly conserved exon/intron architecture. Furthermore, the AlMyoD1 and AlMyoD2 transcription levels were higher in white muscle than in the other tissues. In order to further study AlMyoD function in muscle, promoter sequence analysis found that several E-box binding sites were present. Additionally, binding sites of Almyomixer involved in mammal myoblast fusion, which expression was also the highest in white muscle, were found in the promoter of AlMyoD. Pomoter activity assays further confirmed that both AlMyoD1 and AlMyoD2 can dramatically activate Almyomixer expression, and the AlMyoD1 M2 and AlMyoD2 M5 E-box binding sites were functionally important for Almyomixer transcription based on mutation analysis and electrophoretic mobile shift assays (EMSA). In summary, two MyoDs play a core role in Almyomixer regulation and may promote myofibre formation during muscle development and growth by regulating Almyomixer expression.}, } @article {pmid31754824, year = {2020}, author = {Gabashvili, E and Osepashvili, M and Koulouris, S and Ujmajuridze, L and Tskhitishvili, Z and Kotetishvili, M}, title = {Phage Transduction is Involved in the Intergeneric Spread of Antibiotic Resistance-Associated blaCTX-M, mel, and tetM Loci in Natural Populations of Some Human and Animal Bacterial Pathogens.}, journal = {Current microbiology}, volume = {77}, number = {2}, pages = {185-193}, pmid = {31754824}, issn = {1432-0991}, support = {PhDF2016_97//Shota Rustaveli National Science Foundation/ ; }, mesh = {Anti-Bacterial Agents/*pharmacology ; Bacteria/drug effects/*genetics/virology ; Bacteriophages/*genetics ; DNA, Intergenic ; Databases, Genetic ; Drug Resistance, Microbial/*genetics ; Gene Transfer, Horizontal ; Genes, Bacterial ; Genome, Viral ; *Transduction, Genetic ; beta-Lactamases/*genetics ; }, abstract = {The horizontal genetic transfer (HGT) of antibiotic resistance genes (ARGs) mediated by species-specific bacteriophages contributes to the emergence of antibiotic-resistant strains in natural populations of human and animal bacterial pathogens posing a significant threat to global public health. However, it is unclear and needs to be determined whether polyvalent bacteriophages play any role in the intergeneric transmission of ARGs. In this study, we examined the genome sequences of 2239 bacteriophages from different sources for the presence of ARGs. The identified ARG-carrying bacteriophages were then analyzed by PHACTS, PHAST, and HostPhinder programs to determine their lifestyles, genes coding for bacterial cell lysis, recombinases, and a spectrum of their potential host species, respectively. We employed the SplitsTree, RDP4 and SimPlot software packages in recombination tests to identify HGT events of ARGs between these bacteriophages and bacteria. In our analyses, some ARG-carrying bacteriophages exhibited temperate and/or polyvalent patterns. The bootstrap values (97-100) for the SplitsTree-generated parallelograms, fit values (97-100) for splits networks, Phi P values (< 10[-17] to 3.9 × 10[-16]), RDP4 P values (≤ 7.8 × 10[-03]), and the SimPlot results, provided strong statistical evidence for the phage transduction events of blaCTX-M, mel, and tetM loci on inter-species level. These events involved several host species such as Escherichia coli, Salmonella enterica, Shigella sonnei, Streptococcus pneumoniae and Bacillus coagulans. HGT of mel loci between Erysipelothrix and Streptococcus phages were also detected. These results firmly suggest that certain bacteriophages possibly with temperate properties induce the intergeneric dissemination of blaCTX-M, mel and tetM in the above species.}, } @article {pmid31754100, year = {2019}, author = {Saremi, NF and Supple, MA and Byrne, A and Cahill, JA and Coutinho, LL and Dalén, L and Figueiró, HV and Johnson, WE and Milne, HJ and O'Brien, SJ and O'Connell, B and Onorato, DP and Riley, SPD and Sikich, JA and Stahler, DR and Villela, PMS and Vollmers, C and Wayne, RK and Eizirik, E and Corbett-Detig, RB and Green, RE and Wilmers, CC and Shapiro, B}, title = {Author Correction: Puma genomes from North and South America provide insights into the genomic consequences of inbreeding.}, journal = {Nature communications}, volume = {10}, number = {1}, pages = {5276}, doi = {10.1038/s41467-019-13096-3}, pmid = {31754100}, issn = {2041-1723}, support = {T32 HG008345/HG/NHGRI NIH HHS/United States ; }, abstract = {An amendment to this paper has been published and can be accessed via a link at the top of the paper.}, } @article {pmid31754022, year = {2019}, author = {Li, H and Rukina, D and David, FPA and Li, TY and Oh, CM and Gao, AW and Katsyuba, E and Bou Sleiman, M and Komljenovic, A and Huang, Q and Williams, RW and Robinson-Rechavi, M and Schoonjans, K and Morgenthaler, S and Auwerx, J}, title = {Identifying gene function and module connections by the integration of multispecies expression compendia.}, journal = {Genome research}, volume = {29}, number = {12}, pages = {2034-2045}, pmid = {31754022}, issn = {1549-5469}, support = {R01 AG043930/AG/NIA NIH HHS/United States ; }, mesh = {Animals ; *Databases, Nucleic Acid ; *Gene Expression Profiling ; *Gene Expression Regulation, Fungal ; *Gene Regulatory Networks ; Humans ; Mice ; Rats ; Saccharomyces cerevisiae/*genetics ; *Software ; }, abstract = {The functions of many eukaryotic genes are still poorly understood. Here, we developed and validated a new method, termed GeneBridge, which is based on two linked approaches to impute gene function and bridge genes with biological processes. First, Gene-Module Association Determination (G-MAD) allows the annotation of gene function. Second, Module-Module Association Determination (M-MAD) allows predicting connectivity among modules. We applied the GeneBridge tools to large-scale multispecies expression compendia-1700 data sets with over 300,000 samples from human, mouse, rat, fly, worm, and yeast-collected in this study. G-MAD identifies novel functions of genes-for example, DDT in mitochondrial respiration and WDFY4 in T cell activation-and also suggests novel components for modules, such as for cholesterol biosynthesis. By applying G-MAD on data sets from respective tissues, tissue-specific functions of genes were identified-for instance, the roles of EHHADH in liver and kidney, as well as SLC6A1 in brain and liver. Using M-MAD, we identified a list of module-module associations, such as those between mitochondria and proteasome, mitochondria and histone demethylation, as well as ribosomes and lipid biosynthesis. The GeneBridge tools together with the expression compendia are available as an open resource, which will facilitate the identification of connections linking genes, modules, phenotypes, and diseases.}, } @article {pmid31753906, year = {2019}, author = {Fahlbusch, JA and Harrington, KJ}, title = {A low-cost, open-source inertial movement GPS logger for eco-physiology applications.}, journal = {The Journal of experimental biology}, volume = {222}, number = {Pt 23}, pages = {}, doi = {10.1242/jeb.211136}, pmid = {31753906}, issn = {1477-9145}, mesh = {Animals ; Birds/*physiology ; Ecology/*methods ; Geographic Information Systems/economics/*instrumentation ; *Movement ; Physiology/*methods ; }, abstract = {Open-source technology has been increasingly used for developing low-cost animal-borne bio-loggers; however, a gap remains for a bio-logger that records both inertial movement and GPS positions. We address this need with the Tapered Wings Logger (TWLogger), an archival bio-logger that records high-resolution (e.g. 50 Hz) tri-axial accelerometry and magnetometry, temperature and GPS. The TWLogger can be built for 90 USD, accepts user-defined sampling parameters, and with a 500 mA h battery weighs 25 g. We provide publicly available build instructions and custom analysis scripts. Bench tests recorded 50 Hz inertial movement and 2 min GPS for 31.8±2.2 h (mean±s.d., n=6) with GPS accuracy within 10.9±13.6 m. Field deployments on a medium-sized bird of prey in the wild achieved similar results (n=13). The customizable TWLogger has wide-ranging application across systems and thus offers a practical solution for eco-physiology applications.}, } @article {pmid31751348, year = {2019}, author = {Munyenyiwa, A and Zimba, M and Nhiwatiwa, T and Barson, M}, title = {Plague in Zimbabwe from 1974 to 2018: A review article.}, journal = {PLoS neglected tropical diseases}, volume = {13}, number = {11}, pages = {e0007761}, pmid = {31751348}, issn = {1935-2735}, mesh = {Africa, Southern/epidemiology ; Animals ; Cattle ; Databases, Factual ; *Disease Outbreaks ; Disease Reservoirs ; Disease Susceptibility ; Ecology ; History, 20th Century ; History, 21st Century ; Humans ; Plague/*epidemiology/history/*transmission ; Risk Factors ; Rodent Diseases/epidemiology/microbiology ; Rodentia ; Soil Microbiology ; Yersinia pestis/pathogenicity/*physiology ; Zimbabwe/epidemiology ; }, abstract = {Plague is a zoonotic disease caused by the bacterium Yersinia pestis and is transmitted through the bites of infected rodent fleas. Plague is well known for causing 3 major human pandemics that have killed millions of people since 541 A.D. The aim of this Review is to provide an overview of the epidemiology and ecology of plague in Zimbabwe with special emphasis on its introduction, its potential reservoirs and vectors, and possible causes of its persistence and cyclic outbreaks. To achieve this, we carried out a search and document reported plague outbreaks in Zimbabwe. In the country, human plague cases have been reported in Hwange, Nkayi, and Lupane since 1974. The highest number of cases occurred in 1994 in the Nkayi district of Matabeleland North Province with a total of 329 confirmed human cases and 28 deaths. Plague is encountered in 2 different foci in the country, sylvatic and rural. Risk factors for contracting plague in the country include man-to-rodent contact, cultivation, hunting, cattle herding, handling of infected materials, camping in forests, and anthropic invasion of new areas. Plague is now enzootic in Zimbabwe, and the most recent case was reported in 2012, hence its effective control requires up-to-date information on the epidemiology and ecology of the disease. This can be achieved through continuous monitoring and awareness programs in plague-prone areas.}, } @article {pmid31745111, year = {2019}, author = {Bystriakova, N and Alves De Melo, PH and Moat, J and Lughadha, EN and Monro, AK}, title = {A Preliminary Evaluation of The Karst Flora of Brazil Using Collections Data.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {17037}, pmid = {31745111}, issn = {2045-2322}, abstract = {Karst is defined as landscapes that are underlain by soluble rock in which there is appreciable water movement arising from a combination of high rock solubility and well-developed secondary (fracture) porosity. Karsts occupy approximately 20% of the planet's dry ice-free land and are of great socioeconomic importance, as they supply water to up to 25% of the world's population and represent landscapes of cultural and touristic importance. In Southeast Asia karst is associated with high species-richness and endemism in plants and seen as priority areas for the conservation of biodiversity. There has been little research into the floras associated with karst in South America, most of which occurs in Brazil. We therefore sought to evaluate the importance of Brazilian karst with respect to its species-richness and endemism. We sought to do so using curated plant specimen data in the Botanical Information and Ecology Network (BIEN) dataset. We show that, except for Amazonia, the BIEN dataset is representative of the Brazilian flora with respect to the total number of species and overall patterns of species richness. We found that karst is under-sampled, as is the case for much of Brazil. We also found that whilst karst represent an important source of plant diversity for Brazil, including populations of approximately 1/3 of the Brazilian flora, it is not significantly more species-rich or richer in small-range and endemic species than surrounding landscapes. Similarly, whilst important for conservation, comprising populations of 26.5-37.4% of all Brazilian species evaluated as of conservation concern by International Union for Nature Conservation (IUCN), karst is no more so than the surrounding areas. Whilst experimental error, including map resolution and the precision and accuracy of point data may have under-estimated the species-richness of Brazilian karst, it likely represents an important biodiversity resource for Brazil and one that can play a valuable role in conservation. Our findings are in sharp contrast to those for Southeast Asia where karst represents a more important source of species-richness and endemism. We also show that although BIEN represents a comprehensive and curated source of point data, discrepancies in the application of names compared to current more comprehensive taxonomic backbones, can have profound impacts on estimates of species-richness, distribution ranges and estimates of endemism.}, } @article {pmid31745083, year = {2019}, author = {Peters, KJ and Saltré, F and Friedrich, T and Jacobs, Z and Wood, R and McDowell, M and Ulm, S and Bradshaw, CJA}, title = {FosSahul 2.0, an updated database for the Late Quaternary fossil records of Sahul.}, journal = {Scientific data}, volume = {6}, number = {1}, pages = {272}, pmid = {31745083}, issn = {2052-4463}, mesh = {Animals ; Australia ; *Databases, Factual ; *Fossils ; *Vertebrates ; }, abstract = {The 2016 version of the FosSahul database compiled non-human vertebrate megafauna fossil ages from Sahul published up to 2013 in a standardized format. Its purpose was to create a publicly available, centralized, and comprehensive database for palaeoecological investigations of the continent. Such databases require regular updates and improvements to reflect recent scientific findings. Here we present an updated FosSahul (2.0) containing 11,871 dated non-human vertebrate fossil records from the Late Quaternary published up to 2018. Furthermore, we have extended the information captured in the database to include methodological details and have developed an algorithm to automate the quality-rating process. The algorithm makes the quality-rating more transparent and easier to reproduce, facilitating future database extensions and dissemination. FosSahul has already enabled several palaeoecological analyses, and its updated version will continue to provide a centralized organisation of Sahul's fossil records. As an example of an application of the database, we present the temporal pattern in megafauna genus richness inferred from available data in relation to palaeoclimate indices over the past 180,000 years.}, } @article {pmid31744914, year = {2019}, author = {Zhang, J and Silverstein, KAT and Castaño, JD and Figueroa, M and Schilling, JS}, title = {Gene Regulation Shifts Shed Light on Fungal Adaption in Plant Biomass Decomposers.}, journal = {mBio}, volume = {10}, number = {6}, pages = {}, pmid = {31744914}, issn = {2150-7511}, mesh = {*Adaptation, Biological ; Biodegradation, Environmental ; *Biomass ; Computational Biology/methods ; Fungal Proteins/*genetics ; Fungi/*genetics/*metabolism ; Gene Expression Profiling ; *Gene Expression Regulation, Fungal ; Hydrolysis ; Plants/metabolism/*microbiology ; Wood/chemistry/metabolism/microbiology ; }, abstract = {Fungi dominate the recycling of carbon sequestered in woody biomass. This process of organic turnover was first evolved among "white rot" fungi that degrade lignin to access carbohydrates and later evolved multiple times toward more efficient strategies to selectively target carbohydrates-"brown rot." The brown rot adaption was often explained by mechanisms to deploy reactive oxygen species (ROS) to oxidatively attack wood structures. However, its genetic basis remains unclear, especially in the context of gene contractions of conventional carbohydrate-active enzymes (CAZYs) relative to white rot ancestors. Here, we hypothesized that these apparent gains in brown rot efficiency despite gene losses were due, in part, to upregulation of the retained genes. We applied comparative transcriptomics to multiple species of both rot types grown across a wood wafer to create a gradient of progressive decay and to enable tracking temporal gene expression. Dozens of "decay-stage-dependent" ortho-genes were isolated, narrowing a pool of candidate genes with time-dependent regulation unique to brown rot fungi. A broad comparison of the expression timing of CAZY families indicated a temporal regulatory shift of lignocellulose-oxidizing genes toward early stages in brown rot compared to white rot, enabling the segregation of oxidative treatment ahead of hydrolysis. These key brown rot ROS-generating genes with iron ion binding functions were isolated. Moreover, transcription energy was shifted to be invested on the retained GHs in brown rot fungi to strengthen carbohydrate conversion. Collectively, these results support the hypothesis that gene regulation shifts played a pivotal role in brown rot adaptation.IMPORTANCE Fungi dominate the turnover of wood, Earth's largest pool of aboveground terrestrial carbon. Fungi first evolved this capacity by degrading lignin to access and hydrolyze embedded carbohydrates (white rot). Multiple lineages, however, adapted faster reactive oxygen species (ROS) pretreatments to loosen lignocellulose and selectively extract sugars (brown rot). This brown rot "shortcut" often coincided with losses (>60%) of conventional lignocellulolytic genes, implying that ROS adaptations supplanted conventional pathways. We used comparative transcriptomics to further pursue brown rot adaptations, which illuminated the clear temporal expression shift of ROS genes, as well as the shift toward synthesizing more GHs in brown rot relative to white rot. These imply that gene regulatory shifts, not simply ROS innovations, were key to brown rot fungal evolution. These results not only reveal an important biological shift among these unique fungi, but they may also illuminate a trait that restricts brown rot fungi to certain ecological niches.}, } @article {pmid31744443, year = {2019}, author = {Lutz, EK and Grewal, TS and Riffell, JA}, title = {Computational and experimental insights into the chemosensory navigation of Aedes aegypti mosquito larvae.}, journal = {Proceedings. Biological sciences}, volume = {286}, number = {1915}, pages = {20191495}, pmid = {31744443}, issn = {1471-2954}, support = {R01 DC013693/DC/NIDCD NIH HHS/United States ; R21 AI137947/AI/NIAID NIH HHS/United States ; }, mesh = {Aedes/growth & development/*physiology ; Animals ; *Chemotaxis ; Computational Biology ; Larva/growth & development/physiology ; Mosquito Vectors/growth & development/*physiology ; *Spatial Navigation ; }, abstract = {Mosquitoes are prolific disease vectors that affect public health around the world. Although many studies have investigated search strategies used by host-seeking adult mosquitoes, little is known about larval search behaviour. Larval behaviour affects adult body size and fecundity, and thus the capacity of individual mosquitoes to find hosts and transmit disease. Understanding vector survival at all life stages is crucial for improving disease control. In this study, we use experimental and computational methods to investigate the chemical ecology and search behaviour of Aedes aegypti mosquito larvae. We first show that larvae do not respond to several olfactory cues used by adult Ae. aegypti to assess larval habitat quality, but perceive microbial RNA as a potent foraging attractant. Second, we demonstrate that Ae. aegypti larvae use chemokinesis, an unusual search strategy, to navigate chemical gradients. Finally, we use computational modelling to demonstrate that larvae respond to starvation pressure by optimizing exploration behaviour-possibly critical for exploiting limited larval habitat types. Our results identify key characteristics of foraging behaviour in an important disease vector mosquito. In addition to implications for better understanding and control of disease vectors, this work establishes mosquito larvae as a tractable model for chemosensory behaviour and navigation.}, } @article {pmid31742450, year = {2019}, author = {Carlyle, KE and Guidry, JPD and Dougherty, SA and Burton, CW}, title = {Intimate Partner Violence on Instagram: Visualizing a Public Health Approach to Prevention.}, journal = {Health education & behavior : the official publication of the Society for Public Health Education}, volume = {46}, number = {2_suppl}, pages = {90-96}, doi = {10.1177/1090198119873917}, pmid = {31742450}, issn = {1552-6127}, mesh = {Adolescent ; Adult ; Female ; Health Promotion ; Humans ; Information Storage and Retrieval ; Intimate Partner Violence/*prevention & control ; *Public Health ; *Social Media ; Young Adult ; }, abstract = {Social media platforms like Instagram are often used as venues for discussing relationships, making them ideal channels for promoting healthy relationships and preventing intimate partner violence (IPV). This is particularly relevant for IPV, which has been historically understood as a personal issue and lacked support for consideration as a significant public health issue. To explore a potential platform for IPV prevention, this study examines the ways in which IPV messages on Instagram reflect public health understandings of, and approaches to, prevention and how Instagram users engage with these posts. We analyzed 700 Instagram posts about IPV using the social ecological model as the theoretical framework for conceptualizing framing devices. Posts that mentioned individual causal attribution and individual solution responsibility were both present in the majority of posts and elicited more engagement than posts that did not. Encouragingly, the Instagram sample was more reflective of a range of different types of IPV experiences than previous analyses of traditional media content, possibly indicating that a public health approach to this issue is gaining traction.}, } @article {pmid31741460, year = {2019}, author = {Leskanicova, A and Chovancova, O and Babincak, M and Blicharova, A and Kolesarova, M and Macekova, D and Kostolny, J and Smajda, B and Kiskova, T}, title = {Defining sex differences in selected lipid metabolites of blood plasma in Wistar rats.}, journal = {Journal of physiology and pharmacology : an official journal of the Polish Physiological Society}, volume = {70}, number = {4}, pages = {}, doi = {10.26402/jpp.2019.4.14}, pmid = {31741460}, issn = {1899-1505}, mesh = {Animals ; Female ; *Lipid Metabolism ; Male ; Phosphatidylcholines/blood/metabolism ; Rats, Wistar ; *Sex Characteristics ; Sphingomyelins/blood/metabolism ; }, abstract = {There is an increasing attention to the role that sex/gender plays in health, behavior and outcomes. Even though we know that males and females are not the same, experiments have sometimes been carried out without considering sex in scientific research. It is essential for scientists and clinicians to consider sex differences as one of the underlying physiological determinants of health and disease to provide the building blocks for evidence-based, individualized medicine. Our work aimed to reveal sex-associated differences in lipid metabolite levels of adult female (n = 10) and male (n = 10) Wistar rats, aged 60 days. Partial least square determination analysis (PLS-DA) method and a variance importance in projection (VIP) score was used to identify the key sex-specific metabolites. Our results show that all groups of lipid metabolites: lysophosphatidylcholines (lysoPCs), phosphatidylcholines (PCs), and sphingomyelins (SMs) show a significant sex-dependent pattern. According to our results, more than a half of lysoPCs studied showed sex-specific features. PCs and lysoPCs tend to be significantly elevated in the blood plasma of females. The most distinct increase in more than 90% of SMs has been revealed in female blood plasma, compared with males. According to VIP score, the most important feature was the metabolite PC aa C38:4. Our study points out a sex dimorphism in lipid metabolism. The identification of main lipid features may play a key role in preclinical and clinical practice.}, } @article {pmid31741202, year = {2020}, author = {Fu, R and Niu, R and Li, R and Yue, B and Zhang, X and Cao, Q and Wang, J and Sun, Z}, title = {Fluoride-Induced Alteration in the Diversity and Composition of Bacterial Microbiota in Mice Colon.}, journal = {Biological trace element research}, volume = {196}, number = {2}, pages = {537-544}, doi = {10.1007/s12011-019-01942-w}, pmid = {31741202}, issn = {1559-0720}, support = {Grant No. TYIT201408//the Top Young Innovative Talents of Shanxi Agricultural University/ ; }, mesh = {Administration, Oral ; Animals ; Bacteria/*classification/*drug effects ; Colon/*drug effects/*microbiology ; Computational Biology ; Gastrointestinal Microbiome/*drug effects ; Male ; Mice ; Mice, Inbred ICR ; Sodium Fluoride/administration & dosage/*pharmacology ; }, abstract = {Fluoride, as an environmental toxin, causes damage to intestinal mucosa. It may promote pathogen infection by increasing the intestinal mucosa permeability. In this study, the colonic fecal samples from the control group (C group, 0 mg/L NaF for 60 days) and the fluoride group (F group, 100 mg/L NaF for 60 days) were subjected to high-throughput 16S rRNA sequencing to verify the effects of fluoride on the colonic flora of animals. Results revealed a total of 253 operative taxonomical units (OTUs) in two groups, and 22 unique OTUs occurred in the F group. Fluoride increased the microbiota diversity and species richness of the colon. Concretely, the abundance of the Tenericutes was increased at the level of the phyla in the F group. In addition, in the F group, significant differences at the genus level were observed in Faecalibaculum, Alloprevotella, [Eubacterium]_xylanophilum_group, Prevotellaceae_UCG-001, and Ruminiclostridium_9, compared to the C group. Among them, except for the reduction in Faecalibaculum, the other four bacteria were increased in the F group. In summary, the intestinal microbial composition of mice was reconstituted by the presence of fluoride, and the significantly changing bacteria may partly account for the pathogenesis of fluoride-induced intestinal dysfunction.}, } @article {pmid31738437, year = {2019}, author = {Strijk, JS and Hinsinger, DD and Zhang, F and Cao, K}, title = {Trochodendron aralioides, the first chromosome-level draft genome in Trochodendrales and a valuable resource for basal eudicot research.}, journal = {GigaScience}, volume = {8}, number = {11}, pages = {}, pmid = {31738437}, issn = {2047-217X}, mesh = {Chromosomes, Plant/*genetics ; *Databases, Genetic ; *Genome, Plant ; Magnoliopsida/*genetics ; *Molecular Sequence Annotation ; *Phylogeny ; }, abstract = {BACKGROUND: The wheel tree (Trochodendron aralioides) is one of only 2 species in the basal eudicot order Trochodendrales. Together with Tetracentron sinense, the family is unique in having secondary xylem without vessel elements, long considered to be a primitive character also found in Amborella and Winteraceae. Recent studies however have shown that Trochodendraceae belong to basal eudicots and demonstrate that this represents an evolutionary reversal for the group. Trochodendron aralioides is widespread in cultivation and popular for use in gardens and parks.

FINDINGS: We assembled the T. aralioides genome using a total of 679.56 Gb of clean reads that were generated using both Pacific Biosciences and Illumina short-reads in combination with 10XGenomics and Hi-C data. Nineteen scaffolds corresponding to 19 chromosomes were assembled to a final size of 1.614 Gb with a scaffold N50 of 73.37 Mb in addition to 1,534 contigs. Repeat sequences accounted for 64.226% of the genome, and 35,328 protein-coding genes with an average of 5.09 exons per gene were annotated using de novo, RNA-sequencing, and homology-based approaches. According to a phylogenetic analysis of protein-coding genes, T. aralioides diverged in a basal position relative to core eudicots, ∼121.8-125.8 million years ago.

CONCLUSIONS: Trochodendron aralioides is the first chromosome-scale genome assembled in the order Trochodendrales. It represents the largest genome assembled to date in the basal eudicot grade, as well as the closest order relative to the core-eudicots, as the position of Buxales remains unresolved. This genome will support further studies of wood morphology and floral evolution, and will be an essential resource for understanding rapid changes that took place at the base of the Eudicot tree. Finally, it can further genome-assisted improvement for cultivation and conservation efforts of the wheel tree.}, } @article {pmid31736538, year = {2019}, author = {Podar, D and Macalik, K and Réti, KO and Martonos, I and Török, E and Carpa, R and Weindorf, DC and Csiszár, J and Székely, G}, title = {Morphological, physiological and biochemical aspects of salt tolerance of halophyte Petrosimonia triandra grown in natural habitat.}, journal = {Physiology and molecular biology of plants : an international journal of functional plant biology}, volume = {25}, number = {6}, pages = {1335-1347}, pmid = {31736538}, issn = {0971-5894}, abstract = {Salt tolerance mechanisms of halophyte Petrosimonia triandra, growing in its natural habitat in Cluj County, Romania, were investigated via biomass, growth parameters, water status, ion content, photosynthetic and antioxidative system efficiency, proline accumulation and lipid degradation. Two sampling sites with different soil electrical conductivities were selected: site 1: 3.14 dS m[-1] and site 2: 4.45 dS m[-1]. Higher salinity proved to have a positive effect on growth. The relative water content did not decline severely, Na[+] and K[+] content of the roots, stem and leaves was more, and the functions of the photosynthetic apparatus and photosynthetic pigment contents were not altered. The efficiency of the antioxidative defence system was found to be assured by coordination of several reactive oxygen species scavengers. The presence of higher salinity led to accumulation of the osmolyte proline, while degradation of membrane lipids was reduced. As a whole, P. triandra evolved different adaptational strategies to counteract soil salinity, including morphological and physiological adaptations, preservation of photosynthetic activity, development of an efficient antioxidative system and accumulation of the osmotic compound, proline.}, } @article {pmid31734754, year = {2020}, author = {Ribeiro, T and Vasconcelos, E and Dos Santos, KGB and Vaio, M and Brasileiro-Vidal, AC and Pedrosa-Harand, A}, title = {Diversity of repetitive sequences within compact genomes of Phaseolus L. beans and allied genera Cajanus L. and Vigna Savi.}, journal = {Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology}, volume = {28}, number = {2}, pages = {139-153}, doi = {10.1007/s10577-019-09618-w}, pmid = {31734754}, issn = {1573-6849}, mesh = {Chromosomes, Plant ; Computational Biology/methods ; DNA, Plant ; Data Mining ; Genetic Heterogeneity ; *Genetic Variation ; *Genome, Plant ; *Genomics/methods ; In Situ Hybridization, Fluorescence ; Phaseolus/classification/*genetics ; Phylogeny ; *Repetitive Sequences, Nucleic Acid ; Retroelements ; Tandem Repeat Sequences ; }, abstract = {Repetitive sequences are ubiquitous and fast-evolving elements responsible for size variation and large-scale organization of plant genomes. Within tribe Phaseoleae (Fabaceae), some genera, such as Phaseolus, Vigna, and Cajanus, show small genome and mostly stable chromosome number. Here, we applied a combined computational and cytological approach to study the organization and diversification of repetitive elements in some species of these genera. Sequences were classified in terms of type and repetitiveness and the most abundant were mapped to chromosomes. We identified long terminal repeat (LTR) retrotransposons, especially Ogre and Chromovirus elements, making up most of genomes, other than P. acutifolius and Vigna species. Satellite DNAs (SatDNAs) were less representative, but highly diverse among species, showing a clear phylogenetic relationship. In situ localization revealed preferential location at pericentromeres and centromeres for both types of sequences, suggesting a heterogeneous composition, especially for centromeres. Few elements showed subterminal accumulation. Copy number variation among chromosomes within and among species was observed for all nine identified SatDNAs. Altogether, our data pointed two main elements (Ty3/Gypsy retrotransponsons and SatDNAs) to the diversification on the repetitive landscape in Phaseoleae, with a typical set of repeats in each species. The high turnover of these sequences, however, did not affect total genome size.}, } @article {pmid31732338, year = {2020}, author = {Wang, Y and Qiao, M and Baikeli, Y and Mamat, X and Li, L and Hu, X and Dong, Y and Chang, F and Zhang, H and Hu, G}, title = {Soft-templated mesoporous carbon-modified glassy carbon electrode for sensitive and selective detection of aristolochic acids.}, journal = {Journal of hazardous materials}, volume = {385}, number = {}, pages = {121550}, doi = {10.1016/j.jhazmat.2019.121550}, pmid = {31732338}, issn = {1873-3336}, mesh = {Aristolochic Acids/*analysis ; Asarum/chemistry ; Carbon/*chemistry ; Drugs, Chinese Herbal/analysis ; Electrochemical Techniques/*instrumentation/*methods ; *Electrodes ; Hydrogen-Ion Concentration ; Limit of Detection ; Porosity ; Reproducibility of Results ; }, abstract = {In this study, ordered mesoporous carbon (OMC) was synthesized by applying a soft template method, and its mesoporous structure was characterized by scanning electron microscopy, transmission electron microscopy, and nitrogen adsorption-desorption techniques. X-ray diffraction and Raman spectroscopic analyses were conducted to demonstrate the high graphitization and topological defects at the sample surface. An electrochemical sensor based on an OMC-modified glassy carbon electrode (OMC/GCE) was constructed to detect aristolochic acids (AAs) using cyclic voltammetry and linear sweep voltammetry. The dependence of the experimental parameters including solution pH, scan rate, and accumulation time were examined and optimized. Under the optimal conditions, the response of OMC/GCE was linear over wide concentration ranges of AAs (0.6-10 μM and 10-50 μM), with sensitivities of -1.77 and -0.31 μA/μM, respectively. The limit of detection was calculated to be 0.186 μM (at S/N = 3). Furthermore, the proposed OMC/GCE was applied to detect AAs in Asarum sieboldini and the content of AAs was calculated to be 8.9 μg/g with high accuracy and precision. In addition, the modified electrode also exhibited good selectivity, reproducibility, and stability. Therefore, the OMC/GCE can be used as a platform for the determination of AAs.}, } @article {pmid31730443, year = {2019}, author = {Yancan, L and Tianle, C and Yunhan, F and Delong, L and Guizhi, W}, title = {Population genomics and morphological features underlying the adaptive evolution of the eastern honey bee (Apis cerana).}, journal = {BMC genomics}, volume = {20}, number = {1}, pages = {869}, pmid = {31730443}, issn = {1471-2164}, support = {SDAIT-24-02//Shandong Province Modern Agricultural Industry Technology System Bee Industry Innovation Team Breeding and Resource Protection Post Expert Project/ ; No. 2016LZGC039//Shandong Province Agricultural Variety Project/ ; No. SYL2017YSTD12//Shandong "Double Tops" Program/ ; }, mesh = {Adaptation, Physiological/*genetics ; Alleles ; Animals ; Bayes Theorem ; Bees/classification/*genetics ; Biological Evolution ; China ; Datasets as Topic ; Gene Frequency ; Genetic Variation ; *Genetics, Population ; *Genome, Insect ; *Phylogeny ; Polymorphism, Single Nucleotide ; Principal Component Analysis ; }, abstract = {BACKGROUND: The adaptation of organisms to changing environments is self-evident, with the adaptive evolution of organisms to environmental changes being a fundamental problem in evolutionary biology. Bees can pollinate in various environments and climates and play important roles in maintaining the ecological balance of the earth.

RESULTS: We performed an analysis of 462 Apis cerana (A. cerana) specimens from 31 populations in 11 regions and obtained 39 representative morphological features. We selected 8 A. cerana samples from each population and performed 2b-RAD simplified genome sequencing. A total of 11,506 high-quality single nucleotide polymorphism (SNP) loci were obtained. For these SNPs, the minor allele frequency (MAF) was > 1%, the average number of unique labels for each sample was 49,055, and the average depth was 72.61x. The ratios of the unique labels of all samples were 64.27-86.33%.

CONCLUSIONS: Using 39 morphological characteristics as the data set, we proposed a method for the rapid classification of A. cerana. Using genomics to assess population structure and genetic diversity, we found that A. cerana has a large genetic difference at the ecotype level. A comparison of A. cerana in North China revealed that some physical obstacles, especially the overurbanization of the plains, have isolated the populations of this species. We identified several migration events in North China and Central China. By comparing the differences in the environmental changes in different regions, we found that A. cerana has strong potential for climate change and provides a theoretical basis for investigating and protecting A. cerana.}, } @article {pmid31730190, year = {2020}, author = {Sprengelmeyer, QD and Mansourian, S and Lange, JD and Matute, DR and Cooper, BS and Jirle, EV and Stensmyr, MC and Pool, JE}, title = {Recurrent Collection of Drosophila melanogaster from Wild African Environments and Genomic Insights into Species History.}, journal = {Molecular biology and evolution}, volume = {37}, number = {3}, pages = {627-638}, pmid = {31730190}, issn = {1537-1719}, support = {R35 GM136306/GM/NIGMS NIH HHS/United States ; R01 GM121750/GM/NIGMS NIH HHS/United States ; R35 GM124701/GM/NIGMS NIH HHS/United States ; T32 GM007133/GM/NIGMS NIH HHS/United States ; R01 GM111797/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Databases, Genetic ; Drosophila melanogaster/*genetics/*growth & development ; Europe ; Female ; Genetic Speciation ; Genetic Variation ; Genetics, Population ; Genome, Insect ; Male ; Middle East ; Namibia ; Phylogeography ; Population Dynamics ; Whole Genome Sequencing/*veterinary ; Wilderness ; Zambia ; Zimbabwe ; }, abstract = {A long-standing enigma concerns the geographic and ecological origins of the intensively studied vinegar fly, Drosophila melanogaster. This globally distributed human commensal is thought to originate from sub-Saharan Africa, yet until recently, it had never been reported from undisturbed wilderness environments that could reflect its precommensal niche. Here, we document the collection of 288 D. melanogaster individuals from multiple African wilderness areas in Zambia, Zimbabwe, and Namibia. The presence of D. melanogaster in these remote woodland environments is consistent with an ancestral range in southern-central Africa, as opposed to equatorial regions. After sequencing the genomes of 17 wilderness-collected flies collected from Kafue National Park in Zambia, we found reduced genetic diversity relative to town populations, elevated chromosomal inversion frequencies, and strong differences at specific genes including known insecticide targets. Combining these genomes with existing data, we probed the history of this species' geographic expansion. Demographic estimates indicated that expansion from southern-central Africa began ∼10,000 years ago, with a Saharan crossing soon after, but expansion from the Middle East into Europe did not begin until roughly 1,400 years ago. This improved model of demographic history will provide an important resource for future evolutionary and genomic studies of this key model organism. Our findings add context to the history of D. melanogaster, while opening the door for future studies on the biological basis of adaptation to human environments.}, } @article {pmid31729401, year = {2019}, author = {Mittermayer, FH and Stiasny, MH and Clemmesen, C and Bayer, T and Puvanendran, V and Chierici, M and Jentoft, S and Reusch, TBH}, title = {Transcriptome profiling reveals exposure to predicted end-of-century ocean acidification as a stealth stressor for Atlantic cod larvae.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {16908}, pmid = {31729401}, issn = {2045-2322}, mesh = {Animals ; Computational Biology/methods ; Gadus morhua/*genetics ; *Gene Expression Profiling ; Gene Ontology ; High-Throughput Nucleotide Sequencing ; *Hydrogen-Ion Concentration ; Larva ; Osmoregulation ; Seawater/*analysis/*chemistry ; *Stress, Physiological ; *Transcriptome ; }, abstract = {Ocean acidification (OA), a direct consequence of increasing atmospheric CO2 concentration dissolving in ocean waters, is impacting many fish species. Little is known about the molecular mechanisms underlying the observed physiological impacts in fish. We used RNAseq to characterize the transcriptome of 3 different larval stages of Atlantic cod (Gadus morhua) exposed to simulated OA at levels (1179 µatm CO2) representing end-of-century predictions compared to controls (503 µatm CO2), which were shown to induce tissue damage and elevated mortality in G. morhua. Only few genes were differentially expressed in 6 and 13 days-post-hatching (dph) (3 and 16 genes, respectively), during a period when maximal mortality as a response to elevated pCO2 occurred. At 36 dph, 1413 genes were differentially expressed, most likely caused by developmental asynchrony between the treatment groups, with individuals under OA growing faster. A target gene analysis revealed only few genes of the universal and well-defined cellular stress response to be differentially expressed. We thus suggest that predicted ocean acidification levels constitute a "stealth stress" for early Atlantic cod larvae, with a rapid breakdown of cellular homeostasis leading to organismal death that was missed even with an 8-fold replication implemented in this study.}, } @article {pmid31728526, year = {2020}, author = {Corrêa, FB and Saraiva, JP and Stadler, PF and da Rocha, UN}, title = {TerrestrialMetagenomeDB: a public repository of curated and standardized metadata for terrestrial metagenomes.}, journal = {Nucleic acids research}, volume = {48}, number = {D1}, pages = {D626-D632}, pmid = {31728526}, issn = {1362-4962}, mesh = {Computational Biology/*methods ; Data Mining ; *Databases, Genetic ; Ecology ; Ecosystem ; Genome, Bacterial ; Geography ; Internet ; *Metadata ; *Metagenome ; Soil Microbiology ; User-Computer Interface ; }, abstract = {Microbiome studies focused on the genetic potential of microbial communities (metagenomics) became standard within microbial ecology. MG-RAST and the Sequence Read Archive (SRA), the two main metagenome repositories, contain over 202 858 public available metagenomes and this number has increased exponentially. However, mining databases can be challenging due to misannotated, misleading and decentralized data. The main goal of TerrestrialMetagenomeDB is to make it easier for scientists to find terrestrial metagenomes of interest that could be compared with novel datasets in meta-analyses. We defined terrestrial metagenomes as those that do not belong to marine environments. Further, we curated the database using text mining to assign potential descriptive keywords that better contextualize environmental aspects of terrestrial metagenomes, such as biomes and materials. TerrestrialMetagenomeDB release 1.0 includes 15 022 terrestrial metagenomes from SRA and MG-RAST. Together, the downloadable data amounts to 68 Tbp. In total, 199 terrestrial terms were divided into 14 categories. These metagenomes span 83 countries, 30 biomes and 7 main source materials. The TerrestrialMetagenomeDB is publicly available at https://webapp.ufz.de/tmdb.}, } @article {pmid31727118, year = {2019}, author = {Werner, J and Géron, A and Kerssemakers, J and Matallana-Surget, S}, title = {mPies: a novel metaproteomics tool for the creation of relevant protein databases and automatized protein annotation.}, journal = {Biology direct}, volume = {14}, number = {1}, pages = {21}, pmid = {31727118}, issn = {1745-6150}, mesh = {*Databases, Protein ; Molecular Sequence Annotation/*methods ; *Proteome ; Proteomics/*methods ; }, abstract = {Metaproteomics allows to decipher the structure and functionality of microbial communities. Despite its rapid development, crucial steps such as the creation of standardized protein search databases and reliable protein annotation remain challenging. To overcome those critical steps, we developed a new program named mPies (metaProteomics in environmental sciences). mPies allows the creation of protein databases derived from assembled or unassembled metagenomes, and/or public repositories based on taxon IDs, gene or protein names. For the first time, mPies facilitates the automatization of reliable taxonomic and functional consensus annotations at the protein group level, minimizing the well-known protein inference issue, which is commonly encountered in metaproteomics. mPies' workflow is highly customizable with regards to input data, workflow steps, and parameter adjustment. mPies is implemented in Python 3/Snakemake and freely available on GitHub: https://github.com/johanneswerner/mPies/. REVIEWER: This article was reviewed by Dr. Wilson Wen Bin Goh.}, } @article {pmid31726130, year = {2020}, author = {Zhang, D and Li, WX and Zou, H and Wu, SG and Li, M and Jakovlić, I and Zhang, J and Chen, R and Wang, GT}, title = {Mitochondrial genomes and 28S rDNA contradict the proposed obsoletion of the order Tetraonchidea (Platyhelminthes: Monogenea).}, journal = {International journal of biological macromolecules}, volume = {143}, number = {}, pages = {891-901}, doi = {10.1016/j.ijbiomac.2019.09.150}, pmid = {31726130}, issn = {1879-0003}, mesh = {Animals ; Computational Biology/methods ; Gene Order ; Gene Rearrangement ; *Genome, Mitochondrial ; Genomics/methods ; Molecular Sequence Annotation ; Phylogeny ; Platyhelminths/*classification/*genetics ; RNA, Ribosomal, 28S/*genetics ; RNA, Untranslated/chemistry/genetics ; }, abstract = {Due to the incongruence of morphology-based hypotheses and scarcity of molecular data, validity of the order Tetraonchidea remains contentious. The only complete mitogenome currently available for the entire order is that of Paratetraonchoides inermis (Tetraonchoididae). To study the phylogeny of Tetraonchidea from mitogenomic perspective, we sequenced the first mitogenome for the family Tetraonchidae: Tetraonchus monenteron (Tetraonchidea). To get a nuclear-data perspective, we also sequenced nuclear 28S rDNA gene of both species. The mitogenome of T. monenteron does not have high A + T content, nor tRNA pseudo-genes, both of which were unique features reported in P. inermis. However, T. monenteron exhibits a unique gene order, with a large number of tRNA rearrangements in comparison to P. inermis and other monogeneans. Phylogenetic analyses conducted using Bayesian inference and maximum likelihood methods, complemented with partitioning, consistently support the sister-group relationship of T. monenteron (Tetraonchidae) and P. inermis (Tetraonchoididae). This is also partially supported by the 28S rDNA data and two morphologic apomorphies. This close relationship of Tetraonchidae and Tetraonchoididae challenges the latest major morphology-based classification, which proposed obsoletion of the Tetraonchidea order, and grouped Tetraonchoididae into the Gyrodactylidea clade. The validity of this order shall have to be further confirmed with more data.}, } @article {pmid31725795, year = {2019}, author = {Walker, FM and Tobin, A and Simmons, NB and Sobek, CJ and Sanchez, DE and Chambers, CL and Fofanov, VY}, title = {A fecal sequel: Testing the limits of a genetic assay for bat species identification.}, journal = {PloS one}, volume = {14}, number = {11}, pages = {e0224969}, pmid = {31725795}, issn = {1932-6203}, mesh = {Animals ; Archaeology ; Chiroptera/*genetics ; Feces/*chemistry ; Genetic Testing/*methods ; Humidity ; Mining ; Reproducibility of Results ; Southwestern United States ; Species Specificity ; Time Factors ; }, abstract = {DNA metabarcoding assays are powerful tools for delving into the DNA in wildlife feces, giving unprecedented ability to detect species, understand natural history, and identify pathogens for a range of applications in management, conservation, and research. Next-generation sequencing technology is developing rapidly, which makes it especially important that predictability and reproducibility of DNA metabarcoding assays are explored together with the post-depositional ecology of the target taxon's fecal DNA. Here, we defined the constraints of an assay called 'Species from Feces' used by government agencies, research groups, and non-governmental organizations to identify bat species from guano. We tested assay sensitivity by examining how time and humidity affect the ability to recover and successfully sequence DNA in guano, assessing whether a fecal pellet from a rare bat species could be detected in a background of feces from other bat species, and evaluating the efficacy of Species from Feces as a survey tool for bat roosts in temperate and tropical areas. We found that the assay performs well with feces over two years old in dry, cool environments, and fails by 12 months at 100% relative humidity. We also found that it reliably identifies rare DNA, has great utility for surveying roosts in temperate and tropical regions, and detects more bat species than do visual surveys. We attribute the success of Species from Feces to characteristics of the assay paired with application in taxa that are particularly well-suited for fecal DNA survival. In a time of rapid evolution of DNA metabarcoding approaches and their use with feces, this study illustrates the strengths and limitations of applied assays.}, } @article {pmid31725716, year = {2019}, author = {Almadini, AM and Hassaballa, AA}, title = {Depicting changes in land surface cover at Al-Hassa oasis of Saudi Arabia using remote sensing and GIS techniques.}, journal = {PloS one}, volume = {14}, number = {11}, pages = {e0221115}, pmid = {31725716}, issn = {1932-6203}, mesh = {Agriculture/trends ; Conservation of Natural Resources/trends ; Ecological Parameter Monitoring/methods ; Environmental Monitoring/methods ; Geographic Information Systems ; *Natural Resources ; Remote Sensing Technology ; Saudi Arabia ; Soil ; Spatio-Temporal Analysis ; Urbanization/trends ; }, abstract = {This study assessed the spatial and temporal variations of land cover in the agricultural areas of the Al-Hassa oasis, Kingdom of Saudi Arabia (KSA). Change detection technique was applied in order to classify variations among different surface cover aspects, during three successive stages between 1985 and 2017 (i.e., 1985 to 1999 (14 years), 1999 to 2013 (14 years), and 2013 to 2017 (4 years)), using two scenarios. During the first stage, significant urban sprawl (i.e., 3,200 ha) occurred on bare lands within the old oasis, while only 590 ha of the oasis's vegetation area was occupied by urban cover. However, the final stage revealed rapid urban development (1,270 ha by 2017) within the oasis's vegetation region, while no urban sprawl occurred on bare lands (area of 1,900 ha, same as that in 1999-2013). Vegetation cover of around 1,000 ha changed to the bare soil class, in addition to the areas that were occupied by the urban class (1,700 ha in total). The study provides quantitative information on the influence of urban development on the spatial changes in vegetation cover of the oasis, especially during recent decades.}, } @article {pmid31724703, year = {2020}, author = {Flaudias, V and Zerhouni, O and Chakroun-Baggioni, N and Pires, S and Schmitt, A and De Chazeron, I and Llorca, PM and Brousse, G}, title = {Reducing Attentional Bias in Individuals With Alcohol Use Disorders With a Tablet Application: A Randomized Controlled Trial Pilot Study.}, journal = {Alcohol and alcoholism (Oxford, Oxfordshire)}, volume = {55}, number = {1}, pages = {51-55}, doi = {10.1093/alcalc/agz080}, pmid = {31724703}, issn = {1464-3502}, mesh = {Adult ; Alcoholism/*therapy ; *Attentional Bias ; *Cognitive Behavioral Therapy ; Craving ; Female ; Humans ; Inhibition, Psychological ; Male ; Middle Aged ; Pilot Projects ; Therapy, Computer-Assisted/*methods ; Treatment Outcome ; }, abstract = {AIMS: Cognitive bias modification (CBM) training has been considered a promising and effective intervention tool for reducing cognitive biases toward alcohol. However, the link between the cognitive process and actual behavior remains statistically insignificant because computerized tasks do not have sufficient ecological validity and suffer from high dropout rates. The recent development of 'serious games' has shown encouraging results in maintaining adherence to health-related interventions. We aim to evaluate a CBM program using a gamified attentional bias (AB) training procedure on a touchpad for individuals with alcohol use disorders.

METHODS: Forty-one patients were included in this study, 33 of whom displayed an AB and were randomly assigned into the 'CBM group' (N = 18, 16.7% women) or 'Memory group'-which involved playing a memory game-(N = 15, no woman). Eight other participants (12.5% women) with no AB comprised the 'Without AB group'. Efficacy was assessed for AB, craving, and inhibition and attentional capacities before and after the program.

RESULTS: We observed that the reduction of AB was higher for the 'CBM group' (Mbefore = 153.61, SD = 172.21; Mafter = 18.00, SD = 77.71; t (17) = 4.21, P = 0.001) than for the 'Memory group' (Mbefore = 73.20, SD = 66.65; Mafter =42.47, SD = 113.77; ts < 1). The analysis showed that for the 'Without AB group', there was no significant difference in AB (t (7) = -2.15, P = .07) after the program.

CONCLUSIONS: This study demonstrated an increased reduction of AB for patients included in the CBM program on a touchpad than for patients playing only a memory game.}, } @article {pmid31724378, year = {2019}, author = {Sarkar, S and Singh, P and Lingala, MAL and Verma, P and Dhiman, RC}, title = {Malaria risk map for India based on climate, ecology and geographical modelling.}, journal = {Geospatial health}, volume = {14}, number = {2}, pages = {}, doi = {10.4081/gh.2019.767}, pmid = {31724378}, issn = {1970-7096}, mesh = {Animals ; Anopheles/growth & development ; Climate ; Geographic Information Systems ; *Geographic Mapping ; India/epidemiology ; Malaria/*epidemiology ; Malaria, Falciparum/*epidemiology ; Malaria, Vivax/*epidemiology ; Mosquito Vectors/growth & development ; Plants ; Risk Assessment ; Risk Factors ; Seasons ; Soil/chemistry ; }, abstract = {Mapping the malaria risk at various geographical levels is often undertaken considering climate suitability, infection rate and/or malaria vector distribution, while the ecological factors related to topography and vegetation cover are generally neglected. The present study abides a holistic approach to risk mapping by including topographic, climatic and vegetation components into the framework of malaria risk modelling. This work attempts to delineate the areas of Plasmodium falciparum and Plasmodium vivax malaria transmission risk in India using seven geo-ecological indicators: temperature, relative humidity, rainfall, forest cover, soil, slope, altitude and the normalized difference vegetation index using multi-criteria decision analysis based on geographical information system (GIS). The weight of the risk indicators was assigned by an analytical hierarchical process with the climate suitability (temperature and humidity) data generated using fuzzy logic. Model validation was done through both primary and secondary datasets. The spatio-ecological model was based on GIS to classify the country into five zones characterized by various levels of malaria transmission risk (very high; high; moderate; low; and very low. The study found that about 13% of the country is under very high malaria risk, which includes the malaria- endemic districts of the states of Chhattisgarh, Odisha, Jharkhand, Tripura, Assam, Meghalaya and Manipur. The study also showed that the transmission risk suitability for P. vivax is higher than that for P. falciparum in the Himalayan region. The field study corroborates the identified malaria risk zones and highlights that the low to moderate risk zones are outbreak-prone. It is expected that this information will help the National Vector Borne Disease Control Programme in India to undertake improved surveillance and conduct target based interventions.}, } @article {pmid31722990, year = {2019}, author = {Dominguez-Mirazo, M and Jin, R and Weitz, JS}, title = {Functional and Comparative Genomic Analysis of Integrated Prophage-Like Sequences in "Candidatus Liberibacter asiaticus".}, journal = {mSphere}, volume = {4}, number = {6}, pages = {}, pmid = {31722990}, issn = {2379-5042}, mesh = {Citrus/microbiology ; Computational Biology ; *Genomics ; Plant Diseases/microbiology ; Prophages/*genetics ; Rhizobiaceae/genetics/*growth & development/isolation & purification/*virology ; Virulence ; }, abstract = {Huanglongbing disease (HLB; yellow shoot disease) is a severe worldwide infectious disease for citrus family plants. The pathogen "Candidatus Liberibacter asiaticus" is an alphaproteobacterium of the Rhizobiaceae family that has been identified as the causative agent of HLB. The virulence of "Ca. Liberibacter asiaticus" has been attributed, in part, to prophage-carried genes. Prophage and prophage-like elements have been identified in 12 of the 15 available "Ca. Liberibacter asiaticus" genomes and are classified into three prophage types. Here, we reexamined all 15 "Ca. Liberibacter asiaticus" genomes using a de novo prediction approach and expanded the number of prophage-like elements from 16 to 33. Further, we found that all of the "Ca. Liberibacter asiaticus" genomes contained at least one prophage-like sequence. Comparative analysis revealed a prevalent, albeit previously unknown, prophage-like sequence type that is a remnant of an integrated prophage. Notably, this remnant prophage is found in the Ishi-1 "Ca. Liberibacter asiaticus" strain that had previously been reported as lacking prophages. Our findings provide both a resource for data and new insights into the evolutionary relationship between phage and "Ca. Liberibacter asiaticus" pathogenicity.IMPORTANCE Huanglongbing (HLB) disease is threatening citrus production worldwide. The causative agent is "Candidatus Liberibacter asiaticus." Prior work using mapping-based approaches identified prophage-like sequences in some "Ca. Liberibacter asiaticus" genomes but not all. Here, we utilized a de novo approach that expands the number of prophage-like elements found in "Ca. Liberibacter asiaticus" from 16 to 33 and identified at least one prophage-like sequence in all "Ca. Liberibacter asiaticus" strains. Furthermore, we identified a prophage-like sequence type that is a remnant of an integrated prophage-expanding the number of prophage types in "Ca. Liberibacter asiaticus" from 3 to 4. Overall, the findings will help researchers investigate the role of prophage in the ecology, evolution, and pathogenicity of "Ca. Liberibacter asiaticus."}, } @article {pmid31721236, year = {2020}, author = {Pfaar, O and Karatzas, K and Bastl, K and Berger, U and Buters, J and Darsow, U and Demoly, P and Durham, SR and Galán, C and Gehrig, R and Gerth van Wijk, R and Jacobsen, L and Katsifarakis, N and Klimek, L and Saarto, A and Sofiev, M and Thibaudon, M and Werchan, B and Bergmann, KC}, title = {Pollen season is reflected on symptom load for grass and birch pollen-induced allergic rhinitis in different geographic areas-An EAACI Task Force Report.}, journal = {Allergy}, volume = {75}, number = {5}, pages = {1099-1106}, doi = {10.1111/all.14111}, pmid = {31721236}, issn = {1398-9995}, mesh = {Allergens ; Austria ; *Betula ; Europe ; Finland ; France ; Germany/epidemiology ; Humans ; Poaceae ; Pollen ; *Rhinitis, Allergic ; Seasons ; }, abstract = {BACKGROUND: The effectiveness of allergen immunotherapy (AIT) in seasonal and perennial allergic rhinitis (AR) depends on the definition of pollen exposure intensity or time period. We recently evaluated pollen and symptom data from Germany to examine the new definitions of the European Academy of Allergy and Clinical Immunology (EAACI) on pollen season and peak pollen period start and end. Now, we aim to confirm the feasibility of these definitions to properly mirror symptom loads for grass and birch pollen-induced allergic rhinitis in other European geographical areas such as Austria, Finland and France, and therefore their suitability for AIT and clinical practice support.

METHODS: Data from twenty-three pollen monitoring stations from three countries in Europe and for 3 years (2014-2016) were used to investigate the correlation between birch and grass pollen concentrations during the birch and grass pollen season defined via the EAACI criteria, and total nasal symptom and medication scores as reported with the aid of the patient's hay-fever diary (PHD). In addition, we conducted a statistical analysis, together with a graphical investigation, to reveal correlations and dependencies between the studied parameters.

RESULTS: The analysis demonstrated that the definitions of pollen season as well as peak pollen period start and end as proposed by the EAACI are correlated to pollen-induced symptom loads reported by PHD users during birch and grass pollen season. A statistically significant correlation (slightly higher for birch) has been found between the Total Nasal Symptom and Medication Score (TNSMS) and the pollen concentration levels. Moreover, the maximum symptom levels occurred mostly within the peak pollen periods (PPP) following the EAACI criteria.

CONCLUSIONS: Based on our analyses, we confirm the validity of the EAACI definitions on pollen season for both birch and grass and for a variety of geographical locations for the four European countries (including Germany from a previous publication) analyzed so far. On this basis, the use of the EAACI definitions is supported in future clinical trials on AIT as well as in daily routine for optimal patient care. Further evaluation of the EAACI criteria in other European regions is recommended.}, } @article {pmid31720768, year = {2020}, author = {Abdusamadzoda, D and Abdushukurov, DA and Duliu, OG and Zinicovscaia, I and Yushin, NS and Frontasyeva, MV}, title = {Investigations of the Atmospheric Deposition of Major and Trace Elements in Western Tajikistan by Using the Hylocomium splendens Moss as Bioindicators.}, journal = {Archives of environmental contamination and toxicology}, volume = {78}, number = {1}, pages = {60-67}, doi = {10.1007/s00244-019-00687-w}, pmid = {31720768}, issn = {1432-0703}, mesh = {Air Pollutants/*analysis ; Bryopsida/*chemistry ; Environmental Biomarkers/*drug effects ; Environmental Monitoring/*methods ; Geographic Information Systems ; Spectrophotometry, Atomic ; Tajikistan ; Trace Elements/*analysis ; }, abstract = {The study was performed in a mountainous area of approximately 7000 sq. km of Western Tajikistan, i.e., Turkestan, Zeravshan, Hissar, and Karateghin ridges that are characterized by complex geological settings. Moss biomonitoring was used to assess the concentration level of trace and major elements in atmospheric deposition of the study area. Hylocomium splendens (Hedw.) Schimp. moss was used as biomonitor in this study. 43 major and trace-elements were determined by Epithermal Neutron Activation (ENAA) and Atomic Absorption Spectrometry (AAS). GIS maps of the 43 elements showed that the distribution of Mo, Cd, REE, Th, and U could be most probably associated with the Odjuk pegmatite field. Zr, Hf, and W contents are significantly increased in the vicinity of the Sarbo River washout while Cr, Co, Ni, and As showed a maximum content near Kanchoch gold field. The global pollution index based on the local content of presumed pollutants Cr, Ni, Cu, Zn, As, Cd, Sb, and Pb in some places exceeded the threshold limits for a pristine, unpolluted environment. At the same time, the distribution of incompatible Sc, La, Yb, and Th suggested for the airborne material deposited on mosses a continental component, enriched in few places in felsic components.}, } @article {pmid31720122, year = {2019}, author = {Näpflin, K and O'Connor, EA and Becks, L and Bensch, S and Ellis, VA and Hafer-Hahmann, N and Harding, KC and Lindén, SK and Olsen, MT and Roved, J and Sackton, TB and Shultz, AJ and Venkatakrishnan, V and Videvall, E and Westerdahl, H and Winternitz, JC and Edwards, SV}, title = {Genomics of host-pathogen interactions: challenges and opportunities across ecological and spatiotemporal scales.}, journal = {PeerJ}, volume = {7}, number = {}, pages = {e8013}, pmid = {31720122}, issn = {2167-8359}, abstract = {Evolutionary genomics has recently entered a new era in the study of host-pathogen interactions. A variety of novel genomic techniques has transformed the identification, detection and classification of both hosts and pathogens, allowing a greater resolution that helps decipher their underlying dynamics and provides novel insights into their environmental context. Nevertheless, many challenges to a general understanding of host-pathogen interactions remain, in particular in the synthesis and integration of concepts and findings across a variety of systems and different spatiotemporal and ecological scales. In this perspective we aim to highlight some of the commonalities and complexities across diverse studies of host-pathogen interactions, with a focus on ecological, spatiotemporal variation, and the choice of genomic methods used. We performed a quantitative review of recent literature to investigate links, patterns and potential tradeoffs between the complexity of genomic, ecological and spatiotemporal scales undertaken in individual host-pathogen studies. We found that the majority of studies used whole genome resolution to address their research objectives across a broad range of ecological scales, especially when focusing on the pathogen side of the interaction. Nevertheless, genomic studies conducted in a complex spatiotemporal context are currently rare in the literature. Because processes of host-pathogen interactions can be understood at multiple scales, from molecular-, cellular-, and physiological-scales to the levels of populations and ecosystems, we conclude that a major obstacle for synthesis across diverse host-pathogen systems is that data are collected on widely diverging scales with different degrees of resolution. This disparity not only hampers effective infrastructural organization of the data but also data granularity and accessibility. Comprehensive metadata deposited in association with genomic data in easily accessible databases will allow greater inference across systems in the future, especially when combined with open data standards and practices. The standardization and comparability of such data will facilitate early detection of emerging infectious diseases as well as studies of the impact of anthropogenic stressors, such as climate change, on disease dynamics in humans and wildlife.}, } @article {pmid31719152, year = {2020}, author = {Huang, J and Wang, C and Li, X and Fang, X and Huang, N and Wang, Y and Ma, H and Wang, Y and Copenhaver, GP}, title = {Conservation and Divergence in the Meiocyte sRNAomes of Arabidopsis, Soybean, and Cucumber.}, journal = {Plant physiology}, volume = {182}, number = {1}, pages = {301-317}, pmid = {31719152}, issn = {1532-2548}, mesh = {Arabidopsis/*genetics ; Arabidopsis Proteins/*genetics ; Computational Biology/methods ; Cucumis sativus/*genetics ; Gene Expression Profiling ; Gene Expression Regulation, Plant/genetics ; MicroRNAs/genetics ; Glycine max/*genetics ; }, abstract = {Meiosis is a critical process for sexual reproduction. During meiosis, genetic information on homologous chromosomes is shuffled through meiotic recombination to produce gametes with novel allelic combinations. Meiosis and recombination are orchestrated by several mechanisms including regulation by small RNAs (sRNAs). Our previous work in Arabidopsis (Arabidopsis thaliana) meiocytes showed that meiocyte-specific sRNAs (ms-sRNAs) have distinct characteristics, including positive association with the coding region of genes that are transcriptionally upregulated during meiosis. Here, we characterized the ms-sRNAs in two important crops, soybean (Glycine max) and cucumber (Cucumis sativus). Ms-sRNAs in soybean have the same features as those in Arabidopsis, suggesting that they may play a conserved role in eudicots. We also investigated the profiles of microRNAs (miRNAs) and phased secondary small interfering RNAs in the meiocytes of all three species. Two conserved miRNAs, miR390 and miR167, are highly abundant in the meiocytes of all three species. In addition, we identified three novel cucumber miRNAs. Intriguingly, our data show that the previously identified phased secondary small interfering RNA pathway involving soybean-specific miR4392 is more abundant in meiocytes. These results showcase the conservation and divergence of ms-sRNAs in flowering plants, and broaden our understanding of sRNA function in crop species.}, } @article {pmid31715472, year = {2020}, author = {Bourla, A and Mouchabac, S and Ogorzelec, L and Guinchard, C and Ferreri, F and , }, title = {Are student nurses ready for new technologies in mental health? Mixed-methods study.}, journal = {Nurse education today}, volume = {84}, number = {}, pages = {104240}, doi = {10.1016/j.nedt.2019.104240}, pmid = {31715472}, issn = {1532-2793}, mesh = {Adolescent ; Adult ; Decision Support Techniques ; Depressive Disorder/*diagnosis/nursing ; Ecological Momentary Assessment ; Female ; France ; Humans ; Male ; Psychiatric Nursing/*education ; Reproducibility of Results ; *Smartphone ; Students, Nursing/*psychology ; Surveys and Questionnaires ; Young Adult ; }, abstract = {BACKGROUND: Technical innovations such as ecological momentary assessment (EMA), machine learning (ML), computerized adaptive testing (CAT), Digital Phenotyping, Clinical Decision Support Systems (CDSS), Algorithms, and Biomarkers have caused a paradigm shift in psychiatric care. The aim of the present study was to explore how student nurses view this paradigm shift, by assessing the acceptability of smartphone-based EMA, CAT, and biosensor-based Digital Phenotyping. We also investigated the factors affecting this acceptability.

METHOD: Student nurses recruited via nursing schools participated in a quantitative study involving the screenplay method, in which they were exposed to two scenarios about depression care, one featuring EMA and CAT, the other featuring a connected wristband (CW) for Digital Phenotyping. Four acceptability domains (usefulness, usability, reliability, risk) were investigated.

RESULTS: We recorded 1216 observations for the first scenario and 1106 for the second. Regarding overall acceptability, the CW was viewed less positively than CAT and EMA. Regarding reliability, whereas respondents believed that the CW could correctly detect depressive relapse, they did not think that EMA and CAT were sufficiently reliable for the accurate diagnosis of depressive disorder. More than 70% of respondents stated that they would nevertheless be interested in offering EMA, CAT or CW to their patients, but more than 60% feared that these devices might hinder the therapeutic relationship.

CONCLUSION: This was the first study assessing student nurses' views of EMA, CAT and CW-based digital phenotyping. Respondents were interested in these new technologies and keen to offer them to their patients. However, our study highlighted several issues, as respondents doubted the reliability of these devices and feared that they would hinder the therapeutic relationship. Subgroup analysis revealed correspondences between acceptability profiles and demographic profiles. It is therefore essential for nurses and student nurses to receive training and become involved in the development of this new technologies.}, } @article {pmid31714940, year = {2019}, author = {Li, ZR and Xie, E and Crawford, FW and Warren, JL and McConnell, K and Copple, JT and Johnson, T and Gonsalves, GS}, title = {Suspected heroin-related overdoses incidents in Cincinnati, Ohio: A spatiotemporal analysis.}, journal = {PLoS medicine}, volume = {16}, number = {11}, pages = {e1002956}, pmid = {31714940}, issn = {1549-1676}, support = {DP2 HD091799/HD/NICHD NIH HHS/United States ; R01 MH105203/MH/NIMH NIH HHS/United States ; UL1 TR001863/TR/NCATS NIH HHS/United States ; DP2 DA049282/DA/NIDA NIH HHS/United States ; R37 DA015612/DA/NIDA NIH HHS/United States ; }, mesh = {Bayes Theorem ; Databases, Factual ; Drug Overdose/*epidemiology ; Emergency Medical Services/trends ; Emergency Service, Hospital/trends ; Female ; Heroin/adverse effects ; Heroin Dependence/*epidemiology ; Humans ; Male ; Ohio/epidemiology ; Risk Factors ; Spatio-Temporal Analysis ; Substance-Related Disorders/epidemiology ; United States ; }, abstract = {BACKGROUND: Opioid misuse and deaths are increasing in the United States. In 2017, Ohio had the second highest overdose rates in the US, with the city of Cincinnati experiencing a 50% rise in opioid overdoses since 2015. Understanding the temporal and geographic variation in overdose emergencies may help guide public policy responses to the opioid epidemic.

METHODS AND FINDINGS: We used a publicly available data set of suspected heroin-related emergency calls (n = 6,246) to map overdose incidents to 280 census block groups in Cincinnati between August 1, 2015, and January 30, 2019. We used a Bayesian space-time Poisson regression model to examine the relationship between demographic and environmental characteristics and the number of calls within block groups. Higher numbers of heroin-related incidents were found to be associated with features of the built environment, including the proportion of parks (relative risk [RR] = 2.233; 95% credible interval [CI]: [1.075-4.643]), commercial (RR = 13.200; 95% CI: [4.584-38.169]), manufacturing (RR = 4.775; 95% CI: [1.958-11.683]), and downtown development zones (RR = 11.362; 95% CI: [3.796-34.015]). The number of suspected heroin-related emergency calls was also positively associated with the proportion of male population, the population aged 35-49 years, and distance to pharmacies and was negatively associated with the proportion aged 18-24 years, the proportion of the population with a bachelor's degree or higher, median household income, the number of fast food restaurants, distance to hospitals, and distance to opioid treatment programs. Significant spatial and temporal heterogeneity in the risks of incidents remained after adjusting for covariates. Limitations of this study include lack of information about the nature of incidents after dispatch, which may differ from the initial classification of being related to heroin, and lack of information on local policy changes and interventions.

CONCLUSIONS: We identified areas with high numbers of reported heroin-related incidents and features of the built environment and demographic characteristics that are associated with these events in the city of Cincinnati. Publicly available information about opiate overdoses, combined with data on spatiotemporal risk factors, may help municipalities plan, implement, and target harm-reduction measures. In the US, more work is necessary to improve data availability in other cities and states and the compatibility of data from different sources in order to adequately measure and monitor the risk of overdose and inform health policies.}, } @article {pmid31712730, year = {2019}, author = {Qi, W and Colarusso, A and Olombrada, M and Parrilli, E and Patrignani, A and Tutino, ML and Toll-Riera, M}, title = {New insights on Pseudoalteromonas haloplanktis TAC125 genome organization and benchmarks of genome assembly applications using next and third generation sequencing technologies.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {16444}, pmid = {31712730}, issn = {2045-2322}, support = {/WT_/Wellcome Trust/United Kingdom ; 203141/Z/16/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Aquatic Organisms ; Computational Biology/methods ; *Genome, Bacterial ; *Genomics/methods ; Gram-Negative Bacterial Infections/*microbiology ; *High-Throughput Nucleotide Sequencing ; Molecular Sequence Annotation ; Pseudoalteromonas/*genetics ; Water Microbiology ; }, abstract = {Pseudoalteromonas haloplanktis TAC125 is among the most commonly studied bacteria adapted to cold environments. Aside from its ecological relevance, P. haloplanktis has a potential use for biotechnological applications. Due to its importance, we decided to take advantage of next generation sequencing (Illumina) and third generation sequencing (PacBio and Oxford Nanopore) technologies to resequence its genome. The availability of a reference genome, obtained using whole genome shotgun sequencing, allowed us to study and compare the results obtained by the different technologies and draw useful conclusions for future de novo genome assembly projects. We found that assembly polishing using Illumina reads is needed to achieve a consensus accuracy over 99.9% when using Oxford Nanopore sequencing, but not in PacBio sequencing. However, the dependency of consensus accuracy on coverage is lower in Oxford Nanopore than in PacBio, suggesting that a cost-effective solution might be the use of low coverage Oxford Nanopore sequencing together with Illumina reads. Despite the differences in consensus accuracy, all sequencing technologies revealed the presence of a large plasmid, pMEGA, which was undiscovered until now. Among the most interesting features of pMEGA is the presence of a putative error-prone polymerase regulated through the SOS response. Aside from the characterization of the newly discovered plasmid, we confirmed the sequence of the small plasmid pMtBL and uncovered the presence of a potential partitioning system. Crucially, this study shows that the combination of next and third generation sequencing technologies give us an unprecedented opportunity to characterize our bacterial model organisms at a very detailed level.}, } @article {pmid31712581, year = {2019}, author = {Hebert, FO and Freschi, L and Blackburn, G and Béliveau, C and Dewar, K and Boyle, B and Gundersen-Rindal, DE and Sparks, ME and Cusson, M and Hamelin, RC and Levesque, RC}, title = {Expansion of LINEs and species-specific DNA repeats drives genome expansion in Asian Gypsy Moths.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {16413}, pmid = {31712581}, issn = {2045-2322}, mesh = {Animals ; Computational Biology/methods ; DNA Transposable Elements ; Energy Metabolism ; *Genetic Variation ; *Genome, Insect ; Genome-Wide Association Study ; Genomics/methods ; *Long Interspersed Nucleotide Elements ; Metabolic Networks and Pathways ; Moths/*genetics/metabolism ; *Repetitive Sequences, Nucleic Acid ; Species Specificity ; }, abstract = {Two subspecies of Asian gypsy moth (AGM), Lymantria dispar asiatica and L. dispar japonica, pose a serious alien invasive threat to North American forests. Despite decades of research on the ecology and biology of this pest, limited AGM-specific genomic resources are currently available. Here, we report on the genome sequences and functional content of these AGM subspecies. The genomes of L.d. asiatica and L.d. japonica are the largest lepidopteran genomes sequenced to date, totaling 921 and 999 megabases, respectively. Large genome size in these subspecies is driven by the accumulation of specific classes of repeats. Genome-wide metabolic pathway reconstructions suggest strong genomic signatures of energy-related pathways in both subspecies, dominated by metabolic functions related to thermogenesis. The genome sequences reported here will provide tools for probing the molecular mechanisms underlying phenotypic traits that are thought to enhance AGM invasiveness.}, } @article {pmid31710301, year = {2019}, author = {Bai, J and Jhaney, I and Wells, J}, title = {Developing a Reproducible Microbiome Data Analysis Pipeline Using the Amazon Web Services Cloud for a Cancer Research Group: Proof-of-Concept Study.}, journal = {JMIR medical informatics}, volume = {7}, number = {4}, pages = {e14667}, pmid = {31710301}, issn = {2291-9694}, support = {K99 NR017897/NR/NINR NIH HHS/United States ; }, abstract = {BACKGROUND: Cloud computing for microbiome data sets can significantly increase working efficiencies and expedite the translation of research findings into clinical practice. The Amazon Web Services (AWS) cloud provides an invaluable option for microbiome data storage, computation, and analysis.

OBJECTIVE: The goals of this study were to develop a microbiome data analysis pipeline by using AWS cloud and to conduct a proof-of-concept test for microbiome data storage, processing, and analysis.

METHODS: A multidisciplinary team was formed to develop and test a reproducible microbiome data analysis pipeline with multiple AWS cloud services that could be used for storage, computation, and data analysis. The microbiome data analysis pipeline developed in AWS was tested by using two data sets: 19 vaginal microbiome samples and 50 gut microbiome samples.

RESULTS: Using AWS features, we developed a microbiome data analysis pipeline that included Amazon Simple Storage Service for microbiome sequence storage, Linux Elastic Compute Cloud (EC2) instances (ie, servers) for data computation and analysis, and security keys to create and manage the use of encryption for the pipeline. Bioinformatics and statistical tools (ie, Quantitative Insights Into Microbial Ecology 2 and RStudio) were installed within the Linux EC2 instances to run microbiome statistical analysis. The microbiome data analysis pipeline was performed through command-line interfaces within the Linux operating system or in the Mac operating system. Using this new pipeline, we were able to successfully process and analyze 50 gut microbiome samples within 4 hours at a very low cost (a c4.4xlarge EC2 instance costs $0.80 per hour). Gut microbiome findings regarding diversity, taxonomy, and abundance analyses were easily shared within our research team.

CONCLUSIONS: Building a microbiome data analysis pipeline with AWS cloud is feasible. This pipeline is highly reliable, computationally powerful, and cost effective. Our AWS-based microbiome analysis pipeline provides an efficient tool to conduct microbiome data analysis.}, } @article {pmid31707592, year = {2019}, author = {Mukanyandwi, V and Kurban, A and Hakorimana, E and Nahayo, L and Habiyaremye, G and Gasirabo, A and Sindikubwabo, T}, title = {Seasonal assessment of drinking water sources in Rwanda using GIS, contamination degree (Cd), and metal index (MI).}, journal = {Environmental monitoring and assessment}, volume = {191}, number = {12}, pages = {734}, pmid = {31707592}, issn = {1573-2959}, mesh = {Cadmium/analysis ; Copper/analysis ; Drinking Water/*analysis ; *Environmental Monitoring ; *Geographic Information Systems ; Iron/analysis ; Metals/analysis ; Organic Chemicals/analysis ; Rain ; Rwanda ; Seasons ; Water Pollutants, Chemical/*analysis/standards ; Water Quality ; Water Supply/*statistics & numerical data ; Zinc/analysis ; }, abstract = {The quality of drinking water source remains as a major concern in areas of developing and underdeveloped countries worldwide. The treatment and supply of drinking water in Rwanda are carried out by Water and Sanitation Corporation, a state-owned public company. However, it is not able to supply water to all households. Consequently, the non-serviced households depend on natural water sources, like springs, to meet their water requirements. Nevertheless, the water quality in these springs is scarcely known. Therefore, this study assessed and compared metal elements in drinking water sources in the dry and rainy seasons in 2017 using the contamination degree, metal index, and geographic information systems to reveal the spatial distribution of water quality within the considered water sources of springs in Rwanda. The samples were collected monthly from nine water sources of springs and the measured elements are aluminium, calcium, copper, iron, manganese, and zinc. The metal index indicated that during the dry season and rainy season, the sites of Kibungo (1.10 and 1.26) and Kinigi (1.01 and 1.54) have assessed a metal index which is higher than 1. Thus, the water quality of those sites was getting the threshold of warning. The analysis indicated that pollutants are easily transported into water bodies during the rainy season in urban and rural areas to a greater extent than during the dry season .}, } @article {pmid31706230, year = {2020}, author = {Anne, N and Dunbar, MD and Abuna, F and Simpson, P and Macharia, P and Betz, B and Cherutich, P and Bukusi, D and Carey, F}, title = {Feasibility and acceptability of an iris biometric system for unique patient identification in routine HIV services in Kenya.}, journal = {International journal of medical informatics}, volume = {133}, number = {}, pages = {104006}, pmid = {31706230}, issn = {1872-8243}, support = {D43 TW009783/TW/FIC NIH HHS/United States ; R01 AI099974/AI/NIAID NIH HHS/United States ; }, mesh = {Adult ; *Biometric Identification ; Feasibility Studies ; Female ; *HIV Infections ; Health Information Systems ; Humans ; Iris ; Kenya ; Male ; Middle Aged ; *Records ; }, abstract = {BACKGROUND: Use of routine HIV programme data for surveillance is often limited due to inaccuracies associated with patient misclassification which can be addressed by unique patient identification.We assessed the feasibility and acceptability of integrating an iris recognition biometric identification system into routine HIV care services at 4 sites in Kenya.

METHODS: Patients who had recently tested HIV-positive or were engaged in care were enrolled. Images of the iris were captured using a dual-iris camera connected to a laptop. A prototype iris biometric identification system networked across the sites, analysed the iris patterns; created a template from those patterns; and generated a 12-digit ID number based on the template. During subsequent visits, the patients' irises were re-scanned, and the pattern was matched to stored templates to retrieve the ID number.

RESULTS: Over 55 weeks 8,614 (98%) of 8,794 new patients were assigned a unique ID on their first visit. Among 6,078 return visits, the system correctly re-identified patients' IDs 5,234 times (86%). The false match rate (a new patient given the ID of another patient) was 0·5% while the generalized false reject rate (re-scans assigned a new ID) was 4·7%. Overall, 9 (0·1%) agreed to enrol but declined to have an iris scan. The most common reasons cited for declining an iris scan were concerns about privacy and confidentiality.

CONCLUSION: Implementation of an iris recognition system in routine health information systems is feasible and highly acceptable as part of routine care in Kenya. Scale-up could improve unique patient identification and tracking, enhancing disease surveillance activities.}, } @article {pmid33123540, year = {2019}, author = {Harwell, LC and Vivian, DN and McLaughlin, MD and Hafner, SF}, title = {Scientific Data Management in the Age of Big Data: An Approach Supporting a Resilience Index Development Effort.}, journal = {Frontiers in environmental science}, volume = {7}, number = {Article 72}, pages = {1-13}, pmid = {33123540}, issn = {2296-665X}, support = {EPA999999/ImEPA/Intramural EPA/United States ; }, abstract = {The increased availability of publicly available data is, in many ways, changing our approach to conducting research. Not only are cloud-based information resources providing supplementary data to bolster traditional scientific activities (e.g., field studies, laboratory experiments), they also serve as the foundation for secondary data research projects such as indicator development. Indicators and indices are a convenient way to synthesize disparate information to address complex scientific questions that are difficult to measure directly (e.g., resilience, sustainability, well-being). In the current literature, there is no shortage of indicator or index examples derived from secondary data with a growing number that are scientifically focused. However, little information is provided describing the management approaches and best practices used to govern the data underpinnings supporting these efforts. From acquisition to storage and maintenance, secondary data research products rely on the availability of relevant, high-quality data, repeatable data handling methods and a multi-faceted data flow process to promote and sustain research transparency and integrity. The U.S. Environmental Protection Agency recently published a report describing the development of a climate resilience screening index which used over one million data points to calculate the final index. The pool of data was derived exclusively from secondary sources such as the U.S. Census Bureau, Bureau of Labor Statistics, Postal Service, Housing and Urban Development, Forestry Services and others. Available data were presented in various forms including portable document format (PDF), delimited ASCII and proprietary format (e.g., Microsoft Excel, ESRI ArcGIS). The strategy employed for managing these data in an indicator research and development effort represented a blend of business practices, information science, and the scientific method. This paper describes the approach, highlighting key points unique for managing the data assets of a smaller scale research project in an era of "big data."}, } @article {pmid33500908, year = {2018}, author = {Linson, A and Clark, A and Ramamoorthy, S and Friston, K}, title = {The Active Inference Approach to Ecological Perception: General Information Dynamics for Natural and Artificial Embodied Cognition.}, journal = {Frontiers in robotics and AI}, volume = {5}, number = {}, pages = {21}, pmid = {33500908}, issn = {2296-9144}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {The emerging neurocomputational vision of humans as embodied, ecologically embedded, social agents-who shape and are shaped by their environment-offers a golden opportunity to revisit and revise ideas about the physical and information-theoretic underpinnings of life, mind, and consciousness itself. In particular, the active inference framework (AIF) makes it possible to bridge connections from computational neuroscience and robotics/AI to ecological psychology and phenomenology, revealing common underpinnings and overcoming key limitations. AIF opposes the mechanistic to the reductive, while staying fully grounded in a naturalistic and information-theoretic foundation, using the principle of free energy minimization. The latter provides a theoretical basis for a unified treatment of particles, organisms, and interactive machines, spanning from the inorganic to organic, non-life to life, and natural to artificial agents. We provide a brief introduction to AIF, then explore its implications for evolutionary theory, ecological psychology, embodied phenomenology, and robotics/AI research. We conclude the paper by considering implications for machine consciousness.}, } @article {pmid32214900, year = {2017}, author = {Meiyappan, P and Roy, PS and Sharma, Y and Ramachandran, RM and Joshi, PK and DeFries, RS and Jain, AK}, title = {Dynamics and determinants of land change in India: integrating satellite data with village socioeconomics.}, journal = {Regional environmental change}, volume = {17}, number = {3}, pages = {753-766}, pmid = {32214900}, issn = {1436-3798}, abstract = {We examine the dynamics and spatial determinants of land change in India by integrating decadal land cover maps (1985-1995-2005) from a wall-to-wall analysis of Landsat images with spatiotemporal socioeconomic database for ~630,000 villages in India. We reinforce our results through collective evidence from synthesis of 102 case studies that incorporate field knowledge of the causes of land change in India. We focus on cropland-fallow land conversions, and forest area changes (excludes non-forest tree categories including commercial plantations). We show that cropland to fallow conversions are prominently associated with lack of irrigation and capital, male agricultural labor shortage, and fragmentation of land holdings. We find gross forest loss is substantial and increased from ~23,810 km[2] (1985-1995) to ~25,770 km[2] (1995-2005). The gross forest gain also increased from ~6000 km[2] (1985-1995) to ~7440 km[2] (1995-2005). Overall, India experienced a net decline in forest by ~18,000 km[2] (gross loss-gross gain) consistently during both decades. We show that the major source of forest loss was cropland expansion in areas of low cropland productivity (due to soil degradation and lack of irrigation), followed by industrial development and mining/quarrying activities, and excessive economic dependence of villages on forest resources.}, } @article {pmid32313363, year = {2008}, author = {Janies, D and Habib, F and Alexandrov, B and Hill, A and Pol, D}, title = {Evolution of genomes, host shifts and the geographic spread of SARS-CoV and related coronaviruses.}, journal = {Cladistics : the international journal of the Willi Hennig Society}, volume = {24}, number = {2}, pages = {111-130}, pmid = {32313363}, issn = {0748-3007}, abstract = {Severe acute respiratory syndrome (SARS) is a novel human illness caused by a previously unrecognized coronavirus (CoV) termed SARS-CoV. There are conflicting reports on the animal reservoir of SARS-CoV. Many of the groups that argue carnivores are the original reservoir of SARS-CoV use a phylogeny to support their argument. However, the phylogenies in these studies often lack outgroup and rooting criteria necessary to determine the origins of SARS-CoV. Recently, SARS-CoV has been isolated from various species of Chiroptera from China (e.g., Rhinolophus sinicus) thus leading to reconsideration of the original reservoir of SARS-CoV. We evaluated the hypothesis that SARS-CoV isolated from Chiroptera are the original zoonotic source for SARS-CoV by sampling SARS-CoV and non-SARS-CoV from diverse hosts including Chiroptera, as well as carnivores, artiodactyls, rodents, birds and humans. Regardless of alignment parameters, optimality criteria, or isolate sampling, the resulting phylogenies clearly show that the SARS-CoV was transmitted to small carnivores well after the epidemic of SARS in humans that began in late 2002. The SARS-CoV isolates from small carnivores in Shenzhen markets form a terminal clade that emerged recently from within the radiation of human SARS-CoV. There is evidence of subsequent exchange of SARS-CoV between humans and carnivores. In addition SARS-CoV was transmitted independently from humans to farmed pigs (Sus scrofa). The position of SARS-CoV isolates from Chiroptera are basal to the SARS-CoV clade isolated from humans and carnivores. Although sequence data indicate that Chiroptera are a good candidate for the original reservoir of SARS-CoV, the structural biology of the spike protein of SARS-CoV isolated from Chiroptera suggests that these viruses are not able to interact with the human variant of the receptor of SARS-CoV, angiotensin-converting enzyme 2 (ACE2). In SARS-CoV we study, both visually and statistically, labile genomic fragments and, putative key mutations of the spike protein that may be associated with host shifts. We display host shifts and candidate mutations on trees projected in virtual globes depicting the spread of SARS-CoV. These results suggest that more sampling of coronaviruses from diverse hosts, especially Chiroptera, carnivores and primates, will be required to understand the genomic and biochemical evolution of coronaviruses, including SARS-CoV. © The Willi Hennig Society 2008.}, } @article {pmid32362769, year = {2006}, author = {Carson, E and Feng, DD and Pons, MN and Soncini-Sessa, R and van Straten, G}, title = {Dealing with bio- and ecological complexity: Challenges and opportunities.}, journal = {Annual reviews in control}, volume = {30}, number = {1}, pages = {91-101}, pmid = {32362769}, issn = {1367-5788}, abstract = {The complexities of the dynamic processes and their control associated with biological and ecological systems offer many challenges for the control engineer. Over the past decades the application of dynamic modelling and control has aided understanding of their complexities. At the same time using such complex systems as test-beds for new control methods has highlighted their limitations (e.g. in relation to system identification) and has thus acted as a catalyst for methodological advance. This paper continues the theme of exploring opportunities and achievements in applying modelling and control in the bio- and ecological domains.}, } @article {pmid31704410, year = {2020}, author = {Chen, W and Zhao, H and Li, J and Zhu, L and Wang, Z and Zeng, J}, title = {Land use transitions and the associated impacts on ecosystem services in the Middle Reaches of the Yangtze River Economic Belt in China based on the geo-informatic Tupu method.}, journal = {The Science of the total environment}, volume = {701}, number = {}, pages = {134690}, doi = {10.1016/j.scitotenv.2019.134690}, pmid = {31704410}, issn = {1879-1026}, abstract = {Rapid urbanization in China has greatly exacerbated land use transitions (LUTs), which seriously threaten the ecosystem. The existing literature lacks information on the spatio-temporal analysis of LUTs, and assessments of ecosystem services remain incomplete. This lack of information may limit the formation and implementation of landscape plans and ecologically oriented policies. This study attempts to fill this gap by analysing the geographic features of LUTs with the geo-informatic Tupu method and exploring the responses of ecosystem services to LUTs. A newly revised benefit transfer method that utilizes the land use/land cover change data derived from the Landsat Enhanced Thematic Mapper (ETM) in the Middle Reaches of the Yangtze River Economic Belt (MRYREB) is implemented. The results indicate that the area of construction land continued to increase markedly, while the area of cultivated land declined continuously from 1995 to 2015. This increase in construction land was mainly derived from the occupation of cultivated land. The Tupu units of "forestland → cultivated land," "cultivated land → forestland," "cultivated land → water area," and "water area → cultivated land" were the dominant driving forces of the changes in ecosystem services value (ESV) in the MRYREB. Hotspots of ESV changes were mainly located in the surrounding mountainous areas during 1995-2005 and 2005-2010, while the coldspots during 2010-2015 were mainly located in the plains. The findings in this study have important implications for ecosystem conservation, ecological function zoning, ecological compensation decision-making, and related land development in the MRYREB.}, } @article {pmid31701637, year = {2020}, author = {Ren, Q and Si, H and Yan, X and Liu, C and Ding, L and Long, R and Li, Z and Qiu, Q}, title = {Bacterial communities in the solid, liquid, dorsal, and ventral epithelium fractions of yak (Bos grunniens) rumen.}, journal = {MicrobiologyOpen}, volume = {9}, number = {2}, pages = {e963}, pmid = {31701637}, issn = {2045-8827}, mesh = {Animals ; Biodiversity ; Cattle ; Computational Biology/methods ; Gastric Mucosa/*microbiology ; High-Throughput Nucleotide Sequencing ; Metagenome ; Metagenomics/methods ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Real-Time Polymerase Chain Reaction ; Rumen/*microbiology ; Sequence Analysis, DNA ; }, abstract = {Yak (Bos grunniens) is an important and dominant livestock species in the challenging environment of the Qinghai-Tibetan Plateau. Rumen microbiota of the solid, liquid, and epithelium fractions play key roles in nutrient metabolism and contribute to host adaptation in ruminants. However, there is a little knowledge of the microbiota in these rumen fractions of yak. Therefore, we collected samples of solid, liquid, dorsal, and ventral epithelium fractions from five female yaks, then amplified bacterial 16S rRNA gene V4 regions and sequenced them using an Illumina MiSeq platform. Principal coordinates analysis detected significant differences in bacterial communities between the liquid, solid, and epithelium fractions, and between dorsal and ventral epithelium fractions. Rikenellaceae RC9, the families Lachnospiraceae and Ruminococcaceae, and Fibrobacter spp. were the abundant and enriched bacteria in solid fraction, while the genera Prevotella and Prevotellaceae UCG 003 were higher in the liquid fraction. Campylobacter spp., Comamonas spp., Desulfovibrio spp., and Solobacterium spp. were significantly higher in dorsal epithelium, while Howardella spp., Prevotellaceae UCG 001, Ruminococcaceae UCG 005, and Treponema 2 were enriched in the ventral epithelium. Comparison of predictive functional profiles among the solid, liquid, and dorsal, and ventral epithelium fractions also revealed significant differences. Microbiota in the ventral fraction of yak rumen also significantly differ from reported microbiota of cattle. In conclusion, our results improve our knowledge of the taxonomic composition and roles of yak rumen microbiota.}, } @article {pmid31701533, year = {2020}, author = {Purgato, M and Tedeschi, F and Betancourt, TS and Bolton, P and Bonetto, C and Gastaldon, C and Gordon, J and O'Callaghan, P and Papola, D and Peltonen, K and Punamaki, RL and Richards, J and Staples, JK and Unterhitzenberger, J and de Jong, J and Jordans, MJD and Gross, AL and Tol, WA and Barbui, C}, title = {Mediators of focused psychosocial support interventions for children in low-resource humanitarian settings: analysis from an Individual Participant Dataset with 3,143 participants.}, journal = {Journal of child psychology and psychiatry, and allied disciplines}, volume = {61}, number = {5}, pages = {584-593}, doi = {10.1111/jcpp.13151}, pmid = {31701533}, issn = {1469-7610}, support = {626466/MCCC_/Marie Curie/United Kingdom ; }, mesh = {Adaptation, Psychological ; Child ; *Datasets as Topic ; Hope ; Humans ; *Psychosocial Intervention ; *Psychosocial Support Systems ; Randomized Controlled Trials as Topic ; Social Support ; }, abstract = {BACKGROUND: Research on psychosocial interventions has been focused on the effectiveness of psychosocial interventions on mental health outcomes, without exploring how interventions achieve beneficial effects. Identifying the potential pathways through which interventions work would potentially allow further strengthening of interventions by emphasizing specific components connected with such pathways.

METHODS: We conducted a preplanned mediation analysis using individual participant data from a dataset of 11 randomized controlled trials (RCTs) which compared focused psychosocial support interventions versus control conditions for children living in low- and middle-income countries (LMICs) affected by humanitarian crises. Based on an ecological resilience framework, we hypothesized that (a) coping, (b) hope, (c) social support, and (d) functional impairment mediate the relationship between intervention and outcome PTSD symptoms. A systematic search on the Cochrane Central Register of Controlled Trials (CENTRAL), MEDLINE, PubMed, PyscARTICLES, Web of Science, and the main local LMICs databases was conducted up to August 2018. The hypotheses were tested by using individual participant data obtained from study authors of all the studies included in the systematic review.

RESULTS: We included 3,143 children from 11 studies (100% of data from included studies), of which 1,877 from six studies contributed to the mediation analysis. Functional impairment was the strongest mediator for focused psychosocial interventions on PTSD (mediation coefficient -0.087, standard error 0.040). The estimated proportion of effect mediated by functional impairment, and adjusted for confounders, was 31%.

CONCLUSIONS: Findings did not support the proposed mediation hypotheses for coping, hope, and social support. The mediation through functional impairment may represent unmeasured proxy measures or point to a broader mechanism that impacts self-efficacy and agency.}, } @article {pmid31698858, year = {2019}, author = {Liu, S and Zheng, Y and Ma, Y and Sarwar, A and Zhao, X and Luo, T and Yang, Z}, title = {Evaluation and Proteomic Analysis of Lead Adsorption by Lactic Acid Bacteria.}, journal = {International journal of molecular sciences}, volume = {20}, number = {22}, pages = {}, pmid = {31698858}, issn = {1422-0067}, support = {31871823//National Natural Science Foundation of China/ ; PXM2019_014213_000010//Beijing Talent Cultivation Quality Construction - First-class Professional Construction (Municipal Level) - Food Science and Engineering/ ; }, mesh = {Adsorption ; Bacterial Proteins/metabolism ; Gene Ontology ; Genes, Bacterial ; Lactobacillales/drug effects/growth & development/*metabolism/ultrastructure ; Lead/*metabolism/toxicity ; Molecular Sequence Annotation ; Proteomics/*methods ; Spectrometry, X-Ray Emission ; Water/chemistry ; }, abstract = {Heavy metals are a growing threat to human health due to the resulting damage to the ecology; the removal of heavy metals by lactic acid bacteria (LAB) has been a focus of many studies. In this study, 10 LAB strains were evaluated for their ability to absorb and tolerate lead. Lactobacillus plantarum YW11 was found to possess the strongest ability of lead absorbing and tolerance, with the rate of absorption as high as 99.9% and the minimum inhibitory concentration of lead on YW11 higher than 1000 mg/L. Based on the isobaric tags for relative and absolute quantitation (iTRAQ) proteomics analysis of YW11, a total of 2009 proteins were identified both in the lead-treated strain and the control without the lead treatment. Among these proteins, 44 different proteins were identified. The abundance of 25 proteins increased significantly, and 19 proteins decreased significantly in the treatment group. These significantly differential abundant proteins are involved in the biological processes of amino acid and lipid metabolism, energy metabolism, cell wall biosynthesis, and substance transport. This study contributed further understanding of the molecular mechanism of L. plantarum in the binding and removal of lead to explore its potential application in counteracting heavy metal pollution of environment, food, and other fields.}, } @article {pmid31698527, year = {2020}, author = {Roesch, LFW and Dobbler, PT and Pylro, VS and Kolaczkowski, B and Drew, JC and Triplett, EW}, title = {pime: A package for discovery of novel differences among microbial communities.}, journal = {Molecular ecology resources}, volume = {20}, number = {2}, pages = {415-428}, doi = {10.1111/1755-0998.13116}, pmid = {31698527}, issn = {1755-0998}, support = {//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; //Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; 5R21AI120195-02/GF/NIH HHS/United States ; 1-INO-2018-637-A-N//JDRF/United States ; }, mesh = {Bacteria/classification/genetics/*isolation & purification ; Computational Biology/*methods ; DNA, Bacterial/genetics ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The data used for profiling microbial communities is usually sparse with some microbes having high abundance in a few samples and being nearly absent in others. However, current bioinformatics tools able to deal with this sparsity are lacking. pime (Prevalence Interval for Microbiome Evaluation) was designed to remove those taxa that may be high in relative abundance in just a few samples but have a low prevalence overall. The reliability and robustness of pime were compared against existing methods and tested using 16S rRNA independent data sets. pime filters microbial taxa not shared in a per treatment prevalence interval started at 5% prevalence with increasing increments of 5% at each filtering step. For each prevalence interval, hundreds of decision trees were calculated to predict the likelihood of detecting differences in treatments. The best prevalence-filtered data set was user-selected by choosing the prevalence interval that kept a large portion of the 16S rRNA sequences in the data set while also showing the lowest error rate. To obtain the likelihood of introducing type I error while building prevalence-filtered data sets, an error detection step based was also included. A pime reanalysis of published data sets uncovered other expected microbial associations than previously reported, which may be masked when only relative abundance was considered.}, } @article {pmid31697748, year = {2019}, author = {Liu, Y and Li, L and Chen, L and Cheng, L and Zhou, X and Cui, Y and Li, H and Liu, W}, title = {Urban growth simulation in different scenarios using the SLEUTH model: A case study of Hefei, East China.}, journal = {PloS one}, volume = {14}, number = {11}, pages = {e0224998}, pmid = {31697748}, issn = {1932-6203}, mesh = {Calibration ; China ; *City Planning ; *Computer Simulation ; Geography ; *Models, Theoretical ; *Urban Population ; }, abstract = {As uncontrolled urban growth has increasingly challenged the sustainable use of urban land, it is critically important to model urban growth from different perspectives. Using the SLEUTH (Slope, Land use, Exclusion, Urban, Transportation, and Hill-shade) model, the historical data of Hefei in 2000, 2005, 2010, and 2015 were collected and input to simulate urban growth from 2015 to 2040. Three different urban growth scenarios were considered, namely a historical growth scenario, an urban planning growth scenario, and a land suitability growth scenario. Prediction results show that by 2040 urban built-up land would increase to 1434 km2 in the historical growth scenario, to 1190 km2 in the urban planning growth scenario, and to 1217 km2 in the land suitability growth scenario. We conclude that (1) exclusion layers without effective limits might result in unreasonable prediction of future built-up land; (2) based on the general land use map, the urban growth prediction took the governmental policies into account and could reveal the development hotspots in urban planning; and (3) the land suitability scenario prediction was the result of the trade-off between ecological land and built-up land as it used the MCR -based (minimum cumulative resistance model) land suitability assessment result. It would help to form a compact urban space and avoid excessive protection of farmland and ecological land. Findings derived from this study may provide urban planners with interesting insights on formulating urban planning strategies.}, } @article {pmid31697408, year = {2020}, author = {Igarashi, Y and Shimizu, K and Mizutaka, S and Kagawa, K}, title = {Pregnancy parturition scars in the preauricular area and the association with the total number of pregnancies and parturitions.}, journal = {American journal of physical anthropology}, volume = {171}, number = {2}, pages = {260-274}, pmid = {31697408}, issn = {1096-8644}, support = {08740680//Japan Society for the Promotion of Science/International ; 15K01135//Japan Society for the Promotion of Science/International ; 29019-CR-1025//Cooperative Research/International ; 2018-CR-1021//Cooperative Research/International ; }, mesh = {Adolescent ; Adult ; Aged ; Aged, 80 and over ; Cicatrix/*pathology ; Female ; *Fertility ; Humans ; Japan ; Male ; Middle Aged ; Parturition/*physiology ; Pelvic Bones/*pathology ; Pregnancy ; Young Adult ; }, abstract = {OBJECTIVES: The aim of the present study was to clarify the association between the degree of development of pregnancy parturition scars (PPSs) and the total number of pregnancies and parturitions (TNPPs) on the basis of new identification standards for PPS in the preauricular area.

MATERIALS AND METHODS: Preauricular grooves were macroscopically observed on the pelves of 103 early modern males and 295 females (62 early modern females; 233 present-day females). Three categories of PPS in the preauricular area were defined. The association between the degree of development of PPS in the preauricular area and the TNPP was analyzed in 90 present-day females with detailed lifetime data.

RESULTS: PPS could not estimate the exact TNPP. However, it was shown that no PPS indicated no TNPP, weak PPS indicated a lower TNPP, and developed PPS indicated a higher TNPP.

DISCUSSION: Even though the possibility remains that some PPS indicate no TNPP, the results showed that the percentage of each PPS category indicated fertility in the population, suggesting that the strength of the association between the degree of development of PPS and the TNPP was affected by the classification system, the reliability of lifetime data, and the statistical methods used for analysis.}, } @article {pmid31697362, year = {2019}, author = {Sima, AC and Mendes de Farias, T and Zbinden, E and Anisimova, M and Gil, M and Stockinger, H and Stockinger, K and Robinson-Rechavi, M and Dessimoz, C}, title = {Enabling semantic queries across federated bioinformatics databases.}, journal = {Database : the journal of biological databases and curation}, volume = {2019}, number = {}, pages = {}, pmid = {31697362}, issn = {1758-0463}, mesh = {*Biological Ontologies ; *Computational Biology ; *Databases, Factual ; *Semantic Web ; }, abstract = {MOTIVATION: Data integration promises to be one of the main catalysts in enabling new insights to be drawn from the wealth of biological data available publicly. However, the heterogeneity of the different data sources, both at the syntactic and the semantic level, still poses significant challenges for achieving interoperability among biological databases.

RESULTS: We introduce an ontology-based federated approach for data integration. We applied this approach to three heterogeneous data stores that span different areas of biological knowledge: (i) Bgee, a gene expression relational database; (ii) Orthologous Matrix (OMA), a Hierarchical Data Format 5 orthology DS; and (iii) UniProtKB, a Resource Description Framework (RDF) store containing protein sequence and functional information. To enable federated queries across these sources, we first defined a new semantic model for gene expression called GenEx. We then show how the relational data in Bgee can be expressed as a virtual RDF graph, instantiating GenEx, through dedicated relational-to-RDF mappings. By applying these mappings, Bgee data are now accessible through a public SPARQL endpoint. Similarly, the materialized RDF data of OMA, expressed in terms of the Orthology ontology, is made available in a public SPARQL endpoint. We identified and formally described intersection points (i.e. virtual links) among the three data sources. These allow performing joint queries across the data stores. Finally, we lay the groundwork to enable nontechnical users to benefit from the integrated data, by providing a natural language template-based search interface.}, } @article {pmid31695696, year = {2019}, author = {Salnikova, LE and Chernyshova, EV and Anastasevich, LA and Larin, SS}, title = {Gene- and Disease-Based Expansion of the Knowledge on Inborn Errors of Immunity.}, journal = {Frontiers in immunology}, volume = {10}, number = {}, pages = {2475}, pmid = {31695696}, issn = {1664-3224}, mesh = {Computational Biology/methods ; Databases, Genetic ; *Genetic Association Studies/methods ; Genetic Diseases, Inborn/diagnosis/*genetics/*immunology/therapy ; *Genetic Predisposition to Disease ; Genotype ; Humans ; Immune System Diseases/diagnosis/*genetics/*immunology/therapy ; Immunity/genetics ; Molecular Sequence Annotation ; Phenotype ; Quantitative Trait, Heritable ; Severity of Illness Index ; }, abstract = {The recent report of the International Union of Immunological Societies (IUIS) has provided the categorized list of 354 inborn errors of immunity. We performed a systematic analysis of genes and diseases from the IUIS report with the use of the OMIM, ORPHANET, and HPO resources. To measure phenotypic similarity we applied the Jaccard/Tanimoto (J/T) coefficient for HPO terms and top-level categories. Low J/T coefficients for HPO terms for OMIM or ORPHANET disease pairs associated with the same genes indicated high pleiotropy of these genes. Gene ORGANizer enrichment analysis demonstrated that gene sets related to HPO top-level categories were most often enriched in immune, lymphatic, and corresponding body systems (for example, genes from the category "Cardiovascular" were enriched in cardiovascular system). We presented available data on frequent and very frequent clinical signs and symptoms in inborn errors of immunity. With the use of DisGeNET, we generated the list of 25 IUIS/OMIM diseases with two or more relatively high score gene-disease associations, found for unrelated genes and/or for clusters of genes coding for interacting proteins. Our study showed the enrichment of gene sets related to several IUIS categories with neoplastic and autoimmune diseases from the GWAS Catalog and reported individual genes with phenotypic overlap between inborn errors of immunity and GWAS diseases/traits. We concluded that genetic background may play a role in phenotypic diversity of inborn errors of immunity.}, } @article {pmid31694865, year = {2019}, author = {Greenbaum, G and Rubin, A and Templeton, AR and Rosenberg, NA}, title = {Network-based hierarchical population structure analysis for large genomic data sets.}, journal = {Genome research}, volume = {29}, number = {12}, pages = {2020-2033}, pmid = {31694865}, issn = {1549-5469}, support = {R01 HG005855/HG/NHGRI NIH HHS/United States ; }, mesh = {*Algorithms ; *Databases, Nucleic Acid ; *Genome, Human ; *Genomics ; Humans ; *Sequence Analysis, DNA ; }, abstract = {Analysis of population structure in natural populations using genetic data is a common practice in ecological and evolutionary studies. With large genomic data sets of populations now appearing more frequently across the taxonomic spectrum, it is becoming increasingly possible to reveal many hierarchical levels of structure, including fine-scale genetic clusters. To analyze these data sets, methods need to be appropriately suited to the challenges of extracting multilevel structure from whole-genome data. Here, we present a network-based approach for constructing population structure representations from genetic data. The use of community-detection algorithms from network theory generates a natural hierarchical perspective on the representation that the method produces. The method is computationally efficient, and it requires relatively few assumptions regarding the biological processes that underlie the data. We show the approach by analyzing population structure in the model plant species Arabidopsis thaliana and in human populations. These examples illustrate how network-based approaches for population structure analysis are well-suited to extracting valuable ecological and evolutionary information in the era of large genomic data sets.}, } @article {pmid31690337, year = {2019}, author = {Pisano, SRR and Zimmermann, F and Rossi, L and Capt, S and Akdesir, E and Bürki, R and Kunz, F and Origgi, FC and Ryser-Degiorgis, MP}, title = {Spatiotemporal spread of sarcoptic mange in the red fox (Vulpes vulpes) in Switzerland over more than 60 years: lessons learnt from comparative analysis of multiple surveillance tools.}, journal = {Parasites & vectors}, volume = {12}, number = {1}, pages = {521}, pmid = {31690337}, issn = {1756-3305}, mesh = {Animals ; Communicable Diseases, Emerging/epidemiology/parasitology/*veterinary ; Datasets as Topic ; Female ; Foxes/*parasitology ; Male ; Prevalence ; Prospective Studies ; Retrospective Studies ; Scabies/epidemiology/parasitology/*veterinary ; Spatio-Temporal Analysis ; Surveys and Questionnaires ; Switzerland/epidemiology ; }, abstract = {BACKGROUND: Sarcoptic mange is a contagious skin disease of wild and domestic mammals caused by the mite Sarcoptes scabiei. Reports of sarcoptic mange in wildlife increased worldwide in the second half of the 20th century, especially since the 1990s. The aim of this study was to provide new insights into the epidemiology of mange by (i) documenting the emergence of sarcoptic mange in the red fox (Vulpes vulpes) in the last decades in Switzerland; and (ii) describing its spatiotemporal spread combining data obtained through different surveillance methods.

METHODS: Retrospective analysis of archived material together with prospective data collection delivered a large dataset from the 19th century to 2018. Methods included: (i) a review of historical literature; (ii) screening of necropsy reports from general health surveillance (1958-2018); (iii) screening of data on mange (1968-1992) collected during the sylvatic rabies eradication campaign; (iv) a questionnaire survey (<1980-2017) and (v) evaluation of camera-trap bycatch data (2005-2018).

RESULTS: Sarcoptic mange in red foxes was reported as early as 1835 in Switzerland. The first case diagnosed in the framework of the general health surveillance was in 1959. Prior to 1980, sarcoptic mange occurred in non-adjacent surveillance districts scattered all over the country. During the period of the rabies epidemic (1970s-early 1990s), the percentage of foxes tested for rabies with sarcoptic mange significantly decreased in subregions with rabies, whereas it remained high in the few rabies-free subregions. Sarcoptic mange re-emerged in the mid-1990s and continuously spread during the 2000-2010s, to finally extend to the whole country in 2017. The yearly prevalence of mange in foxes estimated by camera-trapping ranged from 0.1-12%.

CONCLUSIONS: Sarcoptic mange has likely been endemic in Switzerland as well as in other European countries at least since the mid-19th century. The rabies epidemics seem to have influenced the pattern of spread of mange in several locations, revealing an interesting example of disease interaction in free-ranging wildlife populations. The combination of multiple surveillance tools to study the long-term dynamics of sarcoptic mange in red foxes in Switzerland proved to be a successful strategy, which underlined the usefulness of questionnaire surveys.}, } @article {pmid31689942, year = {2019}, author = {Sommers, P and Fontenele, RS and Kringen, T and Kraberger, S and Porazinska, DL and Darcy, JL and Schmidt, SK and Varsani, A}, title = {Single-Stranded DNA Viruses in Antarctic Cryoconite Holes.}, journal = {Viruses}, volume = {11}, number = {11}, pages = {}, pmid = {31689942}, issn = {1999-4915}, mesh = {Antarctic Regions ; DNA Viruses/classification/*genetics/isolation & purification ; DNA, Circular ; *DNA, Single-Stranded ; DNA, Viral/genetics ; Fresh Water/virology ; Genome, Viral/genetics ; Ice Cover/*virology ; Metagenomics ; Microbiota/genetics ; Microviridae/classification/genetics/isolation & purification ; Open Reading Frames ; Phylogeny ; Viral Proteins/genetics ; }, abstract = {Antarctic cryoconite holes, or small melt-holes in the surfaces of glaciers, create habitable oases for isolated microbial communities with tightly linked microbial population structures. Viruses may influence the dynamics of polar microbial communities, but the viromes of the Antarctic cryoconite holes have yet to be characterized. We characterize single-stranded DNA (ssDNA) viruses from three cryoconite holes in the Taylor Valley, Antarctica, using metagenomics. Half of the assembled metagenomes cluster with those in the viral family Microviridae (n = 7), and the rest with unclassified circular replication associated protein (Rep)-encoding single-stranded (CRESS) DNA viruses (n = 7). An additional 18 virus-like circular molecules encoding either a Rep, a capsid protein gene, or other unidentified but viral-like open reading frames were identified. The samples from which the genomes were identified show a strong gradient in microbial diversity and abundances, and the number of viral genomes detected in each sample mirror that gradient. Additionally, one of the CRESS genomes assembled here shares ~90% genome-wide pairwise identity with a virus identified from a freshwater pond on the McMurdo Ice Shelf (Antarctica). Otherwise, the similarity of these viruses to those previously identified is relatively low. Together, these patterns are consistent with the presence of a unique regional virome present in fresh water host populations of the McMurdo Dry Valley region.}, } @article {pmid31688940, year = {2019}, author = {Buble, K and Jung, S and Humann, JL and Yu, J and Cheng, CH and Lee, T and Ficklin, SP and Hough, H and Condon, B and Staton, ME and Wegrzyn, JL and Main, D}, title = {Tripal MapViewer: A tool for interactive visualization and comparison of genetic maps.}, journal = {Database : the journal of biological databases and curation}, volume = {2019}, number = {}, pages = {}, pmid = {31688940}, issn = {1758-0463}, mesh = {*Databases, Genetic ; *Genome, Plant ; Genomics ; *Internet ; *Quantitative Trait Loci ; Rosaceae/*genetics ; *User-Computer Interface ; }, abstract = {Tripal is an open-source, resource-efficient toolkit for construction of genomic, genetic and breeding databases. It facilitates development of biological websites by providing tools to integrate and display biological data using the generic database schema, Chado, together with Drupal, a popular website creation and content management system. Tripal MapViewer is a new interactive tool for visualizing genetic map data. Developed as a Tripal replacement for Comparative Map Viewer (CMap), it enables visualization of entire maps or linkage groups and features such as molecular markers, quantitative trait loci (QTLs) and heritable phenotypic markers. It also provides graphical comparison of maps sharing the same markers as well as dot plot and correspondence matrices. MapViewer integrates directly with the Tripal application programming interface framework, improving data searching capability and providing a more seamless experience for site visitors. The Tripal MapViewer interface can be integrated in any Tripal map page and linked from any Tripal page for markers, QTLs, heritable morphological markers or genes. Configuration of the display is available through a control panel and the administration interface. The administration interface also allows configuration of the custom database query for building materialized views, providing better performance and flexibility in the way data is stored in the Chado database schema. MapViewer is implemented with the D3.js technology and is currently being used at the Genome Database for Rosaceae (https://www.rosaceae.org), CottonGen (https://www.cottongen.org), Citrus Genome Database (https://citrusgenomedb.org), Vaccinium Genome Database (https://www.vaccinium.org) and Cool Season Food Legume Database (https://www.coolseasonfoodlegume.org). It is also currently in development on the Hardwood Genomics Web (https://hardwoodgenomics.org) and TreeGenes (https://treegenesdb.org). Database URL: https://gitlab.com/mainlabwsu/tripal_map.}, } @article {pmid31687752, year = {2019}, author = {Varadharajan, S and Rastas, P and Löytynoja, A and Matschiner, M and Calboli, FCF and Guo, B and Nederbragt, AJ and Jakobsen, KS and Merilä, J}, title = {A High-Quality Assembly of the Nine-Spined Stickleback (Pungitius pungitius) Genome.}, journal = {Genome biology and evolution}, volume = {11}, number = {11}, pages = {3291-3308}, pmid = {31687752}, issn = {1759-6653}, mesh = {Animals ; DNA Transposable Elements ; Evolution, Molecular ; Female ; Fish Proteins/genetics ; *Genome ; Hemoglobins/genetics ; Male ; Microsatellite Repeats ; Molecular Sequence Annotation ; Perciformes/classification/*genetics ; Phylogeny ; Recombination, Genetic ; }, abstract = {The Gasterosteidae fish family hosts several species that are important models for eco-evolutionary, genetic, and genomic research. In particular, a wealth of genetic and genomic data has been generated for the three-spined stickleback (Gasterosteus aculeatus), the "ecology's supermodel," whereas the genomic resources for the nine-spined stickleback (Pungitius pungitius) have remained relatively scarce. Here, we report a high-quality chromosome-level genome assembly of P. pungitius consisting of 5,303 contigs (N50 = 1.2 Mbp) with a total size of 521 Mbp. These contigs were mapped to 21 linkage groups using a high-density linkage map, yielding a final assembly with 98.5% BUSCO completeness. A total of 25,062 protein-coding genes were annotated, and about 23% of the assembly was found to consist of repetitive elements. A comprehensive analysis of repetitive elements uncovered centromere-specific tandem repeats and provided insights into the evolution of retrotransposons. A multigene phylogenetic analysis inferred a divergence time of about 26 million years ago (Ma) between nine- and three-spined sticklebacks, which is far older than the commonly assumed estimate of 13 Ma. Compared with the three-spined stickleback, we identified an additional duplication of several genes in the hemoglobin cluster. Sequencing data from populations adapted to different environments indicated potential copy number variations in hemoglobin genes. Furthermore, genome-wide synteny comparisons between three- and nine-spined sticklebacks identified chromosomal rearrangements underlying the karyotypic differences between the two species. The high-quality chromosome-scale assembly of the nine-spined stickleback genome obtained with long-read sequencing technology provides a crucial resource for comparative and population genomic investigations of stickleback fishes and teleosts.}, } @article {pmid31686138, year = {2020}, author = {Weighman, KK and Moore, PA}, title = {Mapping Dynamic Exposure: Constructing GIS Models of Spatiotemporal Heterogeneity in Artificial Stream Systems.}, journal = {Archives of environmental contamination and toxicology}, volume = {78}, number = {2}, pages = {230-244}, doi = {10.1007/s00244-019-00682-1}, pmid = {31686138}, issn = {1432-0703}, mesh = {Dopamine/analysis ; Ecosystem ; Ecotoxicology/*methods ; *Geographic Information Systems ; Groundwater/analysis/chemistry ; Rivers/*chemistry ; Spatio-Temporal Analysis ; Water Pollutants, Chemical/*analysis/toxicity ; }, abstract = {In flowing environments, the degree of turbulent flow determines the movement and distribution of chemicals. Variation in flow alters the patchiness of toxicant plumes within a stream ecosystem. This patchiness translates into variability in exposure pulses for organisms encountering the toxic plume. Throughout a stream, the processes that give rise to chemical plume structure will vary as a function of local flow characteristics. This research examines the influence of toxicant mode of entry and stream flow velocity on the spatiotemporal patterning of exposure. Two introduction treatments were evaluated: one mimicking groundwater and the other mimicking runoff. The influence of flow regime was examined through the comparison of models constructed under two stream flow velocities. Concentrations of a tracer molecule were recorded using an electrochemical monitoring system. From these localized, direct measurements, geographic information systems (GIS) were used to model exposure throughout the stream. Conceptualizing exposure as a series of toxicant pulses, exposure can be defined using a variety of chemical peak characteristics. Three-dimensional, layered maps were constructed defining exposure as the integrated area of toxicant peaks, the magnitude of peaks, and peak frequency. Differences in the spatial and temporal patterning of exposure were apparent both within treatments and between treatments. No two definitions of exposure yielded the same exposure distributions for any treatment. These models demonstrate that distribution of chemical exposure throughout a stream ecosystem is linked to both toxicant mode of introduction and stream hydrodynamics. Furthermore, these results demonstrate that optimal exposure modeling relies on first defining exposure.}, } @article {pmid31685936, year = {2020}, author = {Bjorbækmo, MFM and Evenstad, A and Røsæg, LL and Krabberød, AK and Logares, R}, title = {The planktonic protist interactome: where do we stand after a century of research?.}, journal = {The ISME journal}, volume = {14}, number = {2}, pages = {544-559}, pmid = {31685936}, issn = {1751-7370}, mesh = {Alveolata ; Animals ; Aquatic Organisms ; Bacteria/*classification ; Biological Evolution ; Databases, Factual ; Ecology ; Ecosystem ; Eukaryota/*classification ; Metagenomics ; Microalgae ; *Microbial Interactions ; *Oceans and Seas ; Parasites ; Phylogeny ; Plankton/classification/microbiology/parasitology ; Rhizaria ; Stramenopiles ; Symbiosis ; }, abstract = {Microbial interactions are crucial for Earth ecosystem function, but our knowledge about them is limited and has so far mainly existed as scattered records. Here, we have surveyed the literature involving planktonic protist interactions and gathered the information in a manually curated Protist Interaction DAtabase (PIDA). In total, we have registered ~2500 ecological interactions from ~500 publications, spanning the last 150 years. All major protistan lineages were involved in interactions as hosts, symbionts (mutualists and commensalists), parasites, predators, and/or prey. Predation was the most common interaction (39% of all records), followed by symbiosis (29%), parasitism (18%), and 'unresolved interactions' (14%, where it is uncertain whether the interaction is beneficial or antagonistic). Using bipartite networks, we found that protist predators seem to be 'multivorous' while parasite-host and symbiont-host interactions appear to have moderate degrees of specialization. The SAR supergroup (i.e., Stramenopiles, Alveolata, and Rhizaria) heavily dominated PIDA, and comparisons against a global-ocean molecular survey (TARA Oceans) indicated that several SAR lineages, which are abundant and diverse in the marine realm, were underrepresented among the recorded interactions. Despite historical biases, our work not only unveils large-scale eco-evolutionary trends in the protist interactome, but it also constitutes an expandable resource to investigate protist interactions and to test hypotheses deriving from omics tools.}, } @article {pmid31683007, year = {2020}, author = {Aandahl, RZ and Bhatia, S and Vaudagnotto, N and Street, AG and Francis, AR and Tanaka, MM}, title = {MERCAT: Visualising molecular epidemiology data combining genetic markers and drug resistance profiles.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {77}, number = {}, pages = {104043}, doi = {10.1016/j.meegid.2019.104043}, pmid = {31683007}, issn = {1567-7257}, mesh = {Bacteria/classification/*genetics/isolation & purification ; Bacterial Proteins/genetics ; Computational Biology/*methods ; *Drug Resistance, Bacterial ; *Genetic Markers ; Genotype ; Humans ; Molecular Epidemiology ; Sequence Analysis, DNA ; Software ; }, abstract = {Molecular epidemiology uses genetic information from bacterial isolates to shed light on the population structure and dynamics of pathogens. Bacterial pathogens can now be studied by whole genome sequencing, but for some well-studied pathogens such as Mycobacterium tuberculosis a wealth of information is also available from other sources such as spoligotyping and multi-locus variable-number-tandem-repeats (VNTR). Isolates are also frequently tested for susceptibility to antibiotics. Methods of analysis are available for each type of data but it would be informative to combine multiple sources of information into a single analysis or visualisation. Here, we propose and implement a simple way to visualise genotypes along with drug resistance profiles for multiple drugs. We also present a way to combine information from different markers to aid in visualising relationships among isolates. These methods help to reveal the origins and spread of multi-drug resistant lineages of pathogens. We introduce a new computational package, MERCAT (Molecular Epidemiology Researcher's Collection of Analytical Tools), for analysing genotypic data from bacterial isolates. The software is available as an open source package in the statistical language R with a user-friendly interface using R Shiny. Although we focus on tuberculosis and the major molecular markers used to understand tuberculosis transmission - multilocus VNTR-typing (MLVA or MIRU) and spoligotyping - the methods and tools can be applied to other bacteria and can be easily tailored to other genetic markers such as SNP data from whole genome sequencing.}, } @article {pmid31679497, year = {2019}, author = {Grace, M and Akçakaya, HR and Bennett, E and Hilton-Taylor, C and Long, B and Milner-Gulland, EJ and Young, R and Hoffmann, M}, title = {Using historical and palaeoecological data to inform ambitious species recovery targets.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {374}, number = {1788}, pages = {20190297}, pmid = {31679497}, issn = {1471-2970}, mesh = {Animal Distribution ; *Biodiversity ; Conservation of Natural Resources/*methods ; Data Collection ; *Databases as Topic ; *Endangered Species ; Plant Dispersal ; }, abstract = {Historical data are a valuable resource for addressing present-day conservation issues, for example by informing the establishment of appropriate recovery targets. However, while the recovery of threatened species is the end goal of many conservation programmes, data made available through the efforts of palaeoecologists and historical ecologists are rarely consulted. The proposal of a 'Green List of Species' by the International Union for Conservation of Nature (IUCN) will soon change this. The Green List of Species measures recovery against historical baselines; in particular, the method requires estimates of species range and abundance in previous centuries. In this paper, we present the case for why setting species recovery against a historical baseline is necessary to produce ambitious conservation targets, and we highlight examples from palaeoecology and historical ecology where fossil and archival data have been used to establish historical species baselines. Finally, we introduce Conservation Archive (https://conservationarchive.shinyapps.io/ConservationArchive/), a database of resources that can be used to infer baseline species conditions, and invite contributions to this database. This article is part of a discussion meeting issue 'The past is a foreign country: how much can the fossil record actually inform conservation?'}, } @article {pmid31677344, year = {2020}, author = {Dumack, K and Fiore-Donno, AM and Bass, D and Bonkowski, M}, title = {Making sense of environmental sequencing data: Ecologically important functional traits of the protistan groups Cercozoa and Endomyxa (Rhizaria).}, journal = {Molecular ecology resources}, volume = {20}, number = {2}, pages = {398-403}, doi = {10.1111/1755-0998.13112}, pmid = {31677344}, issn = {1755-0998}, support = {BO 1907/13-2//Deutsche Forschungsgemeinschaft/ ; BO 1907/18-1//Deutsche Forschungsgemeinschaft/ ; Priority Program 1374//Deutsche Forschungsgemeinschaft/ ; NE/H000887/1//NERC Science of the Environment/ ; NE/H009426/1//NERC Science of the Environment/ ; }, mesh = {Cercozoa/classification/genetics ; DNA, Environmental/genetics ; Databases, Genetic ; Ecosystem ; Phenotype ; Phylogeny ; Rhizaria/classification/*genetics ; Sequence Analysis, DNA ; }, abstract = {We have compiled a database of functional traits for two widespread and ecologically important groups of protists, Cercozoa and Endomyxa (Rhizaria). The functional traits of microorganisms are crucially important for interpreting results from environmental sequencing surveys. Linking morphological and ecological traits to environmental factors is common practice in studies involving micro- and macroorganisms, but is rarely applied to protists. Our database provides functional and ecologically significant traits linked to morphology, nutrition, locomotion and habitats. We discuss how the use of functional traits may help to unveil underlying ecosystem processes. This database is intended as a common reference for the molecular ecology community and will boost the understanding of ecosystem functions, especially those driven by biological interactions.}, } @article {pmid31674643, year = {2019}, author = {Zhao, K and Ishida, Y and Green, CE and Davidson, AG and Sitam, FAT and Donnelly, CL and De Flamingh, A and Perrin-Stowe, TIN and Bourgeois, S and Brandt, AL and Mundis, SJ and van Aarde, RJ and Greenberg, JA and Malhi, RS and Georgiadis, NJ and McEwing, R and Roca, AL}, title = {Loxodonta Localizer: A Software Tool for Inferring the Provenance of African Elephants and Their Ivory Using Mitochondrial DNA.}, journal = {The Journal of heredity}, volume = {110}, number = {7}, pages = {761-768}, doi = {10.1093/jhered/esz058}, pmid = {31674643}, issn = {1465-7333}, mesh = {Africa ; Animals ; Animals, Wild ; Computational Biology/methods ; Conservation of Natural Resources ; *DNA, Mitochondrial ; Elephants/classification/*genetics ; Forensic Genetics ; Genetic Markers ; Haplotypes ; Population Dynamics ; *Software ; *Web Browser ; }, abstract = {Illegal hunting is a major threat to the elephants of Africa, with more elephants killed by poachers than die from natural causes. DNA from tusks has been used to infer the source populations for confiscated ivory, relying on nuclear genetic markers. However, mitochondrial DNA (mtDNA) sequences can also provide information on the geographic origins of elephants due to female elephant philopatry. Here, we introduce the Loxodonta Localizer (LL; www.loxodontalocalizer.org), an interactive software tool that uses a database of mtDNA sequences compiled from previously published studies to provide information on the potential provenance of confiscated ivory. A 316 bp control region sequence, which can be readily generated from DNA extracted from ivory, is used as a query. The software generates a listing of haplotypes reported among 1917 African elephants in 24 range countries, sorted in order of similarity to the query sequence. The African locations from which haplotype sequences have been previously reported are shown on a map. We demonstrate examples of haplotypes reported from only a single locality or country, examine the utility of the program in identifying elephants from countries with varying degrees of sampling, and analyze batches of confiscated ivory. The LL allows for the source of confiscated ivory to be assessed within days, using widely available molecular methods that do not depend on a particular platform or laboratory. The program enables identification of potential regions or localities from which elephants are being poached, with capacity for rapid identification of populations newly or consistently targeted by poachers.}, } @article {pmid31672210, year = {2019}, author = {Chan, S and Li, L and Torous, J and Gratzer, D and Yellowlees, PM}, title = {Review and Implementation of Self-Help and Automated Tools in Mental Health Care.}, journal = {The Psychiatric clinics of North America}, volume = {42}, number = {4}, pages = {597-609}, doi = {10.1016/j.psc.2019.07.001}, pmid = {31672210}, issn = {1558-3147}, mesh = {*Ecological Momentary Assessment ; Humans ; *Mental Health ; *Mobile Applications ; *Patient Education as Topic ; *Self Care ; *Social Media ; *Telemedicine ; }, abstract = {Self-help and automated technologies can be useful for behavioral and mental health education and interventions. These technologies include interactive media, online courses, artificial intelligence-powered chatbots, voice assistants, and video games. Self-help media can include books, videos, audible media like podcasts, blog and print articles, and self-contained Internet sites. Social media, online courses, and mass-market mobile apps also can include such media. These technologies serve to decrease geospatial, temporal, and financial barriers. This article describes different self-help and automated technologies, how to implement such technologies in existing clinical services, and how to implement according to patient needs.}, } @article {pmid31664449, year = {2019}, author = {Garriga, C and Leal, J and Sánchez-Santos, MT and Arden, N and Price, A and Prieto-Alhambra, D and Carr, A and Rangan, A and Cooper, C and Peat, G and Fitzpatrick, R and Barker, K and Judge, A}, title = {Geographical Variation in Outcomes of Primary Hip and Knee Replacement.}, journal = {JAMA network open}, volume = {2}, number = {10}, pages = {e1914325}, pmid = {31664449}, issn = {2574-3805}, support = {MC_U147585827/MRC_/Medical Research Council/United Kingdom ; MC_U147585819/MRC_/Medical Research Council/United Kingdom ; MC_UP_A620_1014/MRC_/Medical Research Council/United Kingdom ; MC_UU_12011/1/MRC_/Medical Research Council/United Kingdom ; G0400491/MRC_/Medical Research Council/United Kingdom ; MC_U147585824/MRC_/Medical Research Council/United Kingdom ; HS&DR/14/46/02/DH_/Department of Health/United Kingdom ; }, mesh = {Aged ; *Arthroplasty, Replacement, Hip ; *Arthroplasty, Replacement, Knee ; England ; Female ; *Geographic Information Systems ; Humans ; Male ; *Outcome Assessment, Health Care ; Patient Reported Outcome Measures ; Registries ; }, abstract = {IMPORTANCE: Little is known about variation in outcomes of surgery or about the factors associated with such variation.

OBJECTIVES: To evaluate variation in patient outcomes and costs for primary hip and knee replacement across health areas in England and to identify whether patient, surgical, or hospital factors are associated with such variation.

This cohort study used data from the National Joint Registry, linked to English Hospital Episode Statistics and Patient Reported Outcome Measures data sets, for 383 382 adult patients who underwent primary total hip replacement (THR) or primary total and unicompartmental knee replacement (TKR) surgical procedures from January 2014 to December 2016. Geographical Information Systems were used to display maps describing adjusted estimates of variation in outcomes across health areas. Data analysis took place from January 2018 to August 2019.

EXPOSURES: Patient characteristics (eg, age, sex, body mass index [BMI], and socioeconomic deprivation), surgical factors (eg, surgeon volume and grade), and hospital organizational factors (eg, number of operating theaters, number of specialist consultants, and hospital volume).

MAIN OUTCOMES AND MEASURES: Length of stay (LOS), bed-day costs, change in Oxford hip or knee scores 6 months after surgery, and complications 6 months after surgery.

RESULTS: A total of 173 107 patients (mean [SD] age, 69.3 [10.7] years; mean [SD] BMI, 28.9 [5.2]) underwent primary THR and 210 275 patients (mean [SD] age 69.7 [9.4] years; mean [SD] BMI, 31.1 [5.5]) underwent primary TKR, nested in 207 health areas. A number of factors were associated with longer LOS, higher bed-day costs, smaller changes in Oxford hip or knee scores, and a higher percentage of complications, including a workforce with a higher number of less experienced physicians (eg, LOS for less experienced surgeons, THR: regression coefficient, 0.02; 95% CI, 0.01 to 0.03; P < .001; TKR: regression coefficient, 0.01; 95% CI, 0.01 to 0.02; P < .001), public hospitals (eg, bed-day costs for private hospitals, THR: regression coefficient, -0.15; 95% CI, -0.15 to -0.14; P < .001; TKR: regression coefficient, -0.19; 95% CI, -0.19 to -0.19; P < .001), low volume of surgical procedures per surgeon (eg, change in Oxford hip or knee scores for lead surgeon with ≤10 vs >150 surgical procedures per year, THR: regression coefficient, -1.03; 95% CI, -1.47 to -0.58; P < .001; TKR: regression coefficient, -0.54; 95% CI, -1.01 to -0.06), and low volume of surgical procedures per hospital (eg, percentage of complications for hospitals with ≤200 vs ≥500 surgical procedures per year, THR: regression coefficient, 0.12; 95% CI, 0.04 to 0.21; P < .001; TKR: regression coefficient, 0.09; 95% CI, 0.01 to 0.18; P = .03). Although these factors did not attenuate the magnitude of variation across health areas, they had ecological correlations with the observed geographical variations in outcomes of surgery by health area. For example, the percentage of public and private hospitals was ecologically correlated at the health area level with longer and shorter stays, respectively (public hospital, THR: ρ, 0.41; public hospital, TKR: ρ, 0.44; private hospital, THR: ρ, -0.37; private hospital, THR: ρ, -0.38). Across health areas, estimated mean length of stay ranged from 3 to 7 days, and associated bed-day costs ranged from £4727 ($5827) to £8800 ($10 848) for both total hip and knee replacement. The absolute estimated mean change in Oxford hip score varied from 18.7 to 24.6 points and, for Oxford knee score, from 13.1 to 18.8. Estimated 6-month complications ranged from 2.9% to 5.8% for both THR and TKR.

CONCLUSIONS AND RELEVANCE: In this study, models indicated that higher surgical volume by surgeon and by hospital as well as private hospitals were associated with better patient outcomes, which could be explained by the changing case mix of public hospitals treating an increasing number of more complex patients. A higher proportion of less experienced physicians was associated with poorer outcomes. This variation was observed geographically.}, } @article {pmid31662345, year = {2020}, author = {Zhang, Y and Holsinger, EE and Prince, L and Rodden, JA and Swanson, SA and Miller, MM and Wintemute, GJ and Studdert, DM}, title = {Assembly of the LongSHOT cohort: public record linkage on a grand scale.}, journal = {Injury prevention : journal of the International Society for Child and Adolescent Injury Prevention}, volume = {26}, number = {2}, pages = {153-158}, pmid = {31662345}, issn = {1475-5785}, mesh = {Adult ; California ; Case-Control Studies ; Cohort Studies ; Female ; Firearms/*statistics & numerical data ; Humans ; Information Storage and Retrieval/methods ; Longitudinal Studies ; Male ; Middle Aged ; Ownership/*statistics & numerical data ; Sex Factors ; }, abstract = {BACKGROUND: Virtually all existing evidence linking access to firearms to elevated risks of mortality and morbidity comes from ecological and case-control studies. To improve understanding of the health risks and benefits of firearm ownership, we launched a cohort study: the Longitudinal Study of Handgun Ownership and Transfer (LongSHOT).

METHODS: Using probabilistic matching techniques we linked three sources of individual-level, state-wide data in California: official voter registration records, an archive of lawful handgun transactions and all-cause mortality data. There were nearly 28.8 million unique voter registrants, 5.5 million handgun transfers and 3.1 million deaths during the study period (18 October 2004 to 31 December 2016). The linkage relied on several identifying variables (first, middle and last names; date of birth; sex; residential address) that were available in all three data sets, deploying them in a series of bespoke algorithms.

RESULTS: Assembly of the LongSHOT cohort commenced in January 2016 and was completed in March 2019. Approximately three-quarters of matches identified were exact matches on all link variables. The cohort consists of 28.8 million adult residents of California followed for up to 12.2 years. A total of 1.2 million cohort members purchased at least one handgun during the study period, and 1.6 million died.

CONCLUSIONS: Three steps taken early may be particularly useful in enhancing the efficiency of large-scale data linkage: thorough data cleaning; assessment of the suitability of off-the-shelf data linkage packages relative to bespoke coding; and careful consideration of the minimum sample size and matching precision needed to support rigorous investigation of the study questions.}, } @article {pmid31657871, year = {2020}, author = {Kaszubinski, SF and Pechal, JL and Schmidt, CJ and Jordan, HR and Benbow, ME and Meek, MH}, title = {Evaluating Bioinformatic Pipeline Performance for Forensic Microbiome Analysis[*,†,‡].}, journal = {Journal of forensic sciences}, volume = {65}, number = {2}, pages = {513-525}, doi = {10.1111/1556-4029.14213}, pmid = {31657871}, issn = {1556-4029}, support = {//Department of Defense SMART Scholarship Program/ ; 2014-DN-BX-K008//National Institute of Justice/ ; }, mesh = {Bacteria/*genetics ; *Computational Biology ; Datasets as Topic ; Forensic Sciences ; High-Throughput Nucleotide Sequencing ; Humans ; *Microbiota ; Mouth/microbiology ; RNA, Ribosomal, 16S ; Rectum/microbiology ; }, abstract = {Microbial communities have potential evidential utility for forensic applications. However, bioinformatic analysis of high-throughput sequencing data varies widely among laboratories. These differences can potentially affect microbial community composition and downstream analyses. To illustrate the importance of standardizing methodology, we compared analyses of postmortem microbiome samples using several bioinformatic pipelines, varying minimum library size or minimum number of sequences per sample, and sample size. Using the same input sequence data, we found that three open-source bioinformatic pipelines, MG-RAST, mothur, and QIIME2, had significant differences in relative abundance, alpha-diversity, and beta-diversity, despite the same input data. Increasing minimum library size and sample size increased the number of low-abundant and infrequent taxa detected. Our results show that bioinformatic pipeline and parameter choice affect results in important ways. Given the growing potential application of forensic microbiology to the criminal justice system, continued research on standardizing computational methodology will be important for downstream applications.}, } @article {pmid31655550, year = {2019}, author = {da Costa, BR and Sutton, AJ}, title = {A comparison of the statistical performance of different meta-analysis models for the synthesis of subgroup effects from randomized clinical trials.}, journal = {BMC medical research methodology}, volume = {19}, number = {1}, pages = {198}, pmid = {31655550}, issn = {1471-2288}, mesh = {Computational Biology/methods ; Data Interpretation, Statistical ; Evidence-Based Medicine/*methods ; Humans ; *Meta-Analysis as Topic ; Models, Statistical ; *Randomized Controlled Trials as Topic ; }, abstract = {BACKGROUND: When investigating subgroup effects in meta-analysis, it is unclear whether accounting in meta-regression for between-trial variation in treatment effects, but not between-trial variation in treatment interaction effects when such effects are present, leads to biased estimates, coverage problems, or wrong standard errors, and whether the use of aggregate data (AD) or individual-patient-data (IPD) influences this assessment.

METHODS: Seven different models were compared in a simulation study. Models differed regarding the use of AD or IPD, whether they accounted for between-trial variation in interaction effects, and whether they minimized the risk of ecological fallacy.

RESULTS: Models that used IPD and that allowed for between-trial variation of the interaction effect had less bias, better coverage, and more accurate standard errors than models that used AD or ignored this variation. The main factor influencing the performance of models was whether they used IPD or AD. The model that used AD had a considerably worse performance than all models that used IPD, especially when a low number of trials was included in the analysis.

CONCLUSIONS: The results indicate that IPD models that allow for the between-trial variation in interaction effects should be given preference whenever investigating subgroup effects within a meta-analysis.}, } @article {pmid31653863, year = {2019}, author = {Hansen, A and Barnett, K and Jantz, P and Phillips, L and Goetz, SJ and Hansen, M and Venter, O and Watson, JEM and Burns, P and Atkinson, S and Rodríguez-Buritica, S and Ervin, J and Virnig, A and Supples, C and De Camargo, R}, title = {Global humid tropics forest structural condition and forest structural integrity maps.}, journal = {Scientific data}, volume = {6}, number = {1}, pages = {232}, pmid = {31653863}, issn = {2052-4463}, support = {80NSSC18K0338/NASA/NASA/United States ; }, mesh = {*Biodiversity ; Conservation of Natural Resources ; *Forests ; Remote Sensing Technology ; *Tropical Climate ; }, abstract = {Remotely sensed maps of global forest extent are widely used for conservation assessment and planning. Yet, there is increasing recognition that these efforts must now include elements of forest quality for biodiversity and ecosystem services. Such data are not yet available globally. Here we introduce two data products, the Forest Structural Condition Index (SCI) and the Forest Structural Integrity Index (FSII), to meet this need for the humid tropics. The SCI integrates canopy height, tree cover, and time since disturbance to distinguish short, open-canopy, or recently deforested stands from tall, closed-canopy, older stands typical of primary forest. The SCI was validated against estimates of foliage height diversity derived from airborne lidar. The FSII overlays a global index of human pressure on SCI to identify structurally complex forests with low human pressure, likely the most valuable for maintaining biodiversity and ecosystem services. These products represent an important step in maturation from conservation focus on forest extent to forest stands that should be considered "best of the last" in international policy settings.}, } @article {pmid31652294, year = {2019}, author = {Tamburello, L and Papa, L and Guarnieri, G and Basconi, L and Zampardi, S and Scipione, MB and Terlizzi, A and Zupo, V and Fraschetti, S}, title = {Are we ready for scaling up restoration actions? An insight from Mediterranean macroalgal canopies.}, journal = {PloS one}, volume = {14}, number = {10}, pages = {e0224477}, pmid = {31652294}, issn = {1932-6203}, mesh = {Conservation of Natural Resources/economics/*methods ; Costs and Cost Analysis ; Herbivory ; *Mediterranean Region ; *Phaeophyceae ; }, abstract = {Extensive loss of macroalgal forests advocates for large-scale restoration interventions, to compensate habitat degradation and recover the associated ecological functions and services. Yet, restoration attempts have generally been limited to small spatial extensions, with the principal aim of developing efficient restoration techniques. Here, the success of outplanting Cystoseira amentacea v. stricta germlings cultured in aquaria was experimentally explored at a scale of tens of kms, by means of a multifactorial experimental design. In the intertidal rocky shores of SE Italy, locations with a continuous distribution for hundreds of meters or with few thalli forming patches of few centimeters of C. amentacea canopy were selected. In each location, the effects of adult conspecifics and the exclusion of macrograzers (salema fish and sea urchins) on the survival of germlings were tested. We evaluated the most critical determinants of mortality for germlings, including the overlooked pressure of mesograzers (e.g. amphipods, small mollusks, polychaetes). Despite the high mortality observed during outplanting and early settlement stages, survival of C. amentacea germlings was consistently favored by the exclusion of macrograzers, while the presence of adult conspecifics had no effects. In addition, the cost analysis of the interventions showed the feasibility of the ex-situ method, representing an essential tool for preserving Cystoseira forests. Large scale restoration is possible but requires baseline information with an in-depth knowledge of the species ecology and of the areas to be restored, together with the development of specific cultivation protocols to make consistently efficient restoration interventions.}, } @article {pmid31652268, year = {2019}, author = {Sheehan, T and Bachelet, D}, title = {A fuzzy logic decision support model for climate-driven biomass loss risk in western Oregon and Washington.}, journal = {PloS one}, volume = {14}, number = {10}, pages = {e0222051}, pmid = {31652268}, issn = {1932-6203}, mesh = {Biomass ; Carbon/metabolism ; *Climate Change ; Computer Simulation ; Decision Support Techniques ; *Ecosystem ; Fires ; Forests ; Fuzzy Logic ; Humans ; *Models, Biological ; Oregon ; Trees ; Washington ; }, abstract = {Dynamic global vegetation model (DGVM) projections are often put forth to aid resource managers in climate change-related decision making. However, interpreting model results and understanding their uncertainty can be difficult. Sources of uncertainty include embedded assumptions about atmospheric CO2 levels, uncertain climate projections driving DGVMs, and DGVM algorithm selection. For western Oregon and Washington, we implemented an Environmental Evaluation Modeling System (EEMS) decision support model using MC2 DGVM results to characterize biomass loss risk. MC2 results were driven by climate projections from 20 General Circulation Models (GCMs) and Earth System Models (ESMs), under Representative Concentration Pathways (RCPs) 4.5 and 8.5, with and without assumed fire suppression, for three different time periods. We produced maps of mean, minimum, and maximum biomass loss risk and uncertainty for each RCP / +/- fire suppression / time period. We characterized the uncertainty due to RCP, fire suppression, and climate projection choice. Finally, we evaluated whether fire or climate maladaptation mortality was the dominant driver of risk for each model run. The risk of biomass loss generally increases in current high biomass areas within the study region through time. The pattern of increased risk is generally south to north and upslope into the Coast and Cascade mountain ranges and along the coast. Uncertainty from climate future choice is greater than that attributable to RCP or +/- fire suppression. Fire dominates as the driving factor for biomass loss risk in more model runs than mortality. This method of interpreting DGVM results and the associated uncertainty provides managers with data in a form directly applicable to their concerns and should prove helpful in adaptive management planning.}, } @article {pmid31650682, year = {2020}, author = {Sommeria-Klein, G and Zinger, L and Coissac, E and Iribar, A and Schimann, H and Taberlet, P and Chave, J}, title = {Latent Dirichlet Allocation reveals spatial and taxonomic structure in a DNA-based census of soil biodiversity from a tropical forest.}, journal = {Molecular ecology resources}, volume = {20}, number = {2}, pages = {371-386}, doi = {10.1111/1755-0998.13109}, pmid = {31650682}, issn = {1755-0998}, support = {//Centre National de la Recherche Scientifique/ ; //Bartin Üniversitesi/ ; ANAEE-France: ANR-11-INBS-0001; Labex CEBA: ANR-10-LABX-25-01; Labex MEMOLIFE: ANR-10-LABX-54; Labex TULIP: ANR-10-LABX-0041; METABAR: ANR-11-BSV7-0020; PSL* Research University: ANR-10-IDEX-0001-02//Agence Nationale de la Recherche/ ; }, mesh = {Bacteria/classification/genetics/*isolation & purification ; Biodiversity ; Computational Biology/*methods ; Eukaryota/*classification/genetics/isolation & purification ; Fungi/classification/genetics/*isolation & purification ; High-Throughput Nucleotide Sequencing ; Soil/*parasitology ; *Soil Microbiology ; }, abstract = {High-throughput sequencing of amplicons from environmental DNA samples permits rapid, standardized and comprehensive biodiversity assessments. However, retrieving and interpreting the structure of such data sets requires efficient methods for dimensionality reduction. Latent Dirichlet Allocation (LDA) can be used to decompose environmental DNA samples into overlapping assemblages of co-occurring taxa. It is a flexible model-based method adapted to uneven sample sizes and to large and sparse data sets. Here, we compare LDA performance on abundance and occurrence data, and we quantify the robustness of the LDA decomposition by measuring its stability with respect to the algorithm's initialization. We then apply LDA to a survey of 1,131 soil DNA samples that were collected in a 12-ha plot of primary tropical forest and amplified using standard primers for bacteria, protists, fungi and metazoans. The analysis reveals that bacteria, protists and fungi exhibit a strong spatial structure, which matches the topographical features of the plot, while metazoans do not, confirming that microbial diversity is primarily controlled by environmental variation at the studied scale. We conclude that LDA is a sensitive, robust and computationally efficient method to detect and interpret the structure of large DNA-based biodiversity data sets. We finally discuss the possible future applications of this approach for the study of biodiversity.}, } @article {pmid31647845, year = {2019}, author = {Takeda, S and Yoza, M and Amano, T and Ohshima, I and Hirano, T and Sato, MH and Sakamoto, T and Kimura, S}, title = {Comparative transcriptome analysis of galls from four different host plants suggests the molecular mechanism of gall development.}, journal = {PloS one}, volume = {14}, number = {10}, pages = {e0223686}, pmid = {31647845}, issn = {1932-6203}, mesh = {Cell Division/genetics ; Computational Biology/methods ; *Gene Expression Profiling ; Gene Expression Regulation, Plant ; Gene Ontology ; Host-Parasite Interactions/*genetics ; Host-Pathogen Interactions/*genetics ; Phenotype ; Plant Tumors/*genetics ; Reactive Oxygen Species ; Signal Transduction ; Species Specificity ; *Transcriptome ; }, abstract = {Galls are plant structures generated by gall-inducing organisms including insects, nematodes, fungi, bacteria and viruses. Those made by insects generally consist of inner callus-like cells surrounded by lignified hard cells, supplying both nutrients and protection to the gall insects living inside. This indicates that gall insects hijack developmental processes in host plants to generate tissues for their own use. Although galls are morphologically diverse, the molecular mechanism for their development remains poorly understood. To identify genes involved in gall development, we performed RNA-sequencing based transcriptome analysis for leaf galls. We examined the young and mature galls of Glochidion obovatum (Phyllanthaceae), induced by the micromoth Caloptilia cecidophora (Lepidoptera: Gracillariidae), the leaf gall from Eurya japonica (Pentaphylacaceae) induced by Borboryctis euryae (Lepidoptera: Gracillariidae), and the strawberry-shaped leaf gall from Artemisia montana (Asteraceae) induced by gall midge Rhopalomyia yomogicola (Oligotrophini: Cecidomyiidae). Gene ontology (GO) analyses suggested that genes related to developmental processes are up-regulated, whereas ones related to photosynthesis are down-regulated in these three galls. Comparison of transcripts in these three galls together with the gall on leaves of Rhus javanica (Anacardiaceae), induced by the aphid Schlechtendalia chinensis (Hemiptera: Aphidoidea), suggested 38 genes commonly up-regulated in galls from different plant species. GO analysis showed that peptide biosynthesis and metabolism are commonly involved in the four different galls. Our results suggest that gall development involves common processes across gall inducers and plant taxa, providing an initial step towards understanding how they manipulate host plant developmental systems.}, } @article {pmid31641158, year = {2019}, author = {Rimet, F and Gusev, E and Kahlert, M and Kelly, MG and Kulikovskiy, M and Maltsev, Y and Mann, DG and Pfannkuchen, M and Trobajo, R and Vasselon, V and Zimmermann, J and Bouchez, A}, title = {Diat.barcode, an open-access curated barcode library for diatoms.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {15116}, pmid = {31641158}, issn = {2045-2322}, mesh = {Base Sequence ; *DNA Barcoding, Taxonomic ; Data Curation ; Databases, Genetic ; Diatoms/*classification/*genetics ; *Gene Library ; Geography ; Ribulose-Bisphosphate Carboxylase/genetics ; }, abstract = {Diatoms (Bacillariophyta) are ubiquitous microalgae which produce a siliceous exoskeleton and which make a major contribution to the productivity of oceans and freshwaters. They display a huge diversity, which makes them excellent ecological indicators of aquatic ecosystems. Usually, diatoms are identified using characteristics of their exoskeleton morphology. DNA-barcoding is an alternative to this and the use of High-Throughput-Sequencing enables the rapid analysis of many environmental samples at a lower cost than analyses under microscope. However, to identify environmental sequences correctly, an expertly curated reference library is needed. Several curated libraries for protists exists; none, however are dedicated to diatoms. Diat.barcode is an open-access library dedicated to diatoms which has been maintained since 2012. Data come from two sources (1) the NCBI nucleotide database and (2) unpublished sequencing data of culture collections. Since 2017, several experts have collaborated to curate this library for rbcL, a chloroplast marker suitable for species-level identification of diatoms. For the latest version of the database (version 7), 605 of the 3482 taxonomical names originally assigned by the authors of the rbcL sequences were modified after curation. The database is accessible at https://www6.inra.fr/carrtel-collection_eng/Barcoding-database .}, } @article {pmid31638156, year = {2020}, author = {He, C and Liang, D and Zhang, P}, title = {Asymmetric Distribution of Gene Trees Can Arise under Purifying Selection If Differences in Population Size Exist.}, journal = {Molecular biology and evolution}, volume = {37}, number = {3}, pages = {881-892}, doi = {10.1093/molbev/msz232}, pmid = {31638156}, issn = {1537-1719}, mesh = {Animals ; Computational Biology/*methods ; Evolution, Molecular ; Gene Flow ; Genetic Speciation ; Models, Genetic ; Phylogeny ; Population Density ; Primates/*genetics ; Rodentia/*genetics ; Scandentia/*genetics ; Selection, Genetic ; }, abstract = {Incomplete lineage sorting (ILS) is an important factor that causes gene tree discordance. For gene trees of three species, under neutrality, random mating, and the absence of interspecific gene flow, ILS creates a symmetric distribution of gene trees: the gene tree that accords with the species tree has the highest frequency, and the two discordant trees are equally frequent. If the neutral condition is violated, the impact of ILS may change, altering the gene tree distribution. Here, we show that under purifying selection, even assuming that the fitness effect of mutations is constant throughout the species tree, if differences in population size exist among species, asymmetric distributions of gene trees will arise, which is different from the expectation under neutrality. In extremes, one of the discordant trees rather than the concordant tree becomes the most frequent gene tree. In addition, we found that in a real case, the position of Scandentia relative to Primate and Glires, the symmetry in the gene tree distribution can be influenced by the strength of purifying selection. In current phylogenetic inference, the impact of purifying selection on the gene tree distribution is rarely considered by researchers. This study highlights the necessity of considering this impact.}, } @article {pmid31637835, year = {2020}, author = {Wilber, MQ and Jani, AJ and Mihaljevic, JR and Briggs, CJ}, title = {Fungal infection alters the selection, dispersal and drift processes structuring the amphibian skin microbiome.}, journal = {Ecology letters}, volume = {23}, number = {1}, pages = {88-98}, doi = {10.1111/ele.13414}, pmid = {31637835}, issn = {1461-0248}, support = {1455873//Division of Integrative Organismal Systems/ ; 1144085//Division of Graduate Education/ ; 0723563//Division of Environmental Biology/ ; }, mesh = {Amphibians ; Animals ; Fungi ; *Microbiota ; *Mycoses ; Skin ; }, abstract = {Symbiotic microbial communities are important for host health, but the processes shaping these communities are poorly understood. Understanding how community assembly processes jointly affect microbial community composition is limited because inflexible community models rely on rejecting dispersal and drift before considering selection. We developed a flexible community assembly model based on neutral theory to ask: How do dispersal, drift and selection concurrently affect the microbiome across environmental gradients? We applied this approach to examine how a fungal pathogen affected the assembly processes structuring the amphibian skin microbiome. We found that the rejection of neutrality for the amphibian microbiome across a fungal gradient was not strictly due to selection processes, but was also a result of species-specific changes in dispersal and drift. Our modelling framework brings the qualitative recognition that niche and neutral processes jointly structure microbiomes into quantitative focus, allowing for improved predictions of microbial community turnover across environmental gradients.}, } @article {pmid31636201, year = {2019}, author = {Palomo, I and Dujardin, Y and Midler, E and Robin, M and Sanz, MJ and Pascual, U}, title = {Modeling trade-offs across carbon sequestration, biodiversity conservation, and equity in the distribution of global REDD+ funds.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {116}, number = {45}, pages = {22645-22650}, pmid = {31636201}, issn = {1091-6490}, mesh = {Biodiversity ; *Carbon Sequestration ; Climate Change ; Conservation of Natural Resources/*economics ; Financial Management/economics ; Forests ; Models, Econometric ; Trees/growth & development ; }, abstract = {The program on Reducing Emissions from Deforestation and Forest Degradation (REDD+) is one of the major attempts to tackle climate change mitigation in developing countries. REDD+ seeks to provide result-based incentives to promote emission reductions and increase carbon sinks in forest land while promoting other cobenefits, such as the conservation of biodiversity. We model different scenarios of international REDD+ funds distribution toward potential recipient countries using 2 carbon emission reduction targets (20% and 50% compared to the baseline scenario, i.e., deforestation and forest degradation without REDD+) by 2030. The model combines the prioritization of environmental outcomes in terms of carbon sequestration and biodiversity conservation and social equity, accounting for the equitable distribution of international REDD+ funds. Results highlight the synergy between carbon sequestration and biodiversity conservation under alternative fund allocation criteria, especially for scenarios of low carbon emission reduction. Trade-offs increase when distributional equity is considered as an additional criterion, especially under higher equity requirements. The analysis helps to better understand the inherent trade-offs between enhancing distributional equity and meeting environmental targets under alternative REDD+ fund allocation options.}, } @article {pmid31635887, year = {2019}, author = {Čanković, M and Žučko, J and Radić, ID and Janeković, I and Petrić, I and Ciglenečki, I and Collins, G}, title = {Microbial diversity and long-term geochemical trends in the euxinic zone of a marine, meromictic lake.}, journal = {Systematic and applied microbiology}, volume = {42}, number = {6}, pages = {126016}, doi = {10.1016/j.syapm.2019.126016}, pmid = {31635887}, issn = {1618-0984}, mesh = {Archaea/classification/genetics/isolation & purification/metabolism ; Bacteria/classification/genetics/isolation & purification/metabolism ; *Biodiversity ; Climate Change ; Databases, Chemical ; Ireland ; Lakes/chemistry/*microbiology ; *Microbiota/genetics ; Oxygen/analysis/*metabolism ; RNA, Ribosomal, 16S/genetics ; Seasons ; Water Microbiology ; }, abstract = {Hypoxic and anoxic niches of meromictic lakes are important sites for studying the microbial ecology of conditions resembling ancient Earth. The expansion and increasing global distribution of such environments also means that information about them serves to understand future phenomena. In this study, a long-term chemical dataset (1996-2015) was explored together with seasonal (in 2015) information on the diversity and abundance of bacterial and archaeal communities residing in the chemocline, monimolimnion and surface sediment of the marine meromictic Rogoznica Lake. The results of quantitative PCR assays, and high-throughput sequencing, targeting 16S rRNA genes and transcripts, revealed a clear vertical structure of the microbial community with Gammaproteobacteria (Halochromatium) and cyanobacteria (Synechococcus spp.) dominating the chemocline, Deltaproteobacteria and Bacteroidetes dominating the monimolimnion, and significantly more abundant archaeal populations in the surface sediment, most of which affiliated to Nanoarchaeota. Seasonal changes in the community structure and abundance were not pronounced. Diversity in Rogoznica Lake was found to be high, presumably as a consequence of stable environmental conditions accompanied by high dissolved carbon and nutrient concentrations. Long-term data indicated that Rogoznica Lake exhibited climate changes that could alter its physico-chemical features and, consequently, induce structural and physiological changes within its microbial community.}, } @article {pmid31633786, year = {2020}, author = {Wang, LG and Lam, TT and Xu, S and Dai, Z and Zhou, L and Feng, T and Guo, P and Dunn, CW and Jones, BR and Bradley, T and Zhu, H and Guan, Y and Jiang, Y and Yu, G}, title = {Treeio: An R Package for Phylogenetic Tree Input and Output with Richly Annotated and Associated Data.}, journal = {Molecular biology and evolution}, volume = {37}, number = {2}, pages = {599-603}, pmid = {31633786}, issn = {1537-1719}, support = {HHSN272201400006C/AI/NIAID NIH HHS/United States ; }, mesh = {Computational Biology/*methods ; Data Mining/*methods ; Internet ; Phylogeny ; Software ; }, abstract = {Phylogenetic trees and data are often stored in incompatible and inconsistent formats. The outputs of software tools that contain trees with analysis findings are often not compatible with each other, making it hard to integrate the results of different analyses in a comparative study. The treeio package is designed to connect phylogenetic tree input and output. It supports extracting phylogenetic trees as well as the outputs of commonly used analytical software. It can link external data to phylogenies and merge tree data obtained from different sources, enabling analyses of phylogeny-associated data from different disciplines in an evolutionary context. Treeio also supports export of a phylogenetic tree with heterogeneous-associated data to a single tree file, including BEAST compatible NEXUS and jtree formats; these facilitate data sharing as well as file format conversion for downstream analysis. The treeio package is designed to work with the tidytree and ggtree packages. Tree data can be processed using the tidy interface with tidytree and visualized by ggtree. The treeio package is released within the Bioconductor and rOpenSci projects. It is available at https://www.bioconductor.org/packages/treeio/.}, } @article {pmid31633780, year = {2020}, author = {Murovec, B and Deutsch, L and Stres, B}, title = {Computational Framework for High-Quality Production and Large-Scale Evolutionary Analysis of Metagenome Assembled Genomes.}, journal = {Molecular biology and evolution}, volume = {37}, number = {2}, pages = {593-598}, pmid = {31633780}, issn = {1537-1719}, mesh = {Computational Biology/*methods ; Evolution, Molecular ; *Genome, Microbial ; Metagenomics ; Phylogeny ; Software ; User-Computer Interface ; }, abstract = {Microbial species play important roles in different environments and the production of high-quality genomes from metagenome data sets represents a major obstacle to understanding their ecological and evolutionary dynamics. Metagenome-Assembled Genomes Orchestra (MAGO) is a computational framework that integrates and simplifies metagenome assembly, binning, bin improvement, bin quality (completeness and contamination), bin annotation, and evolutionary placement of bins via detailed maximum-likelihood phylogeny based on multiple marker genes using different amino acid substitution models, next to average nucleotide identity analysis of genomes for delineation of species boundaries and operational taxonomic units. MAGO offers streamlined execution of the entire metagenomics pipeline, error checking, computational resource distribution and compatibility of data formats, governed by user-tailored pipeline processing. MAGO is an open-source-software package released in three different ways, as a singularity image and a Docker container for HPC purposes as well as for running MAGO on a commodity hardware, and a virtual machine for gaining a full access to MAGO underlying structure and source code. MAGO is open to suggestions for extensions and is amenable for use in both research and teaching of genomics and molecular evolution of genomes assembled from small single-cell projects or large-scale and complex environmental metagenomes.}, } @article {pmid31632690, year = {2019}, author = {Chen, C and Jiang, L and Fu, G and Wang, M and Wang, Y and Shen, B and Liu, Z and Wang, Z and Hou, W and Berceli, SA and Wu, R}, title = {An omnidirectional visualization model of personalized gene regulatory networks.}, journal = {NPJ systems biology and applications}, volume = {5}, number = {}, pages = {38}, pmid = {31632690}, issn = {2056-7189}, support = {K01 AA023321/AA/NIAAA NIH HHS/United States ; KL2 TR002015/TR/NCATS NIH HHS/United States ; UL1 TR002014/TR/NCATS NIH HHS/United States ; }, mesh = {Algorithms ; Computational Biology/*methods ; Computer Simulation ; Gene Expression Regulation/genetics/physiology ; Gene Regulatory Networks/*genetics ; Genomics ; Humans ; Models, Theoretical ; Precision Medicine/methods ; }, abstract = {Gene regulatory networks (GRNs) have been widely used as a fundamental tool to reveal the genomic mechanisms that underlie the individual's response to environmental and developmental cues. Standard approaches infer GRNs as holistic graphs of gene co-expression, but such graphs cannot quantify how gene-gene interactions vary among individuals and how they alter structurally across spatiotemporal gradients. Here, we develop a general framework for inferring informative, dynamic, omnidirectional, and personalized networks (idopNetworks) from routine transcriptional experiments. This framework is constructed by a system of quasi-dynamic ordinary differential equations (qdODEs) derived from the combination of ecological and evolutionary theories. We reconstruct idopNetworks using genomic data from a surgical experiment and illustrate how network structure is associated with surgical response to infrainguinal vein bypass grafting and the outcome of grafting. idopNetworks may shed light on genotype-phenotype relationships and provide valuable information for personalized medicine.}, } @article {pmid31631517, year = {2020}, author = {Li, X and Wang, X and Fang, L and Batbayar, N and Natsagdorj, T and Davaasuren, B and Damba, I and Xu, Z and Cao, L and Fox, AD}, title = {Annual migratory patterns of Far East Greylag Geese (Anser anser rubrirostris) revealed by GPS tracking.}, journal = {Integrative zoology}, volume = {15}, number = {3}, pages = {213-223}, doi = {10.1111/1749-4877.12414}, pmid = {31631517}, issn = {1749-4877}, mesh = {*Animal Migration ; Animals ; China ; Geese/*physiology ; Geographic Information Systems ; Mongolia ; Seasons ; Telemetry/*veterinary ; }, abstract = {Twenty Far East Greylag Geese, Anser anser rubrirostris, were captured and fitted with Global Positioning System/Global System for Mobile Communications (GPS/GSM) loggers to identify breeding and wintering areas, migration routes and stopover sites. Telemetry data for the first time showed linkages between their Yangtze River wintering areas, stopover sites in northeastern China, and breeding/molting grounds in eastern Mongolia and northeast China. 10 of the 20 tagged individuals provided sufficient data. They stopped on migration at the Yellow River Estuary, Beidagang Reservoir and Xar Moron River, confirming these areas as being important stopover sites for this population. The median spring migration duration was 33.7 days (individuals started migrating between 25 February and 16 March and completed migrating from 1 to 9 April) compared to 52.7 days in autumn (26 September-13 October until 4 November-11 December). The median stopover duration was 31.1 and 51.3 days and the median speed of travel was 62.6 and 47.9 km/day for spring and autumn migration, respectively. The significant differences between spring and autumn migration on the migration duration, the stopover duration and the migration speed confirmed that tagged adult Greylag Geese traveled faster in spring than autumn, supporting the hypothesis that they should be more time-limited during spring migration.}, } @article {pmid31629296, year = {2019}, author = {Robinson, CD and Bohannan, BJ and Britton, RA}, title = {Scales of persistence: transmission and the microbiome.}, journal = {Current opinion in microbiology}, volume = {50}, number = {}, pages = {42-49}, pmid = {31629296}, issn = {1879-0364}, support = {P01 GM125576/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Bacteria/genetics ; *Bacterial Physiological Phenomena ; Computational Biology ; Environment ; Humans ; *Microbiota ; }, abstract = {Historically microbiomes have been studied on the scale of the individual host, giving little consideration for the role of extra-host microbial populations in microbiome assembly. However, work in recent years has brought to light the importance of inter-host transmission and its influence on microbiome composition and dynamics. We now appreciate that microbiomes do not exist in isolation, but exchange constituents with the microbial communities of other hosts and the environment. Moving forward, fully understanding the role of transmission in microbiome assembly and dynamics will require a high-resolution view of the colonization and persistence patterns of particular microbial lineages (i.e. strains) across individuals and the environment. Yet, accomplishing this level of resolution will be an immense challenge, requiring improved sampling and bioinformatics approaches as well as employment of tractable experimental models. Insight gained from these investigations will contribute to our understanding of microbiome composition and variation, and lead to improved strategies for modulating microbiomes to improve human health.}, } @article {pmid31629063, year = {2019}, author = {Jiao, T and Yang, TT and Wang, D and Gao, ZQ and Wang, JL and Tang, BP and Liu, QN and Zhang, DZ and Dai, LS}, title = {Characterization and expression analysis of immune-related genes in the red swamp crayfish, Procambarus clarkii in response to lipopolysaccharide challenge.}, journal = {Fish & shellfish immunology}, volume = {95}, number = {}, pages = {140-150}, doi = {10.1016/j.fsi.2019.09.072}, pmid = {31629063}, issn = {1095-9947}, mesh = {Animals ; Astacoidea/drug effects/*genetics/*immunology ; Gene Expression Profiling ; Gene Ontology ; High-Throughput Nucleotide Sequencing ; Lipopolysaccharides/*administration & dosage ; *Transcriptome ; }, abstract = {To learn more about red swamp crayfish related genes in response to bacterial infections, we investigated immune-related genes induced by lipopolysaccharide (LPS) in the hepatopancreas using high-throughput sequencing method. In present the study, a total of 55,107 unigenes were identified, with an average length of 678 bp. A total of 2215 differentially expressed genes (DEGs) were found, including 669 up-regulated genes and 1546 down-regulated genes. The result of Gene ontology (GO) analysis revealed that 3017 DEGs were enriched in 19 biological process subcategories, 17 cellular component subcategories and 15 molecular function subcategories. The top 20 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways showed that "ribosome" was the most abundant group, which had 34 DEGs. KEGG enrichment analysis identified several immune response pathways. Real-time quantitative reverse transcription-PCR (qRT-PCR) results exhibited that several immune responsive genes were greatly up-regulated following LPS stimulation as observed in the results of high-throughput sequencing. Overall, this study provides new insight into the immune defense mechanisms of P. clarkii against LPS infection.}, } @article {pmid31628884, year = {2020}, author = {Hart, AJ and Ginzburg, S and Xu, MS and Fisher, CR and Rahmatpour, N and Mitton, JB and Paul, R and Wegrzyn, JL}, title = {EnTAP: Bringing faster and smarter functional annotation to non-model eukaryotic transcriptomes.}, journal = {Molecular ecology resources}, volume = {20}, number = {2}, pages = {591-604}, doi = {10.1111/1755-0998.13106}, pmid = {31628884}, issn = {1755-0998}, mesh = {Eukaryota/*genetics ; Gene Ontology ; Genome ; Molecular Sequence Annotation/*methods ; *Transcriptome ; }, abstract = {EnTAP (Eukaryotic Non-Model Transcriptome Annotation Pipeline) was designed to improve the accuracy, speed, and flexibility of functional gene annotation for de novo assembled transcriptomes in non-model eukaryotes. This software package addresses the fragmentation and related assembly issues that result in inflated transcript estimates and poor annotation rates of protein-coding transcripts. Following filters applied through assessment of true expression and frame selection, open-source tools are leveraged to functionally annotate the reduced set of translated proteins. Downstream features include fast similarity search across five repositories, protein domain assignment, orthologous gene family assessment, and Gene Ontology (GO) term assignment. The final annotation integrates across multiple databases and selects an optimal assignment from a combination of weighted metrics describing similarity search score, taxonomic relationship, and informativeness. Researchers have the option to include additional filters to identify and remove contaminants, identify associated pathways, and prepare the transcripts for enrichment analysis. This fully featured pipeline is easy to install, configure, and runs significantly faster than comparable annotation packages. EnTAP is optimized to generate extensive functional information for the gene space of organisms with limited or poorly characterized genomic resources.}, } @article {pmid31628318, year = {2019}, author = {Saremi, NF and Supple, MA and Byrne, A and Cahill, JA and Coutinho, LL and Dalén, L and Figueiró, HV and Johnson, WE and Milne, HJ and O'Brien, SJ and O'Connell, B and Onorato, DP and Riley, SPD and Sikich, JA and Stahler, DR and Villela, PMS and Vollmers, C and Wayne, RK and Eizirik, E and Corbett-Detig, RB and Green, RE and Wilmers, CC and Shapiro, B}, title = {Puma genomes from North and South America provide insights into the genomic consequences of inbreeding.}, journal = {Nature communications}, volume = {10}, number = {1}, pages = {4769}, pmid = {31628318}, issn = {2041-1723}, support = {R35 GM128932/GM/NIGMS NIH HHS/United States ; T32 HG008345/HG/NHGRI NIH HHS/United States ; }, mesh = {Animals ; Gene Flow ; Genetic Variation ; Genetics, Population ; Genome-Wide Association Study/*methods ; Genomics/*methods ; Geography ; Inbreeding/*methods ; North America ; Phylogeny ; Puma/classification/*genetics ; South America ; }, abstract = {Pumas are the most widely distributed felid in the Western Hemisphere. Increasingly, however, human persecution and habitat loss are isolating puma populations. To explore the genomic consequences of this isolation, we assemble a draft puma genome and a geographically broad panel of resequenced individuals. We estimate that the lineage leading to present-day North American pumas diverged from South American lineages 300-100 thousand years ago. We find signatures of close inbreeding in geographically isolated North American populations, but also that tracts of homozygosity are rarely shared among these populations, suggesting that assisted gene flow would restore local genetic diversity. The genome of a Florida panther descended from translocated Central American individuals has long tracts of homozygosity despite recent outbreeding. This suggests that while translocations may introduce diversity, sustaining diversity in small and isolated populations will require either repeated translocations or restoration of landscape connectivity. Our approach provides a framework for genome-wide analyses that can be applied to the management of similarly small and isolated populations.}, } @article {pmid31627353, year = {2019}, author = {Priyadarshani, SVGN and Cai, H and Zhou, Q and Liu, Y and Cheng, Y and Xiong, J and Patson, DL and Cao, S and Zhao, H and Qin, Y}, title = {An Efficient Agrobacterium Mediated Transformation of Pineapple with GFP-Tagged Protein Allows Easy, Non-Destructive Screening of Transgenic Pineapple Plants.}, journal = {Biomolecules}, volume = {9}, number = {10}, pages = {}, pmid = {31627353}, issn = {2218-273X}, mesh = {Agrobacterium/*genetics/metabolism ; Ananas/*genetics/growth & development/metabolism ; Computational Biology ; DNA, Plant/genetics/isolation & purification ; Green Fluorescent Proteins/*genetics/metabolism ; Plants, Genetically Modified/*genetics/metabolism ; }, abstract = {Quite a few studies have been conducted to improve the Agrobacterium-mediated transformation of pineapple, which is the second most important commercial tropical fruit crop worldwide. However, pineapple transformation remains challenging, due to technical difficulties, the lengthy regeneration process, and a high labor requirement. There have not been any studies specifically addressing the introduction of GFP-tagged genes into pineapples through Agrobacterium-mediated transformation, which would enable easy, non-destructive expression detection. It would also allow expression localization at the organelle level, which is not possible with GUS a reporter gene that encodes β-glucuronidase or a herbicide resistance reporter gene. Here, we report a method for the introduction of GFP-tagged genes into pineapples through Agrobacterium-mediated transformation. We used embryonic calli for transformation, and plants were regenerated through somatic embryogenesis. In this study, we optimized the incubation time for Agrobacterium infection, the co-cultivation time, the hygromycin concentration for selection, and the callus growth conditions after selection. Our strategy reduced the time required to obtain transgenic plants from 7.6 months to 6.1 months. The expression of GFP-tagged AcWRKY28 was observed in the nuclei of transgenic pineapple root cells. This method allows easy, non-destructive expression detection of transgenic constructs at the organelle level. These findings on pineapple transformation will help accelerate pineapple molecular breeding efforts to introduce new desirable traits.}, } @article {pmid31626658, year = {2019}, author = {Nieuwoudt, SJ and Ngandu, CB and Manderson, L and Norris, SA}, title = {Exclusive breastfeeding policy, practice and influences in South Africa, 1980 to 2018: A mixed-methods systematic review.}, journal = {PloS one}, volume = {14}, number = {10}, pages = {e0224029}, pmid = {31626658}, issn = {1932-6203}, support = {/WT_/Wellcome Trust/United Kingdom ; }, mesh = {*Breast Feeding ; Databases, Factual ; Guidelines as Topic ; *Health Policy ; Health Workforce ; Humans ; Infant ; South Africa ; }, abstract = {BACKGROUND: In 2011, South Africa committed to promoting exclusive breastfeeding (EBF) for six months for all mothers, regardless of HIV status, in line with World Health Organization recommendations. This was a marked shift from earlier policies, and with it, average EBF rates increased from less than 10% in 2011 to 32% by 2016.

OBJECTIVES: The aim of this mixed-methods systematic review was to describe EBF practices in South Africa and their multi-level influences over four policy periods.

METHODS: We applied PRISMA guidelines according to a published protocol (Prospero: CRD42014010512). We searched seven databases [Africa-Wide, PubMed, Popline, PsychINFO, CINAHL, Global Health, and The Cochrane Library] and conducted hand searches for eligible articles (all study designs, conducted in South Africa and published between 1980-2018). The quality of articles was assessed using published tools, as appropriate. Separate policy analysis was conducted to delineate four distinct policy periods. We compared EBF rates by these periods. Then, applying a three-level ecological framework, we analysed EBF influences concurrently by method. Finally, the findings were synthesized to compare breastfeeding influences by policy period, maintaining an ecological framework.

RESULTS: From an initial sample of 20,226 articles, 72 unique articles were reviewed, three of which contributed to both quantitative and qualitative analysis. Despite the large sample, several provinces were poorly represented (if at all) and many studies were assessed as low to moderate quality. Despite these limitations, our historical lens enabled us to explore why South African progress on increasing EBF practices has been slow. The review reflects a context that increasingly supports EBF, but falls short in accounting for family, community, and workplace influences. The findings also highlight the unintended damage caused by rapidly adopting and introducing global guidelines to an unsupported health workforce.

CONCLUSIONS: From a South African perspective, we identified geographic and methodological biases, as well as gaps in our understanding and potential explanations of inequities in EBF. Our recommendations relate to policy, programming, and research to inform changes that would be required to further improve EBF practice rates in South Africa. While our review is South Africa-specific, our findings have broader implications for investing in multi-level interventions and limiting how often infant feeding guidelines are changed.}, } @article {pmid31624847, year = {2020}, author = {Salvatore, S and Dagestad Rand, K and Grytten, I and Ferkingstad, E and Domanska, D and Holden, L and Gheorghe, M and Mathelier, A and Glad, I and Kjetil Sandve, G}, title = {Beware the Jaccard: the choice of similarity measure is important and non-trivial in genomic colocalisation analysis.}, journal = {Briefings in bioinformatics}, volume = {21}, number = {5}, pages = {1523-1530}, doi = {10.1093/bib/bbz083}, pmid = {31624847}, issn = {1477-4054}, mesh = {Algorithms ; Datasets as Topic ; Gene Expression Regulation ; Genetic Variation ; Genomics/*methods ; Humans ; }, abstract = {The generation and systematic collection of genome-wide data is ever-increasing. This vast amount of data has enabled researchers to study relations between a variety of genomic and epigenomic features, including genetic variation, gene regulation and phenotypic traits. Such relations are typically investigated by comparatively assessing genomic co-occurrence. Technically, this corresponds to assessing the similarity of pairs of genome-wide binary vectors. A variety of similarity measures have been proposed for this problem in other fields like ecology. However, while several of these measures have been employed for assessing genomic co-occurrence, their appropriateness for the genomic setting has never been investigated. We show that the choice of similarity measure may strongly influence results and propose two alternative modelling assumptions that can be used to guide this choice. On both simulated and real genomic data, the Jaccard index is strongly altered by dataset size and should be used with caution. The Forbes coefficient (fold change) and tetrachoric correlation are less influenced by dataset size, but one should be aware of increased variance for small datasets. All results on simulated and real data can be inspected and reproduced at https://hyperbrowser.uio.no/sim-measure.}, } @article {pmid31624369, year = {2019}, author = {Habel, JC and Trusch, R and Schmitt, T and Ochse, M and Ulrich, W}, title = {Long-term large-scale decline in relative abundances of butterfly and burnet moth species across south-western Germany.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {14921}, pmid = {31624369}, issn = {2045-2322}, mesh = {Agriculture ; *Animal Distribution ; Animals ; Biodiversity ; Butterflies/*physiology ; *Conservation of Natural Resources ; Datasets as Topic ; Ecological Parameter Monitoring/statistics & numerical data ; Germany ; Grassland ; Moths/*physiology ; Population Dynamics/statistics & numerical data/trends ; }, abstract = {Current studies have shown a severe general decline in insect species diversity, their abundance, and a biomass reduction of flying insects. Most of previous studies have been performed at single sites, or were spatially restricted at the landscape level. In this study, we analyse trends of species richness and shifts in species composition of butterflies and burnet moth species across the federal state of Baden-Württemberg in south-western Germany, covering an area of 35,750 km[2]. The data set consists of 233,474 records and covers a period from 1750 until today. We grouped species according to their species´ specific functional traits and analyse how species with different habitat requirements and behaviour respond to land-use changes over time. Our data document a significant loss of relative abundance for most species, especially since the 1950s until today. Species demanding specific habitat requirements are more seriously suffering under this trend than generalists. This in particular affects taxa adapted to extensively used xerothermic grasslands, bogs or other habitats maintained by traditional low-productivity agricultural practices of the past. Our data indicate large-scale decline in relative abundance of many butterfly and burnet moth species, which happened in particular during the past few decades.}, } @article {pmid31623351, year = {2019}, author = {Wan, X}, title = {Comparative Genome Analyses Reveal the Genomic Traits and Host Plant Adaptations of Flavobacterium akiainvivens IK-1[T].}, journal = {International journal of molecular sciences}, volume = {20}, number = {19}, pages = {}, pmid = {31623351}, issn = {1422-0067}, support = {63191440//This work was supported by the Fundamental Research Funds for the Central Universities, Nankai University/ ; }, mesh = {*Adaptation, Physiological ; Bacterial Physiological Phenomena ; Biological Evolution ; Computational Biology/methods ; Flavobacterium/classification/*physiology ; *Genome, Bacterial ; *Genomics/methods ; *Host-Pathogen Interactions ; Plant Diseases/microbiology ; Plants/*microbiology ; Quorum Sensing ; Synteny ; }, abstract = {The genus Flavobacterium contains a large group of commensal bacteria identified in diverse terrestrial and aquatic habitats. We compared the genome of a new species Flavobacterium akiainvivens IK-1[T] to public available genomes of Flavobacterium species to reveal the genomic traits and ecological roles of IK-1[T]. Principle component analysis (PCA) of carbohydrate-active enzyme classes suggests that IK-1[T] belongs to a terrestrial clade of Flavobacterium. In addition, type 2 and type 9 secretion systems involved in bacteria-environment interactions were identified in the IK-1[T] genome. The IK-1[T] genome encodes eukaryotic-like domain containing proteins including ankyrin repeats, von Willebrand factor type A domain, and major royal jelly proteins, suggesting that IK-1[T] may alter plant host physiology by secreting eukaryotic-like proteins that mimic host proteins. A novel two-component system FaRpfC-FaYpdB was identified in the IK-1[T] genome, which may mediate quorum sensing to regulate global gene expressions. Our findings suggest that comparative genome analyses of Flavobacterium spp. reveal that IK-1[T] has adapted to a terrestrial niche. Further functional characterizations of IK-1[T] secreted proteins and their regulation systems will shed light on molecular basis of bacteria-plant interactions in environments.}, } @article {pmid31623069, year = {2019}, author = {Li, Y and Qin, T and Wei, C and Sun, J and Dong, T and Zhou, R and Chen, Q and Wang, Q}, title = {Using Transcriptome Analysis to Screen for Key Genes and Pathways Related to Cytoplasmic Male Sterility in Cotton (Gossypium hirsutum L.).}, journal = {International journal of molecular sciences}, volume = {20}, number = {20}, pages = {}, pmid = {31623069}, issn = {1422-0067}, support = {National Key Research and Development Program of Thirteenth (Project： 2016YFD0101413）//Ministry of Science and Technology of the People's Republic of China/ ; Major Science and Technology Projects in Henan Province(Project: 161100510100）//Science and Technology Agency, Henan provience/ ; }, mesh = {Computational Biology ; Cytoplasm ; Gene Expression Profiling ; Gene Expression Regulation, Plant ; Gene Ontology ; *Genes, Plant ; Gossypium/*genetics ; Immunohistochemistry ; Metabolic Networks and Pathways ; Molecular Sequence Annotation ; Phenotype ; Plant Infertility/*genetics ; *Transcriptome ; }, abstract = {Cotton (Gossypium hirsutum L.) is one of the most important cash crops worldwide. Cytoplasmic male sterility (CMS) is an excellent breeding system for exploitation of heterosis, which has great potential to increase crop yields. To understand the molecular mechanism of CMS in cotton, we compared transcriptome, cytomorphological, physiological and bioinformatics data between the CMS line C2P5A and its maintainer line C2P5B. By using high-throughput sequencing technology, 178,166 transcripts were assembled and 2013 differentially expression genes (DEGs) were identified at three different stages of C2P5A anther development. In this study, we identified DEGs associated with reactive oxygen species (ROS), peroxisomes, aldehyde dehydrogenases (ALDH), cytochrome oxidase subunit VI, and cytochrome P450, and DEGs associated with tapetum development, Jojoba acyl-CoA reductase-related male sterility protein, basic helix-loop-helix (bHLH) and MYB transcription factors. The abnormal expression of one of these genes may be responsible for the CMS C2P5A line. In gene ontology (GO) annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment, DEGs were mainly related to carbohydrate metabolism, amino acid metabolism, transport and catabolism, and signal transduction. Carbohydrate metabolism provides energy for anther development, starch and sucrose metabolism, fatty acid biosynthesis and metabolism and ascorbate and aldarate metabolism. These results showed that numerous genes and multiple complex metabolic pathways regulate cotton anther development. Weighted correlation network analysis (WGCNA) indicated that three modules, 'turquoise,' 'blue,' and 'green,' were specific for the CMS C2P5A line. The 'turquoise' and 'blue' modules were mainly related to carbohydrate metabolism, amino acid metabolism, energy metabolism, peroxisomes, pyruvate metabolism as well as fatty acid degradation. The 'green' module was mainly related to energy metabolism, carbon metabolism, translation, and lipid metabolism. RNA-sequencing and WGCNA polymerization modules were screened for key genes and pathways related to CMS in cotton. This study presents a new perspective for further research into the metabolic pathways of pollen abortion in the CMS C2P5A line and also provides a theoretical basis for its breeding and production.}, } @article {pmid31622713, year = {2020}, author = {Sharifian, S and Homaei, A and Kamrani, E and Etzerodt, T and Patel, S}, title = {New insights on the marine cytochrome P450 enzymes and their biotechnological importance.}, journal = {International journal of biological macromolecules}, volume = {142}, number = {}, pages = {811-821}, doi = {10.1016/j.ijbiomac.2019.10.022}, pmid = {31622713}, issn = {1879-0003}, mesh = {Animals ; Aquatic Organisms/*chemistry ; Biocatalysis ; Biotechnology ; Biotransformation ; Cytochrome P-450 Enzyme System/*chemistry/genetics/*metabolism ; Gene Expression Regulation ; Humans ; Water Pollutants, Chemical/metabolism ; Xenobiotics/chemistry ; }, abstract = {The monooxygenase enzymes, cytochrome P450s (CYPs), are ubiquitous in their presence and versatile in their functions. They are indispensable for hormone synthesis, dietary metabolism, and detoxification among other roles. CYPs from marine organisms are interesting candidates for recruitment in drug biotransformation, synthesis of therapeutics, bioconversion of xenobiotics, degradation of chemical carcinogens, and for use as ecotoxicological tools. However, excess CYP production in marine organisms indicates a 'stressed condition', which has a negative impact on the ecological balance. This review discusses the CYPs in marine organisms of various phyla, their application potentials, as well as the need to restore normal CYP level in them to regulate the relationship between marine organisms and environment.}, } @article {pmid31622344, year = {2019}, author = {Kaye, TN and Bahm, MA and Thorpe, AS and Gray, EC and Pfingsten, I and Waddell, C}, title = {Population extinctions driven by climate change, population size, and time since observation may make rare species databases inaccurate.}, journal = {PloS one}, volume = {14}, number = {10}, pages = {e0210378}, pmid = {31622344}, issn = {1932-6203}, mesh = {California ; *Climate Change ; Databases, Factual ; *Extinction, Biological ; *Models, Biological ; Orchidaceae/*physiology ; Oregon ; Population Density ; }, abstract = {Loss of biological diversity through population extinctions is a global phenomenon that threatens many ecosystems. Managers often rely on databases of rare species locations to plan land use actions and conserve at-risk taxa, so it is crucial that the information they contain is accurate and dependable. However, small population sizes, long gaps between surveys, and climate change may be leading to undetected extinctions of many populations. We used repeated survey records for a rare but widespread orchid, Cypripedium fasciculatum (clustered lady's slipper), to model population extinction risk based on elevation, population size, and time between observations. Population size and elevation were negatively associated with extinction, while extinction probability increased with time between observations. We interpret population losses at low elevations as a potential signal of climate change impacts. We used this model to estimate the probability of persistence of populations across California and Oregon, and found that 39%-52% of the 2415 populations reported in databases from this region are likely extinct. Managers should be aware that the number of populations of rare species in their databases is potentially an overestimate, and consider resurveying these populations to document their presence and condition, with priority given to older reports of small populations, especially those at low elevations or in other areas with high vulnerability to climate or land cover change.}, } @article {pmid31618851, year = {2019}, author = {Lu, Q and Bian, Z and Tsuchiya, N}, title = {Hydrotransport-Oriented Zn, Cu, and Pb Behavior Assessment and Source Identification in the River Network of a Historically Mined Area in the Hokuroku Basin, Northeast Japan.}, journal = {International journal of environmental research and public health}, volume = {16}, number = {20}, pages = {}, pmid = {31618851}, issn = {1660-4601}, mesh = {Copper/*chemistry ; Ecosystem ; Environmental Monitoring ; Humans ; Japan ; Lead/*chemistry ; Rivers ; Water Pollutants, Chemical/*chemistry ; Zinc/*chemistry ; }, abstract = {Aquatic ecosystems continuously receive potentially hazardous heavy metals from natural and anthropogenic sources. Focusing on the origin of heavy metals, this study aims to estimate the load contribution of tributaries from individual watershed and human drainage and to dissect the source of heavy metals, as commonly required for environmental impact assessment. Using integrated water dynamics, Geographic Information System (GIS), and chemical analysis, we identified and evaluated the heavy metal sources of the Kosaka river system in Hokuroku basin, which is a historically mined area in Northeast Japan, both in the high-water and low-water seasons. The migration and diffusion behaviors of heavy metals along with hydro-transport were analyzed, and the effects of mining activities on regional water quality both in the high-water and low-water seasons were clarified. The results indicate that Zn pollution was obvious in the Kosaka River network, especially in the downstream area. The spatial heterogeneity of heavy metal outflows from tributary watersheds was obvious, and the variations had strong correlations with mine site locations. The heavy metal flows in the mainstream increased sharply in the vicinity downstream of the Kosaka refinery drainage outlets. Compared to the low-water season, the influences of human drainage were slighter in high-water season, with lower contribution rates due to the dilution effect of the greater water discharge. Downscale sampling is effective to identify pollutant sources in regional basins.}, } @article {pmid31613961, year = {2020}, author = {Kim, J and Conroy, DE and Smyth, JM}, title = {Bidirectional Associations of Momentary Affect with Physical Activity and Sedentary Behaviors in Working Adults.}, journal = {Annals of behavioral medicine : a publication of the Society of Behavioral Medicine}, volume = {54}, number = {4}, pages = {268-279}, doi = {10.1093/abm/kaz045}, pmid = {31613961}, issn = {1532-4796}, mesh = {Adult ; Affect/*physiology ; Arousal/*physiology ; Ecological Momentary Assessment ; *Employment ; Exercise/*physiology ; Female ; Humans ; Male ; Middle Aged ; *Sedentary Behavior ; }, abstract = {BACKGROUND: Affective experiences and movement-based behaviors form a system that has been shown to influence exercise adherence and mental health outcomes. Little is known about the naturalistic dynamics of the reciprocal associations in this system.

PURPOSE: We examined the time intervals at which momentary affect precedes and follows movement-based behaviors in everyday life.

METHODS: A community sample of working adults (n = 111) completed ecological momentary assessments (EMA) asking about current affect states (sad, happy, tired, and interested) six times a day for three consecutive days. Ratings were used to generate scores for momentary affective arousal and valence. Participants also wore an activity monitor. Total activity counts and sedentary duration in the shorter to longer time intervals (5-120 min) before or after EMA were used as indicators of movement-based behaviors.

RESULTS: Multilevel modeling showed that current affective arousal predicted higher subsequent activity counts in the longer time intervals (120 min) and less subsequent sedentary behavior in the shorter to longer time intervals (5, 60, and 120 min). For the reversed sequence, neither movement-based behavior predicted subsequent momentary arousal or valence. Affective valence was unrelated to movement-based behaviors in either temporal direction.

CONCLUSIONS: Some naturally occurring affective experiences (i.e., arousal) might precede, rather than follow, movement-based behaviors. Understanding affective arousal may contribute to improved management of subsequent movement-based behaviors in everyday life.}, } @article {pmid31612915, year = {2020}, author = {Kautsar, SA and Blin, K and Shaw, S and Navarro-Muñoz, JC and Terlouw, BR and van der Hooft, JJJ and van Santen, JA and Tracanna, V and Suarez Duran, HG and Pascal Andreu, V and Selem-Mojica, N and Alanjary, M and Robinson, SL and Lund, G and Epstein, SC and Sisto, AC and Charkoudian, LK and Collemare, J and Linington, RG and Weber, T and Medema, MH}, title = {MIBiG 2.0: a repository for biosynthetic gene clusters of known function.}, journal = {Nucleic acids research}, volume = {48}, number = {D1}, pages = {D454-D458}, pmid = {31612915}, issn = {1362-4962}, support = {BB/M008770/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; U41 AT008718/AT/NCCIH NIH HHS/United States ; }, mesh = {Biosynthetic Pathways/genetics ; *Databases, Genetic ; *Genome, Bacterial ; Genomics/*methods ; Molecular Sequence Annotation ; *Multigene Family ; *Software ; }, abstract = {Fueled by the explosion of (meta)genomic data, genome mining of specialized metabolites has become a major technology for drug discovery and studying microbiome ecology. In these efforts, computational tools like antiSMASH have played a central role through the analysis of Biosynthetic Gene Clusters (BGCs). Thousands of candidate BGCs from microbial genomes have been identified and stored in public databases. Interpreting the function and novelty of these predicted BGCs requires comparison with a well-documented set of BGCs of known function. The MIBiG (Minimum Information about a Biosynthetic Gene Cluster) Data Standard and Repository was established in 2015 to enable curation and storage of known BGCs. Here, we present MIBiG 2.0, which encompasses major updates to the schema, the data, and the online repository itself. Over the past five years, 851 new BGCs have been added. Additionally, we performed extensive manual data curation of all entries to improve the annotation quality of our repository. We also redesigned the data schema to ensure the compliance of future annotations. Finally, we improved the user experience by adding new features such as query searches and a statistics page, and enabled direct link-outs to chemical structure databases. The repository is accessible online at https://mibig.secondarymetabolites.org/.}, } @article {pmid31610407, year = {2020}, author = {Reichert, M and Braun, U and Lautenbach, S and Zipf, A and Ebner-Priemer, U and Tost, H and Meyer-Lindenberg, A}, title = {Studying the impact of built environments on human mental health in everyday life: methodological developments, state-of-the-art and technological frontiers.}, journal = {Current opinion in psychology}, volume = {32}, number = {}, pages = {158-164}, doi = {10.1016/j.copsyc.2019.08.026}, pmid = {31610407}, issn = {2352-2518}, mesh = {*Built Environment ; *Digital Technology ; *Ecological Momentary Assessment ; *Geographic Information Systems ; Humans ; *Mental Health ; *Monitoring, Ambulatory ; *Neuroimaging ; *Spatial Analysis ; *Urban Population ; }, abstract = {Rapid worldwide urbanization benefits humans in many aspects, but the prevalence of common psychiatric disorders is increased in urban populations. While the impact of city living and urban upbringing on mental health is well established, it remains elusive which of the multiple factors of urban living convey risk and resilience for mental disorders. For example, air pollutants, traffic noises and fragmented social networks are some of the highly interdependent and complex influences of city living suggested to be detrimental for mental health. In contrast, urban green spaces, social contacts and physical activity have been associated with increased well-being. Knowledge on underlying mechanisms of these associations is crucial for both city planning and healthcare as it informs on how to build environments and to intervene in a way that fosters mental health yet reduces psychiatric disorders. Thus, real-life studies in urban contexts have been launched making use of recent methodological advancements: Mobile devices (e.g. smartphones) to gather intensive longitudinal mental health data, stationary sensor output providing specific context information (e.g. on weather conditions and air pollution), combinations with traditional and modern neuroimaging techniques (e.g. functional near-infrared spectroscopy and portable magnetic-encephalogram caps) and modern virtual reality setups allowing for increasingly realistic and ecological valid simulation of complex urban environments. Here we review selected methodological developments, state-of-the-art approaches as well as technological frontiers and provide examples for their application, highlighting promising potential of these novel methods for tackling the urgent urbanicity societal issue of the 21st century with a view to improve urban contexts conducive to mental health.}, } @article {pmid31608375, year = {2019}, author = {Vitales, D and Fernández, P and Garnatje, T and Garcia, S}, title = {Progress in the study of genome size evolution in Asteraceae: analysis of the last update.}, journal = {Database : the journal of biological databases and curation}, volume = {2019}, number = {}, pages = {}, pmid = {31608375}, issn = {1758-0463}, mesh = {Asteraceae/*genetics ; *Databases, Nucleic Acid ; *Evolution, Molecular ; *Genetic Variation ; *Genome, Plant ; *Polyploidy ; }, abstract = {The Genome Size in Asteraceae Database (GSAD, http://www.asteraceaegenomesize.com) has been recently updated, with data from papers published or in press until July 2018. This constitutes the third release of GSAD, currently containing 4350 data entries for 1496 species, which represent a growth of 22.52% in the number of species with available genome size data compared with the previous release, and a growth of 57.72% in terms of entries. Approximately 6% of Asteraceae species are covered in terms of known genome sizes. The number of source papers included in this release (198) means a 48.87% increase with respect to release 2.0. The significant data increase was exploited to study the genome size evolution in the family from a phylogenetic perspective. Our results suggest that the role of chromosome number in genome size diversity within Asteraceae is basically associated to polyploidy, while dysploidy would only cause minor variation in the DNA amount along the family. Among diploid taxa, we found that the evolution of genome size shows a strong phylogenetic signal. However, this trait does not seem to evolve evenly across the phylogeny, but there could be significant scale and clade-dependent patterns. Our analyses indicate that the phylogenetic signal is stronger at low taxonomic levels, with certain tribes standing out as hotspots of autocorrelation between genome size and phylogeny. Finally, we also observe meaningful associations among nuclear DNA content on Asteraceae species and other phenotypical and ecological traits (i.e. plant habit and invasion ability). Overall, this study emphasizes the need to continue generating and analysing genome size data in order to puzzle out the evolution of this parameter and its many biological correlates.}, } @article {pmid31605926, year = {2019}, author = {Ebrahimi, M and Mohammadi-Dehcheshmeh, M and Ebrahimie, E and Petrovski, KR}, title = {Comprehensive analysis of machine learning models for prediction of sub-clinical mastitis: Deep Learning and Gradient-Boosted Trees outperform other models.}, journal = {Computers in biology and medicine}, volume = {114}, number = {}, pages = {103456}, doi = {10.1016/j.compbiomed.2019.103456}, pmid = {31605926}, issn = {1879-0534}, mesh = {Animals ; *Asymptomatic Infections ; Cattle ; Decision Trees ; *Deep Learning ; Diagnosis, Computer-Assisted/*methods ; Early Diagnosis ; Female ; Mastitis, Bovine/*diagnosis ; Milk/chemistry ; }, abstract = {Sub-clinical bovine mastitis decreases milk quality and production. Moreover, sub-clinical mastitis leads to the use of antibiotics with consequent increased risk of the emergence of antibiotic-resistant bacteria. Therefore, early detection of infected cows is of great importance. The Somatic Cell Count (SCC) day-test used for mastitis surveillance, gives data that fluctuate widely between days, creating questions about its reliability and early prediction power. The recent identification of risk parameters of sub-clinical mastitis based on milking parameters by machine learning models is emerging as a promising new tool to enhance early prediction of mastitis occurrence. To develop the optimal approach for early sub-clinical mastitis prediction, we implemented 2 steps: (1) Finding the best statistical models to accurately link patterns of risk factors to sub-clinical mastitis, and (2) Extending this application from the farms tested to new farms (method generalization). Herein, we applied various machine learning-based prediction systems on a big milking dataset to uncover the best predictive models of sub-clinical mastitis. Data from 364,249 milking instances were collected by an electronic automated in-line monitoring system where milk volume, lactose concentration, electrical conductivity (EC), protein concentration, peak flow and milking time for each sample were measured. To provide a platform for the application of the models developed to other farms, the Z transformation approach was employed. Following this, various prediction systems [Deep Learning (DL), Naïve Bayes, Generalized Liner Model, Logistic Regression, Decision Tree, Gradient-Boosted Tree (GBT) and Random Forest] were applied to the non-transformed milking dataset and to a Z-standardized dataset. ROC (Receiver Operating Characteristics Curve), AUC (Area Under The Curve), and high accuracy demonstrated the high sensitivity of GBT and DL in detecting sub-clinical mastitis. GBT was the most accurate model (accuracy of 84.9%) in prediction of sub-clinical bovine mastitis. These data demonstrate how these models could be applied for prediction of sub-clinical mastitis in multiple bovine herds regardless of the size and sampling techniques.}, } @article {pmid31602942, year = {2019}, author = {Yang, F and Zhou, WZ and Zhao, X and Zhang, JC and Shao, ZL}, title = {[Habitat suitability evaluation for Angelica dahurica planting in Yanting county,Sichuan province based on GIS].}, journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica}, volume = {44}, number = {17}, pages = {3705-3710}, doi = {10.19540/j.cnki.cjcmm.20190701.107}, pmid = {31602942}, issn = {1001-5302}, mesh = {Angelica/*growth & development ; China ; *Ecosystem ; Geographic Information Systems ; Soil ; }, abstract = {It is of great significance to analyze habitable suitability of genuine medicinal materials for Chinese herbal medicine planting according to local environment,for medicinal resources protecting and for reasonable planning introduction. Based on GIS technology,the analytic hierarchy process was applied to analyze the spatial differentiation of habitat suitability of Angelica dahurica in Yanting county of Sichuan province. The evaluation combined local geographical environment characteristics and habitat requirements for A. dahurica planting and adopted the expert experience method to screen out the evaluation index for establishing evaluation system.With the established evaluation system,the index weight of evaluating index was determined by analytic hierarchy process and their grouping values were assigned by Delphi method. The all evaluating index were translated into index distribution maps using Arc GIS software. Using the comprehensive factor weighted evaluating model and spatial index distribution map,the evaluation was obtained by means of the overlay analysis function of Arc GIS 10. 3 software. RESULTS:: showed that A. dahurica had a wide range of suitable planting areas in Yanting county. Highly suitable areas amounted to 165. 01 km2,and mainly distributed in the low hilly area with moderate elevation and fertile soil. Moderately suitable areas amounted to 798. 92 km2 which had extensive distribution in middle and west part of the county. Marginally suitable areas amounted to 0. 33 km2,where the soil was highly viscous with high altitude and low temperature that was not conducive to the growth and development of A. dahurica. Adapting to local conditions and scientific planning plays an important role in the development of local characteristic planting industry of genuine medicinal materials.}, } @article {pmid31602589, year = {2020}, author = {Liu, J and Fitzgerald, M and Liao, H and Luo, Y and Jin, T and Li, X and Yang, X and Hirata, S and Matsuzawa, T}, title = {Modeling habitat suitability for Yunnan Snub-nosed monkeys in Laojun Mountain National Park.}, journal = {Primates; journal of primatology}, volume = {61}, number = {2}, pages = {277-287}, pmid = {31602589}, issn = {1610-7365}, support = {MEXT 24000001 and 16H06283, JSPS core-to-core CCSN//Japan Society for the Promotion of Science/ ; JSPS leading graduate program U04 (PWS) to TM//Japan Society for the Promotion of Science/ ; }, mesh = {Animal Distribution ; Animals ; China ; Climate ; *Ecosystem ; Geographic Information Systems ; Models, Theoretical ; Parks, Recreational ; Presbytini/*virology ; }, abstract = {We provide new information on Yunnan snub-nosed monkey (Rhinopithecus bieti) behavioral ecology, contributing to future conservation efforts within the Laojun Mountain National Park. Habitat evaluation procedures are used to quantify the value of land as a habitat for a species. We analyzed environmental variables hypothesized to influence habitat suitability for Yunnan snub-nosed monkeys, and mapped the distribution of suitable habitats across the study area and adjacent areas. Spatial analysis with GPS data was conducted to investigate home-range change of these monkeys. Predictor variables were generated using ArcMap and R programming language. We prepared 34 environmental variables at 30-m spatial resolution. Maxent was used to analyze environmental variables that contributed to suitability. Using satellite remote sensing and GIS, we modeled the distribution of suitable habitat for Yunnan snub-nosed monkeys in the Jinsichang area of the Laojun Mountains in China. This study did not describe the frequency or intensity of habitat use. Habitat suitability was affected by several variables, the most influential, as determined by permutation importance, being mean diurnal temperature range (31.6%), precipitation during the wettest quarter of the year (30.4%), average annual precipitation (17%), normalized difference vegetation index (5%), wetness (4.6%), and aspect (4.5%). This habitat suitability model provides information about the current distribution of Yunnan snub-nosed monkeys, which is important for appropriate implementation of conservation actions.}, } @article {pmid31599058, year = {2020}, author = {Zhang, D and Gao, F and Jakovlić, I and Zou, H and Zhang, J and Li, WX and Wang, GT}, title = {PhyloSuite: An integrated and scalable desktop platform for streamlined molecular sequence data management and evolutionary phylogenetics studies.}, journal = {Molecular ecology resources}, volume = {20}, number = {1}, pages = {348-355}, doi = {10.1111/1755-0998.13096}, pmid = {31599058}, issn = {1755-0998}, support = {31872604//The National Natural Science Foundation of China/ ; CARS-45-15//The Earmarked Fund for China Agriculture Research System/ ; }, mesh = {Computational Biology/instrumentation/*methods ; Data Management ; Databases, Nucleic Acid ; Molecular Sequence Data ; Phylogeny ; Software ; Workflow ; }, abstract = {Multigene and genomic data sets have become commonplace in the field of phylogenetics, but many existing tools are not designed for such data sets, which often makes the analysis time-consuming and tedious. Here, we present PhyloSuite, a (cross-platform, open-source, stand-alone Python graphical user interface) user-friendly workflow desktop platform dedicated to streamlining molecular sequence data management and evolutionary phylogenetics studies. It uses a plugin-based system that integrates several phylogenetic and bioinformatic tools, thereby streamlining the entire procedure, from data acquisition to phylogenetic tree annotation (in combination with iTOL). It has the following features: (a) point-and-click and drag-and-drop graphical user interface; (b) a workplace to manage and organize molecular sequence data and results of analyses; (c) GenBank entry extraction and comparative statistics; and (d) a phylogenetic workflow with batch processing capability, comprising sequence alignment (mafft and macse), alignment optimization (trimAl, HmmCleaner and Gblocks), data set concatenation, best partitioning scheme and best evolutionary model selection (PartitionFinder and modelfinder), and phylogenetic inference (MrBayes and iq-tree). PhyloSuite is designed for both beginners and experienced researchers, allowing the former to quick-start their way into phylogenetic analysis, and the latter to conduct, store and manage their work in a streamlined way, and spend more time investigating scientific questions instead of wasting it on transferring files from one software program to another.}, } @article {pmid31597944, year = {2019}, author = {Zucchi, MI and Cordeiro, EMG and Allen, C and Novello, M and Viana, JPG and Brown, PJ and Manjunatha, S and Omoto, C and Pinheiro, JB and Clough, SJ}, title = {Patterns of Genome-Wide Variation, Population Differentiation and SNP Discovery of the Red Banded Stink Bug (Piezodorus guildinii).}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {14480}, pmid = {31597944}, issn = {2045-2322}, mesh = {Animals ; Brazil ; Gene Ontology ; Genetic Variation ; Genetics, Population ; Genome, Insect ; Genotype ; Heteroptera/classification/*genetics/pathogenicity ; Models, Genetic ; Polymorphism, Single Nucleotide ; Population Dynamics/trends ; Seasons ; Selection, Genetic ; Glycine max ; United States ; }, abstract = {Unravelling the details of range expansion and ecological dominance shifts of insect pests has been challenging due to the lack of basic knowledge about population structure, gene flow, and most importantly, how natural selection is affecting the adaptive process. Piezodous guildinii is an emerging pest of soybean in the southern region of the United States, and increasingly important in Brazil in recent years. However, the reasons P. guildinii is gradually becoming more of a problem are questions still mostly unanswered. Here, we have genotyped P. guildinii samples and discovered 1,337 loci containing 4,083 variant sites SNPs that were used to estimate genetic structure and to identify gene candidates under natural selection. Our results revealed the existence of a significant genetic structure separating populations according to their broad geographic origin, i.e., U.S. and Brazil, supported by AMOVA (FGT = 0.26), STRUCTURE, PCA, and FST analyses. High levels of gene flow or coancestry within groups (i.e., within countries) can be inferred from the data, and no spatial pattern was apparent at the finer scale in Brazil. Samples from different seasons show more heterogeneous compositions suggesting mixed ancestry and a more complex dynamic. Lastly, we were able to detect and successfully annotated 123 GBS loci (10.5%) under positive selection. The gene ontology (GO) analysis implicated candidate genes under selection with genome reorganization, neuropeptides, and energy mobilization. We discuss how these findings could be related to recent outbreaks and suggest how new efforts directed to better understand P. guildinii population dynamics.}, } @article {pmid31596250, year = {2020}, author = {Kaufman, JH and Elkins, CA and Davis, M and Weis, AM and Huang, BC and Mammel, MK and Patel, IR and Beck, KL and Edlund, S and Chambliss, D and Douglas, J and Bianco, S and Kunitomi, M and Weimer, BC}, title = {Insular Microbiogeography: Three Pathogens as Exemplars.}, journal = {Current issues in molecular biology}, volume = {36}, number = {}, pages = {89-108}, doi = {10.21775/cimb.036.089}, pmid = {31596250}, issn = {1467-3045}, mesh = {Bacteria/classification/*genetics/pathogenicity ; Databases, Genetic ; Ecology ; Evolution, Molecular ; Genetic Variation ; Genome, Bacterial ; Metagenome ; Microbiota/*genetics ; *Phylogeny ; Phylogeography/methods ; Whole Genome Sequencing ; }, abstract = {Traditional taxonomy in biology assumes that life is organized in a simple tree. Attempts to classify microorganisms in this way in the genomics era led microbiologists to look for finite sets of 'core' genes that uniquely group taxa as clades in the tree. However, the diversity revealed by large-scale whole genome sequencing is calling into question the long-held model of a hierarchical tree of life, which leads to questioning of the definition of a species. Large-scale studies of microbial genome diversity reveal that the cumulative number of new genes discovered increases with the number of genomes studied as a power law and subsequently leads to the lack of evidence for a unique core genome within closely related organisms. Sampling 'enough' new genomes leads to the discovery of a replacement or alternative to any gene. This power law behaviour points to an underlying self-organizing critical process that may be guided by mutation and niche selection. Microbes in any particular niche exist within a local web of organism interdependence known as the microbiome. The same mechanism that underpins the macro-ecological scaling first observed by MacArthur and Wilson also applies to microbial communities. Recent metagenomic studies of a food microbiome demonstrate the diverse distribution of community members, but also genotypes for a single species within a more complex community. Collectively, these results suggest that traditional taxonomic classification of bacteria could be replaced with a quasispecies model. This model is commonly accepted in virology and better describes the diversity and dynamic exchange of genes that also hold true for bacteria. This model will enable microbiologists to conduct population-scale studies to describe microbial behaviour, as opposed to a single isolate as a representative.}, } @article {pmid31594929, year = {2019}, author = {Hua, ZS and Wang, YL and Evans, PN and Qu, YN and Goh, KM and Rao, YZ and Qi, YL and Li, YX and Huang, MJ and Jiao, JY and Chen, YT and Mao, YP and Shu, WS and Hozzein, W and Hedlund, BP and Tyson, GW and Zhang, T and Li, WJ}, title = {Insights into the ecological roles and evolution of methyl-coenzyme M reductase-containing hot spring Archaea.}, journal = {Nature communications}, volume = {10}, number = {1}, pages = {4574}, pmid = {31594929}, issn = {2041-1723}, mesh = {Alkanes/metabolism ; Archaea/enzymology/*genetics/isolation & purification ; *Biological Evolution ; China ; Computational Biology ; Genome, Archaeal ; Hot Springs/*microbiology ; Hot Temperature ; Metabolic Networks and Pathways/genetics ; *Metagenome ; Methane/metabolism ; Multigene Family/genetics ; Oxidoreductases/*genetics/metabolism ; Phylogeny ; }, abstract = {Several recent studies have shown the presence of genes for the key enzyme associated with archaeal methane/alkane metabolism, methyl-coenzyme M reductase (Mcr), in metagenome-assembled genomes (MAGs) divergent to existing archaeal lineages. Here, we study the mcr-containing archaeal MAGs from several hot springs, which reveal further expansion in the diversity of archaeal organisms performing methane/alkane metabolism. Significantly, an MAG basal to organisms from the phylum Thaumarchaeota that contains mcr genes, but not those for ammonia oxidation or aerobic metabolism, is identified. Together, our phylogenetic analyses and ancestral state reconstructions suggest a mostly vertical evolution of mcrABG genes among methanogens and methanotrophs, along with frequent horizontal gene transfer of mcr genes between alkanotrophs. Analysis of all mcr-containing archaeal MAGs/genomes suggests a hydrothermal origin for these microorganisms based on optimal growth temperature predictions. These results also suggest methane/alkane oxidation or methanogenesis at high temperature likely existed in a common archaeal ancestor.}, } @article {pmid31593624, year = {2020}, author = {Yii, V and Palermo, C and Kleve, S}, title = {Population-based interventions addressing food insecurity in Australia: A systematic scoping review.}, journal = {Nutrition & dietetics : the journal of the Dietitians Association of Australia}, volume = {77}, number = {1}, pages = {6-18}, doi = {10.1111/1747-0080.12580}, pmid = {31593624}, issn = {1747-0080}, mesh = {Australia ; Databases, Factual ; Family Characteristics ; *Food Insecurity ; Humans ; Northern Territory ; Public Health ; Rural Population ; Socioeconomic Factors ; }, abstract = {AIM: Food insecurity (FI) is a critical public health issue in Australia. Population-based interventions aiming to address the socio-ecological determinants of FI are critical for relieving and preventing it. This review aimed to map and summarise the characteristics of population-based interventions addressing household and/or community FI in Australia.

METHODS: A systematic scoping review was undertaken. Five databases, selected for range and relevance to FI in Australia ("CINAHL plus", "Ovid MEDLINE", "Sociological Abstracts", "Australian Public Affairs Information Service", and "Rural and Remote Health") were searched in May 2018 using the terms and relevant synonyms "FI" and "interventions". In addition a systematic grey literature search using multiple Google searches was undertaken. Data synthesis included categorisation and counting intervention type. Interventions were defined and charted by influence of at least one dimension of food security and impact on the socioeconomic, cultural and environmental conditions.

RESULTS: A total of 3565 published and grey literature records were identified, with the final 60 records describing 98 interventions. Few national interventions were identified, with approaches predominantly in Victoria, Northern Territory and Tasmania. Determinants related to living and working environments, food availability and food utilisation were most frequently addressed. Interventions addressing the key determinant of FI economic access were limited. A number of interventions did not appear to be associated with rigorous evaluation.

CONCLUSIONS: While there is evidence of population responses to FI in Australia, the effectiveness of these remains limited. Importantly there is a lack of coordinated and coherent national responses that address the range of FI determinants.}, } @article {pmid31593620, year = {2019}, author = {Jones, NM and Brymer, M and Silver, RC}, title = {Using Big Data to Study the Impact of Mass Violence: Opportunities for the Traumatic Stress Field.}, journal = {Journal of traumatic stress}, volume = {32}, number = {5}, pages = {653-663}, doi = {10.1002/jts.22434}, pmid = {31593620}, issn = {1573-6598}, mesh = {*Big Data ; California ; Case-Control Studies ; Data Analysis ; *Emotions ; Humans ; Mass Casualty Incidents/*psychology ; Social Media/*statistics & numerical data ; Time Factors ; }, abstract = {Studying the community impact of mass violence using a Big Data approach from social media data (e.g., Twitter) offers traumatic stress researchers an unprecedented opportunity to study and clarify theoretical assumptions using large-scale, observational, ecologically valid data. We describe challenges and benefits of working with Twitter data and briefly review studies that used Twitter data to explore community responses to mass violence. We then demonstrate the use of Twitter data to examine community responses to a specific event: the 2015 San Bernardino terrorist attack, in which 14 people were killed and 22 were wounded. In a 6-week time frame around this attack, we evaluated the time course of community-level negative emotion. We downloaded 1.16 million tweets, representing 25,894 users from San Bernardino, CA, and a matched control community, Stockton, CA. All tweets were coded in R using the Linguistic Inquiry and Word Count (LIWC) negative emotion dictionary. A piecewise regression technique with a discontinuity analysis was used to evaluate pre- and postevent trajectories of negative emotion across the study window. Controlling for within-user variability, negative emotion increased by 6.2%, β = .182, SE = .014, p < .001, in San Bernardino on the day of the attack and remained elevated for 5 days; no elevation was observed in Stockton. We discuss how data-driven text analytic techniques are useful for exploring Twitter content generated after collective traumas and describe challenges and opportunities accompanying analyses of social media data to understand the impact of mass violence on affected populations.}, } @article {pmid31589312, year = {2020}, author = {Arnold, B and Sohail, M and Wadsworth, C and Corander, J and Hanage, WP and Sunyaev, S and Grad, YH}, title = {Fine-Scale Haplotype Structure Reveals Strong Signatures of Positive Selection in a Recombining Bacterial Pathogen.}, journal = {Molecular biology and evolution}, volume = {37}, number = {2}, pages = {417-428}, pmid = {31589312}, issn = {1537-1719}, support = {F32 GM120839/GM/NIGMS NIH HHS/United States ; R01 AI106786/AI/NIAID NIH HHS/United States ; T32 AI007535/AI/NIAID NIH HHS/United States ; U54 GM088558/GM/NIGMS NIH HHS/United States ; R01 AI132606/AI/NIAID NIH HHS/United States ; }, mesh = {Evolution, Molecular ; Gene Frequency ; Gene Transfer, Horizontal ; *Genetic Variation ; Haplotypes ; Linkage Disequilibrium ; Neisseria gonorrhoeae/*genetics ; Recombination, Genetic ; Selection, Genetic ; Sequence Analysis, DNA/*methods ; }, abstract = {Identifying genetic variation in bacteria that has been shaped by ecological differences remains an important challenge. For recombining bacteria, the sign and strength of linkage provide a unique lens into ongoing selection. We show that derived alleles <300 bp apart in Neisseria gonorrhoeae exhibit more coupling linkage than repulsion linkage, a pattern that cannot be explained by limited recombination or neutrality as these couplings are significantly stronger for nonsynonymous alleles than synonymous alleles. This general pattern is driven by a small fraction of highly diverse genes, many of which exhibit evidence of interspecies horizontal gene transfer and an excess of intermediate frequency alleles. Extensive simulations show that two distinct forms of positive selection can create these patterns of genetic variation: directional selection on horizontally transferred alleles or balancing selection that maintains distinct haplotypes in the presence of recombination. Our results establish a framework for identifying patterns of selection in fine-scale haplotype structure that indicate specific ecological processes in species that recombine with distantly related lineages or possess coexisting adaptive haplotypes.}, } @article {pmid31589302, year = {2019}, author = {Yan, CZY and Austin, CM and Ayub, Q and Rahman, S and Gan, HM}, title = {Genomic characterization of Vibrio parahaemolyticus from Pacific white shrimp and rearing water in Malaysia reveals novel sequence types and structural variation in genomic regions containing the Photorhabdus insect-related (Pir) toxin-like genes.}, journal = {FEMS microbiology letters}, volume = {366}, number = {17}, pages = {}, doi = {10.1093/femsle/fnz211}, pmid = {31589302}, issn = {1574-6968}, mesh = {Animal Diseases/epidemiology/*microbiology ; Animals ; Computational Biology/methods ; *Genetic Variation ; *Genomics ; Malaysia ; Multilocus Sequence Typing ; Penaeidae/*microbiology ; Phylogeny ; Phylogeography ; Vibrio Infections/*veterinary ; Vibrio parahaemolyticus/*genetics/isolation & purification ; Water Microbiology ; *Whole Genome Sequencing ; }, abstract = {The Malaysian and global shrimp aquaculture production has been significantly impacted by acute hepatopancreatic necrosis disease (AHPND) typically caused by Vibrio parahaemolyticus harboring the pVA plasmid containing the pirAVp and pirBVp genes, which code for Photorhabdus insect-related (Pir) toxin. The limited genomic resource for V. parahaemolyticus strains from Malaysian aquaculture farms precludes an in-depth understanding of their diversity and evolutionary relationships. In this study, we isolated shrimp-associated and environmental (rearing water) V. parahaemolyticus from three aquaculture farms located in Northern and Central Malaysia followed by whole-genome sequencing of 40 randomly selected isolates on the Illumina MiSeq. Phylogenomic analysis and multilocus sequence typing (MLST) reveal distinct lineages of V. parahaemolyticus that harbor the pirABVp genes. The recovery of pVA plasmid backbone devoid of pirAVp or pirABVp in some V. parahaemolyticus isolates suggests that the toxin genes are prone to deletion. The new insight gained from phylogenomic analysis of Asian V. parahaemolyticus, in addition to the observed genomic instability of pVa plasmid, will have implications for improvements in aquaculture practices to diagnose, treat or limit the impacts of this disease.}, } @article {pmid31588597, year = {2020}, author = {Genin, M and Fumery, M and Occelli, F and Savoye, G and Pariente, B and Dauchet, L and Giovannelli, J and Vignal, C and Body-Malapel, M and Sarter, H and Gower-Rousseau, C and Ficheur, G}, title = {Fine-scale geographical distribution and ecological risk factors for Crohn's disease in France (2007-2014).}, journal = {Alimentary pharmacology & therapeutics}, volume = {51}, number = {1}, pages = {139-148}, doi = {10.1111/apt.15512}, pmid = {31588597}, issn = {1365-2036}, mesh = {Adolescent ; Adult ; Aged ; Aged, 80 and over ; Child ; Child, Preschool ; Crohn Disease/*epidemiology ; Databases, Factual ; *Environment ; Female ; France/epidemiology ; Geography ; History, 21st Century ; Humans ; Infant ; Infant, Newborn ; Male ; Middle Aged ; Patient Discharge/statistics & numerical data ; Prevalence ; Risk Factors ; Social Determinants of Health/statistics & numerical data ; Socioeconomic Factors ; Urban Population/statistics & numerical data ; Young Adult ; }, abstract = {BACKGROUND: Geographical variations in Crohn's disease (CD) suggest that the environment has a role in the pathogenesis of this condition.

AIMS: To describe the spatial distribution and the clustering of CD cases in France, and to assess the relationship between the prevalence of CD and environmental risk factors.

METHODS: We identified all patients with CD included in the French hospital discharge database from 2007 to 2014. Age- and gender-smoothed standardised prevalence ratios over this period were computed for 5610 spatial units. An ecological regression analysis was used to assess the relationship between the risk of CD and ecological variables (health care, latitude, socio-economic deprivation, urbanisation, proportion of agricultural surfaces and density of industries). Local spatial clusters of high-CD prevalence were searched for using elliptic spatial scan statistics and characterised in a hierarchical ascendant classification based on the same ecological variables.

RESULTS: About 129 089 patients with CD were identified, yielding a crude prevalence of 203 per 100 000 inhabitants. The overall spatial heterogeneity was statistically significant (P < .001). An elevated risk of CD was found to be significantly associated with high-social deprivation (relative risk [95% confidence interval] = 1.05 [1.02-1.08]) and high urbanisation (1.09 [1.04-1.14]). Sixteen significant spatial clusters of high-CD prevalence were identified; there were no common ecological variables.

CONCLUSIONS: The geographical distribution of CD prevalence in France is not uniform, and is associated with high levels of social deprivation and urbanisation. Larger ecological databases integrating more detailed environmental and clinical information are needed.}, } @article {pmid31587643, year = {2019}, author = {Ebrahimi, A and Schwartzman, J and Cordero, OX}, title = {Multicellular behaviour enables cooperation in microbial cell aggregates.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {374}, number = {1786}, pages = {20190077}, pmid = {31587643}, issn = {1471-2970}, mesh = {Computational Biology ; *Microbial Interactions ; Models, Biological ; Polysaccharide-Lyases/*biosynthesis ; Vibrio/*enzymology ; }, abstract = {Oligosaccharides produced from the extracellular hydrolysis of biological materials can act as common goods that promote cooperative growth in microbial populations, whereby cell-cell aggregation increases both the per capita availability of resources and the per-cell growth rate. However, aggregation can also have detrimental consequences for growth, as gradients form within aggregates limiting the resource accessibility. We built a computational model, which predicts cooperation is restricted in dense cell aggregates larger than 10 µm because of the emergence of polymer and oligomer counter gradients. We compared these predictions to experiments performed with two well-studied alginate-degrading strains of Vibrio splendidus, which varied in their ability to secrete alginate lyase. We observed that both strains can form large aggregates (less than 50 µm), overcoming diffusion limitation by rearranging their internal structure. The stronger enzyme producer grew non-cooperatively and formed aggregates with internal channels that allowed exchange between the bulk environment and the aggregate, whereas the weak enzyme producer showed strongly cooperative growth and formed dense aggregates in which cells near the core mixed by active swimming. Our simulations suggest that the mixing and channelling reduce diffusion limitation and allow cells to uniformly grow in aggregates. Together, these data demonstrate that bacterial behaviour can help overcome competition imposed by resource gradients within cell aggregates. This article is part of a discussion meeting issue 'Single cell ecology'.}, } @article {pmid31584946, year = {2019}, author = {Kobres, PY and Chretien, JP and Johansson, MA and Morgan, JJ and Whung, PY and Mukundan, H and Del Valle, SY and Forshey, BM and Quandelacy, TM and Biggerstaff, M and Viboud, C and Pollett, S}, title = {A systematic review and evaluation of Zika virus forecasting and prediction research during a public health emergency of international concern.}, journal = {PLoS neglected tropical diseases}, volume = {13}, number = {10}, pages = {e0007451}, pmid = {31584946}, issn = {1935-2735}, mesh = {Databases, Factual ; Disease Outbreaks/statistics & numerical data ; *Forecasting ; Guillain-Barre Syndrome/epidemiology/virology ; Humans ; Models, Statistical ; Models, Theoretical ; Pandemics ; *Public Health ; Reproducibility of Results ; *Zika Virus ; Zika Virus Infection/*epidemiology/virology ; }, abstract = {INTRODUCTION: Epidemic forecasting and prediction tools have the potential to provide actionable information in the midst of emerging epidemics. While numerous predictive studies were published during the 2016-2017 Zika Virus (ZIKV) pandemic, it remains unknown how timely, reproducible, and actionable the information produced by these studies was.

METHODS: To improve the functional use of mathematical modeling in support of future infectious disease outbreaks, we conducted a systematic review of all ZIKV prediction studies published during the recent ZIKV pandemic using the PRISMA guidelines. Using MEDLINE, EMBASE, and grey literature review, we identified studies that forecasted, predicted, or simulated ecological or epidemiological phenomena related to the Zika pandemic that were published as of March 01, 2017. Eligible studies underwent evaluation of objectives, data sources, methods, timeliness, reproducibility, accessibility, and clarity by independent reviewers.

RESULTS: 2034 studies were identified, of which n = 73 met the eligibility criteria. Spatial spread, R0 (basic reproductive number), and epidemic dynamics were most commonly predicted, with few studies predicting Guillain-Barré Syndrome burden (4%), sexual transmission risk (4%), and intervention impact (4%). Most studies specifically examined populations in the Americas (52%), with few African-specific studies (4%). Case count (67%), vector (41%), and demographic data (37%) were the most common data sources. Real-time internet data and pathogen genomic information were used in 7% and 0% of studies, respectively, and social science and behavioral data were typically absent in modeling efforts. Deterministic models were favored over stochastic approaches. Forty percent of studies made model data entirely available, 29% provided all relevant model code, 43% presented uncertainty in all predictions, and 54% provided sufficient methodological detail to allow complete reproducibility. Fifty-one percent of predictions were published after the epidemic peak in the Americas. While the use of preprints improved the accessibility of ZIKV predictions by a median of 119 days sooner than journal publication dates, they were used in only 30% of studies.

CONCLUSIONS: Many ZIKV predictions were published during the 2016-2017 pandemic. The accessibility, reproducibility, timeliness, and incorporation of uncertainty in these published predictions varied and indicates there is substantial room for improvement. To enhance the utility of analytical tools for outbreak response it is essential to improve the sharing of model data, code, and preprints for future outbreaks, epidemics, and pandemics.}, } @article {pmid31584168, year = {2020}, author = {Browne, PD and Kot, W and Jørgensen, TS and Hansen, LH}, title = {The Mobilome: Metagenomic Analysis of Circular Plasmids, Viruses, and Other Extrachromosomal Elements.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2075}, number = {}, pages = {253-264}, doi = {10.1007/978-1-4939-9877-7_18}, pmid = {31584168}, issn = {1940-6029}, mesh = {Computational Biology/methods ; *DNA Transposable Elements ; DNA, Circular ; Databases, Genetic ; Escherichia coli/genetics ; Gene Library ; Gene Transfer, Horizontal ; *Metagenome ; *Metagenomics/methods ; Plasmids/*genetics ; Viruses/*genetics ; }, abstract = {Isolation, sequencing, and analysis of circular genetic elements bring new insights to mobile genetic elements related to microbial ecology. One method used to study circular plasmids, viruses, and other elements is called the mobilome method. The mobilome method presented here is an unamplified mobilome approach allowing fast isolation of circular DNA elements from a variety of samples followed by directly building unamplified Illumina-compatible sequencing libraries using enzymatic tagging and fragmentation. Several methods for bioinformatic analysis of mobilome data are also suggested.}, } @article {pmid31584084, year = {2019}, author = {Tørresen, OK and Star, B and Mier, P and Andrade-Navarro, MA and Bateman, A and Jarnot, P and Gruca, A and Grynberg, M and Kajava, AV and Promponas, VJ and Anisimova, M and Jakobsen, KS and Linke, D}, title = {Tandem repeats lead to sequence assembly errors and impose multi-level challenges for genome and protein databases.}, journal = {Nucleic acids research}, volume = {47}, number = {21}, pages = {10994-11006}, pmid = {31584084}, issn = {1362-4962}, mesh = {Animals ; DNA/*genetics ; *Databases, Nucleic Acid ; *Databases, Protein ; Gadus morhua/genetics ; *Scientific Experimental Error ; Sequence Analysis, DNA ; Tandem Repeat Sequences/*genetics ; }, abstract = {The widespread occurrence of repetitive stretches of DNA in genomes of organisms across the tree of life imposes fundamental challenges for sequencing, genome assembly, and automated annotation of genes and proteins. This multi-level problem can lead to errors in genome and protein databases that are often not recognized or acknowledged. As a consequence, end users working with sequences with repetitive regions are faced with 'ready-to-use' deposited data whose trustworthiness is difficult to determine, let alone to quantify. Here, we provide a review of the problems associated with tandem repeat sequences that originate from different stages during the sequencing-assembly-annotation-deposition workflow, and that may proliferate in public database repositories affecting all downstream analyses. As a case study, we provide examples of the Atlantic cod genome, whose sequencing and assembly were hindered by a particularly high prevalence of tandem repeats. We complement this case study with examples from other species, where mis-annotations and sequencing errors have propagated into protein databases. With this review, we aim to raise the awareness level within the community of database users, and alert scientists working in the underlying workflow of database creation that the data they omit or improperly assemble may well contain important biological information valuable to others.}, } @article {pmid31581264, year = {2019}, author = {Kaur, KM and Malé, PG and Spence, E and Gomez, C and Frederickson, ME}, title = {Using text-mined trait data to test for cooperate-and-radiate co-evolution between ants and plants.}, journal = {PLoS computational biology}, volume = {15}, number = {10}, pages = {e1007323}, pmid = {31581264}, issn = {1553-7358}, mesh = {Animals ; Ants/genetics ; Biological Evolution ; Data Mining/*methods ; Ecosystem ; Genetic Variation/physiology ; Phenotype ; Phylogeny ; Plants/metabolism ; Symbiosis/*physiology ; }, abstract = {Mutualisms may be "key innovations" that spur lineage diversification by augmenting niche breadth, geographic range, or population size, thereby increasing speciation rates or decreasing extinction rates. Whether mutualism accelerates diversification in both interacting lineages is an open question. Research suggests that plants that attract ant mutualists have higher diversification rates than non-ant associated lineages. We ask whether the reciprocal is true: does the interaction between ants and plants also accelerate diversification in ants, i.e. do ants and plants cooperate-and-radiate? We used a novel text-mining approach to determine which ant species associate with plants in defensive or seed dispersal mutualisms. We investigated patterns of lineage diversification across a recent ant phylogeny using BiSSE, BAMM, and HiSSE models. Ants that associate mutualistically with plants had elevated diversification rates compared to non-mutualistic ants in the BiSSE model, with a similar trend in BAMM, suggesting ants and plants cooperate-and-radiate. However, the best-fitting model was a HiSSE model with a hidden state, meaning that diversification models that do not account for unmeasured traits are inappropriate to assess the relationship between mutualism and ant diversification. Against a backdrop of diversification rate heterogeneity, the best-fitting HiSSE model found that mutualism actually decreases diversification: mutualism evolved much more frequently in rapidly diversifying ant lineages, but then subsequently slowed diversification. Thus, it appears that ant lineages first radiated, then cooperated with plants.}, } @article {pmid31581254, year = {2019}, author = {Maffei, A and Angrilli, A}, title = {E-MOVIE - Experimental MOVies for Induction of Emotions in neuroscience: An innovative film database with normative data and sex differences.}, journal = {PloS one}, volume = {14}, number = {10}, pages = {e0223124}, pmid = {31581254}, issn = {1932-6203}, mesh = {Arousal/physiology ; *Databases as Topic ; *Emotions ; Female ; Humans ; Male ; *Motion Pictures ; *Neurosciences ; Recognition, Psychology ; *Sex Characteristics ; Young Adult ; }, abstract = {The need for a validated set of emotional clips to elicit emotions in more ecological experiments is increasing. Here we present the validation of a new database of emotional films, named E-MOVIE, which includes, in this first validation phase, 39 excerpts arranged in six categories, three negative (Fear, Sadness and Compassion), two positive (Erotic and Scenery) and a Neutral category. Notably, Compassion and Scenery are new in the field as they were not included in other databases. The clips in E-MOVIE are characterized by homogenous durations of approximately two minutes, which make them suitable for psychophysiological research. In order to study the affective profile prompted by each category 174 participants (112 women) rated the movies on multiple dimensions, namely valence and arousal, intensity and discreteness of the induction of one of the six basic emotions and, finally, intensity of the experience of the emotional states defined by a series of emotional adjectives. Erotic clips were effective in the elicitation of a positive emotional state, characterized by high levels of arousal and excitement. On the other hand, Fear clips (selected without blood to avoid disgust reaction) prompted an affect characterized by high arousal, low valence and high levels of reported fear and anxiety. Women reported greater unpleasantness, distress, anxiety and jittery than men to the three negative categories. Compassion clips, characterized by the depiction of crying characters, were able to induce an affective state dominated by sadness and feeling touched, consistent with an empathic reaction to emotional sufferance. Sadness clips, instead, elicited an affective state characterized by sadness together with distress and angst. We also demonstrated that clips depicting natural environments (i.e. Scenery) prompted in the viewer a surprised, inspired affective state, characterized by high valence and arousal (especially in males), a result which suggests that their past categorization as neutral stimuli was inaccurate and problematic.}, } @article {pmid31580937, year = {2019}, author = {Qi, D and Chao, Y and Zhang, C and Wang, Z and Wang, W and Chen, Q and Zheng, Z and Zhang, Z}, title = {Duplication of toll-like receptor 22 in teleost fishes.}, journal = {Fish & shellfish immunology}, volume = {94}, number = {}, pages = {752-760}, doi = {10.1016/j.fsi.2019.09.067}, pmid = {31580937}, issn = {1095-9947}, mesh = {Animals ; Computational Biology ; Cyprinidae/genetics ; *Evolution, Molecular ; Fish Proteins/*analysis/genetics ; Fishes/*genetics ; *Gene Duplication ; Phylogeny ; Toll-Like Receptors/*analysis/genetics ; }, abstract = {The TLRs of teleost fishes have distinct features and are highly diverse, but the duplication characteristics and expression patterns of the tlr22 gene remain unclear. Here, we identified paralogous tlr22 genes in 13 teleost fishes by screening available fish genomic resources and using molecular cloning. We then conducted comprehensive bioinformatics analyses and investigated spatiotemporal differences in the expression patterns of the tlr22 genes in G. eckloni. The results indicated that more than three paralogous tlr22 genes were possessed by some teleost fishes. Of these, tlr22c is specific to some subfamilies of the Cyprinidae (e.g., Barbinae, Cyprininae, Schizothoracinae, and Leuciscinae). Phylogenetic and syntenic analyses showed that the paralogous tlr22 genes originated from two single-gene duplication events. Molecular clock calculations dated the two gene duplication events at 49.5 and 39.3 MYA, which is before the common carp-specific genome duplication event and well after the fish-specific genome duplication. Gene duplication of tlr22 was followed by gene loss or pseudogene events in certain lineages. Spatiotemporal expression differences between the three duplicated tlr22 genes from G. eckloni suggested that these genes diverged functionally after gene duplication.}, } @article {pmid31579821, year = {2019}, author = {Huelsmann, M and Hecker, N and Springer, MS and Gatesy, J and Sharma, V and Hiller, M}, title = {Genes lost during the transition from land to water in cetaceans highlight genomic changes associated with aquatic adaptations.}, journal = {Science advances}, volume = {5}, number = {9}, pages = {eaaw6671}, pmid = {31579821}, issn = {2375-2548}, mesh = {*Adaptation, Biological ; Animals ; Cetacea/*genetics ; Computational Biology/methods ; DNA Damage ; DNA Repair ; *Evolution, Molecular ; *Gene Deletion ; *Genome ; *Genomics/methods ; Models, Biological ; Molecular Sequence Annotation ; Open Reading Frames ; Oxidative Stress ; Phylogeny ; }, abstract = {The transition from land to water in whales and dolphins (cetaceans) was accompanied by remarkable adaptations. To reveal genomic changes that occurred during this transition, we screened for protein-coding genes that were inactivated in the ancestral cetacean lineage. We found 85 gene losses. Some of these were likely beneficial for cetaceans, for example, by reducing the risk of thrombus formation during diving (F12 and KLKB1), erroneous DNA damage repair (POLM), and oxidative stress-induced lung inflammation (MAP3K19). Additional gene losses may reflect other diving-related adaptations, such as enhanced vasoconstriction during the diving response (mediated by SLC6A18) and altered pulmonary surfactant composition (SEC14L3), while loss of SLC4A9 relates to a reduced need for saliva. Last, loss of melatonin synthesis and receptor genes (AANAT, ASMT, and MTNR1A/B) may have been a precondition for adopting unihemispheric sleep. Our findings suggest that some genes lost in ancestral cetaceans were likely involved in adapting to a fully aquatic lifestyle.}, } @article {pmid31576380, year = {2019}, author = {Sha, B and Schymanski, EL and Ruttkies, C and Cousins, IT and Wang, Z}, title = {Exploring open cheminformatics approaches for categorizing per- and polyfluoroalkyl substances (PFASs).}, journal = {Environmental science. Processes & impacts}, volume = {21}, number = {11}, pages = {1835-1851}, doi = {10.1039/c9em00321e}, pmid = {31576380}, issn = {2050-7895}, mesh = {*Cheminformatics ; *Fluorocarbons/chemistry/classification ; Humans ; Molecular Structure ; }, abstract = {Per- and polyfluoroalkyl substances (PFASs) are a large and diverse class of chemicals of great interest due to their wide commercial applicability, as well as increasing public concern regarding their adverse impacts. A common terminology for PFASs was recommended in 2011, including broad categorization and detailed naming for many PFASs with rather simple molecular structures. Recent advancements in chemical analysis have enabled identification of a wide variety of PFASs that are not covered by this common terminology. The resulting inconsistency in categorizing and naming of PFASs is preventing efficient assimilation of reported information. This article explores how a combination of expert knowledge and cheminformatics approaches could help address this challenge in a systematic manner. First, the "splitPFAS" approach was developed to systematically subdivide PFASs (for eventual categorization) following a CnF2n+1-X-R pattern into their various parts, with a particular focus on 4 PFAS categories where X is CO, SO2, CH2 and CH2CH2. Then, the open, ontology-based "ClassyFire" approach was tested for potential applicability to categorizing and naming PFASs using five scenarios of original and simplified structures based on the "splitPFAS" output. This workflow was applied to a set of 770 PFASs from the latest OECD PFAS list. While splitPFAS categorized PFASs as intended, the ClassyFire results were mixed. These results reveal that open cheminformatics approaches have the potential to assist in categorizing PFASs in a consistent manner, while much development is needed for future systematic naming of PFASs. The "splitPFAS" tool and related code are publicly available, and include options to extend this proof-of-concept to encompass further PFASs in the future.}, } @article {pmid31575638, year = {2019}, author = {Lanno, SM and Lam, I and Drum, Z and Linde, SC and Gregory, SM and Shimshak, SJ and Becker, MV and Brew, KE and Budhiraja, A and Carter, EA and Chigweshe, L and Collins, KP and Earley, T and Einstein, HL and Fan, AA and Goss, SS and Hagen, ER and Hutcheon, SB and Kim, TT and Mitchell, MA and Neri, NR and Patterson, SE and Ransom, G and Sanchez, GJ and Wiener, BM and Zhao, D and Coolon, JD}, title = {Genomics Analysis of L-DOPA Exposure in Drosophila sechellia.}, journal = {G3 (Bethesda, Md.)}, volume = {9}, number = {12}, pages = {3973-3980}, pmid = {31575638}, issn = {2160-1836}, support = {R15 GM135901/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Caprylates/pharmacology ; Diet ; Drosophila/drug effects/*genetics ; Gene Expression Regulation/drug effects ; Gene Ontology ; Genome, Insect ; *Genomics ; Levodopa/*pharmacology ; Species Specificity ; }, abstract = {Drosophila sechellia is a dietary specialist fruit fly that evolved from a generalist ancestor to specialize on the toxic fruit of Morinda citrifolia This species pair has been the subject of numerous studies where the goal has largely been to determine the genetic basis of adaptations associated with host specialization. Because one of the most striking features of M. citrifolia fruit is the production of toxic volatile compounds that kill insects, most genomic studies in D. sechellia to date have focused on gene expression responses to the toxic compounds in its food. In this study, we aim to identify new genes important for host specialization by profiling gene expression response to 3,4-dihydroxyphenylalanine (L-DOPA). Recent work found it to be highly abundant in M. citrifolia, critical for reproductive success of D. sechellia, and supplementation of diet with the downstream pathway product dopamine can influence toxin resistance phenotypes in related species. Here we used a combination of functional genetics and genomics techniques to identify new genes that are important for D. sechellia ecological adaptation to this new niche. We show that L-DOPA exposure can affect toxin resistance phenotypes, identify genes with plastic responses to L-DOPA exposure, and functionally test an identified candidate gene. We found that knock-down of Esterase 6 (Est6) in a heterologous species alters toxin resistance suggesting Est6 may play an important role in D. sechellia host specialization.}, } @article {pmid31573764, year = {2019}, author = {Boettner, B and Browning, CR and Calder, CA}, title = {Feasibility and Validity of Geographically Explicit Ecological Momentary Assessment With Recall-Aided Space-Time Budgets.}, journal = {Journal of research on adolescence : the official journal of the Society for Research on Adolescence}, volume = {29}, number = {3}, pages = {627-645}, pmid = {31573764}, issn = {1532-7795}, support = {P2C HD042849/HD/NICHD NIH HHS/United States ; P2C HD058484/HD/NICHD NIH HHS/United States ; R01 DA032371/DA/NIDA NIH HHS/United States ; R01 HD088545/HD/NICHD NIH HHS/United States ; }, mesh = {Adolescent ; Adolescent Development/physiology ; Adolescent Health/economics ; Budgets/*statistics & numerical data ; Child ; Compliance ; Ecological Momentary Assessment/*statistics & numerical data ; Feasibility Studies ; Female ; Geographic Information Systems/*statistics & numerical data/trends ; Humans ; Longitudinal Studies ; Male ; Ohio/epidemiology/ethnology ; Smartphone/*instrumentation ; }, abstract = {We employ data from the Adolescent Health and Development in Context Study-a representative sample of urban youth ages 11-17 in and around the Columbus, OH area-to investigate the feasibility and validity of smartphone-based geographically explicit ecological momentary assessment (GEMA). Age, race, household income, familiarity with smartphones, and self-control were associated with missing global positioning systems (GPS) coverage, whereas school day was associated with discordance between percent of time at home based on GPS-only versus recall-aided space-time budget data. Fatigue from protocol compliance increases missing GPS across the week, which results in more discordance. Although some systematic differences were observed, these findings offer evidence that smartphone-based GEMA is a viable method for the collection of activity space data on urban youth.}, } @article {pmid31573385, year = {2020}, author = {Coelho, RV and Dall'Alba, G and de Avila E Silva, S and Echeverrigaray, S and Delamare, APL}, title = {Toward Algorithms for Automation of Postgenomic Data Analyses: Bacillus subtilis Promoter Prediction with Artificial Neural Network.}, journal = {Omics : a journal of integrative biology}, volume = {24}, number = {5}, pages = {300-309}, doi = {10.1089/omi.2019.0041}, pmid = {31573385}, issn = {1557-8100}, mesh = {Algorithms ; Automation/*methods ; Bacillus subtilis/*genetics ; Computational Biology/*methods ; Escherichia coli/genetics ; Gene Expression/genetics ; Genes, Bacterial/genetics ; Genome, Bacterial/genetics ; Neural Networks, Computer ; Pattern Recognition, Automated/*methods ; Promoter Regions, Genetic/*genetics ; Sequence Analysis, DNA/*methods ; }, abstract = {In the present postgenomic era, the capacity to generate big data has far exceeded the capacity to analyze, contextualize, and make sense of the data in clinical, biological, and ecological applications. There is a great unmet need for automation and algorithms to aid in analyses of big data, in biology in particular. In this context, it is noteworthy that computational methods used to analyze the regulation of bacterial gene expression have in the past focused mainly on Escherichia coli promoters due to the large amount of data available. The challenge and prospects of automation in prediction and recognition of bacteria sequences as promoters have not been properly addressed due to the promoter size and degenerate pattern. We report here an original neural network approach for recognition and prediction of Bacillus subtilis promoters. The artificial neural network used as input 767 B. subtilis promoter sequences, while also aiming at identifying the architecture, provides the most optimal prediction. Two multilayer perceptron neural network architectures offered the highest accuracy: one with five, and another with seven neurons in the hidden layer. Each architecture achieved an accuracy of 98.57% and 97.69%, respectively. The results collectively indicate the promise of the application of neural network approaches to the B. subtilis promoter recognition problem, while also suggesting the broader potential of algorithms for automation of data analyses in the postgenomic era.}, } @article {pmid31572789, year = {2019}, author = {Goldenberg, JM and Berthusen, AJ and Cárdenas-Rodríguez, J and Pagel, MD}, title = {Differentiation of Myositis-Induced Models of Bacterial Infection and Inflammation with T2-Weighted, CEST, and DCE-MRI.}, journal = {Tomography (Ann Arbor, Mich.)}, volume = {5}, number = {3}, pages = {283-291}, pmid = {31572789}, issn = {2379-139X}, support = {R01 CA169774/CA/NCI NIH HHS/United States ; P30 CA023074/CA/NCI NIH HHS/United States ; P50 CA095060/CA/NCI NIH HHS/United States ; }, mesh = {Animals ; Area Under Curve ; *Contrast Media ; Disease Models, Animal ; Escherichia coli Infections/*diagnostic imaging/pathology ; Female ; Image Interpretation, Computer-Assisted/*methods ; Machine Learning ; Magnetic Resonance Imaging/*methods ; Mice ; Mice, Inbred CBA ; Myositis/*diagnostic imaging/pathology ; Random Allocation ; Sensitivity and Specificity ; }, abstract = {We used T2 relaxation, chemical exchange saturation transfer (CEST), and dynamic contrast-enhanced (DCE) magnetic resonance imaging (MRI) to assess whether bacterial infection can be differentiated from inflammation in a myositis-induced mouse model. We measured the T2 relaxation time constants, %CEST at 5 saturation frequencies, and area under the curve (AUC) from DCE-MRI after maltose injection from infected, inflamed, and normal muscle tissue models. We applied principal component analysis (PCA) to reduce dimensionality of entire CEST spectra and DCE signal evolutions, which were analyzed using standard classification methods. We extracted features from dimensional reduction as predictors for machine learning classifier algorithms. Normal, inflamed, and infected tissues were evaluated with H&E and gram-staining histological studies, and bacterial-burden studies. The T2 relaxation time constants and AUC of DCE-MRI after injection of maltose differentiated infected, inflamed, and normal tissues. %CEST amplitudes at -1.6 and -3.5 ppm differentiated infected tissues from other tissues, but these did not differentiate inflamed tissue from normal tissue. %CEST amplitudes at 3.5, 3.0, and 2.5 ppm, AUC of DCE-MRI for shorter time periods, and relative K[trans] and kep values from DCE-MRI could not differentiate tissues. PCA and machine learning of CEST-MRI and DCE-MRI did not improve tissue classifications relative to traditional analysis methods. Similarly, PCA and machine learning did not further improve tissue classifications relative to T2 MRI. Therefore, future MRI studies of infection models should focus on T2-weighted MRI and analysis of T2 relaxation times.}, } @article {pmid31571155, year = {2020}, author = {Low, B and Coutinho, D and Gonçalves, B and Rein, R and Memmert, D and Sampaio, J}, title = {A Systematic Review of Collective Tactical Behaviours in Football Using Positional Data.}, journal = {Sports medicine (Auckland, N.Z.)}, volume = {50}, number = {2}, pages = {343-385}, pmid = {31571155}, issn = {1179-2035}, mesh = {Humans ; *Athletic Performance/physiology ; Geographic Information Systems ; Group Processes ; *Spatial Behavior ; Task Performance and Analysis ; *Soccer ; }, abstract = {BACKGROUND: Performance analysis research in association football has recently cusped a paradigmatic shift in the way tactical behaviours are studied. Based on insights from system complexity research, a growing number of studies now analyse tactical behaviours in football based on the collective movements of team players.

OBJECTIVE: The aim of this systematic review is to provide a summary of empirical research on collective tactical behaviours in football, with a particular focus on organising the methods used and their key findings.

METHODS: A systematic search of relevant English-language articles was performed on one database (Web of Science Core Collection) and one search engine (PubMed), based on PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-analyses) guidelines. The keywords 'football' and 'soccer' were each paired with all possible combinations of the following keywords: 'collective movement behaviour', 'collective behaviour', 'tactical behaviour', 'interpersonal coordination', 'space', 'Voronoi', 'synchronisation', 'tactical analysis', 'constraints', 'ecological dynamics', and 'dynamic positioning'. Empirical studies that were related to tactical analyses of footballers' positional data were sought for inclusion and analysis.

RESULTS: Full-text articles of 77 studies were reviewed. A total of 27 tactical variables were identified, which were subsequently organised into 6 categories. In addition to conventional methods of linear analysis, 11 methods of nonlinear analysis were also used, which can be organised into measures of predictability (4 methods) and synchronisation (7 methods). The key findings of the reviewed studies were organised into two themes: levels of analysis, and levels of expertise.

CONCLUSIONS: Some trends in key findings revealed the following collective behaviours as possible indicators of better tactical expertise: higher movement regularity; wider dispersion in youth players and shorter readjustment delay between teammates and opponents. Characteristic behaviours were also observed as an effect of playing position, numerical inequality, and task constraints. Future research should focus on contextualising positional data, incorporating the needs of coaching staff, to better bridge the research-practice gap.}, } @article {pmid31570726, year = {2019}, author = {Bukhari, SA and Saul, MC and James, N and Bensky, MK and Stein, LR and Trapp, R and Bell, AM}, title = {Neurogenomic insights into paternal care and its relation to territorial aggression.}, journal = {Nature communications}, volume = {10}, number = {1}, pages = {4437}, pmid = {31570726}, issn = {2041-1723}, support = {R01 GM082937/GM/NIGMS NIH HHS/United States ; }, mesh = {Aggression/*physiology ; Animals ; Behavior, Animal/physiology ; Brain/physiology ; Evolution, Molecular ; *Fathers ; *Genetics, Behavioral ; Genomics ; Male ; Mice ; Paternal Behavior/*physiology ; Reproduction ; Smegmamorpha/genetics/*physiology ; Social Behavior ; *Territoriality ; Transcription Factors/genetics ; }, abstract = {Motherhood is characterized by dramatic changes in brain and behavior, but less is known about fatherhood. Here we report that male sticklebacks-a small fish in which fathers provide care-experience dramatic changes in neurogenomic state as they become fathers. Some genes are unique to different stages of paternal care, some genes are shared across stages, and some genes are added to the previously acquired neurogenomic state. Comparative genomic analysis suggests that some of these neurogenomic dynamics resemble changes associated with pregnancy and reproduction in mammalian mothers. Moreover, gene regulatory analysis identifies transcription factors that are regulated in opposite directions in response to a territorial challenge versus during paternal care. Altogether these results show that some of the molecular mechanisms of parental care might be deeply conserved and might not be sex-specific, and suggest that tradeoffs between opposing social behaviors are managed at the gene regulatory level.}, } @article {pmid31570119, year = {2019}, author = {Graving, JM and Chae, D and Naik, H and Li, L and Koger, B and Costelloe, BR and Couzin, ID}, title = {DeepPoseKit, a software toolkit for fast and robust animal pose estimation using deep learning.}, journal = {eLife}, volume = {8}, number = {}, pages = {}, pmid = {31570119}, issn = {2050-084X}, support = {IOS-1355061//National Science Foundation/International ; N00014-09-1-1074//Office of Naval Research/International ; N00014-14-1-0635//Office of Naval Research/International ; W911NG-11-1-0385//Army Research Office/International ; W911NF14-1-0431//Army Research Office/International ; DFG Centre of Excellence 2117//Deutsche Forschungsgemeinschaft/International ; Zukunftskolleg Investment Grant//University of Konstanz/International ; The Strukture-und Innovations fonds fur die Forschung of the State of Baden-Wurttemberg//Ministry of Science, Research and Art Baden-Württemberg/International ; Marie Sklodowska-Curie grant agreement No. 748549//Horizon 2020 Framework Programme/International ; GPU Grant//Nvidia/International ; GPU Grant//Nvidia/International ; }, mesh = {Algorithms ; Animals ; Behavior, Animal/*physiology ; Computational Biology/*methods ; *Deep Learning ; Drosophila melanogaster/physiology ; Equidae/physiology ; Grasshoppers/physiology ; Locomotion/physiology ; *Software ; }, abstract = {Quantitative behavioral measurements are important for answering questions across scientific disciplines-from neuroscience to ecology. State-of-the-art deep-learning methods offer major advances in data quality and detail by allowing researchers to automatically estimate locations of an animal's body parts directly from images or videos. However, currently available animal pose estimation methods have limitations in speed and robustness. Here, we introduce a new easy-to-use software toolkit, DeepPoseKit, that addresses these problems using an efficient multi-scale deep-learning model, called Stacked DenseNet, and a fast GPU-based peak-detection algorithm for estimating keypoint locations with subpixel precision. These advances improve processing speed >2x with no loss in accuracy compared to currently available methods. We demonstrate the versatility of our methods with multiple challenging animal pose estimation tasks in laboratory and field settings-including groups of interacting individuals. Our work reduces barriers to using advanced tools for measuring behavior and has broad applicability across the behavioral sciences.}, } @article {pmid31569487, year = {2019}, author = {Yang, Z and Wei, X and He, J and Sun, C and Ju, J and Ma, J}, title = {Characterization of the Noncanonical Regulatory and Transporter Genes in Atratumycin Biosynthesis and Production in a Heterologous Host.}, journal = {Marine drugs}, volume = {17}, number = {10}, pages = {}, pmid = {31569487}, issn = {1660-3397}, mesh = {Antitubercular Agents ; Aquatic Organisms/*genetics/metabolism ; Bacterial Proteins/*genetics/metabolism ; Cloning, Molecular ; Computational Biology ; Depsipeptides/*biosynthesis/genetics/pharmacology ; Gene Expression Regulation, Bacterial ; *Gene Regulatory Networks ; Membrane Transport Proteins/genetics/metabolism ; Multigene Family ; Mycobacterium tuberculosis/drug effects ; Sequence Alignment ; Streptomyces/*genetics/metabolism ; Transcription Factors/genetics/metabolism ; }, abstract = {Atratumycin is a cyclodepsipeptide with activity against Mycobacteria tuberculosis isolated from deep-sea derived Streptomyces atratus SCSIO ZH16NS-80S. Analysis of the atratumycin biosynthetic gene cluster (atr) revealed that its biosynthesis is regulated by multiple factors, including two LuxR regulatory genes (atr1 and atr2), two ABC transporter genes (atr29 and atr30) and one Streptomyces antibiotic regulatory gene (atr32). In this work, three regulatory and two transporter genes were unambiguously determined to provide positive, negative and self-protective roles during biosynthesis of atratumycin through bioinformatic analyses, gene inactivations and trans-complementation studies. Notably, an unusual Streptomyces antibiotic regulatory protein Atr32 was characterized as a negative regulator; the function of Atr32 is distinct from previous studies. Five over-expression mutant strains were constructed by rational application of the regulatory and transporter genes; the resulting strains produced significantly improved titers of atratumycin that were ca. 1.7-2.3 fold greater than wild-type (WT) producer. Furthermore, the atratumycin gene cluster was successfully expressed in Streptomyces coelicolor M1154, thus paving the way for the transfer and recombination of large DNA fragments. Overall, this finding sets the stage for understanding the unique biosynthesis of pharmaceutically important atratumycin and lays the foundation for generating anti-tuberculosis lead compounds possessing novel structures.}, } @article {pmid31564686, year = {2019}, author = {Tanda, N and Washio, J and Kamei, T and Akazawa, K and Takahashi, N and Koseki, T}, title = {Professional Oral Care Reduces Carcinogenic Acetaldehyde Levels in Mouth Air of Perioperative Esophageal Cancer Patients: A Prospective Comparative Study.}, journal = {The Tohoku journal of experimental medicine}, volume = {249}, number = {1}, pages = {75-83}, doi = {10.1620/tjem.249.75}, pmid = {31564686}, issn = {1349-3329}, mesh = {Acetaldehyde/*analysis ; Aged ; Bacteria/isolation & purification ; Breath Tests ; Carcinogens/*analysis ; Case-Control Studies ; Esophageal Neoplasms/*metabolism/*surgery ; Female ; Humans ; Male ; Middle Aged ; Mouth/*chemistry ; *Oral Health ; Perioperative Care ; Prospective Studies ; Saliva/microbiology ; }, abstract = {Acetaldehyde is a potential carcinogen for esophageal cancer, and some oral microorganisms produce acetaldehyde from ethanol or glucose. In this prospective study, we examined the influence of professional oral care on acetaldehyde levels in mouth air of esophageal cancer patients. Acetaldehyde concentrations in mouth air and breath were measured by a portable gas chromatograph, and acetaldehyde production from oral microbiota was also evaluated. Samples were taken from 21 esophageal cancer patients (median age 68 years) and 20 age-matched healthy volunteers (control group) before and after oral care. Post-operative samples were also taken from 17 patients who had undergone surgery. All samples (mouth air, breath, and saliva) were collected 2 to 3 hours after lunch. Oral microbial samples were prepared from saliva. Genotype analysis of alcohol dehydrogenase 1B (ADH1B) and aldehyde dehydrogenase-2 (ALDH2) genes revealed no significant differences in the genotypes between the two groups. In the control group, acetaldehyde levels in mouth air showed no significant changes after oral care, while the amount of microbial acetaldehyde production from ethanol was significantly decreased. By contrast, among the patients, acetaldehyde levels in mouth air were significantly decreased after oral care and after operation, while the amount of microbial acetaldehyde production from ethanol showed no significant changes. Moreover, microbial acetaldehyde production from glucose was significantly decreased after operation. Overall, oral health was poorer in the patient group. In conclusion, professional oral care for esophageal cancer patients is effective for reducing acetaldehyde levels in mouth air due to the reduction of microbial count.}, } @article {pmid31562947, year = {2020}, author = {Hynönen, U and Zoetendal, EG and Virtala, AK and Shetty, S and Hasan, S and Jakava-Viljanen, M and de Vos, WM and Palva, A}, title = {Molecular ecology of the yet uncultured bacterial Ct85-cluster in the mammalian gut.}, journal = {Anaerobe}, volume = {62}, number = {}, pages = {102104}, doi = {10.1016/j.anaerobe.2019.102104}, pmid = {31562947}, issn = {1095-8274}, mesh = {Animals ; Cluster Analysis ; Databases, Genetic ; Female ; *Gastrointestinal Microbiome ; High-Throughput Nucleotide Sequencing ; Humans ; Male ; Mammals ; *Metagenome ; *Metagenomics/methods ; Molecular Typing ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {In our previous studies on irritable bowel syndrome (IBS) -associated microbiota by molecular methods, we demonstrated that a particular 16S rRNA gene amplicon was more abundant in the feces of healthy subjects or mixed type IBS (IBS-M) -sufferers than in the feces of individuals with diarrhea-type IBS (IBS-D). In the current study, we demonstrated that this, so called Ct85-amplicon, consists of a cluster of very heterogeneous 16S rRNA gene sequences, and defined six 16S rRNA gene types, a to f, within this cluster, each representing a novel species-, genus- or family level taxon. We then designed specific PCR primers for these sequence types, mapped the distribution of the Ct85-cluster sequences and that of the newly defined sequence types in several animal species and compared the sequence types present in the feces of healthy individuals and IBS sufferers using two IBS study cohorts, Finnish and Dutch. Various Ct85-cluster sequence types were detected in the fecal samples of several companion and production animal species with remarkably differing prevalences and abundances. The Ct85 sequence type composition of swine closely resembled that of humans. One of the five types (d) shared between humans and swine was not present in any other animals tested, while one sequence type (b) was found only in human samples. In both IBS study cohorts, one type (e) was more prevalent in healthy individuals than in the IBS-M group. By revealing various sequence types in the widespread Ct85-cluster and their distribution, the results improve our understanding of these uncultured bacteria, which is essential for future efforts to cultivate representatives of the Ct85-cluster and reveal their roles in IBS.}, } @article {pmid31561292, year = {2019}, author = {Ding, F and Li, LX and Peng, W and Peng, YK and Liu, BQ}, title = {Molecular basis for the resistance of American sloughgrass to aryloxyphenoxypropionic acid pesticides and its environmental relevance: A combined experimental and computational study.}, journal = {Chemosphere}, volume = {235}, number = {}, pages = {1030-1040}, doi = {10.1016/j.chemosphere.2019.07.044}, pmid = {31561292}, issn = {1879-1298}, mesh = {Acetyl-CoA Carboxylase/*antagonists & inhibitors/genetics/metabolism ; Anilides/toxicity ; Benzoxazoles/toxicity ; Computational Biology/*methods ; Gene Expression Regulation, Enzymologic/drug effects ; Gene Expression Regulation, Plant/drug effects ; Herbicide Resistance/*genetics ; Models, Molecular ; Molecular Docking Simulation ; Mutagenesis, Site-Directed ; Mutation ; Pesticides/*toxicity ; Plant Proteins/*antagonists & inhibitors/genetics/metabolism ; Poaceae/drug effects/enzymology/*growth & development ; Propionates/toxicity ; Protein Conformation ; Pyridines/toxicity ; United States ; }, abstract = {Organic pesticides are one of the main environmental pollutants, and how to reduce their environmental risks is an important issue. In this contribution, we disclose the molecular basis for the resistance of American sloughgrass to aryloxyphenoxypropionic acid pesticides using site-directed mutagenesis and molecular modeling and then construct an effective screening model. The results indicated that the target-site mutation (Trp-1999-Leu) in acetyl-coenzyme A carboxylase (ACCase) can affect the effectiveness of the pesticides (clodinafop, fenoxaprop, cyhalofop, and metamifop), and the plant resistance to fenoxaprop, clodinafop, cyhalofop, and metamifop was found to be 564, 19.5, 10, and 0.19 times, respectively. The established computational models (i.e. wild-type/mutant ACCase models) could be used for rational screening and evaluation of the resistance to pesticides. The resistance induced by target gene mutation can markedly reduce the bioreactivity of the ACCase-clodinafop/fenoxaprop adducts, and the magnitudes are 10 and 102, respectively. Such event will seriously aggravate environmental pollution. However, the biological issue has no distinct effect on cyhalofop (RI＝10), and meanwhile it may markedly increase the bioefficacy of metamifop (RI＝0.19). We could selectively adopt the two chemicals so as to decrease the residual pesticides in the environment. Significantly, research findings from the computational screening models were found to be negatively correlated with the resistance level derived from the bioassay testing, suggesting that the screening models can be used to guide the usage of pesticides. Obviously, this story may shed novel insight on the reduction of environmental risks of pesticides and other organic pollutants.}, } @article {pmid31561049, year = {2019}, author = {Pollmanns, J and Drösler, SE and Geraedts, M and Weyermann, M}, title = {Predictors of hospitalizations for diabetes in Germany: an ecological study on a small-area scale.}, journal = {Public health}, volume = {177}, number = {}, pages = {112-119}, doi = {10.1016/j.puhe.2019.08.003}, pmid = {31561049}, issn = {1476-5616}, mesh = {Adult ; Databases, Factual ; Diabetes Mellitus/epidemiology/*therapy ; Female ; Germany/epidemiology ; Hospitalization/*statistics & numerical data ; Humans ; Logistic Models ; Male ; Middle Aged ; Prevalence ; Primary Health Care/organization & administration ; Small-Area Analysis ; Social Class ; }, abstract = {OBJECTIVES: Our objective was to evaluate the role of potential predictors in explaining spatial variation among diabetes hospitalization rates in Germany.

STUDY DESIGN: This was an ecological analysis using hospital routine data.

METHODS: County-level hospitalization rates (n = 402) in 2015 were calculated based on the German Diagnosis Related Groups database. We used a funnel plot to identify counties with high hospitalization rates. To examine the impact of predictors such as socio-economic status or structure of primary care, we performed linear and logistic regression analyses.

RESULTS: The crude hospitalization rate was 262 admissions per 100,000 population. In multivariable logistic models, we found the percentage of employees with academic degree (odds ratio [OR]: 0.72, 95% confidence interval [CI]: 0.56-0.91), high hospital bed rate (4th quartile vs 1st quartile; OR: 2.73, CI: 1.03-7.24), and diabetes prevalence (OR: 1.49, CI: 1.17-1.90) to be significant predictors for high hospitalization rates. In multivariable linear models, the percentage of unemployed (regression coefficient b: 4.79, CI: 0.81-8.78) and rurality (b: 0.52, CI: 0.19-0.85) explained the variation in addition to predictors from logistic regression. Primary care structure was not a significant predictor in multivariable models.

CONCLUSIONS: The non-significant impact of primary care in adjusted models casts the use of diabetes hospitalizations as indicators for access and quality of primary care into doubt. Diabetes hospitalizations may rather reflect demand for care.}, } @article {pmid31560378, year = {2019}, author = {, and Fitzmaurice, C and Abate, D and Abbasi, N and Abbastabar, H and Abd-Allah, F and Abdel-Rahman, O and Abdelalim, A and Abdoli, A and Abdollahpour, I and Abdulle, ASM and Abebe, ND and Abraha, HN and Abu-Raddad, LJ and Abualhasan, A and Adedeji, IA and Advani, SM and Afarideh, M and Afshari, M and Aghaali, M and Agius, D and Agrawal, S and Ahmadi, A and Ahmadian, E and Ahmadpour, E and Ahmed, MB and Akbari, ME and Akinyemiju, T and Al-Aly, Z and AlAbdulKader, AM and Alahdab, F and Alam, T and Alamene, GM and Alemnew, BTT and Alene, KA and Alinia, C and Alipour, V and Aljunid, SM and Bakeshei, FA and Almadi, MAH and Almasi-Hashiani, A and Alsharif, U and Alsowaidi, S and Alvis-Guzman, N and Amini, E and Amini, S and Amoako, YA and Anbari, Z and Anber, NH and Andrei, CL and Anjomshoa, M and Ansari, F and Ansariadi, A and Appiah, SCY and Arab-Zozani, M and Arabloo, J and Arefi, Z and Aremu, O and Areri, HA and Artaman, A and Asayesh, H and Asfaw, ET and Ashagre, AF and Assadi, R and Ataeinia, B and Atalay, HT and Ataro, Z and Atique, S and Ausloos, M and Avila-Burgos, L and Avokpaho, EFGA and Awasthi, A and Awoke, N and Ayala Quintanilla, BP and Ayanore, MA and Ayele, HT and Babaee, E and Bacha, U and Badawi, A and Bagherzadeh, M and Bagli, E and Balakrishnan, S and Balouchi, A and Bärnighausen, TW and Battista, RJ and Behzadifar, M and Behzadifar, M and Bekele, BB and Belay, YB and Belayneh, YM and Berfield, KKS and Berhane, A and Bernabe, E and Beuran, M and Bhakta, N and Bhattacharyya, K and Biadgo, B and Bijani, A and Bin Sayeed, MS and Birungi, C and Bisignano, C and Bitew, H and Bjørge, T and Bleyer, A and Bogale, KA and Bojia, HA and Borzì, AM and Bosetti, C and Bou-Orm, IR and Brenner, H and Brewer, JD and Briko, AN and Briko, NI and Bustamante-Teixeira, MT and Butt, ZA and Carreras, G and Carrero, JJ and Carvalho, F and Castro, C and Castro, F and Catalá-López, F and Cerin, E and Chaiah, Y and Chanie, WF and Chattu, VK and Chaturvedi, P and Chauhan, NS and Chehrazi, M and Chiang, PP and Chichiabellu, TY and Chido-Amajuoyi, OG and Chimed-Ochir, O and Choi, JJ and Christopher, DJ and Chu, DT and Constantin, MM and Costa, VM and Crocetti, E and Crowe, CS and Curado, MP and Dahlawi, SMA and Damiani, G and Darwish, AH and Daryani, A and das Neves, J and Demeke, FM and Demis, AB and Demissie, BW and Demoz, GT and Denova-Gutiérrez, E and Derakhshani, A and Deribe, KS and Desai, R and Desalegn, BB and Desta, M and Dey, S and Dharmaratne, SD and Dhimal, M and Diaz, D and Dinberu, MTT and Djalalinia, S and Doku, DT and Drake, TM and Dubey, M and Dubljanin, E and Duken, EE and Ebrahimi, H and Effiong, A and Eftekhari, A and El Sayed, I and Zaki, MES and El-Jaafary, SI and El-Khatib, Z and Elemineh, DA and Elkout, H and Ellenbogen, RG and Elsharkawy, A and Emamian, MH and Endalew, DA and Endries, AY and Eshrati, B and Fadhil, I and Fallah Omrani, V and Faramarzi, M and Farhangi, MA and Farioli, A and Farzadfar, F and Fentahun, N and Fernandes, E and Feyissa, GT and Filip, I and Fischer, F and Fisher, JL and Force, LM and Foroutan, M and Freitas, M and Fukumoto, T and Futran, ND and Gallus, S and Gankpe, FG and Gayesa, RT and Gebrehiwot, TT and Gebremeskel, GG and Gedefaw, GA and Gelaw, BK and Geta, B and Getachew, S and Gezae, KE and Ghafourifard, M and Ghajar, A and Ghashghaee, A and Gholamian, A and Gill, PS and Ginindza, TTG and Girmay, A and Gizaw, M and Gomez, RS and Gopalani, SV and Gorini, G and Goulart, BNG and Grada, A and Ribeiro Guerra, M and Guimaraes, ALS and Gupta, PC and Gupta, R and Hadkhale, K and Haj-Mirzaian, A and Haj-Mirzaian, A and Hamadeh, RR and Hamidi, S and Hanfore, LK and Haro, JM and Hasankhani, M and Hasanzadeh, A and Hassen, HY and Hay, RJ and Hay, SI and Henok, A and Henry, NJ and Herteliu, C and Hidru, HD and Hoang, CL and Hole, MK and Hoogar, P and Horita, N and Hosgood, HD and Hosseini, M and Hosseinzadeh, M and Hostiuc, M and Hostiuc, S and Househ, M and Hussen, MM and Ileanu, B and Ilic, MD and Innos, K and Irvani, SSN and Iseh, KR and Islam, SMS and Islami, F and Jafari Balalami, N and Jafarinia, M and Jahangiry, L and Jahani, MA and Jahanmehr, N and Jakovljevic, M and James, SL and Javanbakht, M and Jayaraman, S and Jee, SH and Jenabi, E and Jha, RP and Jonas, JB and Jonnagaddala, J and Joo, T and Jungari, SB and Jürisson, M and Kabir, A and Kamangar, F and Karch, A and Karimi, N and Karimian, A and Kasaeian, A and Kasahun, GG and Kassa, B and Kassa, TD and Kassaw, MW and Kaul, A and Keiyoro, PN and Kelbore, AG and Kerbo, AA and Khader, YS and Khalilarjmandi, M and Khan, EA and Khan, G and Khang, YH and Khatab, K and Khater, A and Khayamzadeh, M and Khazaee-Pool, M and Khazaei, S and Khoja, AT and Khosravi, MH and Khubchandani, J and Kianipour, N and Kim, D and Kim, YJ and Kisa, A and Kisa, S and Kissimova-Skarbek, K and Komaki, H and Koyanagi, A and Krohn, KJ and Bicer, BK and Kugbey, N and Kumar, V and Kuupiel, D and La Vecchia, C and Lad, DP and Lake, EA and Lakew, AM and Lal, DK and Lami, FH and Lan, Q and Lasrado, S and Lauriola, P and Lazarus, JV and Leigh, J and Leshargie, CT and Liao, Y and Limenih, MA and Listl, S and Lopez, AD and Lopukhov, PD and Lunevicius, R and Madadin, M and Magdeldin, S and El Razek, HMA and Majeed, A and Maleki, A and Malekzadeh, R and Manafi, A and Manafi, N and Manamo, WA and Mansourian, M and Mansournia, MA and Mantovani, LG and Maroufizadeh, S and Martini, SMS and Mashamba-Thompson, TP and Massenburg, BB and Maswabi, MT and Mathur, MR and McAlinden, C and McKee, M and Meheretu, HAA and Mehrotra, R and Mehta, V and Meier, T and Melaku, YA and Meles, GG and Meles, HG and Melese, A and Melku, M and Memiah, PTN and Mendoza, W and Menezes, RG and Merat, S and Meretoja, TJ and Mestrovic, T and Miazgowski, B and Miazgowski, T and Mihretie, KMM and Miller, TR and Mills, EJ and Mir, SM and Mirzaei, H and Mirzaei, HR and Mishra, R and Moazen, B and Mohammad, DK and Mohammad, KA and Mohammad, Y and Darwesh, AM and Mohammadbeigi, A and Mohammadi, H and Mohammadi, M and Mohammadian, M and Mohammadian-Hafshejani, A and Mohammadoo-Khorasani, M and Mohammadpourhodki, R and Mohammed, AS and Mohammed, JA and Mohammed, S and Mohebi, F and Mokdad, AH and Monasta, L and Moodley, Y and Moosazadeh, M and Moossavi, M and Moradi, G and Moradi-Joo, M and Moradi-Lakeh, M and Moradpour, F and Morawska, L and Morgado-da-Costa, J and Morisaki, N and Morrison, SD and Mosapour, A and Mousavi, SM and Muche, AA and Muhammed, OSS and Musa, J and Nabhan, AF and Naderi, M and Nagarajan, AJ and Nagel, G and Nahvijou, A and Naik, G and Najafi, F and Naldi, L and Nam, HS and Nasiri, N and Nazari, J and Negoi, I and Neupane, S and Newcomb, PA and Nggada, HA and Ngunjiri, JW and Nguyen, CT and Nikniaz, L and Ningrum, DNA and Nirayo, YL and Nixon, MR and Nnaji, CA and Nojomi, M and Nosratnejad, S and Shiadeh, MN and Obsa, MS and Ofori-Asenso, R and Ogbo, FA and Oh, IH and Olagunju, AT and Olagunju, TO and Oluwasanu, MM and Omonisi, AE and Onwujekwe, OE and Oommen, AM and Oren, E and Ortega-Altamirano, DDV and Ota, E and Otstavnov, SS and Owolabi, MO and P A, M and Padubidri, JR and Pakhale, S and Pakpour, AH and Pana, A and Park, EK and Parsian, H and Pashaei, T and Patel, S and Patil, ST and Pennini, A and Pereira, DM and Piccinelli, C and Pillay, JD and Pirestani, M and Pishgar, F and Postma, MJ and Pourjafar, H and Pourmalek, F and Pourshams, A and Prakash, S and Prasad, N and Qorbani, M and Rabiee, M and Rabiee, N and Radfar, A and Rafiei, A and Rahim, F and Rahimi, M and Rahman, MA and Rajati, F and Rana, SM and Raoofi, S and Rath, GK and Rawaf, DL and Rawaf, S and Reiner, RC and Renzaho, AMN and Rezaei, N and Rezapour, A and Ribeiro, AI and Ribeiro, D and Ronfani, L and Roro, EM and Roshandel, G and Rostami, A and Saad, RS and Sabbagh, P and Sabour, S and Saddik, B and Safiri, S and Sahebkar, A and Salahshoor, MR and Salehi, F and Salem, H and Salem, MR and Salimzadeh, H and Salomon, JA and Samy, AM and Sanabria, J and Santric Milicevic, MM and Sartorius, B and Sarveazad, A and Sathian, B and Satpathy, M and Savic, M and Sawhney, M and Sayyah, M and Schneider, IJC and Schöttker, B and Sekerija, M and Sepanlou, SG and Sepehrimanesh, M and Seyedmousavi, S and Shaahmadi, F and Shabaninejad, H and Shahbaz, M and Shaikh, MA and Shamshirian, A and Shamsizadeh, M and Sharafi, H and Sharafi, Z and Sharif, M and Sharifi, A and Sharifi, H and Sharma, R and Sheikh, A and Shirkoohi, R and Shukla, SR and Si, S and Siabani, S and Silva, DAS and Silveira, DGA and Singh, A and Singh, JA and Sisay, S and Sitas, F and Sobngwi, E and Soofi, M and Soriano, JB and Stathopoulou, V and Sufiyan, MB and Tabarés-Seisdedos, R and Tabuchi, T and Takahashi, K and Tamtaji, OR and Tarawneh, MR and Tassew, SG and Taymoori, P and Tehrani-Banihashemi, A and Temsah, MH and Temsah, O and Tesfay, BE and Tesfay, FH and Teshale, MY and Tessema, GA and Thapa, S and Tlaye, KG and Topor-Madry, R and Tovani-Palone, MR and Traini, E and Tran, BX and Tran, KB and Tsadik, AG and Ullah, I and Uthman, OA and Vacante, M and Vaezi, M and Varona Pérez, P and Veisani, Y and Vidale, S and Violante, FS and Vlassov, V and Vollset, SE and Vos, T and Vosoughi, K and Vu, GT and Vujcic, IS and Wabinga, H and Wachamo, TM and Wagnew, FS and Waheed, Y and Weldegebreal, F and Weldesamuel, GT and Wijeratne, T and Wondafrash, DZ and Wonde, TE and Wondmieneh, AB and Workie, HM and Yadav, R and Yadegar, A and Yadollahpour, A and Yaseri, M and Yazdi-Feyzabadi, V and Yeshaneh, A and Yimam, MA and Yimer, EM and Yisma, E and Yonemoto, N and Younis, MZ and Yousefi, B and Yousefifard, M and Yu, C and Zabeh, E and Zadnik, V and Moghadam, TZ and Zaidi, Z and Zamani, M and Zandian, H and Zangeneh, A and Zaki, L and Zendehdel, K and Zenebe, ZM and Zewale, TA and Ziapour, A and Zodpey, S and Murray, CJL}, title = {Global, Regional, and National Cancer Incidence, Mortality, Years of Life Lost, Years Lived With Disability, and Disability-Adjusted Life-Years for 29 Cancer Groups, 1990 to 2017: A Systematic Analysis for the Global Burden of Disease Study.}, journal = {JAMA oncology}, volume = {5}, number = {12}, pages = {1749-1768}, pmid = {31560378}, issn = {2374-2445}, support = {201900/Z/16/Z/WT_/Wellcome Trust/United Kingdom ; P30 CA014236/CA/NCI NIH HHS/United States ; }, mesh = {Disabled Persons ; Global Burden of Disease ; Global Health ; Humans ; Incidence ; Neoplasms/*epidemiology ; Quality-Adjusted Life Years ; }, abstract = {IMPORTANCE: Cancer and other noncommunicable diseases (NCDs) are now widely recognized as a threat to global development. The latest United Nations high-level meeting on NCDs reaffirmed this observation and also highlighted the slow progress in meeting the 2011 Political Declaration on the Prevention and Control of Noncommunicable Diseases and the third Sustainable Development Goal. Lack of situational analyses, priority setting, and budgeting have been identified as major obstacles in achieving these goals. All of these have in common that they require information on the local cancer epidemiology. The Global Burden of Disease (GBD) study is uniquely poised to provide these crucial data.

OBJECTIVE: To describe cancer burden for 29 cancer groups in 195 countries from 1990 through 2017 to provide data needed for cancer control planning.

EVIDENCE REVIEW: We used the GBD study estimation methods to describe cancer incidence, mortality, years lived with disability, years of life lost, and disability-adjusted life-years (DALYs). Results are presented at the national level as well as by Socio-demographic Index (SDI), a composite indicator of income, educational attainment, and total fertility rate. We also analyzed the influence of the epidemiological vs the demographic transition on cancer incidence.

FINDINGS: In 2017, there were 24.5 million incident cancer cases worldwide (16.8 million without nonmelanoma skin cancer [NMSC]) and 9.6 million cancer deaths. The majority of cancer DALYs came from years of life lost (97%), and only 3% came from years lived with disability. The odds of developing cancer were the lowest in the low SDI quintile (1 in 7) and the highest in the high SDI quintile (1 in 2) for both sexes. In 2017, the most common incident cancers in men were NMSC (4.3 million incident cases); tracheal, bronchus, and lung (TBL) cancer (1.5 million incident cases); and prostate cancer (1.3 million incident cases). The most common causes of cancer deaths and DALYs for men were TBL cancer (1.3 million deaths and 28.4 million DALYs), liver cancer (572 000 deaths and 15.2 million DALYs), and stomach cancer (542 000 deaths and 12.2 million DALYs). For women in 2017, the most common incident cancers were NMSC (3.3 million incident cases), breast cancer (1.9 million incident cases), and colorectal cancer (819 000 incident cases). The leading causes of cancer deaths and DALYs for women were breast cancer (601 000 deaths and 17.4 million DALYs), TBL cancer (596 000 deaths and 12.6 million DALYs), and colorectal cancer (414 000 deaths and 8.3 million DALYs).

CONCLUSIONS AND RELEVANCE: The national epidemiological profiles of cancer burden in the GBD study show large heterogeneities, which are a reflection of different exposures to risk factors, economic settings, lifestyles, and access to care and screening. The GBD study can be used by policy makers and other stakeholders to develop and improve national and local cancer control in order to achieve the global targets and improve equity in cancer care.}, } @article {pmid31560050, year = {2019}, author = {Mao, L and Chen, M and Chu, Q and Jia, L and Sultana, MH and Wu, D and Kong, X and Qiu, J and Ye, CY and Zhu, QH and Chen, X and Fan, L}, title = {RiceRelativesGD: a genomic database of rice relatives for rice research.}, journal = {Database : the journal of biological databases and curation}, volume = {2019}, number = {}, pages = {}, pmid = {31560050}, issn = {1758-0463}, mesh = {*Data Curation ; *Databases, Genetic ; *Genome, Plant ; *Oryza/genetics/metabolism ; }, abstract = {Rice (Oryza sativa L.) is one of the most important crops worldwide. Its relatives, including phylogenetically related species of rice and paddy weeds with a similar ecological niche, can provide crucial genetic resources (such as resistance to biotic and abiotic stresses and high photosynthetic efficiency) for rice research. Although many rice genomic databases have been constructed, a database providing large-scale curated genomic data from rice relatives and offering specific gene resources is still lacking. Here, we present RiceRelativesGD, a user-friendly genomic database of rice relatives. RiceRelativesGD integrates large-scale genomic resources from 2 cultivated rice and 11 rice relatives, including 208 321 specific genes and 13 643 genes related to photosynthesis and responsive to external stimuli. Diverse bioinformatics tools are embedded in the database, which allow users to search, visualize and download the information of interest. To our knowledge, this is the first genomic database providing a centralized genetic resource of rice relatives. RiceRelativesGD will serve as a significant and comprehensive knowledgebase for the rice community.}, } @article {pmid31558710, year = {2019}, author = {Fatima, S and Hu, X and Huang, C and Zhang, W and Cai, J and Huang, M and Gong, RH and Chen, M and Ho, AHM and Su, T and Wong, HLX and Bian, Z and Kwan, HY}, title = {High-fat diet feeding and palmitic acid increase CRC growth in β2AR-dependent manner.}, journal = {Cell death & disease}, volume = {10}, number = {10}, pages = {711}, pmid = {31558710}, issn = {2041-4889}, mesh = {Adrenergic beta-Agonists/pharmacology ; Animals ; Cell Line, Tumor ; Cell Proliferation/drug effects/genetics ; Colorectal Neoplasms/enzymology/genetics/*metabolism/pathology ; Computational Biology ; Cyclic AMP-Dependent Protein Kinases/genetics/metabolism ; Diet, High-Fat/*adverse effects ; Disease Models, Animal ; Humans ; Lipid Metabolism/drug effects/genetics ; Male ; Mice ; Mice, Nude ; Palmitic Acid/*metabolism/pharmacology ; Phosphorylation ; RNA, Small Interfering ; Receptors, Adrenergic, beta/genetics/*metabolism ; Signal Transduction/drug effects/genetics ; Sp1 Transcription Factor/genetics/metabolism ; Stearic Acids/metabolism ; Sterol Esterase/chemistry/metabolism ; }, abstract = {Epidemiology studies indicate that consumption of high-fat diet (HFD) is directly associated with the development of colorectal cancer (CRC). However, the exact component in HFD and the mechanism underlying its effect on CRC growth remained unclear. Our study shows that HFD feeding increases β2AR expression in the xenograft tissues of CRC-bearing mouse model; the elevated β2AR expression is reduced when HFD is replaced by control diet, which strongly suggests an association between HFD feeding and β2AR expression in CRC. HFD feeding increases palmitic acid and stearic acid levels in CRC; however, only palmitic acid increases β2AR expression, which is dependent upon Sp1. β2AR plays the dominant role in promoting CRC cell proliferation among all the β-AR subtypes. More importantly, knockout of β2AR or knockdown of Sp1 abolishes the palmitic acid increased CRC cell proliferation, suggesting palmitic acid increases CRC cell proliferation in β2AR-dependent manner. HFD or palmitic acid-rich diet (PAD) also fails to increase the tumor growth in xenograft mouse models bearing β2AR-knockout CRC cells. β2AR promotes CRC growth by increasing the phosphorylation of HSL at the residue S552. The phosphorylated and activated HSL (S552) changes the metabolic phenotype of CRC and increases energy production, which promotes CRC growth. Our study has revealed the unique tumorigenic properties of palmitic acid in promoting CRC growth, and have delineated the underlying mechanism of action. We are also the first to report the linkage between HFD feeding and β-adrenergic signaling pathway in relation to CRC growth.}, } @article {pmid31558589, year = {2019}, author = {Peckre, LR and Lowie, A and Brewer, D and Ehmke, E and Welser, K and Shaw, E and Wall, C and Pouydebat, E and Fabre, AC}, title = {Food mobility and the evolution of grasping behaviour: a case study in strepsirrhine primates.}, journal = {The Journal of experimental biology}, volume = {222}, number = {Pt 20}, pages = {}, doi = {10.1242/jeb.207688}, pmid = {31558589}, issn = {1477-9145}, mesh = {Animals ; *Biological Evolution ; Databases as Topic ; Female ; *Food ; Hand Strength/*physiology ; Male ; Models, Biological ; Movement ; Primates/*physiology ; }, abstract = {Manual grasping is widespread among tetrapods but is more prominent and dexterous in primates. Whether the selective pressures that drove the evolution of dexterous hand grasping involved the collection of fruit or predation on mobile insects remains an area of debate. One way to explore this question is to examine preferences for manual versus oral grasping of a moving object. Previous studies on strepsirrhines have shown a preference for oral grasping when grasping static food items and a preference for manual grasping when grasping mobile prey such as insects, but little is known about the factors at play. Using a controlled experiment with a simple and predictable motion of a food item, we tested and compared the grasping behaviours of 53 captive individuals belonging to 17 species of strepsirrhines while grasping swinging food items and static food items. The swinging motion increased the frequency of hand-use for all individuals. Our results provide evidence that the swinging motion of the food is a sufficient parameter to increase hand grasping in a wide variety of strepsirrhine primates. From an evolutionary perspective, this result gives some support to the idea that hand-grasping abilities evolved under selective pressure associated with the predation of food items in motion. Looking at a common grasping pattern across a large set of species, this study provides important insight into comparative approaches to understanding the evolution of the hand grasping of food in primates and potentially other tetrapod taxa.}, } @article {pmid31557848, year = {2019}, author = {Kelemen, M and Polishchuk, V and Gavurová, B and Szabo, S and Rozenberg, R and Gera, M and Kozuba, J and Andoga, R and Divoková, A and Bliš'an, P}, title = {Fuzzy Model for Quantitative Assessment of Environmental Start-up Projects in Air Transport.}, journal = {International journal of environmental research and public health}, volume = {16}, number = {19}, pages = {}, pmid = {31557848}, issn = {1660-4601}, mesh = {Aviation/*economics ; Decision Making ; *Environment ; *Fuzzy Logic ; Investments ; *Models, Economic ; }, abstract = {The purpose of this paper is to develop an applied fuzzy model of information technology to obtain quantitative estimates of environmental start-up projects in air transport. The developed model will become a useful tool for venture funds, business angels, or crowdfunding platforms for the development of innovative air transport businesses. Obtaining a quantitative estimate of the environmental start-up projects will increase the sustainability of the decision making on the security of financing of such projects by investors. This article develops a fuzzy evaluation model of project start-ups in air transport as an application of our neuro-fuzzy model in a specific air transport environment. The applied model provides output ranking of start-up project teams in air transport based on a four-layer neuro-fuzzy network. The presented model declares the possibilities of the application to solve these economic problems and offers the space for subsequent research focused on its usability in several areas of start-up development, in sectors and processes differentiated. The benefits are also visible for several types of policies, with an emphasis on decision-making processes in regulatory mechanisms to support the state funding in Slovakia, the EU etc.}, } @article {pmid31555768, year = {2019}, author = {Razzaghi, A and Soori, H and Kavousi, A and Abadi, A and Khosravi, A}, title = {Factors with the Highest Impact on Road Traffic Deaths in Iran; an Ecological Study.}, journal = {Archives of academic emergency medicine}, volume = {7}, number = {1}, pages = {38}, pmid = {31555768}, issn = {2645-4904}, abstract = {INTRODUCTION: The largest proportion of road traffic deaths (RTDs) happen in Low and Middle Income Countries (LMICs). The efforts for decreasing RTDs can be successful if there is precise information about its related risk factors. This study aimed to determine economic, population, road, and vehicle factors with the highest impacts on RTDs in Iran.

METHODS: This is an ecological study, which has been done using covariates including: the population density, economic growth, urbanization, distance traveled (km) in 100 thousand people, the length of urban roads, the length of rural roads and the Vehicle per 1000 population for each province of Iran in 2015. The covariates considered had been gathered from different sources and to determine which one of the covariates has an effect on RTDs, the Negative Binomial (NB) regression model was used.

RESULTS: The mean number of RTDs per 100000 population was 474 ± 70.59 in 2015. The highest and lowest rates of death belonged to Fars and Qom provinces, respectively. The results of the univariate model showed the population density as the only covariate of RTDs (p=0.001). Also, among other covariates, GDP was the only variable with a p-value equal to 0.2. In the multivariate NB model, it was seen that the population density (p=0.001), and GDP (p=0.02) significantly correlated with RTDs. For a unit (Million Rial) increase in the GDP of the province, the number of deaths decreased by as much as 0.0014. In addition, for a unit increase in population density, the number of deaths went up by as much as 30.

CONCLUSION: Population density and GDP had positive and negative effects on the number of fatal road traffic injuries, respectively. By considering these factors in presentational and controlling programs on road traffic injuries, it is possible to decrease the RTDs.}, } @article {pmid31554315, year = {2019}, author = {Polishchuk, V and Kelemen, M and Gavurová, B and Varotsos, C and Andoga, R and Gera, M and Christodoulakis, J and Soušek, R and Kozuba, J and Hospodka, J and Blišťan, P and Szabo, S}, title = {A Fuzzy Model of Risk Assessment for Environmental Start-up Projects in the Air Transport Sector.}, journal = {International journal of environmental research and public health}, volume = {16}, number = {19}, pages = {}, pmid = {31554315}, issn = {1660-4601}, mesh = {*Aviation ; Decision Making ; *Environment ; *Fuzzy Logic ; Investments ; *Risk Assessment ; Software ; }, abstract = {The purpose of this paper is to develop a fuzzy model of the risk assessment for environmental start-up projects in the air transport sector at the stage of business expansion. The model developed for the following software will be a useful tool for the risk decision support system of investment funds in financing environmental start-up projects at the stage of market conquest. Developing a quantitative risk assessment for environmental start-up projects for the air transport sector will increase the resilience of making risk decisions about their financing by the investors. In this paper, a set of 21 criteria for assessing the risk of launching environmental start-up projects in the air transport sector were formulated for the first time by presenting inputs in the form of a linguistic risk assessment and the number of credible expert considerations. The fuzzy risk assessment model, based on expert knowledge, uses linguistic variables, reveals the uncertainty of the input data, and displays a risk assessment with linguistic interpretation. The result of the paper is a fuzzy model that is embedded in a generalized algorithm and tested in an example risk assessment of environmental start-up projects in the air transport sector.}, } @article {pmid31553801, year = {2019}, author = {Hoondert, RPJ and Oldenkamp, R and de Zwart, D and van de Meent, D and Posthuma, L}, title = {QSAR-Based Estimation of Species Sensitivity Distribution Parameters: An Exploratory Investigation.}, journal = {Environmental toxicology and chemistry}, volume = {38}, number = {12}, pages = {2764-2770}, pmid = {31553801}, issn = {1552-8618}, support = {603437//FP7 Environment/International ; }, mesh = {Databases, Chemical ; Ecotoxicology ; Models, Theoretical ; *Quantitative Structure-Activity Relationship ; Risk Assessment ; }, abstract = {Ecological risk assessments are hampered by limited availability of ecotoxicity data. The present study aimed to explore the possibility of deriving species sensitivity distribution (SSD) parameters for nontested compounds, based on simple physicochemical characteristics, known SSDs for data-rich compounds, and a quantitative structure-activity relationship (QSAR)-type approach. The median toxicity of a data-poor chemical for species assemblages significantly varies with values of the physicochemical descriptors, especially when based on high-quality SSD data (from either acute median effect concentrations or chronic no-observed-effect concentrations). Beyond exploratory uses, we discuss how the precision of QSAR-based SSDs can be improved to construct models that accurately predict the SSD parameters of data-poor chemicals. The current models show that the concept of QSAR-based SSDs supports screening-level evaluations of the potential ecotoxicity of compounds for which data are lacking. Environ Toxicol Chem 2019;38:2764-2770. © 2019 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals, Inc. on behalf of SETAC.}, } @article {pmid31547200, year = {2019}, author = {Cheng, L and Li, L and Chen, L and Hu, S and Yuan, L and Liu, Y and Cui, Y and Zhang, T}, title = {Spatiotemporal Variability and Influencing Factors of Aerosol Optical Depth over the Pan Yangtze River Delta during the 2014-2017 Period.}, journal = {International journal of environmental research and public health}, volume = {16}, number = {19}, pages = {}, pmid = {31547200}, issn = {1660-4601}, mesh = {*Aerosols ; Air Pollutants/analysis ; Air Pollution/*statistics & numerical data ; Environmental Monitoring ; Geography ; Particulate Matter/analysis ; Regression Analysis ; *Rivers ; Seasons ; *Spatio-Temporal Analysis ; }, abstract = {Large amounts of aerosol particles suspended in the atmosphere pose a serious challenge to the climate and human health. In this study, we produced a dataset through merging the Moderate Resolution Imaging Spectrometers (MODIS) Collection 6.1 3-km resolution Dark Target aerosol optical depth (DT AOD) with the 10-km resolution Deep Blue aerosol optical depth (DB AOD) data by linear regression and made use of it to unravel the spatiotemporal characteristics of aerosols over the Pan Yangtze River Delta (PYRD) region from 2014 to 2017. Then, the geographical detector method and multiple linear regression analysis were employed to investigate the contributions of influencing factors. Results indicate that: (1) compared to the original Terra DT and Aqua DT AOD data, the average daily spatial coverage of the merged AOD data increased by 94% and 132%, respectively; (2) the values of four-year average AOD were high in the north-east and low in the south-west of the PYRD; (3) the annual average AOD showed a decreasing trend from 2014 to 2017 while the seasonal average AOD reached its maximum in spring; and that (4) Digital Elevation Model (DEM) and slope contributed most to the spatial distribution of AOD, followed by precipitation and population density. Our study highlights the spatiotemporal variability of aerosol optical depth and the contributions of different factors over this large geographical area in the four-year period, and can, therefore, provide useful insights into the air pollution control for decision makers.}, } @article {pmid31545808, year = {2019}, author = {Li, Y and Cazelles, B and Yang, G and Laine, M and Huang, ZXY and Cai, J and Tan, H and Stenseth, NC and Tian, H}, title = {Intrinsic and extrinsic drivers of transmission dynamics of hemorrhagic fever with renal syndrome caused by Seoul hantavirus.}, journal = {PLoS neglected tropical diseases}, volume = {13}, number = {9}, pages = {e0007757}, pmid = {31545808}, issn = {1935-2735}, mesh = {Animals ; China/epidemiology ; Cities ; Climate ; Hemorrhagic Fever with Renal Syndrome/*epidemiology/prevention & control/*transmission ; Humans ; Models, Theoretical ; Rodent Control ; Rodentia/virology ; Seasons ; Seoul virus ; Vaccination ; }, abstract = {Seoul hantavirus (SEOV) has recently raised concern by causing geographic range expansion of hemorrhagic fever with renal syndrome (HFRS). SEOV infections in humans are significantly underestimated worldwide and epidemic dynamics of SEOV-related HFRS are poorly understood because of a lack of field data and empirically validated models. Here, we use mathematical models to examine both intrinsic and extrinsic drivers of disease transmission from animal (the Norway rat) to humans in a SEOV-endemic area in China. We found that rat eradication schemes and vaccination campaigns, but below the local elimination threshold, could diminish the amplitude of the HFRS epidemic but did not modify its seasonality. Models demonstrate population dynamics of the rodent host were insensitive to climate variations in urban settings, while relative humidity had a negative effect on the seasonality in transmission. Our study contributes to a better understanding of the epidemiology of SEOV-related HFRS, demonstrates asynchronies between rodent population dynamics and transmission rate, and identifies potential drivers of the SEOV seasonality.}, } @article {pmid31545804, year = {2019}, author = {Schaber, KL and Paz-Soldan, VA and Morrison, AC and Elson, WHD and Rothman, AL and Mores, CN and Astete-Vega, H and Scott, TW and Waller, LA and Kitron, U and Elder, JP and Barker, CM and Perkins, TA and Vazquez-Prokopec, GM}, title = {Dengue illness impacts daily human mobility patterns in Iquitos, Peru.}, journal = {PLoS neglected tropical diseases}, volume = {13}, number = {9}, pages = {e0007756}, pmid = {31545804}, issn = {1935-2735}, support = {P01 AI098670/AI/NIAID NIH HHS/United States ; }, mesh = {Adolescent ; Dengue/*epidemiology ; Dengue Virus/isolation & purification ; Female ; Fever ; Humans ; *Illness Behavior ; *Locomotion ; Male ; Peru/epidemiology ; Retrospective Studies ; Surveys and Questionnaires ; }, abstract = {BACKGROUND: Human mobility plays a central role in shaping pathogen transmission by generating spatial and/or individual variability in potential pathogen-transmitting contacts. Recent research has shown that symptomatic infection can influence human mobility and pathogen transmission dynamics. Better understanding the complex relationship between symptom severity, infectiousness, and human mobility requires quantification of movement patterns throughout infectiousness. For dengue virus (DENV), human infectiousness peaks 0-2 days after symptom onset, making it paramount to understand human movement patterns from the beginning of illness.

Through community-based febrile surveillance and RT-PCR assays, we identified a cohort of DENV+ residents of the city of Iquitos, Peru (n = 63). Using retrospective interviews, we measured the movements of these individuals when healthy and during each day of symptomatic illness. The most dramatic changes in mobility occurred during the first three days after symptom onset; individuals visited significantly fewer locations (Wilcoxon test, p = 0.017) and spent significantly more time at home (Wilcoxon test, p = 0.005), compared to when healthy. By 7-9 days after symptom onset, mobility measures had returned to healthy levels. Throughout an individual's symptomatic period, the day of illness and their subjective sense of well-being were the most significant predictors for the number of locations and houses they visited.

CONCLUSIONS/SIGNIFICANCE: Our study is one of the first to collect and analyze human mobility data at a daily scale during symptomatic infection. Accounting for the observed changes in human mobility throughout illness will improve understanding of the impact of disease on DENV transmission dynamics and the interpretation of public health-based surveillance data.}, } @article {pmid31545203, year = {2019}, author = {Chen, F and Zeng, S and Ma, J and Li, X and Zhang, S and Zhu, Q}, title = {Interactions between decabromodiphenyl ether and lead in soil-plant system.}, journal = {Chemosphere}, volume = {236}, number = {}, pages = {124406}, doi = {10.1016/j.chemosphere.2019.124406}, pmid = {31545203}, issn = {1879-1298}, mesh = {Biomass ; Chlorophyll/metabolism ; Ecotoxicology/methods ; Festuca/*drug effects/growth & development/metabolism ; Germination/drug effects ; Halogenated Diphenyl Ethers/pharmacokinetics/*toxicity ; Lead/pharmacokinetics/*toxicity ; Plant Exudates/analysis/metabolism ; Plant Roots/drug effects/growth & development/metabolism ; Soil Pollutants/pharmacokinetics/*toxicity ; }, abstract = {Pot experiments were conducted under abiotic conditions to investigate the interactive influence of decabromodiphenyl ether (BDE-209) and lead (Pb) on the seed germination, germ length, root exudation and physiological characteristics of tall fescue (Festuca arundinaceae), and the uptake, accumulation of Pb and BDE-209 in the plant tissues. Results show that seed germination and germ length were impacted by Pb but less influenced by BDE-209. BDE-209 spiking (10 and 50 mg/L) could alleviate the toxicity of high Pb concentration on seed germination and growth. The chlorophyll content was significantly increased at 500 mg/kg Pb but declined at 2000 mg/kg Pb. Low-level Pb contamination (500 mg/kg) activated antioxidase activity; however, 2000 mg/kg Pb significantly reduced the antioxidase activity. Plant biomass slightly decreased at 500 mg/kg Pb but significantly declined at 2000 mg/kg Pb. The addition of a moderate dosage of BDE-209 (10-50 mg/kg) lessened Pb phytotoxicity, leading to improved plant growth relative to the case of Pb spiking alone. The exudate secretion was significantly enhanced by Pb addition, but BDE-209 spiking only caused slightly increased secretion. Pb could interfere with BDE-209 adsorption and translocation of tall fescue by affecting physiological behavior of the plant, but BDE-209 exhibited little influence on the Pb fate in the plant. Overall, BDE-209 had slight interference on the impact of Pb towards tall fescue. The results demonstrate the complex interactive effects of organic pollutants and heavy metals in the soil-plant system.}, } @article {pmid31542415, year = {2019}, author = {Tackmann, J and Matias Rodrigues, JF and von Mering, C}, title = {Rapid Inference of Direct Interactions in Large-Scale Ecological Networks from Heterogeneous Microbial Sequencing Data.}, journal = {Cell systems}, volume = {9}, number = {3}, pages = {286-296.e8}, doi = {10.1016/j.cels.2019.08.002}, pmid = {31542415}, issn = {2405-4720}, support = {/SNSF_/Swiss National Science Foundation/Switzerland ; }, mesh = {Algorithms ; Biodiversity ; Computational Biology/*methods ; Ecosystem ; High-Throughput Nucleotide Sequencing ; Humans ; Metagenome ; Metagenomics ; *Microbial Interactions ; Microbiota/*physiology ; Models, Statistical ; RNA, Ribosomal, 16S/*genetics ; }, abstract = {The availability of large-scale metagenomic sequencing data can facilitate the understanding of microbial ecosystems in unprecedented detail. However, current computational methods for predicting ecological interactions are hampered by insufficient statistical resolution and limited computational scalability. They also do not integrate metadata, which can reduce the interpretability of predicted ecological patterns. Here, we present FlashWeave, a computational approach based on a flexible Probabilistic Graphical Model framework that integrates metadata and predicts direct microbial interactions from heterogeneous microbial abundance data sets with hundreds of thousands of samples. FlashWeave outperforms state-of-the-art methods on diverse benchmarking challenges in terms of runtime and accuracy. We use FlashWeave to analyze a cross-study data set of 69,818 publicly available human gut samples and produce, to the best of our knowledge, the largest and most diverse network of predicted, direct gastrointestinal microbial interactions to date. FlashWeave is freely available for download here: https://github.com/meringlab/FlashWeave.jl.}, } @article {pmid31539968, year = {2019}, author = {He, S and Yang, W and Li, W and Zhang, Y and Qin, M and Mao, Z}, title = {Impacts of salt shocking and the selection of a suitable reversal agent on anammox.}, journal = {The Science of the total environment}, volume = {692}, number = {}, pages = {602-612}, doi = {10.1016/j.scitotenv.2019.07.215}, pmid = {31539968}, issn = {1879-1026}, mesh = {Ammonia/*metabolism ; Bacteria, Anaerobic/*drug effects/metabolism ; Microbiota/*drug effects/physiology ; Oxidation-Reduction ; Sodium Chloride/*toxicity ; Stress, Physiological ; *Waste Disposal, Fluid ; }, abstract = {In this study, an anaerobic ammonium oxidation (anammox) reactor, which was inhibited by a salinity of 50 g NaCl L[-1] during a long-term experiment, was rapidly restarted by decreasing the salinity to 20 g NaCl L[-1] and adding biomass. The effects of exposure time and shock concentrations on the anammox reactor indicate that anammox granular sludge has a high tolerance to salinity and strong ability for self-recovery. The nitrogen removal efficiency was higher than 50% after exposure to 50 g NaCl L[-1] for 66 h. To shorten the time taken for effluent nitrogen concentrations to attain national standards (GB18918-2002) after the anammox reactor was shocked with NaCl, reactor performance (i.e., recovery) after the addition of K[+], glycine betaine, Fe[2+], and hydroxylamine were compared after the reactor was inhibited by 80 g NaCl L[-1]. The results indicate that hydroxylamine was the best reversal agent. The recovery time of the anammox reactor could be shortened by 50% following the addition of hydroxylamine. The most favorable NH2OH-N/NO2[-]-N concentration ratio for improving nitrogen removal of anammox was 1:11. The abundances of Planctomycetes and its genera Candidatus Kuenenia and Brocadiaceae_g_unclassified increased after repeated salinity shock-recovery phases, indicating that Candidatus Kuenenia and Brocadiaceae_g_unclassified are able to adapt to NaCl shocking and recovery.}, } @article {pmid31535335, year = {2020}, author = {Contador, CA and Veas-Castillo, L and Tapia, E and Antipán, M and Miranda, N and Ruiz-Tagle, B and García-Araya, J and Andrews, BA and Marin, M and Dorador, C and Asenjo, JA}, title = {Atacama Database: a platform of the microbiome of the Atacama Desert.}, journal = {Antonie van Leeuwenhoek}, volume = {113}, number = {2}, pages = {185-195}, doi = {10.1007/s10482-019-01328-x}, pmid = {31535335}, issn = {1572-9699}, support = {FB0001//Comisión Nacional de Investigación Científica y Tecnológica/ ; }, mesh = {Archaea/genetics/physiology ; Bacteria/genetics ; Biotechnology ; *Databases, Factual ; Desert Climate ; Microbiota/physiology ; Soil Microbiology ; }, abstract = {The Atacama Desert is one of the oldest and driest places on Earth. In the last decade, microbial richness and diversity has been acknowledged as an important biological resource of this region. Owing to the value of the microbial diversity apparent in potential biotechnology applications and conservation purposes, it is necessary to catalogue these microbial communities to promote research activities and help to preserve the wide range of ecological niches of the Atacama region. A prototype Atacama Database has been designed and it provides a description of the rich microbial diversity of the Atacama Desert, and helps to visualise available literature resources. Data has been collected, curated, and organised into several categories to generate a single record for each organism in the database that covers classification, isolation metadata, morphology, physiology, genome and metabolism information. The current version of Atacama Database contains 2302 microorganisms and includes cultured and uncultured organisms retrieved from different environments within the desert between 1984 and 2016. These organisms are distributed in bacterial, archaeal or eukaryotic domains, along with those that are unclassified taxonomically. The initial prototype of the Atacama Database includes a basic search and taxonomic and advanced search tools to allow identification and comparison of microbial populations, and space distribution within this biome. A geolocation search was implemented to visualise the microbial diversity of the ecological niches defined by sectors and extract general information of the sampling sites. This effort will aid understanding of the microbial ecology of the desert, microbial population dynamics, seasonal behaviour, impact of climate change over time, and reveal further biotechnological applications of these microorganisms. The Atacama Database is freely available at: https://www.atacamadb.cl.}, } @article {pmid31531943, year = {2019}, author = {Niederberger, E and Parnham, MJ and Maas, J and Geisslinger, G}, title = {4 Ds in health research-working together toward rapid precision medicine.}, journal = {EMBO molecular medicine}, volume = {11}, number = {11}, pages = {e10917}, pmid = {31531943}, issn = {1757-4684}, support = {//State of Hessen Landes-Offensive zur Entwicklung Wissenschaftlichökonomischer Exzellenz (LOEWE) Center for Translational Medicine and Pharmacology, TMP/International ; //Fraunhofer Cluster of Excellence for Immune-Mediated Diseases (CIMD)/International ; }, mesh = {Biomedical Research/*methods/*trends ; Databases, Factual ; Diagnostic Tests, Routine/methods ; *Disease Management ; Drug Discovery ; Equipment and Supplies ; Humans ; Precision Medicine/*methods/*trends ; }, abstract = {Patient therapy is based mainly on a combination of diagnosis, suitable monitoring or support devices and drug treatment and is usually employed for a pre-existing disease condition. Therapy remains predominantly symptom-based, although it is increasingly clear that individual treatment is possible and beneficial. However, reasonable precision medicine can only be realized with the coordinated use of diagnostics, devices and drugs in combination with extensive databases (4Ds), an approach that has not yet found sufficient implementation. The practical combination of 4Ds in health care is progressing, but several obstacles still hamper their extended use in precision medicine.}, } @article {pmid31531403, year = {2019}, author = {Kalbfleisch, TS and Rice, ES and DePriest, MS and Walenz, BP and Hestand, MS and Vermeesch, JR and O'Connell, BL and Fiddes, IT and Vershinina, AO and Saremi, NF and Petersen, JL and Finno, CJ and Bellone, RR and McCue, ME and Brooks, SA and Bailey, E and Orlando, L and Green, RE and Miller, DC and Antczak, DF and MacLeod, JN}, title = {Erratum: Author Correction: Improved reference genome for the domestic horse increases assembly contiguity and composition.}, journal = {Communications biology}, volume = {2}, number = {}, pages = {342}, doi = {10.1038/s42003-019-0591-3}, pmid = {31531403}, issn = {2399-3642}, support = {K01 OD015134/OD/NIH HHS/United States ; L40 TR001136/TR/NCATS NIH HHS/United States ; }, abstract = {[This corrects the article DOI: 10.1038/s42003-018-0199-z.].}, } @article {pmid31530813, year = {2019}, author = {Zorz, JK and Sharp, C and Kleiner, M and Gordon, PMK and Pon, RT and Dong, X and Strous, M}, title = {A shared core microbiome in soda lakes separated by large distances.}, journal = {Nature communications}, volume = {10}, number = {1}, pages = {4230}, pmid = {31530813}, issn = {2041-1723}, mesh = {Alkalies/analysis ; Autotrophic Processes ; Bacteria/classification/genetics/*isolation & purification/radiation effects ; Biodiversity ; Canada ; Carbon Cycle ; Lakes/chemistry/*microbiology ; Light ; *Microbiota ; Phototrophic Processes ; *Phylogeny ; Sulfur/metabolism ; }, abstract = {In alkaline soda lakes, concentrated dissolved carbonates establish productive phototrophic microbial mats. Here we show how microbial phototrophs and autotrophs contribute to this exceptional productivity. Amplicon and shotgun DNA sequencing data of microbial mats from four Canadian soda lakes indicate the presence of > 2,000 species of Bacteria and Eukaryotes. We recover metagenome-assembled-genomes for a core microbiome of < 100 abundant bacteria, present in all four lakes. Most of these are related to microbes previously detected in sediments of Asian alkaline lakes, showing that common selection principles drive community assembly from a globally distributed reservoir of alkaliphile biodiversity. Detection of > 7,000 proteins show how phototrophic populations allocate resources to specific processes and occupy complementary niches. Carbon fixation proceeds by the Calvin-Benson-Bassham cycle, in Cyanobacteria, Gammaproteobacteria, and, surprisingly, Gemmatimonadetes. Our study provides insight into soda lake ecology, as well as a template to guide efforts to engineer biotechnology for carbon dioxide conversion.}, } @article {pmid31530397, year = {2019}, author = {Leonardo, L and Bergquist, R and Li, SZ and Lv, S and Khieu, V and Sayasone, S and Xu, J and Olveda, R and Utzinger, J and Sripa, B and Satrija, F and Tangkawattana, S and Ullyartha, H and Wai, KT and Nguyen, H and Zhou, XN}, title = {Multi-disciplinary integration of networking through the RNAS[+]: Research on other target diseases.}, journal = {Advances in parasitology}, volume = {105}, number = {}, pages = {95-110}, doi = {10.1016/bs.apar.2019.07.010}, pmid = {31530397}, issn = {2163-6079}, mesh = {Animals ; Asia ; Community Networks/trends ; *Disease Eradication ; Helminthiasis/*prevention & control ; Humans ; *Interdisciplinary Communication ; }, abstract = {In 2005, the network decided to increase its number of target diseases to include other helminthic zoonoses such as fascioliasis, clonorchiasis, opisthorchiasis, paragonimiasis and cysticercosis and in the process expanding membership to include South Korea, Vietnam, Thailand and Japan. NTDs were eventually included as awareness is heightened on these diseases affecting poor and developing countries. Researches on clonorchiasis and opisthorchiasis unravel the mechanism by which these diseases eventually predispose to cholangiocarcinoma. The liver cancer associated with these liver fluke infections necessitate the need to clarify the global burden of disease of these infections. The magnitude of these liver fluke diseases in endemic countries like China, Vietnam, Laos, Cambodia and Thailand is described. Success in elimination of lymphatic filariasis in PR China and Cambodia is highlighted to show how intensified multisectoral collaboration and strong political become strong ingredients in elimination of parasitic diseases like LF. New advances are presented that clarify species and strain differences in Fasciola spp., Paragonimus spp., Taenia spp. and Echinococcocus spp. Conventional diagnostic techniques are compared with new serologic techniques that are being developed. New control strategies such as the Lawa model are presented.}, } @article {pmid31529065, year = {2019}, author = {Mulvaney, SA and Vaala, SE and Carroll, RB and Williams, LK and Lybarger, CK and Schmidt, DC and Dietrich, MS and Laffel, LM and Hood, KK}, title = {A mobile app identifies momentary psychosocial and contextual factors related to mealtime self-management in adolescents with type 1 diabetes.}, journal = {Journal of the American Medical Informatics Association : JAMIA}, volume = {26}, number = {12}, pages = {1627-1631}, pmid = {31529065}, issn = {1527-974X}, support = {P30 DK036836/DK/NIDDK NIH HHS/United States ; DP3 DK097706/DK/NIDDK NIH HHS/United States ; UL1 TR000445/TR/NCATS NIH HHS/United States ; }, mesh = {Adolescent ; Blood Glucose ; *Blood Glucose Self-Monitoring ; Diabetes Mellitus, Type 1/*psychology/therapy ; *Ecological Momentary Assessment ; Female ; Humans ; Hypoglycemic Agents/administration & dosage ; Insulin/administration & dosage ; Male ; *Meals ; *Mobile Applications ; *Self-Management ; }, abstract = {Effective diabetes problem solving requires identification of risk factors for inadequate mealtime self-management. Ecological momentary assessment was used to enhance identification of factors hypothesized to impact self-management. Adolescents with type 1 diabetes participated in a feasibility trial for a mobile app called MyDay. Meals, mealtime insulin, self-monitored blood glucose, and psychosocial and contextual data were obtained for 30 days. Using 1472 assessments, mixed-effects between-subjects analyses showed that social context, location, and mealtime were associated with missed self-monitored blood glucose. Stress, energy, mood, and fatigue were associated with missed insulin. Within-subjects analyses indicated that all factors were associated with both self-management tasks. Intraclass correlations showed within-subjects accounted for the majority of variance. The ecological momentary assessment method provided specific targets for improving self-management problem solving, phenotyping, or integration within just-in-time adaptive interventions.}, } @article {pmid31527408, year = {2019}, author = {Connor, R and Brister, R and Buchmann, JP and Deboutte, W and Edwards, R and Martí-Carreras, J and Tisza, M and Zalunin, V and Andrade-Martínez, J and Cantu, A and D'Amour, M and Efremov, A and Fleischmann, L and Forero-Junco, L and Garmaeva, S and Giluso, M and Glickman, C and Henderson, M and Kellman, B and Kristensen, D and Leubsdorf, C and Levi, K and Levi, S and Pakala, S and Peddu, V and Ponsero, A and Ribeiro, E and Roy, F and Rutter, L and Saha, S and Shakya, M and Shean, R and Miller, M and Tully, B and Turkington, C and Youens-Clark, K and Vanmechelen, B and Busby, B}, title = {NCBI's Virus Discovery Hackathon: Engaging Research Communities to Identify Cloud Infrastructure Requirements.}, journal = {Genes}, volume = {10}, number = {9}, pages = {}, pmid = {31527408}, issn = {2073-4425}, support = {R35 CA220523/CA/NCI NIH HHS/United States ; }, mesh = {Big Data ; Cloud Computing/*standards ; Genome, Human ; *Genome, Viral ; Humans ; *Metagenome ; Metagenomics/*methods/standards ; Software ; }, abstract = {A wealth of viral data sits untapped in publicly available metagenomic data sets when it might be extracted to create a usable index for the virological research community. We hypothesized that work of this complexity and scale could be done in a hackathon setting. Ten teams comprised of over 40 participants from six countries, assembled to create a crowd-sourced set of analysis and processing pipelines for a complex biological data set in a three-day event on the San Diego State University campus starting 9 January 2019. Prior to the hackathon, 141,676 metagenomic data sets from the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA) were pre-assembled into contiguous assemblies (contigs) by NCBI staff. During the hackathon, a subset consisting of 2953 SRA data sets (approximately 55 million contigs) was selected, which were further filtered for a minimal length of 1 kb. This resulted in 4.2 million (Mio) contigs, which were aligned using BLAST against all known virus genomes, phylogenetically clustered and assigned metadata. Out of the 4.2 Mio contigs, 360,000 contigs were labeled with domains and an additional subset containing 4400 contigs was screened for virus or virus-like genes. The work yielded valuable insights into both SRA data and the cloud infrastructure required to support such efforts, revealing analysis bottlenecks and possible workarounds thereof. Mainly: (i) Conservative assemblies of SRA data improves initial analysis steps; (ii) existing bioinformatic software with weak multithreading/multicore support can be elevated by wrapper scripts to use all cores within a computing node; (iii) redesigning existing bioinformatic algorithms for a cloud infrastructure to facilitate its use for a wider audience; and (iv) a cloud infrastructure allows a diverse group of researchers to collaborate effectively. The scientific findings will be extended during a follow-up event. Here, we present the applied workflows, initial results, and lessons learned from the hackathon.}, } @article {pmid31525198, year = {2019}, author = {Sun, M and Zhang, J}, title = {Chromosome-wide co-fluctuation of stochastic gene expression in mammalian cells.}, journal = {PLoS genetics}, volume = {15}, number = {9}, pages = {e1008389}, pmid = {31525198}, issn = {1553-7404}, support = {R01 GM120093/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Chromatin/genetics ; Chromosome Mapping/methods ; Chromosomes/genetics ; Databases, Genetic ; Evolution, Molecular ; Gene Expression/*genetics ; Gene Expression Regulation/*genetics ; Genetic Linkage/*genetics ; Genome/genetics ; Genomics/methods ; Humans ; Mammals/genetics ; Mice ; Selection, Genetic ; Stochastic Processes ; }, abstract = {Gene expression is subject to stochastic noise, but to what extent and by which means such stochastic variations are coordinated among different genes are unclear. We hypothesize that neighboring genes on the same chromosome co-fluctuate in expression because of their common chromatin dynamics, and verify it at the genomic scale using allele-specific single-cell RNA-sequencing data of mouse cells. Unexpectedly, the co-fluctuation extends to genes that are over 60 million bases apart. We provide evidence that this long-range effect arises in part from chromatin co-accessibilities of linked loci attributable to three-dimensional proximity, which is much closer intra-chromosomally than inter-chromosomally. We further show that genes encoding components of the same protein complex tend to be chromosomally linked, likely resulting from natural selection for intracellular among-component dosage balance. These findings have implications for both the evolution of genome organization and optimal design of synthetic genomes in the face of gene expression noise.}, } @article {pmid31524173, year = {2019}, author = {Mattos, MK and Lingler, JH}, title = {Research Data Disclosure in the Digital Age.}, journal = {Journal of Alzheimer's disease : JAD}, volume = {71}, number = {4}, pages = {1089-1091}, doi = {10.3233/JAD-190725}, pmid = {31524173}, issn = {1875-8908}, mesh = {*Alzheimer Disease ; Biomedical Research/*ethics ; Disclosure/*ethics ; Ecological Momentary Assessment ; Humans ; *Medical Informatics/ethics/trends ; Research Subjects/psychology ; }, abstract = {New advances in digital technologies and data-collection methods support expansion of the traditional research model in the current Digital Age. As researchers continue to explore ways to collect, manage, and share individual-level research study data, investigators must also acknowledge new ethical considerations that arise. To ensure protection of research participants, participants must remain a priority across the research continuum by researchers, institutional review boards, funding agencies, and consumers. Big data and data sharing also require additional investments and oversight to ensure proper management and, and even more important, protection of human subjects.}, } @article {pmid31521200, year = {2019}, author = {Rausch, P and Rühlemann, M and Hermes, BM and Doms, S and Dagan, T and Dierking, K and Domin, H and Fraune, S and von Frieling, J and Hentschel, U and Heinsen, FA and Höppner, M and Jahn, MT and Jaspers, C and Kissoyan, KAB and Langfeldt, D and Rehman, A and Reusch, TBH and Roeder, T and Schmitz, RA and Schulenburg, H and Soluch, R and Sommer, F and Stukenbrock, E and Weiland-Bräuer, N and Rosenstiel, P and Franke, A and Bosch, T and Baines, JF}, title = {Comparative analysis of amplicon and metagenomic sequencing methods reveals key features in the evolution of animal metaorganisms.}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {133}, pmid = {31521200}, issn = {2049-2618}, mesh = {Animals ; Bacteria/classification/genetics ; Databases, Genetic ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Metagenome/genetics/*physiology ; Microbiota/genetics/*physiology ; Phylogeny ; RNA, Ribosomal, 16S/*genetics ; }, abstract = {BACKGROUND: The interplay between hosts and their associated microbiome is now recognized as a fundamental basis of the ecology, evolution, and development of both players. These interdependencies inspired a new view of multicellular organisms as "metaorganisms." The goal of the Collaborative Research Center "Origin and Function of Metaorganisms" is to understand why and how microbial communities form long-term associations with hosts from diverse taxonomic groups, ranging from sponges to humans in addition to plants.

METHODS: In order to optimize the choice of analysis procedures, which may differ according to the host organism and question at hand, we systematically compared the two main technical approaches for profiling microbial communities, 16S rRNA gene amplicon and metagenomic shotgun sequencing across our panel of ten host taxa. This includes two commonly used 16S rRNA gene regions and two amplification procedures, thus totaling five different microbial profiles per host sample.

CONCLUSION: While 16S rRNA gene-based analyses are subject to much skepticism, we demonstrate that many aspects of bacterial community characterization are consistent across methods. The resulting insight facilitates the selection of appropriate methods across a wide range of host taxa. Overall, we recommend single- over multi-step amplification procedures, and although exceptions and trade-offs exist, the V3 V4 over the V1 V2 region of the 16S rRNA gene. Finally, by contrasting taxonomic and functional profiles and performing phylogenetic analysis, we provide important and novel insight into broad evolutionary patterns among metaorganisms, whereby the transition of animals from an aquatic to a terrestrial habitat marks a major event in the evolution of host-associated microbial composition.}, } @article {pmid31520948, year = {2019}, author = {Lv, J and Cao, T and Ji, C and Cong, M and Zhao, J and Wu, H}, title = {Digital gene expression analysis in the gills of Ruditapes philippinarum after nitrite exposure.}, journal = {Ecotoxicology and environmental safety}, volume = {184}, number = {}, pages = {109661}, doi = {10.1016/j.ecoenv.2019.109661}, pmid = {31520948}, issn = {1090-2414}, mesh = {Animals ; Bivalvia/*drug effects/genetics/metabolism ; Gene Expression/*drug effects ; Gene Ontology ; Gills/*drug effects/metabolism ; Glutathione/metabolism ; Glutathione Peroxidase/metabolism ; Glutathione Transferase/metabolism ; Nitrites/*toxicity ; Oxidative Stress/drug effects/genetics ; Seawater/chemistry ; Superoxide Dismutase/metabolism ; Water Pollutants, Chemical/*toxicity ; }, abstract = {Due to the overload of pollutants from highly intensive anthropic activities, nitrite accumulates in offshore seawater and has been a long-lasting pollutant to the healthy aquaculture of the mollusk. In the present study, Ruditapes philippinarum was used as the target bivalve to receive nitrite exposure at environmental concentration for 1 and 7 days. Differentially expressed genes (DEGs) were detected and analyzed by a digital gene expression (DGE) approach to describe the toxicity of nitrite on the bivalve at the gene level. In the N1 group, 185 DEGs were generated and enriched in six Gene Ontology (GO) terms, including oxidoreductase activity, heme binding, tetrapyrrole binding, iron ion binding, metal binding and cation binding. The DEGs in the N1 group were also enriched in two Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, e.g., arachidonic acid metabolism and ovarian steroidogenesis. In the N7 group, 81 DEGs were generated without any GO enrichment but were enriched in five KEGG pathways, including protein processing in the endoplasmic reticulum, protein export, prion diseases, thyroid hormone synthesis and arachidonic acid metabolism. This suggested that nitrite exposure might cause adverse effects to the clams in several aspects, including oxidative damage, depressed immunity, and disorders in cell proliferation, hormone metabolism and tissue regeneration. Evaluation of oxidative stress indicated that nitrite exposure actually induced redox state imbalance by enhancing the contents of thiobarbituric acid reactive substances (TBARSs) and glutathione (GSH), and the activity of glutathione peroxidase (GSH-PX) but not superoxide dismutase (SOD). These results will provide valuable gene references for further study on the toxicology mechanism of bivalves under environmental nitrite stress.}, } @article {pmid31517389, year = {2020}, author = {Walker, NB and Hefley, TJ and Walsh, DP}, title = {Bias correction of bounded location error in binary data.}, journal = {Biometrics}, volume = {76}, number = {2}, pages = {530-539}, doi = {10.1111/biom.13152}, pmid = {31517389}, issn = {1541-0420}, support = {G18AC00317//U.S. Geological Survey/International ; }, mesh = {Animals ; Bias ; Biometry ; Computer Simulation ; *Data Interpretation, Statistical ; Deer ; Female ; Humans ; Likelihood Functions ; Logistic Models ; Male ; *Models, Statistical ; Poisson Distribution ; *Regression Analysis ; Risk Factors ; Wasting Disease, Chronic/epidemiology ; Wisconsin/epidemiology ; }, abstract = {Binary regression models for spatial data are commonly used in disciplines such as epidemiology and ecology. Many spatially referenced binary data sets suffer from location error, which occurs when the recorded location of an observation differs from its true location. When location error occurs, values of the covariates associated with the true spatial locations of the observations cannot be obtained. We show how a change of support (COS) can be applied to regression models for binary data to provide coefficient estimates when the true values of the covariates are unavailable, but the unknown location of the observations are contained within nonoverlapping arbitrarily shaped polygons. The COS accommodates spatial and nonspatial covariates and preserves the convenient interpretation of methods such as logistic and probit regression. Using a simulation experiment, we compare binary regression models with a COS to naive approaches that ignore location error. We illustrate the flexibility of the COS by modeling individual-level disease risk in a population using a binary data set where the locations of the observations are unknown but contained within administrative units. Our simulation experiment and data illustration corroborate that conventional regression models for binary data that ignore location error are unreliable, but that the COS can be used to eliminate bias while preserving model choice.}, } @article {pmid31514979, year = {2019}, author = {Shen, L and Li, XW and Meng, XX and Wu, J and Tang, H and Huang, LF and Xiao, SM and Xu, J and Chen, SL}, title = {Prediction of the globally ecological suitability of Panax quinquefolius by the geographic information system for global medicinal plants (GMPGIS).}, journal = {Chinese journal of natural medicines}, volume = {17}, number = {7}, pages = {481-489}, doi = {10.1016/S1875-5364(19)30069-X}, pmid = {31514979}, issn = {1875-5364}, mesh = {Climate ; Climate Change ; Ecology ; *Geographic Information Systems ; Geography ; Panax/*growth & development ; Plants, Medicinal/*growth & development ; }, abstract = {American ginseng (Panax quinquefolius L.) is a well-known Asian traditional herbal medicine with a large market demand. The plant is native to eastern North America, and its main producing areas worldwide are decreasing due to continuous cropping obstacles and environmental changes. Therefore, the identification of maximum similarities of new ecological distribution of P. quinquefolius, and prediction of its response to climate change in the future are necessary for plant introduction and cultivation. In this study, the areas with potential ecological suitability for P. quinquefolius were predicted using the geographic information system for global medicinal plants (GMPGIS) based on 476 occurrence points and 19 bioclimatic variables. The results indicate that the new ecologically suitable areas for P. quinquefolius are East Asia and the mid-eastern Europe, which are mainly distributed in China, Russia, Japan, Ukraine, Belarus, North Korean, South Korea, andRomania. Under global climate change scenarios, the suitable planting areas for P. quinquefolius would be increased by 9.16%-30.97%, and expandingnorth and west over the current ecologically suitable areas by 2070. The potential increased areas that are ecologically suitable include northern Canada, Eastern Europe, and the Lesser Khingan Mountains of China, and reduced regions are mainly in central China, the southern U.S., and southern Europe. Jackknife tests indicate that the precipitation of the warmest quarter was the important climatic factor controlling the distribution of P. quinquefolius. Our findings can be used as auseful guide for P. quinquefolius introduction and cultivation in ecologically suitable areas.}, } @article {pmid31514603, year = {2019}, author = {Nnawulezi, N and Sullivan, CM and Marcus, S and Young, L and Hacskaylo, M}, title = {Negotiating Participatory Research Processes With Domestic Violence Program Staff to Obtain Ecologically Valid Data.}, journal = {Journal of interpersonal violence}, volume = {34}, number = {23-24}, pages = {4817-4837}, doi = {10.1177/0886260519871535}, pmid = {31514603}, issn = {1552-6518}, mesh = {*Community-Based Participatory Research ; *Data Accuracy ; Data Collection ; Data Interpretation, Statistical ; *Domestic Violence ; Humans ; *Negotiating ; Research Personnel ; Researcher-Subject Relations ; Sexual Partners ; Survivors ; }, abstract = {The choice of research design affects not only internal and external validity but ecological validity as well. Ecological validity refers to the extent to which data are based in and relevant to real-world settings. One way for researchers to maximize the likelihood of achieving ecological validity is to design studies with community partners that use participatory approaches. Engaging deeply with community partners in determining what to study, how to measure constructs of interest, interpreting results, and using findings to create change is one means of conducting research that is likely to produce findings that are meaningful to communities. Conducting in-depth, participatory research within agencies providing crisis supports to individuals who have experienced trauma creates an additional level of complexity in the research process. This article presents a case example of how academic researchers and staff members of a nonprofit organization working with survivors of intimate partner violence collaborated on an evaluation of the community partner agency. As part of this process, the team members had to be continually aware of and responsive to the nature of crisis-focused work. We provide a reflexive account of the lessons learned and recommendations for future research.}, } @article {pmid31513712, year = {2020}, author = {Christman, ZJ and Wilson-Genderson, M and Heid, A and Pruchno, R}, title = {The Effects of Neighborhood Built Environment on Walking for Leisure and for Purpose Among Older People.}, journal = {The Gerontologist}, volume = {60}, number = {4}, pages = {651-660}, pmid = {31513712}, issn = {1758-5341}, support = {R01 AG046463/AG/NIA NIH HHS/United States ; }, mesh = {Aged ; *Built Environment ; Female ; Geographic Information Systems ; Humans ; *Leisure Activities ; Male ; Middle Aged ; New Jersey ; *Residence Characteristics ; Transportation ; Walking/*statistics & numerical data ; }, abstract = {BACKGROUND AND OBJECTIVES: Characteristics of a neighborhood's built environment affect the walking behavior of older people, yet studies typically rely on small nonrepresentative samples that use either subjective reports or aggregate indicators from administrative sources to represent neighborhood characteristics. Our analyses examine the usefulness of a novel method for observing neighborhoods-virtual observations-and assess the extent to which virtual-based observations predict walking among older adults.

RESEARCH DESIGN AND METHODS: Using Google Street View, we observed the neighborhoods of 2,224 older people and examined how characteristics of the neighborhood built environments are associated with the amount of time older people spend walking for leisure and purpose.

RESULTS: Multilevel model analyses revealed that sidewalk characteristics had significant associations with both walking for purpose and leisure. Land use, including the presence of multifamily dwellings, commercial businesses, and parking lots were positively associated with walking for purpose and single-family detached homes were negatively associated with walking for purpose, but none of these characteristics were associated with leisure walking. Gardens/flowers were associated with walking for leisure but not purpose. Garbage/litter was not associated with either type of walking behavior.

DISCUSSION AND IMPLICATIONS: Virtual observations are a useful method that provides meaningful information about neighborhoods. Findings demonstrate how neighborhood characteristics assessed virtually differentially impact walking for leisure and purpose among older adults and are interpreted within a social-ecological model.}, } @article {pmid31513596, year = {2019}, author = {Pearson, GA and Martins, N and Madeira, P and Serrão, EA and Bartsch, I}, title = {Sex-dependent and -independent transcriptional changes during haploid phase gametogenesis in the sugar kelp Saccharina latissima.}, journal = {PloS one}, volume = {14}, number = {9}, pages = {e0219723}, pmid = {31513596}, issn = {1932-6203}, mesh = {Computational Biology/methods ; Gametogenesis/*genetics ; *Gene Expression Profiling ; *Haploidy ; High-Throughput Nucleotide Sequencing ; Molecular Sequence Annotation ; Phaeophyceae/cytology/*genetics/metabolism ; Sugars/metabolism ; *Transcriptome ; }, abstract = {In haplodiplontic lineages, sexual reproduction occurs in haploid parents without meiosis. Although widespread in multicellular lineages such as brown algae (Phaeophyceae), haplodiplontic gametogenesis has been little studied at the molecular level. We addressed this by generating an annotated reference transcriptome for the gametophytic phase of the sugar kelp, Saccharina latissima. Transcriptional profiles of microscopic male and female gametophytes were analysed at four time points during the transition from vegetative growth to gametogenesis. Gametogenic signals resulting from a switch in culture irradiance from red to white light activated a core set of genes in a sex-independent manner, involving rapid activation of ribosome biogenesis, transcription and translation related pathways, with several acting at the post-transcriptional or post-translational level. Additional genes regulating nutrient acquisition and key carbohydrate-energy pathways were also identified. Candidate sex-biased genes under gametogenic conditions had potentially key roles in controlling female- and male-specific gametogenesis. Among these were several sex-biased or -specific E3 ubiquitin-protein ligases that may have important regulatory roles. Females specifically expressed several genes that coordinate gene expression and/or protein degradation, and the synthesis of inositol-containing compounds. Other female-biased genes supported parallels with oogenesis in divergent multicellular lineages, in particular reactive oxygen signalling via an NADPH-oxidase. Males specifically expressed the hypothesised brown algal sex-determining factor. Male-biased expression mainly involved upregulation of genes that control mitotic cell proliferation and spermatogenesis in other systems, as well as multiple flagella-related genes. Our data and results enhance genome-level understanding of gametogenesis in this ecologically and economically important multicellular lineage.}, } @article {pmid31513578, year = {2019}, author = {Becker, AD and Wesolowski, A and Bjørnstad, ON and Grenfell, BT}, title = {Long-term dynamics of measles in London: Titrating the impact of wars, the 1918 pandemic, and vaccination.}, journal = {PLoS computational biology}, volume = {15}, number = {9}, pages = {e1007305}, pmid = {31513578}, issn = {1553-7358}, support = {/WT_/Wellcome Trust/United Kingdom ; DP2 LM013102/LM/NLM NIH HHS/United States ; P2C HD047879/HD/NICHD NIH HHS/United States ; }, mesh = {Computational Biology ; History, 20th Century ; Humans ; Incidence ; Influenza, Human/epidemiology/history ; London/epidemiology ; *Measles/epidemiology/history/prevention & control/transmission ; Pandemics/history/*statistics & numerical data ; Vaccination/history/*statistics & numerical data ; World War I ; World War II ; }, abstract = {A key question in ecology is the relative impact of internal nonlinear dynamics and external perturbations on the long-term trajectories of natural systems. Measles has been analyzed extensively as a paradigm for consumer-resource dynamics due to the oscillatory nature of the host-pathogen life cycle, the abundance of rich data to test theory, and public health relevance. The dynamics of measles in London, in particular, has acted as a prototypical test bed for such analysis using incidence data from the pre-vaccination era (1944-1967). However, during this timeframe there were few external large-scale perturbations, limiting an assessment of the relative impact of internal and extra demographic perturbations to the host population. Here, we extended the previous London analyses to include nearly a century of data that also contains four major demographic changes: the First and Second World Wars, the 1918 influenza pandemic, and the start of a measles mass vaccination program. By combining mortality and incidence data using particle filtering methods, we show that a simple stochastic epidemic model, with minimal historical specifications, can capture the nearly 100 years of dynamics including changes caused by each of the major perturbations. We show that the majority of dynamic changes are explainable by the internal nonlinear dynamics of the system, tuned by demographic changes. In addition, the 1918 influenza pandemic and World War II acted as extra perturbations to this basic epidemic oscillator. Our analysis underlines that long-term ecological and epidemiological dynamics can follow very simple rules, even in a non-stationary population subject to significant perturbations and major secular changes.}, } @article {pmid31512399, year = {2020}, author = {Smith, CCR and Flaxman, SM}, title = {Leveraging whole genome sequencing data for demographic inference with approximate Bayesian computation.}, journal = {Molecular ecology resources}, volume = {20}, number = {1}, pages = {125-139}, doi = {10.1111/1755-0998.13092}, pmid = {31512399}, issn = {1755-0998}, support = {1144083//National Science Foundation/ ; 1627483//National Science Foundation/ ; }, mesh = {Animals ; Bayes Theorem ; Computer Simulation ; Databases, Genetic ; Demography ; Genetics, Population ; *Genome ; Humans ; *Models, Genetic ; Whole Genome Sequencing ; }, abstract = {Accounting for historical demographic features, such as the strength and timing of gene flow and divergence times between closely related lineages, is vital for many inferences in evolutionary biology. Approximate Bayesian computation (ABC) is one method commonly used to estimate demographic parameters. However, the DNA sequences used as input for this method, often microsatellites or RADseq loci, usually represent a small fraction of the genome. Whole genome sequencing (WGS) data, on the other hand, have been used less often with ABC, and questions remain about the potential benefit of, and how to best implement, this type of data; we used pseudo-observed data sets to explore such questions. Specifically, we addressed the potential improvements in parameter estimation accuracy that could be associated with WGS data in multiple contexts; namely, we quantified the effects of (a) more data, (b) haplotype-based summary statistics, and (c) locus length. Compared with a hypothetical RADseq data set with 2.5 Mbp of data, using a 1 Gbp data set consisting of 100 Kbp sequences led to substantial gains in the accuracy of parameter estimates, which was mostly due to haplotype statistics and increased data. We also quantified the effects of including (a) locus-specific recombination rates, and (b) background selection information in ABC analyses. Importantly, assuming uniform recombination or ignoring background selection had a negative effect on accuracy in many cases. Software and results from this method validation study should be useful for future demographic history analyses.}, } @article {pmid31510753, year = {2019}, author = {Yuma, P and Orsi, R and Dunn, JA and Kenyon, V and Tulanowski, E and Stallones, L}, title = {Traumatic injury and access to care in rural areas: leveraging linked data and geographic information systems for planning and advocacy.}, journal = {Rural and remote health}, volume = {19}, number = {3}, pages = {5089}, doi = {10.22605/RRH5089}, pmid = {31510753}, issn = {1445-6354}, mesh = {Colorado ; Geographic Information Systems/*organization & administration ; Health Services Accessibility/*organization & administration ; Health Services Needs and Demand ; Humans ; Rural Population/*statistics & numerical data ; Trauma Centers/*organization & administration ; Wounds and Injuries/*therapy ; }, abstract = {INTRODUCTION: The purpose of this ecological study was to apply Geographic Information System (GIS) methods to patterns of traumatic injury and access to trauma care to facilitate system planning and advocacy.

METHODS: Four US state (Colorado) and national data sources were linked to examine county-level disparities. Average ambulance drive times to trauma centers for populated places in each county were estimated and mapped.

RESULTS: Independent samples t-tests demonstrated Colorado's rural counties had significantly higher injury hospitalization rates (mean (M)=685.4 v M=566.3; p=0.005)) and fatality rates (M=93.8 v M=71.6, p<0.001), indicating residents with the least access to care are the most impacted by the burden of injury; this finding was supported by GIS analyses of drive times to level I and II trauma centers and underlying injury rates, which are visually displayed.

CONCLUSIONS: These methods are useful tools for rural public health professionals to conduct system optimization, identify training and resource needs, assess prevention priorities, and advocate for trauma system support.}, } @article {pmid31508204, year = {2019}, author = {Shome, S and Parra, RG and Fatima, N and Monzon, AM and Cuypers, B and Moosa, Y and Coimbra, NDR and Assis, J and Giner-Delgado, C and Dönertaş, HM and Cuesta-Astroz, Y and Saarunya, G and Allali, I and Gupta, S and Srivastava, A and Kalsan, M and Valdivia, C and J Olguin-Orellana, G and Papadimitriou, S and Parisi, D and Kristensen, NP and Rib, L and Guebila, MB and Bauer, E and Zaffaroni, G and Bekkar, A and Ashano, E and Paladin, L and Necci, M and Moreyra, NN and Rydén, M and Villalobos-Solís, J and Papadopoulos, N and Rafael, C and Karakulak, T and Kaya, Y and Gladbach, Y and Dhanda, SK and Šoštarić, N and Alex, A and DeBlasio, D and Rahman, F}, title = {Global network of computational biology communities: ISCB's Regional Student Groups breaking barriers.}, journal = {F1000Research}, volume = {8}, number = {}, pages = {}, pmid = {31508204}, issn = {2046-1402}, mesh = {*Computational Biology ; Humans ; Interprofessional Relations ; *Students ; }, abstract = {Regional Student Groups (RSGs) of the International Society for Computational Biology Student Council (ISCB-SC) have been instrumental to connect computational biologists globally and to create more awareness about bioinformatics education. This article highlights the initiatives carried out by the RSGs both nationally and internationally to strengthen the present and future of the bioinformatics community. Moreover, we discuss the future directions the organization will take and the challenges to advance further in the ISCB-SC main mission: "Nurture the new generation of computational biologists".}, } @article {pmid31506932, year = {2020}, author = {Wilber, MQ and Webb, CT and Cunningham, FL and Pedersen, K and Wan, XF and Pepin, KM}, title = {Inferring seasonal infection risk at population and regional scales from serology samples.}, journal = {Ecology}, volume = {101}, number = {1}, pages = {e02882}, pmid = {31506932}, issn = {1939-9170}, support = {R01 AI116744/AI/NIAID NIH HHS/United States ; //Animal and Plant Health Inspection Service/International ; }, mesh = {Animals ; Animals, Wild ; Humans ; *Infections ; Seasons ; Seroepidemiologic Studies ; }, abstract = {Accurate estimates of seasonal infection risk can be used by animal health officials to predict future disease risk and improve understanding of the mechanisms driving disease dynamics. It can be difficult to estimate seasonal infection risk in wildlife disease systems because surveillance assays typically target antibodies (serosurveillance), which are not necessarily indicative of current infection, and serosurveillance sampling is often opportunistic. Recently developed methods estimate past time of infection from serosurveillance data using quantitative serological assays that indicate the amount of antibodies in a serology sample. However, current methods do not account for common opportunistic and uneven sampling associated with serosurveillance data. We extended the framework of survival analysis to improve estimates of seasonal infection risk from serosurveillance data across population and regional scales. We found that accounting for the right-censored nature of quantitative serology samples greatly improved estimates of seasonal infection risk, even when sampling was uneven in time. Survival analysis can also be used to account for common challenges when estimating infection risk from serology data, such as biases induced by host demography and continually elevated antibodies following infection. The framework developed herein is widely applicable for estimating seasonal infection risk from serosurveillance data in humans, wildlife, and livestock.}, } @article {pmid31501478, year = {2019}, author = {Charrier, NP and Hermouet, A and Hervet, C and Agoulon, A and Barker, SC and Heylen, D and Toty, C and McCoy, KD and Plantard, O and Rispe, C}, title = {A transcriptome-based phylogenetic study of hard ticks (Ixodidae).}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {12923}, pmid = {31501478}, issn = {2045-2322}, mesh = {Animals ; Biological Evolution ; Computational Biology/methods ; Evolution, Molecular ; Gene Expression Profiling ; Genes, Mitochondrial ; High-Throughput Nucleotide Sequencing ; Ixodidae/*classification/*genetics ; *Phylogeny ; *Transcriptome ; }, abstract = {Hard ticks are widely distributed across temperate regions, show strong variation in host associations, and are potential vectors of a diversity of medically important zoonoses, such as Lyme disease. To address unresolved issues with respect to the evolutionary relationships among certain species or genera, we produced novel RNA-Seq data sets for nine different Ixodes species. We combined this new data with 18 data sets obtained from public databases, both for Ixodes and non-Ixodes hard tick species, using soft ticks as an outgroup. We assembled transcriptomes (for 27 species in total), predicted coding sequences and identified single copy orthologues (SCO). Using Maximum-likelihood and Bayesian frameworks, we reconstructed a hard tick phylogeny for the nuclear genome. We also obtained a mitochondrial DNA-based phylogeny using published genome sequences and mitochondrial sequences derived from the new transcriptomes. Our results confirm previous studies showing that the Ixodes genus is monophyletic and clarify the relationships among Ixodes sub-genera. This work provides a baseline for studying the evolutionary history of ticks: we indeed found an unexpected acceleration of substitutions for mitochondrial sequences of Prostriata, and for nuclear and mitochondrial genes of two species of Rhipicephalus, which we relate with patterns of genome architecture and changes of life-cycle, respectively.}, } @article {pmid31501282, year = {2019}, author = {Umaña, A and Sanders, BE and Yoo, CC and Casasanta, MA and Udayasuryan, B and Verbridge, SS and Slade, DJ}, title = {Utilizing Whole Fusobacterium Genomes To Identify, Correct, and Characterize Potential Virulence Protein Families.}, journal = {Journal of bacteriology}, volume = {201}, number = {23}, pages = {}, pmid = {31501282}, issn = {1098-5530}, support = {R21 CA238630/CA/NCI NIH HHS/United States ; }, mesh = {Adhesins, Bacterial/classification/*genetics/metabolism ; Amino Acid Sequence ; Bacterial Adhesion ; Cell Line ; Computational Biology/methods ; Epithelial Cells/microbiology/pathology ; Fusobacterium/classification/*genetics/metabolism/*pathogenicity ; Fusobacterium Infections/microbiology/pathology ; Gene Expression ; *Genome, Bacterial ; Gingiva/microbiology/pathology ; HCT116 Cells ; Humans ; Phylogeny ; Sequence Alignment ; Sequence Homology, Amino Acid ; Type V Secretion Systems/classification/*genetics/metabolism ; Virulence ; Virulence Factors/classification/*genetics/metabolism ; }, abstract = {Fusobacterium spp. are Gram-negative, anaerobic, opportunistic pathogens involved in multiple diseases, including a link between the oral pathogen Fusobacterium nucleatum and the progression and severity of colorectal cancer. The identification and characterization of virulence factors in the genus Fusobacterium has been greatly hindered by a lack of properly assembled and annotated genomes. Using newly completed genomes from nine strains and seven species of Fusobacterium, we report the identification and corrected annotation of verified and potential virulence factors from the type 5 secreted autotransporter, FadA, and MORN2 protein families, with a focus on the genetically tractable strain F. nucleatum subsp. nucleatum ATCC 23726 and type strain F. nucleatum subsp. nucleatum ATCC 25586. Within the autotransporters, we used sequence similarity networks to identify protein subsets and show a clear differentiation between the prediction of outer membrane adhesins, serine proteases, and proteins with unknown function. These data have identified unique subsets of type 5a autotransporters, which are key proteins associated with virulence in F. nucleatum However, we coupled our bioinformatic data with bacterial binding assays to show that a predicted weakly invasive strain of F. necrophorum that lacks a Fap2 autotransporter adhesin strongly binds human colonocytes. These analyses confirm a gap in our understanding of how autotransporters, MORN2 domain proteins, and FadA adhesins contribute to host interactions and invasion. In summary, we identify candidate virulence genes in Fusobacterium, and caution that experimental validation of host-microbe interactions should complement bioinformatic predictions to increase our understanding of virulence protein contributions in Fusobacterium infections and disease.IMPORTANCEFusobacterium spp. are emerging pathogens that contribute to mammalian and human diseases, including colorectal cancer. Despite a validated connection with disease, few proteins have been characterized that define a direct molecular mechanism for Fusobacterium pathogenesis. We report a comprehensive examination of virulence-associated protein families in multiple Fusobacterium species and show that complete genomes facilitate the correction and identification of multiple, large type 5a secreted autotransporter genes in previously misannotated or fragmented genomes. In addition, we use protein sequence similarity networks and human cell interaction experiments to show that previously predicted noninvasive strains can indeed bind to and potentially invade human cells and that this could be due to the expansion of specific virulence proteins that drive Fusobacterium infections and disease.}, } @article {pmid31500111, year = {2019}, author = {Zhuang, H and Lou, Q and Liu, H and Han, H and Wang, Q and Tang, Z and Ma, Y and Wang, H}, title = {Differential Regulation of Anthocyanins in Green and Purple Turnips Revealed by Combined De Novo Transcriptome and Metabolome Analysis.}, journal = {International journal of molecular sciences}, volume = {20}, number = {18}, pages = {}, pmid = {31500111}, issn = {1422-0067}, support = {xjnkq-2019003//Project of Renovation Capacity Building for the Young Sci-Tech Talents Sponsored by Xinjiang Academy of Agricultural Sciences/ ; }, mesh = {Anthocyanins/*metabolism/pharmacology ; Biosynthetic Pathways ; Brassica napus/*genetics/growth & development/*metabolism ; Chromosome Mapping ; Computational Biology/methods ; Gene Expression Profiling ; *Gene Expression Regulation, Plant/drug effects ; *Metabolome ; Metabolomics/methods ; Molecular Sequence Annotation ; Phenotype ; Plant Development/genetics ; Polymorphism, Single Nucleotide ; *Transcriptome ; }, abstract = {Purple turnip Brassica rapa ssp. rapa is highly appreciated by consumers but the metabolites and molecular mechanisms underlying the root skin pigmentation remain open to study. Herein, we analyzed the anthocyanin composition in purple turnip (PT) and green turnip (GT) at five developmental stages. A total of 21 anthocyanins were detected and classified into the six major anthocynanin aglycones. Distinctly, PT contains 20 times higher levels of anthocyanins than GT, which explain the difference in the root skin pigmentation. We further sequenced the transcriptomes and analyzed the differentially expressed genes between the two turnips. We found that PT essentially diverts dihydroflavonols to the biosynthesis of anthocyanins over flavonols biosynthesis by strongly down-regulating one flavonol synthase gene, while strikingly up-regulating dihydroflavonol 4-reductase (DFR), anthocyanidin synthase and UDP-glucose: flavonoid-3-O-glucosyltransferase genes as compared to GT. Moreover, a nonsense mutation identified in the coding sequence of the DFR gene may lead to a nonfunctional protein, adding another hurdle to the accumulation of anthocyanin in GT. We also uncovered several key members of MYB, bHLH and WRKY families as the putative main drivers of transcriptional changes between the two turnips. Overall, this study provides new tools for modifying anthocyanin content and improving turnip nutritional quality.}, } @article {pmid31499664, year = {2019}, author = {Rashkov, P and Venturino, E and Aguiar, M and Stollenwerk, N and W Kooi, B}, title = {On the role of vector modeling in a minimalistic epidemic model.}, journal = {Mathematical biosciences and engineering : MBE}, volume = {16}, number = {5}, pages = {4314-4338}, doi = {10.3934/mbe.2019215}, pmid = {31499664}, issn = {1551-0018}, mesh = {Aedes/virology ; Animals ; Computer Simulation ; Dengue/epidemiology/transmission ; *Disease Vectors ; *Epidemics/statistics & numerical data ; Heuristics ; Humans ; Mathematical Concepts ; *Models, Biological ; Models, Statistical ; Mosquito Vectors/virology ; Seasons ; Vector Borne Diseases/*epidemiology/*transmission ; }, abstract = {The motivation for the research reported in this paper comes from modeling the spread of vector-borne virus diseases. To study the role of the host versus vector dynamics and their interaction we use the susceptible-infected-removed (SIR) host model and the susceptible-infected (SI) vector model. When the vector dynamical processes occur at a faster scale than those in the host-epidemics dynamics, we can use a time-scale argument to reduce the dimension of the model. This is often implemented as a quasi steady-state assumption (qssa) where the slow varying variable is set at equilibrium and an ode equation is replaced by an algebraic equation. Singular perturbation theory will appear to be a useful tool to perform this derivation. An asymptotic expansion in the small parameter that represents the ratio of the two time scales for the dynamics of the host and vector is obtained using an invariant manifold equation. In the case of a susceptible-infected-susceptible (SIS) host model this algebraic equation is a hyperbolic relationship modeling a saturated incidence rate. This is similar to the Holling type II functional response (Ecology) and the Michaelis-Menten kinetics (Biochemistry). We calculate the value for the force of infection leading to an endemic situation by performing a bifurcation analysis. The effect of seasonality is studied where the force of infection changes sinusoidally to model the annual fluctuations of the vector population. The resulting non-autonomous system is studied in the same way as the autonomous system using bifurcation analysis.}, } @article {pmid31495042, year = {2020}, author = {Pranovi, F and Libralato, S and Zucchetta, M and Anelli Monti, M and Link, JS}, title = {Cumulative biomass curves describe past and present conditions of Large Marine Ecosystems.}, journal = {Global change biology}, volume = {26}, number = {2}, pages = {786-797}, doi = {10.1111/gcb.14827}, pmid = {31495042}, issn = {1365-2486}, mesh = {Biomass ; *Ecosystem ; }, abstract = {Implementing the Ecosystem Approach in marine ecosystems is moving from preliminary steps-dedicated to defining the optimal features for indicators and developing efficient indicator frameworks-towards an operational phase where multisector marine management decisions are executed using this information. Within this operational context, emergent ecosystem properties are becoming quite promising as they have been demonstrated to be globally widespread and repeatable, and to be quite effective in detecting significant state variations of complex systems. Biomass accumulation across TLs (CumB-TL) combines two important emergent properties of an ecosystem (energy flow, in terms of transfer efficiency, and storage, expressed as biomass), both amenable to detecting rapid ecosystem change. However, for further application, it is crucial to understand which types of drivers an indicator is sensitive to and how robust it is in relation to modifications of the external conditions and/or the system state. Here we address some outstanding questions of these CumB-TL curves related to their sensitivity to various drivers by carrying out a global scale assessment (using data from 62 LMEs) over six decades (1950-2010). We confirm the consistency of the S-pattern across all the LMEs, independent from latitude, ecosystem, environmental conditions, and stress level. The dynamics of the curve shape showed a tendency to stretch (i.e. decrease of steepness), in the presence of external disturbance and conversely to increase in steepness and shift towards higher TL in the case of recovery from stressed conditions. Our results suggest the presence of three main types of ecosystem dynamics, those showing an almost continuous increase in ecological state over time, those showing a continuous decrease in ecological state over time, and finally those showing a mixed behaviour flipping between recovering and degrading phases. These robust patterns suggest that the CumB-TL curve approach has some useful properties for use in further advancing the implementation of the Ecosystem Approach, allowing us to detect the state of a given marine ecosystem based on the dynamics of its curve shape, by using readily available time series data. The value of being able to identify conditions that might require management actions is quite high and, in many respects, represents the main objective in the context of an Ecosystem Approach, with large applications for detecting and responding to global changes in marine ecosystems.}, } @article {pmid31494994, year = {2020}, author = {Ran, X and Zhao, F and Wang, Y and Liu, J and Zhuang, Y and Ye, L and Qi, M and Cheng, J and Zhang, Y}, title = {Plant Regulomics: a data-driven interface for retrieving upstream regulators from plant multi-omics data.}, journal = {The Plant journal : for cell and molecular biology}, volume = {101}, number = {1}, pages = {237-248}, doi = {10.1111/tpj.14526}, pmid = {31494994}, issn = {1365-313X}, mesh = {*Databases, Genetic ; Genome, Plant/*genetics ; Genomics ; Plants/*genetics/*metabolism ; Software ; Transcriptome/genetics ; }, abstract = {High-throughput technology has become a powerful approach for routine plant research. Interpreting the biological significance of high-throughput data has largely focused on the functional characterization of a large gene list or genomic loci that involves the following two aspects: the functions of the genes or loci and how they are regulated as a whole, i.e. searching for the upstream regulators. Traditional platforms for functional annotation largely help resolving the first issue. Addressing the second issue is essential for a global understanding of the regulatory mechanism, but is more challenging, and requires additional high-throughput experimental evidence and a unified statistical framework for data-mining. The rapid accumulation of 'omics data provides a large amount of experimental data. We here present Plant Regulomics, an interface that integrates 19 925 transcriptomic and epigenomic data sets and diverse sources of functional evidence (58 112 terms and 695 414 protein-protein interactions) from six plant species along with the orthologous genes from 56 whole-genome sequenced plant species. All pair-wise transcriptomic comparisons with biological significance within the same study were performed, and all epigenomic data were processed to genomic loci targeted by various factors. These data were well organized to gene modules and loci lists, which were further implemented into the same statistical framework. For any input gene list or genomic loci, Plant Regulomics retrieves the upstream factors, treatments, and experimental/environmental conditions regulating the input from the integrated 'omics data. Additionally, multiple tools and an interactive visualization are available through a user-friendly web interface. Plant Regulomics is available at http://bioinfo.sibs.ac.cn/plant-regulomics.}, } @article {pmid31494409, year = {2019}, author = {Reaney, SM and Mackay, EB and Haygarth, PM and Fisher, M and Molineux, A and Potts, M and Benskin, CMH}, title = {Identifying critical source areas using multiple methods for effective diffuse pollution mitigation.}, journal = {Journal of environmental management}, volume = {250}, number = {}, pages = {109366}, doi = {10.1016/j.jenvman.2019.109366}, pmid = {31494409}, issn = {1095-8630}, mesh = {*Agriculture ; Environmental Monitoring ; Fresh Water ; Geographic Information Systems ; Water Pollution ; *Water Quality ; }, abstract = {Diffuse pollution from agriculture constitutes a key pressure on the water quality of freshwaters and is frequently the cause of ecological degradation. The problem of diffuse pollution can be conceptualised with a source-mobilisation-pathway (or delivery)-impact model, whereby the combination of high source risk and strong connected pathways leads to 'critical source areas' (CSAs). These areas are where most diffuse pollution will originate, and hence are the optimal places to implement mitigation measures. However, identifying the locations of these areas is a key problem across different spatial scales within catchments. A number of approaches are frequently used for this assessment, although comparisons of these assessments are rarely carried out. We evaluate the CSAs identified via traditional walkover surveys supported by three different approaches, highlighting their benefits and disadvantages. These include a custom designed smartphone app; a desktop geographic information system (GIS) and terrain analysis-based SCIMAP (Sensitive Catchment Integrated Modelling and Analysis Platform) approach; and the use of a high spatial resolution drone dataset as an improved input data for SCIMAP modelling. Each of these methods captures the locations of the CSAs, revealing similarities and differences in the prioritisation of CSA features. The differences are due to the temporal and spatial resolution of the three methods such as the use of static land cover information, the ability to capture small scale features, such as gateways and the incomplete catchment coverage of the walkover survey. The relative costs and output resolutions of the three methods indicate that they are suitable for application at different catchment scales in conjunction with other methods. Based on the results in this paper, it is recommended that a multi-evidence-based approach to diffuse pollution management is taken across catchment spatial scales, incorporating local knowledge from the walkover with the different data resolutions of the SCIMAP approach.}, } @article {pmid31488068, year = {2019}, author = {Pereira-Flores, E and Glöckner, FO and Fernandez-Guerra, A}, title = {Fast and accurate average genome size and 16S rRNA gene average copy number computation in metagenomic data.}, journal = {BMC bioinformatics}, volume = {20}, number = {1}, pages = {453}, pmid = {31488068}, issn = {1471-2105}, support = {57129354//Deutscher Akademischer Austauschdienst/ ; POS_EXT_2012_1_10105//Agencia Nacional de Investigación e Innovación/ ; 634486//Horizon 2020 Framework Programme/ ; }, mesh = {Benchmarking ; DNA Copy Number Variations ; Databases, Genetic ; *Gene Dosage ; *Genome Size ; Metagenome/*genetics ; Metagenomics/*methods ; Oceans and Seas ; RNA, Ribosomal, 16S/*genetics ; Time Factors ; }, abstract = {BACKGROUND: Metagenomics caused a quantum leap in microbial ecology. However, the inherent size and complexity of metagenomic data limit its interpretation. The quantification of metagenomic traits in metagenomic analysis workflows has the potential to improve the exploitation of metagenomic data. Metagenomic traits are organisms' characteristics linked to their performance. They are measured at the genomic level taking a random sample of individuals in a community. As such, these traits provide valuable information to uncover microorganisms' ecological patterns. The Average Genome Size (AGS) and the 16S rRNA gene Average Copy Number (ACN) are two highly informative metagenomic traits that reflect microorganisms' ecological strategies as well as the environmental conditions they inhabit.

RESULTS: Here, we present the ags.sh and acn.sh tools, which analytically derive the AGS and ACN metagenomic traits. These tools represent an advance on previous approaches to compute the AGS and ACN traits. Benchmarking shows that ags.sh is up to 11 times faster than state-of-the-art tools dedicated to the estimation AGS. Both ags.sh and acn.sh show comparable or higher accuracy than existing tools used to estimate these traits. To exemplify the applicability of both tools, we analyzed the 139 prokaryotic metagenomes of TARA Oceans and revealed the ecological strategies associated with different water layers.

CONCLUSION: We took advantage of recent advances in gene annotation to develop the ags.sh and acn.sh tools to combine easy tool usage with fast and accurate performance. Our tools compute the AGS and ACN metagenomic traits on unassembled metagenomes and allow researchers to improve their metagenomic data analysis to gain deeper insights into microorganisms' ecology. The ags.sh and acn.sh tools are publicly available using Docker container technology at https://github.com/pereiramemo/AGS-and-ACN-tools .}, } @article {pmid31484549, year = {2019}, author = {Matsuzono, K and Mieno, M and Fujimoto, S}, title = {Ramen restaurant prevalence is associated with stroke mortality in Japan: an ecological study.}, journal = {Nutrition journal}, volume = {18}, number = {1}, pages = {53}, pmid = {31484549}, issn = {1475-2891}, mesh = {Diet/*adverse effects/*methods ; Fast Foods/*statistics & numerical data ; Humans ; Japan/epidemiology ; Prevalence ; Restaurants/*statistics & numerical data ; Stroke/*mortality ; }, abstract = {BACKGROUND: The association between stroke and nutrition has recently been investigated. However, the association between diet and stroke in Japan has not been clarified. We hypothesized that there may be an association between consumption of ramen and stroke mortality. Therefore, we investigated the association between the prevalence of ramen restaurants and stroke mortality in Japanese prefectures.

METHODS: We used Pearson's correlation coefficients to evaluate associations between the prevalence of each of four restaurant types (ramen, fast food, French or Italian, and udon or soba) and age- and sex-adjusted stroke mortality rates in each prefecture. We also investigated correlations between acute myocardial infarction and the prevalence of each type of restaurant as a control. We obtained age- and sex-adjusted stroke mortality rates and the acute myocardial infarction mortality rate in each prefecture from the 2017 Trends in National Health published in Japan. Data on the number of restaurants of each type in each prefecture were obtained from the database of the Nippon Telegraph and Telephone Corporation.

RESULTS: The prevalence of ramen restaurants, but not of other restaurant types, positively correlated with stroke mortality in both men and women (r > 0.5). We found no correlation between ramen restaurant prevalence and mortality from acute myocardial infarction.

CONCLUSION: The prevalence of ramen restaurants in Japanese prefectures has a significant correlation with the stroke mortality rate.}, } @article {pmid31484260, year = {2019}, author = {Wang, XF and Zhang, YW and Ma, JJ}, title = {[Factors influencing the incidence of bacterial dysentery in parts of southwest China, using data from the geodetector].}, journal = {Zhonghua liu xing bing xue za zhi = Zhonghua liuxingbingxue zazhi}, volume = {40}, number = {8}, pages = {953-959}, doi = {10.3760/cma.j.issn.0254-6450.2019.08.015}, pmid = {31484260}, issn = {0254-6450}, support = {U1611264//Joint Funds of WHO and National Natural Science Foundation of China/ ; 2016YFC1200703//National Key Research and Development Project/ ; 2017ZX10303401-005//National Science and Technology Major Project of China/ ; }, mesh = {China/epidemiology ; Dysentery, Bacillary/diagnosis/*epidemiology ; Geographic Information Systems ; Humans ; Incidence ; *Meteorological Concepts ; Tibet ; }, abstract = {Objective: To analyze the relationship between the incidence of bacterial dysentery and related meteorological, environmental and socio-economic factors in parts of southwest China, under the geodetector. Methods: Incidence data on bacillary dysentery from 2005 to 2014 was collected from the China infectious disease reporting system and meteorological, terrain environment and socio-economic related data were used for statistical analysis with geodetector also used, in Sichuan province, Yunnan province and the Tibet autonomous region (southwest China). Results: Through geodetector model, results showed that the elevation maximum value of power of determinant (PD) (PD=0.308), ethnicity (PD=0.260), followed by summer mean temperature, topography, elevation standard deviation, slope, population density were noticed. The maximum value of PD of summer average relative humidity, summer average precipitation, and regional GDP were all less than 0.200. In the ecological detector model, value of PD appeared significantly different from multiple factors such as summer average precipitation, regional GDP, average altitude, elevation standard deviation, slope, terrain and ethnicity (P<0.05). In the interactive detector model, after the spatial interaction, factors as: value on PD of summer average relative humidity, population density and regional GDP were larger than the value on the sum of PD of two factors with nonlinear superposition enhancing trend. Results from the risk zone detection showed that areas of moderate average summer temperature, low average precipitation, moderate average summer relative humidity, high average altitude, large elevation standard deviation, high slope, mountain topography, Tibeto-Burmese of ethnicity, low population density, low regional GDP were all related to the high incidence rates of bacterial dysentery. Conclusions: Meteorological conditions and topography environments were related to the bacterial dysentery in southwest China, socio-economic behaviors depends on the level of economic development and sanitary conditions etc. were all directing influencing the transmission and incidence of bacterial dysentery. For developing a better intervention programs on bacillary dysentery, socio-economic means should be used for the control of bacillary dysentery, in the region.}, } @article {pmid31484218, year = {2019}, author = {Goodman, KR and Prost, S and Bi, K and Brewer, MS and Gillespie, RG}, title = {Host and geography together drive early adaptive radiation of Hawaiian planthoppers.}, journal = {Molecular ecology}, volume = {28}, number = {19}, pages = {4513-4528}, pmid = {31484218}, issn = {1365-294X}, support = {S10 OD018174/OD/NIH HHS/United States ; }, mesh = {*Adaptation, Physiological ; Animals ; *Computational Biology ; Ecology ; Exons/genetics ; Genetics, Population ; Geography ; Hawaii ; Hemiptera/genetics/*physiology ; Host Specificity ; Islands ; Male ; *Metagenomics ; Phylogeny ; Plants/*parasitology ; Species Specificity ; *Transcriptome ; }, abstract = {The interactions between insects and their plant host have been implicated in driving diversification of both players. Early arguments highlighted the role of ecological opportunity, with the idea that insects "escape and radiate" on new hosts, with subsequent hypotheses focusing on the interplay between host shifting and host tracking, coupled with isolation and fusion, in generating diversity. Because it is rarely possible to capture the initial stages of diversification, it is particularly difficult to ascertain the relative roles of geographic isolation versus host shifts in initiating the process. The current study examines genetic diversity between populations and hosts within a single species of endemic Hawaiian planthopper, Nesosydne umbratica (Hemiptera, Delphacidae). Given that the species was known as a host generalist occupying unrelated hosts, Clermontia (Campanulaceae) and Pipturus (Urticaceae), we set out to determine the relative importance of geography and host in structuring populations in the early stages of differentiation on the youngest islands of the Hawaiian chain. Results from extensive exon capture data showed that N. umbratica is highly structured, both by geography, with discrete populations on each volcano, and by host plant, with parallel radiations on Clermontia and Pipturus leading to extensive co-occurrence. The marked genetic structure suggests that populations can readily become established on novel hosts provided opportunity; subsequent adaptation allows monopolization of the new host. The results support the role of geographic isolation in structuring populations and with host shifts occurring as discrete events that facilitate subsequent parallel geographic range expansion.}, } @article {pmid31483803, year = {2019}, author = {Singer, AC and Xu, Q and Keller, VDJ}, title = {Translating antibiotic prescribing into antibiotic resistance in the environment: A hazard characterisation case study.}, journal = {PloS one}, volume = {14}, number = {9}, pages = {e0221568}, pmid = {31483803}, issn = {1932-6203}, mesh = {Anti-Bacterial Agents/analysis ; Databases, Factual ; Drug Prescriptions/*statistics & numerical data ; *Drug Resistance, Microbial ; England ; Fluoroquinolones/analysis ; Macrolides/analysis ; Rivers/*microbiology ; Seasons ; Sewage/chemistry ; }, abstract = {The environment receives antibiotics through a combination of direct application (e.g., aquaculture and fruit production), as well as indirect release through pharmaceutical manufacturing, sewage and animal manure. Antibiotic concentrations in many sewage-impacted rivers are thought to be sufficient to select for antibiotic resistance genes. Yet, because antibiotics are nearly always found associated with antibiotic-resistant faecal bacteria in wastewater, it is difficult to distinguish the selective role of effluent antibiotics within a 'sea' of gut-derived resistance genes. Here we examine the potential for macrolide and fluoroquinolone prescribing in England to select for resistance in the River Thames catchment, England. We show that 64% and 74% of the length of the modelled catchment is chronically exposed to putative resistance-selecting concentrations (PNEC) of macrolides and fluoroquinolones, respectively. Under current macrolide usage, 115 km of the modelled River Thames catchment (8% of total length) exceeds the PNEC by 5-fold. Similarly, under current fluoroquinolone usage, 223 km of the modelled River Thames catchment (16% of total length) exceeds the PNEC by 5-fold. Our results reveal that if reduced prescribing was the sole mitigating measure, that macrolide and fluoroquinolone prescribing would need to decline by 77% and 85%, respectively, to limit resistance selection in the catchment. Significant reductions in antibiotic prescribing are feasible, but innovation in sewage-treatment will be necessary for achieving substantially-reduced antibiotic loads and inactivation of DNA-pollution from resistant bacteria. Greater confidence is needed in current risk-based targets for antibiotics, particularly in mixtures, to better inform environmental risk assessments and mitigation.}, } @article {pmid31482680, year = {2020}, author = {Ma, W and Zhao, X and Yin, C and Jiang, F and Du, X and Chen, T and Zhang, Q and Qiu, L and Xu, H and Joe Hull, J and Li, G and Sung, WK and Li, F and Lin, Y}, title = {A chromosome-level genome assembly reveals the genetic basis of cold tolerance in a notorious rice insect pest, Chilo suppressalis.}, journal = {Molecular ecology resources}, volume = {20}, number = {1}, pages = {268-282}, doi = {10.1111/1755-0998.13078}, pmid = {31482680}, issn = {1755-0998}, support = {2016ZX08001001//National Science and Technology Major Project of China/ ; }, mesh = {Animals ; Chromosomes, Insect/*genetics ; Genome Size ; *Genome, Insect ; Moths/classification/*genetics ; Oryza/*parasitology ; Phylogeny ; Plant Diseases/parasitology ; }, abstract = {The rice stem borer, Chilo suppressalis, is one of the most damaging insect pests to rice production worldwide. Although C. suppressalis has been the focus of numerous studies examining cold tolerance and diapause, plant-insect interactions, pesticide targets and resistance, and the development of RNAi-mediated pest management, the absence of a high-quality genome has limited deeper insights. To address this limitation, we generated a draft C. suppressalis genome constructed from both Illumina and PacBio sequences. The assembled genome size was 824.35 Mb with a contig N50 of 307 kb and a scaffold N50 of 1.75 Mb. Hi-C scaffolding assigned 99.2% of the bases to one of 29 chromosomes. Based on universal single-copy orthologues (BUSCO), the draft genome assembly was estimated to be 97% complete and is predicted to encompass 15,653 protein-coding genes. Cold tolerance is an extreme survival strategy found in animals. However, little is known regarding the genetic basis of the winter ecology of C. suppressalis. Here, we focused our orthologous analysis on those gene families associated with animal cold tolerance. Our finding provided the first genomic evidence revealing specific cold-tolerant strategies in C. suppressalis, including those involved in glucose-originated glycerol biosynthesis, triacylglycerol-originated glycerol biosynthesis, fatty acid synthesis and trehalose transport-intermediate cold tolerance. The high-quality C. suppressalis genome provides a valuable resource for research into a broad range of areas in molecular ecology, and subsequently benefits developing modern pest control strategies.}, } @article {pmid31482143, year = {2019}, author = {Roncalli, V and Cieslak, MC and Germano, M and Hopcroft, RR and Lenz, PH}, title = {Regional heterogeneity impacts gene expression in the subarctic zooplankter Neocalanus flemingeri in the northern Gulf of Alaska.}, journal = {Communications biology}, volume = {2}, number = {}, pages = {324}, pmid = {31482143}, issn = {2399-3642}, mesh = {Alaska ; Animals ; Arctic Regions ; Chlorophyll A/metabolism ; Cluster Analysis ; Copepoda/*genetics ; *Gene Expression Regulation ; Gene Ontology ; Lipid Metabolism/genetics ; RNA, Messenger/genetics/metabolism ; Salinity ; Temperature ; Zooplankton/*genetics ; }, abstract = {Marine pelagic species are being increasingly challenged by environmental change. Their ability to persist will depend on their capacity for physiological acclimatization. Little is known about limits of physiological plasticity in key species at the base of the food web. Here we investigate the capacity for acclimatization in the copepod Neocalanus flemingeri, which inhabits the Gulf of Alaska, a heterogeneous and highly seasonal environment. RNA-Seq analysis of field-collected pre-adults identified large regional differences in expression of genes involved in metabolic and developmental processes and response to stressors. We found that lipid synthesis genes were up-regulated in individuals from Prince William Sound and down-regulated in the Gulf of Alaska. Up-regulation of lipid catabolic genes in offshore individuals suggests they are experiencing nutritional deficits. The expression differences demonstrate physiological plasticity in response to a steep gradient in food availability. Our transcriptional analysis reveals mechanisms of acclimatization that likely contribute to the observed resilience of this population.}, } @article {pmid31481743, year = {2020}, author = {Isobe, K and Ise, Y and Kato, H and Oda, T and Vincenot, CE and Koba, K and Tateno, R and Senoo, K and Ohte, N}, title = {Consequences of microbial diversity in forest nitrogen cycling: diverse ammonifiers and specialized ammonia oxidizers.}, journal = {The ISME journal}, volume = {14}, number = {1}, pages = {12-25}, pmid = {31481743}, issn = {1751-7370}, mesh = {Ammonia/*metabolism ; Ammonium Compounds/metabolism ; Biodiversity ; Ecosystem ; *Forests ; Nitrates/metabolism ; *Nitrification ; Nitrogen/metabolism ; *Nitrogen Cycle ; Oxidation-Reduction ; Plants/metabolism ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {We tested the ecosystem functions of microbial diversity with a focus on ammonification (involving diverse microbial taxa) and nitrification (involving only specialized microbial taxa) in forest nitrogen cycling. This study was conducted on a forest slope, in which the soil environment and plant growth gradually changed. We measured the gross and net rates of ammonification and nitrification, the abundance of predicted ammonifiers and nitrifiers, and their community compositions in the soils. The abundance of predicted ammonifiers did not change along the soil environmental gradient, leading to no significant change in the gross ammonification rate. On the other hand, the abundance of nitrifiers and the gross nitrification rate gradually changed. These accordingly determined the spatial distribution of net accumulation of ammonium and nitrate available to plants. The community composition of predicted ammonifiers gradually changed along the slope, implying that diverse ammonifiers were more likely to include taxa that were acclimated to the soil environment and performed ammonification at different slope locations than specialized nitrifiers. Our findings suggest that the abundance of ammonifiers and nitrifiers directly affects the corresponding nitrogen transformation rates, and that their diversity affects the stability of the rates against environmental changes. This study highlights the role of microbial diversity in biogeochemical processes under changing environments and plant growth.}, } @article {pmid31481551, year = {2019}, author = {Kohno, A and Dahlui, M and Nik Farid, ND and Ali, SH and Nakayama, T}, title = {In-depth examination of issues surrounding the reasons for child marriage in Kelantan, Malaysia: a qualitative study.}, journal = {BMJ open}, volume = {9}, number = {9}, pages = {e027377}, pmid = {31481551}, issn = {2044-6055}, mesh = {Adolescent ; Female ; Health Knowledge, Attitudes, Practice ; Humans ; Malaysia ; Male ; *Marriage/legislation & jurisprudence/psychology/statistics & numerical data ; Needs Assessment ; *Poverty ; Qualitative Research ; *Religion ; Reproductive Health/standards ; Social Environment ; Social Validity, Research ; Women's Rights ; }, abstract = {OBJECTIVE: To examine individual, familial, community and societal issues surrounding the reasons for child marriage in Kelantan, Malaysia.

DESIGN: Qualitative study by means of semistructured interviews with women and key informants, using social-ecological model as a conceptual framework.

SETTING: Interviews were conducted in Kota Bharu district, Kelantan, a northeast state in Peninsular Malaysia.

PARTICIPANTS: Eighteen women of reproductive age (18 to 44 years old) that experienced their first marriage below the age of 18, as well as five key informants, consisting of a government officer, a community leader, an officer from religious department and two mothers. The women were recruited from a reproductive health clinic. The key informants who had specialised knowledge related to child marriage were selectively chosen.

RESULTS: Three themes emerged that aligned with the social-ecological model: immaturity in decision-making, family poverty and religious and cultural norms.

CONCLUSIONS: The findings imply that sex education and awareness-building activities regarding the consequences of child marriage must be implemented to eradicate child marriage in Malaysia. Such implementation must be coordinated as a team-based approach involving experts in such fields as law, religion, psychology, social-welfare and public health. In order to increase the awareness of child marriage consequences, the target for awareness must extend not only to the adolescent girls and their families, but also to the community and society at large by clearly communicating the negative consequences of and addressing the drivers for child marriage.}, } @article {pmid31481200, year = {2019}, author = {Nawade, B and Yahyaa, M and Reuveny, H and Shaltiel-Harpaz, L and Eisenbach, O and Faigenboim, A and Bar-Yaakov, I and Holland, D and Ibdah, M}, title = {Profiling of volatile terpenes from almond (Prunus dulcis) young fruits and characterization of seven terpene synthase genes.}, journal = {Plant science : an international journal of experimental plant biology}, volume = {287}, number = {}, pages = {110187}, doi = {10.1016/j.plantsci.2019.110187}, pmid = {31481200}, issn = {1873-2259}, mesh = {Acyclic Monoterpenes/metabolism ; Alkyl and Aryl Transferases/genetics/*metabolism ; Computational Biology ; Cyclohexane Monoterpenes/metabolism ; Fruit/enzymology/genetics ; Phylogeny ; Plant Proteins/genetics/metabolism ; Prunus dulcis/*enzymology/genetics ; Terpenes/*metabolism ; Volatile Organic Compounds/*metabolism ; }, abstract = {Almond (Prunus dulcis) is an agricultural and economically important fruit tree from the Rosaceae family used in the food industry. The monoterpenes and sesquiterpenes perform important ecological functions such as insecticidal and antifeedant activities against various insects. The young fruits of the different almond varieties were found to produce considerable amounts of terpene volatiles, including linalool and geraniol. To identify terpene synthases (TPSs) involved in the production of these volatile terpenes, existing genome databases of the Rosaceae were screened for almond genes with significant sequence similarity to other plants TPSs. Bioinformatics analysis led to the identification of seven putative TPSs genes with complete open reading frames. We characterized the enzymes encoded by these seven complementary DNAs: the monoterpene synthases PdTPS1, PdTPS3, PdTPS5, and PdTPS6 belong to the TPS-b clade, which catalyzes the formation of β-phellandrene, geraniol, linalool, and farnesene, respectively. The sesquiterpene synthases PdTPS2 and PdTPS4, which belong to the TPS-a clade mainly catalyze the formation of bergamotene, while another sesquiterpene synthase, PdTPS7, from the TPS-g clade showed nerolidol synthase activity. The qRT-PCR analysis revealed that the various tissues of almond varieties showed differential transcription for all these PdTPSs genes.}, } @article {pmid31480903, year = {2019}, author = {Willis, KA and Purvis, JH and Myers, ED and Aziz, MM and Karabayir, I and Gomes, CK and Peters, BM and Akbilgic, O and Talati, AJ and Pierre, JF}, title = {Fungi form interkingdom microbial communities in the primordial human gut that develop with gestational age.}, journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology}, volume = {33}, number = {11}, pages = {12825-12837}, pmid = {31480903}, issn = {1530-6860}, mesh = {Female ; *Fungi/classification/growth & development ; *Gastrointestinal Microbiome ; *Gestational Age ; Humans ; Infant ; Infant, Newborn ; *Infant, Premature ; Male ; *Microbiota ; *Mycobiome ; }, abstract = {Fungal and bacterial commensal organisms play a complex role in the health of the human host. Expansion of commensal ecology after birth is a critical period in human immune development. However, the initial fungal colonization of the primordial gut remains undescribed. To investigate primordial fungal ecology, we performed amplicon sequencing and culture-based techniques of first-pass meconium, which forms in the intestine prior to birth, from a prospective observational cohort of term and preterm newborns. Here, we describe fungal ecologies in the primordial gut that develop complexity with advancing gestational age at birth. Our findings suggest homeostasis of fungal commensals may represent an important aspect of human biology present even before birth. Unlike bacterial communities that gradually develop complexity, the domination of the fungal communities of some preterm infants by Saccromycetes, specifically Candida, may suggest a pathologic association with preterm birth.-Willis, K. A., Purvis, J. H., Myers, E. D., Aziz, M. M., Karabayir, I., Gomes, C. K., Peters, B. M., Akbilgic, O., Talati, A. J., Pierre, J. F. Fungi form interkingdom microbial communities in the primordial human gut that develop with gestational age.}, } @article {pmid31479695, year = {2019}, author = {Nerva, L and Forgia, M and Ciuffo, M and Chitarra, W and Chiapello, M and Vallino, M and Varese, GC and Turina, M}, title = {The mycovirome of a fungal collection from the sea cucumber Holothuria polii.}, journal = {Virus research}, volume = {273}, number = {}, pages = {197737}, doi = {10.1016/j.virusres.2019.197737}, pmid = {31479695}, issn = {1872-7492}, mesh = {Animals ; Computational Biology ; Fungal Viruses/*classification/*isolation & purification ; Fungi/*virology ; *Genome, Viral ; High-Throughput Nucleotide Sequencing ; Holothuria/*microbiology ; *Phylogeny ; RNA Viruses/classification ; RNA, Double-Stranded ; RNA, Viral/genetics ; }, abstract = {Holothuria polii is a marine animal with an important ecological and economic impact. In the present study we analysed the presence of mycoviruses associated to fungi that were isolated from different H. polii tissues. Among the 48 fungal isolates analysed we identified 10 viruses in 8 strains belonging to 7 fungal species. Five out of nine viruses have a dsRNA genome: three of them belong to the Partitiviridae family, one belongs to a still undefined clade of bipartite viruses and the last one belongs to the Chrysoviridae family. We also identified two viruses belonging to a recently proposed new mycovirus taxon named polymycovirus. Two viruses belong to the positive single stranded RNA clade: one falls into the new Botourmiaviridae family, specifically in the Magoulivirus genus, and the other one falls into a still undefined clade phylogenetically related to tombusviruses. Finally, we also identified a virus with a negative stranded RNA genome showing similarity to a group of viruses recently proposed as a new family of mycoviruses in the order Bunyavirales. A bioinformatics approach comparing two datasets of contigs containing two closely related mycobunyaviruses allowed us to identify putative nucleocapsids (Nc) and non-structural (Ns) associated proteins. The GenBank/eMBL/DDBJ accession numbers of the sequences reported in this paper are: PRJNA432529, MG913290, MG913291, MG887747, MG887748, MG887749, MG887750, MG887751, MG887752, MG887753, MG887754, MG887755, MG887756, MG887757, MG887758, MG887759, MG887760, MG887761, MG887762, MG887763, MG887764, MG887765, MG887766, MG887767, MH271211, MN163273, MN163274.}, } @article {pmid31479576, year = {2019}, author = {Chak, STC and Rubenstein, DR}, title = {TERAD: Extraction of transposable element composition from RADseq data.}, journal = {Molecular ecology resources}, volume = {19}, number = {6}, pages = {1681-1688}, doi = {10.1111/1755-0998.13080}, pmid = {31479576}, issn = {1755-0998}, support = {//Simons Foundation/ ; //Life Sciences Research Foundation/ ; IOS-1121435//National Science Foundation/ ; IOS-1257530//National Science Foundation/ ; IOS-1439985//National Science Foundation/ ; //Columbia University/ ; //College of William and Mary/ ; }, mesh = {Computational Biology/methods ; DNA Transposable Elements/*genetics ; Genome/genetics ; Genomics/methods ; High-Throughput Nucleotide Sequencing/methods ; Molecular Sequence Annotation/methods ; Sequence Analysis, DNA/methods ; }, abstract = {Transposable elements (TEs) - selfish DNA sequences that can move within the genome - comprise a large proportion of the genomes of many organisms. Although low-coverage whole-genome sequencing can be used to survey TE composition, it is noneconomical for species with large quantities of DNA. Here, we utilize restriction-site associated DNA sequencing (RADSeq) as an alternative method to survey TE composition. First, we demonstrate in silico that double digest restriction-site associated DNA sequencing (ddRADseq) markers contain the same TE compositions as whole genome assemblies across arthropods. Next, we show empirically using eight Synalpheus snapping shrimp species with large genomes that TE compositions from ddRADseq and low-coverage whole-genome sequencing are comparable within and across species. Finally, we develop a new bioinformatic pipeline, TERAD, to extract TE compositions from RADseq data. Our study expands the utility of RADseq to study the repeatome, making comparative studies of genome structure for species with large genomes more tractable and affordable.}, } @article {pmid31479570, year = {2020}, author = {Euclide, PT and McKinney, GJ and Bootsma, M and Tarsa, C and Meek, MH and Larson, WA}, title = {Attack of the PCR clones: Rates of clonality have little effect on RAD-seq genotype calls.}, journal = {Molecular ecology resources}, volume = {20}, number = {1}, pages = {66-78}, doi = {10.1111/1755-0998.13087}, pmid = {31479570}, issn = {1755-0998}, mesh = {Computational Biology ; Genotype ; High-Throughput Nucleotide Sequencing/methods/*standards ; Polymerase Chain Reaction/methods/*standards ; }, abstract = {Interpretation of high-throughput sequence data requires an understanding of how decisions made during bioinformatic data processing can influence results. One source of bias that is often cited is PCR clones (or PCR duplicates). PCR clones are common in restriction site-associated sequencing (RAD-seq) data sets, which are increasingly being used for molecular ecology. To determine the influence PCR clones and the bioinformatic handling of clones have on genotyping, we evaluate four RAD-seq data sets. Data sets were compared before and after clones were removed to estimate the number of clones present in RAD-seq data, quantify how often the presence of clones in a data set causes genotype calls to change compared to when clones were removed, investigate the mechanisms that lead to genotype call changes and test whether clones bias heterozygosity estimates. Our RAD-seq data sets contained 30%-60% PCR clones, but 95% of RAD-tags had five or fewer clones. Relatively few genotypes changed once clones were removed (5%-10%), and the vast majority of these changes (98%) were associated with genotypes switching from a called to no-call state or vice versa. PCR clones had a larger influence on genotype calls in individuals with low read depth but appeared to influence genotype calls at all loci similarly. Removal of PCR clones reduced the number of called genotypes by 2% but had almost no influence on estimates of heterozygosity. As such, while steps should be taken to limit PCR clones during library preparation, PCR clones are likely not a substantial source of bias for most RAD-seq studies.}, } @article {pmid31479467, year = {2019}, author = {Zuykova, EI and Bochkarev, NA and Taylor, DJ and Kotov, AA}, title = {Unexpected endemism in the Daphnia longispina complex (Crustacea: Cladocera) in Southern Siberia.}, journal = {PloS one}, volume = {14}, number = {9}, pages = {e0221527}, pmid = {31479467}, issn = {1932-6203}, mesh = {Animals ; Arctic Regions ; DNA, Mitochondrial/genetics ; Daphnia/*classification/*genetics ; Databases, Nucleic Acid ; Evolution, Molecular ; Genetic Variation ; Genetics, Population ; Haplotypes ; Phylogeny ; Phylogeography ; Polymorphism, Genetic ; RNA, Ribosomal/genetics ; Siberia ; Species Specificity ; }, abstract = {The biological significance of regional cladoceran morphotypes in the montane regions of the central Palearctic remains poorly understood. In the Holarctic Daphnia longispina complex (Cladocera: Daphniidae), several variants, lineages and species have been proposed as endemic for Southern Siberia. Daphnia turbinata Sars, for example, named after its unusual head shape, is known only from Southern Siberia. Here we sequence DNA of Daphnia from three mitochondrial genes (12S rRNA, 16S rRNA, and NADH dehydrogenase subunit 2, ND2) from 57 localities in Russia and Mongolia (the majority being from Southern Siberia) and place them in evolutionary context with existing data. Our aim was to examine regional endemism of the Daphnia longispina complex in Southern Siberian; to improve the phylogenetic understanding with improved taxonomic and regional sampling, and to better understand the influence of Pleistocene glaciation on the biogeography of these lineages. At least three lineages showed genetic evidence for endemism in Southern Siberia. There was strong support for D. turbinata as a sister lineage to to D. longispina/D. dentifera. Another endemic, Siberian D. cf. longispina, is a sister group to the longispina group in general. Within D. longispina s. str. there was an endemic Siberian clade with a western range boundary near the Yenisei River Basin. Gene flow estimates among populations (based on FST values) were very low for clades of D. longispina on a regional (the original 12S dataset), and on a pan-Eurasian (the extended 12S dataset) scale. Negative values of Fu's FS and Tajima's D tests prevailed for the species examined with significant values found for two D. longispina clades, D. dentifera, D. galeata and D. cristata. Our results support the notion that Southern Siberia is an important biogeographic region for cladocerans as it contained unexpected diversity of endemics (such as D. turbinata, D. cf. longispina and lineages of D. umbra and D. longsipina s.str.) and from being the geographic meeting place of expanding postglacial lineages from eastern and western refugia.}, } @article {pmid31479460, year = {2019}, author = {Martinez-Villegas, L and Assis-Geraldo, J and Koerich, LB and Collier, TC and Lee, Y and Main, BJ and Rodrigues, NB and Orfano, AS and Pires, ACAM and Campolina, TB and Nacif-Pimenta, R and Baia-da-Silva, DC and Duarte, APM and Bahia, AC and Rios-Velásquez, CM and Lacerda, MVG and Monteiro, WM and Lanzaro, GC and Secundino, NFC and Pimenta, PFP}, title = {Characterization of the complete mitogenome of Anopheles aquasalis, and phylogenetic divergences among Anopheles from diverse geographic zones.}, journal = {PloS one}, volume = {14}, number = {9}, pages = {e0219523}, pmid = {31479460}, issn = {1932-6203}, support = {S10 OD018174/OD/NIH HHS/United States ; }, mesh = {Animals ; Anopheles/*classification/*genetics ; Base Composition ; Computational Biology/methods ; Evolution, Molecular ; *Genome, Mitochondrial ; *Genomics/methods ; Humans ; Molecular Sequence Annotation ; Mosquito Vectors/classification/genetics ; *Phylogeny ; *Phylogeography ; Sequence Analysis, DNA ; Whole Genome Sequencing ; }, abstract = {Whole mitogenome sequences (mtDNA) have been exploited for insect ecology studies, using them as molecular markers to reconstruct phylogenies, or to infer phylogeographic relationships and gene flow. Recent Anopheles phylogenomic studies have provided information regarding the time of deep lineage divergences within the genus. Here we report the complete 15,393 bp mtDNA sequences of Anopheles aquasalis, a Neotropical human malaria vector. When comparing its structure and base composition with other relevant and available anopheline mitogenomes, high similarity and conserved genomic features were observed. Furthermore, 22 mtDNA sequences comprising anopheline and Dipteran sibling species were analyzed to reconstruct phylogenies and estimate dates of divergence between taxa. Phylogenetic analysis using complete mtDNA sequences suggests that A. aquasalis diverged from the Anopheles albitarsis complex ~28 million years ago (MYA), and ~38 MYA from Anopheles darlingi. Bayesian analysis suggests that the most recent ancestor of Nyssorhynchus and Anopheles + Cellia was extant ~83 MYA, corroborating current estimates of ~79-100 MYA. Additional sampling and publication of African, Asian, and North American anopheline mitogenomes would improve the resolution of the Anopheles phylogeny and clarify early continental dispersal routes.}, } @article {pmid31477173, year = {2019}, author = {Attardo, GM and Abd-Alla, AMM and Acosta-Serrano, A and Allen, JE and Bateta, R and Benoit, JB and Bourtzis, K and Caers, J and Caljon, G and Christensen, MB and Farrow, DW and Friedrich, M and Hua-Van, A and Jennings, EC and Larkin, DM and Lawson, D and Lehane, MJ and Lenis, VP and Lowy-Gallego, E and Macharia, RW and Malacrida, AR and Marco, HG and Masiga, D and Maslen, GL and Matetovici, I and Meisel, RP and Meki, I and Michalkova, V and Miller, WJ and Minx, P and Mireji, PO and Ometto, L and Parker, AG and Rio, R and Rose, C and Rosendale, AJ and Rota-Stabelli, O and Savini, G and Schoofs, L and Scolari, F and Swain, MT and Takáč, P and Tomlinson, C and Tsiamis, G and Van Den Abbeele, J and Vigneron, A and Wang, J and Warren, WC and Waterhouse, RM and Weirauch, MT and Weiss, BL and Wilson, RK and Zhao, X and Aksoy, S}, title = {Comparative genomic analysis of six Glossina genomes, vectors of African trypanosomes.}, journal = {Genome biology}, volume = {20}, number = {1}, pages = {187}, pmid = {31477173}, issn = {1474-760X}, support = {D43 TW007391/TW/FIC NIH HHS/United States ; R01AI051584/NH/NIH HHS/United States ; R01 AI051584/AI/NIAID NIH HHS/United States ; R01 AI068932/AI/NIAID NIH HHS/United States ; R03TW008413/NH/NIH HHS/United States ; U54HG003079/HG/NHGRI NIH HHS/United States ; U01 AI115648/AI/NIAID NIH HHS/United States ; R03TW009444/NH/NIH HHS/United States ; U01AI115648/NH/NIH HHS/United States ; R21AI109263//National Institute of Allergy and Infectious Diseases/International ; }, mesh = {Animals ; DNA Transposable Elements/genetics ; Drosophila melanogaster/genetics ; Female ; Gene Expression Regulation ; Genes, Insect ; Genes, X-Linked ; *Genome, Insect ; *Genomics ; Geography ; Insect Proteins/genetics ; Insect Vectors/*genetics ; Male ; Mutagenesis, Insertional/genetics ; Phylogeny ; Repetitive Sequences, Nucleic Acid/genetics ; Sequence Homology, Amino Acid ; Synteny/genetics ; Trypanosoma/*parasitology ; Tsetse Flies/*genetics ; Wolbachia/genetics ; }, abstract = {BACKGROUND: Tsetse flies (Glossina sp.) are the vectors of human and animal trypanosomiasis throughout sub-Saharan Africa. Tsetse flies are distinguished from other Diptera by unique adaptations, including lactation and the birthing of live young (obligate viviparity), a vertebrate blood-specific diet by both sexes, and obligate bacterial symbiosis. This work describes the comparative analysis of six Glossina genomes representing three sub-genera: Morsitans (G. morsitans morsitans, G. pallidipes, G. austeni), Palpalis (G. palpalis, G. fuscipes), and Fusca (G. brevipalpis) which represent different habitats, host preferences, and vectorial capacity.

RESULTS: Genomic analyses validate established evolutionary relationships and sub-genera. Syntenic analysis of Glossina relative to Drosophila melanogaster shows reduced structural conservation across the sex-linked X chromosome. Sex-linked scaffolds show increased rates of female-specific gene expression and lower evolutionary rates relative to autosome associated genes. Tsetse-specific genes are enriched in protease, odorant-binding, and helicase activities. Lactation-associated genes are conserved across all Glossina species while male seminal proteins are rapidly evolving. Olfactory and gustatory genes are reduced across the genus relative to other insects. Vision-associated Rhodopsin genes show conservation of motion detection/tracking functions and variance in the Rhodopsin detecting colors in the blue wavelength ranges.

CONCLUSIONS: Expanded genomic discoveries reveal the genetics underlying Glossina biology and provide a rich body of knowledge for basic science and disease control. They also provide insight into the evolutionary biology underlying novel adaptations and are relevant to applied aspects of vector control such as trap design and discovery of novel pest and disease control strategies.}, } @article {pmid31477060, year = {2019}, author = {Kim, AM and Kang, S and Park, JH and Yoon, TH and Kim, Y}, title = {Geographic variation and factors associated with rates of knee arthroplasty in Korea-a population based ecological study.}, journal = {BMC musculoskeletal disorders}, volume = {20}, number = {1}, pages = {400}, pmid = {31477060}, issn = {1471-2474}, mesh = {Adolescent ; Adult ; Age Factors ; Aged ; Arthroplasty, Replacement, Knee/economics/*statistics & numerical data ; Child ; Child, Preschool ; Clinical Decision-Making ; Databases, Factual ; Female ; Geography ; Health Expenditures/*statistics & numerical data ; Hospitals/*statistics & numerical data ; Humans ; Infant ; Infant, Newborn ; Male ; Middle Aged ; National Health Programs ; Patient Selection ; Republic of Korea ; Young Adult ; }, abstract = {BACKGROUND: The recent increase in knee arthroplasty (KA) use in Korea is among the highest in the world. The rapid increase in KA use suggests that the KA use in Korea could have been affected by medically unjustifiable factors. This study aimed to examine the geographic variation in the rate of KA and its associated factors in Korea.

METHODS: We used the data from the National Health Insurance in Korea in 2013, from which a total of 67,086 claims for KA were obtained. We calculated the age-sex-standardized KA rates of the entire population and the crude rates of the age groups 0-64 and 65 and over in 251 districts. We assessed the geographic variation of the KA rates and examined the associated factors with a multivariate linear regression with the KA rate as a dependent variable.

RESULTS: The overall rate of KA in Korea was 132.7 per 100,000 persons. The rates of KA showed a four-fold variation. The deprivation index score and the number of beds in the small to medium sized hospitals showed a positive association with the rates of KA while the number of orthopedic surgeons showed a negative association.

CONCLUSIONS: Korea has been experiencing a rapid increase in the use of KA for the last decade or so, which was most prominent among the elderly population aged 65 and older. Our results suggest that the higher rate of KA is strongly related to a higher supply of beds and the socioeconomically deprived conditions. Considering that the decision concerning KA has room for discretion and also affects a considerable portion of health care expenditures, the use of KA should be thoroughly monitored with more emphasis on standardization in the decision making process and preventive measures that can lessen the need for KA.}, } @article {pmid31477015, year = {2019}, author = {Laine, VN and Verhagen, I and Mateman, AC and Pijl, A and Williams, TD and Gienapp, P and van Oers, K and Visser, ME}, title = {Exploration of tissue-specific gene expression patterns underlying timing of breeding in contrasting temperature environments in a song bird.}, journal = {BMC genomics}, volume = {20}, number = {1}, pages = {693}, pmid = {31477015}, issn = {1471-2164}, support = {339092//ERC Advanced Grant/ ; }, mesh = {Animals ; Breeding ; Female ; *Gene Expression Regulation ; Gene Ontology ; Gene Regulatory Networks ; Hypothalamus/metabolism ; Liver/metabolism ; Organ Specificity ; Ovary/metabolism ; Reproduction/*genetics/physiology ; Songbirds/*genetics/metabolism ; Temperature ; Time Factors ; Transcriptome ; }, abstract = {BACKGROUND: Seasonal timing of breeding is a life history trait with major fitness consequences but the genetic basis of the physiological mechanism underlying it, and how gene expression is affected by date and temperature, is not well known. In order to study this, we measured patterns of gene expression over different time points in three different tissues of the hypothalamic-pituitary-gonadal-liver axis, and investigated specifically how temperature affects this axis during breeding. We studied female great tits (Parus major) from lines artificially selected for early and late timing of breeding that were housed in two contrasting temperature environments in climate-controlled aviaries. We collected hypothalamus, liver and ovary samples at three different time points (before and after onset of egg-laying). For each tissue, we sequenced whole transcriptomes of 12 pools (n = 3 females) to analyse gene expression.

RESULTS: Birds from the selection lines differed in expression especially for one gene with clear reproductive functions, zona pellucida glycoprotein 4 (ZP4), which has also been shown to be under selection in these lines. Genes were differentially expressed at different time points in all tissues and most of the differentially expressed genes between the two temperature treatments were found in the liver. We identified a set of hub genes from all the tissues which showed high association to hormonal functions, suggesting that they have a core function in timing of breeding. We also found ample differentially expressed genes with largely unknown functions in birds.

CONCLUSIONS: We found differentially expressed genes associated with selection line and temperature treatment. Interestingly, the latter mainly in the liver suggesting that temperature effects on egg-laying date may happen down-stream in the physiological pathway. These findings, as well as our datasets, will further the knowledge of the mechanisms of tissue-specific avian seasonality in the future.}, } @article {pmid31471958, year = {2019}, author = {Piau, A and Wild, K and Mattek, N and Kaye, J}, title = {Current State of Digital Biomarker Technologies for Real-Life, Home-Based Monitoring of Cognitive Function for Mild Cognitive Impairment to Mild Alzheimer Disease and Implications for Clinical Care: Systematic Review.}, journal = {Journal of medical Internet research}, volume = {21}, number = {8}, pages = {e12785}, pmid = {31471958}, issn = {1438-8871}, support = {P30 AG008017/AG/NIA NIH HHS/United States ; P30 AG024978/AG/NIA NIH HHS/United States ; R01 AG024059/AG/NIA NIH HHS/United States ; U2C AG054397/AG/NIA NIH HHS/United States ; }, mesh = {Accelerometry ; Aged ; Alzheimer Disease/diagnosis/*physiopathology/psychology ; Automobile Driving ; Biomarkers ; Cognition ; Cognitive Dysfunction/diagnosis/*physiopathology/psychology ; Disease Progression ; Early Diagnosis ; Geographic Information Systems ; Humans ; Independent Living ; Surveys and Questionnaires ; *Technology ; Telemedicine ; Wearable Electronic Devices ; }, abstract = {BACKGROUND: Among areas that have challenged the progress of dementia care has been the assessment of change in symptoms over time. Digital biomarkers are defined as objective, quantifiable, physiological, and behavioral data that are collected and measured by means of digital devices, such as embedded environmental sensors or wearables. Digital biomarkers provide an alternative assessment approach, as they allow objective, ecologically valid, and long-term follow-up with continuous assessment. Despite the promise of a multitude of sensors and devices that can be applied, there are no agreed-upon standards for digital biomarkers, nor are there comprehensive evidence-based results for which digital biomarkers may be demonstrated to be most effective.

OBJECTIVE: In this review, we seek to answer the following questions: (1) What is the evidence for real-life, home-based use of technologies for early detection and follow-up of mild cognitive impairment (MCI) or dementia? And (2) What transformation might clinicians expect in their everyday practices?

METHODS: A systematic search was conducted in PubMed, Cochrane, and Scopus databases for papers published from inception to July 2018. We searched for studies examining the implementation of digital biomarker technologies for mild cognitive impairment or mild Alzheimer disease follow-up and detection in nonclinic, home-based settings. All studies that included the following were examined: community-dwelling older adults (aged 65 years or older); cognitively healthy participants or those presenting with cognitive decline, from subjective cognitive complaints to early Alzheimer disease; a focus on home-based evaluation for noninterventional follow-up; and remote diagnosis of cognitive deterioration.

RESULTS: An initial sample of 4811 English-language papers were retrieved. After screening and review, 26 studies were eligible for inclusion in the review. These studies ranged from 12 to 279 participants and lasted between 3 days to 3.6 years. Most common reasons for exclusion were as follows: inappropriate setting (eg, hospital setting), intervention (eg, drugs and rehabilitation), or population (eg, psychiatry and Parkinson disease). We summarized these studies into four groups, accounting for overlap and based on the proposed technological solutions, to extract relevant data: (1) data from dedicated embedded or passive sensors, (2) data from dedicated wearable sensors, (3) data from dedicated or purposive technological solutions (eg, games or surveys), and (4) data derived from use of nondedicated technological solutions (eg, computer mouse movements).

CONCLUSIONS: Few publications dealt with home-based, real-life evaluations. Most technologies were far removed from everyday life experiences and were not mature enough for use under nonoptimal or uncontrolled conditions. Evidence available from embedded passive sensors represents the most relatively mature research area, suggesting that some of these solutions could be proposed to larger populations in the coming decade. The clinical and research communities would benefit from increasing attention to these technologies going forward.}, } @article {pmid31470136, year = {2019}, author = {Hu, X and Dai, Y and Zhang, X and Dai, K and Liu, B and Yuan, R and Feng, Y and Liang, Z and Zhu, M and Zhang, M and Zhang, Y and Zhang, Z and Cao, M and Gu, Y and Pan, J and Yan, B and Zhu, H and Xue, R and Cao, G and Chen, H and Wang, Y and Gong, C}, title = {Identification and characterization of novel type of RNAs, circRNAs in crucian carp Carassius auratus gibelio.}, journal = {Fish & shellfish immunology}, volume = {94}, number = {}, pages = {50-57}, doi = {10.1016/j.fsi.2019.08.070}, pmid = {31470136}, issn = {1095-9947}, mesh = {Animals ; Base Sequence ; Carps/*genetics/immunology ; Computational Biology ; Gene Expression Profiling/veterinary ; RNA, Circular/*genetics/immunology/metabolism ; Signal Transduction/genetics/*immunology ; }, abstract = {Circular RNAs (circRNAs) with regulatory potency activity was identified from varieties of species. Crucian carp (Carassius auratus gibelio) is one of the most freshwater aquaculture species in China. Every year, huge economic damage to the farming was caused by the virus and bacterial infection. Until now, there is any information about circRNA reported from the Crucian carp. In this study, the expression pattern of circRNA in Crucian carp was investigated with transcriptomic analysis. The results showed that only 37 circRNAs were identified from the Crucian carp, and these circRNAs biogenesis was formed with canonical GU-AG splicing mechanism with unevenly distributed on the chromosomes. Wherein, most of the circRNAs were derived from the sense overlapping strategy. Reverse transcript PCR and Sanger sequencing data indicated that these circRNAs were existed authenticity in Crucian carp. The bioinformatics analysis indicated that circRNAs identified from the Crucian carp with potential miRNA sponge regulate the expression level of mRNAs. GO annotation and KEGG pathway analysis of these circRNAs showed that more than 20% circRNAs were related with catalytic activity and binding in the category of molecular function, and these circRNAs were enriched in 9 signaling pathways, such as, Wnt signaling pathway, MAPK signaling pathway, Ubiquitin mediated proteolysis et al. 220 mRNAs would be regulated by the circRNAs via miRNAs mediation. These target mRNAs were further analyzed with functional annotation and KEGG analysis. GO annotation analysis showed that several genes were related with function of nucleotide binding, transcription regulatory activity. KEGG pathway analysis showed that 5 genes were enriched in the pathway of Endocytosis. The circRNA-miRNA-mRNA regulation network indicated that one miRNA can link one or more circRNA and one or more mRNA. Overall, these results will not only help us to further understand the novel RNA transcripts in Crucian carp, but also provide the novel clue to investigate the interaction between host and pathogens from this novel circRNA molecule.}, } @article {pmid31465920, year = {2019}, author = {Giri, S and Zhang, Z and Krasnuk, D and Lathrop, RG}, title = {Evaluating the impact of land uses on stream integrity using machine learning algorithms.}, journal = {The Science of the total environment}, volume = {696}, number = {}, pages = {133858}, doi = {10.1016/j.scitotenv.2019.133858}, pmid = {31465920}, issn = {1879-1026}, abstract = {A general pattern of declining aquatic ecological integrity with increasing urban land use has been well established for a number of watersheds worldwide. A more nuanced characterization of the influence of different urban land uses and the determination of cumulative thresholds will further inform watershed planning and management. To this end, we investigated the utility of two machine learning algorithms (Random Forests (RF) and Boosted Regression Trees (BRT)) to model stream impairment through multimetric macroinvertebrate index known as High Gradient Macroinvertebrate Index (HGMI) in an urbanizing watershed located in north-central New Jersey, United States. These machine learning algorithms were able to explain at least 50% of the variability of stream integrity based on watershed land use/land cover. While comparable in results, RF was found to be easier to train and was somewhat more robust to model overfitting compared to BRT. Our results document the influence of increasing high-medium density (> 30% Impervious Surface cover (ISC)), low density (15-30% ISC) urban and transitional/barren land had in negatively affecting stream biological integrity. The thresholds generated by partial plots suggest that the stream integrity decreased abruptly when the percentage of high-medium and low density urban, and transitional/barren land went above 10%, 8%, and 2% of the watershed, respectively. Additionally, when rural residential surpassed 30% threshold, it behaved similar to low density urban towards stream integrity. Identification of such cumulative thresholds can help watershed managers and policymakers to craft land use zoning regulations and design restoration programs that are grounded by objective scientific criteria.}, } @article {pmid31465440, year = {2019}, author = {Miele, V and Guill, C and Ramos-Jiliberto, R and Kéfi, S}, title = {Non-trophic interactions strengthen the diversity-functioning relationship in an ecological bioenergetic network model.}, journal = {PLoS computational biology}, volume = {15}, number = {8}, pages = {e1007269}, pmid = {31465440}, issn = {1553-7358}, mesh = {Animals ; *Biodiversity ; Biomass ; Biota ; Computational Biology ; Computer Simulation ; *Ecosystem ; Energy Metabolism ; Food Chain ; *Models, Biological ; Predatory Behavior ; }, abstract = {Ecological communities are undeniably diverse, both in terms of the species that compose them as well as the type of interactions that link species to each other. Despite this long recognition of the coexistence of multiple interaction types in nature, little is known about the consequences of this diversity for community functioning. In the ongoing context of global change and increasing species extinction rates, it seems crucial to improve our understanding of the drivers of the relationship between species diversity and ecosystem functioning. Here, using a multispecies dynamical model of ecological communities including various interaction types (e.g. competition for space, predator interference, recruitment facilitation in addition to feeding), we studied the role of the presence and the intensity of these interactions for species diversity, community functioning (biomass and production) and the relationship between diversity and functioning.Taken jointly, the diverse interactions have significant effects on species diversity, whose amplitude and sign depend on the type of interactions involved and their relative abundance. They however consistently increase the slope of the relationship between diversity and functioning, suggesting that species losses might have stronger effects on community functioning than expected when ignoring the diversity of interaction types and focusing on feeding interactions only.}, } @article {pmid31462444, year = {2019}, author = {Udall, JA and Long, E and Hanson, C and Yuan, D and Ramaraj, T and Conover, JL and Gong, L and Arick, MA and Grover, CE and Peterson, DG and Wendel, JF}, title = {De Novo Genome Sequence Assemblies of Gossypium raimondii and Gossypium turneri.}, journal = {G3 (Bethesda, Md.)}, volume = {9}, number = {10}, pages = {3079-3085}, pmid = {31462444}, issn = {2160-1836}, mesh = {*Computational Biology/methods ; *Genome, Plant ; *Genomics/methods ; Gossypium/*classification/*genetics ; Molecular Sequence Annotation ; Repetitive Sequences, Nucleic Acid ; }, abstract = {Cotton is an agriculturally important crop. Because of its importance, a genome sequence of a diploid cotton species (Gossypium raimondii, D-genome) was first assembled using Sanger sequencing data in 2012. Improvements to DNA sequencing technology have improved accuracy and correctness of assembled genome sequences. Here we report a new de novo genome assembly of G. raimondii and its close relative G. turneri The two genomes were assembled to a chromosome level using PacBio long-read technology, HiC, and Bionano optical mapping. This report corrects some minor assembly errors found in the Sanger assembly of G. raimondii We also compare the genome sequences of these two species for gene composition, repetitive element composition, and collinearity. Most of the identified structural rearrangements between these two species are due to intra-chromosomal inversions. More inversions were found in the G. turneri genome sequence than the G. raimondii genome sequence. These findings and updates to the D-genome sequence will improve accuracy and translation of genomics to cotton breeding and genetics.}, } @article {pmid31462233, year = {2019}, author = {Xiong, Q and Zhong, L and Shen, T and Cao, C and He, H and Chen, X}, title = {iTRAQ-based quantitative proteomic and physiological analysis of the response to N deficiency and the compensation effect in rice.}, journal = {BMC genomics}, volume = {20}, number = {1}, pages = {681}, pmid = {31462233}, issn = {1471-2164}, support = {31360309//National Natural Science Foundation of China/ ; 31471441//National Natural Science Foundation of China/ ; }, mesh = {Alanine Transaminase/metabolism ; Carbon Cycle ; Chlorophyll Binding Proteins/metabolism ; Energy Metabolism ; Gene Expression Regulation, Plant ; Gene Ontology ; NADH Dehydrogenase/metabolism ; Nitrogen/*deficiency/*metabolism ; Oryza/*metabolism ; Peroxidase/metabolism ; Phosphoglycerate Kinase/metabolism ; Photosynthesis ; Photosystem II Protein Complex/metabolism ; Plant Leaves/metabolism ; Proteome/metabolism ; Proteomics ; Ribulose-Bisphosphate Carboxylase/metabolism ; }, abstract = {BACKGROUND: The crop growth compensation effect is a naturally biological phenomenon, and nitrogen (N) is essential for crop growth and development, especially for yield formation. Little is known about the molecular mechanism of N deficiency and N compensation in rice. Thus, the N-sensitive stage of rice was selected to study N deficiency at the tillering stage and N compensation at the young panicle differentiation stage. In this study, a proteome analysis was performed to analyze leaf differentially expressed proteins (DEPs), and to investigate the leaf physiological characteristics and yield under N deficiency and after N compensation.

RESULTS: The yield per plant presented an equivalent compensatory effect. The net photosynthetic rate, optimal/maximal quantum yield of photosystem II (Fv/Fm), soil and plant analyzer development (SPAD) value, and glutamic pyruvic transaminase (GPT) activity of T1 (N deficiency at the tillering stage, and N compensation at the young panicle differentiation stage) were lower than those of CK (N at different stages of growth by constant distribution) under N deficiency. However, after N compensation, the net photosynthetic rate, Fv/Fm, SPAD value and GPT activity were increased. Using an iTRAQ-based quantitative approach, a total of 1665 credible proteins were identified in the three 4-plex iTRAQ experiments. Bioinformatics analysis indicated that DEPs were enriched in photosynthesis, photosynthesis-antenna proteins, carbon metabolism and carbon fixation in the photosynthetic organism pathways. Moreover, the photosynthesis-responsive proteins of chlorophyll a-b binding protein, ribulose bisphosphate carboxylase small chain and phosphoglycerate kinase were significantly downregulated under N deficiency. After N compensation, chlorophyll a-b binding protein, NADH dehydrogenase subunit 5, NADH dehydrogenase subunit 7, and peroxidase proteins were significantly upregulated in rice leaves.

CONCLUSION: Through physiological and quantitative proteomic analysis, we concluded that a variety of metabolic pathway changes was induced by N deficiency and N compensation. GO and KEGG enrichment analysis revealed that DEPs were significantly associated with photosynthesis pathway-, energy metabolism pathway- and stress resistance-related proteins. The DEPs play an important role in the regulation of N deficiency and the compensation effect in rice.}, } @article {pmid31461536, year = {2020}, author = {Pereira, L and Bittencourt, PRL and Pacheco, VS and Miranda, MT and Zhang, Y and Oliveira, RS and Groenendijk, P and Machado, EC and Tyree, MT and Jansen, S and Rowland, L and Ribeiro, RV}, title = {The Pneumatron: An automated pneumatic apparatus for estimating xylem vulnerability to embolism at high temporal resolution.}, journal = {Plant, cell & environment}, volume = {43}, number = {1}, pages = {131-142}, doi = {10.1111/pce.13647}, pmid = {31461536}, issn = {1365-3040}, mesh = {Citrus sinensis/physiology ; Databases, Factual ; Droughts ; *Equipment Design ; Eucalyptus ; Plant Leaves/physiology ; Plant Roots/physiology ; Plant Stems/physiology ; Plant Transpiration/physiology ; Reproducibility of Results ; Sensitivity and Specificity ; Trees/physiology ; Water/physiology ; Xylem/*chemistry ; }, abstract = {Xylem vulnerability to embolism represents an important trait to determine species distribution patterns and drought resistance. However, estimating embolism resistance frequently requires time-consuming and ambiguous hydraulic lab measurements. Based on a recently developed pneumatic method, we present and test the "Pneumatron", a device that generates high time-resolution and fully automated vulnerability curves. Embolism resistance is estimated by applying a partial vacuum to extract air from an excised xylem sample, while monitoring the pressure change over time. Although the amount of gas extracted is strongly correlated with the percentage loss of xylem conductivity, validation of the Pneumatron was performed by comparison with the optical method for Eucalyptus camaldulensis leaves. The Pneumatron improved the precision of the pneumatic method considerably, facilitating the detection of small differences in the (percentage of air discharged [PAD] < 0.47%). Hence, the Pneumatron can directly measure the 50% PAD without any fitting of vulnerability curves. PAD and embolism frequency based on the optical method were strongly correlated (r[2] = 0.93) for E. camaldulensis. By providing an open source platform, the Pneumatron represents an easy, low-cost, and powerful tool for field measurements, which can significantly improve our understanding of plant-water relations and the mechanisms behind embolism.}, } @article {pmid31456586, year = {2019}, author = {Vlajinac, HD and Marinković, JM and Maksimović, MZ and Radak, DJ and Arsić, RB and Jorga, JB}, title = {The prevalence of polyvascular disease in patients with carotid artery disease and peripheral artery disease.}, journal = {Kardiologia polska}, volume = {77}, number = {10}, pages = {926-934}, doi = {10.33963/KP.14945}, pmid = {31456586}, issn = {1897-4279}, mesh = {Aged ; Atherosclerosis ; Carotid Artery Diseases/*complications/epidemiology ; Female ; Humans ; Male ; Middle Aged ; Peripheral Arterial Disease/*complications/epidemiology ; Poland ; Prevalence ; Risk Factors ; }, abstract = {BACKGROUND: Cardiovascular disease remains the major cause of mortality in the Western World.

AIMS: We aimed to assess the prevalence of polyvascular disease in patients with carotid artery disease and peripheral artery disease (PAD), and to determine the risk profile of patients with polyvascular disease.

METHODS: The study included 1045 consecutive patients presenting to our department with carotid disease or PAD. Demographic characteristics, anthropometric parameters, and data on cardiovascular risk factors were collected in all patients. On the basis of medical history, patients were classified into those who had only symptomatic carotid disease or symptomatic PAD and those who had symptomatic polyvascular disease.

RESULTS: Carotid disease alone was reported in 366 participants (35%), PAD alone, in 199 (19%), and polyvascular disease, in 480 (46%). Compared with carotid disease, PAD was more often a component of polyvascular disease (P = 0.002) and was combined with a higher number of other atherosclerotic diseases (P = 0.02). Compared with patients with symptomatic atherosclerotic disease in only 1 territory, patients with various types of polyvascular disease more often had hypertension (P from 0.03 to <0.001), dyslipidemia (P <0.001), high‑sensitivity C‑reactive protein levels of 3 mg/l or higher (P = 0.005), and more often were current smokers (P <0.001) or former smokers (P from 0.03 to 0.001).

CONCLUSIONS: We showed a high prevalence of symptomatic polyvascular disease in patients with carotid disease or PAD. The risk profile was worse in patients with polyvascular disease than in those with a disease in a single vascular territory.}, } @article {pmid31451752, year = {2019}, author = {Miura, R and Araki, A and Minatoya, M and Miyake, K and Chen, ML and Kobayashi, S and Miyashita, C and Yamamoto, J and Matsumura, T and Ishizuka, M and Kubota, T and Kishi, R}, title = {An epigenome-wide analysis of cord blood DNA methylation reveals sex-specific effect of exposure to bisphenol A.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {12369}, pmid = {31451752}, issn = {2045-2322}, mesh = {Adult ; Benzhydryl Compounds/*adverse effects ; CpG Islands/genetics ; DNA Methylation/*genetics ; *Epigenome ; Female ; Fetal Blood/*metabolism ; Gene Ontology ; Gene Regulatory Networks ; Humans ; Infant ; Infant, Newborn ; Male ; Phenols/*adverse effects ; Pregnancy ; Prenatal Exposure Delayed Effects/*genetics ; *Sex Characteristics ; }, abstract = {Exposure to bisphenol A (BPA) in utero is associated with adverse health outcome of the offspring. Differential DNA methylation at specific CpG sites may link BPA exposure to health impacts. We examined the association of prenatal BPA exposure with genome-wide DNA methylation changes in cord blood in 277 mother-child pairs in the Hokkaido Study on Environment and Children's Health, using the Illumina HumanMethylation 450 BeadChip. We observed that a large portion of BPA-associated differentially methylated CpGs with p-value < 0.0001 was hypomethylated among all newborns (91%) and female infants (98%), as opposed to being hypermethylated (88%) among males. We found 27 and 16 CpGs with a false discovery rate (FDR) < 0.05 in the analyses for males and females, respectively. Genes annotated to FDR-corrected CpGs clustered into an interconnected genetic network among males, while they rarely exhibited any interactions in females. In contrast, none of the enrichment for gene ontology (GO) terms with FDR < 0.05 was observed for genes annotated to the male-specific CpGs with p < 0.0001, whereas the female-specific genes were significantly enriched for GO terms related to cell adhesion. Our epigenome-wide analysis of cord blood DNA methylation implies potential sex-specific epigenome responses to BPA exposure.}, } @article {pmid31450256, year = {2019}, author = {Duarte-Filho, OB and Bianchi, PHM and Lobel, ALS and Peregrino, PFM and Piccinato, CA and Podgaec, S}, title = {Assisted Reproductive Technologies in Latin America and Europe: a Comparative Analysis of Reported Databases for 2013.}, journal = {Revista brasileira de ginecologia e obstetricia : revista da Federacao Brasileira das Sociedades de Ginecologia e Obstetricia}, volume = {41}, number = {8}, pages = {493-499}, pmid = {31450256}, issn = {1806-9339}, mesh = {Databases, Factual ; Europe ; Female ; Humans ; Latin America ; Male ; Pregnancy ; *Registries ; *Reproductive Techniques, Assisted ; }, abstract = {OBJECTIVE: To compare the Latin American and European assisted reproductive technology (ART) registries regarding data accessibility and quality, treatment utilization, effectiveness, safety, and quality of services.

METHODS:  We performed an ecological study using data from scientific publications of Latin American and European registries that report cycles initiated during 2013 (the most recent registries available until December of 2017). The summarized data are presented as frequencies, percentages, minimum-maximum values, and absolute numbers.

RESULTS:  Reporting clinics and cycle treatments were unevenly distributed between the participating countries for both registries, although access to ART is 15 times greater in Europe. In Latin America, individual services participate voluntarily reporting started cycles until cancellation, birth or miscarriage, while in Europe it varied among countries. It makes the data available from Latin America more uniform, although lesser representative when compared with European ones, given that reporting is compulsory for most countries. The cumulative live birth rate was better in Latin America. Female age, use of intracytoplasmic sperm injection (ICSI), cycles with transfer of ≥ 3 embryos, as well as multiple pregnancy rates were greater in the Latin American Register of Assisted Reproduction (RLA, in the Portuguese acronym). Assisted reproductive technology complications, such as ovarian hyperstimulation syndrome, hemorrhage, and infections were also higher in Latin America, although they are extremely uncommon in both regions.

CONCLUSION:  Both regions have points to improve in the quality of their reports. Latin America has produced a more uniform reporting, their clinical results are generally comparable and sometimes higher than the European ones. In contrast, the safety of the treatment was higher in Europe, with lower rates of complications, especially multiple pregnancies.}, } @article {pmid31446647, year = {2019}, author = {Lemos, LN and Medeiros, JD and Dini-Andreote, F and Fernandes, GR and Varani, AM and Oliveira, G and Pylro, VS}, title = {Genomic signatures and co-occurrence patterns of the ultra-small Saccharimonadia (phylum CPR/Patescibacteria) suggest a symbiotic lifestyle.}, journal = {Molecular ecology}, volume = {28}, number = {18}, pages = {4259-4271}, doi = {10.1111/mec.15208}, pmid = {31446647}, issn = {1365-294X}, support = {BB/P027849/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Bacteria/*genetics ; Base Sequence ; Gene Regulatory Networks ; *Genome, Bacterial ; *Genomics ; Metabolic Networks and Pathways/genetics ; Metagenome ; Microbiota/genetics ; Mining ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Symbiosis/*genetics ; }, abstract = {The size of bacterial genomes is often associated with organismal metabolic capabilities determining ecological breadth and lifestyle. The recently proposed Candidate Phyla Radiation (CPR)/Patescibacteria encompasses mostly unculturable bacterial taxa with relatively small genome sizes with potential for co-metabolism interdependencies. As yet, little is known about the ecology and evolution of CPR, particularly with respect to how they might interact with other taxa. Here, we reconstructed two novel genomes (namely, Candidatus Saccharibacter sossegus and Candidatus Chaer renensis) of taxa belonging to the class Saccharimonadia within the CPR/Patescibacteria using metagenomes obtained from acid mine drainage (AMD). By testing the hypothesis of genome streamlining or symbiotic lifestyle, our results revealed clear signatures of gene losses in these genomes, such as those associated with de novo biosynthesis of essential amino acids, nucleotides, fatty acids and cofactors. In addition, co-occurrence analysis provided evidence supporting potential symbioses of these organisms with Hydrotalea sp. in the AMD system. Together, our findings provide a better understanding of the ecology and evolution of CPR/Patescibacteria and highlight the importance of genome reconstruction for studying metabolic interdependencies between unculturable Saccharimonadia representatives.}, } @article {pmid31444965, year = {2019}, author = {Jaksic, M and Martinovic, M and Gligorovic-Barhanovic, N and Vujacic, A and Djurovic, D and Nedovic-Vukovic, M}, title = {Association between inflammation, oxidative stress, vitamin D, copper and zinc with pre-obesity and obesity in school children from the city of Podgorica, Montenegro.}, journal = {Journal of pediatric endocrinology & metabolism : JPEM}, volume = {32}, number = {9}, pages = {951-957}, doi = {10.1515/jpem-2019-0086}, pmid = {31444965}, issn = {2191-0251}, mesh = {Antioxidants/metabolism ; Biomarkers/blood ; Body Mass Index ; C-Reactive Protein/analysis ; Child ; Copper/*blood ; Female ; Follow-Up Studies ; Humans ; Inflammation/*physiopathology ; Male ; Montenegro/epidemiology ; *Oxidative Stress ; Pediatric Obesity/blood/*epidemiology/pathology ; Prognosis ; Vitamin D/*blood ; Vitamin D Deficiency/*physiopathology ; Vitamins/blood ; Zinc/*blood ; }, abstract = {Background Childhood obesity is a serious health condition with increasing rates worldwide. The aim of this study was to investigate the association between inflammation, oxidative stress, vitamin D, copper and zinc in pre-obese and obese children compared to controls. Methods The study involved 202 children aged 7-15 years (63.9% boys), randomly chosen from 10 elementary schools in Podgorica, Montenegro. Participants were divided into three groups according to their nutritional status (International Obesity Task Force [IOTF] criteria): normal-weight (42.1%), pre-obese (40.6%) and obese (17.3%). Serum biochemical analyses were performed (C-reactive protein [CRP], retinol-binding protein [RBP], total antioxidant status [TAS], total vitamin D [VD], copper and zinc). Results Serum TAS and CRP concentrations were higher in pre-obese and obese children compared to controls (p < 0.001). Serum VD concentrations were lower in pre-obese and obese children compared to their normal-weight peers (p = 0.027 and p = 0.054, respectively). Copper, zinc and RBP concentrations did not differ significantly among the groups (p > 0.05). In pre-obese and obese children, a positive correlation was found between CRP and copper (r = 0.305, p = 0.011 and r = 0.440, p = 0.013, respectively), and TAS and RBP (r = 0.528, p < 0.001 and r = 0.434, p = 0.015, respectively). Standard regression analyses showed that CRP and TAS increase (p < 0.001) whereas VD decreases (p = 0.011) with the body mass index (BMI). Conclusions We show that pre-obesity and obesity in childhood are positively associated with oxidative stress and inflammation, and inversely associated with VD status. Copper and zinc concentrations were not associated with excess fat in children.}, } @article {pmid31444482, year = {2019}, author = {Ranjeva, SL and Mihaljevic, JR and Joseph, MB and Giuliano, AR and Dwyer, G}, title = {Untangling the dynamics of persistence and colonization in microbial communities.}, journal = {The ISME journal}, volume = {13}, number = {12}, pages = {2998-3010}, pmid = {31444482}, issn = {1751-7370}, support = {F30 AI124636/AI/NIAID NIH HHS/United States ; R01 CA214588/CA/NCI NIH HHS/United States ; }, mesh = {Biota ; Humans ; *Microbiota ; Models, Statistical ; Papillomaviridae/classification/genetics/*growth & development/physiology ; Papillomavirus Infections/virology ; }, abstract = {A central goal of community ecology is to infer biotic interactions from observed distributions of co-occurring species. Evidence for biotic interactions, however, can be obscured by shared environmental requirements, posing a challenge for statistical inference. Here, we introduce a dynamic statistical model, based on probit regression, that quantifies the effects of spatial and temporal covariance in longitudinal co-occurrence data. We separate the fixed pairwise effects of species occurrences on persistence and colonization rates, a potential signal of direct interactions, from latent pairwise correlations in occurrence, a potential signal of shared environmental responses. We first validate our modeling framework with several simulation studies. Then, we apply the approach to a pressing epidemiological question by examining how human papillomavirus (HPV) types coexist. Our results suggest that while HPV types respond similarly to common host traits, direct interactions are sparse and weak, so that HPV type diversity depends largely on shared environmental drivers. Our modeling approach is widely applicable to microbial communities and provides valuable insights that should lead to more directed hypothesis testing and mechanistic modeling.}, } @article {pmid31444199, year = {2019}, author = {Loit, K and Adamson, K and Bahram, M and Puusepp, R and Anslan, S and Kiiker, R and Drenkhan, R and Tedersoo, L}, title = {Relative Performance of MinION (Oxford Nanopore Technologies) versus Sequel (Pacific Biosciences) Third-Generation Sequencing Instruments in Identification of Agricultural and Forest Fungal Pathogens.}, journal = {Applied and environmental microbiology}, volume = {85}, number = {21}, pages = {}, pmid = {31444199}, issn = {1098-5336}, mesh = {Agriculture ; Ascomycota/genetics/isolation & purification/pathogenicity ; Biodiversity ; Computational Biology ; Forests ; Fungi/classification/*genetics/*isolation & purification/pathogenicity ; High-Throughput Nucleotide Sequencing/*methods ; Metagenomics/*methods ; *Nanopores ; Oomycetes/genetics/isolation & purification/pathogenicity ; Pathology, Molecular/methods ; Plant Diseases/microbiology ; Sequence Alignment ; Solanum tuberosum ; }, abstract = {Culture-based molecular identification methods have revolutionized detection of pathogens, yet these methods are slow and may yield inconclusive results from environmental materials. The second-generation sequencing tools have much-improved precision and sensitivity of detection, but these analyses are costly and may take several days to months. Of the third-generation sequencing techniques, the portable MinION device (Oxford Nanopore Technologies) has received much attention because of its small size and possibility of rapid analysis at reasonable cost. Here, we compare the relative performances of two third-generation sequencing instruments, MinION and Sequel (Pacific Biosciences), in identification and diagnostics of fungal and oomycete pathogens from conifer (Pinaceae) needles and potato (Solanum tuberosum) leaves and tubers. We demonstrate that the Sequel instrument is efficient for metabarcoding of complex samples, whereas MinION is not suited for this purpose due to a high error rate and multiple biases. However, we find that MinION can be utilized for rapid and accurate identification of dominant pathogenic organisms and other associated organisms from plant tissues following both amplicon-based and PCR-free metagenomics approaches. Using the metagenomics approach with shortened DNA extraction and incubation times, we performed the entire MinION workflow, from sample preparation through DNA extraction, sequencing, bioinformatics, and interpretation, in 2.5 h. We advocate the use of MinION for rapid diagnostics of pathogens and potentially other organisms, but care needs to be taken to control or account for multiple potential technical biases.IMPORTANCE Microbial pathogens cause enormous losses to agriculture and forestry, but current combined culturing- and molecular identification-based detection methods are too slow for rapid identification and application of countermeasures. Here, we develop new and rapid protocols for Oxford Nanopore MinION-based third-generation diagnostics of plant pathogens that greatly improve the speed of diagnostics. However, due to high error rate and technical biases in MinION, the Pacific BioSciences Sequel platform is more useful for in-depth amplicon-based biodiversity monitoring (metabarcoding) from complex environmental samples.}, } @article {pmid31439018, year = {2019}, author = {Li, C and Chng, KR and Kwah, JS and Av-Shalom, TV and Tucker-Kellogg, L and Nagarajan, N}, title = {An expectation-maximization algorithm enables accurate ecological modeling using longitudinal microbiome sequencing data.}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {118}, pmid = {31439018}, issn = {2049-2618}, mesh = {*Algorithms ; Datasets as Topic ; Gastrointestinal Microbiome/genetics/*physiology ; High-Throughput Nucleotide Sequencing/methods ; Humans ; *Microbial Interactions ; *Models, Biological ; }, abstract = {BACKGROUND: The dynamics of microbial communities is driven by a range of interactions from symbiosis to predator-prey relationships, the majority of which are poorly understood. With the increasing availability of high-throughput microbiome taxonomic profiling data, it is now conceivable to directly learn the ecological models that explicitly define microbial interactions and explain community dynamics. The applicability of these approaches is severely limited by the lack of accurate absolute cell density measurements (biomass).

METHODS: We present a new computational approach that resolves this key limitation in the inference of generalized Lotka-Volterra models (gLVMs) by coupling biomass estimation and model inference with an expectation-maximization algorithm (BEEM).

RESULTS: BEEM outperforms the state-of-the-art methods for inferring gLVMs, while simultaneously eliminating the need for additional experimental biomass data as input. BEEM's application to previously inaccessible public datasets (due to the lack of biomass data) allowed us to construct ecological models of microbial communities in the human gut on a per-individual basis, revealing personalized dynamics and keystone species.

CONCLUSIONS: BEEM addresses a key bottleneck in "systems analysis" of microbiomes by enabling accurate inference of ecological models from high throughput sequencing data without the need for experimental biomass measurements.}, } @article {pmid31438841, year = {2019}, author = {Barido-Sottani, J and Chapman, SD and Kosman, E and Mushegian, AR}, title = {Measuring similarity between gene interaction profiles.}, journal = {BMC bioinformatics}, volume = {20}, number = {1}, pages = {435}, pmid = {31438841}, issn = {1471-2105}, support = {xxxx//Stowers Institute for Medical Research/ ; xxxx//Fondation de l'École Polytechnique/ ; xxxx//Colton Foundation/ ; }, mesh = {Algorithms ; Computational Biology/*methods ; *Epistasis, Genetic ; Gene Regulatory Networks ; Genes, Fungal ; Glycosylation ; Molecular Sequence Annotation ; Protein Domains ; Saccharomyces cerevisiae/genetics ; Statistics as Topic ; }, abstract = {BACKGROUND: Gene and protein interaction data are often represented as interaction networks, where nodes stand for genes or gene products and each edge stands for a relationship between a pair of gene nodes. Commonly, that relationship within a pair is specified by high similarity between profiles (vectors) of experimentally defined interactions of each of the two genes with all other genes in the genome; only gene pairs that interact with similar sets of genes are linked by an edge in the network. The tight groups of genes/gene products that work together in a cell can be discovered by the analysis of those complex networks.

RESULTS: We show that the choice of the similarity measure between pairs of gene vectors impacts the properties of networks and of gene modules detected within them. We re-analyzed well-studied data on yeast genetic interactions, constructed four genetic networks using four different similarity measures, and detected gene modules in each network using the same algorithm. The four networks induced different numbers of putative functional gene modules, and each similarity measure induced some unique modules. In an example of a putative functional connection suggested by comparing genetic interaction vectors, we predict a link between SUN-domain proteins and protein glycosylation in the endoplasmic reticulum.

CONCLUSIONS: The discovery of molecular modules in genetic networks is sensitive to the way of measuring similarity between profiles of gene interactions in a cell. In the absence of a formal way to choose the "best" measure, it is advisable to explore the measures with different mathematical properties, which may identify different sets of connections between genes.}, } @article {pmid31438363, year = {2019}, author = {Bakken, S and Arcia, A and Koleck, T and Merrill, JA and Hickey, KT}, title = {Informatics and Data Science for the Precision in Symptom Self-Management Center.}, journal = {Studies in health technology and informatics}, volume = {264}, number = {}, pages = {1827-1828}, doi = {10.3233/SHTI190668}, pmid = {31438363}, issn = {1879-8365}, mesh = {Data Science ; Humans ; Informatics ; *Medical Informatics ; Palliative Care ; Pilot Projects ; *Self-Management ; }, abstract = {The goal of the Precision in Symptom Self-Management (PriSSM) Center is to advance the science of symptom self-management for Latinos through a social ecological lens that takes into account variability in individual, interpersonal, organizational, and environmental factors across the life course. Informatics and data science methods are foundational to PriSSM's research activities including its pilot studies and research resources. This work highlights three areas: Latino Data Repository, Information Visualization, and Center Evaluation.}, } @article {pmid31437230, year = {2019}, author = {Carbone, F and Bruno, L and Perrotta, G and Bitonti, MB and Muzzalupo, I and Chiappetta, A}, title = {Identification of miRNAs involved in fruit ripening by deep sequencing of Olea europaea L. transcriptome.}, journal = {PloS one}, volume = {14}, number = {8}, pages = {e0221460}, pmid = {31437230}, issn = {1932-6203}, mesh = {Conserved Sequence/genetics ; DNA, Complementary/genetics ; Fruit/*genetics/*growth & development ; Gene Expression Regulation, Plant ; Gene Library ; Gene Ontology ; *High-Throughput Nucleotide Sequencing ; MicroRNAs/chemistry/*genetics/metabolism ; Nucleic Acid Conformation ; Olea/*genetics ; RNA, Messenger/genetics/metabolism ; RNA, Plant/chemistry/genetics/metabolism ; Transcriptome/*genetics ; }, abstract = {BACKGROUND: The ripening process of olive fruits is associated with chemical and/or enzymatic specific transformations, making them particularly attractive to animals and humans. In olive drupes, including 'Cassanese' ones, ripening is usually accompanied by progressive chromatic change, resulting in a final red-brown colourization of both epidermis and mesocarp. This event has an exception in the 'Leucocarpa', in which we observed the destabilization in the equilibrium between the chlorophyll metabolism and that of the other pigments, particularly the anthocyanins, whose switch-off during maturation promotes the white colouration of the fruits. Recently, transcription profiling of 'Leucocarpa' and 'Cassanese' olives along ripening, performed through an Illumina RNA-seq approach, has provided useful insights on genes functions involved in fruit maturation such as those related to the biosynthesis of flavonoids and anthocyanins.

METHODOLOGY: To assess expression alterations of genes involved in flavonoids and anthocyanins biosynthetic pathways during ripening, possibly caused by small nuclear RNA (snRNA) in olive drupes, snRNA libraries from 'Leucocarpa' and 'Cassanese' were constructed with RNAs extracted at 100 and 130 Days After Flowering (DAF) and sequenced by an Illumina approach. 130 conserved microRNAs (miRNA) in the Viridiplantae belonging to 14 miRNA families were identified. Regarding the 130 conserved miRNAs, approximately the 48% were identified in all libraries, 5 and 18 miRNAs were shared between the "Cassanese" (C100, C130) and "Leucocarpa" (L100, L130) libraries, respectively.

CONCLUSION: For the remaining reads not-matching with known miRNAs in the Viridiplantae, we combined secondary structure and minimum free energy to discover novel olive miRNAs. Based on these analyses, 492 sequences were considered as putative novel miRNAs. The putative target genes of identified miRNA were computationally predicted by alignment with the olive drupe transcripts obtained from the same samples. A total of 218 transcripts were predicted as targets of 130 known and 492 putative novel miRNAs. Interestingly, some identified target genes are involved in negative regulation of anthocyanin metabolic process. Quantification of the expression pattern of three miRNA and their target transcripts by qRT-PCR assay confirmed the results of Illumina sequencing.}, } @article {pmid31437179, year = {2019}, author = {Faletti, ME and Chacin, DH and Peake, JA and MacDonald, TC and Stallings, CD}, title = {Population dynamics of Pinfish in the eastern Gulf of Mexico (1998-2016).}, journal = {PloS one}, volume = {14}, number = {8}, pages = {e0221131}, pmid = {31437179}, issn = {1932-6203}, mesh = {Animals ; Conservation of Natural Resources ; Datasets as Topic ; Ecosystem ; Estuaries ; Female ; *Food Chain ; Gulf of Mexico ; Male ; Perciformes/*physiology ; Population Dynamics/trends ; Reproduction/*physiology ; }, abstract = {Forage fishes play an important role in marine ecosystems by transferring energy and nutrients through the food web. The population dynamics of forage species can therefore have cascading effects across multiple trophic levels. Here, we analyzed a 19-year dataset on Pinfish (Lagodon rhomboides) across four eastern Gulf of Mexico estuaries to investigate population dynamics, inter- and intra-annual synchrony, metapopulation portfolio effects, growth, and habitat effects. Young-of-year growth rates did not differ among estuaries. The population dynamics of these four systems were stable in the long-term, but highly dynamic inter-annually. Intra-annual dynamics were stable and predictable despite variation in long-term means. Some estuaries exhibited positive inter-annual synchrony, and all four estuaries were synchronous intra-annually. There was evidence for stronger portfolio effects for the entire four-estuary metapopulation, as well as for the two northern estuaries while the southern estuaries appeared to act as a single population. Submerged aquatic vegetation was by far the most important predictor for both presence and abundance of Pinfish. It is important to understand the factors driving forage fish population fluctuations to better predict ecosystem effects, including those to species of economic and ecological importance. These predictors can be useful for the implementation of ecosystem-based management decisions.}, } @article {pmid31435055, year = {2019}, author = {Walker, XJ and Baltzer, JL and Cumming, SG and Day, NJ and Ebert, C and Goetz, S and Johnstone, JF and Potter, S and Rogers, BM and Schuur, EAG and Turetsky, MR and Mack, MC}, title = {Increasing wildfires threaten historic carbon sink of boreal forest soils.}, journal = {Nature}, volume = {572}, number = {7770}, pages = {520-523}, pmid = {31435055}, issn = {1476-4687}, mesh = {Atmosphere/chemistry ; Carbon/*analysis ; *Carbon Sequestration ; Soil/*chemistry ; *Taiga ; Wildfires/*statistics & numerical data ; }, abstract = {Boreal forest fires emit large amounts of carbon into the atmosphere primarily through the combustion of soil organic matter[1-3]. During each fire, a portion of this soil beneath the burned layer can escape combustion, leading to a net accumulation of carbon in forests over multiple fire events[4]. Climate warming and drying has led to more severe and frequent forest fires[5-7], which threaten to shift the carbon balance of the boreal ecosystem from net accumulation to net loss[1], resulting in a positive climate feedback[8]. This feedback will occur if organic-soil carbon that escaped burning in previous fires, termed 'legacy carbon', combusts. Here we use soil radiocarbon dating to quantitatively assess legacy carbon loss in the 2014 wildfires in the Northwest Territories of Canada[2]. We found no evidence for the combustion of legacy carbon in forests that were older than the historic fire-return interval of northwestern boreal forests[9]. In forests that were in dry landscapes and less than 60 years old at the time of the fire, legacy carbon that had escaped burning in the previous fire cycle was combusted. We estimate that 0.34 million hectares of young forests (<60 years) that burned in the 2014 fires could have experienced legacy carbon combustion. This implies a shift to a domain of carbon cycling in which these forests become a net source-instead of a sink-of carbon to the atmosphere over consecutive fires. As boreal wildfires continue to increase in size, frequency and intensity[7], the area of young forests that experience legacy carbon combustion will probably increase and have a key role in shifting the boreal carbon balance.}, } @article {pmid31433817, year = {2019}, author = {Bongers, FJ and Douma, JC and Iwasa, Y and Pierik, R and Evers, JB and Anten, NPR}, title = {Variation in plastic responses to light results from selection in different competitive environments-A game theoretical approach using virtual plants.}, journal = {PLoS computational biology}, volume = {15}, number = {8}, pages = {e1007253}, pmid = {31433817}, issn = {1553-7358}, mesh = {Adaptation, Physiological/genetics/*radiation effects ; Arabidopsis/genetics/growth & development/radiation effects ; Biological Evolution ; Biomass ; Computational Biology ; Computer Simulation ; Game Theory ; Light ; *Models, Biological ; Plant Development/genetics/radiation effects ; Plants/genetics/*radiation effects ; Selection, Genetic ; User-Computer Interface ; }, abstract = {Phenotypic plasticity is a vital strategy for plants to deal with changing conditions by inducing phenotypes favourable in different environments. Understanding how natural selection acts on variation in phenotypic plasticity in plants is therefore a central question in ecology, but is often ignored in modelling studies. Here we present a new modelling approach that allows for the analysis of selection for variation in phenotypic plasticity as a response strategy. We assess selection for shade avoidance strategies of Arabidopsis thaliana in response to future neighbour shading signalled through a decrease in red:far-red (R:FR) ratio. For this, we used a spatially explicit 3D virtual plant model that simulates individual Arabidopsis plants competing for light in different planting densities. Plant structure and growth were determined by the organ-specific interactions with the light environment created by the vegetation structure itself. Shade avoidance plastic responses were defined by a plastic response curve relating petiole elongation and lamina growth to R:FR perceived locally. Different plasticity strategies were represented by different shapes of the response curve that expressed different levels of R:FR sensitivity. Our analyses show that the shape of the selected shade avoidance strategy varies with planting density. At higher planting densities, more sensitive response curves are selected for than at lower densities. In addition, the balance between lamina and petiole responses influences the sensitivity of the response curves selected for. Combining computational virtual plant modelling with a game theoretical analysis represents a new step towards analysing how natural selection could have acted upon variation in shade avoidance as a response strategy, which can be linked to genetic variation and underlying physiological processes.}, } @article {pmid31433524, year = {2019}, author = {Eccles, KM and Pauli, BD and Chan, HM}, title = {The Use of Geographic Information Systems for Spatial Ecological Risk Assessments: An Example from the Athabasca Oil Sands Area in Canada.}, journal = {Environmental toxicology and chemistry}, volume = {38}, number = {12}, pages = {2797-2810}, doi = {10.1002/etc.4577}, pmid = {31433524}, issn = {1552-8618}, support = {//Canada Research Chairs/International ; Joint Oil Sands Monitoring Program//Environment and Climate Change Canada/International ; CREATE grant//Natural Sciences and Engineering Research Council of Canada/International ; Discovery Grant//Natural Sciences and Engineering Research Council of Canada/International ; }, mesh = {Animals ; Canada ; Charadriiformes/growth & development ; Cluster Analysis ; Ecotoxicology ; Environmental Monitoring/*methods ; Environmental Pollutants/analysis ; Geographic Information Systems ; Mercury/analysis ; Oil and Gas Fields/*chemistry ; Ovum/chemistry/metabolism ; Plants/chemistry/metabolism ; Swallows ; }, abstract = {There is an acknowledged need in ecotoxicology for methods that integrate spatial analyses in risk assessment. This has resulted in the emergence of landscape ecotoxicology, a subdiscipline of ecotoxicology. However, landscape ecotoxicology has yet to become common practice in risk assessment due to the underdevelopment of techniques and a lack of standardized methods. In the present study, we demonstrate how geographic information systems (GISs) can serve as a standardized platform to integrate data, assess spatial patterns of ecotoxicological data for multiple species, and assess relationships between chemical mixture exposures and effects on biota for landscape ecotoxicological risks assessment. We use data collected under the Joint Oil Sands Monitoring Program in the Athabasca Oil Sands Region in Alberta, Canada. This dataset is composed of concentrations of contaminants including metals and polycyclic aromatic compounds, and health endpoints measured in 1100 biological samples, including tree swallows, amphibians, gull and tern eggs, plants, and mammals. We present 3 examples using a GIS as a platform and geospatial analysis to: 1) integrate data and assess spatial patterns of contaminant exposure in the region, 2) assess spatial patterns of exposures to complex mixtures, and 3) examine patterns of exposures and responses across the landscape. We summarize the methods used in the present study into a workflow for ease of use. The GIS methods allow researchers to identify hot spots of contamination, use georeferenced monitoring data to derive quantitative exposure-response relationships, and assess complex exposures with more realism. Environ Toxicol Chem 2019;38:2797-2810. © 2019 SETAC.}, } @article {pmid31431616, year = {2019}, author = {Zhang, L and Liu, W and Hou, K and Lin, J and Song, C and Zhou, C and Huang, B and Tong, X and Wang, J and Rhine, W and Jiao, Y and Wang, Z and Ni, R and Liu, M and Zhang, L and Wang, Z and Wang, Y and Li, X and Liu, S and Wang, Y}, title = {Air pollution exposure associates with increased risk of neonatal jaundice.}, journal = {Nature communications}, volume = {10}, number = {1}, pages = {3741}, pmid = {31431616}, issn = {2041-1723}, mesh = {Air Pollutants/analysis/*toxicity ; Air Pollution/*analysis ; Beijing ; Bilirubin/blood ; Female ; Humans ; Infant, Newborn ; Jaundice, Neonatal/*chemically induced ; Maternal Exposure/*adverse effects ; Particulate Matter/analysis/*toxicity ; Pregnancy ; *Prenatal Exposure Delayed Effects ; }, abstract = {Clinical experience suggests increased incidences of neonatal jaundice when air quality worsens, yet no studies have quantified this relationship. Here we reports investigations in 25,782 newborns showing an increase in newborn's bilirubin levels, the indicator of neonatal jaundice risk, by 0.076 (95% CI: 0.027-0.125), 0.029 (0.014-0.044) and 0.009 (95% CI: 0.002-0.016) mg/dL per μg/m[3] for PM2.5 exposure in the concentration ranges of 10-35, 35-75 and 75-200 μg/m[3], respectively. The response is 0.094 (0.077-0.111) and 0.161 (0.07-0.252) mg/dL per μg/m[3] for SO2 exposure at 10-15 and above 15 μg/m[3], respectively, and 0.351 (0.314-0.388) mg/dL per mg/m[3] for CO exposure. Bilirubin levels increase linearly with exposure time between 0 and 48 h. Positive relationship between maternal exposure and newborn bilirubin level is also quantitated. The jaundice-pollution relationship is not affected by top-of-atmosphere incident solar irradiance and atmospheric visibility. Improving air quality may therefore be key to lowering the neonatal jaundice risk.}, } @article {pmid31431594, year = {2019}, author = {Bygholm, A and Kappelsgaard, L}, title = {Avoiding Sedentary Work: Exploring Motivational Issues.}, journal = {Studies in health technology and informatics}, volume = {265}, number = {}, pages = {169-174}, doi = {10.3233/SHTI190158}, pmid = {31431594}, issn = {1879-8365}, mesh = {Exercise ; Humans ; *Motivation ; Qualitative Research ; *Sedentary Behavior ; Workplace ; }, abstract = {In this paper we present a qualitative study on motivations for avoiding sedentary work. Sedentary work has been recognized as a significant public health problem and many workplaces now invest in initiatives to support employees in avoiding it. The initiative in focus here include bikes, treadmills, step machines and adjustable workstations combined with a digital platform to keep track of activities and to make relevant information available. Experiences indicates that while employees are excited at the beginning, the use of exercise tools drop relatively fast. In order to understand motivation for use, clarify challenges and identify opportunities to support use of exercise tools through the digital platform we did interviews with employees and decision makers from four different companies. The overall challenge identified was pressure of busyness and reasons for use was due to individual objectives. Thus, in order to support employees in avoiding sedentary work the digital platform should provide facilities which allow for formulating and pursuing individual objective.}, } @article {pmid31430531, year = {2020}, author = {Souissi, M and Azelmat, J and Chaieb, K and Grenier, D}, title = {Antibacterial and anti-inflammatory activities of cardamom (Elettaria cardamomum) extracts: Potential therapeutic benefits for periodontal infections.}, journal = {Anaerobe}, volume = {61}, number = {}, pages = {102089}, doi = {10.1016/j.anaerobe.2019.102089}, pmid = {31430531}, issn = {1095-8274}, mesh = {Anti-Bacterial Agents/chemistry/*pharmacology ; Anti-Inflammatory Agents/chemistry/*pharmacology ; Biofilms/drug effects ; Cell Membrane Permeability ; Computational Biology/methods ; Cytokines/metabolism ; Elettaria/*chemistry ; Humans ; Lipopolysaccharides/immunology ; Macrophages/drug effects/immunology/metabolism ; Microbial Sensitivity Tests ; NF-kappa B/metabolism ; Periodontitis/diagnosis/drug therapy/microbiology ; Plant Extracts/chemistry/*pharmacology ; }, abstract = {Cardamom (Elettaria cardamomum) is a traditional aromatic plant for which several pharmacological properties have been associated. In this study, the antibacterial activity of two cardamom extracts (fruit and seeds), rich in volatile compounds, against major periodontal pathogens was evaluated. Moreover, the ability of the extracts to exert anti-inflammatory activity was tested. Both cardamom fruit and seed extracts exerted an antibacterial effect against Aggregatibacter actinomycetemcomitans, Fusobacterium nucleatum, Porphyromonas gingivalis, and Prevotella intermedia (minimum inhibitory concentrations: 0.5% [v/v], 0.25%, 0.062%, 0.125%, respectively and minimum bactericidal concentrations: 1%, 0.25%, 0.062%, 0.25%, respectively). The cell membrane of P. gingivalis was disrupted by a treatment with cardamom extracts suggesting the bactericidal mode of action. The extracts also inhibited biofilm formation although it correlated with a growth reduction. Moreover, the cardamom extracts significantly decreased the secretion of IL-1β, TNF-α, and IL-8 by lipopolysaccharide-stimulated macrophages. Evidence were brought that the anti-inflammatory activity may result from inhibition of the NF-κB signaling pathway. This study is the first to provide evidence that cardamom fruit and seed extracts through their antibacterial and anti-inflammatory properties may be therapeutic agents of interest against periodontal infections.}, } @article {pmid31430368, year = {2019}, author = {Sánchez-Herrero, JF and Frías-López, C and Escuer, P and Hinojosa-Alvarez, S and Arnedo, MA and Sánchez-Gracia, A and Rozas, J}, title = {The draft genome sequence of the spider Dysdera silvatica (Araneae, Dysderidae): A valuable resource for functional and evolutionary genomic studies in chelicerates.}, journal = {GigaScience}, volume = {8}, number = {8}, pages = {}, pmid = {31430368}, issn = {2047-217X}, mesh = {Animals ; Chromosome Mapping ; Computational Biology/methods ; Evolution, Molecular ; Gene Ontology ; *Genome ; Genome, Mitochondrial ; *Genomics/methods ; High-Throughput Nucleotide Sequencing ; Molecular Sequence Annotation ; Phenotype ; Phylogeny ; Spiders/*classification/*genetics ; }, abstract = {BACKGROUND: We present the draft genome sequence of Dysdera silvatica, a nocturnal ground-dwelling spider from a genus that has undergone a remarkable adaptive radiation in the Canary Islands.

RESULTS: The draft assembly was obtained using short (Illumina) and long (PaciBio and Nanopore) sequencing reads. Our de novo assembly (1.36 Gb), which represents 80% of the genome size estimated by flow cytometry (1.7 Gb), is constituted by a high fraction of interspersed repetitive elements (53.8%). The assembly completeness, using BUSCO and core eukaryotic genes, ranges from 90% to 96%. Functional annotations based on both ab initio and evidence-based information (including D. silvatica RNA sequencing) yielded a total of 48,619 protein-coding sequences, of which 36,398 (74.9%) have the molecular hallmark of known protein domains, or sequence similarity with Swiss-Prot sequences. The D. silvatica assembly is the first representative of the superfamily Dysderoidea, and just the second available genome of Synspermiata, one of the major evolutionary lineages of the "true spiders" (Araneomorphae).

CONCLUSIONS: Dysderoids, which are known for their numerous instances of adaptation to underground environments, include some of the few examples of trophic specialization within spiders and are excellent models for the study of cryptic female choice. This resource will be therefore useful as a starting point to study fundamental evolutionary and functional questions, including the molecular bases of the adaptation to extreme environments and ecological shifts, as well of the origin and evolution of relevant spider traits, such as the venom and silk.}, } @article {pmid31427469, year = {2019}, author = {Yu, Z and Lin, J and Li, QQ}, title = {Transcriptome Analyses of FY Mutants Reveal Its Role in mRNA Alternative Polyadenylation.}, journal = {The Plant cell}, volume = {31}, number = {10}, pages = {2332-2352}, pmid = {31427469}, issn = {1532-298X}, mesh = {3' Untranslated Regions/genetics ; Arabidopsis/*genetics ; Arabidopsis Proteins/*genetics/*metabolism ; Cleavage And Polyadenylation Specificity Factor/genetics ; Flowers/metabolism ; Gene Expression Profiling ; Gene Expression Regulation, Plant/genetics ; Gene Ontology ; Gene Regulatory Networks ; Mutation ; Phenotype ; Plant Roots/metabolism ; Polyadenylation/*genetics ; Protein Binding ; Protein Domains/genetics ; RNA 3' Polyadenylation Signals/*genetics ; RNA, Messenger/*genetics ; Transcriptome/*genetics ; WD40 Repeats/genetics ; mRNA Cleavage and Polyadenylation Factors/*genetics/*metabolism ; }, abstract = {A crucial step for mRNA polyadenylation is poly(A) signal recognition by trans-acting factors. The mammalian cleavage and polyadenylation specificity factor (CPSF) complex components CPSF30 and WD repeat-containing protein33 (WDR33) recognize the canonical AAUAAA for polyadenylation. In Arabidopsis (Arabidopsis thaliana), the flowering time regulator FY is the homolog of WDR33. However, its role in mRNA polyadenylation is poorly understood. Using poly(A) tag sequencing, we found that >50% of alternative polyadenylation (APA) events are altered in fy single mutants or double mutants with oxt6 (a null mutant of AtCPSF30), but mutation of the FY WD40-repeat has a stronger effect than deletion of the plant-unique Pro-Pro-Leu-Pro-Pro (PPLPP) domain. fy mutations disrupt AAUAAA or AAUAAA-like poly(A) signal recognition. Notably, A-rich signal usage is suppressed in the WD40-repeat mutation but promoted in PPLPP-domain deficiency. However, fy mutations do not aggravate the altered signal usage in oxt6 Furthermore, the WD40-repeat mutation shows a preference for 3' untranslated region shortening, but the PPLPP-domain deficiency shows a preference for lengthening. Interestingly, the WD40-repeat mutant exhibits shortened primary roots and late flowering with alteration of APA of related genes. Importantly, the long transcripts of two APA genes affected in fy are related to abiotic stress responses. These results reveal a conserved and specific role of FY in mRNA polyadenylation.}, } @article {pmid31427456, year = {2019}, author = {Ojeda, DI and Mattila, TM and Ruttink, T and Kujala, ST and Kärkkäinen, K and Verta, JP and Pyhäjärvi, T}, title = {Utilization of Tissue Ploidy Level Variation in de Novo Transcriptome Assembly of Pinus sylvestris.}, journal = {G3 (Bethesda, Md.)}, volume = {9}, number = {10}, pages = {3409-3421}, pmid = {31427456}, issn = {2160-1836}, mesh = {Cluster Analysis ; *Computational Biology/methods ; *Gene Expression Profiling/methods ; Molecular Sequence Annotation ; Organ Specificity/genetics ; Ovule ; Pinus sylvestris/*genetics ; *Ploidies ; *Transcriptome ; }, abstract = {Compared to angiosperms, gymnosperms lag behind in the availability of assembled and annotated genomes. Most genomic analyses in gymnosperms, especially conifer tree species, rely on the use of de novo assembled transcriptomes. However, the level of allelic redundancy and transcript fragmentation in these assembled transcriptomes, and their effect on downstream applications have not been fully investigated. Here, we assessed three assembly strategies for short-reads data, including the utility of haploid megagametophyte tissue during de novo assembly as single-allele guides, for six individuals and five different tissues in Pinus sylvestris We then contrasted haploid and diploid tissue genotype calls obtained from the assembled transcriptomes to evaluate the extent of paralog mapping. The use of the haploid tissue during assembly increased its completeness without reducing the number of assembled transcripts. Our results suggest that current strategies that rely on available genomic resources as guidance to minimize allelic redundancy are less effective than the application of strategies that cluster redundant assembled transcripts. The strategy yielding the lowest levels of allelic redundancy among the assembled transcriptomes assessed here was the generation of SuperTranscripts with Lace followed by CD-HIT clustering. However, we still observed some levels of heterozygosity (multiple gene fragments per transcript reflecting allelic redundancy) in this assembled transcriptome on the haploid tissue, indicating that further filtering is required before using these assemblies for downstream applications. We discuss the influence of allelic redundancy when these reference transcriptomes are used to select regions for probe design of exome capture baits and for estimation of population genetic diversity.}, } @article {pmid31426225, year = {2019}, author = {Isobe, A and Buenaventura, NT and Chastain, S and Chavanich, S and Cózar, A and DeLorenzo, M and Hagmann, P and Hinata, H and Kozlovskii, N and Lusher, AL and Martí, E and Michida, Y and Mu, J and Ohno, M and Potter, G and Ross, PS and Sagawa, N and Shim, WJ and Song, YK and Takada, H and Tokai, T and Torii, T and Uchida, K and Vassillenko, K and Viyakarn, V and Zhang, W}, title = {An interlaboratory comparison exercise for the determination of microplastics in standard sample bottles.}, journal = {Marine pollution bulletin}, volume = {146}, number = {}, pages = {831-837}, doi = {10.1016/j.marpolbul.2019.07.033}, pmid = {31426225}, issn = {1879-3363}, mesh = {Environmental Monitoring ; Laboratories/*standards ; Plastics/*analysis ; Polyethylene/analysis ; Polypropylenes/analysis ; Seawater/analysis ; }, abstract = {An interlaboratory comparison exercise was conducted to assess the consistency of microplastic quantification across several laboratories. The test samples were prepared by mixing one liter seawater free of plastics, microplastics made from polypropylene, high- and low-density polyethylene, and artificial particles in two plastic bottles, and analyzed concurrently in 12 experienced laboratories around the world. The minimum requirements to quantify microplastics were examined by comparing actual numbers of microplastics in these sample bottles with numbers measured in each laboratory. The uncertainty was due to pervasive errors derived from inaccuracies in measuring sizes and/or misidentification of microplastics, including both false recognition and overlooking. The size distribution of microplastics should be smoothed using a running mean with a length of >0.5 mm to reduce uncertainty to less than ±20%. The number of microplastics <1 mm was underestimated by 20% even when using the best practice for measuring microplastics in laboratories.}, } @article {pmid31426188, year = {2019}, author = {Fang, TH and Lin, CW and Kao, CH}, title = {Occurrence and distribution of pharmaceutical compounds in the Danshuei River Estuary and the Northern Taiwan Strait.}, journal = {Marine pollution bulletin}, volume = {146}, number = {}, pages = {509-520}, doi = {10.1016/j.marpolbul.2019.06.069}, pmid = {31426188}, issn = {1879-3363}, mesh = {Aquatic Organisms ; Carbamazepine/analysis ; *Environmental Monitoring ; Erythromycin/analysis ; Estuaries ; Gemfibrozil/analysis ; Pharmaceutical Preparations/*analysis ; Rivers ; Seawater ; Taiwan ; Water Pollutants, Chemical/*analysis ; }, abstract = {Ten pharmaceutically active compounds (PhACs) were determined in northern Taiwan estuarine waters and Taiwan Strait (TS) seawater. The ecological risk of these PhACs was assessed using risk quotient (RQ), which is the ratio of the measured maximum concentration to the predicted no-effect concentration. Six PhACs were detected within the estuarine waters. Caffeine concentration (130-718 ng l[-1]) was the highest among the analyzed PhACs. The distribution of PhACs in the Danshuei River Estuary generally exhibited addition behavior, except that caffeine showed conservative behavior. Carbamazepine, gemfibrozil, caffeine, and ketoprofen were detected in TS seawaters. Their concentrations follow the sequence: gemfibrozil > ketoprofen > caffeine > carbamazepine. The caffeine concentrations in TS seawaters were 2-3 orders of magnitude lower than those in Danshuei estuarine waters. With few exceptions for caffeine, erythromycin, and sulfadiazine posing low risk in some estuarine waters, most of the RQ values were <0.01, suggesting no adverse effects on aquatic organisms.}, } @article {pmid31426134, year = {2019}, author = {Gu, YG and Gao, YP}, title = {An unconstrained ordination- and GIS-based approach for identifying anthropogenic sources of heavy metal pollution in marine sediments.}, journal = {Marine pollution bulletin}, volume = {146}, number = {}, pages = {100-105}, doi = {10.1016/j.marpolbul.2019.06.008}, pmid = {31426134}, issn = {1879-3363}, mesh = {Environmental Monitoring/*methods ; *Geographic Information Systems ; Geologic Sediments/*analysis ; Hong Kong ; Humans ; Metals, Heavy/*analysis ; Multivariate Analysis ; Water Pollutants, Chemical/*analysis ; }, abstract = {A new method consisting of enrichment factor (EF) determination, nonmetric multidimensional scaling (NMS), and the geographic information system (GIS) technique was firstly developed to identify anthropogenic heavy metal sources in marine sediments of Hong Kong. Firstly, the EF was determined to differentiate between heavy metals originating from human and natural sources. Subsequently, NMS was applied to identify various source patterns of heavy metals, and the NMS score was calculated and spatially interpolated using GIS technology to evaluate the spatial influences of anthropogenic impacts in different areas. The concentrations of heavy metals in sediments of Hong Kong substantially exceeded their background values, demonstrating anthropogenic pollution. Two different types of human sources could be identified via NMS, one representing the industrial pollution discharges in the period from the 1960s to the 1980s before pollution control was introduced and one representing sewage discharge before the Tolo Harbour Action Plan in the mid-1980s.}, } @article {pmid31425588, year = {2019}, author = {Liu, Q and Guo, Y and Zhang, Y and Hu, W and Li, Y and Zhu, D and Zhou, Z and Wu, J and Chen, N and Zhou, XN}, title = {A chromosomal-level genome assembly for the insect vector for Chagas disease, Triatoma rubrofasciata.}, journal = {GigaScience}, volume = {8}, number = {8}, pages = {}, pmid = {31425588}, issn = {2047-217X}, mesh = {Animals ; Chagas Disease/parasitology/transmission ; *Chromosomes, Insect ; Computational Biology/methods ; *Genome ; *Genomics/methods ; Insect Vectors/classification/*genetics ; Molecular Sequence Annotation ; Phylogeny ; Repetitive Sequences, Nucleic Acid ; Triatoma/parasitology ; }, abstract = {BACKGROUND: Triatoma rubrofasciata is a widespread pathogen vector for Chagas disease, an illness that affects approximately 7 million people worldwide. Despite its importance to human health, its evolutionary origin has not been conclusively determined. A reference genome for T. rubrofasciata is not yet available.

FINDING: We have sequenced the genome of a female individual with T. rubrofasciatausing a single molecular DNA sequencing technology (i.e., PacBio Sequel platform) and have successfully reconstructed a whole-genome (680-Mb) assembly that covers 90% of the nuclear genome (757 Mb). Through Hi-C analysis, we have reconstructed full-length chromosomes of this female individual that has 13 unique chromosomes (2n = 24 = 22 + X1 + X2) with a contig N50 of 2.72 Mb and a scaffold N50 of 50.7 Mb. This genome has achieved a high base-level accuracy of 99.99%. This platinum-grade genome assembly has 12,691 annotated protein-coding genes. More than 95.1% of BUSCO genes were single-copy completed, indicating a high level of completeness of the genome.

CONCLUSION: The platinum-grade genome assembly and its annotation provide valuable information for future in-depth comparative genomics studies, including sexual determination analysis in T. rubrofasciata and the pathogenesis of Chagas disease.}, } @article {pmid31425547, year = {2019}, author = {Zheng, Y and Liu, H and Zhuo, Y and Li, Z and Liang, C and Wang, L}, title = {Dynamic changes and driving factors of wetlands in Inner Mongolia Plateau, China.}, journal = {PloS one}, volume = {14}, number = {8}, pages = {e0221177}, pmid = {31425547}, issn = {1932-6203}, mesh = {Agriculture/statistics & numerical data ; China ; *Conservation of Natural Resources ; Datasets as Topic ; Environmental Monitoring/*methods ; Linear Models ; Mining/statistics & numerical data ; Satellite Imagery/statistics & numerical data ; *Spatio-Temporal Analysis ; User-Computer Interface ; *Wetlands ; }, abstract = {Wetlands are one of the most critical resources in Inner Mongolia Plateau. However, the region has experienced severe wetland loss in the context of global change. To quantify the dynamic change and the related driving forces, we extracted wetland information using multi-temporal Landsat images between 1993 and 2013 using ArcGIS platform and man-machine interactive interpretation. Dynamically changing characteristics for the past 20 years were analyzed, including wetland types and spatial distribution patterns of the wetlands in Inner Mongolia. We also performed correlation analysis and generalized linear models to quantify the contribution of natural and human factors to the changes in natural wetland area. Our results indicated that the total area of wetlands was 42421.2 km2 in 1993, and decreased to 38912.4 km2 in 2013, a decline ratio of 8.3%. Meanwhile, all types of wetlands showed a trend of transformation into non-wetlands. Anthropogenic factors led to the loss of natural wetlands in Inner Mongolia. In grasslands, mining coal was the dominant driver for natural wetland loss, while in arable lands, agricultural encroachment and irrigation were the primary driving forces. These findings can provide meaningful information for improving sustainable wetlands management strategies according to local conditions in different sub-regions.}, } @article {pmid31422299, year = {2019}, author = {Barnes, MD and Goodell, W and Whittier, R and Falinski, KA and Callender, T and Htun, H and LeViol, C and Slay, H and Oleson, KLL}, title = {Decision analysis to support wastewater management in coral reef priority area.}, journal = {Marine pollution bulletin}, volume = {148}, number = {}, pages = {16-29}, pmid = {31422299}, issn = {1879-3363}, support = {EPA999999//Intramural EPA/United States ; }, mesh = {Animals ; Anthozoa/growth & development ; Conservation of Natural Resources/legislation & jurisprudence/*methods ; *Coral Reefs ; *Decision Support Techniques ; Environmental Exposure/prevention & control ; Hawaii ; Humans ; Sewage ; Waste Disposal, Fluid/legislation & jurisprudence/*methods ; }, abstract = {A cocktail of land-based sources of pollution threatens coral reef ecosystems, and addressing these has become a key management and policy challenge in the State of Hawai'i, other US territories, and globally. In West Maui, Hawai'i, nearly one quarter of all living corals were lost between 1995 and 2008. Onsite disposal systems (OSDS) for sewage leak contaminants into drinking water sources and nearshore waters. In recognition of this risk, the Hawai'i State Department of Health (DOH) is prioritizing areas for cesspool upgrades. Independently, we applied a decision analysis process to identify priority areas to address sewage pollution from OSDS in West Maui, with the objective of reducing nearshore coral reef exposure to pollution. The decision science approach is relevant to a broader context of coastal areas both statewide and worldwide which are struggling with identifying pollution mitigation actions on limited budgets.}, } @article {pmid31422092, year = {2019}, author = {Khan, K and Wahid, S and Khan, NH}, title = {Habitat characterization of sand fly vectors of leishmaniasis in Khyber Pakhtunkhwa, Pakistan.}, journal = {Acta tropica}, volume = {199}, number = {}, pages = {105147}, doi = {10.1016/j.actatropica.2019.105147}, pmid = {31422092}, issn = {1873-6254}, mesh = {Animals ; *Ecosystem ; Geographic Information Systems ; Insect Control ; *Insect Vectors ; Leishmaniasis/*transmission ; Pakistan ; *Phlebotomus ; }, abstract = {Leishmaniasis is currently prevalent in 98 countries including Pakistan, where its wide-spread. Phlebotomus papatasi Scopoli and Phlebotomus sergenti Parrot are suspected vectors of cutaneous leishmaniasis (CL) while P. Phlebotomus major Yakimoff and Phlebotomus hindustanicus Theodor are vectors of visceral leishmaniasis (VL) in the Khyber Pakhtunkhwa (KP) province of Pakistan. The present study identifies the complexity of environmental factors affecting the distribution of these vector sand fly species in KP. Sand fly habitats in the province were characterized from relevant published sources and analyzed using geographic information system (GIS) tools. Specific spatial analysis indicated that P. sergenti and P. papatasi were ecological generalists, found in diverse ecological settings, while P. major and P. hindustanicus were less frequent and had restricted foci in Khyber Pakhtunkhwa. We specifically observed a close association between elevation and existance of several sand fly species. P. sergenti primarily presented at high elevation while P. papatasi had distribution at low altitudinal ranges. P. major and P. hindustanicus were apparently limited to high altitudes in the northern areas of the province. This GIS-based spatial investigation of Phlebotomine vectors of leishmaniasis aims to provide a beneficial tools to medical entomologists, epidemiologists and public health workers for regional control of leishmaniasis. Outcomes from such spatial studies can be utilized in planning vector control initiatives so as to ensure proper allocation of funds for the region's integrated vector control program budget.}, } @article {pmid31421850, year = {2019}, author = {Wang, M and Dong, C and Gao, W}, title = {Evaluation of the growth, photosynthetic characteristics, antioxidant capacity, biomass yield and quality of tomato using aeroponics, hydroponics and porous tube-vermiculite systems in bio-regenerative life support systems.}, journal = {Life sciences in space research}, volume = {22}, number = {}, pages = {68-75}, doi = {10.1016/j.lssr.2019.07.008}, pmid = {31421850}, issn = {2214-5532}, mesh = {Biomass ; *Ecological Systems, Closed ; Hydroponics ; Solanum lycopersicum/chemistry/*growth & development ; Photosynthesis ; Spacecraft ; }, abstract = {The nutrient delivery system is one of the most important hardware components in tomato (Lycopersicon esculentum Mill.) production in Bio-regenerative Life Support Systems (BLSS) for future long-term space mission. The objective of this study was to investigate the influences of different nutrient delivery systems (aeroponics, hydroponics and porous tube-vermiculite) on the growth, photosynthetic characteristics, antioxidant capacity, biomass yield and quality of tomato during its life cycle. The results showed that the dry weight of aeroponics and porous tube-vermiculite treatment group was 1.95 and 1.93 g/fruit, but the value of hydroponics treatment group was only 1.56 g/fruit. Both tomato photosynthesis and stomatal conductance maximized at the development stage and then decreased later in senescent leaves. At the initial stage and the development stage, POD activities in the aeroponics treatment were higher than other two treatments, reached 3.6 U/mg prot and 4.6 U/mg prot, respectively. The fresh yield 431.3 g/plant of hydroponics treatment group was lower. At the same time, there were no significant differences among nutrient delivery systems in the per fruit fresh mass, which was 14.2-17.5 g/fruit.}, } @article {pmid31420657, year = {2020}, author = {Neupert, SD and Hannig, J}, title = {BFF: Bayesian, Fiducial, Frequentist Analysis of Age Effects in Daily Diary Data.}, journal = {The journals of gerontology. Series B, Psychological sciences and social sciences}, volume = {75}, number = {1}, pages = {67-79}, doi = {10.1093/geronb/gbz100}, pmid = {31420657}, issn = {1758-5368}, mesh = {Adolescent ; Adult ; Age Factors ; Aged ; Aged, 80 and over ; Aging/*physiology ; Bayes Theorem ; *Data Interpretation, Statistical ; *Ecological Momentary Assessment ; Emotional Regulation/*physiology ; Female ; Humans ; Male ; Middle Aged ; *Models, Statistical ; Multilevel Analysis ; Stress, Psychological/*physiopathology ; Young Adult ; }, abstract = {OBJECTIVES: We apply new statistical models to daily diary data to advance both methodological and conceptual goals. We examine age effects in within-person slopes in daily diary data and introduce Generalized Fiducial Inference (GFI), which provides a compromise between frequentist and Bayesian inference. We use daily stressor exposure data across six domains to generate within-person emotional reactivity slopes with daily negative affect. We test for systematic age differences and similarities in these reactivity slopes, which are inconsistent in previous research.

METHOD: One hundred and eleven older (aged 60-90) and 108 younger (aged 18-36) adults responded to daily stressor and negative affect questions each day for eight consecutive days, resulting in 1,438 total days. Daily stressor domains included arguments, avoided arguments, work/volunteer stressors, home stressors, network stressors, and health-related stressors.

RESULTS: Using Bayesian, GFI, and frequentist paradigms, we compared results for the six stressor domains with a focus on interpreting age effects in within-person reactivity. Multilevel models suggested null age effects in emotional reactivity across each of the paradigms within the domains of avoided arguments, work/volunteer stressors, home stressors, and health-related stressors. However, the models diverged with respect to null age effects in emotional reactivity to arguments and network stressors.

DISCUSSION: The three paradigms converged on null age effects in reactivity for four of the six stressor domains. GFI is a useful tool that provides additional information when making determinations regarding null age effects in within-person slopes. We provide the code for readers to apply these models to their own data.}, } @article {pmid31420516, year = {2019}, author = {Taylor, MA and Wilczek, AM and Roe, JL and Welch, SM and Runcie, DE and Cooper, MD and Schmitt, J}, title = {Large-effect flowering time mutations reveal conditionally adaptive paths through fitness landscapes in Arabidopsis thaliana.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {116}, number = {36}, pages = {17890-17899}, pmid = {31420516}, issn = {1091-6490}, mesh = {*Adaptation, Biological ; Arabidopsis/*physiology ; Biological Evolution ; Computational Biology/methods ; Flowers/*physiology ; Gene Expression Profiling ; Genetic Association Studies ; Genotype ; *Mutation ; Phenotype ; Seasons ; *Selection, Genetic ; Transcriptome ; }, abstract = {Contrary to previous assumptions that most mutations are deleterious, there is increasing evidence for persistence of large-effect mutations in natural populations. A possible explanation for these observations is that mutant phenotypes and fitness may depend upon the specific environmental conditions to which a mutant is exposed. Here, we tested this hypothesis by growing large-effect flowering time mutants of Arabidopsis thaliana in multiple field sites and seasons to quantify their fitness effects in realistic natural conditions. By constructing environment-specific fitness landscapes based on flowering time and branching architecture, we observed that a subset of mutations increased fitness, but only in specific environments. These mutations increased fitness via different paths: through shifting flowering time, branching, or both. Branching was under stronger selection, but flowering time was more genetically variable, pointing to the importance of indirect selection on mutations through their pleiotropic effects on multiple phenotypes. Finally, mutations in hub genes with greater connectedness in their regulatory networks had greater effects on both phenotypes and fitness. Together, these findings indicate that large-effect mutations may persist in populations because they influence traits that are adaptive only under specific environmental conditions. Understanding their evolutionary dynamics therefore requires measuring their effects in multiple natural environments.}, } @article {pmid31418877, year = {2019}, author = {Parish, CL and Feaster, DJ and Pereyra, MR and Alcaide, M and Cohen, M and Levin, S and Gustafson, D and Merenstein, D and Aouizerat, B and Donohue, J and Webster-Cyriaque, J and Wingood, G and Kempf, M and Metsch, LR}, title = {Dental insurance, dental care utilization, and perceived unmet dental needs in women living with HIV: Results from the Women's Interagency HIV Study.}, journal = {Journal of public health dentistry}, volume = {79}, number = {4}, pages = {343-351}, pmid = {31418877}, issn = {1752-7325}, support = {U01 AI103397/AI/NIAID NIH HHS/United States ; U01 AI031834/AI/NIAID NIH HHS/United States ; U01 AI035004/AI/NIAID NIH HHS/United States ; U01 AI034989/AI/NIAID NIH HHS/United States ; U01 AI034994/AI/NIAID NIH HHS/United States ; UL1 TR000454/TR/NCATS NIH HHS/United States ; U01 AI103401/AI/NIAID NIH HHS/United States ; UL1 TR000004/TR/NCATS NIH HHS/United States ; U01 AI103408/AI/NIAID NIH HHS/United States ; U01 HL146194/HL/NHLBI NIH HHS/United States ; U01 AI103390/AI/NIAID NIH HHS/United States ; U01 AI034993/AI/NIAID NIH HHS/United States ; P30 AI050410/AI/NIAID NIH HHS/United States ; U01 HD032632/HD/NICHD NIH HHS/United States ; U01 AI042590/AI/NIAID NIH HHS/United States ; }, mesh = {Aged ; Dental Care ; Female ; *HIV Infections ; Health Services Accessibility ; Health Services Needs and Demand ; Humans ; Insurance Coverage ; *Insurance, Dental ; Insurance, Health ; Medicaid ; Medicare ; United States ; }, abstract = {OBJECTIVES: Dental care is the most commonly cited unmet health-care service due to cost. Previous research has highlighted the unmet dental needs of people living with HIV (PLWH). Understanding associations among dental insurance availability, dental care utilization, and the presence of unmet dental needs among PLWH is a public health priority.

METHODS: Oral health surveys were collected cross-sectionally (April-October 2016) among 1,442 women living with HIV (WLWH) in the Women's Interagency HIV Study. Logistic regression models were used to analyze the association between having versus not having dental insurance by type (Ryan White, private, Medicaid/Medicare) and two primary outcomes: a) typical frequency of dental visits (at least annually, less than annually) and b) reporting an unmet dental need in the past 6 months.

RESULTS: All dental insurance types were associated with higher odds of receiving annual dental care and, for those with either Medicare/Medicaid or private insurance, lower odds of having an unmet dental need. When WLWH were asked to describe their oral health, poor self-reported condition was associated with both an unmet dental need (odds ratio [OR]: 4.52, 95 percent Confidence Interval [CI] [3.29-6.20]) and lower odds of annual dental care utilization (OR: 0.44, 95 percent CI [0.34-0.57]). Self-reported depressive symptom burden was also linked to having an unmet dental need (OR: 2.10, 95 percent CI [1.46-3.01]).

CONCLUSIONS: Dental insurance coverage increases dental care utilization and is associated with better oral health among WLWH. In the era of health-care reform, dental insurance coverage may be instrumental for enhancing treatment outcomes.}, } @article {pmid31418863, year = {2019}, author = {Serbin, SP and Wu, J and Ely, KS and Kruger, EL and Townsend, PA and Meng, R and Wolfe, BT and Chlus, A and Wang, Z and Rogers, A}, title = {From the Arctic to the tropics: multibiome prediction of leaf mass per area using leaf reflectance.}, journal = {The New phytologist}, volume = {224}, number = {4}, pages = {1557-1568}, doi = {10.1111/nph.16123}, pmid = {31418863}, issn = {1469-8137}, support = {WIS01809//U.S. Department of Agriculture/International ; NNX08AV07H/NASA/NASA/United States ; NNX12AQ28G/NASA/NASA/United States ; 1638720//National Science Foundation/International ; DE-SC0012704//Biological and Environmental Research/International ; NNX08AV07H/NASA/NASA/United States ; NNX12AQ28G/NASA/NASA/United States ; }, mesh = {Arctic Regions ; Databases, Factual ; Ecosystem ; *Models, Biological ; Models, Statistical ; Plant Leaves/*chemistry/*physiology ; Spatio-Temporal Analysis ; Spectrum Analysis/methods ; Tropical Climate ; }, abstract = {Leaf mass per area (LMA) is a key plant trait, reflecting tradeoffs between leaf photosynthetic function, longevity, and structural investment. Capturing spatial and temporal variability in LMA has been a long-standing goal of ecological research and is an essential component for advancing Earth system models. Despite the substantial variation in LMA within and across Earth's biomes, an efficient, globally generalizable approach to predict LMA is still lacking. We explored the capacity to predict LMA from leaf spectra across much of the global LMA trait space, with values ranging from 17 to 393 g m[-2] . Our dataset contained leaves from a wide range of biomes from the high Arctic to the tropics, included broad- and needleleaf species, and upper- and lower-canopy (i.e. sun and shade) growth environments. Here we demonstrate the capacity to rapidly estimate LMA using only spectral measurements across a wide range of species, leaf age and canopy position from diverse biomes. Our model captures LMA variability with high accuracy and low error (R[2] = 0.89; root mean square error (RMSE) = 15.45 g m[-2]). Our finding highlights the fact that the leaf economics spectrum is mirrored by the leaf optical spectrum, paving the way for this technology to predict the diversity of LMA in ecosystems across global biomes.}, } @article {pmid31418456, year = {2020}, author = {Chen, Y and Zhang, S}, title = {A Latent Gaussian process model for analysing intensive longitudinal data.}, journal = {The British journal of mathematical and statistical psychology}, volume = {73}, number = {2}, pages = {237-260}, doi = {10.1111/bmsp.12180}, pmid = {31418456}, issn = {2044-8317}, support = {//Spencer/NAEd postdoctoral fellowship/International ; }, mesh = {Affect ; Algorithms ; Bayes Theorem ; Borderline Personality Disorder/psychology ; Computer Simulation ; Data Interpretation, Statistical ; Depressive Disorder, Major/psychology ; Dysthymic Disorder/psychology ; Humans ; Likelihood Functions ; Longitudinal Studies ; *Models, Statistical ; Normal Distribution ; Probability ; Psychology/*statistics & numerical data ; Stochastic Processes ; Time Factors ; }, abstract = {Intensive longitudinal studies are becoming progressively more prevalent across many social science areas, and especially in psychology. New technologies such as smart-phones, fitness trackers, and the Internet of Things make it much easier than in the past to collect data for intensive longitudinal studies, providing an opportunity to look deep into the underlying characteristics of individuals under a high temporal resolution. In this paper we introduce a new modelling framework for latent curve analysis that is more suitable for the analysis of intensive longitudinal data than existing latent curve models. Specifically, through the modelling of an individual-specific continuous-time latent process, some unique features of intensive longitudinal data are better captured, including intensive measurements in time and unequally spaced time points of observations. Technically, the continuous-time latent process is modelled by a Gaussian process model. This model can be regarded as a semi-parametric extension of the classical latent curve models and falls under the framework of structural equation modelling. Procedures for parameter estimation and statistical inference are provided under an empirical Bayes framework and evaluated by simulation studies. We illustrate the use of the proposed model though the analysis of an ecological momentary assessment data set.}, } @article {pmid31418215, year = {2019}, author = {Wang, QL and Han, YJ and Zhang, LP and Feng, C and Wang, MT}, title = {[GIS-based ecological climate suitability regionalization for Cordyceps sinensis in Shiqu County, Sichuan Province, China.].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {30}, number = {7}, pages = {2137-2144}, doi = {10.13287/j.1001-9332.201907.022}, pmid = {31418215}, issn = {1001-9332}, mesh = {China ; Climate ; *Cordyceps ; Ecology ; *Geographic Information Systems ; Soil ; }, abstract = {Based on the biological characteristics of Cordyceps sinensis, combined with the spatial and temporal distribution characteristics of local agro-climatic resources and the investigation data of C. sinensis resources, we investigated the ecological climate suitability regionalization and the spatial distribution of C. sinensis in Shiqu County using mathematical statistics analysis, optimization method and GIS spatial analysis. We used altitude, mean annual temperature, mean annual precipitation, vegetation, and soil as the leading indicators and topographic gradient as the auxiliary indicators, as the main basis for the suitability zoning of C. sinensis resources. The results showed that C. sinensis grew in most of the townships in Shiqu County, with their distribution areas being fragmented and scattered, showing sporadic patches and blocks. They were mainly distributed in east and west parts of the county and in the Zhaqu River basin in the central part. The suitable distribution area for C. sinensis in Shiqu was 4000-4700 m above sea level, with mean annual temperature of -2.5-3 ℃ and mean annual precipitation of 550-850 mm. The growth environment was generally alpine mea-dow and subalpine meadow with good hydrophobicity and slope of 15°-50°. The suitable growth environment and meteorological conditions were beneficial to the growth and development of feeding plants and bat moths. The unsuitable area was in the high mountain area above the river wide valley area, pastoral area, wetland, or snowline.}, } @article {pmid31417135, year = {2019}, author = {de Melo, AT and Martho, KF and Roberto, TN and Nishiduka, ES and Machado, J and Brustolini, OJB and Tashima, AK and Vasconcelos, AT and Vallim, MA and Pascon, RC}, title = {The regulation of the sulfur amino acid biosynthetic pathway in Cryptococcus neoformans: the relationship of Cys3, Calcineurin, and Gpp2 phosphatases.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {11923}, pmid = {31417135}, issn = {2045-2322}, mesh = {Amino Acids, Sulfur/*biosynthesis ; *Biosynthetic Pathways/genetics ; Calcineurin/*metabolism ; Cryptococcus neoformans/genetics/growth & development/*metabolism/pathogenicity ; Fungal Proteins/*metabolism ; Gene Expression Regulation, Fungal ; Gene Ontology ; Green Fluorescent Proteins/metabolism ; Models, Biological ; Nutritional Status ; Phosphoric Monoester Hydrolases/*metabolism ; Protein Transport ; Proteomics ; Sulfur/metabolism ; Transcription Factors/metabolism ; Transcription, Genetic ; Virulence/genetics ; }, abstract = {Cryptococcosis is a fungal disease caused by C. neoformans. To adapt and survive in diverse ecological niches, including the animal host, this opportunistic pathogen relies on its ability to uptake nutrients, such as carbon, nitrogen, iron, phosphate, sulfur, and amino acids. Genetic circuits play a role in the response to environmental changes, modulating gene expression and adjusting the microbial metabolism to the nutrients available for the best energy usage and survival. We studied the sulfur amino acid biosynthesis and its implications on C. neoformans biology and virulence. CNAG_04798 encodes a BZip protein and was annotated as CYS3, which has been considered an essential gene. However, we demonstrated that CYS3 is not essential, in fact, its knockout led to sulfur amino acids auxotroph. Western blots and fluorescence microscopy indicated that GFP-Cys3, which is expressed from a constitutive promoter, localizes to the nucleus in rich medium (YEPD); the addition of methionine and cysteine as sole nitrogen source (SD-N + Met/Cys) led to reduced nuclear localization and protein degradation. By proteomics, we identified and confirmed physical interaction among Gpp2, Cna1, Cnb1 and GFP-Cys3. Deletion of the calcineurin and GPP2 genes in a GFP-Cys3 background demonstrated that calcineurin is required to maintain Cys3 high protein levels in YEPD and that deletion of GPP2 causes GFP-Cys3 to persist in the presence of sulfur amino acids. Global transcriptional profile of mutant and wild type by RNAseq revealed that Cys3 controls all branches of the sulfur amino acid biosynthesis, and sulfur starvation leads to induction of several amino acid biosynthetic routes. In addition, we found that Cys3 is required for virulence in Galleria mellonella animal model.}, } @article {pmid31415219, year = {2019}, author = {Simon-Soro, A and Sohn, MB and McGinniss, JE and Imai, I and Brown, MC and Knecht, VR and Bailey, A and Clarke, EL and Cantu, E and Li, H and Bittinger, K and Diamond, JM and Christie, JD and Bushman, FD and Collman, RG}, title = {Upper Respiratory Dysbiosis with a Facultative-dominated Ecotype in Advanced Lung Disease and Dynamic Change after Lung Transplant.}, journal = {Annals of the American Thoracic Society}, volume = {16}, number = {11}, pages = {1383-1391}, pmid = {31415219}, issn = {2325-6621}, support = {R01 HL113252/HL/NHLBI NIH HHS/United States ; KL2 TR001879/TR/NCATS NIH HHS/United States ; P30 AI045008/AI/NIAID NIH HHS/United States ; R61 HL137063/HL/NHLBI NIH HHS/United States ; R33 HL137063/HL/NHLBI NIH HHS/United States ; }, mesh = {Adult ; Aged ; Bacteria/classification/*isolation & purification ; Bacterial Infections/*microbiology ; Candida/isolation & purification ; Case-Control Studies ; DNA, Ribosomal Spacer/genetics ; Dysbiosis/*microbiology ; Ecotype ; Female ; Graft Rejection/microbiology ; Humans ; Invasive Pulmonary Aspergillosis/microbiology ; Lung Transplantation/*adverse effects ; Male ; Microbiota ; Middle Aged ; Oropharynx/*microbiology ; Postoperative Complications/microbiology ; RNA, Ribosomal, 16S/genetics ; Respiratory Tract Infections/microbiology ; }, abstract = {Rationale: The oropharyngeal microbiome is a primary source of lung microbiota, contributes to lower respiratory infection, and is also a driver of oral health.Objectives: We sought to understand oropharyngeal microbial communities in advanced lung disease, community dynamics after lung transplantation, and ecological features of dysbiosis.Methods: Oropharyngeal wash samples were obtained from individuals with end-stage disease awaiting transplantation (n = 22) and longitudinally from individuals at 6 weeks, 3 months, and 6 months after transplantation (n = 33), along with healthy control subjects (n = 14). Bacterial 16S and fungal internal transcribed spacer rRNA regions were deep-sequenced, and bacterial community respiratory patterns were imputed from taxonomic composition.Results: Healthy subjects' oropharyngeal microbiomes showed a gradient of community types reflecting relative enrichment of strictly anaerobic, aerobic, or facultative anaerobic bacteria. Patients with end-stage lung disease showed severe dysbiosis by both taxonomic composition and respiration phenotypes, with reduced richness and diversity, increased facultative and decreased aerobic bacteria, and absence of communities characterized by obligate aerobes. In patients at 6 weeks and 3 months post-transplant, richness and diversity were intermediate between healthy and pretransplant subjects, with near-normal distribution of community types. However, by 6 months post-transplant, oropharyngeal wash resembled the low-diversity facultative-dominated profile of pretransplant subjects. Community ecotype correlated with Candida abundance.Conclusions: End-stage lung disease is associated with marked upper respiratory tract dysbiosis involving both community structure and respiratory metabolism profiles of constituent bacteria. Dynamic changes occur after lung transplantation, with partial normalization early but later appearance of severe dysbiosis similar to pretransplant patients. Aberrant oropharyngeal communities may predispose to abnormal lung microbiota and infection risk both in advanced lung disease and after transplantation.}, } @article {pmid31413726, year = {2019}, author = {Kim, J and Marcusson-Clavertz, D and Yoshiuchi, K and Smyth, JM}, title = {Potential benefits of integrating ecological momentary assessment data into mHealth care systems.}, journal = {BioPsychoSocial medicine}, volume = {13}, number = {}, pages = {19}, pmid = {31413726}, issn = {1751-0759}, support = {UH2 AG052167/AG/NIA NIH HHS/United States ; UH3 AG052167/AG/NIA NIH HHS/United States ; }, abstract = {The advancement of wearable/ambulatory technologies has brought a huge change to data collection frameworks in recent decades. Mobile health (mHealth) care platforms, which utilize ambulatory devices to collect naturalistic and often intensively sampled data, produce innovative information of potential clinical relevance. For example, such data can inform clinical study design, recruitment approach, data analysis, and delivery of both "traditional" and novel (e.g., mHealth) interventions. We provide a conceptual overview of how data measured continuously or repeatedly via mobile devices (e.g., smartphone and body sensors) in daily life could be fruitfully used within a mHealth care system. We highlight the potential benefits of integrating ecological momentary assessment (EMA) into mHealth platforms for collecting, processing, and modeling data, and delivering and evaluating novel interventions in everyday life. Although the data obtained from EMA and related approaches may hold great potential benefits for mHealth care system, there are also implementation challenges; we briefly discuss the challenges to integrating EMA into mHealth care system.}, } @article {pmid31407344, year = {2020}, author = {Keenan, TF and Richardson, AD and Hufkens, K}, title = {On quantifying the apparent temperature sensitivity of plant phenology.}, journal = {The New phytologist}, volume = {225}, number = {2}, pages = {1033-1040}, doi = {10.1111/nph.16114}, pmid = {31407344}, issn = {1469-8137}, mesh = {Forests ; Plants/*metabolism ; *Temperature ; }, abstract = {Many plant phenological events are sensitive to temperature, leading to changes in the seasonal cycle of ecosystem function as the climate warms. To evaluate the current and future implications of temperature changes for plant phenology, researchers commonly use a metric of temperature sensitivity, which quantifies the change in phenology per degree change in temperature. Here, we examine the temperature sensitivity of phenology, and highlight conditions under which the widely used days-per-degree sensitivity approach is subject to methodological issues that can generate misleading results. We identify several factors, in particular the length of the period over which temperature is integrated, and changes in the statistical characteristics of the integrated temperature, that can affect the estimated apparent sensitivity to temperature. We show how the resulting artifacts can lead to spurious differences in apparent temperature sensitivity and artificial spatial gradients. Such issues are rarely considered in analyses of the temperature sensitivity of phenology. Given the issues identified, we advocate for process-oriented modelling approaches, informed by observations and with fully characterised uncertainties, as a more robust alternative to the simple days-per-degree temperature sensitivity metric. We also suggest approaches to minimise and assess spurious influences in the days-per-degree metric.}, } @article {pmid31404101, year = {2019}, author = {Meszaros, VA and Miller-Dickson, MD and Ogbunugafor, CB}, title = {Lexical Landscapes as large in silico data for examining advanced properties of fitness landscapes.}, journal = {PloS one}, volume = {14}, number = {8}, pages = {e0220891}, pmid = {31404101}, issn = {1932-6203}, mesh = {*Biological Evolution ; Computer Simulation ; Datasets as Topic ; Genetic Association Studies ; *Genetic Fitness ; *Genetics, Population ; Linguistics ; Models, Genetic ; }, abstract = {In silico approaches have served a central role in the development of evolutionary theory for generations. This especially applies to the concept of the fitness landscape, one of the most important abstractions in evolutionary genetics, and one which has benefited from the presence of large empirical data sets only in the last decade or so. In this study, we propose a method that allows us to generate enormous data sets that walk the line between in silico and empirical: word usage frequencies as catalogued by the Google ngram corpora. These data can be codified or analogized in terms of a multidimensional empirical fitness landscape towards the examination of advanced concepts-adaptive landscape by environment interactions, clonal competition, higher-order epistasis and countless others. We argue that the greater Lexical Landscapes approach can serve as a platform that offers an astronomical number of fitness landscapes for exploration (at least) or theoretical formalism (potentially) in evolutionary biology.}, } @article {pmid31401064, year = {2019}, author = {Zhang, D and Li, WX and Zou, H and Wu, SG and Li, M and Jakovlić, I and Zhang, J and Chen, R and Wang, G}, title = {Homoplasy or plesiomorphy? Reconstruction of the evolutionary history of mitochondrial gene order rearrangements in the subphylum Neodermata.}, journal = {International journal for parasitology}, volume = {49}, number = {10}, pages = {819-829}, doi = {10.1016/j.ijpara.2019.05.010}, pmid = {31401064}, issn = {1879-0135}, mesh = {Animals ; *Biological Evolution ; DNA, Helminth/chemistry/isolation & purification ; Datasets as Topic ; Gene Amplification ; Gene Order/*genetics ; Gene Rearrangement/*genetics ; Molecular Sequence Annotation ; Phylogeny ; Platyhelminths/classification/*genetics ; }, abstract = {Recent mitogenomic studies have exposed a gene order (GO) shared by two classes, four orders and 31 species ('common GO') within the flatworm subphylum Neodermata. There are two possible hypotheses for this phenomenon: convergent evolution (homoplasy) or shared ancestry (plesiomorphy). To test those, we conducted a meta-analysis on all available mitogenomes to infer the evolutionary history of GO in Neodermata. To improve the resolution, we added a newly sequenced mitogenome that exhibited the common GO, Euryhaliotrema johni (Ancyrocephalinae), to the dataset. Phylogenetic analyses conducted on two datasets (nucleotides of all 36 genes and amino acid sequences of 12 protein coding genes) and four algorithms (MrBayes, RAxML, IQ-TREE and PhyloBayes) produced topology instability towards the tips, so ancestral GO reconstructions were conducted using TreeREx and MLGO programs using all eight obtained topologies, plus three unique topologies from previous studies. The results consistently supported the second hypothesis, resolving the common GO as a plesiomorphic ancestral GO for Neodermata, Cestoda, Monopisthocotylea, Cestoda + Trematoda and Cestoda + Trematoda + Monopisthocotylea. This allowed us to trace the evolutionary GO scenarios from each common ancestor to its descendants amongst the Monogenea and Cestoda classes, and propose that the common GO was most likely retained throughout all of the common ancestors, leading to the extant species possessing the common GO. Neodermatan phylogeny inferred from GOs was largely incongruent with all 11 topologies described above, but it did support the mitogenomic dataset in resolving Polyopisthocotylea as the earliest neodermatan branch. Although highly derived GOs might be of some use in resolving isolated taxonomic and phylogenetic uncertainties, we conclude that, due to the discontinuous nature of their evolution, they tend to produce artefactual phylogenetic relationships, which makes them unsuitable for phylogenetic reconstruction in Neodermata. Wider and denser sampling of neodermatan mitogenomic sequences will be needed to infer the evolutionary pathways leading to the observed diversity of GOs with confidence.}, } @article {pmid31399826, year = {2019}, author = {Mariscal, C and Barahona, A and Aubert-Kato, N and Aydinoglu, AU and Bartlett, S and Cárdenas, ML and Chandru, K and Cleland, C and Cocanougher, BT and Comfort, N and Cornish-Bowden, A and Deacon, T and Froese, T and Giovannelli, D and Hernlund, J and Hut, P and Kimura, J and Maurel, MC and Merino, N and Moreno, A and Nakagawa, M and Peretó, J and Virgo, N and Witkowski, O and James Cleaves, H}, title = {Hidden Concepts in the History and Philosophy of Origins-of-Life Studies: a Workshop Report.}, journal = {Origins of life and evolution of the biosphere : the journal of the International Society for the Study of the Origin of Life}, volume = {49}, number = {3}, pages = {111-145}, pmid = {31399826}, issn = {1573-0875}, support = {ELSI Origins Network//John Templeton Foundation/ ; }, mesh = {Biology/*history ; Chemistry/*history ; *Historiography ; History, 16th Century ; History, 17th Century ; History, 18th Century ; History, 19th Century ; History, 20th Century ; History, 21st Century ; Informatics/*history ; Molecular Biology/history ; *Origin of Life ; Paleontology/*history ; Philosophy/*history ; }, abstract = {In this review, we describe some of the central philosophical issues facing origins-of-life research and provide a targeted history of the developments that have led to the multidisciplinary field of origins-of-life studies. We outline these issues and developments to guide researchers and students from all fields. With respect to philosophy, we provide brief summaries of debates with respect to (1) definitions (or theories) of life, what life is and how research should be conducted in the absence of an accepted theory of life, (2) the distinctions between synthetic, historical, and universal projects in origins-of-life studies, issues with strategies for inferring the origins of life, such as (3) the nature of the first living entities (the "bottom up" approach) and (4) how to infer the nature of the last universal common ancestor (the "top down" approach), and (5) the status of origins of life as a science. Each of these debates influences the others. Although there are clusters of researchers that agree on some answers to these issues, each of these debates is still open. With respect to history, we outline several independent paths that have led to some of the approaches now prevalent in origins-of-life studies. These include one path from early views of life through the scientific revolutions brought about by Linnaeus (von Linn.), Wöhler, Miller, and others. In this approach, new theories, tools, and evidence guide new thoughts about the nature of life and its origin. We also describe another family of paths motivated by a" circularity" approach to life, which is guided by such thinkers as Maturana & Varela, Gánti, Rosen, and others. These views echo ideas developed by Kant and Aristotle, though they do so using modern science in ways that produce exciting avenues of investigation. By exploring the history of these ideas, we can see how many of the issues that currently interest us have been guided by the contexts in which the ideas were developed. The disciplinary backgrounds of each of these scholars has influenced the questions they sought to answer, the experiments they envisioned, and the kinds of data they collected. We conclude by encouraging scientists and scholars in the humanities and social sciences to explore ways in which they can interact to provide a deeper understanding of the conceptual assumptions, structure, and history of origins-of-life research. This may be useful to help frame future research agendas and bring awareness to the multifaceted issues facing this challenging scientific question.}, } @article {pmid31399723, year = {2019}, author = {Bolyen, E and Rideout, JR and Dillon, MR and Bokulich, NA and Abnet, CC and Al-Ghalith, GA and Alexander, H and Alm, EJ and Arumugam, M and Asnicar, F and Bai, Y and Bisanz, JE and Bittinger, K and Brejnrod, A and Brislawn, CJ and Brown, CT and Callahan, BJ and Caraballo-Rodríguez, AM and Chase, J and Cope, EK and Da Silva, R and Diener, C and Dorrestein, PC and Douglas, GM and Durall, DM and Duvallet, C and Edwardson, CF and Ernst, M and Estaki, M and Fouquier, J and Gauglitz, JM and Gibbons, SM and Gibson, DL and Gonzalez, A and Gorlick, K and Guo, J and Hillmann, B and Holmes, S and Holste, H and Huttenhower, C and Huttley, GA and Janssen, S and Jarmusch, AK and Jiang, L and Kaehler, BD and Kang, KB and Keefe, CR and Keim, P and Kelley, ST and Knights, D and Koester, I and Kosciolek, T and Kreps, J and Langille, MGI and Lee, J and Ley, R and Liu, YX and Loftfield, E and Lozupone, C and Maher, M and Marotz, C and Martin, BD and McDonald, D and McIver, LJ and Melnik, AV and Metcalf, JL and Morgan, SC and Morton, JT and Naimey, AT and Navas-Molina, JA and Nothias, LF and Orchanian, SB and Pearson, T and Peoples, SL and Petras, D and Preuss, ML and Pruesse, E and Rasmussen, LB and Rivers, A and Robeson, MS and Rosenthal, P and Segata, N and Shaffer, M and Shiffer, A and Sinha, R and Song, SJ and Spear, JR and Swafford, AD and Thompson, LR and Torres, PJ and Trinh, P and Tripathi, A and Turnbaugh, PJ and Ul-Hasan, S and van der Hooft, JJJ and Vargas, F and Vázquez-Baeza, Y and Vogtmann, E and von Hippel, M and Walters, W and Wan, Y and Wang, M and Warren, J and Weber, KC and Williamson, CHD and Willis, AD and Xu, ZZ and Zaneveld, JR and Zhang, Y and Zhu, Q and Knight, R and Caporaso, JG}, title = {Author Correction: Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2.}, journal = {Nature biotechnology}, volume = {37}, number = {9}, pages = {1091}, doi = {10.1038/s41587-019-0252-6}, pmid = {31399723}, issn = {1546-1696}, abstract = {An amendment to this paper has been published and can be accessed via a link at the top of the paper.}, } @article {pmid31398909, year = {2019}, author = {Li, S and Yu, J and Li, Y and Zhang, H and Bao, X and Bian, J and Xu, C and Wang, X and Cai, X and Wang, Q and Wang, P and Guo, S and Miao, Y and Chen, S and Qin, Z and Dai, S}, title = {Heat-Responsive Proteomics of a Heat-Sensitive Spinach Variety.}, journal = {International journal of molecular sciences}, volume = {20}, number = {16}, pages = {}, pmid = {31398909}, issn = {1422-0067}, mesh = {Antioxidants/metabolism ; Computational Biology/methods ; Electrophoresis, Gel, Two-Dimensional ; *Heat-Shock Response/genetics ; Hot Temperature ; Molecular Sequence Annotation ; Phenotype ; Photosynthesis ; Plant Leaves/metabolism ; Plant Proteins/metabolism ; Protein Interaction Mapping ; Protein Interaction Maps ; *Proteome ; *Proteomics/methods ; Reactive Oxygen Species/metabolism ; Spinacia oleracea/*physiology ; }, abstract = {High temperatures seriously limit plant growth and productivity. Investigating heat-responsive molecular mechanisms is important for breeding heat-tolerant crops. In this study, heat-responsive mechanisms in leaves from a heat-sensitive spinach (Spinacia oleracea L.) variety Sp73 were investigated using two-dimensional gel electrophoresis (2DE)-based and isobaric tags for relative and absolute quantification (iTRAQ)-based proteomics approaches. In total, 257 heat-responsive proteins were identified in the spinach leaves. The abundance patterns of these proteins indicated that the photosynthesis process was inhibited, reactive oxygen species (ROS) scavenging pathways were initiated, and protein synthesis and turnover, carbohydrate and amino acid metabolism were promoted in the spinach Sp73 in response to high temperature. By comparing this with our previous results in the heat-tolerant spinach variety Sp75, we found that heat inhibited photosynthesis, as well as heat-enhanced ROS scavenging, stress defense pathways, carbohydrate and energy metabolism, and protein folding and turnover constituting a conservative strategy for spinach in response to heat stress. However, the heat-decreased biosynthesis of chlorophyll and carotenoid as well as soluble sugar content in the variety Sp73 was quite different from that in the variety Sp75, leading to a lower capability for photosynthetic adaptation and osmotic homeostasis in Sp73 under heat stress. Moreover, the heat-reduced activities of SOD and other heat-activated antioxidant enzymes in the heat-sensitive variety Sp73 were also different from the heat-tolerant variety Sp75, implying that the ROS scavenging strategy is critical for heat tolerance.}, } @article {pmid31398190, year = {2019}, author = {Boey, K and Shiokawa, K and Rajeev, S}, title = {Leptospira infection in rats: A literature review of global prevalence and distribution.}, journal = {PLoS neglected tropical diseases}, volume = {13}, number = {8}, pages = {e0007499}, pmid = {31398190}, issn = {1935-2735}, mesh = {Animals ; Databases, Factual ; Geographic Mapping ; Leptospira/classification/genetics/isolation & purification ; Leptospirosis/diagnosis/*epidemiology/*veterinary ; Prevalence ; Rats/*microbiology ; Serogroup ; }, abstract = {BACKGROUND: The role of rodents in Leptospira epidemiology and transmission is well known worldwide. Rats are known to carry different pathogenic serovars of Leptospira spp. capable of causing disease in humans and animals. Wild rats (Rattus spp.), especially the Norway/brown rat (Rattus norvegicus) and the black rat (R. rattus), are the most important sources of Leptospira infection, as they are abundant in urban and peridomestic environments. In this study, we compiled and summarized available data in the literature on global prevalence of Leptospira exposure and infection in rats, as well as compared the global distribution of Leptospira spp. in rats with respect to prevalence, geographic location, method of detection, diversity of serogroups/serovars, and species of rat.

METHODS: We conducted a thorough literature search using PubMed without restrictions on publication date as well as Google Scholar to manually search for other relevant articles. Abstracts were included if they described data pertaining to Leptospira spp. in rats (Rattus spp.) from any geographic region around the world, including reviews. The data extracted from the articles selected included the author(s), year of publication, geographic location, method(s) of detection used, species of rat(s), sample size, prevalence of Leptospira spp. (overall and within each rat species), and information on species, serogroups, and/or serovars of Leptospira spp. detected.

FINDINGS: A thorough search on PubMed retrieved 303 titles. After screening the articles for duplicates and inclusion/exclusion criteria, as well as manual inclusion of relevant articles, 145 articles were included in this review. Leptospira prevalence in rats varied considerably based on geographic location, with some reporting zero prevalence in countries such as Madagascar, Tanzania, and the Faroe Islands, and others reporting as high as >80% prevalence in studies done in Brazil, India, and the Philippines. The top five countries that were reported based on number of articles include India (n = 13), Malaysia (n = 9), Brazil (n = 8), Thailand (n = 7), and France (n = 6). Methods of detecting or isolating Leptospira spp. also varied among studies. Studies among different Rattus species reported a higher Leptospira prevalence in R. norvegicus. The serovar Icterohaemorrhagiae was the most prevalent serovar reported in Rattus spp. worldwide. Additionally, this literature review provided evidence for Leptospira infection in laboratory rodent colonies within controlled environments, implicating the zoonotic potential to laboratory animal caretakers.

CONCLUSIONS: Reports on global distribution of Leptospira infection in rats varies widely, with considerably high prevalence reported in many countries. This literature review emphasizes the need for enhanced surveillance programs using standardized methods for assessing Leptospira exposure or infection in rats. This review also demonstrated several weaknesses to the current methods of reporting the prevalence of Leptospira spp. in rats worldwide. As such, this necessitates a call for standardized protocols for the testing and reporting of such studies, especially pertaining to the diagnostic methods used. A deeper understanding of the ecology and epidemiology of Leptospira spp. in rats in urban environments is warranted. It is also pertinent for rat control programs to be proposed in conjunction with increased efforts for public awareness and education regarding leptospirosis transmission and prevention.}, } @article {pmid31397847, year = {2019}, author = {Marizcurrena, JJ and Herrera, LM and Costábile, A and Morales, D and Villadóniga, C and Eizmendi, A and Davyt, D and Castro-Sowinski, S}, title = {Validating biochemical features at the genome level in the Antarctic bacterium Hymenobacter sp. strain UV11.}, journal = {FEMS microbiology letters}, volume = {366}, number = {14}, pages = {}, doi = {10.1093/femsle/fnz177}, pmid = {31397847}, issn = {1574-6968}, mesh = {Antarctic Regions ; Chromatography, High Pressure Liquid ; Computational Biology/methods ; Cytophagaceae/classification/*genetics/isolation & purification/*metabolism ; *Genome, Bacterial ; *Genomics/methods ; Metabolic Networks and Pathways ; Pigments, Biological/chemistry/metabolism ; Radiation Tolerance ; }, abstract = {We present experimental data that complement and validate some biochemical features at the genome level in the UVC-resistant Antarctic bacterium Hymenobacter sp. UV11 strain. The genome was sequenced, assembled and annotated. It has 6 096 246 bp, a GC content of 60.6% and 5155 predicted genes. The secretome analysis, by combining in silico predictions with shotgun proteomics data, showed that UV11 strain produces extracellular proteases and carbohydrases with potential biotechnological uses. We observed the formation of outer membrane vesicles, mesosomes and carbon-storage compounds by using transmission electron microscopy. The in silico analysis of the genome revealed the presence of genes involved in the metabolism of glycogen-like molecules and starch. By HPLC-UV-Vis analysis and 1H-NMR spectra, we verified that strain UV11 produces xanthophyll-like carotenoids such as 2'-hydroxyflexixanthin, and the in silico analysis showed that this bacterium has genes involved in the biosynthesis of cathaxanthin, zeaxanthin and astaxanthin. We also found genes involved in the repair of UV-damaged DNA such as a photolyase, the nucleotide excision repair system and the production of ATP-dependent proteases that are important cellular components involved in the endurance to physiological stresses. This information will help us to better understand the ecological role played by Hymenobacter strains in the extreme Antarctic environment.}, } @article {pmid31397053, year = {2019}, author = {Liu, Y and Schwalm, CR and Samuels-Crow, KE and Ogle, K}, title = {Ecological memory of daily carbon exchange across the globe and its importance in drylands.}, journal = {Ecology letters}, volume = {22}, number = {11}, pages = {1806-1816}, doi = {10.1111/ele.13363}, pmid = {31397053}, issn = {1461-0248}, support = {DBI#1458867//NSF/ ; DE-AC05-00OR22725 //DOE/ ; }, mesh = {*Carbon ; Carbon Cycle ; Carbon Dioxide ; Ecology ; *Ecosystem ; }, abstract = {How do antecedent (past) conditions influence land-carbon dynamics after those conditions no longer persist? In particular, quantifying such memory effects associated with the influence of past environmental (exogenous) and biological (endogenous) conditions is crucial for understanding and predicting the carbon cycle. Here we show, using data from 42 eddy covariance sites across six major biomes, that ecological memory-decomposed into environmental and biological memory components-of daily net carbon exchange (NEE) is critical for understanding the land-carbon metabolism, especially in drylands for which memory explains ~ 32% of the variation in NEE. The strong environmental memory in drylands was primarily driven by short- and long-term moisture status. Moreover, the strength of environmental memory scales with increasing water stress. This universal scaling relationship, emerging within and among major biomes, suggests a potential adaptive response to water limitation. Our findings underscore the necessity of considering ecological memory in experiments, observations and modelling.}, } @article {pmid31395652, year = {2019}, author = {Madritsch, S and Wischnitzki, E and Kotrade, P and Ashoub, A and Burg, A and Fluch, S and Brüggemann, W and Sehr, EM}, title = {Elucidating Drought Stress Tolerance in European Oaks Through Cross-Species Transcriptomics.}, journal = {G3 (Bethesda, Md.)}, volume = {9}, number = {10}, pages = {3181-3199}, pmid = {31395652}, issn = {2160-1836}, mesh = {*Adaptation, Biological ; Antioxidants/metabolism ; Computational Biology/methods ; Crosses, Genetic ; *Droughts ; Gene Expression Profiling ; *Gene Expression Regulation, Plant ; Gene Ontology ; High-Throughput Nucleotide Sequencing ; Molecular Sequence Annotation ; Quercus/classification/*physiology ; Species Specificity ; Stress, Physiological/*genetics ; *Transcriptome ; }, abstract = {The impact of climate change that comes with a dramatic increase of long periods of extreme summer drought associated with heat is a fundamental challenge for European forests. As a result, forests are expected to shift their distribution patterns toward north-east, which may lead to a dramatic loss in value of European forest land. Consequently, unraveling key processes that underlie drought stress tolerance is not only of great scientific but also of utmost economic importance for forests to withstand future heat and drought wave scenarios. To reveal drought stress-related molecular patterns we applied cross-species comparative transcriptomics of three major European oak species: the less tolerant deciduous pedunculate oak (Quercus robur), the deciduous but quite tolerant pubescent oak (Q. pubescens), and the very tolerant evergreen holm oak (Q. ilex). We found 415, 79, and 222 differentially expressed genes during drought stress in Q. robur, Q. pubescens, and Q. ilex, respectively, indicating species-specific response mechanisms. Further, by comparative orthologous gene family analysis, 517 orthologous genes could be characterized that may play an important role in drought stress adaptation on the genus level. New regulatory candidate pathways and genes in the context of drought stress response were identified, highlighting the importance of the antioxidant capacity, the mitochondrial respiration machinery, the lignification of the water transport system, and the suppression of drought-induced senescence - providing a valuable knowledge base that could be integrated in breeding programs in the face of climate change.}, } @article {pmid31393867, year = {2019}, author = {Funk, F and Hauert, C}, title = {Directed migration shapes cooperation in spatial ecological public goods games.}, journal = {PLoS computational biology}, volume = {15}, number = {8}, pages = {e1006948}, pmid = {31393867}, issn = {1553-7358}, mesh = {Computational Biology ; *Cooperative Behavior ; Ecosystem ; *Game Theory ; Humans ; Microbial Interactions ; Microbiota ; *Models, Biological ; *Population Dynamics/statistics & numerical data ; }, abstract = {From the microscopic to the macroscopic level, biological life exhibits directed migration in response to environmental conditions. Chemotaxis enables microbes to sense and move towards nutrient-rich regions or to avoid toxic ones. Socio-economic factors drive human populations from rural to urban areas. The effect of collective movement is especially significant when triggered in response to the generation of public goods. Microbial communities can, for instance, alter their environment through the secretion of extracellular substances. Some substances provide antibiotic-resistance, others provide access to nutrients or promote motility. However, in all cases the maintenance of public goods requires costly cooperation and is consequently susceptible to exploitation. The threat of exploitation becomes even more acute with motile individuals because defectors can avoid the consequences of their cheating. Here, we propose a model to investigate the effects of targeted migration and analyze the interplay between social conflicts and migration in ecological public goods. In particular, individuals can locate attractive regions by moving towards higher cooperator densities or avoid unattractive regions by moving away from defectors. Both migration patterns not only shape an individual's immediate environment but also affects the entire population. For example, defectors hunting cooperators have a homogenizing effect on population densities. This limits the production of the public good and hence inhibits the growth of the population. In contrast, aggregating cooperators promote the spontaneous formation of patterns through heterogeneous density distributions. The positive feedback between cooperator aggregation and public goods production, however, poses analytical and numerical challenges due to its tendency to develop discontinuous distributions. Thus, different modes of directed migration bear the potential to enhance or inhibit the emergence of complex and sometimes dynamic spatial arrangements. Interestingly, whenever patterns emerge, cooperation is promoted, on average, population densities rise, and the risk of extinction is reduced.}, } @article {pmid31387478, year = {2019}, author = {Levakova, M and Kostal, L and Monsempès, C and Lucas, P and Kobayashi, R}, title = {Adaptive integrate-and-fire model reproduces the dynamics of olfactory receptor neuron responses in a moth.}, journal = {Journal of the Royal Society, Interface}, volume = {16}, number = {157}, pages = {20190246}, pmid = {31387478}, issn = {1742-5662}, mesh = {Action Potentials/*physiology ; *Adaptation, Physiological ; Animals ; Electrophysiological Phenomena ; Male ; Models, Biological ; Moths/*physiology ; Olfactory Receptor Neurons/drug effects/*physiology ; Sex Attractants/*pharmacology ; }, abstract = {In order to understand how olfactory stimuli are encoded and processed in the brain, it is important to build a computational model for olfactory receptor neurons (ORNs). Here, we present a simple and reliable mathematical model of a moth ORN generating spikes. The model incorporates a simplified description of the chemical kinetics leading to olfactory receptor activation and action potential generation. We show that an adaptive spike threshold regulated by prior spike history is an effective mechanism for reproducing the typical phasic-tonic time course of ORN responses. Our model reproduces the response dynamics of individual neurons to a fluctuating stimulus that approximates odorant fluctuations in nature. The parameters of the spike threshold are essential for reproducing the response heterogeneity in ORNs. The model provides a valuable tool for efficient simulations of olfactory circuits.}, } @article {pmid31384683, year = {2019}, author = {Yared, S and Gebresilassie, A and Abbasi, I and Aklilu, E and Kirstein, OD and Balkew, M and Brown, AS and Clouse, RM and Warburg, A and Hailu, A and Gebre-Michael, T}, title = {A molecular analysis of sand fly blood meals in a visceral leishmaniasis endemic region of northwestern Ethiopia reveals a complex host-vector system.}, journal = {Heliyon}, volume = {5}, number = {7}, pages = {e02132}, pmid = {31384683}, issn = {2405-8440}, support = {T32 HG002295/HG/NHGRI NIH HHS/United States ; }, abstract = {BACKGROUND: Visceral leishmaniasis (VL, or "kala-azar") is a major cause of disability and death, especially in East Africa. Its vectors, sand flies (Diptera: Psychodidae: Phlebotominae), are poorly controlled and guarded against in these regions, owing in part to a lack of understanding about their feeding behavior.

METHODS: A total of 746 freshly fed female sand flies were collected in five population centers in Kafta Humera (northwestern Ethiopia), where VL is endemic. Flies were collected from habitats that ranged from inside houses to open fields, using light traps and sticky traps. Sources of sand fly blood meals were identified using enzyme-linked immunosorbent assays (ELISA) and DNA amplification with reverse-line blot analysis (PCR-RLB); 632 specimens were screened using ELISA, 408 of which had identifiable blood meals, and 114 were screened using PCR-RLB, 53 of which yielded identifications. Fly species determinations were based on morphology, and those specimens subjected to PCR-RLB were also screened for Leishmania parasites using conventional PCR to amplify the nuclear marker ITS1 (internal transcribed spacer 1) with Leishmania-specific primers.

RESULTS: More than three-fourths of all sand flies collected were Phlebotomus orientalis, and the remaining portion was comprised of nine other species. Nearly two-thirds of P. orientalis specimens were collected at village peripheries. The most common blood source for all flies was donkey (33.9% of all identifications), followed by cow (24.2%), human (17.6%), dog (11.8%), and goat or sheep (8.6%); mixtures of blood meals from different sources were found in 28.2% of all flies screened. Unidentified blood meals, presumably from wildlife, not domestic animals, were significantly higher in farm fields. Leishmania parasites were not detected in any of the 114 flies screened, not surprising given an expected infection rate of 1-5 out of 1,000. Meals that included a mixture of human and cow blood were significantly more frequent relative to all cow meals than human blood meals were to non-cow meals, suggesting a zoopotentiative interaction between cows and humans in this system.

CONCLUSIONS: Habitat and host preferences of sand fly vectors in Kafta Humera confirmed the finding of previous reports that the main vector in the region, Phlebotomus orientalis, is a highly opportunistic feeder that prefers large animals and is most commonly found at village peripheries. These results were similar to those of a previous study conducted in a nearby region (Tahtay Adiabo), except for the role of cattle on the prevalence of human blood meals. Preliminary examinations of blood meal data from different settings point to the need for additional surveys and field experiments to understand the role of livestock on biting risks.}, } @article {pmid31383970, year = {2019}, author = {Zhang, X and Zhang, S and Zhao, Q and Ming, R and Tang, H}, title = {Assembly of allele-aware, chromosomal-scale autopolyploid genomes based on Hi-C data.}, journal = {Nature plants}, volume = {5}, number = {8}, pages = {833-845}, doi = {10.1038/s41477-019-0487-8}, pmid = {31383970}, issn = {2055-0278}, mesh = {*Algorithms ; *Alleles ; *Chromatin Assembly and Disassembly ; Datasets as Topic ; *Genome, Plant ; Oryza/genetics ; Plants/*genetics ; *Polyploidy ; Saccharum/genetics ; }, abstract = {Construction of chromosome-level assembly is a vital step in achieving the goal of a 'Platinum' genome, but it remains a major challenge to assemble and anchor sequences to chromosomes in autopolyploid or highly heterozygous genomes. High-throughput chromosome conformation capture (Hi-C) technology serves as a robust tool to dramatically advance chromosome scaffolding; however, existing approaches are mostly designed for diploid genomes and often with the aim of reconstructing a haploid representation, thereby having limited power to reconstruct chromosomes for autopolyploid genomes. We developed a novel algorithm (ALLHiC) that is capable of building allele-aware, chromosomal-scale assembly for autopolyploid genomes using Hi-C paired-end reads with innovative 'prune' and 'optimize' steps. Application on simulated data showed that ALLHiC can phase allelic contigs and substantially improve ordering and orientation when compared to other mainstream Hi-C assemblers. We applied ALLHiC on an autotetraploid and an autooctoploid sugar-cane genome and successfully constructed the phased chromosomal-level assemblies, revealing allelic variations present in these two genomes. The ALLHiC pipeline enables de novo chromosome-level assembly of autopolyploid genomes, separating each allele. Haplotype chromosome-level assembly of allopolyploid and heterozygous diploid genomes can be achieved using ALLHiC, overcoming obstacles in assembling complex genomes.}, } @article {pmid31383758, year = {2019}, author = {Guerrieri, R and Belmecheri, S and Ollinger, SV and Asbjornsen, H and Jennings, K and Xiao, J and Stocker, BD and Martin, M and Hollinger, DY and Bracho-Garrillo, R and Clark, K and Dore, S and Kolb, T and Munger, JW and Novick, K and Richardson, AD}, title = {Disentangling the role of photosynthesis and stomatal conductance on rising forest water-use efficiency.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {116}, number = {34}, pages = {16909-16914}, pmid = {31383758}, issn = {1091-6490}, mesh = {Carbon/*metabolism ; Carbon Dioxide/metabolism ; *Forests ; *Models, Biological ; Photosynthesis/*physiology ; Plant Stomata/*physiology ; United States ; Water/*metabolism ; }, abstract = {Multiple lines of evidence suggest that plant water-use efficiency (WUE)-the ratio of carbon assimilation to water loss-has increased in recent decades. Although rising atmospheric CO2 has been proposed as the principal cause, the underlying physiological mechanisms are still being debated, and implications for the global water cycle remain uncertain. Here, we addressed this gap using 30-y tree ring records of carbon and oxygen isotope measurements and basal area increment from 12 species in 8 North American mature temperate forests. Our goal was to separate the contributions of enhanced photosynthesis and reduced stomatal conductance to WUE trends and to assess consistency between multiple commonly used methods for estimating WUE. Our results show that tree ring-derived estimates of increases in WUE are consistent with estimates from atmospheric measurements and predictions based on an optimal balancing of carbon gains and water costs, but are lower than those based on ecosystem-scale flux observations. Although both physiological mechanisms contributed to rising WUE, enhanced photosynthesis was widespread, while reductions in stomatal conductance were modest and restricted to species that experienced moisture limitations. This finding challenges the hypothesis that rising WUE in forests is primarily the result of widespread, CO2-induced reductions in stomatal conductance.}, } @article {pmid31383721, year = {2019}, author = {Dodds, KG and McEwan, JC and Brauning, R and van Stijn, TC and Rowe, SJ and McEwan, KM and Clarke, SM}, title = {Exclusion and Genomic Relatedness Methods for Assignment of Parentage Using Genotyping-by-Sequencing Data.}, journal = {G3 (Bethesda, Md.)}, volume = {9}, number = {10}, pages = {3239-3247}, pmid = {31383721}, issn = {2160-1836}, mesh = {Algorithms ; Alleles ; Breeding ; Databases, Genetic ; Family ; Gene Frequency ; *Genomics/methods ; *Genotype ; *Genotyping Techniques ; Microsatellite Repeats ; Models, Genetic ; *Pedigree ; Sequence Analysis, DNA ; }, abstract = {Genotypes are often used to assign parentage in agricultural and ecological settings. Sequencing can be used to obtain genotypes but does not provide unambiguous genotype calls, especially when sequencing depth is low in order to reduce costs. In that case, standard parentage analysis methods no longer apply. A strategy for using low-depth sequencing data for parentage assignment is developed here. It entails the use of relatedness estimates along with a metric termed excess mismatch rate which, for parent-offspring pairs or trios, is the difference between the observed mismatch rate and the rate expected under a model of inheritance and allele reads without error. When more than one putative parent has similar statistics, bootstrapping can provide a measure of the relatedness similarity. Putative parent-offspring trios can be further checked for consistency by comparing the offspring's estimated inbreeding to half the parent relatedness. Suitable thresholds are required for each metric. These methods were applied to a deer breeding operation consisting of two herds of different breeds. Relatedness estimates were more in line with expectation when the herds were analyzed separately than when combined, although this did not alter which parents were the best matches with each offspring. Parentage results were largely consistent with those based on a microsatellite parentage panel with three discordant parent assignments out of 1561. Two models are investigated to allow the parentage metrics to be calculated with non-random selection of alleles. The tools and strategies given here allow parentage to be assigned from low-depth sequencing data.}, } @article {pmid31381467, year = {2019}, author = {Pasquini, G and Kunej, T}, title = {A Map of the microRNA Regulatory Networks Identified by Experimentally Validated microRNA-Target Interactions in Five Domestic Animals: Cattle, Pig, Sheep, Dog, and Chicken.}, journal = {Omics : a journal of integrative biology}, volume = {23}, number = {9}, pages = {448-456}, doi = {10.1089/omi.2019.0082}, pmid = {31381467}, issn = {1557-8100}, mesh = {Animals ; Animals, Domestic/*genetics ; Cattle ; Chickens ; Computational Biology ; Dogs ; Gene Expression Profiling ; *Gene Expression Regulation ; *Gene Regulatory Networks ; MicroRNAs/*genetics ; *RNA Interference ; RNA, Messenger/*genetics ; Sheep ; Swine ; *Transcriptome ; }, abstract = {Domestic animals are members of the broader ecological context, in which humans are situated. Yet, genomics and systems science research have lagged behind and been relatively underappreciated in domestic animals compared to human genetics/genomics. Harnessing big data calls for omics data mapping studies in a broad range of mammals. To this end, microRNAs (miRNAs) regulate posttranscriptional expression of target genes, hence, governing different biological pathways and physiological processes. The knowledge of miRNA regulatory networks and maps is important for understanding regulation of gene expression and functions in both humans and domestic animals. However, complete miRNA regulatory networks have not yet been described in all species, particularly in domestic animals. We report here an original analysis so as to map the miRNA regulatory networks in domestic animals based on miRNA-target interactions (MTIs). Validated MTIs for five species; cattle, pig, sheep, dog, and chicken were extracted from the miRTarBase. miRNA regulomes were visualized using the Cytoscape software. The data in cattle, chicken, and pig were sufficient to visualize networks, identify central molecules, and subnetworks associated with the same phenotype; however, the MTI data in dog and sheep are still limited. We found several hub genes with large number of interactions, for example, 1 miRNA (bta-miR-17-5p) interacting with 27 genes and 7 miRNAs interacting with the same gene (tumor necrosis factor [TNF]) in cattle. In addition, two single-nucleotide polymorphisms were identified within the seed region of a previously demonstrated MTI, namely, between HMGB3 (high mobility group box 3) gene and bta-miR-17-5p. In summary, this miRNA regulome mapping study will enable and guide further studies of genome function in mammals with a view to applications in human as well as veterinary medicine. Furthermore, these miRNA regulomes can help to clarify fundamental pathways in cell biology and reveal molecular insights on phenotypic trait variability in common complex diseases and response phenotypes of drugs or other health interventions for precision medicine in the future.}, } @article {pmid31380068, year = {2019}, author = {Liu, W and Tanimura, A and Nagara, Y and Watanabe, T and Maegawa, S and Toyohara, H}, title = {Wetland environmental bioreactor system contributes to the decomposition of cellulose.}, journal = {Ecology and evolution}, volume = {9}, number = {14}, pages = {8013-8024}, pmid = {31380068}, issn = {2045-7758}, abstract = {Recently, numerous species of aquatic invertebrates inhabiting wetlands have been shown to possess endogenous cellulase, following the discovery that termites have cellulase genes encoded in their own genome rather than relying on symbiotic bacteria for decomposing cellulose. Wetlands have been empirically shown to play an important role in the decomposition of land-originating hard-to-degrade polysaccharides such as cellulose. However, the mechanism that connects the cellulase producer and the wetlands remains unknown, which makes it very difficult to evaluate the ecological function of wetlands. Here we found that a macrobenthic bivalve, Corbicula japonica, secretes its cellulase to the wetland sediment. Secreted cellulases are immobilized in the components of the sediment. Moreover, adding cellulose or glucose to C. japonica could trigger its cellulase secretion level. These findings suggest a novel wetland cellulose decomposition mechanism. The decomposition ability of wetlands was previously ascribed only to microbes and/or invertebrates that contain cellulases. Our findings suggest that benthic animals supply wetlands with their enzymes as decomposition agents, while wetland sediments serve as immobilization scaffolds for the enzymes. This system, which was named by us an "environmental bioreactor system," could provide a key function in wetlands.}, } @article {pmid31378399, year = {2019}, author = {Corron, L and Adalian, P and Condemi, S and Marchal, F and Navega, D}, title = {Sub-adult aging method selection (SAMS): A decisional tool for selecting and evaluating sub-adult age estimation methods based on standardized methodological parameters.}, journal = {Forensic science international}, volume = {304}, number = {}, pages = {109897}, doi = {10.1016/j.forsciint.2019.109897}, pmid = {31378399}, issn = {1872-6283}, mesh = {Age Determination by Skeleton/*methods ; *Algorithms ; *Databases, Bibliographic ; *Decision Support Techniques ; Forensic Anthropology ; Humans ; Information Storage and Retrieval ; Reproducibility of Results ; }, abstract = {OBJECTIVES: A decisional tool was developed to select sub-adult age estimation methods referenced in a centralized database. Through a freely accessible webpage interface, this tool allows users to evaluate how much the sampling and statistical protocols of these referenced methods comply with methodological recommendations published for building and applying methods in forensic anthropology.

MATERIALS AND METHODS: 261 publications on sub-adult age estimation were collected. Three search parameters describing the anatomical element(s) and the indicators used to obtain age estimates are chosen by the user to filter the database and present the publications that best correspond to the user's selection. A simple algorithm was created to score age estimation methods according to their relevance and validity. "Relevance" and "Validity" parameters indicate how much a publication complies with user queries and published methodological recommendations, respectively; "Score" is a combination of "Relevance" and "Validity". The closer these parameters are to 1, the better the method complies with the user's choice and standardized protocols.

RESULTS: The publications resulting from the user's query appear as search results alphabetically. They are characterized by their "Relevance", "Validity" and "Score" values and descriptors relating to their methodology, sampling and statistical protocols. The reference of the publications and an URL to access them online are also provided.

CONCLUSIONS: SAMS is a decisional tool based on a centralized database for selecting, accessing and evaluating sub-adult age estimation methods based on published methodological recommendations. Protocol validity can be easily and fully accessed to provide the necessary information for method evaluation. The database will be gradually updated and implemented as new sub-adult age estimation methods are made available online.}, } @article {pmid31377928, year = {2019}, author = {Wang, Z and Wang, Y and Peng, S and Niu, B and Cui, C and Wu, J}, title = {Mapping the research of energy subsidies: a bibliometric analysis.}, journal = {Environmental science and pollution research international}, volume = {26}, number = {28}, pages = {28817-28828}, pmid = {31377928}, issn = {1614-7499}, support = {Q20182202//SCIENTIFIC RESEARCH PROJECT OF EDUCATION DEPARTMENT OF HUBEI PROVINCE/ ; }, mesh = {Bibliometrics ; China ; Databases, Factual ; Humans ; Publications/*statistics & numerical data ; *Renewable Energy ; }, abstract = {A review of energy subsidy research from a bibliometric perspective was conducted. Based on the bibliometric method, a statistical analysis of energy subsidy-related publications from 1997 to 2016 was undertaken using the Science Citation Index (SCI) and Social Science Citation Index (SSCI) databases. A total of 1182 publications were retrieved, with a significant increase in the number of publications observed after 2006. The majority of these publications were within the disciplines of Energy & Fuels and Environmental Science & Ecology. Although the USA and China contributed the most papers, authors from 96 countries were involved in the various studies. The USA was the center of global collaborations, while other countries/territories mainly conducted bilateral or regional collaborations in their research activities. Five of the top 11 most productive institutes were from China, followed by the USA. The frequency of collaborations among institutes was relatively low. However, the institute-keyword 2-mode network showed that institutes had great potential to cooperate on a number of common topics. Five major themes were identified from the co-keywords analysis: general renewable energy research, bio-energies, sustainability, subsidies, and welfare. The findings, as a complement to previous conventional reviews, will be useful in future energy subsidy research.}, } @article {pmid31375783, year = {2019}, author = {Katz, R and Sterrett, S}, title = {How a decision-analysis tool helped one scientist couple make some tough career choices.}, journal = {Nature}, volume = {572}, number = {7768}, pages = {275-276}, doi = {10.1038/d41586-019-02106-5}, pmid = {31375783}, issn = {1476-4687}, mesh = {*Career Choice ; *Decision Support Techniques ; Ecology ; Employment/*psychology ; *Family Characteristics ; *Personal Satisfaction ; Quality of Life ; Research Personnel/*psychology ; Software ; Travel ; United States ; Virology ; *Workplace ; }, } @article {pmid31367745, year = {2019}, author = {Farré, M and Li, Q and Darolti, I and Zhou, Y and Damas, J and Proskuryakova, AA and Kulemzina, AI and Chemnick, LG and Kim, J and Ryder, OA and Ma, J and Graphodatsky, AS and Zhang, G and Larkin, DM and Lewin, HA}, title = {An integrated chromosome-scale genome assembly of the Masai giraffe (Giraffa camelopardalis tippelskirchi).}, journal = {GigaScience}, volume = {8}, number = {8}, pages = {}, pmid = {31367745}, issn = {2047-217X}, support = {BB/P020062/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; *Chromosomes, Mammalian ; Computational Biology/methods ; Evolution, Molecular ; *Genome ; *Genomics/methods ; Giraffes/*genetics ; High-Throughput Nucleotide Sequencing ; Karyotyping ; Molecular Sequence Annotation ; Phylogeny ; }, abstract = {BACKGROUND: The Masai giraffe (Giraffa camelopardalis tippelskirchi) is the largest-bodied giraffe and the world's tallest terrestrial animal. With its extreme size and height, the giraffe's unique anatomical and physiological adaptations have long been of interest to diverse research fields. Giraffes are also critical to ecosystems of sub-Saharan Africa, with their long neck serving as a conduit to food sources not shared by other herbivores. Although the genome of a Masai giraffe has been sequenced, the assembly was highly fragmented and suboptimal for genome analysis. Herein we report an improved giraffe genome assembly to facilitate evolutionary analysis of the giraffe and other ruminant genomes.

FINDINGS: Using SOAPdenovo2 and 170 Gbp of Illumina paired-end and mate-pair reads, we generated a 2.6-Gbp male Masai giraffe genome assembly, with a scaffold N50 of 3 Mbp. The incorporation of 114.6 Gbp of Chicago library sequencing data resulted in a HiRise SOAPdenovo + Chicago assembly with an N50 of 48 Mbp and containing 95% of expected genes according to BUSCO analysis. Using the Reference-Assisted Chromosome Assembly tool, we were able to order and orient scaffolds into 42 predicted chromosome fragments (PCFs). Using fluorescence in situ hybridization, we placed 153 cattle bacterial artificial chromosomes onto giraffe metaphase spreads to assess and assign the PCFs on 14 giraffe autosomes and the X chromosome resulting in the final assembly with an N50 of 177.94 Mbp. In this assembly, 21,621 protein-coding genes were identified using both de novo and homology-based predictions.

CONCLUSIONS: We have produced the first chromosome-scale genome assembly for a Giraffidae species. This assembly provides a valuable resource for the study of artiodactyl evolution and for understanding the molecular basis of the unique adaptive traits of giraffes. In addition, the assembly will provide a powerful resource to assist conservation efforts of Masai giraffe, whose population size has declined by 52% in recent years.}, } @article {pmid31359512, year = {2019}, author = {Vizueta, J and Macías-Hernández, N and Arnedo, MA and Rozas, J and Sánchez-Gracia, A}, title = {Chance and predictability in evolution: The genomic basis of convergent dietary specializations in an adaptive radiation.}, journal = {Molecular ecology}, volume = {28}, number = {17}, pages = {4028-4045}, doi = {10.1111/mec.15199}, pmid = {31359512}, issn = {1365-294X}, mesh = {Adaptation, Physiological/*genetics ; Amino Acid Substitution/genetics ; Animals ; *Biological Evolution ; *Diet ; Gene Expression Regulation ; Gene Ontology ; *Genome ; Geography ; Phenotype ; Phylogeny ; Selection, Genetic ; Spain ; Species Specificity ; Spiders/*genetics ; }, abstract = {The coexistence of multiple eco-phenotypes in independently assembled communities makes island adaptive radiations the ideal framework to test convergence and parallelism in evolution. In the radiation of the spider genus Dysdera in the Canary Islands, species diversification occurs concomitant with repeated events of trophic specialization. These dietary shifts, to feed primarily on woodlice, are accompanied by modifications in morphology (mostly in the mouthparts), behaviour and nutritional physiology. To gain insight into the molecular basis of this adaptive radiation, we performed a comprehensive comparative transcriptome analysis of five Canary Island Dysdera endemics representing two evolutionary and geographically independent events of dietary specialization. After controlling for the potential confounding effects of hemiplasy, our differential gene expression and selective constraint analyses identified a number of genetic changes that could be associated with the repeated adaptations to specialized diet of woodlice, including some related to heavy metal detoxification and homeostasis, the metabolism of some important nutrients and venom toxins. Our results shed light on the genomic basis of an extraordinary case of dietary shift convergence associated with species diversification. We uncovered putative molecular substrates of convergent evolutionary changes at different hierarchical levels, including specific genes, genes with equivalent functions and even particular amino acid positions. This study improves our knowledge of rapid adaptive radiations and provides new insights into the predictability of evolution.}, } @article {pmid31355980, year = {2019}, author = {Wright, ES and Vetsigian, KH}, title = {Stochastic exits from dormancy give rise to heavy-tailed distributions of descendants in bacterial populations.}, journal = {Molecular ecology}, volume = {28}, number = {17}, pages = {3915-3928}, doi = {10.1111/mec.15200}, pmid = {31355980}, issn = {1365-294X}, mesh = {DNA Barcoding, Taxonomic ; Selection, Genetic ; Stochastic Processes ; Streptomyces/*genetics ; }, abstract = {Variance in reproductive success is a major determinant of the degree of genetic drift in a population. While many plants and animals exhibit high variance in their number of progeny, far less is known about these distributions for microorganisms. Here, we used a strain barcoding approach to quantify variability in offspring number among replicate bacterial populations and developed a Bayesian method to infer the distribution of descendants from this variability. We applied our approach to measure the offspring distributions for five strains of bacteria from the genus Streptomyces after germination and growth in a homogenous laboratory environment. The distributions of descendants were heavy-tailed, with a few cells effectively 'winning the jackpot' to become a disproportionately large fraction of the population. This extreme variability in reproductive success largely traced back to initial populations of spores stochastically exiting dormancy, which provided early-germinating spores with an exponential advantage. In simulations with multiple dormancy cycles, heavy-tailed distributions of descendants decreased the effective population size by many orders of magnitude and led to allele dynamics differing substantially from classical population genetics models with matching effective population size. Collectively, these results demonstrate that extreme variability in reproductive success can occur even in growth conditions that are far more homogeneous than the natural environment. Thus, extreme variability in reproductive success might be an important factor shaping microbial population dynamics with implications for predicting the fate of beneficial mutations, interpreting sequence variability within populations and explaining variability in infection outcomes across patients.}, } @article {pmid31355954, year = {2019}, author = {Roy, J and Mazel, F and Sosa-Hernández, MA and Dueñas, JF and Hempel, S and Zinger, L and Rillig, MC}, title = {The relative importance of ecological drivers of arbuscular mycorrhizal fungal distribution varies with taxon phylogenetic resolution.}, journal = {The New phytologist}, volume = {224}, number = {2}, pages = {936-948}, doi = {10.1111/nph.16080}, pmid = {31355954}, issn = {1469-8137}, mesh = {*Biodiversity ; DNA, Fungal/genetics ; Databases, Factual ; Mycobiome ; Mycorrhizae/classification/*genetics ; *Phylogeny ; Sequence Analysis, DNA ; *Soil Microbiology ; }, abstract = {The phylogenetic depth at which arbuscular mycorrhizal (AM) fungi harbor a coherent ecological niche is unknown, which has consequences for operational taxonomic unit (OTU) delineation from sequence data and the study of their biogeography. We tested how changes in AM fungi community composition across habitats (beta diversity) vary with OTU phylogenetic resolution. We inferred exact sequence variants (ESVs) to resolve phylotypes at resolutions finer than provided by traditional sequence clustering and analyzed beta diversity profiles up to order-level sequence clusters. At the ESV level, we detected the environmental predictors revealed with traditional OTUs or at higher genetic distances. However, the correlation between environmental predictors and community turnover steeply increased at a genetic distance of c. 0.03 substitutions per site. Furthermore, we observed a turnover of either closely or distantly related taxa (respectively at or above 0.03 substitutions per site) along different environmental gradients. This study suggests that different axes of AM fungal ecological niche are conserved at different phylogenetic depths. Delineating AM fungal phylotypes using DNA sequences should screen different phylogenetic resolutions to better elucidate the factors that shape communities and predict the fate of AM symbioses in a changing environment.}, } @article {pmid31354646, year = {2019}, author = {Beisser, D and Bock, C and Hahn, MW and Vos, M and Sures, B and Rahmann, S and Boenigk, J}, title = {Interaction-Specific Changes in the Transcriptome of Polynucleobacter asymbioticus Caused by Varying Protistan Communities.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {1498}, pmid = {31354646}, issn = {1664-302X}, abstract = {We studied the impact of protist grazing and exudation on the growth and transcriptomic response of the prokaryotic prey species Polynucleobacter asymbioticus. Different single- and multi-species communities of chrysophytes were used to determine a species-specific response to the predators and the effect of chrysophyte diversity. We sequenced the mRNA of Pn. asymbioticus in communities with three single chrysophyte species (Chlorochromonas danica, Poterioochromonas malhamensis and Poteriospumella lacustris) and all combinations. The molecular responses of Pn. asymbioticus significantly changed in the presence of predators with different trophic modes and combinations of species. In the single-species samples we observed significant differences related to the relative importance of grazing and exudation in the protist-bacteria interaction, i.e., to the presence of either the heterotrophic Ps. lacustris or the mixotrophic C. danica. When grazing dominates the interaction, as in the presence of Ps. lacustris, genes acting in stress response are up-regulated. Further genes associated with transcription and translation are down-regulated indicating a reduced growth of Pn. asymbioticus. In contrast, when the potential use of algal exudates dominates the interaction, genes affiliated with iron transport are up-regulated. Rapid phototrophic growth of chrysophytes, with a high demand on soluble iron, could thus lead to iron-limitation and cause changes in the iron metabolism of Pn. asymbioticus. Additionally, we observe a benefit for Pn. asymbioticus from a more diverse protistan community, which could be due to shifts in the relative importance of phototrophy in the mixotrophic chrysophytes when competing for food with other species. Our study highlights the importance of biotic interactions and the specificity of such interactions, in particular the differential effect of grazing and algal exudation in the interaction of bacteria with mixotrophic protists.}, } @article {pmid31350429, year = {2019}, author = {Stewart, FEC and Darlington, S and Volpe, JP and McAdie, M and Fisher, JT}, title = {Corridors best facilitate functional connectivity across a protected area network.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {10852}, pmid = {31350429}, issn = {2045-2322}, mesh = {*Animal Migration ; Animals ; Biodiversity ; Canada ; Conservation of Natural Resources/*methods ; Ecology/methods ; *Ecosystem ; Geographic Information Systems ; Locomotion ; Mustelidae/*physiology ; *Natural Resources ; }, abstract = {Biologging data allow animal ecologists to directly measure species' fine-scale spatiotemporal responses to environments, such as movement - critical for our understanding of biodiversity declines in the Anthropocene. Animal movement between resource patches is a behavioral expression of multiple ecological processes that affect individual fitness. Protected area (PA) networks are a tool used to conserve biodiversity by sustaining habitat patches across vast heterogeneous landscapes. However, our ability to design PA networks that conserve biodiversity relies on our accurate understanding of animal movement and functional connectivity; this understanding is rarely tested in real-world situations due to the large geographic expanse of most PA networks. Using a tractable PA network mesocosm, we employ cutting-edge biologging technology to analyze animal movement decisions in response to a highly heterogeneous landscape. We analyze these data to test, in a novel way, three common hypotheses about functional connectivity - structural corridors, least cost paths, and stepping stones. Consistently, animals moved along structurally self-similar corridors. In reference to the Aichi 2020 Biodiversity Targets, relying on species to "stepping stone" across habitat remnants may not achieve protected area network conservation objectives.}, } @article {pmid31348815, year = {2019}, author = {Yen, HY and Li, C}, title = {Determinants of physical activity: A path model based on an ecological model of active living.}, journal = {PloS one}, volume = {14}, number = {7}, pages = {e0220314}, pmid = {31348815}, issn = {1932-6203}, mesh = {Adult ; *Exercise ; Female ; Healthy Volunteers ; Humans ; Male ; Metabolic Syndrome/complications/*epidemiology ; Middle Aged ; Models, Theoretical ; Obesity/complications/*epidemiology ; Online Systems ; Self Report ; Young Adult ; }, abstract = {Maintaining physical activity is necessary to promote health in our daily lives. The Ecological Model of Active Living was proposed to examine whether individuals participate in active living. The purpose of this study was to understand the determinants of physical activity and create a predictive path model of the intrapersonal, perceived environment, behavior settings, and policy environment domains. Data were obtained from open government data and questionnaires, including the International Physical Activity Questionnaire, Health Belief Model Inventory, Physical Activity Neighborhood Environment Survey, and Accessibility of Open Spaces. Participants comprised 1085 healthy adults who completed a self-reported internet survey. An analysis of the intrapersonal domain revealed that the variables of female, an older age, and a low educational level, and individuals with obesity or cardiometabolic diseases presented lower odds ratios for active living. We found significant statistical support for our path model (The Ecological Model of Active Living), with a predictive power of 23.1%. The predictive path model is a good approach to quantitatively measure the impacts of various determinants on active living that suggests further lines of research in approaches for modeling relationships.}, } @article {pmid31347244, year = {2019}, author = {Fletcher, RJ and Sefair, JA and Wang, C and Poli, CL and Smith, TAH and Bruna, EM and Holt, RD and Barfield, M and Marx, AJ and Acevedo, MA}, title = {Towards a unified framework for connectivity that disentangles movement and mortality in space and time.}, journal = {Ecology letters}, volume = {22}, number = {10}, pages = {1680-1689}, doi = {10.1111/ele.13333}, pmid = {31347244}, issn = {1461-0248}, support = {DEB-1343144//National Science Foundation/ ; DEB-1655555//National Science Foundation/ ; //University of Florida Foundation/ ; }, mesh = {*Animal Distribution ; Animals ; *Ecosystem ; Markov Chains ; *Mortality ; *Movement ; Spatio-Temporal Analysis ; }, abstract = {Predicting connectivity, or how landscapes alter movement, is essential for understanding the scope for species persistence with environmental change. Although it is well known that movement is risky, connectivity modelling often conflates behavioural responses to the matrix through which animals disperse with mortality risk. We derive new connectivity models using random walk theory, based on the concept of spatial absorbing Markov chains. These models decompose the role of matrix on movement behaviour and mortality risk, can incorporate species distribution to predict the amount of flow, and provide both short- and long-term analytical solutions for multiple connectivity metrics. We validate the framework using data on movement of an insect herbivore in 15 experimental landscapes. Our results demonstrate that disentangling the roles of movement behaviour and mortality risk is fundamental to accurately interpreting landscape connectivity, and that spatial absorbing Markov chains provide a generalisable and powerful framework with which to do so.}, } @article {pmid31346192, year = {2019}, author = {Beyrand, V and Voeten, DFAE and Bureš, S and Fernandez, V and Janáček, J and Jirák, D and Rauhut, O and Tafforeau, P}, title = {Multiphase progenetic development shaped the brain of flying archosaurs.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {10807}, pmid = {31346192}, issn = {2045-2322}, mesh = {Alligators and Crocodiles/anatomy & histology/genetics ; Animals ; *Biological Evolution ; Birds/anatomy & histology/*genetics ; Brain/*anatomy & histology/growth & development ; Flight, Animal ; Fossils/*anatomy & histology ; Phylogeny ; Skull/anatomy & histology ; }, abstract = {The growing availability of virtual cranial endocasts of extinct and extant vertebrates has fueled the quest for endocranial characters that discriminate between phylogenetic groups and resolve their neural significances. We used geometric morphometrics to compare a phylogenetically and ecologically comprehensive data set of archosaurian endocasts along the deep evolutionary history of modern birds and found that this lineage experienced progressive elevation of encephalisation through several chapters of increased endocranial doming that we demonstrate to result from progenetic developments. Elevated encephalisation associated with progressive size reduction within Maniraptoriformes was secondarily exapted for flight by stem avialans. Within Mesozoic Avialae, endocranial doming increased in at least some Ornithurae, yet remained relatively modest in early Neornithes. During the Paleogene, volant non-neoavian birds retained ancestral levels of endocast doming where a broad neoavian niche diversification experienced heterochronic brain shape radiation, as did non-volant Palaeognathae. We infer comparable developments underlying the establishment of pterosaurian brain shapes.}, } @article {pmid31344878, year = {2019}, author = {Liu, J and Wu, J and Lin, J and Zhao, J and Xu, T and Yang, Q and Zhao, J and Zhao, Z and Song, X}, title = {Changes in the Microbial Community Diversity of Oil Exploitation.}, journal = {Genes}, volume = {10}, number = {8}, pages = {}, pmid = {31344878}, issn = {2073-4425}, mesh = {DNA Barcoding, Taxonomic ; *Microbiota ; Oil and Gas Fields/*microbiology ; Petroleum/microbiology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {To systematically evaluate the ecological changes of an active offshore petroleum production system, the variation of microbial communities at several sites (virgin field, wellhead, storage tank) of an oil production facility in east China was investigated by sequencing the V3 to V4 regions of 16S ribosomal ribonucleic acid (rRNA) of microorganisms. In general, a decrease of microbial community richness and diversity in petroleum mining was observed, as measured by operational taxonomic unit (OTU) numbers, α (Chao1 and Shannon indices), and β (principal coordinate analysis) diversity. Microbial community structure was strongly affected by environmental factors at the phylum and genus levels. At the phylum level, virgin field and wellhead were dominated by Proteobacteria, while the storage tank had higher presence of Firmicutes (29.3-66.9%). Specifically, the wellhead displayed a lower presentence of Proteobacteria (48.6-53.4.0%) and a higher presence of Firmicutes (24.4-29.6%) than the virgin field. At the genus level, the predominant genera were Ochrobactrum and Acinetobacter in the virgin field, Lactococcus and Pseudomonas in the wellhead, and Prauseria and Bacillus in the storage tank. Our study revealed that the microbial community structure was strongly affected by the surrounding environmental factors, such as temperature, oxygen content, salinity, and pH, which could be altered because of the oil production. It was observed that the various microbiomes produced surfactants, transforming the biohazard and degrading hydro-carbon. Altering the microbiome growth condition by appropriate human intervention and taking advantage of natural microbial resources can further enhance oil recovery technology.}, } @article {pmid31344542, year = {2019}, author = {Saedpanah, S and Amanollahi, J}, title = {Environmental pollution and geo-ecological risk assessment of the Qhorveh mining area in western Iran.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {253}, number = {}, pages = {811-820}, doi = {10.1016/j.envpol.2019.07.049}, pmid = {31344542}, issn = {1873-6424}, mesh = {Ecology ; Environment ; Environmental Monitoring/*methods ; Environmental Pollution/*statistics & numerical data ; Geographic Information Systems ; Iran ; *Mining ; Risk Assessment ; Soil ; Soil Pollutants/analysis ; }, abstract = {In order to evaluate the effect of mining activity on the environment of the Qhorveh mining area in the west of Iran, the geological, ecological and environmental data, related to social development and regional economic status, were used. The geological data included seven sub-indices, such as vegetation coverage, land utilization type, and fault activity; ecological data, with two sub-indices, such as degree of ecological environment recovery; and finally, environmental data, with three sub-indices, such as soil and dust pollutions. These were selected based on the literature and expert opinion which were utilized for environmental pollution and geo-ecological (EPGE) risk assessment of the study site. Remote sensing (RS) image, field sampling, digital elevation map, and data retrieved from different government agencies were used to generate layers for the sub-indices in the geographic information system (GIS) environment. In addition, the analytical hierarchy process (AHP) method was used to determine the weight of sub-indices. Five levels consisting of best, good, middle, poor and worst were used to describe the EPGE risk assessment of the Qhorveh mining area. Results showed that worst and poor levels of EPGE risk are in the east and northeast of the study area where the gold and pumice mines are located while best and good levels of EPGE risk are in its center where the stone mines are located. According to the results of this research, the EPGE risk assessment of the Qhorveh mining area is affected by the environmental pollution index with its highest weight (0.3908). It can be concluded that the integration of the RS, GIS and AHP methods proposed in this study improved the evaluation quality of EPGE risk assessment.}, } @article {pmid31344032, year = {2019}, author = {Sura, SA and Smith, LL and Ambrose, MR and Amorim, CEG and Beichman, AC and Gomez, ACR and Juhn, M and Kandlikar, GS and Miller, JS and Mooney, J and Mummah, RO and Lohmueller, KE and Lloyd-Smith, JO}, title = {Ten simple rules for giving an effective academic job talk.}, journal = {PLoS computational biology}, volume = {15}, number = {7}, pages = {e1007163}, pmid = {31344032}, issn = {1553-7358}, mesh = {Biological Evolution ; Computational Biology/education ; Ecology/education ; Education, Graduate ; *Faculty ; Humans ; *Job Application ; Los Angeles ; Students ; Work Engagement ; Workplace ; }, } @article {pmid31341288, year = {2019}, author = {Bolyen, E and Rideout, JR and Dillon, MR and Bokulich, NA and Abnet, CC and Al-Ghalith, GA and Alexander, H and Alm, EJ and Arumugam, M and Asnicar, F and Bai, Y and Bisanz, JE and Bittinger, K and Brejnrod, A and Brislawn, CJ and Brown, CT and Callahan, BJ and Caraballo-Rodríguez, AM and Chase, J and Cope, EK and Da Silva, R and Diener, C and Dorrestein, PC and Douglas, GM and Durall, DM and Duvallet, C and Edwardson, CF and Ernst, M and Estaki, M and Fouquier, J and Gauglitz, JM and Gibbons, SM and Gibson, DL and Gonzalez, A and Gorlick, K and Guo, J and Hillmann, B and Holmes, S and Holste, H and Huttenhower, C and Huttley, GA and Janssen, S and Jarmusch, AK and Jiang, L and Kaehler, BD and Kang, KB and Keefe, CR and Keim, P and Kelley, ST and Knights, D and Koester, I and Kosciolek, T and Kreps, J and Langille, MGI and Lee, J and Ley, R and Liu, YX and Loftfield, E and Lozupone, C and Maher, M and Marotz, C and Martin, BD and McDonald, D and McIver, LJ and Melnik, AV and Metcalf, JL and Morgan, SC and Morton, JT and Naimey, AT and Navas-Molina, JA and Nothias, LF and Orchanian, SB and Pearson, T and Peoples, SL and Petras, D and Preuss, ML and Pruesse, E and Rasmussen, LB and Rivers, A and Robeson, MS and Rosenthal, P and Segata, N and Shaffer, M and Shiffer, A and Sinha, R and Song, SJ and Spear, JR and Swafford, AD and Thompson, LR and Torres, PJ and Trinh, P and Tripathi, A and Turnbaugh, PJ and Ul-Hasan, S and van der Hooft, JJJ and Vargas, F and Vázquez-Baeza, Y and Vogtmann, E and von Hippel, M and Walters, W and Wan, Y and Wang, M and Warren, J and Weber, KC and Williamson, CHD and Willis, AD and Xu, ZZ and Zaneveld, JR and Zhang, Y and Zhu, Q and Knight, R and Caporaso, JG}, title = {Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2.}, journal = {Nature biotechnology}, volume = {37}, number = {8}, pages = {852-857}, pmid = {31341288}, issn = {1546-1696}, support = {R35 GM133420/GM/NIGMS NIH HHS/United States ; U54 MD012388/MD/NIMHD NIH HHS/United States ; U54 CA143925/CA/NCI NIH HHS/United States ; T32 ES015459/ES/NIEHS NIH HHS/United States ; Z99 CA999999/ImNIH/Intramural NIH HHS/United States ; }, mesh = {*Computational Biology ; *Data Science ; Databases, Factual ; Humans ; *Microbiota ; *Software ; }, } @article {pmid31341142, year = {2019}, author = {Inoue, H and Suzuki, T and Kojima, M and Inoshita, E and Lee, J and Tanaka, S and Fujiyoshi, A and Hayakawa, T and Miura, K}, title = {[Factors related to life expectancy in prefectures: An ecological study using the National Database].}, journal = {[Nihon koshu eisei zasshi] Japanese journal of public health}, volume = {66}, number = {7}, pages = {370-377}, doi = {10.11236/jph.66.7_370}, pmid = {31341142}, issn = {0546-1766}, mesh = {Aged, 80 and over ; Alcohol Drinking/adverse effects/epidemiology ; Anticholesteremic Agents ; Antihypertensive Agents/adverse effects ; Blood Glucose ; Blood Pressure ; Body Mass Index ; *Databases, Factual ; Female ; Humans ; Japan ; *Life Expectancy ; Life Style ; Male ; Regression Analysis ; Risk Factors ; Sex Factors ; Smoking/adverse effects/epidemiology ; Triglycerides/blood ; }, abstract = {Objective In recent years, studies have reported a prefectural-level disparity in life expectancy. Therefore, we analyzed the related factors using the National Database (NDB), which includes data pertaining to the specific health checkup conducted for 20 million individuals. By doing so, we aimed to obtain basic data for developing future health promotion measures.Methods We used specific health checkup items from NDB Open Data for 2014, and life expectancy data from Prefecture Life Table for 2015. The specific health checkup items were adjusted by age using Japanese population data for 2015. A multiple linear regression analysis was conducted using specific health checkup items that were significantly related to average life expectancy as explanatory variables.Results In men, excessive drinking, smoking, antihypertensive drug use, systolic blood pressure, and hyperglycemia were independently and inversely related to life expectancy. In women, smoking and antihypertensive drug use emerged as significant factors.Conclusions Analysis using NDB Open Data showed that lifestyle factors such as smoking and drinking, and cardiovascular risk factors such as high blood pressure and hyperglycemia, were strongly related to life expectancy. These result suggest that it is necessary to focus on the above factors when prefectural authorities implement health promotion measures.}, } @article {pmid31340694, year = {2019}, author = {Rojas Concha, HA and Simões, RT and Dellaretti, M and Rubatino, FVM}, title = {Trends for in-hospital metrics in the treatment of intracranial aneurysms in Minas Gerais, Brazil.}, journal = {Hospital practice (1995)}, volume = {47}, number = {3}, pages = {163-169}, doi = {10.1080/21548331.2019.1646073}, pmid = {31340694}, issn = {2154-8331}, mesh = {Adult ; Aged ; Brazil ; Choice Behavior ; *Clinical Decision-Making ; Databases, Factual ; *Endovascular Procedures/methods/statistics & numerical data ; Female ; Hospital Information Systems ; Humans ; Inpatients ; Intracranial Aneurysm/physiopathology/*surgery ; Linear Models ; Male ; Middle Aged ; *Neurosurgical Procedures/methods/statistics & numerical data ; Treatment Outcome ; }, abstract = {Background: Aneurysmal subarachnoid hemorrhage (ASAH) and unruptured aneurysm (URA) are particularly important because of the high mortality rates, and physical and cognitive impairment, which affect the economically active population. The present work aims at describing the scenario regarding in-hospital indicators related to the following therapeutic approaches: vascular microsurgery (VMS) and endovascular therapy (EVT) in the state of Minas Gerais, Brazil, in order to gather information to construct hypotheses and plan actions. Methods: The study has an ecological design and it is also analytical for the time trends of 2008-2014. Trends for VMS and EVT therapies and mortality are estimated using linear regression, followed by the Prais-Winsten procedure. Data were obtained through Hospital Information System (Sistema de Informações Hospitalares - SIH) of Brazilian Public Health System (Sistema Único de Saúde - SUS). Results: In 2014, 601 procedures were performed, and out of these, 373 (62%) were triggered by SAH and 228 (38%) by URA. The frequency of procedures performed in males and in females results in a ratio of 1:2 for SAH procedures and 1:3 for URA procedures. A heterogeneous distribution of therapeutic approaches was seen among the hospital studied, suggesting a technological preference, which determines the therapeutic approach. Conclusion: Technological bias was observed for aneurysm treatment in Minas Gerais's hospitals. EVT is seen to have a growing trend to detriment of VMS (β1 = 0.024; p = 0.025), with a stable mortality for both therapeutics in both pathologies (SAH and URA). EVT has been associated with a shorter hospital stay, with higher expenses for both ASAH and URA treatment. EVT showed an inverse correlation with in-hospital fatality for ASAH treatment.}, } @article {pmid31340359, year = {2019}, author = {Martinez, EZ and Zucoloto, ML and Silva, ASD and Brunherotti, MAA}, title = {Attributable fraction of congenital syphilis due to the lack of prenatal care.}, journal = {Revista da Sociedade Brasileira de Medicina Tropical}, volume = {52}, number = {}, pages = {e20180532}, doi = {10.1590/0037-8682-0532-2018}, pmid = {31340359}, issn = {1678-9849}, mesh = {Bayes Theorem ; Brazil/epidemiology ; Disease Notification ; Female ; Health Information Systems ; Humans ; Incidence ; Infectious Disease Transmission, Vertical/*statistics & numerical data ; Pregnancy ; Pregnancy Complications, Infectious/*epidemiology ; *Prenatal Care ; Residence Characteristics ; Syphilis, Congenital/*epidemiology ; }, abstract = {INTRODUCTION: Although congenital syphilis is preventable, its incidence has increased in Brazil.

METHODS: In this ecological study, a Bayesian spatio-temporal model was used to estimate the attributable fraction of congenital syphilis cases due to the lack of prenatal care recorded between 2010 and 2015 in the state of São Paulo, Southeast Brazil.

RESULTS: For the year 2016, it was estimated that between 79.4% and 95.3% of the congenital syphilis cases among women who did not have prenatal care could have been prevented.

CONCLUSIONS: A significant proportion of congenital syphilis cases can be prevented if prenatal care coverage is expanded.}, } @article {pmid31339959, year = {2019}, author = {Fernandes, NL and Pandeirada, JNS and Nairne, JS}, title = {Presenting new stimuli to study emotion: Development and validation of the Objects-on-Hands Picture Database.}, journal = {PloS one}, volume = {14}, number = {7}, pages = {e0219615}, pmid = {31339959}, issn = {1932-6203}, mesh = {Adult ; Databases, Factual ; Emotions/*physiology ; Female ; Hand ; Humans ; Image Processing, Computer-Assisted ; Male ; *Photic Stimulation ; Young Adult ; }, abstract = {A long-standing goal shared by researchers has been to design optimal experimental procedures, including the selection of appropriate stimuli. Pictures are commonly used in different research fields. However, until recently, researchers have relied mostly on line-drawings, which can have poor ecological validity. We developed a set of high quality standardized photographs of objects from six different categories, recorded under two camera viewpoints, and five presentation conditions (on its own, held by clean hands, and by hands covered with different substances: sauce, chocolate and mud). These various staging conditions can be used to induce different emotional states while maintaining the object of interest constant. We first report normative data on the objects' name agreement and familiarity collected from North American and Portuguese participants. Results showed high name agreement and familiarity in both samples. Next, arousal, disgust and valence ratings were collected for the stimuli under either an emotional-activating or a neutral context. Subjective ratings varied according to the staging condition and the context, confirming that the same items can effectively be used in different emotional conditions. This database allows researchers to select more ecologically-valid stimuli according to their research purposes while considering several variables of interest and avoiding item-selection problems commonly present when comparing responses to neutral and emotional items.}, } @article {pmid31339876, year = {2019}, author = {Libby, E and Hébert-Dufresne, L and Hosseini, SR and Wagner, A}, title = {Syntrophy emerges spontaneously in complex metabolic systems.}, journal = {PLoS computational biology}, volume = {15}, number = {7}, pages = {e1007169}, pmid = {31339876}, issn = {1553-7358}, support = {P20 GM125498/GM/NIGMS NIH HHS/United States ; }, mesh = {Adaptation, Physiological/genetics ; Algorithms ; Carbon/metabolism ; Computational Biology ; Escherichia coli/genetics/metabolism ; Markov Chains ; *Metabolic Networks and Pathways ; Microbiota/genetics/*physiology ; *Models, Biological ; Monte Carlo Method ; Mutation ; Symbiosis/genetics/*physiology ; }, abstract = {Syntrophy allows a microbial community as a whole to survive in an environment, even though individual microbes cannot. The metabolic interdependence typical of syntrophy is thought to arise from the accumulation of degenerative mutations during the sustained co-evolution of initially self-sufficient organisms. An alternative and underexplored possibility is that syntrophy can emerge spontaneously in communities of organisms that did not co-evolve. Here, we study this de novo origin of syntrophy using experimentally validated computational techniques to predict an organism's viability from its metabolic reactions. We show that pairs of metabolisms that are randomly sampled from a large space of possible metabolism and viable on specific primary carbon sources often become viable on new carbon sources by exchanging metabolites. The same biochemical reactions that are required for viability on primary carbon sources also confer viability on novel carbon sources. Our observations highlight a new and important avenue for the emergence of metabolic adaptations and novel ecological interactions.}, } @article {pmid31337777, year = {2019}, author = {Navarro, J and Grémillet, D and Afán, I and Miranda, F and Bouten, W and Forero, MG and Figuerola, J}, title = {Pathogen transmission risk by opportunistic gulls moving across human landscapes.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {10659}, pmid = {31337777}, issn = {2045-2322}, mesh = {Animal Migration/*physiology ; Animals ; Animals, Wild ; Campylobacter Infections/*transmission ; Charadriiformes ; Chlamydia Infections/*transmission ; Europe ; Geographic Information Systems ; Humans ; Salmonella Infections/*transmission ; Zoonoses/*transmission ; }, abstract = {Wildlife that exploit human-made habitats hosts and spreads bacterial pathogens. This shapes the epidemiology of infectious diseases and facilitates pathogen spill-over between wildlife and humans. This is a global problem, yet little is known about the dissemination potential of pathogen-infected animals. By combining molecular pathogen diagnosis with GPS tracking of pathogen-infected gulls, we show how this knowledge gap could be filled at regional scales. Specifically, we generated pathogen risk maps of Salmonella, Campylobacter and Chlamydia based on the spatial movements of pathogen-infected yellow-legged gulls (Larus michahellis) equipped with GPS recorders. Also, crossing this spatial information with habitat information, we identified critical habitats for the potential transmission of these bacteria in southern Europe. The use of human-made habitats by infected-gulls could potentially increase the potential risk of direct and indirect bidirectional transmission of pathogens between humans and wildlife. Our findings show that pathogen-infected wildlife equipped with GPS recorders can provide accurate information on the spatial spread risk for zoonotic bacteria. Integration of GPS-tracking with classical epidemiological approaches may help to improve zoonosis surveillance and control programs.}, } @article {pmid31337772, year = {2019}, author = {Vimercati, L and Darcy, JL and Schmidt, SK}, title = {The disappearing periglacial ecosystem atop Mt. Kilimanjaro supports both cosmopolitan and endemic microbial communities.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {10676}, pmid = {31337772}, issn = {2045-2322}, mesh = {*Biodiversity ; Comamonadaceae/genetics ; *Ecosystem ; Eukaryota/genetics ; Ice Cover/*microbiology ; Microbiota/*genetics ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 18S/genetics ; *Soil Microbiology ; Tanzania ; }, abstract = {Microbial communities have not been studied using molecular approaches at high elevations on the African continent. Here we describe the diversity of microbial communities from ice and periglacial soils from near the summit of Mt. Kilimanjaro by using both Illumina and Sanger sequencing of 16S and 18S rRNA genes. Ice and periglacial soils contain unexpectedly diverse and rich assemblages of Bacteria and Eukarya indicating that there may be high rates of dispersal to the top of this tropical mountain and/or that the habitat is more conducive to microbial life than was previously thought. Most bacterial OTUs are cosmopolitan and an analysis of isolation by geographic distance patterns of the genus Polaromonas emphasized the importance of global Aeolian transport in the assembly of bacterial communities on Kilimanjaro. The eukaryotic communities were less diverse than the bacterial communities and showed more evidence of dispersal limitations and apparent endemism. Cercozoa dominated the 18S communities, including a high abundance of testate amoebae and a high diversity of endemic OTUs within the Vampyrellida. These results argue for more intense study of this unique high-elevation "island of the cryosphere" before the glaciers of Kilimanjaro disappear forever.}, } @article {pmid31332853, year = {2019}, author = {Broman, E and Raymond, C and Sommer, C and Gunnarsson, JS and Creer, S and Nascimento, FJA}, title = {Salinity drives meiofaunal community structure dynamics across the Baltic ecosystem.}, journal = {Molecular ecology}, volume = {28}, number = {16}, pages = {3813-3829}, pmid = {31332853}, issn = {1365-294X}, mesh = {Animals ; *Biodiversity ; Computational Biology ; Finland ; Nematoda/*classification ; Oceans and Seas ; Population Dynamics ; Rivers ; *Salinity ; Sequence Analysis, DNA ; Sweden ; }, abstract = {Coastal benthic biodiversity is under increased pressure from climate change, eutrophication, hypoxia, and changes in salinity due to increase in river runoff. The Baltic Sea is a large brackish system characterized by steep environmental gradients that experiences all of the mentioned stressors. As such it provides an ideal model system for studying the impact of on-going and future climate change on biodiversity and function of benthic ecosystems. Meiofauna (animals < 1 mm) are abundant in sediment and are still largely unexplored even though they are known to regulate organic matter degradation and nutrient cycling. In this study, benthic meiofaunal community structure was analysed along a salinity gradient in the Baltic Sea proper using high-throughput sequencing. Our results demonstrate that areas with higher salinity have a higher biodiversity, and salinity is probably the main driver influencing meiofauna diversity and community composition. Furthermore, in the more diverse and saline environments a larger amount of nematode genera classified as predators prevailed, and meiofauna-macrofauna associations were more prominent. These findings show that in the Baltic Sea, a decrease in salinity resulting from accelerated climate change will probably lead to decreased benthic biodiversity, and cause profound changes in benthic communities, with potential consequences for ecosystem stability, functions and services.}, } @article {pmid31331270, year = {2019}, author = {Zhong, Z and Kwok, LY and Hou, Q and Sun, Y and Li, W and Zhang, H and Sun, Z}, title = {Comparative genomic analysis revealed great plasticity and environmental adaptation of the genomes of Enterococcus faecium.}, journal = {BMC genomics}, volume = {20}, number = {1}, pages = {602}, pmid = {31331270}, issn = {1471-2164}, support = {31601451//National Natural Science Foundation of China/ ; 31622043//National Natural Science Foundation of China/ ; 31430066//National Natural Science Foundation of China/ ; CARS-36//Agriculture Research System of China/ ; }, mesh = {Adaptation, Physiological/*genetics ; Databases, Genetic ; Drug Resistance, Microbial/genetics ; Enterococcus faecium/drug effects/*genetics/*physiology ; *Environment ; Genes, Bacterial/genetics ; *Genomics ; Phylogeny ; Virulence Factors/genetics ; }, abstract = {BACKGROUND: As an important nosocomial pathogen, Enterococcus faecium has received increasing attention in recent years. However, a large number of studies have focused on the hospital-associated isolates and ignored isolates originated from the natural environments.

RESULTS: In this study, comparative genomic analysis was conducted on 161 isolates originated from human, animal, and naturally fermented dairy products. The results showed that the environment played an important role in shaping the genomes of Enterococcus faecium. The isolates from human had the largest average genome size, while the isolates from dairy products had the smallest average genome size and fewest antibiotic resistance genes. A phylogenetic tree was reconstructed based on the genomes of these isolates, which revealed new insights into the phylogenetic relationships among the dairy isolates and those from hospitals, communities, and animals. Furthermore, 202 environment-specific genes were identified, including 136 dairy-specific, 31 human blood-specific, and 35 human gastrointestinal-specific genes. Interestingly, five dairy-specific genes (namely lacF, lacA/B, lacD, lacG, and lacC) that constituted an integrated lactose metabolism pathway existed in almost all dairy isolates. The pathway conservation demonstrated an active role of the environment in shaping the genomes of Enterococcus faecium.

CONCLUSIONS: This study shows that the Enterococcus faecium species has great genomic plasticity and high versatility to occupy broad ecological roles, dwelling as non-harmful dairy and animal gut commensals as well as significant nosocomial pathogens that disseminate antibiotic resistance genes.}, } @article {pmid31330197, year = {2019}, author = {Brietzke, E and Hawken, ER and Idzikowski, M and Pong, J and Kennedy, SH and Soares, CN}, title = {Integrating digital phenotyping in clinical characterization of individuals with mood disorders.}, journal = {Neuroscience and biobehavioral reviews}, volume = {104}, number = {}, pages = {223-230}, doi = {10.1016/j.neubiorev.2019.07.009}, pmid = {31330197}, issn = {1873-7528}, mesh = {*Biomarkers ; Bipolar Disorder/*diagnosis ; Depressive Disorder, Major/*diagnosis ; *Ecological Momentary Assessment ; Humans ; *Individuality ; *Medical Informatics Applications ; *Phenotype ; }, abstract = {Major Depressive Disorder (MDD) and bipolar disorder (BD) are still under recognized and undertreated, especially in primary care settings. One of the challenges faced by clinicians is the remarkable inter-individual variability among patients with these conditions. In addition, each patient with MDD and BD experiences a unique pattern of longitudinal changes across time, i.e., intra-individual variability can also be problematic. The immense amount of data generated and collected through the use of smartphones or personal devices offers an opportunity to obtain continuous and reliable information on each individual's behavior, a less burdensome way to capture both intra and inter-individual variability over time. Digital phenotypes (DP) are a promising strategy to be integrated with other "Omics" platforms for prediction of relevant outcomes in mood disorders, including but not restricted to, relapse, recurrence, cognitive decline and functional impairment. Despite existing limitations and some skepticism, digital phenotyping represents a field in great expansion and might eventually constitute a feasible strategy in biomarkers research for mood disorders.}, } @article {pmid31330063, year = {2019}, author = {Fountain-Jones, NM and Machado, G and Carver, S and Packer, C and Recamonde-Mendoza, M and Craft, ME}, title = {How to make more from exposure data? An integrated machine learning pipeline to predict pathogen exposure.}, journal = {The Journal of animal ecology}, volume = {88}, number = {10}, pages = {1447-1461}, doi = {10.1111/1365-2656.13076}, pmid = {31330063}, issn = {1365-2656}, mesh = {Animals ; Animals, Wild ; *Distemper Virus, Canine ; Ecology ; *Lions ; Machine Learning ; }, abstract = {Predicting infectious disease dynamics is a central challenge in disease ecology. Models that can assess which individuals are most at risk of being exposed to a pathogen not only provide valuable insights into disease transmission and dynamics but can also guide management interventions. Constructing such models for wild animal populations, however, is particularly challenging; often only serological data are available on a subset of individuals and nonlinear relationships between variables are common. Here we provide a guide to the latest advances in statistical machine learning to construct pathogen-risk models that automatically incorporate complex nonlinear relationships with minimal statistical assumptions from ecological data with missing data. Our approach compares multiple machine learning algorithms in a unified environment to find the model with the best predictive performance and uses game theory to better interpret results. We apply this framework on two major pathogens that infect African lions: canine distemper virus (CDV) and feline parvovirus. Our modelling approach provided enhanced predictive performance compared to more traditional approaches, as well as new insights into disease risks in a wild population. We were able to efficiently capture and visualize strong nonlinear patterns, as well as model complex interactions between variables in shaping exposure risk from CDV and feline parvovirus. For example, we found that lions were more likely to be exposed to CDV at a young age but only in low rainfall years. When combined with our data calibration approach, our framework helped us to answer questions about risk of pathogen exposure that are difficult to address with previous methods. Our framework not only has the potential to aid in predicting disease risk in animal populations, but also can be used to build robust predictive models suitable for other ecological applications such as modelling species distribution or diversity patterns.}, } @article {pmid31328773, year = {2019}, author = {Spoor, S and Cheng, CH and Sanderson, LA and Condon, B and Almsaeed, A and Chen, M and Bretaudeau, A and Rasche, H and Jung, S and Main, D and Bett, K and Staton, M and Wegrzyn, JL and Feltus, FA and Ficklin, SP}, title = {Tripal v3: an ontology-based toolkit for construction of FAIR biological community databases.}, journal = {Database : the journal of biological databases and curation}, volume = {2019}, number = {}, pages = {}, pmid = {31328773}, issn = {1758-0463}, mesh = {Biota/*genetics ; *Databases, Genetic ; Genomics ; *Information Dissemination ; *Internet ; *Software ; *Transcriptome ; }, abstract = {Community biological databases provide an important online resource for both public and private data, analysis tools and community engagement. These sites house genomic, transcriptomic, genetic, breeding and ancillary data for specific species, families or clades. Due to the complexity and increasing quantities of these data, construction of online resources is increasingly difficult especially with limited funding and access to technical expertise. Furthermore, online repositories are expected to promote FAIR data principles (findable, accessible, interoperable and reusable) that presents additional challenges. The open-source Tripal database toolkit seeks to mitigate these challenges by creating both the software and an interactive community of developers for construction of online community databases. Additionally, through coordinated, distributed co-development, Tripal sites encourage community-wide sustainability. Here, we report the release of Tripal version 3 that improves data accessibility and data sharing through systematic use of controlled vocabularies (CVs). Tripal uses the community-developed Chado database as a default data store, but now provides tools to support other data stores, while ensuring that CVs remain the central organizational structure for the data. A new site developer can use Tripal to develop a basic site with little to no programming, with the ability to integrate other data types using extension modules and the Tripal application programming interface. A thorough online User's Guide and Developer's Handbook are available at http://tripal.info, providing download, installation and step-by-step setup instructions.}, } @article {pmid31324000, year = {2019}, author = {Hayes, S and Mahony, J and Vincentelli, R and Ramond, L and Nauta, A and van Sinderen, D and Cambillau, C}, title = {Ubiquitous Carbohydrate Binding Modules Decorate 936 Lactococcal Siphophage Virions.}, journal = {Viruses}, volume = {11}, number = {7}, pages = {}, pmid = {31324000}, issn = {1999-4915}, support = {15/SIRG/3430//Science Foundation Ireland/Ireland ; 13/IA/1953//Science Foundation Ireland/Ireland ; }, mesh = {Bacteriophages/*chemistry/genetics ; Carbohydrates/*chemistry ; Computational Biology ; Host Microbial Interactions ; Lactococcus lactis/*virology ; Models, Molecular ; Protein Binding ; Protein Conformation ; Siphoviridae/*chemistry/genetics ; Viral Tail Proteins/*chemistry/genetics ; Virion/*chemistry/genetics ; }, abstract = {With the availability of an increasing number of 3D structures of bacteriophage components, combined with powerful in silico predictive tools, it has become possible to decipher the structural assembly and functionality of phage adhesion devices. In the current study, we examined 113 members of the 936 group of lactococcal siphophages, and identified a number of Carbohydrate Binding Modules (CBMs) in the neck passage structure and major tail protein, on top of evolved Dit proteins, as recently reported by us. The binding ability of such CBM-containing proteins was assessed through the construction of green fluorescent protein fusion proteins and subsequent binding assays. Two CBMs, one from the phage tail and another from the neck, demonstrated definite binding to their phage-specific host. Bioinformatic analysis of the structural proteins of 936 phages reveals that they incorporate binding modules which exhibit structural homology to those found in other lactococcal phage groups and beyond, indicating that phages utilize common structural "bricks" to enhance host binding capabilities. The omnipresence of CBMs in Siphophages supports their beneficial role in the infection process, as they can be combined in various ways to form appendages with different shapes and functionalities, ensuring their success in host detection in their respective ecological niches.}, } @article {pmid31318965, year = {2019}, author = {Flórián, N and Ladányi, M and Ittzés, A and Kröel-Dulay, G and Ónodi, G and Mucsi, M and Szili-Kovács, T and Gergócs, V and Dányi, L and Dombos, M}, title = {Effects of single and repeated drought on soil microarthropods in a semi-arid ecosystem depend more on timing and duration than drought severity.}, journal = {PloS one}, volume = {14}, number = {7}, pages = {e0219975}, pmid = {31318965}, issn = {1932-6203}, mesh = {Animals ; *Arthropods ; *Biodiversity ; Biomass ; *Droughts ; *Ecosystem ; Soil/chemistry/*parasitology ; }, abstract = {Soil moisture is one of the most important factors affecting soil biota. In arid and semi-arid ecosystems, soil mesofauna is adapted to temporary drought events, but, until now, we have had a limited understanding of the impacts of the different magnitudes and frequencies of drought predicted to occur according to future climate change scenarios. The present study focuses on how springtails and mites respond to simulated repeated drought events of different magnitudes in a field experiment in a Hungarian semi-arid sand steppe. Changes in soil arthropod activities were monitored with soil trapping over two years in a sandy soil. In the first year (2014), we applied an extreme drought pretreatment, and in the consecutive year, we applied less devastating treatments (severe drought, moderate drought, water addition) to these sites. In the first year, the extreme drought pretreatment tended to have a negative effect (either significantly or not significantly) on the capture of all Collembola groups, whereas all mite groups increased in activity density. However, in the consecutive year, between the extreme drought and control treatments, we only detected differences in soil microbial biomass. In the cases of severe drought, moderate drought and water addition, we did not find considerable changes across the microarthropods, except in the case of epedaphic Collembola. In the cases of the water addition and drought treatments, the duration and timing of the manipulation seemed to be more important for soil mesofauna than their severity (i.e., the level of soil moisture decrease). We suggest that in these extreme habitats, soil mesofauna are able to survive extreme conditions, and their populations recover rapidly, but they may not be able to cope with very long drought periods.}, } @article {pmid31316056, year = {2019}, author = {Mallick, H and Franzosa, EA and Mclver, LJ and Banerjee, S and Sirota-Madi, A and Kostic, AD and Clish, CB and Vlamakis, H and Xavier, RJ and Huttenhower, C}, title = {Predictive metabolomic profiling of microbial communities using amplicon or metagenomic sequences.}, journal = {Nature communications}, volume = {10}, number = {1}, pages = {3136}, pmid = {31316056}, issn = {2041-1723}, support = {P30 DK043351/DK/NIDDK NIH HHS/United States ; R01 DK092405/DK/NIDDK NIH HHS/United States ; P30 DK036836/DK/NIDDK NIH HHS/United States ; R01 HG005220/HG/NHGRI NIH HHS/United States ; R24 DK110499/DK/NIDDK NIH HHS/United States ; U54 DK102557/DK/NIDDK NIH HHS/United States ; P30 DK040561/DK/NIDDK NIH HHS/United States ; }, mesh = {Algorithms ; Colitis, Ulcerative/microbiology ; Crohn Disease/microbiology ; Gastrointestinal Microbiome/*genetics ; Humans ; *Metabolomics ; Metagenomics ; Microbiota/*genetics ; *Models, Genetic ; }, abstract = {Microbial community metabolomics, particularly in the human gut, are beginning to provide a new route to identify functions and ecology disrupted in disease. However, these data can be costly and difficult to obtain at scale, while amplicon or shotgun metagenomic sequencing data are readily available for populations of many thousands. Here, we describe a computational approach to predict potentially unobserved metabolites in new microbial communities, given a model trained on paired metabolomes and metagenomes from the environment of interest. Focusing on two independent human gut microbiome datasets, we demonstrate that our framework successfully recovers community metabolic trends for more than 50% of associated metabolites. Similar accuracy is maintained using amplicon profiles of coral-associated, murine gut, and human vaginal microbiomes. We also provide an expected performance score to guide application of the model in new samples. Our results thus demonstrate that this 'predictive metabolomic' approach can aid in experimental design and provide useful insights into the thousands of community profiles for which only metagenomes are currently available.}, } @article {pmid31312027, year = {2019}, author = {Macher, JN and Speksnijder, A and Choo, LQ and van der Hoorn, B and Renema, W}, title = {Uncovering bacterial and functional diversity in macroinvertebrate mitochondrial-metagenomic datasets by differential centrifugation.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {10257}, pmid = {31312027}, issn = {2045-2322}, mesh = {Animals ; Bacteria/classification/genetics ; *Biodiversity ; Centrifugation/methods ; Databases, Genetic ; Invertebrates/genetics/*microbiology ; *Metagenome ; Metagenomics/methods ; Mitochondria/genetics ; }, abstract = {PCR-free techniques such as meta-mitogenomics (MMG) can recover taxonomic composition of macroinvertebrate communities, but suffer from low efficiency, as >90% of sequencing data is mostly uninformative due to the great abundance of nuclear DNA that cannot be identified with current reference databases. Current MMG studies do not routinely check data for information on macroinvertebrate-associated bacteria and gene functions. However, this could greatly increase the efficiency of MMG studies by revealing yet overlooked diversity within ecosystems and making currently unused data available for ecological studies. By analysing six 'mock' communities, each containing three macroinvertebrate taxa, we tested whether this additional data on bacterial taxa and functional potential of communities can be extracted from MMG datasets. Further, we tested whether differential centrifugation, which is known to greatly increase efficiency of macroinvertebrate MMG studies by enriching for mitochondria, impacts on the inferred bacterial community composition. Our results show that macroinvertebrate MMG datasets contain a high number of mostly endosymbiont bacterial taxa and associated gene functions. Centrifugation reduced both the absolute and relative abundance of highly abundant Gammaproteobacteria, thereby facilitating detection of rare taxa and functions. When analysing both taxa and gene functions, the number of features obtained from the MMG dataset increased 31-fold ('enriched') respectively 234-fold ('not enriched'). We conclude that analysing MMG datasets for bacteria and gene functions greatly increases the amount of information available and facilitates the use of shotgun metagenomic techniques for future studies on biodiversity.}, } @article {pmid31310429, year = {2019}, author = {di Porcia E Brugnera, M and Meunier, F and Longo, M and Krishna Moorthy, SM and De Deurwaerder, H and Schnitzer, SA and Bonal, D and Faybishenko, B and Verbeeck, H}, title = {Modeling the impact of liana infestation on the demography and carbon cycle of tropical forests.}, journal = {Global change biology}, volume = {25}, number = {11}, pages = {3767-3780}, pmid = {31310429}, issn = {1365-2486}, mesh = {Carbon Cycle ; Demography ; *Ecosystem ; Forests ; Panama ; Trees ; *Tropical Climate ; }, abstract = {There is mounting empirical evidence that lianas affect the carbon cycle of tropical forests. However, no single vegetation model takes into account this growth form, although such efforts could greatly improve the predictions of carbon dynamics in tropical forests. In this study, we incorporated a novel mechanistic representation of lianas in a dynamic global vegetation model (the Ecosystem Demography Model). We developed a liana-specific plant functional type and mechanisms representing liana-tree interactions (such as light competition, liana-specific allometries, and attachment to host trees) and parameterized them according to a comprehensive literature meta-analysis. We tested the model for an old-growth forest (Paracou, French Guiana) and a secondary forest (Gigante Peninsula, Panama). The resulting model simulations captured many features of the two forests characterized by different levels of liana infestation as revealed by a systematic comparison of the model outputs with empirical data, including local census data from forest inventories, eddy flux tower data, and terrestrial laser scanner-derived forest vertical structure. The inclusion of lianas in the simulations reduced the secondary forest net productivity by up to 0.46 tC ha[-1] year[-1] , which corresponds to a limited relative reduction of 2.6% in comparison with a reference simulation without lianas. However, this resulted in significantly reduced accumulated above-ground biomass after 70 years of regrowth by up to 20 tC /ha (19% of the reference simulation). Ultimately, the simulated negative impact of lianas on the total biomass was almost completely cancelled out when the forest reached an old-growth successional stage. Our findings suggest that lianas negatively influence the forest potential carbon sink strength, especially for young, disturbed, liana-rich sites. In light of the critical role that lianas play in the profound changes currently experienced by tropical forests, this new model provides a robust numerical tool to forecast the impact of lianas on tropical forest carbon sinks.}, } @article {pmid31303914, year = {2019}, author = {Owiny, MO and Obonyo, MO and Gatongi, PM and Fèvre, EM}, title = {Prevalence and spatial distribution of Trematode cercariae in Vector Snails within different Agro-Ecological Zones in Western Kenya, 2016.}, journal = {The Pan African medical journal}, volume = {32}, number = {}, pages = {142}, pmid = {31303914}, issn = {1937-8688}, support = {BB/L019019/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; Cross-Sectional Studies ; *Disease Vectors ; Ecosystem ; *Geographic Information Systems ; Humans ; Kenya ; Prevalence ; Rivers ; Snails/*parasitology ; Trematoda/*isolation & purification ; }, abstract = {INTRODUCTION: Freshwater vector snails' distribution, infection with cercariae, preferred habitat and possible trematodiases transmission foci is not well known in Western Kenya. We sought to determine the distribution and prevalence of infection of snails per agro-ecological zone and environmental factors in vector snail habitats.

METHODS: We conducted a cross-sectional survey from March, 2016 - May, 2016, harvested and identified snails using shell morphology, determined their infection with trematode cercariae using microscopy, used descriptive statistics to estimate the prevalence of infection and relationship between snail abundance and environmental factors.

RESULTS: We sampled a total of 1,678 vector snails from 47 sampling sites of which 42% were Lymnaeid, 23% Biomphalaria, 10% Bulinus, 22% Oncomelaniae and 2% Melanoides. Lower Midland I Ago-Ecological Zones had 44% of the snails and streams from springs had 41% of the snails. Overall, 26.5% (445/1678) (95% CI: 24.4 - 28.6) of the snails shed cercariae. Cercariae were found in 11 (23%) of the sites and in all zones. F. gigantica cercariae were shed by L. natalensis, B. pfeifferi, B. sudanica. Lakeshore had both F. gigantica and S. mansoni cercariae shed by B. sudanica. About 72% (1,202/1,678) of snails were found in water with a pH 6.5 - 7.5. Grass habitat had 54% (912/1,678) of the snails.

CONCLUSION: Lymnaeid snails were present in all the zones, while streams from springs and near neutral habitats had most of the snails. Infection with trematode cercariae was noted in all the zones. Trematodiases control should be focused on all zones especially in freshwater streams and lakeshores.}, } @article {pmid31302400, year = {2019}, author = {Heo, S and Safder, U and Yoo, C}, title = {Deep learning driven QSAR model for environmental toxicology: Effects of endocrine disrupting chemicals on human health.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {253}, number = {}, pages = {29-38}, doi = {10.1016/j.envpol.2019.06.081}, pmid = {31302400}, issn = {1873-6424}, mesh = {Computational Biology ; *Deep Learning ; *Ecotoxicology ; Endocrine Disruptors/metabolism/*toxicity ; Environmental Pollutants/metabolism/*toxicity ; Humans ; Neural Networks, Computer ; *Quantitative Structure-Activity Relationship ; Receptors, Estrogen/metabolism ; Sex Hormone-Binding Globulin ; }, abstract = {Over 80,000 endocrine-disrupting chemicals (EDCs) are considered emerging contaminants (ECs), which are of great concern due to their effects on human health. Quantitative structure-activity relationship (QSAR) models are a promising alternative to in vitro methods to predict the toxicological effects of chemicals on human health. In this study, we assessed a deep-learning based QSAR (DL-QSAR) model to predict the qualitative and the quantitative effects of EDCs on the human endocrine system, and especially sex-hormone binding globulin (SHBG) and estrogen receptor (ER). Statistical analyses of the qualitative responses indicated that the accuracies of all three DL-QSAR methods were above 90%, and greater than the other statistical and machine learning models, indicating excellent classification performance. The quantitative analyses, as assessed using deep-neural-network-based QSAR (DNN-QSAR), resulted in a coefficient of determination (R[2]) of 0.80 and predictive square correlation coefficient (Q[2]) of 0.86, which implied satisfactory goodness of fit and predictive ability. Thus, DNN was able to transform sparse molecular descriptors into higher dimensional spaces, and was superior for assessment qualitative responses. Moreover, DNN-QSAR demonstrated excellent performance in the discipline of computational chemistry by handling multicollinearity and overfitting problems.}, } @article {pmid31301184, year = {2019}, author = {Liow, LH and Taylor, PD}, title = {Cope's Rule in a modular organism: Directional evolution without an overarching macroevolutionary trend.}, journal = {Evolution; international journal of organic evolution}, volume = {73}, number = {9}, pages = {1863-1872}, pmid = {31301184}, issn = {1558-5646}, support = {724324//H2020 European Research Council/International ; }, mesh = {Animals ; *Biological Evolution ; Body Size ; Bryozoa/*classification/ultrastructure ; Costa Rica ; Databases, Factual ; *Fossils ; Microscopy, Electron, Scanning ; Phenotype ; *Phylogeny ; Probability ; Time Factors ; }, abstract = {Cope's Rule describes increasing body size in evolutionary lineages through geological time. This pattern has been documented in unitary organisms but does it also apply to module size in colonial organisms? We address this question using 1169 cheilostome bryozoans ranging through the entire 150 million years of their evolutionary history. The temporal pattern evident in cheilostomes as a whole shows no overall change in zooid (module) size. However, individual subclades show size increases: within a genus, younger species often have larger zooids than older species. Analyses of (paleo)latitudinal shifts show that this pattern cannot be explained by latitudinal effects (Bergmann's Rule) coupled with younger species occupying higher latitudes than older species (an "out of the tropics" hypothesis). While it is plausible that size increase was linked to the advantages of large zooids in feeding, competition for trophic resources and living space, other proposed mechanisms for Cope's Rule in unitary organisms are either inapplicable to cheilostome zooid size or cannot be evaluated. Patterns and mechanisms in colonial organisms cannot and should not be extrapolated from the better-studied unitary organisms. And even if macroevolution simply comprises repeated rounds of microevolution, evolutionary processes occurring within lineages are not always detectable from macroevolutionary patterns.}, } @article {pmid31299282, year = {2019}, author = {Meshgi, B and Majidi-Rad, M and Hanafi-Bojd, AA and Fathi, S}, title = {Ecological niche modeling for predicting the habitat suitability of fascioliasis based on maximum entropy model in southern Caspian Sea littoral, Iran.}, journal = {Acta tropica}, volume = {198}, number = {}, pages = {105079}, doi = {10.1016/j.actatropica.2019.105079}, pmid = {31299282}, issn = {1873-6254}, mesh = {Altitude ; Animals ; Caspian Sea ; Cattle ; Cattle Diseases/epidemiology/*parasitology ; Ecosystem ; *Fasciola ; Fascioliasis/*veterinary ; Geographic Information Systems ; Iran/epidemiology ; Models, Biological ; Sheep ; Sheep Diseases/epidemiology/*parasitology ; }, abstract = {The present study aimed to determine the number of cases of animal fascioliasis per district in the southern littoral of Caspian Sea and to model suitable ecological niches for Fasciola infection in the region. Stool samples (n = 2688) were collected from cattle and sheep in Guilan, Mazandaran and Golestan provinces. The samples were tested using flotation method, and the number of parasite eggs per gram (EPG) of feces was recorded for each sample. Occurrence-only data of Fasciola were collected from the field. A total of 96 points/locations were used to model the ecological niche of Fasciola in maximum entropy (MaxEnt) and geographical information system (GIS). The spatial layers were compiled from 23 bioclimatic and biophysical variables for modeling analysis. Jackknife analysis was used to determine the relative importance of all variables in the model. In the present study, the proportion of fascioliasis in both hosts was highest in Guilan province (sheep: 12.34%, cattle: 15.16%), followed by Mazandaran (sheep: 7.3%, cattle: 6.25%) and Golestan (sheep: 0%, cattle: 0.94%) provinces. The Area Under Curve (AUC) value of the model was 0.909, indicating a good predictive power of the model. Our modeling results indicate that four variables, which were markedly incorporated into the model, are the major predictors of the presence probability of Fasciola spp. in the region: Bio17 (Precipitation of driest quarter; 45.5%), Bio14 (Precipitation of driest month; 24.8%), aspect (9%), and altitude (7.2%). The data presented herein show expansion of the potential high-risk areas of fascioliasis in the northern part of Iran, located at the southern littoral of Caspian Sea, especially in Guilan province. However, the extent of the predicted risk zones varied between the different areas of the region and within provinces, such that at the present, many parts of Golestan province are less environmentally suitable for Fasciola distribution than other areas in the region.}, } @article {pmid31297982, year = {2019}, author = {Barbosa, AJM and Roque, ACA}, title = {Free Marine Natural Products Databases for Biotechnology and Bioengineering.}, journal = {Biotechnology journal}, volume = {14}, number = {11}, pages = {e1800607}, doi = {10.1002/biot.201800607}, pmid = {31297982}, issn = {1860-7314}, support = {SFRH/BPD/112543/2015//Fundação para a Ciência e a Tecnologia/ ; FCT/MCTES (UID/Multi/04378/2019)//Fundação para a Ciência e a Tecnologia/ ; UID/Multi/04378/2019//Fundação para a Ciência e a Tecnologia (FCT)/MCTES/ ; }, mesh = {Agriculture ; Aquatic Organisms/*chemistry ; *Bioengineering ; Biological Products/*chemistry/*classification ; *Biotechnology ; Cosmetics ; *Databases, Chemical ; Food Industry ; Marine Biology ; Oceans and Seas ; Water Microbiology ; }, abstract = {Marine organisms and micro-organisms are a source of natural compounds with unique chemical features. These chemical properties are useful for the discovery of new functions and applications of marine natural products (MNPs). To extensively exploit the potential implementations of MNPs, they are gathered in chemical databases that allow their study and screening for applications of biotechnological interest. However, the classification of MNPs is currently poor in generic chemical databases. The present availability of free-access-focused MNP databases is scarce and the molecular diversity of these databases is still very low when compared to the paid-access ones. In this review paper, the current scenario of free-access MNP databases is presented as well as the hindrances involved in their development, mainly compound dereplication. Examples and opportunities for using freely accessible MNP databases in several important areas of biotechnology are also assessed. The scope of this paper is, as well, to notify the latent potential of these information sources for the discovery and development of new MNPs in biotechnology, and push future efforts to develop a public domain MNP database freely available for the scientific community.}, } @article {pmid31295663, year = {2019}, author = {Pitacco, V and Reizopoulou, S and Sfriso, A and Sfriso, A and Mistri, M and Munari, C}, title = {The difficulty of disentangling natural from anthropogenic forcing factors makes the evaluation of ecological quality problematic: A case study from Adriatic lagoons.}, journal = {Marine environmental research}, volume = {150}, number = {}, pages = {104756}, doi = {10.1016/j.marenvres.2019.104756}, pmid = {31295663}, issn = {1879-0291}, mesh = {Animals ; Ecology ; *Ecosystem ; *Environmental Monitoring ; Invertebrates ; Wetlands ; }, abstract = {The complex and dynamic nature of transitional ecosystems pose problems for the assessment of the Ecological Quality Status required by the European Water Framework Directive (WFD; 2000/60/EC). In six Adriatic lagoons, Ecological Quality Status was studied by comparing a biotic index based on macrophytes (MaQI), and three indices based on invertebrates (M-AMBI, M-bAMBI, and ISD). Ecological Status evaluated though MaQI and ISD resulted in quite degraded ecosystems (moderate/poor/bad), with only opportunistic algae and macrobenthic communities dominated by small size classes. Those results were supported by physico-chemical parameters, indicating high nutrients inputs, and anthropogenic pressures related with agriculture and fishery activities. Ecological Status obtained with M-AMBI and M-bAMBI was higher, with some sites reaching even the "good" status. The best response to anthropogenic pressures, in terms of a pressure index, was obtained by M-AMBI and M-bAMBI. Nevertheless, the response of used metrics (such as AMBI and bAMBI) to environmental variables not related to anthropogenic impact, and the high heterogeneity of physical-chemical conditions within lagoons, represent potential problems for the correct evaluation of Ecological Status of transitional waters. When different metrics give different responses it becomes a problem for managers who cannot easily make a decision on the remedial measures. The disagreement among indices arose because of the different response of biological elements to different stressors, and because the different indices based on macroinvertebrates focused on different aspects of the community, providing complementary information. So urge the need to find alternative approaches for a correct assessment of Ecological Status, with the combination of different biological elements, and considering the development of new indices (e.g. M-bAMBI) or refinement of the existing ones.}, } @article {pmid31291356, year = {2019}, author = {Cheng, K and Cheng, X and Wang, Y and Bi, H and Benfield, MC}, title = {Enhanced convolutional neural network for plankton identification and enumeration.}, journal = {PloS one}, volume = {14}, number = {7}, pages = {e0219570}, pmid = {31291356}, issn = {1932-6203}, mesh = {Animals ; Datasets as Topic ; *Deep Learning ; Ecological Parameter Monitoring/instrumentation/*methods ; Pacific Ocean ; *Support Vector Machine ; Video Recording ; *Zooplankton ; }, abstract = {Despite the rapid increase in the number and applications of plankton imaging systems in marine science, processing large numbers of images remains a major challenge due to large variations in image content and quality in different marine environments. We constructed an automatic plankton image recognition and enumeration system using an enhanced Convolutional Neural Network (CNN) and examined the performance of different network structures on automatic plankton image classification. The procedure started with an adaptive thresholding approach to extract Region of Interest (ROIs) from in situ plankton images, followed by a procedure to suppress the background noise and enhance target features for each extracted ROI. The enhanced ROIs were classified into seven categories by a pre-trained classifier which was a combination of a CNN and a Support Vector Machine (SVM). The CNN was selected to improve feature description and the SVM was utilized to improve classification accuracy. A series of comparison experiments were then conducted to test the effectiveness of the pre-trained classifier including the combination of CNN and SVM versus CNN alone, and the performance of different CNN models. Compared to CNN model alone, the combination of CNN and SVM increased classification accuracy and recall rate by 7.13% and 6.41%, respectively. Among the selected CNN models, the ResNet50 performed the best with accuracy and recall at 94.52% and 94.13% respectively. The present study demonstrates that deep learning technique can improve plankton image recognition and that the results can provide useful information on the selection of different CNN models for plankton recognition. The proposed algorithm could be generally applied to images acquired from different imaging systems.}, } @article {pmid31291095, year = {2019}, author = {Blumensaat, F and Leitão, JP and Ort, C and Rieckermann, J and Scheidegger, A and Vanrolleghem, PA and Villez, K}, title = {How Urban Storm- and Wastewater Management Prepares for Emerging Opportunities and Threats: Digital Transformation, Ubiquitous Sensing, New Data Sources, and Beyond - A Horizon Scan.}, journal = {Environmental science & technology}, volume = {53}, number = {15}, pages = {8488-8498}, doi = {10.1021/acs.est.8b06481}, pmid = {31291095}, issn = {1520-5851}, mesh = {*Industry ; Information Storage and Retrieval ; *Wastewater ; }, abstract = {Ubiquitous sensing will create many opportunities and threats for urban water management, which are only poorly understood today. To identify the most relevant trends, we conducted a horizon scan regarding how ubiquitous sensing will shape the future of urban drainage and wastewater management. Our survey of the international urban water community received an active response from both the academics and the professionals from the water industry. The analysis of the responses demonstrates that emerging topics for urban water will often involve experts from different communities, including aquatic ecologists, urban water system engineers and managers, as well as information and communications technology professionals and computer scientists. Activities in topics that are identified as novel will either require (i) cross-disciplinary training, such as importing new developments from the IT sector, or (ii) research in new areas for urban water specialists, for example, to help solve open questions in aquatic ecology. These results are, therefore, a call for interdisciplinary research beyond our own discipline. They also demonstrate that the water management community is not yet prepared for the digital transformation, where we will experience a data demand, i.e. a "pull" of urban water data into external services. The results suggest that a lot remains to be done to harvest the upcoming opportunities. Horizon scanning should be repeated on a routine basis, under the umbrella of an experienced polling organization.}, } @article {pmid31290101, year = {2019}, author = {Tian, D and Yan, Z and Ma, S and Ding, Y and Luo, Y and Chen, Y and Du, E and Han, W and Kovacs, ED and Shen, H and Hu, H and Kattge, J and Schmid, B and Fang, J}, title = {Family-level leaf nitrogen and phosphorus stoichiometry of global terrestrial plants.}, journal = {Science China. Life sciences}, volume = {62}, number = {8}, pages = {1047-1057}, doi = {10.1007/s11427-019-9584-1}, pmid = {31290101}, issn = {1869-1889}, mesh = {Databases, Factual ; Ecosystem ; Models, Statistical ; Nitrogen/*metabolism ; Phosphorus/*metabolism ; Photosynthesis ; Phylogeny ; Plant Leaves/*chemistry/*metabolism ; Plants/*metabolism ; Soil ; Stereoisomerism ; Temperature ; }, abstract = {Leaf nitrogen (N) and phosphorus (P) concentrations are critical for photosynthesis, growth, reproduction and other ecological processes of plants. Previous studies on large-scale biogeographic patterns of leaf N and P stoichiometric relationships were mostly conducted using data pooled across taxa, while family/genus-level analyses are rarely reported. Here, we examined global patterns of family-specific leaf N and P stoichiometry using a global data set of 12,716 paired leaf N and P records which includes 204 families, 1,305 genera, and 3,420 species. After determining the minimum size of samples (i.e., 35 records), we analyzed leaf N and P concentrations, N:P ratios and N∼P scaling relationships of plants for 62 families with 11,440 records. The numeric values of leaf N and P stoichiometry varied significantly across families and showed diverse trends along gradients of mean annual temperature (MAT) and mean annual precipitation (MAP). The leaf N and P concentrations and N:P ratios of 62 families ranged from 6.11 to 30.30 mg g[-1], 0.27 to 2.17 mg g[-1], and 10.20 to 35.40, respectively. Approximately 1/3-1/2 of the families (22-35 of 62) showed a decrease in leaf N and P concentrations and N:P ratios with increasing MAT or MAP, while the remainder either did not show a significant trend or presented the opposite pattern. Family-specific leaf N∼P scaling exponents did not converge to a certain empirical value, with a range of 0.307-0.991 for 54 out of 62 families which indicated a significant N∼P scaling relationship. Our results for the first time revealed large variation in the family-level leaf N and P stoichiometry of global terrestrial plants and that the stoichiometric relationships for at least one-third of the families were not consistent with the global trends reported previously. The numeric values of the family-specific leaf N and P stoichiometry documented in the current study provide critical synthetic parameters for biogeographic modeling and for further studies on the physiological and ecological mechanisms underlying the nutrient use strategies of plants from different phylogenetic taxa.}, } @article {pmid31290057, year = {2019}, author = {Wright, BR and Grueber, CE and Lott, MJ and Belov, K and Johnson, RN and Hogg, CJ}, title = {Impact of reduced-representation sequencing protocols on detecting population structure in a threatened marsupial.}, journal = {Molecular biology reports}, volume = {46}, number = {5}, pages = {5575-5580}, pmid = {31290057}, issn = {1573-4978}, support = {DP170101253//Australian Research Council/ ; }, mesh = {Animals ; Australia ; Computational Biology/methods ; Genetics, Population/*methods ; Genome/genetics ; Marsupialia/*genetics ; Polymorphism, Single Nucleotide/genetics ; Sequence Analysis, DNA/*methods ; }, abstract = {Reduced-representation sequencing methods have wide utility in conservation genetics of non-model species. Several methods are now available that reduce genome complexity to examine a wide range of markers in a large number of individuals. We produced two datasets collected using different laboratory techniques, comprising a common set of samples from the greater bilby (Macrotis lagotis). We examined the impact of differing data filtering thresholds on downstream population inferences. We found that choice of restriction enzyme and data filtering thresholds, especially the rate of allowable missing data, impacted our ability to detect population structure. Estimates of FST were robust to alterations in laboratory and bioinformatic protocols while principal coordinates and STRUCTURE analyses showed variation according to the number of loci and percent missing data. We advise researchers using reduced-representation sequencing in conservation projects to examine a range of data thresholds, and follow these through to downstream population inferences. Multiple measures of population differentiation should be used in order to fully understand how data filtering thresholds influence the final dataset, paying particular attention to the impact of allowable missing data. Our results indicate that failure to follow these checks could impact conclusions drawn, and conservation management decisions made.}, } @article {pmid31289988, year = {2019}, author = {Parsons, D and Wilson, NJ and Vaz, S and Lee, H and Cordier, R}, title = {Appropriateness of the TOBY Application, an iPad Intervention for Children with Autism Spectrum Disorder: A Thematic Approach.}, journal = {Journal of autism and developmental disorders}, volume = {49}, number = {10}, pages = {4053-4066}, pmid = {31289988}, issn = {1573-3432}, mesh = {Autism Spectrum Disorder/*therapy ; Child ; Computers, Handheld ; Female ; Humans ; Male ; *Mobile Applications ; *Parents ; *Therapy, Computer-Assisted ; }, abstract = {This study aimed to explore the appropriateness of an ICT intervention, the Therapeutic Outcomes by You application (TOBY app), from the perspectives of the parents. Parental experiences of twenty-four parents of a child with ASD who had participated in a three-month trial using the TOBY app were collected using semi-structured interviews. Thematic analysis was conducted and themes were mapped against an appropriateness framework. Collectively, parents felt the TOBY app was relevant and important to them and their children's needs, while expressing partial support of the TOBY app as: a positive experience for them and their children, beneficial for them and their children, a socially and ecological valid intervention, and an intervention that supported change and continuation in the skills learnt.}, } @article {pmid31288571, year = {2020}, author = {Fishe, JN and Bian, J and Chen, Z and Hu, H and Min, J and Modave, F and Prosperi, M}, title = {Prodromal clinical, demographic, and socio-ecological correlates of asthma in adults: a 10-year statewide big data multi-domain analysis.}, journal = {The Journal of asthma : official journal of the Association for the Care of Asthma}, volume = {57}, number = {11}, pages = {1155-1167}, pmid = {31288571}, issn = {1532-4303}, support = {KL2 TR001429/TR/NCATS NIH HHS/United States ; UL1 TR001427/TR/NCATS NIH HHS/United States ; UL1 TR002389/TR/NCATS NIH HHS/United States ; }, mesh = {Administrative Claims, Healthcare/statistics & numerical data ; Adult ; Asthma/*diagnosis/epidemiology ; Big Data ; Case-Control Studies ; Early Diagnosis ; Female ; Florida/epidemiology ; Humans ; Longitudinal Studies ; *Machine Learning ; Male ; Middle Aged ; *Models, Biological ; ROC Curve ; Retrospective Studies ; Risk Assessment/methods/statistics & numerical data ; Risk Factors ; Socioeconomic Factors ; }, abstract = {Objectives: To identify prodromal correlates of asthma as compared to chronic obstructive pulmonary disease and allied-conditions (COPDAC) using a multi domain analysis of socio-ecological, clinical, and demographic domains.Methods: This is a retrospective case-risk-control study using data from Florida's statewide Healthcare Cost and Utilization Project (HCUP). Patients were grouped into three groups: asthma, COPDAC (without asthma), and neither asthma nor COPDAC. To identify socio-ecological, clinical, demographic, and clinical predictors of asthma and COPDAC, we used univariate analysis, feature ranking by bootstrapped information gain ratio, multivariable logistic regression with LogitBoost selection, decision trees, and random forests.Results: A total of 141,729 patients met inclusion criteria, of whom 56,052 were diagnosed with asthma, 85,677 with COPDAC, and 84,737 with neither asthma nor COPDAC. The multi-domain approach proved superior in distinguishing asthma versus COPDAC and non-asthma/non-COPDAC controls (area under the curve (AUROC) 84%). The best domain to distinguish asthma from COPDAC without controls was prior clinical diagnoses (AUROC 82%). Ranking variables from all the domains found the most important predictors for the asthma versus COPDAC and controls were primarily socio-ecological variables, while for asthma versus COPDAC without controls, demographic and clinical variables such as age, CCI, and prior clinical diagnoses, scored better.Conclusions: In this large statewide study using a machine learning approach, we found that a multi-domain approach with demographics, clinical, and socio-ecological variables best predicted an asthma diagnosis. Future work should focus on integrating machine learning-generated predictive models into clinical practice to improve early detection of those common respiratory diseases.}, } @article {pmid31288182, year = {2019}, author = {Bolte, JFB and Clahsen, S and Vercruijsse, W and Houtveen, JH and Schipper, CMA and van Kamp, I and Bogers, R}, title = {Ecological momentary assessment study of exposure to radiofrequency electromagnetic fields and non-specific physical symptoms with self-declared electrosensitives.}, journal = {Environment international}, volume = {131}, number = {}, pages = {104948}, doi = {10.1016/j.envint.2019.104948}, pmid = {31288182}, issn = {1873-6750}, mesh = {Adolescent ; Adult ; Aged ; *Ecological Momentary Assessment ; Electromagnetic Fields/*adverse effects ; *Environmental Exposure/analysis ; Female ; Humans ; Longitudinal Studies ; Male ; Middle Aged ; Self-Assessment ; Surveys and Questionnaires ; Young Adult ; }, abstract = {The main objective of the study is to determine if non-specific physical symptoms (NSPS) in people with self-declared sensitivity to radiofrequency electromagnetic fields (RF EMF) can be explained (across subjects) by exposure to RF EMF. Furthermore, we pioneered whether analysis at the individual level or at the group level may lead to different conclusions. By our knowledge, this is the first longitudinal study exploring the data at the individual level. A group of 57 participants was equipped with a measurement set for five consecutive days. The measurement set consisted of a body worn exposimeter measuring the radiofrequency electromagnetic field in twelve frequency bands used for communication, a GPS logger, and an electronic diary giving cues at random intervals within a two to three hour interval. At every cue, a questionnaire on the most important health complaint and nine NSPS had to be filled out. We analysed the (time-lagged) associations between RF-EMF exposure in the included frequency bands and the total number of NSPS and self-rated severity of the most important health complaint. The manifestation of NSPS was studied during two different time lags - 0-1 h, and 1-4 h - after exposure and for different exposure metrics of RF EMF. The exposure was characterised by exposure metrics describing the central tendency and the intermittency of the signal, i.e. the time-weighted average exposure, the time above an exposure level or the rate of change metric. At group level, there was no statistically significant and relevant (fixed effect) association between the measured personal exposure to RF EMF and NSPS. At individual level, after correction for multiple testing and confounding, we found significant within-person associations between WiFi (the self-declared most important source) exposure metrics and the total NSPS score and severity of the most important complaint in one participant. However, it cannot be ruled out that this association is explained by residual confounding due to imperfect control for location or activities. Therefore, the outcomes have to be regarded very prudently. The significant associations were found for the short and the long time lag, but not always concurrently, so both provide complementary information. We also conclude that analyses at the individual level can lead to different findings when compared to an analysis at group level.}, } @article {pmid31288057, year = {2019}, author = {Szeliga, M and Ciura, J and Grzesik, M and Tyrka, M}, title = {Identification of candidate genes involved in steroidal alkaloids biosynthesis in organ-specific transcriptomes of Veratrum nigrum L.}, journal = {Gene}, volume = {712}, number = {}, pages = {143962}, doi = {10.1016/j.gene.2019.143962}, pmid = {31288057}, issn = {1879-0038}, mesh = {Alkaloids/*biosynthesis ; Contig Mapping ; DNA, Complementary/metabolism ; *Gene Expression Regulation, Plant ; Gene Library ; Gene Ontology ; Genetic Markers ; High-Throughput Nucleotide Sequencing ; Microsatellite Repeats ; Molecular Sequence Annotation ; Oligonucleotide Array Sequence Analysis ; Plant Leaves/metabolism ; Plant Proteins/metabolism ; Plant Roots/metabolism ; Sequence Analysis, RNA ; Steroids/*biosynthesis ; *Transcriptome ; Veratrum/*metabolism ; }, abstract = {Veratrum nigrum is protected plant of Melanthiaceae family, able to synthetize unique steroidal alkaloids important for pharmacy. Transcriptomes from leaves, stems and rhizomes of in vitro maintained V. nigrum plants were sequenced and annotated for genes and markers discovery. Sequencing of samples derived from the different organs resulted in a total of 108,511 contigs with a mean length of 596 bp. Transcripts derived from leaf and stalk were annotated at 28%, and 38% in Nr nucleotide database, respectively. The sequencing revealed 949 unigenes related with lipid metabolism, including 73 transcripts involved in steroids and genus-specific steroid alkaloids biosynthesis. Additionally, 3203 candidate SSRs markers we identified in unigenes with average density of one SSR locus every 6.2 kb sequence. Unraveling of biochemical machinery of the pathway responsible for steroidal alkaloids will open possibility to design and optimize biotechnological process. The transcriptomic data provide valuable resources for biochemical, molecular genetics, comparative transcriptomics, functional genomics, ecological and evolutionary studies of V. nigrum.}, } @article {pmid31287919, year = {2019}, author = {Li, J and Chen, GB and Rasheed, A and Li, D and Sonder, K and Zavala Espinosa, C and Wang, J and Costich, DE and Schnable, PS and Hearne, SJ and Li, H}, title = {Identifying loci with breeding potential across temperate and tropical adaptation via EigenGWAS and EnvGWAS.}, journal = {Molecular ecology}, volume = {28}, number = {15}, pages = {3544-3560}, pmid = {31287919}, issn = {1365-294X}, mesh = {Adaptation, Physiological/*genetics ; *Breeding ; Databases, Genetic ; Ecotype ; *Environment ; *Genetic Loci ; *Genome-Wide Association Study ; Genotype ; Geography ; Models, Genetic ; Molecular Sequence Annotation ; Phylogeny ; Polymorphism, Single Nucleotide/genetics ; Principal Component Analysis ; Sequence Analysis, DNA ; Zea mays/genetics ; }, abstract = {Understanding the genomic basis of adaptation in maize is important for gene discovery and the improvement of breeding germplasm, but much remains a mystery in spite of significant population genetics and archaeological research. Identifying the signals underpinning adaptation are challenging as adaptation often coincided with genetic drift, and the base genomic diversity of the species in massive. In this study, tGBS technology was used to genotype 1,143 diverse maize accessions including landraces collected from 20 countries and elite breeding lines of tropical lowland, highland, subtropical/midaltitude and temperate ecological zones. Based on 355,442 high-quality single nucleotide polymorphisms, 13 genomic regions were detected as being under selection using the bottom-up searching strategy, EigenGWAS. Of the 13 selection regions, 10 were first reported, two were associated with environmental parameters via EnvGWAS, and 146 genes were enriched. Combining large-scale genomic and ecological data in this diverse maize panel, our study supports a polygenic adaptation model of maize and offers a framework to enhance our understanding of both the mechanistic basis and the evolutionary consequences of maize domestication and adaptation. The regions identified here are promising candidates for further, targeted exploration to identify beneficial alleles and haplotypes for deployment in maize breeding.}, } @article {pmid31286860, year = {2019}, author = {Meola, M and Rifa, E and Shani, N and Delbès, C and Berthoud, H and Chassard, C}, title = {DAIRYdb: a manually curated reference database for improved taxonomy annotation of 16S rRNA gene sequences from dairy products.}, journal = {BMC genomics}, volume = {20}, number = {1}, pages = {560}, pmid = {31286860}, issn = {1471-2164}, mesh = {Classification/*methods ; Dairy Products/*microbiology ; *Databases, Genetic ; Microbiota/*genetics ; Phylogeny ; RNA, Ribosomal, 16S/*genetics ; }, abstract = {BACKGROUND: Reads assignment to taxonomic units is a key step in microbiome analysis pipelines. To date, accurate taxonomy annotation of 16S reads, particularly at species rank, is still challenging due to the short size of read sequences and differently curated classification databases. The close phylogenetic relationship between species encountered in dairy products, however, makes it crucial to annotate species accurately to achieve sufficient phylogenetic resolution for further downstream ecological studies or for food diagnostics. Curated databases dedicated to the environment of interest are expected to improve the accuracy and resolution of taxonomy annotation.

RESULTS: We provide a manually curated database composed of 10'290 full-length 16S rRNA gene sequences from prokaryotes tailored for dairy products analysis (https://github.com/marcomeola/DAIRYdb). The performance of the DAIRYdb was compared with the universal databases Silva, LTP, RDP and Greengenes. The DAIRYdb significantly outperformed all other databases independently of the classification algorithm by enabling higher accurate taxonomy annotation down to the species rank. The DAIRYdb accurately annotates over 90% of the sequences of either single or paired hypervariable regions automatically. The manually curated DAIRYdb strongly improves taxonomic annotation accuracy for microbiome studies in dairy environments. The DAIRYdb is a practical solution that enables automatization of this key step, thus facilitating the routine application of NGS microbiome analyses for microbial ecology studies and diagnostics in dairy products.}, } @article {pmid31285584, year = {2019}, author = {Edwards, RA and Vega, AA and Norman, HM and Ohaeri, M and Levi, K and Dinsdale, EA and Cinek, O and Aziz, RK and McNair, K and Barr, JJ and Bibby, K and Brouns, SJJ and Cazares, A and de Jonge, PA and Desnues, C and Díaz Muñoz, SL and Fineran, PC and Kurilshikov, A and Lavigne, R and Mazankova, K and McCarthy, DT and Nobrega, FL and Reyes Muñoz, A and Tapia, G and Trefault, N and Tyakht, AV and Vinuesa, P and Wagemans, J and Zhernakova, A and Aarestrup, FM and Ahmadov, G and Alassaf, A and Anton, J and Asangba, A and Billings, EK and Cantu, VA and Carlton, JM and Cazares, D and Cho, GS and Condeff, T and Cortés, P and Cranfield, M and Cuevas, DA and De la Iglesia, R and Decewicz, P and Doane, MP and Dominy, NJ and Dziewit, L and Elwasila, BM and Eren, AM and Franz, C and Fu, J and Garcia-Aljaro, C and Ghedin, E and Gulino, KM and Haggerty, JM and Head, SR and Hendriksen, RS and Hill, C and Hyöty, H and Ilina, EN and Irwin, MT and Jeffries, TC and Jofre, J and Junge, RE and Kelley, ST and Khan Mirzaei, M and Kowalewski, M and Kumaresan, D and Leigh, SR and Lipson, D and Lisitsyna, ES and Llagostera, M and Maritz, JM and Marr, LC and McCann, A and Molshanski-Mor, S and Monteiro, S and Moreira-Grez, B and Morris, M and Mugisha, L and Muniesa, M and Neve, H and Nguyen, NP and Nigro, OD and Nilsson, AS and O'Connell, T and Odeh, R and Oliver, A and Piuri, M and Prussin Ii, AJ and Qimron, U and Quan, ZX and Rainetova, P and Ramírez-Rojas, A and Raya, R and Reasor, K and Rice, GAO and Rossi, A and Santos, R and Shimashita, J and Stachler, EN and Stene, LC and Strain, R and Stumpf, R and Torres, PJ and Twaddle, A and Ugochi Ibekwe, M and Villagra, N and Wandro, S and White, B and Whiteley, A and Whiteson, KL and Wijmenga, C and Zambrano, MM and Zschach, H and Dutilh, BE}, title = {Global phylogeography and ancient evolution of the widespread human gut virus crAssphage.}, journal = {Nature microbiology}, volume = {4}, number = {10}, pages = {1727-1736}, pmid = {31285584}, issn = {2058-5276}, support = {K99 AI119401/AI/NIAID NIH HHS/United States ; R00 AI119401/AI/NIAID NIH HHS/United States ; T32 AI141346/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Bacteriophages/classification/*genetics ; Bacteroidetes/classification/genetics/virology ; *Biological Coevolution ; DNA, Viral/genetics ; Feces/virology ; Female ; *Gastrointestinal Microbiome ; Genetic Variation ; Humans ; Male ; Phylogeny ; Phylogeography ; Primates/virology ; }, abstract = {Microbiomes are vast communities of microorganisms and viruses that populate all natural ecosystems. Viruses have been considered to be the most variable component of microbiomes, as supported by virome surveys and examples of high genomic mosaicism. However, recent evidence suggests that the human gut virome is remarkably stable compared with that of other environments. Here, we investigate the origin, evolution and epidemiology of crAssphage, a widespread human gut virus. Through a global collaboration, we obtained DNA sequences of crAssphage from more than one-third of the world's countries and showed that the phylogeography of crAssphage is locally clustered within countries, cities and individuals. We also found fully colinear crAssphage-like genomes in both Old-World and New-World primates, suggesting that the association of crAssphage with primates may be millions of years old. Finally, by exploiting a large cohort of more than 1,000 individuals, we tested whether crAssphage is associated with bacterial taxonomic groups of the gut microbiome, diverse human health parameters and a wide range of dietary factors. We identified strong correlations with different clades of bacteria that are related to Bacteroidetes and weak associations with several diet categories, but no significant association with health or disease. We conclude that crAssphage is a benign cosmopolitan virus that may have coevolved with the human lineage and is an integral part of the normal human gut virome.}, } @article {pmid31281881, year = {2019}, author = {Brancalion, PHS and Niamir, A and Broadbent, E and Crouzeilles, R and Barros, FSM and Almeyda Zambrano, AM and Baccini, A and Aronson, J and Goetz, S and Reid, JL and Strassburg, BBN and Wilson, S and Chazdon, RL}, title = {Global restoration opportunities in tropical rainforest landscapes.}, journal = {Science advances}, volume = {5}, number = {7}, pages = {eaav3223}, pmid = {31281881}, issn = {2375-2548}, mesh = {Africa ; Biodiversity ; *Conservation of Natural Resources ; *Rainforest ; Tropical Climate ; }, abstract = {Over 140 Mha of restoration commitments have been pledged across the global tropics, yet guidance is needed to identify those landscapes where implementation is likely to provide the greatest potential benefits and cost-effective outcomes. By overlaying seven recent, peer-reviewed spatial datasets as proxies for socioenvironmental benefits and feasibility of restoration, we identified restoration opportunities (areas with higher potential return of benefits and feasibility) in lowland tropical rainforest landscapes. We found restoration opportunities throughout the tropics. Areas scoring in the top 10% (i.e., restoration hotspots) are located largely within conservation hotspots (88%) and in countries committed to the Bonn Challenge (73%), a global effort to restore 350 Mha by 2030. However, restoration hotspots represented only a small portion (19.1%) of the Key Biodiversity Area network. Concentrating restoration investments in landscapes with high benefits and feasibility would maximize the potential to mitigate anthropogenic impacts and improve human well-being.}, } @article {pmid31279910, year = {2019}, author = {Semenzin, E and Subramanian, V and Pizzol, L and Zabeo, A and Fransman, W and Oksel, C and Hristozov, D and Marcomini, A}, title = {Controlling the risks of nano-enabled products through the life cycle: The case of nano copper oxide paint for wood protection and nano-pigments used in the automotive industry.}, journal = {Environment international}, volume = {131}, number = {}, pages = {104901}, doi = {10.1016/j.envint.2019.06.011}, pmid = {31279910}, issn = {1873-6750}, mesh = {Anti-Bacterial Agents/adverse effects ; Automobiles ; Carbonates/*adverse effects ; Coloring Agents/*adverse effects ; Copper/*adverse effects ; Environmental Exposure/*adverse effects ; Fungicides, Industrial/adverse effects ; Humans ; Metal Nanoparticles/adverse effects ; Nanostructures/*adverse effects ; Paint/*adverse effects ; Risk Assessment ; Soot/adverse effects ; Wood ; }, abstract = {The widespread use of engineered nanomaterials (ENMs) in consumer products and the overwhelming uncertainties in their ecological and human health risks have raised concerns regarding their safety among industries and regulators. There has been an ongoing debate over the past few decades on ways to overcome the challenges in assessing and mitigating nano-related risks, which has reached a phase of general consensus that nanotechnology innovation should be accompanied by the application of the precautionary principle and best practice risk management, even if the risk assessment uncertainties are large. We propose a quantitative methodology for selecting the optimal risk control strategy based on information about human health and ecological risks, efficacy of risk mitigation measures, cost and other contextual factors. The risk control (RC) methodology was developed in the European FP7 research project SUN and successfully demonstrated in two case studies involving real industrial nano-enabled products (NEPs): nano-scale copper oxide (CuO) and basic copper carbonate (Cu2(OH)2CO3) used as antimicrobial and antifungal coatings and impregnations for the preservation of treated wood, and two nanoscale pigments used for colouring plastic automotive parts (i.e. red organic pigment and carbon black). The application of RC for human health risks showed that although nano-related risks could easily be controlled in automotive plastics case study with modifications in production technology or specific type of engineering controls, nano-related risks due to sanding and sawing copper oxide painted wood were non-acceptable in the use lifecycle stage and would need the identification of a more effective risk control strategy.}, } @article {pmid31278828, year = {2019}, author = {Del Campo, J and Pons, MJ and Herranz, M and Wakeman, KC and Del Valle, J and Vermeij, MJA and Leander, BS and Keeling, PJ}, title = {Validation of a universal set of primers to study animal-associated microeukaryotic communities.}, journal = {Environmental microbiology}, volume = {21}, number = {10}, pages = {3855-3861}, doi = {10.1111/1462-2920.14733}, pmid = {31278828}, issn = {1462-2920}, support = {MOP-42517//Canadian Institutes for Health Research/International ; FP7-PEOPLE-2012- IOF - 331450 CAARL//H2020 Marie Skłodowska-Curie Actions/International ; }, mesh = {Animals ; Cnidaria/*genetics ; Ctenophora/*genetics ; DNA Barcoding, Taxonomic/*methods ; DNA Primers/*genetics ; Databases, Nucleic Acid ; Genes, rRNA/genetics ; Humans ; Phylogeny ; Porifera/*genetics ; RNA, Ribosomal, 18S/genetics ; }, abstract = {The application of metabarcoding to study animal-associated microeukaryotes has been restricted because the universal barcode used to study microeukaryotic ecology and distribution in the environment, the Small Subunit of the Ribosomal RNA gene (18S rRNA), is also present in the host. As a result, when host-associated microbial eukaryotes are analysed by metabarcoding, the reads tend to be dominated by host sequences. We have done an in silico validation against the SILVA 18S rRNA database of a non-metazoan primer set (primers that are biased against the metazoan 18S rRNA) that recovers only 2.6% of all the metazoan sequences, while recovering most of the other eukaryotes (80.4%). Among metazoans, the non-metazoan primers are predicted to amplify 74% of Porifera sequences, 4% of Ctenophora, and 15% of Cnidaria, while amplifying almost no sequences within Bilateria. In vivo, these non-metazoan primers reduce significantly the animal signal from coral and human samples, and when compared against universal primers provide at worst a 2-fold decrease in the number of metazoan reads and at best a 2800-fold decrease. This easy, inexpensive, and near-universal method for the study of animal-associated microeukaryotes diversity will contribute to a better understanding of the microbiome.}, } @article {pmid31278668, year = {2019}, author = {Watson, AK and Lannes, R and Pathmanathan, JS and Méheust, R and Karkar, S and Colson, P and Corel, E and Lopez, P and Bapteste, E}, title = {The Methodology Behind Network Thinking: Graphs to Analyze Microbial Complexity and Evolution.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1910}, number = {}, pages = {271-308}, doi = {10.1007/978-1-4939-9074-0_9}, pmid = {31278668}, issn = {1940-6029}, mesh = {Biodiversity ; Biological Evolution ; Computational Biology/methods ; Ecosystem ; Evolution, Molecular ; Gene Ontology ; Gene Regulatory Networks ; High-Throughput Nucleotide Sequencing ; *Metagenome ; *Metagenomics/methods ; Microbiota ; Molecular Sequence Annotation ; Multigene Family ; }, abstract = {In the post genomic era, large and complex molecular datasets from genome and metagenome sequencing projects expand the limits of what is possible for bioinformatic analyses. Network-based methods are increasingly used to complement phylogenetic analysis in studies in molecular evolution, including comparative genomics, classification, and ecological studies. Using network methods, the vertical and horizontal relationships between all genes or genomes, whether they are from cellular chromosomes or mobile genetic elements, can be explored in a single expandable graph. In recent years, development of new methods for the construction and analysis of networks has helped to broaden the availability of these approaches from programmers to a diversity of users. This chapter introduces the different kinds of networks based on sequence similarity that are already available to tackle a wide range of biological questions, including sequence similarity networks, gene-sharing networks and bipartite graphs, and a guide for their construction and analyses.}, } @article {pmid31278639, year = {2019}, author = {Ha, S and Yang, Z}, title = {Evaluation for landscape aesthetic value of the Natural World Heritage Site.}, journal = {Environmental monitoring and assessment}, volume = {191}, number = {8}, pages = {483}, pmid = {31278639}, issn = {1573-2959}, support = {2016YFC0503306//Department of Science and Technology for Social Development/ ; }, mesh = {China ; *Conservation of Natural Resources ; Decision Making ; Environmental Monitoring/*methods ; *Esthetics ; Geographic Information Systems ; Lakes ; Public Opinion ; Rivers ; Wetlands ; }, abstract = {The landscape aesthetic value (LAV) is one essential component of outstanding universal value (OUV) for a Natural World Heritage Site (NWHS). In the identification of LAV, there is the subjectivity of methodology suggested by IUCN in the operation manual, and the expert-led evaluation is insufficient for reflecting all observers' opinions. This study focuses on establishing a universal system combining the subjectivity and objectivity, the experts' and the public's opinions to evaluate the LAV of an NWHS. We used the NWHS criteria, the ecological environment, and the viewing experience as established indicators; nine metrics were applied as corresponding layers respectively to map and give a final spatial evaluation based on the ArcGIS overlay analysis with their comprehensive weights from 3 groups of decision makers. In order to verify the rationality of our model, the LAV of a case study in Bayanbulak of NWHS Xinjiang Tianshan has been evaluated. It is demonstrated that central region of Bayanbulak with unique landscape that taking rivers, lakes, and swamps as base interlacing with wetland meadows has particularly high LAV; it basically shows a concentric circle-like distribution feature that LAV decreases from inside to outside and is consistent with practical protection status. This study responds to the UNESCO's request to monitor and evaluate the OUV of the NWHS; we believe results can provide a useful reference for the planning and decision-making of relevant scenic spots.}, } @article {pmid31277288, year = {2019}, author = {Moreno-Pedraza, A and Gabriel, J and Treutler, H and Winkler, R and Vergara, F}, title = {Effects of Water Availability in the Soil on Tropane Alkaloid Production in Cultivated Datura stramonium.}, journal = {Metabolites}, volume = {9}, number = {7}, pages = {}, pmid = {31277288}, issn = {2218-1989}, abstract = {BACKGROUND: different Solanaceae and Erythroxylaceae species produce tropane alkaloids. These alkaloids are the starting material in the production of different pharmaceuticals. The commercial demand for tropane alkaloids is covered by extracting them from cultivated plants. Datura stramonium is cultivated under greenhouse conditions as a source of tropane alkaloids. Here we investigate the effect of different levels of water availability in the soil on the production of tropane alkaloids by D. stramonium.

METHODS: We tested four irrigation levels on the accumulation of tropane alkaloids. We analyzed the profile of tropane alkaloids using an untargeted liquid chromatography/mass spectrometry method.

RESULTS: Using a combination of informatics and manual interpretation of mass spectra, we generated several structure hypotheses for signals in D. stramonium extracts that we assign as putative tropane alkaloids. Quantitation of mass spectrometry signals for our structure hypotheses across different anatomical organs allowed us to identify patterns of tropane alkaloids associated with different levels of irrigation. Furthermore, we identified anatomic partitioning of tropane alkaloid isomers with pharmaceutical applications.

CONCLUSIONS: Our results show that soil water availability is an effective method for maximizing the production of specific tropane alkaloids for industrial applications.}, } @article {pmid31275319, year = {2019}, author = {Trachsel, J and Briggs, C and Gabler, NK and Allen, HK and Loving, CL}, title = {Dietary Resistant Potato Starch Alters Intestinal Microbial Communities and Their Metabolites, and Markers of Immune Regulation and Barrier Function in Swine.}, journal = {Frontiers in immunology}, volume = {10}, number = {}, pages = {1381}, pmid = {31275319}, issn = {1664-3224}, mesh = {Animals ; *Biomarkers ; Computational Biology/methods ; *Diet ; *Gastrointestinal Microbiome/immunology ; Immunoglobulin A/immunology ; Immunohistochemistry ; *Immunomodulation ; Immunophenotyping ; Intestinal Mucosa/immunology/metabolism/microbiology ; *Metabolome ; Metabolomics/methods ; Metagenome ; Metagenomics/methods ; Models, Biological ; Phenotype ; *Solanum tuberosum/chemistry ; *Starch/chemistry ; Swine ; }, abstract = {Interactions between diet, the microbiota, and the host set the ecological conditions in the gut and have broad implications for health. Prebiotics are dietary compounds that may shift conditions toward health by promoting the growth of beneficial microbes that produce metabolites capable of modulating host cells. This study's objective was to assess how a dietary prebiotic could impact host tissues via modulation of the intestinal microbiota. Pigs fed a diet amended with 5% resistant potato starch (RPS) exhibited alterations associated with gut health relative to swine fed an unamended control diet (CON). RPS intake increased abundances of anaerobic Clostridia in feces and several tissues, as well as intestinal concentrations of butyrate. Functional gene amplicons suggested bacteria similar to Anaerostipes hadrus were stimulated by RPS intake. The CON treatment exhibited increased abundances of several genera of Proteobacteria (which utilize respiratory metabolisms) in several intestinal locations. RPS intake increased the abundance of regulatory T cells in the cecum, but not periphery, and cecal immune status alterations were indicative of enhanced mucosal defenses. A network analysis of host and microbial changes in the cecum revealed that regulatory T cells positively correlated with butyrate concentration, luminal IgA concentration, expression of IL-6 and DEF1B, and several mucosa-associated bacterial taxa. Thus, the administration of RPS modulated the microbiota and host immune status, altering markers of cecal barrier function and immunological tolerance, and suggesting a reduced niche for bacterial respiration.}, } @article {pmid31273536, year = {2019}, author = {Ahmad, I and Dar, MA and Teka, AH and Gebre, T and Gadissa, E and Tolosa, AT}, title = {Application of hydrological indices for erosion hazard mapping using Spatial Analyst tool.}, journal = {Environmental monitoring and assessment}, volume = {191}, number = {8}, pages = {482}, pmid = {31273536}, issn = {1573-2959}, mesh = {Conservation of Natural Resources ; Environmental Monitoring/*methods ; Ethiopia ; Geographic Information Systems ; Geologic Sediments ; Hydrology ; Rivers ; *Software ; Soil ; }, abstract = {Hydrological indices provide excellent input to geographic information systems for the successful mapping of erosion-prone areas. In this research, a digital elevation model was processed and analyzed to obtain the necessary hydrological indices necessary for erosion modeling. The indices (such as sediment transport index, compound topography index, and stream power index) along with other themes (Like Slope gradient, curvature, distance to channels, and channel density) were overlaid using the "Weighted Sum" overlay tool in the geographic information system. The results showed that 33.14 km[2] of the test watershed (sub-basin of Abay, Ethiopia) falls in very high/severe erosion zone and needs immediate conservation measures. A total of 98.26 km[2], 153.40 km[2], and 263.17 km[2] fall in high-, moderate-, and low-erosion hazard zones, respectively. Therefore, the primary and secondary derivatives of the digital elevation model along with morphometric parameters coupled with a Spatial Analyst tool proves to be a powerful integrated approach in demarcating erosion vulnerable zones and could be applied at regional and continental scale for proper watershed management.}, } @article {pmid31270626, year = {2019}, author = {El-Tantawi, AM and Bao, A and Chang, C and Liu, Y}, title = {Monitoring and predicting land use/cover changes in the Aksu-Tarim River Basin, Xinjiang-China (1990-2030).}, journal = {Environmental monitoring and assessment}, volume = {191}, number = {8}, pages = {480}, pmid = {31270626}, issn = {1573-2959}, support = {2017VCA0012//CAS President's International Fellowship Initiative (PIFI) for Visiting Fellows/ ; }, mesh = {Agriculture ; China ; Climate ; Conservation of Natural Resources ; Environmental Monitoring/*methods ; Forests ; Geographic Information Systems ; Neural Networks, Computer ; Population Growth ; Rivers ; Satellite Imagery ; Wetlands ; }, abstract = {Land use/cover (LCLU) is considered as one of the most serious environmental challenges that threatens developed and less developed countries. LCLU changes' monitoring using the integration of remote sensing (RS) and geographical information systems (GIS) and their predicting using an artificial neural network (ANN) in the western part of the Tarim River Basin (Aksu), north-western Xinjiang-China, from 1990 to 2030 have been investigated first time through satellite imageries available. The imageries of 1990, 2000, 2005, 2010, and 2015 were downloaded from GLCF and USGS websites. After digital image processing, the object-oriented image classification approach was applied. The ANN method with MOLUSCE Plugin was used to simulate the LCLU changes in 2020, 2025, and 2030. GIS has also been used to calculate the distance from the road and water and etc. The simulation results of 2010 and 2015 were validated using classification data with Kappa coefficient. The results showed high accuracy of the classification and prediction as the validation of simulated 2010 and 2015 maps to the referenced maps have high accuracy of Kappa 84 and 88%, respectively. The results revealed that the land cover classes forest-, grass-, wet-, and barren land have been decreased from 50.01, 13.06, 8.24, and 1.06% in 1990 to 32.03, 3.06, 6.26, and 0.97% in 2015, respectively, while the land use classes, crop or farm land, and urban land have been increased almost double from 25.5 and 2.13% in 1990 to 53.71 and 3.86% from the total area in 2015, respectively. For the prediction, forest- and wetlands will loss more than half of their areas by 2030, the grass land will be cleared completely to be only 1.3% from the total study area, while the urban land will be increased to be 4.4% or the double of 1990. These results are attributed to population growth and expanding of agriculture land on the grass land, but the effect of climate was weak as the rainfall increased during the study period. Causes and effects of the LCLU changes were briefly discussed. The output of the study serves as useful tools for policy and decision makers combatting natural resources misused in arid lands.}, } @article {pmid31270239, year = {2019}, author = {Darnet, S and Dragalzew, AC and Amaral, DB and Sousa, JF and Thompson, AW and Cass, AN and Lorena, J and Pires, ES and Costa, CM and Sousa, MP and Fröbisch, NB and Oliveira, G and Schneider, PN and Davis, MC and Braasch, I and Schneider, I}, title = {Deep evolutionary origin of limb and fin regeneration.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {116}, number = {30}, pages = {15106-15115}, pmid = {31270239}, issn = {1091-6490}, support = {BB/P027849/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; R01 OD011116/OD/NIH HHS/United States ; }, mesh = {Ambystoma mexicanum/classification/*genetics ; Animal Fins/physiology ; Animals ; *Biological Evolution ; Cichlids/classification/*genetics ; Cyprinidae/classification/*genetics ; Extremities/physiology ; Fish Proteins/classification/*genetics ; Fishes/classification/*genetics ; Gene Ontology ; Molecular Sequence Annotation ; Phylogeny ; Regeneration/*genetics ; Transcriptome ; }, abstract = {Salamanders and lungfishes are the only sarcopterygians (lobe-finned vertebrates) capable of paired appendage regeneration, regardless of the amputation level. Among actinopterygians (ray-finned fishes), regeneration after amputation at the fin endoskeleton has only been demonstrated in polypterid fishes (Cladistia). Whether this ability evolved independently in sarcopterygians and actinopterygians or has a common origin remains unknown. Here we combine fin regeneration assays and comparative RNA-sequencing (RNA-seq) analysis of Polypterus and axolotl blastemas to provide support for a common origin of paired appendage regeneration in Osteichthyes (bony vertebrates). We show that, in addition to polypterids, regeneration after fin endoskeleton amputation occurs in extant representatives of 2 other nonteleost actinopterygians: the American paddlefish (Chondrostei) and the spotted gar (Holostei). Furthermore, we assessed regeneration in 4 teleost species and show that, with the exception of the blue gourami (Anabantidae), 3 species were capable of regenerating fins after endoskeleton amputation: the white convict and the oscar (Cichlidae), and the goldfish (Cyprinidae). Our comparative RNA-seq analysis of regenerating blastemas of axolotl and Polypterus reveals the activation of common genetic pathways and expression profiles, consistent with a shared genetic program of appendage regeneration. Comparison of RNA-seq data from early Polypterus blastema to single-cell RNA-seq data from axolotl limb bud and limb regeneration stages shows that Polypterus and axolotl share a regeneration-specific genetic program. Collectively, our findings support a deep evolutionary origin of paired appendage regeneration in Osteichthyes and provide an evolutionary framework for studies on the genetic basis of appendage regeneration.}, } @article {pmid31269286, year = {2019}, author = {Kienzler, A and Connors, KA and Bonnell, M and Barron, MG and Beasley, A and Inglis, CG and Norberg-King, TJ and Martin, T and Sanderson, H and Vallotton, N and Wilson, P and Embry, MR}, title = {Mode of Action Classifications in the EnviroTox Database: Development and Implementation of a Consensus MOA Classification.}, journal = {Environmental toxicology and chemistry}, volume = {38}, number = {10}, pages = {2294-2304}, pmid = {31269286}, issn = {1552-8618}, mesh = {Animals ; *Consensus ; Databases, Factual ; *Ecotoxicology ; Fishes/physiology ; Invertebrates/physiology ; Risk Assessment ; Toxicity Tests, Acute ; }, abstract = {Multiple mode of action (MOA) frameworks have been developed in aquatic ecotoxicology, mainly based on fish toxicity. These frameworks provide information on a key determinant of chemical toxicity, but the MOA categories and level of specificity remain unique to each of the classification schemes. The present study aimed to develop a consensus MOA assignment within EnviroTox, a curated in vivo aquatic toxicity database, based on the following MOA classification schemes: Verhaar (modified) framework, Assessment Tool for Evaluating Risk, Toxicity Estimation Software Tool, and OASIS. The MOA classifications from each scheme were first collapsed into one of 3 categories: non-specifically acting (i.e., narcosis), specifically acting, or nonclassifiable. Consensus rules were developed based on the degree of concordance among the 4 individual MOA classifications to attribute a consensus MOA to each chemical. A confidence rank was also assigned to the consensus MOA classification based on the degree of consensus. Overall, 40% of the chemicals were classified as narcotics, 17% as specifically acting, and 43% as unclassified. Sixty percent of chemicals had a medium to high consensus MOA assignment. When compared to empirical acute toxicity data, the general trend of specifically acting chemicals being more toxic is clearly observed for both fish and invertebrates but not for algae. EnviroTox is the first approach to establishing a high-level consensus across 4 computationally and structurally distinct MOA classification schemes. This consensus MOA classification provides both a transparent understanding of the variation between MOA classification schemes and an added certainty of the MOA assignment. In terms of regulatory relevance, a reliable understanding of MOA can provide information that can be useful for the prioritization (ranking) and risk assessment of chemicals. Environ Toxicol Chem 2019;38:2294-2304. © 2019 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals, Inc. on behalf of SETAC.}, } @article {pmid31269015, year = {2019}, author = {Komljenovic, A and Li, H and Sorrentino, V and Kutalik, Z and Auwerx, J and Robinson-Rechavi, M}, title = {Cross-species functional modules link proteostasis to human normal aging.}, journal = {PLoS computational biology}, volume = {15}, number = {7}, pages = {e1007162}, pmid = {31269015}, issn = {1553-7358}, support = {R01 AG043930/AG/NIA NIH HHS/United States ; }, mesh = {Adult ; Aged ; Aging/genetics/*metabolism ; Animals ; Caenorhabditis elegans ; Caloric Restriction ; Computational Biology ; Drosophila melanogaster ; Evolution, Molecular ; Female ; Gene Expression Profiling ; Genetic Markers ; Humans ; Longevity/genetics/physiology ; Male ; Mice ; Middle Aged ; Models, Biological ; *Proteostasis/genetics ; Species Specificity ; Young Adult ; }, abstract = {The evolutionarily conserved nature of the few well-known anti-aging interventions that affect lifespan, such as caloric restriction, suggests that aging-related research in model organisms is directly relevant to human aging. Since human lifespan is a complex trait, a systems-level approach will contribute to a more comprehensive understanding of the underlying aging landscape. Here, we integrate evolutionary and functional information of normal aging across human and model organisms at three levels: gene-level, process-level, and network-level. We identify evolutionarily conserved modules of normal aging across diverse taxa, and notably show proteostasis to be conserved in normal aging. Additionally, we find that mechanisms related to protein quality control network are enriched for genes harboring genetic variants associated with 22 age-related human traits and associated to caloric restriction. These results demonstrate that a systems-level approach, combined with evolutionary conservation, allows the detection of candidate aging genes and pathways relevant to human normal aging.}, } @article {pmid31268533, year = {2019}, author = {Whittington, E and Karr, TL and Mongue, AJ and Dorus, S and Walters, JR}, title = {Evolutionary Proteomics Reveals Distinct Patterns of Complexity and Divergence between Lepidopteran Sperm Morphs.}, journal = {Genome biology and evolution}, volume = {11}, number = {7}, pages = {1838-1846}, pmid = {31268533}, issn = {1759-6653}, mesh = {Animals ; Gene Ontology ; Lepidoptera/metabolism ; Male ; Manduca/metabolism ; Proteomics/*methods ; Spermatogenesis/genetics/*physiology ; Spermatozoa/metabolism ; }, abstract = {Spermatozoa are one of the most strikingly diverse animal cell types. One poorly understood example of this diversity is sperm heteromorphism, where males produce multiple distinct morphs of sperm in a single ejaculate. Typically, only one morph is capable of fertilization and the function of the nonfertilizing morph, called parasperm, remains to be elucidated. Sperm heteromorphism has multiple independent origins, including Lepidoptera (moths and butterflies), where males produce a fertilizing eupyrene sperm and an apyrene parasperm, which lacks a nucleus and nuclear DNA. Here we report a comparative proteomic analysis of eupyrene and apyrene sperm between two distantly related lepidopteran species, the monarch butterfly (Danaus plexippus) and Carolina sphinx moth (Manduca sexta). In both species, we identified ∼700 sperm proteins, with half present in both morphs and the majority of the remainder observed only in eupyrene sperm. Apyrene sperm thus have a distinctly less complex proteome. Gene ontology (GO) analysis revealed proteins shared between morphs tend to be associated with canonical sperm cell structures (e.g., flagellum) and metabolism (e.g., ATP production). GO terms for morph-specific proteins broadly reflect known structural differences, but also suggest a role for apyrene sperm in modulating female neurobiology. Comparative analysis indicates that proteins shared between morphs are most conserved between species as components of sperm, whereas morph-specific proteins turn over more quickly, especially in apyrene sperm. The rapid divergence of apyrene sperm content is consistent with a relaxation of selective constraints associated with fertilization and karyogamy. On the other hand, parasperm generally exhibit greater evolutionary lability, and our observations may therefore reflect adaptive responses to shifting regimes of sexual selection.}, } @article {pmid31267637, year = {2019}, author = {Zheng, Y and Luo, L and Gao, Z and Liu, Y and Chen, Q and Kong, X and Yang, Y}, title = {Grafting induces flowering time and tuber formation changes in Brassica species involving FT signalling.}, journal = {Plant biology (Stuttgart, Germany)}, volume = {21}, number = {6}, pages = {1031-1038}, doi = {10.1111/plb.13024}, pmid = {31267637}, issn = {1438-8677}, support = {XXH13506//13th Five-year Informatization Plan of Chinese Academy of Sciences/ ; 31500221 31590820//National Natural Science Foundation of China/ ; }, mesh = {Brassica/genetics/*physiology ; Flowers/genetics/*physiology ; Gene Expression Regulation, Plant/genetics/physiology ; Plant Leaves/genetics/metabolism ; Plant Proteins/genetics/metabolism ; }, abstract = {Brassica species are widely cultivated and important biennial and annual crops. The transition from vegetative to reproductive development in Brassica species is critical in agriculture and horticulture. Grafting is a useful tool for improving agricultural production and investigating the movement of long-range signals. Here we established a hypocotyl micrografting system in B. rapa crops and successfully grafted the rootstock of turnip onto many different scion genotypes. Grafting with turnip rootstock prolonged vegetative growth, delayed flowering and improved seed yield in rapeseed. The late-flowering turnip rootstock could delay flowering of the scion of the early-flowering turnip accession. The BrrFLC1 (FLOWERING LOCUS C1 in B. rapa) transcript levels and H3K4me3 levels at the BrrFLC1 locus were up-regulated and subsequently suppressed the downstream FT (FLOWERING LOCUS T) signals in leaves of the scion to delay flowering. Vernalization treatment can efficiently promote flowering time in turnip. The non-vernalised turnip flowered early after grafting onto the rootstock of the vernalised turnip, which was accompanied by high levels of FT homologue expression in leaves of the scion. Hypocotyl excision experiments revealed that the process of tuber formation was suppressed by removing the hypocotyl tissue, which in turn repressed the expression of tuberization-related genes. Our findings suggest that the rootstock generates mobile signals that are transported from the rootstock to the scion to fine-tune FT signalling and modulate flowering time.}, } @article {pmid31266971, year = {2019}, author = {Fernández-Correa, I and Truchado, DA and Gomez-Lucia, E and Doménech, A and Pérez-Tris, J and Schmidt-Chanasit, J and Cadar, D and Benítez, L}, title = {A novel group of avian astroviruses from Neotropical passerine birds broaden the diversity and host range of Astroviridae.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {9513}, pmid = {31266971}, issn = {2045-2322}, mesh = {Amino Acid Sequence ; Animals ; Astroviridae/classification/*genetics/physiology ; Astroviridae Infections/epidemiology/pathology/virology ; Cloaca/virology ; French Guiana/epidemiology ; Genome, Viral ; *Host Specificity ; Mamastrovirus/genetics ; Open Reading Frames/genetics ; Passeriformes/*virology ; Phylogeny ; Prevalence ; Sequence Alignment ; Viral Proteins/chemistry/classification/metabolism ; }, abstract = {Metagenomics is helping to expand the known diversity of viruses, especially of those with poorly studied hosts in remote areas. The Neotropical region harbors a considerable diversity of avian species that may play a role as both host and short-distance vectors of unknown viruses. Viral metagenomics of cloacal swabs from 50 Neotropical birds collected in French Guiana revealed the presence of four complete astrovirus genomes. They constitute an early diverging novel monophyletic clade within the Avastrovirus phylogeny, representing a putative new astrovirus species (provisionally designated as Avastrovirus 5) according to the International Committee on Taxonomy of Viruses (ICTV) classification criteria. Their genomic organization shares some characteristics with Avastrovirus but also with Mamastrovirus. The pan-astrovirus RT-PCR analysis of the cloacal samples of 406 wild Neotropical birds showed a community-level prevalence of 4.9% (5.1% in passerines, the highest described so far in this order of birds). By screening birds of a remote region, we expanded the known host range of astroviruses to the avian families Cardinalidae, Conopophagidae, Furnariidae, Thamnophilidae, Turdidae and Tyrannidae. Our results provide important first insights into the unexplored viral communities, the ecology, epidemiology and features of host-pathogen interactions that shape the evolution of avastroviruses in a remote Neotropical rainforest.}, } @article {pmid31266879, year = {2019}, author = {Sze, MA and Topçuoğlu, BD and Lesniak, NA and Ruffin, MT and Schloss, PD}, title = {Fecal Short-Chain Fatty Acids Are Not Predictive of Colonic Tumor Status and Cannot Be Predicted Based on Bacterial Community Structure.}, journal = {mBio}, volume = {10}, number = {4}, pages = {}, pmid = {31266879}, issn = {2150-7511}, support = {P30 DK034933/DK/NIDDK NIH HHS/United States ; R01 CA215574/CA/NCI NIH HHS/United States ; UL1 TR002240/TR/NCATS NIH HHS/United States ; }, mesh = {Adenoma/*diagnosis/pathology ; Bacteria/classification/genetics ; Carcinoma/*diagnosis/pathology ; Clinical Decision Rules ; Colonic Neoplasms/*diagnosis/pathology ; Fatty Acids, Volatile/*analysis ; Feces/*chemistry/*microbiology ; *Gastrointestinal Microbiome ; Humans ; Metagenomics ; RNA, Ribosomal, 16S/genetics ; United States ; }, abstract = {Colonic bacterial populations are thought to have a role in the development of colorectal cancer with some protecting against inflammation and others exacerbating inflammation. Short-chain fatty acids (SCFAs) have been shown to have anti-inflammatory properties and are produced in large quantities by colonic bacteria that produce SCFAs by fermenting fiber. We assessed whether there was an association between fecal SCFA concentrations and the presence of colonic adenomas or carcinomas in a cohort of individuals using 16S rRNA gene and metagenomic shotgun sequence data. We measured the fecal concentrations of acetate, propionate, and butyrate within the cohort and found that there were no significant associations between SCFA concentration and tumor status. When we incorporated these concentrations into random forest classification models trained to differentiate between people with healthy colons and those with adenomas or carcinomas, we found that they did not significantly improve the ability of 16S rRNA gene or metagenomic gene sequence-based models to classify individuals. Finally, we generated random forest regression models trained to predict the concentration of each SCFA based on 16S rRNA gene or metagenomic gene sequence data from the same samples. These models performed poorly and were able to explain at most 14% of the observed variation in the SCFA concentrations. These results support the broader epidemiological data that questions the value of fiber consumption for reducing the risks of colorectal cancer. Although other bacterial metabolites may serve as biomarkers to detect adenomas or carcinomas, fecal SCFA concentrations have limited predictive power.IMPORTANCE Considering that colorectal cancer is the third leading cancer-related cause of death within the United States, it is important to detect colorectal tumors early and to prevent the formation of tumors. Short-chain fatty acids (SCFAs) are often used as a surrogate for measuring gut health and for being anticarcinogenic because of their anti-inflammatory properties. We evaluated the fecal SCFA concentrations of a cohort of individuals with different colonic tumor burdens who were previously analyzed to identify microbiome-based biomarkers of tumors. We were unable to find an association between SCFA concentration and tumor burden or use SCFAs to improve our microbiome-based models of classifying people based on their tumor status. Furthermore, we were unable to find an association between the fecal community structure and SCFA concentrations. Our results indicate that the association between fecal SCFAs, the gut microbiome, and tumor burden is weak.}, } @article {pmid31265463, year = {2019}, author = {Ruess, J and Pleška, M and Guet, CC and Tkačik, G}, title = {Molecular noise of innate immunity shapes bacteria-phage ecologies.}, journal = {PLoS computational biology}, volume = {15}, number = {7}, pages = {e1007168}, pmid = {31265463}, issn = {1553-7358}, support = {P 28844/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Bacteria/*immunology/*virology ; Bacteriophages/*immunology ; Computational Biology ; DNA Restriction-Modification Enzymes/immunology ; Ecosystem ; Immunity, Innate ; Microbial Consortia/immunology ; Models, Biological ; Models, Immunological ; Single-Cell Analysis ; Stochastic Processes ; }, abstract = {Mathematical models have been used successfully at diverse scales of biological organization, ranging from ecology and population dynamics to stochastic reaction events occurring between individual molecules in single cells. Generally, many biological processes unfold across multiple scales, with mutations being the best studied example of how stochasticity at the molecular scale can influence outcomes at the population scale. In many other contexts, however, an analogous link between micro- and macro-scale remains elusive, primarily due to the challenges involved in setting up and analyzing multi-scale models. Here, we employ such a model to investigate how stochasticity propagates from individual biochemical reaction events in the bacterial innate immune system to the ecology of bacteria and bacterial viruses. We show analytically how the dynamics of bacterial populations are shaped by the activities of immunity-conferring enzymes in single cells and how the ecological consequences imply optimal bacterial defense strategies against viruses. Our results suggest that bacterial populations in the presence of viruses can either optimize their initial growth rate or their population size, with the first strategy favoring simple immunity featuring a single restriction modification system and the second strategy favoring complex bacterial innate immunity featuring several simultaneously active restriction modification systems.}, } @article {pmid31264965, year = {2019}, author = {Zarin, T and Strome, B and Nguyen Ba, AN and Alberti, S and Forman-Kay, JD and Moses, AM}, title = {Proteome-wide signatures of function in highly diverged intrinsically disordered regions.}, journal = {eLife}, volume = {8}, number = {}, pages = {}, pmid = {31264965}, issn = {2050-084X}, support = {Alexander Graham Bell Scholarship//Natural Sciences and Engineering Research Council of Canada/International ; Discovery Grant//Natural Sciences and Engineering Research Council of Canada/International ; PJT-148532//CIHR/Canada ; FDN-148375//CIHR/Canada ; Postdoctoral Fellowship//Natural Sciences and Engineering Research Council of Canada/International ; Alexander Graham Bell Scholarship//National Sciences and Engineering Research Council/International ; Discovery Grant//National Sciences and Engineering Research Council/International ; }, mesh = {Amino Acid Sequence ; DNA Repair ; Evolution, Molecular ; Gene Ontology ; Intrinsically Disordered Proteins/chemistry/*metabolism ; Mitochondria/metabolism ; Molecular Sequence Annotation ; Protein Sorting Signals ; Proteome/chemistry/*metabolism ; Saccharomyces cerevisiae/metabolism ; }, abstract = {Intrinsically disordered regions make up a large part of the proteome, but the sequence-to-function relationship in these regions is poorly understood, in part because the primary amino acid sequences of these regions are poorly conserved in alignments. Here we use an evolutionary approach to detect molecular features that are preserved in the amino acid sequences of orthologous intrinsically disordered regions. We find that most disordered regions contain multiple molecular features that are preserved, and we define these as 'evolutionary signatures' of disordered regions. We demonstrate that intrinsically disordered regions with similar evolutionary signatures can rescue function in vivo, and that groups of intrinsically disordered regions with similar evolutionary signatures are strongly enriched for functional annotations and phenotypes. We propose that evolutionary signatures can be used to predict function for many disordered regions from their amino acid sequences.}, } @article {pmid31264463, year = {2020}, author = {You, D and Hunter, M and Chen, M and Chow, SM}, title = {A Diagnostic Procedure for Detecting Outliers in Linear State-Space Models.}, journal = {Multivariate behavioral research}, volume = {55}, number = {2}, pages = {231-255}, pmid = {31264463}, issn = {1532-7906}, support = {U24 AA027684/AA/NIAAA NIH HHS/United States ; R01 GM105004/GM/NIGMS NIH HHS/United States ; UL1 TR000127/TR/NCATS NIH HHS/United States ; R01 MH061388/MH/NIMH NIH HHS/United States ; R01 HD076994/HD/NICHD NIH HHS/United States ; }, mesh = {Adolescent ; Adult ; Aged ; Aged, 80 and over ; Behavioral Research/*methods ; Computer Simulation ; *Data Interpretation, Statistical ; Emotions ; Humans ; *Models, Statistical ; Monte Carlo Method ; Reference Standards ; Statistical Distributions ; Young Adult ; }, abstract = {Outliers can be more problematic in longitudinal data than in independent observations due to the correlated nature of such data. It is common practice to discard outliers as they are typically regarded as a nuisance or an aberration in the data. However, outliers can also convey meaningful information concerning potential model misspecification, and ways to modify and improve the model. Moreover, outliers that occur among the latent variables (innovative outliers) have distinct characteristics compared to those impacting the observed variables (additive outliers), and are best evaluated with different test statistics and detection procedures. We demonstrate and evaluate the performance of an outlier detection approach for multi-subject state-space models in a Monte Carlo simulation study, with corresponding adaptations to improve power and reduce false detection rates. Furthermore, we demonstrate the empirical utility of the proposed approach using data from an ecological momentary assessment study of emotion regulation together with an open-source software implementation of the procedures.}, } @article {pmid31263560, year = {2019}, author = {Smith, SP and Phillips, JB and Johnson, ML and Abbot, P and Capra, JA and Rokas, A}, title = {Genome-wide association analysis uncovers variants for reproductive variation across dog breeds and links to domestication.}, journal = {Evolution, medicine, and public health}, volume = {2019}, number = {1}, pages = {93-103}, pmid = {31263560}, issn = {2050-6201}, support = {/WT_/Wellcome Trust/United Kingdom ; R35 GM127087/GM/NIGMS NIH HHS/United States ; T32 GM128596/GM/NIGMS NIH HHS/United States ; }, abstract = {BACKGROUND AND OBJECTIVES: The diversity of eutherian reproductive strategies has led to variation in many traits, such as number of offspring, age of reproductive maturity and gestation length. While reproductive trait variation has been extensively investigated and is well established in mammals, the genetic loci contributing to this variation remain largely unknown. The domestic dog, Canis lupus familiaris is a powerful model for studies of the genetics of inherited disease due to its unique history of domestication. To gain insight into the genetic basis of reproductive traits across domestic dog breeds, we collected phenotypic data for four traits, cesarean section rate, litter size, stillbirth rate and gestation length, from primary literature and breeders' handbooks.

METHODOLOGY: By matching our phenotypic data to genomic data from the Cornell Veterinary Biobank, we performed genome-wide association analyses for these four reproductive traits, using body mass and kinship among breeds as covariates.

RESULTS: We identified 12 genome-wide significant associations between these traits and genetic loci, including variants near CACNA2D3 with gestation length, MSRB3 and MSANTD1 with litter size, SMOC2 with cesarean section rate and UFM1 with stillbirth rate. A few of these loci, such as CACNA2D3 and MSRB3, have been previously implicated in human reproductive pathologies, whereas others have been associated with domestication-related traits, including brachycephaly (SMOC2) and coat curl (KRT71).

CONCLUSIONS AND IMPLICATIONS: We hypothesize that the artificial selection that gave rise to dog breeds also influenced the observed variation in their reproductive traits. Overall, our work establishes the domestic dog as a system for studying the genetics of reproductive biology and disease.

LAY SUMMARY: The genetic contributors to variation in mammalian reproductive traits remain largely unknown. We took advantage of the domestic dog, a powerful model system, to test for associations between genome-wide variants and four reproductive traits (cesarean section rate, litter size, stillbirth rate and gestation length) that vary extensively across breeds. We identified associations at a dozen loci, including ones previously associated with domestication-related traits, suggesting that selection on dog breeds also influenced their reproductive traits.}, } @article {pmid31253856, year = {2019}, author = {Carr, A and Diener, C and Baliga, NS and Gibbons, SM}, title = {Use and abuse of correlation analyses in microbial ecology.}, journal = {The ISME journal}, volume = {13}, number = {11}, pages = {2647-2655}, pmid = {31253856}, issn = {1751-7370}, mesh = {Computational Biology/methods ; Correlation of Data ; *Ecosystem ; *Environmental Microbiology ; Humans ; *Microbial Interactions ; }, abstract = {Correlation analyses are often included in bioinformatic pipelines as methods for inferring taxon-taxon interactions. In this perspective, we highlight the pitfalls of inferring interactions from covariance and suggest methods, study design considerations, and additional data types for improving high-throughput interaction inferences. We conclude that correlation, even when augmented by other data types, almost never provides reliable information on direct biotic interactions in real-world ecosystems. These bioinformatically inferred associations are useful for reducing the number of potential hypotheses that we might test, but will never preclude the necessity for experimental validation.}, } @article {pmid31253826, year = {2019}, author = {Gong, B and Cao, H and Peng, C and Perčulija, V and Tong, G and Fang, H and Wei, X and Ouyang, S}, title = {High-throughput sequencing and analysis of microbial communities in the mangrove swamps along the coast of Beibu Gulf in Guangxi, China.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {9377}, pmid = {31253826}, issn = {2045-2322}, mesh = {Archaea/classification/genetics ; Bacteria/classification/genetics ; *Biodiversity ; China ; Computational Biology/methods ; Ecosystem ; *Environmental Microbiology ; Geography ; High-Throughput Nucleotide Sequencing ; *Metagenome ; *Metagenomics/methods ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Wetlands ; }, abstract = {Mangrove swamp is one of the world's richest and most productive marine ecosystems. This ecosystem also has a great ecological importance, but is highly susceptible to anthropogenic disturbances. The balance of mangrove ecosystem depends largely on the microbial communities in mangrove sediments. Thus, understanding how the mangrove microbial communities respond to spatial differences is essential for more accurate assessment of mangrove ecosystem health. To this end, we performed the first medium-distance (150 km) research on the biogeographic distribution of mangrove microbial communities. The hypervariable regions of 16S rRNA gene was sequenced by Illumina to compare the microbial communities in mangrove sediments collected from six locations (i.e. Zhenzhu harbor, Yuzhouping, Maowei Sea, Qinzhou harbor, Beihai city and Shankou) along the coastline of Beibu Gulf in Guangxi province, China. Collectively, Proteobacteria, Bacteroidetes, Chloroflexi, Actinobacteria, Parvarchaeota, Acidobacteria and Cyanobacteria were the predominant phyla in the mangrove sediments of this area. At genus level, the heat map of microbial communities reflected similarities between study sites and was in agreement with their biogeographic characteristics. Interestingly, the genera Desulfococcus, Arcobacter, Nitrosopumilus and Sulfurimonas showed differences in abundance between study sites. Furthermore, the principal component analysis (PCA) and unweighted UniFrac cluster tree of beta diversity were used to study the biogeographic diversity of the microbial communities. Relatively broader variation of microbial communities was found in Beihai city and Qinzhou harbour, suggesting that environmental condition and historical events may play an important role in shaping the bacterial communities as well. This is the first report on medium-distance range distribution of bacteria in the mangrove swamp ecosystem. Our data is valuable for monitoring and evaluation of the impact of human activity on mangrove habitats from the perspective of microbiome.}, } @article {pmid31253788, year = {2019}, author = {Wu, T and Guan, J and Handel, A and Tscharke, DC and Sidney, J and Sette, A and Wakim, LM and Sng, XYX and Thomas, PG and Croft, NP and Purcell, AW and La Gruta, NL}, title = {Quantification of epitope abundance reveals the effect of direct and cross-presentation on influenza CTL responses.}, journal = {Nature communications}, volume = {10}, number = {1}, pages = {2846}, pmid = {31253788}, issn = {2041-1723}, support = {APP1071916//Department of Health | National Health and Medical Research Council (NHMRC)/International ; U19AI117891//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/International ; R01 AI107625/AI/NIAID NIH HHS/United States ; APP1084283//Department of Health | National Health and Medical Research Council (NHMRC)/International ; APP1137739//Department of Health | National Health and Medical Research Council (NHMRC)/International ; U19 AI117891/AI/NIAID NIH HHS/United States ; APP1104329//Department of Health | National Health and Medical Research Council (NHMRC)/International ; R01 AI136514/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Antigen Presentation/*physiology ; Cell Line ; Epitopes, T-Lymphocyte/immunology/*physiology ; Humans ; Influenza A virus/*immunology ; Mice ; Mice, Inbred C57BL ; Mice, Transgenic ; Models, Biological ; Multivariate Analysis ; Orthomyxoviridae Infections/*immunology/virology ; T-Lymphocytes, Cytotoxic/*physiology ; }, abstract = {The magnitude of T cell responses to infection is a function of the naïve T cell repertoire combined with the context and duration of antigen presentation. Using mass spectrometry, we identify and quantify 21 class 1 MHC-restricted influenza A virus (IAV)-peptides following either direct or cross-presentation. All these peptides, including seven novel epitopes, elicit T cell responses in infected C57BL/6 mice. Directly presented IAV epitopes maintain their relative abundance across distinct cell types and reveal a broad range of epitope abundances. In contrast, cross-presented epitopes are more uniform in abundance. We observe a clear disparity in the abundance of the two key immunodominant IAV antigens, wherein direct infection drives optimal nucleoprotein (NP)366-374 presentation, while cross-presentation is optimal for acid polymerase (PA)224-233 presentation. The study demonstrates how assessment of epitope abundance in both modes of antigen presentation is necessary to fully understand the immunogenicity and response magnitude to T cell epitopes.}, } @article {pmid31251341, year = {2019}, author = {Pepin, KM and Pedersen, K and Wan, XF and Cunningham, FL and Webb, CT and Wilber, MQ}, title = {Individual-Level Antibody Dynamics Reveal Potential Drivers of Influenza A Seasonality in Wild Pig Populations.}, journal = {Integrative and comparative biology}, volume = {59}, number = {5}, pages = {1231-1242}, pmid = {31251341}, issn = {1557-7023}, support = {R01 AI116744/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Antibodies, Viral/*blood ; Influenza A virus/*physiology ; Introduced Species ; Orthomyxoviridae Infections/immunology/*veterinary/virology ; Seasons ; Swine ; Swine Diseases/*immunology/virology ; United States ; }, abstract = {Swine are important in the ecology of influenza A virus (IAV) globally. Understanding the ecological role of wild pigs in IAV ecology has been limited because surveillance in wild pigs is often for antibodies (serosurveillance) rather than IAVs, as in humans and domestic swine. As IAV antibodies can persist long after an infection, serosurveillance data are not necessarily indicative of current infection risk. However, antibody responses to IAV infections cause a predictable antibody response, thus time of infection can be inferred from antibody levels in serological samples, enabling identification of risk factors of infection at estimated times of infection. Recent work demonstrates that these quantitative antibody methods (QAMs) can accurately recover infection dates, even when individual-level variation in antibody curves is moderately high. Also, the methodology can be implemented in a survival analysis (SA) framework to reduce bias from opportunistic sampling. Here we integrated QAMs and SA and applied this novel QAM-SA framework to understand the dynamics of IAV infection risk in wild pigs seasonally and spatially, and identify risk factors. We used national-scale IAV serosurveillance data from 15 US states. We found that infection risk was highest during January-March (54% of 61 estimated peaks), with 24% of estimated peaks occurring from May to July, and some low-level of infection risk occurring year-round. Time-varying IAV infection risk in wild pigs was positively correlated with humidity and IAV infection trends in domestic swine and humans, and did not show wave-like spatial spread of infection among states, nor more similar levels of infection risk among states with more similar meteorological conditions. Effects of host sex on IAV infection risk in wild pigs were generally not significant. Because most of the variation in infection risk was explained by state-level factors or infection risk at long-distances, our results suggested that predicting IAV infection risk in wild pigs is complicated by local ecological factors and potentially long-distance translocation of infection. In addition to revealing factors of IAV infection risk in wild pigs, our framework is broadly applicable for quantifying risk factors of disease transmission using opportunistic serosurveillance sampling, a common methodology in wildlife disease surveillance. Future research on the factors that determine individual-level antibody kinetics will facilitate the design of serosurveillance systems that can extract more accurate estimates of time-varying disease risk from quantitative antibody data.}, } @article {pmid31248178, year = {2019}, author = {Zheng, R and Zhang, ZH and Zhao, YX and Chen, C and Jia, SZ and Cao, XC and Shen, LM and Ni, JZ and Song, GL}, title = {Transcriptomic Insights into the Response of the Olfactory Bulb to Selenium Treatment in a Mouse Model of Alzheimer's Disease.}, journal = {International journal of molecular sciences}, volume = {20}, number = {12}, pages = {}, pmid = {31248178}, issn = {1422-0067}, support = {81400847//Guoli Song/ ; }, mesh = {Alzheimer Disease/drug therapy/*etiology/*metabolism/pathology ; Animals ; Animals, Genetically Modified ; Computational Biology/methods ; Disease Models, Animal ; Gene Expression Profiling ; Gene Expression Regulation/drug effects ; Gene Ontology ; Mice ; Olfactory Bulb/*drug effects/*metabolism ; Reproducibility of Results ; Selenium/*pharmacology/therapeutic use ; *Transcriptome ; }, abstract = {Alzheimer's disease (AD) is a devastating neurodegenerative disorder characterized by the presence of extracellular senile plaques primarily composed of Aβ peptides and intracellular neurofibrillary tangles (NFTs) composed of hyperphosphorylated tau proteins. Olfactory dysfunction is an early clinical phenotype in AD and was reported to be attributable to the presence of NFTs, senile Aβ plaques in the olfactory bulb (OB). Our previous research found that selenomethionine (Se-Met), a major form of selenium (Se) in organisms, effectively increased oxidation resistance as well as reduced the generation and deposition of Aβ and tau hyperphosphorylation in the olfactory bulb of a triple transgenic mouse model of AD (3×Tg-AD), thereby suggesting a potential therapeutic option for AD. In this study, we further investigated changes in the transcriptome data of olfactory bulb tissues of 7-month-old triple transgenic AD (3×Tg-AD) mice treated with Se-Met (6 µg/mL) for three months. Comparison of the gene expression profile between Se-Met-treated and control mice revealed 143 differentially expressed genes (DEGs). Among these genes, 21 DEGs were upregulated and 122 downregulated. The DEGs were then annotated against the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases. The results show that upregulated genes can be roughly classified into three types. Some of them mainly regulate the regeneration of nerves, such as Fabp7, Evt5 and Gal; some are involved in improving cognition and memory, such as Areg; and some are involved in anti-oxidative stress and anti-apoptosis, such as Adcyap1 and Scg2. The downregulated genes are mainly associated with inflammation and apoptosis, such as Lrg1, Scgb3a1 and Pglyrp1. The reliability of the transcriptomic data was validated by quantitative real time polymerase chain reaction (qRT-PCR) for the selected genes. These results were in line with our previous study, which indicated therapeutic effects of Se-Met on AD mice, providing a theoretical basis for further study of the treatment of AD by Se-Met.}, } @article {pmid31246974, year = {2019}, author = {Michalska-Smith, MJ and Allesina, S}, title = {Telling ecological networks apart by their structure: A computational challenge.}, journal = {PLoS computational biology}, volume = {15}, number = {6}, pages = {e1007076}, pmid = {31246974}, issn = {1553-7358}, mesh = {Computational Biology/*methods ; Ecology/*methods ; *Ecosystem ; Machine Learning ; *Models, Biological ; *Symbiosis ; }, abstract = {Ecologists have been compiling ecological networks for over a century, detailing the interactions between species in a variety of ecosystems. To this end, they have built networks for mutualistic (e.g., pollination, seed dispersal) as well as antagonistic (e.g., herbivory, parasitism) interactions. The type of interaction being represented is believed to be reflected in the structure of the network, which would differ substantially between mutualistic and antagonistic networks. Here, we put this notion to the test by attempting to determine the type of interaction represented in a network based solely on its structure. We find that, although it is easy to separate different kinds of nonecological networks, ecological networks display much structural variation, making it difficult to distinguish between mutualistic and antagonistic interactions. We therefore frame the problem as a challenge for the community of scientists interested in computational biology and machine learning. We discuss the features a good solution to this problem should possess and the obstacles that need to be overcome to achieve this goal.}, } @article {pmid31242882, year = {2019}, author = {Iwamoto, Y and Kaucher, S and Lorenz, E and Bärnighausen, T and Winkler, V}, title = {Development of breast cancer mortality considering the implementation of mammography screening programs - a comparison of western European countries.}, journal = {BMC public health}, volume = {19}, number = {1}, pages = {823}, pmid = {31242882}, issn = {1471-2458}, mesh = {Aged ; Breast Neoplasms/ethnology/*mortality ; Cause of Death ; Early Detection of Cancer/*methods ; Europe/epidemiology ; Female ; Government Programs ; Humans ; Interrupted Time Series Analysis ; *Mammography/statistics & numerical data ; *Mass Screening/statistics & numerical data ; Middle Aged ; *Program Evaluation ; Treatment Outcome ; }, abstract = {BACKGROUND: Triggered by the successive implementation of organized mammography screening programs (MSPs) throughout western European countries over the last decades, there is an ongoing debate questioning their effectiveness. Since it is difficult to assess the effect of MSPs on a population level, we rather aim to assess the impact of the implementation itself on breast cancer mortality rates utilizing an ecological study design.

METHODS: We analyzed age group-specific (50-59, 60-69 and 70-79 years) female breast cancer mortality rates in 14 western European countries between 1980 and 2017 using Joinpoint regression, interrupted time series (ITS) regression and multivariable Poisson regression.

RESULTS: The Joinpoint analysis demonstrated decreasing trends resulting in annual percentage changes ranging from - 1.5% to - 5.4% (50-59), - 0.2% to - 8.1% (60-69) and 0% to - 7.1% (70-79) depending on the country within 3 years after MSP implementation. The ITS analysis results in highly significant interaction terms (calendar year * binary MSP indicator) for all age groups. The multivariable regression using "calendar year", "year of MSP implementation" and "years with MSP" as independent variables yielded a significant yearly decrease for "years with MSP" ranging from 0.9 to 1.2%.

CONCLUSIONS: The results of this study suggest a positive association between the implementation of MSPs and the (accelerated) reduction of breast cancer mortality rates. Measuring and quantifying the isolated effect of MSPs on a population level will require additional studies using individual data.}, } @article {pmid31240840, year = {2019}, author = {Bastille-Rousseau, G and Wittemyer, G}, title = {Leveraging multidimensional heterogeneity in resource selection to define movement tactics of animals.}, journal = {Ecology letters}, volume = {22}, number = {9}, pages = {1417-1427}, doi = {10.1111/ele.13327}, pmid = {31240840}, issn = {1461-0248}, support = {//Natural Sciences and Engineering Research Council of Canada/ ; }, mesh = {Animals ; *Behavior, Animal ; *Ecosystem ; *Elephants ; Geographic Information Systems ; Kenya ; *Motor Activity ; }, abstract = {Increasing interest in the complexity, variation and drivers of movement-related behaviours promise new insight into fundamental components of ecology. Resolving the multidimensionality of spatially explicit behaviour remains a challenge for investigating tactics and their relation to niche construction, but high-resolution movement data are providing unprecedented understanding of the diversity of spatially explicit behaviours. We introduce a framework for investigating individual variation in movement-defined resource selection that integrates the behavioural and ecological niche concepts. We apply it to long-term tracking data of 115 African elephants (Loxodonta africana), illustrating how a behavioural hypervolume can be defined based on differences between individuals and their ecological settings, and applied to explore population heterogeneity. While normative movement behaviour is frequently used to characterise population behaviour, we demonstrate the value of leveraging heterogeneity in the behaviour to gain greater insight into population structure and the mechanisms driving space-use tactics.}, } @article {pmid31233650, year = {2019}, author = {Bourgeois, Y and Boissinot, S}, title = {Selection at behavioural, developmental and metabolic genes is associated with the northward expansion of a successful tropical colonizer.}, journal = {Molecular ecology}, volume = {28}, number = {15}, pages = {3523-3543}, doi = {10.1111/mec.15162}, pmid = {31233650}, issn = {1365-294X}, mesh = {Algorithms ; Animals ; Behavior, Animal/*physiology ; Gene Ontology ; *Genes, Developmental ; Genetics, Population ; Humans ; Lizards/*genetics/*metabolism ; Polymorphism, Single Nucleotide/genetics ; Recombination, Genetic/genetics ; *Selection, Genetic ; Time Factors ; *Tropical Climate ; }, abstract = {What makes a species able to colonize novel environments? This question is key to understand the dynamics of adaptive radiations and ecological niche shifts, but the mechanisms that underlie expansion into novel habitats remain poorly understood at a genomic scale. Lizards from the genus Anolis are typically tropical, and the green anole (Anolis carolinensis) constitutes an exception since it expanded into temperate North America from subtropical Florida. Thus, we used the green anole as a model to investigate signatures of selection associated with colonization of a new environment, namely temperate North America. To this end, we analysed 29 whole-genome sequences, covering the entire native range of the species. We used a combination of recent methods to quantify both positive and balancing selection in northern populations, including FST outlier methods, machine learning and ancestral recombination graphs. We naively scanned for genes of interest and assessed the overlap between multiple tests. Strikingly, we identified many genes involved in behaviour, suggesting that the recent successful colonization of northern environments may have been linked to behavioural shifts as well as physiological adaptation. Using a candidate genes strategy, we determined that genes involved in response to cold or behaviour displayed more frequently signals of selection, while controlling for local recombination rate, gene clustering and gene length. In addition, we found signatures of balancing selection at immune genes in all investigated genetic groups, but also at genes involved in neuronal and anatomical development.}, } @article {pmid31233641, year = {2019}, author = {Titus, BM and Blischak, PD and Daly, M}, title = {Genomic signatures of sympatric speciation with historical and contemporary gene flow in a tropical anthozoan (Hexacorallia: Actiniaria).}, journal = {Molecular ecology}, volume = {28}, number = {15}, pages = {3572-3586}, doi = {10.1111/mec.15157}, pmid = {31233641}, issn = {1365-294X}, mesh = {Animals ; Atlantic Ocean ; Cluster Analysis ; Discriminant Analysis ; *Gene Flow ; Gene Ontology ; Genetic Loci ; *Genetic Speciation ; Genetics, Population ; *Genomics ; Geography ; Models, Genetic ; Sea Anemones/*genetics ; Selection, Genetic ; Species Specificity ; Sympatry/*genetics ; }, abstract = {Sympatric diversification is recognized to have played an important role in the evolution of biodiversity. However, an in situ sympatric origin for codistributed taxa is difficult to demonstrate because different evolutionary processes can lead to similar biogeographic outcomes, especially in ecosystems that can readily facilitate secondary contact due to a lack of hard barriers to dispersal. Here we use a genomic (ddRADseq), model-based approach to delimit a species complex of tropical sea anemones that are codistributed on coral reefs throughout the Tropical Western Atlantic. We use coalescent simulations in fastsimcoal2 and ordinary differential equations in Moments to test competing diversification scenarios that span the allopatric-sympatric continuum. Our results suggest that the corkscrew sea anemone Bartholomea annulata is a cryptic species complex whose members are codistributed throughout their range. Simulation and model selection analyses from both approaches suggest these lineages experienced historical and contemporary gene flow, supporting a sympatric origin, but an alternative secondary contact model receives appreciable model support in fastsimcoal2. Leveraging the genome of the closely related Exaiptasia diaphana, we identify five loci under divergent selection between cryptic B. annulata lineages that fall within mRNA transcripts or CDS regions. Our study provides a rare empirical, genomic example of sympatric speciation in a tropical anthozoan and the first range-wide molecular study of a tropical sea anemone, underscoring that anemone diversity is under-described in the tropics, and highlighting the need for additional systematic studies into these ecologically and economically important species.}, } @article {pmid31232488, year = {2019}, author = {Kahnt, B and Hattingh, WN and Theodorou, P and Wieseke, N and Kuhlmann, M and Glennon, KL and van der Niet, T and Paxton, R and Cron, GV}, title = {Should I stay or should I go? Pollinator shifts rather than cospeciation dominate the evolutionary history of South African Rediviva bees and their Diascia host plants.}, journal = {Molecular ecology}, volume = {28}, number = {17}, pages = {4118-4133}, doi = {10.1111/mec.15154}, pmid = {31232488}, issn = {1365-294X}, mesh = {Animals ; Bees/*genetics ; *Biological Evolution ; *Genetic Speciation ; Host-Parasite Interactions/*genetics ; Phylogeny ; Pollination/*physiology ; Quantitative Trait, Heritable ; Scrophulariaceae/*parasitology ; }, abstract = {Plant-pollinator interactions are often highly specialised, which may be a consequence of co-evolution. Yet when plants and pollinators co-evolve, it is not clear if this will also result in frequent cospeciation. Here, we investigate the mutual evolutionary history of South African oil-collecting Rediviva bees and their Diascia host plants, in which the elongated forelegs of female Rediviva have been suggested to coevolve with the oil-producing spurs of their Diascia hosts. After controlling for phylogenetic nonindependence, we found Rediviva foreleg length to be significantly correlated with Diascia spur length, suggestive of co-evolution. However, as trait correlation could also be due to pollinator shifts, we tested if cospeciation or pollinator shifts have dominated the evolution of Rediviva-Diascia interactions by analysing phylogenies in a cophylogenetic framework. Distance-based cophylogenetic analyses (PARAFIT, PACo) indicated significant congruence of the two phylogenies under most conditions. Yet, we found that phylogenetic relatedness was correlated with ecological similarity (the spectrum of partners that each taxon interacted with) only for Diascia but not for Rediviva, suggesting that phylogenetic congruence might be due to phylogenetic tracking by Diascia of Rediviva rather than strict (reciprocal) co-evolution. Furthermore, event-based reconciliation using a parsimony approach (CORE-PA) on average revealed only 11-13 cospeciation events but 58-80 pollinator shifts. Probabilistic cophylogenetic analyses (COALA) supported this trend (8-29 cospeciations vs. 40 pollinator shifts). Our study suggests that diversification of Diascia has been largely driven by Rediviva (phylogenetic tracking, pollinator shifts) but not vice versa. Moreover, our data suggest that, even in co-evolving mutualisms, cospeciation events might occur only infrequently.}, } @article {pmid31231776, year = {2019}, author = {Qi, M and Tan, B and Wang, J and Li, J and Liao, S and Yan, J and Liu, Y and Yin, Y}, title = {Small intestinal transcriptome analysis revealed changes of genes involved in nutrition metabolism and immune responses in growth retardation piglets1.}, journal = {Journal of animal science}, volume = {97}, number = {9}, pages = {3795-3808}, pmid = {31231776}, issn = {1525-3163}, mesh = {Animals ; Gene Expression Profiling/veterinary ; Gene Expression Regulation/*genetics ; Gene Ontology ; Growth Disorders/*veterinary ; Intestinal Mucosa/metabolism ; Intestine, Small/metabolism ; Male ; Nutritional Status ; Sequence Analysis, RNA/veterinary ; Swine/*genetics/immunology/physiology ; *Transcriptome ; }, abstract = {Postnatal growth retardation (PGR) is common in piglets. Abnormal development in small intestine was casually implicated in impaired growth, but the exact mechanism is still implausible. The present study unveiled transcriptome profile of jejunal mucosa, the major site of nutrient absorption, in PGR and healthy piglets using RNA-sequencing (RNA-seq). The middle segments of jejunum and ileum, and jejunal mucosa were obtained from healthy and PGR piglets at 42 d of age. Total RNA samples extracted from jejunal mucosa of healthy and PGR piglets were submitted for RNA-seq. Lower villus height was observed in both jejunum and ileum from PGR piglets suggesting structural impairment in small intestine (P < 0.05). RNA-seq libraries were constructed and sequenced, and produced average 4.8 × 107 clean reads. Analysis revealed a total of 499 differently expressed genes (DEGs), of which 320 DEGs were downregulated in PGR piglets as compared to healthy piglets. The functional annotation based on Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) highlighted that most DEGs were involved in nutrient metabolism and immune responses. Our results further indicated decreased gene expression associated with glucose, lipid, protein, mineral, and vitamin metabolic process, detoxication ability, oxidoreductase activity, and mucosal barrier function; as well as the increased insulin resistance and inflammatory response in the jejunal mucosa of PGR piglets. These results characterized the transcriptomic profile of the jejunal mucosa in PGR piglets, and could provide valuable information with respect to better understanding the nutrition metabolism and immune responses in the small intestine of piglets.}, } @article {pmid31229456, year = {2019}, author = {Senapati, A and Sardar, T and Ganguly, KS and Ganguly, KS and Chattopadhyay, AK and Chattopadhyay, J}, title = {Impact of adult mosquito control on dengue prevalence in a multi-patch setting: A case study in Kolkata (2014-2015).}, journal = {Journal of theoretical biology}, volume = {478}, number = {}, pages = {139-152}, doi = {10.1016/j.jtbi.2019.06.021}, pmid = {31229456}, issn = {1095-8541}, mesh = {Animals ; Dengue/*epidemiology/*parasitology ; Female ; Geography ; India ; Insecticides/toxicity ; Models, Biological ; *Mosquito Control ; Population Density ; Prevalence ; Time Factors ; }, abstract = {Dengue is one of the deadliest mosquito-borne disease prevalent mainly in tropical and sub-tropical regions. Controlling the spread of this disease becomes a major concern to the public health authority. World Health Organization (WHO) adopted several mosquito control strategies to reduce the disease prevalence. In this work, a general multi-patch non-autonomous dengue model is formulated to capture the temporal and spatial transmission mechanism of the disease and the effectiveness of different adult mosquito control strategies in reducing dengue prevalence is evaluated. During the period (2014-2015) the dengue situation of Kolkata which is one of the most dengue affected city in India is considered in our study. Depending on geographical location, Kolkata is divided into five regions and our model is fitted to the monthly dengue cases of these five regions during the above-mentioned period. By considering control specific characteristics (e.g. efficacy, environment persistence) of the mosquito control strategies, we study the efficiency of three adult mosquito controls and their combined effect in reducing dengue prevalence. From our study, it is observed that control with higher environment persistence performs better in comparison to the controls having low environment persistence. It is also observed that, connectedness between the regions play a key role in the effectiveness of the control strategies.}, } @article {pmid31229151, year = {2019}, author = {Borja, A and Chust, G and Muxika, I}, title = {Forever young: The successful story of a marine biotic index.}, journal = {Advances in marine biology}, volume = {82}, number = {}, pages = {93-127}, doi = {10.1016/bs.amb.2019.05.001}, pmid = {31229151}, issn = {2162-5875}, mesh = {Animals ; *Aquatic Organisms ; *Databases as Topic/standards/trends ; Environmental Monitoring/*methods/standards ; *Invertebrates ; }, abstract = {In 2000, the AZTI's Marine Biotic Index (AMBI) was published and was one of a number of marine benthic indices development to assess the ecological status of soft-bottom macroinvertebrates. This index, and its derivatives, has been very successful in its application to different geographical areas, across the world, as well as to different environments, from the intertidal to the abyssal, or from tidal freshwater to offshore habitats. In this review, we explain the story behind the AMBI development, and look for an explanation of the index's success. For doing that, we comment on the current practicalities of the index, we present the new AMBI species list, with 9251 taxa, we dismantle six myths around this index, and examine the past and the future of the index. We show that the solid ecological roots of the index make it a robust tool to assess the status of marine benthic communities, at any time and environment. Hence, we think that it will be 'forever young' helping managers in taking informed decisions to improve benthic marine systems.}, } @article {pmid31229001, year = {2019}, author = {Hassell, JM and Ward, MJ and Muloi, D and Bettridge, JM and Robinson, TP and Kariuki, S and Ogendo, A and Kiiru, J and Imboma, T and Kang'ethe, EK and Öghren, EM and Williams, NJ and Begon, M and Woolhouse, MEJ and Fèvre, EM}, title = {Clinically relevant antimicrobial resistance at the wildlife-livestock-human interface in Nairobi: an epidemiological study.}, journal = {The Lancet. Planetary health}, volume = {3}, number = {6}, pages = {e259-e269}, pmid = {31229001}, issn = {2542-5196}, support = {/WT_/Wellcome Trust/United Kingdom ; G1100783/MRC_/Medical Research Council/United Kingdom ; MR/R015090/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Animals ; Animals, Domestic/*microbiology ; Animals, Wild/*microbiology ; Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Bacterial ; Escherichia coli/*drug effects ; Escherichia coli Infections/epidemiology/*veterinary ; Kenya/epidemiology ; Livestock/microbiology ; Manure/*microbiology ; Prevalence ; Songbirds/microbiology ; }, abstract = {BACKGROUND: Antimicrobial resistance is one of the great challenges facing global health security in the modern era. Wildlife, particularly those that use urban environments, are an important but understudied component of epidemiology of antimicrobial resistance. We investigated antimicrobial resistance overlap between sympatric wildlife, humans, livestock, and their shared environment across the developing city of Nairobi, Kenya. We use these data to examine the role of urban wildlife in the spread of clinically relevant antimicrobial resistance.

METHODS: 99 households across Nairobi were randomly selected on the basis of socioeconomic stratification. A detailed survey was administered to household occupants, and samples (n=2102) were collected from the faeces of 75 wildlife species inhabiting household compounds (ie, the household and its perimeter; n=849), 13 livestock species (n=656), and humans (n=333), and from the external environment (n=288). Escherichia coli, our sentinel organism, was cultured and a single isolate from each sample tested for sensitivity to 13 antibiotics. Diversity of antimicrobial resistant phenotypes was compared between urban wildlife, humans, livestock, and the environment, to investigate whether wildlife are a net source for antimicrobial resistance in Nairobi. Generalised linear mixed models were used to determine whether the prevalence of antimicrobial resistant phenotypes and multidrug-resistant E coli carriage in urban wildlife is linked to variation in ecological traits, such as foraging behaviour, and to determine household-level risk factors for sharing of antimicrobial resistance between humans, wildlife, and livestock.

FINDINGS: E coli were isolated from 485 samples collected from wildlife between Sept 6,2015, and Sept 28, 2016. Wildlife carried a low prevalence of E coli isolates susceptible to all antibiotics tested (45 [9%] of 485 samples) and a high prevalence of clinically relevant multidrug resistance (252 [52%] of 485 samples), which varied between taxa and by foraging traits. Multiple isolates were resistant to one agent from at least seven antimicrobial classes tested for, and a single isolate was resistant to all antibiotics tested for in the study. The phenotypic diversity of antimicrobial-resistant E coli in wildlife was lower than in livestock, humans, and the environment. Within household compounds, statistical models identified two interfaces for exchange of antimicrobial resistance: between both rodents, humans and their rubbish, and seed-eating birds, humans and their rubbish; and between seed-eating birds, cattle, and bovine manure.

INTERPRETATION: Urban wildlife carry a high burden of clinically relevant antimicrobial-resistant E coli in Nairobi, exhibiting resistance to drugs considered crucial for human medicine by WHO. Identifiable traits of the wildlife contribute to this exposure; however, compared with humans, livestock, and the environment, low phenotypic diversity in wildlife is consistent with the hypothesis that wildlife are a net sink rather than source of clinically relevant resistance. Wildlife that interact closely with humans, livestock, and both human and livestock waste within households, are exposed to more antimicrobial resistant phenotypes, and could therefore act as conduits for the dissemination of clinically relevant antimicrobial resistance to the wider environment. These results provide novel insight into the broader epidemiology of antimicrobial resistance in complex urban environments, characteristic of lower-middle-income countries.

FUNDING: UK Medical Research Council and CGIAR Research Program on Agriculture for Nutrition and Health.}, } @article {pmid31228650, year = {2019}, author = {Savelli, B and Li, Q and Webber, M and Jemmat, AM and Robitaille, A and Zamocky, M and Mathé, C and Dunand, C}, title = {RedoxiBase: A database for ROS homeostasis regulated proteins.}, journal = {Redox biology}, volume = {26}, number = {}, pages = {101247}, pmid = {31228650}, issn = {2213-2317}, support = {001/WHO_/World Health Organization/International ; P 31707/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Chromosome Mapping/methods ; Chromosomes ; *Databases, Protein ; Homeostasis/genetics ; Multigene Family ; Oxidoreductases/classification/*genetics/metabolism ; Phylogeny ; Plants/classification/*genetics/metabolism ; Reactive Oxygen Species/*metabolism ; *Software ; }, abstract = {We present a new database, specifically devoted to ROS homeostasis regulated proteins. This database replaced our previous database, the PeroxiBase, which was focused only on various peroxidase families. The addition of 20 new protein families related with ROS homeostasis justifies the new name for this more complex and comprehensive database as RedoxiBase. Besides enlarging the focus of the database, new analysis tools and functionalities have been developed and integrated through the web interface, with which the users can now directly access to orthologous sequences and see the chromosomal localization of sequences when available. OrthoMCL tool, completed with a post-treatment process, provides precise predictions of orthologous gene groups for the sequences present in this database. In order to explore and analyse orthogroups results, taxonomic visualization of organisms containing sequence of a specific orthogroup as well as chromosomal distribution of the orthogroup with one or two organisms have been included.}, } @article {pmid31222061, year = {2019}, author = {Widhelm, TJ and Grewe, F and Huang, JP and Mercado-Díaz, JA and Goffinet, B and Lücking, R and Moncada, B and Mason-Gamer, R and Lumbsch, HT}, title = {Multiple historical processes obscure phylogenetic relationships in a taxonomically difficult group (Lobariaceae, Ascomycota).}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {8968}, pmid = {31222061}, issn = {2045-2322}, mesh = {Ascomycota/*classification/*genetics ; Biological Evolution ; DNA Barcoding, Taxonomic ; Databases, Genetic ; *Evolution, Molecular ; *Phylogeny ; }, abstract = {In the age of next-generation sequencing, the number of loci available for phylogenetic analyses has increased by orders of magnitude. But despite this dramatic increase in the amount of data, some phylogenomic studies have revealed rampant gene-tree discordance that can be caused by many historical processes, such as rapid diversification, gene duplication, or reticulate evolution. We used a target enrichment approach to sample 400 single-copy nuclear genes and estimate the phylogenetic relationships of 13 genera in the lichen-forming family Lobariaceae to address the effect of data type (nucleotides and amino acids) and phylogenetic reconstruction method (concatenation and species tree approaches). Furthermore, we examined datasets for evidence of historical processes, such as rapid diversification and reticulate evolution. We found incongruence associated with sequence data types (nucleotide vs. amino acid sequences) and with different methods of phylogenetic reconstruction (species tree vs. concatenation). The resulting phylogenetic trees provided evidence for rapid and reticulate evolution based on extremely short branches in the backbone of the phylogenies. The observed rapid and reticulate diversifications may explain conflicts among gene trees and the challenges to resolving evolutionary relationships. Based on divergence times, the diversification at the backbone occurred near the Cretaceous-Paleogene (K-Pg) boundary (65 Mya) which is consistent with other rapid diversifications in the tree of life. Although some phylogenetic relationships within the Lobariaceae family remain with low support, even with our powerful phylogenomic dataset of up to 376 genes, our use of target-capturing data allowed for the novel exploration of the mechanisms underlying phylogenetic and systematic incongruence.}, } @article {pmid31221226, year = {2019}, author = {Vogt, L}, title = {Organizing phenotypic data-a semantic data model for anatomy.}, journal = {Journal of biomedical semantics}, volume = {10}, number = {1}, pages = {12}, pmid = {31221226}, issn = {2041-1480}, mesh = {*Anatomy ; Biological Ontologies ; Computer Graphics ; *Phenotype ; *Semantics ; }, abstract = {BACKGROUND: Currently, almost all morphological data are published as unstructured free text descriptions. This not only brings about terminological problems regarding semantic transparency, which hampers their re-use by non-experts, but the data cannot be parsed by computers either, which in turn hampers their integration across many fields in the life sciences, including genomics, systems biology, development, medicine, evolution, ecology, and systematics. With an ever-increasing amount of available ontologies and the development of adequate semantic technology, however, a solution to this problem becomes available. Instead of free text descriptions, morphological data can be recorded, stored, and communicated through the Web in the form of highly formalized and structured directed graphs (semantic graphs) that use ontology terms and URIs as terminology.

RESULTS: After introducing an instance-based approach of recording morphological descriptions as semantic graphs (i.e., Semantic Instance Anatomy Knowledge Graphs) and discussing accompanying metadata graphs, I propose a general scheme of how to efficiently organize the resulting graphs in a tuple store framework based on instances of defined named graph ontology classes. The use of such named graph resources allows meaningful fragmentation of the data, which in turn enables subsequent specification of all kinds of data views for managing and accessing morphological data.

CONCLUSIONS: Morphological data that comply with the here proposed semantic data model will not only be computer-parsable but also re-usable by non-experts and could be better integrated with other sources of data in the life sciences. This would allow morphology as a discipline to further participate in eScience and Big Data.}, } @article {pmid31220587, year = {2020}, author = {Trifi, H and Najjari, A and Achouak, W and Barakat, M and Ghedira, K and Mrad, F and Saidi, M and Sghaier, H}, title = {Metataxonomics of Tunisian phosphogypsum based on five bioinformatics pipelines: Insights for bioremediation.}, journal = {Genomics}, volume = {112}, number = {1}, pages = {981-989}, doi = {10.1016/j.ygeno.2019.06.014}, pmid = {31220587}, issn = {1089-8646}, mesh = {Bacteria/classification/genetics/isolation & purification/*metabolism ; Biodegradation, Environmental ; *Calcium Sulfate/chemistry/metabolism ; Computational Biology ; High-Throughput Nucleotide Sequencing ; Microbiota ; *Phosphorus/chemistry/metabolism ; Sequence Analysis, DNA ; Software ; Tunisia ; }, abstract = {Phosphogypsum (PG) is an acidic by-product from the phosphate fertilizer industry and it is characterized by a low nutrient availability and the presence of radionuclides and heavy metals which pose a serious problem in its management. Here, we have applied Illumina MiSeq sequencing technology and five bioinformatics pipelines to explore the phylogenetic communities in Tunisian PG. Taking One Codex as a reference method, we present the results of 16S-rDNA-gene-based metataxonomics abundances with four other alternative bioinformatics pipelines (MetaGenome Rapid Annotation using Subsystem Technology (MG-RAST), mothur, MICrobial Community Analysis (MICCA) and Quantitative Insights into Microbial Ecology (QIIME)), when analyzing the Tunisian PG. Importantly, based on 16S rDNA datasets, the functional capabilities of microbial communities of PG were deciphered. They suggested the presence of PG autochthonous bacteria valorizable into (1) removal of radioactive elements and toxic heavy metals, (2) promotion of plant growth, (3) oxidation and (4) reduction of sulfate. These bacteria can be explored further for applications in the bioremediation of by-products, like PG, by different processes.}, } @article {pmid31220077, year = {2019}, author = {Mangul, S and Mosqueiro, T and Abdill, RJ and Duong, D and Mitchell, K and Sarwal, V and Hill, B and Brito, J and Littman, RJ and Statz, B and Lam, AK and Dayama, G and Grieneisen, L and Martin, LS and Flint, J and Eskin, E and Blekhman, R}, title = {Challenges and recommendations to improve the installability and archival stability of omics computational tools.}, journal = {PLoS biology}, volume = {17}, number = {6}, pages = {e3000333}, pmid = {31220077}, issn = {1545-7885}, support = {R01 ES021801/ES/NIEHS NIH HHS/United States ; R01 MH101782/MH/NIMH NIH HHS/United States ; K25 HL080079/HL/NHLBI NIH HHS/United States ; P01 HL028481/HL/NHLBI NIH HHS/United States ; R25 MH109172/MH/NIMH NIH HHS/United States ; R35 GM128716/GM/NIGMS NIH HHS/United States ; R01 ES022282/ES/NIEHS NIH HHS/United States ; P01 HL030568/HL/NHLBI NIH HHS/United States ; R01 GM083198/GM/NIGMS NIH HHS/United States ; R01 AI173172/AI/NIAID NIH HHS/United States ; U01 DA024417/DA/NIDA NIH HHS/United States ; }, mesh = {Biomedical Research ; Computational Biology/*methods ; Databases, Factual ; Humans ; Information Dissemination/*methods ; Information Storage and Retrieval/*methods ; Internet ; Software/trends ; }, abstract = {Developing new software tools for analysis of large-scale biological data is a key component of advancing modern biomedical research. Scientific reproduction of published findings requires running computational tools on data generated by such studies, yet little attention is presently allocated to the installability and archival stability of computational software tools. Scientific journals require data and code sharing, but none currently require authors to guarantee the continuing functionality of newly published tools. We have estimated the archival stability of computational biology software tools by performing an empirical analysis of the internet presence for 36,702 omics software resources published from 2005 to 2017. We found that almost 28% of all resources are currently not accessible through uniform resource locators (URLs) published in the paper they first appeared in. Among the 98 software tools selected for our installability test, 51% were deemed "easy to install," and 28% of the tools failed to be installed at all because of problems in the implementation. Moreover, for papers introducing new software, we found that the number of citations significantly increased when authors provided an easy installation process. We propose for incorporation into journal policy several practical solutions for increasing the widespread installability and archival stability of published bioinformatics software.}, } @article {pmid31219681, year = {2020}, author = {Ryo, M and Jeschke, JM and Rillig, MC and Heger, T}, title = {Machine learning with the hierarchy-of-hypotheses (HoH) approach discovers novel pattern in studies on biological invasions.}, journal = {Research synthesis methods}, volume = {11}, number = {1}, pages = {66-73}, pmid = {31219681}, issn = {1759-2887}, support = {01LC1501A//Bundesministerium für Bildung und Forschung/ ; the Grant-in-Aid for JSPS Overseas Research Fellow//Japan Society for the Promotion of Science/ ; JE 288/9-1//Deutsche Forschungsgemeinschaft/ ; JE 288/9-2//Deutsche Forschungsgemeinschaft/ ; 01LC1501A//German Federal Ministry of Education and Research (BMBF)/ ; Az 92807//Volkswagen Foundation/ ; }, mesh = {Algorithms ; Animals ; Artificial Intelligence ; Asia ; Biology/*methods ; Data Interpretation, Statistical ; *Decision Trees ; Ecology ; Ecosystem ; Geography ; *Introduced Species ; *Machine Learning ; Models, Statistical ; Reproducibility of Results ; Research Design ; *Review Literature as Topic ; }, abstract = {Research synthesis on simple yet general hypotheses and ideas is challenging in scientific disciplines studying highly context-dependent systems such as medical, social, and biological sciences. This study shows that machine learning, equation-free statistical modeling of artificial intelligence, is a promising synthesis tool for discovering novel patterns and the source of controversy in a general hypothesis. We apply a decision tree algorithm, assuming that evidence from various contexts can be adequately integrated in a hierarchically nested structure. As a case study, we analyzed 163 articles that studied a prominent hypothesis in invasion biology, the enemy release hypothesis. We explored if any of the nine attributes that classify each study can differentiate conclusions as classification problem. Results corroborated that machine learning can be useful for research synthesis, as the algorithm could detect patterns that had been already focused in previous narrative reviews. Compared with the previous synthesis study that assessed the same evidence collection based on experts' judgement, the algorithm has newly proposed that the studies focusing on Asian regions mostly supported the hypothesis, suggesting that more detailed investigations in these regions can enhance our understanding of the hypothesis. We suggest that machine learning algorithms can be a promising synthesis tool especially where studies (a) reformulate a general hypothesis from different perspectives, (b) use different methods or variables, or (c) report insufficient information for conducting meta-analyses.}, } @article {pmid31219223, year = {2019}, author = {Nieto-Rabiela, F and Wiratsudakul, A and Suzán, G and Rico-Chávez, O}, title = {Viral networks and detection of potential zoonotic viruses in bats and rodents: A worldwide analysis.}, journal = {Zoonoses and public health}, volume = {66}, number = {6}, pages = {655-666}, pmid = {31219223}, issn = {1863-2378}, mesh = {Animals ; Chiroptera/*virology ; Databases, Factual ; Disease Reservoirs/*virology ; Rodentia/*virology ; Virus Diseases/transmission/*veterinary/virology ; Zoonoses ; }, abstract = {Bats and rodents are recognized to host a great diversity of viruses and several important viral zoonoses, but how this viral diversity is structured and how viruses are connected, shared and distributed among host networks is not well understood. To address this gap in knowledge, we compared the associative capacity of the host-virus networks in rodents and bats with the identification of those viruses with zoonotic potential. A virus database, detected by molecular methods, was constructed in the two taxonomic groups. We compiled 5,484 records: 825 in rodents and 4,659 in bats. We identified a total of 173 and 166 viruses, of which 53 and 40 are zoonotic viruses, in rodents and bats, respectively. Based on a network theory, a non-directed bipartite host-virus network was built for each group. Subsequently, the networks were collapsed to represent the connections among hosts and viruses. We identified both discrete and connected communities. We observed a greater degree of connectivity in bat viruses and more discrete communities in rodents. The Coronaviridae recorded in bats have the highest values of degree, betweenness and closeness centralities. In rodents, higher degree positions were distributed homogeneously between viruses and hosts. At least in our database, a higher proportion of rodent viruses were zoonotic. Rodents should thus not be underestimated as important reservoirs of zoonotic disease. We found that viruses were more frequently shared among bats than in rodents. Network theory can reveal some macroecological patterns and identify risks that were previously unrecognized. For example, we found that parvovirus in megabats and Gbagroube virus in rodents may represent a zoonotic risk due to the proximity to humans and other zoonotic viruses. We propose that epidemiological surveillance programmes should consider the connectivity of network actors as a measure of the risks of dispersion and transmission.}, } @article {pmid31217263, year = {2019}, author = {Liedtke, HC and Garrido, JG and Esteve-Codina, A and Gut, M and Alioto, T and Gomez-Mestre, I}, title = {De Novo Assembly and Annotation of the Larval Transcriptome of Two Spadefoot Toads Widely Divergent in Developmental Rate.}, journal = {G3 (Bethesda, Md.)}, volume = {9}, number = {8}, pages = {2647-2655}, pmid = {31217263}, issn = {2160-1836}, mesh = {Animals ; Anura/*genetics ; *Biomarkers ; *Computational Biology/methods ; *Gene Expression Profiling ; Molecular Sequence Annotation ; Species Specificity ; *Transcriptome ; }, abstract = {Amphibians are highly vulnerable and diverse vertebrates for which we still have modest genomic resources. Amphibian larvae are key components of continental wetlands, where they have strong influences on energy fluxes, nutrient cycling, and community structure. Amphibian larvae are highly sensitive to environmental conditions and can often alter their physiology, behavior and even morphology in response to the local conditions experienced, although we still know relatively little about the transcriptomic changes that enable such plasticity. Here we contribute the larval transcriptomes of two spadefoot toad species with divergent developmental rates and degree of developmental plasticity in response to pond drying.}, } @article {pmid31215647, year = {2019}, author = {Mencuccini, M and Rosas, T and Rowland, L and Choat, B and Cornelissen, H and Jansen, S and Kramer, K and Lapenis, A and Manzoni, S and Niinemets, Ü and Reich, P and Schrodt, F and Soudzilovskaia, N and Wright, IJ and Martínez-Vilalta, J}, title = {Leaf economics and plant hydraulics drive leaf : wood area ratios.}, journal = {The New phytologist}, volume = {224}, number = {4}, pages = {1544-1556}, doi = {10.1111/nph.15998}, pmid = {31215647}, issn = {1469-8137}, mesh = {Databases, Factual ; Plant Leaves/*physiology ; Trees/physiology ; Water/metabolism ; Wood/*physiology ; Xylem/physiology ; }, abstract = {Biomass and area ratios between leaves, stems and roots regulate many physiological and ecological processes. The Huber value Hv (sapwood area/leaf area ratio) is central to plant water balance and drought responses. However, its coordination with key plant functional traits is poorly understood, and prevents developing trait-based prediction models. Based on theoretical arguments, we hypothesise that global patterns in Hv of terminal woody branches can be predicted from variables related to plant trait spectra, that is plant hydraulics and size and leaf economics. Using a global compilation of 1135 species-averaged Hv , we show that Hv varies over three orders of magnitude. Higher Hv are seen in short small-leaved low-specific leaf area (SLA) shrubs with low Ks in arid relative to tall large-leaved high-SLA trees with high Ks in moist environments. All traits depend on climate but climatic correlations are stronger for explanatory traits than Hv . Negative isometry is found between Hv and Ks , suggesting a compensation to maintain hydraulic supply to leaves across species. This work identifies the major global drivers of branch sapwood/leaf area ratios. Our approach based on widely available traits facilitates the development of accurate models of above-ground biomass allocation and helps predict vegetation responses to drought.}, } @article {pmid31213173, year = {2019}, author = {Pancerasa, M and Sangiorgio, M and Ambrosini, R and Saino, N and Winkler, DW and Casagrandi, R}, title = {Reconstruction of long-distance bird migration routes using advanced machine learning techniques on geolocator data.}, journal = {Journal of the Royal Society, Interface}, volume = {16}, number = {155}, pages = {20190031}, pmid = {31213173}, issn = {1742-5662}, mesh = {*Animal Migration ; Animals ; Geographic Information Systems ; *Machine Learning ; *Models, Biological ; *Seasons ; Swallows/*physiology ; }, abstract = {Geolocators are a well-established technology to reconstruct migration routes of animals that are too small to carry satellite tags (e.g. passerine birds). These devices record environmental light-level data that enable the reconstruction of daily positions from the time of twilight. However, all current methods for analysing geolocator data require manual pre-processing of raw records to eliminate twilight events showing unnatural variation in light levels, a step that is time-consuming and must be accomplished by a trained expert. Here, we propose and implement advanced machine learning techniques to automate this procedure and we apply them to 108 migration tracks of barn swallows (Hirundo rustica). We show that routes reconstructed from the automated pre-processing are comparable to those obtained from manual selection accomplished by a human expert. This raises the possibility of fully automating light-level geolocator data analysis and possibly analysing the large amount of data already collected on several species.}, } @article {pmid31212899, year = {2019}, author = {Altuwairiqi, M and Jiang, N and Ali, R}, title = {Problematic Attachment to Social Media: Five Behavioural Archetypes.}, journal = {International journal of environmental research and public health}, volume = {16}, number = {12}, pages = {}, pmid = {31212899}, issn = {1660-4601}, mesh = {Adolescent ; Adult ; Age Factors ; Behavior, Addictive/*etiology/*psychology ; Female ; Humans ; Male ; Qualitative Research ; *Screen Time ; Sex Factors ; Social Media/*statistics & numerical data ; Young Adult ; }, abstract = {Today, social media play an important role in people's daily lives. Many people use social media to satisfy their personal and social needs, such as enhancing self-image, acquiring self-esteem, and gaining popularity. However, when social media are used obsessively and excessively, behavioural addiction symptoms can occur, leading to negative impacts on one's life, which is defined as a problematic attachment to social media. Research suggests that tools can be provided to assist the change of problematic attachment behaviour, but it remains unclear how such tools should be designed and personalised to meet individual needs and profiles. This study makes the first attempt to tackle this problem by developing five behavioural archetypes, characterising how social media users differ in their problematic attachments to them. The archetypes are meant to facilitate effective ideation, creativity, and communication during the design process and helping the elicitation and customisation of the variability in the requirements and design of behaviour change tools for combatting problematic usage of social media. This was achieved by using a four-phase qualitative study where the diary study method was considered at the initial stage, and also the refinement and confirmation stage, to enhance ecological validity.}, } @article {pmid31207495, year = {2019}, author = {Wang, J and Liu, S and Liu, H and Chen, K and Zhang, P}, title = {PnSAG1, an E3 ubiquitin ligase of the Antarctic moss Pohlia nutans, enhanced sensitivity to salt stress and ABA.}, journal = {Plant physiology and biochemistry : PPB}, volume = {141}, number = {}, pages = {343-352}, doi = {10.1016/j.plaphy.2019.06.002}, pmid = {31207495}, issn = {1873-2690}, mesh = {Abscisic Acid/*pharmacology ; Antarctic Regions ; Arabidopsis/genetics/*physiology ; Bryophyta/*enzymology/genetics ; Bryopsida/genetics/*physiology ; Computational Biology ; Droughts ; Gene Expression Regulation, Plant ; Germ Cells, Plant/metabolism ; Germination ; Plant Roots/growth & development ; Plants, Genetically Modified/physiology ; *Salt Stress ; Signal Transduction ; Ubiquitin-Protein Ligases/*genetics ; }, abstract = {Plant U-box (PUB) E3 ubiquitin ligases play crucial roles in the plant response to abiotic stress and the phytohormone abscisic acid (ABA) signaling, but little is known about them in bryophytes. Here, a representative U-box armadillo repeat (PUB-ARM) ubiquitin E3 ligase from Antarctic moss Pohlia nutans (PnSAG1), was explored for its role in abiotic stress response in Arabidopsis thaliana and Physcomitrella patens. The expression of PnSAG1 was rapidly induced by exogenous abscisic acid (ABA), salt, cold and drought stresses. PnSAG1 was localized to the cytoplasm and showed E3 ubiquitin ligase activity by in vitro ubiquitination assay. The PnSAG1-overexpressing Arabidopsis enhanced the sensitivity with respect to ABA and salt stress during seed germination and early root growth. Similarly, heterogeneous overexpression of PnSAG1 in P. patens was more sensitive to the salinity and ABA in their gametophyte growth. The analysis by RT-qPCR revealed that the expression of salt stress/ABA-related genes were downregulated in PnSAG1-overexpressing plants after salt treatment. Taken together, our results indicated that PnSAG1 plays a negative role in plant response to ABA and salt stress.}, } @article {pmid31207494, year = {2019}, author = {Ibrahim, HMM and Ahmad, EM and Martínez-Medina, A and Aly, MAM}, title = {Effective approaches to study the plant-root knot nematode interaction.}, journal = {Plant physiology and biochemistry : PPB}, volume = {141}, number = {}, pages = {332-342}, doi = {10.1016/j.plaphy.2019.06.009}, pmid = {31207494}, issn = {1873-2690}, mesh = {Animals ; Chromosome Mapping ; Computational Biology/methods ; Female ; Genome, Plant ; *Host-Parasite Interactions ; Male ; Nematoda/*pathogenicity ; Plant Diseases/parasitology ; Plant Physiological Phenomena ; Plant Roots/genetics/*parasitology ; Plants/genetics/*parasitology ; Plants, Genetically Modified/parasitology ; Quantitative Trait Loci ; RNA Interference ; RNA, Small Interfering/metabolism ; Transcriptome ; Virulence/genetics ; }, abstract = {Plant-parasitic nematodes cause major agricultural losses worldwide. Examining the molecular mechanisms underlying plant-nematode interactions and how plants respond to different invading pathogens is attracting major attention to reduce the expanding gap between agricultural production and the needs of the growing world population. This review summarizes the most recent developments in plant-nematode interactions and the diverse approaches used to improve plant resistance against root knot nematode (RKN). We will emphasize the recent rapid advances in genome sequencing technologies, small interfering RNA techniques (RNAi) and targeted genome editing which are contributing to the significant progress in understanding the plant-nematode interaction mechanisms. Also, molecular approaches to improve plant resistance against nematodes are considered.}, } @article {pmid31207046, year = {2019}, author = {Czechowska, K and Lannigan, J and Wang, L and Arcidiacono, J and Ashhurst, TM and Barnard, RM and Bauer, S and Bispo, C and Bonilla, DL and Brinkman, RR and Cabanski, M and Chang, HD and Chakrabarti, L and Chojnowski, G and Cotleur, B and Degheidy, H and Dela Cruz, GV and Eck, S and Elliott, J and Errington, R and Filby, A and Gagnon, D and Gardner, R and Green, C and Gregory, M and Groves, CJ and Hall, C and Hammes, F and Hedrick, M and Hoffman, R and Icha, J and Ivaska, J and Jenner, DC and Jones, D and Kerckhof, FM and Kukat, C and Lanham, D and Leavesley, S and Lee, M and Lin-Gibson, S and Litwin, V and Liu, Y and Molloy, J and Moore, JS and Müller, S and Nedbal, J and Niesner, R and Nitta, N and Ohlsson-Wilhelm, B and Paul, NE and Perfetto, S and Portat, Z and Props, R and Radtke, S and Rayanki, R and Rieger, A and Rogers, S and Rubbens, P and Salomon, R and Schiemann, M and Sharpe, J and Sonder, SU and Stewart, JJ and Sun, Y and Ulrich, H and Van Isterdael, G and Vitaliti, A and van Vreden, C and Weber, M and Zimmermann, J and Vacca, G and Wallace, P and Tárnok, A}, title = {Cyt-Geist: Current and Future Challenges in Cytometry: Reports of the CYTO 2018 Conference Workshops.}, journal = {Cytometry. Part A : the journal of the International Society for Analytical Cytology}, volume = {95}, number = {6}, pages = {598-644}, doi = {10.1002/cyto.a.23777}, pmid = {31207046}, issn = {1552-4930}, mesh = {Aptamers, Nucleotide ; Biomarkers ; Databases as Topic ; Flow Cytometry/instrumentation/standards/*trends ; Genomics ; Humans ; Mass Spectrometry/instrumentation/methods ; Microbiota/genetics ; Microscopy, Fluorescence ; Reproducibility of Results ; Single-Cell Analysis/*methods ; Software ; Validation Studies as Topic ; }, } @article {pmid31201324, year = {2019}, author = {Hassell, JM and Ward, MJ and Muloi, D and Bettridge, JM and Phan, H and Robinson, TP and Ogendo, A and Imboma, T and Kiiru, J and Kariuki, S and Begon, M and Kang'ethe, EK and Woolhouse, MEJ and Fèvre, EM}, title = {Deterministic processes structure bacterial genetic communities across an urban landscape.}, journal = {Nature communications}, volume = {10}, number = {1}, pages = {2643}, pmid = {31201324}, issn = {2041-1723}, support = {//Wellcome Trust/United Kingdom ; G1100783/MRC_/Medical Research Council/United Kingdom ; MR/R015090/1/MRC_/Medical Research Council/United Kingdom ; G1100783/1//RCUK | Medical Research Council (MRC)/International ; }, mesh = {Adaptation, Biological/genetics ; Animals ; Animals, Wild/microbiology ; Biodiversity ; Birds/microbiology ; Escherichia coli/*genetics ; Genes, Bacterial/*genetics ; Humans ; Interspersed Repetitive Sequences/*genetics ; Kenya ; Livestock/microbiology ; Microbiota/*genetics ; Models, Biological ; Urban Health ; Urbanization ; Whole Genome Sequencing ; Zoonoses/microbiology/*prevention & control/transmission ; }, abstract = {Land-use change is predicted to act as a driver of zoonotic disease emergence through human exposure to novel microbial diversity, but evidence for the effects of environmental change on microbial communities in vertebrates is lacking. We sample wild birds at 99 wildlife-livestock-human interfaces across Nairobi, Kenya, and use whole genome sequencing to characterise bacterial genes known to be carried on mobile genetic elements (MGEs) within avian-borne Escherichia coli (n = 241). By modelling the diversity of bacterial genes encoding virulence and antimicrobial resistance (AMR) against ecological and anthropogenic forms of urban environmental change, we demonstrate that communities of avian-borne bacterial genes are shaped by the assemblage of co-existing avian, livestock and human communities, and the habitat within which they exist. In showing that non-random processes structure bacterial genetic communities in urban wildlife, these findings suggest that it should be possible to forecast the effects of urban land-use change on microbial diversity.}, } @article {pmid31200111, year = {2019}, author = {Dimitrov, KM and Abolnik, C and Afonso, CL and Albina, E and Bahl, J and Berg, M and Briand, FX and Brown, IH and Choi, KS and Chvala, I and Diel, DG and Durr, PA and Ferreira, HL and Fusaro, A and Gil, P and Goujgoulova, GV and Grund, C and Hicks, JT and Joannis, TM and Torchetti, MK and Kolosov, S and Lambrecht, B and Lewis, NS and Liu, H and Liu, H and McCullough, S and Miller, PJ and Monne, I and Muller, CP and Munir, M and Reischak, D and Sabra, M and Samal, SK and Servan de Almeida, R and Shittu, I and Snoeck, CJ and Suarez, DL and Van Borm, S and Wang, Z and Wong, FYK}, title = {Updated unified phylogenetic classification system and revised nomenclature for Newcastle disease virus.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {74}, number = {}, pages = {103917}, pmid = {31200111}, issn = {1567-7257}, support = {BB/R012695/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/M008681/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Bayes Theorem ; Consensus ; Data Curation ; Databases, Genetic ; Genotype ; Guidelines as Topic ; International Cooperation ; Likelihood Functions ; Newcastle disease virus/*classification/genetics ; Phylogeny ; RNA, Viral/*genetics ; Sequence Analysis, RNA/*methods ; }, abstract = {Several Avian paramyxoviruses 1 (synonymous with Newcastle disease virus or NDV, used hereafter) classification systems have been proposed for strain identification and differentiation. These systems pioneered classification efforts; however, they were based on different approaches and lacked objective criteria for the differentiation of isolates. These differences have created discrepancies among systems, rendering discussions and comparisons across studies difficult. Although a system that used objective classification criteria was proposed by Diel and co-workers in 2012, the ample worldwide circulation and constant evolution of NDV, and utilization of only some of the criteria, led to identical naming and/or incorrect assigning of new sub/genotypes. To address these issues, an international consortium of experts was convened to undertake in-depth analyses of NDV genetic diversity. This consortium generated curated, up-to-date, complete fusion gene class I and class II datasets of all known NDV for public use, performed comprehensive phylogenetic neighbor-Joining, maximum-likelihood, Bayesian and nucleotide distance analyses, and compared these inference methods. An updated NDV classification and nomenclature system that incorporates phylogenetic topology, genetic distances, branch support, and epidemiological independence was developed. This new consensus system maintains two NDV classes and existing genotypes, identifies three new class II genotypes, and reduces the number of sub-genotypes. In order to track the ancestry of viruses, a dichotomous naming system for designating sub-genotypes was introduced. In addition, a pilot dataset and sub-trees rooting guidelines for rapid preliminary genotype identification of new isolates are provided. Guidelines for sequence dataset curation and phylogenetic inference, and a detailed comparison between the updated and previous systems are included. To increase the speed of phylogenetic inference and ensure consistency between laboratories, detailed guidelines for the use of a supercomputer are also provided. The proposed unified classification system will facilitate future studies of NDV evolution and epidemiology, and comparison of results obtained across the world.}, } @article {pmid31197805, year = {2019}, author = {Henriksson, N and Rademacher, TT}, title = {Stem Compression: A Means to Reversibly Reduce Phloem Transport in Tree Stems.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2014}, number = {}, pages = {301-310}, doi = {10.1007/978-1-4939-9562-2_24}, pmid = {31197805}, issn = {1940-6029}, mesh = {Biological Transport ; Carbohydrates ; Carbon/metabolism ; Phloem/*physiology ; Photosynthesis ; Plant Development ; Plant Stems/*physiology ; }, abstract = {Stem compression reduces or terminates the phloem-mediated transport of carbohydrates and other solutes in tree stems, without causing permanent damage to phloem functioning (Henriksson et al. Tree Physiol. 35:1075-1085, 2015). This has been tested on two species of pine trees, with diameters ranging from 3 to 26 cm in a forest in northern Sweden (Henriksson et al. Tree Physiol. 35:1075-1085, 2015) and in Harvard Forest, USA. Halting the phloem transport of trees in a forest is useful for studying tree physiological processes related to, or dependent on, phloem-transported compounds as well as downstream processes, in particular interactions with soil microbes. Phloem compression can be deployed in the lab and field on single trees, subsets, or over larger areas, depending on what is relevant for a particular research question.}, } @article {pmid31188063, year = {2019}, author = {Laudadio, I and Fulci, V and Stronati, L and Carissimi, C}, title = {Next-Generation Metagenomics: Methodological Challenges and Opportunities.}, journal = {Omics : a journal of integrative biology}, volume = {23}, number = {7}, pages = {327-333}, doi = {10.1089/omi.2019.0073}, pmid = {31188063}, issn = {1557-8100}, mesh = {Animals ; Big Data ; Biodiversity ; Computational Biology/methods ; Databases, Genetic ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Metagenome ; Metagenomics/*methods ; Microbiological Techniques ; Microbiology/trends ; Microbiota ; }, abstract = {Metagenomics is not only one of the newest omics system science technologies but also one that has arguably the broadest set of applications and impacts globally. Metagenomics has found vast utility not only in environmental sciences, ecology, and public health but also in clinical medicine and looking into the future, in planetary health. In line with the One Health concept, metagenomics solicits collaboration between molecular biologists, geneticists, microbiologists, clinicians, computational biologists, plant biologists, veterinarians, and other health care professionals. Almost every ecological niche of our planet hosts an extremely diverse community of organisms that are still poorly characterized. Detailed characterization of the features of such communities is instrumental to our comprehension of ecological, biological, and clinical complexity. This expert review article evaluates how metagenomics is improving our knowledge of microbiota composition from environmental to human samples. Furthermore, we offer an analysis of the common technical and methodological challenges and potential pitfalls arising from metagenomics approaches, such as metagenomics study design, data processing, and interpretation. All in all, at this critical juncture of further growth of the metagenomics field, it is time to critically reflect on the lessons learned and the future prospects of next-generation metagenomics science, technology, and conceivable applications, particularly from the standpoint of a metagenomics methodology perspective.}, } @article {pmid31184697, year = {2019}, author = {Zhang, H and Zheng, R and Wang, Y and Zhang, Y and Hong, P and Fang, Y and Li, G and Fang, Y}, title = {The effects of Arabidopsis genome duplication on the chromatin organization and transcriptional regulation.}, journal = {Nucleic acids research}, volume = {47}, number = {15}, pages = {7857-7869}, pmid = {31184697}, issn = {1362-4962}, mesh = {Arabidopsis/*genetics/metabolism ; Arabidopsis Proteins/*genetics/metabolism ; Chromatin/metabolism/*ultrastructure ; Gene Duplication ; *Gene Expression Regulation, Plant ; Genetic Loci ; *Genome, Plant ; High-Throughput Nucleotide Sequencing ; Histones/genetics/metabolism ; MADS Domain Proteins/genetics/metabolism ; Polyploidy ; *Transcription, Genetic ; }, abstract = {Autopolyploidy is widespread in higher plants and important for agricultural yield and quality. However, the effects of genome duplication on the chromatin organization and transcriptional regulation are largely unknown in plants. Using High-throughput Chromosome Conformation Capture (Hi-C), we showed that autotetraploid Arabidopsis presented more inter-chromosomal interactions and fewer short-range chromatin interactions compared with its diploid progenitor. In addition, genome duplication contributed to the switching of some loose and compact structure domains with altered H3K4me3 and H3K27me3 histone modification status. 539 genes were identified with altered transcriptions and chromatin interactions in autotetraploid Arabidopsis. Especially, we found that genome duplication changed chromatin looping and H3K27me3 histone modification in Flowering Locus C. We propose that genome doubling modulates the transcription genome-wide by changed chromatin interactions and at the specific locus by altered chromatin loops and histone modifications.}, } @article {pmid31182811, year = {2019}, author = {Humphreys, AM and Govaerts, R and Ficinski, SZ and Nic Lughadha, E and Vorontsova, MS}, title = {Global dataset shows geography and life form predict modern plant extinction and rediscovery.}, journal = {Nature ecology & evolution}, volume = {3}, number = {7}, pages = {1043-1047}, doi = {10.1038/s41559-019-0906-2}, pmid = {31182811}, issn = {2397-334X}, mesh = {Animals ; Birds ; *Ecosystem ; *Extinction, Biological ; Geography ; Humans ; Mammals ; }, abstract = {Most people can name a mammal or bird that has become extinct in recent centuries, but few can name a recently extinct plant. We present a comprehensive, global analysis of modern extinction in plants. Almost 600 species have become extinct, at a higher rate than background extinction, but almost as many have been erroneously declared extinct and then been rediscovered. Reports of extinction on islands, in the tropics and of shrubs, trees or species with narrow ranges are least likely to be refuted by rediscovery. Plant extinctions endanger other organisms, ecosystems and human well-being, and must be understood for effective conservation planning.}, } @article {pmid31178473, year = {2020}, author = {Yamaoka, Y and Fujiwara, T and Fujino, Y and Matsuda, S and Fushimi, K}, title = {Response to the Letter to Editor: "Do Inter-Country Differences in the Frequency of Abusive Head Trauma Reflect Different Proportions of Overdiagnosis of Abuse or True Differences in Abuse?".}, journal = {Journal of epidemiology}, volume = {30}, number = {6}, pages = {278-279}, pmid = {31178473}, issn = {1349-9092}, mesh = {Age Distribution ; Child ; *Child Abuse/diagnosis ; *Craniocerebral Trauma/diagnosis/epidemiology ; Humans ; Incidence ; Infant ; Japan ; Medical Overuse ; }, } @article {pmid31178123, year = {2019}, author = {Brewster, R and Tamburini, FB and Asiimwe, E and Oduaran, O and Hazelhurst, S and Bhatt, AS}, title = {Surveying Gut Microbiome Research in Africans: Toward Improved Diversity and Representation.}, journal = {Trends in microbiology}, volume = {27}, number = {10}, pages = {824-835}, pmid = {31178123}, issn = {1878-4380}, support = {K08 CA184420/CA/NCI NIH HHS/United States ; R25 TW009338/TW/FIC NIH HHS/United States ; T32 HG000044/HG/NHGRI NIH HHS/United States ; }, mesh = {Africa ; *Biodiversity ; Biotechnology ; Communicable Diseases ; Computational Biology ; Diet ; Ecology ; *Gastrointestinal Microbiome/genetics ; Genomics ; Global Health ; Humans ; Life Style ; Nutritional Status ; }, abstract = {Descriptive and translational investigations into the human gut microbiome (GM) are rapidly expanding; however, studies are largely restricted to industrialized populations in the USA and Europe. Little is known about microbial variability and its implications for health and disease in other parts of the world. Populations in Africa are particularly underrepresented. What limited research has been performed has focused on a few subject domains, including the impact of long-term lifestyle and dietary factors on GM ecology, its maturation during infancy, and the interrelationships between the microbiome, infectious disease, and undernutrition. Recently, international consortia have laid the groundwork for large-scale genomics and microbiome studies on the continent, with a particular interest in the epidemiologic transition to noncommunicable disease. Here, we survey the current landscape of GM scholarship in Africa and propose actionable recommendations to improve research capacity and output.}, } @article {pmid31176880, year = {2019}, author = {Zhou, X and Du, J and Liu, Y and Yang, C and Lai, J}, title = {Functional characterization of DiMMS21, a SUMO ligase from Desmodium intortum.}, journal = {Plant physiology and biochemistry : PPB}, volume = {141}, number = {}, pages = {206-214}, doi = {10.1016/j.plaphy.2019.06.003}, pmid = {31176880}, issn = {1873-2690}, mesh = {Abscisic Acid/metabolism ; Arabidopsis/enzymology ; Arabidopsis Proteins/metabolism ; Cell Nucleus/metabolism ; Computational Biology ; Cytoplasm/metabolism ; DNA, Complementary/metabolism ; Fabaceae/*enzymology ; Gene Expression Profiling ; *Gene Expression Regulation, Plant ; Ligases/*metabolism ; Mutation ; Phylogeny ; Plant Leaves/metabolism ; Plant Proteins/*metabolism ; Plant Roots/metabolism ; Seeds/metabolism ; Small Ubiquitin-Related Modifier Proteins/metabolism ; }, abstract = {SUMOylation is an important protein modification that regulates the properties of substrate proteins in a variety of cellular processes. SUMOylation is catalyzed via a cascade of enzymes and is usually stimulated by SUMO E3 ligases. However, the molecular functions and regulatory mechanisms of SUMOylation in forage crops are unknown. Here, we isolated and functionally characterized DiMMS21, a homolog of the Arabidopsis thaliana SUMO ligase AtMMS21, from the forage legume Desmodium intortum. DiMMS21 is expressed ubiquitously in various D. intortum organs and its encoded protein is found in the cytoplasm and nucleus. Bioinformatics analysis indicated that DiMMS21 contains a conserved SP-RING domain that is required for its activity. Biochemical evidence supports the notion that this protein is a functional SUMO ligase. When expressed in an Arabidopsis mms21 mutant, DiMMS21 completely rescued the defects in root, leaf, and silique development. The results from cotyledon greening and marker gene expression suggested that DiMMS21 can only partially complements the role of AtMMS21 in abscisic acid (ABA) responses. In summary, we characterized the molecular features of DiMMS21 and uncovered potential roles of this SUMO ligase in development and ABA responses, increasing our understanding on the function of SUMOylation in forage crops.}, } @article {pmid31173423, year = {2019}, author = {Norton, BA and Bending, GD and Clark, R and Corstanje, R and Dunnett, N and Evans, KL and Grafius, DR and Gravestock, E and Grice, SM and Harris, JA and Hilton, S and Hoyle, H and Lim, E and Mercer, TG and Pawlett, M and Pescott, OL and Richards, JP and Southon, GE and Warren, PH}, title = {Urban meadows as an alternative to short mown grassland: effects of composition and height on biodiversity.}, journal = {Ecological applications : a publication of the Ecological Society of America}, volume = {29}, number = {6}, pages = {e01946}, pmid = {31173423}, issn = {1051-0761}, mesh = {*Biodiversity ; Ecosystem ; *Grassland ; Plants ; Soil ; }, abstract = {There are increasing calls to provide greenspace in urban areas, yet the ecological quality, as well as quantity, of greenspace is important. Short mown grassland designed for recreational use is the dominant form of urban greenspace in temperate regions but requires considerable maintenance and typically provides limited habitat value for most taxa. Alternatives are increasingly proposed, but the biodiversity potential of these is not well understood. In a replicated experiment across six public urban greenspaces, we used nine different perennial meadow plantings to quantify the relative roles of floristic diversity and height of sown meadows on the richness and composition of three taxonomic groups: plants, invertebrates, and soil microbes. We found that all meadow treatments were colonized by plant species not sown in the plots, suggesting that establishing sown meadows does not preclude further locally determined grassland development if management is appropriate. Colonizing species were rarer in taller and more diverse plots, indicating competition may limit invasion rates. Urban meadow treatments contained invertebrate and microbial communities that differed from mown grassland. Invertebrate taxa responded to changes in both height and richness of meadow vegetation, but most orders were more abundant where vegetation height was longer than mown grassland. Order richness also increased in longer vegetation and Coleoptera family richness increased with plant diversity in summer. Microbial community composition seems sensitive to plant species composition at the soil surface (0-10 cm), but in deeper soils (11-20 cm) community variation was most responsive to plant height, with bacteria and fungi responding differently. In addition to improving local residents' site satisfaction, native perennial meadow plantings can produce biologically diverse grasslands that support richer and more abundant invertebrate communities, and restructured plant, invertebrate, and soil microbial communities compared with short mown grassland. Our results suggest that diversification of urban greenspace by planting urban meadows in place of some mown amenity grassland is likely to generate substantial biodiversity benefits, with a mosaic of meadow types likely to maximize such benefits.}, } @article {pmid31171819, year = {2019}, author = {Chavez, DE and Gronau, I and Hains, T and Kliver, S and Koepfli, KP and Wayne, RK}, title = {Comparative genomics provides new insights into the remarkable adaptations of the African wild dog (Lycaon pictus).}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {8329}, pmid = {31171819}, issn = {2045-2322}, mesh = {*Adaptation, Physiological ; Animals ; Animals, Wild/genetics ; *Biological Evolution ; Body Patterning ; Canidae/*genetics ; Computational Biology ; DNA/analysis ; Diet ; Female ; *Genomics ; Genotype ; Hedgehog Proteins/genetics ; Molar ; Monte Carlo Method ; Pigmentation ; Predatory Behavior ; }, abstract = {Within the Canidae, the African wild dog (Lycaon pictus) is the most specialized with regards to cursorial adaptations (specialized for running), having only four digits on their forefeet. In addition, this species is one of the few canids considered to be an obligate meat-eater, possessing a robust dentition for taking down large prey, and displays one of the most variable coat colorations amongst mammals. Here, we used comparative genomic analysis to investigate the evolutionary history and genetic basis for adaptations associated with cursoriality, hypercanivory, and coat color variation in African wild dogs. Genome-wide scans revealed unique amino acid deletions that suggest a mode of evolutionary digit loss through expanded apoptosis in the developing first digit. African wild dog-specific signals of positive selection also uncovered a putative mechanism of molar cusp modification through changes in genes associated with the sonic hedgehog (SHH) signaling pathway, required for spatial patterning of teeth, and three genes associated with pigmentation. Divergence time analyses suggest the suite of genomic changes we identified evolved ~1.7 Mya, coinciding with the diversification of large-bodied ungulates. Our results show that comparative genomics is a powerful tool for identifying the genetic basis of evolutionary changes in Canidae.}, } @article {pmid31165555, year = {2020}, author = {Rácz, P and Passmore, S and Jordan, FM}, title = {Social Practice and Shared History, Not Social Scale, Structure Cross-Cultural Complexity in Kinship Systems.}, journal = {Topics in cognitive science}, volume = {12}, number = {2}, pages = {744-765}, pmid = {31165555}, issn = {1756-8765}, support = {/ERC_/European Research Council/International ; //(ERC)/International ; 47690//Leverhulme Research Fellowship/International ; }, mesh = {Anthropology, Cultural ; *Cross-Cultural Comparison ; *Cultural Evolution ; Databases, Factual ; *Family ; Humans ; *Psycholinguistics ; *Social Cognition ; }, abstract = {Human populations display remarkable diversity in language and culture, but the variation is not without limit. At the population level, variation between societies may be structured by a range of macro-evolutionary factors, including ecological and environmental resources, shared ancestry, spatial proximity, and covarying social practices. Kinship terminology systems are varying linguistic paradigms that denote familial social relationships of kin and non-kin. Systems vary by the kinds of salient distinctions that are made (e.g., age, gender, generation) and the extent to which different kinds of kin are called by the same term. Here, we explore two kinds of explanations for an observed typology of kin terms for cousins. The first one derives the typology from a learning bottleneck linked to population size. This would lead to a correlation between community size and the type of kinship system. The second one derives it from a set of social practices, particularly marriage and transfer of resources that might shape kinship systems. Using a global ethnographic database of over a thousand societies, we show that marriage rules and shared linguistic affiliation have a significant influence on the type of kinship system found in a society. This remains true if we control for the effect of spatial proximity and cultural ancestry. By combining cognitive and historic approaches to this aspect of kinship, we suggest broader implications for the study of human social cognition in general.}, } @article {pmid31165295, year = {2019}, author = {Liu, X and Li, L and Li, A and Li, Y and Wang, W and Zhang, G}, title = {Transcriptome and Gene Coexpression Network Analyses of Two Wild Populations Provides Insight into the High-Salinity Adaptation Mechanisms of Crassostrea ariakensis.}, journal = {Marine biotechnology (New York, N.Y.)}, volume = {21}, number = {5}, pages = {596-612}, pmid = {31165295}, issn = {1436-2236}, support = {XDA23050402//Strategic Priority Research Program of the Chinese Academy of Sciences/ ; CARS-49//Earmarked Fund for Modern Agro-industry Technology Research System/ ; }, mesh = {Animals ; Crassostrea/*drug effects/genetics/growth & development ; Estuaries ; Gene Expression Profiling ; *Gene Expression Regulation, Developmental ; Gene Library ; Gene Ontology ; *Gene Regulatory Networks ; Larva/drug effects/genetics/growth & development ; Molecular Sequence Annotation ; Osmotic Pressure ; Oxidation-Reduction ; Principal Component Analysis ; Salinity ; Salt Tolerance/*genetics ; Signal Transduction ; Sodium Chloride/*pharmacology ; *Transcriptome ; }, abstract = {Crassostrea ariakensis naturally distributes in the intertidal and estuary region with relative low salinity ranging from 10 to 25‰. To understand the adaptive capacity of oysters to salinity stress, we conducted transcriptome analysis to investigate the metabolic pathways of salinity stress effectors in oysters from two different geographical sites, namely at salinities of 16, 23, and 30‰. We completed transcriptome sequencing of 18 samples and a total of 52,392 unigenes were obtained after assembly. Differentially expressed gene (DEG) analysis and weighted gene correlation network analysis (WGCNA) were performed using RNA-Seq transcriptomic data from eye-spot larvae at different salinities and from different populations. The results showed that at moderately high salinities (23 and 30‰), genes related to osmotic agents, oxidation-reduction processes, and related regulatory networks of complex transcriptional regulation and signal transduction pathways dominated to counteract the salinity stress. Moreover, there were adaptive differences in salinity response mechanisms, especially at high salinity, in oyster larvae from different populations. These results provide a framework for understanding the interactions of multiple pathways at the system level and for elucidating the complex cellular processes involved in responding to osmotic stress and maintaining growth. Furthermore, the results facilitate further research into the biological processes underlying physiological adaptations to hypertonic stress in marine invertebrates and provide a molecular basis for our subsequent search for high salinity-tolerant populations.}, } @article {pmid31163047, year = {2019}, author = {Kaczensky, P and Khaliun, S and Payne, J and Boldgiv, B and Buuveibaatar, B and Walzer, C}, title = {Through the eye of a Gobi khulan - Application of camera collars for ecological research of far-ranging species in remote and highly variable ecosystems.}, journal = {PloS one}, volume = {14}, number = {6}, pages = {e0217772}, pmid = {31163047}, issn = {1932-6203}, support = {P 24231/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Animals ; Behavior, Animal/physiology ; Circadian Rhythm/physiology ; *Ecosystem ; Equidae/*physiology ; *Geographic Information Systems ; Geography ; Humans ; Image Processing, Computer-Assisted ; Livestock ; Mongolia ; Photography/*instrumentation ; Rain ; *Remote Sensing Technology ; Species Specificity ; Water ; }, abstract = {The Mongolian Gobi-Eastern Steppe Ecosystem is one of the largest remaining natural drylands and home to a unique assemblage of migratory ungulates. Connectivity and integrity of this ecosystem are at risk if increasing human activities are not carefully planned and regulated. The Gobi part supports the largest remaining population of the Asiatic wild ass (Equus hemionus; locally called "khulan"). Individual khulan roam over areas of thousands of square kilometers and the scale of their movements is among the largest described for terrestrial mammals, making them particularly difficult to monitor. Although GPS satellite telemetry makes it possible to track animals in near-real time and remote sensing provides environmental data at the landscape scale, remotely collected data also harbors the risk of missing important abiotic or biotic environmental variables or life history events. We tested the potential of animal born camera systems ("camera collars") to improve our understanding of the drivers and limitations of khulan movements. Deployment of a camera collar on an adult khulan mare resulted in 7,881 images over a one-year period. Over half of the images showed other khulan and 1,630 images showed enough of the collared khulan to classify the behaviour of the animals seen into several main categories. These khulan images provided us with: i) new insights into important life history events and grouping dynamics, ii) allowed us to calculate time budgets for many more animals than the collared khulan alone, and iii) provided us with a training dataset for calibrating data from accelerometer and tilt sensors in the collar. The images also allowed to document khulan behaviour near infrastructure and to obtain a day-time encounter rate between a specific khulan with semi-nomadic herders and their livestock. Lastly, the images allowed us to ground truth the availability of water by: i) confirming waterpoints predicted from other analyses, ii) detecting new waterpoints, and iii) compare precipitation records for rain and snow from landscape scale climate products with those documented by the camera collar. We discuss the added value of deploying camera collars on a subset of animals in remote, highly variable ecosystems for research and conservation.}, } @article {pmid31160654, year = {2019}, author = {Tan, Y and Zhang, J and Sun, Y and Tong, Z and Peng, C and Chang, L and Guo, A and Wang, X}, title = {Comparative Proteomics of Phytase-transgenic Maize Seeds Indicates Environmental Influence is More Important than that of Gene Insertion.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {8219}, pmid = {31160654}, issn = {2045-2322}, mesh = {6-Phytase/*metabolism ; *Environment ; Gene Expression Regulation, Plant ; Gene Ontology ; Molecular Sequence Annotation ; Mutagenesis, Insertional/*genetics ; Plant Proteins/genetics/metabolism ; Plants, Genetically Modified ; Protein Interaction Maps ; *Proteomics ; Seeds/*enzymology/*genetics ; Zea mays/*enzymology/*genetics ; }, abstract = {Proteomic differences were compared between phytase-transgenic (PT) maize seeds and nontransgenic (NT) maize seeds through two-dimensional electrophoresis (2-DE) with mass spectrometry (MS). When maize was grown under field conditions, 30 differentially accumulated proteins (DAPs) were successfully identified in PT seeds (PT/NT). Clusters of Orthologous Groups (COG) functional classification of these proteins showed that the largest group was associated with posttranslational modifications. To investigate the effects of environmental factors, we further compared the seed protein profiles of the same maize planted in a greenhouse or under field conditions. There were 76 DAPs between the greenhouse- and field-grown NT maize seeds and 77 DAPs between the greenhouse- and field-grown PT maize seeds However, under the same planting conditions, there were only 43 DAPs (planted in the greenhouse) or 37 DAPs (planted in the field) between PT and NT maize seeds. The results revealed that DAPs caused by environmental factors were more common than those caused by the insertion of exogenous genes, indicating that the environment has much more important effects on the seed protein profiles. Our maize seed proteomics results also indicated that the occurrence of unintended effects is not specific to genetically modified crops (GMCs); instead, such effects often occur in traditionally bred plants. Our data may be beneficial for biosafety assessments of GMCs at the protein profile level in the future.}, } @article {pmid31159719, year = {2019}, author = {Li, T and Fang, Z and Peng, H and Zhou, J and Liu, P and Wang, Y and Zhu, W and Li, L and Zhang, Q and Chen, L and Li, L and Liu, Z and Zhang, W and Zhai, W and Lu, L and Gao, L}, title = {Application of high-throughput amplicon sequencing-based SSR genotyping in genetic background screening.}, journal = {BMC genomics}, volume = {20}, number = {1}, pages = {444}, pmid = {31159719}, issn = {1471-2164}, support = {14043//Jianghan University/ ; 1002-0606001//Wuhan City Partner/ ; 31300999//National Natural Science Foundation of China/ ; 31501028//National Natural Science Foundation of China/ ; 31601995//National Natural Science Foundation of China/ ; 31800306//National Natural Science Foundation of China/ ; 2016ZX08001-002//Ministry of Agriculture of the People's Republic of China/ ; 2017CFB229//Natural Science Foundation of Hubei Province/ ; }, mesh = {CRISPR-Cas Systems ; Gene Editing ; Gene Transfer Techniques ; Genetic Engineering ; Genetic Testing/*methods ; High-Throughput Nucleotide Sequencing/*methods ; *Microsatellite Repeats ; Oryza/*genetics ; Plant Proteins/antagonists & inhibitors/*genetics ; Plants, Genetically Modified/*genetics ; Polymorphism, Genetic ; Protein Serine-Threonine Kinases/antagonists & inhibitors/*genetics ; }, abstract = {BACKGROUND: Host genetic backgrounds affect gene functions. The genetic backgrounds of genetically engineered organisms must be identified to confirm their genetic backgrounds identity with those of recipients. Marker-assisted backcrossing (MAB), transgenesis and clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (CRISPR/Cas9) editing are three commonly used genetic engineering techniques. However, methods for genetic background screening between genetically engineered organisms and corresponding recipients suffer from low efficiency, low accuracy or high cost.

RESULTS: Here, we improved our previously reported AmpSeq-SSR method, an amplicon sequencing-based simple sequence repeat (SSR) genotyping method, by selecting SSR loci with high polymorphism among varieties. Ultimately, a set of 396 SSRs was generated and applied to evaluate the genetic backgrounds identity between rice lines developed through MAB, transgenesis, and CRISPR/Cas9 editing and the respective recipient rice. We discovered that the percentage of different SSRs between the MAB-developed rice line and its recipient was as high as 23.5%. In contrast, only 0.8% of SSRs were different between the CRISPR/Cas9-system-mediated rice line and its recipient, while no SSRs showed different genotypes between the transgenic rice line and its recipient. Furthermore, most differential SSRs induced by MAB technology were located in non-coding regions (62.9%), followed by untranslated regions (21.0%) and coding regions (16.1%). Trinucleotide repeats were the most prevalent type of altered SSR. Most importantly, all altered SSRs located in coding regions were trinucleotide repeats.

CONCLUSIONS: This method is not only useful for the background evaluation of genetic resources but also expands our understanding of the unintended effects of different genetic engineering techniques. While the work we present focused on rice, this method can be readily extended to other organisms.}, } @article {pmid31152114, year = {2020}, author = {Hone, T and Szklo, AS and Filippidis, FT and Laverty, AA and Sattamini, I and Been, JV and Vianna, C and Souza, M and de Almeida, LM and Millett, C}, title = {Smoke-free legislation and neonatal and infant mortality in Brazil: longitudinal quasi-experimental study.}, journal = {Tobacco control}, volume = {29}, number = {3}, pages = {312-319}, doi = {10.1136/tobaccocontrol-2019-054923}, pmid = {31152114}, issn = {1468-3318}, support = {CZH/4/1121/CSO_/Chief Scientist Office/United Kingdom ; RP_2014-04-032/DH_/Department of Health/United Kingdom ; }, mesh = {Adolescent ; Adult ; Aged ; Brazil/epidemiology ; Female ; Humans ; Infant ; Infant Death/*etiology ; Infant Health ; *Infant Mortality ; Infant, Newborn ; Linear Models ; Male ; Middle Aged ; Perinatal Death/*etiology ; Pregnancy ; Smoke/adverse effects ; Smoke-Free Policy/*legislation & jurisprudence ; Smoking/*legislation & jurisprudence ; Smoking Cessation ; Smoking Prevention/legislation & jurisprudence/*methods ; Tobacco Products/legislation & jurisprudence ; Tobacco Smoke Pollution/adverse effects/*legislation & jurisprudence ; }, abstract = {OBJECTIVE: To examine the associations of partial and comprehensive smoke-free legislation with neonatal and infant mortality in Brazil using a quasi-experimental study design.

DESIGN: Monthly longitudinal (panel) ecological study from January 2000 to December 2016.

SETTING: All Brazilian municipalities (n=5565).

PARTICIPANTS: Infant populations.

INTERVENTION: Smoke-free legislation in effect in each municipality and month. Legislation was encoded as basic (allowing smoking areas), partial (segregated smoking rooms) or comprehensive (no smoking in public buildings). Associations were quantified by immediate step and longer term slope/trend changes in outcomes.

STATISTICAL ANALYSES: Municipal-level linear fixed-effects regression models.

MAIN OUTCOMES MEASURES: Infant and neonatal mortality.

RESULTS: Implementation of partial smoke-free legislation was associated with a -3.3 % (95% CI -6.2% to -0.4%) step reduction in the municipal infant mortality rate, but no step change in neonatal mortality. Comprehensive smoke-free legislation implementation was associated with -5.2 % (95% CI -8.3% to -2.1%) and -3.4 % (95% CI -6.7% to -0.1%) step reductions in infant and neonatal mortality, respectively, and a -0.36 (95% CI -0.66 to-0.06) annual decline in the infant mortality rate. We estimated that had all smoke-free legislation introduced since 2004 been comprehensive, an additional 10 091 infant deaths (95% CI 1196 to 21 761) could have been averted.

CONCLUSIONS: Strengthening smoke-free legislation in Brazil is associated with improvements in infant health outcomes-particularly under comprehensive legislation. Governments should accelerate implementation of comprehensive smoke-free legislation to protect infant health and achieve the United Nation's Sustainable Development Goal three.}, } @article {pmid31150382, year = {2019}, author = {Boza, G and Worsley, SF and Yu, DW and Scheuring, I}, title = {Efficient assembly and long-term stability of defensive microbiomes via private resources and community bistability.}, journal = {PLoS computational biology}, volume = {15}, number = {5}, pages = {e1007109}, pmid = {31150382}, issn = {1553-7358}, mesh = {Animals ; Anti-Bacterial Agents/biosynthesis ; Computational Biology ; Ecosystem ; Host Microbial Interactions/*physiology ; Microbiota/*physiology ; Models, Biological ; Symbiosis/physiology ; }, abstract = {Understanding the mechanisms that promote the assembly and maintenance of host-beneficial microbiomes is an open problem. Empirical evidence supports the idea that animal and plant hosts can combine 'private resources' with the ecological phenomenon known as 'community bistability' to favour some microbial strains over others. We briefly review evidence showing that hosts can: (i) protect the growth of beneficial strains in an isolated habitat, (ii) use antibiotics to suppress non-beneficial, competitor strains, and (iii) provide resources that only beneficial strains are able to translate into an increased rate of growth, reproduction, or antibiotic production. We then demonstrate in a spatially explicit, individual-based model that these three mechanisms act similarly by selectively promoting the initial proliferation of preferred strains, that is, by acting as a private resource. The faster early growth of preferred strains, combined with the phenomenon of 'community bistability,' allows those strains to continue to dominate the microbiome even after the private resource is withdrawn or made public. This is because after a beneficial colony reaches a sufficiently large size, it can resist invasion by parasites without further private support from the host. We further explicitly model localized microbial interactions and diffusion dynamics, and we show that an intermediate level of antibiotic diffusion is the most efficient mechanism in promoting preferred strains and that there is a wide range of parameters under which hosts can promote the assembly of a self-sustaining defensive microbiome. This in turn supports the idea that hosts readily evolve to promote host-beneficial defensive microbiomes.}, } @article {pmid31148528, year = {2019}, author = {Iwama, R and Oceguera-Figueroa, A and Giribet, G and Kvist, S}, title = {The salivary transcriptome of Limnobdella mexicana (Annelida: Clitellata: Praobdellidae) and orthology determination of major leech anticoagulants.}, journal = {Parasitology}, volume = {146}, number = {10}, pages = {1338-1346}, doi = {10.1017/S0031182019000593}, pmid = {31148528}, issn = {1469-8161}, mesh = {Animals ; Computational Biology ; Factor Xa Inhibitors/*metabolism ; *Genetic Variation ; Leeches/genetics/*metabolism ; Phylogeny ; Salivary Proteins and Peptides/*biosynthesis/classification/genetics ; *Transcriptome ; }, abstract = {Bloodfeeding requires several adaptations that allow the parasite to feed efficiently. Leeches and other hematophagous animals have developed different mechanisms to inhibit hemostasis, one of the main barriers imposed by their hosts. Limnobdella mexicana is a member of the leech family Praobdellidae, a family of host generalists known for their preference to attach on mucosal membranes of mammals, such as those in nasopharyngeal cavities, bladders and ocular orbits. Previous studies have hypothesized a positive relationship between diversity of anticoagulants and diversity of hosts in bloodfeeding leeches. However, orthology determination of putative anticoagulants and the lack of standardization of sequencing effort and method hinder comparisons between publicly available transcriptomes generated in different laboratories. In the present study, we examine the first transcriptome of a praobdellid leech and identify 15 putative anticoagulants using a phylogeny-based inference approach, amino-acid conservation, Pfam domains and BLAST searches. Our phylogenetic analyses suggest that the ancestral leech was able to inhibit factor Xa and that some hirudins that have been reported in previous studies on leech anticoagulants may not be orthologous with the archetypal hirudin.}, } @article {pmid31147679, year = {2019}, author = {Jasrotia, RS and Yadav, PK and Iquebal, MA and Bhatt, SB and Arora, V and Angadi, UB and Tomar, RS and Jaiswal, S and Rai, A and Kumar, D}, title = {VigSatDB: genome-wide microsatellite DNA marker database of three species of Vigna for germplasm characterization and improvement.}, journal = {Database : the journal of biological databases and curation}, volume = {2019}, number = {}, pages = {}, pmid = {31147679}, issn = {1758-0463}, mesh = {DNA, Plant/*genetics ; *Databases, Nucleic Acid ; *Microsatellite Repeats ; Species Specificity ; Vigna/classification/*genetics ; }, abstract = {Genus Vigna represented by more than 100 species is a source of nutritious edible seeds and sprouts that are rich sources of protein and dietary supplements. It is further valuable because of therapeutic attributes due to its antioxidant and anti-diabetic properties. A highly diverse and an extremely ecological niche of different species can be valuable genomic resources for productivity enhancement. It is one of the most underutilized crops for food security and animal feeds. In spite of huge species diversity, only three species of Vigna have been sequenced; thus, there is a need for molecular markers for the remaining species. Computational approach of microsatellite marker discovery along with evaluation of polymorphism utilizing available genomic data of different genotypes can be a quick and an economical approach for genomic resource development. Cross-species transferability by e-PCR over available genomes can further prioritize the potential SSR markers, which could be used for genetic diversity and population differentiation of the remaining species saving cost and time. We present VigSatDB-the world's first comprehensive microsatellite database of genus Vigna, containing >875 K putative microsatellite markers with 772 354 simple and 103 865 compound markers mined from six genome assemblies of three Vigna species, namely, Vigna radiata (Mung bean), Vigna angularis (Adzuki bean) and Vigna unguiculata (Cowpea). It also contains 1976 validated published markers. Markers can be selected on the basis of chromosomes/location specificity, and primers can be generated using Primer3core tool integrated at backend. Efficacy of VigSatDB for microsatellite loci genotyping has been evaluated by 15 markers over a panel of 10 diverse genotype of V. radiata. Our web genomic resources can be used in diversity analysis, population and varietal differentiation, discovery of quantitative trait loci/genes, marker-assisted varietal improvement in endeavor of Vigna crop productivity and management.}, } @article {pmid31146685, year = {2019}, author = {Kubatko, LS and Chifman, J}, title = {An invariants-based method for efficient identification of hybrid species from large-scale genomic data.}, journal = {BMC evolutionary biology}, volume = {19}, number = {1}, pages = {112}, pmid = {31146685}, issn = {1471-2148}, support = {T32 CA079448/CA/NCI NIH HHS/United States ; }, mesh = {Animals ; Butterflies/genetics ; Computer Simulation ; Crotalus/genetics ; *Databases, Genetic ; Genetic Speciation ; *Genomics ; *Hybridization, Genetic ; *Models, Genetic ; Phylogeny ; Species Specificity ; }, abstract = {BACKGROUND: Coalescent-based species tree inference has become widely used in the analysis of genome-scale multilocus and SNP datasets when the goal is inference of a species-level phylogeny. However, numerous evolutionary processes are known to violate the assumptions of a coalescence-only model and complicate inference of the species tree. One such process is hybrid speciation, in which a species shares its ancestry with two distinct species. Although many methods have been proposed to detect hybrid speciation, only a few have considered both hybridization and coalescence in a unified framework, and these are generally limited to the setting in which putative hybrid species must be identified in advance.

RESULTS: Here we propose a method that can examine genome-scale data for a large number of taxa and detect those taxa that may have arisen via hybridization, as well as their potential "parental" taxa. The method is based on a model that considers both coalescence and hybridization together, and uses phylogenetic invariants to construct a test that scales well in terms of computational time for both the number of taxa and the amount of sequence data. We test the method using simulated data for up 20 taxa and 100,000bp, and find that the method accurately identifies both recent and ancient hybrid species in less than 30 s. We apply the method to two empirical datasets, one composed of Sistrurus rattlesnakes for which hybrid speciation is not supported by previous work, and one consisting of several species of Heliconius butterflies for which some evidence of hybrid speciation has been previously found.

CONCLUSIONS: The proposed method is powerful for detecting hybridization for both recent and ancient hybridization events. The computations required can be carried out rapidly for a large number of sequences using genome-scale data, and the method is appropriate for both SNP and multilocus data.}, } @article {pmid31145133, year = {2020}, author = {Ganesan, N and Bambino, K and Boffetta, P and Labgaa, I}, title = {Exploring the potential carcinogenic role of arsenic in gallbladder cancer.}, journal = {European journal of cancer prevention : the official journal of the European Cancer Prevention Organisation (ECP)}, volume = {29}, number = {2}, pages = {100-109}, doi = {10.1097/CEJ.0000000000000521}, pmid = {31145133}, issn = {1473-5709}, support = {T32 HD049311/HD/NICHD NIH HHS/United States ; P30 ES023515/ES/NIEHS NIH HHS/United States ; }, mesh = {Arsenic/analysis/*toxicity ; Carcinogens/analysis/*toxicity ; Datasets as Topic ; Ecological Parameter Monitoring/statistics & numerical data ; Female ; Gallbladder Neoplasms/chemically induced/*epidemiology ; Geography ; *Global Burden of Disease ; Groundwater/chemistry ; Humans ; Incidence ; Male ; Risk Factors ; Sex Factors ; Water Pollutants, Chemical/analysis/*toxicity ; }, abstract = {Gallbladder cancer (GBC) is an aggressive malignancy, associated with dismal outcomes. Although several risk factors including age, sex, and gallstones have been postulated, epidemiologic determinants of the disease remain largely uncovered. Moreover, the implication of environmental toxicants as possible risk factors is increasingly suspected. Arsenic (As), an established human carcinogen, is a natural contaminant of groundwater and has a geographic distribution similar to GBC incidence. This, combined with As metabolites being partially excreted in bile, raised the hypothesis that As may represent a carcinogenic hazard for the gallbladder. We conducted an analysis of the association between As concentration in groundwater and incidence rates of GBC worldwide in 52 countries. The USA, India, and Taiwan were selected on the basis of availability and quality of data for further investigation at a county-level. Relationships between As levels and GBC incidence were assessed using multivariable linear regression analyses. Analyses revealed significant associations between high As concentrations in groundwater and increased GBC incidences. Among women, correlations were observed worldwide (Spearman = 0.31, P = 0.028), in Taiwan (Spearman = 0.57, P = 0.005) and in India (R = 0.23, P = 0.006). In men, a correlation was observed in India (R = 0.26, P = 0.009) and a modest correlation was identified in the USA (Spearman = 0.14, P = 0.026). These results provide some support to the hypothesis of an association between high exposures to As-contaminated water on GBC, which appeared more prominent in women. Further observational and molecular studies, conducted at the individual level, are required to confirm this association and decipher its nature.}, } @article {pmid31138696, year = {2019}, author = {Xu, L and Stige, LC and Leirs, H and Neerinckx, S and Gage, KL and Yang, R and Liu, Q and Bramanti, B and Dean, KR and Tang, H and Sun, Z and Stenseth, NC and Zhang, Z}, title = {Historical and genomic data reveal the influencing factors on global transmission velocity of plague during the Third Pandemic.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {116}, number = {24}, pages = {11833-11838}, pmid = {31138696}, issn = {1091-6490}, mesh = {Animals ; Climate Change ; Databases, Factual ; Genome, Bacterial/*genetics ; Genomics/methods ; Humans ; Pandemics/*statistics & numerical data ; Plague/*genetics/*transmission ; Virulence/*genetics ; Yersinia pestis/genetics ; }, abstract = {Quantitative knowledge about which natural and anthropogenic factors influence the global spread of plague remains sparse. We estimated the worldwide spreading velocity of plague during the Third Pandemic, using more than 200 years of extensive human plague case records and genomic data, and analyzed the association of spatiotemporal environmental factors with spreading velocity. Here, we show that two lineages, 2.MED and 1.ORI3, spread significantly faster than others, possibly reflecting differences among strains in transmission mechanisms and virulence. Plague spread fastest in regions with low population density and high proportion of pasture- or forestland, findings that should be taken into account for effective plague monitoring and control. Temperature exhibited a nonlinear, U-shaped association with spread speed, with a minimum around 20 °C, while precipitation showed a positive association. Our results suggest that global warming may accelerate plague spread in warm, tropical regions and that the projected increased precipitation in the Northern Hemisphere may increase plague spread in relevant regions.}, } @article {pmid31137922, year = {2019}, author = {Koo, SY and Hwang, JH and Yang, SH and Um, JI and Hong, KW and Kang, K and Pan, CH and Hwang, KT and Kim, SM}, title = {Anti-Obesity Effect of Standardized Extract of Microalga Phaeodactylum tricornutum Containing Fucoxanthin.}, journal = {Marine drugs}, volume = {17}, number = {5}, pages = {}, pmid = {31137922}, issn = {1660-3397}, mesh = {Adipocytes/drug effects ; Adipogenesis/*drug effects ; Animals ; Anti-Obesity Agents/isolation & purification/*pharmacology ; Biological Products/*pharmacology ; Diet, High-Fat ; Functional Food/analysis ; Mice, Inbred C57BL ; Microalgae/chemistry ; Stramenopiles/*chemistry ; Xanthophylls/*pharmacology ; }, abstract = {Fucoxanthin (FX), a marine carotenoid found in macroalgae and microalgae, exhibits several beneficial effects to health. The anti-obesity activity of FX is well documented, but FX has not been mass-produced or applied extensively or commercially because of limited availability of raw materials and complex extraction techniques. In this study, we investigated the anti-obesity effect of standardized FX powder (Phaeodactylum extract (PE)) developed from microalga Phaeodactylum tricornutum as a commercial functional food. The effects of PE on adipogenesis inhibition in 3T3-L1 adipocytes and anti-obesity in high-fat diet (HFD)-fed C57BL/6J mice were evaluated. PE and FX dose-dependently decreased intracellular lipid contents in adipocytes without cytotoxicity. In HFD-fed obese mice, PE supplementation for six weeks decreased body weight, organ weight, and adipocyte size. In the serum parameter analysis, the PE-treated groups showed attenuation of lipid metabolism dysfunction and liver damage induced by HFD. In the liver, uncoupling protein-1 (UCP1) upregulation and peroxisome proliferator activated receptor γ (PPARγ) downregulation were detected in the PE-treated groups. Additionally, micro computed tomography revealed lower fat accumulation in PE-treated groups compared to that in the HFD group. These results indicate that PE exerts anti-obesity effects by inhibiting adipocytic lipogenesis, inducing fat mass reduction and decreasing intracellular lipid content, adipocyte size, and adipose weight.}, } @article {pmid31135914, year = {2019}, author = {Cloutier, A and Sackton, TB and Grayson, P and Clamp, M and Baker, AJ and Edwards, SV}, title = {Whole-Genome Analyses Resolve the Phylogeny of Flightless Birds (Palaeognathae) in the Presence of an Empirical Anomaly Zone.}, journal = {Systematic biology}, volume = {68}, number = {6}, pages = {937-955}, pmid = {31135914}, issn = {1076-836X}, mesh = {Animals ; Genome/*genetics ; Genomics ; Palaeognathae/*classification/*genetics ; *Phylogeny ; }, abstract = {Palaeognathae represent one of the two basal lineages in modern birds, and comprise the volant (flighted) tinamous and the flightless ratites. Resolving palaeognath phylogenetic relationships has historically proved difficult, and short internal branches separating major palaeognath lineages in previous molecular phylogenies suggest that extensive incomplete lineage sorting (ILS) might have accompanied a rapid ancient divergence. Here, we investigate palaeognath relationships using genome-wide data sets of three types of noncoding nuclear markers, together totaling 20,850 loci and over 41 million base pairs of aligned sequence data. We recover a fully resolved topology placing rheas as the sister to kiwi and emu + cassowary that is congruent across marker types for two species tree methods (MP-EST and ASTRAL-II). This topology is corroborated by patterns of insertions for 4274 CR1 retroelements identified from multispecies whole-genome screening, and is robustly supported by phylogenomic subsampling analyses, with MP-EST demonstrating particularly consistent performance across subsampling replicates as compared to ASTRAL. In contrast, analyses of concatenated data supermatrices recover rheas as the sister to all other nonostrich palaeognaths, an alternative that lacks retroelement support and shows inconsistent behavior under subsampling approaches. While statistically supporting the species tree topology, conflicting patterns of retroelement insertions also occur and imply high amounts of ILS across short successive internal branches, consistent with observed patterns of gene tree heterogeneity. Coalescent simulations and topology tests indicate that the majority of observed topological incongruence among gene trees is consistent with coalescent variation rather than arising from gene tree estimation error alone, and estimated branch lengths for short successive internodes in the inferred species tree fall within the theoretical range encompassing the anomaly zone. Distributions of empirical gene trees confirm that the most common gene tree topology for each marker type differs from the species tree, signifying the existence of an empirical anomaly zone in palaeognaths.}, } @article {pmid31134596, year = {2019}, author = {Wu, CD}, title = {[Application of Geospatial Information Technologies in Assessing Changes in Regional Health Risks Related to Climate Change].}, journal = {Hu li za zhi The journal of nursing}, volume = {66}, number = {3}, pages = {14-22}, doi = {10.6224/JN.201906_66(3).03}, pmid = {31134596}, issn = {0047-262X}, mesh = {*Climate Change ; *Geographic Information Systems ; Humans ; *Public Health ; Risk Assessment/methods ; Taiwan ; }, abstract = {Changes in climate and global warming trends impact the ecological balance as well as human health. The recent development of geospatial information technologies such as Geographic Information Systems (GIS) and remote sensing provides useful tools to assess the impacts of climate changes on human health over large areas. This article aimed to conduct a literature review related to the application of geospatial information technologies in order to assess climate-change-related health risks in Taiwan, with primary outcomes of interest including physiological and mental health and infectious diseases. Three environmental factors, including temperature, precipitation, and air pollution, and their impacts on human health were considered. Comments were raised for future studies in Taiwan on this subject area. Among the hundred papers reviewed, 28 were related to the target topic, and air pollution and fine particle studies were the focus of most of these 28 papers. Studies related to extreme temperature indicted growing concern with this issue. However, limited research was found related to precipitation and environmental greenness. Therefore, future studies should pay greater attention to these two environmental issues. We hope that the findings of this literature review will encourage more researchers to investigate this subject.}, } @article {pmid31134306, year = {2019}, author = {Picone, M and Corami, F and Vendramin, S and Volpi Ghirardini, A}, title = {A Hybrid Phase I-Phase II Toxicity Identification Evaluation (TIE) for the Simultaneous Characterization and Identification of Toxicants of Concern in Coastal and Estuarine Environments.}, journal = {Archives of environmental contamination and toxicology}, volume = {77}, number = {2}, pages = {223-236}, doi = {10.1007/s00244-019-00639-4}, pmid = {31134306}, issn = {1432-0703}, support = {Fondi IRIDE 2017//Ca' Foscari University Venice/ ; }, mesh = {Ammonia/analysis ; Animals ; Crassostrea/drug effects ; Ecotoxicology/*methods ; Edetic Acid ; Estuaries ; Female ; Male ; Metals/analysis ; Solid Phase Extraction/methods ; Ulva/drug effects ; Water Pollutants, Chemical/*analysis/chemistry/*toxicity ; }, abstract = {A sequential TIE procedure combining in a single framework Phase I manipulations and Phase II methods, including chemical analyses and complementary Phase I treatments, was proposed for characterization and identification of toxicants of concern in estuarine environments. Interstitial water was chosen as test matrix and embryo-larval development with the bivalve Crassostrea gigas as toxicity endpoint. TIE treatments included addition of Ulva rigida and elution through zeolite column for addressing effects due to ammonia, addition of EDTA and elution through a Cation-Exchange Solid-Phase Extraction column for characterize metals, and elution through two different type of polymers (XAD and DPA) with different affinity for polar and nonpolar organic pollutants. Chemical analyses concerned determination of ammonia and trace elements in the untreated sample and after manipulation intended to remove or modify bioavailability of ammonia and metals. The "hybrid" Phase I-Phase II TIE sequence proved to be a reliable and effective tool for the identification of main toxicant of concern in a highly toxic and contaminated interstitial water sample, also in presence of high concentration of potential confounding factors (ammonia). The addition of U. rigida was the more reliable treatment for the removal of ammonia, due to the concurrent release of particles and potentially toxic elements, such as Ba, Rb, and Tl by zeolite column, which may increase toxicity in the post-column sample. The combined use of polymers with different affinity for the various classes of organic pollutants was essential to identify the contribution of polar organic compounds to the observed toxicity.}, } @article {pmid31133727, year = {2019}, author = {Piross, IS and Harnos, A and Rózsa, L}, title = {Rensch's rule in avian lice: contradictory allometric trends for sexual size dimorphism.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {7908}, pmid = {31133727}, issn = {2045-2322}, mesh = {Animals ; Birds/anatomy & histology/*parasitology ; *Body Size ; Female ; Host-Parasite Interactions ; Male ; Parasites/*anatomy & histology/classification/genetics ; Phthiraptera/*anatomy & histology/classification/genetics ; Phylogeny ; *Sex Characteristics ; }, abstract = {Rensch's rule (RR) postulates that in comparisons across closely related species, male body size relative to female size increases with the average size of the species. This holds true in several vertebrate and also in certain free-living invertebrate taxa. Here, we document the validity of RR in avian lice using three families (Philopteridae, Menoponidae, and Ricinidae). Using published data on the body length of 989 louse species, subspecies, or distinct intraspecific lineages, we applied phylogenetic reduced major axis regression to analyse the body size of females vs. males while accounting for phylogenetic non-independence. Our results indicate that philopterid and menoponid lice follow RR, while ricinids exhibit the opposite pattern. In the case of philopterids and menoponids, we argue that larger-bodied bird species tend to host lice that are both larger in size and more abundant. Thus, sexual selection acting on males makes them relatively larger, and this is stronger than fecundity selection acting on females. Ricinids exhibit converse RR, likely because fecundity selection is stronger in their case.}, } @article {pmid31133693, year = {2019}, author = {Gilbert, JA and Lynch, SV}, title = {Community ecology as a framework for human microbiome research.}, journal = {Nature medicine}, volume = {25}, number = {6}, pages = {884-889}, pmid = {31133693}, issn = {1546-170X}, support = {P01 AI089473/AI/NIAID NIH HHS/United States ; R01 DA040532/DA/NIDA NIH HHS/United States ; R21 AI113916/AI/NIAID NIH HHS/United States ; R21 AI133765/AI/NIAID NIH HHS/United States ; }, mesh = {Biodiversity ; Computational Biology ; Ecosystem ; Host Microbial Interactions ; Humans ; *Microbiota ; Models, Biological ; Research ; }, abstract = {The field of human microbiome research has revealed the intimate co-association of humans with diverse communities of microbes in various habitats in the human body, and the necessity of these microbes for the maintenance of human health. Microbial heterogeneity between humans and across spatial and temporal gradients requires multidimensional datasets and a unifying set of theories and statistical tools to analyze the human microbiome and fully realize the potential of this field. Here we consider the utility of community ecology as a framework for the interrogation and interpretation of the human microbiome.}, } @article {pmid31130689, year = {2019}, author = {Sun, C and Bian, Y and Zhou, T and Pan, J}, title = {Using of Multi-Source and Multi-Temporal Remote Sensing Data Improves Crop-Type Mapping in the Subtropical Agriculture Region.}, journal = {Sensors (Basel, Switzerland)}, volume = {19}, number = {10}, pages = {}, pmid = {31130689}, issn = {1424-8220}, support = {No. 41771247//National Natural Science Foundation of China/ ; }, mesh = {*Algorithms ; Crops, Agricultural/*classification ; Geographic Information Systems ; Remote Sensing Technology/*methods ; Satellite Imagery ; Triticum/growth & development ; Tropical Climate ; Zea mays/growth & development ; }, abstract = {Crop-type identification is very important in agricultural regions. Most researchers in this area have focused on exploring the ability of synthetic-aperture radar (SAR) sensors to identify crops. This paper uses multi-source (Sentinel-1, Sentinel-2, and Landsat-8) and multi-temporal data to identify crop types. The change detection method was used to analyze spectral and indices information in time series. Significant differences in crop growth status during the growing season were found. Then, three obviously differentiated time features were extracted. Three advanced machine learning algorithms (Support Vector Machine, Artificial Neural Network, and Random Forest, RF) were used to identify the crop types. The results showed that the detection of (Vertical-vertical) VV, (Vertical-horizontal) VH, and Cross Ratio (CR) changes was effective for identifying land cover. Moreover, the red-edge changes were obviously different according to crop growth periods. Sentinel-2 and Landsat-8 showed different normalized difference vegetation index (NDVI) changes also. By using single remote sensing data to classify crops, Sentinel-2 produced the highest overall accuracy (0.91) and Kappa coefficient (0.89). The combination of Sentinel-1, Sentinel-2, and Landsat-8 data provided the best overall accuracy (0.93) and Kappa coefficient (0.91). The RF method had the best performance in terms of identity classification. In addition, the indices feature dominated the classification results. The combination of phenological period information with multi-source remote sensing data can be used to explore a crop area and its status in the growing season. The results of crop classification can be used to analyze the density and distribution of crops. This study can also allow to determine crop growth status, improve crop yield estimation accuracy, and provide a basis for crop management.}, } @article {pmid31128642, year = {2019}, author = {Blažek, J and Zukal, J and Bandouchova, H and Berková, H and Kovacova, V and Martínková, N and Pikula, J and Řehák, Z and Škrabánek, P and Bartonička, T}, title = {Numerous cold arousals and rare arousal cascades as a hibernation strategy in European Myotis bats.}, journal = {Journal of thermal biology}, volume = {82}, number = {}, pages = {150-156}, doi = {10.1016/j.jtherbio.2019.04.002}, pmid = {31128642}, issn = {0306-4565}, mesh = {Animals ; Arousal ; Behavior, Animal ; Body Temperature ; Chiroptera/*physiology ; Cold Temperature ; *Hibernation ; Seasons ; Torpor ; }, abstract = {Hibernating bats optimise the duration of torpor bouts and arousals in relation to hibernaculum microclimatic conditions and fat reserves. Clustering has significant physiological and ecological benefits, promoting successful hibernation of individuals. Such aggregations may help maintain optimal temperatures, allowing better energy utilisation than in solitarily bats. However, aroused bats in a cluster could conceivably disturb those still hibernating, starting an energy-demanding arousal process. Our study was conducted over two winters in two different hibernacula (cave and mine) in the Czech Republic, where Greater mouse-eared bats (Myotis myotis) have previously been diagnosed with white-nose syndrome. In 118 arousal episodes we recorded 193 individual arousals in which a warming phase was observed, 135 (69.9%) being cold arousals, where bats ceased increasing their body temperatures at ≤ 10 °C. The remaining arousals were standard normothermic arousals, where body (fur) surface temperatures reached > 20 °C. Cold arousals occurred during the mid- and late hibernation periods, suggesting they were a response to disturbance by a neighbour in the same cluster. Arousal cascades, where bats aroused in series, were rare (12.7%) and reached a maximum in mid-January. Our data suggest that Myotis bats prolong their torpor bouts using numerous cold arousals but few arousal cascades. Upon arrival of a bat, the clustered bats show tolerance to disturbing by conspecifics.}, } @article {pmid31127947, year = {2020}, author = {Barylski, J and Enault, F and Dutilh, BE and Schuller, MB and Edwards, RA and Gillis, A and Klumpp, J and Knezevic, P and Krupovic, M and Kuhn, JH and Lavigne, R and Oksanen, HM and Sullivan, MB and Jang, HB and Simmonds, P and Aiewsakun, P and Wittmann, J and Tolstoy, I and Brister, JR and Kropinski, AM and Adriaenssens, EM}, title = {Analysis of Spounaviruses as a Case Study for the Overdue Reclassification of Tailed Phages.}, journal = {Systematic biology}, volume = {69}, number = {1}, pages = {110-123}, pmid = {31127947}, issn = {1076-836X}, support = {HHSN272200700016I/AI/NIAID NIH HHS/United States ; BBS/E/F/000PR10353/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/R012490/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Caudovirales/*classification/genetics ; Classification ; Genome, Viral/genetics ; *Phylogeny ; }, abstract = {Tailed bacteriophages are the most abundant and diverse viruses in the world, with genome sizes ranging from 10 kbp to over 500 kbp. Yet, due to historical reasons, all this diversity is confined to a single virus order-Caudovirales, composed of just four families: Myoviridae, Siphoviridae, Podoviridae, and the newly created Ackermannviridae family. In recent years, this morphology-based classification scheme has started to crumble under the constant flood of phage sequences, revealing that tailed phages are even more genetically diverse than once thought. This prompted us, the Bacterial and Archaeal Viruses Subcommittee of the International Committee on Taxonomy of Viruses (ICTV), to consider overall reorganization of phage taxonomy. In this study, we used a wide range of complementary methods-including comparative genomics, core genome analysis, and marker gene phylogenetics-to show that the group of Bacillus phage SPO1-related viruses previously classified into the Spounavirinae subfamily, is clearly distinct from other members of the family Myoviridae and its diversity deserves the rank of an autonomous family. Thus, we removed this group from the Myoviridae family and created the family Herelleviridae-a new taxon of the same rank. In the process of the taxon evaluation, we explored the feasibility of different demarcation criteria and critically evaluated the usefulness of our methods for phage classification. The convergence of results, drawing a consistent and comprehensive picture of a new family with associated subfamilies, regardless of method, demonstrates that the tools applied here are particularly useful in phage taxonomy. We are convinced that creation of this novel family is a crucial milestone toward much-needed reclassification in the Caudovirales order.}, } @article {pmid31127117, year = {2019}, author = {Lozano-Fernandez, J and Tanner, AR and Giacomelli, M and Carton, R and Vinther, J and Edgecombe, GD and Pisani, D}, title = {Increasing species sampling in chelicerate genomic-scale datasets provides support for monophyly of Acari and Arachnida.}, journal = {Nature communications}, volume = {10}, number = {1}, pages = {2295}, pmid = {31127117}, issn = {2041-1723}, support = {655814//European Commission (EC)/International ; 764840//European Commission (EC)/International ; 764840//European Commission (EC)/International ; STAR studentship//University of Bristol/International ; 11/RFP/EOB/3106//Science Foundation Ireland (SFI)/International ; 11/RFP/EOB/3106//Science Foundation Ireland (SFI)/International ; }, mesh = {Acari/*genetics ; Animals ; Aquatic Organisms/*genetics ; Datasets as Topic ; Evolution, Molecular ; Genome ; Horseshoe Crabs/*genetics ; *Phylogeny ; Spiders/*genetics ; }, abstract = {Chelicerates are a diverse group of arthropods, represented by such forms as predatory spiders and scorpions, parasitic ticks, humic detritivores, and marine sea spiders (pycnogonids) and horseshoe crabs. Conflicting phylogenetic relationships have been proposed for chelicerates based on both morphological and molecular data, the latter usually not recovering arachnids as a clade and instead finding horseshoe crabs nested inside terrestrial Arachnida. Here, using genomic-scale datasets and analyses optimised for countering systematic error, we find strong support for monophyletic Acari (ticks and mites), which when considered as a single group represent the most biodiverse chelicerate lineage. In addition, our analysis recovers marine forms (sea spiders and horseshoe crabs) as the successive sister groups of a monophyletic lineage of terrestrial arachnids, suggesting a single colonisation of land within Chelicerata and the absence of wholly secondarily marine arachnid orders.}, } @article {pmid31126951, year = {2019}, author = {Herren, CM}, title = {Asexual Reproduction Can Account for the High Diversity and Prevalence of Rare Taxa Observed in Microbial Communities.}, journal = {Applied and environmental microbiology}, volume = {85}, number = {15}, pages = {}, pmid = {31126951}, issn = {1098-5336}, mesh = {*Microbiota ; Models, Biological ; Population Density ; *Reproduction, Asexual ; }, abstract = {Recent studies evaluating the community structures of microorganisms and macroorganisms have found greater diversity and rarity within micro-scale communities, compared to macro-scale communities. However, reproductive method has been a confounding factor in these comparisons; the microbes considered generally reproduce asexually, while the macroorganisms considered generally reproduce sexually. Sexual reproduction imposes the constraint of mate finding, which can have significant demographic consequences by depressing birth rates at low population sizes. First, I construct an island biogeography model to study the organization of ecological communities under neutral stochastic processes. Then, I examine theoretically how the effects of mate finding in sexual populations translate to the emergent community properties of diversity, rarity, and dominance (size of the largest population). In mate-limited sexual populations, the decreased growth rates at low population densities translate to a higher extinction rate; this increased extinction rate had a disproportionately strong effect on taxa with low population densities. Thus, mate limitation decreased diversity, primarily by excluding small populations from communities. However, the most abundant taxa were minimally affected by mate limitation. Therefore, mate limitation affected the diversity and rarity of taxa in communities but did not alter the dominance of the largest population. The observed shifts in community structure mirror recent empirical studies of micro-scale versus macro-scale communities, which have shown that microbial communities have greater diversity and rarity than macrobial communities but are not different in dominance. Thus, reproductive method may contribute to observed differences in emergent properties between communities at these two scales.IMPORTANCE There have been numerous recent efforts to integrate microbes into broad-scale ecological theories. Microbial communities are often structurally distinct from macrobial communities, but it is unclear whether these differences are real or whether they are due to the different methodologies used to study communities at these two scales. One major difference between macroorganisms and microorganisms is that microbes are much more likely to reproduce asexually. Sexually reproducing taxa have diminished growth rates at low population size, because they must encounter another member of their species before reproducing. This study shows that communities of asexually reproducing taxa are expected to be more diverse, because taxa persist longer. Furthermore, asexually reproducing taxa can exist at much lower densities than sexually reproducing taxa. Thus, asexual reproduction by microbes can account for two major differences between microbial and macrobial communities, namely, greater diversity and greater prevalence of rare taxa for microbes.}, } @article {pmid31125998, year = {2019}, author = {Jasper, M and Schmidt, TL and Ahmad, NW and Sinkins, SP and Hoffmann, AA}, title = {A genomic approach to inferring kinship reveals limited intergenerational dispersal in the yellow fever mosquito.}, journal = {Molecular ecology resources}, volume = {19}, number = {5}, pages = {1254-1264}, pmid = {31125998}, issn = {1755-0998}, support = {1132412//National Health and Medical Research Council/ ; 202888/Z/16/Z/WT_/Wellcome Trust/United Kingdom ; MC_UU_12014/8/MRC_/Medical Research Council/United Kingdom ; 108508/WT_/Wellcome Trust/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; 1118640//National Health and Medical Research Council/ ; }, mesh = {Aedes/*classification/*genetics ; Animal Distribution ; Animals ; Computational Biology/*methods ; Genomics/*methods ; Malaysia ; Mosquito Vectors/*classification/*genetics ; *Pedigree ; Polymorphism, Single Nucleotide ; }, abstract = {Understanding past dispersal and breeding events can provide insight into ecology and evolution and can help inform strategies for conservation and the control of pest species. However, parent-offspring dispersal can be difficult to investigate in rare species and in small pest species such as mosquitoes. Here, we develop a methodology for estimating parent-offspring dispersal from the spatial distribution of close kin, using pairwise kinship estimates derived from genome-wide single nucleotide polymorphisms (SNPs). SNPs were scored in 162 Aedes aegypti (yellow fever mosquito) collected from eight close-set, high-rise apartment buildings in an area of Malaysia with high dengue incidence. We used the SNPs to reconstruct kinship groups across three orders of kinship. We transformed the geographical distances between all kin pairs within each kinship category into axial standard deviations of these distances, then decomposed these into components representing past dispersal events. From these components, we isolated the axial standard deviation of parent-offspring dispersal and estimated neighbourhood area (129 m), median parent-offspring dispersal distance (75 m) and oviposition dispersal radius within a gonotrophic cycle (36 m). We also analysed genetic structure using distance-based redundancy analysis and linear regression, finding isolation by distance both within and between buildings and estimating neighbourhood size at 268 individuals. These findings indicate the scale required to suppress local outbreaks of arboviral disease and to target releases of modified mosquitoes for mosquito and disease control. Our methodology is readily implementable for studies of other species, including pests and species of conservation significance.}, } @article {pmid31123755, year = {2020}, author = {Kowitt, SD and Lipperman-Kreda, S}, title = {How Is Exposure to Tobacco Outlets Within Activity Spaces Associated With Daily Tobacco Use Among Youth? A Mediation Analysis.}, journal = {Nicotine & tobacco research : official journal of the Society for Research on Nicotine and Tobacco}, volume = {22}, number = {6}, pages = {958-966}, pmid = {31123755}, issn = {1469-994X}, support = {P60 AA006282/AA/NIAAA NIH HHS/United States ; }, mesh = {Adolescent ; Adult ; Commerce/*statistics & numerical data ; Female ; Geographic Information Systems ; Humans ; Male ; *Social Environment ; Tobacco Products/*statistics & numerical data ; Tobacco Smoke Pollution/*prevention & control ; Tobacco Use/*epidemiology ; Young Adult ; }, abstract = {INTRODUCTION: We investigated associations between exposure to tobacco outlets within activity spaces and daily tobacco use, and whether exposure to adults or peers using tobacco mediate these relationships.

METHODS: We used Geographic Ecological Momentary Assessment data over 14 days from 85 youth aged 16-20 years in eight mid-sized California city areas. Tobacco outlet addresses and global positioning systems locations were geocoded and activity spaces were constructed by joining sequential points. We assessed daily number of tobacco outlets within 50 or 100 m of activity space polylines and number of minutes participants were within 50 or 100 m of tobacco outlets each day; daily use of tobacco; and whether participants saw (1) adults and (2) people their age (peers) using tobacco each day.

RESULTS: Controlling for demographics, results of multilevel structural equation models showed no association between number of tobacco outlets within 50 m of polylines and tobacco use (probit regression coefficient: 0.01, p = .82). However, we found evidence of an indirect effect (p = .001) through daily exposure to peers using tobacco. Specifically, greater number of tobacco outlets within 50 m of polylines was positively associated with seeing peers use tobacco (probit regression coefficient: 0.10, p < .001). In turn, seeing peers use tobacco was positively associated with tobacco use on that day (probit regression coefficient: 2.23, p < .001). Similar results were found for number of tobacco outlets within 100 m of polylines.

CONCLUSIONS: Exposure to tobacco outlets within activity spaces affects youth tobacco use through daily exposure to peers who use tobacco.

IMPLICATIONS: Using real-time-ordered data, this article examines whether exposure to adults and peers using tobacco mediate associations between exposure to tobacco outlets within activity spaces and daily tobacco use among youth. Results suggest that exposure to tobacco outlets within activity spaces affects daily tobacco use through exposure to peers who use tobacco. These findings provide additional significant support for policy makers who are considering regulating the number and density of tobacco retailers and point to the importance of interventions focused on peer tobacco use and youths' daily environments to reduce tobacco use.}, } @article {pmid31121967, year = {2019}, author = {Bertini, L and Palazzi, L and Proietti, S and Pollastri, S and Arrigoni, G and Polverino de Laureto, P and Caruso, C}, title = {Proteomic Analysis of MeJa-Induced Defense Responses in Rice against Wounding.}, journal = {International journal of molecular sciences}, volume = {20}, number = {10}, pages = {}, pmid = {31121967}, issn = {1422-0067}, support = {RBNE01KZE7//Ministero dell'Istruzione, dell'Università e della Ricerca/ ; }, mesh = {Cyclopentanes/chemistry/*metabolism ; Disease Resistance ; Esterification ; Gene Ontology ; Oryza/*physiology ; Oxylipins/chemistry/*metabolism ; Plant Growth Regulators/chemistry/*metabolism ; Plant Proteins/*analysis/metabolism ; Proteomics ; Stress, Physiological ; }, abstract = {The role of jasmonates in defense priming has been widely recognized. Priming is a physiological process by which a plant exposed to low doses of biotic or abiotic elicitors activates faster and/or stronger defense responses when subsequently challenged by a stress. In this work, we investigated the impact of MeJA-induced defense responses to mechanical wounding in rice (Oryza sativa). The proteome reprogramming of plants treated with MeJA, wounding or MeJA+wounding has been in-depth analyzed by using a combination of high throughput profiling techniques and bioinformatics tools. Gene Ontology analysis identified protein classes as defense/immunity proteins, hydrolases and oxidoreductases differentially enriched by the three treatments, although with different amplitude. Remarkably, proteins involved in photosynthesis or oxidative stress were significantly affected upon wounding in MeJA-primed plants. Although these identified proteins had been previously shown to play a role in defense responses, our study revealed that they are specifically associated with MeJA-priming. Additionally, we also showed that at the phenotypic level MeJA protects plants from oxidative stress and photosynthetic damage induced by wounding. Taken together, our results add novel insight into the molecular actors and physiological mechanisms orchestrated by MeJA in enhancing rice plants defenses after wounding.}, } @article {pmid31121517, year = {2019}, author = {Gao, Y and Li, G and Qin, Y and Ji, Y and Mai, B and An, T}, title = {New theoretical insight into indirect photochemical transformation of fragrance nitro-musks: Mechanisms, eco-toxicity and health effects.}, journal = {Environment international}, volume = {129}, number = {}, pages = {68-75}, doi = {10.1016/j.envint.2019.05.020}, pmid = {31121517}, issn = {1873-6750}, mesh = {Animals ; Computational Biology ; Ecotoxicology ; Fishes/*metabolism ; Odorants ; Perfume/toxicity ; Photochemical Processes ; Water Pollutants, Chemical/*toxicity ; Xylenes/*toxicity ; }, abstract = {The ubiquitous presence of fragrance-associated synthetic musk is cause for serious concern due to their transformation and environmental impacts. In particular, nitro-musks are frequently detected in various matrices, including water, even though they were restricted because of carcinogenicity. Thus, using musk xylene as a model compound, the mechanism, eco-toxicity and health effects during OH-initiated transformation process were systematically studied using quantum chemistry and computational toxicology. Results indicate that musk xylene can be exclusively transformed via H-abstraction pathways from its methyl group, with total rate constants of 5.65 × 10[8]-8.79 × 10[9] M[-1] s[-1], while the contribution of other pathways, including single-electron transfer and OH-addition pathways, were insignificant. The subsequent dehydrogenation intermediates (MX(H)) could further transform into cyclic, aldehyde and demethylation products. Based on toxicity assessments, all the transformation products exhibited decreased aquatic toxicity to fish in comparison with the parent musk xylene but they were still classified at toxic or very toxic levels, especially the cyclic products. More importantly, these products still exhibited carcinogenic activity during OH-initiated transformation and increased carcinogenicity relative to the parent musk xylene. This is the first time that the transformation mechanism and environmental impacts of nitro-musks have been explored through theoretical calculations.}, } @article {pmid31120160, year = {2019}, author = {Li, F and Zhao, X and Li, M and He, K and Huang, C and Zhou, Y and Li, Z and Walters, JR}, title = {Insect genomes: progress and challenges.}, journal = {Insect molecular biology}, volume = {28}, number = {6}, pages = {739-758}, doi = {10.1111/imb.12599}, pmid = {31120160}, issn = {1365-2583}, mesh = {Animals ; Chromosome Mapping ; *Databases as Topic ; Databases, Genetic ; *Genome, Insect ; *Insect Control ; Insecta/*genetics ; Sequence Analysis, DNA ; }, abstract = {In the wake of constant improvements in sequencing technologies, numerous insect genomes have been sequenced. Currently, 1219 insect genome-sequencing projects have been registered with the National Center for Biotechnology Information, including 401 that have genome assemblies and 155 with an official gene set of annotated protein-coding genes. Comparative genomics analysis showed that the expansion or contraction of gene families was associated with well-studied physiological traits such as immune system, metabolic detoxification, parasitism and polyphagy in insects. Here, we summarize the progress of insect genome sequencing, with an emphasis on how this impacts research on pest control. We begin with a brief introduction to the basic concepts of genome assembly, annotation and metrics for evaluating the quality of draft assemblies. We then provide an overview of genome information for numerous insect species, highlighting examples from prominent model organisms, agricultural pests and disease vectors. We also introduce the major insect genome databases. The increasing availability of insect genomic resources is beneficial for developing alternative pest control methods. However, many opportunities remain for developing data-mining tools that make maximal use of the available insect genome resources. Although rapid progress has been achieved, many challenges remain in the field of insect genomics.}, } @article {pmid31119664, year = {2019}, author = {Gevi, F and Fanelli, G and Zolla, L and Rinalducci, S}, title = {Untargeted Metabolomics of Plant Leaf Tissues.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1978}, number = {}, pages = {187-195}, doi = {10.1007/978-1-4939-9236-2_12}, pmid = {31119664}, issn = {1940-6029}, mesh = {*Chromatography, High Pressure Liquid ; Metabolomics/*methods ; Plant Leaves/*metabolism ; *Tandem Mass Spectrometry ; Triticum/metabolism ; }, abstract = {Untargeted metabolomics is a useful approach for the simultaneous analysis of a vast array of compounds from a single extract. Metabolomic profiling is the relative multi-parallel quantification of a mixture of low molecular weight compounds, or classes of compounds, and it is most often performed by using ultra performance liquid chromatography (UPLC) coupled with mass spectrometry (MS). Being an extension of the classical targeted methods, this approach allows a broader view of the main biochemical events within a particular sample. This chapter exemplifies and provides experimental details on the basic steps to perform a non-targeted metabolomic analysis on plant leaf tissues: sample collection and homogenization, extraction of metabolites, raw data acquisition, and processing into formats for data mining and informatics. In particular, the approach was applied to two spring wheat varieties with different level of drought tolerance (Kavir, drought-resistant; Bahar, drought-sensitive) developed by the CIMMYT (International Center for the Improvement of Corn and Wheat).}, } @article {pmid31119502, year = {2019}, author = {Fonseca, PM and Moura, RD and Wallau, GL and Loreto, ELS}, title = {The mobilome of Drosophila incompta, a flower-breeding species: comparison of transposable element landscapes among generalist and specialist flies.}, journal = {Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology}, volume = {27}, number = {3}, pages = {203-219}, pmid = {31119502}, issn = {1573-6849}, mesh = {Animals ; Breeding ; DNA Transposable Elements/*genetics ; Datasets as Topic ; Drosophila/*genetics ; Ecology ; Feeding Behavior ; Flowers ; Genome, Insect/*genetics ; Solanaceae ; Species Specificity ; }, abstract = {The Drosophila genus is one of the main model organisms in evolutionary studies, including those investigating the role of transposable elements (TE) in genomic evolution both at the nucleotide and chromosome levels. D. incompta is a species with restricted ecology, using Cestrum (Solanaceae) flowers as unique sources for oviposition, feeding and development. In the present study, we deeply characterise the D. incompta mobilome and generate a curated dataset. A total of 277 elements were identified, corresponding to approximately 14% of the genome, and 164 of these elements are new, of which 32.62% are putatively autonomous and 8.9% are transcriptionally active in adult flies. The restricted ecology does not seem to influence the dynamics of TE in this fly, since the proportion and diversity of TEs in its genome are similar to that of other Drosophila species. This result is reinforced by the absence of a clear pattern when comparing the TE landscape between generalist and specialist flies. Using 32 available Drosophila genomes-24 ecologically generalist species and 8 specialist species-no difference was found between their TE landscape patterns. However, differences were found between species of the Sophophora and Drosophila subgenus, indicating there are lineage-specific factors shaping TE landscapes.}, } @article {pmid31114886, year = {2019}, author = {Jovanovic, N and Mikheyev, AS}, title = {Interactive web-based visualization and sharing of phylogenetic trees using phylogeny.IO.}, journal = {Nucleic acids research}, volume = {47}, number = {W1}, pages = {W266-W269}, pmid = {31114886}, issn = {1362-4962}, mesh = {*Computer Graphics ; *Databases, Factual ; Datasets as Topic ; *Internet ; *Phylogeny ; Species Specificity ; *User-Computer Interface ; }, abstract = {Traditional static publication formats make visualization, exploration, and sharing of massive phylogenetic trees difficult. A phylogenetic study often involves hundreds of taxa, and the resulting tree has to be split across multiple journal pages, or be shrunk onto one, which jeopardizes legibility. Furthermore, additional data layers, such as species-specific information or time calibrations are often displayed in separate figures, making the entire picture difficult for readers to grasp. Web-based technologies, such as the Data Driven Document (D3) JavaScript library, were created to overcome such challenges by allowing interactive displays of complex data sets. The new phylogeny.IO web server (https://phylogeny.io) overcomes this issue by allowing users to easily import, annotate, and share interactive phylogenetic trees. It allows a range of static (e.g. such as shapes and colors) and dynamic (e.g. pop-up text and images) annotations. Annotated trees can be saved on the server for subsequent modification or they may be shared as IFrame HTML objects, easily embeddable in any web page. The principal goal of phylogeny.IO is not to produce publication-ready figures, but rather to provide a simple and intuitive annotation interface that allows easy and rapid sharing of figures in blogs, lecture notes, press releases, etc.}, } @article {pmid31112783, year = {2019}, author = {Liu, YY and Jin, WT and Wei, XX and Wang, XQ}, title = {Cryptic speciation in the Chinese white pine (Pinus armandii): Implications for the high species diversity of conifers in the Hengduan Mountains, a global biodiversity hotspot.}, journal = {Molecular phylogenetics and evolution}, volume = {138}, number = {}, pages = {114-125}, doi = {10.1016/j.ympev.2019.05.015}, pmid = {31112783}, issn = {1095-9513}, mesh = {Alleles ; Base Sequence ; *Biodiversity ; Cell Nucleus/genetics ; China ; Databases, Genetic ; Gene Dosage ; Genes, Plant ; *Genetic Speciation ; Genetics, Population ; Geography ; Phylogeny ; Pinus/*genetics ; Polymorphism, Single Nucleotide/genetics ; Principal Component Analysis ; RNA, Messenger/genetics/metabolism ; Species Specificity ; Transcriptome/genetics ; }, abstract = {Conifers are the largest and ecologically and economically most important component group of the gymnosperms. Despite their slow rate of molecular evolution, rapid and recent diversification was unexpectedly prevalent in this ancient group in the Hengduan Mountains, a world's biodiversity hotspot and gymnosperm diversity center in Southwest China. In this study, we investigated the underlying mechanisms and disentangled the interactions of geography and ecology in speciation and evolution in Pinus armandii, an important forest tree species endemic to China, by integrating analyses of population transcriptomics, population genetics and ecological niche modeling. Many lines of evidence suggest that cryptic speciation has occurred in P. armandii. During the process, geologically induced formation of Mount Gongga and other massive peaks might trigger the initial vicariance isolation of the northern and southern subdivisions, and ecologically based selection then reinforced their differentiation and local adaptation. Our ecological niche analysis and earlier reciprocal transplant experiments in P. armandii provided convincing evidences for the critical role of ecology in the process of speciation. These findings suggest that both geography and ecology contributed significantly to the abundance of very recent and rapid species divergences, which promoted the rising of the extremely high conifer diversity in the Hengduan Mountains.}, } @article {pmid31111630, year = {2019}, author = {Pattison, N and Duijts, S}, title = {The value of systematic, rigorous and contemporary literature reviews in advancing cancer care.}, journal = {European journal of cancer care}, volume = {28}, number = {3}, pages = {e13098}, doi = {10.1111/ecc.13098}, pmid = {31111630}, issn = {1365-2354}, mesh = {Adolescent ; Advance Care Planning ; Burnout, Professional ; Cancer Survivors/psychology ; Decision Making, Shared ; Decision Support Techniques ; Delivery of Health Care ; Depression/psychology ; Ecological Momentary Assessment ; Humans ; Needs Assessment ; Neoplasms/psychology/rehabilitation/*therapy ; Oncologists ; Patient Participation ; Patient Preference ; *Review Literature as Topic ; *Systematic Reviews as Topic ; Young Adult ; }, } @article {pmid31109663, year = {2019}, author = {Sackton, TB}, title = {Comparative genomics and transcriptomics of host-pathogen interactions in insects: evolutionary insights and future directions.}, journal = {Current opinion in insect science}, volume = {31}, number = {}, pages = {106-113}, doi = {10.1016/j.cois.2018.12.007}, pmid = {31109663}, issn = {2214-5753}, mesh = {Animals ; Biological Evolution ; Genome, Insect ; Genomics ; Host-Pathogen Interactions/genetics/immunology ; Insecta/*genetics/*immunology/microbiology ; Sequence Analysis, RNA ; Transcriptome ; }, abstract = {Classical evolutionary studies of protein-coding genes have established that genes in the canonical immune system are often among the most rapidly evolving within and between species. As more genomes and transcriptomes across insects are sequenced, it is becoming clear that duplications and losses of immune genes are also a likely consequence of host-pathogen interactions. Furthermore, particular species respond to diverse pathogenic challenges with a wide range of challenge-specific responses that are still poorly understood. Transcriptional studies, using RNA-seq to characterize the infection-regulated transcriptome of diverse insects, are crucial for additional progress in understanding the ecology and evolution of the full complexity of the host response.}, } @article {pmid31107866, year = {2019}, author = {Mainali, K and Bewick, S and Vecchio-Pagan, B and Karig, D and Fagan, WF}, title = {Detecting interaction networks in the human microbiome with conditional Granger causality.}, journal = {PLoS computational biology}, volume = {15}, number = {5}, pages = {e1007037}, pmid = {31107866}, issn = {1553-7358}, mesh = {Causality ; Computational Biology ; Gastrointestinal Microbiome ; Hand/microbiology ; Humans ; *Microbial Interactions ; *Microbiota ; *Models, Biological ; Species Specificity ; Tongue/microbiology ; }, abstract = {Human microbiome research is rife with studies attempting to deduce microbial correlation networks from sequencing data. Standard correlation and/or network analyses may be misleading when taken as an indication of taxon interactions because "correlation is neither necessary nor sufficient to establish causation"; environmental filtering can lead to correlation between non-interacting taxa. Unfortunately, microbial ecologists have generally used correlation as a proxy for causality although there is a general consensus about what constitutes a causal relationship: causes both precede and predict effects. We apply one of the first causal models for detecting interactions in human microbiome samples. Specifically, we analyze a long duration, high resolution time series of the human microbiome to decipher the networks of correlation and causation of human-associated microbial genera. We show that correlation is not a good proxy for biological interaction; we observed a weak negative relationship between correlation and causality. Strong interspecific interactions are disproportionately positive, whereas almost all strong intraspecific interactions are negative. Interestingly, intraspecific interactions also appear to act at a short timescale causing vast majority of the effects within 1-3 days. We report how different taxa are involved in causal relationships with others, and show that strong interspecific interactions are rarely conserved across two body sites whereas strong intraspecific interactions are much more conserved, ranging from 33% between the gut and right-hand to 70% between the two hands. Therefore, in the absence of guiding assumptions about ecological interactions, Granger causality and related techniques may be particularly helpful for understanding the driving factors governing microbiome composition and structure.}, } @article {pmid31104913, year = {2019}, author = {Stamate, D and Katrinecz, A and Stahl, D and Verhagen, SJW and Delespaul, PAEG and van Os, J and Guloksuz, S}, title = {Identifying psychosis spectrum disorder from experience sampling data using machine learning approaches.}, journal = {Schizophrenia research}, volume = {209}, number = {}, pages = {156-163}, doi = {10.1016/j.schres.2019.04.028}, pmid = {31104913}, issn = {1573-2509}, mesh = {Case-Control Studies ; *Ecological Momentary Assessment ; *Emotions ; Female ; Humans ; Logistic Models ; *Machine Learning ; Male ; Monte Carlo Method ; Neural Networks, Computer ; Principal Component Analysis ; Psychotic Disorders/*diagnosis/psychology ; ROC Curve ; Smartphone ; Support Vector Machine ; }, abstract = {The ubiquity of smartphones opened up the possibility of widespread use of the Experience Sampling Method (ESM). The method is used to collect longitudinal data of participants' daily life experiences and is ideal to capture fluctuations in emotions (momentary mental states) as an indicator for later mental ill-health. In this study, ESM data of patients with psychosis spectrum disorder and controls were used to examine daily life emotions and higher order patterns thereof. We attempted to determine whether aggregated ESM data, in which statistical measures represent the distribution and dynamics of the original data, were able to distinguish patients from controls in a predictive modeling framework. Variable importance, recursive feature elimination, and ReliefF methods were used for feature selection. Model training, tuning, and testing were performed in nested cross-validation, based on algorithms such as Random Forests, Support Vector Machines, Gaussian Processes, Logistic Regression, and Neural Networks. ROC analysis was used to post-process these models. Stability of model performance was studied using Monte Carlo simulations. The results provide evidence that patterns in emotion changes can be captured by applying a combination of these techniques. Acceleration in the variables anxious and insecure was particularly successful in adding further predictive power to the models. The best results were achieved by Support Vector Machines with radial kernel (accuracy = 82% and sensitivity = 82%). This proof-of-concept work demonstrates that synergistic machine learning and statistical modeling may be used to harness the power of ESM data in the future.}, } @article {pmid31101818, year = {2019}, author = {Kong, D and Wang, J and Wu, H and Valverde-Barrantes, OJ and Wang, R and Zeng, H and Kardol, P and Zhang, H and Feng, Y}, title = {Nonlinearity of root trait relationships and the root economics spectrum.}, journal = {Nature communications}, volume = {10}, number = {1}, pages = {2203}, pmid = {31101818}, issn = {2041-1723}, support = {31670550//National Natural Science Foundation of China (National Science Foundation of China)/International ; 31870552//National Natural Science Foundation of China (National Science Foundation of China)/International ; 31670545//National Natural Science Foundation of China (National Science Foundation of China)/International ; }, mesh = {*Biological Evolution ; Datasets as Topic ; Nonlinear Dynamics ; Phenotype ; Phylogeny ; Plant Roots/anatomy & histology/*genetics/metabolism ; Plants/anatomy & histology/*genetics/metabolism ; *Quantitative Trait, Heritable ; }, abstract = {The root economics spectrum (RES), a common hypothesis postulating a tradeoff between resource acquisition and conservation traits, is being challenged by conflicting relationships between root diameter, tissue density (RTD) and root nitrogen concentration (RN). Here, we analyze a global trait dataset of absorptive roots for over 800 plant species. For woody species (but not for non-woody species), we find nonlinear relationships between root diameter and RTD and RN, which stem from the allometric relationship between stele and cortical tissues. These nonlinear relationships explain how sampling bias from different ends of the nonlinear curves can result in conflicting trait relationships. Further, the shape of the relationships varies depending on evolutionary context and mycorrhizal affiliation. Importantly, the observed nonlinear trait relationships do not support the RES predictions. Allometry-based nonlinearity of root trait relationships improves our understanding of the ecology, physiology and evolution of absorptive roots.}, } @article {pmid31101652, year = {2019}, author = {Koseva, BS and Hackett, JL and Zhou, Y and Harris, BR and Kelly, JK and Greenfield, MD and Gleason, JM and Macdonald, SJ}, title = {Quantitative Genetic Mapping and Genome Assembly in the Lesser Wax Moth Achroia grisella.}, journal = {G3 (Bethesda, Md.)}, volume = {9}, number = {7}, pages = {2349-2361}, pmid = {31101652}, issn = {2160-1836}, support = {P20 GM103418/GM/NIGMS NIH HHS/United States ; P20 GM103638/GM/NIGMS NIH HHS/United States ; R01 GM085260/GM/NIGMS NIH HHS/United States ; R01 OD010974/OD/NIH HHS/United States ; }, mesh = {Animals ; *Chromosome Mapping ; Computational Biology/methods ; Genetic Linkage ; Genetic Markers ; *Genome ; *Genomics ; Genotype ; High-Throughput Nucleotide Sequencing ; Molecular Sequence Annotation ; Moths/*genetics ; Phenotype ; Quantitative Trait Loci ; }, abstract = {Specific characteristics of the male Achroia grisella acoustic mating signal determine a male's attractiveness toward females. These features are genetically variable in populations, and mapping experiments have been used to identify loci contributing to song variation, and understand the evolutionary forces acting on this important sexual trait. Here we built on this foundation and carried out QTL (Quantitative Trait Locus) mapping using >1,000 recombinant individuals, genotyping this large cohort at thousands of sequence-based markers covering the entire collection of 30 A. grisella chromosomes. This dense marker set, coupled with our development of an annotated, draft genome of A. grisella, allowed us to link >3,000 genome scaffolds, >10,000 predicted genes, and close to 275Mb of genome sequence to chromosomes. Our QTL mapping confirmed a fraction of the QTL identified in a previous study, and additionally revealed novel loci. Collectively, QTL explained only small fractions of the phenotypic variance, suggesting many more causative factors remain below the detection threshold of our study. A surprising, and ultimately challenging feature of our study was the low level of intrachromosomal recombination present in our mapping population. This led to difficulty ordering markers along linkage groups, necessitating a chromosome-by-chromosome mapping approach, rather than true interval mapping, and precluded confident ordering/orienting of scaffolds along each chromosome. Nonetheless, our study increased the genomic resources available for the A. grisella system. Enabled by ever more powerful technologies, future investigators will be able to leverage our data to provide more detailed genetic dissection of male song variation in A. grisella.}, } @article {pmid31099510, year = {2019}, author = {Bergquist, R and Manda, S}, title = {The world in your hands: GeoHealth then and now.}, journal = {Geospatial health}, volume = {14}, number = {1}, pages = {}, doi = {10.4081/gh.2019.779}, pmid = {31099510}, issn = {1970-7096}, mesh = {Animals ; Communicable Diseases/*epidemiology ; Ecosystem ; Environmental Monitoring/instrumentation ; Geographic Information Systems/*organization & administration ; Humans ; Insect Vectors/growth & development ; Soil ; Vector Borne Diseases/*epidemiology ; Weather ; }, abstract = {Infectious diseases transmitted by vectors/intermediate hosts constitute a major part of the economic burden related to public health in the endemic countries of the tropics, which challenges local welfare and hinders development. The World Health Organization, in partnership with pharmaceutical companies, major donors, endemic countries and non-governmental organizations, aims to eliminate the majority of these infections in the near future. To succeed, the ecological requirements and real-time distributions of the causative agents (bacteria, parasites and viruses) and their vectors must not only be known to a high degree of accuracy, but the data must also be updated more rapidly than has so far been the case. Current approaches include data collection through terrestrial capture on site and satellite-generated information. This article provides an update of currently available sources of remotely-sensed data, including specific information on satellite-borne sensors, and how such data can be handled by Geographical Information Systems (GIS). Computers, when equipped with GIS software based on common spatial denominators, can connect remotely-sensed environmental records with terrestrial-captured data and apply spatial statistics in ways uniquely suited to manage control activities in areas where vector-borne infections dominate.}, } @article {pmid31097702, year = {2019}, author = {Youngblut, ND and Reischer, GH and Walters, W and Schuster, N and Walzer, C and Stalder, G and Ley, RE and Farnleitner, AH}, title = {Host diet and evolutionary history explain different aspects of gut microbiome diversity among vertebrate clades.}, journal = {Nature communications}, volume = {10}, number = {1}, pages = {2200}, pmid = {31097702}, issn = {2041-1723}, support = {EP-D-15-016/EPA/EPA/United States ; P 23900/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Animals ; *Biodiversity ; *Biological Evolution ; Datasets as Topic ; Feeding Behavior/*physiology ; Gastrointestinal Microbiome/*genetics ; Host Microbial Interactions/physiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics/isolation & purification ; Vertebrates/*microbiology/physiology ; }, abstract = {Multiple factors modulate microbial community assembly in the vertebrate gut, though studies disagree as to their relative contribution. One cause may be a reliance on captive animals, which can have very different gut microbiomes compared to their wild counterparts. To resolve this disagreement, we analyze a new, large, and highly diverse animal distal gut 16 S rRNA microbiome dataset, which comprises 80% wild animals and includes members of Mammalia, Aves, Reptilia, Amphibia, and Actinopterygii. We decouple the effects of host evolutionary history and diet on gut microbiome diversity and show that each factor modulates different aspects of diversity. Moreover, we resolve particular microbial taxa associated with host phylogeny or diet and show that Mammalia have a stronger signal of cophylogeny. Finally, we find that environmental filtering and microbe-microbe interactions differ among host clades. These findings provide a robust assessment of the processes driving microbial community assembly in the vertebrate intestine.}, } @article {pmid31096696, year = {2019}, author = {Richardson, H and Rhodes, G and Henrys, P and Sedda, L and Weightman, AJ and Pickup, RW}, title = {Presence of Mycobacterium avium Subspecies paratuberculosis Monitored Over Varying Temporal and Spatial Scales in River Catchments: Persistent Routes for Human Exposure.}, journal = {Microorganisms}, volume = {7}, number = {5}, pages = {}, pmid = {31096696}, issn = {2076-2607}, support = {NE/F014791/1//Natural Environment Research Council/ ; }, abstract = {Mycobacterium avium subspecies paratuberculosis (Map) was monitored by quantitative PCR over a range of temporal and spatial scales in the River Tywi catchment. This study shows the persistence of Map over a 10-year period with little change, which correlates with the recognised levels of Johne's disease in British herds over that period (aim 1). Map was quantified within the river at up to 10[8] cell equivalents L[-1] and was shown to be consistently present when monitored over finer timescales (aim 4). Small wastewater treatment plants where the ingress of human-associated Map might be expected had no significant effect (aim 2). Map was found for the first time to be located in natural river foams providing another route for spread via aerosols (aim 5). This study provides evidence for the environmental continuum of Map from the grazing infected animal via rain driven runoff through field drains and streams into main rivers; with detection at a high frequency throughout the year. Should Map need to be monitored in the future, we recommend that weekly or monthly sampling from a fixed location on a river will capture an adequate representation of the flow dynamics of Map in a catchment (aim 3). The human exposure to Map during this process and its impact on human health remains unquantified.}, } @article {pmid31095488, year = {2020}, author = {Karim, MB and Huang, M and Ono, N and Kanaya, S and Amin, MA}, title = {BiClusO: A Novel Biclustering Approach and Its Application to Species-VOC Relational Data.}, journal = {IEEE/ACM transactions on computational biology and bioinformatics}, volume = {17}, number = {6}, pages = {1955-1965}, doi = {10.1109/TCBB.2019.2914901}, pmid = {31095488}, issn = {1557-9964}, mesh = {Algorithms ; Animals ; Bacteria/metabolism ; Cluster Analysis ; Computational Biology/*methods ; Data Mining ; Databases, Chemical ; Gastrointestinal Microbiome/physiology ; Humans ; *Volatile Organic Compounds/analysis/classification/metabolism ; }, abstract = {In this paper, we propose a novel biclustering approach called BiClusO. Biclustering can be applied to various types of bipartite data such as gene-condition or gene-disease relations. For example, we applied BiClusO to bipartite relations between species and volatile organic compounds (VOCs). VOCs, which are emitted by different species, have huge environmental and ecological impacts. The biosynthesis of VOCs depends on different metabolic pathways which can be used to categorize the species. A previous study related to the KNApSAcK VOC database classified microorganisms based on their VOC profiles, which confirmed the consistency between VOC-based and pathogenicity-based classifications. However, due to limited data, classification of all species in terms of VOC profiles was not performed. In this study, we enriched our database with additional data collected from different online sources and journals. Then, by applying BiClusO to species-VOC relational data, we determined that VOC-based classification is consistent with taxonomy-based classification of the species. We also assessed the diversity of VOC pathways across different kingdoms of species.}, } @article {pmid31092658, year = {2019}, author = {Patel, S and Jhass, A and Hopkins, S and Shallcross, L}, title = {Informing the development of a standardised approach to measure antibiotic use in secondary care: a systematic review protocol.}, journal = {BMJ open}, volume = {9}, number = {5}, pages = {e026792}, pmid = {31092658}, issn = {2044-6055}, support = {CS-2016-16-007/DH_/Department of Health/United Kingdom ; }, mesh = {Anti-Bacterial Agents/*therapeutic use ; Antimicrobial Stewardship/*statistics & numerical data ; Bacterial Infections/*drug therapy/prevention & control ; Data Interpretation, Statistical ; Drug Resistance, Microbial ; Humans ; Practice Patterns, Physicians'/*statistics & numerical data ; Reference Standards ; *Research Design ; *Secondary Care ; *Systematic Reviews as Topic ; }, abstract = {INTRODUCTION: Ecological and individual-level evidence indicates that there is an association between level of antibiotic exposure and the emergence and spread of antibiotic resistance. The Global Point Prevalence Survey in 2015 estimated that 34.4% of hospital inpatients globally received at least one antimicrobial. Antimicrobial stewardship to optimise antibiotic use in secondary care can reduce the high risk of patients acquiring and transmitting drug-resistant infections in this setting. However, differences in the availability of data on antibiotic use in this context make it difficult to develop a consensus of how to comparably monitor antibiotic prescribing patterns across secondary care. This review will aim to document and critically evaluate methods and measures to monitor antibiotic use in secondary care.

METHODS AND ANALYSIS: We will search Medline (Ovid), Embase (Ovid), Cumulative Index to Nursing and Allied Health Literature, Cochrane Central Register of Controlled Trials and websites of key organisations for published reports where an attempt to measure antibiotic usage among adult inpatients in high-income hospital settings has been made. Two independent reviewers will screen the studies for eligibility, extract data and assess the study quality using the Newcastle-Ottawa scale. A description of the methods and measures used in antibiotic consumption surveillance will be presented. An adaptation of the Affordability, Practicability, Effectiveness, Acceptability, Side-effects Equity framework will be used to consider the practicality of implementing different approaches to measuring antibiotic usage in secondary care settings. A descriptive comparison of definitions and estimates of (in)appropriate antibiotic usage will also be carried out.

ETHICS AND DISSEMINATION: Ethical approval is not required for this study as no primary data will be collected. The results will be published in relevant peer-reviewed journals and presented at relevant conferences or meetings where possible. This review will inform future approaches to scale up antibiotic consumption surveillance strategies to attempt to maximise impact through standardisation.

PROSPERO REGISTRATION NUMBER: CRD42018103375.}, } @article {pmid31087743, year = {2019}, author = {Medina, D and Hughey, MC and Walke, JB and Becker, MH and Pontarelli, K and Sun, S and Badgley, B and Belden, LK}, title = {Amphibian skin fungal communities vary across host species and do not correlate with infection by a pathogenic fungus.}, journal = {Environmental microbiology}, volume = {21}, number = {8}, pages = {2905-2920}, doi = {10.1111/1462-2920.14682}, pmid = {31087743}, issn = {1462-2920}, support = {DZ10zo-028//Morris Animal Foundation/International ; DEB-1136640//National Science Foundation/International ; //Virginia Tech/International ; }, mesh = {Animals ; Anura/*microbiology ; *Chytridiomycota/genetics ; Fungi/classification/isolation & purification ; Host Specificity ; Microbiota ; Molecular Typing ; *Mycobiome ; Mycoses/microbiology/*veterinary ; Skin/microbiology ; Symbiosis ; }, abstract = {Amphibian population declines caused by the fungus Batrachochytrium dendrobatidis (Bd) have prompted studies on the bacterial community that resides on amphibian skin. However, studies addressing the fungal portion of these symbiont communities have lagged behind. Using ITS1 amplicon sequencing, we examined the fungal portion of the skin microbiome of temperate and tropical amphibian species currently coexisting with Bd in nature. We assessed cooccurrence patterns between bacterial and fungal OTUs using a subset of samples for which bacterial 16S rRNA gene amplicon data were also available. We determined that fungal communities were dominated by members of the phyla Ascomycota and Basidiomycota, and also by Chytridiomycota in the most aquatic amphibian species. Alpha diversity of the fungal communities differed across host species, and fungal community structure differed across species and regions. However, we did not find a correlation between fungal diversity/community structure and Bd infection, though we did identify significant correlations between Bd and specific OTUs. Moreover, positive bacterial-fungal cooccurrences suggest that positive interactions between these organisms occur in the skin microbiome. Understanding the ecology of amphibian skin fungi, and their interactions with bacteria will complement our knowledge of the factors influencing community assembly and the overall function of these symbiont communities.}, } @article {pmid31086738, year = {2019}, author = {Warwick-Dugdale, J and Solonenko, N and Moore, K and Chittick, L and Gregory, AC and Allen, MJ and Sullivan, MB and Temperton, B}, title = {Long-read viral metagenomics captures abundant and microdiverse viral populations and their niche-defining genomic islands.}, journal = {PeerJ}, volume = {7}, number = {}, pages = {e6800}, pmid = {31086738}, issn = {2167-8359}, abstract = {Marine viruses impact global biogeochemical cycles via their influence on host community structure and function, yet our understanding of viral ecology is constrained by limitations in host culturing and a lack of reference genomes and 'universal' gene markers to facilitate community surveys. Short-read viral metagenomic studies have provided clues to viral function and first estimates of global viral gene abundance and distribution, but their assemblies are confounded by populations with high levels of strain evenness and nucleotide diversity (microdiversity), limiting assembly of some of the most abundant viruses on Earth. Such features also challenge assembly across genomic islands containing niche-defining genes that drive ecological speciation. These populations and features may be successfully captured by single-virus genomics and fosmid-based approaches, at least in abundant taxa, but at considerable cost and technical expertise. Here we established a low-cost, low-input, high throughput alternative sequencing and informatics workflow to improve viral metagenomic assemblies using short-read and long-read technology. The 'VirION' (Viral, long-read metagenomics via MinION sequencing) approach was first validated using mock communities where it was found to be as relatively quantitative as short-read methods and provided significant improvements in recovery of viral genomes. We then then applied VirION to the first metagenome from a natural viral community from the Western English Channel. In comparison to a short-read only approach, VirION: (i) increased number and completeness of assembled viral genomes; (ii) captured abundant, highly microdiverse virus populations, and (iii) captured more and longer genomic islands. Together, these findings suggest that VirION provides a high throughput and cost-effective alternative to fosmid and single-virus genomic approaches to more comprehensively explore viral communities in nature.}, } @article {pmid31086670, year = {2019}, author = {Amorim, CA and De Souza, LP and Moreira, JP and Luiz, RR and De V Carneiro, AJ and De Souza, HSP}, title = {Geographic distribution and time trends of esophageal cancer in Brazil from 2005 to 2015.}, journal = {Molecular and clinical oncology}, volume = {10}, number = {6}, pages = {631-638}, pmid = {31086670}, issn = {2049-9450}, abstract = {The purpose of the present study was to investigate the geographical distribution and time trends of the incidence and lethality of esophageal cancer (EC) in Brazil. The present study conducted an ecological study of EC using records from January 2005 to December 2015 in the Health Informatics Department of the Brazilian Ministry of Health (DATASUS) registry. In addition to demographical data on the population, EC incidence and lethality rates were estimated from hospitalizations and in-hospital mortalities and were adjusted by total available hospital beds. The adjusted EC rates per 100,000 increased from 9.1 in 2005 to 12.1 in 2015. The prevalence among males increased from 69 to 78%, while the female rates remained stable over the same period. Although EC was the most common in South and Southeast Brazil, the rates increased proportionately more in the other regions of the country, especially among males. Geographical analysis revealed higher rates of EC in more urbanized areas, with a coast-to-inland gradient. While rates increased in people older than 50 years, they decreased among people below this age. However, the lethality rates remained stable and high during the study period, overlapping with hospital admission rates. The recent increasing trend in the EC incidence, with shifts from the south towards the north and from more urbanized towards rural areas, suggests that environmental factors are crucial in EC pathogenesis. The concentration of EC in South Brazil may reflect the presence of major environmental factors in association with a possible genetic predisposition. The unchanging high mortality associated with EC in the rapidly aging population suggests that EC will continue to impose a significant social and economic burden in the future.}, } @article {pmid31086194, year = {2019}, author = {Galán-Acedo, C and Arroyo-Rodríguez, V and Andresen, E and Arasa-Gisbert, R}, title = {Ecological traits of the world's primates.}, journal = {Scientific data}, volume = {6}, number = {1}, pages = {55}, pmid = {31086194}, issn = {2052-4463}, support = {2015-253946//Consejo Nacional de Ciencia y Tecnología (National Council of Science and Technology, Mexico)/International ; }, mesh = {Animals ; Conservation of Natural Resources ; Databases, Factual ; *Ecosystem ; Population Dynamics ; Primates/*physiology ; }, abstract = {Ecosystems largely depend, for both their functioning and their ecological integrity, on the ecological traits of the species that inhabit them. Non-human primates have a wide geographic distribution and play vital roles in ecosystem structure, function, and resilience. However, there is no comprehensive and updated compilation of information on ecological traits of all the world's primate species to accurately assess such roles at a global scale. Here we present a database on some important ecological traits of the world's primates (504 species), including home range size, locomotion type, diel activity, trophic guild, body mass, habitat type, current conservation status, population trend, and geographic realm. We compiled this information through a careful review of 1,216 studies published between 1941 and 2018, resulting in a comprehensive, easily accessible and user-friendly database. This database has broad applicability in primatological studies, and can potentially be used to address many research questions at all spatial scales, from local to global.}, } @article {pmid31085650, year = {2019}, author = {Staver, AC and Asner, GP and Rodriguez-Iturbe, I and Levin, SA and Smit, IPJ}, title = {Spatial patterning among savanna trees in high-resolution, spatially extensive data.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {116}, number = {22}, pages = {10681-10685}, pmid = {31085650}, issn = {1091-6490}, mesh = {Cluster Analysis ; Databases, Factual ; *Grassland ; Models, Statistical ; Rain ; Rivers ; *Spatial Analysis ; Trees/*physiology ; }, abstract = {In savannas, predicting how vegetation varies is a longstanding challenge. Spatial patterning in vegetation may structure that variability, mediated by spatial interactions, including competition and facilitation. Here, we use unique high-resolution, spatially extensive data of tree distributions in an African savanna, derived from airborne Light Detection and Ranging (LiDAR), to examine tree-clustering patterns. We show that tree cluster sizes were governed by power laws over two to three orders of magnitude in spatial scale and that the parameters on their distributions were invariant with respect to underlying environment. Concluding that some universal process governs spatial patterns in tree distributions may be premature. However, we can say that, although the tree layer may look unpredictable locally, at scales relevant to prediction in, e.g., global vegetation models, vegetation is instead strongly structured by regular statistical distributions.}, } @article {pmid31079748, year = {2019}, author = {López, JC and Porca, E and Collins, G and Clifford, E and Quijano, G and Muñoz, R}, title = {Ammonium influences kinetics and structure of methanotrophic consortia.}, journal = {Waste management (New York, N.Y.)}, volume = {89}, number = {}, pages = {345-353}, doi = {10.1016/j.wasman.2019.04.028}, pmid = {31079748}, issn = {1879-2456}, mesh = {*Ammonium Compounds ; Kinetics ; Methane ; *Methylococcaceae ; Oxidation-Reduction ; Soil Microbiology ; }, abstract = {The literature is conflicted on the influence of ammonium on the kinetics and microbial ecology of methanotrophy. In this study, methanotrophic cultures were enriched, under ammonium concentrations ranging from 0 to 200 mM, from an inoculum comprising leachate and top-cover soil from a landfill. Specific CH4 biodegradation rates were highest (7.8 × 10[-4] ± 6.0 × 10[-5] gCH4 gX[-1] h[-1]) in cultures enriched at 4 mM NH4[+], which were mainly dominated by type II methanotrophs belonging to Methylocystis spp. Lower specific CH4 oxidation rates (average values of 1.8-3.6 × 10[-4] gCH4 gX[-1] h[-1]) were achieved by cultures enriched at higher NH4[+] concentrations (20 and 80 mM), and had higher affinity for CH4 compared to 4 mM enrichments. These lower affinities were attributed to lower diversity dominated by type I methanotrophs, of the Methylosarcina, Methylobacter and Methylomicrobium genera, encountered with increasing concentrations of NH4[+]. The study indicates that CH4 oxidation biotechnologies applied at low NH4[+] concentrations can support efficient abatement of CH4 and high diversity of methanotrophic consortia, whilst enriching type II methanotrophs.}, } @article {pmid31079560, year = {2019}, author = {Petrenko, CLM and Alto, ME and Hart, AR and Freeze, SM and Cole, LL}, title = {"I'm Doing My Part, I Just Need Help From the Community": Intervention Implications of Foster and Adoptive Parents' Experiences Raising Children and Young Adults With FASD.}, journal = {Journal of family nursing}, volume = {25}, number = {2}, pages = {314-347}, pmid = {31079560}, issn = {1552-549X}, support = {K01 AA020486/AA/NIAAA NIH HHS/United States ; }, mesh = {Adolescent ; Adult ; Caregivers/*psychology ; Child ; Child, Adopted/*psychology ; Child, Foster/*psychology ; Child, Preschool ; *Community Networks ; Female ; Fetal Alcohol Spectrum Disorders/*psychology ; Humans ; Male ; Parenting/*psychology ; Parents/*psychology ; *Social Support ; Young Adult ; }, abstract = {Individuals with fetal alcohol spectrum disorders (FASD) have high rates of health care service utilization. It is vital that health care professionals understand FASD and associated family experiences to strengthen their ability to respond to family needs and tailor family-focused interventions. This study included 24 foster and adoptive parents of children and adults (aged 3-33 years) with FASD. Data were collected via individual interviews and focus groups and analyzed thematically. Consistent with a developmental psychopathology perspective, parents' experiences interacted with the individual (with FASD), family, and broader systems ecological levels. Parents undertook protective actions in an attempt to prevent secondary conditions, support their child and family, and mitigate systems barriers. They also experienced stressors at each level, and stress was increased by protective actions. The overall parenting experience was fueled by a protective parenting attitude. Findings can strengthen family-focused care practices with individuals with FASD and their families and inform novel family interventions.}, } @article {pmid31077549, year = {2019}, author = {He, Y and Chang, Y and Bao, L and Yu, M and Li, R and Niu, J and Fan, G and Song, W and Seim, I and Qin, Y and Li, X and Liu, J and Kong, X and Peng, M and Sun, M and Wang, M and Qu, J and Wang, X and Liu, X and Wu, X and Zhao, X and Wang, X and Zhang, Y and Guo, J and Liu, Y and Liu, K and Wang, Y and Zhang, H and Liu, L and Wang, M and Yu, H and Wang, X and Cheng, J and Wang, Z and Xu, X and Wang, J and Yang, H and Lee, SM and Liu, X and Zhang, Q and Qi, J}, title = {A chromosome-level genome of black rockfish, Sebastes schlegelii, provides insights into the evolution of live birth.}, journal = {Molecular ecology resources}, volume = {19}, number = {5}, pages = {1309-1321}, doi = {10.1111/1755-0998.13034}, pmid = {31077549}, issn = {1755-0998}, support = {201822026//Research Funds for Central Universities/ ; 2018YFD0900101//National Key R&D Program of China/ ; 2018YFD0901205//National Key R&D Program of China/ ; 2018YFD0900301//National Key R&D Program of China/ ; }, mesh = {Animals ; *Chromosomes ; Computational Biology ; *Evolution, Molecular ; Genomics/methods ; *Live Birth ; Molecular Sequence Annotation ; Perciformes/*genetics/*physiology ; }, abstract = {The black rockfish (Sebastes schlegelii) is a teleost in which eggs are fertilized internally and retained in the maternal reproductive system, where they undergo development until live birth (viviparity). In the present study, we report a chromosome-level black rockfish genome assembly. High-throughput transcriptome analysis (RNA-seq and ATAC-seq) coupled with in situ hybridization (ISH) and immunofluorescence reveal several candidate genes for maternal preparation, sperm storage and release, and hatching. We propose that zona pellucida (ZP) proteins retain sperm at the oocyte envelope, while genes in two distinct astacin metalloproteinase subfamilies serve to release sperm from the ZP and free the embryo from chorion at prehatching stage. We present a model of black rockfish reproduction, and propose that the rockfish ovarian wall has a similar function to the uterus of mammals. Together, these genomic data reveal unprecedented insights into the evolution of an unusual teleost life history strategy, and provide a sound foundation for studying viviparity in nonmammalian vertebrates and an invaluable resource for rockfish ecological and evolutionary research.}, } @article {pmid31073184, year = {2019}, author = {Subedi, P and Subedi, K and Thapa, B and Subedi, P}, title = {Sinkhole susceptibility mapping in Marion County, Florida: Evaluation and comparison between analytical hierarchy process and logistic regression based approaches.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {7140}, pmid = {31073184}, issn = {2045-2322}, abstract = {Sinkholes are the major cause of concern in Florida for their direct role on aquifer vulnerability and potential loss of lives and property. Mapping sinkhole susceptibility is critical to mitigating these consequences by adopting strategic changes to land use practices. We compared the analytical hierarchy process (AHP) based and logistic regression (LR) based approaches to map the areas prone to sinkhole activity in Marion County, Florida by using long-term sinkhole incident report dataset. For this study, the LR based model was more accurate with an area under the receiver operating characteristic (ROC) curve of 0.8 compared to 0.73 with the AHP based model. Both models performed better when an independent future sinkhole dataset was used for validation. The LR based approach showed a low presence of sinkholes in the very low susceptibility class and low absence of sinkholes in the very high susceptibility class. However, the AHP based model detected sinkhole presence by allocating more area to the high and very high susceptibility classes. For instance, areas susceptible to very high and high sinkhole incidents covered almost 43.4% of the total area under the AHP based approach, whereas the LR based approach allocated 20.7% of the total area to high and very high susceptibility classes. Of the predisposing factors studied, the LR method revealed that closeness to topographic depression was the most important factor for sinkhole susceptibility. Both models classified Ocala city, a populous city of the study area, as being very vulnerable to sinkhole hazard. Using a common test case scenario, this study discusses the applicability and potential limitations of these sinkhole susceptibility mapping approaches in central Florida.}, } @article {pmid31073136, year = {2019}, author = {Bátori, Z and Vojtkó, A and Maák, IE and Lőrinczi, G and Farkas, T and Kántor, N and Tanács, E and Kiss, PJ and Juhász, O and Módra, G and Tölgyesi, C and Erdős, L and Aguilon, DJ and Keppel, G}, title = {Karst dolines provide diverse microhabitats for different functional groups in multiple phyla.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {7176}, pmid = {31073136}, issn = {2045-2322}, mesh = {Animals ; Ants/*physiology ; Biodiversity ; Climate ; Ecosystem ; Humidity ; Hungary ; Temperature ; Tracheophyta/*physiology ; }, abstract = {Fine-scale topographic complexity creates important microclimates that can facilitate species to grow outside their main distributional range and increase biodiversity locally. Enclosed depressions in karst landscapes ('dolines') are topographically complex environments which produce microclimates that are drier and warmer (equator-facing slopes) and cooler and moister (pole-facing slopes and depression bottoms) than the surrounding climate. We show that the distribution patterns of functional groups for organisms in two different phyla, Arthropoda (ants) and Tracheophyta (vascular plants), mirror this variation of microclimate. We found that north-facing slopes and bottoms of solution dolines in northern Hungary provided key habitats for ant and plant species associated with cooler and/or moister conditions. Contrarily, south-facing slopes of dolines provided key habitats for species associated with warmer and/or drier conditions. Species occurring on the surrounding plateau were associated with intermediate conditions. We conclude that karst dolines provide a diversity of microclimatic habitats that may facilitate the persistence of taxa with diverse environmental preferences, indicating these dolines to be potential safe havens for multiple phyla under local and global climate oscillations.}, } @article {pmid31071155, year = {2019}, author = {Hofman, MPG and Hayward, MW and Heim, M and Marchand, P and Rolandsen, CM and Mattisson, J and Urbano, F and Heurich, M and Mysterud, A and Melzheimer, J and Morellet, N and Voigt, U and Allen, BL and Gehr, B and Rouco, C and Ullmann, W and Holand, Ø and Jørgensen, NH and Steinheim, G and Cagnacci, F and Kroeschel, M and Kaczensky, P and Buuveibaatar, B and Payne, JC and Palmegiani, I and Jerina, K and Kjellander, P and Johansson, Ö and LaPoint, S and Bayrakcismith, R and Linnell, JDC and Zaccaroni, M and Jorge, MLS and Oshima, JEF and Songhurst, A and Fischer, C and Mc Bride, RT and Thompson, JJ and Streif, S and Sandfort, R and Bonenfant, C and Drouilly, M and Klapproth, M and Zinner, D and Yarnell, R and Stronza, A and Wilmott, L and Meisingset, E and Thaker, M and Vanak, AT and Nicoloso, S and Graeber, R and Said, S and Boudreau, MR and Devlin, A and Hoogesteijn, R and May-Junior, JA and Nifong, JC and Odden, J and Quigley, HB and Tortato, F and Parker, DM and Caso, A and Perrine, J and Tellaeche, C and Zieba, F and Zwijacz-Kozica, T and Appel, CL and Axsom, I and Bean, WT and Cristescu, B and Périquet, S and Teichman, KJ and Karpanty, S and Licoppe, A and Menges, V and Black, K and Scheppers, TL and Schai-Braun, SC and Azevedo, FC and Lemos, FG and Payne, A and Swanepoel, LH and Weckworth, BV and Berger, A and Bertassoni, A and McCulloch, G and Šustr, P and Athreya, V and Bockmuhl, D and Casaer, J and Ekori, A and Melovski, D and Richard-Hansen, C and van de Vyver, D and Reyna-Hurtado, R and Robardet, E and Selva, N and Sergiel, A and Farhadinia, MS and Sunde, P and Portas, R and Ambarli, H and Berzins, R and Kappeler, PM and Mann, GK and Pyritz, L and Bissett, C and Grant, T and Steinmetz, R and Swedell, L and Welch, RJ and Armenteras, D and Bidder, OR and González, TM and Rosenblatt, A and Kachel, S and Balkenhol, N}, title = {Right on track? Performance of satellite telemetry in terrestrial wildlife research.}, journal = {PloS one}, volume = {14}, number = {5}, pages = {e0216223}, pmid = {31071155}, issn = {1932-6203}, support = {/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Animals ; Animals, Wild/*physiology ; *Ecosystem ; *Environmental Monitoring ; *Geographic Information Systems ; *Spacecraft ; *Telemetry ; }, abstract = {Satellite telemetry is an increasingly utilized technology in wildlife research, and current devices can track individual animal movements at unprecedented spatial and temporal resolutions. However, as we enter the golden age of satellite telemetry, we need an in-depth understanding of the main technological, species-specific and environmental factors that determine the success and failure of satellite tracking devices across species and habitats. Here, we assess the relative influence of such factors on the ability of satellite telemetry units to provide the expected amount and quality of data by analyzing data from over 3,000 devices deployed on 62 terrestrial species in 167 projects worldwide. We evaluate the success rate in obtaining GPS fixes as well as in transferring these fixes to the user and we evaluate failure rates. Average fix success and data transfer rates were high and were generally better predicted by species and unit characteristics, while environmental characteristics influenced the variability of performance. However, 48% of the unit deployments ended prematurely, half of them due to technical failure. Nonetheless, this study shows that the performance of satellite telemetry applications has shown improvements over time, and based on our findings, we provide further recommendations for both users and manufacturers.}, } @article {pmid31067326, year = {2019}, author = {Fitak, RR and Antonides, JD and Baitchman, EJ and Bonaccorso, E and Braun, J and Kubiski, S and Chiu, E and Fagre, AC and Gagne, RB and Lee, JS and Malmberg, JL and Stenglein, MD and Dusek, RJ and Forgacs, D and Fountain-Jones, NM and Gilbertson, MLJ and Worsley-Tonks, KEL and Funk, WC and Trumbo, DR and Ghersi, BM and Grimaldi, W and Heisel, SE and Jardine, CM and Kamath, PL and Karmacharya, D and Kozakiewicz, CP and Kraberger, S and Loisel, DA and McDonald, C and Miller, S and O'Rourke, D and Ott-Conn, CN and Páez-Vacas, M and Peel, AJ and Turner, WC and VanAcker, MC and VandeWoude, S and Pecon-Slattery, J}, title = {The Expectations and Challenges of Wildlife Disease Research in the Era of Genomics: Forecasting with a Horizon Scan-like Exercise.}, journal = {The Journal of heredity}, volume = {110}, number = {3}, pages = {261-274}, doi = {10.1093/jhered/esz001}, pmid = {31067326}, issn = {1465-7333}, mesh = {Animal Diseases/epidemiology/*etiology/transmission ; Animals ; *Animals, Wild ; Biodiversity ; Biological Evolution ; Computational Biology/methods ; Disease Susceptibility ; Ecology ; Environment ; Genome ; *Genomics/methods ; Host-Pathogen Interactions/genetics ; Humans ; *Research ; }, abstract = {The outbreak and transmission of disease-causing pathogens are contributing to the unprecedented rate of biodiversity decline. Recent advances in genomics have coalesced into powerful tools to monitor, detect, and reconstruct the role of pathogens impacting wildlife populations. Wildlife researchers are thus uniquely positioned to merge ecological and evolutionary studies with genomic technologies to exploit unprecedented "Big Data" tools in disease research; however, many researchers lack the training and expertise required to use these computationally intensive methodologies. To address this disparity, the inaugural "Genomics of Disease in Wildlife" workshop assembled early to mid-career professionals with expertise across scientific disciplines (e.g., genomics, wildlife biology, veterinary sciences, and conservation management) for training in the application of genomic tools to wildlife disease research. A horizon scanning-like exercise, an activity to identify forthcoming trends and challenges, performed by the workshop participants identified and discussed 5 themes considered to be the most pressing to the application of genomics in wildlife disease research: 1) "Improving communication," 2) "Methodological and analytical advancements," 3) "Translation into practice," 4) "Integrating landscape ecology and genomics," and 5) "Emerging new questions." Wide-ranging solutions from the horizon scan were international in scope, itemized both deficiencies and strengths in wildlife genomic initiatives, promoted the use of genomic technologies to unite wildlife and human disease research, and advocated best practices for optimal use of genomic tools in wildlife disease projects. The results offer a glimpse of the potential revolution in human and wildlife disease research possible through multi-disciplinary collaborations at local, regional, and global scales.}, } @article {pmid31066811, year = {2019}, author = {Souza, TO and Pinto, LW and Souza, ER}, title = {Hidden deaths: corrected estimates of homicides in Bahia, Brazil, 1996- 2015.}, journal = {Salud colectiva}, volume = {15}, number = {}, pages = {e1639}, doi = {10.18294/sc.2019.1639}, pmid = {31066811}, issn = {1851-8265}, mesh = {Brazil ; Data Interpretation, Statistical ; Health Information Systems ; Homicide/*statistics & numerical data ; Humans ; }, abstract = {The objective of this study was to correct and estimate five-year homicide rates in Bahia, Brazil, for the 1996-2015 period. An ecological study of the homicides was carried out using official data from the Mortality Information System of the Ministry of Health. Deaths due to assault are classified in the codes X85-Y09 of the International Classification of Disease 10th Revision (ICD-10). A proportional redistribution of deaths classified as events of undetermined intent (Y10-Y34) was carried out and mortality correction factors were applied. In the analyzed period, 67,599 homicides were registered in the Mortality Information System; after the second correction, 88,429 homicide deaths were estimated. Comparing the official and adjusted figures, there was an underreporting of 30.8%. The highest corrected homicide rates were observed in the eastern region, in Pojuca (129.8 homicides per 100,000 inhabitants), Lauro de Freitas (117.7) and Simões Filho (114.3); in the southern region, in Santa Luzia (121.4), Valença (87.6) and Itabuna (86.5); and in the far south, Santa Cruz Cabrália (128.2), Itabela (113.3) and Porto Seguro (106.8). After correction, there was an increase in homicides in all of the five-year periods in the municipalities analyzed, which resulted in an even higher mortality rate.}, } @article {pmid31065024, year = {2019}, author = {Lee, TRC and Anderson, SJ and Tran-Nguyen, LTT and Sallam, N and Le Ru, BP and Conlong, D and Powell, K and Ward, A and Mitchell, A}, title = {Towards a global DNA barcode reference library for quarantine identifications of lepidopteran stemborers, with an emphasis on sugarcane pests.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {7039}, pmid = {31065024}, issn = {2045-2322}, mesh = {Animals ; *DNA Barcoding, Taxonomic ; Databases, Genetic ; Lepidoptera/classification/*genetics ; Moths/genetics ; *Pest Control ; Phylogeny ; Quarantine ; Saccharum ; }, abstract = {Lepidopteran stemborers are among the most damaging agricultural pests worldwide, able to reduce crop yields by up to 40%. Sugarcane is the world's most prolific crop, and several stemborer species from the families Noctuidae, Tortricidae, Crambidae and Pyralidae attack sugarcane. Australia is currently free of the most damaging stemborers, but biosecurity efforts are hampered by the difficulty in morphologically distinguishing stemborer species. Here we assess the utility of DNA barcoding in identifying stemborer pest species. We review the current state of the COI barcode sequence library for sugarcane stemborers, assembling a dataset of 1297 sequences from 64 species. Sequences were from specimens collected and identified in this study, downloaded from BOLD or requested from other authors. We performed species delimitation analyses to assess species diversity and the effectiveness of barcoding in this group. Seven species exhibited <0.03 K2P interspecific diversity, indicating that diagnostic barcoding will work well in most of the studied taxa. We identified 24 instances of identification errors in the online database, which has hampered unambiguous stemborer identification using barcodes. Instances of very high within-species diversity indicate that nuclear markers (e.g. 18S, 28S) and additional morphological data (genitalia dissection of all lineages) are needed to confirm species boundaries.}, } @article {pmid31064321, year = {2019}, author = {Beiki, H and Liu, H and Huang, J and Manchanda, N and Nonneman, D and Smith, TPL and Reecy, JM and Tuggle, CK}, title = {Improved annotation of the domestic pig genome through integration of Iso-Seq and RNA-seq data.}, journal = {BMC genomics}, volume = {20}, number = {1}, pages = {344}, pmid = {31064321}, issn = {1471-2164}, support = {3040 - 31000 - 099 - 00D//Agricultural Research Service (US)/ ; 3040 - 31000 - 100 - 00D//Agricultural Research Service/ ; none//NRSP-8 Swine Genome Coordination/ ; }, mesh = {*Alternative Splicing ; Animals ; Chromatin Immunoprecipitation/*methods ; Computational Biology/*methods ; *Genome ; High-Throughput Nucleotide Sequencing/*methods ; *Molecular Sequence Annotation ; Sus scrofa ; }, abstract = {BACKGROUND: Our understanding of the pig transcriptome is limited. RNA transcript diversity among nine tissues was assessed using poly(A) selected single-molecule long-read isoform sequencing (Iso-seq) and Illumina RNA sequencing (RNA-seq) from a single White cross-bred pig.

RESULTS: Across tissues, a total of 67,746 unique transcripts were observed, including 60.5% predicted protein-coding, 36.2% long non-coding RNA and 3.3% nonsense-mediated decay transcripts. On average, 90% of the splice junctions were supported by RNA-seq within tissue. A large proportion (80%) represented novel transcripts, mostly produced by known protein-coding genes (70%), while 17% corresponded to novel genes. On average, four transcripts per known gene (tpg) were identified; an increase over current EBI (1.9 tpg) and NCBI (2.9 tpg) annotations and closer to the number reported in human genome (4.2 tpg). Our new pig genome annotation extended more than 6000 known gene borders (5' end extension, 3' end extension, or both) compared to EBI or NCBI annotations. We validated a large proportion of these extensions by independent pig poly(A) selected 3'-RNA-seq data, or human FANTOM5 Cap Analysis of Gene Expression data. Further, we detected 10,465 novel genes (81% non-coding) not reported in current pig genome annotations. More than 80% of these novel genes had transcripts detected in > 1 tissue. In addition, more than 80% of novel intergenic genes with at least one transcript detected in liver tissue had H3K4me3 or H3K36me3 peaks mapping to their promoter and gene body, respectively, in independent liver chromatin immunoprecipitation data.

CONCLUSIONS: These validated results show significant improvement over current pig genome annotations.}, } @article {pmid31063186, year = {2019}, author = {Mamiya, H and Schmidt, AM and Moodie, EEM and Ma, Y and Buckeridge, DL}, title = {An Area-Level Indicator of Latent Soda Demand: Spatial Statistical Modeling of Grocery Store Transaction Data to Characterize the Nutritional Landscape in Montreal, Canada.}, journal = {American journal of epidemiology}, volume = {188}, number = {9}, pages = {1713-1722}, doi = {10.1093/aje/kwz115}, pmid = {31063186}, issn = {1476-6256}, support = {CPP-137904//Canadian Institute for Health Research/International ; }, mesh = {Bayes Theorem ; Carbonated Beverages/*statistics & numerical data ; Commerce/*statistics & numerical data ; Diabetes Mellitus, Type 2 ; Diet Surveys ; Food Industry ; Food Supply/statistics & numerical data ; Humans ; *Models, Statistical ; Quebec ; Residence Characteristics ; Socioeconomic Factors ; }, abstract = {Measurement of neighborhood dietary patterns at high spatial resolution allows public health agencies to identify and monitor communities with an elevated risk of nutrition-related chronic diseases. Currently, data on diet are obtained primarily through nutrition surveys, which produce measurements at low spatial resolutions. The availability of store-level grocery transaction data provides an opportunity to refine the measurement of neighborhood dietary patterns. We used these data to develop an indicator of area-level latent demand for soda in the Census Metropolitan Area of Montreal in 2012 by applying a hierarchical Bayesian spatial model to data on soda sales from 1,097 chain retail food outlets. The utility of the indicator of latent soda demand was evaluated by assessing its association with the neighborhood relative risk of prevalent type 2 diabetes mellitus. The indicator improved the fit of the disease-mapping model (deviance information criterion: 2,140 with the indicator and 2,148 without) and enables a novel approach to nutrition surveillance.}, } @article {pmid31059560, year = {2019}, author = {Zhang, Y and Zhang, M and Hu, Y and Zhuang, X and Xu, W and Li, P and Wang, Z}, title = {Mining and characterization of novel EST-SSR markers of Parrotia subaequalis (Hamamelidaceae) from the first Illumina-based transcriptome datasets.}, journal = {PloS one}, volume = {14}, number = {5}, pages = {e0215874}, pmid = {31059560}, issn = {1932-6203}, mesh = {*Data Mining ; *Databases, Genetic ; *Expressed Sequence Tags ; *Gene Expression Profiling ; Hamamelidaceae/*genetics ; Microsatellite Repeats/*genetics ; Molecular Sequence Annotation ; Polymorphism, Genetic ; }, abstract = {Parrotia subaequalis is an endangered Tertiary relict tree from eastern China. Despite its important ecological and horticultural value, no transcriptomic data and limited molecular markers are currently available in this species. In this study, we first performed high-throughput transcriptome sequencing of two individuals representing the northernmost (TX) and southernmost (SJD) population of P. subaequalis on the Illumina HiSeq 2500 platform. We gathered a total of 69,135 unigenes for P. subaequalis (TX) and 84,009 unigenes for P. subaequalis (SJD). From two unigenes datasets, 497 candidate polymorphic novel expressed sequence tag-simple sequence repeats (EST-SSRs) were identified using CandiSSR. Among these repeats, di-nucleotide repeats were the most abundant repeat type (62.78%) followed by tri-, tetra- and hexa-nucleotide repeats. We then randomly selected 54 primer pairs for polymorphism validation, of which 27 (50%) were successfully amplified and showed polymorphisms in 96 individuals from six natural populations of P. subaequalis. The average number of alleles per locus and the polymorphism information content values were 3.70 and 0.343; the average observed and expected heterozygosity were 0.378 and 0.394. A relatively high level of genetic diversity (HT = 0.393) and genetic differentiation level (FST = 0.171) were surveyed, indicating P. subaequalis maintained high levels of species diversity in the long-term evolutionary history. Additionally, a high level of cross-transferability (92.59%) was displayed in five congeneric Hamamelidaceae species. Therefore, these new transcriptomic data and novel polymorphic EST-SSR markers will pinpoint genetic resources and facilitate future studies on population genetics and molecular breeding of P. subaequalis and other Hamamelidaceae species.}, } @article {pmid31059547, year = {2019}, author = {Bailly, L and David, R and Chevrier, R and Grebet, J and Moncada, M and Fuch, A and Sciortino, V and Robert, P and Pradier, C}, title = {Alzheimer's disease: Estimating its prevalence rate in a French geographical unit using the National Alzheimer Data Bank and national health insurance information systems.}, journal = {PloS one}, volume = {14}, number = {5}, pages = {e0216221}, pmid = {31059547}, issn = {1932-6203}, mesh = {Age Factors ; Alzheimer Disease/*epidemiology ; Bayes Theorem ; Data Management/methods ; *Databases, Factual ; *Epidemiological Monitoring ; France/epidemiology ; Humans ; National Health Programs/*statistics & numerical data ; Prevalence ; Sex Factors ; }, abstract = {BACKGROUND: Reliable epidemiological data on Alzheimer's disease are scarce. However, these are necessary to adapt healthcare policy in terms of prevention, care and social needs related to this condition. To estimate the prevalence rate in the Alpes-Maritimes on the French Riviera, with a population of one million, we present a capture-recapture procedure applied to cases of Alzheimer's disease, based on two epidemiological surveillance systems.

METHODS: To estimate the total number of patients affected by Alzheimer's disease, a capture-recapture study included a cohort of patients with Alzheimer's disease or receiving medications only eligible for use for this condition, recorded by a specific health insurance information system (Health Insurance Cohort, HIC), and those registered in the French National Alzheimer's Data Bank ("Banque Nationale Alzheimer", BNA) in 2010 and 2011. We applied Bayesian estimation of the Mt ecological model, taking into account age and gender as covariates, i.e. factors of inhomogeneous catchability.

RESULTS: Overall, 5,562 patients with Alzheimer's disease were recorded, of whom only 856 were common to both information systems. Mean age and F/M sex ratio differed between BNA and HIC surveillance systems, 81 vs 84 years and 2.7 vs 3.2, respectively. A Bayesian estimation, with age and gender as covariates, yields an estimate of 15,060 cases of Alzheimer's disease [95%HPDI: 14,490-15,630] in the Alpes-Maritimes. The completeness of the HIC and BNA databases were respectively of 25.4% and 17.2%. The estimated prevalence rate among the population over 65 years old was 6.3% in 2010-2011.

CONCLUSIONS: This study demonstrates that it is possible to determine the number of subjects affected by Alzheimer's disease in a geographical unit, using available data from two existing surveillance systems in France, i.e. 15,060 cases in the Alpes-Maritimes. This is the first stage of a population-based approach in view of adapting available resources to the population's needs.}, } @article {pmid31058458, year = {2019}, author = {McCartney-Melstad, E and Gidiş, M and Shaffer, HB}, title = {An empirical pipeline for choosing the optimal clustering threshold in RADseq studies.}, journal = {Molecular ecology resources}, volume = {19}, number = {5}, pages = {1195-1204}, doi = {10.1111/1755-0998.13029}, pmid = {31058458}, issn = {1755-0998}, support = {//U.S. Fish and Wildlife Service/ ; 1257648//Division of Environmental Biology (National Science Foundation)/ ; //The Scientific and Technological Council of Turkey (TUBITAK)/ ; //Bureau of Reclamation/ ; //California Department of Transportation/ ; }, mesh = {Animals ; *Cluster Analysis ; Computational Biology/*methods ; Genetics, Population/*methods ; Metagenomics/*methods ; *Phylogeny ; Ranidae/classification/genetics ; Sequence Analysis, DNA/*methods ; }, abstract = {Genomic data are increasingly used for high resolution population genetic studies including those at the forefront of biological conservation. A key methodological challenge is determining sequence similarity clustering thresholds for RADseq data when no reference genome is available. These thresholds define the maximum permitted divergence among allelic variants and the minimum divergence among putative paralogues and are central to downstream population genomic analyses. Here we develop a novel set of metrics to determine sequence similarity thresholds that maximize the correct separation of paralogous regions and minimize oversplitting naturally occurring allelic variation within loci. These metrics empirically identify the threshold value at which true alleles at opposite ends of several major axes of genetic variation begin to incorrectly separate into distinct clusters, allowing researchers to choose thresholds just below this value. We test our approach on a recently published data set for the protected foothill yellow-legged frog (Rana boylii). The metrics recover a consistent pattern of roughly 96% similarity as a threshold above which genetic divergence and data missingness become increasingly correlated. We provide scripts for assessing different clustering thresholds and discuss how this approach can be applied across a wide range of empirical data sets.}, } @article {pmid31056485, year = {2019}, author = {Švec, P and Hönig, V and Zubriková, D and Wittmann, M and Pfister, K and Grubhoffer, L}, title = {The use of multi-criteria evaluation for the selection of study plots for monitoring of I. ricinus ticks - Example from Central Europe.}, journal = {Ticks and tick-borne diseases}, volume = {10}, number = {4}, pages = {905-910}, doi = {10.1016/j.ttbdis.2019.04.014}, pmid = {31056485}, issn = {1877-9603}, mesh = {Altitude ; Animals ; Borrelia burgdorferi/isolation & purification ; *Ecosystem ; Encephalitis Viruses, Tick-Borne/isolation & purification ; Female ; Geographic Information Systems ; Geography ; Ixodes/*physiology ; Male ; Sampling Studies ; Tick-Borne Diseases/*epidemiology ; }, abstract = {Research projects in the field of eco-epidemiology of tick-borne diseases often require extensive sampling of arthropod vectors in the field. The aim of our study was to use geographical information systems (GIS) to select appropriate sampling sites of Ixodes ricinus ticks in central European habitat for further ecological studies of vector-borne pathogens (tick-borne encephalitis virus and Borrelia burgdorferi sensu lato). The model area was the Czech-German borderland (the region of South Bohemia and two regions in Germany: the Upper Palatinate and Lower Bavaria) where numerous human tick-borne encephalitis cases are reported annually. We prepared the sampling site design as a multi-criteria evaluation (MCE) task. In the GIS environment, we conducted MCE with a set of environmental, socio-economic and epidemiological data (altitude, vegetation cover, number of tick-borne encephalitis cases recorded in the past, tourist activity). The MCE classified the surveyed area into two classes: suitable for tick collection and unsuitable for tick collection. Subsequently, 50 tick sampling sites were randomly selected in the suitable area: 30 in South Bohemia (Czech Republic) and 20 in the Upper Palatinate and Lower Bavaria regions (Bavaria, Germany). The sampling sites were identified and surveyed in the field. The presence of ticks was confirmed by flagging at each of the selected plots. The described MCE system represents a versatile tool for semi-randomized design of tick sampling sites for research projects in the field of tick-borne pathogen ecology as well as for tick-borne pathogen surveillance programs run by local health authorities.}, } @article {pmid31055079, year = {2019}, author = {Binet, MT and Gissi, F and Stone, S and Trinh, C and McKnight, KS}, title = {Use of scanning and image recognition technology to semi-automate larval development assessment in toxicity tests with a tropical copepod.}, journal = {Ecotoxicology and environmental safety}, volume = {180}, number = {}, pages = {1-11}, doi = {10.1016/j.ecoenv.2019.03.049}, pmid = {31055079}, issn = {1090-2414}, mesh = {Animals ; Australia ; *Automation ; Copepoda/*drug effects ; Ecotoxicology/instrumentation/*methods ; Embryonic Development/*drug effects ; Image Interpretation, Computer-Assisted ; Larva/*drug effects/growth & development ; Microscopy ; Seawater/chemistry ; Software ; Toxicity Tests, Chronic/instrumentation/*methods ; Water Pollutants, Chemical/toxicity ; }, abstract = {There is a high demand for the development of reliable chronic toxicity tests using tropical marine species for subsequent use in tropical risk assessment. However, many chronic test endpoints can be laborious and time-consuming to assess, particularly if the endpoints require measurements of individuals (e.g. growth, size) or advanced taxonomic expertise (e.g. differentiating between larval development stages). In this study, we used scanning and image recognition (SIR) technology to develop and validate a chronic toxicity test with larvae of the tropical euryhaline copepod, Acartia sinjiensis. Optimisation steps are described, and included egg age, and effect of algal food type and salinity on toxicity. Comparisons were made between traditional endpoints measured using microscopy and those measured using SIR. Traditional endpoints of larval development ratio (LDR) and survival achieved using microscope examination and SIR were almost identical (R[2] = 0.96-0.97). Additional endpoints made possible by SIR included larval development index (LDI; based on the number of animals at different stages of development), and a range of size measurements (e.g. surface area, perimeter and length) for individual animals and for total populations (i.e. a proxy for biomass). The SIR-derived endpoints were based on measurements that had concentration-dependant responses to tested toxicants (copper, nickel, ammonia), and were a sub-set of the full range of metrics provided by the software. Toxicity values based on SIR-measurements were similar to or more sensitive than the traditional LDR endpoint. SIR technology provides a major opportunity to improve and modernise larval development tests for a range for species, but comes at a cost of increased data size and complexity. Therefore, as a research tool, SIR has significant advantages over traditional microscope methods, but for routine toxicity testing, SIR incorporation into invertebrate toxicity testing will benefit from further improvements to the associated software and data management systems.}, } @article {pmid31054399, year = {2019}, author = {Pathak, S and Garg, RD and Jato-Espino, D and Lakshmi, V and Ojha, CSP and , }, title = {Evaluating hotspots for stormwater harvesting through participatory sensing.}, journal = {Journal of environmental management}, volume = {242}, number = {}, pages = {351-361}, doi = {10.1016/j.jenvman.2019.04.082}, pmid = {31054399}, issn = {1095-8630}, mesh = {Cities ; *Geographic Information Systems ; Hydrology ; India ; *Rain ; }, abstract = {Geographic Information Systems have been widely accepted to manage and manipulate spatial data associated with the hydrologic response of a watershed. Due to climate change and drought impacts, there is a need to conserve freshwater resources, which can be accomplished by introducing the concept of stormwater harvesting. Apart from hotspot identification and site screening, several economic, social, cultural, environmental aspects need to be considered before finalizing the suitable site for stormwater harvesting. The shortlisted sites are commonly ranked by considering various parameters, i.e. water demand, availability of stormwater and distance to end-use locations, which relate to economic aspects. In the present study, socio-environmental considerations are also constituted by adopting a web-GIS based approach. The geospatial datasets and metadata associated with the study area are organized as a repository in the open source database server (PostgreSQL/PostGIS), which is further assessed and analyzed by using GeoServer. This technique publishes the geospatial datasets to the public domain websites that can be accessed and visualized around the clock and across the world. This will help stakeholders gather and store responses from water planners and inhabitants, while minimizing the time and cost associated with field visits for collecting individual responses. In this respect, a questionnaire is prepared that includes queries associated with site selection and the responses are gathered from various institutions, water professionals, stakeholders and residents. Once the responses are collected, the Analytic Hierarchy Process has been implemented to compute the relative weights of each criterion with respect to the responses collected. The weights thus obtained assisted the planners in deciding the suitable stormwater harvesting site for Dehradun city in India. In context to responses gathered the sites 'B' and 'D' are given the maximum weightage to be the suitable sites in the study region. Also, the socio-environmental criteria such as 'community acceptance', 'recreational activities' and 'need for water reuse' have gathered the maximum weightage from the responses for the specific sites. Hence, the proposed methodology demonstrated how water professionals, civilians, planners, stakeholders and public can be included as participants in water-related decision making processes.}, } @article {pmid31053062, year = {2019}, author = {Gan, HM and Grandjean, F and Jenkins, TL and Austin, CM}, title = {Absence of evidence is not evidence of absence: Nanopore sequencing and complete assembly of the European lobster (Homarus gammarus) mitogenome uncovers the missing nad2 and a new major gene cluster duplication.}, journal = {BMC genomics}, volume = {20}, number = {1}, pages = {335}, pmid = {31053062}, issn = {1471-2164}, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; *Biological Evolution ; Computational Biology/*methods ; *Gene Duplication ; *Genome, Mitochondrial ; High-Throughput Nucleotide Sequencing ; Mitochondrial Proteins/*genetics ; Multigene Family ; *Nanopores ; Nephropidae/*genetics/metabolism ; Phylogeny ; Sequence Analysis, DNA ; Sequence Homology ; }, abstract = {BACKGROUND: The recently published complete mitogenome of the European lobster (Homarus gammarus) that was generated using long-range PCR exhibits unusual gene composition (missing nad2) and gene rearrangements among decapod crustaceans with strong implications in crustacean phylogenetics. Such atypical mitochondrial features will benefit greatly from validation with emerging long read sequencing technologies such as Oxford Nanopore that can more accurately identify structural variation.

RESULTS: We re-sequenced the H. gammarus mitogenome on an Oxford Nanopore Minion flowcell and performed a long-read only assembly, generating a complete mitogenome assembly for H. gammarus. In contrast to previous reporting, we found an intact mitochondrial nad2 gene in the H. gammarus mitogenome and showed that its gene organization is broadly similar to that of the American lobster (H. americanus) except for the presence of a large tandemly duplicated region with evidence of pseudogenization in one of each duplicated protein-coding genes.

CONCLUSIONS: Using the European lobster as an example, we demonstrate the value of Oxford Nanopore long read technology in resolving problematic mitogenome assemblies. The increasing accessibility of Oxford Nanopore technology will make it an attractive and useful tool for evolutionary biologists to verify new and existing unusual mitochondrial gene rearrangements recovered using first and second generation sequencing technologies, particularly those used to make phylogenetic inferences of evolutionary scenarios.}, } @article {pmid31052562, year = {2019}, author = {Bartas, M and Čutová, M and Brázda, V and Kaura, P and Šťastný, J and Kolomazník, J and Coufal, J and Goswami, P and Červeň, J and Pečinka, P}, title = {The Presence and Localization of G-Quadruplex Forming Sequences in the Domain of Bacteria.}, journal = {Molecules (Basel, Switzerland)}, volume = {24}, number = {9}, pages = {}, pmid = {31052562}, issn = {1420-3049}, support = {18-15548S//Grant Agency of the Czech Republic/ ; LO1208 TEWEP//Ministry of Education, Youth and Sports of the Czech Republic in the "National Feasibility Program I"/ ; CZ.1.05/2.1.00/19.0388//EU structural funding Operational Programme Research and Development for innovation/ ; SGS/09/PrF/2019//University of Ostrava/ ; }, mesh = {Bacteria/*genetics ; DNA, Bacterial/*chemistry ; *G-Quadruplexes ; Genome, Bacterial ; Humans ; Nucleic Acid Conformation ; Phylogeny ; }, abstract = {The role of local DNA structures in the regulation of basic cellular processes is an emerging field of research. Amongst local non-B DNA structures, the significance of G-quadruplexes was demonstrated in the last decade, and their presence and functional relevance has been demonstrated in many genomes, including humans. In this study, we analyzed the presence and locations of G-quadruplex-forming sequences by G4Hunter in all complete bacterial genomes available in the NCBI database. G-quadruplex-forming sequences were identified in all species, however the frequency differed significantly across evolutionary groups. The highest frequency of G-quadruplex forming sequences was detected in the subgroup Deinococcus-Thermus, and the lowest frequency in Thermotogae. G-quadruplex forming sequences are non-randomly distributed and are favored in various evolutionary groups. G-quadruplex-forming sequences are enriched in ncRNA segments followed by mRNAs. Analyses of surrounding sequences showed G-quadruplex-forming sequences around tRNA and regulatory sequences. These data point to the unique and non-random localization of G-quadruplex-forming sequences in bacterial genomes.}, } @article {pmid31043324, year = {2019}, author = {Danaei, G and Farzadfar, F and Kelishadi, R and Rashidian, A and Rouhani, OM and Ahmadnia, S and Ahmadvand, A and Arabi, M and Ardalan, A and Arhami, M and Azizi, MH and Bahadori, M and Baumgartner, J and Beheshtian, A and Djalalinia, S and Doshmangir, L and Haghdoost, AA and Haghshenas, R and Hosseinpoor, AR and Islami, F and Kamangar, F and Khalili, D and Madani, K and Masoumi-Asl, H and Mazyaki, A and Mirchi, A and Moradi, E and Nayernouri, T and Niemeier, D and Omidvari, AH and Peykari, N and Pishgar, F and Qorbani, M and Rahimi, K and Rahimi-Movaghar, A and Tehrani, FR and Rezaei, N and Shahraz, S and Takian, A and Tootee, A and Ezzati, M and Jamshidi, HR and Larijani, B and Majdzadeh, R and Malekzadeh, R}, title = {Iran in transition.}, journal = {Lancet (London, England)}, volume = {393}, number = {10184}, pages = {1984-2005}, doi = {10.1016/S0140-6736(18)33197-0}, pmid = {31043324}, issn = {1474-547X}, support = {001/WHO_/World Health Organization/International ; MR/L01341X/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Health Transition ; *History of Medicine ; History, Ancient ; Humans ; Iran/epidemiology ; Noncommunicable Diseases/*epidemiology ; Persia ; Quality-Adjusted Life Years ; }, abstract = {Being the second-largest country in the Middle East, Iran has a long history of civilisation during which several dynasties have been overthrown and established and health-related structures have been reorganised. Iran has had the replacement of traditional practices with modern medical treatments, emergence of multiple pioneer scientists and physicians with great contributions to the advancement of science, environmental and ecological changes in addition to large-scale natural disasters, epidemics of multiple communicable diseases, and the shift towards non-communicable diseases in recent decades. Given the lessons learnt from political instabilities in the past centuries and the approaches undertaken to overcome health challenges at the time, Iran has emerged as it is today. Iran is now a country with a population exceeding 80 million, mainly inhabiting urban regions, and has an increasing burden of non-communicable diseases, including cardiovascular diseases, hypertension, diabetes, malignancies, mental disorders, substance abuse, and road injuries.}, } @article {pmid31042745, year = {2019}, author = {Niku, J and Brooks, W and Herliansyah, R and Hui, FKC and Taskinen, S and Warton, DI}, title = {Efficient estimation of generalized linear latent variable models.}, journal = {PloS one}, volume = {14}, number = {5}, pages = {e0216129}, pmid = {31042745}, issn = {1932-6203}, mesh = {Algorithms ; Computer Simulation ; Data Interpretation, Statistical ; Likelihood Functions ; *Linear Models ; *Multivariate Analysis ; Software ; }, abstract = {Generalized linear latent variable models (GLLVM) are popular tools for modeling multivariate, correlated responses. Such data are often encountered, for instance, in ecological studies, where presence-absences, counts, or biomass of interacting species are collected from a set of sites. Until very recently, the main challenge in fitting GLLVMs has been the lack of computationally efficient estimation methods. For likelihood based estimation, several closed form approximations for the marginal likelihood of GLLVMs have been proposed, but their efficient implementations have been lacking in the literature. To fill this gap, we show in this paper how to obtain computationally convenient estimation algorithms based on a combination of either the Laplace approximation method or variational approximation method, and automatic optimization techniques implemented in R software. An extensive set of simulation studies is used to assess the performances of different methods, from which it is shown that the variational approximation method used in conjunction with automatic optimization offers a powerful tool for estimation.}, } @article {pmid31042732, year = {2019}, author = {Fechter, D and Ciuti, S and Kelle, D and Pratje, P and Dormann, CF and Storch, I}, title = {Spatial behavior in rehabilitated orangutans in Sumatra: Where do they go?.}, journal = {PloS one}, volume = {14}, number = {5}, pages = {e0215284}, pmid = {31042732}, issn = {1932-6203}, mesh = {Age Factors ; Animals ; Animals, Wild/*physiology ; Behavior, Animal/physiology ; Conservation of Natural Resources ; Female ; Geographic Information Systems ; Humans ; Indonesia ; Male ; Pongo/*physiology ; Spatial Behavior/*physiology ; }, abstract = {Wildlife restoration is one of the key components of conservation strategies, and this includes the rehabilitation and release of animals confiscated from wildlife traffickers. When primates are re-introduced, most individuals need a pre-release training to acquire the skills needed to survive in the wild. Pre-release training may either negatively or positively affect primate post-release behavior and survival. Post-release behavior, however, has rarely been monitored even though it is the only means to assess the survival of released individuals. Here, we present a thorough analysis of data from a 3-year radio tracking study on 32 orangutans (Pongo abelii) released in Sumatra after their rehabilitation. We investigated whether and how the age at release, the duration of the pre-release rehabilitation and training, and the release location affected the post-release individual spatial behavior. Orangutans released at older age exhibited post-release habitat selection patterns that were more comparable to that shown by wild conspecifics, i.e., they chose areas closer to rivers and at lower elevations (150-250 meters a.s.l.) where previous research had documented greater food availability. In contrast, individuals released at younger age showed a stronger spatial dependency on the rehabilitation station and exhibited disrupted habitat selection patterns; although after several months after the release all individuals tended to decrease their spatial reliance on the rehabilitation facility. This study indicates that the rehabilitation of individuals for a longer period and their release further from the rehabilitation station have facilitated the subsequent development of more natural spatial behavior, i.e. driven by food availability rather than by the dependence on care-giving human facility. Our study provides indications on how to improve the rehabilitation and release of confiscated orangutans, highlighting the importance of the age at release, the length of the rehabilitation program, and the location of the release site.}, } @article {pmid31042286, year = {2019}, author = {Falster, DS and FitzJohn, RG and Pennell, MW and Cornwell, WK}, title = {Datastorr: a workflow and package for delivering successive versions of 'evolving data' directly into R.}, journal = {GigaScience}, volume = {8}, number = {5}, pages = {}, pmid = {31042286}, issn = {2047-217X}, mesh = {*Computational Biology ; Humans ; *Information Dissemination ; *Software ; Workflow ; }, abstract = {The sharing and re-use of data has become a cornerstone of modern science. Multiple platforms now allow easy publication of datasets. So far, however, platforms for data sharing offer limited functions for distributing and interacting with evolving datasets- those that continue to grow with time as more records are added, errors fixed, and new data structures are created. In this article, we describe a workflow for maintaining and distributing successive versions of an evolving dataset, allowing users to retrieve and load different versions directly into the R platform. Our workflow utilizes tools and platforms used for development and distribution of successive versions of an open source software program, including version control, GitHub, and semantic versioning, and applies these to the analogous process of developing successive versions of an open source dataset. Moreover, we argue that this model allows for individual research groups to achieve a dynamic and versioned model of data delivery at no cost.}, } @article {pmid31039751, year = {2019}, author = {Fu, B and Yu, X and Tong, J and Pang, M and Zhou, Y and Liu, Q and Tao, W}, title = {Comparative transcriptomic analysis of hypothalamus-pituitary-liver axis in bighead carp (Hypophthalmichthys nobilis) with differential growth rate.}, journal = {BMC genomics}, volume = {20}, number = {1}, pages = {328}, pmid = {31039751}, issn = {1471-2164}, support = {31472268//National Natural Science Foundation of China/ ; 31502147//National Natural Science Foundation of China/ ; 2016FBZ05//State Key Laboratory of Freshwater Ecology and Biotechnology/ ; XDJK2018B025//Fundamental Research Funds for the Central Universities (Ministry of Education of China)/ ; }, mesh = {Animals ; Carps/*genetics/*growth & development ; Computational Biology ; High-Throughput Nucleotide Sequencing ; Hypothalamus/*growth & development/metabolism ; Liver/*growth & development/metabolism ; Molecular Sequence Annotation ; Phenotype ; Pituitary Gland/*growth & development/metabolism ; *Transcriptome ; }, abstract = {BACKGROUND: Growth rate is one of the most important features for aquaculture species and deciphering its regulation mechanism has great significance both in genetics and in economics. Hypothalamus-pituitary growth axis (HP growth axis) or neuro-endocrine axis plays a vital role in growth regulation in different aquaculture animals.

RESULTS: In this study, the HP and liver transcriptomes of two female groups (H and L) with phenotypically extreme growth rate were sequenced using RNA-Seq. A total of 30,524 and 22,341 genes were found expressed in the two tissues, respectively. The average expression levels for the two tissues were almost the same, but the median differed significantly. A differential expression analysis between H and L groups identified 173 and 204 differentially expressed genes (DEGs) in HP and liver tissue, respectively. Pathway analysis revealed that DEGs in HP tissue were enriched in regulation of cell proliferation and angiogenesis while in liver tissue these genes were overrepresented in sterol biosynthesis and transportation. Genomic overlapping analyses found that 4 and 5 DEGs were within growth-related QTL in HP and liver tissue respectively. A deeper analysis of these 9 genes revealed 3 genes were functionally linked to the trait of interest. The expression of 2075 lncRNAs in HP tissue and 1490 in liver tissue were also detected, and some of lncRNAs were highly expressed in the two tissues.

CONCLUSIONS: Above all, the results of the present study greatly contributed to the knowledge of the regulation of growth and then assisted the design of new selection strategies for bighead carp with improved growth-related traits.}, } @article {pmid31039147, year = {2019}, author = {Fogarty, L and Creanza, N and Feldman, MW}, title = {The life history of learning: Demographic structure changes cultural outcomes.}, journal = {PLoS computational biology}, volume = {15}, number = {4}, pages = {e1006821}, pmid = {31039147}, issn = {1553-7358}, mesh = {Agriculture ; Anthropology/methods ; *Biological Evolution ; Computational Biology/*methods ; *Cultural Evolution ; Demography/*methods ; Feeding Behavior ; Humans ; }, abstract = {Human populations show rich cultural diversity. Underpinning this diversity of tools, rituals, and cultural norms are complex interactions between cultural evolutionary and demographic processes. Most models of cultural change assume that individuals use the same learning modes and methods throughout their lives. However, empirical data on 'learning life histories'-the balance of dominant modes of learning (for example, learning from parents, peers, or unrelated elders) throughout an individual's lifetime-suggest that age structure may play a crucial role in determining learning modes and cultural evolutionary trajectories. Thus, studied in isolation, demographic and cultural evolutionary models show only part of the picture. This paper describes a mathematical and computational framework that combines demographic and cultural evolutionary methods. Using this general framework, we examine interactions between the ways in which culture is spread throughout an individual's lifetime and cultural change across generations. We show that including demographic structure alongside cultural dynamics can help to explain domain-specific patterns of cultural evolution that are a persistent feature of cultural data, and can shed new light on rare but significant demographic events.}, } @article {pmid31038630, year = {2019}, author = {Covre, ER and Melo, WA and Tostes, MFDP and Fernandes, CAM}, title = {Permanence, cost and mortality related to surgical admissions by the Unified Health System.}, journal = {Revista latino-americana de enfermagem}, volume = {27}, number = {}, pages = {e3136}, pmid = {31038630}, issn = {1518-8345}, mesh = {Brazil/epidemiology ; Costs and Cost Analysis ; Hospitalization/*economics/statistics & numerical data ; Humans ; Length of Stay ; National Health Programs/*economics/statistics & numerical data ; Patient Admission/statistics & numerical data ; Surgical Procedures, Operative/*economics/mortality ; }, abstract = {OBJECTIVE: to analyze the time trend of surgical admissions by the Unified Health System according to hospital stay, costs and mortality by subgroups of surgical procedures in Brazil.

METHOD: ecological study of time series. The variables surgical hospitalization, permanence, cost and mortality were obtained from the Department of Informatics of the Unified Health System. The trend analysis used the polynomial regression model.

RESULTS: in nine years, 37,565,785 surgical admissions were recorded. The mean duration of surgical admissions was constant (p = 0.449); the mean stay (3.8 days) was decreasing and significant (p <0.01); the mean cost (389.16 dollars) and mortality (1.63%) were increasing and significant (p <0.01). In subgroups of eye, thoracic, oncological and other surgeries, the temporal evolution of surgeries was increasing and significant (p <0.05). In contrast, endocrine glands, digestive tract, genitourinary, breast, reconstruction and buco-maxillofacial surgeries showed a significant trend of decline (p <0.05). In the other subgroups, the trend was constant.

CONCLUSION: evidence shows the trend of surgical admissions in the last decade in the country and provide subsidies for the efficient elaboration of public policies, planning and management towards universal coverage in surgical care.}, } @article {pmid31038614, year = {2019}, author = {Queiroz, PR and Lima, KC and Oliveira, TC and Santos, MMD and Jacob, JF and Oliveira, AMBM}, title = {Notifiable Diseases Information System and human poisoning by pesticides in Brazil.}, journal = {Revista brasileira de epidemiologia = Brazilian journal of epidemiology}, volume = {22}, number = {}, pages = {e190033}, doi = {10.1590/1980-549720190033}, pmid = {31038614}, issn = {1980-5497}, mesh = {Brazil/epidemiology ; Disease Notification/*statistics & numerical data ; Female ; Health Information Systems/*statistics & numerical data ; Humans ; Incidence ; Male ; Pesticides/*poisoning ; Regression Analysis ; Sex Distribution ; Statistics, Nonparametric ; Time Factors ; }, abstract = {OBJECTIVE: To analyze trends in pesticide poisoning incidence rates in Brazilian regions, according to sex and circumstances of poisoning, between 2001 and 2014.

METHOD: Ecological time-series study, with data from the national Notifiable Diseases Information System (SINAN). The incidence rates were calculated by dividing the number of confirmed new cases of pesticide poisoning by the total resident population in the same period and location. Both Polynomial regression analysis and Mann-Whitney and Kruskal-Wallis tests were performed. When significant differences were found, these tests were followed by the Bonferroni penalty, in order to identify the difference more precisely.

RESULTS: In Brazil, 80,069 notified poisoning cases were recorded from 2001 to 2014. There was a steadily increasing growth of pesticide poisoning in this population, whose growth trend was 0,377 for 100,000 inhabitants per year. The highest incidence of poisoning occurred in the South and Midest Regions. Regarding sex, no significant differences were found (p < 0,347), and attempted suicide was the most significant circumstance of poisoning (p < 0,001).

CONCLUSION: The incidence of pesticide poisoning in Brazil has been continuously increasing in the twenty-first century.}, } @article {pmid31035578, year = {2019}, author = {Banguera-Hinestroza, E and Ferrada, E and Sawall, Y and Flot, JF}, title = {Computational Characterization of the mtORF of Pocilloporid Corals: Insights into Protein Structure and Function in Stylophora Lineages from Contrasting Environments.}, journal = {Genes}, volume = {10}, number = {5}, pages = {}, pmid = {31035578}, issn = {2073-4425}, mesh = {Animals ; Anthozoa/*genetics ; *Computational Biology ; DNA, Mitochondrial/*genetics ; Ecosystem ; Indian Ocean ; Mitochondria/*genetics ; Open Reading Frames/genetics ; Phylogeny ; Phylogeography ; Protein Conformation ; Tandem Repeat Sequences/genetics ; }, abstract = {More than a decade ago, a new mitochondrial Open Reading Frame (mtORF) was discovered in corals of the family Pocilloporidae and has been used since then as an effective barcode for these corals. Recently, mtORF sequencing revealed the existence of two differentiated Stylophora lineages occurring in sympatry along the environmental gradient of the Red Sea (18.5°C to 33.9°C). In the endemic Red Sea lineage RS_LinB, the mtORF and the heat shock protein gene hsp70 uncovered similar phylogeographic patterns strongly correlated with environmental variations. This suggests that the mtORF too might be involved in thermal adaptation. Here, we used computational analyses to explore the features and putative function of this mtORF. In particular, we tested the likelihood that this gene encodes a functional protein and whether it may play a role in adaptation. Analyses of full mitogenomes showed that the mtORF originated in the common ancestor of Madracis and other pocilloporids, and that it encodes a transmembrane protein differing in length and domain architecture among genera. Homology-based annotation and the relative conservation of metal-binding sites revealed traces of an ancient hydrolase catalytic activity. Furthermore, signals of pervasive purifying selection, lack of stop codons in 1830 sequences analyzed, and a codon-usage bias similar to that of other mitochondrial genes indicate that the protein is functional, i.e., not a pseudogene. Other features, such as intrinsically disordered regions, tandem repeats, and signals of positive selection particularly in StylophoraRS_LinB populations, are consistent with a role of the mtORF in adaptive responses to environmental changes.}, } @article {pmid31035218, year = {2019}, author = {Tsao, WY and Hsu, JW and Huang, KL and Bai, YM and Su, TP and Li, CT and Tsai, SJ and Lin, WC and Chen, TJ and Pan, TL and Chen, MH}, title = {Risk of cardiometabolic diseases among siblings of patients with bipolar disorder.}, journal = {Journal of affective disorders}, volume = {253}, number = {}, pages = {171-175}, doi = {10.1016/j.jad.2019.04.094}, pmid = {31035218}, issn = {1573-2517}, mesh = {Adult ; Bipolar Disorder/*genetics ; Databases, Factual ; Diabetes Mellitus, Type 2/*epidemiology/genetics ; Dyslipidemias/*epidemiology/genetics ; Female ; Genetic Predisposition to Disease/*epidemiology ; Humans ; Male ; Middle Aged ; Odds Ratio ; Pedigree ; Prevalence ; Risk Factors ; Siblings ; Stroke/*epidemiology/genetics ; Taiwan/epidemiology ; }, abstract = {BACKGROUND: Cardiometabolic diseases are suggested to be associated with bipolar disorder. However, the risk of metabolic disorders in unaffected siblings of patients with bipolar disorder remains unclear.

METHODS: From the Taiwan National Health Insurance Research Database, 7,225 unaffected siblings of bipolar probands and 28,900 age-/sex-/income-/residence-matched control individuals were included and followed until the end of 2011. Individuals who developed metabolic disorders during the follow-up period were identified.

RESULTS: The unaffected siblings of bipolar probands had a higher prevalence of dyslipidemia (5.4% vs. 4.5%, p = 0.001), younger age at diagnosis of type 2 diabetes mellitus (34.81 vs. 37.22, p = 0.024), and higher prevalence of any stroke (1.5% vs. 1.1%, p = 0.007) than the controls. Moreover, only male siblings of bipolar probands had an increased risk of dyslipidemia (odds ratio [OR]: 1.28, 95% confidence interval [CI]: 1.10-1.48) and higher rates of any stroke (OR: 1.38, 95% CI: 1.02-1.85) and ischemic stroke (OR: 2.43, 95% CI: 1.60-3.70) during the follow-up compared with the controls.

DISCUSSION: Unaffected siblings of bipolar patients, particularly brothers, had a higher prevalence of dyslipidemia and ischemic stroke compared with the controls. The result suggests the familial association between cardiometabolic diseases and bipolar disorder. Further research may be necessary to identify this shared etiology between the disorders.}, } @article {pmid31034467, year = {2019}, author = {Qanbari, S and Rubin, CJ and Maqbool, K and Weigend, S and Weigend, A and Geibel, J and Kerje, S and Wurmser, C and Peterson, AT and Brisbin, IL and Preisinger, R and Fries, R and Simianer, H and Andersson, L}, title = {Genetics of adaptation in modern chicken.}, journal = {PLoS genetics}, volume = {15}, number = {4}, pages = {e1007989}, pmid = {31034467}, issn = {1553-7404}, mesh = {*Adaptation, Biological ; Alleles ; Animals ; Chickens/*genetics ; Computational Biology/methods ; Gene Frequency ; Genetic Variation ; *Genome ; *Genomics/methods ; Molecular Sequence Annotation ; Polymorphism, Single Nucleotide ; }, abstract = {We carried out whole genome resequencing of 127 chicken including red jungle fowl and multiple populations of commercial broilers and layers to perform a systematic screening of adaptive changes in modern chicken (Gallus gallus domesticus). We uncovered >21 million high quality SNPs of which 34% are newly detected variants. This panel comprises >115,000 predicted amino-acid altering substitutions as well as 1,100 SNPs predicted to be stop-gain or -loss, several of which reach high frequencies. Signatures of selection were investigated both through analyses of fixation and differentiation to reveal selective sweeps that may have had prominent roles during domestication and breed development. Contrasting wild and domestic chicken we confirmed selection at the BCO2 and TSHR loci and identified 34 putative sweeps co-localized with ALX1, KITLG, EPGR, IGF1, DLK1, JPT2, CRAMP1, and GLI3, among others. Analysis of enrichment between groups of wild vs. commercials and broilers vs. layers revealed a further panel of candidate genes including CORIN, SKIV2L2 implicated in pigmentation and LEPR, MEGF10 and SPEF2, suggestive of production-oriented selection. SNPs with marked allele frequency differences between wild and domestic chicken showed a highly significant deficiency in the proportion of amino-acid altering mutations (P<2.5×10-6). The results contribute to the understanding of major genetic changes that took place during the evolution of modern chickens and in poultry breeding.}, } @article {pmid31034053, year = {2019}, author = {Ayres, DL and Cummings, MP and Baele, G and Darling, AE and Lewis, PO and Swofford, DL and Huelsenbeck, JP and Lemey, P and Rambaut, A and Suchard, MA}, title = {BEAGLE 3: Improved Performance, Scaling, and Usability for a High-Performance Computing Library for Statistical Phylogenetics.}, journal = {Systematic biology}, volume = {68}, number = {6}, pages = {1052-1061}, pmid = {31034053}, issn = {1076-836X}, support = {U19 AI135995/AI/NIAID NIH HHS/United States ; R01 AI107034/AI/NIAID NIH HHS/United States ; R01 HG006139/HG/NHGRI NIH HHS/United States ; 206298/Z/17/Z/WT_/Wellcome Trust/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; }, mesh = {Classification/*methods ; Data Interpretation, Statistical ; Phylogeny ; Software/*standards ; }, abstract = {BEAGLE is a high-performance likelihood-calculation library for phylogenetic inference. The BEAGLE library defines a simple, but flexible, application programming interface (API), and includes a collection of efficient implementations for calculation under a variety of evolutionary models on different hardware devices. The library has been integrated into recent versions of popular phylogenetics software packages including BEAST and MrBayes and has been widely used across a diverse range of evolutionary studies. Here, we present BEAGLE 3 with new parallel implementations, increased performance for challenging data sets, improved scalability, and better usability. We have added new OpenCL and central processing unit-threaded implementations to the library, allowing the effective utilization of a wider range of modern hardware. Further, we have extended the API and library to support concurrent computation of independent partial likelihood arrays, for increased performance of nucleotide-model analyses with greater flexibility of data partitioning. For better scalability and usability, we have improved how phylogenetic software packages use BEAGLE in multi-GPU (graphics processing unit) and cluster environments, and introduced an automated method to select the fastest device given the data set, evolutionary model, and hardware. For application developers who wish to integrate the library, we also have developed an online tutorial. To evaluate the effect of the improvements, we ran a variety of benchmarks on state-of-the-art hardware. For a partitioned exemplar analysis, we observe run-time performance improvements as high as 5.9-fold over our previous GPU implementation. BEAGLE 3 is free, open-source software licensed under the Lesser GPL and available at https://beagle-dev.github.io.}, } @article {pmid31031001, year = {2019}, author = {Gregory, AC and Zayed, AA and Conceição-Neto, N and Temperton, B and Bolduc, B and Alberti, A and Ardyna, M and Arkhipova, K and Carmichael, M and Cruaud, C and Dimier, C and Domínguez-Huerta, G and Ferland, J and Kandels, S and Liu, Y and Marec, C and Pesant, S and Picheral, M and Pisarev, S and Poulain, J and Tremblay, JÉ and Vik, D and , and Babin, M and Bowler, C and Culley, AI and de Vargas, C and Dutilh, BE and Iudicone, D and Karp-Boss, L and Roux, S and Sunagawa, S and Wincker, P and Sullivan, MB}, title = {Marine DNA Viral Macro- and Microdiversity from Pole to Pole.}, journal = {Cell}, volume = {177}, number = {5}, pages = {1109-1123.e14}, pmid = {31031001}, issn = {1097-4172}, support = {T32 AI112542/AI/NIAID NIH HHS/United States ; }, mesh = {Aquatic Organisms/*genetics ; *Biodiversity ; DNA Viruses/*genetics ; DNA, Viral/*genetics ; *Metagenome ; *Water Microbiology ; }, abstract = {Microbes drive most ecosystems and are modulated by viruses that impact their lifespan, gene flow, and metabolic outputs. However, ecosystem-level impacts of viral community diversity remain difficult to assess due to classification issues and few reference genomes. Here, we establish an ∼12-fold expanded global ocean DNA virome dataset of 195,728 viral populations, now including the Arctic Ocean, and validate that these populations form discrete genotypic clusters. Meta-community analyses revealed five ecological zones throughout the global ocean, including two distinct Arctic regions. Across the zones, local and global patterns and drivers in viral community diversity were established for both macrodiversity (inter-population diversity) and microdiversity (intra-population genetic variation). These patterns sometimes, but not always, paralleled those from macro-organisms and revealed temperate and tropical surface waters and the Arctic as biodiversity hotspots and mechanistic hypotheses to explain them. Such further understanding of ocean viruses is critical for broader inclusion in ecosystem models.}, } @article {pmid31026273, year = {2019}, author = {Park, DS and Akuffo, AA and Muench, DE and Grimes, HL and Epling-Burnette, PK and Maini, PK and Anderson, ARA and Bonsall, MB}, title = {Clonal hematopoiesis of indeterminate potential and its impact on patient trajectories after stem cell transplantation.}, journal = {PLoS computational biology}, volume = {15}, number = {4}, pages = {e1006913}, pmid = {31026273}, issn = {1553-7358}, support = {R01 HL122661/HL/NHLBI NIH HHS/United States ; U54 CA193489/CA/NCI NIH HHS/United States ; P30 CA076292/CA/NCI NIH HHS/United States ; U01 CA232382/CA/NCI NIH HHS/United States ; I01 CX000114/CX/CSRD VA/United States ; }, mesh = {Animals ; Computational Biology ; Hematopoiesis/*physiology ; *Hematopoietic Stem Cells/cytology/physiology ; Humans ; Mice ; *Models, Biological ; Stem Cell Transplantation/*statistics & numerical data ; }, abstract = {Clonal hematopoiesis of indeterminate potential (CHIP) is a recently identified process where older patients accumulate distinct subclones defined by recurring somatic mutations in hematopoietic stem cells. CHIP's implications for stem cell transplantation have been harder to identify due to the high degree of mutational heterogeneity that is present within the genetically distinct subclones. In order to gain a better understanding of CHIP and the impact of clonal dynamics on transplantation outcomes, we created a mathematical model of clonal competition dynamics. Our analyses highlight the importance of understanding competition intensity between healthy and mutant clones. Importantly, we highlight the risk that CHIP poses in leading to dominance of precancerous mutant clones and the risk of donor derived leukemia. Furthermore, we estimate the degree of competition intensity and bone marrow niche decline in mice during aging by using our modeling framework. Together, our work highlights the importance of better characterizing the ecological and clonal composition in hematopoietic donor populations at the time of stem cell transplantation.}, } @article {pmid31025942, year = {2019}, author = {Rozet, A and Kronish, IM and Schwartz, JE and Davidson, KW}, title = {Using Machine Learning to Derive Just-In-Time and Personalized Predictors of Stress: Observational Study Bridging the Gap Between Nomothetic and Ideographic Approaches.}, journal = {Journal of medical Internet research}, volume = {21}, number = {4}, pages = {e12910}, pmid = {31025942}, issn = {1438-8871}, support = {R01 HL115941/HL/NHLBI NIH HHS/United States ; UL1 TR001873/TR/NCATS NIH HHS/United States ; }, mesh = {Adult ; Data Collection ; Female ; Humans ; Machine Learning/*standards ; Male ; Middle Aged ; Stress, Psychological/*diagnosis ; Young Adult ; }, abstract = {BACKGROUND: Investigations into person-specific predictors of stress have typically taken either a population-level nomothetic approach or an individualized ideographic approach. Nomothetic approaches can quickly identify predictors but can be hindered by the heterogeneity of these predictors across individuals and time. Ideographic approaches may result in more predictive models at the individual level but require a longer period of data collection to identify robust predictors.

OBJECTIVE: Our objectives were to compare predictors of stress identified through nomothetic and ideographic models and to assess whether sequentially combining nomothetic and ideographic models could yield more accurate and actionable predictions of stress than relying on either model. At the same time, we sought to maintain the interpretability necessary to retrieve individual predictors of stress despite using nomothetic models.

METHODS: Data collected in a 1-year observational study of 79 participants performing low levels of exercise were used. Physical activity was continuously and objectively monitored by actigraphy. Perceived stress was recorded by participants via daily ecological momentary assessments on a mobile app. Environmental variables including daylight time, temperature, and precipitation were retrieved from the public archives. Using these environmental, actigraphy, and mobile assessment data, we built machine learning models to predict individual stress ratings using linear, decision tree, and neural network techniques employing nomothetic and ideographic approaches. The accuracy of the approaches for predicting individual stress ratings was compared based on classification errors.

RESULTS: Across the group of patients, an individual's recent history of stress ratings was most heavily weighted in predicting a future stress rating in the nomothetic recurrent neural network model, whereas environmental factors such as temperature and daylight, as well as duration and frequency of bouts of exercise, were more heavily weighted in the ideographic models. The nomothetic recurrent neural network model was the highest performing nomothetic model and yielded 72% accuracy for an 80%/20% train/test split. Using the same 80/20 split, the ideographic models yielded 75% accuracy. However, restricting ideographic models to participants with more than 50 valid days in the training set, with the same 80/20 split, yielded 85% accuracy.

CONCLUSIONS: We conclude that for some applications, nomothetic models may be useful for yielding higher initial performance while still surfacing personalized predictors of stress, before switching to ideographic models upon sufficient data collection.}, } @article {pmid31025880, year = {2019}, author = {Togo, A and Dufour, JC and Lagier, JC and Dubourg, G and Raoult, D and Million, M}, title = {Repertoire of human breast and milk microbiota: a systematic review.}, journal = {Future microbiology}, volume = {14}, number = {}, pages = {623-641}, doi = {10.2217/fmb-2018-0317}, pmid = {31025880}, issn = {1746-0921}, mesh = {Abscess/microbiology ; Archaea/classification/isolation & purification ; Bacteria/classification/isolation & purification ; Breast/*microbiology ; Breast Feeding ; Colostrum/microbiology ; Databases, Factual ; Dysbiosis ; Female ; Humans ; Mastitis/microbiology ; *Microbiota ; Milk, Human/*microbiology ; Symbiosis ; }, abstract = {Breastfeeding is a major determinant of human health. Breast milk is not sterile and ecological large-scale sequencing methods have revealed an unsuspected microbial diversity that plays an important role. However, microbiological analysis at the species level has been neglected while it is a prerequisite before understanding which microbe is associated with symbiosis or dysbiosis, and health or disease. We review the currently known bacterial repertoire from the human breast and milk microbiota using a semiautomated strategy. Total 242 articles from 38 countries, 11,124 women and 15,489 samples were included. Total 820 species were identified mainly composed of Proteobacteria and Firmicutes. We report variations according to the analytical method (culture or molecular method), the anatomical site (breast, colostrum or milk) and the infectious status (healthy control, mastitis, breast abscess, neonatal infection). In addition, we compared it with the other human repertoires. Finally, we discuss its putative origin and role in health and disease.}, } @article {pmid31024153, year = {2019}, author = {Jensen, EL and Clement, R and Kosta, A and Maberly, SC and Gontero, B}, title = {A new widespread subclass of carbonic anhydrase in marine phytoplankton.}, journal = {The ISME journal}, volume = {13}, number = {8}, pages = {2094-2106}, pmid = {31024153}, issn = {1751-7370}, mesh = {Amino Acid Sequence ; Carbon/*metabolism ; Carbon Dioxide/*metabolism ; Carbonic Anhydrases/*genetics/metabolism ; Chloroplasts/enzymology/ultrastructure ; Coenzymes ; Databases, Nucleic Acid ; Diatoms/*enzymology/genetics/ultrastructure ; Geography ; Microscopy, Electron, Transmission ; Oceans and Seas ; Photosynthesis ; Phylogeny ; Phytoplankton/*enzymology/genetics/ultrastructure ; Sequence Alignment ; }, abstract = {Most aquatic photoautotrophs depend on CO2-concentrating mechanisms (CCMs) to maintain productivity at ambient concentrations of CO2, and carbonic anhydrase (CA) plays a key role in these processes. Here we present different lines of evidence showing that the protein LCIP63, identified in the marine diatom Thalassiosira pseudonana, is a CA. However, sequence analysis showed that it has a low identity with any known CA and therefore belongs to a new subclass that we designate as iota-CA. Moreover, LCIP63 unusually prefers Mn[2+] to Zn[2+] as a cofactor, which is potentially of ecological relevance since Mn[2+] is more abundant than Zn[2+] in the ocean. LCIP63 is located in the chloroplast and only expressed at low concentrations of CO2. When overexpressed using biolistic transformation, the rate of photosynthesis at limiting concentrations of dissolved inorganic carbon increased, confirming its role in the CCM. LCIP63 homologs are present in the five other sequenced diatoms and in other algae, bacteria, and archaea. Thus LCIP63 is phylogenetically widespread but overlooked. Analysis of the Tara Oceans database confirmed this and showed that LCIP63 is widely distributed in marine environments and is therefore likely to play an important role in global biogeochemical carbon cycling.}, } @article {pmid31024020, year = {2019}, author = {Milleret, C and Ordiz, A and Sanz-Pérez, A and Uzal, A and Carricondo-Sanchez, D and Eriksen, A and Sand, H and Wabakken, P and Wikenros, C and Åkesson, M and Zimmermann, B}, title = {Testing the influence of habitat experienced during the natal phase on habitat selection later in life in Scandinavian wolves.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {6526}, pmid = {31024020}, issn = {2045-2322}, mesh = {Animals ; Behavior ; *Ecosystem ; Geographic Information Systems ; Geography ; Humans ; Models, Theoretical ; Principal Component Analysis ; Scandinavian and Nordic Countries ; Wolves/*physiology ; }, abstract = {Natal habitat preference induction (NHPI) occurs when characteristics of the natal habitat influence the future habitat selection of an animal. However, the influence of NHPI after the dispersal phase has received remarkably little attention. We tested whether exposure to humans in the natal habitat helps understand why some adult wolves Canis lupus may approach human settlements more than other conspecifics, a question of both ecological and management interest. We quantified habitat selection patterns within home ranges using resource selection functions and GPS data from 21 wolf pairs in Scandinavia. We identified the natal territory of each wolf with genetic parental assignment, and we used human-related characteristics within the natal territory to estimate the degree of anthropogenic influence in the early life of each wolf. When the female of the adult wolf pair was born in an area with a high degree of anthropogenic influence, the wolf pair tended to select areas further away from humans, compared to wolf pairs from natal territories with a low degree of anthropogenic influence. Yet the pattern was statistically weak, we suggest that our methodological approach can be useful in other systems to better understand NHPI and to inform management about human-wildlife interactions.}, } @article {pmid31024009, year = {2019}, author = {Rund, SSC and Braak, K and Cator, L and Copas, K and Emrich, SJ and Giraldo-Calderón, GI and Johansson, MA and Heydari, N and Hobern, D and Kelly, SA and Lawson, D and Lord, C and MacCallum, RM and Roche, DG and Ryan, SJ and Schigel, D and Vandegrift, K and Watts, M and Zaspel, JM and Pawar, S}, title = {MIReAD, a minimum information standard for reporting arthropod abundance data.}, journal = {Scientific data}, volume = {6}, number = {1}, pages = {40}, pmid = {31024009}, issn = {2052-4463}, support = {HHSN272201400029C/AI/NIAID NIH HHS/United States ; R01 AI122284/AI/NIAID NIH HHS/United States ; R01 AI136035/AI/NIAID NIH HHS/United States ; U01 CK000510/CK/NCEZID CDC HHS/United States ; }, mesh = {Animals ; *Arthropods/physiology ; Biodiversity ; Ecosystem ; Information Dissemination ; Information Storage and Retrieval/*standards ; Population Dynamics ; }, abstract = {Arthropods play a dominant role in natural and human-modified terrestrial ecosystem dynamics. Spatially-explicit arthropod population time-series data are crucial for statistical or mathematical models of these dynamics and assessment of their veterinary, medical, agricultural, and ecological impacts. Such data have been collected world-wide for over a century, but remain scattered and largely inaccessible. In particular, with the ever-present and growing threat of arthropod pests and vectors of infectious diseases, there are numerous historical and ongoing surveillance efforts, but the data are not reported in consistent formats and typically lack sufficient metadata to make reuse and re-analysis possible. Here, we present the first-ever minimum information standard for arthropod abundance, Minimum Information for Reusable Arthropod Abundance Data (MIReAD). Developed with broad stakeholder collaboration, it balances sufficiency for reuse with the practicality of preparing the data for submission. It is designed to optimize data (re)usability from the "FAIR," (Findable, Accessible, Interoperable, and Reusable) principles of public data archiving (PDA). This standard will facilitate data unification across research initiatives and communities dedicated to surveillance for detection and control of vector-borne diseases and pests.}, } @article {pmid31022924, year = {2019}, author = {Wang, L and Sun, W and Zhou, K and Zhang, M and Bao, P}, title = {Spatial Analysis of Built Environment Risk for Respiratory Health and Its Implication for Urban Planning: A Case Study of Shanghai.}, journal = {International journal of environmental research and public health}, volume = {16}, number = {8}, pages = {}, pmid = {31022924}, issn = {1660-4601}, mesh = {Aged ; Aged, 80 and over ; *Built Environment ; China/epidemiology ; Cities/epidemiology ; *City Planning ; Female ; Geographic Information Systems ; Humans ; Industry ; Lung Neoplasms/*epidemiology ; Male ; Middle Aged ; }, abstract = {Urban planning has been proven and is expected to promote public health by improving the built environment. With a focus on respiratory health, this paper explores the impact of the built environment on the incidence of lung cancer and its planning implications. While the occurrence of lung cancer is a complicated and cumulative process, it would be valuable to discover the potential risks of the built environment. Based on the data of 52,009 lung cancer cases in Shanghai, China from 2009 to 2013, this paper adopts spatial analytical methods to unravel the spatial distribution of lung cancer cases. With the assistance of geographic information system and Geo-Detector, this paper identifies certain built environments that are correlated with the distribution pattern of lung cancer cases in Shanghai, including the percentage of industrial land (which explains 28% of the cases), location factors (11%), and the percentages of cultivated land and green space (6% and 5%, respectively). Based on the quantitative study, this paper facilitates additional consideration and planning intervention measures for respiratory health such as green buffering. It is an ecological study to illustrate correlation that provides approaches for further study to unravel the causality of disease incidence and the built environment.}, } @article {pmid31022507, year = {2019}, author = {Noleto-Filho, EM and Pennino, MG and Gauy, ACDS and Bolognesi, MC and Gonçalves-de-Freitas, E}, title = {The Bias of combining variables on fish's aggressive behavior studies.}, journal = {Behavioural processes}, volume = {164}, number = {}, pages = {65-77}, doi = {10.1016/j.beproc.2019.04.006}, pmid = {31022507}, issn = {1872-8308}, mesh = {*Aggression ; Animals ; Bayes Theorem ; *Behavior, Animal ; Bias ; Cichlids ; *Data Interpretation, Statistical ; Markov Chains ; Monte Carlo Method ; Probability ; }, abstract = {Quantifying animal aggressive behavior by behavioral units, either displays or attacks, is a common practice in animal behavior studies. However, this practice can generate a bias in data analysis, especially when the variables have different temporal patterns. This study aims to use Bayesian Hierarchical Linear Models (B-HLMs) to analyze the feasibility of pooling the aggressive behavior variables of four cichlids species. Additionally, this paper discusses the feasibility of combining variables by examining the usage of different sample sizes and family distributions to aggressive behaviour variables. The subject species were: the angelfish (Pterophyllum scalare), the tiger oscar (Astronotus ocellatus), the Cichlasoma paranaense and the Nile tilapia (Oreochromis niloticus). For each species, 15 groups of 3 individuals were assigned to daily observations (10-min recordings) for 5 days. Aggressive behavior data was labeled according to its aggressive intensity. The variables chase (C), tail beating (TB), push (P), lateral attack (LA) and bite (B) were classified as high intensity. The variables undulation (U), lateral threat (LT) and frontal displays (FD) were classified as low intensity. These behaviors, however, were not present in all species. Model parameters were estimated by Monte Carlo Markov chains using non-informative priors. B-HLMs were performed to assess the impact probability of each variable in the analysis. Results revealed that when combining variables, the resulting distribution is strongly influenced by only one variable in each category. Moreover, in some cases the aggregate values altered the results, which changed the probabilities of the main variables. Species with low aggressive behavior frequencies, such as A. ocellatus, are more sensitive to this bias. LT was the main low intensity variable for all species, while B was the main high intensity variable for the P. scalare and the O. niloticus. LA was the high intensity category variable that was the most relevant for the C. paranaense and A. ocellatus. Moreover, combining the variables did not impact the feasibility of reducing the sample size when compared to using the most quantitative variable. For all species a sample size of 12 did not change the study conclusions. With respect to family distribution, based on DIC values the Gaussian model is more suitable for most of the studied species. However, caution should be taken, because the Gaussian posterior probability distribution overlapped 0 in some cases, which is biologically impossible in aggressive behaviors. The only exception is the A. ocellatus, which, based on DIC values, was the only species better modeled by a Poisson distribution. Bayesian analysis can be therefore considered a strong tool for analyzing aggressive behavior.}, } @article {pmid31014305, year = {2019}, author = {Terahara, F and Nishiura, H}, title = {Fluoroquinolone consumption and Escherichia coli resistance in Japan: an ecological study.}, journal = {BMC public health}, volume = {19}, number = {1}, pages = {426}, pmid = {31014305}, issn = {1471-2458}, support = {JP18fk0108050//Japan Agency for Medical Research and Development/ ; JPMJCR1413//Core Research for Evolutional Science and Technology/ ; 16KT0130 and 17H04701//Japan Society for the Promotion of Science/ ; NA//Telecommunications Advancement Foundation/ ; }, mesh = {Anti-Bacterial Agents/*supply & distribution ; Cross Infection/drug therapy/epidemiology ; Databases, Pharmaceutical/statistics & numerical data ; *Drug Resistance, Bacterial ; Escherichia coli/*drug effects ; Escherichia coli Infections/drug therapy/*epidemiology ; Fluoroquinolones/*supply & distribution ; Geography ; Humans ; Japan/epidemiology ; Levofloxacin/pharmacology ; Microbial Sensitivity Tests ; }, abstract = {BACKGROUND: The frequency of antimicrobial resistance has steadily increased worldwide, induced by inappropriate use of antibiotics in a variety of settings. We analyzed the ecological correlation between fluoroquinolone consumption and levofloxacin resistance in Escherichia coli in Japan.

METHODS: We collected information on cases of E. coli resistant to levofloxacin in 2015-2016 in all 47 prefectures from the Japan Nosocomial Infections Surveillance system. Information on fluoroquinolone consumption was obtained from pharmaceutical sales data. To address potential confounding, we also collected information on the number of physicians, nurses, and medical facilities per 100,000 individuals.

RESULTS: We identified higher fluoroquinolone consumption and higher resistance in western prefectures, and lower consumption and resistance in eastern prefectures. Multivariate analysis identified a positive correlation between fluoroquinolone consumption and levofloxacin resistance in both 2015 and 2016.

CONCLUSIONS: Fluoroquinolone consumption and levofloxacin-resistant E. coli are potentially associated on a nationwide scale. The relationship between the two must be elucidated using additional studies with different epidemiological designs, so that any possible counter-measures, including alternative prescription, can be considered in the future.}, } @article {pmid31014224, year = {2019}, author = {Kopperud, BT and Lidgard, S and Liow, LH}, title = {Text-mined fossil biodiversity dynamics using machine learning.}, journal = {Proceedings. Biological sciences}, volume = {286}, number = {1901}, pages = {20190022}, pmid = {31014224}, issn = {1471-2954}, mesh = {Animals ; *Biodiversity ; Biological Evolution ; Bryozoa/*physiology ; Data Mining/*statistics & numerical data ; *Fossils ; Machine Learning/*statistics & numerical data ; Paleontology ; }, abstract = {Documented occurrences of fossil taxa are the empirical foundation for understanding large-scale biodiversity changes and evolutionary dynamics in deep time. The fossil record contains vast amounts of understudied taxa. Yet the compilation of huge volumes of data remains a labour-intensive impediment to a more complete understanding of Earth's biodiversity history. Even so, many occurrence records of species and genera in these taxa can be uncovered in the palaeontological literature. Here, we extract observations of fossils and their inferred ages from unstructured text in books and scientific articles using machine-learning approaches. We use Bryozoa, a group of marine invertebrates with a rich fossil record, as a case study. Building on recent advances in computational linguistics, we develop a pipeline to recognize taxonomic names and geologic time intervals in published literature and use supervised learning to machine-read whether the species in question occurred in a given age interval. Intermediate machine error rates appear comparable to human error rates in a simple trial, and resulting genus richness curves capture the main features of published fossil diversity studies of bryozoans. We believe our automated pipeline, that greatly reduced the time required to compile our dataset, can help others compile similar data for other taxa.}, } @article {pmid31010824, year = {2019}, author = {Campbell, MA and Hale, MC and McKinney, GJ and Nichols, KM and Pearse, DE}, title = {Long-Term Conservation of Ohnologs Through Partial Tetrasomy Following Whole-Genome Duplication in Salmonidae.}, journal = {G3 (Bethesda, Md.)}, volume = {9}, number = {6}, pages = {2017-2028}, pmid = {31010824}, issn = {2160-1836}, mesh = {Animals ; Computational Biology/methods ; *Evolution, Molecular ; Female ; *Gene Duplication ; Gene Expression Profiling ; Gene Expression Regulation ; Gene Ontology ; *Genome ; *Genomics/methods ; Inheritance Patterns ; Male ; Salmonidae/*genetics ; *Tetrasomy ; }, abstract = {Whole-genome duplications (WGDs) have occurred repeatedly and broadly throughout the evolutionary history of eukaryotes. However, the effects of WGD on genome function and evolution remain unclear. The salmonid WGD that occurred approximately 88 million years ago presents an excellent opportunity for studying the effects of WGD as ∼10-15% of each salmonid genome still exhibits tetrasomic inheritance. Herein, we utilized the rainbow trout (Oncorhynchus mykiss) genome assembly and brain transcriptome data to examine the fate of gene pairs (ohnologs) following the salmonid whole-genome duplication. We find higher sequence identity between ohnologs located within known tetrasomic regions than between ohnologs found in disomic regions, and that tetrasomically inherited ohnologs showed greater similarity in patterns of gene expression and per ohnolog were lower expressed, than disomically inherited ohnologs. Enrichment testing for Gene Ontology terms identified 49 over-represented terms in tetrasomically inherited ohnologs compared to disomic ohnologs. However, why these ohnologs are retained as tetrasomic is difficult to answer. It could be that we have identified salmonid specific "dangerous duplicates", that is, genes that cannot take on new roles following WGD. Alternatively, there may be adaptive advantages for retaining genes as functional duplicates in tetrasomic regions, as presumably, movement of these genes into disomic regions would affect both their sequence identity and their gene expression patterns.}, } @article {pmid31010316, year = {2021}, author = {Merz, ZC and Van Patten, R and Hurless, N and Grant, A and McGrath, AB}, title = {Furthering the Understanding of Wechsler Adult Intelligence Scale-Fourth Edition Factor Structure in a Clinical Sample.}, journal = {Applied neuropsychology. Adult}, volume = {28}, number = {1}, pages = {12-23}, doi = {10.1080/23279095.2019.1585351}, pmid = {31010316}, issn = {2327-9109}, mesh = {Adolescent ; Adult ; *Behavioral Symptoms/physiopathology ; *Data Interpretation, Statistical ; Factor Analysis, Statistical ; Female ; Humans ; *Intelligence/physiology ; Male ; *Mental Disorders/physiopathology ; Middle Aged ; Psychometrics/*standards ; Reproducibility of Results ; Wechsler Scales/*standards ; Young Adult ; }, abstract = {The Wechsler Adult Intelligence Scale, Fourth Edition (WAIS-IV) is a commonly administered battery for assessing intellectual and cognitive abilities. Despite its popularity, construct validation studies primarily utilize the WAIS-IV normative sample rather than ecologically-valid clinical samples. The current study expands the literature on the validity of WAIS-IV by testing a bifactor model in such a sample. We examined archival data from 300 concurrent psychological evaluations performed at a university-based community clinic. Participants received the full WAIS-IV standard battery. Consistent with recent literature, confirmatory factor analyses (CFAs) favored a direct hierarchical model, where the g factor has a direct influence on WAIS-IV subtest performance and index scores explain only modest degrees of residual variance. Results challenge traditional intelligence nosologies and suggest consideration of a two-step method of WAIS-IV interpretation in clinical samples, whereby the Full Scale IQ score (FSIQ) score is examined first and individual subtest scores are analyzed second.}, } @article {pmid31009481, year = {2019}, author = {Wangara, F and Kipruto, H and Ngesa, O and Kayima, J and Masini, E and Sitienei, J and Ngari, F}, title = {The spatial epidemiology of leprosy in Kenya: A retrospective study.}, journal = {PLoS neglected tropical diseases}, volume = {13}, number = {4}, pages = {e0007329}, pmid = {31009481}, issn = {1935-2735}, support = {001/WHO_/World Health Organization/International ; }, mesh = {Adolescent ; Adult ; Age Distribution ; Aged ; Aged, 80 and over ; Chi-Square Distribution ; Child ; Child, Preschool ; Databases, Factual ; Disease Notification/*statistics & numerical data ; Female ; Humans ; Incidence ; Infant ; Infant, Newborn ; Kenya/epidemiology ; Leprosy/diagnosis/*epidemiology/prevention & control ; Male ; Middle Aged ; Poisson Distribution ; Population Surveillance ; Prevalence ; Retrospective Studies ; Sex Distribution ; *Spatial Analysis ; Young Adult ; }, abstract = {BACKGROUND: Leprosy elimination defined as a registered prevalence rate of less than 1 case per 10,000 persons was achieved in Kenya at the national level in 1989. However, there are still pockets of leprosy in some counties where late diagnosis and consequent physical disability persist. The epidemiology of leprosy in Kenya for the period 2012 through to 2015 was defined using spatial methods.

METHODS: This was a retrospective ecological correlational study that utilized leprosy case based data extracted from the National Leprosy Control Program database. Geographic information system and demographic data were obtained from Kenya National Bureau of Statistics (KNBS). Chi square tests were carried out to check for association between sociodemographic factors and disease indicators. Two Spatial Poisson Conditional Autoregressive (CAR) models were fitted in WinBUGS 1.4 software. The first model included all leprosy cases (new, retreatment, transfers from another health facility) and the second one included only new leprosy cases. These models were used to estimate leprosy relative risks per county as compared to the whole country i.e. the risk of presenting with leprosy given the geographical location.

PRINCIPAL FINDINGS: Children aged less than 15 years accounted for 7.5% of all leprosy cases indicating active leprosy transmission in Kenya. The risk of leprosy notification increased by about 5% for every 1 year increase in age, whereas a 1% increase in the proportion of MB cases increased the chances of new leprosy case notification by 4%. When compared to the whole country, counties with the highest risk of leprosy include Kwale (relative risk of 15), Kilifi (RR;8.9) and Homabay (RR;4.1), whereas Turkana had the lowest relative risk of 0.005.

CONCLUSION: Leprosy incidence exhibits geographical variation and there is need to institute tailored local control measures in these areas to reduce the burden of disability.}, } @article {pmid31007605, year = {2019}, author = {Thomas, HJD and Myers-Smith, IH and Bjorkman, AD and Elmendorf, SC and Blok, D and Cornelissen, JHC and Forbes, BC and Hollister, RD and Normand, S and Prevéy, JS and Rixen, C and Schaepman-Strub, G and Wilmking, M and Wipf, S and Cornwell, WK and Kattge, J and Goetz, SJ and Guay, KC and Alatalo, JM and Anadon-Rosell, A and Angers-Blondin, S and Berner, LT and Björk, RG and Buchwal, A and Buras, A and Carbognani, M and Christie, K and Siegwart Collier, L and Cooper, EJ and Eskelinen, A and Frei, ER and Grau, O and Grogan, P and Hallinger, M and Heijmans, MMPD and Hermanutz, L and Hudson, JMG and Hülber, K and Iturrate-Garcia, M and Iversen, CM and Jaroszynska, F and Johnstone, JF and Kaarlejärvi, E and Kulonen, A and Lamarque, LJ and Lévesque, E and Little, CJ and Michelsen, A and Milbau, A and Nabe-Nielsen, J and Nielsen, SS and Ninot, JM and Oberbauer, SF and Olofsson, J and Onipchenko, VG and Petraglia, A and Rumpf, SB and Semenchuk, PR and Soudzilovskaia, NA and Spasojevic, MJ and Speed, JDM and Tape, KD and Te Beest, M and Tomaselli, M and Trant, A and Treier, UA and Venn, S and Vowles, T and Weijers, S and Zamin, T and Atkin, OK and Bahn, M and Blonder, B and Campetella, G and Cerabolini, BEL and Chapin Iii, FS and Dainese, M and de Vries, FT and Díaz, S and Green, W and Jackson, RB and Manning, P and Niinemets, Ü and Ozinga, WA and Peñuelas, J and Reich, PB and Schamp, B and Sheremetev, S and van Bodegom, PM}, title = {Traditional plant functional groups explain variation in economic but not size-related traits across the tundra biome.}, journal = {Global ecology and biogeography : a journal of macroecology}, volume = {28}, number = {2}, pages = {78-95}, pmid = {31007605}, issn = {1466-822X}, abstract = {AIM: Plant functional groups are widely used in community ecology and earth system modelling to describe trait variation within and across plant communities. However, this approach rests on the assumption that functional groups explain a large proportion of trait variation among species. We test whether four commonly used plant functional groups represent variation in six ecologically important plant traits.

LOCATION: Tundra biome.

TIME PERIOD: Data collected between 1964 and 2016.

MAJOR TAXA STUDIED: 295 tundra vascular plant species.

METHODS: We compiled a database of six plant traits (plant height, leaf area, specific leaf area, leaf dry matter content, leaf nitrogen, seed mass) for tundra species. We examined the variation in species-level trait expression explained by four traditional functional groups (evergreen shrubs, deciduous shrubs, graminoids, forbs), and whether variation explained was dependent upon the traits included in analysis. We further compared the explanatory power and species composition of functional groups to alternative classifications generated using post hoc clustering of species-level traits.

RESULTS: Traditional functional groups explained significant differences in trait expression, particularly amongst traits associated with resource economics, which were consistent across sites and at the biome scale. However, functional groups explained 19% of overall trait variation and poorly represented differences in traits associated with plant size. Post hoc classification of species did not correspond well with traditional functional groups, and explained twice as much variation in species-level trait expression.

MAIN CONCLUSIONS: Traditional functional groups only coarsely represent variation in well-measured traits within tundra plant communities, and better explain resource economic traits than size-related traits. We recommend caution when using functional group approaches to predict tundra vegetation change, or ecosystem functions relating to plant size, such as albedo or carbon storage. We argue that alternative classifications or direct use of specific plant traits could provide new insights for ecological prediction and modelling.}, } @article {pmid31002665, year = {2019}, author = {Canino-Koning, R and Wiser, MJ and Ofria, C}, title = {Fluctuating environments select for short-term phenotypic variation leading to long-term exploration.}, journal = {PLoS computational biology}, volume = {15}, number = {4}, pages = {e1006445}, pmid = {31002665}, issn = {1553-7358}, mesh = {*Biological Variation, Population ; Computational Biology ; Computer Simulation ; Environment ; Evolution, Molecular ; *Gene-Environment Interaction ; Genetic Fitness ; Genetics, Population ; *Models, Genetic ; Mutation ; Phylogeny ; Software ; }, abstract = {Genetic spaces are often described in terms of fitness landscapes or genotype-to-phenotype maps, where each genetic sequence is associated with phenotypic properties and linked to other genotypes that are a single mutational step away. The positions close to a genotype make up its "mutational landscape" and, in aggregate, determine the short-term evolutionary potential of a population. Populations with wider ranges of phenotypes in their mutational neighborhood are known to be more evolvable. Likewise, those with fewer phenotypic changes available in their local neighborhoods are more mutationally robust. Here, we examine whether forces that change the distribution of phenotypes available by mutation profoundly alter subsequent evolutionary dynamics. We compare evolved populations of digital organisms that were subject to either static or cyclically-changing environments. For each of these, we examine diversity of the phenotypes that are produced through mutations in order to characterize the local genotype-phenotype map. We demonstrate that environmental change can push populations toward more evolvable mutational landscapes where many alternate phenotypes are available, though purely deleterious mutations remain suppressed. Further, we show that populations in environments with harsh changes switch phenotypes more readily than those in environments with more benign changes. We trace this effect to repeated population bottlenecks in the harsh environments, which result in shorter coalescence times and keep populations in regions of the mutational landscape where the phenotypic shifts in question are more likely to occur. Typically, static environments select solely for immediate optimization, at the expensive of long-term evolvability. In contrast, we show that with changing environments, short-term pressures to deal with immediate challenges can align with long-term pressures to explore a more productive portion of the mutational landscape.}, } @article {pmid31002569, year = {2019}, author = {Memarzadeh, M and Boettiger, C}, title = {Resolving the Measurement Uncertainty Paradox in Ecological Management.}, journal = {The American naturalist}, volume = {193}, number = {5}, pages = {645-660}, doi = {10.1086/702704}, pmid = {31002569}, issn = {1537-5323}, mesh = {*Conservation of Natural Resources ; *Decision Support Techniques ; Ecology/*methods ; *Fisheries ; *Uncertainty ; }, abstract = {Ecological management and decision-making typically focus on uncertainty about the future, but surprisingly little is known about how to account for uncertainty of the present: that is, the realities of having only partial or imperfect measurements. Our primary paradigms for handling decisions under uncertainty-the precautionary principle and optimal control-have so far given contradictory results. This paradox is best illustrated in the example of fisheries management, where many ideas that guide thinking about ecological decision-making were first developed. We find that simplistic optimal control approaches have repeatedly concluded that a manager should increase catch quotas when faced with greater uncertainty about the fish biomass. Current best practices take a more precautionary approach, decreasing catch quotas by a fixed amount to account for uncertainty. Using comparisons to both simulated and historical catch data, we find that neither approach is sufficient to avoid stock collapses under moderate observational uncertainty. Using partially observed Markov decision process (POMDP) methods, we demonstrate how this paradox arises from flaws in the standard theory, which contributes to overexploitation of fisheries and increased probability of economic and ecological collapse. In contrast, we find that POMDP-based management avoids such overexploitation while also generating higher economic value. These results have significant implications for how we handle uncertainty in both fisheries and ecological management more generally.}, } @article {pmid30998739, year = {2019}, author = {Šaffa, G and Kubicka, AM and Hromada, M and Kramer, KL}, title = {Is the timing of menarche correlated with mortality and fertility rates?.}, journal = {PloS one}, volume = {14}, number = {4}, pages = {e0215462}, pmid = {30998739}, issn = {1932-6203}, mesh = {Adolescent ; Adult ; Age Factors ; Birth Rate ; Databases, Factual ; Demography ; Female ; *Fertility ; Humans ; Maternal Age ; *Menarche ; *Models, Biological ; *Mortality ; }, abstract = {Timing of menarche has largely been studied in the context of a secular trend. However, since mortality and fertility rates are fundamental demographic factors linked to a population's developmental and reproductive characteristics, we expect that the timing of menarche, a precondition to reproduction, is also associated with these vital rates. We conduct an analysis of 89 countries and 21 demographic, socioeconomic, nutritional, and educational variables selected for their known influence on menarche. Model results predict that a country's fertility and adult female mortality rates are significant predictors of mean age at menarche, while other covariates are not. Specifically, menarche is delayed in countries with high mortality and high fertility, which may be proxies for assessing overall environmental quality. We emphasize that, for a comprehensive understanding of the timing of menarche, it is critical to take into account both individual- and population-level influences.}, } @article {pmid30998676, year = {2019}, author = {Villa Martín, P and Muñoz, MA and Pigolotti, S}, title = {Bet-hedging strategies in expanding populations.}, journal = {PLoS computational biology}, volume = {15}, number = {4}, pages = {e1006529}, pmid = {30998676}, issn = {1553-7358}, mesh = {*Biological Evolution ; Computational Biology/*methods ; Ecology ; *Genetic Fitness ; *Models, Biological ; Models, Statistical ; Population Dynamics ; }, abstract = {In ecology, species can mitigate their extinction risks in uncertain environments by diversifying individual phenotypes. This observation is quantified by the theory of bet-hedging, which provides a reason for the degree of phenotypic diversity observed even in clonal populations. Bet-hedging in well-mixed populations is rather well understood. However, many species underwent range expansions during their evolutionary history, and the importance of phenotypic diversity in such scenarios still needs to be understood. In this paper, we develop a theory of bet-hedging for populations colonizing new, unknown environments that fluctuate either in space or time. In this case, we find that bet-hedging is a more favorable strategy than in well-mixed populations. For slow rates of variation, temporal and spatial fluctuations lead to different outcomes. In spatially fluctuating environments, bet-hedging is favored compared to temporally fluctuating environments. In the limit of frequent environmental variation, no opportunity for bet-hedging exists, regardless of the nature of the environmental fluctuations. For the same model, bet-hedging is never an advantageous strategy in the well-mixed case, supporting the view that range expansions strongly promote diversification. These conclusions are robust against stochasticity induced by finite population sizes. Our findings shed light on the importance of phenotypic heterogeneity in range expansions, paving the way to novel approaches to understand how biodiversity emerges and is maintained.}, } @article {pmid30998040, year = {2019}, author = {Setodji, CM and Martino, SC and Dunbar, MS and Shadel, WG}, title = {An exponential effect persistence model for intensive longitudinal data.}, journal = {Psychological methods}, volume = {24}, number = {5}, pages = {622-636}, pmid = {30998040}, issn = {1939-1463}, support = {R01 CA175209/CA/NCI NIH HHS/United States ; R21 CA137286/CA/NCI NIH HHS/United States ; }, mesh = {Adolescent ; Adult ; Advertising/statistics & numerical data ; Behavioral Sciences/*methods ; *Data Interpretation, Statistical ; Ecological Momentary Assessment ; Humans ; *Longitudinal Studies ; *Models, Statistical ; Smoking/epidemiology ; Young Adult ; }, abstract = {We develop an effect persistence model for intensive longitudinal data under a general assumption of an exponential loss of association between exposure and outcome over time. The working model proposed may be useful for understanding the complexity of phenomena for which subjects can be repeatedly exposed to an intervention or a naturally occurring event, while, the effect of any one exposure is expected to diminish over time. Under the main assumption, we specify a semilinear model with extensions to generalized linear models. These methods are motivated by, and applied to, data from a study of adolescent exposure to prosmoking advertisement in which the impact of prosmoking media exposure on young adults' susceptibility to smoking is assessed along with the decay of the effect over time. We investigate the performance of the proposed method when the model assumptions are correctly specified or not. (PsycINFO Database Record (c) 2019 APA, all rights reserved).}, } @article {pmid30997489, year = {2019}, author = {Axtner, J and Crampton-Platt, A and Hörig, LA and Mohamed, A and Xu, CCY and Yu, DW and Wilting, A}, title = {An efficient and robust laboratory workflow and tetrapod database for larger scale environmental DNA studies.}, journal = {GigaScience}, volume = {8}, number = {4}, pages = {}, pmid = {30997489}, issn = {2047-217X}, mesh = {Computational Biology/methods ; *DNA Barcoding, Taxonomic/methods ; *Databases, Nucleic Acid ; Laboratories ; *Metagenome ; Metagenomics/*methods ; Quality Control ; Workflow ; }, abstract = {BACKGROUND: The use of environmental DNA for species detection via metabarcoding is growing rapidly. We present a co-designed lab workflow and bioinformatic pipeline to mitigate the 2 most important risks of environmental DNA use: sample contamination and taxonomic misassignment. These risks arise from the need for polymerase chain reaction (PCR) amplification to detect the trace amounts of DNA combined with the necessity of using short target regions due to DNA degradation.

FINDINGS: Our high-throughput workflow minimizes these risks via a 4-step strategy: (i) technical replication with 2 PCR replicates and 2 extraction replicates; (ii) using multi-markers (12S,16S,CytB); (iii) a "twin-tagging," 2-step PCR protocol; and (iv) use of the probabilistic taxonomic assignment method PROTAX, which can account for incomplete reference databases. Because annotation errors in the reference sequences can result in taxonomic misassignment, we supply a protocol for curating sequence datasets. For some taxonomic groups and some markers, curation resulted in >50% of sequences being deleted from public reference databases, owing to (i) limited overlap between our target amplicon and reference sequences, (ii) mislabelling of reference sequences, and (iii) redundancy. Finally, we provide a bioinformatic pipeline to process amplicons and conduct PROTAX assignment and tested it on an invertebrate-derived DNA dataset from 1,532 leeches from Sabah, Malaysia. Twin-tagging allowed us to detect and exclude sequences with non-matching tags. The smallest DNA fragment (16S) amplified most frequently for all samples but was less powerful for discriminating at species rank. Using a stringent and lax acceptance criterion we found 162 (stringent) and 190 (lax) vertebrate detections of 95 (stringent) and 109 (lax) leech samples.

CONCLUSIONS: Our metabarcoding workflow should help research groups increase the robustness of their results and therefore facilitate wider use of environmental and invertebrate-derived DNA, which is turning into a valuable source of ecological and conservation information on tetrapods.}, } @article {pmid30993333, year = {2019}, author = {Dabos, L and Patiño-Navarrete, R and Nastro, M and Famiglietti, A and Glaser, P and Rodriguez, CH and Naas, T}, title = {SME-4-producing Serratia marcescens from Argentina belonging to clade 2 of the S. marcescens phylogeny.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {74}, number = {7}, pages = {1836-1841}, doi = {10.1093/jac/dkz115}, pmid = {30993333}, issn = {1460-2091}, mesh = {Argentina ; Bacterial Proteins/*analysis ; Carbapenem-Resistant Enterobacteriaceae/*classification/enzymology/*isolation & purification ; Computational Biology ; Genome, Bacterial ; Genomic Islands ; *Genotype ; Humans ; Male ; Microbial Sensitivity Tests ; Middle Aged ; Phylogeny ; Serratia Infections/*microbiology ; Serratia marcescens/*classification/enzymology/*isolation & purification ; Whole Genome Sequencing ; beta-Lactamases/*analysis ; }, abstract = {BACKGROUND: SME carbapenemases are increasingly reported, especially from North and South America. Here, we describe an SME-4-producing Serratia marcescens (SME-Sm) clinical isolate from Argentina and compare its genome with other SME-Sm and Sm isolates recovered from public databases.

METHODS: Sm isolates were characterized by WGS using Illumina technology, susceptibility testing and MIC determination. Carbapenemase activity was revealed by biochemical tests based on imipenem hydrolysis. A whole-genome phylogeny was estimated for all the Sm isolates retrieved from public databases with kSNP3 and a whole-genome phylogenetic analysis based on non-recombinant core SNPs was inferred for Sm complete genomes and for those encoding any blaSME variants.

RESULTS: Sm163 was resistant to amoxicillin, temocillin, aztreonam and carbapenems, remaining susceptible to extended-spectrum cephalosporins. WGS analysis of Sm163 revealed a genome of 5139329 bp and a chromosomally encoded blaSME-4 carbapenemase gene located on a genomic island closely related to SmarGI1-1 of Sm N11-02820. Comparison of the Sm genomes revealed that the 14 SME-Sm isolates possess this genomic island inserted at the same loci, that 13/14 belong to clade 1 and that 11/14 form a well-defined subcluster of cluster I of Sm clade 1, while Sm163 belongs to clade 2, suggesting that an SME-encoding genomic island may have been transferred between isolates from different clades.

CONCLUSIONS: To the best of our knowledge this is the first report of an SME-4-encoding Sm from Argentina. The blaSME-4 gene is located on a SmarGI1-1-like genomic island. The genome of Sm163 belongs to clade 2, unlike all the other SME-Sm isolates, which belong to clade 1.}, } @article {pmid30989204, year = {2019}, author = {Gelaw, YA and Williams, G and Assefa, Y and Asressie, M and Soares Magalhães, RJ}, title = {Sociodemographic profiling of tuberculosis hotspots in Ethiopia, 2014-2017.}, journal = {Transactions of the Royal Society of Tropical Medicine and Hygiene}, volume = {113}, number = {7}, pages = {379-391}, doi = {10.1093/trstmh/trz017}, pmid = {30989204}, issn = {1878-3503}, mesh = {Adolescent ; Child ; Child, Preschool ; *Cluster Analysis ; Demography ; Ethiopia/epidemiology ; Female ; Geographic Information Systems ; Humans ; Male ; Tuberculosis/*epidemiology ; }, abstract = {BACKGROUND: Tuberculosis (TB) notification rates vary across regions in Ethiopia and districts within the Amhara Region. The Amhara Region is one of the main TB hotspot regions in the country. In this study we identified the spatial distribution of TB and characterized the sociodemographic factors of spatial clusters in the Amhara Region.

METHODS: An ecological spatial analysis of TB notifications from 2014 to 2017 was conducted to quantify the presence and location of spatial clusters of TB notifications at the district level within the Amhara Region. Global Moran's I statistics and local indicators of spatial association were used to explore the spatial clustering of TB notifications. Notifications from hotspots and low-risk districts were compared to identify significant sociodemographic factors using analysis of variance and Classification and Regression Tree analysis. The geographic information system and 'sp' packages of R software were used for spatial analysis.

RESULTS: From 2014 to 2017 the average notification rate of all forms of TB in the Amhara Region was 107/100 000 population (range 18-614 per 100 000 population). District-level TB notification rates were positively spatially autocorrelated, with Moran's I value ranging from 0.207 to 0.276 (p=0.01). Hotspot TB clusters were found in the northwest and central part of the region. The proportion of migrants (F(3,124)=23.21, p<0.001, d=1.4) was found to be the most important factor associated with hotspot TB clustering.

CONCLUSIONS: TB notification rates in the Amhara Region of Ethiopia over the past 4 y were significantly clustered. Distinguishing high-risk areas from low-risk areas and characterizing the proportion of migrants and other risk factors is important for targeted TB prevention and control in the region.}, } @article {pmid30986215, year = {2019}, author = {Flagel, LE and Blackman, BK and Fishman, L and Monnahan, PJ and Sweigart, A and Kelly, JK}, title = {GOOGA: A platform to synthesize mapping experiments and identify genomic structural diversity.}, journal = {PLoS computational biology}, volume = {15}, number = {4}, pages = {e1006949}, pmid = {30986215}, issn = {1553-7358}, support = {R01 GM073990/GM/NIGMS NIH HHS/United States ; }, mesh = {Algorithms ; Animals ; Biological Evolution ; Chromosome Mapping/*methods ; Computational Biology/*methods ; Drosophila/genetics ; Genetic Variation/*genetics ; Genetics, Population/methods ; Genome/physiology ; Genomics ; Hybridization, Genetic/genetics ; Markov Chains ; Mimulus/genetics ; Phenotype ; Quantitative Trait Loci/genetics ; }, abstract = {Understanding genomic structural variation such as inversions and translocations is a key challenge in evolutionary genetics. We develop a novel statistical approach to comparative genetic mapping to detect large-scale structural mutations from low-level sequencing data. The procedure, called Genome Order Optimization by Genetic Algorithm (GOOGA), couples a Hidden Markov Model with a Genetic Algorithm to analyze data from genetic mapping populations. We demonstrate the method using both simulated data (calibrated from experiments on Drosophila melanogaster) and real data from five distinct crosses within the flowering plant genus Mimulus. Application of GOOGA to the Mimulus data corrects numerous errors (misplaced sequences) in the M. guttatus reference genome and confirms or detects eight large inversions polymorphic within the species complex. Finally, we show how this method can be applied in genomic scans to improve the accuracy and resolution of Quantitative Trait Locus (QTL) mapping.}, } @article {pmid30986212, year = {2019}, author = {Zhang, Y and Pechal, JL and Schmidt, CJ and Jordan, HR and Wang, WW and Benbow, ME and Sze, SH and Tarone, AM}, title = {Machine learning performance in a microbial molecular autopsy context: A cross-sectional postmortem human population study.}, journal = {PloS one}, volume = {14}, number = {4}, pages = {e0213829}, pmid = {30986212}, issn = {1932-6203}, mesh = {Adolescent ; Adult ; Aged ; Aged, 80 and over ; Autopsy/*methods ; Cross-Sectional Studies ; DNA, Archaeal/isolation & purification ; DNA, Bacterial/isolation & purification ; Datasets as Topic ; Female ; High-Throughput Nucleotide Sequencing ; Humans ; *Machine Learning ; Male ; Microbiota/*physiology ; Middle Aged ; *Postmortem Changes ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA/*methods ; Time Factors ; Young Adult ; }, abstract = {BACKGROUND: The postmortem microbiome can provide valuable information to a death investigation and to the human health of the once living. Microbiome sequencing produces, in general, large multi-dimensional datasets that can be difficult to analyze and interpret. Machine learning methods can be useful in overcoming this analytical challenge. However, different methods employ distinct strategies to handle complex datasets. It is unclear whether one method is more appropriate than others for modeling postmortem microbiomes and their ability to predict attributes of interest in death investigations, which require understanding of how the microbial communities change after death and may represent those of the once living host.

METHODS AND FINDINGS: Postmortem microbiomes were collected by swabbing five anatomical areas during routine death investigation, sequenced and analyzed from 188 death cases. Three machine learning methods (boosted algorithms, random forests, and neural networks) were compared with respect to their abilities to predict case attributes: postmortem interval (PMI), location of death, and manner of death. Accuracy depended on the method used, the numbers of anatomical areas analyzed, and the predicted attribute of death.

CONCLUSIONS: All algorithms performed well but with distinct features to their performance. Xgboost often produced the most accurate predictions but may also be more prone to overfitting. Random forest was the most stable across predictions that included more anatomic areas. Analysis of postmortem microbiota from more than three anatomic areas appears to yield limited returns on accuracy, with the eyes and rectum providing the most useful information correlating with circumstances of death in most cases for this dataset.}, } @article {pmid30980778, year = {2019}, author = {Bay, RA and Taylor, EB and Schluter, D}, title = {Parallel introgression and selection on introduced alleles in a native species.}, journal = {Molecular ecology}, volume = {28}, number = {11}, pages = {2802-2813}, doi = {10.1111/mec.15097}, pmid = {30980778}, issn = {1365-294X}, mesh = {*Alleles ; Animals ; Canada ; Gene Frequency/genetics ; Gene Ontology ; Geography ; *Inbreeding ; Oncorhynchus/genetics ; Polymorphism, Single Nucleotide/genetics ; *Selection, Genetic ; Species Specificity ; United States ; }, abstract = {As humans cause the redistribution of species ranges, hybridization between previously allopatric species is on the rise. Such hybridization can have complex effects on overall fitness of native species as new allelic combinations are tested. Widespread species introductions provide a unique opportunity to study selection on introgressed alleles in independent, replicated populations. We examined selection on alleles that repeatedly introgressed from introduced rainbow trout (Oncorhynchus mykiss) into native westslope cutthroat trout (Oncorhynchus clarkii lewisi) populations in western Canada. We found that the degree of introgression of individual single nucleotide polymorphisms from the invasive species into the native is correlated between independent watersheds. A number of rainbow trout alleles have repeatedly swept to high frequency in native populations, suggesting parallel adaptive advantages. Using simulations, we estimated large selection coefficients up to 0.05 favoring several rainbow trout alleles in the native background. Although previous studies have found reduced hybrid fitness and genome-wide resistance to introgression in westslope cutthroat trout, our results suggest that some introduced genomic regions are strongly favored by selection. Our study demonstrates the utility of replicated introductions as case studies for understanding parallel adaptation and the interactions between selection and introgression across the genome. We suggest that understanding this variation, including consideration of beneficial alleles, can inform management strategies for hybridizing species.}, } @article {pmid30974346, year = {2019}, author = {Gan, Y and Rong, Y and Huang, F and Hu, L and Yu, X and Duan, P and Xiong, S and Liu, H and Peng, J and Yuan, X}, title = {Automatic hierarchy classification in venation networks using directional morphological filtering for hierarchical structure traits extraction.}, journal = {Computational biology and chemistry}, volume = {80}, number = {}, pages = {187-194}, doi = {10.1016/j.compbiolchem.2019.03.012}, pmid = {30974346}, issn = {1476-928X}, mesh = {Algorithms ; Botany/*methods ; Datasets as Topic ; Image Processing, Computer-Assisted/*methods/statistics & numerical data ; Plant Leaves/*anatomy & histology/*classification ; Glycine max/anatomy & histology ; }, abstract = {The extraction of vein traits from venation networks is of great significance to the development of a variety of research fields, such as evolutionary biology. However, traditional studies normally target to the extraction of reticulate structure traits (ReSTs), which is not sufficient enough to distinguish the difference between vein orders. For hierarchical structure traits (HiSTs), only a few tools have made attempts with human assistance, and obviously are not practical for large-scale traits extraction. Thus, there is a necessity to develop the method of automated vein hierarchy classification, raising a new challenge yet to be addressed. We propose a novel vein hierarchy classification method based on directional morphological filtering to automatically classify vein orders. Different from traditional methods, our method classify vein orders from highly dense venation networks for the extraction of traits with ecological significance. To the best of our knowledge, this is the first attempt to automatically classify vein hierarchy. To evaluate the performance of our method, we prepare a soybean transmission image dataset (STID) composed of 1200 soybean leaf images and the vein orders of these leaves are manually coarsely annotated by experts as ground truth. We apply our method to classify vein orders of each leaf in the dataset. Compared with ground truth, the proposed method achieves great performance, while the average deviation on major vein is less than 5 pixels and the average completeness on second-order veins reaches 54.28%.}, } @article {pmid30973936, year = {2019}, author = {Luo, X and Lin, F and Zhu, S and Yu, M and Zhang, Z and Meng, L and Peng, J}, title = {Mine landslide susceptibility assessment using IVM, ANN and SVM models considering the contribution of affecting factors.}, journal = {PloS one}, volume = {14}, number = {4}, pages = {e0215134}, pmid = {30973936}, issn = {1932-6203}, mesh = {Environmental Monitoring/*methods ; Geographic Information Systems/*statistics & numerical data ; Landslides/*prevention & control/*statistics & numerical data ; *Neural Networks, Computer ; Risk Assessment/*methods ; *Support Vector Machine ; }, abstract = {The fragile ecological environment near mines provide advantageous conditions for the development of landslides. Mine landslide susceptibility mapping is of great importance for mine geo-environment control and restoration planning. In this paper, a total of 493 landslides in Shangli County, China were collected through historical landslide inventory. 16 spectral, geomorphic and hydrological predictive factors, mainly derived from Landsat 8 imagery and Global Digital Elevation Model (ASTER GDEM), were prepared initially for landslide susceptibility assessment. Predictive capability of these factors was evaluated by using the value of variance inflation factor and information gain ratio. Three models, namely artificial neural network (ANN), support vector machine (SVM) and information value model (IVM), were applied to assess the mine landslide sensitivity. The receiver operating characteristic curve (ROC) and rank probability score were used to validate and compare the comprehensive predictive capabilities of three models involving uncertainty. Results showed that ANN model achieved higher prediction capability, proving its advantage of solve nonlinear and complex problems. Comparing the estimated landslide susceptibility map with the ground-truth one, the high-prone area tends to be located in the middle area with multiple fault distributions and the steeply sloped hill.}, } @article {pmid30973867, year = {2019}, author = {Stone, L and Simberloff, D and Artzy-Randrup, Y}, title = {Network motifs and their origins.}, journal = {PLoS computational biology}, volume = {15}, number = {4}, pages = {e1006749}, pmid = {30973867}, issn = {1553-7358}, mesh = {Computational Biology ; Ecosystem ; Gene Regulatory Networks ; Humans ; Models, Biological ; Neural Networks, Computer ; Social Networking ; *Systems Biology ; }, abstract = {Modern network science is a new and exciting research field that has transformed the study of complex systems over the last 2 decades. Of particular interest is the identification of small "network motifs" that might be embedded in a larger network and that indicate the presence of evolutionary design principles or have an overly influential role on system-wide dynamics. Motifs are patterns of interconnections, or subgraphs, that appear in an observed network significantly more often than in compatible randomized networks. The concept of network motifs was introduced into Systems Biology by Milo, Alon and colleagues in 2002, quickly revolutionized the field, and it has had a huge impact in wider scientific domains ever since. Here, we argue that the same concept and tools for the detection of motifs were well known in the ecological literature decades into the last century, a fact that is generally not recognized. We review the early history of network motifs, their evolution in the mathematics literature, and their recent rediscoveries.}, } @article {pmid30972949, year = {2019}, author = {Elbers, JP and Rogers, MF and Perelman, PL and Proskuryakova, AA and Serdyukova, NA and Johnson, WE and Horin, P and Corander, J and Murphy, D and Burger, PA}, title = {Improving Illumina assemblies with Hi-C and long reads: An example with the North African dromedary.}, journal = {Molecular ecology resources}, volume = {19}, number = {4}, pages = {1015-1026}, pmid = {30972949}, issn = {1755-0998}, support = {17-00-00146//Russian Foundation for Basic Research/ ; P 29623/FWF_/Austrian Science Fund FWF/Austria ; RPG-2017-287//Leverhulme Trust/ ; P29623-B25//Austrian Science Fund/ ; 16-14-10009//Russian Science Foundation/ ; }, mesh = {Animals ; Camelus/*genetics ; Computational Biology/*methods ; Desert Climate ; *Genome ; Genomics/*methods ; Sequence Analysis, DNA/*methods ; }, abstract = {Researchers have assembled thousands of eukaryotic genomes using Illumina reads, but traditional mate-pair libraries cannot span all repetitive elements, resulting in highly fragmented assemblies. However, both chromosome conformation capture techniques, such as Hi-C and Dovetail Genomics Chicago libraries and long-read sequencing, such as Pacific Biosciences and Oxford Nanopore, help span and resolve repetitive regions and therefore improve genome assemblies. One important livestock species of arid regions that does not have a high-quality contiguous reference genome is the dromedary (Camelus dromedarius). Draft genomes exist but are highly fragmented, and a high-quality reference genome is needed to understand adaptation to desert environments and artificial selection during domestication. Dromedaries are among the last livestock species to have been domesticated, and together with wild and domestic Bactrian camels, they are the only representatives of the Camelini tribe, which highlights their evolutionary significance. Here we describe our efforts to improve the North African dromedary genome. We used Chicago and Hi-C sequencing libraries from Dovetail Genomics to resolve the order of previously assembled contigs, producing almost chromosome-level scaffolds. Remaining gaps were filled with Pacific Biosciences long reads, and then scaffolds were comparatively mapped to chromosomes. Long reads added 99.32 Mbp to the total length of the new assembly. Dovetail Chicago and Hi-C libraries increased the longest scaffold over 12-fold, from 9.71 Mbp to 124.99 Mbp and the scaffold N50 over 50-fold, from 1.48 Mbp to 75.02 Mbp. We demonstrate that Illumina de novo assemblies can be substantially upgraded by combining chromosome conformation capture and long-read sequencing.}, } @article {pmid30970071, year = {2019}, author = {Fernandes, CM and Boing, AC}, title = {Pedestrian mortality in road traffic accidents in Brazil: time trend analysis, 1996-2015.}, journal = {Epidemiologia e servicos de saude : revista do Sistema Unico de Saude do Brasil}, volume = {28}, number = {1}, pages = {e2018079}, doi = {10.5123/S1679-49742019000100021}, pmid = {30970071}, issn = {2237-9622}, mesh = {Accidents, Traffic/*mortality/statistics & numerical data ; Adolescent ; Adult ; Age Distribution ; Brazil/epidemiology ; Child ; Child, Preschool ; Female ; Humans ; Infant ; Infant, Newborn ; Information Systems/statistics & numerical data ; Linear Models ; Male ; Middle Aged ; Pedestrians/*statistics & numerical data ; Sex Distribution ; Time Factors ; Wounds and Injuries/epidemiology/etiology/*mortality ; Young Adult ; }, abstract = {OBJECTIVE: to analyze the mortality coefficient trend for road traffic accidents involving pedestrians in Brazil, by sex, age range and macro-region, between 1996 and 2015.

METHODS: this was an ecological time series study using data from the Ministry of Health's Mortality Information System (SIM); Prais-Winstein generalized linear regression was used to calculate annual percentage change.

RESULTS: pedestrian deaths corresponded to 26.5% of deaths due to road traffic accidents; mortality among pedestrians decreased 63.2% in the country as a whole, with the standardized coefficient varying between 8.9 to 3.3 per 100,000 inhabitants, although the decrease in the country's North and the Northeast regions was slower than the national average; being run over was significantly higher among men and the elderly.

CONCLUSION: although mortality among pedestrians is decreasing in all regions of the country, current figures still account for a large part of road traffic mortality.}, } @article {pmid30968297, year = {2019}, author = {Obeidavi, Z and Rangzan, K and Kabolizade, M and Mirzaei, R}, title = {A web-based GIS system for wildlife species: a case study from Khouzestan Province, Iran.}, journal = {Environmental science and pollution research international}, volume = {26}, number = {16}, pages = {16026-16039}, pmid = {30968297}, issn = {1614-7499}, mesh = {Algorithms ; Amphibians ; Animals ; *Animals, Wild ; Biodiversity ; Birds ; Environmental Monitoring/*methods ; *Geographic Information Systems ; *Internet ; Iran ; Mammals ; Reptiles ; User-Computer Interface ; }, abstract = {Recent efforts to aggregate, process, and use biodiversity information have appended novel opportunities and challenges for the field, and a rapid increase in studies that integrate and analyze data in the biological-ecological realm. We developed a web-based GIS system for the wildlife of Khouzestan Province that provides potential distribution maps and other spatial and nonspatial data on the wildlife of Khouzestan Province and its protected areas. We used MaxEnt and a fuzzy inference system to model distributions of species. Our application was structured using a client/server architecture, and the database design and construction was carried out using PostgreSQL/PostGIS, and GeoServer to serve maps. The mapping interface was developed using OpenLayers; ASP.NET was selected for designing the user interface. We used qualitative-quantitative methods to develop, design, refine, and finalize our system particularly as regards usability. The design approach resulted in a user-friendly interface that allows both specialists and non-specialists to quickly and efficiently run models to estimate potential distributions of species. Our application highlights what can be accomplished with a biodiversity-oriented web application.}, } @article {pmid30967543, year = {2019}, author = {Utazi, CE and Thorley, J and Alegana, VA and Ferrari, MJ and Takahashi, S and Metcalf, CJE and Lessler, J and Cutts, FT and Tatem, AJ}, title = {Mapping vaccination coverage to explore the effects of delivery mechanisms and inform vaccination strategies.}, journal = {Nature communications}, volume = {10}, number = {1}, pages = {1633}, pmid = {30967543}, issn = {2041-1723}, support = {/WT_/Wellcome Trust/United Kingdom ; 211208/Z/18/Z/WT_/Wellcome Trust/United Kingdom ; P2C HD047879/HD/NICHD NIH HHS/United States ; U19 AI089674/AI/NIAID NIH HHS/United States ; }, mesh = {Cambodia ; Child, Preschool ; Datasets as Topic ; Democratic Republic of the Congo ; Demography/*statistics & numerical data ; Diphtheria-Tetanus-Pertussis Vaccine/administration & dosage ; Ethiopia ; Global Health/*statistics & numerical data ; Humans ; Income ; Infant ; Infant, Newborn ; Mass Vaccination/methods/organization & administration/*statistics & numerical data ; Measles Vaccine/administration & dosage ; Models, Statistical ; Mozambique ; Multivariate Analysis ; Nigeria ; Strategic Planning ; Vaccination Coverage/*statistics & numerical data ; }, abstract = {The success of vaccination programs depends largely on the mechanisms used in vaccine delivery. National immunization programs offer childhood vaccines through fixed and outreach services within the health system and often, additional supplementary immunization activities (SIAs) are undertaken to fill gaps and boost coverage. Here, we map predicted coverage at 1 × 1 km spatial resolution in five low- and middle-income countries to identify areas that are under-vaccinated via each delivery method using Demographic and Health Surveys data. We compare estimates of the coverage of the third dose of diphtheria-tetanus-pertussis-containing vaccine (DTP3), which is typically delivered through routine immunization (RI), with those of measles-containing vaccine (MCV) for which SIAs are also undertaken. We find that SIAs have boosted MCV coverage in some places, but not in others, particularly where RI had been deficient, as depicted by DTP coverage. The modelling approaches outlined here can help to guide geographical prioritization and strategy design.}, } @article {pmid30967539, year = {2019}, author = {McCluney, JK and Anderson, CM and Anderson, JL}, title = {The fishery performance indicators for global tuna fisheries.}, journal = {Nature communications}, volume = {10}, number = {1}, pages = {1641}, pmid = {30967539}, issn = {2041-1723}, mesh = {Animals ; Conservation of Natural Resources/economics/statistics & numerical data ; Databases, Factual/statistics & numerical data ; Fisheries/economics/*organization & administration/statistics & numerical data ; Seafood/economics/*statistics & numerical data ; Total Quality Management/economics/*statistics & numerical data ; *Tuna ; }, abstract = {We characterize the ecological, economic, and community performance of 21 major tuna fisheries, accounting for at least 77% of global tuna production, using the Fishery Performance Indicators. Our analysis reveals that the biggest variations in performance among tuna fisheries are driven by the final markets that they target: international sashimi market tuna fisheries considerably outperform a comparison set of 62 non-tuna fisheries in the Fishery Performance Indicator database, international canned tuna market fisheries perform similarly to the comparison set, and tuna fisheries supplying local markets in coastal states considerably underperform the comparison set. Differences among regional fishery management organizations primarily reflect regional species composition and market access, despite stark variation in governance, management, and other enabling conditions. With a legacy of open access, tuna's harvest sector performance is similar across all fisheries, reflecting only a normal return on the capital and skill invested: industrial vessels slightly outperform semi-industrial and artisanal vessels. Differences emerge in the post-harvest sector however, as value chains able to preserve quality and transport fish to high value markets outperform others.}, } @article {pmid30967122, year = {2019}, author = {Ai, D and Li, X and Pan, H and Chen, J and Cram, JA and Xia, LC}, title = {Explore mediated co-varying dynamics in microbial community using integrated local similarity and liquid association analysis.}, journal = {BMC genomics}, volume = {20}, number = {Suppl 2}, pages = {185}, pmid = {30967122}, issn = {1471-2164}, support = {R01 HG006137/HG/NHGRI NIH HHS/United States ; }, mesh = {*Algorithms ; Bacteria/*classification/genetics ; Biodiversity ; Computational Biology/*methods ; *Metagenome ; *Microbial Interactions ; *Microbiota ; *Software ; }, abstract = {BACKGROUND: Discovering the key microbial species and environmental factors of microbial community and characterizing their relationships with other members are critical to ecosystem studies. The microbial co-occurrence patterns across a variety of environmental settings have been extensively characterized. However, previous studies were limited by their restriction toward pairwise relationships, while there was ample evidence of third-party mediated co-occurrence in microbial communities.

METHODS: We implemented and applied the triplet-based liquid association analysis in combination with the local similarity analysis procedure to microbial ecology data. We developed an intuitive scheme to visualize those complex triplet associations along with pairwise correlations. Using a time series from the marine microbial ecosystem as example, we identified pairs of operational taxonomic units (OTUs) where the strength of their associations appeared to relate to the values of a third "mediator" variable. These "mediator" variables appear to modulate the associations between pairs of bacteria.

RESULTS: Using this analysis, we were able to assess the OTUs' ability to regulate its functional partners in the community, typically not manifested in the pairwise correlation patterns. For example, we identified Flavobacteria as a multifaceted player in the marine microbial ecosystem, and its clades were involved in mediating other OTU pairs. By contrast, SAR11 clades were not active mediators of the community, despite being abundant and highly correlated with other OTUs. Our results suggested that Flavobacteria are more likely to respond to situations where particles and unusual sources of dissolved organic material are prevalent, such as after a plankton bloom. On the other hand, SAR11s are oligotrophic chemoheterotrophs with inflexible metabolisms, and their relationships with other organisms may be less governed by environmental or biological factors.

CONCLUSIONS: By integrating liquid association with local similarity analysis to explore the mediated co-varying dynamics, we presented a novel perspective and a useful toolkit to analyze and interpret time series data from microbial community. Our augmented association network analysis is thus more representative of the true underlying dynamic structure of the microbial community. The analytic software in this study was implemented as new functionalities of the ELSA (Extended local similarity analysis) tool, which is available for free download (http://bitbucket.org/charade/elsa).}, } @article {pmid30966628, year = {2018}, author = {Lin, G and Li, D and Liu, M and Zhang, X and Zheng, Y}, title = {Rheology, Non-Isothermal Crystallization Behavior, Mechanical and Thermal Properties of PMMA-Modified Carbon Fiber-Reinforced Poly(Ethylene Terephthalate) Composites.}, journal = {Polymers}, volume = {10}, number = {6}, pages = {}, pmid = {30966628}, issn = {2073-4360}, support = {41672278//the National Natural Science Foundation of China/ ; JAT160340//the Projects of Fujian Provincial Department of Education/ ; GY-Z160065//the scientific research projects funded start-up funds of Fujian University of Technology/ ; 2017Y4001//the Fujian Provincial Natural Science Foundation Projects/ ; 2017-G-96//the Science and Technology Plan Projects of Fuzhou/ ; }, abstract = {Poly(ethylene terephthalate) (PET) composites containing carbon fiber (CF) or polymethyl methacrylate (PMMA)-grafted carbon fiber (PMMA-g-CF) were prepared by melt compounding. The rheology, non-isothermal crystallization behavior, and mechanical and thermal properties of pure PET, PET/CF and PET/PMMA-g-CF composites were investigated. The results show that the addition of CF or PMMA-g-CF significantly increases the storage modulus (G'), loss modulus (G″), and complex viscosity (η*) of the composites at low frequency. The Cole-Cole plots confirm that the surface modification of CF leads to a better interaction between the CF and PET, and then decreases the heterogeneity of the polymeric systems, which is confirmed by the SEM observation on the tensile fracture surface of the composites. Non-isothermal crystallization analysis shows that the CF or PMMA-g-CF could serve as nucleation agent to accelerate the crystallization rate of the composites, and the effect of PMMA-g-CF is stronger than that of CF. The result is further confirmed by the analysis of the crystallization activation energy for all composites calculated by the Flynn-Wall-Ozawa method. Moreover, the tensile and impact strength and the thermal stability of the composites are improved by CF, while the incorporation of PMMA-g-CF further enhances the tensile and impact strength and thermal stability.}, } @article {pmid30965551, year = {2019}, author = {Soares, S and Terêncio, D and Fernandes, L and Machado, J and Pacheco, FAL}, title = {The Potential of Small Dams for Conjunctive Water Management in Rural Municipalities.}, journal = {International journal of environmental research and public health}, volume = {16}, number = {7}, pages = {}, pmid = {30965551}, issn = {1660-4601}, mesh = {Cities ; Environmental Monitoring ; Forests ; Geographic Information Systems ; Groundwater ; Hydrology/*instrumentation ; Portugal ; Rain ; Rivers ; *Rural Population ; Water ; *Water Supply ; }, abstract = {The drinking water supply to Vila Pouca de Aguiar municipality in North Portugal is based on high quality groundwater, namely on nearly one hundred artesian springs and fifty boreholes. The groundwater resources are plentiful on a municipal level, but evidence some deficits at the sub-municipal (village) level, especially during the dry period (July- August) that coincides with the return of many emigrants for holiday time. The deficits affect mostly the municipal capital (Vila Pouca de Aguiar) and a neighboring village (Pedras Salgadas), which populations nearly double or even triple during that period. The estimated annual deficits approach 55,000 m[3]/yr in those villages. If the anticipated increase in consumption/habitant and decrease in annual rainfall become reality in the next two decades, then the deficits may raise to approximately 90,000 m[3]/yr. To balance the water supply system, this study proposes its transition towards a conjunctive water management based on surface water stored in small dams and groundwater. A hydrologic modeling involving small forested catchments (< 15 km[2]) elected the Cabouço watershed as most suited basin to store stream water, because surface water availability is large (2.4 Mm[3]/yr) and forest cover is dominant (84.8%). Estimated nutrient loads are also compatible with drinking water supply.}, } @article {pmid30963208, year = {2019}, author = {Brink, DP and Ravi, K and Lidén, G and Gorwa-Grauslund, MF}, title = {Mapping the diversity of microbial lignin catabolism: experiences from the eLignin database.}, journal = {Applied microbiology and biotechnology}, volume = {103}, number = {10}, pages = {3979-4002}, pmid = {30963208}, issn = {1432-0614}, support = {RBP14-0052//Stiftelsen f?r?Strategisk Forskning/ ; }, mesh = {*Databases, Factual ; *Databases, Genetic ; Lignin/*metabolism ; Metabolic Networks and Pathways/*genetics ; *Microbial Consortia ; }, abstract = {Lignin is a heterogeneous aromatic biopolymer and a major constituent of lignocellulosic biomass, such as wood and agricultural residues. Despite the high amount of aromatic carbon present, the severe recalcitrance of the lignin macromolecule makes it difficult to convert into value-added products. In nature, lignin and lignin-derived aromatic compounds are catabolized by a consortia of microbes specialized at breaking down the natural lignin and its constituents. In an attempt to bridge the gap between the fundamental knowledge on microbial lignin catabolism, and the recently emerging field of applied biotechnology for lignin biovalorization, we have developed the eLignin Microbial Database (www.elignindatabase.com), an openly available database that indexes data from the lignin bibliome, such as microorganisms, aromatic substrates, and metabolic pathways. In the present contribution, we introduce the eLignin database, use its dataset to map the reported ecological and biochemical diversity of the lignin microbial niches, and discuss the findings.}, } @article {pmid30956159, year = {2019}, author = {Gehlen, M and Nicola, MRC and Costa, ERD and Cabral, VK and de Quadros, ELL and Chaves, CO and Lahm, RA and Nicolella, ADR and Rossetti, MLR and Silva, DR}, title = {Geospatial intelligence and health analitycs: Its application and utility in a city with high tuberculosis incidence in Brazil.}, journal = {Journal of infection and public health}, volume = {12}, number = {5}, pages = {681-689}, doi = {10.1016/j.jiph.2019.03.012}, pmid = {30956159}, issn = {1876-035X}, mesh = {Brazil/epidemiology ; Cities/epidemiology ; Cluster Analysis ; *Epidemiological Monitoring ; Female ; *Geographic Information Systems ; Humans ; Incidence ; Male ; Residence Characteristics ; Risk Factors ; Socioeconomic Factors ; *Spatial Analysis ; Tuberculosis/*epidemiology ; }, abstract = {BACKGROUND: Geospatial Intelligence and Health Analysis have been used to identify tuberculosis (TB) hotspots and to better understand their relationship to social and economic factors. The purpose of this study was to use geospatial intelligence to assess the distribution of TB and its correlations with Human Development Index (HDI) in a city with high TB incidence in Brazil.

METHODS: We conducted an ecological study, using National System of Information on Noticeable Disease (SINAN) to identify TB cases. Geocoding was performed using QGIS 2.0 software and Google Maps API 3.0. We applied geospatial intelligence to detect where in the city clustering of TB cases occurred, and assessed the association of an area's HDI (each one of the components - longevity, education, and income) with TB spatial distribution.

RESULTS: During the study period (2011-2013), there were 737 TB cases. TB cases showed heterogeneity across the 29 neighborhoods. The neighborhoods with HDI-income lower than the mean had higher TB incidence (p = 0.036).

CONCLUSIONS: We found several hotspots of TB across the 29 neighborhoods, and an inverse association between HDI-income and TB incidence. These findings provide useful information and may help to guide TB control programs.}, } @article {pmid30954655, year = {2019}, author = {Desprez, B and Birk, B and Blaauboer, B and Boobis, A and Carmichael, P and Cronin, MTD and Curie, R and Daston, G and Hubesch, B and Jennings, P and Klaric, M and Kroese, D and Mahony, C and Ouédraogo, G and Piersma, A and Richarz, AN and Schwarz, M and van Benthem, J and van de Water, B and Vinken, M}, title = {A mode-of-action ontology model for safety evaluation of chemicals: Outcome of a series of workshops on repeated dose toxicity.}, journal = {Toxicology in vitro : an international journal published in association with BIBRA}, volume = {59}, number = {}, pages = {44-50}, doi = {10.1016/j.tiv.2019.04.005}, pmid = {30954655}, issn = {1879-3177}, mesh = {*Animal Testing Alternatives ; Animals ; *Biological Ontologies ; Consumer Product Safety ; Cosmetics/toxicity ; Hazardous Substances/toxicity ; Humans ; Risk Assessment/*methods ; Toxicity Tests ; }, abstract = {Repeated dose toxicity evaluation aims at assessing the occurrence of adverse effects following chronic or repeated exposure to chemicals. Non-animal approaches have gained importance in the last decades because of ethical considerations as well as due to scientific reasons calling for more human-based strategies. A critical aspect of this challenge is linked to the capacity to cover a comprehensive set of interdependent mechanisms of action, link them to adverse effects and interpret their probability to be triggered in the light of the exposure at the (sub)cellular level. Inherent to its structured nature, an ontology addressing repeated dose toxicity could be a scientific and transparent way to achieve this goal. Additionally, repeated dose toxicity evaluation through the use of a harmonized ontology should be performed in a reproducible and consistent manner, while mimicking as accurately as possible human physiology and adaptivity. In this paper, the outcome of a series of workshops organized by Cosmetics Europe on this topic is reported. As such, this manuscript shows how experts set critical elements and ways of establishing a mode-of-action ontology model as a support to risk assessors aiming to perform animal-free safety evaluation of chemicals based on repeated dose toxicity data.}, } @article {pmid30953568, year = {2019}, author = {Chen, W and Shakir, S and Bigham, M and Richter, A and Fei, Z and Jander, G}, title = {Genome sequence of the corn leaf aphid (Rhopalosiphum maidis Fitch).}, journal = {GigaScience}, volume = {8}, number = {4}, pages = {}, pmid = {30953568}, issn = {2047-217X}, mesh = {Animals ; Aphids/classification/drug effects/*genetics/metabolism ; Computational Biology/methods ; Gene Expression Profiling ; Gene Transfer, Horizontal ; *Genome ; *Genomics/methods ; Inactivation, Metabolic ; Insecticide Resistance ; Molecular Sequence Annotation ; Phylogeny ; Sequence Analysis, DNA ; Transcriptome ; }, abstract = {BACKGROUND: The corn leaf aphid (Rhopalosiphum maidis Fitch) is the most economically damaging aphid pest on maize (Zea mays), one of the world's most important grain crops. In addition to causing direct damage by removing photoassimilates, R. maidis transmits several destructive maize viruses, including maize yellow dwarf virus, barley yellow dwarf virus, sugarcane mosaic virus, and cucumber mosaic virus.

FINDINGS: The genome of a parthenogenetically reproducing R. maidis clone was assembled with a combination of Pacific Biosciences (207-fold coverage) and Illumina (83-fold coverage) sequencing. The 689 assembled contigs, which have an N50 size of 9.0 megabases (Mb) and a low level of heterozygosity, were clustered using Phase Genomics Hi-C interaction maps. Consistent with the commonly observed 2n = 8 karyotype of R. maidis, most of the contigs (473 spanning 321 Mb) were successfully oriented into 4 scaffolds. The genome assembly captured the full length of 95.8% of the core eukaryotic genes, indicating that it is highly complete. Repetitive sequences accounted for 21.2% of the assembly, and a total of 17,629 protein-coding genes were predicted with integrated evidence from ab initio and homology-based gene predictions and transcriptome sequences generated with both Pacific Biosciences and Illumina. An analysis of likely horizontally transferred genes identified 2 from bacteria, 7 from fungi, 2 from protozoa, and 9 from algae. Repeat elements, transposons, and genes encoding likely detoxification enzymes (cytochrome P450s, glutathione S-transferases, carboxylesterases, uridine diphosphate-glucosyltransferases, and ABC transporters) were identified in the genome sequence. Other than Buchnera aphidicola (642,929 base pairs, 602 genes), no endosymbiont bacteria were found in R. maidis.

CONCLUSIONS: A high-quality R. maidis genome was assembled at the chromosome level. This genome sequence will enable further research related to ecological interactions, virus transmission, pesticide resistance, and other aspects of R. maidis biology. It also serves as a valuable resource for comparative investigation of other aphid species.}, } @article {pmid30953526, year = {2019}, author = {Ikeda, E and Hinckson, E and Witten, K and Smith, M}, title = {Assessment of direct and indirect associations between children active school travel and environmental, household and child factors using structural equation modelling.}, journal = {The international journal of behavioral nutrition and physical activity}, volume = {16}, number = {1}, pages = {32}, pmid = {30953526}, issn = {1479-5868}, mesh = {Adolescent ; Child ; Cross-Sectional Studies ; *Family Characteristics ; Geographic Information Systems ; Humans ; Latent Class Analysis ; New Zealand ; Parents ; *Schools ; *Social Environment ; Students ; *Travel ; }, abstract = {BACKGROUND: Active school travel (AST) is influenced by multiple factors including built and social environments, households and individual variables. A holistic theory such as Mitra's Behavioural Model of School Transportation (BMST) is vital to comprehensively understand these complex interrelationships. This study aimed to assess direct and indirect associations between children's AST and environmental, household and child factors based on the BMST using structural equation modelling (SEM).

METHODS: Data were drawn from Neighbourhoods for Active Kids (NfAK), a cross-sectional study of 1102 children aged 8-13 years (school years 5-8) and their parents from nine intermediate and 10 primary schools in Auckland, New Zealand between February 2015 and December 2016. Data were collected using an online participatory mapping survey (softGIS) with children, a computer-assisted telephone interviewing survey (CATI) with parents, and ArcGIS for built environment attributes. Based on the BMST a conceptual model of children's school travel behaviour was specified for SEM analyses ('hypothesised SEM'), and model modification was made to improve the model ('modified SEM'). SEM analyses using Mplus were performed to test the hypothesised/modified SEM and to assess direct and indirect relationships among variables.

RESULTS: The overall fit of the modified SEM was acceptable (N = 542; Root mean square error of approximation = 0.04, Comparative fit index = 0.94, Tucker-Lewis index = 0.92). AST was positively associated with child independent mobility, child-perceived neighbourhood safety, and parent-perceived importance of social interaction and neighbourhood social environment. Distance to school, and parental perceptions of convenience and concerns about traffic safety were negatively associated with AST. Parental fears of stranger danger were indirectly related to AST through those of traffic safety. Distance to school and child independent mobility mediated relationships between AST and child school year and sex.

CONCLUSIONS: Increasing children's AST requires action on multiple fronts including communities that support independent mobility by providing child friendly social and built environments, safety from traffic, and policies that promote local schools and safe vehicle-free zones around school.}, } @article {pmid30951528, year = {2019}, author = {Lau, MSY and Grenfell, BT and Worby, CJ and Gibson, GJ}, title = {Model diagnostics and refinement for phylodynamic models.}, journal = {PLoS computational biology}, volume = {15}, number = {4}, pages = {e1006955}, pmid = {30951528}, issn = {1553-7358}, support = {P2C HD047879/HD/NICHD NIH HHS/United States ; }, mesh = {Animals ; Computational Biology/*methods ; Computer Simulation ; Disease Outbreaks/statistics & numerical data ; Humans ; Models, Statistical ; Molecular Epidemiology/*methods/statistics & numerical data ; Phylogeny ; Viruses/pathogenicity ; }, abstract = {Phylodynamic modelling, which studies the joint dynamics of epidemiological and evolutionary processes, has made significant progress in recent years due to increasingly available genomic data and advances in statistical modelling. These advances have greatly improved our understanding of transmission dynamics of many important pathogens. Nevertheless, there remains a lack of effective, targetted diagnostic tools for systematically detecting model mis-specification. Development of such tools is essential for model criticism, refinement, and calibration. The idea of utilising latent residuals for model assessment has already been exploited in general spatio-temporal epidemiological settings. Specifically, by proposing appropriately designed non-centered, re-parameterizations of a given epidemiological process, one can construct latent residuals with known sampling distributions which can be used to quantify evidence of model mis-specification. In this paper, we extend this idea to formulate a novel model-diagnostic framework for phylodynamic models. Using simulated examples, we show that our framework may effectively detect a particular form of mis-specification in a phylodynamic model, particularly in the event of superspreading. We also exemplify our approach by applying the framework to a dataset describing a local foot-and-mouth (FMD) outbreak in the UK, eliciting strong evidence against the assumption of no within-host-diversity in the outbreak. We further demonstrate that our framework can facilitate model calibration in real-life scenarios, by proposing a within-host-diversity model which appears to offer a better fit to data than one that assumes no within-host-diversity of FMD virus.}, } @article {pmid30949808, year = {2019}, author = {Pan, H and Tian, X and Shao, M and Xie, Y and Huang, H and Hu, J and Ju, J}, title = {Genome mining and metabolic profiling illuminate the chemistry driving diverse biological activities of Bacillus siamensis SCSIO 05746.}, journal = {Applied microbiology and biotechnology}, volume = {103}, number = {10}, pages = {4153-4165}, doi = {10.1007/s00253-019-09759-2}, pmid = {30949808}, issn = {1432-0614}, support = {41576136//National Natural Science Foundation of China/ ; 31872036//National Natural Science Foundation of China/ ; U1501223//National Natural Science Foundation of China/ ; 81425022//National Outstanding Youth Foundation of China/ ; }, mesh = {Bacillus/*chemistry/genetics ; Biological Products/*analysis ; Data Mining ; *Genome, Bacterial ; *Genomics ; Metabolic Networks and Pathways/*genetics ; *Metabolomics ; }, abstract = {Bacillus spp. are important producers of bioactive natural products with potential applications in medicine and agriculture. Bacillus sp. SCSIO 05476 from a deep-sea sediment exhibits broad-spectrum antimicrobial activities and strong cytotoxic activity. Here, an integrative approach combining genome mining and metabolic profiling has been applied to decipher the chemical origins of this strain's varied and significant biological activities. First, genome mining revealed 19 candidate gene clusters encoding the biosynthesis of diverse secondary metabolites. Then, a series of bacillibactins, fengycins, bacillomycins, surfactins, bacillaenes, macrolactins, and related species were found by LC-DAD-MS. Finally, three new linear bacillibactins, linbacillibactins A-C (1-3), along with 11 known secondary metabolites, bacillibactin (4), normal-C13 Val7 surfactin (5), anteiso-C13 Leu7 surfactin (6), iso-C14 Leu7 surfactin (7), normal-C14 Leu7 surfactin (8), anteiso-C14 Leu7 surfactin (9), macrolactin D (10), normal-C14 bacillomycin D (11), iso-C16 bacillomycin D (12), normal-C17 bacillomycin D (13), and iso-C17 bacillomycin D (14), were obtained and elucidated by bioactivity and structure-guided isolation from the fermentation of strain SCSIO 05746. Among them, new compounds 1-3 show significant siderophore activities comparable to that of bacillibactin (4), compounds 13 and 14 exhibit strong cytotoxic activity. At the same time, the strain classification status was confirmed by genomic analyses, and the complete genome sequence of Bacillus siamensis was presented firstly. This study provides a foundation for understanding the mechanisms driving SCSIO 05746's multiple bioactivities and demonstrates a successful way of discovering bioactive metabolites using a combination of genome mining and metabolic profiling methods.}, } @article {pmid30949441, year = {2019}, author = {Buetti-Dinh, A and Galli, V and Bellenberg, S and Ilie, O and Herold, M and Christel, S and Boretska, M and Pivkin, IV and Wilmes, P and Sand, W and Vera, M and Dopson, M}, title = {Deep neural networks outperform human expert's capacity in characterizing bioleaching bacterial biofilm composition.}, journal = {Biotechnology reports (Amsterdam, Netherlands)}, volume = {22}, number = {}, pages = {e00321}, pmid = {30949441}, issn = {2215-017X}, abstract = {BACKGROUND: Deep neural networks have been successfully applied to diverse fields of computer vision. However, they only outperform human capacities in a few cases.

METHODS: The ability of deep neural networks versus human experts to classify microscopy images was tested on biofilm colonization patterns formed on sulfide minerals composed of up to three different bioleaching bacterial species attached to chalcopyrite sample particles.

RESULTS: A low number of microscopy images per category (<600) was sufficient for highly efficient computational analysis of the biofilm's bacterial composition. The use of deep neural networks reached an accuracy of classification of ∼90% compared to ∼50% for human experts.

CONCLUSIONS: Deep neural networks outperform human experts' capacity in characterizing bacterial biofilm composition involved in the degradation of chalcopyrite. This approach provides an alternative to standard, time-consuming biochemical methods.}, } @article {pmid30948549, year = {2019}, author = {Sackton, TB and Grayson, P and Cloutier, A and Hu, Z and Liu, JS and Wheeler, NE and Gardner, PP and Clarke, JA and Baker, AJ and Clamp, M and Edwards, SV}, title = {Convergent regulatory evolution and loss of flight in paleognathous birds.}, journal = {Science (New York, N.Y.)}, volume = {364}, number = {6435}, pages = {74-78}, doi = {10.1126/science.aat7244}, pmid = {30948549}, issn = {1095-9203}, support = {R01 GM122080/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Bayes Theorem ; *Biological Evolution ; Chromatin/metabolism ; Conserved Sequence ; Enhancer Elements, Genetic ; *Epigenesis, Genetic ; Epigenomics ; *Evolution, Molecular ; Exons/genetics ; Extinction, Biological ; *Flight, Animal ; Forelimb/anatomy & histology ; Palaeognathae/*anatomy & histology/*genetics/physiology ; Phenotype ; Phylogeny ; }, abstract = {A core question in evolutionary biology is whether convergent phenotypic evolution is driven by convergent molecular changes in proteins or regulatory regions. We combined phylogenomic, developmental, and epigenomic analysis of 11 new genomes of paleognathous birds, including an extinct moa, to show that convergent evolution of regulatory regions, more so than protein-coding genes, is prevalent among developmental pathways associated with independent losses of flight. A Bayesian analysis of 284,001 conserved noncoding elements, 60,665 of which are corroborated as enhancers by open chromatin states during development, identified 2355 independent accelerations along lineages of flightless paleognaths, with functional consequences for driving gene expression in the developing forelimb. Our results suggest that the genomic landscape associated with morphological convergence in ratites has a substantial shared regulatory component.}, } @article {pmid30945190, year = {2019}, author = {Sablok, G and Sun, K and Sun, H}, title = {NAMS: Noncoding Assessment of long RNAs in Magnoliophyta Species.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1933}, number = {}, pages = {257-264}, doi = {10.1007/978-1-4939-9045-0_15}, pmid = {30945190}, issn = {1940-6029}, mesh = {Computational Biology/*methods ; Gene Expression Regulation, Plant ; High-Throughput Nucleotide Sequencing/*methods ; Magnoliopsida/*genetics ; RNA, Long Noncoding/*genetics ; RNA, Plant/*genetics ; Sequence Analysis, RNA/*methods ; *Software ; Transcriptome ; }, abstract = {Regulation of plant transcriptional machinery has been recently demonstrated to be widely regulated by a class of long noncoding RNAs (lncRNAs) with size larger than 200 nt. The lncRNAs have been demonstrated to play key roles in abiotic stress. Taking into account the rapid pace in the development of the sequencing technologies, accelerated identification of lncRNAs with potential involvement in regulating the gene expression has been witnessed. Although progress has been made to identify the lncRNAs, however, accurate classification of the lncRNAs particularly in the case of plants is still challenging. In this protocol chapter, we present NAMS, which provides large-scale noncoding assessment of the lncRNAs specifically designed for Magnoliophyta species. We describe the approach and the usage of NAMS with potential applications for the lncRNA discovery.}, } @article {pmid30944336, year = {2019}, author = {Figgener, C and Bernardo, J and Plotkin, PT}, title = {MarTurtSI, a global database of stable isotope analyses of marine turtles.}, journal = {Scientific data}, volume = {6}, number = {1}, pages = {16}, pmid = {30944336}, issn = {2052-4463}, mesh = {Animals ; *Databases, Factual ; Feeding Behavior ; Female ; Isotope Labeling ; Male ; Reproduction ; Turtles/*physiology ; }, abstract = {Marine turtles are both flagship species of conservation concern and indicators of ocean health. As highly migratory species, and despite substantial research effort focusing on nesting females and satellite tagging studies, we still know little about the trophic ecology and habitat use of immature stages and males. Consequently, marine turtle biologists began using stable isotope analyses in the last decade to elucidate various aspects of trophic ecology, including habitat use and trophic position. This has resulted in a burgeoning but largely disconnected literature of mostly single-species case studies. Here we comprehensively synthesize this body of work into a unified data repository, the MarTurtSI database. MarTurtSI contains stable isotope data from six of seven marine turtle species ranging from juveniles to adults, in different developmental, feeding, and breeding habitats across multiple ocean basins. MarTurtSI will be curated and updated with the aim of enabling continued comprehensive and global investigations into the trophic ecology of marine turtles especially in the face of climate change and other conservation challenges.}, } @article {pmid30943236, year = {2019}, author = {Broekhuis, F and Madsen, EK and Keiwua, K and Macdonald, DW}, title = {Using GPS collars to investigate the frequency and behavioural outcomes of intraspecific interactions among carnivores: A case study of male cheetahs in the Maasai Mara, Kenya.}, journal = {PloS one}, volume = {14}, number = {4}, pages = {e0213910}, pmid = {30943236}, issn = {1932-6203}, mesh = {Acinonyx/*physiology ; *Animal Communication ; Animals ; Geographic Information Systems ; Homing Behavior/*physiology ; Kenya ; Male ; Remote Sensing Technology/*instrumentation/methods ; *Wearable Electronic Devices ; }, abstract = {Intraspecific interactions between individuals or groups of individuals of the same species are an important component of population dynamics. Interactions can be static, such as spatial overlap, or dynamic based on the interactions of movements, and can be mediated through communication, such as the deployment of scent marks. Interactions and their behavioural outcomes can be difficult to determine, especially for species that live at low densities. With the use of GPS collars we quantify both static and dynamic interactions between male cheetahs (Acinonyx jubatus) and the behavioural outcomes. The 99% home-ranges of males overlapped significantly while there was little overlap of the 50% home-ranges. Despite this overlap, male cheetahs rarely came into close proximity of one another, possibly because presence was communicated through frequent visits to marking posts. The minimum distance between individuals in a dyad ranged from 89m to 196m but the average proximity between individuals ranged from 17,145 ± 6,865m to 26,367 ± 11,288m. Possible interactions took place more frequently at night than by day and occurred mostly in the 50% home-range of one individual of a dyad or where cores of both individuals overlapped. After a possible encounter male cheetahs stayed in close proximity to each other for up to 6 hours, which could be the result of a territory defence strategy or the presence of a receptive female. We believe that one of the encounters between a singleton and a 5-male coalition resulted in the death of the singleton. Our results give new insights into cheetah interactions, which could help our understanding of ecological processes such as disease transmission.}, } @article {pmid30943204, year = {2019}, author = {Hernández-Hernández, R and Kluge, J and Ah-Peng, C and González-Mancebo, JM}, title = {Natural and human-impacted diversity of bryophytes along an elevational gradient on an oceanic island (La Palma, Canarias).}, journal = {PloS one}, volume = {14}, number = {4}, pages = {e0213823}, pmid = {30943204}, issn = {1932-6203}, mesh = {Agriculture ; Altitude ; *Biodiversity ; Bryophyta/*physiology ; Datasets as Topic ; Ecological Parameter Monitoring/*statistics & numerical data ; Forests ; Humans ; Islands ; Plant Dispersal/*physiology ; Spain ; }, abstract = {Bryophytes have been proposed as ideal indicators of ecosystem change, because they are important components of forest integrity, and considerable research indicates that some groups are sensitive to the changes associated with specific human disturbances. Bryophyte richness and abundance have been found to vary predictably along elevational gradients, but the role of human impacts on these distribution patterns remains unclear. The aim of this study is to explore the impact of human disturbance on the elevational patterns of bryophyte diversity, along an elevational gradient. Along the gradient we collected three datasets in the following sites: preserved (P), forest track roadsides (R) and disturbed by agriculture/silviculture practices (D). Two survey plots of 100 m2 were established at every 200 m elevational step for each sites P, R, D, and in each plot bryophytes were sampled in a stratified manner. At each plot we recorded all species on available substrates and estimated their percentage cover. Our results showed that species number did not differ among studied sites, but that species diversity pattern differs among the three gradient types and species life strategy composition along the elevational gradient showed a clear response to the disturbance of mature communities. We conclude that human impact has strongly changed the elevational pattern of diversity, and that these changes vary depending on the ecological and taxonomical group considered.}, } @article {pmid30942334, year = {2019}, author = {Nascimento, FAD and Silva, SAD and Jaime, PC}, title = {Coverage of food intake assessment in the Brazilian Food and Nutrition Surveillance System: 2008 to 2013.}, journal = {Revista brasileira de epidemiologia = Brazilian journal of epidemiology}, volume = {22}, number = {}, pages = {e190028}, doi = {10.1590/1980-549720190028}, pmid = {30942334}, issn = {1980-5497}, mesh = {Adolescent ; Adult ; Brazil/epidemiology ; Child ; Child, Preschool ; Databases as Topic ; Epidemiologic Studies ; Female ; Humans ; Middle Aged ; National Health Programs/*statistics & numerical data ; Nutrition Surveys/*statistics & numerical data ; *Nutritional Status ; Population Surveillance/*methods ; Pregnancy ; Program Evaluation ; Young Adult ; }, abstract = {INTRODUCTION: In Brazil, the Food and Nutrition Surveillance System (Sistema de Vigilância Alimentar e Nutricional - SISVAN) provides continuous data on the nutritional status and food intake of the population user of primary health care to elaborate actions, programs, and policies.

OBJECTIVE: This article describes the percentage of registration in the system, percentage of use, and coverage of food intake monitoring between 2008 and 2013.

METHODS: This is an ecological study that characterizes the registered population according to federation units, macro-regions, and/or life stages. The indicators used were percentage of registration and use and coverage. The analysis used descriptive statistics, a linear regression model, and Spearman's correlation.

RESULTS: In 2010, approximately 100.00% of the cities had at least one individual registered in the system while the percentage of use was 22.4%. National coverage ranged from 0.13 to 0.4% between 2008 and 2013, with a statistically significant increasing trend. The Midwest showed the highest regional coverage. All life stages presented increasing coverage trend, especially children and pregnant women.

CONCLUSION: Despite the continuous data collection, food intake assessment proved to be incipient, and its distribution in the cities was low. Implementation of the National Food and Nutrition Policy can be enhanced by overcoming central issues, such as physical structure and training of professionals, which prevent the progress of system consolidation.}, } @article {pmid30941640, year = {2019}, author = {Wu, JJ and Zhou, YL and Wang, ZW and Li, GH and Jin, FP and Cui, LL and Gao, HT and Li, XP and Zhou, L and Gui, JF}, title = {Comparative Transcriptome Analysis Reveals Differentially Expressed Genes and Signaling Pathways Between Male and Female Red-Tail Catfish (Mystus wyckioides).}, journal = {Marine biotechnology (New York, N.Y.)}, volume = {21}, number = {4}, pages = {463-474}, pmid = {30941640}, issn = {1436-2236}, support = {QYZDY-SSW-SMC025//Key Program of Frontier Sciences of the Chinese Academy of Sciences/ ; Y73Z04-1-301//Yunnan Academician Workstation/ ; NYCYTX-49//Earmarked Fund for Modern Agro-industry Technology Research System/ ; 2016FBZ01//Autonomous Project of the State Key Laboratory of Freshwater Ecology and Biotechnology/ ; }, mesh = {Animals ; Catfishes/*genetics/growth & development/metabolism ; Cyclic AMP/metabolism ; Female ; Fish Proteins/classification/*genetics/metabolism ; Gene Expression Profiling ; *Gene Expression Regulation, Developmental ; Gene Ontology ; Glutamic Acid/metabolism ; Hypothalamus/growth & development/metabolism ; Male ; Molecular Sequence Annotation ; Ovary/growth & development/metabolism ; Pituitary Gland/growth & development/metabolism ; *Sex Characteristics ; Sex Differentiation ; Signal Transduction/*genetics ; Testis/growth & development/metabolism ; *Transcriptome ; }, abstract = {Sexual dimorphism is widespread in fish species. The red-tail catfish (Mystus wyckioides) is a commercially important catfish in the lower reaches of the Lancang River and the Mekong basin, and it shows a growth advantage in males. Here, RNA-seq was for the first time used to explore the gene expression difference between the sexes in the hypothalamus and pituitary of red-tail catfish, respectively. In the hypothalamus, 5732 and 271 unigenes have significantly higher and lower expressions, respectively, in males compared with females. KEGG analysis showed that 212 DEGs were annotated to 216 signaling pathways, and enrichment analysis suggested different levels of cAMP and glutamatergic synapse signaling between male and female hypothalami and some of the DEGs appear involved in gonad development and growth. In the pituitary, we found only 19 differentially expressed unigenes, which were annotated to 32 signaling pathways, most of which play important roles in gonad development.}, } @article {pmid30940820, year = {2019}, author = {Šmíd, J and Tolley, KA}, title = {Calibrating the tree of vipers under the fossilized birth-death model.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {5510}, pmid = {30940820}, issn = {2045-2322}, mesh = {Animals ; Biological Evolution ; Computational Biology/*methods ; Fossils ; *Genetic Markers ; Models, Biological ; Phylogeny ; Sequence Analysis, DNA ; Viperidae/*classification/genetics ; }, abstract = {Scaling evolutionary trees to time is essential for understanding the origins of clades. Recently developed methods allow including the entire fossil record known for the group of interest and eliminated the need for specifying prior distributions for node ages. Here we apply the fossilized birth-death (FBD) approach to reconstruct the diversification timeline of the viperines (subfamily Viperinae). Viperinae are an Old World snake subfamily comprising 102 species from 13 genera. The fossil record of vipers is fairly rich and well assignable to clades due to the unique vertebral and fang morphology. We use an unprecedented sampling of 83 modern species and 13 genetic markers in combination with 197 fossils representing 28 extinct taxa to reconstruct a time-calibrated phylogeny of the Viperinae. Our results suggest a late Eocene-early Oligocene origin with several diversification events following soon after the group's establishment. The age estimates inferred with the FBD model correspond to those from previous studies that were based on node dating but FBD provides notably narrower credible intervals around the node ages. Viperines comprise two African and an Eurasian clade, but the ancestral origin of the subfamily is ambiguous. The most parsimonious scenarios require two transoceanic dispersals over the Tethys Sea during the Oligocene.}, } @article {pmid30940400, year = {2019}, author = {Buck, B and Scherer, E and Brian, R and Wang, R and Wang, W and Campbell, A and Choudhury, T and Hauser, M and Kane, JM and Ben-Zeev, D}, title = {Relationships between smartphone social behavior and relapse in schizophrenia: A preliminary report.}, journal = {Schizophrenia research}, volume = {208}, number = {}, pages = {167-172}, pmid = {30940400}, issn = {1573-2509}, support = {R01 MH103148/MH/NIMH NIH HHS/United States ; }, mesh = {Adult ; Diagnosis, Computer-Assisted ; Female ; Humans ; Male ; Preliminary Data ; Prognosis ; Recurrence ; Schizophrenia/*diagnosis ; *Schizophrenic Psychology ; Secondary Prevention ; *Smartphone ; *Social Behavior ; Telemedicine ; }, abstract = {Social dysfunction is a hallmark of schizophrenia. Social isolation may increase individuals' risk for psychotic symptom exacerbation and relapse. Monitoring and timely detection of shifts in social functioning are hampered by the limitations of traditional clinic-based assessment strategies. Ubiquitous mobile technologies such as smartphones introduce new opportunities to capture objective digital indicators of social behavior. The goal of this study was to evaluate whether smartphone-collected digital measures of social behavior can provide early indication of relapse events among individuals with schizophrenia. Sixty-one individuals with schizophrenia with elevated risk for relapse were given smartphones with the CrossCheck behavioral sensing system for a year of remote monitoring. CrossCheck leveraged the device's microphone, call record, and text messaging log to capture digital socialization data. Relapse events including psychiatric hospitalizations, suicidal ideation, and significant psychiatric symptom exacerbations were recorded by trained assessors. Exploratory mixed effects models examined relationships of social behavior to relapse, finding that reductions in number and duration of outgoing calls, as well as number of text messages were associated with relapses. Number and duration of incoming phone calls and in-person conversations were not. Smartphone enabled social activity may provide an important metric in determining relapse risk in schizophrenia and provide access to sensitive, meaningful and ecologically valid data streams never before available in routine care.}, } @article {pmid30939153, year = {2019}, author = {Hoffmann, EM and Konerding, V and Nautiyal, S and Buerkert, A}, title = {Is the push-pull paradigm useful to explain rural-urban migration? A case study in Uttarakhand, India.}, journal = {PloS one}, volume = {14}, number = {4}, pages = {e0214511}, pmid = {30939153}, issn = {1932-6203}, mesh = {Demography ; Developing Countries ; Economics ; *Emigration and Immigration ; Employment ; Forests ; Geographic Information Systems ; Geography ; Humans ; Income ; India ; Life Style ; Motivation ; *Population Dynamics ; *Rural Population ; Socioeconomic Factors ; Surveys and Questionnaires ; *Transients and Migrants ; *Urban Population ; }, abstract = {The present study explored the motivation of rural-urban migrants who moved from the Himalaya foothills of Uttarakhand to its capital city, Dehradun. A survey of 100 migrant families reported their socio-economic profile before and after migration, personal and general reasons for migration, problems in the village and in the city, and perception of push- and pull factors. A remote sensing-based analysis of land cover and forest changes was conducted for two villages of the migrants' origin, aiming to link the reasons for migration to land cover changes. This was contextualised by reported large scale changes in forest cover. Major reasons for migration mentioned in this study were education, employment opportunities with the associated income, and facilities. These were perceived as both, push and pull factors, whereas environmental factors ranked very low. Declining environment or agriculture were never mentioned spontaneously as personal reason, and only occasionally as a presumed general reason for migration, but were frequently confirmed as a major problem in the village. Thus, although such problems existed, they seemed not a major driver of rural-urban migration. For most of the respondents their migration resulted in a profound change of livelihoods and significantly improved their socio-economic situation. Land and forest cover around the chosen villages fluctuated by up to 15% with a trend to increasing forest cover in recent years. At the district and state scales, forest cover was rather stable. These results question the narrative of deforestation and environmental degradation in the Himalayas as major push-factors for rural-urban migration in Uttarakhand. Even if environmental constraints were felt, it was rather the differences in socio-economic opportunities (education, employment, facilities) that drove people to migrate to the city. Regarding the push-pull paradigm, we conclude that scenarios of external conditions under which people migrate cannot be evaluated without taking the migrants' attitudes and choices into account.}, } @article {pmid30937225, year = {2019}, author = {Lorieul, T and Pearson, KD and Ellwood, ER and Goëau, H and Molino, JF and Sweeney, PW and Yost, JM and Sachs, J and Mata-Montero, E and Nelson, G and Soltis, PS and Bonnet, P and Joly, A}, title = {Toward a large-scale and deep phenological stage annotation of herbarium specimens: Case studies from temperate, tropical, and equatorial floras.}, journal = {Applications in plant sciences}, volume = {7}, number = {3}, pages = {e01233}, pmid = {30937225}, issn = {2168-0450}, abstract = {PREMISE OF THE STUDY: Phenological annotation models computed on large-scale herbarium data sets were developed and tested in this study.

METHODS: Herbarium specimens represent a significant resource with which to study plant phenology. Nevertheless, phenological annotation of herbarium specimens is time-consuming, requires substantial human investment, and is difficult to mobilize at large taxonomic scales. We created and evaluated new methods based on deep learning techniques to automate annotation of phenological stages and tested these methods on four herbarium data sets representing temperate, tropical, and equatorial American floras.

RESULTS: Deep learning allowed correct detection of fertile material with an accuracy of 96.3%. Accuracy was slightly decreased for finer-scale information (84.3% for flower and 80.5% for fruit detection).

DISCUSSION: The method described has the potential to allow fine-grained phenological annotation of herbarium specimens at large ecological scales. Deeper investigation regarding the taxonomic scalability of this approach is needed.}, } @article {pmid30937220, year = {2019}, author = {Richardson, AD and Hufkens, K and Li, X and Ault, TR}, title = {Testing Hopkins' Bioclimatic Law with PhenoCam data.}, journal = {Applications in plant sciences}, volume = {7}, number = {3}, pages = {e01228}, pmid = {30937220}, issn = {2168-0450}, abstract = {PREMISE OF THE STUDY: We investigated the spatial and temporal patterns of vegetation phenology with phenometrics derived from PhenoCam imagery. Specifically, we evaluated the Bioclimatic Law proposed by Hopkins, which relates phenological transitions to latitude, longitude, and elevation.

METHODS: "Green-up" and "green-down" dates-representing the start and end of the annual cycles of vegetation activity-were estimated from measures of canopy greenness calculated from digital repeat photography. We used data from 65 deciduous broadleaf (DB) forest sites, 18 evergreen needleleaf (EN) forest sites, and 21 grassland (GR) sites.

RESULTS: DB green-up dates were well correlated with mean annual temperature and varied along spatial gradients consistent with the Bioclimatic Law. Interannual variation in DB phenology was most strongly associated with temperature anomalies during a relatively narrow window of time. EN phenology was not well correlated with either climatic factors or spatial gradients, but similar to DB phenology, interannual variation was most closely associated with temperature anomalies. For GR sites, mean annual precipitation explained most of the spatial variation in the duration of vegetation activity, whereas both temperature and precipitation anomalies explained interannual variation in phenology.

DISCUSSION: PhenoCam data provide an objective and consistent means by which spatial and temporal patterns in vegetation phenology can be investigated.}, } @article {pmid30937143, year = {2019}, author = {Chiu, CY and Chan, YL and Tsai, MH and Wang, CJ and Chiang, MH and Chiu, CC}, title = {Gut microbial dysbiosis is associated with allergen-specific IgE responses in young children with airway allergies.}, journal = {The World Allergy Organization journal}, volume = {12}, number = {3}, pages = {100021}, pmid = {30937143}, issn = {1939-4551}, abstract = {BACKGROUND: There is increasing evidence linking alterations of the gut microbial composition during early infancy to the development of atopic diseases and asthma. However, few studies have addressed the association of dysbiotic gut microbiota with allergic reactions through evaluation of feces in young children with allergic airway diseases.

METHODS: We sought to evaluate relationships among gut microbiota, total fecal immunoglobulin E (IgE) levels, serum allergic sensitization, and their relevance to childhood allergic rhinitis and asthma. Microbial composition and diversity were analyzed with Illumina-based 16S rRNA gene sequencing of 89 stool samples collected from children with asthma (n = 35) and allergic rhinitis (n = 28), and from healthy controls (n = 26). Data analysis was performed using Quantitative Insights into Microbial Ecology (QIIME) software.

RESULTS: A significantly lower abundance of organisms of the phylum Firmicutes were found in children with asthma and allergic rhinitis than in the healthy controls. Relatively lower Chao1 and Shannon indices were also found in children with allergic airway diseases but without any significant difference. Total fecal IgE levels in early childhood were strongly correlated with serum D. pteronyssinus- and D. farinae-specific IgE but not with food-specific IgE levels. In comparison with healthy controls, the genus Dorea was less abundant and negatively correlated with total fecal IgE levels in children with rhinitis, whereas the genus Clostridium was abundant and positively correlated with fecal IgE levels in children with asthma.

CONCLUSIONS: An interaction between particular subsets of gut microbial dysbiosis and IgE-mediated responses to allergens may contribute to the susceptibility to allergic rhinitis and asthma in early childhood.}, } @article {pmid30935422, year = {2019}, author = {Panfilio, KA and Vargas Jentzsch, IM and Benoit, JB and Erezyilmaz, D and Suzuki, Y and Colella, S and Robertson, HM and Poelchau, MF and Waterhouse, RM and Ioannidis, P and Weirauch, MT and Hughes, DST and Murali, SC and Werren, JH and Jacobs, CGC and Duncan, EJ and Armisén, D and Vreede, BMI and Baa-Puyoulet, P and Berger, CS and Chang, CC and Chao, H and Chen, MM and Chen, YT and Childers, CP and Chipman, AD and Cridge, AG and Crumière, AJJ and Dearden, PK and Didion, EM and Dinh, H and Doddapaneni, HV and Dolan, A and Dugan, S and Extavour, CG and Febvay, G and Friedrich, M and Ginzburg, N and Han, Y and Heger, P and Holmes, CJ and Horn, T and Hsiao, YM and Jennings, EC and Johnston, JS and Jones, TE and Jones, JW and Khila, A and Koelzer, S and Kovacova, V and Leask, M and Lee, SL and Lee, CY and Lovegrove, MR and Lu, HL and Lu, Y and Moore, PJ and Munoz-Torres, MC and Muzny, DM and Palli, SR and Parisot, N and Pick, L and Porter, ML and Qu, J and Refki, PN and Richter, R and Rivera-Pomar, R and Rosendale, AJ and Roth, S and Sachs, L and Santos, ME and Seibert, J and Sghaier, E and Shukla, JN and Stancliffe, RJ and Tidswell, O and Traverso, L and van der Zee, M and Viala, S and Worley, KC and Zdobnov, EM and Gibbs, RA and Richards, S}, title = {Molecular evolutionary trends and feeding ecology diversification in the Hemiptera, anchored by the milkweed bug genome.}, journal = {Genome biology}, volume = {20}, number = {1}, pages = {64}, pmid = {30935422}, issn = {1474-760X}, support = {R01 GM080203/GM/NIGMS NIH HHS/United States ; R01 HG004483/HG/NHGRI NIH HHS/United States ; U54 HG003273/HG/NHGRI NIH HHS/United States ; R01 GM113230/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Animals ; CYS2-HIS2 Zinc Fingers ; *Evolution, Molecular ; Feeding Behavior ; Gene Dosage ; Gene Expression Profiling ; Gene Transfer, Horizontal ; Genes, Homeobox ; *Genome, Insect ; Hemiptera/*genetics/growth & development/metabolism ; Pigmentation/genetics ; Smell ; Transcription Factors/genetics ; }, abstract = {BACKGROUND: The Hemiptera (aphids, cicadas, and true bugs) are a key insect order, with high diversity for feeding ecology and excellent experimental tractability for molecular genetics. Building upon recent sequencing of hemipteran pests such as phloem-feeding aphids and blood-feeding bed bugs, we present the genome sequence and comparative analyses centered on the milkweed bug Oncopeltus fasciatus, a seed feeder of the family Lygaeidae.

RESULTS: The 926-Mb Oncopeltus genome is well represented by the current assembly and official gene set. We use our genomic and RNA-seq data not only to characterize the protein-coding gene repertoire and perform isoform-specific RNAi, but also to elucidate patterns of molecular evolution and physiology. We find ongoing, lineage-specific expansion and diversification of repressive C2H2 zinc finger proteins. The discovery of intron gain and turnover specific to the Hemiptera also prompted the evaluation of lineage and genome size as predictors of gene structure evolution. Furthermore, we identify enzymatic gains and losses that correlate with feeding biology, particularly for reductions associated with derived, fluid nutrition feeding.

CONCLUSIONS: With the milkweed bug, we now have a critical mass of sequenced species for a hemimetabolous insect order and close outgroup to the Holometabola, substantially improving the diversity of insect genomics. We thereby define commonalities among the Hemiptera and delve into how hemipteran genomes reflect distinct feeding ecologies. Given Oncopeltus's strength as an experimental model, these new sequence resources bolster the foundation for molecular research and highlight technical considerations for the analysis of medium-sized invertebrate genomes.}, } @article {pmid30935258, year = {2019}, author = {Michou, M and Panagiotakos, DB and Lionis, C and Costarelli, V}, title = {Socioeconomic inequalities in relation to health and nutrition literacy in Greece.}, journal = {International journal of food sciences and nutrition}, volume = {70}, number = {8}, pages = {1007-1013}, doi = {10.1080/09637486.2019.1593951}, pmid = {30935258}, issn = {1465-3478}, mesh = {Adolescent ; Adult ; Cross-Sectional Studies ; Databases, Factual ; Female ; Greece ; *Health Literacy ; *Health Status ; Humans ; Income ; Linear Models ; Male ; Middle Aged ; *Nutritional Status ; Regression Analysis ; Self Report ; Social Class ; *Socioeconomic Factors ; Surveys and Questionnaires ; Young Adult ; }, abstract = {Poor health literacy (HL) is associated with poor health behaviours and outcomes. The aim of the study was to investigate the effect of socioeconomic status on HL and nutrition literacy (NL) in Greece. This is a cross-sectional study which took place in Attica, Greece. 1281 individuals, aged ≥18 years of both sexes, participated. The European Health Literacy Questionnaire and the Greek version of the Nutrition Literacy Scale were used. Linear regression analysis revealed that education was significantly positively associated with HL (p = 0.002) and medium annual income was significantly associated with higher HL (p = 0.024), in contrast to low annual income. Education (p < 0.001) was significantly positively associated with NL. Unskilled particpants had lower NL compared to skilled paricipants (p = 0.021) and participants with medium annual income had significantly higher NL (p = 0.003) in comparison to participants with low annual income. Socioeconomic inequalities seem to negatively associate with HL and NL in Greece.}, } @article {pmid30935053, year = {2019}, author = {Lei, J and Jia, Y and Zuo, A and Zeng, Q and Shi, L and Zhou, Y and Zhang, H and Lu, C and Lei, G and Wen, L}, title = {Bird Satellite Tracking Revealed Critical Protection Gaps in East Asian[-]Australasian Flyway.}, journal = {International journal of environmental research and public health}, volume = {16}, number = {7}, pages = {}, pmid = {30935053}, issn = {1660-4601}, mesh = {*Animal Migration ; Animals ; *Conservation of Natural Resources ; *Geese ; Geographic Information Systems ; Grassland ; Population Dynamics ; Satellite Communications ; Seasons ; Wetlands ; }, abstract = {Most migratory birds depend on stopover sites, which are essential for refueling during migration and affect their population dynamics. In the East Asian[-]Australasian Flyway (EAAF), however, the stopover ecology of migratory waterfowl is severely under-studied. The knowledge gaps regarding the timing, intensity and duration of stopover site usages prevent the development of effective and full annual cycle conservation strategies for migratory waterfowl in EAAF. In this study, we obtained a total of 33,493 relocations and visualized 33 completed spring migratory paths of five geese species using satellite tracking devices. We delineated 2,192,823 ha as the key stopover sites along the migration routes and found that croplands were the largest land use type within the stopover sites, followed by wetlands and natural grasslands (62.94%, 17.86% and 15.48% respectively). We further identified the conservation gaps by overlapping the stopover sites with the World Database on Protected Areas (PA). The results showed that only 15.63% (or 342,757 ha) of the stopover sites are covered by the current PA network. Our findings fulfil some key knowledge gaps for the conservation of the migratory waterbirds along the EAAF, thus enabling an integrative conservation strategy for migratory water birds in the flyway.}, } @article {pmid30934677, year = {2019}, author = {Pawlaczyk, A and Gajek, M and Jozwik, K and Szynkowska, MI}, title = {Multielemental Analysis of Various Kinds of Whisky.}, journal = {Molecules (Basel, Switzerland)}, volume = {24}, number = {7}, pages = {}, pmid = {30934677}, issn = {1420-3049}, mesh = {Alcoholic Beverages/*analysis ; Data Interpretation, Statistical ; Mass Spectrometry ; Multivariate Analysis ; }, abstract = {Whisky (whiskey) consists of many trace elements coming from the raw materials used in its fermentation, distillation and maturation processes. These ingredients assure the exceptional organoleptic characteristics of the beverage. Their analysis is important to better control the stages of fermentation, distillation, taste repeatability and for product quality assurance as well as from the brand protection point of view. This article presents the usefulness of modern analytical techniques based on elemental analysis. ICP mass spectrometry and CV atomic absorption spectroscopy were applied to distinguish whisky produced in Scotland from whisky coming from Ireland and the United States. The collected semi-quantitative data were used for multivariate analysis performed using the Statistica 10.0 software. The results showed that Irish whiskey is characterized by quite a high amount of Ba and Ti compared with other samples, which made it possible to distinguish this sample from the others. No strict correlation was found between the type of whisky and the amount of trace elements, however, the projection of objects on the first two components revealed that single malt samples created one cluster.}, } @article {pmid30934615, year = {2019}, author = {Fang, Z and Hou, Z and Wang, S and Liu, Z and Wei, S and Zhang, Y and Song, J and Yin, J}, title = {Transcriptome Analysis Reveals the Accumulation Mechanism of Anthocyanins in Buckwheat (Fagopyrum esculentum Moench) Cotyledons and Flowers.}, journal = {International journal of molecular sciences}, volume = {20}, number = {6}, pages = {}, pmid = {30934615}, issn = {1422-0067}, support = {31671755, 31571736//National Natural Science Foundation of China/ ; }, mesh = {Anthocyanins/chemistry/*metabolism ; Cotyledon/*genetics ; Fagopyrum/*genetics/*metabolism ; Flowers/anatomy & histology/*genetics ; *Gene Expression Profiling ; Gene Expression Regulation, Plant ; Gene Ontology ; Molecular Sequence Annotation ; Open Reading Frames/genetics ; Plant Leaves/anatomy & histology ; Sequence Analysis, RNA ; }, abstract = {Buckwheat (Fagopyrum esculentum) is a valuable crop which can produce multiple human beneficial secondary metabolites, for example, the anthocyanins in sprouts and flowers. However, as the predominant group of visible polyphenols in pigmentation, little is known about the molecular mechanisms underlying the anthocyanin biosynthesis within buckwheat. In this study, a comparative transcriptome analysis of green and red common buckwheat cultivars was carried out through RNA sequencing. Overall, 3727 and 5323 differently expressed genes (DEGs) were identified in flowers and cotyledons, respectively. Through GO and KEGG analysis, we revealed that DEGs in flowers and cotyledons are predominately involved in biosynthesis of anthocyanin. A total of 42 unigenes encoding 11 structural enzymes of the anthocyanin biosynthesis were identified as DEGs. We also identified some transcription factor families involved in the regulation of anthocyanin biosynthesis. Real-time qPCR validation of candidate genes was performed in flowers and cotyledons, and the results suggested that the high expression level of structural genes involved in anthocyanin biosynthetic pathway promotes anthocyanin accumulation. Our results provide the insight understanding for coloration of red common buckwheat.}, } @article {pmid30932209, year = {2019}, author = {Lee, E and Smathers, C and Zubieta, AC and Ginnetti, S and Shah, A and Freedman, DA}, title = {Identifying Indicators of Readiness and Capacity for Implementing Farm-to-School Interventions.}, journal = {The Journal of school health}, volume = {89}, number = {5}, pages = {373-381}, pmid = {30932209}, issn = {1746-1561}, mesh = {Agriculture ; Capacity Building ; Child ; Community Networks ; *Diet, Healthy ; Female ; Focus Groups ; *Health Promotion ; Humans ; Interviews as Topic ; Male ; Pediatric Obesity/prevention & control ; Qualitative Research ; *Schools ; }, abstract = {BACKGROUND: Farm-to-school interventions are recommended strategies to improve dietary behaviors among school-aged children. Tools are needed to assess community readiness and capacity to optimize farm-to-school implementation. The objective of this study was to identify and prioritize factors to inform tailored farm-to-school implementation by practitioners working in diverse contexts.

METHODS: Practitioners and community residents (N = 194) participated in semistructured interviews (N = 18) and focus groups (N = 23). Thematic analysis was conducted to identify themes and subthemes influencing farm-to-school implementation. The subthemes were operationalized into measureable indicators. The themes and their associated indicators were prioritized through a consensus conference with an expert panel (N = 18).

RESULTS: The qualitative data analysis and consensus conference yielded 4 themes and 17 indicators associated with community readiness and capacity to implement farm-to-school. The themes represent school capacity, networks and relationships, organizational and practitioner capacity, and community resources and motivations.

CONCLUSIONS: Findings highlight a range of indicators of community readiness and capacity needed to support farm-to-school implementation. Results offer guidance for tailoring intervention delivery based on levels of community, school, practitioner, and organizational readiness and capacity.}, } @article {pmid30930924, year = {2019}, author = {Klisz, M and Buras, A and Sass-Klaassen, U and Puchałka, R and Koprowski, M and Ukalska, J}, title = {Limitations at the Limit? Diminishing of Genetic Effects in Norway Spruce Provenance Trials.}, journal = {Frontiers in plant science}, volume = {10}, number = {}, pages = {306}, pmid = {30930924}, issn = {1664-462X}, abstract = {Provenance trials are used to study the effects of tree origin on climate-growth relationships. Thereby, they potentially identify provenances which appear more resilient to anticipated climate change. However, when studying between provenance variability in growth behavior it becomes important to address potential effects related to site marginality in the context of provenance trials. In our study we focus on provenance-specific climate sensitivity manifested under marginal growth conditions. We hypothesized that the provenance effects are masked if trials are located at marginal environmental conditions of the natural species distribution. Under this framework, we investigate 10 Norway spruce provenances growing at two contrasting locations, i.e., a relatively drought-prone site in western Poland (at the climatic margin of Norway spruce's natural distribution) and a mild and moist site in north-eastern Poland (within its natural range). Combining principal component analysis with climate-growth relationships, we found distinguishable growth patterns and climate correlations among provenances. That is, at the mild and moist north-eastern site, we observed provenance-specific growth patterns and thus a varying drought susceptibility. In contrast, at the dryer western site, provenance-specific growth patterns were less pronounced and all provenances expressed a common and strong sensitivity to drought. Our results indicate that the genetic specificity of growth reactions diminishes toward the distributional margins of a given species. We conclude that the climate conditions at the margins of a species' distribution are constraining tree growth independently of tree origin. Because of this, the marginality of a site has to be considered when evaluating climate sensitivity of provenances within trials. As a consequence, the yet different responses of provenances to adverse growing conditions may synchronize under more extreme conditions in course of the anticipated climate change.}, } @article {pmid30929192, year = {2019}, author = {Long, M and Shen, B}, title = {Evolution of genes and genomes: an emerging paradigm in life science.}, journal = {Science China. Life sciences}, volume = {62}, number = {4}, pages = {435-436}, doi = {10.1007/s11427-018-9448-x}, pmid = {30929192}, issn = {1869-1889}, mesh = {Biological Science Disciplines/*trends ; Computational Biology ; Evolution, Molecular ; Genetics, Population ; Genome/*genetics ; Genomics ; History, 20th Century ; History, 21st Century ; Humans ; }, } @article {pmid30928604, year = {2019}, author = {Okutani, A and Inoue, S and Morikawa, S}, title = {Comparative genomics and phylogenetic analysis of Bacillus anthracis strains isolated from domestic animals in Japan.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {71}, number = {}, pages = {128-139}, doi = {10.1016/j.meegid.2019.03.022}, pmid = {30928604}, issn = {1567-7257}, mesh = {Animals ; Animals, Domestic/microbiology ; Anthrax/*veterinary ; Bacillus anthracis/*classification/*genetics ; Cattle ; Computational Biology ; Genome, Bacterial ; Genomics ; Horses ; Japan/epidemiology ; Molecular Epidemiology ; Phylogeny ; Phylogeography ; Polymorphism, Single Nucleotide ; Swine ; Whole Genome Sequencing ; }, abstract = {Anthrax, caused by Bacillus anthracis, is a severe zoonosis with a great impact on both human and animal health. In the present study, we identified the phylogenetic relationships among 16 Japanese strains of B. anthracis, including eight bovine strains, two equine strains, five swine strains, and one former vaccine strain, using in silico canonical single nucleotide polymorphism (canSNP) and core genome SNP analyses. The results of our in silico canSNP analysis suggest that these 16 Japanese strains could be divided into four lineages: i) one equine strain in A.Br.Ames, ii) one equine and six bovine strains in A.Br.001/002, iii) five swine and one bovine strain in A.Br.Aust94, and iv) one bovine and one vaccine strain in A.Br.008/011. A comparison with non-Japanese B. anthracis strains revealed a total of 3787 SNPs identified from the whole genome sequences of the Japanese strains; these SNP data were subjected to a phylogenetic analysis using the maximum parsimony (MP) method. Our core genome SNP analysis was also able to detect differences of a few chromosomal SNPs across clonal strains from the same cases that had different storage and passage histories. Additionally, our whole genome SNP analysis clearly indicated that the Japanese swine anthrax cases of 1982 were caused by at least three independent strains; however, their phylogeny revealed no clear relationship with swine strains from other countries. The bovine strain belonging to the A.Br.008/011 lineage differed from a former Japanese vaccine strain by only 12 SNPs. Together with the phylogenic results and epidemiological circumstances, the diversity of strains reveals that the B. anthracis available in Japan probably resulted from multiple relatively recent import events, rather than reflecting the persistence of a more ancient ecologically established group.}, } @article {pmid30928035, year = {2019}, author = {Louro, R and Santos-Silva, C and Nobre, T}, title = {What is in a name? Terfezia classification revisited.}, journal = {Fungal biology}, volume = {123}, number = {4}, pages = {267-273}, doi = {10.1016/j.funbio.2019.01.003}, pmid = {30928035}, issn = {1878-6146}, mesh = {Ascomycota/*classification/*genetics/growth & development ; Computational Biology ; DNA, Fungal/*genetics ; DNA, Ribosomal Spacer/*genetics ; *Phylogeny ; *Terminology as Topic ; }, abstract = {Desert truffles (mycorrhizal hypogeous Ascomycota) are found in arid and semi-arid areas of the globe and have great ecological and economic importance. Terfezia is undoubtedly the most diversified of all desert truffle genera, but its taxonomy is far from resolved. Specifically, the large number of newly described species plus the high intraspecific morphological variability observed within some Terfezia lineages as rendered the use of molecular techniques mandatory for specimen's discrimination. But the subsequent increasing amount of sequence data produced also a huge number of undescribed taxa that required determination. We compiled and used the public available ITS data on Terfezia spp. on the custom-curated UNITE database to reconstruct the genus phylogeny. We found at least 17 distinct lineages within the genus and successfully resolved some of the more pressing taxonomic issues, namely the T. leptoderma/olbiensis complex and some misapplied synonymy. Based on this resolved phylogeny, and motivated by the recent new described species, we proposed an identification key to Terfezia genus highlighting the importance of morphological and ecological characterization.}, } @article {pmid30927270, year = {2019}, author = {Fletcher, RJ and Hefley, TJ and Robertson, EP and Zuckerberg, B and McCleery, RA and Dorazio, RM}, title = {A practical guide for combining data to model species distributions.}, journal = {Ecology}, volume = {100}, number = {6}, pages = {e02710}, doi = {10.1002/ecy.2710}, pmid = {30927270}, issn = {1939-9170}, mesh = {Animals ; *Birds ; *Ecology ; Information Storage and Retrieval ; }, abstract = {Understanding and accurately modeling species distributions lies at the heart of many problems in ecology, evolution, and conservation. Multiple sources of data are increasingly available for modeling species distributions, such as data from citizen science programs, atlases, museums, and planned surveys. Yet reliably combining data sources can be challenging because data sources can vary considerably in their design, gradients covered, and potential sampling biases. We review, synthesize, and illustrate recent developments in combining multiple sources of data for species distribution modeling. We identify five ways in which multiple sources of data are typically combined for modeling species distributions. These approaches vary in their ability to accommodate sampling design, bias, and uncertainty when quantifying environmental relationships in species distribution models. Many of the challenges for combining data are solved through the prudent use of integrated species distribution models: models that simultaneously combine different data sources on species locations to quantify environmental relationships for explaining species distribution. We illustrate these approaches using planned survey data on 24 species of birds coupled with opportunistically collected eBird data in the southeastern United States. This example illustrates some of the benefits of data integration, such as increased precision in environmental relationships, greater predictive accuracy, and accounting for sample bias. Yet it also illustrates challenges of combining data sources with vastly different sampling methodologies and amounts of data. We provide one solution to this challenge through the use of weighted joint likelihoods. Weighted joint likelihoods provide a means to emphasize data sources based on different criteria (e.g., sample size), and we find that weighting improves predictions for all species considered. We conclude by providing practical guidance on combining multiple sources of data for modeling species distributions.}, } @article {pmid30926861, year = {2019}, author = {Brandt, A and Bast, J and Scheu, S and Meusemann, K and Donath, A and Schütte, K and Machida, R and Kraaijeveld, K}, title = {No signal of deleterious mutation accumulation in conserved gene sequences of extant asexual hexapods.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {5338}, pmid = {30926861}, issn = {2045-2322}, mesh = {Animals ; *Conserved Sequence ; Evolution, Molecular ; Insecta/classification/*genetics ; *Mutation Accumulation ; Reproduction, Asexual/*genetics ; Selection, Genetic ; Silent Mutation ; Species Specificity ; }, abstract = {Loss of sex and recombination is generally assumed to impede the effectiveness of purifying selection and to result in the accumulation of slightly deleterious mutations. Empirical evidence for this has come from several studies investigating mutational load in a small number of individual genes. However, recent whole transcriptome based studies have yielded inconsistent results, hence questioning the validity of the assumption of mutational meltdown in asexual populations. Here, we study the effectiveness of purifying selection in eight asexual hexapod lineages and their sexual relatives, as present in the 1 K Insect Transcriptome Evolution (1KITE) project, covering eight hexapod groups. We analyse the accumulation of slightly deleterious nonsynonymous and synonymous point mutations in 99 single copy orthologue protein-coding loci shared among the investigated taxa. While accumulation rates of nonsynonymous mutations differed between genes and hexapod groups, we found no effect of reproductive mode on the effectiveness of purifying selection acting at nonsynonymous and synonymous sites. Although the setup of this study does not fully rule out nondetection of subtle effects, our data does not support the established consensus of asexual lineages undergoing 'mutational meltdown'.}, } @article {pmid30926723, year = {2019}, author = {Martinson, EO and Peyton, J and Kelkar, YD and Jennings, EC and Benoit, JB and Werren, JH and Denlinger, DL}, title = {Genome and Ontogenetic-Based Transcriptomic Analyses of the Flesh Fly, Sarcophaga bullata.}, journal = {G3 (Bethesda, Md.)}, volume = {9}, number = {5}, pages = {1313-1320}, pmid = {30926723}, issn = {2160-1836}, support = {R01 GM098667/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Computational Biology/methods ; Exons ; *Gene Expression Profiling/methods ; *Genome, Insect ; *Genomics/methods ; High-Throughput Nucleotide Sequencing ; Introns ; Molecular Sequence Annotation ; Phylogeny ; Sarcophagidae/classification/*genetics ; *Transcriptome ; }, abstract = {The flesh fly, Sarcophaga bullata, is a widely-used model for examining the physiology of insect diapause, development, stress tolerance, neurobiology, and host-parasitoid interactions. Flies in this taxon are implicated in myiasis (larval infection of vertebrates) and feed on carrion, aspects that are important in forensic studies. Here we present the genome of S. bullata, along with developmental- and reproduction-based RNA-Seq analyses. We predict 15,768 protein coding genes, identify orthology in relation to closely related flies, and establish sex and developmental-specific gene sets based on our RNA-Seq analyses. Genomic sequences, predicted genes, and sequencing data sets have been deposited at the National Center for Biotechnology Information. Our results provide groundwork for genomic studies that will expand the flesh fly's utility as a model system.}, } @article {pmid30926662, year = {2019}, author = {Fournier, A and Penone, C and Pennino, MG and Courchamp, F}, title = {Predicting future invaders and future invasions.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {116}, number = {16}, pages = {7905-7910}, pmid = {30926662}, issn = {1091-6490}, mesh = {Algorithms ; Animals ; Ants/physiology ; Biodiversity ; Computational Biology/*methods ; Humans ; *Introduced Species/statistics & numerical data/trends ; *Models, Statistical ; Risk Assessment ; }, abstract = {Invasive alien species are a great threat to biodiversity and human livelihoods worldwide. The most effective way to limit their impacts and costs is to prevent their introduction into new areas. Identifying invaders and invasions before their occurrence would arguably be the most efficient strategy. Here, we provide a profiling method to predict which species-with which particular ecological characteristics-will invade, and where they could invade. We illustrate our approach with ants, which are among the most detrimental invasive species, as they are responsible for declines of numerous taxa, are involved in local extinctions, disturb ecosystem functioning, and impact multiple human activities. Based on statistical profiling of 1,002 ant species from an extensive trait database, we identify 13 native ant species with an ecological profile that matches that of known invasive ants. Even though they are not currently described as such, these species are likely to become the next global invaders. We couple these predictions with species distribution models to identify the regions most at risk from the invasion of these species: Florida and Central America, Brazil, Central Africa and Madagascar, Southeast Asia, Papua New Guinea Northeast Australia, and many islands worldwide. This framework, applicable to any other taxa, represents a remarkable opportunity to implement timely and specifically shaped proactive management strategies against biological invasions.}, } @article {pmid30925776, year = {2019}, author = {Magalhães Filho, FJC and de Queiroz, AAFSL and Machado, BS and Paulo, PL}, title = {Sustainable Sanitation Management Tool for Decision Making in Isolated Areas in Brazil.}, journal = {International journal of environmental research and public health}, volume = {16}, number = {7}, pages = {}, pmid = {30925776}, issn = {1660-4601}, mesh = {Brazil ; *Decision Making, Computer-Assisted ; *Guidelines as Topic ; Humans ; Information Dissemination/*methods ; Pilot Projects ; Rural Population ; Sanitation/*methods/*standards ; *Software ; }, abstract = {There is a worldwide range of technical sanitation guidelines focusing on small or traditional and isolated communities for ecological alternatives at the household level. However, a computational tool (software) that has a database and connects these guidelines in a single reference for resource-oriented sanitation concept decision making is still lacking. In this regard, an easy-to-use tool was developed using a participatory approach for the decision-making process from a choice of technical solutions to a type of system management. The results obtained from a pilot study indicate that the proposed tool in this paper will help with the decision-making process to aid in not only choosing sustainable sanitation solutions, but also sustainable operation and maintenance options for the systems. When presenting and discussing the tool with research groups and technicians, the potential for participatory application was noticed. The proposed tool can be used in the elaboration of municipal sanitation plans, assisting local technicians and environmental licensing agencies, designers and engineering students, among others. The software can be applied with other management tools, such as 5W2H and Canvas business model.}, } @article {pmid30925592, year = {2019}, author = {Kerns, EK and Staggs, VS and Fouquet, SD and McCulloh, RJ}, title = {Estimating the impact of deploying an electronic clinical decision support tool as part of a national practice improvement project.}, journal = {Journal of the American Medical Informatics Association : JAMIA}, volume = {26}, number = {7}, pages = {630-636}, pmid = {30925592}, issn = {1527-974X}, support = {UG1 OD024953/OD/NIH HHS/United States ; }, mesh = {Anti-Bacterial Agents/therapeutic use ; Bacterial Infections/complications/*diagnosis/drug therapy ; *Decision Support Systems, Clinical ; Diagnostic Errors ; Fever of Unknown Origin/drug therapy/*etiology ; Hospitalization ; Humans ; Infant ; *Mobile Applications ; Pediatrics/standards ; Practice Guidelines as Topic ; Quality Improvement ; Radiography, Thoracic ; Sepsis/diagnosis ; Smartphone ; United States ; }, abstract = {OBJECTIVE: Estimate the impact on clinical practice of using a mobile device-based electronic clinical decision support (mECDS) tool within a national standardization project.

MATERIALS AND METHODS: An mECDS tool (app) was released as part of a change package to provide febrile infant management guidance to clinicians. App usage was analyzed using 2 measures: metric hits per case (metric-related screen view count divided by site-reported febrile infant cases in each designated market area [DMA] monthly) and cumulative prior metric hits per site (DMA metric hits summed from study month 1 until the month preceding the index, divided by sites in the DMA). For each metric, a mixed logistic regression model was fit to model site performance as a function of app usage.

RESULTS: An increase of 200 cumulative prior metric hits per site was associated with increased odds of adherence to 3 metrics: appropriate admission (odds ratio [OR], 1.12; 95% confidence interval [CI], 1.06-1.18), appropriate length of stay (OR, 1.20; 95% CI, 1.12-1.28), and inappropriate chest x-ray (OR, 0.82; 95% CI, 0.75-0.91). Ten additional metric hits per case were also associated: OR were 1.18 (95% CI, 1.02-1.36), 1.36 (95% CI, 1.14-1.62), and 0.74 (95% CI, 0.62-0.89).

DISCUSSION: mECDS tools are increasingly being implemented, but their impact on clinical practice is poorly described. To our knowledge, although ecologic in nature, this report is the first to link clinical practice to mECDS use on a national scale and outside of an electronic health record.

CONCLUSIONS: mECDS use was associated with changes in adherence to targeted metrics. Future studies should seek to link mECDS usage more directly to clinical practice and assess other site-level factors.}, } @article {pmid30923136, year = {2019}, author = {Jørgensen, TS and Nielsen, BLH and Petersen, B and Browne, PD and Hansen, BW and Hansen, LH}, title = {The Whole Genome Sequence and mRNA Transcriptome of the Tropical Cyclopoid Copepod Apocyclops royi.}, journal = {G3 (Bethesda, Md.)}, volume = {9}, number = {5}, pages = {1295-1302}, pmid = {30923136}, issn = {2160-1836}, mesh = {Animals ; Computational Biology/methods ; Copepoda/classification/*genetics ; Genome ; Genomics/methods ; Phylogeny ; RNA, Messenger ; *Transcriptome ; *Whole Genome Sequencing ; }, abstract = {Copepoda is one of the most ecologically important animal groups on Earth, yet very few genetic resources are available for this Subclass. Here, we present the first whole genome sequence (WGS, acc. UYDY01) and the first mRNA transcriptome assembly (TSA, Acc. GHAJ01) for the tropical cyclopoid copepod species Apocyclops royi Until now, only the 18S small subunit of ribosomal RNA gene and the COI gene has been available from A. royi, and WGS resources was only available from one other cyclopoid copepod species. Overall, the provided resources are the 8[th] copepod species to have WGS resources available and the 19[th] copepod species with TSA information available. We analyze the length and GC content of the provided WGS scaffolds as well as the coverage and gene content of both the WGS and the TSA assembly. Finally, we place the resources within the copepod order Cyclopoida as a member of the Apocyclops genus. We estimate the total genome size of A. royi to 450 Mb, with 181 Mb assembled nonrepetitive sequence, 76 Mb assembled repeats and 193 Mb unassembled sequence. The TSA assembly consists of 29,737 genes and an additional 45,756 isoforms. In the WGS and TSA assemblies, >80% and >95% of core genes can be found, though many in fragmented versions. The provided resources will allow researchers to conduct physiological experiments on A. royi, and also increase the possibilities for copepod gene set analysis, as it adds substantially to the copepod datasets available.}, } @article {pmid30922854, year = {2019}, author = {Li, Y and Xie, J and Li, Y and Yang, Y and Yang, L}, title = {Literature data based systems pharmacology uncovers the essence of "body fire" in traditional Chinese medicine: A case by Huang-Lian-Jie-Du-Tang.}, journal = {Journal of ethnopharmacology}, volume = {237}, number = {}, pages = {266-285}, doi = {10.1016/j.jep.2019.03.037}, pmid = {30922854}, issn = {1872-7573}, mesh = {Databases, Factual ; Drugs, Chinese Herbal/chemistry/*pharmacology ; Humans ; Medicine, Chinese Traditional ; Proteins/metabolism ; Systems Biology ; }, abstract = {ETHNOPHARMACOLOGY RELEVANCE: Like other concepts in traditional Chinese medical theory, "body fire", a concept that has already been well-known and widely used in describing the symptoms and the treatment of corresponding diseases, is, however, still under suspicions in the western medicine due to its vague essence and symptoms. Presently, Huang-Lian-Jie-Du-Tang (HLJDT), a typical popular TCM formula in cleansing the "body fire", is studied as a probe by a systems pharmacology method we produced, with purpose to explore the mechanisms of the potion, as well as to interpret the essence of "body fire" disease.

METHODS: The systematic process includes a pharmacokinetics prescreening, pharmacodynamics targets and pathways identification, and candidate-target-pathway network construction.

RESULTS: Through this method, 145 chemicals and 91 proteins are identified as active ingredients and "body fire"-related targets. And we find that the mechanism of HLJDT prescription for cleansing "body fire" lies in three, i.e., anti-OS/NS, anti-inflammation and anti-infection function modules, which are mainly executed through four, i.e., PI3K-AKT, MAPK, VEGF as well as Calcium signaling pathways.

CONCLUSIONS: Accordingly, the essence of "body fire" is a gradual process which is an integration of OS/NS, inflammation and infection. This work, we hope, may not only offer a systemic methodology for exploring and elucidating TCM concepts from a multi-scale perspective, but also provide an efficient way for herbal drug discovery.}, } @article {pmid30920277, year = {2019}, author = {Wright, AGC and Gates, KM and Arizmendi, C and Lane, ST and Woods, WC and Edershile, EA}, title = {Focusing personality assessment on the person: Modeling general, shared, and person specific processes in personality and psychopathology.}, journal = {Psychological assessment}, volume = {31}, number = {4}, pages = {502-515}, pmid = {30920277}, issn = {1939-134X}, support = {F32 MH097325/MH/NIMH NIH HHS/United States ; L30 MH101760/MH/NIMH NIH HHS/United States ; R01 MH080086/MH/NIMH NIH HHS/United States ; }, mesh = {Data Interpretation, Statistical ; Diaries as Topic ; Humans ; Longitudinal Studies ; *Models, Psychological ; *Personality ; *Personality Assessment ; Personality Disorders/*diagnosis/psychology ; }, abstract = {Personality and psychopathology are composed of dynamic and interactive processes among diverse psychological systems, manifesting over time and in response to an individual's natural environment. Ambulatory assessment techniques promise to revolutionize assessment practices by allowing access to the dynamic data necessary to study these processes directly. Assessing manifestations of personality and psychopathology naturalistically in an individual's own ecology allows for dynamic modeling of key behavioral processes. However, advances in dynamic data collection have highlighted the challenges of both fully understanding an individual (via idiographic models) and how s/he compares with others (as seen in nomothetic models). Methods are needed that can simultaneously model idiographic (i.e., person-specific) processes and nomothetic (i.e., general) structure from intensive longitudinal personality assessments. Here we present a method, group iterative multiple model estimation (GIMME) for simultaneously studying general, shared (i.e., in subgroups), and person-specific processes in intensive longitudinal behavioral data. We first provide an introduction to the GIMME method, followed by a demonstration of its use in a sample of individuals diagnosed with personality disorder who completed daily diaries over 100 consecutive days. (PsycINFO Database Record (c) 2019 APA, all rights reserved).}, } @article {pmid30919506, year = {2019}, author = {Fridrich, A and Hazan, Y and Moran, Y}, title = {Too Many False Targets for MicroRNAs: Challenges and Pitfalls in Prediction of miRNA Targets and Their Gene Ontology in Model and Non-model Organisms.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {41}, number = {4}, pages = {e1800169}, pmid = {30919506}, issn = {1521-1878}, support = {637456/ERC_/European Research Council/International ; }, mesh = {Animals ; Computational Biology ; *Gene Ontology ; Humans ; MicroRNAs/*genetics/metabolism ; *Models, Biological ; Phylogeny ; }, abstract = {Short ("seed") or extended base pairing between microRNAs (miRNAs) and their target RNAs enables post-transcriptional silencing in many organisms. These interactions allow the computational prediction of potential targets. In model organisms, predicted targets are frequently validated experimentally; hence meaningful miRNA-regulated processes are reported. However, in non-models, these reports mostly rely on computational prediction alone. Many times, further bioinformatic analyses such as Gene Ontology (GO) enrichment are based on these in silico projections. Here such approaches are reviewed, their caveats are highlighted and the ease of picking false targets from predicted lists is demonstrated. Discoveries that shed new light on how miRNAs evolved to regulate targets in various phyletic groups are discussed, in addition to the pitfalls of target identification in non-model organisms. The goal is to prevent the misuse of bioinformatic tools, as they cannot bypass the biological understanding of miRNA-target regulation.}, } @article {pmid30919281, year = {2019}, author = {Zhang, W and Gao, Y and Long, M and Shen, B}, title = {Origination and evolution of orphan genes and de novo genes in the genome of Caenorhabditis elegans.}, journal = {Science China. Life sciences}, volume = {62}, number = {4}, pages = {579-593}, doi = {10.1007/s11427-019-9482-0}, pmid = {30919281}, issn = {1869-1889}, mesh = {Animals ; Caenorhabditis elegans/classification/*genetics/growth & development ; Caenorhabditis elegans Proteins/*genetics ; Computational Biology ; DNA Transposable Elements ; Evolution, Molecular ; *Genes, Helminth ; Genetic Variation ; Genome, Helminth/genetics ; Phylogeny ; Reading Frames ; Species Specificity ; }, abstract = {Orphan genes that lack detectable homologues in other lineages could contribute to a variety of biological functions. However, their origination and function mechanisms remain largely unknown. Herein, through a comprehensive and systematic computational pipeline, we identified 893 orphan genes in the lineage of C. elegans, of which only a low fraction (0.9%) were derived from transposon elements. Six new protein-coding genes that de novo originated from non-coding DNA sequences in the genome of C. elegans were also identified. The authenticity and functionality of these orphan genes and de novo genes are supported by three lines of evidences, consisting of transcriptional data, and in silico proteomic data, and the fixation status data in wild populations. Orphan genes and de novo genes exhibited simple gene structures, such as, short in protein length, of fewer exons, and are frequently X-linked. RNA-seq data analysis showed these orphan genes are enriched with expression in embryo development and gonad, and their potential function in early development was further supported by gene ontology enrichment analysis results. Meanwhile, de novo genes were found to be with significant expression in gonad, and functional enrichment analysis of the co-expression genes of these de novo genes suggested they may be functionally involved in signaling transduction pathway and metabolism process. Our results presented the first systematic evidence on the evolution of orphan genes and de novo origin of genes in nematodes and their impacts on the functional and phenotypic evolution, and thus could shed new light on our appreciation of the importance of these new genes.}, } @article {pmid30919186, year = {2019}, author = {Cui, Y and Dong, B and Chen, L and Gao, X and Cui, Y}, title = {Study on habitat suitability of overwintering cranes based on landscape pattern change-a case study of typical lake wetlands in the middle and lower reaches of the Yangtze River.}, journal = {Environmental science and pollution research international}, volume = {26}, number = {15}, pages = {14962-14975}, pmid = {30919186}, issn = {1614-7499}, support = {41571101//National Natural Science Foundation of China/ ; }, mesh = {Animal Migration ; Animals ; *Birds ; China ; Conservation of Natural Resources ; Ecosystem ; Geographic Information Systems ; Lakes ; Population Density ; Rivers ; Seasons ; *Wetlands ; }, abstract = {Shengjin Lake wetland is located in the middle and lower reaches of the Yangtze River in China. It is a typical lake-type wetland and is also an ideal place for rare cranes to overwintering. The changes of wetland landscape are closely related to the habitat quality of wintering cranes. It is of great significance to study the habitat change of wintering cranes in wetland for wetland ecological restoration and restoration. In this paper, we analyze four kinds of winter cranes and wetland landscape pattern types from the years 1986 to 2015. Also, we adopted the Pearson correlation analysis method to analyze the relationship between wetland landscape types and crane population, and the main landscape types of cranes habitat were obtained. We selected disturbance degree, food richness, vegetation cover, and hydrological condition as the main factors affecting wintering habitat of cranes. We established a habitat suitability index model for wintering cranes and generated habitat suitability assessment maps by ArcGIS. The results show that the change of landscape pattern in Shengjin Lake protected area was obvious, the number of wetland patches increased, the fragmentation degree of landscape increased, the landscape patch difference became smaller, and the diversity index and evenness index increased gradually. From 1986 to 2015, the number of wintering cranes decreased and the habitat suitability index of wintering cranes decreased from 0.845 to 0.465, and the habitat suitability of wintering cranes fell from 13,577.11 to 7424.42 ha, which showed the overall habitat deteriorated significantly and had a positive correlation between the crane population and habitat suitability.}, } @article {pmid30918448, year = {2019}, author = {Stucky, BJ and Balhoff, JP and Barve, N and Barve, V and Brenskelle, L and Brush, MH and Dahlem, GA and Gilbert, JDJ and Kawahara, AY and Keller, O and Lucky, A and Mayhew, PJ and Plotkin, D and Seltmann, KC and Talamas, E and Vaidya, G and Walls, R and Yoder, M and Zhang, G and Guralnick, R}, title = {Developing a vocabulary and ontology for modeling insect natural history data: example data, use cases, and competency questions.}, journal = {Biodiversity data journal}, volume = {7}, number = {}, pages = {e33303}, pmid = {30918448}, issn = {1314-2828}, abstract = {Insects are possibly the most taxonomically and ecologically diverse class of multicellular organisms on Earth. Consequently, they provide nearly unlimited opportunities to develop and test ecological and evolutionary hypotheses. Currently, however, large-scale studies of insect ecology, behavior, and trait evolution are impeded by the difficulty in obtaining and analyzing data derived from natural history observations of insects. These data are typically highly heterogeneous and widely scattered among many sources, which makes developing robust information systems to aggregate and disseminate them a significant challenge. As a step towards this goal, we report initial results of a new effort to develop a standardized vocabulary and ontology for insect natural history data. In particular, we describe a new database of representative insect natural history data derived from multiple sources (but focused on data from specimens in biological collections), an analysis of the abstract conceptual areas required for a comprehensive ontology of insect natural history data, and a database of use cases and competency questions to guide the development of data systems for insect natural history data. We also discuss data modeling and technology-related challenges that must be overcome to implement robust integration of insect natural history data.}, } @article {pmid30918402, year = {2019}, author = {Peters, MK and Hemp, A and Appelhans, T and Becker, JN and Behler, C and Classen, A and Detsch, F and Ensslin, A and Ferger, SW and Frederiksen, SB and Gebert, F and Gerschlauer, F and Gütlein, A and Helbig-Bonitz, M and Hemp, C and Kindeketa, WJ and Kühnel, A and Mayr, AV and Mwangomo, E and Ngereza, C and Njovu, HK and Otte, I and Pabst, H and Renner, M and Röder, J and Rutten, G and Schellenberger Costa, D and Sierra-Cornejo, N and Vollstädt, MGR and Dulle, HI and Eardley, CD and Howell, KM and Keller, A and Peters, RS and Ssymank, A and Kakengi, V and Zhang, J and Bogner, C and Böhning-Gaese, K and Brandl, R and Hertel, D and Huwe, B and Kiese, R and Kleyer, M and Kuzyakov, Y and Nauss, T and Schleuning, M and Tschapka, M and Fischer, M and Steffan-Dewenter, I}, title = {Climate-land-use interactions shape tropical mountain biodiversity and ecosystem functions.}, journal = {Nature}, volume = {568}, number = {7750}, pages = {88-92}, pmid = {30918402}, issn = {1476-4687}, mesh = {Agriculture/*statistics & numerical data ; *Altitude ; Animals ; *Biodiversity ; *Ecosystem ; Humidity ; Microbiology ; Plants ; Rain ; Tanzania ; Temperature ; *Tropical Climate ; }, abstract = {Agriculture and the exploitation of natural resources have transformed tropical mountain ecosystems across the world, and the consequences of these transformations for biodiversity and ecosystem functioning are largely unknown[1-3]. Conclusions that are derived from studies in non-mountainous areas are not suitable for predicting the effects of land-use changes on tropical mountains because the climatic environment rapidly changes with elevation, which may mitigate or amplify the effects of land use[4,5]. It is of key importance to understand how the interplay of climate and land use constrains biodiversity and ecosystem functions to determine the consequences of global change for mountain ecosystems. Here we show that the interacting effects of climate and land use reshape elevational trends in biodiversity and ecosystem functions on Africa's largest mountain, Mount Kilimanjaro (Tanzania). We find that increasing land-use intensity causes larger losses of plant and animal species richness in the arid lowlands than in humid submontane and montane zones. Increases in land-use intensity are associated with significant changes in the composition of plant, animal and microorganism communities; stronger modifications of plant and animal communities occur in arid and humid ecosystems, respectively. Temperature, precipitation and land use jointly modulate soil properties, nutrient turnover, greenhouse gas emissions, plant biomass and productivity, as well as animal interactions. Our data suggest that the response of ecosystem functions to land-use intensity depends strongly on climate; more-severe changes in ecosystem functioning occur in the arid lowlands and the cold montane zone. Interactions between climate and land use explained-on average-54% of the variation in species richness, species composition and ecosystem functions, whereas only 30% of variation was related to single drivers. Our study reveals that climate can modulate the effects of land use on biodiversity and ecosystem functioning, and points to a lowered resistance of ecosystems in climatically challenging environments to ongoing land-use changes in tropical mountainous regions.}, } @article {pmid30918042, year = {2019}, author = {Nemat-Gorgani, N and Guethlein, LA and Henn, BM and Norberg, SJ and Chiaroni, J and Sikora, M and Quintana-Murci, L and Mountain, JL and Norman, PJ and Parham, P}, title = {Diversity of KIR, HLA Class I, and Their Interactions in Seven Populations of Sub-Saharan Africans.}, journal = {Journal of immunology (Baltimore, Md. : 1950)}, volume = {202}, number = {9}, pages = {2636-2647}, pmid = {30918042}, issn = {1550-6606}, support = {R01 AI017892/AI/NIAID NIH HHS/United States ; U01 AI090905/AI/NIAID NIH HHS/United States ; }, mesh = {Africa South of the Sahara ; *Black People ; Female ; HLA-A Antigens/*genetics ; HLA-B Antigens/*genetics ; HLA-C Antigens/*genetics ; *Haplotypes ; Humans ; Male ; Receptors, KIR/*genetics ; }, abstract = {HLA class I and KIR sequences were determined for Dogon, Fulani, and Baka populations of western Africa, Mbuti of central Africa, and Datooga, Iraqw, and Hadza of eastern Africa. Study of 162 individuals identified 134 HLA class I alleles (41 HLA-A, 60 HLA-B, and 33 HLA-C). Common to all populations are three HLA-C alleles (C1[+]C*07:01, C1[+]C*07:02, and C2[+]C*06:02) but no HLA-A or -B Unexpectedly, no novel HLA class I was identified in these previously unstudied and anthropologically distinctive populations. In contrast, of 227 KIR detected, 22 are present in all seven populations and 28 are novel. A high diversity of HLA A-C-B haplotypes was observed. In six populations, most haplotypes are represented just once. But in the Hadza, a majority of haplotypes occur more than once, with 2 having high frequencies and 10 having intermediate frequencies. The centromeric (cen) part of the KIR locus exhibits an even balance between cenA and cenB in all seven populations. The telomeric (tel) part has an even balance of telA to telB in East Africa, but this changes across the continent to where telB is vestigial in West Africa. All four KIR ligands (A3/11, Bw4, C1, and C2) are present in six of the populations. HLA haplotypes of the Iraqw and Hadza encode two KIR ligands, whereas the other populations have an even balance between haplotypes encoding one and two KIR ligands. Individuals in these African populations have a mean of 6.8-8.4 different interactions between KIR and HLA class I, compared with 2.9-6.5 for non-Africans.}, } @article {pmid30917178, year = {2019}, author = {Velásquez-Tibatá, J and Olaya-Rodríguez, MH and López-Lozano, D and Gutiérrez, C and González, I and Londoño-Murcia, MC}, title = {BioModelos: A collaborative online system to map species distributions.}, journal = {PloS one}, volume = {14}, number = {3}, pages = {e0214522}, pmid = {30917178}, issn = {1932-6203}, mesh = {*Biodiversity ; *Internet ; *Models, Statistical ; Online Systems ; Publications ; Software ; }, abstract = {Information on species distribution is recognized as a crucial input for biodiversity conservation and management. To that end, considerable resources have been dedicated towards increasing the quantity and availability of species occurrence data, boosting their use in species distribution modeling and online platforms for their dissemination. Currently, those platforms face the challenge of bringing biology into modeling by making informed decisions that result in meaningful models, based on limited occurrence and ecological data. Here we describe BioModelos, a modeling approach supported by an online system and a core team of modelers, whereby a network of experts contributes to the development of species distribution models by assessing the quality of occurrence data, identifying potentially limiting environmental variables, establishing species' accessible areas and validating modeling predictions qualitatively. Models developed through BioModelos become freely and publicly available once validated by experts, furthering their use in conservation applications. Our approach has been implemented in Colombia since 2013 and it currently consist of a network of nearly 500 experts that collaboratively contribute to enhance the knowledge on the distribution of a growing number of species and it has aided the development of several decision support products such as national risk assessments and biodiversity compensation manuals. BioModelos is an example of operationalization of an essential biodiversity variable at a national level through the implementation of a research infrastructure that enhances the value of open access species data.}, } @article {pmid30917146, year = {2019}, author = {Parker, L and Bourgoin, C and Martinez-Valle, A and Läderach, P}, title = {Vulnerability of the agricultural sector to climate change: The development of a pan-tropical Climate Risk Vulnerability Assessment to inform sub-national decision making.}, journal = {PloS one}, volume = {14}, number = {3}, pages = {e0213641}, pmid = {30917146}, issn = {1932-6203}, mesh = {Agriculture/*methods ; *Climate Change ; Crops, Agricultural ; *Decision Making ; Droughts ; Floods ; *Food Supply ; Geographic Information Systems ; Geography ; Health Policy ; Nicaragua ; Public Policy ; *Risk Assessment ; Rural Population ; Tropical Climate ; Uganda ; Vietnam ; Zea mays ; }, abstract = {As climate change continues to exert increasing pressure upon the livelihoods and agricultural sector of many developing and developed nations, a need exists to understand and prioritise at the sub national scale which areas and communities are most vulnerable. The purpose of this study is to develop a robust, rigorous and replicable methodology that is flexible to data limitations and spatially prioritizes the vulnerability of agriculture and rural livelihoods to climate change. We have applied the methodology in Vietnam, Uganda and Nicaragua, three contrasting developing countries that are particularly threatened by climate change. We conceptualize vulnerability to climate change following the widely adopted combination of sensitivity, exposure and adaptive capacity. We used Ecocrop and Maxent ecological models under a high emission climate scenario to assess the sensitivity of the main food security and cash crops to climate change. Using a participatory approach, we identified exposure to natural hazards and the main indicators of adaptive capacity, which were modelled and analysed using geographic information systems. We finally combined the components of vulnerability using equal-weighting to produce a crop specific vulnerability index and a final accumulative score. We have mapped the hotspots of climate change vulnerability and identified the underlying driving indicators. For example, in Vietnam we found the Mekong delta to be one of the vulnerable regions due to a decline in the climatic suitability of rice and maize, combined with high exposure to flooding, sea level rise and drought. However, the region is marked by a relatively high adaptive capacity due to developed infrastructure and comparatively high levels of education. The approach and information derived from the study informs public climate change policies and actions, as vulnerability assessments are the bases of any National Adaptation Plans (NAP), National Determined Contributions (NDC) and for accessing climate finance.}, } @article {pmid30916642, year = {2019}, author = {Luo, J and Ren, Q and Chen, Z and Liu, W and Qu, Z and Xiao, R and Chen, R and Lin, H and Wu, Z and Luo, J and Yin, H and Wang, H and Liu, G}, title = {Comparative analysis of microRNA profiles between wild and cultured Haemaphysalis longicornis (Acari, Ixodidae) ticks.}, journal = {Parasite (Paris, France)}, volume = {26}, number = {}, pages = {18}, pmid = {30916642}, issn = {1776-1042}, mesh = {Animals ; Computational Biology ; Gene Ontology ; Host-Pathogen Interactions/genetics ; Ixodidae/*genetics ; MicroRNAs/*genetics ; Polymerase Chain Reaction ; Rabbits/parasitology ; }, abstract = {The miRNA profiles of a Haemaphysalis longicornis wild-type (HLWS) and of a Haemaphysalis longicornis cultured population (HLCS) were sequenced using the Illumina Hiseq 4000 platform combined with bioinformatics analysis and real-time polymerase chain reaction (RT-PCR). A total of 15.63 and 15.48 million raw reads were acquired for HLWS and HLCS, respectively. The data identified 1517 and 1327 known conserved miRNAs, respectively, of which 342 were differentially expressed between the two libraries. Thirty-six novel candidate miRNAs were predicted. To explain the functions of these novel miRNAs, Gene Ontology (GO) analysis was performed. Target gene function prediction identified a significant set of genes related to salivary gland development, pathogen-host interaction and regulation of the defence response to pathogens expressed by wild H. longicornis ticks. Cellular component biogenesis, the immune system process, and responses to stimuli were represented at high percentages in the two tick libraries. GO enrichment analysis showed that the percentages of most predicted functions of the target genes of miRNA were similar, as were certain specific categories of functional enhancements, and that these genes had different numbers and specific functions (e.g., auxiliary transport protein and electron carrier functions). This study provides novel findings showing that miRNA regulation affects the expression of immune genes, indicating a considerable influence of environment-induced stressful stimulation on immune homeostasis. Differences in the living environments of ticks can lead to differences in miRNAs between ticks and provide a basis and a convenient means to screen for genes encoding immune factors in ticks.}, } @article {pmid30915794, year = {2019}, author = {Peng, WT and Liu, WQ and Cai, WB and Wang, X and Huang, Z and Wu, CZ}, title = {[Evaluation of ecosystem cultural services of urban protected areas based on public participation GIS (PPGIS): A case study of Gongqing Forest Park in Shanghai, China].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {30}, number = {2}, pages = {439-448}, doi = {10.13287/j.1001-9332.201902.011}, pmid = {30915794}, issn = {1001-9332}, mesh = {China ; Community Participation ; *Ecosystem ; Forests ; *Geographic Information Systems ; }, abstract = {Quantitative evaluation of ecosystem service value and its spatial mapping is an effective way to determine priority conservation areas of cultural ecosystem services (CES). We used a combination of questionnaires and structured interviews with public participatory GIS (PPGIS) in Gongqing Forest Park in Shanghai to connect non-monetary CES values with spatially explicit information. This method applied spatial indicators of abundance, diversity and rarity to quantitatively assess the value of CES and their spatial distribution, and identified priority CES areas. The results showed the value of CES varied among landscape types. Relatively open grassland, riverside, and shrub areas were associated with high aesthetic value. Riverside areas were associated with the CES category concerned with inspiration and supporting social relationships. High diversity values mainly distributed in riverside areas, while forest and grassland areas were associated with high rarity values. The areas with the highest values for the abundance, diversity, and rarity indices were overlaid with eight gradient thresholds, which indicated that defining the 25% of ecological areas with the highest overall rating as CES priority areas was an effective threshold for CES identification and management. The methodology in this study leveraged PPGIS to spatially refe-rence, quantify, and user perception to establish relationships between landscape attributes, space, and experience. These results could provide an important basis for identifying, planning for, and managing priority conservation areas in urban protected areas.}, } @article {pmid30914730, year = {2019}, author = {Tragin, M and Vaulot, D}, title = {Novel diversity within marine Mamiellophyceae (Chlorophyta) unveiled by metabarcoding.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {5190}, pmid = {30914730}, issn = {2045-2322}, mesh = {Aquatic Organisms/*classification/*genetics ; Base Sequence ; *Biodiversity ; Chlorophyta/*classification/*genetics ; *DNA Barcoding, Taxonomic ; Databases, Genetic ; Geography ; *Metagenomics ; Phylogeny ; }, abstract = {Mamiellophyceae (unicellular green algae) are a key phytoplankton group in coastal waters. Although extensively studied over the last 20 years, the overall oceanic distribution of the major species/clades is still poorly known. To address this problem, we analyzed the 2014 Ocean Sampling Day (OSD) metabarcoding dataset providing sequences from the V4 hypervariable region of the 18S rRNA gene for 157 samples collected at 143 mostly coastal stations. Mamiellophyceae were found at nearly all OSD stations and represented 55% of the green microalgae (Chlorophyta) reads. We performed phylogenetic analyses of unique OSD metabarcodes (amplicon single variants, ASVs) and GenBank reference sequences from cultures and from the environment, focusing on the four most represented genera: Ostreococcus (45% of the Mamiellophyceae reads), Micromonas (34%), Bathycoccus (10%) and Mantoniella (8.7%). These analyses uncovered novel diversity within each genus except Bathycoccus. In Ostreococcus, a new clade (E) was the second most represented clade after Ostreococcus "lucimarinus". Micromonas could be separated into nine clades, exceeding the six species and candidate species already described. Finally, we found two new environmental clades within Mantoniella. Each Mamiellophyceae clade had a specific distribution in the OSD dataset suggesting that they are adapted to different ecological niches.}, } @article {pmid30912762, year = {2019}, author = {Bangerter, A and Manyakov, NV and Lewin, D and Boice, M and Skalkin, A and Jagannatha, S and Chatterjee, M and Dawson, G and Goodwin, MS and Hendren, R and Leventhal, B and Shic, F and Ness, S and Pandina, G}, title = {Caregiver Daily Reporting of Symptoms in Autism Spectrum Disorder: Observational Study Using Web and Mobile Apps.}, journal = {JMIR mental health}, volume = {6}, number = {3}, pages = {e11365}, pmid = {30912762}, issn = {2368-7959}, abstract = {BACKGROUND: Currently, no medications are approved to treat core symptoms of autism spectrum disorder (ASD). One barrier to ASD medication development is the lack of validated outcome measures able to detect symptom change. Current ASD interventions are often evaluated using retrospective caregiver reports that describe general clinical presentation but often require recall of specific behaviors weeks after they occur, potentially reducing accuracy of the ratings. My JAKE, a mobile and Web-based mobile health (mHealth) app that is part of the Janssen Autism Knowledge Engine-a dynamically updated clinical research system-was designed to help caregivers of individuals with ASD to continuously log symptoms, record treatments, and track progress, to mitigate difficulties associated with retrospective reporting.

OBJECTIVE: My JAKE was deployed in an exploratory, noninterventional clinical trial to evaluate its utility and acceptability to monitor clinical outcomes in ASD. Hypotheses regarding relationships among daily tracking of symptoms, behavior, and retrospective caregiver reports were tested.

METHODS: Caregivers of individuals with ASD aged 6 years to adults (N=144) used the My JAKE app to make daily reports on their child's sleep quality, affect, and other self-selected specific behaviors across the 8- to 10-week observational study. The results were compared with commonly used paper-and-pencil scales acquired over a concurrent period at regular 4-week intervals.

RESULTS: Caregiver reporting of behaviors in real time was successfully captured by My JAKE. On average, caregivers made reports 2-3 days per week across the study period. Caregivers were positive about their use of the system, with over 50% indicating that they would like to use My JAKE to track behavior outside of a clinical trial. More positive average daily reporting of overall type of day was correlated with 4 weekly reports of lower caregiver burden made at 4-week intervals (r=-0.27, P=.006, n=88) and with ASD symptoms (r=-0.42, P<.001, n=112).

CONCLUSIONS: My JAKE reporting aligned with retrospective Web-based or paper-and-pencil scales. Use of mHealth apps, such as My JAKE, has the potential to increase the validity and accuracy of caregiver-reported outcomes and could be a useful way of identifying early changes in response to intervention. Such systems may also assist caregivers in tracking symptoms and behavior outside of a clinical trial, help with personalized goal setting, and monitoring of progress, which could collectively improve understanding of and quality of life for individuals with ASD and their families.

TRIAL REGISTRATION: ClinicalTrials.gov NCT02668991; https://clinicaltrials.gov/ct2/show/NCT02668991.}, } @article {pmid30912756, year = {2019}, author = {Manini, TM and Mendoza, T and Battula, M and Davoudi, A and Kheirkhahan, M and Young, ME and Weber, E and Fillingim, RB and Rashidi, P}, title = {Perception of Older Adults Toward Smartwatch Technology for Assessing Pain and Related Patient-Reported Outcomes: Pilot Study.}, journal = {JMIR mHealth and uHealth}, volume = {7}, number = {3}, pages = {e10044}, pmid = {30912756}, issn = {2291-5222}, support = {P30 AG028740/AG/NIA NIH HHS/United States ; R21 AG059207/AG/NIA NIH HHS/United States ; }, mesh = {Aged ; Aged, 80 and over ; Female ; Focus Groups/methods ; Humans ; Male ; Mobile Applications/*standards/statistics & numerical data ; Pain Measurement/*methods/standards ; Patient Reported Outcome Measures ; *Perception ; Pilot Projects ; Qualitative Research ; Technology Assessment, Biomedical/methods ; }, abstract = {BACKGROUND: Chronic pain, including arthritis, affects about 100 million adults in the United States. Complexity and diversity of the pain experience across time and people and its fluctuations across and within days show the need for valid pain reports that do not rely on patient's long-term recall capability. Smartwatches can be used as digital ecological momentary assessment (EMA) tools for real-time collection of pain scores. Smartwatches are generally less expensive than smartphones, are highly portable, and have a simpler user interface, providing an excellent medium for continuous data collection and enabling a higher compliance rate.

OBJECTIVE: The aim of this study was to explore the attitudes and perceptions of older adults towards design and technological aspects of a smartwatch framework for measuring patient report outcomes (PRO) as an EMA tool.

METHODS: A focus group session was conducted to explore the perception of participants towards smartwatch technology and its utility for PRO assessment. Participants included older adults (age 65+), with unilateral or bilateral symptomatic knee osteoarthritis. A preliminary user interface with server communication capability was developed and deployed on 10 Samsung Gear S3 smartwatches and provided to the users during the focus group. Pain was designated as the main PRO, while fatigue, mood, and sleep quality were included as auxiliary PROs. Pre-planned topics included participants' attitude towards the smartwatch technology, usability of the custom-designed app interface, and suitability of the smartwatch technology for PRO assessment. Discussions were transcribed, and content analysis with theme characterization was performed to identify and code the major themes.

RESULTS: We recruited 19 participants (age 65+) who consented to take part in the focus group study. The overall attitude of the participants toward the smartwatch technology was positive. They showed interest in the direct phone-call capability, availability of extra apps such as the weather apps and sensors for tracking health and wellness such as accelerometer and heart rate sensor. Nearly three-quarters of participants showed willingness to participate in a one-year study to wear the watch daily. Concerns were raised regarding usability, including accessibility (larger icons), notification customization, and intuitive interface design (unambiguous icons and assessment scales). Participants expressed interest in using smartwatch technology for PRO assessment and the availability of methods for sharing data with health care providers.

CONCLUSIONS: All participants had overall positive views of the smartwatch technology for measuring PROs to facilitate patient-provider communications and to provide more targeted treatments and interventions in the future. Usability concerns were the major issues that will require special consideration in future smartwatch PRO user interface designs, especially accessibility issues, notification design, and use of intuitive assessment scales.}, } @article {pmid30910089, year = {2019}, author = {Chaix, E and Deléger, L and Bossy, R and Nédellec, C}, title = {Text mining tools for extracting information about microbial biodiversity in food.}, journal = {Food microbiology}, volume = {81}, number = {}, pages = {63-75}, pmid = {30910089}, issn = {1095-9998}, mesh = {Algorithms ; *Biodiversity ; Biological Ontologies ; Computational Biology/*methods ; Data Mining/*methods ; Databases, Bibliographic ; Databases, Factual ; Ecosystem ; *Food Microbiology ; Humans ; Information Services ; Information Storage and Retrieval ; Internet ; Literature ; MEDLINE ; National Library of Medicine (U.S.) ; Phenotype ; Phylogeny ; PubMed ; Software ; United States ; }, abstract = {Information on food microbial diversity is scattered across millions of scientific papers. Researchers need tools to assist their bibliographic search in such large collections. Text mining and knowledge engineering methods are useful to automatically and efficiently find relevant information in Life Science. This work describes how the Alvis text mining platform has been applied to a large collection of PubMed abstracts of scientific papers in the food microbiology domain. The information targeted by our work is microorganisms, their habitats and phenotypes. Two knowledge resources, the NCBI taxonomy and the OntoBiotope ontology were used to detect this information in texts. The result of the text mining process was indexed and is presented through the AlvisIR Food on-line semantic search engine. In this paper, we also show through two illustrative examples the great potential of this new tool to assist in studies on ecological diversity and the origin of microbial presence in food.}, } @article {pmid30908812, year = {2019}, author = {Coady, K and Browne, P and Embry, M and Hill, T and Leinala, E and Steeger, T and Maślankiewicz, L and Hutchinson, T}, title = {When Are Adverse Outcome Pathways and Associated Assays "Fit for Purpose" for Regulatory Decision-Making and Management of Chemicals?.}, journal = {Integrated environmental assessment and management}, volume = {15}, number = {4}, pages = {633-647}, pmid = {30908812}, issn = {1551-3793}, support = {//funding support from the Society of Environmental Toxicology and Chemistry, United States Environmental Protection Agency, American Cleaning Institute, Cefic-LRI (European Chemical Industry Council Long-Range Research Initiative), Chevron-Environmental, ECETOC (European Center for Ecotoxicology and Toxicology of Chemicals), European Commission Joint Research Centre, European Crop Protection, ExxonMobil, Health and Environmental Sciences Institute, Humane Society International, The Humane Society/ ; }, mesh = {Adverse Outcome Pathways/*statistics & numerical data ; Databases, Factual/statistics & numerical data ; Decision Making ; Ecotoxicology/*methods ; Environmental Policy/*legislation & jurisprudence ; *Government Regulation ; *Hazardous Substances ; Humans ; Risk Assessment/methods ; }, abstract = {There have been increasing demands for chemical hazard and risk assessments in recent years. Chemical companies have expanded internal product stewardship initiatives, and jurisdictions have increased the regulatory requirements for the manufacture and sale of chemicals. There has also been a shift in chemical toxicity evaluations within the same time frame, with new methodologies being developed to improve chemical safety assessments for both human health and the environment. With increased needs for chemical assessments coupled with more diverse data streams from new technologies, regulators and others tasked with chemical management activities are faced with increasing workloads and more diverse types of data to consider. The Adverse Outcome Pathway (AOP) framework can be applied in different scenarios to integrate data and guide chemical assessment and management activities. In this paper, scenarios of how AOPs can be used to guide chemical management decisions during research and development, chemical registration, and subsequent regulatory activities such as prioritization and risk assessment are considered. Furthermore, specific criteria (e.g., the type and level of AOP complexity, confidence in the AOP, as well as external review and assay validation) are proposed to examine whether AOPs and associated tools are fit for purpose when applied in different contexts. Certain toxicity pathways are recommended as priority areas for AOP research and development, and the continued use of AOPs and defined approaches in regulatory activities are recommended. Furthermore, a call for increased outreach, education, and enhanced use of AOP databases is proposed to increase their utility in chemicals management. Integr Environ Assess Manag 2019;15:633-647. © 2019 The Authors. Integrated Environmental Assessment and Management published by Wiley Periodicals, Inc. on behalf of Society of Environmental Toxicology & Chemistry (SETAC).}, } @article {pmid30903698, year = {2019}, author = {Iida, J and Desaki, Y and Hata, K and Uemura, T and Yasuno, A and Islam, M and Maffei, ME and Ozawa, R and Nakajima, T and Galis, I and Arimura, GI}, title = {Tetranins: new putative spider mite elicitors of host plant defense.}, journal = {The New phytologist}, volume = {224}, number = {2}, pages = {875-885}, doi = {10.1111/nph.15813}, pmid = {30903698}, issn = {1469-8137}, mesh = {Agrobacterium tumefaciens ; Animals ; Calcium ; Databases, Genetic ; Female ; Gene Expression Regulation ; Phaseolus/immunology/*parasitology ; Plant Diseases/immunology/*parasitology ; Plant Leaves/immunology/parasitology ; Reactive Oxygen Species ; Solanum melongena/immunology/*parasitology ; Tetranychidae/*physiology ; }, abstract = {The two-spotted spider mite (Tetranychus urticae) is a plant-sucking arthropod herbivore that feeds on a wide array of cultivated plants. In contrast to the well-characterized classical chewing herbivore salivary elicitors that promote plant defense responses, little is known about sucking herbivores' elicitors. To characterize the sucking herbivore elicitors, we explored putative salivary gland proteins of spider mites by using an Agrobacterium-mediated transient expression system or protein infiltration in damaged bean leaves. Two candidate elicitors (designated as tetranin1 (Tet1) and tetranin2 (Tet2)) triggered early leaf responses (cytosolic calcium influx and membrane depolarization) and increased the transcript abundances of defense genes in the leaves, eventually resulting in reduced survivability of T. urticae on the host leaves as well as induction of indirect plant defenses by attracting predatory mites. Tet1 and/or Tet2 also induced jasmonate, salicylate and abscisic acid biosynthesis. Notably, Tet2-induced signaling cascades were also activated via the generation of reactive oxygen species. The signaling cascades of these two structurally dissimilar elicitors are mostly overlapping but partially distinct and thus they would coordinate the direct and indirect defense responses in host plants under spider mite attack in both shared and distinct manners.}, } @article {pmid30902616, year = {2019}, author = {Han, BA and Majumdar, S and Calmon, FP and Glicksberg, BS and Horesh, R and Kumar, A and Perer, A and von Marschall, EB and Wei, D and Mojsilović, A and Varshney, KR}, title = {Confronting data sparsity to identify potential sources of Zika virus spillover infection among primates.}, journal = {Epidemics}, volume = {27}, number = {}, pages = {59-65}, doi = {10.1016/j.epidem.2019.01.005}, pmid = {30902616}, issn = {1878-0067}, mesh = {Animals ; Bayes Theorem ; Humans ; Primates/*virology ; Risk ; Zika Virus/*pathogenicity ; Zika Virus Infection/*epidemiology/pathology ; Zoonoses/*epidemiology/pathology/*virology ; }, abstract = {The recent Zika virus (ZIKV) epidemic in the Americas ranks among the largest outbreaks in modern times. Like other mosquito-borne flaviviruses, ZIKV circulates in sylvatic cycles among primates that can serve as reservoirs of spillover infection to humans. Identifying sylvatic reservoirs is critical to mitigating spillover risk, but relevant surveillance and biological data remain limited for this and most other zoonoses. We confronted this data sparsity by combining a machine learning method, Bayesian multi-label learning, with a multiple imputation method on primate traits. The resulting models distinguished flavivirus-positive primates with 82% accuracy and suggest that species posing the greatest spillover risk are also among the best adapted to human habitations. Given pervasive data sparsity describing animal hosts, and the virtual guarantee of data sparsity in scenarios involving novel or emerging zoonoses, we show that computational methods can be useful in extracting actionable inference from available data to support improved epidemiological response and prevention.}, } @article {pmid30902045, year = {2019}, author = {Du, H and Li, X and Ning, L and Qin, R and Du, Q and Wang, Q and Song, H and Huang, F and Wang, H and Yu, D}, title = {RNA-Seq analysis reveals transcript diversity and active genes after common cutworm (Spodoptera litura Fabricius) attack in resistant and susceptible wild soybean lines.}, journal = {BMC genomics}, volume = {20}, number = {1}, pages = {237}, pmid = {30902045}, issn = {1471-2164}, support = {31671715//National Natural Science Foundation of China/ ; 31701453//National Natural Science Foundation of China/ ; Y0201600116//Fundamental Research Funds for the Central Universities/ ; 2016ZX08004-003//Key Transgenic Breeding Program of China/ ; BK20160584//Natural Science Foundation of Jiangsu Provence/ ; }, mesh = {Animals ; Gene Expression Profiling ; Gene Ontology ; *Genetic Variation ; RNA, Messenger/genetics ; *Sequence Analysis, RNA ; Glycine max/*genetics/immunology ; Spodoptera/*physiology ; Transcription Factors/genetics ; }, abstract = {BACKGROUND: Common cutworm (CCW) is highly responsible for destabilizing soybean productivity. Wild soybean is a resource used by breeders to discover elite defensive genes.

RESULTS: The transcriptomes of two wild accessions (W11 and W99) with different resistance to CCW were analyzed at early- and late-induction time points. After induction, the susceptible accession W11 differentially expressed 1268 and 508 genes at the early and late time points, respectively. Compared with W11, the resistant accession W99 differentially expressed 1270 genes at the early time point and many more genes (2308) at the late time point. In total, 3836 non-redundant genes were identified in both lines. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses revealed that the differentially expressed genes (DEGs) in W99 at the late time point were mostly associated with specific processes and pathways. Among the non-redundant genes, 146 genes were commonly up-regulated in the treatment condition compared with the control condition at the early- and late-induction time points in both accessions used in this experiment. Approximately 40% of the common DEGs were related to secondary metabolism, disease resistance, and signal transduction based on their putative function. Excluding the common DEGs, W99 expressed more unique DEGs than W11. Further analysis of the 3836 DEGs revealed that the induction of CCW not only up-regulated defense-related genes, including 37 jasmonic acid (JA)-related genes, 171 plant-pathogen-related genes, and 17 genes encoding protease inhibitors, but also down-regulated growth-related genes, including 35 photosynthesis-related genes, 48 nutrition metabolism genes, and 28 auxin metabolism genes. Therefore, representative defense-related and growth-related genes were chosen for binding site prediction via co-expression of transcription factors (TFs) and spatial expression pattern analyses. In total, 53 binding sites of 28 TFs were identified based on 3 defense-related genes and 3 growth-related genes. Phosphate transporter PT1, which is a representative growth-related gene, was transformed into soybean, and the transgenic soybean plants were susceptible to CCW.

CONCLUSIONS: In summary, we described transcriptome reprograming after herbivore induction in wild soybean, identified the susceptibility of growth-related genes, and provided new resources for the breeding of herbivore-resistant cultivated soybeans.}, } @article {pmid30898326, year = {2019}, author = {Kmiec, J and Suffoletto, B}, title = {Implementations of a text-message intervention to increase linkage from the emergency department to outpatient treatment for substance use disorders.}, journal = {Journal of substance abuse treatment}, volume = {100}, number = {}, pages = {39-44}, pmid = {30898326}, issn = {1873-6483}, support = {K23 AA023284/AA/NIAAA NIH HHS/United States ; R01 AA023650/AA/NIAAA NIH HHS/United States ; }, mesh = {Adult ; *Ambulatory Care/organization & administration ; *Ecological Momentary Assessment ; *Emergency Service, Hospital/organization & administration ; Female ; Humans ; Male ; Middle Aged ; *Outcome Assessment, Health Care ; *Patient Acceptance of Health Care ; *Reminder Systems ; Retrospective Studies ; Substance-Related Disorders/*therapy ; *Text Messaging ; }, abstract = {AIM: To determine acceptability and explore potential usefulness of a text messaging (SMS) program aimed at increasing attendance at outpatient treatment for substance use disorders (SUD) after emergency department (ED) referral.

METHOD: A retrospective analysis of 377 adult patients from 2 urban EDs seeking treatment for SUD (opioids (n = 168), alcohol (n = 188), benzodiazepines (n = 21)) referred to outpatient treatment and offered an SMS program which included daily (1) motivational messages focused on positive thinking, (2) ecological momentary assessments (EMA) related to craving with tailored behavioral strategy messages, (3) EMA of drug use with tailored feedback to reduce abstinence violation effects, and (4) reminders about treatment location and phone number. We assessed acceptability by examining opt-in rates, EMA completion rates over the first week and end-of-program qualitative feedback. We assessed how individuals who opt in differ in outcomes from those who opt out by examining rates of outpatient SUD treatment attendance recorded from the medical record.

RESULTS: 167 patients (44%) opted in to the SMS program. Over 7 days, around 33% of EMA were completed. Median helpfulness score was 8 (IQR 6 to 10) out of 10 and 84% would recommend the SMS program to someone else. Individuals who opted in to the SMS program had higher rates of SUD treatment initiation than individuals who did not opt-in (70.7% vs. 40.9%).

CONCLUSIONS: We found evidence supporting acceptability and potential usefulness of an automated text message program to assist treatment attendance for some individuals with SUDs discharged from the ED. A controlled trial is needed to examine whether SMS program exposure is associated with improved treatment attendance compared to standard care.}, } @article {pmid30897417, year = {2019}, author = {Szabó, B and Lang, Z and Bakonyi, G and Mariën, J and Roelofs, D and van Gestel, CAM and Seres, A}, title = {Transgenerational and multigenerational stress gene responses to the insecticide etofenprox in Folsomia candida (Collembola).}, journal = {Ecotoxicology and environmental safety}, volume = {175}, number = {}, pages = {181-191}, doi = {10.1016/j.ecoenv.2019.03.052}, pmid = {30897417}, issn = {1090-2414}, mesh = {Acclimatization ; Animals ; Arthropods/*drug effects/genetics/metabolism ; Electron Transport Complex IV/genetics/metabolism ; *Epigenesis, Genetic ; *Gene Expression Regulation ; HSP70 Heat-Shock Proteins/genetics/metabolism ; Insecticides/*adverse effects ; Pyrethrins/*adverse effects ; Reproduction/drug effects ; Soil ; }, abstract = {Insecticide exposure may cause both transgenerational and multigenerational effects on populations, but the molecular mechanisms of these changes remain largely unclear. Many studies have focused on either transgenerational or multigenerational mechanisms but did neglect the comparative aspects. This study assessed whether the pyrethroid insecticide etofenprox (formulation Trebon[®] 30 EC) shows transgenerational and/or multigenerational effects on the survival and reproduction of Folsomia candida (Collembola). The activation of stress-related genes was studied to detect whether etofenprox modifies the expression of reproduction-associated genes in trans- and multigenerational treatments. A laboratory study was carried out for three generations with five insecticide concentrations in LUFA 2.2 soil. In the transgenerational treatment, only the parent generation (P) was exposed, but the subsequent generations were not. In the multigenerational treatment, all three generations were exposed to the insecticide in the same manner. Multigenerational exposure resulted in reduced reproduction effects over generations, suggesting that F. candida is capable of acclimating to enhanced concentration levels of etofenprox during prolonged exposure over multiple generations. In the transgenerational treatment, the heat shock protein 70 was up-regulated and cytochrome oxidase 6N4v1 expression down-regulated in a dose-dependent manner in the F2 generation. This finding raises the possibility of the epigenetic inheritance of insecticide impacts on parents. Furthermore, CYP6N4v1 expression was oppositely regulated in the trans- and multigenerational treatments. Our results draw attention to the differences in molecular level responses of F. candida to trans- and multigenerational etofenprox exposure.}, } @article {pmid30895926, year = {2019}, author = {Sohail, M and Maier, RM and Ganna, A and Bloemendal, A and Martin, AR and Turchin, MC and Chiang, CW and Hirschhorn, J and Daly, MJ and Patterson, N and Neale, B and Mathieson, I and Reich, D and Sunyaev, SR}, title = {Polygenic adaptation on height is overestimated due to uncorrected stratification in genome-wide association studies.}, journal = {eLife}, volume = {8}, number = {}, pages = {}, pmid = {30895926}, issn = {2050-084X}, support = {GM100233/NH/NIH HHS/United States ; Investigator/HHMI/Howard Hughes Medical Institute/United States ; Sloan Research Fellowship//Alfred P. Sloan Foundation/International ; R01 GM100233/GM/NIGMS NIH HHS/United States ; New Investigator Research Grant//Charles E Kaufman Foundation/International ; R01 HG006399/HG/NHGRI NIH HHS/United States ; Allen Discovery Center//Paul Allen Foundation/International ; R01 DK075787/DK/NIDDK NIH HHS/United States ; R35 GM127131/GM/NIGMS NIH HHS/United States ; MH101244/NH/NIH HHS/United States ; GM127131/NH/NIH HHS/United States ; R01 MH101244/MH/NIMH NIH HHS/United States ; U01 HG009088/HG/NHGRI NIH HHS/United States ; HG009088/NH/NIH HHS/United States ; HG006399/NH/NIH HHS/United States ; }, mesh = {Adaptation, Biological ; Biostatistics ; *Body Height ; Computational Biology/*methods ; Databases, Factual ; Genome-Wide Association Study/*methods ; Humans ; *Multifactorial Inheritance ; Phylogeny ; Polymorphism, Single Nucleotide ; United Kingdom ; }, abstract = {UNLABELLED: Genetic predictions of height differ among human populations and these differences have been interpreted as evidence of polygenic adaptation. These differences were first detected using SNPs genome-wide significantly associated with height, and shown to grow stronger when large numbers of sub-significant SNPs were included, leading to excitement about the prospect of analyzing large fractions of the genome to detect polygenic adaptation for multiple traits. Previous studies of height have been based on SNP effect size measurements in the GIANT Consortium meta-analysis. Here we repeat the analyses in the UK Biobank, a much more homogeneously designed study. We show that polygenic adaptation signals based on large numbers of SNPs below genome-wide significance are extremely sensitive to biases due to uncorrected population stratification. More generally, our results imply that typical constructions of polygenic scores are sensitive to population stratification and that population-level differences should be interpreted with caution.

EDITORIAL NOTE: This article has been through an editorial process in which the authors decide how to respond to the issues raised during peer review. The Reviewing Editor's assessment is that all the issues have been addressed (see decision letter).}, } @article {pmid30895923, year = {2019}, author = {Berg, JJ and Harpak, A and Sinnott-Armstrong, N and Joergensen, AM and Mostafavi, H and Field, Y and Boyle, EA and Zhang, X and Racimo, F and Pritchard, JK and Coop, G}, title = {Reduced signal for polygenic adaptation of height in UK Biobank.}, journal = {eLife}, volume = {8}, number = {}, pages = {}, pmid = {30895923}, issn = {2050-084X}, support = {Fellowship//Stanford Center for Computational, Evolutionary and Human Genomics/International ; R01 HG008140/HG/NHGRI NIH HHS/United States ; F32 GM126787/NH/NIH HHS/United States ; R01 GM115889/NH/NIH HHS/United States ; R01 GM121372/GM/NIGMS NIH HHS/United States ; Graduate Fellowship//Stanford University/International ; National Defense Science and Engineering Gran//U.S. Department of Defense/International ; F32 GM126787/GM/NIGMS NIH HHS/United States ; R01 GM108779/GM/NIGMS NIH HHS/United States ; National Defense Science and Engineering Grant//U.S. Department of Defense/International ; T32 HG000044/HG/NHGRI NIH HHS/United States ; R01 GM121372/NH/NIH HHS/United States ; R01 GM108779/NH/NIH HHS/United States ; Young Investigator award//Villum Fonden/International ; R01 HG008140/NH/NIH HHS/United States ; R01 GM115889/GM/NIGMS NIH HHS/United States ; }, mesh = {*Adaptation, Biological ; Biostatistics ; *Body Height ; Databases, Factual ; Europe ; Humans ; *Multifactorial Inheritance ; *Selection, Genetic ; }, abstract = {UNLABELLED: Several recent papers have reported strong signals of selection on European polygenic height scores. These analyses used height effect estimates from the GIANT consortium and replication studies. Here, we describe a new analysis based on the the UK Biobank (UKB), a large, independent dataset. We find that the signals of selection using UKB effect estimates are strongly attenuated or absent. We also provide evidence that previous analyses were confounded by population stratification. Therefore, the conclusion of strong polygenic adaptation now lacks support. Moreover, these discrepancies highlight (1) that methods for correcting for population stratification in GWAS may not always be sufficient for polygenic trait analyses, and (2) that claims of differences in polygenic scores between populations should be treated with caution until these issues are better understood.

EDITORIAL NOTE: This article has been through an editorial process in which the authors decide how to respond to the issues raised during peer review. The Reviewing Editor's assessment is that all the issues have been addressed (see decision letter).}, } @article {pmid30894750, year = {2019}, author = {Whitehouse, H and François, P and Savage, PE and Currie, TE and Feeney, KC and Cioni, E and Purcell, R and Ross, RM and Larson, J and Baines, J and Ter Haar, B and Covey, A and Turchin, P}, title = {Complex societies precede moralizing gods throughout world history.}, journal = {Nature}, volume = {568}, number = {7751}, pages = {226-229}, pmid = {30894750}, issn = {1476-4687}, mesh = {Databases, Factual ; *Geographic Mapping ; History, Ancient ; Humans ; *Morals ; Religion/*history ; Social Sciences ; }, abstract = {The origins of religion and of complex societies represent evolutionary puzzles[1-8]. The 'moralizing gods' hypothesis offers a solution to both puzzles by proposing that belief in morally concerned supernatural agents culturally evolved to facilitate cooperation among strangers in large-scale societies[9-13]. Although previous research has suggested an association between the presence of moralizing gods and social complexity[3,6,7,9-18], the relationship between the two is disputed[9-13,19-24], and attempts to establish causality have been hampered by limitations in the availability of detailed global longitudinal data. To overcome these limitations, here we systematically coded records from 414 societies that span the past 10,000 years from 30 regions around the world, using 51 measures of social complexity and 4 measures of supernatural enforcement of morality. Our analyses not only confirm the association between moralizing gods and social complexity, but also reveal that moralizing gods follow-rather than precede-large increases in social complexity. Contrary to previous predictions[9,12,16,18], powerful moralizing 'big gods' and prosocial supernatural punishment tend to appear only after the emergence of 'megasocieties' with populations of more than around one million people. Moralizing gods are not a prerequisite for the evolution of social complexity, but they may help to sustain and expand complex multi-ethnic empires after they have become established. By contrast, rituals that facilitate the standardization of religious traditions across large populations[25,26] generally precede the appearance of moralizing gods. This suggests that ritual practices were more important than the particular content of religious belief to the initial rise of social complexity.}, } @article {pmid30894575, year = {2019}, author = {Unmack, PJ and Adams, M and Bylemans, J and Hardy, CM and Hammer, MP and Georges, A}, title = {Perspectives on the clonal persistence of presumed 'ghost' genomes in unisexual or allopolyploid taxa arising via hybridization.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {4730}, pmid = {30894575}, issn = {2045-2322}, mesh = {Animals ; Clone Cells ; DNA, Mitochondrial ; Databases, Nucleic Acid ; Fishes ; Genome/*genetics ; *Hybridization, Genetic ; Isoenzymes ; Perciformes/*genetics ; *Phylogeny ; Polymorphism, Single Nucleotide ; *Polyploidy ; }, abstract = {Although hybridization between non-sibling species rarely results in viable or fertile offspring, it occasionally produces self-perpetuating or sexually-parasitic lineages in which ancestral genomes are inherited clonally and thus may persist as 'ghost species' after ancestor extinction. Ghost species have been detected in animals and plants, for polyploid and diploid organisms, and across clonal, semi-clonal, and even sexual reproductive modes. Here we use a detailed investigation of the evolutionary and taxonomic status of a newly-discovered, putative ghost lineage (HX) in the fish genus Hypseleotris to provide perspectives on several important issues not previously explored by other studies on ghost species, but relevant to ongoing discussions about their detection, conservation, and artificial re-creation. Our comprehensive genetic (allozymes, mtDNA) and genomic (SNPs) datasets successfully identified a threatened sexual population of HX in one tiny portion of the extensive distribution displayed by two hemi-clonal HX-containing lineages. We also discuss what confidence should be placed on any assertion that an ancestral species is actually extinct, and how to assess whether any putative sexual ancestor represents a pure remnant, as shown here, or a naturally-occurring resurrection via the crossing of compatible clones or hemi-clones.}, } @article {pmid30894330, year = {2019}, author = {Talamantes-Becerra, B and Carling, J and Kennedy, K and Gahan, ME and Georges, A}, title = {Identification of bacterial isolates from a public hospital in Australia using complexity-reduced genotyping.}, journal = {Journal of microbiological methods}, volume = {160}, number = {}, pages = {11-19}, doi = {10.1016/j.mimet.2019.03.016}, pmid = {30894330}, issn = {1872-8359}, mesh = {Australia ; *Bacteria/classification/isolation & purification ; Bacterial Typing Techniques/*methods ; Databases, Nucleic Acid ; Genome, Bacterial/genetics ; Hospitals, Public ; Humans ; Sequence Analysis, DNA/methods ; }, abstract = {Bacterial identification methods used in routine identification of pathogens in medical microbiology include a combination approach of biochemical tests, mass spectrometry or molecular biology techniques. Extensive publicly-available databases of DNA sequence data from pathogenic bacteria have been amassed in recent years; this provides an opportunity for using bacterial genome sequencing for identification purposes. Whole genome sequencing is increasing in popularity, although at present it remains a relatively expensive approach to bacterial identification and typing. Complexity-reduced bacterial genome sequencing provides an alternative. We evaluate genomic complexity-reduction using restriction enzymes and sequencing to identify bacterial isolates. A total of 165 bacterial isolates from hospital patients in the Australian Capital Territory, between 2013 and 2015 were used in this study. They were identified and typed by the Microbiology Department of Canberra Public Hospital, and represented 14 bacterial species. DNA extractions from these samples were processed using a combination of the restriction enzymes PstI with MseI, PstI with HpaII and MseI with HpaII. The resulting sequences (length 30-69 bp) were aligned against publicly available bacterial genome and plasmid sequences. Results of the alignment were processed using a bioinformatics pipeline developed for this project, Currito3.1 DNA Fragment Analysis Software. All 165 samples were correctly identified to genus and species by each of the three combinations of restriction enzymes. A further 35 samples typed to the level of strain identified and compared for consistency with MLST typing data and in silico MLST data derived from the nearest sequenced candidate reference. The high level of agreement between bacterial identification using complexity-reduced genome sequencing and standard hospital identifications indicating that this new approach is a viable alternative for identification of bacterial isolates derived from pathology specimens. The effectiveness of species identification and in particular, strain typing, depends on access to a comprehensive and taxonomically accurate bacterial genome sequence database containing relevant bacterial species and strains.}, } @article {pmid30893737, year = {2019}, author = {Ramirez-Reyes, C and Brauman, KA and Chaplin-Kramer, R and Galford, GL and Adamo, SB and Anderson, CB and Anderson, C and Allington, GRH and Bagstad, KJ and Coe, MT and Cord, AF and Dee, LE and Gould, RK and Jain, M and Kowal, VA and Muller-Karger, FE and Norriss, J and Potapov, P and Qiu, J and Rieb, JT and Robinson, BE and Samberg, LH and Singh, N and Szeto, SH and Voigt, B and Watson, K and Wright, TM}, title = {Reimagining the potential of Earth observations for ecosystem service assessments.}, journal = {The Science of the total environment}, volume = {665}, number = {}, pages = {1053-1063}, doi = {10.1016/j.scitotenv.2019.02.150}, pmid = {30893737}, issn = {1879-1026}, abstract = {The benefits nature provides to people, called ecosystem services, are increasingly recognized and accounted for in assessments of infrastructure development, agricultural management, conservation prioritization, and sustainable sourcing. These assessments are often limited by data, however, a gap with tremendous potential to be filled through Earth observations (EO), which produce a variety of data across spatial and temporal extents and resolutions. Despite widespread recognition of this potential, in practice few ecosystem service studies use EO. Here, we identify challenges and opportunities to using EO in ecosystem service modeling and assessment. Some challenges are technical, related to data awareness, processing, and access. These challenges require systematic investment in model platforms and data management. Other challenges are more conceptual but still systemic; they are byproducts of the structure of existing ecosystem service models and addressing them requires scientific investment in solutions and tools applicable to a wide range of models and approaches. We also highlight new ways in which EO can be leveraged for ecosystem service assessments, identifying promising new areas of research. More widespread use of EO for ecosystem service assessment will only be achieved if all of these types of challenges are addressed. This will require non-traditional funding and partnering opportunities from private and public agencies to promote data exploration, sharing, and archiving. Investing in this integration will be reflected in better and more accurate ecosystem service assessments worldwide.}, } @article {pmid30892517, year = {2019}, author = {Tanaka, OY and Drumond Júnior, M and Gontijo, TL and Louvison, MCP and Rosa, TEC}, title = {Arterial hypertension as a tracer for the evaluation of access to health care.}, journal = {Ciencia & saude coletiva}, volume = {24}, number = {3}, pages = {963-972}, doi = {10.1590/1413-81232018243.07312017}, pmid = {30892517}, issn = {1678-4561}, mesh = {Brazil ; Databases, Factual ; Delivery of Health Care/*organization & administration ; *Health Services Accessibility ; Humans ; Hypertension/*therapy ; National Health Programs/organization & administration ; *Public Health ; }, abstract = {This study evaluated the use of and access to different services involved in the care of patients with arterial hypertension in the Public Health System in the municipality of São Paulo, Brazil. This is an ecological study that addressed the magnitude, trend and relationships of outpatient procedures linked to the arterial hypertension care Data were retrieved from the SIA/SUS and the Estabsus from the Municipal Health Secretariat, and were processed with PostgreSQL relational database linking the different information by the indicators chosen and analyzed by territories. The statistical analysis were performed by the R program with the trend significance analysis of the historical series of indicators defined and the relationships between them. Essential changes in the care model were found in the period under study in São Paulo, with a declining general trend of primary medical visits and increased specialized cardiology procedures. Production was heterogeneous in the different regional coordination offices in the city. The study shows the potential use of SUS databases and it allows the identification of gaps in the access, coverage and use of high complexity services in health care for chronic conditions in the Brazilian Unified Health System (SUS).}, } @article {pmid30892468, year = {2019}, author = {Souza, TO and Souza, ER and Pinto, LW}, title = {Analysis of the quality of information on mortality by homicide from deaths with undetermined intent. Bahia, Brazil, from 2002-2013.}, journal = {Revista brasileira de epidemiologia = Brazilian journal of epidemiology}, volume = {22}, number = {}, pages = {e190005}, doi = {10.1590/1980-549720190005}, pmid = {30892468}, issn = {1980-5497}, mesh = {Brazil/epidemiology ; Cause of Death ; Data Accuracy ; *Health Information Systems ; Homicide/*statistics & numerical data ; Humans ; Residence Characteristics ; Violence/statistics & numerical data ; Wounds and Injuries/*mortality ; }, abstract = {OBJECTIVE: To identify patterns in the spatial distribution of homicide death rates, considering the proportion of deaths of undetermined intent in the municipalities of the State of Bahia, from 2002 to 2013.

METHOD: An ecological study was carried out, using data from the Mortality Information System (SIM). Theproportional mortality of undetermined intent on the total external causes and the homicide rate were analyzed in several municipalities of Bahia and considering the Health Macro-regions (HMRs).

RESULTS: A-non-random mortality distribution pattern was observed, according to the overall Moran index, which was clearer in the 2005-2007, 2008-2010 and 2011-2013 triennia. The highest proportions of undetermined deaths, ≥ 50%, were concentrated in the State's Western region. On the other hand, the highest homicide rates were observed in the Far South, South and East regions - coastal municipalities.

CONCLUSION: The same municipalities and regions identified with low homicide rates concomitantly presented high proportions of undetermined deaths, and conversely, where there were high rates, there was also a low proportion of undetermined death. Therefore,it is essential to take into account the quality of information about the underlying cause.}, } @article {pmid30891006, year = {2019}, author = {Chan, MA and Bowen, BB and Corsetti, FA and Farrand, WH and Law, ES and Newsom, HE and Spear, JR and Thompson, DR}, title = {Exploring, Mapping, and Data Management Integration of Habitable Environments in Astrobiology.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {147}, pmid = {30891006}, issn = {1664-302X}, abstract = {New approaches to blending geoscience, planetary science, microbiology-geobiology/ecology, geoinformatics and cyberinfrastructure technology disciplines in a holistic effort can be transformative to astrobiology explorations. Over the last two decades, overwhelming orbital evidence has confirmed the abundance of authigenic (in situ, formed in place) minerals on Mars. On Earth, environments where authigenic minerals form provide a substrate for the preservation of microbial life. Similarly, extraterrestrial life is likely to be preserved where crustal minerals can record and preserve the biochemical mechanisms (i.e., biosignatures). The search for astrobiological evidence on Mars has focused on identifying past or present habitable environments - places that could support some semblance of life. Thus, authigenic minerals represent a promising habitable environment where extraterrestrial life could be recorded and potentially preserved over geologic time scales. Astrobiology research necessarily takes place over vastly different scales; from molecules to viruses and microbes to those of satellites and solar system exploration, but the differing scales of analyses are rarely connected quantitatively. The mismatch between the scales of these observations- from the macro- satellite mineralogical observations to the micro- microbial observations- limits the applicability of our astrobiological understanding as we search for records of life beyond Earth. Each-scale observation requires knowledge of the geologic context and the environmental parameters important for assessing habitability. Exploration efforts to search for extraterrestrial life should attempt to quantify both the geospatial context and the temporal/spatial relationships between microbial abundance and diversity within authigenic minerals at multiple scales, while assimilating resolutions from satellite observations to field measurements to microscopic analyses. Statistical measures, computer vision, and the geospatial synergy of Geographic Information Systems (GIS), can allow analyses of objective data-driven methods to locate, map, and predict where the "sweet spots" of habitable environments occur at multiple scales. This approach of science information architecture or an "Astrobiology Information System" can provide the necessary maps to guide researchers to discoveries via testing, visualizing, documenting, and collaborating on significant data relationships that will advance explorations for evidence of life in our solar system and beyond.}, } @article {pmid30889889, year = {2019}, author = {Abuasad, S and Yildirim, A and Hashim, I and Abdul Karim, SA and Gómez-Aguilar, JF}, title = {Fractional Multi-Step Differential Transformed Method for Approximating a Fractional Stochastic SIS Epidemic Model with Imperfect Vaccination.}, journal = {International journal of environmental research and public health}, volume = {16}, number = {6}, pages = {}, pmid = {30889889}, issn = {1660-4601}, mesh = {*Data Interpretation, Statistical ; Epidemics/*prevention & control ; Humans ; Mathematics ; *Models, Statistical ; *Vaccination ; Vaccines/*administration & dosage ; }, abstract = {In this paper, we applied a fractional multi-step differential transformed method, which is a generalization of the multi-step differential transformed method, to find approximate solutions to one of the most important epidemiology and mathematical ecology, fractional stochastic SIS epidemic model with imperfect vaccination, subject to appropriate initial conditions. The fractional derivatives are described in the Caputo sense. Numerical results coupled with graphical representations indicate that the proposed method is robust and precise which can give new interpretations for various types of dynamical systems.}, } @article {pmid30889192, year = {2019}, author = {Kumar, G and Langa, J and Montes, I and Conklin, D and Kocour, M and Kohlmann, K and Estonba, A}, title = {A novel transcriptome-derived SNPs array for tench (Tinca tinca L.).}, journal = {PloS one}, volume = {14}, number = {3}, pages = {e0213992}, pmid = {30889192}, issn = {1932-6203}, mesh = {Animals ; Breeding ; Cyprinidae/classification/*genetics ; Czech Republic ; Female ; Fisheries ; Gene Ontology ; Genetic Markers ; Genetics, Population ; Genome ; Male ; Phylogeny ; Polymorphism, Single Nucleotide ; Species Specificity ; Transcriptome ; }, abstract = {Tench (Tinca tinca L.) has great economic potential due to its high rate of fecundity and long-life span. Population genetic studies based on allozymes, microsatellites, PCR-RFLP and sequence analysis of genes and DNA fragments have revealed the presence of Eastern and Western phylogroups. However, the lack of genomic resources for this species has complicated the development of genetic markers. In this study, the tench transcriptome and genome were sequenced by high-throughput sequencing. A total of 60,414 putative SNPs were identified in the tench transcriptome using a computational pipeline. A set of 96 SNPs was selected for validation and a total of 92 SNPs was validated, resulting in the highest conversion and validation rate for a non-model species obtained to date (95.83%). The validated SNPs were used to genotype 140 individuals belonging to two tench breeds (Tabor and Hungarian), showing low (FST = 0.0450) but significant (<0.0001) genetic differentiation between the two tench breeds. This implies that set of validated SNPs array can be used to distinguish the tench breeds and that it might be useful for studying a range of associations between DNA sequence and traits of importance. These genomic resources created for the tench will provide insight into population genetics, conservation fish stock management, and aquaculture.}, } @article {pmid30888231, year = {2019}, author = {Schofield, PN and Kulka, U and Tapio, S and Grosche, B}, title = {Big data in radiation biology and epidemiology; an overview of the historical and contemporary landscape of data and biomaterial archives.}, journal = {International journal of radiation biology}, volume = {95}, number = {7}, pages = {861-878}, doi = {10.1080/09553002.2019.1589026}, pmid = {30888231}, issn = {1362-3095}, mesh = {Animals ; Archives ; *Big Data ; Ecology ; Epidemiology ; History, 20th Century ; History, 21st Century ; Humans ; Information Dissemination ; Occupational Exposure ; Radiation Injuries ; Radiobiology/*history/*methods ; Reproducibility of Results ; Tissue Banks ; }, abstract = {Over the past 60 years a great number of very large datasets have been generated from the experimental exposure of animals to external radiation and internal contamination. This accumulation of 'big data' has been matched by increasingly large epidemiological studies from accidental and occupational radiation exposure, and from plants, humans and other animals affected by environmental contamination. We review the creation, sustainability and reuse of this legacy data, and discuss the importance of Open data and biomaterial archives for contemporary radiobiological sciences, radioecology and epidemiology. We find evidence for the ongoing utility of legacy datasets and biological materials, but that the availability of these resources depends on uncoordinated, often institutional, initiatives to curate and archive them. The importance of open data from contemporary experiments and studies is also very clear, and yet there are few stable platforms for their preservation, sharing, and reuse. We discuss the development of the ERA and STORE data sharing platforms for the scientific community, and their contribution to FAIR sharing of data. The contribution of funding agency and journal policies to the support of data sharing is critical for the maximum utilisation and reproducibility of publicly funded research, but this needs to be matched by training in data management and cultural changes in the attitudes of investigators to ensure the sustainability of the data and biomaterial commons.}, } @article {pmid30886704, year = {2019}, author = {Heard, KL and Hughes, S and Mughal, N and Azadian, BS and Moore, LSP}, title = {Evaluating the impact of the ICNET® clinical decision support system for antimicrobial stewardship.}, journal = {Antimicrobial resistance and infection control}, volume = {8}, number = {}, pages = {51}, pmid = {30886704}, issn = {2047-2994}, mesh = {Administration, Intravenous ; Administration, Oral ; Anti-Bacterial Agents/*administration & dosage ; Antimicrobial Stewardship/*methods ; Decision Support Systems, Clinical/*organization & administration ; Drug Prescriptions ; Humans ; Inappropriate Prescribing ; Practice Patterns, Physicians'/statistics & numerical data ; Retrospective Studies ; }, abstract = {BACKGROUND: Antimicrobial resistance (AMR) is an ecological and economic crisis and stewardship of available antimicrobials is required. Electronic prescribing, where available, enables auditing of practice, yet in order to be efficient and effective in addressing inappropriate antimicrobial prescribing, better use of current and new technological interventions is needed. This retrospective observational evaluation looked at the impact of a commercial clinical decision support system (CDSS) on the workflow of an established antimicrobial stewardship (AMS) team.

MATERIAL/METHODS: Clinical, workflow, and pharmaceutical data from 3 months post implementation of CDSS were collated, and compared to the same 3 month periods in preceding years. The evaluation considered total interventions made, the types of intervention made, impact of said interventions, and time spent executing interventions. All antimicrobial data were adjusted for total daily defined doses (DDD) of intravenous antimicrobials.

RESULTS: Productivity: In the 3 month evaluation period (Jun-Aug 2016) a total of 264 case reviews resulting in 298 AMS interventions were made. Compared to preceding years where 138 and 169 interventions were made (2013 and 2014 respectively). In 2013 49% of interventions were stopping medication and 30% change of therapy based on cultures and sensitivities compared to 25 and 17% in 2016. In contrast to previous years', the CDSS instead enabled a greater number of dose/drug optimisation (13%), escalation of antimicrobials (12%) and intravenous (IV) to oral switch (11%) interventions.Patient Identification: Despite increased patient numbers post-CDSS, on average 46 min per day was spent compiling a patient list for review, compared to 59 min in 2014. The use of CDSS facilitated 15 interventions/1000DDD, compared to pre-intervention (9.4/1000DDD in 2013; 11.5/1000DDD in 2014).

CONCLUSIONS: Initial evaluation of the impact of this CDSS on AMS at the organisation has demonstrated effectiveness in terms of case finding, AMS team productivity, and workflow auditing. More importantly, patient infection management has been optimised with a shift in the emphasis of AMS interventions. It has contributed to the success of the healthcare provider achieving nationally set remunerated AMS targets.}, } @article {pmid30886374, year = {2019}, author = {Varga, T and Krizsán, K and Földi, C and Dima, B and Sánchez-García, M and Sánchez-Ramírez, S and Szöllősi, GJ and Szarkándi, JG and Papp, V and Albert, L and Andreopoulos, W and Angelini, C and Antonín, V and Barry, KW and Bougher, NL and Buchanan, P and Buyck, B and Bense, V and Catcheside, P and Chovatia, M and Cooper, J and Dämon, W and Desjardin, D and Finy, P and Geml, J and Haridas, S and Hughes, K and Justo, A and Karasiński, D and Kautmanova, I and Kiss, B and Kocsubé, S and Kotiranta, H and LaButti, KM and Lechner, BE and Liimatainen, K and Lipzen, A and Lukács, Z and Mihaltcheva, S and Morgado, LN and Niskanen, T and Noordeloos, ME and Ohm, RA and Ortiz-Santana, B and Ovrebo, C and Rácz, N and Riley, R and Savchenko, A and Shiryaev, A and Soop, K and Spirin, V and Szebenyi, C and Tomšovský, M and Tulloss, RE and Uehling, J and Grigoriev, IV and Vágvölgyi, C and Papp, T and Martin, FM and Miettinen, O and Hibbett, DS and Nagy, LG}, title = {Megaphylogeny resolves global patterns of mushroom evolution.}, journal = {Nature ecology & evolution}, volume = {3}, number = {4}, pages = {668-678}, pmid = {30886374}, issn = {2397-334X}, mesh = {Agaricales/*genetics ; Genetic Variation ; *Genome, Fungal ; Phylogeny ; }, abstract = {Mushroom-forming fungi (Agaricomycetes) have the greatest morphological diversity and complexity of any group of fungi. They have radiated into most niches and fulfil diverse roles in the ecosystem, including wood decomposers, pathogens or mycorrhizal mutualists. Despite the importance of mushroom-forming fungi, large-scale patterns of their evolutionary history are poorly known, in part due to the lack of a comprehensive and dated molecular phylogeny. Here, using multigene and genome-based data, we assemble a 5,284-species phylogenetic tree and infer ages and broad patterns of speciation/extinction and morphological innovation in mushroom-forming fungi. Agaricomycetes started a rapid class-wide radiation in the Jurassic, coinciding with the spread of (sub)tropical coniferous forests and a warming climate. A possible mass extinction, several clade-specific adaptive radiations and morphological diversification of fruiting bodies followed during the Cretaceous and the Paleogene, convergently giving rise to the classic toadstool morphology, with a cap, stalk and gills (pileate-stipitate morphology). This morphology is associated with increased rates of lineage diversification, suggesting it represents a key innovation in the evolution of mushroom-forming fungi. The increase in mushroom diversity started during the Mesozoic-Cenozoic radiation event, an era of humid climate when terrestrial communities dominated by gymnosperms and reptiles were also expanding.}, } @article {pmid30884039, year = {2019}, author = {Piao, S and Liu, Q and Chen, A and Janssens, IA and Fu, Y and Dai, J and Liu, L and Lian, X and Shen, M and Zhu, X}, title = {Plant phenology and global climate change: Current progresses and challenges.}, journal = {Global change biology}, volume = {25}, number = {6}, pages = {1922-1940}, doi = {10.1111/gcb.14619}, pmid = {30884039}, issn = {1365-2486}, mesh = {*Climate Change ; Ecosystem ; Plant Development ; Plant Leaves/physiology ; *Plant Physiological Phenomena ; Seasons ; Temperature ; }, abstract = {Plant phenology, the annually recurring sequence of plant developmental stages, is important for plant functioning and ecosystem services and their biophysical and biogeochemical feedbacks to the climate system. Plant phenology depends on temperature, and the current rapid climate change has revived interest in understanding and modeling the responses of plant phenology to the warming trend and the consequences thereof for ecosystems. Here, we review recent progresses in plant phenology and its interactions with climate change. Focusing on the start (leaf unfolding) and end (leaf coloring) of plant growing seasons, we show that the recent rapid expansion in ground- and remote sensing- based phenology data acquisition has been highly beneficial and has supported major advances in plant phenology research. Studies using multiple data sources and methods generally agree on the trends of advanced leaf unfolding and delayed leaf coloring due to climate change, yet these trends appear to have decelerated or even reversed in recent years. Our understanding of the mechanisms underlying the plant phenology responses to climate warming is still limited. The interactions between multiple drivers complicate the modeling and prediction of plant phenology changes. Furthermore, changes in plant phenology have important implications for ecosystem carbon cycles and ecosystem feedbacks to climate, yet the quantification of such impacts remains challenging. We suggest that future studies should primarily focus on using new observation tools to improve the understanding of tropical plant phenology, on improving process-based phenology modeling, and on the scaling of phenology from species to landscape-level.}, } @article {pmid30883574, year = {2019}, author = {Giezendanner, J and Bertuzzo, E and Pasetto, D and Guisan, A and Rinaldo, A}, title = {A minimalist model of extinction and range dynamics of virtual mountain species driven by warming temperatures.}, journal = {PloS one}, volume = {14}, number = {3}, pages = {e0213775}, pmid = {30883574}, issn = {1932-6203}, mesh = {*Climate Change ; Ecosystem ; *Models, Biological ; Temperature ; }, abstract = {A longstanding question in ecology concerns the prediction of the fate of mountain species under climate change, where climatic and geomorphic factors but also endogenous species characteristics are jointly expected to control species distributions. A significant step forward would single out reliably landscape effects, given their constraining role and relative ease of theoretical manipulation. Here, we address population dynamics in ecosystems where the substrates for ecological interactions are mountain landscapes subject to climate warming. We use a minimalist model of metapopulation dynamics based on virtual species (i.e. a suitable assemblage of focus species) where dispersal processes interact with the spatial structure of the landscape. Climate warming is subsumed by an upward shift of species habitat altering the metapopulation capacity of the landscape and hence species viability. We find that the landscape structure is a powerful determinant of species survival, owing to the specific role of the predictably evolving connectivity of the various habitats. Range shifts and lags in tracking suitable habitat experienced by virtual species under warming conditions are singled out in different landscapes. The range of parameters is identified for which these virtual species (characterized by comparable viability thus restricting their possible fitnesses and niche widths) prove unable to cope with environmental change. The statistics of the proportion of species bound to survive is identified for each landscape, providing the temporal evolution of species range shifts and the related expected occupation patterns. A baseline dynamic model for predicting species fates in evolving habitats is thus provided.}, } @article {pmid30880511, year = {2020}, author = {Nyári, TA and McNally, R}, title = {Seasonal variation in childhood mortality.}, journal = {The journal of maternal-fetal & neonatal medicine : the official journal of the European Association of Perinatal Medicine, the Federation of Asia and Oceania Perinatal Societies, the International Society of Perinatal Obstetricians}, volume = {33}, number = {24}, pages = {4055-4061}, doi = {10.1080/14767058.2019.1594765}, pmid = {30880511}, issn = {1476-4954}, mesh = {Adolescent ; Child ; *Child Mortality ; Child, Preschool ; Female ; Humans ; Hungary/epidemiology ; Infant ; *Infant Mortality ; Infant, Newborn ; Male ; Pregnancy ; Regression Analysis ; Seasons ; }, abstract = {Aim: This ecological study was carried out to determine the cyclic trends in the rate of perinatal and infant mortality and among children aged under 15 years who died in traffic accidents or from drowning, respiratory disease or cancer.Methods: Monthly data on the numbers of live births, perinatal and infant deaths, and deaths from respiratory disease, cancer, traffic accidents, accidental drowning, and submersion in children aged under 15 years were obtained from the Hungarian nationwide population register. The data were aggregated over the study period and cyclic trends were investigated using the Walter-Elwood and negative binomial regression methods.Results: Significant double-peak (May and November) trends were found in mortality rates for perinatal and infant deaths, respectively. Additionally, significant (p-value < .001) seasonal variation in monthly mortality rates for deaths from respiratory diseases was observed with a peak in February, and a significant single peak was observed in mortality rates in July in both deaths from traffic accidents and drowning among children aged 0-14 years. However, there was no seasonal variation in monthly mortality rates for deaths from childhood cancer.Conclusions: Since cyclic trends in mortality suggest some effect of environmental factors in etiology, we might speculate that perinatal mortality may have been related to respiratory infections. A significant single peak was observed in mortality rates in July in both deaths from traffic accidents and drowning among children aged 0-14 years which could be related to environmental factors, such as temperature, air masses, and fronts. However, there was no seasonal variation in monthly mortality rates for deaths from childhood cancer. All of these novel findings could prove useful in preventive strategies, but further cohort studies are needed to investigate this hypothesis.What is knownSeasonality in infant mortality is known.What is newA significant cyclic trend was found in infants' mortality, with a peak in deaths in winter during the post-perinatal period and double peaks in May and November during the perinatal period, which might be associated with respiratory syncytial virus infections.Winter-peak cyclic trends were observed in both preterm and low birthweight mortality.A significant cyclic trend was observed in mortality, with a peak in deaths from traffic accidents and drowning in July for children aged 0-14 years, but seasonal variation was not found in monthly deaths from childhood cancer.}, } @article {pmid30875864, year = {2019}, author = {Uritskiy, G and DiRuggiero, J}, title = {Applying Genome-Resolved Metagenomics to Deconvolute the Halophilic Microbiome.}, journal = {Genes}, volume = {10}, number = {3}, pages = {}, pmid = {30875864}, issn = {2073-4425}, support = {T32 GM007231/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacteria/classification/genetics ; Base Composition ; Computational Biology/*methods ; High-Throughput Nucleotide Sequencing/methods ; Metagenomics/*methods ; Sequence Analysis, RNA/methods ; Whole Genome Sequencing/*methods ; }, abstract = {In the past decades, the study of microbial life through shotgun metagenomic sequencing has rapidly expanded our understanding of environmental, synthetic, and clinical microbial communities. Here, we review how shotgun metagenomics has affected the field of halophilic microbial ecology, including functional potential reconstruction, virus[-]host interactions, pathway selection, strain dispersal, and novel genome discoveries. However, there still remain pitfalls and limitations from conventional metagenomic analysis being applied to halophilic microbial communities. Deconvolution of halophilic metagenomes has been difficult due to the high G + C content of these microbiomes and their high intraspecific diversity, which has made both metagenomic assembly and binning a challenge. Halophiles are also underrepresented in public genome databases, which in turn slows progress. With this in mind, this review proposes experimental and analytical strategies to overcome the challenges specific to the halophilic microbiome, from experimental designs to data acquisition and the computational analysis of metagenomic sequences. Finally, we speculate about the potential applications of other next-generation sequencing technologies in halophilic communities. RNA sequencing, long-read technologies, and chromosome conformation assays, not initially intended for microbiomes, are becoming available in the study of microbial communities. Together with recent analytical advancements, these new methods and technologies have the potential to rapidly advance the field of halophile research.}, } @article {pmid30875367, year = {2019}, author = {Cougoul, A and Bailly, X and Vourc'h, G and Gasqui, P}, title = {Rarity of microbial species: In search of reliable associations.}, journal = {PloS one}, volume = {14}, number = {3}, pages = {e0200458}, pmid = {30875367}, issn = {1932-6203}, mesh = {Animals ; Computational Biology ; Computer Simulation ; Ecosystem ; Humans ; *Microbial Interactions ; *Microbiota ; Models, Biological ; }, abstract = {The role of microbial interactions in defining the properties of microbiota is a topic of key interest in microbial ecology. Microbiota contain hundreds to thousands of operational taxonomic units (OTUs), most of them rare. This feature of community structure can lead to methodological difficulties: simulations have shown that methods for detecting pairwise associations between OTUs, which presumably reflect interactions, yield problematic results. The performance of association detection tools is impaired when there is a high proportion of zeros in OTU tables. Our goal was to understand the impact of OTU rarity on the detection of associations. We explored the utility of common statistics for testing associations; the sensitivity of alternative association measures; and the performance of network inference tools. We found that a large proportion of pairwise associations, especially negative associations, cannot be reliably tested. This constraint could hamper the identification of candidate biological agents that could be used to control rare pathogens. Identifying testable associations could serve as an objective method for filtering datasets in lieu of current empirical approaches. This trimming strategy could significantly reduce the computational time needed to infer networks and network inference quality. Different possibilities for improving the analysis of associations within microbiota are discussed.}, } @article {pmid30874558, year = {2019}, author = {Jakobson, CM and She, R and Jarosz, DF}, title = {Pervasive function and evidence for selection across standing genetic variation in S. cerevisiae.}, journal = {Nature communications}, volume = {10}, number = {1}, pages = {1222}, pmid = {30874558}, issn = {2041-1723}, support = {DP2 GM119140/GM/NIGMS NIH HHS/United States ; F32 GM125162/GM/NIGMS NIH HHS/United States ; }, mesh = {Adaptation, Biological/*genetics ; Computational Biology ; Ecosystem ; Genotype ; Phenotype ; Phylogeny ; Polymorphism, Single Nucleotide/*genetics ; Quantitative Trait Loci/*genetics ; Saccharomyces cerevisiae/*genetics ; *Selection, Genetic ; }, abstract = {Quantitative genetics aims to map genotype to phenotype, often with the goal of understanding how organisms evolved. However, it remains unclear whether the genetic variants identified are exemplary of evolution. Here we analyzed progeny of two wild Saccharomyces cerevisiae isolates to identify 195 loci underlying complex metabolic traits, resolving 107 to single polymorphisms with diverse molecular mechanisms. More than 20% of causal variants exhibited patterns of emergence inconsistent with neutrality. Moreover, contrary to drift-centric expectation, variation in diverse wild yeast isolates broadly exhibited this property: over 30% of shared natural variants exhibited phylogenetic signatures suggesting that they are not neutral. This pattern is likely attributable to both homoplasy and balancing selection on ancestral polymorphism. Variants that emerged repeatedly were more likely to have done so in isolates from the same ecological niche. Our results underscore the power of super-resolution mapping of ecologically relevant traits in understanding adaptation and evolution.}, } @article {pmid30874304, year = {2019}, author = {Song, C and Rohr, RP and Saavedra, S}, title = {Beware z-scores.}, journal = {The Journal of animal ecology}, volume = {88}, number = {5}, pages = {808-809}, doi = {10.1111/1365-2656.12964}, pmid = {30874304}, issn = {1365-2656}, mesh = {Data Interpretation, Statistical ; *Ecology/statistics & numerical data ; }, abstract = {Song, Rohr, and Saavedra (2017) have proposed a methodology to compare network properties across systems with different sizes and constraints, in response to the fact that z-scores cannot be used for such purposes. Simmons, Hoeppke, and Sutherland (2019) have shown that part of the methodology can be improved. Here, we show that all previous results hold and are strengthened by the new methodology.}, } @article {pmid30872328, year = {2019}, author = {Mehjabin, R and Xiong, L and Huang, R and Yang, C and Chen, G and He, L and Liao, L and Zhu, Z and Wang, Y}, title = {Full-Length Transcriptome Sequencing and the Discovery of New Transcripts in the Unfertilized Eggs of Zebrafish (Danio rerio).}, journal = {G3 (Bethesda, Md.)}, volume = {9}, number = {6}, pages = {1831-1838}, pmid = {30872328}, issn = {2160-1836}, mesh = {Animals ; Cluster Analysis ; Computational Biology/methods ; Embryonic Development/genetics ; *Gene Expression Profiling ; Gene Expression Regulation, Developmental ; Genome ; Genomics/methods ; Ovum/*metabolism ; Sequence Analysis, RNA ; *Transcriptome ; *Exome Sequencing ; Zebrafish/*genetics ; }, abstract = {Understanding early gene expression in zebrafish embryos is a prerequisite for developmental biology research. In this study, 1,629,447 polymerase reads were obtained from the unfertilized eggs of zebrafish via full-length transcriptome sequencing using the PacBio RS II platform first. Then, 102,920 unique isoforms were obtained by correction, clustering and comparison with the zebrafish genome. 12,782 genes in the genome were captured, accounting for 39.71% of the all annotated genes. Approximately 62.27% of the 12,782 genes have been alternatively spliced. GO and KEGG annotations revealed that the unfertilized eggs primarily stored genes that participate in RNA processing and nuclear protein complex composition. According to this PacBio data that aligned with the genome, 3,970 fusion genes, 819 ncRNAs, and 84 new transcripts were predicted. Illumina RNA-seq and RT-qPCR detection found that the expression of two new transcripts, PB.5289.1 and PB.10209.1, were significantly up-regulated at the 2-cell stage and down-regulated rapidly thereafter, suggesting their involvement in minor ZGA during early embryonic development. This study indicated that the unfertilized eggs of zebrafish may have retained genes directly related to cell division and development to initiate the subsequent development in a limited space and time. On the other hand, NTRs or new transcriptome regions in the genome were discovered, which provided new clues regarding ZGA of MZT during early embryonic development in fish.}, } @article {pmid30864657, year = {2019}, author = {Meng, G and Li, Y and Yang, C and Liu, S}, title = {MitoZ: a toolkit for animal mitochondrial genome assembly, annotation and visualization.}, journal = {Nucleic acids research}, volume = {47}, number = {11}, pages = {e63}, pmid = {30864657}, issn = {1362-4962}, mesh = {Animals ; Computational Biology/*methods ; DNA, Mitochondrial/chemistry/*genetics ; Genes, Mitochondrial ; Genome, Mitochondrial/*genetics ; Genomics ; High-Throughput Nucleotide Sequencing/*methods ; Internet ; Molecular Sequence Annotation ; Sequence Analysis, DNA/*methods ; Software ; }, abstract = {Mitochondrial genome (mitogenome) plays important roles in evolutionary and ecological studies. It becomes routine to utilize multiple genes on mitogenome or the entire mitogenomes to investigate phylogeny and biodiversity of focal groups with the onset of High Throughput Sequencing (HTS) technologies. We developed a mitogenome toolkit MitoZ, consisting of independent modules of de novo assembly, findMitoScaf (find Mitochondrial Scaffolds), annotation and visualization, that can generate mitogenome assembly together with annotation and visualization results from HTS raw reads. We evaluated its performance using a total of 50 samples of which mitogenomes are publicly available. The results showed that MitoZ can recover more full-length mitogenomes with higher accuracy compared to the other available mitogenome assemblers. Overall, MitoZ provides a one-click solution to construct the annotated mitogenome from HTS raw data and will facilitate large scale ecological and evolutionary studies. MitoZ is free open source software distributed under GPLv3 license and available at https://github.com/linzhi2013/MitoZ.}, } @article {pmid30864613, year = {2019}, author = {Meira, KC and Santos, JD and Silva, CMFPD and Ferreira, AA and Guimarães, RM and Simões, TC}, title = {[Effects of age-period and cohort on mortality due to ovarian cancer in Brazil and its regions].}, journal = {Cadernos de saude publica}, volume = {35}, number = {3}, pages = {e00087018}, doi = {10.1590/0102-311X00087018}, pmid = {30864613}, issn = {1678-4464}, mesh = {Adult ; Age Factors ; Aged ; Brazil/epidemiology ; Epidemiologic Methods ; Female ; Humans ; Middle Aged ; Ovarian Neoplasms/diagnosis/*mortality ; Young Adult ; }, abstract = {This article sought to evaluate the effects of age, period and birth cohort (APC) on the temporal evolution of mortality due to ovarian cancer in Brazil and its regions from 1980 to 2014. This is an ecological, time-trend study using APC models with a Baysean approach and INLA (Integrated Nested Laplace Approximations) deterministic method for parameter inference. Mortality data and population data were obtained from the Brazilian Health Informatics Department. Rates of mortality due to ovarian cancer, according to geographical region, were standardized using the direct method, after correcting deaths for undefined causes and incomplete cancer diagnosis. In the period we studied, Brazil had 4.91 deaths due to ovarian cancer per 100,000 women, the Southern (5.66) and Southeastern regions (5.70) had higher rates per 100,000 women and the Northern region had the lowest rate (3.13/100,000 women). In all regions, there was a progressive increase in mortality as ages advanced. The multivariate best fit APC model showed positive risk of death in the Central and Northeast between 2010-2014 and, beginning in 1995-1999, in the South. We also observed a positive and significant risk of death for older cohorts in the South and Southeast and a reduced risk for younger cohorts. The inverse was opposed in the Northern and Northeastern regions. The data shows a heterogeneous pattern in the temporal evolution of mortality due to ovarian cancer in the Brazilian geographical regions, which may be related to the distinct demographic and epidemiological transition processes experienced in these regions.}, } @article {pmid30863868, year = {2019}, author = {Plantinga, AM and Chen, J and Jenq, RR and Wu, MC}, title = {pldist: ecological dissimilarities for paired and longitudinal microbiome association analysis.}, journal = {Bioinformatics (Oxford, England)}, volume = {35}, number = {19}, pages = {3567-3575}, pmid = {30863868}, issn = {1367-4811}, support = {R01 GM129512/GM/NIGMS NIH HHS/United States ; S10 OD020069/OD/NIH HHS/United States ; F31 AI131595/AI/NIAID NIH HHS/United States ; }, mesh = {Humans ; *Microbiota ; Phylogeny ; Research Design ; }, abstract = {MOTIVATION: The human microbiome is notoriously variable across individuals, with a wide range of 'healthy' microbiomes. Paired and longitudinal studies of the microbiome have become increasingly popular as a way to reduce unmeasured confounding and to increase statistical power by reducing large inter-subject variability. Statistical methods for analyzing such datasets are scarce.

RESULTS: We introduce a paired UniFrac dissimilarity that summarizes within-individual (or within-pair) shifts in microbiome composition and then compares these compositional shifts across individuals (or pairs). This dissimilarity depends on a novel transformation of relative abundances, which we then extend to more than two time points and incorporate into several phylogenetic and non-phylogenetic dissimilarities. The data transformation and resulting dissimilarities may be used in a wide variety of downstream analyses, including ordination analysis and distance-based hypothesis testing. Simulations demonstrate that tests based on these dissimilarities retain appropriate type 1 error and high power. We apply the method in two real datasets.

The R package pldist is available on GitHub at https://github.com/aplantin/pldist.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, } @article {pmid30862862, year = {2019}, author = {Dos Santos Figueiredo, FW and Adami, F}, title = {Effects of the high-inequality of income on the breast cancer mortality in Brazil.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {4173}, pmid = {30862862}, issn = {2045-2322}, mesh = {Adult ; Brazil/epidemiology ; Breast Neoplasms/*mortality ; Female ; Geography ; Humans ; Income/*statistics & numerical data ; Models, Theoretical ; *Socioeconomic Factors ; }, abstract = {As well as breast cancer mortality, the income inequality in Brazil is different between Federative units, including between units of the same region. To assess the effects of the high-inequality of income on breast cancer mortality in Brazilian Federative Units, in the 2010 year. This is an ecologic study. Deaths from breast cancer in Brazilian women according to Federative units were obtained from the Department of Informatics of the Unified Health System. Mortality by breast cancer was estimated per 100,000 women and age-standardized by the direct method according to World Health Organization population. Income inequality was measured by the Gini index obtained from the United Nations Development Programme. The High-inequality of income was classified by the third tercile of the distribution from the Gini index of the Federative units. Univariate analysis was performed according to data normality. Linear regressions were performed by the stepwise backward method. The confidence level was 5%. Stata® (Stata Corp, LC) 11.0. was used. The High-inequality of income was associated with worse social and demographic indicators. The age-standardized breast cancer mortality was larger in the high-inequality of income Federative units. In the adjusted analysis, these Federative units presented a mean of 2 more deaths (ranging from the 0.4 to 3.7 deaths, r[2] = 0.79; p = 0.018) by breast cancer per 100,000 women when compared to the Federative units without high-inequality of income. In the Brazilian Federative units, the high-inequality of income was associated with age-standardized breast cancer mortality more.}, } @article {pmid30862821, year = {2019}, author = {Chanda, MM and Carpenter, S and Prasad, G and Sedda, L and Henrys, PA and Gajendragad, MR and Purse, BV}, title = {Livestock host composition rather than land use or climate explains spatial patterns in bluetongue disease in South India.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {4229}, pmid = {30862821}, issn = {2045-2322}, support = {BB/H009205/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/I/00007036/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/I/00007038/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/H009167/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; *Bluetongue/epidemiology/transmission ; *Bluetongue virus ; Buffaloes/*virology ; *Disease Outbreaks ; India/epidemiology ; Livestock/*virology ; Models, Biological ; Seroepidemiologic Studies ; Sheep/virology ; }, abstract = {Culicoides-borne arboviruses of livestock impair animal health, livestock production and livelihoods worldwide. As these arboviruses are multi-host, multi-vector systems, predictions to improve targeting of disease control measures require frameworks that quantify the relative impacts of multiple abiotic and biotic factors on disease patterns. We develop such a framework to predict long term (1992-2009) average patterns in bluetongue (BT), caused by bluetongue virus (BTV), in sheep in southern India, where annual BT outbreaks constrain the livelihoods and production of small-holder farmers. In Bayesian spatial general linear mixed models, host factors outperformed landscape and climate factors as predictors of disease patterns, with more BT outbreaks occurring on average in districts with higher densities of susceptible sheep breeds and buffalo. Since buffalo are resistant to clinical signs of BT, this finding suggests they are a source of infection for sympatric susceptible sheep populations. Sero-monitoring is required to understand the role of buffalo in maintaining BTV transmission and whether they must be included in vaccination programs to protect sheep adequately. Landscape factors, namely the coverage of post-flooding, irrigated and rain-fed croplands, had weak positive effects on outbreaks. The intimate links between livestock host, vector composition and agricultural practices in India require further investigation at the landscape scale.}, } @article {pmid30854451, year = {2019}, author = {Stringfield, O and Arrington, JA and Johnston, SK and Rognin, NG and Peeri, NC and Balagurunathan, Y and Jackson, PR and Clark-Swanson, KR and Swanson, KR and Egan, KM and Gatenby, RA and Raghunand, N}, title = {Multiparameter MRI Predictors of Long-Term Survival in Glioblastoma Multiforme.}, journal = {Tomography (Ann Arbor, Mich.)}, volume = {5}, number = {1}, pages = {135-144}, pmid = {30854451}, issn = {2379-139X}, support = {R01 CA116174/CA/NCI NIH HHS/United States ; R01 CA164371/CA/NCI NIH HHS/United States ; R01 NS060752/NS/NINDS NIH HHS/United States ; U54 CA193489/CA/NCI NIH HHS/United States ; U01 CA220378/CA/NCI NIH HHS/United States ; P30 CA076292/CA/NCI NIH HHS/United States ; U54 CA143970/CA/NCI NIH HHS/United States ; U54 CA210180/CA/NCI NIH HHS/United States ; }, mesh = {Adult ; Aged ; Brain Neoplasms/*diagnostic imaging/pathology ; Contrast Media ; Female ; Glioblastoma/*diagnostic imaging/pathology ; Humans ; Image Interpretation, Computer-Assisted/methods ; Kaplan-Meier Estimate ; Magnetic Resonance Imaging/methods ; Male ; Middle Aged ; Predictive Value of Tests ; Prognosis ; Retrospective Studies ; Young Adult ; }, abstract = {Standard-of-care multiparameter magnetic resonance imaging (MRI) scans of the brain were used to objectively subdivide glioblastoma multiforme (GBM) tumors into regions that correspond to variations in blood flow, interstitial edema, and cellular density. We hypothesized that the distribution of these distinct tumor ecological "habitats" at the time of presentation will impact the course of the disease. We retrospectively analyzed initial MRI scans in 2 groups of patients diagnosed with GBM, a long-term survival group comprising subjects who survived >36 month postdiagnosis, and a short-term survival group comprising subjects who survived ≤19 month postdiagnosis. The single-institution discovery cohort contained 22 subjects in each group, while the multi-institution validation cohort contained 15 subjects per group. MRI voxel intensities were calibrated, and tumor voxels clustered on contrast-enhanced T1-weighted and fluid-attenuated inversion-recovery (FLAIR) images into 6 distinct "habitats" based on low- to medium- to high-contrast enhancement and low-high signal on FLAIR scans. Habitat 6 (high signal on calibrated contrast-enhanced T1-weighted and FLAIR sequences) comprised a significantly higher volume fraction of tumors in the long-term survival group (discovery cohort, 35% ± 6.5%; validation cohort, 34% ± 4.8%) compared with tumors in the short-term survival group (discovery cohort, 17% ± 4.5%, P < .03; validation cohort, 16 ± 4.0%, P < .007). Of the 6 distinct MRI-defined habitats, the fractional tumor volume of habitat 6 at diagnosis was significantly predictive of long- or short-term survival. We discuss a possible mechanistic basis for this association and implications for habitat-driven adaptive therapy of GBM.}, } @article {pmid30854028, year = {2019}, author = {Clifton-Brown, J and Harfouche, A and Casler, MD and Dylan Jones, H and Macalpine, WJ and Murphy-Bokern, D and Smart, LB and Adler, A and Ashman, C and Awty-Carroll, D and Bastien, C and Bopper, S and Botnari, V and Brancourt-Hulmel, M and Chen, Z and Clark, LV and Cosentino, S and Dalton, S and Davey, C and Dolstra, O and Donnison, I and Flavell, R and Greef, J and Hanley, S and Hastings, A and Hertzberg, M and Hsu, TW and Huang, LS and Iurato, A and Jensen, E and Jin, X and Jørgensen, U and Kiesel, A and Kim, DS and Liu, J and McCalmont, JP and McMahon, BG and Mos, M and Robson, P and Sacks, EJ and Sandu, A and Scalici, G and Schwarz, K and Scordia, D and Shafiei, R and Shield, I and Slavov, G and Stanton, BJ and Swaminathan, K and Taylor, G and Torres, AF and Trindade, LM and Tschaplinski, T and Tuskan, GA and Yamada, T and Yeon Yu, C and Zalesny, RS and Zong, J and Lewandowski, I}, title = {Breeding progress and preparedness for mass-scale deployment of perennial lignocellulosic biomass crops switchgrass, miscanthus, willow and poplar.}, journal = {Global change biology. Bioenergy}, volume = {11}, number = {1}, pages = {118-151}, pmid = {30854028}, issn = {1757-1693}, support = {BB/E006833/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/G00580X/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/C/00004158/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/C/00004975/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, abstract = {Genetic improvement through breeding is one of the key approaches to increasing biomass supply. This paper documents the breeding progress to date for four perennial biomass crops (PBCs) that have high output-input energy ratios: namely Panicum virgatum (switchgrass), species of the genera Miscanthus (miscanthus), Salix (willow) and Populus (poplar). For each crop, we report on the size of germplasm collections, the efforts to date to phenotype and genotype, the diversity available for breeding and on the scale of breeding work as indicated by number of attempted crosses. We also report on the development of faster and more precise breeding using molecular breeding techniques. Poplar is the model tree for genetic studies and is furthest ahead in terms of biological knowledge and genetic resources. Linkage maps, transgenesis and genome editing methods are now being used in commercially focused poplar breeding. These are in development in switchgrass, miscanthus and willow generating large genetic and phenotypic data sets requiring concomitant efforts in informatics to create summaries that can be accessed and used by practical breeders. Cultivars of switchgrass and miscanthus can be seed-based synthetic populations, semihybrids or clones. Willow and poplar cultivars are commercially deployed as clones. At local and regional level, the most advanced cultivars in each crop are at technology readiness levels which could be scaled to planting rates of thousands of hectares per year in about 5 years with existing commercial developers. Investment in further development of better cultivars is subject to current market failure and the long breeding cycles. We conclude that sustained public investment in breeding plays a key role in delivering future mass-scale deployment of PBCs.}, } @article {pmid30851363, year = {2019}, author = {Cai, C and Zhang, Z and Morales, M and Wang, Y and Khafipour, E and Friel, J}, title = {Feeding practice influences gut microbiome composition in very low birth weight preterm infants and the association with oxidative stress: A prospective cohort study.}, journal = {Free radical biology & medicine}, volume = {142}, number = {}, pages = {146-154}, doi = {10.1016/j.freeradbiomed.2019.02.032}, pmid = {30851363}, issn = {1873-4596}, support = {/CAPMC/CIHR/Canada ; }, mesh = {Biomarkers/urine ; Clostridiales/classification/genetics/isolation & purification ; Computational Biology/methods ; Diet/*methods ; Enteral Nutrition/*methods ; Enterobacteriaceae/classification/genetics/isolation & purification ; F2-Isoprostanes/*urine ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*genetics ; Gestational Age ; High-Throughput Nucleotide Sequencing ; Humans ; Infant ; Infant Formula/chemistry ; Infant, Newborn ; Infant, Premature ; Infant, Very Low Birth Weight ; Male ; Milk, Human/chemistry ; *Oxidative Stress ; Prospective Studies ; RNA, Ribosomal, 16S/genetics ; Veillonella/classification/genetics/isolation & purification ; }, abstract = {Knowledge about the development of the preterm infant gut microbiota is emerging and is critical to their health. Very-low-birth-weight (VLBW; birth weight, <1500 g) infants usually have special dietary needs while showing increased oxidative stress related to intensive care. This prospective cohort study assessed the effect of feeding practice on gut microbiome development and oxidative stress in preterm infants. Fecal samples were collected from each infant in the early (1-2 weeks of enteral feeding) and late (2-4 weeks of enteral feeding) feeding stages. We performed high-throughput sequencing of V3-V4 regions of the 16S rRNA gene to analyze the fecal microbiome composition of 20 VLBW preterm infants and to determine the association of gut bacterial composition with feeding practice using an oxidative stress marker (urinary F2-isoprostane). Our results showed that feeding practices in the late stage significantly influenced the gut microbiome composition and oxidative stress in preterm infants. Preterm infants fed human milk + human milk fortifier and only formula diets showed a significant increase in F2-isoprostane levels (P < 0.05) compared with those fed human milk + formula diet. The gut microbiome of the infants fed the human milk + Human milk fortifier diet showed the lower relative abundance of Veillonella (P < 0.05) compared with that of the infants fed the human milk + formula diet. The gut microbiome of the infants fed the only formula diet showed the lowest microbial diversity and the highest relative abundance of Terrisporobacter (P < 0.05) compared with the gut microbiome of the infants fed the other diets. Correlation network analysis showed that urinary F2-isoprostane level was positively correlated with Terrisporobacter and Enterobacteriaceae abundance (P < 0.05) in the preterm infants. In conclusion, these data suggest that feeding practice affects the bacterial diversity and composition in the gut microbiome and is associated with oxidative stress in VLBW preterm infants.}, } @article {pmid30849302, year = {2019}, author = {Pratumchart, K and Suwannatrai, K and Sereewong, C and Thinkhamrop, K and Chaiyos, J and Boonmars, T and Suwannatrai, AT}, title = {Ecological Niche Model based on Maximum Entropy for mapping distribution of Bithynia siamensis goniomphalos, first intermediate host snail of Opisthorchis viverrini in Thailand.}, journal = {Acta tropica}, volume = {193}, number = {}, pages = {183-191}, doi = {10.1016/j.actatropica.2019.03.004}, pmid = {30849302}, issn = {1873-6254}, mesh = {Altitude ; Animals ; *Ecosystem ; Entropy ; Geographic Information Systems ; Humans ; *Models, Biological ; Opisthorchiasis/epidemiology ; *Opisthorchis ; *Snails ; Soil ; Temperature ; Thailand/epidemiology ; }, abstract = {The snail Bithynia siamensis goniomphalos acts as first intermediate host of the liver fluke, Opisthorchis viverrini, which causes opisthorchiasis in humans. In this study, we used a geographic information system (GIS), remote sensing (RS) and software using the maximum entropy (MaxEnt) algorithm to predict the distribution of B. s. goniomphalos in Thailand on the basis of environmental and climatic factors. The MaxEnt model for B. s. goniomphalos was excellent, with average test AUC values of 0.89. The predicted distribution of B. s. goniomphalos was affected by altitude, land cover, normalized difference vegetation index (NDVI), precipitation in the driest month (BIO 14), land surface temperature (LST) and soil pH. The areas suitable for B. s. goniomphalos were mostly in Northeast Thailand and some northern parts of the country. The presence of B. s. goniomphalos decreases with increasing altitude and increasing NDVI value. Bithynia s. goniomphalos is most likely to occur in paddy fields and cropland. Opisthorchiasis prevalence was directly proportional to the likelihood of snail occurrence as predicted by the model. This is the first time this ecological niche model has been used to predict Bithynia snail distribution and hence to provide a basis for future work of opisthorchiasis prevention in opisthorchiasis-endemic countries.}, } @article {pmid30846683, year = {2019}, author = {George, PBL and Lallias, D and Creer, S and Seaton, FM and Kenny, JG and Eccles, RM and Griffiths, RI and Lebron, I and Emmett, BA and Robinson, DA and Jones, DL}, title = {Divergent national-scale trends of microbial and animal biodiversity revealed across diverse temperate soil ecosystems.}, journal = {Nature communications}, volume = {10}, number = {1}, pages = {1107}, pmid = {30846683}, issn = {2041-1723}, mesh = {Animals ; *Biodiversity ; Computational Biology ; DNA Barcoding, Taxonomic ; *Ecosystem ; Microbiota/genetics ; *Soil ; *Soil Microbiology ; Wales ; }, abstract = {Soil biota accounts for ~25% of global biodiversity and is vital to nutrient cycling and primary production. There is growing momentum to study total belowground biodiversity across large ecological scales to understand how habitat and soil properties shape belowground communities. Microbial and animal components of belowground communities follow divergent responses to soil properties and land use intensification; however, it is unclear whether this extends across heterogeneous ecosystems. Here, a national-scale metabarcoding analysis of 436 locations across 7 different temperate ecosystems shows that belowground animal and microbial (bacteria, archaea, fungi, and protists) richness follow divergent trends, whereas β-diversity does not. Animal richness is governed by intensive land use and unaffected by soil properties, while microbial richness was driven by environmental properties across land uses. Our findings demonstrate that established divergent patterns of belowground microbial and animal diversity are consistent across heterogeneous land uses and are detectable using a standardised metabarcoding approach.}, } @article {pmid30846610, year = {2019}, author = {Kühl, HS and Boesch, C and Kulik, L and Haas, F and Arandjelovic, M and Dieguez, P and Bocksberger, G and McElreath, MB and Agbor, A and Angedakin, S and Ayimisin, EA and Bailey, E and Barubiyo, D and Bessone, M and Brazzola, G and Chancellor, R and Cohen, H and Coupland, C and Danquah, E and Deschner, T and Dowd, D and Dunn, A and Egbe, VE and Eshuis, H and Goedmakers, A and Granjon, AC and Head, J and Hedwig, D and Hermans, V and Imong, I and Jeffery, KJ and Jones, S and Junker, J and Kadam, P and Kambere, M and Kambi, M and Kienast, I and Kujirakwinja, D and Langergraber, KE and Lapuente, J and Larson, B and Lee, K and Leinert, V and Llana, M and Maretti, G and Marrocoli, S and Martin, R and Mbi, TJ and Meier, AC and Morgan, B and Morgan, D and Mulindahabi, F and Murai, M and Neil, E and Niyigaba, P and Ormsby, LJ and Orume, R and Pacheco, L and Piel, A and Preece, J and Regnaut, S and Rundus, A and Sanz, C and van Schijndel, J and Sommer, V and Stewart, F and Tagg, N and Vendras, E and Vergnes, V and Welsh, A and Wessling, EG and Willie, J and Wittig, RM and Yuh, YG and Yurkiw, K and Zuberbühler, K and Kalan, AK}, title = {Human impact erodes chimpanzee behavioral diversity.}, journal = {Science (New York, N.Y.)}, volume = {363}, number = {6434}, pages = {1453-1455}, doi = {10.1126/science.aau4532}, pmid = {30846610}, issn = {1095-9203}, mesh = {Animals ; Conservation of Natural Resources/*methods ; Datasets as Topic ; Humans ; Pan troglodytes/*psychology ; *Social Behavior ; }, abstract = {Chimpanzees possess a large number of behavioral and cultural traits among nonhuman species. The "disturbance hypothesis" predicts that human impact depletes resources and disrupts social learning processes necessary for behavioral and cultural transmission. We used a dataset of 144 chimpanzee communities, with information on 31 behaviors, to show that chimpanzees inhabiting areas with high human impact have a mean probability of occurrence reduced by 88%, across all behaviors, compared to low-impact areas. This behavioral diversity loss was evident irrespective of the grouping or categorization of behaviors. Therefore, human impact may not only be associated with the loss of populations and genetic diversity, but also affects how animals behave. Our results support the view that "culturally significant units" should be integrated into wildlife conservation.}, } @article {pmid30842894, year = {2019}, author = {Sumsion, GR and Bradshaw, MS and Hill, KT and Pinto, LDG and Piccolo, SR}, title = {Remote sensing tree classification with a multilayer perceptron.}, journal = {PeerJ}, volume = {7}, number = {}, pages = {e6101}, pmid = {30842894}, issn = {2167-8359}, abstract = {To accelerate scientific progress on remote tree classification-as well as biodiversity and ecology sampling-The National Institute of Science and Technology created a community-based competition where scientists were invited to contribute informatics methods for classifying tree species and genus using crown-level images of trees. We classified tree species and genus at the pixel level using hyperspectral and LiDAR observations. We compared three algorithms that have been implemented extensively across a broad range of research applications: support vector machines, random forests, and multilayer perceptron. At the pixel level, the multilayer perceptron algorithm classified species or genus with high accuracy (92.7% and 95.9%, respectively) on the training data and performed better than the other two algorithms (85.8-93.5%). This indicates promise for the use of the multilayer perceptron (MLP) algorithm for tree-species classification based on hyperspectral and LiDAR observations and coincides with a growing body of research in which neural network-based algorithms outperform other types of classification algorithm for machine vision. To aggregate patterns across the images, we used an ensemble approach that averages the pixel-level outputs of the MLP algorithm to classify species at the crown level. The average accuracy of these classifications on the test set was 68.8% for the nine species.}, } @article {pmid30836614, year = {2019}, author = {Huang, C and Yang, C and Fang, Z and Zhang, L and Zhang, W and Zhu, Y and Zhang, C}, title = {Discovery of Stealthin Derivatives and Implication of the Amidotransferase FlsN3 in the Biosynthesis of Nitrogen-Containing Fluostatins.}, journal = {Marine drugs}, volume = {17}, number = {3}, pages = {}, pmid = {30836614}, issn = {1660-3397}, support = {31820103003, 31700042, 41676165//National Natural Science Foundation of China/ ; GDME-2018C005, 2015A030308013//Guangdong Province/ ; }, mesh = {Aquatic Organisms/*metabolism ; Bacterial Proteins/genetics/*metabolism ; Biosynthetic Pathways ; Computational Biology ; Crystallography, X-Ray ; Fluorenes/chemistry/*isolation & purification/metabolism ; Heterocyclic Compounds, 4 or More Rings/chemistry ; Magnetic Resonance Spectroscopy ; Micromonospora/*metabolism ; Molecular Structure ; Nitrogen/chemistry ; Streptomyces ; Transaminases/genetics/*metabolism ; }, abstract = {Diazobenzofluorene-containing atypical angucyclines exhibit promising biological activities. Here we report the inactivation of an amidotransferase-encoding gene flsN3 in Micromonospora rosaria SCSIO N160, a producer of fluostatins. Bioinformatics analysis indicated that FlsN3 was involved in the diazo formation. Chemical investigation of the flsN3-inactivation mutant resulted in the isolation of a variety of angucycline aromatic polyketides, including four racemic aminobenzo[b]fluorenes stealthins D[-]G (9[-]12) harboring a stealthin C-like core skeleton with an acetone or butanone-like side chain. Their structures were elucidated on the basis of nuclear magnetic resonance (NMR) spectroscopic data and X-ray diffraction analysis. A plausible mechanism for the formation of stealthins D[-]G (9[-]12) was proposed. These results suggested a functional role of FlsN3 in the formation/modification of N[-]N bond-containing fluostatins.}, } @article {pmid30833739, year = {2019}, author = {Kwok, R}, title = {AI empowers conservation biology.}, journal = {Nature}, volume = {567}, number = {7746}, pages = {133-134}, doi = {10.1038/d41586-019-00746-1}, pmid = {30833739}, issn = {1476-4687}, mesh = {Animals ; *Artificial Intelligence/standards ; Automation ; Big Data ; Birds/physiology ; Conservation of Natural Resources/*methods ; Ecology/*methods ; Environmental Monitoring/*methods ; Machine Learning/standards ; Software ; }, } @article {pmid30832740, year = {2019}, author = {Song, W and Wemheuer, B and Zhang, S and Steensen, K and Thomas, T}, title = {MetaCHIP: community-level horizontal gene transfer identification through the combination of best-match and phylogenetic approaches.}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {36}, pmid = {30832740}, issn = {2049-2618}, mesh = {Bacteria/classification/*genetics ; Computational Biology/*methods ; Databases, Genetic ; Drug Resistance, Bacterial ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Humans ; Metagenomics ; Phylogeny ; Soil Microbiology ; }, abstract = {BACKGROUND: Metagenomic datasets provide an opportunity to study horizontal gene transfer (HGT) on the level of a microbial community. However, current HGT detection methods cannot be applied to community-level datasets or require reference genomes. Here, we present MetaCHIP, a pipeline for reference-independent HGT identification at the community level.

RESULTS: Assessment of MetaCHIP's performance on simulated datasets revealed that it can predict HGTs with various degrees of genetic divergence from metagenomic datasets. The results also indicated that the detection of very recent gene transfers (i.e. those with low levels of genetic divergence) from metagenomics datasets is largely affected by the read assembly step. Comparison of MetaCHIP with a previous analysis on soil bacteria showed a high level of consistency for the prediction of recent HGTs and revealed a large number of additional non-recent gene transfers, which can provide new biological and ecological insight. Assessment of MetaCHIP's performance on real metagenomic datasets confirmed the role of HGT in the spread of genes related to antibiotic resistance in the human gut microbiome. Further testing also showed that functions related to energy production and conversion as well as carbohydrate transport and metabolism are frequently transferred among free-living microorganisms.

CONCLUSION: MetaCHIP provides an opportunity to study HGTs among members of a microbial community and therefore has several applications in the field of microbial ecology and evolution. MetaCHIP is implemented in Python and freely available at https://github.com/songweizhi/MetaCHIP .}, } @article {pmid30832282, year = {2019}, author = {Wu, Z and Lei, S and He, BJ and Bian, Z and Wang, Y and Lu, Q and Peng, S and Duo, L}, title = {Assessment of Landscape Ecological Health: A CaseStudy of a Mining City in a Semi-Arid Steppe.}, journal = {International journal of environmental research and public health}, volume = {16}, number = {5}, pages = {}, pmid = {30832282}, issn = {1660-4601}, mesh = {Biodiversity ; China ; Cities ; *City Planning ; *Conservation of Natural Resources ; *Ecosystem ; Humans ; *Mining ; }, abstract = {The ecological status of the semi-arid steppes in China is fragile. Under the long-term and high-intensity development of mining, the ecological integrity and biodiversity of steppe landscapes have been destroyed, causing soil pollution, grassland degradation, landscape function defect, and so on. Previous studies have mainly focused on ecosystem health assessment in mining areas. Landscape ecological health (LEH) pays more attention to the interactions between different ecosystems. Therefore, the ecological assessment of mining cities is more suitable on a landscape scale. Meanwhile, the existing LEH assessment index systems are not applicable in ecologically fragile areas with sparse population, underdeveloped economy, and in relatively small research areas. The purpose of this study was to construct a LEH assessment index system and evaluate the LEH of a mining city located in a semi-arid steppe. Xilinhot is a typical semi-arid steppe mining city in China. The contradictions between the human, land and ecological environment are serious. A new model Condition, Vigor, Organization, Resilience, and Ecosystem (CVORE) model was constructed that integrated five subsystems (services) from the perspectives of ecology, landscape ecology, mining science, and geography. This study used the CVORE model to systematically evaluate the LEH in Xilinhot city in terms of five LEH levels, including very healthy, healthy, sub-healthy, unhealthy and morbid landscape. Research results show that the areas of the very healthy, healthy, sub-healthy, unhealthy and morbid landscapes are 13.23, 736.35, 184.5, 66.76 and 20.63 km[2], respectively. The healthy landscapes area accounts for 72.08% and most grasslands are healthy. The sub-healthy landscapes are mainly located around areas with higher disturbances due to human activities. The morbid or unhealthy landscapes are concentrated in the mining areas. The proposed CVORE model can enrich the foundations for the quantitative assessment of Landscape Ecological Health of Mining Cities in Semi-arid Steppe (LEHMCSS). This study provided a new LEH assessment approach (CVORE model), which can support landscape ecological restoration, ecological environmental protection and urban planning of the semi-arid steppe mining cities.}, } @article {pmid30830765, year = {2019}, author = {Sebestyen, SD and Ross, DS and Shanley, JB and Elliott, EM and Kendall, C and Campbell, JL and Dail, DB and Fernandez, IJ and Goodale, CL and Lawrence, GB and Lovett, GM and McHale, PJ and Mitchell, MJ and Nelson, SJ and Shattuck, MD and Wickman, TR and Barnes, RT and Bostic, JT and Buda, AR and Burns, DA and Eshleman, KN and Finlay, JC and Nelson, DM and Ohte, N and Pardo, LH and Rose, LA and Sabo, RD and Schiff, SL and Spoelstra, J and Williard, KWJ}, title = {Unprocessed Atmospheric Nitrate in Waters of the Northern Forest Region in the U.S. and Canada.}, journal = {Environmental science & technology}, volume = {53}, number = {7}, pages = {3620-3633}, doi = {10.1021/acs.est.9b01276}, pmid = {30830765}, issn = {1520-5851}, mesh = {Canada ; Environmental Monitoring ; *Forests ; *Nitrates ; Nitrogen ; Rivers ; }, abstract = {Little is known about the regional extent and variability of nitrate from atmospheric deposition that is transported to streams without biological processing in forests. We measured water chemistry and isotopic tracers (δ[18]O and δ[15]N) of nitrate sources across the Northern Forest Region of the U.S. and Canada and reanalyzed data from other studies to determine when, where, and how unprocessed atmospheric nitrate was transported in catchments. These inputs were more widespread and numerous than commonly recognized, but with high spatial and temporal variability. Only 6 of 32 streams had high fractions (>20%) of unprocessed atmospheric nitrate during baseflow. Seventeen had high fractions during stormflow or snowmelt, which corresponded to large fractions in near-surface soil waters or groundwaters, but not deep groundwater. The remaining 10 streams occasionally had some (<20%) unprocessed atmospheric nitrate during stormflow or baseflow. Large, sporadic events may continue to be cryptic due to atmospheric deposition variation among storms and a near complete lack of monitoring for these events. A general lack of observance may bias perceptions of occurrence; sustained monitoring of chronic nitrogen pollution effects on forests with nitrate source apportionments may offer insights needed to advance the science as well as assess regulatory and management schemes.}, } @article {pmid30814591, year = {2019}, author = {da Silva Paiva, L and Oliveira, FR and de Alcantara Sousa, LV and Dos Santos Figueiredo, FW and de Sá, TH and Adami, F}, title = {Decline in Stroke Mortality Between 1997 and 2012 by Sex: Ecological Study in Brazilians Aged 15 to 49 Years.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {2962}, pmid = {30814591}, issn = {2045-2322}, mesh = {Adolescent ; Adult ; Brazil/epidemiology ; Databases, Factual ; Female ; Humans ; International Classification of Diseases ; Linear Models ; Male ; Middle Aged ; Mortality/trends ; Sex Factors ; Stroke/epidemiology/*mortality ; }, abstract = {This study aimed to analyse the time trends of stroke mortality between 1997 and 2012 according to sex in Brazilians aged 15 to 49 years. This ecological study used data obtained from the Mortality Information System, which is available from the National Health System Department of Informatics - DATASUS and maintained by the Brazilian Ministry of Health. Stroke definition included International Classification of Disease version 10 (ICD-10) codes I60, I61, I63, and I64. Crude and age-standardized mortality rates and respective 95% confidence intervals were estimated per 100,000 inhabitants and stratified by age, region, year, and sex. Linear regression models were used to analyse the time trends with a confidence level of 95%. The statistical program used was Stata 11.0. Between 1997 and 2012, there were 124,866 deaths due to stroke in Brazilians aged 15 to 49 years. There was a decreasing linear trend in stroke mortality among men (β = -0.46, p < 0.001, R[2] = 0.95) and women (β = -0.40, p < 0.001, R[2] = 0.98) during this period. Overall there was no significant difference in stroke mortality trends by sex, except with respect to the age group of 40 to 49 years where there was a difference in the decrease of stroke mortality between men and women (interaction sex * year: β = 0.238, p = 0.012, R[2] = 0.96). Mortality rates decrease significantly over time in men and women in the age group 15 to 49 years old, but there is only significant difference in the decrease of rates by sex only in the age group from 40 to 49 years old.}, } @article {pmid30813962, year = {2019}, author = {Mangul, S and Martin, LS and Eskin, E and Blekhman, R}, title = {Improving the usability and archival stability of bioinformatics software.}, journal = {Genome biology}, volume = {20}, number = {1}, pages = {47}, pmid = {30813962}, issn = {1474-760X}, support = {K25 HL080079/HL/NHLBI NIH HHS/United States ; R01 ES022282/ES/NIEHS NIH HHS/United States ; P01 HL030568/HL/NHLBI NIH HHS/United States ; R01 ES021801/ES/NIEHS NIH HHS/United States ; R35 GM128716/GM/NIGMS NIH HHS/United States ; U01 DA024417/DA/NIDA NIH HHS/United States ; P01 HL028481/HL/NHLBI NIH HHS/United States ; R01 GM083198/GM/NIGMS NIH HHS/United States ; R01 MH101782/MH/NIMH NIH HHS/United States ; }, mesh = {Archives ; Computational Biology/*standards ; Software/*standards ; }, abstract = {Implementation of bioinformatics software involves numerous unique challenges; a rigorous standardized approach is needed to examine software tools prior to their publication.}, } @article {pmid30810209, year = {2019}, author = {Yang, W and Jiang, C and Zhu, Y and Chen, K and Wang, G and Yuan, D and Miao, W and Xiong, J}, title = {Tetrahymena Comparative Genomics Database (TCGD): a community resource for Tetrahymena.}, journal = {Database : the journal of biological databases and curation}, volume = {2019}, number = {}, pages = {}, pmid = {30810209}, issn = {1758-0463}, mesh = {*Databases, Genetic ; Genome, Protozoan ; *Genomics ; Macronucleus/genetics ; Synteny/genetics ; Tetrahymena/*genetics ; }, abstract = {Ciliates are a large and diverse group of unicellular organisms characterized by having the following two distinct type of nuclei within a single cell: micronucleus (MIC) and macronucleus (MAC). Although the genomes of several ciliates in different groups have been sequenced, comparative genomics data for multiple species within a ciliate genus are not yet available. Here we collected the genome information and comparative genomics analysis results for 10 species in the Tetrahymena genus, including the previously sequenced model organism Tetrahymena thermophila and 9 newly sequenced species, and constructed a genus-level comparative analysis platform, the Tetrahymena Comparative Genomics Database (TCGD). Genome sequences, transcriptomic data, gene models, functional annotation, ortholog groups and synteny maps were built into this database and a user-friendly interface was developed for searching, visualizing and analyzing these data. In summary, the TCGD (http://ciliate.ihb.ac.cn) will be an important and useful resource for the ciliate research community.}, } @article {pmid30809013, year = {2019}, author = {Yu, X and Polz, MF and Alm, EJ}, title = {Interactions in self-assembled microbial communities saturate with diversity.}, journal = {The ISME journal}, volume = {13}, number = {6}, pages = {1602-1617}, pmid = {30809013}, issn = {1751-7370}, mesh = {Bacteria/classification/genetics/*isolation & purification ; Bacterial Physiological Phenomena ; *Biodiversity ; Ecology ; Microbiota ; Seawater/*microbiology ; }, abstract = {How the diversity of organisms competing for or sharing resources influences community function is an important question in ecology but has rarely been explored in natural microbial communities. These generally contain large numbers of species making it difficult to disentangle how the effects of different interactions scale with diversity. Here, we show that changing diversity affects measures of community function in relatively simple communities but that increasing richness beyond a threshold has little detectable effect. We generated self-assembled communities with a wide range of diversity by growth of cells from serially diluted seawater on brown algal leachate. We subsequently isolated the most abundant taxa from these communities via dilution-to-extinction in order to compare productivity functions of the entire community to those of individual taxa. To parse the effect of different types of organismal interactions, we defined relative total function (RTF) as an index for positive or negative effects of diversity on community function. Our analysis identified three overall regimes with increasing diversity. At low richness (<12 taxa), positive and negative effects of interactions were both weak, while at moderate richness (12-26 taxa), community resource uptake increased but the carbon use efficiency decreased. Finally, beyond 26 taxa, the effect of interactions on community function saturated and further diversity increases did not affect community function. Although more diverse communities had overall greater access to resources, on average individual taxa within these communities had lower resource availability and reduced carbon use efficiency. Our results thus suggest competition and complementation simultaneously increase with diversity but both saturate at a threshold.}, } @article {pmid30808697, year = {2019}, author = {Kothari, A and Wu, YW and Chandonia, JM and Charrier, M and Rajeev, L and Rocha, AM and Joyner, DC and Hazen, TC and Singer, SW and Mukhopadhyay, A}, title = {Large Circular Plasmids from Groundwater Plasmidomes Span Multiple Incompatibility Groups and Are Enriched in Multimetal Resistance Genes.}, journal = {mBio}, volume = {10}, number = {1}, pages = {}, pmid = {30808697}, issn = {2150-7511}, mesh = {Bacteria/classification/genetics ; Cluster Analysis ; DNA, Ribosomal/chemistry/genetics ; *Drug Resistance, Bacterial ; *Genes, Bacterial ; Genetic Variation ; Groundwater/*microbiology ; Metals/*toxicity ; Phylogeny ; Plasmids/*analysis/*chemistry ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Naturally occurring plasmids constitute a major category of mobile genetic elements responsible for harboring and transferring genes important in survival and fitness. A targeted evaluation of plasmidomes can reveal unique adaptations required by microbial communities. We developed a model system to optimize plasmid DNA isolation procedures targeted to groundwater samples which are typically characterized by low cell density (and likely variations in the plasmid size and copy numbers). The optimized method resulted in successful identification of several hundred circular plasmids, including some large plasmids (11 plasmids more than 50 kb in size, with the largest being 1.7 Mb in size). Several interesting observations were made from the analysis of plasmid DNA isolated in this study. The plasmid pool (plasmidome) was more conserved than the corresponding microbiome distribution (16S rRNA based). The circular plasmids were diverse as represented by the presence of seven plasmid incompatibility groups. The genes carried on these groundwater plasmids were highly enriched in metal resistance. Results from this study confirmed that traits such as metal, antibiotic, and phage resistance along with toxin-antitoxin systems are encoded on abundant circular plasmids, all of which could confer novel and advantageous traits to their hosts. This study confirms the ecological role of the plasmidome in maintaining the latent capacity of a microbiome, enabling rapid adaptation to environmental stresses.IMPORTANCE Plasmidomes have been typically studied in environments abundant in bacteria, and this is the first study to explore plasmids from an environment characterized by low cell density. We specifically target groundwater, a significant source of water for human/agriculture use. We used samples from a well-studied site and identified hundreds of circular plasmids, including one of the largest sizes reported in plasmidome studies. The striking similarity of the plasmid-borne ORFs in terms of taxonomical and functional classifications across several samples suggests a conserved plasmid pool, in contrast to the observed variability in the 16S rRNA-based microbiome distribution. Additionally, the stress response to environmental factors has stronger conservation via plasmid-borne genes as marked by abundance of metal resistance genes. Last, identification of novel and diverse plasmids enriches the existing plasmid database(s) and serves as a paradigm to increase the repertoire of biological parts that are available for modifying novel environmental strains.}, } @article {pmid30801984, year = {2019}, author = {Ostendorf, DM and Caldwell, AE and Creasy, SA and Pan, Z and Lyden, K and Bergouignan, A and MacLean, PS and Wyatt, HR and Hill, JO and Melanson, EL and Catenacci, VA}, title = {Physical Activity Energy Expenditure and Total Daily Energy Expenditure in Successful Weight Loss Maintainers.}, journal = {Obesity (Silver Spring, Md.)}, volume = {27}, number = {3}, pages = {496-504}, pmid = {30801984}, issn = {1930-739X}, support = {P30 DK048520/DK/NIDDK NIH HHS/United States ; UL1 TR002535/TR/NCATS NIH HHS/United States ; K99 DK100465/DK/NIDDK NIH HHS/United States ; R00 DK100465/DK/NIDDK NIH HHS/United States ; P30 DK056336/DK/NIDDK NIH HHS/United States ; T32 HL116276/HL/NHLBI NIH HHS/United States ; K23 DK078913/DK/NIDDK NIH HHS/United States ; P50 HD073063/HD/NICHD NIH HHS/United States ; }, mesh = {Adult ; Case-Control Studies ; Energy Metabolism/*physiology ; Exercise/*physiology ; Female ; Humans ; Male ; Middle Aged ; Weight Loss/*physiology ; }, abstract = {OBJECTIVE: The objective of this study was to compare physical activity energy expenditure (PAEE) and total daily energy expenditure (TDEE) in successful weight loss maintainers (WLM) with normal weight controls (NC) and controls with overweight/obesity (OC).

METHODS: Participants were recruited in three groups: WLM (n = 25, BMI 24.1 ± 2.3 kg/m[2] ; maintaining ≥ 13.6-kg weight loss for ≥ 1 year), NC (n = 27, BMI 23.0 ± 2.0 kg/m[2] ; similar to current BMI of WLM), and OC (n = 28, BMI 34.3 ± 4.8 kg/m[2] ; similar to pre-weight loss BMI of WLM). TDEE was measured using the doubly labeled water method. Resting energy expenditure (REE) was measured using indirect calorimetry. PAEE was calculated as (TDEE - [0.1 × TDEE] - REE).

RESULTS: PAEE in WLM (812 ± 268 kcal/d, mean ± SD) was significantly higher compared with that in both NC (621 ± 285 kcal/d, P < 0.01) and OC (637 ± 271 kcal/d, P = 0.02). As a result, TDEE in WLM (2,495 ± 366 kcal/d) was higher compared with that in NC (2,195 ± 521 kcal/d, P = 0.01) but was not significantly different from that in OC (2,573 ± 391 kcal/d).

CONCLUSIONS: The high levels of PAEE and TDEE observed in individuals maintaining a substantial weight loss (-26.2 ± 9.8 kg maintained for 9.0 ± 10.2 years) suggest that this group relies on high levels of energy expended in physical activity to remain in energy balance (and avoid weight regain) at a reduced body weight.}, } @article {pmid30801709, year = {2019}, author = {Taylor, PG and Cleveland, CC and Soper, F and Wieder, WR and Dobrowski, SZ and Doughty, CE and Townsend, AR}, title = {Greater stem growth, woody allocation, and aboveground biomass in Paleotropical forests than in Neotropical forests.}, journal = {Ecology}, volume = {100}, number = {3}, pages = {e02589}, doi = {10.1002/ecy.2589}, pmid = {30801709}, issn = {0012-9658}, support = {//National Science Foundation/International ; //U.S. Department of Agriculture/International ; }, mesh = {Africa ; Asia ; Biomass ; Carbon/analysis ; *Forests ; South America ; Trees ; *Tropical Climate ; }, abstract = {Forest dynamics and tree species composition vary substantially between Paleotropical and Neotropical forests, but these broad biogeographic regions are treated uniformly in many land models. To assess whether these regional differences translate into variation in productivity and carbon (C) storage, we compiled a database of climate, tree stem growth, litterfall, aboveground net primary production (ANPP), and aboveground biomass across tropical rainforest sites spanning 33 countries throughout Central and South America, Asia, and Australasia, but excluding Africa due to a paucity of available data. Though the sum of litterfall and stem growth (ANPP) did not differ between regions, both stem growth and the ratio of stem growth to litterfall were higher in Paleotropical forests compared to Neotropical forests across the full observed range of ANPP. Greater C allocation to woody growth likely explains the much larger aboveground biomass estimates in Paleotropical forests (~29%, or ~80 Mg DW/ha, greater than in the Neotropics). Climate was similar in Paleo- and Neotropical forests, thus the observed differences in C likely reflect differences in the evolutionary history of species and forest structure and function between regions. Our analysis suggests that Paleotropical forests, which can be dominated by tall-statured Dipterocarpaceae species, may be disproportionate hotspots for aboveground C storage. Land models typically treat these distinct tropical forests with differential structures as a single functional unit, but our findings suggest that this may overlook critical biogeographic variation in C storage potential among regions.}, } @article {pmid30799699, year = {2019}, author = {Baranzini, SE}, title = {Insights into microbiome research 4: The computational analysis.}, journal = {Multiple sclerosis (Houndmills, Basingstoke, England)}, volume = {25}, number = {1}, pages = {21-22}, doi = {10.1177/1352458518811205}, pmid = {30799699}, issn = {1477-0970}, mesh = {Biomedical Research ; *Computational Biology/methods ; Humans ; *Microbiota ; *Multiple Sclerosis ; }, abstract = {The computational analysis of microbiome samples is a highly specialized task, requiring powerful hardware and deep know-how not only in informatics and statistics but also in ecology and taxonomy. Different approaches must be followed based on the sequencing method (16S or shotgun) and while these can provide partially overlapping information, they are conceptually distinct. Understanding their differences and similarities can be useful in the interpretation of the results of microbiome studies.}, } @article {pmid30799165, year = {2020}, author = {Mine, Y and Fujino, Y and Sabanai, K and Muramatsu, K and Otani, M and Kubo, T and Fushimi, K and Matsuda, S}, title = {Effectiveness of regional clinical pathways on postoperative length of stay for hip fracture patients: A retrospective observational study using the Japanese Diagnosis Procedure Combination database.}, journal = {Journal of orthopaedic science : official journal of the Japanese Orthopaedic Association}, volume = {25}, number = {1}, pages = {127-131}, doi = {10.1016/j.jos.2019.02.002}, pmid = {30799165}, issn = {1436-2023}, mesh = {Aged ; Aged, 80 and over ; *Arthroplasty, Replacement, Hip ; *Critical Pathways ; Cross-Sectional Studies ; Female ; Hip Fractures/*surgery ; Humans ; Japan ; Length of Stay/*statistics & numerical data ; Male ; Postoperative Period ; Retrospective Studies ; }, abstract = {BACKGROUND: Regional clinical pathways, a new type of clinical pathway, are practiced with the aim of standardizing and optimizing medical care by cooperation among multiple medical institutions in a region. However, current evaluation of the effectiveness of regional clinical pathways for hip fracture, a major health problem requiring hospitalization for orthopedic surgery, is insufficient. This study aimed to determine the association between regional clinical pathways and postoperative hospital length of stay (LOS) among hip fracture patients. In particular, we focused on the variation in postoperative LOS of hip fracture patients among hospitals and the contribution of regional clinical pathways to this variation.

METHODS: Using data from the Diagnosis Procedure Combination (DPC) database in Japan from April 2011 to March 2013, patients who were diagnosed with "fracture of head and neck of femur" (ICD10 code S72.0) or "pertrochanteric fracture" (S72.1) and received "bipolar hip arthroplasty" or "open reduction and internal fixation" were extracted. A total of 110,133 patients were included. Associations between regional clinical pathways and postoperative LOS were analyzed using cross-sectional analysis with multilevel regression models.

RESULTS: Hospitals that implemented a regional clinical pathway showed a significant reduction (13 days) in the postoperative LOS of hip fracture patients. We found a 16% inter-hospital variation in postoperative LOS, which might be explained by hospital-level implementation of regional clinical pathways. Application of regional clinical pathways at the patient level resulted in a 4-day decrease in postoperative LOS.

CONCLUSIONS: Implementation of regional clinical pathways for hip fracture patients at the hospital level was associated with reduced postoperative LOS, regardless of whether or not pathways were implemented at the patient level. This suggests that regional clinical pathways are effective for patient care management in hospitals.}, } @article {pmid30797477, year = {2019}, author = {Singh, NS and Sharma, R and Singh, DK}, title = {Identification of enzyme(s) capable of degrading endosulfan and endosulfan sulfate using in silico techniques.}, journal = {Enzyme and microbial technology}, volume = {124}, number = {}, pages = {32-40}, doi = {10.1016/j.enzmictec.2019.01.003}, pmid = {30797477}, issn = {1879-0909}, mesh = {Bacillus subtilis/enzymology/metabolism ; Bacterial Proteins/metabolism ; Basidiomycota/enzymology/growth & development/*metabolism ; Biodegradation, Environmental ; Databases, Protein ; Endosulfan/*analogs & derivatives/*metabolism ; Fungal Proteins/metabolism ; Insecticides/*metabolism ; Laccase/metabolism ; Mixed Function Oxygenases/antagonists & inhibitors/*metabolism ; *Molecular Docking Simulation ; }, abstract = {Endosulfan is one of the most widely used organochlorine cyclodiene insecticides. Microbial oxidation of endosulfan forms endosulfan sulfate, which is more or less toxic and persistent as endosulfan. Due to lack of specificity and efficiency of microbial bioremediation technique in the field conditions, enzymatic bioremediation is receiving huge attention to clean-up the environment. In the present study, X-ray crystal structures of enzymes from Brookhaven Protein Data Bank were screened for their potential to degrade endosulfan and endosulfan sulfate using molecular docking and molecular dynamics simulation techniques. A phenol hydroxylase, 1PN0 from Trichosporon cutaneum was found to have the potential to degrade both α-endosulfan and endosulfan sulfate while a bacterial CotA laccase, 3ZDW from Bacillus subtilis has the potential to degrade α-endosulfan. The in silico result correlate with in vitro degradation study using two different strains of Trichosporon cutaneum. In vitro degradation study found that the fungal strain was capable of degrading 60.36% α-endosulfan, 70.73% β-endosulfan, and 52.08% endosulfan sulfate. The presence of phenol hydroxylase inhibitor in the sulfur-free medium with endosulfan and endosulfan sulfate as sole sulfur source inhibits the growth of both the fungal strains. Such in silico techniques can provide an easy and reliable way to speed up the development of bioremediation processes through rapid identification of potential enzymes and microbes to counter the ever-increasing number of toxic compounds in the environment.}, } @article {pmid30793451, year = {2019}, author = {Yu, R and Ruddell, BL and Kang, M and Kim, J and Childers, D}, title = {Anticipating global terrestrial ecosystem state change using FLUXNET.}, journal = {Global change biology}, volume = {25}, number = {7}, pages = {2352-2367}, doi = {10.1111/gcb.14602}, pmid = {30793451}, issn = {1365-2486}, mesh = {Carbon Cycle ; Climate Change ; *Ecosystem ; *Forests ; Temperature ; }, abstract = {Ecosystems can be characterized as complex systems that traverse a variety of functional and structural states in response to changing bioclimatic forcings. A central challenge of global change biology is the robust empirical description of these states and state transitions. An ecosystem's functional state can be empirically described using Process Networks (PN) that use timeseries observations to determine the strength of process-level functional couplings between ecosystem components. A globally extensive source of in-situ observations of terrestrial ecosystem dynamics is the FLUXNET eddy-covariance network that provides standardized observations of micrometeorology and carbon, water, and energy flux dynamics. We employ the LaThuile FLUXNET synthesis dataset to delineate each month's functional state for 204 sites, yielding the LaThuile PN version 1.0 database that describes the strength of an ecosystem's functional couplings from air temperature and precipitation to carbon fluxes during each site-month. Then we calculate the elasticity of these couplings to seasonal scale forcings: air temperature, precipitation, solar radiation, and phenophase. Finally, we train artificial neural networks to extrapolate these elasticities from 204 sites to the globe, yielding maps of the estimated functional elasticity of every terrestrial ecosystem's functional states to changing seasonal bioclimatic forcings. These maps provide theoretically novel resource that can be used to anticipate ecological state transitions in response to climate change and to validate process-based models of ecological change. These elasticity maps show that each ecosystem can be expected to respond uniquely to changing forcings. Tropical forests, hot deserts, savannas, and high elevations are most elastic to climate change, and elasticity of ecosystems to seasonal air temperature is on average an order of magnitude higher than elasticity to other bioclimatic forcings. We also observed a reasonable amount of moderate relationships between functional elasticity and structural state change across different ecosystems.}, } @article {pmid30786881, year = {2019}, author = {Aguilar, C and Raina, JB and Fôret, S and Hayward, DC and Lapeyre, B and Bourne, DG and Miller, DJ}, title = {Transcriptomic analysis reveals protein homeostasis breakdown in the coral Acropora millepora during hypo-saline stress.}, journal = {BMC genomics}, volume = {20}, number = {1}, pages = {148}, pmid = {30786881}, issn = {1471-2164}, support = {CE14100020//Centre of Excellence for Coral Reef Studies, Australian Research Council/ ; }, mesh = {Amino Acids/metabolism ; Animals ; Anthozoa/*genetics/*metabolism ; Computational Biology/methods ; Endoplasmic Reticulum/metabolism ; *Gene Expression Profiling ; Gene Expression Regulation ; Gene Ontology ; Oxidative Stress ; Proteolysis ; *Proteostasis ; *Salinity ; Stress, Physiological/*genetics ; *Transcriptome ; }, abstract = {BACKGROUND: Coral reefs can experience salinity fluctuations due to rainfall and runoff; these events can have major impacts on the corals and lead to bleaching and mortality. On the Great Barrier Reef (GBR), low salinity events, which occur during summer seasons and can involve salinity dropping ~ 10 PSU correlate with declines in coral cover, and these events are predicted to increase in frequency and severity under future climate change scenarios. In other marine invertebrates, exposure to low salinity causes increased expression of genes involved in proteolysis, responses to oxidative stress, and membrane transport, but the effects that changes in salinity have on corals have so far received only limited attention. To better understand the coral response to hypo-osmotic stress, here we investigated the transcriptomic response of the coral Acropora millepora in both adult and juvenile life stages to acute (1 h) and more prolonged (24 h) exposure to low salinity.

RESULTS: Differential gene expression analysis revealed the involvement of both common and specific response mechanisms in Acropora. The general response to environmental stressors included up-regulation of genes involved in the mitigation of macromolecular and oxidative damage, while up-regulation of genes involved in amino acid metabolism and transport represent specific responses to salinity stress.

CONCLUSIONS: This study is the first comprehensive transcriptomic analysis of the coral response to low salinity stress and provides important insights into the likely consequences of heavy rainfall and runoff events on coral reefs.}, } @article {pmid30785570, year = {2019}, author = {Covre, ER and Melo, WA and Tostes, MFDP and Fernandes, CAM}, title = {Trend of hospitalizations and mortality from surgical causes in Brazil, 2008 to 2016.}, journal = {Revista do Colegio Brasileiro de Cirurgioes}, volume = {46}, number = {1}, pages = {e1979}, doi = {10.1590/0100-6991e-20191979}, pmid = {30785570}, issn = {1809-4546}, mesh = {Brazil/epidemiology ; Health Services Accessibility ; Healthcare Disparities ; Hospitalization/*statistics & numerical data/*trends ; Humans ; Mortality/*trends ; National Health Programs ; Residence Characteristics ; Surgical Procedures, Operative/*mortality ; }, abstract = {OBJECTIVE: to evaluate the trend of hospitalazions for surgical procedures and surgical mortality in Brazil, from 2008 to 2016.

METHODS: we conducted an ecological, time-series study. We obtained the data on surgical hospitalizations and mortality between 2008 and 2016 from the Department of Informatics of the Unified Health System (SUS). We performed the trend analysis using polynomial regression models.

RESULTS: in the period of the study, 37,565,785 surgical procedures were performed in the SUS, an average of 4,151,050 surgeries/year. The mean coefficient of the surgical procedures was 2.12 surgeries per 100 inhabitants/year, with a variation of 1.92 to 2.56 inhabitants/year among the country regions. The surgical mortality rate was 1.63%, ranging from 1.07% to 2.02% between the regions.

CONCLUSION: there was a significant trend towards increasing number of surgical procedures carried out and of surgical mortality; however, the coefficient of surgical procedures is lower than recommended by international standards, with regional disparities in access to surgical care and mortality, which undermines the guarantee of universal health coverage expect from the Unified Health System.}, } @article {pmid30783007, year = {2019}, author = {Keshri, V and Diene, SM and Estienne, A and Dardaillon, J and Chabrol, O and Tichit, L and Rolain, JM and Raoult, D and Pontarotti, P}, title = {An Integrative Database of β-Lactamase Enzymes: Sequences, Structures, Functions, and Phylogenetic Trees.}, journal = {Antimicrobial agents and chemotherapy}, volume = {63}, number = {5}, pages = {}, pmid = {30783007}, issn = {1098-6596}, mesh = {*Databases, Protein ; Kinetics ; Microbial Sensitivity Tests ; Phylogeny ; Protein Conformation ; beta-Lactamases/*metabolism ; }, abstract = {β-Lactamase enzymes have attracted substential medical attention from researchers and clinicians because of their clinical, ecological, and evolutionary interest. Here, we present a comprehensive online database of β-lactamase enzymes. The current database is manually curated and incorporates the primary amino acid sequences, closest structural information in an external structure database (the Protein Data Bank [PDB]) and the functional profiles and phylogenetic trees of the four molecular classes (A, B, C, and D) of β-lactamases. The functional profiles are presented according to the MICs and kinetic parameters that make them more useful for the investigators. Here, a total of 1,147 β-lactam resistance genes are analyzed and described in the database. The database is implemented in MySQL and the related website is developed with Zend Framework 2 on an Apache server, supporting all major web browsers. Users can easily retrieve and visualize biologically important information using a set of efficient queries from a graphical interface. This database is freely accessible at http://ifr48.timone.univ-mrs.fr/beta-lactamase/public/.}, } @article {pmid30782660, year = {2019}, author = {López-Pérez, M and Jayakumar, JM and Haro-Moreno, JM and Zaragoza-Solas, A and Reddi, G and Rodriguez-Valera, F and Shapiro, OH and Alam, M and Almagro-Moreno, S}, title = {Evolutionary Model of Cluster Divergence of the Emergent Marine Pathogen Vibrio vulnificus: From Genotype to Ecotype.}, journal = {mBio}, volume = {10}, number = {1}, pages = {}, pmid = {30782660}, issn = {2150-7511}, mesh = {Aquaculture ; Aquatic Organisms/microbiology ; Cluster Analysis ; Computational Biology ; *Ecotype ; Evolution, Molecular ; Gene Flow ; Gene Transfer, Horizontal ; *Genetic Variation ; Genome, Bacterial ; *Genotype ; Phenotype ; Recombination, Genetic ; Vibrio vulnificus/*classification/*genetics/isolation & purification/physiology ; }, abstract = {Vibrio vulnificus, an opportunistic pathogen, is the causative agent of a life-threatening septicemia and a rising problem for aquaculture worldwide. The genetic factors that differentiate its clinical and environmental strains remain enigmatic. Furthermore, clinical strains have emerged from every clade of V. vulnificus In this work, we investigated the underlying genomic properties and population dynamics of the V. vulnificus species from an evolutionary and ecological point of view. Genome comparisons and bioinformatic analyses of 113 V. vulnificus isolates indicate that the population of V. vulnificus is made up of four different clusters. We found evidence that recombination and gene flow between the two largest clusters (cluster 1 [C1] and C2) have drastically decreased to the point where they are diverging independently. Pangenome and phenotypic analyses showed two markedly different lifestyles for these two clusters, indicating commensal (C2) and bloomer (C1) ecotypes, with differences in carbohydrate utilization, defense systems, and chemotaxis, among other characteristics. Nonetheless, we identified frequent intra- and interspecies exchange of mobile genetic elements (e.g., antibiotic resistance plasmids, novel "chromids," or two different and concurrent type VI secretion systems) that provide high levels of genetic diversity in the population. Surprisingly, we identified strains from both clusters in the mucosa of aquaculture species, indicating that manmade niches are bringing strains from the two clusters together. We propose an evolutionary model of V. vulnificus that could be broadly applicable to other pathogenic vibrios and facultative bacterial pathogens to pursue strategies to prevent their infections and emergence.IMPORTANCEVibrio vulnificus is an emergent marine pathogen and is the cause of a deadly septicemia. However, the genetic factors that differentiate its clinical and environmental strains and its several biotypes remain mostly enigmatic. In this work, we investigated the underlying genomic properties and population dynamics of the V. vulnificus species to elucidate the traits that make these strains emerge as a human pathogen. The acquisition of different ecological determinants could have allowed the development of highly divergent clusters with different lifestyles within the same environment. However, we identified strains from both clusters in the mucosa of aquaculture species, indicating that manmade niches are bringing strains from the two clusters together, posing a potential risk of recombination and of emergence of novel variants. We propose a new evolutionary model that provides a perspective that could be broadly applicable to other pathogenic vibrios and facultative bacterial pathogens to pursue strategies to prevent their infections.}, } @article {pmid30781813, year = {2019}, author = {Cheng, M and Huang, B and Kong, L and Ouyang, Z}, title = {Ecosystem Spatial Changes and Driving Forces in the Bohai Coastal Zone.}, journal = {International journal of environmental research and public health}, volume = {16}, number = {4}, pages = {}, pmid = {30781813}, issn = {1660-4601}, mesh = {Agriculture ; China ; Conservation of Natural Resources ; *Ecosystem ; *Environmental Monitoring/methods ; Geographic Information Systems ; Geological Phenomena ; Urbanization ; Wetlands ; }, abstract = {Landscape change is an important aspect of coastal ecological conservation and has an essential influence on the sustainable development of the coastal economy. With remoting-sensing (RS) images between 2000, 2005, 2010, and 2015, using geographic information system (GIS) technologies, we examined ecosystem spatial changes in the Bohai coastal zone. Results showed that wetlands, mainly constituted by reservoirs/ponds, were the dominant landscape types. The urban ecosystem has the largest area increment and the fastest growth rate from 2000 to 2015. The quantification of landscape metrics revealed that spatial patterns have changed significantly, and the change direction of these ecosystems had moved toward increased heterogeneity and fragmentation. In addition, natural and socio-economic data were used to analyze the major driving forces triggering ecosystem spatial changes through redundancy analysis (RDA). The results revealed that the output of aquatic products (AQ) and population (Pop) were the main factors related to wetland ecosystem change. Pop and gross domestic product per capita (GDPpc) were closely related to the urban ecosystem change. Annual mean temperature (ATm), crop acreage (CA), and grain yield (GY) had positive correlations with the agriculture ecosystem changes.}, } @article {pmid30781408, year = {2019}, author = {Yoon, H and Shin, C}, title = {Cross-Device Computation Coordination for Mobile Collocated Interactions with Wearables.}, journal = {Sensors (Basel, Switzerland)}, volume = {19}, number = {4}, pages = {}, pmid = {30781408}, issn = {1424-8220}, support = {NRF-2018R1D1A1B07043983//National Research Foundation of Korea/ ; }, mesh = {*Big Data ; Data Mining/*statistics & numerical data ; Electric Power Supplies ; Humans ; Internet ; *Machine Learning ; Mobile Applications ; Wearable Electronic Devices ; }, abstract = {Mobile devices, wearables and Internet-of-Things are crammed into smaller form factors and batteries, yet they encounter demanding applications such as big data analysis, data mining, machine learning, augmented reality and virtual reality. To meet such high demands in the multi-device ecology, multiple devices should communicate collectively to share computation burdens and stay energy-efficient. In this paper, we present a cross-device computation coordination method for scenarios of mobile collocated interactions with wearables. We formally define a cross-device computation coordination problem and propose a method for solving this problem. Lastly, we demonstrate the feasibility of our approach through experiments and exemplar cases using 12 commercial Android devices with varying computation capabilities.}, } @article {pmid30769104, year = {2019}, author = {Conrads, G and Abdelbary, MMH}, title = {Challenges of next-generation sequencing targeting anaerobes.}, journal = {Anaerobe}, volume = {58}, number = {}, pages = {47-52}, doi = {10.1016/j.anaerobe.2019.02.006}, pmid = {30769104}, issn = {1095-8274}, mesh = {Archaea/*genetics ; Bacteria, Anaerobic/*genetics ; Computational Biology/methods ; High-Throughput Nucleotide Sequencing/*methods ; Metagenomics/*methods ; Sequence Analysis, DNA/*methods ; }, abstract = {Next-generation sequencing allows for investigating the composition of microbiomes that are associated with infection (clinical microbiology) or dysbiosis (microbial ecology). The most commonly applied short-read sequencing technologies are Illumina MiSeq/HiSeq and Ion Torrent PGM, however, other platforms that generate long-reads are under way and optimized. A pre-condition for representative results is an appropriate method for contamination-free collection, homogenization, storage of specimens and a subsequent efficient DNA extraction protocol. As some of the anaerobes such as Clostridia or anaerobe Archaea are robust while others of the same environment, such as spirochetes, possess a very thin cell wall, a chemico-mechanical lysing strategy is recommended but with some precautions to avoid DNA-sheering and overheating. For amplicon sequencing, the Silva-TestPrime online tool helps to find the optimal 16S directed primers for individual studies. For metagenome profiling, the classifier tool has to be selected with helpful decision trees available but a combination based on different strategies seems to be indispensable. Further development of both hard- and software is needed before microbiome results become free of a substantial technology-dependent bias.}, } @article {pmid30768612, year = {2019}, author = {García Antón, A and Garza, V and Hernández Justribó, J and Traba, J}, title = {Factors affecting Dupont´s lark distribution and range regression in Spain.}, journal = {PloS one}, volume = {14}, number = {2}, pages = {e0211549}, pmid = {30768612}, issn = {1932-6203}, mesh = {*Animal Distribution ; Animals ; Climate ; Climate Change ; *Endangered Species ; Geographic Information Systems ; Homing Behavior ; Models, Theoretical ; Passeriformes/*physiology ; Population Density ; Population Dynamics ; Spain ; }, abstract = {In this work, we analyse factors explaining the distribution and range regression of Dupont's lark in Spain, the only European country in which this threatened alaudid is present. Dupont's lark is an extremely elusive and scarce species, distributed across a reduced and strongly fragmented range, showing a metapopulational structure with unknown dispersive and connective mechanisms. We used maximum entropy modelling (Maxent) on nearly 15,000 Dupont's lark observations (1985-2015) to assess the probability of presence at a 1 km resolution across its European range. Moreover, we tested the probability of extinction by comparing pre- and post-2000 observations by means of a GLM over a subset of cells with presence-absence data. We obtained strong model fitting (AUC = 0.919), in which species occurrence was explained by low values of plant productivity (NDVI), climate (high temperature range and medium annual precipitation), land use (increasing with sclerophyllous scrubland), flat topography and human disturbance (associated with low human population density). The species also tolerates dry farming, but not other farm types or forest cover. The probability map identified two main regions known as the species' core areas: the steppes of the Iberian System and the Ebro Valley. The North Plateau is characterised by a dispersed structure of small and very fragmented patches of suitable habitat, while a succession of discontinuous probability patches form an Eastern Corridor connecting the central core areas to the southernmost populations. Finally, the model identified small and isolated patches of high probability of presence along the eastern coastline. The species tends to occur in the best available areas but, at the same time, the model revealed a large area of suitable but unoccupied habitat. Our results correct the previous estimation of occupation area from 1,480 to 1,010.78 km2, a reduction of 26.22%. The current distribution of Dupont's lark is almost completely covered by Important Bird Areas (IBAs), highlighting their importance for bird conservation, but only 44.89% is included in Natura 2000 Special Protection Areas (SPAs). A comparison of pre- and post-2000 periods revealed a range contraction of 44%. Probability of extinction increased with higher temperature range and lower annual precipitation, and with decreases in population density, which suggests that this species is extremely vulnerable to both climate change and rural abandonment, due to its dependence on traditional grazing. These results suggest the need for a re-evaluation of the conservation status of Dupont's lark in Spain. They urge the preservation of not only current extant populations, but also the unoccupied suitable areas that could be critical for metapopulation structure, and the development of policies addressing the preservation of traditional grazing.}, } @article {pmid30768364, year = {2019}, author = {Kain, V and Van Der Pol, W and Mariappan, N and Ahmad, A and Eipers, P and Gibson, DL and Gladine, C and Vigor, C and Durand, T and Morrow, C and Halade, GV}, title = {Obesogenic diet in aging mice disrupts gut microbe composition and alters neutrophil:lymphocyte ratio, leading to inflamed milieu in acute heart failure.}, journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology}, volume = {33}, number = {5}, pages = {6456-6469}, pmid = {30768364}, issn = {1530-6860}, support = {UL1 TR003096/TR/NCATS NIH HHS/United States ; R01 HL132989/HL/NHLBI NIH HHS/United States ; R00 AT006704/AT/NCCIH NIH HHS/United States ; P30 AR050948/AR/NIAMS NIH HHS/United States ; UL1 TR001417/TR/NCATS NIH HHS/United States ; K99 AT006704/AT/NCCIH NIH HHS/United States ; }, mesh = {Acute Disease ; Aging/drug effects/*metabolism/pathology ; Animals ; Diet, High-Fat/adverse effects ; Dietary Fats/*adverse effects/pharmacology ; Firmicutes/classification/*metabolism ; *Gastrointestinal Microbiome ; Heart Failure/chemically induced/*metabolism/pathology ; Inflammation/chemically induced/metabolism/pathology ; Lymphocytes/*metabolism ; Male ; Mice ; Neutrophils/*metabolism/pathology ; *Obesity/chemically induced/metabolism/microbiology/pathology ; }, abstract = {Calorie-dense obesogenic diet (OBD) is a prime risk factor for cardiovascular disease in aging. However, increasing age coupled with changes in the diet can affect the interaction of intestinal microbiota influencing the immune system, which can lead to chronic inflammation. How age and calorie-enriched OBD interact with microbial flora and impact leukocyte profiling is currently under investigated. Here, we tested the interorgan hypothesis to determine whether OBD in young and aging mice alters the gut microbe composition and the splenic leukocyte profile in acute heart failure (HF). Young (2-mo-old) and aging (18-mo-old) mice were supplemented with standard diet (STD, ∼4% safflower oil diet) and OBD (10% safflower oil) for 2 mo and then subjected to coronary artery ligation to induce myocardial infarction. Fecal samples were collected pre- and post-diet intervention, and the microbial flora were analyzed using 16S variable region 4 rRNA gene DNA sequencing and Quantitative Insights Into Microbial Ecology informatics. The STD and OBD in aging mice resulted in an expansion of the genus Allobaculum in the fecal microbiota. However, we found a pathologic change in the neutrophil:lymphocyte ratio in aging mice in comparison with their young counterparts. Thus, calorie-enriched OBD dysregulated splenic leukocytes by decreasing immune-responsive F4/80[+] and CD169[+] macrophages in aging mice. OBD programmed neutrophil swarming with an increase in isoprostanoid levels, with dysregulation of lipoxygenases, cytokines, and metabolite-sensing receptor expression. In summary, calorie-dense OBD in aging mice disrupted the composition of the gut microbiome, which correlates with the development of integrative and system-wide nonresolving inflammation in acute HF.-Kain, V., Van Der Pol, W., Mariappan, N., Ahmad, A., Eipers, P., Gibson, D. L., Gladine, C., Vigor, C., Durand, T., Morrow, C., Halade, G. V. Obesogenic diet in aging mice disrupts gut microbe composition and alters neutrophil:lymphocyte ratio, leading to inflamed milieu in acute heart failure.}, } @article {pmid30767761, year = {2019}, author = {Cao, X and Hu, L and Chen, X and Zhang, R and Cheng, D and Li, H and Xu, Z and Li, L and Zhou, Y and Liu, A and Song, J and Liu, C and Liu, J and Zhao, Z and Chen, M and Ma, Y}, title = {Genome-wide analysis and identification of the low potassium stress responsive gene SiMYB3 in foxtail millet (Setariaitalica L.).}, journal = {BMC genomics}, volume = {20}, number = {1}, pages = {136}, pmid = {30767761}, issn = {1471-2164}, support = {ZR2016CQ33//Shandong Provincial Natural Science Foundation/ ; 2016YFD0101802, 2016YFE0108600//The National Key Research and Development Program of China/ ; NO NUMBER//the Yong Talents Training Program of Shandong Academy of Agricultural Sciences./ ; CXGC2018E13//Agricultural scientific and technological innovation project of Shandong Academy of Agricultural Sciences/ ; }, mesh = {Arabidopsis/genetics ; Databases, Genetic ; Gene Expression Profiling ; *Gene Expression Regulation, Plant ; *Genes, Plant ; Genetic Variation ; High-Throughput Screening Assays ; Oryza/genetics ; Phenotype ; Plant Proteins/genetics/*physiology ; Plant Roots/growth & development ; Plants, Genetically Modified/genetics ; Potassium/*metabolism ; Seedlings/genetics ; Setaria Plant/*genetics/*metabolism ; Stress, Physiological/*genetics ; Transcription Factors/genetics/*physiology ; }, abstract = {BACKGROUND: Potassium (K) is essential to plant growth and development. Foxtail millet (Setaria italic L.) is an important fodder grain crop in arid and semi-arid regions of Asia and Africa because of its strong tolerance to drought and barren stresses. The molecular mechanisms of physiological and biochemical responses and regulations to various abiotic stresses such as low potassium conditions in foxtail millet are not fully understood, which hinders the research and exploitation of this valuable resource.

RESULTS: In this research, we demonstrated that the millet variety Longgu 25 was the most insensitive variety to low potassium stress among other five varieties. The transcriptome analysis of Longgu 25 variety revealed a total of 26,192 and 26,849 genes from the K[+]-deficient and normal transcriptomic libraries by RNA-seq, respectively. A total of 1982 differentially expressed genes (DEGs) were identified including 866 up-regulated genes and 1116 down-regulated genes. We conducted a comparative analysis of these DEGs under low-K[+] stress conditions and discovered 248 common DEGs for potassium deprivation among foxtail millet, rice and Arabidopsis. Further Gene Ontology (GO) enrichment analysis identified a series of candidate genes that may involve in K[+]-deficient response and in intersection of molecular functions among foxtail millet, rice and Arabidopsis. The expression profiles of randomly selected 18 candidate genes were confirmed as true DEGs with RT-qPCR. Furthermore, one of the 18 DEGs, SiMYB3, is specifically expressed only in the millet under low-K[+] stress conditions. Overexpression of SiMYB3 promoted the main root elongation and improved K[+] deficiency tolerance in transgenic Arabidopsis plants. The fresh weight of the transgenic plants was higher, the primary root length was longer and the root surface-area was larger than those of control plants after K[+] deficiency treatments.

CONCLUSIONS: This study provides a global view of transcriptomic resources relevant to the K[+]-deficient tolerance in foxtail millet, and shows that SiMYB3 is a valuable genetic resource for the improvement of K[+] deficiency tolerance in foxtail millet.}, } @article {pmid30767225, year = {2019}, author = {Feng, Z and Yuan, X and Fares, S and Loreto, F and Li, P and Hoshika, Y and Paoletti, E}, title = {Isoprene is more affected by climate drivers than monoterpenes: A meta-analytic review on plant isoprenoid emissions.}, journal = {Plant, cell & environment}, volume = {42}, number = {6}, pages = {1939-1949}, doi = {10.1111/pce.13535}, pmid = {30767225}, issn = {1365-3040}, mesh = {Butadienes/*metabolism ; Carbon Dioxide ; *Climate Change ; Databases, Factual ; Droughts ; Global Warming ; Hemiterpenes/*metabolism ; Monoterpenes/*metabolism ; Ozone ; Photosynthesis/physiology ; Plants/*metabolism ; Terpenes/*metabolism ; Volatile Organic Compounds/metabolism ; }, abstract = {Isoprene and monoterpenes (MTs) are among the most abundant and reactive volatile organic compounds produced by plants (biogenic volatile organic compounds). We conducted a meta-analysis to quantify the mean effect of environmental factors associated to climate change (warming, drought, elevated CO2 , and O3) on the emission of isoprene and MTs. Results indicated that all single factors except warming inhibited isoprene emission. When subsets of data collected in experiments run under similar change of a given environmental factor were compared, isoprene and photosynthesis responded negatively to elevated O3 (-8% and -10%, respectively) and drought (-15% and -42%), and in opposite ways to elevated CO2 (-23% and +55%) and warming (+53% and -23%, respectively). Effects on MTs emission were usually not significant, with the exceptions of a significant stimulation caused by warming (+39%) and by elevated O3 (limited to O3 -insensitive plants, and evergreen species with storage organs). Our results clearly highlight individual effects of environmental factors on isoprene and MT emissions, and an overall uncoupling between these secondary metabolites produced by the same methylerythritol 4-phosphate pathway. Future results from manipulative experiments and long-term observations may help untangling the interactive effects of these factors and filling gaps featured in the current meta-analysis.}, } @article {pmid30766677, year = {2019}, author = {Signer, J and Fieberg, J and Avgar, T}, title = {Animal movement tools (amt): R package for managing tracking data and conducting habitat selection analyses.}, journal = {Ecology and evolution}, volume = {9}, number = {2}, pages = {880-890}, pmid = {30766677}, issn = {2045-7758}, abstract = {Advances in tracking technology have led to an exponential increase in animal location data, greatly enhancing our ability to address interesting questions in movement ecology, but also presenting new challenges related to data management and analysis. Step-selection functions (SSFs) are commonly used to link environmental covariates to animal location data collected at fine temporal resolution. SSFs are estimated by comparing observed steps connecting successive animal locations to random steps, using a likelihood equivalent of a Cox proportional hazards model. By using common statistical distributions to model step length and turn angle distributions, and including habitat- and movement-related covariates (functions of distances between points, angular deviations), it is possible to make inference regarding habitat selection and movement processes or to control one process while investigating the other. The fitted model can also be used to estimate utilization distributions and mechanistic home ranges. Here, we present the R package amt (animal movement tools) that allows users to fit SSFs to data and to simulate space use of animals from fitted models. The amt package also provides tools for managing telemetry data. Using fisher (Pekania pennanti) data as a case study, we illustrate a four-step approach to the analysis of animal movement data, consisting of data management, exploratory data analysis, fitting of models, and simulating from fitted models.}, } @article {pmid30761130, year = {2019}, author = {Velazquez-Caldelas, TE and Alcalá-Corona, SA and Espinal-Enríquez, J and Hernandez-Lemus, E}, title = {Unveiling the Link Between Inflammation and Adaptive Immunity in Breast Cancer.}, journal = {Frontiers in immunology}, volume = {10}, number = {}, pages = {56}, pmid = {30761130}, issn = {1664-3224}, mesh = {*Adaptive Immunity ; Biomarkers ; Breast Neoplasms/*etiology/metabolism/*pathology ; CD8-Positive T-Lymphocytes/immunology/metabolism ; Cellular Microenvironment/genetics/immunology ; Computational Biology/methods ; Disease Susceptibility ; Female ; Gene Expression Profiling ; Gene Expression Regulation ; Gene Ontology ; Gene Regulatory Networks ; Humans ; Inflammation/*complications/immunology/metabolism ; Models, Biological ; Signal Transduction ; }, abstract = {Inflammation has been recognized as an important driver in the development and growth of malignancies. Inflammatory signaling in cancer emerges from the combinatorial interaction of several deregulated pathways. Pathway deregulation is often driven by changes in the underlying gene regulatory networks. Confronted with such complex scenario, it can be argued that a closer analysis of the structure of such regulatory networks will shed some light on how gene deregulation led to sustained inflammation in cancer. Here, we inferred an inflammation-associated gene regulatory network from 641 breast cancer and 78 healthy samples. A modular structure analysis of the regulatory network was carried out, revealing a hierarchical modular structure. Modules show significant overrepresentation score p-values for biological processes unveiling a definite association between inflammatory processes and adaptive immunity. Other modules are enriched for T-cell activation, differentiation of CD8[+] lymphocytes and immune cell migration, thus reinforcing the aforementioned association. These analyses suggest that in breast cancer tumors, the balance between antitumor response and immune tolerance involving CD8[+] T cells is tipped in favor of the tumor. One possible mechanism is the induction of tolerance and anergization of these cells by persistent antigen exposure.}, } @article {pmid30760923, year = {2019}, author = {Wu, L and Wang, D and Evans, JA}, title = {Large teams develop and small teams disrupt science and technology.}, journal = {Nature}, volume = {566}, number = {7744}, pages = {378-382}, doi = {10.1038/s41586-019-0941-9}, pmid = {30760923}, issn = {1476-4687}, mesh = {Cooperative Behavior ; Databases, Factual ; *Diffusion of Innovation ; *Group Processes ; Interdisciplinary Research/*organization & administration/statistics & numerical data/trends ; Nobel Prize ; Patents as Topic/statistics & numerical data ; Research Support as Topic ; Science/*organization & administration/*statistics & numerical data/trends ; Software/supply & distribution ; Technology/*organization & administration/*statistics & numerical data/trends ; }, abstract = {One of the most universal trends in science and technology today is the growth of large teams in all areas, as solitary researchers and small teams diminish in prevalence[1-3]. Increases in team size have been attributed to the specialization of scientific activities[3], improvements in communication technology[4,5], or the complexity of modern problems that require interdisciplinary solutions[6-8]. This shift in team size raises the question of whether and how the character of the science and technology produced by large teams differs from that of small teams. Here we analyse more than 65 million papers, patents and software products that span the period 1954-2014, and demonstrate that across this period smaller teams have tended to disrupt science and technology with new ideas and opportunities, whereas larger teams have tended to develop existing ones. Work from larger teams builds on more-recent and popular developments, and attention to their work comes immediately. By contrast, contributions by smaller teams search more deeply into the past, are viewed as disruptive to science and technology and succeed further into the future-if at all. Observed differences between small and large teams are magnified for higher-impact work, with small teams known for disruptive work and large teams for developing work. Differences in topic and research design account for a small part of the relationship between team size and disruption; most of the effect occurs at the level of the individual, as people move between smaller and larger teams. These results demonstrate that both small and large teams are essential to a flourishing ecology of science and technology, and suggest that, to achieve this, science policies should aim to support a diversity of team sizes.}, } @article {pmid30759619, year = {2019}, author = {Grinn-Gofroń, A and Nowosad, J and Bosiacka, B and Camacho, I and Pashley, C and Belmonte, J and De Linares, C and Ianovici, N and Manzano, JMM and Sadyś, M and Skjøth, C and Rodinkova, V and Tormo-Molina, R and Vokou, D and Fernández-Rodríguez, S and Damialis, A}, title = {Airborne Alternaria and Cladosporium fungal spores in Europe: Forecasting possibilities and relationships with meteorological parameters.}, journal = {The Science of the total environment}, volume = {653}, number = {}, pages = {938-946}, doi = {10.1016/j.scitotenv.2018.10.419}, pmid = {30759619}, issn = {1879-1026}, mesh = {Air Microbiology/*standards ; Air Pollutants/*analysis/immunology ; Air Pollution/analysis ; Allergens/analysis/immunology ; Alternaria/immunology/*physiology ; Cladosporium/immunology/*physiology ; Environmental Monitoring/statistics & numerical data ; Europe ; Forecasting ; *Meteorological Concepts ; Models, Statistical ; Spores, Fungal/immunology/*isolation & purification ; }, abstract = {Airborne fungal spores are prevalent components of bioaerosols with a large impact on ecology, economy and health. Their major socioeconomic effects could be reduced by accurate and timely prediction of airborne spore concentrations. The main aim of this study was to create and evaluate models of Alternaria and Cladosporium spore concentrations based on data on a continental scale. Additional goals included assessment of the level of generalization of the models spatially and description of the main meteorological factors influencing fungal spore concentrations. Aerobiological monitoring was carried out at 18 sites in six countries across Europe over 3 to 21 years depending on site. Quantile random forest modelling was used to predict spore concentrations. Generalization of the Alternaria and Cladosporium models was tested using (i) one model for all the sites, (ii) models for groups of sites, and (iii) models for individual sites. The study revealed the possibility of reliable prediction of fungal spore levels using gridded meteorological data. The classification models also showed the capacity for providing larger scale predictions of fungal spore concentrations. Regression models were distinctly less accurate than classification models due to several factors, including measurement errors and distinct day-to-day changes of concentrations. Temperature and vapour pressure proved to be the most important variables in the regression and classification models of Alternaria and Cladosporium spore concentrations. Accurate and operational daily-scale predictive models of bioaerosol abundances contribute to the assessment and evaluation of relevant exposure and consequently more timely and efficient management of phytopathogenic and of human allergic diseases.}, } @article {pmid30759567, year = {2019}, author = {Anderson, EC and Minor, ES}, title = {Assessing social and biophysical drivers of spontaneous plant diversity and structure in urban vacant lots.}, journal = {The Science of the total environment}, volume = {653}, number = {}, pages = {1272-1281}, doi = {10.1016/j.scitotenv.2018.11.006}, pmid = {30759567}, issn = {1879-1026}, mesh = {*Biodiversity ; Chicago ; Cities ; Ecosystem ; Environmental Monitoring ; Geographic Information Systems ; Plants/classification ; Seasons ; }, abstract = {Vacant lots are typically viewed as urban blight but are also green spaces that provide wildlife habitat and ecosystem services in urban landscapes. Vacant lot vegetation results from interacting biophysical and social forces, and studying vacant lot ecology is an opportunity to examine urban socio-environmental intersections. Here, we assess vegetation patterns in vacant lots across Chicago, IL (USA), and ask two questions: 1) How does diversity and structure vary, and 2) how do social and biophysical drivers contribute to this variation? We conducted vegetation surveys in 35 vacant lots in the summer of 2015. In each lot, we identified all herbaceous plants (excluding turf grasses) and woody seedlings and measured species richness, evenness, vegetation height, and total vegetated area. We used field sampled data about human activities and land use in vacant lots (e.g., presence of a path, trash and turf), coupled with sociodemographic data (e.g., income, ethnicity), and fine-scale land cover to construct two models for each vegetation measure: a best-fit biophysical model and a best-fit social model. We then used variation partitioning to compare the relative strength of these models and any overlap between them. In total, we identified 109 plant species. Species evenness was high, suggesting that there are few rare species in this system. Species richness and vegetation height were better explained by social models, while vegetated area and evenness were better explained by biophysical models. We saw evidence of overlapping explanatory power between the social and biophysical domains. The amount of trash in a lot was the most significant variable, explaining three of our vegetation measures. Lots with higher amounts of trash had higher richness and evenness, and lower vegetated area. This assessment of patterns of vegetation in Chicago's vacant lots provides insight into how habitat differs across the city and informs urban conservation paradigms.}, } @article {pmid30758819, year = {2019}, author = {Shekhar, K and Menon, V}, title = {Identification of Cell Types from Single-Cell Transcriptomic Data.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1935}, number = {}, pages = {45-77}, doi = {10.1007/978-1-4939-9057-3_4}, pmid = {30758819}, issn = {1940-6029}, support = {K99 EY028625/EY/NEI NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; }, mesh = {Animals ; Cluster Analysis ; Computational Biology/methods ; Gene Expression Profiling/methods ; Genome/genetics ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Mice ; RNA/genetics ; Sequence Analysis, RNA/methods ; Single-Cell Analysis/methods ; Transcriptome/*genetics ; }, abstract = {Unprecedented technological advances in single-cell RNA-sequencing (scRNA-seq) technology have now made it possible to profile genome-wide expression in single cells at low cost and high throughput. There is substantial ongoing effort to use scRNA-seq measurements to identify the "cell types" that form components of a complex tissue, akin to taxonomizing species in ecology. Cell type classification from scRNA-seq data involves the application of computational tools rooted in dimensionality reduction and clustering, and statistical analysis to identify molecular signatures that are unique to each type. As datasets continue to grow in size and complexity, computational challenges abound, requiring analytical methods to be scalable, flexible, and robust. Moreover, careful consideration needs to be paid to experimental biases and statistical challenges that are unique to these measurements to avoid artifacts. This chapter introduces these topics in the context of cell-type identification, and outlines an instructive step-by-step example bioinformatic pipeline for researchers entering this field.}, } @article {pmid30758452, year = {2019}, author = {Thum, MA and Baldisserotto, J and Celeste, RK}, title = {[e-SUS AB use and factors associated with recording primary care procedures and consultations in Brazilian municipalities].}, journal = {Cadernos de saude publica}, volume = {35}, number = {2}, pages = {e00029418}, doi = {10.1590/0102-311X00029418}, pmid = {30758452}, issn = {1678-4464}, mesh = {Brazil ; Cities ; Electronic Health Records/*instrumentation ; Family Health ; Health Information Systems/*instrumentation ; Humans ; National Health Programs ; Primary Health Care/methods ; *Referral and Consultation/statistics & numerical data ; }, abstract = {This article sought to evaluate e-SUS AB's impact on procedure and consultation notification in the Outpatient Information System of the Brazilian Unified National Health System (SIA/SUS) in Brazilian municipalities. This is an ecological study with longitudinal comparisons before, during and after the e-SUS AB implementation period (June 2013 to May 2015) and, during implementation, cross-sectional comparison between municipalities in completed, intermediary and initial implementation stages. Rates were described using means and standard deviations and analyzed through negative binomial regression. Municipalities where e-SUS AB had been implemented in November 2014 were small, with lower Municipal Human Development Index (HDI-M), lower per capita income, higher rates of nurses, high Family Health Strategy - (FHS) coverage (> 80%). We did not observe differences in rates of procedures or consultations between municipalities according to implementation stage and there was no increase over time. Municipalities with 100% FHS coverage had higher rates of procedures (rate ratio [RR] = 1.44; 95%CI: 1.29-1.62) and consultations (RR = 1.26; 95%CI: 1.15-1.39); municipalities with more than 100 thousand inhabitants had lower rates of procedures (RR = 0.68; 95%CI: 0.57-0.81) and consultations (RR = 0.54; 95%CI: 0.47-0.63). We found lower procedure rates in all regions when compared with the Northern Region, with the Northeastern RR of 0.34 (95%CI: 0.30-0.40) lower and the Southern Region RR of 0.35 (95%CI: 0.30-0.41) lower than the Northern Region. Further analyses of system use and its implications in teams' work processes should be carried out in order to support managers in using and maintaining the system.}, } @article {pmid30756333, year = {2019}, author = {Wang, H and Xin, H and Guo, J and Gao, Y and Liu, C and Dai, D and Tang, L}, title = {Genome-wide screening of hexokinase gene family and functional elucidation of HXK2 response to cold stress in Jatropha curcas.}, journal = {Molecular biology reports}, volume = {46}, number = {2}, pages = {1649-1660}, pmid = {30756333}, issn = {1573-4978}, support = {31460179//National Natural Science Foundation of China/ ; 31460561//National Natural Science Foundation of China/ ; }, mesh = {Cloning, Molecular/methods ; Cold Temperature ; Cold-Shock Response/*genetics ; Computational Biology/methods ; Gene Expression Regulation, Plant ; Genes, Plant ; Genome-Wide Association Study/methods ; Hexokinase/*genetics ; Jatropha/*genetics/metabolism ; Phylogeny ; Plant Proteins/genetics ; Plants, Genetically Modified/genetics ; }, abstract = {Hexokinase, the key rate-limiting enzyme of plant respiration and glycolysis metabolism, has been found to play a vital role in plant sugar sensing and sugar signal transduction. Using Jatropha curcas genome database and bioinformatics method, J. curcas HXK gene family (JcHXK) was identified and its phylogenetic evolution, functional domain, signal peptide at the N-terminal, and expression analysis were conducted. The results showed that a total of 4 HXK genes (JcHXK1, JcHXK2, JcHXK3, and JcHKL1) with 9 exons were systematically identified from J. curcas. JcHXK1, JcHXK3, and JcHKL1 with putative transmembrane domain at the N-terminal belonged to the type of secretory pathway protein, and JcHXK2 contained putative chloroplast targeting peptide. Quantitative real-time PCR (qRT-PCR) analysis revealed that all the four JcHXKs were expressed in different tissues of the leaves, roots, and seeds; however, JcHXK1 and JcHKL1 expression were higher in the roots, whereas JcHXK2 and JcHXK3 showed over-expression in the leaves and seeds, respectively. Furthermore, all the four JcHXKs were up-regulated in the leaves after cold stress at 12 °C; however, only JcHXK3 remarkably demonstrated cold-induced expression in the roots, which reached the highest expression level at 12 h (2.28-fold). According to the cis-acting element analysis results, JcHXK2 contained the most low temperature responsive elements, which was closely related to the cold resistance in J. curcas. A pET-28a-JcHXK2 prokaryotic recombinant expression vector was successfully constructed and a 57.0 kDa protein was obtained, JcHXK2 revealed catalytic activity towards glucose and fructose, with a higher affinity for glucose than fructose. The subcellular localization assays revealed that JcHXK2 was localized in the chloroplast. The results of this study might provide theoretical foundation for further studies on gene cloning and functional verification of HXK family in J. curcas.}, } @article {pmid30755671, year = {2019}, author = {Schultz, JC and Edger, PP and Body, MJA and Appel, HM}, title = {A galling insect activates plant reproductive programs during gall development.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {1833}, pmid = {30755671}, issn = {2045-2322}, mesh = {Animals ; *Aphids ; Arabidopsis/genetics ; Base Sequence ; Female ; Flowers/physiology ; Gene Expression Profiling ; *Gene Expression Regulation, Plant ; Gene Ontology ; Host-Parasite Interactions ; Insecta ; Meristem ; Phenotype ; Plant Leaves/genetics/parasitology ; Reproduction ; Sequence Analysis, RNA ; Vitis/*parasitology/*physiology ; }, abstract = {Many insect species have acquired the ability to redirect plant development to form unique organs called galls, which provide these insects with unique, enhanced food and protection from enemies and the elements. Many galls resemble flowers or fruits, suggesting that elements of reproductive development may be involved. We tested this hypothesis using RNA sequencing to quantify the transcriptional responses of wild grapevine (Vitis riparia) leaves to a galling parasite, phylloxera (Daktulosphaira vitifoliae). If development of reproductive structures is part of gall formation, we expected to find significantly elevated expression of genes involved in flower and/or fruit development in developing galls as opposed to ungalled leaves. We found that reproductive gene ontology categories were significantly enriched in developing galls, and that expression of many candidate genes involved in floral development were significantly increased, particularly in later gall stages. The patterns of gene expression found in galls suggest that phylloxera exploits vascular cambium to provide meristematic tissue and redirects leaf development towards formation of carpels. The phylloxera leaf gall appears to be phenotypically and transcriptionally similar to the carpel, due to the parasite hijacking underlying genetic machinery in the host plant.}, } @article {pmid30747566, year = {2020}, author = {Greig, M and Child, B}, title = {Submaximal Cricket Fast Bowling Offers a Disproportionate Reduction in Loading Versus Performance: An Alternative Workload Intervention.}, journal = {Journal of sport rehabilitation}, volume = {29}, number = {4}, pages = {483-487}, doi = {10.1123/jsr.2018-0266}, pmid = {30747566}, issn = {1543-3072}, mesh = {Acceleration ; Adolescent ; Back Injuries/physiopathology ; Biomechanical Phenomena ; Cricket Sport/injuries/*physiology ; Geographic Information Systems ; Humans ; Lumbar Vertebrae/injuries/*physiology ; Male ; Motor Skills/physiology ; Sports Medicine ; }, abstract = {CONTEXT: Cricket fast bowlers are particularly susceptible to lumbar spine loading and injury. Quantitative analysis of technique typically involves laboratory-based biomechanical systems with limited ecological validity, whereas contemporary developments in global positioning satellite microtechnologies facilitate an on-field evaluation of loading.

OBJECTIVE: To quantify the influence of submaximal bowling from reduced approach lengths on performance and loading.

DESIGN: Repeated-measures, field-based design.

SETTING: Regulation cricket pitch.

PARTICIPANTS: A total of 12 male cricket academy fast bowlers (18.7 [0.7] y), injury free with ≥3 years of competitive experience.

INTERVENTIONS: Each bowler wore 2 global positioning satellite units placed at C7 and L4 to measure triaxial acceleration (100 Hz). Bowlers completed an over (6 deliveries) from a randomized 3-, 6-, 9-, and 12-stride approach.

MAIN OUTCOME MEASURES: Ball speed was recorded as the performance measure, with PlayerLoad in the anteroposterior, mediolateral, and vertical planes also calculated for each delivery length.

RESULTS: In ball speed, there was a significant main effect for delivery length (P = .02), with a 3-stride approach eliciting significantly less ball speed than a 9-stride (P = .03) or 12-stride (P = .002) approach. In loading, there was a significant main effect for delivery length (P < .001) in the anteroposterior, mediolateral, and vertical planes, with loading increasing linearly as a function of delivery strides. The 6-stride approach elicited a 44% reduction in loading, with a disproportionately small 3.5% decrease in performance. There was a significant main effect for global positioning satellite location (P ≤ .023) in all planes, with L4 eliciting greater loading than C7.

CONCLUSIONS: A submaximal 6-stride approach yielded the optimum balance between reduced loading and performance inhibition. Reduced delivery length, therefore, offers an alternative to reduced overs in reducing loading in young bowlers and might also have practicable value in the rehabilitation of bowlers postinjury.}, } @article {pmid30740899, year = {2019}, author = {Hume, BCC and Smith, EG and Ziegler, M and Warrington, HJM and Burt, JA and LaJeunesse, TC and Wiedenmann, J and Voolstra, CR}, title = {SymPortal: A novel analytical framework and platform for coral algal symbiont next-generation sequencing ITS2 profiling.}, journal = {Molecular ecology resources}, volume = {19}, number = {4}, pages = {1063-1080}, pmid = {30740899}, issn = {1755-0998}, support = {NE/K00641X/1//Natural Environment Research Council/ ; Baseline funding//King Abdullah University of Science and Technology (KAUST)/ ; FP7/2007-013/ERC 311179//FP7 Ideas: European Research Council/ ; }, mesh = {Animals ; Anthozoa/*parasitology ; Computational Biology/*methods ; DNA, Protozoan/chemistry/*genetics ; DNA, Ribosomal Spacer/chemistry/*genetics ; Dinoflagellida/*classification/genetics/isolation & purification ; High-Throughput Nucleotide Sequencing/*methods ; *Phylogeny ; }, abstract = {We present SymPortal (SymPortal.org), a novel analytical framework and platform for genetically resolving the algal symbionts of reef corals using next-generation sequencing (NGS) data of the ITS2 rDNA. Although the ITS2 marker is widely used to genetically characterize taxa within the family Symbiodiniaceae (formerly the genus Symbiodinium), the multicopy nature of the marker complicates its use. Commonly, the intragenomic diversity resultant from this multicopy nature is collapsed by analytical approaches, thereby focusing on only the most abundant sequences. In contrast, SymPortal employs logic to identify within-sample informative intragenomic sequences, which we have termed 'defining intragenomic variants' (DIVs), to identify ITS2-type profiles representative of putative Symbiodiniaceae taxa. By making use of this intragenomic ITS2 diversity, SymPortal is able to resolve genetic delineations using the ITS2 marker at a level that was previously only possible by using additional genetic markers. We demonstrate this by comparing this novel approach to the most commonly used alternative approach for NGS ITS2 data, the 97% similarity clustering to operational taxonomic units (OTUs). The SymPortal platform accepts NGS raw sequencing data as input to provide an easy-to-use, standardization-enforced, and community-driven framework that integrates with a database to gain resolving power with increased use. We consider that SymPortal, in conjunction with ongoing large-scale sampling and sequencing efforts, should play an instrumental role in making future sampling efforts more comparable and in maximizing their efficacy in working towards the classification of the global Symbiodiniaceae diversity.}, } @article {pmid30739152, year = {2019}, author = {Robinson, KF and Fuller, AK and Stedman, RC and Siemer, WF and Decker, DJ}, title = {Integration of social and ecological sciences for natural resource decision making: challenges and opportunities.}, journal = {Environmental management}, volume = {63}, number = {5}, pages = {565-573}, pmid = {30739152}, issn = {1432-1009}, support = {WE-173-G//New York Federal Aid in Wildlife Restoration Grant/International ; }, mesh = {*Conservation of Natural Resources ; Decision Making ; Decision Support Techniques ; *Ecology ; Humans ; Natural Resources ; }, abstract = {The last 25 years have witnessed growing recognition that natural resource management decisions depend as much on understanding humans and their social interactions as on understanding the interactions between non-human organisms and their environment. Decision science provides a framework for integrating ecological and social factors into a decision, but challenges to integration remain. The decision-analytic framework elicits values and preferences to help articulate objectives, and then evaluates the outcomes of alternative management actions to achieve these objectives. Integrating social science into these steps can be hindered by failing to include social scientists as more than stakeholder-process facilitators, assuming that specific decision-analytic skills are commonplace for social scientists, misperceptions of social data as inherently qualitative, timescale mismatches for iterating through decision analysis and collecting relevant social data, difficulties in predicting human behavior, and failures of institutions to recognize the importance of this integration. We engage these challenges, and suggest solutions to them, helping move forward the integration of social and biological/ecological knowledge and considerations in decision-making.}, } @article {pmid30738158, year = {2019}, author = {Yu, P and Zhou, L and Zhou, XY and Yang, WT and Zhang, J and Zhang, XJ and Wang, Y and Gui, JF}, title = {Unusual AT-skew of Sinorhodeus microlepis mitogenome provides new insights into mitogenome features and phylogenetic implications of bitterling fishes.}, journal = {International journal of biological macromolecules}, volume = {129}, number = {}, pages = {339-350}, doi = {10.1016/j.ijbiomac.2019.01.200}, pmid = {30738158}, issn = {1879-0003}, mesh = {Animals ; Base Composition ; Base Sequence ; Codon ; Computational Biology/methods ; Conserved Sequence ; Evolution, Molecular ; Fishes/classification/*genetics ; *Genome, Mitochondrial ; *Genomics/methods ; High-Throughput Nucleotide Sequencing ; Molecular Sequence Annotation ; Nucleic Acid Conformation ; Phylogeny ; }, abstract = {Sinorhodeus microlepis (S. microlepis) is recently described as a new species and represents a new genus Sinorhodeu of the subfamily Acheilognathinae. In this study, we first sequenced the complete mitogenome of S. microlepis and compared with the other 29 bitterling mitogenomes. The S. microlepis mitogenome is 16,591 bp in length and contains 37 genes. Gene distribution pattern is identical among 30 bitterling mitogenomes. A significant linear correlation between A+T% and AT-skew were found among 29 bitterling mitogenomes, except S. microlepis shows unusual AT-skew with slightly negative in tRNAs and PCGs. Bitterling mitogenomes exhibit highly conserved usage bias of start codon, relative synonymous codons and amino acids, overlaps and non-coding intergenic spacers. Phylogenetic trees constructed by 13 PCGs strongly support the polyphyly of the genus Acheilognathus and the paraphyly of Rhodeus and Tanakia. Together with the unusual characters of S. microlepis mitogenomes and phylogenetic trees, S. microlepis should be a sister species to the genus Rhodeu that might diverge about 13.69 Ma (95% HPD: 12.96-14.48 Ma).}, } @article {pmid30735725, year = {2019}, author = {Yao, G and Jin, JJ and Li, HT and Yang, JB and Mandala, VS and Croley, M and Mostow, R and Douglas, NA and Chase, MW and Christenhusz, MJM and Soltis, DE and Soltis, PS and Smith, SA and Brockington, SF and Moore, MJ and Yi, TS and Li, DZ}, title = {Plastid phylogenomic insights into the evolution of Caryophyllales.}, journal = {Molecular phylogenetics and evolution}, volume = {134}, number = {}, pages = {74-86}, doi = {10.1016/j.ympev.2018.12.023}, pmid = {30735725}, issn = {1095-9513}, mesh = {Caryophyllales/*genetics ; Databases, Genetic ; *Evolution, Molecular ; Genome, Plastid/*genetics ; Likelihood Functions ; *Phylogeny ; }, abstract = {The Caryophyllales includes 40 families and 12,500 species, representing a large and diverse clade of angiosperms. Collectively, members of the clade grow on all continents and in all terrestrial biomes and often occupy extreme habitats (e.g., xeric, salty). The order is characterized by many taxa with unusual adaptations including carnivory, halophytism, and multiple origins of C4 photosynthesis. However, deep phylogenetic relationships within the order have long been problematic due to putative rapid divergence. To resolve the deep-level relationships of Caryophyllales, we performed phylogenomic analyses of all 40 families of Caryophyllales. We time-calibrated the molecular phylogeny of this clade, and evaluated putative correlations among plastid structural changes and rates of molecular substitution. We recovered a well-resolved and well-supported phylogeny of the Caryophyllales that was largely congruent with previous estimates of this order. Our results provide improved support for the phylogenetic position of several key families within this clade. The crown age of Caryophyllales was estimated at ca. 114.4 million years ago (Ma), with periods of rapid divergence in the mid-Cretaceous. A strong, positive correlation between nucleotide substitution rate and plastid structural changes was detected. Our study highlights the importance of broad taxon sampling in phylogenomic inference and provides a firm basis for future investigations of molecular, morphological, and ecophysiological evolution in Caryophyllales.}, } @article {pmid30734102, year = {2019}, author = {Zhang, Z and Shu, A and Zhang, K and Liu, H and Wang, J and Dai, J}, title = {Quantification of river bank erosion by RTK GPS monitoring: case studies along the Ningxia-Inner Mongolia reaches of the Yellow River, China.}, journal = {Environmental monitoring and assessment}, volume = {191}, number = {3}, pages = {140}, pmid = {30734102}, issn = {1573-2959}, support = {41730748//National Natural Science Foundation of China/ ; 2011CB403304//Ministry of Science and Technology of China/ ; }, mesh = {Biomechanical Phenomena ; China ; Environmental Monitoring/*methods ; Floods/statistics & numerical data ; *Geographic Information Systems ; *Geological Phenomena ; Rivers ; Water Movements ; }, abstract = {The Ningxia-Inner Mongolia reaches of the Yellow River suffer from bank erosion problems; in order to identify the bank erosion dynamics, Real Time Kinematic Global Positioning System (RTK GPS) was applied to monitor bank morphology at three sites: Taole Cropland (TC), Maobula Shrubland (MS), and Maobula Cropland (MC). The measured data were analyzed using the Geographical Information System (GIS) to quantify the volume and amount of bank erosion. To verify the feasibility of other means quantifying bank erosion including remote sensing image interpretation and Bank-Stability and Toe-Erosion Model (BSTEM) simulation, their results were compared with the directly monitored results by RTK GPS. Results show that the bank erosion moduli at the TC, MS, and MC sites are 12,762, 6681 and 44,142 t km[-1] a[-1] respectively based on RTK GPS measurements from 2011 to 2014, with the bank erosion amount varying between flood and non-flood seasons and among different years. The bank erosion quantified by remote sensing interpretation and BSTEM simulation agreed well with results from RTK GPS measurement. The main factors that influence bank erosion on the upper reaches of the Yellow River include land use in the bank area, bank height, and bank curvature. More rational land use along the Yellow River and stabilization of the river bank are required for this area. This study shows that RTK GPS monitoring is reliable and useful for bank erosion research, which has not yet been fully exploited. There is potential of applying remote sensing and model simulation to determine bank erosion of large rivers, while they should be combined and supported by field investigated data.}, } @article {pmid30728607, year = {2018}, author = {Crous, PW and Luangsa-Ard, JJ and Wingfield, MJ and Carnegie, AJ and Hernández-Restrepo, M and Lombard, L and Roux, J and Barreto, RW and Baseia, IG and Cano-Lira, JF and Martín, MP and Morozova, OV and Stchigel, AM and Summerell, BA and Brandrud, TE and Dima, B and García, D and Giraldo, A and Guarro, J and Gusmão, LFP and Khamsuntorn, P and Noordeloos, ME and Nuankaew, S and Pinruan, U and Rodríguez-Andrade, E and Souza-Motta, CM and Thangavel, R and van Iperen, AL and Abreu, VP and Accioly, T and Alves, JL and Andrade, JP and Bahram, M and Baral, HO and Barbier, E and Barnes, CW and Bendiksen, E and Bernard, E and Bezerra, JDP and Bezerra, JL and Bizio, E and Blair, JE and Bulyonkova, TM and Cabral, TS and Caiafa, MV and Cantillo, T and Colmán, AA and Conceição, LB and Cruz, S and Cunha, AOB and Darveaux, BA and da Silva, AL and da Silva, GA and da Silva, GM and da Silva, RMF and de Oliveira, RJV and Oliveira, RL and De Souza, JT and Dueñas, M and Evans, HC and Epifani, F and Felipe, MTC and Fernández-López, J and Ferreira, BW and Figueiredo, CN and Filippova, NV and Flores, JA and Gené, J and Ghorbani, G and Gibertoni, TB and Glushakova, AM and Healy, R and Huhndorf, SM and Iturrieta-González, I and Javan-Nikkhah, M and Juciano, RF and Jurjević, Ž and Kachalkin, AV and Keochanpheng, K and Krisai-Greilhuber, I and Li, YC and Lima, AA and Machado, AR and Madrid, H and Magalhães, OMC and Marbach, PAS and Melanda, GCS and Miller, AN and Mongkolsamrit, S and Nascimento, RP and Oliveira, TGL and Ordoñez, ME and Orzes, R and Palma, MA and Pearce, CJ and Pereira, OL and Perrone, G and Peterson, SW and Pham, THG and Piontelli, E and Pordel, A and Quijada, L and Raja, HA and Rosas de Paz, E and Ryvarden, L and Saitta, A and Salcedo, SS and Sandoval-Denis, M and Santos, TAB and Seifert, KA and Silva, BDB and Smith, ME and Soares, AM and Sommai, S and Sousa, JO and Suetrong, S and Susca, A and Tedersoo, L and Telleria, MT and Thanakitpipattana, D and Valenzuela-Lopez, N and Visagie, CM and Zapata, M and Groenewald, JZ}, title = {Fungal Planet description sheets: 785-867.}, journal = {Persoonia}, volume = {41}, number = {}, pages = {238-417}, pmid = {30728607}, issn = {0031-5850}, abstract = {Novel species of fungi described in this study include those from various countries as follows: Angola, Gnomoniopsis angolensis and Pseudopithomyces angolensis on unknown host plants. Australia, Dothiora corymbiae on Corymbia citriodora, Neoeucasphaeria eucalypti (incl. Neoeucasphaeria gen. nov.) on Eucalyptus sp., Fumagopsis stellae on Eucalyptus sp., Fusculina eucalyptorum (incl. Fusculinaceae fam. nov.) on Eucalyptus socialis, Harknessia corymbiicola on Corymbia maculata, Neocelosporium eucalypti (incl. Neocelosporium gen. nov., Neocelosporiaceae fam. nov. and Neocelosporiales ord. nov.) on Eucalyptus cyanophylla, Neophaeomoniella corymbiae on Corymbia citriodora, Neophaeomoniella eucalyptigena on Eucalyptus pilularis, Pseudoplagiostoma corymbiicola on Corymbia citriodora, Teratosphaeria gracilis on Eucalyptus gracilis, Zasmidium corymbiae on Corymbia citriodora. Brazil, Calonectria hemileiae on pustules of Hemileia vastatrix formed on leaves of Coffea arabica, Calvatia caatinguensis on soil, Cercospora solani-betacei on Solanum betaceum, Clathrus natalensis on soil, Diaporthe poincianellae on Poincianella pyramidalis, Geastrum piquiriunense on soil, Geosmithia carolliae on wing of Carollia perspicillata, Henningsia resupinata on wood, Penicillium guaibinense from soil, Periconia caespitosa from leaf litter, Pseudocercospora styracina on Styrax sp., Simplicillium filiforme as endophyte from Citrullus lanatus, Thozetella pindobacuensis on leaf litter, Xenosonderhenia coussapoae on Coussapoa floccosa. Canary Islands (Spain), Orbilia amarilla on Euphorbia canariensis. Cape Verde Islands, Xylodon jacobaeus on Eucalyptus camaldulensis. Chile, Colletotrichum arboricola on Fuchsia magellanica. Costa Rica, Lasiosphaeria miniovina on tree branch. Ecuador, Ganoderma chocoense on tree trunk. France, Neofitzroyomyces nerii (incl. Neofitzroyomyces gen. nov.) on Nerium oleander. Ghana, Castanediella tereticornis on Eucalyptus tereticornis, Falcocladium africanum on Eucalyptus brassiana, Rachicladosporium corymbiae on Corymbia citriodora. Hungary, Entoloma silvae-frondosae in Carpinus betulus-Pinus sylvestris mixed forest. Iran, Pseudopyricularia persiana on Cyperus sp. Italy, Inocybe roseascens on soil in mixed forest. Laos, Ophiocordyceps houaynhangensis on Coleoptera larva. Malaysia, Monilochaetes melastomae on Melastoma sp. Mexico, Absidia terrestris from soil. Netherlands, Acaulium pannemaniae, Conioscypha boutwelliae, Fusicolla septimanifiniscientiae, Gibellulopsis simonii, Lasionectria hilhorstii, Lectera nordwiniana, Leptodiscella rintelii, Parasarocladium debruynii and Sarocladium dejongiae (incl. Sarocladiaceae fam. nov.) from soil. New Zealand, Gnomoniopsis rosae on Rosa sp. and Neodevriesia metrosideri on Metrosideros sp. Puerto Rico, Neodevriesia coccolobae on Coccoloba uvifera, Neodevriesia tabebuiae and Alfaria tabebuiae on Tabebuia chrysantha. Russia, Amanita paludosa on bogged soil in mixed deciduous forest, Entoloma tiliae in forest of Tilia × europaea, Kwoniella endophytica on Pyrus communis. South Africa, Coniella diospyri on Diospyros mespiliformis, Neomelanconiella combreti (incl. Neomelanconiellaceae fam. nov. and Neomelanconiella gen. nov.) on Combretum sp., Polyphialoseptoria natalensis on unidentified plant host, Pseudorobillarda bolusanthi on Bolusanthus speciosus, Thelonectria pelargonii on Pelargonium sp. Spain, Vermiculariopsiella lauracearum and Anungitopsis lauri on Laurus novocanariensis, Geosmithia xerotolerans from a darkened wall of a house, Pseudopenidiella gallaica on leaf litter. Thailand, Corynespora thailandica on wood, Lareunionomyces loeiensis on leaf litter, Neocochlearomyces chromolaenae (incl. Neocochlearomyces gen. nov.) on Chromolaena odorata, Neomyrmecridium septatum (incl. Neomyrmecridium gen. nov.), Pararamichloridium caricicola on Carex sp., Xenodactylaria thailandica (incl. Xenodactylariaceae fam. nov. and Xenodactylaria gen. nov.), Neomyrmecridium asiaticum and Cymostachys thailandica from unidentified vine. USA, Carolinigaster bonitoi (incl. Carolinigaster gen. nov.) from soil, Penicillium fortuitum from house dust, Phaeotheca shathenatiana (incl. Phaeothecaceae fam. nov.) from twig and cone litter, Pythium wohlseniorum from stream water, Superstratomyces tardicrescens from human eye, Talaromyces iowaense from office air. Vietnam, Fistulinella olivaceoalba on soil. Morphological and culture characteristics along with DNA barcodes are provided.}, } @article {pmid30726461, year = {2019}, author = {Ferreira, FR and Nascimento, LFC}, title = {Spatial approach of leprosy in the State of São Paulo, 2009-2012.}, journal = {Anais brasileiros de dermatologia}, volume = {94}, number = {1}, pages = {37-41}, pmid = {30726461}, issn = {1806-4841}, mesh = {Bayes Theorem ; Brazil/epidemiology ; Cities/epidemiology ; Female ; Geographic Information Systems ; Humans ; Leprosy/*epidemiology ; Male ; Socioeconomic Factors ; *Spatial Analysis ; }, abstract = {BACKGROUND: Leprosy is a chronic, infectious disease that affects the skin and the peripheral nervous system and can lead to permanent disability and/or deformity.

OBJECTIVES: To identify the distribution and to quantify the spatial dependence of the detection rates of new cases of Hansen's disease in the State of São Paulo, correlating with socioeconomic variables.

METHODS: Ecological and exploratory study with data on the detection rates of new cases of Hansen's disease among residents of São Paulo State municipalities between 2009-2012. The average rate per 10,0000 inhabitants was estimated. Information on the proportion of the population with low-income and the values of the Gini index were obtained. Thematic maps were constructed with the average rates and with those obtained by the Bayesian estimator; Moran and Kernel maps were also constructed. Spatial analysis by TerraView program. An alpha of 5% was adopted.

RESULTS: In total, 7163 new cases of Hansen's disease were recorded throughout the state. The average rate per 10,000 inhabitants, was 0.71 (SD = 1.06), ranging from zero to 12.87, with higher rates in the west of the State, in the metropolitan area of the capital and the Paraiba Valley. Municipalities with high priority for intervention were located in the west and northwest of the State. There was no correlation between rates with Gini index and low income.

STUDY LIMITATIONS: Possible inconsistency of Hansen's disease notification database regarding information quantity, quality and processing.

CONCLUSIONS: This study identified the distribution and quantified the spatial dependence of the detection rates of new cases of Hansen's disease in the State of São Paulo, corroborating previous studies and serving as a subsidy to health managers.}, } @article {pmid30726240, year = {2019}, author = {Jäger, G and Füllsack, M}, title = {Systematically false positives in early warning signal analysis.}, journal = {PloS one}, volume = {14}, number = {2}, pages = {e0211072}, pmid = {30726240}, issn = {1932-6203}, mesh = {Computer Simulation ; *Data Analysis ; *Data Interpretation, Statistical ; False Positive Reactions ; *Models, Theoretical ; }, abstract = {Many systems in various scientific fields like medicine, ecology, economics or climate science exhibit so-called critical transitions, through which a system abruptly changes from one state to a different state. Typical examples are epileptic seizures, changes in the climate system or catastrophic shifts in ecosystems. In order to predict imminent critical transitions, a mathematical apparatus called early warning signals has been developed and this method is used successfully in many scientific areas. However, not all critical transitions can be detected by this approach (false negative) and the appearance of early warning signals does not necessarily proof that a critical transition is imminent (false positive). Furthermore, there are whole classes of systems that always show early warning signals, even though they do not feature critical transitions. In this study we identify such classes in order to provide a safeguard against a misinterpretation of the results of an early warning signal analysis of such systems. Furthermore, we discuss strategies to avoid such systematic false positives and test our theoretical insights by applying them to real world data.}, } @article {pmid30726213, year = {2019}, author = {Diao, X and Wu, K and Zhou, D and Wang, J and Duan, Z and Yu, Z}, title = {Combining subsidence theory and slope stability analysis method for building damage assessment in mountainous mining subsidence regions.}, journal = {PloS one}, volume = {14}, number = {2}, pages = {e0210021}, pmid = {30726213}, issn = {1932-6203}, mesh = {China ; *Coal Mining ; *Construction Industry ; *Construction Materials ; *Models, Theoretical ; *Structure Collapse ; }, abstract = {Ground subsidence and surface cracks caused by coal mining are typical man-made geological hazards that can severely damage the ecological environment and buildings. In China, within the theme of sustained and stable development, accurate assessment of mining-related building damage is paramount in order to address the contradiction between coal mining enterprises and building owners. Previous research in China focused mainly on the mining areas of plains, and only a few studies have considered building damage caused by intensive mining in mountainous areas. First, based on field investigation, this study located ground surface cracks and assessed the damage to buildings in the village of Nanyetou in Shanxi Province (China) attributable to the exploitation of the 15110 working face of the Baiyangling coal mine. Second, based on the mining subsidence law and boundary angle, the surface influenced boundary caused by underground mining was determined. However, as the existing subsidence theory cannot adequately explain the phenomenon of building damage, the damage was investigated from the perspective of slope stability analysis, and the slope safety factor before and after working face mining were calculated using the Janbu method. The analytical results showed that slope instability due to a decrease of the safety factor because of the coal mining activity was the principal reason for damage to the village buildings, a finding that was confirmed by field survey and InSAR monitoring displacement. The results of this study could provide guidance and reference for the assessment of building damage caused by underground mining in mountain areas.}, } @article {pmid30721922, year = {2019}, author = {Brázda, V and Kolomazník, J and Lýsek, J and Bartas, M and Fojta, M and Šťastný, J and Mergny, JL}, title = {G4Hunter web application: a web server for G-quadruplex prediction.}, journal = {Bioinformatics (Oxford, England)}, volume = {35}, number = {18}, pages = {3493-3495}, pmid = {30721922}, issn = {1367-4811}, mesh = {Computers ; DNA ; *G-Quadruplexes ; Guanine ; Internet ; Sequence Analysis, DNA ; Software ; }, abstract = {MOTIVATION: Expanding research highlights the importance of guanine quadruplex structures. Therefore, easy-accessible tools for quadruplex analyses in DNA and RNA molecules are important for the scientific community.

RESULTS: We developed a web version of the G4Hunter application. This new web-based server is a platform-independent and user-friendly application for quadruplex analyses. It allows retrieval of gene/nucleotide sequence entries from NCBI databases and provides complete characterization of localization and quadruplex propensity of quadruplex-forming sequences. The G4Hunter web application includes an interactive graphical data representation with many useful options including visualization, sorting, data storage and export.

G4Hunter web application can be accessed at: http://bioinformatics.ibp.cz.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, } @article {pmid30721227, year = {2019}, author = {Marsland, R and Cui, W and Goldford, J and Sanchez, A and Korolev, K and Mehta, P}, title = {Available energy fluxes drive a transition in the diversity, stability, and functional structure of microbial communities.}, journal = {PLoS computational biology}, volume = {15}, number = {2}, pages = {e1006793}, pmid = {30721227}, issn = {1553-7358}, support = {R35 GM119461/GM/NIGMS NIH HHS/United States ; }, mesh = {Computational Biology ; Databases, Factual ; *Ecosystem ; Energy Metabolism/*physiology ; Microbial Consortia/*physiology ; Models, Biological ; Stochastic Processes ; Thermodynamics ; }, abstract = {A fundamental goal of microbial ecology is to understand what determines the diversity, stability, and structure of microbial ecosystems. The microbial context poses special conceptual challenges because of the strong mutual influences between the microbes and their chemical environment through the consumption and production of metabolites. By analyzing a generalized consumer resource model that explicitly includes cross-feeding, stochastic colonization, and thermodynamics, we show that complex microbial communities generically exhibit a transition as a function of available energy fluxes from a "resource-limited" regime where community structure and stability is shaped by energetic and metabolic considerations to a diverse regime where the dominant force shaping microbial communities is the overlap between species' consumption preferences. These two regimes have distinct species abundance patterns, different functional profiles, and respond differently to environmental perturbations. Our model reproduces large-scale ecological patterns observed across multiple experimental settings such as nestedness and differential beta diversity patterns along energy gradients. We discuss the experimental implications of our results and possible connections with disorder-induced phase transitions in statistical physics.}, } @article {pmid30721163, year = {2019}, author = {Morrison, CN and Byrnes, HF and Miller, BA and Kaner, E and Wiehe, SE and Ponicki, WR and Wiebe, DJ}, title = {Assessing Individuals' Exposure to Environmental Conditions Using Residence-based Measures, Activity Location-based Measures, and Activity Path-based Measures.}, journal = {Epidemiology (Cambridge, Mass.)}, volume = {30}, number = {2}, pages = {166-176}, pmid = {30721163}, issn = {1531-5487}, support = {R01 HD078415/HD/NICHD NIH HHS/United States ; }, mesh = {Adolescent ; *Alcoholic Beverages ; *Anomie ; *Cultural Deprivation ; Data Collection ; Ecological Momentary Assessment ; Female ; Geographic Information Systems ; Humans ; Male ; Parent-Child Relations ; Poverty/statistics & numerical data ; San Francisco/epidemiology ; Student Dropouts/statistics & numerical data ; Surveys and Questionnaires ; Underage Drinking/*statistics & numerical data ; Unemployment/statistics & numerical data ; }, abstract = {BACKGROUND: Many approaches are available to researchers who wish to measure individuals' exposure to environmental conditions. Different approaches may yield different estimates of associations with health outcomes. Taking adolescents' exposure to alcohol outlets as an example, we aimed to (1) compare exposure measures and (2) assess whether exposure measures were differentially associated with alcohol consumption.

METHODS: We tracked 231 adolescents 14-16 years of age from the San Francisco Bay Area for 4 weeks in 2015/2016 using global positioning systems (GPS). Participants were texted ecologic momentary assessment surveys six times per week, including assessment of alcohol consumption. We used GPS data to calculate exposure to alcohol outlets using three approach types: residence-based (e.g., within the home census tract), activity location-based (e.g., within buffer distances of frequently attended places), and activity path-based (e.g., average outlets per hour within buffer distances of GPS route lines). Spearman correlations compared exposure measures, and separate Tobit models assessed associations with the proportion of ecologic momentary assessment responses positive for alcohol consumption.

RESULTS: Measures were mostly strongly correlated within approach types (ρ ≥ 0.7), but weakly (ρ < 0.3) to moderately (0.3 ≤ ρ < 0.7) correlated between approach types. Associations with alcohol consumption were mostly inconsistent within and between approach types. Some of the residence-based measures (e.g., census tract: β = 8.3, 95% CI = 2.8, 13.8), none of the activity location-based approaches, and most of the activity path-based approaches (e.g., outlet-hours per hour, 100 m buffer: β = 8.3, 95% CI = 3.3, 13.3) were associated with alcohol consumption.

CONCLUSIONS: Methodologic decisions regarding measurement of exposure to environmental conditions may affect study results.}, } @article {pmid30716633, year = {2019}, author = {Li, S and Zhou, C and Wang, S}, title = {Does modernization affect carbon dioxide emissions? A panel data analysis.}, journal = {The Science of the total environment}, volume = {663}, number = {}, pages = {426-435}, doi = {10.1016/j.scitotenv.2019.01.373}, pmid = {30716633}, issn = {1879-1026}, abstract = {Modernization refers to the general trend of developmental progress that occurs within human societies. We now know that global warming, a result of carbon dioxide emissions, severely threatens the sustainability of human society. It is therefore of significant theoretical and practical implications that the scientific community more thoroughly investigate the impacts of modernization on CO2 emissions. Surprisingly, only a limited number of studies have addressed this topic previously. As the world's largest developing economy and carbon emitter, China faces the dual challenge of peaking carbon emissions by 2030 while realizing basic modernization by 2035. With the purpose of identifying the implications of China's 2035 modernization goal for its 2030 emission peak goal, this study explored the effects of modernization on carbon dioxide emissions in China. Using a comprehensive indicator system, five modernization indexes-addressing industrialization, agricultural modernization, informatization, urbanization, and ecological modernization-were estimated, along with carbon dioxide emissions, for the period 1997-2016, for 30 Chinese provinces. Panel data modeling was then used to examine the impacts of the five modernization indexes on CO2 emissions in China. The results demonstrate that industrialization, agricultural modernization, informatization, and urbanization exerted positive effects on CO2 emissions during the study period, suggesting these aspects of modernization led to increased carbon dioxide emissions. A negative correlation between ecological modernization and carbon dioxide emission was identified, indicating that ecological modernization helped to abate CO2 emissions. The findings emerging from this study hold significant implications for China's policy makers in promoting decarbonization, suggesting the utility of pursuing new-type industrialization, developing organic agriculture and eco-agriculture, popularizing electronic equipment with low power dissipation, building low-carbon cities, and promoting the ecology-oriented transformation of the modernization model.}, } @article {pmid30716128, year = {2019}, author = {Amor, JM and Newman, R and Jensen, WF and Rundquist, BC and Walter, WD and Boulanger, JR}, title = {Seasonal home ranges and habitat selection of three elk (Cervus elaphus) herds in North Dakota.}, journal = {PloS one}, volume = {14}, number = {2}, pages = {e0211650}, pmid = {30716128}, issn = {1932-6203}, mesh = {Animals ; Animals, Wild/physiology ; Canada ; Deer/*physiology ; Ecosystem ; Feeding Behavior/physiology ; Female ; Geographic Information Systems ; Homing Behavior/*physiology ; Models, Biological ; North Dakota ; Seasons ; }, abstract = {Changes in land use have resulted in range shifts of many wildlife species, including those entering novel environments, resulting in the critical need to understand their spatial ecology to inform ecosystem effects and management decisions. Dispersing elk (Cervus elaphus) were colonizing areas of suitable habitat in the Northern Great Plains, USA, resulting in crop depredation complaints in these areas. Although state resource managers had little information on these elk herds, limited evidence suggested temporal movements into Canada. We collected and analyzed essential information on home range and habitat selection for 3 elk herds residing in North Dakota. We captured 5 adult female elk in each study area, affixed global positioning system collars, and monitored them for 1 year (2016-2017). We estimated diel period, seasonal, and hunting season home ranges using Brownian Bridge Movement Models for each individual. We analyzed habitat selection using multinomial logit models to test for differences in use of land classes, and for departures from proportionate use based on random sampling; our predictor variables included individual elk, diel period, and season. Home ranges differed between the 3 herds, seasons, and diel period; gun and winter season home ranges were both larger than in summer, as was night when compared with day. Female elk generally restricted themselves to cover during the day and entered open areas at night and during winter months. Our results also suggest that elk in our study areas tended to seek more cover, and in the case of our Turtle Mountain study area, some cross into Canada during gun season. Our study provides a better understanding of the spatial ecology of elk in the Northern Great Plains while highlighting the need for enhanced international cooperative management efforts.}, } @article {pmid30716065, year = {2019}, author = {Louca, S and Mazel, F and Doebeli, M and Parfrey, LW}, title = {A census-based estimate of Earth's bacterial and archaeal diversity.}, journal = {PLoS biology}, volume = {17}, number = {2}, pages = {e3000106}, pmid = {30716065}, issn = {1545-7885}, mesh = {Archaea/*genetics ; Bacteria/*genetics ; *Biodiversity ; Databases, Genetic ; *Earth, Planet ; Phylogeny ; Prokaryotic Cells/metabolism ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The global diversity of Bacteria and Archaea, the most ancient and most widespread forms of life on Earth, is a subject of intense controversy. This controversy stems largely from the fact that existing estimates are entirely based on theoretical models or extrapolations from small and biased data sets. Here, in an attempt to census the bulk of Earth's bacterial and archaeal ("prokaryotic") clades and to estimate their overall global richness, we analyzed over 1.7 billion 16S ribosomal RNA amplicon sequences in the V4 hypervariable region obtained from 492 studies worldwide, covering a multitude of environments and using multiple alternative primers. From this data set, we recovered 739,880 prokaryotic operational taxonomic units (OTUs, 16S-V4 gene clusters at 97% similarity), a commonly used measure of microbial richness. Using several statistical approaches, we estimate that there exist globally about 0.8-1.6 million prokaryotic OTUs, of which we recovered somewhere between 47%-96%, representing >99.98% of prokaryotic cells. Consistent with this conclusion, our data set independently "recaptured" 91%-93% of 16S sequences from multiple previous global surveys, including PCR-independent metagenomic surveys. The distribution of relative OTU abundances is consistent with a log-normal model commonly observed in larger organisms; the total number of OTUs predicted by this model is also consistent with our global richness estimates. By combining our estimates with the ratio of full-length versus partial-length (V4) sequence diversity in the SILVA sequence database, we further estimate that there exist about 2.2-4.3 million full-length OTUs worldwide. When restricting our analysis to the Americas, while controlling for the number of studies, we obtain similar richness estimates as for the global data set, suggesting that most OTUs are globally distributed. Qualitatively similar results are also obtained for other 16S similarity thresholds (90%, 95%, and 99%). Our estimates constrain the extent of a poorly quantified rare microbial biosphere and refute recent predictions that there exist trillions of prokaryotic OTUs.}, } @article {pmid30715467, year = {2019}, author = {Saad-Roy, CM and McDermott, AB and Grenfell, BT}, title = {Dynamic Perspectives on the Search for a Universal Influenza Vaccine.}, journal = {The Journal of infectious diseases}, volume = {219}, number = {Suppl_1}, pages = {S46-S56}, pmid = {30715467}, issn = {1537-6613}, mesh = {Computational Biology/methods ; Cross Protection/immunology ; Hemagglutinin Glycoproteins, Influenza Virus/immunology ; Humans ; Influenza A virus/genetics/*immunology/isolation & purification ; Influenza B virus/genetics/*immunology/isolation & purification ; Influenza Vaccines/*immunology ; Influenza, Human/epidemiology/*prevention & control/transmission ; Models, Theoretical ; Pandemics/*prevention & control ; Phylogeny ; Vaccination ; }, abstract = {A universal influenza vaccine (UIV) could considerably alleviate the public health burden of both seasonal and pandemic influenza. Although significant progress has been achieved in clarifying basic immunology and virology relating to UIV, several important questions relating to the dynamics of infection, immunity, and pathogen evolution remain unsolved. In this study, we review these gaps, which span integrative levels, from cellular to global and timescales from molecular events to decades. We argue that they can be best addressed by a tight integration of empirical (laboratory, epidemiological) research and theory and suggest fruitful areas for this synthesis. In particular, quantifying natural and vaccinal limitations on viral transmission are central to this effort.}, } @article {pmid30715292, year = {2019}, author = {Chen, L and Lu, Y and Li, W and Ren, Y and Yu, M and Jiang, S and Fu, Y and Wang, J and Peng, S and Bilyk, KT and Murphy, KR and Zhuang, X and Hune, M and Zhai, W and Wang, W and Xu, Q and Cheng, CC}, title = {The genomic basis for colonizing the freezing Southern Ocean revealed by Antarctic toothfish and Patagonian robalo genomes.}, journal = {GigaScience}, volume = {8}, number = {4}, pages = {}, pmid = {30715292}, issn = {2047-217X}, mesh = {Adaptation, Physiological ; Animals ; Antarctic Regions ; Biological Evolution ; Computational Biology/methods ; Data Curation ; Environment ; Fishes/classification/*genetics ; Freezing ; Gene Expression Profiling ; *Genome ; *Genomics/methods ; Molecular Sequence Annotation ; Osteogenesis ; Phylogeny ; Transcriptome ; Vertebrates ; Whole Genome Sequencing ; }, abstract = {BACKGROUND: The Southern Ocean is the coldest ocean on Earth but a hot spot of evolution. The bottom-dwelling Eocene ancestor of Antarctic notothenioid fishes survived polar marine glaciation and underwent adaptive radiation, forming >120 species that fill all water column niches today. Genome-wide changes enabling physiological adaptations and the rapid expansion of the Antarctic notothenioids remain poorly understood.

RESULTS: We sequenced and compared 2 notothenioid genomes-the cold-adapted and neutrally buoyant Antarctic toothfish Dissostichus mawsoni and the basal Patagonian robalo Eleginops maclovinus, representing the temperate ancestor. We detected >200 protein gene families that had expanded and thousands of genes that had evolved faster in the toothfish, with diverse cold-relevant functions including stress response, lipid metabolism, protein homeostasis, and freeze resistance. Besides antifreeze glycoprotein, an eggshell protein had functionally diversified to aid in cellular freezing resistance. Genomic and transcriptomic comparisons revealed proliferation of selcys-transfer RNA genes and broad transcriptional upregulation across anti-oxidative selenoproteins, signifying their prominent role in mitigating oxidative stress in the oxygen-rich Southern Ocean. We found expansion of transposable elements, temporally correlated to Antarctic notothenioid diversification. Additionally, the toothfish exhibited remarkable shifts in genetic programs towards enhanced fat cell differentiation and lipid storage, and promotion of chondrogenesis while inhibiting osteogenesis in bone development, collectively contributing to the achievement of neutral buoyancy and pelagicism.

CONCLUSIONS: Our study revealed a comprehensive landscape of evolutionary changes essential for Antarctic notothenioid cold adaptation and ecological expansion. The 2 genomes are valuable resources for further exploration of mechanisms underlying the spectacular notothenioid radiation in the coldest marine environment.}, } @article {pmid30714190, year = {2019}, author = {Connors, KA and Beasley, A and Barron, MG and Belanger, SE and Bonnell, M and Brill, JL and de Zwart, D and Kienzler, A and Krailler, J and Otter, R and Phillips, JL and Embry, MR}, title = {Creation of a Curated Aquatic Toxicology Database: EnviroTox.}, journal = {Environmental toxicology and chemistry}, volume = {38}, number = {5}, pages = {1062-1073}, pmid = {30714190}, issn = {1552-8618}, support = {//Health and Environmental Sciences Institute Animal Alternatives in Environmental Risk Assessment Technical Committee/International ; }, mesh = {Animals ; Aquatic Organisms/drug effects ; *Databases, Factual ; *Ecotoxicology ; Risk Assessment ; Toxicity Tests, Acute ; Toxicity Tests, Chronic ; Water Pollutants, Chemical/*toxicity ; }, abstract = {Flexible, rapid, and predictive approaches that do not require the use of large numbers of vertebrate test animals are needed because the chemical universe remains largely untested for potential hazards. Development of robust new approach methodologies and nontesting approaches requires the use of existing information via curated, integrated data sets. The ecological threshold of toxicological concern (ecoTTC) represents one such new approach methodology that can predict a conservative de minimis toxicity value for chemicals with little or no information available. For the creation of an ecoTTC tool, a large, diverse environmental data set was developed from multiple sources, with harmonization, characterization, and information quality assessment steps to ensure that the information could be effectively organized and mined. The resulting EnviroTox database contains 91 217 aquatic toxicity records representing 1563 species and 4016 unique Chemical Abstracts Service numbers and is a robust, curated database containing high-quality aquatic toxicity studies that are traceable to the original information source. Chemical-specific information is also linked to each record and includes physico-chemical information, chemical descriptors, and mode of action classifications. Toxicity data are associated with the physico-chemical data, mode of action classifications, and curated taxonomic information for the organisms tested. The EnviroTox platform also includes 3 analysis tools: a predicted-no-effect concentration calculator, an ecoTTC distribution tool, and a chemical toxicity distribution tool. Although the EnviroTox database and tools were originally developed to support ecoTTC analysis and development, they have broader applicability to the field of ecological risk assessment. Environ Toxicol Chem 2019;9999:1-12. © 2019 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals, Inc. on behalf of SETAC.}, } @article {pmid30713261, year = {2020}, author = {Yamaoka, Y and Fujiwara, T and Fujino, Y and Matsuda, S and Fushimi, K}, title = {Incidence and Age Distribution of Hospitalized Presumptive and Possible Abusive Head Trauma of Children Under 12 Months Old in Japan.}, journal = {Journal of epidemiology}, volume = {30}, number = {2}, pages = {91-97}, pmid = {30713261}, issn = {1349-9092}, mesh = {Age Distribution ; Child Abuse/*diagnosis ; Craniocerebral Trauma/*epidemiology/*therapy ; Cross-Sectional Studies ; Databases, Factual ; Female ; *Hospitalization ; Humans ; Incidence ; Infant ; International Classification of Diseases ; Japan/epidemiology ; Male ; }, abstract = {BACKGROUND: Abusive head trauma (AHT) is the leading cause of fatal maltreatment among young children. The incidence of AHT in Japan, however, remains unknown. This study examined the incidence and distribution of age in months among young children under 12 months of age hospitalized with intracranial injury in Japan.

METHODS: We conducted a multicenter cross-sectional study of children under 36 months old admitted with intracranial injury to hospitals that employed the Diagnostic Procedure Combination (DPC) payment system between 2010 and 2013. Presumptive and possible AHT were defined using the combination of ICD-10 codes modified from the coding system recommended by the United States Centers for Disease Control and Prevention.

RESULTS: The average incidence was 7.2 (95% confidence interval [CI], 7.18-7.26) for presumptive and 41.7 (95% CI, 41.7-41.8) for possible AHT per 100,000 children less than 12 months old from 2010 to 2013. The distributions of age in months for both presumptive AHT and possible AHT had peaks at around 2 and 8 months.

CONCLUSIONS: This is the first study to report the incidence of hospitalized children with presumptive and possible AHT using population-based data. Further datasets are needed to evaluate the incidence and specific preventive strategies to prevent AHT in infants during the months of highest risk.}, } @article {pmid30713051, year = {2019}, author = {Reiczigel, J and Marozzi, M and Fábián, I and Rózsa, L}, title = {Biostatistics for Parasitologists - A Primer to Quantitative Parasitology.}, journal = {Trends in parasitology}, volume = {35}, number = {4}, pages = {277-281}, doi = {10.1016/j.pt.2019.01.003}, pmid = {30713051}, issn = {1471-5007}, mesh = {*Biostatistics ; Parasitology/*methods ; *Software ; }, abstract = {The aggregated distributions of host-parasite systems require several different infection parameters to characterize them. We advise readers how to choose infection indices with clear and distinct biological interpretations, and recommend statistical tests to compare them across samples. A user-friendly and free software is available online to overcome technical difficulties.}, } @article {pmid30711775, year = {2019}, author = {Lai, Y and Kontokosta, CE}, title = {The impact of urban street tree species on air quality and respiratory illness: A spatial analysis of large-scale, high-resolution urban data.}, journal = {Health & place}, volume = {56}, number = {}, pages = {80-87}, doi = {10.1016/j.healthplace.2019.01.016}, pmid = {30711775}, issn = {1873-2054}, mesh = {Air Pollutants ; Air Pollution/*statistics & numerical data ; Allergens ; Asthma/epidemiology ; Cities ; Emergency Medical Services/statistics & numerical data ; Environmental Health ; Humans ; New York City/epidemiology ; Public Health ; *Residence Characteristics ; Respiratory Tract Diseases/*epidemiology ; *Spatial Analysis ; Trees/*adverse effects ; }, abstract = {Urban trees play a key role in reducing greenhouse gas emissions, cleaning air, promoting physical activity, and improving mental health. However, it is still largely unknown how the density and species of urban street trees may impact local public health. This study demonstrates how open data mining and large-scale spatial data integration can contribute to deeper insights into the effects of urban forestry. We analyze the impact of the spatial distribution of street trees by species in New York City by combining crowd-sourced tree census data - which includes geolocation, species, size, and condition for each of 652,169 street trees - with pollen activity, allergen severity, land use, housing conditions, and neighborhood demographic data. We further integrate neighborhood asthma hospitalization and emergency department visit rates and air quality data (PM2.5) to investigate how street trees impact local air quality and the prevalence of acute respiratory illness. Using a geographically weighted regression model, the results indicate that although a greater concentration of trees contributes to better local air quality, species with severe allergenicity can increase local asthma hospitalization rates in vulnerable populations, controlling for other covariates.}, } @article {pmid30707878, year = {2019}, author = {Qin, J and Liu, H and Dong, Y and Yi, Q and Zhang, C and Yu, S and Huang, Q and Zhao, Y and Mo, S}, title = {[Integration of clinical pathway construction and hospital information system in intensive care unit is the core of digitalized hospital: experience of clinical pathway construction in Liuzhou Worker's Hospital from 2016 to 2018].}, journal = {Zhonghua wei zhong bing ji jiu yi xue}, volume = {31}, number = {1}, pages = {102-107}, doi = {10.3760/cma.j.issn.2095-4352.2019.01.020}, pmid = {30707878}, issn = {2095-4352}, mesh = {China ; Critical Pathways/*organization & administration ; Hospital Information Systems/*organization & administration ; Humans ; Intensive Care Units/*organization & administration ; Pilot Projects ; }, abstract = {OBJECTIVE: To explore the effective strategies of clinical pathway construction in intensive care unit (ICU).

METHODS: From January 2016 to July 2018, 1 488 patients were discharged from ICU of Liuzhou Worker's Hospital of Guangxi Zhuang Autonomous Region. The pilot project of "postoperative monitoring of heart disease" with simpler route and less variation was selected first, and then the pilot project was promoted to "post-operative monitoring" after its success. The implementation of the clinical pathway was divided into three stages: the first stage, January 2016 to May 2017, for the pilot phase, a total of 87 patients were enrolled in the clinical pathway trial; the second stage, June 2017 to December 2017, surgical ICU "postoperative monitoring of heart disease" was put into the pathway 111 times; the third stage, January 2018 to July 2018, surgical ICU "postoperative monitoring of heart disease" was entered in the path 116 times; comprehensive ICU "postoperative care" was put into the path 96 times. After carefully analyzed the reasons and sum up the experience, internet+medical treatment (Liuzhou Worker's Hospital became the fifth deep partner of Tencent Inc in the internet+medical field, and carried out the plan and practice of "WeChat wisdom hospital 3.0" in 2017) was used, four aspects of connection, payment, security and ecological cooperation were upgraded, and the construction of 6 level of electronic medical record (EMR) was accelerated. At the same time, through diagnosis related groups system (DRGs), the concept of evidence-based medicine, quality management and continuous improvement as the leading factor, and combined with the construction status of hospital information system (HIS) and EMR system, step by step implementation and design of information management platform for clinical pathway were formulated. The completion rate of clinical pathway, average length of hospital stay, average cost, cure rate and improvement rate were the main observation parameters.

RESULTS: In the first stage, none of the 87 patients who entered the clinical pathway completed the clinical pathway. In the second stage, the completion rate of surgical ICU clinical pathway was increased from 33.33% in June 2017 to 94.44% in December 2017, and up to 100% in October 2017, and the average completion rate from January to July 2018 was 94.00%. The completion rate of ICU clinical pathway was increased from 81.82% in January 2008 to 92.86% in July 2008. There was a significant difference in the overall clinical pathway completion rate from 2016 to 2018 (χ[2] = 204.300, P = 0.000). After the effective implementation of clinical pathway in June 2017, the length of hospital stay of patients was significantly shortened as compared with that before implementation (days: 2.96±0.43 vs. 6.66±0.75, P < 0.01), and the daily cost was significantly reduced (Yuan: 3 550.92±755.51 vs. 6 171.48±377.29, P < 0.01). The average length of hospital stay was shortened by about 3.84 days (P < 0.01), and the average daily cost was reduced by about 2 108.39 Yuan (P < 0.01) after the implementation of clinical pathway by surgical ICU "postoperative monitoring of heart disease" as compared with those before implementation. The average length of hospital stay was shortened by about 2.98 days (P < 0.01) and the average daily cost was reduced by 5 094.13 Yuan (P < 0.01) after the implementation of clinical pathway by comprehensive ICU "post-operative monitoring" as compared with those before implementation. At the same time, the cure rate was increased from 1.16% (7/603) to 42.26% (105/227), and the improvement rate was decreased from 94.36% (569/603) to 52.86% (120/227, both P < 0.01) after the implementation of surgical ICU clinical pathway, but there was no significant difference in the cure rate or the improvement rate after the implementation of comprehensive ICU [2.77% (33/1 193) vs. 2.22% (2/90), 79.21% (945/1 193) vs. 97.78% (88/90), both P > 0.05].

CONCLUSIONS: Application of clinical pathway to control ICU quality and guide diagnosis and treatment, more refined diagnosis and treatment schemes including clinical guidelines, average length of stay, average cost of hospitalization, cost-efficiency ratio and so on were completed, which confirmed that the improvement of clinical pathway management strategy originated from clinical were needed. Informatization, intellectualization, standardization and effective control of medical cost of clinical pathway could improve medical quality and accurate management. The integration of ICU clinical pathway construction and HIS could promote the development of digital hospitals.}, } @article {pmid30707720, year = {2019}, author = {Fagua, JC and Ramsey, RD}, title = {Geospatial modeling of land cover change in the Chocó-Darien global ecoregion of South America; One of most biodiverse and rainy areas in the world.}, journal = {PloS one}, volume = {14}, number = {2}, pages = {e0211324}, pmid = {30707720}, issn = {1932-6203}, mesh = {*Biodiversity ; Conservation of Natural Resources ; Environmental Monitoring/*methods ; *Rainforest ; South America ; }, abstract = {The tropical rain forests of northwest South America fall within the Chocó-Darien Global Ecoregion (CGE). The CGE is one of 25 global biodiversity hotspots prioritized for conservation due to its high biodiversity and endemism as well as threats due to deforestation. The analysis of land-use and land-cover (LULC) change within the CGE using remotely sensed imagery is challenging because this area is considered to be one of the rainiest places on the planet (hence high frequency of cloud cover). Furthermore, the availability of high-resolution remotely sensed data is low for developing countries before 2015. Using the Random Forest ensemble learning classification tree system, we developed annual LULC maps in the CGE from 2002 to 2015 using a time series of cloud-free MODIS vegetation index products. The MODIS imagery was processed through a Gaussian weighted filter to further correct for cloud pollution and matched to visual interpretations of land cover and land use from available high spatial resolution imagery (WorldView-2, Quick Bird, Ikonos and GeoEye-1). Validation of LULC maps resulted in a Kappa of 0.87 (Sd = 0.008). We detected a gradual replacement of forested areas with agriculture (mainly grassland planted to support livestock grazing), and secondary vegetation (agriculture reverting to forest) across the CGE. Forest loss was higher between 2010-2015 when compared to 2002-2010. LULC change trends, deforestation drivers, and reforestation transitions varied according to administrative organization (countries: Panamanian CGE, Colombian CGE, and Ecuadorian CGE).}, } @article {pmid30707687, year = {2019}, author = {Koch, S and Kohrs, F and Lahmann, P and Bissinger, T and Wendschuh, S and Benndorf, D and Reichl, U and Klamt, S}, title = {RedCom: A strategy for reduced metabolic modeling of complex microbial communities and its application for analyzing experimental datasets from anaerobic digestion.}, journal = {PLoS computational biology}, volume = {15}, number = {2}, pages = {e1006759}, pmid = {30707687}, issn = {1553-7358}, mesh = {Anaerobiosis/physiology ; Biofuels ; Bioreactors ; Biotechnology ; Computational Biology/*methods ; Metabolic Networks and Pathways/*physiology ; Methane/metabolism ; Microbiota/*physiology ; Models, Biological ; Proteomics ; }, abstract = {Constraint-based modeling (CBM) is increasingly used to analyze the metabolism of complex microbial communities involved in ecology, biomedicine, and various biotechnological processes. While CBM is an established framework for studying the metabolism of single species with linear stoichiometric models, CBM of communities with balanced growth is more complicated, not only due to the larger size of the multi-species metabolic network but also because of the bilinear nature of the resulting community models. Moreover, the solution space of these community models often contains biologically unrealistic solutions, which, even with model linearization and under application of certain objective functions, cannot easily be excluded. Here we present RedCom, a new approach to build reduced community models in which the metabolisms of the participating organisms are represented by net conversions computed from the respective single-species networks. By discarding (single-species) net conversions that violate a minimality criterion in the exchange fluxes, it is ensured that unrealistic solutions in the community model are excluded where a species altruistically synthesizes large amounts of byproducts (instead of biomass) to fulfill the requirements of other species. We employed the RedCom approach for modeling communities of up to nine organisms involved in typical degradation steps of anaerobic digestion in biogas plants. Compared to full (bilinear and linearized) community models, we found that the reduced community models obtained with RedCom are not only much smaller but allow, also in the largest model with nine species, extensive calculations required to fully characterize the solution space and to reveal key properties of communities with maximum methane yield and production rates. Furthermore, the predictive power of the reduced community models is significantly larger because they predict much smaller ranges of feasible community compositions and exchange fluxes still being consistent with measurements obtained from enrichment cultures. For an enrichment culture for growth on ethanol, we also used metaproteomic data to further constrain the solution space of the community models. Both model and proteomic data indicated a dominance of acetoclastic methanogens (Methanosarcinales) and Desulfovibrionales being the least abundant group in this microbial community.}, } @article {pmid30706201, year = {2019}, author = {Danesh, G and Monavari, SM and Omrani, GA and Karbasi, A and Farsad, F}, title = {Compilation of a model for hazardous waste disposal site selection using GIS-based multi-purpose decision-making models.}, journal = {Environmental monitoring and assessment}, volume = {191}, number = {2}, pages = {122}, pmid = {30706201}, issn = {1573-2959}, mesh = {*Decision Making ; Decision Support Techniques ; Environmental Monitoring/*methods ; Geographic Information Systems ; Hazardous Waste/*analysis ; *Hazardous Waste Sites ; *Models, Theoretical ; Refuse Disposal/*methods ; Software ; }, abstract = {Nowadays, given the high production volume of industrial and dangerous materials and their impacts on the human society and environment, disposal of waste materials in the environment and finding the best disposal site for industrial and hazardous wastes, as the most significant managerial measure, have become one of the most important and complex decisions in urban management. In order to find a disposal site, analysis of spatial data, laws, and large socioeconomic and environmental criteria is required. Multi-criteria analysis techniques coupled with GIS capabilities can be a good solution for this. Due to numerous industrial units, especially refineries in Bushehr province, it is essential to find a management solution for hazardous wastes of this province. The main objective of this study is to find an optimal location which has the lowest environmental risk and economically favorable. For this purpose, ecological and socioeconomic criteria were identified and normalized by fuzzy method. The weight of the parameters was determined by analytical network process method combined with the weighted linear combination method. In the capability of the area to locate the hazardous waste disposal, the results showed that the highest weight belonged to ecological criteria (61.34%) and land use (0.27), respectively. Also, 6.13% of the province areas are identified with high potentials for disposal of hazardous wastes. The results of this study showed the importance and significant weight of environmental criteria in prioritizing the proposed areas for disposal of this type of waste. Efficiency of the employed models, integrated with GIS and MCDM, was also proven.}, } @article {pmid30703281, year = {2019}, author = {Gill, BA and Musili, PM and Kurukura, S and Hassan, AA and Goheen, JR and Kress, WJ and Kuzmina, M and Pringle, RM and Kartzinel, TR}, title = {Plant DNA-barcode library and community phylogeny for a semi-arid East African savanna.}, journal = {Molecular ecology resources}, volume = {19}, number = {4}, pages = {838-846}, doi = {10.1111/1755-0998.13001}, pmid = {30703281}, issn = {1755-0998}, support = {//The Nature Conservancy/ ; DEB-1355122//National Science Foundation/ ; DEB-1457679//National Science Foundation/ ; DEB-1556728//National Science Foundation/ ; IOS-1656527//National Science Foundation/ ; Natural Sciences and Engineering Council Research Tools and Instruments Grant//National Science Foundation/ ; }, mesh = {*DNA Barcoding, Taxonomic ; DNA, Plant/chemistry/*genetics ; DNA, Ribosomal Spacer ; *Databases, Genetic ; Grassland ; Kenya ; *Phylogeny ; Plant Proteins/genetics ; Plants/*classification/*genetics ; }, abstract = {Applications of DNA barcoding include identifying species, inferring ecological and evolutionary relationships between species, and DNA metabarcoding. These applications require reference libraries that are not yet available for many taxa and geographic regions. We collected, identified, and vouchered plant specimens from Mpala Research Center in Laikipia, Kenya, to develop an extensive DNA-barcode library for a savanna ecosystem in equatorial East Africa. We amassed up to five DNA barcode markers (rbcL, matK, trnL-F, trnH-psbA, and ITS) for 1,781 specimens representing up to 460 species (~92% of the known flora), increasing the number of plant DNA barcode records for Africa by ~9%. We evaluated the ability of these markers, singly and in combination, to delimit species by calculating intra- and interspecific genetic distances. We further estimated a plant community phylogeny and demonstrated its utility by testing if evolutionary relatedness could predict the tendency of members of the Mpala plant community to have or lack "barcode gaps", defined as disparities between the maximum intra- and minimum interspecific genetic distances. We found barcode gaps for 72%-89% of taxa depending on the marker or markers used. With the exception of the markers rbcL and ITS, we found that evolutionary relatedness was an important predictor of barcode-gap presence or absence for all of the markers in combination and for matK, trnL-F, and trnH-psbA individually. This plant DNA barcode library and community phylogeny will be a valuable resource for future investigations.}, } @article {pmid30702740, year = {2019}, author = {Zhu, Q and Song, Y and Huang, H and Li, Q and Ju, J}, title = {Characterization of MtdV as a chorismate lyase essential to A201A biosynthesis and precursor-directed biosynthesis of new analogs.}, journal = {Organic & biomolecular chemistry}, volume = {17}, number = {15}, pages = {3760-3764}, doi = {10.1039/c8ob02852d}, pmid = {30702740}, issn = {1477-0539}, mesh = {Actinobacteria/*enzymology ; Aminoglycosides/*biosynthesis/chemistry ; Biocatalysis ; Computational Biology ; Molecular Structure ; Mutation ; Oxo-Acid-Lyases/genetics/*metabolism ; }, abstract = {The antimicrobial nucleoside antibiotic A201A is produced by the deep-sea derived Marinactinospora thermotolerans SCSIO 00652. Bioinformatics analysis revealed that mtdV, downstream within the A201A biosynthetic gene cluster, encodes a protein with low homology to a group of chorismate pyruvate-lyases. To explore the role of mtdV in A201A biosynthesis, mtdV was inactivated and HPLC analysis revealed that the resulting ΔmtdV mutant failed to produce A201A; production was partially restored by adding exogenous 4-hydroxybenzoic acid (4HB) to the fermentation. In vitro biochemical assays showed that MtdV catalyzes the conversion of chorismate into 4HB, thereby firmly demonstrating that MtdV is a chorismate lyase involved in A201A biosynthesis. In addition, supplementation of the ΔmtdV mutant with various 4HB analogs enabled production of seven new A201A analogs. Antimicrobial assays showed that the purified A201A analogs 3'-F-A201A and 3'-Cl-A201A were just as active as A201A against the test strains with MIC values of 1-8 μg mL-1.}, } @article {pmid30702199, year = {2019}, author = {Nahayo, L and Ndayisaba, F and Karamage, F and Nsengiyumva, JB and Kalisa, E and Mind'je, R and Mupenzi, C and Li, L}, title = {Estimating landslides vulnerability in Rwanda using analytic hierarchy process and geographic information system.}, journal = {Integrated environmental assessment and management}, volume = {15}, number = {3}, pages = {364-373}, doi = {10.1002/ieam.4132}, pmid = {30702199}, issn = {1551-3793}, mesh = {*Geographic Information Systems ; Landslides/*statistics & numerical data ; Risk Assessment/*methods ; Rwanda ; Soil ; }, abstract = {Landslides are among hazards that undermine the social, economic, and environmental well-being of the vulnerable community. Assessment of landslides vulnerability reveals the damages that could be recorded, estimates the severity of the impact, and increases the preparedness, response, recovery, and mitigation as well. This study aims to estimate landslides vulnerability for the western province of Rwanda. Field survey and secondary data sources identified 96 landslides used to prepare a landslides inventory map. Ten factors-altitude, slope angles, normalized difference vegetation index (NVDI), land use, distance to roads, soil texture, rainfall, lithology, population density, and possession rate of communication tools-were analyzed. The Analytical Hierarchy Process (AHP) model was used to weight and rank the vulnerability conditioning factors. Then the Weighted Linear Combination (WLC) in geographic information system (GIS) spatially estimated landslides vulnerability over the study area. The results indicated the altitude (19.7%), slope angles (16.1%), soil texture (14.3%), lithology (13.5%), and rainfall (12.2%) as the major vulnerability conditioning parameters. The produced landslides vulnerability map is divided into 5 classes: very low, low, moderate, high and very high. The proposed method is validated by using the relative landslides density index (R-index) method, which revealed that 35.4%, 25%, and 23.9% of past landslides are observed within moderate, high, and very high vulnerability zones, respectively. The consistency of validation indicates good performance of the methodology used and the vulnerability map prepared. The results can be used by policy makers to recognize hazard vulnerability lessening and future planning needs. Integr Environ Assess Manag 2019;00:000-000. © 2019 SETAC.}, } @article {pmid30701707, year = {2019}, author = {Jerde, CL and Wilson, EA and Dressler, TL}, title = {Measuring global fish species richness with eDNA metabarcoding.}, journal = {Molecular ecology resources}, volume = {19}, number = {1}, pages = {19-22}, doi = {10.1111/1755-0998.12929}, pmid = {30701707}, issn = {1755-0998}, support = {AID-OAA-A-16-00057//United States Agency for International Development/ ; }, mesh = {Animals ; *Biodiversity ; Computational Biology ; DNA/chemistry/genetics/isolation & purification ; DNA Barcoding, Taxonomic/*methods ; Fishes/*classification/*genetics ; French Guiana ; High-Throughput Nucleotide Sequencing ; Metagenomics/*methods ; Water/chemistry ; }, abstract = {Despite mounting threats to global freshwater and marine biodiversity, including climate change, habitat alteration, overharvesting and pollution, we struggle to know which species are present below the water's surface that are suffering from these stressors. However, the idea that a water sample containing environmental DNA (eDNA) can be screened using high-throughput sequencing and bioinformatics to reveal the identity of aquatic species is a revolutionary advance for studying the patterns of species extirpation, invasive species establishment and the dynamics of species richness. To date, many of the critical tests of fisheries diversity using this metabarcoding approach have been conducted in lower diversity systems (<40 fish species), but in this issue of Molecular Ecology Resources, Cilleros et al. (2018) described their eDNA application in the species-rich French Guiana fishery (>200 fish species) and showed the greater potential and some limitations of using eDNA in species-rich environments.}, } @article {pmid30698537, year = {2019}, author = {Winsall, M and Orlowski, S and Vogl, G and Blake, V and Nicholas, M and Antezana, G and Schrader, G and Bidargaddi, N}, title = {Designing Online Interventions in Consideration of Young People's Concepts of Well-Being: Exploratory Qualitative Study.}, journal = {JMIR human factors}, volume = {6}, number = {1}, pages = {e10106}, pmid = {30698537}, issn = {2292-9495}, abstract = {BACKGROUND: A key challenge in developing online well-being interventions for young people is to ensure that they are based on theory and reflect adolescent concepts of well-being.

OBJECTIVE: This exploratory qualitative study aimed to understand young people's concepts of well-being in Australia.

METHODS: Data were collected via workshops at five sites across rural and metropolitan sites with 37 young people from 15 to 21 years of age, inclusive. Inductive, data-driven coding was then used to analyze transcripts and artifacts (ie, written or image data).

RESULTS: Young adults' conceptions of well-being were diverse, personally contextualized, and shaped by ongoing individual experiences related to physical and mental health, along with ecological accounts acknowledging the role of family, community, and social factors. Key emerging themes were (1) positive emotions and enjoyable activities, (2) physical wellness, (3) relationships and social connectedness, (4) autonomy and control, (5) goals and purpose, (6) being engaged and challenged, and (7) self-esteem and confidence. Participants had no difficulty describing actions that led to positive well-being; however, they only considered their own well-being at times of stress.

CONCLUSIONS: In this study, young people appeared to think mostly about their well-being at times of stress. The challenge for online interventions is to encourage young people to monitor well-being prior to it becoming compromised. A more proactive focus that links the overall concept of well-being to everyday, concrete actions and activities young people engage in, and that encourages the creation of routine good habits, may lead to better outcomes from online well-being interventions.}, } @article {pmid30698111, year = {2018}, author = {Zhang, Y and Dong, D and Li, D and Lu, L and Li, J and Zhang, Y and Chen, L}, title = {Computational Method for the Identification of Molecular Metabolites Involved in Cereal Hull Color Variations.}, journal = {Combinatorial chemistry & high throughput screening}, volume = {21}, number = {10}, pages = {760-770}, doi = {10.2174/1386207322666190129105441}, pmid = {30698111}, issn = {1875-5402}, mesh = {Amino Acids/metabolism ; Anthocyanins/metabolism ; *Computational Biology ; Edible Grain/genetics/*metabolism ; Flavonoids/metabolism ; Humans ; *Metabolomics ; Plant Growth Regulators/metabolism ; Vitamins/metabolism ; }, abstract = {BACKGROUND: Cereal hull color is an important quality specification characteristic. Many studies were conducted to identify genetic changes underlying cereal hull color diversity. However, these studies mainly focused on the gene level. Recent studies have suggested that metabolomics can accurately reflect the integrated and real-time cell processes that contribute to the formation of different cereal colors.

METHODS: In this study, we exploited published metabolomics databases and applied several advanced computational methods, such as minimum redundancy maximum relevance (mRMR), incremental forward search (IFS), random forest (RF) to investigate cereal hull color at the metabolic level. First, the mRMR was applied to analyze cereal hull samples represented by metabolite features, yielding a feature list. Then, the IFS and RF were used to test several feature sets, constructed according to the aforementioned feature list. Finally, the optimal feature sets and RF classifier were accessed based on the testing results.

RESULTS AND CONCLUSION: A total of 158 key metabolites were found to be useful in distinguishing white cereal hulls from colorful cereal hulls. A prediction model constructed with these metabolites and a random forest algorithm generated a high Matthews coefficient correlation value of 0.701. Furthermore, 24 of these metabolites were previously found to be relevant to cereal color. Our study can provide new insights into the molecular basis of cereal hull color formation.}, } @article {pmid30697746, year = {2019}, author = {Gibert, A and Tozer, W and Westoby, M}, title = {Plant performance response to eight different types of symbiosis.}, journal = {The New phytologist}, volume = {222}, number = {1}, pages = {526-542}, doi = {10.1111/nph.15392}, pmid = {30697746}, issn = {1469-8137}, support = {//Australian Research Council/International ; }, mesh = {Databases as Topic ; Plant Development ; Plants/*microbiology ; Publication Bias ; Symbiosis/*physiology ; }, abstract = {Almost all plant species interact with one or more symbioses somewhere within their distribution range. Bringing together plant trait data and growth responses to symbioses spanning 552 plant species, we provide for the first time on a large scale (597 studies) a quantitative synthesis on plant performance differences between eight major types of symbiosis, including mycorrhizas, N-fixing bacteria, fungal endophytes and ant-plant interactions. Frequency distributions of plant growth responses varied considerably between different types of symbiosis, in terms of both mean effect and 'risk', defined here as percentage of experiments reporting a negative effect of symbiosis on plants. Contrary to expectation, plant traits were poor predictors of growth response across and within all eight symbiotic associations. Our analysis showed no systematic additive effect when a host plant engaged in two functionally different symbioses. This synthesis suggests that plant species' ecological strategies have little effect in determining the influence of a symbiosis on host plant growth. Reliable quantification of differences in plant performance across symbioses will prove valuable for developing general hypotheses on how species become engaged in mutualisms without a guarantee of net returns.}, } @article {pmid30696775, year = {2019}, author = {Austin, RM and Sholts, SB and Williams, L and Kistler, L and Hofman, CA}, title = {Opinion: To curate the molecular past, museums need a carefully considered set of best practices.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {116}, number = {5}, pages = {1471-1474}, pmid = {30696775}, issn = {1091-6490}, mesh = {Anthropology/*legislation & jurisprudence/methods ; Attitude ; Body Remains/*chemistry ; Computational Biology/legislation & jurisprudence/methods ; Humans ; Museums/*legislation & jurisprudence ; Science/legislation & jurisprudence/methods ; }, } @article {pmid30695030, year = {2019}, author = {Yenni, GM and Christensen, EM and Bledsoe, EK and Supp, SR and Diaz, RM and White, EP and Ernest, SKM}, title = {Developing a modern data workflow for regularly updated data.}, journal = {PLoS biology}, volume = {17}, number = {1}, pages = {e3000125}, pmid = {30695030}, issn = {1545-7885}, mesh = {Animals ; Big Data ; Computational Biology/methods ; Data Curation/*methods/*trends ; Humans ; Publications ; Reproducibility of Results ; Software ; Workflow ; }, abstract = {Over the past decade, biology has undergone a data revolution in how researchers collect data and the amount of data being collected. An emerging challenge that has received limited attention in biology is managing, working with, and providing access to data under continual active collection. Regularly updated data present unique challenges in quality assurance and control, data publication, archiving, and reproducibility. We developed a workflow for a long-term ecological study that addresses many of the challenges associated with managing this type of data. We do this by leveraging existing tools to 1) perform quality assurance and control; 2) import, restructure, version, and archive data; 3) rapidly publish new data in ways that ensure appropriate credit to all contributors; and 4) automate most steps in the data pipeline to reduce the time and effort required by researchers. The workflow leverages tools from software development, including version control and continuous integration, to create a modern data management system that automates the pipeline.}, } @article {pmid30694965, year = {2021}, author = {Fernandes-Da-Silva, J and Castagna, C and Teixeira, AS and Carminatti, LJ and Francini, L and Póvoas, SCA and Antonacci Guglielmo, LG}, title = {Ecological and Construct Validity of a Repeated Sprint Test in Male Youth Soccer Players.}, journal = {Journal of strength and conditioning research}, volume = {35}, number = {7}, pages = {2000-2009}, doi = {10.1519/JSC.0000000000003047}, pmid = {30694965}, issn = {1533-4287}, mesh = {Adolescent ; *Athletic Performance ; *Football ; Geographic Information Systems ; Humans ; Male ; *Running ; *Soccer ; }, abstract = {Fernandes-Da-Silva, J, Castagna, C, Teixeira, AS, Carminatti, LJ, Francini, L, Póvoas, SCA, and Antonacci Guglielmo, LG. Ecological and construct validity of a repeated sprint test in male youth soccer players. J Strength Cond Res 35(7): 2000-2009, 2021-This study aimed to examine the relationship between a repeated sprint ability (RSA) test (5 bouts of 30-m sprints interspersed by 30 seconds of recovery) and match-related physical performance in male youth soccer players. Although 60 outfield players were evaluated, only data from players who participated in the full matches (n = 39) were retained (8 central defenders, 7 external defenders, 8 central midfielders, 8 external midfielders, and 8 forwards). To verify the ecological validity of this RSA protocol, the association between the best (RSAbest) and mean (RSAmean) sprint time in the 5 × 30-m and physical match performance during friendly youth soccer games was examined. Physical match demands were assessed using global positioning system technology (10 Hz) considering distance covered in selected arbitrary speed categories. The absolute speed thresholds were the same for all the players. Players were categorized into 2 groups based on the 5 × 30-m performance: RSAmean times below (i.e., faster) and above (i.e., slower) the median value. Players with faster RSAmean times covered significantly more distance sprinting during friendly matches (606 ± 204 m, +47.0%; t = 4.953; effect size = 1.88, 1.24; 2.52, p ≤ 0.001) compared to their slower counterparts (322 ± 145 m). A large negative correlation (r = -0.63, -0.77; -0.44, p ≤ 0.001) was found between RSAbest time (4.59 ± 0.27 seconds) and match sprint distance (457 ± 229 m). Likewise, RSAmean time (4.76 ± 0.25 seconds) was also largely associated (r = -0.60, -0.75; -0.39; p ≤ 0.001) with in-game sprinting performance. The results of this study provided evidence to support the construct and ecological validity of the 5 × 30-m protocol in male youth soccer players. Furthermore, differences in 5 × 30-m performance explained the amount of sprinting activity performed during the match.}, } @article {pmid30694508, year = {2019}, author = {Pérez-Cobas, AE and Buchrieser, C}, title = {Analysis of the Pulmonary Microbiome Composition of Legionella pneumophila-Infected Patients.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1921}, number = {}, pages = {429-443}, doi = {10.1007/978-1-4939-9048-1_27}, pmid = {30694508}, issn = {1940-6029}, mesh = {Computational Biology/methods ; DNA, Ribosomal Spacer ; Data Interpretation, Statistical ; High-Throughput Nucleotide Sequencing ; Humans ; Legionella pneumophila/*physiology ; Legionnaires' Disease/*microbiology ; *Microbiota ; Molecular Sequence Annotation ; Pneumonia, Bacterial/*microbiology ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S ; }, abstract = {The analysis of the lung microbiome composition is a field of research that recently emerged. It gained great interest in pulmonary diseases such as pneumonia since the microbiome seems to be involved in host immune responses, inflammation, and protection against pathogens. Thus, it is possible that the microbial communities living in the lungs play a role in the outcome and severity of lung infections such as Legionella-caused pneumonia and in the response to antibiotic therapy. In this chapter, all steps necessary for the characterization of the bacterial and fungal fraction of the lung microbiome using high-throughput sequencing approaches are explained, starting from the selection of clinical samples to the analysis of the taxonomic composition, diversity, and ecology of the microbiome.}, } @article {pmid30692535, year = {2019}, author = {Cheng, J and Demeulemeester, J and Wedge, DC and Vollan, HKM and Pitt, JJ and Russnes, HG and Pandey, BP and Nilsen, G and Nord, S and Bignell, GR and White, KP and Børresen-Dale, AL and Campbell, PJ and Kristensen, VN and Stratton, MR and Lingjærde, OC and Moreau, Y and Van Loo, P}, title = {Author Correction: Pan-cancer analysis of homozygous deletions in primary tumours uncovers rare tumour suppressors.}, journal = {Nature communications}, volume = {10}, number = {1}, pages = {525}, doi = {10.1038/s41467-019-08512-7}, pmid = {30692535}, issn = {2041-1723}, abstract = {The original version of this Article omitted a declaration from the competing interests statement, which should have included the following: 'K.P.W. is President of Tempus Lab, Inc., Chicago, IL, USA'. This has now been corrected in both the PDF and HTML versions of the Article.}, } @article {pmid30691911, year = {2019}, author = {Malinowski, M and Wolny-Koładka, K and Vaverková, MD}, title = {Effect of biochar addition on the OFMSW composting process under real conditions.}, journal = {Waste management (New York, N.Y.)}, volume = {84}, number = {}, pages = {364-372}, doi = {10.1016/j.wasman.2018.12.011}, pmid = {30691911}, issn = {1879-2456}, mesh = {Charcoal ; *Composting ; Czech Republic ; Nitrogen ; Soil ; }, abstract = {The article evaluates the effect of small selected doses of biochar addition (0%, 1.5%, 3% and 5%, wet weight) on the composting process of the organic fraction of municipal solid waste (OFMSW) with a low initial C/N ratio under real conditions. The low C/N composting mixtures with addition of biochar at low rates can have a positive effect on the compost quality and on the reduction of N losses in compost. The novelty of this work consists in studying the impact of small biochar doses on the composting process at full-scale. The research was conducted under real conditions in the Brno Central Composting Plant (Czech Republic) receiving food waste, grass, straw, sawdust, mineral waste, paper, wood and sewage sludge for processing. The experimental processing time was 12 weeks. We evaluated changes in carbon (C), nitrogen (N), moisture content (MC), organic matter (OM), respiration activity (AT4), as well as changes in the microbiocenotic composition of microorganisms colonizing the processed waste. OFMSW with the addition of biochar and compost were assessed for the content of heavy metals (HM). It was found out that biochar reduced the compost toxicity. The resulting compost with the addition of biochar exhibited higher moisture content and lower waste density. Biochar had an impact on N retention during composting but it did not change the course or accelerate the composting process. The highest OM loss (62.6%) was observed in the OFMSW with no biochar addition. The abundance of potentially pathogenic microorganisms clearly decreased during the OFMSW composting process with the addition of biochar.}, } @article {pmid30691184, year = {2019}, author = {Xi, X and Zong, Y and Li, S and Cao, D and Sun, X and Liu, B}, title = {Transcriptome Analysis Clarified Genes Involved in Betalain Biosynthesis in the Fruit of Red Pitayas (Hylocereus costaricensis).}, journal = {Molecules (Basel, Switzerland)}, volume = {24}, number = {3}, pages = {}, pmid = {30691184}, issn = {1420-3049}, support = {2018-NK-133, 2018-ZJ-T08, 2019-ZJ-982Q//QingHai Department of Science and Technology/ ; 2018-KF-06//West Light Talent Program of the Chinese Academy of Sciences, the Open Project of State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University/ ; }, mesh = {Anthocyanins/biosynthesis ; Betalains/*biosynthesis ; Biosynthetic Pathways/genetics ; Cactaceae/classification/*genetics/*metabolism ; Computational Biology/methods ; Fruit/*genetics/*metabolism ; Gene Expression Profiling ; *Gene Expression Regulation, Plant ; Genes, Plant ; High-Throughput Nucleotide Sequencing ; Phylogeny ; *Transcriptome ; }, abstract = {The red flesh trait gives red pitayas more healthful components and a higher price, while the genetic mechanism behind this trait is unknown. In this manuscript, transcriptome analysis was employed to discover the genetic differences between white and red flesh in pitayas. A total of 27.99 Gb clean data were obtained for four samples. Unigenes, 79,049 in number, were generated with an average length of 1333 bp, and 52,618 Unigenes were annotated. Compared with white flesh, the expression of 10,215 Unigenes was up-regulated, and 4853 Unigenes were down-regulated in red flesh. The metabolic pathways accounted for 64.6% of all differentially expressed Unigenes in KEGG pathways. The group with high betalain content in red flesh and all structural genes, related to betalain biosynthesis, had a higher expression in red flesh than white flesh. The expression of the key gene, tyrosine hydroxylase CYP76AD1, was up-regulated 245.08 times, while 4,5-DOPA dioxygenase DODA was up-regulated 6.46 times. Moreover, the special isomers CYP76AD1α and DODAα were only expressed in red flesh. The competitive anthocyanin biosynthesis pathway had a lower expression in red flesh. Two MYB transcription factors were of the same branch as BvMYB1, regulating betalain biosynthesis in beet, and those transcription factors had expression differences in two kinds of pitayas, which indicated that they should be candidate genes controlling betalain accumulation in red pitayas. This research would benefit from identifying the major gene controlling red flesh trait and breed new cultivars with the red flesh trait. Future research should aim to prove the role of each candidate gene in betalain biosynthesis in red pitayas.}, } @article {pmid30690450, year = {2019}, author = {Prim, JH and Favorov, OV and Cecchini, AS and Scherer, MR and Weightman, MM and McCulloch, KL}, title = {Clinical Utility and Analysis of the Run-Roll-Aim Task: Informing Return-to-Duty Readiness Decisions in Active-Duty Service Members.}, journal = {Military medicine}, volume = {184}, number = {5-6}, pages = {e268-e277}, doi = {10.1093/milmed/usy425}, pmid = {30690450}, issn = {1930-613X}, mesh = {Adolescent ; Adult ; Analysis of Variance ; Cross-Sectional Studies ; *Decision Support Techniques ; *Disability Evaluation ; Female ; Humans ; Male ; Military Personnel/*statistics & numerical data ; Reproducibility of Results ; Return to Work/*statistics & numerical data ; }, abstract = {INTRODUCTION: The Assessment of Military Multitasking Performance (AMMP1) consists of six dual-task and multitask military-relevant performance-based assessments which were developed to provide assistance in making return-to-duty decisions after concussion or mild traumatic brain injury (mTBI.) The Run-Roll-Aim (RRA) task, one component of the AMMP, was developed to target vulnerabilities following mTBI including attention, visual function, dynamic stability, rapid transition, and vestibular function. One aim of this study was to assess the known-group and construct validity of the RRA, and additionally to further explore reliability limitations reported previously.

MATERIALS AND METHODS: A cross-sectional study consisting of 84 Active Duty service members in two groups (healthy control - HC and individuals experiencing persistent mTBI symptoms) completed neurocognitive tests and the RRA. The RRA task requires a high level of mobility and resembles military training activities in a maneuver that includes combat rolls, fast transitions, obstacle avoidance, and visual search. Observational and inertial sensor data were compared between groups and performance across four trial times was compared within groups. Correlations between RRA results and neurocognitive test scores were analyzed.

RESULTS: Simple observational measures (time, errors) did not differ between groups. Spectral power analysis of the inertial sensor data showed significant differences in motor performance between groups. Within group one-way ANOVAs showed that in HC trial 1, time was significantly different than trials 2,3 and 4 (F(3,47) = 4.60, p < 0.01, Tukey HSD p < 0.05) while the mTBI group showed no significant difference in time between trials. During testing individuals with mTBI were less likely to complete the multiple test trials or required additional rest between trials than HCs (χ2 = 10.78, p < 0.01). Small but significant correlations were seen with two neurocognitive tests of attention and RRA performance time.

CONCLUSION: While observational scores were not sensitive to group differences, inertial sensor data showed motor performance on the forward run, combat roll, and backward run differed significantly between groups. The RRA task appeared challenging and provoked symptoms in the mTBI group, causing 8 of 33 mTBI participants to stop the task or require additional rest between trials while none of the HC participants had to stop. Individuals with mTBI demonstrated slower learning of the complex motor sequence compared to HCs who had significant improvement after one trial of RRA. Complex novel training maneuvers like RRA may aid clinicians in informing return to duty decisions.}, } @article {pmid30689651, year = {2019}, author = {Duncan, DT and Park, SH and Goedel, WC and Sheehan, DM and Regan, SD and Chaix, B}, title = {Acceptability of smartphone applications for global positioning system (GPS) and ecological momentary assessment (EMA) research among sexual minority men.}, journal = {PloS one}, volume = {14}, number = {1}, pages = {e0210240}, pmid = {30689651}, issn = {1932-6203}, support = {R25 MH083620/MH/NIMH NIH HHS/United States ; R01 MH112406/MH/NIMH NIH HHS/United States ; R21 MH110190/MH/NIMH NIH HHS/United States ; R03 DA039748/DA/NIDA NIH HHS/United States ; U01 PS005122/PS/NCHHSTP CDC HHS/United States ; K01 MD013770/MD/NIMHD NIH HHS/United States ; }, mesh = {Adolescent ; Adult ; Ecological Momentary Assessment ; France ; *Geographic Information Systems ; HIV Infections ; Humans ; Male ; Middle Aged ; *Mobile Applications ; Paris ; Sexual Behavior/psychology ; Sexual and Gender Minorities/*psychology ; *Smartphone ; Young Adult ; }, abstract = {BACKGROUND: Emerging research is using global positioning system (GPS) and ecological momentary assessment (EMA) methods among sexual minority men (SMM), a population that experiences multiple health disparities. However, we are not aware of any research that has combined these approaches among SMM, highlighting the need for acceptability and feasibility research. The purpose of this study was to examine the acceptability of implementing GPS and EMA research protocols using smartphone applications among SMM as well as related socio-demographic correlates.

METHODS: Data come from a sample of SMM on a popular geosocial-networking app in Paris, France (n = 580). We assessed the acceptability of implementing GPS and EMA research protocols on smartphone apps as well as socio-demographic characteristics (i.e., age, sexual orientation, country of origin, employment status, and relationship status). We examined the anticipated acceptability of GPS and EMA data collection methods as well as socio-demographic correlates of acceptability of GPS and EMA methods.

RESULTS: We found that over half (54.1%) of the sample was willing to download a smartphone app for GPS-based research and we found that almost 60% of the participants were willing to download a smartphone app for EMA-based research. In total, 44.0% reported that they were willing to download both GPS and EMA apps. In addition, we found that older participants were less willing to download a smartphone app for EMA research than younger participants aged 18-24 (40-49 years: aPR = 0.40; 95% CI = 0.20, 0.78) and students were more willing to download smartphone apps for both GPS and EMA research (aPR = 1.41; 95% CI = 1.02, 1.95).

CONCLUSION: Results from this study suggest that using smartphone apps to implement GPS and EMA methods among some SMM are acceptable. However, care should be taken as segments of SMM are less likely to be willing to engage in this type of research.}, } @article {pmid30689307, year = {2019}, author = {Wackett, LP}, title = {Evolutionary microbial ecology: An annotated selection of World Wide Web sites relevant to the topics in environmental microbiology.}, journal = {Environmental microbiology reports}, volume = {11}, number = {1}, pages = {48-49}, doi = {10.1111/1758-2229.12734}, pmid = {30689307}, issn = {1758-2229}, mesh = {*Biological Evolution ; Databases, Factual ; *Environmental Microbiology ; *Internet ; }, } @article {pmid30683860, year = {2019}, author = {Zou, C and Li, L and Miki, D and Li, D and Tang, Q and Xiao, L and Rajput, S and Deng, P and Peng, L and Jia, W and Huang, R and Zhang, M and Sun, Y and Hu, J and Fu, X and Schnable, PS and Chang, Y and Li, F and Zhang, H and Feng, B and Zhu, X and Liu, R and Schnable, JC and Zhu, JK and Zhang, H}, title = {The genome of broomcorn millet.}, journal = {Nature communications}, volume = {10}, number = {1}, pages = {436}, pmid = {30683860}, issn = {2041-1723}, mesh = {Adaptation, Physiological/genetics ; Base Sequence ; Biological Evolution ; Carbon Cycle ; Chromosome Mapping ; Chromosomes, Plant/*chemistry ; Gene Ontology ; *Genome, Plant ; High-Throughput Nucleotide Sequencing ; MicroRNAs/classification/genetics ; Molecular Sequence Annotation ; Panicum/classification/*genetics ; *Phylogeny ; Plant Breeding ; Plant Proteins/*genetics ; RNA, Plant/genetics ; Stress, Physiological ; Synteny ; Ubiquitin-Protein Ligases/genetics ; }, abstract = {Broomcorn millet (Panicum miliaceum L.) is the most water-efficient cereal and one of the earliest domesticated plants. Here we report its high-quality, chromosome-scale genome assembly using a combination of short-read sequencing, single-molecule real-time sequencing, Hi-C, and a high-density genetic map. Phylogenetic analyses reveal two sets of homologous chromosomes that may have merged ~5.6 million years ago, both of which exhibit strong synteny with other grass species. Broomcorn millet contains 55,930 protein-coding genes and 339 microRNA genes. We find Paniceae-specific expansion in several subfamilies of the BTB (broad complex/tramtrack/bric-a-brac) subunit of ubiquitin E3 ligases, suggesting enhanced regulation of protein dynamics may have contributed to the evolution of broomcorn millet. In addition, we identify the coexistence of all three C4 subtypes of carbon fixation candidate genes. The genome sequence is a valuable resource for breeders and will provide the foundation for studying the exceptional stress tolerance as well as C4 biology.}, } @article {pmid30682820, year = {2019}, author = {Mantravadi, PK and Kalesh, KA and Dobson, RCJ and Hudson, AO and Parthasarathy, A}, title = {The Quest for Novel Antimicrobial Compounds: Emerging Trends in Research, Development, and Technologies.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {8}, number = {1}, pages = {}, pmid = {30682820}, issn = {2079-6382}, support = {R15 GM120653/GM/NIGMS NIH HHS/United States ; R15GM120653/NH/NIH HHS/United States ; }, abstract = {Pathogenic antibiotic resistant bacteria pose one of the most important health challenges of the 21st century. The overuse and abuse of antibiotics coupled with the natural evolutionary processes of bacteria has led to this crisis. Only incremental advances in antibiotic development have occurred over the last 30 years. Novel classes of molecules, such as engineered antibodies, antibiotic enhancers, siderophore conjugates, engineered phages, photo-switchable antibiotics, and genome editing facilitated by the CRISPR/Cas system, are providing new avenues to facilitate the development of antimicrobial therapies. The informatics revolution is transforming research and development efforts to discover novel antibiotics. The explosion of nanotechnology and micro-engineering is driving the invention of antimicrobial materials, enabling the cultivation of "uncultivable" microbes and creating specific and rapid diagnostic technologies. Finally, a revival in the ecological aspects of microbial disease management, the growth of prebiotics, and integrated management based on the "One Health" model, provide additional avenues to manage this health crisis. These, and future scientific and technological developments, must be coupled and aligned with sound policy and public awareness to address the risks posed by rising antibiotic resistance.}, } @article {pmid30682013, year = {2019}, author = {Chuard, PJC and Vrtílek, M and Head, ML and Jennions, MD}, title = {Evidence that nonsignificant results are sometimes preferred: Reverse P-hacking or selective reporting?.}, journal = {PLoS biology}, volume = {17}, number = {1}, pages = {e3000127}, pmid = {30682013}, issn = {1545-7885}, mesh = {Bias ; Data Analysis ; *Data Interpretation, Statistical ; Humans ; Knowledge ; Probability ; Publication Bias/*statistics & numerical data/trends ; Publishing ; Research Personnel ; Statistics as Topic/*methods ; Surveys and Questionnaires ; }, abstract = {There is increased concern about poor scientific practices arising from an excessive focus on P-values. Two particularly worrisome practices are selective reporting of significant results and 'P-hacking'. The latter is the manipulation of data collection, usage, or analyses to obtain statistically significant outcomes. Here, we introduce the novel, to our knowledge, concepts of selective reporting of nonsignificant results and 'reverse P-hacking' whereby researchers ensure that tests produce a nonsignificant result. We test whether these practices occur in experiments in which researchers randomly assign subjects to treatment and control groups to minimise differences in confounding variables that might affect the focal outcome. By chance alone, 5% of tests for a group difference in confounding variables should yield a significant result (P < 0.05). If researchers less often report significant findings and/or reverse P-hack to avoid significant outcomes that undermine the ethos that experimental and control groups only differ with respect to actively manipulated variables, we expect significant results from tests for group differences to be under-represented in the literature. We surveyed the behavioural ecology literature and found significantly more nonsignificant P-values reported for tests of group differences in potentially confounding variables than the expected 95% (P = 0.005; N = 250 studies). This novel, to our knowledge, publication bias could result from selective reporting of nonsignificant results and/or from reverse P-hacking. We encourage others to test for a bias toward publishing nonsignificant results in the equivalent context in their own research discipline.}, } @article {pmid30679468, year = {2019}, author = {Glatz, C and Chuang, LL}, title = {The time course of auditory looming cues in redirecting visuo-spatial attention.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {743}, pmid = {30679468}, issn = {2045-2322}, mesh = {Acoustic Stimulation ; Attention/*physiology ; Auditory Perception/*physiology ; Female ; Humans ; Male ; Orientation, Spatial/physiology ; Photic Stimulation ; Reaction Time/*physiology ; Space Perception/*physiology ; }, abstract = {By orienting attention, auditory cues can improve the discrimination of spatially congruent visual targets. Looming sounds that increase in intensity are processed preferentially by the brain. Thus, we investigated whether auditory looming cues can orient visuo-spatial attention more effectively than static and receding sounds. Specifically, different auditory cues could redirect attention away from a continuous central visuo-motor tracking task to peripheral visual targets that appeared occasionally. To investigate the time course of crossmodal cuing, Experiment 1 presented visual targets at different time-points across a 500 ms auditory cue's presentation. No benefits were found for simultaneous audio-visual cue-target presentation. The largest crossmodal benefit occurred at early cue-target asynchrony onsets (i.e., CTOA = 250 ms), regardless of auditory cue type, which diminished at CTOA = 500 ms for static and receding cues. However, auditory looming cues showed a late crossmodal cuing benefit at CTOA = 500 ms. Experiment 2 showed that this late auditory looming cue benefit was independent of the cue's intensity when the visual target appeared. Thus, we conclude that the late crossmodal benefit throughout an auditory looming cue's presentation is due to its increasing intensity profile. The neural basis for this benefit and its ecological implications are discussed.}, } @article {pmid30678078, year = {2019}, author = {Ziemińska-Stolarska, A and Imbierowicz, M and Jaskulski, M and Szmidt, A and Zbiciński, I}, title = {Continuous and Periodic Monitoring System of Surface Water Quality of an Impounding Reservoir: Sulejow Reservoir, Poland.}, journal = {International journal of environmental research and public health}, volume = {16}, number = {3}, pages = {}, pmid = {30678078}, issn = {1660-4601}, mesh = {Biological Oxygen Demand Analysis ; Environmental Monitoring/*methods ; Eutrophication ; Fresh Water/*chemistry ; *Online Systems ; Poland ; Rain ; Seasons ; }, abstract = {The paper presents results of water quality monitoring conducted within the frame of the MONSUL project. The main goal was to analyse and assess the impact of factors determining the ecological status of a dam reservoir on the basis of the Sulejow Reservoir located in Central Poland. The project implementation plan based on comprehensive research-based monitoring covered the following parameters characterising the ecological potential of the reservoir: water temperature, pH, oxygen concentration, chlorophyll “a” and blue-green algae, concentration of ammonium ion, nitrate nitrogen phosphates as well as total organic carbon, chemical oxygen demand and biochemical oxygen demand. The parameters were measured with a mobile and stationary monitoring system and supplemented by an off-line analysis of water samples in the laboratory. The study was carried out during two seasons: May–October 2015 and April–November 2016; the results were analysed also with regard to the weather conditions. Despite the similar temperatures of water and air in the analysed seasons, significant differences were observed for atmospheric precipitation; 2015 was a dry year, and the climatic water balance for the analysed area was negative, which caused limited surface runoff and decreased the concentrations of nutrient in the reservoir waters. Data from continuous monitoring, supplemented with the results of laboratory measurements, indicated that the values of TOC (Total Organic Carbon) and COD (Chemical Oxygen Demand) parameters were within the purity class I; exceedances refer to the BOD (Biochemical Oxygen Demand) value, which confirmed the presence of biodegradable organic compounds in the reservoir waters. The values of chlorophyll “a” and the presence of algae during the vegetation season testify to eutrophication of the Sulejow Reservoir.}, } @article {pmid30678021, year = {2019}, author = {Song, Y and Wang, Y and Mao, G and Gao, G and Wang, Y}, title = {Impact of planktonic low nucleic acid-content bacteria to bacterial community structure and associated ecological functions in a shallow lake.}, journal = {The Science of the total environment}, volume = {658}, number = {}, pages = {868-878}, doi = {10.1016/j.scitotenv.2018.12.274}, pmid = {30678021}, issn = {1879-1026}, mesh = {*Bacterial Physiological Phenomena ; China ; Computational Biology ; Flow Cytometry ; Lakes/*microbiology ; *Microbiota ; Nucleic Acids/analysis ; Phytoplankton/*physiology ; RNA, Bacterial/analysis ; RNA, Ribosomal, 16S/analysis ; }, abstract = {In this study, 0.45 μm filtration, flow cytometric fingerprint, 16S rRNA amplicon sequencing, and bioinformation tools were adopted to analyze the structural diversity and potential functions of planktonic low nucleic acid (LNA)- content bacteria in a shallow lake. Three bacterial groups, namely, "LNA," "high nucleic acid (HNA)-Small," and "HNA-Large," were classified through flow cytometric fingerprint, among which the "HNA-Small" group was possibly in the proliferation stage of the "LNA" group. Total nitrogen and phosphate were the key factors that influence the growth of LNA bacteria. Results of 16S rRNA amplicon sequencing showed that LNA bacteria were phylogenetically less diverse than HNA bacteria, and Actinobacteria and Proteobacteria (especially Gamma-Proteobacteria) were the dominant phyla in LNA bacterial operational taxonomic units (OTUs). Accordingly, hgcI_clade and Pseudomonas were the most abundant bacterial genera in LNA bacterial OTUs. The fraction of low-abundance LNA bacteria was sensitive to several environmental factors, indicating that environmental factors only determined the fraction distribution of low-abundance bacteria. The prediction of metabolic and ecological functions showed that LNA and HNA bacteria had distinct metabolic and ecological functions, which were mainly attributed to the dominant and exclusive bacterial groups.}, } @article {pmid30678004, year = {2019}, author = {Liversage, K and Kotta, J and Aps, R and Fetissov, M and Nurkse, K and Orav-Kotta, H and Rätsep, M and Forsström, T and Fowler, A and Lehtiniemi, M and Normant-Saremba, M and Puntila-Dodd, R and Arula, T and Hubel, K and Ojaveer, H}, title = {Knowledge to decision in dynamic seas: Methods to incorporate non-indigenous species into cumulative impact assessments for maritime spatial planning.}, journal = {The Science of the total environment}, volume = {658}, number = {}, pages = {1452-1464}, doi = {10.1016/j.scitotenv.2018.12.123}, pmid = {30678004}, issn = {1879-1026}, mesh = {*Animal Distribution ; Animals ; *Brachyura ; Conservation of Natural Resources/*methods ; *Decision Support Techniques ; Estonia ; *Introduced Species ; Models, Biological ; *Perciformes ; Spatial Analysis ; }, abstract = {Incorporating ecosystem changes from non-indigenous species (NIS) is an important task of maritime spatial planning. Maritime spatial planning requires a framework that emphasises ecological functioning in a state of dynamic change, including changes to ecosystem services from functions introduced by new NIS. Adaptable modelling toolsets should be developed that can readily incorporate knowledge of new NIS. In the Baltic Sea, recent NIS examples are the North American mud crab Rhithropanopeus harrisii and the Ponto-Caspian round goby Neogobius melanostomus. We performed environmental niche modelling that predicted N. melanostomus will spread across large areas of the Baltic Sea coast while R. harrisii will be limited to regions with high temperature and low salinity conditions. We then performed a meta-analysis on literature showing effects in the Baltic Sea from these NIS and calculated the standardised effect-sizes on relevant ecosystem services. Half the impacts identified for N. melanostomus were considered to increase ecosystem service outcomes, while all R. harrisii impacts caused apparent decreases. Effect coefficients were incorporated into an online impact assessment tool developed by the Estonian Marine Institute. Users with or without science training can use the portal to estimate areas impacted and changes to natural assets (km[2]) caused by these NIS and cumulative effects from other pressure-types. Impact estimates are based on best available knowledge from manipulative and correlative experiments and thus form a link between science and management. Dynamic modelling techniques informed from varied ecological and methodological perspectives will effectively advise spatial planners about rapid maritime changes and mitigation actions to reduce NIS impacts especially in the focus areas.}, } @article {pmid30677922, year = {2019}, author = {Chen, D and Ali, A and Yong, XH and Lin, CG and Niu, XH and Cai, AM and Dong, BC and Zhou, ZX and Wang, YJ and Yu, FH}, title = {A multi-species comparison of selective placement patterns of ramets in invasive alien and native clonal plants to light, soil nutrient and water heterogeneity.}, journal = {The Science of the total environment}, volume = {657}, number = {}, pages = {1568-1577}, doi = {10.1016/j.scitotenv.2018.12.099}, pmid = {30677922}, issn = {1879-1026}, mesh = {Adaptation, Physiological ; Amaranthaceae/growth & development/*physiology/radiation effects ; Araliaceae/growth & development/*physiology/radiation effects ; Biomass ; China ; *Cloning, Organism ; *Introduced Species ; Paspalum/growth & development/*physiology/radiation effects ; Plant Development/radiation effects ; Soil/chemistry ; Water ; Wedelia/growth & development/*physiology/radiation effects ; }, abstract = {A worth noticing pattern in current invasive biology is the clonal ability of many of the world's worst invasive plants. Selective placement of ramets (i.e. foraging behavior) can intensify ramet performance and allocation, and place more ramets in the more favorable microhabitats, which can maximum utilize resource and share risk in heterogeneous environments. Still little is known about whether invasive alien and native clonal plants differ in the selective placement patterns of ramets in invasive clonal plants or not. We used five congeneric pairs of naturally co-occurring invasive alien and native clonal plant species in China. In a glasshouse, we grew all species in pots under a homogeneous and three heterogeneous conditions (i.e. light, soil nutrients or water) subjected to resource-high or -low patches. All biomass parameters and number of ramets significantly increased in resource-high patches in all three types of heterogeneous environments. Interestingly, growth of invasive alien plants benefited significantly more from resource-high patches than native plants in all heterogeneous environments. Overall, invasive had higher biomass parameters per ramet than natives. Ramet parameters of invasive plants also benefited more from resource-low patches than natives. Three different selective placement patterns of ramets in resource-low patches were exhibited in invasive plants: ramet increasing shoot investment (above pattern), increasing root investment (below pattern) and increasing both investments (complete pattern) in the light, soil water and nutrient heterogeneity, respectively. Investment on less, larger ramet was the adaptive strategy of invasive plants in resource-poor patches. The results suggest that adaptively selective placement patterns of ramets promote a higher morphology plasticity and performance in invasive clonal plants over natives. When alien clonal plants spread new areas with light, soil nutrients or water heterogeneity, selective placement patterns of ramets might play an important role in plant performance and competitive superior by capitalizing more on additional resources.}, } @article {pmid30677210, year = {2019}, author = {Kim, SH and Lee, SJ and Kim, SH and Kang, SE and Lee, DS and Lim, SR}, title = {Environmental effects of the technology transformation from hard-disk to solid-state drives from resource depletion and toxicity management perspectives.}, journal = {Integrated environmental assessment and management}, volume = {15}, number = {2}, pages = {292-298}, doi = {10.1002/ieam.4127}, pmid = {30677210}, issn = {1551-3793}, support = {//Basic Science Research Programs/ ; NRF-2017R1D1A1A09000632//National Research Foundation of Korea/ ; NRF-2018R1A6A1A03024962//National Research Foundation of Korea/ ; }, mesh = {*Computers ; *Environment ; Environmental Pollutants/*analysis/*toxicity ; Humans ; Information Storage and Retrieval ; Inventions ; Metals/*analysis/*toxicity ; Risk Assessment ; }, abstract = {Solid-state drives (SSDs) are used as data storage systems in various electronic devices in place of hard-disk drives (HDDs) due to their higher speed and durability and lower noise and power consumption. Although SSDs have these advantages, the environmental consequences of the technology transformation from HDD to SSD need to be examined from resource depletion and toxicity management perspectives because most electronic components and devices contain rare, precious, and toxic metals. Thus, the objective of this study was to assess and compare resource depletion and toxicity potentials from metals in an HDD and an SSD on a same capacity basis. The environmental impact potentials were evaluated based on the metal contents and masses of the drives and environmental impact characterization factors used in life cycle impact assessments. The SSD had 86% to 94% lower resource depletion potentials than the HDD, due primarily to the lower contents of Au, Cu, Pd, Ru, and Pt, whereas the SSD had 33% higher potential for only In. The SSD also had 87% to 94% lower toxicity potentials due primarily to the lower contents of Ni, Pb, Cu, and Cr. Thus, this study showed that the technology transformation is environmentally desirable to conserve resources and to protect human and ecological health. Integr Environ Assess Manag 2019;15:292-298. © 2019 SETAC.}, } @article {pmid30677035, year = {2019}, author = {Lortie, CJ}, title = {Ten simple rules for writing statistical book reviews.}, journal = {PLoS computational biology}, volume = {15}, number = {1}, pages = {e1006562}, pmid = {30677035}, issn = {1553-7358}, mesh = {*Books ; Computational Biology/education/organization & administration ; Humans ; Reading ; Statistics as Topic/*education ; *Writing ; }, abstract = {Statistical books can provide deep insights into statistics and software. There are, however, many resources available to the practitioner. Book reviews have the capacity to function as a critical mechanism for the learner to assess the merits of engaging in part, in full, or at all with a book. The "ten simple rules" format, pioneered in computational biology, was applied here to writing effective book reviews for statistics because of the wide breadth of offerings in this domain, including topical introductions, computational solutions, and theory. Learning by doing is a popular paradigm in statistics and computation, but there is still a niche for books in the pedagogy of self-taught and instruction-based learning. Primarily, these rules ensure that book reviews function as a form of short syntheses to inform and guide readers in deciding to use a specific book relative to other options for resolving statistical challenges.}, } @article {pmid30675523, year = {2019}, author = {Fujisawa, R and Ichinose, G and Dobata, S}, title = {Regulatory mechanism predates the evolution of self-organizing capacity in simulated ant-like robots.}, journal = {Communications biology}, volume = {2}, number = {}, pages = {25}, pmid = {30675523}, issn = {2399-3642}, mesh = {*Algorithms ; *Models, Theoretical ; }, abstract = {The evolution of complexity is one of the prime features of life on Earth. Although well accepted as the product of adaptation, the dynamics underlying the evolutionary build-up of complex adaptive systems remains poorly resolved. Using simulated robot swarms that exhibit ant-like group foraging with trail pheromones, we show that their self-organizing capacity paradoxically involves regulatory behavior that arises in advance. We focus on a traffic rule on their foraging trail as a regulatory trait. We allow the simulated robot swarms to evolve pheromone responsiveness and traffic rules simultaneously. In most cases, the traffic rule, initially arising as selectively neutral component behaviors, assists the group foraging system to bypass a fitness valley caused by overcrowding on the trail. Our study reveals a hitherto underappreciated role of regulatory mechanisms in the origin of complex adaptive systems, as well as highlights the importance of embodiment in the study of their evolution.}, } @article {pmid30674899, year = {2019}, author = {Sarwar, MB and Ahmad, Z and Rashid, B and Hassan, S and Gregersen, PL and Leyva, MO and Nagy, I and Asp, T and Husnain, T}, title = {De novo assembly of Agave sisalana transcriptome in response to drought stress provides insight into the tolerance mechanisms.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {396}, pmid = {30674899}, issn = {2045-2322}, mesh = {*Agave/genetics/metabolism ; Dehydration/genetics/metabolism ; *Gene Expression Regulation, Plant ; *Gene Ontology ; *Stress, Physiological ; *Transcriptome ; }, abstract = {Agave, monocotyledonous succulent plants, is endemic to arid regions of North America, exhibiting exceptional tolerance to their xeric environments. They employ various strategies to overcome environmental constraints, such as crassulacean acid metabolism, wax depositions, and protective leaf morphology. Genomic resources of Agave species have received little attention irrespective of their cultural, economic and ecological importance, which so far prevented the understanding of the molecular bases underlying their adaptations to the arid environment. In this study, we aimed to elucidate molecular mechanism(s) using transcriptome sequencing of A. sisalana. A de novo approach was applied to assemble paired-end reads. The expression study unveiled 3,095 differentially expressed unigenes between well-irrigated and drought-stressed leaf samples. Gene ontology and KEGG analysis specified a significant number of abiotic stress responsive genes and pathways involved in processes like hormonal responses, antioxidant activity, response to stress stimuli, wax biosynthesis, and ROS metabolism. We also identified transcripts belonging to several families harboring important drought-responsive genes. Our study provides the first insight into the genomic structure of A. sisalana underlying adaptations to drought stress, thus providing diverse genetic resources for drought tolerance breeding research.}, } @article {pmid30670614, year = {2019}, author = {González-Torres, P and Rodríguez-Mateos, F and Antón, J and Gabaldón, T}, title = {Impact of Homologous Recombination on the Evolution of Prokaryotic Core Genomes.}, journal = {mBio}, volume = {10}, number = {1}, pages = {}, pmid = {30670614}, issn = {2150-7511}, mesh = {*Adaptation, Biological ; Archaea/*genetics ; Bacteria/*genetics ; Computational Biology ; *Evolution, Molecular ; *Genome, Archaeal ; *Genome, Bacterial ; *Homologous Recombination ; }, abstract = {Homologous recombination (HR) enables the exchange of genetic material between and within species. Recent studies suggest that this process plays a major role in the microevolution of microbial genomes, contributing to core genome homogenization and to the maintenance of cohesive population structures. However, we still have a very poor understanding of the possible adaptive roles of intraspecific HR and of the factors that determine its differential impact across clades and lifestyles. Here we used a unified methodological framework to assess HR in 338 complete genomes from 54 phylogenetically diverse and representative prokaryotic species, encompassing different lifestyles and a broad phylogenetic distribution. Our results indicate that lifestyle and presence of restriction-modification (RM) machineries are among the main factors shaping HR patterns, with symbionts and intracellular pathogens having the lowest HR levels. Similarly, the size of exchanged genomic fragments correlated with the presence of RM and competence machineries. Finally, genes exchanged by HR showed functional enrichments which could be related to adaptations to different environments and ecological strategies. Taken together, our results clarify the factors underlying HR impact and suggest important adaptive roles of genes exchanged through this mechanism. Our results also revealed that the extent of genetic exchange correlated with lifestyle and some genomic features. Moreover, the genes in exchanged regions were enriched for functions that reflected specific adaptations, supporting identification of HR as one of the main evolutionary mechanisms shaping prokaryotic core genomes.IMPORTANCE Microbial populations exchange genetic material through a process called homologous recombination. Although this process has been studied in particular organisms, we lack an understanding of its differential impact over the genome and across microbes with different life-styles. We used a common analytical framework to assess this process in a representative set of microorganisms. Our results uncovered important trends. First, microbes with different lifestyles are differentially impacted, with endosymbionts and obligate pathogens being those less prone to undergo this process. Second, certain genetic elements such as restriction-modification systems seem to be associated with higher rates of recombination. Most importantly, recombined genomes show the footprints of natural selection in which recombined regions preferentially contain genes that can be related to specific ecological adaptations. Taken together, our results clarify the relative contributions of factors modulating homologous recombination and show evidence for a clear a role of this process in shaping microbial genomes and driving ecological adaptations.}, } @article {pmid30670006, year = {2019}, author = {Cardinal-McTeague, WM and Wurdack, KJ and Sigel, EM and Gillespie, LJ}, title = {Seed size evolution and biogeography of Plukenetia (Euphorbiaceae), a pantropical genus with traditionally cultivated oilseed species.}, journal = {BMC evolutionary biology}, volume = {19}, number = {1}, pages = {29}, pmid = {30670006}, issn = {1471-2148}, mesh = {Bayes Theorem ; Biodiversity ; *Biological Evolution ; Data Mining ; Euphorbiaceae/*anatomy & histology/genetics ; Genome, Plant ; Phylogeny ; *Phylogeography ; Plant Oils/*chemistry ; Regression Analysis ; Seeds/*anatomy & histology ; Transcriptome/genetics ; *Tropical Climate ; }, abstract = {BACKGROUND: Plukenetia is a small pantropical genus of lianas and vines with variably sized edible oil-rich seeds that presents an ideal system to investigate neotropical and pantropical diversification patterns and seed size evolution. We assessed the biogeography and seed evolution of Plukenetia through phylogenetic analyses of a 5069 character molecular dataset comprising five nuclear and two plastid markers for 86 terminals in subtribe Plukenetiinae (representing 20 of ~ 23 Plukenetia species). Two nuclear genes, KEA1 and TEB, were used for phylogenetic reconstruction for the first time. Our goals were: (1) produce a robust, time-dependent evolutionary framework for Plukenetia using BEAST; (2) reconstruct its biogeographical history with ancestral range estimation in BIOGEOBEARS; (3) define seed size categories; (4) identify patterns of seed size evolution using ancestral state estimation; and (5) conduct regression analyses with putative drivers of seed size using the threshold model.

RESULTS: Plukenetia was resolved into two major groups, which we refer to as the pinnately- and palmately-veined clades. Our analyses suggest Plukenetia originated in the Amazon or Atlantic Forest of Brazil during the Oligocene (28.7 Mya) and migrated/dispersed between those regions and Central America/Mexico throughout the Miocene. Trans-oceanic dispersals explain the pantropical distribution of Plukenetia, including from the Amazon to Africa in the Early Miocene (17.4 Mya), followed by Africa to Madagascar and Africa to Southeast Asia in the Late Miocene (9.4 Mya) and Pliocene (4.5 Mya), respectively. We infer a single origin of large seeds in the ancestor of Plukenetia. Seed size fits a Brownian motion model of trait evolution and is moderately to strongly associated with plant size, fruit type/dispersal syndrome, and seedling ecology. Biome shifts were not drivers of seed size, although there was a weak association with a transition to fire prone semi-arid savannas.

CONCLUSIONS: The major relationships among the species of Plukenetia are now well-resolved. Our biogeographical analyses support growing evidence that many pantropical distributions developed by periodic trans-oceanic dispersals throughout the Miocene and Pliocene. Selection on a combination of traits contributed to seed size variation, while movement between forest edge/light gap and canopy niches likely contributed to the seed size extremes in Plukenetia.}, } @article {pmid30668562, year = {2019}, author = {D'Andrea, R and Riolo, M and Ostling, AM}, title = {Generalizing clusters of similar species as a signature of coexistence under competition.}, journal = {PLoS computational biology}, volume = {15}, number = {1}, pages = {e1006688}, pmid = {30668562}, issn = {1553-7358}, mesh = {Animals ; *Biological Evolution ; Cluster Analysis ; Computational Biology/*methods ; Ecosystem ; *Models, Biological ; }, abstract = {Patterns of trait distribution among competing species can potentially reveal the processes that allow them to coexist. It has been recently proposed that competition may drive the spontaneous emergence of niches comprising clusters of similar species, in contrast with the dominant paradigm of greater-than-chance species differences. However, current clustering theory relies largely on heuristic rather than mechanistic models. Furthermore, studies of models incorporating demographic stochasticity and immigration, two key players in community assembly, did not observe clusters. Here we demonstrate clustering under partitioning of resources, partitioning of environmental gradients, and a competition-colonization tradeoff. We show that clusters are robust to demographic stochasticity, and can persist under immigration. While immigration may sustain clusters that are otherwise transient, too much dilutes the pattern. In order to detect and quantify clusters in nature, we introduce and validate metrics which have no free parameters nor require arbitrary trait binning, and weigh species by their abundances rather than relying on a presence-absence count. By generalizing beyond the circumstances where clusters have been observed, our study contributes to establishing them as an update to classical trait patterning theory.}, } @article {pmid30660845, year = {2019}, author = {Jin, Y and O'Connor, D and Ok, YS and Tsang, DCW and Liu, A and Hou, D}, title = {Assessment of sources of heavy metals in soil and dust at children's playgrounds in Beijing using GIS and multivariate statistical analysis.}, journal = {Environment international}, volume = {124}, number = {}, pages = {320-328}, doi = {10.1016/j.envint.2019.01.024}, pmid = {30660845}, issn = {1873-6750}, mesh = {Beijing ; Child ; Cluster Analysis ; Dust/*analysis ; Environmental Monitoring/methods ; Geographic Information Systems ; Humans ; Metals, Heavy/*analysis ; Multivariate Analysis ; *Parks, Recreational ; Seasons ; Soil ; Soil Pollutants/*analysis ; }, abstract = {Potentially toxic elements such as heavy metals are ubiquitous in the environment. Risk-based environmental management relies upon identifying pollution sources, pathways, and the exposed population. In a Chinese urban setting, many residents live in high-rise buildings without private gardens. Therefore, the main residential risk of exposure to contaminated soils and dusts may be associated with public open spaces. As children are the most vulnerable receptor, playgrounds represent an important yet often overlooked exposure point. The present study assessed plausible sources of heavy metals at children's playgrounds in a representative metropolitan environment. Soil and equipment dust samples were collected from 71 playgrounds across Beijing, which were analyzed for 11 different heavy metals. Principal component analysis (PCA) was used to identify the latent constructs which control heavy metal variability and reflect potential sources. Cluster analysis (CA) was conducted to group sampled locations, which provided further insights on plausible sources. The main factors extracted from the PCA were then subject to geostatistical analysis. The systematic combination of GIS with multivariate statistical analysis proved valuable for elucidating anthropogenic and natural sources. Elevated Be, V, Cr, Mn, Co, Ni, As in playground soils were found to derive mainly from the natural background (spatial autocorrelation = 2 km), while elevated Cu and Pb was attributed to traffic activities (spatial autocorrelation = 17 km), especially along the routes of Beijing's inner ring-roads, the major roads toward the northwest and northeast, and the international airport. These results suggest that heavy metals in playground equipment dust may derive mainly from atmospheric deposition of air pollution of both natural and anthropogenic origin (spatial autocorrelation = 11-13 km). Among them, Be, V, Mn, Co, Cu, As, Pb were attributed to atmospheric pollution deriving from the north of Beijing, brought by the prevailing northern wind in the winter season; whereas, Cr and Ni may possibly be brought from the southeast by the summer season winds. Knowledge of anthropogenic vs. natural origins of heavy metals in playgrounds is critical in assessing health impact and designing policy instruments for metropolitan areas.}, } @article {pmid30660143, year = {2018}, author = {Stanković, A and Bogdanović, D and Nikolić, M and Anđelković Apostolović, M}, title = {Does short-term air pollution exposure have effects on blood pressure and heart rate in healthy women in the city of Niš, Serbia?.}, journal = {Central European journal of public health}, volume = {26}, number = {4}, pages = {310-315}, doi = {10.21101/cejph.a5104}, pmid = {30660143}, issn = {1210-7778}, mesh = {Air Pollution/adverse effects/*analysis ; Blood Pressure/*physiology ; Cities ; Environmental Exposure/adverse effects/*statistics & numerical data ; Female ; Heart Rate/*physiology ; Humans ; Serbia ; Smoke/analysis ; Sulfur Dioxide/analysis ; Time Factors ; }, abstract = {OBJECTIVE: Epidemiological research has shown that air pollution is associated with cardiovascular events, but little is known about short-term effects on blood pressure (BP) and heart rate (HR) in Serbian population. The present study assessed the short-term association between black smoke (BS) and sulphur dioxide (SO2) levels in urban air and the daily values of blood pressure and heart rate in 98 healthy nonsmoking female volunteers.

METHODS: Generalized regression model was fitted controlling for temperature, relative humidity, air pressure, season, and the day of the week.

RESULTS: There was no association between short-term air pollution exposure and BP and HR, the exposure showed a tendency toward a decrease of diastolic BP and HR, but with no statistical significance.

CONCLUSION: The present findings did not support the conclusion that current levels of ambient BS and SO2 may have an effect on blood pressure and heart rate in women.}, } @article {pmid30659755, year = {2019}, author = {Linck, E and Battey, CJ}, title = {Minor allele frequency thresholds strongly affect population structure inference with genomic data sets.}, journal = {Molecular ecology resources}, volume = {19}, number = {3}, pages = {639-647}, doi = {10.1111/1755-0998.12995}, pmid = {30659755}, issn = {1755-0998}, support = {32 CFR 168a//U.S. Army/ ; }, mesh = {Animals ; Computational Biology/*methods ; Computer Simulation ; *Gene Frequency ; Genetics, Population/*methods ; Genomics/*methods ; Passeriformes/classification/genetics ; Polymorphism, Single Nucleotide ; }, abstract = {A common method of minimizing errors in large DNA sequence data sets is to drop variable sites with a minor allele frequency (MAF) below some specified threshold. Although widespread, this procedure has the potential to alter downstream population genetic inferences and has received relatively little rigorous analysis. Here we use simulations and an empirical single nucleotide polymorphism data set to demonstrate the impacts of MAF thresholds on inference of population structure-often the first step in analysis of population genomic data. We find that model-based inference of population structure is confounded when singletons are included in the alignment, and that both model-based and multivariate analyses infer less distinct clusters when more stringent MAF cutoffs are applied. We propose that this behaviour is caused by the combination of a drop in the total size of the data matrix and by correlations between allele frequencies and mutational age. We recommend a set of best practices for applying MAF filters in studies seeking to describe population structure with genomic data.}, } @article {pmid30659289, year = {2019}, author = {Jefferson, A}, title = {Shutdown will cast a long shadow over research.}, journal = {Nature}, volume = {565}, number = {7740}, pages = {399}, doi = {10.1038/d41586-019-00207-9}, pmid = {30659289}, issn = {1476-4687}, mesh = {*Costs and Cost Analysis ; Datasets as Topic/economics ; *Federal Government ; Financing, Government/economics/*legislation & jurisprudence ; Hydrology/education ; Ohio ; Parks, Recreational/economics/legislation & jurisprudence ; *Politics ; Rain ; Research/*economics/*legislation & jurisprudence ; Research Personnel/*economics/legislation & jurisprudence/psychology ; Research Support as Topic/economics/legislation & jurisprudence ; Time Factors ; Uncertainty ; United States ; }, } @article {pmid30658626, year = {2019}, author = {Lavoie, JG and Wong, ST and Ibrahim, N and O'Neil, JD and Green, M and Ward, A}, title = {Underutilized and undertheorized: the use of hospitalization for ambulatory care sensitive conditions for assessing the extent to which primary healthcare services are meeting needs in British Columbia First Nation communities.}, journal = {BMC health services research}, volume = {19}, number = {1}, pages = {50}, pmid = {30658626}, issn = {1472-6963}, support = {230563//Institute of Aboriginal Peoples Health/ ; }, mesh = {Adolescent ; Adult ; Aged ; Child ; Child, Preschool ; Female ; Humans ; Infant ; Male ; Middle Aged ; Young Adult ; *Ambulatory Care ; British Columbia ; Community Health Services ; Databases, Factual ; *Hospitalization/trends ; Population Groups ; *Primary Health Care ; Indigenous Canadians ; }, abstract = {BACKGROUND: Since the 1960s, the federal government has been providing or funding a selection of community-based primary healthcare (PHC) programs on First Nations reserves. A key question is whether local access to PHC can help address health inequities in First Nations on-reserve communities in British Columbia (BC).

OBJECTIVES: This paper examines whether hospitalization for Ambulatory Care Sensitive Conditions (1) can be used as a proxy measure for the organization of PHC in First Nations reserve areas; and (2) is associated with premature mortality rates.

METHODS: In this descriptive correlational study, we used administrative data available through Population Data BC, including demographic and ecological information (i.e. geo-codes indicating location of residence). We used two different measures of hospitalization: rates of episodic hospital care and rates of length of stay. We correlated hospitalization rates with premature mortality rates and the level of care available in First Nations communities, which depends on a federal funding formula based upon community size and, more specifically, the level of isolation from a provincial point of care.

RESULTS: First Nations communities in BC that have local 24/7 access to PHC services have similar rates of hospitalization for ACSC to those living in urban centres. This is demonstrated by the similarities in the strengths of the correlation between premature mortality rates and rates of avoidable hospitalization for conditions treatable in a PHC setting. This is not the case for communities served by a Health Centre (weaker correlation) and for communities serviced by a Health Station or with no on-reserve point of care (no correlation).

CONCLUSIONS: Improving access to PHC services in First Nations communities can be associated with a significant reduction in avoidable hospitalization and premature mortality rates. The method we tested is an important tool that could serve health care planning decisions in small communities.}, } @article {pmid30658302, year = {2019}, author = {Liu, Z and Tai, P and Li, X and Kong, L and Matthews, TG and Lester, RE and Mondon, JA}, title = {Deriving site-specific water quality criteria for ammonia from national versus international toxicity data.}, journal = {Ecotoxicology and environmental safety}, volume = {171}, number = {}, pages = {665-676}, doi = {10.1016/j.ecoenv.2018.12.078}, pmid = {30658302}, issn = {1090-2414}, mesh = {Ammonia/*toxicity ; Animals ; China ; Chironomidae/drug effects ; Copepoda/drug effects ; Daphnia/drug effects ; Databases, Factual ; Endpoint Determination ; Fishes ; Fresh Water/chemistry ; Geologic Sediments/chemistry ; Models, Theoretical ; Palaemonidae/drug effects ; Rivers/chemistry ; Toxicity Tests ; Water Pollutants, Chemical/*toxicity ; Water Quality/*standards ; }, abstract = {A key question to be asked when developing regional water quality criteria with scarce toxicity data is whether such data need to be locally derived. To address this, ammonia toxicity data from local aquatic species in the Liao River were compared against data from species native and non-native to China, based on comparisons of the overall trends of species sensitivity distributions and derived water quality criteria. Liao River data were acquired by acute and chronic tests using five local freshwater invertebrate species, and then compiled alongside published data from Chinese national guidelines and international literature. Models of best fit using three species sensitivity distribution approaches (log-logistic, log-normal, and Burr III) did not vary markedly (r[2] >0.9), and no specific model provided a best fit across all data sets. The comparisons of the overall trend of species sensitivity distribution curves showed no significant differences at either a national (Chinese native taxa tested in China versus non-native taxa) or regional level (Liao River taxa versus non-Liao River taxa). The comparisons also revealed that the inclusion or exclusions of different ecological groups had little influence on the overall trends of species sensitivity distributions. These findings suggested data on non-local and non-native species, and data from local species tested elsewhere, could be appropriate for guiding the derivation of ammonia water quality criteria for regions such as Liao River. However, caution is needed when using hazardous concentration 5% values in the development of site-specific water quality criteria for a river basin due to the considerable variation observed for ammonia (16.8-56.6 mg/L), although these differences were not statistically significant. Based on the toxicity test evaluation, a preliminary acute value of 10.0 mg/L and chronic value of 1.7 mg/L (at pH of 7.0 and 20 °C) are proposed as site-specific ammonia water quality criteria for the Liao River, China.}, } @article {pmid30658089, year = {2019}, author = {Liu, X and Mubayi, A and Reinhold, D and Zhu, L}, title = {Approximation methods for analyzing multiscale stochastic vector-borne epidemic models.}, journal = {Mathematical biosciences}, volume = {309}, number = {}, pages = {42-65}, doi = {10.1016/j.mbs.2019.01.003}, pmid = {30658089}, issn = {1879-3134}, mesh = {Animals ; *Epidemics ; Humans ; *Models, Biological ; Stochastic Processes ; Vector Borne Diseases/*transmission ; }, abstract = {Stochastic epidemic models, generally more realistic than deterministic counterparts, have often been seen too complex for rigorous mathematical analysis because of level of details it requires to comprehensively capture the dynamics of diseases. This problem further becomes intense when complexity of diseases increases as in the case of vector-borne diseases (VBD). The VBDs are human illnesses caused by pathogens transmitted among humans by intermediate species, which are primarily arthropods. In this study, a stochastic VBD model is developed and novel mathematical methods are described and evaluated to systematically analyze the model and understand its complex dynamics. The VBD model incorporates some relevant features of the VBD transmission process including demographical, ecological and social mechanisms, and different host and vector dynamic scales. The analysis is based on dimensional reductions and model simplifications via scaling limit theorems. The results suggest that the dynamics of the stochastic VBD depends on a threshold quantity R0, the initial size of infectives, and the type of scaling in terms of host population size. The quantity R0 for deterministic counterpart of the model is interpreted as a threshold condition for infection persistence as is mentioned in the literature for many infectious disease models. Different scalings yield different approximations of the model, and in particular, if vectors have much faster dynamics, the effect of the vector dynamics on the host population averages out, which largely reduces the dimension of the model. Specific scenarios are also studied using simulations for some fixed sets of parameters to draw conclusions on dynamics.}, } @article {pmid30651533, year = {2019}, author = {Perkins, DM and Perna, A and Adrian, R and Cermeño, P and Gaedke, U and Huete-Ortega, M and White, EP and Yvon-Durocher, G}, title = {Energetic equivalence underpins the size structure of tree and phytoplankton communities.}, journal = {Nature communications}, volume = {10}, number = {1}, pages = {255}, pmid = {30651533}, issn = {2041-1723}, mesh = {Autotrophic Processes ; Biomass ; Biota/*physiology ; Energy Metabolism/*physiology ; Forests ; *Models, Biological ; Phytoplankton/*physiology ; Trees/*physiology ; }, abstract = {The size structure of autotroph communities - the relative abundance of small vs. large individuals - shapes the functioning of ecosystems. Whether common mechanisms underpin the size structure of unicellular and multicellular autotrophs is, however, unknown. Using a global data compilation, we show that individual body masses in tree and phytoplankton communities follow power-law distributions and that the average exponents of these individual size distributions (ISD) differ. Phytoplankton communities are characterized by an average ISD exponent consistent with three-quarter-power scaling of metabolism with body mass and equivalence in energy use among mass classes. Tree communities deviate from this pattern in a manner consistent with equivalence in energy use among diameter size classes. Our findings suggest that whilst universal metabolic constraints ultimately underlie the emergent size structure of autotroph communities, divergent aspects of body size (volumetric vs. linear dimensions) shape the ecological outcome of metabolic scaling in forest vs. pelagic ecosystems.}, } @article {pmid30649166, year = {2019}, author = {Schiffer, L and Azhar, R and Shepherd, L and Ramos, M and Geistlinger, L and Huttenhower, C and Dowd, JB and Segata, N and Waldron, L}, title = {HMP16SData: Efficient Access to the Human Microbiome Project Through Bioconductor.}, journal = {American journal of epidemiology}, volume = {188}, number = {6}, pages = {1023-1026}, pmid = {30649166}, issn = {1476-6256}, support = {R01 HG005220/HG/NHGRI NIH HHS/United States ; R21 AI121784/AI/NIAID NIH HHS/United States ; U24 CA180996/CA/NCI NIH HHS/United States ; U54 DE023798/DE/NIDCR NIH HHS/United States ; }, mesh = {Adolescent ; Adult ; Computational Biology ; Databases, Genetic/*statistics & numerical data ; Female ; Humans ; Male ; Microbiota/*physiology ; RNA, Ribosomal, 16S/*metabolism ; Young Adult ; }, abstract = {Phase 1 of the Human Microbiome Project (HMP) investigated 18 body subsites of 242 healthy American adults to produce the first comprehensive reference for the composition and variation of the "healthy" human microbiome. Publicly available data sets from amplicon sequencing of two 16S ribosomal RNA variable regions, with extensive controlled-access participant data, provide a reference for ongoing microbiome studies. However, utilization of these data sets can be hindered by the complex bioinformatic steps required to access, import, decrypt, and merge the various components in formats suitable for ecological and statistical analysis. The HMP16SData package provides count data for both 16S ribosomal RNA variable regions, integrated with phylogeny, taxonomy, public participant data, and controlled participant data for authorized researchers, using standard integrative Bioconductor data objects. By removing bioinformatic hurdles of data access and management, HMP16SData enables epidemiologists with only basic R skills to quickly analyze HMP data.}, } @article {pmid30638174, year = {2019}, author = {Ágh, N and Piross, IS and Majoros, G and Csörgő, T and Szöllősi, E}, title = {Malaria infection status of European Robins seems to associate with timing of autumn migration but not with actual condition.}, journal = {Parasitology}, volume = {146}, number = {6}, pages = {814-820}, doi = {10.1017/S0031182018002184}, pmid = {30638174}, issn = {1469-8161}, mesh = {*Animal Migration ; Animals ; Bird Diseases/*epidemiology ; Body Size ; Europe/epidemiology ; Female ; Malaria/epidemiology/*veterinary ; Male ; Prevalence ; *Seasons ; Sex Factors ; *Songbirds ; }, abstract = {Avian malaria parasites can negatively affect many aspects of the life of the passerines. Though these parasites may strongly affect the health and thus migration patterns of the birds also during autumn, previous studies on avian malaria focused mainly on the spring migration and the breeding periods of the birds. We investigated whether the prevalence of blood parasites varies in relation to biometrical traits, body condition and arrival time in the European Robin (Erithacus rubecula) during autumn migration. We found no sex or age related differences in avian malaria prevalence and no relationship between infection status and body size or actual condition of the birds was found either. However, the timing of autumn migration differed marginally between infected and non-infected juveniles, so that parasitized individuals arrived later at the Hungarian stopover site. This is either because avian malaria infections adversely affect the migration timing or migration speed of the birds, or because later arriving individuals come from more distant populations with possibly higher blood parasite prevalence. The possible delay that parasites cause in the arrival time of the birds during autumn migration could affect the whole migratory strategy and the breeding success of the birds in the next season.}, } @article {pmid30637945, year = {2019}, author = {Becheler, A and Coron, C and Dupas, S}, title = {The Quetzal Coalescence template library: A C++ programmers resource for integrating distributional, demographic and coalescent models.}, journal = {Molecular ecology resources}, volume = {19}, number = {3}, pages = {788-793}, doi = {10.1111/1755-0998.12992}, pmid = {30637945}, issn = {1755-0998}, support = {ANR-11-LABX-0034//French Government/ ; }, mesh = {Computational Biology/*methods ; Genetics, Population/*methods ; *Software ; }, abstract = {Genetic samples can be used to understand and predict the behaviour of species living in a fragmented and temporally changing environment. In this regard, models of coalescence conditioned to an environment through an explicit modelling of population growth and migration have been developed in recent years, and simulators implementing these models have been developed, enabling biologists to estimate parameters of interest with Approximate Bayesian Computation techniques. However, model choice remains limited, and developing new coalescence simulators is extremely time consuming because code re-use is limited. We present Quetzal, a C++ library composed of re-usable components, which is sufficiently general to efficiently implement a wide range of spatially explicit coalescence-based environmental models of population genetics and to embed the simulation in an Approximate Bayesian Computation framework. Quetzal is not a simulation program, but a toolbox for programming simulators aimed at the community of scientific coders and research software engineers in molecular ecology and phylogeography. This new code resource is open-source and available at https://becheler.github.io/pages/quetzal.html along with other documentation resources.}, } @article {pmid30634914, year = {2019}, author = {Liu, W and Chen, L and Zhang, S and Hu, F and Wang, Z and Lyu, J and Wang, B and Xiang, H and Zhao, R and Tian, Z and Ge, S and Wang, W}, title = {Decrease of gene expression diversity during domestication of animals and plants.}, journal = {BMC evolutionary biology}, volume = {19}, number = {1}, pages = {19}, pmid = {30634914}, issn = {1471-2148}, mesh = {Animals ; Bombyx/genetics ; Chickens/genetics ; Databases, Genetic ; Dogs/genetics ; *Domestication ; *Gene Expression Regulation ; *Genetic Variation ; Humans ; Linkage Disequilibrium/genetics ; Plants/*genetics ; Selection, Genetic ; Transcriptome/genetics ; Zea mays/genetics ; }, abstract = {BACKGROUND: The genetic mechanisms underlying the domestication of animals and plants have been of great interest to biologists since Darwin. To date, little is known about the global pattern of gene expression changes during domestication.

RESULTS: We generated and collected transcriptome data for seven pairs of domestic animals and plants including dog, silkworm, chicken, rice, cotton, soybean and maize and their wild progenitors and compared the expression profiles between the domestic and wild species. Intriguingly, although the number of expressed genes varied little, the domestic species generally exhibited lower gene expression diversity than did the wild species, and this lower diversity was observed for both domestic plants and different kinds of domestic animals including insect, bird and mammal in the whole-genome gene set (WGGS), candidate selected gene set (CSGS) and non-CSGS, with CSGS exhibiting a higher degree of decreased expression diversity. Moreover, different from previous reports which found 2 to 4% of genes were selected by human, we identified 6892 candidate selected genes accounting for 7.57% of the whole-genome genes in rice and revealed that fewer than 8% of the whole-genome genes had been affected by domestication.

CONCLUSIONS: Our results showed that domestication affected the pattern of variation in gene expression throughout the genome and generally decreased the expression diversity across species, and this decrease may have been associated with decreased genetic diversity. This pattern might have profound effects on the phenotypic and physiological changes of domestic animals and plants and provide insights into the genetic mechanisms at the transcriptome level other than decreased genetic diversity and increased linkage disequilibrium underpinning artificial selection.}, } @article {pmid30631311, year = {2018}, author = {Christel, S and Herold, M and Bellenberg, S and Buetti-Dinh, A and El Hajjami, M and Pivkin, IV and Sand, W and Wilmes, P and Poetsch, A and Vera, M and Dopson, M}, title = {Weak Iron Oxidation by Sulfobacillus thermosulfidooxidans Maintains a Favorable Redox Potential for Chalcopyrite Bioleaching.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {3059}, pmid = {30631311}, issn = {1664-302X}, abstract = {Bioleaching is an emerging technology, describing the microbially assisted dissolution of sulfidic ores that provides a more environmentally friendly alternative to many traditional metal extraction methods, such as roasting or smelting. Industrial interest is steadily increasing and today, circa 15-20% of the world's copper production can be traced back to this method. However, bioleaching of the world's most abundant copper mineral chalcopyrite suffers from low dissolution rates, often attributed to passivating layers, which need to be overcome to use this technology to its full potential. To prevent these passivating layers from forming, leaching needs to occur at a low oxidation/reduction potential (ORP), but chemical redox control in bioleaching heaps is difficult and costly. As an alternative, selected weak iron-oxidizers could be employed that are incapable of scavenging exceedingly low concentrations of iron and therefore, raise the ORP just above the onset of bioleaching, but not high enough to allow for the occurrence of passivation. In this study, we report that microbial iron oxidation by Sulfobacillus thermosulfidooxidans meets these specifications. Chalcopyrite concentrate bioleaching experiments with S. thermosulfidooxidans as the sole iron oxidizer exhibited significantly lower redox potentials and higher release of copper compared to communities containing the strong iron oxidizer Leptospirillum ferriphilum. Transcriptomic response to single and co-culture of these two iron oxidizers was studied and revealed a greatly decreased number of mRNA transcripts ascribed to iron oxidation in S. thermosulfidooxidans when cultured in the presence of L. ferriphilum. This allowed for the identification of genes potentially responsible for S. thermosulfidooxidans' weaker iron oxidation to be studied in the future, as well as underlined the need for new mechanisms to control the microbial population in bioleaching heaps.}, } @article {pmid30626123, year = {2019}, author = {Mollalo, A and Mao, L and Rashidi, P and Glass, GE}, title = {A GIS-Based Artificial Neural Network Model for Spatial Distribution of Tuberculosis across the Continental United States.}, journal = {International journal of environmental research and public health}, volume = {16}, number = {1}, pages = {}, pmid = {30626123}, issn = {1660-4601}, mesh = {Cluster Analysis ; *Geographic Information Systems ; Humans ; Linear Models ; *Neural Networks, Computer ; Spatial Analysis ; Tuberculosis/*epidemiology ; United States/epidemiology ; }, abstract = {Despite the usefulness of artificial neural networks (ANNs) in the study of various complex problems, ANNs have not been applied for modeling the geographic distribution of tuberculosis (TB) in the US. Likewise, ecological level researches on TB incidence rate at the national level are inadequate for epidemiologic inferences. We collected 278 exploratory variables including environmental and a broad range of socio-economic features for modeling the disease across the continental US. The spatial pattern of the disease distribution was statistically evaluated using the global Moran's I, Getis[-]Ord General G, and local Gi* statistics. Next, we investigated the applicability of multilayer perceptron (MLP) ANN for predicting the disease incidence. To avoid overfitting, L1 regularization was used before developing the models. Predictive performance of the MLP was compared with linear regression for test dataset using root mean square error, mean absolute error, and correlations between model output and ground truth. Results of clustering analysis showed that there is a significant spatial clustering of smoothed TB incidence rate (p < 0.05) and the hotspots were mainly located in the southern and southeastern parts of the country. Among the developed models, single hidden layer MLP had the best test accuracy. Sensitivity analysis of the MLP model showed that immigrant population (proportion), underserved segments of the population, and minimum temperature were among the factors with the strongest contributions. The findings of this study can provide useful insight to health authorities on prioritizing resource allocation to risk-prone areas.}, } @article {pmid30625983, year = {2019}, author = {Yao, Y and Chen, SB and Ding, G and Dai, J}, title = {Evaluation of Reliability of the Recomputed Nutrient Intake Data in the National Heart, Lung, and Blood Institute Twin Study.}, journal = {Nutrients}, volume = {11}, number = {1}, pages = {}, pmid = {30625983}, issn = {2072-6643}, mesh = {Adult ; *Databases, Factual ; Datasets as Topic ; *Diet ; Energy Intake ; *Food Analysis ; Humans ; Male ; Middle Aged ; Nutrients/*administration & dosage ; *Nutritive Value ; Reproducibility of Results ; }, abstract = {The nutrient intake dataset is crucial in epidemiological studies. The latest version of the food composition database includes more types of nutrients than previous ones and can be used to obtain data on nutrient intake that could not be estimated before. Usual food consumption data were collected among 910 twins between 1969 and 1973 through dietary history interviews, and then used to calculate intake of eight types of nutrients (energy intake, carbohydrate, protein, cholesterol, total fat, and saturated, monounsaturated, and polyunsaturated fatty acids) in the National Heart, Lung, and Blood Institute Twin Study. We recalculated intakes using the food composition database updated in 2008. Several different statistical methods were used to evaluate the validity and the reliability of the recalculated intake data. Intra-class correlation coefficients between recalculated and original intake values were above 0.99 for all nutrients. R[2] values for regression models were above 0.90 for all nutrients except polyunsaturated fatty acids (R[2] = 0.63). In Bland[-]Altman plots, the percentage of scattering points that outlay the mean plus or minus two standard deviations lines was less than 5% for all nutrients. The arithmetic mean percentage of quintile agreement was 78.5% and that of the extreme quintile disagreement was 0.1% for all nutrients between the two datasets. Recalculated nutrient intake data is in strong agreement with the original one, supporting the reliability of the recalculated data. It is also implied that recalculation is a cost-efficient approach to obtain the intake of nutrients unavailable at baseline.}, } @article {pmid30625219, year = {2019}, author = {Ožana, S and Burda, M and Hykel, M and Malina, M and Prášek, M and Bárta, D and Dolný, A}, title = {Dragonfly Hunter CZ: Mobile application for biological species recognition in citizen science.}, journal = {PloS one}, volume = {14}, number = {1}, pages = {e0210370}, pmid = {30625219}, issn = {1932-6203}, mesh = {Altitude ; Animals ; Biodiversity ; Czech Republic ; Ecosystem ; Expert Systems ; Female ; Fuzzy Logic ; Male ; *Mobile Applications ; *Odonata/anatomy & histology/classification ; Seasons ; Volunteers ; }, abstract = {Citizen science and data collected from various volunteers have an interesting potential in aiding the understanding of many biological and ecological processes. We describe a mobile application that allows the public to map and report occurrences of the odonata species (dragonflies and damselflies) found in the Czech Republic. The application also helps in species classification based on observation details such as date, GPS coordinates, and the altitude, biotope, suborder, and colour. Dragonfly Hunter CZ is a free Android application built on the open-source framework NativeScript using the JavaScript programming language which is now fully available on Google Play. The server side is powered by Apache Server with PHP and MariaDB SQL database. A mobile application is a fast and accurate way to obtain data pertaining to the odonata species, which can be used after expert verification for ecological studies and conservation basis like Red Lists and policy instruments. We expect it to be effective in encouraging Citizen Science and in promoting the proactive reporting of odonates. It can also be extended to the reporting and monitoring of other plant and animal species.}, } @article {pmid30625112, year = {2019}, author = {Brooks, LE and Kaze, M and Sistrom, M}, title = {Where the plasmids roam: large-scale sequence analysis reveals plasmids with large host ranges.}, journal = {Microbial genomics}, volume = {5}, number = {1}, pages = {}, pmid = {30625112}, issn = {2057-5858}, mesh = {Corynebacterium/*genetics ; *Databases, Nucleic Acid ; Enterobacteriaceae/*genetics ; Plasmids/*genetics ; }, abstract = {Describing the role of plasmids and their contribution to the exchange of genetic material among bacteria is essential for understanding the fields of plasmid epidemiology, microbial ecology, and commercial and synthetic microbiology. Broad-host-range (BHR) plasmids are those that are found not only in a single bacterial species, but in members of different taxonomic groups and are of significant interest to researchers in many fields. We applied a novel approach to computationally identify new BHR plasmids, in which we searched for highly similar cognate plasmids within a comprehensive plasmid database. After identifying 125 plasmid groups with highly similar cognates found in multiple taxa, we closely examined BHR plasmids found in multiple families. The majority of our identified BHR plasmids are found in members of the Enterobacteriaceae and closely related taxa, while three BHR plasmids of potential commercial significance were found in two species of Cyanobacteria. One plasmid with an exceptionally broad host range was found in both Gram-positive and Gram-negative bacterial species. This analysis demonstrates the utility of this method in identifying new BHR plasmids while highlighting unknown ranges of previously documented plasmids.}, } @article {pmid30623332, year = {2019}, author = {Liao, Z and Zhou, C and Tian, W and Hu, T and Guo, R}, title = {CBR-based integration of a hydrodynamic and water quality model and GIS-a case study of Chaohu City.}, journal = {Environmental science and pollution research international}, volume = {26}, number = {7}, pages = {6436-6449}, pmid = {30623332}, issn = {1614-7499}, support = {2016YFE0123300//National Key R&D Program of China/ ; 51578396 and 51778451//National Natural Science Foundation of China/ ; }, mesh = {China ; Decision Making ; Environmental Monitoring/*methods ; *Geographic Information Systems ; Hydrodynamics ; *Models, Theoretical ; Software ; Water Quality ; }, abstract = {Monitoring on urban water environment and analysis of engineering improvement measures are intricate and time-consuming tasks. In previous studies, the integration of hydrodynamic and water quality models and geographical information system (GIS) usually takes three approaches: loose coupling, tight coupling, and full coupling. However, this paper adopted a special loose coupling approach-case-based reasoning (CBR) to develop an integrated decision support system. This was characterized by invoking the case base stored in the GIS platform as the output of the model. The fused capability of model's water quality predication and strong spatial data processing analysis of GIS can be realized at the same time by integration. The functionality of the integrated system was illustrated through a case study of Chaohu, a medium-sized city in China, which includes case retrieval, result interpretation, and the visual display in the GIS platform. Results verified the feasibility and operability of the developed method. As a useful tool, the integrated decision support system makes it simpler and more convenient for decision makers to make decisions efficiently and quickly.}, } @article {pmid30617886, year = {2019}, author = {Li, X and Du, J and Long, H}, title = {Dynamic analysis of international green behavior from the perspective of the mapping knowledge domain.}, journal = {Environmental science and pollution research international}, volume = {26}, number = {6}, pages = {6087-6098}, pmid = {30617886}, issn = {1614-7499}, support = {18VSJ038//Special Funds of the National Social Science Fund of China/ ; }, mesh = {Bibliometrics ; Databases, Factual ; *Environment ; Humans ; International Cooperation ; Knowledge ; Research/*statistics & numerical data ; Serial Publications/*statistics & numerical data ; Spatio-Temporal Analysis ; }, abstract = {Green behavior is an important part of the study of green development. To promote green development, it is necessary to engage in further innovation on the basis of lessons from international advancements in green behavior. To clarify the spatial and temporal distribution characteristics of international researchers in the study of green behavior, the research focus, and the research frontiers, a visual analysis was performed on 22,114 articles cited in the SSCI and SCI-EXPANDED databases from 2000 to 2017. This analysis was based on bibliometrics and mapping knowledge domain (MKD) analysis with CiteSpace 5.3.R4, a scientific and technological text-mining and visualization software. The results show that international green behavior research has the following main characteristics. First, a positive correlation was found between the number of papers and time. Second, research is highly valued by researchers in the natural sciences, such as ecology. The USA is involved in major research efforts and maintains a high level of cooperation with other countries and regions. International cooperation among institutions needs to be strengthened. The co-cited journals are primarily academic journals in the natural sciences. Third, research hotspots mainly focus on the theory of planned behavior (TPB), consumers, attitudes, performance, and environment, all of which evolve according to the phase path of "germination-growth." Fourth, the research frontier issues are largely related to management science and environmental science, and the research objects and methods will become increasingly complex and interdisciplinary over time.}, } @article {pmid30616526, year = {2019}, author = {Maselli-Schoueri, JH and Affonso-Kaufman, FA and de Melo Sette, CV and Dos Santos Figueiredo, FW and Adami, F}, title = {Time trend of breast cancer mortality in BRAZILIAN men: 10-year data analysis from 2005 to 2015.}, journal = {BMC cancer}, volume = {19}, number = {1}, pages = {23}, pmid = {30616526}, issn = {1471-2407}, mesh = {Adult ; Age Factors ; Aged ; Aged, 80 and over ; Brazil ; Breast Neoplasms, Male/*mortality ; Data Analysis ; Humans ; Male ; Middle Aged ; Mortality/trends ; Young Adult ; }, abstract = {BACKGROUND: Male Breast Cancer (MBC) is rare, which makes its understanding and treatment be extrapolated from what is known about the occurrence in women, with few epidemiological studies, with few epidemiological studies. Therefore, the aim of the present paper was to study breast cancer mortality in adult males in Brazil and its administrative regions between 2005 and 2015.

METHODS: Ecological study with data on MBC mortality in adults between 2005 and 2015. Data were obtained from the Mortality Information System of the Department of Informatics of SUS (the Unified Health System of the country). Descriptive statistics were used for MBC mortality and linear regression to analyze the relationship between mortality and the country's administrative regions. Percentage Change (PC) and Annual Percentage Change (APC) were the trend measures used for MBC mortality for the period.

RESULTS: Between 2005 and 2015, there were 1521 deaths due to MBC in adults in Brazil. Regarding mortality by region, there was great oscillation in the rates of the country as a whole (PC = 113,87; β = 0,009 (IC95% 0,000 - 0,018); r[2] = 0,381; P = 0,043). The highest increase in MBC mortality occurred in patients aged 80 years or older (PC = 161,04; β = 0,201 (IC95% 0,640 - 0,339); r[2] = 0,550; P = 0,009) and there was significant increase in deaths for the 50-54-year age group (PC = 224,01; β = 0,135 (CI95% 0,052; 0,218); r[2] = 0,601; P = 0,005).

CONCLUSION: Mortality in adults due to MBC increased in Brazil during the study period with the highest percentage increase occurring for individuals aged 80 years or older.}, } @article {pmid30616481, year = {2019}, author = {Brennecke, P and Rasina, D and Aubi, O and Herzog, K and Landskron, J and Cautain, B and Vicente, F and Quintana, J and Mestres, J and Stechmann, B and Ellinger, B and Brea, J and Kolanowski, JL and Pilarski, R and Orzaez, M and Pineda-Lucena, A and Laraia, L and Nami, F and Zielenkiewicz, P and Paruch, K and Hansen, E and von Kries, JP and Neuenschwander, M and Specker, E and Bartunek, P and Simova, S and Leśnikowski, Z and Krauss, S and Lehtiö, L and Bilitewski, U and Brönstrup, M and Taskén, K and Jirgensons, A and Lickert, H and Clausen, MH and Andersen, JH and Vicent, MJ and Genilloud, O and Martinez, A and Nazaré, M and Fecke, W and Gribbon, P}, title = {EU-OPENSCREEN: A Novel Collaborative Approach to Facilitate Chemical Biology.}, journal = {SLAS discovery : advancing life sciences R & D}, volume = {24}, number = {3}, pages = {398-413}, pmid = {30616481}, issn = {2472-5560}, mesh = {*Cooperative Behavior ; Drug Discovery/*methods ; Drug Evaluation, Preclinical ; Europe ; High-Throughput Screening Assays ; Humans ; Structure-Activity Relationship ; }, abstract = {Compound screening in biological assays and subsequent optimization of hits is indispensable for the development of new molecular research tools and drug candidates. To facilitate such discoveries, the European Research Infrastructure EU-OPENSCREEN was founded recently with the support of its member countries and the European Commission. Its distributed character harnesses complementary knowledge, expertise, and instrumentation in the discipline of chemical biology from 20 European partners, and its open working model ensures that academia and industry can readily access EU-OPENSCREEN's compound collection, equipment, and generated data. To demonstrate the power of this collaborative approach, this perspective article highlights recent projects from EU-OPENSCREEN partner institutions. These studies yielded (1) 2-aminoquinazolin-4(3 H)-ones as potential lead structures for new antimalarial drugs, (2) a novel lipodepsipeptide specifically inducing apoptosis in cells deficient for the pVHL tumor suppressor, (3) small-molecule-based ROCK inhibitors that induce definitive endoderm formation and can potentially be used for regenerative medicine, (4) potential pharmacological chaperones for inborn errors of metabolism and a familiar form of acute myeloid leukemia (AML), and (5) novel tankyrase inhibitors that entered a lead-to-candidate program. Collectively, these findings highlight the benefits of small-molecule screening, the plethora of assay designs, and the close connection between screening and medicinal chemistry within EU-OPENSCREEN.}, } @article {pmid30616091, year = {2019}, author = {Calabrese, EJ and Agathokleous, E and Kozumbo, WJ and Stanek, EJ and Leonard, D}, title = {Estimating the range of the maximum hormetic stimulatory response.}, journal = {Environmental research}, volume = {170}, number = {}, pages = {337-343}, doi = {10.1016/j.envres.2018.12.020}, pmid = {30616091}, issn = {1096-0953}, mesh = {Animals ; Databases, Factual ; Dose-Response Relationship, Drug ; *Hormesis ; Humans ; *Plants ; }, abstract = {An ever-expanding hormetic database (HDB) was used to demonstrate that the median maximal hormetic stimulatory response (MHSR) of biphasic dose-response relationships increases in value with an increase in the number of stimulatory doses/concentrations that are administered below the estimated threshold/ZEP (zero equivalent point - i.e., the dose where the response crosses the control group value). With only one dose or concentration administered below the ZEP, the median MHSR for microbes (in vitro), animals (in vitro and in vivo), and plants (in vitro and in vivo) ranged between 120% and 125% of the control response. However, when individual agents having at least six doses below the ZEP were mined from the HDB (and a median MHSR then determined), the median MHSR increased to 160-190%. This progressive increase in the MHSR appears to be due to several factors, including (i) the enhanced capacity of additional doses in the stimulatory hormetic zone to better estimate the response optima, and (ii) enhanced variability due to the presence of more doses in the stimulatory zone. This study offers a novel perspective for improving research protocols, unraveling the limits of biological plasticity, understanding low-level stress biology, advancing human and ecological health, and enhancing human performance.}, } @article {pmid30609942, year = {2019}, author = {Yang, SH and Tandon, K and Lu, CY and Wada, N and Shih, CJ and Hsiao, SS and Jane, WN and Lee, TC and Yang, CM and Liu, CT and Denis, V and Wu, YT and Wang, LT and Huang, L and Lee, DC and Wu, YW and Yamashiro, H and Tang, SL}, title = {Metagenomic, phylogenetic, and functional characterization of predominant endolithic green sulfur bacteria in the coral Isopora palifera.}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {3}, pmid = {30609942}, issn = {2049-2618}, mesh = {Animals ; Anthozoa/*microbiology ; Chlorobi/*classification/genetics/isolation & purification ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Metagenomics/*methods ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: Endolithic microbes in coral skeletons are known to be a nutrient source for the coral host. In addition to aerobic endolithic algae and Cyanobacteria, which are usually described in the various corals and form a green layer beneath coral tissues, the anaerobic photoautotrophic green sulfur bacteria (GSB) Prosthecochloris is dominant in the skeleton of Isopora palifera. However, due to inherent challenges in studying anaerobic microbes in coral skeleton, the reason for its niche preference and function are largely unknown.

RESULTS: This study characterized a diverse and dynamic community of endolithic microbes shaped by the availability of light and oxygen. In addition, anaerobic bacteria isolated from the coral skeleton were cultured for the first time to experimentally clarify the role of these GSB. This characterization includes GSB's abundance, genetic and genomic profiles, organelle structure, and specific metabolic functions and activity. Our results explain the advantages endolithic GSB receive from living in coral skeletons, the potential metabolic role of a clade of coral-associated Prosthecochloris (CAP) in the skeleton, and the nitrogen fixation ability of CAP.

CONCLUSION: We suggest that the endolithic microbial community in coral skeletons is diverse and dynamic and that light and oxygen are two crucial factors for shaping it. This study is the first to demonstrate the ability of nitrogen uptake by specific coral-associated endolithic bacteria and shed light on the role of endolithic bacteria in coral skeletons.}, } @article {pmid30609726, year = {2019}, author = {Moreno, C and Aquino, R and Ibarreche, J and Pérez, I and Castellanos, E and Álvarez, E and Rentería, R and Anguiano, L and Edwards, A and Lepper, P and Edwards, RM and Clark, B}, title = {RiverCore: IoT Device for River Water Level Monitoring over Cellular Communications.}, journal = {Sensors (Basel, Switzerland)}, volume = {19}, number = {1}, pages = {}, pmid = {30609726}, issn = {1424-8220}, mesh = {Cloud Computing ; Environmental Monitoring/*instrumentation/*methods ; Floods/*prevention & control/statistics & numerical data ; Hydrology/*statistics & numerical data ; Information Storage and Retrieval ; Internet/*instrumentation ; Mexico ; Mobile Applications ; *Rivers ; Telemetry/*instrumentation ; }, abstract = {Flooding is one of the most frequent and costly natural disasters affecting mankind. However, implementing Internet of Things (IoT) technology to monitor river behavior may help mitigate or prevent future disasters. This article outlines the hardware development of an IoT system (RiverCore) and defines an application scenario in a specific hydrological region of the state of Colima (Mexico), highlighting the characteristics of data acquisition and data processing used. Both fixed position and moving drifter node systems are described along with web-based data acquisition platform developments integrated with IoT techniques to retrieve data through 3G cellular networks. The developed architecture uses the Message Queuing Telemetry Transport (MQTT) protocol, along with encryption and security mechanisms, to send real-time data packages from fixed nodes to a server that stores retrieved data in a non-relational database. From this, data can be accessed and displayed through different customizable queries and graphical representations, allowing future use in flood analysis and prediction systems. All of these features are presented along with graphical evidence of the deployment of the different devices and of several cellular communication and on-site data acquisition tests.}, } @article {pmid30602025, year = {2019}, author = {Heras, J and Aguilar, A}, title = {Comparative Transcriptomics Reveals Patterns of Adaptive Evolution Associated with Depth and Age Within Marine Rockfishes (Sebastes).}, journal = {The Journal of heredity}, volume = {110}, number = {3}, pages = {340-350}, pmid = {30602025}, issn = {1465-7333}, support = {S10 RR027303/RR/NCRR NIH HHS/United States ; S10 RR029668/RR/NCRR NIH HHS/United States ; }, mesh = {Animals ; Computational Biology/methods ; *Evolution, Molecular ; Fishes/classification/*genetics ; *Gene Expression Profiling ; High-Throughput Nucleotide Sequencing ; Molecular Sequence Annotation ; Phylogeny ; Repetitive Sequences, Nucleic Acid ; Selection, Genetic ; *Transcriptome ; }, abstract = {The genetic underpinnings that contribute to ecological adaptation and speciation are not completely understood, especially within marine ecosystems. These evolutionary processes can be elucidated by studying adaptive radiations, because they provide replicates of divergence within a given environment or time-frame. Marine rockfishes (genus Sebastes) are an adaptive radiation and unique model system for studying adaptive evolution in the marine realm. We investigated molecular evolution associated with ecological (depth) and life history (lifespan) divergence in 2 closely related clades of Sebastes. Brain transcriptomes were sequenced via RNA-Seq from 3 species within the subgenus Pteropodus and a pair of related congeners from the subgenus Sebastosomus in order to identify patterns of adaptive evolution. De novo assemblies from these transcriptomes were used to identify 3867 orthologous clusters, and genes subject to positive selection were identified based on all 5 species, depth, and lifespan. Within all our analyses, we identified hemoglobin subunit α to be under strong positive selection and is associated with the depth of occurrence. In our lifespan analysis we identified immune function genes under positive selection in association with maximum lifespan. This study provides insight on the molecular evolution of rockfishes and these candidate genes may provide a better understanding of how these subgenera radiated within the Northeast Pacific.}, } @article {pmid30600455, year = {2019}, author = {Shacham, E and Lew, D and Xiao, T and López, J and Trull, T and Schootman, M and Presti, R}, title = {Testing the Feasibility of Using Ecological Momentary Assessment to Collect Real-Time Behavior and Mood to Predict Technology-Measured HIV Medication Adherence.}, journal = {AIDS and behavior}, volume = {23}, number = {8}, pages = {2176-2184}, doi = {10.1007/s10461-018-2378-9}, pmid = {30600455}, issn = {1573-3254}, support = {1R21AA022064//National Institute on Alcohol Abuse and Alcoholism/ ; }, mesh = {Adult ; *Affect ; Alcohol Drinking/*psychology ; Data Collection ; *Ecological Momentary Assessment ; Feasibility Studies ; Female ; HIV Infections/*drug therapy ; Humans ; Male ; Medical Informatics Applications ; Medication Adherence/*psychology ; Missouri ; Pilot Projects ; Prospective Studies ; Smartphone ; }, abstract = {Identifying distinct patterns of behavior and mood in natural environments that interrupt medication adherence among individuals with HIV will be useful in informing intervention development. This pilot study assessed the initial efficacy of using ecologic momentary assessment to define patterns of alcohol use, mood, and medication adherence. Participants reported intraday alcohol use and mood using app-enabled smartphones and MEMSCap pill bottles to measure medication adherence. There were 34 enrolled participants, 29 of whom completed the 28-day study. Participants drank a mean of 7.75 days of the study period. The positive and negative affect scores ranged from 10 to 50, with a mean of 25.7 and 11.4 for each, respectively. The average medication adherence for the sample was 94.1%. These findings suggest these types of data collection methods are increasingly acceptable in measuring real-time mood and behavior, which may better inform interventions addressed at increasing HIV adherence practices.}, } @article {pmid30598535, year = {2019}, author = {Allen, JM and Folk, RA and Soltis, PS and Soltis, DE and Guralnick, RP}, title = {Biodiversity synthesis across the green branches of the tree of life.}, journal = {Nature plants}, volume = {5}, number = {1}, pages = {11-13}, pmid = {30598535}, issn = {2055-0278}, mesh = {*Biodiversity ; *Databases, Factual ; Ecology/*methods ; Phylogeny ; *Plant Physiological Phenomena ; }, abstract = {Advances in biodiversity science, coupled with new technologies and big data platforms, are expanding our ability to explore and understand the natural world. For the first time, biologists can link data from growing repositories and computational approaches to better integrate plant evolution and ecology at the broadest extents. The emerging synthesis is reshaping our views of plant diversification and guiding new approaches to conservation.}, } @article {pmid30598532, year = {2019}, author = {Hübner, S and Bercovich, N and Todesco, M and Mandel, JR and Odenheimer, J and Ziegler, E and Lee, JS and Baute, GJ and Owens, GL and Grassa, CJ and Ebert, DP and Ostevik, KL and Moyers, BT and Yakimowski, S and Masalia, RR and Gao, L and Ćalić, I and Bowers, JE and Kane, NC and Swanevelder, DZH and Kubach, T and Muños, S and Langlade, NB and Burke, JM and Rieseberg, LH}, title = {Sunflower pan-genome analysis shows that hybridization altered gene content and disease resistance.}, journal = {Nature plants}, volume = {5}, number = {1}, pages = {54-62}, pmid = {30598532}, issn = {2055-0278}, mesh = {Crops, Agricultural/genetics/microbiology ; Disease Resistance/genetics ; Gene Ontology ; Genes, Plant ; Genetic Variation ; Genome, Plant ; Helianthus/*genetics/*microbiology ; *Hybridization, Genetic ; Plant Diseases/*genetics/microbiology ; Recombination, Genetic ; Selection, Genetic ; }, abstract = {Domesticated plants and animals often display dramatic responses to selection, but the origins of the genetic diversity underlying these responses remain poorly understood. Despite domestication and improvement bottlenecks, the cultivated sunflower remains highly variable genetically, possibly due to hybridization with wild relatives. To characterize genetic diversity in the sunflower and to quantify contributions from wild relatives, we sequenced 287 cultivated lines, 17 Native American landraces and 189 wild accessions representing 11 compatible wild species. Cultivar sequences failing to map to the sunflower reference were assembled de novo for each genotype to determine the gene repertoire, or 'pan-genome', of the cultivated sunflower. Assembled genes were then compared to the wild species to estimate origins. Results indicate that the cultivated sunflower pan-genome comprises 61,205 genes, of which 27% vary across genotypes. Approximately 10% of the cultivated sunflower pan-genome is derived through introgression from wild sunflower species, and 1.5% of genes originated solely through introgression. Gene ontology functional analyses further indicate that genes associated with biotic resistance are over-represented among introgressed regions, an observation consistent with breeding records. Analyses of allelic variation associated with downy mildew resistance provide an example in which such introgressions have contributed to resistance to a globally challenging disease.}, } @article {pmid30597116, year = {2019}, author = {Nakagawa, S and De Villemereuil, P}, title = {A General Method for Simultaneously Accounting for Phylogenetic and Species Sampling Uncertainty via Rubin's Rules in Comparative Analysis.}, journal = {Systematic biology}, volume = {68}, number = {4}, pages = {632-641}, doi = {10.1093/sysbio/syy089}, pmid = {30597116}, issn = {1076-836X}, mesh = {Classification/*methods ; Data Interpretation, Statistical ; *Phylogeny ; }, abstract = {Phylogenetic comparative methods (PCMs), especially ones based on linear models, have played a central role in understanding species' trait evolution. These methods, however, usually assume that phylogenetic trees are known without error or uncertainty, but this assumption is most likely incorrect. So far, Markov chain Monte Carlo (MCMC)-based Bayesian methods have mainly been deployed to account for such "phylogenetic uncertainty" in PCMs. Herein, we propose an approach with which phylogenetic uncertainty is incorporated in a simple, readily implementable and reliable manner. Our approach uses Rubin's rules, which are an integral part of a standard multiple imputation procedure, often employed to recover missing data. We see true phylogenetic trees as missing data under this approach. Further, unmeasured species in comparative data (i.e., missing trait data) can be seen as another source of uncertainty in PCMs because arbitrary sampling of species in a given taxon or "species sampling uncertainty" can affect estimation in PCMs. Using two simulation studies, we show our method can account for phylogenetic uncertainty under many different scenarios (e.g., uncertainty in topology and branch lengths) and, at the same time, it can handle missing trait data (i.e., species sampling uncertainty). A unique property of the multiple imputation procedure is that an index, named "relative efficiency," could be used to quantify the number of trees required for incorporating phylogenetic uncertainty. Thus, by using the relative efficiency, we show the required tree number is surprisingly small ($\sim$50 trees). However, the most notable advantage of our method is that it could be combined seamlessly with PCMs that utilize multiple imputation to handle simultaneously phylogenetic uncertainty (i.e., missing true trees) and species sampling uncertainty (i.e., missing trait data) in PCMs.}, } @article {pmid30596704, year = {2018}, author = {Kim, YA and Park, YS and Youk, T and Lee, H and Lee, K}, title = {Trends in South Korean antimicrobial use and association with changes in Escherichia coli resistance rates: 12-year ecological study using a nationwide surveillance and antimicrobial prescription database.}, journal = {PloS one}, volume = {13}, number = {12}, pages = {e0209580}, pmid = {30596704}, issn = {1932-6203}, mesh = {Anti-Bacterial Agents/*pharmacology/therapeutic use ; Cefoxitin/pharmacology/therapeutic use ; Databases, Factual ; *Drug Resistance, Bacterial ; *Drug Utilization ; *Escherichia coli/drug effects ; Escherichia coli Infections/drug therapy/*epidemiology/microbiology ; Fluoroquinolones/pharmacology/therapeutic use ; Humans ; Public Health Surveillance ; Republic of Korea/epidemiology ; }, abstract = {The purpose of this study is to determine the correlation between use of antimicrobials, such as fluoroquinolone, cefoxitin, and cefotaxime, and Escherichia coli resistance using a nationwide database. Nationwide data on antimicrobial consumption for 12 years (2002 to 2013) were acquired from a database of subjects (n = 1,025,340) included in the National Health Insurance Service-National Sample Cohort. National antimicrobial resistance rates of E. coli were obtained from the Korean Antimicrobial Resistance Monitoring System, which has been administered by the Korean Centers for Disease Control and Prevention since 2002. Fluoroquinolone-resistance rates of E. coli isolated from general hospitals have continuously increased since 2002 and were correlated with nationwide fluoroquinolone use (r = 0.82, P = 0.0012) or ciprofloxacin use (r = 0.90, P<0.0001). Cefotaxime-resistance rates of E. coli isolated from general hospitals markedly increased since 2008 and were correlated with nationwide cefotaxime use (r = 0.94, P<0.0001) or third-generation cephalosporin use (r = 0.96, P<0.0001). Cefoxitin-resistance rates of E. coli isolated from general hospitals peaked in 2010 and significantly correlated with cephamycin use at a two-year interval (r = 0.64, P = 0.0256). In conclusion, consumption of antimicrobials such as fluoroquinolone, cefoxitin, and cefotaxime is well correlated with the resistance rates of E. coli to these agents. This study provides background data for national antimicrobial management policies to reduce antimicrobial resistance.}, } @article {pmid30594777, year = {2019}, author = {Cao, M and Zhao, J and Hu, G}, title = {Genome-wide methods for investigating long noncoding RNAs.}, journal = {Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie}, volume = {111}, number = {}, pages = {395-401}, pmid = {30594777}, issn = {1950-6007}, support = {R01 DA043138/DA/NIDA NIH HHS/United States ; R01 MH112848/MH/NIMH NIH HHS/United States ; R21 DA042704/DA/NIDA NIH HHS/United States ; R21 DA046831/DA/NIDA NIH HHS/United States ; R01 DA033150/DA/NIDA NIH HHS/United States ; }, mesh = {Animals ; *Databases, Genetic ; Genome-Wide Association Study/*methods ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; RNA, Long Noncoding/*genetics ; }, abstract = {Long noncoding RNAs (lncRNAs) are large RNA transcripts that do not code for proteins but exert their effects in the form of RNA. To date many thousands of lncRNAs have been identified, their molecular functions and mechanisms of action however are largely unknown. The development of high-throughput experimental technologies, such as ChIRP (Chromatin isolation by RNA purification), CHART (Capture Hybridization Analysis of RNA Targets), RAP (RNA antisense purification), RIP (RNA Immunoprecipitation), CLIP (cross-linking and immunoprecipitation) and RNA pull-down, has led to a rapid expansion of lncRNA research and resulted in many publicly-available databases. This review provides an overview of the current methodologies available for discovering and investigating functions of lncRNAs in various human diseases. A comparison and application of these methods are also included. Finally, this paper surveys current databases containing annotations, interactome networks and functions of lncRNAs. The appropriate use of these methods and databases will provide not only high-resolution functional features of lncRNAs, but also enhance our understanding of the underlying mechanisms by which lncRNAs regulate a variety of biological processes.}, } @article {pmid30593598, year = {2018}, author = {Sadeghi, SH and Kazemi Kia, S and Erfanian, M and Movahed, SMS}, title = {Identifying representative watershed for the Urmia Lake Basin, Iran.}, journal = {Environmental monitoring and assessment}, volume = {191}, number = {1}, pages = {45}, pmid = {30593598}, issn = {1573-2959}, mesh = {*Ecosystem ; Environmental Monitoring/*methods ; Geographic Information Systems ; Hydrology ; Iran ; *Lakes ; }, abstract = {Designation of representative watersheds (RWs) as a reference area representing key behavior of the whole region is an essential tool to provide a time and cost-effective basis for monitoring watershed performance against different driving forces. It is more important in developing countries facing lack of necessary investments in one hand and ever-increasing human interventions and need to assess the outcome behavior of the system in another hand. However, this serious affair has been less considered worldwide, in general, and in developing countries, in particular. Therefore, in the present study, a quantitative-based method of Representative Watershed Index (RWI) with potential range from 0 to 100 has been formulated using four important criteria and available national-wide raster data of elevation (meter), slope (%), rainfall erosivity factor (t m ha[-1] cm h[-1]), and land use. The approach was then applied to the data prepared for the unique and invaluable global water ecosystem of the Urmia Lake Basin (ULB), north-western Iran, as a case study. The input raster was overlaid via matrices programming in the MATrix LABoratory (MATLAB) 2016 and Geographic Information System (GIS) 9.3 software environments. The RWIs were accordingly computed for 61 sub-watersheds of the ULB. The RWIs resulted from quadri-partite dimensional matrices that varied from 5.54 to 53.46 with respective maximum dissimilarity and resemblance with the entire 61 study sub-watersheds in the region. However, the sub-watershed with RWI of 40.65 (No. 57) was proposed as the final RW for the whole ULB due to hydrological independency, appropriate locality, and existence of functioning meteorological and hydrometric stations. The identified RW would be suggested to be considered as the basis for future insight monitoring and assessing environmental issues for the region eventually leading to an appropriate adaptive watershed management. Graphical abstract ᅟ.}, } @article {pmid30593356, year = {2019}, author = {Giannakopoulos, A and Vasileiou, NGC and Gougoulis, DA and Cripps, PJ and Ioannidi, KS and Chatzopoulos, DC and Billinis, C and Mavrogianni, VS and Petinaki, E and Fthenakis, GC}, title = {Use of geographical information system and ecological niche modelling for predicting potential space distribution of subclinical mastitis in ewes.}, journal = {Veterinary microbiology}, volume = {228}, number = {}, pages = {119-128}, doi = {10.1016/j.vetmic.2018.11.021}, pmid = {30593356}, issn = {1873-2542}, mesh = {Animals ; Ecosystem ; Farms ; Female ; Geographic Information Systems ; Greece/epidemiology ; Mastitis/epidemiology/microbiology/*veterinary ; Prevalence ; Sheep ; Sheep Diseases/*epidemiology/microbiology ; Staphylococcal Infections/epidemiology/microbiology/*veterinary ; Staphylococcus/*isolation & purification ; }, abstract = {Objective was to recognise areas potentially of high risk for increased frequency of subclinical mastitis in ewes. Milk samples were collected, for bacteriological and cytological examination, from 2198 clinically healthy ewes in 111 farms in all administrative regions of Greece. Data on farms were located in the field using hand-held Global Positioning System Garmin units. Collected data were analysed by an Ecological Niche Model under the framework of a geographic information system. Two separate analyses were performed: one for subclinical mastitis independently of causal agent (prevalence in population sampled: 0.260) and one for subclinical mastitis caused specifically by slime-producing staphylococci (prevalence in population sampled: 0.153). A model was constructed in which sheep farms were divided into two clusters, according to prevalence of subclinical mastitis: farms in the upper three quartiles of prevalence were used as occurrence points for the Ecological niche modelling procedure ('infected farms'); farms in the lower quartile of prevalence within each category were (pseudo)negative points. Significant differences in environmental parametres prevailing in locations of farms into the study, were identified for up to 13 parametres between locations of farms according to management system applied in farms. When farms in each management system were considered separately, differences became evident between farms in each management system, as well as between the two infections. The factor with the highest relative contribution in the analyses was the distance from other sheep farms; other factors also of importance in the predictive models were the altitude, the maximum temperature of warmest month and the total precipitation of driest month. Verification of the model revealed that ≥ 0.760 of infected farms' were located in areas predicted as high risk for prevalence of subclinical mastitis or slime staphylococcal subclinical mastitis. The paper describes for the first time potential association of mastitis with environmental factors and presents predictive models for mastitis in ewes taking into account environmental parametres.}, } @article {pmid30592378, year = {2019}, author = {Gong, L and Fan, G and Ren, Y and Chen, Y and Qiu, Q and Liu, L and Qin, Y and Liu, B and Jiang, L and Li, H and Zeng, Y and Gao, Q and Zhang, C and Wang, Z and Jiang, H and Tian, J and Zhang, H and Liu, X and Xu, X and Wang, W and Lü, Z and Li, Y}, title = {Chromosomal level reference genome of Tachypleus tridentatus provides insights into evolution and adaptation of horseshoe crabs.}, journal = {Molecular ecology resources}, volume = {19}, number = {3}, pages = {744-756}, doi = {10.1111/1755-0998.12988}, pmid = {30592378}, issn = {1755-0998}, support = {GREKF17-04//Chinese Academy of Sciences/ ; GREKF16-03//Chinese Academy of Sciences/ ; }, mesh = {Animals ; Aquatic Organisms/*classification/*genetics ; *Computational Biology ; *Evolution, Molecular ; *Genomics ; Horseshoe Crabs/*classification/*genetics ; }, abstract = {Horseshoe crabs including Tachypleus tridentatus are a group of marine arthropods and living fossil species which have existed on the earth for ~500 million years. However, the genetic mechanisms underlying their unique adaptive ability are still unclear. Here, we assembled the first chromosome-level T. tridentatus genome, and proved that this genome is of high quality with contig N50 1.69 Mb. By comparison with other arthropods, some gene families of T. tridentatus experienced significant expansion, which are related to several signaling pathways, endonuclease activities, and metabolic processes. Based on the results of comparative analysis of genomics and 27 transcriptomes from nine tissues, we found that the expanded Dscam genes are located at key hub positions of immune network. Furthermore, the Dscam genes showed higher levels of expression in the yellow connective tissue (the birthplace of blood cells with strong differentiation capability) than the other eight tissues. Besides, the Dscam genes are positively correlated with the expression of the core immunity gene, clotting factor B, which is involved in the coagulation cascade reaction. The effective and unusual immune ability endowed by the expansion and expression of Dscam genes in the horseshoe crab may be a factor that makes the species have a strong environmental adaptability within ~500 million years. The high quality chromosome level genome of a horseshoe crab and unique genomic features reported in this study provide important data resources for future studies on the evolution of marine ecological systems.}, } @article {pmid30589896, year = {2018}, author = {Shimamoto, CY and Padial, AA and da Rosa, CM and Marques, MCM}, title = {Restoration of ecosystem services in tropical forests: A global meta-analysis.}, journal = {PloS one}, volume = {13}, number = {12}, pages = {e0208523}, pmid = {30589896}, issn = {1932-6203}, mesh = {Carbon/chemistry ; Databases, Factual ; Ecology ; *Ecosystem ; *Environmental Restoration and Remediation ; *Forests ; Soil/chemistry ; Tropical Climate ; }, abstract = {To reverse the effects of deforestation, tropical areas have expanded restoration efforts in recent years. As ecological restoration positively affects the structure and function of degraded ecosystems, understanding to what extent restoration recovers ecosystem services (ES) is an important step in directing large-scale restoration actions. We evaluated the effect of restoration in increasing the provision of ES in tropical forests. We performed a global meta-analysis of ecological indicators of the ES provided in restored areas, degraded areas and reference ecosystems. We tested for the effects of different restoration strategies, different types of degradation and for the effects of restoration over time. Overall, restoration actions contributed to a significant increase in levels of ecological indicators of ES (carbon pool, soil attributes and biodiversity protection) compared to disturbed areas. Among the restoration strategies, the natural regeneration was the most effective. Biodiversity protection and carbon recovered better than soil attributes. All other restoration strategies recovered ES to a substantially lesser degree, and reforestation with exotics decreased the ES of areas degraded by agriculture. In areas degraded by pasture, restoration was more effective in recovering the biodiversity protection, whereas in areas degraded by agriculture, the restoration recovered mainly the carbon pool. Our results show that by choosing the correct strategy, restoration can recover much of the ES lost by the degradation of tropical forests. These results should be considered for large-scale conservation and management efforts for this biome.}, } @article {pmid30589858, year = {2018}, author = {Kosmala, M and Hufkens, K and Richardson, AD}, title = {Integrating camera imagery, crowdsourcing, and deep learning to improve high-frequency automated monitoring of snow at continental-to-global scales.}, journal = {PloS one}, volume = {13}, number = {12}, pages = {e0209649}, pmid = {30589858}, issn = {1932-6203}, mesh = {*Crowdsourcing ; *Deep Learning ; Humans ; Reproducibility of Results ; *Satellite Imagery ; Sensitivity and Specificity ; *Snow ; }, abstract = {Snow is important for local to global climate and surface hydrology, but spatial and temporal heterogeneity in the extent of snow cover make accurate, fine-scale mapping and monitoring of snow an enormous challenge. We took 184,453 daily near-surface images acquired by 133 automated cameras and processed them using crowdsourcing and deep learning to determine whether snow was present or absent in each image. We found that the crowdsourced data had an accuracy of 99.1% when compared with expert evaluation of the same imagery. We then used the image classification to train a deep convolutional neural network via transfer learning, with accuracies of 92% to 98%, depending on the image set and training method. The majority of neural network errors were due to snow that was present not being detected. We used the results of the neural networks to validate the presence or absence of snow inferred from the MODIS satellite sensor and obtained similar results to those from other validation studies. This method of using automated sensors, crowdsourcing, and deep learning in combination produced an accurate high temporal dataset of snow presence across a continent. It holds broad potential for real-time large-scale acquisition and processing of ecological and environmental data in support of monitoring, management, and research objectives.}, } @article {pmid30589836, year = {2018}, author = {B George, A and Korolev, KS}, title = {Chirality provides a direct fitness advantage and facilitates intermixing in cellular aggregates.}, journal = {PLoS computational biology}, volume = {14}, number = {12}, pages = {e1006645}, pmid = {30589836}, issn = {1553-7358}, mesh = {Cell Aggregation/*physiology ; Cell Movement/physiology ; Cell Polarity/physiology ; Cell Proliferation/physiology ; Cell Shape/physiology ; Computational Biology ; Computer Simulation ; Humans ; Microbiota/physiology ; *Models, Biological ; Neoplasm Invasiveness/pathology/physiopathology ; Neoplasms/pathology/physiopathology ; Stochastic Processes ; }, abstract = {Chirality in shape and motility can evolve rapidly in microbes and cancer cells. To determine how chirality affects cell fitness, we developed a model of chiral growth in compact aggregates such as microbial colonies and solid tumors. Our model recapitulates previous experimental findings and shows that mutant cells can invade by increasing their chirality or switching their handedness. The invasion results either in a takeover or stable coexistence between the mutant and the ancestor depending on their relative chirality. For large chiralities, the coexistence is accompanied by strong intermixing between the cells, while spatial segregation occurs otherwise. We show that the competition within the aggregate is mediated by bulges in regions where the cells with different chiralities meet. The two-way coupling between aggregate shape and natural selection is described by the chiral Kardar-Parisi-Zhang equation coupled to the Burgers' equation with multiplicative noise. We solve for the key features of this theory to explain the origin of selection on chirality. Overall, our work suggests that chirality could be an important ecological trait that mediates competition, invasion, and spatial structure in cellular populations.}, } @article {pmid30589201, year = {2019}, author = {D'Agostino, PM and Woodhouse, JN and Liew, HT and Sehnal, L and Pickford, R and Wong, HL and Burns, BP and Neilan, BA}, title = {Bioinformatic, phylogenetic and chemical analysis of the UV-absorbing compounds scytonemin and mycosporine-like amino acids from the microbial mat communities of Shark Bay, Australia.}, journal = {Environmental microbiology}, volume = {21}, number = {2}, pages = {702-715}, doi = {10.1111/1462-2920.14517}, pmid = {30589201}, issn = {1462-2920}, support = {//Australian Research Council/International ; }, mesh = {Amino Acids/*metabolism ; Australia ; Bays/*microbiology ; Computational Biology ; Cyanobacteria/classification/genetics/*isolation & purification/metabolism ; Glycine/metabolism ; Indoles/*metabolism ; Microbiota/radiation effects ; Phenols/*metabolism ; Photosynthesis ; *Phylogeny ; Tandem Mass Spectrometry ; Ultraviolet Rays ; }, abstract = {Shark Bay, Western Australia is a World Heritage area with extensive microbial mats and stromatolites. Microbial communities that comprise these mats have developed a range of mitigation strategies against changing levels of photosynthetically active and ultraviolet radiation, including the ability to biosynthesise the UV-absorbing natural products scytonemin and mycosporine-like amino acids (MAAs). To this end, the distribution of photoprotective pigments within Shark Bay microbial mats was delineated in the present study. This involved amplicon sequencing of bacterial 16S rDNA from communities at the surface and subsurface in three distinct mat types (smooth, pustular and tufted), and correlating this data with the chemical and molecular distribution of scytonemin and MAAs. Employing UV spectroscopy and MS/MS fragmentation, mycosporine-glycine, asterina and an unknown MAA were identified based on typical fragmentation patterns. Marker genes for scytonemin and MAA production (scyC and mysC) were amplified from microbial mat DNA and placed into phylogenetic context against a broad screen throughout 363 cyanobacterial genomes. Results indicate that occurrence of UV screening compounds is associated with the upper layer of Shark Bay microbial mats, and the occurrence of scytonemin is closely dependent on the abundance of cyanobacteria.}, } @article {pmid30587126, year = {2018}, author = {Bochkareva, OO and Moroz, EV and Davydov, II and Gelfand, MS}, title = {Genome rearrangements and selection in multi-chromosome bacteria Burkholderia spp.}, journal = {BMC genomics}, volume = {19}, number = {1}, pages = {965}, pmid = {30587126}, issn = {1471-2164}, support = {18-14-00358//Russian Science Foundation/ ; 16-54-21004//Russian Foundation of Basic Research/ ; IZLRZ3\163872//Swiss National Science Foundation/ ; }, mesh = {Burkholderia/classification/*genetics ; *Chromosomes, Bacterial ; Databases, Genetic ; Gene Rearrangement/*genetics ; Phylogeny ; }, abstract = {BACKGROUND: The genus Burkholderia consists of species that occupy remarkably diverse ecological niches. Its best known members are important pathogens, B. mallei and B. pseudomallei, which cause glanders and melioidosis, respectively. Burkholderia genomes are unusual due to their multichromosomal organization, generally comprised of 2-3 chromosomes.

RESULTS: We performed integrated genomic analysis of 127 Burkholderia strains. The pan-genome is open with the saturation to be reached between 86,000 and 88,000 genes. The reconstructed rearrangements indicate a strong avoidance of intra-replichore inversions that is likely caused by selection against the transfer of large groups of genes between the leading and the lagging strands. Translocated genes also tend to retain their position in the leading or the lagging strand, and this selection is stronger for large syntenies. Integrated reconstruction of chromosome rearrangements in the context of strains phylogeny reveals parallel rearrangements that may indicate inversion-based phase variation and integration of new genomic islands. In particular, we detected parallel inversions in the second chromosomes of B. pseudomallei with breakpoints formed by genes encoding membrane components of multidrug resistance complex, that may be linked to a phase variation mechanism. Two genomic islands, spreading horizontally between chromosomes, were detected in the B. cepacia group.

CONCLUSIONS: This study demonstrates the power of integrated analysis of pan-genomes, chromosome rearrangements, and selection regimes. Non-random inversion patterns indicate selective pressure, inversions are particularly frequent in a recent pathogen B. mallei, and, together with periods of positive selection at other branches, may indicate adaptation to new niches. One such adaptation could be a possible phase variation mechanism in B. pseudomallei.}, } @article {pmid30585386, year = {2019}, author = {Cholet, F and Ijaz, UZ and Smith, CJ}, title = {Differential ratio amplicons (Ramp) for the evaluation of RNA integrity extracted from complex environmental samples.}, journal = {Environmental microbiology}, volume = {21}, number = {2}, pages = {827-844}, pmid = {30585386}, issn = {1462-2920}, support = {//Univeristy of Glasgow, School of Engineering Doctoral Scholarship/International ; NE/L011956/1//NERC IRF/International ; RCSRF1718643//Royal Academy of Engineering under the Research Chairs and Senior Research Fellowships scheme/International ; }, mesh = {Bacteria/classification/*genetics/metabolism ; Computational Biology ; Environmental Microbiology ; Geologic Sediments/analysis/*microbiology ; Humans ; RNA Stability ; RNA, Bacterial/*genetics/metabolism ; RNA, Messenger/genetics/metabolism ; RNA, Ribosomal, 16S/genetics/metabolism ; }, abstract = {Reliability and reproducibility of transcriptomics-based studies are dependent on RNA integrity. In microbial ecology, microfluidics-based techniques, such as the Ribosomal Integrity Number (RIN), targeting rRNA are currently the only approaches to evaluate RNA integrity. However, the relationship between rRNA and mRNA integrity is unknown. Here, we present an integrity index, the Ratio Amplicon, Ramp , adapted from human clinical studies, to directly monitor mRNA integrity from complex environmental samples. We show, in a suite of experimental degradations of RNA extracted from sediment, that while the RIN generally reflected the degradation status of RNA the Ramp mapped mRNA degradation better. Furthermore, we examined the effect of degradation on transcript community structure by amplicon sequencing of 16S rRNA, amoA and glnA transcripts. We successfully sequenced transcripts for all three targets even from highly-degraded RNA samples. While RNA degradation changed the community structure of the mRNA profiles, no changes were observed for the 16S rRNA transcript profiles. Since both RT-Q-PCR and sequencing results were obtained, even from highly degraded samples, we strongly recommend evaluating RNA integrity prior to downstream processing to ensure meaningful results. For this, both the RIN and Ramp are useful, with the Ramp better evaluating mRNA integrity in this study.}, } @article {pmid30582844, year = {2018}, author = {Ivanova, OM and Kovgan, LM and Masiuk, SV}, title = {METHODOLOGY OF RECONSTRUCTION OF INDIVIDUALIZED EXPOSURE DOSES FOR PERSONS RESIDING AT RADIOACTIVELY CONTAMINATED TERRITORIES OF UKRAINE.}, journal = {Problemy radiatsiinoi medytsyny ta radiobiolohii}, volume = {23}, number = {}, pages = {164-187}, doi = {10.33145/2304-8336-2018-23-164-187}, pmid = {30582844}, issn = {2304-8336}, mesh = {Adolescent ; Adult ; Aged ; Animals ; Body Burden ; Cesium Radioisotopes/*analysis ; *Chernobyl Nuclear Accident ; Child ; Child, Preschool ; Databases, Factual ; Environmental Exposure/*analysis ; Female ; Food Contamination, Radioactive/*analysis ; Gamma Rays/adverse effects ; Humans ; Infant ; Longitudinal Studies ; Male ; Middle Aged ; *Models, Statistical ; Radiation Dosage ; Radiation Exposure/*analysis ; Radiation Monitoring/methods/*statistics & numerical data ; Risk Assessment ; Ukraine ; }, abstract = {OBJECTIVE: Development of methodology for reconstruction of individualized exposure doses for persons residing atradioactively contaminated after Chornobyl accident territories.Materials and methods of research. The methodology is based on the data of radio-ecological (ground, meal) anddosimetric (WBC measurements) monitoring held in Ukraine in 1986-2013, the results of which are saved in databases of Central Ecological and Dosimetric Register of Radiation Protection Laboratory of NRCRM. It is presentedfour levels of individualization of exposure doses. Each subsequent level of the model is based on the previous oneand takes into account additional parameters, and as a result a model of the next level comprises more number ofexposure situations and provides more accurate estimates. Using the methodology it is necessary to select a modelof such level that enables to solve in the best way the assignments posed before a researcher. For the population ofradioactively contaminated territories, two main ways of exposure are considered: (a) external gamma-exposurefrom radionuclides in the ground, and (b) internal exposure from consumption of radioactively contaminated meal.The dose is evaluated from all the main radionuclides of radioactive accident deposition, and in case of internalexposure after 1986 - only from radio-isotopes of cesium (134Cs and 137Cs).

RESULTS: Individualized doses are evaluated for different age groups of population residing in 10 raions of the mostcontaminated after Chornobyl accident Oblasts of Ukraine: Zhytomyr, Kyiv, Rivne and Chernihiv Oblasts. Dose esti-mates are presented weighted by the number of residents in settlements of specific raions. Among them are: thedose for 1986, doses accumulated during the first 15 years after the accident (1986-2000), and during the periodof 32 years after the accident (1986-2017).

CONCLUSIONS: Average raion dose reconstructed for adult residents of the most radioactively contaminatedNarodychy Raion of Zhytomyr Oblast in 1986 was 18 mSv, and accumulated during the whole period after the acci-dent was 51 mSv. The lowest doses among abovementioned 10 raions were obtained by persons residing at the ter-ritory of Kozelets and Ripky Raions of Chernihiv Oblast. Average dose for them in 1986 constituted 1.3 and 1.7 mSv,and the one accumulated during 32 years was 6.1 and 6.2, respectively.}, } @article {pmid30582232, year = {2019}, author = {de Macedo Bernardino, Í and da Nóbrega, LM and da Silva, JRC and de Alencar, CRB and de Olinda, RA and d'Ávila, S}, title = {Social determinants of health and maxillofacial injuries in children and adolescents victims of violence: A novel GIS-based modelling application.}, journal = {International journal of paediatric dentistry}, volume = {29}, number = {3}, pages = {375-383}, doi = {10.1111/ipd.12461}, pmid = {30582232}, issn = {1365-263X}, mesh = {Adolescent ; Brazil ; Child ; *Geographic Information Systems ; Humans ; *Maxillofacial Injuries ; Social Determinants of Health ; Violence ; }, abstract = {BACKGROUND: Physical violence against children and adolescents comprises a serious public health problem and often results in oral and maxillofacial traumas. Social determinants may favour the occurrence of these events, but few studies have critically evaluated the interaction between social and geographical risk factors.

AIMS: To investigate the spatiotemporal distribution of oral and maxillofacial traumas resulting from violence against children and adolescents through geostatistical techniques.

METHODS: This study was an ecological analysis of cases of trauma caused by violence against Brazilian children and adolescents using aggregated data from victims attended at a Center of Forensic Medicine and Forensic Dentistry between January 2012 and December 2015. Data were analysed through modelling based on geographic information system (GIS).

RESULTS: Two distinct patterns of longitudinal trajectory of oral and maxillofacial trauma related to violence against children and adolescents were identified (TP1 and TP2, P < 0.05). The spatial regression analysis revealed a statistically significant association between higher incidence of cases and areas with worse socioeconomic conditions (β = 0.047, SE = 0.020, P < 0.05).

CONCLUSION: Neighbourhoods with considerable socio-spatial vulnerability for violence against children and adolescents and maxillofacial traumas were identified.}, } @article {pmid30577099, year = {2019}, author = {Rova, S and Meire, P and Müller, F and Simeoni, M and Pranovi, F}, title = {A Petri net modeling approach to explore the temporal dynamics of the provision of multiple ecosystem services.}, journal = {The Science of the total environment}, volume = {655}, number = {}, pages = {1047-1061}, doi = {10.1016/j.scitotenv.2018.11.184}, pmid = {30577099}, issn = {1879-1026}, abstract = {The representation of the temporal dynamics of ecosystem services (ES) is a crucial research frontier in the field of ES modeling. In fact, most current ES models focus on static ES assessments, that need to be repeated with different inputs per time step to explore potential changes in ES. Here, we present a new approach for the dynamic modeling of multiple ES, based on the Petri Net modeling framework. The key features are: (i) multiple ES are modeled together as a single network, using a social-ecological systems (SES) perspective; (ii) the model accounts for the interactions occurring among ES, by distinguishing between the ES whose provision is mediated by some type of human input, which can produce some side-effects on the system, and those that are generated directly through ecosystem functions and do not generate side-effects; (iii) the model can reproduce the effects of changing drivers on the elements of the SES. These features allow to use the model to explore how ES can evolve over time under different "what-if" scenarios. The importance of considering the ES interactions is tested, showing that failing to include them in the model remarkably affects the results. Due to its complexity, the model should be used as an exploratory tool, focusing on the analysis of the general trends of multiple ES provision, rather than on the generation of quantitative projections. A first conceptual application to the Venice lagoon, Italy, is presented, in which the trends of 13 different ES are simulated. This application shows the potential of the model in exploring the development produced by climate change and socio-economic pressures, and the effects of a set of possible management actions. This modeling approach can contribute to generate new perspectives on the dynamic modeling of multiple ES and on the integrated management of SES.}, } @article {pmid30576494, year = {2018}, author = {Yi, F and Ling, J and Xiao, Y and Zhang, H and Ouyang, F and Wang, J}, title = {ConTEdb: a comprehensive database of transposable elements in conifers.}, journal = {Database : the journal of biological databases and curation}, volume = {2018}, number = {}, pages = {}, pmid = {30576494}, issn = {1758-0463}, mesh = {*Databases, Genetic ; Genes, Plant/*genetics ; Internet ; Software ; Tracheophyta/*genetics ; }, abstract = {Conifers are the largest and most ubiquitous group of gymnosperms and have significant ecological significance and economic importance. However, the huge and complex genomes have hindered the sequencing and mining of conifer genomes. In this study, we identified 413 423 transposable elements (TEs) from Picea abies, Picea glauca and Pinus taeda using a combination of multiple approaches and classified them into 11 133 families. A comprehensive web-based database, ConTEdb, was constructed and served for researchers. ConTEdb enables users to browse, retrieve and download the TE sequences from the database. Several analysis tools are integrated into ConTEdb to help users mine the TE data easily and effectively. In summary, ConTEdb provides a platform to study TE biology and functional genomics in conifers.}, } @article {pmid30574668, year = {2018}, author = {Halecki, W and Stachura, T and Fudała, W and Rusnak, M}, title = {Evaluating the applicability of MESS (matrix exponential spatial specification) model to assess water quality using GIS technique in agricultural mountain catchment (Western Carpathian).}, journal = {Environmental monitoring and assessment}, volume = {191}, number = {1}, pages = {26}, pmid = {30574668}, issn = {1573-2959}, mesh = {Agriculture ; Chemical Phenomena ; Environmental Monitoring/*methods ; *Geographic Information Systems ; Multivariate Analysis ; Nitrates/analysis ; Nitrogen/analysis ; Phosphorus/analysis ; Rivers/chemistry ; Seasons ; Soil/chemistry ; Water Pollutants, Chemical/*analysis ; Water Pollution/*analysis ; *Water Quality ; }, abstract = {The formation of many sources of pollution in a short period of time is due to mountain soil erosion by water. One of the major mechanisms decisive in the intensification of such erosion is the loosening of soil material on the slope. Water quality studies show the impact of diversified spatial management and allow making the right decisions in environmental management in mountain areas with high variability of use and land cover. The research undertaken as part of the paper was carried out in order to determine the dependency between total suspended solids (TSS) and the physicochemical parameters of surface waters and the amount of soil losses in the use structure within the mountain catchment. The paper focused on the frequency of phenomena in time and the possibility of stopping the surface runoff on the slope and on the soil's susceptibility to water erosion. The dependencies between multipoint sampling and the concentration of material washed off the slope due to precipitation were verified with a multivariate analysis. Sampling took place in hydrometric sections, and during small floods, in the waterbed cross section. Research shows that such sampling is the basis for the calculation of the transported load, reflecting the average variation in concentration. The variation in the volume of the load from the individual parts of the catchment was assessed by the spatial autoregressive model. It was found that the use of river basin areas affects water chemistry. Water reservoirs are an important ecological barrier for the migration of nitrate nitrogen (N-NO3) and phosphate phosphorus (P-PO4), which is marked by changes in the growing season. Water along the sections of the river near the quarry with a high degree of sodding showed good quality condition. Despite significant differences between measurement sampling sites, high total dissolved solid (TDS) values were found in communities adjacent to forests and meadows. However, the highest electrical conductivity (EC) and TSS concentrations were found in the interface with cultivated areas. Biogenic indices showed variation depending on the way the adjacent areas were used. GIS linked spatial variables with the formation of water pollution. The analysis of spatial autoregression pointed to the impact of arable land. Moreover, the analysis of spatial autoregression with the MESS function designated a connection between agricultural land use and nitrite nitrogen (N-NO2), EC, TSS, and dissolved oxygen (DO). Graphical abstract ᅟ.}, } @article {pmid30571696, year = {2018}, author = {Somveille, M and Firth, JA and Aplin, LM and Farine, DR and Sheldon, BC and Thompson, RN}, title = {Movement and conformity interact to establish local behavioural traditions in animal populations.}, journal = {PLoS computational biology}, volume = {14}, number = {12}, pages = {e1006647}, pmid = {30571696}, issn = {1553-7358}, support = {//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; *Behavior, Animal ; Computational Biology ; Ecosystem ; England ; Learning ; *Models, Biological ; Models, Psychological ; Passeriformes/physiology ; Population Dynamics ; *Social Behavior ; }, abstract = {The social transmission of information is critical to the emergence of animal culture. Two processes are predicted to play key roles in how socially-transmitted information spreads in animal populations: the movement of individuals across the landscape and conformist social learning. We develop a model that, for the first time, explicitly integrates these processes to investigate their impacts on the spread of behavioural preferences. Our results reveal a strong interplay between movement and conformity in determining whether locally-variable traditions establish across a landscape or whether a single preference dominates the whole population. The model is able to replicate a real-world cultural diffusion experiment in great tits Parus major, but also allows for a range of predictions for the emergence of animal culture under various initial conditions, habitat structure and strength of conformist bias to be made. Integrating social behaviour with ecological variation will be important for understanding the stability and diversity of culture in animals.}, } @article {pmid30568285, year = {2019}, author = {Strassburg, BBN and Beyer, HL and Crouzeilles, R and Iribarrem, A and Barros, F and de Siqueira, MF and Sánchez-Tapia, A and Balmford, A and Sansevero, JBB and Brancalion, PHS and Broadbent, EN and Chazdon, RL and Filho, AO and Gardner, TA and Gordon, A and Latawiec, A and Loyola, R and Metzger, JP and Mills, M and Possingham, HP and Rodrigues, RR and Scaramuzza, CAM and Scarano, FR and Tambosi, L and Uriarte, M}, title = {Strategic approaches to restoring ecosystems can triple conservation gains and halve costs.}, journal = {Nature ecology & evolution}, volume = {3}, number = {1}, pages = {62-70}, pmid = {30568285}, issn = {2397-334X}, mesh = {Brazil ; Carbon Sequestration ; Conservation of Natural Resources/*economics ; Cost-Benefit Analysis ; *Ecosystem ; }, abstract = {International commitments for ecosystem restoration add up to one-quarter of the world's arable land. Fulfilling them would ease global challenges such as climate change and biodiversity decline but could displace food production and impose financial costs on farmers. Here, we present a restoration prioritization approach capable of revealing these synergies and trade-offs, incorporating ecological and economic efficiencies of scale and modelling specific policy options. Using an actual large-scale restoration target of the Atlantic Forest hotspot, we show that our approach can deliver an eightfold increase in cost-effectiveness for biodiversity conservation compared with a baseline of non-systematic restoration. A compromise solution avoids 26% of the biome's current extinction debt of 2,864 plant and animal species (an increase of 257% compared with the baseline). Moreover, this solution sequesters 1 billion tonnes of CO2-equivalent (a 105% increase) while reducing costs by US$28 billion (a 57% decrease). Seizing similar opportunities elsewhere would offer substantial contributions to some of the greatest challenges for humankind.}, } @article {pmid30568252, year = {2018}, author = {Fourdrilis, S and de Frias Martins, AM and Backeljau, T}, title = {Relation between mitochondrial DNA hyperdiversity, mutation rate and mitochondrial genome evolution in Melarhaphe neritoides (Gastropoda: Littorinidae) and other Caenogastropoda.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {17964}, pmid = {30568252}, issn = {2045-2322}, mesh = {Animals ; Base Composition ; Chromosome Mapping ; Codon ; Computational Biology/methods ; *DNA, Mitochondrial ; *Evolution, Molecular ; Gastropoda/*classification/*genetics ; *Genome, Mitochondrial ; Genomics/methods ; Molecular Sequence Annotation ; *Mutation Rate ; Nucleic Acid Conformation ; Open Reading Frames ; RNA, Transfer/chemistry/genetics ; }, abstract = {Mitochondrial DNA hyperdiversity is primarily caused by high mutation rates (µ) and has potential implications for mitogenome architecture and evolution. In the hyperdiverse mtDNA of Melarhaphe neritoides (Gastropoda: Littorinidae), high mutational pressure generates unusually large amounts of synonymous variation, which is expected to (1) promote changes in synonymous codon usage, (2) reflect selection at synonymous sites, (3) increase mtDNA recombination and gene rearrangement, and (4) be correlated with high mtDNA substitution rates. The mitogenome of M. neritoides was sequenced, compared to closely related littorinids and put in the phylogenetic context of Caenogastropoda, to assess the influence of mtDNA hyperdiversity and high µ on gene content and gene order. Most mitogenome features are in line with the trend in Mollusca, except for the atypical secondary structure of the methionine transfer RNA lacking the TΨC-loop. Therefore, mtDNA hyperdiversity and high µ in M. neritoides do not seem to affect its mitogenome architecture. Synonymous sites are under positive selection, which adds to the growing evidence of non-neutral evolution at synonymous sites. Under such non-neutrality, substitution rate involves neutral and non-neutral substitutions, and high µ is not necessarily associated with high substitution rate, thus explaining that, unlike high µ, a high substitution rate is associated with gene order rearrangement.}, } @article {pmid30566939, year = {2019}, author = {Esser, D and Lange, J and Marinos, G and Sieber, M and Best, L and Prasse, D and Bathia, J and Rühlemann, MC and Boersch, K and Jaspers, C and Sommer, F}, title = {Functions of the Microbiota for the Physiology of Animal Metaorganisms.}, journal = {Journal of innate immunity}, volume = {11}, number = {5}, pages = {393-404}, pmid = {30566939}, issn = {1662-8128}, mesh = {Aging ; Animals ; Computational Biology ; Health Status ; Host Microbial Interactions/*physiology ; Humans ; Microbiota/*physiology ; Models, Biological ; Mucus/microbiology/virology ; Symbiosis/physiology ; }, abstract = {Animals are usually regarded as independent entities within their respective environments. However, within an organism, eukaryotes and prokaryotes interact dynamically to form the so-called metaorganism or holobiont, where each partner fulfils its versatile and crucial role. This review focuses on the interplay between microorganisms and multicellular eukaryotes in the context of host physiology, in particular aging and mucus-associated crosstalk. In addition to the interactions between bacteria and the host, we highlight the importance of viruses and nonmodel organisms. Moreover, we discuss current culturing and computational methodologies that allow a deeper understanding of underlying mechanisms controlling the physiology of metaorganisms.}, } @article {pmid30565882, year = {2019}, author = {Haller, BC and Galloway, J and Kelleher, J and Messer, PW and Ralph, PL}, title = {Tree-sequence recording in SLiM opens new horizons for forward-time simulation of whole genomes.}, journal = {Molecular ecology resources}, volume = {19}, number = {2}, pages = {552-566}, pmid = {30565882}, issn = {1755-0998}, support = {R01GM127418/NH/NIH HHS/United States ; 100956/Z/13/Z/WT_/Wellcome Trust/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; R01 GM127418/GM/NIGMS NIH HHS/United States ; R21 AI130635/AI/NIAID NIH HHS/United States ; R21AI130635/NH/NIH HHS/United States ; }, mesh = {*Biological Evolution ; Computational Biology ; Computer Simulation ; Genetics, Population/*methods ; Software ; }, abstract = {There is an increasing demand for evolutionary models to incorporate relatively realistic dynamics, ranging from selection at many genomic sites to complex demography, population structure, and ecological interactions. Such models can generally be implemented as individual-based forward simulations, but the large computational overhead of these models often makes simulation of whole chromosome sequences in large populations infeasible. This situation presents an important obstacle to the field that requires conceptual advances to overcome. The recently developed tree-sequence recording method (Kelleher, Thornton, Ashander, & Ralph, 2018), which stores the genealogical history of all genomes in the simulated population, could provide such an advance. This method has several benefits: (1) it allows neutral mutations to be omitted entirely from forward-time simulations and added later, thereby dramatically improving computational efficiency; (2) it allows neutral burn-in to be constructed extremely efficiently after the fact, using "recapitation"; (3) it allows direct examination and analysis of the genealogical trees along the genome; and (4) it provides a compact representation of a population's genealogy that can be analysed in Python using the msprime package. We have implemented the tree-sequence recording method in SLiM 3 (a free, open-source evolutionary simulation software package) and extended it to allow the recording of non-neutral mutations, greatly broadening the utility of this method. To demonstrate the versatility and performance of this approach, we showcase several practical applications that would have been beyond the reach of previously existing methods, opening up new horizons for the modelling and exploration of evolutionary processes.}, } @article {pmid30563290, year = {2018}, author = {Ribeiro, AI and Hoffimann, E}, title = {Development of a Neighbourhood Walkability Index for Porto Metropolitan Area. How Strongly Is Walkability Associated with Walking for Transport?.}, journal = {International journal of environmental research and public health}, volume = {15}, number = {12}, pages = {}, pmid = {30563290}, issn = {1660-4601}, mesh = {Adolescent ; Adult ; Cross-Sectional Studies ; *Environment Design ; Female ; Geographic Information Systems ; Health Promotion/*methods ; Humans ; Male ; Middle Aged ; Portugal ; Residence Characteristics/*statistics & numerical data ; Transportation/*methods ; Urban Population/*statistics & numerical data ; Walking/*psychology/*statistics & numerical data ; Young Adult ; }, abstract = {The creation of walkable communities constitutes a cost-effective health promotion strategy, as walking is an accessible and free intervention for increasing physical activity and health. In this cross-sectional ecological study, we developed a walkability index for the Porto Metropolitan Area and we validated it by assessing its association with walking for transportation. Neighborhood walkability was measured using a geographic information system and resulted from the weighted sum of residential density, street connectivity, and a destination-based entropy index. The index was categorized into quintiles of increasing walkability. Among the 1,112,555 individuals living in the study area, 28.1% resided in neighborhoods in the upper quintile of walkability and 15.8% resided in the least walkable neighborhoods. Adjusted regression models revealed that individuals residing in the most walkable neighborhoods are 81% more likely to report walking for transportation, compared with those from the least walkable neighborhoods (odds ratio: 1.81; 95% confidence intervals: 1.76[-]1.87). These results suggest that community design strategies to improve walkability may promote walking behavior.}, } @article {pmid30563097, year = {2018}, author = {Arbuckle, K}, title = {Phylogenetic Comparative Methods can Provide Important Insights into the Evolution of Toxic Weaponry.}, journal = {Toxins}, volume = {10}, number = {12}, pages = {}, pmid = {30563097}, issn = {2072-6651}, mesh = {Data Interpretation, Statistical ; Models, Biological ; *Phylogeny ; *Toxins, Biological ; }, abstract = {The literature on chemical weaponry of organisms is vast and provides a rich understanding of the composition and mechanisms of the toxins and other components involved. However, an ecological or evolutionary perspective has often been lacking and is largely limited to (1) molecular evolutionary studies of particular toxins (lacking an ecological view); (2) comparisons across different species that ignore phylogenetic relatedness (lacking an evolutionary view); or (3) descriptive studies of venom composition and toxicology that contain post hoc and untested ecological or evolutionary interpretations (a common event but essentially uninformative speculation). Conveniently, comparative biologists have prolifically been developing and using a wide range of phylogenetic comparative methods that allow us to explicitly address many ecological and evolutionary questions relating to venoms and poisons. Nevertheless, these analytical tools and approaches are rarely used and poorly known by biological toxinologists and toxicologists. In this review I aim to (1) introduce phylogenetic comparative methods to the latter audience; (2) highlight the range of questions that can be addressed using them; and (3) encourage biological toxinologists and toxicologists to either seek out adequate training in comparative biology or seek collaboration with comparative biologists to reap the fruits of a powerful interdisciplinary approach to the field.}, } @article {pmid30559362, year = {2018}, author = {Cheng, J and Demeulemeester, J and Wedge, DC and Vollan, HKM and Pitt, JJ and Russnes, HG and Pandey, BP and Nilsen, G and Nord, S and Bignell, GR and White, KP and Børresen-Dale, AL and Campbell, PJ and Kristensen, VN and Stratton, MR and Lingjærde, OC and Moreau, Y and Van Loo, P}, title = {Author Correction: Pan-cancer analysis of homozygous deletions in primary tumours uncovers rare tumour suppressors.}, journal = {Nature communications}, volume = {9}, number = {1}, pages = {5397}, doi = {10.1038/s41467-018-07842-2}, pmid = {30559362}, issn = {2041-1723}, abstract = {The original version of this Article contained an error in the author affiliations. The affiliation of Kevin P. White with Tempus Labs, Inc., Chicago, IL, USA was inadvertently omitted.This has now been corrected in both the PDF and HTML versions of the Article.}, } @article {pmid30557757, year = {2019}, author = {Zhao, D and Zhang, X and Li, X and Ru, S and Wang, Y and Yin, J and Liu, D}, title = {Oxidative damage induced by copper in testis of the red swamp crayfish Procambarus clarkii and its underlying mechanisms.}, journal = {Aquatic toxicology (Amsterdam, Netherlands)}, volume = {207}, number = {}, pages = {120-131}, doi = {10.1016/j.aquatox.2018.12.006}, pmid = {30557757}, issn = {1879-1514}, mesh = {Animals ; Astacoidea/genetics/*metabolism ; Copper/*toxicity ; DNA/metabolism ; Environmental Exposure ; Gene Expression Profiling ; Gene Ontology ; Glutathione/metabolism ; Male ; Malondialdehyde/metabolism ; Molecular Sequence Annotation ; Oxidation-Reduction ; *Oxidative Stress/drug effects ; Reactive Oxygen Species/metabolism ; Reproducibility of Results ; Spermatozoa/drug effects/metabolism ; Testis/drug effects/metabolism/*pathology ; Transcriptome/genetics ; Water Pollutants, Chemical/toxicity ; }, abstract = {Copper (Cu) is one of the most widespread environmental pollutants and is known to exert multiple toxic effects including reproductive toxicity. In this study, we investigated the toxic effect of Cu on reproduction of the red swamp crayfish (Procambarus clarkii), an economic crustacean species, by exposing adult male crayfish to 0.03 and 3.00 mg/L Cu[2+] for 7 days. The results showed that Cu[2+] exposure induced oxidative stress accompanied by elevated reactive oxygen species (ROS) and malondialdehyde (MDA) levels in testes, and resulted in decreased sperm quality and abnormal testicular structures with apoptotic germ cells and vacuolisation in Sertoli cells. To reveal the molecular mechanism of Cu[2+]-induced oxidative damage in crayfish testes, we sequenced, assembled and annotated the transcriptome for crayfish testes, using the Illumina sequencing approach. After the 3.00 mg/L Cu[2+] treatment, 6745 genes with differentially expressed profile were identified, of which many genes were involved in cellular response to ROS based on Gene Ontology enrichment analysis. Further, KEGG analysis demonstrated that genes with up-regulated expression levels significantly enriched in mitochondria oxidative phosphorylation pathway, suggesting disturbed mitochondrial electron transport chain was probably a main source of Cu[2+]-induced ROS production in testes. This study represented the first use of transcriptome to investigate the toxic effect of Cu[2+] on male crayfish reproduction, and the pathways identified underlying Cu[2+] toxicity at molecular level provide a novel insight into the reproductive toxicity of Cu in crustaceans.}, } @article {pmid30556814, year = {2019}, author = {Roux, S and Adriaenssens, EM and Dutilh, BE and Koonin, EV and Kropinski, AM and Krupovic, M and Kuhn, JH and Lavigne, R and Brister, JR and Varsani, A and Amid, C and Aziz, RK and Bordenstein, SR and Bork, P and Breitbart, M and Cochrane, GR and Daly, RA and Desnues, C and Duhaime, MB and Emerson, JB and Enault, F and Fuhrman, JA and Hingamp, P and Hugenholtz, P and Hurwitz, BL and Ivanova, NN and Labonté, JM and Lee, KB and Malmstrom, RR and Martinez-Garcia, M and Mizrachi, IK and Ogata, H and Páez-Espino, D and Petit, MA and Putonti, C and Rattei, T and Reyes, A and Rodriguez-Valera, F and Rosario, K and Schriml, L and Schulz, F and Steward, GF and Sullivan, MB and Sunagawa, S and Suttle, CA and Temperton, B and Tringe, SG and Thurber, RV and Webster, NS and Whiteson, KL and Wilhelm, SW and Wommack, KE and Woyke, T and Wrighton, KC and Yilmaz, P and Yoshida, T and Young, MJ and Yutin, N and Allen, LZ and Kyrpides, NC and Eloe-Fadrosh, EA}, title = {Minimum Information about an Uncultivated Virus Genome (MIUViG).}, journal = {Nature biotechnology}, volume = {37}, number = {1}, pages = {29-37}, pmid = {30556814}, issn = {1546-1696}, support = {R21 HD086833/HD/NICHD NIH HHS/United States ; HHSN272200700016I/AI/NIAID NIH HHS/United States ; P30 DK058404/DK/NIDDK NIH HHS/United States ; R01 AI132581/AI/NIAID NIH HHS/United States ; R01 GM117361/GM/NIGMS NIH HHS/United States ; }, mesh = {Databases, Genetic ; *Genome, Viral ; Genomics/*methods ; *Virus Cultivation ; Viruses/*genetics/*isolation & purification ; }, abstract = {We present an extension of the Minimum Information about any (x) Sequence (MIxS) standard for reporting sequences of uncultivated virus genomes. Minimum Information about an Uncultivated Virus Genome (MIUViG) standards were developed within the Genomic Standards Consortium framework and include virus origin, genome quality, genome annotation, taxonomic classification, biogeographic distribution and in silico host prediction. Community-wide adoption of MIUViG standards, which complement the Minimum Information about a Single Amplified Genome (MISAG) and Metagenome-Assembled Genome (MIMAG) standards for uncultivated bacteria and archaea, will improve the reporting of uncultivated virus genomes in public databases. In turn, this should enable more robust comparative studies and a systematic exploration of the global virosphere.}, } @article {pmid30550813, year = {2019}, author = {Shi, H and Liu, S and Chen, J and Li, X and Ma, Q and Yu, B}, title = {Predicting drug-target interactions using Lasso with random forest based on evolutionary information and chemical structure.}, journal = {Genomics}, volume = {111}, number = {6}, pages = {1839-1852}, doi = {10.1016/j.ygeno.2018.12.007}, pmid = {30550813}, issn = {1089-8646}, mesh = {*Databases, Protein ; Drug Development ; Ion Channels/*genetics ; *Machine Learning ; Position-Specific Scoring Matrices ; Protein Conformation ; Receptors, Cytoplasmic and Nuclear/*genetics ; Receptors, G-Protein-Coupled/*genetics ; *Software ; }, abstract = {The identification of drug-target interactions has great significance for pharmaceutical scientific research. Since traditional experimental methods identifying drug-target interactions is costly and time-consuming, the use of machine learning methods to predict potential drug-target interactions has attracted widespread attention. This paper presents a novel drug-target interactions prediction method called LRF-DTIs. Firstly, the pseudo-position specific scoring matrix (PsePSSM) and FP2 molecular fingerprinting were used to extract the features of drug-target. Secondly, using Lasso to reduce the dimension of the extracted feature information and then the Synthetic Minority Oversampling Technique (SMOTE) method was used to deal with unbalanced data. Finally, the processed feature vectors were input into a random forest (RF) classifier to predict drug-target interactions. Through 10 trials of 5-fold cross-validation, the overall prediction accuracies on the enzyme, ion channel (IC), G-protein-coupled receptor (GPCR) and nuclear receptor (NR) datasets reached 98.09%, 97.32%, 95.69%, and 94.88%, respectively, and compared with other prediction methods. In addition, we have tested and verified that our method not only could be applied to predict the new interactions but also could obtain a satisfactory result on the new dataset. All the experimental results indicate that our method can significantly improve the prediction accuracy of drug-target interactions and play a vital role in the new drug research and target protein development. The source code and all datasets are available at https://github.com/QUST-AIBBDRC/LRF-DTIs/ for academic use.}, } @article {pmid30549365, year = {2019}, author = {Richardson, RT and Curtis, HR and Matcham, EG and Lin, CH and Suresh, S and Sponsler, DB and Hearon, LE and Johnson, RM}, title = {Quantitative multi-locus metabarcoding and waggle dance interpretation reveal honey bee spring foraging patterns in Midwest agroecosystems.}, journal = {Molecular ecology}, volume = {28}, number = {3}, pages = {686-697}, doi = {10.1111/mec.14975}, pmid = {30549365}, issn = {1365-294X}, support = {//Project Apis m.-Costco Honey Bee Biology Fellowship/International ; //Pollinator Partnership Corn Dust Research Consortium grant/International ; OHO01277//state and federal funds appropriated to The Ohio State University, Ohio Agricultural Research and Development Center/International ; }, mesh = {Animals ; *Appetitive Behavior ; Bees/*physiology ; *Behavior, Animal ; DNA Barcoding, Taxonomic ; Databases, Nucleic Acid ; Ohio ; Pollen/*genetics ; Seasons ; }, abstract = {We explored the pollen foraging behaviour of honey bee colonies situated in the corn and soybean dominated agroecosystems of central Ohio over a month-long period using both pollen metabarcoding and waggle dance inference of spatial foraging patterns. For molecular pollen analysis, we developed simple and cost-effective laboratory and bioinformatics methods. Targeting four plant barcode loci (ITS2, rbcL, trnL and trnH), we implemented metabarcoding library preparation and dual-indexing protocols designed to minimize amplification biases and index mistagging events. We constructed comprehensive, curated reference databases for hierarchical taxonomic classification of metabarcoding data and used these databases to train the metaxa2 DNA sequence classifier. Comparisons between morphological and molecular palynology provide strong support for the quantitative potential of multi-locus metabarcoding. Results revealed consistent foraging habits between locations and show clear trends in the phenological progression of honey bee spring foraging in these agricultural areas. Our data suggest that three key taxa, woody Rosaceae such as pome fruits and hawthorns, Salix, and Trifolium provided the majority of pollen nutrition during the study. Spatially, these foraging patterns were associated with a significant preference for forests and tree lines relative to herbaceous land cover and nonflowering crop fields.}, } @article {pmid30548685, year = {2019}, author = {Whalen, A and Gorjanc, G and Hickey, JM}, title = {Parentage assignment with genotyping-by-sequencing data.}, journal = {Journal of animal breeding and genetics = Zeitschrift fur Tierzuchtung und Zuchtungsbiologie}, volume = {136}, number = {2}, pages = {102-112}, pmid = {30548685}, issn = {1439-0388}, support = {BB/J004235/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/L020467/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/L020726/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/M009254/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/N004728/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/N004736/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/N006178/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; MR/M000370/1//Medical Research Council/United Kingdom ; }, mesh = {Animals ; *Computational Biology ; Genotype ; *Genotyping Techniques ; Polymorphism, Single Nucleotide/*genetics ; Sequence Analysis, DNA ; }, abstract = {In this paper, we evaluate using genotype-by-sequencing (GBS) data to perform parentage assignment in lieu of traditional array data. The use of GBS data raises two issues: First, for low-coverage (e.g., <2×) GBS data, it may not be possible to call the genotype at many loci, a critical first step for detecting opposing homozygous markers. Second, the amount of sequencing coverage may vary across individuals, making it challenging to directly compare the likelihood scores between putative parents. To address these issues, we extend the probabilistic framework of Huisman (Molecular Ecology Resources, 2017, 17, 1009) and evaluate putative parents by comparing their (potentially noisy) genotypes to a series of proposal distributions. These distributions describe the expected genotype probabilities for the relatives of an individual. We assign putative parents as a parent if they are classified as a parent (as opposed to e.g., an unrelated individual), and if the assignment score passes a threshold. We evaluated this method on simulated data and found that (a) high-coverage (>2×) GBS data performs similarly to array data and requires only a small number of markers to correctly assign parents and (b) low-coverage GBS data (as low as 0.1×) can also be used, provided that it is obtained across a large number of markers. When analysing the low-coverage GBS data, we also found a high number of false positives if the true parent is not contained within the list of candidate parents, but that this false positive rate can be greatly reduced by hand tuning the assignment threshold. We provide this parentage assignment method as a standalone program called AlphaAssign.}, } @article {pmid30545097, year = {2018}, author = {Geuss, D and Lortzing, T and Schwachtje, J and Kopka, J and Steppuhn, A}, title = {Oviposition by Spodoptera exigua on Solanum dulcamara Alters the Plant's Response to Herbivory and Impairs Larval Performance.}, journal = {International journal of molecular sciences}, volume = {19}, number = {12}, pages = {}, pmid = {30545097}, issn = {1422-0067}, support = {SFB973 project B2//Deutsche Forschungsgemeinschaft/ ; }, mesh = {Animals ; Gene Expression Profiling ; Gene Expression Regulation, Plant/drug effects ; Gene Ontology ; Herbivory/drug effects/*physiology ; Larva/drug effects/physiology ; Oviposition/drug effects/*physiology ; Plant Growth Regulators/pharmacology ; Propanols/metabolism ; Protease Inhibitors/pharmacology ; Solanum/drug effects/genetics/*physiology ; Spodoptera/drug effects/*physiology ; Transcription, Genetic/drug effects ; }, abstract = {Plant resistance traits against insect herbivores are extremely plastic. Plants respond not only to the herbivory itself, but also to oviposition by herbivorous insects. How prior oviposition affects plant responses to larval herbivory is largely unknown. Combining bioassays and defense protein activity assays with microarray analyses and metabolite profiling, we investigated the impact of preceding oviposition on the interaction of Solanum dulcamara with the generalist lepidopteran herbivore Spodoptera exigua at the levels of the plant's resistance, transcriptome and metabolome. We found that oviposition increased plant resistance to the subsequent feeding larvae. While constitutive and feeding-induced levels of defensive protease inhibitor activity remained unaffected, pre-exposure to eggs altered S. dulcamara's transcriptional and metabolic response to larval feeding in leaves local and systemic to oviposition. In particular, genes involved in phenylpropanoid metabolism were more strongly expressed in previously oviposited plants, which was reflected by reciprocal changes of primary metabolites upstream and within these pathways. Our data highlight that plants integrate signals from non-threatening life stages of their natural enemies to optimize their response when they become actually attacked. The observed transcriptional and metabolic reshaping of S. dulcamara's response to S. exigua herbivory suggests a role of phenylpropanoids in oviposition-primed plant resistance.}, } @article {pmid30523083, year = {2018}, author = {Schmitz, OJ and Wilmers, CC and Leroux, SJ and Doughty, CE and Atwood, TB and Galetti, M and Davies, AB and Goetz, SJ}, title = {Animals and the zoogeochemistry of the carbon cycle.}, journal = {Science (New York, N.Y.)}, volume = {362}, number = {6419}, pages = {}, doi = {10.1126/science.aar3213}, pmid = {30523083}, issn = {1095-9203}, mesh = {*Animal Migration ; Animals ; Atmosphere/*chemistry ; *Carbon Cycle ; Ecosystem ; Soil/*chemistry ; }, abstract = {Predicting and managing the global carbon cycle requires scientific understanding of ecosystem processes that control carbon uptake and storage. It is generally assumed that carbon cycling is sufficiently characterized in terms of uptake and exchange between ecosystem plant and soil pools and the atmosphere. We show that animals also play an important role by mediating carbon exchange between ecosystems and the atmosphere, at times turning ecosystem carbon sources into sinks, or vice versa. Animals also move across landscapes, creating a dynamism that shapes landscape-scale variation in carbon exchange and storage. Predicting and measuring carbon cycling under such dynamism is an important scientific challenge. We explain how to link analyses of spatial ecosystem functioning, animal movement, and remote sensing of animal habitats with carbon dynamics across landscapes.}, } @article {pmid30540835, year = {2018}, author = {Hollingdale, E and Pérez-Barbería, FJ and Walker, DM}, title = {Inferring symmetric and asymmetric interactions between animals and groups from positional data.}, journal = {PloS one}, volume = {13}, number = {12}, pages = {e0208202}, pmid = {30540835}, issn = {1932-6203}, mesh = {Animals ; Animals, Wild/physiology ; Behavior, Animal/*physiology ; Datasets as Topic ; Deer/physiology ; Ecological Parameter Monitoring/*methods/standards ; Ecosystem ; Geographic Information Systems ; Locomotion/physiology ; *Models, Spatial Interaction ; Remote Sensing Technology/methods ; Sheep/physiology ; Spatial Behavior/*physiology ; }, abstract = {Interactions between domestic and wild species has become a global problem of growing interest. Global Position Systems (GPS) allow collection of vast records of time series of animal spatial movement, but there is need for developing analytical methods to efficiently use this information to unravel species interactions. This study assesses different methods to infer interactions and their symmetry between individual animals, social groups or species. We used two data sets, (i) a simulated one of the movement of two grazing species under different interaction scenarios by-species and by-individual, and (ii) a real time series of GPS data on the movements of sheep and deer grazing a large moorland plot. Different time series transformations were applied to capture the behaviour of the data (convex hull area, kth nearest neighbour distance, distance to centre of mass, Voronoi tessellation area, distance to past position) to assess their efficiency in inferring the interactions using different techniques (cross correlation, Granger causality, network properties). The results indicate that the methods are more efficient assessing by-group interaction than by-individual interaction, and different transformations produce different outputs of the nature of the interaction. Both species maintained a consistent by-species grouping structure. The results do not provide clear evidence of inter-species interaction based on the traditional framework of niche partitioning in the guild of large herbivores. In view of the transformation-dependent results, it seems that in our experimental framework both species co-exist showing complex interactions. We provide guidelines for the use of the different transformations with respect to study aims and data quality. The study attempts to provide behavioural ecologists with tools to infer animal interactions and their symmetry based on positional data recorded by visual observation, conventional telemetry or GPS technology.}, } @article {pmid30540766, year = {2018}, author = {Taff, CC and Freeman-Gallant, CR and Streby, HM and Kramer, GR}, title = {Geolocator deployment reduces return rate, alters selection, and impacts demography in a small songbird.}, journal = {PloS one}, volume = {13}, number = {12}, pages = {e0207783}, pmid = {30540766}, issn = {1932-6203}, mesh = {Animal Migration/physiology ; Animals ; Behavior, Animal/physiology ; Breeding ; Conservation of Natural Resources/methods ; Demography/*methods ; Ecology/instrumentation/methods ; Geographic Information Systems/*instrumentation/trends ; Reproduction ; Seasons ; Songbirds/physiology ; }, abstract = {In the past few years, miniature light-level geolocators have been developed for tracking wild bird species that were previously too small to track during their full annual cycle. Geolocators offer an exciting opportunity to study the full annual cycle for many species. However, the potential detrimental effects of carrying geolocators are still poorly understood, especially for small-bodied birds. Here, we deployed light-level geolocators on common yellowthroat warblers (Geothlypis trichas). Over two years, we monitored return rates and neighborhood demography for 40 warblers carrying a geolocator and 20 reference birds that did not carry a geolocator. We compared the two groups with long-term data from 108 unmanipulated birds breeding at the same location in previous and subsequent years. Overall, we found that individuals carrying a geolocator were less likely to return to the study site in the following year (21% to 33% returned, depending on inclusion criteria) than either contemporaneous controls (55%) or long-term controls (55%). Among birds marked with geolocators, we also detected viability selection for greater wing length, whereas this pattern was not present in control birds. Finally, in each year after geolocator deployment, inexperienced breeders colonized vacant territories and this demographic effect persisted for two years after deployment. Sexual selection and ornamentation are strongly age-dependent in this system, and behavioral data collected after geolocator deployment is likely to differ systematically from natural conditions. Clearly geolocators will continue to be useful tools, but we suggest that future studies should carefully consider the potential for biased returns and the ecological validity of behavioral data collected from geolocator marked populations.}, } @article {pmid30540352, year = {2019}, author = {Merikangas, KR and Swendsen, J and Hickie, IB and Cui, L and Shou, H and Merikangas, AK and Zhang, J and Lamers, F and Crainiceanu, C and Volkow, ND and Zipunnikov, V}, title = {Real-time Mobile Monitoring of the Dynamic Associations Among Motor Activity, Energy, Mood, and Sleep in Adults With Bipolar Disorder.}, journal = {JAMA psychiatry}, volume = {76}, number = {2}, pages = {190-198}, pmid = {30540352}, issn = {2168-6238}, support = {R01 HL123407/HL/NHLBI NIH HHS/United States ; R01 HL130483/HL/NHLBI NIH HHS/United States ; R01 NS060910/NS/NINDS NIH HHS/United States ; }, mesh = {Actigraphy ; Adult ; Affect/*physiology ; Bipolar Disorder/*physiopathology ; Case-Control Studies ; Computers, Handheld ; Ecological Momentary Assessment ; Female ; Humans ; Male ; Middle Aged ; *Monitoring, Ambulatory ; Motor Activity/*physiology ; Self Report ; Sleep/*physiology ; }, abstract = {IMPORTANCE: Biologic systems involved in the regulation of motor activity are intricately linked with other homeostatic systems such as sleep, feeding behavior, energy, and mood. Mobile monitoring technology (eg, actigraphy and ecological momentary assessment devices) allows the assessment of these multiple systems in real time. However, most clinical studies of mental disorders that use mobile devices have not focused on the dynamic associations between these systems.

OBJECTIVES: To examine the directional associations among motor activity, energy, mood, and sleep using mobile monitoring in a community-identified sample, and to evaluate whether these within-day associations differ between people with a history of bipolar or other mood disorders and controls without mood disorders.

This study used a nested case-control design of 242 adults, a subsample of a community-based sample of adults. Probands were recruited by mail from the greater Washington, DC, metropolitan area from January 2005 to June 2013. Enrichment of the sample for mood disorders was provided by volunteers or referrals from the National Institutes of Health Clinical Center or by participants in the National Institute of Mental Health Mood and Anxiety Disorders Program. The inclusion criteria were the ability to speak English, availability to participate, and consent to contact at least 2 living first-degree relatives. Data analysis was performed from June 2013 through July 2018.

MAIN OUTCOMES AND MEASURES: Motor activity and sleep duration data were obtained from minute-to-minute activity counts from an actigraphy device worn on the nondominant wrist for 2 weeks. Mood and energy levels were assessed by subjective analogue ratings on the ecological momentary assessment (using a personal digital assistant) by participants 4 times per day for 2 weeks.

RESULTS: Of the total 242 participants, 92 (38.1%) were men and 150 (61.9%) were women, with a mean (SD) age of 48 (16.9) years. Among the participants, 54 (22.3%) had bipolar disorder (25 with bipolar I; 29 with bipolar II), 91 (37.6%) had major depressive disorder, and 97 (40.1%) were controls with no history of mood disorders. A unidirectional association was found between motor activity and subjective mood level (β = -0.018, P = .04). Bidirectional associations were observed between motor activity (β = 0.176; P = .03) and subjective energy level (β = 0.027; P = .03) as well as between motor activity (β = -0.027; P = .04) and sleep duration (β = -0.154; P = .04). Greater cross-domain reactivity was observed in bipolar disorder across all outcomes, including motor activity, sleep, mood, and energy.

CONCLUSIONS AND RELEVANCE: These findings suggest that interventions focused on motor activity and energy may have greater efficacy than current approaches that target depressed mood; both active and passive tracking of multiple regulatory systems are important in designing therapeutic targets.}, } @article {pmid30537086, year = {2019}, author = {Bastounes, ER and Rando, HM and Johnson, JL and Trut, LN and Sacks, BN and Driscoll, CA and vonHoldt, B and Kukekova, AV}, title = {Four structural variants associated with human-directed sociability in dogs are not found in tame red foxes (Vulpes vulpes).}, journal = {Animal genetics}, volume = {50}, number = {1}, pages = {116-118}, pmid = {30537086}, issn = {1365-2052}, support = {R01 GM120782/GM/NIGMS NIH HHS/United States ; GM120782//National Institutes of Health/ ; 538922//USDA Federal Hatch Project/ ; 0324-2018-0016//Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences/ ; }, mesh = {Animals ; DNA Transposable Elements ; Dogs ; Foxes/*genetics ; Genotyping Techniques/veterinary ; Sequence Analysis, DNA/veterinary ; *Social Behavior ; }, } @article {pmid30535911, year = {2019}, author = {Azevedo, Á and Pereira, ML and Gouveia, S and Tavares, JN and Caldas, IM}, title = {Sex estimation using the mandibular canine index components.}, journal = {Forensic science, medicine, and pathology}, volume = {15}, number = {2}, pages = {191-197}, pmid = {30535911}, issn = {1556-2891}, mesh = {Adolescent ; Adult ; Cuspid/*anatomy & histology ; Female ; Forensic Dentistry ; Humans ; Male ; Mandible ; Models, Dental ; Multivariate Analysis ; ROC Curve ; *Sex Characteristics ; Young Adult ; }, abstract = {The mandibular canine index (MCI) has been described as a suitable methodology for sex estimation in forensic scenarios but there are contradictory reports about its accuracy. Moreover, the two mandibular canine teeth must be available, which is not always a viable option. The aim of this study was to strip the MCI by analyzing the MCI itself and its components, in order to optimize its use for sex estimation. The mesiodistal dimensions of the mandibular canine crown and the mandibular canine arch width were measured in a sample of 120 cast models. Five predictor variables were considered in this study: the standard MCI, a variation of the MCI using the left canine, and MCI components (MD43, MD33 and D33-43). Multivariate binary logistic regression was performed using stepwise forward approach to select the most statistical relevant variables on the probability of a cast being from a female. The estimated probability was then analyzed with respect to performance in sex classification (ROC analysis and optimal cut-offs accuracy) and compared with the performance of the univariate variables. MCI43 and MCI33 presented the lowest performance (64.2% and 63.3% respectively), and the highest overall accuracy was attained using the MD43 and MD33 (85.8% in both cases). The multivariate logistic model obtained (using MD43 and MD33) exhibited the same accuracy as the logistic model based solely on MD43 (85.8%). Our results suggest that MD43 should be used instead of MCI for sex estimation.}, } @article {pmid30535819, year = {2019}, author = {Chen, J and Mortola, E and Du, X and Zhao, S and Liu, X}, title = {Excess of retrogene traffic in pig X chromosome.}, journal = {Genetica}, volume = {147}, number = {1}, pages = {23-32}, pmid = {30535819}, issn = {1573-6857}, support = {31572375//National Natural Science Foundation of China (CN)/ ; 31361140365//National Natural Science Foundation of China/ ; 2662016PY006//unversity/ ; }, mesh = {Animals ; Evolution, Molecular ; Female ; Male ; Multigene Family ; *Retroelements ; Selection, Genetic ; Swine/*genetics ; X Chromosome/*genetics ; }, abstract = {Despite the insights into retrogene evolution in multiple species provided by trans-traffic retrogenes (trans-retrogenes), cis-traffic retrogenes (cis-retrogenes) are hitherto understudied and thus limit our understanding of genetic novelty. Here we used the pig genome as a model to compare cis- and trans-retrogenes. We found that cis- and trans-retrogenes have similar patterns in terms of excessive X-chromosome representation, testis expression preference, and metabolic functional enrichment. Despite these similarities, lower levels of selective pressure were found in cis- than in trans-retrogenes. The evolutionary dating evidence revealed that more cis-retrogenes have originated after pig-cattle divergence than trans-retrogenes, suggesting a more recent origination of cis-retrogenes. The gene family clustering confirmed that excesses of X-derived cis-retrogenes may be driven by their rapid expansion in the recent times. Thus, the different selective constraints between cis- and trans-retrogenes may be due to different evolutionary time-scales rather than any differential functional importance. Thus, this study highlights the ongoing functional contributions from cis- and trans-traffic retrogenes during the reshaping of pig genome.}, } @article {pmid30535251, year = {2018}, author = {Mak, SST and Gopalakrishnan, S and Carøe, C and Geng, C and Liu, S and Sinding, MS and Kuderna, LFK and Zhang, W and Fu, S and Vieira, FG and Germonpré, M and Bocherens, H and Fedorov, S and Petersen, B and Sicheritz-Pontén, T and Marques-Bonet, T and Zhang, G and Jiang, H and Gilbert, MTP}, title = {Erratum to: Comparative performance of the BGISEQ-500 vs Illumina HiSeq2500 sequencing platforms for palaeogenomic sequencing.}, journal = {GigaScience}, volume = {7}, number = {12}, pages = {}, pmid = {30535251}, issn = {2047-217X}, } @article {pmid30533308, year = {2018}, author = {Jenkins, MF and White, EP and Hurlbert, AH}, title = {The proportion of core species in a community varies with spatial scale and environmental heterogeneity.}, journal = {PeerJ}, volume = {6}, number = {}, pages = {e6019}, pmid = {30533308}, issn = {2167-8359}, abstract = {Ecological communities are composed of a combination of core species that maintain local viable populations and transient species that occur infrequently due to dispersal from surrounding regions. Preliminary work indicates that while core and transient species are both commonly observed in community surveys of a wide range of taxonomic groups, their relative prevalence varies substantially from one community to another depending upon the spatial scale at which the community was characterized and its environmental context. We used a geographically extensive dataset of 968 bird community time series to quantitatively describe how the proportion of core species in a community varies with spatial scale and environmental heterogeneity. We found that the proportion of core species in an assemblage increased with spatial scale in a positive decelerating fashion with a concomitant decrease in the proportion of transient species. Variation in the shape of this scaling relationship between sites was related to regional environmental heterogeneity, with lower proportions of core species at a given scale associated with high environmental heterogeneity. Understanding this influence of scale and environmental heterogeneity on the proportion of core species may help resolve discrepancies between studies of biotic interactions, resource availability, and mass effects conducted at different scales, because the importance of these and other ecological processes are expected to differ substantially between core and transient species.}, } @article {pmid30531940, year = {2019}, author = {Cho, J and Benoit, M and Catoni, M and Drost, HG and Brestovitsky, A and Oosterbeek, M and Paszkowski, J}, title = {Sensitive detection of pre-integration intermediates of long terminal repeat retrotransposons in crop plants.}, journal = {Nature plants}, volume = {5}, number = {1}, pages = {26-33}, pmid = {30531940}, issn = {2055-0278}, mesh = {Arabidopsis/genetics ; Computational Biology/methods ; Crops, Agricultural/*genetics ; Gene Expression Regulation, Plant ; Heat-Shock Response/genetics ; Solanum lycopersicum/genetics ; Oryza/genetics ; Retroelements/*genetics ; Sequence Analysis, DNA/*methods ; *Terminal Repeat Sequences ; }, abstract = {Retrotransposons have played an important role in the evolution of host genomes[1,2]. Their impact is mainly deduced from the composition of DNA sequences that have been fixed over evolutionary time[2]. Such studies provide important 'snapshots' reflecting the historical activities of transposons but do not predict current transposition potential. We previously reported sequence-independent retrotransposon trapping (SIRT) as a method that, by identification of extrachromosomal linear DNA (eclDNA), revealed the presence of active long terminal repeat (LTR) retrotransposons in Arabidopsis[3]. However, SIRT cannot be applied to large and transposon-rich genomes, as found in crop plants. We have developed an alternative approach named ALE-seq (amplification of LTR of eclDNAs followed by sequencing) for such situations. ALE-seq reveals sequences of 5' LTRs of eclDNAs after two-step amplification: in vitro transcription and subsequent reverse transcription. Using ALE-seq in rice, we detected eclDNAs for a novel Copia family LTR retrotransposon, Go-on, which is activated by heat stress. Sequencing of rice accessions revealed that Go-on has preferentially accumulated in Oryza sativa ssp. indica rice grown at higher temperatures. Furthermore, ALE-seq applied to tomato fruits identified a developmentally regulated Gypsy family of retrotransposons. A bioinformatic pipeline adapted for ALE-seq data analyses is used for the direct and reference-free annotation of new, active retroelements. This pipeline allows assessment of LTR retrotransposon activities in organisms for which genomic sequences and/or reference genomes are either unavailable or of low quality.}, } @article {pmid30530665, year = {2018}, author = {Lin, M and Siford, RL and Martin, AR and Nakagome, S and Möller, M and Hoal, EG and Bustamante, CD and Gignoux, CR and Henn, BM}, title = {Rapid evolution of a skin-lightening allele in southern African KhoeSan.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {115}, number = {52}, pages = {13324-13329}, pmid = {30530665}, issn = {1091-6490}, support = {R01 GM118652/GM/NIGMS NIH HHS/United States ; T32 GM007790/GM/NIGMS NIH HHS/United States ; }, mesh = {Adult ; Africa, Southern ; Alleles ; Antiporters/*genetics/metabolism ; Asian People/genetics ; Black People/genetics ; Demography/methods ; Evolution, Molecular ; Female ; Gene Flow ; Genetic Variation/genetics ; Genetics, Population/methods ; Genotype ; Haplotypes ; Humans ; Male ; Phenotype ; Phylogeny ; Polymorphism, Single Nucleotide/genetics ; Skin Pigmentation/*genetics ; White People/genetics ; }, abstract = {Skin pigmentation is under strong directional selection in northern European and Asian populations. The indigenous KhoeSan populations of far southern Africa have lighter skin than other sub-Saharan African populations, potentially reflecting local adaptation to a region of Africa with reduced UV radiation. Here, we demonstrate that a canonical Eurasian skin pigmentation gene, SLC24A5, was introduced to southern Africa via recent migration and experienced strong adaptive evolution in the KhoeSan. To reconstruct the evolution of skin pigmentation, we collected phenotypes from over 400 ≠Khomani San and Nama individuals and high-throughput sequenced candidate pigmentation genes. The derived causal allele in SLC24A5, p.Ala111Thr, significantly lightens basal skin pigmentation in the KhoeSan and explains 8 to 15% of phenotypic variance in these populations. The frequency of this allele (33 to 53%) is far greater than expected from colonial period European gene flow; however, the most common derived haplotype is identical among European, eastern African, and KhoeSan individuals. Using four-population demographic simulations with selection, we show that the allele was introduced into the KhoeSan only 2,000 y ago via a back-to-Africa migration and then experienced a selective sweep (s = 0.04 to 0.05 in ≠Khomani and Nama). The SLC24A5 locus is both a rare example of intense, ongoing adaptation in very recent human history, as well as an adaptive gene flow at a pigmentation locus in humans.}, } @article {pmid30521641, year = {2018}, author = {Tian, H and Feng, Y and Vrancken, B and Cazelles, B and Tan, H and Gill, MS and Yang, Q and Li, Y and Yang, W and Zhang, Y and Zhang, Y and Lemey, P and Pybus, OG and Stenseth, NC and Zhang, H and Dellicour, S}, title = {Transmission dynamics of re-emerging rabies in domestic dogs of rural China.}, journal = {PLoS pathogens}, volume = {14}, number = {12}, pages = {e1007392}, pmid = {30521641}, issn = {1553-7374}, mesh = {Animals ; China/epidemiology ; Dog Diseases/*epidemiology/*transmission/virology ; Dogs ; Pets ; Phylogeny ; Phylogeography ; Rabies/*epidemiology/*transmission ; Rabies virus/genetics ; Rural Population ; Zoonoses/*epidemiology/*transmission ; }, abstract = {Despite ongoing efforts to control transmission, rabies prevention remains a challenge in many developing countries, especially in rural areas of China where re-emerging rabies is under-reported due to a lack of sustained animal surveillance. By taking advantage of detailed genomic and epidemiological data for the re-emerging rabies outbreak in Yunnan Province, China, collected between 1999 and 2015, we reconstruct the demographic and dispersal history of domestic dog rabies virus (RABV) as well as the dynamics of dog-to-dog and dog-to-human transmission. Phylogeographic analyses reveal a lower diffusion coefficient than previously estimated for dog RABV dissemination in northern Africa. Furthermore, epidemiological analyses reveal transmission rates between dogs, as well as between dogs and humans, lower than estimates for Africa. Finally, we show that reconstructed epidemic history of RABV among dogs and the dynamics of rabid dogs are consistent with the recorded human rabies cases. This work illustrates the benefits of combining phylogeographic and epidemic modelling approaches for uncovering the spatiotemporal dynamics of zoonotic diseases, with both approaches providing estimates of key epidemiological parameters.}, } @article {pmid30518164, year = {2018}, author = {Mennis, J and Mason, M and Coffman, DL and Henry, K}, title = {Geographic Imputation of Missing Activity Space Data from Ecological Momentary Assessment (EMA) GPS Positions.}, journal = {International journal of environmental research and public health}, volume = {15}, number = {12}, pages = {}, pmid = {30518164}, issn = {1660-4601}, support = {R01 DA031724/DA/NIDA NIH HHS/United States ; R01 CA229542/CA/NCI NIH HHS/United States ; }, mesh = {Adolescent ; *Data Interpretation, Statistical ; *Ecological Momentary Assessment ; Female ; *Geographic Information Systems ; Humans ; Longitudinal Studies ; Male ; Pilot Projects ; Residence Characteristics ; Spatial Analysis ; Stress, Psychological/diagnosis/*epidemiology ; United States/epidemiology ; Urban Health/*statistics & numerical data ; }, abstract = {This research presents a pilot study to develop and compare methods of geographic imputation for estimating the location of missing activity space data collected using geographic ecological momentary assessment (GEMA). As a demonstration, we use data from a previously published analysis of the effect of neighborhood disadvantage, captured at the U.S. Census Bureau tract level, on momentary psychological stress among a sample of 137 urban adolescents. We investigate the impact of listwise deletion on model results and test two geographic imputation techniques adapted for activity space data from hot deck and centroid imputation approaches. Our results indicate that listwise deletion can bias estimates of place effects on health, and that these impacts are mitigated by the use of geographic imputation, particularly regarding inflation of the standard errors. These geographic imputation techniques may be extended in future research by incorporating approaches from the non-spatial imputation literature as well as from conventional geographic imputation and spatial interpolation research that focus on non-activity space data.}, } @article {pmid30506631, year = {2019}, author = {Lambert, SM and Streicher, JW and Fisher-Reid, MC and Méndez de la Cruz, FR and Martínez-Méndez, N and García-Vázquez, UO and Nieto Montes de Oca, A and Wiens, JJ}, title = {Inferring introgression using RADseq and DFOIL : Power and pitfalls revealed in a case study of spiny lizards (Sceloporus).}, journal = {Molecular ecology resources}, volume = {19}, number = {4}, pages = {818-837}, doi = {10.1111/1755-0998.12972}, pmid = {30506631}, issn = {1755-0998}, support = {2012117663//National Science Foundation/ ; 1655690//National Science Foundation/ ; //Society for the Study of Evolution/ ; //Society of Systematic Biologists/ ; }, mesh = {Animals ; Biostatistics/methods ; Computational Biology/*methods ; DNA, Mitochondrial/genetics ; *Evolution, Molecular ; *Gene Flow ; Lizards/*genetics ; Mexico ; Sequence Analysis, DNA/*methods ; }, abstract = {Introgression is now commonly reported in studies across the Tree of Life, aided by recent advancements in data collection and analysis. Nevertheless, researchers working with nonmodel species lacking reference genomes may be stymied by a mismatch between available resources and methodological demands. In this study, we demonstrate a fast and simple approach for inferring introgression using RADseq data, and apply it to a case study involving spiny lizards (Sceloporus) from northeastern México. First, we find evidence for recurrent mtDNA introgression between the two focal species based on patterns of mito-nuclear discordance. We then test for nuclear introgression by exhaustively applying the "five-taxon" D-statistic (DFOIL) to all relevant individuals sampled for RADseq data. In our case, this exhaustive approach (dubbed "ExDFOIL ") entails testing up to ~250,000 unique four-taxon combinations of individuals across species. To facilitate use of this ExDFOIL approach, we provide scripts for many relevant tasks, including the selection of appropriate four-taxon combinations, execution of DFOIL tests in parallel and visualization of introgression results in phylogenetic and geographic space. Using ExDFOIL , we find evidence for ancient introgression between the focal species. Furthermore, we reveal geographic variation in patterns of introgression that is consistent with patterns of mito-nuclear discordance and with recurrent introgression. Overall, our study demonstrates that the combination of DFOIL and RADseq data can effectively detect introgression under a variety of sampling conditions (for individuals, populations and loci). Importantly, we also find evidence that batch-specific error and linkage in RADseq data may mislead inferences of introgression under certain conditions.}, } @article {pmid30503825, year = {2019}, author = {Wang, Z and Wang, M and Wang, T and Zhang, Y and Zhang, X}, title = {Genome-wide probing RNA structure with the modified DMS-MaPseq in Arabidopsis.}, journal = {Methods (San Diego, Calif.)}, volume = {155}, number = {}, pages = {30-40}, doi = {10.1016/j.ymeth.2018.11.018}, pmid = {30503825}, issn = {1095-9130}, mesh = {Arabidopsis/*genetics/metabolism ; Arabidopsis Proteins/genetics/metabolism ; Base Pairing ; Base Sequence ; Computational Biology/*methods ; *Genome, Plant ; High-Throughput Nucleotide Sequencing/*methods ; Light-Harvesting Protein Complexes/genetics/metabolism ; Mutation ; Nucleic Acid Conformation ; Photosystem II Protein Complex/genetics/metabolism ; RNA, Messenger/*chemistry/genetics/metabolism ; RNA, Plant/*chemistry/genetics/metabolism ; Sulfuric Acid Esters/chemistry ; }, abstract = {Transcripts have intrinsic propensity to form stable secondary structure that is fundamental to regulate RNA transcription, splicing, translation, RNA localization and turnover. Numerous methods that integrate chemical reactions with next-generation sequencing (NGS) have been applied to study in vivo RNA structure, providing new insights into RNA biology. Dimethyl sulfate (DMS) probing coupled with mutational profiling through NGS (DMS-MaPseq) is a newly developed method for revealing genome-wide or target-specific RNA structure. Herein, we present our experimental protocol of a modified DMS-MaPseq method for plant materials. The DMS treatment condition was optimized, and library preparation procedures were simplified. We also provided custom scripts for bioinformatic analysis of genome-wide DMS-MaPseq data. Bioinformatic results showed that our method could generate high-quality and reproducible data. Further, we assessed sequencing depth and coverage for genome-wide RNA structure profiling in Arabidopsis, and provided two examples of in vivo structure of mobile RNAs. We hope that our modified DMS-MaPseq method will serve as a powerful tool for analyzing in vivo RNA structurome in plants.}, } @article {pmid30503684, year = {2019}, author = {Xavier, J and Guedjou, H and Anzalone, SM and Boucenna, S and Guigon, E and Chetouani, M and Cohen, D}, title = {Toward a motor signature in autism: Studies from human-machine interaction.}, journal = {L'Encephale}, volume = {45}, number = {2}, pages = {182-187}, doi = {10.1016/j.encep.2018.08.002}, pmid = {30503684}, issn = {0013-7006}, mesh = {Autism Spectrum Disorder/classification/*diagnosis/physiopathology ; Child ; *Computer Simulation ; Diagnosis, Computer-Assisted/methods/trends ; Diagnostic Techniques, Neurological/*trends ; Female ; Humans ; Machine Learning ; Male ; Motor Activity/*physiology ; Motor Skills Disorders/*diagnosis/psychology ; Posture/*physiology ; *Robotics/methods/trends ; }, abstract = {BACKGROUND: Autism spectrum disorder (ASD) is a heterogeneous group of neurodevelopmental disorders which core symptoms are impairments in socio-communication and repetitive symptoms and stereotypies. Although not cardinal symptoms per se, motor impairments are fundamental aspects of ASD. These impairments are associated with postural and motor control disabilities that we investigated using computational modeling and developmental robotics through human-machine interaction paradigms.

METHOD: First, in a set of studies involving a human-robot posture imitation, we explored the impact of 3 different groups of partners (including a group of children with ASD) on robot learning by imitation. Second, using an ecological task, i.e. a real-time motor imitation with a tightrope walker (TW) avatar, we investigated interpersonal synchronization, motor coordination and motor control during the task in children with ASD (n=29), TD children (n=39) and children with developmental coordination disorder (n=17, DCD).

RESULTS: From the human-robot experiments, we evidenced that motor signature at both groups' and individuals' levels had a key influence on imitation learning, posture recognition and identity recognition. From the more dynamic motor imitation paradigm with a TW avatar, we found that interpersonal synchronization, motor coordination and motor control were more impaired in children with ASD compared to both TD children and children with DCD. Taken together these results confirm the motor peculiarities of children with ASD despite imitation tasks were adequately performed.

DISCUSSION: Studies from human-machine interaction support the idea of a behavioral signature in children with ASD. However, several issues need to be addressed. Is this behavioral signature motoric in essence? Is it possible to ascertain that these peculiarities occur during all motor tasks (e.g. posture, voluntary movement)? Could this motor signature be considered as specific to autism, notably in comparison to DCD that also display poor motor coordination skills? We suggest that more work comparing the two conditions should be implemented, including analysis of kinematics and movement smoothness with sufficient measurement quality to allow spectral analysis.}, } @article {pmid30503563, year = {2019}, author = {Starodubtseva, MN and Mitsura, EF and Starodubtsev, IE and Chelnokova, IA and Yegorenkov, NI and Volkova, LI and Kharin, YS}, title = {Nano- and microscale mechanical properties of erythrocytes in hereditary spherocytosis.}, journal = {Journal of biomechanics}, volume = {83}, number = {}, pages = {1-8}, doi = {10.1016/j.jbiomech.2018.11.017}, pmid = {30503563}, issn = {1873-2380}, mesh = {Biomechanical Phenomena ; Child ; Elastic Modulus ; Erythrocytes/*pathology ; Female ; Friction ; Humans ; Male ; *Mechanical Phenomena ; *Microtechnology ; *Nanotechnology ; Spherocytosis, Hereditary/*blood ; }, abstract = {Hereditary spherocytosis (HS), an erythrocyte membranopathy, is a heterogeneous disease, even at the level of the erythrocyte population. The paper aims at studying the mechanical properties (the Young's modulus, median and RMS roughness of friction force maps; fractal dimension, lacunarity and spatial distribution parameters of lateral force maps) of the cell surface layer of the erythrocytes of two different morphologies (discocytes and spherocytes) in HS using atomic force microscopy. The results of spatial-spectral and fractal analysis showed that the mechanical property maps of the HS spherocyte surface were more structurally homogeneous compared to the maps of HS discocytes. HS spherocytes also had a reduced RMS roughness and lacunarity of the mechanical property maps. The Young's modulus and averaged friction forces over the microscale HS spherocyte surface regions were approximately 20% higher than that of HS discocytes. The revealed significant difference at the nano- and microscales in the structural and mechanical properties of main (discoidal and spheroidal) morphological types of HS erythrocytes can potentially cause blood flow disturbance in the vascular system in HS.}, } @article {pmid30503468, year = {2018}, author = {Radomyski, A and Lei, K and Giubilato, E and Critto, A and Lin, C and Marcomini, A}, title = {Bioaccumulation of trace metals in aquatic food web. A case study, Liaodong Bay, NE China.}, journal = {Marine pollution bulletin}, volume = {137}, number = {}, pages = {555-565}, doi = {10.1016/j.marpolbul.2018.11.002}, pmid = {30503468}, issn = {1879-3363}, mesh = {Animals ; Bays ; Body Weight ; China ; Estuaries ; *Fishes ; *Food Chain ; Geologic Sediments/analysis ; Intestines/chemistry ; Invertebrates/*chemistry ; Liver/chemistry ; Metals/analysis/*pharmacokinetics ; Models, Theoretical ; Muscles/chemistry ; Rivers ; Tissue Distribution ; Urbanization ; Water Pollutants, Chemical/analysis/*pharmacokinetics ; }, abstract = {The recently developed modelling tool MERLIN-Expo was applied to support the exposure assessment of an aquatic food web to trace metals in a coastal environment. The exposure scenario, built on the data from Daliao River estuary in the Liaodong Bay (Bohai Sea, China), affected by long-term and large-scale industrial activities as well as rapid urbanization in Liao River watershed, represents an interesting case-study for ecological exposure modelling due to the availability of local data on metal concentrations in water and sediment. The bioaccumulation of selected trace metals in aquatic organisms was modelled and compared with field data from local aquatic organisms. Both model results and experimental data demonstrated that As, Cd, Cu, Ni, Pb and Zn, out of examined metals, were accumulated most abundantly by invertebrates and less by higher trophic level species. The body parts of the sampled animals with the highest measured concentration of metals were predominantly muscles, intestine and liver and fish skin in the case of Cr. The Morris and extended Fourier Analysis (EFAST) were used to account for variability in selected parameters of the bioaccumulation model. Food assimilation efficiency and slopes and intercepts of two sub-models for calculating metal specific BCFs (BCFmetal-exposure concentration) and fish weight (Weightfish-Lengthfish) were identified as the most influential parameters on ecological exposure to selected metals.}, } @article {pmid30502396, year = {2019}, author = {Fassio, G and Modica, MV and Alvaro, MC and Buge, B and Salvi, D and Oliverio, M and Schiaparelli, S}, title = {An Antarctic flock under the Thorson's rule: Diversity and larval development of Antarctic Velutinidae (Mollusca: Gastropoda).}, journal = {Molecular phylogenetics and evolution}, volume = {132}, number = {}, pages = {1-13}, doi = {10.1016/j.ympev.2018.11.017}, pmid = {30502396}, issn = {1095-9513}, mesh = {Animals ; Antarctic Regions ; Bayes Theorem ; *Biodiversity ; Cell Nucleus/genetics ; Databases, Genetic ; Electron Transport Complex IV/genetics ; Larva/growth & development ; Mollusca/classification/genetics/*growth & development/ultrastructure ; Phylogeny ; Species Specificity ; Urochordata ; }, abstract = {In most marine gastropods, the duration of the larval phase is a key feature, strongly influencing species distribution and persistence. Antarctic lineages, in agreement with Thorson's rule, generally show a short pelagic developmental phase (or lack it completely), with very few exceptions. Among them is the ascidian-feeding gastropod family Velutinidae, a quite understudied group. Based on a multilocus (COI, 16S, 28S and ITS2) dataset for 182 specimens collected in Antarctica and other regions worldwide, we investigated the actual Antarctic velutinid diversity, inferred their larval development, tested species genetic connectivity and produced a first phylogenetic framework of the family. We identified 15 Antarctic Molecular Operational Taxonomic Units (MOTUs), some of which represented undescribed species, which show two different types of larval shell, indicating different duration of the Pelagic Larval Phase (PLD). Antarctic velutinids stand as an independent lineage, sister to the rest of the family, with extensive hidden diversity likely produced by rapid radiation. Our phylogenetic framework indicates that this Antarctic flock underwent repeated events of pelagic phase shortening, in agreement with Thorson's rule, yielding species with restricted geographic ranges.}, } @article {pmid30517350, year = {2018}, author = {Souza, CDF and Santos, FGB and Marques, CS and Leal, TC and Paiva, JPS and Araújo, EMCF}, title = {Spatial study of leprosy in Bahia, Brazil, 2001-2012: an approach based on the local empirical Bayesian model.}, journal = {Epidemiologia e servicos de saude : revista do Sistema Unico de Saude do Brasil}, volume = {27}, number = {4}, pages = {e2017479}, doi = {10.5123/S1679-49742018000400013}, pmid = {30517350}, issn = {2237-9622}, mesh = {Adolescent ; Age Distribution ; Bayes Theorem ; Brazil/epidemiology ; Child ; Child, Preschool ; Cities/statistics & numerical data ; Disabled Persons/statistics & numerical data ; Disease Notification/*statistics & numerical data ; Health Information Systems/*statistics & numerical data ; Humans ; Infant ; Leprosy/*epidemiology ; Risk Factors ; *Spatial Analysis ; }, abstract = {OBJECTIVE: to compare the temporal evolution and spatial distribution of epidemiological indicators of leprosy, both crude and also corrected using the empirical Bayesian model, Bahia, Brazil, 2001-2012.

METHODS: this was an ecological study using data from the Notifiable Diseases Information System; all 417 municipalities in Bahia were included and the following indicators per 100,000 inhabitants were analyzed - detection rate of new cases in the general population, in those <15 years old, and in those with grade 2 physical disability -; the local empirical Bayesian model was used to smoothen the indicators, and Student's t-test was used to compare means.

RESULTS: indicators estimated by the model were higher than crude indicators; estimated detection rates in the general population and in those <15 years old were higher than crude rates in 253 (60.7%) and 209 (50.1%) municipalities, respectively; areas of greatest risk were concentrated in the northwestern and southern regions of the state.

CONCLUSION: spatial distribution of the disease was heterogeneous and there was possible underreporting of cases.}, } @article {pmid30517348, year = {2018}, author = {Vieira, ILV and Kupek, E}, title = {The impact of pneumococcal vaccine in reducing pneumonia hospitalizations in children under 5 years old, in Santa Catarina, Brazil, 2006 a 2014.}, journal = {Epidemiologia e servicos de saude : revista do Sistema Unico de Saude do Brasil}, volume = {27}, number = {4}, pages = {e2017378}, doi = {10.5123/S1679-49742018000400012}, pmid = {30517348}, issn = {2237-9622}, mesh = {Age Factors ; Brazil/epidemiology ; Child, Preschool ; Health Information Systems ; Hospitalization/*statistics & numerical data ; Humans ; Infant ; National Health Programs ; Pneumococcal Vaccines/*administration & dosage ; Pneumonia, Pneumococcal/epidemiology/*prevention & control ; Poisson Distribution ; }, abstract = {OBJECTIVE: to analyze the impact of pneumococcal conjugate vaccine (PCV10) on pneumonia hospital admissions among children in Santa Catarina, Brazil, 2006-2014.

METHODS: this was an ecological study using data obtained from Brazilian National Health System Information Technology Department (Datasus) for 2006-2009 (pre-vaccination period) and 2010-2014 (post-vaccination period); time trends were evaluated using the Poisson regression coefficient.

RESULTS: in the comparison between pre- and post-vaccination periods, the percentage difference in the hospitalization rate for children under 1 year old ranged from -44.1% in the Western region to -1.4% in the Serrano Plateau region, and in children between 1-4 years old it ranged from -37.1% in the Northern Plateau region to 16.9% in the Serrano Plateau region (p<0.05); hospitalization rates in the state reduced by 23.3% in children under 1 year old and by 8.4% in those aged 1-4 years.

CONCLUSION: a significant reduction in the rate of pneumonia hospitalization in children under 1 year old age was found, suggesting the effectiveness of the vaccine in reducing hospitalizations.}, } @article {pmid30517152, year = {2018}, author = {Huang, W and Li, H and Cheng, C and Ren, C and Chen, T and Jiang, X and Cheng, K and Luo, P and Hu, C}, title = {Analysis of the transcriptome data in Litopenaeus vannamei reveals the immune basis and predicts the hub regulation-genes in response to high-pH stress.}, journal = {PloS one}, volume = {13}, number = {12}, pages = {e0207771}, pmid = {30517152}, issn = {1932-6203}, mesh = {Animals ; Cyclic Nucleotide-Gated Cation Channels/genetics/immunology/metabolism ; Gene Expression Profiling ; Gene Expression Regulation ; Gene Ontology ; HSP70 Heat-Shock Proteins/genetics/immunology/metabolism ; Hydrogen-Ion Concentration ; Patched-1 Receptor/genetics/immunology/metabolism ; Penaeidae/*genetics/*immunology/metabolism ; Protein Interaction Maps/genetics/immunology ; Sequence Analysis, RNA ; Signal Transduction ; Stress, Physiological/genetics/immunology ; }, abstract = {Soil salinization erodes the farmlands and poses a serious threat to human life, reuse of the saline-alkali lands as cultivated resources becomes increasingly prominent. Pacific white shrimp (Litopenaeus vannamei) is an important farmed aquatic species for the development and utilization of the saline-alkali areas. However, little is known about the adaptation mechanism of this species in terms of high-pH stress. In the present study, a transcriptome analysis on the gill tissues of L. vannamei in response to high-pH stress (pH 9.3 ± 0.1) was conducted. After analyzing, the cyclic nucleotide gated channel-Ca2+ (CNGC-Ca2+) and patched 1 (Ptc1) were detected as the majority annotated components in the cAMP signaling pathway (KO04024), indicating that the CNGC-Ca2+ and Ptc1 might be the candidate components for transducing and maintaining the high-pH stress signals, respectively. The immunoglobulin superfamily (IgSF), heat shock protein (HSP), glutathione s-transferase (GST), prophenoloxidase/phenoloxidase (proPO/PO), superoxide dismutase (SOD), anti-lipopolysaccharide factor (ALF) and lipoprotein were discovered as the major transcribed immune factors in response to high-pH stress. To further detect hub regulation-genes, protein-protein interaction (PPI) networks were constructed; the genes/proteins "Polymerase (RNA) II (DNA directed) polypeptide A" (POLR2A), "Histone acetyltransferase p300" (EP300) and "Heat shock 70kDa protein 8" (HSPA8) were suggested as the top three hub regulation-genes in response to acute high-pH stress; the genes/proteins "Heat shock 70kDa protein 4" (HSPA4), "FBJ murine osteosarcoma viral oncogene homolog" (FOS) and "Nucleoporin 54kDa" (NUP54) were proposed as the top three hub regulation-genes involved in adapting endurance high-pH stress; the protein-interactions of "EP300-HSPA8" and "HSPA4-NUP54" were detected as the most important biological interactions in response to the high-pH stress; and the HSP70 family genes might play essential roles in the adaptation of the high-pH stress environment in L. vannamei. These findings provide the first insight into the molecular and immune basis of L. vannamei in terms of high-pH environments, and the construction of a PPI network might improve our understanding in revealing the hub regulation-genes in response to abiotic stress in shrimp species and might be beneficial for further studies.}, } @article {pmid30510239, year = {2019}, author = {Wang, M and Tu, L and Yuan, D and Zhu, D and Shen, C and Li, J and Liu, F and Pei, L and Wang, P and Zhao, G and Ye, Z and Huang, H and Yan, F and Ma, Y and Zhang, L and Liu, M and You, J and Yang, Y and Liu, Z and Huang, F and Li, B and Qiu, P and Zhang, Q and Zhu, L and Jin, S and Yang, X and Min, L and Li, G and Chen, LL and Zheng, H and Lindsey, K and Lin, Z and Udall, JA and Zhang, X}, title = {Reference genome sequences of two cultivated allotetraploid cottons, Gossypium hirsutum and Gossypium barbadense.}, journal = {Nature genetics}, volume = {51}, number = {2}, pages = {224-229}, doi = {10.1038/s41588-018-0282-x}, pmid = {30510239}, issn = {1546-1718}, mesh = {Chromosome Mapping/methods ; Chromosomes, Plant/genetics ; Cotton Fiber ; Genetic Variation/genetics ; Genome, Plant/*genetics ; Gossypium/*genetics ; Phylogeny ; Plant Breeding/methods ; Quantitative Trait Loci/genetics ; }, abstract = {Allotetraploid cotton species (Gossypium hirsutum and Gossypium barbadense) have long been cultivated worldwide for natural renewable textile fibers. The draft genome sequences of both species are available but they are highly fragmented and incomplete[1-4]. Here we report reference-grade genome assemblies and annotations for G. hirsutum accession Texas Marker-1 (TM-1) and G. barbadense accession 3-79 by integrating single-molecule real-time sequencing, BioNano optical mapping and high-throughput chromosome conformation capture techniques. Compared with previous assembled draft genomes[1,3], these genome sequences show considerable improvements in contiguity and completeness for regions with high content of repeats such as centromeres. Comparative genomics analyses identify extensive structural variations that probably occurred after polyploidization, highlighted by large paracentric/pericentric inversions in 14 chromosomes. We constructed an introgression line population to introduce favorable chromosome segments from G. barbadense to G. hirsutum, allowing us to identify 13 quantitative trait loci associated with superior fiber quality. These resources will accelerate evolutionary and functional genomic studies in cotton and inform future breeding programs for fiber improvement.}, } @article {pmid30509188, year = {2018}, author = {Fritz, S and Rajaonison, A and Chabrol, O and Raoult, D and Rolain, JM and Merhej, V}, title = {Full-length title: NRPPUR database search and in vitro analysis identify an NRPS-PKS biosynthetic gene cluster with a potential antibiotic effect.}, journal = {BMC bioinformatics}, volume = {19}, number = {1}, pages = {463}, pmid = {30509188}, issn = {1471-2105}, mesh = {Anti-Bacterial Agents/*chemistry ; Databases, Factual ; Humans ; Multigene Family/*genetics ; Peptide Synthases/*genetics ; }, abstract = {BACKGROUND: Growing concern about the emergence of antibiotic resistance is compelling the pharmaceutical industry to search for new antimicrobial agents. The availability of genome sequences has enabled the development of computational mining as an important tool in the discovery of natural products with antibiotic effect.

RESULTS: NRPPUR (Non-Ribosomal Peptide and Polyketide Urmite) is a new bioinformatic tool that was created to detect polyketides and non-ribosomal peptide gene clusters (PKS and NRPS) in bacterial genomes using the rpsBlast program. The NRPPUR database was constructed locally by assembling all 3505 available sequences of NRPS-PKS that have been identified by in silico approaches to date, with 164 Biosynthetic Gene Clusters (BGCs) derived from the published literature that have demonstrated antimicrobial activity in vitro. The in silico analysis of 49 intestinal human bacterial genomes using the NRPPUR made it possible to identify 91 BGCs including 89 clusters that had never previously been described. On average, intestinal human bacterial genomes devote nearly 0.8% (±1.4% s.d.) of their genome to NRPS/PKS biosynthesis, with Bacillus vallismortis, Streptomyces massiliensis and Bacillus subtilis genomes apportioning 8.4, 3.6 and 3.15% of their genomes, respectively. When using the cross-streak method, S. massiliensis displayed antibacterial activity against many Gram-positive and negative bacteria including methicillin-resistant Staphylococcus aureus (MRSA).

CONCLUSIONS: NRPPUR has proven to be a very useful tool for the primary in silico selection of species with potential antimicrobial activity and human microbiota could be the future source of new antimicrobial discoveries. Further exploration of this and other ecological niches, coupled with high-throughput antibacterial activity screening should be envisaged.}, } @article {pmid30500872, year = {2019}, author = {Lippmann, C and Ultsch, A and Lötsch, J}, title = {Computational functional genomics-based reduction of disease-related gene sets to their key components.}, journal = {Bioinformatics (Oxford, England)}, volume = {35}, number = {14}, pages = {2362-2370}, doi = {10.1093/bioinformatics/bty986}, pmid = {30500872}, issn = {1367-4811}, mesh = {Computational Biology ; Gene Expression ; *Genomics ; *Knowledge Bases ; Software ; }, abstract = {MOTIVATION: The genetic architecture of diseases becomes increasingly known. This raises difficulties in picking suitable targets for further research among an increasing number of candidates. Although expression based methods of gene set reduction are applied to laboratory-derived genetic data, the analysis of topical sets of genes gathered from knowledge bases requires a modified approach as no quantitative information about gene expression is available.

RESULTS: We propose a computational functional genomics-based approach at reducing sets of genes to the most relevant items based on the importance of the gene within the polyhierarchy of biological processes characterizing the disease. Knowledge bases about the biological roles of genes can provide a valid description of traits or diseases represented as a directed acyclic graph (DAG) picturing the polyhierarchy of disease relevant biological processes. The proposed method uses a gene importance score derived from the location of the gene-related biological processes in the DAG. It attempts to recreate the DAG and thereby, the roles of the original gene set, with the least number of genes in descending order of importance. This obtained precision and recall of over 70% to recreate the components of the DAG charactering the biological functions of n=540 genes relevant to pain with a subset of only the k=29 best-scoring genes.

CONCLUSIONS: A new method for reduction of gene sets is shown that is able to reproduce the biological processes in which the full gene set is involved by over 70%; however, by using only ∼5% of the original genes.

The necessary numerical parameters for the calculation of gene importance are implemented in the R package dbtORA at https://github.com/IME-TMP-FFM/dbtORA.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, } @article {pmid30499218, year = {2019}, author = {Taylor, SD and Meiners, JM and Riemer, K and Orr, MC and White, EP}, title = {Comparison of large-scale citizen science data and long-term study data for phenology modeling.}, journal = {Ecology}, volume = {100}, number = {2}, pages = {e02568}, pmid = {30499218}, issn = {0012-9658}, support = {GBMF4563//Gordon and Betty Moore Foundation/International ; //University of Florida Biodiversity Institute Graduate Research Fellowship/International ; }, mesh = {*Climate Change ; Longitudinal Studies ; *Models, Theoretical ; Seasons ; }, abstract = {Large-scale observational data from citizen science efforts are becoming increasingly common in ecology, and researchers often choose between these and data from intensive local-scale studies for their analyses. This choice has potential trade-offs related to spatial scale, observer variance, and interannual variability. Here we explored this issue with phenology by comparing models built using data from the large-scale, citizen science USA National Phenology Network (USA-NPN) effort with models built using data from more intensive studies at Long Term Ecological Research (LTER) sites. We built statistical and process based phenology models for species common to each data set. From these models, we compared parameter estimates, estimates of phenological events, and out-of-sample errors between models derived from both USA-NPN and LTER data. We found that model parameter estimates for the same species were most similar between the two data sets when using simple models, but parameter estimates varied widely as model complexity increased. Despite this, estimates for the date of phenological events and out-of-sample errors were similar, regardless of the model chosen. Predictions for USA-NPN data had the lowest error when using models built from the USA-NPN data, while LTER predictions were best made using LTER-derived models, confirming that models perform best when applied at the same scale they were built. This difference in the cross-scale model comparison is likely due to variation in phenological requirements within species. Models using the USA-NPN data set can integrate parameters over a large spatial scale while those using an LTER data set can only estimate parameters for a single location. Accordingly, the choice of data set depends on the research question. Inferences about species-specific phenological requirements are best made with LTER data, and if USA-NPN or similar data are all that is available, then analyses should be limited to simple models. Large-scale predictive modeling is best done with the larger-scale USA-NPN data, which has high spatial representation and a large regional species pool. LTER data sets, on the other hand, have high site fidelity and thus characterize inter-annual variability extremely well. Future research aimed at forecasting phenology events for particular species over larger scales should develop models that integrate the strengths of both data sets.}, } @article {pmid30498254, year = {2018}, author = {Dutta, A and Dutta Gupta, S and Gupta, A and Sarkar, J and Roy, S and Mukherjee, A and Sar, P}, title = {Exploration of deep terrestrial subsurface microbiome in Late Cretaceous Deccan traps and underlying Archean basement, India.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {17459}, pmid = {30498254}, issn = {2045-2322}, support = {MoES/P.O.(Seismo)/1(181)/2013//Ministry of Earth Sciences (MoES)/International ; }, mesh = {Biodiversity ; Computational Biology/methods ; *Environmental Microbiology ; Geologic Sediments/*microbiology ; India ; Metagenome ; Metagenomics/methods ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Scientific deep drilling at Koyna, western India provides a unique opportunity to explore microbial life within deep biosphere hosted by ~65 Myr old Deccan basalt and Archaean granitic basement. Characteristic low organic carbon content, mafic/felsic nature but distinct trend in sulfate and nitrate concentrations demarcates the basaltic and granitic zones as distinct ecological habitats. Quantitative PCR indicates a depth independent distribution of microorganisms predominated by bacteria. Abundance of dsrB and mcrA genes are relatively higher (at least one order of magnitude) in basalt compared to granite. Bacterial communities are dominated by Alpha-, Beta-, Gammaproteobacteria, Actinobacteria and Firmicutes, whereas Euryarchaeota is the major archaeal group. Strong correlation among the abundance of autotrophic and heterotrophic taxa is noted. Bacteria known for nitrite, sulfur and hydrogen oxidation represent the autotrophs. Fermentative, nitrate/sulfate reducing and methane metabolising microorganisms represent the heterotrophs. Lack of shared operational taxonomic units and distinct clustering of major taxa indicate possible community isolation. Shotgun metagenomics corroborate that chemolithoautotrophic assimilation of carbon coupled with fermentation and anaerobic respiration drive this deep biosphere. This first report on the geomicrobiology of the subsurface of Deccan traps provides an unprecedented opportunity to understand microbial composition and function in the terrestrial, igneous rock-hosted, deep biosphere.}, } @article {pmid30497508, year = {2018}, author = {Meerstein-Kessel, L and Andolina, C and Carrio, E and Mahamar, A and Sawa, P and Diawara, H and van de Vegte-Bolmer, M and Stone, W and Collins, KA and Schneider, P and Dicko, A and Drakeley, C and Felger, I and Voss, T and Lanke, K and Bousema, T}, title = {A multiplex assay for the sensitive detection and quantification of male and female Plasmodium falciparum gametocytes.}, journal = {Malaria journal}, volume = {17}, number = {1}, pages = {441}, pmid = {30497508}, issn = {1475-2875}, support = {202769/Z/16/Z//Wellcome Trust/United Kingdom ; BSCGI0_157729//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; U19AI089674//National Institute of Allergy and Infectious Diseases/ ; OPP1173572//Bill & Melinda Gates Foundation/ ; ERC-2014-StG 639776//European Research Council/International ; U19 AI089674/AI/NIAID NIH HHS/United States ; //Wellcome Trust/United Kingdom ; }, mesh = {Female ; Humans ; Malaria, Falciparum/*parasitology ; Male ; Molecular Diagnostic Techniques/*methods ; Parasite Load/*methods ; Parasitemia/*parasitology ; Plasmodium falciparum/classification/genetics/*isolation & purification ; Real-Time Polymerase Chain Reaction/*methods ; }, abstract = {BACKGROUND: The transmission of malaria to mosquitoes depends on the presence of gametocytes that circulate in the peripheral blood of infected human hosts. Sensitive estimates of the densities of female gametocytes (FG) and male gametocytes (MG) may allow the prediction of infectivity to mosquitoes and thus a molecular estimate of the human infectious reservoir for transmission.

METHODS: A novel multiplex qRT-PCR assay with intron-spanning primers was developed for the parallel quantification of FG and MG. CCp4 (PF3D7_0903800) transcripts specific for FG and PfMGET (PF3D7_1469900) transcripts specific for MG were quantified in total nucleic acids. The assay was validated on sex-sorted gametocytes from culture material and on samples from clinical trials with gametocytocidal drugs. Synthetic RNA standards were generated for the two targets genes and calibrated against known gametocyte quantities.

RESULTS: The limit of detection was determined at 0.1 male and 0.1 female gametocyte/µL, which was equal to the limit of quantification (LOQ) for MG, while the LOQ for FG was 1 FG/µL. Results from previously reported clinical trials that used separate gametocyte qRT-PCR assays for FG (targeting Pfs25) and MG (targeting PfMGET) were reproduced with the multiplex assay. High levels of agreement between separate assays and the multiplex approach were observed (R[2] = 0.9473, 95% CI 0.9314-0.9632, for FG measured by transcript levels of Pfs25 in qRT-PCR or CCp4 in multiplex; R[2] = 0.8869, 95% CI 0.8541-0.9197, for MG measured by PfMGET in either single or multiplex qRT-PCR). FG and MG transcripts were detected in pure ring stage parasites at 10,000- and 100,000-fold reduced frequency for CCp4 and PfMGET, respectively. The CCp4 and PfMGET transcripts were equally stable under suboptimal storage conditions.

CONCLUSIONS: Gametocyte densities and their sex ratios can be determined in the presented one-step multiplex assay with higher throughput than single assays. The interpretation of low gametocyte densities at asexual parasite densities above 1000 parasites/µL requires caution to avoid false positive gametocyte signals from spurious transcript levels in ring stage parasites.}, } @article {pmid30497363, year = {2018}, author = {Sperlea, T and Füser, S and Boenigk, J and Heider, D}, title = {SEDE-GPS: socio-economic data enrichment based on GPS information.}, journal = {BMC bioinformatics}, volume = {19}, number = {Suppl 15}, pages = {440}, pmid = {30497363}, issn = {1471-2105}, mesh = {Algorithms ; Biodiversity ; *Geographic Information Systems ; Lakes ; Machine Learning ; Microbiota ; Socioeconomic Factors ; }, abstract = {BACKGROUND: Microbes are essentail components of all ecosystems because they drive many biochemical processes and act as primary producers. In freshwater ecosystems, the biodiversity in and the composition of microbial communities can be used as indicators for environmental quality. Recently, some environmental features have been identified that influence microbial ecosystems. However, the impact of human action on lake microbiomes is not well understood. This is, in part, due to the fact that environmental data is, albeit theoretically accessible, not easily available.

RESULTS: In this work, we present SEDE-GPS, a tool that gathers data that are relevant to the environment of an user-provided GPS coordinate. To this end, it accesses a list of public and corporate databases and aggregates the information in a single file, which can be used for further analysis. To showcase the use of SEDE-GPS, we enriched a lake microbial ecology sequencing dataset with around 18,000 socio-economic, climate, and geographic features. The sources of SEDE-GPS are public databases such as Eurostat, the Climate Data Center, and OpenStreetMap, as well as corporate sources such as Twitter. Using machine learning and feature selection methods, we were able to identify features in the data provided by SEDE-GPS that can be used to predict lake microbiome alpha diversity.

CONCLUSION: The results presented in this study show that SEDE-GPS is a handy and easy-to-use tool for comprehensive data enrichment for studies of ecology and other processes that are affected by environmental features. Furthermore, we present lists of environmental, socio-economic, and climate features that are predictive for microbial biodiversity in lake ecosystems. These lists indicate that human action has a major impact on lake microbiomes. SEDE-GPS and its source code is available for download at http://SEDE-GPS.heiderlab.de.}, } @article {pmid30497032, year = {2019}, author = {Assefa, A and Tysklind, M and Bignert, A and Josefsson, S and Wiberg, K}, title = {Sources of polychlorinated dibenzo-p-dioxins and dibenzofurans to Baltic Sea herring.}, journal = {Chemosphere}, volume = {218}, number = {}, pages = {493-500}, doi = {10.1016/j.chemosphere.2018.11.051}, pmid = {30497032}, issn = {1879-1298}, mesh = {Animals ; Chlorophenols/analysis ; Databases, Factual ; Dibenzofurans, Polychlorinated/*analysis ; Ecotoxicology/methods ; Environmental Monitoring/methods ; Fish Products ; *Fishes ; Food Contamination ; Models, Theoretical ; Polychlorinated Dibenzodioxins/*analysis ; Sweden ; Water Pollutants, Chemical/*analysis ; }, abstract = {Levels of polychlorinated dibenzo-p-dioxins and dibenzofurans (PCDD/Fs) in herring (Clupea harengus) remain high in several parts of the Baltic Sea, despite declines in PCDD/F emissions since the 1980s. The reasons behind this are not well understood. This study applied a statistical modeling approach where sources of PCDD/Fs that contaminate Baltic biota were quantitatively assessed by analyzing existing datasets. PCDD/F patterns were extracted from a herring dataset using positive matrix factorization (PMF). The extracted biota patterns were transformed into sediment patterns using fish-to-sediment transformation factors, and the resulting patterns were compared with known source PCDD/F patterns. The model distinguished three model patterns, which explained 85% of the data. These patterns were matched to tetra-chlorophenol (TCP), penta-chlorophenol/atmospheric background (PCP/AB), and thermal source patterns, respectively. The thermal source was the largest contributor to toxic equivalents (TEQ) in herring, but the level decreased from 42 ± 9.0 pg TEQ g[-1] lipid weight (lw) before year 2000 (pre-2000) to 15 ± 2.4 pg TEQ g[-1] lw post-2000, i.e., a decline of around one-third in the original TEQ concentration. The contribution of TCP more than doubled, from 2.1 ± 0.62 pg TEQ g[-1] lw to 5.6 ± 1.1 pg TEQ g[-1] lw, and the relative contribution of PCP/AB also increased. These increasing trends suggest that, as primary air emissions of PCDD/Fs are managed and levels decline, the impact of TCP and PCP/AB sources on Baltic Sea biota will become more important over time and that PCDD/F-contaminated sites in coastal areas and marine environments require more attention.}, } @article {pmid30488481, year = {2019}, author = {Jones-Todd, CM and Caie, P and Illian, JB and Stevenson, BC and Savage, A and Harrison, DJ and Bown, JL}, title = {Identifying prognostic structural features in tissue sections of colon cancer patients using point pattern analysis.}, journal = {Statistics in medicine}, volume = {38}, number = {8}, pages = {1421-1441}, doi = {10.1002/sim.8046}, pmid = {30488481}, issn = {1097-0258}, mesh = {Algorithms ; Colorectal Neoplasms/*diagnosis/*pathology ; Data Interpretation, Statistical ; Humans ; Prognosis ; }, abstract = {Diagnosis and prognosis of cancer are informed by the architecture inherent in cancer patient tissue sections. This architecture is typically identified by pathologists, yet advances in computational image analysis facilitate quantitative assessment of this structure. In this article, we develop a spatial point process approach to describe patterns in cell distribution within tissue samples taken from colorectal cancer (CRC) patients. In particular, our approach is centered on the Palm intensity function. This leads to taking an approximate-likelihood technique in fitting point processes models. We consider two Neyman-Scott point processes and a void process, fitting these point process models to the CRC patient data. We find that the parameter estimates of these models may be used to quantify the spatial arrangement of cells. Importantly, we observe characteristic differences in the spatial arrangement of cells between patients who died from CRC and those alive at follow up.}, } @article {pmid30485303, year = {2018}, author = {Tanaka, Y and Nakamura, K and Yokomizo, H}, title = {Relative robustness of NOEC and ECx against large uncertainties in data.}, journal = {PloS one}, volume = {13}, number = {11}, pages = {e0206901}, pmid = {30485303}, issn = {1932-6203}, mesh = {Data Interpretation, Statistical ; Ecotoxicology/*methods ; Environmental Pollutants/*toxicity ; Hazardous Substances/*toxicity ; Monte Carlo Method ; No-Observed-Adverse-Effect Level ; Risk Assessment/methods ; *Uncertainty ; }, abstract = {The relative ability of the NOEC (no-observed-effect concentration) and ECx (the effect concentration corresponding to x-percent response) to determine benchmark toxicant concentrations, which are expected to ensure environmental safety, when there are large uncertainties in data was investigated with Monte Carlo simulations. We assumed a hypothetical true concentration-response function, and examined how random fluctuations of responses around the true responses affected the NOEC and ECx values. For assessment of the relative performances of these endpoints, we adopted two criteria: how large uncertainties were allowed for the minimum requirement for safety to be met, and the probability with which the estimated endpoints exceeded the minimum requirement for safety. The results of simulations indicated that, when there were small uncertainties in the data, performance of the NOEC was comparable with or slightly better than the ECx (EC5 and EC10) in providing benchmark concentrations that satisfied the minimum requirement for safety. With larger random variation of data (the coefficient of variation in responses between replicates within treatments or in the control was noticeably larger than 10 percent), the NOEC performed considerably worse than the ECx in terms of the frequency of simulated runs in which the endpoints exceeded the minimum requirement of safety. We conclude that the NOEC is as relevant as the ECx for risk assessment of chemicals under limited situations.}, } @article {pmid30484217, year = {2019}, author = {Geyer, K and Ellis, DA and Piwek, L}, title = {A simple location-tracking app for psychological research.}, journal = {Behavior research methods}, volume = {51}, number = {6}, pages = {2840-2846}, pmid = {30484217}, issn = {1554-3528}, mesh = {Adult ; *Geographic Information Systems ; Humans ; *Mobile Applications ; Smartphone ; }, abstract = {Location data gathered from a variety of sources are particularly valuable when it comes to understanding individuals and groups. However, much of this work has relied on participants' active engagement in regularly reporting their location. More recently, smartphones have been used to assist with this process, but although commercial smartphone applications are available, these are often expensive and are not designed with researchers in mind. To overcome these and other related issues, we have developed a freely available Android application that logs location accurately, stores the data securely, and ensures that participants can provide consent or withdraw from a study at any time. Further recommendations and R code are provided in order to assist with subsequent data analysis.}, } @article {pmid30483906, year = {2019}, author = {Chan, CK and Rosic, N and Lorenc, MT and Visendi, P and Lin, M and Kaniewska, P and Ferguson, BJ and Gresshoff, PM and Batley, J and Edwards, D}, title = {A differential k-mer analysis pipeline for comparing RNA-Seq transcriptome and meta-transcriptome datasets without a reference.}, journal = {Functional & integrative genomics}, volume = {19}, number = {2}, pages = {363-371}, pmid = {30483906}, issn = {1438-7948}, mesh = {Algorithms ; Animals ; Anthozoa/genetics ; Datasets as Topic ; Gene Expression Profiling/*methods/standards ; *Metagenome ; Reference Standards ; Sequence Analysis, RNA/*methods/standards ; *Transcriptome ; }, abstract = {Next-generation DNA sequencing technologies, such as RNA-Seq, currently dominate genome-wide gene expression studies. A standard approach to analyse this data requires mapping sequence reads to a reference and counting the number of reads which map to each gene. However, for many transcriptome studies, a suitable reference genome is unavailable, especially for meta-transcriptome studies which assay gene expression from mixed populations of organisms. Where a reference is unavailable, it is possible to generate a reference by the de novo assembly of the sequence reads. However, the high cost of generating high-coverage data for de novo assembly hinders this approach and more importantly the accurate assembly of such data is challenging, especially for meta-transcriptome data, and resulting assemblies frequently suffer from collapsed regions or chimeric sequences. As an alternative to the standard reference mapping approach, we have developed a k-mer-based analysis pipeline (DiffKAP) to identify differentially expressed reads between RNA-Seq datasets without the requirement for a reference. We compared the DiffKAP approach with the traditional Tophat/Cuffdiff method using RNA-Seq data from soybean, which has a suitable reference genome. We subsequently examined differential gene expression for a coral meta-transcriptome where no reference is available, and validated the results using qRT-PCR. We conclude that DiffKAP is an accurate method to study differential gene expression in complex meta-transcriptomes without the requirement of a reference genome.}, } @article {pmid30483277, year = {2018}, author = {Mohammadi-Dehcheshmeh, M and Niazi, A and Ebrahimi, M and Tahsili, M and Nurollah, Z and Ebrahimi Khaksefid, R and Ebrahimi, M and Ebrahimie, E}, title = {Unified Transcriptomic Signature of Arbuscular Mycorrhiza Colonization in Roots of Medicago truncatula by Integration of Machine Learning, Promoter Analysis, and Direct Merging Meta-Analysis.}, journal = {Frontiers in plant science}, volume = {9}, number = {}, pages = {1550}, pmid = {30483277}, issn = {1664-462X}, abstract = {Plant root symbiosis with Arbuscular mycorrhizal (AM) fungi improves uptake of water and mineral nutrients, improving plant development under stressful conditions. Unraveling the unified transcriptomic signature of a successful colonization provides a better understanding of symbiosis. We developed a framework for finding the transcriptomic signature of Arbuscular mycorrhiza colonization and its regulating transcription factors in roots of Medicago truncatula. Expression profiles of roots in response to AM species were collected from four separate studies and were combined by direct merging meta-analysis. Batch effect, the major concern in expression meta-analysis, was reduced by three normalization steps: Robust Multi-array Average algorithm, Z-standardization, and quartiling normalization. Then, expression profile of 33685 genes in 18 root samples of Medicago as numerical features, as well as study ID and Arbuscular mycorrhiza type as categorical features, were mined by seven models: RELIEF, UNCERTAINTY, GINI INDEX, Chi Squared, RULE, INFO GAIN, and INFO GAIN RATIO. In total, 73 genes selected by machine learning models were up-regulated in response to AM (Z-value difference > 0.5). Feature weighting models also documented that this signature is independent from study (batch) effect. The AM inoculation signature obtained was able to differentiate efficiently between AM inoculated and non-inoculated samples. The AP2 domain class transcription factor, GRAS family transcription factors, and cyclin-dependent kinase were among the highly expressed meta-genes identified in the signature. We found high correspondence between the AM colonization signature obtained in this study and independent RNA-seq experiments on AM colonization, validating the repeatability of the colonization signature. Promoter analysis of upregulated genes in the transcriptomic signature led to the key regulators of AM colonization, including the essential transcription factors for endosymbiosis establishment and development such as NF-YA factors. The approach developed in this study offers three distinct novel features: (I) it improves direct merging meta-analysis by integrating supervised machine learning models and normalization steps to reduce study-specific batch effects; (II) seven attribute weighting models assessed the suitability of each gene for the transcriptomic signature which contributes to robustness of the signature (III) the approach is justifiable, easy to apply, and useful in practice. Our integrative framework of meta-analysis, promoter analysis, and machine learning provides a foundation to reveal the transcriptomic signature and regulatory circuits governing Arbuscular mycorrhizal symbiosis and is transferable to the other biological settings.}, } @article {pmid30478111, year = {2018}, author = {Tashiro, A and Sakisaka, K and Okamoto, E and Yoshida, H}, title = {Differences in infant and child mortality before and after the Great East Japan Earthquake and Tsunami: a large population-based ecological study.}, journal = {BMJ open}, volume = {8}, number = {11}, pages = {e022737}, pmid = {30478111}, issn = {2044-6055}, mesh = {Age Factors ; Child ; *Child Mortality ; Child, Preschool ; Earthquakes/*mortality/statistics & numerical data ; Female ; Geographic Information Systems ; Health Services Accessibility/statistics & numerical data ; Humans ; Infant ; *Infant Mortality ; Infant, Newborn ; Japan/epidemiology ; Male ; Natural Disasters/*mortality ; Sex Factors ; Tsunamis/*statistics & numerical data ; }, abstract = {OBJECTIVES: To examine associations between access to medical care, geological data, and infant and child mortality in the area of North-Eastern Japan that was impacted by the Great East Japan Earthquake and Tsunami (GEJET) in 2011.

DESIGN: A population-based ecological study using publicly available data.

SETTING: Twenty secondary medical areas (SMAs) in the disaster-affected zones in the north-eastern prefectures of Japan (Iwate, Fukushima and Miyagi).

PARTICIPANTS: Children younger than 10 years who died in the 20 SMAs between 2008 and 2014 (n=1 748). Primary and secondary outcome measures: Multiple regression analysis for infant and child mortality rate. The mean values were applied for infant and child mortality rates and other factors before GEJET (2008-2010) and after GEJET (2012-2014).

RESULTS: Between 2008 and 2014, the most common cause of death among children younger than 10 years was accidents. The mortality rate per 100 000 persons was 39.1±41.2 before 2011, 226.7±43.4 in 2011 and 31.4±39.1 after 2011. Regression analysis revealed that the mortality rate was positively associated with low age in each period, while the coastal zone was negatively associated with fewer disaster base hospitals in 2011. By contrast, the number of obstetrics and gynaecology centres (β=-189.9, p=0.02) and public health nurses (β=-1.7, p=0.01) was negatively associated with mortality rate per person in 2011.

CONCLUSIONS: In 2011, the mortality rate among children younger than 10 years was 6.4 times higher than that before and after 2011. Residence in a coastal zone was significantly associated with higher child mortality rates.}, } @article {pmid30476557, year = {2019}, author = {Yi, Y and Lv, Y and You, X and Chen, J and Bian, C and Huang, Y and Xu, J and Deng, L and Shi, Q}, title = {High throughput screening of small immune peptides and antimicrobial peptides from the Fish-T1K database.}, journal = {Genomics}, volume = {111}, number = {3}, pages = {215-221}, doi = {10.1016/j.ygeno.2018.11.023}, pmid = {30476557}, issn = {1089-8646}, mesh = {Animals ; Antimicrobial Cationic Peptides/*genetics/metabolism ; Databases, Genetic ; Fish Proteins/*genetics/metabolism ; Fishes/*genetics/immunology ; Genetic Variation ; Gills/metabolism ; *Transcriptome ; }, abstract = {Analyses of transcriptomic datasets have the potential to reveal genetic markers underlying ecological adaptations. In the present study, we leverage the expanding dataset generated by the Fish-T1K Project (Transcriptomes of 1000 Fishes) to characterize small peptides that may be implicated in the immune system of fishes. We focused our analyses on sequences smaller than 360 bp obtained from gill transcriptomes of 87 ray-finned fishes (Actinopterygii). Functional annotation of short transcripts revealed that the number of small immune peptides varied significantly among the studied species. High-throughput screening of antimicrobial peptides (AMPs) with homologous searches was used to characterize the composition of innate immune defense factors present in fishes. We analyzed the putative effects of habitat, climatic zone and genetic system on the distribution of small peptides among species. Our results highlight the utility of large transcriptomic datasets such as Fish-T1K to explore patterns of variation at macroevolutionary scales and to discover novel peptides that may be used for further investigation and drug development.}, } @article {pmid30472648, year = {2019}, author = {Bergier, I and Silva, APS and Abreu, UGP and Oliveira, LOF and Tomazi, M and Dias, FRT and Urbanetz, C and Nogueira, É and Borges-Silva, JC}, title = {Could bovine livestock intensification in Pantanal be neutral regarding enteric methane emissions?.}, journal = {The Science of the total environment}, volume = {655}, number = {}, pages = {463-472}, doi = {10.1016/j.scitotenv.2018.11.178}, pmid = {30472648}, issn = {1879-1026}, mesh = {Animal Husbandry/*methods/*trends ; Animals ; Brazil ; Cattle ; Conservation of Natural Resources ; Geographic Information Systems ; Greenhouse Gases/*analysis ; Methane/*analysis ; Multivariate Analysis ; Principal Component Analysis ; *Wetlands ; }, abstract = {Bovine livestock is a major anthropogenic greenhouse gas source via enteric methane. Brazilian bovine livestock is also responsible for emissions from land-use changes. In contrast, enteric emissions from extensive cattle systems in wetlands might have been overestimated. We provide scientific evidences that the human footprint of bovine products delivered by the Pantanal can be much lower. To assess this, a historical cloud-free imagery of the Landsat-5, spanning 26 years, were processed for mapping spatiotemporal landscapes in a Pantanal farm under cattle intensification studies. Eight landscape categories were identified according to spatiotemporal dynamics of interannual floods. The spatiotemporal map allowed in the field the adoption of stratified random samplings of chamber gas fluxes. The combination of stratified sampled landscapes with Monte Carlo simulations of measured methane emissions in wet and dry soils permitted to integrate landscapes emissions at annual basis with biased uncertainties. Assuming enteric emissions obtained for the Pantanal region, our results suggest that the landscapes methane emissions are 10- to 23-fold superior than the enteric emissions of traditional bovine systems. While enteric emissions seem negligible with respect to net farmland emissions, cattle livestock provide important environmental services like carbon recycling through non-competing herbivory. Moreover, cattle might be making use of a biomass that would undergo decomposition during the flooding phase. Our analysis thus indicate that enteric emissions from traditional bovine systems in flooding farmlands could be considered neutral. By contrast, intensification to improve the stocking rate should be accounted as net anthropogenic emissions. A case study of intensification allowed an increase of 48% in the stocking rate, which is associated with net anthropogenic emissions from 534 bovine animals or about 27 to 63 Mg of enteric CH4 per year. In short, the competition between traditional and distinct levels of cattle intensification will result from a trade-off between public policies and strategic market niches (organic, sustainable) for the optimal landscape management of the Pantanal.}, } @article {pmid30469060, year = {2019}, author = {Zou, YA and Zhang, PY and Zhang, SQ and Chen, XS and Li, F and Deng, ZM and Yang, S and Zhang, H and Li, FY and Xie, YH}, title = {Crucial sites and environmental variables for wintering migratory waterbird population distributions in the natural wetlands in East Dongting Lake, China.}, journal = {The Science of the total environment}, volume = {655}, number = {}, pages = {147-157}, doi = {10.1016/j.scitotenv.2018.11.185}, pmid = {30469060}, issn = {1879-1026}, mesh = {Animals ; China ; *Conservation of Natural Resources ; Ecosystem ; Geese/classification/*growth & development ; Geographic Information Systems ; *Lakes ; Population Dynamics ; Remote Sensing Technology ; Seasons ; *Wetlands ; }, abstract = {Dongting Lake is the second largest freshwater lake in China and is one of the globally important wintering sites for migratory waterbirds in the East Asian-Australasian Flyway. Crucial sites and environmental variables for wintering migratory waterbirds are of great concern in the Dongting Lake wetlands. In this research, based on annual (2003/2004-2016/2017) waterbird and habitat census data, we recognized the crucial sites for waterbirds during wintering seasons by comparing the difference of waterbird populations at the community, foraging guild and species levels in different natural wetlands within East Dongting Lake, and then identified the crucial environmental variables affecting waterbird distributions by analyzing the relationship between waterbird populations and the environmental variables, including vegetation area, mudflat area, water area with the depth of 0-20 cm, water area with the depth of 20-50 cm, water area with the depth of 50-100 cm, water area with the depth >100 cm, growth status of vegetation (Min, Mean and Max NDVI), and the human disturbance. Results indicated that five natural wetlands, i.e., Daxiaoxi, Chunfeng, Baihu lakes, Dingzi dyke and Tanjiaweizi, were recognized as the crucial wintering sites for migratory waterbirds in the East Dongting Lake. Among the ten selected environmental variables, water areas with the depth of 0-20 cm, 20-50 cm and >100 cm, human disturbance, Min and Mean NDVIs were identified as the crucial environmental variables overall. Waterbirds at different levels exhibited significant linear relationship with certain environmental variables, with the exception of Bean goose and Lesser White-fronted goose at the species level, which showed Gaussian distribution with changes in mean NDVI. The crucial environmental variables appeared to be foraging guild- and species-specific. These findings provide significant information for managers to understand the differences of wetlands and waterbird populations within East Dongting Lake, and to make more targeted conservation efforts.}, } @article {pmid30459085, year = {2019}, author = {Nuttall, PA}, title = {Wonders of tick saliva.}, journal = {Ticks and tick-borne diseases}, volume = {10}, number = {2}, pages = {470-481}, doi = {10.1016/j.ttbdis.2018.11.005}, pmid = {30459085}, issn = {1877-9603}, mesh = {Animals ; Arthropod Proteins/analysis/*chemistry ; Computational Biology ; Female ; Guinea Pigs ; Humans ; Male ; Mice ; Saliva/*chemistry ; Salivary Glands/chemistry ; Salivary Proteins and Peptides/analysis/*chemistry ; Ticks/*chemistry ; }, abstract = {Saliva of ticks is arguably the most complex saliva of any animal. This is particularly the case for ixodid species that feed for many days firmly attached to the same skin site of their obliging host. Sequencing and spectrometry technologies combined with bioinformatics are enumerating ingredients in the saliva cocktail. The dynamic and expanding saliva recipe is helping decipher the wonderous activities of tick saliva, revealing how ticks stealthily hide from their hosts while satisfying their gluttony and sharing their individual resources. This review takes a tick perspective on the composition and functions of tick saliva, covering water balance, gasket and holdfast, control of host responses, dynamics, individuality, mate guarding, saliva-assisted transmission, and redundancy. It highlights areas sometimes overlooked - feeding aggregation and sharing of sialomes, and the contribution of salivary gland storage granules - and questions whether the huge diversity of tick saliva molecules is 'redundant' or more a reflection on the enormous adaptability wonderous saliva confers on ticks.}, } @article {pmid30457843, year = {2019}, author = {Cao, X and Hamilton, JJ and Venturelli, OS}, title = {Understanding and Engineering Distributed Biochemical Pathways in Microbial Communities.}, journal = {Biochemistry}, volume = {58}, number = {2}, pages = {94-107}, pmid = {30457843}, issn = {1520-4995}, support = {R35 GM124774/GM/NIGMS NIH HHS/United States ; }, mesh = {Biological Evolution ; Computational Biology/*methods ; Game Theory ; Genome, Microbial ; Microbiota/*physiology ; *Models, Biological ; Spatio-Temporal Analysis ; Synthetic Biology/*methods ; }, abstract = {Microbiomes impact nearly every environment on Earth by modulating the molecular composition of the environment. Temporally changing environmental stimuli and spatial organization are major variables shaping the structure and function of microbiomes. The web of interactions among members of these communities and between the organisms and the environment dictates microbiome functions. Microbial interactions are major drivers of microbiomes and are modulated by spatiotemporal parameters. A mechanistic and quantitative understanding of ecological, molecular, and environmental forces shaping microbiomes could inform strategies to control microbiome dynamics and functions. Major challenges for harnessing the potential of microbiomes for diverse applications include the development of predictive modeling frameworks and tools for precise manipulation of microbiome behaviors.}, } @article {pmid30457567, year = {2018}, author = {Bennett, JM and Steets, JA and Burns, JH and Durka, W and Vamosi, JC and Arceo-Gómez, G and Burd, M and Burkle, LA and Ellis, AG and Freitas, L and Li, J and Rodger, JG and Wolowski, M and Xia, J and Ashman, TL and Knight, TM}, title = {GloPL, a global data base on pollen limitation of plant reproduction.}, journal = {Scientific data}, volume = {5}, number = {}, pages = {180249}, pmid = {30457567}, issn = {2052-4463}, mesh = {*Databases, Factual ; *Pollination ; }, abstract = {Plant reproduction relies on transfer of pollen from anthers to stigmas, and the majority of flowering plants depend on biotic or abiotic agents for this transfer. A key metric for characterizing if pollen receipt is insufficient for reproduction is pollen limitation, which is assessed by pollen supplementation experiments. In a pollen supplementation experiment, fruit or seed production by flowers exposed to natural pollination is compared to that following hand pollination either by pollen supplementation (i.e. manual outcross pollen addition without bagging) or manual outcrossing of bagged flowers, which excludes natural pollination. The GloPL database brings together data from 2969 unique pollen supplementation experiments reported in 927 publications published from 1981 to 2015, allowing assessment of the strength and variability of pollen limitation in 1265 wild plant species across all biomes and geographic regions globally. The GloPL database will be updated and curated with the aim of enabling the continued study of pollen limitation in natural ecosystems and highlighting significant gaps in our understanding of pollen limitation.}, } @article {pmid30456315, year = {2018}, author = {Kalbfleisch, TS and Rice, ES and DePriest, MS and Walenz, BP and Hestand, MS and Vermeesch, JR and O Connell, BL and Fiddes, IT and Vershinina, AO and Saremi, NF and Petersen, JL and Finno, CJ and Bellone, RR and McCue, ME and Brooks, SA and Bailey, E and Orlando, L and Green, RE and Miller, DC and Antczak, DF and MacLeod, JN}, title = {Improved reference genome for the domestic horse increases assembly contiguity and composition.}, journal = {Communications biology}, volume = {1}, number = {}, pages = {197}, pmid = {30456315}, issn = {2399-3642}, support = {K01 OD015134/OD/NIH HHS/United States ; L40 TR001136/TR/NCATS NIH HHS/United States ; }, abstract = {Recent advances in genomic sequencing technology and computational assembly methods have allowed scientists to improve reference genome assemblies in terms of contiguity and composition. EquCab2, a reference genome for the domestic horse, was released in 2007. Although of equal or better quality compared to other first-generation Sanger assemblies, it had many of the shortcomings common to them. In 2014, the equine genomics research community began a project to improve the reference sequence for the horse, building upon the solid foundation of EquCab2 and incorporating new short-read data, long-read data, and proximity ligation data. Here, we present EquCab3. The count of non-N bases in the incorporated chromosomes is improved from 2.33 Gb in EquCab2 to 2.41 Gb in EquCab3. Contiguity has also been improved nearly 40-fold with a contig N50 of 4.5 Mb and scaffold contiguity enhanced to where all but one of the 32 chromosomes is comprised of a single scaffold.}, } @article {pmid30455442, year = {2018}, author = {Doughty, CE and Santos-Andrade, PE and Shenkin, A and Goldsmith, GR and Bentley, LP and Blonder, B and Díaz, S and Salinas, N and Enquist, BJ and Martin, RE and Asner, GP and Malhi, Y}, title = {Tropical forest leaves may darken in response to climate change.}, journal = {Nature ecology & evolution}, volume = {2}, number = {12}, pages = {1918-1924}, doi = {10.1038/s41559-018-0716-y}, pmid = {30455442}, issn = {2397-334X}, support = {NE/J023418/1//Natural Environment Research Council (NERC)/International ; }, mesh = {Altitude ; Carbon Dioxide/analysis ; *Climate Change ; Forests ; Hot Temperature ; Models, Theoretical ; Peru ; Plant Leaves/chemistry/*physiology ; Trees/chemistry/*physiology ; *Tropical Climate ; }, abstract = {Tropical forest leaf albedo (reflectance) greatly impacts how much energy the planet absorbs; however; little is known about how it might be impacted by climate change. Here, we measure leaf traits and leaf albedo at ten 1-ha plots along a 3,200-m elevation gradient in Peru. Leaf mass per area (LMA) decreased with warmer temperatures along the elevation gradient; the distribution of LMA was positively skewed at all sites indicating a shift in LMA towards a warmer climate and future reduced tropical LMA. Reduced LMA was significantly (P < 0.0001) correlated with reduced leaf near-infrared (NIR) albedo; community-weighted mean NIR albedo significantly (P < 0.01) decreased as temperature increased. A potential future 2 °C increase in tropical temperatures could reduce lowland tropical leaf LMA by 6-7 g m[-2] (5-6%) and reduce leaf NIR albedo by 0.0015-0.002 units. Reduced NIR albedo means that leaves are darker and absorb more of the Sun's energy. Climate simulations indicate this increased absorbed energy will warm tropical forests more at high CO2 conditions with proportionately more energy going towards heating and less towards evapotranspiration and cloud formation.}, } @article {pmid30453986, year = {2018}, author = {Cazer, CL and Volkova, VV and Gröhn, YT}, title = {Expanding behavior pattern sensitivity analysis with model selection and survival analysis.}, journal = {BMC veterinary research}, volume = {14}, number = {1}, pages = {355}, pmid = {30453986}, issn = {1746-6148}, support = {T32 OD011000/OD/NIH HHS/United States ; 2016-68003-24607//National Institute of Food and Agriculture/ ; T32ODO011000//NIH Office of the Director/ ; }, mesh = {Administration, Oral ; Animals ; Anti-Bacterial Agents/pharmacokinetics/pharmacology/therapeutic use ; Cattle/microbiology ; Chlortetracycline/pharmacokinetics/pharmacology/therapeutic use ; Data Interpretation, Statistical ; Gastrointestinal Microbiome/drug effects ; Linear Models ; Male ; *Models, Theoretical ; Proportional Hazards Models ; *Survival Analysis ; Tetracycline Resistance ; }, abstract = {BACKGROUND: Sensitivity analysis is an essential step in mathematical modeling because it identifies parameters with a strong influence on model output, due to natural variation or uncertainty in the parameter values. Recently behavior pattern sensitivity analysis has been suggested as a method for sensitivity analyses on models with more than one mode of output behavior. The model output is classified by behavior mode and several behavior pattern measures, defined by the researcher, are calculated for each behavior mode. Significant associations between model inputs and outputs are identified by building linear regression models with the model parameters as independent variables and the behavior pattern measures as the dependent variables. We applied the behavior pattern sensitivity analysis to a mathematical model of tetracycline-resistant enteric bacteria in beef cattle administered chlortetracycline orally. The model included 29 parameters related to bacterial population dynamics, chlortetracycline pharmacokinetics and pharmacodynamics. The prevalence of enteric resistance during and after chlortetracycline administration was the model output. Cox proportional hazard models were used when linear regression assumptions were not met.

RESULTS: We have expanded the behavior pattern sensitivity analysis procedure by incorporating model selection techniques to produce parsimonious linear regression models that efficiently prioritize input parameters. We also demonstrate how to address common violations of linear regression model assumptions. Finally, we explore the semi-parametric Cox proportional hazards model as an alternative to linear regression for situations with censored data. In the example mathematical model, the resistant bacteria exhibited three behaviors during the simulation period: (1) increasing, (2) decreasing, and (3) increasing during antimicrobial therapy and decreasing after therapy ceases. The behavior pattern sensitivity analysis identified bacterial population parameters as high importance in determining the trajectory of the resistant bacteria population.

CONCLUSIONS: Interventions aimed at the enteric bacterial population ecology, such as diet changes, may be effective at reducing the prevalence of tetracycline-resistant enteric bacteria in beef cattle. Behavior pattern sensitivity analysis is a useful and flexible tool for conducting a sensitivity analysis on models with varied output behavior, enabling prioritization of input parameters via regression model selection techniques. Cox proportional hazard models are an alternative to linear regression when behavior pattern measures are censored or linear regression assumptions cannot be met.}, } @article {pmid30446977, year = {2019}, author = {VanDam, M and De Palma, P}, title = {A modular, extensible approach to massive ecologically valid behavioral data.}, journal = {Behavior research methods}, volume = {51}, number = {4}, pages = {1754-1765}, doi = {10.3758/s13428-018-1167-8}, pmid = {30446977}, issn = {1554-3528}, support = {R01 DC004969/DC/NIDCD NIH HHS/United States ; }, mesh = {Adult ; Automation ; *Behavior ; Child ; Databases, Factual ; Female ; Humans ; Male ; *Speech ; Speech Perception ; Speech Recognition Software ; }, abstract = {We explore here the application of modern computer hardware and software to the collection and analysis of behavioral data. We discuss the issues of ecological validity, storage and processing, data permanence, automation, validity, and algorithmic determinism. Taking the modern landscape into account, we demonstrate several varying projects we have recently undertaken as proofs of concept of the viability and utility of this approach. In particular, we describe four research projects, which involve work on child-directed speech; the application of automatic methods to clinical populations, including children with hearing loss; quality control and the assessment of validity; and the sharing of data in a public database. We conclude by pointing out how the methodology described here can be extended to a wide variety of interdisciplinary and detailed projects that are likely to lead to better science and improved outcomes for populations served by the behavioral, social, and health sciences.}, } @article {pmid30446752, year = {2018}, author = {Felipe-Lucia, MR and Soliveres, S and Penone, C and Manning, P and van der Plas, F and Boch, S and Prati, D and Ammer, C and Schall, P and Gossner, MM and Bauhus, J and Buscot, F and Blaser, S and Blüthgen, N and de Frutos, A and Ehbrecht, M and Frank, K and Goldmann, K and Hänsel, F and Jung, K and Kahl, T and Nauss, T and Oelmann, Y and Pena, R and Polle, A and Renner, S and Schloter, M and Schöning, I and Schrumpf, M and Schulze, ED and Solly, E and Sorkau, E and Stempfhuber, B and Tschapka, M and Weisser, WW and Wubet, T and Fischer, M and Allan, E}, title = {Multiple forest attributes underpin the supply of multiple ecosystem services.}, journal = {Nature communications}, volume = {9}, number = {1}, pages = {4839}, pmid = {30446752}, issn = {2041-1723}, mesh = {Conservation of Natural Resources/*methods ; Ecosystem ; Europe ; Forestry/*methods/trends ; *Forests ; Humans ; Trees/*physiology ; }, abstract = {Trade-offs and synergies in the supply of forest ecosystem services are common but the drivers of these relationships are poorly understood. To guide management that seeks to promote multiple services, we investigated the relationships between 12 stand-level forest attributes, including structure, composition, heterogeneity and plant diversity, plus 4 environmental factors, and proxies for 14 ecosystem services in 150 temperate forest plots. Our results show that forest attributes are the best predictors of most ecosystem services and are also good predictors of several synergies and trade-offs between services. Environmental factors also play an important role, mostly in combination with forest attributes. Our study suggests that managing forests to increase structural heterogeneity, maintain large trees, and canopy gaps would promote the supply of multiple ecosystem services. These results highlight the potential for forest management to encourage multifunctional forests and suggest that a coordinated landscape-scale strategy could help to mitigate trade-offs in human-dominated landscapes.}, } @article {pmid30446680, year = {2018}, author = {Dettori, S and Filigheddu, MR and Deplano, G and Molgora, JE and Ruiu, M and Sedda, L}, title = {Employing a spatio-temporal contingency table for the analysis of cork oak cover change in the Sa Serra region of Sardinia.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {16946}, pmid = {30446680}, issn = {2045-2322}, mesh = {Agriculture/*methods ; Algorithms ; Conservation of Natural Resources/methods ; Ecosystem ; *Forests ; Geography ; Italy ; Models, Theoretical ; Quercus/*growth & development ; *Spatio-Temporal Analysis ; }, abstract = {Land cover change analyses are common and, especially in the absence of explanatory variables, they are mainly carried out by employing qualitative methods such as transition matrices or raster operations. These methods do not provide any estimation of the statistical significance of the changes, or the uncertainty of the model and data, and are usually limited in supporting explicit biological/ecological interpretation of the processes determining the changes. Here we show how the original nearest-neighbour contingency table, proposed by Dixon to evaluate spatial segregation, has been extended to the temporal domain to map the intensity, statistical significance and uncertainty of land cover changes. This index was then employed to quantify the changes in cork oak forest cover between 1998 and 2016 in the Sa Serra region of Sardinia (Italy). The method showed that most statistically significant cork oak losses were concentrated in the centre of Sa Serra and characterised by high intensity. A spatial binomial-logit generalised linear model estimated the probability of changes occurring in the area but not the type of change. We show how the spatio-temporal Dixon's index can be an attractive alternative to other land cover change analysis methods, since it provides a robust statistical framework and facilitates direct biological/ecological interpretation.}, } @article {pmid30446557, year = {2019}, author = {Srikumar, S and Cao, Y and Yan, Q and Van Hoorde, K and Nguyen, S and Cooney, S and Gopinath, GR and Tall, BD and Sivasankaran, SK and Lehner, A and Stephan, R and Fanning, S}, title = {RNA Sequencing-Based Transcriptional Overview of Xerotolerance in Cronobacter sakazakii SP291.}, journal = {Applied and environmental microbiology}, volume = {85}, number = {3}, pages = {}, pmid = {30446557}, issn = {1098-5336}, mesh = {Bacterial Proteins/genetics/metabolism ; Cronobacter sakazakii/classification/*genetics/isolation & purification/metabolism ; Enterobacteriaceae Infections/*microbiology ; Humans ; Infant Formula/microbiology ; RNA, Bacterial/*genetics/metabolism ; Sequence Analysis, RNA ; Transcription, Genetic ; Trehalose/metabolism ; }, abstract = {Cronobacter sakazakii is a xerotolerant neonatal pathogen epidemiologically linked to powdered infant food formula, often resulting in high mortality rates. Here, we used transcriptome sequencing (RNA-seq) to provide transcriptional insights into the survival of C. sakazakii in desiccated conditions. Our RNA-seq data show that about 22% of the total C. sakazakii genes were significantly upregulated and 9% were downregulated during desiccation survival. When reverse transcription-quantitative PCR (qRT-PCR) was used to validate the RNA-seq data, we found that the primary desiccation response was gradually downregulated during the tested 4 hours of desiccation, while the secondary response remained constitutively upregulated. The 4-hour desiccation tolerance of C. sakazakii was dependent on the immediate microenvironment surrounding the bacterial cell. The removal of Trypticase soy broth (TSB) salts and the introduction of sterile infant formula residues in the microenvironment enhanced the desiccation survival of C. sakazakii SP291. The trehalose biosynthetic pathway encoded by otsA and otsB, a prominent secondary bacterial desiccation response, was highly upregulated in desiccated C. sakazakiiC. sakazakii SP291 ΔotsAB was significantly inhibited compared with the isogenic wild type in an 8-hour desiccation survival assay, confirming the physiological importance of trehalose in desiccation survival. Overall, we provide a comprehensive RNA-seq-based transcriptional overview along with confirmation of the phenotypic importance of trehalose metabolism in Cronobacter sakazakii during desiccation.IMPORTANCECronobacter sakazakii is a pathogen of importance to neonatal health and is known to persist in dry food matrices, such as powdered infant formula (PIF) and its associated production environment. When infections are reported in neonates, mortality rates can be high. The success of this bacterium in surviving these low-moisture environments suggests that Cronobacter species can respond to a variety of environmental signals. Therefore, understanding those signals that aid the persistence of this pathogen in these ecological niches is an important step toward the development of strategies to reduce the risk of contamination of PIF. This research led to the identification of candidate genes that play a role in the persistence of this pathogen in desiccated conditions and, thereby, serve as a model target to design future strategies to mitigate PIF-associated survival of C. sakazakii.}, } @article {pmid30445133, year = {2019}, author = {Zheng, C and Li, Z and Yang, H and Zhang, T and Niu, H and Liu, D and Wang, J and Ying, H}, title = {Computation-aided rational design of a halophilic choline kinase for cytidine diphosphate choline production in high-salt condition.}, journal = {Journal of biotechnology}, volume = {290}, number = {}, pages = {59-66}, doi = {10.1016/j.jbiotec.2018.11.008}, pmid = {30445133}, issn = {1873-4863}, mesh = {Bacterial Proteins/chemistry/genetics/metabolism ; *Choline Kinase/chemistry/genetics/metabolism ; Computational Biology/*methods ; Cytidine Diphosphate Choline/*metabolism ; Enzyme Stability ; Escherichia coli/genetics ; Models, Molecular ; Protein Engineering/*methods ; Recombinant Proteins/chemistry/genetics/metabolism ; Salts/*chemistry ; Surface Properties ; }, abstract = {Biocatalysis has become the main approach to produce cytidine diphosphate choline (CDP-choline), which has been applied for treatment of acute craniocerebral injury and consciousness after brain surgery. However, salt accumulates with the production and inhibits enzyme activity, and eventually reduces yield and product accumulation rate. Our work provided a possible solution to this problem by applying a computational designed halophilic choline kinase. The halotolerant CKI (choline kinase) was designed following a unique strategy considering the most variable residue positions on the protein surface among target enzymes from different sources. The basic and neutral surface residues were replaced with acidic ones. This approach was enlightened by features of natural halophilic enzymes. Mutants in the work represented higher catalytic activities and IC50 (inhibit activity by 50%) at high salt concentrations (over 1200 mM). Furthermore, when the mutant was used in fed-batch production, the CDP-choline accumulation rate doubled comparing with process using wild-type CKI at acetate concentration of over 700 mM. The maximum titer was 151 ± 3.2 mM, the productivity was 5.8 ± 0.1 mM·L[-1] h[-1], and molar yield to CMP and utilization efficiency of energy were 85.3 and 63.5%. The idea of computational design in our work can also be applied to modify other enzymes in industry, and sheds light on alleviating effect of salt accumulation during industrial manufacturing process.}, } @article {pmid30442308, year = {2018}, author = {Khuntikeo, N and Thinkhamrop, B and Bundhamcharoen, K and Andrews, RH and Grundy-Warr, C and Yongvanit, P and Loilome, W and Chamadol, N and Kosuwan, W and Sithithaworn, P and Petney, TN}, title = {The Socioeconomic Burden of Cholangiocarcinoma Associated With Opisthorchis viverrini Sensu Lato Infection in Northeast Thailand: A Preliminary Analysis.}, journal = {Advances in parasitology}, volume = {102}, number = {}, pages = {141-163}, doi = {10.1016/bs.apar.2018.06.003}, pmid = {30442308}, issn = {2163-6079}, mesh = {Adult ; Animals ; Bile Duct Neoplasms/economics/epidemiology/*etiology ; Cholangiocarcinoma/economics/epidemiology/*etiology ; Female ; Humans ; Male ; Middle Aged ; Opisthorchiasis/*complications/economics/epidemiology ; Opisthorchis ; Socioeconomic Factors ; Thailand ; }, abstract = {The northeast of Thailand, which is the poorest region of the country, has the highest incidence of cholangiocarcinoma (CCA) worldwide. This is associated with infection with the liver fluke Opisthorchis viverrini. Although an estimated 20,000 people die every year of this disease, the socioeconomic impact of this mortality on the victims' family and the community in which he or she lived remains unknown. Here, we provide background information on the socioeconomic groups most effected by CCA and provide a qualitative estimate of the likely financial burden on the family and community. Most victims of CCA are small-scale farmers. Mortality occurs most commonly in males between the ages of 40 and 65, having either children or grandchildren to support. Costs can be divided between premortality with the family paying for transport and accommodation to the hospital, as well as costs not covered by the Thai Universal Health Coverage scheme. The main costs, however, are likely to be postmortem with loss of income and potentially the loss of a major contributor to farm work. What is urgently required is a quantitative estimate of the costs of CCA and long-term studies of the families and communities affected to determine where and how the burden of CCA falls.}, } @article {pmid30431668, year = {2018}, author = {Portnoy, GA and Relyea, MR and Decker, S and Shamaskin-Garroway, A and Driscoll, M and Brandt, CA and Haskell, SG}, title = {Understanding Gender Differences in Resilience Among Veterans: Trauma History and Social Ecology.}, journal = {Journal of traumatic stress}, volume = {31}, number = {6}, pages = {845-855}, doi = {10.1002/jts.22341}, pmid = {30431668}, issn = {1573-6598}, support = {VA IIR 12-118//Health Services Research and Development/International ; }, mesh = {Adult ; Afghan Campaign 2001- ; Exposure to Violence/psychology ; Female ; Humans ; Iraq War, 2003-2011 ; Longitudinal Studies ; Male ; *Resilience, Psychological ; Sex Factors ; Sex Offenses/psychology ; Social Environment ; Stress Disorders, Post-Traumatic/etiology/*psychology ; Surveys and Questionnaires ; United States/epidemiology ; Veterans/*psychology ; }, abstract = {A social-ecological framework for resilience underscores the importance of conceptualizing individuals embedded within their context when evaluating a person's vulnerability and adaptation to stress. Despite a high level of trauma exposure, most veterans exhibit psychological resilience following a traumatic event. Interpersonal trauma is associated with poorer psychological outcomes than noninterpersonal trauma and is experienced more frequently across the lifespan by women as compared to men. In the present study, we examined gender differences in trauma exposure, resilience, and protective factors among veterans. Participants included 665 veterans who completed a baseline survey assessing traumatic events; 544 veterans (81.8%) completed a 1-year follow-up survey assessing resilience, combat exposure, deployment social support, deployment preparedness, and military sexual trauma (MST). Principal component analyses revealed the Traumatic Life Events Questionnaire categorized into four meaningful components: sexual abuse, interpersonal violence, stranger violence, and accidents/unexpected trauma. Women reported greater exposure to sexual abuse, d = 0.76; interpersonal violence, d = 0.31; and MST, Cramer's V = 0.54; men reported greater exposure to stranger violence, accidents/unexpected trauma, and combat exposure, ds = 0.24-0.55. Compared to women, men also reported greater social support during deployment, d = 0.46. Hierarchical linear regression indicated that men's resilience scores were higher than women's, β = .10, p = .032, yet this association was no longer significant once we accounted for trauma type, β = .07, p = .197. Results indicate that trauma type is central to resilience and suggest one must consider the social-ecological context that can promote or inhibit resilient processes.}, } @article {pmid30430701, year = {2019}, author = {Varela, MR and Patrício, AR and Anderson, K and Broderick, AC and DeBell, L and Hawkes, LA and Tilley, D and Snape, RTE and Westoby, MJ and Godley, BJ}, title = {Assessing climate change associated sea-level rise impacts on sea turtle nesting beaches using drones, photogrammetry and a novel GPS system.}, journal = {Global change biology}, volume = {25}, number = {2}, pages = {753-762}, doi = {10.1111/gcb.14526}, pmid = {30430701}, issn = {1365-2486}, mesh = {Aircraft ; Animals ; *Climate Change ; *Ecosystem ; Environmental Monitoring/instrumentation/*methods ; Geographic Information Systems/instrumentation ; *Nesting Behavior ; Photogrammetry/methods ; Turtles/*physiology ; }, abstract = {Climate change associated sea-level rise (SLR) is expected to have profound impacts on coastal areas, affecting many species, including sea turtles which depend on these habitats for egg incubation. Being able to accurately model beach topography using digital terrain models (DTMs) is therefore crucial to project SLR impacts and develop effective conservation strategies. Traditional survey methods are typically low-cost with low accuracy or high-cost with high accuracy. We present a novel combination of drone-based photogrammetry and a low-cost and portable real-time kinematic (RTK) GPS to create DTMs which are highly accurate (<10 cm error) and visually realistic. This methodology is ideal for surveying coastal sites, can be broadly applied to other species and habitats, and is a relevant tool in supporting the development of Specially Protected Areas. Here, we applied this method as a case-study to project three SLR scenarios (0.48, 0.63 and 1.20 m) and assess the future vulnerability and viability of a key nesting habitat for sympatric loggerhead (Caretta caretta) and green turtle (Chelonia mydas) at a key rookery in the Mediterranean. We combined the DTM with 5 years of nest survey data describing location and clutch depth, to identify (a) regions with highest nest densities, (b) nest elevation by species and beach, and (c) estimated proportion of nests inundated under each SLR scenario. On average, green turtles nested at higher elevations than loggerheads (1.8 m vs. 1.32 m, respectively). However, because green turtles dig deeper nests than loggerheads (0.76 m vs. 0.50 m, respectively), these were at similar risk of inundation. For a SLR of 1.2 m, we estimated a loss of 67.3% for loggerhead turtle nests and 59.1% for green turtle nests. Existing natural and artificial barriers may affect the ability of these nesting habitats to remain suitable for nesting through beach migration.}, } @article {pmid30429613, year = {2018}, author = {Fadrique, B and Báez, S and Duque, Á and Malizia, A and Blundo, C and Carilla, J and Osinaga-Acosta, O and Malizia, L and Silman, M and Farfán-Ríos, W and Malhi, Y and Young, KR and Cuesta C, F and Homeier, J and Peralvo, M and Pinto, E and Jadan, O and Aguirre, N and Aguirre, Z and Feeley, KJ}, title = {Widespread but heterogeneous responses of Andean forests to climate change.}, journal = {Nature}, volume = {564}, number = {7735}, pages = {207-212}, pmid = {30429613}, issn = {1476-4687}, support = {DEB-1350125//US National Science Foundation/International ; DEB-1754647//US National Science Foundation/International ; DEB-1258112//US National Science Foundation/International ; EAR-1338694//US National Science Foundation/International ; }, mesh = {*Acclimatization ; *Altitude ; *Biodiversity ; Databases, Factual ; Disaster Planning/trends ; Disasters/prevention & control ; Forecasting/methods ; *Forests ; *Global Warming ; Species Specificity ; *Temperature ; Trees/*classification/*physiology ; Tropical Climate ; }, abstract = {Global warming is forcing many species to shift their distributions upward, causing consequent changes in the compositions of species that occur at specific locations. This prediction remains largely untested for tropical trees. Here we show, using a database of nearly 200 Andean forest plot inventories spread across more than 33.5° latitude (from 26.8° S to 7.1° N) and 3,000-m elevation (from 360 to 3,360 m above sea level), that tropical and subtropical tree communities are experiencing directional shifts in composition towards having greater relative abundances of species from lower, warmer elevations. Although this phenomenon of 'thermophilization' is widespread throughout the Andes, the rates of compositional change are not uniform across elevations. The observed heterogeneity in thermophilization rates is probably because of different warming rates and/or the presence of specialized tree communities at ecotones (that is, at the transitions between distinct habitats, such as at the timberline or at the base of the cloud forest). Understanding the factors that determine the directions and rates of compositional changes will enable us to better predict, and potentially mitigate, the effects of climate change on tropical forests.}, } @article {pmid30427897, year = {2018}, author = {McCurrie, CH and Crone, DL and Bigelow, F and Laham, SM}, title = {Moral and Affective Film Set (MAAFS): A normed moral video database.}, journal = {PloS one}, volume = {13}, number = {11}, pages = {e0206604}, pmid = {30427897}, issn = {1932-6203}, mesh = {Adult ; *Affect ; Crowdsourcing ; *Databases as Topic ; Female ; Humans ; Male ; *Morals ; *Motion Pictures ; Psychological Theory ; }, abstract = {Moral psychology has relied nearly exclusively on text stimuli in the development and testing of theories. However, text stimuli lack the rich variety of morally-relevant social and contextual cues available in everyday interactions. A consequence of this pervasive ecological invalidity may be that moral psychological theories are mischaracterized by an overreliance on cue-impoverished moral stimuli. We address this limitation by developing a cue-rich Moral and Affective Film Set (MAAFS). We crowd-sourced videos of moral behaviours, using previously validated text stimuli and definitions of moral foundations as a guide for content. Crowd-sourced clips were rated by 322 American and 253 Australian participants on a range of moral and affective dimensions, including wrongness, moral foundation relevance, punishment, arousal, discrete emotion-relevance, clarity, previous exposure, and how weird/uncommon the moral acts were. The final stimulus set contained sixty nine moral videos. Ratings confirmed that the videos are reliably rated as morally wrong and feature a variety of moral concerns. The validation process revealed features that make the MAAFS useful for future research: (1) the MAAFS includes a range of videos that depict everyday transgressions, (2) certain videos evoke negative emotions at an intensity comparable to mood induction films, (3) the videos are largely novel: participants had never seen more than 90% of the videos. We anticipate the MAAFS will be a particularly valuable tool for researchers in moral psychology who seek to study morality in scenarios that approximate real-life. However, the MAAFS may be valuable for other fields of psychology, for example, affective scientists may use these videos as a mood induction procedure. The complete stimulus set, links to videos, and normative statistics can be accessed at osf.io/8w3en.}, } @article {pmid30427852, year = {2018}, author = {Brito, TL and Campos, AB and Bastiaan von Meijenfeldt, FA and Daniel, JP and Ribeiro, GB and Silva, GGZ and Wilke, DV and de Moraes, DT and Dutilh, BE and Meirelles, PM and Trindade-Silva, AE}, title = {The gill-associated microbiome is the main source of wood plant polysaccharide hydrolases and secondary metabolite gene clusters in the mangrove shipworm Neoteredo reynei.}, journal = {PloS one}, volume = {13}, number = {11}, pages = {e0200437}, pmid = {30427852}, issn = {1932-6203}, mesh = {Animals ; Bivalvia/*microbiology/physiology ; Gammaproteobacteria/*enzymology/genetics/*physiology ; Genomics ; Gills/microbiology ; Glycoside Hydrolases/genetics/*metabolism ; Metagenome ; Microbiota ; Multigene Family ; Phylogeny ; Polysaccharides/*metabolism ; Secondary Metabolism ; *Symbiosis ; Wood/metabolism/parasitology ; }, abstract = {Teredinidae are a family of highly adapted wood-feeding and wood-boring bivalves, commonly known as shipworms, whose evolution is linked to the acquisition of cellulolytic gammaproteobacterial symbionts harbored in bacteriocytes within the gills. In the present work we applied metagenomics to characterize microbiomes of the gills and digestive tract of Neoteredo reynei, a mangrove-adapted shipworm species found over a large range of the Brazilian coast. Comparative metagenomics grouped the gill symbiont community of different N. reynei specimens, indicating closely related bacterial types are shared. Similarly, the intestine and digestive gland communities were related, yet were more diverse than and showed no overlap with the gill community. Annotation of assembled metagenomic contigs revealed that the gill symbiotic community of N. reynei encodes a plethora of plant cell wall polysaccharides degrading glycoside hydrolase encoding genes, and Biosynthetic Gene Clusters (BGCs). In contrast, the digestive tract microbiomes seem to play little role in wood digestion and secondary metabolites biosynthesis. Metagenome binning recovered the nearly complete genome sequences of two symbiotic Teredinibacter strains from the gills, a representative of Teredinibacter turnerae "clade I" strain, and a yet to be cultivated Teredinibacter sp. type. These Teredinibacter genomes, as well as un-binned gill-derived gammaproteobacteria contigs, also include an endo-β-1,4-xylanase/acetylxylan esterase multi-catalytic carbohydrate-active enzyme, and a trans-acyltransferase polyketide synthase (trans-AT PKS) gene cluster with the gene cassette for generating β-branching on complex polyketides. Finally, we use multivariate analyses to show that the secondary metabolome from the genomes of Teredinibacter representatives, including genomes binned from N. reynei gills' metagenomes presented herein, stands out within the Cellvibrionaceae family by size, and enrichments for polyketide, nonribosomal peptide and hybrid BGCs. Results presented here add to the growing characterization of shipworm symbiotic microbiomes and indicate that the N. reynei gill gammaproteobacterial community is a prolific source of biotechnologically relevant enzymes for wood-digestion and bioactive compounds production.}, } @article {pmid30427452, year = {2018}, author = {Amaral, TLM and Amaral, CA and Miranda Filho, AL and Monteiro, GTR}, title = {Trends and multiple causes of death due to chronic renal failure in a municipality in the Brazilian Amazon.}, journal = {Ciencia & saude coletiva}, volume = {23}, number = {11}, pages = {3821-3828}, doi = {10.1590/1413-812320182311.29902016}, pmid = {30427452}, issn = {1678-4561}, support = {001/WHO_/World Health Organization/International ; }, mesh = {Adult ; Aged ; Aged, 80 and over ; Brazil/epidemiology ; Cause of Death/*trends ; Databases, Factual ; Diabetes Mellitus/epidemiology/etiology/*mortality ; Female ; Humans ; Hypertension/epidemiology/etiology/*mortality ; Kidney Failure, Chronic/complications/epidemiology/*mortality ; Linear Models ; Male ; Middle Aged ; Poisson Distribution ; Respiratory Tract Diseases/epidemiology/mortality ; }, abstract = {This study examined the mortality trend due to chronic renal failure (CRF) and verified the underlying and associated causes for this trend in the capital of the state of Acre in the Brazilian Amazon. This ecological study used data provided by DATASUS related to mortality due to CRF, which occurred between 1986 and 2012 for male and female residents of the city of Rio Branco, Acre, Brazil. The estimated annual percentage chance (EAPC) was calculated by using Poisson log-linear regression and utilizing the Joinpoint program. The results showed that the adjusted mortality rates due to CRF, with correction, ranged from 15.4 per 100,000 inhabitants in 1986 to 4.0 per 100,000 inhabitants in 2012. The EAPC was -3.5% from 1986- 2012. Deaths by CRF presented associated causes such as respiratory diseases, pneumonia and pulmonary edema, septicemias and poorly defined signs and symptoms. When CRF was analyzed as an associated cause of death, the main primary causes of death were hypertensive diseases and diabetes. Thus, there was a decrease in mortality due to CRF as an underlying cause during the period studied; however, preventive and heath care measures should be maintained.}, } @article {pmid30426377, year = {2018}, author = {Al-Weshah, RA and Yihdego, Y}, title = {Multi-criteria decision approach for evaluation, ranking, and selection of remediation options: case of polluted groundwater, Kuwait.}, journal = {Environmental science and pollution research international}, volume = {25}, number = {36}, pages = {36039-36045}, pmid = {30426377}, issn = {1614-7499}, mesh = {Cities ; Decision Support Techniques ; Environmental Monitoring ; Environmental Restoration and Remediation/economics/*methods ; Groundwater/*chemistry ; Kuwait ; Petroleum Pollution ; Seawater ; *Water Pollution, Chemical/analysis ; Water Purification/economics/*methods ; }, abstract = {Freshwater groundwater resources at north Kuwait were contaminated by infiltrated oil as well as sea water that was used to fight the oil-well fires during the liberation of Kuwait in 1991. This paper investigates the feasibility of five remediation options to restore the polluted aquifers. These options include: (i) pump and treat of contaminated groundwater; (ii) cleaning the aquifer formation; (iii) construction of additional desalination plant; (iv) constructing additional storage tanks, and (v) development of artificial aquifer recharge schemes. The basis for this assessment study is to supply minimum basic drinking water to Kuwait City at a total rate of 50,000 m[3]/day in an emergency for up to one year based on essential basic need of 32 liters per capita per day. To compare these options, a decision matrix to select suitable remediation options using Multiple Criteria Decision Analysis (MCDA) approach is developed. The cost was given a relative weight of 20 whereas other criteria are given weight of 10. Based on these MCDA scores, it was found that option 3, namely, establishing an additional water desalination plant, is the most feasible option followed by option 5, artificial recharge of aquifers.}, } @article {pmid30425147, year = {2018}, author = {Su, X and Jing, G and McDonald, D and Wang, H and Wang, Z and Gonzalez, A and Sun, Z and Huang, S and Navas, J and Knight, R and Xu, J}, title = {Identifying and Predicting Novelty in Microbiome Studies.}, journal = {mBio}, volume = {9}, number = {6}, pages = {}, pmid = {30425147}, issn = {2150-7511}, mesh = {*Computational Biology ; *Databases, Factual ; Humans ; Microbiota/*genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {With the expansion of microbiome sequencing globally, a key challenge is to relate new microbiome samples to the existing space of microbiome samples. Here, we present Microbiome Search Engine (MSE), which enables the rapid search of query microbiome samples against a large, well-curated reference microbiome database organized by taxonomic similarity at the whole-microbiome level. Tracking the microbiome novelty score (MNS) over 8 years of microbiome depositions based on searching in more than 100,000 global 16S rRNA gene amplicon samples, we detected that the structural novelty of human microbiomes is approaching saturation and likely bounded, whereas that in environmental habitats remains 5 times higher. Via the microbiome focus index (MFI), which is derived from the MNS and microbiome attention score (MAS), we objectively track and compare the structural-novelty and attracted-attention scores of individual microbiome samples and projects, and we predict future trends in the field. For example, marine and indoor environments and mother-baby interactions are likely to receive disproportionate additional attention based on recent trends. Therefore, MNS, MAS, and MFI are proposed "alt-metrics" for evaluating a microbiome project or prospective developments in the microbiome field, both of which are done in the context of existing microbiome big data.IMPORTANCE We introduce two concepts to quantify the novelty of a microbiome. The first, the microbiome novelty score (MNS), allows identification of microbiomes that are especially different from what is already sequenced. The second, the microbiome attention score (MAS), allows identification of microbiomes that have many close neighbors, implying that considerable scientific attention is devoted to their study. By computing a microbiome focus index based on the MNS and MAS, we objectively track and compare the novelty and attention scores of individual microbiome samples and projects over time and predict future trends in the field; i.e., we work toward yielding fundamentally new microbiomes rather than filling in the details. Therefore, MNS, MAS, and MFI can serve as "alt-metrics" for evaluating a microbiome project or prospective developments in the microbiome field, both of which are done in the context of existing microbiome big data.}, } @article {pmid30422394, year = {2018}, author = {Feindt, W and Oppenheim, SJ and DeSalle, R and Mehr, S}, title = {Good Citizenship Made Easy: A Step-by-Step Guide to Submitting RNA-Seq Data to NCBI.}, journal = {Current protocols in bioinformatics}, volume = {64}, number = {1}, pages = {e67}, doi = {10.1002/cpbi.67}, pmid = {30422394}, issn = {1934-340X}, support = {//American Museum of Natural History/International ; //Annette Kade Charitable Trust (W.F.)/International ; //Lewis and Dorothy Cullman Program for Molecular Systematics/International ; //Korein Foundation/International ; DBI-1307844//NSF/International ; }, mesh = {*Computational Biology ; *Databases, Genetic ; *Sequence Analysis, RNA ; Transcriptome/genetics ; }, abstract = {The analysis of transcriptome data from non-model organisms contributes to our understanding of diverse aspects of evolutionary biology, including developmental processes, speciation, adaptation, and extinction. Underlying this diversity is one shared feature, the generation of enormous amounts of sequence data. Data availability requirements in most journals oblige researchers to make their raw transcriptome data publicly available, and the databases housed at the National Center for Biotechnology Information (NCBI) are a popular choice for data deposition. Unfortunately, the successful submission of raw sequences to the Sequence Read Archive (SRA) and transcriptome assemblies to the Transcriptome Shotgun Assembly (TSA) can be challenging for novice users, significantly delaying data availability and publication. Here we present two comprehensive protocols for submitting RNA-Seq data to NCBI databases, accompanied by an easy-to-use website that facilitates the timely submission of data by researchers of any experience level. © 2018 by John Wiley & Sons, Inc.}, } @article {pmid30419993, year = {2019}, author = {Lozano-Jaramillo, M and Bastiaansen, JWM and Dessie, T and Komen, H}, title = {Use of geographic information system tools to predict animal breed suitability for different agro-ecological zones.}, journal = {Animal : an international journal of animal bioscience}, volume = {13}, number = {7}, pages = {1536-1543}, pmid = {30419993}, issn = {1751-732X}, mesh = {Animal Husbandry/instrumentation/*methods ; Animals ; Breeding/methods ; *Chickens ; *Environment ; Ethiopia ; Geographic Information Systems/*statistics & numerical data ; }, abstract = {Predicting breed-specific environmental suitability has been problematic in livestock production. Native breeds have low productivity but are thought to be more robust to perform under local conditions than exotic breeds. Attempts to introduce genetically improved exotic breeds are generally unsuccessful, mainly due to the antagonistic environmental conditions. Knowledge of the environmental conditions that are shaping the breed would be needed to determine its suitability to different locations. Here, we present a methodology to predict the suitability of breeds for different agro-ecological zones using Geographic Information Systems tools and predictive habitat distribution models. This methodology was tested on the current distribution of two introduced chicken breeds in Ethiopia: the Koekoek, originally from South Africa, and the Fayoumi, originally from Egypt. Cross-validation results show this methodology to be effective in predicting breed suitability for specific environmental conditions. Furthermore, the model predicts suitable areas of the country where the breeds could be introduced. The specific climatic parameters that explained the potential distribution of each of the breeds were similar to the environment from which the breeds originated. This novel methodology finds application in livestock programs, allowing for a more informed decision when designing breeding programs and introduction programs, and increases our understanding of the role of the environment in livestock productivity.}, } @article {pmid30419142, year = {2018}, author = {Muthye, V and Lavrov, DV}, title = {Characterization of mitochondrial proteomes of nonbilaterian animals.}, journal = {IUBMB life}, volume = {70}, number = {12}, pages = {1289-1301}, doi = {10.1002/iub.1961}, pmid = {30419142}, issn = {1521-6551}, mesh = {Animals ; Cell Nucleus/genetics ; Computational Biology ; Ctenophora/*genetics ; DNA, Mitochondrial ; *Evolution, Molecular ; Humans ; Mitochondria/*genetics ; Mitochondrial Proteins/*genetics ; Phylogeny ; Proteome/genetics ; }, abstract = {Mitochondria require ~1,500 proteins for their maintenance and proper functionality, which constitute the mitochondrial proteome (mt-proteome). Although a few of these proteins, mostly subunits of the electron transport chain complexes, are encoded in mitochondrial DNA (mtDNA), the vast majority are encoded in the nuclear genome and imported to the organelle. Previous studies have shown a continuous and complex evolution of mt-proteome among eukaryotes. However, there was less attention paid to mt-proteome evolution within Metazoa, presumably because animal mtDNA and, by extension, animal mitochondria are often considered to be uniform. In this analysis, two bioinformatic approaches (Orthologue-detection and Mitochondrial Targeting Sequence prediction) were used to identify mt-proteins in 23 species from four nonbilaterian phyla: Cnidaria, Ctenophora, Placozoa, and Porifera, as well as two choanoflagellates, the closest animal relatives. Our results revealed a large variation in mt-proteome in nonbilaterian animals in size and composition. Myxozoans, highly reduced cnidarian parasites, possessed the smallest inferred mitochondrial proteomes, while calcareous sponges possessed the largest. About 513 mitochondrial orthologous groups were present in all nonbilaterian phyla and human. Interestingly, 42 human mitochondrial proteins were not identified in any nonbilaterian species studied and represent putative innovations along the bilaterian branch. Several of these proteins were involved in apoptosis and innate immunity, two processes known to evolve within Metazoa. Conversely, several proteins identified as mitochondrial in nonbilaterian phyla and animal outgroups were absent in human, representing cases of possible loss. Finally, a few human cytosolic proteins, such as histones and cytosolic ribosomal proteins, were predicted to be targeted to mitochondria in nonbilaterian animals. Overall, our analysis provides the first step in characterization of mt-proteomes in nonbilaterian animals and understanding evolution of animal mt-proteome. © 2018 IUBMB Life, 70(12):1289-1301, 2018.}, } @article {pmid30418376, year = {2018}, author = {Okpala, P}, title = {Balancing Quality Healthcare Services and Costs Through Collaborative Leadership.}, journal = {Journal of healthcare management / American College of Healthcare Executives}, volume = {63}, number = {6}, pages = {e148-e157}, doi = {10.1097/JHM-D-18-00020}, pmid = {30418376}, issn = {1096-9012}, mesh = {Community Health Services/*economics/*standards ; *Cooperative Behavior ; Cost Control/*organization & administration ; Databases, Factual ; *Health Care Costs ; Humans ; *Leadership ; *Quality of Health Care ; }, abstract = {This review assesses the effectiveness of collaborative leadership strategies in balancing quality healthcare services and costs. Quantitative analysis of 39 studies answered research questions to identify collaborative leadership strategies employed by healthcare managers to address the cost of care, determine the most effective strategies for managing this cost, and evaluate how collaborative leadership's cost-reduction strategies affect quality of care. The intrahospital collaboration strategy was noted to be the most frequently used strategy (53.8%). The other strategies included patient-based collaboration (41.0%) and interorganizational collaboration (17.9%). The patient-based collaborative strategy offered significantly higher cost-reduction effectiveness (31.9% ± 6.005). The cost effectiveness of the intrahospital collaboration (25.3% ± 2.014) and interorganizational collaboration strategy (20.2% ± 4.229) were also significant. The adoption of the patient-based collaboration strategy was associated with enhanced quality of healthcare (62.5%), while the interorganizational collaboration strategy had a greater proportion of noneffect on quality of services (71.4%). Therefore, healthcare leaders should facilitate the adoption of patient-based and interorganizational collaboration strategies to manage healthcare costs.}, } @article {pmid30417109, year = {2018}, author = {Mazel, F and Davis, KM and Loudon, A and Kwong, WK and Groussin, M and Parfrey, LW}, title = {Is Host Filtering the Main Driver of Phylosymbiosis across the Tree of Life?.}, journal = {mSystems}, volume = {3}, number = {5}, pages = {}, pmid = {30417109}, issn = {2379-5077}, abstract = {Host-associated microbiota composition can be conserved over evolutionary time scales. Indeed, closely related species often host similar microbiota; i.e., the composition of their microbiota harbors a phylogenetic signal, a pattern sometimes referred to as "phylosymbiosis." Elucidating the origins of this pattern is important to better understand microbiota ecology and evolution. However, this is hampered by our lack of theoretical expectations and a comprehensive overview of phylosymbiosis prevalence in nature. Here, we use simulations to provide a simple expectation for when we should expect this pattern to occur and then review the literature to document the prevalence and strength of phylosymbiosis across the host tree of life. We demonstrate that phylosymbiosis can readily emerge from a simple ecological filtering process, whereby a given host trait (e.g., gut pH) that varies with host phylogeny (i.e., harbors a phylogenetic signal) filters preadapted microbes. We found marked differences between methods used to detect phylosymbiosis, so we proposed a series of practical recommendations based on using multiple best-performing approaches. Importantly, we found that, while the prevalence of phylosymbiosis is mixed in nature, it appears to be stronger for microbiotas living in internal host compartments (e.g., the gut) than those living in external compartments (e.g., the rhizosphere). We show that phylosymbiosis can theoretically emerge without any intimate, long-term coevolutionary mechanisms and that most phylosymbiosis patterns observed in nature are compatible with a simple ecological process. Deviations from baseline ecological expectations might be used to further explore more complex hypotheses, such as codiversification. IMPORTANCE Phylosymbiosis is a pattern defined as the tendency of closely related species to host microbiota whose compositions resemble each other more than host species drawn at random from the same tree. Understanding the mechanisms behind phylosymbiosis is important because it can shed light on rules governing the assembly of host-associated microbiotas and, potentially, their coevolutionary dynamics with hosts. For example, is phylosymbiosis a result of coevolution, or can it be generated by simple ecological filtering processes? Beyond qualitative theoretical models, quantitative theoretical expectations can provide new insights. For example, deviations from a simple baseline of ecological filtering may be used to test more-complex hypotheses (e.g., coevolution). Here, we use simulations to provide evidence that simple host-related ecological filtering can readily generate phylosymbiosis, and we contrast these predictions with real-world data. We find that while phylosymbiosis is widespread in nature, phylosymbiosis patterns are compatible with a simple ecological model in the majority of taxa. Internal compartments of hosts, such as the animal gut, often display stronger phylosymbiosis than expected from a purely ecological filtering process, suggesting that other mechanisms are also involved.}, } @article {pmid30415649, year = {2019}, author = {Chen, MH and Hsu, JW and Huang, KL and Su, TP and Li, CT and Lin, WC and Tsai, SJ and Cheng, CM and Chang, WH and Pan, TL and Chen, TJ and Bai, YM}, title = {Risk and coaggregation of major psychiatric disorders among first-degree relatives of patients with bipolar disorder: a nationwide population-based study.}, journal = {Psychological medicine}, volume = {49}, number = {14}, pages = {2397-2404}, doi = {10.1017/S003329171800332X}, pmid = {30415649}, issn = {1469-8978}, mesh = {Adolescent ; Adult ; Attention Deficit Disorder with Hyperactivity/genetics ; Autism Spectrum Disorder/genetics ; Bipolar Disorder/*genetics ; Databases, Factual ; Depressive Disorder, Major/genetics ; Diseases in Twins/genetics ; Family Health ; Female ; Genetic Predisposition to Disease/genetics ; Humans ; Male ; Mental Disorders/*genetics ; Middle Aged ; Risk ; Schizophrenia/genetics ; Taiwan ; Young Adult ; }, abstract = {BACKGROUND: Bipolar disorder is a highly heritable mental illness that transmits intergeneratively. Previous studies supported that first-degree relatives (FDRs), such as parents, offspring, and siblings, of patients with bipolar disorder, had a higher risk of bipolar disorder. However, whether FDRs of bipolar patients have an increased risk of schizophrenia, major depressive disorder (MDD), autism spectrum disorder (ASD), and attention deficit hyperactivity disorder (ADHD) remains unclear.

METHODS: Among the entire population in Taiwan, 87 639 patients with bipolar disorder and 188 290 FDRs of patients with bipolar disorder were identified in our study. The relative risks (RRs) of major psychiatric disorders were assessed among FDRs of patients with bipolar disorder.

RESULTS: FDRs of patients with bipolar disorder were more likely to have a higher risk of major psychiatric disorders, including bipolar disorder (RR 6.12, 95% confidence interval (CI) 5.95-6.30), MDD (RR 2.89, 95% CI 2.82-2.96), schizophrenia (RR 2.64, 95% CI 2.55-2.73), ADHD (RR 2.21, 95% CI 2.13-2.30), and ASD (RR 2.10, 95% CI 1.92-2.29), than the total population did. These increased risks for major psychiatric disorders were consistent across different familial kinships, such as parents, offspring, siblings, and twins. A dose-dependent relationship was also found between risk of each major psychiatric disorder and numbers of bipolar patients.

CONCLUSIONS: Our study was the first study to support the familial coaggregation of bipolar disorder with other major psychiatric disorders, including schizophrenia, MDD, ADHD, and ASD, in a Taiwanese (non-Caucasian) population. Given the elevated risks of major psychiatric disorders, the public health government should pay more attention to the mental health of FDRs of patients with bipolar disorder.}, } @article {pmid30415488, year = {2019}, author = {Feng, S and Ru, D and Sun, Y and Mao, K and Milne, R and Liu, J}, title = {Trans-lineage polymorphism and nonbifurcating diversification of the genus Picea.}, journal = {The New phytologist}, volume = {222}, number = {1}, pages = {576-587}, doi = {10.1111/nph.15590}, pmid = {30415488}, issn = {1469-8137}, support = {31590821//National Natural Science Foundation of China/International ; 91731301//National Natural Science Foundation of China/International ; 2017YFC0505203//National Key Research and Development program/International ; //International Collaboration 111 Projects of China/International ; }, mesh = {Cell Nucleus/genetics ; Databases, Genetic ; Gene Flow ; *Genetic Variation ; Genome, Plant ; Haplotypes/genetics ; *Phylogeny ; Picea/*genetics ; *Polymorphism, Genetic ; }, abstract = {Nonbifurcating divergence caused by introgressive hybridization is continuously reported for groups of closely related species. In this study, we aimed to reconstruct the genome-scale classification of deep lineages of the conifer genus Picea, establish their phylogenetic relationships and test the bifurcating hypothesis between deeply branching lineages based on genomic data. We sequenced the transcriptomes of 35 individuals of 27 taxa covering all main lineages of the genus. Four major lineages, comprising three to 12 taxa each, largely consistent with morphological evidence, were recovered across the coalescent and integrated nuclear phylogeny. However, many of the individual gene trees recovered contradict one another. Moreover, the well-supported coalescent tree inferred here differs from previous studies based on various DNA markers, with respect to topology and inter-lineage relationships. We identified the shared polymorphisms between four major lineages. ABBA-BABA tests confirmed the inter-lineage gene flow and thus violated the bifurcating divergence model. Gene flow occurred more frequently between lineages distributed in the same continent than those disjunct between continents. Our results indicate that introgression and nonbifurcating diversification apply, even between deeply branching lineages of the conifer genus Picea.}, } @article {pmid30414117, year = {2019}, author = {Asselman, J}, title = {Bioinformatic Analysis of Methylation Patterns Using Bisulfite Sequencing Data.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1858}, number = {}, pages = {157-175}, doi = {10.1007/978-1-4939-8775-7_12}, pmid = {30414117}, issn = {1940-6029}, mesh = {Animals ; Computational Biology/*methods ; *DNA Methylation ; Epigenesis, Genetic ; *Genome, Insect ; High-Throughput Nucleotide Sequencing/methods ; Insecta/*genetics ; Sequence Analysis, DNA/*methods ; Software ; Sulfites/*chemistry ; }, abstract = {Epigenetic factors, including DNA methylation, play a crucial role in the development, behavior, and stress response of insects yet the analysis of DNA methylation patterns remains quite challenging. This chapter will introduce the different technologies for DNA methylation analysis and present a general methodology for the analysis of DNA methylation patterns using the commonly used technology of bisulfite sequencing. The chapter will give a short overview of the sequencing technology itself and will primarily focus on presenting the bioinformatic and statistical analysis methodology of bisulfite sequencing data to study DNA methylation patterns.}, } @article {pmid30414111, year = {2019}, author = {Waterhouse, RM and Seppey, M and Simão, FA and Zdobnov, EM}, title = {Using BUSCO to Assess Insect Genomic Resources.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1858}, number = {}, pages = {59-74}, doi = {10.1007/978-1-4939-8775-7_6}, pmid = {30414111}, issn = {1940-6029}, mesh = {Animals ; Benchmarking ; Computational Biology/*methods ; Gene Dosage ; *Genome, Insect ; High-Throughput Nucleotide Sequencing/methods ; Insecta/*genetics ; Molecular Sequence Annotation/*methods ; Sequence Analysis, DNA/*methods ; *Software ; *Transcriptome ; }, abstract = {The increasing affordability of sequencing technologies offers many new and exciting opportunities to address a diverse array of biological questions. This is evidenced in entomological research by numerous genomics and transcriptomics studies that attempt to decipher the often complex relationships among different species or orders and to build "omics" resources to drive advancement of the molecular understanding of insect biology. Being able to gauge the quality of the sequencing data is of critical importance to understanding the potential limitations on the types of questions that these data can be reliably used to address. This chapter details the use of the Benchmarking Universal Single-Copy Orthologue (BUSCO) assessment tool to estimate the completeness of transcriptomes, genome assemblies, and annotated gene sets in terms of their expected gene content.}, } @article {pmid30413903, year = {2019}, author = {Sánchez-Giraldo, C and Daza, JM}, title = {Getting better temporal and spatial ecology data for threatened species: using lightweight GPS devices for small primate monitoring in the northern Andes of Colombia.}, journal = {Primates; journal of primatology}, volume = {60}, number = {1}, pages = {93-102}, pmid = {30413903}, issn = {1610-7365}, mesh = {Animals ; Colombia ; Ecology/*methods ; Endangered Species ; Female ; Geographic Information Systems/*instrumentation ; *Homing Behavior ; Male ; Saguinus/*physiology ; }, abstract = {The use of GPS telemetry has been a reliable research tool for the study of primate biology in recent years. Although in the past technological restrictions limited its use mainly to large primates, recent improvements in battery size make it possible to use this technology for small species. We used GPS devices for monitoring two adult white-footed tamarins (Saguinus leucopus) from a free-ranging group, and assessed its applicability for recording spatial and ecological data. GPS devices were operational for 66 and 85 days, recording 221 positions (36.6% acquisition rate; 73% of which were highly accurate) and 3195 activity values for both individuals. Depending on the estimation method, we calculated the home range size for the group to be 19.4 and 22.9 ha, which were within the range for the species in other localities. The animals were active each day for 11 h, with high activity during the early morning. The monkeys showed a constant and alternate use of four sleeping sites with a limited reuse of the same site on consecutive nights. These daily activity and sleeping site use patterns are similar to those reported for other Saguinus species. Based on the kind and quality of the data recorded, we consider GPS telemetry to be an efficient and advantageous method for tracking and obtaining ecological information from S. leucopus. In comparison to other data collection methods, GPS telemetry required fewer personnel and less time commitment to record data without compromising the accuracy of the spatial and activity information we obtained.}, } @article {pmid30413766, year = {2018}, author = {Amiri Moghaddam, J and Crüsemann, M and Alanjary, M and Harms, H and Dávila-Céspedes, A and Blom, J and Poehlein, A and Ziemert, N and König, GM and Schäberle, TF}, title = {Analysis of the Genome and Metabolome of Marine Myxobacteria Reveals High Potential for Biosynthesis of Novel Specialized Metabolites.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {16600}, pmid = {30413766}, issn = {2045-2322}, mesh = {Bacterial Proteins/*genetics ; Computational Biology ; *Genome, Bacterial ; *Metabolome ; Multigene Family ; Myxococcales/classification/genetics/*metabolism ; Phylogeny ; Seawater/*microbiology ; }, abstract = {Comparative genomic/metabolomic analysis is a powerful tool to disclose the potential of microbes for the biosynthesis of novel specialized metabolites. In the group of marine myxobacteria only a limited number of isolated species and sequenced genomes is so far available. However, the few compounds isolated thereof so far show interesting bioactivities and even novel chemical scaffolds; thereby indicating a huge potential for natural product discovery. In this study, all marine myxobacteria with accessible genome data (n = 5), including Haliangium ochraceum DSM 14365, Plesiocystis pacifica DSM 14875, Enhygromyxa salina DSM 15201 and the two newly sequenced species Enhygromyxa salina SWB005 and SWB007, were analyzed. All of these accessible genomes are large (~10 Mb), with a relatively small core genome and many unique coding sequences in each strain. Genome analysis revealed a high variety of biosynthetic gene clusters (BGCs) between the strains and several resistance models and essential core genes indicated the potential to biosynthesize antimicrobial molecules. Polyketides (PKs) and terpenes represented the majority of predicted specialized metabolite BGCs and contributed to the highest share between the strains. BGCs coding for non-ribosomal peptides (NRPs), PK/NRP hybrids and ribosomally synthesized and post-translationally modified peptides (RiPPs) were mostly strain specific. These results were in line with the metabolomic analysis, which revealed a high diversity of the chemical features between the strains. Only 6-11% of the metabolome was shared between all the investigated strains, which correlates to the small core genome of these bacteria (13-16% of each genome). In addition, the compound enhygrolide A, known from E. salina SWB005, was detected for the first time and structurally elucidated from Enhygromyxa salina SWB006. The here acquired data corroborate that these microorganisms represent a most promising source for the detection of novel specialized metabolites.}, } @article {pmid30413497, year = {2018}, author = {Gadroen, K and Dodd, CN and Masclee, GMC and de Ridder, MAJ and Weibel, D and Mina, MJ and Grenfell, BT and Sturkenboom, MCJM and van de Vijver, DAMC and de Swart, RL}, title = {Impact and longevity of measles-associated immune suppression: a matched cohort study using data from the THIN general practice database in the UK.}, journal = {BMJ open}, volume = {8}, number = {11}, pages = {e021465}, pmid = {30413497}, issn = {2044-6055}, support = {P2C HD047879/HD/NICHD NIH HHS/United States ; }, mesh = {Adolescent ; Anti-Infective Agents/therapeutic use ; Case-Control Studies ; Child ; Child, Preschool ; Communicable Diseases/*epidemiology ; Databases, Factual ; Female ; Hospitalization/statistics & numerical data ; Humans ; Immunologic Memory ; *Immunosuppression Therapy ; Incidence ; Infant ; Longitudinal Studies ; Male ; Measles/epidemiology/*immunology ; Measles Vaccine ; Risk Assessment ; Statistics, Nonparametric ; Time Factors ; United Kingdom/epidemiology ; Vaccination/statistics & numerical data ; }, abstract = {OBJECTIVE: To test the hypothesis that measles infection increases the incidence of non-measles infectious diseases over a prolonged period of time.

DESIGN: A population-based matched cohort study.

DATA SOURCES: This study examined children aged 1-15 years in The Health Improvement Network UK general practice medical records database. Participants included 2228 patients diagnosed with measles between 1990 and 2014, which were matched on age, sex, general practitioner practice and calendar year with 19 930 children without measles. All controls had received at least one measles vaccination. Children with a history of immune-compromising conditions or with immune-suppressive treatment were excluded.

PRIMARY OUTCOME MEASURES: Incidence rate ratio (IRR) of infections, anti-infective prescriptions and all-cause hospitalisations following measles in predetermined periods using multivariate analysis to adjust for confounding variables.

RESULTS: In children with measles, the incidence rate for non-measles infectious disease was significantly increased in each time period assessed up to 5 years postmeasles: 43% in the first month (IRR: 1.43; 95% CI 1.22 to 1.68), 22% from month one to the first year (IRR: 1.22; 95% CI 1.14 to 1.31), 10% from year 1 to 2.5 years (IRR: 1.10; 95% CI 1.02 to 1.19) and 15% (IRR: 1.15; 95% CI 1.06 to 1.25) in years 2.5 to 5 years of follow-up. Children with measles were more than three times as likely to receive an anti-infective prescription in the first month and 15%-24% more likely between the first month and 5 years. The rate of hospitalisation in children with measles was increased only in the month following diagnosis but not thereafter (IRR: 2.83; 95% CI 1.72 to 4.67).

CONCLUSION: Following measles, children had increased rates of diagnosed infections, requiring increased prescribing of antimicrobial therapies. This population-based matched cohort study supports the hypothesis that measles has a prolonged impact on host resistance to non-measles infectious diseases.}, } @article {pmid30413098, year = {2018}, author = {Trotter, RT and Lininger, MR and Camplain, R and Fofanov, VY and Camplain, C and Baldwin, JA}, title = {A Survey of Health Disparities, Social Determinants of Health, and Converging Morbidities in a County Jail: A Cultural-Ecological Assessment of Health Conditions in Jail Populations.}, journal = {International journal of environmental research and public health}, volume = {15}, number = {11}, pages = {}, pmid = {30413098}, issn = {1660-4601}, support = {U54 MD012388/MD/NIMHD NIH HHS/United States ; U54MD012388/MD/NIMHD NIH HHS/United States ; }, mesh = {Adult ; Female ; *Health Status Disparities ; Health Surveys ; Humans ; Male ; Morbidity ; *Prisoners ; Prisons ; *Social Determinants of Health ; United States ; }, abstract = {The environmental health status of jail populations in the United States constitutes a significant public health threat for prisoners and the general population. The ecology of jails creates a dynamic condition in relation to general population health due to the concentrated potential exposure to infectious diseases, difficult access to treatment for chronic health conditions, interruption in continuity of care for serious behavioral health conditions, as well as on-going issues for the prevention and treatment of substance abuse disorders. This paper reports on elements of a cross-sectional survey embedded in a parent project, "Health Disparities in Jail Populations." The overall project includes a comprehensive secondary data analysis of the health status of county jail populations, along with primary data collection that includes a cross-sectional health and health care services survey of incarcerated individuals, coupled with collection of biological samples to investigate infectious disease characteristics of a county jail population. This paper reports on the primary results of the survey data collection that indicate that this is a population with complex and interacting co-morbidities, as well as significant health disparities compared to the general population.}, } @article {pmid30411561, year = {2018}, author = {Luan, XL and Wei, S and Han, SR and Li, XT and Yang, WY and Liu, MS and Xu, C}, title = {[A multi-scale study on the formation mechanism and main controlling factors of urban thermal field based on urban big data.].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {29}, number = {9}, pages = {2861-2868}, doi = {10.13287/j.1001-9332.201809.015}, pmid = {30411561}, issn = {1001-9332}, mesh = {*Big Data ; Cities ; Environmental Monitoring/*methods ; Hot Temperature ; Humans ; Regression Analysis ; *Temperature ; }, abstract = {The composition and structure of urban landscape and human activity intensity are key factors shaping urban thermal fields, whereas the relative importance of influencing factors for urban thermal distribution remains unclear. We carried out a case study in Yixing City. Land surface temperature (LST), ecological infrastructure (including vegetation and water cover), building volume and point of interest data were extracted from the RS interpretation, field mapping and programming technique. Using Pearson correlation analysis, univariete regression analysis, multiple regression analysis and relative weight analysis, we quantitatively analyzed the relationships between urban land surface temperature to ecological infrastructure, building volume, POI density at multiple scales (500, 1000, 2000 m) as well as their relative importance. The results showed that ecological infrastructure had a significant cooling effect, and the building volume and POI density were positively correlated with LST. Among the influence factors of urban heat field, ecological infrastructure had the highest relative weight (21.3%-43.8%), followed by building volume (20.7%-22.6%) and POI density (13.7%-21.7%). Our results would help to understand the relative importance of factors driving urban thermal field and offer important reference for taking mitigation measures to alleviate urban heat island effect.}, } @article {pmid30411285, year = {2019}, author = {Patel, S and Sangeeta, S}, title = {Pesticides as the drivers of neuropsychotic diseases, cancers, and teratogenicity among agro-workers as well as general public.}, journal = {Environmental science and pollution research international}, volume = {26}, number = {1}, pages = {91-100}, pmid = {30411285}, issn = {1614-7499}, mesh = {Abnormalities, Drug-Induced/epidemiology/*etiology ; Africa ; Agricultural Workers' Diseases/*chemically induced ; Farmers ; Female ; Humans ; India ; Male ; Neoplasms/*chemically induced/epidemiology ; Occupational Exposure/*adverse effects ; Pesticides/analysis/*toxicity ; Psychotic Disorders/epidemiology/*etiology ; Suicide/trends ; United States ; }, abstract = {The need to maximize agricultural productivity has made pesticides an indispensable part of current times. Farmers are unaware of the lurking consequences of the pesticide exposure, which endanger their health. It also puts the unsuspecting consumers in peril. The pesticides (from organophosphates, organochlorine, and carbamate class) disrupt the immune and hormonal signaling, causing recurrent inflammation, which leads to a wide array pathologies, including teratogenicity. Numerous farmers have fallen victim to neural disorders-driven suicides and lungs, prostate/breast cancer-caused untimely deaths. Green revolution which significantly escalated agricultural productivity is backfiring now. It is high time that environmental and agricultural authorities act to restrain the excessive usage of the detrimental chemicals and educate farmers regarding the crisis. This review discusses the biological mechanisms of pesticide-driven pathogenesis (such as the activation or inhibition of caspase, serine protease, acetylcholinesterase) and presents the pesticide-exposure-caused health deterioration in USA, India, and Africa. This holistic and critical review should be an eye-opener for general public, and a guide for researchers.}, } @article {pmid30410743, year = {2018}, author = {Munos, MK and Maiga, A and Do, M and Sika, GL and Carter, ED and Mosso, R and Dosso, A and Leyton, A and Khan, SM}, title = {Linking household survey and health facility data for effective coverage measures: a comparison of ecological and individual linking methods using the Multiple Indicator Cluster Survey in Côte d'Ivoire.}, journal = {Journal of global health}, volume = {8}, number = {2}, pages = {020803}, pmid = {30410743}, issn = {2047-2986}, mesh = {Adolescent ; Adult ; Child, Preschool ; Cote d'Ivoire ; Ecology ; Feasibility Studies ; Female ; *Health Care Surveys ; Health Services Needs and Demand ; Humans ; Infant ; Infant, Newborn ; Information Storage and Retrieval/*methods ; *Medical Record Linkage ; Middle Aged ; Patient Acceptance of Health Care/*statistics & numerical data ; Pregnancy ; Quality of Health Care ; Reproducibility of Results ; Young Adult ; }, abstract = {BACKGROUND: Population-based measures of intervention coverage are used in low- and middle-income countries for program planning, prioritization, and evaluation. There is increased interest in effective coverage, which integrates information about service quality or health outcomes. Approaches proposed for quality-adjusted effective coverage include linking data on need and service contact from population-based surveys with data on service quality from health facility surveys. However, there is limited evidence about the validity of different linking methods for effective coverage estimation.

METHODS: We collaborated with the 2016 Côte d'Ivoire Multiple Indicator Cluster Survey (MICS) to link data from a health provider assessment to care-seeking data collected by the MICS in the Savanes region of Côte d'Ivoire. The provider assessment was conducted in a census of public and non-public health facilities and pharmacies in Savanes in May-June 2016. We also included community health workers managing sick children who served the clusters sampled for the MICS. The provider assessment collected information on structural and process quality for antenatal care, delivery and immediate newborn care, postnatal care, and sick child care. We linked the MICS and provider data using exact-match and ecological linking methods, including aggregate linking and geolinking methods. We compared the results obtained from exact-match and ecological methods.

RESULTS: We linked 731 of 786 care-seeking episodes (93%) from the MICS to a structural quality score for the provider named by the respondent. Effective coverage estimates computed using exact-match methods were 13%-63% lower than the care-seeking estimates from the MICS. Absolute differences between exact match and ecological linking methods were ±7 percentage points for all ecological methods. Incorporating adjustments for provider category and weighting by service-specific utilization into the ecological methods generally resulted in better agreement between ecological and exact match estimates.

CONCLUSIONS: Ecological linking may be a feasible and valid approach for estimating quality-adjusted effective coverage when a census of providers is used. Adjusting for provider type and caseload may improve agreement with exact match results. There remain methodological questions to be addressed to develop guidance on using linking methods for estimating quality-adjusted effective coverage, including the effect of facility sampling and time displacement.}, } @article {pmid30410073, year = {2018}, author = {Jin, C and Bao, J and Wang, Y and Chen, W and Wu, T and Wang, L and Lv, X and Gao, W and Wang, B and Zhu, G and Dai, G and Sun, W}, title = {Changes in long non-coding RNA expression profiles related to the antagonistic effects of Escherichia coli F17 on lamb spleens.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {16514}, pmid = {30410073}, issn = {2045-2322}, mesh = {Animals ; Escherichia coli/classification/*pathogenicity ; Escherichia coli Infections/genetics/microbiology/*veterinary ; Gene Expression Profiling/*veterinary ; Gene Expression Regulation ; Gene Ontology ; Gene Regulatory Networks ; RNA, Long Noncoding/*genetics ; RNA, Messenger/genetics ; Sequence Analysis, RNA/veterinary ; Sheep ; Sheep Diseases/*genetics/microbiology ; Spleen/*chemistry/microbiology ; }, abstract = {Sheep colibacillosis is one of the most common bacterial diseases found at large-scale sheep farms. The aim of this study was to employ RNA-seq to screen differentially expressed (DE) long non-coding RNAs (lncRNAs) that impart antagonistic or sensitive effects on Escherichia coli F17. In this study, individuals who had antagonistic or sensitive responses to E. coli F17 were identified by feeding E. coli F17 strains to Hu lambs. The sensitive group had higher levels of intestinal bacteria than that in the antagonistic group (P < 0.05), the jejunum showed various levels of mucosal tissue damage and had a dark colour, and disintegration of part of the small intestinal villi was observed. Totals of 34 DE lncRNAs and 703 DE mRNAs in two groups were identified. qRT-PCR results for 12 randomly selected DE lncRNAs and DE mRNAs were consistent with the RNA-seq data. Gene Ontology (GO), KEGG Pathway enrichment and lncRNA-mRNA interaction analyses identified 6 co-expressed genes, namely, MYO1G, TIMM29, CARM1, ADGRB1, SEPT4, and DESI2. This is the first study that has performed expression profiling of lncRNAs in the spleen of antagonistic and sensitive lambs. The identification of DE lncRNAs can facilitate investigations into the molecular mechanism underlying resistance to diarrhoea in sheep.}, } @article {pmid30409881, year = {2018}, author = {Kubelka, V and Šálek, M and Tomkovich, P and Végvári, Z and Freckleton, RP and Székely, T}, title = {Global pattern of nest predation is disrupted by climate change in shorebirds.}, journal = {Science (New York, N.Y.)}, volume = {362}, number = {6415}, pages = {680-683}, doi = {10.1126/science.aat8695}, pmid = {30409881}, issn = {1095-9203}, mesh = {Animals ; Birds/*physiology ; *Climate Change ; Databases, Factual ; Nesting Behavior/*physiology ; Predatory Behavior/*physiology ; }, abstract = {Ongoing climate change is thought to disrupt trophic relationships, with consequences for complex interspecific interactions, yet the effects of climate change on species interactions are poorly understood, and such effects have not been documented at a global scale. Using a single database of 38,191 nests from 237 populations, we found that shorebirds have experienced a worldwide increase in nest predation over the past 70 years. Historically, there existed a latitudinal gradient in nest predation, with the highest rates in the tropics; however, this pattern has been recently reversed in the Northern Hemisphere, most notably in the Arctic. This increased nest predation is consistent with climate-induced shifts in predator-prey relationships.}, } @article {pmid30407542, year = {2019}, author = {Delprat, A and Guillén, Y and Ruiz, A}, title = {Computational Sequence Analysis of Inversion Breakpoint Regions in the Cactophilic Drosophila mojavensis Lineage.}, journal = {The Journal of heredity}, volume = {110}, number = {1}, pages = {102-117}, doi = {10.1093/jhered/esy057}, pmid = {30407542}, issn = {1465-7333}, mesh = {Animals ; *Chromosome Breakpoints ; *Chromosome Inversion ; *Chromosomes, Insect ; Computational Biology ; Drosophila/*genetics ; *Evolution, Molecular ; Female ; Male ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {We investigated rates of chromosomal evolution in Drosophila mojavensis using whole-genome sequence information from D. mojavensis, Drosophila buzzatii, and Drosophila virilis. Drosophila mojavensis is a cactophilic species of the repleta group living under extreme ecological conditions in the deserts of the Southwestern United States and Northwestern México. The genome of D. buzzatii, another member of the repleta group, was recently sequenced and the largest scaffolds anchored to all chromosomes using diverse procedures. Chromosome organization between D. mojavensis and D. buzzatii was compared using MUMmer and GRIMM software. Our results corroborate previous cytological analyses that indicated chromosome 2 differed between these 2 species by 10 inversions, chromosomes X and 5 differed by one inversion each, and chromosome 4 was homosequential. In contrast, we found that chromosome 3 differed by 5 inversions instead of the expected 2 that were previously inferred by cytological analyses. Thirteen of these inversions occurred in the D. mojavensis lineage: 12 are fixed and one of them is a polymorphic inversion previously described in populations from Sonora and Baja California, México. We previously investigated the breakpoints of chromosome 2 inversions fixed in D. mojavensis. Here we characterized the breakpoint regions of the 5 inversions found in chromosome 3 in order to infer the molecular mechanism that generated each inversion and its putative functional consequences. Overall, our results reveal a number of gene alterations at the inversion breakpoints with putative adaptive consequences that point to natural selection as the cause for fast chromosomal evolution in D. mojavensis.}, } @article {pmid30407532, year = {2019}, author = {Portwood, JL and Woodhouse, MR and Cannon, EK and Gardiner, JM and Harper, LC and Schaeffer, ML and Walsh, JR and Sen, TZ and Cho, KT and Schott, DA and Braun, BL and Dietze, M and Dunfee, B and Elsik, CG and Manchanda, N and Coe, E and Sachs, M and Stinard, P and Tolbert, J and Zimmerman, S and Andorf, CM}, title = {MaizeGDB 2018: the maize multi-genome genetics and genomics database.}, journal = {Nucleic acids research}, volume = {47}, number = {D1}, pages = {D1146-D1154}, pmid = {30407532}, issn = {1362-4962}, mesh = {Computational Biology/*methods ; *Databases, Genetic ; Gene Expression Regulation, Plant ; Genetic Variation ; Genome, Plant/*genetics ; Genomics/*methods ; Information Storage and Retrieval/methods ; Internet ; Polymorphism, Single Nucleotide ; Proteomics/methods ; User-Computer Interface ; Zea mays/*genetics/metabolism ; }, abstract = {Since its 2015 update, MaizeGDB, the Maize Genetics and Genomics database, has expanded to support the sequenced genomes of many maize inbred lines in addition to the B73 reference genome assembly. Curation and development efforts have targeted high quality datasets and tools to support maize trait analysis, germplasm analysis, genetic studies, and breeding. MaizeGDB hosts a wide range of data including recent support of new data types including genome metadata, RNA-seq, proteomics, synteny, and large-scale diversity. To improve access and visualization of data types several new tools have been implemented to: access large-scale maize diversity data (SNPversity), download and compare gene expression data (qTeller), visualize pedigree data (Pedigree Viewer), link genes with phenotype images (MaizeDIG), and enable flexible user-specified queries to the MaizeGDB database (MaizeMine). MaizeGDB also continues to be the community hub for maize research, coordinating activities and providing technical support to the maize research community. Here we report the changes MaizeGDB has made within the last three years to keep pace with recent software and research advances, as well as the pan-genomic landscape that cheaper and better sequencing technologies have made possible. MaizeGDB is accessible online at https://www.maizegdb.org.}, } @article {pmid30404937, year = {2018}, author = {Worthing, KA and Schwendener, S and Perreten, V and Saputra, S and Coombs, GW and Pang, S and Davies, MR and Abraham, S and Trott, DJ and Norris, JM}, title = {Characterization of Staphylococcal Cassette Chromosome mec Elements from Methicillin-Resistant Staphylococcus pseudintermedius Infections in Australian Animals.}, journal = {mSphere}, volume = {3}, number = {6}, pages = {}, pmid = {30404937}, issn = {2379-5042}, mesh = {Animal Diseases/*microbiology ; Animals ; Anti-Bacterial Agents/pharmacology ; Australia ; *Chromosomes, Bacterial ; Computational Biology ; *Genomic Islands ; *Methicillin Resistance ; Microbial Sensitivity Tests ; Oxacillin/pharmacology ; Staphylococcal Infections/microbiology/*veterinary ; Staphylococcus/drug effects/*genetics/isolation & purification ; Whole Genome Sequencing ; }, abstract = {We examined the oxacillin resistance phenotype and genomic structure of staphylococcal cassette chromosome mec (SCCmec) elements from 77 veterinary methicillin-resistant Staphylococcus pseudintermedius (MRSP) isolates. Isolates were characterized by oxacillin broth microdilution, whole-genome sequencing, and bioformatics analysis. Five previously described SCCmec elements, and a sixth novel element, were identified: SCCmec III (also known as II-III), ΨSCCmec57395, and SCCmecNA45 (a SCCmec VII variant), all previously described in MRSP, and SCCmec IVg and SCCmec VT, previously described in both methicillin-resistant Staphylococcus aureus (MRSA) and MRSP. The sixth element was novel and found among nine geographically clustered isolates. This novel pseudostaphylococcal cassette chromosome (ΨSCCmecKW21) contained a class A mec gene complex but lacked ccr genes. It also harbored heavy metal (cadmium) resistance determinants. The median oxacillin MIC values among ΨSCCmecKW21, SCCmec III, and SCCmec VT isolates were significantly higher than those determined for the SCCmecNA45 VII variant isolates and ΨSCCmec57395 and SCCmec IVg isolates. ΨSCCmecKW21 was found exclusively in sequence type 497 (ST497), an MRSP clone that is locally successful in Victoria, Australia. Future studies are necessary to determine if this clone has disseminated further afield and if ΨSCCmecKW21 has moved into other MRSP lineages or staphylococcal species.IMPORTANCEStaphylococcus pseudintermedius is a significant veterinary pathogen and occasional cause of infections in humans. β-Lactams are an important group of antimicrobials used to treat staphylococcal infections in humans and animals. However, when staphylococci become methicillin resistant via the acquisition of a mobile genetic element called staphylococcal cassette chromosome mec (SCCmec), they become resistant to all β-lactams. This study detected a novel SCCmec element among a cluster of methicillin-resistant S. pseudintermedius isolates from animals in Australia. It also detected SCCmec elements in S. pseudintermedius that had high similarity to those identified in methicillin-resistant Staphylococcus aureus, demonstrating how human and animal pathogens can share the same resistance determinants.}, } @article {pmid30404247, year = {2018}, author = {Chi, C and Giri, SS and Jun, JW and Kim, HJ and Kim, SW and Kang, JW and Park, SC}, title = {Detoxification and Immune Transcriptomic Response of the Gill Tissue of Bay Scallop (Argopecten irradians) Following Exposure to the Algicide Palmitoleic Acid.}, journal = {Biomolecules}, volume = {8}, number = {4}, pages = {}, pmid = {30404247}, issn = {2218-273X}, mesh = {Activation, Metabolic/drug effects ; Animals ; Fatty Acids, Monounsaturated/*toxicity ; Gene Expression Profiling ; Gene Library ; Gene Ontology ; Gills/drug effects/*immunology/metabolism ; Pectinidae/drug effects/*genetics/*immunology ; RNA, Messenger/genetics/metabolism ; Stress, Physiological/drug effects/genetics ; Transcriptome/drug effects/*genetics ; }, abstract = {Palmitoleic acid (PA) is an effective algicide against Alexandrium tamarense. However, the toxicological mechanism of PA exposure is unclear. The transcript abundance and differentially expressed genes (DEGs) in gills of bay scallop were investigated following 80 mg/L PA exposure up to 48 h using the Illumina HiSeq 4000 deep-sequencing platform with the recommended read length of 100 bp. De novo assembly of paired-end reads yielded 62,099 unigenes; 5414 genes were identified as being significantly increased, and 4452 were decreased. Based on gene ontology classification and enrichment analysis, the 'cellular process', 'metabolic process', 'response to stimulus', and 'catalytic process' with particularly high functional enrichment were revealed. The DEGs, which are related to detoxification and immune responses, revealed that acid phosphatase, fibrinogen C domain-containing protein, cyclic AMP-responsive element-binding protein, glutathione reductase, ATP-binding cassette, nuclear factor erythroid 2-related factor, NADPH2:quinone reductase, and cytochrome P450 4F22, 4B1, and 2C8-related gene expression decreased. In contrast, some genes related to glutathione S-transferase, C-type lectin, superoxide dismutase, toll-like receptors, and cytochrome P450 2C14, 2U1, 3A24 and 4A2 increased. The results of current research will be a valuable resource for the investigation of gene expression stimulated by PA, and will help understanding of the molecular mechanisms underlying the scallops' response to PA exposure.}, } @article {pmid30404215, year = {2018}, author = {Yuan, Y and Peng, Q and Yang, S and Zhang, S and Fu, Y and Wu, Y and Gao, M}, title = {Isolation of A Novel Bacillus thuringiensis Phage Representing A New Phage Lineage and Characterization of Its Endolysin.}, journal = {Viruses}, volume = {10}, number = {11}, pages = {}, pmid = {30404215}, issn = {1999-4915}, mesh = {Bacillus Phages/classification/*isolation & purification/*physiology/ultrastructure ; Bacillus thuringiensis/*virology ; Bacteriolysis ; Computational Biology/methods ; Endopeptidases/*genetics ; Genome, Viral ; Phylogeny ; Viral Plaque Assay ; Whole Genome Sequencing ; }, abstract = {Phages, the parasites of bacteria, are considered as a new kind of antimicrobial agent due to their ability to lyse pathogenic bacteria. Due to the increase of available phage isolates, the newly isolated phage showed increasing genomic similarities with previously isolated phages. In this study, the novel phage vB_BthS_BMBphi, infecting the Bacillus thuringiensis strain BMB171, is isolated and characterized together with its endolysin. This phage is the first tadpole-like phage infecting the Bacillus strains. Genomic analysis shows that the phage genome is dissimilar to all those of previously characterized phages, only exhibiting low similarities with partial regions of the B. thuringiensis prophages. Phylogenetic analysis revealed that the phage was distant from the other Bacillus phages in terms of evolution. The novel genome sequence, the distant evolutionary relationship, and the special virion morphology together suggest that the phage vB_BthS_BMBphi could be classified as a new phage lineage. The genome of the phage is found to contain a restriction modification system, which might endow the phage with immunity to the restriction modification system of the host bacterium. The function of the endolysin PlyBMB encoded by the phage vB_BthS_BMBphi was analyzed, and the endolysin could lyse all the tested Bacillus cereus group strains, suggesting that the endolysin might be used in controlling pathogenic B. cereus group strains. The findings of this study enrich the understanding of phage diversity and provide a resource for controlling the B. cereus group pathogenic bacteria.}, } @article {pmid30404207, year = {2018}, author = {Chmurzynska, A and Mlodzik-Czyzewska, MA and Malinowska, AM and Czarnocinska, J and Wiebe, D}, title = {Use of a Smartphone Application Can Improve Assessment of High-Fat Food Consumption in Overweight Individuals.}, journal = {Nutrients}, volume = {10}, number = {11}, pages = {}, pmid = {30404207}, issn = {2072-6643}, support = {grant number 2014/15/B/NZ9/02134//Narodowe Centrum Nauki/ ; }, mesh = {Adult ; Dietary Fats/*administration & dosage ; Eating ; Female ; *Food Analysis ; Humans ; Male ; *Mobile Applications ; Overweight ; Poland ; *Smartphone ; Young Adult ; }, abstract = {BACKGROUND: We evaluated the feasibility of an application for measuring the frequency of consumption of high-fat foods and compared this application with standard methods.

METHODS: Twenty-six females and thirty six males aged 20⁻40 were enrolled in Poland. Participants completed the Block Screening Questionnaire for Fat Intake (BSQF; Q1) and a second questionnaire (Q2) with additional high-fat foods. The participants were then monitored for ten days in a real-time manner using a smartphone application that employed the same lists of food as Q2.

RESULTS: Most subjects (84%) gave replies to at least three prompts on at least 5 days. The results from Q1 and the application were correlated (r = 0.42, p < 0.001). Energy intake and the frequency of consumption of high-fat foods were correlated in the overweight/obese group (r = 0.83, p < 0.001). The mean differences between Q2 and the app were similar in both groups but the agreement limits were wider in the overweight/obese group than in the normal weight group.

CONCLUSIONS: An application for mobile devices is a feasible tool for capturing the frequency of high-fat food consumption and it seems to improve the measured variable, especially in overweight or obese people.}, } @article {pmid30401458, year = {2018}, author = {Mooney, JA and Huber, CD and Service, S and Sul, JH and Marsden, CD and Zhang, Z and Sabatti, C and Ruiz-Linares, A and Bedoya, G and , and Freimer, N and Lohmueller, KE}, title = {Understanding the Hidden Complexity of Latin American Population Isolates.}, journal = {American journal of human genetics}, volume = {103}, number = {5}, pages = {707-726}, pmid = {30401458}, issn = {1537-6605}, support = {R01 MH095454/MH/NIMH NIH HHS/United States ; P30 NS062691/NS/NINDS NIH HHS/United States ; R35 GM119856/GM/NIGMS NIH HHS/United States ; K01 ES028064/ES/NIEHS NIH HHS/United States ; R01 MH075007/MH/NIMH NIH HHS/United States ; }, mesh = {Colombia ; Consanguinity ; Costa Rica ; Female ; Genetics, Population/methods ; Genome, Human/*genetics ; Genomics/methods ; Homozygote ; Humans ; Male ; Pedigree ; White People/genetics ; Whole Genome Sequencing/methods ; }, abstract = {Most population isolates examined to date were founded from a single ancestral population. Consequently, there is limited knowledge about the demographic history of admixed population isolates. Here we investigate genomic diversity of recently admixed population isolates from Costa Rica and Colombia and compare their diversity to a benchmark population isolate, the Finnish. These Latin American isolates originated during the 16[th] century from admixture between a few hundred European males and Amerindian females, with a limited contribution from African founders. We examine whole-genome sequence data from 449 individuals, ascertained as families to build mutigenerational pedigrees, with a mean sequencing depth of coverage of approximately 36×. We find that Latin American isolates have increased genetic diversity relative to the Finnish. However, there is an increase in the amount of identity by descent (IBD) segments in the Latin American isolates relative to the Finnish. The increase in IBD segments is likely a consequence of a very recent and severe population bottleneck during the founding of the admixed population isolates. Furthermore, the proportion of the genome that falls within a long run of homozygosity (ROH) in Costa Rican and Colombian individuals is significantly greater than that in the Finnish, suggesting more recent consanguinity in the Latin American isolates relative to that seen in the Finnish. Lastly, we find that recent consanguinity increased the number of deleterious variants found in the homozygous state, which is relevant if deleterious variants are recessive. Our study suggests that there is no single genetic signature of a population isolate.}, } @article {pmid30399430, year = {2019}, author = {Tang, P and Zhu, JC and Zheng, BY and Wei, SJ and Sharkey, M and Chen, XX and Vogler, AP}, title = {Mitochondrial phylogenomics of the Hymenoptera.}, journal = {Molecular phylogenetics and evolution}, volume = {131}, number = {}, pages = {8-18}, doi = {10.1016/j.ympev.2018.10.040}, pmid = {30399430}, issn = {1095-9513}, mesh = {Animals ; Base Composition/genetics ; Base Sequence ; Bayes Theorem ; Databases, Genetic ; Fossils ; *Genome, Mitochondrial ; Hymenoptera/*genetics ; Likelihood Functions ; *Phylogeny ; Time Factors ; }, abstract = {The insect order Hymenoptera presents marvelous morphological and ecological diversity. Higher-level hymenopteran relationships remain controversial, even after recent phylogenomic analyses, as their taxon sampling was limited. To shed light on the origin and diversification of Hymenoptera, in particular the poorly studied Parasitica, we undertook phylogenetic analyses of 40 newly and 43 previously sequenced mitochondrial genomes representing all major clades of Hymenoptera. Various Bayesian inferences using different data partitions and phylogenetic methods recovered similar phylogenetic trees with strong statistical support for almost all nodes. Novel findings of the mitogenomic phylogeny mainly affected the three infraorders Ichneumonomorpha, Proctotrupomorpha and Evaniomorpha, the latter of which was split into three clades. Basal relationships of Parasitica recovered Stephanoidea + (Gasteruptiidae + Aulacidae) as the sister group to Ichneumonomorpha + (Trigonalyoidea + Megalyroidea). This entire clade is sister to Proctotrupomorpha, and Ceraphronoidea + Evaniidae is sister to Aculeata (stinging wasps). Our divergence time analysis indicates that major hymenopteran lineages originated in the Mesozoic. The radiation of early apocritans may have been triggered by the Triassic-Jurassic mass extinction; all extant families were present by the Cretaceous.}, } @article {pmid30397464, year = {2018}, author = {Alhaddad, H and Alhajeri, BH}, title = {SamplEase: a simple application for collection and organization of biological specimen data in the field.}, journal = {Ecology and evolution}, volume = {8}, number = {20}, pages = {10266-10271}, pmid = {30397464}, issn = {2045-7758}, abstract = {Careful collection and organization of biological specimens and their associated data are at the core of field research (e.g., ecology, genetics). Fieldwork data are often collected by handwriting or unsystematically via an electronic device (e.g., laptop), a process that is time-intensive, disorganized, and may lead to transcription errors, as data are copied to a more permanent repository. SamplEase is an iOS and Android application that is designed to ease the process of collecting biological specimen data in the field (data associated with biological samples, such as location, age, and sex). In addition to biological specimen data, SamplEase allows for the assignment of photographs to each collected sample, which provides visual records of each specimen in its environment. SamplEase outputs biological specimen data in a tabular format, facilitating subsequent analyses and dissemination. Despite the simplicity of SamplEase, no similar data management application is readily available for researchers.}, } @article {pmid30390527, year = {2019}, author = {Khan, K and Benfenati, E and Roy, K}, title = {Consensus QSAR modeling of toxicity of pharmaceuticals to different aquatic organisms: Ranking and prioritization of the DrugBank database compounds.}, journal = {Ecotoxicology and environmental safety}, volume = {168}, number = {}, pages = {287-297}, doi = {10.1016/j.ecoenv.2018.10.060}, pmid = {30390527}, issn = {1090-2414}, mesh = {Animals ; Aquatic Organisms/*drug effects ; Chlorophyceae/drug effects ; *Consensus ; Cyprinidae ; Daphnia/drug effects ; Databases, Factual ; *Ecotoxicology ; Oncorhynchus mykiss ; Organic Chemicals/*toxicity ; Pharmaceutical Preparations/analysis ; *Quantitative Structure-Activity Relationship ; Toxicity Tests ; Water Pollutants, Chemical/*toxicity ; }, abstract = {In the present work, quantitative structure-activity relationship (QSAR) models have been developed for ecotoxicity of pharmaceuticals on four different aquatic species namely Pseudokirchneriella subcapitata, Daphnia magna, Oncorhynchus mykiss and Pimephales promelas using genetic algorithm (GA) for feature selection followed by Partial Least Squares regression technique according to the Organization for Economic Co-operation and Development (OECD) guidelines. Double cross-validation methodology was employed for selecting suitable models. Only 2D descriptors were used for capturing chemical information and model building, whereas validation of the models was performed by considering various stringent internal and external validation metrics. Interestingly, models could be developed even without using any LogP terms in contrary to the usual dependence of toxicity on lipophilicity. However, the current manuscript proposes highly robust and more predictive models employing computed logP descriptors. The applicability domain study was performed in order to set a predefined chemical zone of applicability for the obtained QSAR models, and the test compounds falling outside the domain were not taken for further analysis while making a prioritized list. An additional comparison was made with ECOSAR, an online expert system for toxicity prediction of organic pollutants, in order to prove predictability of the obtained models. The obtained robust consensus models were utilized to predict the toxicity of a large dataset of approximately 9300 drug-like molecules in order to prioritize the existing drug-like substances in accordance to their acute predicted aquatic toxicities following a scaling technique. Finally, prioritized lists of 500 most toxic chemicals obtained by respective consensus models and those predicted from ECOSAR tool have been reported.}, } @article {pmid30387920, year = {2019}, author = {Grandjean, P and Abdennebi-Najar, L and Barouki, R and Cranor, CF and Etzel, RA and Gee, D and Heindel, JJ and Hougaard, KS and Hunt, P and Nawrot, TS and Prins, GS and Ritz, B and Soffritti, M and Sunyer, J and Weihe, P}, title = {Timescales of developmental toxicity impacting on research and needs for intervention.}, journal = {Basic & clinical pharmacology & toxicology}, volume = {125 Suppl 3}, number = {Suppl 3}, pages = {70-80}, pmid = {30387920}, issn = {1742-7843}, support = {P42ES027706//STEEP Superfund Center/ ; R13 ES029385/ES/NIEHS NIH HHS/United States ; R01 ES026596/ES/NIEHS NIH HHS/United States ; R13ES029385/ES/NIEHS NIH HHS/United States ; P42 ES027706/ES/NIEHS NIH HHS/United States ; }, mesh = {Animals ; Big Data ; Computational Chemistry/methods ; Congresses as Topic ; Disease Models, Animal ; Ecotoxicology/*methods ; Endocrine Disruptors/*adverse effects ; Environmental Exposure/*adverse effects ; Environmental Medicine/*methods ; Epigenesis, Genetic/drug effects ; Epigenomics/methods ; Female ; Fetal Development/drug effects/genetics ; Humans ; Metabolomics/methods ; Pregnancy ; Prenatal Exposure Delayed Effects/*diagnosis/etiology/prevention & control ; Research Design ; Risk Assessment/methods ; Time Factors ; }, abstract = {Much progress has happened in understanding developmental vulnerability to preventable environmental hazards. Along with the improved insight, the perspective has widened, and developmental toxicity now involves latent effects that can result in delayed adverse effects in adults or at old age and additional effects that can be transgenerationally transferred to future generations. Although epidemiology and toxicology to an increasing degree are exploring the adverse effects from developmental exposures in human beings, the improved documentation has resulted in little progress in protection, and few environmental chemicals are currently regulated to protect against developmental toxicity, whether it be neurotoxicity, endocrine disruption or other adverse outcome. The desire to obtain a high degree of certainty and verification of the evidence used for decision-making must be weighed against the costs and necessary duration of research, as well as the long-term costs to human health because of delayed protection of vulnerable early-life stages of human development and, possibly, future generations. Although two-generation toxicology tests may be useful for initial test purposes, other rapidly emerging tools need to be seriously considered from computational chemistry and metabolomics to CLARITY-BPA-type designs, big data and population record linkage approaches that will allow efficient generation of new insight; epigenetic mechanisms may necessitate a set of additional regulatory tests to reveal such effects. As reflected by the Prenatal Programming and Toxicity (PPTOX) VI conference, the current scientific understanding and the timescales involved require an intensified approach to protect against preventable adverse health effects that can harm the next generation and generations to come. While further research is needed, the main emphasis should be on research translation and timely public health intervention to avoid serious, irreversible and perhaps transgenerational harm.}, } @article {pmid30386588, year = {2018}, author = {Young, S and Rode-Margono, J and Amin, R}, title = {Software to facilitate and streamline camera trap data management: A review.}, journal = {Ecology and evolution}, volume = {8}, number = {19}, pages = {9947-9957}, pmid = {30386588}, issn = {2045-7758}, abstract = {Improving technology and increasing affordability mean that camera trapping-the use of remotely triggered cameras to photograph wildlife-is becoming an increasingly common tool in the monitoring and conservation of wild populations. Each camera trap study generates a vast amount of data, which need to be processed and labeled before analysis. Traditionally, processing camera trap data has been performed manually by entering data into a spreadsheet. This is time-consuming, prone to human error, and data management may be inconsistent between projects, hindering collaboration. Recently, several programs have become available to facilitate and quicken data processing. Here, we review available software and assess their ability to better standardize camera trap data management and facilitate data sharing and collaboration. To identify available software for camera trap data management, we used internet searches and contacted researchers and practitioners working on large camera trap projects, as well as software developers. We tested all available programs against a range of software characteristics in addition to their ability to record a suite of important data variables extracted from images. We identified and reviewed 12 available programs for the management of camera trap data. These ranged from simple software assisting with the extraction of metadata from an image, through to comprehensive programs that facilitate data entry and analysis. Many of the programs tested were developed for use on specific studies and so do not cover all possible software or data collection requirements that different projects may have. We highlight the importance of a standardized software solution for camera trap data management. This approach would allow all possible data to be collected, enabling researchers to share data and contribute to other studies, as well as facilitating multi-project comparisons. By standardizing camera trap data collection and management in this way, future studies would be better placed to guide conservation policy on a global level.}, } @article {pmid30384907, year = {2018}, author = {Bamisile, BS and Dash, CK and Akutse, KS and Keppanan, R and Afolabi, OG and Hussain, M and Qasim, M and Wang, L}, title = {Prospects of endophytic fungal entomopathogens as biocontrol and plant growth promoting agents: An insight on how artificial inoculation methods affect endophytic colonization of host plants.}, journal = {Microbiological research}, volume = {217}, number = {}, pages = {34-50}, doi = {10.1016/j.micres.2018.08.016}, pmid = {30384907}, issn = {1618-0623}, mesh = {*Agricultural Inoculants ; Animals ; Beauveria/physiology ; Biological Control Agents/*pharmacology ; Databases, Factual ; Endophytes/growth & development/*physiology ; Host-Pathogen Interactions/physiology ; Insecta/drug effects ; Pest Control, Biological/*methods ; *Plant Development ; Plant Diseases/microbiology/*prevention & control ; Plant Roots/microbiology ; Plant Stems/microbiology ; Plants/*microbiology ; Seedlings/microbiology ; Soil ; Sorghum/microbiology ; }, abstract = {Entomopathogenic fungi (EPF) can be established as endophytes in the host plants to offer a long-term preventive measure for pests and diseases. This practice serves as a better alternative to the common practice of periodic direct application of EPF on plants or the target pests as a short-term defense strategy against pests and diseases. These fungal endophytes, aside from their role in pests and diseases prevention, also act as plant growth promoters. Several fungal endophytes have been associated with improvement in plant height, dry and wet weight and other growth parameters. However, many limiting factors have been identified as mitigating the successful colonization of the host plants by EPF. The inoculation methods used have been identified as one, but sadly, this has received little or less attention. Some previous studies carried out comparison between various artificial inoculation methods; foliar application, seedling dipping, soil drenching, seed inoculation, direct injection and others. In separate studies, some authors had suggested different application methods that are best suitable for certain fungal entomopathogens. For instance, leaf inoculation with conidial suspensions was suggested to be the best inoculation method for Beauveria bassiana in sorghum, stem injection was suggested as the most suitable for coffee, while, root dipping method proved the most successful for B. bassiana colonization of tomato plants for the management of Helicoverpa armigera. Here, we discussed entomopathogenic fungal endophytes as bio-control agents, plant growth promoters and highlighted the effect of various artificial inoculation methods on their endophytic colonization of the host plants.}, } @article {pmid30383757, year = {2018}, author = {Kelleher, J and Thornton, KR and Ashander, J and Ralph, PL}, title = {Efficient pedigree recording for fast population genetics simulation.}, journal = {PLoS computational biology}, volume = {14}, number = {11}, pages = {e1006581}, pmid = {30383757}, issn = {1553-7358}, support = {R01 GM115564/GM/NIGMS NIH HHS/United States ; 100956/Z/13/Z//Wellcome Trust/United Kingdom ; }, mesh = {Algorithms ; Computational Biology/*methods ; Computer Simulation ; Gene Frequency ; *Genetic Variation ; *Genetics, Population ; Genome ; Genotype ; Humans ; Models, Genetic ; Pedigree ; Polymorphism, Genetic ; *Software ; }, abstract = {In this paper we describe how to efficiently record the entire genetic history of a population in forwards-time, individual-based population genetics simulations with arbitrary breeding models, population structure and demography. This approach dramatically reduces the computational burden of tracking individual genomes by allowing us to simulate only those loci that may affect reproduction (those having non-neutral variants). The genetic history of the population is recorded as a succinct tree sequence as introduced in the software package msprime, on which neutral mutations can be quickly placed afterwards. Recording the results of each breeding event requires storage that grows linearly with time, but there is a great deal of redundancy in this information. We solve this storage problem by providing an algorithm to quickly 'simplify' a tree sequence by removing this irrelevant history for a given set of genomes. By periodically simplifying the history with respect to the extant population, we show that the total storage space required is modest and overall large efficiency gains can be made over classical forward-time simulations. We implement a general-purpose framework for recording and simplifying genealogical data, which can be used to make simulations of any population model more efficient. We modify two popular forwards-time simulation frameworks to use this new approach and observe efficiency gains in large, whole-genome simulations of one to two orders of magnitude. In addition to speed, our method for recording pedigrees has several advantages: (1) All marginal genealogies of the simulated individuals are recorded, rather than just genotypes. (2) A population of N individuals with M polymorphic sites can be stored in O(N log N + M) space, making it feasible to store a simulation's entire final generation as well as its history. (3) A simulation can easily be initialized with a more efficient coalescent simulation of deep history. The software for recording and processing tree sequences is named tskit.}, } @article {pmid30382813, year = {2018}, author = {Qiu, CZ and Zhou, QZ and Liu, TT and Fang, SM and Wang, YW and Fang, X and Huang, CL and Yu, QY and Chen, CH and Zhang, Z}, title = {Evidence of peripheral olfactory impairment in the domestic silkworms: insight from the comparative transcriptome and population genetics.}, journal = {BMC genomics}, volume = {19}, number = {1}, pages = {788}, pmid = {30382813}, issn = {1471-2164}, support = {20152062//Promoting Cooperation of Scientific Research with the Region of America and Oceania and High-level Talents Training in Ministry of Education of China/ ; }, mesh = {Animals ; *Animals, Domestic ; Bombyx/*genetics ; Computational Biology/methods ; Gene Expression Profiling ; Gene Expression Regulation ; Genetics, Population ; Molecular Sequence Annotation ; Mutation ; Olfactory Perception/*genetics ; Phylogeny ; Transcriptome ; }, abstract = {BACKGROUND: The insect olfactory system is a highly specific and sensitive chemical detector, which plays important roles in feeding, mating and finding an appropriate oviposition site. The ecological niche of Bombyx mori has changed greatly since domestication from B. mandarina, and its olfactory response to environmental odorants clearly decreased. However, the mechanisms that result in the olfactory impairment are largely unknown.

RESULTS: The antennal transcriptomes were compared between the domestic and wild silkworms. Comparison of the same sex between the domestic and wild silkworms revealed 1410 and 1173 differentially expressed genes (DEGs) in males and females, respectively. To understand the olfactory impairment, we mainly focused on the olfactory-related genes. In total, 30 olfactory genes and 19 odorant-degrading enzymes (ODEs) showed differential expression in the two comparisons, in which 19 and 14 were down-regulated in the domestic silkworm, respectively. Based on population genomic data, the down-regulated odorant receptors (ORs) showed a higher ratio of unique non-synonymous polymorphisms to synonymous polymorphisms (N/S ratio) in the domestic populations than that in the wild silkworms. Furthermore, one deleterious mutation was found in OR30 of the domestic population, which was located in transmembrane helix 6 (TM6).

CONCLUSIONS: Our results suggested that down-regulation of the olfactory-related genes and relaxed selection might be the major reasons for olfactory impairment of the domestic silkworm reared completely indoor environment. Reversely, wild silkworm may increase expression and remove deleterious polymorphisms of olfactory-related genes to retain sensitive olfaction.}, } @article {pmid30382197, year = {2018}, author = {Wagner, FB and Mignardot, JB and Le Goff-Mignardot, CG and Demesmaeker, R and Komi, S and Capogrosso, M and Rowald, A and Seáñez, I and Caban, M and Pirondini, E and Vat, M and McCracken, LA and Heimgartner, R and Fodor, I and Watrin, A and Seguin, P and Paoles, E and Van Den Keybus, K and Eberle, G and Schurch, B and Pralong, E and Becce, F and Prior, J and Buse, N and Buschman, R and Neufeld, E and Kuster, N and Carda, S and von Zitzewitz, J and Delattre, V and Denison, T and Lambert, H and Minassian, K and Bloch, J and Courtine, G}, title = {Targeted neurotechnology restores walking in humans with spinal cord injury.}, journal = {Nature}, volume = {563}, number = {7729}, pages = {65-71}, pmid = {30382197}, issn = {1476-4687}, mesh = {Activities of Daily Living ; *Biomedical Technology ; Computer Simulation ; *Electric Stimulation Therapy ; Electromyography ; Epidural Space ; Humans ; Leg/innervation/physiology/physiopathology ; Locomotion/physiology ; Male ; Motor Neurons/physiology ; Muscle, Skeletal/innervation/physiology/physiopathology ; Paralysis/physiopathology/*rehabilitation/surgery ; Spinal Cord/cytology/physiology/physiopathology ; Spinal Cord Injuries/physiopathology/*rehabilitation/surgery ; Walking/*physiology ; }, abstract = {Spinal cord injury leads to severe locomotor deficits or even complete leg paralysis. Here we introduce targeted spinal cord stimulation neurotechnologies that enabled voluntary control of walking in individuals who had sustained a spinal cord injury more than four years ago and presented with permanent motor deficits or complete paralysis despite extensive rehabilitation. Using an implanted pulse generator with real-time triggering capabilities, we delivered trains of spatially selective stimulation to the lumbosacral spinal cord with timing that coincided with the intended movement. Within one week, this spatiotemporal stimulation had re-established adaptive control of paralysed muscles during overground walking. Locomotor performance improved during rehabilitation. After a few months, participants regained voluntary control over previously paralysed muscles without stimulation and could walk or cycle in ecological settings during spatiotemporal stimulation. These results establish a technological framework for improving neurological recovery and supporting the activities of daily living after spinal cord injury.}, } @article {pmid30382153, year = {2018}, author = {Cunning, R and Bay, RA and Gillette, P and Baker, AC and Traylor-Knowles, N}, title = {Comparative analysis of the Pocillopora damicornis genome highlights role of immune system in coral evolution.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {16134}, pmid = {30382153}, issn = {2045-2322}, support = {OCE-1358699//National Science Foundation (NSF)/International ; OCE-1358699//National Science Foundation (NSF)/International ; }, mesh = {Animals ; Anthozoa/*genetics/*immunology ; *Biological Evolution ; Gene Ontology ; Genetic Variation ; *Genome ; Immune System/*metabolism ; Molecular Sequence Annotation ; Multigene Family ; Phylogeny ; Species Specificity ; }, abstract = {Comparative analysis of the expanding genomic resources for scleractinian corals may provide insights into the evolution of these organisms, with implications for their continued persistence under global climate change. Here, we sequenced and annotated the genome of Pocillopora damicornis, one of the most abundant and widespread corals in the world. We compared this genome, based on protein-coding gene orthology, with other publicly available coral genomes (Cnidaria, Anthozoa, Scleractinia), as well as genomes from other anthozoan groups (Actiniaria, Corallimorpharia), and two basal metazoan outgroup phlya (Porifera, Ctenophora). We found that 46.6% of P. damicornis genes had orthologs in all other scleractinians, defining a coral 'core' genome enriched in basic housekeeping functions. Of these core genes, 3.7% were unique to scleractinians and were enriched in immune functionality, suggesting an important role of the immune system in coral evolution. Genes occurring only in P. damicornis were enriched in cellular signaling and stress response pathways, and we found similar immune-related gene family expansions in each coral species, indicating that immune system diversification may be a prominent feature of scleractinian coral evolution at multiple taxonomic levels. Diversification of the immune gene repertoire may underlie scleractinian adaptations to symbiosis, pathogen interactions, and environmental stress.}, } @article {pmid30381312, year = {2018}, author = {Hognert, H and Skjeldestad, FE and Gemzell-Danielsson, K and Heikinheimo, O and Milsom, I and Lidegaard, Ø and Lindh, I}, title = {Ecological study on the use of hormonal contraception, abortions and births among teenagers in the Nordic countries.}, journal = {BMJ open}, volume = {8}, number = {10}, pages = {e022473}, pmid = {30381312}, issn = {2044-6055}, mesh = {Abortion, Induced/*statistics & numerical data ; Adolescent ; Birth Rate ; Condoms/statistics & numerical data ; Contraception Behavior/*statistics & numerical data ; Contraceptives, Oral, Hormonal/therapeutic use ; Contraceptives, Oral, Synthetic/therapeutic use ; Databases, Factual ; Female ; Humans ; Intrauterine Devices/statistics & numerical data ; Levonorgestrel/therapeutic use ; Pregnancy ; Scandinavian and Nordic Countries/epidemiology ; Young Adult ; }, abstract = {OBJECTIVES: Compare hormonal contraceptive use, birth and abortion rates among teenagers in the Nordic countries. A secondary aim was to explore plausible explanations for possible differences between countries.

DESIGN: Ecological study using national registry data concerning births and abortions among all women aged 15-19 years residing in Denmark, Finland, Iceland, Norway and Sweden 2008-2015. Age-specific data on prescriptions for hormonal contraceptives for the period 2008-2015 were obtained from national databases in Denmark, Norway and Sweden.

SETTING: Denmark, Finland, Iceland, Norway and Sweden.

PARTICIPANTS: Women 15-19 years old in all Nordic countries (749 709) and 13-19 years old in Denmark, Norway and Sweden (815 044).

RESULTS: Both annual birth rates and abortion rates fell in all the Nordic countries during the study period. The highest user rate of hormonal contraceptives among 15-19-year-olds was observed in Denmark (from 51% to 47%) followed by Sweden (from 39% to 42%) and Norway (from 37% to 41%). Combined oral contraceptives were the most commonly used methods in all countries. The use of long-acting reversible contraceptives (LARC), implants and the levonorgestrel-releasing intrauterine systems, were increasing, especially in Sweden and Norway. In the subgroup of 18-19-year-old teenagers, the user rates of hormonal contraceptives varied between 63% and 61% in Denmark, 56% and 61% in Norway and 54% and 56% in Sweden. In the same subgroup, the steepest increase of LARC was seen, from 2% to 6% in Denmark, 2% to 9% in Norway and 7% to 17% in Sweden.

CONCLUSIONS: Birth and abortion rates continuously declined in the Nordic countries among teenagers. There was a high user rate of hormonal contraceptives, with an increase in the use of LARC especially among the oldest teenagers.}, } @article {pmid30379893, year = {2018}, author = {Bovo, S and Ribani, A and Utzeri, VJ and Schiavo, G and Bertolini, F and Fontanesi, L}, title = {Shotgun metagenomics of honey DNA: Evaluation of a methodological approach to describe a multi-kingdom honey bee derived environmental DNA signature.}, journal = {PloS one}, volume = {13}, number = {10}, pages = {e0205575}, pmid = {30379893}, issn = {1932-6203}, mesh = {Animals ; Bees ; *DNA ; High-Throughput Nucleotide Sequencing ; *Honey ; *Metagenome ; *Metagenomics/methods ; }, abstract = {Honey bees are considered large-scale monitoring tools due to their environmental exploration and foraging activities. Traces of these activities can be recovered in the honey that also may reflect the hive ecological micro-conditions in which it has been produced. This study applied a next generation sequencing platform (Ion Torrent) for shotgun metagenomic analysis of honey environmental DNA (eDNA). The study tested a methodological framework to interpret DNA sequence information useful to describe the complex ecosystems of the honey bee colony superorganism, its pathosphere and the heterogeneity of the agroecological environments and environmental sources that left DNA marks in the honey. Analysis of two honeys reported sequence reads from five main organism groups (kingdoms or phyla): arthropods (that mainly included reads from Apis mellifera, several other members of the Hymenotpera, in addition to members of the Diptera, Coleoptera and Lepidoptera, as well as aphids and mites), plants (that clearly confirmed the botanical origin of the two honeys, i.e. orange tree blossom and eucalyptus tree blossom honeys), fungi and bacteria (including common hive and honey bee gut microorganisms, honey bee pathogens and plant pathogens), and viruses (which accounted for the largest number of reads in both honeys, mainly assigned to Apis mellifera filamentous virus). The shotgun metagenomic approach that was used in this study can be applied in large scale experiments that might have multiple objectives according to the multi-kingdom derived eDNA that is contained in the honey.}, } @article {pmid30379842, year = {2018}, author = {Osazuwa-Peters, OL and Stevens, WD and Jiménez, I}, title = {Using museum specimens to estimate broad-scale species richness: Exploring the performance of individual-based and spatially explicit rarefaction.}, journal = {PloS one}, volume = {13}, number = {10}, pages = {e0204484}, pmid = {30379842}, issn = {1932-6203}, mesh = {*Biodiversity ; Computer Simulation ; Databases, Factual ; *Models, Biological ; *Museums ; Nicaragua ; Plants ; Spatial Analysis ; }, abstract = {Estimates of spatial patterns of broad-scale species richness are central to major questions in ecology, evolution and conservation. Yet, they are scarce due to incomplete information on species distributions. Often the only germane data derives from museum specimens collected during non-standardized sampling. Rarefaction, a promising approach to estimate broad-scale richness with these data, estimates the expected number of species represented in subsets of n specimens drawn from N specimens collected in a sampling unit. One version of rarefaction, known as individual-based rarefaction, assumes that the N specimens collected in a sampling unit constitute a random sample of individuals in that sampling unit. Another version, known as spatially explicit rarefaction, assumes that the N specimens collected in a sampling unit are spatially aggregated. We examined the working hypothesis that, when applied to museum specimen data, spatially explicit rarefaction is less biased than individual-based rarefaction because it reduces overestimation due to spatially aggregated sampling. We derived five predictions from this working hypothesis and tested them using computer simulation experiments based on a database of 129,782 plant specimens from Nicaragua, and sampling units of 5 x 5, 50 x 50, and 100 x 100 km. One experiment was a negative control, whereby we simulated collection of randomly chosen individuals from each sampling unit. In contrast, three other experiments included spatially aggregated sampling. In all experiments we applied individual-based and spatially explicit rarefaction to estimate richness, with n = 200 and n = 500 specimens. As expected, the experiment designed as a negative control did not support the working hypothesis. The other three experiments supported the working hypothesis in analyses of larger sampling units, but not in 5 x 5 km sampling units. The predictions we derived from the working hypothesis can be used to assess which rarefaction version is best in particular systems.}, } @article {pmid30377776, year = {2019}, author = {Scheirs, S and Hevink, B and Ortega-Sánchez, M and Jordana, X and McGlynn, H and Rodriguez-Baeza, A and Malgosa, A and Galtés, I}, title = {Intra vitam trauma pattern: changing the paradigm of forensic anthropology?.}, journal = {International journal of legal medicine}, volume = {133}, number = {2}, pages = {661-668}, pmid = {30377776}, issn = {1437-1596}, mesh = {Aged ; Aged, 80 and over ; *Death ; Forensic Anthropology ; Fractures, Bone/*pathology ; Humans ; Logistic Models ; Middle Aged ; Models, Biological ; }, abstract = {This study aims to improve a previous study that reported new traits to characterize a perimortem fracture pattern in human long bones. This second study aims to acquire further knowledge about these perimortem traits, specifically by improving the experimental setting-by using a Blunt Force Trauma Simulator-and increasing the sample size with a total of 43 autopsy specimens and 57 reproduced fractures. Additionally, we investigated whether these traits could be related to muscular contractions by adding axial compression in the experimentally fractured specimens. If intra vitam traits can be found, it would consequentially be more valuable for forensic anthropologists to shorten the perimortem period. We demonstrate that all traits are perimortem traits. Furthermore, based on our results, we see the tendency that the combination of traits-instead of the presence of each trait individually-may make it possible to distinguish intra vitam from perimortem fractures. This study confirms these distinct characteristics that can be valuable to utilize in the distinction between peri- and postmortem fractures.}, } @article {pmid30376128, year = {2018}, author = {Landhäusser, SM and Chow, PS and Dickman, LT and Furze, ME and Kuhlman, I and Schmid, S and Wiesenbauer, J and Wild, B and Gleixner, G and Hartmann, H and Hoch, G and McDowell, NG and Richardson, AD and Richter, A and Adams, HD}, title = {Standardized protocols and procedures can precisely and accurately quantify non-structural carbohydrates.}, journal = {Tree physiology}, volume = {38}, number = {12}, pages = {1764-1778}, pmid = {30376128}, issn = {1758-4469}, mesh = {Acids ; Carbohydrates/*analysis/chemistry ; Chemistry Techniques, Analytical ; Chromatography, Ion Exchange ; Enzymes ; Plants/*chemistry ; Specimen Handling ; Starch/analysis ; Sugars/analysis ; }, abstract = {Non-structural carbohydrates (NSCs), the stored products of photosynthesis, building blocks for growth and fuel for respiration, are central to plant metabolism, but their measurement is challenging. Differences in methods and procedures among laboratories can cause results to vary widely, limiting our ability to integrate and generalize patterns in plant carbon balance among studies. A recent assessment found that NSC concentrations measured for a common set of samples can vary by an order of magnitude, but sources for this variability were unclear. We measured a common set of nine plant material types, and two synthetic samples with known NSC concentrations, using a common protocol for sugar extraction and starch digestion, and three different sugar quantification methods (ion chromatography, enzyme, acid) in six laboratories. We also tested how sample handling, extraction solvent and centralizing parts of the procedure in one laboratory affected results. Non-structural carbohydrate concentrations measured for synthetic samples were within about 11.5% of known values for all three methods. However, differences among quantification methods were the largest source of variation in NSC measurements for natural plant samples because the three methods quantify different NSCs. The enzyme method quantified only glucose, fructose and sucrose, with ion chromatography we additionally quantified galactose, while the acid method quantified a large range of mono- and oligosaccharides. For some natural samples, sugars quantified with the acid method were two to five times higher than with other methods, demonstrating that trees allocate carbon to a range of sugar molecules. Sample handling had little effect on measurements, while ethanol sugar extraction improved accuracy over water extraction. Our results demonstrate that reasonable accuracy of NSC measurements can be achieved when different methods are used, as long as protocols are robust and standardized. Thus, we provide detailed protocols for the extraction, digestion and quantification of NSCs in plant samples, which should improve the comparability of NSC measurements among laboratories.}, } @article {pmid30374157, year = {2018}, author = {Gutleb, DR and Ostner, J and Schülke, O and Wajjwalku, W and Sukmak, M and Roos, C and Noll, A}, title = {Non-invasive genotyping with a massively parallel sequencing panel for the detection of SNPs in HPA-axis genes.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {15944}, pmid = {30374157}, issn = {2045-2322}, support = {OS201/8-1 and 254142454/GRK 2070//Deutsche Forschungsgemeinschaft (German Research Foundation)/International ; }, mesh = {Animals ; Computational Biology ; DNA/chemistry/isolation & purification/metabolism ; Feces/chemistry ; Female ; Genotype ; High-Throughput Nucleotide Sequencing/methods ; Hypothalamo-Hypophyseal System/*metabolism ; Macaca/*genetics ; Male ; Pituitary-Adrenal System/*metabolism ; *Polymorphism, Single Nucleotide ; Sequence Analysis, DNA ; }, abstract = {We designed a genotyping panel for the investigation of the genetic underpinnings of inter-individual differences in aggression and the physiological stress response. The panel builds on single nucleotide polymorphisms (SNPs) in genes involved in the three subsystems of the hypothalamic-pituitary-adrenal (HPA)-axis: the catecholamine, serotonin and corticoid metabolism. To promote the pipeline for use with wild animal populations, we used non-invasively collected faecal samples from a wild population of Assamese macaques (Macaca assamensis). We targeted loci of 46 previously reported SNPs in 21 candidate genes coding for elements of the HPA-axis and amplified and sequenced them using next-generation Illumina sequencing technology. We compared multiple bioinformatics pipelines for variant calling and variant effect prediction. Based on this strategy and the application of different quality thresholds, we identified up to 159 SNPs with different types of predicted functional effects among our natural study population. This study provides a massively parallel sequencing panel that will facilitate integrating large-scale SNP data into behavioural and physiological studies. Such a multi-faceted approach will promote understanding of flexibility and constraints of animal behaviour and hormone physiology.}, } @article {pmid30372522, year = {2019}, author = {Zhang, S and Lehmann, A and Zheng, W and You, Z and Rillig, MC}, title = {Arbuscular mycorrhizal fungi increase grain yields: a meta-analysis.}, journal = {The New phytologist}, volume = {222}, number = {1}, pages = {543-555}, doi = {10.1111/nph.15570}, pmid = {30372522}, issn = {1469-8137}, support = {//German Federal Ministry of Education and Research for the BonaRes project INPLAMINT/International ; BK20160689//Natural Science Foundation of Jiangsu Province/International ; //Green Talents Research Stay of the German Federal Ministry of Education and Research/International ; }, mesh = {Crops, Agricultural/growth & development/microbiology ; Databases as Topic ; Edible Grain/*growth & development ; Mycorrhizae/*physiology ; }, abstract = {Increasing grain yields of food cereal crops is a major goal in future sustainable agriculture. We quantitatively analyzed the potential role of arbuscular mycorrhizal (AM) fungi in enhancing grain yields of seven cereal crops with exceptional importance for human nutrition across the globe: corn, wheat, rice, barley, sorghum, millet and oat. We conducted a meta-analysis for three datasets including both English and Chinese language publications: the 'whole' dataset including both laboratory and field studies (168 articles); the 'field' dataset comprising only field studies (97 studies); and the 'field-inoculation' dataset including only AM fungal inoculation studies conducted in field conditions (70 articles). We found that the AM fungal effect on grain yield was less pronounced in field and noninoculation studies. AM fungal inoculation in field led to a 16% increase (overall effect) based on the 'field-inoculation' dataset; this effect was variable (77% trials had positive values), crop-specific, lower for new cultivars released after 1950 and further modulated by soil pH. Although there are neutral and negative effects of AM fungi on grain yields, we emphasize the importance of integrating AM fungi in sustainable agriculture to increase grain yields of cereal crops.}, } @article {pmid30372479, year = {2018}, author = {Cruz, M and González-Villa, J}, title = {Simplified procedure for efficient and unbiased population size estimation.}, journal = {PloS one}, volume = {13}, number = {10}, pages = {e0206091}, pmid = {30372479}, issn = {1932-6203}, mesh = {Algorithms ; Computer Simulation ; Data Interpretation, Statistical ; Humans ; Models, Statistical ; Monte Carlo Method ; *Population Density ; Sample Size ; }, abstract = {Population size estimation is relevant to social and ecological sciences. Exhaustive manual counting, the density method and automated computer vision are some of the estimation methods that are currently used. Some of these methods may work in concrete cases but they do not provide a fast, efficient and unbiased estimation in general. Recently, the CountEm method, based on systematic sampling with a grid of quadrats, was proposed. It offers an unbiased estimation that can be applied to any population. However, choosing suitable grid parameters is sometimes cumbersome. Here we define a more intuitive grid parametrization, using initial number of quadrats and sampling fraction. A crowd counting dataset with 51 images and their corresponding, manually annotated position point patterns, are used to analyze the variation of the coefficient of error with respect to different parameter choices. Our Monte Carlo resampling results show that the error depends on the sample size and the number of nonempty quadrats, but not on the size of the target population. A procedure to choose suitable parameter values is described, and the expected coefficients of error are given. Counting about 100 particles in 30 nonempty quadrats usually yields coefficients of error below 10%.}, } @article {pmid30371820, year = {2019}, author = {Nilsson, RH and Larsson, KH and Taylor, AFS and Bengtsson-Palme, J and Jeppesen, TS and Schigel, D and Kennedy, P and Picard, K and Glöckner, FO and Tedersoo, L and Saar, I and Kõljalg, U and Abarenkov, K}, title = {The UNITE database for molecular identification of fungi: handling dark taxa and parallel taxonomic classifications.}, journal = {Nucleic acids research}, volume = {47}, number = {D1}, pages = {D259-D264}, pmid = {30371820}, issn = {1362-4962}, mesh = {Computational Biology/*methods ; DNA Barcoding, Taxonomic/*methods ; *Databases, Nucleic Acid ; Fungi/*classification/*genetics ; *Genome, Fungal ; *Genomics/methods ; Software ; Web Browser ; }, abstract = {UNITE (https://unite.ut.ee/) is a web-based database and sequence management environment for the molecular identification of fungi. It targets the formal fungal barcode-the nuclear ribosomal internal transcribed spacer (ITS) region-and offers all ∼1 000 000 public fungal ITS sequences for reference. These are clustered into ∼459 000 species hypotheses and assigned digital object identifiers (DOIs) to promote unambiguous reference across studies. In-house and web-based third-party sequence curation and annotation have resulted in more than 275 000 improvements to the data over the past 15 years. UNITE serves as a data provider for a range of metabarcoding software pipelines and regularly exchanges data with all major fungal sequence databases and other community resources. Recent improvements include redesigned handling of unclassifiable species hypotheses, integration with the taxonomic backbone of the Global Biodiversity Information Facility, and support for an unlimited number of parallel taxonomic classification systems.}, } @article {pmid30371751, year = {2019}, author = {Lötsch, J and Kringel, D and Hummel, T}, title = {Machine Learning in Human Olfactory Research.}, journal = {Chemical senses}, volume = {44}, number = {1}, pages = {11-22}, pmid = {30371751}, issn = {1464-3553}, mesh = {Biomarkers/analysis ; Databases, Factual ; Electronic Nose ; Humans ; *Machine Learning ; Odorants/*analysis ; Smell/*physiology ; Volatile Organic Compounds/chemistry ; }, abstract = {The complexity of the human sense of smell is increasingly reflected in complex and high-dimensional data, which opens opportunities for data-driven approaches that complement hypothesis-driven research. Contemporary developments in computational and data science, with its currently most popular implementation as machine learning, facilitate complex data-driven research approaches. The use of machine learning in human olfactory research included major approaches comprising 1) the study of the physiology of pattern-based odor detection and recognition processes, 2) pattern recognition in olfactory phenotypes, 3) the development of complex disease biomarkers including olfactory features, 4) odor prediction from physico-chemical properties of volatile molecules, and 5) knowledge discovery in publicly available big databases. A limited set of unsupervised and supervised machine-learned methods has been used in these projects, however, the increasing use of contemporary methods of computational science is reflected in a growing number of reports employing machine learning for human olfactory research. This review provides key concepts of machine learning and summarizes current applications on human olfactory data.}, } @article {pmid30367000, year = {2019}, author = {Šulčius, S and Šimoliūnas, E and Alzbutas, G and Gasiūnas, G and Jauniškis, V and Kuznecova, J and Miettinen, S and Nilsson, E and Meškys, R and Roine, E and Paškauskas, R and Holmfeldt, K}, title = {Genomic Characterization of Cyanophage vB_AphaS-CL131 Infecting Filamentous Diazotrophic Cyanobacterium Aphanizomenon flos-aquae Reveals Novel Insights into Virus-Bacterium Interactions.}, journal = {Applied and environmental microbiology}, volume = {85}, number = {1}, pages = {}, pmid = {30367000}, issn = {1098-5336}, mesh = {Aphanizomenon/*virology ; Base Sequence ; Clustered Regularly Interspaced Short Palindromic Repeats ; DNA, Viral/analysis ; Genome, Viral/*genetics ; Lithuania ; Phylogeny ; Siphoviridae/classification/*genetics ; }, abstract = {While filamentous cyanobacteria play a crucial role in food web dynamics and biogeochemical cycling of many aquatic ecosystems around the globe, the knowledge regarding the phages infecting them is limited. Here, we describe the complete genome of the virulent cyanophage vB_AphaS-CL131 (here, CL 131), a Siphoviridae phage that infects the filamentous diazotrophic bloom-forming cyanobacterium Aphanizomenon flos-aquae in the brackish Baltic Sea. CL 131 features a 112,793-bp double-stranded DNA (dsDNA) genome encompassing 149 putative open reading frames (ORFs), of which the majority (86%) lack sequence homology to genes with known functions in other bacteriophages or bacteria. Phylogenetic analysis revealed that CL 131 possibly represents a new evolutionary lineage within the group of cyanophages infecting filamentous cyanobacteria, which form a separate cluster from phages infecting unicellular cyanobacteria. CL 131 encodes a putative type V-U2 CRISPR-Cas system with one spacer (out of 10) targeting a DNA primase pseudogene in a cyanobacterium and a putative type II toxin-antitoxin system, consisting of a GNAT family N-acetyltransferase and a protein of unknown function containing the PRK09726 domain (characteristic of HipB antitoxins). Comparison of CL 131 proteins to reads from Baltic Sea and other available fresh- and brackish-water metagenomes and analysis of CRISPR-Cas arrays in publicly available A. flos-aquae genomes demonstrated that phages similar to CL 131 are present and dynamic in the Baltic Sea and share a common history with their hosts dating back at least several decades. In addition, different CRISPR-Cas systems within individual A. flos-aquae genomes targeted several sequences in the CL 131 genome, including genes related to virion structure and morphogenesis. Altogether, these findings revealed new genomic information for exploring viral diversity and provide a model system for investigation of virus-host interactions in filamentous cyanobacteria.IMPORTANCE The genomic characterization of novel cyanophage vB_AphaS-CL131 and the analysis of its genomic features in the context of other viruses, metagenomic data, and host CRISPR-Cas systems contribute toward a better understanding of aquatic viral diversity and distribution in general and of brackish-water cyanophages infecting filamentous diazotrophic cyanobacteria in the Baltic Sea in particular. The results of this study revealed previously undescribed features of cyanophage genomes (e.g., self-excising intein-containing putative dCTP deaminase and putative cyanophage-encoded CRISPR-Cas and toxin-antitoxin systems) and can therefore be used to predict potential interactions between bloom-forming cyanobacteria and their cyanophages.}, } @article {pmid30366463, year = {2018}, author = {Nicosia, A and Mikov, A and Cammarata, M and Colombo, P and Andreev, Y and Kozlov, S and Cuttitta, A}, title = {The Anemonia viridis Venom: Coupling Biochemical Purification and RNA-Seq for Translational Research.}, journal = {Marine drugs}, volume = {16}, number = {11}, pages = {}, pmid = {30366463}, issn = {1660-3397}, support = {16-15-00167//Russian Science Foundation/ ; }, mesh = {Animals ; Cnidarian Venoms/*chemistry/*genetics/isolation & purification/pharmacology ; Data Mining ; Marine Toxins/*chemistry/genetics/isolation & purification/pharmacology ; Neurotoxins/*chemistry/*genetics/isolation & purification/pharmacology ; RNA/chemistry/genetics ; Sea Anemones/*chemistry/*genetics ; Sequence Analysis, RNA ; Translational Research, Biomedical ; }, abstract = {Blue biotechnologies implement marine bio-resources for addressing practical concerns. The isolation of biologically active molecules from marine animals is one of the main ways this field develops. Strikingly, cnidaria are considered as sustainable resources for this purpose, as they possess unique cells for attack and protection, producing an articulated cocktail of bioactive substances. The Mediterranean sea anemone Anemonia viridis has been studied extensively for years. In this short review, we summarize advances in bioprospecting of the A. viridis toxin arsenal. A. viridis RNA datasets and toxin data mining approaches are briefly described. Analysis reveals the major pool of neurotoxins of A. viridis, which are particularly active on sodium and potassium channels. This review therefore integrates progress in both RNA-Seq based and biochemical-based bioprospecting of A. viridis toxins for biotechnological exploitation.}, } @article {pmid30366399, year = {2018}, author = {Meng, X and Wang, F and Xie, Y and Song, G and Ma, S and Hu, S and Bai, J and Yang, Y}, title = {An Ontology-Driven Approach for Integrating Intelligence to Manage Human and Ecological Health Risks in the Geospatial Sensor Web.}, journal = {Sensors (Basel, Switzerland)}, volume = {18}, number = {11}, pages = {}, pmid = {30366399}, issn = {1424-8220}, support = {41501441//National Natural Science Foundation of China/ ; 2014HB04//Hubei Provincial Environment Protection Project/ ; GDGTKJ2017001//Guangdong Provincial Land Resource Research Project/ ; 2042017kf0212//Wuhan University Grant/ ; }, mesh = {Ecology ; Environmental Monitoring/*methods ; *Geographic Information Systems ; Humans ; Intelligence ; Software ; }, abstract = {Due to the rapid installation of a massive number of fixed and mobile sensors, monitoring machines are intentionally or unintentionally involved in the production of a large amount of geospatial data. Environmental sensors and related software applications are rapidly altering human lifestyles and even impacting ecological and human health. However, there are rarely specific geospatial sensor web (GSW) applications for certain ecological public health questions. In this paper, we propose an ontology-driven approach for integrating intelligence to manage human and ecological health risks in the GSW. We design a Human and Ecological health Risks Ontology (HERO) based on a semantic sensor network ontology template. We also illustrate a web-based prototype, the Human and Ecological Health Risk Management System (HaEHMS), which helps health experts and decision makers to estimate human and ecological health risks. We demonstrate this intelligent system through a case study of automatic prediction of air quality and related health risk.}, } @article {pmid30366337, year = {2019}, author = {Shi, Y and Shi, S and Wang, H}, title = {Reconsideration of the methodology for estimation of land population carrying capacity in Shanghai metropolis.}, journal = {The Science of the total environment}, volume = {652}, number = {}, pages = {367-381}, doi = {10.1016/j.scitotenv.2018.10.210}, pmid = {30366337}, issn = {1879-1026}, abstract = {How to estimate the urban land carrying capacity (ULCC)? Based on our previous research, this paper made improvements in two aspects: One is to subdivide land use types from four subspaces to seven subspaces (i.e. urban construction, industrial development, agricultural production, rural living, green ecological, other ecological and other subspaces), so as to distinguish more detailed the urban functional and spatial heterogeneities; the other is to reconstructing evaluation index system and estimate both maximum and appropriate population carrying capacities. The results demonstrate as follows: ① There is a significant difference between the population capacities in different types of subspaces. The urban construction and industrial development subspaces are the main carrier of population and economy. The agricultural production and rural living subspaces have low population capacities. The ecological protection and other subspaces have only a very low share of load. ② The appropriate and maximum population capacities of Shanghai metropolis are estimated to be approximately 20-23 million persons and 27-30 million persons, respectively, in 2009. There were 22.1028 million permanent residents of Shanghai in 2009, approaching the limit of the appropriate population capacity but lower than the limit of the maximum population capacity. ③ The methodology for estimation of maximum and appropriate ULCC in this paper not only gives the quantitative range, but also can provide the basis for growth control of urban population.}, } @article {pmid30366121, year = {2019}, author = {Rowe, M and Skerget, S and Rosenow, MA and Karr, TL}, title = {Identification and characterization of the zebra finch (Taeniopygia guttata) sperm proteome.}, journal = {Journal of proteomics}, volume = {193}, number = {}, pages = {192-204}, doi = {10.1016/j.jprot.2018.10.009}, pmid = {30366121}, issn = {1876-7737}, mesh = {Animals ; Avian Proteins/*metabolism ; Finches/*metabolism ; Gene Ontology ; Male ; Proteome/*metabolism ; *Proteomics ; Sperm Motility ; Sperm-Ovum Interactions ; Spermatozoa/*metabolism ; }, abstract = {Spermatozoa exhibit remarkable variability in size, shape, and performance. Our understanding of the molecular basis of this variation, however, is limited, especially in avian taxa. The zebra finch (Taeniopygia guttata) is a model organism in the study of avian sperm biology and sperm competition. Using LC-MS based proteomics, we identify and describe 494 proteins of the zebra finch sperm proteome (ZfSP). Gene ontology and associated bioinformatics analyses revealed a rich repertoire of proteins essential to sperm structure and function, including proteins linked to metabolism and energetics, as well as tubulin binding and microtubule related functions. The ZfSP also contained a number of immunity and defense proteins and proteins linked to sperm motility and sperm-egg interactions. Additionally, while most proteins in the ZfSP appear to be evolutionarily constrained, a small subset of proteins are evolving rapidly. Finally, in a comparison with the sperm proteome of the domestic chicken, we found an enrichment of proteins linked to catalytic activity and cytoskeleton related processes. As the first described passerine sperm proteome, and one of only two characterized avian sperm proteomes, the ZfSP provides a significant step towards a platform for studies of the molecular basis of sperm function and evolution in birds. SIGNIFICANCE: Using highly purified spermatozoa and LC-MS proteomics, we characterise the sperm proteome of the Zebra finch; the main model species for the avian order Passeriformes, the largest and most diverse of the avian clades. As the first described passerine sperm proteome, and one of only two reported avian sperm proteomes, these results will facilitate studies of sperm biology and mechanisms of fertilisation in passerines, as well as comparative studies of sperm evolution and reproduction across birds and other vertebrates.}, } @article {pmid30365710, year = {2018}, author = {Hashemi, SA}, title = {Ecological capability evaluation for afforestation and forest expansion using Geographic Information System (GIS) in management area of Caspian Sea.}, journal = {Anais da Academia Brasileira de Ciencias}, volume = {90}, number = {4}, pages = {3761-3768}, doi = {10.1590/0001-3765201820170805}, pmid = {30365710}, issn = {1678-2690}, mesh = {Caspian Sea ; Environmental Monitoring/*methods ; Forestry/methods ; *Forests ; Fuzzy Logic ; *Geographic Information Systems ; Iran ; }, abstract = {Ecological capability evaluation is referred to as evaluation of potential capability of land and determination of its natural land use. In this paper, ecological capability of Lille Basin in Lahijan was evaluated for afforestation and forest expansion using Geographical Information Systems (GIS). For this purpose, information layers (slope, elevation, geographical directions, temperature, rainfall, humidity, soil type, and canopy cover) were prepared by digitizing the data obtained from concerned organizations. First, the layers were prepared based on coordinate systems and pixel value. Then, they were standardized using fuzzy membership functions. The evaluation criteria were prioritized with regard to expert opinion, and by using multi-criteria evaluation method (MCE) and analysis of hierarchic process (AHP), and the final weight of each criterion was determined. The weight for 8 criteria including elevation, soil type, canopy cover (%), directions, slope, temperature, humidity, rainfall were 0.330, 0.210, 0.128, 0.117, 0.076, 0.054, 0.046 and 0.210, respectively. According to these weights, elevation has the highest value and the slope is the lowest. The results suggest that ecological capability exhibits sensitivity to variations of different criteria and its distribution is directly correlated to ecological factors especially climatic and physiographical ones. The incompatibility index (0.09) also indicated that the weights were logical. Then valuation of the maps performed. Finally, based on these values, capabilities of each environmental unit were identified and potentials of the area for afforestation were determined in five capability classes.}, } @article {pmid30365005, year = {2018}, author = {Cannataro, VL and Gaffney, SG and Townsend, JP}, title = {Effect Sizes of Somatic Mutations in Cancer.}, journal = {Journal of the National Cancer Institute}, volume = {110}, number = {11}, pages = {1171-1177}, pmid = {30365005}, issn = {1460-2105}, support = {T32 CA193200/CA/NCI NIH HHS/United States ; }, mesh = {*Biomarkers, Tumor ; Computational Biology/methods ; Genetic Association Studies ; Genetic Predisposition to Disease ; Genomics/methods ; Humans ; *Mutation ; Mutation Rate ; Neoplasms/diagnosis/*genetics ; Polymorphism, Single Nucleotide ; }, abstract = {A major goal of cancer biology is determination of the relative importance of the genetic alterations that confer selective advantage to cancer cells. Tumor sequence surveys have frequently ranked the importance of substitutions to cancer growth by P value or a false-discovery conversion thereof. However, P values are thresholds for belief, not metrics of effect. Their frequent misuse as metrics of effect has often been vociferously decried, even in cases when the only attributable mistake was omission of effect sizes. Here, we propose an appropriate ranking-the cancer effect size, which is the selection intensity for somatic variants in cancer cell lineages. The selection intensity is a metric of the survival and reproductive advantage conferred by mutations in somatic tissue. Thus, they are of fundamental importance to oncology, and have immediate relevance to ongoing decision making in precision medicine tumor boards, to the selection and design of clinical trials, to the targeted development of pharmaceuticals, and to basic research prioritization. Within this commentary, we first discuss the scope of current methods that rank confidence in the overrepresentation of specific mutated genes in cancer genomes. Then we bring to bear recent advances that draw upon an understanding of the development of cancer as an evolutionary process to estimate the effect size of somatic variants leading to cancer. We demonstrate the estimation of the effect sizes of all recurrent single nucleotide variants in 22 cancer types, quantifying relative importance within and between driver genes.}, } @article {pmid30362076, year = {2019}, author = {Almeida, OGG and De Martinis, ECP}, title = {Bioinformatics tools to assess metagenomic data for applied microbiology.}, journal = {Applied microbiology and biotechnology}, volume = {103}, number = {1}, pages = {69-82}, doi = {10.1007/s00253-018-9464-9}, pmid = {30362076}, issn = {1432-0614}, support = {17/13759-6//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 6762/2006-4//Conselho Nacional de Desenvolvimento Científico e Tecnológico (BR)/ ; }, mesh = {Biodiversity ; Computational Biology/*methods ; Gene Library ; High-Throughput Nucleotide Sequencing/methods ; Industrial Microbiology/*methods ; Metagenomics/*methods/statistics & numerical data ; Phylogeny ; Quality Control ; }, abstract = {The reduction of the price of DNA sequencing has resulted in the emergence of large data sets to handle and analyze, especially in microbial ecosystems, which are characterized by high taxonomic and functional diversities. To assess the properties of these complex ecosystems, a conceptual background of the application of NGS technology and bioinformatics analysis to metagenomics is required. Accordingly, this article presents an overview of the evolution of knowledge of microbial ecology from traditional culture-dependent methods to culture-independent methods and the last frontier in knowledge, metagenomics. Topics that will be covered include sample preparation for NGS, starting with total DNA extraction and library preparation, followed by a brief discussion of the chemistry of NGS to help provide an understanding of which bioinformatics pipeline approach may be helpful for achieving a researcher's goals. The importance of selecting appropriate sequencing coverage and depth parameters to obtain a suitable measure of microbial diversity is discussed. As all DNA sequencing processes produce base-calling errors that compromise data analysis, including genome assembly and microbial functional analysis, dedicated software is presented and conceptually discussed with regard to potential applications in the general microbial ecology field.}, } @article {pmid30357347, year = {2019}, author = {Jung, S and Lee, T and Cheng, CH and Buble, K and Zheng, P and Yu, J and Humann, J and Ficklin, SP and Gasic, K and Scott, K and Frank, M and Ru, S and Hough, H and Evans, K and Peace, C and Olmstead, M and DeVetter, LW and McFerson, J and Coe, M and Wegrzyn, JL and Staton, ME and Abbott, AG and Main, D}, title = {15 years of GDR: New data and functionality in the Genome Database for Rosaceae.}, journal = {Nucleic acids research}, volume = {47}, number = {D1}, pages = {D1137-D1145}, pmid = {30357347}, issn = {1362-4962}, mesh = {Computational Biology/*methods/statistics & numerical data ; *Databases, Genetic ; Gene Expression Profiling/methods ; Genes, Plant/genetics ; Genome, Plant/*genetics ; Genomics/*methods ; Information Storage and Retrieval/methods ; Internet ; Plant Breeding/methods ; Quantitative Trait Loci/genetics ; Rosaceae/classification/*genetics ; Species Specificity ; Synteny ; Time Factors ; User-Computer Interface ; }, abstract = {The Genome Database for Rosaceae (GDR, https://www.rosaceae.org) is an integrated web-based community database resource providing access to publicly available genomics, genetics and breeding data and data-mining tools to facilitate basic, translational and applied research in Rosaceae. The volume of data in GDR has increased greatly over the last 5 years. The GDR now houses multiple versions of whole genome assembly and annotation data from 14 species, made available by recent advances in sequencing technology. Annotated and searchable reference transcriptomes, RefTrans, combining peer-reviewed published RNA-Seq as well as EST datasets, are newly available for major crop species. Significantly more quantitative trait loci, genetic maps and markers are available in MapViewer, a new visualization tool that better integrates with other pages in GDR. Pathways can be accessed through the new GDR Cyc Pathways databases, and synteny among the newest genome assemblies from eight species can be viewed through the new synteny browser, SynView. Collated single-nucleotide polymorphism diversity data and phenotypic data from publicly available breeding datasets are integrated with other relevant data. Also, the new Breeding Information Management System allows breeders to upload, manage and analyze their private breeding data within the secure GDR server with an option to release data publicly.}, } @article {pmid30356291, year = {2018}, author = {Xiao, H and Tong, X and Gao, L and Hu, S and Tan, H and Huang, ZYX and Zhang, G and Yang, Q and Li, X and Huang, R and Tong, S and Tian, H}, title = {Spatial heterogeneity of hemorrhagic fever with renal syndrome is driven by environmental factors and rodent community composition.}, journal = {PLoS neglected tropical diseases}, volume = {12}, number = {10}, pages = {e0006881}, pmid = {30356291}, issn = {1935-2735}, mesh = {Animals ; China/epidemiology ; *Environmental Exposure ; Hemorrhagic Fever with Renal Syndrome/*epidemiology ; Humans ; Incidence ; Risk Factors ; Rodentia/*growth & development ; Spatial Analysis ; *Topography, Medical ; Zoonoses/*epidemiology ; }, abstract = {Hemorrhagic fever with renal syndrome (HFRS) is a rodent-borne disease caused mainly by two hantaviruses in China: Hantaan virus and Seoul virus. Environmental factors can significantly affect the risk of contracting hantavirus infections, primarily through their effects on rodent population dynamics and human-rodent contact. We aimed to clarify the environmental risk factors favoring rodent-to-human transmission to provide scientific evidence for developing effective HFRS prevention and control strategies. The 10-year (2006-2015) field surveillance data from the rodent hosts for hantavirus, the epidemiological and environmental data extracted from satellite images and meteorological stations, rodent-to-human transmission rates and impacts of the environment on rodent community composition were used to quantify the relationships among environmental factors, rodent species and HFRS occurrence. The study included 709 cases of HFRS. Rodent species in Chenzhou, a hantavirus hotspot, comprise mainly Rattus norvegicus, Mus musculus, R. flavipectus and some other species (R. losea and Microtus fortis calamorum). The rodent species played different roles across the various land types we examined, but all of them were associated with transmission risks. Some species were associated with HFRS occurrence risk in forest and water bodies. R. norvegicus and R. flavipectus were associated with risk of HFRS incidence in grassland, whereas M. musculus and R. flavipectus were associated with this risk in built-on land. The rodent community composition was also associated with environmental variability. The predictive risk models based on these significant factors were validated by a good-fit model, where: cultivated land was predicted to represent the highest risk for HFRS incidence, which accords with the statistics for HFRS cases in 2014-2015. The spatial heterogeneity of HFRS disease may be influenced by rodent community composition, which is associated with local environmental conditions. Therefore, future work should focus on preventing HFRS is moist, warm environments.}, } @article {pmid30356117, year = {2018}, author = {Fourati, S and Talla, A and Mahmoudian, M and Burkhart, JG and Klén, R and Henao, R and Yu, T and Aydın, Z and Yeung, KY and Ahsen, ME and Almugbel, R and Jahandideh, S and Liang, X and Nordling, TEM and Shiga, M and Stanescu, A and Vogel, R and , and Pandey, G and Chiu, C and McClain, MT and Woods, CW and Ginsburg, GS and Elo, LL and Tsalik, EL and Mangravite, LM and Sieberts, SK}, title = {A crowdsourced analysis to identify ab initio molecular signatures predictive of susceptibility to viral infection.}, journal = {Nature communications}, volume = {9}, number = {1}, pages = {4418}, pmid = {30356117}, issn = {2041-1723}, support = {R01 GM126019/GM/NIGMS NIH HHS/United States ; W911NF-15-1-0107//DOD | Defense Advanced Research Projects Agency (DARPA)/International ; U54 HL127624/HL/NHLBI NIH HHS/United States ; R01GM114434//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/International ; G0902266/MRC_/Medical Research Council/United Kingdom ; R01 GM114434/GM/NIGMS NIH HHS/United States ; T15 LM007088/LM/NLM NIH HHS/United States ; S10 OD018164/OD/NIH HHS/United States ; }, mesh = {Gene Expression/*genetics ; Healthy Volunteers ; Heme/metabolism ; Humans ; Influenza A Virus, H1N2 Subtype/immunology/pathogenicity ; Influenza A Virus, H3N2 Subtype/immunology/pathogenicity ; Respiratory Syncytial Viruses/immunology/pathogenicity ; Rhinovirus/immunology/pathogenicity ; }, abstract = {The response to respiratory viruses varies substantially between individuals, and there are currently no known molecular predictors from the early stages of infection. Here we conduct a community-based analysis to determine whether pre- or early post-exposure molecular factors could predict physiologic responses to viral exposure. Using peripheral blood gene expression profiles collected from healthy subjects prior to exposure to one of four respiratory viruses (H1N1, H3N2, Rhinovirus, and RSV), as well as up to 24 h following exposure, we find that it is possible to construct models predictive of symptomatic response using profiles even prior to viral exposure. Analysis of predictive gene features reveal little overlap among models; however, in aggregate, these genes are enriched for common pathways. Heme metabolism, the most significantly enriched pathway, is associated with a higher risk of developing symptoms following viral exposure. This study demonstrates that pre-exposure molecular predictors can be identified and improves our understanding of the mechanisms of response to respiratory viruses.}, } @article {pmid30355288, year = {2018}, author = {Gysi, DM and Voigt, A and Fragoso, TM and Almaas, E and Nowick, K}, title = {wTO: an R package for computing weighted topological overlap and a consensus network with integrated visualization tool.}, journal = {BMC bioinformatics}, volume = {19}, number = {1}, pages = {392}, pmid = {30355288}, issn = {1471-2105}, support = {GDE 204111/2014-5//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; }, mesh = {Algorithms ; Computational Biology/*methods ; *Consensus ; Escherichia coli/metabolism ; Gene Ontology ; *Gene Regulatory Networks ; Humans ; *Metabolic Networks and Pathways ; Metagenomics ; Oceans and Seas ; ROC Curve ; *Software ; Time Factors ; Transcription Factors/metabolism ; }, abstract = {BACKGROUND: Network analyses, such as of gene co-expression networks, metabolic networks and ecological networks have become a central approach for the systems-level study of biological data. Several software packages exist for generating and analyzing such networks, either from correlation scores or the absolute value of a transformed score called weighted topological overlap (wTO). However, since gene regulatory processes can up- or down-regulate genes, it is of great interest to explicitly consider both positive and negative correlations when constructing a gene co-expression network.

RESULTS: Here, we present an R package for calculating the weighted topological overlap (wTO), that, in contrast to existing packages, explicitly addresses the sign of the wTO values, and is thus especially valuable for the analysis of gene regulatory networks. The package includes the calculation of p-values (raw and adjusted) for each pairwise gene score. Our package also allows the calculation of networks from time series (without replicates). Since networks from independent datasets (biological repeats or related studies) are not the same due to technical and biological noise in the data, we additionally, incorporated a novel method for calculating a consensus network (CN) from two or more networks into our R package. To graphically inspect the resulting networks, the R package contains a visualization tool, which allows for the direct network manipulation and access of node and link information. When testing the package on a standard laptop computer, we can conduct all calculations for systems of more than 20,000 genes in under two hours. We compare our new wTO package to state of art packages and demonstrate the application of the wTO and CN functions using 3 independently derived datasets from healthy human pre-frontal cortex samples. To showcase an example for the time series application we utilized a metagenomics data set.

CONCLUSION: In this work, we developed a software package that allows the computation of wTO networks, CNs and a visualization tool in the R statistical environment. It is publicly available on CRAN repositories under the GPL -2 Open Source License (https://cran.r-project.org/web/packages/wTO/).}, } @article {pmid30355067, year = {2019}, author = {Yu, L and Guo, R and Jiang, Y and Ye, X and Yang, Z and Meng, Y and Shao, C}, title = {Genome-wide identification and characterization of novel microRNAs in seed development of soybean.}, journal = {Bioscience, biotechnology, and biochemistry}, volume = {83}, number = {2}, pages = {233-242}, doi = {10.1080/09168451.2018.1536513}, pmid = {30355067}, issn = {1347-6947}, mesh = {Cotyledon/genetics ; Data Mining/methods ; *Genome, Plant ; High-Throughput Nucleotide Sequencing ; MicroRNAs/*genetics ; RNA Interference ; Seeds/*genetics/*growth & development ; Software Design ; Glycine max/embryology/*genetics ; }, abstract = {MicroRNAs (miRNAs) are important and ubiquitous regulators of gene expression in eukaryotes. However, the information about miRNAs population and their regulatory functions involving in soybean seed development remains incomplete. Base on the Dicer-like1-mediated cleavage signals during miRNA processing could be employed for novel miRNA discovery, a genome-wide search for miRNA candidates involved in seed development was carried out. As a result, 17 novel miRNAs, 14 isoforms of miRNA (isomiRs) and 31 previously validated miRNAs were discovered. These novel miRNAs and isomiRs represented tissue-specific expression and the isomiRs showed significantly higher abundance than that of their miRNA counterparts in different tissues. After target prediction and degradome sequencing data-based validation, 13 novel miRNA-target pairs were further identified. Besides, five targets of 22-nt iso-gma-miR393h were found to be triggered to produce secondary trans-acting siRNA (ta-siRNAs). Summarily, our results could expand the repertoire of miRNAs with potentially important functions in soybean.}, } @article {pmid30352804, year = {2019}, author = {Yao, Z and Guo, Z and Wang, Y and Li, W and Fu, Y and Lin, Y and Lin, W and Lin, X}, title = {Integrated Succinylome and Metabolome Profiling Reveals Crucial Role of S-Ribosylhomocysteine Lyase in Quorum Sensing and Metabolism of Aeromonas hydrophila.}, journal = {Molecular & cellular proteomics : MCP}, volume = {18}, number = {2}, pages = {200-215}, pmid = {30352804}, issn = {1535-9484}, mesh = {Aeromonas hydrophila/*physiology ; Bacterial Proteins/chemistry/genetics/*metabolism ; Carbon-Sulfur Lyases/chemistry/genetics/*metabolism ; Chromatography, Liquid ; Gene Ontology ; Homoserine/analogs & derivatives/metabolism ; Lactones/metabolism ; Lysine/*chemistry/genetics ; Metabolome ; Metabolomics/*methods ; Mutagenesis, Site-Directed ; Protein Processing, Post-Translational ; *Quorum Sensing ; Tandem Mass Spectrometry ; }, abstract = {Protein modification by lysine succinylation is a newly identified post-translational modification (PTM) of lysine residues and plays an important role in diverse physiological functions, although their associated biological characteristics are still largely unknown. Here, we investigated the effects of lysine succinylation on the physiological regulation within a well-known fish pathogen, Aeromonas hydrophila A high affinity purification method was used to enrich peptides with lysine succinylation in A. hydrophila ATCC 7966, and a total of 2,174 lysine succinylation sites were identified on 666 proteins using LC-MS/MS. Gene ontology analysis indicated that these succinylated proteins are involved in diverse metabolic pathways and biological processes, including translation, protein export, and central metabolic pathways. The modifications of several selected candidates were further validated by Western blotting. Using site-directed mutagenesis, we observed that the succinylation of lysines on S-ribosylhomocysteine lyase (LuxS) at the K23 and K30 sites positively regulate the production of the quorum sensing autoinducer AI-2, and that these PTMs ultimately alter its competitiveness with another pathogen, Vibrio alginolyticus Moreover, subsequent metabolomic analyses indicated that K30 succinylation on LuxS may suppress the activated methyl cycle (AMC) and that both the K23 and K30 sites are involved in amino acid metabolism. Taken together, the results from this study provide significant insights into the functions of lysine succinylation and its critical roles on LuxS in regulating the cellular physiology of A. hydrophila.}, } @article {pmid30348785, year = {2018}, author = {Lindsey, PA and Miller, JRB and Petracca, LS and Coad, L and Dickman, AJ and Fitzgerald, KH and Flyman, MV and Funston, PJ and Henschel, P and Kasiki, S and Knights, K and Loveridge, AJ and Macdonald, DW and Mandisodza-Chikerema, RL and Nazerali, S and Plumptre, AJ and Stevens, R and Van Zyl, HW and Hunter, LTB}, title = {More than $1 billion needed annually to secure Africa's protected areas with lions.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {115}, number = {45}, pages = {E10788-E10796}, pmid = {30348785}, issn = {1091-6490}, mesh = {Africa ; Animals ; Conservation of Natural Resources/*economics/legislation & jurisprudence ; Datasets as Topic ; Ecosystem ; Lions/*physiology ; *Models, Statistical ; }, abstract = {Protected areas (PAs) play an important role in conserving biodiversity and providing ecosystem services, yet their effectiveness is undermined by funding shortfalls. Using lions (Panthera leo) as a proxy for PA health, we assessed available funding relative to budget requirements for PAs in Africa's savannahs. We compiled a dataset of 2015 funding for 282 state-owned PAs with lions. We applied three methods to estimate the minimum funding required for effective conservation of lions, and calculated deficits. We estimated minimum required funding as $978/km[2] per year based on the cost of effectively managing lions in nine reserves by the African Parks Network; $1,271/km[2] based on modeled costs of managing lions at ≥50% carrying capacity across diverse conditions in 115 PAs; and $2,030/km[2] based on Packer et al.'s [Packer et al. (2013) Ecol Lett 16:635-641] cost of managing lions in 22 unfenced PAs. PAs with lions require a total of $1.2 to $2.4 billion annually, or ∼$1,000 to 2,000/km[2], yet received only $381 million annually, or a median of $200/km[2] Ninety-six percent of range countries had funding deficits in at least one PA, with 88 to 94% of PAs with lions funded insufficiently. In funding-deficit PAs, available funding satisfied just 10 to 20% of PA requirements on average, and deficits total $0.9 to $2.1 billion. African governments and the international community need to increase the funding available for management by three to six times if PAs are to effectively conserve lions and other species and provide vital ecological and economic benefits to neighboring communities.}, } @article {pmid30348161, year = {2018}, author = {Jeanne, I and Chambers, LE and Kazazic, A and Russell, TL and Bobogare, A and Bugoro, H and Otto, F and Fafale, G and Amjadali, A}, title = {Mapping a Plasmodium transmission spatial suitability index in Solomon Islands: a malaria monitoring and control tool.}, journal = {Malaria journal}, volume = {17}, number = {1}, pages = {381}, pmid = {30348161}, issn = {1475-2875}, mesh = {*Animal Distribution ; Animals ; Anopheles/growth & development/*physiology ; Communicable Disease Control/*methods ; Geographic Information Systems ; Geographic Mapping ; Humans ; Larva/physiology ; Malaria/*transmission ; Melanesia ; Mosquito Control/*methods ; Mosquito Vectors/growth & development/*physiology ; Plasmodium/*physiology ; }, abstract = {BACKGROUND: Malaria remains a challenge in Solomon Islands, despite government efforts to implement a coordinated control programme. This programme resulted in a dramatic decrease in the number of cases and mortality however, malaria incidence remains high in the three most populated provinces. Anopheles farauti is the primary malaria vector and a better understanding of the spatial patterns parasite transmission is required in order to implement effective control measures. Previous entomological studies provide information on the ecological preferences of An. farauti but this information has never before been gathered and "translated" in useful tools as maps that provide information at both the national level and at the scale of villages, thus enabling local targeted control measures.

METHODS: A literature review and consultation with entomology experts were used to determine and select environmental preferences of An. farauti. Remote sensing images were processed to translate these preferences into geolocated information to allow them to be used as the basis for a Transmission Suitability Index (TSI). Validation was developed from independent previous entomological studies with georeferenced locations of An. farauti. Then, TSI was autoscaled to ten classes for mapping.

RESULTS: Key environmental preferences for the An. farauti were: distance to coastline, elevation, and availability of water sources. Based on these variables, a model was developed to provide a TSI. This TSI was developed using GIS and remote sensing image processing, resulting in maps and GIS raster layer for all the eight provinces and Honiara City at a 250 m spatial resolution. For a TSI ranging from 0 as not suitable to 13 as most suitable, all the previous collections of An. farauti had mean TSI value between 9 and 11 and were significantly higher than where the vector was searched for and absent. Resulting maps were provided after autoscaling the TSI into ten classes from 0 to 9 for visual clarity.

CONCLUSIONS: The TSI model developed here provides useful predictions of likely malaria transmission larval sources based on the environmental preferences of the mosquito, An. farauti. These predictions can provide sufficient lead-time for agencies to target malaria prevention and control measures and can assist with effective deployment of limited resources. As the model is built on the known environmental preferences of An. farauti, the model should be completed and updated as soon as new information is available. Because the model did not include any other malaria transmission factors such as care availability, diagnostic time, treatment, prevention, and entomological parameters other than the ecological preferences neither, our suitability mapping represents the upper bound of transmission areas. The results of this study can now being used as the basis of a malaria monitoring system which has been jointly implemented by the Solomon Islands National Vector Borne Disease Control Programme, the Solomon Islands Meteorological Services and the Australian Bureau of Meteorology. The TSI model development method can be applied to other regions of the world where this mosquito occurs and could be adapted for other species.}, } @article {pmid30346402, year = {2018}, author = {Borjon, JI and Schroer, SE and Bambach, S and Slone, LK and Abney, DH and Crandall, DJ and Smith, LB}, title = {A View of Their Own: Capturing the Egocentric View of Infants and Toddlers with Head-Mounted Cameras.}, journal = {Journal of visualized experiments : JoVE}, volume = {}, number = {140}, pages = {}, pmid = {30346402}, issn = {1940-087X}, support = {F32 HD093280/HD/NICHD NIH HHS/United States ; R01 HD028675/HD/NICHD NIH HHS/United States ; R01 HD074601/HD/NICHD NIH HHS/United States ; T32 HD007475/HD/NICHD NIH HHS/United States ; }, mesh = {*Child Development ; Child, Preschool ; Female ; Hand/physiology ; Humans ; Infant ; Male ; Video Recording/*instrumentation/*methods ; Vision, Ocular/*physiology ; Visual Perception/physiology ; }, abstract = {Infants and toddlers view the world, at a basic sensory level, in a fundamentally different way from their parents. This is largely due to biological constraints: infants possess different body proportions than their parents and the ability to control their own head movements is less developed. Such constraints limit the visual input available. This protocol aims to provide guiding principles for researchers using head-mounted cameras to understand the changing visual input experienced by the developing infant. Successful use of this protocol will allow researchers to design and execute studies of the developing child's visual environment set in the home or laboratory. From this method, researchers can compile an aggregate view of all the possible items in a child's field of view. This method does not directly measure exactly what the child is looking at. By combining this approach with machine learning, computer vision algorithms, and hand-coding, researchers can produce a high-density dataset to illustrate the changing visual ecology of the developing infant.}, } @article {pmid30344120, year = {2018}, author = {Gopalakrishnan, S and Sinding, MS and Ramos-Madrigal, J and Niemann, J and Samaniego Castruita, JA and Vieira, FG and Carøe, C and Montero, MM and Kuderna, L and Serres, A and González-Basallote, VM and Liu, YH and Wang, GD and Marques-Bonet, T and Mirarab, S and Fernandes, C and Gaubert, P and Koepfli, KP and Budd, J and Rueness, EK and Sillero, C and Heide-Jørgensen, MP and Petersen, B and Sicheritz-Ponten, T and Bachmann, L and Wiig, Ø and Hansen, AJ and Gilbert, MTP}, title = {Interspecific Gene Flow Shaped the Evolution of the Genus Canis.}, journal = {Current biology : CB}, volume = {28}, number = {21}, pages = {3441-3449.e5}, pmid = {30344120}, issn = {1879-0445}, support = {U01 MH106874/MH/NIMH NIH HHS/United States ; }, mesh = {Animals ; *Biological Evolution ; Canidae/*genetics ; *Gene Flow ; *Hybridization, Genetic ; *Phylogeny ; }, abstract = {The evolutionary history of the wolf-like canids of the genus Canis has been heavily debated, especially regarding the number of distinct species and their relationships at the population and species level [1-6]. We assembled a dataset of 48 resequenced genomes spanning all members of the genus Canis except the black-backed and side-striped jackals, encompassing the global diversity of seven extant canid lineages. This includes eight new genomes, including the first resequenced Ethiopian wolf (Canis simensis), one dhole (Cuon alpinus), two East African hunting dogs (Lycaon pictus), two Eurasian golden jackals (Canis aureus), and two Middle Eastern gray wolves (Canis lupus). The relationships between the Ethiopian wolf, African golden wolf, and golden jackal were resolved. We highlight the role of interspecific hybridization in the evolution of this charismatic group. Specifically, we find gene flow between the ancestors of the dhole and African hunting dog and admixture between the gray wolf, coyote (Canis latrans), golden jackal, and African golden wolf. Additionally, we report gene flow from gray and Ethiopian wolves to the African golden wolf, suggesting that the African golden wolf originated through hybridization between these species. Finally, we hypothesize that coyotes and gray wolves carry genetic material derived from a "ghost" basal canid lineage.}, } @article {pmid30343430, year = {2019}, author = {Patel, S and Homaei, A and Patil, S and Daverey, A}, title = {Microbial biosurfactants for oil spill remediation: pitfalls and potentials.}, journal = {Applied microbiology and biotechnology}, volume = {103}, number = {1}, pages = {27-37}, doi = {10.1007/s00253-018-9434-2}, pmid = {30343430}, issn = {1432-0614}, mesh = {Bacteria/*chemistry/metabolism ; Environmental Restoration and Remediation/*methods ; Fungi/*chemistry/metabolism ; Glycolipids/chemistry ; Lipopeptides/chemistry ; Oleic Acids/chemistry ; *Petroleum Pollution ; *Surface-Active Agents/chemistry ; }, abstract = {Spillage of fossil-based oils during their conveyance through water conduits are sporadic, but significant environmental disasters. As the viscous hydrocarbons of the crude oils spread on water surface and choke aquatic life to death, their effective degradation is crucial for ecological balance. Though chemical and mechanical means are conventional ways to tackle the issues, they are riddled with limitations. In this scenario, coercing the biosurfactant-producing bacteria and fungi are promising avenues. Biosurfactants, the amphiphilic compounds, are capable of reducing interfacial tension, dispersing the oil particles, and degrading them into non-toxic debris. Among the vast array of biosurfactants, the trio of rhamnolipid, sophorolipid, and surfactin have been characterized well. Among the microbes, only Pseudomonas, Bacillus, and Candida have been evaluated, while there can be other exploitable candidates. In this regard, this review discusses the scopes and hurdles in utilization of the microbial surface-active compounds for oil spill management.}, } @article {pmid30343232, year = {2019}, author = {Bock, C and Zimmermann, S and Beisser, D and Dinglinger, SM and Engelskirchen, S and Giesemann, P and Klink, S and Olefeld, JL and Rahmann, S and Vos, M and Boenigk, J and Sures, B}, title = {Silver stress differentially affects growth of phototrophic and heterotrophic chrysomonad flagellate populations.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {244}, number = {}, pages = {314-322}, doi = {10.1016/j.envpol.2018.09.146}, pmid = {30343232}, issn = {1873-6424}, mesh = {Animals ; Ecosystem ; Eukaryota/*growth & development ; Heterotrophic Processes/*drug effects ; Invertebrates/*growth & development ; Light ; Phototrophic Processes/*drug effects ; Plankton/*growth & development ; Silver/*toxicity ; Water Pollutants, Chemical/*toxicity ; }, abstract = {Silver ions are among the predominant anthropogenic introduced pollutants in aquatic systems. As silver has effects on species at all trophic levels the community composition in aquatic habitats can be changed as a result of silver stress. The response of planktonic protists to environmental stressors is particularly important as they act both as producers and consumers in complex planktonic communities. Chrysomonad flagellates are of major interest, since this group includes heterotrophic, mixotrophic and phototrophic taxa, and therefore allows analysis of silver stress in organisms with contrasting nutritional strategies independent of a potential taxonomic bias. In a series of lab experiments, we compared the response of different trophic chrysophyte strains to low (5 μg L[-1]), medium (10 μg L[-1]) and high (20 μg L[-1]) nominal Ag concentrations in combination with changes in temperature and light intensity (phototrophs), temperature and food concentration (heterotrophs), or a combination of the above settings (mixotrophs). All tested strains were negatively affected by silver in their growth rates. The phototrophic strains reacted strongly to silver stress, whereas light intensity and temperature had only minor effects on growth rates. For heterotrophic strains, high food concentration toned down the effect of silver, whereas temperatures outside the growth optimum had a combined stress effect. The mixotrophic strains reacted differently depending on whether their nutritional mode was dominated by heterotrophy or by phototrophy. The precise response pattern across all variables was uniquely different for every single species we tested. The present work contributes to a deeper understanding of the effects of environmental stressors on complex planktonic communities. It indicates that silver will negatively impact planktonic communities and may create shifts in their composition and functioning.}, } @article {pmid30339216, year = {2018}, author = {Wang, H and Yan, H and Liu, H and Liu, R and Chen, J and Xiang, Y}, title = {GFDP: the gene family database in poplar.}, journal = {Database : the journal of biological databases and curation}, volume = {2018}, number = {}, pages = {}, pmid = {30339216}, issn = {1758-0463}, mesh = {*Databases, Genetic ; *Genes, Plant ; Molecular Sequence Annotation ; *Multigene Family ; Populus/*genetics ; }, abstract = {A gene family is formed by duplication of a single original gene. Poplar trees (genus Populus) are important, principally because of their ecological and economic benefits, and are one of the most widely distributed and adaptable trees in the world. Systematic identification and annotation of gene family members are primary steps in studying the function and evolution of poplar genomes. Here, we describe the construction of the Gene Family Database in Poplar (GFDP), which contains information that systematically describes 6551 genes distributed in 145 gene families. GFDP is designed to present important biological information, such as gene structure, protein length, isoelectric point and functional and evolutionary information, using highly visual displays. Data and graphs are visualized by a web-based interface. Users can browse and download data through all the major browsers. GFDP provides a comprehensive platform with a solid foundation for further study of poplar gene families. GFDP is free available.}, } @article {pmid30336592, year = {2018}, author = {Yuan, X and Sun, W and Zou, X and Liu, B and Huang, W and Chen, Z and Li, Y and Qiu, MY and Liu, ZJ and Mao, Y and Zou, SQ}, title = {Sequencing of Euscaphis konishii Endocarp Transcriptome Points to Molecular Mechanisms of Endocarp Coloration.}, journal = {International journal of molecular sciences}, volume = {19}, number = {10}, pages = {}, pmid = {30336592}, issn = {1422-0067}, support = {118-KRC16006A//Fujian Science and Technology Innovation Leading Talent Support Project/ ; CXZX2016072//Special fund for science and technology innovation of Fujian Agriculture and Forestry University/ ; CXZX2016073//Special fund for science and technology innovation of Fujian Agriculture and Forestry University/ ; CXZX2016074//Special fund for science and technology innovation of Fujian Agriculture and Forestry University/ ; 31700292//National Science Foundation of China Projects/ ; }, mesh = {Anthocyanins/biosynthesis ; Carotenoids/biosynthesis ; Chlorophyll/metabolism ; Fruit/*genetics ; Gene Expression Profiling ; Gene Expression Regulation, Plant ; Gene Ontology ; Genes, Plant ; Malvaceae/*genetics ; Molecular Sequence Annotation ; Multigene Family ; Pigmentation/*genetics ; Protein Interaction Maps/genetics ; Reproducibility of Results ; *Sequence Analysis, RNA ; Transcription Factors/metabolism ; Transcriptome/*genetics ; }, abstract = {Flower and fruit colors are of vital importance to the ecology and economic market value of plants. The mechanisms of flower and fruit coloration have been well studied, especially among ornamental flower plants and cultivated fruits. As people pay more attention to exocarp coloration, the endocarp coloration in some species has often been ignored. Here, we report on the molecular mechanism of endocarp coloration in three development stages of Euscaphis konishii. The results show that endocarp reddening is closely related to anthocyanin accumulation, and a total of 86,120 unigenes were assembled, with a mean length of 893 bp (N50 length of 1642 bp). We identified a large number of differentially expressed genes associated with endocarp coloration, including anthocyanin biosynthesis, carotenoid biosynthesis, and chlorophyll breakdown. The genes participating in each step of the anthocyanin biosynthesis were found in the transcriptome dataset, but a few genes were found in the carotenoid biosynthesis and chlorophyll breakdown. In addition, the candidate R2R3-MYB transcription factors and candidate glutathione S-transferase transport genes, which likely regulate the anthocyanin biosynthesis, were identified. This study offers a platform for E. konishii functional genomic research and provides a reference for revealing the regulatory mechanisms of endocarp reddening.}, } @article {pmid30335763, year = {2018}, author = {Orantes, LC and Monroy, C and Dorn, PL and Stevens, L and Rizzo, DM and Morrissey, L and Hanley, JP and Rodas, AG and Richards, B and Wallin, KF and Helms Cahan, S}, title = {Uncovering vector, parasite, blood meal and microbiome patterns from mixed-DNA specimens of the Chagas disease vector Triatoma dimidiata.}, journal = {PLoS neglected tropical diseases}, volume = {12}, number = {10}, pages = {e0006730}, pmid = {30335763}, issn = {1935-2735}, mesh = {Animals ; Archaea/genetics/isolation & purification ; Bacteria/genetics/isolation & purification ; Central America ; Cluster Analysis ; Computational Biology ; DNA/*genetics/*isolation & purification ; *Feeding Behavior ; Fungi/genetics/isolation & purification ; *Gastrointestinal Microbiome ; High-Throughput Nucleotide Sequencing ; Humans ; Nematoda/genetics/isolation & purification ; Phylogeny ; Sequence Analysis, DNA ; Triatoma/*genetics/microbiology/parasitology/physiology ; Trypanosoma cruzi/genetics/*isolation & purification ; Viruses/genetics/isolation & purification ; }, abstract = {Chagas disease, considered a neglected disease by the World Health Organization, is caused by the protozoan parasite Trypanosoma cruzi, and transmitted by >140 triatomine species across the Americas. In Central America, the main vector is Triatoma dimidiata, an opportunistic blood meal feeder inhabiting both domestic and sylvatic ecotopes. Given the diversity of interacting biological agents involved in the epidemiology of Chagas disease, having simultaneous information on the dynamics of the parasite, vector, the gut microbiome of the vector, and the blood meal source would facilitate identifying key biotic factors associated with the risk of T. cruzi transmission. In this study, we developed a RADseq-based analysis pipeline to study mixed-species DNA extracted from T. dimidiata abdomens. To evaluate the efficacy of the method across spatial scales, we used a nested spatial sampling design that spanned from individual villages within Guatemala to major biogeographic regions of Central America. Information from each biotic source was distinguished with bioinformatics tools and used to evaluate the prevalence of T. cruzi infection and predominant Discrete Typing Units (DTUs) in the region, the population genetic structure of T. dimidiata, gut microbial diversity, and the blood meal history. An average of 3.25 million reads per specimen were obtained, with approximately 1% assigned to the parasite, 20% to the vector, 11% to bacteria, and 4% to putative blood meals. Using a total of 6,405 T. cruzi SNPs, we detected nine infected vectors harboring two distinct DTUs: TcI and a second unidentified strain, possibly TcIV. Vector specimens were sufficiently variable for population genomic analyses, with a total of 25,710 T. dimidiata SNPs across all samples that were sufficient to detect geographic genetic structure at both local and regional scales. We observed a diverse microbiotic community, with significantly higher bacterial species richness in infected T. dimidiata abdomens than those that were not infected. Unifrac analysis suggests a common assemblage of bacteria associated with infection, which co-occurs with the typical gut microbial community derived from the local environment. We identified vertebrate blood meals from five T. dimidiata abdomens, including chicken, dog, duck and human; however, additional detection methods would be necessary to confidently identify blood meal sources from most specimens. Overall, our study shows this method is effective for simultaneously generating genetic data on vectors and their associated parasites, along with ecological information on feeding patterns and microbial interactions that may be followed up with complementary approaches such as PCR-based parasite detection, 18S eukaryotic and 16S bacterial barcoding.}, } @article {pmid30335747, year = {2018}, author = {Wodarz, D and Skinner, PJ and Levy, DN and Connick, E}, title = {Virus and CTL dynamics in the extrafollicular and follicular tissue compartments in SIV-infected macaques.}, journal = {PLoS computational biology}, volume = {14}, number = {10}, pages = {e1006461}, pmid = {30335747}, issn = {1553-7358}, support = {R01 AI096966/AI/NIAID NIH HHS/United States ; UM1 AI126617/AI/NIAID NIH HHS/United States ; R24 OD010976/OD/NIH HHS/United States ; P51 OD011106/OD/NIH HHS/United States ; }, mesh = {Animals ; Computational Biology ; Host-Pathogen Interactions/*immunology ; Macaca ; Models, Immunological ; *Simian Acquired Immunodeficiency Syndrome/immunology/virology ; *Simian Immunodeficiency Virus/pathogenicity/physiology ; *T-Lymphocytes, Cytotoxic/immunology/virology ; }, abstract = {Data from SIV-infected macaques indicate that virus-specific cytotoxic T lymphocytes (CTL) are mostly present in the extrafollicular (EF) compartment of the lymphoid tissue, with reduced homing to the follicular (F) site. This contributes to the majority of the virus being present in the follicle and represents a barrier to virus control. Using mathematical models, we investigate these dynamics. Two models are analyzed. The first assumes that CTL can only become stimulated and expand in the extrafollicular compartment, with migration accounting for the presence of CTL in the follicle. In the second model, follicular CTL can also undergo antigen-induced expansion. Consistent with experimental data, both models predict increased virus compartmentalization in the presence of stronger CTL responses and lower virus loads, and a more pronounced rise of extrafollicular compared to follicular virus during CD8 cell depletion experiments. The models, however, differ in other aspects. The follicular expansion model results in dynamics that promote the clearance of productive infection in the extrafollicular site, with any productively infected cells found being the result of immigration from the follicle. This is not observed in the model without follicular CTL expansion. The models further predict different consequences of introducing engineered, follicular-homing CTL, which has been proposed as a therapeutic means to improve virus control. Without follicular CTL expansion, this is predicted to result in a reduction of virus load in both compartments. The follicular CTL expansion model, however, makes the counter-intuitive prediction that addition of F-homing CTL not only results in a reduction of follicular virus load, but also in an increase in extrafollicular virus replication. These predictions remain to be experimentally tested, which will be relevant for distinguishing between models and for understanding how therapeutic introduction of F-homing CTL might impact the overall dynamics of the infection.}, } @article {pmid30333512, year = {2018}, author = {Clark, CR and Maile, M and Blaney, P and Hellweg, SR and Strauss, A and Durose, W and Priya, S and Habicht, J and Burns, MB and Blekhman, R and Abrahante, JE and Starr, TK}, title = {Transposon mutagenesis screen in mice identifies TM9SF2 as a novel colorectal cancer oncogene.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {15327}, pmid = {30333512}, issn = {2045-2322}, support = {KL2 TR000113/TR/NCATS NIH HHS/United States ; P30 CA077598/CA/NCI NIH HHS/United States ; R00 CA151672/CA/NCI NIH HHS/United States ; 5R00CA1516723-03//U.S. Department of Health & Human Services | NIH | National Cancer Institute (NCI)/International ; }, mesh = {Animals ; Cell Cycle ; Cell Line, Tumor ; Ceramides/metabolism ; Colorectal Neoplasms/*metabolism/physiopathology ; *Gene Expression Regulation, Neoplastic ; Humans ; Membrane Proteins/genetics/*metabolism ; Mice ; Nuclear Proteins/metabolism ; Oncogenes ; Oxidative Phosphorylation ; *Signal Transduction ; Transcription Factors/metabolism ; Xenograft Model Antitumor Assays ; }, abstract = {New therapeutic targets for advanced colorectal cancer (CRC) are critically needed. Our laboratory recently performed an insertional mutagenesis screen in mice to identify novel CRC driver genes and, thus, potential drug targets. Here, we define Transmembrane 9 Superfamily 2 (TM9SF2) as a novel CRC oncogene. TM9SF2 is an understudied protein, belonging to a well conserved protein family characterized by their nine putative transmembrane domains. Based on our transposon screen we found that TM9SF2 is a candidate progression driver in digestive tract tumors. Analysis of The Cancer Genome Atlas (TCGA) data revealed that approximately 35% of CRC patients have elevated levels of TM9SF2 mRNA, data we validated using an independent set of CRC samples. RNAi silencing of TM9SF2 reduced CRC cell growth in an anchorage-independent manner, a hallmark of cancer. Furthermore, CRISPR/Cas9 knockout of TM9SF2 substantially diminished CRC tumor fitness in vitro and in vivo. Transcriptome analysis of TM9SF2 knockout cells revealed a potential role for TM9SF2 in cell cycle progression, oxidative phosphorylation, and ceramide signaling. Lastly, we report that increased TM9SF2 expression correlates with disease stage and low TM9SF2 expression correlate with a more favorable relapse-free survival. Taken together, this study provides evidence that TM9SF2 is a novel CRC oncogene.}, } @article {pmid30329222, year = {2019}, author = {Hoff, SNK and Baalsrud, HT and Tooming-Klunderud, A and Skage, M and Richmond, T and Obernosterer, G and Shirzadi, R and Tørresen, OK and Jakobsen, KS and Jentoft, S}, title = {Long-read sequence capture of the haemoglobin gene clusters across codfish species.}, journal = {Molecular ecology resources}, volume = {19}, number = {1}, pages = {245-259}, pmid = {30329222}, issn = {1755-0998}, support = {222378//Norges Forskningsråd/ ; }, mesh = {Animals ; Computational Biology ; Evolution, Molecular ; Gadiformes/*classification/*genetics ; Gadus morhua ; Gene Order ; *Genetic Loci ; Genetic Variation ; Genomics/*methods ; Hemoglobins/*genetics ; High-Throughput Nucleotide Sequencing/*methods ; *Multigene Family ; Synteny ; }, abstract = {Combining high-throughput sequencing with targeted sequence capture has become an attractive tool to study specific genomic regions of interest. Most studies have so far focused on the exome using short-read technology. These approaches are not designed to capture intergenic regions needed to reconstruct genomic organization, including regulatory regions and gene synteny. Here, we demonstrate the power of combining targeted sequence capture with long-read sequencing technology for comparative genomic analyses of the haemoglobin (Hb) gene clusters across eight species separated by up to 70 million years. Guided by the reference genome assembly of the Atlantic cod (Gadus morhua) together with genome information from draft assemblies of selected codfishes, we designed probes covering the two Hb gene clusters. Use of custom-made barcodes combined with PacBio RSII sequencing led to highly continuous assemblies of the LA (~100 kb) and MN (~200 kb) clusters, which include syntenic regions of coding and intergenic sequences. Our results revealed an overall conserved genomic organization of the Hb genes within this lineage, yet with several, lineage-specific gene duplications. Moreover, for some of the species examined, we identified amino acid substitutions at two sites in the Hbb1 gene as well as length polymorphisms in its regulatory region, which has previously been linked to temperature adaptation in Atlantic cod populations. This study highlights the use of targeted long-read capture as a versatile approach for comparative genomic studies by generation of a cross-species genomic resource elucidating the evolutionary history of the Hb gene family across the highly divergent group of codfishes.}, } @article {pmid30329134, year = {2019}, author = {Kahn, R and Hitchings, M and Wang, R and Bellan, SE and Lipsitch, M}, title = {Analyzing Vaccine Trials in Epidemics With Mild and Asymptomatic Infection.}, journal = {American journal of epidemiology}, volume = {188}, number = {2}, pages = {467-474}, pmid = {30329134}, issn = {1476-6256}, support = {K01 AI125830/AI/NIAID NIH HHS/United States ; R37 AI051164/AI/NIAID NIH HHS/United States ; U54 GM088558/GM/NIGMS NIH HHS/United States ; }, mesh = {Asymptomatic Infections/*epidemiology ; Basic Reproduction Number ; Data Interpretation, Statistical ; Epidemics ; Humans ; Proportional Hazards Models ; Randomized Controlled Trials as Topic/*methods/standards ; *Research Design ; Risk ; Seroepidemiologic Studies ; Vaccines/*immunology ; Virus Diseases/*epidemiology/*prevention & control ; Zika Virus Infection/epidemiology/prevention & control ; }, abstract = {Vaccine efficacy against susceptibility to infection (VES), regardless of symptoms, is an important endpoint of vaccine trials for pathogens with a high proportion of asymptomatic infection, because such infections may contribute to onward transmission and long-term sequelae, such as congenital Zika syndrome. However, estimating VES is resource-intensive. We aimed to identify approaches for accurately estimating VES when limited information is available and resources are constrained. We modeled an individually randomized vaccine trial by generating a network of individuals and simulating an epidemic. The disease natural history followed a "susceptible-exposed-infectious/symptomatic (or infectious/asymptomatic)-recovered" model. We then used 7 approaches to estimate VES, and we also estimated vaccine efficacy against progression to symptoms (VEP). A corrected relative risk and an interval-censored Cox model accurately estimate VES and only require serological testing of participants once, while a Cox model using only symptomatic infections returns biased estimates. Only acquiring serological endpoints in a 10% sample and imputing the remaining infection statuses yields unbiased VES estimates across values of the basic reproduction number (R0) and accurate estimates of VEP for higher R0 values. Identifying resource-preserving methods for accurately estimating VES and VEP is important in designing trials for diseases with a high proportion of asymptomatic infection.}, } @article {pmid30329081, year = {2019}, author = {Passot, S and Couvreur, V and Meunier, F and Draye, X and Javaux, M and Leitner, D and Pagès, L and Schnepf, A and Vanderborght, J and Lobet, G}, title = {Connecting the dots between computational tools to analyse soil-root water relations.}, journal = {Journal of experimental botany}, volume = {70}, number = {9}, pages = {2345-2357}, doi = {10.1093/jxb/ery361}, pmid = {30329081}, issn = {1460-2431}, mesh = {*Computer Simulation ; *Plant Roots ; *Soil ; *Water ; }, abstract = {In recent years, many computational tools, such as image analysis, data management, process-based simulation, and upscaling tools, have been developed to help quantify and understand water flow in the soil-root system, at multiple scales (tissue, organ, plant, and population). Several of these tools work together or at least are compatible. However, for the uninformed researcher, they might seem disconnected, forming an unclear and disorganized succession of tools. In this article, we show how different studies can be further developed by connecting them to analyse soil-root water relations in a comprehensive and structured network. This 'explicit network of soil-root computational tools' informs readers about existing tools and helps them understand how their data (past and future) might fit within the network. We also demonstrate the novel possibilities of scale-consistent parameterizations made possible by the network with a set of case studies from the literature. Finally, we discuss existing gaps in the network and how we can move forward to fill them.}, } @article {pmid30327529, year = {2018}, author = {Curry, A}, title = {The internet of animals that could help to save vanishing wildlife.}, journal = {Nature}, volume = {562}, number = {7727}, pages = {322-326}, doi = {10.1038/d41586-018-07036-2}, pmid = {30327529}, issn = {1476-4687}, mesh = {*Animal Identification Systems/economics ; *Animal Migration ; Animals ; Animals, Wild/*physiology ; Astronauts ; Birds ; Cell Phone ; Conservation of Natural Resources/*methods ; Cues ; Earthquakes/statistics & numerical data ; Endangered Species/*statistics & numerical data ; Energy Metabolism ; Environmental Monitoring/economics/*instrumentation/*methods ; Geographic Information Systems ; Germany ; *Internet ; Light ; Magnetic Fields ; Mobile Applications ; Moscow ; Radio ; Satellite Communications/instrumentation/trends ; Spacecraft ; United States ; United States National Aeronautics and Space Administration/organization & administration ; }, } @article {pmid30326457, year = {2019}, author = {Moustakas, A and Daliakopoulos, IN and Benton, TG}, title = {Data-driven competitive facilitative tree interactions and their implications on nature-based solutions.}, journal = {The Science of the total environment}, volume = {651}, number = {Pt 2}, pages = {2269-2280}, doi = {10.1016/j.scitotenv.2018.09.349}, pmid = {30326457}, issn = {1879-1026}, mesh = {Big Data ; Data Science ; *Grassland ; Longevity ; Population Density ; Population Dynamics ; Seasons ; Soil/chemistry ; South Africa ; Temperature ; Trees/*physiology ; }, abstract = {Spatio-temporal data are more ubiquitous and richer than even before and the availability of such data poses great challenges in data analytics. Ecological facilitation, the positive effect of density of individuals on the individual's survival across a stress gradient, is a complex phenomenon. A large number of tree individuals coupled with soil moisture, temperature, and water stress data across a long temporal period were followed. Data-driven analysis in the absence of hypothesis was performed. Information theoretic analysis of multiple statistical models was employed in order to quantify the best data-driven index of vegetation density and spatial scale of interactions. Sequentially, tree survival was quantified as a function of the size of the individual, vegetation density, and time at the optimal spatial interaction scale. Land surface temperature and soil moisture were also statistically explained by tree size, density, and time. Results indicated that in space both facilitation and competition co-exist in the same ecosystem and the sign and magnitude of this depend on the spatial scale. Overall, within the optimal data-driven spatial scale, tree survival was best explained by the interaction between density and year, sifting overall from facilitation to competition through time. However, small sized trees were always facilitated by increased densities, while large sized trees had either negative or no density effects. Tree size was more important predictor than density in survival and this has implications for nature-based solutions: maintaining large tree individuals or planting species that can become large-sized can safeguard against tree-less areas by promoting survival at long time periods through harsh environmental conditions. Large trees had also a significant effect in moderating land surface temperature and this effect was higher than the one of vegetation density on temperature.}, } @article {pmid30325353, year = {2018}, author = {Du, E}, title = {A database of annual atmospheric acid and nutrient deposition to China's forests.}, journal = {Scientific data}, volume = {5}, number = {}, pages = {180223}, pmid = {30325353}, issn = {2052-4463}, mesh = {Acid Rain ; Air Pollutants/*analysis ; China ; *Databases, Factual ; *Environmental Monitoring ; *Forests ; }, abstract = {Anthropogenic emissions have substantially altered atmospheric acid and nutrient deposition in China. Understanding the status and characteristics of acid and nutrient deposition to China's forests is crucial to assess the consequent impacts, and to better guide forest management options. Based on a comprehensive literature review, here I present an updated database for annual acid and nutrient deposition during the period 1991-2015 in China's forests (CFAND 2.0). The database includes information from 56 forested sites on the water fluxes of bulk precipitation and throughfall, the concentrations of H[+] (pH), dissolved inorganic nitrogen (N) (NH4[+] and NO3[-]), sulfur (S), dissolved phosphorus (P), potassium (K[+]), calcium (Ca[2+]) and magnesium (Mg[2+]) in bulk precipitation and throughfall, and the fluxes of dissolved inorganic N, S, dissolved P, K[+], Ca[2+] and Mg[2+] in bulk deposition and throughfall. This database will help to understand the spatial patterns of acid and nutrient deposition, validate modelling results of acid and nutrient deposition and assess the ecological effects of acid and nutrient deposition in China's forests.}, } @article {pmid30324133, year = {2018}, author = {Song, H and Wignall, PB and Dunhill, AM}, title = {Decoupled taxonomic and ecological recoveries from the Permo-Triassic extinction.}, journal = {Science advances}, volume = {4}, number = {10}, pages = {eaat5091}, pmid = {30324133}, issn = {2375-2548}, mesh = {Animals ; Aquatic Organisms/*classification/genetics/physiology ; Biological Evolution ; Databases, Factual ; Ecosystem ; *Extinction, Biological ; Food Chain ; *Fossils ; Genetic Variation ; Oceans and Seas ; Predatory Behavior ; Reptiles ; }, abstract = {The Permian-Triassic mass extinction was the worst crisis faced by life; it killed >90% of marine species in less than 0.1 million years (Ma). However, knowledge of its macroecological impact over prolonged time scales is limited. We show that marine ecosystems dominated by non-motile animals shifted to ones dominated by nektonic groups after the extinction. In Triassic oceans, animals at high trophic levels recovered faster than those at lower levels. The top-down rebuilding of marine ecosystems was still underway in the latest Triassic, ~50 Ma after the extinction, and contrasts with the ~5-Ma recovery required for taxonomic diversity. The decoupling between taxonomic and ecological recoveries suggests that a process of vacant niche filling before reaching the maximum environmental carrying capacity is independent of ecosystem structure building.}, } @article {pmid30318637, year = {2019}, author = {Cursio, JF and Mermelstein, RJ and Hedeker, D}, title = {Latent trait shared-parameter mixed models for missing ecological momentary assessment data.}, journal = {Statistics in medicine}, volume = {38}, number = {4}, pages = {660-673}, doi = {10.1002/sim.7989}, pmid = {30318637}, issn = {1097-0258}, support = {P01CA098262/CA/NCI NIH HHS/United States ; }, mesh = {Affect ; *Data Interpretation, Statistical ; Humans ; Longitudinal Studies ; *Models, Statistical ; Reminder Systems ; Students/psychology ; Time Factors ; }, abstract = {Latent trait shared-parameter mixed models for ecological momentary assessment (EMA) data containing missing values are developed in which data are collected in an intermittent manner. In such studies, data are often missing due to unanswered prompts. Using item response theory models, a latent trait is used to represent the missing prompts and modeled jointly with a mixed model for bivariate longitudinal outcomes. Both one- and two-parameter latent trait shared-parameter mixed models are presented. These new models offer a unique way to analyze missing EMA data with many response patterns. Here, the proposed models represent missingness via a latent trait that corresponds to the students' "ability" to respond to the prompting device. Data containing more than 10 300 observations from an EMA study involving high school students' positive and negative affects are presented. The latent trait representing missingness was a significant predictor of both positive affect and negative affect outcomes. The models are compared to a missing at random mixed model. A simulation study indicates that the proposed models can provide lower bias and increased efficiency compared to the standard missing at random approach commonly used with intermittent missing longitudinal data.}, } @article {pmid30314778, year = {2018}, author = {Singleton, DA and Sánchez-Vizcaíno, F and Arsevska, E and Dawson, S and Jones, PH and Noble, PJM and Pinchbeck, GL and Williams, NJ and Radford, AD}, title = {New approaches to pharmacosurveillance for monitoring prescription frequency, diversity, and co-prescription in a large sentinel network of companion animal veterinary practices in the United Kingdom, 2014-2016.}, journal = {Preventive veterinary medicine}, volume = {159}, number = {}, pages = {153-161}, pmid = {30314778}, issn = {1873-1716}, mesh = {Animals ; Anti-Bacterial Agents/*administration & dosage ; Cat Diseases/*drug therapy ; Cats ; *Data Mining ; Dog Diseases/*drug therapy ; Dogs ; Electronic Health Records/*statistics & numerical data ; Practice Patterns, Physicians'/*statistics & numerical data ; *Rabbits ; United Kingdom ; }, abstract = {Pharmaceutical agents (PAs) are commonly prescribed in companion animal practice in the United Kingdom. However, little is known about PA prescription on a population-level, particularly with respect to PAs authorised for human use alone prescribed via the veterinary cascade; this raises important questions regarding the efficacy and safety of PAs prescribed to companion animals. This study explored new approaches for describing PA prescription, diversity and co-prescription in dogs, cats and rabbits utilising electronic health records (EHRs) from a sentinel network of 457 companion animal-treating veterinary sites throughout the UK over a 2-year period (2014-2016). A novel text mining-based identification and classification methodology was utilised to semi-automatically map practitioner-defined product descriptions recorded in 918,333 EHRs from 413,870 dogs encompassing 1,242,270 prescriptions; 352,730 EHRs from 200,541 cats encompassing 491,554 prescriptions, and 22,526 EHRS from 13,398 rabbits encompassing 18,490 prescriptions respectively. PA prescription as a percentage of booked consultations was 65.4% (95% confidence interval, CI, 64.6-66.3) in dogs; in cats it was 69.1% (95% CI, 67.9-70.2) and in rabbits, 56.3% (95% CI, 54.7-57.8). Vaccines were the most commonly prescribed PAs in all three species, with antibiotics, antimycotics, and parasiticides also commonly prescribed. PA prescription utilising products authorised for human use only (hence, 'human-authorised') comprised 5.1% (95% CI, 4.7-5.5) of total canine prescription events; in cats it was 2.8% (95% CI, 2.6-3.0), and in rabbits, 7.8% (95% CI, 6.5-9.0). The most commonly prescribed human-authorised PA in dogs was metronidazole (antibiotic); in cats and rabbits it was ranitidine (H2 histamine receptor antagonist). Using a new approach utilising the Simpson's Diversity Index (an ecological measure of relative animal, plant etc. species abundance), we identified differences in prescription based on presenting complaint and species, with rabbits generally exposed to a less diverse range of PAs than dogs or cats, potentially reflecting the paucity of authorised PAs for use in rabbits. Finally, through a novel application of network analysis, we demonstrated the existence of three major co-prescription groups (preventive health; treatment of disease, and euthanasia); a trend commonly observed in practice. This study represents the first time PA prescription has been described across all pharmaceutical families in a large population of companion animals, encompassing PAs authorised for both veterinary and human-only use. These data form a baseline against which future studies could be compared, and provides some useful tools for understanding PA comparative efficacy and risks when prescribed in the varied setting of clinical practice.}, } @article {pmid30313373, year = {2018}, author = {Bartlett, CR and Passos, EMD and Da Silva, FG and Diniz, LEC and Dollet, M}, title = {A new species of Oecleus Stål (Hemiptera: Fulgoroidea: Cixiidae) from coconut in Brazil.}, journal = {Zootaxa}, volume = {4472}, number = {2}, pages = {358-364}, doi = {10.11646/zootaxa.4472.2.8}, pmid = {30313373}, issn = {1175-5334}, mesh = {Animals ; Brazil ; *Cocos ; Databases, Nucleic Acid ; *Hemiptera ; Mitochondria ; }, abstract = {A new species of cixiid planthopper (Hemiptera: Fulgoroidea) in the genus Oecleus Stål, Oecleus sergipensis n. sp., is described from Sergipe State, Brazil. This new taxon is associated with coconut (Cocos nucifera L.) and date palm (Phoenix L). The species was detected in Auchenorrhyncha surveys to find potential vectors of lethal yellowing type syndrome. This is the first report of the genus Oecleus in Brazil. Sequence data from the mitochondrial cytochrome c oxidase subunit I (COI) barcoding region was obtained and accessioned into GenBank.}, } @article {pmid30312000, year = {2019}, author = {Stobie, CS and Cunningham, MJ and Oosthuizen, CJ and Bloomer, P}, title = {Finding stories in noise: Mitochondrial portraits from RAD data.}, journal = {Molecular ecology resources}, volume = {19}, number = {1}, pages = {191-205}, doi = {10.1111/1755-0998.12953}, pmid = {30312000}, issn = {1755-0998}, support = {77240//National Research Foundation/ ; //Genomics Research Institute, University of Pretoria/ ; }, mesh = {Animals ; Computational Biology/*methods ; Cyprinidae/classification/genetics ; DNA, Mitochondrial/*chemistry/*genetics ; Genetics, Population/*methods ; High-Throughput Nucleotide Sequencing/*methods ; Metagenomics/*methods ; }, abstract = {Mitochondrial DNA (mtDNA) has formed the backbone of phylogeographic research for many years; however, recent trends focus on genome-wide analyses. One method proposed for calibrating inferences from noisy next-generation data, such as RAD sequencing, is to compare these results with analyses of mitochondrial sequences. Most researchers using this approach appear to be unaware that many single nucleotide polymorphisms (SNPs) identified from genome-wide sequence data are themselves mitochondrial, or assume that these are too few to bias analyses. Here, we demonstrate two methods for mining mitochondrial markers using RAD sequence data from three South African species of yellowfish, Labeobarbus. First, we use a rigorous SNP discovery pipeline using the program stacks, to identify variant sites in mtDNA, which we then combine into haplotypes. Second, we directly map sequence reads against a mitochondrial genome reference. This method allowed us to reconstruct up to 98% of the Labeobarbus mitogenome. We validated these mitogenome reconstructions through blast database searches and by comparison with cytochrome b gene sequences obtained through Sanger sequencing. Finally, we investigate the organismal consequences of these data including ancient genetic exchange and a recent translocation among populations of L. natalensis, as well as interspecific hybridization between L. aeneus and L. kimberleyensis.}, } @article {pmid30311911, year = {2018}, author = {Fischer, J and Müller, SY and Netzker, T and Jäger, N and Gacek-Matthews, A and Scherlach, K and Stroe, MC and García-Altares, M and Pezzini, F and Schoeler, H and Reichelt, M and Gershenzon, J and Krespach, MK and Shelest, E and Schroeckh, V and Valiante, V and Heinzel, T and Hertweck, C and Strauss, J and Brakhage, AA}, title = {Chromatin mapping identifies BasR, a key regulator of bacteria-triggered production of fungal secondary metabolites.}, journal = {eLife}, volume = {7}, number = {}, pages = {}, pmid = {30311911}, issn = {2050-084X}, support = {SFB-F3703//Austrian Science Fund FWF/Austria ; }, mesh = {Acetylation ; Aspergillus nidulans/genetics/*metabolism ; Chromatin/*metabolism ; Fungal Proteins/genetics/*metabolism ; Gene Expression Regulation, Fungal ; Gene Ontology ; Genome, Fungal ; Histidine/metabolism ; Histones/metabolism ; Lysine/metabolism ; Mitochondria/metabolism ; Multigene Family ; Nitrogen/metabolism ; Phylogeny ; *Secondary Metabolism ; Signal Transduction ; Streptomyces/*metabolism ; Transcription Factors/metabolism ; }, abstract = {The eukaryotic epigenetic machinery can be modified by bacteria to reprogram the response of eukaryotes during their interaction with microorganisms. We discovered that the bacterium Streptomyces rapamycinicus triggered increased chromatin acetylation and thus activation of the silent secondary metabolism ors gene cluster in the fungus Aspergillus nidulans. Using this model, we aim understanding mechanisms of microbial communication based on bacteria-triggered chromatin modification. Using genome-wide ChIP-seq analysis of acetylated histone H3, we uncovered the unique chromatin landscape in A. nidulans upon co-cultivation with S. rapamycinicus and relate changes in the acetylation to that in the fungal transcriptome. Differentially acetylated histones were detected in genes involved in secondary metabolism, in amino acid and nitrogen metabolism, in signaling, and encoding transcription factors. Further molecular analyses identified the Myb-like transcription factor BasR as the regulatory node for transduction of the bacterial signal in the fungus and show its function is conserved in other Aspergillus species.}, } @article {pmid30309989, year = {2018}, author = {Wendt, J and Schmidt, MF and König, J and Patzlaff, R and Huss, M and Urschitz, MS}, title = {Young age at school entry and attention-deficit hyperactivity disorder-related symptoms during primary school: results of a prospective cohort study conducted at German Rudolf Steiner Schools.}, journal = {BMJ open}, volume = {8}, number = {10}, pages = {e020820}, pmid = {30309989}, issn = {2044-6055}, mesh = {*Age Factors ; Attention Deficit Disorder with Hyperactivity/*diagnosis/epidemiology ; Child ; Child, Preschool ; Female ; Germany/epidemiology ; Humans ; Linear Models ; Male ; *Mass Screening ; Multivariate Analysis ; Pilot Projects ; Prospective Studies ; Risk Factors ; *School Health Services ; Schools ; }, abstract = {OBJECTIVES: Young age at school entry (ASE) for students has been related to their impaired mental health in higher grades. To avoid the negative health consequences of young ASE, preschool examinations and individual school entry deferral for young children are routinely performed by some school authorities. We aimed to investigate whether ASE was associated with attention-deficit hyperactivity disorder (ADHD)-related symptoms in pupils attending schools using a selective school enrolment procedure.

DESIGN: Prospective open cohort study with baseline assessments at school entry and two follow-ups in the second and fourth grades.

SETTING: Up to 128 Rudolf Steiner Schools (Waldorf Schools) located within Germany.

PARTICIPANTS: Of the 3079 children from whom data were gathered in the second or fourth grade, 2671 children born between 1 July 2001 and 31 October 2002 (age at baseline: mean 6.7, min 5.91, max 7.24 years, 50% girls) were selected for analysis to avoid bias introduced by individuals at the edges of the ASE distribution.

MAIN OUTCOME MEASURES: ADHD-related symptoms were assessed at school entry and second and fourth grades by parent-reported and teacher-reported versions of the Strengths and Difficulties Questionnaire (Hyperactivity-Inattention Subscale).

RESULTS: The agreement between parent-reported and teacher-reported symptoms was poor (intra-class correlation: 0.41 and 0.44 in second and fourth grade assessments, respectively). Regarding teacher reports, ASE was negatively associated with ADHD-related symptoms in the second grade (regression coefficient β=-0.66 per year, P=0.0006) and fourth grade (β=-0.56, P=0.0014). Associations remained after adjusting for potential confounders and pre-existing symptoms at baseline. Regarding parent reports, associations were markedly weaker in both grades (second grade: β=-0.22, P=0.12; fourth grade: β=-0.09, P=0.48).

CONCLUSIONS: Using a prospective study design and comprehensive adjustment for confounding and baseline symptoms, we confirmed prior evidence of the association between young ASE and teacher-reported ADHD symptoms in primary school.}, } @article {pmid30308403, year = {2019}, author = {Lin, W and Wu, K and Lao, Z and Hu, W and Lin, B and Li, Y and Fan, H and Hu, J}, title = {Assessment of trace metal contamination and ecological risk in the forest ecosystem of dexing mining area in northeast Jiangxi Province, China.}, journal = {Ecotoxicology and environmental safety}, volume = {167}, number = {}, pages = {76-82}, doi = {10.1016/j.ecoenv.2018.10.001}, pmid = {30308403}, issn = {1090-2414}, mesh = {Animals ; China ; Environmental Monitoring ; *Forests ; Geographic Information Systems ; Metals, Heavy/*analysis ; *Mining ; Multivariate Analysis ; Oligochaeta/chemistry ; Plant Roots/chemistry ; Risk Assessment ; Soil/chemistry ; Soil Pollutants/*analysis ; Trees/chemistry ; }, abstract = {Samples of soil, earthworms, and tree roots from the forest ecosystem in the Dexing Pb/Zn mining area of Jiangxi Province were collected and the status of trace metal pollution analyzed to assess potential ecological risks. Chemometric and geographic information system methods were used to identify and describe the spatial distributions and the main contamination sources of trace metals. The order of potential ecological risks of trace metals in this area are as follows: cadmium (Cd) > arsenic (As) > copper (Cu) > nickel (Ni) > lead (Pb) > chromium (Cr) > zinc (Zn). Elemental spatial distribution maps showed the existence of zones heavily polluted by trace metals around the mining area. Earthworms and roots of three tree species were also heavily contaminated, with concentrations of trace metals in earthworms much higher than in previous studies. The potential ecological risk index and other soil quality indices indicated that soil had moderate to severe contamination and there were high ecological risks, with Cd making the greatest contribution. Multivariate statistical analyses showed that Cd, As, Cu, Pb, and Zn in soil came from a mining activity source, whereas Ni and Cr primarily originated from a natural source.}, } @article {pmid30305460, year = {2018}, author = {Dzubakova, K and Peter, H and Bertuzzo, E and Juez, C and Franca, MJ and Rinaldo, A and Battin, TJ}, title = {Environmental heterogeneity promotes spatial resilience of phototrophic biofilms in streambeds.}, journal = {Biology letters}, volume = {14}, number = {10}, pages = {}, pmid = {30305460}, issn = {1744-957X}, mesh = {Biodiversity ; *Biofilms ; Conservation of Natural Resources ; *Ecosystem ; Periphyton/*physiology ; *Rivers ; Water Movements ; }, abstract = {The loss of environmental heterogeneity threatens biodiversity and ecosystem functioning. It is therefore important to understand the relationship between environmental heterogeneity and spatial resilience as the capacity of ecological communities embedded in a landscape matrix to reorganize following disturbance. We experimented with phototrophic biofilms colonizing streambed landscapes differing in spatial heterogeneity and exposed to flow-induced disturbance. We show how streambed roughness and related features promote growth-related trait diversity and the recovery of biofilms towards carrying capacity (CC) and spatial resilience. At the scale of streambed landscapes, roughness and exposure to water flow promoted biofilm CC and growth trait diversity. Structural equation modelling identified roughness, post-disturbance biomass and a 'neighbourhood effect' to drive biofilm CC. Our findings suggest that the environment selecting for adaptive capacities prior to disturbance (that is, memory effects) and biofilm connectivity into spatial networks (that is, mobile links) contribute to the spatial resilience of biofilms in streambed landscapes. These findings are critical given the key functions biofilms fulfil in streams, now increasingly experiencing shifts in sedimentary and hydrological regimes.}, } @article {pmid30302053, year = {2018}, author = {Knight, A and Jarrad, GA and Schrader, GD and Strobel, J and Horton, D and Bidargaddi, N}, title = {Monte Carlo Simulations Demonstrate Algorithmic Interventions Over Time Reduce Hospitalisation in Patients With Schizophrenia and Bipolar Disorder.}, journal = {Biomedical informatics insights}, volume = {10}, number = {}, pages = {1178222618803076}, pmid = {30302053}, issn = {1178-2226}, abstract = {Non-adherence with pharmacologic treatment is associated with increased rates of relapse and rehospitalisation among patients with schizophrenia and bipolar disorder. To improve treatment response, remission, and recovery, research efforts are still needed to elucidate how to effectively map patient's response to medication treatment including both therapeutic and adverse effects, compliance, and satisfaction in the prodromal phase of illness (ie, the time period in between direct clinical consultation and relapse). The Actionable Intime Insights (AI[2]) application draws information from Australian Medicare administrative claims records in real time when compliance with treatment does not meet best practice guidelines for managing chronic severe mental illness. Subsequently, the AI[2] application alerts clinicians and patients when patients do not adhere to guidelines for treatment. The aim of this study was to evaluate the impact of the AI[2] application on the risk of hospitalisation among simulated patients with schizophrenia and bipolar disorder. Monte Carlo simulation methodology was used to estimate the impact of the AI[2] intervention on the probability of hospitalisation over a 2-year period. Results indicated that when the AI[2] algorithmic intervention had an efficacy level of (>0.6), over 80% of actioned alerts were contributing to reduced hospitalisation risk among the simulated patients. Such findings indicate the potential utility of the AI[2] application should replication studies validate its methodologic and ecological rigour in real-world settings.}, } @article {pmid30301821, year = {2018}, author = {Thompson, M and Van Wassenbergh, S and Rogers, SM and Seamone, SG and Higham, TE}, title = {Angling-induced injuries have a negative impact on suction feeding performance and hydrodynamics in marine shiner perch, Cymatogaster aggregata.}, journal = {The Journal of experimental biology}, volume = {221}, number = {Pt 19}, pages = {}, doi = {10.1242/jeb.180935}, pmid = {30301821}, issn = {1477-9145}, mesh = {Animals ; Computational Biology ; Conservation of Natural Resources ; *Feeding Behavior ; *Fisheries ; Hydrodynamics ; Perciformes/*injuries/*physiology ; Video Recording ; }, abstract = {Fishing is a popular and lucrative sport around the world and, in some cases, may contribute to declining fish stocks. To mediate this problem and maintain fish biomass in aquatic ecosystems, catch-and-release fishing, whereby a fish is caught and immediately released, has been implemented in many countries. It is unclear whether the injuries to the mouth that are caused by the hook have an impact on feeding performance of fishes. Using high-speed video and computational fluid dynamics (CFD), we asked whether injuries around the mouth caused by fishing hooks have a negative impact on suction feeding performance (measured as maximum prey velocity) of the commonly angled marine shiner perch (Cymatogaster aggregata). We hypothesized that fish with mouth injuries would exhibit decreased feeding performance compared with controls. Ten shiner perch were caught using scientific angling and 10 were caught using a seine net. Feeding events were then recorded at 500 frames per second using a high-speed camera. Compared with the control group, maximum prey velocity was significantly lower in the injured group (P<0.01). Maximum gape, time to peak gape, maximum jaw protrusion and predator-prey distance were comparable between the control and injured groups, leading us to conclude that the injury-induced hole in the buccal cavity wall reduced the pressure gradient during mouth expansion, thereby reducing the velocity of water entering the fish's mouth. This was confirmed with our CFD modelling. Fishing injuries in nature are likely to depress feeding performance of fish after they have been released, although it is currently unclear whether this has a significant impact on survival.}, } @article {pmid30298259, year = {2018}, author = {Layeghifard, M and Hwang, DM and Guttman, DS}, title = {Constructing and Analyzing Microbiome Networks in R.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1849}, number = {}, pages = {243-266}, doi = {10.1007/978-1-4939-8728-3_16}, pmid = {30298259}, issn = {1940-6029}, mesh = {Bacteria/classification/*genetics ; Biological Evolution ; Computational Biology/*methods ; *Gene Regulatory Networks ; *Host Microbial Interactions ; Humans ; *Microbiota ; *Software ; }, abstract = {Microbiomes are complex microbial communities whose structure and function are heavily influenced by microbe-microbe and microbe-host interactions mediated by a range of mechanisms, all of which have been implicated in the modulation of disease progression and clinical outcome. Therefore, understanding the microbiome as a whole, including both the complex interplay among microbial taxa and interactions with their hosts, is essential for understanding the spectrum of roles played by microbiomes in host health, development, dysbiosis, and polymicrobial infections. Network theory, in the form of systems-oriented, graph-theoretical approaches, is an exciting holistic methodology that can facilitate microbiome analysis and enhance our understanding of the complex ecological and evolutionary processes involved. Using network theory, one can model and analyze a microbiome and all its complex interactions in a single network. Here, we describe in detail and step by step, the process of building, analyzing and visualizing microbiome networks from operational taxonomic unit (OTU) tables in R and RStudio, using several different approaches and extensively commented code snippets.}, } @article {pmid30298251, year = {2018}, author = {Hall, M and Beiko, RG}, title = {16S rRNA Gene Analysis with QIIME2.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1849}, number = {}, pages = {113-129}, doi = {10.1007/978-1-4939-8728-3_8}, pmid = {30298251}, issn = {1940-6029}, mesh = {Bacteria/classification/*genetics/isolation & purification ; Biodiversity ; Computational Biology/methods ; *Genetic Markers ; High-Throughput Nucleotide Sequencing/*methods ; Phylogeny ; RNA, Ribosomal, 16S/*genetics ; *Software ; }, abstract = {Microbial marker-gene sequence data can be used to generate comprehensive taxonomic profiles of the microorganisms present in a given community and for other community diversity analyses. The process of going from raw gene sequences to taxonomic profiles or diversity measures involves a series of data transformations performed by numerous computational tools. This includes tools for sequence quality checking, denoising, taxonomic classification, alignment, and phylogenetic tree building. In this chapter, we demonstrate how the Quantitative Insights Into Microbial Ecology version 2 (QIIME2) software suite can simplify 16S rRNA marker-gene analysis. We walk through an example data set extracted from the guts of bumblebees in order to show how QIIME2 can transform raw sequences into taxonomic bar plots, phylogenetic trees, principal co-ordinates analyses, and other visualizations of microbial diversity.}, } @article {pmid30295812, year = {2018}, author = {Vitousek, MN and Johnson, MA and Husak, JF}, title = {Illuminating Endocrine Evolution: The Power and Potential of Large-Scale Comparative Analyses.}, journal = {Integrative and comparative biology}, volume = {58}, number = {4}, pages = {712-719}, doi = {10.1093/icb/icy098}, pmid = {30295812}, issn = {1557-7023}, mesh = {Animals ; Biological Evolution ; Databases as Topic ; Endocrine System/*physiology ; Hormones/*physiology ; *Phenotype ; Phylogeny ; Vertebrates/growth & development/*physiology ; }, abstract = {Hormones are central mediators of genotype-phenotype and organism-environment interactions. Despite these important functions, the role of selection in shaping hormonal mediators of phenotype remains poorly understood. Thanks to decades of work by endocrinologists, circulating hormone levels have been measured in a diversity of organisms. Variation in other endocrine traits and mediators (e.g., receptor expression and binding globulins), and the hormonal response to standardized challenges (e.g., restraint, pharmacological challenges) are also increasingly measured in both captive and free-living populations. Large-scale comparative analyses of the multitude of available endocrine data represent a particularly promising approach to addressing the function and evolution of these key phenotypic mediators, and their potential to serve as indicators of disturbance. Several recent phylogenetic comparative analyses and meta-analyses have begun to reveal the power and potential of these approaches to address key questions in integrative biology. Here we highlight two recent developments that are facilitating such analyses: increasingly powerful and flexible phylogenetic comparative methods, and the release of two endocrine trait databases-HormoneBase (currently 474 species) and the Wildlife Endocrinology Information Network (currently 25 species)-that contain compiled measures of endocrine traits across vertebrates. Increasingly comprehensive comparative analyses of endocrine data could provide insight into many interesting questions, including how rapidly changing environments are impacting phenotypes, why endocrine traits differ so remarkably within and across populations, and the evolution of plasticity. The endocrine system mediates interactions between genotypes and phenotypes, and between organisms and their environment. Environmentally induced hormonal responses regulate phenotypic flexibility across timescales by altering physiological state, gene expression, and epigenetic marks. A staggering diversity of phenotypic traits are mediated by hormones from early development through senescence. Through their actions on behavior, hormones also exert widespread influence over how organisms interact with their biotic and abiotic environments. Because hormones are responsive to the environment, there has long been interest in their use as biomarkers of exposure to challenges. More recently, increasing attention has been paid to the potential for within and among-population variation in endocrine regulation or responsiveness to serve as indicators of resistance or resilience to future challenges, or measures of evolutionary potential.}, } @article {pmid30295749, year = {2019}, author = {da Fonseca, NJ and Afonso, MQL and de Oliveira, LC and Bleicher, L}, title = {A new method bridging graph theory and residue co-evolutionary networks for specificity determinant positions detection.}, journal = {Bioinformatics (Oxford, England)}, volume = {35}, number = {9}, pages = {1478-1485}, doi = {10.1093/bioinformatics/bty846}, pmid = {30295749}, issn = {1367-4811}, mesh = {*Algorithms ; Computational Biology ; Proteins ; Sequence Alignment ; *Software ; }, abstract = {MOTIVATION: Computational studies of molecular evolution are usually performed from a multiple alignment of homologous sequences, on which sequences resulting from a common ancestor are aligned so that equivalent residues are placed in the same position. Residues frequency patterns of a full alignment or from a subset of its sequences can be highly useful for suggesting positions under selection. Most methods mapping co-evolving or specificity determinant sites are focused on positions, however, they do not consider the case for residues that are specificity determinants in one subclass, but variable in others. In addition, many methods are impractical for very large alignments, such as those obtained from Pfam, or require a priori information of the subclasses to be analyzed.

RESULTS: In this paper we apply the complex networks theory, widely used to analyze co-affiliation systems in the social and ecological contexts, to map groups of functional related residues. This methodology was initially evaluated in simulated environments and then applied to four different protein families datasets, in which several specificity determinant sets and functional motifs were successfully detected.

The algorithms and datasets used in the development of this project are available on http://www.biocomp.icb.ufmg.br/biocomp/software-and-databases/networkstats/.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, } @article {pmid30293475, year = {2019}, author = {Ge, Y and Zhao, G and Zhang, Y and Houston, RJ and Song, J}, title = {A standardised database of Chinese emotional film clips.}, journal = {Cognition & emotion}, volume = {33}, number = {5}, pages = {976-990}, doi = {10.1080/02699931.2018.1530197}, pmid = {30293475}, issn = {1464-0600}, mesh = {Adolescent ; Adult ; China ; Culture ; Databases, Factual/*statistics & numerical data ; Emotions/*physiology ; Female ; Humans ; Male ; Motion Pictures/*statistics & numerical data ; Young Adult ; }, abstract = {Film clips are widely used in emotion research due to their relatively high ecological validity. Although researchers have established various film clip sets for different cultures, the few that exist related to Chinese culture do not adequately address positive emotions. The main purposes of the present study were to establish a standardised database of Chinese emotional film clips that could elicit more categories of reported positive emotions compared to the existing databases and to expand the available film clips that can be used as neutral materials. Two experiments were conducted to construct the database. In experiment 1, 111 film clips were selected from more than one thousand Chinese movies for preliminary screening. After 315 participants viewed and evaluated these film clips, 39 excerpts were selected for further validation. In experiment 2, 147 participants watched and rated these 39 film clips, as well as another 8 excerpts chosen from the existing databases, to compare their validity. Eventually, 22 film excerpts that successfully evoked three positive emotions (joy, amusement, and tenderness), four negative emotions (moral disgust, anger, fear, and sadness), and neutrality formed the standardised database of Chinese emotional film clips.}, } @article {pmid30291357, year = {2018}, author = {Stein, JC and Yu, Y and Copetti, D and Zwickl, DJ and Zhang, L and Zhang, C and Chougule, K and Gao, D and Iwata, A and Goicoechea, JL and Wei, S and Wang, J and Liao, Y and Wang, M and Jacquemin, J and Becker, C and Kudrna, D and Zhang, J and Londono, CEM and Song, X and Lee, S and Sanchez, P and Zuccolo, A and Ammiraju, JSS and Talag, J and Danowitz, A and Rivera, LF and Gschwend, AR and Noutsos, C and Wu, CC and Kao, SM and Zeng, JW and Wei, FJ and Zhao, Q and Feng, Q and El Baidouri, M and Carpentier, MC and Lasserre, E and Cooke, R and da Rosa Farias, D and da Maia, LC and Dos Santos, RS and Nyberg, KG and McNally, KL and Mauleon, R and Alexandrov, N and Schmutz, J and Flowers, D and Fan, C and Weigel, D and Jena, KK and Wicker, T and Chen, M and Han, B and Henry, R and Hsing, YC and Kurata, N and de Oliveira, AC and Panaud, O and Jackson, SA and Machado, CA and Sanderson, MJ and Long, M and Ware, D and Wing, RA}, title = {Publisher Correction: Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza.}, journal = {Nature genetics}, volume = {50}, number = {11}, pages = {1618}, doi = {10.1038/s41588-018-0261-2}, pmid = {30291357}, issn = {1546-1718}, abstract = {This article was not made open access when initially published online, which was corrected before print publication. In addition, ORCID links were missing for 12 authors and have been added to the HTML and PDF versions of the article.}, } @article {pmid30288922, year = {2019}, author = {Savojardo, C and Luchetti, A and Martelli, PL and Casadio, R and Mantovani, B}, title = {Draft genomes and genomic divergence of two Lepidurus tadpole shrimp species (Crustacea, Branchiopoda, Notostraca).}, journal = {Molecular ecology resources}, volume = {19}, number = {1}, pages = {235-244}, doi = {10.1111/1755-0998.12952}, pmid = {30288922}, issn = {1755-0998}, support = {//Canziani funding/ ; }, mesh = {Animals ; Computational Biology ; Crustacea/*genetics ; Genetic Variation ; *Genome ; High-Throughput Nucleotide Sequencing ; Larva/*genetics ; Whole Genome Sequencing ; }, abstract = {Crustaceans of the order Notostraca (Branchiopoda) are distributed worldwide and are known for the remarkable morphological stasis between their extant and Permian fossil species. Moreover, these crustaceans show relevant ecological traits and a wide range of reproductive strategies. However, genomic studies on notostracans are fairly limited. Here, we present the genome sequences of two notostracan taxa, Lepidurus arcticus and Lepidurus apus lubbocki. Taking advantage of the small genome sizes (~0.11 pg) of these taxa, genomes were sequenced for one individual per species with one run on the Illumina HiSeq X platform. We finally assembled 73.2 Mbp (L. arcticus) and 90.3 Mbp (L. apus lubbocki) long genomes. Assemblies cover up to 84% of the estimated genome size, with a gene completeness >97% for both genomes. In total, 13%-16% of the assembled genomes consist of repeats, and based on read mapping, L. apus lubbocki shows a significantly lower transposable element content than L. arcticus. The analysis of 2,376 orthologous genes indicates an ~7% divergence between the two Lepidurus taxa, with a nucleotide substitution rate significantly lower than that of Daphnia taxa. Ka /Ks analysis suggests purifying selection in both branchiopod lineages, raising the question of whether the low substitution rate of Lepidurus is correlated with morphological conservation or is linked to specific biological traits. Our analysis demonstrates that, in these organisms, it is possible to obtain high-quality draft genomes from single individuals with a relatively low sequencing effort. This result makes Lepidurus and Notostraca interesting models for genomic studies at taxonomic, ecological and evolutionary levels.}, } @article {pmid30288122, year = {2018}, author = {Medenwald, D and Vordermark, D and Dietzel, CT}, title = {Number of radiotherapy treatment machines in the population and cancer mortality: an ecological study.}, journal = {Clinical epidemiology}, volume = {10}, number = {}, pages = {1249-1273}, pmid = {30288122}, issn = {1179-1349}, abstract = {OBJECTIVES: The aim of this study was to assess the association between the number of radiotherapy treatment machines (RTMs) in the population and incidence-adjusted cancer mortality.

METHODS: Data on cancer incidence and mortality were obtained from the GLOBOCAN project (only high-quality data, C3, or higher according to GLOBOCAN quality label), information on the number of RTMs from the Directory of Radiotherapy Centers database, and remaining data from the World Bank and World Health Organization database. We used linear regression models to assess the associations between RTM per 10,000,000 inhabitants (logarithmized) and the log-transformed mortality/incidence ratio. Models were adjusted for public health variables. To assess the bias due to unobserved confounders, mortality from leukemia was considered as a negative control. Here radiotherapy treatment is less frequently applied, but a common set of confounders is shared with cancer types where radiotherapy plays a stronger role, enabling us to estimate the bias due to confounding of unmeasured parameters. To assess an exposure-effect size relationship, estimated cancer type-specific estimates were related to the proportion of subjects receiving radiotherapy.

RESULTS: We found an inverse linear relationship between RTM in the population and the cancer mortality to incidence ratio for prostate cancer (14.1% per doubling of RTM; 95% CI: 0.1%-26.1%), female breast cancer (12.3%; 95% CI: 2.7%-20.9%), and lung cancer in women (11.2%; 95% CI: 4.3%-17.6%). There was no evidence for bias due to unobserved confounders after covariate adjustment. For women, an exposure-effect size relationship was found (P=0.02).

CONCLUSION: In this ecological study, we found evidence that the population density of RTM is related to cancer mortality independently of other public health parameters.}, } @article {pmid30287354, year = {2018}, author = {Staley, C and Sadowsky, MJ}, title = {Practical considerations for sampling and data analysis in contemporary metagenomics-based environmental studies.}, journal = {Journal of microbiological methods}, volume = {154}, number = {}, pages = {14-18}, doi = {10.1016/j.mimet.2018.09.020}, pmid = {30287354}, issn = {1872-8359}, mesh = {Algorithms ; Biodiversity ; Biostatistics/methods ; Computational Biology/methods ; DNA/analysis/isolation & purification ; *Data Analysis ; Ecology ; Ecosystem ; Environment ; *Environmental Microbiology ; High-Throughput Nucleotide Sequencing/methods ; Humans ; *Metagenome ; Metagenomics/*methods ; Microbiota/genetics ; Phylogeography ; Sequence Analysis, DNA/methods ; Specimen Handling/*methods ; }, abstract = {Recent advancements in metagenomic-based studies, especially analyses of amplicon-based DNA sequencing targeting taxonomic marker genes, has led to an unprecedented characterization of microbial communities from diverse ecosystems around the world. While originally constrained by a lack of appropriate analytical tools and sequencing depth, new technologies and computational and statistical algorithms have been developed to handle highly dimensional, next-generation sequencing datasets. Both these tools allow for the robust analysis of structural and distributional patterns of microbiota essential for the understanding of microbial ecology and biogeography. Furthermore, consortia of individual laboratories working on large interdisciplinary research programs, like the Human and Earth Microbiome Projects, have developed standardized protocols for DNA extraction, sequencing pipelines, and bioinformatics. These approaches provide large repositories of publicly available data to serve as references for on-going and future, hypothesis-driven studies to better characterize the roles of microbial communities in diverse ecosystems. In this review, we outline the currently available statistical approaches and tools to aid in statistically powered study designs and analyses. Given what is now known about the enormous diversity and variability of the microbial communities in aquatic and terrestrial habitats, we also discuss practical considerations for sample collection. Due to the extensive advances made in the field of metagenomics over the last decade, rigorous, well replicated, hypothesis-driven studies are: 1) needed, 2) now possible, and 3) essential to make best use of sequencing-based technologies to characterize the roles of microbial communities in the structure and function of diverse ecosystems.}, } @article {pmid30285843, year = {2018}, author = {Ziganshina, EE and Mohammed, WS and Shagimardanova, EI and Shigapova, LH and Ziganshin, AM}, title = {Draft genome sequence of Staphylococcus sp. EZ-P03 isolated from a mesophilic anaerobic digester.}, journal = {BMC research notes}, volume = {11}, number = {1}, pages = {694}, pmid = {30285843}, issn = {1756-0500}, support = {16-34-60093//Russian Foundation for Basic Research/ ; }, mesh = {Animals ; Chickens ; DNA, Bacterial/*genetics ; Databases, Genetic ; *Firmicutes ; Genome, Bacterial/*genetics ; Manure/*microbiology ; RNA, Ribosomal, 16S/*genetics ; Staphylococcus/*genetics ; }, abstract = {OBJECTIVES: Staphylococcus species of the family Staphylococcaceae are facultatively anaerobic Gram-positive cocci growing in clusters, pairs and occasionally in short chains. Staphylococci can be detected in different environments. They are common commensals, but some can also cause infections in humans. Hence, their investigation is required to understand ecology and genetics and to create an opportunity for comparative studies.

DATA DESCRIPTION: In this study, we report the determination of a draft genome sequence of Staphylococcus sp. strain EZ-P03 which was isolated from anaerobically digested chicken waste materials. The draft genome of Staphylococcus sp. EZ-P03 constituted a total of 62 contigs (> 500 bp) amounting to 2,689,358 bp with a G+C content of 37.3% and a N50 contig size of 126,562 bp. The whole genome shotgun project of Staphylococcus sp. strain EZ-P03 has been deposited at DDBJ/ENA/GenBank under the accession number QPMO00000000.}, } @article {pmid30283105, year = {2018}, author = {Buermann, W and Forkel, M and O'Sullivan, M and Sitch, S and Friedlingstein, P and Haverd, V and Jain, AK and Kato, E and Kautz, M and Lienert, S and Lombardozzi, D and Nabel, JEMS and Tian, H and Wiltshire, AJ and Zhu, D and Smith, WK and Richardson, AD}, title = {Widespread seasonal compensation effects of spring warming on northern plant productivity.}, journal = {Nature}, volume = {562}, number = {7725}, pages = {110-114}, pmid = {30283105}, issn = {1476-4687}, mesh = {Computer Simulation ; Geographic Mapping ; *Plant Development ; *Plant Physiological Phenomena ; Plant Transpiration ; Plants ; *Seasons ; *Temperature ; }, abstract = {Climate change is shifting the phenological cycles of plants[1], thereby altering the functioning of ecosystems, which in turn induces feedbacks to the climate system[2]. In northern (north of 30° N) ecosystems, warmer springs lead generally to an earlier onset of the growing season[3,4] and increased ecosystem productivity early in the season[5]. In situ[6] and regional[7-9] studies also provide evidence for lagged effects of spring warmth on plant productivity during the subsequent summer and autumn. However, our current understanding of these lagged effects, including their direction (beneficial or adverse) and geographic distribution, is still very limited. Here we analyse satellite, field-based and modelled data for the period 1982-2011 and show that there are widespread and contrasting lagged productivity responses to spring warmth across northern ecosystems. On the basis of the observational data, we find that roughly 15 per cent of the total study area of about 41 million square kilometres exhibits adverse lagged effects and that roughly 5 per cent of the total study area exhibits beneficial lagged effects. By contrast, current-generation terrestrial carbon-cycle models predict much lower areal fractions of adverse lagged effects (ranging from 1 to 14 per cent) and much higher areal fractions of beneficial lagged effects (ranging from 9 to 54 per cent). We find that elevation and seasonal precipitation patterns largely dictate the geographic pattern and direction of the lagged effects. Inadequate consideration in current models of the effects of the seasonal build-up of water stress on seasonal vegetation growth may therefore be able to explain the differences that we found between our observation-constrained estimates and the model-constrained estimates of lagged effects associated with spring warming. Overall, our results suggest that for many northern ecosystems the benefits of warmer springs on growing-season ecosystem productivity are effectively compensated for by the accumulation of seasonal water deficits, despite the fact that northern ecosystems are thought to be largely temperature- and radiation-limited[10].}, } @article {pmid30281913, year = {2019}, author = {Jusino, MA and Banik, MT and Palmer, JM and Wray, AK and Xiao, L and Pelton, E and Barber, JR and Kawahara, AY and Gratton, C and Peery, MZ and Lindner, DL}, title = {An improved method for utilizing high-throughput amplicon sequencing to determine the diets of insectivorous animals.}, journal = {Molecular ecology resources}, volume = {19}, number = {1}, pages = {176-190}, doi = {10.1111/1755-0998.12951}, pmid = {30281913}, issn = {1755-0998}, support = {//United States Forest Service, Northern Research Station/ ; Hatch Formula Funds//University of Wisconsin-Madison, Wisconsin Agricultural Experiment Station/ ; IOS-1121739//National Science Foundation/ ; IOS-1121807//National Science Foundation/ ; }, mesh = {Animals ; *Chiroptera ; Computational Biology/*methods ; DNA/chemistry/genetics/isolation & purification ; Electron Transport Complex IV/genetics ; Feces/chemistry ; *Feeding Behavior ; High-Throughput Nucleotide Sequencing/*methods ; Metagenomics/*methods ; }, abstract = {DNA analysis of predator faeces using high-throughput amplicon sequencing (HTS) enhances our understanding of predator-prey interactions. However, conclusions drawn from this technique are constrained by biases that occur in multiple steps of the HTS workflow. To better characterize insectivorous animal diets, we used DNA from a diverse set of arthropods to assess PCR biases of commonly used and novel primer pairs for the mitochondrial gene, cytochrome oxidase C subunit 1 (COI). We compared diversity recovered from HTS of bat guano samples using a commonly used primer pair "ZBJ" to results using the novel primer pair "ANML." To parameterize our bioinformatics pipeline, we created an arthropod mock community consisting of single-copy (cloned) COI sequences. To examine biases associated with both PCR and HTS, mock community members were combined in equimolar amounts both pre- and post-PCR. We validated our system using guano from bats fed known diets and using composite samples of morphologically identified insects collected in pitfall traps. In PCR tests, the ANML primer pair amplified 58 of 59 arthropod taxa (98%), whereas ZBJ amplified 24-40 of 59 taxa (41%-68%). Furthermore, in an HTS comparison of field-collected samples, the ANML primers detected nearly fourfold more arthropod taxa than the ZBJ primers. The additional arthropods detected include medically and economically relevant insect groups such as mosquitoes. Results revealed biases at both the PCR and sequencing levels, demonstrating the pitfalls associated with using HTS read numbers as proxies for abundance. The use of an arthropod mock community allowed for improved bioinformatics pipeline parameterization.}, } @article {pmid30281592, year = {2018}, author = {Erickson, RA and Fienen, MN and McCalla, SG and Weiser, EL and Bower, ML and Knudson, JM and Thain, G}, title = {Wrangling distributed computing for high-throughput environmental science: An introduction to HTCondor.}, journal = {PLoS computational biology}, volume = {14}, number = {10}, pages = {e1006468}, pmid = {30281592}, issn = {1553-7358}, mesh = {*Computational Biology ; *Computing Methodologies ; *Ecology ; High-Throughput Screening Assays ; Humans ; Internet ; Research ; *Software ; }, abstract = {Biologists and environmental scientists now routinely solve computational problems that were unimaginable a generation ago. Examples include processing geospatial data, analyzing -omics data, and running large-scale simulations. Conventional desktop computing cannot handle these tasks when they are large, and high-performance computing is not always available nor the most appropriate solution for all computationally intense problems. High-throughput computing (HTC) is one method for handling computationally intense research. In contrast to high-performance computing, which uses a single "supercomputer," HTC can distribute tasks over many computers (e.g., idle desktop computers, dedicated servers, or cloud-based resources). HTC facilities exist at many academic and government institutes and are relatively easy to create from commodity hardware. Additionally, consortia such as Open Science Grid facilitate HTC, and commercial entities sell cloud-based solutions for researchers who lack HTC at their institution. We provide an introduction to HTC for biologists and environmental scientists. Our examples from biology and the environmental sciences use HTCondor, an open source HTC system.}, } @article {pmid30280477, year = {2019}, author = {Bolam, FC and Grainger, MJ and Mengersen, KL and Stewart, GB and Sutherland, WJ and Runge, MC and McGowan, PJK}, title = {Using the Value of Information to improve conservation decision making.}, journal = {Biological reviews of the Cambridge Philosophical Society}, volume = {94}, number = {2}, pages = {629-647}, doi = {10.1111/brv.12471}, pmid = {30280477}, issn = {1469-185X}, mesh = {Animals ; *Biodiversity ; *Conservation of Natural Resources/trends ; *Decision Making ; Decision Support Techniques ; *Ecology ; Humans ; Population Density ; Uncertainty ; }, abstract = {Conservation decisions are challenging, not only because they often involve difficult conflicts among outcomes that people value, but because our understanding of the natural world and our effects on it is fraught with uncertainty. Value of Information (VoI) methods provide an approach for understanding and managing uncertainty from the standpoint of the decision maker. These methods are commonly used in other fields (e.g. economics, public health) and are increasingly used in biodiversity conservation. This decision-analytical approach can identify the best management alternative to select where the effectiveness of interventions is uncertain, and can help to decide when to act and when to delay action until after further research. We review the use of VoI in the environmental domain, reflect on the need for greater uptake of VoI, particularly for strategic conservation planning, and suggest promising areas for new research. We also suggest common reporting standards as a means of increasing the leverage of this powerful tool. The environmental science, ecology and biodiversity categories of the Web of Knowledge were searched using the terms 'Value of Information,' 'Expected Value of Perfect Information,' and the abbreviation 'EVPI.' Google Scholar was searched with the same terms, and additionally the terms decision and biology, biodiversity conservation, fish, or ecology. We identified 1225 papers from these searches. Included studies were limited to those that showed an application of VoI in biodiversity conservation rather than simply describing the method. All examples of use of VOI were summarised regarding the application of VoI, the management objectives, the uncertainties, the models used, how the objectives were measured, and the type of VoI. While the use of VoI appears to be on the increase in biodiversity conservation, the reporting of results is highly variable, which can make it difficult to understand the decision context and which uncertainties were considered. Moreover, it was unclear if, and how, the papers informed management and policy interventions, which is why we suggest a range of reporting standards that would aid the use of VoI. The use of VoI in conservation settings is at an early stage. There are opportunities for broader applications, not only for species-focussed management problems, but also for setting local or global research priorities for biodiversity conservation, making funding decisions, or designing or improving protected area networks and management. The long-term benefits of applying VoI methods to biodiversity conservation include a more structured and decision-focused allocation of resources to research.}, } @article {pmid30279590, year = {2018}, author = {Walter, WD and Evans, TS and Stainbrook, D and Wallingford, BD and Rosenberry, CS and Diefenbach, DR}, title = {Heterogeneity of a landscape influences size of home range in a North American cervid.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {14667}, pmid = {30279590}, issn = {2045-2322}, mesh = {Animal Migration/*physiology ; Animals ; Deer/*physiology ; Ecological Parameter Monitoring/instrumentation/methods ; Forests ; Geographic Information Systems ; Homing Behavior/*physiology ; Linear Models ; *Models, Biological ; New England ; Remote Sensing Technology/instrumentation/methods ; Seasons ; Spatial Analysis ; Wasting Disease, Chronic/*prevention & control/transmission ; Wearable Electronic Devices ; }, abstract = {In the northeastern United States, chronic wasting disease has recently been detected in white-tailed deer (Odocoileus virginianus) populations, and understanding the relationship between landscape configuration and home range may improve disease surveillance and containment efforts. The objectives of our study were to compare size of home range for deer occupying a continuum of forested landscapes and to investigate relationships between size of home range and measures of landscape configuration. We used a movement-based kernel density estimator to estimate home range at five spatial scales among deer across study areas. We developed 7 linear regression models that used measures of the configuration of the forested landscape to explain size of home range. We observed differences in size of home range between sexes among areas that differed based on landscape configuration. We documented size of home range changed with various metrics that identifying connectivity of forested patches. Generally, size of home range increased with an increasing proportion of homogenous forest. Our results suggest that deer in our region occupy a landscape at hierarchically-nested scales that is controlled by the connectivity of the forested landscape across local or broad geographical regions.}, } @article {pmid30277072, year = {2018}, author = {Han, J and Chen, WQ and Zhang, L and Liu, G}, title = {Uncovering the Spatiotemporal Dynamics of Urban Infrastructure Development: A High Spatial Resolution Material Stock and Flow Analysis.}, journal = {Environmental science & technology}, volume = {52}, number = {21}, pages = {12122-12132}, doi = {10.1021/acs.est.8b03111}, pmid = {30277072}, issn = {1520-5851}, mesh = {China ; Cities ; *Construction Materials ; Geographic Information Systems ; Humans ; *Recycling ; }, abstract = {Understanding the complexity and sustainability of infrastructure development is crucial for reconciling economic growth, human well-being, and environmental conservation. However, previous studies on infrastructure's material metabolism were mainly conducted on a global or national scale, due largely to lack of more spatially refined data, and thus could not reveal the spatial patterns and dynamics on a city scale. Here, we integrated material flow analysis (MFA) and geographical information system (GIS) data to uncover the spatiotemporal patterns of the material stocks and flows accompanying the infrastructure development at a high spatial resolution for the case of Shanghai, China. From 1980 to 2010, material stocks and waste output flows of Shanghai's infrastructure system exhibited a significant increase from 83 to 561 million metric tons (Mt) and from 2 to 17 Mt, respectively. Input flows peaked in 2005 because of the economic slowdown and stepped-up policies to cool the housing market. Spatially, the center and peri-urban areas were the largest container of material stocks and biggest generator of demolition waste, while suburban areas absorbed 58%-76% of material inputs. Plans to make the city more compact will enhance the service capacity of stocks but may also increase the use of more energy and emissions-intensive construction materials (e.g., steel). Prolonging the service lifetime of infrastructure through proper management and increasing the recycling and reuse rate of demolition waste are also identified as highly efficient strategies.}, } @article {pmid30273336, year = {2018}, author = {Handel, A and Li, Y and McKay, B and Pawelek, KA and Zarnitsyna, V and Antia, R}, title = {Exploring the impact of inoculum dose on host immunity and morbidity to inform model-based vaccine design.}, journal = {PLoS computational biology}, volume = {14}, number = {10}, pages = {e1006505}, pmid = {30273336}, issn = {1553-7358}, support = {P20 GM103499/GM/NIGMS NIH HHS/United States ; U19 AI117891/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Computational Biology ; *Dose-Response Relationship, Immunologic ; Drug Design ; Host-Pathogen Interactions/*immunology ; Humans ; Mice ; *Models, Immunological ; Rats ; Vaccines/*administration & dosage/*immunology ; Viral Load ; }, abstract = {Vaccination is an effective method to protect against infectious diseases. An important consideration in any vaccine formulation is the inoculum dose, i.e., amount of antigen or live attenuated pathogen that is used. Higher levels generally lead to better stimulation of the immune response but might cause more severe side effects and allow for less population coverage in the presence of vaccine shortages. Determining the optimal amount of inoculum dose is an important component of rational vaccine design. A combination of mathematical models with experimental data can help determine the impact of the inoculum dose. We illustrate the concept of using data and models to inform inoculum dose determination for vaccines, wby fitting a mathematical model to data from influenza A virus (IAV) infection of mice and human parainfluenza virus (HPIV) infection of cotton rats at different inoculum doses. We use the model to map inoculum dose to the level of immune protection and morbidity and to explore how such a framework might be used to determine an optimal inoculum dose. We show how a framework that combines mathematical models with experimental data can be used to study the impact of inoculum dose on important outcomes such as immune protection and morbidity. Our findings illustrate that the impact of inoculum dose on immune protection and morbidity can depend on the specific pathogen and that both protection and morbidity do not necessarily increase monotonically with increasing inoculum dose. Once vaccine design goals are specified with required levels of protection and acceptable levels of morbidity, our proposed framework can help in the rational design of vaccines and determination of the optimal amount of inoculum.}, } @article {pmid30273332, year = {2018}, author = {Cai, FY and Fussell, T and Cobey, S and Lipsitch, M}, title = {Use of an individual-based model of pneumococcal carriage for planning a randomized trial of a whole-cell vaccine.}, journal = {PLoS computational biology}, volume = {14}, number = {10}, pages = {e1006333}, pmid = {30273332}, issn = {1553-7358}, mesh = {*Carrier State/epidemiology/microbiology/prevention & control ; Computational Biology/*methods ; Host-Pathogen Interactions/immunology ; Humans ; Incidence ; *Models, Immunological ; *Pneumococcal Infections/epidemiology/microbiology/prevention & control ; *Pneumococcal Vaccines ; Prevalence ; Randomized Controlled Trials as Topic ; Streptococcus pneumoniae/immunology/pathogenicity ; }, abstract = {For encapsulated bacteria such as Streptococcus pneumoniae, asymptomatic carriage is more common and longer in duration than disease, and hence is often a more convenient endpoint for clinical trials of vaccines against these bacteria. However, using a carriage endpoint entails specific challenges. Carriage is almost always measured as prevalence, whereas the vaccine may act by reducing incidence or duration. Thus, to determine sample size requirements, its impact on prevalence must first be estimated. The relationship between incidence and prevalence (or duration and prevalence) is convex, saturating at 100% prevalence. For this reason, the proportional effect of a vaccine on prevalence is typically less than its proportional effect on incidence or duration. This relationship is further complicated in the presence of multiple pathogen strains. In addition, host immunity to carriage accumulates rapidly with frequent exposures in early years of life, creating potentially complex interactions with the vaccine's effect. We conducted a simulation study to predict the impact of an inactivated whole cell pneumococcal vaccine-believed to reduce carriage duration-on carriage prevalence in different age groups and trial settings. We used an individual-based model of pneumococcal carriage that incorporates relevant immunological processes, both vaccine-induced and naturally acquired. Our simulations showed that for a wide range of vaccine efficacies, sampling time and age at vaccination are important determinants of sample size. There is a window of favorable sampling times during which the required sample size is relatively low, and this window is prolonged with a younger age at vaccination, and in a trial setting with lower transmission intensity. These results illustrate the ability of simulation studies to inform the planning of vaccine trials with carriage endpoints, and the methods we present here can be applied to trials evaluating other pneumococcal vaccine candidates or comparing alternative dosing schedules for the existing conjugate vaccines.}, } @article {pmid30269352, year = {2019}, author = {Saatkamp, A and Cochrane, A and Commander, L and Guja, LK and Jimenez-Alfaro, B and Larson, J and Nicotra, A and Poschlod, P and Silveira, FAO and Cross, AT and Dalziell, EL and Dickie, J and Erickson, TE and Fidelis, A and Fuchs, A and Golos, PJ and Hope, M and Lewandrowski, W and Merritt, DJ and Miller, BP and Miller, RG and Offord, CA and Ooi, MKJ and Satyanti, A and Sommerville, KD and Tangney, R and Tomlinson, S and Turner, S and Walck, JL}, title = {A research agenda for seed-trait functional ecology.}, journal = {The New phytologist}, volume = {221}, number = {4}, pages = {1764-1775}, doi = {10.1111/nph.15502}, pmid = {30269352}, issn = {1469-8137}, support = {R-90470-01//Commonwealth Scientific and Industrial Research Organisation/International ; }, mesh = {Biodiversity ; Conservation of Natural Resources ; Databases, Factual ; Ecosystem ; Germination/*physiology ; Seed Dispersal/*physiology ; Seedlings/physiology ; Seeds/*physiology ; }, abstract = {Trait-based approaches have improved our understanding of plant evolution, community assembly and ecosystem functioning. A major challenge for the upcoming decades is to understand the functions and evolution of early life-history traits, across levels of organization and ecological strategies. Although a variety of seed traits are critical for dispersal, persistence, germination timing and seedling establishment, only seed mass has been considered systematically. Here we suggest broadening the range of morphological, physiological and biochemical seed traits to add new understanding on plant niches, population dynamics and community assembly. The diversity of seed traits and functions provides an important challenge that will require international collaboration in three areas of research. First, we present a conceptual framework for a seed ecological spectrum that builds upon current understanding of plant niches. We then lay the foundation for a seed-trait functional network, the establishment of which will underpin and facilitate trait-based inferences. Finally, we anticipate novel insights and challenges associated with incorporating diverse seed traits into predictive evolutionary ecology, community ecology and applied ecology. If the community invests in standardized seed-trait collection and the implementation of rigorous databases, major strides can be made at this exciting frontier of functional ecology.}, } @article {pmid30269263, year = {2018}, author = {Li, W and Liu, S and Pei, Y and He, J and Wang, Q}, title = {Zoning for eco-geological environment before mining in Yushenfu mining area, northern Shaanxi, China.}, journal = {Environmental monitoring and assessment}, volume = {190}, number = {10}, pages = {619}, pmid = {30269263}, issn = {1573-2959}, support = {2015CB251601//the National Basic Research Program of China (973 Program)/ ; 41430643//the State Key Program of the National Natural Science Foundation of China/ ; }, mesh = {China ; Ecology/*methods ; Ecosystem ; Environment ; Environmental Monitoring/*methods ; Geographic Information Systems ; Geology ; Groundwater ; *Mining ; Remote Sensing Technology/methods ; }, abstract = {Zoning for the eco-geological environment (EGE) aims to protect and improve the regional ecological environment. It is the basis for evaluating the ecological characteristics of a mining area prior to mining activities and has the purpose of implementing water-preserved mining according to zoning type. In this study, four EGE types were proposed following field investigation in the Yushenfu mining area: oasis type with phreatic water and bottomland in desert (OTPWBD), oasis type with surface water and valley river (OTSWVR), loess gully type with surface runoff (LGTSR), and regional deep groundwater enrichment type (RDGET). Nine EGE evaluation indices were selected: rainfall, evaporation capacity, Luohe formation thickness, surface elevation, Sara Wusu aquifer water abundance, surface lithology, topography, slope, and normalized difference vegetation index (NDVI). Remote sensing technology and geographic information systems were first used to generate the evaluation index thematic maps. Then, the weight of each evaluation index was determined based on an analytic hierarchy process (AHP). Third, the index weight was used to form an improved weighted fuzzy C s clustering algorithm, and EGE zones were assigned using the MATLAB computing platform. For comparison, the AHP was also adopted for EGE zoning and a map of zoning differences was obtained. Finally, EGE field surveys of typical mines were carried out, which verified that EGE zoning using fuzzy clustering was accurate and reasonable.}, } @article {pmid30269196, year = {2018}, author = {Papadopoulos, AV and Kati, V and Chachalis, D and Kotoulas, V and Stamatiadis, S}, title = {Weed mapping in cotton using ground-based sensors and GIS.}, journal = {Environmental monitoring and assessment}, volume = {190}, number = {10}, pages = {622}, pmid = {30269196}, issn = {1573-2959}, support = {LIFE08 ENV/GR/0000570: HydroSense//European Commission/ ; }, mesh = {Environmental Monitoring/*methods ; *Geographic Information Systems ; Greece ; Photography ; Weed Control/*methods ; }, abstract = {Site-specific weed management presupposes the careful monitoring and mapping of weed infestation areas. Cut-edge sensor technologies coupled with geographical information systems (GIS) provide the means for reliable decision-making concerning weed management even in sub-field level. In present research, two different spectral sensing systems were engaged in order to digitally map weed patches as grown in four different cotton fields in Central Greece. The systems used were a set of two Crop Circle multispectral sensors ACS-430 and a digital camera Nikon D300S. The spaces between cotton rows were scanned and photographed with the two systems accordingly. Raw recorded data were stored and analyzed in GIS environment producing spatially interpolated maps of red-edge normalized difference vegetation index (NDVI) and weed cover percentage values. Both mapping approaches were satisfactorily related to weed distribution as occurred in the fields; however, the photographic method tended to underestimate weed populations. Correlation of red-edge NDVI and weed cover values, at the points where photographs were taken, as revealed by Pearson's correlation coefficient was high (r > 0.83) and statistically significant at the 0.01 level. A first-degree linear equation adequately modeled (R[2] > 0.7) the between value pair relations, strengthening the validity of the two methodologies in spatially monitoring weed patches. The methodologies and the technologies used in the study can be used for yearly mapping weed flora in cotton cultivation and potentially constitute a means of rationalizing herbicide application in terms of doses and spatio-temporal decision-making.}, } @article {pmid30267313, year = {2018}, author = {Song, EJ and Lee, ES and Nam, YD}, title = {Progress of analytical tools and techniques for human gut microbiome research.}, journal = {Journal of microbiology (Seoul, Korea)}, volume = {56}, number = {10}, pages = {693-705}, pmid = {30267313}, issn = {1976-3794}, mesh = {Computational Biology/*trends ; Data Analysis ; Feces/microbiology ; *Gastrointestinal Microbiome ; Humans ; Metagenomics/*trends ; Microbiota ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Massive DNA sequencing studies have expanded our insights and understanding of the ecological and functional characteristics of the gut microbiome. Advanced sequencing technologies allow us to understand the close association of the gut microbiome with human health and critical illnesses. In the future, analyses of the gut microbiome will provide key information associating with human individual health, which will help provide personalized health care for diseases. Numerous molecular biological analysis tools have been rapidly developed and employed for the gut microbiome researches; however, methodological differences among researchers lead to inconsistent data, limiting extensive share of data. It is therefore very essential to standardize the current methodologies and establish appropriate pipelines for human gut microbiome research. Herein, we review the methods and procedures currently available for studying the human gut microbiome, including fecal sample collection, metagenomic DNA extraction, massive DNA sequencing, and data analyses with bioinformatics. We believe that this review will contribute to the progress of gut microbiome research in the clinical and practical aspects of human health.}, } @article {pmid30266931, year = {2018}, author = {Van Echelpoel, W and Goethals, PLM}, title = {Variable importance for sustaining macrophyte presence via random forests: data imputation and model settings.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {14557}, pmid = {30266931}, issn = {2045-2322}, mesh = {Araceae/*physiology ; Computer Simulation ; Data Mining ; Ecosystem ; Hydrogen-Ion Concentration ; *Machine Learning ; *Models, Biological ; Nuphar/*physiology ; Probability ; Temperature ; }, abstract = {Data sets plagued with missing data and performance-affecting model parameters represent recurrent issues within the field of data mining. Via random forests, the influence of data reduction, outlier and correlated variable removal and missing data imputation technique on the performance of habitat suitability models for three macrophytes (Lemna minor, Spirodela polyrhiza and Nuphar lutea) was assessed. Higher performances (Cohen's kappa values around 0.2-0.3) were obtained for a high degree of data reduction, without outlier or correlated variable removal and with imputation of the median value. Moreover, the influence of model parameter settings on the performance of random forest trained on this data set was investigated along a range of individual trees (ntree), while the number of variables to be considered (mtry), was fixed at two. Altering the number of individual trees did not have a uniform effect on model performance, but clearly changed the required computation time. Combining both criteria provided an ntree value of 100, with the overall effect of ntree on performance being relatively limited. Temperature, pH and conductivity remained as variables and showed to affect the likelihood of L. minor, S. polyrhiza and N. lutea being present. Generally, high likelihood values were obtained when temperature is high (>20 °C), conductivity is intermediately low (50-200 mS m[-1]) or pH is intermediate (6.9-8), thereby also highlighting that a multivariate management approach for supporting macrophyte presence remains recommended. Yet, as our conclusions are only based on a single freshwater data set, they should be further tested for other data sets.}, } @article {pmid30265733, year = {2018}, author = {Droste, N and D'Amato, D and Goddard, JJ}, title = {Where communities intermingle, diversity grows - The evolution of topics in ecosystem service research.}, journal = {PloS one}, volume = {13}, number = {9}, pages = {e0204749}, pmid = {30265733}, issn = {1932-6203}, mesh = {*Algorithms ; *Conservation of Natural Resources/methods/trends ; *Data Mining ; *Databases, Bibliographic ; *Ecology/methods/trends ; *Ecosystem ; }, abstract = {We analyze how the content of ecosystem service research has evolved since the early 1990s. Conducting a computational bibliometric content analysis we process a corpus of 14,118 peer-reviewed scientific article abstracts on ecosystem services (ES) from Web of Science records. To provide a comprehensive content analysis of ES research literature, we employ a latent Dirichlet allocation algorithm. For three different time periods (1990-2000, 2001-2010, 2011-2016), we derive nine main ES topics arising from content analysis and elaborate on how they are related over time. The results show that natural science-based ES research analyzes oceanic, freshwater, agricultural, forest, and soil ecosystems. Pollination and land cover emerge as traceable standalone topics around 2001. Social science ES literature demonstrates a reflexive and critical lens on the role of ES research and includes critiques of market-oriented perspectives. The area where social and natural science converge most is about land use systems such as agriculture. Overall, we provide evidence of the strong natural science foundation, the highly interdisciplinary nature of ES research, and a shift in social ES research towards integrated assessments and governance approaches. Furthermore, we discuss potential reasons for observable topic developments.}, } @article {pmid30264359, year = {2019}, author = {Hu, J and Lin, B and Yuan, M and Lao, Z and Wu, K and Zeng, Y and Liang, Z and Li, H and Li, Y and Zhu, D and Liu, J and Fan, H}, title = {Trace metal pollution and ecological risk assessment in agricultural soil in Dexing Pb/Zn mining area, China.}, journal = {Environmental geochemistry and health}, volume = {41}, number = {2}, pages = {967-980}, pmid = {30264359}, issn = {1573-2983}, support = {NSFC-81273127//National Natural Science Foundation of China/ ; GC200109-1//high level talent researcher for dongguan university of technology/ ; }, mesh = {Agriculture ; China ; Environmental Monitoring/methods ; Geographic Information Systems ; Lead/analysis ; Metals, Heavy/*analysis ; Mining ; Multivariate Analysis ; Risk Assessment ; Soil Pollutants/*analysis ; Zinc/analysis ; }, abstract = {Surface agricultural soil samples obtained from Dexing Pb/Zn mining area in Jiangxi province were analyzed for trace metals to assess their pollution status and potential ecological risk. The spatial distributions and the major trace metals pollution sources were described and identified with the combination of chemical measures and geographic information systems technology. The level of pollution in seven metals is decreasing in the following order: zinc (Zn 128.9 mg/kg) > chromium (Cr 64.1 mg/kg) > lead (Pb 58.4 mg/kg) > arsenic (As 45.3 mg/kg) > copper (Cu 41.9 mg/kg) > nickel (Ni 31.3 mg/kg) > cadmium (Cd 1.5 mg/kg). Trace metal spatial distribution maps established by geographic information system techniques displayed two high-pollution zones around mining sites in the study area. Multivariate statistical analyses were also applied, and the results demonstrated that Cd, As, Pb, Cu and Zn in the soils originated from mining activities, whereas Cr and Ni primarily originated from natural sources. The values of pollution index ranged from 4.79 to 71.59, and the values of modified pollution index ranged from 1.98 to 24.69. Moreover, the potential ecological risk values ranged from 264.0 to 3263.5, which indicated considerable ecological risk to very high ecological risk. The potential ecological risk values and other soil contamination indices showed similar patterns that the high-risk areas were around Dexing Pb/Zn mining site. The surface agricultural soil in study area is heavily to extremely polluted , with Cd that made the most dominant contribution.}, } @article {pmid30264342, year = {2018}, author = {Wang, C and Bourland, WA and Mu, W and Pan, X}, title = {Transcriptome analysis on chlorpyrifos detoxification in Uronema marinum (Ciliophora, Oligohymenophorea).}, journal = {Environmental science and pollution research international}, volume = {25}, number = {33}, pages = {33402-33414}, pmid = {30264342}, issn = {1614-7499}, support = {31501844//The National Natural Science Funds of China/ ; 31601866//The National Natural Science Funds of China/ ; QC2017017//Program of Natural Science of Heilongjiang Province of R. P. China/ ; UNPYSCT-2017178//University Nursing Program for Young Scholars with Creative Talents in Heilongjiang Province/ ; }, mesh = {Animals ; Antioxidants/*metabolism ; Biodegradation, Environmental ; Chlorpyrifos/*analysis/toxicity ; Gene Expression Profiling ; Gene Ontology ; Inactivation, Metabolic ; Oligohymenophorea/*drug effects/genetics/metabolism ; Transcriptome/*drug effects ; Water Pollutants, Chemical/*analysis/toxicity ; }, abstract = {Chlorpyrifos (CPF) pollution has drawn widespread concerns in aquatic environments due to its risks to ecologic system, however, the response mechanisms of ciliates to CPF pollution were poorly studied. In our current work, the degradation of CPF by ciliates and the morphological changes of ciliates after CPF exposure were investigated. In addition, the transcriptomic profiles of the ciliate Uronema marinum, with and without exposure with CPF, were detected using digital gene expression technologies. De novo transcriptome assembly 166,829,634 reads produced from three groups (untreated, CPF treatment at 12 h and 24 h) by whole transcriptome sequencing (RNA-Seq). Gene ontology (GO) and Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathways were analyzed in all unigenes and different expression genes to identify their biological functions and processes. Furthermore, the results indicated that genes related to the stress response, cytoskeleton and cell structure proteins, and antioxidant systems might play an important role in the resistance mechanism of ciliates. The enzyme activities of SOD and GST after CPF stress were also analyzed, and the result showed the good antioxidant capacity of SOD and GST in ciliates inferred from the increase of the activities of the two enzymes. The ciliate Uronema marinum showed a resistance response to chlorpyrifos stress at the transcriptomic level in the present work, which indicates that ciliates can be considered as a potential bioremediation agent.}, } @article {pmid30262689, year = {2018}, author = {Song, H and Zhang, YX and Yang, MJ and Sun, JC and Zhang, T and Wang, HY}, title = {Genome survey on invasive veined rapa whelk (Rapana venosa) and development of microsatellite loci on large scale.}, journal = {Journal of genetics}, volume = {97}, number = {4}, pages = {e79-e86}, pmid = {30262689}, issn = {0973-7731}, mesh = {Animals ; China ; Computational Biology ; Gastropoda/*genetics ; Genetic Variation ; Genome/*genetics ; *Genomics ; High-Throughput Nucleotide Sequencing ; Microsatellite Repeats/*genetics ; Polymorphism, Genetic ; Sequence Analysis, DNA ; }, abstract = {The veined rapa whelk (Rapana venosa) is an economically important gastropod in China, but is considered as an invasive species globally. Only a few studies have examined the R. venosa genome, a genomewide survey is necessary for improving our understanding of the genome structure and size of this organism. Microsatellite markers are powerful tools for characterizing germplasms, genetic diversity and kinship among individuals. The resultant data are applicable to breeding efforts in commercial aquaculture or for understanding invasion mechanisms. Here, we investigated the genome structure of R. venosa on an Illumina Hi-seq platform with ∼92× sequencing depth. We performed a K-mer analysis to estimate genome size, repeat sequences and heterozygosity. Clean reads were de novo assembled for the identification of simple-sequence repeat (SSR) loci that are suitable as markers. The estimated genome size of R. venosa was 2200.07 Mb, with a 1.41% heterozygosity rate and 67.04% repeats. We detected 5,477,450 simple-sequence repeats (SSRs), with 3,400,602 loci present as pure tandem repeats and 2,076,848 as compound motifs. We further selected and characterized 28 polymorphic markers in 78 individuals from Dandong, Laizhou, Weihai and Zhoushan in China. The range of alleles was 2-28 and the observed heterozygosity was 0.2857-0.8676. The data obtained from our genomic survey will aid the design of R. venosa whole-genome sequencing projects and advance the identification of SSR markers. Both these developments are valuable for further studies on ecological, evolutionary and genetic breeding in R. venosa.}, } @article {pmid30258229, year = {2018}, author = {Bjorkman, AD and Myers-Smith, IH and Elmendorf, SC and Normand, S and Rüger, N and Beck, PSA and Blach-Overgaard, A and Blok, D and Cornelissen, JHC and Forbes, BC and Georges, D and Goetz, SJ and Guay, KC and Henry, GHR and HilleRisLambers, J and Hollister, RD and Karger, DN and Kattge, J and Manning, P and Prevéy, JS and Rixen, C and Schaepman-Strub, G and Thomas, HJD and Vellend, M and Wilmking, M and Wipf, S and Carbognani, M and Hermanutz, L and Lévesque, E and Molau, U and Petraglia, A and Soudzilovskaia, NA and Spasojevic, MJ and Tomaselli, M and Vowles, T and Alatalo, JM and Alexander, HD and Anadon-Rosell, A and Angers-Blondin, S and Beest, MT and Berner, L and Björk, RG and Buchwal, A and Buras, A and Christie, K and Cooper, EJ and Dullinger, S and Elberling, B and Eskelinen, A and Frei, ER and Grau, O and Grogan, P and Hallinger, M and Harper, KA and Heijmans, MMPD and Hudson, J and Hülber, K and Iturrate-Garcia, M and Iversen, CM and Jaroszynska, F and Johnstone, JF and Jørgensen, RH and Kaarlejärvi, E and Klady, R and Kuleza, S and Kulonen, A and Lamarque, LJ and Lantz, T and Little, CJ and Speed, JDM and Michelsen, A and Milbau, A and Nabe-Nielsen, J and Nielsen, SS and Ninot, JM and Oberbauer, SF and Olofsson, J and Onipchenko, VG and Rumpf, SB and Semenchuk, P and Shetti, R and Collier, LS and Street, LE and Suding, KN and Tape, KD and Trant, A and Treier, UA and Tremblay, JP and Tremblay, M and Venn, S and Weijers, S and Zamin, T and Boulanger-Lapointe, N and Gould, WA and Hik, DS and Hofgaard, A and Jónsdóttir, IS and Jorgenson, J and Klein, J and Magnusson, B and Tweedie, C and Wookey, PA and Bahn, M and Blonder, B and van Bodegom, PM and Bond-Lamberty, B and Campetella, G and Cerabolini, BEL and Chapin, FS and Cornwell, WK and Craine, J and Dainese, M and de Vries, FT and Díaz, S and Enquist, BJ and Green, W and Milla, R and Niinemets, Ü and Onoda, Y and Ordoñez, JC and Ozinga, WA and Penuelas, J and Poorter, H and Poschlod, P and Reich, PB and Sandel, B and Schamp, B and Sheremetev, S and Weiher, E}, title = {Plant functional trait change across a warming tundra biome.}, journal = {Nature}, volume = {562}, number = {7725}, pages = {57-62}, pmid = {30258229}, issn = {1476-4687}, mesh = {Biometry ; Geographic Mapping ; *Global Warming ; Humidity ; Phenotype ; *Plant Physiological Phenomena ; Plants/*anatomy & histology ; Soil/chemistry ; Spatio-Temporal Analysis ; Temperature ; *Tundra ; Water/analysis ; }, abstract = {The tundra is warming more rapidly than any other biome on Earth, and the potential ramifications are far-reaching because of global feedback effects between vegetation and climate. A better understanding of how environmental factors shape plant structure and function is crucial for predicting the consequences of environmental change for ecosystem functioning. Here we explore the biome-wide relationships between temperature, moisture and seven key plant functional traits both across space and over three decades of warming at 117 tundra locations. Spatial temperature-trait relationships were generally strong but soil moisture had a marked influence on the strength and direction of these relationships, highlighting the potentially important influence of changes in water availability on future trait shifts in tundra plant communities. Community height increased with warming across all sites over the past three decades, but other traits lagged far behind predicted rates of change. Our findings highlight the challenge of using space-for-time substitution to predict the functional consequences of future warming and suggest that functions that are tied closely to plant height will experience the most rapid change. They also reveal the strength with which environmental factors shape biotic communities at the coldest extremes of the planet and will help to improve projections of functional changes in tundra ecosystems with climate warming.}, } @article {pmid30257009, year = {2019}, author = {Fu, X and Meinzer, FC}, title = {Metrics and proxies for stringency of regulation of plant water status (iso/anisohydry): a global data set reveals coordination and trade-offs among water transport traits.}, journal = {Tree physiology}, volume = {39}, number = {1}, pages = {122-134}, doi = {10.1093/treephys/tpy087}, pmid = {30257009}, issn = {1758-4469}, mesh = {Databases, Factual ; Datasets as Topic ; *Ecosystem ; Plant Leaves/*metabolism ; *Plant Transpiration ; Plants/*metabolism ; Water/*metabolism ; }, abstract = {Plants operate along a continuum of stringency of regulation of plant water potential from isohydry to anisohydry. However, most metrics and proxies of plant iso/anisohydric behavior have been developed from limited sets of site-specific experiments. Understanding the underlying mechanisms that determine species' operating ranges along this continuum, independent of site and growing conditions, remains challenging. We compiled a global database to assess the global patterns of metrics and proxies of plant iso/anisohydry and then explored some of the underlying functional traits and trade-offs associated with stringency of regulation that determines where species operate along the continuum. Our results showed that arid and semi-arid biomes were associated with greater anisohydry than more mesic biomes, and angiosperms showed marginally greater anisohydry than gymnosperms. Leaf water potential at the turgor loss point (Ψtlp) and wood density were the two most powerful proxies for ranking the degree of plant iso/anisohydry for a wide range of species and biomes. Both of these simple traits can be easily and rapidly determined, and therefore show promise for a priori mapping and understanding of the global distribution pattern of the degree of plant iso/anisohydry. Generally, the most anisohydric species had the most negative values of Ψtlp and highest wood density, greatest resistance to embolism, lowest hydraulic capacitance and lowest leaf-specific hydraulic conductivity of their branches. Wood density in particular appeared to be central to a coordinated series of traits, trade-offs and behaviors along a continuum of iso/anisohydry. Quantification of species' operating ranges along a continuum of iso/anisohydry and identification of associated trade-offs among functional traits may hold promise for mechanistic modeling of species-specific responses to the anticipated more frequent and severe droughts under global climate change scenarios.}, } @article {pmid30256939, year = {2018}, author = {Gong, G and Dan, C and Xiao, S and Guo, W and Huang, P and Xiong, Y and Wu, J and He, Y and Zhang, J and Li, X and Chen, N and Gui, JF and Mei, J}, title = {Chromosomal-level assembly of yellow catfish genome using third-generation DNA sequencing and Hi-C analysis.}, journal = {GigaScience}, volume = {7}, number = {11}, pages = {}, pmid = {30256939}, issn = {2047-217X}, mesh = {Animals ; Catfishes/classification/*genetics ; *Chromosomes ; *Computational Biology/methods ; Female ; Gene Library ; *Genome ; *Genomics/methods ; Male ; Molecular Sequence Annotation ; Multigene Family ; Phylogeny ; }, abstract = {BACKGROUND: The yellow catfish, Pelteobagrus fulvidraco, belonging to the Siluriformes order, is an economically important freshwater aquaculture fish species in Asia, especially in Southern China. The aquaculture industry has recently been facing tremendous challenges in germplasm degeneration and poor disease resistance. As the yellow catfish exhibits notable sex dimorphism in growth, with adult males about two- to three-fold bigger than females, the way in which the aquaculture industry takes advantage of such sex dimorphism is another challenge. To address these issues, a high-quality reference genome of the yellow catfish would be a very useful resource.

FINDINGS: To construct a high-quality reference genome for the yellow catfish, we generated 51.2 Gb short reads and 38.9 Gb long reads using Illumina and Pacific Biosciences (PacBio) sequencing platforms, respectively. The sequencing data were assembled into a 732.8 Mb genome assembly with a contig N50 length of 1.1 Mb. Additionally, we applied Hi-C technology to identify contacts among contigs, which were then used to assemble contigs into scaffolds, resulting in a genome assembly with 26 chromosomes and a scaffold N50 length of 25.8 Mb. Using 24,552 protein-coding genes annotated in the yellow catfish genome, the phylogenetic relationships of the yellow catfish with other teleosts showed that yellow catfish separated from the common ancestor of channel catfish ∼81.9 million years ago. We identified 1,717 gene families to be expanded in the yellow catfish, and those gene families are mainly enriched in the immune system, signal transduction, glycosphingolipid biosynthesis, and fatty acid biosynthesis.

CONCLUSIONS: Taking advantage of Illumina, PacBio, and Hi-C technologies, we constructed the first high-quality chromosome-level genome assembly for the yellow catfish P. fulvidraco. The genomic resources generated in this work not only offer a valuable reference genome for functional genomics studies of yellow catfish to decipher the economic traits and sex determination but also provide important chromosome information for genome comparisons in the wider evolutionary research community.}, } @article {pmid30256807, year = {2018}, author = {Korpilo, S and Jalkanen, J and Virtanen, T and Lehvävirta, S}, title = {Where are the hotspots and coldspots of landscape values, visitor use and biodiversity in an urban forest?.}, journal = {PloS one}, volume = {13}, number = {9}, pages = {e0203611}, pmid = {30256807}, issn = {1932-6203}, mesh = {Biodiversity ; *Ecosystem ; *Forests ; Geographic Information Systems ; }, abstract = {Cities and urban green areas therein can be considered as complex social-ecological systems that provide various ecosystem services with different synergies and trade-offs among them. In this article, we show that multiple stakeholder perspectives and data sources should be used to capture key values for sustainable planning and management of urban green spaces. Using an urban forest in Helsinki, Finland as a case study, we incorporated data collected using public participation GIS, expert elicitation and forest inventories in order to investigate the guidance that the different types of data, and their integration, can provide for landscape planning. We examined the relationship and spatial concurrence between two social variables i.e. visitors' perceived landscape values and green space use, and two ecological variables i.e. forest habitat quality and urban biodiversity, using hot/coldspot analysis. We found weak correlations and low mean spatial coincidence between the social and ecological data, indicating great complementary importance to multi-criteria decision-making. In addition, there was a higher level of spatial agreement between the ecological datasets than between the social datasets. Forest habitat quality and urban biodiversity were positively correlated and spatially coincided moderately, while we found a negative correlation and very low overlap between visitor use and landscape values. This highlights the conceptual and spatial distinction between the general preferences and values citizens assign to public green spaces and the realized everyday use of these areas and their services. The resulting maps can inform planners on overall social and environmental quality of the landscape, and point out potential threats to areas of high ecological value due to intensive recreational use, which is crucial information for natural resource management. In the end, we discuss different strategies for managing overlaps and discrepancies between the social and ecological values.}, } @article {pmid30254267, year = {2018}, author = {O'Dea, RE and Lagisz, M and Jennions, MD and Nakagawa, S}, title = {Gender differences in individual variation in academic grades fail to fit expected patterns for STEM.}, journal = {Nature communications}, volume = {9}, number = {1}, pages = {3777}, pmid = {30254267}, issn = {2041-1723}, mesh = {Academic Performance/*statistics & numerical data ; Adolescent ; Adult ; Child ; Datasets as Topic ; Engineering/*statistics & numerical data ; Female ; Humans ; Male ; Mathematics/*statistics & numerical data ; Models, Statistical ; Motivation ; Sex Distribution ; Sex Factors ; Students/*statistics & numerical data ; Technology/*statistics & numerical data ; Young Adult ; }, abstract = {Fewer women than men pursue careers in science, technology, engineering and mathematics (STEM), despite girls outperforming boys at school in the relevant subjects. According to the 'variability hypothesis', this over-representation of males is driven by gender differences in variance; greater male variability leads to greater numbers of men who exceed the performance threshold. Here, we use recent meta-analytic advances to compare gender differences in academic grades from over 1.6 million students. In line with previous studies we find strong evidence for lower variation among girls than boys, and of higher average grades for girls. However, the gender differences in both mean and variance of grades are smaller in STEM than non-STEM subjects, suggesting that greater variability is insufficient to explain male over-representation in STEM. Simulations of these differences suggest the top 10% of a class contains equal numbers of girls and boys in STEM, but more girls in non-STEM subjects.}, } @article {pmid30252850, year = {2018}, author = {Wu, B and Zhou, L}, title = {Individualised aspiration dynamics: Calculation by proofs.}, journal = {PLoS computational biology}, volume = {14}, number = {9}, pages = {e1006035}, pmid = {30252850}, issn = {1553-7358}, mesh = {Algorithms ; *Aspirations, Psychological ; Biological Evolution ; Computational Biology/*methods ; Computer Simulation ; Cooperative Behavior ; Decision Making ; *Game Theory ; Humans ; Interpersonal Relations ; Markov Chains ; Models, Statistical ; Models, Theoretical ; Probability ; Systems Biology ; }, abstract = {Cooperation is key for the evolution of biological systems ranging from bacteria communities to human societies. Evolutionary processes can dramatically alter the cooperation level. Evolutionary processes are typically of two classes: comparison based and self-evaluation based. The fate of cooperation is extremely sensitive to the details of comparison based processes. For self-evaluation processes, however, it is still unclear whether the sensitivity remains. We concentrate on a class of self-evaluation processes based on aspiration, where all the individuals adjust behaviors based on their own aspirations. We prove that the evolutionary outcome with heterogeneous aspirations is the same as that of the homogeneous one for regular networks under weak selection limit. Simulation results further suggest that it is also valid for general networks across various distributions of personalised aspirations. Our result clearly indicates that self-evaluation processes are robust in contrast with comparison based rules. In addition, our result greatly simplifies the calculation of the aspiration dynamics, which is computationally expensive.}, } @article {pmid30247613, year = {2018}, author = {Wen, M and Ng, JHJ and Zhu, F and Chionh, YT and Chia, WN and Mendenhall, IH and Lee, BP and Irving, AT and Wang, LF}, title = {Exploring the genome and transcriptome of the cave nectar bat Eonycteris spelaea with PacBio long-read sequencing.}, journal = {GigaScience}, volume = {7}, number = {10}, pages = {}, pmid = {30247613}, issn = {2047-217X}, mesh = {Alternative Splicing ; Animals ; Chiroptera/classification/*genetics ; Computational Biology/methods ; Evolution, Molecular ; Female ; *Genome ; *Genomics/methods ; High-Throughput Nucleotide Sequencing ; Molecular Sequence Annotation ; Phylogeny ; *Transcriptome ; }, abstract = {BACKGROUND: In the past two decades, bats have emerged as an important model system to study host-pathogen interactions. More recently, it has been shown that bats may also serve as a new and excellent model to study aging, inflammation, and cancer, among other important biological processes. The cave nectar bat or lesser dawn bat (Eonycteris spelaea) is known to be a reservoir for several viruses and intracellular bacteria. It is widely distributed throughout the tropics and subtropics from India to Southeast Asia and pollinates several plant species, including the culturally and economically important durian in the region. Here, we report the whole-genome and transcriptome sequencing, followed by subsequent de novo assembly, of the E. spelaea genome solely using the Pacific Biosciences (PacBio) long-read sequencing platform.

FINDINGS: The newly assembled E. spelaea genome is 1.97 Gb in length and consists of 4,470 sequences with a contig N50 of 8.0 Mb. Identified repeat elements covered 34.65% of the genome, and 20,640 unique protein-coding genes with 39,526 transcripts were annotated.

CONCLUSIONS: We demonstrated that the PacBio long-read sequencing platform alone is sufficient to generate a comprehensive de novo assembled genome and transcriptome of an important bat species. These results will provide useful insights and act as a resource to expand our understanding of bat evolution, ecology, physiology, immunology, viral infection, and transmission dynamics.}, } @article {pmid30246797, year = {2018}, author = {Wu, N and Wang, B and Cui, ZW and Zhang, XY and Cheng, YY and Xu, X and Li, XM and Wang, ZX and Chen, DD and Zhang, YA}, title = {Integrative Transcriptomic and microRNAomic Profiling Reveals Immune Mechanism for the Resilience to Soybean Meal Stress in Fish Gut and Liver.}, journal = {Frontiers in physiology}, volume = {9}, number = {}, pages = {1154}, pmid = {30246797}, issn = {1664-042X}, abstract = {In aquafeeds, fish-meal has been commonly replaced with plant protein, which often causes enteritis. Currently, foodborne enteritis has few solutions in regards to prevention or cures. The recovery mechanism from enteritis in herbivorous fish may further help understand prevention or therapy. However, few reports could be found regarding the recovery or resilience to fish foodborne enteritis. In this study, grass carp was used as an animal model for soybean meal induced enteritis and it was found that the fish could adapt to the soybean meal at a moderate level of substitution. Resilience to soybean meal stress was found in the 40% soybean meal group for juvenile fish at growth performance, morphological and gene expression levels, after a 7-week feeding trial. Furthermore, the intestinal transcriptomic data, including transcriptome and miRNAome, was applied to demonstrate resilience mechanisms. The result of this study revealed that in juvenile grass carp after a 7-week feeding cycle with 40% soybean meal, the intestine recovered via enhancing both an immune tolerance and wound healing, the liver gradually adapted via re-balancing immune responses, such as phagosome and complement cascades. Also, many immune factors in the gut and liver were systemically revealed among stages of on-setting, remising, and recovering (or relief). In addition, miRNA regulation played a key role in switching immune states. Thus, the present data systemically demonstrated that the molecular adaptation mechanism of fish gut-liver immunity is involved in the resilience to soybean meal stress.}, } @article {pmid30240120, year = {2019}, author = {de La Harpe, M and Hess, J and Loiseau, O and Salamin, N and Lexer, C and Paris, M}, title = {A dedicated target capture approach reveals variable genetic markers across micro- and macro-evolutionary time scales in palms.}, journal = {Molecular ecology resources}, volume = {19}, number = {1}, pages = {221-234}, doi = {10.1111/1755-0998.12945}, pmid = {30240120}, issn = {1755-0998}, support = {CRSII3_147630//Swiss National Science Foundation (SNSF)/ ; //University of Zurich/ ; //Illumina/ ; //National Science Foundation/ ; }, mesh = {Arecaceae/*classification/*genetics ; Computational Biology ; Evolution, Molecular ; *Genetic Markers ; *Genetic Variation ; Genetics, Population/*methods ; Genome, Plant ; Genotype ; Genotyping Techniques/*methods ; Molecular Biology/methods ; Whole Genome Sequencing ; }, abstract = {Understanding the genetics of biological diversification across micro- and macro-evolutionary time scales is a vibrant field of research for molecular ecologists as rapid advances in sequencing technologies promise to overcome former limitations. In palms, an emblematic, economically and ecologically important plant family with high diversity in the tropics, studies of diversification at the population and species levels are still hampered by a lack of genomic markers suitable for the genotyping of large numbers of recently diverged taxa. To fill this gap, we used a whole genome sequencing approach to develop target sequencing for molecular markers in 4,184 genome regions, including 4,051 genes and 133 non-genic putatively neutral regions. These markers were chosen to cover a wide range of evolutionary rates allowing future studies at the family, genus, species and population levels. Special emphasis was given to the avoidance of copy number variation during marker selection. In addition, a set of 149 well-known sequence regions previously used as phylogenetic markers by the palm biological research community were included in the target regions, to open the possibility to combine and jointly analyse already available data sets with genomic data to be produced with this new toolkit. The bait set was effective for species belonging to all three palm sub-families tested (Arecoideae, Ceroxyloideae and Coryphoideae), with high mapping rates, specificity and efficiency. The number of high-quality single nucleotide polymorphisms (SNPs) detected at both the sub-family and population levels facilitates efficient analyses of genomic diversity across micro- and macro-evolutionary time scales.}, } @article {pmid30239729, year = {2018}, author = {Varadharajan, S and Sandve, SR and Gillard, GB and Tørresen, OK and Mulugeta, TD and Hvidsten, TR and Lien, S and Asbjørn Vøllestad, L and Jentoft, S and Nederbragt, AJ and Jakobsen, KS}, title = {The Grayling Genome Reveals Selection on Gene Expression Regulation after Whole-Genome Duplication.}, journal = {Genome biology and evolution}, volume = {10}, number = {10}, pages = {2785-2800}, pmid = {30239729}, issn = {1759-6653}, mesh = {Animals ; Biological Evolution ; Chloride Channels/genetics ; Gene Expression ; *Gene Expression Regulation ; *Genome ; Male ; *Polyploidy ; Salmonidae/*genetics ; *Selection, Genetic ; }, abstract = {Whole-genome duplication (WGD) has been a major evolutionary driver of increased genomic complexity in vertebrates. One such event occurred in the salmonid family ∼80 Ma (Ss4R) giving rise to a plethora of structural and regulatory duplicate-driven divergence, making salmonids an exemplary system to investigate the evolutionary consequences of WGD. Here, we present a draft genome assembly of European grayling (Thymallus thymallus) and use this in a comparative framework to study evolution of gene regulation following WGD. Among the Ss4R duplicates identified in European grayling and Atlantic salmon (Salmo salar), one-third reflect nonneutral tissue expression evolution, with strong purifying selection, maintained over ∼50 Myr. Of these, the majority reflect conserved tissue regulation under strong selective constraints related to brain and neural-related functions, as well as higher-order protein-protein interactions. A small subset of the duplicates have evolved tissue regulatory expression divergence in a common ancestor, which have been subsequently conserved in both lineages, suggestive of adaptive divergence following WGD. These candidates for adaptive tissue expression divergence have elevated rates of protein coding- and promoter-sequence evolution and are enriched for immune- and lipid metabolism ontology terms. Lastly, lineage-specific duplicate divergence points toward underlying differences in adaptive pressures on expression regulation in the nonanadromous grayling versus the anadromous Atlantic salmon. Our findings enhance our understanding of the role of WGD in genome evolution and highlight cases of regulatory divergence of Ss4R duplicates, possibly related to a niche shift in early salmonid evolution.}, } @article {pmid30239679, year = {2018}, author = {Harper, L and Campbell, J and Cannon, EKS and Jung, S and Poelchau, M and Walls, R and Andorf, C and Arnaud, E and Berardini, TZ and Birkett, C and Cannon, S and Carson, J and Condon, B and Cooper, L and Dunn, N and Elsik, CG and Farmer, A and Ficklin, SP and Grant, D and Grau, E and Herndon, N and Hu, ZL and Humann, J and Jaiswal, P and Jonquet, C and Laporte, MA and Larmande, P and Lazo, G and McCarthy, F and Menda, N and Mungall, CJ and Munoz-Torres, MC and Naithani, S and Nelson, R and Nesdill, D and Park, C and Reecy, J and Reiser, L and Sanderson, LA and Sen, TZ and Staton, M and Subramaniam, S and Tello-Ruiz, MK and Unda, V and Unni, D and Wang, L and Ware, D and Wegrzyn, J and Williams, J and Woodhouse, M and Yu, J and Main, D}, title = {AgBioData consortium recommendations for sustainable genomics and genetics databases for agriculture.}, journal = {Database : the journal of biological databases and curation}, volume = {2018}, number = {}, pages = {}, pmid = {30239679}, issn = {1758-0463}, support = {R01 GM080203/GM/NIGMS NIH HHS/United States ; R01 HG004483/HG/NHGRI NIH HHS/United States ; }, mesh = {*Agriculture ; Breeding ; *Databases, Genetic ; Gene Ontology ; *Genomics ; Metadata ; Surveys and Questionnaires ; }, abstract = {The future of agricultural research depends on data. The sheer volume of agricultural biological data being produced today makes excellent data management essential. Governmental agencies, publishers and science funders require data management plans for publicly funded research. Furthermore, the value of data increases exponentially when they are properly stored, described, integrated and shared, so that they can be easily utilized in future analyses. AgBioData (https://www.agbiodata.org) is a consortium of people working at agricultural biological databases, data archives and knowledgbases who strive to identify common issues in database development, curation and management, with the goal of creating database products that are more Findable, Accessible, Interoperable and Reusable. We strive to promote authentic, detailed, accurate and explicit communication between all parties involved in scientific data. As a step toward this goal, we present the current state of biocuration, ontologies, metadata and persistence, database platforms, programmatic (machine) access to data, communication and sustainability with regard to data curation. Each section describes challenges and opportunities for these topics, along with recommendations and best practices.}, } @article {pmid30239664, year = {2018}, author = {Falk, T and Herndon, N and Grau, E and Buehler, S and Richter, P and Zaman, S and Baker, EM and Ramnath, R and Ficklin, S and Staton, M and Feltus, FA and Jung, S and Main, D and Wegrzyn, JL}, title = {Growing and cultivating the forest genomics database, TreeGenes.}, journal = {Database : the journal of biological databases and curation}, volume = {2018}, number = {}, pages = {1-11}, pmid = {30239664}, issn = {1758-0463}, mesh = {Data Mining ; *Databases, Genetic ; *Forests ; Gene Ontology ; *Genomics ; Phenotype ; Phylogeny ; Search Engine ; Software ; Trees/genetics/growth & development ; }, abstract = {Forest trees are valued sources of pulp, timber and biofuels, and serve a role in carbon sequestration, biodiversity maintenance and watershed stability. Examining the relationships among genetic, phenotypic and environmental factors for these species provides insight on the areas of concern for breeders and researchers alike. The TreeGenes database is a web-based repository that is home to 1790 tree species and over 1500 registered users. The database provides a curated archive for high-throughput genomics, including reference genomes, transcriptomes, genetic maps and variant data. These resources are paired with extensive phenotypic information and environmental layers. TreeGenes recently migrated to Tripal, an integrated and open-source database schema and content management system. This migration enabled developments focused on data exchange, data transfer and improved analytical capacity, as well as providing TreeGenes the opportunity to communicate with the following partner databases: Hardwood Genomics Web, Genome Database for Rosaceae, and the Citrus Genome Database. Recent development in TreeGenes has focused on coordinating information for georeferenced accessions, including metadata acquisition and ontological frameworks, to improve integration across studies combining genetic, phenotypic and environmental data. This focus was paired with the development of tools to enable comparative genomics and data visualization. By combining advanced data importers, relevant metadata standards and integrated analytical frameworks, TreeGenes provides a platform for researchers to store, submit and analyze forest tree data.}, } @article {pmid30232812, year = {2018}, author = {Anderson, KC and Knuckey, R and Cánepa, M and Elizur, A}, title = {A transcriptomic investigation of appetite-regulation and digestive processes in giant grouper Epinephelus lanceolatus during early larval development.}, journal = {Journal of fish biology}, volume = {93}, number = {4}, pages = {694-710}, doi = {10.1111/jfb.13798}, pmid = {30232812}, issn = {1095-8649}, support = {FIS-2012-101//Australian Centre for International Agricultural Research (ACIAR)/ ; }, mesh = {Animals ; Appetite ; *Appetite Regulation ; Aquaculture ; Bass/*growth & development/*metabolism ; Chitinases/metabolism ; Databases, Factual ; *Digestion ; Endopeptidases/metabolism ; Female ; Larva/metabolism ; Lipase/metabolism ; Male ; Neuropeptide Y/metabolism ; Peptide Hydrolases/metabolism ; Seafood ; *Transcriptome ; Trypsinogen/metabolism ; }, abstract = {The giant grouper Epinephelus lanceolatus is an ecologically vulnerable species with high market demand. However, efforts to improve larval husbandry are hindered by a lack of knowledge surrounding larval developmental physiology. To address this shortfall, a transcriptomic approach was applied to larvae between 1 and 14 days post hatch (dph) to characterise the molecular ontogenesis of genes that influence appetite and digestion. Appetite regulating factors were detected from 1 dph, including neuropeptide Y, nesfatin-1, cocaine and amphetamine regulated transcript, cholecystokinin and pituitary adenylate cyclase activating peptide and the expression level of several genes changed sharply with the onset of exogenous feeding. The level of expression for proteases, chitinases, lipases and amylases typically followed one of two expression patterns, a general increase as development progressed, or an inverted U-shape with maximal expression at c. 6 dph. Similarly, the tendency among both expression patterns was for the level of expression to increase around the time of mouth-opening. There was also evidence to suggest the presence of putative isoforms for several digestion-related genes. We have provided an insight into appetite-regulation and digestive processes in groupers during early larval development and have developed a transcriptomic database that will aid future efforts to rear this species in an aquaculture setting.}, } @article {pmid30232462, year = {2018}, author = {Aguirre de Cárcer, D}, title = {The human gut pan-microbiome presents a compositional core formed by discrete phylogenetic units.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {14069}, pmid = {30232462}, issn = {2045-2322}, mesh = {Bacteria/*classification/genetics/isolation & purification ; Cluster Analysis ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Databases, Genetic ; Ecosystem ; Gastrointestinal Microbiome ; Humans ; Phylogeny ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, DNA/*methods ; }, abstract = {The complex community of microbes living in the human gut plays an important role in host wellbeing. However, defining a 'healthy' gut microbiome in terms of composition has remained an elusive task, despite its anticipated medical and scientific importance. In this regard, a central question has been if there is a 'core' microbiome consisting of bacterial groups common to all healthy humans. Recent studies have been able to define a compositional core in human gut microbiome datasets in terms of taxonomic assignments. However, the description of the core microbiome in terms of taxonomic assignments may not be adequate when considering subsequent analyses and applications. Through the implementation of a dynamic clustering approach in the meta-analyisis of comprehensive 16S rRNA marker gene datasets, this study found that the human gut pan-microbiome presents a preeminent compositional core comprised of discrete units of varying phylogenetic depth present in all individuals studied. Since both microbial traits and ecological coherence show signs of phylogenetic conservation, this outcome provides a new conceptual framework in the study of the ecosystem, as well as important practical considerations which should be taken into account in future research.}, } @article {pmid30232358, year = {2018}, author = {Tragin, M and Vaulot, D}, title = {Green microalgae in marine coastal waters: The Ocean Sampling Day (OSD) dataset.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {14020}, pmid = {30232358}, issn = {2045-2322}, support = {Bourse doctorale//Université Pierre et Marie Curie (UPMC)/International ; ARED GreenPhy//Conseil Régional de Bretagne (Regional Council of Brittany)/International ; MicroB3//EC | Seventh Framework Programme (European Union Seventh Framework Programme)/International ; }, mesh = {Chlorophyta/*classification/genetics ; Databases, Factual ; Microalgae/classification/genetics ; Phylogeny ; RNA, Ribosomal, 18S/genetics ; Seawater/*parasitology ; Sequence Analysis, DNA/methods ; }, abstract = {The ecology and distribution of green phytoplankton (Chlorophyta) in the ocean is poorly known because most studies have focused on groups with large cell size such as diatoms or dinoflagellates that are easily recognized by traditional techniques such as microscopy. The Ocean Sampling Day (OSD) project sampled surface waters quasi-simultaneously at 141 marine locations, mostly in coastal waters. The analysis of the 18S V4 region OSD metabarcoding dataset reveals that Chlorophyta are ubiquitous and can be locally dominant in coastal waters. Chlorophyta represented 29% of the global photosynthetic reads (Dinoflagellates excluded) and their contribution was especially high at oligotrophic stations (up to 94%) and along the European Atlantic coast. Mamiellophyceae dominated most coastal stations. At some coastal stations, they were replaced by Chlorodendrophyceae, Ulvophyceae, Trebouxiophyceae or Chlorophyceae as the dominating group, while oligotrophic stations were dominated either by Chloropicophyceae or the uncultured prasinophytes clade IX. Several Chlorophyta classes showed preferences in terms of nitrate concentration, distance to the coast, temperature and salinity. For example, Chlorophyceae preferred cold and low salinity coastal waters, and prasinophytes clade IX warm, high salinity, oligotrophic oceanic waters.}, } @article {pmid30229698, year = {2019}, author = {Utazi, CE and Thorley, J and Alegana, VA and Ferrari, MJ and Nilsen, K and Takahashi, S and Metcalf, C and Lessler, J and Tatem, AJ}, title = {A spatial regression model for the disaggregation of areal unit based data to high-resolution grids with application to vaccination coverage mapping.}, journal = {Statistical methods in medical research}, volume = {28}, number = {10-11}, pages = {3226-3241}, pmid = {30229698}, issn = {1477-0334}, support = {106866/Z/15/Z/WT_/Wellcome Trust/United Kingdom ; 204613/Z/16/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Afghanistan ; Bayes Theorem ; Datasets as Topic ; Diphtheria-Tetanus-Pertussis Vaccine/*administration & dosage ; Humans ; Maps as Topic ; Measles Vaccine/*administration & dosage ; Pakistan ; Predictive Value of Tests ; *Spatial Regression ; Vaccination Coverage/*statistics & numerical data ; }, abstract = {The growing demand for spatially detailed data to advance the Sustainable Development Goals agenda of 'leaving no one behind' has resulted in a shift in focus from aggregate national and province-based metrics to small areas and high-resolution grids in the health and development arena. Vaccination coverage is customarily measured through aggregate-level statistics, which mask fine-scale heterogeneities and 'coldspots' of low coverage. This paper develops a methodology for high-resolution mapping of vaccination coverage using areal data in settings where point-referenced survey data are inaccessible. The proposed methodology is a binomial spatial regression model with a logit link and a combination of covariate data and random effects modelling two levels of spatial autocorrelation in the linear predictor. The principal aspect of the model is the melding of the misaligned areal data and the prediction grid points using the regression component and each of the conditional autoregressive and the Gaussian spatial process random effects. The Bayesian model is fitted using the INLA-SPDE approach. We demonstrate the predictive ability of the model using simulated data sets. The results obtained indicate a good predictive performance by the model, with correlations of between 0.66 and 0.98 obtained at the grid level between true and predicted values. The methodology is applied to predicting the coverage of measles and diphtheria-tetanus-pertussis vaccinations at 5 × 5 km[2] in Afghanistan and Pakistan using subnational Demographic and Health Surveys data. The predicted maps are used to highlight vaccination coldspots and assess progress towards coverage targets to facilitate the implementation of more geographically precise interventions. The proposed methodology can be readily applied to wider disaggregation problems in related contexts, including mapping other health and development indicators.}, } @article {pmid30222734, year = {2018}, author = {Del Campo, J and Kolisko, M and Boscaro, V and Santoferrara, LF and Nenarokov, S and Massana, R and Guillou, L and Simpson, A and Berney, C and de Vargas, C and Brown, MW and Keeling, PJ and Wegener Parfrey, L}, title = {EukRef: Phylogenetic curation of ribosomal RNA to enhance understanding of eukaryotic diversity and distribution.}, journal = {PLoS biology}, volume = {16}, number = {9}, pages = {e2005849}, pmid = {30222734}, issn = {1545-7885}, mesh = {Ciliophora/genetics ; *Data Curation ; Databases, Genetic ; Eukaryota/*classification/*genetics ; *Genetic Variation ; *Phylogeny ; RNA, Ribosomal/*genetics ; }, abstract = {Environmental sequencing has greatly expanded our knowledge of micro-eukaryotic diversity and ecology by revealing previously unknown lineages and their distribution. However, the value of these data is critically dependent on the quality of the reference databases used to assign an identity to environmental sequences. Existing databases contain errors and struggle to keep pace with rapidly changing eukaryotic taxonomy, the influx of novel diversity, and computational challenges related to assembling the high-quality alignments and trees needed for accurate characterization of lineage diversity. EukRef (eukref.org) is an ongoing community-driven initiative that addresses these challenges by bringing together taxonomists with expertise spanning the eukaryotic tree of life and microbial ecologists, who use environmental sequence data to develop reliable reference databases across the diversity of microbial eukaryotes. EukRef organizes and facilitates rigorous mining and annotation of sequence data by providing protocols, guidelines, and tools. The EukRef pipeline and tools allow users interested in a particular group of microbial eukaryotes to retrieve all sequences belonging to that group from International Nucleotide Sequence Database Collaboration (INSDC) (GenBank, the European Nucleotide Archive [ENA], or the DNA DataBank of Japan [DDBJ]), to place those sequences in a phylogenetic tree, and to curate taxonomic and environmental information for the group. We provide guidelines to facilitate the process and to standardize taxonomic annotations. The final outputs of this process are (1) a reference tree and alignment, (2) a reference sequence database, including taxonomic and environmental information, and (3) a list of putative chimeras and other artifactual sequences. These products will be useful for the broad community as they become publicly available (at eukref.org) and are shared with existing reference databases.}, } @article {pmid30222493, year = {2019}, author = {Greig, M and Emmerson, H and McCreadie, J}, title = {Quantifying Functional Ankle Rehabilitation Progression Criteria Using GPS: A Preliminary Study.}, journal = {Journal of sport rehabilitation}, volume = {28}, number = {7}, pages = {729-734}, doi = {10.1123/jsr.2018-0045}, pmid = {30222493}, issn = {1543-3072}, mesh = {Ankle/physiopathology ; Ankle Injuries/*rehabilitation ; Athletes ; Athletic Injuries/*rehabilitation ; Exercise Test ; Female ; *Geographic Information Systems ; Humans ; *Physical Therapy Modalities ; Weight-Bearing ; }, abstract = {CONTEXT: Contemporary developments in Global Positioning System (GPS) technology present a means of quantifying mechanical loading in a clinical environment with high ecological validity. However, applications to date have typically focused on performance rather than rehabilitation.

OBJECTIVE: To examine the efficacy of GPS microtechnology in quantifying the progression of loading during functional rehabilitation from ankle sprain injury, given the prevalence of reinjury and need for quantifiable monitoring. Furthermore, to examine the influence of unit placement on the clinical interpretation of loading during specific functional rehabilitation drills.

DESIGN: Repeated measures.

SETTING: University athletic facilities.

PARTICIPANTS: Twenty-two female intermittent team sports players.

INTERVENTION: All players completed a battery of 5 drills (anterior hop, inversion hop, eversion hop, diagonal hop, and diagonal hurdle hop) designed to reflect the mechanism of ankle sprain injury, and progress functional challenge and loading.

MAIN OUTCOME MEASURES: GPS-mounted accelerometers quantified uniaxial PlayerLoad for each drill, with units placed at C7 and the tibia. Main effects for drill type and GPS location were investigated.

RESULTS: There was a significant main effect for drill type (P < .001) in the mediolateral (η2 = .436), anteroposterior (η2 = .480), and vertical planes (η2 = .516). The diagonal hurdle hop elicited significantly greater load than all other drills, highlighting a nonlinear progression of load. Only the mediolateral load showed evidence of progressive increase in loading. PlayerLoad was significantly greater at the tibia than at C7 for all drills, and in all planes (P < .001, η2 ≥ .662). Furthermore, the tibia placement was more sensitive to between-drill changes in mediolateral load than the C7 placement.

CONCLUSIONS: The placement of the GPS unit is imperative to clinical interpretation, with both magnitude and sensitivity influenced by the unit location. GPS does provide efficacy in quantifying multiplanar loading during (p)rehabilitation, in a field or clinical setting, with potential in extending GPS analyses (beyond performance metrics) to functional injury rehabilitation and prevention.}, } @article {pmid30220204, year = {2018}, author = {Fingerhut, LCHW and Strugnell, JM and Faou, P and Labiaga, ÁR and Zhang, J and Cooke, IR}, title = {Shotgun Proteomics Analysis of Saliva and Salivary Gland Tissue from the Common Octopus Octopus vulgaris.}, journal = {Journal of proteome research}, volume = {17}, number = {11}, pages = {3866-3876}, doi = {10.1021/acs.jproteome.8b00525}, pmid = {30220204}, issn = {1535-3907}, mesh = {Animals ; Female ; *Gene Expression Regulation, Developmental ; Gene Ontology ; Larva/chemistry/genetics/growth & development/metabolism ; Male ; Molecular Sequence Annotation ; Mollusk Venoms/classification/*genetics/metabolism ; Neurotoxins/classification/genetics/metabolism ; Octopodiformes/chemistry/*genetics/growth & development/metabolism ; Phylogeny ; Proteogenomics/*methods ; Proteome/genetics/metabolism ; Saliva/chemistry/*metabolism ; Salivary Glands/chemistry/growth & development/metabolism ; Serine Proteases/classification/genetics/metabolism ; *Transcriptome ; }, abstract = {The salivary apparatus of the common octopus (Octopus vulgaris) has been the subject of biochemical study for over a century. A combination of bioassays, behavioral studies and molecular analysis on O. vulgaris and related species suggests that its proteome should contain a mixture of highly potent neurotoxins and degradative proteins. However, a lack of genomic and transcriptomic data has meant that the amino acid sequences of these proteins remain almost entirely unknown. To address this, we assembled the posterior salivary gland transcriptome of O. vulgaris and combined it with high resolution mass spectrometry data from the posterior and anterior salivary glands of two adults, the posterior salivary glands of six paralarvae and the saliva from a single adult. We identified a total of 2810 protein groups from across this range of salivary tissues and age classes, including 84 with homology to known venom protein families. Additionally, we found 21 short secreted cysteine rich protein groups of which 12 were specific to cephalopods. By combining protein expression data with phylogenetic analysis we demonstrate that serine proteases expanded dramatically within the cephalopod lineage and that cephalopod specific proteins are strongly associated with the salivary apparatus.}, } @article {pmid30216600, year = {2018}, author = {Lennox, GD and Gardner, TA and Thomson, JR and Ferreira, J and Berenguer, E and Lees, AC and Mac Nally, R and Aragão, LEOC and Ferraz, SFB and Louzada, J and Moura, NG and Oliveira, VHF and Pardini, R and Solar, RRC and Vaz-de Mello, FZ and Vieira, ICG and Barlow, J}, title = {Second rate or a second chance? Assessing biomass and biodiversity recovery in regenerating Amazonian forests.}, journal = {Global change biology}, volume = {24}, number = {12}, pages = {5680-5694}, doi = {10.1111/gcb.14443}, pmid = {30216600}, issn = {1365-2486}, mesh = {Animals ; *Biodiversity ; *Biomass ; Birds/physiology ; Carbon Cycle ; Coleoptera/physiology ; Conservation of Natural Resources ; Datasets as Topic ; Ecosystem ; *Forests ; Trees ; Tropical Climate ; }, abstract = {Secondary forests (SFs) regenerating on previously deforested land account for large, expanding areas of tropical forest cover. Given that tropical forests rank among Earth's most important reservoirs of carbon and biodiversity, SFs play an increasingly pivotal role in the carbon cycle and as potential habitat for forest biota. Nevertheless, their capacity to regain the biotic attributes of undisturbed primary forests (UPFs) remains poorly understood. Here, we provide a comprehensive assessment of SF recovery, using extensive tropical biodiversity, biomass, and environmental datasets. These data, collected in 59 naturally regenerating SFs and 30 co-located UPFs in the eastern Amazon, cover >1,600 large- and small-stemmed plant, bird, and dung beetles species and a suite of forest structure, landscape context, and topoedaphic predictors. After up to 40 years of regeneration, the SFs we surveyed showed a high degree of biodiversity resilience, recovering, on average among taxa, 88% and 85% mean UPF species richness and composition, respectively. Across the first 20 years of succession, the period for which we have accurate SF age data, biomass recovered at 1.2% per year, equivalent to a carbon uptake rate of 2.25 Mg/ha per year, while, on average, species richness and composition recovered at 2.6% and 2.3% per year, respectively. For all taxonomic groups, biomass was strongly associated with SF species distributions. However, other variables describing habitat complexity-canopy cover and understory stem density-were equally important occurrence predictors for most taxa. Species responses to biomass revealed a successional transition at approximately 75 Mg/ha, marking the influx of high-conservation-value forest species. Overall, our results show that naturally regenerating SFs can accumulate substantial amounts of carbon and support many forest species. However, given that the surveyed SFs failed to return to a typical UPF state, SFs are not substitutes for UPFs.}, } @article {pmid30213659, year = {2018}, author = {Costello, MJ and Horton, T and Kroh, A}, title = {Sustainable Biodiversity Databasing: International, Collaborative, Dynamic, Centralised.}, journal = {Trends in ecology & evolution}, volume = {33}, number = {11}, pages = {803-805}, doi = {10.1016/j.tree.2018.08.006}, pmid = {30213659}, issn = {1872-8383}, mesh = {Aquatic Organisms/*classification ; *Biodiversity ; *Databases, Factual ; Informatics ; Registries ; Terminology as Topic ; }, abstract = {The World Register of Marine Species (WoRMS) is a sustainable model of international collaboration around a centralised database that provides expert validated biodiversity data freely online. This model could be replicated for the over 1.2 million terrestrial and freshwater species to improve quality control and data management in biology and ecology globally.}, } @article {pmid30208069, year = {2018}, author = {Mariac, C and Vigouroux, Y and Duponchelle, F and García-Dávila, C and Nunez, J and Desmarais, E and Renno, JF}, title = {Metabarcoding by capture using a single COI probe (MCSP) to identify and quantify fish species in ichthyoplankton swarms.}, journal = {PloS one}, volume = {13}, number = {9}, pages = {e0202976}, pmid = {30208069}, issn = {1932-6203}, mesh = {Animals ; Biodiversity ; DNA Barcoding, Taxonomic/*methods ; Databases, Genetic ; Fishes/*classification/genetics ; High-Throughput Nucleotide Sequencing ; Larva/*genetics ; }, abstract = {The ability to determine the composition and relative frequencies of fish species in large ichthyoplankton swarms could have extremely important ecological applications However, this task is currently hampered by methodological limitations. We proposed a new method for Amazonian species based on hybridization capture of the COI gene DNA from a distant species (Danio rerio), absent from our study area (the Amazon basin). The COI sequence of this species is approximately equidistant from all COI of Amazonian species available. By using this sequence as probe we successfully facilitated the simultaneous identification of fish larvae belonging to the order Siluriformes and to the Characiformes represented in our ichthyoplankton samples. Species relative frequencies, estimated by the number of reads, showed almost perfect correlations with true frequencies estimated by a Sanger approach, allowing the development of a quantitative approach. We also proposed a further improvement to a previous protocol, which enables lowering the sequencing effort by 40 times. This new Metabarcoding by Capture using a Single Probe (MCSP) methodology could have important implications for ecology, fisheries management and conservation in fish biodiversity hotspots worldwide. Our approach could easily be extended to other plant and animal taxa.}, } @article {pmid30207406, year = {2019}, author = {Hamadi, H and Apatu, E and Loh, CA and Farah, H and Walker, K and Spaulding, A}, title = {Does level of minority presence and hospital reimbursement policy influence hospital referral region health rankings in the United States.}, journal = {The International journal of health planning and management}, volume = {34}, number = {1}, pages = {e354-e368}, doi = {10.1002/hpm.2654}, pmid = {30207406}, issn = {1099-1751}, mesh = {Adolescent ; Adult ; Databases, Factual ; Fee-for-Service Plans ; *Health Policy ; Humans ; Middle Aged ; *Minority Groups ; Patient Protection and Affordable Care Act ; Quality of Health Care ; *Referral and Consultation/statistics & numerical data ; *Reimbursement Mechanisms ; Reimbursement, Incentive ; United States ; Young Adult ; }, abstract = {The shift from a fee-for-service payment to a value-based payment scheme, sparked by the Patient Protection and Affordable Care Act, introduced pay-for-performance programs such Hospital Value Based Purchasing. Previous inquiry has not considered how local community factors may affect hospital system performance. This study investigated the association between local health performance and minority population in a hospital referral region (HRR). The primary objective was to ascertain whether community diversity levels are significantly associated to local health performance guided by the ecological model. Secondary data analysis collected from the 2016 American Hospital Association, Area Health Resource File, Commonwealth Fund Scorecard on Local Health System Performance, and the Dartmouth Atlas HRR dataset was used. Our primary findings show that the more diverse a HRR is, the more likely it is to be associated with lower ranking for access and affordability prevention and treatment avoidable hospital use and cost as well as healthy lives. Total performance score was significantly related to a better health ranking on prevention and treatment, hospital use, and cost, as well as healthy lives. This research supports the assertion that communities, particularly minorities in those communities, affect local health care performance in a variety of ways.}, } @article {pmid30206171, year = {2018}, author = {Gaulke, CA and Arnold, HK and Humphreys, IR and Kembel, SW and O'Dwyer, JP and Sharpton, TJ}, title = {Ecophylogenetics Clarifies the Evolutionary Association between Mammals and Their Gut Microbiota.}, journal = {mBio}, volume = {9}, number = {5}, pages = {}, pmid = {30206171}, issn = {2150-7511}, mesh = {Algorithms ; Animals ; Bacteria/*classification ; Biodiversity ; *Biological Evolution ; Computational Biology ; *Gastrointestinal Microbiome ; Host Microbial Interactions ; Mammals/*microbiology ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Our knowledge of how the gut microbiome relates to mammalian evolution benefits from the identification of gut microbial taxa that are unexpectedly prevalent or unexpectedly conserved across mammals. Such taxa enable experimental determination of the traits needed for such microbes to succeed as gut generalists, as well as those traits that impact mammalian fitness. However, the punctuated resolution of microbial taxonomy may limit our ability to detect conserved gut microbes, especially in cases in which broadly related microbial lineages possess shared traits that drive their apparent ubiquity across mammals. To advance the discovery of conserved mammalian gut microbes, we developed a novel ecophylogenetic approach to taxonomy that groups microbes into taxonomic units based on their shared ancestry and their common distribution across mammals. Applying this approach to previously generated gut microbiome data uncovered monophyletic clades of gut bacteria that are conserved across mammals. It also resolved microbial clades exclusive to and conserved among particular mammalian lineages. Conserved clades often manifest phylogenetic patterns, such as cophylogeny with their host, that indicate that they are subject to selective processes, such as host filtering. Moreover, this analysis identified variation in the rate at which mammals acquire or lose conserved microbial clades and resolved a human-accelerated loss of conserved clades. Collectively, the data from this study reveal mammalian gut microbiota that possess traits linked to mammalian phylogeny, point to the existence of a core set of microbes that comprise the mammalian gut microbiome, and clarify potential evolutionary or ecologic mechanisms driving the gut microbiome's diversification throughout mammalian evolution.IMPORTANCE Our understanding of mammalian evolution has become microbiome-aware. While emerging research links mammalian biodiversity and the gut microbiome, we lack insight into which microbes potentially impact mammalian evolution. Microbes common to diverse mammalian species may be strong candidates, as their absence in the gut may affect how the microbiome functionally contributes to mammalian physiology to adversely affect fitness. Identifying such conserved gut microbes is thus important to ultimately assessing the microbiome's potential role in mammalian evolution. To advance their discovery, we developed an approach that identifies ancestrally related groups of microbes that distribute across mammals in a way that indicates their collective conservation. These conserved clades are presumed to have evolved a trait in their ancestor that matters to their distribution across mammals and which has been retained among clade members. We found not only that such clades do exist among mammals but also that they appear to be subject to natural selection and characterize human evolution.}, } @article {pmid30203521, year = {2019}, author = {Lehmann, R and Lightfoot, DJ and Schunter, C and Michell, CT and Ohyanagi, H and Mineta, K and Foret, S and Berumen, ML and Miller, DJ and Aranda, M and Gojobori, T and Munday, PL and Ravasi, T}, title = {Finding Nemo's Genes: A chromosome-scale reference assembly of the genome of the orange clownfish Amphiprion percula.}, journal = {Molecular ecology resources}, volume = {19}, number = {3}, pages = {570-585}, pmid = {30203521}, issn = {1755-0998}, support = {OCRF-2014-CRG3-62140408//King Abdullah University of Science and Technology/ ; }, mesh = {Animals ; *Chromosomes ; Computational Biology ; Fishes/*genetics ; *Gene Order ; Genomics ; Pacific Ocean ; Sequence Analysis, DNA ; }, abstract = {The iconic orange clownfish, Amphiprion percula, is a model organism for studying the ecology and evolution of reef fishes, including patterns of population connectivity, sex change, social organization, habitat selection and adaptation to climate change. Notably, the orange clownfish is the only reef fish for which a complete larval dispersal kernel has been established and was the first fish species for which it was demonstrated that antipredator responses of reef fishes could be impaired by ocean acidification. Despite its importance, molecular resources for this species remain scarce and until now it lacked a reference genome assembly. Here, we present a de novo chromosome-scale assembly of the genome of the orange clownfish Amphiprion percula. We utilized single-molecule real-time sequencing technology from Pacific Biosciences to produce an initial polished assembly comprised of 1,414 contigs, with a contig N50 length of 1.86 Mb. Using Hi-C-based chromatin contact maps, 98% of the genome assembly were placed into 24 chromosomes, resulting in a final assembly of 908.8 Mb in length with contig and scaffold N50s of 3.12 and 38.4 Mb, respectively. This makes it one of the most contiguous and complete fish genome assemblies currently available. The genome was annotated with 26,597 protein-coding genes and contains 96% of the core set of conserved actinopterygian orthologs. The availability of this reference genome assembly as a community resource will further strengthen the role of the orange clownfish as a model species for research on the ecology and evolution of reef fishes.}, } @article {pmid30203454, year = {2018}, author = {Berry, N and Emsley, R and Lobban, F and Bucci, S}, title = {Social media and its relationship with mood, self-esteem and paranoia in psychosis.}, journal = {Acta psychiatrica Scandinavica}, volume = {138}, number = {6}, pages = {558-570}, pmid = {30203454}, issn = {1600-0447}, support = {MR/K006665/1/MRC_/Medical Research Council/United Kingdom ; PB-PG-0807-14075/DH_/Department of Health/United Kingdom ; }, mesh = {Adult ; *Affect ; Ecological Momentary Assessment ; Female ; Hierarchy, Social ; Humans ; Male ; Middle Aged ; Paranoid Disorders/*psychology ; Psychotic Disorders/*psychology ; *Schizophrenia ; *Self Concept ; *Social Behavior ; *Social Media ; Young Adult ; }, abstract = {OBJECTIVE: An evidence-base is emerging indicating detrimental and beneficial effects of social media. Little is known about the impact of social media use on people who experience psychosis.

METHOD: Forty-four participants with and without psychosis completed 1084 assessments of social media use, perceived social rank, mood, self-esteem and paranoia over a 6-day period using an experience sampling method (ESM).

RESULTS: Social media use predicted low mood, but did not predict self-esteem and paranoia. Posting about feelings and venting on social media predicted low mood and self-esteem and high paranoia, whilst posting about daily activities predicted increases in positive affect and self-esteem and viewing social media newsfeeds predicted reductions in negative affect and paranoia. Perceptions of low social rank when using social media predicted low mood and self-esteem and high paranoia. The impact of social media use did not differ between participants with and without psychosis; although, experiencing psychosis moderated the relationship between venting and negative affect. Social media use frequency was lower in people with psychosis.

CONCLUSION: Findings show the potential detrimental impact of social media use for people with and without psychosis. Despite few between-group differences, overall negative psychological consequences highlight the need to consider use in clinical practice.}, } @article {pmid30201488, year = {2018}, author = {Mollalo, A and Sadeghian, A and Israel, GD and Rashidi, P and Sofizadeh, A and Glass, GE}, title = {Machine learning approaches in GIS-based ecological modeling of the sand fly Phlebotomus papatasi, a vector of zoonotic cutaneous leishmaniasis in Golestan province, Iran.}, journal = {Acta tropica}, volume = {188}, number = {}, pages = {187-194}, doi = {10.1016/j.actatropica.2018.09.004}, pmid = {30201488}, issn = {1873-6254}, mesh = {Animals ; Area Under Curve ; Ecosystem ; Environment ; Geographic Information Systems ; Insect Vectors ; Iran/epidemiology ; Leishmaniasis, Cutaneous/epidemiology/*transmission ; *Machine Learning ; *Phlebotomus ; }, abstract = {The distribution and abundance of Phlebotomus papatasi, the primary vector of zoonotic cutaneous leishmaniasis in most semi-/arid countries, is a major public health challenge. This study compares several approaches to model the spatial distribution of the species in an endemic region of the disease in Golestan province, northeast of Iran. The intent is to assist decision makers for targeted interventions. We developed a geo-database of the collected Phlebotominae sand flies from different parts of the study region. Sticky paper traps coated with castor oil were used to collect sand flies. In 44 out of 142 sampling sites, Ph. papatasi was present. We also gathered and prepared data on related environmental factors including topography, weather variables, distance to main rivers and remotely sensed data such as normalized difference vegetation cover and land surface temperature (LST) in a GIS framework. Applicability of three classifiers: (vanilla) logistic regression, random forest and support vector machine (SVM) were compared for predicting presence/absence of the vector. Predictive performances were compared using an independent dataset to generate area under the ROC curve (AUC) and Kappa statistics. All three models successfully predicted the presence/absence of the vector, however, the SVM classifier (Accuracy = 0.906, AUC = 0.974, Kappa = 0.876) outperformed the other classifiers on predicting accuracy. Moreover, this classifier was the most sensitive (85%), and the most specific (93%) model. Sensitivity analysis of the most accurate model (i.e. SVM) revealed that slope, nighttime LST in October and mean temperature of the wettest quarter were among the most important predictors. The findings suggest that machine learning techniques, especially the SVM classifier, when coupled with GIS and remote sensing data can be a useful and cost-effective way for identifying habitat suitability of the species.}, } @article {pmid30199691, year = {2019}, author = {Liu, J and An, Z}, title = {Variations in hydrogen isotopic fractionation in higher plants and sediments across different latitudes: Implications for paleohydrological reconstruction.}, journal = {The Science of the total environment}, volume = {650}, number = {Pt 1}, pages = {470-478}, doi = {10.1016/j.scitotenv.2018.09.047}, pmid = {30199691}, issn = {1879-1026}, mesh = {Alkanes/analysis ; Databases, Factual ; *Environmental Monitoring ; Geologic Sediments/*chemistry ; Hydrogen/*analysis ; *Hydrology ; Isotopes/*analysis ; Lakes/chemistry ; Plant Leaves/chemistry ; Plants/*chemistry ; }, abstract = {Sedimentary δDn-alkane value is widely utilized as a reliable proxy for paleo-hydrological reconstruction. Applications of this proxy must be based upon a globally clear understanding of the relationship between leaf wax δDn-alkane values and precipitation δD (δDp), defined as apparent fractionation (εapp). However, there is a critical concern about whether relatively constant εapp values exist across different latitudes. In this study, we systematically analyzed the variations of available εapp with latitudes based upon two compiled-new databases of higher plants and sediments over the world. We found that the total average εapp was relatively constant, i.e., -116 ± 5‰ (n = 941), in higher plants across different latitudes without consideration of plant types (e.g., dicots, monocots, gymnosperms), and was still constant but slightly lower average εapp, i.e., -125 ± 6‰ (n = 460), in sediments across the latitudes. The slightly lower average εapp in sediments relative to higher plants probably derived from the contribution of aquatic plants with isotopically D-depleted εapp in lake sediments. Interestingly, with consideration of plant types, average εapp increased in dicots but decreased in monocots slightly from low to high latitudes. The counteraction of these competing trends generates relatively constant average εapp values in higher plants, and resultantly constant average εapp values occur in sediments at the global scale. It is important to elaborate relatively constant εapp values from higher plants and sediments across different latitudes when sedimentary δDn-alkane is utilized as a proxy for paleohydrological reconstruction.}, } @article {pmid30197411, year = {2018}, author = {Mise, K and Fujita, K and Kunito, T and Senoo, K and Otsuka, S}, title = {Phosphorus-mineralizing Communities Reflect Nutrient-Rich Characteristics in Japanese Arable Andisols.}, journal = {Microbes and environments}, volume = {33}, number = {3}, pages = {282-289}, pmid = {30197411}, issn = {1347-4405}, mesh = {Alkaline Phosphatase/*genetics/metabolism ; Bacteria/classification/enzymology/genetics/*metabolism ; Bacterial Proteins/*genetics/metabolism ; Biodiversity ; Computational Biology ; DNA, Bacterial/genetics ; Genes, Bacterial/genetics ; Geography ; Japan ; Metagenome/genetics ; Phosphorus/analysis/*metabolism ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {Elucidating the soil phosphorus cycle driven by soil microbes is a vital question in soil microbial ecology. The Japanese arable Andisols, occupying half of the Japanese cropland, are known for their high phosphorus sorption capacity. However, limited information is currently available on microbially driven phosphorus mineralization in arable Andisols. We herein report that the phosphorus-mineralizing community in the Japanese arable Andisols showed characteristic distribution and composition patterns, from those in other types of soils. We performed a chemical analysis and microbial community analysis of 43 arable Andisols along the Japanese archipelago. Soil phosphomonoesterase activities measured at pH 11 were approximately 70% of those at pH 6.5, which indicates that alkaline phosphatase contributes to phosphorus cycling, although most soil samples were acidic. Functional gene predictions based on 16S rRNA gene sequencing indicated that the alkaline phosphatase gene phoD was more abundant than other alkaline phosphatase genes and, thus, plays major roles. Hence, amplicon sequencing targeting phoD was performed and the results obtained showed that alphaproteobacterial phoD was dominant. This is in contrast to previously reported phoD compositions in other soils and may be attributed to the nutrient conditions in arable Andisols, which favor copiotrophic Alphaproteobacteria. Furthermore, the composition of phoD correlated with soil pH and bioavailable phosphorus concentrations rather than carbon or nitrogen concentrations. These results were partly different from previous findings, varying in the soil types and geographic ranges of sampling sites. Collectively, the present results indicate that the phosphorus-mineralizing community in the Japanese arable Andisols is regulated differently from those in other soil types.}, } @article {pmid30196122, year = {2018}, author = {Cheon, SH and Lee, YN and Kang, SI and Kye, SJ and Lee, EK and Heo, GB and Lee, MH and Kim, JW and Lee, KN and Son, HM and Lee, YJ}, title = {Genetic evidence for the intercontinental movement of avian influenza viruses possessing North American-origin nonstructural gene allele B into South Korea.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {66}, number = {}, pages = {18-25}, doi = {10.1016/j.meegid.2018.09.001}, pmid = {30196122}, issn = {1567-7257}, mesh = {*Alleles ; Animal Migration ; Animals ; Animals, Wild ; Birds/virology ; Geese/virology ; *Genetic Variation ; Geographic Information Systems ; Influenza A virus/*classification/*genetics/isolation & purification ; Influenza in Birds/*epidemiology/transmission/*virology ; North America/epidemiology ; Phylogeny ; Republic of Korea/epidemiology ; Viral Nonstructural Proteins/*genetics ; }, abstract = {Avian influenza viruses (AIVs) are genetically separated by geographical barriers, resulting in the independent evolution of North American and Eurasian lineages. In the present study, to determine whether AIVs possessing the North American-origin nonstructural (NS) gene were previously introduced into South Korea, we performed a genetic analysis of AIVs isolated from fecal samples of migratory birds. We detected seven viruses possessing the North American-origin NS allele B among 413 AIV-positive samples obtained during AI surveillance between 2012 and 2017. We found evidence for the intercontinental transmission of at least three genetically distinct clusters of the B allele of the North American-origin NS gene into Eurasia at a low frequency. The host species of three viruses were identified as the greater white-fronted goose (Anser albifrons) using a DNA barcoding technique. Moreover, we used GPS-CDMA-based telemetry to determine the migration route of the greater white-fronted goose between the Far East of Russia and South Korea and found that this species may play an important role as an intermediate vector in the intercontinental transmission of AIVs. To improve our understanding of the role of wild birds in the ecology of AIVs, advanced AIV surveillance is required in the Far East of Russia as well as in Alaska region of Beringia accompanied by host identification and wild bird tracking.}, } @article {pmid30194403, year = {2018}, author = {Rokas, A and Wisecaver, JH and Lind, AL}, title = {The birth, evolution and death of metabolic gene clusters in fungi.}, journal = {Nature reviews. Microbiology}, volume = {16}, number = {12}, pages = {731-744}, doi = {10.1038/s41579-018-0075-3}, pmid = {30194403}, issn = {1740-1534}, mesh = {Evolution, Molecular ; Fungi/*genetics/*metabolism ; *Genome, Fungal ; Metabolic Networks and Pathways ; *Multigene Family ; *Phylogeny ; }, abstract = {Fungi contain a remarkable diversity of both primary and secondary metabolic pathways involved in ecologically specialized or accessory functions. Genes in these pathways are frequently physically linked on fungal chromosomes, forming metabolic gene clusters (MGCs). In this Review, we describe the diversity in the structure and content of fungal MGCs, their population-level and species-level variation, the evolutionary mechanisms that underlie their formation, maintenance and decay, and their ecological and evolutionary impact on fungal populations. We also discuss MGCs from other eukaryotes and the reasons for their preponderance in fungi. Improved knowledge of the evolutionary life cycle of MGCs will advance our understanding of the ecology of specialized metabolism and of the interplay between the lifestyle of an organism and genome architecture.}, } @article {pmid30193672, year = {2018}, author = {Kumar, N and Pandey, A and Garg, N and Sampene, E and Lavie, CJ}, title = {Seasonal and Geographic Patterns in Seeking Cardiovascular Health Information: An Analysis of the Online Search Trends.}, journal = {Mayo Clinic proceedings}, volume = {93}, number = {9}, pages = {1185-1190}, pmid = {30193672}, issn = {1942-5546}, support = {UL1 TR000427/TR/NCATS NIH HHS/United States ; UL1 TR002373/TR/NCATS NIH HHS/United States ; }, mesh = {Australia ; *Cardiovascular Diseases ; *Consumer Health Information ; Geography ; Humans ; *Information Seeking Behavior ; Internet/*trends ; Linear Models ; Search Engine/*trends ; Seasons ; United States ; }, abstract = {OBJECTIVE: To ascertain whether temporal and geographic interest in seeking cardiovascular disease (CVD) information online follows seasonal and geographic patterns similar to those observed in real-world data.

METHODS: We searched Google Trends for popular search terms relating to CVD. Relative search volumes (RSVs) were obtained for the period January 4, 2004, to April 19, 2014, for the United States and Australia. We compared average RSVs by month and season and used cosinor analysis to test for seasonal variation in RSVs. We also assessed correlations between state-level RSVs and CVD burden using an ecological correlational design.

RESULTS: RSVs were 15% higher in the United States and 45% higher in Australia for winter compared with summer (P<.001 for difference for both). In the United States, RSVs were 36% higher in February compared with August, while in Australia, RSVs were 75% higher in August compared with January. On cosinor analysis, we found a significant seasonal variability in RSVs, with winter peaks and summer troughs for both the United States and Australia (P<.001 for zero amplitude test for both). We found a significant correlation between state-level RSVs and mortality from CVD (r=0.62; P<.001), heart disease (r=0.58; P<.001), coronary heart disease (r=0.48; P<.001), heart failure (r=0.51; P<.001), and stroke (r=0.60; P<.001).

CONCLUSION: Google search query volumes related to CVD follow strong seasonal patterns with winter peaks and summer troughs. There is moderate to strong positive correlation between state-level search query volumes and burden of CVD mortality.}, } @article {pmid30192445, year = {2018}, author = {Wang, LJ and Lee, SY and Chou, MC and Yang, KC and Lee, TL and Shyu, YC}, title = {Impact of Drug Adherence on Oppositional Defiant Disorder and Conduct Disorder Among Patients With Attention-Deficit/Hyperactivity Disorder.}, journal = {The Journal of clinical psychiatry}, volume = {79}, number = {5}, pages = {}, doi = {10.4088/JCP.17m11784}, pmid = {30192445}, issn = {1555-2101}, mesh = {Adolescent ; Attention Deficit Disorder with Hyperactivity/drug therapy/*epidemiology/*psychology ; Attention Deficit and Disruptive Behavior Disorders/drug therapy/*epidemiology/*psychology ; Child ; Child, Preschool ; Comorbidity ; Conduct Disorder/drug therapy/*epidemiology/*psychology ; Databases, Factual ; Female ; Humans ; Male ; Medication Adherence/*psychology ; Taiwan/epidemiology ; }, abstract = {OBJECTIVE: Attention-deficit/hyperactivity disorder (ADHD) may be a predecessor of oppositional defiant disorder (ODD) and conduct disorder (CD), and medication is an effective treatment option for ADHD. This study aims to examine whether adherence to medication treatment is associated with developing ODD and CD among youths with ADHD.

METHODS: A total of 33,835 youths (4 years ≤ age of diagnosis ≤ 18 years) with ADHD (ICD-9-CM code 314.X) undergoing medication treatment for at least 90 days were selected from Taiwan's National Health Insurance Research Database during the period of January 2000 through December 2009. Patients' medical records were monitored through December 31, 2011, or until they had a diagnosis of ODD or CD. We categorized participants as compliant or noncompliant on the basis of a medication possession ratio (MPR) of 50%.

RESULTS: The patients with better drug adherence (MPR ≥ 50%) exhibited a significantly decreased probability of developing ODD (53% reduction, P < .001) or CD (58% reduction, P < .001) when compared to the patients with poor drug adherence (MPR < 50%). The results in our sensitivity analyses showed that good drug adherence consistently exerted protective effects on ODD or CD, irrespective of patients' characteristics. Moreover, the patients with the best drug adherence (MPR ≥ 75%) had the lowest risks of developing ODD or CD.

CONCLUSION: Among patients with ADHD undergoing drug therapy, a better drug adherence is associated with a lower likelihood of their developing ODD or CD in later life.}, } @article {pmid30191440, year = {2018}, author = {Chu, P and Wilson, GM and Michael, TP and Vaiciunas, J and Honig, J and Lam, E}, title = {Sequence-guided approach to genotyping plant clones and species using polymorphic NB-ARC-related genes.}, journal = {Plant molecular biology}, volume = {98}, number = {3}, pages = {219-231}, pmid = {30191440}, issn = {1573-5028}, support = {DGE-0903675//Directorate for Biological Sciences/ ; 12116//New Jersey Agricultural Experiment Station/ ; }, mesh = {Araceae/*genetics ; *Cloning, Organism ; DNA Fingerprinting ; DNA, Plant/genetics ; Gene Expression Regulation, Plant/*physiology ; *Genotype ; Nucleic Acid Amplification Techniques ; Plant Proteins/genetics/*metabolism ; *Polymorphism, Single Nucleotide ; }, abstract = {Leveraging the heightened levels of polymorphism in NB-ARC-related protein encoding genes in higher plants, a bioinformatic pipeline was created to identify regions in this gene family from sequenced plant genomes that exhibit fragment length or single nucleotide differences in different accessions of the same species. Testing this approach with the aquatic plant Spirodela polyrhiza demonstrated its superior performance in comparison with currently available genotyping technologies based on PCR amplification. Rapid and economical genotyping tools that can reliably distinguish species and intraspecific variations in plants can be powerful tools for biogeographical and ecological studies. Clones of the cosmopolitan duckweed species, Spirodela polyrhiza, are difficult to distinguish morphologically due to their highly abbreviated architecture and inherently low levels of sequence variation. The use of plastidic markers and generic Amplification Fragment Length Polymorphism approaches have met with limited success in resolving clones of S. polyrhiza from diverse geographical locales. Using whole genome sequencing data from nine S. polyrhiza clones as a training set, we created an informatic pipeline to identify and rank polymorphic regions from nuclear-encoded NB-ARC-related genes to design markers for PCR, Sanger sequencing (barcoding), and fragment length analysis. With seven primer sets, we found 21 unique fingerprints from a set of 23 S. polyrhiza clones. However, three of these clones share the same fingerprint and are indistinguishable by these markers. These primer sets can also be used as interspecific barcoding tools to rapidly resolve S. polyrhiza from the closely related S. intermedia species without the need for DNA sequencing. Our work demonstrates a general approach of using hyper-polymorphic loci within genomes as a resource to produce facile tools that can have high resolving power for genotyping applications.}, } @article {pmid30186704, year = {2018}, author = {Mohamad-Matrol, AA and Chang, SW and Abu, A}, title = {Plant data visualisation using network graphs.}, journal = {PeerJ}, volume = {6}, number = {}, pages = {e5579}, pmid = {30186704}, issn = {2167-8359}, abstract = {BACKGROUND: The amount of plant data such as taxonomical classification, morphological characteristics, ecological attributes and geological distribution in textual and image forms has increased rapidly due to emerging research and technologies. Therefore, it is crucial for experts as well as the public to discern meaningful relationships from this vast amount of data using appropriate methods. The data are often presented in lengthy texts and tables, which make gaining new insights difficult. The study proposes a visual-based representation to display data to users in a meaningful way. This method emphasises the relationships between different data sets.

METHOD: This study involves four main steps which translate text-based results from Extensible Markup Language (XML) serialisation format into graphs. The four steps include: (1) conversion of ontological dataset as graph model data; (2) query from graph model data; (3) transformation of text-based results in XML serialisation format into a graphical form; and (4) display of results to the user via a graphical user interface (GUI). Ontological data for plants and samples of trees and shrubs were used as the dataset to demonstrate how plant-based data could be integrated into the proposed data visualisation.

RESULTS: A visualisation system named plant visualisation system was developed. This system provides a GUI that enables users to perform the query process, as well as a graphical viewer to display the results of the query in the form of a network graph. The efficiency of the developed visualisation system was measured by performing two types of user evaluations: a usability heuristics evaluation, and a query and visualisation evaluation.

DISCUSSION: The relationships between the data were visualised, enabling the users to easily infer the knowledge and correlations between data. The results from the user evaluation show that the proposed visualisation system is suitable for both expert and novice users, with or without computer skills. This technique demonstrates the practicability of using a computer assisted-tool by providing cognitive analysis for understanding relationships between data. Therefore, the results benefit not only botanists, but also novice users, especially those that are interested to know more about plants.}, } @article {pmid30185798, year = {2018}, author = {Doizy, A and Barter, E and Memmott, J and Varnham, K and Gross, T}, title = {Impact of cyber-invasive species on a large ecological network.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {13245}, pmid = {30185798}, issn = {2045-2322}, mesh = {Animals ; Carnivory ; Cluster Analysis ; Databases, Factual ; Ecosystem ; Feeding Behavior/*physiology ; Food Chain ; Herbivory ; Introduced Species ; Rats ; United Kingdom ; }, abstract = {As impacts of introduced species cascade through trophic levels, they can cause indirect and counter-intuitive effects. To investigate the impact of invasive species at the network scale, we use a generalized food web model, capable of propagating changes through networks with a series of ecologically realistic criteria. Using data from a small British offshore island, we quantify the impacts of four virtual invasive species (an insectivore, a herbivore, a carnivore and an omnivore whose diet is based on a rat) and explore which clusters of species react in similar ways. We find that the predictions for the impacts of invasive species are ecologically plausible, even in large networks. Species in the same taxonomic group are similarly impacted by a virtual invasive species. However, interesting differences within a given taxonomic group can occur. The results suggest that some native species may be at risk from a wider range of invasives than previously believed. The implications of these results for ecologists and land managers are discussed.}, } @article {pmid30185609, year = {2018}, author = {Marshall, CR and Finnegan, S and Clites, EC and Holroyd, PA and Bonuso, N and Cortez, C and Davis, E and Dietl, GP and Druckenmiller, PS and Eng, RC and Garcia, C and Estes-Smargiassi, K and Hendy, A and Hollis, KA and Little, H and Nesbitt, EA and Roopnarine, P and Skibinski, L and Vendetti, J and White, LD}, title = {Quantifying the dark data in museum fossil collections as palaeontology undergoes a second digital revolution.}, journal = {Biology letters}, volume = {14}, number = {9}, pages = {}, pmid = {30185609}, issn = {1744-957X}, mesh = {Animals ; California ; Databases, Factual/*statistics & numerical data ; *Fossils ; *Invertebrates ; Museums/statistics & numerical data ; Oregon ; Paleontology/methods ; Washington ; }, abstract = {Large-scale analysis of the fossil record requires aggregation of palaeontological data from individual fossil localities. Prior to computers, these synoptic datasets were compiled by hand, a laborious undertaking that took years of effort and forced palaeontologists to make difficult choices about what types of data to tabulate. The advent of desktop computers ushered in palaeontology's first digital revolution-online literature-based databases, such as the Paleobiology Database (PBDB). However, the published literature represents only a small proportion of the palaeontological data housed in museum collections. Although this issue has long been appreciated, the magnitude, and thus potential significance, of these so-called 'dark data' has been difficult to determine. Here, in the early phases of a second digital revolution in palaeontology--the digitization of museum collections-we provide an estimate of the magnitude of palaeontology's dark data. Digitization of our nine institutions' holdings of Cenozoic marine invertebrate collections from California, Oregon and Washington in the USA reveals that they represent 23 times the number of unique localities than are currently available in the PBDB. These data, and the vast quantity of similarly untapped dark data in other museum collections, will, when digitally mobilized, enhance palaeontologists' ability to make inferences about the patterns and processes of past evolutionary and ecological changes.}, } @article {pmid30185512, year = {2018}, author = {Rohwer, RR and Hamilton, JJ and Newton, RJ and McMahon, KD}, title = {TaxAss: Leveraging a Custom Freshwater Database Achieves Fine-Scale Taxonomic Resolution.}, journal = {mSphere}, volume = {3}, number = {5}, pages = {}, pmid = {30185512}, issn = {2379-5042}, mesh = {Algorithms ; Animals ; Bacteria/*classification ; DNA, Bacterial/genetics ; Databases as Topic ; *Databases, Genetic ; Ecosystem ; Fresh Water/*microbiology ; *Metagenomics ; Mice ; *Microbial Consortia ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Taxonomy assignment of freshwater microbial communities is limited by the minimally curated phylogenies used for large taxonomy databases. Here we introduce TaxAss, a taxonomy assignment workflow that classifies 16S rRNA gene amplicon data using two taxonomy reference databases: a large comprehensive database and a small ecosystem-specific database rigorously curated by scientists within a field. We applied TaxAss to five different freshwater data sets using the comprehensive SILVA database and the freshwater-specific FreshTrain database. TaxAss increased the percentage of the data set classified compared to using only SILVA, especially at fine-resolution family to species taxon levels, while across the freshwater test data sets classifications increased by as much as 11 to 40% of total reads. A similar increase in classifications was not observed in a control mouse gut data set, which was not expected to contain freshwater bacteria. TaxAss also maintained taxonomic richness compared to using only the FreshTrain across all taxon levels from phylum to species. Without TaxAss, most organisms not represented in the FreshTrain were unclassified, but at fine taxon levels, incorrect classifications became significant. We validated TaxAss using simulated amplicon data derived from full-length clone libraries and found that 96 to 99% of test sequences were correctly classified at fine resolution. TaxAss splits a data set's sequences into two groups based on their percent identity to reference sequences in the ecosystem-specific database. Sequences with high similarity to sequences in the ecosystem-specific database are classified using that database, and the others are classified using the comprehensive database. TaxAss is free and open source and is available at https://www.github.com/McMahonLab/TaxAssIMPORTANCE Microbial communities drive ecosystem processes, but microbial community composition analyses using 16S rRNA gene amplicon data sets are limited by the lack of fine-resolution taxonomy classifications. Coarse taxonomic groupings at the phylum, class, and order levels lump ecologically distinct organisms together. To avoid this, many researchers define operational taxonomic units (OTUs) based on clustered sequences, sequence variants, or unique sequences. These fine-resolution groupings are more ecologically relevant, but OTU definitions are data set dependent and cannot be compared between data sets. Microbial ecologists studying freshwater have curated a small, ecosystem-specific taxonomy database to provide consistent and up-to-date terminology. We created TaxAss, a workflow that leverages this database to assign taxonomy. We found that TaxAss improves fine-resolution taxonomic classifications (family, genus, and species). Fine taxonomic groupings are more ecologically relevant, so they provide an alternative to OTU-based analyses that is consistent and comparable between data sets.}, } @article {pmid30184106, year = {2018}, author = {Didelot, X and Croucher, NJ and Bentley, SD and Harris, SR and Wilson, DJ}, title = {Bayesian inference of ancestral dates on bacterial phylogenetic trees.}, journal = {Nucleic acids research}, volume = {46}, number = {22}, pages = {e134}, pmid = {30184106}, issn = {1362-4962}, support = {MR/N010760/1/MRC_/Medical Research Council/United Kingdom ; MR/R015600/1/MRC_/Medical Research Council/United Kingdom ; 101237/Z/13/Z/WT_/Wellcome Trust/United Kingdom ; MR/N010760/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {*Bayes Theorem ; Benchmarking ; Computer Simulation ; DNA, Bacterial/genetics ; Datasets as Topic ; *Evolution, Molecular ; *Genome, Bacterial ; Markov Chains ; *Models, Genetic ; Monte Carlo Method ; Mycobacterium leprae/genetics ; *Phylogeny ; Recombination, Genetic ; Shigella sonnei/genetics ; Software ; Streptococcus pneumoniae/genetics ; Time Factors ; }, abstract = {The sequencing and comparative analysis of a collection of bacterial genomes from a single species or lineage of interest can lead to key insights into its evolution, ecology or epidemiology. The tool of choice for such a study is often to build a phylogenetic tree, and more specifically when possible a dated phylogeny, in which the dates of all common ancestors are estimated. Here, we propose a new Bayesian methodology to construct dated phylogenies which is specifically designed for bacterial genomics. Unlike previous Bayesian methods aimed at building dated phylogenies, we consider that the phylogenetic relationships between the genomes have been previously evaluated using a standard phylogenetic method, which makes our methodology much faster and scalable. This two-step approach also allows us to directly exploit existing phylogenetic methods that detect bacterial recombination, and therefore to account for the effect of recombination in the construction of a dated phylogeny. We analysed many simulated datasets in order to benchmark the performance of our approach in a wide range of situations. Furthermore, we present applications to three different real datasets from recent bacterial genomic studies. Our methodology is implemented in a R package called BactDating which is freely available for download at https://github.com/xavierdidelot/BactDating.}, } @article {pmid30183869, year = {2018}, author = {Braz, RM and Barcellos, C}, title = {Analysis of the process of malaria transmission elimination with a spatial approach to incidence variation in the Brazilian Amazon, 2016.}, journal = {Epidemiologia e servicos de saude : revista do Sistema Unico de Saude do Brasil}, volume = {27}, number = {3}, pages = {e2017253}, doi = {10.5123/S1679-49742018000300010}, pmid = {30183869}, issn = {2237-9622}, mesh = {Brazil/epidemiology ; Cities ; *Epidemiological Monitoring ; Humans ; Incidence ; *Information Systems ; Malaria/*epidemiology/prevention & control/transmission ; Spatial Analysis ; }, abstract = {OBJECTIVE: to identify areas where malaria transmission has been eliminated and levels of malaria incidence variation in the Brazilian Amazon in 2016, and to present an indicator of priorities for control actions.

METHODS: an ecological study was conducted with data from the Malaria Epidemiological Surveillance Information System (Sivep-Malaria); municipalities were classified into three groups - elimination achieved, in the process of elimination and in search of reduction -; a composite indicator was created to stratify municipalities prioritized for control actions.

RESULTS: a total of 337 (41.7%) municipalities were found to have achieved elimination, 398 (49.3%) were in the process of elimination and 73 (9.0%) were in search of reduction; the priority indicator created identified 71 municipalities that accounted for 95% of cases.

CONCLUSION: the vast majority of municipalities have already achieved elimination of malaria transmission or are in the process of eliminating transmission; the priority indicator may contribute to targeting malaria control actions.}, } @article {pmid30181062, year = {2019}, author = {de Jonge, PA and Nobrega, FL and Brouns, SJJ and Dutilh, BE}, title = {Molecular and Evolutionary Determinants of Bacteriophage Host Range.}, journal = {Trends in microbiology}, volume = {27}, number = {1}, pages = {51-63}, doi = {10.1016/j.tim.2018.08.006}, pmid = {30181062}, issn = {1878-4380}, mesh = {Bacteria/genetics/*virology ; Bacteriophages/genetics/*growth & development ; *Host Specificity ; }, abstract = {The host range of a bacteriophage is the taxonomic diversity of hosts it can successfully infect. Host range, one of the central traits to understand in phages, is determined by a range of molecular interactions between phage and host throughout the infection cycle. While many well studied model phages seem to exhibit a narrow host range, recent ecological and metagenomics studies indicate that phages may have specificities that range from narrow to broad. There is a growing body of studies on the molecular mechanisms that enable phages to infect multiple hosts. These mechanisms, and their evolution, are of considerable importance to understanding phage ecology and the various clinical, industrial, and biotechnological applications of phage. Here we review knowledge of the molecular mechanisms that determine host range, provide a framework defining broad host range in an evolutionary context, and highlight areas for additional research.}, } @article {pmid30172483, year = {2019}, author = {Isigonis, P and Critto, A and Zabeo, A and Ciffroy, P}, title = {"AMORE" Decision Support System for probabilistic Ecological Risk Assessment - Part II: Effect assessment of the case study on cyanide.}, journal = {The Science of the total environment}, volume = {648}, number = {}, pages = {1665-1672}, doi = {10.1016/j.scitotenv.2018.08.227}, pmid = {30172483}, issn = {1879-1026}, abstract = {Ecotoxicological data are highly important for risk assessment processes and are used for deriving environmental quality criteria, which are enacted for assuring the good quality of waters, soils or sediments and achieving desirable environmental quality objectives. Therefore, it is of significant importance the evaluation of the reliability and relevance of available data for analysing their possible use in the aforementioned processes. In this context, a new methodology which has been developed based on Multi-Criteria Decision Analysis (MCDA) techniques, is being used, demonstrated and tested for analysing the reliability and relevance of ecotoxicological data of cyanide (which are produced through laboratory biotests for individual effects). The proposed methodology is also used for the production of Weighted by Data Quality Species Sensitivity Distributions (SSD-WDQ), as a component of the Ecological Risk Assessment of chemicals in aquatic systems. The SSD-WDQ production resulted in the estimation of environmental quality criteria (hazard concentration affecting 5% and 50% of the species). The proposed work is part of the development of the AMORE Decision Support System (DSS) for the application of probabilistic Ecological Risk Assessment (ERA), presented in the companion paper (Isigonis et al., 2019). The DSS has been tested through a case study on ERA of cyanide in the watershed of river Selune in France. The paper presents the 'Effect Assessment' of cyanide, based on the aforementioned methodologies. The main results presented in the paper are the probabilistic analysis of the estimated species sensitivity on cyanide (Effect Assessment) and the calculation of Hazardous Concentration (HCx) of the same contaminant in the Selune river area, based on the functionalities of the DSS. The results are described and discussed in detail, with the use of various graphs and indices. The indices are calculated for all the available ecotoxicological data, as well as for the data on trophic levels or taxonomic groups separately. An effect comparison is presented between the innovative methodologies included in the DSS and the currently existing methodologies.}, } @article {pmid30171327, year = {2018}, author = {Lovette, JP and Duncan, JM and Smart, LS and Fay, JP and Olander, LP and Urban, DL and Daly, N and Blackwell, J and Hoos, AB and García, AM and Band, LE}, title = {Leveraging Big Data Towards Functionally-Based, Catchment Scale Restoration Prioritization.}, journal = {Environmental management}, volume = {62}, number = {6}, pages = {1007-1024}, pmid = {30171327}, issn = {1432-1009}, mesh = {*Big Data ; *Conservation of Water Resources ; Ecosystem ; Environmental Monitoring ; Hydrology ; Nitrogen/analysis ; North Carolina ; Phosphorus/analysis ; Rivers/*chemistry ; Water Quality ; Wetlands ; }, abstract = {The persistence of freshwater degradation has necessitated the growth of an expansive stream and wetland restoration industry, yet restoration prioritization at broad spatial extents is still limited and ad-hoc restoration prevails. The River Basin Restoration Prioritization tool has been developed to incorporate vetted, distributed data models into a catchment scale restoration prioritization framework. Catchment baseline condition and potential improvement with restoration activity is calculated for all National Hydrography Dataset stream reaches and catchments in North Carolina and compared to other catchments within the river subbasin to assess where restoration efforts may best be focused. Hydrologic, water quality, and aquatic habitat quality conditions are assessed with peak flood flow, nitrogen and phosphorus loading, and aquatic species distribution models. The modular nature of the tool leaves ample opportunity for future incorporation of novel and improved datasets to better represent the holistic health of a watershed, and the nature of the datasets used herein allow this framework to be applied at much broader scales than North Carolina.}, } @article {pmid30171211, year = {2020}, author = {Nunes, A and Schnack, HG and Ching, CRK and Agartz, I and Akudjedu, TN and Alda, M and Alnæs, D and Alonso-Lana, S and Bauer, J and Baune, BT and Bøen, E and Bonnin, CDM and Busatto, GF and Canales-Rodríguez, EJ and Cannon, DM and Caseras, X and Chaim-Avancini, TM and Dannlowski, U and Díaz-Zuluaga, AM and Dietsche, B and Doan, NT and Duchesnay, E and Elvsåshagen, T and Emden, D and Eyler, LT and Fatjó-Vilas, M and Favre, P and Foley, SF and Fullerton, JM and Glahn, DC and Goikolea, JM and Grotegerd, D and Hahn, T and Henry, C and Hibar, DP and Houenou, J and Howells, FM and Jahanshad, N and Kaufmann, T and Kenney, J and Kircher, TTJ and Krug, A and Lagerberg, TV and Lenroot, RK and López-Jaramillo, C and Machado-Vieira, R and Malt, UF and McDonald, C and Mitchell, PB and Mwangi, B and Nabulsi, L and Opel, N and Overs, BJ and Pineda-Zapata, JA and Pomarol-Clotet, E and Redlich, R and Roberts, G and Rosa, PG and Salvador, R and Satterthwaite, TD and Soares, JC and Stein, DJ and Temmingh, HS and Trappenberg, T and Uhlmann, A and van Haren, NEM and Vieta, E and Westlye, LT and Wolf, DH and Yüksel, D and Zanetti, MV and Andreassen, OA and Thompson, PM and Hajek, T and , }, title = {Using structural MRI to identify bipolar disorders - 13 site machine learning study in 3020 individuals from the ENIGMA Bipolar Disorders Working Group.}, journal = {Molecular psychiatry}, volume = {25}, number = {9}, pages = {2130-2143}, pmid = {30171211}, issn = {1476-5578}, support = {R56 MH097940/MH/NIMH NIH HHS/United States ; R01 MH083968/MH/NIMH NIH HHS/United States ; R01 MH101111/MH/NIMH NIH HHS/United States ; U54 EB020403/EB/NIBIB NIH HHS/United States ; R01 MH107248/MH/NIMH NIH HHS/United States ; K23 MH085096/MH/NIMH NIH HHS/United States ; R01 MH078143/MH/NIMH NIH HHS/United States ; U01 MH105630/MH/NIMH NIH HHS/United States ; MR/L010305/1/MRC_/Medical Research Council/United Kingdom ; R01 MH107703/MH/NIMH NIH HHS/United States ; R01 MH080912/MH/NIMH NIH HHS/United States ; R01 AG058464/AG/NIA NIH HHS/United States ; R01 MH083824/MH/NIMH NIH HHS/United States ; }, mesh = {*Bipolar Disorder/diagnostic imaging ; Brain/diagnostic imaging ; Humans ; Machine Learning ; Magnetic Resonance Imaging ; Neuroimaging ; }, abstract = {Bipolar disorders (BDs) are among the leading causes of morbidity and disability. Objective biological markers, such as those based on brain imaging, could aid in clinical management of BD. Machine learning (ML) brings neuroimaging analyses to individual subject level and may potentially allow for their diagnostic use. However, fair and optimal application of ML requires large, multi-site datasets. We applied ML (support vector machines) to MRI data (regional cortical thickness, surface area, subcortical volumes) from 853 BD and 2167 control participants from 13 cohorts in the ENIGMA consortium. We attempted to differentiate BD from control participants, investigated different data handling strategies and studied the neuroimaging/clinical features most important for classification. Individual site accuracies ranged from 45.23% to 81.07%. Aggregate subject-level analyses yielded the highest accuracy (65.23%, 95% CI = 63.47-67.00, ROC-AUC = 71.49%, 95% CI = 69.39-73.59), followed by leave-one-site-out cross-validation (accuracy = 58.67%, 95% CI = 56.70-60.63). Meta-analysis of individual site accuracies did not provide above chance results. There was substantial agreement between the regions that contributed to identification of BD participants in the best performing site and in the aggregate dataset (Cohen's Kappa = 0.83, 95% CI = 0.829-0.831). Treatment with anticonvulsants and age were associated with greater odds of correct classification. Although short of the 80% clinically relevant accuracy threshold, the results are promising and provide a fair and realistic estimate of classification performance, which can be achieved in a large, ecologically valid, multi-site sample of BD participants based on regional neurostructural measures. Furthermore, the significant classification in different samples was based on plausible and similar neuroanatomical features. Future multi-site studies should move towards sharing of raw/voxelwise neuroimaging data.}, } @article {pmid30166779, year = {2018}, author = {Babaie, J and Barati, M and Azizi, M and Ephtekhari, A and Sadat, SJ}, title = {A systematic evidence review of the effect of climate change on malaria in Iran.}, journal = {Journal of parasitic diseases : official organ of the Indian Society for Parasitology}, volume = {42}, number = {3}, pages = {331-340}, pmid = {30166779}, issn = {0971-7196}, abstract = {Climate is an effective factor in the ecological structure which plays an important role in control and outbreak of the diseases caused by biological factors like malaria. With regard to the occurring climatic change, this study aimed to review the effects of climate change on malaria in Iran. In this systematic review, Cochrane, PubMed and ScienceDirect (as international databases), SID and Magiran as Persian databases were investigated through MESH keywords including climate change, global warming, malaria, Anopheles, and Iran. The related articles were screened and finally their results were extracted using data extraction sheets. Totally 41 papers were resulted through databases searching process. Finally 14 papers which met inclusion criteria were included in data extraction stage. The findings indicated that Anopheles mosquitoes are present at least in 115 places in Iran; they are compatible with climatic zones of Iran. Malaria and it's vectors are affected by climate change. Temperature, precipitation, relative humidity, wind intensity and direction are the most important climatic factors affecting the growth and proliferation of Anopheles, Plasmodium and the prevalence of malaria. The transmission of malaria in Iran is associated with the climatic factors of temperature, rainfall, and humidity. Therefore, with regard to the occurring climatic change, the incidence of the disease may also change which needs to be taken into consideration while planning of malaria control.}, } @article {pmid30166629, year = {2018}, author = {de Barros Damgaard, P and Marchi, N and Rasmussen, S and Peyrot, M and Renaud, G and Korneliussen, T and Moreno-Mayar, JV and Pedersen, MW and Goldberg, A and Usmanova, E and Baimukhanov, N and Loman, V and Hedeager, L and Pedersen, AG and Nielsen, K and Afanasiev, G and Akmatov, K and Aldashev, A and Alpaslan, A and Baimbetov, G and Bazaliiskii, VI and Beisenov, A and Boldbaatar, B and Boldgiv, B and Dorzhu, C and Ellingvag, S and Erdenebaatar, D and Dajani, R and Dmitriev, E and Evdokimov, V and Frei, KM and Gromov, A and Goryachev, A and Hakonarson, H and Hegay, T and Khachatryan, Z and Khaskhanov, R and Kitov, E and Kolbina, A and Kubatbek, T and Kukushkin, A and Kukushkin, I and Lau, N and Margaryan, A and Merkyte, I and Mertz, IV and Mertz, VK and Mijiddorj, E and Moiyesev, V and Mukhtarova, G and Nurmukhanbetov, B and Orozbekova, Z and Panyushkina, I and Pieta, K and Smrčka, V and Shevnina, I and Logvin, A and Sjogren, KG and Štolcova, T and Taravella, AM and Tashbaeva, K and Tkachev, A and Tulegenov, T and Voyakin, D and Yepiskoposyan, L and Undrakhbold, S and Varfolomeev, V and Weber, A and Wilson Sayres, MA and Kradin, N and Allentoft, ME and Orlando, L and Nielsen, R and Sikora, M and Heyer, E and Kristiansen, K and Willerslev, E}, title = {Author Correction: 137 ancient human genomes from across the Eurasian steppes.}, journal = {Nature}, volume = {563}, number = {7729}, pages = {E16}, doi = {10.1038/s41586-018-0488-1}, pmid = {30166629}, issn = {1476-4687}, abstract = {with In this Article, Angela M. Taravella and Melissa A. Wilson Sayres have been added to the author list (associated with: School of Life Sciences, Center for Evolution and Medicine, The Biodesign Institute, Arizona State University, Tempe, AZ, USA). The author list and Author Information section have been corrected online.}, } @article {pmid30166491, year = {2018}, author = {Nolan, C and Overpeck, JT and Allen, JRM and Anderson, PM and Betancourt, JL and Binney, HA and Brewer, S and Bush, MB and Chase, BM and Cheddadi, R and Djamali, M and Dodson, J and Edwards, ME and Gosling, WD and Haberle, S and Hotchkiss, SC and Huntley, B and Ivory, SJ and Kershaw, AP and Kim, SH and Latorre, C and Leydet, M and Lézine, AM and Liu, KB and Liu, Y and Lozhkin, AV and McGlone, MS and Marchant, RA and Momohara, A and Moreno, PI and Müller, S and Otto-Bliesner, BL and Shen, C and Stevenson, J and Takahara, H and Tarasov, PE and Tipton, J and Vincens, A and Weng, C and Xu, Q and Zheng, Z and Jackson, ST}, title = {Past and future global transformation of terrestrial ecosystems under climate change.}, journal = {Science (New York, N.Y.)}, volume = {361}, number = {6405}, pages = {920-923}, doi = {10.1126/science.aan5360}, pmid = {30166491}, issn = {1095-9203}, mesh = {*Biodiversity ; *Climate Change ; }, abstract = {Impacts of global climate change on terrestrial ecosystems are imperfectly constrained by ecosystem models and direct observations. Pervasive ecosystem transformations occurred in response to warming and associated climatic changes during the last glacial-to-interglacial transition, which was comparable in magnitude to warming projected for the next century under high-emission scenarios. We reviewed 594 published paleoecological records to examine compositional and structural changes in terrestrial vegetation since the last glacial period and to project the magnitudes of ecosystem transformations under alternative future emission scenarios. Our results indicate that terrestrial ecosystems are highly sensitive to temperature change and suggest that, without major reductions in greenhouse gas emissions to the atmosphere, terrestrial ecosystems worldwide are at risk of major transformation, with accompanying disruption of ecosystem services and impacts on biodiversity.}, } @article {pmid30166151, year = {2018}, author = {Mataragas, M and Alessandria, V and Ferrocino, I and Rantsiou, K and Cocolin, L}, title = {A bioinformatics pipeline integrating predictive metagenomics profiling for the analysis of 16S rDNA/rRNA sequencing data originated from foods.}, journal = {Food microbiology}, volume = {76}, number = {}, pages = {279-286}, doi = {10.1016/j.fm.2018.05.009}, pmid = {30166151}, issn = {1095-9998}, mesh = {Algorithms ; Cheese/microbiology ; *Computational Biology ; DNA, Ribosomal ; Food Microbiology/methods ; High-Throughput Nucleotide Sequencing ; Metabolic Networks and Pathways ; Metagenomics/*methods ; Microbial Consortia/*genetics ; RNA, Ribosomal, 16S/*genetics ; *Sequence Analysis, DNA ; Software ; }, abstract = {The recent advances in molecular biology, such as the advent of next-generation sequencing (NGS) platforms, have paved the way to new exciting tools which rapidly transform food microbiology. Nowadays, NGS methods such as 16S rDNA/rRNA metagenomics or amplicon sequencing are used for the taxonomic profiling of the food microbial communities. Although 16S rDNA/rRNA NGS-based microbial data are not suited for the investigation of the functional potential of the identified operational taxonomic units as compared to shotgun metagenomics, advances in the bioinformatics discipline allow now the performance of such studies. In this paper, a bioinformatics workflow is described integrating predictive metagenomics profiling with specific application to food microbiology data. Bioinformatics tools pertinent to each sub-module of the pipeline are suggested as well. The published 16S rDNA/rRNA amplicon data originated from an Italian Grana-type cheese, using an NGS platform, was employed to demonstrate the predictive metagenomics profiling approach. The pipeline identified the microbial community and the changes that occurred in the microbial profile during manufacture of the food product studied (taxonomic profiling). The workflow also indicated significant changes in the functional profiling of the community. The tool may help to investigate the functional potential, alterations, and interactions of a microbial community. The proposed workflow may also find an application in the investigation of the ecology of foodborne pathogens encountered in various food products.}, } @article {pmid30165481, year = {2019}, author = {Tu, Q and Lin, L and Cheng, L and Deng, Y and He, Z}, title = {NCycDB: a curated integrative database for fast and accurate metagenomic profiling of nitrogen cycling genes.}, journal = {Bioinformatics (Oxford, England)}, volume = {35}, number = {6}, pages = {1040-1048}, doi = {10.1093/bioinformatics/bty741}, pmid = {30165481}, issn = {1367-4811}, mesh = {Databases, Factual ; Ecosystem ; *Metagenome ; *Metagenomics ; Nitrogen ; }, abstract = {MOTIVATION: The nitrogen (N) cycle is a collection of important biogeochemical pathways in the Earth ecosystem and has gained extensive foci in ecology and environmental studies. Currently, shotgun metagenome sequencing has been widely applied to explore gene families responsible for N cycle processes. However, there are problems in applying publically available orthology databases to profile N cycle gene families in shotgun metagenomes, such as inefficient database searching, unspecific orthology groups and low coverage of N cycle genes and/or gene (sub)families.

RESULTS: To solve these issues, this study built a manually curated integrative database (NCycDB) for fast and accurate profiling of N cycle gene (sub)families from shotgun metagenome sequencing data. NCycDB contains a total of 68 gene (sub)families and covers eight N cycle processes with 84 759 and 219 146 representative sequences at 95 and 100% identity cutoffs, respectively. We also identified 1958 homologous orthology groups and included corresponding sequences in the database to avoid false positive assignments due to 'small database' issues. We applied NCycDB to characterize N cycle gene (sub)families in 52 shotgun metagenomes from the Global Ocean Sampling expedition. Further analysis showed that the structure and composition of N cycle gene families were most strongly correlated with latitude and temperature. NCycDB is expected to facilitate N cycle studies via shotgun metagenome sequencing approaches in various environments. The framework developed in this study can be served as a good reference to build similar knowledge-based functional gene databases in various processes and pathways.

NCycDB database files are available at https://github.com/qichao1984/NCyc.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, } @article {pmid30159889, year = {2019}, author = {Boulabeiz, M and Klebingat, S and Agaguenia, S}, title = {A GIS-Based GOD Model and Hazard Index Analysis: The Quaternary Coastal Collo Aquifer (NE-Algeria).}, journal = {Ground water}, volume = {57}, number = {1}, pages = {166-176}, doi = {10.1111/gwat.12824}, pmid = {30159889}, issn = {1745-6584}, mesh = {Algeria ; Environmental Monitoring ; Geographic Information Systems ; *Groundwater ; *Water Pollutants, Chemical ; Water Pollution ; }, abstract = {The quaternary coastal Collo aquifer in northeast Algeria (NE Algeria) marks an important local water resource supporting domestic, industrial and agricultural activities. The aquifer shows signs of contamination due to the existence of various pollution sources, especially nitrogen compounds. Focusing the local identification of key vulnerable zones and related main hazard types for wise future water management, the present study highlights results from a coupled analysis of the well-established Geographical Information System (GIS)-based GOD (groundwater occurrence, overall aquifer class, depth to groundwater) hazard index analysis and the COST Action 620 plan. Most prevalent hazard types in the study area were identified as the urban/residential areas without public sewage systems, landfill and agricultural/pasturing areas. Regarding the vulnerability analysis particularly the northern aquifer region is endangered, dominated by high (22.4%) and moderate (27.4%) vulnerability classes. Central, western and southern aquifer regions are characterized by low (23.3%) and very low (26.9%) vulnerability classes. Overall, these GOD-derived results are in good agreement with earlier results obtained by the more complex DRASTIC approach. Final risk assessment and validation related to 2014/2015 nitrate sampling campaigns indicate that "high risk" and "very high risk" classes only apply to a small part of the study area in the northern sector (8%), whereas the main part (>60%) broadly affecting the central, western and southern sector only bears a low to very low risk of water pollution. Apart from a future-oriented groundwater abstraction strategy it is recommended to update the evaluation regularly to effectively consider dynamic changes of local anthropogenic activities and hazards.}, } @article {pmid30157296, year = {2018}, author = {Benedetti-Cecchi, L and Bulleri, F and Dal Bello, M and Maggi, E and Ravaglioli, C and Rindi, L}, title = {Hybrid datasets: integrating observations with experiments in the era of macroecology and big data.}, journal = {Ecology}, volume = {99}, number = {12}, pages = {2654-2666}, doi = {10.1002/ecy.2504}, pmid = {30157296}, issn = {0012-9658}, support = {PRA_2017_19//Università di Pisa/International ; RBFR12RXWL//Italian Ministry for Education, University and Research through project HI-BEF/International ; }, mesh = {*Big Data ; Ecology ; *Ecosystem ; Research ; }, abstract = {Understanding how increasing human domination of the biosphere affects life on earth is a critical research challenge. This task is facilitated by the increasing availability of open-source data repositories, which allow ecologists to address scientific questions at unprecedented spatial and temporal scales. Large datasets are mostly observational, so they may have limited ability to uncover causal relations among variables. Experiments are better suited at attributing causation, but they are often limited in scope. We propose hybrid datasets, resulting from the integration of observational with experimental data, as an approach to leverage the scope and ability to attribute causality in ecological studies. We show how the analysis of hybrid datasets with emerging techniques in time series analysis (Convergent Cross-mapping) and macroecology (Joint Species Distribution Models) can generate novel insights into causal effects of abiotic and biotic processes that would be difficult to achieve otherwise. We illustrate these principles with two case studies in marine ecosystems and discuss the potential to generalize across environments, species and ecological processes. If used wisely, the analysis of hybrid datasets may become the standard approach for research goals that seek causal explanations for large-scale ecological phenomena.}, } @article {pmid30156039, year = {2018}, author = {An, S and Zhu, X and Shen, M and Wang, Y and Cao, R and Chen, X and Yang, W and Chen, J and Tang, Y}, title = {Mismatch in elevational shifts between satellite observed vegetation greenness and temperature isolines during 2000-2016 on the Tibetan Plateau.}, journal = {Global change biology}, volume = {24}, number = {11}, pages = {5411-5425}, doi = {10.1111/gcb.14432}, pmid = {30156039}, issn = {1365-2486}, mesh = {Acclimatization ; Carbon Sequestration ; *Climate Change ; *Ecosystem ; Environmental Monitoring/methods ; Seasons ; Spacecraft ; *Temperature ; Tibet ; Water ; }, abstract = {Climate warming on the Tibetan Plateau tends to induce an uphill shift of temperature isolines. Observations and process-based models have both shown that climate warming has resulted in an increase in vegetation greenness on the Tibetan Plateau in recent decades. However, it is unclear whether the uphill shift of temperature isolines has caused greenness isolines to shift upward and whether the two shifts match each other. Our analysis of satellite observed vegetation greenness during the growing season (May-Sep) and gridded climate data for 2000-2016 documented a substantial mismatch between the elevational shifts of greenness and temperature isolines. This mismatch is probably associated with a lagging response of greenness to temperature change and with the elevational gradient of greenness. The lagging response of greenness may be associated with water limitation, resources availability, and acclimation. This lag may weaken carbon sequestration by Tibetan ecosystems, given that greenness is closely related to primary carbon uptake and ecosystem respiration increases exponentially with temperature. We also found that differences in terrain slope angle accounted for large spatial variations in the elevational gradient of greenness and thus the velocity of elevational shifts of greenness isolines and the sensitivity of elevational shifts of greenness isolines to temperature, highlighting the role of terrain effects on the elevational shifts of greenness isolines. The mismatches and the terrain effect found in this study suggest that there is potentially large micro-topographical difference in response and acclimation/adaptation of greenness to temperature changes in plants. More widespread in situ measurements and fine-resolution remote sensing observations and fine-gridded climate data are required to attribute the mismatch to specific environmental drivers and ecological processes such as vertical changes in community structure, plant physiology, and distribution of species.}, } @article {pmid30155713, year = {2018}, author = {Li, R and Jiang, GF and Dong, SY}, title = {A head transcriptome provides insights into odorant binding proteins of the bamboo grasshopper.}, journal = {Genes & genomics}, volume = {40}, number = {9}, pages = {991-1000}, pmid = {30155713}, issn = {2092-9293}, support = {30970339 and 31572246//National Natural Sciences Foundation of China/International ; }, mesh = {Amino Acid Sequence ; Animals ; Bambusa/*parasitology ; Databases, Genetic ; Gene Expression Profiling ; Gene Ontology ; Grasshoppers/*genetics/*metabolism ; Head ; High-Throughput Nucleotide Sequencing ; Insect Proteins/chemistry/*genetics/*metabolism ; Microsatellite Repeats ; Phylogeny ; Protein Binding ; Receptors, Odorant/chemistry/*genetics/*metabolism ; Sequence Homology, Amino Acid ; *Transcriptome ; }, abstract = {The bamboo grasshopper Ceracris kiangsu is a famous bamboo pest in China. The identification of genes involved in olfactory behavior of C. kiangsu is necessary for better understanding the molecular basis and expression profiles of behavior ecology. However, necessary genomic and transcriptomic data are lacking in the species, limiting control efficiency. The primary objective of this study was to find and describe odorant binding proteins in the head of the bamboo grasshopper. We performed the paired-end sequencing on an Illumina Hiseq2000 following the vendor's recommended protocol. Functional annotation was performed by comparison with public databases. OBP genes were first identified using BLASTN and BLASTX results from our C. kiangsu datebase, which was established from the date of transcriptome sequencing. The gene-specific primers were used to conduct RT-PCR to detect the tissue distribution of OBPs using a SYBR Premix ExTaq kit following the manufacturer's instructions with a real-time thermal cycler. We obtained more than 133 million clean reads derived from the C. Kiangsu heads using the next-generation sequencing, which were assembled into 260,822 unique sequences (average 814 bp). We have detected eight putative odorant binding protein genes (OBPs) of C. kiangsu for the first time, and analyzed the expression profiles of the OBPs in different tissues (head, antenna, mouthpart, body and leg). Our results reveal that the eight OBPs display a clear divergence, strongly indicating that they possessed diverse functions, and thus provides comprehensive sequence analysis for elucidating the molecular basis of OBPs in C. kiangsu. In addition, we find that the relative expression levels of OBP1, OBP2 and OBP8 are significantly higher in the antennae as compared to the other OBP genes, suggesting that these three OBP genes play crucial roles in the locust's odorant discrimination. In general, this is the first study to characterize the complete head transcriptome of C. kiangsu using high-throughput sequencing. The study opens a window for functional characterization of the OBPs of C. kiangsu, with potential for new or refined applications of semiochemicals for control of this notorious pest.}, } @article {pmid30148503, year = {2018}, author = {Parks, DH and Chuvochina, M and Waite, DW and Rinke, C and Skarshewski, A and Chaumeil, PA and Hugenholtz, P}, title = {A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life.}, journal = {Nature biotechnology}, volume = {36}, number = {10}, pages = {996-1004}, pmid = {30148503}, issn = {1546-1696}, mesh = {Bacteria/*classification/*genetics ; Databases, Genetic ; *Genome, Bacterial ; Genomics ; *Phylogeny ; Software ; }, abstract = {Taxonomy is an organizing principle of biology and is ideally based on evolutionary relationships among organisms. Development of a robust bacterial taxonomy has been hindered by an inability to obtain most bacteria in pure culture and, to a lesser extent, by the historical use of phenotypes to guide classification. Culture-independent sequencing technologies have matured sufficiently that a comprehensive genome-based taxonomy is now possible. We used a concatenated protein phylogeny as the basis for a bacterial taxonomy that conservatively removes polyphyletic groups and normalizes taxonomic ranks on the basis of relative evolutionary divergence. Under this approach, 58% of the 94,759 genomes comprising the Genome Taxonomy Database had changes to their existing taxonomy. This result includes the description of 99 phyla, including six major monophyletic units from the subdivision of the Proteobacteria, and amalgamation of the Candidate Phyla Radiation into a single phylum. Our taxonomy should enable improved classification of uncultured bacteria and provide a sound basis for ecological and evolutionary studies.}, } @article {pmid30147447, year = {2018}, author = {Dornelas, M and Antão, LH and Moyes, F and Bates, AE and Magurran, AE and Adam, D and Akhmetzhanova, AA and Appeltans, W and Arcos, JM and Arnold, H and Ayyappan, N and Badihi, G and Baird, AH and Barbosa, M and Barreto, TE and Bässler, C and Bellgrove, A and Belmaker, J and Benedetti-Cecchi, L and Bett, BJ and Bjorkman, AD and Błażewicz, M and Blowes, SA and Bloch, CP and Bonebrake, TC and Boyd, S and Bradford, M and Brooks, AJ and Brown, JH and Bruelheide, H and Budy, P and Carvalho, F and Castañeda-Moya, E and Chen, CA and Chamblee, JF and Chase, TJ and Siegwart Collier, L and Collinge, SK and Condit, R and Cooper, EJ and Cornelissen, JHC and Cotano, U and Kyle Crow, S and Damasceno, G and Davies, CH and Davis, RA and Day, FP and Degraer, S and Doherty, TS and Dunn, TE and Durigan, G and Duffy, JE and Edelist, D and Edgar, GJ and Elahi, R and Elmendorf, SC and Enemar, A and Ernest, SKM and Escribano, R and Estiarte, M and Evans, BS and Fan, TY and Turini Farah, F and Loureiro Fernandes, L and Farneda, FZ and Fidelis, A and Fitt, R and Fosaa, AM and Daher Correa Franco, GA and Frank, GE and Fraser, WR and García, H and Cazzolla Gatti, R and Givan, O and Gorgone-Barbosa, E and Gould, WA and Gries, C and Grossman, GD and Gutierréz, JR and Hale, S and Harmon, ME and Harte, J and Haskins, G and Henshaw, DL and Hermanutz, L and Hidalgo, P and Higuchi, P and Hoey, A and Van Hoey, G and Hofgaard, A and Holeck, K and Hollister, RD and Holmes, R and Hoogenboom, M and Hsieh, CH and Hubbell, SP and Huettmann, F and Huffard, CL and Hurlbert, AH and Macedo Ivanauskas, N and Janík, D and Jandt, U and Jażdżewska, A and Johannessen, T and Johnstone, J and Jones, J and Jones, FAM and Kang, J and Kartawijaya, T and Keeley, EC and Kelt, DA and Kinnear, R and Klanderud, K and Knutsen, H and Koenig, CC and Kortz, AR and Král, K and Kuhnz, LA and Kuo, CY and Kushner, DJ and Laguionie-Marchais, C and Lancaster, LT and Min Lee, C and Lefcheck, JS and Lévesque, E and Lightfoot, D and Lloret, F and Lloyd, JD and López-Baucells, A and Louzao, M and Madin, JS and Magnússon, B and Malamud, S and Matthews, I and McFarland, KP and McGill, B and McKnight, D and McLarney, WO and Meador, J and Meserve, PL and Metcalfe, DJ and Meyer, CFJ and Michelsen, A and Milchakova, N and Moens, T and Moland, E and Moore, J and Mathias Moreira, C and Müller, J and Murphy, G and Myers-Smith, IH and Myster, RW and Naumov, A and Neat, F and Nelson, JA and Paul Nelson, M and Newton, SF and Norden, N and Oliver, JC and Olsen, EM and Onipchenko, VG and Pabis, K and Pabst, RJ and Paquette, A and Pardede, S and Paterson, DM and Pélissier, R and Peñuelas, J and Pérez-Matus, A and Pizarro, O and Pomati, F and Post, E and Prins, HHT and Priscu, JC and Provoost, P and Prudic, KL and Pulliainen, E and Ramesh, BR and Mendivil Ramos, O and Rassweiler, A and Rebelo, JE and Reed, DC and Reich, PB and Remillard, SM and Richardson, AJ and Richardson, JP and van Rijn, I and Rocha, R and Rivera-Monroy, VH and Rixen, C and Robinson, KP and Ribeiro Rodrigues, R and de Cerqueira Rossa-Feres, D and Rudstam, L and Ruhl, H and Ruz, CS and Sampaio, EM and Rybicki, N and Rypel, A and Sal, S and Salgado, B and Santos, FAM and Savassi-Coutinho, AP and Scanga, S and Schmidt, J and Schooley, R and Setiawan, F and Shao, KT and Shaver, GR and Sherman, S and Sherry, TW and Siciński, J and Sievers, C and da Silva, AC and Rodrigues da Silva, F and Silveira, FL and Slingsby, J and Smart, T and Snell, SJ and Soudzilovskaia, NA and Souza, GBG and Maluf Souza, F and Castro Souza, V and Stallings, CD and Stanforth, R and Stanley, EH and Mauro Sterza, J and Stevens, M and Stuart-Smith, R and Rondon Suarez, Y and Supp, S and Yoshio Tamashiro, J and Tarigan, S and Thiede, GP and Thorn, S and Tolvanen, A and Teresa Zugliani Toniato, M and Totland, Ø and Twilley, RR and Vaitkus, G and Valdivia, N and Vallejo, MI and Valone, TJ and Van Colen, C and Vanaverbeke, J and Venturoli, F and Verheye, HM and Vianna, M and Vieira, RP and Vrška, T and Quang Vu, C and Van Vu, L and Waide, RB and Waldock, C and Watts, D and Webb, S and Wesołowski, T and White, EP and Widdicombe, CE and Wilgers, D and Williams, R and Williams, SB and Williamson, M and Willig, MR and Willis, TJ and Wipf, S and Woods, KD and Woehler, EJ and Zawada, K and Zettler, ML and Hickler, T}, title = {BioTIME: A database of biodiversity time series for the Anthropocene.}, journal = {Global ecology and biogeography : a journal of macroecology}, volume = {27}, number = {7}, pages = {760-786}, pmid = {30147447}, issn = {1466-822X}, support = {/WT_/Wellcome Trust/United Kingdom ; 250189/ERC_/European Research Council/International ; }, abstract = {MOTIVATION: The BioTIME database contains raw data on species identities and abundances in ecological assemblages through time. These data enable users to calculate temporal trends in biodiversity within and amongst assemblages using a broad range of metrics. BioTIME is being developed as a community-led open-source database of biodiversity time series. Our goal is to accelerate and facilitate quantitative analysis of temporal patterns of biodiversity in the Anthropocene.

The database contains 8,777,413 species abundance records, from assemblages consistently sampled for a minimum of 2 years, which need not necessarily be consecutive. In addition, the database contains metadata relating to sampling methodology and contextual information about each record.

SPATIAL LOCATION AND GRAIN: BioTIME is a global database of 547,161 unique sampling locations spanning the marine, freshwater and terrestrial realms. Grain size varies across datasets from 0.0000000158 km[2] (158 cm[2]) to 100 km[2] (1,000,000,000,000 cm[2]).

TIME PERIOD AND GRAIN: BioTIME records span from 1874 to 2016. The minimal temporal grain across all datasets in BioTIME is a year.

BioTIME includes data from 44,440 species across the plant and animal kingdoms, ranging from plants, plankton and terrestrial invertebrates to small and large vertebrates.

SOFTWARE FORMAT: .csv and .SQL.}, } @article {pmid30146795, year = {2018}, author = {Montagna, M and Berruti, A and Bianciotto, V and Cremonesi, P and Giannico, R and Gusmeroli, F and Lumini, E and Pierce, S and Pizzi, F and Turri, F and Gandini, G}, title = {Differential biodiversity responses between kingdoms (plants, fungi, bacteria and metazoa) along an Alpine succession gradient.}, journal = {Molecular ecology}, volume = {27}, number = {18}, pages = {3671-3685}, doi = {10.1111/mec.14817}, pmid = {30146795}, issn = {1365-294X}, mesh = {Bacteria/*classification ; *Biodiversity ; Computational Biology ; *Ecosystem ; Fungi/*classification ; Italy ; Plants/*classification ; Rhizosphere ; Soil Microbiology ; }, abstract = {Biological diversities of multiple kingdoms potentially respond in similar ways to environmental changes. However, studies either compare details of microbial diversity across general vegetation or land use classes or relate details of plant community diversity with the extent of microbially governed soil processes, via physiological profiling. Here, we test the hypothesis of shared responses of plant and rhizosphere bacterial, fungal and metazoan biodiversities (especially across-habitat β-diversity patterns) along a disturbance gradient encompassing grazed to abandoned Alpine pasture, on acid soil in the European Central Alps. Rhizosphere biological diversity was inferred from eDNA fractions specific to bacteria, fungi and metazoans from contrasting plant habitats indicative of different disturbance levels. We found that soil β-diversity patterns were weakly correlated with plant diversity measures and similarly ordinated along an evident edaphic (pH, C:N, assimilable P) and disturbance gradient but, contrary to our hypothesis, did not demonstrate the same diversity patterns. While plant communities were well separated along the disturbance gradient, correlating with fungal diversity, the majority of bacterial taxa were shared between disturbance levels (75% of bacteria were ubiquitous, cf. 29% plant species). Metazoa exhibited an intermediate response, with communities at the lowest levels of disturbance partially overlapping. Thus, plant and soil biological diversities were only loosely dependent and did not exhibit strictly linked environmental responses. This probably reflects the different spatial scales of organisms (and their habitats) and capacity to invest resources in persistent multicellular tissues, suggesting that vegetation responses to environmental change are unreliable indicators of below-ground biodiversity responses.}, } @article {pmid30145758, year = {2018}, author = {Pastuszak, M and Kowalkowski, T and Kopiński, J and Doroszewski, A and Jurga, B and Buszewski, B}, title = {Long-term changes in nitrogen and phosphorus emission into the Vistula and Oder catchments (Poland)-modeling (MONERIS) studies.}, journal = {Environmental science and pollution research international}, volume = {25}, number = {29}, pages = {29734-29751}, pmid = {30145758}, issn = {1614-7499}, mesh = {Agriculture ; Environmental Monitoring/*methods ; Geographic Information Systems ; Groundwater/chemistry ; *Models, Theoretical ; Nitrogen/*analysis ; Phosphorus/*analysis ; Poland ; Rivers/*chemistry ; Wastewater/chemistry ; Water Pollutants, Chemical/*analysis ; Water Purification/methods ; }, abstract = {Modeling (MONERIS) studies allowed calculation of nitrogen (N) and phosphorus (P) emission into the Vistula and Oder basins (Poland), and facilitated estimation of N and P retention in these catchments in 1995-2015. In the discussion of results, data of other authors were used in order to get an insight into N (1880-2015) and P emission (1955-2015) into the Oder basin. Population growth and agricultural intensification were responsible for respective 5.3-fold and 3.5-fold increase in N and P emission into the Oder basin, with the maximum (135,000 tons N year[-1]; 14,000 tons P year[-1]) observed at the turn of the 1980s/1990s. Pro-ecological activities during the economic transition period (since 1989) covered various sectors of the economy including agriculture, environmental protection related to, e.g., construction of a large number of waste water treatment plants (WWTPs). Consequently, in 1985-2015, the emission into the Oder basin decreased from the abovementioned maxima to 94,000 tons N year[-1] and to 5000 tons P year[-1], whereas in 1995-2015, the emission into the Vistula basin decreased from 170,000 to 140,000 tons N year[-1] and from 14,200 to 10,600 tons P year[-1]. In 1995-2015, groundwater, tile drainage, and WWTPs played a key role in N emission, while erosion, overland flow, WWTPs, and urban areas played a predominant role in P emission. The relative shares of nutrient emission pathways in overall N and P emission were considerably changing over time. Extreme weather conditions have a great impact on increased (floods) or decreased (droughts) nutrient emission; particularly, N emission is susceptible to variable weather conditions. In total, approximately 91,000 tons of N and 7600 tons of P were retained annually in the river basins.}, } @article {pmid30145518, year = {2018}, author = {D'Alessandro, M and Esposito, V and Porporato, EMD and Berto, D and Renzi, M and Giacobbe, S and Scotti, G and Consoli, P and Valastro, G and Andaloro, F and Romeo, T}, title = {Relationships between plastic litter and chemical pollutants on benthic biodiversity.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {242}, number = {Pt B}, pages = {1546-1556}, doi = {10.1016/j.envpol.2018.08.002}, pmid = {30145518}, issn = {1873-6424}, mesh = {Animals ; *Biodiversity ; Ecology ; Environmental Monitoring ; Introduced Species ; Mediterranean Sea ; Mollusca/classification ; Plastics/*analysis ; Polychaeta/classification ; Water Pollutants, Chemical/*analysis ; }, abstract = {Five Descriptors (D) of Marine Strategy Framework Directive (MSFD): marine litter (D10), non-indigenous species (D2) and organic and inorganic pollutants (D8), were estimated in a coastal area of GSA 16 (Augusta harbour, Central Mediterranean Sea) in order to study their effects on the biodiversity (D1) of the benthic community D6) and to improve data for the MSFD. Investigation of plastic debris had led to the identification of 38 fragments divided into four categories, among which microplastics resulted as the most abundant. Six non-indigenous species, belonging to Polychaeta (Kirkegaardia dorsobranchialis, Notomastus aberans, Pista unibranchia, Pseudonereis anomala, Branchiomma bairdi) and Mollusca (Brachidontes pharaonis) were found. Biodiversity and benthic indices suggested a generalised, slightly disturbed ecological status. Anthracene, Zinc and Chrome were the most abundant chemical compounds in analysed sediments. Significant correlations were found between the abundance of trace elements vs biotic indices and between plastic debris vs biodiversity and benthic indices. This study represents the first report about the abundance of plastic debris and its relationship to contaminants and infauna in Augusta harbour. Our results can provide useful information for national and international laws and directives.}, } @article {pmid30143789, year = {2018}, author = {Signor, S and Nuzhdin, S}, title = {Dynamic changes in gene expression and alternative splicing mediate the response to acute alcohol exposure in Drosophila melanogaster.}, journal = {Heredity}, volume = {121}, number = {4}, pages = {342-360}, pmid = {30143789}, issn = {1365-2540}, support = {R01 GM102227/GM/NIGMS NIH HHS/United States ; }, mesh = {Alcohol-Related Disorders/genetics ; *Alternative Splicing ; Animals ; Computational Biology/methods ; Drosophila melanogaster/*drug effects/*genetics ; Environment ; Ethanol/*pharmacology ; Exons ; Female ; Gene Expression Profiling ; Gene Expression Regulation/*drug effects ; Gene Ontology ; Gene-Environment Interaction ; Genotype ; Male ; Time Factors ; }, abstract = {Environmental changes typically cause rapid gene expression responses in the exposed organisms, including changes in the representation of gene isoforms with different functions or properties. Identifying the genes that respond to environmental change, including in genotype-specific ways, is an important step in treating the undesirable physiological effects of stress, such as exposure to toxins or ethanol. Ethanol is a unique environmental stress in that chronic exposure results in permanent physiological changes and the development of alcohol use disorders. Drosophila is a classic model for deciphering the mechanisms of the response to alcohol exposure, as it meets the criteria for the development of alcohol use disorders, and has similar physiological underpinnings with vertebrates. Because many studies on the response to ethanol have relied on a priori candidate genes, broad surveys of gene expression and splicing are required and have been investigated here. Further, we expose Drosophila to ethanol in an environment that is genetically, socially, and ecologically relevant. Both expression and splicing differences, inasmuch as they can be decomposed, contribute to the response to ethanol in Drosophila melanogaster. However, we find that while D. melanogaster responds to ethanol, there is very little genetic variation in how it responds to ethanol. In addition, the response to alcohol over time is dynamic, suggesting that incorporating time into studies on the response to the environment is important.}, } @article {pmid30143714, year = {2018}, author = {Giannattasio, S and Giacovazzo, G and Bonato, A and Caruso, C and Luvisetto, S and Coccurello, R and Caruso, M}, title = {Lack of cyclin D3 induces skeletal muscle fiber-type shifting, increased endurance performance and hypermetabolism.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {12792}, pmid = {30143714}, issn = {2045-2322}, mesh = {Animals ; Cell Line ; Cyclin D3/*deficiency/genetics/metabolism ; Energy Metabolism ; Gene Ontology ; Mice, Knockout ; Muscle Fibers, Skeletal/*metabolism ; Myosin Heavy Chains/metabolism ; Phenotype ; *Physical Endurance ; Protein Isoforms/metabolism ; Reproducibility of Results ; Respiration ; Transcriptome/genetics ; Up-Regulation/genetics ; }, abstract = {The mitogen-induced D-type cyclins (D1, D2 and D3) are regulatory subunits of the cyclin-dependent kinases CDK4 and CDK6 that drive progression through the G1 phase of the cell cycle. In skeletal muscle, cyclin D3 plays a unique function in controlling the proliferation/differentiation balance of myogenic progenitor cells. Here, we show that cyclin D3 also performs a novel function, regulating muscle fiber type-specific gene expression. Mice lacking cyclin D3 display an increased number of myofibers with higher oxidative capacity in fast-twitch muscle groups, primarily composed of myofibers that utilize glycolytic metabolism. The remodeling of myofibers toward a slower, more oxidative phenotype is accompanied by enhanced running endurance and increased energy expenditure and fatty acid oxidation. In addition, gene expression profiling of cyclin D3-/- muscle reveals the upregulation of genes encoding proteins involved in the regulation of contractile function and metabolic markers specifically expressed in slow-twitch and fast-oxidative myofibers, many of which are targets of MEF2 and/or NFAT transcription factors. Furthermore, cyclin D3 can repress the calcineurin- or MEF2-dependent activation of a slow fiber-specific promoter in cultured muscle cells. These data suggest that cyclin D3 regulates muscle fiber type phenotype, and consequently whole body metabolism, by antagonizing the activity of MEF2 and/or NFAT.}, } @article {pmid30142582, year = {2018}, author = {Yang, J and Zhang, B}, title = {Air pollution and healthcare expenditure: Implication for the benefit of air pollution control in China.}, journal = {Environment international}, volume = {120}, number = {}, pages = {443-455}, doi = {10.1016/j.envint.2018.08.011}, pmid = {30142582}, issn = {1873-6750}, mesh = {Air Pollutants/*analysis/economics ; Air Pollution/*analysis/economics ; China ; Databases, Factual ; *Health Expenditures ; Humans ; Particulate Matter/*analysis/economics ; }, abstract = {Quantitating the health effects of air pollution is important for understanding the benefits of environmental regulations. Using the China Urban Household Survey (UHS) Database, this paper estimated the effect of air pollution exposure on household healthcare expenditure. To address potential endogeneity concerns, we performed household healthcare expenditure regressions using an instrumental variables (IV) strategy based on spatial air pollution spillovers. Our research revealed that a 1% increase in yearly exposure to fine particulate matter (PM2.5) corresponds to a 2.942% (95% confidence interval: 1.084%, 4.799%) increase in household healthcare expenditure. The estimates suggest that the 13th Five-Year Plan for Ecological and Environmental Protection (the 13th FYP) would reduce annual national healthcare expenditure by 47.36 Billion Dollar (95% confidence interval: 17.45 Billion Dollar, 77.25 Billion Dollar), which accounts for 0.64% (95% confidence interval: 0.24%, 1.04%) of China's gross domestic product (GDP).}, } @article {pmid30140690, year = {2018}, author = {Brázda, V and Lýsek, J and Bartas, M and Fojta, M}, title = {Complex Analyses of Short Inverted Repeats in All Sequenced Chloroplast DNAs.}, journal = {BioMed research international}, volume = {2018}, number = {}, pages = {1097018}, pmid = {30140690}, issn = {2314-6141}, mesh = {Chloroplasts/*genetics ; *DNA, Chloroplast ; Evolution, Molecular ; Genome, Chloroplast ; Introns ; *Inverted Repeat Sequences ; Phylogeny ; }, abstract = {Chloroplasts are key organelles in the management of oxygen in algae and plants and are therefore crucial for all living beings that consume oxygen. Chloroplasts typically contain a circular DNA molecule with nucleus-independent replication and heredity. Using "palindrome analyser" we performed complete analyses of short inverted repeats (S-IRs) in all chloroplast DNAs (cpDNAs) available from the NCBI genome database. Our results provide basic parameters of cpDNAs including comparative information on localization, frequency, and differences in S-IR presence. In a total of 2,565 cpDNA sequences available, the average frequency of S-IRs in cpDNA genomes is 45 S-IRs/per kbp, significantly higher than that found in mitochondrial DNA sequences. The frequency of S-IRs in cpDNAs generally decreased with S-IR length, but not for S-IRs 15, 22, 24, or 27 bp long, which are significantly more abundant than S-IRs with other lengths. These results point to the importance of specific S-IRs in cpDNA genomes. Moreover, comparison by Levenshtein distance of S-IR similarities showed that a limited number of S-IR sequences are shared in the majority of cpDNAs. S-IRs are not located randomly in cpDNAs, but are length-dependently enriched in specific locations, including the repeat region, stem, introns, and tRNA regions. The highest enrichment was found for 12 bp and longer S-IRs in the stem-loop region followed by 12 bp and longer S-IRs located before the repeat region. On the other hand, S-IRs are relatively rare in rRNA sequences and around introns. These data show nonrandom and conserved arrangements of S-IRs in chloroplast genomes.}, } @article {pmid30140020, year = {2018}, author = {Batool, K and Alam, I and Wu, S and Liu, W and Zhao, G and Chen, M and Wang, J and Xu, J and Huang, T and Pan, X and Yu, X and Guan, X and Xu, L and Zhang, L}, title = {Transcriptomic Analysis of Aedes aegypti in Response to Mosquitocidal Bacillus thuringiensis LLP29 Toxin.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {12650}, pmid = {30140020}, issn = {2045-2322}, support = {R21 AI117808/AI/NIAID NIH HHS/United States ; 31301724//National Natural Science Foundation of China (National Science Foundation of China)/International ; }, mesh = {Aedes/*genetics/microbiology ; Animals ; Bacillus thuringiensis/*physiology ; Computational Biology ; Gene Expression Profiling/*methods ; Gene Library ; High-Throughput Nucleotide Sequencing ; Real-Time Polymerase Chain Reaction ; Transcriptome/*genetics ; }, abstract = {Globally, Aedes aegypti is one of the most dangerous mosquitoes that plays a crucial role as a vector for human diseases, such as yellow fever, dengue, and chikungunya. To identify (1) transcriptomic basis of midgut (2) key genes that are involved in the toxicity process by a comparative transcriptomic analysis between the control and Bacillus thuringiensis (Bt) toxin (LLP29 proteins)-treated groups. Next-generation sequencing technology was used to sequence the midgut transcriptome of A. aegypti. A total of 17130 unigenes, including 574 new unigenes, were identified containing 16358 (95.49%) unigenes that were functionally annotated. According to differentially expressed gene (DEG) analysis, 557 DEGs were annotated, including 226 upregulated and 231 downregulated unigenes in the Bt toxin-treated group. A total of 442 DEGs were functionally annotated; among these, 33 were specific to multidrug resistance, 6 were immune-system-related (Lectin, Defensin, Lysozyme), 28 were related to putative proteases, 7 were lipase-related, 8 were related to phosphatases, and 30 were related to other transporters. In addition, the relative expression of 28 DEGs was further confirmed through quantitative real time polymerase chain reaction. The results provide a transcriptomic basis for the identification and functional authentication of DEGs in A. aegypti.}, } @article {pmid30133659, year = {2018}, author = {Abreu, DROM and Souza, EM and Mathias, TAF}, title = {[Impact of the Brazilian Traffic Code and the Law Against Drinking and Driving on mortality from motor vehicle accidents].}, journal = {Cadernos de saude publica}, volume = {34}, number = {8}, pages = {e00122117}, doi = {10.1590/0102-311X00122117}, pmid = {30133659}, issn = {1678-4464}, mesh = {Accidents, Traffic/*mortality ; Adolescent ; Adult ; Alcohol Drinking/*legislation & jurisprudence ; Brazil/epidemiology ; Driving Under the Influence/*legislation & jurisprudence ; Female ; Humans ; Information Systems ; Linear Models ; Male ; Middle Aged ; Motorcycles/*statistics & numerical data ; Pedestrians ; Risk Factors ; Young Adult ; }, abstract = {The objective was to analyze the impact of the Brazilian Traffic Code and the Law Against Drinking and Driving on mortality from traffic accidents in the State of Paraná, Brazil, from 1980 to 2014. This was an ecological time series study on mortality from traffic accidents in residents 15 to 49 years of age, stratified by the sex, age, and categories of victims, with data from the Mortality Information System. The time trend study used a segmented linear regression model and the Cochrane-Orcutt iterative procedure. The assumption of independence of residuals was verified by correlograms and the Box-Pierce test. The highest mortality rates during the period were in males 20 to 29 years of age. After enactment of the Brazilian Traffic Code, there was a decrease of 9.69 deaths/100,000 inhabitants per year for all categories of traffic accidents (p < 0.001), 6.90 for pedestrians (p = 0.001), and 1.96 for vehicle occupants (p < 0.001). As for age bracket, the greatest impact on mortality was in pedestrians 15 to 19 years of age (p < 0.001) and all victims 20 to 29 years of age (p < 0.001). Following enactment of the Drinking and Driving Law, the data displayed variability and the trends were not significant. However, there was a decrease in overall and pedestrian mortality. The rates for motorcyclists and vehicle occupants stabilized. The results showed an impact on traffic accident mortality after enactment of the new Brazilian Traffic Code and Drinking and Driving Law, followed by an increase in the rates. The study evidenced the need for more effective enforcement and progress with public policies in order to avoid a reversal of the gains achieved.}, } @article {pmid30128999, year = {2018}, author = {Vázquez-Castellanos, JF}, title = {Diversity Analysis in Viral Metagenomes.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1838}, number = {}, pages = {203-230}, doi = {10.1007/978-1-4939-8682-8_15}, pmid = {30128999}, issn = {1940-6029}, mesh = {Biomarkers ; *Computational Biology/methods ; Databases, Genetic ; Humans ; *Metagenome ; *Metagenomics/methods ; Software ; Viruses/*classification/*genetics ; }, abstract = {Viruses are the most abundant and diverse biological entity in the earth. Nowadays, there are several viral metagenomes from different ecological niches which have been used to characterize new viral particles and to determine their diversity. However, viral metagenomic data have the disadvantage to be high-dimensional compositional and sparse. This type of data renders many of the conventional multivariate statistical analyses inoperative. Fortunately, different libraries and statistical packages have been developed to deal with this problem and perform the different ecological and statistical analyses. In the present chapter, it is analyzed simulated viral metagenomes, based on real human gut-associated viral metagenomes, using different R and python packages. The example presented here includes the estimation and comparison of different indexes of diversity, evenness, and richness; perform different ordination and statistical analysis using different dissimilarity metrics; determine the optimal cluster configuration and perform biomarker discovery. The scripts and the simulated datasets are in https://github.com/jorgevazcast/Viromic-diversity.}, } @article {pmid30126456, year = {2018}, author = {Milani, C and Casey, E and Lugli, GA and Moore, R and Kaczorowska, J and Feehily, C and Mangifesta, M and Mancabelli, L and Duranti, S and Turroni, F and Bottacini, F and Mahony, J and Cotter, PD and McAuliffe, FM and van Sinderen, D and Ventura, M}, title = {Tracing mother-infant transmission of bacteriophages by means of a novel analytical tool for shotgun metagenomic datasets: METAnnotatorX.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {145}, pmid = {30126456}, issn = {2049-2618}, mesh = {Bacteriophages/*classification/genetics/isolation & purification ; Computational Biology/*methods/standards ; Feces/*virology ; Female ; Gastrointestinal Microbiome ; Genotype ; Humans ; Infant, Newborn ; Male ; Metagenomics/*methods/standards ; Mothers ; Sequence Analysis, DNA/methods ; Software ; }, abstract = {BACKGROUND: Despite the relevance of viral populations, our knowledge of (bacterio) phage populations, i.e., the phageome, suffers from the absence of a "gold standard" protocol for viral DNA extraction with associated in silico sequence processing analyses. To overcome this apparent hiatus, we present here a comprehensive performance evaluation of various protocols and propose an optimized pipeline that covers DNA extraction, sequencing, and bioinformatic analysis of phageome data.

RESULTS: Five widely used protocols for viral DNA extraction from fecal samples were tested for their performance in removal of non-viral DNA. Moreover, we developed a novel bioinformatic platform, METAnnotatorX, for metagenomic dataset analysis. This in silico tool facilitates a range of read- and assembly-based analyses, including taxonomic profiling using an iterative multi-database pipeline, classification of contigs at genus and species level, as well as functional characterizations of reads and assembled data. Performances of METAnnotatorX were assessed through investigation of seven mother-newborn pairs, leading to the identification of shared phage genotypes, of which two were genomically decoded and characterized. METAnnotatorX was furthermore employed to evaluate a protocol for the identification of contaminant non-viral DNA in sequenced datasets and was exploited to determine the amount of metagenomic data needed for robust evaluation of human adult-derived (fecal) phageomes.

CONCLUSIONS: Results obtained in this study demonstrate that a comprehensive pipeline for analysis of phageomes will be pivotal for future explorations of the ecology of phages in the gut environment as well as for understanding their impact on the physiology and bacterial community kinetics as players of dysbiosis and homeostasis in the gut microbiota.}, } @article {pmid30125851, year = {2019}, author = {Isigonis, P and Critto, A and Stefan, M and Zabeo, A and Ciffroy, P and Marcomini, A}, title = {"AMORE" Decision Support System for probabilistic Ecological Risk Assessment - Part I: Exposure and risk assessment of the case study on cyanide.}, journal = {The Science of the total environment}, volume = {648}, number = {}, pages = {693-702}, doi = {10.1016/j.scitotenv.2018.08.124}, pmid = {30125851}, issn = {1879-1026}, abstract = {Ecological Risk Assessment of chemicals in fluvial systems is a highly researched topic, but its importance for the environmental protection of our planet is vital. Thus, new developments and improvements to existing methodologies are proposed constantly, for providing more advanced tools and more accurate results to researchers and other interested parties. In the field of probabilistic Ecological Risk Assessment, a new Decision Support System is proposed, developed, tested and evaluated. The AMORE DSS is a modular DSS, which incorporates a series of new methodologies, and is built upon the notions of 'Exposure Assessment', 'Effect Assessment' and 'Risk Assessment'. The AMORE Decision Support System has been developed as part of the AMORE research project (French National Research Agency project). The DSS provides a set of tools for analysing and integrating both exposure and effect information in order to evaluate the risk for species living on a given contaminated aquatic system in terms of the Potentially Affected Fraction. The DSS has been tested through a case study on ERA of cyanide in the watershed of river Selune in France. The paper presents the 'Exposure Assessment' and 'Risk Assessment' of the cyanide case study, as well as the complete functionalities of the AMORE DSS. The main results presented in the paper are the statistical analysis of the measured environmental concentrations of cyanide (Exposure Assessment) and the probabilistic 'Risk assessment' of the same contaminant in the area of interest, based on the functionalities of the DSS. The results are described and discussed in detail with the use of various graphs and risk indices. The risk indices are calculated for all the available ecotoxicological data, as well as for the data on trophic levels or taxonomic groups separately. A risk comparison is presented between the innovative methodologies included in the DSS and the currently existing methodologies.}, } @article {pmid30124858, year = {2018}, author = {Alba, S and Rood, E and Bakker, MI and Straetemans, M and Glaziou, P and Sismanidis, C}, title = {Development and validation of a predictive ecological model for TB prevalence.}, journal = {International journal of epidemiology}, volume = {47}, number = {5}, pages = {1645-1657}, pmid = {30124858}, issn = {1464-3685}, support = {001/WHO_/World Health Organization/International ; }, mesh = {Adolescent ; Adult ; Africa/epidemiology ; Aged ; Aged, 80 and over ; Asia/epidemiology ; Child ; Child, Preschool ; Comorbidity ; Cross-Sectional Studies ; Databases, Factual ; Developing Countries ; Female ; Humans ; India/epidemiology ; Infant ; Infant, Newborn ; Male ; Middle Aged ; *Models, Biological ; Multivariate Analysis ; Prevalence ; Regression Analysis ; Tuberculosis/*epidemiology ; Young Adult ; }, abstract = {BACKGROUND: Nationally representative tuberculosis (TB) prevalence surveys provide invaluable empirical measurements of TB burden but are a massive and complex undertaking. Therefore, methods that capitalize on data from these surveys are both attractive and imperative. The aim of this study was to use existing TB prevalence estimates to develop and validate an ecological predictive statistical model to indirectly estimate TB prevalence in low- and middle-income countries without survey data.

METHODS: We included national and subnational estimates from 30 nationally representative surveys and 2 district-level surveys in India, resulting in 50 data points for model development (training set). Ecological predictors included TB notification and programmatic data, co-morbidities and socio-environmental factors extracted from online data repositories. A random-effects multivariable binomial regression model was developed using the training set and was used to predict bacteriologically confirmed TB prevalence in 63 low- and middle-income countries across Africa and Asia in 2015.

RESULTS: Out of the 111 ecological predictors considered, 14 were retained for model building (due to incompleteness or collinearity). The final model retained for predictions included five predictors: continent, percentage retreated cases out of all notified, all forms TB notification rates per 100 000 population, population density and proportion of the population under the age of 15. Cross-fold validations in the training set showed very good average fit (R-sq = 0.92).

CONCLUSION: Predictive ecological modelling is a useful complementary approach to indirectly estimating TB burden and can be considered alongside other methods in countries with limited robust empirical measurements of TB among the general population.}, } @article {pmid30120682, year = {2019}, author = {Jacobson, NC and Chow, SM and Newman, MG}, title = {The Differential Time-Varying Effect Model (DTVEM): A tool for diagnosing and modeling time lags in intensive longitudinal data.}, journal = {Behavior research methods}, volume = {51}, number = {1}, pages = {295-315}, pmid = {30120682}, issn = {1554-3528}, support = {R01 GM105004/GM/NIGMS NIH HHS/United States ; U24 AA027684/AA/NIAAA NIH HHS/United States ; }, mesh = {*Data Interpretation, Statistical ; Humans ; *Longitudinal Studies ; *Models, Statistical ; Time Factors ; }, abstract = {With the recent growth in intensive longitudinal designs and the corresponding demand for methods to analyze such data, there has never been a more pressing need for user-friendly analytic tools that can identify and estimate optimal time lags in intensive longitudinal data. The available standard exploratory methods to identify optimal time lags within univariate and multivariate multiple-subject time series are greatly underpowered at the group (i.e., population) level. We describe a hybrid exploratory-confirmatory tool, referred to herein as the Differential Time-Varying Effect Model (DTVEM), which features a convenient user-accessible function to identify optimal time lags and estimate these lags within a state-space framework. Data from an empirical ecological momentary assessment study are then used to demonstrate the utility of the proposed tool in identifying the optimal time lag for studying the linkages between nervousness and heart rate in a group of undergraduate students. Using a simulation study, we illustrate the effectiveness of DTVEM in identifying optimal lag structures in multiple-subject time-series data with missingness, as well as its strengths and limitations as a hybrid exploratory-confirmatory approach, relative to other existing approaches.}, } @article {pmid30120589, year = {2018}, author = {Chaiyos, J and Suwannatrai, K and Thinkhamrop, K and Pratumchart, K and Sereewong, C and Tesana, S and Kaewkes, S and Sripa, B and Wongsaroj, T and Suwannatrai, AT}, title = {MaxEnt modeling of soil-transmitted helminth infection distributions in Thailand.}, journal = {Parasitology research}, volume = {117}, number = {11}, pages = {3507-3517}, pmid = {30120589}, issn = {1432-1955}, support = {TRG5790198//Thailand Research Fund/ ; }, mesh = {Ancylostomatoidea/*isolation & purification ; Animals ; Ascariasis/epidemiology/parasitology/transmission ; Ascaris lumbricoides/*isolation & purification ; Child ; Climate ; Entropy ; Gastrointestinal Diseases/*parasitology ; Geographic Information Systems ; Helminthiasis/*epidemiology/parasitology/*transmission ; Hookworm Infections/epidemiology/parasitology/transmission ; Humans ; Prevalence ; Remote Sensing Technology ; Soil/*parasitology ; Strongyloides stercoralis/*isolation & purification ; Strongyloidiasis/epidemiology/parasitology/transmission ; Thailand/epidemiology ; Trichuriasis/epidemiology/parasitology/transmission ; Trichuris/*isolation & purification ; }, abstract = {Infections due to soil-transmitted helminths (STHs), i.e. Ascaris lumbricoides, Trichuris trichiura, hookworms, and Strongyloides stercoralis, are widely distributed in tropical and subtropical areas in which approximately 1.5 billion people are infected. A clear understanding of the epidemiology and distribution of diseases is an important aid for control and prevention. The aim of our study was to identify the effects of environmental and climatic factors on distribution patterns of STHs and to develop a risk map for STH infections under current environmental and climate regimes in Thailand. Geographical information systems (GIS), remote sensing, and Maximum Entropy (MaxEnt) algorithm software were used to determine the significant factors and to create predictive risk maps for STH infections in Thailand. The disease data from Thailand covered the years from 1969 to 2014, while environmental and climatic data were compiled from the Worldclim database, MODIS satellite imagery, Soilgrids and ISCGM. The models predicted that STHs occur mainly in southern Thailand. Mean annual precipitation was the factor most affecting the current distribution of A. lumbricoides, T. trichiura, and S. stercoralis. Land cover class was the main predictor for distribution of S. stercoralis and important for hookworms. Altitude was the dominant factor affecting the distribution of hookworms, and mean temperature of the wettest quarter was significantly associated with A. lumbricoides distribution. A predicted distribution map of STHs to identify environmental risk factors in Thailand is presented. This work provides a model for use in STH monitoring and health planning not only in Thailand but also in other countries with similar disease conditions.}, } @article {pmid30118479, year = {2018}, author = {Modepalli, V and Fridrich, A and Agron, M and Moran, Y}, title = {The methyltransferase HEN1 is required in Nematostella vectensis for microRNA and piRNA stability as well as larval metamorphosis.}, journal = {PLoS genetics}, volume = {14}, number = {8}, pages = {e1007590}, pmid = {30118479}, issn = {1553-7404}, mesh = {Animals ; Computational Biology ; Female ; Gene Deletion ; Gene Expression Regulation ; Gene Library ; Larva/genetics/metabolism ; Male ; Metamorphosis, Biological/*genetics ; Methylation ; Methyltransferases/genetics/*metabolism ; MicroRNAs/*genetics ; *RNA Stability ; RNA, Messenger/genetics/metabolism ; RNA, Small Interfering/*genetics ; Sea Anemones/embryology/*genetics/metabolism ; }, abstract = {Small non-coding RNAs (sRNAs) such as microRNAs (miRNAs), small interfering RNAs (siRNAs) and piwi-interacting RNAs (piRNAs) regulate the levels of endogenous, viral and transposable element RNA in plants (excluding piRNAs) and animals. These pathways are explored mainly in bilaterian animals, such as vertebrates, arthropods and nematodes, where siRNAs and piRNAs, but not miRNAs bind their targets with a perfect match and mediate the cleavage of the target RNA. Methylation of the 3' ends of piRNAs and siRNAs by the methyltransferase HEN1 protects these sRNAs from degradation. There is a noticeable selection in bilaterian animals against miRNA-mRNA perfect matching, as it leads to the degradation of miRNAs. Cnidarians (sea anemones, corals, hydroids and jellyfish), are separated from bilaterians by more than 600 million years. As opposed to bilaterians, cnidarian miRNAs frequently bind their targets with a nearly perfect match. Knowing that an ortholog of HEN1 is widely expressed in the sea anemone Nematostella vectensis, we tested in this work whether it mediates the stabilization of its sRNAs. We show that the knockdown of HEN1 in Nematostella results in a developmental arrest. Small RNA sequencing revealed that the levels of both miRNAs and piRNAs drop dramatically in the morphant animals. Moreover, knockdown experiments of Nematostella Dicer1 and PIWI2, homologs of major bilaterian biogenesis components of miRNAs and piRNAs, respectively, resulted in developmental arrest similar to HEN1 morphants. Our findings suggest that HEN1 mediated methylation of sRNAs reflects the ancestral state, where miRNAs were also methylated. Thus, we provide the first evidence of a methylation mechanism that stabilizes miRNAs in animals, and highlight the importance of post-transcriptional regulation in non-bilaterian animals.}, } @article {pmid30115014, year = {2018}, author = {Chou, HC and Acevedo-Luna, N and Kuhlman, JA and Schneider, SQ}, title = {PdumBase: a transcriptome database and research tool for Platynereis dumerilii and early development of other metazoans.}, journal = {BMC genomics}, volume = {19}, number = {1}, pages = {618}, pmid = {30115014}, issn = {1471-2164}, support = {12-3985//Roy J. Carver Charitable Trust/ ; 1455185//National Science Foundation/ ; }, mesh = {Algorithms ; Animals ; Annelida/classification/genetics ; Biomedical Research/*methods ; Computational Biology/*methods ; *Databases, Genetic ; Embryo, Nonmammalian ; Embryonic Development/*genetics ; Gene Expression Profiling ; Genes, Developmental ; Polychaeta/*embryology/*genetics ; *Transcriptome ; }, abstract = {BACKGROUND: The marine polychaete annelid Platynereis dumerilii has recently emerged as a prominent organism for the study of development, evolution, stem cells, regeneration, marine ecology, chronobiology and neurobiology within metazoans. Its phylogenetic position within the spiralian/ lophotrochozoan clade, the comparatively high conservation of ancestral features in the Platynereis genome, and experimental access to any stage within its life cycle, make Platynereis an important model for elucidating the complex regulatory and functional molecular mechanisms governing early development, later organogenesis, and various features of its larval and adult life. High resolution RNA-seq gene expression data obtained from specific developmental stages can be used to dissect early developmental mechanisms. However, the potential for discovery of these mechanisms relies on tools to search, retrieve, and compare genome-wide information within Platynereis, and across other metazoan taxa.

RESULTS: To facilitate exploration and discovery by the broader scientific community, we have developed a web-based, searchable online research tool, PdumBase, featuring the first comprehensive transcriptome database for Platynereis dumerilii during early stages of development (2 h ~ 14 h). Our database also includes additional stages over the P. dumerilii life cycle and provides access to the expression data of 17,213 genes (31,806 transcripts) along with annotation information sourced from Swiss-Prot, Gene Ontology, KEGG pathways, Pfam domains, TmHMM, SingleP, and EggNOG orthology. Expression data for each gene includes the stage, the normalized FPKM, the raw read counts, and information that can be leveraged for statistical analyses of differential gene expression and the construction of genome-wide co-expression networks. In addition, PdumBase offers early stage transcriptome expression data from five further species as a valuable resource for investigators interested in comparing early development in different organisms. To understand conservation of Platynereis gene models and to validate gene annotation, most Platynereis gene models include a comprehensive phylogenetic analysis across 18 species representing diverse metazoan taxa.

CONCLUSIONS: PdumBase represents the first online resource for the early developmental transcriptome of Platynereis dumerilii. It serves as a research platform for discovery and exploration of gene expression during early stages, throughout the Platynereis life cycle, and enables comparison to other model organisms. PdumBase is freely available at http://pdumbase.gdcb.iastate.edu .}, } @article {pmid30109017, year = {2017}, author = {Griffin, PC and Khadake, J and LeMay, KS and Lewis, SE and Orchard, S and Pask, A and Pope, B and Roessner, U and Russell, K and Seemann, T and Treloar, A and Tyagi, S and Christiansen, JH and Dayalan, S and Gladman, S and Hangartner, SB and Hayden, HL and Ho, WWH and Keeble-Gagnère, G and Korhonen, PK and Neish, P and Prestes, PR and Richardson, MF and Watson-Haigh, NS and Wyres, KL and Young, ND and Schneider, MV}, title = {Best practice data life cycle approaches for the life sciences.}, journal = {F1000Research}, volume = {6}, number = {}, pages = {1618}, pmid = {30109017}, issn = {2046-1402}, abstract = {Throughout history, the life sciences have been revolutionised by technological advances; in our era this is manifested by advances in instrumentation for data generation, and consequently researchers now routinely handle large amounts of heterogeneous data in digital formats. The simultaneous transitions towards biology as a data science and towards a 'life cycle' view of research data pose new challenges. Researchers face a bewildering landscape of data management requirements, recommendations and regulations, without necessarily being able to access data management training or possessing a clear understanding of practical approaches that can assist in data management in their particular research domain. Here we provide an overview of best practice data life cycle approaches for researchers in the life sciences/bioinformatics space with a particular focus on 'omics' datasets and computer-based data processing and analysis. We discuss the different stages of the data life cycle and provide practical suggestions for useful tools and resources to improve data management practices.}, } @article {pmid30111595, year = {2018}, author = {Väli, Ü and Mirski, P and Sellis, U and Dagys, M and Maciorowski, G}, title = {Genetic determination of migration strategies in large soaring birds: evidence from hybrid eagles.}, journal = {Proceedings. Biological sciences}, volume = {285}, number = {1884}, pages = {}, pmid = {30111595}, issn = {1471-2954}, mesh = {*Animal Migration ; Animals ; Eagles/genetics/*physiology ; Female ; Flight, Animal ; Geographic Information Systems ; *Hybridization, Genetic ; Male ; Telemetry/veterinary ; }, abstract = {The relative contributions of genetic and social factors in shaping the living world are a crucial question in ecology. The annual migration of birds to their wintering grounds and back provides significant knowledge in this field of research. Migratory movements are predominantly genetically determined in passerine birds, while in large soaring birds, it is presumed that social (cultural) factors play the largest role. In this study, we show that genetic factors in soaring birds are more important than previously assumed. We used global positioning system (GPS)-telemetry to compare the autumn journeys and wintering ranges of two closely related large raptorial bird species, the greater spotted eagle Clanga clanga and the lesser spotted eagle Clanga pomarina, and hybrids between them. The timing of migration in hybrids was similar to that of one parental species, but the wintering distributions and home range sizes were similar to those of the other. Tracking data were supported by habitat suitability modelling, based on GPS fixes and ring recoveries. These results suggest a strong genetic influence on migration strategy via a trait-dependent dominance effect, although we cannot rule out the contribution of social interactions.}, } @article {pmid30110640, year = {2018}, author = {Kearney, SM and Gibbons, SM and Erdman, SE and Alm, EJ}, title = {Orthogonal Dietary Niche Enables Reversible Engraftment of a Gut Bacterial Commensal.}, journal = {Cell reports}, volume = {24}, number = {7}, pages = {1842-1851}, pmid = {30110640}, issn = {2211-1247}, support = {P30 DK043351/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; Bacterial Load ; Bacteroides/isolation & purification/*physiology ; Diet/*methods ; Eating/physiology ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*physiology ; Mice ; Mice, Inbred C57BL ; Seaweed/*chemistry ; Symbiosis/*physiology ; Verrucomicrobia/isolation & purification/physiology ; }, abstract = {Interest in manipulating the gut microbiota to treat disease has led to a need for understanding how organisms can establish themselves when introduced into a host with an intact microbial community. Here, we employ the concept of orthogonal niche engineering: a resource typically absent from the diet, seaweed, creates a customized niche for an introduced organism. In the short term, co-introduction of this resource at 1% in the diet along with an organism with exclusive access to this resource, Bacteroides plebeius DSM 17135, enables it to colonize at a median abundance of 1% and frequently up to 10 or more percent, both on pulsed and constant seaweed diets. In a two-month follow-up after the initial treatment period, B. plebeius stops responding to seaweed in mice initially on the constant seaweed diet, suggesting treatment regime will affect controllability. These results offer potential for diet-based intervention to introduce and control target organisms.}, } @article {pmid30110370, year = {2018}, author = {Campos, MC and Dombrowski, JG and Phelan, J and Marinho, CRF and Hibberd, M and Clark, TG and Campino, S}, title = {Zika might not be acting alone: Using an ecological study approach to investigate potential co-acting risk factors for an unusual pattern of microcephaly in Brazil.}, journal = {PloS one}, volume = {13}, number = {8}, pages = {e0201452}, pmid = {30110370}, issn = {1932-6203}, support = {MR/K000551/1/MRC_/Medical Research Council/United Kingdom ; MR/M01360X/1/MRC_/Medical Research Council/United Kingdom ; MC_PC_15103//Medical Research Council/United Kingdom ; MR/N010469/1//Medical Research Council/United Kingdom ; }, mesh = {Aedes/*growth & development ; Animals ; Brazil ; *Databases, Factual ; *Ecosystem ; Female ; Humans ; Incidence ; Infant ; Infant, Newborn ; Larva/growth & development ; Male ; Microcephaly ; *Poverty ; *Zika Virus ; Zika Virus Infection/*epidemiology/*transmission ; }, abstract = {Zika virus infections can cause a range of neurologic disorders including congenital microcephaly. However, while Zika infections have been notified across all regions in Brazil, there has been an unusual number of congenital microcephaly case notifications concentrated in the Northeast of the country. To address this observation, we investigated epidemiological data (2014-2016) on arbovirus co-distribution, environmental and socio-economic factors for each region in Brazil. Data on arbovirus reported cases and microcephaly were collected from several Brazilian Ministry of Health databases for each Federal unit. These were complemented by environmental management, social economic and Aedes aegypti infestation index data, extracted from multiple databases. Spatial time "ecological" analysis on the number of arboviruses transmitted by Aedes mosquitoes in Brazil show that the distribution of dengue and Zika was widespread in the whole country, with higher incidence in the West-Central region. However, reported chikungunya cases were higher in the Northeast, the region also with the highest number of microcephaly cases registered. Social economic factors (human development index and poverty index) and environmental management (water supply/storage and solid waste management) pointed the Northeast as the less wealthy region. The Northeast is also the region with the highest risk of Aedes aegypti house infestation due to the man-made larval habitats. In summary, the results of our ecological analysis support the hypothesis that the unusual distribution of microcephaly might not be due to Zika infection alone and could be accentuated by poverty and previous or co-infection with other pathogens. Our study reinforces the link between poverty and the risk of disease and the need to understand the effect on pathogenesis of sequential exposure to arboviruses and co-viral infections. Comprehensive large-scale cohort studies are required to corroborate our findings. We recommend that the list of infectious diseases screened, particularly during pregnancy, be regularly updated to include and effectively differentiate all viruses from ongoing outbreaks.}, } @article {pmid30110075, year = {2018}, author = {Rakić, JG and Maksimović, M and Janković, J and Vlajinac, H and Marinković, J}, title = {Relationship between socioeconomic and nutritional status in the Serbian adult population: a cross-sectional study.}, journal = {Sao Paulo medical journal = Revista paulista de medicina}, volume = {136}, number = {4}, pages = {310-318}, pmid = {30110075}, issn = {1806-9460}, mesh = {Adult ; Aged ; Cross-Sectional Studies ; Female ; Health Surveys ; Humans ; Interviews as Topic ; Male ; Middle Aged ; *Nutritional Status ; Obesity/*epidemiology ; Serbia/epidemiology ; *Socioeconomic Factors ; }, abstract = {BACKGROUND: Socioeconomic status is a well-known risk factor for obesity. The aim of this study was to assess the relationship between socioeconomic and nutritional status in the Serbian adult population.

DESIGN AND SETTING: Cross-sectional study on data from the 2013 National Health Survey performed in Serbia.

METHODS: The study population consisted of adults aged ≥ 20 years. Face-to-face interviews and anthropometric measurements were conducted by trained staff. Associations between body mass index and sociodemographic variables were analyzed using multivariable logistic regression analyses.

RESULTS: Out of 12,461 subjects of both sexes, 36.4% were overweight and 22.4% were obese. The prevalences of overweight and obesity differed significantly between the sexes, regarding all sociodemographic characteristics. Among women, educational attainment was associated with lower risk of being overweight (odds ratio, OR = 0.82; 95% confidence interval, CI: 0.69-0.98 for medium-level and OR = 0.77; CI: 0.62-0.97 for higher education) or obese (OR = 0.68; CI: 0.57-0.82 for medium-level and OR = 0.41; CI: 0.31-0.54 for higher education). In contrast, medium-level (OR = 1.28; CI: 1.08-1.52) and highly educated men (OR = 1.39; CI: 1.11-1.74) were more frequently overweight than were those with low education. Among men, grade I obesity was positively related to the richest wealth index group (OR = 1.27), while the opposite was true for grade II obesity among women (OR = 0.61).

CONCLUSION: This study showed significant socioeconomic inequalities in nutritional status between men and women. Continuous monitoring of socioeconomic patterns relating to weight is important, especially with further exploration of the link between education and obesity.}, } @article {pmid30108295, year = {2018}, author = {Liebhold, AM and Yamanaka, T and Roques, A and Augustin, S and Chown, SL and Brockerhoff, EG and Pyšek, P}, title = {Plant diversity drives global patterns of insect invasions.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {12095}, pmid = {30108295}, issn = {2045-2322}, mesh = {*Animal Distribution ; Animals ; Datasets as Topic ; Geography ; Insecta/*physiology ; Introduced Species/*statistics & numerical data ; *Models, Biological ; *Plants ; Population Dynamics/statistics & numerical data ; }, abstract = {During the last two centuries, thousands of insect species have been transported (largely inadvertently) and established outside of their native ranges worldwide, some with catastrophic ecological and economic impacts. Global variation in numbers of invading species depends on geographic variation in propagule pressure and heterogeneity of environmental resistance to invasions. Elton's diversity-invasibility hypothesis, proposed over sixty years ago, has been widely explored for plants but little is known on how biodiversity affects insect invasions. Here we use species inventories from 44 land areas, ranging from small oceanic islands to entire continents in various world regions, to show that numbers of established insect species are primarily driven by diversity of plants, with both native and non-native plant species richness being the strongest predictor of insect invasions. We find that at large spatial scales, plant diversity directly explains variation in non-native insect species richness among world regions, while geographic factors such as land area, climate and insularity largely affect insect invasions indirectly via their effects on local plant richness.}, } @article {pmid30108240, year = {2018}, author = {Argiriadis, E and Battistel, D and McWethy, DB and Vecchiato, M and Kirchgeorg, T and Kehrwald, NM and Whitlock, C and Wilmshurst, JM and Barbante, C}, title = {Lake sediment fecal and biomass burning biomarkers provide direct evidence for prehistoric human-lit fires in New Zealand.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {12113}, pmid = {30108240}, issn = {2045-2322}, mesh = {Archaeology ; Biomarkers/analysis/chemistry ; Charcoal/analysis/chemistry ; Conservation of Natural Resources/*history ; Feces/*chemistry ; Fires/*history ; Fossils ; Geologic Sediments/*analysis/chemistry ; History, Ancient ; Humans ; Lakes ; New Zealand ; Phytosterols/analysis/chemistry ; Plants/chemistry ; Polycyclic Aromatic Hydrocarbons/analysis/chemistry ; }, abstract = {Deforestation associated with the initial settlement of New Zealand is a dramatic example of how humans can alter landscapes through fire. However, evidence linking early human presence and land-cover change is inferential in most continental sites. We employed a multi-proxy approach to reconstruct anthropogenic land use in New Zealand's South Island over the last millennium using fecal and plant sterols as indicators of human activity and monosaccharide anhydrides, polycyclic aromatic hydrocarbons, charcoal and pollen as tracers of fire and vegetation change in lake-sediment cores. Our data provide a direct record of local human presence in Lake Kirkpatrick and Lake Diamond watersheds at the time of deforestation and a new and stronger case of human agency linked with forest clearance. The first detection of human presence matches charcoal and biomarker evidence for initial burning at c. AD 1350. Sterols decreased shortly after to values suggesting the sporadic presence of people and then rose to unprecedented levels after the European settlement. Our results confirm that initial human arrival in New Zealand was associated with brief and intense burning activities. Testing our approach in a context of well-established fire history provides a new tool for understanding cause-effect relationships in more complex continental reconstructions.}, } @article {pmid30107434, year = {2018}, author = {Ou, S and Chen, J and Jiang, N}, title = {Assessing genome assembly quality using the LTR Assembly Index (LAI).}, journal = {Nucleic acids research}, volume = {46}, number = {21}, pages = {e126}, pmid = {30107434}, issn = {1362-4962}, mesh = {Chromosomes, Artificial, Bacterial ; Computational Biology/methods ; *Genome, Plant ; Genomics/*methods ; Oryza/genetics ; Retroelements/*genetics ; *Software ; Solanum/genetics ; }, abstract = {Assembling a plant genome is challenging due to the abundance of repetitive sequences, yet no standard is available to evaluate the assembly of repeat space. LTR retrotransposons (LTR-RTs) are the predominant interspersed repeat that is poorly assembled in draft genomes. Here, we propose a reference-free genome metric called LTR Assembly Index (LAI) that evaluates assembly continuity using LTR-RTs. After correcting for LTR-RT amplification dynamics, we show that LAI is independent of genome size, genomic LTR-RT content, and gene space evaluation metrics (i.e., BUSCO and CEGMA). By comparing genomic sequences produced by various sequencing techniques, we reveal the significant gain of assembly continuity by using long-read-based techniques over short-read-based methods. Moreover, LAI can facilitate iterative assembly improvement with assembler selection and identify low-quality genomic regions. To apply LAI, intact LTR-RTs and total LTR-RTs should contribute at least 0.1% and 5% to the genome size, respectively. The LAI program is freely available on GitHub: https://github.com/oushujun/LTR_retriever.}, } @article {pmid30107371, year = {2018}, author = {Wang, Q and Xiong, X and Wang, X and Tu, Q and Li, J and Ding, X and Li, Y and Huang, P and He, S and Yin, Y and Yang, H}, title = {Suckling Piglet Intestinal Enterocyte Nutrient Metabolism Changes.}, journal = {Cellular physiology and biochemistry : international journal of experimental cellular physiology, biochemistry, and pharmacology}, volume = {48}, number = {5}, pages = {2103-2113}, doi = {10.1159/000492552}, pmid = {30107371}, issn = {1421-9778}, mesh = {Amino Acids/analysis/metabolism ; Animals ; Animals, Suckling ; Cells, Cultured ; Chromatography, High Pressure Liquid ; Citric Acid Cycle/genetics ; Databases, Factual ; Enterocytes/cytology/*metabolism ; Fatty Acids/analysis/metabolism ; Glucose/analysis/metabolism ; Jejunum/cytology ; Peptides/analysis ; Swine ; Tandem Mass Spectrometry ; }, abstract = {BACKGROUND/AIMS: Intestinal morphology and the types of enterocytes are changed in piglets during the suckling period, but it is unclear whether these changes are associated with metabolic changes in epithelium. The present study was conducted to test the hypothesis that glucose, fatty acids, and amino acid metabolism in differentiated piglet enterocytes changed during suckling.

METHODS: Twenty-four piglets (Duroc × [Landrace × Yorkshire]) from 8 litters (3 piglets/litter) were selected. A single piglet from each litter was randomly selected and euthanized at days 7, 14, and 21. Differentiated enterocytes (DE) were isolated from their mid-jejunum. Isobaric tags for relative and absolute quantification and subsequent liquid chromatography-tandem mass spectrometry were used to identify and measure protein synthesis.

RESULTS: The results showed that various activities, including: cellular processes; metabolic processes; biological regulation; pigmentation; and, localization, in DEs changed during suckling. Metabolic process analyses revealed that protein expression related to glycolysis and citrate cycle was decreased from day 7 to day 14. The number of differentiated enterocytes of 21 d piglets increased compared to 7 d piglets. Most of the proteins involved in fatty acid and amino acids metabolism had decreased DE expression between day 7 and day 14. Some, but not all, detected proteins down-regulated in DEs of 21 day piglets compared to 7 day piglets.

CONCLUSION: These results indicate that glucose, fatty acids, and amino acids metabolism changed during suckling. This may provide useful information for designing feed formulas and regulating piglet intestinal growth and development.}, } @article {pmid30106998, year = {2018}, author = {Pilipovic-Broceta, N and Vasiljevic, N and Marinkovic, J and Todorovic, N and Jankovic, J and Ostric, I and Kalimanovska-Ostric, D and Racic, M}, title = {Assessment of hypertension chronic care model: Pacic application in Bosnia and Herzegovina.}, journal = {PloS one}, volume = {13}, number = {8}, pages = {e0202250}, pmid = {30106998}, issn = {1932-6203}, mesh = {Adult ; Aged ; Attitude to Health ; Bosnia and Herzegovina ; Chronic Disease ; Cross-Sectional Studies ; Family Practice ; Female ; Humans ; Hypertension/*therapy ; Male ; Middle Aged ; Patient Satisfaction ; Practice Guidelines as Topic ; Primary Health Care ; Quality of Health Care ; Surveys and Questionnaires ; }, abstract = {The objectives of this study were to evaluate patients' attitudes towards hypertension treatment according to the chronic care model and to assess the implementation of hypertension clinical guidelines in family medicine. The cross-sectional study was carried out in two randomly selected primary health care centers (Bijeljina and Prijedor), respectively in Bosnia and Herzegovina, covering the period between March and April 2016. This study sample consists of 791 respondents with hypertension purposing to measure specific actions and quality of care for hypertensive patients. The Patient Assessment of Chronic Illness Care (PACIC) was used. Treatment for the indicators of hypertension was assessed by analyzing patients' medical charts according to the recommendations of clinical guidelines. More than half of the evaluated indicators of treatment for hypertension were documented in medical charts of 84.07% patients. The average overall PACIC score was 4.18 (SD 0.59), being an average of the separate scores of 4.19 (SD 0.57) in men and 4.17 (SD 0.60) in women. Subscale means of PACIC were as follows: patient activation 4.33, delivery system design 4.36; goal setting 4.03; problem solving 4.51; follow-up and co-ordination 3.67. No statistically significant correlations in the overall score and subscale scores were found by demographic characteristics. Non-smokers had a significantly higher overall score compared to smokers (p = 0.001). As implementation of the guidelines became stronger, the reported PACIC scores rose. Continuing the education of patients in order to achieve better health care outcomes is imperative.}, } @article {pmid30106390, year = {2018}, author = {Duarte, G and Moreira, M and Branco, P and da Costa, L and Ferreira, MT and Segurado, P}, title = {One millennium of historical freshwater fish occurrence data for Portuguese rivers and streams.}, journal = {Scientific data}, volume = {5}, number = {}, pages = {180163}, pmid = {30106390}, issn = {2052-4463}, mesh = {Animals ; Databases, Factual ; Ecology/history ; Ecosystem ; *Fishes ; History, 15th Century ; History, 16th Century ; History, 17th Century ; History, 18th Century ; History, 19th Century ; History, 20th Century ; History, Medieval ; Portugal ; Rivers ; Datasets as Topic ; }, abstract = {The insights that historical evidence of human presence and man-made documents provide are unique. For example, using historical data may be critical to adequately understand the ecological requirements of species. However, historical information about freshwater species distribution remains largely a knowledge gap. In this Data Descriptor, we present the Portuguese Historical Fish Database (PHish-DB), a compilation of 2214 records (557 at the basin scale, 184 at the sub-basin scale and 1473 at the segment scale) resulting from a survey of 194 historical documents. The database was developed using a three-scale approach that maximises the inclusion of information by allowing different degrees of spatial acuity. PHish database contains records of 25 taxonomical groups and covers a time span of one millennium, from the 11th until the 20th century. This database has already proven useful for two scientific studies, and PHish further use will contribute to correctly assess the full range of conditions tolerated by species, by establishing adequate benchmark conditions, and/or to improve existing knowledge of the species distribution limits.}, } @article {pmid30104690, year = {2018}, author = {Nobrega, FL and Vlot, M and de Jonge, PA and Dreesens, LL and Beaumont, HJE and Lavigne, R and Dutilh, BE and Brouns, SJJ}, title = {Targeting mechanisms of tailed bacteriophages.}, journal = {Nature reviews. Microbiology}, volume = {16}, number = {12}, pages = {760-773}, doi = {10.1038/s41579-018-0070-8}, pmid = {30104690}, issn = {1740-1534}, mesh = {Bacteria/genetics/*virology ; Bacteriophages/classification/genetics/*physiology ; *Genetic Variation ; Host Specificity ; Protein Binding ; }, abstract = {Phages differ substantially in the bacterial hosts that they infect. Their host range is determined by the specific structures that they use to target bacterial cells. Tailed phages use a broad range of receptor-binding proteins, such as tail fibres, tail spikes and the central tail spike, to target their cognate bacterial cell surface receptors. Recent technical advances and new structure-function insights have begun to unravel the molecular mechanisms and temporal dynamics that govern these interactions. Here, we review the current understanding of the targeting machinery and mechanisms of tailed phages. These new insights and approaches pave the way for the application of phages in medicine and biotechnology and enable deeper understanding of their ecology and evolution.}, } @article {pmid30103527, year = {2018}, author = {Lucas, RM and Rodney Harris, RM}, title = {On the Nature of Evidence and 'Proving' Causality: Smoking and Lung Cancer vs. Sun Exposure, Vitamin D and Multiple Sclerosis.}, journal = {International journal of environmental research and public health}, volume = {15}, number = {8}, pages = {}, pmid = {30103527}, issn = {1660-4601}, mesh = {Causality ; Data Interpretation, Statistical ; Environmental Exposure/*statistics & numerical data ; Humans ; Lung Neoplasms/*etiology ; Multiple Sclerosis/*etiology ; Risk Factors ; Smoking/*adverse effects ; *Sunlight ; Tobacco Smoking ; Vitamin D Deficiency/*complications/prevention & control ; }, abstract = {If environmental exposures are shown to cause an adverse health outcome, reducing exposure should reduce the disease risk. Links between exposures and outcomes are typically based on 'associations' derived from observational studies, and causality may not be clear. Randomized controlled trials to 'prove' causality are often not feasible or ethical. Here the history of evidence that tobacco smoking causes lung cancer-from observational studies-is compared to that of low sun exposure and/or low vitamin D status as causal risk factors for the autoimmune disease, multiple sclerosis (MS). Evidence derives from in vitro and animal studies, as well as ecological, case-control and cohort studies, in order of increasing strength. For smoking and lung cancer, the associations are strong, consistent, and biologically plausible-the evidence is coherent or 'in harmony'. For low sun exposure/vitamin D as risk factors for MS, the evidence is weaker, with smaller effect sizes, but coherent across a range of sources of evidence, and biologically plausible. The association is less direct-smoking is directly toxic and carcinogenic to the lung, but sun exposure/vitamin D modulate the immune system, which in turn may reduce the risk of immune attack on self-proteins in the central nervous system. Opinion about whether there is sufficient evidence to conclude that low sun exposure/vitamin D increase the risk of multiple sclerosis, is divided. General public health advice to receive sufficient sun exposure to avoid vitamin D deficiency (<50 nmol/L) should also ensure any benefits for multiple sclerosis, but must be tempered against the risk of skin cancers.}, } @article {pmid30103194, year = {2018}, author = {Hu, X and Zhu, M and Liu, B and Liang, Z and Huang, L and Xu, J and Yu, L and Li, K and Jiang, M and Xue, R and Cao, G and Gong, C}, title = {Circular RNA alterations in the Bombyx mori midgut following B. mori nucleopolyhedrovirus infection.}, journal = {Molecular immunology}, volume = {101}, number = {}, pages = {461-470}, doi = {10.1016/j.molimm.2018.08.008}, pmid = {30103194}, issn = {1872-9142}, mesh = {Animals ; Base Sequence ; Bombyx/*genetics/*virology ; Digestive System/*virology ; Down-Regulation/genetics ; Gene Expression Profiling ; Gene Ontology ; Gene Regulatory Networks ; MicroRNAs/genetics/metabolism ; Nucleopolyhedroviruses/*physiology ; RNA/genetics/*metabolism ; RNA, Circular ; RNA, Messenger/genetics/metabolism ; Reproducibility of Results ; Up-Regulation/genetics ; }, abstract = {Thus far, no systematic studies have examined circRNA expression profiles in the silkworm following B.mori nucleopolyhedrovirus (BmNPV) infection. To explore the expression patterns of circRNAs in the silkworm midgut following BmNPV infection, circRNAs in normal midguts and BmNPV-infected midguts were analyzed by high-throughput sequencing. A total of 353 circRNAs were significantly differentially expressed, of which 241 were upregulated and 112 were downregulated following infection. GO annotation and KEGG pathways analyses of these circRNAs showed that many key immunity pathways and metabolism pathways were enriched in the BmNPV-infected midguts. The potential roles of the predicted targets of the miRNAs that interacted with the circRNAs showed that ubiquitin, apoptosis, and endocytosis signaling pathways were enriched significantly by BmNPV infection.}, } @article {pmid30098166, year = {2019}, author = {Stanková, K and Brown, JS and Dalton, WS and Gatenby, RA}, title = {Optimizing Cancer Treatment Using Game Theory: A Review.}, journal = {JAMA oncology}, volume = {5}, number = {1}, pages = {96-103}, pmid = {30098166}, issn = {2374-2445}, support = {P30 CA076292/CA/NCI NIH HHS/United States ; R01 CA170595/CA/NCI NIH HHS/United States ; U54 CA143970/CA/NCI NIH HHS/United States ; U54 CA193489/CA/NCI NIH HHS/United States ; }, mesh = {Antineoplastic Agents/adverse effects/*therapeutic use ; *Clinical Decision-Making ; Disease Progression ; *Drug Resistance, Neoplasm/genetics ; Drug Substitution ; *Game Theory ; Humans ; Medical Oncology/*methods ; Neoplasms/*drug therapy/genetics/mortality/pathology ; *Patient Selection ; Quality of Life ; Risk Assessment ; Risk Factors ; Time Factors ; Treatment Outcome ; }, abstract = {IMPORTANCE: While systemic therapy for disseminated cancer is often initially successful, malignant cells, using diverse adaptive strategies encoded in the human genome, almost invariably evolve resistance, leading to treatment failure. Thus, the Darwinian dynamics of resistance are formidable barriers to all forms of systemic cancer treatment but rarely integrated into clinical trial design or included within precision oncology initiatives.

OBSERVATIONS: We investigate cancer treatment as a game theoretic contest between the physician's therapy and the cancer cells' resistance strategies. This game has 2 critical asymmetries: (1) Only the physician can play rationally. Cancer cells, like all evolving organisms, can only adapt to current conditions; they can neither anticipate nor evolve adaptations for treatments that the physician has not yet applied. (2) It has a distinctive leader-follower (or "Stackelberg") dynamics; the "leader" oncologist plays first and the "follower" cancer cells then respond and adapt to therapy. Current treatment protocols for metastatic cancer typically exploit neither asymmetry. By repeatedly administering the same drug(s) until disease progression, the physician "plays" a fixed strategy even as the opposing cancer cells continuously evolve successful adaptive responses. Furthermore, by changing treatment only when the tumor progresses, the physician cedes leadership to the cancer cells and treatment failure becomes nearly inevitable. Without fundamental changes in strategy, standard-of-care cancer therapy typically results in "Nash solutions" in which no unilateral change in treatment can favorably alter the outcome.

CONCLUSIONS AND RELEVANCE: Physicians can exploit the advantages inherent in the asymmetries of the cancer treatment game, and likely improve outcomes, by adopting more dynamic treatment protocols that integrate eco-evolutionary dynamics and modulate therapy accordingly. Implementing this approach will require new metrics of tumor response that incorporate both ecological (ie, size) and evolutionary (ie, molecular mechanisms of resistance and relative size of resistant population) changes.}, } @article {pmid30096916, year = {2018}, author = {Allende-Prieto, C and Méndez-Fernández, BI and Sañudo-Fontaneda, LA and Charlesworth, SM}, title = {Development of a Geospatial Data-Based Methodology for Stormwater Management in Urban Areas Using Freely-Available Software.}, journal = {International journal of environmental research and public health}, volume = {15}, number = {8}, pages = {}, pmid = {30096916}, issn = {1660-4601}, mesh = {Cities ; City Planning/*methods ; Geographic Information Systems ; *Geographic Mapping ; Hydrology ; *Rain ; *Software ; Spain ; *Urbanization ; Water Movements ; }, abstract = {Intense urbanisation, combined with climate change impacts such as increased rainfall intensity, is overloading conventional drainage systems, increasing the number of combined sewer overflow events and making treatment plants outdated. There is a need for better urban planning, incorporating stormwater and flood management design in order to accurately design urban drainage networks. Geographic Information System (GIS) tools are capable of identifying and delineating the runoff flow direction, as well as accurately defining small-sized urban catchments using geospatial data. This study explores the synergies between GIS and stormwater management design tools for better land-use planning, providing a new methodology which has the potential to incorporate hydraulic and hydrological calculations into the design of urban areas. From data collection to final results, only freely available software and open platforms have been used: the U.S. EPA Storm Water Management Model (SWMM), QGis, PostgreSQL, PostGIS, SagaGIS, and GrassGIS. Each of these tools alone cannot provide all the necessary functionalities for large-scale projects, but once linked to GISWATER, a unique, fast, efficient, and accurate work methodology results. A case study of a newly urbanised area in the city of Gijón (northern Spain) has been utilised to apply this new methodology.}, } @article {pmid30096816, year = {2018}, author = {Liu, Y and Liu, Y and Li, J and Lu, W and Wei, X and Sun, C}, title = {Evolution of Landscape Ecological Risk at the Optimal Scale: A Case Study of the Open Coastal Wetlands in Jiangsu, China.}, journal = {International journal of environmental research and public health}, volume = {15}, number = {8}, pages = {}, pmid = {30096816}, issn = {1660-4601}, mesh = {China ; Conservation of Natural Resources/*methods ; Ecology ; Environmental Monitoring/*methods ; Geographic Information Systems ; Geological Phenomena ; Human Activities ; Humans ; Remote Sensing Technology ; Risk ; *Wetlands ; }, abstract = {Detailed analysis of the evolution characteristics of landscape ecological risk is crucial for coastal sustainable management and for understanding the potential environmental impacts of a man-made landform landscapes (MMLL). As a typical open coastal wetland, large-scale human activities (e.g., tidal reclamation, fishery activities, wind farm construction, and port construction) have substantially affected the evolution of the coastal ecological environment. Previous landscape ecological risk assessment studies have documented the effectiveness of assessing the quality of ecological environment processes. However, these studies have either focused on the noncoastal zone, or they have not considered the evolution of the spatial characteristics and ecological risk evolution of the landscape at an optimal scale. Here, we present a landscape ecological risk pattern (LERP) evolution model, based on two successive steps: first, we constructed an optimal scale method with an appropriate extent and grain using multi[-]temporal Landsat TM/OLI images acquired in the years 2000, 2004, 2008, 2013 and 2017, and then we calculated landscape ecological risk indices. Based on this model, the entire process of the spatiotemporal evolution of ecological risk patterns of the open coastal wetlands in Jiangsu, China, was determined. The principal findings are as follows: (1) The main landscape types in the study area are tidal flats and farmland, and the main features of the landscape evolution are a significant increase in aquafarming and a substantial decrease in the tidal flat area, while the landscape heterogeneity increased; (2) In the past 20 years, the areas of low and relatively low ecological risk in the study region were greatly reduced, while the areas of medium, relatively high, and high ecological risk greatly increased; the areas of high-grade ecological risk areas are mainly around Dongtai and Dafeng; (3) The area of ecological risk from low-grade to high-grade occupied 71.75% of the study area during 2000[-]2017. During the previous periods (2000[-]2004 and 2004[-]2008), the areas of low-grade ecological risk were transformed to areas of middle-grade ecological risk area, while during the later periods (2008[-]2013 and 2013[-]2017) there was a substantial increase in the proportion of areas of high-grade ecological risk. Our results complement the official database of coastal landscape planning, and provide important information for assessing the potential effects of MMLL processes on coastal environments.}, } @article {pmid30094953, year = {2019}, author = {Huggett, MJ and Apprill, A}, title = {Coral microbiome database: Integration of sequences reveals high diversity and relatedness of coral-associated microbes.}, journal = {Environmental microbiology reports}, volume = {11}, number = {3}, pages = {372-385}, pmid = {30094953}, issn = {1758-2229}, support = {OCE-1233612//NSF/International ; OCE-1736288//NSF/International ; //Edith Cowan University/International ; }, mesh = {Animals ; Anthozoa/*microbiology ; Archaea/classification/genetics ; Bacteria/classification/genetics ; Biodiversity ; Biological Evolution ; *Databases, Genetic ; Genes, rRNA/genetics ; Host Specificity ; Microbiota/*genetics ; Phylogeny ; }, abstract = {Coral-associated microorganisms are thought to play a fundamental role in the health and ecology of corals, but understanding of specific coral-microbial interactions are lacking. In order to create a framework to examine coral-microbial specificity, we integrated and phylogenetically compared 21,100 SSU rRNA gene Sanger-produced sequences from bacteria and archaea associated with corals from previous studies, and accompanying host, location and publication metadata, to produce the Coral Microbiome Database. From this database, we identified 39 described and candidate phyla of Bacteria and two Archaea phyla associated with corals, demonstrating that corals are one of the most phylogenetically diverse animal microbiomes. Secondly, this new phylogenetic resource shows that certain microorganisms are indeed specific to corals, including evolutionary distinct hosts. Specifically, we identified 2-37 putative monophyletic, coral-specific sequence clusters within bacterial genera associated with the greatest number of coral species (Vibrio, Endozoicomonas and Ruegeria) as well as functionally relevant microbial taxa ("Candidatus Amoebophilus", "Candidatus Nitrosopumilus" and under recognized cyanobacteria). This phylogenetic resource provides a framework for more targeted studies of corals and their specific microbial associates, which is timely given the escalated need to understand the role of the coral microbiome and its adaptability to changing ocean and reef conditions.}, } @article {pmid30093613, year = {2018}, author = {Albrecht, J and Classen, A and Vollstädt, MGR and Mayr, A and Mollel, NP and Schellenberger Costa, D and Dulle, HI and Fischer, M and Hemp, A and Howell, KM and Kleyer, M and Nauss, T and Peters, MK and Tschapka, M and Steffan-Dewenter, I and Böhning-Gaese, K and Schleuning, M}, title = {Plant and animal functional diversity drive mutualistic network assembly across an elevational gradient.}, journal = {Nature communications}, volume = {9}, number = {1}, pages = {3177}, pmid = {30093613}, issn = {2041-1723}, support = {For1246//Deutsche Forschungsgemeinschaft (German Research Foundation)/International ; FOR1246//Deutsche Forschungsgemeinschaft (German Research Foundation)/International ; FOR1246//Deutsche Forschungsgemeinschaft (German Research Foundation)/International ; FOR1246//Deutsche Forschungsgemeinschaft (German Research Foundation)/International ; FOR1246//Deutsche Forschungsgemeinschaft (German Research Foundation)/International ; FOR1246//Deutsche Forschungsgemeinschaft (German Research Foundation)/International ; FOR1246//Deutsche Forschungsgemeinschaft (German Research Foundation)/International ; FOR1246//Deutsche Forschungsgemeinschaft (German Research Foundation)/International ; FOR1246//Deutsche Forschungsgemeinschaft (German Research Foundation)/International ; FOR1246//Deutsche Forschungsgemeinschaft (German Research Foundation)/International ; FOR1246//Deutsche Forschungsgemeinschaft (German Research Foundation)/International ; FOR1246//Deutsche Forschungsgemeinschaft (German Research Foundation)/International ; FOR1246//Deutsche Forschungsgemeinschaft (German Research Foundation)/International ; FOR1246//Deutsche Forschungsgemeinschaft (German Research Foundation)/International ; }, mesh = {Altitude ; Animals ; Bayes Theorem ; *Biodiversity ; Birds/*physiology ; Climate ; *Ecosystem ; Feeding Behavior ; Flowers/*physiology ; Fruit ; Insecta/*physiology ; Phylogeny ; Plants ; Research Design ; Species Specificity ; *Symbiosis ; Tanzania ; }, abstract = {Species' functional traits set the blueprint for pair-wise interactions in ecological networks. Yet, it is unknown to what extent the functional diversity of plant and animal communities controls network assembly along environmental gradients in real-world ecosystems. Here we address this question with a unique dataset of mutualistic bird-fruit, bird-flower and insect-flower interaction networks and associated functional traits of 200 plant and 282 animal species sampled along broad climate and land-use gradients on Mt. Kilimanjaro. We show that plant functional diversity is mainly limited by precipitation, while animal functional diversity is primarily limited by temperature. Furthermore, shifts in plant and animal functional diversity along the elevational gradient control the niche breadth and partitioning of the respective other trophic level. These findings reveal that climatic constraints on the functional diversity of either plants or animals determine the relative importance of bottom-up and top-down control in plant-animal interaction networks.}, } @article {pmid30093419, year = {2018}, author = {Li, J and Levitan, B and Gomez-Jimenez, S and Kültz, D}, title = {Development of a Gill Assay Library for Ecological Proteomics of Threespine Sticklebacks (Gasterosteus aculeatus).}, journal = {Molecular & cellular proteomics : MCP}, volume = {17}, number = {11}, pages = {2146-2163}, pmid = {30093419}, issn = {1535-9484}, mesh = {Animals ; Fish Proteins/metabolism ; *Gene Library ; Gene Ontology ; Gills/*metabolism ; Proteome/metabolism ; Proteomics/*methods ; Reproducibility of Results ; Smegmamorpha/*metabolism ; }, abstract = {A data-independent acquisition (DIA) assay library for quantitative analyses of proteome dynamics has been developed for gills of threespine sticklebacks (Gasterosteus aculeatus). A raw spectral library was generated by data-dependent acquisition (DDA) and annotation of tryptic peptides to MSMS spectra and protein database identifiers. The assay library was constructed from the raw spectral library by removal of low-quality, ambiguous, and low-signal peptides. Only unique proteins represented by at least two peptides are included in the assay library, which consists of 1506 proteins, 5074 peptides, 5104 precursors, and 25,322 transitions. This assay library was used with DIA data to identify biochemical differences in gill proteomes of four populations representing different eco- and morpho-types of threespine sticklebacks. The assay library revealed unique and reproducible proteome signatures. Warm-adapted, low-plated, brackish-water fish from Laguna de la Bocana del Rosario (Mexico) show elevated HSP47, extracellular matrix, and innate immunity proteins whereas several immunoglobulins, interferon-induced proteins, ubiquitins, proteolytic enzymes, and nucleic acid remodeling proteins are reduced. Fully-plated, brackish-water fish from Westchester Lagoon (Alaska) display elevated ion regulation, GTPase signaling, and contractile cytoskeleton proteins, altered abundances of many ribosomal, calcium signaling and immunity proteins, and depleted transcriptional regulators and metabolic enzymes. Low-plated freshwater fish from Lake Solano (California) have elevated inflammasomes and proteolytic proteins whereas several iron containing and ion regulatory proteins are reduced. Gills of fully-plated, marine fish from Bodega Harbor (California) have elevated oxidative metabolism enzymes and reduced transglutaminase 2, collagens, and clathrin heavy chains. These distinct proteome signatures represent targets for testing ecological and evolutionary influences on molecular mechanisms of gill function in threespine sticklebacks. Furthermore, the gill assay library represents a model for other tissues and paves the way for accurate and reproducible network analyses of environmental context-dependent proteome dynamics in complex organisms.}, } @article {pmid30088464, year = {2018}, author = {Gil-Pulido, B and Tarpey, E and Finnegan, W and Zhan, X and Dobson, AD and O'Leary, N}, title = {Dominance of the genus Polaromonas in the microbial ecology of an Intermittently Aerated Sequencing Batch Reactor (IASBR) treating dairy processing wastewater under varying aeration rates.}, journal = {The Journal of dairy research}, volume = {85}, number = {3}, pages = {388-390}, doi = {10.1017/S0022029918000572}, pmid = {30088464}, issn = {1469-7629}, mesh = {Comamonadaceae/classification/isolation & purification/*physiology ; DNA, Bacterial/analysis ; *Dairy Products ; Food-Processing Industry/*methods ; Oxygen/*administration & dosage ; Sewage/microbiology ; Wastewater/*microbiology ; Water Purification/*instrumentation/methods ; }, abstract = {In this Research Communication we investigate potential correlations between key bacterial groups and nutrient removal efficiency in an Intermittently Aerated Sequencing Batch Reactor (IASBR) treating synthetic dairy processing wastewater. Reactor aeration rates of 0·6 and 0·4 litre per minute (LPM) were applied to an 8 l laboratory scale system and the relative impacts on IASBR microbial community structure and orthophosphate (PO4-P) and ammonium (NH4-N) removal efficiencies compared. Aeration at 0·6 LPM over several sludge retention times (SRTs) resulted in approximately 92% removal efficiencies for both PO4-P and NH4-N. Biomass samples subjected to next-generation sequencing (NGS), 16S rRNA profiling revealed a concomitant enrichment of Polaromonas under 0·6 LPM conditions, up to ~50% relative abundance within the reactor biomass. The subsequent shift in reactor aeration to 0·4 LPM, over a period of 3 SRTs, resulted in markedly reduced nutrient removal efficiencies for PO4-P (50%) and NH4-N (45%). An 85·7% reduction in the genus level relative abundance of Polaromonas was observed under 0·4 LPM aeration conditions over the same period.}, } @article {pmid30088318, year = {2018}, author = {Stoner, DC and Sexton, JO and Choate, DM and Nagol, J and Bernales, HH and Sims, SA and Ironside, KE and Longshore, KM and Edwards, TC}, title = {Climatically driven changes in primary production propagate through trophic levels.}, journal = {Global change biology}, volume = {24}, number = {10}, pages = {4453-4463}, doi = {10.1111/gcb.14364}, pmid = {30088318}, issn = {1365-2486}, support = {NNH10ZDA001N/NASA/NASA/United States ; W-65-M//Utah Division of Wildlife Resources/International ; W-170-R//Utah Division of Wildlife Resources/International ; //Utah Army National Guard/International ; //Kennecott Utah Copper Corporation/International ; //African Safari Club of Florida/International ; //Utah's Hogle Zoo/International ; //Utah Chapter of the American Association of Zoo Keepers, Cabela's, Sportsman's Warehouse/International ; //USGS Park-Oriented Biological Support Program/International ; //USGS Colorado Plateau Research Station/International ; //NPS Cooperative Conservation Initiative/International ; //Summerlee Foundation/International ; //Wilburforce Foundation/International ; //USGS Southwest Biological Science Center/International ; //USGS Western Ecological Science Center/International ; //USGS Fire Research Program/International ; //US Fish & Wildlife Service/International ; //Johnson Family Foundation/International ; //Department of Energy/International ; //Southern Nevada Public Lands Management Act/International ; //Arizona Game and Fish Department/International ; //USDA Wildlife Services/International ; //Grand Canyon Trust/International ; //Northern Arizona University/International ; }, mesh = {Animals ; *Climate Change ; Conservation of Natural Resources ; Deer/*physiology ; *Ecosystem ; Female ; Geographic Information Systems ; Homing Behavior ; Humans ; North America ; Plants ; Population Density ; Puma/*physiology ; Reproduction ; }, abstract = {Climate and land-use change are the major drivers of global biodiversity loss. Their effects are particularly acute for wide-ranging consumers, but little is known about how these factors interact to affect the abundance of large carnivores and their herbivore prey. We analyzed population densities of a primary and secondary consumer (mule deer, Odocoileus hemionus, and mountain lion, Puma concolor) across a climatic gradient in western North America by combining satellite-based maps of plant productivity with estimates of animal abundance and foraging area derived from Global Positioning Systems telemetry data (GPS). Mule deer density exhibited a positive, linear relationship with plant productivity (r[2] = 0.58), varying by a factor of 18 across the climate-vegetation gradient (range: 38-697 individuals/100 km[2]). Mountain lion home range size decreased in response to increasing primary productivity and consequent changes in the abundance of their herbivore prey (range: 20-450 km[2]). This pattern resulted in a strong, positive association between plant productivity and mountain lion density (r[2] = 0.67). Despite varying densities, the ratio of prey to predator remained constant across the climatic gradient (mean ± SE = 363 ± 29 mule deer/mountain lion), suggesting that the determinacy of the effect of primary productivity on consumer density was conserved across trophic levels. As droughts and longer term climate changes reduce the suitability of marginal habitats, consumer home ranges will expand in order for individuals to meet basic nutritional requirements. These changes portend decreases in the abundance of large-bodied, wide-ranging wildlife through climatically driven reductions in carrying capacity, as well as increased human-wildlife interactions stemming from anthropogenic land use and habitat fragmentation.}, } @article {pmid30087482, year = {2018}, author = {Gewin, V}, title = {Earth hacker.}, journal = {Nature}, volume = {560}, number = {7717}, pages = {273}, doi = {10.1038/d41586-018-05897-1}, pmid = {30087482}, issn = {1476-4687}, mesh = {Animals ; *Artificial Intelligence/economics ; *Big Data/economics ; Ecology/economics/*trends ; Endangered Species ; Financing, Organized/organization & administration ; Food Chain ; Human Activities ; Humans ; Satellite Imagery ; Sustainable Development/economics/*trends ; Technology/economics/*trends ; }, } @article {pmid30084019, year = {2018}, author = {Potgieter, LJ and Gaertner, M and Irlich, UM and O'Farrell, PJ and Stafford, L and Vogt, H and Richardson, DM}, title = {Managing Urban Plant Invasions: a Multi-Criteria Prioritization Approach.}, journal = {Environmental management}, volume = {62}, number = {6}, pages = {1168-1185}, pmid = {30084019}, issn = {1432-1009}, support = {85417//National Research Foundation/International ; }, mesh = {Agriculture ; Biodiversity ; Cities ; *Decision Support Techniques ; Ecology ; *Ecosystem ; Geographic Information Systems ; Introduced Species/*statistics & numerical data ; *Plant Development ; South Africa ; }, abstract = {Alien plant invasions in urban areas can have considerable impact on biodiversity and ecosystem services (ES). Managing urban plant invasions is particularly challenging given the complex interactions between ecological, economic and social elements that exist in the urban milieu. Strategic landscape-scale insights are crucial for guiding management, as are tactical site-scale perspectives to plan and coordinate control efforts on the ground. Integrating these requirements to enhance management efficiency is a major challenge. Decision-support models have considerable potential for guiding and informing management strategies when problems are complex. This study uses multi-criteria decision tools to develop a prioritization framework for managing invasive alien plants (IAPs) in urban areas at landscape and local scales. We used the Analytic Hierarchy Process (AHP; a multi-criteria decision support model) to develop and rank criteria for prioritising IAP management in the City of Cape Town (CoCT), South Africa. Located within a global biodiversity hotspot, Cape Town has a long history of alien plant introductions and a complex socio-political make-up, creating a useful system to explore the challenges associated with managing urban plant invasions. To guide the prioritization of areas for IAP management across the CoCT, a stakeholder workshop was held to identify a goal and criteria for consideration, and to assess the relative importance given to each criterion in IAP management. Workshop attendees were drawn from multiple disciplines involved with different aspects of IAP research and management: government departments, scientists and researchers, and managers with a diverse set of skills and interests. We selected spatial datasets and applied our multi-criteria decision analysis in a Geographic Information System (GIS) to develop a landscape-scale prioritization map. To address issues relevant in an urban setting, we also modified an existing IAP management framework to develop a tactical (site-level) prioritization scheme for guiding on-the-ground control operations. High-priority sites for IAP management were identified at landscape- and local scales across the study area. Factors related to safety and security emerged as pivotal features for setting spatially-explicit priorities for management. The approach applied in this study can be useful for managers in all urban settings to guide the selection and prioritization of areas for IAP management.}, } @article {pmid30083468, year = {2018}, author = {Macrander, J and Panda, J and Janies, D and Daly, M and Reitzel, AM}, title = {Venomix: a simple bioinformatic pipeline for identifying and characterizing toxin gene candidates from transcriptomic data.}, journal = {PeerJ}, volume = {6}, number = {}, pages = {e5361}, pmid = {30083468}, issn = {2167-8359}, abstract = {The advent of next-generation sequencing has resulted in transcriptome-based approaches to investigate functionally significant biological components in a variety of non-model organism. This has resulted in the area of "venomics": a rapidly growing field using combined transcriptomic and proteomic datasets to characterize toxin diversity in a variety of venomous taxa. Ultimately, the transcriptomic portion of these analyses follows very similar pathways after transcriptome assembly often including candidate toxin identification using BLAST, expression level screening, protein sequence alignment, gene tree reconstruction, and characterization of potential toxin function. Here we describe the Python package Venomix, which streamlines these processes using common bioinformatic tools along with ToxProt, a publicly available annotated database comprised of characterized venom proteins. In this study, we use the Venomix pipeline to characterize candidate venom diversity in four phylogenetically distinct organisms, a cone snail (Conidae; Conus sponsalis), a snake (Viperidae; Echis coloratus), an ant (Formicidae; Tetramorium bicarinatum), and a scorpion (Scorpionidae; Urodacus yaschenkoi). Data on these organisms were sampled from public databases, with each original analysis using different approaches for transcriptome assembly, toxin identification, or gene expression quantification. Venomix recovered numerically more candidate toxin transcripts for three of the four transcriptomes than the original analyses and identified new toxin candidates. In summary, we show that the Venomix package is a useful tool to identify and characterize the diversity of toxin-like transcripts derived from transcriptomic datasets. Venomix is available at: https://bitbucket.org/JasonMacrander/Venomix/.}, } @article {pmid30081949, year = {2018}, author = {Montassier, E and Al-Ghalith, GA and Hillmann, B and Viskocil, K and Kabage, AJ and McKinlay, CE and Sadowsky, MJ and Khoruts, A and Knights, D}, title = {CLOUD: a non-parametric detection test for microbiome outliers.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {137}, pmid = {30081949}, issn = {2049-2618}, mesh = {Bacteria/*classification ; Clostridioides difficile/pathogenicity ; Clostridium Infections/microbiology/*therapy ; Computational Biology/*methods ; Dysbiosis/*diagnosis ; Enterocolitis/microbiology/*therapy ; Fecal Microbiota Transplantation ; Gastrointestinal Microbiome ; Humans ; }, abstract = {BACKGROUND: Dysbiosis of the human gut microbiome is defined as a maladaptive or clinically relevant deviation of the community profile from the healthy or normal state. Dysbiosis has been implicated in an extensive set of metabolic, auto-immune, and infectious diseases, and yet there is substantial inter-individual variation in microbiome composition even within body sites of healthy humans. An individual's microbiome varies over time in a high-dimensional space to form their personal microbiome cloud. This cloud may or may not be similar to that of other people, both in terms of the average microbiome profile (conformity) and the diameter of the cloud (stability). However, there is currently no robust non-parametric test that determines whether a patient's microbiome cloud is an outlier with respect to a reference group of healthy individuals with widely varying microbiome profiles.

METHODS: Here, we propose a test for outliers' detection in the human gut microbiome that accounts for the wide range of microbiome phenotypes observed in a typical set of healthy individuals and for intra-individual temporal variation. Our robust nonparametric outlier detection test, the CLOUD test, performs two assessments of a patient's microbiome health: conformity, the extent to which the patient's microbiome cloud is ecologically similar to a subset of healthy subjects; and stability, which compares the cloud diameter of a patient to those of healthy subjects. The CLOUD test is based on locally linear embedded ecological distances, allowing it to account for widely varying microbiome compositions among reference individuals. It also leverages temporal variability within patients and reference individuals to increase the robustness of the test.

RESULTS: We describe the CLOUD test, and we apply it to one novel and two previously published cohorts of patients receiving fecal microbiota transplantation for recurrent Clostridium difficile colitis, as well as to two known healthy cohorts, demonstrating high concordance of the CLOUD conformity and stability indices with clinical outcomes.

CONCLUSIONS: Although the CLOUD test is not, on its own, a test for clinical dysbiosis, it nonetheless provides a framework for outlier testing that could be incorporated into evaluation of suspected dysbiosis, which may play a role in diagnosis and prognosis of numerous pediatric and adult diseases.}, } @article {pmid30078708, year = {2018}, author = {Atkinson, EG and Audesse, AJ and Palacios, JA and Bobo, DM and Webb, AE and Ramachandran, S and Henn, BM}, title = {No Evidence for Recent Selection at FOXP2 among Diverse Human Populations.}, journal = {Cell}, volume = {174}, number = {6}, pages = {1424-1435.e15}, pmid = {30078708}, issn = {1097-4172}, support = {K12 GM102778/GM/NIGMS NIH HHS/United States ; P20 GM109035/GM/NIGMS NIH HHS/United States ; R01 GM118652/GM/NIGMS NIH HHS/United States ; T32 MH020068/MH/NIMH NIH HHS/United States ; }, mesh = {Brain/cytology/metabolism ; Cell Line ; Databases, Genetic ; Exons ; Female ; Forkhead Transcription Factors/*genetics ; Genome, Human ; Haplotypes ; Humans ; Introns ; Male ; Markov Chains ; Polymorphism, Single Nucleotide ; Prefrontal Cortex/metabolism ; }, abstract = {FOXP2, initially identified for its role in human speech, contains two nonsynonymous substitutions derived in the human lineage. Evidence for a recent selective sweep in Homo sapiens, however, is at odds with the presence of these substitutions in archaic hominins. Here, we comprehensively reanalyze FOXP2 in hundreds of globally distributed genomes to test for recent selection. We do not find evidence of recent positive or balancing selection at FOXP2. Instead, the original signal appears to have been due to sample composition. Our tests do identify an intronic region that is enriched for highly conserved sites that are polymorphic among humans, compatible with a loss of function in humans. This region is lowly expressed in relevant tissue types that were tested via RNA-seq in human prefrontal cortex and RT-PCR in immortalized human brain cells. Our results represent a substantial revision to the adaptive history of FOXP2, a gene regarded as vital to human evolution.}, } @article {pmid30076986, year = {2018}, author = {Reiser, L and Harper, L and Freeling, M and Han, B and Luan, S}, title = {FAIR: A Call to Make Published Data More Findable, Accessible, Interoperable, and Reusable.}, journal = {Molecular plant}, volume = {11}, number = {9}, pages = {1105-1108}, doi = {10.1016/j.molp.2018.07.005}, pmid = {30076986}, issn = {1752-9867}, mesh = {Botany/*standards ; Databases, Factual/*standards ; Guidelines as Topic ; *Information Dissemination ; Manuscripts as Topic ; }, } @article {pmid30076910, year = {2018}, author = {Ellis, VA and Bensch, S}, title = {Host specificity of avian haemosporidian parasites is unrelated among sister lineages but shows phylogenetic signal across larger clades.}, journal = {International journal for parasitology}, volume = {48}, number = {12}, pages = {897-902}, doi = {10.1016/j.ijpara.2018.05.005}, pmid = {30076910}, issn = {1879-0135}, mesh = {Animals ; Birds/*parasitology ; Data Mining ; Databases, Factual ; Databases, Genetic ; Haemosporida/*classification/genetics/isolation & purification/*physiology ; *Host Specificity ; *Phylogeny ; }, abstract = {Parasites can vary in the number of host species they infect, a trait known as "host specificity". Here we quantify phylogenetic signal-the tendency for closely related species to resemble each other more than distantly related species-in host specificity of avian haemosporidian parasites (genera Plasmodium, Haemoproteus and Leucocytozoon) using data from MalAvi, the global avian haemosporidian database. We used the genetic data (479 base pairs of cytochrome b) that define parasite lineages to produce genus level phylogenies. Combining host specificity data with those phylogenies revealed significant levels of phylogenetic signal while controlling for sampling effects; phylogenetic signal was higher when the phylogenetic diversity of hosts was taken into account. We then tested for correlations in the host specificity of pairs of sister lineages. Correlations were generally close to zero for all three parasite genera. These results suggest that while the host specificity of parasite sister lineages differ, larger clades may be relatively specialised or generalised.}, } @article {pmid30076905, year = {2019}, author = {Tasian, GE and Ross, M and Song, L and Audrain-McGovern, J and Wiebe, D and Warner, SG and Henderson, B and Patel, A and Furth, SL}, title = {Ecological Momentary Assessment of Factors Associated with Water Intake among Adolescents with Kidney Stone Disease.}, journal = {The Journal of urology}, volume = {201}, number = {3}, pages = {606-614}, pmid = {30076905}, issn = {1527-3792}, support = {K23 DK106428/DK/NIDDK NIH HHS/United States ; K24 DK078737/DK/NIDDK NIH HHS/United States ; }, mesh = {Adolescent ; Adolescent Behavior ; Beverages ; Child ; *Drinking ; *Ecological Momentary Assessment ; Female ; Health Behavior ; Humans ; Kidney Calculi/*prevention & control/psychology ; Male ; }, abstract = {PURPOSE: Maintaining high water intake decreases kidney stone recurrence but is difficult to do. Strategies to reduce stone recurrence among adolescents are lacking. We conducted an ecological momentary assessment study to identify factors associated with water intake in adolescents with nephrolithiasis.

MATERIALS AND METHODS: The study population consisted of 15 female and 10 male patients 12 to 18 years old with at least 1 prior kidney stone. For 7 days participants used "smart" bottles to self-monitor water intake and received questionnaires randomly 4 times daily, which were completed in real time on mobile devices. The questionnaires ascertained awareness of water intake volume, awareness of water intake goals, perceived need to drink, access to water, alternative beverage consumption and attitudes toward bathrooms. Linear mixed effects models were fit to estimate the association between momentary responses and daily water intake.

RESULTS: During 175 person-days 595 assessments (85%) were completed. Median daily water intake was 1,304 ml (IQR 848-1,832) and 20% of participants met their intake goal for 4 days or more. Unawareness of water intake volume was associated with drinking 690 ml less water per day (p = 0.04). A strong self-perceived need to drink more was associated with drinking 1,954 ml less water each day compared to no self-perceived need to drink more (p <0.01). Unawareness of intake goals was weakly associated with drinking 1,129 ml less water each day (p = 0.1). Access to water, alternative beverage consumption and bathroom aversion were not associated with water intake.

CONCLUSIONS: Unawareness of water volume consumed and low responsiveness to perceived need to drink more were associated with low water intake. Interventions that help adolescents recognize when and identify how to increase water intake may be effective in decreasing stone recurrence.}, } @article {pmid30076195, year = {2018}, author = {Bellenberg, S and Buetti-Dinh, A and Galli, V and Ilie, O and Herold, M and Christel, S and Boretska, M and Pivkin, IV and Wilmes, P and Sand, W and Vera, M and Dopson, M}, title = {Automated Microscopic Analysis of Metal Sulfide Colonization by Acidophilic Microorganisms.}, journal = {Applied and environmental microbiology}, volume = {84}, number = {20}, pages = {}, pmid = {30076195}, issn = {1098-5336}, mesh = {Acidithiobacillus/metabolism ; Algorithms ; Automation, Laboratory/instrumentation/*methods ; Bacteria/*metabolism ; *Bacterial Adhesion ; Biofilms/growth & development ; Copper/metabolism ; Iron/metabolism ; Metals/*metabolism ; Microbial Consortia ; Microscopy/*methods ; Sulfides/*metabolism ; Sulfur/metabolism ; }, abstract = {Industrial biomining processes are currently focused on metal sulfides and their dissolution, which is catalyzed by acidophilic iron(II)- and/or sulfur-oxidizing microorganisms. Cell attachment on metal sulfides is important for this process. Biofilm formation is necessary for seeding and persistence of the active microbial community in industrial biomining heaps and tank reactors, and it enhances metal release. In this study, we used a method for direct quantification of the mineral-attached cell population on pyrite or chalcopyrite particles in bioleaching experiments by coupling high-throughput, automated epifluorescence microscopy imaging of mineral particles with algorithms for image analysis and cell quantification, thus avoiding human bias in cell counting. The method was validated by quantifying cell attachment on pyrite and chalcopyrite surfaces with axenic cultures of Acidithiobacillus caldus, Leptospirillum ferriphilum, and Sulfobacillus thermosulfidooxidans. The method confirmed the high affinity of L. ferriphilum cells to colonize pyrite and chalcopyrite surfaces and indicated that biofilm dispersal occurs in mature pyrite batch cultures of this species. Deep neural networks were also applied to analyze biofilms of different microbial consortia. Recent analysis of the L. ferriphilum genome revealed the presence of a diffusible soluble factor (DSF) family quorum sensing system. The respective signal compounds are known as biofilm dispersal agents. Biofilm dispersal was confirmed to occur in batch cultures of L. ferriphilum and S. thermosulfidooxidans upon the addition of DSF family signal compounds.IMPORTANCE The presented method for the assessment of mineral colonization allows accurate relative comparisons of the microbial colonization of metal sulfide concentrate particles in a time-resolved manner. Quantitative assessment of the mineral colonization development is important for the compilation of improved mathematical models for metal sulfide dissolution. In addition, deep-learning algorithms proved that axenic or mixed cultures of the three species exhibited characteristic biofilm patterns and predicted the biofilm species composition. The method may be extended to the assessment of microbial colonization on other solid particles and may serve in the optimization of bioleaching processes in laboratory scale experiments with industrially relevant metal sulfide concentrates. Furthermore, the method was used to demonstrate that DSF quorum sensing signals directly influence colonization and dissolution of metal sulfides by mineral-oxidizing bacteria, such as L. ferriphilum and S. thermosulfidooxidans.}, } @article {pmid30072227, year = {2018}, author = {Ramirez, KS and Geisen, S and Morriën, E and Snoek, BL and van der Putten, WH}, title = {Network Analyses Can Advance Above-Belowground Ecology.}, journal = {Trends in plant science}, volume = {23}, number = {9}, pages = {759-768}, doi = {10.1016/j.tplants.2018.06.009}, pmid = {30072227}, issn = {1878-4372}, mesh = {Big Data ; Biodiversity ; Correlation of Data ; *Ecology ; *Ecosystem ; Plant Components, Aerial/*physiology ; *Plant Physiological Phenomena ; Plant Roots/physiology ; *Plants ; }, abstract = {An understanding of above-belowground (AG-BG) ecology is important for evaluating how plant interactions with enemies, symbionts, and decomposers affect species diversity and will respond to global changes. However, research questions and experiments often focus on only a limited number of interactions, creating an incomplete picture of how entire communities may be involved in AG-BG community ecology. Therefore, a pressing challenge is to formulate hypotheses of AG-BG interactions when considering communities in their full complexity. Here we discuss how network analyses can be a powerful tool to progress AG-BG research, link across scales from individual to community and ecosystem, visualize community interactions between the two (AG and BG) subsystems, and develop testable hypotheses.}, } @article {pmid30071675, year = {2018}, author = {Kim, D and Seo, S and Min, S and Simoni, Z and Kim, S and Kim, M}, title = {A Closer Look at the Bivariate Association between Ambient Air Pollution and Allergic Diseases: The Role of Spatial Analysis.}, journal = {International journal of environmental research and public health}, volume = {15}, number = {8}, pages = {}, pmid = {30071675}, issn = {1660-4601}, mesh = {Air Pollutants/analysis ; Air Pollution/*adverse effects/analysis ; Asthma/epidemiology ; Female ; Geographic Information Systems ; Humans ; Hypersensitivity/*epidemiology/*etiology ; Prevalence ; Rhinitis, Allergic/epidemiology ; Seoul/epidemiology ; Spatial Analysis ; }, abstract = {Although previous ecological studies investigating the association between air pollution and allergic diseases accounted for temporal or seasonal relationships, few studies address spatial non-stationarity or autocorrelation explicitly. Our objective was to examine bivariate correlation between outdoor air pollutants and the prevalence of allergic diseases, highlighting the limitation of a non-spatial correlation measure, and suggesting an alternative to address spatial autocorrelation. The 5-year prevalence data (2011[-]2015) of allergic rhinitis, atopic dermatitis, and asthma were integrated with the measures of four major air pollutants (SO2, NO2, CO, and PM10) for each of the 423 sub-districts of Seoul. Lee's L statistics, which captures how much bivariate associations are spatially clustered, was calculated and compared with Pearson's correlation coefficient for each pair of the air pollutants and allergic diseases. A series of maps showing spatiotemporal patterns of allergic diseases at the sub-district level reveals a substantial degree of spatial heterogeneity. A high spatial autocorrelation was observed for all pollutants and diseases, leading to significant dissimilarities between the two bivariate association measures. The local L statistics identifies the areas where a specific air pollutant is considered to be contributing to a type of allergic disease. This study suggests that a bivariate correlation measure between air pollutants and allergic diseases should capture spatially-clustered phenomenon of the association, and detect the local instability in their relationships. It highlights the role of spatial analysis in investigating the contribution of the local-level spatiotemporal dynamics of air pollution to trends and the distribution of allergic diseases.}, } @article {pmid30071007, year = {2018}, author = {Zhang, P and Rhodes, JS and Garland, T and Perez, SD and Southey, BR and Rodriguez-Zas, SL}, title = {Brain region-dependent gene networks associated with selective breeding for increased voluntary wheel-running behavior.}, journal = {PloS one}, volume = {13}, number = {8}, pages = {e0201773}, pmid = {30071007}, issn = {1932-6203}, support = {P30 DA018310/DA/NIDA NIH HHS/United States ; R21 MH096030/MH/NIMH NIH HHS/United States ; }, mesh = {Animals ; Behavior, Addictive/genetics/metabolism ; Cerebellum/*metabolism ; Corpus Striatum/*metabolism ; Gene Expression ; *Gene Regulatory Networks ; Male ; Mice, Inbred Strains ; Reward ; Running/*physiology/psychology ; *Selective Breeding ; Species Specificity ; *Transcriptome/genetics/physiology ; Volition ; }, abstract = {Mouse lines selectively bred for high voluntary wheel-running behavior are helpful models for uncovering gene networks associated with increased motivation for physical activity and other reward-dependent behaviors. The fact that multiple brain regions are hypothesized to contribute to distinct behavior components necessitates the simultaneous study of these regions. The goals of this study were to identify brain-region dependent and independent gene expression patterns, regulators, and networks associated with increased voluntary wheel-running behavior. The cerebellum and striatum from a high voluntary running line and a non-selected control line were compared. Neuropeptide genes annotated to reward-dependent processes including neuropeptide S receptor 1 (Npsr1), neuropeptide Y (Npy), and proprotein convertase subtilisin/kexin type 9 (Pcsk9), and genes implicated in motor coordination including vitamin D receptor (Vdr) and keratin, type I cytoskeletal 25 (Krt25) were among the genes exhibiting activity line-by-region interaction effects. Genes annotated to the Parkinson pathway presented consistent line patterns, albeit at different orders of magnitude between brain regions, suggesting some parallel events in response to selection for high voluntary activity. The comparison of gene networks between brain regions highlighted genes including transcription factor AP-2-delta (Tfap2d), distal-less homeobox 5 gene (Dlx5) and sine oculis homeobox homolog 3 (Six3) that exhibited line differential expression in one brain region and are associated with reward-dependent behaviors. Transcription factors including En2, Stat6 and Eomes predominated among regulators of genes that differed in expression between lines. Results from the simultaneous study of striatum and cerebellum confirm the necessity to study molecular mechanisms associated with voluntary activity and reward-dependent behaviors in consideration of brain region dependencies.}, } @article {pmid30069646, year = {2019}, author = {Duong, MH and Tran, HM and Han, TA}, title = {On the distribution of the number of internal equilibria in random evolutionary games.}, journal = {Journal of mathematical biology}, volume = {78}, number = {1-2}, pages = {331-371}, pmid = {30069646}, issn = {1432-1416}, mesh = {Algorithms ; *Biological Evolution ; Computational Biology ; Computer Simulation ; *Game Theory ; Humans ; Mathematical Concepts ; *Models, Biological ; Probability ; }, abstract = {The analysis of equilibrium points is of great importance in evolutionary game theory with numerous practical ramifications in ecology, population genetics, social sciences, economics and computer science. In contrast to previous analytical approaches which primarily focus on computing the expected number of internal equilibria, in this paper we study the distribution of the number of internal equilibria in a multi-player two-strategy random evolutionary game. We derive for the first time a closed formula for the probability that the game has a certain number of internal equilibria, for both normal and uniform distributions of the game payoff entries. In addition, using Descartes' rule of signs and combinatorial methods, we provide several universal upper and lower bound estimates for this probability, which are independent of the underlying payoff distribution. We also compare our analytical results with those obtained from extensive numerical simulations. Many results of this paper are applicable to a wider class of random polynomials that are not necessarily from evolutionary games.}, } @article {pmid30067749, year = {2018}, author = {Kavanagh, L and Galbraith, E}, title = {Links between fish abundance and ocean biogeochemistry as recorded in marine sediments.}, journal = {PloS one}, volume = {13}, number = {8}, pages = {e0199420}, pmid = {30067749}, issn = {1932-6203}, mesh = {Animals ; Carbon/metabolism ; Carbon Cycle ; Databases, Factual ; Ecosystem ; Fishes/*physiology ; Geologic Sediments/*chemistry ; Oceans and Seas ; Phytoplankton/growth & development ; }, abstract = {Fish populations are linked to ocean biogeochemistry by their reliance on primary production for food, and dissolved oxygen to breathe. It is also possible that marine fish modify biogeochemical dynamics, as do freshwater fish, through top-down trophic cascades, but there has been relatively little consideration of this possibility. This lack of consideration may reflect a lack of importance; alternatively, it may simply reflect the lack of appropriate observations with which to constrain such relationships. Here, we draw attention to the potential use of marine sediments as long-term simultaneous monitors of both fish abundance and marine biogeochemical dynamics. We compile published sediment proxy records of fish abundance from the west coasts of the Americas, and compare them with biogeochemical proxy measurements made at the same sites. Despite the challenges of using sediment records and the potential convolution of ecological and climatic signals, we find a small number of statistically significant relationships between fish debris and biogeochemical variables, at least some of which are likely to reflect causal relationships. Considering TOC, the most commonly-measured biogeochemical variable, some positive correlations with fish abundance are found, consistent with bottom-up control of fish abundance by primary production, or a planktivore-herbivore-phytoplankton trophic cascade. Negative correlations are also found, which could reflect sedimentary processes, the influence of upwelling-driven oxygen and nutrient dynamics on primary production and fish populations, and/or impacts of fish stocks on carbon fluxes by altering the recycling of carbon within the water column. Although the number of available measurements is too small to draw strong conclusions, the results point to plausible cases of bottom-up forcing, trophic cascades, and influence of dissolved oxygen concentrations on fish habitat.}, } @article {pmid30066225, year = {2018}, author = {Zadbagher, E and Becek, K and Berberoglu, S}, title = {Modeling land use/land cover change using remote sensing and geographic information systems: case study of the Seyhan Basin, Turkey.}, journal = {Environmental monitoring and assessment}, volume = {190}, number = {8}, pages = {494}, pmid = {30066225}, issn = {1573-2959}, mesh = {Agriculture/methods ; Biodiversity ; Climate ; Conservation of Natural Resources/methods ; Environmental Monitoring/*methods ; Forests ; *Geographic Information Systems ; Hydrology ; *Models, Theoretical ; Remote Sensing Technology/*methods ; Soil ; Turkey ; }, abstract = {Land use and land cover (LULC) changes affect several natural environmental factors, including soil erosion, hydrological balance, biodiversity, and the climate, which ultimately impact societal well-being. Therefore, LULC changes are an important aspect of land management. One method used to analyze LULC changes is the mathematical modeling approach. In this study, Cellular Automata and Markov Chain (CA-MC) models were used to predict the LULC changes in the Seyhan Basin in Turkey that are likely to occur by 2036. Satellite multispectral imagery acquired in the years 1995, 2006, and 2016 were classified using the object-based classification method and used as the input data for the CA-MC model. Subsequently, the post-classification comparison technique was used to determine the parameters of the model to be simulated. The Markov Chain analyses and the multi-criteria evaluation (MCE) method were used to produce a transition probability matrix and land suitability maps, respectively. The model was validated using the Kappa index, which reached an overall level of 77%. Finally, the LULC changes were mapped for the year 2036 based on transition rules and a transition area matrix. The LULC prediction for the year 2036 showed a 50% increase in the built-up area class and a 7% decrease in the open spaces class compared to the LULC status of the reference year 2016. About an 8% increase in agricultural land is also likely to occur in 2036. About a 4% increase in shrub land and a 5% decrease in forest areas are also predicted.}, } @article {pmid30066019, year = {2018}, author = {Baumann, K and Dashevsky, D and Sunagar, K and Fry, B}, title = {Scratching the Surface of an Itch: Molecular Evolution of Aculeata Venom Allergens.}, journal = {Journal of molecular evolution}, volume = {86}, number = {7}, pages = {484-500}, pmid = {30066019}, issn = {1432-1432}, mesh = {Allergens/immunology ; Animals ; Databases, Genetic ; Evolution, Molecular ; Hymenoptera/*genetics/*metabolism ; Phylogeny ; Venoms/*genetics/immunology ; }, abstract = {Hymenopteran insects are infamous for their sting, and their ability to cause severe anaphylaxis and in some cases death. This allergic reaction is a result of allergens present in the venom. Hymenopterans have many common venom allergens, the most widespread of which include phospholipase A1, phospholipase A2, acid phosphatase, hyaluronidase, serine protease and antigen 5. While there have been studies that look at the phylogenetic histories of allergens within closely related species, to our knowledge, this is the first study using evolutionary analyses to compare across Hymenoptera the types of selection that are occurring on allergens. This research examined the publicly available sequences of six different groups of allergens and found that allergens had diverged and formed closely related clades which share greater sequence similarities. We also analysed the patterns of selection and found that they are predominately under the influence of negative selection.}, } @article {pmid30063710, year = {2018}, author = {Fischer, M and Parkins, K and Maizels, K and Sutherland, DR and Allan, BM and Coulson, G and Di Stefano, J}, title = {Biotelemetry marches on: A cost-effective GPS device for monitoring terrestrial wildlife.}, journal = {PloS one}, volume = {13}, number = {7}, pages = {e0199617}, pmid = {30063710}, issn = {1932-6203}, mesh = {Animals ; *Animals, Wild ; Australia ; Cost-Benefit Analysis ; *Geographic Information Systems ; Geography ; Telemetry/*methods ; }, abstract = {The availability of low-cost wildlife trackers increases the capacity to collect valuable ecological data when research budgets are limited. We converted a commercially available global positioning system (GPS) product into a low-cost tracking device that sends data via the mobile phone network, and assessed its performance under varying conditions. We established a stationary test, deploying devices along a continuum from open urban areas to topographically and structurally complex forested sites. We tested three features of the device: (a) the GPS, by measuring fix success rate, fix precision and horizontal dilution of precision (HDOP), (b) remote download capacity via the mobile phone network and (c) battery drain. Measures of GPS performance demonstrated high fix success rates and precision. HDOP values were influenced by habitat type and topographical position, but generally remained very low, giving an acceptable degree of error for most applications in wildlife research. Devices experienced delayed data transmission at sites with less phone reception, and faster battery drain at sites with denser vegetation. We recorded device malfunctions in 8.2% of the 110 sampling locations, but these were not associated with habitat type or topography. Our device was effective under a wide range of conditions, and the development process we used provides guidance to other researchers aiming to develop cost-effective wildlife trackers. Reducing the financial and labour costs of acquiring high-quality movement data will improve the capacity to increase sample size in animal movement studies.}, } @article {pmid30061811, year = {2018}, author = {Amaral, C and Mouga, S and Simões, M and Pereira, HC and Bernardino, I and Quental, H and Playle, R and McNamara, R and Oliveira, G and Castelo-Branco, M}, title = {A Feasibility Clinical Trial to Improve Social Attention in Autistic Spectrum Disorder (ASD) Using a Brain Computer Interface.}, journal = {Frontiers in neuroscience}, volume = {12}, number = {}, pages = {477}, pmid = {30061811}, issn = {1662-4548}, abstract = {Deficits in the interpretation of others' intentions from gaze-direction or other social attention cues are well-recognized in ASD. Here we investigated whether an EEG brain computer interface (BCI) can be used to train social cognition skills in ASD patients. We performed a single-arm feasibility clinical trial and enrolled 15 participants (mean age 22y 2m) with high-functioning ASD (mean full-scale IQ 103). Participants were submitted to a BCI training paradigm using a virtual reality interface over seven sessions spread over 4 months. The first four sessions occurred weekly, and the remainder monthly. In each session, the subject was asked to identify objects of interest based on the gaze direction of an avatar. Attentional responses were extracted from the EEG P300 component. A final follow-up assessment was performed 6-months after the last session. To analyze responses to joint attention cues participants were assessed pre and post intervention and in the follow-up, using an ecologic "Joint-attention task." We used eye-tracking to identify the number of social attention items that a patient could accurately identify from an avatar's action cues (e.g., looking, pointing at). As secondary outcome measures we used the Autism Treatment Evaluation Checklist (ATEC) and the Vineland Adaptive Behavior Scale (VABS). Neuropsychological measures related to mood and depression were also assessed. In sum, we observed a decrease in total ATEC and rated autism symptoms (Sociability; Sensory/Cognitive Awareness; Health/Physical/Behavior); an evident improvement in Adapted Behavior Composite and in the DLS subarea from VABS; a decrease in Depression (from POMS) and in mood disturbance/depression (BDI). BCI online performance and tolerance were stable along the intervention. Average P300 amplitude and alpha power were also preserved across sessions. We have demonstrated the feasibility of BCI in this kind of intervention in ASD. Participants engage successfully and consistently in the task. Although the primary outcome (rate of automatic responses to joint attention cues) did not show changes, most secondary neuropsychological outcome measures showed improvement, yielding promise for a future efficacy trial. (clinical-trial ID: NCT02445625-clinicaltrials.gov).}, } @article {pmid30061690, year = {2018}, author = {Horsthemke, B}, title = {A critical view on transgenerational epigenetic inheritance in humans.}, journal = {Nature communications}, volume = {9}, number = {1}, pages = {2973}, pmid = {30061690}, issn = {2041-1723}, mesh = {Animals ; Biological Evolution ; Culture ; *DNA Methylation ; Databases, Genetic ; Drosophila ; Ecology ; *Epigenesis, Genetic ; Gene-Environment Interaction ; Germ Cells ; Humans ; *Inheritance Patterns ; Models, Genetic ; Mutation ; Nematoda ; Phenotype ; Plants/genetics ; Proteome ; Proteomics ; }, abstract = {Transgenerational epigenetic inheritance refers to the transmission of epigenetic information through the germline. While it has been observed in plants, nematodes and fruit flies, its occurrence in mammals-and humans in particular-is the matter of controversial debate, mostly because the study of transgenerational epigenetic inheritance is confounded by genetic, ecological and cultural inheritance. In this comment, I discuss the phenomenon of transgenerational epigenetic inheritance and the difficulty of providing conclusive proof for it in experimental and observational studies.}, } @article {pmid30061657, year = {2018}, author = {Butler, S and O'Dwyer, JP}, title = {Stability criteria for complex microbial communities.}, journal = {Nature communications}, volume = {9}, number = {1}, pages = {2970}, pmid = {30061657}, issn = {2041-1723}, mesh = {Algorithms ; Computational Biology ; *Ecology ; *Microbiota ; Models, Biological ; Software ; *Symbiosis ; }, abstract = {Competition and mutualism are inevitable processes in microbial ecology, and a central question is which and how many taxa will persist in the face of these interactions. Ecological theory has demonstrated that when direct, pairwise interactions among a group of species are too numerous, or too strong, then the coexistence of these species will be unstable to any slight perturbation. Here, we refine and to some extent overturn that understanding, by considering explicitly the resources that microbes consume and produce. In contrast to more complex organisms, microbial cells consume primarily abiotic resources, and mutualistic interactions are often mediated through the mechanism of crossfeeding. We show that if microbes consume, but do not produce resources, then any positive equilibrium will always be stable to small perturbations. We go on to show that in the presence of crossfeeding, stability is no longer guaranteed. However, positive equilibria remain stable whenever mutualistic interactions are either sufficiently weak, or when all pairs of taxa reciprocate each other's assistance.}, } @article {pmid30061425, year = {2018}, author = {Hivert, V and Leblois, R and Petit, EJ and Gautier, M and Vitalis, R}, title = {Measuring Genetic Differentiation from Pool-seq Data.}, journal = {Genetics}, volume = {210}, number = {1}, pages = {315-330}, pmid = {30061425}, issn = {1943-2631}, mesh = {Alleles ; Computer Simulation ; DNA/genetics ; Databases, Genetic ; Gene Frequency/genetics ; Genetic Variation/*genetics ; Genomics ; Genotype ; High-Throughput Nucleotide Sequencing ; Polymorphism, Single Nucleotide/genetics ; Sequence Analysis, DNA/*methods/*statistics & numerical data ; }, abstract = {The advent of high throughput sequencing and genotyping technologies enables the comparison of patterns of polymorphisms at a very large number of markers. While the characterization of genetic structure from individual sequencing data remains expensive for many nonmodel species, it has been shown that sequencing pools of individual DNAs (Pool-seq) represents an attractive and cost-effective alternative. However, analyzing sequence read counts from a DNA pool instead of individual genotypes raises statistical challenges in deriving correct estimates of genetic differentiation. In this article, we provide a method-of-moments estimator of [Formula: see text] for Pool-seq data, based on an analysis-of-variance framework. We show, by means of simulations, that this new estimator is unbiased and outperforms previously proposed estimators. We evaluate the robustness of our estimator to model misspecification, such as sequencing errors and uneven contributions of individual DNAs to the pools. Finally, by reanalyzing published Pool-seq data of different ecotypes of the prickly sculpin Cottus asper, we show how the use of an unbiased [Formula: see text] estimator may question the interpretation of population structure inferred from previous analyses.}, } @article {pmid30060454, year = {2018}, author = {Zhang, X and Zhou, L and Liu, Y}, title = {Modeling Land Use Changes and their Impacts on Non-Point Source Pollution in a Southeast China Coastal Watershed.}, journal = {International journal of environmental research and public health}, volume = {15}, number = {8}, pages = {}, pmid = {30060454}, issn = {1660-4601}, mesh = {China ; Environmental Monitoring ; Forests ; Geographic Information Systems ; *Models, Theoretical ; Non-Point Source Pollution/*analysis ; Rivers ; }, abstract = {Changes in landscape patterns in a river basin play a crucial role in the change on load of non-point source pollution. The spatial distribution of various land use types affects the transmission of non-point source pollutants on the basis of source-sink theory in landscape ecology. Jiulong River basin in southeast of China was selected as the study area in this paper. Aiming to analyze the correlation between changing landscape patterns and load of non-point source pollution in this area, traditional landscape metrics and the improved location-weighted landscape contrast index based on the minimum hydrological response unit (HRULCI) were applied in this study, in combination with remote sensing and geographic information system (GIS) technique. The results of the landscape metrics showed the enhanced fragmentation extent and the decreasing polymerization degree of the overall landscape in the watershed. High values of HRULCI were concentrated in cultivated land, while low HRULCI values mostly appeared in forestland, indicating that cultivated land substantially enhanced non-point source pollution, while forestland inhibited the pollution process.}, } @article {pmid30060110, year = {2018}, author = {Doering, JA and Lee, S and Kristiansen, K and Evenseth, L and Barron, MG and Sylte, I and LaLone, CA}, title = {In Silico Site-Directed Mutagenesis Informs Species-Specific Predictions of Chemical Susceptibility Derived From the Sequence Alignment to Predict Across Species Susceptibility (SeqAPASS) Tool.}, journal = {Toxicological sciences : an official journal of the Society of Toxicology}, volume = {166}, number = {1}, pages = {131-145}, pmid = {30060110}, issn = {1096-0929}, support = {EPA999999//Intramural EPA/United States ; }, mesh = {Acetylcholinesterase/*genetics ; Amino Acid Sequence ; Amino Acids/*genetics ; Animals ; Computational Biology/*methods ; Computer Simulation ; Hazardous Substances/toxicity ; Humans ; Molecular Docking Simulation ; *Mutagenesis, Site-Directed ; Receptors, Steroid/*genetics ; Sequence Alignment ; Species Specificity ; Toxicity Tests/*methods ; }, abstract = {Chemical hazard assessment requires extrapolation of information from model organisms to all species of concern. The Sequence Alignment to Predict Across Species Susceptibility (SeqAPASS) tool was developed as a rapid, cost-effective method to aid cross-species extrapolation of susceptibility to chemicals acting on specific protein targets through evaluation of protein structural similarities and differences. The greatest resolution for extrapolation of chemical susceptibility across species involves comparisons of individual amino acid residues at key positions involved in protein-chemical interactions. However, a lack of understanding of whether specific amino acid substitutions among species at key positions in proteins affect interaction with chemicals made manual interpretation of alignments time consuming and potentially inconsistent. Therefore, this study used in silico site-directed mutagenesis coupled with docking simulations of computational models for acetylcholinesterase (AChE) and ecdysone receptor (EcR) to investigate how specific amino acid substitutions impact protein-chemical interaction. This study found that computationally derived substitutions in identities of key amino acids caused no change in protein-chemical interaction if residues share the same side chain functional properties and have comparable molecular dimensions, while differences in these characteristics can change protein-chemical interaction. These findings were considered in the development of capabilities for automatically generated species-specific predictions of chemical susceptibility in SeqAPASS. These predictions for AChE and EcR were shown to agree with SeqAPASS predictions comparing the primary sequence and functional domain sequence of proteins for more than 90% of the investigated species, but also identified dramatic species-specific differences in chemical susceptibility that align with results from standard toxicity tests. These results provide a compelling line of evidence for use of SeqAPASS in deriving screening level, species-specific, susceptibility predictions across broad taxonomic groups for application to human and ecological hazard assessment.}, } @article {pmid30055354, year = {2018}, author = {Linard, B and Crampton-Platt, A and Moriniere, J and Timmermans, MJTN and Andújar, C and Arribas, P and Miller, KE and Lipecki, J and Favreau, E and Hunter, A and Gómez-Rodríguez, C and Barton, C and Nie, R and Gillett, CPDT and Breeschoten, T and Bocak, L and Vogler, AP}, title = {The contribution of mitochondrial metagenomics to large-scale data mining and phylogenetic analysis of Coleoptera.}, journal = {Molecular phylogenetics and evolution}, volume = {128}, number = {}, pages = {1-11}, doi = {10.1016/j.ympev.2018.07.008}, pmid = {30055354}, issn = {1095-9513}, mesh = {Algorithms ; Animals ; Base Sequence ; Coleoptera/classification/*genetics ; Databases, Genetic ; *Metagenomics ; Mitochondria/*genetics ; *Phylogeny ; }, abstract = {A phylogenetic tree at the species level is still far off for highly diverse insect orders, including the Coleoptera, but the taxonomic breadth of public sequence databases is growing. In addition, new types of data may contribute to increasing taxon coverage, such as metagenomic shotgun sequencing for assembly of mitogenomes from bulk specimen samples. The current study explores the application of these techniques for large-scale efforts to build the tree of Coleoptera. We used shotgun data from 17 different ecological and taxonomic datasets (5 unpublished) to assemble a total of 1942 mitogenome contigs of >3000 bp. These sequences were combined into a single dataset together with all mitochondrial data available at GenBank, in addition to nuclear markers widely used in molecular phylogenetics. The resulting matrix of nearly 16,000 species with two or more loci produced trees (RAxML) showing overall congruence with the Linnaean taxonomy at hierarchical levels from suborders to genera. We tested the role of full-length mitogenomes in stabilizing the tree from GenBank data, as mitogenomes might link terminals with non-overlapping gene representation. However, the mitogenome data were only partly useful in this respect, presumably because of the purely automated approach to assembly and gene delimitation, but improvements in future may be possible by using multiple assemblers and manual curation. In conclusion, the combination of data mining and metagenomic sequencing of bulk samples provided the largest phylogenetic tree of Coleoptera to date, which represents a summary of existing phylogenetic knowledge and a defensible tree of great utility, in particular for studies at the intra-familial level, despite some shortcomings for resolving basal nodes.}, } @article {pmid30054764, year = {2018}, author = {Venturini, C and Ginn, AN and Wilson, BE and Tsafnat, G and Paulsen, I and Partridge, SR and Iredell, JR}, title = {Ecological effects of cefepime use during antibiotic cycling on the Gram-negative enteric flora of ICU patients.}, journal = {Intensive care medicine experimental}, volume = {6}, number = {1}, pages = {19}, pmid = {30054764}, issn = {2197-425X}, support = {NHMRC_1001020//National Health and Medical Research Council/ ; NHMRC_1046889//National Health and Medical Research Council/ ; }, abstract = {This study examines the impact of cefepime and APP-β (antipseudomonal penicillin/ β-lactamase inhibitor combinations) on Gram-negative bacterial colonization and resistance in two Australian ICUs. While resistance did not cumulatively increase, cefepime (but not APP-β treatment) was associated with acquisition of antibiotic resistant Enterobacteriaceae, consistent with an ecological effect. Analysis of the resident gut E. coli population in a subset of patients showed an increase in markers of horizontal gene transfer after cefepime exposure that helps explain the increase in APP-β resistance and reminds us that unmeasured impacts on the microbiome are key outcome determinants that need to be fully explored.}, } @article {pmid30054531, year = {2018}, author = {Simões, T and Novais, SC and Natal-da-Luz, T and Devreese, B and de Boer, T and Roelofs, D and Sousa, JP and van Straalen, NM and Lemos, MFL}, title = {An integrative omics approach to unravel toxicity mechanisms of environmental chemicals: effects of a formulated herbicide.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {11376}, pmid = {30054531}, issn = {2045-2322}, support = {SFRH/BPD/94500/2013//Ministry of Education and Science | Fundação para a Ciência e a Tecnologia (Portuguese Science and Technology Foundation)/International ; SFRH/BPD/110943/2015//Ministry of Education and Science | Fundação para a Ciência e a Tecnologia (Portuguese Science and Technology Foundation)/International ; PTDC/AGR-PRO/3496/2012//Ministry of Education and Science | Fundação para a Ciência e a Tecnologia (Portuguese Science and Technology Foundation)/International ; UID/MAR/04292/2013//Ministry of Education and Science | Fundação para a Ciência e a Tecnologia (Portuguese Science and Technology Foundation)/International ; 604305//EC | Seventh Framework Programme (European Union Seventh Framework Programme)/International ; }, mesh = {Animals ; Arthropods/drug effects/genetics ; Environmental Pollutants/*toxicity ; Gene Expression Regulation/drug effects ; Gene Ontology ; Gene Regulatory Networks/drug effects ; Genomics/*methods ; Herbicides/*toxicity ; RNA, Messenger/genetics/metabolism ; Reproduction/drug effects ; Survival Analysis ; *Toxicity Tests ; Transcriptome/genetics ; }, abstract = {The use of integrative molecular approaches can aid in a comprehensive understanding of the effects of toxicants at different levels of biological organization, also supporting risk assessment. The present study aims to unravel the toxicity mechanisms of a widely used herbicide to the arthropod Folsomia candida exposed in a natural soil, by linking effects on reproduction, proteomics and genome-wide gene expression. The EC50 effects on reproduction over 4 weeks was 4.63 mg glyphosate/kg of soil. The formulation included a polyethoxylated tallowamine as an adjuvant, which at 50% effect on reproduction had an estimated concentration of 0.87-1.49 mg/kg of soil. No effects were observed on survival and reproduction when using the isolated active substance, pointing the toxicity of the formulated product to the co-formulant instead of the active ingredient, glyphosate. RNA sequencing and shotgun proteomics were applied to assess differential transcript and protein expressions between exposed and control organisms in time, respectively. Specific functional categories at protein and transcriptome levels were concordant with each other, despite overall limited correlations between datasets. The exposure to this formulation affected normal cellular respiration and lipid metabolism, inducing oxidative stress and leading to impairment in biological life cycle mechanisms such as molting and reproduction.}, } @article {pmid30053133, year = {2018}, author = {Trujillo, JT and Seetharam, AS and Hufford, MB and Beilstein, MA and Mosher, RA}, title = {Evidence for a Unique DNA-Dependent RNA Polymerase in Cereal Crops.}, journal = {Molecular biology and evolution}, volume = {35}, number = {10}, pages = {2454-2462}, pmid = {30053133}, issn = {1537-1719}, support = {T32 GM008659/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; DNA-Directed RNA Polymerases/*genetics ; Edible Grain/*enzymology/genetics ; *Gene Duplication ; Grain Proteins ; Phylogeny ; Poaceae/*enzymology/genetics ; *Selection, Genetic ; }, abstract = {Gene duplication is an important driver for the evolution of new genes and protein functions. Duplication of DNA-dependent RNA polymerase (Pol) II subunits within plants led to the emergence of RNA Pol IV and V complexes, each of which possess unique functions necessary for RNA-directed DNA Methylation. Comprehensive identification of Pol V subunit orthologs across the monocot radiation revealed a duplication of the largest two subunits within the grasses (Poaceae), including critical cereal crops. These paralogous Pol subunits display sequence conservation within catalytic domains, but their carboxy terminal domains differ in length and character of the Ago-binding platform, suggesting unique functional interactions. Phylogenetic analysis of the catalytic region indicates positive selection on one paralog following duplication, consistent with retention via neofunctionalization. Positive selection on residue pairs that are predicted to interact between subunits suggests that paralogous subunits have evolved specific assembly partners. Additional Pol subunits as well as Pol-interacting proteins also possess grass-specific paralogs, supporting the hypothesis that a novel Pol complex with distinct function has evolved in the grass family, Poaceae.}, } @article {pmid30052988, year = {2018}, author = {Martin, LB and Vitousek, M and Donald, JW and Flock, T and Fuxjager, MJ and Goymann, W and Hau, M and Husak, J and Johnson, MA and Kircher, B and Knapp, R and Miller, ET and Schoenle, LA and Williams, T and Francis, CD}, title = {IUCN Conservation Status Does Not Predict Glucocorticoid Concentrations in Reptiles and Birds.}, journal = {Integrative and comparative biology}, volume = {58}, number = {4}, pages = {800-813}, doi = {10.1093/icb/icy102}, pmid = {30052988}, issn = {1557-7023}, mesh = {Animal Distribution ; Animals ; Birds/*physiology ; *Conservation of Natural Resources ; Databases as Topic ; Glucocorticoids/*metabolism ; Reptiles/*physiology ; }, abstract = {Circulating glucocorticoids (GCs) are the most commonly used biomarkers of stress in wildlife. However, their utility as a tool for identifying and/or managing at-risk species has varied. Here, we took a very broad approach to conservation physiology, asking whether International Union for the Conservation of Nature (IUCN) listing status (concern versus no obvious concern) and/or location within a geographic range (edge versus non-edge) predicted baseline and post-restraint concentrations of corticosterone (CORT) among many species of birds and reptiles. Even though such an approach can be viewed as coarse, we asked in this analysis whether CORT concentrations might be useful to implicate species at risk. Indeed, our effort, relying on HormoneBase, a repository of data on wildlife steroids, complements several other large-scale efforts in this issue to describe and understand GC variation. Using a phylogenetically informed Bayesian approach, we found little evidence that either IUCN status or edge/non-edge location in a geographic distribution were related to GC levels. However, we did confirm patterns described in previous studies, namely that breeding condition and evolutionary relatedness among species predicted some GC variation. Given the broad scope of our work, we are reluctant to conclude that IUCN status and location within a range are unrelated to GC regulation. We encourage future more targeted efforts on GCs in at-risk populations to reveal how factors leading to IUCN listing or the environmental conditions at range edges impact individual performance and fitness, particularly in the mammals, amphibians, and fish species we could not study here because data are currently unavailable.}, } @article {pmid30052543, year = {2018}, author = {Tsuda, T and Tokinobu, A and Yamamoto, E and Suzuki, E}, title = {Re: Associations Between Childhood Thyroid Cancer and External Radiation Dose After the Fukushima Daiichi Nuclear Power Plant Accident.}, journal = {Epidemiology (Cambridge, Mass.)}, volume = {29}, number = {6}, pages = {e56-e57}, doi = {10.1097/EDE.0000000000000898}, pmid = {30052543}, issn = {1531-5487}, mesh = {Child ; *Fukushima Nuclear Accident ; Humans ; Japan ; *Nuclear Power Plants ; Radiation Dosage ; Thyroid Neoplasms ; }, } @article {pmid30051848, year = {2018}, author = {Senner, NR and Stager, M and Verhoeven, MA and Cheviron, ZA and Piersma, T and Bouten, W}, title = {High-altitude shorebird migration in the absence of topographical barriers: avoiding high air temperatures and searching for profitable winds.}, journal = {Proceedings. Biological sciences}, volume = {285}, number = {1881}, pages = {}, pmid = {30051848}, issn = {1471-2954}, mesh = {Africa ; Air ; *Altitude ; *Animal Migration ; Animals ; Charadriiformes/*physiology ; Europe ; Female ; Geographic Information Systems ; Geography ; Netherlands ; *Temperature ; *Wind ; }, abstract = {Nearly 20% of all bird species migrate between breeding and nonbreeding sites annually. Their migrations include storied feats of endurance and physiology, from non-stop trans-Pacific crossings to flights at the cruising altitudes of jetliners. Despite intense interest in these performances, there remains great uncertainty about which factors most directly influence bird behaviour during migratory flights. We used GPS trackers that measure an individual's altitude and wingbeat frequency to track the migration of black-tailed godwits (Limosa limosa) and identify the abiotic factors influencing their in-flight migratory behaviour. We found that godwits flew at altitudes above 5000 m during 21% of all migratory flights, and reached maximum flight altitudes of nearly 6000 m. The partial pressure of oxygen at these altitudes is less than 50% of that at sea level, yet these extremely high flights occurred in the absence of topographical barriers. Instead, they were associated with high air temperatures at lower altitudes and increasing wind support at higher altitudes. Our results therefore suggest that wind, temperature and topography all play a role in determining migratory behaviour, but that their relative importance is context dependent. Extremely high-altitude flights may thus not be especially rare, but they may only occur in very specific environmental contexts.}, } @article {pmid30050986, year = {2018}, author = {Leonardi, M and Boschin, F and Giampoudakis, K and Beyer, RM and Krapp, M and Bendrey, R and Sommer, R and Boscato, P and Manica, A and Nogues-Bravo, D and Orlando, L}, title = {Late Quaternary horses in Eurasia in the face of climate and vegetation change.}, journal = {Science advances}, volume = {4}, number = {7}, pages = {eaar5589}, pmid = {30050986}, issn = {2375-2548}, mesh = {Adaptation, Physiological ; Animals ; Archaeology ; Asia ; *Climate Change ; Databases, Factual ; Ecosystem ; Europe ; Horses/*physiology ; }, abstract = {Wild horses thrived across Eurasia until the Last Glacial Maximum to collapse after the beginning of the Holocene. The interplay of climate change, species adaptability to different environments, and human domestication in horse history is still lacking coherent continental-scale analysis integrating different lines of evidence. We assembled temporal and geographical information on 3070 horse occurrences across Eurasia, frequency data for 1120 archeological layers in Europe, and matched them to paleoclimatic and paleoenvironmental simulations for the Late Quaternary. Climate controlled the distribution of horses, and they inhabited regions in Europe and Asia with different climates and ecosystem productivity, suggesting plasticity to populate different environments. Their decline in Europe during the Holocene appears associated with an increasing loss and fragmentation of open habitats. Europe was the most likely source for the spread of horses toward more temperate regions, and we propose both Iberia and central Asia as potential centers of domestication.}, } @article {pmid30048939, year = {2018}, author = {Ribeiro, AG and Baquero, OS and Freitas, CU and Chiaravalotti Neto, F and Cardoso, MRA and Latorre, MDRDO and Nardocci, AC}, title = {Incidence and mortality risk for respiratory tract cancer in the city of São Paulo, Brazil: Bayesian analysis of the association with traffic density.}, journal = {Cancer epidemiology}, volume = {56}, number = {}, pages = {53-59}, doi = {10.1016/j.canep.2018.07.005}, pmid = {30048939}, issn = {1877-783X}, mesh = {Adult ; Air Pollutants/adverse effects ; Air Pollution/adverse effects ; Bayes Theorem ; Brazil/epidemiology ; Cities/epidemiology ; Databases, Factual ; Humans ; Incidence ; Lung Neoplasms/*epidemiology/etiology ; Male ; Risk ; Traffic-Related Pollution/*adverse effects ; Young Adult ; }, abstract = {BACKGROUND: There is evidence that exposure to traffic-related air pollution is related to the incidence of and mortality associated with lung cancer. The aim of this study was to perform a spatial analysis, with a Bayesian approach, to test the hypothesis that high traffic density is associated with increased respiratory tract cancer incidence and mortality risk among individuals over 20 years of age residing in the city of São Paulo, Brazil.

METHODS: We employed data from two different databases: the São Paulo Municipal Population-Based Cancer Registry (2002-2011 cancer incidence data); and the Mortality Database of the São Paulo Municipal Health Department (2002-2013 cancer mortality data). The relationships between the number of cases of respiratory tract cancer in each area analyzed and the standardized covariates-traffic density and the Municipal Human Development Index (MHDI)-were evaluated with a Besag-York-Mollié ecological model with relative risks (RRs) estimates.

RESULTS: Per 1-unit standard-deviation increase in traffic density and in the MHDI, the RR for respiratory tract cancer incidence was 1.07 (95% CI: 1.02-1.13) and 1.25 (95% CI: 1.18-1.32), respectively, whereas the RR for mortality was 1.04 (95% CI: 0.99-1.09) and 1.23 (95% CI: 1.16-1.30), respectively.

CONCLUSION: Our findings support the hypothesis that residing in areas with high traffic density is associated with increased respiratory tract cancer incidence and mortality risk in the city of São Paulo.}, } @article {pmid30046636, year = {2018}, author = {Bird, SM and King, R}, title = {Multiple Systems Estimation (or Capture-Recapture Estimation) to Inform Public Policy.}, journal = {Annual review of statistics and its application}, volume = {5}, number = {}, pages = {95-118}, pmid = {30046636}, issn = {2326-8298}, support = {MC_U105260794/MRC_/Medical Research Council/United Kingdom ; }, abstract = {Estimating population sizes has long been of interest, from the estimation of the human or ecological population size within regions or countries to the hidden number of civilian casualties in a war. Total enumeration of the population, for example, via a census, is often infeasible or simply impractical. However, a series of partial enumerations or observations of the population is often possible. This has led to the ideas of capture-recapture methods, which have been extensively used within ecology to estimate the size of wildlife populations, with an associated measure of uncertainty, and are most effectively applied when there are multiple capture occasions. Capture-recapture ideology can be more widely applied to multiple data-sources, by the linkage of individuals across the multiple lists. This is often referred to as Multiple Systems Estimation (MSE). The MSE approach has been preferred when estimating "capture-shy" or hard-to-reach populations, including those caught up in the criminal justice system; or homeless; or trafficked; or civilian casualties of war. Motivated by a range of public policy applications of MSE, each briefly introduced, we discuss practical problems with potentially substantial methodological implications. They include: "period" definition; "case" definition; when an observed count is not a true count of the population of interest but an upper bound due to mismatched definitions; exact or probabilistic matching of "cases" across different lists; demographic or other information about the "case" which may influence capture-propensities; required permissions to access extant-lists; list-creation by research-teams or interested parties; referrals (if presence on list A results - almost surely - in presence on list B); different mathematical models leading to widely different estimated population sizes; uncertainty in estimation; computational efficiency; external validation; hypothesis-generation; and additional independent external information. Returning to our motivational applications, we focus on whether the uncertainty which qualified their estimates was sufficiently narrow to orient public policy; and, if not, what options were available and/or taken to reduce the uncertainty or to seek external validation. We also consider whether MSE was hypothesis-generating: in the sense of having spawned new lines of inquiry.}, } @article {pmid30046167, year = {2018}, author = {Spagnolo, F and Cristofari, P and Tatonetti, NP and Ginzburg, LR and Dykhuizen, DE}, title = {Pathogen population structure can explain hospital outbreaks.}, journal = {The ISME journal}, volume = {12}, number = {12}, pages = {2835-2843}, pmid = {30046167}, issn = {1751-7370}, mesh = {Computer Simulation ; Cross Infection/*epidemiology ; *Disease Outbreaks ; Hospitals ; Humans ; *Models, Theoretical ; Monte Carlo Method ; Population Dynamics ; }, abstract = {Hospitalized patients are at risk for increased length of stay, illness, or death due to hospital acquired infections. The majority of hospital transmission models describe dynamics on the level of the host rather than on the level of the pathogens themselves. Accordingly, epidemiologists often cannot complete transmission chains without direct evidence of either host-host contact or a large reservoir population. Here, we propose an ecology-based model to explain the transmission of pathogens in hospitals. The model is based upon metapopulation biology, which describes a group of interacting localized populations and island biogeography, which provides a basis for how pathogens may be moving between locales. Computational simulation trials are used to assess the applicability of the model. Results indicate that pathogens survive for extended periods without the need for large reservoirs by living in localized ephemeral populations while continuously transmitting pathogens to new seed populations. Computational simulations show small populations spending significant portions of time at sizes too small to be detected by most surveillance protocols and that the number and type of these ephemeral populations enable the overall pathogen population to be sustained. By modeling hospital pathogens as a metapopulation, many observations characteristic of hospital acquired infection outbreaks for which there has previously been no sufficient biological explanation, including how and why empirically successful interventions work, can now be accounted for using population dynamic hypotheses. Epidemiological links between temporally isolated outbreaks are explained via pathogen population dynamics and potential outbreak intervention targets are identified.}, } @article {pmid30044711, year = {2018}, author = {Bryant, GA and Fessler, DMT and Fusaroli, R and Clint, E and Amir, D and Chávez, B and Denton, KK and Díaz, C and Duran, LT and Fanćovićová, J and Fux, M and Ginting, EF and Hasan, Y and Hu, A and Kamble, SV and Kameda, T and Kuroda, K and Li, NP and Luberti, FR and Peyravi, R and Prokop, P and Quintelier, KJP and Shin, HJ and Stieger, S and Sugiyama, LS and van den Hende, EA and Viciana-Asensio, H and Yildizhan, SE and Yong, JC and Yuditha, T and Zhou, Y}, title = {The Perception of Spontaneous and Volitional Laughter Across 21 Societies.}, journal = {Psychological science}, volume = {29}, number = {9}, pages = {1515-1525}, doi = {10.1177/0956797618778235}, pmid = {30044711}, issn = {1467-9280}, mesh = {Adult ; Auditory Perception/*physiology ; *Cross-Cultural Comparison ; *Emotions ; Female ; Humans ; Laughter/*psychology ; Linear Models ; Male ; Nonverbal Communication/psychology ; Volition ; Young Adult ; }, abstract = {Laughter is a nonverbal vocalization occurring in every known culture, ubiquitous across all forms of human social interaction. Here, we examined whether listeners around the world, irrespective of their own native language and culture, can distinguish between spontaneous laughter and volitional laughter-laugh types likely generated by different vocal-production systems. Using a set of 36 recorded laughs produced by female English speakers in tests involving 884 participants from 21 societies across six regions of the world, we asked listeners to determine whether each laugh was real or fake, and listeners differentiated between the two laugh types with an accuracy of 56% to 69%. Acoustic analysis revealed that sound features associated with arousal in vocal production predicted listeners' judgments fairly uniformly across societies. These results demonstrate high consistency across cultures in laughter judgments, underscoring the potential importance of nonverbal vocal communicative phenomena in human affiliation and cooperation.}, } @article {pmid30042705, year = {2018}, author = {de Jong, M and Jolij, J and Pimenta, A and Lorist, MM}, title = {Age Modulates the Effects of Mental Fatigue on Typewriting.}, journal = {Frontiers in psychology}, volume = {9}, number = {}, pages = {1113}, pmid = {30042705}, issn = {1664-1078}, abstract = {In the present study, we examined whether age influences the effects of mental fatigue on task performance, and if we could validate the use of measures based on typing behavior as an index of the effects of mental fatigue on different aspects of cognition. Young (N = 24, 18-30 years) and middle-aged (N = 24, 50-67 years) participants performed a typewriting task and a mouse targeting task for 120 min. At the beginning and at the end of the experiment the level of subjective fatigue was assessed. During task performance measures based on typing behavior and EEG were recorded. Results showed that subjective fatigue increased over the experiment in both the young and the middle-aged group. Typing speed decreased with time-on-task (ToT) in both age groups, reflected in larger general interkey intervals and in an increase in typing time. In addition, typing accuracy decreased with ToT in the young group, however, not in the middle-aged group, reflected by an increase in typing errors. Moreover, the young group used the backspace key more often with ToT due to delayed error-correction, reflected in larger backspace sequences, resulting in larger interkey intervals and increased typing time. This effect was absent in the middle-aged group. In the young group, the P3 brain potential amplitude decreased over the experiment, which was related to an increase in typing time, longer general interkey intervals, and an increase in typing errors, suggesting that decreased task engagement was related to less efficient typewriting, at least in the young group. These results indicate that measures based on typing behavior could give information about the process of mental fatigue, and in addition suggest that age influences the effect of mental fatigue on typewriting. More specifically, younger adults more often adopt a strategy that emphasizes speed, while middle-aged adults act more error-aversive than younger adults.}, } @article {pmid30041026, year = {2018}, author = {Bogarín, D and Pérez-Escobar, OA and Groenenberg, D and Holland, SD and Karremans, AP and Lemmon, EM and Lemmon, AR and Pupulin, F and Smets, E and Gravendeel, B}, title = {Anchored hybrid enrichment generated nuclear, plastid and mitochondrial markers resolve the Lepanthes horrida (Orchidaceae: Pleurothallidinae) species complex.}, journal = {Molecular phylogenetics and evolution}, volume = {129}, number = {}, pages = {27-47}, doi = {10.1016/j.ympev.2018.07.014}, pmid = {30041026}, issn = {1095-9513}, mesh = {Cell Nucleus/*genetics ; Cluster Analysis ; Databases, Genetic ; Flowers/anatomy & histology ; Genetic Loci ; Genetic Markers ; *Hybridization, Genetic ; Likelihood Functions ; Mitochondria/*genetics ; Orchidaceae/*genetics ; Phylogeny ; Plastids/*genetics ; Species Specificity ; }, abstract = {Phylogenetic relationships in species complexes and lineages derived from rapid diversifications are often challenging to resolve using morphology or standard DNA barcoding markers. The hyper-diverse genus Lepanthes from Neotropical cloud forest includes over 1200 species and many recent, explosive diversifications that have resulted in poorly supported nodes and morphological convergence across clades. Here, we assess the performance of 446 nuclear-plastid-mitochondrial markers derived from an anchored hybrid enrichment approach (AHE) coupled with coalescence- and species network-based inferences to resolve phylogenetic relationships and improve species recognition in the Lepanthes horrida species group. In addition to using orchid-specific probes to increase enrichment efficiency, we improved gene tree resolution by extending standard angiosperm targets into adjacent exons. We found high topological discordance among individual gene trees, suggesting that hybridization/polyploidy may have promoted speciation in the lineage via formation of new hybrid taxa. In addition, we identified ten loci with the highest phylogenetic informativeness values from these genomes. Most previous phylogenetic sampling in the Pleurothallidinae relies on two regions (ITS and matK), therefore, the evaluation of other markers such as those shown here may be useful in future phylogenetic studies in the orchid family. Coalescent-based species tree estimation methods resolved the phylogenetic relationships of the L. horrida species group. The resolution of the phylogenetic estimations was improved with the inclusion of extended anchor targets. This approach produced longer loci with higher discriminative power. These analyses also disclosed two undescribed species, L. amicitiae and L. genetoapophantica, formally described here, which are also supported by morphology. Our study demonstrates the utility of combined genomic evidence to disentangle phylogenetic relationships at very shallow levels of the tree of life, and in clades showing convergent trait evolution. With a fully resolved phylogeny, is it possible to disentangle traits evolving in parallel or convergently across these orchid lineages such as flower color and size from diagnostic traits such as the shape and orientation of the lobes of the petals and lip.}, } @article {pmid30040720, year = {2018}, author = {Yao, F and Hong, X and Li, S and Zhang, Y and Zhao, Q and Du, W and Wang, Y and Ni, J}, title = {Urine-Based Biomarkers for Alzheimer's Disease Identified Through Coupling Computational and Experimental Methods.}, journal = {Journal of Alzheimer's disease : JAD}, volume = {65}, number = {2}, pages = {421-431}, doi = {10.3233/JAD-180261}, pmid = {30040720}, issn = {1875-8908}, mesh = {Aged ; Aged, 80 and over ; Alzheimer Disease/*urine ; Biomarkers/urine ; Brain/metabolism ; Chromatography, Liquid ; Computational Biology ; Computer Simulation ; Enzyme-Linked Immunosorbent Assay ; Female ; Gene Expression ; Humans ; Insulin-Like Growth Factor Binding Proteins/urine ; Male ; Models, Biological ; Osteopontin/urine ; Tandem Mass Spectrometry ; }, abstract = {Alzheimer's disease (AD) is a chronic neurodegenerative disorder contributing to nearly 70% of dementia cases. However, no diagnostic protein biomarkers are available in urine. In this study, we combined computational and experimental methods to identify urinary biomarkers for AD. First, by analyzing brain tissue-based gene expression data of AD, 2,754 differentially expressed genes were identified, 559 of which were predicted to encode urine-excretory proteins that might act as candidate protein biomarkers of AD. GO enrichment analyses implied that they were mainly involved in microtubule-based process, myelin sheath, and calcium ion binding, suggesting that they might be associated with AD pathogenesis. In order to verify these proteins in urine, an iTRAQ experiment was carried out to analyze urine samples from AD patients and healthy controls, and 15 proteins were detected. Based on the expression changes of these proteins, 4 proteins were chosen for further validation by ELISA experiment, and SPP1, GSN, and IGFBP7 were found to be differentially expressed in the urine of AD patients. After a literature survey, we found that they were involved in AD pathophysiology and might serve as new urine biomarkers for AD. To our knowledge, this is the first time that urine biomarkers for AD were identified by combining computational and experimental methods. Furthermore, this is the first time SPP1, GSN, and IGFBP7 have been reported as potential urine protein biomarkers for AD. Therefore, our findings might provide significant guidance for finding early biomarkers of AD in urine.}, } @article {pmid30038903, year = {2018}, author = {Estrada-Peña, A and Cabezas-Cruz, A and Pollet, T and Vayssier-Taussat, M and Cosson, JF}, title = {High Throughput Sequencing and Network Analysis Disentangle the Microbial Communities of Ticks and Hosts Within and Between Ecosystems.}, journal = {Frontiers in cellular and infection microbiology}, volume = {8}, number = {}, pages = {236}, pmid = {30038903}, issn = {2235-2988}, mesh = {Animals ; Arvicolinae/*microbiology/*parasitology ; Bacteria/*classification/genetics ; Cluster Analysis ; Computational Biology ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Ecosystem ; High-Throughput Nucleotide Sequencing ; Ixodes/*growth & development/*microbiology ; Metagenomics/*methods ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Spleen/microbiology ; }, abstract = {We aimed to develop a framework, based on graph theory, to capture the ecological meaning behind pure pair comparisons of microbiome-derived data. As a proof of concept, we applied the framework to analyze the co-occurrence of bacteria in either Ixodes ricinus ticks or the spleen of one of their main hosts, the vole Myodes glareolus. As a secondary lymphoid organ, the spleen acts as a filter of blood and represents well the exposure to microorganisms circulating in the blood; including those acquired and transmitted by ticks during feeding. The microbiome of 301 and 269 individual tick and vole samples, respectively, were analyzed using next generation sequencing (NGS) of 16S rRNA. To assess the effect of habitat on ecological communities of bacteria associated to ticks and voles, two different biotopes were included in the study, forest, and ecotone. An innovative approach of NGS data analysis combining network analysis and phylogenies of co-occuring of bacteria was used to study associations between bacteria in individual samples. Of the 126 bacterial genera found in ticks and voles, 62% were shared by both species. Communities of co-occurring bacteria were always more phylogenetically diverse in ticks than in voles. Interestingly, ~80% of bacterial phylogenetic diversity was found in ~20% of ticks. This pattern was not observed in vole-associated bacteria. Results revealed that the microbiome of I. ricinus is only slightly related to that of M. glareolus and that the biotope plays the most important role in shaping the bacterial communities of either ticks or voles. The analysis of the phylogenetic signal of the network indexes across the 16S rRNA-derived tree of bacteria suggests that the microbiome of both ticks and voles has high phylogenetic diversity and that closest bacterial genera do not co-occur. This study shows that network analysis is a promising tool to unravel complex microbial communities associated to arthropod vectors and vertebrate hosts.}, } @article {pmid30036369, year = {2018}, author = {Nad'o, L and Kaňuch, P}, title = {Why sampling ratio matters: Logistic regression and studies of habitat use.}, journal = {PloS one}, volume = {13}, number = {7}, pages = {e0200742}, pmid = {30036369}, issn = {1932-6203}, mesh = {Animals ; Chiroptera/*physiology ; Ecology ; *Ecosystem ; *Environment ; Geographic Information Systems ; *Logistic Models ; Probability ; Random Allocation ; Species Specificity ; Zoology ; }, abstract = {Logistic regression (LR) models are among the most frequently used statistical tools in ecology. With LR one can infer if a species' habitat use is related to environmental factors and estimate the probability of species occurrence based on the values of these factors. However, studies often use inadequate sampling with regards to the arbitrarily chosen ratio between occupied and unoccupied (or available) locations, and this has a profound effect on the inference and predictive power of LR models. To demonstrate the effect of various sampling strategies/efforts on the quality of LR models, we used a unique census dataset containing all the used roosting cavities of the tree-dwelling bat Nyctalus leisleri and all cavities where the species was absent. We compared models constructed from randomly selected data subsets with varying ratios of occupied and unoccupied cavities (1:1, 1:5, 1:10) with a full dataset model (ratio 1:31). These comparisons revealed that the power of LR models was low when the sampling did not reflect the population ratio of occupied and unoccupied cavities. The use of weights improved the subsampled models. Thus, this study warns against inadequate data sampling and highly encourages a randomized sampling procedure to estimate the true ratio of occupied:unoccupied locations, which can then be used to optimize a manageable sampling effort and apply weights to improve the LR model. Such an approach may provide robust and reliable models suitable for both inference and prediction.}, } @article {pmid30029348, year = {2018}, author = {Ridding, LE and Redhead, JW and Oliver, TH and Schmucki, R and McGinlay, J and Graves, AR and Morris, J and Bradbury, RB and King, H and Bullock, JM}, title = {The importance of landscape characteristics for the delivery of cultural ecosystem services.}, journal = {Journal of environmental management}, volume = {206}, number = {}, pages = {1145-1154}, doi = {10.1016/j.jenvman.2017.11.066}, pmid = {30029348}, issn = {1095-8630}, mesh = {*Conservation of Natural Resources ; Ecology ; *Ecosystem ; England ; *Geographic Information Systems ; Humans ; }, abstract = {The importance of Cultural Ecosystem Services (CES) to human wellbeing is widely recognised. However, quantifying these non-material benefits is challenging and consequently they are often not assessed. Mapping approaches are increasingly being used to understand the spatial distribution of different CES and how this relates to landscape characteristics. This study uses an online Public Participation Geographic Information System (PPGIS) to elicit information on outdoor locations important to respondents in Wiltshire, a dynamic lowland landscape in southern England. We analysed these locations in a GIS with spatial datasets representing potential influential factors, including protected areas, land use, landform, and accessibility. We assess these characteristics at different spatial and visual scales for different types of cultural engagement. We find that areas that are accessible, near to urban centres, with larger views, and a high diversity of protected habitats, are important for the delivery of CES. Other characteristics including a larger area of woodland and the presence of sites of historic interest in the surrounding landscape were also influential. These findings have implications for land-use planning and the management of ecosystems, by demonstrating the benefits of high quality ecological sites near to towns. The importance of maintaining and restoring landscape features, such as woodlands, to enhance the delivery of CES were also highlighted.}, } @article {pmid30029345, year = {2018}, author = {He, L and Shen, J and Zhang, Y}, title = {Ecological vulnerability assessment for ecological conservation and environmental management.}, journal = {Journal of environmental management}, volume = {206}, number = {}, pages = {1115-1125}, doi = {10.1016/j.jenvman.2017.11.059}, pmid = {30029345}, issn = {1095-8630}, mesh = {China ; *Climate Change ; *Conservation of Natural Resources ; Ecology ; Ecosystem ; *Geographic Information Systems ; Humans ; }, abstract = {Identifying ecological vulnerable regions is a significant aspect in ecological conservation and environmental management. This paper presents a first attempt to provide a prototype framework that can assess ecological vulnerability and evaluate potential impacts of natural, social, economic, environmental pollution, and human health elements on ecological vulnerability with integrating spatial analysis of Geographic Information System (GIS) method and multi-criteria decision analysis (MCDA). A general ecological vulnerability index was constructed to describe the vulnerability status in an ecological hotspot of China. The assessment results of this study confirm the poor ecological vulnerability in China that only 1.32% of the China's population lives in not vulnerable ecosystem. A very high percentage (98.68%) of Chinese with 1.34 billion people lives in vulnerable and highly vulnerable area. This situation is mainly caused by increasing population pressure, exhausted nature resources, extensive economic growth, severe environmental pollution, insufficient environmental protection investment, and accelerating population aging. The spatial comparison indicates that spatial disparity existed in China with the central and northwestern provinces showing higher ecological vulnerability than the northeastern and southern provinces. The results of ecological vulnerability assessment can support effective guidance for mid- or long-term ecologic management. The developed framework can be replicated at different spatial and temporal scales using context-specific datasets to support ecological managers and government with decision-making. With available robust climate change models, future research might incorporate climate change into the ecological vulnerability framework.}, } @article {pmid30029326, year = {2018}, author = {Djikanović, V and Skorić, S and Spasić, S and Naunovic, Z and Lenhardt, M}, title = {Ecological risk assessment for different macrophytes and fish species in reservoirs using biota-sediment accumulation factors as a useful tool.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {241}, number = {}, pages = {1167-1174}, doi = {10.1016/j.envpol.2018.06.054}, pmid = {30029326}, issn = {1873-6424}, mesh = {Animals ; Aquatic Organisms/*chemistry ; Biota ; Canada ; Catfishes ; Cyprinidae ; Ecology ; Environmental Monitoring/*methods ; Gills/chemistry ; Liver/chemistry ; Metals/analysis ; Metals, Heavy/analysis ; Muscles/chemistry ; Netherlands ; Risk Assessment ; Serbia ; Trace Elements/analysis ; Water Pollutants, Chemical/*analysis ; }, abstract = {Metal content was evaluated in the sediment, macrophytes and fish in the Medjuvršje reservoir (Western Serbia). Concentrations of 16 trace elements (Ag; Al; As; B; Ba; Cd; Co; Cr; Cu; Fe; Li; Mn; Ni; Pb; Sr; Zn) were analysed in the sediment, macrophytes and fish of an aquatic ecosystem. Five macrophyte species and three fish tissues (liver, muscle, gills) from five fish species (freshwater bream, common nase, Prussian carp, chub, wels catfish) were sampled and the metal content was analysed with ICP-OES. The sediment concentrations of Cu, Cd, and Zn exceeded the Canadian sediment quality guidelines while concentrations of Cr and Ni were above the Netherlands' target values. Bioaccumulation factors (BSAF) were calculated for analysed macrophytes and fish tissue. The BSAF had higher values for macrophytes for all investigated elements except for Cu and Zn; Cu had a higher value in the liver of the freshwater bream (0.823) and Zn had a higher value in the liver of freshwater bream (0.914) and chub (0.834) as well as in gills of Prussian carp (2.58) and chub (1.26). Potamogeton pectinatus, Ceratophylum demersum and the root of Phragmites communis showed higher accumulation of elements than Trapa natans and Potamogeton fluitans and the body of P. communis. The highest BSAF values for Ba, Mn, Sr and Ni were recorded in the gills. Cd and Cu had the highest BSAF values in the liver. Results confirmed that particular macrophyte and fish species could be a good indicator of reservoir water and sediment pollution.}, } @article {pmid30027688, year = {2018}, author = {Dallas, T and Decker, RR and Hastings, A}, title = {Multiple data sources and freely available code is critical when investigating species distributions and diversity: a response to Knouft (2018).}, journal = {Ecology letters}, volume = {21}, number = {9}, pages = {1423-1424}, doi = {10.1111/ele.13105}, pmid = {30027688}, issn = {1461-0248}, mesh = {Biodiversity ; *Databases, Factual ; }, abstract = {A recent comment from Knouft () has suggested that our original article (Dallas et al.) was an 'inappropriate application of biodiversity data'. Here, we affirm our results, and address the more general point about biodiversity data use.}, } @article {pmid31213752, year = {2018}, author = {Eremić-Kojić, N and Đerić, M and Govorčin, ML and Balać, D and Kresoja, M and Kojić-Damjanov, S}, title = {Assessment of hepatic steatosis algorithms in non-alcoholic fatty liver disease.}, journal = {Hippokratia}, volume = {22}, number = {1}, pages = {10-16}, pmid = {31213752}, issn = {1108-4189}, abstract = {BACKGROUND: In order to optimize the identification of persons with non-alcoholic fatty liver disease (NAFLD), several algorithms for hepatic steatosis were developed. These available algorithms, as well as an algorithm, derived using biochemical and anthropometric data of our participants, are compared in a cross-sectional pilot study.

MATERIAL AND METHODS: We included 77 participants with abdominal obesity: 43 with NAFLD and 33 without NAFLD. Body mass index (BMI), waist circumference (WC) and hip circumference (HC), systolic and diastolic blood pressure were assessed. Fibrinogen, high sensitive C-reactive protein (hsCRP), aspartate aminotransferase (AST), alanine transaminase (ALT), gamma-glutamyl transferase (GGT), uric acid, ferritin, glucose, insulin, homocysteine, lipid status parameters, apolipoprotein A-I, apolipoprotein B and Lp(a)-lipoprotein were measured. Fatty liver was assessed by ultrasound with the presence or absence of hepatic steatosis. Discovering the most significant factor in the presence of NAFLD is assessed through logistic regression modeling. The predictor variables were chosen according to an algorithm derived from conducted factor analysis and other available algorithms for hepatic steatosis.

RESULTS: Participants with NAFLD had significantly higher BMI (34.38 ± 9.73 vs 28.05 ± 4.79 kg/m[2], p =0.001), WC (108.05 ± 11.47 vs 96.15 ± 14.27 cm, p =0.001), HC (114.93 ± 11.01 vs 108.21 ± 9.82 cm, p =0.050), systolic (128.98 ± 8.67 vs 122.42 ± 10.62 mmHg, p =0.010) and diastolic blood pressure (83.64 ± 5.94 vs 78.33 ± 7.57 mmHg, p =0.001), AST (23.93 ± 6.91 vs 21.70 ± 5.21 U/L, p =0.014), ALT (30.50 ± 13.70 vs 23.00 ± 11.75 U/L, p =0.007), hsCRP (4.34 ± 5.56 vs 2.98 ± 2.34mg/l, p =0.004) and uric acid (358.02 ± 83.29 vs 296.78 ± 84.54µmol/l, p =0.001), in comparison non NAFLD. Logistic regression model with algorithm derived from factor analysis showed the best performance. From other available algorithms, only fatty liver index (FLI) and hepatic steatosis index (HSI) had statistically significant discriminatory power.   Conclusions: Elevation of WC, HC, BMI, DBP, SBP, Fbg, hsCRP, glucose, and uric acid, incorporated in our hepatic steatosis prediction model, had the best predictive power among all assessed algorithms. HIPPOKRATIA 2018, 22(1): 10-16.}, } @article {pmid30980045, year = {2018}, author = {Benjamin, DJ and Berger, JO and Johannesson, M and Nosek, BA and Wagenmakers, EJ and Berk, R and Bollen, KA and Brembs, B and Brown, L and Camerer, C and Cesarini, D and Chambers, CD and Clyde, M and Cook, TD and De Boeck, P and Dienes, Z and Dreber, A and Easwaran, K and Efferson, C and Fehr, E and Fidler, F and Field, AP and Forster, M and George, EI and Gonzalez, R and Goodman, S and Green, E and Green, DP and Greenwald, AG and Hadfield, JD and Hedges, LV and Held, L and Hua Ho, T and Hoijtink, H and Hruschka, DJ and Imai, K and Imbens, G and Ioannidis, JPA and Jeon, M and Jones, JH and Kirchler, M and Laibson, D and List, J and Little, R and Lupia, A and Machery, E and Maxwell, SE and McCarthy, M and Moore, DA and Morgan, SL and Munafó, M and Nakagawa, S and Nyhan, B and Parker, TH and Pericchi, L and Perugini, M and Rouder, J and Rousseau, J and Savalei, V and Schönbrodt, FD and Sellke, T and Sinclair, B and Tingley, D and Van Zandt, T and Vazire, S and Watts, DJ and Winship, C and Wolpert, RL and Xie, Y and Young, C and Zinman, J and Johnson, VE}, title = {Redefine statistical significance.}, journal = {Nature human behaviour}, volume = {2}, number = {1}, pages = {6-10}, doi = {10.1038/s41562-017-0189-z}, pmid = {30980045}, issn = {2397-3374}, mesh = {*Data Interpretation, Statistical ; Models, Statistical ; Reproducibility of Results ; Scholarly Communication ; }, } @article {pmid30888267, year = {2018}, author = {}, title = {Realizing the promise of computational prediction in toxicology applications.}, journal = {Journal of environmental science and health. Part C, Environmental carcinogenesis & ecotoxicology reviews}, volume = {36}, number = {4}, pages = {167-168}, doi = {10.1080/10590501.2018.1537560}, pmid = {30888267}, issn = {1532-4095}, mesh = {Computational Biology ; Ecotoxicology/*methods ; Software ; }, } @article {pmid30026187, year = {2018}, author = {Bradburd, GS and Coop, GM and Ralph, PL}, title = {Inferring Continuous and Discrete Population Genetic Structure Across Space.}, journal = {Genetics}, volume = {210}, number = {1}, pages = {33-52}, pmid = {30026187}, issn = {1943-2631}, support = {R01 GM108779/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Cluster Analysis ; Data Interpretation, Statistical ; Gene Flow/genetics ; Genetic Variation/genetics ; Genetics, Population/*methods/*statistics & numerical data ; Humans ; Models, Genetic ; North America ; Population Groups/genetics ; Populus/genetics ; Ursidae/genetics ; }, abstract = {A classic problem in population genetics is the characterization of discrete population structure in the presence of continuous patterns of genetic differentiation. Especially when sampling is discontinuous, the use of clustering or assignment methods may incorrectly ascribe differentiation due to continuous processes (e.g., geographic isolation by distance) to discrete processes, such as geographic, ecological, or reproductive barriers between populations. This reflects a shortcoming of current methods for inferring and visualizing population structure when applied to genetic data deriving from geographically distributed populations. Here, we present a statistical framework for the simultaneous inference of continuous and discrete patterns of population structure. The method estimates ancestry proportions for each sample from a set of two-dimensional population layers, and, within each layer, estimates a rate at which relatedness decays with distance. This thereby explicitly addresses the "clines versus clusters" problem in modeling population genetic variation, and remedies some of the overfitting to which nonspatial models are prone. The method produces useful descriptions of structure in genetic relatedness in situations where separated, geographically distributed populations interact, as after a range expansion or secondary contact. We demonstrate the utility of this approach using simulations and by applying it to empirical datasets of poplars and black bears in North America.}, } @article {pmid30026186, year = {2018}, author = {Willis, S and Masel, J}, title = {Gene Birth Contributes to Structural Disorder Encoded by Overlapping Genes.}, journal = {Genetics}, volume = {210}, number = {1}, pages = {303-313}, pmid = {30026186}, issn = {1943-2631}, support = {R01 GM104040/GM/NIGMS NIH HHS/United States ; }, mesh = {Base Sequence/genetics ; Biological Evolution ; Codon ; Databases, Genetic ; Evolution, Molecular ; Genes, Overlapping/*genetics/*physiology ; Genes, Viral/genetics ; Genetic Variation/genetics ; Humans ; Intrinsically Disordered Proteins ; Mutation Rate ; Open Reading Frames/genetics ; Phylogeny ; Proteins/genetics ; Reading Frames/genetics ; Sequence Homology, Nucleic Acid ; }, abstract = {The same nucleotide sequence can encode two protein products in different reading frames. Overlapping gene regions encode higher levels of intrinsic structural disorder (ISD) than nonoverlapping genes (39% vs. 25% in our viral dataset). This might be because of the intrinsic properties of the genetic code, because one member per pair was recently born de novo in a process that favors high ISD, or because high ISD relieves increased evolutionary constraint imposed by dual-coding. Here, we quantify the relative contributions of these three alternative hypotheses. We estimate that the recency of de novo gene birth explains [Formula: see text] or more of the elevation in ISD in overlapping regions of viral genes. While the two reading frames within a same-strand overlapping gene pair have markedly different ISD tendencies that must be controlled for, their effects cancel out to make no net contribution to ISD. The remaining elevation of ISD in the older members of overlapping gene pairs, presumed due to the need to alleviate evolutionary constraint, was already present prior to the origin of the overlap. Same-strand overlapping gene birth events can occur in two different frames, favoring high ISD either in the ancestral gene or in the novel gene; surprisingly, most de novo gene birth events contained completely within the body of an ancestral gene favor high ISD in the ancestral gene (23 phylogenetically independent events vs. 1). This can be explained by mutation bias favoring the frame with more start codons and fewer stop codons.}, } @article {pmid30024958, year = {2018}, author = {Takagi, J and Ichikawa, K and Arai, N and Miyamoto, Y and Uchida, K and Shoji, J and Mitamura, H}, title = {Simultaneous observation of intermittent locomotion of multiple fish by fine-scale spatiotemporal three-dimensional positioning.}, journal = {PloS one}, volume = {13}, number = {7}, pages = {e0201029}, pmid = {30024958}, issn = {1932-6203}, mesh = {Animal Migration/*physiology ; Animals ; *Ecology ; Fishes/*physiology ; Locomotion/*physiology ; *Models, Statistical ; Spatio-Temporal Analysis ; }, abstract = {Recent advances in biotelemetry techniques, especially positioning methods, have revealed the detailed behaviour and movement of aquatic organisms. Behavioural intermittence in animal locomotion, such as the Lévy walk, is a popular topic in the field of movement ecology. Previous attempts to describe intermittent locomotion quantitatively have been constrained by the spatial and temporal resolution possible with conventional biotelemetry systems. This study developed a fine-scale spatiotemporal three-dimensional positioning method using a new biotelemetry system with a positional precision of <10 cm and positioning interval of <10 s. Using this proposed positioning method, the intermittent stop-and-go locomotion of Siebold's wrasses (Pseudolabrus sieboldi) was observed during travel from an unsuitable to a suitable location following displacement. The fish displayed behavioural intermittence in relocating to a suitable location. Initially, their movement halted for reorientation, after which they moved intermittently yet in a straight line to the suitable location. To test the positioning ability of the proposed method, data sets were resampled at intervals of 5, 10, 30, 60, and 300 s. Longer sampling intervals failed to identify reorientations and underestimated the number of stops, distance travelled, and speed. Overall, the results highlighted the adequacy and ability of the proposed positioning method to observe the intermittent locomotion of fish, such as stop-and-go behaviour, in a natural environment.}, } @article {pmid30021534, year = {2018}, author = {Quinn, TP and Crowley, TM and Richardson, MF}, title = {Benchmarking differential expression analysis tools for RNA-Seq: normalization-based vs. log-ratio transformation-based methods.}, journal = {BMC bioinformatics}, volume = {19}, number = {1}, pages = {274}, pmid = {30021534}, issn = {1471-2105}, mesh = {Base Sequence ; *Benchmarking ; Computer Simulation ; Databases, Genetic ; Gene Expression Profiling/*methods ; High-Throughput Nucleotide Sequencing ; Humans ; RNA, Messenger/genetics/metabolism ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, RNA/*methods ; *Software ; }, abstract = {BACKGROUND: Count data generated by next-generation sequencing assays do not measure absolute transcript abundances. Instead, the data are constrained to an arbitrary "library size" by the sequencing depth of the assay, and typically must be normalized prior to statistical analysis. The constrained nature of these data means one could alternatively use a log-ratio transformation in lieu of normalization, as often done when testing for differential abundance (DA) of operational taxonomic units (OTUs) in 16S rRNA data. Therefore, we benchmark how well the ALDEx2 package, a transformation-based DA tool, detects differential expression in high-throughput RNA-sequencing data (RNA-Seq), compared to conventional RNA-Seq methods such as edgeR and DESeq2.

RESULTS: To evaluate the performance of log-ratio transformation-based tools, we apply the ALDEx2 package to two simulated, and two real, RNA-Seq data sets. One of the latter was previously used to benchmark dozens of conventional RNA-Seq differential expression methods, enabling us to directly compare transformation-based approaches. We show that ALDEx2, widely used in meta-genomics research, identifies differentially expressed genes (and transcripts) from RNA-Seq data with high precision and, given sufficient sample sizes, high recall too (regardless of the alignment and quantification procedure used). Although we show that the choice in log-ratio transformation can affect performance, ALDEx2 has high precision (i.e., few false positives) across all transformations. Finally, we present a novel, iterative log-ratio transformation (now implemented in ALDEx2) that further improves performance in simulations.

CONCLUSIONS: Our results suggest that log-ratio transformation-based methods can work to measure differential expression from RNA-Seq data, provided that certain assumptions are met. Moreover, these methods have very high precision (i.e., few false positives) in simulations and perform well on real data too. With previously demonstrated applicability to 16S rRNA data, ALDEx2 can thus serve as a single tool for data from multiple sequencing modalities.}, } @article {pmid30020436, year = {2018}, author = {Chen, F and Zhang, J and Chen, J and Li, X and Dong, W and Hu, J and Lin, M and Liu, Y and Li, G and Wang, Z and Zhang, L}, title = {realDB: a genome and transcriptome resource for the red algae (phylum Rhodophyta).}, journal = {Database : the journal of biological databases and curation}, volume = {2018}, number = {}, pages = {}, pmid = {30020436}, issn = {1758-0463}, mesh = {Algal Proteins/chemistry/genetics/metabolism ; *Databases, Genetic ; *Genome ; Internet ; Molecular Sequence Annotation ; Rhodophyta/*genetics ; Sequence Alignment ; Transcriptome/*genetics ; }, abstract = {With over 6000 species in seven classes, red algae (Rhodophyta) have diverse economic, ecological, experimental and evolutionary values. However, red algae are usually absent or rare in comparative analyses because genomic information of this phylum is often under-represented in various comprehensive genome databases. To improve the accessibility to the ome data and omics tools for red algae, we provided 10 genomes and 27 transcriptomes representing all seven classes of Rhodophyta. Three genomes and 18 transcriptomes were de novo assembled and annotated in this project. User-friendly BLAST suit, Jbrowse tools and search system were developed for online analyses. Detailed introductions to red algae taxonomy and the sequencing status are also provided. In conclusion, realDB (realDB.algaegenome.org) provides a platform covering the most genome and transcriptome data for red algae and a suite of tools for online analyses, and will attract both red algal biologists and those working on plant ecology, evolution and development.Database URL: http://realdb.algaegenome.org/.}, } @article {pmid30020357, year = {2018}, author = {Niño, L}, title = {[Health risk zoning: yellow fever from a geographical perspective in La Macarena, Department of Meta, Colombia].}, journal = {Salud colectiva}, volume = {14}, number = {1}, pages = {19-32}, doi = {10.18294/sc.2018.1087}, pmid = {30020357}, issn = {1851-8265}, mesh = {Colombia/epidemiology ; Geographic Information Systems ; *Geographic Mapping ; Humans ; Risk Assessment ; Risk Factors ; Yellow Fever/*epidemiology/etiology ; }, abstract = {This paper attempts to zone yellow fever risk in La Macarena (department of Meta, Colombia) in terms of environmental hazards and socio-economic vulnerabilities. An ecological study was carried out, in which data published from 2007 to 2013 on conditions of the municipality were integrated into a geographic information system. Through a superposition of map layers, magnitudes of hazard and vulnerability proportional to the degree of severity were obtained. As a result the spatial heterogeneity of the risk of yellow fever was described, suggesting that the areas surrounding populated centers, roads and rivers present the highest probability of transmission. It is concluded that the cartographic representation of the spatial distribution of risk in the municipality constitutes a methodological contribution to health risk zoning - in concrete geographical areas and based on hazards and vulnerabilities - which facilitates decision-making in public health.}, } @article {pmid30018084, year = {2018}, author = {Solares, EA and Chakraborty, M and Miller, DE and Kalsow, S and Hall, K and Perera, AG and Emerson, JJ and Hawley, RS}, title = {Rapid Low-Cost Assembly of the Drosophila melanogaster Reference Genome Using Low-Coverage, Long-Read Sequencing.}, journal = {G3 (Bethesda, Md.)}, volume = {8}, number = {10}, pages = {3143-3154}, pmid = {30018084}, issn = {2160-1836}, support = {S10 OD021718/OD/NIH HHS/United States ; S10 RR025496/RR/NCRR NIH HHS/United States ; R01 RR024862/RR/NCRR NIH HHS/United States ; R01 GM123303/GM/NIGMS NIH HHS/United States ; S10 OD010794/OD/NIH HHS/United States ; P30 CA062203/CA/NCI NIH HHS/United States ; }, mesh = {Animals ; *Computational Biology/methods ; Drosophila melanogaster/*genetics ; Gene Library ; Genetic Variation ; *Genome, Insect ; Genome, Mitochondrial ; *Genomics/methods ; High-Throughput Nucleotide Sequencing ; Molecular Sequence Annotation ; Sequence Analysis, DNA ; }, abstract = {Accurate and comprehensive characterization of genetic variation is essential for deciphering the genetic basis of diseases and other phenotypes. A vast amount of genetic variation stems from large-scale sequence changes arising from the duplication, deletion, inversion, and translocation of sequences. In the past 10 years, high-throughput short reads have greatly expanded our ability to assay sequence variation due to single nucleotide polymorphisms. However, a recent de novo assembly of a second Drosophila melanogaster reference genome has revealed that short read genotyping methods miss hundreds of structural variants, including those affecting phenotypes. While genomes assembled using high-coverage long reads can achieve high levels of contiguity and completeness, concerns about cost, errors, and low yield have limited widespread adoption of such sequencing approaches. Here we resequenced the reference strain of D. melanogaster (ISO1) on a single Oxford Nanopore MinION flow cell run for 24 hr. Using only reads longer than 1 kb or with at least 30x coverage, we assembled a highly contiguous de novo genome. The addition of inexpensive paired reads and subsequent scaffolding using an optical map technology achieved an assembly with completeness and contiguity comparable to the D. melanogaster reference assembly. Comparison of our assembly to the reference assembly of ISO1 uncovered a number of structural variants (SVs), including novel LTR transposable element insertions and duplications affecting genes with developmental, behavioral, and metabolic functions. Collectively, these SVs provide a snapshot of the dynamics of genome evolution. Furthermore, our assembly and comparison to the D. melanogaster reference genome demonstrates that high-quality de novo assembly of reference genomes and comprehensive variant discovery using such assemblies are now possible by a single lab for under $1,000 (USD).}, } @article {pmid30017551, year = {2018}, author = {Longbottom, J and Shearer, FM and Devine, M and Alcoba, G and Chappuis, F and Weiss, DJ and Ray, SE and Ray, N and Warrell, DA and Ruiz de Castañeda, R and Williams, DJ and Hay, SI and Pigott, DM}, title = {Vulnerability to snakebite envenoming: a global mapping of hotspots.}, journal = {Lancet (London, England)}, volume = {392}, number = {10148}, pages = {673-684}, pmid = {30017551}, issn = {1474-547X}, support = {/WT_/Wellcome Trust/United Kingdom ; 095066/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Africa, Northern/epidemiology ; Animals ; Antivenins/therapeutic use ; Geographic Mapping ; Health Resources/economics/statistics & numerical data ; Health Services Accessibility/standards ; Humans ; Indonesia/epidemiology ; Neglected Diseases/drug therapy/epidemiology/prevention & control ; Public Health/education ; Quality of Health Care/standards ; Snake Bites/*drug therapy/*epidemiology/mortality/prevention & control ; Snakes/*classification/injuries ; Vulnerable Populations/*statistics & numerical data ; }, abstract = {BACKGROUND: Snakebite envenoming is a frequently overlooked cause of mortality and morbidity. Data for snake ecology and existing snakebite interventions are scarce, limiting accurate burden estimation initiatives. Low global awareness stunts new interventions, adequate health resources, and available health care. Therefore, we aimed to synthesise currently available data to identify the most vulnerable populations at risk of snakebite, and where additional data to manage this global problem are needed.

METHODS: We assembled a list of snake species using WHO guidelines. Where relevant, we obtained expert opinion range (EOR) maps from WHO or the Clinical Toxinology Resources. We also obtained occurrence data for each snake species from a variety of websites, such as VertNet and iNaturalist, using the spocc R package (version 0.7.0). We removed duplicate occurrence data and categorised snakes into three groups: group A (no available EOR map or species occurrence records), group B (EOR map but <5 species occurrence records), and group C (EOR map and ≥5 species occurrence records). For group C species, we did a multivariate environmental similarity analysis using the 2008 WHO EOR maps and newly available evidence. Using these data and the EOR maps, we produced contemporary range maps for medically important venomous snake species at a 5 × 5 km resolution. We subsequently triangulated these data with three health system metrics (antivenom availability, accessibility to urban centres, and the Healthcare Access and Quality [HAQ] Index) to identify the populations most vulnerable to snakebite morbidity and mortality.

FINDINGS: We provide a map showing the ranges of 278 snake species globally. Although about 6·85 billion people worldwide live within range of areas inhabited by snakes, about 146·70 million live within remote areas lacking quality health-care provisioning. Comparing opposite ends of the HAQ Index, 272·91 million individuals (65·25%) of the population within the lowest decile are at risk of exposure to any snake for which no effective therapy exists compared with 519·46 million individuals (27·79%) within the highest HAQ Index decile, showing a disproportionate coverage in reported antivenom availability. Antivenoms were available for 119 (43%) of 278 snake species evaluated by WHO, while globally 750·19 million (10·95%) of those living within snake ranges live more than 1 h from population centres. In total, we identify about 92·66 million people living within these vulnerable geographies, including many sub-Saharan countries, Indonesia, and other parts of southeast Asia.

INTERPRETATION: Identifying exact populations vulnerable to the most severe outcomes of snakebite envenoming at a subnational level is important for prioritising new data collection and collation, reinforcing envenoming treatment, existing health-care systems, and deploying currently available and future interventions. These maps can guide future research efforts on snakebite envenoming from both ecological and public health perspectives and better target future estimates of the burden of this neglected tropical disease.

FUNDING: Bill & Melinda Gates Foundation.}, } @article {pmid30016947, year = {2018}, author = {Song, Z and Stajich, JE and Xie, Y and Liu, X and He, Y and Chen, J and Hicks, GR and Wang, G}, title = {Comparative analysis reveals unexpected genome features of newly isolated Thraustochytrids strains: on ecological function and PUFAs biosynthesis.}, journal = {BMC genomics}, volume = {19}, number = {1}, pages = {541}, pmid = {30016947}, issn = {1471-2164}, support = {IOS-1027542//National Science Foundation/ ; CA-R-PPA-5062-H//National Institute of Food and Agriculture Hatch project/ ; 31670044//National Natural Science Foundation of China/ ; 91751115//National Natural Science Foundation of China/ ; S10 OD016290/OD/NIH HHS/United States ; # 2016YFA0601401//The National Key Research Program of China/ ; 201305022//National Marine Public Welfare Industry Special Scientific Research Project/ ; }, mesh = {Biosynthetic Pathways/genetics ; Docosahexaenoic Acids/*biosynthesis ; Ecological and Environmental Phenomena ; Fatty Acids, Unsaturated/biosynthesis ; Gene Ontology ; *Genome ; Genomics ; Molecular Sequence Annotation ; Multigene Family ; Phylogeny ; Stramenopiles/classification/enzymology/*genetics/metabolism ; }, abstract = {BACKGROUND: Thraustochytrids are unicellular fungal-like marine protists with ubiquitous existence in marine environments. They are well-known for their ability to produce high-valued omega-3 polyunsaturated fatty acids (ω-3-PUFAs) (e.g., docosahexaenoic acid (DHA)) and hydrolytic enzymes. Thraustochytrid biomass has been estimated to surpass that of bacterioplankton in both coastal and oceanic waters indicating they have an important role in microbial food-web. Nevertheless, the molecular pathway and regulatory network for PUFAs production and the molecular mechanisms underlying ecological functions of thraustochytrids remain largely unknown.

RESULTS: The genomes of two thraustochytrids strains (Mn4 and SW8) with ability to produce DHA were sequenced and assembled with a hybrid sequencing approach utilizing Illumina short paired-end reads and Pacific Biosciences long reads to generate a highly accurate genome assembly. Phylogenomic and comparative genomic analyses found that DHA-producing thraustochytrid strains were highly similar and possessed similar gene content. Analysis of the conventional fatty acid synthesis (FAS) and the polyketide synthase (PKS) systems for PUFAs production only detected incomplete and fragmentary pathways in the genome of these two strains. Surprisingly, secreted carbohydrate active enzymes (CAZymes) were found to be significantly depleted in the genomes of these 2 strains as compared to other sequenced relatives. Furthermore, these two strains possess an expanded gene repertoire for signal transduction and self-propelled movement, which could be important for their adaptations to dynamic marine environments.

CONCLUSIONS: Our results demonstrate the possibility of a third PUFAs synthesis pathway besides previously described FAS and PKS pathways encoded in the genome of these two thraustochytrid strains. Moreover, lack of a complete set of hydrolytic enzymatic machinery for degrading plant-derived organic materials suggests that these two DHA-producing strains play an important role as a nutritional source rather than a nutrient-producer in marine microbial-food web. Results of this study suggest the existence of two types of saprobic thraustochytrids in the world's ocean. The first group, which does not produce cellulosic enzymes and live as 'left-over' scavenger of bacterioplankton, serves as a dietary source for the plankton of higher trophic levels and the other possesses capacity to live on detrital organic matters in the marine ecosystems.}, } @article {pmid30016149, year = {2018}, author = {Piccolo, BD and Graham, JL and Stanhope, KL and Nookaew, I and Mercer, KE and Chintapalli, SV and Wankhade, UD and Shankar, K and Havel, PJ and Adams, SH}, title = {Diabetes-associated alterations in the cecal microbiome and metabolome are independent of diet or environment in the UC Davis Type 2 Diabetes Mellitus Rat model.}, journal = {American journal of physiology. Endocrinology and metabolism}, volume = {315}, number = {5}, pages = {E961-E972}, pmid = {30016149}, issn = {1522-1555}, support = {R01 DK050603/DK/NIDDK NIH HHS/United States ; P20 GM125503/GM/NIGMS NIH HHS/United States ; R01 DK078328/DK/NIDDK NIH HHS/United States ; R01 HL121324/HL/NHLBI NIH HHS/United States ; R01 HL121324/HL/NHLBI NIH HHS/United States ; P20 GM121293/GM/NIGMS NIH HHS/United States ; R01 HL107256/HL/NHLBI NIH HHS/United States ; R01 HL091333/HL/NHLBI NIH HHS/United States ; P20 GM125503/GM/NIGMS NIH HHS/United States ; U24 DK092993/DK/NIDDK NIH HHS/United States ; RC1 DK087307/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; Bacteroides/isolation & purification ; Cecum/metabolism/*microbiology ; Diabetes Mellitus, Type 2/metabolism/*microbiology ; Diet ; Disease Models, Animal ; Firmicutes/isolation & purification ; Gastrointestinal Microbiome/*physiology ; Male ; *Metabolome ; Metabolomics ; Metagenomics ; Prediabetic State/metabolism/*microbiology ; Rats ; Rats, Sprague-Dawley ; }, abstract = {The composition of the gut microbiome is altered in obesity and type 2 diabetes; however, it is not known whether these alterations are mediated by dietary factors or related to declines in metabolic health. To address this, cecal contents were collected from age-matched, chow-fed male University of California, Davis Type 2 Diabetes Mellitus (UCD-T2DM) rats before the onset of diabetes (prediabetic PD; n = 15), 2 wk recently diabetic (RD; n = 10), 3 mo (D3M; n = 11), and 6 mo (D6M; n = 8) postonset of diabetes. Bacterial species and functional gene counts were assessed by shotgun metagenomic sequencing of bacterial DNA in cecal contents, while metabolites were identified by gas chromatography-quadrupole time-off-flight-mass spectrometry. Metagenomic analysis showed a shift from Firmicutes species in early stages of diabetes (PD + RD) toward an enrichment of Bacteroidetes species in later stages of diabetes (D3M + D6M). In total, 45 bacterial species discriminated early and late stages of diabetes with 25 of these belonging to either Bacteroides or Prevotella genera. Furthermore, 61 bacterial gene clusters discriminated early and later stages of diabetes with elevations of enzymes related to stress response (e.g., glutathione and glutaredoxin) and amino acid, carbohydrate, and bacterial cell wall metabolism. Twenty-five cecal metabolites discriminated early vs. late stages of diabetes, with the largest differences observed in abundances of dehydroabietic acid and phosphate. Alterations in the gut microbiota and cecal metabolome track diabetes progression in UCD-T2DM rats when controlling for diet, age, and housing environment. Results suggest that diabetes-specific host signals impact the ecology and end product metabolites of the gut microbiome when diet is held constant.}, } @article {pmid30015809, year = {2018}, author = {Noble, DWA and Stenhouse, V and Riley, JL and Warner, DA and While, GM and Du, WG and Uller, T and Schwanz, LE}, title = {A comprehensive database of thermal developmental plasticity in reptiles.}, journal = {Scientific data}, volume = {5}, number = {}, pages = {180138}, pmid = {30015809}, issn = {2052-4463}, mesh = {Adaptation, Physiological ; Animals ; Behavior, Animal ; *Climate Change ; Databases, Factual ; Female ; Male ; Reptiles/embryology/*physiology ; }, abstract = {How temperature influences development has direct relevance to ascertaining the impact of climate change on natural populations. Reptiles have served as empirical models for understanding how the environment experienced by embryos can influence phenotypic variation, including sex ratio, phenology and survival. Such an understanding has important implications for basic eco-evolutionary theory and conservation efforts worldwide. While there is a burgeoning empirical literature of experimental manipulations of embryonic thermal environments, addressing widespread patterns at a comparative level has been hampered by the lack of accessible data in a format that is amendable to updates as new studies emerge. Here, we describe a database with nearly 10, 000 phenotypic estimates from 155 species of reptile, collected from 300 studies manipulating incubation temperature (published between 1974-2016). The data encompass various morphological, physiological, behavioural and performance traits along with growth rates, developmental timing, sex ratio and survival (e.g., hatching success). This resource will serve as an important data repository for addressing overarching questions about thermal plasticity of reptile embryos.}, } @article {pmid30014979, year = {2018}, author = {Tomczyk, NJ and Parr, TB and Wenger, SJ and Capps, KA}, title = {The influence of land cover on the sensitivity of streams to metal pollution.}, journal = {Water research}, volume = {144}, number = {}, pages = {55-63}, doi = {10.1016/j.watres.2018.06.058}, pmid = {30014979}, issn = {1879-2448}, mesh = {Carbon/analysis ; Databases, Factual ; *Ecosystem ; Ecotoxicology/*methods ; Fresh Water/chemistry ; *Metals/analysis/pharmacokinetics/toxicity ; *Models, Theoretical ; Rivers ; Temperature ; United States ; Water Pollutants, Chemical/analysis/pharmacokinetics/toxicity ; *Water Pollution, Chemical ; Wetlands ; }, abstract = {Identifying freshwater systems that are at risk from anthropogenic stressors is a pressing management problem. In particular, the detection of metal pollution is often constrained by data availability and resources. To address this challenge and develop a tool to identify susceptible systems, we tested whether land cover could be predictive of stream sensitivity to metal pollution, as determined by the biotic ligand model (BLM). We used water chemistry data from the conterminous United States to estimate metal sensitivity in streams using two BLMs (i.e., HydoQual, Bio-Met). Subsequently, we combined the sensitivity estimates with land cover and physiochemical data from the GAGES-II database to build predictive models of sensitivity to metals in streams. When combined, our predictor variables (e.g., land cover, mean annual temperature, mean annual precipitation) generally explained about half of the variation in our dataset. In each model, the percent of wetlands in a watershed was strongly correlated with reduced sensitivity to metals, likely due to increased concentrations of dissolved organic carbon associated with wetlands. To validate the utility of the models, we used them to predict metal sensitivity in sites where metal concentrations had been collected, but where the full suite of BLM parameters were unknown. We were able to classify several hundred sites which are likely at risk to metal pollution. Our work highlights the value in considering metal toxicity at the landscape-scale and describes a new approach to estimate metal sensitivity when site-specific chemical parameters are unknown.}, } @article {pmid30013185, year = {2018}, author = {Feijen, FAA and Vos, RA and Nuytinck, J and Merckx, VSFT}, title = {Evolutionary dynamics of mycorrhizal symbiosis in land plant diversification.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {10698}, pmid = {30013185}, issn = {2045-2322}, mesh = {Ascomycota/genetics ; Basidiomycota/genetics ; Bayes Theorem ; DNA, Chloroplast/genetics/isolation & purification ; DNA, Fungal/genetics/isolation & purification ; Datasets as Topic ; Embryophyta/*genetics/microbiology ; *Genetic Speciation ; Glomeromycota/genetics ; Mycorrhizae/*genetics ; *Phylogeny ; Soil Microbiology ; Symbiosis ; }, abstract = {Mycorrhizal symbiosis between soil fungi and land plants is one of the most widespread and ecologically important mutualisms on earth. It has long been hypothesized that the Glomeromycotina, the mycorrhizal symbionts of the majority of plants, facilitated colonization of land by plants in the Ordovician. This view was recently challenged by the discovery of mycorrhiza-like associations with Mucoromycotina in several early diverging lineages of land plants. Utilizing a large, species-level database of plants' mycorrhiza-like associations and a Bayesian approach to state transition dynamics we here show that the recruitment of Mucoromycotina is the best supported transition from a non-mycorrhizal state. We further found that transitions between different combinations of either or both of Mucoromycotina and Glomeromycotina occur at high rates, and found similar promiscuity among combinations that include either or both of Glomeromycotina and Ascomycota with a nearly fixed association with Basidiomycota. Our results portray an evolutionary scenario of evolution of mycorrhizal symbiosis with a prominent role for Mucoromycotina in the early stages of land plant diversification.}, } @article {pmid30011006, year = {2018}, author = {Garamszegi, LZ and Donald, J and Francis, CD and Fuxjager, MJ and Goymann, W and Hau, M and Husak, JF and Johnson, MA and Kircher, B and Knapp, R and Martin, LB and Miller, ET and Schoenle, LA and Vitousek, MN and Williams, TD}, title = {Species-Specific Means and Within-Species Variance in Glucocorticoid Hormones and Speciation Rates in Birds.}, journal = {Integrative and comparative biology}, volume = {58}, number = {4}, pages = {763-776}, doi = {10.1093/icb/icy086}, pmid = {30011006}, issn = {1557-7023}, mesh = {Animals ; Birds/*physiology ; Databases as Topic ; Ecosystem ; *Genetic Speciation ; Glucocorticoids/*metabolism ; Species Specificity ; }, abstract = {At macroevolutionary scales, stress physiology may have consequences for species diversification and subspecies richness. Populations that exploit new resources or undergo range expansion should cope with new environmental challenges, which could favor higher mean stress responses. Within-species variation in the stress response may also play a role in mediating the speciation process: in species with broad variation, there will always be some individuals that can tolerate an unpredictable environment, whereas in species with narrow variation there will be fewer individuals that are able to thrive in a new ecological niche. We tested for the evolutionary relationship between stress response, speciation rate, and subspecies richness in birds by relying on the HormoneBase repository, from which we calculated within- and among-species variation in baseline (BL) and stress-induced (SI) corticosterone levels. To estimate speciation rates, we applied Bayesian analysis of macroevolutionary mixtures that can account for variation in diversification rate among clades and through time. Contrary to our predictions, lineages with higher diversification rates were not characterized by higher BL or SI levels of corticosterone either at the tips or at the deeper nodes of the phylogeny. We also found no association between mean hormone levels and subspecies richness. Within-species variance in corticosterone levels showed close to zero repeatability, thus it is highly unlikely that this is a species-specific trait that influences diversification rates. These results imply that stress physiology may play a minor, if any, role in determining speciation rates in birds.}, } @article {pmid30010236, year = {2018}, author = {Drori, M and Rice, A and Einhorn, M and Chay, O and Glick, L and Mayrose, I}, title = {OneTwoTree: An online tool for phylogeny reconstruction.}, journal = {Molecular ecology resources}, volume = {18}, number = {6}, pages = {1492-1499}, doi = {10.1111/1755-0998.12927}, pmid = {30010236}, issn = {1755-0998}, support = {2016550//United States-Israel Binational Science Foundation/ ; 961/17//Israel Science Foundation/ ; //Edmond J. Safra Center for Bioinformatics/ ; }, mesh = {Computational Biology/*methods ; Internet ; *Phylogeny ; Plantaginaceae/classification/genetics ; }, abstract = {Phylogeny reconstruction is a key instrument in numerous biological analyses, ranging from evolutionary and ecology research, to conservation and systems biology. The increasing accumulation of genomic data makes it possible to reconstruct phylogenies with both high accuracy and at increasingly finer resolution. Yet, taking advantage of the enormous amount of sequence data available requires the use of computational tools for efficient data retrieval and processing, or else the process could quickly become an error-prone endeavour. Here, we present OneTwoTree (http://onetwotree.tau.ac.il/), a Web-based tool for tree reconstruction based on the supermatrix paradigm. Given a list of taxa names of interest as the sole input requirement, OneTwoTree retrieves all available sequence data from NCBI GenBank, clusters these into orthology groups, identifies the most informative set of markers, searches for an appropriate outgroup, and assembles a partitioned sequence matrix that is then used for the final phylogeny reconstruction step. OneTwoTree further allows users to control various steps of the process, such as the merging of sequences from similar clusters, or phylogeny reconstruction based on markers from a specific genome type. By comparing the performance of OneTwoTree to a manually reconstructed phylogeny of the Antirrhineae tribe, we show that the use of OneTwoTree resulted in substantially higher data coverage in terms of both taxon sampling and the number of informative markers assembled. OneTwoTree provides a flexible online tool for species-tree reconstruction, aimed to assist researchers ranging in their level of prior expertise in the task of phylogeny reconstruction.}, } @article {pmid30008248, year = {2018}, author = {Adams, WB and Rovito, MJ and Craycraft, M}, title = {The Connection Between Testicular Cancer, Minority Males, and Planned Parenthood.}, journal = {American journal of men's health}, volume = {12}, number = {5}, pages = {1774-1783}, pmid = {30008248}, issn = {1557-9891}, mesh = {Adolescent ; Adult ; Black or African American/statistics & numerical data ; Cohort Studies ; Databases, Factual ; Early Detection of Cancer/*methods ; Health Services Accessibility/statistics & numerical data ; Humans ; Incidence ; International Planned Parenthood Federation/organization & administration ; Male ; Medically Uninsured/*statistics & numerical data ; *Men's Health ; Needs Assessment ; Poverty ; Retrospective Studies ; Risk Assessment ; Sexual and Gender Minorities ; Testicular Neoplasms/*diagnosis/*epidemiology/therapy ; United States ; Vulnerable Populations/*statistics & numerical data ; Young Adult ; }, abstract = {Testicular cancer (TCa) is the most prevalent neoplasm diagnosed in males aged 15-40 years. Lack of access to care is a key impediment to early-stage TCa diagnosis. Health equity concerns arise, however, as poor access largely manifests within underserved male populations, therefore, placing them at a higher risk to develop late-stage TCa. Planned Parenthood Federation of America (PPFA) offers a myriad of male reproductive/sexual health care options, including TCa screening and referral services. Therefore, expanding these amenities in traditionally underserved communities may address the concern of TCa screening opportunities. An ecological analysis was performed using data from the United States Cancer Statistics, American Community Survey, and PPFA databases to assess the impact of TCa upon minority males, identify associations between PPFA services and minority males, and provide future implications on the role PPFA may play in bridging health-care access gaps pertaining to TCa screenings. Results indicate that states with higher rates of poverty and uninsured individuals, as well as specifically Black/African American males, have lower TCa incidence and limited access to screening services. PPFA service presence and Black/African American, as well as uninsured, males had a negative association but revealed positive correlations with TCa incidence. Considering the emerging TCa outcome disparities among minority males, expanding PPFA men's health services is crucial in providing affordable options to help identify testicular abnormalities that are early stage or carcinoma in situ. Many at-risk males have limited means to obtain TCa screening services. Expanding this discussion could provide a foundation for future advocacy.}, } @article {pmid30007868, year = {2018}, author = {Edwards, CJ and Cella, M and Emsley, R and Tarrier, N and Wykes, THM}, title = {Exploring the relationship between the anticipation and experience of pleasure in people with schizophrenia: An experience sampling study.}, journal = {Schizophrenia research}, volume = {202}, number = {}, pages = {72-79}, pmid = {30007868}, issn = {1573-2509}, support = {MR/K015516/1//Medical Research Council/United Kingdom ; }, mesh = {Adult ; Anticipation, Psychological/*physiology ; Ecological Momentary Assessment ; Female ; Humans ; Male ; Middle Aged ; Pleasure/*physiology ; Schizophrenia/*physiopathology ; }, abstract = {BACKGROUND: It has been hypothesised that a reduction in anticipatory pleasure contributes to reduced levels of functioning in people with schizophrenia. Previous research on anticipatory pleasure, however, reports mixed findings and has not yet examined the link between anticipatory pleasure and activity. The aim of this study is to examine how pleasure anticipation is related to difficulties engaging in activity in people with schizophrenia.

METHOD: A healthy control group (n = 44) and a group of individuals with schizophrenia (n = 36) completed an experience sampling study using portable devices. Participants rated motivation, mood, functional, leisure and social activity levels; anticipatory and consummatory pleasure seven times a day for six consecutive days. Multi-level regression models were constructed to examine the role of anticipatory pleasure and/or motivation in predicting future activities.

RESULTS: The findings showed no evidence for a motivation or pleasure deficit in people with schizophrenia. Yet, people with schizophrenia did fewer functional activities and spent more time "resting" or "doing nothing". In the control group, expectation was the only significant predictor of future activity. In contrast, none of the parameters assessed could predict experiences occurring in people with schizophrenia.

CONCLUSIONS: In contrast with controls people with schizophrenia did not show a link between their predictions and the activities they engaged in. This appears to be an important process influencing functioning in people with psychosis. Future interventions targeting reduced functioning should focus on reinforcing the link between pleasure anticipation and goal-directed behaviour.}, } @article {pmid30006621, year = {2018}, author = {Tagami, K and Uchida, S and Wood, MD and Beresford, NA}, title = {Radiocaesium transfer and radiation exposure of frogs in Fukushima Prefecture.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {10662}, pmid = {30006621}, issn = {2045-2322}, support = {NE/L000520/1//Natural Environment Research Council (NERC)/International ; NE/L000318/1//Natural Environment Research Council (NERC)/International ; }, mesh = {Age Factors ; Animals ; *Anura ; Cesium Radioisotopes/*toxicity ; Datasets as Topic ; *Fukushima Nuclear Accident ; Japan ; Larva/radiation effects ; Radiation Dosage ; Radiation Exposure/statistics & numerical data ; Radiation Monitoring/*methods/statistics & numerical data ; Water Pollutants, Radioactive/*toxicity ; }, abstract = {The International Commission on Radiological Protection has proposed an environmental assessment framework. This includes ionising radiation exposure assessment for different frog life-stages, but radiocaesium transfer parameters are unavailable. We collate data from the Fukushima Prefecture (contaminated by the Fukushima accident) and estimate radiocaesium concentration ratio (CRwo-water) values for tadpoles and adult frogs, presenting the largest available amphibian CRwo-water dataset. In total, 513 adult frogs and 2540 tadpoles were analysed in 62 and 59 composite samples respectively. Results suggest that equilibrium was reached between water and amphibian radiocaesium activity concentrations circa one-year after the accident. Radiocaesium transfer to tadpoles was higher than to adult frogs. Dose rates were estimated for different life-stages and species in both the aquatic and terrestrial environment. Estimated dose rates to adults and tadpoles were typically similar because external exposure dominated for both organisms; frogspawn dose rates were estimated to be orders of magnitude lower than other life-stages. For the two sites assessed, which were outside of the most contaminated areas of the Fukushima Prefecture, estimated dose rates were below those anticipated to present a risk to wildlife populations; it is likely that dose rates in more contaminated areas were in excess of some effects benchmark values.}, } @article {pmid30005602, year = {2018}, author = {Caniglia, R and Fabbri, E and Hulva, P and Bolfíková, BČ and Jindřichová, M and Stronen, AV and Dykyy, I and Camatta, A and Carnier, P and Randi, E and Galaverni, M}, title = {Wolf outside, dog inside? The genomic make-up of the Czechoslovakian Wolfdog.}, journal = {BMC genomics}, volume = {19}, number = {1}, pages = {533}, pmid = {30005602}, issn = {1471-2164}, support = {1337-00007//Danish Natural Science Research Council/ ; 20175018//IGA CULS/ ; 20175006//CIGA/ ; 20175018//IGA CULS/ ; }, mesh = {Animals ; Bayes Theorem ; Catechol O-Methyltransferase/genetics ; Circadian Rhythm/genetics ; Czechoslovakia ; DNA/isolation & purification/metabolism ; Dogs/*genetics ; Gene Ontology ; Genetics, Population ; *Genome ; Hybridization, Genetic ; Linkage Disequilibrium ; Lipid Metabolism/genetics ; Polymorphism, Single Nucleotide ; Principal Component Analysis ; Wolves/*genetics ; }, abstract = {BACKGROUND: Genomic methods can provide extraordinary tools to explore the genetic background of wild species and domestic breeds, optimize breeding practices, monitor and limit the spread of recessive diseases, and discourage illegal crossings. In this study we analysed a panel of 170k Single Nucleotide Polymorphisms with a combination of multivariate, Bayesian and outlier gene approaches to examine the genome-wide diversity and inbreeding levels in a recent wolf x dog cross-breed, the Czechoslovakian Wolfdog, which is becoming increasingly popular across Europe.

RESULTS: Pairwise FST values, multivariate and assignment procedures indicated that the Czechoslovakian Wolfdog was significantly differentiated from all the other analysed breeds and also well-distinguished from both parental populations (Carpathian wolves and German Shepherds). Coherently with the low number of founders involved in the breed selection, the individual inbreeding levels calculated from homozygosity regions were relatively high and comparable with those derived from the pedigree data. In contrast, the coefficient of relatedness between individuals estimated from the pedigrees often underestimated the identity-by-descent scores determined using genetic profiles. The timing of the admixture and the effective population size trends estimated from the LD patterns reflected the documented history of the breed. Ancestry reconstruction methods identified more than 300 genes with excess of wolf ancestry compared to random expectations, mainly related to key morphological features, and more than 2000 genes with excess of dog ancestry, playing important roles in lipid metabolism, in the regulation of circadian rhythms, in learning and memory processes, and in sociability, such as the COMT gene, which has been described as a candidate gene for the latter trait in dogs.

CONCLUSIONS: In this study we successfully applied genome-wide procedures to reconstruct the history of the Czechoslovakian Wolfdog, assess individual wolf ancestry proportions and, thanks to the availability of a well-annotated reference genome, identify possible candidate genes for wolf-like and dog-like phenotypic traits typical of this breed, including commonly inherited disorders. Moreover, through the identification of ancestry-informative markers, these genomic approaches could provide tools for forensic applications to unmask illegal crossings with wolves and uncontrolled trades of recent and undeclared wolfdog hybrids.}, } @article {pmid29996779, year = {2018}, author = {Greer, JB and Schmale, MC and Fieber, LA}, title = {Whole-transcriptome changes in gene expression accompany aging of sensory neurons in Aplysia californica.}, journal = {BMC genomics}, volume = {19}, number = {1}, pages = {529}, pmid = {29996779}, issn = {1471-2164}, support = {P40 OD010952/OD/NIH HHS/United States ; }, mesh = {Aging/*genetics ; Animals ; Aplysia/*genetics/metabolism ; Down-Regulation ; Gene Ontology ; Ion Channels/genetics/metabolism ; Principal Component Analysis ; RNA/chemistry/isolation & purification/metabolism ; Sensory Receptor Cells/*metabolism ; Sequence Analysis, RNA ; Signal Transduction/genetics ; *Transcriptome ; Up-Regulation ; }, abstract = {BACKGROUND: Large-scale molecular changes occur during aging and have many downstream consequences on whole-organism function, such as motor function, learning, and memory. The marine mollusk Aplysia californica can be used to study transcriptional changes that occur with age in identified neurons of the brain, because its simplified nervous system allows for more direct correlations between molecular changes, physiological changes, and their phenotypic outcomes. Behavioral deficits in the tail-withdrawal reflex of aged animals have been correlated with reduced excitation in sensory neurons that control the reflex. RNASeq was used to investigate whole-transcriptome changes in tail-withdrawal sensory neurons of sexually mature and aged Aplysia to correlate transcriptional changes with reduced behavioral and physiological responses.

RESULTS: Paired-end sequencing resulted in 210 million reads used for differential expression analysis. Aging significantly altered expression of 1202 transcripts in sensory neurons underlying the tail-withdrawal reflex, with an approximately equal number of these genes up- and down regulated with age. Despite overall bidirectionality of expression changes, > 80% of ion channel genes that were differentially expressed had decreased expression with age. In particular, several voltage-gated K[+] and Ca[2+] channels were down regulated. This marked decrease in ion channel expression may play an important role in previously observed declines in aged sensory neuron excitability. We also observed decreased expression of genes and pathways involved in learning and memory. Genes involved in the stress response showed increased expression in aged Aplysia neurons.

CONCLUSIONS: Significantly altered expression of many genes between sexually mature and aged Aplysia suggests large molecular changes that may impact neuronal function. Decreased ion channel mRNA observed could mean fewer receptors present in aged neurons, resulting in reduced excitability of PVC sensory neurons, ultimately leading to reduced tail-withdrawal reflex observed in aged Aplysia. Significant changes in other genes and pathways, such as stress response and learning and memory, have previously been shown to occur with age in many vertebrate organisms. This suggests that some effects of aging are common across many animal phyla.}, } @article {pmid29995174, year = {2018}, author = {Gan, HM and Austin, C and Linton, S}, title = {Transcriptome-Guided Identification of Carbohydrate Active Enzymes (CAZy) from the Christmas Island Red Crab, Gecarcoidea natalis and a Vote for the Inclusion of Transcriptome-Derived Crustacean CAZys in Comparative Studies.}, journal = {Marine biotechnology (New York, N.Y.)}, volume = {20}, number = {5}, pages = {654-665}, pmid = {29995174}, issn = {1436-2236}, mesh = {Amino Acid Sequence ; Animals ; Arthropod Proteins/chemistry/classification/*genetics/metabolism ; Brachyura/classification/enzymology/*genetics ; Carbohydrate Metabolism/*genetics ; Cellulase/chemistry/classification/*genetics/metabolism ; Databases, Genetic ; Diet ; Gene Expression ; Gene Ontology ; Isoenzymes/chemistry/classification/genetics/metabolism ; Models, Molecular ; Molecular Sequence Annotation ; Phylogeny ; Protein Conformation, alpha-Helical ; Protein Conformation, beta-Strand ; RNA, Messenger/genetics/metabolism ; Sequence Alignment ; Structural Homology, Protein ; *Transcriptome ; }, abstract = {The Christmas Island red crab, Gecarcoidea natalis, is an herbivorous land crab that consumes mostly fallen leaf litter. In order to subsist, G. natalis would need to have developed specialised digestive enzymes capable of supplying significant amounts of metabolisable sugars from this diet. To gain insights into the carbohydrate metabolism of G. natalis, a transcriptome assembly was performed, with a specific focus on identifying transcripts coding for carbohydrate active enzyme (CAZy) using in silico approaches. Transcriptome sequencing of the midgut gland identified 70 CAZy-coding transcripts with varying expression values. At least three newly discovered putative GH9 endo-β-1,4-glucanase ("classic cellulase") transcripts were highly expressed in the midgut gland in addition to the previously characterised GH9 and GH16 (β-1,3-glucanase) transcripts, and underscoring the utility of whole transcriptome in uncovering new CAZy-coding transcripts. A highly expressed transcript coding for GH5_10 previously missed by conventional screening of cellulase activity was inferred to be a novel endo-β-1,4-mannase in G. natalis with in silico support from homology modelling and amino acid alignment with other functionally validated GH5_10 proteins. Maximum likelihood tree reconstruction of the GH5_10 proteins demonstrates the phylogenetic affiliation of the G. natalis GH5_10 transcript to that of other decapods, supporting endogenous expression. Surprisingly, crustacean-derived GH5_10 transcripts were near absent in the current CAZy database and yet mining of the transcriptome shotgun assembly (TSA) recovered more than 100 crustacean GH5_10s in addition to several other biotechnological relevant CAZys, underscoring the unappreciated potential of the TSA database as a valuable resource for crustacean CAZys.}, } @article {pmid29992097, year = {2018}, author = {Gil-Pulido, B and Tarpey, E and Almeida, EL and Finnegan, W and Zhan, X and Dobson, ADW and O'Leary, N}, title = {Evaluation of dairy processing wastewater biotreatment in an IASBR system: Aeration rate impacts on performance and microbial ecology.}, journal = {Biotechnology reports (Amsterdam, Netherlands)}, volume = {19}, number = {}, pages = {e00263}, pmid = {29992097}, issn = {2215-017X}, abstract = {Dairy processing generates large volumes of wastewater that require extensive nutrient remediation prior to discharge. Significant commercial opportunities exist therefore for cost-effective biotechnologies capable of achieving this requirement. In this study the authors evaluated the use of intermittently aerated sequencing batch reactors, (IASBRs), as a single-tank biotreatment system for co-removal of COD, nitrogen and phosphorus from synthetic dairy processing wastewater. Variation of the IASBR aeration rates, (0.8, 0.6 and 0.4 L/min), had significant impacts on the respective nutrient removal efficiencies and underlying microbial diversity profiles. Aeration at 0.6 L/min was most effective and resulted in >90% co-removal of orthophosphate and ammonium. 16S rRNA based pyrosequencing of biomass DNA samples revealed the family Comamonadaceae was notably enriched (>80% relative abundance) under these conditions. In silico predictive metabolic modelling also identified Comamonadaceae as the major contributor of several known genes for nitrogen and phosphorus assimilation (nirK, nosZ, norB, ppK, ppX and phbC).}, } @article {pmid29991804, year = {2018}, author = {Reich, I and Ijaz, UZ and Gormally, M and Smith, CJ}, title = {16S rRNA sequencing reveals likely beneficial core microbes within faecal samples of the EU protected slug Geomalacus maculosus.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {10402}, pmid = {29991804}, issn = {2045-2322}, mesh = {Animals ; Biodiversity ; Computational Biology ; Feces/microbiology ; Gastropoda/genetics/*microbiology ; High-Throughput Nucleotide Sequencing ; Ireland ; Microbiota/*genetics ; *Phylogeny ; Portugal ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, DNA ; Spain ; }, abstract = {The EU-protected slug Geomalacus maculosus Allman occurs only in the West of Ireland and in northern Spain and Portugal. We explored the microbial community found within the faeces of Irish specimens with a view to determining whether a core microbiome existed among geographically isolated slugs which could give insight into the adaptations of G. maculosus to the available food resources within its habitat. Faecal samples of 30 wild specimens were collected throughout its Irish range and the V3 region of the bacterial 16S rRNA gene was sequenced using Illumina MiSeq. To investigate the influence of diet on the microbial composition, faecal samples were taken and sequenced from six laboratory reared slugs which were raised on two different foods. We found a widely diverse microbiome dominated by Enterobacteriales with three core OTUs shared between all specimens. While the reared specimens appeared clearly separated by diet in NMDS plots, no significant difference between the slugs fed on the two different diets was found. Our results indicate that while the majority of the faecal microbiome of G. maculosus is probably dependent on the microhabitat of the individual slugs, parts of it are likely selected for by the host.}, } @article {pmid29991352, year = {2018}, author = {Vidulin, V and Šmuc, T and Džeroski, S and Supek, F}, title = {The evolutionary signal in metagenome phyletic profiles predicts many gene functions.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {129}, pmid = {29991352}, issn = {2049-2618}, mesh = {Evolution, Molecular ; Gene Ontology ; Genomics ; Humans ; Metagenomics/*methods ; *Multigene Family ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA/*methods ; Water Microbiology ; }, abstract = {BACKGROUND: The function of many genes is still not known even in model organisms. An increasing availability of microbiome DNA sequencing data provides an opportunity to infer gene function in a systematic manner.

RESULTS: We evaluated if the evolutionary signal contained in metagenome phyletic profiles (MPP) is predictive of a broad array of gene functions. The MPPs are an encoding of environmental DNA sequencing data that consists of relative abundances of gene families across metagenomes. We find that such MPPs can accurately predict 826 Gene Ontology functional categories, while drawing on human gut microbiomes, ocean metagenomes, and DNA sequences from various other engineered and natural environments. Overall, in this task, the MPPs are highly accurate, and moreover they provide coverage for a set of Gene Ontology terms largely complementary to standard phylogenetic profiles, derived from fully sequenced genomes. We also find that metagenomes approximated from taxon relative abundance obtained via 16S rRNA gene sequencing may provide surprisingly useful predictive models. Crucially, the MPPs derived from different types of environments can infer distinct, non-overlapping sets of gene functions and therefore complement each other. Consistently, simulations on > 5000 metagenomes indicate that the amount of data is not in itself critical for maximizing predictive accuracy, while the diversity of sampled environments appears to be the critical factor for obtaining robust models.

CONCLUSIONS: In past work, metagenomics has provided invaluable insight into ecology of various habitats, into diversity of microbial life and also into human health and disease mechanisms. We propose that environmental DNA sequencing additionally constitutes a useful tool to predict biological roles of genes, yielding inferences out of reach for existing comparative genomics approaches.}, } @article {pmid29989590, year = {2018}, author = {Tavşanoğlu, Ç and Pausas, JG}, title = {A functional trait database for Mediterranean Basin plants.}, journal = {Scientific data}, volume = {5}, number = {}, pages = {180135}, pmid = {29989590}, issn = {2052-4463}, mesh = {*Databases, Factual ; Ecosystem ; Mediterranean Region ; *Plants ; }, abstract = {Functional trait databases are emerging as crucial tools for a wide range of ecological studies across the world. Here, we provide a database of functional traits for vascular plant species of the Mediterranean Basin. The database includes 25,764 individual records of 44 traits from 2,457 plant taxa distributed in 119 taxonomic families. This database (BROT 2.0) is an updated and enlarged version of a previous database (BROT 1.0; 8,263 records, 14 traits, 952 taxa). Trait data were obtained from a comprehensive literature review, plus some field and experimental observations. All records are fully referenced and, in many cases, include geographic coordinates. The database is structured to include different levels of accuracy of trait information for each entry. BROT 2.0 should facilitate testing hypotheses on plant functional ecology within the Mediterranean Basin, and comparing this region with other ecosystems worldwide. The BROT 2.0 database and its trait definitions can be used as a template for creating similar trait databases in other regions of the world.}, } @article {pmid29988159, year = {2018}, author = {Stein, LR and Bukhari, SA and Bell, AM}, title = {Personal and transgenerational cues are nonadditive at the phenotypic and molecular level.}, journal = {Nature ecology & evolution}, volume = {2}, number = {8}, pages = {1306-1311}, pmid = {29988159}, issn = {2397-334X}, support = {R01 GM082937/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Brain/physiology ; *Cues ; Male ; *Paternal Behavior ; Perciformes/physiology ; Phenotype ; *Predatory Behavior ; Smegmamorpha/*physiology ; }, abstract = {Organisms can gain information about their environment from their ancestors, their parents or their own personal experience. 'Cue integration' models often start with the simplifying assumption that information from different sources is additive. Here, we test key assumptions and predictions of cue integration theory at both the phenotypic and molecular level in threespined sticklebacks (Gasterosteus aculeatus). We show that regardless of whether cues about predation risk were provided by their father or acquired through personal experience, sticklebacks produced the same set of predator-adapted phenotypes. Moreover, there were nonadditive effects of personal and paternal experience: animals that received cues from both sources resembled animals that received cues from a single source. A similar pattern was detected at the molecular level: there was a core set of genes that were differentially expressed in the brains of offspring regardless of whether risk was experienced by their father, themselves or both. These results provide strong support for cue integration theory because they show that cues provided by parents and personal experience are comparable at both the phenotypic and molecular level, and draw attention to the importance of nonadditive responses to multiple cues.}, } @article {pmid29985552, year = {2018}, author = {Ma, ZS and Li, L}, title = {Measuring metagenome diversity and similarity with Hill numbers.}, journal = {Molecular ecology resources}, volume = {18}, number = {6}, pages = {1339-1355}, doi = {10.1111/1755-0998.12923}, pmid = {29985552}, issn = {1755-0998}, support = {//Industry Technology Talent Grant/ ; //A China-US International Collaborative Project/ ; 71473243//National Science Foundation of China/ ; }, mesh = {Cluster Analysis ; Computational Biology/*methods ; DNA, Ribosomal/chemistry/genetics ; *Genetic Variation ; *Metagenome ; Metagenomics/*methods ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {The first step of any metagenome sequencing project is to get the inventory of OTU abundances (operational taxonomic units) and/or metagenomic gene abundances. The former is generated with 16S-rRNA-tagged amplicon sequencing technology, and the latter can be generated from either gene-targeted or whole-sample shotgun metagenomics technologies. With 16S-rRNA data sets, measuring community diversity with diversity indexes such as species richness and Shannon's index has been a de facto standard analysis; nevertheless, similarly comprehensive approaches to metagenomic gene abundances are still largely missing, despite that both OTU and gene abundances are DNA reads. Here, we adapt the Hill numbers, which were reintroduced to macrocommunity ecology recently and are now widely regarded as a most appropriate measure system for ecological diversity, for measuring metagenome alpha-, beta- and gamma-diversities, and similarity. Our proposal includes the following: (a) Metagenomic gene (MG) diversity measures the single-gene-level metagenome diversity; (b) Type-I metagenome functional gene cluster (MFGC) diversity measures the diversity of functional gene clusters but ignoring within-cluster gene abundance information; (c) Type-II MFGC diversity considers within-cluster gene abundances information and integrates gene-cluster-level metagenome diversity and functional gene redundancy information; and (d) Four classes of Hill-numbers-based similarity metrics, including local gene overlap, regional gene overlap, gene homogeneity measure and gene turnover complement, were introduced in terms of MG and MFGC, respectively. We demonstrate the proposal with the gut metagenomes from healthy and IBD (inflammatory bowel disease) cohorts. The Hill numbers offer a unified approach to cohesively and comprehensively measuring the ecological and metagenome diversities of microbiomes.}, } @article {pmid29985386, year = {2018}, author = {Kakar, KU and Nawaz, Z and Cui, Z and Cao, P and Jin, J and Shu, Q and Ren, X}, title = {Evolutionary and expression analysis of CAMTA gene family in Nicotiana tabacum yielded insights into their origin, expansion and stress responses.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {10322}, pmid = {29985386}, issn = {2045-2322}, mesh = {Amino Acid Motifs ; Evolution, Molecular ; Gene Expression Regulation, Plant ; Genome, Plant ; MicroRNAs/metabolism ; Phylogeny ; Plant Leaves/genetics/metabolism ; Plant Proteins/classification/*genetics/metabolism ; Plant Roots/genetics/metabolism ; Stress, Physiological ; Nicotiana/genetics/growth & development/*metabolism ; Transcription Factors/classification/*genetics/metabolism ; }, abstract = {Calmodulin-binding transcription activators (CAMTAs) represent the novel gene family of transcriptional regulators, which play important biological functions. Though, the first ever plant CAMTA gene was evidenced in Nicotiana tabacum in 2002. But, the systematic identification, origin and function of this gene family has not been performed due to the lack of reference genome information until now. Here, we identified 29 CAMTA genes in four Nicotiana species, including thirteen NtabCAMTAs, six NsylCAMTAs, and five NtomCAMTAs and NbenCAMTAs. These CAMTA families were classified into five phylogenetic groups (I-V), among which, the group-IV CAMTAs probably emerged the earliest. The NtabCAMTA family genes have diverse structures, and are randomly localized on five chromosomes and scaffolds. N. tabacum acquired 11 copies of homolog CAMATA genes from the parental genomes of N. tomentosiformis and N. sylvestris, followed by expansion through polyploidization and duplication. The NtabCAMTA genes were differentially expressed in different plant parts, and showed sensitivity towards different abiotic and biotic stresses. Co-expression network analysis revealed that some NtabCAMTA subunits interact with each other, and co-expressed. The current study is the first report presenting a comprehensive overview of Nicotiana CAMTA families, and opens a new avenue for the improvement of the cultivated tobacco.}, } @article {pmid29982597, year = {2018}, author = {Akbarzadeh, K and Saghafipour, A and Jesri, N and Karami-Jooshin, M and Arzamani, K and Hazratian, T and Kordshouli, RS and Afshar, AA}, title = {Spatial Distribution of Necrophagous Flies of Infraorder Muscomorpha in Iran Using Geographical Information System.}, journal = {Journal of medical entomology}, volume = {55}, number = {5}, pages = {1071-1085}, doi = {10.1093/jme/tjy098}, pmid = {29982597}, issn = {1938-2928}, mesh = {*Animal Distribution ; Animals ; Geographic Information Systems ; Iran ; *Sarcophagidae ; }, abstract = {Medically important flies that majority of them are classified to synanthropic flies can be mechanical vectors for some of contagious diseases to human and many animals. Also some species of their larvae are cause of myiasis in human and livestock animals. The aim of this study was to determine the geographical distribution of medically important flies in Iran using Geographical Information System (GIS). All published English and Persian documents on medically important flies of Iran from reliable medical sciences resources were gathered. A database was then designed in Excel format, including all available information regarding flies. The valid data were transferred to ArcGIS 10.3 to prepare the first spatial database of medically important flies and human myiasis foci of Iran. The Iran Medical Important Flies base includes 71 papers and three PhD/MSc theses, reporting studies conducted during 1977-2017. This database contains different available data covering their faunistic and all myiasis data reports related to flies of 102 species in nine families of medical important flies in Iran. Twenty-three out of the 31 provinces of Iran, had some reports of medically important flies. However, these flies have high species diversity, wide geographical distribution and with various ecological niches in different provinces in Iran. Besides that, there are many high-risk foci of human myiasis in a number of provinces of Iran.}, } @article {pmid29982387, year = {2019}, author = {Dumitrascu, B and Darnell, G and Ayroles, J and Engelhardt, BE}, title = {Statistical tests for detecting variance effects in quantitative trait studies.}, journal = {Bioinformatics (Oxford, England)}, volume = {35}, number = {2}, pages = {200-210}, pmid = {29982387}, issn = {1367-4811}, support = {R01 HL133218/HL/NHLBI NIH HHS/United States ; R01 MH101822/MH/NIMH NIH HHS/United States ; R35 GM124881/GM/NIGMS NIH HHS/United States ; U01 HG007900/HG/NHGRI NIH HHS/United States ; }, mesh = {Analysis of Variance ; *Bayes Theorem ; Computational Biology ; Genomics/*methods ; Humans ; *Linear Models ; *Models, Genetic ; Phenotype ; *Quantitative Trait Loci ; }, abstract = {MOTIVATION: Identifying variants, both discrete and continuous, that are associated with quantitative traits, or QTs, is the primary focus of quantitative genetics. Most current methods are limited to identifying mean effects, or associations between genotype or covariates and the mean value of a quantitative trait. It is possible, however, that a variant may affect the variance of the quantitative trait in lieu of, or in addition to, affecting the trait mean. Here, we develop a general methodology to identify covariates with variance effects on a quantitative trait using a Bayesian heteroskedastic linear regression model (BTH). We compare BTH with existing methods to detect variance effects across a large range of simulations drawn from scenarios common to the analysis of quantitative traits.

RESULTS: We find that BTH and a double generalized linear model (dglm) outperform classical tests used for detecting variance effects in recent genomic studies. We show BTH and dglm are less likely to generate spurious discoveries through simulations and application to identifying methylation variance QTs and expression variance QTs. We identify four variance effects of sex in the Cardiovascular and Pharmacogenetics study. Our work is the first to offer a comprehensive view of variance identifying methodology. We identify shortcomings in previously used methodology and provide a more conservative and robust alternative. We extend variance effect analysis to a wide array of covariates that enables a new statistical dimension in the study of sex and age specific quantitative trait effects.

https://github.com/b2du/bth.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, } @article {pmid29981081, year = {2018}, author = {Khan, Y and Leung, GJ and Belanger, P and Gournis, E and Buckeridge, DL and Liu, L and Li, Y and Johnson, IL}, title = {Comparing Twitter data to routine data sources in public health surveillance for the 2015 Pan/Parapan American Games: an ecological study.}, journal = {Canadian journal of public health = Revue canadienne de sante publique}, volume = {109}, number = {3}, pages = {419-426}, pmid = {29981081}, issn = {1920-7476}, mesh = {Canada ; Crowding ; Feasibility Studies ; Humans ; Public Health Surveillance/*methods ; *Social Media ; *Sports ; }, abstract = {OBJECTIVES: This study examined Twitter for public health surveillance during a mass gathering in Canada with two objectives: to explore the feasibility of acquiring, categorizing and using geolocated Twitter data and to compare Twitter data against other data sources used for Pan Parapan American Games (P/PAG) surveillance.

METHODS: Syndrome definitions were created using keyword categorization to extract posts from Twitter. Categories were developed iteratively for four relevant syndromes: respiratory, gastrointestinal, heat-related illness, and influenza-like illness (ILI). All data sources corresponded to the location of Toronto, Canada. Twitter data were acquired from a publicly available stream representing a 1% random sample of tweets from June 26 to September 10, 2015. Cross-correlation analyses of time series data were conducted between Twitter and comparator surveillance data sources: emergency department visits, telephone helpline calls, laboratory testing positivity rate, reportable disease data, and temperature.

RESULTS: The frequency of daily tweets that were classified into syndromes was low, with the highest mean number of daily tweets being for ILI and respiratory syndromes (22.0 and 21.6, respectively) and the lowest, for the heat syndrome (4.1). Cross-correlation analyses of Twitter data demonstrated significant correlations for heat syndrome with two data sources: telephone helpline calls (r = 0.4) and temperature data (r = 0.5).

CONCLUSION: Using simple syndromes based on keyword classification of geolocated tweets, we found a correlation between tweets and two routine data sources for heat alerts, the only public health event detected during P/PAG. Further research is needed to understand the role for Twitter in surveillance.}, } @article {pmid29981010, year = {2019}, author = {Lant, C and Baggio, J and Konar, M and Mejia, A and Ruddell, B and Rushforth, R and Sabo, JL and Troy, TJ}, title = {The U.S. food-energy-water system: A blueprint to fill the mesoscale gap for science and decision-making.}, journal = {Ambio}, volume = {48}, number = {3}, pages = {251-263}, pmid = {29981010}, issn = {1654-7209}, support = {1639529//National Science Foundation/ ; }, mesh = {Cities ; Decision Making ; *Ecology ; Food ; Humans ; *Water ; }, abstract = {Food, energy, and water (FEW) are interdependent and must be examined as a coupled natural-human system. This perspective essay defines FEW systems and outlines key findings about them as a blueprint for future models to satisfy six key objectives. The first three focus on linking the FEW production and consumption to impacts on Earth cycles in a spatially specific manner in order to diagnose problems and identify potential solutions. The second three focus on describing the evolution of FEW systems to identify risks, thus empowering the FEW actors to better achieve the goals of resilience and sustainability. Four key findings about the FEW systems that guide future model development are (1) that they engage ecological, carbon, water, and nutrient cycles most powerfully among all human systems; (2) that they operate primarily at a mesoscale best captured by counties, districts, and cities; (3) that cities are hubs within the FEW system; and (4) that the FEW system forms a complex network.}, } @article {pmid29980501, year = {2018}, author = {Meyers, L and Ginocchio, CC and Faucett, AN and Nolte, FS and Gesteland, PH and Leber, A and Janowiak, D and Donovan, V and Dien Bard, J and Spitzer, S and Stellrecht, KA and Salimnia, H and Selvarangan, R and Juretschko, S and Daly, JA and Wallentine, JC and Lindsey, K and Moore, F and Reed, SL and Aguero-Rosenfeld, M and Fey, PD and Storch, GA and Melnick, SJ and Robinson, CC and Meredith, JF and Cook, CV and Nelson, RK and Jones, JD and Scarpino, SV and Althouse, BM and Ririe, KM and Malin, BA and Poritz, MA}, title = {Automated Real-Time Collection of Pathogen-Specific Diagnostic Data: Syndromic Infectious Disease Epidemiology.}, journal = {JMIR public health and surveillance}, volume = {4}, number = {3}, pages = {e59}, pmid = {29980501}, issn = {2369-2960}, support = {U01 AI074419/AI/NIAID NIH HHS/United States ; }, abstract = {BACKGROUND: Health care and public health professionals rely on accurate, real-time monitoring of infectious diseases for outbreak preparedness and response. Early detection of outbreaks is improved by systems that are comprehensive and specific with respect to the pathogen but are rapid in reporting the data. It has proven difficult to implement these requirements on a large scale while maintaining patient privacy.

OBJECTIVE: The aim of this study was to demonstrate the automated export, aggregation, and analysis of infectious disease diagnostic test results from clinical laboratories across the United States in a manner that protects patient confidentiality. We hypothesized that such a system could aid in monitoring the seasonal occurrence of respiratory pathogens and may have advantages with regard to scope and ease of reporting compared with existing surveillance systems.

METHODS: We describe a system, BioFire Syndromic Trends, for rapid disease reporting that is syndrome-based but pathogen-specific. Deidentified patient test results from the BioFire FilmArray multiplex molecular diagnostic system are sent directly to a cloud database. Summaries of these data are displayed in near real time on the Syndromic Trends public website. We studied this dataset for the prevalence, seasonality, and coinfections of the 20 respiratory pathogens detected in over 362,000 patient samples acquired as a standard-of-care testing over the last 4 years from 20 clinical laboratories in the United States.

RESULTS: The majority of pathogens show influenza-like seasonality, rhinovirus has fall and spring peaks, and adenovirus and the bacterial pathogens show constant detection over the year. The dataset can also be considered in an ecological framework; the viruses and bacteria detected by this test are parasites of a host (the human patient). Interestingly, the rate of pathogen codetections, on average 7.94% (28,741/362,101), matches predictions based on the relative abundance of organisms present.

CONCLUSIONS: Syndromic Trends preserves patient privacy by removing or obfuscating patient identifiers while still collecting much useful information about the bacterial and viral pathogens that they harbor. Test results are uploaded to the database within a few hours of completion compared with delays of up to 10 days for other diagnostic-based reporting systems. This work shows that the barriers to establishing epidemiology systems are no longer scientific and technical but rather administrative, involving questions of patient privacy and data ownership. We have demonstrated here that these barriers can be overcome. This first look at the resulting data stream suggests that Syndromic Trends will be able to provide high-resolution analysis of circulating respiratory pathogens and may aid in the detection of new outbreaks.}, } @article {pmid29980049, year = {2018}, author = {Morin, CW and Stoner-Duncan, B and Winker, K and Scotch, M and Hess, JJ and Meschke, JS and Ebi, KL and Rabinowitz, PM}, title = {Avian influenza virus ecology and evolution through a climatic lens.}, journal = {Environment international}, volume = {119}, number = {}, pages = {241-249}, doi = {10.1016/j.envint.2018.06.018}, pmid = {29980049}, issn = {1873-6750}, mesh = {Animals ; Asia ; Birds/*virology ; *Climate ; Ecology ; Ecosystem ; Influenza in Birds/*virology ; North America ; *Orthomyxoviridae ; }, abstract = {Avian influenza virus (AIV) is a major health threat to both avian and human populations. The ecology of the virus is driven by numerous factors, including climate and avian migration patterns, yet relatively little is known about these drivers. Long-distance transport of the virus is tied to inter- and intra-continental bird migration, while enhanced viral reassortment is linked to breeding habitats in Beringia shared by migrant species from North America and Asia. Furthermore, water temperature, pH, salinity, and co-existing biota all impact the viability and persistence of the virus in the environment. Changes in climate can potentially alter the ecology of AIV through multiple pathways. Warming temperatures can change the timing and patterns of bird migration, creating novel assemblages of species and new opportunities for viral transport and reassortment. Water temperature and chemistry may also be altered, resulting in changes in virus survival. In this review, we explain how these shifts have the potential to increase viral persistence, pathogenicity, and transmissibility and amplify the threat of pandemic disease in animal and human hosts. Better understanding of climatic influences on viral ecology is essential to developing strategies to limit adverse health effects in humans and animals.}, } @article {pmid29979688, year = {2018}, author = {Mzobe, P and Berggren, M and Pilesjö, P and Lundin, E and Olefeldt, D and Roulet, NT and Persson, A}, title = {Dissolved organic carbon in streams within a subarctic catchment analysed using a GIS/remote sensing approach.}, journal = {PloS one}, volume = {13}, number = {7}, pages = {e0199608}, pmid = {29979688}, issn = {1932-6203}, mesh = {Carbon/*analysis ; Climate Change ; Environmental Monitoring ; Fresh Water/analysis/chemistry ; *Geographic Information Systems ; Geography ; Models, Theoretical ; Organic Chemicals/*analysis ; *Remote Sensing Technology ; Rivers/*chemistry ; Spatial Analysis ; Sweden ; }, abstract = {Climate change projections show that temperature and precipitation increases can alter the exchange of greenhouse gases between the atmosphere and high latitude landscapes, including their freshwaters. Dissolved organic carbon (DOC) plays an important role in greenhouse gas emissions, but the impact of catchment productivity on DOC release to subarctic waters remains poorly known, especially at regional scales. We test the hypothesis that increased terrestrial productivity, as indicated by the normalized difference vegetation index (NDVI), generates higher stream DOC concentrations in the Stordalen catchment in subarctic Sweden. Furthermore, we aimed to determine the degree to which other generic catchment properties (elevation, slope) explain DOC concentration, and whether or not land cover variables representing the local vegetation type (e.g., mire, forest) need to be included to obtain adequate predictive models for DOC delivered into rivers. We show that the land cover type, especially the proportion of mire, played a dominant role in the catchment's release of DOC, while NDVI, slope, and elevation were supporting predictor variables. The NDVI as a single predictor showed weak and inconsistent relationships to DOC concentrations in recipient waters, yet NDVI was a significant positive regulator of DOC in multiple regression models that included land cover variables. Our study illustrates that vegetation type exerts primary control in DOC regulation in Stordalen, while productivity (NDVI) is of secondary importance. Thus, predictive multiple linear regression models for DOC can be utilized combining these different types of explanatory variables.}, } @article {pmid29978939, year = {2018}, author = {Förster, DW and Bull, JK and Lenz, D and Autenrieth, M and Paijmans, JLA and Kraus, RHS and Nowak, C and Bayerl, H and Kuehn, R and Saveljev, AP and Sindičić, M and Hofreiter, M and Schmidt, K and Fickel, J}, title = {Targeted resequencing of coding DNA sequences for SNP discovery in nonmodel species.}, journal = {Molecular ecology resources}, volume = {18}, number = {6}, pages = {1356-1373}, doi = {10.1111/1755-0998.12924}, pmid = {29978939}, issn = {1755-0998}, support = {SAW-2011-SGN-3//Leibniz-Gemeinschaft/ ; A/11/93927//Deutscher Akademischer Austauschdienst/ ; 2014/15/B/NZ8/00212//Narodowe Centrum Nauki/ ; }, mesh = {Animals ; Cats/genetics ; Computational Biology/*methods ; Genotype ; Genotyping Techniques/*methods ; Lynx/*classification/*genetics ; *Polymorphism, Single Nucleotide ; Sequence Analysis, DNA/*methods ; }, abstract = {Targeted capture coupled with high-throughput sequencing can be used to gain information about nuclear sequence variation at hundreds to thousands of loci. Divergent reference capture makes use of molecular data of one species to enrich target loci in other (related) species. This is particularly valuable for nonmodel organisms, for which often no a priori knowledge exists regarding these loci. Here, we have used targeted capture to obtain data for 809 nuclear coding DNA sequences (CDS) in a nonmodel organism, the Eurasian lynx Lynx lynx, using baits designed with the help of the published genome of a related model organism (the domestic cat Felis catus). Using this approach, we were able to survey intraspecific variation at hundreds of nuclear loci in L. lynx across the species' European range. A large set of biallelic candidate SNPs was then evaluated using a high-throughput SNP genotyping platform (Fluidigm), which we then reduced to a final 96 SNP-panel based on assay performance and reliability; validation was carried out with 100 additional Eurasian lynx samples not included in the SNP discovery phase. The 96 SNP-panel developed from CDS performed very successfully in the identification of individuals and in population genetic structure inference (including the assignment of individuals to their source population). In keeping with recent studies, our results show that genic SNPs can be valuable for genetic monitoring of wildlife species.}, } @article {pmid29978606, year = {2018}, author = {Xiong, W and Zhan, A}, title = {Testing clustering strategies for metabarcoding-based investigation of community-environment interactions.}, journal = {Molecular ecology resources}, volume = {18}, number = {6}, pages = {1326-1338}, doi = {10.1111/1755-0998.12922}, pmid = {29978606}, issn = {1755-0998}, support = {31572228//National Natural Science Foundation of China/ ; ZDRW-ZS-2016-5-6//The Key Research Program of the Chinese Academy of Sciences/ ; 2015//The Innovation in Cross-functional Team Program of the Chinese Academy of Sciences/ ; 2015ZX07201-008-09//Water Pollution Control and Treatment Special Project/ ; 15K01ESPCR//The State Key Joint Laboratory of Environment Simulation and Pollution Control (RCEES, Chinese Academy of Sciences)/ ; 2017M620927//China Postdoctoral Science Foundation/ ; }, mesh = {Animals ; China ; *Cluster Analysis ; Computational Biology/*methods ; DNA Barcoding, Taxonomic/*methods ; *Environmental Exposure ; Environmental Monitoring/*methods ; Metagenomics/*methods ; Rivers ; Water Pollutants/toxicity ; Zooplankton/drug effects ; }, abstract = {The degradation of freshwater ecosystems has become a common ecological and environmental problem globally. Owing to the complexity of biological communities, there remain tremendous technical challenges for investigating influence of environmental stressors (e.g., chemical pollution) on biological communities. High-throughput sequencing-based metabarcoding provides a powerful tool to reveal complex interactions between environments and biological communities. Among many technical issues, the clustering strategies for operational taxonomic units (OTUs) which are crucial for assessing biodiversity of communities, may affect final conclusions. Here, we used zooplankton communities along an environmental pollution gradient in the Chaobai River in Northern China to test different clustering strategies, including nonclustering and clustering with varied thresholds. Our results showed that though the number of OTUs estimated by nonclustering strategies and clustering strategies with divergence thresholds of 99%-97% largely varied, they were able to identify the same set of significant environmental and spatial variables responsible for geographical distributions of zooplankton communities. In addition, the ecological conclusions obtained by clustering thresholds of 99%-97% were consistent with nonclustering strategies, where for all eight clustering scenarios we detected that species sorting predicted by environmental variables overrode dispersal as the dominant factor in structuring zooplankton communities. However, clustering with the divergence thresholds of <95% affected the environmental and spatial variables identified. We conclude that both newly developed nonclustering methods and traditional clustering methods with divergence thresholds ≥97% were reliable to reveal mechanisms of complex community-environment interactions, although different clustering strategies could lead to largely varied biodiversity estimates such as those for α-diversity.}, } @article {pmid29978422, year = {2018}, author = {Gavarāne, I and Trofimova, J and Mališevs, A and Valciņa, O and Kirjušina, M and Rubeniņa, I and Bērziņš, A}, title = {DNA extraction from amoebal isolates and genotype determination of Acanthamoeba from tap water in Latvia.}, journal = {Parasitology research}, volume = {117}, number = {10}, pages = {3299-3303}, pmid = {29978422}, issn = {1432-1955}, mesh = {Acanthamoeba/classification/genetics/*isolation & purification ; Animals ; DNA, Protozoan/*genetics ; Databases, Nucleic Acid ; Genotype ; Invertebrates/genetics ; Latvia ; RNA, Ribosomal, 18S/genetics ; Water/*parasitology ; Water Pollution ; }, abstract = {Acanthamoeba are free-living amoebae found in various ecological environments, and they are major microbial predators. Some Acanthamoeba species can cause keratitis, granulomatous amoebic encephalitis, and infections of the organs. This is the first study in Latvia describing Acanthamoeba detection by molecular techniques and genotyping using tap water from different sources. An 18S rRNA gene investigation of the 20 Acanthamoeba isolates suggested that 19 belonged to the hazardous T4 genotype and one sample was T12. The results indicate that tap water in Latvia may be a source of Acanthamoeba that is potentially pathogenic to humans. All obtained sequences were submitted to the GenBank database under the following accession numbers: MG386295-MG386314.}, } @article {pmid29973596, year = {2018}, author = {Bramon Mora, B and Gravel, D and Gilarranz, LJ and Poisot, T and Stouffer, DB}, title = {Identifying a common backbone of interactions underlying food webs from different ecosystems.}, journal = {Nature communications}, volume = {9}, number = {1}, pages = {2603}, pmid = {29973596}, issn = {2041-1723}, mesh = {Animals ; Competitive Behavior/*physiology ; Datasets as Topic ; Ecosystem ; *Food Chain ; *Models, Statistical ; Predatory Behavior/*physiology ; Principal Component Analysis ; }, abstract = {Although the structure of empirical food webs can differ between ecosystems, there is growing evidence of multiple ways in which they also exhibit common topological properties. To reconcile these contrasting observations, we postulate the existence of a backbone of interactions underlying all ecological networks-a common substructure within every network comprised of species playing similar ecological roles-and a periphery of species whose idiosyncrasies help explain the differences between networks. To test this conjecture, we introduce a new approach to investigate the structural similarity of 411 food webs from multiple environments and biomes. We first find significant differences in the way species in different ecosystems interact with each other. Despite these differences, we then show that there is compelling evidence of a common backbone of interactions underpinning all food webs. We expect that identifying a backbone of interactions will shed light on the rules driving assembly of different ecological communities.}, } @article {pmid29972280, year = {2018}, author = {Steevensz, A and Gombar, R and Vergilino, R and Cristescu, ME and Vacratsis, PO}, title = {Proteomic Profile of Daphnia pulex using Data-Independent Acquisition Mass Spectrometry and Ion Mobility Separation.}, journal = {Proteomics}, volume = {18}, number = {16}, pages = {e1700460}, doi = {10.1002/pmic.201700460}, pmid = {29972280}, issn = {1615-9861}, mesh = {Animals ; Computational Biology ; Daphnia/*metabolism ; Mass Spectrometry/*methods ; Proteins/*metabolism ; Proteome/*analysis ; }, abstract = {Daphnia pulex is a keystone species for aquatic habitats and an ecological/evolution model organism. Although significant progress has been made on characterizing its genome, the D. pulex proteome remains largely uncharacterized partially due to abnormally high protein degradation during homogenization and emphasis on genomic analysis. In this study, various sample preparation and mass spectrometry acquisition methods are performed for the purpose of improving D. pulex proteome exploration. Benefits for employing both in-gel and in-solution methods of trypsin digestion are observed. Furthermore, acquisition methods employing ion mobility separation greatly increase peptide identification and more than doubled the proteome coverage. Bioinformatic analysis suggests that mitochondrial and hydrolytic activities are enriched in D. pulex compared to closely related invertebrates or Homo sapiens. Also, novel D. pulex proteins possessing putative genome modifying functional domains are identified. Data are available via ProteomeXchange with identifier PXD008455.}, } @article {pmid29969113, year = {2018}, author = {Nohe, A and Knockaert, C and Goffin, A and Dewitte, E and De Cauwer, K and Desmit, X and Vyverman, W and Tyberghein, L and Lagring, R and Sabbe, K}, title = {Marine phytoplankton community composition data from the Belgian part of the North Sea, 1968-2010.}, journal = {Scientific data}, volume = {5}, number = {}, pages = {180126}, pmid = {29969113}, issn = {2052-4463}, mesh = {Belgium ; *Databases, Factual ; North Sea ; *Phytoplankton ; }, abstract = {The Belgian Phytoplankton Database (BPD) is a comprehensive data collection comprising quantitative phytoplankton cell counts from multiple research projects conducted since 1968. The collection is focused on the Belgian part of the North Sea, but also includes data from the French and the Dutch part of the North Sea. The database includes almost 300 unique sampling locations and more than 3,000 sampling events resulting in more than 86,000 phytoplankton cell count records. The dataset covers two periods: 1968 to 1978 and 1994 to 2010. The BPD can be accessed online and provides high quality phytoplankton count data. The species taxonomy is updated, and the count values are quality checked and standardized. Important metadata like sampling date, sampling location, sampling depth and methodology is provided and standardized. Additionally, associated abiotic data and biovolume values are available. The dataset allows to conduct analyses of long-term temporal and spatial trends in phytoplankton community structure in the southern part of the North Sea, including changes in phytoplankton phenology and seasonality.}, } @article {pmid29968727, year = {2018}, author = {Utzeri, VJ and Schiavo, G and Ribani, A and Tinarelli, S and Bertolini, F and Bovo, S and Fontanesi, L}, title = {Entomological signatures in honey: an environmental DNA metabarcoding approach can disclose information on plant-sucking insects in agricultural and forest landscapes.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {9996}, pmid = {29968727}, issn = {2045-2322}, support = {RFO//Università di Bologna (University of Bologna)/International ; }, mesh = {Agriculture ; Animals ; Bees ; DNA ; DNA Barcoding, Taxonomic/methods ; Electron Transport Complex IV/genetics ; Entomology/*methods ; Flowers ; Forests ; Hemiptera/classification/*metabolism ; Honey/*analysis ; Insecta ; Plants ; Polymerase Chain Reaction/methods ; }, abstract = {Honeydew produced from the excretion of plant-sucking insects (order Hemiptera) is a carbohydrate-rich material that is foraged by honey bees to integrate their diets. In this study, we used DNA extracted from honey as a source of environmental DNA to disclose its entomological signature determined by honeydew producing Hemiptera that was recovered not only from honeydew honey but also from blossom honey. We designed PCR primers that amplified a fragment of mitochondrial cytochrome c oxidase subunit 1 (COI) gene of Hemiptera species using DNA isolated from unifloral, polyfloral and honeydew honeys. Ion Torrent next generation sequencing metabarcoding data analysis assigned Hemiptera species using a customized bioinformatic pipeline. The forest honeydew honeys reported the presence of high abundance of Cinara pectinatae DNA, confirming their silver fir forest origin. In all other honeys, most of the sequenced reads were from the planthopper Metcalfa pruinosa for which it was possible to evaluate the frequency of different mitotypes. Aphids of other species were identified from honeys of different geographical and botanical origins. This unique entomological signature derived by environmental DNA contained in honey opens new applications for honey authentication and to disclose and monitor the ecology of plant-sucking insects in agricultural and forest landscapes.}, } @article {pmid29968347, year = {2019}, author = {Saul, MC and Blatti, C and Yang, W and Bukhari, SA and Shpigler, HY and Troy, JM and Seward, CH and Sloofman, L and Chandrasekaran, S and Bell, AM and Stubbs, L and Robinson, GE and Zhao, SD and Sinha, S}, title = {Cross-species systems analysis of evolutionary toolkits of neurogenomic response to social challenge.}, journal = {Genes, brain, and behavior}, volume = {18}, number = {1}, pages = {e12502}, pmid = {29968347}, issn = {1601-183X}, support = {U54 GM114838/GM/NIGMS NIH HHS/United States ; 1U54GM114838/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Bees ; Brain/metabolism/physiology ; *Evolution, Molecular ; Female ; Gene Regulatory Networks ; Genetics, Behavioral/*methods ; Genome ; Genomics/*methods ; Male ; Mice ; Smegmamorpha ; *Social Behavior ; *Systems Analysis ; Transcriptome ; }, abstract = {Social challenges like territorial intrusions evoke behavioral responses in widely diverging species. Recent work has showed that evolutionary "toolkits"-genes and modules with lineage-specific variations but deep conservation of function-participate in the behavioral response to social challenge. Here, we develop a multispecies computational-experimental approach to characterize such a toolkit at a systems level. Brain transcriptomic responses to social challenge was probed via RNA-seq profiling in three diverged species-honey bees, mice and three-spined stickleback fish-following a common methodology, allowing fair comparisons across species. Data were collected from multiple brain regions and multiple time points after social challenge exposure, achieving anatomical and temporal resolution substantially greater than previous work. We developed statistically rigorous analyses equipped to find homologous functional groups among these species at the levels of individual genes, functional and coexpressed gene modules, and transcription factor subnetworks. We identified six orthogroups involved in response to social challenge, including groups represented by mouse genes Npas4 and Nr4a1, as well as common modulation of systems such as transcriptional regulators, ion channels, G-protein-coupled receptors and synaptic proteins. We also identified conserved coexpression modules enriched for mitochondrial fatty acid metabolism and heat shock that constitute the shared neurogenomic response. Our analysis suggests a toolkit wherein nuclear receptors, interacting with chaperones, induce transcriptional changes in mitochondrial activity, neural cytoarchitecture and synaptic transmission after social challenge. It shows systems-level mechanisms that have been repeatedly co-opted during evolution of analogous behaviors, thus advancing the genetic toolkit concept beyond individual genes.}, } @article {pmid29959647, year = {2019}, author = {Marzec-Wróblewska, U and Kamiński, P and Łakota, P and Szymański, M and Wasilow, K and Ludwikowski, G and Jerzak, L and Stuczyński, T and Woźniak, A and Buciński, A}, title = {Human Sperm Characteristics with Regard to Cobalt, Chromium, and Lead in Semen and Activity of Catalase in Seminal Plasma.}, journal = {Biological trace element research}, volume = {188}, number = {2}, pages = {251-260}, doi = {10.1007/s12011-018-1416-9}, pmid = {29959647}, issn = {1559-0720}, mesh = {Catalase/*metabolism ; Chromium/*analysis ; Cobalt/*analysis ; Humans ; Infertility, Male/*diagnosis/enzymology ; Lead/*analysis ; Male ; Semen/*chemistry/enzymology ; Semen Analysis ; Sperm Count ; Sperm Motility ; Spermatozoa/*chemistry/enzymology ; }, abstract = {We analyzed cobalt (Co), chromium (Cr), and lead (Pb) concentrations in human semen and catalase CAT activity in seminal plasma and the effects of their relations on the sperm quality. We obtained semen samples from men (n = 168) undergoing routine infertility evaluation. Studies included two groups based on the ejaculate parameters: I (n = 39; normal ejaculate; normozoospermia); II (n = 129; pathological spermiogram). We examined relationships and differences between Co, Cr, and Pb concentrations in seminal plasma, CAT activity, and semen parameters. We did not establish differences in Co, Cr, and Pb concentrations and CAT activity from men between normozoospermic and those with pathological spermiogram. We found a significantly lower Co concentration and CAT activity in males with normal sperm motility than in asthenozoospermic males. We found significantly lower Co and a higher Pb concentration in males with normal morphology of spermatozoa than in teratozoospermic males. We found a significantly higher Pb concentration in the individuals with consumption of alcohol than in those without consumption. There were significant correlations between Co and Pb concentrations, sperm progressive motility (A + B, i.e., fast and slow progressive motility; Co-negatively; Pb-positively), and normal morphology of spermatozoa (Co-negatively; Pb-positively). We found a significant negative correlation between Cr concentration and slow progressive motility, and between CAT activity and volume of ejaculate. Co, Cr, and Pb levels and CAT activity were related to sperm characteristics and male fertility. The impact of alcohol may be manifested by a disturbance in Pb equilibrium in the body. Co and Pb influence progressive motility and normal morphology of human spermatozoa. Thus, Co and Pb levels in semen may be a useful diagnostic in male infertility. Most of the results of this study are in contrast to expectations. Namely, Pb is a toxic element and its harmful effects (poor semen quality) may be expected already at relatively low level of Pb exposure and are particularly visible with increasing of Pb. Co and Cr(III) are essential elements and harmful effects may be expected at their deficiency and/or overexposure.}, } @article {pmid29957426, year = {2018}, author = {Sfriso, AA and Chiesa, S and Sfriso, A and Buosi, A and Gobbo, L and Boscolo Gnolo, A and Argese, E}, title = {Spatial distribution, bioaccumulation profiles and risk for consumption of edible bivalves: a comparison among razor clam, Manila clam and cockles in the Venice Lagoon.}, journal = {The Science of the total environment}, volume = {643}, number = {}, pages = {579-591}, doi = {10.1016/j.scitotenv.2018.06.057}, pmid = {29957426}, issn = {1879-1026}, mesh = {Animals ; Bivalvia/*metabolism ; Cardiidae/metabolism ; *Environmental Monitoring ; Geologic Sediments ; Humans ; Seafood/statistics & numerical data ; Water Pollutants, Chemical/*metabolism ; }, abstract = {Despite their ecological and economical relevance, a lack of data is still occurring about the distribution, abundance, bioaccumulation and risks for consumption of some edible bivalves. The present study has been carried out in the Venice Lagoon taking into account three bivalve species to investigate i) the possible relationship among the biological features-distribution, abundance and bioaccumulation patterns- of razor clams (Solen marginatus Pulteney, 1799), Manila clams (Ruditapes philippinarum Adams and Reeve, 1850) and lagoon cockles (Cerastoderma glaucum Poiret, 1789) and the hydrological features, namely sediment physico-chemical characteristics and contamination; ii) their specific role as bioindicators of inorganic contamination; iii) the possible risks for human health associated with the consumption of these edible bivalves. Results showed that species distribution and abundance, especially for razor clams, was mainly influenced by environmental conditions and sediment granulometric composition, above metal(loid) contamination. The contamination patterns were different among species, as Manila clam generally showed higher bioaccumulation values for most of the metal(loid)s, whilst lagoon cockles preferentially accumulated Ni. Eventually, a serious concern exists for the human consumption, for all species and investigated sites regarding As. This study will raise attention on the effects of bioaccumulation of inorganic pollutants by edible bivalves and risks for consumers' safety, especially concerning razor clams and cockles, for which a critical lack of data on metal(loid) bioaccumulation occurs from the Northern Adriatic Sea.}, } @article {pmid29957336, year = {2018}, author = {Pimenta, L and Dutra, VGP and de Castro, ALB and Guimarães, RM}, title = {Analysis of conditions sensitive to primary care in a successful experience of primary healthcare expansion in Brazil, 1998-2015.}, journal = {Public health}, volume = {162}, number = {}, pages = {32-40}, doi = {10.1016/j.puhe.2018.05.011}, pmid = {29957336}, issn = {1476-5616}, mesh = {Brazil ; Cerebrovascular Disorders/therapy ; Health Information Systems ; Health Services Research ; Heart Failure/therapy ; Hospitalization/*trends ; Humans ; Pneumonia, Bacterial/therapy ; Primary Health Care/*organization & administration ; }, abstract = {OBJECTIVE: To analyze trends in expansion of coverage of the family health strategy and hospitalization for conditions sensitive to primary care (CSPC) in a successful experience of primary healthcare expansion in Brazil.

STUDY DESIGN: Ecological study with data from the Brazilian National Health Information System.

METHODS: CSPC were analyzed between 1998 and 2015 in Rio de Janeiro, Brazil, by cause groups. Trends, variation, and correlation between indicators in the period were evaluated.

RESULTS: Most of the cause groups showed a reduction in hospitalization rate, particularly cardiovascular diseases and asthma, but an increase was seen for obstetric causes. The main causes of hospitalization were heart failure, cerebrovascular diseases, and bacterial pneumonia. The contribution of vaccine-preventable diseases, cardiovascular diseases, diabetes, nutritional deficiencies, and chronic lung diseases to the total number of hospitalizations was seen to decrease.

CONCLUSIONS: Analysis demonstrates that the family health strategy, as access to the healthcare system, decreases the majority of CSPC hospitalization rates.}, } @article {pmid29956221, year = {2018}, author = {Yang, S and Zhong, Q and Tian, J and Wang, L and Zhao, M and Li, L and Sun, X}, title = {Characterization and development of EST-SSR markers to study the genetic diversity and populations analysis of Jerusalem artichoke (Helianthus tuberosus L.).}, journal = {Genes & genomics}, volume = {40}, number = {10}, pages = {1023-1032}, pmid = {29956221}, issn = {2092-9293}, support = {31460523//National Natural Science Foundation of China/International ; 31660528//National Natural Science Foundation of China/International ; 31660569//National Natural Science Foundation of China/International ; 31760600//National Natural Science Foundation of China/International ; 2016-ZJ-751//The Fundamental Research Program of Qinghai/International ; 2015-HZ-805//The Fundamental Research Program of Qinghai/International ; }, mesh = {Cluster Analysis ; DNA Primers/genetics ; Databases, Genetic ; Evolution, Molecular ; *Expressed Sequence Tags ; Genetic Markers ; Genetic Variation ; Helianthus/*genetics ; *Microsatellite Repeats ; Plant Breeding ; Seeds/*genetics ; }, abstract = {In recent years, Jerusalem artichoke has received widespread attention as a novel source of sugar, biofuel, and animal feed. Currently, only few gDNA-SSRs derived from sunflower were verified in the Jerusalem artichoke; therefore, it is particularly important to develop SSR primer markers that belonged to Jerusalem artichoke resources. Using EST data to develop EST-SSR markers is simple and effective. In order to understand the general characteristics of SSR markers in Jerusalem artichoke EST sequences and accelerate the use of SSR markers in Jerusalem artichoke research. This study used 40,370 sequenced unigene fragments and MISA software to identify SSR loci. The 48 pairs of EST-SSR primers assessed for the identification of 45 varieties of Jerusalem artichoke. Cluster, genetic diversity parameters and AMOVA analysis was conducted using the genetic similarity coefficient, revealing genetic differences between 48 genetic material. A total of 1204 SSR loci were identified with 13 different types of repeats, distributed among 1020 EST sequences, of which trinucleotide repeats were the most common, accounting for 38.21% of the total SSR loci. Among the 44 repeat motifs, AG/CT, AAG/CTT, and ATC/ATG motifs had the highest frequencies, accounting for 22.45, 14.71, and 7.84% of all motifs, respectively. From these sequences, 48 pairs of EST-SSR primers were designed, and 22 primer pairs for loci with high polymorphism were selected to analyze the genetic diversity of 45 Jerusalem artichoke germplasm sources. The results indicated that the variation range of the effective number of alleles for 22 primers ranged between 1.7502 and 4.5660. The Shannon's information index ranged between 0.6200 and 1.6423. The variation range of PIC ranged between 0.3121 and 0.6662 with an average of 0.5184. Cluster analysis was conducted using the genetic similarity coefficient, revealing significant genetic differences between Asian and European genetic material. Cluster analysis revealed a relationship between the genotypes and geographic origins of the Jerusalem artichoke. The results of AMOVA as well as the genetic identity and genetic distance in the Jerusalem artichoke population showed that there presented certain genetic heterogeneity in Jerusalem artichoke genetic structure of 45 samples from seven different geographic populations. The Jerusalem artichoke EST-SSR marker system established in this study provides an effective molecular marker system for future research focused on Jerusalem artichoke genetic diversity and the breeding of new varieties.}, } @article {pmid29955341, year = {2017}, author = {Nakileza, BR and Majaliwa, MJ and Wandera, A and Nantumbwe, CM}, title = {Enhancing resilience to landslide disaster risks through rehabilitation of slide scars by local communities in Mt Elgon, Uganda.}, journal = {Jamba (Potchefstroom, South Africa)}, volume = {9}, number = {1}, pages = {390}, pmid = {29955341}, issn = {1996-1421}, abstract = {Mass movements are key drivers affecting the utilisation of many farmlands and consequently the livelihoods in mountains' ecosystems. Numerous expansive landslide scars can for years remain unusable for crop farming purposes, which is a major livelihood activity. This article examined the approaches and challenges faced by local communities in the rehabilitation of landslide-degraded areas in selected areas of Mt Elgon. Data were collected through field surveys of purposively selected scars, key informant interviews and focus group discussions with the local communities. The findings indicate that the local communities have initiated the rehabilitation of some scars to stabilise the slopes and also accelerate their quick recovery for beneficial purposes. Community trainings coupled with awareness and participatory actions during rehabilitation enhance community preparedness to landslide risks. However, there were noted constraints including limited resources, incidences of secondary slides, cracks and lack of adequate knowledge on the existing best practices for the rehabilitation of scars on deeply weathered soils. Further research should be focussed on generating relevant knowledge on regeneration rates under different socio-ecological conditions and for guiding sustainable utilisation of fragile areas.}, } @article {pmid29950008, year = {2018}, author = {Asgari, E and Garakani, K and McHardy, AC and Mofrad, MRK}, title = {MicroPheno: predicting environments and host phenotypes from 16S rRNA gene sequencing using a k-mer based representation of shallow sub-samples.}, journal = {Bioinformatics (Oxford, England)}, volume = {34}, number = {13}, pages = {i32-i42}, pmid = {29950008}, issn = {1367-4811}, mesh = {*Databases, Nucleic Acid ; Genes, rRNA ; Humans ; Microbiota/*genetics ; *Phenotype ; RNA, Ribosomal, 16S/*genetics ; Sequence Alignment/methods ; Sequence Analysis, DNA/*methods ; *Software ; }, abstract = {MOTIVATION: Microbial communities play important roles in the function and maintenance of various biosystems, ranging from the human body to the environment. A major challenge in microbiome research is the classification of microbial communities of different environments or host phenotypes. The most common and cost-effective approach for such studies to date is 16S rRNA gene sequencing. Recent falls in sequencing costs have increased the demand for simple, efficient and accurate methods for rapid detection or diagnosis with proved applications in medicine, agriculture and forensic science. We describe a reference- and alignment-free approach for predicting environments and host phenotypes from 16S rRNA gene sequencing based on k-mer representations that benefits from a bootstrapping framework for investigating the sufficiency of shallow sub-samples. Deep learning methods as well as classical approaches were explored for predicting environments and host phenotypes.

RESULTS: A k-mer distribution of shallow sub-samples outperformed Operational Taxonomic Unit (OTU) features in the tasks of body-site identification and Crohn's disease prediction. Aside from being more accurate, using k-mer features in shallow sub-samples allows (i) skipping computationally costly sequence alignments required in OTU-picking and (ii) provided a proof of concept for the sufficiency of shallow and short-length 16S rRNA sequencing for phenotype prediction. In addition, k-mer features predicted representative 16S rRNA gene sequences of 18 ecological environments, and 5 organismal environments with high macro-F1 scores of 0.88 and 0.87. For large datasets, deep learning outperformed classical methods such as Random Forest and Support Vector Machine.

The software and datasets are available at https://llp.berkeley.edu/micropheno.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, } @article {pmid29946138, year = {2018}, author = {Gemmell, MR and Berry, S and Mukhopadhya, I and Hansen, R and Nielsen, HL and Bajaj-Elliott, M and Nielsen, H and Hold, GL}, title = {Comparative genomics of Campylobacter concisus: Analysis of clinical strains reveals genome diversity and pathogenic potential.}, journal = {Emerging microbes & infections}, volume = {7}, number = {1}, pages = {116}, pmid = {29946138}, issn = {2222-1751}, mesh = {Campylobacter/*classification/*genetics/isolation & purification/pathogenicity ; Campylobacter Infections/*microbiology ; Cluster Analysis ; Computational Biology/methods ; Feces/microbiology ; *Genetic Variation ; *Genome, Bacterial ; *Genomics/methods ; Host-Pathogen Interactions ; Humans ; Molecular Sequence Annotation ; Phenotype ; Phylogeny ; Reproducibility of Results ; Virulence ; Virulence Factors/genetics ; Whole Genome Sequencing ; }, abstract = {In recent years, an increasing number of Campylobacter species have been associated with human gastrointestinal (GI) diseases including gastroenteritis, inflammatory bowel disease, and colorectal cancer. Campylobacter concisus, an oral commensal historically linked to gingivitis and periodontitis, has been increasingly detected in the lower GI tract. In the present study, we generated robust genome sequence data from C. concisus strains and undertook a comprehensive pangenome assessment to identify C. concisus virulence properties and to explain potential adaptations acquired while residing in specific ecological niche(s) of the GI tract. Genomes of 53 new C. concisus strains were sequenced, assembled, and annotated including 36 strains from gastroenteritis patients, 13 strains from Crohn's disease patients and four strains from colitis patients (three collagenous colitis and one lymphocytic colitis). When compared with previous published sequences, strains clustered into two main groups/genomospecies (GS) with phylogenetic clustering explained neither by disease phenotype nor sample location. Paired oral/faecal isolates, from the same patient, indicated that there are few genetic differences between oral and gut isolates which suggests that gut isolates most likely reflect oral strain relocation. Type IV and VI secretion systems genes, genes known to be important for pathogenicity in the Campylobacter genus, were present in the genomes assemblies, with 82% containing Type VI secretion system genes. Our findings indicate that C. concisus strains are genetically diverse, and the variability in bacterial secretion system content may play an important role in their virulence potential.}, } @article {pmid29940835, year = {2018}, author = {Devlin, JC and Battaglia, T and Blaser, MJ and Ruggles, KV}, title = {WHAM!: a web-based visualization suite for user-defined analysis of metagenomic shotgun sequencing data.}, journal = {BMC genomics}, volume = {19}, number = {1}, pages = {493}, pmid = {29940835}, issn = {1471-2164}, support = {U01 AI22285//Foundation for the National Institutes of Health/ ; }, mesh = {Computational Biology/*methods ; High-Throughput Nucleotide Sequencing/methods ; Metagenomics/*methods ; Microbiota/*genetics ; }, abstract = {BACKGROUND: Exploration of large data sets, such as shotgun metagenomic sequence or expression data, by biomedical experts and medical professionals remains as a major bottleneck in the scientific discovery process. Although tools for this purpose exist for 16S ribosomal RNA sequencing analysis, there is a growing but still insufficient number of user-friendly interactive visualization workflows for easy data exploration and figure generation. The development of such platforms for this purpose is necessary to accelerate and streamline microbiome laboratory research.

RESULTS: We developed the Workflow Hub for Automated Metagenomic Exploration (WHAM!) as a web-based interactive tool capable of user-directed data visualization and statistical analysis of annotated shotgun metagenomic and metatranscriptomic data sets. WHAM! includes exploratory and hypothesis-based gene and taxa search modules for visualizing differences in microbial taxa and gene family expression across experimental groups, and for creating publication quality figures without the need for command line interface or in-house bioinformatics.

CONCLUSIONS: WHAM! is an interactive and customizable tool for downstream metagenomic and metatranscriptomic analysis providing a user-friendly interface allowing for easy data exploration by microbiome and ecological experts to facilitate discovery in multi-dimensional and large-scale data sets.}, } @article {pmid29939286, year = {2018}, author = {Mamiya, H and Moodie, EEM and Ma, Y and Buckeridge, DL}, title = {Susceptibility to price discounting of soda by neighbourhood educational status: an ecological analysis of disparities in soda consumption using point-of-purchase transaction data in Montreal, Canada.}, journal = {International journal of epidemiology}, volume = {47}, number = {6}, pages = {1877-1886}, doi = {10.1093/ije/dyy108}, pmid = {29939286}, issn = {1464-3685}, mesh = {Carbonated Beverages/*economics ; Commerce/*statistics & numerical data ; Consumer Behavior/*statistics & numerical data ; Diet, Healthy ; *Educational Status ; *Food Preferences ; Humans ; Obesity/economics/prevention & control ; Population Surveillance/methods ; Quebec ; }, abstract = {INTRODUCTION: Price discounting is a marketing tactic used frequently by food industries and retailers, but the extent to which education modifies the effect of discounting on the purchasing of unhealthy foods has received little attention. We investigated whether there was a differential association of price discounting of soda with store-level soda purchasing records between 2008 and 2013 by store-neighbourhood education in Montreal, Canada.

METHODS: Using data on grocery purchase transactions from a sample of supermarkets, pharmacies, supercentres and convenience stores, we performed an ecological time-series analysis, modelling weekly store-level sales of soda as a function of store-level price discounting, store- and neighbourhood-level confounders and an interaction term between discounting and categorical education in the neighbourhood of each store.

RESULTS: Analysis by store type (n = 18 743, 12 437, 3965 and 49 533 store-weeks for superstores, pharmacies, supercentres and convenience stores, respectively) revealed that the effect measure modification of discounting by neighbourhood education on soda purchasing was lower in stores in the more educated neighbourhoods, most notably in pharmacies: -0.020 [95% confidence interval (CI): -0.028, -0.012] and -0.038 (95% CI: -0.051, -0.025), for middle- and high-education categories, respectively). Weaker effect modification was observed in convenience stores. There was no evidence of effect modification in supercentres or superstores.

CONCLUSIONS: Price discounting is an important environmental risk factor for soda purchasing and can widen education inequalities in excess sugar intake across levels of education. Interventions to regulate price discounting warrant further investigation as a public health strategy to improve population nutrition, particularly in lower-education neighbourhoods.}, } @article {pmid29939251, year = {2018}, author = {Francis, CD and Donald, JW and Fuxjager, MJ and Goymann, W and Hau, M and Husak, JF and Johnson, MA and Kircher, BK and Knapp, R and Martin, LB and Miller, ET and Schoenle, LA and Vitousek, MN and Williams, TD and Downs, CJ}, title = {Metabolic Scaling of Stress Hormones in Vertebrates.}, journal = {Integrative and comparative biology}, volume = {58}, number = {4}, pages = {729-738}, doi = {10.1093/icb/icy063}, pmid = {29939251}, issn = {1557-7023}, mesh = {Animals ; Corticosterone/*metabolism ; Databases as Topic ; Glucocorticoids/*metabolism ; Hydrocortisone/*metabolism ; *Phylogeny ; Vertebrates/classification/*metabolism ; }, abstract = {Glucocorticoids (GCs) are stress hormones that can strongly influence physiology, behavior, and an organism's ability to cope with environmental change. Despite their importance, and the wealth of studies that have sought to understand how and why GC concentrations vary within species, we do not have a clear understanding of how circulating GC levels vary within and across the major vertebrate clades. New research has proposed that much interspecific variation in GC concentrations can be explained by variation in metabolism and body mass. Specifically, GC concentrations should vary proportionally with mass-specific metabolic rates and, given known scaling relationships between body mass and metabolic rate, GC concentrations should scale to the -1/4 power of body mass and to the power of 1 with mass-specific metabolic rate. Here, we use HormoneBase, the newly compiled database that includes plasma GC concentrations from free-living and unmanipulated vertebrates, to evaluate this hypothesis. Specifically, we explored the relationships between body mass or mass-specific metabolic rate and either baseline or stress-induced GC (cortisol or corticosterone) concentrations in tetrapods. Our phylogenetically-informed models suggest that, whereas the relationship between GC concentrations and body mass across tetrapods and among mammals is close to -1/4 power, this relationship does not exist in amphibians, reptiles, and birds. Moreover, with the exception of a positive association between stress-induced GC concentrations and mass-specific metabolic rate in birds, we found little evidence that GC concentrations are linked to metabolic rate, although the number of species sampled was quite limited for amphibians and somewhat so for reptiles and mammals. Nevertheless, these results stand in contrast to the generally accepted association between the two and suggest that our observed positive association between body mass and GC concentrations may not be due to the well-established link between mass and metabolism. Large-scale comparative approaches can come with drawbacks, such as pooling and pairing observations from separate sources. However, these broad analyses provide an important counterbalance to the majority of studies examining variation in GC concentrations at the population or species level, and can be a powerful approach to testing both long-standing and new questions in biology.}, } @article {pmid29936291, year = {2018}, author = {Venter, PC and Nitsche, F and Scherwass, A and Arndt, H}, title = {Discrepancies Between Molecular and Morphological Databases of Soil Ciliates Studied for Temperate Grasslands of Central Europe.}, journal = {Protist}, volume = {169}, number = {4}, pages = {521-538}, doi = {10.1016/j.protis.2018.04.001}, pmid = {29936291}, issn = {1618-0941}, mesh = {Ciliophora/*classification ; *Databases, Factual/standards ; Databases, Genetic ; Europe ; *Grassland ; High-Throughput Nucleotide Sequencing ; Molecular Typing ; *Soil Microbiology ; }, abstract = {By measuring the change in soil protist communities, the effect of human land use on grasslands can be monitored to promote sustainable ecosystem functioning. Protists form the active link in the rhizosphere between the plant roots and higher trophic organisms; however, only few morphological species and their ecological values have yet been described in this context. To investigate the communicability between morphological and molecular databases used in the molecular barcoding of protists and in the biomonitoring of grassland soil, the present high-throughput sequencing (HTS) study (N=150) covered the area of central Europe (mesoscale) known to be well studied for ciliated protists. HTS delivered 2,404 unique reads identifying taxa in all major ciliophoran classes but exact reference matches were few. The study identified clear discrepancies between databases for well-studied taxa, where molecular databases contained multiple gene variants for single morphospecies of dominant taxa. Gene variants presented own biogeography - the eukaryotic microdiversity along gradients (e.g., land-use intensity, soil water). It is possible that many of the so called novel phylogenetic lineages and hidden diversity pointed out in environmental surveys could be evidence for the severe lack of molecular data for already known and morphologically described species, present in morphological databases.}, } @article {pmid29935958, year = {2018}, author = {Shier, AP and Morita, PP and Dickie, C and Islam, M and Burns, CM and Cafazzo, JA}, title = {Design and evaluation of a safety-centered user interface for radiation therapy.}, journal = {Practical radiation oncology}, volume = {8}, number = {5}, pages = {e346-e354}, doi = {10.1016/j.prro.2018.01.009}, pmid = {29935958}, issn = {1879-8519}, mesh = {Equipment Design ; Humans ; Medical Errors/*prevention & control ; Neoplasms/*radiotherapy ; Patient Positioning/instrumentation/methods ; Patient Safety ; Patient-Specific Modeling ; Radiation Injuries/*prevention & control ; Radiation Oncologists ; Radiotherapy Planning, Computer-Assisted/*instrumentation/methods ; *User-Computer Interface ; }, abstract = {PURPOSE: As radiation therapy treatment grows more complex over time, treatment delivery has become more susceptible to adverse events and patient safety risks from use error. The radiation therapy monitoring and treatment delivery user interface explored in this study was redesigned using ecological interface design, a human factors engineering method, and evaluated to improve treatment safety.

METHODS AND MATERIALS: An initial design concept was created based on previously completed analysis and informally evaluated in focus groups with radiation therapists. Sixteen newly graduated radiation therapists used both the redesigned and current system in a usability test to determine if the redesigned system better supported detection of errors.

RESULTS: The redesigned system successfully improved the error detection rate of 2 errors: wrong treatment volume and wrong treatment site (P < .03 and P < .01, respectively). It also improved level 2 and level 3 situation awareness (ie, comprehension of the meaning of the information and the projection of the behavior of the technology: P < .01 and P < .01, respectively) and achieved a higher user satisfaction.

CONCLUSIONS: The ecological interface design approach was found to be effective in redesigning a radiation therapy treatment delivery interface. Radiation therapists were able to deliver simulated radiation therapy with a higher rate of error detection and improved higher-level situation awareness, and participants preferred the redesigned interface to the current interface. Overall, the redesigned interface improved the radiation therapists' system understanding and ability to detect errors that affect patient safety.}, } @article {pmid29934904, year = {2018}, author = {Kar, S and Roy, K and Leszczynski, J}, title = {Impact of Pharmaceuticals on the Environment: Risk Assessment Using QSAR Modeling Approach.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1800}, number = {}, pages = {395-443}, pmid = {29934904}, issn = {1940-6029}, mesh = {Animals ; Computer Simulation ; Databases, Factual ; *Drug Discovery ; Ecotoxicology/methods ; *Environment ; Environmental Monitoring ; Health Policy ; Humans ; Models, Theoretical ; *Pharmaceutical Preparations/analysis ; *Quantitative Structure-Activity Relationship ; Risk Assessment ; Risk Management ; Software ; Waste Management ; }, abstract = {An extensive use of pharmaceuticals and the widespread practices of their erroneous disposal measures have made these products contaminants of emerging concern (CEC). Especially, active pharmaceutical ingredients (APIs) are ubiquitously detected in surface water and soil, mainly in the aquatic compartment, where they do affect the living systems. Unfortunately, there is a huge gap in the availability of ecotoxicological data on pharmaceuticals' environmental behavior and ecotoxicity which force EMEA (European Medicines Agency) to release guidelines for their risk assessment. In silico modeling approaches are vital tools to exploit the existing information to rapidly emphasize the potentially most hazardous and toxic pharmaceuticals and prioritize the most environmentally hazardous ones for focusing further on their experimental studies. The quantitative structure-activity relationship (QSAR) models are capable of predicting missing properties for toxic end-points required to prioritize existing, or newly synthesized chemicals for their potential hazard. This chapter reviews the information regarding occurrence and impact of pharmaceuticals and their metabolites in the environment along with their persistence, environmental fate, risk assessment, and risk management. A bird's eye view about the necessity of in silico methods for fate prediction of pharmaceuticals in the environment as well as existing successful models regarding ecotoxicity of pharmaceuticals are discussed. Available toxicity endpoints, ecotoxicity databases, and expert systems frequently used for ecotoxicity predictions of pharmaceuticals are also reported. The overall discussion justifies the requirement to build up additional in silico models for quick prediction of ecotoxicity of pharmaceuticals economically, without or involving only limited animal testing.}, } @article {pmid29934651, year = {2018}, author = {Lane, BA and Sandoval-Solis, S and Stein, ED and Yarnell, SM and Pasternack, GB and Dahlke, HE}, title = {Beyond Metrics? The Role of Hydrologic Baseline Archetypes in Environmental Water Management.}, journal = {Environmental management}, volume = {62}, number = {4}, pages = {678-693}, pmid = {29934651}, issn = {1432-1009}, mesh = {California ; *Climate Change ; Conservation of Water Resources/*methods ; Databases, Factual ; Environmental Monitoring/*methods ; Humans ; *Hydrology ; Rivers ; Water Movements ; Water Resources/*supply & distribution ; Water Supply/standards/*statistics & numerical data ; }, abstract = {Balancing ecological and human water needs often requires characterizing key aspects of the natural flow regime and then predicting ecological response to flow alterations. Flow metrics are generally relied upon to characterize long-term average statistical properties of the natural flow regime (hydrologic baseline conditions). However, some key aspects of hydrologic baseline conditions may be better understood through more complete consideration of continuous patterns of daily, seasonal, and inter-annual variability than through summary metrics. Here we propose the additional use of high-resolution dimensionless archetypes of regional stream classes to improve understanding of baseline hydrologic conditions and inform regional environmental flows assessments. In an application to California, we describe the development and analysis of hydrologic baseline archetypes to characterize patterns of flow variability within and between stream classes. We then assess the utility of archetypes to provide context for common flow metrics and improve understanding of linkages between aquatic patterns and processes and their hydrologic controls. Results indicate that these archetypes may offer a distinct and complementary tool for researching mechanistic flow-ecology relationships, assessing regional patterns for streamflow management, or understanding impacts of changing climate.}, } @article {pmid29933691, year = {2018}, author = {Froemelt, A and Dürrenmatt, DJ and Hellweg, S}, title = {Using Data Mining To Assess Environmental Impacts of Household Consumption Behaviors.}, journal = {Environmental science & technology}, volume = {52}, number = {15}, pages = {8467-8478}, doi = {10.1021/acs.est.8b01452}, pmid = {29933691}, issn = {1520-5851}, mesh = {*Data Mining ; *Environment ; }, abstract = {Household consumption is a main driver of economy and might be regarded as ultimately responsible for environmental impacts occurring over the life cycle of products and services. Given that purchase decisions are made on household levels and are highly behavior-driven, the derivation of targeted environmental measures requires an understanding of household behavior patterns and the resulting environmental impacts. To provide an appropriate basis in support of effective environmental policymaking, we propose a new approach to capture the variability of lifestyle-induced environmental impacts. Lifestyle-archetypes representing prevailing consumption patterns are derived in a two-tiered clustering that applies a Ward-clustering on top of a preconditioning self-organizing map. The environmental impacts associated with specific archetypical behavior are then assessed in a hybrid life cycle assessment framework. The application of this approach to the Swiss Household Budget Survey reveals a global picture of consumption that is in line with previous studies, but also demonstrates that different archetypes can be found within similar socio-economic household types. The appearance of archetypes diverging from general macro-trends indicates that the proposed approach might be useful for an enhanced understanding of consumption patterns and for the future support of policymakers in devising effective environmental measures targeting specific consumer groups.}, } @article {pmid29932122, year = {2018}, author = {Lu, W and Bian, X and Yang, W and Cheng, T and Wang, J and Zhang, Q and Pan, H}, title = {Transcriptomics Investigation into the Mechanisms of Self-Incompatibility between Pin and Thrum Morphs of Primula maximowiczii.}, journal = {International journal of molecular sciences}, volume = {19}, number = {7}, pages = {}, pmid = {29932122}, issn = {1422-0067}, mesh = {Flowers/genetics ; Gene Expression Profiling/*methods ; *Gene Expression Regulation, Plant ; Gene Ontology ; Pollen/genetics ; Pollen Tube/genetics ; Pollination/genetics ; Primula/*genetics ; Self-Incompatibility in Flowering Plants/*genetics ; }, abstract = {Heteromorphic self-incompatibility (SI) is an important system for preventing inbreeding in the genus Primula. However, investigations into the molecular mechanisms of Primula SI are lacking. To explore the mechanisms of SI in Primula maximowiczii, the pollen germination and fruiting rates of self- and cross-pollinations between pin and thrum morphs were investigated, and transcriptomics analyses of the pistils after pollination were performed to assess gene expression patterns in pin and thrum SI. The results indicated that P. maximowiczii exhibits strong SI and that the mechanisms of pollen tube inhibition differ between pin and thrum morphs. While self-pollen tubes of the pin morph were able to occasionally, though rarely, enter the style, those of the thrum morph were never observed to enter the style. The transcriptomics analysis of the pistils revealed 1311 and 1048 differentially expressed genes (DEGs) that were identified by comparing pin self-pollination (PS) vs. pin cross-pollination (PT) and thrum self-pollination (TS) vs. thrum cross-pollination (TP). Notably, about 90% of these DEGs exhibited different expression patterns in the two comparisons. Moreover, pin and thrum DEGs were associated with different Gene Ontology (GO) categories and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways following enrichment analyses. Based on our results, the molecular mechanisms underlying the pin and thrum SI in P. maximowiczii appear to be distinct. Furthermore, the genes involved in the SI processes are commonly associated with carbohydrate metabolism and environmental adaptation. These results provide new insight into the molecular mechanisms of Primula SI.}, } @article {pmid29931324, year = {2018}, author = {Qi, M and Li, Z and Liu, C and Hu, W and Ye, L and Xie, Y and Zhuang, Y and Zhao, F and Teng, W and Zheng, Q and Fan, Z and Xu, L and Lang, Z and Tong, Y and Zhang, Y}, title = {CGT-seq: epigenome-guided de novo assembly of the core genome for divergent populations with large genome.}, journal = {Nucleic acids research}, volume = {46}, number = {18}, pages = {e107}, pmid = {29931324}, issn = {1362-4962}, mesh = {Computational Biology/methods ; Epigenesis, Genetic/*physiology ; Epigenomics/*methods ; *Genetic Speciation ; Genetic Variation/*genetics ; Genome/genetics ; Genome Size/*physiology ; Genotyping Techniques/methods ; High-Throughput Nucleotide Sequencing/methods ; Molecular Sequence Annotation/methods ; Oryza/classification/genetics ; Sequence Analysis, DNA/methods ; Transcriptome ; Triticum/classification/genetics ; Whole Genome Sequencing/*methods ; }, abstract = {Genetic diversity in plants is remarkably high. Recent whole genome sequencing (WGS) of 67 rice accessions recovered 10,872 novel genes. Comparison of the genetic architecture among divergent populations or between crops and wild relatives is essential for obtaining functional components determining crucial traits. However, many major crops have gigabase-scale genomes, which are not well-suited to WGS. Existing cost-effective sequencing approaches including re-sequencing, exome-sequencing and restriction enzyme-based methods all have difficulty in obtaining long novel genomic sequences from highly divergent population with large genome size. The present study presented a reference-independent core genome targeted sequencing approach, CGT-seq, which employed epigenomic information from both active and repressive epigenetic marks to guide the assembly of the core genome mainly composed of promoter and intragenic regions. This method was relatively easily implemented, and displayed high sensitivity and specificity for capturing the core genome of bread wheat. 95% intragenic and 89% promoter region from wheat were covered by CGT-seq read. We further demonstrated in rice that CGT-seq captured hundreds of novel genes and regulatory sequences from a previously unsequenced ecotype. Together, with specific enrichment and sequencing of regions within and nearby genes, CGT-seq is a time- and resource-effective approach to profiling functionally relevant regions in sequenced and non-sequenced populations with large genomes.}, } @article {pmid29931218, year = {2018}, author = {Kedzierska, KZ and Gerber, L and Cagnazzi, D and Krützen, M and Ratan, A and Kistler, L}, title = {SONiCS: PCR stutter noise correction in genome-scale microsatellites.}, journal = {Bioinformatics (Oxford, England)}, volume = {34}, number = {23}, pages = {4115-4117}, pmid = {29931218}, issn = {1367-4811}, support = {P30 CA044579/CA/NCI NIH HHS/United States ; }, mesh = {Alleles ; Animals ; Computational Biology ; *Genotyping Techniques ; *Microsatellite Repeats ; Monte Carlo Method ; *Polymerase Chain Reaction ; *Software ; }, abstract = {MOTIVATION: Massively parallel capture of short tandem repeats (STRs, or microsatellites) provides a strategy for population genomic and demographic analyses at high resolution with or without a reference genome. However, the high Polymerase Chain Reaction (PCR) cycle numbers needed for target capture experiments create genotyping noise through polymerase slippage known as PCR stutter.

RESULTS: We developed SONiCS-Stutter mONte Carlo Simulation-a solution for stutter correction based on dense forward simulations of PCR and capture experimental conditions. To test SONiCS, we genotyped a 2499-marker STR panel in 22 humpback dolphins (Sousa sahulensis) using target capture, and generated capillary-based genotypes to validate five of these markers. In these 110 comparisons, SONiCS showed a 99.1% accuracy rate and a 98.2% genotyping success rate, miscalling a single allele in a marker with low sequence coverage and rejecting another as un-callable.

Source code and documentation for SONiCS is freely available at https://github.com/kzkedzierska/sonics. Raw read data used in experimental validation of SONiCS have been deposited in the Sequence Read Archive under accession number SRP135756.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, } @article {pmid29930200, year = {2018}, author = {Venturelli, OS and Carr, AC and Fisher, G and Hsu, RH and Lau, R and Bowen, BP and Hromada, S and Northen, T and Arkin, AP}, title = {Deciphering microbial interactions in synthetic human gut microbiome communities.}, journal = {Molecular systems biology}, volume = {14}, number = {6}, pages = {e8157}, pmid = {29930200}, issn = {1744-4292}, support = {R35 GM124774/GM/NIGMS NIH HHS/United States ; T32 GM008349/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacterial Physiological Phenomena ; Computational Biology/methods ; Gastrointestinal Microbiome/*physiology ; Humans ; Metabolomics ; *Microbial Interactions ; Models, Biological ; }, abstract = {The ecological forces that govern the assembly and stability of the human gut microbiota remain unresolved. We developed a generalizable model-guided framework to predict higher-dimensional consortia from time-resolved measurements of lower-order assemblages. This method was employed to decipher microbial interactions in a diverse human gut microbiome synthetic community. We show that pairwise interactions are major drivers of multi-species community dynamics, as opposed to higher-order interactions. The inferred ecological network exhibits a high proportion of negative and frequent positive interactions. Ecological drivers and responsive recipient species were discovered in the network. Our model demonstrated that a prevalent positive and negative interaction topology enables robust coexistence by implementing a negative feedback loop that balances disparities in monospecies fitness levels. We show that negative interactions could generate history-dependent responses of initial species proportions that frequently do not originate from bistability. Measurements of extracellular metabolites illuminated the metabolic capabilities of monospecies and potential molecular basis of microbial interactions. In sum, these methods defined the ecological roles of major human-associated intestinal species and illuminated design principles of microbial communities.}, } @article {pmid29928036, year = {2018}, author = {Lehnen, L and Schorcht, W and Karst, I and Biedermann, M and Kerth, G and Puechmaille, SJ}, title = {Using Approximate Bayesian Computation to infer sex ratios from acoustic data.}, journal = {PloS one}, volume = {13}, number = {6}, pages = {e0199428}, pmid = {29928036}, issn = {1932-6203}, mesh = {*Acoustics ; Animals ; Bayes Theorem ; Chiroptera/*physiology ; *Computer Simulation ; Databases as Topic ; Female ; Male ; *Sex Ratio ; Vocalization, Animal/physiology ; }, abstract = {Population sex ratios are of high ecological relevance, but are challenging to determine in species lacking conspicuous external cues indicating their sex. Acoustic sexing is an option if vocalizations differ between sexes, but is precluded by overlapping distributions of the values of male and female vocalizations in many species. A method allowing the inference of sex ratios despite such an overlap will therefore greatly increase the information extractable from acoustic data. To meet this demand, we developed a novel approach using Approximate Bayesian Computation (ABC) to infer the sex ratio of populations from acoustic data. Additionally, parameters characterizing the male and female distribution of acoustic values (mean and standard deviation) are inferred. This information is then used to probabilistically assign a sex to a single acoustic signal. We furthermore develop a simpler means of sex ratio estimation based on the exclusion of calls from the overlap zone. Applying our methods to simulated data demonstrates that sex ratio and acoustic parameter characteristics of males and females are reliably inferred by the ABC approach. Applying both the ABC and the exclusion method to empirical datasets (echolocation calls recorded in colonies of lesser horseshoe bats, Rhinolophus hipposideros) provides similar sex ratios as molecular sexing. Our methods aim to facilitate evidence-based conservation, and to benefit scientists investigating ecological or conservation questions related to sex- or group specific behaviour across a wide range of organisms emitting acoustic signals. The developed methodology is non-invasive, low-cost and time-efficient, thus allowing the study of many sites and individuals. We provide an R-script for the easy application of the method and discuss potential future extensions and fields of applications. The script can be easily adapted to account for numerous biological systems by adjusting the type and number of groups to be distinguished (e.g. age, social rank, cryptic species) and the acoustic parameters investigated.}, } @article {pmid29927925, year = {2018}, author = {Estrela, S and Brown, SP}, title = {Community interactions and spatial structure shape selection on antibiotic resistant lineages.}, journal = {PLoS computational biology}, volume = {14}, number = {6}, pages = {e1006179}, pmid = {29927925}, issn = {1553-7358}, mesh = {Anti-Bacterial Agents/*pharmacology/therapeutic use ; *Bacteria/drug effects/pathogenicity ; Bacterial Infections/drug therapy/*microbiology ; Biofilms/drug effects ; Computational Biology ; Drug Resistance, Bacterial ; Humans ; *Microbial Interactions/drug effects/physiology ; *Models, Biological ; Symbiosis/drug effects/physiology ; }, abstract = {Polymicrobial interactions play an important role in shaping the outcome of antibiotic treatment, yet how multispecies communities respond to antibiotic assault is still little understood. Here we use an individual-based simulation model of microbial biofilms to investigate how competitive and mutualistic interactions between an antibiotic-resistant and a susceptible strain (or species) influence the two-lineage community response to antibiotic exposure. Our model predicts that while increasing competition and antibiotics leads to increasing competitive release of the antibiotic-resistant strain, hitting a mutualistic community of cross-feeding species with antibiotics leads to a mutualistic suppression effect where both susceptible and resistant species are harmed. We next show that the impact of antibiotics is further governed by emergent spatial feedbacks within communities. Mutualistic cross-feeding communities can rescue susceptible members by subsidizing their growth inside the biofilm despite lack of access to the nutrient-rich and high-antibiotic growing front. Moreover, we show that antibiotic detoxification by resistant cells can protect nearby susceptible cells, but such cross-protection is more effective in mutualistic communities because mutualism drives mixing of resistant and susceptible cells. In contrast, competition leads to segregation, which ultimately prevents susceptible cells to profit from detoxification. Understanding how the interplay between microbial metabolic interactions and community spatial structuring shapes the outcome of antibiotic treatment can be key to effectively leverage the power of antibiotics and promote microbiome health.}, } @article {pmid29926380, year = {2019}, author = {Long, C and Kubatko, L}, title = {Identifiability and Reconstructibility of Species Phylogenies Under a Modified Coalescent.}, journal = {Bulletin of mathematical biology}, volume = {81}, number = {2}, pages = {408-430}, doi = {10.1007/s11538-018-0456-9}, pmid = {29926380}, issn = {1522-9602}, mesh = {Computational Biology ; Computer Simulation ; Evolution, Molecular ; Genetic Speciation ; Mathematical Concepts ; *Models, Genetic ; Models, Statistical ; *Phylogeny ; Probability ; }, abstract = {Coalescent models of evolution account for incomplete lineage sorting by specifying a species tree parameter which determines a distribution on gene trees, and consequently, a site pattern probability distribution. It has been shown that the unrooted topology of the species tree parameter of the multispecies coalescent is generically identifiable, and a reconstruction method called SVDQuartets has been developed to infer this topology. In this paper, we describe a modified multispecies coalescent model that allows for varying effective population size and violations of the molecular clock. We show that the unrooted topology of the species tree parameter for these models is generically identifiable and that SVDQuartets can still be used to infer this topology.}, } @article {pmid29925783, year = {2018}, author = {Rando, HM and Farré, M and Robson, MP and Won, NB and Johnson, JL and Buch, R and Bastounes, ER and Xiang, X and Feng, S and Liu, S and Xiong, Z and Kim, J and Zhang, G and Trut, LN and Larkin, DM and Kukekova, AV}, title = {Construction of Red Fox Chromosomal Fragments from the Short-Read Genome Assembly.}, journal = {Genes}, volume = {9}, number = {6}, pages = {}, pmid = {29925783}, issn = {2073-4425}, support = {R01 GM120782/GM/NIGMS NIH HHS/United States ; }, abstract = {The genome of a red fox (Vulpes vulpes) was recently sequenced and assembled using next-generation sequencing (NGS). The assembly is of high quality, with 94X coverage and a scaffold N50 of 11.8 Mbp, but is split into 676,878 scaffolds, some of which are likely to contain assembly errors. Fragmentation and misassembly hinder accurate gene prediction and downstream analysis such as the identification of loci under selection. Therefore, assembly of the genome into chromosome-scale fragments was an important step towards developing this genomic model. Scaffolds from the assembly were aligned to the dog reference genome and compared to the alignment of an outgroup genome (cat) against the dog to identify syntenic sequences among species. The program Reference-Assisted Chromosome Assembly (RACA) then integrated the comparative alignment with the mapping of the raw sequencing reads generated during assembly against the fox scaffolds. The 128 sequence fragments RACA assembled were compared to the fox meiotic linkage map to guide the construction of 40 chromosomal fragments. This computational approach to assembly was facilitated by prior research in comparative mammalian genomics, and the continued improvement of the red fox genome can in turn offer insight into canid and carnivore chromosome evolution. This assembly is also necessary for advancing genetic research in foxes and other canids.}, } @article {pmid29925614, year = {2018}, author = {Brothers, CJ and Van Der Pol, WJ and Morrow, CD and Hakim, JA and Koo, H and McClintock, JB}, title = {Ocean warming alters predicted microbiome functionality in a common sea urchin.}, journal = {Proceedings. Biological sciences}, volume = {285}, number = {1881}, pages = {}, pmid = {29925614}, issn = {1471-2954}, support = {P30 AI027767/AI/NIAID NIH HHS/United States ; P30 AR050948/AR/NIAMS NIH HHS/United States ; UL1 TR001417/TR/NCATS NIH HHS/United States ; }, mesh = {Animals ; *Climate Change ; Hot Temperature/*adverse effects ; Lytechinus/*microbiology ; *Microbiota ; Oceans and Seas ; Random Allocation ; Seawater/*analysis ; }, abstract = {The microbiome of sea urchins plays a role in maintaining digestive health and innate immunity. Here, we investigated the effects of long-term (90 day) exposure to elevated seawater temperatures on the microbiome of the common, subtropical sea urchin Lytechinus variegatus The community composition and diversity of microbes varied according to the type of sample collected from the sea urchin (seawater, feed, intestines, coelomic fluid, digested pellet and faeces), with the lowest microbial diversity (predominately the order Campylobacterales) located in the intestinal tissue. Sea urchins exposed to near-future seawater temperatures maintained the community structure and diversity of microbes associated with their tissues. However, marginal, non-significant shifts in microbial community structure with elevated temperature resulted in significant changes in predicted metagenomic functions such as membrane transport and amino acid and carbohydrate metabolism. The predicted changes in key metabolic categories suggest that near-future climate-induced increases in seawater temperature could shift microbial community function and impact sea urchin digestive and immune physiology.}, } @article {pmid29924794, year = {2018}, author = {Burns, MB and Montassier, E and Abrahante, J and Priya, S and Niccum, DE and Khoruts, A and Starr, TK and Knights, D and Blekhman, R}, title = {Colorectal cancer mutational profiles correlate with defined microbial communities in the tumor microenvironment.}, journal = {PLoS genetics}, volume = {14}, number = {6}, pages = {e1007376}, pmid = {29924794}, issn = {1553-7404}, support = {R01 AI121383/AI/NIAID NIH HHS/United States ; UL1 TR000114/TR/NCATS NIH HHS/United States ; }, mesh = {Adult ; Bacteria/genetics ; Colonic Neoplasms ; Colorectal Neoplasms/*genetics ; Female ; Gastrointestinal Microbiome/*genetics ; Genetic Variation/genetics ; Humans ; Male ; Middle Aged ; Mutation ; Transcriptome/genetics ; Tumor Microenvironment/*genetics/physiology ; }, abstract = {Variation in the gut microbiome has been linked to colorectal cancer (CRC), as well as to host genetic variation. However, we do not know whether, in addition to baseline host genetics, somatic mutational profiles in CRC tumors interact with the surrounding tumor microbiome, and if so, whether these changes can be used to understand microbe-host interactions with potential functional biological relevance. Here, we characterized the association between CRC microbial communities and tumor mutations using microbiome profiling and whole-exome sequencing in 44 pairs of tumors and matched normal tissues. We found statistically significant associations between loss-of-function mutations in tumor genes and shifts in the abundances of specific sets of bacterial taxa, suggestive of potential functional interaction. This correlation allows us to statistically predict interactions between loss-of-function tumor mutations in cancer-related genes and pathways, including MAPK and Wnt signaling, solely based on the composition of the microbiome. In conclusion, our study shows that CRC microbiomes are correlated with tumor mutational profiles, pointing towards possible mechanisms of molecular interaction.}, } @article {pmid29924690, year = {2019}, author = {Gawarkiewicz, G and Malek Mercer, A}, title = {Partnering with Fishing Fleets to Monitor Ocean Conditions.}, journal = {Annual review of marine science}, volume = {11}, number = {}, pages = {391-411}, doi = {10.1146/annurev-marine-010318-095201}, pmid = {29924690}, issn = {1941-0611}, mesh = {Animals ; Conservation of Water Resources/*methods ; Cooperative Behavior ; Ecosystem ; Environmental Monitoring/*methods ; *Fisheries ; Humans ; Oceanography/*methods ; Oceans and Seas ; }, abstract = {Engaging ocean users, including fishing fleets, in oceanographic and ecological research is a valuable method for collecting high-quality data, improving cost efficiency, and increasing societal appreciation for scientific research. As research partners, fishing fleets provide broad access to and knowledge of the ocean, and fishers are highly motivated to use the data collected to better understand the ecosystems in which they harvest. Here, we discuss recent trends in collaborative research that have increased the capacity of and access to scientific data collection. We also describe common elements of successful collaborative research programs, including definition of a scientific problem and goals, choice of technology, data collection and sampling design, data management and dissemination, and data analysis and communication. Finally, we review four case studies that demonstrate the general principles of effective collaborative research as well as the utility of citizen-collected data for academic research and fisheries management. We also discuss the challenge of funding, particularly as it relates to maintaining collaborative research programs in the long term. We conclude with a discussion of likely future trends. Ultimately, we predict that collaborative research will continue to grow in importance as climate change increasingly impacts ocean ecosystems, commercial fisheries, and the global food supply.}, } @article {pmid29923638, year = {2018}, author = {Jucker, T and Wintle, B and Shackelford, G and Bocquillon, P and Geffert, JL and Kasoar, T and Kovacs, E and Mumby, HS and Orland, C and Schleicher, J and Tew, ER and Zabala, A and Amano, T and Bell, A and Bongalov, B and Chambers, JM and Corrigan, C and Durán, AP and Duvic-Paoli, LA and Emilson, C and Emilson, EJS and da Silva, JF and Garnett, EE and Green, EJ and Guth, MK and Hacket-Pain, A and Hinsley, A and Igea, J and Kunz, M and Luke, SH and Lynam, W and Martin, PA and Nunes, MH and Ockendon, N and Pavitt, A and Payne, CLR and Plutshack, V and Rademacher, TT and Robertson, RJ and Rose, DC and Serban, A and Simmons, BI and Tayleur, C and Wordley, CFR and Mukherjee, N}, title = {Ten-year assessment of the 100 priority questions for global biodiversity conservation.}, journal = {Conservation biology : the journal of the Society for Conservation Biology}, volume = {32}, number = {6}, pages = {1457-1463}, doi = {10.1111/cobi.13159}, pmid = {29923638}, issn = {1523-1739}, mesh = {Biodiversity ; *Conservation of Natural Resources ; *Ecosystem ; Fresh Water ; }, abstract = {In 2008, a group of conservation scientists compiled a list of 100 priority questions for the conservation of the world's biodiversity. However, now almost a decade later, no one has yet published a study gauging how much progress has been made in addressing these 100 high-priority questions in the peer-reviewed literature. We took a first step toward reexamining the 100 questions to identify key knowledge gaps that remain. Through a combination of a questionnaire and a literature review, we evaluated each question on the basis of 2 criteria: relevance and effort. We defined highly relevant questions as those that - if answered - would have the greatest impact on global biodiversity conservation and quantified effort based on the number of review publications addressing a particular question, which we used as a proxy for research effort. Using this approach, we identified a set of questions that, despite being perceived as highly relevant, have been the focus of relatively few review publications over the past 10 years. These questions covered a broad range of topics but predominantly tackled 3 major themes: conservation and management of freshwater ecosystems, role of societal structures in shaping interactions between people and the environment, and impacts of conservation interventions. We believe these questions represent important knowledge gaps that have received insufficient attention and may need to be prioritized in future research.}, } @article {pmid29923321, year = {2018}, author = {Keck, F and Vasselon, V and Rimet, F and Bouchez, A and Kahlert, M}, title = {Boosting DNA metabarcoding for biomonitoring with phylogenetic estimation of operational taxonomic units' ecological profiles.}, journal = {Molecular ecology resources}, volume = {18}, number = {6}, pages = {1299-1309}, doi = {10.1111/1755-0998.12919}, pmid = {29923321}, issn = {1755-0998}, mesh = {Computational Biology/*methods ; DNA Barcoding, Taxonomic/*methods ; Diatoms/classification/genetics ; Environmental Monitoring/*methods ; Metagenomics/*methods ; Microscopy ; Phylogeny ; Rivers/microbiology ; Sensitivity and Specificity ; }, abstract = {DNA metabarcoding has been introduced as a revolutionary way to identify organisms and monitor ecosystems. However, the potential of this approach for biomonitoring remains partially unfulfilled because a significant part of the sampled DNA cannot be affiliated to species due to incomplete reference libraries. Thus, biotic indices, which are based on the estimated abundances of species in a community and their ecological profiles, can be inaccurate. We propose to compute biotic indices using phylogenetic imputation of operational taxonomic units (OTUs') ecological profiles (OTU-PITI approach). First, OTUs sequences are inserted within a reference phylogeny. Second, OTUs' ecological profiles are estimated on the basis of their phylogenetic relationships with reference species whose ecology is known. Based on these ecological profiles, biotic indices can be computed using all available OTUs. Using freshwater diatoms as a case study, we show that short DNA barcodes can be placed accurately within a phylogeny and their ecological preferences estimated with a satisfactory level of precision. In the light of these results, we tested the approach with a data set of 139 environmental samples of benthic river diatoms for which the same biotic index (specific sensitivity index) was calculated using (a) traditional microscopy, (b) OTUs with taxonomic assignment approach, (c) OTUs with phylogenetic estimation of ecological profiles (OTU-PITI) and (d) OTU with taxonomic assignment completed by the phylogenetic approach (OTU-PITI) for unclassified OTUs. Using traditional microscopy as a reference, we found that the combination of the OTUs' taxonomic assignment completed by the phylogenetic method performed satisfactorily and substantially better than the other methods tested.}, } @article {pmid29922245, year = {2018}, author = {Mercado-Blanco, J and Abrantes, I and Barra Caracciolo, A and Bevivino, A and Ciancio, A and Grenni, P and Hrynkiewicz, K and Kredics, L and Proença, DN}, title = {Belowground Microbiota and the Health of Tree Crops.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {1006}, pmid = {29922245}, issn = {1664-302X}, abstract = {Trees are crucial for sustaining life on our planet. Forests and land devoted to tree crops do not only supply essential edible products to humans and animals, but also additional goods such as paper or wood. They also prevent soil erosion, support microbial, animal, and plant biodiversity, play key roles in nutrient and water cycling processes, and mitigate the effects of climate change acting as carbon dioxide sinks. Hence, the health of forests and tree cropping systems is of particular significance. In particular, soil/rhizosphere/root-associated microbial communities (known as microbiota) are decisive to sustain the fitness, development, and productivity of trees. These benefits rely on processes aiming to enhance nutrient assimilation efficiency (plant growth promotion) and/or to protect against a number of (a)biotic constraints. Moreover, specific members of the microbial communities associated with perennial tree crops interact with soil invertebrate food webs, underpinning many density regulation mechanisms. This review discusses belowground microbiota interactions influencing the growth of tree crops. The study of tree-(micro)organism interactions taking place at the belowground level is crucial to understand how they contribute to processes like carbon sequestration, regulation of ecosystem functioning, and nutrient cycling. A comprehensive understanding of the relationship between roots and their associate microbiota can also facilitate the design of novel sustainable approaches for the benefit of these relevant agro-ecosystems. Here, we summarize the methodological approaches to unravel the composition and function of belowground microbiota, the factors influencing their interaction with tree crops, their benefits and harms, with a focus on representative examples of Biological Control Agents (BCA) used against relevant biotic constraints of tree crops. Finally, we add some concluding remarks and suggest future perspectives concerning the microbiota-assisted management strategies to sustain tree crops.}, } @article {pmid29920527, year = {2018}, author = {Saarman, ET and Owens, B and Murray, SN and Weisberg, SB and Ambrose, RF and Field, JC and Nielsen, KJ and Carr, MH}, title = {An ecological framework for informing permitting decisions on scientific activities in protected areas.}, journal = {PloS one}, volume = {13}, number = {6}, pages = {e0199126}, pmid = {29920527}, issn = {1932-6203}, mesh = {Animals ; Aquatic Organisms ; Biodiversity ; California ; *Conservation of Natural Resources ; Decision Making ; *Decision Support Systems, Management ; *Decision Support Techniques ; *Ecosystem ; *Environment ; Models, Theoretical ; Program Evaluation ; *Research/organization & administration ; }, abstract = {There are numerous reasons to conduct scientific research within protected areas, but research activities may also negatively impact organisms and habitats, and thus conflict with a protected area's conservation goals. We developed a quantitative ecological decision-support framework that estimates these potential impacts so managers can weigh costs and benefits of proposed research projects and make informed permitting decisions. The framework generates quantitative estimates of the ecological impacts of the project and the cumulative impacts of the proposed project and all other projects in the protected area, and then compares the estimated cumulative impacts of all projects with policy-based acceptable impact thresholds. We use a series of simplified equations (models) to assess the impacts of proposed research to: a) the population of any targeted species, b) the major ecological assemblages that make up the community, and c) the physical habitat that supports protected area biota. These models consider both targeted and incidental impacts to the ecosystem and include consideration of the vulnerability of targeted species, assemblages, and habitats, based on their recovery time and ecological role. We parameterized the models for a wide variety of potential research activities that regularly occur in the study area using a combination of literature review and expert judgment with a precautionary approach to uncertainty. We also conducted sensitivity analyses to examine the relationships between model input parameters and estimated impacts to understand the dominant drivers of the ecological impact estimates. Although the decision-support framework was designed for and adopted by the California Department of Fish and Wildlife for permitting scientific studies in the state-wide network of marine protected areas (MPAs), the framework can readily be adapted for terrestrial and freshwater protected areas.}, } @article {pmid29917104, year = {2018}, author = {Celis, JS and Wibberg, D and Ramírez-Portilla, C and Rupp, O and Sczyrba, A and Winkler, A and Kalinowski, J and Wilke, T}, title = {Binning enables efficient host genome reconstruction in cnidarian holobionts.}, journal = {GigaScience}, volume = {7}, number = {7}, pages = {}, pmid = {29917104}, issn = {2047-217X}, mesh = {Algorithms ; Animals ; Anthozoa/*physiology ; Cnidaria/*genetics ; Computational Biology ; Coral Reefs ; DNA/analysis ; Ecology ; *Genome ; Genomics/*methods ; High-Throughput Nucleotide Sequencing ; Metagenomics/*methods ; Phylogeny ; RNA, Ribosomal, 16S/analysis ; Sequence Analysis, DNA ; Symbiosis ; Transcriptome ; }, abstract = {BACKGROUND: Many cnidarians, including stony corals, engage in complex symbiotic associations, comprising the eukaryotic host, photosynthetic algae, and highly diverse microbial communities-together referred to as holobiont. This taxonomic complexity makes sequencing and assembling coral host genomes extremely challenging. Therefore, previous cnidarian genomic projects were based on symbiont-free tissue samples. However, this approach may not be applicable to the majority of cnidarian species for ecological reasons. We therefore evaluated the performance of an alternative method based on sequence binning for reconstructing the genome of the stony coral Porites rus from a hologenomic sample and compared it to traditional approaches.

RESULTS: Our results demonstrate that binning performs well for hologenomic data, producing sufficient reads for assembling the draft genome of P. rus. An assembly evaluation based on operational criteria showed results that were comparable to symbiont-free approaches in terms of completeness and usefulness, despite a high degree of fragmentation in our assembly. In addition, we found that binning provides sufficient data for exploratory k-mer estimation of genomic features, such as genome size and heterozygosity.

CONCLUSIONS: Binning constitutes a powerful approach for disentangling taxonomically complex coral hologenomes. Considering the recent decline of coral reefs on the one hand and previous limitations to coral genome sequencing on the other hand, binning may facilitate rapid and reliable genome assembly. This study also provides an important milestone in advancing binning from the metagenomic to the hologenomic and from the prokaryotic to the eukaryotic level.}, } @article {pmid29916185, year = {2018}, author = {Lee, C and Ahn, JW and Kim, JB and Kim, JY and Choi, YE}, title = {Comparative transcriptome analysis of Haematococcus pluvialis on astaxanthin biosynthesis in response to irradiation with red or blue LED wavelength.}, journal = {World journal of microbiology & biotechnology}, volume = {34}, number = {7}, pages = {96}, pmid = {29916185}, issn = {1573-0972}, support = {2016R1D1A1B03932773//National Research Foundation of Korea/ ; Project No. C38703//Korea Basic Science Institute/ ; }, mesh = {Biosynthetic Pathways/genetics/radiation effects ; Cell Division/radiation effects ; Chlorophyta/*genetics/growth & development/*metabolism/*radiation effects ; Cluster Analysis ; Color ; Gene Expression Profiling ; Gene Expression Regulation, Plant/*radiation effects ; Gene Ontology ; Genes, Plant/genetics/radiation effects ; Industrial Microbiology ; *Light ; Lighting ; Reactive Oxygen Species/metabolism ; Sequence Analysis, RNA ; *Transcriptome ; Up-Regulation ; Xanthophylls/biosynthesis/genetics ; }, abstract = {The unicellular green microalga Haematococcus pluvialis has the highest content of the natural antioxidant, astaxanthin. Previously, it was determined that astaxanthin accumulation in H. pluvialis could be induced by blue-wavelength irradiation; however, the molecular mechanism remains unknown. The present study aimed to compare the transcriptome of H. pluvialis, with respect to astaxanthin biosynthesis, under the monochromatic red (660 nm) or blue (450 nm) light-emitting diode (LED) irradiation. Among a total of 165,372 transcripts, we identified 67,703 unigenes, of which 2245 and 171 were identified as differentially expressed genes (DEGs) in response to blue and red irradiation, respectively. Interestingly, expressional changes of blue light receptor cryptochromes were detected in response to blue and/or red LED irradiation in H. pluvialis, which may directly and indirectly regulate astaxanthin biosynthesis. In accordance with this observation, expression of the BKT and CHY genes, which are part of the downstream section of the astaxanthin biosynthetic pathway, was significantly upregulated by blue LED irradiation compared with their expression under control white irradiation. Contrastingly, they were downregulated by red LED irradiation. Our transcriptome study provided molecular insights that highlighted the different of responses of H. pluvialis to red and blue irradiation, especially for astaxanthin biosynthesis.}, } @article {pmid29915339, year = {2018}, author = {Culina, A and Crowther, TW and Ramakers, JJC and Gienapp, P and Visser, ME}, title = {How to do meta-analysis of open datasets.}, journal = {Nature ecology & evolution}, volume = {2}, number = {7}, pages = {1053-1056}, doi = {10.1038/s41559-018-0579-2}, pmid = {29915339}, issn = {2397-334X}, mesh = {*Datasets as Topic ; Ecology/*methods ; *Ecosystem ; *Meta-Analysis as Topic ; }, } @article {pmid29914367, year = {2018}, author = {Lu, Z and Huang, Q and Zhang, T and Hu, B and Chang, Y}, title = {Global transcriptome analysis and characterization of Dryopteris fragrans (L.) Schott sporangium in different developmental stages.}, journal = {BMC genomics}, volume = {19}, number = {1}, pages = {471}, pmid = {29914367}, issn = {1471-2164}, support = {31570189//National Natural Science Foundation of China/ ; }, mesh = {Databases, Protein ; Dryopteris/*genetics/*growth & development ; Gene Expression Profiling/*methods ; *Gene Expression Regulation, Developmental ; *Gene Expression Regulation, Plant ; High-Throughput Nucleotide Sequencing ; Molecular Sequence Annotation ; Plant Proteins/*genetics ; *Transcriptome ; }, abstract = {BACKGROUND: Dryopteris fragrans (D. fragrans) is a potential medicinal fern distributed in volcanic magmatic rock areas under tough environmental condition. Sporangia are important organs for fern reproduction. This study was designed to characterize the transcriptome characteristics of the wild D. fragrans sporangia in three stages (stage A, B, and C) with the aim of uncovering its molecular mechanism of growth and development.

RESULTS: Using a HiSeq 4000, 79.81 Gb clean data (each sample is at least 7.95 GB) were obtained from nine samples, with three being supplied from each period, and assembled into 94,705 Unigenes, among which 44,006 Unigenes were annotated against public protein databases (NR, Swiss-Prot, KEGG, COG, KOG, GO, eggNOG and Pfam). Furthermore, we observed 7126 differentially expressed genes (DEG) (Fold Change > 4, FDR < 0.001), 349,885 SNP loci, and 10,584 SSRs. DEGs involved in DNA replication and homologous recombination were strongly expressed in stage A, and several DEGs involved in cutin, suberin and wax biosynthesis had undergone dramatic changes during development, which was consistent with morphological observations. DEGs responsible for secondary metabolism and plant hormone signal transduction changed clearly in the last two stages. DEGs homologous to those known genes associated with the development of reproductive organs of flowering plants have also been validated and discussed, such as AGL61, AGL62, ONAC010. In particular, a Unigene encoding TFL1, an important flower-development regulator in flowering plants, was identified and exhibited the highest expression level in stage B in D. fragrans sporangia.

CONCLUSIONS: This study is the first report on global transcriptome analysis in the development of sporangia of wild D. fragrans. DEGs related to development and homologous to flower-seed development in flowering plants were discussed. All DEGs involved in DNA replication and homologous recombination were consistent with morphological observations of paraffin slices. The results of this study provide rare resources for further investigation of the D. fragrans sporangium development, stress resistance and secondary metabolism.}, } @article {pmid29914364, year = {2018}, author = {Kennedy, EM and Goehring, GN and Nichols, MH and Robins, C and Mehta, D and Klengel, T and Eskin, E and Smith, AK and Conneely, KN}, title = {An integrated -omics analysis of the epigenetic landscape of gene expression in human blood cells.}, journal = {BMC genomics}, volume = {19}, number = {1}, pages = {476}, pmid = {29914364}, issn = {1471-2164}, support = {UL1TR000454//National Center for Advancing Translational Sciences/ ; T32GM008490//National Institute of General Medical Sciences/ ; UL1 TR000454/TR/NCATS NIH HHS/United States ; UL1 TR002378/TR/NCATS NIH HHS/United States ; 1008188//Burroughs Wellcome Fund/ ; T32 GM008490/GM/NIGMS NIH HHS/United States ; }, mesh = {Adolescent ; Adult ; Aged ; Blood Cells/*metabolism ; Cohort Studies ; CpG Islands ; *DNA Methylation ; *Epigenesis, Genetic ; Female ; Gene Expression Profiling ; Gene Ontology ; Genomics ; Humans ; Male ; Middle Aged ; Young Adult ; }, abstract = {BACKGROUND: Gene expression can be influenced by DNA methylation 1) distally, at regulatory elements such as enhancers, as well as 2) proximally, at promoters. Our current understanding of the influence of distal DNA methylation changes on gene expression patterns is incomplete. Here, we characterize genome-wide methylation and expression patterns for ~ 13 k genes to explore how DNA methylation interacts with gene expression, throughout the genome.

RESULTS: We used a linear mixed model framework to assess the correlation of DNA methylation at ~ 400 k CpGs with gene expression changes at ~ 13 k transcripts in two independent datasets from human blood cells. Among CpGs at which methylation significantly associates with transcription (eCpGs), > 50% are distal (> 50 kb) or trans (different chromosome) to the correlated gene. Many eCpG-transcript pairs are consistent between studies and ~ 90% of neighboring eCpGs associate with the same gene, within studies. We find that enhancers (P < 5e-18) and microRNA genes (P = 9e-3) are overrepresented among trans eCpGs, and insulators and long intergenic non-coding RNAs are enriched among cis and distal eCpGs. Intragenic-eCpG-transcript correlations are negative in 60-70% of occurrences and are enriched for annotated gene promoters and enhancers (P < 0.002), highlighting the importance of intragenic regulation. Gene Ontology analysis indicates that trans eCpGs are enriched for transcription factor genes and chromatin modifiers, suggesting that some trans eCpGs represent the influence of gene networks and higher-order transcriptional control.

CONCLUSIONS: This work sheds new light on the interplay between epigenetic changes and gene expression, and provides useful data for mining biologically-relevant results from epigenome-wide association studies.}, } @article {pmid29914169, year = {2018}, author = {Watkins, SC and Sible, E and Putonti, C}, title = {Pseudomonas PB1-Like Phages: Whole Genomes from Metagenomes Offer Insight into an Abundant Group of Bacteriophages.}, journal = {Viruses}, volume = {10}, number = {6}, pages = {}, pmid = {29914169}, issn = {1999-4915}, mesh = {Computational Biology ; Environmental Microbiology ; *Genetic Variation ; *Genome, Viral ; Metagenomics ; Pseudomonas Phages/*classification/*genetics/isolation & purification ; }, abstract = {Despite the abundance, ubiquity and impact of environmental viruses, their inherent genomic plasticity and extreme diversity pose significant challenges for the examination of bacteriophages on Earth. Viral metagenomic studies have offered insight into broader aspects of phage ecology and repeatedly uncover genes to which we are currently unable to assign function. A combined effort of phage isolation and metagenomic survey of Chicago’s nearshore waters of Lake Michigan revealed the presence of Pbunaviruses, relatives of the Pseudomonas phage PB1. This prompted our expansive investigation of PB1-like phages. Genomic signatures of PB1-like phages and Pbunaviruses were identified, permitting the unambiguous distinction between the presence/absence of these phages in soils, freshwater and wastewater samples, as well as publicly available viral metagenomic datasets. This bioinformatic analysis led to the de novo assembly of nine novel PB1-like phage genomes from a metagenomic survey of samples collected from Lake Michigan. While this study finds that Pbunaviruses are abundant in various environments of Northern Illinois, genomic variation also exists to a considerable extent within individual communities.}, } @article {pmid29913567, year = {2018}, author = {Siebielec, S and Siebielec, G and Stuczyński, T and Sugier, P and Grzęda, E and Grządziel, J}, title = {Long term insight into biodiversity of a smelter wasteland reclaimed with biosolids and by-product lime.}, journal = {The Science of the total environment}, volume = {636}, number = {}, pages = {1048-1057}, doi = {10.1016/j.scitotenv.2018.04.372}, pmid = {29913567}, issn = {1879-1026}, mesh = {Biodiversity ; Calcium Compounds ; Environmental Monitoring ; Environmental Restoration and Remediation/*methods ; *Hazardous Waste Sites ; *Metallurgy ; Metals ; Oxides ; Poland ; Soil Pollutants/analysis ; Trace Elements ; }, abstract = {Smelter wastelands containing high amounts of zinc, lead, cadmium, and arsenic constitute a major problem worldwide. Serious hazards for human health and ecosystem functioning are related to a lack of vegetative cover, causing fugitive dust fluxes, runoff and leaching of metals, affecting post-industrial ecosystems, often in heavily populated areas. Previous studies demonstrated the short term effectiveness of assisted phytostabilisation of zinc and lead smelter slags, using biosolids and liming. However, a long term persistence of plant communities introduced for remediation and risk reduction has not been adequately evaluated. The work was aimed at characterising trace element solubility, plant and microbial communities of the top layer of the reclaimed zinc and lead smelter waste heaps in Piekary Slaskie, Poland, 20 years after the treatment and revegetation. The surface layer of the waste heaps treated with various rates of biosolids and the by-product lime was sampled for measuring chemical and biochemical parameters, which are indicative for metals bioavailability as well as for microorganisms activity. Microbial processes were characterised by enzyme activities, abundance of specific groups of microorganisms and identification of N fixing bacteria. Plant communities of the area were characterised by a percent coverage of the surface and by a composition of plant species and plant diversity. The study provides a strong evidence that the implemented remediation approach enables a sustainable functioning of the ecosystem established on the toxic waste heaps. Enzyme activities and the count of various groups of microorganisms were the highest in areas treated with both biosolids and lime, regardless their rates. A high plant species diversity and microbial activities are sustainable after almost two decades from the treatment, which is indicative of a strong resistance of the established ecosystem to a metal stress and a poor physical quality of the anthropogenic soil formed by the treatment.}, } @article {pmid29912385, year = {2018}, author = {Bengtsson-Palme, J and Richardson, RT and Meola, M and Wurzbacher, C and Tremblay, ÉD and Thorell, K and Kanger, K and Eriksson, KM and Bilodeau, GJ and Johnson, RM and Hartmann, M and Nilsson, RH}, title = {Metaxa2 Database Builder: enabling taxonomic identification from metagenomic or metabarcoding data using any genetic marker.}, journal = {Bioinformatics (Oxford, England)}, volume = {34}, number = {23}, pages = {4027-4033}, pmid = {29912385}, issn = {1367-4811}, mesh = {Computational Biology ; *DNA Barcoding, Taxonomic ; *Genetic Markers ; *Metagenomics ; *Phylogeny ; *Software ; }, abstract = {MOTIVATION: Correct taxonomic identification of DNA sequences is central to studies of biodiversity using both shotgun metagenomic and metabarcoding approaches. However, no genetic marker gives sufficient performance across all the biological kingdoms, hampering studies of taxonomic diversity in many groups of organisms. This has led to the adoption of a range of genetic markers for DNA metabarcoding. While many taxonomic classification software tools can be re-trained on these genetic markers, they are often designed with assumptions that impair their utility on genes other than the SSU and LSU rRNA. Here, we present an update to Metaxa2 that enables the use of any genetic marker for taxonomic classification of metagenome and amplicon sequence data.

RESULTS: We evaluated the Metaxa2 Database Builder on 11 commonly used barcoding regions and found that while there are wide differences in performance between different genetic markers, our software performs satisfactorily provided that the input taxonomy and sequence data are of high quality.

Freely available on the web as part of the Metaxa2 package at http://microbiology.se/software/metaxa2/.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, } @article {pmid29909752, year = {2020}, author = {Subramaniam, A and Van Der Pol, WJ and Ptacek, T and Lobashevsky, E and Neely, C and Biggio, JR and Lefkowitz, EJ and Morrow, CD and Edwards, RK}, title = {Midtrimester microbial DNA variations in maternal serum of women who experience spontaneous preterm birth.}, journal = {The journal of maternal-fetal & neonatal medicine : the official journal of the European Association of Perinatal Medicine, the Federation of Asia and Oceania Perinatal Societies, the International Society of Perinatal Obstetricians}, volume = {33}, number = {3}, pages = {359-367}, pmid = {29909752}, issn = {1476-4954}, support = {P30 AI027767/AI/NIAID NIH HHS/United States ; P30 AR050948/AR/NIAMS NIH HHS/United States ; UL1 TR001417/TR/NCATS NIH HHS/United States ; UL1 TR003096/TR/NCATS NIH HHS/United States ; }, mesh = {Adult ; DNA, Bacterial/*blood ; Female ; Humans ; *Microbiota ; Pregnancy ; Pregnancy Trimester, Second ; Premature Birth/blood/*microbiology ; Retrospective Studies ; Young Adult ; }, abstract = {Objectives: To evaluate if midtrimester maternal serum contains microbial DNA and whether it differs between women with spontaneous preterm birth (SPTB) and those delivering at term.Study design: In this retrospective case-control study, we identified 20 healthy nulliparas with SPTB at 24-33 weeks of a nonanomalous singleton in 2014. Each case was matched by race/ethnicity to a control delivering at 39-40 weeks. Serum samples, collected at 15-20 weeks and stored at -80 C, were thawed and DNA extracted. PCR with primers targeting the 16S rDNA V4 region were used to prepare an amplicon library, sequenced using Illumina MiSeq, and analyzed using quantitative insight into microbial ecology (QIIME). Taxonomy was assigned using Ribosomal Database program (RDP) Classifier (threshold 0.8) against a modified Greengenes database. Differences in number of observed species, microbial alpha-diversity and beta-diversity, and taxa level analyses were undertaken.Results: All 40 samples were included. Women with SPTB had more unique observed species (p = .046) and higher mean alpha-diversity by Shannon index (but not Chao1 or Simpson) (p = .024). Microbial composition was different between groups by Bray-Curtis clustering (p = .03) but not by weighted (p = .13) or unweighted Unifrac (p = .11). Numerous taxa in the Firmicutes, Proteobacteria, and Actinobacteria phyla differed between groups (p < .05).Conclusions: SPTB is associated with distinct microbial DNA changes detected in midtrimester maternal serum.}, } @article {pmid29908576, year = {2018}, author = {Gilca, M and Tiplica, GS and Salavastru, CM}, title = {Traditional and ethnobotanical dermatology practices in Romania and other Eastern European countries.}, journal = {Clinics in dermatology}, volume = {36}, number = {3}, pages = {338-352}, doi = {10.1016/j.clindermatol.2018.03.008}, pmid = {29908576}, issn = {1879-1131}, mesh = {Databases as Topic ; *Ethnobotany ; Humans ; *Medicine, Traditional ; *Phytotherapy ; Romania ; Skin Diseases/*drug therapy ; }, abstract = {The geographic and ecologic specificity of Romania and other Eastern European countries has resulted in the development of an exceptional diversity of medicinal plants. The purpose of this study was to provide an overview of the ethnobotanical dermatology practices based on the use of medicinal plants in this region. The indications, ethnopharmacologic activities, parts used, and administration of 106 medicinal plants are provided. We also discuss the relative importance of these species, using two modified indices of quantitative ethnobotany: Use Value Index and Relative Dermatologic Importance, which were calculated on the basis of etic constructions (indications and ethnopharmacologic activities). The species identified to have the highest dermatologic importance (on a scale of 100) were Brassica oleracea L. (100), Matricaria chamomilla L. (79.17), Arctium lappa L. (74.82), Daucus carota L. (72.28), Equisetum arvense L. (70.47), Juglans regia L. (69.93), Populous nigra L. (65.94), Symphytum officinale L. (63.59), Chelidonium majus L. (57.78), Calendula officinalis L. (57.78), Achillea millefolium L. (57.43), Melilotus officinalis L. (55.25), Allium cepa L. (51.45), Quercus robur L. (51.08), and Betula spp. (50.91). This preliminary study on ethnobotanical dermatology practices indicates that Eastern European traditional medical knowledge represents an important heritage that is currently underexploited.}, } @article {pmid29908452, year = {2018}, author = {Chao, W and Zhang, Y and Chai, L and Wang, H}, title = {Transcriptomics provides mechanistic indicators of fluoride toxicology on endochondral ossification in the hind limb of Bufo gargarizans.}, journal = {Aquatic toxicology (Amsterdam, Netherlands)}, volume = {201}, number = {}, pages = {138-150}, doi = {10.1016/j.aquatox.2018.06.006}, pmid = {29908452}, issn = {1879-1514}, mesh = {Animals ; Bufonidae/*genetics/growth & development/*physiology ; Fluorides/*toxicity ; Gene Expression Profiling ; Gene Expression Regulation, Developmental/drug effects ; Gene Ontology ; Hindlimb/*physiology ; Metamorphosis, Biological/drug effects/genetics ; Molecular Sequence Annotation ; Osteogenesis/drug effects/*genetics ; RNA, Messenger/genetics/metabolism ; Sequence Analysis, RNA ; Thyroid Hormones/metabolism ; Transcriptome/drug effects/*genetics ; Water Pollutants, Chemical/toxicity ; Water Quality ; }, abstract = {Endochondral ossification, the process by which most of the bone is formed, is regulated by many specific groups of molecules and extracellular matrix components. Hind limb of Bufo gargarizans is a model to study endochondral ossification during metamorphosis. Chinese toad (Bufo gargarizans) were exposed to different fluoride concentrations (0, 1, 5, 10 and 20 mg L[-1]) from G3 to G42. The development of hind limb of B. gargarizans was observed using the double staining methodology. The transcriptome of hind limb of B. gargarizans was conducted using RNA-seq approach, and differentially expressed gene was also validated. In addition, the location of Sox9 and Ihh in the growth cartilage was determined using in situ hybridization. Our results showed that 5 mg L[-1] stimulated bone mineralization, while 10 and 20 mg L[-1] exposure could inhibit the tibio-fibula, tarsus and metacarpals ossification. Besides, 10 mg F/L treatment could down-regulate Ihh, Sox9, D2, D3, TRα, TRβ, Wnt10, FGF3 and BMP6 expression, while up-regulate ObRb and HHAT mRNA expression in the hind limb of B. gargarizans. Transcript level changes of Ihh, Sox9, D2, D3, TRα, TRβ, Wnt10, FGF3 and BMP6 were consistent with the results of RT-qPCR. In situ hybridization revealed that Ihh was expressed in prehypertrophic chondrocytes, while Sox9 was abundantly expressed in proliferous, prehypertrophic and hypertrophic chondrocytes. However, 10 mg F-/L did not cause any affect in the location of the Ihh and Sox9 mRNA. Therefore, high concentration of fluoride could affect the ossification-related genes mRNA expression and then inhibit the endochondral ossification. The present study thus will greatly contribute to our understanding of the effect of environmental contaminant on ossification in amphibian.}, } @article {pmid29906269, year = {2018}, author = {Parkinson, JH and Kutil, R and Kuppler, J and Junker, RR and Trutschnig, W and Bathke, AC}, title = {A Fast and Robust Way to Estimate Overlap of Niches, and Draw Inference.}, journal = {The international journal of biostatistics}, volume = {14}, number = {2}, pages = {}, doi = {10.1515/ijb-2017-0028}, pmid = {29906269}, issn = {1557-4679}, mesh = {Animals ; *Biostatistics ; *Data Interpretation, Statistical ; *Ecosystem ; Finches ; *Models, Biological ; *Models, Statistical ; }, abstract = {The problem of quantifying the overlap of Hutchinsonian niches has received much attention lately, in particular in quantitative ecology, from where it also originates. However, the niche concept has the potential to also be useful in many other application areas, as for example in economics. We are presenting a fully nonparametric, robust solution to this problem, along with exact shortcut formulas based on rank-statistics, and with a rather intuitive probabilistic interpretation. Furthermore, by deriving the asymptotic sampling distribution of the estimators, we are proposing the first asymptotically valid inference method, providing confidence intervals for the niche overlap. The theoretical considerations are supplemented by simulation studies and a real data example.}, } @article {pmid29905922, year = {2018}, author = {Castro-Prieto, J and Andrade-Núñez, MJ}, title = {Health and Ecological Aspects of Stray Cats in Old San Juan, Puerto Rico: Baseline Information to Develop an Effective Control Program.}, journal = {Puerto Rico health sciences journal}, volume = {37}, number = {2}, pages = {110-114}, pmid = {29905922}, issn = {0738-0658}, mesh = {Animals ; *Animals, Wild ; Cat Diseases/*epidemiology/physiopathology ; Cats ; Databases, Factual ; Female ; Male ; Program Development/*methods ; Program Evaluation ; Puerto Rico/epidemiology ; Spatial Analysis ; }, abstract = {The overpopulation of stray cats in urban areas represents a potential risk for humans, as stray cats may carry diseases, such as toxoplasmosis, and virus such as rabies, the feline immunodeficiency, and the feline leukemia. In Old San Juan, a historic neighborhood and one of the most touristic places in Puerto Rico, there is an overpopulation of stray cats. In this study, we generated baseline information fundamental to developing a successful control program by estimating the stray cat population size, density, and spatial distribution. Furthermore, we quantified the number of neutered cats and developed a spatial database to include information about the external physical condition of each individual. We estimated a population of 178 (±21) cats, with a density of 3.6 cats/ha. Overall, we observed 209 cats, from which 149 (71%) were identified as new and 60 (29%) were recaptured. We found stray cats had a significant non-random and clustered spatial distribution (z-score = -19.39 SD; ratio = 0.29; p<0.0001), with an observable larger abundance in residential zones where food was provided. A total of 105 (70%) cats were neutered, and 32 (21%) individuals exhibited very poor physical conditions, including skin problems, scars, underweight, and blindness. We concluded that the ecological and descriptive data generated in this study are essential for an effective control of stray cats and their potential impacts on humans living in this neighborhood.}, } @article {pmid29899513, year = {2018}, author = {Kearney, SM and Gibbons, SM and Poyet, M and Gurry, T and Bullock, K and Allegretti, JR and Clish, CB and Alm, EJ}, title = {Endospores and other lysis-resistant bacteria comprise a widely shared core community within the human microbiota.}, journal = {The ISME journal}, volume = {12}, number = {10}, pages = {2403-2416}, pmid = {29899513}, issn = {1751-7370}, support = {P30 DK040561/DK/NIDDK NIH HHS/United States ; P30 DK043351/DK/NIDDK NIH HHS/United States ; }, mesh = {Bacteria/*classification/genetics ; Biodiversity ; Feces/microbiology ; Gastrointestinal Microbiome/*physiology ; Humans ; Spores, Bacterial/physiology ; }, abstract = {Endospore-formers in the human microbiota are well adapted for host-to-host transmission, and an emerging consensus points to their role in determining health and disease states in the gut. The human gut, more than any other environment, encourages the maintenance of endospore formation, with recent culture-based work suggesting that over 50% of genera in the microbiome carry genes attributed to this trait. However, there has been limited work on the ecological role of endospores and other stress-resistant cellular states in the human gut. In fact, there is no data to indicate whether organisms with the genetic potential to form endospores actually form endospores in situ and how sporulation varies across individuals and over time. Here we applied a culture-independent protocol to enrich for endospores and other stress-resistant cells in human feces to identify variation in these states across people and within an individual over time. We see that cells with resistant states are more likely than those without to be shared among multiple individuals, which suggests that these resistant states are particularly adapted for cross-host dissemination. Furthermore, we use untargeted fecal metabolomics in 24 individuals and within a person over time to show that these organisms respond to shared environmental signals, and in particular, dietary fatty acids, that likely mediate colonization of recently disturbed human guts.}, } @article {pmid29898550, year = {2018}, author = {Mirtl, M and T Borer, E and Djukic, I and Forsius, M and Haubold, H and Hugo, W and Jourdan, J and Lindenmayer, D and McDowell, WH and Muraoka, H and Orenstein, DE and Pauw, JC and Peterseil, J and Shibata, H and Wohner, C and Yu, X and Haase, P}, title = {Genesis, goals and achievements of Long-Term Ecological Research at the global scale: A critical review of ILTER and future directions.}, journal = {The Science of the total environment}, volume = {626}, number = {}, pages = {1439-1462}, doi = {10.1016/j.scitotenv.2017.12.001}, pmid = {29898550}, issn = {1879-1026}, abstract = {Since its founding in 1993 the International Long-term Ecological Research Network (ILTER) has gone through pronounced development phases. The current network comprises 44 active member LTER networks representing 700 LTER Sites and ~80 LTSER Platforms across all continents, active in the fields of ecosystem, critical zone and socio-ecological research. The critical challenges and most important achievements of the initial phase have now become state-of-the-art in networking for excellent science. At the same time increasing integration, accelerating technology, networking of resources and a strong pull for more socially relevant scientific information have been modifying the mission and goals of ILTER. This article provides a critical review of ILTER's mission, goals, development and impacts. Major characteristics, tools, services, partnerships and selected examples of relative strengths relevant for advancing ILTER are presented. We elaborate on the tradeoffs between the needs of the scientific community and stakeholder expectations. The embedding of ILTER in an increasingly collaborative landscape of global environmental observation and ecological research networks and infrastructures is also reflected by developments of pioneering regional and national LTER networks such as SAEON in South Africa, CERN/CEOBEX in China, TERN in Australia or eLTER RI in Europe. The primary role of ILTER is currently seen as a mechanism to investigate ecosystem structure, function, and services in response to a wide range of environmental forcings using long-term, place-based research. We suggest four main fields of activities and advancements for the next decade through development/delivery of a: (1) Global multi-disciplinary community of researchers and research institutes; (2) Strategic global framework and strong partnerships in ecosystem observation and research; (3) Global Research Infrastructure (GRI); and (4) a scientific knowledge factory for societally relevant information on sustainable use of natural resources.}, } @article {pmid29898034, year = {2018}, author = {Ma, YH and Ye, GS}, title = {Determination of multidrug resistance mechanisms in Clostridium perfringens type A isolates using RNA sequencing and 2D-electrophoresis.}, journal = {Brazilian journal of medical and biological research = Revista brasileira de pesquisas medicas e biologicas}, volume = {51}, number = {8}, pages = {e7044}, pmid = {29898034}, issn = {1414-431X}, mesh = {Animals ; Bacterial Proteins/*genetics/metabolism ; Clostridium perfringens/classification/drug effects/*genetics/metabolism ; DNA, Complementary ; Drug Resistance, Multiple, Bacterial/*genetics ; Electrophoresis, Gel, Two-Dimensional/methods ; Gene Expression Regulation, Bacterial/genetics ; Gene Ontology ; *Genes, MDR ; Genome, Bacterial/genetics ; Mass Spectrometry/methods ; Proteome/genetics ; Sequence Analysis, RNA/*methods ; Transcriptome/genetics ; }, abstract = {In this study, we screened differentially expressed genes in a multidrug-resistant isolate strain of Clostridium perfringens by RNA sequencing. We also separated and identified differentially expressed proteins (DEPs) in the isolate strain by two-dimensional electrophoresis (2-DE) and mass spectrometry (MS). The RNA sequencing results showed that, compared with the control strain, 1128 genes were differentially expressed in the isolate strain, and these included 227 up-regulated genes and 901 down-regulated genes. Bioinformatics analysis identified the following genes and gene categories that are potentially involved in multidrug resistance (MDR) in the isolate strain: drug transport, drug response, hydrolase activity, transmembrane transporter, transferase activity, amidase transmembrane transporter, efflux transmembrane transporter, bacterial chemotaxis, ABC transporter, and others. The results of the 2-DE showed that 70 proteins were differentially expressed in the isolate strain, 45 of which were up-regulated and 25 down-regulated. Twenty-seven DEPs were identified by MS and these included the following protein categories: ribosome, antimicrobial peptide resistance, and ABC transporter, all of which may be involved in MDR in the isolate strain of C. perfringens. The results provide reference data for further investigations on the drug resistant molecular mechanisms of C. perfringens.}, } @article {pmid29897905, year = {2018}, author = {Rorick, MM and Baskerville, EB and Rask, TS and Day, KP and Pascual, M}, title = {Identifying functional groups among the diverse, recombining antigenic var genes of the malaria parasite Plasmodium falciparum from a local community in Ghana.}, journal = {PLoS computational biology}, volume = {14}, number = {6}, pages = {e1006174}, pmid = {29897905}, issn = {1553-7358}, support = {R01 AI084156/AI/NIAID NIH HHS/United States ; R01 TW009670/TW/FIC NIH HHS/United States ; }, mesh = {Animals ; Antigenic Variation/genetics ; Antigens, Protozoan/genetics ; Computational Biology/methods ; Conserved Sequence ; Female ; Genetic Variation/genetics ; Ghana ; Humans ; Malaria, Falciparum/parasitology ; Male ; Parasites/genetics ; Plasmodium falciparum/*genetics ; Protozoan Proteins/*genetics/metabolism ; Sequence Analysis, DNA/methods ; }, abstract = {A challenge in studying diverse multi-copy gene families is deciphering distinct functional types within immense sequence variation. Functional changes can in some cases be tracked through the evolutionary history of a gene family; however phylogenetic approaches are not possible in cases where gene families diversify primarily by recombination. We take a network theoretical approach to functionally classify the highly recombining var antigenic gene family of the malaria parasite Plasmodium falciparum. We sample var DBLα sequence types from a local population in Ghana, and classify 9,276 of these variants into just 48 functional types. Our approach is to first decompose each sequence type into its constituent, recombining parts; we then use a stochastic block model to identify functional groups among the parts; finally, we classify the sequence types based on which functional groups they contain. This method for functional classification does not rely on an inferred phylogenetic history, nor does it rely on inferring function based on conserved sequence features. Instead, it infers functional similarity among recombining parts based on the sharing of similar co-occurrence interactions with other parts. This method can therefore group sequences that have undetectable sequence homology or even distinct origination. Describing these 48 var functional types allows us to simplify the antigenic diversity within our dataset by over two orders of magnitude. We consider how the var functional types are distributed in isolates, and find a nonrandom pattern reflecting that common var functional types are non-randomly distinct from one another in terms of their functional composition. The coarse-graining of var gene diversity into biologically meaningful functional groups has important implications for understanding the disease ecology and evolution of this system, as well as for designing effective epidemiological monitoring and intervention.}, } @article {pmid29897884, year = {2018}, author = {Platzer, A and Polzin, J and Rembart, K and Han, PP and Rauer, D and Nussbaumer, T}, title = {BioSankey: Visualization of Microbial Communities Over Time.}, journal = {Journal of integrative bioinformatics}, volume = {15}, number = {4}, pages = {}, pmid = {29897884}, issn = {1613-4516}, mesh = {*Computer Graphics ; Databases, Factual ; Genome, Bacterial ; High-Throughput Nucleotide Sequencing ; Metagenomics/*methods ; *Microbiota ; *Software ; }, abstract = {Metagenomics provides quantitative measurements for microbial species over time. To obtain a global overview of an experiment and to explore the full potential of a given dataset, intuitive and interactive visualization tools are needed. Therefore, we established BioSankey to visualize microbial species in microbiome studies over time as a Sankey diagram. These diagrams are embedded into a project-specific webpage which depends only on JavaScript and Google API to allow searches of interesting species without requiring a web server or connection to a database. BioSankey is a valuable tool to visualize different data elements from single or dual RNA-seq datasets and additionally enables a straightforward exchange of results among collaboration partners.}, } @article {pmid29893801, year = {2018}, author = {Chen, P and Jing, X and Ren, J and Cao, H and Hao, P and Li, X}, title = {Modelling BioNano optical data and simulation study of genome map assembly.}, journal = {Bioinformatics (Oxford, England)}, volume = {34}, number = {23}, pages = {3966-3974}, pmid = {29893801}, issn = {1367-4811}, mesh = {*Chromosome Mapping ; Computational Biology ; Computer Simulation ; *Genomics ; Sequence Analysis, DNA ; *Software ; }, abstract = {MOTIVATION: The launch of the BioNano next-generation mapping system has greatly enhanced the performance of physical map construction, thus rapidly expanding the application of optical mapping in genome research. Data biases have profound implications for downstream applications. However, very little is known about the properties and biases of BioNano data, and the very factors that contribute to whole-genome optical map assembly.

RESULTS: We generated BioNano molecule data from eight organisms with diverse base compositions. We first characterized the properties/biases of BioNano molecule data, i.e. molecule length distribution, false labelling signal, variation of optical resolution and coverage distribution bias, and their inducing factors such as chimeric molecules, fragile sites and DNA molecule stretching. Second, we developed the BioNano Molecule SIMulator (BMSIM), a novel computer simulation program for optical data. BMSIM, is of great use for future genome mapping projects. Third, we evaluated the experimental variables that impact whole-genome optical map assembly. Specifically, the effects of coverage depth, molecule length, false-positive and false-negative labelling signals, chimeric molecules and nicking enzyme and nick site density were investigated. Our simulation study provides the empirical findings on how to control experimental variables and gauge analytical parameters to maximize benefit and minimize cost on whole-genome optical map assembly.

BMSIM is freely available on: https://github.com/pingchen09990102/BMSIM.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, } @article {pmid29892920, year = {2018}, author = {Han, C and Li, Q and Li, X and Zhang, Z and Huang, J}, title = {De novo assembly, characterization and annotation for the transcriptome of Sphaeroma terebrans and microsatellite marker discovery.}, journal = {Genes & genomics}, volume = {40}, number = {2}, pages = {167-176}, pmid = {29892920}, issn = {2092-9293}, support = {2016-0244//GEF China Wetlands System Project, the biology diversity and environmental monitoring of FuTian mangrove natural reserve/International ; 2015B020235006//the science and technology project of Guangdong Province, China/International ; }, mesh = {Animals ; Gene Expression Profiling ; Gene Expression Regulation ; Gene Ontology ; High-Throughput Nucleotide Sequencing ; Isopoda/genetics/*metabolism ; Lignin/*metabolism ; *Metabolic Networks and Pathways ; *Microsatellite Repeats ; Molecular Sequence Annotation ; Polymorphism, Genetic ; Sequence Analysis, RNA ; *Transcriptome ; }, abstract = {Sphaeroma terebrans, an economically and ecologically important marine wood-boring isopod, is mainly distributed in tropical and subtropical mangroves. Nevertheless, available genomic and transcriptomic information for this isopod is extremely deficient. Here, we first performed the assembly of S. terebrans transcriptome by Illumina sequencing. A total of 51,092 high-quality unigenes with an average length of 641 bp were obtained and 19,915 unigenes were successfully annotated in four public databases. Only 9932 out of 19915 unigenes were commonly annotated by all four databases. In addition, 9609 unigenes were categorized into 54 function categories of Gene Ontology (GO), and 14,512 unigenes were successfully grouped into 25 functional categories of the EuKaryotic Orthologous Groups (KOG) database. Moreover, 11,507 unigenes were assigned to 228 pathways of the Kyoto Encyclopedia of Genes and Genomes (KEGG). Out of 51,092 unigenes, a total of 4257 different microsatellites with motifs range from di- to hexa-nucleotide were identified from 3324 unigene sequences. Among 64 primer pairs selected for validation, 35 were successful in PCR amplification and 13 exhibited obvious repeat polymorphisms in the wild population of S. terebrans in Dongzhaigang (Hainan Island). The transcriptome dataset and the identified microsatellite markers (SSRs) will provide abundant information for researches on the discovery of new genes, metabolic mechanism and genetic diversity of S. terebrans.}, } @article {pmid29892831, year = {2018}, author = {Buisine, N and Kerdivel, G and Sachs, LM}, title = {De Novo Transcriptomic Approach to Study Thyroid Hormone Receptor Action in Non-mammalian Models.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1801}, number = {}, pages = {265-285}, doi = {10.1007/978-1-4939-7902-8_21}, pmid = {29892831}, issn = {1940-6029}, mesh = {Animals ; Computational Biology/methods ; *Gene Expression Profiling/methods ; *Gene Expression Regulation ; High-Throughput Nucleotide Sequencing ; Molecular Sequence Annotation ; Receptors, Thyroid Hormone/*genetics/metabolism ; Software ; *Transcriptome ; Workflow ; }, abstract = {Thyroid hormones are pleiotropic hormones involved in chordates physiology. Understanding their functions and mechanisms is also instrumental to diagnose dys-regulations and get a predictive power that can applied to medicine, ecology, etc. Today, high-throughput sequencing technologies offer the opportunity to address this issue not only in model organisms but also in non-model organisms. Here, we describe a method that makes use of RNA-seq to address differential expression analysis in non-model organism.}, } @article {pmid29892433, year = {2018}, author = {Li, S and Mou, Q and Xu, X and Qi, S and Leung, PHM}, title = {Synergistic antibacterial activity between penicillenols and antibiotics against methicillin-resistant Staphylococcus aureus.}, journal = {Royal Society open science}, volume = {5}, number = {5}, pages = {172466}, pmid = {29892433}, issn = {2054-5703}, abstract = {Penicillenol A2 (isolated from deep-sea fungus Penicillium biourgeianum DFFSCS023) has good antibacterial activity against methicillin-sensitive Staphylococcus aureus and in combination with beta-lactam antibiotics it could significantly decrease methicillin-resistant Staphylococcus aureus (MRSA) survival, which provides a novel treatment consideration for MRSA-caused infections.}, } @article {pmid29890590, year = {2018}, author = {Dick, J and Orenstein, DE and Holzer, JM and Wohner, C and Achard, AL and Andrews, C and Avriel-Avni, N and Beja, P and Blond, N and Cabello, J and Chen, C and Díaz-Delgado, R and Giannakis, GV and Gingrich, S and Izakovicova, Z and Krauze, K and Lamouroux, N and Leca, S and Melecis, V and Miklós, K and Mimikou, M and Niedrist, G and Piscart, C and Postolache, C and Psomas, A and Santos-Reis, M and Tappeiner, U and Vanderbilt, K and Van Ryckegem, G}, title = {What is socio-ecological research delivering? A literature survey across 25 international LTSER platforms.}, journal = {The Science of the total environment}, volume = {622-623}, number = {}, pages = {1225-1240}, doi = {10.1016/j.scitotenv.2017.11.324}, pmid = {29890590}, issn = {1879-1026}, abstract = {With an overarching goal of addressing global and regional sustainability challenges, Long Term Socio-Ecological Research Platforms (LTSER) aim to conduct place-based research, to collect and synthesize both environmental and socio-economic data, and to involve a broader stakeholder pool to set the research agenda. To date there have been few studies examining the output from LTSER platforms. In this study we enquire if the socio-ecological research from 25 self-selected LTSER platforms of the International Long-Term Ecological Research (ILTER) network has produced research products which fulfil the aims and ambitions of the paradigm shift from ecological to socio-ecological research envisaged at the turn of the century. In total we assessed 4983 publically available publications, of which 1112 were deemed relevant to the socio-ecological objectives of the platform. A series of 22 questions were scored for each publication, assessing relevance of responses in terms of the disciplinary focus of research, consideration of human health and well-being, degree of stakeholder engagement, and other relevant variables. The results reflected the diverse origins of the individual platforms and revealed a wide range in foci, temporal periods and quantity of output from participating platforms, supporting the premise that there is a growing trend in socio-ecological research at long-term monitoring platforms. Our review highlights the challenges of realizing the top-down goal to harmonize international network activities and objectives and the need for bottom-up, self-definition for research platforms. This provides support for increasing the consistency of LTSER research while preserving the diversity of regional experiences.}, } @article {pmid29890495, year = {2018}, author = {Vaverková, MD and Elbl, J and Radziemska, M and Adamcová, D and Kintl, A and Baláková, L and Bartoň, S and Hladký, J and Kynický, J and Brtnický, M}, title = {Environmental risk assessment and consequences of municipal solid waste disposal.}, journal = {Chemosphere}, volume = {208}, number = {}, pages = {569-578}, doi = {10.1016/j.chemosphere.2018.06.026}, pmid = {29890495}, issn = {1879-1298}, mesh = {Environmental Monitoring ; *Environmental Pollution ; Metals, Heavy/*analysis/pharmacokinetics ; Plants/*metabolism ; *Refuse Disposal ; Risk Assessment ; Soil Pollutants/analysis/pharmacokinetics ; Waste Disposal Facilities ; }, abstract = {Effective and efficient assessments of the site conditions are required for the sustainable management of landfills. In this study we propose an evaluation method to determine the degree of environmental contamination by the contest of heavy metals (HM) concentrations in soil and plants (Tanacetum vulgare L., Carduus L., Plantago major L.). We compared HM concentrations in the soil, leaves, stem and roots of those native plants. Content of HM in samples was at the same level in all localities, except content of Zn. These values confirm that the area is not naturally burdened by increased HM content in the soil, and also that the deposited municipal waste or the material used for reclamation and composting does not contain risk elements. The content of selected HM was monitored in plants naturally occurring in the area of interest. We can state that the content of individual HM was in the plant biomass at the same level. The measured values confirmed that the largest number of HM was in roots, then in stem and the least in leaves. In addition, specific indexes were determined: BAC, TF, CF, PLI and Igeo. The BAC values confirmed that the individual plants had the ability to accumulate Pb and Cd (BAC> 2) but were limited to bind Mn and Zn (BAC <1). TF values confirmed that plants had a different ability to transport HM from roots to aboveground biomass. Potential soil contamination was detected using CF, PLI and Igeo indexes but contamination by HM was not confirmed.}, } @article {pmid29886941, year = {2018}, author = {Lamb, JS and Fiorello, CV and Satgé, YG and Mills, K and Ziccardi, M and Jodice, PGR}, title = {Movement patterns of California brown pelicans (Pelecanus occidentalis californicus) following oiling and rehabilitation.}, journal = {Marine pollution bulletin}, volume = {131}, number = {Pt A}, pages = {22-31}, doi = {10.1016/j.marpolbul.2018.03.043}, pmid = {29886941}, issn = {1879-3363}, mesh = {Animals ; *Birds ; California ; Ecotoxicology/methods ; Environmental Monitoring/methods ; Female ; Geographic Information Systems ; Male ; Movement ; *Petroleum Pollution ; }, abstract = {Direct mortality of wildlife is generally used to quantify the damage caused by pollution events. However, free-ranging wildlife that survive initial exposure to pollutants may also experience long-term consequences. Individuals that are rehabilitated following oil exposure have a known history of oiling and provide a useful study population for understanding behavior following pollution events. We GPS-tracked 12 rehabilitated brown pelicans and compared their movements to those of eight non-oiled, non-rehabilitated controls over 87-707 (mean = 271) days. Rehabilitated pelicans traveled farther, spent more time in long-distance movements, and occupied more productive waters than controls. These differences were more apparent among females than males. Rehabilitated pelicans also visited breeding colonies and nest sites at lower rates than controls. Our results indicate that, although rehabilitated pelicans undertake long-distance movements, they may display increased dispersion and reduced breeding investment, particularly among females. Such behavioral changes could have long-term effects on populations.}, } @article {pmid29886108, year = {2018}, author = {Xu, C and Zhang, J}, title = {Alternative Polyadenylation of Mammalian Transcripts Is Generally Deleterious, Not Adaptive.}, journal = {Cell systems}, volume = {6}, number = {6}, pages = {734-742.e4}, pmid = {29886108}, issn = {2405-4712}, support = {R01 GM120093/GM/NIGMS NIH HHS/United States ; }, mesh = {3' Untranslated Regions/genetics ; Alternative Splicing/genetics ; Animals ; Databases, Genetic ; Gene Expression/genetics ; Humans ; Mammals/genetics ; Poly A/genetics/*metabolism ; Polyadenylation/*genetics ; RNA, Messenger/*genetics/metabolism ; Selection, Genetic/genetics ; }, abstract = {Alternative polyadenylation (APA) produces from the same gene multiple mature RNAs with varying 3' ends. Although APA is commonly believed to generate beneficial functional diversity and be adaptive, we hypothesize that most genes have one optimal polyadenylation site and that APA is caused largely by deleterious polyadenylation errors. The error hypothesis, but not the adaptive hypothesis, predicts that, as the expression level of a gene increases, its polyadenylation diversity declines, relative use of the major (presumably optimal) polyadenylation site increases, and that of each minor (presumably nonoptimal) site decreases. It further predicts that the number of polyadenylation signals per gene is smaller than the random expectation and that polyadenylation signals for major but not minor sites are under purifying selection. All of these predictions are confirmed in mammals, suggesting that numerous defective RNAs are produced in normal cells, many phenotypic variations at the molecular level are nonadaptive, and cellular life is noisier than is appreciated.}, } @article {pmid29885666, year = {2018}, author = {Meng, A and Marchet, C and Corre, E and Peterlongo, P and Alberti, A and Da Silva, C and Wincker, P and Pelletier, E and Probert, I and Decelle, J and Le Crom, S and Not, F and Bittner, L}, title = {A de novo approach to disentangle partner identity and function in holobiont systems.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {105}, pmid = {29885666}, issn = {2049-2618}, support = {ANR-15-CE02-0011//Agence Nationale de la Recherche (FR)/International ; }, mesh = {Animals ; Cnidaria/*parasitology ; Computational Biology ; *Coral Reefs ; Microalgae/metabolism ; Plankton/parasitology ; Porifera/*microbiology ; Rhizaria/*parasitology ; Symbiosis/*physiology ; Transcriptome/genetics ; }, abstract = {BACKGROUND: Study of meta-transcriptomic datasets involving non-model organisms represents bioinformatic challenges. The production of chimeric sequences and our inability to distinguish the taxonomic origins of the sequences produced are inherent and recurrent difficulties in de novo assembly analyses. As the study of holobiont meta-transcriptomes is affected by challenges invoked above, we propose an innovative bioinformatic approach to tackle such difficulties and tested it on marine models as a proof of concept.

RESULTS: We considered three holobiont models, of which two transcriptomes were previously published and a yet unpublished transcriptome, to analyze and sort their raw reads using Short Read Connector, a k-mer based similarity method. Before assembly, we thus defined four distinct categories for each holobiont meta-transcriptome: host reads, symbiont reads, shared reads, and unassigned reads. Afterwards, we observed that independent de novo assemblies for each category led to a diminution of the number of chimeras compared to classical assembly methods. Moreover, the separation of each partner's transcriptome offered the independent and comparative exploration of their functional diversity in the holobiont. Finally, our strategy allowed to propose new functional annotations for two well-studied holobionts (a Cnidaria-Dinophyta, a Porifera-Bacteria) and a first meta-transcriptome from a planktonic Radiolaria-Dinophyta system forming widespread symbiotic association for which our knowledge is considerably limited.

CONCLUSIONS: In contrast to classical assembly approaches, our bioinformatic strategy generates less de novo assembled chimera and allows biologists to study separately host and symbiont data from a holobiont mixture. The pre-assembly separation of reads using an efficient tool as Short Read Connector is an effective way to tackle meta-transcriptomic challenges and offers bright perpectives to study holobiont systems composed of either well-studied or poorly characterized symbiotic lineages and ultimately expand our knowledge about these associations.}, } @article {pmid29885636, year = {2018}, author = {Patel, S and Homaei, A and El-Seedi, HR and Akhtar, N}, title = {Cathepsins: Proteases that are vital for survival but can also be fatal.}, journal = {Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie}, volume = {105}, number = {}, pages = {526-532}, pmid = {29885636}, issn = {1950-6007}, mesh = {Animals ; Cathepsins/antagonists & inhibitors/*metabolism ; Cell Death/drug effects ; Cell Survival/drug effects ; Humans ; Protease Inhibitors/pharmacology ; Substrate Specificity/drug effects ; }, abstract = {The state of enzymes in the human body determines the normal physiology or pathology, so all the six classes of enzymes are crucial. Proteases, the hydrolases, can be of several types based on the nucleophilic amino acid or the metal cofactor needed for their activity. Cathepsins are proteases with serine, cysteine, or aspartic acid residues as the nucleophiles, which are vital for digestion, coagulation, immune response, adipogenesis, hormone liberation, peptide synthesis, among a litany of other functions. But inflammatory state radically affects their normal roles. Released from the lysosomes, they degrade extracellular matrix proteins such as collagen and elastin, mediating parasite infection, autoimmune diseases, tumor metastasis, cardiovascular issues, and neural degeneration, among other health hazards. Over the years, the different types and isoforms of cathepsin, their optimal pH and functions have been studied, yet much information is still elusive. By taming and harnessing cathepsins, by inhibitors and judicious lifestyle, a gamut of malignancies can be resolved. This review discusses these aspects, which can be of clinical relevance.}, } @article {pmid29883444, year = {2018}, author = {Brett, TS and O'Dea, EB and Marty, É and Miller, PB and Park, AW and Drake, JM and Rohani, P}, title = {Anticipating epidemic transitions with imperfect data.}, journal = {PLoS computational biology}, volume = {14}, number = {6}, pages = {e1006204}, pmid = {29883444}, issn = {1553-7358}, support = {U01 GM110744/GM/NIGMS NIH HHS/United States ; U01GM110744/NH/NIH HHS/United States ; }, mesh = {Area Under Curve ; Cluster Analysis ; Computational Biology ; Computer Simulation ; Databases, Factual ; Epidemics/*prevention & control/*statistics & numerical data ; Humans ; *Models, Statistical ; }, abstract = {Epidemic transitions are an important feature of infectious disease systems. As the transmissibility of a pathogen increases, the dynamics of disease spread shifts from limited stuttering chains of transmission to potentially large scale outbreaks. One proposed method to anticipate this transition are early-warning signals (EWS), summary statistics which undergo characteristic changes as the transition is approached. Although theoretically predicted, their mathematical basis does not take into account the nature of epidemiological data, which are typically aggregated into periodic case reports and subject to reporting error. The viability of EWS for epidemic transitions therefore remains uncertain. Here we demonstrate that most EWS can predict emergence even when calculated from imperfect data. We quantify performance using the area under the curve (AUC) statistic, a measure of how well an EWS distinguishes between numerical simulations of an emerging disease and one which is stationary. Values of the AUC statistic are compared across a range of different reporting scenarios. We find that different EWS respond to imperfect data differently. The mean, variance and first differenced variance all perform well unless reporting error is highly overdispersed. The autocorrelation, autocovariance and decay time perform well provided that the aggregation period of the data is larger than the serial interval and reporting error is not highly overdispersed. The coefficient of variation, skewness and kurtosis are found to be unreliable indicators of emergence. Overall, we find that seven of ten EWS considered perform well for most realistic reporting scenarios. We conclude that imperfect epidemiological data is not a barrier to using EWS for many potentially emerging diseases.}, } @article {pmid29882677, year = {2018}, author = {Mulvaney, SA and Vaala, S and Hood, KK and Lybarger, C and Carroll, R and Williams, L and Schmidt, DC and Johnson, K and Dietrich, MS and Laffel, L}, title = {Mobile Momentary Assessment and Biobehavioral Feedback for Adolescents with Type 1 Diabetes: Feasibility and Engagement Patterns.}, journal = {Diabetes technology & therapeutics}, volume = {20}, number = {7}, pages = {465-474}, pmid = {29882677}, issn = {1557-8593}, support = {P30 DK036836/DK/NIDDK NIH HHS/United States ; P30 DK092986/DK/NIDDK NIH HHS/United States ; UL1 TR000445/TR/NCATS NIH HHS/United States ; DP3 DK097706/DK/NIDDK NIH HHS/United States ; }, mesh = {Adolescent ; Blood Glucose Self-Monitoring/methods ; Diabetes Mellitus, Type 1/*blood/drug therapy ; Ecological Momentary Assessment ; Feasibility Studies ; Feedback, Psychological/*physiology ; Female ; Humans ; Hypoglycemic Agents/therapeutic use ; Insulin/therapeutic use ; Male ; Patient Compliance ; Young Adult ; }, abstract = {BACKGROUND: Integration of momentary contextual and psychosocial factors within self-management feedback may provide more specific, engaging, and personalized targets for problem solving.

METHODS: Forty-four youth ages 13-19 with type 1 diabetes (T1D) were provided a Bluetooth meter and completed the 30-day protocol. Participants were randomized to "app + meter" or "meter-only" groups. App + meter participants completed mealtime and bedtime assessment each day. Assessments focused on psychosocial and contextual information relevant for self-management. Graphical feedback integrated self-monitored blood glucose (SMBG), insulin, and Bluetooth-transmitted blood glucose data with the psychosocial and contextual data. App + meter participants completed an interview to identify data patterns.

RESULTS: The median number of momentary assessments per participant was 80.0 (range 32-120) with 2.60 per day. By 2 weeks participants had an average of 40.77 (SD 12.23) assessments. Dose-response analyses indicated that the number of app assessments submitted were significantly related to higher mean daily SMBG (r = -0.44, P < 0.05) and to lower% missed mealtime SMBG (r = -0.47, P < 0.01). Number of feedback viewing sessions was also significantly related to a lower% missed mealtime SMBG (r = -0.44, P < 0.05). Controlling for baseline variables, mixed-effects analyses did not indicate group × time differences in mean daily SMBG. Engagement analyses resulted in three trajectory groups distinguished by assessment frequencies and rates of decline. Engagement group membership was significantly related to gender, mean daily SMBG, and HbA1c values.

CONCLUSIONS: Momentary assessment combined with device data provided a feasible means to provide novel personalized biobehavioral feedback for adolescents with T1D. A 2-week protocol provided sufficient data for self-management problem identification. In addition to feedback, more intensive intervention may need to be integrated for those patients with the lowest self-management at baseline.}, } @article {pmid29880761, year = {2018}, author = {Lamm, SH and Boroje, IJ and Ferdosi, H and Ahn, J}, title = {Lung Cancer Risk and Low (≤50 μg/L) Drinking Water Arsenic Levels for US Counties (2009[-]2013)-A Negative Association.}, journal = {International journal of environmental research and public health}, volume = {15}, number = {6}, pages = {}, pmid = {29880761}, issn = {1660-4601}, mesh = {Arsenic/*analysis/standards ; Databases, Factual ; Dietary Exposure/*analysis/standards ; Drinking Water/*chemistry/standards ; Epidemiologic Studies ; Female ; Groundwater/analysis/*chemistry ; Humans ; Incidence ; Lung Neoplasms/*epidemiology ; Male ; Risk Factors ; United States/epidemiology ; Water Pollutants, Chemical/*analysis/standards ; }, abstract = {While epidemiologic studies clearly demonstrate drinking water with high levels of arsenic as a significant risk factor for lung cancer, the evidence at low levels (≤50 μg/L) is uncertain. Therefore, we have conducted an ecological analysis of recent lung cancer incidence for US counties with a groundwater supply of.}, } @article {pmid29879149, year = {2018}, author = {Ottensmann, M and Stoffel, MA and Nichols, HJ and Hoffman, JI}, title = {GCalignR: An R package for aligning gas-chromatography data for ecological and evolutionary studies.}, journal = {PloS one}, volume = {13}, number = {6}, pages = {e0198311}, pmid = {29879149}, issn = {1932-6203}, mesh = {Animals ; Bees/*classification ; Breeding ; Databases, Factual ; Female ; Fur Seals/*classification ; Gas Chromatography-Mass Spectrometry/*methods ; Male ; Software ; }, abstract = {Chemical cues are arguably the most fundamental means of animal communication and play an important role in mate choice and kin recognition. Consequently, there is growing interest in the use of gas chromatography (GC) to investigate the chemical basis of eco-evolutionary interactions. Both GC-MS (mass spectrometry) and FID (flame ionization detection) are commonly used to characterise the chemical composition of biological samples such as skin swabs. The resulting chromatograms comprise peaks that are separated according to their retention times and which represent different substances. Across chromatograms of different samples, homologous substances are expected to elute at similar retention times. However, random and often unavoidable experimental variation introduces noise, making the alignment of homologous peaks challenging, particularly with GC-FID data where mass spectral data are lacking. Here we present GCalignR, a user-friendly R package for aligning GC-FID data based on retention times. The package was developed specifically for ecological and evolutionary studies that seek to investigate similarity patterns across multiple and often highly variable biological samples, for example representing different sexes, age classes or reproductive stages. The package also implements dynamic visualisations to facilitate inspection and fine-tuning of the resulting alignments and can be integrated within a broader workflow in R to facilitate downstream multivariate analyses. We demonstrate an example workflow using empirical data from Antarctic fur seals and explore the impact of user-defined parameter values by calculating alignment error rates for multiple datasets. The resulting alignments had low error rates for most of the explored parameter space and we could also show that GCalignR performed equally well or better than other available software. We hope that GCalignR will help to simplify the processing of chemical datasets and improve the standardization and reproducibility of chemical analyses in studies of animal chemical communication and related fields.}, } @article {pmid29878056, year = {2018}, author = {Martinez-Vernon, AS and Farrell, F and Soyer, OS}, title = {MetQy-an R package to query metabolic functions of genes and genomes.}, journal = {Bioinformatics (Oxford, England)}, volume = {34}, number = {23}, pages = {4134-4137}, pmid = {29878056}, issn = {1367-4811}, support = {BB/K003240/2/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/M017982/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Computational Biology ; Genome ; Genomics ; Metabolic Networks and Pathways/*genetics ; *Metagenomics ; *Software ; }, abstract = {SUMMARY: With the rapid accumulation of sequencing data from genomic and metagenomic studies, there is an acute need for better tools that facilitate their analyses against biological functions. To this end, we developed MetQy, an open-source R package designed for query-based analysis of functional units in [meta]genomes and/or sets of genes using the The Kyoto Encyclopedia of Genes and Genomes (KEGG). Furthermore, MetQy contains visualization and analysis tools and facilitates KEGG's flat file manipulation. Thus, MetQy enables better understanding of metabolic capabilities of known genomes or user-specified [meta]genomes by using the available information and can help guide studies in microbial ecology, metabolic engineering and synthetic biology.

The MetQy R package is freely available and can be downloaded from our group's website (http://osslab.lifesci.warwick.ac.uk) or GitHub (https://github.com/OSS-Lab/MetQy).}, } @article {pmid29875442, year = {2018}, author = {She, Z and Li, L and Meng, J and Jia, Z and Que, H and Zhang, G}, title = {Population resequencing reveals candidate genes associated with salinity adaptation of the Pacific oyster Crassostrea gigas.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {8683}, pmid = {29875442}, issn = {2045-2322}, mesh = {Animals ; Crassostrea/*genetics/physiology ; Gene Expression Profiling ; *Gene Expression Regulation ; Gene Ontology ; Phenotype ; Polymorphism, Single Nucleotide ; Salinity ; *Salt Tolerance ; Transcriptome ; }, abstract = {The Pacific oyster Crassostrea gigas is an important cultivated shellfish. As a euryhaline species, it has evolved adaptive mechanisms responding to the complex and changeable intertidal environment that it inhabits. To investigate the genetic basis of this salinity adaptation mechanism, we conducted a genome-wide association study using phenotypically differentiated populations (hyposalinity and hypersalinity adaptation populations, and control population), and confirmed our results using an independent population, high-resolution melting, and mRNA expression analysis. For the hyposalinity adaptation, we determined 24 genes, including Cg_CLCN7 (chloride channel protein 7) and Cg_AP1 (apoptosis 1 inhibitor), involved in the ion/water channel and transporter mechanisms, free amino acid and reactive oxygen species metabolism, immune responses, and chemical defence. Three SNPs located on these two genes were significantly differentiated between groups, as was Cg_CLCN7. For the hypersalinity adaptation, the biological process for positive regulating the developmental process was enriched. Enriched gene functions were focused on transcriptional regulation, signal transduction, and cell growth and differentiation, including calmodulin (Cg_CaM) and ficolin-2 (Cg_FCN2). These genes and polymorphisms possibly play an important role in oyster hyposalinity and hypersalinity adaptation. They not only further our understanding of salinity adaptation mechanisms but also provide markers for highly adaptable oyster strains suitable for breeding.}, } @article {pmid29874297, year = {2018}, author = {Santos, CC and Coelho, R}, title = {Migrations and habitat use of the smooth hammerhead shark (Sphyrna zygaena) in the Atlantic Ocean.}, journal = {PloS one}, volume = {13}, number = {6}, pages = {e0198664}, pmid = {29874297}, issn = {1932-6203}, mesh = {Animal Migration/*physiology ; Animals ; Atlantic Ocean ; Behavior, Animal/*physiology ; Ecological Parameter Monitoring/methods ; Female ; Fisheries ; Geographic Information Systems ; Male ; Motor Activity/*physiology ; Remote Sensing Technology ; Risk Assessment/methods ; Sharks/*physiology ; }, abstract = {The smooth hammerhead shark, Sphyrna zygaena, is a cosmopolitan semipelagic shark captured as bycatch in pelagic oceanic fisheries, especially pelagic longlines targeting swordfish and/or tunas. From 2012 to 2016, eight smooth hammerheads were tagged with Pop-up Satellite Archival Tags in the inter-tropical region of the Northeast Atlantic Ocean, with successful transmissions received from seven tags (total of 319 tracking days). Results confirmed the smooth hammerhead is a highly mobile species, as the longest migration ever documented for this species (> 6600 km) was recorded. An absence of a diel vertical movement behavior was noted, with the sharks spending most of their time at surface waters (0-50 m) above 23°C. The operating depth of the pelagic longline gear was measured with Minilog Temperature and Depth Recorders, and the overlap with the species vertical distribution was calculated. The overlap is taking place mainly during the night and is higher for juveniles (~40% of overlap time). The novel information presented can now be used to contribute to the provision of sustainable management tools and serve as input for Ecological Risk Assessments for smooth hammerheads caught in Atlantic pelagic longline fisheries.}, } @article {pmid29873731, year = {2018}, author = {Johnson, MA and Francis, CD and Miller, ET and Downs, CJ and Vitousek, MN}, title = {Detecting Bias in Large-Scale Comparative Analyses: Methods for Expanding the Scope of Hypothesis-Testing with HormoneBase.}, journal = {Integrative and comparative biology}, volume = {58}, number = {4}, pages = {720-728}, doi = {10.1093/icb/icy045}, pmid = {29873731}, issn = {1557-7023}, mesh = {Animals ; Classification/*methods ; *Databases as Topic ; Hormones/*physiology ; *Phylogeny ; *Research Design ; Vertebrates/*classification/growth & development/physiology ; }, abstract = {To address large-scale questions in evolutionary biology, the compilation of data from a variety of sources is often required. This is a major challenge in the development of databases in organismal biology. Here, we describe the procedure we used to reconstruct the phylogeny of the 474 species represented in HormoneBase, including fish, amphibians, mammals, birds, and reptiles. We also provide the methodology used to compile vertebrate environmental, life history, and metabolic rate data for use in conjunction with the HormoneBase database to test hypotheses of the evolution of steroid hormone traits. We then report a series of analyses using these data to determine the extent to which field measures of circulating hormones and associated life history data exhibit taxonomic and geographic bias. By providing a detailed description of the approaches used to compile and evaluate these data and identifying potential biases in the collection of these data, we hope to make the HormoneBase database a more broadly useful resource for the scientific community to address a diversity of comparative questions.}, } @article {pmid29872428, year = {2018}, author = {Wagner, BD and Grunwald, GK and Zerbe, GO and Mikulich-Gilbertson, SK and Robertson, CE and Zemanick, ET and Harris, JK}, title = {On the Use of Diversity Measures in Longitudinal Sequencing Studies of Microbial Communities.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {1037}, pmid = {29872428}, issn = {1664-302X}, support = {K24 DA032555/DA/NIDA NIH HHS/United States ; R01 DA035804/DA/NIDA NIH HHS/United States ; UL1 TR001082/TR/NCATS NIH HHS/United States ; R01 HL124103/HL/NHLBI NIH HHS/United States ; K23 HL114883/HL/NHLBI NIH HHS/United States ; }, abstract = {Identification of the majority of organisms present in human-associated microbial communities is feasible with the advent of high throughput sequencing technology. As substantial variability in microbiota communities is seen across subjects, the use of longitudinal study designs is important to better understand variation of the microbiome within individual subjects. Complex study designs with longitudinal sample collection require analytic approaches to account for this additional source of variability. A common approach to assessing community changes is to evaluate the change in alpha diversity (the variety and abundance of organisms in a community) over time. However, there are several commonly used alpha diversity measures and the use of different measures can result in different estimates of magnitude of change and different inferences. It has recently been proposed that diversity profile curves are useful for clarifying these differences, and may provide a more complete picture of the community structure. However, it is unclear how to utilize these curves when interest is in evaluating changes in community structure over time. We propose the use of a bi-exponential function in a longitudinal model that accounts for repeated measures on each subject to compare diversity profiles over time. Furthermore, it is possible that no change in alpha diversity (single community/sample) may be observed despite the presence of a highly divergent community composition. Thus, it is also important to use a beta diversity measure (similarity between multiple communities/samples) that captures changes in community composition. Ecological methods developed to evaluate temporal turnover have currently only been applied to investigate changes of a single community over time. We illustrate the extension of this approach to multiple communities of interest (i.e., subjects) by modeling the beta diversity measure over time. With this approach, a rate of change in community composition is estimated. There is a need for the extension and development of analytic methods for longitudinal microbiota studies. In this paper, we discuss different approaches to model alpha and beta diversity indices in longitudinal microbiota studies and provide both a review of current approaches and a proposal for new methods.}, } @article {pmid29866836, year = {2018}, author = {Frank, KT and Petrie, B and Leggett, WC and Boyce, DG}, title = {Exploitation drives an ontogenetic-like deepening in marine fish.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {115}, number = {25}, pages = {6422-6427}, pmid = {29866836}, issn = {1091-6490}, mesh = {Animals ; Biological Ontologies ; Fisheries ; Fishes/*physiology ; Gadus morhua ; North Sea ; Population Dynamics ; Seafood ; }, abstract = {Virtually all studies reporting deepening with increasing size or age by fishes involve commercially harvested species. Studies of North Sea plaice in the early 1900s first documented this phenomenon (named Heincke's law); it occurred at a time of intensive harvesting and rapid technological changes in fishing methods. The possibility that this deepening might be the result of harvesting has never been evaluated. Instead, age- or size-related deepening have been credited to interactions between density-dependent food resources and density-independent environmental factors. Recently, time-dependent depth variations have been ascribed to ocean warming. We use a model, initialized from observations of Atlantic cod (Gadus morhua) on the eastern Scotian Shelf, where an age-dependent deepening of ∼60 m was observed, to assess the effect of size- and depth-selective exploitation on fish distribution. Exploitation restricted to the upper 80 m can account for ∼72% of the observed deepening; by extending exploitation to 120 m, all of the deepening can be accounted for. In the absence of fishing, the model indicated no age-related deepening. Observations of depth distributions of older cod during a moratorium on fishing supported this prediction; however, younger cod exhibited low-amplitude deepening (10-15 m) suggestive of an ontogenetic response. The implications of these findings are manifold, particularly as they relate to hypotheses advanced to explain the ecological and evolutionary basis for ontogenetic deepening and to recent calls for the adoption of evidence of species deepening as a biotic indicator or "footprint" of warming seas.}, } @article {pmid29862438, year = {2018}, author = {Al-Nasrawi, AKM and Hamylton, SM and Jones, BG}, title = {An assessment of anthropogenic and climatic stressors on estuaries using a spatio-temporal GIS-modelling approach for sustainability: Towamba estuary, southeastern Australia.}, journal = {Environmental monitoring and assessment}, volume = {190}, number = {7}, pages = {375}, pmid = {29862438}, issn = {1573-2959}, support = {University of Wollongong, Australia//GeoQuEST Research Centre,/ ; }, mesh = {Climate Change ; Conservation of Natural Resources ; Ecosystem ; Environmental Monitoring/*methods ; *Estuaries ; *Geographic Information Systems ; Human Activities ; Humans ; New South Wales ; Spatio-Temporal Analysis ; Wetlands ; }, abstract = {Monitoring estuarine ecological-geomorphological dynamics has become a crucial aspect of studying the impacts of climate change and worldwide infrastructure development in coastal zones. Together, these factors have changed the natural eco-geomorphic processes that affect estuarine regimes and comprehensive modelling of coastal resources can assist managers to make appropriate decisions about their sustainable use. This study has utilised Towamba estuary (southeastern NSW, Australia), to demonstrate the value and priority of modelling estuarine dynamism as a measure of the rates and consequences of eco-geomorphic changes. This research employs several geoinformatic modelling approaches over time to investigate and assess how climate change and human activities have altered this estuarine eco-geomorphic setting. Multitemporal trend/change analysis of sediment delivery, shoreline positions and land cover, determined from fieldwork and GIS analysis of remote sensing datasets, shows significant spatio-temporal changes to the elevation and areal extent of sedimentary facies in the Towamba estuary over the past 65 years. Geomorphic growth (~ 2600 m[2] annually) has stabilised the estuarine habitats, particularly within native vegetation, salt marsh and mangrove areas. Geomorphic changes have occurred because of a combination of sediment runoff from the mostly unmodified terrestrial catchment, nearshore processes (ocean dynamics) and human activities. The construction of GIS models, verified with water and sediment samples, can characterise physical processes and quantify changes within the estuarine ecosystem. Such robust models will allow resource managers to evaluate the potential effects of changes to the current coastal ecosystems.}, } @article {pmid29860499, year = {2018}, author = {Casagrande, S and Zsolt Garamszegi, L and Goymann, W and Donald, J and Francis, CD and Fuxjager, MJ and Husak, JF and Johnson, MA and Kircher, B and Knapp, R and Martin, LB and Miller, ET and Schoenle, LA and Vitousek, MN and Williams, TD and Hau, M}, title = {Do Seasonal Glucocorticoid Changes Depend on Reproductive Investment? A Comparative Approach in Birds.}, journal = {Integrative and comparative biology}, volume = {58}, number = {4}, pages = {739-750}, doi = {10.1093/icb/icy022}, pmid = {29860499}, issn = {1557-7023}, mesh = {Animals ; Birds/*physiology ; Databases as Topic ; Glucocorticoids/*metabolism ; *Phylogeny ; *Reproduction ; Seasons ; }, abstract = {Animals go through different life history stages such as reproduction, moult, or migration, of which some are more energy-demanding than others. Baseline concentrations of glucocorticoid hormones increase during moderate, predictable challenges and thus are expected to be higher when seasonal energy demands increase, such as during reproduction. By contrast, stress-induced glucocorticoids prioritize a survival mode that includes reproductive inhibition. Thus, many species down-regulate stress-induced glucocorticoid concentrations during the breeding season. Interspecific variation in glucocorticoid levels during reproduction has been successfully mapped onto reproductive investment, with species investing strongly in current reproduction (fast pace of life) showing higher baseline and lower stress-induced glucocorticoid concentrations than species that prioritize future reproduction over current attempts (slow pace of life). Here we test the "glucocorticoid seasonal plasticity hypothesis", in which we propose that interspecific variation in seasonal changes in glucocorticoid concentrations from the non-breeding to the breeding season will be related to the degree of reproductive investment (and thus pace of life). We extracted population means for baseline (for 54 species) and stress-induced glucocorticoids (for 32 species) for the breeding and the non-breeding seasons from the database "HormoneBase", also calculating seasonal glucocorticoid changes. We focused on birds because this group offered the largest sample size. Using phylogenetic comparative methods, we first showed that species differed consistently in both average glucocorticoid concentrations and their changes between the two seasons, while controlling for sex, latitude, and hemisphere. Second, as predicted seasonal changes in baseline glucocorticoids were explained by clutch size (our proxy for reproductive investment), with species laying larger clutches showing a greater increase during the breeding season-especially in passerine species. In contrast, changes in seasonal stress-induced levels were not explained by clutch size, but sample sizes were more limited. Our findings highlight that seasonal changes in baseline glucocorticoids are associated with a species' reproductive investment, representing an overlooked physiological trait that may underlie the pace of life.}, } @article {pmid29859932, year = {2018}, author = {Clark, AT and Neuhauser, C}, title = {Harnessing uncertainty to approximate mechanistic models of interspecific interactions.}, journal = {Theoretical population biology}, volume = {123}, number = {}, pages = {35-44}, doi = {10.1016/j.tpb.2018.05.002}, pmid = {29859932}, issn = {1096-0325}, mesh = {*Ecosystem ; Humans ; *Models, Theoretical ; Population Dynamics ; Stochastic Processes ; Uncertainty ; }, abstract = {Because the Lotka-Volterra competitive equations posit no specific competitive mechanisms, they are exceedingly general, and can theoretically approximate any underlying mechanism of competition near equilibrium. In practice, however, these models rarely generate accurate predictions in diverse communities. We propose that this difference between theory and practice may be caused by how uncertainty propagates through Lotka-Volterra systems. In approximating mechanistic relationships with Lotka-Volterra models, associations among parameters are lost, and small variation can correspond to large and unrealistic changes in predictions. We demonstrate that constraining Lotka-Volterra models using correlations among parameters expected from hypothesized underlying mechanisms can reintroduce some of the underlying structure imposed by those mechanisms, thereby improving model predictions by both reducing bias and increasing precision. Our results suggest that this hybrid approach may combine some of the generality of phenomenological models with the broader applicability and meaningful interpretability of mechanistic approaches. These methods could be useful in poorly understood systems for identifying important coexistence mechanisms, or for making more accurate predictions.}, } @article {pmid29857243, year = {2018}, author = {Chen, L and Tsui, MMP and Shi, Q and Hu, C and Wang, Q and Zhou, B and Lam, PKS and Lam, JCW}, title = {Accumulation of perfluorobutane sulfonate (PFBS) and impairment of visual function in the eyes of marine medaka after a life-cycle exposure.}, journal = {Aquatic toxicology (Amsterdam, Netherlands)}, volume = {201}, number = {}, pages = {1-10}, doi = {10.1016/j.aquatox.2018.05.018}, pmid = {29857243}, issn = {1879-1514}, mesh = {Acetylcholine/metabolism ; Animals ; *Environmental Exposure ; Eye/*metabolism ; Female ; Fluorocarbons/*metabolism ; Gene Ontology ; *Life Cycle Stages ; Male ; Neurotransmitter Agents/metabolism ; Organ Size ; Oryzias/*growth & development/*metabolism ; Proteomics ; Signal Transduction ; Visual Pathways/*physiology ; Water Pollutants, Chemical/metabolism ; }, abstract = {As an alternative to perfluorooctane sulfonate (PFOS), increasing usage of perfluorobutane sulfonate (PFBS) has led to ubiquitous presence in the environment. PFBS is also shown to potently disrupt the thyroid endocrine system. Considering the regulation of thyroid hormones in visual development, PFBS is likely to adversely affect the development and function of visual systems, which is a sensitive target of environmental pollutants. Therefore, the present study exposed marine medaka embryos to environmentally realistic concentrations of PFBS (0, 1.0, 2.9 and 9.5 μg/L) for an entire life-cycle. After exposure until sexual maturity, eyes of adult medaka were dissected to directly investigate the ocular accumulation and toxicity of PFBS. For the first time, substantial accumulation of an environmental pollutant (i.e., PFBS) was observed in the eye tissue. PFBS exposure was also found to impair the visual development and function in a sex-dependent manner. In female medaka, weight of eyes was significantly decreased, while content of water was increased, probably resulting in higher intraocular pressure. Multiple neural signaling processes were also disturbed by PFBS life-cycle exposure, including cholinergic, glutamatergic, GABAergic and monoaminergic systems. Increased levels of norepinephrine and epinephrine neurotransmitters may adaptively decrease the intraocular hypertension in female eyes. In addition, proteomic profiling identified the visual proteins of differential expressions (e.g., beta and gamma crystallins, arrestin and lumican), which were significantly associated with visual perception and motor activity of eyes. Overall, this study found that PFBS was able to accumulate in the eyes and induce ocular toxicities. The susceptibility and sex-specific responses of visual systems to environmental pollutants warrants more works for a comprehensive risk assessment.}, } @article {pmid29855518, year = {2018}, author = {Grüss, A and Biggs, C and Heyman, WD and Erisman, B}, title = {Prioritizing monitoring and conservation efforts for fish spawning aggregations in the U.S. Gulf of Mexico.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {8473}, pmid = {29855518}, issn = {2045-2322}, mesh = {Animals ; *Conservation of Water Resources ; Databases, Factual ; Ecosystem ; Fishes/*physiology ; Gulf of Mexico ; Linear Models ; United States ; }, abstract = {In the U.S. Gulf of Mexico (U.S. GOM), the identification and characterization of transient fish spawning aggregation (FSA) sites is recognized as a regional priority for conservation, but progress is hindered by a lack of understanding of FSA distributions for most exploited species. We employed information compiled in regional databases on FSAs and monitoring for the U.S. GOM to fit species distribution models and produce maps showing the areas likely to host single- and multi-species transient FSA sites. Our results revealed two distinct regions of the U.S. GOM for prioritizing monitoring and conservation efforts for transient FSAs: the coastal waters surrounding major bay systems, particularly those of Texas and Louisiana, and portions of the continental shelf edge (the Flower Garden Banks area and the West Florida shelf edge). The next step would be to locate and characterize actual transient FSA sites in the U.S. GOM by surveying within the areas we identified.}, } @article {pmid29854945, year = {2018}, author = {Hazen, EL and Scales, KL and Maxwell, SM and Briscoe, DK and Welch, H and Bograd, SJ and Bailey, H and Benson, SR and Eguchi, T and Dewar, H and Kohin, S and Costa, DP and Crowder, LB and Lewison, RL}, title = {A dynamic ocean management tool to reduce bycatch and support sustainable fisheries.}, journal = {Science advances}, volume = {4}, number = {5}, pages = {eaar3001}, pmid = {29854945}, issn = {2375-2548}, mesh = {Animals ; *Conservation of Natural Resources ; Demography ; Ecosystem ; Environmental Monitoring ; *Fisheries ; Models, Theoretical ; }, abstract = {Seafood is an essential source of protein for more than 3 billion people worldwide, yet bycatch of threatened species in capture fisheries remains a major impediment to fisheries sustainability. Management measures designed to reduce bycatch often result in significant economic losses and even fisheries closures. Static spatial management approaches can also be rendered ineffective by environmental variability and climate change, as productive habitats shift and introduce new interactions between human activities and protected species. We introduce a new multispecies and dynamic approach that uses daily satellite data to track ocean features and aligns scales of management, species movement, and fisheries. To accomplish this, we create species distribution models for one target species and three bycatch-sensitive species using both satellite telemetry and fisheries observer data. We then integrate species-specific probabilities of occurrence into a single predictive surface, weighing the contribution of each species by management concern. We find that dynamic closures could be 2 to 10 times smaller than existing static closures while still providing adequate protection of endangered nontarget species. Our results highlight the opportunity to implement near real-time management strategies that would both support economically viable fisheries and meet mandated conservation objectives in the face of changing ocean conditions. With recent advances in eco-informatics, dynamic management provides a new climate-ready approach to support sustainable fisheries.}, } @article {pmid29848201, year = {2018}, author = {Mellor, J and Stone, MA and Keane, J}, title = {Application of Data Mining to a Large Hearing-Aid Manufacturer's Dataset to Identify Possible Benefits for Clinicians, Manufacturers, and Users.}, journal = {Trends in hearing}, volume = {22}, number = {}, pages = {2331216518773632}, pmid = {29848201}, issn = {2331-2165}, support = {MR/M026132/1//Medical Research Council/United Kingdom ; }, mesh = {Acoustics ; *Data Mining ; Female ; *Hearing Aids ; Humans ; Male ; Middle Aged ; *Prosthesis Fitting ; *Signal Processing, Computer-Assisted ; }, abstract = {Modern hearing instruments contain logging technology to record data, such as the acoustic environments in which the device is being used and how the signal processing is consequently operating. Combined with patient data, such as the audiogram, this information gives a more comprehensive picture of the user and their relationship with the aid. Here, a relatively large, anonymized dataset (>300,000 devices, >150,000 wearers) from a hearing-aid manufacturer was data mined for connections between subsets of the logged varieties of data. Apart from replicating links that have previously been reported in labor-intensive studies, a link between device style (in-the-ear/behind-the-ear) and the sound levels of encountered environments was demonstrated, suggesting that some device types are more successful from a lifestyle perspective. Furthermore, the data also suggested links between the audiogram and the sound environments in which the aid was operated. Modeling the expected link between the environment and the microphone directionality settings revealed patterns of either abnormal fitting or where the aid was not operating correctly-factors that may indicate a failed fitting. Given the necessarily redacted nature of the dataset, the reported findings represent a proof-of-concept of the use of relatively large-scale data mining to guide and assess hearing-aid fitting procedures for possible benefits to the clinician, manufacturer, and patient.}, } @article {pmid29848183, year = {2018}, author = {Mellor, JC and Stone, MA and Keane, J}, title = {Application of Data Mining to "Big Data" Acquired in Audiology: Principles and Potential.}, journal = {Trends in hearing}, volume = {22}, number = {}, pages = {2331216518776817}, pmid = {29848183}, issn = {2331-2165}, support = {MR/M026132/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {*Audiology ; *Big Data ; Data Mining/*methods ; *Hearing Aids ; Hearing Tests ; Humans ; Signal Processing, Computer-Assisted ; }, abstract = {The ubiquity and cheapness of miniature low-power sensors, digital processing, and large amounts of storage contained in small packages has heralded the ability to acquire large amounts of data about systems during their course of operation. The size and complexity of the data sets so generated have colloquially been labeled "big data." The computer science field of "data mining" has arisen with the purpose of extracting meaning from such data, expressly looking for patterns that not only link historic observations but also predict future behavior. This overview article considers the process, techniques, and interpretation of data mining, with specific focus on its application in audiology. Modern hearing instruments contain data-logging technology to record data separate from the audio stream, such as the acoustic environments in which the device was being used and how the signal processing was consequently operating. Combined with details about the patient, such as the audiogram, the variety of data generated lends itself to a data mining approach. To date, reports of the use and interpretation of these data have been mostly constrained to questions such as looking for changes in patterns of daily use, or the degree and direction of volume control manipulation as the patient's experience with a hearing aid changes. In this, and an accompanying results paper, the practical applications of some data mining techniques are described as applied to a large data set of examples of real-world device usage, as supplied by a hearing aid manufacturer.}, } @article {pmid29847023, year = {2018}, author = {Dellicour, S and Flot, JF}, title = {The hitchhiker's guide to single-locus species delimitation.}, journal = {Molecular ecology resources}, volume = {18}, number = {6}, pages = {1234-1246}, doi = {10.1111/1755-0998.12908}, pmid = {29847023}, issn = {1755-0998}, mesh = {Computational Biology/*methods ; DNA Barcoding, Taxonomic/*methods ; Metagenomics/*methods ; *Phylogeny ; }, abstract = {Molecular approaches to species delimitation are increasingly used to ascertain the number of species in a sample prior to taxonomic, ecological or physiological studies. Although multilocus approaches are gaining fast in popularity, single-gene methods still predominate in the literature. However, available simulation benchmarks of these methods focus exclusively on species-poor samples and/or tree-based approaches: as a result, travellers in the land of single-locus species delimitation lack a comprehensive "hitchhiker's guide" highlighting the sweet spots and dangers on their road. To fill this gap, we compared the performances of distance-based (ABGD, "automatic barcode gap discovery"), allele sharing-based (haplowebs) and tree-based approaches (GMYC, "generalized mixed Yule-coalescent" and PTP, "Poisson tree processes") to detect interspecific boundaries in samples of 6, 60 and 120 simulated species with various speciation rates, effective population sizes, mutation rates and sampling patterns. We found that all approaches performed poorly when population sizes and speciation rates were large, with haplowebs yielding best results followed by ABGD then tree-based approaches. The latter's error type was mostly oversplitting, whereas ABGD chiefly overlumped and haplowebs leaned either way depending on simulation parameters: such widely divergent error patterns suggest that, if all three types of methods agree, then the resulting delimitation is probably correct. Perfect congruence being quite rare, travellers in search of a one-size-fit-all approach to single-locus species delimitation should forget it; however, our hitchhiker's guide raises hope that such species delimitation's Holy Grail may be found in the relatively uncharted nearby land of multilocus species delimitation.}, } @article {pmid29844443, year = {2018}, author = {Kula, A and Saelens, J and Cox, J and Schubert, AM and Travisano, M and Putonti, C}, title = {The Evolution of Molecular Compatibility between Bacteriophage ΦX174 and its Host.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {8350}, pmid = {29844443}, issn = {2045-2322}, mesh = {Bacteriophage phi X 174/*genetics/metabolism ; Bacteriophages/genetics ; Codon/genetics ; Computational Biology/methods ; Evolution, Molecular ; Genome, Viral/*genetics ; RNA, Transfer/genetics ; RNA, Viral/genetics ; Viruses/genetics ; }, abstract = {Viruses rely upon their hosts for biosynthesis of viral RNA, DNA and protein. This dependency frequently engenders strong selection for virus genome compatibility with potential hosts, appropriate gene regulation and expression necessary for a successful infection. While bioinformatic studies have shown strong correlations between codon usage in viral and host genomes, the selective factors by which this compatibility evolves remain a matter of conjecture. Engineered to include codons with a lesser usage and/or tRNA abundance within the host, three different attenuated strains of the bacterial virus ФX174 were created and propagated via serial transfers. Molecular sequence data indicate that biosynthetic compatibility was recovered rapidly. Extensive computational simulations were performed to assess the role of mutational biases as well as selection for translational efficiency in the engineered phage. Using bacteriophage as a model system, we can begin to unravel the evolutionary processes shaping codon compatibility between viruses and their host.}, } @article {pmid29813067, year = {2018}, author = {Funikov, SY and Kulikova, DA and Krasnov, GS and Rezvykh, AP and Chuvakova, LN and Shostak, NG and Zelentsova, ES and Blumenstiel, JP and Evgen'ev, MB}, title = {Spontaneous gain of susceptibility suggests a novel mechanism of resistance to hybrid dysgenesis in Drosophila virilis.}, journal = {PLoS genetics}, volume = {14}, number = {5}, pages = {e1007400}, pmid = {29813067}, issn = {1553-7404}, mesh = {Animals ; Chromatin/*genetics ; Computational Biology ; DNA Copy Number Variations/genetics ; DNA Transposable Elements/*genetics ; Drosophila/*genetics ; Female ; Genomic Instability ; High-Throughput Nucleotide Sequencing ; Infertility/*genetics ; Male ; Ovary/metabolism ; RNA, Small Interfering/*genetics/metabolism ; Real-Time Polymerase Chain Reaction ; Sequence Analysis, RNA ; }, abstract = {Syndromes of hybrid dysgenesis (HD) have been critical for our understanding of the transgenerational maintenance of genome stability by piRNA. HD in D. virilis represents a special case of HD since it includes simultaneous mobilization of a set of TEs that belong to different classes. The standard explanation for HD is that eggs of the responder strains lack an abundant pool of piRNAs corresponding to the asymmetric TE families transmitted solely by sperm. However, there are several strains of D. virilis that lack asymmetric TEs, but exhibit a "neutral" cytotype that confers resistance to HD. To characterize the mechanism of resistance to HD, we performed a comparative analysis of the landscape of ovarian small RNAs in strains that vary in their resistance to HD mediated sterility. We demonstrate that resistance to HD cannot be solely explained by a maternal piRNA pool that matches the assemblage of TEs that likely cause HD. In support of this, we have witnessed a cytotype shift from neutral (N) to susceptible (M) in a strain devoid of all major TEs implicated in HD. This shift occurred in the absence of significant change in TE copy number and expression of piRNAs homologous to asymmetric TEs. Instead, this shift is associated with a change in the chromatin profile of repeat sequences unlikely to be causative of paternal induction. Overall, our data suggest that resistance to TE-mediated sterility during HD may be achieved by mechanisms that are distinct from the canonical syndromes of HD.}, } @article {pmid29808518, year = {2019}, author = {Pastick, NJ and Jorgenson, MT and Goetz, SJ and Jones, BM and Wylie, BK and Minsley, BJ and Genet, H and Knight, JF and Swanson, DK and Jorgenson, JC}, title = {Spatiotemporal remote sensing of ecosystem change and causation across Alaska.}, journal = {Global change biology}, volume = {25}, number = {3}, pages = {1171-1189}, doi = {10.1111/gcb.14279}, pmid = {29808518}, issn = {1365-2486}, support = {NNX17AE44G/NASA/NASA/United States ; }, mesh = {Alaska ; Arctic Regions ; *Climate Change ; *Ecosystem ; Environmental Monitoring/*methods ; Permafrost ; Plant Development ; *Remote Sensing Technology ; Spatio-Temporal Analysis ; Temperature ; }, abstract = {Contemporary climate change in Alaska has resulted in amplified rates of press and pulse disturbances that drive ecosystem change with significant consequences for socio-environmental systems. Despite the vulnerability of Arctic and boreal landscapes to change, little has been done to characterize landscape change and associated drivers across northern high-latitude ecosystems. Here we characterize the historical sensitivity of Alaska's ecosystems to environmental change and anthropogenic disturbances using expert knowledge, remote sensing data, and spatiotemporal analyses and modeling. Time-series analysis of moderate-and high-resolution imagery was used to characterize land- and water-surface dynamics across Alaska. Some 430,000 interpretations of ecological and geomorphological change were made using historical air photos and satellite imagery, and corroborate land-surface greening, browning, and wetness/moisture trend parameters derived from peak-growing season Landsat imagery acquired from 1984 to 2015. The time series of change metrics, together with climatic data and maps of landscape characteristics, were incorporated into a modeling framework for mapping and understanding of drivers of change throughout Alaska. According to our analysis, approximately 13% (~174,000 ± 8700 km[2]) of Alaska has experienced directional change in the last 32 years (±95% confidence intervals). At the ecoregions level, substantial increases in remotely sensed vegetation productivity were most pronounced in western and northern foothills of Alaska, which is explained by vegetation growth associated with increasing air temperatures. Significant browning trends were largely the result of recent wildfires in interior Alaska, but browning trends are also driven by increases in evaporative demand and surface-water gains that have predominately occurred over warming permafrost landscapes. Increased rates of photosynthetic activity are associated with stabilization and recovery processes following wildfire, timber harvesting, insect damage, thermokarst, glacial retreat, and lake infilling and drainage events. Our results fill a critical gap in the understanding of historical and potential future trajectories of change in northern high-latitude regions.}, } @article {pmid29804262, year = {2018}, author = {Ma, K and Zhang, Q and Cheng, T and Wang, J}, title = {Identification of transposons near predicted lncRNA and mRNA pools of Prunus mume using an integrative transposable element database constructed from Rosaceae plant genomes.}, journal = {Molecular genetics and genomics : MGG}, volume = {293}, number = {5}, pages = {1301-1316}, pmid = {29804262}, issn = {1617-4623}, support = {NO. 31501787//National Natural Science Foundation of China (CN)/ ; NO. 2016ZCQ02//Fundamental Research Funds for the Central Universities/ ; }, mesh = {Chromosome Mapping ; *DNA Transposable Elements ; Databases, Genetic ; *Genome, Plant ; Molecular Sequence Annotation ; Prunus/*genetics ; RNA, Long Noncoding/*genetics ; RNA, Messenger/*genetics ; Rosaceae/*genetics ; Whole Genome Sequencing ; }, abstract = {This study focused on the construction of a database of transposable elements (TEs) from Rosaceae plants, the third most economically important plant family in temperate regions, and its transcriptomics applications. The evolutionary effects of TEs on gene regulation have been explored, and TE insertions can be the molecular bases of changes in gene structure and function. However, a specific Rosaceae plant TE database (RPTEdb) is lacking. The genomes of several Rosaceae plants have been sequenced, providing the opportunity to mine TE data at a whole-genome level. Therefore, we constructed the RPTEdb, a collective and comprehensive database of 19,596 annotated TEs in the genomes of Rosaceae plants using previously described identification and annotation methods and published genome sequences. The user-friendly web-based database provides access to research tools through hyperlinks, including Browse, TE tree, tools, JBrowse, and search sections, and through the inputting of sequences on the main webpage. Next, we performed one advanced application in which TEs near predicted long non-coding RNA (lncRNA) and mRNA domains within white and red petal-tissue transcriptomes of Prunus mume 'Fuban Tiaozhi' were identified, revealing 16 TEs that overlapped or were near 16 differentially expressed lncRNA domains, and 54 TEs that overlapped or were near 54 differentially expressed mRNA domains, and the TEs' possible functions were also discussed. We believe that the RPTEdb will contribute to the understanding of TE roles in the structural, functional and evolutionary dynamics of Rosaceae plant genomes.}, } @article {pmid29804162, year = {2018}, author = {Rydberg, DM and Mejyr, S and Loikas, D and Schenck-Gustafsson, K and von Euler, M and Malmström, RE}, title = {Sex differences in spontaneous reports on adverse drug events for common antihypertensive drugs.}, journal = {European journal of clinical pharmacology}, volume = {74}, number = {9}, pages = {1165-1173}, pmid = {29804162}, issn = {1432-1041}, support = {SKL 08/2254//Sveriges Kommuner och Landsting (SE)/ ; }, mesh = {*Adverse Drug Reaction Reporting Systems ; Antihypertensive Agents/administration & dosage/*adverse effects ; Cross-Sectional Studies ; Databases, Factual ; Dose-Response Relationship, Drug ; Drug-Related Side Effects and Adverse Reactions/diagnosis/*epidemiology ; Female ; Humans ; Male ; *Pharmacovigilance ; Prevalence ; Risk Factors ; Sex Factors ; Sweden/epidemiology ; }, abstract = {PURPOSE: To explore sex differences in spontaneously reported adverse drug events (ADEs) for antihypertensives in routine care.

METHODS: A cross sectional analysis combining number of reports from the national pharmacovigilance database with data from the Swedish Prescribed Drug Register, from 2005 to 2012 for ACE inhibitors (ACE-I) and angiotensin receptor blockers (ARB), with or without thiazide, diuretics (thiazides, potassium-sparing agents, sulfonamides, aldosterone antagonists), selective betablockers, and dihydropyridine calcium-channel-blockers (DHPs). The total number of reports was adjusted to exposed patients and dispensed DDDs among women and men. Dose exposures, co-medications, and co-prescriptions were also analyzed.

RESULTS: In women, a higher prevalence of ADE-reports was seen in ACE-I (odds ratio, OR 1.21; 95% CI 1.09-1.35), ACE-I-combinations (OR 1.61; 1.44-1.79), ARB-combinations (OR 2.12; 1.47-3.06), thiazides (OR 1.78; 1.33-2.39), diuretics and potassium-sparing agents (OR 1.62; 1.22-2.17), and DHPs (OR 1.40; 1.17-1.67), with a potential linkage to dose exposure. For aldosterone antagonists, we observed a higher prevalence of ADE reports in men (OR 0.75; 0.59-0.97) but without any sex difference in dose exposure.

CONCLUSIONS: This ecological study of reported ADEs showed a higher prevalence of reports in women in six out of ten groups of antihypertensive drugs, and this may potentially be linked to dose exposure. Aldosterone antagonists was the only group with a higher prevalence of ADE-reports in men with a similar dose exposure between women and men.}, } @article {pmid29802785, year = {2018}, author = {Capblancq, T and Luu, K and Blum, MGB and Bazin, E}, title = {Evaluation of redundancy analysis to identify signatures of local adaptation.}, journal = {Molecular ecology resources}, volume = {18}, number = {6}, pages = {1223-1233}, doi = {10.1111/1755-0998.12906}, pmid = {29802785}, issn = {1755-0998}, support = {ANR-15-CE02-0004//Agence Nationale de la Recherche/ ; ANR-15-IDEX-02//Agence Nationale de la Recherche/ ; }, mesh = {*Adaptation, Biological ; Biostatistics/methods ; Computational Biology/methods ; Genetic Loci ; *Genetic Variation ; Genetics, Population/*methods ; Genomics/*methods ; Genotype ; Polymorphism, Single Nucleotide ; }, abstract = {Ordination is a common tool in ecology that aims at representing complex biological information in a reduced space. In landscape genetics, ordination methods such as principal component analysis (PCA) have been used to detect adaptive variation based on genomic data. Taking advantage of environmental data in addition to genotype data, redundancy analysis (RDA) is another ordination approach that is useful to detect adaptive variation. This study aims at proposing a test statistic based on RDA to search for loci under selection. We compare redundancy analysis to pcadapt, which is a nonconstrained ordination method, and to a latent factor mixed model (LFMM), which is a univariate genotype-environment association method. Individual-based simulations identify evolutionary scenarios where RDA genome scans have a greater statistical power than genome scans based on PCA. By constraining the analysis with environmental variables, RDA performs better than PCA in identifying adaptive variation when selection gradients are weakly correlated with population structure. In addition, we show that if RDA and LFMM have a similar power to identify genetic markers associated with environmental variables, the RDA-based procedure has the advantage to identify the main selective gradients as a combination of environmental variables. To give a concrete illustration of RDA in population genomics, we apply this method to the detection of outliers and selective gradients on an SNP data set of Populus trichocarpa (Geraldes et al.,). The RDA-based approach identifies the main selective gradient contrasting southern and coastal populations to northern and continental populations in the north-western American coast.}, } @article {pmid29802772, year = {2018}, author = {Snell Taylor, SJ and Evans, BS and White, EP and Hurlbert, AH}, title = {The prevalence and impact of transient species in ecological communities.}, journal = {Ecology}, volume = {99}, number = {8}, pages = {1825-1835}, doi = {10.1002/ecy.2398}, pmid = {29802772}, issn = {0012-9658}, mesh = {*Biota ; *Ecosystem ; Prevalence ; }, abstract = {Transient species occur infrequently in a community over time and do not maintain viable local populations. Because transient species interact differently than non-transients with their biotic and abiotic environment, it is important to characterize the prevalence of these species and how they impact our understanding of ecological systems. We quantified the prevalence and impact of transient species in communities using data on over 19,000 community time series spanning an array of ecosystems, taxonomic groups, and spatial scales. We found that transient species are a general feature of communities regardless of taxa or ecosystem. The proportion of these species decreases with increasing spatial scale leading to a need to control for scale in comparative work. Removing transient species from analyses influences the form of a suite of commonly studied ecological patterns including species-abundance distributions, species-energy relationships, species-area relationships, and temporal turnover. Careful consideration should be given to whether transient species are included in analyses depending on the theoretical and practical relevance of these species for the question being studied.}, } @article {pmid29796788, year = {2018}, author = {Lin, SL and Wei, T and Lin, JF and Guo, LQ and Wu, GP and Wei, JB and Huang, JJ and Ouyang, PL}, title = {Bio-production of Baccatin III, an Important Precursor of Paclitaxel by a Cost-Effective Approach.}, journal = {Molecular biotechnology}, volume = {60}, number = {7}, pages = {492-505}, pmid = {29796788}, issn = {1559-0305}, support = {2014B050505018, 2014B020205003//Science and Technology Program of Guangdong Province/ ; 31071837, 31372116, 31572178//National Natural Science Foundation of China/ ; }, mesh = {Acetyltransferases/chemistry/*genetics/metabolism ; Alkaloids/*biosynthesis/economics ; Antineoplastic Agents, Phytogenic/*biosynthesis/economics ; Bioengineering ; Biosynthetic Pathways ; Computational Biology ; Cost-Benefit Analysis ; Genetic Engineering ; Models, Molecular ; Mutagenesis ; Paclitaxel/biosynthesis/economics ; Substrate Specificity ; Taxoids/economics/metabolism ; Taxus/chemistry/*enzymology/genetics/metabolism ; Vinyl Compounds/chemistry/metabolism ; }, abstract = {Natural production of anti-cancer drug taxol from Taxus has proved to be environmentally unsustainable and economically unfeasible. Currently, bioengineering the biosynthetic pathway of taxol is an attractive alternative production approach. 10-deacetylbaccatin III-10-O-acetyl transferase (DBAT) was previously characterized as an acyltransferase, using 10-deacetylbaccatin III (10-DAB) and acetyl CoA as natural substrates, to form baccatin III in the taxol biosynthesis. Here, we report that other than the natural acetyl CoA (Ac-CoA) substrate, DBAT can also utilize vinyl acetate (VA), which is commercially available at very low cost, acylate quickly and irreversibly, as acetyl donor in the acyl transfer reaction to produce baccatin III. Furthermore, mutants were prepared via a semi-rational design in this work. A double mutant, I43S/D390R was constructed to combine the positive effects of the different single mutations on catalytic activity, and its catalytic efficiency towards 10-DAB and VA was successfully improved by 3.30-fold, compared to that of wild-type DBAT, while 2.99-fold higher than the catalytic efficiency of WT DBAT towards 10-DAB and Ac-CoA. These findings can provide a promising economically and environmentally friendly method for exploring novel acyl donors to engineer natural product pathways.}, } @article {pmid29795657, year = {2018}, author = {Monnahan, CC and Kristensen, K}, title = {No-U-turn sampling for fast Bayesian inference in ADMB and TMB: Introducing the adnuts and tmbstan R packages.}, journal = {PloS one}, volume = {13}, number = {5}, pages = {e0197954}, pmid = {29795657}, issn = {1932-6203}, mesh = {*Algorithms ; Animals ; *Bayes Theorem ; Computational Biology/*methods ; Humans ; Markov Chains ; *Models, Biological ; *Models, Statistical ; Monte Carlo Method ; }, abstract = {Statistical inference is a widely-used, powerful tool for learning about natural processes in diverse fields. The statistical software platforms AD Model Builder (ADMB) and Template Model Builder (TMB) are particularly popular in the ecological literature, where they are typically used to perform frequentist inference of complex models. However, both lack capabilities for flexible and efficient Markov chain Monte Carlo (MCMC) integration. Recently, the no-U-turn sampler (NUTS) MCMC algorithm has gained popularity for Bayesian inference through the software Stan because it is efficient for high dimensional, complex hierarchical models. Here, we introduce the R packages adnuts and tmbstan, which provide NUTS sampling in parallel and interactive diagnostics with ShinyStan. The ADMB source code was modified to provide NUTS, while TMB models are linked directly into Stan. We describe the packages, provide case studies demonstrating their use, and contrast performance against Stan. For TMB models, we show how to test the accuracy of the Laplace approximation using NUTS. For complex models, the performance of ADMB and TMB was typically within +/- 50% the speed of Stan. In one TMB case study we found inaccuracies in the Laplace approximation, potentially leading to biased inference. adnuts provides a new method for estimating hierarchical ADMB models which previously were infeasible. TMB users can fit the same model in both frequentist and Bayesian paradigms, including using NUTS to test the validity of the Laplace approximation of the marginal likelihood for arbitrary subsets of parameters. These software developments extend the available statistical methods of the ADMB and TMB user base with no additional effort by the user.}, } @article {pmid29795571, year = {2018}, author = {Haney, S and Konen, J and Marcus, AI and Bazhenov, M}, title = {The complex ecosystem in non small cell lung cancer invasion.}, journal = {PLoS computational biology}, volume = {14}, number = {5}, pages = {e1006131}, pmid = {29795571}, issn = {1553-7358}, support = {R01 CA194027/CA/NCI NIH HHS/United States ; U54 CA209992/CA/NCI NIH HHS/United States ; R21 CA201744/CA/NCI NIH HHS/United States ; T32 HL134632/HL/NHLBI NIH HHS/United States ; R01 DC012943/DC/NIDCD NIH HHS/United States ; }, mesh = {*Carcinoma, Non-Small-Cell Lung/genetics/metabolism ; Cell Line, Tumor ; Computational Biology ; Ecosystem ; Humans ; *Lung Neoplasms/genetics/metabolism ; Microscopy, Fluorescence ; *Models, Biological ; Signal Transduction ; *Tumor Microenvironment/genetics/physiology ; }, abstract = {Many tumors are characterized by genetic instability, producing an assortment of genetic variants of tumor cells called subclones. These tumors and their surrounding environments form complex multi-cellular ecosystems, where subclones compete for resources and cooperate to perform multiple tasks, including cancer invasion. Our recent empirical studies revealed existence of such distinct phenotypes of cancer cells, leaders and followers, in lung cancer. These two cellular subclones exchange a complex array of extracellular signals demonstrating a symbiotic relationship at the cellular level. Here, we develop a computational model of the microenvironment of the lung cancer ecosystem to explore how the interactions between subclones can advance or inhibit invasion. We found that, due to the complexity of the ecosystem, invasion may have very different dynamics characterized by the different levels of aggressiveness. By altering the signaling environment, we could alter the ecological relationship between the cell types and the overall ecosystem development. Competition between leader and follower cell populations (defined by the limited amount of resources), positive feedback within the leader cell population (controlled by the focal adhesion kinase and fibronectin signaling), and impact of the follower cells to the leaders (represented by yet undetermined proliferation signal) all had major effects on the outcome of the collective dynamics. Specifically, our analysis revealed a class of tumors (defined by the strengths of fibronectin signaling and competition) that are particularly sensitive to manipulations of the signaling environment. These tumors can undergo irreversible changes to the tumor ecosystem that outlast the manipulations of feedbacks and have a profound impact on invasive potential. Our study predicts a complex division of labor between cancer cell subclones and suggests new treatment strategies targeting signaling within the tumor ecosystem.}, } @article {pmid29794166, year = {2018}, author = {Couger, MB and Arévalo, L and Campbell, P}, title = {A High Quality Genome for Mus spicilegus, a Close Relative of House Mice with Unique Social and Ecological Adaptations.}, journal = {G3 (Bethesda, Md.)}, volume = {8}, number = {7}, pages = {2145-2152}, pmid = {29794166}, issn = {2160-1836}, mesh = {Animals ; Computational Biology/methods ; Ecology ; Gene Expression Profiling ; *Genome ; *Genomics/methods ; Geography ; Hungary ; Mice ; Molecular Sequence Annotation ; Phylogeny ; Species Specificity ; Transcriptome ; }, abstract = {Genomic data for the closest relatives of house mice (Mus musculus species complex) are surprisingly limited. Here, we present the first complete genome for a behaviorally and ecologically unique member of the sister clade to house mice, the mound-building mouse, Mus spicilegus Using read cloud sequencing and de novo assembly we produced a 2.50 Gbp genome with a scaffold N50 of 2.27 Mbp. We constructed >25 000 gene models, of which the majority had high homology to other Mus species. To evaluate the utility of the M. spicilegus genome for behavioral and ecological genomics, we extracted 196 vomeronasal receptor (VR) sequences from our genome and analyzed phylogenetic relationships between M. spicilegus VRs and orthologs from M. musculus and the Algerian mouse, M. spretus While most M. spicilegus VRs clustered with orthologs in M. musculus and M. spretus, 10 VRs with evidence of rapid divergence in M. spicilegus are strong candidate modulators of species-specific chemical communication. A high quality assembly and genome for M. spicilegus will help to resolve discordant ancestry patterns in house mouse genomes, and will provide an essential foundation for genetic dissection of phenotypes that distinguish commensal from non-commensal species, and the social and ecological characteristics that make M. spicilegus unique.}, } @article {pmid29792315, year = {2018}, author = {Stevens, KA and Woeste, K and Chakraborty, S and Crepeau, MW and Leslie, CA and Martínez-García, PJ and Puiu, D and Romero-Severson, J and Coggeshall, M and Dandekar, AM and Kluepfel, D and Neale, DB and Salzberg, SL and Langley, CH}, title = {Genomic Variation Among and Within Six Juglans Species.}, journal = {G3 (Bethesda, Md.)}, volume = {8}, number = {7}, pages = {2153-2165}, pmid = {29792315}, issn = {2160-1836}, mesh = {Computational Biology/methods ; Evolution, Molecular ; *Genetic Variation ; Genome Size ; *Genome, Plant ; *Genomics/methods ; Genotype ; High-Throughput Nucleotide Sequencing ; Juglans/*classification/*genetics ; Molecular Sequence Annotation ; Phylogeny ; Polymorphism, Single Nucleotide ; }, abstract = {Genomic analysis in Juglans (walnuts) is expected to transform the breeding and agricultural production of both nuts and lumber. To that end, we report here the determination of reference sequences for six additional relatives of Juglans regia: Juglans sigillata (also from section Dioscaryon), Juglans nigra, Juglans microcarpa, Juglans hindsii (from section Rhysocaryon), Juglans cathayensis (from section Cardiocaryon), and the closely related Pterocarya stenoptera While these are 'draft' genomes, ranging in size between 640Mbp and 990Mbp, their contiguities and accuracies can support powerful annotations of genomic variation that are often the foundation of new avenues of research and breeding. We annotated nucleotide divergence and synteny by creating complete pairwise alignments of each reference genome to the remaining six. In addition, we have re-sequenced a sample of accessions from four Juglans species (including regia). The variation discovered in these surveys comprises a critical resource for experimentation and breeding, as well as a solid complementary annotation. To demonstrate the potential of these resources the structural and sequence variation in and around the polyphenol oxidase loci, PPO1 and PPO2 were investigated. As reported for other seed crops variation in this gene is implicated in the domestication of walnuts. The apparently Juglandaceae specific PPO1 duplicate shows accelerated divergence and an excess of amino acid replacement on the lineage leading to accessions of the domesticated nut crop species, Juglans regia and sigillata.}, } @article {pmid29792109, year = {2018}, author = {Lippmann, C and Kringel, D and Ultsch, A and Lötsch, J}, title = {Computational functional genomics-based approaches in analgesic drug discovery and repurposing.}, journal = {Pharmacogenomics}, volume = {19}, number = {9}, pages = {783-797}, doi = {10.2217/pgs-2018-0036}, pmid = {29792109}, issn = {1744-8042}, mesh = {Analgesics/*therapeutic use ; Animals ; Computational Biology/methods ; Data Mining/methods ; Drug Discovery/*methods ; Drug Repositioning/methods ; Gene Expression/genetics ; Genomics/methods ; Humans ; Pain/*drug therapy/genetics ; Proteomics/methods ; }, abstract = {Persistent pain is a major healthcare problem affecting a fifth of adults worldwide with still limited treatment options. The search for new analgesics increasingly includes the novel research area of functional genomics, which combines data derived from various processes related to DNA sequence, gene expression or protein function and uses advanced methods of data mining and knowledge discovery with the goal of understanding the relationship between the genome and the phenotype. Its use in drug discovery and repurposing for analgesic indications has so far been performed using knowledge discovery in gene function and drug target-related databases; next-generation sequencing; and functional proteomics-based approaches. Here, we discuss recent efforts in functional genomics-based approaches to analgesic drug discovery and repurposing and highlight the potential of computational functional genomics in this field including a demonstration of the workflow using a novel R library 'dbtORA'.}, } @article {pmid29791528, year = {2018}, author = {Pelissari, DM and Bartholomay, P and Jacobs, MG and Arakaki-Sanchez, D and Anjos, DSOD and Costa, MLDS and Cavalcanti, PCDS and Diaz-Quijano, FA}, title = {Offer of primary care services and detection of tuberculosis incidence in Brazil.}, journal = {Revista de saude publica}, volume = {52}, number = {}, pages = {53}, pmid = {29791528}, issn = {1518-8787}, mesh = {Brazil/epidemiology ; Disease Notification ; Health Services ; Humans ; Incidence ; Information Systems ; *Primary Health Care ; Tuberculosis/*diagnosis/*epidemiology ; }, abstract = {OBJECTIVE To evaluate the association between the health services offered by primary care teams and the detection of new tuberculosis cases in Brazil. METHODS This was an ecological study covering all Brazilian municipalities that registered at least one new tuberculosis case (diagnosed between 2012 to 2014 and notified in the Information System of Notifiable Diseases) and with at least one primary care team evaluated by the second cycle of the National Program for Improving Access and Quality of Primary Care (PMAQ-AB). The variables of the PMAQ-AB were classified as proximal or distal, according to their relation with the tuberculosis diagnosis. Then, they were tested hierarchically in multiple models (adjusted by States) using negative binomial regression. RESULTS An increase of 10% in the primary health care coverage was associated with a decrease of 2.24% in the tuberculosis detection rate (95%CI -3.35- -1.11). Regarding the proximal variables in relation to diagnosis, in the multiple model, the detection of tuberculosis was associated with the proportion of teams that conduct contact investigation (increase in Incidence Rate Ratio [IRR] = 2.97%, 95%CI 2.41-3.53), carry out tuberculosis active case finding (increase in IRR = 2.17%, 95%CI 1.48-2.87), and request culture for mycobacteria (increase in IRR = 1.87%, 95%CI 0.98-2.76). CONCLUSIONS The variables related to the search actions were positively associated with the detection of new tuberculosis cases, which suggests a significant contribution to the strengthening of the sensitivity of the surveillance system. On the other hand, primary care coverage was inversely associated with the tuberculosis detection rate, which could represent the overall effect of the primary care on transmission control, probably from the identification and early treatment of cases.}, } @article {pmid29791436, year = {2018}, author = {Ravinet, M and Yoshida, K and Shigenobu, S and Toyoda, A and Fujiyama, A and Kitano, J}, title = {The genomic landscape at a late stage of stickleback speciation: High genomic divergence interspersed by small localized regions of introgression.}, journal = {PLoS genetics}, volume = {14}, number = {5}, pages = {e1007358}, pmid = {29791436}, issn = {1553-7404}, mesh = {Animals ; Atlantic Ocean ; Bayes Theorem ; Datasets as Topic ; Female ; Gene Flow/*genetics ; *Genetic Speciation ; Genome ; Genomics/methods ; Hybridization, Genetic/*genetics ; Japan ; Male ; Pacific Ocean ; Recombination, Genetic/genetics ; Smegmamorpha/*genetics ; Sympatry/*genetics ; }, abstract = {Speciation is a continuous process and analysis of species pairs at different stages of divergence provides insight into how it unfolds. Previous genomic studies on young species pairs have revealed peaks of divergence and heterogeneous genomic differentiation. Yet less known is how localised peaks of differentiation progress to genome-wide divergence during the later stages of speciation in the presence of persistent gene flow. Spanning the speciation continuum, stickleback species pairs are ideal for investigating how genomic divergence builds up during speciation. However, attention has largely focused on young postglacial species pairs, with little knowledge of the genomic signatures of divergence and introgression in older stickleback systems. The Japanese stickleback species pair, composed of the Pacific Ocean three-spined stickleback (Gasterosteus aculeatus) and the Japan Sea stickleback (G. nipponicus), which co-occur in the Japanese islands, is at a late stage of speciation. Divergence likely started well before the end of the last glacial period and crosses between Japan Sea females and Pacific Ocean males result in hybrid male sterility. Here we use coalescent analyses and Approximate Bayesian Computation to show that the two species split approximately 0.68-1 million years ago but that they have continued to exchange genes at a low rate throughout divergence. Population genomic data revealed that, despite gene flow, a high level of genomic differentiation is maintained across the majority of the genome. However, we identified multiple, small regions of introgression, occurring mainly in areas of low recombination rate. Our results demonstrate that a high level of genome-wide divergence can establish in the face of persistent introgression and that gene flow can be localized to small genomic regions at the later stages of speciation with gene flow.}, } @article {pmid29791432, year = {2018}, author = {Tao, Y and Shea, K and Ferrari, M}, title = {Logistical constraints lead to an intermediate optimum in outbreak response vaccination.}, journal = {PLoS computational biology}, volume = {14}, number = {5}, pages = {e1006161}, pmid = {29791432}, issn = {1553-7358}, support = {BB/K010972/4/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; R01 GM105247/GM/NIGMS NIH HHS/United States ; 1 R01 GM105247-01/NH/NIH HHS/United States ; }, mesh = {Computational Biology ; *Computer Simulation ; Disease Outbreaks/*prevention & control/*statistics & numerical data ; Humans ; *Immunity, Herd ; *Models, Biological ; Time Factors ; Vaccination/*statistics & numerical data ; Vaccines/administration & dosage/supply & distribution ; }, abstract = {Dynamic models in disease ecology have historically evaluated vaccination strategies under the assumption that they are implemented homogeneously in space and time. However, this approach fails to formally account for operational and logistical constraints inherent in the distribution of vaccination to the population at risk. Thus, feedback between the dynamic processes of vaccine distribution and transmission might be overlooked. Here, we present a spatially explicit, stochastic Susceptible-Infected-Recovered-Vaccinated model that highlights the density-dependence and spatial constraints of various diffusive strategies of vaccination during an outbreak. The model integrates an agent-based process of disease spread with a partial differential process of vaccination deployment. We characterize the vaccination response in terms of a diffusion rate that describes the distribution of vaccination to the population at risk from a central location. This generates an explicit trade-off between slow diffusion, which concentrates effort near the central location, and fast diffusion, which spreads a fixed vaccination effort thinly over a large area. We use stochastic simulation to identify the optimum vaccination diffusion rate as a function of population density, interaction scale, transmissibility, and vaccine intensity. Our results show that, conditional on a timely response, the optimal strategy for minimizing outbreak size is to distribute vaccination resource at an intermediate rate: fast enough to outpace the epidemic, but slow enough to achieve local herd immunity. If the response is delayed, however, the optimal strategy for minimizing outbreak size changes to a rapidly diffusive distribution of vaccination effort. The latter may also result in significantly larger outbreaks, thus suggesting a benefit of allocating resources to timely outbreak detection and response.}, } @article {pmid29787608, year = {2018}, author = {Silva-Brandão, KL and Peruchi, A and Seraphim, N and Murad, NF and Carvalho, RA and Farias, JR and Omoto, C and Cônsoli, FL and Figueira, A and Brandão, MM}, title = {Loci under selection and markers associated with host plant and host-related strains shape the genetic structure of Brazilian populations of Spodoptera frugiperda (Lepidoptera, Noctuidae).}, journal = {PloS one}, volume = {13}, number = {5}, pages = {e0197378}, pmid = {29787608}, issn = {1932-6203}, mesh = {Adenosine Triphosphate/chemistry ; Alleles ; Animals ; Bacillus thuringiensis/*genetics ; Bayes Theorem ; Brazil ; Ecology ; Gene Library ; Gene Ontology ; *Genetic Markers ; *Genetics, Population ; Genotype ; Geography ; Insecticide Resistance/*genetics ; Oryza/genetics ; Plant Diseases/genetics ; Polymorphism, Single Nucleotide ; Principal Component Analysis ; Protein Binding ; *Selection, Genetic ; Sequence Analysis, DNA ; Spodoptera/*genetics ; Transcriptome ; Zea mays/genetics ; }, abstract = {We applied the ddRAD genotyping-by-sequencing technique to investigate the genetic distinctiveness of Brazilian populations of the noctuid moth Spodoptera frugiperda, the fall armyworm (FAW), and the role of host-plant association as a source of genetic diversification. By strain-genotyping all field-collected individuals we found that populations collected from corn were composed primarily of corn-strain individuals, while the population collected from rice was composed almost entirely of rice-strain individuals. Outlier analyses indicated 1,184 loci putatively under selection (ca. 15% of the total) related to 194 different Gene Ontologies (GOs); the most numerous GOs were nucleotide binding, ATP binding, metal-ion binding and nucleic-acid binding. The association analyses indicated 326 loci associated with the host plant, and 216 loci associated with the individual strain, including functions related to Bacillus thuringiensis and insecticide resistance. The genetic-structure analyses indicated a moderate level of differentiation among all populations, and lower genetic structure among populations collected exclusively from corn, which suggests that the population collected from rice has a strong influence on the overall genetic structure. Populations of S. frugiperda are structured partially due to the host plant, and pairs of populations using the same host plant are more genetically similar than pairs using different hosts. Loci putatively under selection are the main factors responsible for the genetic structure of these populations, which indicates that adaptive selection on important traits, including the response to control tactics, is acting in the genetic differentiation of FAW populations in Brazil.}, } @article {pmid29786693, year = {2018}, author = {Vitousek, MN and Johnson, MA and Donald, JW and Francis, CD and Fuxjager, MJ and Goymann, W and Hau, M and Husak, JF and Kircher, BK and Knapp, R and Martin, LB and Miller, ET and Schoenle, LA and Uehling, JJ and Williams, TD}, title = {HormoneBase, a population-level database of steroid hormone levels across vertebrates.}, journal = {Scientific data}, volume = {5}, number = {}, pages = {180097}, pmid = {29786693}, issn = {2052-4463}, mesh = {Androgens/*blood ; Animals ; Biological Evolution ; *Databases, Factual ; Female ; Glucocorticoids/*blood ; Male ; Species Specificity ; *Vertebrates ; }, abstract = {Hormones are central regulators of organismal function and flexibility that mediate a diversity of phenotypic traits from early development through senescence. Yet despite these important roles, basic questions about how and why hormone systems vary within and across species remain unanswered. Here we describe HormoneBase, a database of circulating steroid hormone levels and their variation across vertebrates. This database aims to provide all available data on the mean, variation, and range of plasma glucocorticoids (both baseline and stress-induced) and androgens in free-living and un-manipulated adult vertebrates. HormoneBase (www.HormoneBase.org) currently includes >6,580 entries from 476 species, reported in 648 publications from 1967 to 2015, and unpublished datasets. Entries are associated with data on the species and population, sex, year and month of study, geographic coordinates, life history stage, method and latency of hormone sampling, and analysis technique. This novel resource could be used for analyses of the function and evolution of hormone systems, and the relationships between hormonal variation and a variety of processes including phenotypic variation, fitness, and species distributions.}, } @article {pmid29785479, year = {2018}, author = {Kulsum, U and Kapil, A and Singh, H and Kaur, P}, title = {NGSPanPipe: A Pipeline for Pan-genome Identification in Microbial Strains from Experimental Reads.}, journal = {Advances in experimental medicine and biology}, volume = {1052}, number = {}, pages = {39-49}, doi = {10.1007/978-981-10-7572-8_4}, pmid = {29785479}, issn = {0065-2598}, mesh = {Bacteria/classification/*genetics/isolation & purification ; Databases, Genetic ; *Genome, Bacterial ; High-Throughput Nucleotide Sequencing ; }, abstract = {Recent advancements in sequencing technologies have decreased both time span and cost for sequencing the whole bacterial genome. High-throughput Next-Generation Sequencing (NGS) technology has led to the generation of enormous data concerning microbial populations publically available across various repositories. As a consequence, it has become possible to study and compare the genomes of different bacterial strains within a species or genus in terms of evolution, ecology and diversity. Studying the pan-genome provides insights into deciphering microevolution, global composition and diversity in virulence and pathogenesis of a species. It can also assist in identifying drug targets and proposing vaccine candidates. The effective analysis of these large genome datasets necessitates the development of robust tools. Current methods to develop pan-genome do not support direct input of raw reads from the sequencer machine but require preprocessing of reads as an assembled protein/gene sequence file or the binary matrix of orthologous genes/proteins. We have designed an easy-to-use integrated pipeline, NGSPanPipe, which can directly identify the pan-genome from short reads. The output from the pipeline is compatible with other pan-genome analysis tools. We evaluated our pipeline with other methods for developing pan-genome, i.e. reference-based assembly and de novo assembly using simulated reads of Mycobacterium tuberculosis. The single script pipeline (pipeline.pl) is applicable for all bacterial strains. It integrates multiple in-house Perl scripts and is freely accessible from https://github.com/Biomedinformatics/NGSPanPipe .}, } @article {pmid29785463, year = {2018}, author = {Smith, WB and Cuenca Lara, RA and Delgado Caballero, CE and Godínez Valdivia, CI and Kapron, JS and Leyva Reyes, JC and Meneses Tovar, CL and Miles, PD and Oswalt, SN and Ramírez Salgado, M and Song, XA and Stinson, G and Villela Gaytán, SA}, title = {The North American Forest Database: going beyond national-level forest resource assessment statistics.}, journal = {Environmental monitoring and assessment}, volume = {190}, number = {6}, pages = {350}, pmid = {29785463}, issn = {1573-2959}, mesh = {*Conservation of Natural Resources ; *Databases, Factual ; Ecosystem ; Environmental Monitoring/*methods ; Forestry ; Forests ; Trees/*growth & development ; United States ; }, abstract = {Forests cannot be managed sustainably without reliable data to inform decisions. National Forest Inventories (NFI) tend to report national statistics, with sub-national stratification based on domestic ecological classification systems. It is becoming increasingly important to be able to report statistics on ecosystems that span international borders, as global change and globalization expand stakeholders' spheres of concern. The state of a transnational ecosystem can only be properly assessed by examining the entire ecosystem. In global forest resource assessments, it may be useful to break national statistics down by ecosystem, especially for large countries. The Inventory and Monitoring Working Group (IMWG) of the North American Forest Commission (NAFC) has begun developing a harmonized North American Forest Database (NAFD) for managing forest inventory data, enabling consistent, continental-scale forest assessment supporting ecosystem-level reporting and relational queries. The first iteration of the database contains data describing 1.9 billion ha, including 677.5 million ha of forest. Data harmonization is made challenging by the existence of definitions and methodologies tailored to suit national circumstances, emerging from each country's professional forestry development. This paper reports the methods used to synchronize three national forest inventories, starting with a small suite of variables and attributes.}, } @article {pmid29784002, year = {2018}, author = {Kawaguchi, H and Koike, S and Sakurai, R and Ohe, K}, title = {Association between number of institutions with coronary computed tomography angiography and regional mortality ratio of acute myocardial infarction: a nationwide ecological study using a spatial Bayesian model.}, journal = {International journal of health geographics}, volume = {17}, number = {1}, pages = {13}, pmid = {29784002}, issn = {1476-072X}, support = {JP16K00432//Japan Society for the Promotion of Science/International ; H26 Research on Statistics//Ministry of Health, Labour and Welfare/International ; Information 001//Ministry of Health, Labour and Welfare/International ; }, mesh = {Adolescent ; Adult ; Aged ; Aged, 80 and over ; Bayes Theorem ; Computed Tomography Angiography/*mortality/statistics & numerical data ; Coronary Artery Disease/*diagnostic imaging/*mortality ; Cross-Sectional Studies ; Female ; Humans ; Japan/epidemiology ; Male ; Middle Aged ; Mortality/trends ; Myocardial Infarction/*diagnostic imaging/*mortality ; Young Adult ; }, abstract = {BACKGROUND: Coronary computed tomography angiography (CTA) has demonstrated high diagnostic accuracy for detection of coronary artery stenosis, and healthcare providers can detect coronary artery disease in earlier stages before it develops into more serious clinical conditions such as acute myocardial infarction (AMI). We hypothesized that the mortality ratio of AMI in regions with a higher density of coronary CTA is lower than that in regions with a lower density of coronary CTA.

METHODS: This ecological and cross-sectional study using secondary data targeted all secondary medical service areas (SMSAs) in Japan (n = 349). We obtained the numbers of cardiologists, institutions with coronary CTA, and institutions with a cardiac catheterization laboratory (CCL) as medical resources, socioeconomic factors, lifestyle factors, exercise habit factors, and AMI mortality data from a Japanese national database. We evaluated the association between the number of these medical resources and the standardized mortality ratio (SMR) of AMI in each SMSA using a hierarchical Bayesian model accounting for spatial autocorrelation (i.e., a conditional autoregressive model). We assumed a Poisson distribution for the observed number of AMI-related deaths and set the expected number of AMI-related deaths as the offset variable.

RESULTS: The number of institutions with coronary CTA was negatively and significantly associated with the SMR of AMI (relative risk [RR] 0.900; 95% credible interval [CI] 0.848-0.953), while the SMR in each SMSA was not significantly associated with the number of either cardiologists (RR 0.997; 95% CI 0.988-1.004) or institutions with a CCL (RR 1.026; 95% CI 0.963-1.096).

CONCLUSIONS: We observed a significant association between the number of institutions with coronary CTA and the SMR of AMI. Effective allocation of coronary CTA in each region is recommended, and it would be important to clarify the standing position of coronary CTA in regional networking for AMI treatment in the future.}, } @article {pmid29782923, year = {2019}, author = {Wong, SH and Kwong, TNY and Wu, CY and Yu, J}, title = {Clinical applications of gut microbiota in cancer biology.}, journal = {Seminars in cancer biology}, volume = {55}, number = {}, pages = {28-36}, doi = {10.1016/j.semcancer.2018.05.003}, pmid = {29782923}, issn = {1096-3650}, mesh = {Computational Biology ; Gastrointestinal Microbiome/*genetics ; Humans ; *Metagenomics ; Neoplasms/diagnosis/*genetics/microbiology/therapy ; }, abstract = {The involvement of microorganisms in cancer has been increasing recognized. Collectively, microorganisms have been estimated to account for ∼20% of all cancers worldwide. Recent advances in metagenomics and bioinformatics have provided new insights on the microbial ecology in different tumors, pinpointing the roles of microorganisms in cancer formation, development and response to treatments. Furthermore, studies have emphasized the importance of host-microbial and inter-microbial interactions in the cancer microbiota. These studies have not only revolutionized our understanding of cancer biology, but also opened up new opportunities for cancer prevention, diagnosis, prognostication and treatment. This review article aims to summarize the microbiota in various cancers and their treatments, and explore clinical applications for such relevance.}, } @article {pmid29780034, year = {2018}, author = {Soyiri, IN and Sheikh, A and Reis, S and Kavanagh, K and Vieno, M and Clemens, T and Carnell, EJ and Pan, J and King, A and Beck, RC and Ward, HJT and Dibben, C and Robertson, C and Simpson, CR}, title = {Improving predictive asthma algorithms with modelled environment data for Scotland: an observational cohort study protocol.}, journal = {BMJ open}, volume = {8}, number = {5}, pages = {e023289}, pmid = {29780034}, issn = {2044-6055}, support = {//Medical Research Council/United Kingdom ; //Chief Scientist Office/United Kingdom ; }, mesh = {Air Pollutants/*analysis ; *Algorithms ; Asthma/*epidemiology ; Databases, Factual ; Environmental Monitoring/*methods ; Female ; Humans ; Logistic Models ; Longitudinal Studies ; Male ; Multicenter Studies as Topic ; Observational Studies as Topic ; Primary Health Care/organization & administration ; Research Design ; Retrospective Studies ; Scotland/epidemiology ; }, abstract = {INTRODUCTION: Asthma has a considerable, but potentially, avoidable burden on many populations globally. Scotland has some of the poorest health outcomes from asthma. Although ambient pollution, weather changes and sociodemographic factors have been associated with asthma attacks, it remains unclear whether modelled environment data and geospatial information can improve population-based asthma predictive algorithms. We aim to create the afferent loop of a national learning health system for asthma in Scotland. We will investigate the associations between ambient pollution, meteorological, geospatial and sociodemographic factors and asthma attacks.

METHODS AND ANALYSIS: We will develop and implement a secured data governance and linkage framework to incorporate primary care health data, modelled environment data, geospatial population and sociodemographic data. Data from 75 recruited primary care practices (n=500 000 patients) in Scotland will be used. Modelled environment data on key air pollutants at a horizontal resolution of 5 km×5 km at hourly time steps will be generated using the EMEP4UK atmospheric chemistry transport modelling system for the datazones of the primary care practices' populations. Scottish population census and education databases will be incorporated into the linkage framework for analysis. We will then undertake a longitudinal retrospective observational analysis. Asthma outcomes include asthma hospitalisations and oral steroid prescriptions. Using a nested case-control study design, associations between all covariates will be measured using conditional logistic regression to account for the matched design and to identify suitable predictors and potential candidate algorithms for an asthma learning health system in Scotland.Findings from this study will contribute to the development of predictive algorithms for asthma outcomes and be used to form the basis for our learning health system prototype.

ETHICS AND DISSEMINATION: The study received National Health Service Research Ethics Committee approval (16/SS/0130) and also obtained permissions via the Public Benefit and Privacy Panel for Health and Social Care in Scotland to access, collate and use the following data sets: population and housing census for Scotland; Scottish education data via the Scottish Exchange of Data and primary care data from general practice Data Custodians. Analytic code will be made available in the open source GitHub website. The results of this study will be published in international peer reviewed journals.}, } @article {pmid29779713, year = {2018}, author = {Kawaguchi, H and Koike, S and Ohe, K}, title = {Regional differences in electronic medical record adoption in Japan: A nationwide longitudinal ecological study.}, journal = {International journal of medical informatics}, volume = {115}, number = {}, pages = {114-119}, doi = {10.1016/j.ijmedinf.2018.05.002}, pmid = {29779713}, issn = {1872-8243}, mesh = {*Diffusion of Innovation ; *Electronic Health Records ; Health Facilities ; Hospitals, Private ; Humans ; Japan ; Longitudinal Studies ; Physicians ; }, abstract = {PURPOSE: Regional differences in the adoption of electronic medical records (EMR) are a major problem, yet little is known about these differences internationally. We analyzed regional differences in EMR adoption in Japan and evaluated factors associated with these differences.

METHODS: This nationwide ecological study used secondary data from all secondary medical service areas (SMSAs) in fiscal years 2008 (n = 348) and 2014 (n = 344). For each SMSA we collected the following information from a Japanese national database: the number of medical facilities that had adopted EMR, the population density, the average per capita income, the number of working doctors per 1000 people, and the proportion of interns to all working doctors. To adjust for medical facility characteristics in each SMSA, such as number of beds, public versus private hospital, and hospital type (psychiatric or other), we estimated the standardized adoption ratio (SAR) for EMR adoption, modeled on the standardized mortality ratio. We calculated Moran's I for the SAR and investigated whether the SAR had spatial autocorrelations. We evaluated the association between the SAR and regional factors with a conditional autoregressive model. We compared these results in 2008 and 2014, for both hospitals and clinics.

RESULTS: While the EMR adoption rate in SMSAs increased, Moran's I of the SAR in hospitals was close to 1 in both 2008 and 2014, and Moran's I of the SAR in clinics increased from 2008 to 2014. For hospitals, there was a significant association between the proportion of interns to all working doctors and the SAR only in 2008. For clinics, average income in the SMSA was positively associated with the SAR, whereas the number of working doctors was negatively associated with the SAR in both 2008 and 2014. Population density was positively associated with the SAR only in 2014.

CONCLUSION: From 2008 to 2014, EMR adoption in Japan generally increased, but geographical differences did not improve. Regional factors associated with the SAR were different for hospitals than for clinics. Therefore, the government should take different approaches for clinics and hospitals to improve regional differences in EMR adoption, especially in providing financial and technical support.}, } @article {pmid29778844, year = {2018}, author = {Zheng, J and Cao, J and Mao, Y and Su, Y and Wang, J}, title = {Identification of microRNAs with heat stress responsive and immune properties in Marsupenaeus japonicus based on next-generation sequencing and bioinformatics analysis: Essential regulators in the heat stress-host interactions.}, journal = {Fish & shellfish immunology}, volume = {81}, number = {}, pages = {390-398}, doi = {10.1016/j.fsi.2018.05.030}, pmid = {29778844}, issn = {1095-9947}, mesh = {Animals ; Computational Biology ; Genes, Viral ; *Heat-Shock Response/genetics/immunology ; Host-Pathogen Interactions ; *MicroRNAs/genetics/immunology ; *Penaeidae/genetics/immunology/virology ; Sequence Analysis, RNA ; White spot syndrome virus 1/*genetics ; }, abstract = {Summer mortality syndrome is one of the most serious issue for Marsupenaeus japonicus aquaculture in China. Since it causes massive economic loss and threatens sustainability of M. japonicus aquaculture industry, thus, there is an urgent desire to reveal the heat stress-host interactions mechanisms that lead to mass mortalities of M. japonicus in hot summer months. MicroRNAs (miRNAs) are small noncoding RNAs that involved in regulation of diverse biological processes, including stress and immune response, and might serve as potential regulators in the heat stress-host interactions. In the present study, miRNAs with heat stress responsive and immune properties were identified and characterized in M. japonicus by small RNA sequencing and bioinformatics analysis. In total, 79 host miRNAs were identified, among which 15 miRNAs were differentially expressed in response to heat stress. Target genes prediction and function annotation revealed that a variety of host cellular processes, such as signal transduction, transcription, anti-stress response, ribosomal biogenesis, lipid metabolism, cytoskeleton, etc, were potentially subject to miRNA-mediated regulation in response to heat stress. Furthermore, a total of 30 host miRNAs that potentially involved in interaction with white spot syndrome virus (WSSV) were obtained via predicting and analyzing the target genes from WSSV. The results showed that a batch of WSSV genes that code for structural proteins and enzymes that are essential for WSSV infection and proliferation, such as envelope proteins, capsid proteins, immediate-early proteins, collagen-like protein, protein kinase, thymidylate synthetase, TATA-box bind protein, etc, were predicted to be targeted by host miRNAs. Several of the host miRNAs with predicted antiviral capacity were down-regulated under heat stress, indicating a repression of host miRNA-mediated antiviral immune response. This study highlighted the essential roles of host miRNAs in the heat stress-host interactions and provided valuable information for further investigation on the mechanism of miRNA-mediated heat stress and immune response of shrimp.}, } @article {pmid29777837, year = {2018}, author = {Kropinski, AM}, title = {Bacteriophage research - What we have learnt and what still needs to be addressed.}, journal = {Research in microbiology}, volume = {169}, number = {9}, pages = {481-487}, doi = {10.1016/j.resmic.2018.05.002}, pmid = {29777837}, issn = {1769-7123}, mesh = {Anti-Bacterial Agents/administration & dosage/adverse effects/history ; *Bacteriophages/classification ; Classification ; Computational Biology/history ; Genomics/history ; History, 20th Century ; History, 21st Century ; Phage Therapy/history ; Research/*history ; Research Design ; }, abstract = {Research on bacteriophages has significantly enhanced our understanding of molecular biology, the genomes of prokaryotic cells, and viral ecology. Phages and lysins offer a viable alternative to the declining utility of antibiotics in this post-antibiotic era. They also provide ideal teaching tools for genomics and bioinformatics. This article touches on the first 100 years of phage research with the author commenting on what he thinks are the highlights, and what needs to be addressed.}, } @article {pmid29776375, year = {2018}, author = {Kaufman, EL and Stone, NE and Scoles, GA and Hepp, CM and Busch, JD and Wagner, DM}, title = {Range-wide genetic analysis of Dermacentor variabilis and its Francisella-like endosymbionts demonstrates phylogeographic concordance between both taxa.}, journal = {Parasites & vectors}, volume = {11}, number = {1}, pages = {306}, pmid = {29776375}, issn = {1756-3305}, support = {2010-65104-20386//National Institute of Food and Agriculture/International ; }, mesh = {Animals ; Arachnid Vectors/microbiology ; Canada ; Coxiella burnetii/genetics/pathogenicity ; DNA, Bacterial/genetics ; Dermacentor/classification/*genetics/*microbiology ; Disease Vectors ; Francisella/classification/*genetics/pathogenicity ; Genes, Mitochondrial/genetics ; Humans ; *Phylogeny ; Phylogeography ; RNA, Ribosomal, 16S/genetics ; Rickettsia/genetics/pathogenicity ; Sequence Analysis, DNA/methods ; Symbiosis/genetics ; United States ; }, abstract = {BACKGROUND: The American dog tick, Dermacentor variabilis, is an important vector of pathogens to humans, wildlife and domestic animals in North America. Although this tick species is widely distributed in the USA and Canada, knowledge of its range-wide phylogeographic patterns remains incomplete.

METHODS: We carried out a phylogenetic analysis of D. variabilis using samples collected from 26 USA states and five Canadian provinces. Tick samples (n = 1053 in total) originated from two main sources: existing archives (2000-2011), and new collections made from 2012 to 2013. We sequenced a 691 bp fragment of the cox1 gene from a subset (n = 332) of geographically diverse D. variabilis. DNA extracted from individual ticks (n = 1053) was also screened for a Francisella-like endosymbiont, using a targeted 16S rRNA sequencing approach, and important pathogens (Rickettsia spp. and Coxiella burnetii), using species-specific quantitative PCR assays.

RESULTS: Maximum parsimony analysis of cox1 sequences revealed two major groups within D. variabilis with distinct geographical distributions: one from the eastern USA/Canada (Group 1) and one from the west coast states of the USA (California and Washington; Group 2). However, genetic subdivisions within both of these two major groups were weak to moderate and not tightly correlated with geography. We found molecular signatures consistent with Francisella-like endosymbionts in 257 of the DNA extracts from the 1053 individual ticks, as well as Rickettsia spp. and Coxiella burnetii in a small number of ticks (n = 29 and 2, respectively). Phylogenetic patterns for Francisella-like endosymbionts, constructed using sequence data from the bacterial 16S rRNA locus, were similar to those for D. variabilis, with two major groups that had a nearly perfect one-to-one correlation with the two major groups within D. variabilis.

CONCLUSIONS: Our findings reveal a distinct phylogenetic split between the two major D. variabilis populations. However, high levels of genetic mixture among widely separated geographical localities occur within each of these two major groups. Furthermore, our phylogenetic analyses provide evidence of long-term tick-symbiont co-evolution. This work has implications for understanding the dispersal and evolutionary ecology of D. variabilis and associated vector-borne diseases.}, } @article {pmid29776351, year = {2018}, author = {Buetti-Dinh, A and Jensen, R and Friedman, R}, title = {A computational study of hedgehog signalling involved in basal cell carcinoma reveals the potential and limitation of combination therapy.}, journal = {BMC cancer}, volume = {18}, number = {1}, pages = {569}, pmid = {29776351}, issn = {1471-2407}, support = {CAN 2015/387//Cancerfonden/ ; }, mesh = {Anilides/pharmacology/therapeutic use ; Antineoplastic Combined Chemotherapy Protocols/pharmacology/*therapeutic use ; Carcinoma, Basal Cell/*drug therapy/genetics/pathology ; Computational Biology ; Computer Simulation ; Datasets as Topic ; Drug Resistance, Neoplasm/genetics ; Hedgehog Proteins/*metabolism ; Humans ; Mutation ; Phosphatidylinositol 3-Kinases/metabolism ; Phosphodiesterase Inhibitors/therapeutic use ; Phosphoinositide-3 Kinase Inhibitors ; Phosphoric Diester Hydrolases/metabolism ; Proto-Oncogene Proteins c-akt/antagonists & inhibitors/metabolism ; Pyridines/pharmacology/therapeutic use ; Signal Transduction/*drug effects/genetics ; Skin Neoplasms/*drug therapy/genetics/pathology ; Smoothened Receptor/antagonists & inhibitors/metabolism ; }, abstract = {BACKGROUND: The smoothened (SMO) receptor is an essential component of the Sonic hedgehog (SHH) signalling, which is associated with the development of skin basal cell carcinoma (BCC). SMO inhibitors are indicated for BCC patients when surgical treatment or radiation therapy are not possible. Unfortunately, SMO inhibitors are not always well tolerated due to severe side effects, and their therapeutical success is limited by resistance mutations.

METHODS: We investigated how common are resistance-causing mutations in two genomic databases which are not linked to BCC or other cancers, namely 1000 Genomes and ExAC. To examine the potential for combination therapy or other treatments, we further performed knowledge-based simulations of SHH signalling, in the presence or absence of SMO and PI3K/Akt inhibitors.

RESULTS: The database analysis revealed that of 18 known mutations associated with Vismodegib-resistance, three were identified in the databases. Treatment of individuals carrying such mutations is thus liable to fail a priori. Analysis of the simulations suggested that a combined inhibition of SMO and the PI3K/Akt signalling pathway may provide an effective reduction in tumour proliferation. However, the inhibition dosage of SMO and PI3K/Akt depended on the activity of phosphodiesterases (PDEs). Under high PDEs activities, SMO became the most important control node of the network. By applying PDEs inhibition, the control potential of SMO decreased and PI3K appeared as a significant factor in controlling tumour proliferation.

CONCLUSIONS: Our systems biology approach employs knowledge-based computer simulations to help interpret the large amount of data available in public databases, and provides application-oriented solutions for improved cancer resistance treatments.}, } @article {pmid29774660, year = {2018}, author = {Kato, Y and Kondoh, M and Ishikawa, NF and Togashi, H and Kohmatsu, Y and Yoshimura, M and Yoshimizu, C and Haraguchi, TF and Osada, Y and Ohte, N and Tokuchi, N and Okuda, N and Miki, T and Tayasu, I}, title = {Using food network unfolding to evaluate food-web complexity in terms of biodiversity: theory and applications.}, journal = {Ecology letters}, volume = {21}, number = {7}, pages = {1065-1074}, doi = {10.1111/ele.12973}, pmid = {29774660}, issn = {1461-0248}, mesh = {*Biodiversity ; Biomass ; Ecosystem ; *Food Chain ; }, abstract = {Food-web complexity often hinders disentangling functionally relevant aspects of food-web structure and its relationships to biodiversity. Here, we present a theoretical framework to evaluate food-web complexity in terms of biodiversity. Food network unfolding is a theoretical method to transform a complex food web into a linear food chain based on ecosystem processes. Based on this method, we can define three biodiversity indices, horizontal diversity (DH), vertical diversity (DV) and range diversity (DR), which are associated with the species diversity within each trophic level, diversity of trophic levels, and diversity in resource use, respectively. These indices are related to Shannon's diversity index (H'), where H' = DH + DV - DR . Application of the framework to three riverine macroinvertebrate communities revealed that D indices, calculated from biomass and stable isotope features, captured well the anthropogenic, seasonal, or other within-site changes in food-web structures that could not be captured with H' alone.}, } @article {pmid29773560, year = {2018}, author = {Tomasini, M and Peischl, S}, title = {Establishment of Locally Adapted Mutations Under Divergent Selection.}, journal = {Genetics}, volume = {209}, number = {3}, pages = {885-895}, pmid = {29773560}, issn = {1943-2631}, mesh = {Adaptation, Biological ; Animals ; Computational Biology/*methods ; Gene Flow ; Genetics, Population ; Humans ; Models, Genetic ; *Mutation ; Population Dynamics ; *Selection, Genetic ; }, abstract = {We study the establishment probabilities of locally adapted mutations using a multi-type branching process framework. We find a surprisingly simple and intuitive analytical approximation for the establishment probabilities in a symmetric two-deme model under the assumption of weak (positive) selection. This is the first analytical closed-form approximation for arbitrary migration rate to appear in the literature. We find that the establishment probability lies between the weak and the strong migration limits if we condition the origin of the mutation to the deme where it is advantageous. This is not the case when we condition the mutation to first occur in a deme where it is disadvantageous. In this case we find that an intermediate migration rate maximizes the probability of establishment. We extend our results to the cases of multiple demes, two demes with asymmetric rates of gene flow, and asymmetric carrying capacities. The latter case allows us to illustrate how density regulation can affect establishment probabilities. Finally, we use our results to investigate the role of gene flow on the rate of local adaptation and identify cases in which intermediate amounts of gene flow facilitate the rate of local adaptation as compared to two populations without gene flow.}, } @article {pmid29764375, year = {2018}, author = {Chou, CH and Huang, HY and Huang, WC and Hsu, SD and Hsiao, CD and Liu, CY and Chen, YH and Liu, YC and Huang, WY and Lee, ML and Chen, YC and Huang, HD}, title = {The aquatic animals' transcriptome resource for comparative functional analysis.}, journal = {BMC genomics}, volume = {19}, number = {Suppl 2}, pages = {103}, pmid = {29764375}, issn = {1471-2164}, mesh = {Animals ; Aquatic Organisms/*genetics ; Databases, Genetic ; Gene Expression Profiling/*methods ; Gene Regulatory Networks ; Genomics/*methods ; High-Throughput Nucleotide Sequencing/methods ; Molecular Sequence Annotation ; Phylogeny ; Sequence Analysis, RNA/methods ; Software ; }, abstract = {BACKGROUND: Aquatic animals have great economic and ecological importance. Among them, non-model organisms have been studied regarding eco-toxicity, stress biology, and environmental adaptation. Due to recent advances in next-generation sequencing techniques, large amounts of RNA-seq data for aquatic animals are publicly available. However, currently there is no comprehensive resource exist for the analysis, unification, and integration of these datasets. This study utilizes computational approaches to build a new resource of transcriptomic maps for aquatic animals. This aquatic animal transcriptome map database dbATM provides de novo assembly of transcriptome, gene annotation and comparative analysis of more than twenty aquatic organisms without draft genome.

RESULTS: To improve the assembly quality, three computational tools (Trinity, Oases and SOAPdenovo-Trans) were employed to enhance individual transcriptome assembly, and CAP3 and CD-HIT-EST software were then used to merge these three assembled transcriptomes. In addition, functional annotation analysis provides valuable clues to gene characteristics, including full-length transcript coding regions, conserved domains, gene ontology and KEGG pathways. Furthermore, all aquatic animal genes are essential for comparative genomics tasks such as constructing homologous gene groups and blast databases and phylogenetic analysis.

CONCLUSION: In conclusion, we establish a resource for non model organism aquatic animals, which is great economic and ecological importance and provide transcriptomic information including functional annotation and comparative transcriptome analysis. The database is now publically accessible through the URL http://dbATM.mbc.nctu.edu.tw/ .}, } @article {pmid29762668, year = {2018}, author = {Almeida, A and Mitchell, AL and Tarkowska, A and Finn, RD}, title = {Benchmarking taxonomic assignments based on 16S rRNA gene profiling of the microbiota from commonly sampled environments.}, journal = {GigaScience}, volume = {7}, number = {5}, pages = {}, pmid = {29762668}, issn = {2047-217X}, mesh = {Bacteria/*classification/*genetics ; Biodiversity ; Databases, Genetic ; *Environmental Microbiology ; Gastrointestinal Microbiome/genetics ; Humans ; Microbiota/*genetics ; Oceans and Seas ; Phylogeny ; Principal Component Analysis ; RNA, Ribosomal, 16S/*genetics ; Soil ; }, abstract = {BACKGROUND: Taxonomic profiling of ribosomal RNA (rRNA) sequences has been the accepted norm for inferring the composition of complex microbial ecosystems. Quantitative Insights Into Microbial Ecology (QIIME) and mothur have been the most widely used taxonomic analysis tools for this purpose, with MAPseq and QIIME 2 being two recently released alternatives. However, no independent and direct comparison between these four main tools has been performed. Here, we compared the default classifiers of MAPseq, mothur, QIIME, and QIIME 2 using synthetic simulated datasets comprised of some of the most abundant genera found in the human gut, ocean, and soil environments. We evaluate their accuracy when paired with both different reference databases and variable sub-regions of the 16S rRNA gene.

FINDINGS: We show that QIIME 2 provided the best recall and F-scores at genus and family levels, together with the lowest distance estimates between the observed and simulated samples. However, MAPseq showed the highest precision, with miscall rates consistently <2%. Notably, QIIME 2 was the most computationally expensive tool, with CPU time and memory usage almost 2 and 30 times higher than MAPseq, respectively. Using the SILVA database generally yielded a higher recall than using Greengenes, while assignment results of different 16S rRNA variable sub-regions varied up to 40% between samples analysed with the same pipeline.

CONCLUSIONS: Our results support the use of either QIIME 2 or MAPseq for optimal 16S rRNA gene profiling, and we suggest that the choice between the two should be based on the level of recall, precision, and/or computational performance required.}, } @article {pmid29760203, year = {2018}, author = {Feulner, PGD and Schwarzer, J and Haesler, MP and Meier, JI and Seehausen, O}, title = {A Dense Linkage Map of Lake Victoria Cichlids Improved the Pundamilia Genome Assembly and Revealed a Major QTL for Sex-Determination.}, journal = {G3 (Bethesda, Md.)}, volume = {8}, number = {7}, pages = {2411-2420}, pmid = {29760203}, issn = {2160-1836}, mesh = {Animals ; *Chromosome Mapping ; Cichlids/*genetics ; Databases, Genetic ; Evolution, Molecular ; *Genetic Linkage ; Genetic Markers ; *Genomics/methods ; Genotype ; High-Throughput Nucleotide Sequencing ; Lakes ; *Quantitative Trait Loci ; Recombination, Genetic ; *Sex Determination Processes ; Synteny ; }, abstract = {Genetic linkage maps are essential for comparative genomics, high quality genome sequence assembly and fine scale quantitative trait locus (QTL) mapping. In the present study we identified and genotyped markers via restriction-site associated DNA (RAD) sequencing and constructed a genetic linkage map based on 1,597 SNP markers of an interspecific F2 cross of two closely related Lake Victoria cichlids (Pundamilia pundamilia and P sp. 'red head'). The SNP markers were distributed on 22 linkage groups and the total map size was 1,594 cM with an average marker distance of 1.01 cM. This high-resolution genetic linkage map was used to anchor the scaffolds of the Pundamilia genome and estimate recombination rates along the genome. Via QTL mapping we identified a major QTL for sex in a ∼1.9 Mb region on Pun-LG10, which is homologous to Oreochromis niloticus LG 23 (Ore-LG23) and includes a well-known vertebrate sex-determination gene (amh).}, } @article {pmid29758899, year = {2018}, author = {Feng, Y and Yang, Q and Tong, X and Chen, L}, title = {Evaluating land ecological security and examining its relationships with driving factors using GIS and generalized additive model.}, journal = {The Science of the total environment}, volume = {633}, number = {}, pages = {1469-1479}, doi = {10.1016/j.scitotenv.2018.03.272}, pmid = {29758899}, issn = {1879-1026}, abstract = {Land ecological security (LES) refers to the environmental health and sustainability of the land resources and ecosystems, which are substantially affected by biophysical and socio-economic factors. We assess the spatiotemporal patterns of LES in Ningbo city on the southeast coast of China from 1975 to 2015 and explore the effects of driving factors. Expert evaluation is used to estimate the LES score for each 2×2km grid and map the patterns by Kriging. Five levels of LES are used: very secure, secure, neutral, insecure and very insecure. A generalized additive model (GAM) captures the relationships between LES and driving factors, and identifies the dominant factors. Our results show that the Ningbo LES has been deteriorating since 1975, and it is now very insecure in Ningbo city center and the central area of the satellite city Cixi. The dominant factors affecting LES are distances to city center (Dcity), district center (Ddistrict) and road networks (Droads), and the moving window built-up area (Dndbi). Among these, Dndbi is most important as inferred by the highest explained deviance of the GAM. This study improves our understanding of the spatiotemporal patterns of LES in Ningbo and how LES changes. As a result, it provides insight to help local governments optimize land-use configuration, potentially improving the environment and ecosystems and creating a more environmentally friendly city.}, } @article {pmid29757994, year = {2018}, author = {Ibrahim, B and Arkhipova, K and Andeweg, AC and Posada-Céspedes, S and Enault, F and Gruber, A and Koonin, EV and Kupczok, A and Lemey, P and McHardy, AC and McMahon, DP and Pickett, BE and Robertson, DL and Scheuermann, RH and Zhernakova, A and Zwart, MP and Schönhuth, A and Dutilh, BE and Marz, M}, title = {Bioinformatics Meets Virology: The European Virus Bioinformatics Center's Second Annual Meeting.}, journal = {Viruses}, volume = {10}, number = {5}, pages = {}, pmid = {29757994}, issn = {1999-4915}, support = {MC_UU_12014/12/MRC_/Medical Research Council/United Kingdom ; }, mesh = {*Computational Biology ; Congresses as Topic ; DNA Viruses ; Ecology ; Genomics ; Humans ; Societies, Scientific ; Software ; *Virology ; }, abstract = {The Second Annual Meeting of the European Virus Bioinformatics Center (EVBC), held in Utrecht, Netherlands, focused on computational approaches in virology, with topics including (but not limited to) virus discovery, diagnostics, (meta-)genomics, modeling, epidemiology, molecular structure, evolution, and viral ecology. The goals of the Second Annual Meeting were threefold: (i) to bring together virologists and bioinformaticians from across the academic, industrial, professional, and training sectors to share best practice; (ii) to provide a meaningful and interactive scientific environment to promote discussion and collaboration between students, postdoctoral fellows, and both new and established investigators; (iii) to inspire and suggest new research directions and questions. Approximately 120 researchers from around the world attended the Second Annual Meeting of the EVBC this year, including 15 renowned international speakers. This report presents an overview of new developments and novel research findings that emerged during the meeting.}, } @article {pmid29752497, year = {2018}, author = {Hornseth, ML and Pigeon, KE and MacNearney, D and Larsen, TA and Stenhouse, G and Cranston, J and Finnegan, L}, title = {Motorized Activity on Legacy Seismic Lines: A Predictive Modeling Approach to Prioritize Restoration Efforts.}, journal = {Environmental management}, volume = {62}, number = {3}, pages = {595-607}, pmid = {29752497}, issn = {1432-1009}, mesh = {Alberta ; Animals ; *Conservation of Natural Resources ; *Ecosystem ; Endangered Species ; *Environmental Monitoring ; Forests ; Geographic Information Systems ; Human Activities ; Humans ; *Models, Theoretical ; *Reindeer ; }, abstract = {Natural regeneration of seismic lines, cleared for hydrocarbon exploration, is slow and often hindered by vegetation damage, soil compaction, and motorized human activity. There is an extensive network of seismic lines in western Canada which is known to impact forest ecosystems, and seismic lines have been linked to declines in woodland caribou (Rangifer tarandus caribou). Seismic line restoration is costly, but necessary for caribou conservation to reduce cumulative disturbance. Understanding where motorized activity may be impeding regeneration of seismic lines will aid in prioritizing restoration. Our study area in west-central Alberta, encompassed five caribou ranges where restoration is required under federal species at risk recovery strategies, hence prioritizing seismic lines for restoration is of immediate conservation value. To understand patterns of motorized activity on seismic lines, we evaluated five a priori hypotheses using a predictive modeling framework and Geographic Information System variables across three landscapes in the foothills and northern boreal regions of Alberta. In the northern boreal landscape, motorized activity was most common in dry areas with a large industrial footprint. In highly disturbed areas of the foothills, motorized activity on seismic lines increased with low vegetation heights, relatively dry soils, and further from forest cutblocks, while in less disturbed areas of the foothills, motorized activity on seismic lines decreased proportional to seismic line density, slope steepness, and white-tailed deer abundance, and increased proportional with distance to roads. We generated predictive maps of high motorized activity, identifying 21,777 km of seismic lines where active restoration could expedite forest regeneration.}, } @article {pmid29751427, year = {2018}, author = {Meng, L and Huang, J and Dong, J}, title = {Assessment of rural ecosystem health and type classification in Jiangsu province, China.}, journal = {The Science of the total environment}, volume = {615}, number = {}, pages = {1218-1228}, doi = {10.1016/j.scitotenv.2017.09.312}, pmid = {29751427}, issn = {1879-1026}, mesh = {China ; Conservation of Natural Resources ; *Ecosystem ; *Environmental Monitoring ; Geographic Information Systems ; Urbanization ; }, abstract = {Quantitative analysis of rural ecosystem health (REH) is required to comprehend the spatial differentiation of rural landscape and promote rural sustainable development under the pressure of urbanization and industrialization, especially those with dramatic changes in rural ecology of China and other developing countries. In this study, taking Jiangsu province as the case study, appropriate indicators were selected in the perspective of compound ecosystem and the rural ecosystem health index (REHI) was developed including four rural ecological subsystems of resource, environmental, social and economic. The comprehensive indicator assessment models and geographic information system (GIS) spatial methods were used to analyze the REH status and spatial differentiation of 57 counties in Jiangsu province. The REH scores of 57 rural counties were in a higher range of 0.686-0.882 and fluctuating increased from north to south, indicating that the rural ecosystem in Jiangsu province was at a relatively healthy level and counties in southern Jiangsu were healthier than those in central and northern regions. The spatial concentration of REH in Jiangsu was poor and the spatial distribution of four subsystems health levels were significantly different by spatial Gini coefficient analysis. The REH of 57 counties in Jiangsu province were classified into 13 types according to the identification of the health levels and quantity of four subsystems. Moreover, we analyzed the influencing factors of each type and proposed paths to promote the development and management of rural ecosystem.}, } @article {pmid29751021, year = {2018}, author = {Ibrahim, B and McMahon, DP and Hufsky, F and Beer, M and Deng, L and Mercier, PL and Palmarini, M and Thiel, V and Marz, M}, title = {A new era of virus bioinformatics.}, journal = {Virus research}, volume = {251}, number = {}, pages = {86-90}, doi = {10.1016/j.virusres.2018.05.009}, pmid = {29751021}, issn = {1872-7492}, support = {MC_UU_12014/10/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Computational Biology/*methods/trends ; Virology/*methods/trends ; Viruses/*genetics/*growth & development ; }, abstract = {Despite the recognized excellence of virology and bioinformatics, these two communities have interacted surprisingly sporadically, aside from some pioneering work on HIV-1 and influenza. Bringing together the expertise of bioinformaticians and virologists is crucial, since very specific but fundamental computational approaches are required for virus research, particularly in an era of big data. Collaboration between virologists and bioinformaticians is necessary to improve existing analytical tools, cloud-based systems, computational resources, data sharing approaches, new diagnostic tools, and bioinformatic training. Here, we highlight current progress and discuss potential avenues for future developments in this promising era of virus bioinformatics. We end by presenting an overview of current technologies, and by outlining some of the major challenges and advantages that bioinformatics will bring to the field of virology.}, } @article {pmid29748988, year = {2018}, author = {Metcalfe, DB and Rocha, W and Balch, JK and Brando, PM and Doughty, CE and Malhi, Y}, title = {Impacts of fire on sources of soil CO2 efflux in a dry Amazon rain forest.}, journal = {Global change biology}, volume = {24}, number = {8}, pages = {3629-3641}, doi = {10.1111/gcb.14305}, pmid = {29748988}, issn = {1365-2486}, mesh = {Brazil ; Carbon ; Carbon Dioxide/*chemistry ; Climate Change ; Environmental Monitoring ; *Fires ; Human Activities ; Rain ; *Rainforest ; Soil/*chemistry ; Time Factors ; Trees ; }, abstract = {Fire at the dry southern margin of the Amazon rainforest could have major consequences for regional soil carbon (C) storage and ecosystem carbon dioxide (CO2) emissions, but relatively little information exists about impacts of fire on soil C cycling within this sensitive ecotone. We measured CO2 effluxes from different soil components (ground surface litter, roots, mycorrhizae, soil organic matter) at a large-scale burn experiment designed to simulate a severe but realistic potential future scenario for the region (Fire plot) in Mato Grosso, Brazil, over 1 year, and compared these measurements to replicated data from a nearby, unmodified Control plot. After four burns over 5 years, soil CO2 efflux (Rs) was ~5.5 t C ha[-1] year[-1] lower on the Fire plot compared to the Control. Most of the Fire plot Rs reduction was specifically due to lower ground surface litter and root respiration. Mycorrhizal respiration on both plots was around ~20% of Rs . Soil surface temperature appeared to be more important than moisture as a driver of seasonal patterns in Rs at the site. Regular fire events decreased the seasonality of Rs at the study site, due to apparent differences in environmental sensitivities among biotic and abiotic soil components. These findings may contribute toward improved predictions of the amount and temporal pattern of C emissions across the large areas of tropical forest facing increasing fire disturbances associated with climate change and human activities.}, } @article {pmid29745294, year = {2018}, author = {McDaniel, JT}, title = {Prevalence of chronic obstructive pulmonary disease: county-level risk factors based on the Social Ecological Model.}, journal = {Perspectives in public health}, volume = {138}, number = {4}, pages = {200-208}, doi = {10.1177/1757913918772598}, pmid = {29745294}, issn = {1757-9147}, mesh = {Adult ; Black or African American/statistics & numerical data ; Censuses ; Female ; Geographic Information Systems ; Hispanic or Latino/statistics & numerical data ; Humans ; Linear Models ; Local Government ; Male ; Middle Aged ; Poverty ; Prevalence ; Pulmonary Disease, Chronic Obstructive/*epidemiology ; Risk Factors ; Social Environment ; United States/epidemiology ; Young Adult ; }, abstract = {AIMS: Chronic obstructive pulmonary disease (COPD) was the third leading cause of death among Americans in 2014. Multiple factors, ranging from proximal (i.e. biological characteristics and behaviors) to distal (i.e. environmental characteristics and policies), have been shown to predict COPD outcomes. The Social Ecological Model (SEM), which specifies that five levels of influence (i.e. intrapersonal, interpersonal, institutional, community, and public policy factors) are implicated in the development of ill health, has not been used in epidemiological studies of COPD prevalence. A better understanding of the community-level correlates of COPD prevalence may improve community health practice.

METHODS: Using several sources of county-level secondary data (n = 646), changes in COPD prevalence from 2012 to 2014 were predicted from the five levels of the SEM using ordinary least squares (OLS) hierarchical linear regression. The geographic distribution of county-level changes in COPD prevalence was analyzed with a choropleth map.

RESULTS: County-level COPD prevalence increased by 4.76% between 2012 and 2014 overall; however, the greatest increases were observed among counties within the Appalachian region (i.e. counties in West Virginia). Results showed that the SEM, with five levels of influence, was a statistically significant framework for examining changes in county-level COPD prevalence, F = 10.21, p < .001, R[2] = 0.28. Statistically significant county-level predictors of changes in COPD prevalence included racial composition, ethnic composition, poverty, altitude, air pollution, and smoking policy.

CONCLUSION: COPD prevention may be assisted by the implementation of community-based programs rooted in a multilevel approach.}, } @article {pmid29745169, year = {2017}, author = {Shi, Y and Yun, YX and Liu, C and Chu, YQ}, title = {[Carbon footprint of buildings in the urban agglomeration of central Liaoning, China].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {28}, number = {6}, pages = {2040-2046}, doi = {10.13287/j.1001-9332.201706.007}, pmid = {29745169}, issn = {1001-9332}, mesh = {*Carbon Footprint ; China ; Environmental Monitoring ; Geographic Information Systems ; *Urbanization ; }, abstract = {With the development of urbanization in China, buildings consumed lots of material and energy. How to estimate carbon emission of buildings is an important scientific problem. Carbon footprint of the central Liaoning agglomeration was studied with carbon footprint approach, geographic information system (GIS) and high-resolution remote sensing (HRRS) technology. The results showed that the construction carbon footprint coefficient of central Liaoning urban agglomeration was 269.16 kg·m[-2]. The approach of interpreting total building area and spatial distribution with HRRS was effective, and the accuracy was 89%. The extraction approach was critical for total carbon footprint and spatial distribution estimation. The building area and total carbon footprint of central Liaoning urban agglomeration in descending order was Shenyang, Anshan, Fushun, Liao-yang, Yingkou, Tieling and Benxi. The annual average increment of footprint from 2011 to 2013 in descending order was Shenyang, Benxi, Fushun, Anshan, Tieling, Yingkou and Liaoyang. The accurate estimation of construction carbon footprint spatial and its distribution was of significance for the planning and optimization of carbon emission reduction.}, } @article {pmid29744581, year = {2018}, author = {Zeller, KA and Wattles, DW and DeStefano, S}, title = {Incorporating Road Crossing Data into Vehicle Collision Risk Models for Moose (Alces americanus) in Massachusetts, USA.}, journal = {Environmental management}, volume = {62}, number = {3}, pages = {518-528}, pmid = {29744581}, issn = {1432-1009}, mesh = {Accidents, Traffic/*statistics & numerical data ; Animals ; Deer/*physiology ; Geographic Information Systems ; Humans ; Massachusetts ; Models, Theoretical ; Population Density ; Probability ; }, abstract = {Wildlife-vehicle collisions are a human safety issue and may negatively impact wildlife populations. Most wildlife-vehicle collision studies predict high-risk road segments using only collision data. However, these data lack biologically relevant information such as wildlife population densities and successful road-crossing locations. We overcome this shortcoming with a new method that combines successful road crossings with vehicle collision data, to identify road segments that have both high biological relevance and high risk. We used moose (Alces americanus) road-crossing locations from 20 moose collared with Global Positioning Systems as well as moose-vehicle collision (MVC) data in the state of Massachusetts, USA, to create multi-scale resource selection functions. We predicted the probability of moose road crossings and MVCs across the road network and combined these surfaces to identify road segments that met the dual criteria of having high biological relevance and high risk for MVCs. These road segments occurred mostly on larger roadways in natural areas and were surrounded by forests, wetlands, and a heterogenous mix of land cover types. We found MVCs resulted in the mortality of 3% of the moose population in Massachusetts annually. Although there have been only three human fatalities related to MVCs in Massachusetts since 2003, the human fatality rate was one of the highest reported in the literature. The rate of MVCs relative to the size of the moose population and the risk to human safety suggest a need for road mitigation measures, such as fencing, animal detection systems, and large mammal-crossing structures on roadways in Massachusetts.}, } @article {pmid29743675, year = {2018}, author = {Damgaard, PB and Marchi, N and Rasmussen, S and Peyrot, M and Renaud, G and Korneliussen, T and Moreno-Mayar, JV and Pedersen, MW and Goldberg, A and Usmanova, E and Baimukhanov, N and Loman, V and Hedeager, L and Pedersen, AG and Nielsen, K and Afanasiev, G and Akmatov, K and Aldashev, A and Alpaslan, A and Baimbetov, G and Bazaliiskii, VI and Beisenov, A and Boldbaatar, B and Boldgiv, B and Dorzhu, C and Ellingvag, S and Erdenebaatar, D and Dajani, R and Dmitriev, E and Evdokimov, V and Frei, KM and Gromov, A and Goryachev, A and Hakonarson, H and Hegay, T and Khachatryan, Z and Khaskhanov, R and Kitov, E and Kolbina, A and Kubatbek, T and Kukushkin, A and Kukushkin, I and Lau, N and Margaryan, A and Merkyte, I and Mertz, IV and Mertz, VK and Mijiddorj, E and Moiyesev, V and Mukhtarova, G and Nurmukhanbetov, B and Orozbekova, Z and Panyushkina, I and Pieta, K and Smrčka, V and Shevnina, I and Logvin, A and Sjögren, KG and Štolcová, T and Taravella, AM and Tashbaeva, K and Tkachev, A and Tulegenov, T and Voyakin, D and Yepiskoposyan, L and Undrakhbold, S and Varfolomeev, V and Weber, A and Wilson Sayres, MA and Kradin, N and Allentoft, ME and Orlando, L and Nielsen, R and Sikora, M and Heyer, E and Kristiansen, K and Willerslev, E}, title = {137 ancient human genomes from across the Eurasian steppes.}, journal = {Nature}, volume = {557}, number = {7705}, pages = {369-374}, doi = {10.1038/s41586-018-0094-2}, pmid = {29743675}, issn = {1476-4687}, mesh = {Asia/ethnology ; Asian People/*genetics ; Europe/ethnology ; Farmers/history ; Genome, Human/*genetics ; *Grassland ; History, Ancient ; Human Migration/history ; Humans ; *Phylogeny ; White People/*genetics ; }, abstract = {For thousands of years the Eurasian steppes have been a centre of human migrations and cultural change. Here we sequence the genomes of 137 ancient humans (about 1× average coverage), covering a period of 4,000 years, to understand the population history of the Eurasian steppes after the Bronze Age migrations. We find that the genetics of the Scythian groups that dominated the Eurasian steppes throughout the Iron Age were highly structured, with diverse origins comprising Late Bronze Age herders, European farmers and southern Siberian hunter-gatherers. Later, Scythians admixed with the eastern steppe nomads who formed the Xiongnu confederations, and moved westward in about the second or third century BC, forming the Hun traditions in the fourth-fifth century AD, and carrying with them plague that was basal to the Justinian plague. These nomads were further admixed with East Asian groups during several short-term khanates in the Medieval period. These historical events transformed the Eurasian steppes from being inhabited by Indo-European speakers of largely West Eurasian ancestry to the mostly Turkic-speaking groups of the present day, who are primarily of East Asian ancestry.}, } @article {pmid29743352, year = {2018}, author = {de Barros Damgaard, P and Martiniano, R and Kamm, J and Moreno-Mayar, JV and Kroonen, G and Peyrot, M and Barjamovic, G and Rasmussen, S and Zacho, C and Baimukhanov, N and Zaibert, V and Merz, V and Biddanda, A and Merz, I and Loman, V and Evdokimov, V and Usmanova, E and Hemphill, B and Seguin-Orlando, A and Yediay, FE and Ullah, I and Sjögren, KG and Iversen, KH and Choin, J and de la Fuente, C and Ilardo, M and Schroeder, H and Moiseyev, V and Gromov, A and Polyakov, A and Omura, S and Senyurt, SY and Ahmad, H and McKenzie, C and Margaryan, A and Hameed, A and Samad, A and Gul, N and Khokhar, MH and Goriunova, OI and Bazaliiskii, VI and Novembre, J and Weber, AW and Orlando, L and Allentoft, ME and Nielsen, R and Kristiansen, K and Sikora, M and Outram, AK and Durbin, R and Willerslev, E}, title = {The first horse herders and the impact of early Bronze Age steppe expansions into Asia.}, journal = {Science (New York, N.Y.)}, volume = {360}, number = {6396}, pages = {}, pmid = {29743352}, issn = {1095-9203}, support = {/WT_/Wellcome Trust/United Kingdom ; 206194/WT_/Wellcome Trust/United Kingdom ; 207492/Z/17/Z/WT_/Wellcome Trust/United Kingdom ; T32 GM007197/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Asia ; Asian People/*genetics ; Chromosomes, Human, Y/genetics ; DNA, Ancient ; DNA, Mitochondrial/genetics ; *Domestication ; Europe ; *Genetic Drift ; *Genome, Human ; Grassland ; History, Ancient ; *Horses ; Human Migration/*history ; Humans ; Language ; Whole Genome Sequencing ; }, abstract = {The Yamnaya expansions from the western steppe into Europe and Asia during the Early Bronze Age (~3000 BCE) are believed to have brought with them Indo-European languages and possibly horse husbandry. We analyzed 74 ancient whole-genome sequences from across Inner Asia and Anatolia and show that the Botai people associated with the earliest horse husbandry derived from a hunter-gatherer population deeply diverged from the Yamnaya. Our results also suggest distinct migrations bringing West Eurasian ancestry into South Asia before and after, but not at the time of, Yamnaya culture. We find no evidence of steppe ancestry in Bronze Age Anatolia from when Indo-European languages are attested there. Thus, in contrast to Europe, Early Bronze Age Yamnaya-related migrations had limited direct genetic impact in Asia.}, } @article {pmid29739657, year = {2018}, author = {Barbosa-Lorenzo, R and Ruano-Ravina, A and Fernández-Villar, A and López-Pardo, E and Carballeira-Roca, C and Barros-Dios, JM}, title = {COPD prevalence and hospital admissions in Galicia (Spain). An analysis using the potential of new health information systems.}, journal = {Pulmonology}, volume = {24}, number = {6}, pages = {323-329}, doi = {10.1016/j.pulmoe.2018.03.005}, pmid = {29739657}, issn = {2531-0437}, mesh = {Aged ; Cross-Sectional Studies ; Female ; *Health Information Systems ; Humans ; Male ; Middle Aged ; Patient Admission/*statistics & numerical data ; Prevalence ; Pulmonary Disease, Chronic Obstructive/*epidemiology ; Spain/epidemiology ; }, abstract = {INTRODUCTION AND OBJECTIVES: Chronic obstructive pulmonary disease (COPD) is a major public health problem. The aim of this study was to ascertain the prevalence of COPD and whether such prevalence was positively or negatively associated with COPD admissions, using all the data of a regional health care system.

MATERIALS AND METHODS: We designed a descriptive cross-sectional study which included all subjects aged over 45 years, diagnosed with COPD in primary care in 2013. We also calculated the number of such patients who had a record of hospital admissions due to this disease. COPD prevalence and incidence of admissions were calculated. Poisson regression models were then used to analyse the association between cases with diagnosis of COPD and admissions due to COPD, by sex, adjusting for socio-demographic variables and distance to hospital. Sensitivity subanalyses were performed by reference to the respective municipal rurality indices.

RESULTS: Median municipal prevalence of COPD was 5.29% in men and 2.19% in women. Among patients with COPD, 28.22% of men and 16.00% of women had at least one hospital admission. The relative risk of admission per unit of the standardised prevalence ratio was 0.37 (95% CI 0.34-0.41) for men and 0.39 (95% CI 0.34-0.45) for women.

CONCLUSIONS: There is a significant negative association between COPD prevalence and hospital admissions due to this disease. The proportion of admissions is lower in municipalities lying furthest from hospitals. There is considerable municipal variability in terms of COPD prevalence and proportion of admissions. In-depth attention should be given to disease-management training programmes.}, } @article {pmid29737630, year = {2018}, author = {Freeman, SC and Fisher, D and Tierney, JF and Carpenter, JR}, title = {A framework for identifying treatment-covariate interactions in individual participant data network meta-analysis.}, journal = {Research synthesis methods}, volume = {9}, number = {3}, pages = {393-407}, pmid = {29737630}, issn = {1759-2887}, support = {MC_UU_12023/21/MRC_/Medical Research Council/United Kingdom ; MC_UU_12023/25/MRC_/Medical Research Council/United Kingdom ; MC UU 12023/21//MRC Clinical Trials Unit Methodology Programme/ ; }, mesh = {*Bias ; *Data Interpretation, Statistical ; Female ; Humans ; Models, Statistical ; *Network Meta-Analysis ; Randomized Controlled Trials as Topic ; Reproducibility of Results ; Research Design ; Treatment Outcome ; Uterine Cervical Neoplasms/drug therapy/radiotherapy ; }, abstract = {BACKGROUND: Stratified medicine seeks to identify patients most likely to respond to treatment. Individual participant data (IPD) network meta-analysis (NMA) models have greater power than individual trials to identify treatment-covariate interactions (TCIs). Treatment-covariate interactions contain "within" and "across" trial interactions, where the across-trial interaction is more susceptible to confounding and ecological bias.

METHODS: We considered a network of IPD from 37 trials (5922 patients) for cervical cancer (2394 events), where previous research identified disease stage as a potential interaction covariate. We compare 2 models for NMA with TCIs: (1) 2 effects separating within- and across-trial interactions and (2) a single effect combining within- and across-trial interactions. We argue for a visual assessment of consistency of within- and across-trial interactions and consider more detailed aspects of interaction modelling, eg, common vs trial-specific effects of the covariate. This leads us to propose a practical framework for IPD NMA with TCIs.

RESULTS: Following our framework, we found no evidence in the cervical cancer network for a treatment-stage interaction on the basis of the within-trial interaction. The NMA provided additional power for an across-trial interaction over and above the pairwise evidence. Following our proposed framework, we found that the within- and across-trial interactions should not be combined.

CONCLUSION: Across-trial interactions are susceptible to confounding and ecological bias. It is important to separate the sources of evidence to check their consistency and identify which sources of evidence are driving the conclusion. Our framework provides practical guidance for researchers, reducing the risk of unduly optimistic interpretation of TCIs.}, } @article {pmid29736767, year = {2018}, author = {Hale, BW}, title = {Mapping Potential Environmental Impacts from Tourists Using Data from Social Media: A Case Study in the Westfjords of Iceland.}, journal = {Environmental management}, volume = {62}, number = {3}, pages = {446-457}, pmid = {29736767}, issn = {1432-1009}, support = {IZK0Z2_171645//Swiss National Science Foundation/Switzerland ; }, mesh = {Ecology ; *Environment ; Estuaries ; Geographic Information Systems ; Humans ; Iceland ; *Social Media ; *Travel ; }, abstract = {With tourism increasing in remote regions, it is important to be able to estimate potential environmental impacts from the tourists in order to plan and manage natural areas. This study combines measures of ecological sensitivity with data from publicly available geotagged photographs posted on the social media site Flickr to assess the vulnerability of the locations frequented by foreign tourists in the Westfjords region of Iceland between 2014 and 2016. The results suggest that tourists cluster primarily around six hotspots that represented some of the major known tourist destinations of the region. Although tourists generally frequented areas with lower ecological sensitivity and rarely went far beyond the main roads, one of the hotspots was in an area of higher ecological sensitivity. Further, tourists also appeared to have higher intensity stays when they entered areas of higher ecological sensitivity. Overall, these findings highlight the usefulness of combining data from social media in assessing potential environmental impacts of tourism. However, natural resource managers should be aware of limitations in the use of such data.}, } @article {pmid29736651, year = {2018}, author = {He, K and Zhang, J and Wang, X and Zeng, Y and Zhang, L}, title = {A scientometric review of emerging trends and new developments in agricultural ecological compensation.}, journal = {Environmental science and pollution research international}, volume = {25}, number = {17}, pages = {16522-16532}, pmid = {29736651}, issn = {1614-7499}, support = {71703051//Natural Sciences Foundation of China/ ; 71333006//Natural Sciences Foundation of China/ ; 41501213//Natural Sciences Foundation of China/ ; 2662017QD009//Fundamental Research Funds for the Central Universities/ ; 15JZD014//Key Program of Philosophy and Social Sciences Research, Ministry of Education of China/ ; 2018ADC036//Soft Science Research Project of Technology Innovation in Hubei Province/ ; }, mesh = {Agriculture/*economics/*trends ; Compensation and Redress ; Conservation of Natural Resources/*economics/*trends ; Databases, Factual ; Ecology ; Ecosystem ; Humans ; }, abstract = {Agricultural ecological compensation has drawn an increasingly broad range of interest since early 1990s. In recent years, the volume of the literature grows rapidly. As a result, a systematic review of the diverse research field and its current trends becomes essential. This paper surveys the literature of agricultural ecological compensation between 1990 and 2016. Specifically, by employing CiteSpace information visualization software, we firstly identified the research hotspots and evolution path and then illustrated the frontier and developing trend of the domain in core and broader perspectives. It is found that the focus of the academic community has always been researches on the theoretical policy and application of the payment for agro-ecosystem services, agricultural ecological compensation based on contingent valuation method, and ecological compensation of farmland landscape and organic food production as well as willingness to accept/pay for land use and ecological protection. Meanwhile, we also found that, in recent years, qualitative research has received more and more attention in the field of agricultural ecological compensation, since global warming, agricultural carbon emissions, and other emerging environmental issues have aroused widespread concern of the people around the world. Moreover, we believed that more and more scholars will employ case study methodology to analyze agricultural ecological compensation in specific systems, regions, or circumstances in the future.}, } @article {pmid29734799, year = {2018}, author = {Peters, K and Worrich, A and Weinhold, A and Alka, O and Balcke, G and Birkemeyer, C and Bruelheide, H and Calf, OW and Dietz, S and Dührkop, K and Gaquerel, E and Heinig, U and Kücklich, M and Macel, M and Müller, C and Poeschl, Y and Pohnert, G and Ristok, C and Rodríguez, VM and Ruttkies, C and Schuman, M and Schweiger, R and Shahaf, N and Steinbeck, C and Tortosa, M and Treutler, H and Ueberschaar, N and Velasco, P and Weiß, BM and Widdig, A and Neumann, S and Dam, NMV}, title = {Current Challenges in Plant Eco-Metabolomics.}, journal = {International journal of molecular sciences}, volume = {19}, number = {5}, pages = {}, pmid = {29734799}, issn = {1422-0067}, mesh = {*Ecology ; Metabolomics/*trends ; Plants/*genetics/metabolism ; }, abstract = {The relatively new research discipline of Eco-Metabolomics is the application of metabolomics techniques to ecology with the aim to characterise biochemical interactions of organisms across different spatial and temporal scales. Metabolomics is an untargeted biochemical approach to measure many thousands of metabolites in different species, including plants and animals. Changes in metabolite concentrations can provide mechanistic evidence for biochemical processes that are relevant at ecological scales. These include physiological, phenotypic and morphological responses of plants and communities to environmental changes and also interactions with other organisms. Traditionally, research in biochemistry and ecology comes from two different directions and is performed at distinct spatiotemporal scales. Biochemical studies most often focus on intrinsic processes in individuals at physiological and cellular scales. Generally, they take a bottom-up approach scaling up cellular processes from spatiotemporally fine to coarser scales. Ecological studies usually focus on extrinsic processes acting upon organisms at population and community scales and typically study top-down and bottom-up processes in combination. Eco-Metabolomics is a transdisciplinary research discipline that links biochemistry and ecology and connects the distinct spatiotemporal scales. In this review, we focus on approaches to study chemical and biochemical interactions of plants at various ecological levels, mainly plant[-]organismal interactions, and discuss related examples from other domains. We present recent developments and highlight advancements in Eco-Metabolomics over the last decade from various angles. We further address the five key challenges: (1) complex experimental designs and large variation of metabolite profiles; (2) feature extraction; (3) metabolite identification; (4) statistical analyses; and (5) bioinformatics software tools and workflows. The presented solutions to these challenges will advance connecting the distinct spatiotemporal scales and bridging biochemistry and ecology.}, } @article {pmid29733879, year = {2018}, author = {Bartas, M and Brázda, V and Karlický, V and Červeň, J and Pečinka, P}, title = {Bioinformatics analyses and in vitro evidence for five and six stacked G-quadruplex forming sequences.}, journal = {Biochimie}, volume = {150}, number = {}, pages = {70-75}, doi = {10.1016/j.biochi.2018.05.002}, pmid = {29733879}, issn = {1638-6183}, mesh = {Circular Dichroism ; Computational Biology/*methods ; *G-Quadruplexes ; Nucleic Acid Conformation ; }, abstract = {Quadruplexes are noncanonical DNA structures that arise in guanine rich loci and have important biological functions. Classically, quadruplexes contain four stacked intramolecular G-tetrads. Surprisingly, although some algorithms allow searching for longer than 4G tracts for quadruplex formation, these have not yet been systematically studied. Therefore, we analyzed the human genome for sequences that are predicted to adopt stacked intramolecular G-tetrads with greater than four stacks. The data provide evidence for numerous G-quadruplexes that contain five or six stacked intramolecular G-tetrads. These sequences are predominantly found in known gene regulatory regions. Electrophoretic mobility assays and circular dichroism spectroscopy indicate that these sequences form quadruplex structures in vitro under physiological conditions. The localization and in vitro stability of these G-quadruplexes indicate their potentially important roles in gene regulation and their potential for therapeutic applications.}, } @article {pmid29732259, year = {2018}, author = {Botella, C and Joly, A and Bonnet, P and Monestiez, P and Munoz, F}, title = {Species distribution modeling based on the automated identification of citizen observations.}, journal = {Applications in plant sciences}, volume = {6}, number = {2}, pages = {e1029}, pmid = {29732259}, issn = {2168-0450}, abstract = {PREMISE OF THE STUDY: A species distribution model computed with automatically identified plant observations was developed and evaluated to contribute to future ecological studies.

METHODS: We used deep learning techniques to automatically identify opportunistic plant observations made by citizens through a popular mobile application. We compared species distribution modeling of invasive alien plants based on these data to inventories made by experts.

RESULTS: The trained models have a reasonable predictive effectiveness for some species, but they are biased by the massive presence of cultivated specimens.

DISCUSSION: The method proposed here allows for fine-grained and regular monitoring of some species of interest based on opportunistic observations. More in-depth investigation of the typology of the observations and the sampling bias should help improve the approach in the future.}, } @article {pmid29732255, year = {2018}, author = {James, SA and Soltis, PS and Belbin, L and Chapman, AD and Nelson, G and Paul, DL and Collins, M}, title = {Herbarium data: Global biodiversity and societal botanical needs for novel research.}, journal = {Applications in plant sciences}, volume = {6}, number = {2}, pages = {e1024}, pmid = {29732255}, issn = {2168-0450}, abstract = {Building on centuries of research based on herbarium specimens gathered through time and around the globe, a new era of discovery, synthesis, and prediction using digitized collections data has begun. This paper provides an overview of how aggregated, open access botanical and associated biological, environmental, and ecological data sets, from genes to the ecosystem, can be used to document the impacts of global change on communities, organisms, and society; predict future impacts; and help to drive the remediation of change. Advocacy for botanical collections and their expansion is needed, including ongoing digitization and online publishing. The addition of non-traditional digitized data fields, user annotation capability, and born-digital field data collection enables the rapid access of rich, digitally available data sets for research, education, informed decision-making, and other scholarly and creative activities. Researchers are receiving enormous benefits from data aggregators including the Global Biodiversity Information Facility (GBIF), Integrated Digitized Biocollections (iDigBio), the Atlas of Living Australia (ALA), and the Biodiversity Heritage Library (BHL), but effective collaboration around data infrastructures is needed when working with large and disparate data sets. Tools for data discovery, visualization, analysis, and skills training are increasingly important for inspiring novel research that improves the intrinsic value of physical and digital botanical collections.}, } @article {pmid29729991, year = {2018}, author = {Wang, D and Sun, Y and Chang, L and Tong, Z and Xie, Q and Jin, X and Zhu, L and He, P and Li, H and Wang, X}, title = {Subcellular proteome profiles of different latex fractions revealed washed solutions from rubber particles contain crucial enzymes for natural rubber biosynthesis.}, journal = {Journal of proteomics}, volume = {182}, number = {}, pages = {53-64}, doi = {10.1016/j.jprot.2018.05.002}, pmid = {29729991}, issn = {1876-7737}, mesh = {Gene Ontology ; Hevea/chemistry/*enzymology ; Latex/*biosynthesis ; Membrane Proteins/metabolism ; Plant Proteins/metabolism ; Proteome/*analysis ; Proteomics/*methods ; Rubber/chemistry ; Solutions/chemistry ; }, abstract = {UNLABELLED: Rubber particle (RP) is a specific organelle for natural rubber biosynthesis (NRB) and storage in rubber tree Hevea brasiliensis. NRB is processed by RP membrane-localized proteins, which were traditionally purified by repeated washing. However, we noticed many proteins in the discarded washing solutions (WS) from RP. Here, we compared the proteome profiles of WS, C-serum (CS) and RP by 2-DE, and identified 233 abundant proteins from WS by mass spectrometry. Many spots on 2-DE gels were identified as different protein species. We further performed shotgun analysis of CS, WS and RP and identified 1837, 1799 and 1020 unique proteins, respectively. Together with 2-DE, we finally identified 1825 proteins from WS, 246 were WS-specific. These WS-specific proteins were annotated in Gene Ontology, indicating most abundant pathways are organic substance metabolic process, protein degradation, primary metabolic process, and energy metabolism. Protein-protein interaction analysis revealed these WS-specific proteins are mainly involved in ribosomal metabolism, proteasome system, vacuolar protein sorting and endocytosis. Label free and Western blotting revealed many WS-specific proteins and protein complexes are crucial for NRB initiation. These findings not only deepen our understanding of WS proteome, but also provide new evidences on the roles of RP membrane proteins in NRB.

SIGNIFICANCE: Natural rubber is stored in rubber particle from the rubber tree. Rubber particles were traditionally purified by repeated washing, but many proteins were identified from the washing solutions (WS). We obtained the first visualization proteome profiles with 1825 proteins from WS, including 246 WS-specific ones. These WS proteins contain almost all enzymes for polyisoprene initiation and may play important roles in rubber biosynthesis.}, } @article {pmid29727060, year = {2018}, author = {Boscaro, V and Santoferrara, LF and Zhang, Q and Gentekaki, E and Syberg-Olsen, MJ and Del Campo, J and Keeling, PJ}, title = {EukRef-Ciliophora: a manually curated, phylogeny-based database of small subunit rRNA gene sequences of ciliates.}, journal = {Environmental microbiology}, volume = {20}, number = {6}, pages = {2218-2230}, doi = {10.1111/1462-2920.14264}, pmid = {29727060}, issn = {1462-2920}, support = {RGPIN-2014-03994//Natural Sciences and Engineering Research Council of Canada/International ; //Centre for Microbial Diversity and Evolution from the Tula Foundation/International ; OCE1435515//U.S. National Science Foundation/International ; 31672251//National Natural Science Foundation of China/International ; FP7-PEOPLE-2012-IOF-331450 CAARL//Marie Curie International Outgoing Fellowship/International ; }, mesh = {Ciliophora/*genetics ; *Databases, Nucleic Acid ; High-Throughput Nucleotide Sequencing ; *Phylogeny ; RNA, Ribosomal/*genetics ; }, abstract = {High-throughput sequencing (HTS) surveys, among the most common approaches currently used in environmental microbiology, require reliable reference databases to be correctly interpreted. The EukRef Initiative (eukref.org) is a community effort to manually screen available small subunit (SSU) rRNA gene sequences and produce a public, high-quality and informative framework of phylogeny-based taxonomic annotations. In the context of EukRef, we present a database for the monophyletic phylum Ciliophora, one of the most complex, diverse and ubiquitous protist groups. We retrieved more than 11 500 sequences of ciliates present in GenBank (28% from identified isolates and 72% from environmental surveys). Our approach included the inference of phylogenetic trees for every ciliate lineage and produced the largest SSU rRNA tree of the phylum Ciliophora to date. We flagged approximately 750 chimeric or low-quality sequences, improved the classification of 70% of GenBank entries and enriched environmental and literature metadata by 30%. The performance of EukRef-Ciliophora is superior to the current SILVA database in classifying HTS reads from a global marine survey. Comprehensive outputs are publicly available to make the new tool a useful guide for non-specialists and a quick reference for experts.}, } @article {pmid29725101, year = {2018}, author = {Toju, H and Peay, KG and Yamamichi, M and Narisawa, K and Hiruma, K and Naito, K and Fukuda, S and Ushio, M and Nakaoka, S and Onoda, Y and Yoshida, K and Schlaeppi, K and Bai, Y and Sugiura, R and Ichihashi, Y and Minamisawa, K and Kiers, ET}, title = {Core microbiomes for sustainable agroecosystems.}, journal = {Nature plants}, volume = {4}, number = {5}, pages = {247-257}, doi = {10.1038/s41477-018-0139-4}, pmid = {29725101}, issn = {2055-0278}, mesh = {*Agriculture/methods ; *Ecosystem ; *Microbiota ; Plants/microbiology ; Symbiosis ; }, abstract = {In an era of ecosystem degradation and climate change, maximizing microbial functions in agroecosystems has become a prerequisite for the future of global agriculture. However, managing species-rich communities of plant-associated microbiomes remains a major challenge. Here, we propose interdisciplinary research strategies to optimize microbiome functions in agroecosystems. Informatics now allows us to identify members and characteristics of 'core microbiomes', which may be deployed to organize otherwise uncontrollable dynamics of resident microbiomes. Integration of microfluidics, robotics and machine learning provides novel ways to capitalize on core microbiomes for increasing resource-efficiency and stress-resistance of agroecosystems.}, } @article {pmid29722621, year = {2018}, author = {Hotta, K and Behnke, BJ and Masamoto, K and Shimotsu, R and Onodera, N and Yamaguchi, A and Poole, DC and Kano, Y}, title = {Microvascular permeability of skeletal muscle after eccentric contraction-induced muscle injury: in vivo imaging using two-photon laser scanning microscopy.}, journal = {Journal of applied physiology (Bethesda, Md. : 1985)}, volume = {125}, number = {2}, pages = {369-380}, doi = {10.1152/japplphysiol.00046.2018}, pmid = {29722621}, issn = {1522-1601}, mesh = {Animals ; Capillary Permeability/*physiology ; Electric Stimulation/methods ; Male ; Microcirculation/physiology ; Microscopy, Confocal/methods ; Muscle Contraction/*physiology ; Muscle Fibers, Skeletal/*physiology ; Rats ; Rats, Wistar ; Wounds and Injuries/*physiopathology ; }, abstract = {Via modulation of endothelial integrity and vascular permeability in response to damage, skeletal muscle microvessels play a crucial permissive role in tissue leukocyte invasion. However, direct visual evidence of altered microvascular permeability of skeletal muscle has not been technically feasible, impairing mechanistic understanding of these responses. Two-photon laser scanning microscopy (TPLSM) allows three-dimensional in vivo imaging of skeletal muscle microcirculation. We hypothesized that the regulation of microvascular permeability in vivo is temporally related to acute inflammatory and regenerative processes following muscle injury. To test our hypothesis, tibialis anterior muscles of anesthetized male Wistar rats were subjected to eccentric contractions (ECCs) via electrical stimulation. The skeletal muscle microcirculation was imaged by an intravenously infused fluorescent dye (rhodamine B isothiocyanate-dextran) to assess microvascular permeability via TPLSM 1, 3, and 7 days after ECC. Immunohistochemistry on serial muscle sections was performed to determine the proportion of VEGF-A-positive muscle fibers in the damaged muscle. Compared with control rats, the volumetrically determined interstitial leakage of fluorescent dye (5.1 ± 1.4, 5.3 ± 1.2 vs. 0.51 ± 0.14 μm[3] × 10[6]; P < 0.05, days 1 and 3, respectively, vs. control) and percentage of VEGF-A-positive fibers in the damaged muscle (10 ± 0.4%, 22 ± 1.1% vs. 0%; days 1 and 3, respectively, vs. control) were significantly higher on days 1 and 3 after ECC. The interstitial leakage volume returned to control by day 7. These results suggest that microvascular hyperpermeability assessed by in vivo TPLSM imaging is associated with ECC-induced muscle damage and increased VEGF expression. NEW & NOTEWORTHY This investigation employed a novel in vivo imaging technique for skeletal muscle microcirculation using two-photon laser scanning microscopy that enabled microvascular permeability to be assessed by four-dimensional image analysis. By combining in vivo imaging and histological analysis, we found the temporal profile of microvascular hyperpermeability to be related to that of eccentric contraction-induced skeletal muscle injury and pronounced novel myocyte VEGF expression.}, } @article {pmid29717679, year = {2019}, author = {Toni, M and Manciocco, A and Angiulli, E and Alleva, E and Cioni, C and Malavasi, S}, title = {Review: Assessing fish welfare in research and aquaculture, with a focus on European directives.}, journal = {Animal : an international journal of animal bioscience}, volume = {13}, number = {1}, pages = {161-170}, doi = {10.1017/S1751731118000940}, pmid = {29717679}, issn = {1751-732X}, mesh = {Animal Welfare/*standards ; Animals ; Aquaculture/*standards ; Biomedical Research/standards ; European Union ; *Fishes ; Laboratory Animal Science/*standards ; }, abstract = {The number of farmed fish in the world has increased considerably. Aquaculture is a growing industry that will in the future provide a large portion of fishery products. Moreover, in recent years, the number of teleost fish used as animal models for scientific research in both biomedical and ecological fields has increased. Therefore, it is increasingly important to implement measures designed to enhance the welfare of these animals. Currently, a number of European rules exist as requirements for the establishment, care and accommodation of fish maintained for human purposes. As far as (teleost) fish are concerned, the fact that the number of extant species is much greater than that of all other vertebrates must be considered. Of further importance is that each species has its own specific physical and chemical requirements. These factors make it difficult to provide generalized recommendations or requirements for all fish species. An adequate knowledge is required of the physiology and ecology of each species bred. This paper integrates and discusses, in a single synthesis, the current issues related to fish welfare, considering that teleosts are target species for both aquaculture and experimental models in biological and biomedical research. We first focus on the practical aspects, which must be considered when assessing fish welfare in both research and aquaculture contexts. Next, we address husbandry and the care of fish housed in research laboratories and aquaculture facilities in relation to their physiological and behavioural requirements, as well as in reference to the suggestions provided by European regulations. Finally, to evaluate precisely which parameters described by Directive 2010/63/EU are reported in scientific papers, we analysed 82 articles published by European researchers in 2014 and 2015. This review found that there is a general lack of information related to the optimal environmental conditions that should be provided for the range of species covered by this directive.}, } @article {pmid29717136, year = {2018}, author = {Krause-Kyora, B and Nutsua, M and Boehme, L and Pierini, F and Pedersen, DD and Kornell, SC and Drichel, D and Bonazzi, M and Möbus, L and Tarp, P and Susat, J and Bosse, E and Willburger, B and Schmidt, AH and Sauter, J and Franke, A and Wittig, M and Caliebe, A and Nothnagel, M and Schreiber, S and Boldsen, JL and Lenz, TL and Nebel, A}, title = {Ancient DNA study reveals HLA susceptibility locus for leprosy in medieval Europeans.}, journal = {Nature communications}, volume = {9}, number = {1}, pages = {1569}, pmid = {29717136}, issn = {2041-1723}, mesh = {*DNA, Ancient ; DNA, Bacterial/genetics ; Denmark ; Fossils ; *Genetic Predisposition to Disease ; Genome, Bacterial ; HLA-DQ beta-Chains/genetics ; HLA-DRB1 Chains/genetics ; High-Throughput Screening Assays ; Humans ; Leprosy/*genetics ; Mycobacterium leprae/genetics ; White People/*genetics ; }, abstract = {Leprosy, a chronic infectious disease caused by Mycobacterium leprae (M. leprae), was very common in Europe till the 16th century. Here, we perform an ancient DNA study on medieval skeletons from Denmark that show lesions specific for lepromatous leprosy (LL). First, we test the remains for M. leprae DNA to confirm the infection status of the individuals and to assess the bacterial diversity. We assemble 10 complete M. leprae genomes that all differ from each other. Second, we evaluate whether the human leukocyte antigen allele DRB1*15:01, a strong LL susceptibility factor in modern populations, also predisposed medieval Europeans to the disease. The comparison of genotype data from 69 M. leprae DNA-positive LL cases with those from contemporary and medieval controls reveals a statistically significant association in both instances. In addition, we observe that DRB1*15:01 co-occurs with DQB1*06:02 on a haplotype that is a strong risk factor for inflammatory diseases today.}, } @article {pmid29716955, year = {2018}, author = {Bod'ová, K and Priklopil, T and Field, DL and Barton, NH and Pickup, M}, title = {Evolutionary Pathways for the Generation of New Self-Incompatibility Haplotypes in a Nonself-Recognition System.}, journal = {Genetics}, volume = {209}, number = {3}, pages = {861-883}, pmid = {29716955}, issn = {1943-2631}, mesh = {Evolution, Molecular ; Haplotypes ; Models, Genetic ; Phylogeny ; Plant Breeding ; *Plant Physiological Phenomena ; Plant Proteins/*genetics ; Plants/*genetics ; Pollination ; *Self-Incompatibility in Flowering Plants ; Stochastic Processes ; }, abstract = {Self-incompatibility (SI) is a genetically based recognition system that functions to prevent self-fertilization and mating among related plants. An enduring puzzle in SI is how the high diversity observed in nature arises and is maintained. Based on the underlying recognition mechanism, SI can be classified into two main groups: self-recognition (SR) and nonself-recognition (NSR). Most work has focused on diversification within SR systems despite expected differences between the two groups in the evolutionary pathways and outcomes of diversification. Here, we use a deterministic population genetic model and stochastic simulations to investigate how novel S-haplotypes evolve in a gametophytic NSR [SRNase/S Locus F-box (SLF)] SI system. For this model, the pathways for diversification involve either the maintenance or breakdown of SI and can vary in the order of mutations of the female (SRNase) and male (SLF) components. We show analytically that diversification can occur with high inbreeding depression and self-pollination, but this varies with evolutionary pathway and level of completeness (which determines the number of potential mating partners in the population), and, in general, is more likely for lower haplotype number. The conditions for diversification are broader in stochastic simulations of finite population size. However, the number of haplotypes observed under high inbreeding and moderate-to-high self-pollination is less than that commonly observed in nature. Diversification was observed through pathways that maintain SI as well as through self-compatible intermediates. Yet the lifespan of diversified haplotypes was sensitive to their level of completeness. By examining diversification in a NSR SI system, this model extends our understanding of the evolution and maintenance of haplotype diversity observed in a recognition system common in flowering plants.}, } @article {pmid29716616, year = {2018}, author = {Socorro de Almeida Viana, MND and Santos Nobre, AF and Costa, E and Silva, IC and Pinheiro, BT and Pereira, CCC and de Souza Canto Ferreira, L and de Almeida, DS and de Araújo, MWL and da Silva Borges, M and da Costa, CA and Ishikawa, EAY and Ferrari, SF and Silva de Sousa, M}, title = {Stability of the HTLV-1 glycoprotein 46 (gp46) gene in an endemic region of the Brazilian Amazon and the presence of a significant mutation (N93D) in symptomatic patients.}, journal = {Virology journal}, volume = {15}, number = {1}, pages = {80}, pmid = {29716616}, issn = {1743-422X}, mesh = {Adult ; Amino Acid Substitution ; Base Sequence ; Bayes Theorem ; Brazil/epidemiology ; Computational Biology ; *Endemic Diseases ; Female ; Gene Expression ; Gene Products, env/*genetics ; Genotype ; HTLV-I Infections/diagnosis/*epidemiology/physiopathology/virology ; Heterozygote ; Human T-lymphotropic virus 1/*genetics/isolation & purification/pathogenicity ; Humans ; Male ; Middle Aged ; *Mutation ; Pain/diagnosis/*epidemiology/physiopathology/virology ; Primary Dysautonomias/diagnosis/*epidemiology/physiopathology/virology ; Protein Domains ; Retrospective Studies ; Retroviridae Proteins, Oncogenic/*genetics ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: The human T-lymphotropic virus type 1 (HTLV-1) affects 2-5 million people worldwide, and is associated with a number of degenerative and infectious diseases. The Envelope glycoproteins (gp) are highly conserved among the different HTLV-1 isolates, although nucleotide substitutions in the region that codifies these proteins may influence both the infectivity and the replication of the virus. The gp46 gene has functional domains which have been associated with the inhibition of the formation of the syncytium, cell-cell transmission, and the production of antibodies. The present study investigated the genetic stability of the gp46 gene of HTLV-1 in an endemic region of Brazilian Amazonia.

METHODS: Index case (IC - a sample of a given family group) carriers of HTLV-1 were investigated in the metropolitan region of Belém (Pará, Brazil) between January 2010 (registered retrospectively) and December 2015. The sequences that codify the gp46 were amplified by PCR, purified and sequenced (MF084788-MF084825). The gene was characterized using bioinformatics and Bayesian Inference.

RESULTS: The 40 patients analyzed had a mean age of 45.2 years and 70% presented some type of symptom, with a predominance of pain and sensitivity, dysautonomia, and motor disorders. All patients presented the aA (Transcontinental Cosmopolitan) genotype, with an extremely low mutation rate, which is characteristic of the codifying region (aA - 1.83 × 10-[4] mutations per site per year). The gp46 gene had a nucleotide diversity of between 0.00% and 2.0%. Amino acid mutations were present in 66.6% of the samples of individuals with signs/symptoms or diseases associated with HTLV-1 (p = 0.0091). Of the three most frequent mutations, the previously undescribed N93D mutant was invariably associated with symptomatic cases.

CONCLUSIONS: The aA HTLV-1 subtype is predominant in the metropolitan region of Belém and presented a high degree of genetic stability in the codifying region. The rare N93D amino acid mutation may be associated with the clinical manifestations of this viral infection.

IMPORTANCE: Little is known of the phylogeny of HTLV-1 in the endemic region of Brazilian Amazonia, and few complete gene sequences are available for the gp46 glycoprotein from the local population. The nucleotide sequences of the viral gp46 gene recorded in the present study confirmed the genetic stability of the region, and pointed to a homogeneous viral group, with local geographic characteristics. Further research will be necessary to more fully understand the molecular diversity of this protein, given the potential of this codifying region as a model for an effective HTLV-1 vaccine. The identification of a rare mutation (N93D), present only in symptomatic patients, should also be investigated further as a potential clinical marker.

TRIAL REGISTRATION: ISRCTN 12345678, registered 28 September 2014.}, } @article {pmid29709223, year = {2018}, author = {Wills, TA and Soneji, SS}, title = {Individual-Level and Ecological Studies.}, journal = {The Journal of adolescent health : official publication of the Society for Adolescent Medicine}, volume = {62}, number = {5}, pages = {507-508}, doi = {10.1016/j.jadohealth.2018.03.002}, pmid = {29709223}, issn = {1879-1972}, support = {P30 CA071789/CA/NCI NIH HHS/United States ; }, mesh = {*Cigarette Smoking ; Data Interpretation, Statistical ; *Electronic Nicotine Delivery Systems ; Environment ; Humans ; }, } @article {pmid29706901, year = {2018}, author = {Waris, MI and Younas, A and Ul Qamar, MT and Hao, L and Ameen, A and Ali, S and Abdelnabby, HE and Zeng, FF and Wang, MQ}, title = {Silencing of Chemosensory Protein Gene NlugCSP8 by RNAi Induces Declining Behavioral Responses of Nilaparvata lugens.}, journal = {Frontiers in physiology}, volume = {9}, number = {}, pages = {379}, pmid = {29706901}, issn = {1664-042X}, abstract = {Chemosensory proteins (CSPs) play imperative functions in chemical and biochemical signaling of insects, as they distinguish and transfer ecological chemical indications to a sensory system in order to initiate behavioral responses. The brown planthopper (BPH), Nilaparvata lugens Stål (Hemiptera: Delphacidae), has emerged as the most destructive pest, causing serious damage to rice in extensive areas throughout Asia. Biotic characteristics like monophagy, dual wing forms, and annual long-distance migration imply a critical role of chemoreception in N. lugens. In this study, we cloned the full-length CSP8 gene from N. lugens. Protein sequence analysis indicated that NlugCSP8 shared high sequence resemblance with the CSPs of other insect family members and had the typical four-cysteine signature. Analysis of gene expression indicated that NlugCSP8 mRNA was specifically expressed in the wings of mated 3-day brachypterous females with a 175-fold difference compare to unmated 3-day brachypterous females. The NlugCSP8 mRNA was also highly expressed in the abdomen of unmated 5-day brachypterous males and correlated to the age, gender, adult wing form, and mating status. A competitive ligand-binding assay demonstrated that ligands with long chain carbon atoms, nerolidol, hexanal, and trans-2-hexenal were able to bind to NlugCSP8 in declining order of affinity. By using bioinformatics techniques, three-dimensional protein structure modeling and molecular docking, the binding sites of NlugCSP8 to the volatiles which had high binding affinity were predicted. In addition, behavioral experiments using the compounds displaying the high binding affinity for the NlugCSP8, revealed four compounds able to elicit significant behavioral responses from N. lugens. The in vivo functions of NlugCSP8 were further confirmed through the testing of RNAi and post-RNAi behavioral experiments. The results revealed that reduction in NlugCSP8 transcript abundance caused a decrease in behavioral response to representative attractants. An enhanced understanding of the NlugCSP8 is expected to contribute in the improvement of more effective and eco-friendly control strategies of BPH.}, } @article {pmid29706773, year = {2018}, author = {Moritz, L and Wesener, T and Koch, M}, title = {An apparently non-swinging tentorium in the Diplopoda (Myriapoda): comparative morphology of the tentorial complex in giant pill-millipedes (Sphaerotheriida).}, journal = {ZooKeys}, volume = {}, number = {741}, pages = {77-91}, pmid = {29706773}, issn = {1313-2989}, abstract = {The presence of a swinging tentorium is a key apomorphy of Myriapoda, but this character has been studied in detail in only few species. Here the tentorium, i.e., the peristomatic skeleton of the preoral chamber, is comparatively studied in three species of the millipede order Sphaerotheriida Brandt, 1833. Since dissections of the fragile tentorial components proved to be difficult, despite the large head size, they were analysed mainly in situ via micro-computed tomography. Our results confirm previous observations of large differences in the tentorial construction in the giant pill-millipedes compared to chilognathan diplopods. The tentorium of Sphaerotheriida consists of a curved, plate-like epipharyngeal bar with distal projections, an elongate and thin hypopharyngeal bar, and a plate-like triangular posterior process; a transverse bar is absent. Only seven muscles attach at the tentorium in giant pill-millipedes, including two antennal muscles and two muscles of the gnathochilarium. Within the order Sphaerotheriida, the composition of the tentorium and its muscular equipment seems to be conserved, except for some variability in the shape of the epipharyngeal bar. As the transverse bar has been considered essential for the mobility of the tentorium in myriapods, its absence in Sphaerotheriida may indicate that their tentorium is not capable of performing a swing. Loss of tentorial mobility may also pertain to the order Glomerida Brandt, 1833, inferred here from the absence of a posterior process. An apparently immobile tentorium in Glomerida and Sphaerotheriida can straightforwardly be correlated with transformations of the head related to their ability of volvation. The different transformations of the tentorium, here hypothesised to cause immobility, may support current assumptions that the ability of volvation evolved convergently in Glomerida and Sphaerotheriida. This conclusion, however, still requires more detailed studies of the head anatomy in Glomerida and Glomeridesmida Cook, 1895.}, } @article {pmid29704459, year = {2018}, author = {Rupp, O and MacDonald, ML and Li, S and Dhiman, H and Polson, S and Griep, S and Heffner, K and Hernandez, I and Brinkrolf, K and Jadhav, V and Samoudi, M and Hao, H and Kingham, B and Goesmann, A and Betenbaugh, MJ and Lewis, NE and Borth, N and Lee, KH}, title = {A reference genome of the Chinese hamster based on a hybrid assembly strategy.}, journal = {Biotechnology and bioengineering}, volume = {115}, number = {8}, pages = {2087-2100}, pmid = {29704459}, issn = {1097-0290}, support = {P20 GM103446/GM/NIGMS NIH HHS/United States ; R35 GM119850/GM/NIGMS NIH HHS/United States ; W 1224/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Animals ; Computational Biology ; Cricetulus/*genetics ; *Genome ; High-Throughput Nucleotide Sequencing ; Sequence Analysis, DNA ; *Whole Genome Sequencing ; }, abstract = {Accurate and complete genome sequences are essential in biotechnology to facilitate genome-based cell engineering efforts. The current genome assemblies for Cricetulus griseus, the Chinese hamster, are fragmented and replete with gap sequences and misassemblies, consistent with most short-read-based assemblies. Here, we completely resequenced C. griseus using single molecule real time sequencing and merged this with Illumina-based assemblies. This generated a more contiguous and complete genome assembly than either technology alone, reducing the number of scaffolds by >28-fold, with 90% of the sequence in the 122 longest scaffolds. Most genes are now found in single scaffolds, including up- and downstream regulatory elements, enabling improved study of noncoding regions. With >95% of the gap sequence filled, important Chinese hamster ovary cell mutations have been detected in draft assembly gaps. This new assembly will be an invaluable resource for continued basic and pharmaceutical research.}, } @article {pmid29703247, year = {2018}, author = {Zeng, Q and Rodrigo, A}, title = {Neutral models of short-term microbiome dynamics with host subpopulation structure and migration limitation.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {80}, pmid = {29703247}, issn = {2049-2618}, mesh = {Biological Evolution ; Computational Biology/*methods ; *Computer Simulation ; Host Microbial Interactions/*physiology ; Humans ; Microbiota/*physiology ; *Models, Biological ; }, abstract = {BACKGROUND: Most empirical studies tend to focus on microbiome dynamics within hosts or microbiome compositional differences between hosts over short periods. However, there is still a dearth of formal models that allow us to investigate the observed short-term dynamics of microbiomes under a unified ecological and evolutionary framework. In our previous study, we developed a computational agent-based neutral framework that simulates microbiome dynamics spanning many host generations with the added dimension of a genealogy of hosts. Although this long-term framework revealed interesting microbial diversity patterns under a simple but plausible evolutionary process and provided a platform for future elaboration of more complex systems, it does not allow us to explore microbiome dynamics within a single host generation.

METHODS: In this paper, we developed a computational, agent-based, forward-time framework of microbiome dynamics within a single host generation. As we have done under our neutral long-term models, we incorporate neutral processes of environmental microbiome assembly and microbe acquisition from parents and environment. We also incorporate a Moran genealogical model of hosts, so that the dynamics of microbiome evolution can be studied within a single host generation. Furthermore, we allow host subpopulation structure and host migration to affect microbiome recruitment.

RESULTS: We show that microbiome diversity within hosts increases monotonically with increases in environmental contribution, while microbiome diversity between hosts increases with increasing parental inheritance. Host population division and dispersal limitation under high host contribution further shaped the patterns by elevating microbiome differences between hosts and depressing microbial diversity within hosts. Microbiome diversity within the whole population showed strong temporal stability regardless of the modes of microbiome acquisition and subpopulation structures.

CONCLUSIONS: We present a computational framework that integrates various processes including host genealogy, microbe recruitment, and host dispersal limitation acting on the short-term dynamics of microbiomes. Our framework demonstrates that the neutral dynamics of microbiomes within a population of hosts is strongly influenced by transmission mode and shared environment.}, } @article {pmid29703146, year = {2018}, author = {Chen, F and Zhang, L and Lin, Z and Cheng, ZM}, title = {Identification of a novel fused gene family implicates convergent evolution in eukaryotic calcium signaling.}, journal = {BMC genomics}, volume = {19}, number = {1}, pages = {306}, pmid = {29703146}, issn = {1471-2164}, support = {CX(14)2051//Priority Academic Program Development of Modern Horticulture Science in Jiangsu Province/ ; SKB2017004//State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops/ ; 1009395//Tennessee Agricultural Experiment Station, University of Tennessee/ ; //Wellcome Trust/United Kingdom ; 201406850018//China Scholarship Council/ ; }, mesh = {Animals ; *Biological Evolution ; Calcium/*metabolism ; Calcium Signaling ; *Computational Biology ; Eukaryota/*genetics ; Gene Expression Regulation ; *Gene Fusion ; *Multigene Family ; Phylogeny ; Plants/*genetics ; }, abstract = {BACKGROUND: Both calcium signals and protein phosphorylation responses are universal signals in eukaryotic cell signaling. Currently three pathways have been characterized in different eukaryotes converting the Ca[2+] signals to the protein phosphorylation responses. All these pathways have based mostly on studies in plants and animals.

RESULTS: Based on the exploration of genomes and transcriptomes from all the six eukaryotic supergroups, we report here in Metakinetoplastina protists a novel gene family. This family, with a proposed name SCAMK, comprises SnRK3 fused calmodulin-like III kinase genes and was likely evolved through the insertion of a calmodulin-like3 gene into an SnRK3 gene by unequal crossover of homologous chromosomes in meiosis cell. Its origin dated back to the time intersection at least 450 million-year-ago when Excavata parasites, Vertebrata hosts, and Insecta vectors evolved. We also analyzed SCAMK's unique expression pattern and structure, and proposed it as one of the leading calcium signal conversion pathways in Excavata parasite. These characters made SCAMK gene as a potential drug target for treating human African trypanosomiasis.

CONCLUSIONS: This report identified a novel gene fusion and dated its precise fusion time in Metakinetoplastina protists. This potential fourth eukaryotic calcium signal conversion pathway complements our current knowledge that convergent evolution occurs in eukaryotic calcium signaling.}, } @article {pmid29702724, year = {2018}, author = {Soltis, DE and Moore, MJ and Sessa, EB and Smith, SA and Soltis, PS}, title = {Using and navigating the plant tree of life.}, journal = {American journal of botany}, volume = {105}, number = {3}, pages = {287-290}, doi = {10.1002/ajb2.1071}, pmid = {29702724}, issn = {1537-2197}, mesh = {Big Data ; Biodiversity ; *Biological Evolution ; Classification ; DNA, Plant ; *Datasets as Topic ; Evolution, Molecular ; Genes, Plant ; Genome, Plant ; Genome, Plastid ; Genomics/methods ; *Phylogeny ; Plants/*genetics ; }, } @article {pmid29702162, year = {2018}, author = {Fink, A and Rominger, C and Benedek, M and Perchtold, CM and Papousek, I and Weiss, EM and Seidel, A and Memmert, D}, title = {EEG alpha activity during imagining creative moves in soccer decision-making situations.}, journal = {Neuropsychologia}, volume = {114}, number = {}, pages = {118-124}, doi = {10.1016/j.neuropsychologia.2018.04.025}, pmid = {29702162}, issn = {1873-3514}, support = {I 2901/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Adult ; Attention ; Brain/*physiology ; Brain Mapping ; *Creativity ; Decision Making/*physiology ; Electroencephalography ; Humans ; Imagination/*physiology ; Male ; Movement/*physiology ; Psychometrics ; Psychomotor Performance ; Soccer/*psychology ; Task Performance and Analysis ; Young Adult ; }, abstract = {This study investigated task-related changes of EEG alpha power while participants were imagining creative moves in soccer decision-making situations. After presenting brief video clips of a soccer scene, participants had to imagine themselves as the acting player and to think either of a creative/original or an obvious/conventional move (control condition) that might lead to a goal. Performance of the soccer task generally elicited comparatively strong alpha power decreases at parietal and occipital sites, indicating high visuospatial processing demands. This power decrease was less pronounced in the creative vs. control condition, reflecting a more internally oriented state of information processing characterized by more imaginative mental simulation rather than stimulus-driven bottom-up processing. In addition, more creative task performance in the soccer task was associated with stronger alpha desynchronization at left cortical sites, most prominently over motor related areas. This finding suggests that individuals who generated more creative moves were more intensively engaged in processes related to movement imagery. Unlike the domain-specific creativity measure, individual's trait creative potential, as assessed by a psychometric creativity test, was globally positively associated with alpha power at all cortical sites. In investigating creative processes implicated in complex creative behavior involving more ecologically valid demands, this study showed that thinking creatively in soccer decision-making situations recruits specific brain networks supporting processes related to visuospatial attention and movement imagery, while the relative increase in alpha power in more creative conditions and in individuals with higher creative potential might reflect a pattern relevant across different creativity domains.}, } @article {pmid29700429, year = {2018}, author = {Borruso, L and Sannino, C and Selbmann, L and Battistel, D and Zucconi, L and Azzaro, M and Turchetti, B and Buzzini, P and Guglielmin, M}, title = {A thin ice layer segregates two distinct fungal communities in Antarctic brines from Tarn Flat (Northern Victoria Land).}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {6582}, pmid = {29700429}, issn = {2045-2322}, mesh = {Antarctic Regions ; *Biodiversity ; *Environmental Microbiology ; Fungi/*classification ; Ice Cover/*microbiology ; *Mycobiome ; Phylogeny ; Salts/*chemistry ; }, abstract = {Brines are hypersaline solutions which have been found within the Antarctic permafrost from the Tarn Flat area (Northern Victoria Land). Here, an investigation on the possible presence and diversity of fungal life within those peculiar ecosystems has been carried out for the first time. Brines samples were collected at 4- and 5-meter depths (TF1 and TF2, respectively), from two brines separated by a thin ice layer. The samples were analyzed via Illumina MiSeq targeting the ITS region specific for both yeasts and filamentous fungi. An unexpected high alpha diversity was found. Beta diversity analysis revealed that the two brines were inhabited by two phylogenetically diverse fungal communities (Unifrac value: 0.56, p value < 0.01; Martin's P-test p-value < 0.001) characterized by several specialist taxa. The most abundant fungal genera were Candida sp., Leucosporidium sp., Naganishia sp. and Sporobolomyces sp. in TF1, and Leucosporidium sp., Malassezia sp., Naganishia sp. and Sporobolomyces sp. in TF2. A few hypotheses on such differentiation have been done: i) the different chemical and physical composition of the brines; ii) the presence in situ of a thin layer of ice, acting as a physical barrier; and iii) the diverse geological origin of the brines.}, } @article {pmid29699481, year = {2018}, author = {Buetti-Dinh, A and Friedman, R}, title = {Computer simulations of the signalling network in FLT3 [+]-acute myeloid leukaemia - indications for an optimal dosage of inhibitors against FLT3 and CDK6.}, journal = {BMC bioinformatics}, volume = {19}, number = {1}, pages = {155}, pmid = {29699481}, issn = {1471-2105}, support = {CAN 2015/387//Cancerfonden/International ; }, mesh = {Apoptosis/drug effects ; Cell Proliferation/drug effects ; *Computer Simulation ; Cyclin-Dependent Kinase 6/*antagonists & inhibitors/genetics ; Gene Expression Regulation, Neoplastic/*drug effects ; Humans ; Leukemia, Myeloid, Acute/drug therapy/genetics/*pathology ; Mutation ; Protein Kinase Inhibitors/*pharmacology/*standards ; Signal Transduction/drug effects ; fms-Like Tyrosine Kinase 3/*antagonists & inhibitors/genetics ; }, abstract = {BACKGROUND: Mutations in the FMS-like tyrosine kinase 3 (FLT3) are associated with uncontrolled cellular functions that contribute to the development of acute myeloid leukaemia (AML). We performed computer simulations of the FLT3-dependent signalling network in order to study the pathways that are involved in AML development and resistance to targeted therapies.

RESULTS: Analysis of the simulations revealed the presence of alternative pathways through phosphoinositide 3 kinase (PI3K) and SH2-containing sequence proteins (SHC), that could overcome inhibition of FLT3. Inhibition of cyclin dependent kinase 6 (CDK6), a related molecular target, was also tested in the simulation but was not found to yield sufficient benefits alone.

CONCLUSIONS: The PI3K pathway provided a basis for resistance to treatments. Alternative signalling pathways could not, however, restore cancer growth signals (proliferation and loss of apoptosis) to the same levels as prior to treatment, which may explain why FLT3 resistance mutations are the most common resistance mechanism. Finally, sensitivity analysis suggested the existence of optimal doses of FLT3 and CDK6 inhibitors in terms of efficacy and toxicity.}, } @article {pmid29697785, year = {2018}, author = {Izak, D and Klim, J and Kaczanowski, S}, title = {Host-parasite interactions and ecology of the malaria parasite-a bioinformatics approach.}, journal = {Briefings in functional genomics}, volume = {17}, number = {6}, pages = {451-457}, doi = {10.1093/bfgp/ely013}, pmid = {29697785}, issn = {2041-2657}, mesh = {Animals ; Computational Biology/*methods ; Databases as Topic ; Genome-Wide Association Study ; *Host-Parasite Interactions ; Humans ; Malaria/*parasitology ; Parasites/physiology ; }, abstract = {Malaria remains one of the highest mortality infectious diseases. Malaria is caused by parasites from the genus Plasmodium. Most deaths are caused by infections involving Plasmodium falciparum, which has a complex life cycle. Malaria parasites are extremely well adapted for interactions with their host and their host's immune system and are able to suppress the human immune system, erase immunological memory and rapidly alter exposed antigens. Owing to this rapid evolution, parasites develop drug resistance and express novel forms of antigenic proteins that are not recognized by the host immune system. There is an emerging need for novel interventions, including novel drugs and vaccines. Designing novel therapies requires knowledge about host-parasite interactions, which is still limited. However, significant progress has recently been achieved in this field through the application of bioinformatics analysis of parasite genome sequences. In this review, we describe the main achievements in 'malarial' bioinformatics and provide examples of successful applications of protein sequence analysis. These examples include the prediction of protein functions based on homology and the prediction of protein surface localization via domain and motif analysis. Additionally, we describe PlasmoDB, a database that stores accumulated experimental data. This tool allows data mining of the stored information and will play an important role in the development of malaria science. Finally, we illustrate the application of bioinformatics in the development of population genetics research on malaria parasites, an approach referred to as reverse ecology.}, } @article {pmid29694592, year = {2018}, author = {Almeida, TSO and Fook, SML and Mariz, SR and Camêlo, ELS and Gomes, LCF}, title = {Suicide attempts: epidemiologic trends towards geoprocessing.}, journal = {Ciencia & saude coletiva}, volume = {23}, number = {4}, pages = {1183-1192}, doi = {10.1590/1413-81232018234.12452016}, pmid = {29694592}, issn = {1678-4561}, mesh = {Adult ; Age Factors ; Brazil/epidemiology ; Female ; Geographic Information Systems ; *Geographic Mapping ; Humans ; Incidence ; Male ; Middle Aged ; *Public Policy ; Risk Factors ; Sex Factors ; Spatial Analysis ; Suicide, Attempted/*statistics & numerical data ; Urban Population/*statistics & numerical data ; Young Adult ; }, abstract = {In order to study data about suicide attempts and do the mapping of occurrence areas, it was developed an ecologic and exploring study, making use of techniques of geoprocessing, based on confirmed cases of suicide attempts. Cases of self-poisoning were included in the urban area of Campina Grande county, in the period of 2010-2013. A total of 446 suicide attempts were geo-referred, pointing up an incidence of 120 cases out of each 100,000 inhabitants. The sample was mostly feminine (66.4%), and 62.3% being up to 30 years old. Kernel's map remarked hot spot areas. Compared to surrounding areas the suicide risk of populations within the hot spots was increased (38%; Relative Risk = 1.38; p= 0.0029), with an average estimative of 165 suicide attempts out of 100,000 inhabitants. Through identification of hot spots and index of living conditions of the neighborhoods, it is possible to set priorities in terms of public policies for the prevention of suicide attempts and control of the marketing of substances that are potentially toxic.}, } @article {pmid29694414, year = {2018}, author = {Bridgeman, B and Morgan-Richards, M and Wheeler, D and Trewick, SA}, title = {First detection of Wolbachia in the New Zealand biota.}, journal = {PloS one}, volume = {13}, number = {4}, pages = {e0195517}, pmid = {29694414}, issn = {1932-6203}, mesh = {Animals ; Bacterial Proteins/genetics ; Bayes Theorem ; Biological Evolution ; *Biota/genetics ; Computational Biology ; DNA, Bacterial/analysis ; High-Throughput Nucleotide Sequencing ; New Zealand ; Orthoptera/microbiology ; Phylogeny ; Wasps/microbiology ; Wolbachia/genetics/*isolation & purification ; }, abstract = {Wolbachia is one of the most widespread intracellular bacteria on earth, estimated to infect between 40 and 66% of arthropod species in most ecosystems that have been surveyed. Their significance rests not only in their vast distribution, but also in their ability to modify the reproductive biology of their hosts, which can ultimately affect genetic diversity and speciation of infected populations. Wolbachia has yet to be formally identified in the fauna of New Zealand which has high levels of endemic biodiversity and this represents a gap in our understanding of the global biology of Wolbachia. Using High Throughput Sequencing (HTS) of host DNA in conjunction with traditional molecular techniques we identified six endemic Orthoptera species that were positive for Wolbachia infection. In addition, short-sequence amplification with Wolbachia specific primers applied to New Zealand and introduced invertebrates detected a further 153 individuals positive for Wolbachia. From these short-range DNA amplification products sequence data was obtained for the ftsZ gene region from 86 individuals representing 10 host species. Phylogenetic analysis using the sequences obtained in this study reveals that there are two distinct Wolbachia bacteria lineages in New Zealand hosts belonging to recognised Wolbachia supergroups (A and B). These represent the first described instances of Wolbachia in the New Zealand native fauna, including detection in putative parasitoids of infected Orthoptera suggesting a possible transmission path. Our detection of Wolbachia infections of New Zealand species provides the opportunity to study local transmission of Wolbachia and explore their role in the evolution of New Zealand invertebrates.}, } @article {pmid29688462, year = {2018}, author = {Nekrutenko, A and Team, G and Goecks, J and Taylor, J and Blankenberg, D}, title = {Biology Needs Evolutionary Software Tools: Let's Build Them Right.}, journal = {Molecular biology and evolution}, volume = {35}, number = {6}, pages = {1372-1375}, pmid = {29688462}, issn = {1537-1719}, support = {R01 AI134384/AI/NIAID NIH HHS/United States ; U41 HG006620/HG/NHGRI NIH HHS/United States ; }, mesh = {*Biological Evolution ; *Computational Biology ; Software/*standards ; }, abstract = {Research in population genetics and evolutionary biology has always provided a computational backbone for life sciences as a whole. Today evolutionary and population biology reasoning are essential for interpretation of large complex datasets that are characteristic of all domains of today's life sciences ranging from cancer biology to microbial ecology. This situation makes algorithms and software tools developed by our community more important than ever before. This means that we, developers of software tool for molecular evolutionary analyses, now have a shared responsibility to make these tools accessible using modern technological developments as well as provide adequate documentation and training.}, } @article {pmid29688343, year = {2018}, author = {Tobin, TC and Shade, A}, title = {A town on fire! Integrating 16S rRNA gene amplicon analyses into an undergraduate microbiology lecture class.}, journal = {FEMS microbiology letters}, volume = {365}, number = {10}, pages = {}, pmid = {29688343}, issn = {1574-6968}, support = {R25 GM115335/GM/NIGMS NIH HHS/United States ; }, mesh = {Adult ; Bacteria/classification/*genetics/isolation & purification ; Computational Biology/*education ; Female ; Humans ; Male ; Metagenomics ; Microbiology/*education ; Microbiota ; Phylogeny ; RNA, Bacterial/*genetics ; RNA, Ribosomal, 16S/*genetics ; Soil Microbiology ; Students ; Teaching ; Young Adult ; }, abstract = {Microbiology increasingly relies upon bioinformatics to understand complex microbial interactions. Nevertheless, biology undergraduates often lack the basic quantitative and computer-based skills required for bioinformatics analyses. To address these issues, the course module 'A Town on Fire! 16S rRNA Gene Amplicon Analysis of Microbial Communities Overlying the Centralia, PA Mine Fire' was developed for an undergraduate microbiology lecture course. In this module, microbiology students used Quantitative Insights into Microbial Ecology to perform taxonomic, phylogenetic and statistical analyses on bacterial communities from three hot mine fire-impacted surface soils using 16S rRNA gene amplicon sequences. Pre- and post-module assessment data for each of 2 years were compiled, and indirect assessment indicated that students' confidence regarding their ability to perform bioinformatics analyses, as well as their ability to interpret bioinformatics data both increased, as did their enthusiasm for bioinformatics. Direct assessment demonstrated that students' understanding of topics that they actually used in the module, such as the statistical analyses that underlie bioinformatics investigations and the ability to infer phylogenetic relationships, improved during the module, but that their underlying understanding of techniques that they did not directly perform, such as sequencing and library construction, did not.}, } @article {pmid29688221, year = {2018}, author = {Ceccarelli, S and Balsalobre, A and Medone, P and Cano, ME and Gurgel Gonçalves, R and Feliciangeli, D and Vezzani, D and Wisnivesky-Colli, C and Gorla, DE and Marti, GA and Rabinovich, JE}, title = {DataTri, a database of American triatomine species occurrence.}, journal = {Scientific data}, volume = {5}, number = {}, pages = {180071}, pmid = {29688221}, issn = {2052-4463}, mesh = {Animals ; Chagas Disease/transmission ; Databases, Factual ; Humans ; *Insect Vectors ; *Triatominae ; Trypanosoma cruzi ; United States ; }, abstract = {Trypanosoma cruzi, the causative agent of Chagas disease, is transmitted to mammals - including humans - by insect vectors of the subfamily Triatominae. We present the results of a compilation of triatomine occurrence and complementary ecological data that represents the most complete, integrated and updated database (DataTri) available on triatomine species at a continental scale. This database was assembled by collecting the records of triatomine species published from 1904 to 2017, spanning all American countries with triatomine presence. A total of 21815 georeferenced records were obtained from published literature, personal fieldwork and data provided by colleagues. The data compiled includes 24 American countries, 14 genera and 135 species. From a taxonomic perspective, 67.33% of the records correspond to the genus Triatoma, 20.81% to Panstrongylus, 9.01% to Rhodnius and the remaining 2.85% are distributed among the other 11 triatomine genera. We encourage using DataTri information in various areas, especially to improve knowledge of the geographical distribution of triatomine species and its variations in time.}, } @article {pmid29686079, year = {2018}, author = {Muscente, AD and Prabhu, A and Zhong, H and Eleish, A and Meyer, MB and Fox, P and Hazen, RM and Knoll, AH}, title = {Quantifying ecological impacts of mass extinctions with network analysis of fossil communities.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {115}, number = {20}, pages = {5217-5222}, pmid = {29686079}, issn = {1091-6490}, mesh = {Animals ; *Biodiversity ; Biological Evolution ; *Databases, Factual ; *Ecosystem ; *Extinction, Biological ; *Fossils ; Geology ; Invertebrates ; *Paleontology ; }, abstract = {Mass extinctions documented by the fossil record provide critical benchmarks for assessing changes through time in biodiversity and ecology. Efforts to compare biotic crises of the past and present, however, encounter difficulty because taxonomic and ecological changes are decoupled, and although various metrics exist for describing taxonomic turnover, no methods have yet been proposed to quantify the ecological impacts of extinction events. To address this issue, we apply a network-based approach to exploring the evolution of marine animal communities over the Phanerozoic Eon. Network analysis of fossil co-occurrence data enables us to identify nonrandom associations of interrelated paleocommunities. These associations, or evolutionary paleocommunities, dominated total diversity during successive intervals of relative community stasis. Community turnover occurred largely during mass extinctions and radiations, when ecological reorganization resulted in the decline of one association and the rise of another. Altogether, we identify five evolutionary paleocommunities at the generic and familial levels in addition to three ordinal associations that correspond to Sepkoski's Cambrian, Paleozoic, and Modern evolutionary faunas. In this context, we quantify magnitudes of ecological change by measuring shifts in the representation of evolutionary paleocommunities over geologic time. Our work shows that the Great Ordovician Biodiversification Event had the largest effect on ecology, followed in descending order by the Permian-Triassic, Cretaceous-Paleogene, Devonian, and Triassic-Jurassic mass extinctions. Despite its taxonomic severity, the Ordovician extinction did not strongly affect co-occurrences of taxa, affirming its limited ecological impact. Network paleoecology offers promising approaches to exploring ecological consequences of extinctions and radiations.}, } @article {pmid29685579, year = {2018}, author = {Sukumaran, J and Knowles, LL}, title = {Trait-Dependent Biogeography: (Re)Integrating Biology into Probabilistic Historical Biogeographical Models.}, journal = {Trends in ecology & evolution}, volume = {33}, number = {6}, pages = {390-398}, doi = {10.1016/j.tree.2018.03.010}, pmid = {29685579}, issn = {1872-8383}, mesh = {*Animal Distribution ; Computational Biology ; *Life History Traits ; Models, Biological ; Models, Statistical ; *Phenotype ; *Phylogeny ; *Phylogeography ; *Plant Dispersal ; }, abstract = {The development of process-based probabilistic models for historical biogeography has transformed the field by grounding it in modern statistical hypothesis testing. However, most of these models abstract away biological differences, reducing species to interchangeable lineages. We present here the case for reintegration of biology into probabilistic historical biogeographical models, allowing a broader range of questions about biogeographical processes beyond ancestral range estimation or simple correlation between a trait and a distribution pattern, as well as allowing us to assess how inferences about ancestral ranges themselves might be impacted by differential biological traits. We show how new approaches to inference might cope with the computational challenges resulting from the increased complexity of these trait-based historical biogeographical models.}, } @article {pmid29684033, year = {2018}, author = {You, C and Lin, DKJ and Young, SS}, title = {Time series smoother for effect detection.}, journal = {PloS one}, volume = {13}, number = {4}, pages = {e0195360}, pmid = {29684033}, issn = {1932-6203}, mesh = {Air Pollution ; Computer Simulation ; Data Interpretation, Statistical ; *Ecological and Environmental Phenomena ; *Epidemiologic Methods ; Factor Analysis, Statistical ; Humans ; Los Angeles ; Mortality ; Ozone ; Regression Analysis ; Temperature ; Time Factors ; Time and Motion Studies ; Weather ; }, abstract = {In environmental epidemiology, it is often encountered that multiple time series data with a long-term trend, including seasonality, cannot be fully adjusted by the observed covariates. The long-term trend is difficult to separate from abnormal short-term signals of interest. This paper addresses how to estimate the long-term trend in order to recover short-term signals. Our case study demonstrates that the current spline smoothing methods can result in significant positive and negative cross-correlations from the same dataset, depending on how the smoothing parameters are chosen. To circumvent this dilemma, three classes of time series smoothers are proposed to detrend time series data. These smoothers do not require fine tuning of parameters and can be applied to recover short-term signals. The properties of these smoothers are shown with both a case study using a factorial design and a simulation study using datasets generated from the original dataset. General guidelines are provided on how to discover short-term signals from time series with a long-term trend. The benefit of this research is that a problem is identified and characteristics of possible solutions are determined.}, } @article {pmid29682730, year = {2018}, author = {Adams, DC and Collyer, ML}, title = {Phylogenetic ANOVA: Group-clade aggregation, biological challenges, and a refined permutation procedure.}, journal = {Evolution; international journal of organic evolution}, volume = {72}, number = {6}, pages = {1204-1215}, doi = {10.1111/evo.13492}, pmid = {29682730}, issn = {1558-5646}, mesh = {*Analysis of Variance ; Animals ; *Data Interpretation, Statistical ; Multivariate Analysis ; *Phylogeny ; Urodela/*genetics ; }, abstract = {Phylogenetic regression is frequently used in macroevolutionary studies, and its statistical properties have been thoroughly investigated. By contrast, phylogenetic ANOVA has received relatively less attention, and the conditions leading to incorrect statistical and biological inferences when comparing multivariate phenotypes among groups remain underexplored. Here, we propose a refined method of randomizing residuals in a permutation procedure (RRPP) for evaluating phenotypic differences among groups while conditioning the data on the phylogeny. We show that RRPP displays appropriate statistical properties for both phylogenetic ANOVA and regression models, and for univariate and multivariate datasets. For ANOVA, we find that RRPP exhibits higher statistical power than methods utilizing phylogenetic simulation. Additionally, we investigate how group dispersion across the phylogeny affects inferences, and reveal that highly aggregated groups generate strong and significant correlations with the phylogeny, which reduce statistical power and subsequently affect biological interpretations. We discuss the broader implications of this phylogenetic group aggregation, and its relation to challenges encountered with other comparative methods where one or a few transitions in discrete traits are observed on the phylogeny. Finally, we recommend that phylogenetic comparative studies of continuous trait data use RRPP for assessing the significance of indicator variables as sources of trait variation.}, } @article {pmid29681934, year = {2018}, author = {Liu, Y and Xia, C and Fan, Z and Wu, R and Chen, X and Liu, Z}, title = {Implementation of Fractal Dimension and Self-Organizing Map to Detect Toxic Effects of Toluene on Movement Tracks of Daphnia magna.}, journal = {Journal of toxicology}, volume = {2018}, number = {}, pages = {2637209}, pmid = {29681934}, issn = {1687-8191}, abstract = {Movement behaviors of an indicator species, Daphnia magna, in response to contaminants have been implemented to monitor environmental disturbances. Complexity in movement tracks of Daphnia magna was characterized by use of fractal dimension and self-organizing map. The individual movement tracks of D. magna were continuously recorded for 24 hours before and after treatments with toluene at the concentration of 10 mg/L, respectively. The general complexity in movement tracks (10 minutes) was characterized by fractal dimension. Results showed that average fractal dimension of movement tracks was decreased from 1.62 to 1.22 after treatments. The instantaneous movement parameters of movement segments in 5 s were input into the self-organizing map to investigate the swimming pattern changes under stresses of toluene. Abnormal behaviors of D. magna are more frequently observed after treatments than before treatments. Computational methods in ecological informatics could be utilized to obtain the useful information in behavioral data of D. magna and would be further applied as an in situ monitoring tool in water environment.}, } @article {pmid29681497, year = {2018}, author = {Vvedenskaya, IO and Bird, JG and Zhang, Y and Zhang, Y and Jiao, X and Barvík, I and Krásný, L and Kiledjian, M and Taylor, DM and Ebright, RH and Nickels, BE}, title = {CapZyme-Seq Comprehensively Defines Promoter-Sequence Determinants for RNA 5' Capping with NAD.}, journal = {Molecular cell}, volume = {70}, number = {3}, pages = {553-564.e9}, pmid = {29681497}, issn = {1097-4164}, support = {R01 GM041376/GM/NIGMS NIH HHS/United States ; R01 GM067005/GM/NIGMS NIH HHS/United States ; R35 GM118059/GM/NIGMS NIH HHS/United States ; R37 GM041376/GM/NIGMS NIH HHS/United States ; }, mesh = {DNA-Directed RNA Polymerases/metabolism ; Endoribonucleases/metabolism ; Escherichia coli/genetics/metabolism ; Gene Expression/genetics ; High-Throughput Nucleotide Sequencing/*methods ; NAD/*metabolism ; Nucleotides/genetics ; Promoter Regions, Genetic/*genetics ; RNA Caps/*genetics ; Transcription Initiation Site/physiology ; Transcription, Genetic/genetics ; Transcriptome/genetics ; }, abstract = {Nucleoside-containing metabolites such as NAD[+] can be incorporated as 5' caps on RNA by serving as non-canonical initiating nucleotides (NCINs) for transcription initiation by RNA polymerase (RNAP). Here, we report CapZyme-seq, a high-throughput-sequencing method that employs NCIN-decapping enzymes NudC and Rai1 to detect and quantify NCIN-capped RNA. By combining CapZyme-seq with multiplexed transcriptomics, we determine efficiencies of NAD[+] capping by Escherichia coli RNAP for ∼16,000 promoter sequences. The results define preferred transcription start site (TSS) positions for NAD[+] capping and define a consensus promoter sequence for NAD[+] capping: HRRASWW (TSS underlined). By applying CapZyme-seq to E. coli total cellular RNA, we establish that sequence determinants for NCIN capping in vivo match the NAD[+]-capping consensus defined in vitro, and we identify and quantify NCIN-capped small RNAs (sRNAs). Our findings define the promoter-sequence determinants for NCIN capping with NAD[+] and provide a general method for analysis of NCIN capping in vitro and in vivo.}, } @article {pmid29677204, year = {2018}, author = {Zhang, J and Basso, B and Price, RF and Putman, G and Shuai, G}, title = {Estimating plant distance in maize using Unmanned Aerial Vehicle (UAV).}, journal = {PloS one}, volume = {13}, number = {4}, pages = {e0195223}, pmid = {29677204}, issn = {1932-6203}, mesh = {Agriculture/instrumentation/*methods ; *Aircraft ; Crops, Agricultural/*growth & development/physiology ; Geographic Information Systems ; Models, Theoretical ; *Remote Sensing Technology ; *Spatial Analysis ; Statistics as Topic ; Zea mays/*growth & development/physiology ; }, abstract = {Distance between rows and plants are essential parameters that affect the final grain yield in row crops. This paper presents the results of research intended to develop a novel method to quantify the distance between maize plants at field scale using an Unmanned Aerial Vehicle (UAV). Using this method, we can recognize maize plants as objects and calculate the distance between plants. We initially developed our method by training an algorithm in an indoor facility with plastic corn plants. Then, the method was scaled up and tested in a farmer's field with maize plant spacing that exhibited natural variation. The results of this study demonstrate that it is possible to precisely quantify the distance between maize plants. We found that accuracy of the measurement of the distance between maize plants depended on the height above ground level at which UAV imagery was taken. This study provides an innovative approach to quantify plant-to-plant variability and, thereby final crop yield estimates.}, } @article {pmid29673182, year = {2018}, author = {Li, C and Liu, M and Hu, Y and Shi, T and Zong, M and Walter, MT}, title = {Assessing the Impact of Urbanization on Direct Runoff Using Improved Composite CN Method in a Large Urban Area.}, journal = {International journal of environmental research and public health}, volume = {15}, number = {4}, pages = {}, pmid = {29673182}, issn = {1660-4601}, mesh = {China ; Geographic Information Systems ; Hydrology ; *Models, Theoretical ; Remote Sensing Technology ; Urbanization/*trends ; }, abstract = {Urbanization is one of the most widespread anthropogenic activities, which brings a range of physical and biochemical changes to hydrological system and processes. Increasing direct runoff caused by land use change has become a major challenge for urban ecological security. Reliable prediction of the quantity and rate of surface runoff is an inherently difficult and time-consuming task for large ungauged urban areas. In this study, we combined Geographic Information System and remote sensing technology with an improved Soil Conservation Service curve number model to evaluate the effects of land use change on direct runoff volume of the four-ring area in Shenyang, China, and analyzed trends of direct runoff at different scales. Through analyzing trends of direct runoff from 1984 to 2015 at different scales, we explored how urbanization and other potential factors affect direct runoff changes. Total direct runoff volume increased over time, and trends varied from the inner urban area to suburban area. Zones 1 and 2 had a tendency toward decreasing direct runoff volume and risks, while Zones 3 and 4 showed gradual increases at both regional and pixel scales. The most important influence on direct runoff change was urban surface change caused by urbanization. This study presents a framework for identifying hotspots of runoff increase, which can provide important guidance to urban managers in future green infrastructure planning, in the hopes of improving the security of urban water ecological patterns.}, } @article {pmid29672581, year = {2018}, author = {Franklin, NT and Frank, MJ}, title = {Compositional clustering in task structure learning.}, journal = {PLoS computational biology}, volume = {14}, number = {4}, pages = {e1006116}, pmid = {29672581}, issn = {1553-7358}, support = {R01 MH080066/MH/NIMH NIH HHS/United States ; S10 OD016366/OD/NIH HHS/United States ; R01MH080066/NH/NIH HHS/United States ; }, mesh = {Bayes Theorem ; Cluster Analysis ; Computational Biology ; Computer Simulation ; Humans ; Information Theory ; *Learning ; Models, Psychological ; Reward ; Statistics, Nonparametric ; Stochastic Processes ; *Task Performance and Analysis ; }, abstract = {Humans are remarkably adept at generalizing knowledge between experiences in a way that can be difficult for computers. Often, this entails generalizing constituent pieces of experiences that do not fully overlap, but nonetheless share useful similarities with, previously acquired knowledge. However, it is often unclear how knowledge gained in one context should generalize to another. Previous computational models and data suggest that rather than learning about each individual context, humans build latent abstract structures and learn to link these structures to arbitrary contexts, facilitating generalization. In these models, task structures that are more popular across contexts are more likely to be revisited in new contexts. However, these models can only re-use policies as a whole and are unable to transfer knowledge about the transition structure of the environment even if only the goal has changed (or vice-versa). This contrasts with ecological settings, where some aspects of task structure, such as the transition function, will be shared between context separately from other aspects, such as the reward function. Here, we develop a novel non-parametric Bayesian agent that forms independent latent clusters for transition and reward functions, affording separable transfer of their constituent parts across contexts. We show that the relative performance of this agent compared to an agent that jointly clusters reward and transition functions depends environmental task statistics: the mutual information between transition and reward functions and the stochasticity of the observations. We formalize our analysis through an information theoretic account of the priors, and propose a meta learning agent that dynamically arbitrates between strategies across task domains to optimize a statistical tradeoff.}, } @article {pmid29671403, year = {2018}, author = {Lyu, M and Chen, J and Jiang, Y and Dong, W and Fang, Z and Li, S}, title = {KDiamend: a package for detecting key drivers in a molecular ecological network of disease.}, journal = {BMC systems biology}, volume = {12}, number = {Suppl 1}, pages = {5}, pmid = {29671403}, issn = {1752-0509}, mesh = {Arthritis, Rheumatoid/microbiology ; Computational Biology/*methods ; Diabetes Mellitus, Type 2/microbiology ; Gastrointestinal Microbiome ; Humans ; *Microbiota ; Mouth/microbiology ; Phenotype ; }, abstract = {BACKGROUND: Microbial abundance profiles are applied widely to understand diseases from the aspect of microbial communities. By investigating the abundance associations of species or genes, we can construct molecular ecological networks (MENs). The MENs are often constructed by calculating the Pearson correlation coefficient (PCC) between genes. In this work, we also applied multimodal mutual information (MMI) to construct MENs. The members which drive the concerned MENs are referred to as key drivers.

RESULTS: We proposed a novel method to detect the key drivers. First, we partitioned the MEN into subnetworks. Then we identified the most pertinent subnetworks to the disease by measuring the correlation between the abundance pattern and the delegated phenotype-the variable representing the disease phenotypes. Last, for each identified subnetwork, we detected the key driver by PageRank. We developed a package named KDiamend and applied it to the gut and oral microbial data to detect key drivers for Type 2 diabetes (T2D) and Rheumatoid Arthritis (RA). We detected six T2D-relevant subnetworks and three key drivers of them are related to the carbohydrate metabolic process. In addition, we detected nine subnetworks related to RA, a disease caused by compromised immune systems. The extracted subnetworks include InterPro matches (IPRs) concerned with immunoglobulin, Sporulation, biofilm, Flaviviruses, bacteriophage, etc., while the development of biofilms is regarded as one of the drivers of persistent infections.

CONCLUSION: KDiamend is feasible to detect key drivers and offers insights to uncover the development of diseases. The package is freely available at http://www.deepomics.org/pipelines/3DCD6955FEF2E64A/ .}, } @article {pmid29669512, year = {2018}, author = {Kwok, KO and Read, JM and Tang, A and Chen, H and Riley, S and Kam, KM}, title = {A systematic review of transmission dynamic studies of methicillin-resistant Staphylococcus aureus in non-hospital residential facilities.}, journal = {BMC infectious diseases}, volume = {18}, number = {1}, pages = {188}, pmid = {29669512}, issn = {1471-2334}, support = {200861/Z/16/Z/WT_/Wellcome Trust/United Kingdom ; U01 GM110721/GM/NIGMS NIH HHS/United States ; R01 TW008246/TW/FIC NIH HHS/United States ; /WT_/Wellcome Trust/United Kingdom ; HHSN266200700005C/AI/NIAID NIH HHS/United States ; 093488/Z/10/Z/WT_/Wellcome Trust/United Kingdom ; U54 GM088558/GM/NIGMS NIH HHS/United States ; MR/J008761/1/MRC_/Medical Research Council/United Kingdom ; N01AI70005/AI/NIAID NIH HHS/United States ; 200187/Z/15/Z/WT_/Wellcome Trust/United Kingdom ; MR/R015600/1/MRC_/Medical Research Council/United Kingdom ; U01 GM110721-01/GM/NIGMS NIH HHS/United States ; }, mesh = {Disease Outbreaks ; Hand Hygiene ; Health Personnel ; Hospitals ; Humans ; Infection Control/*methods ; Methicillin-Resistant Staphylococcus aureus/*pathogenicity ; Nursing Homes ; Prevalence ; Residential Facilities ; Staphylococcal Infections/epidemiology/microbiology/*transmission ; }, abstract = {BACKGROUND: Non-hospital residential facilities are important reservoirs for MRSA transmission. However, conclusions and public health implications drawn from the many mathematical models depicting nosocomial MRSA transmission may not be applicable to these settings. Therefore, we reviewed the MRSA transmission dynamics studies in defined non-hospital residential facilities to: (1) provide an overview of basic epidemiology which has been addressed; (2) identify future research direction; and (3) improve future model implementation.

METHODS: A review was conducted by searching related keywords in PUBMED without time restriction as well as internet searches via Google search engine. We included only articles describing the epidemiological transmission pathways of MRSA/community-associated MRSA within and between defined non-hospital residential settings.

RESULTS: Among the 10 included articles, nursing homes (NHs) and correctional facilities (CFs) were two settings considered most frequently. Importation of colonized residents was a plausible reason for MRSA outbreaks in NHs, where MRSA was endemic without strict infection control interventions. The importance of NHs over hospitals in increasing nosocomial MRSA prevalence was highlighted. Suggested interventions in NHs included: appropriate staffing level, screening and decolonizing, and hand hygiene. On the other hand, the small population amongst inmates in CFs has no effect on MRSA community transmission. Included models ranged from system-level compartmental models to agent-based models. There was no consensus over the course of disease progression in these models, which were mainly featured with NH residents /CF inmates/ hospital patients as transmission pathways. Some parameters used by these models were outdated or unfit.

CONCLUSIONS: Importance of NHs has been highlighted from these current studies addressing scattered aspects of MRSA epidemiology. However, the wide variety of non-hospital residential settings suggest that more work is needed before robust conclusions can be drawn. Learning from existing work for hospitals, we identified critical future research direction in this area from infection control, ecological and economic perspectives. From current model deficiencies, we suggest more transmission pathways be specified to depict MRSA transmission, and further empirical studies be stressed to support evidence-based mathematical models of MRSA in non-hospital facilities. Future models should be ready to cope with the aging population structure.}, } @article {pmid29668682, year = {2018}, author = {Hannigan, GD and Duhaime, MB and Koutra, D and Schloss, PD}, title = {Biogeography and environmental conditions shape bacteriophage-bacteria networks across the human microbiome.}, journal = {PLoS computational biology}, volume = {14}, number = {4}, pages = {e1006099}, pmid = {29668682}, issn = {1553-7358}, support = {T32AI007528/NH/NIH HHS/United States ; T32 AI007528/AI/NIAID NIH HHS/United States ; U01 AI124255/AI/NIAID NIH HHS/United States ; P30 DK034933/DK/NIDDK NIH HHS/United States ; P30DK034933/NH/NIH HHS/United States ; U01AI124255/NH/NIH HHS/United States ; U19AI09087/NH/NIH HHS/United States ; }, mesh = {Bacteria/*genetics ; *Bacterial Physiological Phenomena ; Bacteriophages/*genetics/*physiology ; Computational Biology ; Diet ; Humans ; Metagenomics ; Microbial Consortia/genetics/physiology ; Microbiota/*genetics/*physiology ; Models, Biological ; Phylogeography ; Skin/microbiology/virology ; }, abstract = {Viruses and bacteria are critical components of the human microbiome and play important roles in health and disease. Most previous work has relied on studying bacteria and viruses independently, thereby reducing them to two separate communities. Such approaches are unable to capture how these microbial communities interact, such as through processes that maintain community robustness or allow phage-host populations to co-evolve. We implemented a network-based analytical approach to describe phage-bacteria network diversity throughout the human body. We built these community networks using a machine learning algorithm to predict which phages could infect which bacteria in a given microbiome. Our algorithm was applied to paired viral and bacterial metagenomic sequence sets from three previously published human cohorts. We organized the predicted interactions into networks that allowed us to evaluate phage-bacteria connectedness across the human body. We observed evidence that gut and skin network structures were person-specific and not conserved among cohabitating family members. High-fat diets appeared to be associated with less connected networks. Network structure differed between skin sites, with those exposed to the external environment being less connected and likely more susceptible to network degradation by microbial extinction events. This study quantified and contrasted the diversity of virome-microbiome networks across the human body and illustrated how environmental factors may influence phage-bacteria interactive dynamics. This work provides a baseline for future studies to better understand system perturbations, such as disease states, through ecological networks.}, } @article {pmid29668677, year = {2018}, author = {De Maio, N and Worby, CJ and Wilson, DJ and Stoesser, N}, title = {Bayesian reconstruction of transmission within outbreaks using genomic variants.}, journal = {PLoS computational biology}, volume = {14}, number = {4}, pages = {e1006117}, pmid = {29668677}, issn = {1553-7358}, support = {/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Bayes Theorem ; Communicable Diseases/*epidemiology/genetics/*transmission ; Computational Biology ; Computer Simulation ; Disease Outbreaks/*statistics & numerical data ; Evolution, Molecular ; Genetic Variation ; Hemorrhagic Fever, Ebola/epidemiology/genetics/transmission ; Host-Pathogen Interactions/*genetics ; Humans ; Models, Genetic ; Sierra Leone/epidemiology ; Software ; }, abstract = {Pathogen genome sequencing can reveal details of transmission histories and is a powerful tool in the fight against infectious disease. In particular, within-host pathogen genomic variants identified through heterozygous nucleotide base calls are a potential source of information to identify linked cases and infer direction and time of transmission. However, using such data effectively to model disease transmission presents a number of challenges, including differentiating genuine variants from those observed due to sequencing error, as well as the specification of a realistic model for within-host pathogen population dynamics. Here we propose a new Bayesian approach to transmission inference, BadTrIP (BAyesian epiDemiological TRansmission Inference from Polymorphisms), that explicitly models evolution of pathogen populations in an outbreak, transmission (including transmission bottlenecks), and sequencing error. BadTrIP enables the inference of host-to-host transmission from pathogen sequencing data and epidemiological data. By assuming that genomic variants are unlinked, our method does not require the computationally intensive and unreliable reconstruction of individual haplotypes. Using simulations we show that BadTrIP is robust in most scenarios and can accurately infer transmission events by efficiently combining information from genetic and epidemiological sources; thanks to its realistic model of pathogen evolution and the inclusion of epidemiological data, BadTrIP is also more accurate than existing approaches. BadTrIP is distributed as an open source package (https://bitbucket.org/nicofmay/badtrip) for the phylogenetic software BEAST2. We apply our method to reconstruct transmission history at the early stages of the 2014 Ebola outbreak, showcasing the power of within-host genomic variants to reconstruct transmission events.}, } @article {pmid29667323, year = {2018}, author = {Pei, J and Chu, C and Li, X and Lu, B and Wu, Y}, title = {CLADES: A classification-based machine learning method for species delimitation from population genetic data.}, journal = {Molecular ecology resources}, volume = {}, number = {}, pages = {}, doi = {10.1111/1755-0998.12887}, pmid = {29667323}, issn = {1755-0998}, abstract = {Species are considered to be the basic unit of ecological and evolutionary studies. As multilocus genomic data are increasingly available, there have been considerable interests in the use of DNA sequence data to delimit species. In this study, we show that machine learning can be used for species delimitation. Our method treats the species delimitation problem as a classification problem for identifying the category of a new observation on the basis of training data. Extensive simulation is first conducted over a broad range of evolutionary parameters for training purposes. Each pair of known populations is combined to form training samples with a label of "same species" or "different species". We use support vector machine (SVM) to train a classifier using a set of summary statistics computed from training samples as features. The trained classifier can classify a test sample to two outcomes: "same species" or "different species". Given multilocus genomic data of multiple related organisms or populations, our method (called CLADES) performs species delimitation by first classifying pairs of populations. CLADES then delimits species by maximizing the likelihood of species assignment for multiple populations. CLADES is evaluated through extensive simulation and also tested on real genetic data. We show that CLADES is both accurate and efficient for species delimitation when compared with existing methods. CLADES can be useful especially when existing methods have difficulty in delimitation, for example with short species divergence time and gene flow.}, } @article {pmid29666315, year = {2018}, author = {Chen, S and Wang, W and Xu, W and Wang, Y and Wan, H and Chen, D and Tang, Z and Tang, X and Zhou, G and Xie, Z and Zhou, D and Shangguan, Z and Huang, J and He, JS and Wang, Y and Sheng, J and Tang, L and Li, X and Dong, M and Wu, Y and Wang, Q and Wang, Z and Wu, J and Chapin, FS and Bai, Y}, title = {Plant diversity enhances productivity and soil carbon storage.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {115}, number = {16}, pages = {4027-4032}, pmid = {29666315}, issn = {1091-6490}, mesh = {*Biodiversity ; Biomass ; Carbon/*analysis ; *Carbon Sequestration ; China ; Conservation of Natural Resources ; Datasets as Topic ; *Ecosystem ; Farms ; Forests ; Grassland ; Human Activities ; Humans ; Hydrogen-Ion Concentration ; Nitrogen/analysis ; Plant Dispersal ; Plants/chemistry/classification/*metabolism ; Rain ; Soil/*chemistry ; Temperature ; }, abstract = {Despite evidence from experimental grasslands that plant diversity increases biomass production and soil organic carbon (SOC) storage, it remains unclear whether this is true in natural ecosystems, especially under climatic variations and human disturbances. Based on field observations from 6,098 forest, shrubland, and grassland sites across China and predictions from an integrative model combining multiple theories, we systematically examined the direct effects of climate, soils, and human impacts on SOC storage versus the indirect effects mediated by species richness (SR), aboveground net primary productivity (ANPP), and belowground biomass (BB). We found that favorable climates (high temperature and precipitation) had a consistent negative effect on SOC storage in forests and shrublands, but not in grasslands. Climate favorability, particularly high precipitation, was associated with both higher SR and higher BB, which had consistent positive effects on SOC storage, thus offsetting the direct negative effect of favorable climate on SOC. The indirect effects of climate on SOC storage depended on the relationships of SR with ANPP and BB, which were consistently positive in all biome types. In addition, human disturbance and soil pH had both direct and indirect effects on SOC storage, with the indirect effects mediated by changes in SR, ANPP, and BB. High soil pH had a consistently negative effect on SOC storage. Our findings have important implications for improving global carbon cycling models and ecosystem management: Maintaining high levels of diversity can enhance soil carbon sequestration and help sustain the benefits of plant diversity and productivity.}, } @article {pmid29666240, year = {2018}, author = {Tian, H and Hu, S and Cazelles, B and Chowell, G and Gao, L and Laine, M and Li, Y and Yang, H and Li, Y and Yang, Q and Tong, X and Huang, R and Bjornstad, ON and Xiao, H and Stenseth, NC}, title = {Urbanization prolongs hantavirus epidemics in cities.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {115}, number = {18}, pages = {4707-4712}, pmid = {29666240}, issn = {1091-6490}, mesh = {Animals ; China ; *Databases, Factual ; Female ; *Orthohantavirus ; Hantavirus Infections/*epidemiology ; *Human Migration ; Humans ; Incidence ; Male ; *Urban Renewal ; Zoonoses/*epidemiology/virology ; }, abstract = {Urbanization and rural-urban migration are two factors driving global patterns of disease and mortality. There is significant concern about their potential impact on disease burden and the effectiveness of current control approaches. Few attempts have been made to increase our understanding of the relationship between urbanization and disease dynamics, although it is generally believed that urban living has contributed to reductions in communicable disease burden in industrialized countries. To investigate this relationship, we carried out spatiotemporal analyses using a 48-year-long dataset of hemorrhagic fever with renal syndrome incidence (HFRS; mainly caused by two serotypes of hantavirus in China: Hantaan virus and Seoul virus) and population movements in an important endemic area of south China during the period 1963-2010. Our findings indicate that epidemics coincide with urbanization, geographic expansion, and migrant movement over time. We found a biphasic inverted U-shaped relationship between HFRS incidence and urbanization, with various endemic turning points associated with economic growth rates in cities. Our results revealed the interrelatedness of urbanization, migration, and hantavirus epidemiology, potentially explaining why urbanizing cities with high economic growth exhibit extended epidemics. Our results also highlight contrasting effects of urbanization on zoonotic disease outbreaks during periods of economic development in China.}, } @article {pmid29666195, year = {2018}, author = {Crofton, AE and Cartwright, EL and Feitzinger, AA and Lott, SE}, title = {Effect of Larval Nutrition on Maternal mRNA Contribution to the Drosophila Egg.}, journal = {G3 (Bethesda, Md.)}, volume = {8}, number = {6}, pages = {1933-1941}, pmid = {29666195}, issn = {2160-1836}, support = {R01 GM111362/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Cluster Analysis ; Drosophila melanogaster/genetics/*metabolism ; Female ; Gene Ontology ; Genes, Insect ; Larva/genetics ; *Nutritional Physiological Phenomena ; Ovum/*metabolism ; Principal Component Analysis ; Protein Interaction Maps ; RNA, Messenger, Stored/genetics/*metabolism ; }, abstract = {Embryonic development begins under the control of maternal gene products, mRNAs and proteins that the mother deposits into the egg; the zygotic genome is activated some time later. Maternal control of early development is conserved across metazoans. Gene products contributed by mothers are critical to many early developmental processes, and set up trajectories for the rest of development. Maternal deposition of these factors is an often-overlooked aspect of parental investment. If the mother experiences challenging environmental conditions, such as poor nutrition, previous studies in Drosophila melanogaster have demonstrated a plastic response wherein these mothers may produce larger eggs to buffer the offspring against the same difficult environment. This additional investment can produce offspring that are more fit in the challenging environment. With this study, we ask whether D. melanogaster mothers who experience poor nutrition during their own development change their gene product contribution to the egg. We perform mRNA-Seq on eggs at a stage where all mRNAs are maternally derived, from mothers with different degrees of nutritional limitation. We find that nutritional limitation produces similar transcript changes at all degrees of limitation tested. Genes that have lower transcript abundance in nutritionally limited mothers are those involved in translation, which is likely one of the most energetically costly processes occurring in the early embryo. We find an increase in transcripts for transport and localization of macromolecules, and for the electron transport chain. The eggs produced by nutrition-limited mothers show a plastic response in mRNA deposition, which may better prepare the future embryo for development in a nutrition-limited environment.}, } @article {pmid29664998, year = {2018}, author = {Bible, RC and Peterson, AT}, title = {Compatible ecological niche signals between biological and archaeological datasets for late-surviving Neandertals.}, journal = {American journal of physical anthropology}, volume = {166}, number = {4}, pages = {968-974}, doi = {10.1002/ajpa.23482}, pmid = {29664998}, issn = {1096-8644}, mesh = {Animals ; *Anthropology, Physical ; Databases, Factual ; *Ecosystem ; Europe ; Fossils ; Humans ; Neanderthals/*physiology ; Research ; }, abstract = {OBJECTIVES: To assess ecological niche similarity for biological and archaeological samples representing late-surviving Neandertals in Europe to evaluate the validity of combining these two types of data in ecological niche modeling analyses.

MATERIALS AND METHODS: Tests of niche conservatism were used to assess niche similarity and niche identity of samples of morphologically diagnostic Neandertal remains and Middle Paleolithic (MP) archaeological sites dating to the time period leading up to Neandertal extinction. Paleoenvironmental reconstructions for the Pre-H4 (43.3-40.2 ky cal BP) were used as environmental space analyses.

RESULTS: Null hypotheses of niche similarity and identity of the two types of samples could not be rejected.

CONCLUSIONS: As primary and secondary evidence of Neandertal occurrence during the Pre-H4 show high levels of niche similarity and identity, combining the two types of occurrence data to create larger samples for niche analyses is justified without the concern that different environmental signals could complicate future research.}, } @article {pmid29664397, year = {2018}, author = {Stein, RR and Tanoue, T and Szabady, RL and Bhattarai, SK and Olle, B and Norman, JM and Suda, W and Oshima, K and Hattori, M and Gerber, GK and Sander, C and Honda, K and Bucci, V}, title = {Computer-guided design of optimal microbial consortia for immune system modulation.}, journal = {eLife}, volume = {7}, number = {}, pages = {}, pmid = {29664397}, issn = {2050-084X}, support = {R15 AI112985/AI/NIAID NIH HHS/United States ; R01 GM106303/GM/NIGMS NIH HHS/United States ; P41 GM103504/GM/NIGMS NIH HHS/United States ; P41 GM103504/NH/NIH HHS/United States ; P30 DK034854/DK/NIDDK NIH HHS/United States ; 5R01 GM106303/GM/NIGMS NIH HHS/United States ; R15-AI112985-01A1/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Computer Simulation ; Firmicutes/*immunology ; *Host Microbial Interactions ; *Immunity, Cellular ; Lymphocyte Activation ; Mice ; *Microbial Consortia ; T-Lymphocytes, Regulatory/*immunology ; }, abstract = {Manipulation of the gut microbiota holds great promise for the treatment of diseases. However, a major challenge is the identification of therapeutically potent microbial consortia that colonize the host effectively while maximizing immunologic outcome. Here, we propose a novel workflow to select optimal immune-inducing consortia from microbiome compositicon and immune effectors measurements. Using published and newly generated microbial and regulatory T-cell (Treg) data from germ-free mice, we estimate the contributions of twelve Clostridia strains with known immune-modulating effect to Treg induction. Combining this with a longitudinal data-constrained ecological model, we predict the ability of every attainable and ecologically stable subconsortium in promoting Treg activation and rank them by the Treg Induction Score (TrIS). Experimental validation of selected consortia indicates a strong and statistically significant correlation between predicted TrIS and measured Treg. We argue that computational indexes, such as the TrIS, are valuable tools for the systematic selection of immune-modulating bacteriotherapeutics.}, } @article {pmid29659792, year = {2018}, author = {Dahlö, M and Scofield, DG and Schaal, W and Spjuth, O}, title = {Tracking the NGS revolution: managing life science research on shared high-performance computing clusters.}, journal = {GigaScience}, volume = {7}, number = {5}, pages = {}, pmid = {29659792}, issn = {2047-217X}, mesh = {Biological Science Disciplines/*methods ; Computational Biology/*methods ; High-Throughput Nucleotide Sequencing/*methods ; *Research ; Software ; }, abstract = {BACKGROUND: Next-generation sequencing (NGS) has transformed the life sciences, and many research groups are newly dependent upon computer clusters to store and analyze large datasets. This creates challenges for e-infrastructures accustomed to hosting computationally mature research in other sciences. Using data gathered from our own clusters at UPPMAX computing center at Uppsala University, Sweden, where core hour usage of ∼800 NGS and ∼200 non-NGS projects is now similar, we compare and contrast the growth, administrative burden, and cluster usage of NGS projects with projects from other sciences.

RESULTS: The number of NGS projects has grown rapidly since 2010, with growth driven by entry of new research groups. Storage used by NGS projects has grown more rapidly since 2013 and is now limited by disk capacity. NGS users submit nearly twice as many support tickets per user, and 11 more tools are installed each month for NGS projects than for non-NGS projects. We developed usage and efficiency metrics and show that computing jobs for NGS projects use more RAM than non-NGS projects, are more variable in core usage, and rarely span multiple nodes. NGS jobs use booked resources less efficiently for a variety of reasons. Active monitoring can improve this somewhat.

CONCLUSIONS: Hosting NGS projects imposes a large administrative burden at UPPMAX due to large numbers of inexperienced users and diverse and rapidly evolving research areas. We provide a set of recommendations for e-infrastructures that host NGS research projects. We provide anonymized versions of our storage, job, and efficiency databases.}, } @article {pmid29659582, year = {2018}, author = {Reppell, M and Novembre, J}, title = {Using pseudoalignment and base quality to accurately quantify microbial community composition.}, journal = {PLoS computational biology}, volume = {14}, number = {4}, pages = {e1006096}, pmid = {29659582}, issn = {1553-7358}, support = {R01 HG007089/HG/NHGRI NIH HHS/United States ; R01 HG007089/NH/NIH HHS/United States ; }, mesh = {Base Composition ; Computational Biology ; Computer Simulation ; DNA/chemistry/genetics ; Databases, Genetic ; Humans ; Microbial Consortia/*genetics ; Microbiota/genetics ; Quantitative Trait Loci ; RNA, Ribosomal, 16S/*genetics ; Sequence Alignment/statistics & numerical data ; Software ; }, abstract = {Pooled DNA from multiple unknown organisms arises in a variety of contexts, for example microbial samples from ecological or human health research. Determining the composition of pooled samples can be difficult, especially at the scale of modern sequencing data and reference databases. Here we propose a novel method for taxonomic profiling in pooled DNA that combines the speed and low-memory requirements of k-mer based pseudoalignment with a likelihood framework that uses base quality information to better resolve multiply mapped reads. We apply the method to the problem of classifying 16S rRNA reads using a reference database of known organisms, a common challenge in microbiome research. Using simulations, we show the method is accurate across a variety of read lengths, with different length reference sequences, at different sample depths, and when samples contain reads originating from organisms absent from the reference. We also assess performance in real 16S data, where we reanalyze previous genetic association data to show our method discovers a larger number of quantitative trait associations than other widely used methods. We implement our method in the software Karp, for k-mer based analysis of read pools, to provide a novel combination of speed and accuracy that is uniquely suited for enhancing discoveries in microbial studies.}, } @article {pmid29659578, year = {2018}, author = {Martínez-García, R and Nadell, CD and Hartmann, R and Drescher, K and Bonachela, JA}, title = {Cell adhesion and fluid flow jointly initiate genotype spatial distribution in biofilms.}, journal = {PLoS computational biology}, volume = {14}, number = {4}, pages = {e1006094}, pmid = {29659578}, issn = {1553-7358}, support = {P20 GM113132/GM/NIGMS NIH HHS/United States ; P20-GM113132/NH/NIH HHS/United States ; }, mesh = {Bacterial Adhesion/physiology ; Biofilms/*growth & development ; Computational Biology ; Genetic Engineering ; Genotype ; Humans ; Hydrodynamics ; *Models, Biological ; Surface Properties ; Vibrio cholerae/genetics/pathogenicity/physiology ; }, abstract = {Biofilms are microbial collectives that occupy a diverse array of surfaces. It is well known that the function and evolution of biofilms are strongly influenced by the spatial arrangement of different strains and species within them, but how spatiotemporal distributions of different genotypes in biofilm populations originate is still underexplored. Here, we study the origins of biofilm genetic structure by combining model development, numerical simulations, and microfluidic experiments using the human pathogen Vibrio cholerae. Using spatial correlation functions to quantify the differences between emergent cell lineage segregation patterns, we find that strong adhesion often, but not always, maximizes the size of clonal cell clusters on flat surfaces. Counterintuitively, our model predicts that, under some conditions, investing in adhesion can reduce rather than increase clonal group size. Our results emphasize that a complex interaction between fluid flow and cell adhesiveness can underlie emergent patterns of biofilm genetic structure. This structure, in turn, has an outsize influence on how biofilm-dwelling populations function and evolve.}, } @article {pmid29658778, year = {2018}, author = {Boenn, M}, title = {ShRangeSim: Simulation of Single Nucleotide Polymorphism Clusters in Next-Generation Sequencing Data.}, journal = {Journal of computational biology : a journal of computational molecular cell biology}, volume = {25}, number = {6}, pages = {613-622}, doi = {10.1089/cmb.2018.0007}, pmid = {29658778}, issn = {1557-8666}, mesh = {*Algorithms ; Animals ; Computational Biology/*methods ; *Computer Simulation ; Drosophila melanogaster/*genetics ; Female ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Male ; *Polymorphism, Single Nucleotide ; Sequence Analysis, DNA/*methods ; }, abstract = {Genomic variations are in the focus of research to uncover mechanisms of host-pathogen interactions and diseases such as cancer. Nowadays, next-generation sequencing (NGS) data are analyzed through dedicated pipelines to detect them. Surrogate NGS data in conjunction with genomic variations help to evaluate pipelines and validate their outcomes, fostering selection of proper tools for a given scientific question. I describe how existing approaches for simulating NGS data in conjunction with genomic variations fail to model local enrichments of single nucleotide polymorphisms (SNPs), so called SNP clusters. Two distributions for count data are applied to publicly available collections of genomic variations. The results suggest modeling of SNP cluster sizes by overdispersion-aware distributions.}, } @article {pmid29652811, year = {2018}, author = {Zhang, Z and Zhou, Y and Wang, S and Huang, X}, title = {Spatial Distribution of Stony Desertification and Key Influencing Factors on Different Sampling Scales in Small Karst Watersheds.}, journal = {International journal of environmental research and public health}, volume = {15}, number = {4}, pages = {}, pmid = {29652811}, issn = {1660-4601}, mesh = {China ; *Conservation of Natural Resources ; Ecosystem ; Geographic Information Systems ; Geological Phenomena ; Soil ; }, abstract = {Karst areas are typical ecologically fragile areas, and stony desertification has become the most serious ecological and economic problems in these areas worldwide as well as a source of disasters and poverty. A reasonable sampling scale is of great importance for research on soil science in karst areas. In this paper, the spatial distribution of stony desertification characteristics and its influencing factors in karst areas are studied at different sampling scales using a grid sampling method based on geographic information system (GIS) technology and geo-statistics. The rock exposure obtained through sampling over a 150 m &times; 150 m grid in the Houzhai River Basin was utilized as the original data, and five grid scales (300 m &times; 300 m, 450 m &times; 450 m, 600 m &times; 600 m, 750 m &times; 750 m, and 900 m &times; 900 m) were used as the subsample sets. The results show that the rock exposure does not vary substantially from one sampling scale to another, while the average values of the five subsamples all fluctuate around the average value of the entire set. As the sampling scale increases, the maximum value and the average value of the rock exposure gradually decrease, and there is a gradual increase in the coefficient of variability. At the scale of 150 m &times; 150 m, the areas of minor stony desertification, medium stony desertification, and major stony desertification in the Houzhai River Basin are 7.81 km[2], 4.50 km[2], and 1.87 km[2], respectively. The spatial variability of stony desertification at small scales is influenced by many factors, and the variability at medium scales is jointly influenced by gradient, rock content, and rock exposure. At large scales, the spatial variability of stony desertification is mainly influenced by soil thickness and rock content.}, } @article {pmid29652573, year = {2018}, author = {Laudadio, I and Fulci, V and Palone, F and Stronati, L and Cucchiara, S and Carissimi, C}, title = {Quantitative Assessment of Shotgun Metagenomics and 16S rDNA Amplicon Sequencing in the Study of Human Gut Microbiome.}, journal = {Omics : a journal of integrative biology}, volume = {22}, number = {4}, pages = {248-254}, doi = {10.1089/omi.2018.0013}, pmid = {29652573}, issn = {1557-8100}, mesh = {Adolescent ; Child ; Computational Biology/methods ; Female ; *Gastrointestinal Microbiome ; High-Throughput Nucleotide Sequencing ; Humans ; Male ; *Metagenome ; *Metagenomics/methods ; *RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {The analysis of microbiota composition in humans, animals, and built environments is important because of emerging roles and applications in a broad range of disease and ecological phenotypes. Next Generation Sequencing is the current method of choice to characterize microbial community composition. The taxonomic profile of a microbial community can be obtained either by shotgun analysis of random DNA fragments or through 16S ribosomal RNA gene (rDNA) amplicon sequencing. It has been previously shown that the 16S rDNA amplicon sequencing approach yields quantitatively and qualitatively different results compared to shotgun metagenomics when the two techniques are used to assess microbial community composition on the same samples. However, most of such comparisons were either based on the recovery of 16S rDNA sequences in the shotgun metagenomics data or limited to a single microbiome or synthetic samples. Direct comparison of shotgun metagenomics and 16S rDNA amplicon sequencing on the same samples was performed only once in the recent literature, suggesting that the two methods yield comparable results. Here, we set out to compare the outcome of these two alternative approaches to the microbiome characterization in human gut microbiomes from stool samples. To this end, we processed six different samples with both techniques. We report here that shotgun next generation sequencing metagenomics allows much deeper characterization of the microbiome complexity, allowing identification of a larger number of species for each sample, compared to 16S rDNA amplicon sequencing. Further comparative studies in independent samples are called for.}, } @article {pmid29652093, year = {2018}, author = {Wilson, K and Sheldon, BC and Gaillard, JM and Sanders, NJ and Hoggart, SPG and Newton, E}, title = {And the winner of the inaugural Sidnie Manton Award is….}, journal = {The Journal of animal ecology}, volume = {87}, number = {3}, pages = {527-529}, doi = {10.1111/1365-2656.12825}, pmid = {29652093}, issn = {1365-2656}, mesh = {Animals ; *Awards and Prizes ; Ecology/*history ; History, 21st Century ; Image Interpretation, Computer-Assisted/*methods ; Oregon ; Societies, Scientific ; United Kingdom ; }, } @article {pmid29651320, year = {2018}, author = {Bakalár, P and Zvonar, M and Sedlacek, J and Lenkova, R and Sagat, P and Vojtasko, L and Liptakova, E and Barcalova, M}, title = {Movement Activity Determination with Health-related Variables of University Students in Kosice.}, journal = {Zdravstveno varstvo}, volume = {57}, number = {2}, pages = {88-95}, pmid = {29651320}, issn = {0351-0026}, abstract = {INTRODUCTION: There is currently a strong scientific evidence about the negative health consequences of physical inactivity. One of the potential tools for promoting physical activity at the institutional level of the Ecological model is to create conditions and settings that would enable pupils, students and employees engage in some form of physical activity. However, physical activities as a subject are being eliminated from the study programs at Slovak universities. The purpose of the study was to find current evidence about the level of structured physical activity and health-related variables in university students in Košice.

MATERIAL AND METHODS: The sample consisted of 1,993 or, more precisely, 1,398 students who attended two universities in Košice. To collect data, students completed a questionnaire and were tested for body height, body weight, circumferential measures and percentage body fat.

RESULTS: The university students did not sufficiently engage in a structured physical activity. A large number of students had either low or high values of percentage body fat and BMI and high WHR values.

CONCLUSIONS: Our findings have shown that the research into physical activity of university students should receive more attention.}, } @article {pmid29644621, year = {2018}, author = {Gould, RK and Coleman, K and Gluck, SB}, title = {Exploring dynamism of cultural ecosystems services through a review of environmental education research.}, journal = {Ambio}, volume = {47}, number = {8}, pages = {869-883}, pmid = {29644621}, issn = {1654-7209}, support = {1003495//USDA National Institute of Food and Agriculture, McIntire-Stennis/ ; EXPRESS Research Grant//University of Vermont/ ; }, mesh = {*Attitude ; *Awareness ; Behavior Observation Techniques ; Data Mining ; *Ecosystem ; *Education ; Humans ; *Intention ; *Recreation ; *Social Responsibility ; Surveys and Questionnaires ; }, abstract = {The field of cultural ecosystem services (CES) explores the non-material benefits that ecosystems provide to people. Human perceptions and valuations change, for many reasons and in many ways; research on CES, however, rarely accounts for this dynamism. In an almost entirely separate academic world, research on environmental education (EE) explores how EE programming affects peoples' attitudes and values toward the natural world. In this review of 119 EE research publications, we explore whether CES (and the adjacent concept of relational values) can be dynamic. We approach this via two lines of inquiry that explore whether EE may instigate this change. First, we investigate whether the EE community measures (and tries to affect) CES-related outcomes. Second, we ask: Has EE research detected changes in CES-related outcomes? We find the EE programs measure many CES outcomes (e.g., aesthetic appreciation, social connectedness), and that in most cases studies observe increases in these outcomes after EE experiences.}, } @article {pmid29643352, year = {2018}, author = {Pfaller, JB and Chaloupka, M and Bolten, AB and Bjorndal, KA}, title = {Phylogeny, biogeography and methodology: a meta-analytic perspective on heterogeneity in adult marine turtle survival rates.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {5852}, pmid = {29643352}, issn = {2045-2322}, mesh = {Animals ; Data Interpretation, Statistical ; Oceans and Seas ; *Phylogeny ; Phylogeography/*methods/statistics & numerical data/trends ; Population Dynamics/statistics & numerical data/trends ; Survival Rate/trends ; Turtles/*genetics ; }, abstract = {Comparative syntheses of key demographic parameters are critical not only for identifying data gaps, but also for evaluating sources of heterogeneity among estimates. Because demographic studies frequently exhibit heterogeneity, evaluating sources of heterogeneity among estimates can inform biological patterns and conservation actions more broadly. To better understand adult survival in marine turtles and avoid drawing inaccurate conclusions from current estimates, we conducted a comprehensive meta-analysis to test how heterogeneity among estimates was partitioned among phylogenetic, biogeographic and methodological factors. Fifty-nine studies from five marine turtle species met the minimum selection criteria for inclusion in our meta-analysis. Heterogeneity among survival estimates was first partitioned between differences in ocean basin (Indo-Pacific versus Atlantic), then by differences among family/tribe within the Indo-Pacific (Chelonini versus Carettini and Dermochelidae). However, apparent differences attributed to biogeography (ocean basin effect) and phylogeny (family/tribe effect) were highly correlated with methodological differences in tag type, model type, habitat type and study duration, thereby confounding biological interpretations and complicating efforts to use many current survival estimates in population assessments. Our results highlight the importance of evaluating sources of heterogeneity when interpreting patterns among similar demographic studies and directly inform efforts to identify research priorities for marine turtles globally.}, } @article {pmid29643269, year = {2018}, author = {Mori, S and Matsunami, M}, title = {Signature of positive selection in mitochondrial DNA in Cetartiodactyla.}, journal = {Genes & genetic systems}, volume = {93}, number = {2}, pages = {65-73}, doi = {10.1266/ggs.17-00015}, pmid = {29643269}, issn = {1880-5779}, mesh = {Amino Acid Substitution ; Animals ; Artiodactyla/*genetics ; Biological Evolution ; Cetacea/*genetics ; DNA, Mitochondrial/*genetics ; Databases, Genetic ; Evolution, Molecular ; Genomics ; Mammals/genetics ; Mitochondria/genetics ; Phylogeny ; Selection, Genetic/genetics ; }, abstract = {Acceleration of the amino acid substitution rate is a good indicator of positive selection in adaptive evolutionary changes of functional genes. Genomic information about mammals has become readily available in recent years, as many researchers have attempted to clarify the adaptive evolution of mammals by examining evolutionary rate change based on multiple loci. The order Cetartiodactyla (Artiodactyla and Cetacea) is one of the most diverse orders of mammals. Species in this order are found throughout all continents and seas, except Antarctica, and they exhibit wide variation in morphology and habitat. Here, we focused on the metabolism-related genes of mitochondrial DNA (mtDNA) in species of the order Cetartiodactyla using 191 mtDNA sequences available in databases. Based on comparisons of the dN/dS ratio (ω) in 12 protein-coding genes, ATP8 was shown to have a higher ω value (ω = 0.247) throughout Cetartiodactyla than the other 11 genes (ω < 0.05). In a branch-site analysis of ATP8 sequences, a markedly higher ω value of 0.801 was observed in the ancestral lineage of the clade of Cetacea, which is indicative of adaptive evolution. Through efforts to detect positively selected amino acids, codon positions 52 and 54 of ATP8 were shown to have experienced positive selective pressure during the course of evolution; multiple substitutions have occurred at these sites throughout the cetacean lineage. At position 52, glutamic acid was replaced with asparagine, and, at position 54, lysine was replaced with non-charged amino acids. These sites are conserved in most Artiodactyla. These results imply that the ancestor of cetaceans underwent accelerated amino acid changes in ATP8 and replacements at codons 52 and 54, which adjusted metabolism to adapt to the marine environment.}, } @article {pmid29642940, year = {2018}, author = {Dai, Z and Coker, OO and Nakatsu, G and Wu, WKK and Zhao, L and Chen, Z and Chan, FKL and Kristiansen, K and Sung, JJY and Wong, SH and Yu, J}, title = {Multi-cohort analysis of colorectal cancer metagenome identified altered bacteria across populations and universal bacterial markers.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {70}, pmid = {29642940}, issn = {2049-2618}, support = {766613, 14106145, 14111216//RGC-GRF/International ; 2016YFC1303200//135 Program Project China/International ; 2013CB531401//973 Program China/International ; 2014BAI09B05//National Key Technology R&D Program/International ; }, mesh = {Aged ; Bacteria/*classification/*genetics ; Cell Transformation, Neoplastic ; Colorectal Neoplasms/diagnosis/*etiology ; Computational Biology/methods ; Female ; *Gastrointestinal Microbiome ; Gene Ontology ; Humans ; Male ; *Metagenome ; *Metagenomics/methods ; Middle Aged ; }, abstract = {BACKGROUND: Alterations of gut microbiota are associated with colorectal cancer (CRC) in different populations and several bacterial species were found to contribute to the tumorigenesis. The potential use of gut microbes as markers for early diagnosis has also been reported. However, cohort specific noises may distort the structure of microbial dysbiosis in CRC and lead to inconsistent results among studies. In this regard, our study targeted at exploring changes in gut microbiota that are universal across populations at species level.

RESULTS: Based on the combined analysis of 526 metagenomic samples from Chinese, Austrian, American, and German and French cohorts, seven CRC-enriched bacteria (Bacteroides fragilis, Fusobacterium nucleatum, Porphyromonas asaccharolytica, Parvimonas micra, Prevotella intermedia, Alistipes finegoldii, and Thermanaerovibrio acidaminovorans) have been identified across populations. The seven enriched bacterial markers classified cases from controls with an area under the receiver-operating characteristics curve (AUC) of 0.80 across the different populations. Abundance correlation analysis demonstrated that CRC-enriched and CRC-depleted bacteria respectively formed their own mutualistic networks, in which the latter was disjointed in CRC. The CRC-enriched bacteria have been found to be correlated with lipopolysaccharide and energy biosynthetic pathways.

CONCLUSIONS: Our study identified potential diagnostic bacterial markers that are robust across populations, indicating their potential universal use for non-invasive CRC diagnosis. We also elucidated the ecological networks and functional capacities of CRC-associated microbiota.}, } @article {pmid29642841, year = {2018}, author = {Sivade Dumousseau, M and Alonso-López, D and Ammari, M and Bradley, G and Campbell, NH and Ceol, A and Cesareni, G and Combe, C and De Las Rivas, J and Del-Toro, N and Heimbach, J and Hermjakob, H and Jurisica, I and Koch, M and Licata, L and Lovering, RC and Lynn, DJ and Meldal, BHM and Micklem, G and Panni, S and Porras, P and Ricard-Blum, S and Roechert, B and Salwinski, L and Shrivastava, A and Sullivan, J and Thierry-Mieg, N and Yehudi, Y and Van Roey, K and Orchard, S}, title = {Encompassing new use cases - level 3.0 of the HUPO-PSI format for molecular interactions.}, journal = {BMC bioinformatics}, volume = {19}, number = {1}, pages = {134}, pmid = {29642841}, issn = {1471-2105}, support = {/WT_/Wellcome Trust/United Kingdom ; R01 GM071909/GM/NIGMS NIH HHS/United States ; R01 GM123126/GM/NIGMS NIH HHS/United States ; BB/L024179/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Databases, Protein ; Humans ; Mutation/genetics ; *Protein Interaction Maps ; Proteome/*metabolism ; *Proteomics ; Systems Biology ; }, abstract = {BACKGROUND: Systems biologists study interaction data to understand the behaviour of whole cell systems, and their environment, at a molecular level. In order to effectively achieve this goal, it is critical that researchers have high quality interaction datasets available to them, in a standard data format, and also a suite of tools with which to analyse such data and form experimentally testable hypotheses from them. The PSI-MI XML standard interchange format was initially published in 2004, and expanded in 2007 to enable the download and interchange of molecular interaction data. PSI-XML2.5 was designed to describe experimental data and to date has fulfilled this basic requirement. However, new use cases have arisen that the format cannot properly accommodate. These include data abstracted from more than one publication such as allosteric/cooperative interactions and protein complexes, dynamic interactions and the need to link kinetic and affinity data to specific mutational changes.

RESULTS: The Molecular Interaction workgroup of the HUPO-PSI has extended the existing, well-used XML interchange format for molecular interaction data to meet new use cases and enable the capture of new data types, following extensive community consultation. PSI-MI XML3.0 expands the capabilities of the format beyond simple experimental data, with a concomitant update of the tool suite which serves this format. The format has been implemented by key data producers such as the International Molecular Exchange (IMEx) Consortium of protein interaction databases and the Complex Portal.

CONCLUSIONS: PSI-MI XML3.0 has been developed by the data producers, data users, tool developers and database providers who constitute the PSI-MI workgroup. This group now actively supports PSI-MI XML2.5 as the main interchange format for experimental data, PSI-MI XML3.0 which additionally handles more complex data types, and the simpler, tab-delimited MITAB2.5, 2.6 and 2.7 for rapid parsing and download.}, } @article {pmid29641291, year = {2018}, author = {Moran, LM and Kowalczyk, WJ and Phillips, KA and Vahabzadeh, M and Lin, JL and Mezghanni, M and Epstein, DH and Preston, KL}, title = {Sex differences in daily life stress and craving in opioid-dependent patients.}, journal = {The American journal of drug and alcohol abuse}, volume = {44}, number = {5}, pages = {512-523}, pmid = {29641291}, issn = {1097-9891}, support = {Z01 DA000175-14//Intramural NIH HHS/United States ; ZIA DA000499-12//Intramural NIH HHS/United States ; }, mesh = {Adult ; Affect ; Analgesics, Opioid/administration & dosage ; Cocaine-Related Disorders/psychology ; *Craving ; Cues ; *Ecological Momentary Assessment ; Female ; Humans ; Male ; Middle Aged ; Opiate Substitution Treatment/methods ; Opioid-Related Disorders/*psychology/rehabilitation ; Outpatients ; Sex Factors ; Smartphone ; Stress, Psychological/*epidemiology ; }, abstract = {BACKGROUND: Responses to stress and drug craving differ between men and women. Differences in the momentary experience of stress in relation to craving are less well-understood.

OBJECTIVES: Using ecological momentary assessment (EMA), we examined sex differences in real-time in two areas: (1) causes and contexts associated with stress, and (2) the extent to which stress and drug cues are associated with craving.

METHODS: Outpatients on opioid-agonist treatment (135 males, 47 females) reported stress, craving, and behavior on smartphones for 16 weeks. They initiated an entry each time they felt more stressed than usual (stress event) and made randomly prompted entries 3 times/day. In stress-event entries, they identified the causes and context (location, activity, companions), and rated stress and craving severity.

RESULTS: The causes reported for stress events did not differ significantly by sex. Women reported arguing and being in a store more often during stress events, and men reported working more often during stress events, compared to base rates (assessed via random prompts). Women showed a greater increase in opioid craving as a function of stress (p < 0.0001) and had higher stress ratings in the presence of both stress and drug cues relative to men (p < 0.01). Similar effects were found for cocaine craving in men (p < 0.0001).

CONCLUSION: EMA methods provide evidence based on real-time activities and moods that opioid-dependent men and women experience similar contexts and causes for stress but differ in stress- and cue-induced craving. These findings support sex-based tailoring of treatment, but because not all participants conformed to the overall pattern of sex differences, any such tailoring should also consider person-level differences.}, } @article {pmid29638009, year = {2018}, author = {Visser, MA}, title = {Care Like Kin: Community Based Youth Serving Organizations and the Social Reproduction of Disconnected Youth in Rural America.}, journal = {American journal of community psychology}, volume = {61}, number = {3-4}, pages = {472-487}, doi = {10.1002/ajcp.12244}, pmid = {29638009}, issn = {1573-2770}, mesh = {Adolescent ; California ; *Community Networks/organization & administration ; Economic Recession ; Homeless Youth ; Humans ; Interviews as Topic ; Mental Health ; Qualitative Research ; *Rural Population ; *Unemployment ; United States ; Young Adult ; }, abstract = {Increasing economic insecurity faced by older youth in rural America presents a crisis of social reproduction for disconnected youth in these areas. Increasingly community based youth serving organizations (CBYSOs) are recognizing and responding to the social reproduction needs of this particularly vulnerable youth population. Such responses are often hidden from funders, government agencies, and community residents. Yet these institutions play an important substitution function for disconnected youth and provide critical social support and social leverage for this population. Based on case studies of three CBYSOs in the San Joaquin Valley of California, this article explores how and why CBYSOs play a substitution function for disconnected youth in rural communities. It is the argument of this article that the social reproduction work of CBYSOs is undertaken with a ethic of care that may have the capacity to transform the political, social, and economic contexts that face this marginalized youth population.}, } @article {pmid29636512, year = {2018}, author = {Pechal, JL and Schmidt, CJ and Jordan, HR and Benbow, ME}, title = {A large-scale survey of the postmortem human microbiome, and its potential to provide insight into the living health condition.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {5724}, pmid = {29636512}, issn = {2045-2322}, mesh = {*Autopsy ; Computational Biology/methods ; Cross-Sectional Studies ; Humans ; Metagenome ; Metagenomics/methods ; *Microbiota ; Time Factors ; }, abstract = {The microbiome plays many roles in human health, often through the exclusive lens of clinical interest. The inevitable end point for all living hosts, death, has its own altered microbiome configurations. However, little is understood about the ecology and changes of microbial communities after death, or their potential utility for understanding the health condition of the recently living. Here we reveal distinct postmortem microbiomes of human hosts from a large-scale survey of death cases representing a predominantly urban population, and demonstrated these microbiomes reflected antemortem health conditions within 24-48 hours of death. Our results characterized microbial community structure and predicted function from 188 cases representing a cross-section of an industrial-urban population. We found strong niche differentiation of anatomic habitat and microbial community turnover based on topographical distribution. Microbial community stability was documented up to two days after death. Additionally, we observed a positive relationship between cell motility and time since host death. Interestingly, we discovered evidence that microbial biodiversity is a predictor of antemortem host health condition (e.g., heart disease). These findings improve the understanding of postmortem host microbiota dynamics, and provide a robust dataset to test the postmortem microbiome as a tool for assessing health conditions in living populations.}, } @article {pmid29636401, year = {2018}, author = {Vakkalanka, JP and Harland, KK and Swanson, MB and Mohr, NM}, title = {Clinical and epidemiological variability in severe sepsis: an ecological study.}, journal = {Journal of epidemiology and community health}, volume = {72}, number = {8}, pages = {741-745}, pmid = {29636401}, issn = {1470-2738}, support = {T32 GM007337/GM/NIGMS NIH HHS/United States ; }, mesh = {Adult ; Aged ; Aged, 80 and over ; Databases, Factual ; Emergency Service, Hospital ; Humans ; Incidence ; Iowa/epidemiology ; Middle Aged ; Retrospective Studies ; Sepsis/*epidemiology/mortality/*physiopathology ; }, abstract = {BACKGROUND: To assess clinical and epidemiological trends of severe sepsis.

METHODS: Ecological study of patients presenting to the emergency department with severe sepsis or septic shock between 2005 and 2013. Patients were identified using the state-wide hospital administrative database. Key outcomes included incidence rates (IRs) and mortality rates (per 1000 population) by age and medically underserved areas (MUAs), sepsis case fatality rate (deaths per 100 sepsis cases), and proportions of transfer and comorbidities.

RESULTS: There were 154 019 sepsis cases identified. In 2005, 85+ yo in non-MUAs had a 44% increase in IR compared with those in MUAs, and this difference rose to 74% by 2013. Mortality rates were 1.6 (95% CI 1.3 to 1.8) times greater among 85+ yo in non-MUAs. Mortality rates increased by 1.8% annually, while the sepsis case fatality rate decreased by 7.7%. The proportion of transfer among sepsis cases decreased by 2.1% per year (3.8% in non-MUAs, 0.7% in MUAs).

CONCLUSIONS: Sepsis incidence varies geographically, and access to healthcare is one proposed mechanism that may explain heterogeneity. Over time, we may be capturing higher acuity sepsis cases with better recognition and management, as well as observing differential diagnostic coding documentation by location.}, } @article {pmid29636007, year = {2018}, author = {Woods, LC and Li, Y and Ding, Y and Liu, J and Reading, BJ and Fuller, SA and Song, J}, title = {DNA methylation profiles correlated to striped bass sperm fertility.}, journal = {BMC genomics}, volume = {19}, number = {1}, pages = {244}, pmid = {29636007}, issn = {1471-2164}, support = {Seed grant//USDA/NRAC/International ; Seed grant//USDA/NRAC/International ; }, mesh = {Animals ; Bass/*genetics/physiology ; *DNA Methylation ; Fertility/*genetics ; Gene Ontology ; Male ; Sequence Analysis, DNA ; Spermatozoa/*physiology ; }, abstract = {BACKGROUND: Striped bass (Morone saxatilis) spermatozoa are used to fertilize in vitro the eggs of white bass (M. chrysops) to produce the preferred hybrid for the striped bass aquaculture industry. Currently, only one source of domestic striped bass juveniles is available to growers that is not obtained from wild-caught parents and is thus devoid of any genetic improvement in phenotypic traits of importance to aquaculture. Sperm epigenetic modification has been predicted to be associated with fertility, which could switch genes on and off without changing the DNA sequence itself. DNA methylation is one of the most common epigenetic modification types and changes in sperm epigenetics can be correlated to sub-fertility or infertility in male striped bass. The objective of this study was to find the differentially methylated regions (DMRs) between high-fertility and sub-fertility male striped bass, which could potentially regulate the fertility performance.

RESULTS: In our present study, we performed DNA methylation analysis of high-fertility and sub-fertility striped bass spermatozoa through MBD-Seq methods. A total of 171 DMRs were discovered in striped bass sperm correlated to fertility. Based on the annotation of these DMRs, we conducted a functional classification analysis and two important groups of genes including the WDR3/UTP12 and GPCR families, were discovered to be related to fertility performance of striped bass. Proteins from the WDR3/UTP12 family are involved in forming the sperm flagella apparatus in vertebrates and GPCRs are involved in hormonal signaling and regulation of tissue development, proliferation and differentiation.

CONCLUSIONS: Our results contribute insights into understanding the mechanism of fertility in striped bass, which will provide powerful tools to maximize reproductive efficiencies and to identify those males with superior gametes for this important aquaculture species.}, } @article {pmid29636006, year = {2018}, author = {Tørresen, OK and Brieuc, MSO and Solbakken, MH and Sørhus, E and Nederbragt, AJ and Jakobsen, KS and Meier, S and Edvardsen, RB and Jentoft, S}, title = {Genomic architecture of haddock (Melanogrammus aeglefinus) shows expansions of innate immune genes and short tandem repeats.}, journal = {BMC genomics}, volume = {19}, number = {1}, pages = {240}, pmid = {29636006}, issn = {1471-2164}, support = {#222378/F20//Norges Forskningsråd/ ; #234367/E40//Norges Forskningsråd/ ; }, mesh = {Animals ; Fish Proteins/*genetics ; Gadiformes/*genetics ; Genetic Variation ; *Genome ; Histocompatibility Antigens Class I/genetics ; Immunity, Innate/*genetics ; *Microsatellite Repeats ; NLR Proteins/genetics ; Population Density ; Toll-Like Receptors/genetics ; }, abstract = {BACKGROUND: Increased availability of genome assemblies for non-model organisms has resulted in invaluable biological and genomic insight into numerous vertebrates, including teleosts. Sequencing of the Atlantic cod (Gadus morhua) genome and the genomes of many of its relatives (Gadiformes) demonstrated a shared loss of the major histocompatibility complex (MHC) II genes 100 million years ago. An improved version of the Atlantic cod genome assembly shows an extreme density of tandem repeats compared to other vertebrate genome assemblies. Highly contiguous assemblies are therefore needed to further investigate the unusual immune system of the Gadiformes, and whether the high density of tandem repeats found in Atlantic cod is a shared trait in this group.

RESULTS: Here, we have sequenced and assembled the genome of haddock (Melanogrammus aeglefinus) - a relative of Atlantic cod - using a combination of PacBio and Illumina reads. Comparative analyses reveal that the haddock genome contains an even higher density of tandem repeats outside and within protein coding sequences than Atlantic cod. Further, both species show an elevated number of tandem repeats in genes mainly involved in signal transduction compared to other teleosts. A characterization of the immune gene repertoire demonstrates a substantial expansion of MCHI in Atlantic cod compared to haddock. In contrast, the Toll-like receptors show a similar pattern of gene losses and expansions. For the NOD-like receptors (NLRs), another gene family associated with the innate immune system, we find a large expansion common to all teleosts, with possible lineage-specific expansions in zebrafish, stickleback and the codfishes.

CONCLUSIONS: The generation of a highly contiguous genome assembly of haddock revealed that the high density of short tandem repeats as well as expanded immune gene families is not unique to Atlantic cod - but possibly a feature common to all, or most, codfishes. A shared expansion of NLR genes in teleosts suggests that the NLRs have a more substantial role in the innate immunity of teleosts than other vertebrates. Moreover, we find that high copy number genes combined with variable genome assembly qualities may impede complete characterization of these genes, i.e. the number of NLRs in different teleost species might be underestimates.}, } @article {pmid29635297, year = {2018}, author = {Geib, SM and Hall, B and Derego, T and Bremer, FT and Cannoles, K and Sim, SB}, title = {Genome Annotation Generator: a simple tool for generating and correcting WGS annotation tables for NCBI submission.}, journal = {GigaScience}, volume = {7}, number = {4}, pages = {1-5}, pmid = {29635297}, issn = {2047-217X}, mesh = {Computational Biology/*methods ; Databases, Genetic ; Molecular Sequence Annotation ; *Software ; Whole Genome Sequencing ; }, abstract = {BACKGROUND: One of the most overlooked, yet critical, components of a whole genome sequencing (WGS) project is the submission and curation of the data to a genomic repository, most commonly the National Center for Biotechnology Information (NCBI). While large genome centers or genome groups have developed software tools for post-annotation assembly filtering, annotation, and conversion into the NCBI's annotation table format, these tools typically require back-end setup and connection to an Structured Query Language (SQL) database and/or some knowledge of programming (Perl, Python) to implement. With WGS becoming commonplace, genome sequencing projects are moving away from the genome centers and into the ecology or biology lab, where fewer resources are present to support the process of genome assembly curation. To fill this gap, we developed software to assess, filter, and transfer annotation and convert a draft genome assembly and annotation set into the NCBI annotation table (.tbl) format, facilitating submission to the NCBI Genome Assembly database. This software has no dependencies, is compatible across platforms, and utilizes a simple command to perform a variety of simple and complex post-analysis, pre-NCBI submission WGS project tasks.

FINDINGS: The Genome Annotation Generator is a consistent and user-friendly bioinformatics tool that can be used to generate a .tbl file that is consistent with the NCBI submission pipeline.

CONCLUSIONS: The Genome Annotation Generator achieves the goal of providing a publicly available tool that will facilitate the submission of annotated genome assemblies to the NCBI. It is useful for any individual researcher or research group that wishes to submit a genome assembly of their study system to the NCBI.}, } @article {pmid29634425, year = {2018}, author = {Kowalczyk, WJ and Moran, LM and Bertz, JW and Phillips, KA and Ghitza, UE and Vahabzadeh, M and Lin, JL and Epstein, DH and Preston, KL}, title = {Using ecological momentary assessment to examine the relationship between craving and affect with opioid use in a clinical trial of clonidine as an adjunct medication to buprenorphine treatment.}, journal = {The American journal of drug and alcohol abuse}, volume = {44}, number = {5}, pages = {502-511}, pmid = {29634425}, issn = {1097-9891}, support = {Z01 DA000175-14//Intramural NIH HHS/United States ; ZIA DA000175-22//Intramural NIH HHS/United States ; ZIA DA000499-12//Intramural NIH HHS/United States ; ZIA DA000536-12//Intramural NIH HHS/United States ; }, mesh = {Adrenergic alpha-2 Receptor Agonists/administration & dosage ; Adult ; Affect/drug effects ; Buprenorphine/*administration & dosage ; Clonidine/*administration & dosage ; Craving/drug effects ; Double-Blind Method ; Drug Therapy, Combination ; *Ecological Momentary Assessment ; Female ; Humans ; Linear Models ; Male ; Middle Aged ; Narcotic Antagonists/administration & dosage ; Opiate Substitution Treatment/methods ; Opioid-Related Disorders/*drug therapy/psychology ; }, abstract = {BACKGROUND: In a recent clinical trial (NCT00295308), we demonstrated that clonidine decreased the association between opioid craving and moderate levels of stress and affect in patients receiving buprenorphine-based opioid agonist therapy.

OBJECTIVES: To examine the relationship between illicit opioid use and craving and affect during the evaluation of clonidine as an adjunct medication in buprenorphine treatment for opioid use disorder. Secondarily, to examine whether those relationships are driven by within- or between-participant factors.

METHODS: This was a secondary data analysis from our original trial. Participants (N = 108, female: n = 23, male n = 85) receiving buprenorphine were randomized to receive adjunct clonidine or placebo. Participants used portable electronic devices to rate stress, mood, and craving via ecological momentary assessment (EMA) four times randomly each day. To associate the EMA data with illicit opioid use, each EMA report was linked to participants' next urine drug screen (thrice weekly). We used generalized linear mixed models to examine the interaction between treatment group and illicit opioid use, as well as to decompose the analysis into within- and between-participant effects.

RESULTS: Craving for opioids and cocaine was increased when participants were using illicit opioids; this effect was greater in the clonidine group. For affect, mood was poorer during periods preceding opioid-positive urines than opioid-negative urines for clonidine-treated participants, whereas there was no difference for placebo participants.

CONCLUSION: This secondary analysis provides evidence that for participants maintained on opioid agonist therapy, clonidine minimized the behavioral impact of moderate levels of negative affect and craving.}, } @article {pmid29630562, year = {2018}, author = {Olivieri, I and Meriggi, P and Fedeli, C and Brazzoli, E and Castagna, A and Roidi, MLR and Angelini, L}, title = {Computer Assisted REhabilitation (CARE) Lab: A novel approach towards Pediatric Rehabilitation 2.0.}, journal = {Journal of pediatric rehabilitation medicine}, volume = {11}, number = {1}, pages = {43-51}, pmid = {29630562}, issn = {1875-8894}, mesh = {Adolescent ; Child ; Humans ; Paresis/congenital/rehabilitation ; Rehabilitation/*methods ; Therapy, Computer-Assisted/*methods ; User-Computer Interface ; }, abstract = {Pediatric Rehabilitation therapists have always worked using a variety of off-the-shelf or custom-made objects and devices, more recently including computer based systems. These Information and Communication Technology (ICT) solutions vary widely in complexity, from easy-to-use interactive videogame consoles originally intended for entertainment purposes to sophisticated systems specifically developed for rehabilitation.This paper describes the principles underlying an innovative "Pediatric Rehabilitation 2.0" approach, based on the combination of suitable ICT solutions and traditional rehabilitation, which has been progressively refined while building up and using a computer-assisted rehabilitation laboratory. These principles are thus summarized in the acronym EPIQ, to account for the terms Ecological, Personalized, Interactive and Quantitative. The paper also presents the laboratory, which has been designed to meet the children's rehabilitation needs and to empower therapists in their work. The laboratory is equipped with commercial hardware and specially developed software called VITAMIN: a virtual reality platform for motor and cognitive rehabilitation.}, } @article {pmid29624439, year = {2018}, author = {Settanni, M and Azucar, D and Marengo, D}, title = {Predicting Individual Characteristics from Digital Traces on Social Media: A Meta-Analysis.}, journal = {Cyberpsychology, behavior and social networking}, volume = {21}, number = {4}, pages = {217-228}, doi = {10.1089/cyber.2017.0384}, pmid = {29624439}, issn = {2152-2723}, mesh = {*Databases, Factual ; Humans ; *Internet ; Social Behavior ; *Social Media ; }, abstract = {The increasing utilization of social media provides a vast and new source of user-generated ecological data (digital traces), which can be automatically collected for research purposes. The availability of these data sets, combined with the convergence between social and computer sciences, has led researchers to develop automated methods to extract digital traces from social media and use them to predict individual psychological characteristics and behaviors. In this article, we reviewed the literature on this topic and conducted a series of meta-analyses to determine the strength of associations between digital traces and specific individual characteristics; personality, psychological well-being, and intelligence. Potential moderator effects were analyzed with respect to type of social media platform, type of digital traces examined, and study quality. Our findings indicate that digital traces from social media can be studied to assess and predict theoretically distant psychosocial characteristics with remarkable accuracy. Analysis of moderators indicated that the collection of specific types of information (i.e., user demographics), and the inclusion of different types of digital traces, could help improve the accuracy of predictions.}, } @article {pmid29620755, year = {2018}, author = {Kwok, R}, title = {Ecology's remote-sensing revolution.}, journal = {Nature}, volume = {556}, number = {7699}, pages = {137-138}, doi = {10.1038/d41586-018-03924-9}, pmid = {29620755}, issn = {1476-4687}, mesh = {Animals ; Cloud Computing ; Conservation of Natural Resources ; Data Interpretation, Statistical ; *Datasets as Topic ; Ecology/instrumentation/*methods ; Machine Learning ; Satellite Imagery/instrumentation/*methods/*statistics & numerical data ; Software ; United States ; United States National Aeronautics and Space Administration ; }, } @article {pmid29618526, year = {2018}, author = {Ching, T and Himmelstein, DS and Beaulieu-Jones, BK and Kalinin, AA and Do, BT and Way, GP and Ferrero, E and Agapow, PM and Zietz, M and Hoffman, MM and Xie, W and Rosen, GL and Lengerich, BJ and Israeli, J and Lanchantin, J and Woloszynek, S and Carpenter, AE and Shrikumar, A and Xu, J and Cofer, EM and Lavender, CA and Turaga, SC and Alexandari, AM and Lu, Z and Harris, DJ and DeCaprio, D and Qi, Y and Kundaje, A and Peng, Y and Wiley, LK and Segler, MHS and Boca, SM and Swamidass, SJ and Huang, A and Gitter, A and Greene, CS}, title = {Opportunities and obstacles for deep learning in biology and medicine.}, journal = {Journal of the Royal Society, Interface}, volume = {15}, number = {141}, pages = {}, pmid = {29618526}, issn = {1742-5662}, support = {U54 AI117924/AI/NIAID NIH HHS/United States ; UL1 TR001409/TR/NCATS NIH HHS/United States ; T32 GM007753/GM/NIGMS NIH HHS/United States ; P30 ES013508/ES/NIEHS NIH HHS/United States ; DP2 GM123485/GM/NIGMS NIH HHS/United States ; R01 GM089753/GM/NIGMS NIH HHS/United States ; R21 CA220398/CA/NCI NIH HHS/United States ; R35 GM122547/GM/NIGMS NIH HHS/United States ; T32 HG000046/HG/NHGRI NIH HHS/United States ; }, mesh = {Algorithms ; Biomedical Research/methods/*trends ; Biomedical Technology/*trends ; Decision Making ; Deep Learning/*trends ; Delivery of Health Care/methods/trends ; Disease/genetics ; Drug Design ; Electronic Health Records/trends ; Humans ; Terminology as Topic ; }, abstract = {Deep learning describes a class of machine learning algorithms that are capable of combining raw inputs into layers of intermediate features. These algorithms have recently shown impressive results across a variety of domains. Biology and medicine are data-rich disciplines, but the data are complex and often ill-understood. Hence, deep learning techniques may be particularly well suited to solve problems of these fields. We examine applications of deep learning to a variety of biomedical problems-patient classification, fundamental biological processes and treatment of patients-and discuss whether deep learning will be able to transform these tasks or if the biomedical sphere poses unique challenges. Following from an extensive literature review, we find that deep learning has yet to revolutionize biomedicine or definitively resolve any of the most pressing challenges in the field, but promising advances have been made on the prior state of the art. Even though improvements over previous baselines have been modest in general, the recent progress indicates that deep learning methods will provide valuable means for speeding up or aiding human investigation. Though progress has been made linking a specific neural network's prediction to input features, understanding how users should interpret these models to make testable hypotheses about the system under study remains an open challenge. Furthermore, the limited amount of labelled data for training presents problems in some domains, as do legal and privacy constraints on work with sensitive health records. Nonetheless, we foresee deep learning enabling changes at both bench and bedside with the potential to transform several areas of biology and medicine.}, } @article {pmid29618314, year = {2018}, author = {Dobrin, BH and Zwickl, DJ and Sanderson, MJ}, title = {The prevalence of terraced treescapes in analyses of phylogenetic data sets.}, journal = {BMC evolutionary biology}, volume = {18}, number = {1}, pages = {46}, pmid = {29618314}, issn = {1471-2148}, support = {DEB-1353815//National Science Foundation/International ; }, mesh = {*Databases, Genetic ; Genes ; Models, Genetic ; *Phylogeny ; }, abstract = {BACKGROUND: The pattern of data availability in a phylogenetic data set may lead to the formation of terraces, collections of equally optimal trees. Terraces can arise in tree space if trees are scored with parsimony or with partitioned, edge-unlinked maximum likelihood. Theory predicts that terraces can be large, but their prevalence in contemporary data sets has never been surveyed. We selected 26 data sets and phylogenetic trees reported in recent literature and investigated the terraces to which the trees would belong, under a common set of inference assumptions. We examined terrace size as a function of the sampling properties of the data sets, including taxon coverage density (the proportion of taxon-by-gene positions with any data present) and a measure of gene sampling "sufficiency". We evaluated each data set in relation to the theoretical minimum gene sampling depth needed to reduce terrace size to a single tree, and explored the impact of the terraces found in replicate trees in bootstrap methods.

RESULTS: Terraces were identified in nearly all data sets with taxon coverage densities < 0.90. They were not found, however, in high-coverage-density (i.e., ≥ 0.94) transcriptomic and genomic data sets. The terraces could be very large, and size varied inversely with taxon coverage density and with gene sampling sufficiency. Few data sets achieved a theoretical minimum gene sampling depth needed to reduce terrace size to a single tree. Terraces found during bootstrap resampling reduced overall support.

CONCLUSIONS: If certain inference assumptions apply, trees estimated from empirical data sets often belong to large terraces of equally optimal trees. Terrace size correlates to data set sampling properties. Data sets seldom include enough genes to reduce terrace size to one tree. When bootstrap replicate trees lie on a terrace, statistical support for phylogenetic hypotheses may be reduced. Although some of the published analyses surveyed were conducted with edge-linked inference models (which do not induce terraces), unlinked models have been used and advocated. The present study describes the potential impact of that inference assumption on phylogenetic inference in the context of the kinds of multigene data sets now widely assembled for large-scale tree construction.}, } @article {pmid29617811, year = {2018}, author = {Hao, Y and Washburn, JD and Rosenthal, J and Nielsen, B and Lyons, E and Edger, PP and Pires, JC and Conant, GC}, title = {Patterns of Population Variation in Two Paleopolyploid Eudicot Lineages Suggest That Dosage-Based Selection on Homeologs Is Long-Lived.}, journal = {Genome biology and evolution}, volume = {10}, number = {3}, pages = {999-1011}, pmid = {29617811}, issn = {1759-6653}, mesh = {Arabidopsis/genetics ; Brassica/genetics ; *Evolution, Molecular ; Gene Dosage/genetics ; Gene Duplication ; Genes, Plant/genetics ; Genome, Plant/*genetics ; Phylogeny ; Polyploidy ; Selection, Genetic/*genetics ; }, abstract = {Genes that are inherently subject to strong selective constraints tend to be overretained in duplicate after polyploidy. They also continue to experience similar, but somewhat relaxed, constraints after that polyploidy event. We sought to assess for how long the influence of polyploidy is felt on these genes' selective pressures. We analyzed two nested polyploidy events in Brassicaceae: the At-α genome duplication that is the most recent polyploidy in the model plant Arabidopsis thaliana and a more recent hexaploidy shared by the genus Brassica and its relatives. By comparing the strength and direction of the natural selection acting at the population and at the species level, we find evidence for continued intensified purifying selection acting on retained duplicates from both polyploidies even down to the present. The constraint observed in preferentially retained genes is not a result of the polyploidy event: the orthologs of such genes experience even stronger constraint in nonpolyploid outgroup genomes. In both the Arabidopsis and Brassica lineages, we further find evidence for segregating mildly deleterious variants, confirming that the population-level data uncover patterns not visible with between-species comparisons. Using the A. thaliana metabolic network, we also explored whether network position was correlated with the measured selective constraint. At both the population and species level, nodes/genes tended to show similar constraints to their neighbors. Our results paint a picture of the long-lived effects of polyploidy on plant genomes, suggesting that even yesterday's polyploids still have distinct evolutionary trajectories.}, } @article {pmid29608592, year = {2018}, author = {Chang, LM}, title = {webpic: A flexible web application for collecting distance and count measurements from images.}, journal = {PloS one}, volume = {13}, number = {4}, pages = {e0195184}, pmid = {29608592}, issn = {1932-6203}, mesh = {Data Collection ; Data Mining ; Image Processing, Computer-Assisted/methods ; *Software ; *Web Browser ; }, abstract = {Despite increasing ability to store and analyze large amounts of data for organismal and ecological studies, the process of collecting distance and count measurements from images has largely remained time consuming and error-prone, particularly for tasks for which automation is difficult or impossible. Improving the efficiency of these tasks, which allows for more high quality data to be collected in a shorter amount of time, is therefore a high priority. The open-source web application, webpic, implements common web languages and widely available libraries and productivity apps to streamline the process of collecting distance and count measurements from images. In this paper, I introduce the framework of webpic and demonstrate one readily available feature of this application, linear measurements, using fossil leaf specimens. This application fills the gap between workflows accomplishable by individuals through existing software and those accomplishable by large, unmoderated crowds. It demonstrates that flexible web languages can be used to streamline time-intensive research tasks without the use of specialized equipment or proprietary software and highlights the potential for web resources to facilitate data collection in research tasks and outreach activities with improved efficiency.}, } @article {pmid29605834, year = {2018}, author = {Vargová, B and Majláth, I and Kurimský, J and Cimbala, R and Kosterec, M and Tryjanowski, P and Jankowiak, Ł and Raši, T and Majláthová, V}, title = {Electromagnetic radiation and behavioural response of ticks: an experimental test.}, journal = {Experimental & applied acarology}, volume = {75}, number = {1}, pages = {85-95}, pmid = {29605834}, issn = {1572-9702}, support = {26220220116//Research & Development Operational Programme funded by the ERDF/ ; 1/0417/14//Scientific Grant Agency of the Ministry of Education of the Slovak Republic and the Slovak Academy of Sciences/ ; 1/0311/15//Scientific Grant Agency of the Ministry of Education of the Slovak Republic and the Slovak Academy of Sciences/ ; 2/0141/16//Scientific Grant Agency of the Ministry of Education of the Slovak Republic and the Slovak Academy of Sciences/ ; 26220120055//Ministry of Education Agency for structural funds of EU/ ; APVV-15-0438//Slovak Research and Development Agency/ ; }, mesh = {Animal Distribution/*radiation effects ; Animals ; Dermacentor/*radiation effects ; Electromagnetic Fields/*adverse effects ; Female ; Male ; Radio Waves/*adverse effects ; Slovakia ; }, abstract = {Factors associated with the increased usage of electronic devices, wireless technologies and mobile phones nowadays are present in increasing amounts in our environment. All living organisms are constantly affected by electromagnetic radiation which causes serious environmental pollution. The distribution and density of ticks in natural habitats is influenced by a complex of abiotic and biotic factors. Exposure to radio-frequency electromagnetic field (RF-EMF) constitutes a potential cause altering the presence and distribution of ticks in the environment. Our main objective was to determine the affinity of Dermacentor reticulatus ticks towards RF-EMF exposure. Originally designed and constructed radiation-shielded tube (RST) test was used to test the affinity of ticks under controlled laboratory conditions. All test were performed in an electromagnetic compatibility laboratory in an anechoic chamber. Ticks were irradiated using a Double-Ridged Waveguide Horn Antenna to RF-EMF at 900 and 5000 MHz, 0 MHz was used as control. The RF-EMF exposure to 900 MHz induced a higher concentration of ticks on irradiated arm of RST as opposed to the RF-EMF at 5000 MHz, which caused an escape of ticks to the shielded arm. This study represents the first experimental evidence of RF-EMF preference in D. reticulatus. The projection of obtained results to the natural environment could help assess the risk of tick borne diseases and could be a tool of preventive medicine.}, } @article {pmid29605386, year = {2018}, author = {Redston, S and de Botte, S and Smith, C}, title = {Resolving embarrassing medical conditions with online health information.}, journal = {International journal of medical informatics}, volume = {114}, number = {}, pages = {101-105}, doi = {10.1016/j.ijmedinf.2018.03.010}, pmid = {29605386}, issn = {1872-8243}, mesh = {Bayes Theorem ; Data Collection ; *Disease ; *Embarrassment ; Humans ; Internet/*statistics & numerical data ; Medical Informatics/*methods ; *Problem Solving ; }, abstract = {PURPOSE: Reliance on online health information is proliferating and the Internet has the potential to revolutionize the provision of public health information. The anonymity of online health information may be particularly appealing to people seeking advice on 'embarrassing' health problems. The purpose of this study was to investigate (1) whether data generated by the embarrassingproblems.com health information site showed any temporal patterns in problem resolution, and (2) whether successful resolution of a medical problem using online information varied with the type of medical problem.

METHODS: We analyzed the responses of visitors to the embarrassingproblems.com website on the resolution of their problems. The dataset comprised 100,561 responses to information provided on 77 different embarrassing problems grouped into 9 classes of medical problem over an 82-month period. Data were analyzed with a Bernoulli Generalized Linear Model using Bayesian inference.

RESULTS: We detected a statistically important interaction between embarrassing problem type and the time period in which data were collected, with an improvement in problem resolution over time for all of the classes of medical problem on the website but with a lower rate of increase in resolution for urinary health problems and medical problems associated with the mouth and face. As far as we are aware, this is the first analysis of data of this nature.

CONCLUSIONS: Findings support the growing recognition that online health information can contribute to the resolution of embarrassing medical problems, but demonstrate that outcomes may vary with medical problem type. The results indicate that building data collection into online information provision can help to refine and focus health information for online users.}, } @article {pmid29603732, year = {2018}, author = {Foglia, L and Borsi, I and Mehl, S and De Filippis, G and Cannata, M and Vasquez-Suñe, E and Criollo, R and Rossetto, R}, title = {FREEWAT, a Free and Open Source, GIS-Integrated, Hydrological Modeling Platform.}, journal = {Ground water}, volume = {56}, number = {4}, pages = {521-523}, doi = {10.1111/gwat.12654}, pmid = {29603732}, issn = {1745-6584}, mesh = {*Geographic Information Systems ; *Groundwater ; Hydrology ; }, } @article {pmid29603138, year = {2018}, author = {Eiserhardt, WL and Antonelli, A and Bennett, DJ and Botigué, LR and Burleigh, JG and Dodsworth, S and Enquist, BJ and Forest, F and Kim, JT and Kozlov, AM and Leitch, IJ and Maitner, BS and Mirarab, S and Piel, WH and Pérez-Escobar, OA and Pokorny, L and Rahbek, C and Sandel, B and Smith, SA and Stamatakis, A and Vos, RA and Warnow, T and Baker, WJ}, title = {A roadmap for global synthesis of the plant tree of life.}, journal = {American journal of botany}, volume = {105}, number = {3}, pages = {614-622}, doi = {10.1002/ajb2.1041}, pmid = {29603138}, issn = {1537-2197}, mesh = {DNA, Plant ; Humans ; *Information Dissemination ; *Information Management ; Information Technology ; *Phylogeny ; Plants/*genetics ; Sequence Analysis, DNA ; }, abstract = {Providing science and society with an integrated, up-to-date, high quality, open, reproducible and sustainable plant tree of life would be a huge service that is now coming within reach. However, synthesizing the growing body of DNA sequence data in the public domain and disseminating the trees to a diverse audience are often not straightforward due to numerous informatics barriers. While big synthetic plant phylogenies are being built, they remain static and become quickly outdated as new data are published and tree-building methods improve. Moreover, the body of existing phylogenetic evidence is hard to navigate and access for non-experts. We propose that our community of botanists, tree builders, and informaticians should converge on a modular framework for data integration and phylogenetic analysis, allowing easy collaboration, updating, data sourcing and flexible analyses. With support from major institutions, this pipeline should be re-run at regular intervals, storing trees and their metadata long-term. Providing the trees to a diverse global audience through user-friendly front ends and application development interfaces should also be a priority. Interactive interfaces could be used to solicit user feedback and thus improve data quality and to coordinate the generation of new data. We conclude by outlining a number of steps that we suggest the scientific community should take to achieve global phylogenetic synthesis.}, } @article {pmid29602265, year = {2018}, author = {Stanford, BCM and Rogers, SM}, title = {R(NA)-tistic expression: The art of matching unknown mRNA and proteins to environmental response in ecological genomics.}, journal = {Molecular ecology}, volume = {27}, number = {4}, pages = {827-830}, doi = {10.1111/mec.14419}, pmid = {29602265}, issn = {1365-294X}, mesh = {Animals ; *Daphnia ; Ecology ; Gene Ontology ; Genomics ; *RNA, Messenger ; }, abstract = {A challenge of modern ecological genomics is reducing uncertainty surrounding the biological inferences from gene expression. For example, approximately 40% of proteins in eukaryotic model organisms do not contain characterized domains (Gollery et al., 2006). Even proteins of "known function" are typically only characterized in the sense that they have a domain function, but provide no information on their biological role within the cell (e.g., activation, pathways or targets). Yet, as molecular ecologists, a common objective is to elucidate how organisms respond to environmental variation through changes in gene expression, including homoeostatic, acclimatory, and adaptive responses to environmental stressors, a challenge increased by poor protein ecological annotation. Now, in this issue of Molecular Ecology, Orsini et al. (2017) use the quintessential Daphnia system to characterize the differences in stress response in three genotypic backgrounds to common biotic and abiotic stressors found in nature. Using an optimized weighted gene co-expression network analysis, they link genes of unknown function to genes that they co-activate with and enrich for gene ontology. Determining the functional networks of genes that behave in genotype- and treatment-specific responses gives insight into possible pathways and respective ecological roles, helping pave the way for the next generation of transcriptomic studies in molecular ecology.}, } @article {pmid29600646, year = {2018}, author = {Yu, J and Ye, Q and Ning, SJ and Li, Q and Tan, HX and Feng, JX and Chen, RB and Ma, XL and Gong, PM and Zhao, XX and Zhang, L and Wei, DZ}, title = {[Bioinformation analysis of chorismate synthase in Baphicacantus cusia and other 78 species of plants].}, journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica}, volume = {43}, number = {4}, pages = {721-730}, doi = {10.19540/j.cnki.cjcmm.20180105.002}, pmid = {29600646}, issn = {1001-5302}, mesh = {Acanthaceae/*enzymology ; Amino Acid Sequence ; Computational Biology ; Phosphorus-Oxygen Lyases/*chemistry ; Phylogeny ; Plant Proteins/*chemistry ; Protein Structure, Secondary ; }, abstract = {Chorismate synthase(CS, EC:4.2.3.5) catalyses 5-enolpyruvy-shikimate-3-phosphate to form chorismate, which is the essential enzyme for chorismate biosynthesis in organisms. The amino acid sequences of CS from 79 species of higher plants were reported in GenBank at present. 125 amino acid sequences of CS from Baphicacanthus cusia and other 78 species of plants were predicted and analyzed by using various bioinformatics software, including the composition of amino acid sequences, signal peptide, leader peptide, hydrophobic/hydrophilic, transmembrane structure, coiled-coil domain, protein secondary structure, tertiary structure and functional domains. The phylogenetic tree of CS protein family was constructed and divided into eight groups by phylogenetic analysis. The homology comparison indicated that B. cusia shared a high homology with several plants such as Sesamum indicum, Nicotiana tabacum, Solanum tuberosum and so on. The open reading frame(ORF) of all samples is about 1 300 bp, the molecular weight is about 50 kDa, the isoelectric point(pI) is 5.0-8.0 which illustrated that CS protein is slightly basic. The ORF of CS we cloned in B. cusia is 1 326 bp, the amino acid residues are 442, the molecular weight is 47 kDa and pI is 8.11. The CS in B.cusia showed obvious hydrophobicity area and hydrophilicity area, no signal peptide, and may exists transmembrane structure areas. The main secondary structures of CS protein are random coil and Alpha helix, also contain three main structural domains which are an active structural domain, a PLN02754 conserved domain and a FMN binding site. The acquired information in this study would provide certain scientific basis for further study on structure-activity relationship and structure modification of CS in plants in the future.}, } @article {pmid29599464, year = {2018}, author = {Muška, M and Tušer, M and Frouzová, J and Mrkvička, T and Ricard, D and Seďa, J and Morelli, F and Kubečka, J}, title = {Real-time distribution of pelagic fish: combining hydroacoustics, GIS and spatial modelling at a fine spatial scale.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {5381}, pmid = {29599464}, issn = {2045-2322}, mesh = {Acoustics ; Animals ; Ecosystem ; Environmental Monitoring ; Fishes/*physiology ; Geographic Information Systems ; Population Dynamics ; *Spatial Analysis ; }, abstract = {Understanding spatial distribution of organisms in heterogeneous environment remains one of the chief issues in ecology. Spatial organization of freshwater fish was investigated predominantly on large-scale, neglecting important local conditions and ecological processes. However, small-scale processes are of an essential importance for individual habitat preferences and hence structuring trophic cascades and species coexistence. In this work, we analysed the real-time spatial distribution of pelagic freshwater fish in the Římov Reservoir (Czechia) observed by hydroacoustics in relation to important environmental predictors during 48 hours at 3-h interval. Effect of diurnal cycle was revealed of highest significance in all spatial models with inverse trends between fish distribution and predictors in day and night in general. Our findings highlighted daytime pelagic fish distribution as highly aggregated, with general fish preferences for central, deep and highly illuminated areas, whereas nighttime distribution was more disperse and fish preferred nearshore steep sloped areas with higher depth. This turnover suggests prominent movements of significant part of fish assemblage between pelagic and nearshore areas on a diel basis. In conclusion, hydroacoustics, GIS and spatial modelling proved as valuable tool for predicting local fish distribution and elucidate its drivers, which has far reaching implications for understanding freshwater ecosystem functioning.}, } @article {pmid29599447, year = {2018}, author = {Baert, JM and Stienen, EWM and Heylen, BC and Kavelaars, MM and Buijs, RJ and Shamoun-Baranes, J and Lens, L and Müller, W}, title = {High-resolution GPS tracking reveals sex differences in migratory behaviour and stopover habitat use in the Lesser Black-backed Gull Larus fuscus.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {5391}, pmid = {29599447}, issn = {2045-2322}, mesh = {Animal Migration/*physiology ; Animals ; Charadriiformes/*physiology ; *Ecosystem ; Female ; Geographic Information Systems ; Male ; Seasons ; Sex Characteristics ; }, abstract = {Sex-, size- or age-dependent variation in migration strategies in birds is generally expected to reflect differences in competitive abilities. Theoretical and empirical studies thereby focus on differences in wintering areas, by which individuals may benefit from avoiding food competition during winter or ensuring an early return and access to prime nesting sites in spring. Here, we use GPS tracking to assess sex- and size-related variation in the spatial behaviour of adult Lesser Black-backed Gulls (Larus fuscus) throughout their annual cycle. We did not find sex- or size-dependent differences in wintering area or the timing of spring migration. Instead, sexual differences occurred prior to, and during, autumn migration, when females strongly focussed on agricultural areas. Females exhibited a more protracted autumn migration strategy, hence spent more time on stopover sites and arrived 15 days later at their wintering areas, than males. This shift in habitat use and protracted autumn migration coincided with the timing of moult, which overlaps with chick rearing and migration. Our results suggest that this overlap between energy-demanding activities may lead females to perform a more prolonged autumn migration, which results in spatiotemporal differences in foraging habitat use between the sexes.}, } @article {pmid29597054, year = {2018}, author = {Parra-Henao, G and Amioka, E and Franco-Paredes, C and Colborn, KL and Henao-Martínez, AF}, title = {Heart Failure Symptoms and Ecological Factors as Predictors of Chagas Disease Among Indigenous Communities in the Sierra Nevada de Santa Marta, Colombia.}, journal = {Journal of cardiac failure}, volume = {24}, number = {12}, pages = {864-866}, doi = {10.1016/j.cardfail.2018.03.007}, pmid = {29597054}, issn = {1532-8414}, mesh = {Adult ; Chagas Disease/*complications/epidemiology ; Colombia/epidemiology ; Cross-Sectional Studies ; Echocardiography ; Electrocardiography ; Environmental Exposure/*adverse effects ; Female ; Heart Failure/diagnosis/epidemiology/*etiology ; Humans ; Incidence ; Male ; Population Groups/*statistics & numerical data ; Prognosis ; Risk Factors ; }, } @article {pmid29596744, year = {2018}, author = {Li, SY and Liu, JK and Zhao, GP and Wang, J}, title = {CADS: CRISPR/Cas12a-Assisted DNA Steganography for Securing the Storage and Transfer of DNA-Encoded Information.}, journal = {ACS synthetic biology}, volume = {7}, number = {4}, pages = {1174-1178}, doi = {10.1021/acssynbio.8b00074}, pmid = {29596744}, issn = {2161-5063}, mesh = {CRISPR-Cas Systems/*genetics ; Computer Security ; *DNA ; DNA Primers ; DNA, Single-Stranded ; Escherichia coli/genetics ; HEK293 Cells ; Humans ; Information Storage and Retrieval/*methods ; Polymerase Chain Reaction ; RNA ; }, abstract = {Because DNA has the merit of high capacity and complexity, DNA steganography, which conceals DNA-encoded messages, is very promising in information storage. The classical DNA steganography method hides DNA with a "secret message" in a mount of junk DNA, and the message can be extracted by polymerase chain reaction (PCR) using specific primers (key), followed by DNA sequencing and sequence decoding. As leakage of the primer information may result in message insecurity, new methods are needed to better secure the DNA information. Here, we develop a pre-key by either mixing specific primers (real key) with nonspecific primers (fake key) or linking a real key with 3'-end redundant sequences. Then, the single-stranded DNA (ssDNA) trans cleavage activity of CRISPR/Cas12a is employed to cut a fake key or remove the 3'-end redundant sequences, generating a real key for further information extraction. Therefore, with the Cas12a-assisted DNA steganography method, both storage and transfer of DNA-encoding data can be better protected.}, } @article {pmid29596482, year = {2018}, author = {Slater, K and Barrett, A and Brown, LR}, title = {Home range utilization by chacma baboon (Papio ursinus) troops on Suikerbosrand Nature Reserve, South Africa.}, journal = {PloS one}, volume = {13}, number = {3}, pages = {e0194717}, pmid = {29596482}, issn = {1932-6203}, mesh = {Animals ; *Conservation of Natural Resources ; Geographic Information Systems ; *Homing Behavior ; Movement ; *Papio ursinus ; Seasons ; South Africa ; }, abstract = {Rapid urbanization coupled with decreasing areas of natural habitat are causing baboon populations to become scattered and isolated, often resulting in increased levels of human-baboon conflict. To implement baboon-human conflict management strategies, it is essential to formulate realistic conservation policies that deal with all stakeholder concerns and ensure the conservation of viable baboon populations. A study was initiated in response to complaints of perceived excessive baboon numbers and associated lack of food resources on Suikerbosrand Nature Reserve in South Africa. Data obtained from GPS tracking collars fitted to one baboon from each of 10 identified troops were analyzed to determine home range size and utilization. The spatial representation of home ranges generated from this study will allow reserve management to identify areas of potential high and low human-baboon conflict and will contribute to the development of a formal baboon management plan to reduce human-baboon conflict on and around the reserve. Home ranges were unevenly distributed and had a mean size of 26.72 km2 ± 13.91 SD in the cold/dry season and 26.54 km2 ± 12.76 SD in the warm/wet season. Troop home ranges overlapped to some degree and five troops utilized areas outside the reserve. Although no significant relationship between troop size and home range was found, there was a positive relationship between troop size and daily distance travelled. All troops had significantly longer mean daily distances during the warm/wet season than during the cold/dry season (P ≤ 0.02).}, } @article {pmid29596446, year = {2018}, author = {Barengolts, E and Green, SJ and Eisenberg, Y and Akbar, A and Reddivari, B and Layden, BT and Dugas, L and Chlipala, G}, title = {Gut microbiota varies by opioid use, circulating leptin and oxytocin in African American men with diabetes and high burden of chronic disease.}, journal = {PloS one}, volume = {13}, number = {3}, pages = {e0194171}, pmid = {29596446}, issn = {1932-6203}, support = {IK2 BX001587/BX/BLRD VA/United States ; R01 DK104927/DK/NIDDK NIH HHS/United States ; R01DK104927-01A1/NH/NIH HHS/United States ; }, mesh = {*Black or African American ; Bacteria/genetics/growth & development ; Chronic Disease ; Cost of Illness ; Cross-Sectional Studies ; *Diabetes Mellitus, Type 2/blood/microbiology ; *Gastrointestinal Microbiome ; Humans ; Leptin/*blood ; Male ; Metformin/administration & dosage ; *Opioid-Related Disorders/blood/microbiology ; Oxytocin/*blood ; }, abstract = {OBJECTIVE: The gut microbiota is known to be related to type 2 diabetes (T2D), psychiatric conditions, and opioid use. In this study, we tested the hypothesis that variability in gut microbiota in T2D is associated with psycho-metabolic health.

METHODS: A cross-sectional study was conducted among African American men (AAM) (n = 99) that were outpatients at a Chicago VA Medical Center. The main outcome measures included fecal microbiota ecology (by 16S rRNA gene sequencing), psychiatric disorders including opioid use, and circulating leptin and oxytocin as representative hormone biomarkers for obesity and psychological pro-social behavior.

RESULTS: The study subjects had prevalent overweight/obesity (78%), T2D (50%) and co-morbid psychiatric (65%) and opioid use (45%) disorders. In the analysis of microbiota, the data showed interactions of opioids, T2D and metformin with Bifidobacterium and Prevotella genera. The differential analysis of Bifidobacterium stratified by opioids, T2D and metformin, showed significant interactions among these factors indicating that the effect of one factor was changed by the other (FDR-adjusted p [q] < 0.01). In addition, the pair-wise comparison showed that participants with T2D not taking metformin had a significant 6.74 log2 fold increase in Bifidobacterium in opioid users as compared to non-users (q = 2.2 x 10-8). Since metformin was not included in this pair-wise comparison, the significant 'q' suggested association of opioid use with Bifidobacterium abundance. The differences in Bifidobacterium abundance could possibly be explained by opioids acting as organic cation transporter 1 (OCT1) inhibitors. Analysis stratified by lower and higher leptin and oxytocin (divided by the 50th percentile) in the subgroup without T2D showed lower Dialister in High-Leptin vs. Low-Leptin (p = 0.03). Contrary, the opposite was shown for oxytocin, higher Dialister in High-Oxytocin vs. Low-Oxytocin (p = 0.04).

CONCLUSIONS: The study demonstrated for the first time that Bifidobacterium and Prevotella abundance was affected by interactions of T2D, metformin and opioid use. Also, in subjects without T2D Dialister abundance varied according to circulating leptin and oxytocin.}, } @article {pmid29595363, year = {2019}, author = {Holland, CAC and Ebner, NC and Lin, T and Samanez-Larkin, GR}, title = {Emotion identification across adulthood using the Dynamic FACES database of emotional expressions in younger, middle aged, and older adults.}, journal = {Cognition & emotion}, volume = {33}, number = {2}, pages = {245-257}, pmid = {29595363}, issn = {1464-0600}, support = {R00 AG042596/AG/NIA NIH HHS/United States ; }, mesh = {Adolescent ; Adult ; Age Factors ; Aged ; Aged, 80 and over ; Databases, Factual ; Emotions/*physiology ; *Facial Expression ; Female ; Humans ; Male ; Middle Aged ; Photic Stimulation/*methods ; Young Adult ; }, abstract = {Facial stimuli are widely used in behavioural and brain science research to investigate emotional facial processing. However, some studies have demonstrated that dynamic expressions elicit stronger emotional responses compared to static images. To address the need for more ecologically valid and powerful facial emotional stimuli, we created Dynamic FACES, a database of morphed videos (n = 1026) from younger, middle-aged, and older adults displaying naturalistic emotional facial expressions (neutrality, sadness, disgust, fear, anger, happiness). To assess adult age differences in emotion identification of dynamic stimuli and to provide normative ratings for this modified set of stimuli, healthy adults (n = 1822, age range 18-86 years) categorised for each video the emotional expression displayed, rated the expression distinctiveness, estimated the age of the face model, and rated the naturalness of the expression. We found few age differences in emotion identification when using dynamic stimuli. Only for angry faces did older adults show lower levels of identification accuracy than younger adults. Further, older adults outperformed middle-aged adults' in identification of sadness. The use of dynamic facial emotional stimuli has previously been limited, but Dynamic FACES provides a large database of high-resolution naturalistic, dynamic expressions across adulthood. Information on using Dynamic FACES for research purposes can be found at http://faces.mpib-berlin.mpg.de .}, } @article {pmid29593680, year = {2018}, author = {Ren, M and Zhang, Z and Wang, X and Zhou, Z and Chen, D and Zeng, H and Zhao, S and Chen, L and Hu, Y and Zhang, C and Liang, Y and She, Q and Zhang, Y and Peng, N}, title = {Diversity and Contributions to Nitrogen Cycling and Carbon Fixation of Soil Salinity Shaped Microbial Communities in Tarim Basin.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {431}, pmid = {29593680}, issn = {1664-302X}, abstract = {Arid and semi-arid regions comprise nearly one-fifth of the earth's terrestrial surface. However, the diversities and functions of their soil microbial communities are not well understood, despite microbial ecological importance in driving biogeochemical cycling. Here, we analyzed the geochemistry and microbial communities of the desert soils from Tarim Basin, northwestern China. Our geochemical data indicated half of these soils are saline. Metagenomic analysis showed that bacterial phylotypes (89.72% on average) dominated the community, with relatively small proportions of Archaea (7.36%) and Eukaryota (2.21%). Proteobacteria, Firmicutes, Actinobacteria, and Euryarchaeota were most abundant based on metagenomic data, whereas genes attributed to Proteobacteria, Actinobacteria, Euryarchaeota, and Thaumarchaeota most actively transcribed. The most abundant phylotypes (Halobacterium, Halomonas, Burkholderia, Lactococcus, Clavibacter, Cellulomonas, Actinomycetospora, Beutenbergia, Pseudomonas, and Marinobacter) in each soil sample, based on metagenomic data, contributed marginally to the population of all microbial communities, whereas the putative halophiles, which contributed the most abundant transcripts, were in the majority of the active microbial population and is consistent with the soil salinity. Sample correlation analyses according to the detected and active genotypes showed significant differences, indicating high diversity of microbial communities among the Tarim soil samples. Regarding ecological functions based on the metatranscriptomic data, transcription of genes involved in various steps of nitrogen cycling, as well as carbon fixation, were observed in the tested soil samples. Metatranscriptomic data also indicated that Thaumarchaeota are crucial for ammonia oxidation and Proteobacteria play the most important role in other steps of nitrogen cycle. The reductive TCA pathway and dicarboxylate-hydroxybutyrate cycle attributed to Proteobacteria and Crenarchaeota, respectively, were highly represented in carbon fixation. Our study reveals that the microbial communities could provide carbon and nitrogen nutrients for higher plants in the sandy saline soils of Tarim Basin.}, } @article {pmid29590103, year = {2018}, author = {Emery, M and Willis, MMS and Hao, Y and Barry, K and Oakgrove, K and Peng, Y and Schmutz, J and Lyons, E and Pires, JC and Edger, PP and Conant, GC}, title = {Preferential retention of genes from one parental genome after polyploidy illustrates the nature and scope of the genomic conflicts induced by hybridization.}, journal = {PLoS genetics}, volume = {14}, number = {3}, pages = {e1007267}, pmid = {29590103}, issn = {1553-7404}, mesh = {Brassicaceae/*genetics ; Evolution, Molecular ; *Genes, Plant ; *Genomic Imprinting ; *Hybridization, Genetic ; Models, Genetic ; *Polyploidy ; }, abstract = {Polyploidy is increasingly seen as a driver of both evolutionary innovation and ecological success. One source of polyploid organisms' successes may be their origins in the merging and mixing of genomes from two different species (e.g., allopolyploidy). Using POInT (the Polyploid Orthology Inference Tool), we model the resolution of three allopolyploidy events, one from the bakers' yeast (Saccharomyces cerevisiae), one from the thale cress (Arabidopsis thaliana) and one from grasses including Sorghum bicolor. Analyzing a total of 21 genomes, we assign to every gene a probability for having come from each parental subgenome (i.e., derived from the diploid progenitor species), yielding orthologous segments across all genomes. Our model detects statistically robust evidence for the existence of biased fractionation in all three lineages, whereby genes from one of the two subgenomes were more likely to be lost than those from the other subgenome. We further find that a driver of this pattern of biased losses is the co-retention of genes from the same parental genome that share functional interactions. The pattern of biased fractionation after the Arabidopsis and grass allopolyploid events was surprisingly constant in time, with the same parental genome favored throughout the lineages' history. In strong contrast, the yeast allopolyploid event shows evidence of biased fractionation only immediately after the event, with balanced gene losses more recently. The rapid loss of functionally associated genes from a single subgenome is difficult to reconcile with the action of genetic drift and suggests that selection may favor the removal of specific duplicates. Coupled to the evidence for continuing, functionally-associated biased fractionation after the A. thaliana At-α event, we suggest that, after allopolyploidy, there are functional conflicts between interacting genes encoded in different subgenomes that are ultimately resolved through preferential duplicate loss.}, } @article {pmid29581009, year = {2018}, author = {Ouellet, É and Boller, B and Corriveau-Lecavalier, N and Cloutier, S and Belleville, S}, title = {The Virtual Shop: A new immersive virtual reality environment and scenario for the assessment of everyday memory.}, journal = {Journal of neuroscience methods}, volume = {303}, number = {}, pages = {126-135}, doi = {10.1016/j.jneumeth.2018.03.010}, pmid = {29581009}, issn = {1872-678X}, support = {MOP81302//CIHR/Canada ; RN109554 − 246831//CIHR/Canada ; RN205414 − 315174//CIHR/Canada ; }, mesh = {*Activities of Daily Living ; Adult ; Aged ; Aging/physiology ; Diagnosis, Computer-Assisted/instrumentation/*methods ; Feasibility Studies ; Female ; Humans ; Male ; Memory/*physiology ; Memory Disorders/diagnosis ; Middle Aged ; *Neuropsychological Tests ; Reproducibility of Results ; *Virtual Reality ; Young Adult ; }, abstract = {BACKGROUND: Assessing and predicting memory performance in everyday life is a common assignment for neuropsychologists. However, most traditional neuropsychological tasks are not conceived to capture everyday memory performance.

NEW METHOD: The Virtual Shop is a fully immersive task developed to assess memory in a more ecological way than traditional neuropsychological assessments. Two studies were undertaken to assess the feasibility of the Virtual Shop and to appraise its ecological and construct validity. In study 1, 20 younger and 19 older adults completed the Virtual Shop task to evaluate its level of difficulty and the way the participants interacted with the VR material. The construct validity was examined with the contrasted-group method, by comparing the performance of younger and older adults. In study 2, 35 individuals with subjective cognitive decline completed the Virtual Shop task. Performance was correlated with an existing questionnaire evaluating everyday memory in order to appraise its ecological validity. To add further support to its construct validity, performance was correlated with traditional episodic memory and executive tasks.

RESULTS: All participants successfully completed the Virtual Shop. The task had an appropriate level of difficulty that helped differentiate younger and older adults, supporting the feasibility and construct validity of the task.

The performance on the Virtual Shop was significantly and moderately correlated with the performance on the questionnaire and on the traditional memory and executive tasks.

CONCLUSIONS: Results support the feasibility and both the ecological and construct validity of the Virtual Shop.}, } @article {pmid29579103, year = {2018}, author = {Geldenhuys, M and Mortlock, M and Weyer, J and Bezuidt, O and Seamark, ECJ and Kearney, T and Gleasner, C and Erkkila, TH and Cui, H and Markotter, W}, title = {A metagenomic viral discovery approach identifies potential zoonotic and novel mammalian viruses in Neoromicia bats within South Africa.}, journal = {PloS one}, volume = {13}, number = {3}, pages = {e0194527}, pmid = {29579103}, issn = {1932-6203}, mesh = {Adenoviridae/genetics/pathogenicity ; Animals ; Chiroptera/physiology/*virology ; Computational Biology ; Coronavirus/genetics/pathogenicity ; Coronavirus Infections/veterinary/*virology ; Gastrointestinal Tract/physiology/virology ; Genetic Variation ; Genome, Viral/*genetics ; Herpesviridae/genetics/pathogenicity ; High-Throughput Nucleotide Sequencing ; Humans ; Mammals/*virology ; Metagenomics/methods ; Phylogeny ; Phylogeography ; Sequence Analysis, DNA ; South Africa ; Zoonoses/*virology ; }, abstract = {Species within the Neoromicia bat genus are abundant and widely distributed in Africa. It is common for these insectivorous bats to roost in anthropogenic structures in urban regions. Additionally, Neoromicia capensis have previously been identified as potential hosts for Middle East respiratory syndrome (MERS)-related coronaviruses. This study aimed to ascertain the gastrointestinal virome of these bats, as viruses excreted in fecal material or which may be replicating in rectal or intestinal tissues have the greatest opportunities of coming into contact with other hosts. Samples were collected in five regions of South Africa over eight years. Initial virome composition was determined by viral metagenomic sequencing by pooling samples and enriching for viral particles. Libraries were sequenced on the Illumina MiSeq and NextSeq500 platforms, producing a combined 37 million reads. Bioinformatics analysis of the high throughput sequencing data detected the full genome of a novel species of the Circoviridae family, and also identified sequence data from the Adenoviridae, Coronaviridae, Herpesviridae, Parvoviridae, Papillomaviridae, Phenuiviridae, and Picornaviridae families. Metagenomic sequencing data was insufficient to determine the viral diversity of certain families due to the fragmented coverage of genomes and lack of suitable sequencing depth, as some viruses were detected from the analysis of reads-data only. Follow up conventional PCR assays targeting conserved gene regions for the Adenoviridae, Coronaviridae, and Herpesviridae families were used to confirm metagenomic data and generate additional sequences to determine genetic diversity. The complete coding genome of a MERS-related coronavirus was recovered with additional amplicon sequencing on the MiSeq platform. The new genome shared 97.2% overall nucleotide identity to a previous Neoromicia-associated MERS-related virus, also from South Africa. Conventional PCR analysis detected diverse adenovirus and herpesvirus sequences that were widespread throughout Neoromicia populations in South Africa. Furthermore, similar adenovirus sequences were detected within these populations throughout several years. With the exception of the coronaviruses, the study represents the first report of sequence data from several viral families within a Southern African insectivorous bat genus; highlighting the need for continued investigations in this regard.}, } @article {pmid29574273, year = {2018}, author = {Psonis, N and Antoniou, A and Karameta, E and Leaché, AD and Kotsakiozi, P and Darriba, D and Kozlov, A and Stamatakis, A and Poursanidis, D and Kukushkin, O and Jablonski, D and Crnobrnja-Isailović, J and Gherghel, I and Lymberakis, P and Poulakakis, N}, title = {Resolving complex phylogeographic patterns in the Balkan Peninsula using closely related wall-lizard species as a model system.}, journal = {Molecular phylogenetics and evolution}, volume = {125}, number = {}, pages = {100-115}, doi = {10.1016/j.ympev.2018.03.021}, pmid = {29574273}, issn = {1095-9513}, mesh = {Animals ; Balkan Peninsula ; Bayes Theorem ; Biodiversity ; Calibration ; DNA, Mitochondrial/genetics ; Genetic Variation ; Genetics, Population ; Genomics ; Haplotypes/genetics ; Lizards/*classification/genetics ; Microsatellite Repeats/genetics ; *Models, Biological ; Phylogeny ; *Phylogeography ; Species Specificity ; }, abstract = {The Balkan Peninsula constitutes a biodiversity hotspot with high levels of species richness and endemism. The complex geological history of the Balkans in conjunction with the climate evolution are hypothesized as the main drivers generating this biodiversity. We investigated the phylogeography, historical demography, and population structure of closely related wall-lizard species from the Balkan Peninsula and southeastern Europe to better understand diversification processes of species with limited dispersal ability, from Late Miocene to the Holocene. We used several analytical methods integrating genome-wide SNPs (ddRADseq), microsatellites, mitochondrial and nuclear DNA data, as well as species distribution modelling. Phylogenomic analysis resulted in a completely resolved species level phylogeny, population level analyses confirmed the existence of at least two cryptic evolutionary lineages and extensive within species genetic structuring. Divergence time estimations indicated that the Messinian Salinity Crisis played a key role in shaping patterns of species divergence, whereas intraspecific genetic structuring was mainly driven by Pliocene tectonic events and Quaternary climatic oscillations. The present work highlights the effectiveness of utilizing multiple methods and data types coupled with extensive geographic sampling to uncover the evolutionary processes that shaped the species over space and time.}, } @article {pmid29572469, year = {2018}, author = {Fuselli, S and Baptista, RP and Panziera, A and Magi, A and Guglielmi, S and Tonin, R and Benazzo, A and Bauzer, LG and Mazzoni, CJ and Bertorelle, G}, title = {A new hybrid approach for MHC genotyping: high-throughput NGS and long read MinION nanopore sequencing, with application to the non-model vertebrate Alpine chamois (Rupicapra rupicapra).}, journal = {Heredity}, volume = {121}, number = {4}, pages = {293-303}, pmid = {29572469}, issn = {1365-2540}, mesh = {Alleles ; Animals ; Computational Biology/methods ; Exons ; Genes, MHC Class II ; Genomics/methods ; Haplotypes ; High-Throughput Nucleotide Sequencing/methods/standards ; Histocompatibility Testing/*methods/standards ; Major Histocompatibility Complex/*genetics ; Polymerase Chain Reaction ; Polymorphism, Genetic ; Recombination, Genetic ; Rupicapra/genetics ; Sequence Analysis, DNA/methods ; }, abstract = {The major histocompatibility complex (MHC) acts as an interface between the immune system and infectious diseases. Accurate characterization and genotyping of the extremely variable MHC loci are challenging especially without a reference sequence. We designed a combination of long-range PCR, Illumina short-reads, and Oxford Nanopore MinION long-reads approaches to capture the genetic variation of the MHC II DRB locus in an Italian population of the Alpine chamois (Rupicapra rupicapra). We utilized long-range PCR to generate a 9 Kb fragment of the DRB locus. Amplicons from six different individuals were fragmented, tagged, and simultaneously sequenced with Illumina MiSeq. One of these amplicons was sequenced with the MinION device, which produced long reads covering the entire amplified fragment. A pipeline that combines short and long reads resolved several short tandem repeats and homopolymers and produced a de novo reference, which was then used to map and genotype the short reads from all individuals. The assembled DRB locus showed a high level of polymorphism and the presence of a recombination breakpoint. Our results suggest that an amplicon-based NGS approach coupled with single-molecule MinION nanopore sequencing can efficiently achieve both the assembly and the genotyping of complex genomic regions in multiple individuals in the absence of a reference sequence.}, } @article {pmid29571418, year = {2018}, author = {Struckhoff, MA and Orazio, CE and Tillitt, DE and Shaver, DK and Papoulias, DM}, title = {Mapping elemental contamination on Palmyra Atoll National Wildlife Refuge.}, journal = {Marine pollution bulletin}, volume = {128}, number = {}, pages = {97-105}, doi = {10.1016/j.marpolbul.2017.12.065}, pmid = {29571418}, issn = {1879-3363}, mesh = {Animals ; Animals, Wild ; Conservation of Natural Resources/*methods ; Coral Reefs ; Ecosystem ; Environmental Monitoring/instrumentation/*methods ; Environmental Pollutants/*analysis ; Geographic Information Systems ; Geologic Sediments/*chemistry ; Pacific Islands ; Pacific Ocean ; Satellite Imagery ; Soil/*chemistry ; Spectrometry, X-Ray Emission ; Trace Elements/*analysis ; United States ; }, abstract = {Palmyra Atoll, once a WWII U.S. Navy air station, is now a U.S. National Wildlife Refuge with nearly 50km[2] of coral reef and 275ha of emergent lands with forests of Pisonia grandis trees and colonies of several bird species. Due to the known elemental and organic contamination from chemicals associated with aviation, power generation and transmission, waste management, and other air station activities, a screening survey to map elemental concentrations was conducted. A map of 1944 Navy facilities was georeferenced and identifiable features were digitized. These data informed a targeted survey of 25 elements in soils and sediment at locations known or suspected to be contaminated, using a hand-held X-ray fluorescence spectrometer. At dozens of locations, concentrations of elements exceeded established soil and marine sediment thresholds for adverse ecological effects. Results were compiled into a publically available geospatial dataset to inform potential remediation and habitat restoration activities.}, } @article {pmid29571390, year = {2018}, author = {Xu, F and Gao, Z and Jiang, X and Shang, W and Ning, J and Song, D and Ai, J}, title = {A UAV and S2A data-based estimation of the initial biomass of green algae in the South Yellow Sea.}, journal = {Marine pollution bulletin}, volume = {128}, number = {}, pages = {408-414}, doi = {10.1016/j.marpolbul.2018.01.061}, pmid = {29571390}, issn = {1879-3363}, mesh = {*Aquaculture ; *Biomass ; China ; Chlorophyta/*growth & development ; Databases, Factual ; Environmental Monitoring/*methods ; Eutrophication ; Oceans and Seas ; Satellite Imagery ; Seawater/chemistry ; }, abstract = {Previous studies have shown that the initial biomass of green tide was the green algae attaching to Pyropia aquaculture rafts in the Southern Yellow Sea. In this study, the green algae was identified with unmanned aerial vehicle (UAV), an biomass estimation model was proposed for green algae biomass in the radial sand ridge area based on Sentinel-2A image (S2A) and UAV images. The result showed that the green algae was detected highly accurately with the normalized green-red difference index (NGRDI); approximately 1340 tons and 700 tons of green algae were attached to rafts and raft ropes respectively, and the lower biomass might be the main cause for the smaller scale of green tide in 2017. In addition, UAV play an important role in raft-attaching green algae monitoring and long-term research of its biomass would provide a scientific basis for the control and forecast of green tide in the Yellow Sea.}, } @article {pmid29569818, year = {2018}, author = {Anderegg, LDL and Berner, LT and Badgley, G and Sethi, ML and Law, BE and HilleRisLambers, J}, title = {Within-species patterns challenge our understanding of the leaf economics spectrum.}, journal = {Ecology letters}, volume = {21}, number = {5}, pages = {734-744}, doi = {10.1111/ele.12945}, pmid = {29569818}, issn = {1461-0248}, mesh = {*Biological Evolution ; Ecology ; Phenotype ; *Plant Leaves ; Plant Physiological Phenomena ; Plants ; }, abstract = {The utility of plant functional traits for predictive ecology relies on our ability to interpret trait variation across multiple taxonomic and ecological scales. Using extensive data sets of trait variation within species, across species and across communities, we analysed whether and at what scales leaf economics spectrum (LES) traits show predicted trait-trait covariation. We found that most variation in LES traits is often, but not universally, at high taxonomic levels (between families or genera in a family). However, we found that trait covariation shows distinct taxonomic scale dependence, with some trait correlations showing opposite signs within vs. across species. LES traits responded independently to environmental gradients within species, with few shared environmental responses across traits or across scales. We conclude that, at small taxonomic scales, plasticity may obscure or reverse the broad evolutionary linkages between leaf traits, meaning that variation in LES traits cannot always be interpreted as differences in resource use strategy.}, } @article {pmid29569108, year = {2018}, author = {Pérez, V and Dorador, C and Molina, V and Yáñez, C and Hengst, M}, title = {Rhodobacter sp. Rb3, an aerobic anoxygenic phototroph which thrives in the polyextreme ecosystem of the Salar de Huasco, in the Chilean Altiplano.}, journal = {Antonie van Leeuwenhoek}, volume = {111}, number = {8}, pages = {1449-1465}, doi = {10.1007/s10482-018-1067-z}, pmid = {29569108}, issn = {1572-9699}, support = {1140179//Fondo Nacional de Desarrollo Científico y Tecnológico/ ; 1140356//Fondo Nacional de Desarrollo Científico y Tecnológico/ ; FB0001//Centro de Biotecnología y Bioingeniería/ ; }, mesh = {Adaptation, Physiological/*genetics ; Altitude ; Chile ; Computational Biology ; DNA, Bacterial/genetics ; *Ecosystem ; *Extreme Environments ; Genes, Bacterial ; Models, Biological ; RNA, Ribosomal, 16S/genetics ; RNA, Transfer/genetics ; Rhodobacter/genetics/metabolism/*physiology ; Species Specificity ; *Water Microbiology ; }, abstract = {The Salar de Huasco is an evaporitic basin located in the Chilean Altiplano, which presents extreme environmental conditions for life, i.e. high altitude (3800 m.a.s.l.), negative water balance, a wide salinity range, high daily temperature changes and the occurrence of the highest registered solar radiation on the planet (> 1200 W m[-2]). This ecosystem is considered as a natural laboratory to understand different adaptations of microorganisms to extreme conditions. Rhodobacter, an anoxygenic aerobic phototrophic bacterial genus, represents one of the most abundant groups reported based on taxonomic diversity surveys in this ecosystem. The bacterial mat isolate Rhodobacter sp. strain Rb3 was used to study adaptation mechanisms to stress-inducing factors potentially explaining its success in a polyextreme ecosystem. We found that the Rhodobacter sp. Rb3 genome was characterized by a high abundance of genes involved in stress tolerance and adaptation strategies, among which DNA repair and oxidative stress were the most conspicuous. Moreover, many other molecular mechanisms associated with oxidative stress, photooxidation and antioxidants; DNA repair and protection; motility, chemotaxis and biofilm synthesis; osmotic stress, metal, metalloid and toxic anions resistance; antimicrobial resistance and multidrug pumps; sporulation; cold shock and heat shock stress; mobile genetic elements and toxin-antitoxin system were detected and identified as potential survival mechanism features in Rhodobacter sp. Rb3. In total, these results reveal a wide set of strategies used by the isolate to adapt and thrive under environmental stress conditions as a model of polyextreme environmental resistome.}, } @article {pmid29566239, year = {2018}, author = {Ueno, S and Nakamura, Y and Kobayashi, M and Terashima, S and Ishizuka, W and Uchiyama, K and Tsumura, Y and Yano, K and Goto, S}, title = {TodoFirGene: Developing Transcriptome Resources for Genetic Analysis of Abies sachalinensis.}, journal = {Plant & cell physiology}, volume = {59}, number = {6}, pages = {1276-1284}, doi = {10.1093/pcp/pcy058}, pmid = {29566239}, issn = {1471-9053}, mesh = {Abies/*genetics ; *Databases, Nucleic Acid ; Flowers/genetics ; Genetic Variation/*genetics ; High-Throughput Nucleotide Sequencing ; Molecular Sequence Annotation ; Plant Bark/genetics ; Plant Leaves/genetics ; Sequence Analysis, RNA ; *Transcriptome ; }, abstract = {Todo-matsu (Abies sachalinensis) is one of the most important forestry species in Hokkaido, Japan and is distributed from near sea level to the alpine zone. Due to its wide spatial distribution, the species adapts to its environment, displaying phenotypes of ecological relevance. In order to identify candidate genes under natural selection, we collected the transcriptome from the female and male flower, leaf and inner bark. De novo assembly with 34.7 Gb of sequencing reads produced 158,542 transcripts from 69,618 loci, whose estimated coverage reached 95.6% of conserved eukaryotic genes. Homology searches against publicly available databases identified 134,190 (84.6%) transcripts with at least one hit. In total, 28,944 simple sequence repeats (SSRs) and 80,758 single nucleotide variants (SNVs) were detected from 23,570 (14.9%) and 25,366 (16.0%) transcripts, which were valuable for use in genetic analysis of the species. All the annotations were included in a relational database, TodoFirGene, which provides an interface for various queries and homology search, and can be accessed at http://plantomics.mind.meiji.ac.jp/todomatsu/. This database hosts not only the A. sachalinensis transcriptome but also links to the proteomes of 13 other species, allowing a comparative genomic study of plant species.}, } @article {pmid29566054, year = {2018}, author = {Jablonski, KE and Boone, RB and Meiman, PJ}, title = {An agent-based model of cattle grazing toxic Geyer's larkspur.}, journal = {PloS one}, volume = {13}, number = {3}, pages = {e0194450}, pmid = {29566054}, issn = {1932-6203}, mesh = {Agriculture/*methods ; Alkaloids/toxicity ; Animals ; Behavior, Animal ; Biological Variation, Population ; Cattle ; Cattle Diseases/etiology/*prevention & control ; Computational Biology ; Delphinium/chemistry/*toxicity ; *Models, Biological ; Plant Poisoning/etiology/*prevention & control/veterinary ; United States ; }, abstract = {By killing cattle and otherwise complicating management, the many species of larkspur (Delphinium spp.) present a serious, intractable, and complex challenge to livestock grazing management in the western United States. Among the many obstacles to improving our understanding of cattle-larkspur dynamics has been the difficulty of testing different grazing management strategies in the field, as the risk of dead animals is too great. Agent-based models (ABMs) provide an effective method of testing alternate management strategies without risk to livestock. ABMs are especially useful for modeling complex systems such as livestock grazing management, and allow for realistic bottom-up encoding of cattle behavior. Here, we introduce a spatially-explicit, behavior-based ABM of cattle grazing in a pasture with a dangerous amount of Geyer's larkspur (D. geyeri). This model tests the role of herd cohesion and stocking density in larkspur intake, finds that both are key drivers of larkspur-induced toxicosis, and indicates that alteration of these factors within realistic bounds can mitigate risk. Crucially, the model points to herd cohesion, which has received little attention in the discipline, as playing an important role in lethal acute toxicosis. As the first ABM to model grazing behavior at realistic scales, this study also demonstrates the tremendous potential of ABMs to illuminate grazing management dynamics, including fundamental aspects of livestock behavior amidst ecological heterogeneity.}, } @article {pmid29566035, year = {2018}, author = {Du, B and Kreuzwieser, J and Dannenmann, M and Junker, LV and Kleiber, A and Hess, M and Jansen, K and Eiblmeier, M and Gessler, A and Kohnle, U and Ensminger, I and Rennenberg, H and Wildhagen, H}, title = {Foliar nitrogen metabolism of adult Douglas-fir trees is affected by soil water availability and varies little among provenances.}, journal = {PloS one}, volume = {13}, number = {3}, pages = {e0194684}, pmid = {29566035}, issn = {1932-6203}, mesh = {Acclimatization ; Adaptation, Physiological ; Climate ; Ecosystem ; Geography ; Germany ; Nitrogen/*metabolism ; North America ; Plant Leaves/*metabolism ; Pseudotsuga/*growth & development/*metabolism ; Soil/*chemistry ; Trees/growth & development/metabolism ; Water/analysis/*metabolism ; }, abstract = {The coniferous forest tree Douglas-fir (Pseudotsuga menziesii) is native to the pacific North America, and is increasingly planted in temperate regions worldwide. Nitrogen (N) metabolism is of great importance for growth, resistance and resilience of trees. In the present study, foliar N metabolism of adult trees of three coastal and one interior provenance of Douglas-fir grown at two common gardens in southwestern Germany (Wiesloch, W; Schluchsee, S) were characterized in two subsequent years. Both the native North American habitats of the seed sources and the common garden sites in Germany differ in climate conditions. Total and mineral soil N as well as soil water content were higher in S compared to W. We hypothesized that i) provenances differ constitutively in N pool sizes and composition, ii) N pools are affected by environmental conditions, and iii) that effects of environmental factors on N pools differ among interior and coastal provenances. Soil water content strongly affected the concentrations of total N, soluble protein, total amino acids (TAA), arginine and glutamate. Foliar concentrations of total N, soluble protein, structural N and TAA of trees grown at W were much higher than in trees at S. Provenance effects were small but significant for total N and soluble protein content (interior provenance showed lowest concentrations), as well as arginine, asparagine and glutamate. Our data suggest that needle N status of adult Douglas-fir is independent from soil N availability and that low soil water availability induces a re-allocation of N from structural N to metabolic N pools. Small provenance effects on N pools suggest that local adaptation of Douglas-fir is not dominated by N conditions at the native habitats.}, } @article {pmid29565658, year = {2018}, author = {Kauh, TJ and Dawkins-Lyn, N and Dooyema, C and Harris, C and Jernigan, J and Kettel Khan, L and Ottley, P and Young-Hyman, D}, title = {Childhood Obesity Declines Project: An Effort of the National Collaborative on Childhood Obesity Research to Explore Progress in Four Communities.}, journal = {Childhood obesity (Print)}, volume = {14}, number = {S1}, pages = {S1-S4}, pmid = {29565658}, issn = {2153-2176}, mesh = {Adolescent ; Child ; Child, Preschool ; Community Health Services/*organization & administration ; Diet, Healthy ; Exercise ; Female ; *Health Promotion/methods ; Humans ; Male ; Pediatric Obesity/epidemiology/*prevention & control ; Prevalence ; Qualitative Research ; Retrospective Studies ; Stakeholder Participation ; United States/epidemiology ; }, abstract = {BACKGROUND: Recent findings show that national childhood obesity prevalence overall is improving among some age groups, but that disparities continue to persist, particularly among populations that have historically been at higher risk of obesity and overweight. Over the past several years, many jurisdictions at the city or county level across the nation have also reported declines. Little evaluation has focused on understanding the factors that influence the implementation of efforts to reduce childhood obesity rates. This article summarizes the rationale, aims, and overall design of the Childhood Obesity Declines Project (COBD), which was the first of its kind to systematically study and document the what, how, when, and where of community-based obesity strategies in four distinct communities across the nation.

METHODS: COBD was initiated by the National Collaborative on Childhood Obesity Research (NCCOR), was led by a subset of NCCOR advisors and a research team at ICF, and was guided by external advisors made up of researchers, decision makers, and other key stakeholders. The research team used an adapted version of the Systematic Screening and Assessment method to review and collect retrospective implementation data in four communities.

RESULTS: COBD found that sites implemented strategies across the many levels and environments that impact children's well being (akin to the social-ecological framework), building a Culture of Health in their communities.

CONCLUSIONS: COBD demonstrates how collaboratives of major funders with the support of other experts and key stakeholders, can help to accelerate progress in identifying and disseminating strategies that promote healthy eating and physical activity.}, } @article {pmid29565654, year = {2018}, author = {Jernigan, J and Kettel Khan, L and Dooyema, C and Ottley, P and Harris, C and Dawkins-Lyn, N and Kauh, T and Young-Hyman, D}, title = {Childhood Obesity Declines Project: Highlights of Community Strategies and Policies.}, journal = {Childhood obesity (Print)}, volume = {14}, number = {S1}, pages = {S32-S39}, pmid = {29565654}, issn = {2153-2176}, mesh = {Adolescent ; Child ; Child, Preschool ; Community Health Services/*organization & administration ; Female ; Guideline Adherence/*statistics & numerical data ; *Health Policy ; Health Promotion/*organization & administration ; Humans ; Male ; Pediatric Obesity/epidemiology/*prevention & control ; Prevalence ; Program Evaluation ; Retrospective Studies ; United States/epidemiology ; }, abstract = {BACKGROUND: The social ecological model (SEM) is a framework for understanding the interactive effects of personal and environmental factors that determine behavior. The SEM has been used to examine childhood obesity interventions and identify factors at each level that impact behaviors. However, little is known about how those factors interact both within and across levels of the SEM.

METHODS: The Childhood Obesity Declines (COBD) project was exploratory, attempting to capture retrospectively policies and programs that occurred in four communities that reported small declines in childhood obesity. It also examined contextual factors that may have influenced initiatives, programs, or policies. Data collection included policy and program assessments, key informant interviews, and document reviews. These data were aggregated by the COBD project team to form a site report for each community (available at www.nccor.org/projects/obesity-declines). These reports were used to develop site summaries that illustrate how policies, programs, and activities worked to address childhood obesity in each study site.

RESULTS/CONCLUSIONS: Site summaries for Anchorage, AK; Granville County, NC; Philadelphia, PA; and New York City, NY, describe those policies and programs implemented across the levels of the SEM to address childhood obesity and examine interactions both across and within levels of the model to better understand what factors appear important for implementation success.}, } @article {pmid29564821, year = {2018}, author = {Henry, IM and Comai, L and Tan, EH}, title = {Detection of Chromothripsis in Plants.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1769}, number = {}, pages = {119-132}, doi = {10.1007/978-1-4939-7780-2_8}, pmid = {29564821}, issn = {1940-6029}, mesh = {*Chromosome Aberrations ; *Chromothripsis ; Computational Biology/methods ; Epigenesis, Genetic ; Genome, Plant ; Genomic Instability ; Genomic Library ; Plants/*genetics ; Ploidies ; Software ; }, abstract = {Chromothripsis, or chromosome shattering, occurs after chromosomes missegregate, are pulverized and subsequently repaired erroneously, leading to highly complex structural rearrangements. In plants, chromothripsis has been observed as a result of mitotic malfunction connected with the incomplete loss of haploid inducer chromosomes during uniparental genome elimination. Uniparental genome elimination, a process that results in haploid induction, is a phenomenon that typically results in the loss of an entire parental chromosome set in early embryos, resulting in haploid plants. In Arabidopsis thaliana, genome elimination can be achieved via the manipulation of the centromere-specific histone H3 variant, CENH3. Genomic characterization of F1 progeny resulting from CENH3-mediated genome elimination crosses in Arabidopsis revealed haploids (~39%), diploids (~25%), and aneuploids (~37%). Within the aneuploid class, ~11% show evidence for chromothripsis. Here, we present a protocol to identify Arabidopsis aneuploids that have inherited chromothriptic chromosomes during genome elimination crosses and describe in detail how to perform in silico reconstructions for individuals with chromothripsis using the somatic mutation finder (SMuFin) tool.}, } @article {pmid29564395, year = {2018}, author = {Lind, AL and Lim, FY and Soukup, AA and Keller, NP and Rokas, A}, title = {An LaeA- and BrlA-Dependent Cellular Network Governs Tissue-Specific Secondary Metabolism in the Human Pathogen Aspergillus fumigatus.}, journal = {mSphere}, volume = {3}, number = {2}, pages = {}, pmid = {29564395}, issn = {2379-5042}, support = {T15 LM007450/LM/NLM NIH HHS/United States ; R01 AI065728/AI/NIAID NIH HHS/United States ; T32 GM007133/GM/NIGMS NIH HHS/United States ; T32 HL007899/HL/NHLBI NIH HHS/United States ; T32 AI055397/AI/NIAID NIH HHS/United States ; }, abstract = {Biosynthesis of many ecologically important secondary metabolites (SMs) in filamentous fungi is controlled by several global transcriptional regulators, like the chromatin modifier LaeA, and tied to both development and vegetative growth. In Aspergillus molds, asexual development is regulated by the BrlA > AbaA > WetA transcriptional cascade. To elucidate BrlA pathway involvement in SM regulation, we examined the transcriptional and metabolic profiles of ΔbrlA, ΔabaA, and ΔwetA mutant and wild-type strains of the human pathogen Aspergillus fumigatus. We find that BrlA, in addition to regulating production of developmental SMs, regulates vegetative SMs and the SrbA-regulated hypoxia stress response in a concordant fashion to LaeA. We further show that the transcriptional and metabolic equivalence of the ΔbrlA and ΔlaeA mutations is mediated by an LaeA requirement preventing heterochromatic marks in the brlA promoter. These results provide a framework for the cellular network regulating not only fungal SMs but diverse cellular processes linked to virulence of this pathogen. IMPORTANCE Filamentous fungi produce a spectacular variety of small molecules, commonly known as secondary or specialized metabolites (SMs), which are critical to their ecologies and lifestyles (e.g., penicillin, cyclosporine, and aflatoxin). Elucidation of the regulatory network that governs SM production is a major question of both fundamental and applied research relevance. To shed light on the relationship between regulation of development and regulation of secondary metabolism in filamentous fungi, we performed global transcriptomic and metabolomic analyses on mutant and wild-type strains of the human pathogen Aspergillus fumigatus under conditions previously shown to induce the production of both vegetative growth-specific and asexual development-specific SMs. We find that the gene brlA, previously known as a master regulator of asexual development, is also a master regulator of secondary metabolism and other cellular processes. We further show that brlA regulation of SM is mediated by laeA, one of the master regulators of SM, providing a framework for the cellular network regulating not only fungal SMs but diverse cellular processes linked to virulence of this pathogen.}, } @article {pmid29563074, year = {2018}, author = {Ehrler, F and Weinhold, T and Joe, J and Lovis, C and Blondon, K}, title = {A Mobile App (BEDSide Mobility) to Support Nurses' Tasks at the Patient's Bedside: Usability Study.}, journal = {JMIR mHealth and uHealth}, volume = {6}, number = {3}, pages = {e57}, pmid = {29563074}, issn = {2291-5222}, abstract = {BACKGROUND: The introduction of clinical information systems has increased the amount of clinical documentation. Although this documentation generally improves patient safety, it has become a time-consuming task for nurses, which limits their time with the patient. On the basis of a user-centered methodology, we have developed a mobile app named BEDSide Mobility to support nurses in their daily workflow and to facilitate documentation at the bedside.

OBJECTIVE: The aim of the study was to assess the usability of the BEDSide Mobility app in terms of the navigation and interaction design through usability testing.

METHODS: Nurses were asked to complete a scenario reflecting their daily work with patients. Their interactions with the app were captured with eye-tracking glasses and by using the think aloud protocol. After completing the tasks, participants filled out the system usability scale questionnaire. Descriptive statistics were used to summarize task completion rates and the users' performance.

RESULTS: A total of 10 nurses (aged 21-50) participated in the study. Overall, they were satisfied with the navigation, layout, and interaction design of the app, with the exception of one user who was unfamiliar with smartphones. The problems identified were related to the ambiguity of some icons, the navigation logic, and design inconsistency.

CONCLUSIONS: Besides the usability issues identified in the app, the participants' results do indicate good usability, high acceptance, and high satisfaction with the developed app. However, the results must be taken with caution because of the poor ecological validity of the experimental setting.}, } @article {pmid29562307, year = {2018}, author = {Blischak, PD and Chifman, J and Wolfe, AD and Kubatko, LS}, title = {HyDe: A Python Package for Genome-Scale Hybridization Detection.}, journal = {Systematic biology}, volume = {67}, number = {5}, pages = {821-829}, pmid = {29562307}, issn = {1076-836X}, support = {T32 CA079448/CA/NCI NIH HHS/United States ; }, mesh = {Computational Biology/*methods ; *Gene Flow ; *Genetic Speciation ; *Hybridization, Genetic ; Software ; }, abstract = {The analysis of hybridization and gene flow among closely related taxa is a common goal for researchers studying speciation and phylogeography. Many methods for hybridization detection use simple site pattern frequencies from observed genomic data and compare them to null models that predict an absence of gene flow. The theory underlying the detection of hybridization using these site pattern probabilities exploits the relationship between the coalescent process for gene trees within population trees and the process of mutation along the branches of the gene trees. For certain models, site patterns are predicted to occur in equal frequency (i.e., their difference is 0), producing a set of functions called phylogenetic invariants. In this article, we introduce HyDe, a software package for detecting hybridization using phylogenetic invariants arising under the coalescent model with hybridization. HyDe is written in Python and can be used interactively or through the command line using pre-packaged scripts. We demonstrate the use of HyDe on simulated data, as well as on two empirical data sets from the literature. We focus in particular on identifying individual hybrids within population samples and on distinguishing between hybrid speciation and gene flow. HyDe is freely available as an open source Python package under the GNU GPL v3 on both GitHub (https://github.com/pblischak/HyDe) and the Python Package Index (PyPI: https://pypi.python.org/pypi/phyde).}, } @article {pmid29560524, year = {2018}, author = {Cardellini, G and Valada, T and Cornillier, C and Vial, E and Dragoi, M and Goudiaby, V and Mues, V and Lasserre, B and Gruchala, A and Rørstad, PK and Neumann, M and Svoboda, M and Sirgmets, R and Näsärö, OP and Mohren, F and Achten, WMJ and Vranken, L and Muys, B}, title = {EFO-LCI: A New Life Cycle Inventory Database of Forestry Operations in Europe.}, journal = {Environmental management}, volume = {61}, number = {6}, pages = {1031-1047}, pmid = {29560524}, issn = {1432-1009}, mesh = {*Conservation of Natural Resources/economics/methods ; Databases, Factual ; Europe ; *Forestry/economics/methods ; *Forests ; Reproducibility of Results ; Time Factors ; Trees/*growth & development ; Wood/*economics ; }, abstract = {Life cycle assessment (LCA) has become a common methodology to analyze environmental impacts of forestry systems. Although LCA has been widely applied to forestry since the 90s, the LCAs are still often based on generic Life Cycle Inventory (LCI). With the purpose of improving LCA practices in the forestry sector, we developed a European Life Cycle Inventory of Forestry Operations (EFO-LCI) and analyzed the available information to check if within the European forestry sector national differences really exist. We classified the European forests on the basis of "Forest Units" (combinations of tree species and silvicultural practices). For each Forest Unit, we constructed the LCI of their forest management practices on the basis of a questionnaire filled out by national silvicultural experts. We analyzed the data reported to evaluate how they vary over Europe and how they affect LCA results and made freely available the inventory data collected for future use. The study shows important variability in rotation length, type of regeneration, amount and assortments of wood products harvested, and machinery used due to the differences in management practices. The existing variability on these activities sensibly affect LCA results of forestry practices and raw wood production. Although it is practically unfeasible to collect site-specific data for all the LCAs involving forest-based products, the use of less generic LCI data of forestry practice is desirable to improve the reliability of the studies. With the release of EFO-LCI we made a step toward the construction of regionalized LCI for the European forestry sector.}, } @article {pmid29553073, year = {2018}, author = {Fukai, N and Hiraoka, K and Kajiki, S and Kobayashi, Y and Thanachokswang, C and Arphorn, S and Uehara, M and Nakanishi, S and Mori, K}, title = {[The System and Human Resources for Occupational Health in Thailand - For Japanese Enterprises to Manage Proper Occupational Health Activities at Overseas Workplaces].}, journal = {Journal of UOEH}, volume = {40}, number = {1}, pages = {33-44}, doi = {10.7888/juoeh.40.33}, pmid = {29553073}, issn = {0387-821X}, mesh = {Humans ; Information Storage and Retrieval ; *Occupational Health/legislation & jurisprudence ; Occupational Health Physicians/education ; Thailand ; *Workplace ; }, abstract = {We collected information necessary for conducting occupational health activities in Thailand with regard to occupational safety and health management systems (OSHMS). Based on an information collection check sheet developed in our previous research, we conducted a literature research and visited four local business bases, one ISO certification body and two higher educational institutions. The legal framework concerning occupational health in Thailand consists of the Occupational Safety, Health and Environment Act of 2011 and 13 ordinances from the Ministry of Labor under that act. The original OSHMS standards for Thailand have been published, and the number of companies, especially large ones, introducing systems conforming to these standards has increased in recent years. For occupational health specialists, there are training programs for specialized occupational health physicians, professional safety officers and occupational nurses. Professional safety officers also play a central role in occupational health in the workplace. In Thailand, it is necessary to ensure compliance with related acts and regulations, and to conduct voluntary activities that satisfy workplace conditions as based on the OSHMS standards. Additionally, to improve occupational health performance, it is essential to use high-quality external services and/or occupational health professionals. Headquarters of Japanese companies have considered taking countermeasures such as recommending active use of professional safety officers, as well as issuing global standards.}, } @article {pmid29551950, year = {2017}, author = {Oliveira, C and Gunderman, L and Coles, CA and Lochmann, J and Parks, M and Ballard, E and Glazko, G and Rahmatallah, Y and Tackett, AJ and Thomas, DJ}, title = {16S rRNA Gene-Based Metagenomic Analysis of Ozark Cave Bacteria.}, journal = {Diversity}, volume = {9}, number = {3}, pages = {}, pmid = {29551950}, issn = {1424-2818}, support = {P20 GM103429/GM/NIGMS NIH HHS/United States ; P20 RR016460/RR/NCRR NIH HHS/United States ; }, abstract = {The microbial diversity within cave ecosystems is largely unknown. Ozark caves maintain a year-round stable temperature (12-14 °C), but most parts of the caves experience complete darkness. The lack of sunlight and geological isolation from surface-energy inputs generate nutrient-poor conditions that may limit species diversity in such environments. Although microorganisms play a crucial role in sustaining life on Earth and impacting human health, little is known about their diversity, ecology, and evolution in community structures. We used five Ozark region caves as test sites for exploring bacterial diversity and monitoring long-term biodiversity. Illumina MiSeq sequencing of five cave soil samples and a control sample revealed a total of 49 bacterial phyla, with seven major phyla: Proteobacteria, Acidobacteria, Actinobacteria, Firmicutes, Chloroflexi, Bacteroidetes, and Nitrospirae. Variation in bacterial composition was observed among the five caves studied. Sandtown Cave had the lowest richness and most divergent community composition. 16S rRNA gene-based metagenomic analysis of cave-dwelling microbial communities in the Ozark caves revealed that species abundance and diversity are vast and included ecologically, agriculturally, and economically relevant taxa.}, } @article {pmid29549589, year = {2018}, author = {Gikonyo, S and Kimani, T and Matere, J and Kimutai, J and Kiambi, SG and Bitek, AO and Juma Ngeiywa, KJZ and Makonnen, YJ and Tripodi, A and Morzaria, S and Lubroth, J and Rugalema, G and Fasina, FO}, title = {Mapping Potential Amplification and Transmission Hotspots for MERS-CoV, Kenya.}, journal = {EcoHealth}, volume = {15}, number = {2}, pages = {372-387}, pmid = {29549589}, issn = {1612-9210}, support = {OSRO/GLO/505/USA//United States Agency for International Development/International ; }, mesh = {Animal Diseases/*epidemiology/transmission ; Animals ; Camelus/*virology ; Coronavirus Infections/epidemiology/transmission/*veterinary ; Disease Reservoirs/*veterinary/virology ; Geographic Information Systems ; *Geographic Mapping ; Kenya/epidemiology ; Middle East Respiratory Syndrome Coronavirus ; Prevalence ; Public Health Surveillance ; Seroepidemiologic Studies ; }, abstract = {Dromedary camels have been implicated consistently as the source of Middle East respiratory syndrome coronavirus (MERS-CoV) human infections and attention to prevent and control it has focused on camels. To understanding the epidemiological role of camels in the transmission of MERS-CoV, we utilized an iterative empirical process in Geographic Information System (GIS) to identify and qualify potential hotspots for maintenance and circulation of MERS-CoV, and produced risk-based surveillance sites in Kenya. Data on camel population and distribution were used to develop camel density map, while camel farming system was defined using multi-factorial criteria including the agro-ecological zones (AEZs), production and marketing practices. Primary and secondary MERS-CoV seroprevalence data from specific sites were analyzed, and location-based prevalence matching with camel densities was conducted. High-risk convergence points (migration zones, trade routes, camel markets, slaughter slabs) were profiled and frequent cross-border camel movement mapped. Results showed that high camel-dense areas and interaction (markets and migration zones) were potential hotspot for transmission and spread. Cross-border contacts occurred with in-migrated herds at hotspot locations. AEZ differential did not influence risk distribution and plausible risk factors for spatial MERS-CoV hotspots were camel densities, previous cases of MERS-CoV, high seroprevalence and points of camel convergences. Although Kenyan camels are predisposed to MERS-CoV, no shedding is documented to date. These potential hotspots, determined using anthropogenic, system and trade characterizations should guide selection of sampling/surveillance sites, high-risk locations, critical areas for interventions and policy development in Kenya, as well as instigate further virological examination of camels.}, } @article {pmid29543878, year = {2018}, author = {Göke, C and Dahl, K and Mohn, C}, title = {Maritime Spatial Planning supported by systematic site selection: Applying Marxan for offshore wind power in the western Baltic Sea.}, journal = {PloS one}, volume = {13}, number = {3}, pages = {e0194362}, pmid = {29543878}, issn = {1932-6203}, mesh = {Baltic States ; Computational Biology/*methods ; Conservation of Natural Resources/*methods ; Ecosystem ; Geography ; Humans ; Oceans and Seas ; *Wind ; }, abstract = {The development of offshore wind energy and other competing interests in sea space are a major incentive for designating marine and coastal areas for specific human activities. Maritime Spatial Planning (MSP) considers human activities at sea in a more integrated way by analysing and designating spatial and temporal distributions of human activities based on ecological, economic and social targets. However, specific tools supporting spatial decisions at sea incorporating all relevant sectors are rarely adopted. The decision support tool Marxan is traditionally used for systematic selection and designation of nature protection and conservation areas. In this study, Marxan was applied as a support tool to identify suitable sites for offshore wind power in the pilot area Pomeranian Bight / Arkona Basin in the western Baltic Sea. The software was successfully tested and scenarios were developed that support the sites indicated in existing national plans, but also show options for alternative developments of offshore wind power in the Pomeranian Bight / Arkona Basin area.}, } @article {pmid29541867, year = {2018}, author = {Heider, K and Lopez, JMR and Scheffran, J}, title = {The potential of volunteered geographic information to investigate peri-urbanization in the conservation zone of Mexico City.}, journal = {Environmental monitoring and assessment}, volume = {190}, number = {4}, pages = {219}, pmid = {29541867}, issn = {1573-2959}, support = {10th call//Center for a Sustainable University/ ; }, mesh = {Cities ; Conservation of Natural Resources/*methods ; Ecology ; Environmental Monitoring/methods ; *Geographic Information Systems ; Mexico ; Rural Population ; Urbanization/*trends ; }, abstract = {Due to the availability of Web 2.0 technologies, volunteered geographic information (VGI) is on the rise. This new type of data is available on many topics and on different scales. Thus, it has become interesting for research. This article deals with the collective potential of VGI and remote sensing to detect peri-urbanization in the conservation zone of Mexico City. On the one hand, remote sensing identifies horizontal urban expansion, and on the other hand, VGI of ecological complaints provides data about informal settlements. This enables the combination of top-down approaches (remote sensing) and bottom-up approaches (ecological complaints). Within the analysis, we identify areas of high urbanization as well as complaint densities and bring them together in a multi-scale analysis using Geographic Information Systems (GIS). Furthermore, we investigate the influence of settlement patterns and main roads on the peri-urbanization process in Mexico City using OpenStreetMap. Peri-urbanization is detected especially in the transition zone between the urban and rural (conservation) area and near main roads as well as settlements.}, } @article {pmid29540790, year = {2018}, author = {Ushio, M and Murata, K and Sado, T and Nishiumi, I and Takeshita, M and Iwasaki, W and Miya, M}, title = {Demonstration of the potential of environmental DNA as a tool for the detection of avian species.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {4493}, pmid = {29540790}, issn = {2045-2322}, mesh = {Animals ; Biodiversity ; Birds/*classification/*genetics ; Computational Biology/methods ; *DNA ; DNA Barcoding, Taxonomic ; Metagenomics/methods ; Phylogeny ; }, abstract = {Birds play unique functional roles in the maintenance of ecosystems, such as pollination and seed dispersal, and thus monitoring bird species diversity is a first step towards avoiding undesirable consequences of anthropogenic impacts on bird communities. In the present study, we hypothesized that birds, regardless of their main habitats, must have frequent contact with water and that tissues that contain their DNA that persists in the environment (environmental DNA; eDNA) could be used to detect the presence of avian species. To this end, we applied a set of universal PCR primers (MiBird, a modified version of fish/mammal universal primers) for metabarcoding avian eDNA. We confirmed the versatility of MiBird primers by performing in silico analyses and by amplifying DNAs extracted from bird tissues. Analyses of water samples from zoo cages of birds with known species composition suggested that the use of MiBird primers combined with Illumina MiSeq could successfully detect avian species from water samples. Additionally, analysis of water samples collected from a natural pond detected five avian species common to the sampling areas. The present findings suggest that avian eDNA metabarcoding would be a complementary detection/identification tool in cases where visual census of bird species is difficult.}, } @article {pmid29540568, year = {2018}, author = {Liu, XY and Koba, K and Koyama, LA and Hobbie, SE and Weiss, MS and Inagaki, Y and Shaver, GR and Giblin, AE and Hobara, S and Nadelhoffer, KJ and Sommerkorn, M and Rastetter, EB and Kling, GW and Laundre, JA and Yano, Y and Makabe, A and Yano, M and Liu, CQ}, title = {Nitrate is an important nitrogen source for Arctic tundra plants.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {115}, number = {13}, pages = {3398-3403}, pmid = {29540568}, issn = {1091-6490}, mesh = {Denitrification ; Nitrates/*metabolism ; Nitrogen/*analysis ; Plant Leaves/growth & development/*metabolism ; Soil/*chemistry ; *Tundra ; }, abstract = {Plant nitrogen (N) use is a key component of the N cycle in terrestrial ecosystems. The supply of N to plants affects community species composition and ecosystem processes such as photosynthesis and carbon (C) accumulation. However, the availabilities and relative importance of different N forms to plants are not well understood. While nitrate (NO3[-]) is a major N form used by plants worldwide, it is discounted as a N source for Arctic tundra plants because of extremely low NO3[-] concentrations in Arctic tundra soils, undetectable soil nitrification, and plant-tissue NO3[-] that is typically below detection limits. Here we reexamine NO3[-] use by tundra plants using a sensitive denitrifier method to analyze plant-tissue NO3[-] Soil-derived NO3[-] was detected in tundra plant tissues, and tundra plants took up soil NO3[-] at comparable rates to plants from relatively NO3[-]-rich ecosystems in other biomes. Nitrate assimilation determined by [15]N enrichments of leaf NO3[-] relative to soil NO3[-] accounted for 4 to 52% (as estimated by a Bayesian isotope-mixing model) of species-specific total leaf N of Alaskan tundra plants. Our finding that in situ soil NO3[-] availability for tundra plants is high has important implications for Arctic ecosystems, not only in determining species compositions, but also in determining the loss of N from soils via leaching and denitrification. Plant N uptake and soil N losses can strongly influence C uptake and accumulation in tundra soils. Accordingly, this evidence of NO3[-] availability in tundra soils is crucial for predicting C storage in tundra.}, } @article {pmid29537089, year = {2018}, author = {Paris, JR and Sherman, KD and Bell, E and Boulenger, C and Delord, C and El-Mahdi, MBM and Fairfield, EA and Griffiths, AM and Gutmann Roberts, C and Hedger, RD and Holman, LE and Hooper, LH and Humphries, NE and Katsiadaki, I and King, RA and Lemopoulos, A and Payne, CJ and Peirson, G and Richter, KK and Taylor, MI and Trueman, CN and Hayden, B and Stevens, JR}, title = {Understanding and managing fish populations: keeping the toolbox fit for purpose.}, journal = {Journal of fish biology}, volume = {92}, number = {3}, pages = {727-751}, doi = {10.1111/jfb.13549}, pmid = {29537089}, issn = {1095-8649}, support = {NC/K001086/1/NC3RS_/National Centre for the Replacement, Refinement and Reduction of Animals in Research/United Kingdom ; }, mesh = {Animals ; Congresses as Topic ; Conservation of Natural Resources/methods ; *Fisheries ; Fishes/*physiology ; Interdisciplinary Communication ; Models, Biological ; Policy ; Population Dynamics ; Telemetry ; }, abstract = {Wild fish populations are currently experiencing unprecedented pressures, which are projected to intensify in the coming decades. Developing a thorough understanding of the influences of both biotic and abiotic factors on fish populations is a salient issue in contemporary fish conservation and management. During the 50th Anniversary Symposium of The Fisheries Society of the British Isles at the University of Exeter, UK, in July 2017, scientists from diverse research backgrounds gathered to discuss key topics under the broad umbrella of 'Understanding Fish Populations'. Below, the output of one such discussion group is detailed, focusing on tools used to investigate natural fish populations. Five main groups of approaches were identified: tagging and telemetry; molecular tools; survey tools; statistical and modelling tools; tissue analyses. The appraisal covered current challenges and potential solutions for each of these topics. In addition, three key themes were identified as applicable across all tool-based applications. These included data management, public engagement, and fisheries policy and governance. The continued innovation of tools and capacity to integrate interdisciplinary approaches into the future assessment and management of fish populations is highlighted as an important focus for the next 50 years of fisheries research.}, } @article {pmid29537088, year = {2018}, author = {Jacobs, A and Doran, C and Murray, DS and Duffill Telsnig, J and Laskowski, KL and Jones, NAR and Auer, SK and Praebel, K}, title = {On the challenges and opportunities facing fish biology: a discussion of five key knowledge gaps.}, journal = {Journal of fish biology}, volume = {92}, number = {3}, pages = {690-698}, doi = {10.1111/jfb.13545}, pmid = {29537088}, issn = {1095-8649}, mesh = {Animals ; *Aquaculture ; Climate Change ; Fisheries ; Fishes/*physiology ; Food Supply ; Knowledge Bases ; }, abstract = {Many fish species face increasing challenges associated with climate change and overfishing. At the same time, aquaculture is becoming vital for food security. Gaining a deeper understanding of the basic biology of fish is therefore more important than ever. Here we synthesize and summarize key questions, opportunities and challenges in fish biology highlighted during a round-table discussion at the 50th Anniversary Symposium of The Fisheries Society of the British Isles, held at the University of Exeter, U.K., in July 2017. We identified several knowledge gaps but also key opportunities for fish biology to inform food security, for collective behaviour, evolutionary history and trait correlations to predict responses to environmental change and for novel analytical approaches to mine existing data sets. Overall, more integrative approaches through stronger collaborations across different fields are needed to advance our understanding of the basic biology of fish.}, } @article {pmid29536423, year = {2018}, author = {Kennedy, RC and Fling, RR and Robeson, MS and Saxton, AM and Schneider, LG and Darcy, JL and Bemis, DA and Zhao, L and Chen, J}, title = {Temporal dynamics of gut microbiota in triclocarban-exposed weaned rats.}, journal = {Environmental science and pollution research international}, volume = {25}, number = {15}, pages = {14743-14751}, pmid = {29536423}, issn = {1614-7499}, support = {1R21ES017475-01A1//National Institute of Environmental Health Sciences/ ; }, mesh = {Animals ; Anti-Infective Agents/*toxicity ; Carbanilides/*toxicity ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*drug effects ; Lactation ; Rats ; Rats, Sprague-Dawley ; Water Pollutants, Chemical/*toxicity ; Weaning ; }, abstract = {Widely used as an antimicrobial in antibacterial bar soaps, triclocarban (3,4,4'-trichlorocarbanilide; TCC) is effective against Gram-positive bacteria but shows little efficacy against Gram-negative strains, potentially altering the composition of indigenous microflora within and on the human body. To date, the consequence of continuous or previous nonprescription antimicrobial exposure from compounds in personal care products on commensal microflora is still elusive. Previous research has shown that TCC exposure during gestation and lactation induced dysbiosis of gut microbial communities among exposed dams and neonates. However, the impact of antimicrobial exposure specifically after discontinuation of the use of TCC on the gut microbiota has not been investigated. In this study, weaned Sprague Dawley rats (postnatal day, PND 22) were provided ad lib access to TCC-supplemented diet (0.2% w/w or 0.5% w/w) for 4 weeks (phase I) followed by a 4-week washout period (phase II) to determine gut microflora changes both during continuous exposure to TCC and to determine the potential rebound following TCC withdrawal. Fecal samples were collected at baseline (PND 22) prior to TCC exposure and throughout phase I and phase II. The V4 region of 16S rDNA was sequenced from extracted total fecal DNA with the MiSeq platform. Exposure to both 0.2% w/w and 0.5% w/w TCC was sufficient to alter diversity of microbiota during phase I of treatment. This effect was further prolonged into phase II, even when TCC exposure was discontinued. Collectively, these data highlight the impact of both continuous and prior TCC exposure on gut microbial ecology and shed light onto the potential long-term health risk of daily nonprescription antimicrobial personal care product use.}, } @article {pmid29535148, year = {2018}, author = {Molinier, C and Reisser, CMO and Fields, P and Ségard, A and Galimov, Y and Haag, CR}, title = {Identification of General Patterns of Sex-Biased Expression in Daphnia, a Genus with Environmental Sex Determination.}, journal = {G3 (Bethesda, Md.)}, volume = {8}, number = {5}, pages = {1523-1533}, pmid = {29535148}, issn = {2160-1836}, support = {R24 GM078274/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Daphnia/*genetics ; *Environment ; Female ; Gene Expression Regulation ; Gene Ontology ; Male ; *Sex Characteristics ; Sex Determination Processes/*genetics ; Species Specificity ; }, abstract = {Daphnia reproduce by cyclic-parthenogenesis, where phases of asexual reproduction are intermitted by sexual production of diapause stages. This life cycle, together with environmental sex determination, allow the comparison of gene expression between genetically identical males and females. We investigated gene expression differences between males and females in four genotypes of Daphnia magna and compared the results with published data on sex-biased gene expression in two other Daphnia species, each representing one of the major phylogenetic clades within the genus. We found that 42% of all annotated genes showed sex-biased expression in D. magna This proportion is similar both to estimates from other Daphnia species as well as from species with genetic sex determination, suggesting that sex-biased expression is not reduced under environmental sex determination. Among 7453 single copy, one-to-one orthologs in the three Daphnia species, 707 consistently showed sex-biased expression and 675 were biased in the same direction in all three species. Hence these genes represent a core-set of genes with consistent sex-differential expression in the genus. A functional analysis identified that several of them are involved in known sex determination pathways. Moreover, 75% were overexpressed in females rather than males, a pattern that appears to be a general feature of sex-biased gene expression in Daphnia.}, } @article {pmid29530087, year = {2018}, author = {Feng, X and Zhou, X and Zhou, S and Wang, J and Hu, W}, title = {Analysis of microRNA profile of Anopheles sinensis by deep sequencing and bioinformatic approaches.}, journal = {Parasites & vectors}, volume = {11}, number = {1}, pages = {172}, pmid = {29530087}, issn = {1756-3305}, support = {No.81271867 and 91431104//National Natural Science Foundation of China/International ; No.2014DFA31130//International Science and Technology Cooperation Program of China/International ; No.2009ZX10004-302//National Science& Technology Major Program/International ; No.20174Y0089//Shanghai Municipal Commission of Health and Family Planning Grant/International ; }, mesh = {Animals ; Anopheles/*genetics ; Computational Biology/*methods ; Gene Expression Profiling ; High-Throughput Nucleotide Sequencing/*methods ; *MicroRNAs ; Transcriptome ; }, abstract = {BACKGROUND: microRNAs (miRNAs) are small non-coding RNAs widely identified in many mosquitoes. They are reported to play important roles in development, differentiation and innate immunity. However, miRNAs in Anopheles sinensis, one of the Chinese malaria mosquitoes, remain largely unknown.

METHODS: We investigated the global miRNA expression profile of An. sinensis using Illumina Hiseq 2000 sequencing. Meanwhile, we applied a bioinformatic approach to identify potential miRNAs in An. sinensis. The identified miRNA profiles were compared and analyzed by two approaches. The selected miRNAs from the sequencing result and the bioinformatic approach were confirmed with qRT-PCR. Moreover, target prediction, GO annotation and pathway analysis were carried out to understand the role of miRNAs in An. sinensis.

RESULTS: We identified 49 conserved miRNAs and 12 novel miRNAs by next-generation high-throughput sequencing technology. In contrast, 43 miRNAs were predicted by the bioinformatic approach, of which two were assigned as novel. Comparative analysis of miRNA profiles by two approaches showed that 21 miRNAs were shared between them. Twelve novel miRNAs did not match any known miRNAs of any organism, indicating that they are possibly species-specific. Forty miRNAs were found in many mosquito species, indicating that these miRNAs are evolutionally conserved and may have critical roles in the process of life. Both the selected known and novel miRNAs (asi-miR-281, asi-miR-184, asi-miR-14, asi-miR-nov5, asi-miR-nov4, asi-miR-9383, and asi-miR-2a) could be detected by quantitative real-time PCR (qRT-PCR) in the sequenced sample, and the expression patterns of these miRNAs measured by qRT-PCR were in concordance with the original miRNA sequencing data. The predicted targets for the known and the novel miRNAs covered many important biological roles and pathways indicating the diversity of miRNA functions. We also found 21 conserved miRNAs and eight counterparts of target immune pathway genes in An. sinensis based on the analysis of An. gambiae.

CONCLUSIONS: Our results provide the first lead to the elucidation of the miRNA profile in An. sinensis. Unveiling the roles of mosquito miRNAs will undoubtedly lead to a better understanding of mosquito biology and mosquito-pathogen interactions. This work lays the foundation for the further functional study of An. sinensis miRNAs and will facilitate their application in vector control.}, } @article {pmid29529097, year = {2018}, author = {Virgili, A and Authier, M and Monestiez, P and Ridoux, V}, title = {How many sightings to model rare marine species distributions.}, journal = {PloS one}, volume = {13}, number = {3}, pages = {e0193231}, pmid = {29529097}, issn = {1932-6203}, mesh = {Animals ; *Aquatic Organisms ; Area Under Curve ; Conservation of Natural Resources ; Databases, Factual ; Demography ; Dolphins/growth & development ; Ecosystem ; *Models, Biological ; }, abstract = {Despite large efforts, datasets with few sightings are often available for rare species of marine megafauna that typically live at low densities. This paucity of data makes modelling the habitat of these taxa particularly challenging. We tested the predictive performance of different types of species distribution models fitted to decreasing numbers of sightings. Generalised additive models (GAMs) with three different residual distributions and the presence only model MaxEnt were tested on two megafauna case studies differing in both the number of sightings and ecological niches. From a dolphin (277 sightings) and an auk (1,455 sightings) datasets, we simulated rarity with a sighting thinning protocol by random sampling (without replacement) of a decreasing fraction of sightings. Better prediction of the distribution of a rarely sighted species occupying a narrow habitat (auk dataset) was expected compared to the distribution of a rarely sighted species occupying a broad habitat (dolphin dataset). We used the original datasets to set up a baseline model and fitted additional models on fewer sightings but keeping effort constant. Model predictive performance was assessed with mean squared error and area under the curve. Predictions provided by the models fitted to the thinned-out datasets were better than a homogeneous spatial distribution down to a threshold of approximately 30 sightings for a GAM with a Tweedie distribution and approximately 130 sightings for the other models. Thinning the sighting data for the taxon with narrower habitats seemed to be less detrimental to model predictive performance than for the broader habitat taxon. To generate reliable habitat modelling predictions for rarely sighted marine predators, our results suggest (1) using GAMs with a Tweedie distribution with presence-absence data and (2) implementing, as a conservative empirical measure, at least 50 sightings in the models.}, } @article {pmid29526926, year = {2018}, author = {Do, TH and Le, NG and Dao, TK and Nguyen, TMP and Le, TL and Luu, HL and Nguyen, KHV and Nguyen, VL and Le, LA and Phung, TN and van Straalen, NM and Roelofs, D and Truong, NH}, title = {Metagenomic insights into lignocellulose-degrading genes through Illumina-based de novo sequencing of the microbiome in Vietnamese native goats' rumen.}, journal = {The Journal of general and applied microbiology}, volume = {64}, number = {3}, pages = {108-116}, doi = {10.2323/jgam.2017.08.004}, pmid = {29526926}, issn = {1349-8037}, mesh = {Amino Acid Sequence ; Animals ; Bacteria/classification/*enzymology/*genetics ; Base Sequence ; DNA, Bacterial/genetics ; Databases, Genetic ; Gastrointestinal Microbiome/*genetics ; Genome, Bacterial/genetics ; Glycoside Hydrolases/*genetics/metabolism ; Goats/*microbiology ; Lignin/metabolism ; Metagenome/*genetics ; Metagenomics ; Open Reading Frames ; Rumen/*microbiology ; Vietnam ; }, abstract = {The scarcity of enzymes having an optimal activity in lignocellulose deconstruction is an obstacle for industrial-scale conversion of cellulosic biomass into biofuels. With the aim of mining novel lignocellulolytic enzymes, a ~9 Gb metagenome of bacteria in Vietnamese native goats' rumen was sequenced by Illumina platform. From the data, 821 ORFs encoding carbohydrate esterases (CEs) and polysaccharide lyases (PLs) serving for lignocellulose pre-treatment, 816 ORFs encoding 11 glycoside hydrolase families (GHs) of cellulases, and 2252 ORFs encoding 22 GHs of hemicellulases, were mined. The carbohydrate binding module (CBM) was also abundant with 763 ORFs, of which 480 ORFs are located with lignocellulolytic enzymes. The enzyme modularity analysis showed that CBMs are usually present in endoglucanase, endo 1,3-beta-D-glucosidase, and endoxylanase, whereas fibronectin 3-like module (FN3) mainly represents in GH3 and immunoglobulin-like domain (Ig) was located in GH9 only. Every domain located in each ORF was analyzed in detail to contribute enzymes' modularity which is valuable for modelling, to study the structure, and for recombinant production. With the aim of confirming the annotated results, a mined ORF encoding CBM63 was highly expressed in E. coli in soluble form. The purified recombinant CBM63 exhibited no cellulase activity, but enhanced a commercial cellulase activity in the destruction of a paper filter.}, } @article {pmid29523839, year = {2018}, author = {Butler, JB and Freeman, JS and Potts, BM and Vaillancourt, RE and Grattapaglia, D and Silva-Junior, OB and Simmons, BA and Healey, AL and Schmutz, J and Barry, KW and Lee, DJ and Henry, RJ and King, GJ and Baten, A and Shepherd, M}, title = {Annotation of the Corymbia terpene synthase gene family shows broad conservation but dynamic evolution of physical clusters relative to Eucalyptus.}, journal = {Heredity}, volume = {121}, number = {1}, pages = {87-104}, pmid = {29523839}, issn = {1365-2540}, mesh = {Alkyl and Aryl Transferases/*genetics ; Chromosome Mapping ; *Computational Biology/methods ; *Evolution, Molecular ; Gene Dosage ; Gene Expression Profiling ; Gene Expression Regulation, Plant ; *Genetic Variation ; Genome, Plant ; Genomics/methods ; Molecular Sequence Annotation ; *Multigene Family ; Myrtaceae/classification/enzymology/*genetics ; Phylogeny ; Quantitative Trait Loci ; }, abstract = {Terpenes are economically and ecologically important phytochemicals. Their synthesis is controlled by the terpene synthase (TPS) gene family, which is highly diversified throughout the plant kingdom. The plant family Myrtaceae are characterised by especially high terpene concentrations, and considerable variation in terpene profiles. Many Myrtaceae are grown commercially for terpene products including the eucalypts Corymbia and Eucalyptus. Eucalyptus grandis has the largest TPS gene family of plants currently sequenced, which is largely conserved in the closely related E. globulus. However, the TPS gene family has been well studied only in these two eucalypt species. The recent assembly of two Corymbia citriodora subsp. variegata genomes presents an opportunity to examine the conservation of this important gene family across more divergent eucalypt lineages. Manual annotation of the TPS gene family in C. citriodora subsp. variegata revealed a similar overall number, and relative subfamily representation, to that previously reported in E. grandis and E. globulus. Many of the TPS genes were in physical clusters that varied considerably between Eucalyptus and Corymbia, with several instances of translocation, expansion/contraction and loss. Notably, there was greater conservation in the subfamilies involved in primary metabolism than those involved in secondary metabolism, likely reflecting different selective constraints. The variation in cluster size within subfamilies and the broad conservation between the eucalypts in the face of this variation are discussed, highlighting the potential contribution of selection, concerted evolution and stochastic processes. These findings provide the foundation to better understand terpene evolution within the ecologically and economically important Myrtaceae.}, } @article {pmid29523074, year = {2018}, author = {Mata, AR and Pacheco, CM and Cruz Pérez, JF and Sáenz, MM and Baca, BE}, title = {In silico comparative analysis of GGDEF and EAL domain signaling proteins from the Azospirillum genomes.}, journal = {BMC microbiology}, volume = {18}, number = {1}, pages = {20}, pmid = {29523074}, issn = {1471-2180}, mesh = {Adaptation, Biological ; Azospirillum/enzymology/*genetics/*metabolism ; Bacterial Proteins/*genetics/*metabolism ; Biofilms/growth & development ; Computational Biology ; Cyclic GMP/*analogs & derivatives/metabolism ; Escherichia coli Proteins/metabolism ; Gene Expression Regulation, Bacterial ; Models, Molecular ; Phosphoric Diester Hydrolases/metabolism ; Phosphorus-Oxygen Lyases/metabolism ; Protein Conformation ; *Protein Domains ; Second Messenger Systems/genetics ; *Signal Transduction ; }, abstract = {BACKGROUND: The cyclic-di-GMP (c-di-GMP) second messenger exemplifies a signaling system that regulates many bacterial behaviors of key importance; among them, c-di-GMP controls the transition between motile and sessile life-styles in bacteria. Cellular c-di-GMP levels in bacteria are regulated by the opposite enzymatic activities of diguanylate cyclases and phosphodiesterases, which are proteins that have GGDEF and EAL domains, respectively. Azospirillum is a genus of plant-growth-promoting bacteria, and members of this genus have beneficial effects in many agronomically and ecologically essential plants. These bacteria also inhabit aquatic ecosystems, and have been isolated from humus-reducing habitats. Bioinformatic and structural approaches were used to identify genes predicted to encode GG[D/E]EF, EAL and GG[D/E]EF-EAL domain proteins from nine genome sequences.

RESULTS: The analyzed sequences revealed that the genomes of A. humicireducens SgZ-5[T], A. lipoferum 4B, Azospirillum sp. B510, A. thiophilum BV-S[T], A. halopraeferens DSM3675, A. oryzae A2P, and A. brasilense Sp7, Sp245 and Az39 encode for 29 to 41 of these predicted proteins. Notably, only 15 proteins were conserved in all nine genomes: eight GGDEF, three EAL and four GGDEF-EAL hybrid domain proteins, all of which corresponded to core genes in the genomes. The predicted proteins exhibited variable lengths, architectures and sensor domains. In addition, the predicted cellular localizations showed that some of the proteins to contain transmembrane domains, suggesting that these proteins are anchored to the membrane. Therefore, as reported in other soil bacteria, the Azospirillum genomes encode a large number of proteins that are likely involved in c-di-GMP metabolism. In addition, the data obtained here strongly suggest host specificity and environment specific adaptation.

CONCLUSIONS: Bacteria of the Azospirillum genus cope with diverse environmental conditions to survive in soil and aquatic habitats and, in certain cases, to colonize and benefit their host plant. Gaining information on the structures of proteins involved in c-di-GMP metabolism in Azospirillum appears to be an important step in determining the c-di-GMP signaling pathways, involved in the transition of a motile cell towards a biofilm life-style, as an example of microbial genome plasticity under diverse in situ environments.}, } @article {pmid29519937, year = {2018}, author = {Rohde, PD and Østergaard, S and Kristensen, TN and Sørensen, P and Loeschcke, V and Mackay, TFC and Sarup, P}, title = {Functional Validation of Candidate Genes Detected by Genomic Feature Models.}, journal = {G3 (Bethesda, Md.)}, volume = {8}, number = {5}, pages = {1659-1668}, pmid = {29519937}, issn = {2160-1836}, support = {R01 AA016560/AA/NIAAA NIH HHS/United States ; R01 AG043490/AG/NIA NIH HHS/United States ; }, mesh = {Animals ; Drosophila melanogaster/*genetics ; Gene Expression Regulation ; Gene Ontology ; *Genes, Insect ; *Genetic Association Studies ; *Genomics ; Male ; *Models, Genetic ; Motor Activity/genetics ; Reproducibility of Results ; }, abstract = {Understanding the genetic underpinnings of complex traits requires knowledge of the genetic variants that contribute to phenotypic variability. Reliable statistical approaches are needed to obtain such knowledge. In genome-wide association studies, variants are tested for association with trait variability to pinpoint loci that contribute to the quantitative trait. Because stringent genome-wide significance thresholds are applied to control the false positive rate, many true causal variants can remain undetected. To ameliorate this problem, many alternative approaches have been developed, such as genomic feature models (GFM). The GFM approach tests for association of set of genomic markers, and predicts genomic values from genomic data utilizing prior biological knowledge. We investigated to what degree the findings from GFM have biological relevance. We used the Drosophila Genetic Reference Panel to investigate locomotor activity, and applied genomic feature prediction models to identify gene ontology (GO) categories predictive of this phenotype. Next, we applied the covariance association test to partition the genomic variance of the predictive GO terms to the genes within these terms. We then functionally assessed whether the identified candidate genes affected locomotor activity by reducing gene expression using RNA interference. In five of the seven candidate genes tested, reduced gene expression altered the phenotype. The ranking of genes within the predictive GO term was highly correlated with the magnitude of the phenotypic consequence of gene knockdown. This study provides evidence for five new candidate genes for locomotor activity, and provides support for the reliability of the GFM approach.}, } @article {pmid29518701, year = {2018}, author = {McQuoid, J and Thrul, J and Ling, P}, title = {A geographically explicit ecological momentary assessment (GEMA) mixed method for understanding substance use.}, journal = {Social science & medicine (1982)}, volume = {202}, number = {}, pages = {89-98}, pmid = {29518701}, issn = {1873-5347}, support = {T32 CA113710/CA/NCI NIH HHS/United States ; U01 CA154240/CA/NCI NIH HHS/United States ; }, mesh = {Adolescent ; Adult ; Ecological Momentary Assessment ; Female ; Geographic Information Systems ; *Health Status Disparities ; Health Surveys ; Humans ; Male ; Qualitative Research ; Risk Factors ; Sexual and Gender Minorities/*psychology/statistics & numerical data ; Smokers/*psychology/statistics & numerical data ; Tobacco Use/*epidemiology ; United States/epidemiology ; Young Adult ; }, abstract = {Tobacco use is increasingly concentrated within marginalized groups, including LGBTQ+ young adults. Developing tailored interventions to reduce tobacco-related health disparities requires understanding the mechanisms linking individual and contextual factors associated with tobacco use to behavior. This paper presents an in-depth exploration of three cases from a novel mixed method study designed to identify the situational factors and place-based practices of substance use among high-risk individuals. We combined geographically explicit ecological momentary assessment (GEMA) with an adapted travel diary-interview method. Participants (young adult bisexual smokers, ages 18-26) reported on non-smoking and smoking situations for 30 days with a smartphone app. GEMA surveys captured internal and external situational factors (e.g., craving intensity, location type, seeing others smoking). Continuous locational data was collected via smartphone GPS. Subsequently, participants completed in-depth interviews reviewing maps of their own GEMA data. GEMA data and transcripts were analyzed separately and integrated at the case level in a matrix. Using GEMA maps to guide the interview grounded discussion in participants' everyday smoking situations and routines. Interviews clarified participant interpretation of GEMA measures and revealed experiences and meanings of smoking locations and practices. The GEMA method identified the most frequent smoking locations/times for each participant (e.g., afternoons at university). Interviews provided description of associated situational factors and perceptions of smoking contexts (e.g., peer rejection of bisexual identity) and the roles of smoking therein (e.g., physically escape uncomfortable environments). In conclusion, this mixed method contributes to advancing qualitative GIS and other hypothesis-generating approaches working to reveal the richness of individuals' experiences of the everyday contexts of health behavior, while also providing reliable measures of situational predictors of behaviors of interest, such as substance use. Limitations of and future directions for the method are discussed.}, } @article {pmid29518076, year = {2018}, author = {Mac Aodha, O and Gibb, R and Barlow, KE and Browning, E and Firman, M and Freeman, R and Harder, B and Kinsey, L and Mead, GR and Newson, SE and Pandourski, I and Parsons, S and Russ, J and Szodoray-Paradi, A and Szodoray-Paradi, F and Tilova, E and Girolami, M and Brostow, G and Jones, KE}, title = {Bat detective-Deep learning tools for bat acoustic signal detection.}, journal = {PLoS computational biology}, volume = {14}, number = {3}, pages = {e1005995}, pmid = {29518076}, issn = {1553-7358}, mesh = {Algorithms ; Animals ; Chiroptera/classification/*physiology ; Computational Biology ; Echolocation/classification/*physiology ; Endangered Species ; Environmental Monitoring/*methods ; *Machine Learning ; Neural Networks, Computer ; *Signal Processing, Computer-Assisted ; Zoology ; }, abstract = {Passive acoustic sensing has emerged as a powerful tool for quantifying anthropogenic impacts on biodiversity, especially for echolocating bat species. To better assess bat population trends there is a critical need for accurate, reliable, and open source tools that allow the detection and classification of bat calls in large collections of audio recordings. The majority of existing tools are commercial or have focused on the species classification task, neglecting the important problem of first localizing echolocation calls in audio which is particularly problematic in noisy recordings. We developed a convolutional neural network based open-source pipeline for detecting ultrasonic, full-spectrum, search-phase calls produced by echolocating bats. Our deep learning algorithms were trained on full-spectrum ultrasonic audio collected along road-transects across Europe and labelled by citizen scientists from www.batdetective.org. When compared to other existing algorithms and commercial systems, we show significantly higher detection performance of search-phase echolocation calls with our test sets. As an example application, we ran our detection pipeline on bat monitoring data collected over five years from Jersey (UK), and compared results to a widely-used commercial system. Our detection pipeline can be used for the automatic detection and monitoring of bat populations, and further facilitates their use as indicator species on a large scale. Our proposed pipeline makes only a small number of bat specific design decisions, and with appropriate training data it could be applied to detecting other species in audio. A crucial novelty of our work is showing that with careful, non-trivial, design and implementation considerations, state-of-the-art deep learning methods can be used for accurate and efficient monitoring in audio.}, } @article {pmid29516246, year = {2018}, author = {Nibert, ML and Manny, AR and Debat, HJ and Firth, AE and Bertini, L and Caruso, C}, title = {A barnavirus sequence mined from a transcriptome of the Antarctic pearlwort Colobanthus quitensis.}, journal = {Archives of virology}, volume = {163}, number = {7}, pages = {1921-1926}, pmid = {29516246}, issn = {1432-8798}, support = {R01 GM033050/GM/NIGMS NIH HHS/United States ; T32 AI007245/AI/NIAID NIH HHS/United States ; 5R01GM033050/NH/NIH HHS/United States ; 2T32AI007245/NH/NIH HHS/United States ; /WT_/Wellcome Trust/United Kingdom ; 106207/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Capsid Proteins/genetics ; Caryophyllaceae/*genetics/*virology ; Data Mining/methods ; Databases, Genetic ; Frameshifting, Ribosomal ; Fungi/virology ; Genome, Viral ; *Open Reading Frames ; Plant Viruses/*genetics ; RNA Viruses/*genetics ; RNA, Viral/*genetics ; RNA-Dependent RNA Polymerase/genetics ; Transcriptome ; }, abstract = {Because so few viruses in the family Barnaviridae have been reported, we searched for more of them in public sequence databases. Here, we report the complete coding sequence of Colobanthus quitensis associated barnavirus 1, mined from a transcriptome of the Antarctic pearlwort Colobanthus quitensis. The 4.2-kb plus-strand sequence of this virus encompasses four main open reading frames (ORFs), as expected for barnaviruses, including ORFs for a protease-containing polyprotein, an RNA-dependent RNA polymerase whose translation appears to rely on - 1 ribosomal frameshifting, and a capsid protein that is likely to be translated from a subgenomic RNA. The possible derivation of this virus from a fungus associated with C. quitensis is discussed.}, } @article {pmid29513661, year = {2018}, author = {Lee, EC and Arab, A and Goldlust, SM and Viboud, C and Grenfell, BT and Bansal, S}, title = {Deploying digital health data to optimize influenza surveillance at national and local scales.}, journal = {PLoS computational biology}, volume = {14}, number = {3}, pages = {e1006020}, pmid = {29513661}, issn = {1553-7358}, support = {P2C HD047879/HD/NICHD NIH HHS/United States ; }, mesh = {Bayes Theorem ; Computer Simulation ; Databases, Factual ; Humans ; Influenza A Virus, H1N1 Subtype/pathogenicity ; Influenza, Human/*epidemiology ; Medical Records ; Models, Theoretical ; Online Systems ; Pandemics ; Population Surveillance/*methods ; Selection Bias ; Sentinel Surveillance ; United States ; }, abstract = {The surveillance of influenza activity is critical to early detection of epidemics and pandemics and the design of disease control strategies. Case reporting through a voluntary network of sentinel physicians is a commonly used method of passive surveillance for monitoring rates of influenza-like illness (ILI) worldwide. Despite its ubiquity, little attention has been given to the processes underlying the observation, collection, and spatial aggregation of sentinel surveillance data, and its subsequent effects on epidemiological understanding. We harnessed the high specificity of diagnosis codes in medical claims from a database that represented 2.5 billion visits from upwards of 120,000 United States healthcare providers each year. Among influenza seasons from 2002-2009 and the 2009 pandemic, we simulated limitations of sentinel surveillance systems such as low coverage and coarse spatial resolution, and performed Bayesian inference to probe the robustness of ecological inference and spatial prediction of disease burden. Our models suggest that a number of socio-environmental factors, in addition to local population interactions, state-specific health policies, as well as sampling effort may be responsible for the spatial patterns in U.S. sentinel ILI surveillance. In addition, we find that biases related to spatial aggregation were accentuated among areas with more heterogeneous disease risk, and sentinel systems designed with fixed reporting locations across seasons provided robust inference and prediction. With the growing availability of health-associated big data worldwide, our results suggest mechanisms for optimizing digital data streams to complement traditional surveillance in developed settings and enhance surveillance opportunities in developing countries.}, } @article {pmid29510660, year = {2018}, author = {Lie, KK and Tørresen, OK and Solbakken, MH and Rønnestad, I and Tooming-Klunderud, A and Nederbragt, AJ and Jentoft, S and Sæle, Ø}, title = {Loss of stomach, loss of appetite? Sequencing of the ballan wrasse (Labrus bergylta) genome and intestinal transcriptomic profiling illuminate the evolution of loss of stomach function in fish.}, journal = {BMC genomics}, volume = {19}, number = {1}, pages = {186}, pmid = {29510660}, issn = {1471-2164}, support = {900554//Fiskeri- og Havbruksnæringens Forskningsfond/International ; 901135//Fiskeri- og Havbruksnæringens Forskningsfond (NO)/International ; }, mesh = {Animals ; Appetite ; *Biological Evolution ; Digestion ; Gastrointestinal Tract ; *Gene Expression Profiling ; Genome ; Perciformes/*genetics/physiology ; Phylogeny ; Stomach/*physiology ; }, abstract = {BACKGROUND: The ballan wrasse (Labrus bergylta) belongs to a large teleost family containing more than 600 species showing several unique evolutionary traits such as lack of stomach and hermaphroditism. Agastric fish are found throughout the teleost phylogeny, in quite diverse and unrelated lineages, indicating stomach loss has occurred independently multiple times in the course of evolution. By assembling the ballan wrasse genome and transcriptome we aimed to determine the genetic basis for its digestive system function and appetite regulation. Among other, this knowledge will aid the formulation of aquaculture diets that meet the nutritional needs of agastric species.

RESULTS: Long and short read sequencing technologies were combined to generate a ballan wrasse genome of 805 Mbp. Analysis of the genome and transcriptome assemblies confirmed the absence of genes that code for proteins involved in gastric function. The gene coding for the appetite stimulating protein ghrelin was also absent in wrasse. Gene synteny mapping identified several appetite-controlling genes and their paralogs previously undescribed in fish. Transcriptome profiling along the length of the intestine found a declining expression gradient from the anterior to the posterior, and a distinct expression profile in the hind gut.

CONCLUSIONS: We showed gene loss has occurred for all known genes related to stomach function in the ballan wrasse, while the remaining functions of the digestive tract appear intact. The results also show appetite control in ballan wrasse has undergone substantial changes. The loss of ghrelin suggests that other genes, such as motilin, may play a ghrelin like role. The wrasse genome offers novel insight in to the evolutionary traits of this large family. As the stomach plays a major role in protein digestion, the lack of genes related to stomach digestion in wrasse suggests it requires formulated diets with higher levels of readily digestible protein than those for gastric species.}, } @article {pmid29509685, year = {2018}, author = {Liao, X and Zhang, C and Sun, G and Li, Z and Shang, L and Fu, Y and He, Y and Yang, Y}, title = {Assessment of Metalloid and Metal Contamination in Soils from Hainan, China.}, journal = {International journal of environmental research and public health}, volume = {15}, number = {3}, pages = {}, pmid = {29509685}, issn = {1660-4601}, mesh = {Arsenic/*analysis ; China ; Coal ; Environmental Monitoring ; Geographic Information Systems ; Metals, Heavy/*analysis ; Mining ; Power Plants ; Soil Pollutants/*analysis ; }, abstract = {The characterization of the concentrations and sources of metals and metalloids in soils is necessary to establish quality standards on a regional level and to assess the potential threat of metals to food safety and human health. A total of 8713 soil samples throughout Hainan Island, China were collected at a density of one sample per 4 km[2], and concentrations of As, Cd, Cr, Cu, Hg, Ni, Pb, Se, and Zn were analyzed. The geometric mean values of the elements were 2.17, 0.60, 26.5, 9.43, 0.033, 8.74, 22.2, 0.26, and 39.6 mg·· kg[-1] for As, Cd, Cr, Cu, Hg, Ni, Pb, Se, and Zn, respectively, significantly lower than the background values of Chinese soils with the exception of Se. Principal component analysis (PCA) suggested that multiple anthropogenic sources regulated the elemental compositions of the Hainan environment. Coal combustion and mining are important anthropogenic sources of metals for Hainan. The geochemical maps of elements in Hainan soils were produced using the Geographic Information System (GIS) method, and several hot-spot areas were identified. The ecological impact of As, Cd, Cu, Cr, Hg, Pb, Ni, and Zn pollution to the soils was extremely "low".}, } @article {pmid29507262, year = {2018}, author = {Knight, A and Fouyaxis, J and Jarrad, G and Beski, K and Cho, G and Bidargaddi, N}, title = {Systems to Harness Digital Footprint to Elucidate and Facilitate Ageing in Place.}, journal = {Studies in health technology and informatics}, volume = {246}, number = {}, pages = {91-101}, pmid = {29507262}, issn = {1879-8365}, mesh = {Aged ; *Aging ; Chronic Disease ; Humans ; *Independent Living ; Internet ; *Mobile Applications ; *Quality of Life ; }, abstract = {The rapid ageing of the population is a worldwide inexorable demographic transformation. At a time of immense social, political and economic change, the growing elderly population is at the forefront of global burden, placing an increasing strain on the federal, state, and local budgets. Many public policy responses to the impending ageing epidemic have begun, particularly with regards to dementia prevention and quality of life for older adults. However, to date, the fruition of such efforts remains to be discovered. Indeed, there is a need to find more novel and multifaceted ways of understanding the fragmentary changes and underlying mechanisms in the biopsychosocial contexts of ageing. Discovering better ways to measure these intricate domains will create better insight into how to improve clinical and public health information systems for the development of more personalisation support and services across the continuum of aged care. Technology now permeates all aspects of our everyday living. Digital footprints are data arising as a by-product of interactions we do as part of everyday living. The digital traces we live behind, be it on internet, social media, on mobile phone apps, as well as in health records (EHRs) could be used to infer how we behave and interact with environment, and how we feel in different situations. Commercial sector has very successfully used these footprints in the advertisement and marketing space. This type of information may provide clinicians with an unobtrusive way of monitoring older adults in their daily living, and provide an alternative means to traditional self-report and expert-rated assessment. In this paper we present two innovative digital footprint applications, Actionable Intime Insights and the SAIL Mobile app, which aim to facilitate "Ageing in Place" through adaptive, dynamic, early intervention strategies. These systems are devised to unveil contextual indicators of how a person is functioning mentally, socially, behaviourally and physically in their own environment, as to as assist those with chronic conditions better self-manage by facilitating assistance with care and medication needs just in time.}, } @article {pmid29506476, year = {2018}, author = {Ip, JCH and Mu, H and Chen, Q and Sun, J and Ituarte, S and Heras, H and Van Bocxlaer, B and Ganmanee, M and Huang, X and Qiu, JW}, title = {AmpuBase: a transcriptome database for eight species of apple snails (Gastropoda: Ampullariidae).}, journal = {BMC genomics}, volume = {19}, number = {1}, pages = {179}, pmid = {29506476}, issn = {1471-2164}, support = {JCYJ20170307161326613//Shenzhen Science and Technology Innovation Committee/International ; HKBU 12301415//General Research Fund of Hong Kong/International ; 0850 and 0122//Agencia Nacional de Promoción Científica y Tecnológica/International ; }, mesh = {Animals ; *Databases, Genetic ; Gene Expression Profiling ; Gene Ontology ; Genomics/methods ; High-Throughput Nucleotide Sequencing/methods ; Molecular Sequence Annotation ; Snails/*classification/*genetics ; *Transcriptome ; }, abstract = {BACKGROUND: Gastropoda, with approximately 80,000 living species, is the largest class of Mollusca. Among gastropods, apple snails (family Ampullariidae) are globally distributed in tropical and subtropical freshwater ecosystems and many species are ecologically and economically important. Ampullariids exhibit various morphological and physiological adaptations to their respective habitats, which make them ideal candidates for studying adaptation, population divergence, speciation, and larger-scale patterns of diversity, including the biogeography of native and invasive populations. The limited availability of genomic data, however, hinders in-depth ecological and evolutionary studies of these non-model organisms.

RESULTS: Using Illumina Hiseq platforms, we sequenced 1220 million reads for seven species of apple snails. Together with the previously published RNA-Seq data of two apple snails, we conducted de novo transcriptome assembly of eight species that belong to five genera of Ampullariidae, two of which represent Old World lineages and the other three New World lineages. There were 20,730 to 35,828 unigenes with predicted open reading frames for the eight species, with N50 (shortest sequence length at 50% of the unigenes) ranging from 1320 to 1803 bp. 69.7% to 80.2% of these unigenes were functionally annotated by searching against NCBI's non-redundant, Gene Ontology database and the Kyoto Encyclopaedia of Genes and Genomes. With these data we developed AmpuBase, a relational database that features online BLAST functionality for DNA/protein sequences, keyword searching for unigenes/functional terms, and download functions for sequences and whole transcriptomes.

CONCLUSIONS: In summary, we have generated comprehensive transcriptome data for multiple ampullariid genera and species, and created a publicly accessible database with a user-friendly interface to facilitate future basic and applied studies on ampullariids, and comparative molecular studies with other invertebrates.}, } @article {pmid29506361, year = {2018}, author = {Badaloni, C and Cattani, G and De' Donato, F and Gaeta, A and Leone, G and Michelozzi, P and Davoli, M and Forastiere, F and Stafoggia, M}, title = {[Big data in environmental epidemiology. Satellite and land use data for the estimation of environmental exposures at national level].}, journal = {Epidemiologia e prevenzione}, volume = {42}, number = {1}, pages = {46-59}, doi = {10.19191/EP18.1.P046.015}, pmid = {29506361}, issn = {1120-9763}, mesh = {Aerosols ; *Big Data ; Cities ; Climate ; Dust ; Ecology/*methods ; Environmental Exposure/analysis ; *Epidemiologic Methods ; Farms ; Forests ; Fresh Water ; Geographic Information Systems ; Housing ; Humans ; Italy ; Meteorological Concepts ; Natural Resources ; Particulate Matter/analysis ; Plant Dispersal ; }, abstract = {OBJECTIVES: to define a national geographic domain, with high spatial (1 km[2]) and temporal (daily) resolution, and to build a list of georeferenced environmental and temporal indicators useful for environmental epidemiology applications at national level.

DESIGN: geographic study.

SETTING AND PARTICIPANTS: study domain: Italian territory divided into 307,635 1-km² grid cells; study period: 2006-2012, divided into 2,557 daily time windows.

MAIN OUTCOME MEASURES: for each grid cell and day, an extensive number of indicators has been computed. These indicators include spatial (administrative layers, resident population, presence of water bodies, climatic zones, land use variables, impervious surfaces, orography, viability, point and areal emissions of air pollutants) and spatio-temporal predictors (particulate matter data from monitoring stations, meteorological parameters, desert dust advection episodes, aerosol optical depth, normalized difference vegetation index, planetary boundary layer) potentially useful to characterize population environmental exposures and to estimate their health effects, at national level.

RESULTS AND CONCLUSIONS: this study represents the first example of relational big data in environmental epidemiology at national level, where multiple sources of data (satellite, environmental, meteorology, land use, population) have been linked on a common spatial and temporal domain, aimed at promoting environmental epidemiology applications at national and local level.}, } @article {pmid29504186, year = {2018}, author = {Bolton, TAW and Jochaut, D and Giraud, AL and Van De Ville, D}, title = {Brain dynamics in ASD during movie-watching show idiosyncratic functional integration and segregation.}, journal = {Human brain mapping}, volume = {39}, number = {6}, pages = {2391-2404}, pmid = {29504186}, issn = {1097-0193}, mesh = {Adolescent ; Adult ; Autism Spectrum Disorder/*pathology ; Brain/*diagnostic imaging ; *Brain Mapping ; Comprehension/*physiology ; Female ; Humans ; Image Processing, Computer-Assisted ; Magnetic Resonance Imaging ; Male ; *Motion Pictures ; Neural Pathways/diagnostic imaging ; Oxygen/blood ; Time Factors ; Young Adult ; }, abstract = {To refine our understanding of autism spectrum disorders (ASD), studies of the brain in dynamic, multimodal and ecological experimental settings are required. One way to achieve this is to compare the neural responses of ASD and typically developing (TD) individuals when viewing a naturalistic movie, but the temporal complexity of the stimulus hampers this task, and the presence of intrinsic functional connectivity (FC) may overshadow movie-driven fluctuations. Here, we detected inter-subject functional correlation (ISFC) transients to disentangle movie-induced functional changes from underlying resting-state activity while probing FC dynamically. When considering the number of significant ISFC excursions triggered by the movie across the brain, connections between remote functional modules were more heterogeneously engaged in the ASD population. Dynamically tracking the temporal profiles of those ISFC changes and tying them to specific movie subparts, this idiosyncrasy in ASD responses was then shown to involve functional integration and segregation mechanisms such as response inhibition, background suppression, or multisensory integration, while low-level visual processing was spared. Through the application of a new framework for the study of dynamic experimental paradigms, our results reveal a temporally localized idiosyncrasy in ASD responses, specific to short-lived episodes of long-range functional interplays.}, } @article {pmid29502222, year = {2018}, author = {Scheirs, S and Langenhorst, W and Malgosa, A and Ortega-Sánchez, M and McGlynn, H and Santos, C and Jordana, X and Rodriguez-Baeza, A and Galtés, I}, title = {Perimortem fracture pattern in ribs by blunt force trauma.}, journal = {International journal of legal medicine}, volume = {132}, number = {4}, pages = {1205-1213}, pmid = {29502222}, issn = {1437-1596}, mesh = {Accidents ; Adult ; Aged ; Aged, 80 and over ; Cardiopulmonary Resuscitation/adverse effects ; Female ; Forensic Pathology ; Humans ; Male ; Middle Aged ; Models, Biological ; Rib Fractures/etiology/*pathology ; Time Factors ; Wounds, Nonpenetrating/*complications ; Young Adult ; }, abstract = {Literature on timing of rib trauma is scarce but remains challenging during forensic cases. This study analysed the macroscopic fracture patterns of perimortem rib fractures and compared them to experimentally reproduced rib fractures on fresh and dry ribs. Six distinctive macroscopic traits were found in ribs that might provide information about the timing of trauma, fracture mechanism and/or trauma circumstances. These traits are peels, folds, differential fracture edges, incomplete fractures, plastic deformation and longitudinal lines. Peels, folds and plastic deformation might provide information about trauma timing. Folds and different fracture edges might provide information about the fracture mechanism. Statistical analyses showed that longitudinal lines, folds and incomplete fractures might provide information about the trauma circumstances and that age might have an influence on the occurrence of complete fractures, longitudinal lines and peels (p ≤ 0.05). The new insights presented in this study might be valuable for forensic anthropologists in rib trauma analysis.}, } @article {pmid29502218, year = {2018}, author = {Reichert, F and Chen, J and Torney-Purta, J}, title = {Profiles of Adolescents' Perceptions of Democratic Classroom Climate and Students' Influence: The Effect of School and Community Contexts.}, journal = {Journal of youth and adolescence}, volume = {47}, number = {6}, pages = {1279-1298}, pmid = {29502218}, issn = {1573-6601}, mesh = {Adolescent ; Adolescent Behavior/*psychology ; *Adolescent Development ; Adult ; Databases, Factual ; *Democracy ; Female ; Humans ; Interpersonal Relations ; Male ; *Peer Influence ; Politics ; Scandinavian and Nordic Countries ; School Teachers ; Schools ; Social Responsibility ; Students/*psychology ; }, abstract = {Students' learning experiences and outcomes are shaped by school and classroom contexts. Many studies have shown how an open, democratic classroom climate relates to learning in the citizenship domain and helps nurture active and engaged citizens. However, little research has been undertaken to look at how such a favorable classroom climate may work together with broader school factors. The current study examines data from 14,292 Nordic eighth graders (51% female) who had participated in the International Civic and Citizenship Education Study in 2009, as well as contextual data from 5,657 teachers and 618 principals. Latent class analysis identifies profiles of students' perceptions of school context, which are further examined with respect to the contextual correlates at the school level using two-level fixed effects multinomial regression analyses. Five distinct student profiles are identified and labeled "alienated", "indifferent", "activist", "debater", and "communitarian". Compared to indifferent students, debaters and activists appear more frequently at schools with relatively few social problems; being in the communitarian group is associated with aspects of the wider community. Furthermore, being in one of these three groups (and not in the indifferent group) is more likely when teachers act as role models by engaging in school governance. The results are discussed within the framework of ecological assets and developmental niches for emergent participatory citizenship. The implications are that adults at school could enhance multiple contexts that shape adolescents' developmental niches to nurture active and informed citizens for democracies.}, } @article {pmid29502094, year = {2018}, author = {Yumoto, T and Naito, H and Yorifuji, T and Maeyama, H and Kosaki, Y and Yamamoto, H and Tsukahara, K and Osako, T and Nakao, A}, title = {Cushing's sign and severe traumatic brain injury in children after blunt trauma: a nationwide retrospective cohort study in Japan.}, journal = {BMJ open}, volume = {8}, number = {3}, pages = {e020781}, pmid = {29502094}, issn = {2044-6055}, mesh = {Adolescent ; Bradycardia/*epidemiology ; Brain Injuries, Traumatic/complications/mortality/*surgery ; Cause of Death ; Child ; Child, Preschool ; Craniotomy/*classification ; Critical Care ; Databases, Factual ; Female ; Glasgow Coma Scale ; Hospital Mortality ; Humans ; Hypertension/*epidemiology ; Injury Severity Score ; Japan/epidemiology ; Logistic Models ; Male ; Multivariate Analysis ; Retrospective Studies ; Tomography, X-Ray Computed ; Vital Signs ; Wounds, Nonpenetrating/complications/mortality/*surgery ; }, abstract = {OBJECTIVE: We tested whether Cushing's sign could predict severe traumatic brain injury (TBI) requiring immediate neurosurgical intervention (BI-NSI) in children after blunt trauma.

DESIGN: Retrospective cohort study using Japan Trauma Data Bank.

SETTING: Emergency and critical care centres in secondary and tertiary hospitals in Japan.

PARTICIPANTS: Children between the ages of 2 and 15 years with Glasgow Coma Scale motor scores of 5 or less at presentation after blunt trauma from 2004 to 2015 were included. A total of 1480 paediatric patients were analysed.

PRIMARY OUTCOME MEASURES: Patients requiring neurosurgical intervention within 24 hours of hospital arrival and patients who died due to isolated severe TBI were defined as BI-NSI. The combination of systolic blood pressure (SBP) and heart rate (HR) on arrival, which were respectively divided into tertiles, and its correlation with BI-NSI were investigated using a multiple logistic regression model.

RESULTS: In the study cohort, 297 (20.1%) exhibited BI-NSI. After adjusting for sex, age category and with or without haemorrhage shock, groups with higher SBP and lower HR (SBP ≥135 mm Hg; HR ≤92 bpm) were significantly associated with BI-NSI (OR 2.84, 95% CI 1.68 to 4.80, P<0.001) compared with the patients with normal vital signs. In age-specific analysis, hypertension and bradycardia were significantly associated with BI-NSI in a group of 7-10 and 11-15 years of age; however, no significant association was observed in a group of 2-6 years of age.

CONCLUSIONS: Cushing's sign after blunt trauma was significantly associated with BI-NSI in school-age children and young adolescents.}, } @article {pmid29502016, year = {2018}, author = {Giri, S and Qiu, Z and Zhang, Z}, title = {Assessing the impacts of land use on downstream water quality using a hydrologically sensitive area concept.}, journal = {Journal of environmental management}, volume = {213}, number = {}, pages = {309-319}, doi = {10.1016/j.jenvman.2018.02.075}, pmid = {29502016}, issn = {1095-8630}, mesh = {Hydrology ; New Jersey ; Nitrogen ; Phosphorus ; *Water Movements ; *Water Quality ; }, abstract = {Understanding the relationship between land use and water quality is essential to improve water quality through carefully managing landscape change. This study applies a linear mixed model at both watershed and hydrologically sensitive areas (HSAs) scales to assess such a relationship in 28 northcentral New Jersey watersheds located in a rapidly urbanizing region in the United States. Two models differ in terms of the geographic scope used to derive land use matrices that quantify land use conditions. The land use matrices at the watershed and HSAs scales represent the land use conditions in these watersheds and their HSAs, respectively. HSAs are the hydrological "hotspots" in a watershed that are prone to runoff generation during storm events. HSAs are derived using a soil topographic index (STI) that predicts hydrological sensitivity of a landscape based on a variable source area hydrology concept. The water quality indicators in these models are total nitrogen (TN), total phosphorus (TP) and total suspended solids (TSS) concentrations in streams observed at the watershed outlets. The modeling results suggest that presence of low density urban land, agricultural land and wetlands elevate while forest decreases TN, TP and/or TSS concentrations in streams. The watershed scale model tends to emphasize the role of agricultural lands in water quality degradation while the HSA scale model highlights the role of forest in water quality improvement. This study supports the hypothesis that even though HSAs are relatively smaller area compared to watershed, still the land uses within HSAs have similar impacts on downstream water quality as the land uses in entire watersheds, since both models have negligible differences in model evaluation parameters. Inclusion of HSAs brings an interesting perspective to understand the dynamic relationships between land use and water quality.}, } @article {pmid29498741, year = {2018}, author = {Valeriani, F and Crognale, S and Protano, C and Gianfranceschi, G and Orsini, M and Vitali, M and Spica, VR}, title = {Metagenomic analysis of bacterial community in a travertine depositing hot spring.}, journal = {The new microbiologica}, volume = {41}, number = {2}, pages = {126-135}, pmid = {29498741}, issn = {1121-7138}, mesh = {Bacteria/*genetics/isolation & purification ; Biodiversity ; Computational Biology ; DNA, Bacterial/genetics ; Hot Springs/*microbiology ; Metagenomics/*methods ; Phylogeny ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; *Water Microbiology ; }, abstract = {Several factors influence bacteria biodiversity in hot springs. The impact of biotic and abiotic pathways on travertine deposition plays a key role in microbial ecology and in the final composition of the waterborne microbiota. The metabolism of some bacterial groups such as photoautotrophs or lithoautotrophs influences water chemistry, favoring carbonate precipitation processes. The role of microbial mats in mineral precipitation processes is not fully clarified. For the first time, a comprehensive metagenomic analysis has been undertaken in the historical Bullicame hot spring. Bacterial biodiversity was characterized and biomineralization activities were assigned to different genera. A higher biodiversity in mat samples compared to water samples was observed: Shannon index of 3.34 and 0.86, respectively. Based on the functional assignment of each Operational Taxonomic Unit, the bacteria involved in biologically- induced mineralization are prevalent in mat and released in the water. According to the principle that each geothermal water specimen has distinctive physic-chemical characteristics, our results suggest new interacting bio-actions within these ecosystems. The saturation index and the chemical composition, as the high concentration of sulfur species and HCO3, can be linked to create a selective environment where pioneer communities are able to live and shape the ecosystem.}, } @article {pmid29497508, year = {2018}, author = {Willey, B and Waiswa, P and Kajjo, D and Munos, M and Akuze, J and Allen, E and Marchant, T}, title = {Linking data sources for measurement of effective coverage in maternal and newborn health: what do we learn from individual- vs ecological-linking methods?.}, journal = {Journal of global health}, volume = {8}, number = {1}, pages = {010601}, pmid = {29497508}, issn = {2047-2986}, mesh = {Adolescent ; Adult ; Delivery, Obstetric/*statistics & numerical data ; Female ; Health Care Surveys ; Health Services Accessibility/*statistics & numerical data ; Humans ; Infant, Newborn ; Information Storage and Retrieval/*methods ; Maternal Health Services/*statistics & numerical data ; Middle Aged ; Pregnancy ; Uganda ; Young Adult ; }, abstract = {BACKGROUND: Improving maternal and newborn health requires improvements in the quality of facility-based care. This is challenging to measure: routine data may be unreliable; respondents in population surveys may be unable to accurately report on quality indicators; and facility assessments lack population level denominators. We explored methods for linking access to skilled birth attendance (SBA) from household surveys to data on provision of care from facility surveys with the aim of estimating population level effective coverage reflecting access to quality care.

METHODS: We used data from Mayuge District, Uganda. Data from household surveys on access to SBA were linked to health facility assessment census data on readiness to provide basic emergency obstetric and newborn care (BEmONC) in the same district. One individual- and two ecological-linking methods were applied. All methods used household survey reports on where care at birth was accessed. The individual-linking method linked this to data about facility readiness from the specific facility where each woman delivered. The first ecological-linking approach used a district-wide mean estimate of facility readiness. The second used an estimate of facility readiness adjusted by level of health facility accessed. Absolute differences between estimates derived from the different linking methods were calculated, and agreement examined using Lin's concordance correlation coefficient.

RESULTS: A total of 1177 women resident in Mayuge reported a birth during 2012-13. Of these, 664 took place in facilities within Mayuge, and were eligible for linking to the census of the district's 38 facilities. 55% were assisted by a SBA in a facility. Using the individual-linking method, effective coverage of births that took place with an SBA in a facility ready to provide BEmONC was just 10% (95% confidence interval CI 3-17). The absolute difference between the individual- and ecological-level linking method adjusting for facility level was one percentage point (11%), and tests suggested good agreement. The ecological method using the district-wide estimate demonstrated poor agreement.

CONCLUSIONS: The proportion of women accessing appropriately equipped facilities for care at birth is far lower than the coverage of facility delivery. To realise the life-saving potential of health services, countries need evidence to inform actions that address gaps in the provision of quality care. Linking household and facility-based information provides a simple but innovative method for estimating quality of care at the population level. These encouraging findings suggest that linking data sets can result in meaningful evidence even when the exact location of care seeking is not known.}, } @article {pmid29495440, year = {2018}, author = {Torina, A and Blanda, V and Blanda, M and Auteri, M and La Russa, F and Scimeca, S and D'Agostino, R and Disclafani, R and Villari, S and Currò, V and Caracappa, S}, title = {A Geographical Information System Based Approach for Integrated Strategies of Tick Surveillance and Control in the Peri-Urban Natural Reserve of Monte Pellegrino (Palermo, Southern Italy).}, journal = {International journal of environmental research and public health}, volume = {15}, number = {3}, pages = {}, pmid = {29495440}, issn = {1660-4601}, mesh = {Animals ; Conservation of Natural Resources ; *Geographic Information Systems ; Italy ; Spatio-Temporal Analysis ; Tick Control/*methods ; *Ticks ; Urban Health ; }, abstract = {Ticks (Acari: Ixodidae) are bloodsucking arthropods involved in pathogen transmission in animals and humans. Tick activity depends on various ecological factors such as vegetation, hosts, and temperature. The aim of this study was to analyse the spatial/temporal distribution of ticks in six sites within a peri-urban area of Palermo (Natural Reserve of Monte Pellegrino) and correlate it with field data using Geographical Information System (GIS) data. A total of 3092 ticks were gathered via dragging method from June 2012 to May 2014. The species collected were: Ixodes ventalloi (46.09%), Hyalomma lusitanicum (19.99%), Rhipicephalus sanguineus (17.34%), Rhipicephalus pusillus (16.11%), Haemaphisalis sulcata (0.36%), Dermacentor marginatus (0.10%), and Rhipicephalus turanicus (0.03%). GIS analysis revealed environmental characteristics of each site, and abundance of each tick species was analysed in relation to time (monthly trend) and space (site-specific abundance). A relevant presence of I. ventalloi in site 2 and H. lusitanicum in site 5 was observed, suggesting the possible exposure of animals and humans to tick-borne pathogens. Our study shows the importance of surveillance of ticks in peri-urban areas and the useful implementation of GIS analysis in vector ecology; studies on temporal and spatial distribution of ticks correlated to GIS-based ecological analysis represent an integrated strategy for decision support in public health.}, } @article {pmid29495413, year = {2018}, author = {Jiang, C and Zhang, SB}, title = {A Novel Adaptively-Robust Strategy Based on the Mahalanobis Distance for GPS/INS Integrated Navigation Systems.}, journal = {Sensors (Basel, Switzerland)}, volume = {18}, number = {3}, pages = {}, pmid = {29495413}, issn = {1424-8220}, abstract = {As an optimal estimation method, the Kalman filter is the most frequently-used data fusion strategy in the field of dynamic navigation and positioning. Nevertheless, the abnormal model errors seriously degrade performance of the conventional Kalman filter. The adaptive Kalman filter was put forward to control the influences of model errors. However, the adaptive Kalman filter based on the predicted residuals (innovation vector) requires reliable observation information, and its performance is significantly affected by outliers in the measurements. In this paper, a novel adaptively-robust strategy based on the Mahalanobis distance is proposed to weaken the effects of abnormal model deviations and outliers in the measurements. In the proposed scheme, the judging index is defined based on the Mahalanobis distance, and the adaptively-robust filtering is performed when the observations are reliable, otherwise, the robust filtering is performed based on the robust estimation method. Various experiments with the actual data of GPS/INS integrated navigation systems are implemented to examine validity of the proposed scheme. Results show that both the influences of model deviations and outliers are weakened effectively by using the proposed adaptive robust filtering scheme. Moreover, the proposed scheme is easy to implement with a reasonable calculation burden.}, } @article {pmid29495282, year = {2018}, author = {Stoltenburg, R and Strehlitz, B}, title = {Refining the Results of a Classical SELEX Experiment by Expanding the Sequence Data Set of an Aptamer Pool Selected for Protein A.}, journal = {International journal of molecular sciences}, volume = {19}, number = {2}, pages = {}, pmid = {29495282}, issn = {1422-0067}, mesh = {Aptamers, Nucleotide/chemistry/*genetics/*metabolism ; Base Sequence ; Computational Biology/methods ; High-Throughput Nucleotide Sequencing ; High-Throughput Screening Assays ; Humans ; Ligands ; Nucleic Acid Conformation ; Protein Binding ; SELEX Aptamer Technique ; Staphylococcal Protein A/chemistry/*metabolism ; Staphylococcus aureus/metabolism ; }, abstract = {New, as yet undiscovered aptamers for Protein A were identified by applying next generation sequencing (NGS) to a previously selected aptamer pool. This pool was obtained in a classical SELEX (Systematic Evolution of Ligands by EXponential enrichment) experiment using the FluMag-SELEX procedure followed by cloning and Sanger sequencing. PA#2/8 was identified as the only Protein A-binding aptamer from the Sanger sequence pool, and was shown to be able to bind intact cells of Staphylococcus aureus. In this study, we show the extension of the SELEX results by re-sequencing of the same aptamer pool using a medium throughput NGS approach and data analysis. Both data pools were compared. They confirm the selection of a highly complex and heterogeneous oligonucleotide pool and show consistently a high content of orphans as well as a similar relative frequency of certain sequence groups. But in contrast to the Sanger data pool, the NGS pool was clearly dominated by one sequence group containing the known Protein A-binding aptamer PA#2/8 as the most frequent sequence in this group. In addition, we found two new sequence groups in the NGS pool represented by PA-C10 and PA-C8, respectively, which also have high specificity for Protein A. Comparative affinity studies reveal differences between the aptamers and confirm that PA#2/8 remains the most potent sequence within the selected aptamer pool reaching affinities in the low nanomolar range of KD = 20 ± 1 nM.}, } @article {pmid29494552, year = {2018}, author = {Park, M and Park, H and Lee, H and Lee, BH and Lee, J}, title = {The Complete Plastome Sequence of an Antarctic Bryophyte Sanionia uncinata (Hedw.) Loeske.}, journal = {International journal of molecular sciences}, volume = {19}, number = {3}, pages = {}, pmid = {29494552}, issn = {1422-0067}, mesh = {Antarctic Regions ; Bryopsida/classification/*genetics ; Computational Biology/methods ; Gene Ontology ; Genes, Chloroplast ; *Genome, Plant ; *Genomics/methods ; Molecular Sequence Annotation ; Phylogeny ; RNA Editing ; Whole Genome Sequencing ; }, abstract = {Organellar genomes of bryophytes are poorly represented with chloroplast genomes of only four mosses, four liverworts and two hornworts having been sequenced and annotated. Moreover, while Antarctic vegetation is dominated by the bryophytes, there are few reports on the plastid genomes for the Antarctic bryophytes. Sanionia uncinata (Hedw.) Loeske is one of the most dominant moss species in the maritime Antarctic. It has been researched as an important marker for ecological studies and as an extremophile plant for studies on stress tolerance. Here, we report the complete plastome sequence of S. uncinata, which can be exploited in comparative studies to identify the lineage-specific divergence across different species. The complete plastome of S. uncinata is 124,374 bp in length with a typical quadripartite structure of 114 unique genes including 82 unique protein-coding genes, 37 tRNA genes and four rRNA genes. However, two genes encoding the α subunit of RNA polymerase (rpoA) and encoding the cytochrome b6/f complex subunit VIII (petN) were absent. We could identify nuclear genes homologous to those genes, which suggests that rpoA and petN might have been relocated from the chloroplast genome to the nuclear genome.}, } @article {pmid29492895, year = {2018}, author = {Rampelli, S and Turroni, S}, title = {From Whole-Genome Shotgun Sequencing to Viral Community Profiling: The ViromeScan Tool.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1746}, number = {}, pages = {181-185}, doi = {10.1007/978-1-4939-7683-6_14}, pmid = {29492895}, issn = {1940-6029}, mesh = {Computational Biology ; DNA, Viral/*analysis/genetics ; *Genome, Viral ; Metagenomics/*methods ; *Software ; Viruses/*classification/*genetics ; Whole Genome Sequencing/*methods ; }, abstract = {ViromeScan is an innovative metagenomic analysis tool that allows the viral community characterization in terms of taxonomy from raw data of metagenomics sequencing. It efficiently denoises samples from reads of other microorganisms. Users can adopt the same shotgun metagenomic sequencing data to fully characterize complex microbial ecosystems, including bacteria and viruses. Here we apply ViromeScan pipeline to some examples, thus illustrating the processes computed from raw data to the final output.}, } @article {pmid29491990, year = {2017}, author = {Lehmann, KDS and Montgomery, TM and MacLachlan, SM and Parker, JM and Spagnuolo, OS and VandeWetering, KJ and Bills, PS and Holekamp, KE}, title = {Lions, hyenas and mobs (oh my!).}, journal = {Current zoology}, volume = {63}, number = {3}, pages = {313-322}, pmid = {29491990}, issn = {1674-5507}, abstract = {Understanding the factors that facilitate the emergence of cooperation among organisms is central to the study of social evolution. Spotted hyenas Crocuta crocuta frequently cooperate to mob lions Panthera leo, approaching the lions as a tightknit group while vocalizing loudly in an attempt to overwhelm them and drive them away. Whereas cooperative mobbing behavior has been well documented in birds and some mammals, to our knowledge it has never been described during interactions between 2 apex predators. Using a 27-year dataset, we characterize lion-hyena encounters, assess rates of mobbing behavior observed during these interactions, and inquire whether mobbing results in successful acquisition of food. Lions and hyenas interacted most often at fresh kills, especially as prey size and the number of hyenas present increased. Possession of food at the beginning of an interaction positively affected retention of that food by each predator species. The presence of male lions increased the probability of an interspecific interaction but decreased the likelihood of hyenas obtaining or retaining possession of the food. Hyena mobbing rates were highest at fresh kills, but lower when adult male lions were present. The occurrence of mobbing was predicted by an increase in the number of hyenas present. Whether or not mobbing resulted in acquisition of food from lions was predicted by an increase in the number of mobs formed by the hyenas present, suggesting that cooperation among hyenas enhances their fitness.}, } @article {pmid29491180, year = {2018}, author = {Reeves, DB and Magaret, AS and Greninger, AL and Johnston, C and Schiffer, JT}, title = {Model-based estimation of superinfection prevalence from limited datasets.}, journal = {Journal of the Royal Society, Interface}, volume = {15}, number = {139}, pages = {}, pmid = {29491180}, issn = {1742-5662}, support = {U19 AI096111/AI/NIAID NIH HHS/United States ; }, mesh = {*Databases, Factual ; Female ; HIV Infections/*epidemiology ; *HIV-1 ; Herpes Genitalis/*epidemiology ; *Herpesvirus 2, Human ; Humans ; Male ; *Models, Biological ; Prevalence ; Superinfection/*epidemiology ; }, abstract = {Humans can be infected sequentially by different strains of the same virus. Estimating the prevalence of so-called 'superinfection' for a particular pathogen is vital because superinfection implies a failure of immunologic memory against a given virus despite past exposure, which may signal challenges for future vaccine development. Increasingly, viral deep sequencing and phylogenetic inference can discriminate distinct strains within a host. Yet, a population-level study may misrepresent the true prevalence of superinfection for several reasons. First, certain infections such as herpes simplex virus (HSV-2) only reactivate single strains, making multiple samples necessary to detect superinfection. Second, the number of samples collected in a study may be fewer than the actual number of independently acquired strains within a single person. Third, detecting strains that are relatively less abundant can be difficult, even for other infections such as HIV-1 where deep sequencing may identify multiple strains simultaneously. Here we develop a model of superinfection inspired by ecology. We define an infected individual's richness as the number of infecting strains and use ecological evenness to quantify the relative strain abundances. The model uses an EM methodology to infer the true prevalence of superinfection from limited clinical datasets. Simulation studies with known true prevalence are used to contrast our EM method to a standard (naive) calculation. While varying richness, evenness and sampling we quantify the accuracy and precision of our method. The EM method outperforms in all cases, particularly when sampling is low, and richness or unevenness is high. Here, sensitivity to our assumptions about clinical data is considered. The simulation studies also provide insight into optimal study designs; estimates of prevalence improve equally by enrolling more participants or gathering more samples per person. Finally, we apply our method to data from published studies of HSV-2 and HIV-1 superinfection.}, } @article {pmid29488217, year = {2018}, author = {Coggan, NV and Hayward, MW and Gibb, H}, title = {A global database and "state of the field" review of research into ecosystem engineering by land animals.}, journal = {The Journal of animal ecology}, volume = {87}, number = {4}, pages = {974-994}, doi = {10.1111/1365-2656.12819}, pmid = {29488217}, issn = {1365-2656}, mesh = {Animals ; *Biodiversity ; Databases as Topic ; *Ecosystem ; Invertebrates/*physiology ; Vertebrates/*physiology ; }, abstract = {Ecosystem engineers have been widely studied for terrestrial systems, but global trends in research encompassing the range of taxa and functions have not previously been synthesised. We reviewed contemporary understanding of engineer fauna in terrestrial habitats and assessed the methods used to document patterns and processes, asking: (a) which species act as ecosystem engineers and with whom do they interact? (b) What are the impacts of ecosystem engineers in terrestrial habitats and how are they distributed? (c) What are the primary methods used to examine engineer effects and how have these developed over time? We considered the strengths, weaknesses and gaps in knowledge related to each of these questions and suggested a conceptual framework to delineate "significant impacts" of engineering interactions for all terrestrial animals. We collected peer-reviewed publications examining ecosystem engineer impacts and created a database of engineer species to assess experimental approaches and any additional covariates that influenced the magnitude of engineer impacts. One hundred and twenty-two species from 28 orders were identified as ecosystem engineers, performing five ecological functions. Burrowing mammals were the most researched group (27%). Half of all studies occurred in dry/arid habitats. Mensurative studies comparing sites with and without engineers (80%) were more common than manipulative studies (20%). These provided a broad framework for predicting engineer impacts upon abundance and species diversity. However, the roles of confounding factors, processes driving these patterns and the consequences of experimentally adjusting variables, such as engineer density, have been neglected. True spatial and temporal replication has also been limited, particularly for emerging studies of engineer reintroductions. Climate change and habitat modification will challenge the roles that engineers play in regulating ecosystems, and these will become important avenues for future research. We recommend future studies include simulation of engineer effects and experimental manipulation of engineer densities to determine the potential for ecological cascades through trophic and engineering pathways due to functional decline. We also recommend improving knowledge of long-term engineering effects and replication of engineer reintroductions across landscapes to better understand how large-scale ecological gradients alter the magnitude of engineering impacts.}, } @article {pmid29485018, year = {2018}, author = {Durkin, MJ and Jafarzadeh, SR and Hsueh, K and Sallah, YH and Munshi, KD and Henderson, RR and Fraser, VJ}, title = {Outpatient Antibiotic Prescription Trends in the United States: A National Cohort Study.}, journal = {Infection control and hospital epidemiology}, volume = {39}, number = {5}, pages = {584-589}, pmid = {29485018}, issn = {1559-6834}, support = {U54 CK000609/CK/NCEZID CDC HHS/United States ; KL2 TR002346/TR/NCATS NIH HHS/United States ; U54 CK000482/CK/NCEZID CDC HHS/United States ; L30 AI133778/AI/NIAID NIH HHS/United States ; U54CK000482/ACL/ACL HHS/United States ; }, mesh = {Ambulatory Care ; Anti-Bacterial Agents/*therapeutic use ; Cohort Studies ; Databases, Factual ; Drug Utilization/*statistics & numerical data/trends ; Insurance Claim Reporting ; Outpatients/*statistics & numerical data ; Poisson Distribution ; Prescriptions ; Retrospective Studies ; Seasons ; United States ; }, abstract = {OBJECTIVETo characterize trends in outpatient antibiotic prescriptions in the United StatesDESIGNRetrospective ecological and temporal trend study evaluating outpatient antibiotic prescriptions from 2013 to 2015SETTINGNational administrative claims data from a pharmacy benefits manager PARTICIPANTS. Prescription pharmacy beneficiaries from Express Scripts Holding CompanyMEASUREMENTSAnnual and seasonal percent change in antibiotic prescriptionsRESULTSApproximately 98 million outpatient antibiotic prescriptions were filled by 39 million insurance beneficiaries during the 3-year study period. The most commonly prescribed antibiotics were azithromycin, amoxicillin, amoxicillin/clavulanate, ciprofloxacin, and cephalexin. No significant changes in individual or overall annual antibiotic prescribing rates were found during the study period. Significant seasonal variation was observed, with antibiotics being 42% more likely to be prescribed during February than September (peak-to-trough ratio [PTTR], 1.42; 95% confidence interval [CI], 1.39-1.61). Similar seasonal trends were found for azithromycin (PTTR, 2.46; 95% CI, 2.44-3.47), amoxicillin (PTTR, 1.52; 95% CI, 1.42-1.89), and amoxicillin/clavulanate (PTTR, 1.78; 95% CI, 1.68-2.29).CONCLUSIONSThis study demonstrates that annual national outpatient antibiotic prescribing practices remained unchanged during our study period. Furthermore, seasonal peaks in antibiotics generally used to treat viral upper respiratory tract infections remained unchanged during cold and influenza season. These results suggest that inappropriate prescribing of antibiotics remains widespread, despite the concurrent release of several guideline-based best practices intended to reduce inappropriate antibiotic consumption; however, further research linking national outpatient antibiotic prescriptions to associated medical conditions is needed to confirm these findings.Infect Control Hosp Epidemiol 2018;39:584-589.}, } @article {pmid29483242, year = {2018}, author = {Sequeira, AMM and Rodríguez, JP and Eguíluz, VM and Harcourt, R and Hindell, M and Sims, DW and Duarte, CM and Costa, DP and Fernández-Gracia, J and Ferreira, LC and Hays, GC and Heupel, MR and Meekan, MG and Aven, A and Bailleul, F and Baylis, AMM and Berumen, ML and Braun, CD and Burns, J and Caley, MJ and Campbell, R and Carmichael, RH and Clua, E and Einoder, LD and Friedlaender, A and Goebel, ME and Goldsworthy, SD and Guinet, C and Gunn, J and Hamer, D and Hammerschlag, N and Hammill, M and Hückstädt, LA and Humphries, NE and Lea, MA and Lowther, A and Mackay, A and McHuron, E and McKenzie, J and McLeay, L and McMahon, CR and Mengersen, K and Muelbert, MMC and Pagano, AM and Page, B and Queiroz, N and Robinson, PW and Shaffer, SA and Shivji, M and Skomal, GB and Thorrold, SR and Villegas-Amtmann, S and Weise, M and Wells, R and Wetherbee, B and Wiebkin, A and Wienecke, B and Thums, M}, title = {Convergence of marine megafauna movement patterns in coastal and open oceans.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {115}, number = {12}, pages = {3072-3077}, pmid = {29483242}, issn = {1091-6490}, mesh = {*Animal Migration ; Animals ; *Databases, Factual ; Ecosystem ; *Oceans and Seas ; *Vertebrates ; }, abstract = {The extent of increasing anthropogenic impacts on large marine vertebrates partly depends on the animals' movement patterns. Effective conservation requires identification of the key drivers of movement including intrinsic properties and extrinsic constraints associated with the dynamic nature of the environments the animals inhabit. However, the relative importance of intrinsic versus extrinsic factors remains elusive. We analyze a global dataset of ∼2.8 million locations from >2,600 tracked individuals across 50 marine vertebrates evolutionarily separated by millions of years and using different locomotion modes (fly, swim, walk/paddle). Strikingly, movement patterns show a remarkable convergence, being strongly conserved across species and independent of body length and mass, despite these traits ranging over 10 orders of magnitude among the species studied. This represents a fundamental difference between marine and terrestrial vertebrates not previously identified, likely linked to the reduced costs of locomotion in water. Movement patterns were primarily explained by the interaction between species-specific traits and the habitat(s) they move through, resulting in complex movement patterns when moving close to coasts compared with more predictable patterns when moving in open oceans. This distinct difference may be associated with greater complexity within coastal microhabitats, highlighting a critical role of preferred habitat in shaping marine vertebrate global movements. Efforts to develop understanding of the characteristics of vertebrate movement should consider the habitat(s) through which they move to identify how movement patterns will alter with forecasted severe ocean changes, such as reduced Arctic sea ice cover, sea level rise, and declining oxygen content.}, } @article {pmid29479643, year = {2018}, author = {Hervé, MR and Nicolè, F and Lê Cao, KA}, title = {Multivariate Analysis of Multiple Datasets: a Practical Guide for Chemical Ecology.}, journal = {Journal of chemical ecology}, volume = {44}, number = {3}, pages = {215-234}, doi = {10.1007/s10886-018-0932-6}, pmid = {29479643}, issn = {1573-1561}, mesh = {*Databases, Chemical ; Ecology/*methods ; *Guidelines as Topic ; Models, Statistical ; Multivariate Analysis ; }, abstract = {Chemical ecology has strong links with metabolomics, the large-scale study of all metabolites detectable in a biological sample. Consequently, chemical ecologists are often challenged by the statistical analyses of such large datasets. This holds especially true when the purpose is to integrate multiple datasets to obtain a holistic view and a better understanding of a biological system under study. The present article provides a comprehensive resource to analyze such complex datasets using multivariate methods. It starts from the necessary pre-treatment of data including data transformations and distance calculations, to the application of both gold standard and novel multivariate methods for the integration of different omics data. We illustrate the process of analysis along with detailed results interpretations for six issues representative of the different types of biological questions encountered by chemical ecologists. We provide the necessary knowledge and tools with reproducible R codes and chemical-ecological datasets to practice and teach multivariate methods.}, } @article {pmid29476118, year = {2018}, author = {Stuhr, M and Blank-Landeshammer, B and Reymond, CE and Kollipara, L and Sickmann, A and Kucera, M and Westphal, H}, title = {Disentangling thermal stress responses in a reef-calcifier and its photosymbionts by shotgun proteomics.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {3524}, pmid = {29476118}, issn = {2045-2322}, mesh = {Aquatic Organisms ; Calcification, Physiologic/genetics ; Coral Reefs ; Diatoms/*genetics/growth & development/metabolism ; Ecosystem ; Foraminifera/*genetics/growth & development/metabolism ; Gene Expression Regulation ; Gene Ontology ; Hot Temperature ; Molecular Sequence Annotation ; Oceans and Seas ; Photosynthesis/genetics ; Proteome/classification/*genetics/metabolism ; Proteomics/*methods ; *Stress, Physiological ; Symbiosis ; }, abstract = {The proliferation of key marine ecological engineers and carbonate producers often relies on their association with photosymbiotic algae. Evaluating stress responses of these organisms is important to predict their fate under future climate projections. Physiological approaches are limited in their ability to resolve the involved molecular mechanisms and attribute stress effects to the host or symbiont, while probing and partitioning of proteins cannot be applied in organisms where the host and symbiont are small and cannot be physically separated. Here we apply a label-free quantitative proteomics approach to detect changes of proteome composition in the diatom-bearing benthic foraminifera Amphistegina gibbosa experimentally exposed to three thermal-stress scenarios. We developed a workflow for protein extraction from less than ten specimens and simultaneously analysed host and symbiont proteomes. Despite little genomic data for the host, 1,618 proteins could be partially assembled and assigned. The proteomes revealed identical pattern of stress response among stress scenarios as that indicated by physiological measurements, but allowed identification of compartment-specific stress reactions. In the symbiont, stress-response and proteolysis-related proteins were up regulated while photosynthesis-related proteins declined. In contrast, host homeostasis was maintained through chaperone up-regulation associated with elevated proteosynthesis and proteolysis, and the host metabolism shifted to heterotrophy.}, } @article {pmid29474862, year = {2018}, author = {Ma, S and Wu, Q and Hu, Y and Wei, F}, title = {Patterns and effects of GC3 heterogeneity and parsimony informative sites on the phylogenetic tree of genes.}, journal = {Gene}, volume = {655}, number = {}, pages = {56-60}, doi = {10.1016/j.gene.2018.02.037}, pmid = {29474862}, issn = {1879-0038}, mesh = {Animals ; Base Composition/*genetics ; Computational Biology ; *Evolution, Molecular ; *Genetic Heterogeneity ; Humans ; Mammals/*genetics ; *Pedigree ; *Phylogeny ; }, abstract = {The explosive growth in genomic data has provided novel insights into the conflicting signals hidden in phylogenetic trees. Although some studies have explored the effects of the GC content and parsimony informative sites (PIS) on the phylogenetic tree, the effect of the heterogeneity of the GC content at the first/second/third codon position on parsimony informative sites (GC1/2/3PIS) among different species and the effect of PIS on phylogenetic tree construction remain largely unexplored. Here, we used two different mammal genomic datasets to explore the patterns of GC1/2/3PIS heterogeneity and the effect of PIS on the phylogenetic tree of genes: (i) all GC1/2/3PIS have obvious heterogeneity between different mammals, and the levels of heterogeneity are GC3PIS > GC2PIS > GC1PIS; (ii) the number of PIS is positively correlated with the metrics of "good" gene tree topologies, and excluding the third codon position (C3) decreases the quality of gene trees by removing too many PIS. These results provide novel insights into the heterogeneity pattern of GC1/2/3PIS in mammals and the relationship between GC3/PIS and gene trees. Additionally, it is necessary to carefully consider whether to exclude C3 to improve the quality of gene trees, especially in the super-tree method.}, } @article {pmid29474419, year = {2018}, author = {Yang, H and Cai, Y and Zhuo, Z and Yang, W and Yang, C and Zhang, J and Yang, Y and Wang, B and Guan, F}, title = {Transcriptome analysis in different developmental stages of Batocera horsfieldi (Coleoptera: Cerambycidae) and comparison of candidate olfactory genes.}, journal = {PloS one}, volume = {13}, number = {2}, pages = {e0192730}, pmid = {29474419}, issn = {1932-6203}, mesh = {Animals ; Arthropod Antennae/growth & development/physiology ; Coleoptera/*genetics/*growth & development/physiology ; Databases, Genetic ; Female ; Gene Expression Profiling ; Gene Expression Regulation, Developmental ; Gene Ontology ; *Genes, Insect ; Insect Proteins/genetics ; Male ; Phylogeny ; Receptors, Odorant/genetics ; Sex Characteristics ; Smell/*genetics ; }, abstract = {The white-striped longhorn beetle Batocera horsfieldi (Coleoptera: Cerambycidae) is a polyphagous wood-boring pest that causes substantial damage to the lumber industry. Moreover olfactory proteins are crucial components to function in related processes, but the B. horsfieldi genome is not readily available for olfactory proteins analysis. In the present study, developmental transcriptomes of larvae from the first instar to the prepupal stage, pupae, and adults (females and males) from emergence to mating were built by RNA sequencing to establish a genetic background that may help understand olfactory genes. Approximately 199 million clean reads were obtained and assembled into 171,664 transcripts, which were classified into 23,380, 26,511, 22,393, 30,270, and 87, 732 unigenes for larvae, pupae, females, males, and combined datasets, respectively. The unigenes were annotated against NCBI's non-redundant nucleotide and protein sequences, Swiss-Prot, Gene Ontology (GO), Pfam, Clusters of Eukaryotic Orthologous Groups (KOG), and KEGG Orthology (KO) databases. A total of 43,197 unigenes were annotated into 55 sub-categories under the three main GO categories; 25,237 unigenes were classified into 26 functional KOG categories, and 25,814 unigenes were classified into five functional KEGG Pathway categories. RSEM software identified 2,983, 3,097, 870, 2,437, 5,161, and 2,882 genes that were differentially expressed between larvae and males, larvae and pupae, larvae and females, males and females, males and pupae, and females and pupae, respectively. Among them, genes encoding seven candidate odorant binding proteins (OBPs) and three chemosensory proteins (CSPs) were identified. RT-PCR and RT-qPCR analyses showed that BhorOBP3, BhorCSP2, and BhorOBPC1/C3/C4 were highly expressed in the antenna of males, indicating these genes may may play key roles in foraging and host-orientation in B. horsfieldi. Our results provide valuable molecular information about the olfactory system in B. horsfieldi and will help guide future functional studies on olfactory genes.}, } @article {pmid29467741, year = {2018}, author = {Knelman, JE and Graham, EB and Prevéy, JS and Robeson, MS and Kelly, P and Hood, E and Schmidt, SK}, title = {Interspecific Plant Interactions Reflected in Soil Bacterial Community Structure and Nitrogen Cycling in Primary Succession.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {128}, pmid = {29467741}, issn = {1664-302X}, abstract = {Past research demonstrating the importance plant-microbe interactions as drivers of ecosystem succession has focused on how plants condition soil microbial communities, impacting subsequent plant performance and plant community assembly. These studies, however, largely treat microbial communities as a black box. In this study, we sought to examine how emblematic shifts from early successional Alnus viridus ssp. sinuata (Sitka alder) to late successional Picea sitchensis (Sitka spruce) in primary succession may be reflected in specific belowground changes in bacterial community structure and nitrogen cycling related to the interaction of these two plants. We examined early successional alder-conditioned soils in a glacial forefield to delineate how alders alter the soil microbial community with increasing dominance. Further, we assessed the impact of late-successional spruce plants on these early successional alder-conditioned microbiomes and related nitrogen cycling through a leachate addition microcosm experiment. We show how increasingly abundant alder select for particular bacterial taxa. Additionally, we found that spruce leachate significantly alters the composition of these microbial communities in large part by driving declines in taxa that are enriched by alder, including bacterial symbionts. We found these effects to be spruce specific, beyond a general leachate effect. Our work also demonstrates a unique influence of spruce on ammonium availability. Such insights bolster theory relating the importance of plant-microbe interactions with late-successional plants and interspecific plant interactions more generally.}, } @article {pmid29466331, year = {2018}, author = {Ma, Z and Guo, D and Xu, X and Lu, M and Bardgett, RD and Eissenstat, DM and McCormack, ML and Hedin, LO}, title = {Evolutionary history resolves global organization of root functional traits.}, journal = {Nature}, volume = {555}, number = {7694}, pages = {94-97}, pmid = {29466331}, issn = {1476-4687}, mesh = {Biodiversity ; *Biological Evolution ; Carbon/metabolism ; Databases, Factual ; Desert Climate ; *Ecosystem ; Mycorrhizae/physiology ; Photosynthesis ; Phylogeny ; Plant Roots/*anatomy & histology/classification/microbiology/*physiology ; Seasons ; Soil/chemistry ; Species Specificity ; Symbiosis ; Tropical Climate ; }, abstract = {Plant roots have greatly diversified in form and function since the emergence of the first land plants, but the global organization of functional traits in roots remains poorly understood. Here we analyse a global dataset of 10 functionally important root traits in metabolically active first-order roots, collected from 369 species distributed across the natural plant communities of 7 biomes. Our results identify a high degree of organization of root traits across species and biomes, and reveal a pattern that differs from expectations based on previous studies of leaf traits. Root diameter exerts the strongest influence on root trait variation across plant species, growth forms and biomes. Our analysis suggests that plants have evolved thinner roots since they first emerged in land ecosystems, which has enabled them to markedly improve their efficiency of soil exploration per unit of carbon invested and to reduce their dependence on symbiotic mycorrhizal fungi. We also found that diversity in root morphological traits is greatest in the tropics, where plant diversity is highest and many ancestral phylogenetic groups are preserved. Diversity in root morphology declines sharply across the sequence of tropical, temperate and desert biomes, presumably owing to changes in resource supply caused by seasonally inhospitable abiotic conditions. Our results suggest that root traits have evolved along a spectrum bounded by two contrasting strategies of root life: an ancestral 'conservative' strategy in which plants with thick roots depend on symbiosis with mycorrhizal fungi for soil resources and a more-derived 'opportunistic' strategy in which thin roots enable plants to more efficiently leverage photosynthetic carbon for soil exploration. These findings imply that innovations of belowground traits have had an important role in preparing plants to colonize new habitats, and in generating biodiversity within and across biomes.}, } @article {pmid29461564, year = {2018}, author = {Beger, C and Merker, A and Mumm, R and Gausche, R}, title = {Growth prediction of small for gestational age infants within the first weeks after birth.}, journal = {Anthropologischer Anzeiger; Bericht uber die biologisch-anthropologische Literatur}, volume = {74}, number = {5}, pages = {377-382}, doi = {10.1127/anthranz/2018/0820}, pmid = {29461564}, issn = {0003-5548}, mesh = {*Body Height ; Child ; Female ; Forecasting ; Gestational Age ; Humans ; Infant ; Infant, Newborn ; *Infant, Small for Gestational Age ; Pregnancy ; }, abstract = {Being born small for gestational age (SGA) in length is a sign of growth failure due to malnutrition in pregnancy or other serious disorders. In previous publications it was shown that SGA born neonates may experience a compensatory growth spurt (catch-up growth) in infancy and childhood (Olbertz et al. in press). The timing of this growth spurt, however, was not well described. We analyzed longitudinal data of 5,138 SGA infants and children, collected by licensed physicians in Germany and centrally stored in the Database Management System of CrescNet at the University of Leipzig. We confirm that SGA born infants undergo a catch-up in height SDS after birth and up to 2 years of life. 2,712 SGA newborns out of 2,846 showed catch-up in length SDS. The catch-up occurred already during the 4[th] to 16[th] postnatal weeks. We analyzed infants who did not show a catch-up within this time period, or even had a loss in height SDS. These infants have a significant lower height SDS throughout the first 5 years after birth and especially in the timeframe of 60[th] to 64[th] month after birth (-1.33 mean height SDS in catch-up group, -2.49 in non-catch-up group, p-value < 0.001, CI = [0.827, 1.483]). Even though the medical reasons for the lack of catch-up growth in young SGA infants may not be known, absence of this catch-up within the 4[th] to 16[th] postnatal week can be used to early identify SGA infants with high risk of growth failure within the following 5 years.}, } @article {pmid29461516, year = {2018}, author = {Davies, CH and Ajani, P and Armbrecht, L and Atkins, N and Baird, ME and Beard, J and Bonham, P and Burford, M and Clementson, L and Coad, P and Crawford, C and Dela-Cruz, J and Doblin, MA and Edgar, S and Eriksen, R and Everett, JD and Furnas, M and Harrison, DP and Hassler, C and Henschke, N and Hoenner, X and Ingleton, T and Jameson, I and Keesing, J and Leterme, SC and James McLaughlin, M and Miller, M and Moffatt, D and Moss, A and Nayar, S and Patten, NL and Patten, R and Pausina, SA and Proctor, R and Raes, E and Robb, M and Rothlisberg, P and Saeck, EA and Scanes, P and Suthers, IM and Swadling, KM and Talbot, S and Thompson, P and Thomson, PG and Uribe-Palomino, J and van Ruth, P and Waite, AM and Wright, S and Richardson, AJ}, title = {A database of chlorophyll a in Australian waters.}, journal = {Scientific data}, volume = {5}, number = {}, pages = {180018}, pmid = {29461516}, issn = {2052-4463}, mesh = {Australia ; *Chlorophyll ; Databases, Factual ; Ecosystem ; Phytoplankton ; Seawater ; }, abstract = {Chlorophyll a is the most commonly used indicator of phytoplankton biomass in the marine environment. It is relatively simple and cost effective to measure when compared to phytoplankton abundance and is thus routinely included in many surveys. Here we collate 173, 333 records of chlorophyll a collected since 1965 from Australian waters gathered from researchers on regular coastal monitoring surveys and ocean voyages into a single repository. This dataset includes the chlorophyll a values as measured from samples analysed using spectrophotometry, fluorometry and high performance liquid chromatography (HPLC). The Australian Chlorophyll a database is freely available through the Australian Ocean Data Network portal (https://portal.aodn.org.au/). These data can be used in isolation as an index of phytoplankton biomass or in combination with other data to provide insight into water quality, ecosystem state, and relationships with other trophic levels such as zooplankton or fish.}, } @article {pmid29460198, year = {2018}, author = {Ohta, T and Kawashima, T and Shinozaki, NO and Dobashi, A and Hiraoka, S and Hoshino, T and Kanno, K and Kataoka, T and Kawashima, S and Matsui, M and Nemoto, W and Nishijima, S and Suganuma, N and Suzuki, H and Taguchi, YH and Takenaka, Y and Tanigawa, Y and Tsuneyoshi, M and Yoshitake, K and Sato, Y and Yamashita, R and Arakawa, K and Iwasaki, W}, title = {Collaborative environmental DNA sampling from petal surfaces of flowering cherry Cerasus × yedoensis 'Somei-yoshino' across the Japanese archipelago.}, journal = {Journal of plant research}, volume = {131}, number = {4}, pages = {709-717}, pmid = {29460198}, issn = {1618-0860}, mesh = {Chloroplasts/genetics ; Cyanobacteria/genetics ; DNA/*genetics ; DNA, Plant/*genetics ; *Environment ; Flowers/*genetics/microbiology ; Japan ; Proteobacteria/genetics ; Prunus/*genetics/microbiology ; Sequence Alignment ; Sequence Analysis, DNA ; }, abstract = {Recent studies have shown that environmental DNA is found almost everywhere. Flower petal surfaces are an attractive tissue to use for investigation of the dispersal of environmental DNA in nature as they are isolated from the external environment until the bud opens and only then can the petal surface accumulate environmental DNA. Here, we performed a crowdsourced experiment, the "Ohanami Project", to obtain environmental DNA samples from petal surfaces of Cerasus × yedoensis 'Somei-yoshino' across the Japanese archipelago during spring 2015. C. × yedoensis is the most popular garden cherry species in Japan and clones of this cultivar bloom simultaneously every spring. Data collection spanned almost every prefecture and totaled 577 DNA samples from 149 collaborators. Preliminary amplicon-sequencing analysis showed the rapid attachment of environmental DNA onto the petal surfaces. Notably, we found DNA of other common plant species in samples obtained from a wide distribution; this DNA likely originated from the pollen of the Japanese cedar. Our analysis supports our belief that petal surfaces after blossoming are a promising target to reveal the dynamics of environmental DNA in nature. The success of our experiment also shows that crowdsourced environmental DNA analyses have considerable value in ecological studies.}, } @article {pmid29455155, year = {2018}, author = {Chyra Kufova, Z and Sevcikova, T and Januska, J and Vojta, P and Boday, A and Vanickova, P and Filipova, J and Growkova, K and Jelinek, T and Hajduch, M and Hajek, R}, title = {Newly designed 11-gene panel reveals first case of hereditary amyloidosis captured by massive parallel sequencing.}, journal = {Journal of clinical pathology}, volume = {71}, number = {8}, pages = {687-694}, pmid = {29455155}, issn = {1472-4146}, mesh = {Adult ; Aged ; Aged, 80 and over ; Amyloidosis, Familial/diagnosis/*genetics ; Cardiomyopathy, Hypertrophic/diagnosis/*genetics ; Computational Biology ; Czech Republic ; DNA Mutational Analysis/*methods ; Female ; Gene Expression Profiling/*methods ; Gene Frequency ; Genetic Markers ; Genetic Predisposition to Disease ; *High-Throughput Nucleotide Sequencing ; Humans ; Male ; Middle Aged ; *Mutation ; Phenotype ; Pilot Projects ; *Polymorphism, Single Nucleotide ; Predictive Value of Tests ; Reproducibility of Results ; Risk Factors ; *Transcriptome ; }, abstract = {AIMS: Amyloidosis is caused by deposition of abnormal protein fibrils, leading to damage of organ function. Hereditary amyloidosis represents a monogenic disease caused by germline mutations in 11 amyloidogenic precursor protein genes. One of the important but non-specific symptoms of amyloidosis is hypertrophic cardiomyopathy. Diagnostics of hereditary amyloidosis is complicated and the real cause can remain overlooked. We aimed to design hereditary amyloidosis gene panel and to introduce new next-generation sequencing (NGS) approach to investigate hereditary amyloidosis in a cohort of patients with hypertrophic cardiomyopathy of unknown significance.

METHODS: Design of target enrichment DNA library preparation using Haloplex Custom Kit containing 11 amyloidogenic genes was followed by MiSeq Illumina sequencing and bioinformatics identification of germline variants using tool VarScan in a cohort of 40 patients.

RESULTS: We present design of NGS panel for 11 genes (TTR, FGA, APOA1, APOA2, LYZ, GSN, CST3, PRNP, APP, B2M, ITM2B) connected to various forms of amyloidosis. We detected one mutation, which is responsible for hereditary amyloidosis. Some other single nucleotide variants are so far undescribed or rare variants or represent common polymorphisms in European population.

CONCLUSIONS: We report one positive case of hereditary amyloidosis in a cohort of patients with hypertrophic cardiomyopathy of unknown significance and set up first panel for NGS in hereditary amyloidosis. This work may facilitate successful implementation of the NGS method by other researchers or clinicians and may improve the diagnostic process after validation.}, } @article {pmid29453350, year = {2018}, author = {Culina, A and Baglioni, M and Crowther, TW and Visser, ME and Woutersen-Windhouwer, S and Manghi, P}, title = {Navigating the unfolding open data landscape in ecology and evolution.}, journal = {Nature ecology & evolution}, volume = {2}, number = {3}, pages = {420-426}, doi = {10.1038/s41559-017-0458-2}, pmid = {29453350}, issn = {2397-334X}, mesh = {*Biological Evolution ; *Datasets as Topic ; Ecology/*methods ; *Online Systems ; }, abstract = {Open access to data is revolutionizing the sciences. To allow ecologists and evolutionary biologists to confidently find and use the existing data, we provide an overview of the landscape of online data infrastructures, and highlight the key points to consider when using open data. We introduce an online collaborative platform to keep a community-driven, updated list of the best sources that enable search for data in one interface. In doing so, our aim is to lower the barrier to accessing open data, and encourage its use by researchers hoping to increase the scope, reliability and value of their findings.}, } @article {pmid29451365, year = {2018}, author = {Kim, HS and Lee, BY and Han, J and Jeong, CB and Hwang, DS and Lee, MC and Kang, HM and Kim, DH and Kim, HJ and Papakostas, S and Declerck, SAJ and Choi, IY and Hagiwara, A and Park, HG and Lee, JS}, title = {The genome of the freshwater monogonont rotifer Brachionus calyciflorus.}, journal = {Molecular ecology resources}, volume = {18}, number = {3}, pages = {646-655}, doi = {10.1111/1755-0998.12768}, pmid = {29451365}, issn = {1755-0998}, mesh = {Animals ; *Databases, Genetic ; *Genome ; Molecular Sequence Annotation ; Rotifera/*genetics ; Sequence Analysis, DNA ; }, abstract = {Monogononta is the most speciose class of rotifers, with more than 2,000 species. The monogonont genus Brachionus is widely distributed at a global scale, and a few of its species are commonly used as ecological and evolutionary models to address questions related to aquatic ecology, cryptic speciation, evolutionary ecology, the evolution of sex and ecotoxicology. With the importance of Brachionus species in many areas of research, it is remarkable that the genome has not been characterized. This study aims to address this lacuna by presenting, for the first time, the whole-genome assembly of the freshwater species Brachionus calyciflorus. The total length of the assembled genome was 129.6 Mb, with 1,041 scaffolds. The N50 value was 786.6 kb, and the GC content was 24%. A total of 16,114 genes were annotated with repeat sequences, accounting for 21% of the assembled genome. This assembled genome may form a basis for future studies addressing key questions on the evolution of monogonont rotifers. It will also provide the necessary molecular resources to mechanistically investigate ecophysiological and ecotoxicological responses.}, } @article {pmid29451313, year = {2018}, author = {McDowell, N and Allen, CD and Anderson-Teixeira, K and Brando, P and Brienen, R and Chambers, J and Christoffersen, B and Davies, S and Doughty, C and Duque, A and Espirito-Santo, F and Fisher, R and Fontes, CG and Galbraith, D and Goodsman, D and Grossiord, C and Hartmann, H and Holm, J and Johnson, DJ and Kassim, AR and Keller, M and Koven, C and Kueppers, L and Kumagai, T and Malhi, Y and McMahon, SM and Mencuccini, M and Meir, P and Moorcroft, P and Muller-Landau, HC and Phillips, OL and Powell, T and Sierra, CA and Sperry, J and Warren, J and Xu, C and Xu, X}, title = {Drivers and mechanisms of tree mortality in moist tropical forests.}, journal = {The New phytologist}, volume = {219}, number = {3}, pages = {851-869}, doi = {10.1111/nph.15027}, pmid = {29451313}, issn = {1469-8137}, mesh = {Carbon Dioxide/metabolism ; *Forests ; *Humidity ; Models, Theoretical ; Trees/*physiology ; *Tropical Climate ; }, abstract = {Tree mortality rates appear to be increasing in moist tropical forests (MTFs) with significant carbon cycle consequences. Here, we review the state of knowledge regarding MTF tree mortality, create a conceptual framework with testable hypotheses regarding the drivers, mechanisms and interactions that may underlie increasing MTF mortality rates, and identify the next steps for improved understanding and reduced prediction. Increasing mortality rates are associated with rising temperature and vapor pressure deficit, liana abundance, drought, wind events, fire and, possibly, CO2 fertilization-induced increases in stand thinning or acceleration of trees reaching larger, more vulnerable heights. The majority of these mortality drivers may kill trees in part through carbon starvation and hydraulic failure. The relative importance of each driver is unknown. High species diversity may buffer MTFs against large-scale mortality events, but recent and expected trends in mortality drivers give reason for concern regarding increasing mortality within MTFs. Models of tropical tree mortality are advancing the representation of hydraulics, carbon and demography, but require more empirical knowledge regarding the most common drivers and their subsequent mechanisms. We outline critical datasets and model developments required to test hypotheses regarding the underlying causes of increasing MTF mortality rates, and improve prediction of future mortality under climate change.}, } @article {pmid29447149, year = {2018}, author = {Alvarado, C and Fider, NA and Wearing, HJ and Komarova, NL}, title = {Optimizing homeostatic cell renewal in hierarchical tissues.}, journal = {PLoS computational biology}, volume = {14}, number = {2}, pages = {e1005967}, pmid = {29447149}, issn = {1553-7358}, support = {U01 CA187956/CA/NCI NIH HHS/United States ; 1 U01 CA187956-01/NH/NIH HHS/United States ; }, mesh = {Animals ; Cell Differentiation/*physiology ; Cell Division ; Cell Proliferation ; Computational Biology ; *Computer Simulation ; Genes, Tumor Suppressor ; Hematopoiesis ; Homeostasis ; Humans ; Models, Biological ; Mutation ; Neoplasms/*genetics/metabolism ; Probability ; Risk ; Stem Cells/*cytology ; *Stochastic Processes ; }, abstract = {In order to maintain homeostasis, mature cells removed from the top compartment of hierarchical tissues have to be replenished by means of differentiation and self-renewal events happening in the more primitive compartments. As each cell division is associated with a risk of mutation, cell division patterns have to be optimized, in order to minimize or delay the risk of malignancy generation. Here we study this optimization problem, focusing on the role of division tree length, that is, the number of layers of cells activated in response to the loss of terminally differentiated cells, which is related to the balance between differentiation and self-renewal events in the compartments. Using both analytical methods and stochastic simulations in a metapopulation-style model, we find that shorter division trees are advantageous if the objective is to minimize the total number of one-hit mutants in the cell population. Longer division trees on the other hand minimize the accumulation of two-hit mutants, which is a more likely evolutionary goal given the key role played by tumor suppressor genes in cancer initiation. While division tree length is the most important property determining mutant accumulation, we also find that increasing the size of primitive compartments helps to delay two-hit mutant generation.}, } @article {pmid29441230, year = {2018}, author = {Harris, DJ and Taylor, SD and White, EP}, title = {Forecasting biodiversity in breeding birds using best practices.}, journal = {PeerJ}, volume = {6}, number = {}, pages = {e4278}, pmid = {29441230}, issn = {2167-8359}, abstract = {Biodiversity forecasts are important for conservation, management, and evaluating how well current models characterize natural systems. While the number of forecasts for biodiversity is increasing, there is little information available on how well these forecasts work. Most biodiversity forecasts are not evaluated to determine how well they predict future diversity, fail to account for uncertainty, and do not use time-series data that captures the actual dynamics being studied. We addressed these limitations by using best practices to explore our ability to forecast the species richness of breeding birds in North America. We used hindcasting to evaluate six different modeling approaches for predicting richness. Hindcasts for each method were evaluated annually for a decade at 1,237 sites distributed throughout the continental United States. All models explained more than 50% of the variance in richness, but none of them consistently outperformed a baseline model that predicted constant richness at each site. The best practices implemented in this study directly influenced the forecasts and evaluations. Stacked species distribution models and "naive" forecasts produced poor estimates of uncertainty and accounting for this resulted in these models dropping in the relative performance compared to other models. Accounting for observer effects improved model performance overall, but also changed the rank ordering of models because it did not improve the accuracy of the "naive" model. Considering the forecast horizon revealed that the prediction accuracy decreased across all models as the time horizon of the forecast increased. To facilitate the rapid improvement of biodiversity forecasts, we emphasize the value of specific best practices in making forecasts and evaluating forecasting methods.}, } @article {pmid29441154, year = {2018}, author = {Bourla, A and Mouchabac, S and El Hage, W and Ferreri, F}, title = {e-PTSD: an overview on how new technologies can improve prediction and assessment of Posttraumatic Stress Disorder (PTSD).}, journal = {European journal of psychotraumatology}, volume = {9}, number = {sup1}, pages = {1424448}, pmid = {29441154}, issn = {2000-8066}, abstract = {Background: New technologies may profoundly change our way of understanding psychiatric disorders including posttraumatic stress disorder (PTSD). Imaging and biomarkers, along with technological and medical informatics developments, might provide an answer regarding at-risk patient's identification. Recent advances in the concept of 'digital phenotype', which refers to the capture of characteristics of a psychiatric disorder by computerized measurement tools, is one paradigmatic example. Objective: The impact of the new technologies on health professionals practice in PTSD care remains to be determined. The recent evolutions could disrupt the clinical practices and practitioners in their beliefs, ethics and representations, going as far as questioning their professional culture. In the present paper, we conducted an extensive search to highlight the articles which reflect the potential of these new technologies. Method: We conducted an overview by querying PubMed database with the terms [PTSD] [Posttraumatic stress disorder] AND [Computer] OR [Computerized] OR [Mobile] OR [Automatic] OR [Automated] OR [Machine learning] OR [Sensor] OR [Heart rate variability] OR [HRV] OR [actigraphy] OR [actimetry] OR [digital] OR [motion] OR [temperature] OR [virtual reality]. Results: We summarized the synthesized literature in two categories: prediction and assessment (including diagnostic, screening and monitoring). Two independent reviewers screened, extracted data and quality appraised the sources. Results were synthesized narratively. Conclusions: This overview shows that many studies are underway allowing researchers to start building a PTSD digital phenotype using passive data obtained by biometric sensors. Active data obtained from Ecological Momentary Assessment (EMA) could allow clinicians to assess PTSD patients. The place of connected objects, Artificial Intelligence and remote monitoring of patients with psychiatric pathology remains to be defined. These tools must be explained and adapted to the different profiles of physicians and patients. The involvement of patients, caregivers and health professionals is essential to the design and evaluation of these new tools.}, } @article {pmid29438679, year = {2018}, author = {Doxey, AC and Mansfield, MJ and Montecucco, C}, title = {Discovery of novel bacterial toxins by genomics and computational biology.}, journal = {Toxicon : official journal of the International Society on Toxinology}, volume = {147}, number = {}, pages = {2-12}, doi = {10.1016/j.toxicon.2018.02.002}, pmid = {29438679}, issn = {1879-3150}, mesh = {Animals ; Bacteria/*metabolism ; Bacterial Proteins/genetics/metabolism/toxicity ; Bacterial Toxins/*chemistry/*toxicity ; *Computational Biology ; Gene Expression Regulation, Bacterial ; *Genomics ; Humans ; }, abstract = {Hundreds and hundreds of bacterial protein toxins are presently known. Traditionally, toxin identification begins with pathological studies of bacterial infectious disease. Following identification and cultivation of a bacterial pathogen, the protein toxin is purified from the culture medium and its pathogenic activity is studied using the methods of biochemistry and structural biology, cell biology, tissue and organ biology, and appropriate animal models, supplemented by bioimaging techniques. The ongoing and explosive development of high-throughput DNA sequencing and bioinformatic approaches have set in motion a revolution in many fields of biology, including microbiology. One consequence is that genes encoding novel bacterial toxins can be identified by bioinformatic and computational methods based on previous knowledge accumulated from studies of the biology and pathology of thousands of known bacterial protein toxins. Starting from the paradigmatic cases of diphtheria toxin, tetanus and botulinum neurotoxins, this review discusses traditional experimental approaches as well as bioinformatics and genomics-driven approaches that facilitate the discovery of novel bacterial toxins. We discuss recent work on the identification of novel botulinum-like toxins from genera such as Weissella, Chryseobacterium, and Enteroccocus, and the implications of these computationally identified toxins in the field. Finally, we discuss the promise of metagenomics in the discovery of novel toxins and their ecological niches, and present data suggesting the existence of uncharacterized, botulinum-like toxin genes in insect gut metagenomes.}, } @article {pmid29437638, year = {2018}, author = {Gardner, K and Fulford, T and Silver, N and Rooks, H and Angelis, N and Allman, M and Nkya, S and Makani, J and Howard, J and Kesse-Adu, R and Rees, DC and Stuart-Smith, S and Yeghen, T and Awogbade, M and Sangeda, RZ and Mgaya, J and Patel, H and Newhouse, S and Menzel, S and Thein, SL}, title = {g(HbF): a genetic model of fetal hemoglobin in sickle cell disease.}, journal = {Blood advances}, volume = {2}, number = {3}, pages = {235-239}, pmid = {29437638}, issn = {2473-9537}, support = {//British Heart Foundation/United Kingdom ; ID62593//Medical Research Council/United Kingdom ; D43 TW009343/TW/FIC NIH HHS/United States ; //Cancer Research UK/United Kingdom ; MR/K006584/1//Wellcome Trust/United Kingdom ; //Arthritis Research UK/United Kingdom ; //Wellcome Trust/United Kingdom ; //Chief Scientist Office/United Kingdom ; G0001249//Medical Research Council/United Kingdom ; }, mesh = {Adolescent ; Adult ; Aged ; Aged, 80 and over ; Alleles ; Anemia, Sickle Cell/*genetics ; Child ; Child, Preschool ; England ; Fetal Hemoglobin/*genetics ; Genetic Loci ; Genetic Variation ; Genotype ; Hemoglobin, Sickle/genetics ; Humans ; Middle Aged ; *Models, Genetic ; Young Adult ; }, abstract = {Fetal hemoglobin (HbF) is a strong modifier of sickle cell disease (SCD) severity and is associated with 3 common genetic loci. Quantifying the genetic effects of the 3 loci would specifically address the benefits of HbF increases in patients. Here, we have applied statistical methods using the most representative variants: rs1427407 and rs6545816 in BCL11A, rs66650371 (3-bp deletion) and rs9376090 in HMIP-2A, rs9494142 and rs9494145 in HMIP-2B, and rs7482144 (Xmn1-HBG2 in the β-globin locus) to create g(HbF), a genetic quantitative variable for HbF in SCD. Only patients aged ≥5 years with complete genotype and HbF data were studied. Five hundred eighty-one patients with hemoglobin SS (HbSS) or HbSβ[0] thalassemia formed the "discovery" cohort. Multiple linear regression modeling rationalized the 7 variants down to 4 markers (rs6545816, rs1427407, rs66650371, and rs7482144) each independently contributing HbF-boosting alleles, together accounting for 21.8% of HbF variability (r[2]) in the HbSS or HbSβ[0] patients. The model was replicated with consistent r[2] in 2 different cohorts: 27.5% in HbSC patients (N = 186) and 23% in 994 Tanzanian HbSS patients. g(HbF), our 4-variant model, provides a robust approach to account for the genetic component of HbF in SCD and is of potential utility in sickle genetic and clinical studies.}, } @article {pmid29433218, year = {2018}, author = {Higgins, D and Pal, C and Sulaiman, IM and Jia, C and Zerwekh, T and Dowd, SE and Banerjee, P}, title = {Application of high-throughput pyrosequencing in the analysis of microbiota of food commodities procured from small and large retail outlets in a U.S. metropolitan area - A pilot study.}, journal = {Food research international (Ottawa, Ont.)}, volume = {105}, number = {}, pages = {29-40}, doi = {10.1016/j.foodres.2017.10.057}, pmid = {29433218}, issn = {1873-7145}, support = {U54 FD004330/FD/FDA HHS/United States ; }, mesh = {Aeromonas/isolation & purification ; Bacillus/isolation & purification ; Computational Biology ; DNA, Bacterial/genetics/*isolation & purification ; Enterobacter/isolation & purification ; Firmicutes/isolation & purification ; *Food Microbiology ; *High-Throughput Nucleotide Sequencing ; Meat Products/microbiology ; *Microbiota ; Pantoea/isolation & purification ; Pilot Projects ; Proteobacteria/isolation & purification ; RNA, Ribosomal, 16S/genetics/isolation & purification ; Sequence Analysis, DNA ; Tennessee ; Vegetables/microbiology ; }, abstract = {With the advent of high-throughput sequencing technologies, it is possible to comprehensively analyze the microbial community of foods without culturing them in the laboratory. The estimation of all microbes inhabiting a food commodity (food microbiota) therefore may shed light on the microbial quality and safety of foods. In this study, we utilized high-throughput pyrosequencing of 16S rRNA genes as well as traditional microbiological methods to evaluate the bacterial diversity and the predicted metabolic pathways associated with the bacterial communities of selected foods (romaine lettuce, cabbage, deli meat, and chicken legs, total 200 samples) procured from small and large retail outlets located in Memphis-Shelby County, Tennessee, USA. For high-throughput sequencing, microbial genomic DNA was directly extracted from the food products and subjected to genetic sequencing. Aerobic plate count of all food samples was also performed. Foods from small stores (such as corner stores) were found to contain higher bacterial counts as compared to large stores (such as supermarkets). High-throughput pyrosequencing in tandem with bioinformatics analyses revealed a comprehensive picture of the bacterial ecology of foods at different taxonomic levels. Firmicutes and Proteobacteria were the most abundant phyla across all products. At the genus level, Enterobacter and Pantoea in vegetables, and Bacillus and Aeromonas in animal products were found to be the most abundant. The bacterial predicted metabolic pathways such as inosine-5'-phosphate biosynthesis I, methylglyoxal (MG) degradation pathways, urea cycle, dTDP-l-rhamnose biosynthesis I, and mevalonate pathway I differed in foods procured from small stores as compared to large groceries or supermarkets. The results from this study revealed that the bacterial ecology (both in terms of numbers and types of bacteria) of food commodities might differ based on the vending outlet type (large vs. small) of retail stores. The overall estimation bacterial communities in foods by high-throughput sequencing method may be useful to identify potential taxa responsible for food spoilage. Moreover, the data from pyrosequencing of 16S rRNA genes can also be applied to infer major metabolic pathways in bacteria inhabiting different foods. This may reflect the role of these pathways in food-bacteria interaction and adaptation.}, } @article {pmid29432851, year = {2018}, author = {Gates, DJ and Pilson, D and Smith, SD}, title = {Filtering of target sequence capture individuals facilitates species tree construction in the plant subtribe Iochrominae (Solanaceae).}, journal = {Molecular phylogenetics and evolution}, volume = {123}, number = {}, pages = {26-34}, doi = {10.1016/j.ympev.2018.02.002}, pmid = {29432851}, issn = {1095-9513}, mesh = {Base Sequence ; Cluster Analysis ; Databases, Genetic ; High-Throughput Nucleotide Sequencing/methods ; Likelihood Functions ; *Phylogeny ; Sequence Analysis, DNA ; Solanaceae/*classification/*genetics ; Species Specificity ; }, abstract = {Advances in sequencing technology have made it possible to produce large multi-locus datasets required for species tree analyses. One challenge with constructing high throughput sequencing datasets, however, is that missing information is propagated at different steps in the sequence preparation process. To date, species tree studies have focused on filtering and removing errors that occur at particular loci. Given the way that high throughput sequencing datasets are constructed, however, large amounts of error or ambiguity may also manifest across individuals. Here we use a novel tree-based multivariate clustering method to identify and remove individuals with low phylogenetic signal in a nuclear sequence capture dataset for the Iochrominae clade (Solanaceae). Our results suggest that the low quality tips are the result of the library preparation process (e.g. unequal pooling) rather than poor capture due to phylogenetic distance from the reference species. After implementing the clustering approach and removing low quality tips, we construct an Iochrominae species tree that resolves a number of unknown relationships. We propose this pipeline as a valuable tool for species tree reconstruction with phylogenomic datasets containing variable levels of missing data.}, } @article {pmid29431888, year = {2018}, author = {Hackett, SC and Bonsall, MB}, title = {Management of a stage-structured insect pest: an application of approximate optimization.}, journal = {Ecological applications : a publication of the Ecological Society of America}, volume = {28}, number = {4}, pages = {938-952}, doi = {10.1002/eap.1700}, pmid = {29431888}, issn = {1051-0761}, support = {BB/H01814X/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; *Ceratitis capitata ; *Decision Support Techniques ; Female ; Insecticides/*economics ; Male ; Models, Biological ; Pest Control, Biological/*economics ; }, abstract = {Ecological decision problems frequently require the optimization of a sequence of actions over time where actions may have both immediate and downstream effects. Dynamic programming can solve such problems only if the dimensionality is sufficiently low. Approximate dynamic programming (ADP) provides a suite of methods applicable to problems of arbitrary complexity at the expense of guaranteed optimality. The most easily generalized method is the look-ahead policy: a brute-force algorithm that identifies reasonable actions by constructing and solving a series of temporally truncated approximations of the full problem over a defined planning horizon. We develop and apply this approach to a pest management problem inspired by the Mediterranean fruit fly, Ceratitis capitata. The model aims to minimize the cumulative costs of management actions and medfly-induced losses over a single 16-week season. The medfly population is stage-structured and grows continuously while management decisions are made at discrete, weekly intervals. For each week, the model chooses between inaction, insecticide application, or one of six sterile insect release ratios. Look-ahead policy performance is evaluated over a range of planning horizons, two levels of crop susceptibility to medfly and three levels of pesticide persistence. In all cases, the actions proposed by the look-ahead policy are contrasted to those of a myopic policy that minimizes costs over only the current week. We find that look-ahead policies always out-performed a myopic policy and decision quality is sensitive to the temporal distribution of costs relative to the planning horizon: it is beneficial to extend the planning horizon when it excludes pertinent costs. However, longer planning horizons may reduce decision quality when major costs are resolved imminently. ADP methods such as the look-ahead-policy-based approach developed here render questions intractable to dynamic programming amenable to inference but should be applied carefully as their flexibility comes at the expense of guaranteed optimality. However, given the complexity of many ecological management problems, the capacity to propose a strategy that is "good enough" using a more representative problem formulation may be preferable to an optimal strategy derived from a simplified model.}, } @article {pmid29431231, year = {2019}, author = {Daly, MR and Mellor, JM and Millones, M}, title = {Defining Primary Care Shortage Areas: Do GIS-based Measures Yield Different Results?.}, journal = {The Journal of rural health : official journal of the American Rural Health Association and the National Rural Health Care Association}, volume = {35}, number = {1}, pages = {22-34}, doi = {10.1111/jrh.12294}, pmid = {29431231}, issn = {1748-0361}, mesh = {Geographic Information Systems/trends ; *Geographic Mapping ; Humans ; *Medically Underserved Area ; Primary Health Care/methods/*trends ; Virginia ; }, abstract = {PURPOSE: To examine whether geographic information systems (GIS)-based physician-to-population ratios (PPRs) yield determinations of geographic primary care shortage areas that differ from those based on bounded-area PPRs like those used in the Health Professional Shortage Area (HPSA) designation process.

METHODS: We used geocoded data on primary care physician (PCP) locations and census block population counts from 1 US state to construct 2 shortage area indicators. The first is a bounded-area shortage indicator defined without GIS methods; the second is a GIS-based measure that measures the populations' spatial proximity to PCP locations. We examined agreement and disagreement between bounded shortage areas and GIS-based shortage areas.

FINDINGS: Bounded shortage area indicators and GIS-based shortage area indicators agree for the census blocks where the vast majority of our study populations reside. Specifically, 95% and 98% of the populations in our full and urban samples, respectively, reside in census blocks where the 2 indicators agree. Although agreement is generally high in rural areas (ie, 87% of the rural population reside in census blocks where the 2 indicators agree), agreement is significantly lower compared to urban areas. One source of disagreement suggests that bounded-area measures may "overlook" some shortages in rural areas; however, other aspects of the HPSA designation process likely mitigate this concern. Another source of disagreement arises from the border-crossing problem, and it is more prevalent.

CONCLUSIONS: The GIS-based PPRs we employed would yield shortage area determinations that are similar to those based on bounded-area PPRs defined for Primary Care Service Areas. Disagreement rates were lower than previous studies have found.}, } @article {pmid29426939, year = {2018}, author = {Sablok, G and Hayward, RJ and Davey, PA and Santos, RP and Schliep, M and Larkum, A and Pernice, M and Dolferus, R and Ralph, PJ}, title = {SeagrassDB: An open-source transcriptomics landscape for phylogenetically profiled seagrasses and aquatic plants.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {2749}, pmid = {29426939}, issn = {2045-2322}, mesh = {Aquatic Organisms/*classification/*genetics ; *Databases, Genetic ; Marine Biology ; Phylogeny ; Plants/*classification/*genetics ; Transcriptome/genetics ; }, abstract = {Seagrasses and aquatic plants are important clades of higher plants, significant for carbon sequestration and marine ecological restoration. They are valuable in the sense that they allow us to understand how plants have developed traits to adapt to high salinity and photosynthetically challenged environments. Here, we present a large-scale phylogenetically profiled transcriptomics repository covering seagrasses and aquatic plants. SeagrassDB encompasses a total of 1,052,262 unigenes with a minimum and maximum contig length of 8,831 bp and 16,705 bp respectively. SeagrassDB provides access to 34,455 transcription factors, 470,568 PFAM domains, 382,528 prosite models and 482,121 InterPro domains across 9 species. SeagrassDB allows for the comparative gene mining using BLAST-based approaches and subsequent unigenes sequence retrieval with associated features such as expression (FPKM values), gene ontologies, functional assignments, family level classification, Interpro domains, KEGG orthology (KO), transcription factors and prosite information. SeagrassDB is available to the scientific community for exploring the functional genic landscape of seagrass and aquatic plants at: http://115.146.91.129/index.php .}, } @article {pmid29426887, year = {2018}, author = {Liu, Y and Crawford, FW}, title = {Estimating dose-specific cell division and apoptosis rates from chemo-sensitivity experiments.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {2705}, pmid = {29426887}, issn = {2045-2322}, support = {DP2 HD091799/HD/NICHD NIH HHS/United States ; }, mesh = {Apoptosis/*drug effects ; Cell Division/*drug effects ; Cell Proliferation/*drug effects ; Data Interpretation, Statistical ; Drug Therapy/methods ; Humans ; Research Design ; Software ; }, abstract = {In-vitro chemo-sensitivity experiments are an essential step in the early stages of cancer therapy development, but existing data analysis methods suffer from problems with fitting, do not permit assessment of uncertainty, and can give misleading estimates of cell growth inhibition. We present an approach (bdChemo) based on a mechanistic model of cell division and death that permits rigorous statistical analyses of chemo-sensitivity experiment data by simultaneous estimation of cell division and apoptosis rates as functions of dose, without making strong assumptions about the shape of the dose-response curve. We demonstrate the utility of this method using a large-scale NCI-DREAM challenge dataset. We developed an R package "bdChemo" implementing this method, available at https://github.com/YiyiLiu1/bdChemo .}, } @article {pmid29426200, year = {2018}, author = {Stefanidis, K and Panagopoulos, Y and Mimikou, M}, title = {Response of a multi-stressed Mediterranean river to future climate and socio-economic scenarios.}, journal = {The Science of the total environment}, volume = {627}, number = {}, pages = {756-769}, doi = {10.1016/j.scitotenv.2018.01.282}, pmid = {29426200}, issn = {1879-1026}, mesh = {*Climate Change ; Ecosystem ; *Environmental Monitoring ; Europe ; Greece ; Mediterranean Region ; *Models, Theoretical ; Rivers/*chemistry ; Socioeconomic Factors ; Water Pollution/*statistics & numerical data ; }, abstract = {Streams and rivers are among the most threatened ecosystems in Europe due to the combined effects of multiple pressures related to anthropogenic activities. Particularly in the Mediterranean region, changes in hydromorphology along with increased nutrient loadings are known to affect the ecological functions and ecosystem services of streams and rivers with the anticipated climate change being likely to further impair their functionality and structure. In this study, we investigated the combined effects of agricultural driven stressors on the ecology and delivered services of the Pinios river basin in Greece under three future world scenarios developed within the EU funded MARS project. Scenarios are based on combinations of Representative Concentration Pathways and Shared Socioeconomic Pathways and refer to early century (2030) and mid-century (2060) representing future climate worlds with particular socioeconomic characteristics. To assess the responses of ecological and ecosystem service indicators to the scenarios we first simulated hydrology and water quality in Pinios with a process-based model. Simulated abiotic stressor parameters (predictors) were linked to two biotic indicators, the macroinvertebrate indicators ASPT and EPT, with empirical modelling based on boosted regression trees and general linear models. Our results showed that the techno world scenario driven by fast economic growth and intensive exploitation of energy resources had the largest impact on both the abiotic status (nutrient loads and concentrations in water) and the biotic indicators. In contrast, the predicted changes under the other two future worlds, consensus and fragmented, were more diverse and were mostly dictated by the projected climate. This work showed that the future scenarios, especially the mid-century ones, had significant impact on both abiotic status and biotic responses underpinning the need for implementing catchment management practices able to mitigate the ecological threat on waters in the long-term.}, } @article {pmid29423631, year = {2018}, author = {Yu, Y and Tang, B and Dai, R and Zhang, B and Chen, L and Yang, H and Zhao, G and Ding, X}, title = {Identification of the streptothricin and tunicamycin biosynthetic gene clusters by genome mining in Streptomyces sp. strain fd1-xmd.}, journal = {Applied microbiology and biotechnology}, volume = {102}, number = {6}, pages = {2621-2633}, doi = {10.1007/s00253-018-8748-4}, pmid = {29423631}, issn = {1432-0614}, support = {2016YFA0500600//National Key R&D Program of China/ ; 17JC1401800//Basic Research Project of Science and Technology Commission of Shanghai Municipality/ ; 2017R19R08E01//Youth Talent Training Program of Zhejiang Academy of Agricultural Sciences/ ; }, mesh = {Bacteria/drug effects ; Biosynthetic Pathways/*genetics ; China ; Computational Biology ; Culture Media/chemistry ; Data Mining ; Eukaryota/drug effects ; *Genomics ; *Multigene Family ; Soil Microbiology ; Streptomyces/classification/*genetics/isolation & purification/*metabolism ; Streptothricins/*biosynthesis ; Tunicamycin/*biosynthesis ; Whole Genome Sequencing ; }, abstract = {The genus Streptomyces have been highly regarded for their important source of natural products. Combined with the technology of genome sequencing and mining, we could identify the active ingredients from fermentation broth quickly. Here, we report on Streptomyces sp. strain fd1-xmd, which was isolated from a soil sample collected in Shanghai. Interestingly, the fermentation broth derived from this strain demonstrated broad-spectrum antimicrobial activity against gram-positive bacteria, gram-negative bacteria, and eukaryotes. To identify the antimicrobial substances and their biosynthetic gene clusters, we sequenced the fd1-xmd strain and obtained a genome 7,929,999 bp in length. The average GC content of the chromosome was 72.5 mol%. Knockout experiments demonstrated that out of eight biosynthetic gene clusters we could identify, two are responsible for the biosynthesis of the antibiotics streptothricin (ST) and tunicamycin (TM). The ST biosynthetic gene cluster from fd1-xmd was verified via successful heterologous expression in Streptomyces coelicolor M1146. ST production had a yield of up to 0.5 g/L after the optimization of culture conditions. This study describes a novel producer of ST and TM and outlines the complete process undertaken for Streptomyces sp. strain fd1-xmd genome mining.}, } @article {pmid29420617, year = {2018}, author = {Hufsky, F and Ibrahim, B and Beer, M and Deng, L and Mercier, PL and McMahon, DP and Palmarini, M and Thiel, V and Marz, M}, title = {Virologists-Heroes need weapons.}, journal = {PLoS pathogens}, volume = {14}, number = {2}, pages = {e1006771}, pmid = {29420617}, issn = {1553-7374}, support = {MC_UU_12014/10/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Animals ; Biomedical Research/*methods/trends ; Computational Biology/methods/trends ; Europe ; Humans ; Professional Role ; Virology/*methods/trends ; Workforce ; }, } @article {pmid29415502, year = {2018}, author = {Chen, G and He, L and Luo, L and Huang, R and Liao, L and Li, Y and Zhu, Z and Wang, Y}, title = {Transcriptomics Sequencing Provides Insights into Understanding the Mechanism of Grass Carp Reovirus Infection.}, journal = {International journal of molecular sciences}, volume = {19}, number = {2}, pages = {}, pmid = {29415502}, issn = {1422-0067}, mesh = {Animals ; Cell Survival ; Computational Biology ; Cytopathogenic Effect, Viral ; Fish Diseases/*genetics/*virology ; Gene Expression Regulation ; Gene Ontology ; *High-Throughput Nucleotide Sequencing ; *Reoviridae ; Reoviridae Infections/*veterinary ; Reproducibility of Results ; *Transcriptome ; }, abstract = {Grass carp is an important aquaculture fish species in China that is affected by severe diseases, especially haemorrhagic disease caused by grass carp reovirus (GCRV). However, the mechanisms of GCRV invasion and infection remain to be elucidated. In the present study, Ctenopharyngodon idellus kidney (CIK) cells were infected with GCRV, harvested at 0, 8, 24, and 72 h post infection, respectively, and then subjected to transcriptomics sequencing. Each sample yielded more than 6 Gb of clean data and 40 million clean reads. To better understand GCRV infection, the process was divided into three phases: the early (0-8 h post infection), middle (8-24 h post infection), and late (24-72 h) stages of infection. A total of 76 (35 up-regulated, 41 down-regulated), 553 (463 up-regulated, 90 down-regulated), and 284 (150 up-regulated, 134 down-regulated) differently expressed genes (DEGs) were identified during the early, middle, and late stages of infection, respectively. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis revealed that DEGs were mainly involved in carbohydrate biosynthesis, transport, and endocytosis in the early stage, phagocytosis and lysosome pathways were mainly enriched in the middle stage, and programmed cell death, apoptosis, and inflammation were largely associated with the late stage. These results suggest GCRV infection is a gradual process involving adsorption on the cell surface, followed by endocytosis into cells, transport by lysosomes, and eventually resulted in cell necrosis and/or apoptosis. Our findings provide insight into the mechanisms of grass carp reovirus infection.}, } @article {pmid29414353, year = {2018}, author = {Zuo, H and Chen, L and Kong, M and Yang, Y and Lü, P and Qiu, L and Wang, Q and Ma, S and Chen, K}, title = {The toxic effect of sodium fluoride on Spodoptera frugiperda 9 cells and differential protein analysis following NaF treatment of cells.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {236}, number = {}, pages = {313-323}, doi = {10.1016/j.envpol.2018.01.054}, pmid = {29414353}, issn = {1873-6424}, mesh = {Animals ; Apoptosis/*drug effects ; Cell Survival/drug effects ; Dose-Response Relationship, Drug ; Environmental Pollutants/*toxicity ; Gene Expression Regulation/drug effects ; Gene Ontology ; Humans ; Insect Proteins/*genetics ; Necrosis ; Sf9 Cells ; Sodium Fluoride/*toxicity ; }, abstract = {Accumulation of excess fluoride has a destructive effect on the environment, endangering human health, affecting organism growth and development, and leading to damage to the biological chain, thereby affecting ecological environment balance. In recent years, numerous studies focused on the molecular mechanisms associated with fluoride toxicity; however, fluoride-toxicity mechanisms in insect cells remain unclear. This study explored the toxic impact of sodium fluoride (NaF) on Spodoptera frugiperda 9 (Sf9) insect cells. High concentrations of NaF (10[-4] M, 10[-3] M and 10[-2] M) resulted in cell enlargement, cell membrane blurring and breakage, and release of cellular contents. Dose-response curves indicated that NaF-specific inhibition rates on Sf9-cell activity increased along with increases in NaF concentration, with a half-inhibitory concentration (IC50) for NaF of 5.919 × 10[-3] M at 72 h. Compared with controls, the percentages of early and late apoptotic and necrotic cells clearly increased based on observed increases in NaF concentrations. Two-dimensional gel electrophoresis combined with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry was used to detect differentially expressed proteins in Sf9 cells treated with IC50 NaF, identifying 17 proteins, seven of which were upregulated and 10 downregulated. These results demonstrated that Sf9 cells showed signs of NaF-mediated toxicity through alterations in cell morphology, apoptosis rates, and protein expression.}, } @article {pmid29413986, year = {2018}, author = {Gross, M}, title = {Eyes on our planet.}, journal = {Current biology : CB}, volume = {28}, number = {3}, pages = {R89-R92}, doi = {10.1016/j.cub.2018.01.046}, pmid = {29413986}, issn = {1879-0445}, mesh = {*Big Data ; Climate ; Conservation of Natural Resources/*methods ; *Fisheries/statistics & numerical data ; *Machine Learning ; Meteorology/*instrumentation ; Oceans and Seas ; Remote Sensing Technology/*statistics & numerical data ; *Spacecraft ; }, abstract = {Combining several satellite-based tracking technologies with big data methods and machine learning, fisheries experts can now efficiently monitor the entirety of the oceans and ensure that legal limits and protected areas are respected. Observing our planet from space is also proving a fruitful approach in other areas of conservation, ecology and climate research. Michael Gross reports.}, } @article {pmid29413870, year = {2018}, author = {Kreitz, C and Schnuerch, R and Furley, PA and Memmert, D}, title = {What's past is past: Neither perceptual preactivation nor prior motivational relevance decrease subsequent inattentional blindness.}, journal = {Consciousness and cognition}, volume = {59}, number = {}, pages = {1-9}, doi = {10.1016/j.concog.2018.01.003}, pmid = {29413870}, issn = {1090-2376}, mesh = {Adult ; Attention/*physiology ; Awareness/*physiology ; Female ; Humans ; Male ; Motivation/*physiology ; Visual Perception/*physiology ; Young Adult ; }, abstract = {Inattentional blindness-the phenomenon that clearly visible, yet currently unexpected objects go unnoticed when our attention is focused elsewhere-is an ecologically valid failure of awareness. It is currently subject to debate whether previous events and experiences determine whether or not inattentional blindness occurs. Using a simple two-phase paradigm in the present study, we found that the likelihood of missing an unexpected object due to inattention did not change when its defining characteristic (its color) was perceptually preactivated (Experiment 1; N = 188). Likewise, noticing rates were not significantly reduced if the object's color was previously motivationally relevant during an unrelated detection task (Experiment 2; N = 184). These results corroborate and extend recent findings questioning the influence of previous experience on subsequent inattentional blindness. This has implications for possible countermeasures intended to thwart the potentially harmful effects of inattention.}, } @article {pmid29412350, year = {2018}, author = {Carmo, ÉA and Santos, PHS and Ribeiro, BS and Soares, CJ and Santana, MLAD and Bomfim, EDS and Oliveira, BG and Oliveira, JDS}, title = {Sociodemographic characteristics and time series of mortality due to suicide among elderly individuals in Bahia State, Brazil, 1996-2013.}, journal = {Epidemiologia e servicos de saude : revista do Sistema Unico de Saude do Brasil}, volume = {27}, number = {1}, pages = {e20171971}, doi = {10.5123/S1679-49742018000100001}, pmid = {29412350}, issn = {2237-9622}, mesh = {Aged ; Aged, 80 and over ; Asphyxia/*epidemiology/mortality ; Brazil/epidemiology ; Cause of Death ; Female ; Humans ; Information Systems ; Male ; Middle Aged ; Poisoning/*epidemiology/mortality ; Regression Analysis ; Sex Factors ; Suicide/*statistics & numerical data/trends ; Time Factors ; }, abstract = {OBJECTIVE: to describe sociodemographic aspects and time evolution of mortality due to suicide among elderly individuals in Bahia State, Brazil, from 1996 to 2013.

METHODS: time series descriptive and ecological study, with data from the Mortality Information System (SIM); Prais-Winsten regression was used for trend analysis and to calculate annual percent change (APC).

RESULTS: 858 deaths due to suicide were identified in elderly in Bahia; 85.4% were men, and 53.8% were in the 60-69 age group; 64.3% of deaths resulted from hanging/strangulation, followed by self-poisoning by pesticides and chemical products (13.1%); there was an increasing trend in suicide mortality rate in the general elderly population (APC 11.0; 95%CI 6.9;15.3) and in the male sex (APC 12.1; 95%CI 7.1;17.3), whilst in the female population it remained stable.

CONCLUSION: in Bahia, mortality due to suicide among elderly individuals presented an increasing trend in the period studied and was higher among males.}, } @article {pmid29412314, year = {2018}, author = {Paiva, RFDPS and Souza, MFDP}, title = {[Association between socioeconomic, health, and primary care conditions and hospital morbidity due to waterborne diseases in Brazil].}, journal = {Cadernos de saude publica}, volume = {34}, number = {1}, pages = {e00017316}, doi = {10.1590/0102-311X00017316}, pmid = {29412314}, issn = {1678-4464}, mesh = {Brazil/epidemiology ; Child ; Educational Status ; Family Health/economics/*statistics & numerical data ; Hospitalization/economics/*statistics & numerical data ; Humans ; Morbidity ; Primary Health Care/economics/*statistics & numerical data ; Sanitation/economics/*statistics & numerical data ; Sewage ; Socioeconomic Factors ; Waterborne Diseases/economics/*mortality/*transmission ; }, abstract = {The current study aimed to assess the association between socioeconomic conditions, basic sanitation, and coverage by family health teams and hospitalizations for waterborne diseases. The analysis of socioeconomic conditions and sanitation was based on an ecological study with data from the Brazilian National Household Sample Survey (PNAD) and the Brazilian Health Informatics Departament (DATASUS) database (observations for the States and Federal District) for the year 2013. Associations between family health teams and hospitalization were assessed by simple regressions, with data from DATASUS and the Department of Primary Care of Ministry of Health from 1998 to 2014. Connection to the public sewage system, low schooling, and family health team coverage were significantly associated (p < 0.05) with hospitalizations for waterborne diseases. Based on attributable risk analysis, for Brazil as a whole in 2013, 57,574 (16.3%) of hospital admissions for waterborne diseases could have been avoided by adequate sewage disposal, which would also have avoided BRL 20,372,559.90 in treatment costs and 172,722 days lost to hospitalization. The results emphasize the importance of integrated sanitation policies, education, and health care that consider regional inequalities, thereby contributing to improvement of the population's health conditions.}, } @article {pmid29412052, year = {2018}, author = {Lane, SD and Keefe, RH and Rubinstein, RA and Hall, M and Kelly, KA and Satterly, LB and Shaw, A and Fisher, J}, title = {Integrating the social determinants of health into two interprofessional courses: Findings from a pilot study.}, journal = {Journal of interprofessional care}, volume = {32}, number = {4}, pages = {505-508}, doi = {10.1080/13561820.2018.1435517}, pmid = {29412052}, issn = {1469-9567}, mesh = {Clinical Competence ; Cooperative Behavior ; Curriculum ; Health Knowledge, Attitudes, Practice ; Health Occupations/*education ; Health Status Disparities ; Humans ; *Interprofessional Relations ; New York ; *Peer Group ; Pilot Projects ; *Social Determinants of Health ; Socioeconomic Factors ; Teaching/*organization & administration ; }, abstract = {Five colleges and universities in Upstate New York, United States, created the 'Route-90 Collaborative' to support faculty implementing the Institute of Medicine's (IOM) Framework for Educating Health Professionals to Address the Social Determinants of Health. The two courses described herein used a flipped classroom approach in which students from 14 different nations were responsible for facilitating individual classes. This descriptive study used an educational intervention in two interprofessional courses - reproductive health and global health - based on the IOM Framework into two courses. The evaluation used quantitative and open-ended text response data from students. Course evaluations indicated the students found the courses helped them to learn more about health issues and service delivery in various countries, expand their knowledge base on sociocultural and ecological influences on health care, and broaden their perspectives on various health topics so they will be able to provide higher quality healthcare. Although this is the first effort of our Collaborative to implement the Framework, given the student feedback, we believe implementing the Framework in various courses has the potential to enhance healthcare service delivery and reduce the negative impact of social determinants of health.}, } @article {pmid29411442, year = {2018}, author = {Leal, L and Talla, V and Källman, T and Friberg, M and Wiklund, C and Dincă, V and Vila, R and Backström, N}, title = {Gene expression profiling across ontogenetic stages in the wood white (Leptidea sinapis) reveals pathways linked to butterfly diapause regulation.}, journal = {Molecular ecology}, volume = {27}, number = {4}, pages = {935-948}, doi = {10.1111/mec.14501}, pmid = {29411442}, issn = {1365-294X}, mesh = {Animals ; Butterflies/*genetics/*physiology/radiation effects ; Circadian Clocks/genetics ; Cluster Analysis ; Diapause/*genetics/radiation effects ; Female ; *Gene Expression Profiling ; Gene Expression Regulation, Developmental/radiation effects ; Gene Ontology ; Light ; *Wood ; }, abstract = {In temperate latitudes, many insects enter diapause (dormancy) during the cold season, a period during which developmental processes come to a standstill. The wood white (Leptidea sinapis) is a butterfly species distributed across western Eurasia that shows photoperiod-induced diapause with variation in critical day-length across populations at different latitudes. We assembled transcriptomes and estimated gene expression levels at different developmental stages in experimentally induced directly developing and diapausing cohorts of a single Swedish population of L. sinapis to investigate the regulatory mechanisms underpinning diapause initiation. Different day lengths resulted in expression changes of developmental genes and affected the rate of accumulation of signal molecules, suggesting that diapause induction might be controlled by increased activity of monoamine neurotransmitters in larvae reared under short-day light conditions. Expression differences between light treatment groups of two monoamine regulator genes (DDC and ST) were observed already in instar III larvae. Once developmental pathways were irreversibly set at instar V, a handful of genes related to dopamine production were differentially expressed leading to a significant decrease in expression of global metabolic genes and increase in expression of genes related to fatty acid synthesis and sequestration. This is in line with a time-dependent (hour-glass) model of diapause regulation where a gradual shift in the concentration of monoamine neurotransmitters and their metabolites during development of larvae under short-day conditions leads to increased storage of fat, decreased energy expenditures, and ultimately developmental stasis at the pupal stage.}, } @article {pmid29411440, year = {2018}, author = {Noguerales, V and Cordero, PJ and Ortego, J}, title = {Integrating genomic and phenotypic data to evaluate alternative phylogenetic and species delimitation hypotheses in a recent evolutionary radiation of grasshoppers.}, journal = {Molecular ecology}, volume = {27}, number = {5}, pages = {1229-1244}, doi = {10.1111/mec.14504}, pmid = {29411440}, issn = {1365-294X}, mesh = {Animals ; *Biological Evolution ; Cluster Analysis ; Computational Biology ; *Genome ; Genotype ; Grasshoppers/anatomy & histology/classification/*genetics ; *Phenotype ; Phylogeny ; Species Specificity ; }, abstract = {Although resolving phylogenetic relationships and establishing species limits are primary goals of systematics, these tasks remain challenging at both conceptual and analytical levels. Here, we integrated genomic and phenotypic data and employed a comprehensive suite of coalescent-based analyses to develop and evaluate competing phylogenetic and species delimitation hypotheses in a recent evolutionary radiation of grasshoppers (Chorthippus binotatus group) composed of two species and eight putative subspecies. To resolve the evolutionary relationships within this complex, we first evaluated alternative phylogenetic hypotheses arising from multiple schemes of genomic data processing and contrasted genetic-based inferences with different sources of phenotypic information. Second, we examined the importance of number of loci, demographic priors, number and kind of phenotypic characters and sex-based trait variation for developing alternative species delimitation hypotheses. The best-supported topology was largely compatible with phenotypic data and showed the presence of two clades corresponding to the nominative species groups, one including three well-resolved lineages and the other comprising a four-lineage polytomy and a well-differentiated sister taxon. Integrative species delimitation analyses indicated that the number of employed loci had little impact on the obtained inferences but revealed the higher power provided by an increasing number of phenotypic characters and the usefulness of assessing their phylogenetic information content and differences between sexes in among-taxa trait variation. Overall, our study highlights the importance of integrating multiple sources of information to test competing phylogenetic hypotheses and elucidate the evolutionary history of species complexes representing early stages of divergence where conflicting inferences are more prone to appear.}, } @article {pmid29411379, year = {2018}, author = {Obregón, C and Lyndon, AR and Barker, J and Christiansen, H and Godley, BJ and Kurland, S and Piccolo, JJ and Potts, R and Short, R and Tebb, A and Mariani, S}, title = {Valuing and understanding fish populations in the Anthropocene: key questions to address.}, journal = {Journal of fish biology}, volume = {92}, number = {3}, pages = {828-845}, doi = {10.1111/jfb.13536}, pmid = {29411379}, issn = {1095-8649}, mesh = {Animals ; Biodiversity ; Conservation of Natural Resources/*methods ; Ecosystem ; Fisheries ; Fishes/*physiology ; Knowledge Bases ; Population Dynamics ; }, abstract = {Research on the values of fish populations and fisheries has primarily focused on bio-economic aspects; a more nuanced and multidimensional perspective is mostly neglected. Although a range of social aspects is increasingly being considered in fisheries research, there is still no clear understanding as to how to include these additional values within management policies nor is there a cogent appreciation of the major knowledge gaps that should be tackled by future research. This paper results from a workshop held during the 50th anniversary symposium of the Fisheries Society of the British Isles at the University of Exeter, UK, in July 2017. Here, we aim to highlight the current knowledge gaps on the values of fish populations and fisheries thus directing future research. To this end, we present eight questions that are deeply relevant to understanding the values of fish populations and fisheries. These can be applied to all habitats and fisheries, including freshwater, estuarine and marine.}, } @article {pmid29411121, year = {2018}, author = {Kangabam, RD and Selvaraj, M and Govindaraju, M}, title = {Spatio-temporal analysis of floating islands and their behavioral changes in Loktak Lake with respect to biodiversity using remote sensing and GIS techniques.}, journal = {Environmental monitoring and assessment}, volume = {190}, number = {3}, pages = {118}, pmid = {29411121}, issn = {1573-2959}, support = {Ramsar Research Grant 2013//Society of Wetland Scientists (US)/ ; TM04_1415//Ocean Park Conservaton Foundation, Hong Kong/ ; }, mesh = {Agriculture ; *Biodiversity ; Conservation of Natural Resources ; Ecosystem ; Environmental Monitoring/*methods ; *Geographic Information Systems ; Islands ; Lakes/*chemistry ; Myanmar ; *Remote Sensing Technology ; Spatio-Temporal Analysis ; Urbanization ; }, abstract = {The presence of floating islands is a unique characteristic of Loktak Lake. Floating islands play a significant role in ecosystem services and ecological processes and functioning. Rapid urbanization, industrialization, and a demand for more resources have led to changes in the landscape patterns at Loktak Lake in past three decades, thereby degrading and threatening the fragile ecosystem. The aim of the present study is to assess the changes in land use practices of the Phumdis by analyzing data from the past 38 years with remote sensing techniques. Landsat images from 1977, 1988, 1999 and an Indian remote sensing image from 2015 were used to assess the land use/land cover changes. The methodology adopted is a supervised classification using the maximum likelihood technique in ERDAS software. Five land used classes were employed: open water bodies, agricultural areas, Phumdis with thick vegetation, and Phumdis with thin vegetation and settlements. The results indicate that the highest loss of land used class was in Phumdis with thin vegetation (49.38 km[2]) followed by Phumdis with thick vegetation (8.59 km[2]), while there was an overall increase in open water bodies (27.00 km[2]), agricultural areas (25.33 km[2]), and settlement (5.75 km[2]). Our study highlights the loss of floating islands from the Loktak as a major concern that will lead to the destruction of the only "floating national park in the world." There is a high probability of extinction of the Sangai, an important keystone species found in the Indo-Burma biodiversity hotspot, if floating islands are not protected through sustainable development.}, } @article {pmid29408193, year = {2018}, author = {Veisani, Y and Jenabi, E and Khazaei, S and Nematollahi, S}, title = {Global incidence and mortality rates in pancreatic cancer and the association with the Human Development Index: decomposition approach.}, journal = {Public health}, volume = {156}, number = {}, pages = {87-91}, doi = {10.1016/j.puhe.2017.12.015}, pmid = {29408193}, issn = {1476-5616}, mesh = {Adult ; Age Distribution ; Databases, Factual ; Developed Countries ; Developing Countries ; Female ; Global Health/*statistics & numerical data ; *Health Status Disparities ; Humans ; Incidence ; Male ; Pancreatic Neoplasms/*epidemiology/*mortality ; Socioeconomic Factors ; }, abstract = {OBJECTIVES: Pancreatic cancer has a lower morbidity yet higher case fatality rates (CFRs) compared with other gastrointestinal cancers. The effects of socio-economic components on pancreatic cancer rates have been acknowledged; however, the effects of the Human Development Index (HDI) inequality are not. In this study, we aimed to determine the contribution of important socio-economic components on pancreatic cancer rates using a decomposition approach.

STUDY DESIGN: Global ecological study.

METHODS: Incidence and mortality rates of pancreatic cancer were obtained for 172 countries from GLOBOCAN and the United Nations Development Program. The World Bank database was also used to obtain the HDI and its gradient for 169 countries. Inequality in pancreatic cancer age-specific incidence and mortality rates was calculated according to the HDI using the concentration index (CI). We decomposed the CI to determine main contributors of the inequality.

RESULTS: The CI for incidence and mortality of pancreatic cancer in both genders according to the HDI was 0.26 (95% confidence interval: 0.21-0.30) and 0.25 (95% confidence interval: 0.21-0.30), respectively, which indicated more concentrated inequality in advantaged countries. About 80% of the inequality sources were predicted by socio-economic component in both rates of pancreatic cancer. The main contributors to inequality were the mean years of schooling, life expectancy at birth, expected years of schooling, and urbanization.

CONCLUSION: Global inequalities exist in pancreatic cancer incidence and mortality rates according to the HDI; in addition, inequality was more concentrated in countries with higher score of HDI.}, } @article {pmid29406730, year = {2018}, author = {Mendoza Beltran, A and Prado, V and Font Vivanco, D and Henriksson, PJG and Guinée, JB and Heijungs, R}, title = {Quantified Uncertainties in Comparative Life Cycle Assessment: What Can Be Concluded?.}, journal = {Environmental science & technology}, volume = {52}, number = {4}, pages = {2152-2161}, pmid = {29406730}, issn = {1520-5851}, mesh = {*Data Interpretation, Statistical ; Probability ; *Recycling ; Uncertainty ; }, abstract = {Interpretation of comparative Life Cycle Assessment (LCA) results can be challenging in the presence of uncertainty. To aid in interpreting such results under the goal of any comparative LCA, we aim to provide guidance to practitioners by gaining insights into uncertainty-statistics methods (USMs). We review five USMs-discernibility analysis, impact category relevance, overlap area of probability distributions, null hypothesis significance testing (NHST), and modified NHST-and provide a common notation, terminology, and calculation platform. We further cross-compare all USMs by applying them to a case study on electric cars. USMs belong to a confirmatory or an exploratory statistics' branch, each serving different purposes to practitioners. Results highlight that common uncertainties and the magnitude of differences per impact are key in offering reliable insights. Common uncertainties are particularly important as disregarding them can lead to incorrect recommendations. On the basis of these considerations, we recommend the modified NHST as a confirmatory USM. We also recommend discernibility analysis as an exploratory USM along with recommendations for its improvement, as it disregards the magnitude of the differences. While further research is necessary to support our conclusions, the results and supporting material provided can help LCA practitioners in delivering a more robust basis for decision-making.}, } @article {pmid29405981, year = {2018}, author = {Kikuchi, J and Ito, K and Date, Y}, title = {Environmental metabolomics with data science for investigating ecosystem homeostasis.}, journal = {Progress in nuclear magnetic resonance spectroscopy}, volume = {104}, number = {}, pages = {56-88}, doi = {10.1016/j.pnmrs.2017.11.003}, pmid = {29405981}, issn = {1873-3301}, mesh = {Animals ; Biota/*physiology ; Databases, Factual ; *Ecology ; *Ecosystem ; Homeostasis/*physiology ; Humans ; Machine Learning ; *Metabolomics ; Multivariate Analysis ; Nuclear Magnetic Resonance, Biomolecular ; }, abstract = {A natural ecosystem can be viewed as the interconnections between complex metabolic reactions and environments. Humans, a part of these ecosystems, and their activities strongly affect the environments. To account for human effects within ecosystems, understanding what benefits humans receive by facilitating the maintenance of environmental homeostasis is important. This review describes recent applications of several NMR approaches to the evaluation of environmental homeostasis by metabolic profiling and data science. The basic NMR strategy used to evaluate homeostasis using big data collection is similar to that used in human health studies. Sophisticated metabolomic approaches (metabolic profiling) are widely reported in the literature. Further challenges include the analysis of complex macromolecular structures, and of the compositions and interactions of plant biomass, soil humic substances, and aqueous particulate organic matter. To support the study of these topics, we also discuss sample preparation techniques and solid-state NMR approaches. Because NMR approaches can produce a number of data with high reproducibility and inter-institution compatibility, further analysis of such data using machine learning approaches is often worthwhile. We also describe methods for data pretreatment in solid-state NMR and for environmental feature extraction from heterogeneously-measured spectroscopic data by machine learning approaches.}, } @article {pmid29393597, year = {2018}, author = {Narum, S and Chambers, K}, title = {Editorial 2018.}, journal = {Molecular ecology resources}, volume = {18}, number = {1}, pages = {1-13}, doi = {10.1111/1755-0998.12753}, pmid = {29393597}, issn = {1755-0998}, mesh = {Computational Biology/*methods ; Ecology/*methods ; *Editorial Policies ; Molecular Biology/*methods ; *Periodicals as Topic ; }, } @article {pmid29391497, year = {2018}, author = {Li, D and Chou, WC and Shih, YY and Chen, GY and Chang, Y and Chow, CH and Lin, TY and Hung, CC}, title = {Elevated particulate organic carbon export flux induced by internal waves in the oligotrophic northern South China Sea.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {2042}, pmid = {29391497}, issn = {2045-2322}, abstract = {To understand the biogeochemical response to internal waves in the deep basin of the northern South China Sea (NSCS), particulate organic carbon (POC) export fluxes were quantified for the first time during the passage of large internal waves using drifting sediment traps attached with hydrographic sensors. Results revealed large variations in temperature, nitrate and chlorophyll a (Chl a) concentrations during and after internal waves, suggesting that cold nutrient-replete waters may be brought to the euphotic zone in the dissipation zone during and after the passage of internal wave packets, resulted in phytoplankton flourished. Most importantly, POC export fluxes (110.9 ± 10.7 mg C m[-2] d[-1]) were significantly enhanced after internal waves compared to non-internal wave area (32.6-73.0 mg C m[-2] d[-1]) in the NSCS. Such elevated POC fluxes may be induced by downward flourished biogenic particles, particle aggregation or converged particles from mixed layer triggered by internal waves.}, } @article {pmid29389330, year = {2018}, author = {Noe, MH and Gelfand, JM}, title = {Research Techniques Made Simple: Pharmacoepidemiology Research Methods in Dermatology.}, journal = {The Journal of investigative dermatology}, volume = {138}, number = {2}, pages = {e13-e18}, pmid = {29389330}, issn = {1523-1747}, support = {K24 AR064310/AR/NIAMS NIH HHS/United States ; P30 AR069589/AR/NIAMS NIH HHS/United States ; T32 GM075766/GM/NIGMS NIH HHS/United States ; }, mesh = {Biomedical Research/*methods ; Dermatologic Agents/*therapeutic use ; Dermatology/*methods ; Humans ; Pharmacoepidemiology/*methods ; Research Design ; Skin Diseases/*drug therapy/epidemiology ; }, abstract = {Clinical trials have several important limitations for evaluating the safety of new medications, leading to many adverse events not being identified until the postmarketing period. Descriptive studies, including case reports, case series, cross-sectional, and ecologic studies, help identify potential safety signals and generate hypotheses. Further research using analytic study methods, including case-control studies and cohort studies, are necessary to determine if an association truly exists and to better understand the potential for causation. Pharmacoepidemiology research examines the use and effects of drugs when used in large populations of patients, using a variety of study designs and biostatistical techniques to reduce the confounding and systematic error associated with observational research. Understanding the strengths and limitations of pharmacoepidemiology research techniques is necessary to interpret the validity of drug safety studies, guiding both individual patient decisions and broader public health decisions.}, } @article {pmid29386578, year = {2018}, author = {Schoville, SD and Chen, YH and Andersson, MN and Benoit, JB and Bhandari, A and Bowsher, JH and Brevik, K and Cappelle, K and Chen, MM and Childers, AK and Childers, C and Christiaens, O and Clements, J and Didion, EM and Elpidina, EN and Engsontia, P and Friedrich, M and García-Robles, I and Gibbs, RA and Goswami, C and Grapputo, A and Gruden, K and Grynberg, M and Henrissat, B and Jennings, EC and Jones, JW and Kalsi, M and Khan, SA and Kumar, A and Li, F and Lombard, V and Ma, X and Martynov, A and Miller, NJ and Mitchell, RF and Munoz-Torres, M and Muszewska, A and Oppert, B and Palli, SR and Panfilio, KA and Pauchet, Y and Perkin, LC and Petek, M and Poelchau, MF and Record, É and Rinehart, JP and Robertson, HM and Rosendale, AJ and Ruiz-Arroyo, VM and Smagghe, G and Szendrei, Z and Thomas, GWC and Torson, AS and Vargas Jentzsch, IM and Weirauch, MT and Yates, AD and Yocum, GD and Yoon, JS and Richards, S}, title = {A model species for agricultural pest genomics: the genome of the Colorado potato beetle, Leptinotarsa decemlineata (Coleoptera: Chrysomelidae).}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {1931}, pmid = {29386578}, issn = {2045-2322}, support = {R01 GM080203/GM/NIGMS NIH HHS/United States ; R01 GM070559/GM/NIGMS NIH HHS/United States ; K12 GM000708/GM/NIGMS NIH HHS/United States ; R01 HG004483/HG/NHGRI NIH HHS/United States ; U54 HG003273/HG/NHGRI NIH HHS/United States ; }, mesh = {*Agriculture ; Animals ; Coleoptera/*genetics ; DNA Transposable Elements/genetics ; Evolution, Molecular ; Female ; Gene Expression Regulation ; Genetic Variation ; Genetics, Population ; *Genome, Insect ; *Genomics ; Host-Parasite Interactions/genetics ; Insect Proteins/genetics/metabolism ; Insecticide Resistance/genetics ; Male ; Molecular Sequence Annotation ; Multigene Family ; Pest Control, Biological ; Phylogeny ; RNA Interference ; Solanum tuberosum/*parasitology ; Transcription Factors/metabolism ; }, abstract = {The Colorado potato beetle is one of the most challenging agricultural pests to manage. It has shown a spectacular ability to adapt to a variety of solanaceaeous plants and variable climates during its global invasion, and, notably, to rapidly evolve insecticide resistance. To examine evidence of rapid evolutionary change, and to understand the genetic basis of herbivory and insecticide resistance, we tested for structural and functional genomic changes relative to other arthropod species using genome sequencing, transcriptomics, and community annotation. Two factors that might facilitate rapid evolutionary change include transposable elements, which comprise at least 17% of the genome and are rapidly evolving compared to other Coleoptera, and high levels of nucleotide diversity in rapidly growing pest populations. Adaptations to plant feeding are evident in gene expansions and differential expression of digestive enzymes in gut tissues, as well as expansions of gustatory receptors for bitter tasting. Surprisingly, the suite of genes involved in insecticide resistance is similar to other beetles. Finally, duplications in the RNAi pathway might explain why Leptinotarsa decemlineata has high sensitivity to dsRNA. The L. decemlineata genome provides opportunities to investigate a broad range of phenotypes and to develop sustainable methods to control this widely successful pest.}, } @article {pmid29385403, year = {2018}, author = {Ji, G and Chen, M and Ye, W and Zhu, S and Ye, C and Su, Y and Peng, H and Wu, X}, title = {TSAPA: identification of tissue-specific alternative polyadenylation sites in plants.}, journal = {Bioinformatics (Oxford, England)}, volume = {34}, number = {12}, pages = {2123-2125}, doi = {10.1093/bioinformatics/bty044}, pmid = {29385403}, issn = {1367-4811}, mesh = {Computational Biology/*methods ; Machine Learning ; Plants/*metabolism ; Poly A ; *Polyadenylation ; Sequence Analysis, DNA ; Sequence Analysis, RNA ; *Software ; }, abstract = {SUMMARY: Alternative polyadenylation (APA) is now emerging as a widespread mechanism modulated tissue-specifically, which highlights the need to define tissue-specific poly(A) sites for profiling APA dynamics across tissues. We have developed an R package called TSAPA based on the machine learning model for identifying tissue-specific poly(A) sites in plants. A feature space including more than 200 features was assembled to specifically characterize poly(A) sites in plants. The classification model in TSAPA can be customized by selecting desirable features or classifiers. TSAPA is also capable of predicting tissue-specific poly(A) sites in unannotated intergenic regions. TSAPA will be a valuable addition to the community for studying dynamics of APA in plants.

https://github.com/BMILAB/TSAPA.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, } @article {pmid29385096, year = {2018}, author = {Nsengiyumva, JB and Luo, G and Nahayo, L and Huang, X and Cai, P}, title = {Landslide Susceptibility Assessment Using Spatial Multi-Criteria Evaluation Model in Rwanda.}, journal = {International journal of environmental research and public health}, volume = {15}, number = {2}, pages = {}, pmid = {29385096}, issn = {1660-4601}, mesh = {Disasters ; Geographic Information Systems ; *Landslides ; *Models, Theoretical ; Risk Assessment ; Rwanda ; }, abstract = {Landslides susceptibility assessment has to be conducted to identify prone areas and guide risk management. Landslides in Rwanda are very deadly disasters. The current research aimed to conduct landslide susceptibility assessment by applying Spatial Multi-Criteria Evaluation Model with eight layers of causal factors including: slope, distance to roads, lithology, precipitation, soil texture, soil depth, altitude and land cover. In total, 980 past landslide locations were mapped. The relationship between landslide factors and inventory map was calculated using the Spatial Multi-Criteria Evaluation. The results revealed that susceptibility is spatially distributed countrywide with 42.3% of the region classified from moderate to very high susceptibility, and this is inhabited by 49.3% of the total population. In addition, Provinces with high to very high susceptibility are West, North and South (40.4%, 22.8% and 21.5%, respectively). Subsequently, the Eastern Province becomes the peak under low susceptibility category (87.8%) with no very high susceptibility (0%). Based on these findings, the employed model produced accurate and reliable outcome in terms of susceptibility, since 49.5% of past landslides fell within the very high susceptibility category, which confirms the model's performance. The outcomes of this study will be useful for future initiatives related to landslide risk reduction and management.}, } @article {pmid29382768, year = {2018}, author = {Zachar, I and Szilágyi, A and Számadó, S and Szathmáry, E}, title = {Farming the mitochondrial ancestor as a model of endosymbiotic establishment by natural selection.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {115}, number = {7}, pages = {E1504-E1510}, pmid = {29382768}, issn = {1091-6490}, support = {294332/ERC_/European Research Council/International ; }, mesh = {Animals ; Bacteria/pathogenicity ; *Biological Evolution ; Computational Biology ; Erythrocytes/*microbiology ; Eukaryota ; Humans ; Mitochondria/*physiology ; *Models, Biological ; Predatory Behavior ; *Selection, Genetic ; Symbiosis/*physiology ; }, abstract = {The origin of mitochondria was a major evolutionary transition leading to eukaryotes, and is a hotly debated issue. It is unknown whether mitochondria were acquired early or late, and whether it was captured via phagocytosis or syntrophic integration. We present dynamical models to directly simulate the emergence of mitochondria in an ecoevolutionary context. Our results show that regulated farming of prey bacteria and delayed digestion can facilitate the establishment of stable endosymbiosis if prey-rich and prey-poor periods alternate. Stable endosymbiosis emerges without assuming any initial metabolic benefit provided by the engulfed partner, in a wide range of parameters, despite that during good periods farming is costly. Our approach lends support to the appearance of mitochondria before any metabolic coupling has emerged, but after the evolution of primitive phagocytosis by the urkaryote.}, } @article {pmid29382745, year = {2018}, author = {Dietze, MC and Fox, A and Beck-Johnson, LM and Betancourt, JL and Hooten, MB and Jarnevich, CS and Keitt, TH and Kenney, MA and Laney, CM and Larsen, LG and Loescher, HW and Lunch, CK and Pijanowski, BC and Randerson, JT and Read, EK and Tredennick, AT and Vargas, R and Weathers, KC and White, EP}, title = {Iterative near-term ecological forecasting: Needs, opportunities, and challenges.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {115}, number = {7}, pages = {1424-1432}, pmid = {29382745}, issn = {1091-6490}, mesh = {Bayes Theorem ; Climate Change ; Ecology/*education/*methods/trends ; Ecosystem ; Forecasting ; Humans ; Models, Theoretical ; }, abstract = {Two foundational questions about sustainability are "How are ecosystems and the services they provide going to change in the future?" and "How do human decisions affect these trajectories?" Answering these questions requires an ability to forecast ecological processes. Unfortunately, most ecological forecasts focus on centennial-scale climate responses, therefore neither meeting the needs of near-term (daily to decadal) environmental decision-making nor allowing comparison of specific, quantitative predictions to new observational data, one of the strongest tests of scientific theory. Near-term forecasts provide the opportunity to iteratively cycle between performing analyses and updating predictions in light of new evidence. This iterative process of gaining feedback, building experience, and correcting models and methods is critical for improving forecasts. Iterative, near-term forecasting will accelerate ecological research, make it more relevant to society, and inform sustainable decision-making under high uncertainty and adaptive management. Here, we identify the immediate scientific and societal needs, opportunities, and challenges for iterative near-term ecological forecasting. Over the past decade, data volume, variety, and accessibility have greatly increased, but challenges remain in interoperability, latency, and uncertainty quantification. Similarly, ecologists have made considerable advances in applying computational, informatic, and statistical methods, but opportunities exist for improving forecast-specific theory, methods, and cyberinfrastructure. Effective forecasting will also require changes in scientific training, culture, and institutions. The need to start forecasting is now; the time for making ecology more predictive is here, and learning by doing is the fastest route to drive the science forward.}, } @article {pmid29381785, year = {2018}, author = {Dzubur, E and Huh, J and Maher, JP and Intille, SS and Dunton, GF}, title = {Response patterns and intra-dyadic factors related to compliance with ecological momentary assessment among mothers and children.}, journal = {Translational behavioral medicine}, volume = {8}, number = {2}, pages = {233-242}, pmid = {29381785}, issn = {1613-9860}, support = {R01 HL119255/HL/NHLBI NIH HHS/United States ; T32 CA009492/CA/NCI NIH HHS/United States ; }, mesh = {Adult ; Child ; Ecological Momentary Assessment/*statistics & numerical data ; Female ; Hispanic or Latino/statistics & numerical data ; Humans ; Male ; Mothers/*statistics & numerical data ; Patient Compliance/*statistics & numerical data ; Poverty/statistics & numerical data ; Reminder Systems/*statistics & numerical data ; *Socioeconomic Factors ; Surveys and Questionnaires ; }, abstract = {Ecological momentary assessment (EMA) is a real-time sampling strategy that may address limitations in health research, such as the inability to examine how processes unfold on a daily basis. However, EMA studies are prone to limited data availability due to difficulties in implementing sophisticated protocols and systematic non-compliance with prompts, resulting in biased estimates and limited statistical power. The objectives of this study were to describe the availability of data, to examine response patterns, and to analyze factors related to EMA prompt compliance in a dyadic EMA study with mothers and children. Participants (N = 404) each received up to eight EMA prompts (i.e., audible pings) per day for a total of 7 days. Each EMA survey consisted of items assessing affect, perceived stress, and social context. Participants responded to approximately 80% (range: 3.4%-100%) of prompted EMA surveys, and completed 92.6% of surveys once started. Mothers and children identifying as Hispanic, as well as mothers in lower-income households, were less likely to comply with any given EMA prompt. Participant dyads were more likely to comply with prompts when they were together. Understanding factors related to systematic EMA prompt non-compliance is an important step to reduce the likelihood of biased estimates and improve statistical power. Socioeconomic factors may impede mothers' compliance with EMA protocols. Furthermore, mothers' presence and involvement may enhance children's compliance with EMA protocols.}, } @article {pmid29378821, year = {2018}, author = {Hekman, JP and Johnson, JL and Edwards, W and Vladimirova, AV and Gulevich, RG and Ford, AL and Kharlamova, AV and Herbeck, Y and Acland, GM and Raetzman, LT and Trut, LN and Kukekova, AV}, title = {Anterior Pituitary Transcriptome Suggests Differences in ACTH Release in Tame and Aggressive Foxes.}, journal = {G3 (Bethesda, Md.)}, volume = {8}, number = {3}, pages = {859-873}, pmid = {29378821}, issn = {2160-1836}, support = {R01 DK076647/DK/NIDDK NIH HHS/United States ; R01 GM120782/GM/NIGMS NIH HHS/United States ; T32 ES007326/ES/NIEHS NIH HHS/United States ; }, mesh = {Adrenocorticotropic Hormone/*metabolism ; *Aggression ; Alternative Splicing ; Animals ; *Behavior, Animal ; Computational Biology/methods ; Domestication ; Foxes/*genetics/*metabolism ; Gene Expression Profiling ; Gene Expression Regulation ; Gene Ontology ; Gene Regulatory Networks ; Hypothalamo-Hypophyseal System ; Pituitary Gland, Anterior/*metabolism ; Pituitary-Adrenal System ; *Transcriptome ; }, abstract = {Domesticated species exhibit a suite of behavioral, endocrinological, and morphological changes referred to as "domestication syndrome." These changes may include a reduction in reactivity of the hypothalamic-pituitary-adrenal (HPA) axis and specifically reduced adrenocorticotropic hormone release from the anterior pituitary. To investigate the biological mechanisms targeted during domestication, we investigated gene expression in the pituitaries of experimentally domesticated foxes (Vulpes vulpes). RNA was sequenced from the anterior pituitary of six foxes selectively bred for tameness ("tame foxes") and six foxes selectively bred for aggression ("aggressive foxes"). Expression, splicing, and network differences identified between the two lines indicated the importance of genes related to regulation of exocytosis, specifically mediated by cAMP, organization of pseudopodia, and cell motility. These findings provide new insights into biological mechanisms that may have been targeted when these lines of foxes were selected for behavior and suggest new directions for research into HPA axis regulation and the biological underpinnings of domestication.}, } @article {pmid29378241, year = {2018}, author = {Zhang, L and Wang, MY and Li, XP and Wang, XT and Jia, CL and Yang, XZ and Feng, RQ and Yuan, ML}, title = {A small set of differentially expressed genes was associated with two color morphs in natural populations of the pea aphid Acyrthosiphon pisum.}, journal = {Gene}, volume = {651}, number = {}, pages = {23-32}, doi = {10.1016/j.gene.2018.01.079}, pmid = {29378241}, issn = {1879-0038}, mesh = {Animals ; Aphids/*genetics ; Cold Temperature ; Gene Expression Regulation, Enzymologic ; Gene Ontology ; *Genes, Insect ; Medicago sativa ; Pigmentation/genetics ; Polymorphism, Genetic ; Real-Time Polymerase Chain Reaction ; Sequence Analysis, RNA ; Transcriptome ; beta-Carotene 15,15'-Monooxygenase/genetics ; }, abstract = {Color polymorphism is an ecologically important trait, which is related to local adaptation and ecological speciation. The pea aphid Acyrthosiphon pisum shows color polymorphism: the red and green color morphs where differences in ecological adaptation have been observed. Here, we measured genome-wide gene expression profiles of two color morphs in natural populations of A. pisum to explore the genetic basis of differentiated ecological adaptation. The results showed that only 32 genes were significantly differentially expressed between the two morphs, of which 18 had functional annotations. Among them, 13 genes were up-regulated [e.g. genes encoding protoheme IX farnesyltransferase (LOC100570971), carotene dehydrogenase (tor) and V-type proton ATPase subunit B (LOC100169462)] and 5 genes were down-regulated in the red morph (e.g. genes encoding transcription factors and heat shock proteins). To assess the functional importance of these differentially expressed genes (DEGs), we selected three highly expressed DEGs (LOC100169462, LOC100570971 and tor) with functional annotations and analyzed their expression levels in the red morph under three low temperatures (1 °C, 4 °C, and 8 °C) for 24 h. These three DEGs showed an interesting expression response to the cold acclimating conditions which resulted in an obvious phenotypic change of the red individuals to be greenish variants. This study suggests a link between gene expressions and body color polymorphisms in the pea aphid and provides important clues for further studying molecular mechanisms of ecological adaptation in aphids.}, } @article {pmid29376638, year = {2018}, author = {Amorim, MJB and Lin, S and Schlich, K and Navas, JM and Brunelli, A and Neubauer, N and Vilsmeier, K and Costa, AL and Gondikas, A and Xia, T and Galbis, L and Badetti, E and Marcomini, A and Hristozov, D and Kammer, FV and Hund-Rinke, K and Scott-Fordsmand, JJ and Nel, A and Wohlleben, W}, title = {Environmental Impacts by Fragments Released from Nanoenabled Products: A Multiassay, Multimaterial Exploration by the SUN Approach.}, journal = {Environmental science & technology}, volume = {52}, number = {3}, pages = {1514-1524}, doi = {10.1021/acs.est.7b04122}, pmid = {29376638}, issn = {1520-5851}, mesh = {Animals ; Ecotoxicology ; Environment ; *Nanostructures ; *Nanotubes, Carbon ; Plastics ; }, abstract = {Nanoenabled products (NEPs) have numerous outdoor uses in construction, transportation or consumer scenarios, and there is evidence that their fragments are released in the environment at low rates. We hypothesized that the lower surface availability of NEPs fragment reduced their environmental effects with respect to pristine nanomaterials. This hypothesis was explored by testing fragments generated by intentional micronisation ("the SUN approach"; Nowack et al. Meeting the Needs for Released Nanomaterials Required for Further Testing: The SUN Approach. Environmental Science & Technology, 2016 (50), 2747). The NEPs were composed of four matrices (epoxy, polyolefin, polyoxymethylene, and cement) with up to 5% content of three nanomaterials (carbon nanotubes, iron oxide, and organic pigment). Regardless of the type of nanomaterial or matrix used, it was observed that nanomaterials were only partially exposed at the NEP fragment surface, indicating that mostly the intrinsic and extrinsic properties of the matrix drove the NEP fragment toxicity. Ecotoxicity in multiple assays was done covering relevant media from terrestrial to aquatic, including sewage treatment plant (biological activity), soil worms (Enchytraeus crypticus), and fish (zebrafish embryo and larvae and trout cell lines). We designed the studies to explore the possible modulation of ecotoxicity by nanomaterial additives in plastics/polymer/cement, finding none. The results support NEPs grouping by the matrix material regarding ecotoxicological effect during the use phase. Furthermore, control results on nanomaterial-free polymer fragments representing microplastic had no significant adverse effects up to the highest concentration tested.}, } @article {pmid29371471, year = {2018}, author = {Tucker, MA and Böhning-Gaese, K and Fagan, WF and Fryxell, JM and Van Moorter, B and Alberts, SC and Ali, AH and Allen, AM and Attias, N and Avgar, T and Bartlam-Brooks, H and Bayarbaatar, B and Belant, JL and Bertassoni, A and Beyer, D and Bidner, L and van Beest, FM and Blake, S and Blaum, N and Bracis, C and Brown, D and de Bruyn, PJN and Cagnacci, F and Calabrese, JM and Camilo-Alves, C and Chamaillé-Jammes, S and Chiaradia, A and Davidson, SC and Dennis, T and DeStefano, S and Diefenbach, D and Douglas-Hamilton, I and Fennessy, J and Fichtel, C and Fiedler, W and Fischer, C and Fischhoff, I and Fleming, CH and Ford, AT and Fritz, SA and Gehr, B and Goheen, JR and Gurarie, E and Hebblewhite, M and Heurich, M and Hewison, AJM and Hof, C and Hurme, E and Isbell, LA and Janssen, R and Jeltsch, F and Kaczensky, P and Kane, A and Kappeler, PM and Kauffman, M and Kays, R and Kimuyu, D and Koch, F and Kranstauber, B and LaPoint, S and Leimgruber, P and Linnell, JDC and López-López, P and Markham, AC and Mattisson, J and Medici, EP and Mellone, U and Merrill, E and de Miranda Mourão, G and Morato, RG and Morellet, N and Morrison, TA and Díaz-Muñoz, SL and Mysterud, A and Nandintsetseg, D and Nathan, R and Niamir, A and Odden, J and O'Hara, RB and Oliveira-Santos, LGR and Olson, KA and Patterson, BD and Cunha de Paula, R and Pedrotti, L and Reineking, B and Rimmler, M and Rogers, TL and Rolandsen, CM and Rosenberry, CS and Rubenstein, DI and Safi, K and Saïd, S and Sapir, N and Sawyer, H and Schmidt, NM and Selva, N and Sergiel, A and Shiilegdamba, E and Silva, JP and Singh, N and Solberg, EJ and Spiegel, O and Strand, O and Sundaresan, S and Ullmann, W and Voigt, U and Wall, J and Wattles, D and Wikelski, M and Wilmers, CC and Wilson, JW and Wittemyer, G and Zięba, F and Zwijacz-Kozica, T and Mueller, T}, title = {Moving in the Anthropocene: Global reductions in terrestrial mammalian movements.}, journal = {Science (New York, N.Y.)}, volume = {359}, number = {6374}, pages = {466-469}, doi = {10.1126/science.aam9712}, pmid = {29371471}, issn = {1095-9203}, mesh = {*Animal Migration ; Animals ; Geographic Information Systems ; *Human Activities ; Humans ; *Mammals ; }, abstract = {Animal movement is fundamental for ecosystem functioning and species survival, yet the effects of the anthropogenic footprint on animal movements have not been estimated across species. Using a unique GPS-tracking database of 803 individuals across 57 species, we found that movements of mammals in areas with a comparatively high human footprint were on average one-half to one-third the extent of their movements in areas with a low human footprint. We attribute this reduction to behavioral changes of individual animals and to the exclusion of species with long-range movements from areas with higher human impact. Global loss of vagility alters a key ecological trait of animals that affects not only population persistence but also ecosystem processes such as predator-prey interactions, nutrient cycling, and disease transmission.}, } @article {pmid29370206, year = {2018}, author = {Si, Y and Li, X and Yin, D and Liu, R and Wei, J and Huang, Y and Li, T and Liu, J and Gu, S and Wang, G}, title = {Evaluating and optimizing the operation of the hydropower system in the Upper Yellow River: A general LINGO-based integrated framework.}, journal = {PloS one}, volume = {13}, number = {1}, pages = {e0191483}, pmid = {29370206}, issn = {1932-6203}, mesh = {China ; Data Interpretation, Statistical ; Hydrology ; Models, Theoretical ; Nonlinear Dynamics ; Power Plants/*organization & administration/*statistics & numerical data ; Renewable Energy ; Rivers ; Software ; }, abstract = {The hydropower system in the Upper Yellow River (UYR), one of the largest hydropower bases in China, plays a vital role in the energy structure of the Qinghai Power Grid. Due to management difficulties, there is still considerable room for improvement in the joint operation of this system. This paper presents a general LINGO-based integrated framework to study the operation of the UYR hydropower system. The framework is easy to use for operators with little experience in mathematical modeling, takes full advantage of LINGO's capabilities (such as its solving capacity and multi-threading ability), and packs its three layers (the user layer, the coordination layer, and the base layer) together into an integrated solution that is robust and efficient and represents an effective tool for data/scenario management and analysis. The framework is general and can be easily transferred to other hydropower systems with minimal effort, and it can be extended as the base layer is enriched. The multi-objective model that represents the trade-off between power quantity (i.e., maximum energy production) and power reliability (i.e., firm output) of hydropower operation has been formulated. With equivalent transformations, the optimization problem can be solved by the nonlinear programming (NLP) solvers embedded in the LINGO software, such as the General Solver, the Multi-start Solver, and the Global Solver. Both simulation and optimization are performed to verify the model's accuracy and to evaluate the operation of the UYR hydropower system. A total of 13 hydropower plants currently in operation are involved, including two pivotal storage reservoirs on the Yellow River, which are the Longyangxia Reservoir and the Liujiaxia Reservoir. Historical hydrological data from multiple years (2000-2010) are provided as input to the model for analysis. The results are as follows. 1) Assuming that the reservoirs are all in operation (in fact, some reservoirs were not operational or did not collect all of the relevant data during the study period), the energy production is estimated as 267.7, 357.5, and 358.3×108 KWh for the Qinghai Power Grid during dry, normal, and wet years, respectively. 2) Assuming that the hydropower system is operated jointly, the firm output can reach 3110 MW (reliability of 100%) and 3510 MW (reliability of 90%). Moreover, a decrease in energy production from the Longyangxia Reservoir can bring about a very large increase in firm output from the hydropower system. 3) The maximum energy production can reach 297.7, 363.9, and 411.4×108 KWh during dry, normal, and wet years, respectively. The trade-off curve between maximum energy production and firm output is also provided for reference.}, } @article {pmid29365166, year = {2018}, author = {Radomski, MV and Davidson, LF and Smith, L and Finkelstein, M and Cecchini, A and Heaton, KJ and McCulloch, K and Scherer, M and Weightman, MM}, title = {Toward Return to Duty Decision-Making After Military Mild Traumatic Brain Injury: Preliminary Validation of the Charge of Quarters Duty Test.}, journal = {Military medicine}, volume = {183}, number = {7-8}, pages = {e214-e222}, doi = {10.1093/milmed/usx045}, pmid = {29365166}, issn = {1930-613X}, mesh = {Adolescent ; Adult ; Ambulatory Care/methods/statistics & numerical data ; Brain Concussion/*complications/epidemiology/psychology ; *Decision Making ; Decision Support Techniques ; Female ; Humans ; Male ; Neuropsychological Tests ; North Carolina/epidemiology ; Reproducibility of Results ; Return to Work/*statistics & numerical data ; Statistics, Nonparametric ; Surveys and Questionnaires ; }, abstract = {INTRODUCTION: Determining duty-readiness after mild traumatic brain injury (mTBI) remains a priority of the United States Department of Defense as warfighters in both deployed and non-deployed settings continue to sustain these injuries in relatively large numbers. Warfighters with mTBI may experience unresolved sensorimotor, emotional, cognitive sequelae including problems with executive functions, a category of higher order cognitive processes that enable people to regulate goal-directed behavior. Persistent mTBI sequelae interfere with warfighters' proficiency in performing military duties and signal the need for graded return to activity and possibly rehabilitative services. Although significant strides have been carried out in recent years to enhance the identification and management of mTBI in garrison (EXORD 165-13) and deployed settings (EXORD 242-11; DoDI 6,490.11), the Department of Defense still lacks reliable, valid, and clinically feasible functional assessments to help inform duty-readiness decisions. Traditional functional assessments lack face validity for warfighters and may have ceiling effects, especially as related to executive functions. Performance-based multitasking assessments have been shown to be sensitive to executive dysfunction after acquired brain injury but no multitasking assessments have been validated in adults with mTBI. Existing multitasking assessments are not ecologically valid relative to military contexts. A multidisciplinary military-civilian team of researchers developed and evaluated a performance-based assessment called the Assessment of Military Multitasking Performance. One of the Assessment of Military Multitasking Performance multitasks, the Charge of Quarters Duty Test (CQDT), was designed to challenge the divided attention, foresight, and planning dimensions of executive functions. Here, we report on the preliminary validation results of the CQDT.

MATERIALS AND METHODS: The team conducted a measurement development study at Fort Bragg, NC, enrolling 83 service members (33 with mTBI and 50 healthy controls). Discriminant validity was evaluated by comparing differences in CQDT sub-scores of warfighters with mTBI and healthy controls. Associations between CQDT sub-scores and neurocognitive measures known to be sensitive to mTBI were examined to explore convergent validity. The study was approved by the Womack Army Medical Center Institutional Review Board (Fort Bragg).

RESULTS: There were significant between-group differences in two of the four CQDT sub-scores (number of visits, p = 0.012; and performance accuracy, p = 0.020). Correlations between the CQDT sub-scores and some neurocognitive measures were statistically significant but weak, ranging from 0.287 (CQDT performance accuracy and NAB Numbers and Letters, Part D) to -0.421 (CQDT total number of visits and Automated Neuropsychological Assessment Metrics Tower Task). There were group differences in terms of participants' reading level, education, years in military, and stress symptoms; some of these characteristics may have influenced CQDT performance.

CONCLUSIONS: The CQDT demonstrated initial evidence of discriminant validity. Further study is warranted to more formally evaluate convergent/divergent validity and ultimately how and whether this performance-based multitasking measure can inform readiness to return to duty after mTBI.}, } @article {pmid29363430, year = {2018}, author = {Cao, Y and Cao, R and Huang, Y and Zhou, H and Liu, Y and Li, X and Zhong, W and Hao, P}, title = {A comprehensive study on cellular RNA editing activity in response to infections with different subtypes of influenza a viruses.}, journal = {BMC genomics}, volume = {19}, number = {Suppl 1}, pages = {925}, pmid = {29363430}, issn = {1471-2164}, mesh = {Animals ; Birds/*genetics/physiology/virology ; Cells, Cultured ; Computational Biology/*methods ; Epithelial Cells/virology ; Gene Expression Regulation ; Humans ; Influenza A virus/classification/*genetics ; Influenza in Birds/*genetics/virology ; Influenza, Human/*genetics/virology ; RNA Editing/*genetics ; RNA-Binding Proteins/genetics/metabolism ; Virus Replication ; }, abstract = {BACKGROUND: RNA editing is an important mechanism that expands the diversity and complexity of genetic codes. The conversions of adenosine (A) to inosine (I) and cytosine (C) to uridine (U) are two prominent types of RNA editing in animals. The roles of RNA editing events have been implicated in important biological pathways. Cellular RNA editing activity in response to influenza A virus infection has not been fully characterized in human and avian hosts. This study was designed as a big data analysis to investigate the role and response of RNA editing in epithelial cells during the course of infection with various subtypes of influenza A viruses.

RESULTS: Using a bioinformatics pipeline modified from our previous study, we characterized the profiles of A-to-I and C-to-U RNA editing events in human epithelial cells during the course of influenza A virus infection. Our results revealed a striking diversity of A-to-I RNA editing activities in human epithelial cells in responses to different subtypes of influenza A viruses. The infection of H1N1 and H3N2 significantly up-regulated normalized A-to-I RNA editing levels in human epithelial cells, whereas that of H5N1 did not change it and H7N9 infection significantly down-regulated normalized A-to-I editing level in A549 cells. Next, the expression levels of ADAR and APOBEC enzymes responsible for A-to-I and C-to-U RNA editing during the course of virus infection were examined. The increase of A-to-I RNA editing activities in infections with some influenza A viruses (H1N1 and H3N2) is linked to the up-regulation of ADAR1 but not ADAR2. Further, the pattern recognition receptors of human epithelial cells infected with H1N1, H3N2, H5N1 and H7N9 were examined. Variable responsive changes in gene expression were observed with RIG-I like receptors and Toll like receptors. Finally, the effect of influenza A virus infection on cellular RNA editing activity was also analyzed in avian hosts.

CONCLUSION: This work represents the first comprehensive study of cellular RNA editing activity in response to different influenza A virus infections in human and avian hosts, highlighting the critical role of RNA editing in innate immune response and the pathogenicity of different subtypes of influenza A viruses.}, } @article {pmid29362551, year = {2017}, author = {Filippova, N and Bulyonkova, T}, title = {The communities of terrestrial macrofungi in different forest types in vicinities of Khanty-Mansiysk (middle taiga zone of West Siberia).}, journal = {Biodiversity data journal}, volume = {}, number = {5}, pages = {e20732}, pmid = {29362551}, issn = {1314-2828}, abstract = {BACKGROUND: The diversity of macrofungi in the vicinities of Khanty-Mansiysk (Yugra, Russia) was surveyed using a method of permanent sampling plots. Ten plots, each consisting of a number of micro-plots, were established in several different communities ranging from old-growth mixed taiga forest to its derivatives in cutting succession and bogged areas. For more complete registration of the mycota, plots were supplemented with random walking routes directly nearby. Survey results were subjected to various quantitative analyses which allowed not only to evaluate the diversity of fungi but also to obtain valuable information on occurrence, abundance and ecology of individual species as well as community structure and its dynamics in the course of ecological succession. The paper reports the results of the first year of observations.

NEW INFORMATION: 460 species of terrestrial macrofungi revealed in a poorly explored area in middle taiga of West Siberia. The plot-based study revealed differences between communities of terrestrial macrofungi of old coniferous forests, their after-cutting secondary formations and bogged stages. The survey allowed to reveal records of 3 species listed in the Red Data Book of Russia and 9 species listed in the Red Data Book of Yugra.}, } @article {pmid29358651, year = {2018}, author = {Stein, JC and Yu, Y and Copetti, D and Zwickl, DJ and Zhang, L and Zhang, C and Chougule, K and Gao, D and Iwata, A and Goicoechea, JL and Wei, S and Wang, J and Liao, Y and Wang, M and Jacquemin, J and Becker, C and Kudrna, D and Zhang, J and Londono, CEM and Song, X and Lee, S and Sanchez, P and Zuccolo, A and Ammiraju, JSS and Talag, J and Danowitz, A and Rivera, LF and Gschwend, AR and Noutsos, C and Wu, CC and Kao, SM and Zeng, JW and Wei, FJ and Zhao, Q and Feng, Q and El Baidouri, M and Carpentier, MC and Lasserre, E and Cooke, R and Rosa Farias, DD and da Maia, LC and Dos Santos, RS and Nyberg, KG and McNally, KL and Mauleon, R and Alexandrov, N and Schmutz, J and Flowers, D and Fan, C and Weigel, D and Jena, KK and Wicker, T and Chen, M and Han, B and Henry, R and Hsing, YC and Kurata, N and de Oliveira, AC and Panaud, O and Jackson, SA and Machado, CA and Sanderson, MJ and Long, M and Ware, D and Wing, RA}, title = {Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza.}, journal = {Nature genetics}, volume = {50}, number = {2}, pages = {285-296}, doi = {10.1038/s41588-018-0040-0}, pmid = {29358651}, issn = {1546-1718}, mesh = {Conserved Sequence ; Crops, Agricultural/*genetics ; Domestication ; *Evolution, Molecular ; Genetic Speciation ; *Genetic Variation ; Genome, Plant ; Oryza/*classification/*genetics ; Phylogeny ; }, abstract = {The genus Oryza is a model system for the study of molecular evolution over time scales ranging from a few thousand to 15 million years. Using 13 reference genomes spanning the Oryza species tree, we show that despite few large-scale chromosomal rearrangements rapid species diversification is mirrored by lineage-specific emergence and turnover of many novel elements, including transposons, and potential new coding and noncoding genes. Our study resolves controversial areas of the Oryza phylogeny, showing a complex history of introgression among different chromosomes in the young 'AA' subclade containing the two domesticated species. This study highlights the prevalence of functionally coupled disease resistance genes and identifies many new haplotypes of potential use for future crop protection. Finally, this study marks a milestone in modern rice research with the release of a complete long-read assembly of IR 8 'Miracle Rice', which relieved famine and drove the Green Revolution in Asia 50 years ago.}, } @article {pmid29356990, year = {2018}, author = {Adriaenssens, EM and Wittmann, J and Kuhn, JH and Turner, D and Sullivan, MB and Dutilh, BE and Jang, HB and van Zyl, LJ and Klumpp, J and Lobocka, M and Moreno Switt, AI and Rumnieks, J and Edwards, RA and Uchiyama, J and Alfenas-Zerbini, P and Petty, NK and Kropinski, AM and Barylski, J and Gillis, A and Clokie, MRC and Prangishvili, D and Lavigne, R and Aziz, RK and Duffy, S and Krupovic, M and Poranen, MM and Knezevic, P and Enault, F and Tong, Y and Oksanen, HM and Rodney Brister, J}, title = {Taxonomy of prokaryotic viruses: 2017 update from the ICTV Bacterial and Archaeal Viruses Subcommittee.}, journal = {Archives of virology}, volume = {163}, number = {4}, pages = {1125-1129}, doi = {10.1007/s00705-018-3723-z}, pmid = {29356990}, issn = {1432-8798}, support = {HHSN272200700016I//Battelle Memorial Institute's prime contract with the US National Institute of Allergy and Infectious Diseases (NIAID)/ ; Vidi Grant 864.14.004//Netherlands Organization for Scientific Research (NWO)/ ; MCB-1330800//National Science Foundation/ ; not given//Intramural Research Program of the National Institutes of Health, National Library of Medicine/ ; not given//FWO Vlaanderen/ ; 272507//Academy of Finland (FI)/ ; not given//National Fund for Scientific Research (FNRS)/ ; not given//University of Helsinki funding for Instruct-F1 research infrastructure/ ; }, mesh = {Archaeal Viruses/*classification ; Bacteriophages/*classification ; }, } @article {pmid29353173, year = {2018}, author = {Zeinali, F and Homaei, A and Kamrani, E and Patel, S}, title = {Use of Cu/Zn-superoxide dismutase tool for biomonitoring marine environment pollution in the Persian Gulf and the Gulf of Oman.}, journal = {Ecotoxicology and environmental safety}, volume = {151}, number = {}, pages = {236-241}, doi = {10.1016/j.ecoenv.2018.01.029}, pmid = {29353173}, issn = {1090-2414}, mesh = {Avicennia/*enzymology ; *Environmental Monitoring ; Hydrogen-Ion Concentration ; Indian Ocean ; Oman ; Oxidative Stress ; Plant Leaves/*enzymology ; Stress, Physiological ; Superoxide Dismutase-1/*metabolism ; Temperature ; Water Pollutants, Chemical/*analysis ; }, abstract = {Superoxide dismutase (SOD) is the pivotal antioxidant enzyme that defends organisms against the oxidative stresses of superoxide radicals. In this experimental study, purification of SOD from the leaves of Avicennia marina (grey mangrove or white mangrove) from the family Acanthaceae, located in Sirik mangrove forest on the shore of the Gulf of Oman was performed, for the intended characterization of SOD. The Sirik AmSOD (A. marina SOD) expressed optimum activity in the pH range of 6-9 with the maximum activity at pH 8. The optimal temperature for Sirik AmSOD activity was 70°C. Comparison of the pH and temperature optima in two regions (the Persian Gulf and the Gulf of Oman) showed significant differences with P<0.05. The SOD from the Persian Gulf was more resistant against the environmental stressors, because of the biochemical adaption to this environment, which is harsher. The evidence from these results suggests that AmSOD has different characteristics in each place, and mangroves undergo different adaptations and require different protections. The results of the enzymatic research can be useful for ecological management of organisms.}, } @article {pmid29353015, year = {2018}, author = {Goldenberg, J and Cipriani, V and Jackson, TNW and Arbuckle, K and Debono, J and Dashevsky, D and Panagides, N and Ikonomopoulou, MP and Koludarov, I and Li, B and Santana, RC and Nouwens, A and Jones, A and Hay, C and Dunstan, N and Allen, L and Bush, B and Miles, JJ and Ge, L and Kwok, HF and Fry, BG}, title = {Proteomic and functional variation within black snake venoms (Elapidae: Pseudechis).}, journal = {Comparative biochemistry and physiology. Toxicology & pharmacology : CBP}, volume = {205}, number = {}, pages = {53-61}, doi = {10.1016/j.cbpc.2018.01.001}, pmid = {29353015}, issn = {1532-0456}, mesh = {Animals ; Australia ; Coagulants/chemistry/metabolism/toxicity ; Databases, Protein ; Elapid Venoms/chemistry/genetics/*metabolism/toxicity ; Electrophoresis, Polyacrylamide Gel ; Evolution, Molecular ; Hydrophiidae/growth & development/*physiology ; *Models, Molecular ; Molecular Conformation ; New Guinea ; Phospholipases A2/chemistry/genetics/metabolism/toxicity ; Phylogeny ; Proteomics/methods ; Reptilian Proteins/chemistry/genetics/*metabolism/toxicity ; Species Specificity ; Two-Dimensional Difference Gel Electrophoresis ; }, abstract = {Pseudechis (black snakes) is an Australasian elapid snake genus that inhabits much of mainland Australia, with two representatives confined to Papua New Guinea. The present study is the first to analyse the venom of all 9 described Pseudechis species (plus one undescribed species) to investigate the evolution of venom composition and functional activity. Proteomic results demonstrated that the typical Pseudechis venom profile is dominated by phospholipase A2 toxins. Strong cytotoxicity was the dominant function for most species. P. porphyriacus, the most basal member of the genus, also exhibited the most divergent venom composition, being the only species with appreciable amounts of procoagulant toxins. The relatively high presence of factor Xa recovered in P. porphyriacus venom may be related to a predominantly amphibian diet. Results of this study provide important insights to guide future ecological and toxinological investigations.}, } @article {pmid29352727, year = {2018}, author = {McGrath, JA and Fanelli, CJ and Di Toro, DM and Parkerton, TF and Redman, AD and Paumen, ML and Comber, M and Eadsforth, CV and den Haan, K}, title = {Re-evaluation of target lipid model-derived HC5 predictions for hydrocarbons.}, journal = {Environmental toxicology and chemistry}, volume = {37}, number = {6}, pages = {1579-1593}, doi = {10.1002/etc.4100}, pmid = {29352727}, issn = {1552-8618}, mesh = {Animals ; Body Burden ; Databases, Chemical ; Fishes ; Hydrocarbons/toxicity ; Invertebrates/chemistry/drug effects ; Lipids/*analysis ; Organic Chemicals/*toxicity ; Plants/chemistry/drug effects ; Risk Assessment/methods ; Species Specificity ; Toxicity Tests, Acute ; Toxicity Tests, Chronic ; Water Pollutants, Chemical/*toxicity ; }, abstract = {The target lipid model (TLM) has been previously applied to predict the aquatic toxicity of hydrocarbons and other nonionic organic chemicals and for deriving the concentrations above which 95% of species should be protected (HC5 values). Several concerns have been identified with the TLM-derived HC5 when it is applied in a substance risk assessment context. These shortcomings were addressed by expanding the acute and chronic toxicity databases to include more diverse taxonomic groups and increase the number of species. The TLM was recalibrated with these expanded databases, resulting in critical target lipid body burdens and acute-to-chronic ratios that met the required guidelines for using species sensitivity distributions in substance risk assessment. The HC5 equation was further revised to consider covarying model parameters. The calculated HC5 values derived from the revised TLM framework were validated using an independent data set for hydrocarbons comprising 106 chronic values across plants, invertebrates, and fish. Assuming a sum binomial distribution, the 95% confidence limit for a 5% failure is between 0.8 and 9.2%. Eight chronic values fell below the HC5, corresponding to an excursion of 7.5%, which falls within the expected uncertainty bounds. Thus, calculated HC5s derived from the revised TLM framework were found to be consistent with the intended protection goals. Environ Toxicol Chem 2018;37:1579-1593. © 2018 SETAC.}, } @article {pmid29352182, year = {2018}, author = {Bi, Y and Zhang, MF and Xue, J and Dong, R and Du, YP and Zhang, XH}, title = {Chloroplast genomic resources for phylogeny and DNA barcoding: a case study on Fritillaria.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {1184}, pmid = {29352182}, issn = {2045-2322}, mesh = {Computational Biology/methods ; *DNA Barcoding, Taxonomic ; DNA, Chloroplast ; Fritillaria/*classification/*genetics ; *Genome, Chloroplast ; Microsatellite Repeats ; *Phylogeny ; Repetitive Sequences, Nucleic Acid ; Whole Genome Sequencing ; }, abstract = {The genus Fritillaria comprises approximately 130 perennial herbaceous species. In the Pharmacopoeia of the People's Republic of China, the bulbs of 11 Fritillaria species are used in Chinese herbal medicines. However, the traditional methods of morphological classification cannot accurately identify closely related species of Fritillaria. Previous studies have attempted to identify these species with universal molecular markers, but insufficient phylogenetic signal was available. In this study, the complete chloroplast genomes of eight Fritillaria species were compared. The length of the eight Fritillaria chloroplast genomes ranges from 151,009 bp to 152,224 bp. A total of 136 SSR loci were identified, including 124 polymorphic SSR loci. For large repeat sequences, 108 repeat loci and four types of repeats were observed. Ten highly variable regions were identified as potential molecular markers. These SSRs, large repeat sequences and highly variable regions provide important information for the development of genetic markers and DNA fingerprints. Phylogenetic analyses showed that the topological structures of all data sets (except the IR regions) were in complete agreement and well resolved. Overall, this study provides comprehensive chloroplast genomic resources, which will be valuable for future studies of evolution and species identification in Fritillaria.}, } @article {pmid29351548, year = {2018}, author = {Geltsch, N and Elek, Z and Manczinger, L and Vágvölgyi, C and Moskát, C}, title = {Common cuckoos (Cuculus canorus) affect the bacterial diversity of the eggshells of their great reed warbler (Acrocephalus arundinaceus) hosts.}, journal = {PloS one}, volume = {13}, number = {1}, pages = {e0191364}, pmid = {29351548}, issn = {1932-6203}, mesh = {Animals ; Biodiversity ; Birds/*microbiology/physiology ; Egg Shell/*microbiology ; Female ; Host-Parasite Interactions/genetics ; Microbiota/genetics ; Nesting Behavior ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Songbirds/*microbiology/*parasitology/physiology ; Species Specificity ; }, abstract = {The common cuckoo (Cuculus canorus) is an avian brood parasite, laying its eggs in the nests of other bird species, where these hosts incubate the parasitic eggs, feed and rear the nestlings. The appearance of a cuckoo egg in a host nest may change the bacterial community in the nest. This may have consequences on the hatchability of host eggs, even when hosts reject the parasitic egg, typically within six days after parasitism. The present study revealed the bacterial community of cuckoo eggshells and those of the great reed warbler (Acrocephalus arundinaceus), one of the main hosts of cuckoos. We compared host eggs from non-parasitized clutches, as well as host and cuckoo eggs from parasitized clutches. As incubation may change bacterial assemblages on eggshells, we compared these egg types in two stages: the egg-laying stage, when incubation has not been started, and the mid-incubation stage (ca. on days 5-7 in incubation), where heat from the incubating female dries eggshells. Our results obtained by the 16S rRNA gene sequencing technique showed that fresh host and cuckoo eggs had partially different bacterial communities, but they became more similar during incubation in parasitized nests. Cluster analysis revealed that fresh cuckoo eggs and incubated host eggs in unparasitized nests (where no cuckoo effect could have happened) were the most dissimilar from the other groups of eggs. Cuckoo eggs did not reduce the hatchability of great reed warbler eggs. Our results on the cuckoo-great reed warbler relationship supported the idea that brood parasites may change bacterial microbiota in the host nest. Further studies should reveal how bacterial communities of cuckoo eggshells may vary by host-specific races (gentes) of cuckoos.}, } @article {pmid29351302, year = {2018}, author = {Bzhalava, Z and Hultin, E and Dillner, J}, title = {Extension of the viral ecology in humans using viral profile hidden Markov models.}, journal = {PloS one}, volume = {13}, number = {1}, pages = {e0190938}, pmid = {29351302}, issn = {1932-6203}, mesh = {Algorithms ; Computational Biology ; Contig Mapping/statistics & numerical data ; Databases, Protein/statistics & numerical data ; Humans ; Markov Chains ; Metagenomics/statistics & numerical data ; *Microbiota ; Phylogeny ; Viral Proteins/genetics ; Viruses/classification/*genetics/*isolation & purification ; }, abstract = {When human samples are sequenced, many assembled contigs are "unknown", as conventional alignments find no similarity to known sequences. Hidden Markov models (HMM) exploit the positions of specific nucleotides in protein-encoding codons in various microbes. The algorithm HMMER3 implements HMM using a reference set of sequences encoding viral proteins, "vFam". We used HMMER3 analysis of "unknown" human sample-derived sequences and identified 510 contigs distantly related to viruses (Anelloviridae (n = 1), Baculoviridae (n = 34), Circoviridae (n = 35), Caulimoviridae (n = 3), Closteroviridae (n = 5), Geminiviridae (n = 21), Herpesviridae (n = 10), Iridoviridae (n = 12), Marseillevirus (n = 26), Mimiviridae (n = 80), Phycodnaviridae (n = 165), Poxviridae (n = 23), Retroviridae (n = 6) and 89 contigs related to described viruses not yet assigned to any taxonomic family). In summary, we find that analysis using the HMMER3 algorithm and the "vFam" database greatly extended the detection of viruses in biospecimens from humans.}, } @article {pmid29350561, year = {2018}, author = {De Filippis, F and Parente, E and Ercolini, D}, title = {Recent Past, Present, and Future of the Food Microbiome.}, journal = {Annual review of food science and technology}, volume = {9}, number = {}, pages = {589-608}, doi = {10.1146/annurev-food-030117-012312}, pmid = {29350561}, issn = {1941-1413}, mesh = {Computational Biology ; Fermentation ; *Food Microbiology ; Food Safety ; Food Technology/*methods ; High-Throughput Nucleotide Sequencing/methods ; Metagenomics ; Microbiota/*genetics ; }, abstract = {Sequencing technologies have deeply changed our approach to the study of food microbial communities. This review describes recent exploitations of high-throughput sequencing applications to improve our knowledge of food microbial consortia. In the past 10 years, target amplicon sequencing has become routinely used in many food microbiology laboratories, providing a detailed picture of food-associated microbiota. Metagenomics and metatranscriptomics approaches are still underexploited in food microbial ecology, despite their potential to uncover the functionality of complex communities. In a near future, sequencing technologies will surely advance our understanding of how to effectively use the invaluable microbial resources to improve food quality and safety.}, } @article {pmid29350398, year = {2018}, author = {Lötsch, J and Kringel, D}, title = {Use of Computational Functional Genomics in Drug Discovery and Repurposing for Analgesic Indications.}, journal = {Clinical pharmacology and therapeutics}, volume = {103}, number = {6}, pages = {975-978}, pmid = {29350398}, issn = {1532-6535}, mesh = {Analgesics/pharmacology ; Animals ; Computational Biology/*methods ; Data Mining ; Databases, Genetic ; Drug Discovery/*methods ; Drug Repositioning/*methods ; Genomics/*methods ; Humans ; Machine Learning ; Mice ; Pain/*drug therapy/*genetics ; Phenotype ; }, abstract = {The novel research area of functional genomics investigates biochemical, cellular, or physiological properties of gene products with the goal of understanding the relationship between the genome and the phenotype. These developments have made analgesic drug research a data-rich discipline mastered only by making use of parallel developments in computer science, including the establishment of knowledge bases, mining methods for big data, machine-learning, and artificial intelligence, (Table) which will be exemplarily introduced in the following.}, } @article {pmid29348510, year = {2018}, author = {Lin, R and Qin, F and Shen, B and Shi, Q and Liu, C and Zhang, X and Jiao, Y and Lu, J and Gao, Y and Suarez-Fernandez, M and Lopez-Moya, F and Lopez-Llorca, LV and Wang, G and Mao, Z and Ling, J and Yang, Y and Cheng, X and Xie, B}, title = {Genome and secretome analysis of Pochonia chlamydosporia provide new insight into egg-parasitic mechanisms.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {1123}, pmid = {29348510}, issn = {2045-2322}, mesh = {Chromosomes, Fungal ; Computational Biology/methods ; Gene Duplication ; Gene Transfer, Horizontal ; Genomics/methods ; High-Throughput Nucleotide Sequencing ; Host-Parasite Interactions ; Host-Pathogen Interactions ; Hypocreales/*genetics/*metabolism ; *Metabolome ; Phylogeny ; Plants/microbiology/parasitology ; *Proteome ; Selection, Genetic ; *Transcriptome ; }, abstract = {Pochonia chlamydosporia infects eggs and females of economically important plant-parasitic nematodes. The fungal isolates parasitizing different nematodes are genetically distinct. To understand their intraspecific genetic differentiation, parasitic mechanisms, and adaptive evolution, we assembled seven putative chromosomes of P. chlamydosporia strain 170 isolated from root-knot nematode eggs (~44 Mb, including 7.19% of transposable elements) and compared them with the genome of the strain 123 (~41 Mb) isolated from cereal cyst nematode. We focus on secretomes of the fungus, which play important roles in pathogenicity and fungus-host/environment interactions, and identified 1,750 secreted proteins, with a high proportion of carboxypeptidases, subtilisins, and chitinases. We analyzed the phylogenies of these genes and predicted new pathogenic molecules. By comparative transcriptome analysis, we found that secreted proteins involved in responses to nutrient stress are mainly comprised of proteases and glycoside hydrolases. Moreover, 32 secreted proteins undergoing positive selection and 71 duplicated gene pairs encoding secreted proteins are identified. Two duplicated pairs encoding secreted glycosyl hydrolases (GH30), which may be related to fungal endophytic process and lost in many insect-pathogenic fungi but exist in nematophagous fungi, are putatively acquired from bacteria by horizontal gene transfer. The results help understanding genetic origins and evolution of parasitism-related genes.}, } @article {pmid29348447, year = {2018}, author = {Horel, S}, title = {Browsing a corporation's mind.}, journal = {Journal of public health policy}, volume = {39}, number = {1}, pages = {12-14}, doi = {10.1057/s41271-017-0103-y}, pmid = {29348447}, issn = {1745-655X}, mesh = {Big Data ; Commerce/legislation & jurisprudence/*organization & administration/standards ; *Databases, Factual ; Ecology ; Government Regulation ; Hazardous Substances/*toxicity ; Humans ; Information Storage and Retrieval ; Public Health ; Public Policy ; Tobacco Industry/organization & administration ; }, } @article {pmid29348446, year = {2018}, author = {Robbins, A and Freeman, P}, title = {ToxicDocs (www.ToxicDocs.org) goes live: A giant step toward leveling the playing field for efforts to combat toxic exposures.}, journal = {Journal of public health policy}, volume = {39}, number = {1}, pages = {1-3}, doi = {10.1057/s41271-017-0102-z}, pmid = {29348446}, issn = {1745-655X}, mesh = {*Big Data ; Commerce/legislation & jurisprudence/*organization & administration/standards ; *Databases, Factual ; Ecology ; Government Regulation ; Hazardous Substances/*toxicity ; Humans ; Information Storage and Retrieval ; Public Health ; Public Policy ; }, } @article {pmid29348445, year = {2018}, author = {Freudenberg, N}, title = {ToxicDocs: a new resource for assessing the impact of corporate practices on health.}, journal = {Journal of public health policy}, volume = {39}, number = {1}, pages = {30-33}, doi = {10.1057/s41271-017-0101-0}, pmid = {29348445}, issn = {1745-655X}, mesh = {Big Data ; Commerce/legislation & jurisprudence/*organization & administration/standards ; *Databases, Factual ; Ecology ; Government Regulation ; Hazardous Substances/*toxicity ; Humans ; Information Storage and Retrieval ; Public Health ; Public Policy ; }, } @article {pmid29346509, year = {2018}, author = {Zhang, J and Wei, Z and Chen, J}, title = {A distance-based approach for testing the mediation effect of the human microbiome.}, journal = {Bioinformatics (Oxford, England)}, volume = {34}, number = {11}, pages = {1875-1883}, doi = {10.1093/bioinformatics/bty014}, pmid = {29346509}, issn = {1367-4811}, mesh = {Bacteria/genetics ; Computational Biology/*methods ; Computer Simulation ; Gastrointestinal Microbiome/genetics ; Microbiota/*genetics ; *Phylogeny ; *Software ; }, abstract = {MOTIVATION: Recent studies have revealed a complex interplay between environment, the human microbiome and health and disease. Mediation analysis of the human microbiome in these complex relationships could potentially provide insights into the role of the microbiome in the etiology of disease and, more importantly, lead to novel clinical interventions by modulating the microbiome. However, due to the high dimensionality, sparsity, non-normality and phylogenetic structure of microbiome data, none of the existing methods are suitable for testing such clinically important mediation effect.

RESULTS: We propose a distance-based approach for testing the mediation effect of the human microbiome. In the framework, the nonlinear relationship between the human microbiome and independent/dependent variables is captured implicitly through the use of sample-wise ecological distances, and the phylogenetic tree information is conveniently incorporated by using phylogeny-based distance metrics. Multiple distance metrics are utilized to maximize the power to detect various types of mediation effect. Simulation studies demonstrate that our method has correct Type I error control, and is robust and powerful under various mediation models. Application to a real gut microbiome dataset revealed that the association between the dietary fiber intake and body mass index was mediated by the gut microbiome.

An R package 'MedTest' is freely available at https://github.com/jchen1981/MedTest.

CONTACT: zhiwei@njit.edu or chen.jun2@mayo.edu.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, } @article {pmid29343494, year = {2018}, author = {Gloria-Soria, A and Dunn, WA and Yu, X and Vigneron, A and Lee, KY and Li, M and Weiss, BL and Zhao, H and Aksoy, S and Caccone, A}, title = {Uncovering Genomic Regions Associated with Trypanosoma Infections in Wild Populations of the Tsetse Fly Glossina fuscipes.}, journal = {G3 (Bethesda, Md.)}, volume = {8}, number = {3}, pages = {887-897}, pmid = {29343494}, issn = {2160-1836}, support = {D43 TW007391/TW/FIC NIH HHS/United States ; R01 AI068932/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Chromosome Mapping ; Computational Biology/methods ; Gene Expression Profiling ; Genes, Insect ; *Genetic Predisposition to Disease ; Genetic Variation ; *Genome, Insect ; *Genomics/methods ; High-Throughput Nucleotide Sequencing ; Host-Pathogen Interactions/*genetics ; Polymorphism, Single Nucleotide ; Transcriptome ; *Trypanosoma ; Tsetse Flies/*genetics/*parasitology ; }, abstract = {Vector-borne diseases are responsible for > 1 million deaths every year but genomic resources for most species responsible for their transmission are limited. This is true for neglected diseases such as sleeping sickness (Human African Trypanosomiasis), a disease caused by Trypanosoma parasites vectored by several species of tseste flies within the genus Glossina We describe an integrative approach that identifies statistical associations between trypanosome infection status of Glossina fuscipes fuscipes (Gff) flies from Uganda, for which functional studies are complicated because the species cannot be easily maintained in laboratory colonies, and ∼73,000 polymorphic sites distributed across the genome. Then, we identify candidate genes involved in Gff trypanosome susceptibility by taking advantage of genomic resources from a closely related species, G. morsitans morsitans (Gmm). We compiled a comprehensive transcript library from 72 published and unpublished RNAseq experiments of trypanosome-infected and uninfected Gmm flies, and improved the current Gmm transcriptome assembly. This new assembly was then used to enhance the functional annotations on the Gff genome. As a consequence, we identified 56 candidate genes in the vicinity of the 18 regions associated with Trypanosoma infection status in Gff Twenty-nine of these genes were differentially expressed (DE) among parasite-infected and uninfected Gmm, suggesting that their orthologs in Gff may correlate with disease transmission. These genes were involved in DNA regulation, neurophysiological functions, and immune responses. We highlight the power of integrating population and functional genomics from related species to enhance our understanding of the genetic basis of physiological traits, particularly in nonmodel organisms.}, } @article {pmid29339507, year = {2018}, author = {Zhang, Y and Harris, CJ and Liu, Q and Liu, W and Ausin, I and Long, Y and Xiao, L and Feng, L and Chen, X and Xie, Y and Chen, X and Zhan, L and Feng, S and Li, JJ and Wang, H and Zhai, J and Jacobsen, SE}, title = {Large-scale comparative epigenomics reveals hierarchical regulation of non-CG methylation in Arabidopsis.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {115}, number = {5}, pages = {E1069-E1074}, pmid = {29339507}, issn = {1091-6490}, support = {R01 GM060398/GM/NIGMS NIH HHS/United States ; R37 GM060398/GM/NIGMS NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; }, mesh = {Arabidopsis/*genetics ; Cluster Analysis ; Computational Biology ; CpG Islands ; *DNA Methylation ; Epigenesis, Genetic ; *Epigenomics ; *Gene Expression Regulation, Plant ; Gene Library ; Genome, Plant ; Heterochromatin/chemistry ; High-Throughput Nucleotide Sequencing ; Plants, Genetically Modified ; Sequence Analysis, DNA ; Sequence Analysis, RNA ; Software ; }, abstract = {Genome-wide characterization by next-generation sequencing has greatly improved our understanding of the landscape of epigenetic modifications. Since 2008, whole-genome bisulfite sequencing (WGBS) has become the gold standard for DNA methylation analysis, and a tremendous amount of WGBS data has been generated by the research community. However, the systematic comparison of DNA methylation profiles to identify regulatory mechanisms has yet to be fully explored. Here we reprocessed the raw data of over 500 publicly available Arabidopsis WGBS libraries from various mutant backgrounds, tissue types, and stress treatments and also filtered them based on sequencing depth and efficiency of bisulfite conversion. This enabled us to identify high-confidence differentially methylated regions (hcDMRs) by comparing each test library to over 50 high-quality wild-type controls. We developed statistical and quantitative measurements to analyze the overlapping of DMRs and to cluster libraries based on their effect on DNA methylation. In addition to confirming existing relationships, we revealed unanticipated connections between well-known genes. For instance, MET1 and CMT3 were found to be required for the maintenance of asymmetric CHH methylation at nonoverlapping regions of CMT2 targeted heterochromatin. Our comparative methylome approach has established a framework for extracting biological insights via large-scale comparison of methylomes and can also be adopted for other genomics datasets.}, } @article {pmid29338736, year = {2018}, author = {Moukam Kakmeni, FM and Guimapi, RYA and Ndjomatchoua, FT and Pedro, SA and Mutunga, J and Tonnang, HEZ}, title = {Spatial panorama of malaria prevalence in Africa under climate change and interventions scenarios.}, journal = {International journal of health geographics}, volume = {17}, number = {1}, pages = {2}, pmid = {29338736}, issn = {1476-072X}, mesh = {Africa/epidemiology ; Animals ; *Climate Change/statistics & numerical data ; *Geographic Information Systems/statistics & numerical data ; Geographic Mapping ; Humans ; Malaria/*epidemiology/prevention & control/*transmission ; *Models, Theoretical ; Mosquito Vectors ; Plasmodium falciparum/isolation & purification ; Prevalence ; }, abstract = {BACKGROUND: Malaria is highly sensitive to climatic variables and is strongly influenced by the presence of vectors in a region that further contribute to parasite development and sustained disease transmission. Mathematical analysis of malaria transmission through the use and application of the value of the basic reproduction number (R0) threshold is an important and useful tool for the understanding of disease patterns.

METHODS: Temperature dependence aspect of R0 obtained from dynamical mathematical network model was used to derive the spatial distribution maps for malaria transmission under different climatic and intervention scenarios. Model validation was conducted using MARA map and the Annual Plasmodium falciparum Entomological Inoculation Rates for Africa.

RESULTS: The inclusion of the coupling between patches in dynamical model seems to have no effects on the estimate of the optimal temperature (about 25 °C) for malaria transmission. In patches environment, we were able to establish a threshold value (about α = 5) representing the ratio between the migration rates from one patch to another that has no effect on the magnitude of R0. Such findings allow us to limit the production of the spatial distribution map of R0 to a single patch model. Future projections using temperature changes indicated a shift in malaria transmission areas towards the southern and northern areas of Africa and the application of the interventions scenario yielded a considerable reduction in transmission within malaria endemic areas of the continent.

CONCLUSIONS: The approach employed here is a sole study that defined the limits of contemporary malaria transmission, using R0 derived from a dynamical mathematical model. It has offered a unique prospect for measuring the impacts of interventions through simple manipulation of model parameters. Projections at scale provide options to visualize and query the results, when linked to the human population could potentially deliver adequate highlight on the number of individuals at risk of malaria infection across Africa. The findings provide a reasonable basis for understanding the fundamental effects of malaria control and could contribute towards disease elimination, which is considered as a challenge especially in the context of climate change.}, } @article {pmid29337419, year = {2018}, author = {Grogan, LF and Cashins, SD and Skerratt, LF and Berger, L and McFadden, MS and Harlow, P and Hunter, DA and Scheele, BC and Mulvenna, J}, title = {Evolution of resistance to chytridiomycosis is associated with a robust early immune response.}, journal = {Molecular ecology}, volume = {27}, number = {4}, pages = {919-934}, doi = {10.1111/mec.14493}, pmid = {29337419}, issn = {1365-294X}, mesh = {Animals ; Anura/genetics/*immunology/*microbiology ; Chytridiomycota/*physiology ; Cluster Analysis ; Clutch Size ; Disease Resistance/*immunology ; Down-Regulation/genetics ; Female ; Gene Ontology ; *Immunity ; Male ; Molecular Sequence Annotation ; Multigene Family ; Mycoses/*immunology/*microbiology ; Survival Analysis ; Transcriptome/genetics ; Up-Regulation/genetics ; }, abstract = {Potentiating the evolution of immunity is a promising strategy for addressing biodiversity diseases. Assisted selection for infection resistance may enable the recovery and persistence of amphibians threatened by chytridiomycosis, a devastating fungal skin disease threatening hundreds of species globally. However, knowledge of the mechanisms involved in the natural evolution of immunity to chytridiomycosis is limited. Understanding the mechanisms of such resistance may help speed-assisted selection. Using a transcriptomics approach, we examined gene expression responses of endangered alpine tree frogs (Litoria verreauxii alpina) to subclinical infection, comparing two long-exposed populations with a naïve population. We performed a blinded, randomized and controlled exposure experiment, collecting skin, liver and spleen tissues at 4, 8 and 14 days postexposure from 51 wild-caught captively reared infection-naïve adult frogs for transcriptome assembly and differential gene expression analyses. We analysed our results in conjunction with infection intensity data, and the results of a large clinical survival experiment run concurrently with individuals from the same clutches. Here, we show that frogs from an evolutionarily long-exposed and phenotypically more resistant population of the highly susceptible alpine tree frog demonstrate a more robust innate and adaptive immune response at the critical early subclinical stage of infection when compared with two more susceptible populations. These results are consistent with the occurrence of evolution of resistance against chytridiomycosis, help to explain underlying resistance mechanisms, and provide genes of potential interest and sequence data for future research. We recommend further investigation of cell-mediated immunity pathways, the role of interferons and mechanisms of lymphocyte suppression.}, } @article {pmid29335027, year = {2018}, author = {Tipton, L and Müller, CL and Kurtz, ZD and Huang, L and Kleerup, E and Morris, A and Bonneau, R and Ghedin, E}, title = {Fungi stabilize connectivity in the lung and skin microbial ecosystems.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {12}, pmid = {29335027}, issn = {2049-2618}, support = {K24 HL123342/HL/NHLBI NIH HHS/United States ; PN2 EY016586/EY/NEI NIH HHS/United States ; U01 HL098962/HL/NHLBI NIH HHS/United States ; GM32877-21/22//National Institutes of Health (US)/International ; EY016586-06/NH/NIH HHS/United States ; U54 CA143907/CA/NCI NIH HHS/United States ; K24 HL123342/NH/NIH HHS/United States ; PN2-EY016586/NH/NIH HHS/United States ; U01HL098962//National Institutes of Health (US)/International ; IU54CA143907-01/NH/NIH HHS/United States ; K24 HL087713/HL/NHLBI NIH HHS/United States ; IOS-1126971//National Science Foundation/International ; R01 HL090339/HL/NHLBI NIH HHS/United States ; R01 GM032877/GM/NIGMS NIH HHS/United States ; PN1 EY016586/EY/NEI NIH HHS/United States ; R01HL090339/NH/NIH HHS/United States ; }, mesh = {Adult ; Bacteria/*classification/genetics/isolation & purification ; Computational Biology/*methods ; Female ; Fungi/*classification/genetics/isolation & purification ; Humans ; Lung/*microbiology ; Male ; Microbial Consortia ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Skin/*microbiology ; }, abstract = {BACKGROUND: No microbe exists in isolation, and few live in environments with only members of their own kingdom or domain. As microbiome studies become increasingly more interested in the interactions between microbes than in cataloging which microbes are present, the variety of microbes in the community should be considered. However, the majority of ecological interaction networks for microbiomes built to date have included only bacteria. Joint association inference across multiple domains of life, e.g., fungal communities (the mycobiome) and bacterial communities, has remained largely elusive.

RESULTS: Here, we present a novel extension of the SParse InversE Covariance estimation for Ecological ASsociation Inference (SPIEC-EASI) framework that allows statistical inference of cross-domain associations from targeted amplicon sequencing data. For human lung and skin micro- and mycobiomes, we show that cross-domain networks exhibit higher connectivity, increased network stability, and similar topological re-organization patterns compared to single-domain networks. We also validate in vitro a small number of cross-domain interactions predicted by the skin association network.

CONCLUSIONS: For the human lung and skin micro- and mycobiomes, our findings suggest that fungi play a stabilizing role in ecological network organization. Our study suggests that computational efforts to infer association networks that include all forms of microbial life, paired with large-scale culture-based association validation experiments, will help formulate concrete hypotheses about the underlying biological mechanisms of species interactions and, ultimately, help understand microbial communities as a whole.}, } @article {pmid29334414, year = {2018}, author = {Fišer, C and Robinson, CT and Malard, F}, title = {Cryptic species as a window into the paradigm shift of the species concept.}, journal = {Molecular ecology}, volume = {27}, number = {3}, pages = {613-635}, doi = {10.1111/mec.14486}, pmid = {29334414}, issn = {1365-294X}, mesh = {Amphipoda/physiology ; Animals ; Biodiversity ; Databases as Topic ; *Genetic Speciation ; Phylogeny ; Species Specificity ; }, abstract = {The species concept is the cornerstone of biodiversity science, and any paradigm shift in the delimitation of species affects many research fields. Many biologists now are embracing a new "species" paradigm as separately evolving populations using different delimitation criteria. Individual criteria can emerge during different periods of speciation; some may never evolve. As such, a paradigm shift in the species concept relates to this inherent heterogeneity in the speciation process and species category-which is fundamentally overlooked in biodiversity research. Cryptic species fall within this paradigm shift: they are continuously being reported from diverse animal phyla but are poorly considered in current tests of ecological and evolutionary theory. The aim of this review is to integrate cryptic species in biodiversity science. In the first section, we address that the absence of morphological diversification is an evolutionary phenomenon, a "process" counterpart to the long-studied mechanisms of morphological diversification. In the next section regarding taxonomy, we show that molecular delimitation of cryptic species is heavily biased towards distance-based methods. We also stress the importance of formally naming of cryptic species for better integration into research fields that use species as units of analysis. Finally, we show that incorporating cryptic species leads to novel insights regarding biodiversity patterns and processes, including large-scale biodiversity assessments, geographic variation in species distribution and species coexistence. It is time for incorporating multicriteria species approaches aiming to understand speciation across space and taxa, thus allowing integration into biodiversity conservation while accommodating for species uncertainty.}, } @article {pmid29332298, year = {2018}, author = {Garay, J and Cressman, R and Móri, TF and Varga, T}, title = {The ESS and replicator equation in matrix games under time constraints.}, journal = {Journal of mathematical biology}, volume = {76}, number = {7}, pages = {1951-1973}, pmid = {29332298}, issn = {1432-1416}, support = {K 108615//Hungarian National Research, Development and Innovation Office NKFIH/International ; GINOP 2.3.2-15-2016-00057//Hungarian National Research, Development and Innovation Office NKFIH/International ; 690817//Horizon 2020: The EU Framework Programme for Research and Innovation, Marie Skłodowska-Curie Actions/International ; 690817//Horizon 2020: The EU Framework Programme for Research and Innovation, Marie Skłodowska-Curie Actions/International ; }, mesh = {Animals ; *Biological Evolution ; Computational Biology ; Ecosystem ; *Game Theory ; Humans ; Mathematical Concepts ; *Models, Biological ; Mutation ; Phenotype ; Population Dynamics ; Time Factors ; }, abstract = {Recently, we introduced the class of matrix games under time constraints and characterized the concept of (monomorphic) evolutionarily stable strategy (ESS) in them. We are now interested in how the ESS is related to the existence and stability of equilibria for polymorphic populations. We point out that, although the ESS may no longer be a polymorphic equilibrium, there is a connection between them. Specifically, the polymorphic state at which the average strategy of the active individuals in the population is equal to the ESS is an equilibrium of the polymorphic model. Moreover, in the case when there are only two pure strategies, a polymorphic equilibrium is locally asymptotically stable under the replicator equation for the pure-strategy polymorphic model if and only if it corresponds to an ESS. Finally, we prove that a strict Nash equilibrium is a pure-strategy ESS that is a locally asymptotically stable equilibrium of the replicator equation in n-strategy time-constrained matrix games.}, } @article {pmid29331627, year = {2018}, author = {Haara, A and Pykäläinen, J and Tolvanen, A and Kurttila, M}, title = {Use of interactive data visualization in multi-objective forest planning.}, journal = {Journal of environmental management}, volume = {210}, number = {}, pages = {71-86}, doi = {10.1016/j.jenvman.2018.01.002}, pmid = {29331627}, issn = {1095-8630}, mesh = {Decision Making ; *Decision Support Techniques ; Ecosystem ; *Forestry ; Forests ; }, abstract = {Common to multi-objective forest planning situations is that they all require comparisons, searches and evaluation among decision alternatives. Through these actions, the decision maker can learn from the information presented and thus make well-justified decisions. Interactive data visualization is an evolving approach that supports learning and decision making in multidimensional decision problems and planning processes. Data visualization contributes the formation of mental image data and this process is further boosted by allowing interaction with the data. In this study, we introduce a multi-objective forest planning decision problem framework and the corresponding characteristics of data. We utilize the framework with example planning data to illustrate and evaluate the potential of 14 interactive data visualization techniques to support multi-objective forest planning decisions. Furthermore, broader utilization possibilities of these techniques to incorporate the provisioning of ecosystem services into forest management and planning are discussed.}, } @article {pmid29331591, year = {2018}, author = {Rakitov, R and Moysa, AA and Kopylov, AT and Moshkovskii, SA and Peters, RS and Meusemann, K and Misof, B and Dietrich, CH and Johnson, KP and Podsiadlowski, L and Walden, KKO}, title = {Brochosomins and other novel proteins from brochosomes of leafhoppers (Insecta, Hemiptera, Cicadellidae).}, journal = {Insect biochemistry and molecular biology}, volume = {94}, number = {}, pages = {10-17}, doi = {10.1016/j.ibmb.2018.01.001}, pmid = {29331591}, issn = {1879-0240}, mesh = {Animals ; Chromatography, Liquid ; Computational Biology ; Electrophoresis, Polyacrylamide Gel ; Hemiptera/*physiology ; High-Throughput Nucleotide Sequencing ; Insect Proteins/*genetics/metabolism ; Malpighian Tubules/*metabolism ; Multigene Family/*genetics ; Tandem Mass Spectrometry ; }, abstract = {Brochosomes (BS) are secretory granules resembling buckyballs, produced intracellularly in specialized glandular segments of the Malpighian tubules and forming superhydrophobic coatings on the integuments of leafhoppers (Hemiptera, Cicadellidae). Their composition is poorly known. Using a combination of SDS-PAGE, LC-MS/MS, next-generation sequencing (RNAseq) and bioinformatics we demonstrate that the major structural component of BS of the leafhopper Graphocephala fennahi Young is a novel family of 21-40-kDa secretory proteins, referred to herein as brochosomins (BSM), apparently cross-linked by disulfide bonds. At least 28 paralogous BSM were identified in a transcriptome assembly of this species, most of which were detected in BS. Multiple additional BS-associated proteins (BSAP), possibly loosely attached to the outer and inner surfaces of BS, were also identified; some of these were glycine-, tyrosine- and proline-rich. BSM and BSAP together accounted for half of the 100 most expressed transcripts in the Malpighian tubules of G. fennahi. Except for several minor BSAP possibly related to cyclases, BSM and BSAP had no homologs among known proteins, thus representing taxonomically restricted gene families (orphans). Searching in 50 whole-body transcriptome assemblies of Hemiptera found homologs of BSM in representatives of all five families of the superfamily Membracoidea (Cicadellidae, Myerslopiidae, Aetalionidae, Membracidae, and Melizoderidae), but not in other lineages. Among the identified proteins only BSM were shared in common between all 17 surveyed leafhoppers known to produce BS. Combined CHN elemental and aminoacid analyses estimated the total protein content of BS from the integument of G. fennahi to be 60-70%.}, } @article {pmid29330422, year = {2018}, author = {Nunes, GT and Bertrand, S and Bugoni, L}, title = {Seabirds fighting for land: phenotypic consequences of breeding area constraints at a small remote archipelago.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {665}, pmid = {29330422}, issn = {2045-2322}, mesh = {Animals ; Birds/*physiology ; Body Size ; Breeding ; Databases, Factual ; Feeding Behavior/*physiology ; Female ; Genetic Fitness ; Male ; Nesting Behavior/*physiology ; Phenotype ; }, abstract = {Identifying associations between phenotypes and environmental parameters is crucial for understanding how natural selection acts at the individual level. In this context, genetically isolated populations can be useful models for identifying the forces selecting fitness-related traits. Here, we use a comprehensive dataset on a genetically and ecologically isolated population of the strictly marine bird, the brown booby Sula leucogaster, at the tropical and remote Saint Peter and Saint Paul Archipelago, mid-Atlantic Ocean, in order to detect phenotypic adjustments from interindividual differences in diet, foraging behaviour, and nest quality. For this, we took biometrics of all individuals of the colony breeding in 2014 and 2015 and tested their associations with nest quality, diet parameters, and foraging behaviour. While body size was not related to the foraging parameters, the body size of the females (responsible for nest acquisition and defence) was significantly associated with the nest quality, as larger females occupied high-quality nests. Our findings suggest that the small breeding area, rather than prey availability, is a limiting factor, emphasizing the role of on-land features in shaping phenotypic characteristics and fitness in land-dependent marine vertebrates.}, } @article {pmid29329394, year = {2018}, author = {Miller, JR and Koren, S and Dilley, KA and Puri, V and Brown, DM and Harkins, DM and Thibaud-Nissen, F and Rosen, B and Chen, XG and Tu, Z and Sharakhov, IV and Sharakhova, MV and Sebra, R and Stockwell, TB and Bergman, NH and Sutton, GG and Phillippy, AM and Piermarini, PM and Shabman, RS}, title = {Analysis of the Aedes albopictus C6/36 genome provides insight into cell line utility for viral propagation.}, journal = {GigaScience}, volume = {7}, number = {3}, pages = {1-13}, pmid = {29329394}, issn = {2047-217X}, support = {R01 AI123338/AI/NIAID NIH HHS/United States ; }, mesh = {Aedes/genetics/*virology ; Animals ; Base Sequence/genetics ; Cell Line ; Genome, Insect/genetics ; Humans ; Larva/genetics/virology ; Mosquito Vectors/genetics/virology ; Virus Replication/*genetics ; Zika Virus/*genetics/growth & development ; Zika Virus Infection/*genetics/virology ; }, abstract = {BACKGROUND: The 50-year-old Aedes albopictus C6/36 cell line is a resource for the detection, amplification, and analysis of mosquito-borne viruses including Zika, dengue, and chikungunya. The cell line is derived from an unknown number of larvae from an unspecified strain of Aedes albopictus mosquitoes. Toward improved utility of the cell line for research in virus transmission, we present an annotated assembly of the C6/36 genome.

RESULTS: The C6/36 genome assembly has the largest contig N50 (3.3 Mbp) of any mosquito assembly, presents the sequences of both haplotypes for most of the diploid genome, reveals independent null mutations in both alleles of the Dicer locus, and indicates a male-specific genome. Gene annotation was computed with publicly available mosquito transcript sequences. Gene expression data from cell line RNA sequence identified enrichment of growth-related pathways and conspicuous deficiency in aquaporins and inward rectifier K+ channels. As a test of utility, RNA sequence data from Zika-infected cells were mapped to the C6/36 genome and transcriptome assemblies. Host subtraction reduced the data set by 89%, enabling faster characterization of nonhost reads.

CONCLUSIONS: The C6/36 genome sequence and annotation should enable additional uses of the cell line to study arbovirus vector interactions and interventions aimed at restricting the spread of human disease.}, } @article {pmid29324887, year = {2018}, author = {Irigoyen, AJ and Rojo, I and Calò, A and Trobbiani, G and Sánchez-Carnero, N and García-Charton, JA}, title = {The "Tracked Roaming Transect" and distance sampling methods increase the efficiency of underwater visual censuses.}, journal = {PloS one}, volume = {13}, number = {1}, pages = {e0190990}, pmid = {29324887}, issn = {1932-6203}, mesh = {Animals ; Biodiversity ; Coral Reefs ; Environmental Monitoring/instrumentation/*methods ; *Fishes/classification ; Geographic Information Systems ; Humans ; *Vision, Ocular ; }, abstract = {Underwater visual census (UVC) is the most common approach for estimating diversity, abundance and size of reef fishes in shallow and clear waters. Abundance estimation through UVC is particularly problematic in species occurring at low densities and/or highly aggregated because of their high variability at both spatial and temporal scales. The statistical power of experiments involving UVC techniques may be increased by augmenting the number of replicates or the area surveyed. In this work we present and test the efficiency of an UVC method based on diver towed GPS, the Tracked Roaming Transect (TRT), designed to maximize transect length (and thus the surveyed area) with respect to diving time invested in monitoring, as compared to Conventional Strip Transects (CST). Additionally, we analyze the effect of increasing transect width and length on the precision of density estimates by comparing TRT vs. CST methods using different fixed widths of 6 and 20 m (FW3 and FW10, respectively) and the Distance Sampling (DS) method, in which perpendicular distance of each fish or group of fishes to the transect line is estimated by divers up to 20 m from the transect line. The TRT was 74% more time and cost efficient than the CST (all transect widths considered together) and, for a given time, the use of TRT and/or increasing the transect width increased the precision of density estimates. In addition, since with the DS method distances of fishes to the transect line have to be estimated, and not measured directly as in terrestrial environments, errors in estimations of perpendicular distances can seriously affect DS density estimations. To assess the occurrence of distance estimation errors and their dependence on the observer's experience, a field experiment using wooden fish models was performed. We tested the precision and accuracy of density estimators based on fixed widths and the DS method. The accuracy of the estimates was measured comparing the actual total abundance with those estimated by divers using FW3, FW10, and DS estimators. Density estimates differed by 13% (range 0.1-31%) from the actual values (average = 13.09%; median = 14.16%). Based on our results we encourage the use of the Tracked Roaming Transect with Distance Sampling (TRT+DS) method for improving density estimates of species occurring at low densities and/or highly aggregated, as well as for exploratory rapid-assessment surveys in which divers could gather spatial ecological and ecosystem information on large areas during UVC.}, } @article {pmid29322387, year = {2018}, author = {Zhang, M and Zhang, Z and Li, Z and Hong, M and Zhou, X and Zhou, S and Zhang, J and Hull, V and Huang, J and Zhang, H}, title = {Giant panda foraging and movement patterns in response to bamboo shoot growth.}, journal = {Environmental science and pollution research international}, volume = {25}, number = {9}, pages = {8636-8643}, pmid = {29322387}, issn = {1614-7499}, support = {WPC-20 (15-18) -03//Wolong Club Foundation/ ; SD1115//Giant Panda International Cooperation Research Project/ ; }, mesh = {Animals ; Biological Phenomena ; China ; Diet ; Ecosystem ; Environmental Monitoring/*methods ; Geographic Information Systems ; Herbivory/*physiology ; Poaceae/*growth & development ; Seasons ; Spatio-Temporal Analysis ; Ursidae/*physiology ; }, abstract = {Diet plays a pivotal role in dictating behavioral patterns of herbivorous animals, particularly specialist species. The giant panda (Ailuropoda melanoleuca) is well-known as a bamboo specialist. In the present study, the response of giant pandas to spatiotemporal variation of bamboo shoots was explored using field surveys and GPS collar tracking. Results show the dynamics in panda-bamboo space-time relationships that have not been previously articulated. For instance, we found a higher bamboo stump height of foraged bamboo with increasing elevation, places where pandas foraged later in spring when bamboo shoots become more fibrous and woody. The time required for shoots to reach optimum height for foraging was significantly delayed as elevation increased, a pattern which corresponded with panda elevational migration patterns beginning from the lower elevational end of Fargesia robusta distribution and gradually shifting upward until the end of the shooting season. These results indicate that giant pandas can respond to spatiotemporal variation of bamboo resources, such as available shoots. Anthropogenic interference of low-elevation F. robusta habitat should be mitigated, and conservation attention and increased monitoring should be given to F. robusta areas at the low- and mid-elevation ranges, particularly in the spring shooting season.}, } @article {pmid29321916, year = {2018}, author = {Suzuki, R and Matsubayashi, S and Saito, F and Murate, T and Masuda, T and Yamamoto, K and Kojima, R and Nakadai, K and Okuno, HG}, title = {A spatiotemporal analysis of acoustic interactions between great reed warblers (Acrocephalus arundinaceus) using microphone arrays and robot audition software HARK.}, journal = {Ecology and evolution}, volume = {8}, number = {1}, pages = {812-825}, pmid = {29321916}, issn = {2045-7758}, abstract = {Acoustic interactions are important for understanding intra- and interspecific communication in songbird communities from the viewpoint of soundscape ecology. It has been suggested that birds may divide up sound space to increase communication efficiency in such a manner that they tend to avoid overlap with other birds when they sing. We are interested in clarifying the dynamics underlying the process as an example of complex systems based on short-term behavioral plasticity. However, it is very problematic to manually collect spatiotemporal patterns of acoustic events in natural habitats using data derived from a standard single-channel recording of several species singing simultaneously. Our purpose here was to investigate fine-scale spatiotemporal acoustic interactions of the great reed warbler. We surveyed spatial and temporal patterns of several vocalizing color-banded great reed warblers (Acrocephalus arundinaceus) using an open-source software for robot audition HARK (Honda Research Institute Japan Audition for Robots with Kyoto University) and three new 16-channel, stand-alone, and water-resistant microphone arrays, named DACHO spread out in the bird's habitat. We first show that our system estimated the location of two color-banded individuals' song posts with mean error distance of 5.5 ± 4.5 m from the location of observed song posts. We then evaluated the temporal localization accuracy of the songs by comparing the duration of localized songs around the song posts with those annotated by human observers, with an accuracy score of average 0.89 for one bird that stayed at one song post. We further found significant temporal overlap avoidance and an asymmetric relationship between songs of the two singing individuals, using transfer entropy. We believe that our system and analytical approach contribute to a better understanding of fine-scale acoustic interactions in time and space in bird communities.}, } @article {pmid29321862, year = {2018}, author = {Robeson, MS and Khanipov, K and Golovko, G and Wisely, SM and White, MD and Bodenchuck, M and Smyser, TJ and Fofanov, Y and Fierer, N and Piaggio, AJ}, title = {Assessing the utility of metabarcoding for diet analyses of the omnivorous wild pig (Sus scrofa).}, journal = {Ecology and evolution}, volume = {8}, number = {1}, pages = {185-196}, pmid = {29321862}, issn = {2045-7758}, abstract = {Wild pigs (Sus scrofa) are an invasive species descended from both domestic swine and Eurasian wild boar that was introduced to North America during the early 1500s. Wild pigs have since become the most abundant free-ranging exotic ungulate in the United States. Large and ever-increasing populations of wild pigs negatively impact agriculture, sport hunting, and native ecosystems with costs estimated to exceed $1.5 billion/year within the United States. Wild pigs are recognized as generalist feeders, able to exploit a broad array of locally available food resources, yet their feeding behaviors remain poorly understood as partially digested material is often unidentifiable through traditional stomach content analyses. To overcome the limitation of stomach content analyses, we developed a DNA sequencing-based protocol to describe the plant and animal diet composition of wild pigs. Additionally, we developed and evaluated blocking primers to reduce the amplification and sequencing of host DNA, thus providing greater returns of sequences from diet items. We demonstrate that the use of blocking primers produces significantly more sequencing reads per sample from diet items, which increases the robustness of ascertaining animal diet composition with molecular tools. Further, we show that the overall plant and animal diet composition is significantly different between the three areas sampled, demonstrating this approach is suitable for describing differences in diet composition among the locations.}, } @article {pmid29321298, year = {2018}, author = {Hung, KJ and Kingston, JM and Albrecht, M and Holway, DA and Kohn, JR}, title = {The worldwide importance of honey bees as pollinators in natural habitats.}, journal = {Proceedings. Biological sciences}, volume = {285}, number = {1870}, pages = {}, pmid = {29321298}, issn = {1471-2954}, mesh = {Animals ; Bees/*physiology ; Behavior, Animal/*physiology ; Crops, Agricultural/physiology ; Datasets as Topic ; *Ecosystem ; Flowers/physiology ; Honey ; Pollen ; *Pollination ; Regression Analysis ; }, abstract = {The western honey bee (Apis mellifera) is the most frequent floral visitor of crops worldwide, but quantitative knowledge of its role as a pollinator outside of managed habitats is largely lacking. Here we use a global dataset of 80 published plant-pollinator interaction networks as well as pollinator effectiveness measures from 34 plant species to assess the importance of A. mellifera in natural habitats. Apis mellifera is the most frequent floral visitor in natural habitats worldwide, averaging 13% of floral visits across all networks (range 0-85%), with 5% of plant species recorded as being exclusively visited by A. mellifera For 33% of the networks and 49% of plant species, however, A. mellifera visitation was never observed, illustrating that many flowering plant taxa and assemblages remain dependent on non-A. mellifera visitors for pollination. Apis mellifera visitation was higher in warmer, less variable climates and on mainland rather than island sites, but did not differ between its native and introduced ranges. With respect to single-visit pollination effectiveness, A. mellifera did not differ from the average non-A. mellifera floral visitor, though it was generally less effective than the most effective non-A. mellifera visitor. Our results argue for a deeper understanding of how A. mellifera, and potential future changes in its range and abundance, shape the ecology, evolution, and conservation of plants, pollinators, and their interactions in natural habitats.}, } @article {pmid29320533, year = {2018}, author = {Bouwer, FL and Burgoyne, JA and Odijk, D and Honing, H and Grahn, JA}, title = {What makes a rhythm complex? The influence of musical training and accent type on beat perception.}, journal = {PloS one}, volume = {13}, number = {1}, pages = {e0190322}, pmid = {29320533}, issn = {1932-6203}, mesh = {Adolescent ; Adult ; Aged ; *Auditory Perception ; Female ; Humans ; Male ; Middle Aged ; *Music ; }, abstract = {Perception of a regular beat in music is inferred from different types of accents. For example, increases in loudness cause intensity accents, and the grouping of time intervals in a rhythm creates temporal accents. Accents are expected to occur on the beat: when accents are "missing" on the beat, the beat is more difficult to find. However, it is unclear whether accents occurring off the beat alter beat perception similarly to missing accents on the beat. Moreover, no one has examined whether intensity accents influence beat perception more or less strongly than temporal accents, nor how musical expertise affects sensitivity to each type of accent. In two experiments, we obtained ratings of difficulty in finding the beat in rhythms with either temporal or intensity accents, and which varied in the number of accents on the beat as well as the number of accents off the beat. In both experiments, the occurrence of accents on the beat facilitated beat detection more in musical experts than in musical novices. In addition, the number of accents on the beat affected beat finding more in rhythms with temporal accents than in rhythms with intensity accents. The effect of accents off the beat was much weaker than the effect of accents on the beat and appeared to depend on musical expertise, as well as on the number of accents on the beat: when many accents on the beat are missing, beat perception is quite difficult, and adding accents off the beat may not reduce beat perception further. Overall, the different types of accents were processed qualitatively differently, depending on musical expertise. Therefore, these findings indicate the importance of designing ecologically valid stimuli when testing beat perception in musical novices, who may need different types of accent information than musical experts to be able to find a beat. Furthermore, our findings stress the importance of carefully designing rhythms for social and clinical applications of beat perception, as not all listeners treat all rhythms alike.}, } @article {pmid29318843, year = {2017}, author = {Xiao, JL and Zhang, XB and Liu, YC and Li, M and Li, B and Shan, YQ and Qu, XB}, title = {[Quality of Schisandrae Chinensis Fructus regionalization based on GIS technology].}, journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica}, volume = {42}, number = {22}, pages = {4408-4413}, doi = {10.19540/j.cnki.cjcmm.2017.0192}, pmid = {29318843}, issn = {1001-5302}, mesh = {China ; Drugs, Chinese Herbal/*standards ; Fruit/chemistry ; *Geographic Information Systems ; Plants, Medicinal/chemistry ; Quality Control ; Schisandra/*chemistry ; }, abstract = {This paper is aims to clarify the spatial distribution of high quality medicinal materials Schisandrae Chinensis Fructus. Based on investigation and field investigation, the samples and distribution information of Schisandrae Chinensis Fructus were collected. Based on the data of four kinds of lignin chemical constituents, ecological environment factors and spatial distribution data of Schisandrae Chinensis Fructus, using GIS technology, maximum information entropy model and SPSS statistical analysis method for regionalizing the quality of Schisandrae Chinensis Fructus. The results showed that Schisandrae Chinensis Fructus was mainly distributed in the northeast of Liaoning, east of Jilin, east of Heilongjiang. The content of schisandrin was higher in the samples from northeastern part of Jilin province and the northeastern part of Liaoning province, The content of deoxyschizandrin was higher in the samples from middle of Jilin province and northeastern Hebei province, where the content of schisandrin B was higher in the samples from Jilin area, The higher schisantherin A sample were from southeast of Jilin and northeast of Liaoning. Considering the content of four components in Schisandrae Chinensis Fructus, the quality of Schisandrae Chinensis Fructus was concentrated in the southeast of Jilin and the northeastern part of Liaoning.}, } @article {pmid29318840, year = {2017}, author = {Dong, YB and Luo, Y and Zhu, C and Peng, WF and Xu, XL and Fang, QM}, title = {[Application of remote sensing and GIS in study of suitability distribution of Swertia mussotii, a Tibetan medicine in Sichuan province].}, journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica}, volume = {42}, number = {22}, pages = {4387-4394}, doi = {10.19540/j.cnki.cjcmm.2017.0189}, pmid = {29318840}, issn = {1001-5302}, mesh = {China ; Ecology ; *Geographic Information Systems ; Medicine, Tibetan Traditional ; *Plant Dispersal ; Plants, Medicinal/growth & development ; *Remote Sensing Technology ; Swertia/*growth & development ; }, abstract = {Swertia mussotii is a kind of rare medicinal materials, the relevant researches are mainly concentrated on its medicinal efficacy and medicinal value till now, researches of adaptive distribution by applying remote sensing and GIS are relatively less. This study is to analyze the adaptive distribution of S.mussotii in Sichuan province by applying remote sensing and GIS technology, and provide scientific basis for the protection and development of wild resources, artificial cultivation and adjustment of Chinese medicine industrial distribution in Sichuan province. Based on literature review and ecological factors such as altitude, annual precipitation and annual average temperature, this study extracted ecological factors, overlay analysis in GIS, as well as combining GPS field validation data by means of remote sensing and GIS, discusses the adaptive distribution of SMF sin Sichuan province. ①The area of adaptive distribution of S. mussotii in Sichuan province is 1 543.749 km[2], mainly in Dege county, Ganzi county, Daofu county, Kangding county, Barkam, Jinchuan county, Xiaojin county, Danba county, Daocheng county, Xiangcheng county, Xinlong county, Aba county, Muli county and other counties and cities, accounts for about 7.25% in total area. ② Combining statistical information and field validation, this study found that S. mussotii adaptive distribution gained by remote sensing and GIS is in conformity with its actual distribution. The study shows that remote sensing and GIS technology are feasible to obtain the S. mussotii adaptive distribution, they can further be applied to studies on adaptive distributions of other rare Chinese medicinal herb.}, } @article {pmid29318839, year = {2017}, author = {Luo, Y and Dong, YB and Zhu, C and Peng, WF and Fang, QM and Xu, XL}, title = {[Research on suitable distribution of Paris yunnanensis based on remote sensing and GIS].}, journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica}, volume = {42}, number = {22}, pages = {4378-4386}, doi = {10.19540/j.cnki.cjcmm.2017.0188}, pmid = {29318839}, issn = {1001-5302}, mesh = {China ; *Geographic Information Systems ; Melanthiaceae/*growth & development ; *Plant Dispersal ; Plants, Medicinal/growth & development ; *Remote Sensing Technology ; Soil ; }, abstract = {Paris yunnanensis is a kind of rare medicinal herb, having a very high medicinal value. Studying its suitable ecological condition can provide a basis for its rational exploitation, artificial cultivation, and sustainable utilization. A practicable method in this paper has been proposed to research the suitable regional distribution of P. yunnanensis in Sichuan province. By the case study of P. yunnanensis in Sichuan province, and according to related literatures, the suitable ecological condition of P. yunnanensis such as altitude, mean annual temperature (MAT), annual precipitation, regional slope, slope ranges, vegetative cover, and soil types was analyzed following remote sensing (RS) and GIS.The appropriate distribution regionof P. yunnanensis and its area were extracted based on RS and GIS technology,combing with the information of the field validation data. The results showed that the concentrated distribution regions in counties of Sichuan province were, Liangshan prefecture, Aba prefecture, Sertar county of Ganzi prefecture, Panzhihua city, Ya'an city, Chengdu city, Meishan city, Leshan city, Yibin city, Neijiang city, Luzhou city, Bazhong city, Nanchong city, Guangyuan city and other cities and counties area.The suitable distribution area in Sichuan is about 7 338 km[2], accounting for 3.02% of the total study regional area. The analysis result has high consistency with the filed validation data, and the research method for P. yunnanensis distribution region based onspatial overlay analysis and the extracted the information of land usage and ecological factors following the RS and GIS is reliable.}, } @article {pmid29318837, year = {2017}, author = {Wu, XJ and Zhang, XB and Guo, LP and Yu, Y and Huang, LQ}, title = {[Study on distribution division of Codonopsis Radix].}, journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica}, volume = {42}, number = {22}, pages = {4368-4372}, doi = {10.19540/j.cnki.cjcmm.2017.0186}, pmid = {29318837}, issn = {1001-5302}, mesh = {Altitude ; China ; Codonopsis/*growth & development ; Ecology ; Geographic Information Systems ; *Plant Dispersal ; Plants, Medicinal/*growth & development ; }, abstract = {This paper is aimed to clarify the distribution of Codonopsis Radix in China and search the main ecological factors that affect the suitability distribution. Through literature reading, National Specimen Information Infrastructure researching, field investigation and general survey of Chinese medicine resources, the distribution information was acquired. The MaxEnt model and ArcGIS technology were applied to analyze the main environmental factors influencing the suitability of Codonopsis Radix with integrated 55 environmental factors. The results showed the precipitation and altitude were the major factors impacting the ecology suitable of Codonopsis Radix. The ecological suitable region of C. pilosula was mainly concentrated in south Gansu, Shanxi, Shanxi, Ningxia and, and the ecological suitable region of C. pilosula var. modesta was mainly concentrated in south Gansu, northwest Guizhou, northeast Sichuan, and the ecological suitable region of C. tangshen was mainly concentrated in west Hubei, east Chongqing, middle Sichuan. Combined with the investigation and cultivation of Codonopsis Radix distribution information, the results of ecological suitability of Codonopsis Radix were verified. The ecological suitability distribution result of Codonopsis Radix was consistent with each species actual distribution, which could provide scientific basis for carrying out the rational cultivation of Codonopsis Radix.}, } @article {pmid29316977, year = {2018}, author = {Pragman, AA and Lyu, T and Baller, JA and Gould, TJ and Kelly, RF and Reilly, CS and Isaacson, RE and Wendt, CH}, title = {The lung tissue microbiota of mild and moderate chronic obstructive pulmonary disease.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {7}, pmid = {29316977}, issn = {2049-2618}, support = {1IK2CX001095//U.S. Department of Veterans Affairs/International ; NA//Minnesota Veterans Medical Research and Education Foundation/International ; UL1 TR000114/TR/NCATS NIH HHS/United States ; 348261//American Lung Association/International ; IK2 CX001095/CX/CSRD VA/United States ; T32 AI055433/AI/NIAID NIH HHS/United States ; 5T32AI055433//National Institute of Allergy and Infectious Diseases/International ; 8UL1TR000114/TR/NCATS NIH HHS/United States ; }, mesh = {Aged ; Aged, 80 and over ; Animals ; Bacteria/*classification/genetics/isolation & purification ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Female ; Humans ; Lung/*microbiology ; Male ; Microbiota ; Middle Aged ; Moths/microbiology ; Nose/microbiology ; Pulmonary Disease, Chronic Obstructive/*microbiology/*surgery ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: Oral taxa are often found in the chronic obstructive pulmonary disease (COPD) lung microbiota, but it is not clear if this is due to a physiologic process such as aspiration or experimental contamination at the time of specimen collection.

METHODS: Microbiota samples were obtained from nine subjects with mild or moderate COPD by swabbing lung tissue and upper airway sites during lung lobectomy. Lung specimens were not contaminated with upper airway taxa since they were obtained surgically. The microbiota were analyzed with 16S rRNA gene qPCR and 16S rRNA gene hypervariable region 3 (V3) sequencing. Data analyses were performed using QIIME, SourceTracker, and R.

RESULTS: Streptococcus was the most common genus in the oral, bronchial, and lung tissue samples, and multiple other taxa were present in both the upper and lower airways. Each subject's own bronchial and lung tissue microbiota were more similar to each other than were the bronchial and lung tissue microbiota of two different subjects (permutation test, p = 0.0139), indicating more within-subject similarity than between-subject similarity at these two lung sites. Principal coordinate analysis of all subject samples revealed clustering by anatomic sampling site (PERMANOVA, p = 0.001), but not by subject. SourceTracker analysis found that the sources of the lung tissue microbiota were 21.1% (mean) oral microbiota, 8.7% nasal microbiota, and 70.1% unknown. An analysis using the neutral theory of community ecology revealed that the lung tissue microbiota closely reflects the bronchial, oral, and nasal microbiota (immigration parameter estimates 0.69, 0.62, and 0.74, respectively), with some evidence of ecologic drift occurring in the lung tissue.

CONCLUSION: This is the first study to evaluate the mild-moderate COPD lung tissue microbiota without potential for upper airway contamination of the lung samples. In our small study of subjects with COPD, we found oral and nasal bacteria in the lung tissue microbiota, confirming that aspiration is a source of the COPD lung microbiota.}, } @article {pmid29315317, year = {2018}, author = {Marshall, HH and Griffiths, DJ and Mwanguhya, F and Businge, R and Griffiths, AGF and Kyabulima, S and Mwesige, K and Sanderson, JL and Thompson, FJ and Vitikainen, EIK and Cant, MA}, title = {Data collection and storage in long-term ecological and evolutionary studies: The Mongoose 2000 system.}, journal = {PloS one}, volume = {13}, number = {1}, pages = {e0190740}, pmid = {29315317}, issn = {1932-6203}, mesh = {Animals ; *Biological Evolution ; Computers ; Data Collection ; Databases, Factual ; *Ecosystem ; Environmental Monitoring/*methods ; Female ; Herpestidae ; Humans ; Male ; Pregnancy ; Smartphone ; Uganda ; }, abstract = {Studying ecological and evolutionary processes in the natural world often requires research projects to follow multiple individuals in the wild over many years. These projects have provided significant advances but may also be hampered by needing to accurately and efficiently collect and store multiple streams of the data from multiple individuals concurrently. The increase in the availability and sophistication of portable computers (smartphones and tablets) and the applications that run on them has the potential to address many of these data collection and storage issues. In this paper we describe the challenges faced by one such long-term, individual-based research project: the Banded Mongoose Research Project in Uganda. We describe a system we have developed called Mongoose 2000 that utilises the potential of apps and portable computers to meet these challenges. We discuss the benefits and limitations of employing such a system in a long-term research project. The app and source code for the Mongoose 2000 system are freely available and we detail how it might be used to aid data collection and storage in other long-term individual-based projects.}, } @article {pmid29315312, year = {2018}, author = {Cyronak, T and Andersson, AJ and Langdon, C and Albright, R and Bates, NR and Caldeira, K and Carlton, R and Corredor, JE and Dunbar, RB and Enochs, I and Erez, J and Eyre, BD and Gattuso, JP and Gledhill, D and Kayanne, H and Kline, DI and Koweek, DA and Lantz, C and Lazar, B and Manzello, D and McMahon, A and Meléndez, M and Page, HN and Santos, IR and Schulz, KG and Shaw, E and Silverman, J and Suzuki, A and Teneva, L and Watanabe, A and Yamamoto, S}, title = {Taking the metabolic pulse of the world's coral reefs.}, journal = {PloS one}, volume = {13}, number = {1}, pages = {e0190872}, pmid = {29315312}, issn = {1932-6203}, mesh = {Acids/analysis ; Carbon/analysis ; *Coral Reefs ; Ecosystem ; Eutrophication ; Global Warming ; Hydrogen-Ion Concentration ; Seawater/chemistry ; }, abstract = {Worldwide, coral reef ecosystems are experiencing increasing pressure from a variety of anthropogenic perturbations including ocean warming and acidification, increased sedimentation, eutrophication, and overfishing, which could shift reefs to a condition of net calcium carbonate (CaCO3) dissolution and erosion. Herein, we determine the net calcification potential and the relative balance of net organic carbon metabolism (net community production; NCP) and net inorganic carbon metabolism (net community calcification; NCC) within 23 coral reef locations across the globe. In light of these results, we consider the suitability of using these two metrics developed from total alkalinity (TA) and dissolved inorganic carbon (DIC) measurements collected on different spatiotemporal scales to monitor coral reef biogeochemistry under anthropogenic change. All reefs in this study were net calcifying for the majority of observations as inferred from alkalinity depletion relative to offshore, although occasional observations of net dissolution occurred at most locations. However, reefs with lower net calcification potential (i.e., lower TA depletion) could shift towards net dissolution sooner than reefs with a higher potential. The percent influence of organic carbon fluxes on total changes in dissolved inorganic carbon (DIC) (i.e., NCP compared to the sum of NCP and NCC) ranged from 32% to 88% and reflected inherent biogeochemical differences between reefs. Reefs with the largest relative percentage of NCP experienced the largest variability in seawater pH for a given change in DIC, which is directly related to the reefs ability to elevate or suppress local pH relative to the open ocean. This work highlights the value of measuring coral reef carbonate chemistry when evaluating their susceptibility to ongoing global environmental change and offers a baseline from which to guide future conservation efforts aimed at preserving these valuable ecosystems.}, } @article {pmid29314756, year = {2018}, author = {Wang, WY and Srivathsan, A and Foo, M and Yamane, SK and Meier, R}, title = {Sorting specimen-rich invertebrate samples with cost-effective NGS barcodes: Validating a reverse workflow for specimen processing.}, journal = {Molecular ecology resources}, volume = {18}, number = {3}, pages = {490-501}, doi = {10.1111/1755-0998.12751}, pmid = {29314756}, issn = {1755-0998}, mesh = {Animals ; Ants/classification/*genetics ; Biodiversity ; Classification/methods ; DNA Barcoding, Taxonomic/methods ; Databases, Genetic ; Invertebrates/classification/*genetics ; Sequence Analysis, DNA ; Workflow ; }, abstract = {Biologists frequently sort specimen-rich samples to species. This process is daunting when based on morphology, and disadvantageous if performed using molecular methods that destroy vouchers (e.g., metabarcoding). An alternative is barcoding every specimen in a bulk sample and then presorting the specimens using DNA barcodes, thus mitigating downstream morphological work on presorted units. Such a "reverse workflow" is too expensive using Sanger sequencing, but we here demonstrate that is feasible with an next-generation sequencing (NGS) barcoding pipeline that allows for cost-effective high-throughput generation of short specimen-specific barcodes (313 bp of COI; laboratory cost <$0.50 per specimen) through next-generation sequencing of tagged amplicons. We applied our approach to a large sample of tropical ants, obtaining barcodes for 3,290 of 4,032 specimens (82%). NGS barcodes and their corresponding specimens were then sorted into molecular operational taxonomic units (mOTUs) based on objective clustering and Automated Barcode Gap Discovery (ABGD). High diversity of 88-90 mOTUs (4% clustering) was found and morphologically validated based on preserved vouchers. The mOTUs were overwhelmingly in agreement with morphospecies (match ratio 0.95 at 4% clustering). Because of lack of coverage in existing barcode databases, only 18 could be accurately identified to named species, but our study yielded new barcodes for 48 species, including 28 that are potentially new to science. With its low cost and technical simplicity, the NGS barcoding pipeline can be implemented by a large range of laboratories. It accelerates invertebrate species discovery, facilitates downstream taxonomic work, helps with building comprehensive barcode databases and yields precise abundance information.}, } @article {pmid29313491, year = {2018}, author = {Riemer, K and Guralnick, RP and White, EP}, title = {No general relationship between mass and temperature in endothermic species.}, journal = {eLife}, volume = {7}, number = {}, pages = {}, pmid = {29313491}, issn = {2050-084X}, mesh = {Animals ; Biological Variation, Population ; Birds ; *Body Weights and Measures ; *Environmental Exposure ; Mammals ; Temperature ; }, abstract = {Bergmann's rule is a widely-accepted biogeographic rule stating that individuals within a species are smaller in warmer environments. While there are many single-species studies and integrative reviews documenting this pattern, a data-intensive approach has not been used yet to determine the generality of this pattern. We assessed the strength and direction of the intraspecific relationship between temperature and individual mass for 952 bird and mammal species. For eighty-seven percent of species, temperature explained less than 10% of variation in mass, and for 79% of species the correlation was not statistically significant. These results suggest that Bergmann's rule is not general and temperature is not a dominant driver of biogeographic variation in mass. Further understanding of size variation will require integrating multiple processes that influence size. The lack of dominant temperature forcing weakens the justification for the hypothesis that global warming could result in widespread decreases in body size.}, } @article {pmid29311639, year = {2018}, author = {Segobola, J and Adriaenssens, E and Tsekoa, T and Rashamuse, K and Cowan, D}, title = {Exploring Viral Diversity in a Unique South African Soil Habitat.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {111}, pmid = {29311639}, issn = {2045-2322}, mesh = {Bacteriophages/classification/genetics ; *Biodiversity ; Computational Biology/methods ; Genome, Viral ; Metagenome ; Metagenomics/methods ; Phylogeny ; *Soil Microbiology ; South Africa ; Viruses/*classification/genetics/ultrastructure ; }, abstract = {The Kogelberg Biosphere Reserve in the Cape Floral Kingdom in South Africa is known for its unique plant biodiversity. The potential presence of unique microbial and viral biodiversity associated with this unique plant biodiversity led us to explore the fynbos soil using metaviromic techniques. In this study, metaviromes of a soil community from the Kogelberg Biosphere Reserve has been characterised in detail for the first time. Metaviromic DNA was recovered from soil and sequenced by Next Generation Sequencing. The MetaVir, MG-RAST and VIROME bioinformatics pipelines were used to analyse taxonomic composition, phylogenetic and functional assessments of the sequences. Taxonomic composition revealed members of the order Caudovirales, in particular the family Siphoviridae, as prevalent in the soil samples and other compared viromes. Functional analysis and other metaviromes showed a relatively high frequency of phage-related and structural proteins. Phylogenetic analysis of PolB, PolB2, terL and T7gp17 genes indicated that many viral sequences are closely related to the order Caudovirales, while the remainder were distinct from known isolates. The use of single virome which only includes double stranded DNA viruses limits this study. Novel phage sequences were detected, presenting an opportunity for future studies aimed at targeting novel genetic resources for applied biotechnology.}, } @article {pmid29309185, year = {2017}, author = {Brinberg, M and Fosco, GM and Ram, N}, title = {Examining inter-family differences in intra-family (parent-adolescent) dynamics using grid-sequence analysis.}, journal = {Journal of family psychology : JFP : journal of the Division of Family Psychology of the American Psychological Association (Division 43)}, volume = {31}, number = {8}, pages = {994-1004}, pmid = {29309185}, issn = {1939-1293}, support = {R01 HD076994/HD/NICHD NIH HHS/United States ; T32 LM012415/LM/NLM NIH HHS/United States ; //Karl R. and Diane Wendle Fink Early Career Professorship for the Study of Families/ ; UL1 TR000127/TR/NCATS NIH HHS/United States ; //Penn State Social Science Research Institute/ ; P2C HD041025/HD/NICHD NIH HHS/United States ; UL1 TR002014/TR/NCATS NIH HHS/United States ; /NH/NIH HHS/United States ; }, mesh = {Adolescent ; *Adolescent Behavior ; Adult ; *Data Interpretation, Statistical ; *Ecological Momentary Assessment ; Female ; Humans ; Male ; Middle Aged ; *Parent-Child Relations ; Systems Theory ; }, abstract = {Family systems theorists have forwarded a set of theoretical principles meant to guide family scientists and practitioners in their conceptualization of patterns of family interaction-intra-family dynamics-that, over time, give rise to family and individual dysfunction and/or adaptation. In this article, we present an analytic approach that merges state space grid methods adapted from the dynamic systems literature with sequence analysis methods adapted from molecular biology into a "grid-sequence" method for studying inter-family differences in intra-family dynamics. Using dyadic data from 86 parent-adolescent dyads who provided up to 21 daily reports about connectedness, we illustrate how grid-sequence analysis can be used to identify a typology of intrafamily dynamics and to inform theory about how specific types of intrafamily dynamics contribute to adolescent behavior problems and family members' mental health. Methodologically, grid-sequence analysis extends the toolbox of techniques for analysis of family experience sampling and daily diary data. Substantively, we identify patterns of family level microdynamics that may serve as new markers of risk/protective factors and potential points for intervention in families. (PsycINFO Database Record}, } @article {pmid29305629, year = {2018}, author = {Solon, AJ and Vimercati, L and Darcy, JL and Arán, P and Porazinska, D and Dorador, C and Farías, ME and Schmidt, SK}, title = {Microbial Communities of High-Elevation Fumaroles, Penitentes, and Dry Tephra "Soils" of the Puna de Atacama Volcanic Zone.}, journal = {Microbial ecology}, volume = {76}, number = {2}, pages = {340-351}, pmid = {29305629}, issn = {1432-184X}, support = {DEB-1258160//National Science Foundation/ ; FA9550-14-1-0006//Air Force Office of Scientific Research/ ; }, mesh = {Archaea/classification/genetics ; Bacteria/classification/genetics ; *Bacterial Physiological Phenomena ; Biodiversity ; Chile ; Cluster Analysis ; Computational Biology ; Cyanobacteria/classification ; Desert Climate ; Exobiology ; *Extreme Environments ; *Microbiota/genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Soil ; *Soil Microbiology ; Temperature ; }, abstract = {The aim of this study was to understand the spatial distribution of microbial communities (18S and 16S rRNA genes) across one of the harshest terrestrial landscapes on Earth. We carried out Illumina sequencing using samples from two expeditions to the high slopes (up to 6050 m.a.s.l.) of Volcán Socompa and Llullaillaco to describe the microbial communities associated with the extremely dry tephra compared to areas that receive water from fumaroles and ice fields made up of nieves penitentes. There were strong spatial patterns relative to these landscape features with the most diverse (alpha diversity) communities being associated with fumaroles. Penitentes did not significantly increase alpha diversity compared to dry tephra at the same elevation (5825 m.a.s.l.) on Volcán Socompa, but the structure of the 18S community (beta diversity) was significantly affected by the presence of penitentes on both Socompa and Llullaillaco. In addition, the 18S community was significantly different in tephra wetted by penitentes versus dry tephra sites across many elevations on Llullaillaco. Traditional phototrophs (algae and cyanobacteria) were abundant in wetter tephra associated with fumaroles, and algae (but not cyanobacteria) were common in tephra associated with penitentes. Dry tephra had neither algae nor cyanobacteria but did host potential phototrophs in the Rhodospirillales on Volcán Llullaillaco, but not on Socompa. These results provide new insights into the distribution of microbes across one of the most extreme terrestrial environments on Earth and provide the first ever glimpse of life associated with nieves penitentes, spire-shaped ice structures that are widespread across the mostly unexplored high-elevation Andean Central Volcanic Zone.}, } @article {pmid29300904, year = {2018}, author = {Tanser, F and Bärnighausen, T and Dobra, A and Sartorius, B}, title = {Identifying 'corridors of HIV transmission' in a severely affected rural South African population: a case for a shift toward targeted prevention strategies.}, journal = {International journal of epidemiology}, volume = {47}, number = {2}, pages = {537-549}, pmid = {29300904}, issn = {1464-3685}, support = {R01 AI124389/AI/NIAID NIH HHS/United States ; R01 HD084233/HD/NICHD NIH HHS/United States ; }, mesh = {Adolescent ; Adult ; Age Distribution ; Cluster Analysis ; Cohort Studies ; Female ; HIV Infections/*epidemiology/prevention & control ; HIV Seropositivity/*epidemiology ; Humans ; Incidence ; Linear Models ; Logistic Models ; Male ; Middle Aged ; Rural Population ; Sex Distribution ; South Africa/epidemiology ; Young Adult ; }, abstract = {BACKGROUND: In the context of a severe generalized African HIV epidemic, the value of geographically targeted prevention interventions has only recently been given serious consideration. However, to date no study has performed a population-based analysis of the micro-geographical clustering of HIV incident infections, limiting the evidential support for such a strategy.

METHODS: We followed 17 984 HIV-uninfected individuals aged 15-54 in a population-based cohort in rural KwaZulu-Natal, South Africa, and observed individual HIV sero-conversions between 2004 and 2014. We geo-located all individuals to an exact homestead of residence (accuracy <2 m). We then employed a two-dimensional Gaussian kernel of radius 3 km to produce robust estimates of HIV incidence which vary across continuous geographical space. We also applied Tango's flexibly shaped spatial scan statistic to identify irregularly shaped clusters of high HIV incidence.

RESULTS: Between 2004 and 2014, we observed a total of 2 311 HIV sero-conversions over 70 534 person-years of observation, at an overall incidence of 3.3 [95% confidence interval (CI), 3.1-3.4] per 100 person-years. Three large irregularly-shaped clusters of new HIV infections (relative risk = 1.6, 1.7 and 2.3) were identified in two adjacent peri-urban communities near the National Road (P = 0.001, 0.015) as well as in a rural node bordering a recent coal mine development (P = 0.020), respectively. Together the clusters had a significantly higher age-sex standardized incidence of 5.1 (95% CI, 4.7-5.6) per 100 person-years compared with a standardized incidence of 3.0 per 100 person-years (95% CI, 2.9-3.2) in the remainder of the study area. Though these clusters comprise just 6.8% of the study area, they account for one out of every four sero-conversions observed over the study period.

CONCLUSIONS: Our study has revealed clear 'corridors of transmission' in this typical rural, hyper-endemic population. Even in a severely affected rural African population, an approach that seeks to provide preventive interventions to the most vulnerable geographies could be more effective and cost-effective in reducing the overall rate of new HIV infections. There is an urgent need to develop and test such interventions as part of an overall combination prevention approach.}, } @article {pmid29298748, year = {2018}, author = {Berrouiguet, S and Perez-Rodriguez, MM and Larsen, M and Baca-García, E and Courtet, P and Oquendo, M}, title = {From eHealth to iHealth: Transition to Participatory and Personalized Medicine in Mental Health.}, journal = {Journal of medical Internet research}, volume = {20}, number = {1}, pages = {e2}, pmid = {29298748}, issn = {1438-8871}, support = {KL2 TR001435/TR/NCATS NIH HHS/United States ; }, mesh = {Cell Phone/*instrumentation ; Data Mining/*methods ; Decision Making ; Humans ; Mental Health/*standards ; Precision Medicine/*standards ; Telemedicine/*methods ; }, abstract = {Clinical assessment in psychiatry is commonly based on findings from brief, regularly scheduled in-person appointments. Although critically important, this approach reduces assessment to cross-sectional observations that miss essential information about disease course. The mental health provider makes all medical decisions based on this limited information. Thanks to recent technological advances such as mobile phones and other personal devices, electronic health (eHealth) data collection strategies now can provide access to real-time patient self-report data during the interval between visits. Since mobile phones are generally kept on at all times and carried everywhere, they are an ideal platform for the broad implementation of ecological momentary assessment technology. Integration of these tools into medical practice has heralded the eHealth era. Intelligent health (iHealth) further builds on and expands eHealth by adding novel built-in data analysis approaches based on (1) incorporation of new technologies into clinical practice to enhance real-time self-monitoring, (2) extension of assessment to the patient's environment including caregivers, and (3) data processing using data mining to support medical decision making and personalized medicine. This will shift mental health care from a reactive to a proactive and personalized discipline.}, } @article {pmid29295652, year = {2019}, author = {Cavallo, M and Angilletta, C}, title = {Long-Lasting Neuropsychological Effects of a Computerized Cognitive Training in Patients Affected by Early Stage Alzheimer's Disease: Are They Stable Over Time?.}, journal = {Journal of applied gerontology : the official journal of the Southern Gerontological Society}, volume = {38}, number = {7}, pages = {1035-1044}, doi = {10.1177/0733464817750276}, pmid = {29295652}, issn = {1552-4523}, mesh = {Aged ; Alzheimer Disease/*psychology/*rehabilitation ; Cognitive Behavioral Therapy/*methods ; Early Diagnosis ; Executive Function ; Female ; Humans ; Male ; *Neuropsychological Tests ; Psychomotor Performance ; Therapy, Computer-Assisted/*methods ; Treatment Outcome ; }, abstract = {INTRODUCTION: We investigated the stability of effects of a computerized cognitive training previously administered to a large group of early stage Alzheimer's disease (AD) patients, as compared with a control group.

METHOD: Eighty AD patients were randomized in two groups and underwent a computerized cognitive training, or a control intervention.

RESULTS: A Repeated Measures General Linear Model (RM-GLM) showed a significant interaction effect for the following neuropsychological tests: the digit span forward and backward, and the two-syllable words test, as measures of short-term memory and working memory; the Rivermead Behavioural Memory Test (RBMT) story immediate and the RBMT story delayed, as measures of ecologically oriented memory; the Token test, as measure of language comprehension; and the Brixton test, as an executive functions measure.

CONCLUSION: Patients in the experimental group showed a significant improvement in various neuropsychological domains due to the training, and these effects decreased after 12 months.}, } @article {pmid29290833, year = {2017}, author = {Sousa, LVA and Paiva, LDS and Figueiredo, FWDS and Almeida, TCDC and Oliveira, FR and Adami, F}, title = {Trends in Stroke-Related Mortality in the ABC Region, São Paulo, Brazil: An Ecological Study Between 1997 and 2012.}, journal = {The open cardiovascular medicine journal}, volume = {11}, number = {}, pages = {111-119}, pmid = {29290833}, issn = {1874-1924}, abstract = {BACKGROUND: Stroke is the second leading cause of death and the third leading cause of physical disability in the world, with a high burden of morbidity and mortality, but it has been shown a reduction in mortality worldwide over the past two decades, especially in regions with higher income.

OBJECTIVE: The study analyzed the temporal trend and the factors associated with stroke-related mortality in the cities that make up the ABC region of São Paulo (Santo André, São Bernardo do Campo, São Caetano do Sul, Diadema, Mauá, Ribeirão Pires, and Rio Grande da Serra), in comparison to data from the capital city of São Paulo, in the state of São Paulo, Brazil.

METHOD: This was an ecological study conducted in 2017 using data from 1997 to 2012. Data were collected in 2017 from the Department of Informatics of the Brazilian Unified National Health System (DATASUS), where the Mortality Information System (SIM/SUS) was accessed. Linear regression analysis was used to estimate the temporal trend of stroke-related mortality according to sex, stroke subtypes, and regions. The confidence level adopted was 95%.

RESULTS: There was a reduction in the mortality rates stratified according to sex, age groups above 15 years, and subtypes of stroke. Mortality from hemorrhagic and non-specified stroke decreased in all regions. However, a significant reduction in ischemic stroke-related mortality was observed only in the ABC region and in Brazil.

CONCLUSION: The ABC region showed greater mortality due to stroke in males, the age group above 49 years, and non-specified stroke between 1997 and 2012.}, } @article {pmid29288361, year = {2018}, author = {Jiao, JY and Salam, N and Liu, L and Rao, MPN and Zhang, XT and Fang, BZ and Han, MX and Zhang, ZT and Chen, J and Zhao, J and Zhou, Y and Alkhalifah, DHM and Liu, Q and Xiao, M and Klenk, HP and Li, WJ}, title = {Genome sequence and comparative analysis of Jiangella alba YIM 61503[T] isolated from a medicinal plant Maytenus austroyunnanensis.}, journal = {Antonie van Leeuwenhoek}, volume = {111}, number = {5}, pages = {667-678}, doi = {10.1007/s10482-017-1010-8}, pmid = {29288361}, issn = {1572-9699}, support = {31670009//National Natural Science Foundation of China/ ; RGP-1438-0004//Deanship of Scientific Research at Princess Nourah bint Abdulrahman University/ ; }, mesh = {Actinobacteria/*classification/*genetics ; Computational Biology ; DNA, Bacterial/genetics ; Genome, Bacterial/*genetics ; Maytenus/*microbiology ; Models, Biological ; *Phylogeny ; Plants, Medicinal/*microbiology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {A draft genome sequence of Jiangella alba YIM 61503[T] revealed a genome size of 7,664,864 bp arranged in 33 scaffolds. The genome was predicted to contain 7196 predicted genes, including 51 coding for RNA. Phylogenetic and comparative analyses of the draft genome of J. alba YIM 61503[T] with the available genomes of other Jiangella species suggested a proximal similarity between strains J. alba YIM 61503[T] and J. muralis DSM 45357[T], while indicating a high divergence between J. gansuensis YIM 002[T] and other Jiangella species. The genome of J. alba YIM 61503[T] also revealed genes involved in indole-3-acetic acid biosynthesis and an alkylresorcinols gene cluster. Further, detection of phosphotransferase genes in the genome of all Jiangella species indicated that they can uptake and phosphorylate sugars. The presences of TreX-Z, TreS and OtsA-OtsB genes in some of the Jiangella strains also indicated a possible mechanism for their tolerance of high salinity. Besides providing new insights into its genetic features, our results suggested that J. alba YIM 61503[T] could be a potential strain for further genome mining studies. The release of this genome may, therefore, provide a better prospect for understanding "evolutionary taxonomy" about this genus in future.}, } @article {pmid29287805, year = {2018}, author = {Ghatee, MA and Haghdoost, AA and Kooreshnia, F and Kanannejad, Z and Parisaie, Z and Karamian, M and Moshfe, A}, title = {Role of environmental, climatic risk factors and livestock animals on the occurrence of cutaneous leishmaniasis in newly emerging focus in Iran.}, journal = {Journal of infection and public health}, volume = {11}, number = {3}, pages = {425-433}, doi = {10.1016/j.jiph.2017.12.004}, pmid = {29287805}, issn = {1876-035X}, mesh = {Animals ; Cattle/parasitology ; Cattle Diseases/epidemiology/parasitology/transmission ; *Climate ; *Environment ; Geographic Information Systems ; Leishmaniasis, Cutaneous/epidemiology/parasitology/transmission/*veterinary ; Livestock/*parasitology ; Rain ; Risk Factors ; Sheep/parasitology ; Sheep Diseases/*epidemiology/parasitology/transmission ; Temperature ; }, abstract = {INTRODUCTION: Occurrence of leishmaniasis is affected by various biological and environmental factors. Kohgiluye and Boyerahmad (K-B) province is an emerging focus of cutaneous leishmaniasis (CL) in Southwest Iran.

SUBJECTS AND METHODS: To elucidate some angles of occurrence of CL in this province, climatic and environmental factors and close proximity to livestock were studied by univariate and two multivariate logistic regression models. The dwelling addresses of 275 CL patients were obtained from Health Centers records for a 5 years period. The effect of mean annual temperature, minimum mean annual temperature, maximum mean annual temperature, mean annual rainfall, slope, elevation, land covers and close proximity to cattle and sheep/goat sheds on the occurrence of CL were analysed using geographical information systems (GIS) approach.

RESULTS: CL occurred in all counties with the most cases in Northwest, West and South semi-arid and warm regions. Land cover, slope, elevation and close proximity to cattle sheds, were the most effective factors. Urban, dry farm and thin rangeland were found as the most important land covers. Slope and elevation decreased the probability of disease. Close proximity to cattle sheds notably increased the chance of CL. The importance of other factors such as rainfall, temperature and close proximity to sheep/goat sheds only were shown when their effects were evaluated independently from other factors. So regions with urban, dry farm and thin rangeland covers with lower slope and altitude where in close proximity of cattle sheds seems to be potentially most high risk areas.

CONCLUSION: Distribution of CL cases is influenced by combination of environmental, ecological factors and close proximity to livestock sheds but control programs should be focused on cities and villages in the above-mentioned most high risk regions.}, } @article {pmid29286182, year = {2018}, author = {Lian, Y and Xiao, C and Yan, C and Chen, D and Huang, Q and Fan, Y and Li, Z and Xu, H}, title = {Knockdown of pseudogene derived from lncRNA DUXAP10 inhibits cell proliferation, migration, invasion, and promotes apoptosis in pancreatic cancer.}, journal = {Journal of cellular biochemistry}, volume = {119}, number = {4}, pages = {3671-3682}, doi = {10.1002/jcb.26578}, pmid = {29286182}, issn = {1097-4644}, mesh = {Animals ; Apoptosis/genetics/physiology ; Cell Cycle/genetics/physiology ; Cell Line, Tumor ; Cell Proliferation/genetics/physiology ; Cell Survival/genetics/physiology ; Computational Biology ; Flow Cytometry ; Gene Expression Regulation, Neoplastic/genetics/physiology ; Humans ; Immunoprecipitation ; Mice ; Mice, Inbred BALB C ; Mice, Nude ; Pancreatic Neoplasms/genetics/*metabolism ; RNA, Long Noncoding/*genetics/physiology ; Reverse Transcriptase Polymerase Chain Reaction ; }, abstract = {Current evidence suggests that pseudogene derived lncRNAs may be important players in human cancer progression. Our previous study showed that DUXAP10 could promote cell proliferation in colorectal cancer. However, the clinical significance and potential role of DUXAP10 in human pancreatic cancer (PC) has not been uncovered. In this study, we found that DUXAP10 was overexpressed in PC tissues compared with normal tissues. DUXAP10 expression was significantly higher in patients with an advanced TNM stage and positive lymph node metastasis. Bioinformatic analysis showed that cell cycle progression was increased in patients with high DUXAP10 expression. In vitro and in vivo assays of DUXAP10 alterations revealed a complex integrated phenotype affecting cell growth, apoptosis, migration, and invasion. Mechanistic studies revealed that DUXAP10 has a crucial role in G2/M arrest. We further showed that DUXAP10 regulated PC cell proliferation through interact with RNA-binding protein EZH2 and LSD1. Overall, our findings indicates that DUXAP10 is an oncogenic lncRNA that promotes PC proliferation and metastasis.}, } @article {pmid29284191, year = {2018}, author = {Becknell, JM and Porder, S and Hancock, S and Chazdon, RL and Hofton, MA and Blair, JB and Kellner, JR}, title = {Chronosequence predictions are robust in a Neotropical secondary forest, but plots miss the mark.}, journal = {Global change biology}, volume = {24}, number = {3}, pages = {933-943}, doi = {10.1111/gcb.14036}, pmid = {29284191}, issn = {1365-2486}, mesh = {Biomass ; Carbon/metabolism ; Carbon Sequestration ; Databases, Factual ; *Forests ; Time Factors ; }, abstract = {Tropical secondary forests (TSF) are a global carbon sink of 1.6 Pg C/year. However, TSF carbon uptake is estimated using chronosequence studies that assume differently aged forests can be used to predict change in aboveground biomass density (AGBD) over time. We tested this assumption using two airborne lidar datasets separated by 11.5 years over a Neotropical landscape. Using data from 1998, we predicted canopy height and AGBD within 1.1 and 10.3% of observations in 2009, with higher accuracy for forest height than AGBD and for older TSFs in comparison to younger ones. This result indicates that the space-for-time assumption is robust at the landscape-scale. However, since lidar measurements of secondary tropical forest are rare, we used the 1998 lidar dataset to test how well plot-based studies quantify the mean TSF height and biomass in a landscape. We found that the sample area required to produce estimates of height or AGBD close to the landscape mean is larger than the typical area sampled in secondary forest chronosequence studies. For example, estimating AGBD within 10% of the landscape mean requires more than thirty 0.1 ha plots per age class, and more total area for larger plots. We conclude that under-sampling in ground-based studies may introduce error into estimations of the TSF carbon sink, and that this error can be reduced by more extensive use of lidar measurements.}, } @article {pmid29283024, year = {2019}, author = {Gilboa, Y and Jansari, A and Kerrouche, B and Uçak, E and Tiberghien, A and Benkhaled, O and Aligon, D and Mariller, A and Verdier, V and Mintegui, A and Abada, G and Canizares, C and Goldstein, A and Chevignard, M}, title = {Assessment of executive functions in children and adolescents with acquired brain injury (ABI) using a novel complex multi-tasking computerised task: The Jansari assessment of Executive Functions for Children (JEF-C[©]).}, journal = {Neuropsychological rehabilitation}, volume = {29}, number = {9}, pages = {1359-1382}, doi = {10.1080/09602011.2017.1411819}, pmid = {29283024}, issn = {1464-0694}, mesh = {Adolescent ; Brain Injuries/*complications ; Child ; Cognitive Dysfunction/*diagnosis/etiology/physiopathology ; Diagnosis, Computer-Assisted/standards ; *Executive Function/physiology ; Female ; Humans ; Male ; *Memory, Episodic ; Neuropsychological Tests/*standards ; Reproducibility of Results ; Sensitivity and Specificity ; Thinking/*physiology ; Virtual Reality ; }, abstract = {Objectives: The Jansari assessment of Executive Functions for Children (JEF-C[©]) is a new non-immersive computerised assessment of executive functions. The objectives of the study were to test the feasibility and validity of JEF-C[©] in children and adolescents with acquired brain injury (ABI). Methods: Twenty-nine patients with ABI aged 10-18 years and 30 age-and gender-matched controls were tested. Participants performed JEF-C[©], Wechsler Abbreviated Scale of Intelligence (WASI) and the Behavioural Assessment of the Dysexecutive Syndrome for Children (BADS-C), while parents completed the Behaviour Rating Inventory of Executive Function (BRIEF) questionnaire. Results: The JEF-C[©] task proved feasible in patients with ABI. The internal consistency was medium (Cronbach's alpha = 0.62 and significant intercorrelations between individual JEF-C[©] constructs). Patients performed significantly worse than controls on most of the JEF-C[©] subscales and total score, with 41.4% of participants with ABI classified as having severe executive dysfunction. No significant correlations were found between JEF-C[©] total score, the BRIEF indices, and the BADS-C. Significant correlations were found between JEF-C[©] and demographic characteristics of the sample and intellectual ability, but not with severity/medical variables. Conclusion: JEF-C[©] is a playful complex task that appears to be a sensitive and ecologically valid assessment tool, especially for relatively high-functioning individuals.}, } @article {pmid29277542, year = {2018}, author = {Springer, MS and Gatesy, J}, title = {Evolution of the MC5R gene in placental mammals with evidence for its inactivation in multiple lineages that lack sebaceous glands.}, journal = {Molecular phylogenetics and evolution}, volume = {120}, number = {}, pages = {364-374}, doi = {10.1016/j.ympev.2017.12.010}, pmid = {29277542}, issn = {1095-9513}, mesh = {Animals ; Base Sequence ; Databases, Genetic ; *Evolution, Molecular ; Female ; Mammals/classification/*metabolism ; Phylogeny ; Placenta/metabolism ; Pregnancy ; Receptors, Melanocortin/classification/*genetics ; Sebaceous Glands/*physiology ; Sequence Alignment ; }, abstract = {MC5R is one of five melanocortin receptor genes found in placental mammals. MC5R plays an important role in energy homeostasis and is also expressed in the terminal differentiation of sebaceous glands. Among placental mammals there are multiple lineages that either lack or have degenerative sebaceous glands including Cetacea (whales, dolphins, and porpoises), Hippopotamidae (hippopotamuses), Sirenia (manatees and dugongs), Proboscidea (elephants), Rhinocerotidae (rhinos), and Heterocephalus glaber (naked mole rat). Given the loss or diminution of sebaceous glands in these taxa, we procured MC5R sequences from publicly available genomes and transcriptomes, supplemented by a newly generated sequence for Choeropsis liberiensis (pygmy hippopotamus), to determine if this gene remains intact or is inactivated in association with loss/reduction of sebaceous glands. Our data set includes complete MC5R sequences for 114 placental mammal species including two individuals of Mammuthus primigenius (woolly mammoth) from Oimyakon and Wrangel Island. Complete loss or inactivation of the MC5R gene occurs in multiple placental lineages that have lost sebaceous glands (Cetacea, West Indian manatee, African elephant, white rhinoceros) or are characterized by unusual skin (pangolins, aardvarks). Both M. primigenius individuals share inactivating mutations with the African elephant even though sebaceous glands have been reported in the former. MC5R remains intact in hippopotamuses and the naked mole rat, although slightly elevated dN/dS ratios in these lineages allow for the possibility that the accumulation of inactivating mutations in MC5R may lag behind the relaxation of purifying selection. For Cetacea and Hippopotamidae, the absence of shared inactivating mutations in two different skin genes (MC5R, PSORS1C2) is consistent with the hypothesis that semi-aquatic lifestyles were acquired independently in these clades following divergence from a common ancestor.}, } @article {pmid29273806, year = {2018}, author = {Demenais, F and Margaritte-Jeannin, P and Barnes, KC and Cookson, WOC and Altmüller, J and Ang, W and Barr, RG and Beaty, TH and Becker, AB and Beilby, J and Bisgaard, H and Bjornsdottir, US and Bleecker, E and Bønnelykke, K and Boomsma, DI and Bouzigon, E and Brightling, CE and Brossard, M and Brusselle, GG and Burchard, E and Burkart, KM and Bush, A and Chan-Yeung, M and Chung, KF and Couto Alves, A and Curtin, JA and Custovic, A and Daley, D and de Jongste, JC and Del-Rio-Navarro, BE and Donohue, KM and Duijts, L and Eng, C and Eriksson, JG and Farrall, M and Fedorova, Y and Feenstra, B and Ferreira, MA and , and Freidin, MB and Gajdos, Z and Gauderman, J and Gehring, U and Geller, F and Genuneit, J and Gharib, SA and Gilliland, F and Granell, R and Graves, PE and Gudbjartsson, DF and Haahtela, T and Heckbert, SR and Heederik, D and Heinrich, J and Heliövaara, M and Henderson, J and Himes, BE and Hirose, H and Hirschhorn, JN and Hofman, A and Holt, P and Hottenga, J and Hudson, TJ and Hui, J and Imboden, M and Ivanov, V and Jaddoe, VWV and James, A and Janson, C and Jarvelin, MR and Jarvis, D and Jones, G and Jonsdottir, I and Jousilahti, P and Kabesch, M and Kähönen, M and Kantor, DB and Karunas, AS and Khusnutdinova, E and Koppelman, GH and Kozyrskyj, AL and Kreiner, E and Kubo, M and Kumar, R and Kumar, A and Kuokkanen, M and Lahousse, L and Laitinen, T and Laprise, C and Lathrop, M and Lau, S and Lee, YA and Lehtimäki, T and Letort, S and Levin, AM and Li, G and Liang, L and Loehr, LR and London, SJ and Loth, DW and Manichaikul, A and Marenholz, I and Martinez, FJ and Matheson, MC and Mathias, RA and Matsumoto, K and Mbarek, H and McArdle, WL and Melbye, M and Melén, E and Meyers, D and Michel, S and Mohamdi, H and Musk, AW and Myers, RA and Nieuwenhuis, MAE and Noguchi, E and O'Connor, GT and Ogorodova, LM and Palmer, CD and Palotie, A and Park, JE and Pennell, CE and Pershagen, G and Polonikov, A and Postma, DS and Probst-Hensch, N and Puzyrev, VP and Raby, BA and Raitakari, OT and Ramasamy, A and Rich, SS and Robertson, CF and Romieu, I and Salam, MT and Salomaa, V and Schlünssen, V and Scott, R and Selivanova, PA and Sigsgaard, T and Simpson, A and Siroux, V and Smith, LJ and Solodilova, M and Standl, M and Stefansson, K and Strachan, DP and Stricker, BH and Takahashi, A and Thompson, PJ and Thorleifsson, G and Thorsteinsdottir, U and Tiesler, CMT and Torgerson, DG and Tsunoda, T and Uitterlinden, AG and van der Valk, RJP and Vaysse, A and Vedantam, S and von Berg, A and von Mutius, E and Vonk, JM and Waage, J and Wareham, NJ and Weiss, ST and White, WB and Wickman, M and Widén, E and Willemsen, G and Williams, LK and Wouters, IM and Yang, JJ and Zhao, JH and Moffatt, MF and Ober, C and Nicolae, DL}, title = {Multiancestry association study identifies new asthma risk loci that colocalize with immune-cell enhancer marks.}, journal = {Nature genetics}, volume = {50}, number = {1}, pages = {42-53}, pmid = {29273806}, issn = {1546-1718}, support = {G0401540/MRC_/Medical Research Council/United Kingdom ; MR/K002449/2/MRC_/Medical Research Council/United Kingdom ; R01 HL129735/HL/NHLBI NIH HHS/United States ; R01 HL077612/HL/NHLBI NIH HHS/United States ; MR/K002449/1/MRC_/Medical Research Council/United Kingdom ; G0601361/MRC_/Medical Research Council/United Kingdom ; MC_UU_12015/1/MRC_/Medical Research Council/United Kingdom ; RC2 HL101651/HL/NHLBI NIH HHS/United States ; 648916/ERC_/European Research Council/International ; G0902125/MRC_/Medical Research Council/United Kingdom ; P01 CA196569/CA/NCI NIH HHS/United States ; P30 ES006694/ES/NIEHS NIH HHS/United States ; U01 HL130114/HL/NHLBI NIH HHS/United States ; G9815508/MRC_/Medical Research Council/United Kingdom ; P30 ES009089/ES/NIEHS NIH HHS/United States ; }, mesh = {Alleles ; Asthma/ethnology/*genetics/immunology ; *Enhancer Elements, Genetic ; Epigenesis, Genetic ; Genetic Loci ; Genetic Predisposition to Disease ; Genome-Wide Association Study ; Histone Code ; Humans ; Leukocytes/metabolism ; Phenotype ; Promoter Regions, Genetic ; Rhinitis, Allergic, Seasonal/genetics ; Risk ; }, abstract = {We examined common variation in asthma risk by conducting a meta-analysis of worldwide asthma genome-wide association studies (23,948 asthma cases, 118,538 controls) of individuals from ethnically diverse populations. We identified five new asthma loci, found two new associations at two known asthma loci, established asthma associations at two loci previously implicated in the comorbidity of asthma plus hay fever, and confirmed nine known loci. Investigation of pleiotropy showed large overlaps in genetic variants with autoimmune and inflammatory diseases. The enrichment in enhancer marks at asthma risk loci, especially in immune cells, suggested a major role of these loci in the regulation of immunologically related mechanisms.}, } @article {pmid29273717, year = {2017}, author = {Albanese, D and Donati, C}, title = {Strain profiling and epidemiology of bacterial species from metagenomic sequencing.}, journal = {Nature communications}, volume = {8}, number = {1}, pages = {2260}, pmid = {29273717}, issn = {2041-1723}, mesh = {Bacteria/*genetics ; Bifidobacterium longum/genetics ; *Computational Biology ; Databases, Genetic ; Enterococcus faecalis/genetics ; Escherichia coli/genetics ; High-Throughput Nucleotide Sequencing ; Humans ; Metagenome/*genetics ; *Metagenomics ; Microbiota/*genetics ; Neisseria meningitidis/genetics ; Polymorphism, Single Nucleotide ; Propionibacterium acnes/genetics ; Staphylococcus aureus/genetics ; Staphylococcus epidermidis/genetics ; Streptococcus pneumoniae/genetics ; }, abstract = {Microbial communities are often composed by complex mixtures of multiple strains of the same species, characterized by a wide genomic and phenotypic variability. Computational methods able to identify, quantify and classify the different strains present in a sample are essential to fully exploit the potential of metagenomic sequencing in microbial ecology, with applications that range from the epidemiology of infectious diseases to the characterization of the dynamics of microbial colonization. Here we present a computational approach that uses the available genomic data to reconstruct complex strain profiles from metagenomic sequencing, quantifying the abundances of the different strains and cataloging them according to the population structure of the species. We validate the method on synthetic data sets and apply it to the characterization of the strain distribution of several important bacterial species in real samples, showing how its application provides novel insights on the structure and complexity of the microbiota.}, } @article {pmid29272799, year = {2018}, author = {DeBofsky, AR and Klingler, RH and Mora-Zamorano, FX and Walz, M and Shepherd, B and Larson, JK and Anderson, D and Yang, L and Goetz, F and Basu, N and Head, J and Tonellato, P and Armstrong, BM and Murphy, C and Carvan, MJ}, title = {Female reproductive impacts of dietary methylmercury in yellow perch (Perca flavescens) and zebrafish (Danio rerio).}, journal = {Chemosphere}, volume = {195}, number = {}, pages = {301-311}, pmid = {29272799}, issn = {1879-1298}, support = {P30 ES004184/ES/NIEHS NIH HHS/United States ; R21 ES024879/ES/NIEHS NIH HHS/United States ; }, mesh = {Animals ; *Diet/adverse effects ; *Environmental Exposure/adverse effects ; Female ; Lakes ; Liver/drug effects ; Methylmercury Compounds/*pharmacology ; Ovary/drug effects ; Perches/*physiology ; Real-Time Polymerase Chain Reaction ; Reproduction/*drug effects ; Zebrafish/*physiology ; }, abstract = {The purpose of this study was to evaluate the effects of environmentally relevant dietary MeHg exposures on adult female yellow perch (Perca flavescens) and female zebrafish (Danio rerio) ovarian development and reproduction. Yellow perch were used in the study for their socioeconomic and ecological importance within the Great Lakes basin, and the use of zebrafish allowed for a detailed analysis of the molecular effects of MeHg following a whole life-cycle exposure. Chronic whole life dietary exposure of F1 zebrafish to MeHg mimics realistic wildlife exposure scenarios, and the twenty-week adult yellow perch exposure (where whole life-cycle exposures are difficult) captures early seasonal ovarian development. For both species, target dietary accumulation values were achieved prior to analyses. In zebrafish, several genes involved in reproductive processes were shown to be dysregulated by RNA-sequencing and quantitative real-time polymerase chain reaction (QPCR), but no significant phenotypic changes were observed regarding ovarian staging, fecundity, or embryo mortality. Yellow perch were exposed to dietary MeHg for 12, 16, or 20 weeks. In this species, a set of eight genes were assessed by QPCR in the pituitary, liver, and ovary, and no exposure-related changes were observed. The lack of genomic resources in yellow perch hinders the characterization of subtle molecular impacts. The ovarian somatic index, circulating estradiol and testosterone, and ovarian staging were not significantly altered by MeHg exposure in yellow perch. These results suggest that environmentally relevant MeHg exposures do not drastically reduce the reproductively important endpoints in these fish, but to capture realistic exposure scenarios, whole life-cycle yellow perch exposures are needed.}, } @article {pmid29269415, year = {2018}, author = {Langenegger, N and Koua, D and Schürch, S and Heller, M and Nentwig, W and Kuhn-Nentwig, L}, title = {Identification of a precursor processing protease from the spider Cupiennius salei essential for venom neurotoxin maturation.}, journal = {The Journal of biological chemistry}, volume = {293}, number = {6}, pages = {2079-2090}, pmid = {29269415}, issn = {1083-351X}, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Computational Biology ; Enzyme Stability ; Hydrogen-Ion Concentration ; Molecular Sequence Data ; Neurotoxins/chemistry/genetics/*metabolism ; Protein Processing, Post-Translational ; Serine Proteases/chemistry/genetics/isolation & purification/*metabolism ; Spider Venoms/*enzymology/genetics/metabolism ; Spiders/*enzymology/genetics/metabolism ; }, abstract = {Spider venom neurotoxins and cytolytic peptides are expressed as elongated precursor peptides, which are post-translationally processed by proteases to yield the active mature peptides. The recognition motifs for these processing proteases, first published more than 10 years ago, include the processing quadruplet motif (PQM) and the inverted processing quadruplet motif (iPQM). However, the identification of the relevant proteases was still pending. Here we describe the purification of a neurotoxin precursor processing protease from the venom of the spider Cupiennius salei The chymotrypsin-like serine protease is a 28-kDa heterodimer with optimum activity at venom's pH of 6.0. We designed multiple synthetic peptides mimicking the predicted cleavage sites of neurotoxin precursors. Using these peptides as substrates, we confirm the biochemical activity of the protease in propeptide removal from neurotoxin precursors by cleavage C-terminal of the PQM. Furthermore, the PQM protease also cleaves the iPQM relevant for heterodimerization of a subgroup of neurotoxins. An involvement in the maturing of cytolytic peptides is very likely, due to high similarity of present protease recognition motifs. Finally, bioinformatics analysis, identifying sequences of homolog proteins from 18 spiders of 9 families, demonstrate the wide distribution and importance of the isolated enzyme for spiders. In summary, we establish the first example of a PQM protease, essential for maturing of spider venom neurotoxins. In the future, the here described protease may be established as a powerful tool for production strategies of recombinant toxic peptides, adapted to the maturing of spider venom toxins.}, } @article {pmid29255013, year = {2018}, author = {Bradshaw, WE and Burkhart, J and Colbourne, JK and Borowczak, R and Lopez, J and Denlinger, DL and Reynolds, JA and Pfrender, ME and Holzapfel, CM}, title = {Evolutionary transition from blood feeding to obligate nonbiting in a mosquito.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {115}, number = {5}, pages = {1009-1014}, pmid = {29255013}, issn = {1091-6490}, mesh = {Animals ; Blood ; Blood-Borne Pathogens ; Culicidae/*genetics/*pathogenicity/physiology ; *Evolution, Molecular ; *Feeding Behavior/physiology ; Female ; Gene Expression ; Genes, Insect ; Genetics, Population ; Humans ; Insect Bites and Stings/parasitology ; Insect Proteins/genetics ; Metabolic Networks and Pathways/genetics ; Models, Biological ; Mosquito Vectors/genetics/pathogenicity/physiology ; Rats ; Rats, Inbred SHR ; }, abstract = {The spread of blood-borne pathogens by mosquitoes relies on their taking a blood meal; if there is no bite, there is no disease transmission. Although many species of mosquitoes never take a blood meal, identifying genes that distinguish blood feeding from obligate nonbiting is hampered by the fact that these different lifestyles occur in separate, genetically incompatible species. There is, however, one unique extant species with populations that share a common genetic background but blood feed in one region and are obligate nonbiters in the rest of their range: Wyeomyia smithii Contemporary blood-feeding and obligate nonbiting populations represent end points of divergence between fully interfertile southern and northern populations. This divergence has undoubtedly resulted in genetic changes that are unrelated to blood feeding, and the challenge is to winnow out the unrelated genetic factors to identify those related specifically to the evolutionary transition from blood feeding to obligate nonbiting. Herein, we determine differential gene expression resulting from directional selection on blood feeding within a polymorphic population to isolate genetic differences between blood feeding and obligate nonbiting. We show that the evolution of nonbiting has resulted in a greatly reduced metabolic investment compared with biting populations, a greater reliance on opportunistic metabolic pathways, and greater reliance on visual rather than olfactory sensory input. W. smithii provides a unique starting point to determine if there are universal nonbiting genes in mosquitoes that could be manipulated as a means to control vector-borne disease.}, } @article {pmid29253532, year = {2018}, author = {Choi, H and Shin, S and Jung, S and Clarke, DJ and Lee, S}, title = {Molecular phylogeny of Macrosiphini (Hemiptera: Aphididae): An evolutionary hypothesis for the Pterocomma-group habitat adaptation.}, journal = {Molecular phylogenetics and evolution}, volume = {121}, number = {}, pages = {12-22}, doi = {10.1016/j.ympev.2017.12.021}, pmid = {29253532}, issn = {1095-9513}, mesh = {*Adaptation, Physiological ; Animals ; Aphids/*classification ; Base Sequence ; Bayes Theorem ; Databases as Topic ; *Ecosystem ; Likelihood Functions ; *Models, Biological ; *Phylogeny ; }, abstract = {The aphid tribe Macrosiphini Wilson, 1910 (Hemiptera: Aphididae: Aphidinae) is one of the most controversial groups within Aphididae. We sequenced 2876 bp from one nuclear gene (EF-1α) and four mitochondrial genes (COI, tRNA + COII, 16S) from 107 terminal taxa representing 57 genera of Macrosiphini s.l. (the former Macrosiphini + genera in former Pterocommatini), including all of the recognized major genera and outgroups, and reconstructed the phylogeny using maximum likelihood, maximum parsimony and Bayesian methods. The stepping-stone method was used to evaluate various topological hypotheses regarding Macrosiphini s.l. and related groups. Our findings support both the monophyly of Macrosiphini s.l., and of two subordinate groups (Macrosiphini s.str and the Pterocomma-group), as well as the transfer of Capitophorus, Pleotrichophorus, Liosomaphis and Vesiculaphis to the Pterocomma-group-a result not previously suggested by analyses of molecular data. Ancestral state reconstructions for Macrosiphini and the Pterocomma-group suggest an ancestral primary host association with Rosales and Malpighiales, respectively, and other host associations within the tribe. Host transitions independently occurred more than once in Macrosiphini s.str. Furthermore, host-shifts between Rosales and Malpighiales may have occurred at least once in the Pterocomma-group. Additionally, the Macrosiphini phylogeny indicates that host associations are consistent also with host ecology, with a partitioning of aphid-host relationships into riparian and periaquatic habitats versus drier forest/shrubland habitats.}, } @article {pmid29253216, year = {2018}, author = {Silva-Junior, OB and Grattapaglia, D and Novaes, E and Collevatti, RG}, title = {Genome assembly of the Pink Ipê (Handroanthus impetiginosus, Bignoniaceae), a highly valued, ecologically keystone Neotropical timber forest tree.}, journal = {GigaScience}, volume = {7}, number = {1}, pages = {1-16}, pmid = {29253216}, issn = {2047-217X}, mesh = {Brazil ; Chromosome Mapping/*methods ; DNA Transposable Elements ; *Databases, Genetic ; Forests ; Genome Size ; *Genome, Plant ; Haplotypes ; Heterozygote ; High-Throughput Nucleotide Sequencing ; Quinones/*metabolism ; Tabebuia/*genetics/growth & development ; Trees/*genetics/growth & development ; Tropical Climate ; }, abstract = {BACKGROUND: Handroanthus impetiginosus (Mart. ex DC.) Mattos is a keystone Neotropical hardwood tree widely distributed in seasonally dry tropical forests of South and Mesoamerica. Regarded as the "new mahogany," it is the second most expensive timber, the most logged species in Brazil, and currently under significant illegal trading pressure. The plant produces large amounts of quinoids, specialized metabolites with documented antitumorous and antibiotic effects. The development of genomic resources is needed to better understand and conserve the diversity of the species, to empower forensic identification of the origin of timber, and to identify genes for important metabolic compounds.

FINDINGS: The genome assembly covers 503.7 Mb (N50 = 81 316 bp), 90.4% of the 557-Mbp genome, with 13 206 scaffolds. A repeat database with 1508 sequences was developed, allowing masking of ∼31% of the assembly. Depth of coverage indicated that consensus determination adequately removed haplotypes assembled separately due to the extensive heterozygosity of the species. Automatic gene prediction provided 31 688 structures and 35 479 messenger RNA transcripts, while external evidence supported a well-curated set of 28 603 high-confidence models (90% of total). Finally, we used the genomic sequence and the comprehensive gene content annotation to identify genes related to the production of specialized metabolites.

CONCLUSIONS: This genome assembly is the first well-curated resource for a Neotropical forest tree and the first one for a member of the Bignoniaceae family, opening exceptional opportunities to empower molecular, phytochemical, and breeding studies. This work should inspire the development of similar genomic resources for the largely neglected forest trees of the mega-diverse tropical biomes.}, } @article {pmid29253147, year = {2018}, author = {Edger, PP and VanBuren, R and Colle, M and Poorten, TJ and Wai, CM and Niederhuth, CE and Alger, EI and Ou, S and Acharya, CB and Wang, J and Callow, P and McKain, MR and Shi, J and Collier, C and Xiong, Z and Mower, JP and Slovin, JP and Hytönen, T and Jiang, N and Childs, KL and Knapp, SJ}, title = {Single-molecule sequencing and optical mapping yields an improved genome of woodland strawberry (Fragaria vesca) with chromosome-scale contiguity.}, journal = {GigaScience}, volume = {7}, number = {2}, pages = {1-7}, pmid = {29253147}, issn = {2047-217X}, mesh = {DNA Methylation ; Fragaria/*genetics ; Gene Ontology ; Genome Size ; *Genome, Plant ; High-Throughput Nucleotide Sequencing/*methods ; Molecular Sequence Annotation ; Optical Imaging/instrumentation/*methods ; Physical Chromosome Mapping/instrumentation/*methods ; Synteny ; }, abstract = {BACKGROUND: Although draft genomes are available for most agronomically important plant species, the majority are incomplete, highly fragmented, and often riddled with assembly and scaffolding errors. These assembly issues hinder advances in tool development for functional genomics and systems biology.

FINDINGS: Here we utilized a robust, cost-effective approach to produce high-quality reference genomes. We report a near-complete genome of diploid woodland strawberry (Fragaria vesca) using single-molecule real-time sequencing from Pacific Biosciences (PacBio). This assembly has a contig N50 length of ∼7.9 million base pairs (Mb), representing a ∼300-fold improvement of the previous version. The vast majority (>99.8%) of the assembly was anchored to 7 pseudomolecules using 2 sets of optical maps from Bionano Genomics. We obtained ∼24.96 Mb of sequence not present in the previous version of the F. vesca genome and produced an improved annotation that includes 1496 new genes. Comparative syntenic analyses uncovered numerous, large-scale scaffolding errors present in each chromosome in the previously published version of the F. vesca genome.

CONCLUSIONS: Our results highlight the need to improve existing short-read based reference genomes. Furthermore, we demonstrate how genome quality impacts commonly used analyses for addressing both fundamental and applied biological questions.}, } @article {pmid29247477, year = {2018}, author = {Haas, TC and Ferreira, SM}, title = {Finding politically feasible conservation policies: the case of wildlife trafficking.}, journal = {Ecological applications : a publication of the Ecological Society of America}, volume = {28}, number = {2}, pages = {473-494}, doi = {10.1002/eap.1662}, pmid = {29247477}, issn = {1051-0761}, mesh = {Animals ; Commerce ; Conservation of Natural Resources/*legislation & jurisprudence ; *Decision Support Techniques ; *Perissodactyla ; Politics ; Population Dynamics ; South Africa ; Uncertainty ; }, abstract = {Conservation management is of increasing importance in ecology as most ecosystems nowadays are essentially managed ecosystems. Conservation managers work within a political-ecological system when they develop and attempt to implement a conservation plan that is designed to meet particular conservation goals. In this article, we develop a decision support tool that can identify a conservation policy for a managed wildlife population that is both sustainable and politically feasible. Part of our tool consists of a simulation model composed of interacting influence diagrams. We build, fit, and use our tool on the case of rhino horn trafficking between South Africa and Asia. Using these diagrams, we show how a rhino poacher's belief system can be modified by such a policy and locate it in a perceived risks-benefits space before and after policy implementation. We statistically fit our model to observations on group actions and rhino abundance. We then use this fitted model to compute a politically feasible conservation policy.}, } @article {pmid29247237, year = {2017}, author = {Navarro-Domínguez, B and Ruiz-Ruano, FJ and Camacho, JPM and Cabrero, J and López-León, MD}, title = {Transcription of a B chromosome CAP-G pseudogene does not influence normal Condensin Complex genes in a grasshopper.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {17650}, pmid = {29247237}, issn = {2045-2322}, mesh = {Adenosine Triphosphatases/*genetics ; Animals ; Chromosomal Proteins, Non-Histone/*genetics ; Chromosomes, Insect/*genetics ; Computational Biology ; DNA-Binding Proteins/*genetics ; Female ; Gene Expression Regulation ; Grasshoppers/*genetics ; In Situ Hybridization, Fluorescence ; Insect Proteins/*genetics ; Male ; Multiprotein Complexes/*genetics ; Pseudogenes/*genetics ; }, abstract = {Parasitic B chromosomes invade and persist in natural populations through several mechanisms for transmission advantage (drive). They may contain gene-derived sequences which, in some cases, are actively transcribed. A further interesting question is whether B-derived transcripts become functional products. In the grasshopper Eyprepocnemis plorans, one of the gene-derived sequences located on the B chromosome shows homology with the gene coding for the CAP-G subunit of condensin I. We show here, by means of fluorescent in situ hybridization coupled with tyramide signal amplification (FISH-TSA), that this gene is located in the distal region of the B24 chromosome variant. The DNA sequence located in the B chromosome is a pseudogenic version of the CAP-G gene (B-CAP-G). In two Spanish populations, we found active transcription of B-CAP-G, but it did not influence the expression of CAP-D2 and CAP-D3 genes coding for corresponding condensin I and II subunits, respectively. Our results indicate that the transcriptional regulation of the B-CAP-G pseudogene is uncoupled from the standard regulation of the genes that constitute the condensin complex, and suggest that some of the B chromosome known effects may be related with its gene content and transcriptional activity, thus opening new exciting avenues for research.}, } @article {pmid29247217, year = {2017}, author = {Blut, C and Crespi, A and Mersch, D and Keller, L and Zhao, L and Kollmann, M and Schellscheidt, B and Fülber, C and Beye, M}, title = {Automated computer-based detection of encounter behaviours in groups of honeybees.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {17663}, pmid = {29247217}, issn = {2045-2322}, support = {MC_U105188491/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Animals ; Automation, Laboratory ; Bees/*physiology ; Behavior, Animal/*physiology ; Data Curation/*methods ; Diagnosis, Computer-Assisted ; *Machine Learning ; Social Behavior ; Software ; }, abstract = {Honeybees form societies in which thousands of members integrate their behaviours to act as a single functional unit. We have little knowledge on how the collaborative features are regulated by workers' activities because we lack methods that enable collection of simultaneous and continuous behavioural information for each worker bee. In this study, we introduce the Bee Behavioral Annotation System (BBAS), which enables the automated detection of bees' behaviours in small observation hives. Continuous information on position and orientation were obtained by marking worker bees with 2D barcodes in a small observation hive. We computed behavioural and social features from the tracking information to train a behaviour classifier for encounter behaviours (interaction of workers via antennation) using a machine learning-based system. The classifier correctly detected 93% of the encounter behaviours in a group of bees, whereas 13% of the falsely classified behaviours were unrelated to encounter behaviours. The possibility of building accurate classifiers for automatically annotating behaviours may allow for the examination of individual behaviours of worker bees in the social environments of small observation hives. We envisage that BBAS will be a powerful tool for detecting the effects of experimental manipulation of social attributes and sub-lethal effects of pesticides on behaviour.}, } @article {pmid29245494, year = {2017}, author = {Samuel, VKD and Krishnan, P and Sreeraj, CR and Chamundeeswari, K and Parthiban, C and Sekar, V and Patro, S and Saravanan, R and Abhilash, KR and Ramachandran, P and Ramesh, R}, title = {An updated checklist of Echinoderms from Indian waters.}, journal = {Zootaxa}, volume = {4354}, number = {1}, pages = {1-68}, doi = {10.11646/zootaxa.4354.1.1}, pmid = {29245494}, issn = {1175-5334}, mesh = {Animals ; *Biodiversity ; Databases, Factual ; *Echinodermata ; Ecology ; India ; }, abstract = {Species checklists enlist the species available within the defined geographical region and thus serve as essential input for developing conservation and management strategies. The fields of conservation biology and ecology confront the challenge of inflated biodiversity, attributed to non-recognition of taxonomic inconsistencies such as synonyms, alternate representation, emendations etc. Critical review of the checklists and distributional records of Phylum Echinodermata from Indian waters and subsequent validation of species names with World Register of Marine Species (WoRMS) database, revealed that the current literature included 236 incorrect entries comprising of 162 synonyms, 15 emendations, 5 nomina dubia, 1 nomen nudum, 40 species under alternate representation, 9 species with author misnomer, 1 subspecies and 1 unaccepted. The 226 species found to be mixed with valid names and a revised checklist was prepared. The revised and updated checklist holds 741 species of echinoderms comprising of 182 asteroids (24.56%), 70 crinoids (9.45%), 138 echinoids (18.62%), 179 holothuroids (24.16%) and 172 ophiuroids (23.21%), placed under 28 orders and 107 families. This paper discusses the cause for taxonomic inflation and argues that such taxonomic inconsistencies alter our interpretations of a species including its inaccurate distribution and, could possibly impede the country's conservation and management efforts.}, } @article {pmid29244862, year = {2017}, author = {Mumba, C and Skjerve, E and Rich, M and Rich, KM}, title = {Application of system dynamics and participatory spatial group model building in animal health: A case study of East Coast Fever interventions in Lundazi and Monze districts of Zambia.}, journal = {PloS one}, volume = {12}, number = {12}, pages = {e0189878}, pmid = {29244862}, issn = {1932-6203}, mesh = {*Animal Husbandry ; Animals ; Antibodies, Protozoan/administration & dosage ; Cattle ; Geographic Information Systems ; Immunization ; Theileriasis/epidemiology/physiopathology/*virology ; Zambia ; }, abstract = {East Coast Fever (ECF) is the most economically important production disease among traditional beef cattle farmers in Zambia. Despite the disease control efforts by the government, donors, and farmers, ECF cases are increasing. Why does ECF oscillate over time? Can alternative approaches such as systems thinking contribute solutions to the complex ECF problem, avoid unintended consequences, and achieve sustainable results? To answer these research questions and inform the design and implementation of ECF interventions, we qualitatively investigated the influence of dynamic socio-economic, cultural, and ecological factors. We used system dynamics modelling to specify these dynamics qualitatively, and an innovative participatory framework called spatial group model building (SGMB). SGMB uses participatory geographical information system (GIS) concepts and techniques to capture the role of spatial phenomenon in the context of complex systems, allowing stakeholders to identify spatial phenomenon directly on physical maps and integrate such information in model development. Our SGMB process convened focus groups of beef value chain stakeholders in two distinct production systems. The focus groups helped to jointly construct a series of interrelated system dynamics models that described ECF in a broader systems context. Thus, a complementary objective of this study was to demonstrate the applicability of system dynamics modelling and SGMB in animal health. The SGMB process revealed policy leverage points in the beef cattle value chain that could be targeted to improve ECF control. For example, policies that develop sustainable and stable cattle markets and improve household income availability may have positive feedback effects on investment in animal health. The results obtained from a SGMB process also demonstrated that a "one-size-fits-all" approach may not be equally effective in policing ECF in different agro-ecological zones due to the complex interactions of socio-ecological context with important, and often ignored, spatial patterns.}, } @article {pmid29244812, year = {2017}, author = {Chang, SS and Tu, S and Baek, KI and Pietersen, A and Liu, YH and Savage, VM and Hwang, SL and Hsiai, TK and Roper, M}, title = {Optimal occlusion uniformly partitions red blood cells fluxes within a microvascular network.}, journal = {PLoS computational biology}, volume = {13}, number = {12}, pages = {e1005892}, pmid = {29244812}, issn = {1553-7358}, support = {1R01 GM126556/NH/NIH HHS/United States ; R01 HL129727/HL/NHLBI NIH HHS/United States ; R01 HL129727/NH/NIH HHS/United States ; R01 HL111437/NH/NIH HHS/United States ; R01 GM126556/GM/NIGMS NIH HHS/United States ; R01 HL083015/HL/NHLBI NIH HHS/United States ; R01 HL083015/NH/NIH HHS/United States ; R01 HL118650/HL/NHLBI NIH HHS/United States ; R01 HL111437/HL/NHLBI NIH HHS/United States ; T32 GM008185/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Animals, Genetically Modified ; Blood Flow Velocity/physiology ; Computational Biology ; Erythrocytes/physiology ; Feedback, Physiological ; Hemorheology ; Microcirculation/*physiology ; Microvessels/anatomy & histology/*physiology ; *Models, Cardiovascular ; Zebrafish ; }, abstract = {In animals, gas exchange between blood and tissues occurs in narrow vessels, whose diameter is comparable to that of a red blood cell. Red blood cells must deform to squeeze through these narrow vessels, transiently blocking or occluding the vessels they pass through. Although the dynamics of vessel occlusion have been studied extensively, it remains an open question why microvessels need to be so narrow. We study occlusive dynamics within a model microvascular network: the embryonic zebrafish trunk. We show that pressure feedbacks created when red blood cells enter the finest vessels of the trunk act together to uniformly partition red blood cells through the microvasculature. Using mathematical models as well as direct observation, we show that these occlusive feedbacks are tuned throughout the trunk network to prevent the vessels closest to the heart from short-circuiting the network. Thus occlusion is linked with another open question of microvascular function: how are red blood cells delivered at the same rate to each micro-vessel? Our analysis shows that tuning of occlusive feedbacks increase the total dissipation within the network by a factor of 11, showing that uniformity of flows rather than minimization of transport costs may be prioritized by the microvascular network.}, } @article {pmid29243391, year = {2018}, author = {Bromham, L and Duchêne, S and Hua, X and Ritchie, AM and Duchêne, DA and Ho, SYW}, title = {Bayesian molecular dating: opening up the black box.}, journal = {Biological reviews of the Cambridge Philosophical Society}, volume = {93}, number = {2}, pages = {1165-1191}, doi = {10.1111/brv.12390}, pmid = {29243391}, issn = {1469-185X}, mesh = {Animals ; Bayes Theorem ; Computational Biology/methods ; *Evolution, Molecular ; Models, Genetic ; *Phylogeny ; }, abstract = {Molecular dating analyses allow evolutionary timescales to be estimated from genetic data, offering an unprecedented capacity for investigating the evolutionary past of all species. These methods require us to make assumptions about the relationship between genetic change and evolutionary time, often referred to as a 'molecular clock'. Although initially regarded with scepticism, molecular dating has now been adopted in many areas of biology. This broad uptake has been due partly to the development of Bayesian methods that allow complex aspects of molecular evolution, such as variation in rates of change across lineages, to be taken into account. But in order to do this, Bayesian dating methods rely on a range of assumptions about the evolutionary process, which vary in their degree of biological realism and empirical support. These assumptions can have substantial impacts on the estimates produced by molecular dating analyses. The aim of this review is to open the 'black box' of Bayesian molecular dating and have a look at the machinery inside. We explain the components of these dating methods, the important decisions that researchers must make in their analyses, and the factors that need to be considered when interpreting results. We illustrate the effects that the choices of different models and priors can have on the outcome of the analysis, and suggest ways to explore these impacts. We describe some major research directions that may improve the reliability of Bayesian dating. The goal of our review is to help researchers to make informed choices when using Bayesian phylogenetic methods to estimate evolutionary rates and timescales.}, } @article {pmid29242166, year = {2018}, author = {Campillo, LC and Oliveros, CH and Sheldon, FH and Moyle, RG}, title = {Genomic data resolve gene tree discordance in spiderhunters (Nectariniidae, Arachnothera).}, journal = {Molecular phylogenetics and evolution}, volume = {120}, number = {}, pages = {151-157}, doi = {10.1016/j.ympev.2017.12.011}, pmid = {29242166}, issn = {1095-9513}, mesh = {Animals ; Biological Evolution ; Computational Biology ; DNA/chemistry/isolation & purification/metabolism ; Genetic Loci ; *Genome ; Likelihood Functions ; Passeriformes/*classification/genetics ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {Reduced representation genomic sequencing methods efficiently gather sequence data from thousands of loci throughout the genome. These data can be used to test previous phylogenetic hypotheses produced from limited numbers of mitochondrial and nuclear loci that often reveal intriguing, but conflicting, results. In this paper, we use phylogenomic data to revisit recent molecular phylogenetic work that clarified many taxonomic relationships within spiderhunters, but also questioned the monophyly of this distinctive genus of sunbirds (AVES: Nectariniidae; Arachnothera). DNA sequence data were produced by target-capture sequencing of ultraconserved elements (UCEs) to infer the evolutionary history of 11 species of Arachnothera and six outgroups, including the Purple-naped Sunbird (Hypogramma hypogrammicum), which previous work suggested might lie within Arachnothera. Although we recovered many different gene tree topologies, concatenated and coalescent methods of analysis converged on a species tree that strongly supports the monophyly of Arachnothera, with Hypogramma as its sister taxon.}, } @article {pmid29242164, year = {2018}, author = {Dauphin, B and Grant, JR and Farrar, DR and Rothfels, CJ}, title = {Rapid allopolyploid radiation of moonwort ferns (Botrychium; Ophioglossaceae) revealed by PacBio sequencing of homologous and homeologous nuclear regions.}, journal = {Molecular phylogenetics and evolution}, volume = {120}, number = {}, pages = {342-353}, doi = {10.1016/j.ympev.2017.11.025}, pmid = {29242164}, issn = {1095-9513}, mesh = {Bayes Theorem ; Cell Nucleus/genetics ; Computational Biology ; Cryptochromes/chemistry/classification/genetics ; DNA, Plant/chemistry/isolation & purification/metabolism ; Ferns/*classification/genetics ; Phylogeny ; Polyploidy ; Sequence Analysis, DNA ; }, abstract = {Polyploidy is a major speciation process in vascular plants, and is postulated to be particularly important in shaping the diversity of extant ferns. However, limitations in the availability of bi-parental markers for ferns have greatly limited phylogenetic investigation of polyploidy in this group. With a large number of allopolyploid species, the genus Botrychium is a classic example in ferns where recurrent polyploidy is postulated to have driven frequent speciation events. Here, we use PacBio sequencing and the PURC bioinformatics pipeline to capture all homeologous or allelic copies of four long (∼1 kb) low-copy nuclear regions from a sample of 45 specimens (25 diploids and 20 polyploids) representing 37 Botrychium taxa, and three outgroups. This sample includes most currently recognized Botrychium species in Europe and North America, and the majority of our specimens were genotyped with co-dominant nuclear allozymes to ensure species identification. We analyzed the sequence data using maximum likelihood (ML) and Bayesian inference (BI) concatenated-data ("gene tree") approaches to explore the relationships among Botrychium species. Finally, we estimated divergence times among Botrychium lineages and inferred the multi-labeled polyploid species tree showing the origins of the polyploid taxa, and their relationships to each other and to their diploid progenitors. We found strong support for the monophyly of the major lineages within Botrychium and identified most of the parental donors of the polyploids; these results largely corroborate earlier morphological and allozyme-based investigations. Each polyploid had at least two distinct homeologs, indicating that all sampled polyploids are likely allopolyploids (rather than autopolyploids). Our divergence-time analyses revealed that these allopolyploid lineages originated recently-within the last two million years-and thus that the genus has undergone a recent radiation, correlated with multiple independent allopolyploidizations across the phylogeny. Also, we found strong parental biases in the formation of allopolyploids, with individual diploid species participating multiple times as either the maternal or paternal donor (but not both). Finally, we discuss the role of polyploidy in the evolutionary history of Botrychium and the interspecific reproductive barriers possibly involved in these parental biases.}, } @article {pmid29241736, year = {2018}, author = {Suzuki, E and Tsuda, T and Yamamoto, E}, title = {Covariate balance for no confounding in the sufficient-cause model.}, journal = {Annals of epidemiology}, volume = {28}, number = {1}, pages = {48-53.e2}, doi = {10.1016/j.annepidem.2017.11.005}, pmid = {29241736}, issn = {1873-2585}, mesh = {*Bias ; *Causality ; *Confounding Factors, Epidemiologic ; Data Interpretation, Statistical ; Epidemiologic Methods ; Humans ; *Models, Statistical ; }, abstract = {PURPOSE: To show conditions of covariate balance for no confounding in the sufficient-cause model and discuss its relationship with exchangeability conditions.

METHODS: We consider the link between the sufficient-cause model and the counterfactual model, emphasizing that the target population plays a key role when discussing these conditions. Furthermore, we incorporate sufficient causes within the directed acyclic graph framework. We propose to use each of the background factors in sufficient causes as representing a set of covariates of interest and discuss the presence of covariate balance by comparing joint distributions of the relevant background factors between the exposed and the unexposed groups.

RESULTS: We show conditions for partial covariate balance, covariate balance, and full covariate balance, each of which is stronger than partial exchangeability, exchangeability, and full exchangeability, respectively. This is consistent with the fact that the sufficient-cause model is a "finer" model than the counterfactual model.

CONCLUSIONS: Covariate balance is a sufficient, but not a necessary, condition for no confounding irrespective of the target population. Although our conceptualization of covariate imbalance is closely related to the recently proposed counterfactual-based definition of a confounder, the concepts of covariate balance and confounder should be clearly distinguished.}, } @article {pmid29240930, year = {2018}, author = {Vigo, M and Hassan, L and Vance, W and Jay, C and Brass, A and Cruickshank, S}, title = {Britain Breathing: using the experience sampling method to collect the seasonal allergy symptoms of a country.}, journal = {Journal of the American Medical Informatics Association : JAMIA}, volume = {25}, number = {1}, pages = {88-92}, pmid = {29240930}, issn = {1527-974X}, support = {MC_PC_13042/MRC_/Medical Research Council/United Kingdom ; 105610/Z/14/Z//Wellcome Trust/United Kingdom ; MR/K006665/1//Medical Research Council/United Kingdom ; }, mesh = {Adult ; Cross-Sectional Studies ; *Ecological Momentary Assessment ; Female ; Humans ; Hypersensitivity/*epidemiology ; Male ; Mobile Applications ; Rhinitis, Allergic, Seasonal/*epidemiology ; Sampling Studies ; Seasons ; Symptom Assessment ; United Kingdom/epidemiology ; }, abstract = {OBJECTIVE: Allergies are increasing, but the reasons for this are unclear. Although environmental factors are thought to be important, there is a lack of data on how they contribute to symptom development. To understand this relationship better, we need accurate data about both symptoms and environmental factors. Our objective here is to ascertain whether experience sampling is a reliable approach for collecting allergy symptom data in the general population, allowing us to map symptoms and understand etiology.

MATERIALS AND METHODS: We conducted a 32-week cross-sectional study where individuals reported their seasonal allergy symptoms and severity via a mobile application. Symptom geographical location and timestamp were also collected automatically.

RESULTS: The experience sampling method reliably infers the incidence of seasonal allergies as indicated by the strong correlation (r = 0.93, P < .003) between the reported lack of wellness and the number of antihistamines prescribed by General Practitioners.

DISCUSSION AND CONCLUSION: The project has resulted in the first dataset to map allergy symptoms over time and place and reveals periods of peak hay fever symptoms in the UK.}, } @article {pmid29240763, year = {2017}, author = {Radeva, T and Dornhaus, A and Lynch, N and Nagpal, R and Su, HH}, title = {Costs of task allocation with local feedback: Effects of colony size and extra workers in social insects and other multi-agent systems.}, journal = {PLoS computational biology}, volume = {13}, number = {12}, pages = {e1005904}, pmid = {29240763}, issn = {1553-7358}, mesh = {Algorithms ; Animals ; Behavior, Animal/physiology ; Body Temperature Regulation ; Computational Biology ; Computer Simulation ; Feedback, Physiological ; Insecta/*physiology ; *Models, Biological ; *Social Behavior ; Systems Biology ; Task Performance and Analysis ; }, abstract = {Adaptive collective systems are common in biology and beyond. Typically, such systems require a task allocation algorithm: a mechanism or rule-set by which individuals select particular roles. Here we study the performance of such task allocation mechanisms measured in terms of the time for individuals to allocate to tasks. We ask: (1) Is task allocation fundamentally difficult, and thus costly? (2) Does the performance of task allocation mechanisms depend on the number of individuals? And (3) what other parameters may affect their efficiency? We use techniques from distributed computing theory to develop a model of a social insect colony, where workers have to be allocated to a set of tasks; however, our model is generalizable to other systems. We show, first, that the ability of workers to quickly assess demand for work in tasks they are not currently engaged in crucially affects whether task allocation is quickly achieved or not. This indicates that in social insect tasks such as thermoregulation, where temperature may provide a global and near instantaneous stimulus to measure the need for cooling, for example, it should be easy to match the number of workers to the need for work. In other tasks, such as nest repair, it may be impossible for workers not directly at the work site to know that this task needs more workers. We argue that this affects whether task allocation mechanisms are under strong selection. Second, we show that colony size does not affect task allocation performance under our assumptions. This implies that when effects of colony size are found, they are not inherent in the process of task allocation itself, but due to processes not modeled here, such as higher variation in task demand for smaller colonies, benefits of specialized workers, or constant overhead costs. Third, we show that the ratio of the number of available workers to the workload crucially affects performance. Thus, workers in excess of those needed to complete all tasks improve task allocation performance. This provides a potential explanation for the phenomenon that social insect colonies commonly contain inactive workers: these may be a 'surplus' set of workers that improves colony function by speeding up optimal allocation of workers to tasks. Overall our study shows how limitations at the individual level can affect group level outcomes, and suggests new hypotheses that can be explored empirically.}, } @article {pmid29239835, year = {2018}, author = {Figueiredo, FWDS and Adami, F}, title = {Income Inequality and Mortality Owing to Breast Cancer: Evidence From Brazil.}, journal = {Clinical breast cancer}, volume = {18}, number = {4}, pages = {e651-e658}, doi = {10.1016/j.clbc.2017.11.005}, pmid = {29239835}, issn = {1938-0666}, mesh = {Brazil/epidemiology ; Breast Neoplasms/economics/epidemiology/*mortality ; Female ; Humans ; Income/*statistics & numerical data ; Linear Models ; Socioeconomic Factors ; }, abstract = {BACKGROUND: The relationship between breast cancer and inequality income is unclear. This study analyzed the correlation between income inequality and mortality standardized by age and proportional mortality owing to breast cancer among Brazilian women.

PATIENTS AND METHODS: This is an ecological study using data of the federative units and Federal District of Brazil in 2010. The age-standardized mortality owing to breast cancer was estimated using data from the Department of Informatics of Brazil's Unified Health System. Income inequality indicators used included the Gini index, Theil-L index, Palma index, and the ratio of income distribution quintiles obtained from the United Nations Development Program. We used Pearson correlation and linear regression adjusted for income per capita and other variables.

RESULTS: An increase of 0.1 in the Gini index was associated with increases of 9.8 deaths per 100,000 women (95% confidence interval [CI], 1.7-17.9); an increase in the Palma index was associated with increases in mortality of 0.7 deaths per 100,000 women (95% CI, 0.1-1.4), an increase in the Theil-L index was associated with increases in mortality of 4.9 deaths per 100,000 women (95% CI, 1.9-7.9), and of 0.8 (95% CI, 0.2-1.5) in the proportional mortality.

CONCLUSION: Income inequality, as assessed by the Gini, Palma, and Theil-L indexes, is positively associated with an increase in breast cancer mortality in Brazil.}, } @article {pmid29237244, year = {2018}, author = {Valdebenito, B and Tullume-Vergara, PO and González, W and Kreth, J and Giacaman, RA}, title = {In silico analysis of the competition between Streptococcus sanguinis and Streptococcus mutans in the dental biofilm.}, journal = {Molecular oral microbiology}, volume = {33}, number = {2}, pages = {168-180}, doi = {10.1111/omi.12209}, pmid = {29237244}, issn = {2041-1014}, mesh = {Bacterial Proteins/*genetics/*metabolism ; Bacteriocins/metabolism ; *Biofilms ; Computer Simulation ; Databases, Genetic ; Dental Caries/microbiology ; Dental Plaque/*microbiology ; Genes, Bacterial/genetics ; Gluconeogenesis ; Humans ; Hydrogen Peroxide/metabolism ; Metabolic Networks and Pathways ; Mouth/microbiology ; Streptococcus mutans/*genetics/*metabolism ; Streptococcus sanguis/*genetics/*metabolism ; }, abstract = {During dental caries, the dental biofilm modifies the composition of the hundreds of involved bacterial species. Changing environmental conditions influence competition. A pertinent model to exemplify the complex interplay of the microorganisms in the human dental biofilm is the competition between Streptococcus sanguinis and Streptococcus mutans. It has been reported that children and adults harbor greater numbers of S. sanguinis in the oral cavity, associated with caries-free teeth. Conversely, S. mutans is predominant in individuals with a high number of carious lesions. Competition between both microorganisms stems from the production of H2 O2 by S. sanguinis and mutacins, a type of bacteriocins, by S. mutans. There is limited evidence on how S. sanguinis survives its own H2 O2 levels, or if it has other mechanisms that might aid in the competition against S. mutans, nonetheless. We performed a genomic and metabolic pathway comparison, coupled with a comprehensive literature review, to better understand the competition between these two species. Results indicated that S. sanguinis can outcompete S. mutans by the production of an enzyme capable of metabolizing H2 O2 . S. mutans, however, lacks the enzyme and is susceptible to the peroxide from S. sanguinis. In addition, S. sanguinis can generate energy through gluconeogenesis and seems to have evolved different communication mechanisms, indicating that novel proteins may be responsible for intra-species communication.}, } @article {pmid29235427, year = {2018}, author = {Wunderlich, J and Acuña-Soto, R and Alonso, WJ}, title = {Dengue hospitalisations in Brazil: annual wave from West to East and recent increase among children.}, journal = {Epidemiology and infection}, volume = {146}, number = {2}, pages = {236-245}, pmid = {29235427}, issn = {1469-4409}, mesh = {Adolescent ; Adult ; Aged ; Aged, 80 and over ; Brazil/epidemiology ; Child ; Child, Preschool ; Databases, Factual ; Dengue/*epidemiology ; Dengue Virus/genetics ; Female ; Fourier Analysis ; Genotype ; Hospitalization/*statistics & numerical data ; Humans ; Incidence ; Infant ; Male ; Middle Aged ; Seasons ; Young Adult ; }, abstract = {The number of dengue epidemics in Brazil has increased dramatically in the last 15 years. In this study, we analysed the seasonal patterns in the incidence of hospitalisations due to dengue across the different states of Brazil and compared these with the corresponding climatic patterns. We discovered that the seasonality of dengue hospitalisations in Brazil has a clear zonal gradient, characterised by the progression of primary peaks from West to East during the first half of the year, which may be associated with the increased vapour pressure and rainfall during this period, leading to increased mosquito abundance and activity. We also found that the proportion of children among hospitalised individuals was especially high during the peak outbreaks in 2007/2008 and 2010. This may be due to the emergence and spread of the new DENV-2 Southeast Asian genotype lineage II from 2007, which has probably arrived from the Caribbean and may have caused an increase in incidence and severity of the disease, particularly among children. Our findings may allow health systems to improve control interventions and contribute to reducing dengue morbidity and mortality by using integrated vector control in conjunction with early diagnosis and prompt supportive care.}, } @article {pmid29234011, year = {2017}, author = {Wesolowski, A and Zu Erbach-Schoenberg, E and Tatem, AJ and Lourenço, C and Viboud, C and Charu, V and Eagle, N and Engø-Monsen, K and Qureshi, T and Buckee, CO and Metcalf, CJE}, title = {Multinational patterns of seasonal asymmetry in human movement influence infectious disease dynamics.}, journal = {Nature communications}, volume = {8}, number = {1}, pages = {2069}, pmid = {29234011}, issn = {2041-1723}, support = {/WT_/Wellcome Trust/United Kingdom ; P2C HD047879/HD/NICHD NIH HHS/United States ; U54 GM088558/GM/NIGMS NIH HHS/United States ; 106866/Z/15/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Cell Phone ; Communicable Diseases/*epidemiology/transmission ; Geographic Information Systems ; Human Migration/*statistics & numerical data/trends ; Humans ; Incidence ; Kenya/epidemiology ; *Models, Biological ; Namibia/epidemiology ; Pakistan/epidemiology ; Rural Population/statistics & numerical data/trends ; *Seasons ; Travel/*statistics & numerical data/trends ; Urban Population/statistics & numerical data/trends ; }, abstract = {Seasonal variation in human mobility is globally ubiquitous and affects the spatial spread of infectious diseases, but the ability to measure seasonality in human movement has been limited by data availability. Here, we use mobile phone data to quantify seasonal travel and directional asymmetries in Kenya, Namibia, and Pakistan, across a spectrum from rural nomadic populations to highly urbanized communities. We then model how the geographic spread of several acute pathogens with varying life histories could depend on country-wide connectivity fluctuations through the year. In all three countries, major national holidays are associated with shifts in the scope of travel. Within this broader pattern, the relative importance of particular routes also fluctuates over the course of the year, with increased travel from rural to urban communities after national holidays, for example. These changes in travel impact how fast communities are likely to be reached by an introduced pathogen.}, } @article {pmid29232365, year = {2017}, author = {Gini, R and Schuemie, MJ and Pasqua, A and Carlini, E and Profili, F and Cricelli, I and Dazzi, P and Barletta, V and Francesconi, P and Lapi, F and Donatini, A and Dal Co, G and Visca, M and Bellentani, M and Sturkenboom, M and Klazinga, N}, title = {Monitoring compliance with standards of care for chronic diseases using healthcare administrative databases in Italy: Strengths and limitations.}, journal = {PloS one}, volume = {12}, number = {12}, pages = {e0188377}, pmid = {29232365}, issn = {1932-6203}, mesh = {Chronic Disease/*therapy ; Diabetes Mellitus, Type 2/therapy ; Female ; *Guideline Adherence ; Humans ; Hypertension/therapy ; Italy ; Male ; Myocardial Ischemia/therapy ; }, abstract = {BACKGROUND: A recent comprehensive report on healthcare quality in Italy published by the Organization of Economic Co-operation and Development (OECD) recommended that regular monitoring of quality of primary care by means of compliance with standards of care for chronic diseases is performed. A previous ecological study demonstrated that compliance with standards of care could be reliably estimated on regional level using administrative databases. This study compares estimates based on administrative data with estimates based on GP records for the same persons, to understand whether ecological fallacy played a role in the results of the previous study.

METHODS: We compared estimates of compliance with diagnostic and therapeutic standards of care for type 2 diabetes (T2DM), hypertension and ischaemic heart disease (IHD) from administrative data (IAD) with estimates from medical records (MR) for the same persons registered with 24 GP's in 2012. Data were linked at an individual level.

RESULTS: 32,688 persons entered the study, 12,673 having at least one of the three diseases according to at least one data source. Patients not detected by IAD were many, for all three conditions: adding MR increased the number of cases of T2DM, hypertension, and IHD by +40%, +42%, and +104%, respectively. IAD had imperfect sensitivity in detecting population compliance with therapies (adding MR increased the estimate, from +11.5% for statins to +14.7% for antithrombotics), and, more substantially, with diagnostic recommendations (adding MR increased the estimate, from +23.7% in glycated hemoglobin tests, to +50.5% in electrocardiogram). Patients not detected by IAD were less compliant with respect to those that IAD correctly identified (from -4.8 percentage points in proportion of IHD patients compliant with a yearly glycated hemoglobin test, to -40.1 points in the proportion of T2DM patients compliant with the same recommendation). IAD overestimated indicators of compliance with therapeutic standards (significant differences ranged from 3.3. to 3.6 percentage points) and underestimated indicators of compliance with diagnostic standards (significant differences ranged from -2.3 to -14.1 percentage points).

CONCLUSION: IAD overestimated the percentage of patients compliant with therapeutic standards by less than 6 percentage points, and underestimated the percentage of patients compliant with diagnostic standards by a maximum of 14 percentage points. Therefore, both discussions at local level between GP's and local health unit managers and discussions at central level between national and regional policy makers can be informed by indicators of compliance estimated by IAD, which, based on those results, have the ability of signalling critical or excellent clusters. However, this study found that estimates are partly flawed, because a high number of patients with chronic diseases are not detected by IAD, patients detected are not representative of the whole population of patients, and some categories of diagnostic tests are markedly underrecorded in IAD (up to 50% in the case of electrocardiograms). Those results call to caution when interpreting IAD estimates. Audits based on medical records, on the local level, and an interpretation taking into account information external to IAD, on the central level, are needed to assess a more comprehensive compliance with standards.}, } @article {pmid29228262, year = {2017}, author = {Cossu, RM and Casola, C and Giacomello, S and Vidalis, A and Scofield, DG and Zuccolo, A}, title = {LTR Retrotransposons Show Low Levels of Unequal Recombination and High Rates of Intraelement Gene Conversion in Large Plant Genomes.}, journal = {Genome biology and evolution}, volume = {9}, number = {12}, pages = {3449-3462}, pmid = {29228262}, issn = {1759-6653}, mesh = {Computational Biology ; Evolution, Molecular ; Gene Conversion ; Genome Size ; Magnoliopsida/genetics ; Picea/*genetics ; *Recombination, Genetic ; *Retroelements ; *Terminal Repeat Sequences ; Zea mays/*genetics ; }, abstract = {The accumulation and removal of transposable elements (TEs) is a major driver of genome size evolution in eukaryotes. In plants, long terminal repeat (LTR) retrotransposons (LTR-RTs) represent the majority of TEs and form most of the nuclear DNA in large genomes. Unequal recombination (UR) between LTRs leads to removal of intervening sequence and formation of solo-LTRs. UR is a major mechanism of LTR-RT removal in many angiosperms, but our understanding of LTR-RT-associated recombination within the large, LTR-RT-rich genomes of conifers is quite limited. We employ a novel read-based methodology to estimate the relative rates of LTR-RT-associated UR within the genomes of four conifer and seven angiosperm species. We found the lowest rates of UR in the largest genomes studied, conifers and the angiosperm maize. Recombination may also resolve as gene conversion, which does not remove sequence, so we analyzed LTR-RT-associated gene conversion events (GCEs) in Norway spruce and six angiosperms. Opposite the trend for UR, we found the highest rates of GCEs in Norway spruce and maize. Unlike previous work in angiosperms, we found no evidence that rates of UR correlate with retroelement structural features in the conifers, suggesting that another process is suppressing UR in these species. Recent results from diverse eukaryotes indicate that heterochromatin affects the resolution of recombination, by favoring gene conversion over crossing-over, similar to our observation of opposed rates of UR and GCEs. Control of LTR-RT proliferation via formation of heterochromatin would be a likely step toward large genomes in eukaryotes carrying high LTR-RT content.}, } @article {pmid29226627, year = {2017}, author = {Lötsch, J}, title = {Data visualizations to detect systematic errors in laboratory assay results.}, journal = {Pharmacology research & perspectives}, volume = {5}, number = {6}, pages = {}, pmid = {29226627}, issn = {2052-1707}, mesh = {Clinical Laboratory Services ; Data Interpretation, Statistical ; Programming Languages ; *Quality Control ; }, abstract = {The measurement of concentrations of drugs and endogenous substances is widely used in basic and clinical pharmacology research and service tasks. Using data science-derived visualizations of laboratory data, it is demonstrated on a real-life example that basic statistical exploration of laboratory assay results or advised standard visual methods of data inspection may fall short in detecting systematic laboratory errors. For example, data pathologies such as generating always the same value in all probes of a particular assay run may pass undetected when using standard methods of data quality check. It is shown that the use of different data visualizations that emphasize different views of the data may enhance the detection of systematic laboratory errors. A dotplot of single data in the order of assay is proposed that provides an overview on the data range, outliers and a particular type of systematic errors where similar values are wrongly measured in all probes.}, } @article {pmid29220487, year = {2017}, author = {Lassalle, F and Planel, R and Penel, S and Chapulliot, D and Barbe, V and Dubost, A and Calteau, A and Vallenet, D and Mornico, D and Bigot, T and Guéguen, L and Vial, L and Muller, D and Daubin, V and Nesme, X}, title = {Ancestral Genome Estimation Reveals the History of Ecological Diversification in Agrobacterium.}, journal = {Genome biology and evolution}, volume = {9}, number = {12}, pages = {3413-3431}, pmid = {29220487}, issn = {1759-6653}, mesh = {Agrobacterium/*cytology/*genetics ; *Biological Evolution ; Computational Biology ; *Ecology ; *Genetic Variation ; *Genome, Bacterial ; High-Throughput Nucleotide Sequencing ; Phylogeny ; Software ; }, abstract = {Horizontal gene transfer (HGT) is considered as a major source of innovation in bacteria, and as such is expected to drive adaptation to new ecological niches. However, among the many genes acquired through HGT along the diversification history of genomes, only a fraction may have actively contributed to sustained ecological adaptation. We used a phylogenetic approach accounting for the transfer of genes (or groups of genes) to estimate the history of genomes in Agrobacterium biovar 1, a diverse group of soil and plant-dwelling bacterial species. We identified clade-specific blocks of cotransferred genes encoding coherent biochemical pathways that may have contributed to the evolutionary success of key Agrobacterium clades. This pattern of gene coevolution rejects a neutral model of transfer, in which neighboring genes would be transferred independently of their function and rather suggests purifying selection on collectively coded acquired pathways. The acquisition of these synapomorphic blocks of cofunctioning genes probably drove the ecological diversification of Agrobacterium and defined features of ancestral ecological niches, which consistently hint at a strong selective role of host plant rhizospheres.}, } @article {pmid29220486, year = {2017}, author = {Hawkins, AK and Garza, ER and Dietz, VA and Hernandez, OJ and Hawkins, WD and Burrell, AM and Pepper, AE}, title = {Transcriptome Signatures of Selection, Drift, Introgression, and Gene Duplication in the Evolution of an Extremophile Endemic Plant.}, journal = {Genome biology and evolution}, volume = {9}, number = {12}, pages = {3478-3494}, pmid = {29220486}, issn = {1759-6653}, mesh = {Adaptation, Physiological ; Computational Biology ; *Evolution, Molecular ; Extremophiles/*genetics/growth & development/physiology ; *Gene Duplication ; Gene Expression Profiling ; *Genetic Drift ; Genetic Variation ; Genomics ; Metals, Heavy ; Phylogeny ; Selection, Genetic ; Transcriptome ; }, abstract = {Plants on serpentine soils provide extreme examples of adaptation to environment, and thus offer excellent models for the study of evolution at the molecular and genomic level. Serpentine outcrops are derived from ultramafic rock and have extremely low levels of essential plant nutrients (e.g., N, P, K, and Ca), as well as toxic levels of heavy metals (e.g., Ni, Cr, and Co) and low moisture availability. These outcrops provide habitat to a number of endemic plant species, including the annual mustard Caulanthus amplexicaulis var. barbarae (Cab) (Brassicaceae). Its sister taxon, C. amplexicaulis var. amplexicaulis (Caa), is intolerant to serpentine soils. Here, we assembled and annotated comprehensive reference transcriptomes of both Caa and Cab for use in protein coding sequence comparisons. A set of 29,443 reciprocal best Blast hit (RBH) orthologs between Caa and Cab was compared with identify coding sequence variants, revealing a high genome-wide dN/dS ratio between the two taxa (mean = 0.346). We show that elevated dN/dS likely results from the composite effects of genetic drift, positive selection, and the relaxation of negative selection. Further, analysis of paralogs within each taxon revealed the signature of a period of elevated gene duplication (∼10 Ma) that is shared with other species of the tribe Thelypodieae, and may have played a role in the striking morphological and ecological diversity of this tribe. In addition, distribution of the synonymous substitution rate, dS, is strongly bimodal, indicating a history of reticulate evolution that may have contributed to serpentine adaptation.}, } @article {pmid29220469, year = {2017}, author = {Hausen, J and Scholz-Starke, B and Burkhardt, U and Lesch, S and Rick, S and Russell, D and Roß-Nickoll, M and Ottermanns, R}, title = {Edaphostat: interactive ecological analysis of soil organism occurrences and preferences from the Edaphobase data warehouse.}, journal = {Database : the journal of biological databases and curation}, volume = {2017}, number = {}, pages = {}, pmid = {29220469}, issn = {1758-0463}, mesh = {*Databases, Factual ; *Soil ; }, abstract = {Edaphostat is part of the Edaphobase Web Application available at https://portal.edaphobase.org.}, } @article {pmid29220446, year = {2017}, author = {Chen, M and Henry, N and Almsaeed, A and Zhou, X and Wegrzyn, J and Ficklin, S and Staton, M}, title = {New extension software modules to enhance searching and display of transcriptome data in Tripal databases.}, journal = {Database : the journal of biological databases and curation}, volume = {2017}, number = {}, pages = {}, pmid = {29220446}, issn = {1758-0463}, mesh = {*Databases, Genetic ; Gene Expression Profiling/*methods ; Genomics/*methods ; Sequence Analysis, RNA ; *Software ; Transcriptome/*genetics ; }, abstract = {https://github.com/tripal/tripal_elasticsearch.

https://github.com/tripal/tripal_analysis_expression.}, } @article {pmid29213056, year = {2017}, author = {D'Amico, G and Rabadan, R and Kleban, M}, title = {A Random Categorization Model for Hierarchical Taxonomies.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {17051}, pmid = {29213056}, issn = {2045-2322}, support = {R01 GM117591/GM/NIGMS NIH HHS/United States ; U54 CA193313/CA/NCI NIH HHS/United States ; }, mesh = {Databases, Factual ; *Models, Biological ; Statistical Distributions ; }, abstract = {A taxonomy is a standardized framework to classify and organize items into categories. Hierarchical taxonomies are ubiquitous, ranging from the classification of organisms to the file system on a computer. Characterizing the typical distribution of items within taxonomic categories is an important question with applications in many disciplines. Ecologists have long sought to account for the patterns observed in species-abundance distributions (the number of individuals per species found in some sample), and computer scientists study the distribution of files per directory. Is there a universal statistical distribution describing how many items are typically found in each category in large taxonomies? Here, we analyze a wide array of large, real-world datasets - including items lost and found on the New York City transit system, library books, and a bacterial microbiome - and discover such an underlying commonality. A simple, non-parametric branching model that randomly categorizes items and takes as input only the total number of items and the total number of categories is quite successful in reproducing the observed abundance distributions. This result may shed light on patterns in species-abundance distributions long observed in ecology. The model also predicts the number of taxonomic categories that remain unrepresented in a finite sample.}, } @article {pmid29212070, year = {2018}, author = {Löckenhoff, CE}, title = {Aging and Decision-Making: A Conceptual Framework for Future Research - A Mini-Review.}, journal = {Gerontology}, volume = {64}, number = {2}, pages = {140-148}, pmid = {29212070}, issn = {1423-0003}, support = {P30 AG022845/AG/NIA NIH HHS/United States ; }, mesh = {Aging/physiology/*psychology ; Cognition ; *Decision Making/physiology ; Decision Support Techniques ; Emotions ; Functional Neuroimaging ; Geriatrics/trends ; Humans ; Motivation ; Research Design/trends ; Social Environment ; }, abstract = {Age differences in decision-making are of theoretical interest and have important practical implications, but relevant lines of work are distributed across multiple disciplines and often lack integration. The present review proposes an overarching conceptual framework with the aim of connecting disjointed aspects of this field of research. The framework builds on process models of decision-making and specifies potential mechanisms behind age effects as well as relevant moderators including task characteristics and contextual factors. After summarizing the extant literature for each aspect of the framework, compensatory mechanisms and ecological fit between different components of the model are considered. Implications for real-life decision-making, remaining research gaps, and directions for future research are discussed.}, } @article {pmid29211144, year = {2017}, author = {Chaves, EC and Costa, SV and Flores, RLDR and Neves, EOSD}, title = {Social deprivation index and leprosy in Pará State, Brazil, in 2013: spatial analysis.}, journal = {Epidemiologia e servicos de saude : revista do Sistema Unico de Saude do Brasil}, volume = {26}, number = {4}, pages = {807-816}, doi = {10.5123/S1679-49742017000400012}, pmid = {29211144}, issn = {2237-9622}, mesh = {Brazil/epidemiology ; Cities ; Cross-Sectional Studies ; Disease Notification ; *Endemic Diseases ; Factor Analysis, Statistical ; Humans ; *Information Systems ; Leprosy/diagnosis/*epidemiology/psychology ; *Psychosocial Deprivation ; Spatial Analysis ; }, abstract = {OBJECTIVE: to analyze the ecological association between the condition of social deprivation and leprosy detection rate in Pará State, Brazil.

METHODS: cross-sectional ecological study with data from the Information System for Notifiable Diseases (Sinan); global and local bivariate Moran's factor analysis and autocorrelation were used to identify spatial patterns associated with the distribution of the social deprivation index (SDI) and leprosy detection rate (LDR).

RESULTS: in 2013, 3,358 new cases of leprosy were reported in Pará, with LDR of 41.98 cases/100,000 inhabitants; higher rates were observed in the municipalities of the Araguaia region; 17.5% of the 143 municipalities of the state were considered hyperendemic (LDR>40.00) and 30.8% presented poor SDI; there was spatial autocorrelation between LDR and SDI (p<0.05).

CONCLUSION: there was spatial association between SDI and LDR, with higher leprosy detection in the municipalities with higher social deprivation.}, } @article {pmid29202384, year = {2018}, author = {Tang, SF and Chen, IH and Chiang, HY and Wu, CT and Hsueh, IP and Yu, WH and Hsieh, CL}, title = {A comparison between the original and Tablet-based Symbol Digit Modalities Test in patients with schizophrenia: Test-retest agreement, random measurement error, practice effect, and ecological validity.}, journal = {Psychiatry research}, volume = {260}, number = {}, pages = {199-206}, doi = {10.1016/j.psychres.2017.11.066}, pmid = {29202384}, issn = {1872-7123}, mesh = {*Activities of Daily Living ; Adult ; Cognitive Dysfunction/*diagnosis/etiology ; *Computers, Handheld ; Diagnosis, Computer-Assisted/*standards ; Female ; Humans ; Male ; Middle Aged ; Neuropsychological Tests/*standards ; Psychometrics/instrumentation/*standards ; Psychomotor Performance/*physiology ; Reproducibility of Results ; Schizophrenia/complications/*diagnosis ; }, abstract = {We aimed to compare the test-retest agreement, random measurement error, practice effect, and ecological validity of the original and Tablet-based Symbol Digit Modalities Test (T-SDMT) over five serial assessments, and to examine the concurrent validity of the T-SDMT in patients with schizophrenia. Sixty patients with chronic schizophrenia completed five serial assessments (one week apart) of the SDMT and T-SDMT and one assessment of the Activities of Daily Living Rating Scale III at the first time point. Both measures showed high test-retest agreement, similar levels of random measurement error over five serial assessments. Moreover, the practice effects of the two measures did not reach a plateau phase after five serial assessments in young and middle-aged participants. Nevertheless, only the practice effect of the T-SDMT became trivial after the first assessment. Like the SDMT, the T-SDMT had good ecological validity. The T-SDMT also had good concurrent validity with the SDMT. In addition, only the T-SDMT had discriminative validity to discriminate processing speed in young and middle-aged participants. Compared to the SDMT, the T-SDMT had overall slightly better psychometric properties, so it can be an alternative measure to the SDMT for assessing processing speed in patients with schizophrenia.}, } @article {pmid29198378, year = {2018}, author = {Matz, MV}, title = {Fantastic Beasts and How To Sequence Them: Ecological Genomics for Obscure Model Organisms.}, journal = {Trends in genetics : TIG}, volume = {34}, number = {2}, pages = {121-132}, doi = {10.1016/j.tig.2017.11.002}, pmid = {29198378}, issn = {0168-9525}, mesh = {Adaptation, Biological/genetics ; Animals ; Biological Evolution ; DNA Methylation ; Ecology ; Gene Ontology ; *Genetics, Population ; *Genome ; Genomics/instrumentation/*methods ; High-Throughput Nucleotide Sequencing/economics/*methods/trends ; *Models, Animal ; Molecular Sequence Annotation ; }, abstract = {The application of genomic approaches to 'obscure model organisms' (OMOs), meaning species with no prior genomic resources, enables increasingly sophisticated studies of the genomic basis of evolution, acclimatization, and adaptation in real ecological contexts. I consider here ecological questions that can be addressed using OMOs, and indicate optimal sequencing and data-handling solutions for each case. With this I hope to promote the diversity of OMO-based projects that would capitalize on the peculiarities of the natural history of OMOs and could feasibly be completed within the scope of a single PhD thesis.}, } @article {pmid29197740, year = {2018}, author = {Mühleisen, TW and Reinbold, CS and Forstner, AJ and Abramova, LI and Alda, M and Babadjanova, G and Bauer, M and Brennan, P and Chuchalin, A and Cruceanu, C and Czerski, PM and Degenhardt, F and Fischer, SB and Fullerton, JM and Gordon, SD and Grigoroiu-Serbanescu, M and Grof, P and Hauser, J and Hautzinger, M and Herms, S and Hoffmann, P and Kammerer-Ciernioch, J and Khusnutdinova, E and Kogevinas, M and Krasnov, V and Lacour, A and Laprise, C and Leber, M and Lissowska, J and Lucae, S and Maaser, A and Maier, W and Martin, NG and Mattheisen, M and Mayoral, F and McKay, JD and Medland, SE and Mitchell, PB and Moebus, S and Montgomery, GW and Müller-Myhsok, B and Oruc, L and Pantelejeva, G and Pfennig, A and Pojskic, L and Polonikov, A and Reif, A and Rivas, F and Rouleau, GA and Schenk, LM and Schofield, PR and Schwarz, M and Streit, F and Strohmaier, J and Szeszenia-Dabrowska, N and Tiganov, AS and Treutlein, J and Turecki, G and Vedder, H and Witt, SH and Schulze, TG and Rietschel, M and Nöthen, MM and Cichon, S}, title = {Gene set enrichment analysis and expression pattern exploration implicate an involvement of neurodevelopmental processes in bipolar disorder.}, journal = {Journal of affective disorders}, volume = {228}, number = {}, pages = {20-25}, doi = {10.1016/j.jad.2017.11.068}, pmid = {29197740}, issn = {1573-2517}, support = {001/WHO_/World Health Organization/International ; 084703/WT_/Wellcome Trust/United Kingdom ; MOP-13506/CAPMC/CIHR/Canada ; }, mesh = {Algorithms ; Bipolar Disorder/*genetics/metabolism/physiopathology ; Brain/*growth & development/metabolism ; Female ; GRB2 Adaptor Protein/genetics/*metabolism ; Gene Expression ; Genes, erbB-2/physiology ; Genetic Predisposition to Disease ; Genome-Wide Association Study ; Humans ; Male ; Phenotype ; Polymorphism, Single Nucleotide ; RNA/metabolism ; Receptor, ErbB-2/*metabolism ; *Signal Transduction ; }, abstract = {BACKGROUND: Bipolar disorder (BD) is a common and highly heritable disorder of mood. Genome-wide association studies (GWAS) have identified several independent susceptibility loci. In order to extract more biological information from GWAS data, multi-locus approaches represent powerful tools since they utilize knowledge about biological processes to integrate functional sets of genes at strongly to moderately associated loci.

METHODS: We conducted gene set enrichment analyses (GSEA) using 2.3 million single-nucleotide polymorphisms, 397 Reactome pathways and 24,025 patients with BD and controls. RNA expression of implicated individual genes and gene sets were examined in post-mortem brains across lifespan.

RESULTS: Two pathways showed a significant enrichment after correction for multiple comparisons in the GSEA: GRB2 events in ERBB2 signaling, for which 6 of 21 genes were BD associated (PFDR = 0.0377), and NCAM signaling for neurite out-growth, for which 11 out of 62 genes were BD associated (PFDR = 0.0451). Most pathway genes showed peaks of RNA co-expression during fetal development and infancy and mapped to neocortical areas and parts of the limbic system.

LIMITATIONS: Pathway associations were technically reproduced by two methods, although they were not formally replicated in independent samples. Gene expression was explored in controls but not in patients.

CONCLUSIONS: Pathway analysis in large GWAS data of BD and follow-up of gene expression patterns in healthy brains provide support for an involvement of neurodevelopmental processes in the etiology of this neuropsychiatric disease. Future studies are required to further evaluate the relevance of the implicated genes on pathway functioning and clinical aspects of BD.}, } @article {pmid29197686, year = {2018}, author = {Yoshida, Y and Schmaltz, CL and Jackson-Thompson, J and Simoes, EJ}, title = {The impact of screening on cancer incidence and mortality in Missouri, USA, 2004-2013.}, journal = {Public health}, volume = {154}, number = {}, pages = {51-58}, doi = {10.1016/j.puhe.2017.10.015}, pmid = {29197686}, issn = {1476-5616}, mesh = {Adult ; Aged ; Breast Neoplasms/epidemiology/mortality ; Colorectal Neoplasms/epidemiology/mortality ; Early Detection of Cancer/*statistics & numerical data ; Female ; Health Care Surveys ; Humans ; Incidence ; Male ; Middle Aged ; Missouri/epidemiology ; Neoplasms/*epidemiology/mortality ; Uterine Cervical Neoplasms/epidemiology/mortality ; Young Adult ; }, abstract = {OBJECTIVES: Population-based evidence regarding impact of cancer screenings and cancer rates in Missouri is lacking. This study examined whether screenings of breast cancer, cervical cancer, and colorectal cancer impact early-stage cancer incidence and mortality in Missouri.

STUDY DESIGN: This is an ecological study based on county-specific estimates of selected cancer screening prevalence and early-stage cancer incidence and cancer mortality.

METHODS: County-specific prevalence of clinical breast examination, mammography, Pap test, sigmoidoscopy or colonoscopy, and fecal occult blood test (FOBT) were generated from Missouri County-Level Study (2003, 2007, and 2011). County-specific crude incidence and mortality were calculated (2004-2013). Pearson's correlation and Poisson regression were used to test association between cancer rate and screening prevalence. Covariates included county-level mean age, percentage of whites, percentage with low income, percentage with less than high school education high school, percentage with no insurance, and percentage having difficulties accessing care.

RESULTS: In the adjusted model, 'ever had Pap test' was significantly associated with an increase of 8% in early-stage cervical cancer incidence. Having clinical breast examination or Pap test in the past was also associated with decreases in mortality by 3% and 4%, respectively, although the association was not significant for Pap test. In addition, having mammography was statistically significantly associated with early-stage breast cancer incidence, and having FOBT or sigmoidoscopy or colonoscopy was associated with decreased colorectal cancer mortality; however, magnitude for these associations was only around 1%.

CONCLUSIONS: This study provides ecological evidence of the effectiveness of screening services in predicting early stage cancer incidence and in reducing mortality across Missouri counties. Further incentive to promote these screenings in Missouri is needed.}, } @article {pmid29196950, year = {2018}, author = {Kim, D and Park, HJ and Sul, WJ and Park, H}, title = {Transcriptome analysis of Pseudomonas sp. from subarctic tundra soil: pathway description and gene discovery for humic acids degradation.}, journal = {Folia microbiologica}, volume = {63}, number = {3}, pages = {315-323}, pmid = {29196950}, issn = {1874-9356}, mesh = {Biodegradation, Environmental ; Databases, Protein ; *Gene Expression Profiling ; Gene Expression Regulation, Bacterial ; Genes, Bacterial ; Humic Substances/*microbiology ; Lignin/metabolism ; *Metabolic Networks and Pathways ; Pseudomonas/*genetics/metabolism ; *Soil Microbiology ; *Tundra ; }, abstract = {Although humic acids (HA) are involved in many biological processes in soils and thus their ecological importance has received much attention, the degradative pathways and corresponding catalytic genes underlying the HA degradation by bacteria remain unclear. To unveil those uncertainties, we analyzed transcriptomes extracted from Pseudomonas sp. PAMC 26793 cells time-dependently induced in the presence of HA in a lab flask. Out of 6288 genes, 299 (microarray) and 585 (RNA-seq) were up-regulated by > 2.0-fold in HA-induced cells, compared with controls. A significant portion (9.7% in microarray and 24.1% in RNA-seq) of these genes are predicted to function in the transport and metabolism of small molecule compounds, which could result from microbial HA degradation. To further identify lignin (a surrogate for HA)-degradative genes, 6288 protein sequences were analyzed against carbohydrate-active enzyme database and a self-curated list of putative lignin degradative genes. Out of 19 genes predicted to function in lignin degradation, several genes encoding laccase, dye-decolorizing peroxidase, vanillate O-demethylase oxygenase and reductase, and biphenyl 2,3-dioxygenase were up-regulated > 2.0-fold in RNA-seq. This induction was further confirmed by qRT-PCR, validating the likely involvement of these genes in the degradation of HA.}, } @article {pmid29194875, year = {2018}, author = {Crüsemann, M and Reher, R and Schamari, I and Brachmann, AO and Ohbayashi, T and Kuschak, M and Malfacini, D and Seidinger, A and Pinto-Carbó, M and Richarz, R and Reuter, T and Kehraus, S and Hallab, A and Attwood, M and Schiöth, HB and Mergaert, P and Kikuchi, Y and Schäberle, TF and Kostenis, E and Wenzel, D and Müller, CE and Piel, J and Carlier, A and Eberl, L and König, GM}, title = {Heterologous Expression, Biosynthetic Studies, and Ecological Function of the Selective Gq-Signaling Inhibitor FR900359.}, journal = {Angewandte Chemie (International ed. in English)}, volume = {57}, number = {3}, pages = {836-840}, doi = {10.1002/anie.201707996}, pmid = {29194875}, issn = {1521-3773}, mesh = {Animals ; Bombyx/metabolism ; Chromosomes, Artificial, Bacterial ; Computational Biology ; Depsipeptides/*biosynthesis/metabolism/*pharmacology ; Escherichia coli/genetics ; GTP-Binding Protein alpha Subunits, Gq-G11/*metabolism ; Gene Transfer Techniques ; HEK293 Cells ; Humans ; Insect Proteins/*metabolism ; Multigene Family ; Peptide Synthases/genetics ; Primulaceae/chemistry ; Sf9 Cells ; Signal Transduction/*drug effects ; Tandem Mass Spectrometry ; }, abstract = {The cyclic depsipeptide FR900359 (FR), isolated from the tropical plant Ardisia crenata, is a strong and selective inhibitor of Gq proteins, making it an indispensable pharmacological tool to study Gq-related processes, as well as a promising drug candidate. Gq inhibition is a novel mode of action for defense chemicals and crucial for the ecological function of FR, as shown by in vivo experiments in mice, its affinity to insect Gq proteins, and insect toxicity studies. The uncultured endosymbiont of A. crenata was sequenced, revealing the FR nonribosomal peptide synthetase (frs) gene cluster. We here provide a detailed model of FR biosynthesis, supported by in vitro enzymatic and bioinformatic studies, and the novel analogue AC-1, which demonstrates the flexibility of the FR starter condensation domains. Finally, expression of the frs genes in E. coli led to heterologous FR production in a cultivable, bacterial host for the first time.}, } @article {pmid29194457, year = {2017}, author = {Jacob, V and Monsempès, C and Rospars, JP and Masson, JB and Lucas, P}, title = {Olfactory coding in the turbulent realm.}, journal = {PLoS computational biology}, volume = {13}, number = {12}, pages = {e1005870}, pmid = {29194457}, issn = {1553-7358}, mesh = {Animals ; Appetitive Behavior/*physiology ; Arthropod Antennae/cytology/*physiology ; Computational Biology/methods ; Male ; Moths/physiology ; Olfactory Pathways/*physiology ; Olfactory Receptor Neurons/metabolism/*physiology ; Pheromones/*metabolism ; }, abstract = {Long-distance olfactory search behaviors depend on odor detection dynamics. Due to turbulence, olfactory signals travel as bursts of variable concentration and spacing and are characterized by long-tail distributions of odor/no-odor events, challenging the computing capacities of olfactory systems. How animals encode complex olfactory scenes to track the plume far from the source remains unclear. Here we focus on the coding of the plume temporal dynamics in moths. We compare responses of olfactory receptor neurons (ORNs) and antennal lobe projection neurons (PNs) to sequences of pheromone stimuli either with white-noise patterns or with realistic turbulent temporal structures simulating a large range of distances (8 to 64 m) from the odor source. For the first time, we analyze what information is extracted by the olfactory system at large distances from the source. Neuronal responses are analyzed using linear-nonlinear models fitted with white-noise stimuli and used for predicting responses to turbulent stimuli. We found that neuronal firing rate is less correlated with the dynamic odor time course when distance to the source increases because of improper coding during long odor and no-odor events that characterize large distances. Rapid adaptation during long puffs does not preclude however the detection of puff transitions in PNs. Individual PNs but not individual ORNs encode the onset and offset of odor puffs for any temporal structure of stimuli. A higher spontaneous firing rate coupled to an inhibition phase at the end of PN responses contributes to this coding property. This allows PNs to decode the temporal structure of the odor plume at any distance to the source, an essential piece of information moths can use in their tracking behavior.}, } @article {pmid29190686, year = {2017}, author = {Morris, G and Conner, LM}, title = {Assessment of accuracy, fix success rate, and use of estimated horizontal position error (EHPE) to filter inaccurate data collected by a common commercially available GPS logger.}, journal = {PloS one}, volume = {12}, number = {11}, pages = {e0189020}, pmid = {29190686}, issn = {1932-6203}, mesh = {Data Collection ; *Geographic Information Systems ; }, abstract = {Global positioning system (GPS) technologies have improved the ability of researchers to monitor wildlife; however, use of these technologies is often limited by monetary costs. Some researchers have begun to use commercially available GPS loggers as a less expensive means of tracking wildlife, but data regarding performance of these devices are limited. We tested a commercially available GPS logger (i-gotU GT-120) by placing loggers at ground control points with locations known to < 30 cm. In a preliminary investigation, we collected locations every 15 minutes for several days to estimate location error (LE) and circular error probable (CEP). Using similar methods, we then investigated the influence of cover on LE, CEP, and fix success rate (FSR) by constructing cover over ground control points. We found mean LE was < 10 m and mean 50% CEP was < 7 m. FSR was not significantly influenced by cover and in all treatments remained near 100%. Cover had a minor but significant effect on LE. Denser cover was associated with higher mean LE, but the difference in LE between the no cover and highest cover treatments was only 2.2 m. Finally, the most commonly used commercially available devices provide a measure of estimated horizontal position error (EHPE) which potentially may be used to filter inaccurate locations. Using data combined from the preliminary and cover investigations, we modeled LE as a function of EHPE and number of satellites. We found support for use of both EHPE and number of satellites in predicting LE; however, use of EHPE to filter inaccurate locations resulted in the loss of many locations with low error in return for only modest improvements in LE. Even without filtering, the accuracy of the logger was likely sufficient for studies which can accept average location errors of approximately 10 m.}, } @article {pmid29187508, year = {2018}, author = {Peischl, S and Dupanloup, I and Foucal, A and Jomphe, M and Bruat, V and Grenier, JC and Gouy, A and Gilbert, KJ and Gbeha, E and Bosshard, L and Hip-Ki, E and Agbessi, M and Hodgkinson, A and Vézina, H and Awadalla, P and Excoffier, L}, title = {Relaxed Selection During a Recent Human Expansion.}, journal = {Genetics}, volume = {208}, number = {2}, pages = {763-777}, pmid = {29187508}, issn = {1943-2631}, support = {MR/L016311/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Algorithms ; Alleles ; Biological Evolution ; Computer Simulation ; Demography ; Evolution, Molecular ; Gene Frequency ; Gene Ontology ; Genetic Fitness ; Genetic Variation ; *Genetics, Population ; Humans ; *Models, Genetic ; Mutation ; Polymorphism, Single Nucleotide ; Quebec ; *Selection, Genetic ; }, abstract = {Humans have colonized the planet through a series of range expansions, which deeply impacted genetic diversity in newly settled areas and potentially increased the frequency of deleterious mutations on expanding wave fronts. To test this prediction, we studied the genomic diversity of French Canadians who colonized Quebec in the 17th century. We used historical information and records from ∼4000 ascending genealogies to select individuals whose ancestors lived mostly on the colonizing wave front and individuals whose ancestors remained in the core of the settlement. Comparison of exomic diversity reveals that: (i) both new and low-frequency variants are significantly more deleterious in front than in core individuals, (ii) equally deleterious mutations are at higher frequencies in front individuals, and (iii) front individuals are two times more likely to be homozygous for rare very deleterious mutations present in Europeans. These differences have emerged in the past six to nine generations and cannot be explained by differential inbreeding, but are consistent with relaxed selection mainly due to higher rates of genetic drift on the wave front. Demographic inference and modeling of the evolution of rare variants suggest lower effective size on the front, and lead to an estimation of selection coefficients that increase with conservation scores. Even though range expansions have had a relatively limited impact on the overall fitness of French Canadians, they could explain the higher prevalence of recessive genetic diseases in recently settled regions of Quebec.}, } @article {pmid29186623, year = {2017}, author = {Hoffman, DJ and Reynolds, RM and Hardy, DB}, title = {Developmental origins of health and disease: current knowledge and potential mechanisms.}, journal = {Nutrition reviews}, volume = {75}, number = {12}, pages = {951-970}, doi = {10.1093/nutrit/nux053}, pmid = {29186623}, issn = {1753-4887}, mesh = {Animals ; Body Composition ; Databases, Factual ; Diet ; Dyslipidemias/*epidemiology/etiology ; Female ; Gastrointestinal Microbiome ; Gastrointestinal Tract/microbiology ; Glucocorticoids/administration & dosage/adverse effects ; Humans ; Infant ; *Infant Nutritional Physiological Phenomena ; Malnutrition/complications/*epidemiology ; *Maternal Nutritional Physiological Phenomena ; Metabolic Diseases/*epidemiology/etiology ; Models, Animal ; Nutritional Status ; Obesity/*epidemiology ; Observational Studies as Topic ; Prevalence ; Randomized Controlled Trials as Topic ; Socioeconomic Factors ; }, abstract = {Epidemiologic and clinical research has provided a large body of evidence supporting the developmental origins of health and disease (DOHaD), but there has been a relative dearth of mechanistic studies in humans due to the complexity of working with large, longitudinal cohorts. Nonetheless, animal models of undernutrition have provided substantial evidence for the potential epigenetic, metabolic, and endocrine mechanisms behind DOHaD. Furthermore, recent research has explored the interaction between the environment and the gastrointestinal system by investigating how the gut microbial ecology may impact the capacity for nutrient processing and absorption in a manner that may limit growth. This review presents a summary of current research that supports the concept of DOHaD, as well as potential mechanisms and interactions that explain how nutrition in utero and during early childhood influences lifelong health.}, } @article {pmid29186473, year = {2018}, author = {Dobrzynski, L and Fornalski, KW and Reszczynska, J}, title = {Meta-analysis of thirty-two case-control and two ecological radon studies of lung cancer.}, journal = {Journal of radiation research}, volume = {59}, number = {2}, pages = {149-163}, pmid = {29186473}, issn = {1349-9157}, mesh = {Bayes Theorem ; Case-Control Studies ; Databases as Topic ; Humans ; Linear Models ; Lung Neoplasms/*etiology ; Radon/*adverse effects ; }, abstract = {A re-analysis has been carried out of thirty-two case-control and two ecological studies concerning the influence of radon, a radioactive gas, on the risk of lung cancer. Three mathematically simplest dose-response relationships (models) were tested: constant (zero health effect), linear, and parabolic (linear-quadratic). Health effect end-points reported in the analysed studies are odds ratios or relative risk ratios, related either to morbidity or mortality. In our preliminary analysis, we show that the results of dose-response fitting are qualitatively (within uncertainties, given as error bars) the same, whichever of these health effect end-points are applied. Therefore, we deemed it reasonable to aggregate all response data into the so-called Relative Health Factor and jointly analysed such mixed data, to obtain better statistical power. In the second part of our analysis, robust Bayesian and classical methods of analysis were applied to this combined dataset. In this part of our analysis, we selected different subranges of radon concentrations. In view of substantial differences between the methodology used by the authors of case-control and ecological studies, the mathematical relationships (models) were applied mainly to the thirty-two case-control studies. The degree to which the two ecological studies, analysed separately, affect the overall results when combined with the thirty-two case-control studies, has also been evaluated. In all, as a result of our meta-analysis of the combined cohort, we conclude that the analysed data concerning radon concentrations below ~1000 Bq/m3 (~20 mSv/year of effective dose to the whole body) do not support the thesis that radon may be a cause of any statistically significant increase in lung cancer incidence.}, } @article {pmid29186423, year = {2018}, author = {Richardson, MF and Sequeira, F and Selechnik, D and Carneiro, M and Vallinoto, M and Reid, JG and West, AJ and Crossland, MR and Shine, R and Rollins, LA}, title = {Improving amphibian genomic resources: a multitissue reference transcriptome of an iconic invader.}, journal = {GigaScience}, volume = {7}, number = {1}, pages = {1-7}, pmid = {29186423}, issn = {2047-217X}, mesh = {Animals ; Aquatic Organisms/*genetics/growth & development ; Benchmarking ; Bufonidae/*genetics/growth & development ; Chromosome Mapping ; Female ; Gene Library ; Gene Ontology ; *Genome ; High-Throughput Nucleotide Sequencing ; *Introduced Species ; Life Cycle Stages/*genetics ; Male ; Molecular Sequence Annotation ; Sequence Analysis, RNA ; *Transcriptome ; }, abstract = {BACKGROUND: Cane toads (Rhinella marina) are an iconic invasive species introduced to 4 continents and well utilized for studies of rapid evolution in introduced environments. Despite the long introduction history of this species, its profound ecological impacts, and its utility for demonstrating evolutionary principles, genetic information is sparse. Here we produce a de novo transcriptome spanning multiple tissues and life stages to enable investigation of the genetic basis of previously identified rapid phenotypic change over the introduced range.

FINDINGS: Using approximately 1.9 billion reads from developing tadpoles and 6 adult tissue-specific cDNA libraries, as well as a transcriptome assembly pipeline encompassing 100 separate de novo assemblies, we constructed 62 202 transcripts, of which we functionally annotated ∼50%. Our transcriptome assembly exhibits 90% full-length completeness of the Benchmarking Universal Single-Copy Orthologs data set. Robust assembly metrics and comparisons with several available anuran transcriptomes and genomes indicate that our cane toad assembly is one of the most complete anuran genomic resources available.

CONCLUSIONS: This comprehensive anuran transcriptome will provide a valuable resource for investigation of genes under selection during invasion in cane toads, but will also greatly expand our general knowledge of anuran genomes, which are underrepresented in the literature. The data set is publically available in NCBI and GigaDB to serve as a resource for other researchers.}, } @article {pmid29184540, year = {2017}, author = {Walter, JM and Coutinho, FH and Dutilh, BE and Swings, J and Thompson, FL and Thompson, CC}, title = {Ecogenomics and Taxonomy of Cyanobacteria Phylum.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {2132}, pmid = {29184540}, issn = {1664-302X}, abstract = {Cyanobacteria are major contributors to global biogeochemical cycles. The genetic diversity among Cyanobacteria enables them to thrive across many habitats, although only a few studies have analyzed the association of phylogenomic clades to specific environmental niches. In this study, we adopted an ecogenomics strategy with the aim to delineate ecological niche preferences of Cyanobacteria and integrate them to the genomic taxonomy of these bacteria. First, an appropriate phylogenomic framework was established using a set of genomic taxonomy signatures (including a tree based on conserved gene sequences, genome-to-genome distance, and average amino acid identity) to analyse ninety-nine publicly available cyanobacterial genomes. Next, the relative abundances of these genomes were determined throughout diverse global marine and freshwater ecosystems, using metagenomic data sets. The whole-genome-based taxonomy of the ninety-nine genomes allowed us to identify 57 (of which 28 are new genera) and 87 (of which 32 are new species) different cyanobacterial genera and species, respectively. The ecogenomic analysis allowed the distinction of three major ecological groups of Cyanobacteria (named as i. Low Temperature; ii. Low Temperature Copiotroph; and iii. High Temperature Oligotroph) that were coherently linked to the genomic taxonomy. This work establishes a new taxonomic framework for Cyanobacteria in the light of genomic taxonomy and ecogenomic approaches.}, } @article {pmid29181443, year = {2017}, author = {Reino, L and Figueira, R and Beja, P and Araújo, MB and Capinha, C and Strubbe, D}, title = {Networks of global bird invasion altered by regional trade ban.}, journal = {Science advances}, volume = {3}, number = {11}, pages = {e1700783}, pmid = {29181443}, issn = {2375-2548}, mesh = {Animals ; Birds ; Commerce ; Conservation of Natural Resources ; Databases, Factual ; Endangered Species/*economics ; }, abstract = {Wildlife trade is a major pathway for introduction of invasive species worldwide. However, how exactly wildlife trade influences invasion risk, beyond the transportation of individuals to novel areas, remains unknown. We analyze the global trade network of wild-caught birds from 1995 to 2011 as reported by CITES (Convention on International Trade in Endangered Species of Wild Fauna and Flora). We found that before the European Union ban on imports of wild-caught birds, declared in 2005, invasion risk was closely associated with numbers of imported birds, diversity of import sources, and degree of network centrality of importer countries. After the ban, fluxes of global bird trade declined sharply. However, new trade routes emerged, primarily toward the Nearctic, Afrotropical, and Indo-Malay regions. Although regional bans can curtail invasion risk globally, to be fully effective and prevent rerouting of trade flows, bans should be global.}, } @article {pmid29179052, year = {2018}, author = {Suffoletto, B and Gharani, P and Chung, T and Karimi, H}, title = {Using phone sensors and an artificial neural network to detect gait changes during drinking episodes in the natural environment.}, journal = {Gait & posture}, volume = {60}, number = {}, pages = {116-121}, pmid = {29179052}, issn = {1879-2219}, support = {K23 AA023284/AA/NIAAA NIH HHS/United States ; R01 AA023650/AA/NIAAA NIH HHS/United States ; }, mesh = {Accelerometry/methods ; Adult ; Alcohol Drinking/*physiopathology ; Bayes Theorem ; *Blood Alcohol Content ; Environment ; Feasibility Studies ; Female ; Gait/*physiology ; Humans ; Magnetometry/methods ; Male ; Mobile Applications ; Neural Networks, Computer ; Pilot Projects ; Smartphone/statistics & numerical data ; Young Adult ; }, abstract = {BACKGROUND: Phone sensors could be useful in assessing changes in gait that occur with alcohol consumption. This study determined (1) feasibility of collecting gait-related data during drinking occasions in the natural environment, and (2) how gait-related features measured by phone sensors relate to estimated blood alcohol concentration (eBAC).

METHODS: Ten young adult heavy drinkers were prompted to complete a 5-step gait task every hour from 8pm to 12am over four consecutive weekends. We collected 3-axis accelerometer, gyroscope, and magnetometer data from phone sensors, and computed 24 gait-related features using a sliding window technique. eBAC levels were calculated at each time point based on Ecological Momentary Assessment (EMA) of alcohol use. We used an artificial neural network model to analyze associations between sensor features and eBACs in training (70% of the data) and validation and test (30% of the data) datasets.

RESULTS: We analyzed 128 data points where both eBAC and gait-related sensor data were captured, either when not drinking (n=60), while eBAC was ascending (n=55) or eBAC was descending (n=13). 21 data points were captured at times when the eBAC was greater than the legal limit (0.08mg/dl). Using a Bayesian regularized neural network, gait-related phone sensor features showed a high correlation with eBAC (Pearson's r>0.9), and >95% of estimated eBAC would fall between -0.012 and +0.012 of actual eBAC.

CONCLUSIONS: It is feasible to collect gait-related data from smartphone sensors during drinking occasions in the natural environment. Sensor-based features can be used to infer gait changes associated with elevated blood alcohol content.}, } @article {pmid29178828, year = {2017}, author = {Qin, J and Hu, Y and Ma, KY and Jiang, X and Ho, CH and Tsang, LM and Yi, L and Leung, RWT and Chu, KH}, title = {CrusTF: a comprehensive resource of transcriptomes for evolutionary and functional studies of crustacean transcription factors.}, journal = {BMC genomics}, volume = {18}, number = {1}, pages = {908}, pmid = {29178828}, issn = {1471-2164}, support = {41606143//National Natural Science Foundation of China/ ; 11601343//National Natural Science Foundation of China/ ; 4053187//Direct Grant for Research from The Chinese University of Hong Kong/ ; C4042-14G//Collaborative Research Fund of the Research Grants Council/ ; 2016A030310038//Natural Science Foundation of Guangdong Province/ ; }, mesh = {Animals ; Crustacea/*genetics ; *Databases, Genetic ; Phylogeny ; Transcription Factors/chemistry/classification/genetics/*physiology ; *Transcriptome ; }, abstract = {BACKGROUND: Crustacea, the second largest subphylum of Arthropoda, includes species of major ecological and economic importance, such as crabs, lobsters, crayfishes, shrimps, and barnacles. With the rapid development of crustacean aquaculture and biodiversity loss, understanding the gene regulatory mechanisms of growth, reproduction, and development of crustaceans is crucial to both aquaculture development and biodiversity conservation of this group of organisms. In these biological processes, transcription factors (TFs) play a vital role in regulating gene expression. However, crustacean transcription factors are still largely unknown, because the lack of complete genome sequences of most crustacean species hampers the studies on their transcriptional regulation on a system-wide scale. Thus, the current TF databases derived from genome sequences contain TF information for only a few crustacean species and are insufficient to elucidate the transcriptional diversity of such a large animal group.

RESULTS: Our database CrusTF (http://qinlab.sls.cuhk.edu.hk/CrusTF) provides comprehensive information for evolutionary and functional studies on the crustacean transcriptional regulatory system. CrusTF fills the knowledge gap of transcriptional regulation in crustaceans by exploring publicly available and newly sequenced transcriptomes of 170 crustacean species and identifying 131,941 TFs within 63 TF families. CrusTF features three categories of information: sequence, function, and evolution of crustacean TFs. The database enables searching, browsing and downloading of crustacean TF sequences. CrusTF infers DNA binding motifs of crustacean TFs, thus facilitating the users to predict potential downstream TF targets. The database also presents evolutionary analyses of crustacean TFs, which improve our understanding of the evolution of transcriptional regulatory systems in crustaceans.

CONCLUSIONS: Given the importance of TF information in evolutionary and functional studies on transcriptional regulatory systems of crustaceans, this database will constitute a key resource for the research community of crustacean biology and evolutionary biology. Moreover, CrusTF serves as a model for the construction of TF database derived from transcriptome data. A similar approach could be applied to other groups of organisms, for which transcriptomes are more readily available than genomes.}, } @article {pmid29178196, year = {2018}, author = {Yuan, YY and Li, M and Fan, F and Qiu, XH}, title = {Comparative transcriptomic analysis of larval and adult Malpighian tubules from the cotton bollworm Helicoverpa armigera.}, journal = {Insect science}, volume = {25}, number = {6}, pages = {991-1005}, doi = {10.1111/1744-7917.12561}, pmid = {29178196}, issn = {1744-7917}, support = {31601644//National Natural Science Foundation of China/ ; ChineseIPM1502//State Key Laboratory of Integrated Management of Pest Insects and Rodents/ ; }, mesh = {Animals ; Diuresis/genetics ; *Gene Expression Profiling ; Gene Ontology ; Larva/*genetics ; Malpighian Tubules/*metabolism ; Molecular Sequence Annotation ; Moths/anatomy & histology/*genetics/growth & development/physiology ; }, abstract = {Malpighian tubules (MTs) are usually considered the key excretory and osmoregulatory organs of insects. However, increasing evidence has suggested that MTs perform many more functions than just osmoregulation. Until now, the molecular and physiological functions of MTs in the cotton bollworm (Helicoverpa armigera), a very important agricultural pest, are largely unknown. In this study, the transcriptomes of H. armigera MTs from larvae, male adults and female adults were sequenced using RNA-Seq technology, and comparative analyses of transcriptomes between two life stages (larval and adult) and between adult sexes were conducted. We generated a total of 84 643 high-quality unigenes, and identified a large number of abundant transcripts putatively encoding proteins involved in diuresis, detoxification, immunity, carbohydrate transport and metabolism, development and reproduction. We found that the expression pattern of unigenes was relatively similar between female and male adult MTs, but different between larval and adult MTs. Our data suggest that insect MTs may take multiple physiological functions as versatile organs. The extensive alterations in gene expression in MTs occurred from larvae to adults reflect an ecological adaptation to different feeding habits. Sexual dimorphism in the cotton bollworm is somewhat indicated by the transcriptional difference of genes related to carbohydrate metabolism, detoxification, immunity and reproduction in the MTs of male and female adults.}, } @article {pmid29176825, year = {2017}, author = {Farhang-Sardroodi, S and Darooneh, AH and Nikbakht, M and Komarova, NL and Kohandel, M}, title = {The effect of spatial randomness on the average fixation time of mutants.}, journal = {PLoS computational biology}, volume = {13}, number = {11}, pages = {e1005864}, pmid = {29176825}, issn = {1553-7358}, support = {U01 CA187956/CA/NCI NIH HHS/United States ; }, mesh = {Computational Biology ; *Evolution, Molecular ; Genetic Fitness ; Models, Biological ; Models, Statistical ; *Mutation ; *Population Dynamics ; }, abstract = {The mean conditional fixation time of a mutant is an important measure of stochastic population dynamics, widely studied in ecology and evolution. Here, we investigate the effect of spatial randomness on the mean conditional fixation time of mutants in a constant population of cells, N. Specifically, we assume that fitness values of wild type cells and mutants at different locations come from given probability distributions and do not change in time. We study spatial arrangements of cells on regular graphs with different degrees, from the circle to the complete graph, and vary assumptions on the fitness probability distributions. Some examples include: identical probability distributions for wild types and mutants; cases when only one of the cell types has random fitness values while the other has deterministic fitness; and cases where the mutants are advantaged or disadvantaged. Using analytical calculations and stochastic numerical simulations, we find that randomness has a strong impact on fixation time. In the case of complete graphs, randomness accelerates mutant fixation for all population sizes, and in the case of circular graphs, randomness delays mutant fixation for N larger than a threshold value (for small values of N, different behaviors are observed depending on the fitness distribution functions). These results emphasize fundamental differences in population dynamics under different assumptions on cell connectedness. They are explained by the existence of randomly occurring "dead zones" that can significantly delay fixation on networks with low connectivity; and by the existence of randomly occurring "lucky zones" that can facilitate fixation on networks of high connectivity. Results for death-birth and birth-death formulations of the Moran process, as well as for the (haploid) Wright Fisher model are presented.}, } @article {pmid29176663, year = {2017}, author = {Quinn, TP and Richardson, MF and Lovell, D and Crowley, TM}, title = {propr: An R-package for Identifying Proportionally Abundant Features Using Compositional Data Analysis.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {16252}, pmid = {29176663}, issn = {2045-2322}, mesh = {Algorithms ; Animals ; *Data Analysis ; Data Interpretation, Statistical ; Genomics/*methods ; Humans ; }, abstract = {In the life sciences, many assays measure only the relative abundances of components in each sample. Such data, called compositional data, require special treatment to avoid misleading conclusions. Awareness of the need for caution in analyzing compositional data is growing, including the understanding that correlation is not appropriate for relative data. Recently, researchers have proposed proportionality as a valid alternative to correlation for calculating pairwise association in relative data. Although the question of how to best measure proportionality remains open, we present here a computationally efficient R package that implements three measures of proportionality. In an effort to advance the understanding and application of proportionality analysis, we review the mathematics behind proportionality, demonstrate its application to genomic data, and discuss some ongoing challenges in the analysis of relative abundance data.}, } @article {pmid29171224, year = {2017}, author = {Zhang, F and Chen, SQ and Wang, LL and Zhang, T and Zhang, XB and Zhu, SD}, title = {[Study on ecological suitability regionalization of Corni Fructus based on Maxent and ArcGIS model].}, journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica}, volume = {42}, number = {16}, pages = {3078-3083}, doi = {10.19540/j.cnki.cjcmm.20170714.017}, pmid = {29171224}, issn = {1001-5302}, mesh = {China ; Climate ; Cornus/*growth & development ; Ecology ; Geographic Information Systems ; Plants, Medicinal/*growth & development ; Soil ; }, abstract = {Through planting regionalization the scientific basis for planting area of high-quality medicinal materials was predicted. Through interview investigation and field survey, the distribution information of Corni Fructus in China was collected,and 89 sampling point from 14 producing areas were collected. Climate and topography of Corni Fructus were analyzed, the ecological adaptability of study was conducted based on ArcGIS and Maxent. Different suitability grade at potential areas and regionalization map were formulated. There are nine ecological factors affecting the growth of Corni Fructus, for example precipitation in November and March and vegetation type. The results showed that the most suitable habitats are Henan, Shaanxi, Zhejiang, Chongqing, Hubei, Sichuan, Anhui, Hunan and Shandong province. Using the spatial analysis method,the study not only illustrates the most suitable for the surroundings of Corni Fructus,but also provides a scientific reference for wild resource tending, introduction and cultivation, and artificial planting base and directing production layout.}, } @article {pmid29171165, year = {2018}, author = {Gómez-Sánchez, D and Schlötterer, C}, title = {ReadTools: A universal toolkit for handling sequence data from different sequencing platforms.}, journal = {Molecular ecology resources}, volume = {18}, number = {3}, pages = {676-680}, doi = {10.1111/1755-0998.12741}, pmid = {29171165}, issn = {1755-0998}, mesh = {Computational Biology ; Internet ; Sequence Analysis/*methods ; Sequence Analysis, DNA ; *Software ; }, abstract = {Sequencing whole genomes has become a standard research tool in many disciplines including Molecular Ecology, but the rapid technological advances in combination with several competing platforms have resulted in a confusing diversity of formats. This lack of standard formats causes several problems, such as undocumented preprocessing steps or the loss of information in downstream software tools, which do not account for the specifics of the different available formats. ReadTools is an open-source Java toolkit designed to standardize and preprocess read data from different platforms. It manages FASTQ- and SAM-formatted inputs while dealing with platform-specific peculiarities and provides a standard SAM compliant output. The code and executable are available at https://github.com/magicDGS/ReadTools.}, } @article {pmid29171072, year = {2018}, author = {Pérez-Acosta, JA and Martínez-Porchas, M and Elizalde-Contreras, JM and Leyva, JM and Ruiz-May, E and Gollas-Galván, T and Martínez-Córdova, LR and Huerta-Ocampo, JÁ}, title = {Proteomic profiling of integral membrane proteins associated to pathogenicity in Vibrio parahaemolyticus strains.}, journal = {Microbiology and immunology}, volume = {62}, number = {1}, pages = {14-23}, doi = {10.1111/1348-0421.12556}, pmid = {29171072}, issn = {1348-0421}, mesh = {Adhesins, Bacterial/genetics/metabolism ; Animals ; Bacterial Proteins/genetics/isolation & purification ; Bacterial Secretion Systems/genetics/metabolism ; Cell Division ; Gene Ontology ; Hepatopancreas/microbiology ; Humans ; Membrane Proteins/genetics/*metabolism ; Penaeidae/microbiology ; *Proteomics ; RNA, Ribosomal, 16S/genetics ; Vibrio Infections/microbiology/veterinary ; Vibrio parahaemolyticus/genetics/isolation & purification/*metabolism/*pathogenicity ; Virulence ; Virulence Factors/genetics/*metabolism ; }, abstract = {Vibrio parahaemolyticus has been recognized as the causal agent of early mortality syndrome and is currently considered an emerging shrimp disease causing losses of millions in the aquaculture industry. Integral membrane proteins are widely recognized as pathogenicity factors involved in essential mechanisms for V. parahaemolyticus infection, which makes them attractive as therapeutic targets. However, their physico-chemical properties and weak expression has resulted in under-representation of these proteins in conventional bottom-up proteomics, making integral membrane proteomics a challenging task. Integral membrane proteins from a bacterial strain isolated from the hepatopancreases of white shrimp with early mortality syndrome and identified by 16S rRNA sequencing as V. parahaemolyticus and an ATCC strain that is pathogenic for humans were obtained by a sequential extraction method and subjected to relative quantification and identification by isobaric Tags for Relative and Absolute Quantitation. A homology database search resulted in identification of more than two hundred proteins, 35 of which are recognized as pathogenic factors showed statistically significant differential accumulation between the strains. These proteins are mainly associated with adherence, secretion systems, cell division, transport, lysogenization, movement and virulence. Identification of pathogenicity-related proteins in V. parahaemolyticus provides valuable information for developing strategies based on molecular mechanisms that inhibit these proteins, which may be useful therapeutic targets for assisting the shrimp and aquaculture industry.}, } @article {pmid29167538, year = {2017}, author = {Suzuki, K and Roseboom, W and Schwartzman, DJ and Seth, AK}, title = {A Deep-Dream Virtual Reality Platform for Studying Altered Perceptual Phenomenology.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {15982}, pmid = {29167538}, issn = {2045-2322}, mesh = {Consciousness ; Humans ; *Neural Networks, Computer ; Virtual Reality ; }, abstract = {Altered states of consciousness, such as psychotic or pharmacologically-induced hallucinations, provide a unique opportunity to examine the mechanisms underlying conscious perception. However, the phenomenological properties of these states are difficult to isolate experimentally from other, more general physiological and cognitive effects of psychoactive substances or psychopathological conditions. Thus, simulating phenomenological aspects of altered states in the absence of these other more general effects provides an important experimental tool for consciousness science and psychiatry. Here we describe such a tool, which we call the Hallucination Machine. It comprises a novel combination of two powerful technologies: deep convolutional neural networks (DCNNs) and panoramic videos of natural scenes, viewed immersively through a head-mounted display (panoramic VR). By doing this, we are able to simulate visual hallucinatory experiences in a biologically plausible and ecologically valid way. Two experiments illustrate potential applications of the Hallucination Machine. First, we show that the system induces visual phenomenology qualitatively similar to classical psychedelics. In a second experiment, we find that simulated hallucinations do not evoke the temporal distortion commonly associated with altered states. Overall, the Hallucination Machine offers a valuable new technique for simulating altered phenomenology without directly altering the underlying neurophysiology.}, } @article {pmid29167366, year = {2017}, author = {Kılınç, GM and Koptekin, D and Atakuman, Ç and Sümer, AP and Dönertaş, HM and Yaka, R and Bilgin, CC and Büyükkarakaya, AM and Baird, D and Altınışık, E and Flegontov, P and Götherström, A and Togan, İ and Somel, M}, title = {Archaeogenomic analysis of the first steps of Neolithization in Anatolia and the Aegean.}, journal = {Proceedings. Biological sciences}, volume = {284}, number = {1867}, pages = {}, pmid = {29167366}, issn = {1471-2954}, mesh = {Agriculture/*history ; Archaeology ; Farmers/history ; *Gene Flow ; *Genome, Human ; Genomics ; Greece ; History, Ancient ; Human Migration/*history ; Humans ; Turkey ; }, abstract = {The Neolithic transition in west Eurasia occurred in two main steps: the gradual development of sedentism and plant cultivation in the Near East and the subsequent spread of Neolithic cultures into the Aegean and across Europe after 7000 cal BCE. Here, we use published ancient genomes to investigate gene flow events in west Eurasia during the Neolithic transition. We confirm that the Early Neolithic central Anatolians in the ninth millennium BCE were probably descendants of local hunter-gatherers, rather than immigrants from the Levant or Iran. We further study the emergence of post-7000 cal BCE north Aegean Neolithic communities. Although Aegean farmers have frequently been assumed to be colonists originating from either central Anatolia or from the Levant, our findings raise alternative possibilities: north Aegean Neolithic populations may have been the product of multiple westward migrations, including south Anatolian emigrants, or they may have been descendants of local Aegean Mesolithic groups who adopted farming. These scenarios are consistent with the diversity of material cultures among Aegean Neolithic communities and the inheritance of local forager know-how. The demographic and cultural dynamics behind the earliest spread of Neolithic culture in the Aegean could therefore be distinct from the subsequent Neolithization of mainland Europe.}, } @article {pmid29167363, year = {2017}, author = {Turvey, ST and Crees, JJ and Li, Z and Bielby, J and Yuan, J}, title = {Long-term archives reveal shifting extinction selectivity in China's postglacial mammal fauna.}, journal = {Proceedings. Biological sciences}, volume = {284}, number = {1867}, pages = {}, pmid = {29167363}, issn = {1471-2954}, mesh = {Animals ; Archaeology ; *Biodiversity ; China ; Databases, Factual ; *Extinction, Biological ; *Mammals ; Paleontology ; Phylogeny ; }, abstract = {Ecosystems have been modified by human activities for millennia, and insights about ecology and extinction risk based only on recent data are likely to be both incomplete and biased. We synthesize multiple long-term archives (over 250 archaeological and palaeontological sites dating from the early Holocene to the Ming Dynasty and over 4400 historical records) to reconstruct the spatio-temporal dynamics of Holocene-modern range change across China, a megadiverse country experiencing extensive current-day biodiversity loss, for 34 mammal species over three successive postglacial time intervals. Our combined zooarchaeological, palaeontological, historical and current-day datasets reveal that both phylogenetic and spatial patterns of extinction selectivity have varied through time in China, probably in response both to cumulative anthropogenic impacts (an 'extinction filter' associated with vulnerable species and accessible landscapes being affected earlier by human activities) and also to quantitative and qualitative changes in regional pressures. China has experienced few postglacial global species-level mammal extinctions, and most species retain over 50% of their maximum estimated Holocene range despite millennia of increasing regional human pressures, suggesting that the potential still exists for successful species conservation and ecosystem restoration. Data from long-term archives also demonstrate that herbivores have experienced more historical extinctions in China, and carnivores have until recently displayed greater resilience. Accurate assessment of patterns of biodiversity loss and the likely predictive power of current-day correlates of faunal vulnerability and resilience is dependent upon novel perspectives provided by long-term archives.}, } @article {pmid29166656, year = {2017}, author = {Pichugin, Y and Peña, J and Rainey, PB and Traulsen, A}, title = {Fragmentation modes and the evolution of life cycles.}, journal = {PLoS computational biology}, volume = {13}, number = {11}, pages = {e1005860}, pmid = {29166656}, issn = {1553-7358}, mesh = {Animals ; Bacteria/cytology ; *Biological Evolution ; Cell Physiological Phenomena/*physiology ; Computational Biology ; Life Cycle Stages/*physiology ; *Models, Biological ; Reproduction/physiology ; }, abstract = {Reproduction is a defining feature of living systems. To reproduce, aggregates of biological units (e.g., multicellular organisms or colonial bacteria) must fragment into smaller parts. Fragmentation modes in nature range from binary fission in bacteria to collective-level fragmentation and the production of unicellular propagules in multicellular organisms. Despite this apparent ubiquity, the adaptive significance of fragmentation modes has received little attention. Here, we develop a model in which groups arise from the division of single cells that do not separate but stay together until the moment of group fragmentation. We allow for all possible fragmentation patterns and calculate the population growth rate of each associated life cycle. Fragmentation modes that maximise growth rate comprise a restrictive set of patterns that include production of unicellular propagules and division into two similar size groups. Life cycles marked by single-cell bottlenecks maximise population growth rate under a wide range of conditions. This surprising result offers a new evolutionary explanation for the widespread occurrence of this mode of reproduction. All in all, our model provides a framework for exploring the adaptive significance of fragmentation modes and their associated life cycles.}, } @article {pmid29163090, year = {2017}, author = {Kersten, L and Vriends, N and Steppan, M and Raschle, NM and Praetzlich, M and Oldenhof, H and Vermeiren, R and Jansen, L and Ackermann, K and Bernhard, A and Martinelli, A and Gonzalez-Madruga, K and Puzzo, I and Wells, A and Rogers, JC and Clanton, R and Baker, RH and Grisley, L and Baumann, S and Gundlach, M and Kohls, G and Gonzalez-Torres, MA and Sesma-Pardo, E and Dochnal, R and Lazaratou, H and Kalogerakis, Z and Bigorra Gualba, A and Smaragdi, A and Siklósi, R and Dikeos, D and Hervás, A and Fernández-Rivas, A and De Brito, SA and Konrad, K and Herpertz-Dahlmann, B and Fairchild, G and Freitag, CM and Popma, A and Kieser, M and Stadler, C}, title = {Community Violence Exposure and Conduct Problems in Children and Adolescents with Conduct Disorder and Healthy Controls.}, journal = {Frontiers in behavioral neuroscience}, volume = {11}, number = {}, pages = {219}, pmid = {29163090}, issn = {1662-5153}, abstract = {Exposure to community violence through witnessing or being directly victimized has been associated with conduct problems in a range of studies. However, the relationship between community violence exposure (CVE) and conduct problems has never been studied separately in healthy individuals and individuals with conduct disorder (CD). Therefore, it is not clear whether the association between CVE and conduct problems is due to confounding factors, because those with high conduct problems also tend to live in more violent neighborhoods, i.e., an ecological fallacy. Hence, the aim of the present study was: (1) to investigate whether the association between recent CVE and current conduct problems holds true for healthy controls as well as adolescents with a diagnosis of CD; (2) to examine whether the association is stable in both groups when including effects of aggression subtypes (proactive/reactive aggression), age, gender, site and socioeconomic status (SES); and (3) to test whether proactive or reactive aggression mediate the link between CVE and conduct problems. Data from 1178 children and adolescents (62% female; 44% CD) aged between 9 years and 18 years from seven European countries were analyzed. Conduct problems were assessed using the Kiddie-Schedule of Affective Disorders and Schizophrenia diagnostic interview. Information about CVE and aggression subtypes was obtained using self-report questionnaires (Social and Health Assessment and Reactive-Proactive aggression Questionnaire (RPQ), respectively). The association between witnessing community violence and conduct problems was significant in both groups (adolescents with CD and healthy controls). The association was also stable after examining the mediating effects of aggression subtypes while including moderating effects of age, gender and SES and controlling for effects of site in both groups. There were no clear differences between the groups in the strength of the association between witnessing violence and conduct problems. However, we found evidence for a ceiling effect, i.e., individuals with very high levels of conduct problems could not show a further increase if exposed to CVE and vice versa. Results indicate that there was no evidence for an ecological fallacy being the primary cause of the association, i.e., CVE must be considered a valid risk factor in the etiology of CD.}, } @article {pmid29160928, year = {2018}, author = {Attard, CRM and Beheregaray, LB and Möller, LM}, title = {Genotyping-by-sequencing for estimating relatedness in nonmodel organisms: Avoiding the trap of precise bias.}, journal = {Molecular ecology resources}, volume = {18}, number = {3}, pages = {381-390}, doi = {10.1111/1755-0998.12739}, pmid = {29160928}, issn = {1755-0998}, mesh = {Alleles ; Animals ; Balaenoptera/*genetics ; Bias ; Classification/methods ; Computer Simulation ; Datasets as Topic ; Genetics, Population ; *Genotyping Techniques ; Polymorphism, Single Nucleotide ; Sequence Analysis, DNA ; }, abstract = {There has been remarkably little attention to using the high resolution provided by genotyping-by-sequencing (i.e., RADseq and similar methods) for assessing relatedness in wildlife populations. A major hurdle is the genotyping error, especially allelic dropout, often found in this type of data that could lead to downward-biased, yet precise, estimates of relatedness. Here, we assess the applicability of genotyping-by-sequencing for relatedness inferences given its relatively high genotyping error rate. Individuals of known relatedness were simulated under genotyping error, allelic dropout and missing data scenarios based on an empirical ddRAD data set, and their true relatedness was compared to that estimated by seven relatedness estimators. We found that an estimator chosen through such analyses can circumvent the influence of genotyping error, with the estimator of Ritland (Genetics Research, 67, 175) shown to be unaffected by allelic dropout and to be the most accurate when there is genotyping error. We also found that the choice of estimator should not rely solely on the strength of correlation between estimated and true relatedness as a strong correlation does not necessarily mean estimates are close to true relatedness. We also demonstrated how even a large SNP data set with genotyping error (allelic dropout or otherwise) or missing data still performs better than a perfectly genotyped microsatellite data set of tens of markers. The simulation-based approach used here can be easily implemented by others on their own genotyping-by-sequencing data sets to confirm the most appropriate and powerful estimator for their data.}, } @article {pmid29160520, year = {2017}, author = {Berra, TZ and Queiroz, AAR and Yamamura, M and Arroyo, LH and Garcia, MCDC and Popolin, MP and Santos, DTD and Ramos, ACV and Alves, LS and Fronteira, IE and Chiaravalloti, F and Palha, PF and Arcêncio, RA}, title = {Spatial risk of tuberculosis mortality and social vulnerability in Northeast Brazil.}, journal = {Revista da Sociedade Brasileira de Medicina Tropical}, volume = {50}, number = {5}, pages = {693-697}, doi = {10.1590/0037-8682-0160-2017}, pmid = {29160520}, issn = {1678-9849}, mesh = {Adolescent ; Adult ; Age Distribution ; Brazil/epidemiology ; Child ; Child, Preschool ; Demography ; Female ; Geographic Information Systems ; Humans ; Infant ; Male ; Middle Aged ; Risk Assessment/methods ; Risk Factors ; Sex Distribution ; Socioeconomic Factors ; Spatial Analysis ; Tuberculosis/*etiology/*mortality ; Vulnerable Populations/*statistics & numerical data ; Young Adult ; }, abstract = {INTRODUCTION: Tuberculosis (TB) is the most common infectious disease in the world. We aimed to analyze the spatial risk of tuberculosis mortality and to verify associations in high-risk areas with social vulnerability.

METHODS: This was an ecological study. The scan statistic was used to detect areas at risk, and the Bivariate Moran Index was used to verify relationships between variables.

RESULTS: High-risk areas of tuberculosis mortality were statistically significantly associated with domain 2 of the Social Vulnerability Index (I=0.010; p=0.001).

CONCLUSIONS: This study provides evidence regarding areas with high risk and that vulnerability is a determinant of TB mortality.}, } @article {pmid29153398, year = {2017}, author = {Dornburg, A and Townsend, JP and Wang, Z}, title = {Maximizing Power in Phylogenetics and Phylogenomics: A Perspective Illuminated by Fungal Big Data.}, journal = {Advances in genetics}, volume = {100}, number = {}, pages = {1-47}, doi = {10.1016/bs.adgen.2017.09.007}, pmid = {29153398}, issn = {0065-2660}, mesh = {Evolution, Molecular ; Fungi/*genetics ; *Genome, Fungal ; *Genomics ; Information Systems ; Models, Genetic ; *Phylogeny ; Phylogeography ; }, abstract = {Since its original inception over 150 years ago by Darwin, we have made tremendous progress toward the reconstruction of the Tree of Life. In particular, the transition from analyzing datasets comprised of small numbers of loci to those comprised of hundreds of loci, if not entire genomes, has aided in resolving some of the most vexing of evolutionary problems while giving us a new perspective on biodiversity. Correspondingly, phylogenetic trees have taken a central role in fields that span ecology, conservation, and medicine. However, the rise of big data has also presented phylogenomicists with a new set of challenges to experimental design, quantitative analyses, and computation. The sequencing of a number of very first genomes presented significant challenges to phylogenetic inference, leading fungal phylogenomicists to begin addressing pitfalls and postulating solutions to the issues that arise from genome-scale analyses relevant to any lineage across the Tree of Life. Here we highlight insights from fungal phylogenomics for topics including systematics and species delimitation, ecological and phenotypic diversification, and biogeography while providing an overview of progress made on the reconstruction of the fungal Tree of Life. Finally, we provide a review of considerations to phylogenomic experimental design for robust tree inference. We hope that this special issue of Advances in Genetics not only excites the continued progress of fungal evolutionary biology but also motivates the interdisciplinary development of new theory and methods designed to maximize the power of genomic scale data in phylogenetic analyses.}, } @article {pmid29150650, year = {2017}, author = {Zhao, JS and Wang, AY and Zhao, HB and Chen, YH}, title = {Transcriptome sequencing and differential gene expression analysis of the schistosome-transmitting snail Oncomelania hupensis inhabiting hilly and marshland regions.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {15809}, pmid = {29150650}, issn = {2045-2322}, mesh = {Animals ; China ; Cluster Analysis ; *Ecosystem ; *Gene Expression Profiling ; Gene Expression Regulation ; Gene Ontology ; Geography ; Molecular Sequence Annotation ; Polymorphism, Single Nucleotide/genetics ; Reproducibility of Results ; Schistosoma/*physiology ; *Sequence Analysis, RNA ; Snails/*genetics/*parasitology ; Transcriptome/*genetics ; }, abstract = {The freshwater snail Oncomelania hupensis is the unique intermediate host of the blood fluke Schistosoma japonicum, which is the major cause of schistosomiasis. The snail inhabits two contrasting environments: the hilly and marshland regions. The hilly snails are smaller in size and have the typical smooth shell, whereas the marshland snails are larger and possess the ribbed shell. To reveal the differences in gene expression between the hilly and marshland snails, a total of six snails, three per environment, were individually examined by RNA sequencing technology. All paired-end reads were assembled into contigs from which 34,760 unigenes were predicted. Based on single nucleotide polymorphisms, principal component analysis and neighbor-joining clustering revealed two distinct clusters of hilly and marshland snails. Analysis of expression changes between environments showed that upregulated genes relating to immunity and development were enriched in hilly snails, while those associated with reproduction were over-represented in marshland snails. Eight differentially expressed genes between the two types of snails were validated by qRT-PCR. Our study identified candidate genes that could be targets for future functional studies, and provided a link between expression profiling and ecological adaptation of the snail that may have implications for schistosomiasis control.}, } @article {pmid29150517, year = {2018}, author = {Christel, S and Herold, M and Bellenberg, S and El Hajjami, M and Buetti-Dinh, A and Pivkin, IV and Sand, W and Wilmes, P and Poetsch, A and Dopson, M}, title = {Multi-omics Reveals the Lifestyle of the Acidophilic, Mineral-Oxidizing Model Species Leptospirillum ferriphilum[T].}, journal = {Applied and environmental microbiology}, volume = {84}, number = {3}, pages = {}, pmid = {29150517}, issn = {1098-5336}, mesh = {Bacteria/classification/*genetics/metabolism ; Copper/metabolism ; *Genome, Bacterial ; Hydrogen-Ion Concentration ; Iron/*metabolism ; Oxidation-Reduction ; Phylogeny ; *Proteome ; Proteomics ; RNA, Bacterial/*genetics/metabolism ; *Transcriptome ; }, abstract = {Leptospirillum ferriphilum plays a major role in acidic, metal-rich environments, where it represents one of the most prevalent iron oxidizers. These milieus include acid rock and mine drainage as well as biomining operations. Despite its perceived importance, no complete genome sequence of the type strain of this model species is available, limiting the possibilities to investigate the strategies and adaptations that Leptospirillum ferriphilum DSM 14647[T] (here referred to as Leptospirillum ferriphilum[T]) applies to survive and compete in its niche. This study presents a complete, circular genome of Leptospirillum ferriphilum[T] obtained by PacBio single-molecule real-time (SMRT) long-read sequencing for use as a high-quality reference. Analysis of the functionally annotated genome, mRNA transcripts, and protein concentrations revealed a previously undiscovered nitrogenase cluster for atmospheric nitrogen fixation and elucidated metabolic systems taking part in energy conservation, carbon fixation, pH homeostasis, heavy metal tolerance, the oxidative stress response, chemotaxis and motility, quorum sensing, and biofilm formation. Additionally, mRNA transcript counts and protein concentrations were compared between cells grown in continuous culture using ferrous iron as the substrate and those grown in bioleaching cultures containing chalcopyrite (CuFeS2). Adaptations of Leptospirillum ferriphilum[T] to growth on chalcopyrite included the possibly enhanced production of reducing power, reduced carbon dioxide fixation, as well as elevated levels of RNA transcripts and proteins involved in heavy metal resistance, with special emphasis on copper efflux systems. Finally, the expression and translation of genes responsible for chemotaxis and motility were enhanced.IMPORTANCELeptospirillum ferriphilum is one of the most important iron oxidizers in the context of acidic and metal-rich environments during moderately thermophilic biomining. A high-quality circular genome of Leptospirillum ferriphilum[T] coupled with functional omics data provides new insights into its metabolic properties, such as the novel identification of genes for atmospheric nitrogen fixation, and represents an essential step for further accurate proteomic and transcriptomic investigation of this acidophile model species in the future. Additionally, light is shed on adaptation strategies of Leptospirillum ferriphilum[T] for growth on the copper mineral chalcopyrite. These data can be applied to deepen our understanding and optimization of bioleaching and biooxidation, techniques that present sustainable and environmentally friendly alternatives to many traditional methods for metal extraction.}, } @article {pmid29149350, year = {2018}, author = {Nymark, P and Rieswijk, L and Ehrhart, F and Jeliazkova, N and Tsiliki, G and Sarimveis, H and Evelo, CT and Hongisto, V and Kohonen, P and Willighagen, E and Grafström, RC}, title = {A Data Fusion Pipeline for Generating and Enriching Adverse Outcome Pathway Descriptions.}, journal = {Toxicological sciences : an official journal of the Society of Toxicology}, volume = {162}, number = {1}, pages = {264-275}, doi = {10.1093/toxsci/kfx252}, pmid = {29149350}, issn = {1096-0929}, mesh = {Adverse Outcome Pathways/*trends ; Biomedical Research/*methods/statistics & numerical data/trends ; Computer Simulation ; Data Mining/statistics & numerical data/trends ; Databases, Factual/statistics & numerical data/*trends ; Drug-Related Side Effects and Adverse Reactions/genetics ; Ecotoxicology/*methods/statistics & numerical data/trends ; Hazardous Substances/toxicity ; Humans ; Pulmonary Fibrosis/genetics ; }, abstract = {Increasing amounts of systems toxicology data, including omics results, are becoming publically available and accessible in databases. Data-driven and informatics-tool supported pipeline schemas for fitting such data into Adverse Outcome Pathway (AOP) descriptions could potentially aid the development of nonanimal-based hazard and risk assessment methods. We devised a 6-step workflow that integrated diverse types of toxicology data into a novel AOP scheme for pulmonary fibrosis. Mining of literature references and diverse data sources covering previous pathway descriptions and molecular results were coupled in a stepwise manner with informatics tools applications that enabled gene linkage and pathway identification in molecular interaction maps. Ultimately, a network of functional elements coupled 64 pulmonary fibrosis-associated genes into a novel, open-source AOP-linked molecular pathway, now available for commenting and improvements in WikiPathways (WP3624). Applying in silico-based knowledge extraction and modeling, the pipeline enabled screening and fusion of many different complex data types, including the integration of omics results. Overall, the taken, stepwise approach should be generally useful to construct novel AOP descriptions as well as to enrich developing AOP descriptions in progress.}, } @article {pmid29149169, year = {2017}, author = {Neufeld, Z and von Witt, W and Lakatos, D and Wang, J and Hegedus, B and Czirok, A}, title = {The role of Allee effect in modelling post resection recurrence of glioblastoma.}, journal = {PLoS computational biology}, volume = {13}, number = {11}, pages = {e1005818}, pmid = {29149169}, issn = {1553-7358}, support = {R01 GM102801/GM/NIGMS NIH HHS/United States ; }, mesh = {Algorithms ; Brain Neoplasms/*metabolism/surgery ; Cell Proliferation ; Computational Biology/*methods ; Diffusion ; Glioblastoma/*metabolism/surgery ; Humans ; *Models, Biological ; Neoplasm Recurrence, Local/*metabolism ; }, abstract = {Resection of the bulk of a tumour often cannot eliminate all cancer cells, due to their infiltration into the surrounding healthy tissue. This may lead to recurrence of the tumour at a later time. We use a reaction-diffusion equation based model of tumour growth to investigate how the invasion front is delayed by resection, and how this depends on the density and behaviour of the remaining cancer cells. We show that the delay time is highly sensitive to qualitative details of the proliferation dynamics of the cancer cell population. The typically assumed logistic type proliferation leads to unrealistic results, predicting immediate recurrence. We find that in glioblastoma cell cultures the cell proliferation rate is an increasing function of the density at small cell densities. Our analysis suggests that cooperative behaviour of cancer cells, analogous to the Allee effect in ecology, can play a critical role in determining the time until tumour recurrence.}, } @article {pmid29145425, year = {2017}, author = {Mainali, KP and Bewick, S and Thielen, P and Mehoke, T and Breitwieser, FP and Paudel, S and Adhikari, A and Wolfe, J and Slud, EV and Karig, D and Fagan, WF}, title = {Statistical analysis of co-occurrence patterns in microbial presence-absence datasets.}, journal = {PloS one}, volume = {12}, number = {11}, pages = {e0187132}, pmid = {29145425}, issn = {1932-6203}, mesh = {*Datasets as Topic ; *Microbiota ; }, abstract = {Drawing on a long history in macroecology, correlation analysis of microbiome datasets is becoming a common practice for identifying relationships or shared ecological niches among bacterial taxa. However, many of the statistical issues that plague such analyses in macroscale communities remain unresolved for microbial communities. Here, we discuss problems in the analysis of microbial species correlations based on presence-absence data. We focus on presence-absence data because this information is more readily obtainable from sequencing studies, especially for whole-genome sequencing, where abundance estimation is still in its infancy. First, we show how Pearson's correlation coefficient (r) and Jaccard's index (J)-two of the most common metrics for correlation analysis of presence-absence data-can contradict each other when applied to a typical microbiome dataset. In our dataset, for example, 14% of species-pairs predicted to be significantly correlated by r were not predicted to be significantly correlated using J, while 37.4% of species-pairs predicted to be significantly correlated by J were not predicted to be significantly correlated using r. Mismatch was particularly common among species-pairs with at least one rare species (<10% prevalence), explaining why r and J might differ more strongly in microbiome datasets, where there are large numbers of rare taxa. Indeed 74% of all species-pairs in our study had at least one rare species. Next, we show how Pearson's correlation coefficient can result in artificial inflation of positive taxon relationships and how this is a particular problem for microbiome studies. We then illustrate how Jaccard's index of similarity (J) can yield improvements over Pearson's correlation coefficient. However, the standard null model for Jaccard's index is flawed, and thus introduces its own set of spurious conclusions. We thus identify a better null model based on a hypergeometric distribution, which appropriately corrects for species prevalence. This model is available from recent statistics literature, and can be used for evaluating the significance of any value of an empirically observed Jaccard's index. The resulting simple, yet effective method for handling correlation analysis of microbial presence-absence datasets provides a robust means of testing and finding relationships and/or shared environmental responses among microbial taxa.}, } @article {pmid29145027, year = {2018}, author = {Zhang, L and Feng, Q and Sun, L and Ding, K and Huo, D and Fang, Y and Zhang, T and Yang, H}, title = {Differential gene expression in the intestine of sea cucumber (Apostichopus japonicus) under low and high salinity conditions.}, journal = {Comparative biochemistry and physiology. Part D, Genomics & proteomics}, volume = {25}, number = {}, pages = {34-41}, doi = {10.1016/j.cbd.2017.11.001}, pmid = {29145027}, issn = {1878-0407}, mesh = {Acclimatization ; Animals ; *Gene Expression Profiling ; Gene Ontology ; *Intestines ; Probability ; Reproducibility of Results ; *Salinity ; Sequence Analysis, RNA ; Stichopus/*metabolism/physiology ; }, abstract = {Sea cucumber, Apostichopus japonicus is an important species for aquaculture, and its behavior and physiology can change in response to changing salinity conditions. For this reason, it is important to understand the molecular responses of A. japonicus when exposed to ambient changes in salinity. In this study, RNA-Seq provided a general overview of the gene expression profiles in the intestine of A. japonicus exposed to high salinity (SD40), normal salinity (SD30) and low salinity (SD20) environments. Screening for differentially expressed genes (DEGs) using the NOISeq method identified 109, 100, and 89 DEGs based on a fold change of ≥2 and divergence probability ≥0.8 according to the comparisons of SD20 vs. SD30, SD20 vs.SD40, and SD30 vs. SD40, respectively. Gene ontology analysis showed that the terms "metabolic process" and "catalytic activity" comprised the most enriched DEGs. These fell into the categories of "biological process" and "molecular function". While "cell" and "cell part" had the most enriched DEGs in the category of "cellular component". With these DEGs mapping to 2119, 159, and 160 pathways in the Kyoto Encyclopedia of Genes and Genomes database. Of these 51, 2, and 57 pathways were significantly enriched, respectively. The osmosis-specific DEGs identified in this study of A. japonicus will be important targets for further studies to understand the biochemical mechanisms involved with the adaption of sea cucumbers to changes in salinity.}, } @article {pmid29144284, year = {2017}, author = {Yin, S and Dongjie, G and Weici, S and Weijun, G}, title = {Integrated assessment and scenarios simulation of urban water security system in the southwest of China with system dynamics analysis.}, journal = {Water science and technology : a journal of the International Association on Water Pollution Research}, volume = {76}, number = {9-10}, pages = {2255-2267}, doi = {10.2166/wst.2017.333}, pmid = {29144284}, issn = {0273-1223}, mesh = {China ; Cities ; Conservation of Water Resources/*methods ; Geographic Information Systems ; Models, Theoretical ; Soil/chemistry ; Systems Analysis ; Water/*chemistry ; Water Quality ; Water Resources/supply & distribution ; Water Supply/*standards ; }, abstract = {The demand for global freshwater is growing, while global freshwater available for human use is limited within a certain time and space. Its security has significant impacts on both the socio-economic system and ecological system. Recently, studies have focused on the urban water security system (UWSS) in terms of either water quantity or water quality. In this study, water resources, water environment, and water disaster issues in the UWSS were combined to establish an evaluation index system with system dynamics (SD) and geographic information systems (GIS). The GIS method performs qualitative analysis from the perspective of the spatial dimension; meanwhile, the SD method performs quantitative calculation about related water security problems from the perspective of the temporal dimension. We established a UWSS model for Guizhou province, China to analyze influencing factors, main driving factors, and system variation law, by using the SD method. We simulated the water security system from 2005 to 2025 under four scenarios (Guiyang scenario, Zunyi scenario, Bijie scenario and combined scenario). The results demonstrate that: (1) the severity of water security in cities is ranked as follows: three cities are secure in Guizhou province, four cities are in basic security and two cities are in a situation of insecurity from the spatial dimension of GIS through water security synthesis; and (2) the major driving factors of UWSS in Guizhou province include agricultural irrigation water demand, soil and water losses area, a ratio increase to the standard of water quality, and investment in environmental protection. A combined scenario is the best solution for UWSS by 2025 in Guizhou province under the four scenarios from the temporal dimension of SD. The results of this study provide a useful suggestion for the management of freshwater for the cities of Guizhou province in southwest China.}, } @article {pmid29143457, year = {2018}, author = {Baetscher, DS and Clemento, AJ and Ng, TC and Anderson, EC and Garza, JC}, title = {Microhaplotypes provide increased power from short-read DNA sequences for relationship inference.}, journal = {Molecular ecology resources}, volume = {18}, number = {2}, pages = {296-305}, doi = {10.1111/1755-0998.12737}, pmid = {29143457}, issn = {1755-0998}, mesh = {Animals ; Computational Biology/*methods ; Fishes/*classification/*genetics ; Genetics, Population/*methods ; Genotyping Techniques/*methods ; *Haplotypes ; Polymorphism, Single Nucleotide ; Sequence Analysis, DNA/*methods ; }, abstract = {The accelerating rate at which DNA sequence data are now generated by high-throughput sequencing instruments provides both opportunities and challenges for population genetic and ecological investigations of animals and plants. We show here how the common practice of calling genotypes from a single SNP per sequenced region ignores substantial additional information in the phased short-read sequences that are provided by these sequencing instruments. We target sequenced regions with multiple SNPs in kelp rockfish (Sebastes atrovirens) to determine "microhaplotypes" and then call these microhaplotypes as alleles at each locus. We then demonstrate how these multi-allelic marker data from such loci dramatically increase power for relationship inference. The microhaplotype approach decreases false-positive rates by several orders of magnitude, relative to calling bi-allelic SNPs, for two challenging analytical procedures, full-sibling and single parent-offspring pair identification. We also show how the identification of half-sibling pairs requires so much data that physical linkage becomes a consideration, and that most published studies that attempt to do so are dramatically underpowered. The advent of phased short-read DNA sequence data, in conjunction with emerging analytical tools for their analysis, promises to improve efficiency by reducing the number of loci necessary for a particular level of statistical confidence, thereby lowering the cost of data collection and reducing the degree of physical linkage amongst markers used for relationship estimation. Such advances will facilitate collaborative research and management for migratory and other widespread species.}, } @article {pmid29140991, year = {2017}, author = {Schwager, E and Mallick, H and Ventz, S and Huttenhower, C}, title = {A Bayesian method for detecting pairwise associations in compositional data.}, journal = {PLoS computational biology}, volume = {13}, number = {11}, pages = {e1005852}, pmid = {29140991}, issn = {1553-7358}, support = {R01 HG005220/HG/NHGRI NIH HHS/United States ; T32 GM074897/GM/NIGMS NIH HHS/United States ; U54 DE023798/DE/NIDCR NIH HHS/United States ; U54 DK102557/DK/NIDDK NIH HHS/United States ; }, mesh = {Algorithms ; *Bayes Theorem ; Computational Biology/*methods ; *Computer Simulation ; Ecology ; Humans ; Markov Chains ; Microbiota ; *Models, Biological ; Proteobacteria ; }, abstract = {Compositional data consist of vectors of proportions normalized to a constant sum from a basis of unobserved counts. The sum constraint makes inference on correlations between unconstrained features challenging due to the information loss from normalization. However, such correlations are of long-standing interest in fields including ecology. We propose a novel Bayesian framework (BAnOCC: Bayesian Analysis of Compositional Covariance) to estimate a sparse precision matrix through a LASSO prior. The resulting posterior, generated by MCMC sampling, allows uncertainty quantification of any function of the precision matrix, including the correlation matrix. We also use a first-order Taylor expansion to approximate the transformation from the unobserved counts to the composition in order to investigate what characteristics of the unobserved counts can make the correlations more or less difficult to infer. On simulated datasets, we show that BAnOCC infers the true network as well as previous methods while offering the advantage of posterior inference. Larger and more realistic simulated datasets further showed that BAnOCC performs well as measured by type I and type II error rates. Finally, we apply BAnOCC to a microbial ecology dataset from the Human Microbiome Project, which in addition to reproducing established ecological results revealed unique, competition-based roles for Proteobacteria in multiple distinct habitats.}, } @article {pmid29140522, year = {2018}, author = {Verbruggen, B and Gunnarsson, L and Kristiansson, E and Österlund, T and Owen, SF and Snape, JR and Tyler, CR}, title = {ECOdrug: a database connecting drugs and conservation of their targets across species.}, journal = {Nucleic acids research}, volume = {46}, number = {D1}, pages = {D930-D936}, pmid = {29140522}, issn = {1362-4962}, mesh = {Amino Acid Sequence ; Animals ; Antineoplastic Agents/adverse effects/*pharmacology/therapeutic use ; Conservation of Natural Resources ; Conserved Sequence ; Data Collection ; Data Display ; *Databases, Pharmaceutical ; Drug Delivery Systems ; *Drug Discovery ; Drug Evaluation, Preclinical ; Fishes/genetics ; Forecasting ; Humans ; Invertebrates/genetics ; Mammals/genetics ; *Molecular Targeted Therapy ; Neoplasm Proteins/*antagonists & inhibitors/chemistry ; Neoplasms/drug therapy/*genetics ; RNA, Neoplasm/*genetics ; Risk Assessment ; Species Specificity ; User-Computer Interface ; }, abstract = {Pharmaceuticals are designed to interact with specific molecular targets in humans and these targets generally have orthologs in other species. This provides opportunities for the drug discovery community to use alternative model species for drug development. It also means, however, there is potential for mode of action related effects in non-target wildlife species as many pharmaceuticals reach the environment through patient use and manufacturing wastes. Acquiring insight in drug target ortholog predictions across species and taxonomic groups has proven difficult because of the lack of an optimal strategy and because necessary information is spread across multiple and diverse sources and platforms. We introduce a new research platform tool, ECOdrug, that reliably connects drugs to their protein targets across divergent species. It harmonizes ortholog predictions from multiple sources via a simple user interface underpinning critical applications for a wide range of studies in pharmacology, ecotoxicology and comparative evolutionary biology. ECOdrug can be used to identify species with drug targets and identify drugs that interact with those targets. As such, it can be applied to support intelligent targeted drug safety testing by ensuring appropriate and relevant species are selected in ecological risk assessments. ECOdrug is freely accessible and available at: http://www.ecodrug.org.}, } @article {pmid29139261, year = {2017}, author = {Cheng, WX and Dong, G and Wu, MY and He, L and Chen, JL}, title = {[Study on suitable distribution areas of Sichuan safflower in Sichuan province based on 3S technologies].}, journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica}, volume = {42}, number = {15}, pages = {2939-2945}, doi = {10.19540/j.cnki.cjcmm.20170714.020}, pmid = {29139261}, issn = {1001-5302}, mesh = {Carthamus tinctorius/*growth & development ; China ; Drugs, Chinese Herbal ; Geographic Information Systems ; Medicine, Chinese Traditional ; Plants, Medicinal/*growth & development ; Soil ; Telemetry ; Temperature ; }, abstract = {Sichuan safflower (Carthamus tinctorius) is a traditional Chinese medicine for promoting blood circulation and removing blood stasis. In this paper, taking Sichuan province as an example, based on TM image, digital elevation model (DEM), meteorology, soil and other data, and using remote sensing and GIS technology to extract grassland, elevation, temperature and precipitation, soil and other influencing factors, the spatial distribution of the suitability of safflower was studied, and the field investigation was carried out. The results indicate that Sichuan safflower resources are mainly concentrated in the eastern and northeastern parts of Sichuan, and the suitable distribution area is about 6 277.14 km2. The area of suitable area of Dazhou is 1 143.45 km[2], which is suitable for the province area of 18.22%. From the county point of view, the suitable area of Dachuan is about 507.15 km[2], and accounting for 17.9% of county. In addition, Naxi, Qingshen, Jiangan and other 12 counties of the suitable area of more than 100 km[2], and accounted for more than 10% of the county. The results of remote sensing and GIS analysis are in accordance with the real area of Sichuan safflower resources. It is feasible to find out the area suitable for the growth of Sichuan safflower by 3S technologies. It can provide a scientific basis for the monitoring and development of Chinese herbal resources.}, } @article {pmid29136109, year = {2019}, author = {Wang, Y and Pirani, M and Hansell, AL and Richardson, S and Blangiardo, M}, title = {Using ecological propensity score to adjust for missing confounders in small area studies.}, journal = {Biostatistics (Oxford, England)}, volume = {20}, number = {1}, pages = {1-16}, pmid = {29136109}, issn = {1468-4357}, support = {G0801056/MRC_/Medical Research Council/United Kingdom ; MR/M025195/1/MRC_/Medical Research Council/United Kingdom ; MC_UU_00002/10/MRC_/Medical Research Council/United Kingdom ; MR/L01341X/1/MRC_/Medical Research Council/United Kingdom ; MC_UP_0801/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Air Pollution/statistics & numerical data ; Biostatistics/*methods ; Computer Simulation ; Coronary Disease/epidemiology ; *Data Interpretation, Statistical ; *Epidemiologic Methods ; Humans ; London ; Patient Admission/statistics & numerical data ; *Propensity Score ; *Small-Area Analysis ; }, abstract = {Small area ecological studies are commonly used in epidemiology to assess the impact of area level risk factors on health outcomes when data are only available in an aggregated form. However, the resulting estimates are often biased due to unmeasured confounders, which typically are not available from the standard administrative registries used for these studies. Extra information on confounders can be provided through external data sets such as surveys or cohorts, where the data are available at the individual level rather than at the area level; however, such data typically lack the geographical coverage of administrative registries. We develop a framework of analysis which combines ecological and individual level data from different sources to provide an adjusted estimate of area level risk factors which is less biased. Our method (i) summarizes all available individual level confounders into an area level scalar variable, which we call ecological propensity score (EPS), (ii) implements a hierarchical structured approach to impute the values of EPS whenever they are missing, and (iii) includes the estimated and imputed EPS into the ecological regression linking the risk factors to the health outcome. Through a simulation study, we show that integrating individual level data into small area analyses via EPS is a promising method to reduce the bias intrinsic in ecological studies due to unmeasured confounders; we also apply the method to a real case study to evaluate the effect of air pollution on coronary heart disease hospital admissions in Greater London.}, } @article {pmid29135940, year = {2017}, author = {Guo, H and Zhang, J and Wang, Y and Bu, C and Zhou, Y and Fang, Q}, title = {Comparative Proteomic Analysis of Lysine Acetylation in Fish CIK Cells Infected with Aquareovirus.}, journal = {International journal of molecular sciences}, volume = {18}, number = {11}, pages = {}, pmid = {29135940}, issn = {1422-0067}, mesh = {Acetylation ; Amino Acid Motifs ; Animals ; Benzoates/pharmacology/therapeutic use ; Carps/*physiology ; Cell Line ; Cluster Analysis ; Cytokine-Induced Killer Cells/drug effects/*metabolism/*virology ; Fish Diseases/metabolism/*virology ; Fish Proteins/chemistry/metabolism ; Gene Ontology ; Hydroxamic Acids/pharmacology/therapeutic use ; Lysine/*metabolism ; Nitrobenzenes ; Protein Domains ; Protein Interaction Maps/drug effects ; Proteome/metabolism ; *Proteomics ; Pyrazoles/pharmacology/therapeutic use ; Pyrazolones ; Reoviridae/*physiology ; Subcellular Fractions/metabolism ; Virus Replication/drug effects ; Vorinostat ; }, abstract = {Grass carp (Ctenopharyngodon idellus) is an important worldwide commercial freshwater culture species. However, grass carp reovirus (GCRV) causes serious hemorrhagic disease in fingerlings and yearlings of fishes. To understand the molecular pathogenesis of host cells during GCRV infection, intensive proteomic quantification analysis of lysine acetylation in Ctenopharyngodon idella kidney (CIK) cells was performed. Using dimethylation labeling-based quantitative proteomics, 832 acetylated proteins with 1391 lysine acetylation sites were identified in response to GCRV infection, among which 792 proteins with 1323 sites were quantifiable. Bioinformatics analysis showed that differentially expressed lysine acetylated proteins are involved in diverse cellular processes and associated with multifarious functions, suggesting that extensive intracellular activities were changed upon viral infection. In addition, extensive alterations on host-protein interactions at the lysine acetylation level were also detected. Further biological experiments showed that the histone deacetylases (HDAC) inhibitor suberoylanilide hydroxamic acid (SAHA) could significantly suppress the GCRV replication. To our knowledge, this is the first to reveal the proteome-wide changes in host cell acetylome with aquatic virus infection. The results provided in this study laid a basis for further understanding the host response to aquareovirus infection in the post-translational modification aspect by regulating cell lysine acetylation conducive to viral replication.}, } @article {pmid29134195, year = {2017}, author = {Crouzeilles, R and Ferreira, MS and Chazdon, RL and Lindenmayer, DB and Sansevero, JBB and Monteiro, L and Iribarrem, A and Latawiec, AE and Strassburg, BBN}, title = {Ecological restoration success is higher for natural regeneration than for active restoration in tropical forests.}, journal = {Science advances}, volume = {3}, number = {11}, pages = {e1701345}, pmid = {29134195}, issn = {2375-2548}, mesh = {Animals ; Biodiversity ; *Environmental Restoration and Remediation ; *Forests ; Plants/metabolism ; }, abstract = {Is active restoration the best approach to achieve ecological restoration success (the return to a reference condition, that is, old-growth forest) when compared to natural regeneration in tropical forests? Our meta-analysis of 133 studies demonstrated that natural regeneration surpasses active restoration in achieving tropical forest restoration success for all three biodiversity groups (plants, birds, and invertebrates) and five measures of vegetation structure (cover, density, litter, biomass, and height) tested. Restoration success for biodiversity and vegetation structure was 34 to 56% and 19 to 56% higher in natural regeneration than in active restoration systems, respectively, after controlling for key biotic and abiotic factors (forest cover, precipitation, time elapsed since restoration started, and past disturbance). Biodiversity responses were based primarily on ecological metrics of abundance and species richness (74%), both of which take far less time to achieve restoration success than similarity and composition. This finding challenges the widely held notion that natural forest regeneration has limited conservation value and that active restoration should be the default ecological restoration strategy. The proposition that active restoration achieves greater restoration success than natural regeneration may have arisen because previous comparisons lacked controls for biotic and abiotic factors; we also did not find any difference between active restoration and natural regeneration outcomes for vegetation structure when we did not control for these factors. Future policy priorities should align the identified patterns of biophysical and ecological conditions where each or both restoration approaches are more successful, cost-effective, and compatible with socioeconomic incentives for tropical forest restoration.}, } @article {pmid29133028, year = {2018}, author = {Ling, J and Smura, T and Tamarit, D and Huitu, O and Voutilainen, L and Henttonen, H and Vaheri, A and Vapalahti, O and Sironen, T}, title = {Evolution and postglacial colonization of Seewis hantavirus with Sorex araneus in Finland.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {57}, number = {}, pages = {88-97}, doi = {10.1016/j.meegid.2017.11.010}, pmid = {29133028}, issn = {1567-7257}, mesh = {Animal Diseases/*epidemiology/*virology ; Animals ; Computational Biology/methods ; Evolution, Molecular ; Finland/epidemiology ; Orthohantavirus/*genetics ; Hantavirus Infections/*veterinary ; Phylogeny ; Phylogeography ; RNA, Viral ; Sequence Analysis, DNA ; Shrews/*virology ; }, abstract = {Hantaviruses have co-existed with their hosts for millions of years. Seewis virus (SWSV), a soricomorph-borne hantavirus, is widespread in Eurasia, ranging from Central Siberia to Western Europe. To gain insight into the phylogeography and evolutionary history of SWSV in Finland, lung tissue samples of 225 common shrews (Sorex araneus) trapped from different parts of Finland were screened for the presence of SWSV RNA. Forty-two of the samples were positive. Partial small (S), medium (M) and large (L) segments of the virus were sequenced, and analyzed together with all SWSV sequences available in Genbank. The phylogenetic analysis of the partial S-segment sequences suggested that all Finnish SWSV strains shared their most recent common ancestor with the Eastern European strains, while the L-segment suggested multiple introductions. The difference between the L- and S-segment phylogenies implied that reassortment events play a role in the evolution of SWSV. Of the Finnish strains, variants from Eastern Finland occupied the root position in the phylogeny, and had the highest genetic diversity, supporting the hypothesis that SWSV reached Finland first form the east. During the spread in Finland, the virus has formed three separate lineages, identified here by correlation analysis of genetic versus geographic distance combined with median-joining network analysis. These results support the hypothesis that Finnish SWSV recolonized Finland with its host, the common shrew, from east after the last ice age 12,000-8000years ago, and then subsequently spread along emerging land bridges towards west or north with the migration and population expansion of its host.}, } @article {pmid29132403, year = {2017}, author = {Wang, L and Beissinger, TM and Lorant, A and Ross-Ibarra, C and Ross-Ibarra, J and Hufford, MB}, title = {The interplay of demography and selection during maize domestication and expansion.}, journal = {Genome biology}, volume = {18}, number = {1}, pages = {215}, pmid = {29132403}, issn = {1474-760X}, support = {2009-65300-05668//U.S. Department of Agriculture/International ; 1546719//National Science Foundation/International ; CA-D-PLS-2066-H//USDA Hatch project/International ; }, mesh = {Alleles ; *Domestication ; Inbreeding ; Mutation/genetics ; Population Density ; *Selection, Genetic ; Zea mays/*genetics/*growth & development ; }, abstract = {BACKGROUND: The history of maize has been characterized by major demographic events, including population size changes associated with domestication and range expansion, and gene flow with wild relatives. The interplay between demographic history and selection has shaped diversity across maize populations and genomes.

RESULTS: We investigate these processes using high-depth resequencing data from 31 maize landraces spanning the pre-Columbian distribution of maize, and four wild teosinte individuals (Zea mays ssp. parviglumis). Genome-wide demographic analyses reveal that maize experienced pronounced declines in effective population size due to both a protracted domestication bottleneck and serial founder effects during post-domestication spread, while parviglumis in the Balsas River Valley experienced population growth. The domestication bottleneck and subsequent spread led to an increase in deleterious alleles in the domesticate compared to the wild progenitor. This cost is particularly pronounced in Andean maize, which has experienced a more dramatic founder event compared to other maize populations. Additionally, we detect introgression from the wild teosinte Zea mays ssp. mexicana into maize in the highlands of Mexico, Guatemala, and the southwestern USA, which reduces the prevalence of deleterious alleles likely due to the higher long-term effective population size of teosinte.

CONCLUSIONS: These findings underscore the strong interaction between historical demography and the efficiency of selection and illustrate how domesticated species are particularly useful for understanding these processes. The landscape of deleterious alleles and therefore evolutionary potential is clearly influenced by recent demography, a factor that could bear importantly on many species that have experienced recent demographic shifts.}, } @article {pmid29131508, year = {2018}, author = {Ahlstrand, E and Buetti-Dinh, A and Friedman, R}, title = {An interactive computer lab of the galvanic cell for students in biochemistry.}, journal = {Biochemistry and molecular biology education : a bimonthly publication of the International Union of Biochemistry and Molecular Biology}, volume = {46}, number = {1}, pages = {58-65}, doi = {10.1002/bmb.21091}, pmid = {29131508}, issn = {1539-3429}, mesh = {Biochemistry/*education ; Electrochemical Techniques/*instrumentation ; Humans ; *Laboratories ; Learning ; *Software ; *Students ; Thermodynamics ; }, abstract = {We describe an interactive module that can be used to teach basic concepts in electrochemistry and thermodynamics to first year natural science students. The module is used together with an experimental laboratory and improves the students' understanding of thermodynamic quantities such as Δr G, Δr H, and Δr S that are calculated but not directly measured in the lab. We also discuss how new technologies can substitute some parts of experimental chemistry courses, and improve accessibility to course material. Cloud computing platforms such as CoCalc facilitate the distribution of computer codes and allow students to access and apply interactive course tools beyond the course's scope. Despite some limitations imposed by cloud computing, the students appreciated the approach and the enhanced opportunities to discuss study questions with their classmates and instructor as facilitated by the interactive tools. © 2017 by The International Union of Biochemistry and Molecular Biology, 46(1):58-65, 2018.}, } @article {pmid29130757, year = {2017}, author = {Adamowicz, SJ and Hollingsworth, PM and Ratnasingham, S and van der Bank, M}, title = {International Barcode of Life: Focus on big biodiversity in South Africa.}, journal = {Genome}, volume = {60}, number = {11}, pages = {875-879}, doi = {10.1139/gen-2017-0210}, pmid = {29130757}, issn = {1480-3321}, mesh = {Animals ; *Biodiversity ; Computational Biology ; Congresses as Topic ; Conservation of Natural Resources ; *DNA Barcoding, Taxonomic ; *Evolution, Molecular ; High-Throughput Nucleotide Sequencing ; Lepidoptera/genetics ; Phylogeography ; Plants, Medicinal/genetics ; South Africa ; }, abstract = {Participants in the 7th International Barcode of Life Conference (Kruger National Park, South Africa, 20-24 November 2017) share the latest findings in DNA barcoding research and its increasingly diversified applications. Here, we review prevailing trends synthesized from among 429 invited and contributed abstracts, which are collated in this open-access special issue of Genome. Hosted for the first time on the African continent, the 7th Conference places special emphasis on the evolutionary origins, biogeography, and conservation of African flora and fauna. Within Africa and elsewhere, DNA barcoding and related techniques are being increasingly used for wildlife forensics and for the validation of commercial products, such as medicinal plants and seafood species. A striking trend of the conference is the dramatic rise of studies on environmental DNA (eDNA) and on diverse uses of high-throughput sequencing techniques. Emerging techniques in these areas are opening new avenues for environmental biomonitoring, managing species-at-risk and invasive species, and revealing species interaction networks in unprecedented detail. Contributors call for the development of validated community standards for high-throughput sequence data generation and analysis, to enable the full potential of these methods to be realized for understanding and managing biodiversity on a global scale.}, } @article {pmid29130343, year = {2017}, author = {Thomson, JP and Ottaviano, R and Buesen, R and Moggs, JG and Schwarz, M and Meehan, RR}, title = {Defining baseline epigenetic landscapes in the rat liver.}, journal = {Epigenomics}, volume = {9}, number = {12}, pages = {1503-1527}, pmid = {29130343}, issn = {1750-192X}, support = {MC_PC_U127574433/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Animals ; Chromatin/metabolism ; CpG Islands ; *DNA Methylation ; Databases, Genetic ; *Epigenesis, Genetic ; Female ; *Genetic Variation ; *Histone Code ; Liver/*metabolism ; Male ; Rats ; Rats, Sprague-Dawley ; Rats, Wistar ; Sex Factors ; }, abstract = {Characterization of the hepatic epigenome following exposure to chemicals and therapeutic drugs provides novel insights into toxicological and pharmacological mechanisms, however appreciation of genome-wide inter- and intra-strain baseline epigenetic variation, particularly in under-characterized species such as the rat is limited. Material & methods: To enhance the utility of epigenomic endpoints safety assessment, we map both DNA modifications (5-methyl-cytosine and 5-hydroxymethyl-cytosine) and enhancer related chromatin marks (H3K4me1 and H3K27ac) across multiple male and female rat livers for two important outbred laboratory rat strains (Sprague-Dawley and Wistar). Results & conclusion: Integration of DNA modification, enhancer chromatin marks and gene expression profiles reveals clear gender-specific chromatin states at genes which exhibit gender-specific transcription. Taken together this work provides a valuable baseline liver epigenome resource for rat strains that are commonly used in chemical and pharmaceutical safety assessment.}, } @article {pmid29127278, year = {2017}, author = {Hammond, SA and Warren, RL and Vandervalk, BP and Kucuk, E and Khan, H and Gibb, EA and Pandoh, P and Kirk, H and Zhao, Y and Jones, M and Mungall, AJ and Coope, R and Pleasance, S and Moore, RA and Holt, RA and Round, JM and Ohora, S and Walle, BV and Veldhoen, N and Helbing, CC and Birol, I}, title = {The North American bullfrog draft genome provides insight into hormonal regulation of long noncoding RNA.}, journal = {Nature communications}, volume = {8}, number = {1}, pages = {1433}, pmid = {29127278}, issn = {2041-1723}, support = {R01 HG007182/HG/NHGRI NIH HHS/United States ; }, mesh = {Animals ; Computational Biology ; *Genome ; Genome, Mitochondrial ; Male ; Molecular Sequence Annotation ; North America ; Phylogeny ; RNA, Long Noncoding/*genetics/metabolism ; Rana catesbeiana/*genetics/metabolism ; Thyroid Hormones/metabolism ; }, abstract = {Frogs play important ecological roles, and several species are important model organisms for scientific research. The globally distributed Ranidae (true frogs) are the largest frog family, and have substantial evolutionary distance from the model laboratory Xenopus frog species. Unfortunately, there are currently no genomic resources for the former, important group of amphibians. More widely applicable amphibian genomic data is urgently needed as more than two-thirds of known species are currently threatened or are undergoing population declines. We report a 5.8 Gbp (NG50 = 69 kbp) genome assembly of a representative North American bullfrog (Rana [Lithobates] catesbeiana). The genome contains over 22,000 predicted protein-coding genes and 6,223 candidate long noncoding RNAs (lncRNAs). RNA-Seq experiments show thyroid hormone causes widespread transcriptional change among protein-coding and putative lncRNA genes. This initial bullfrog draft genome will serve as a key resource with broad utility including amphibian research, developmental biology, and environmental research.}, } @article {pmid29126205, year = {2018}, author = {Cechová, J and Lýsek, J and Bartas, M and Brázda, V}, title = {Complex analyses of inverted repeats in mitochondrial genomes revealed their importance and variability.}, journal = {Bioinformatics (Oxford, England)}, volume = {34}, number = {7}, pages = {1081-1085}, pmid = {29126205}, issn = {1367-4811}, mesh = {Eukaryota/genetics ; *Evolution, Molecular ; *Genome, Mitochondrial ; *Genomics ; *Inverted Repeat Sequences ; Sequence Analysis, DNA ; }, abstract = {MOTIVATION: The NCBI database contains mitochondrial DNA (mtDNA) genomes from numerous species. We investigated the presence and locations of inverted repeat sequences (IRs) in these mtDNA sequences, which are known to be important for regulating nuclear genomes.

RESULTS: IRs were identified in mtDNA in all species. IR lengths and frequencies correlate with evolutionary age and the greatest variability was detected in subgroups of plants and fungi and the lowest variability in mammals. IR presence is non-random and evolutionary favoured. The frequency of IRs generally decreased with IR length, but not for IRs 24 or 30 bp long, which are 1.5 times more abundant. IRs are enriched in sequences from the replication origin, followed by D-loop, stem-loop and miscellaneous sequences, pointing to the importance of IRs in regulatory regions of mitochondrial DNA.

Data were produced using Palindrome analyser, freely available on the web at http://bioinformatics.ibp.cz.

CONTACT: vaclav@ibp.cz.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, } @article {pmid29126115, year = {2017}, author = {Lynch, J and Tang, K and Priya, S and Sands, J and Sands, M and Tang, E and Mukherjee, S and Knights, D and Blekhman, R}, title = {HOMINID: a framework for identifying associations between host genetic variation and microbiome composition.}, journal = {GigaScience}, volume = {6}, number = {12}, pages = {1-7}, pmid = {29126115}, issn = {2047-217X}, mesh = {Animals ; Bacteria/*classification ; Bacterial Physiological Phenomena ; Computational Biology/*methods ; Host-Pathogen Interactions ; Humans ; Linear Models ; Microbiota ; *Polymorphism, Single Nucleotide ; }, abstract = {Recent studies have uncovered a strong effect of host genetic variation on the composition of host-associated microbiota. Here, we present HOMINID, a computational approach based on Lasso linear regression, that given host genetic variation and microbiome taxonomic composition data, identifies host single nucleotide polymorphisms (SNPs) that are correlated with microbial taxa abundances. Using simulated data, we show that HOMINID has accuracy in identifying associated SNPs and performs better compared with existing methods. We also show that HOMINID can accurately identify the microbial taxa that are correlated with associated SNPs. Lastly, by using HOMINID on real data of human genetic variation and microbiome composition, we identified 13 human SNPs in which genetic variation is correlated with microbiome taxonomic composition across body sites. In conclusion, HOMINID is a powerful method to detect host genetic variants linked to microbiome composition and can facilitate discovery of mechanisms controlling host-microbiome interactions.}, } @article {pmid29126086, year = {2018}, author = {Han, J and Kim, DH and Kim, HS and Kim, HJ and Declerck, SAJ and Hagiwara, A and Lee, JS}, title = {Genome-wide identification of 31 cytochrome P450 (CYP) genes in the freshwater rotifer Brachionus calyciflorus and analysis of their benzo[α]pyrene-induced expression patterns.}, journal = {Comparative biochemistry and physiology. Part D, Genomics & proteomics}, volume = {25}, number = {}, pages = {26-33}, doi = {10.1016/j.cbd.2017.10.003}, pmid = {29126086}, issn = {1878-0407}, mesh = {Amino Acid Sequence ; Animals ; Benzo(a)pyrene/*toxicity ; Cytochrome P-450 Enzyme System/*genetics ; Databases, Genetic ; Fresh Water ; Gene Expression/*drug effects ; *Genome ; Phylogeny ; Rotifera/*genetics ; Sequence Analysis, RNA ; Sequence Homology, Amino Acid ; Water Pollutants, Chemical/*toxicity ; }, abstract = {While marine invertebrate cytochrome P450 (CYP) genes and their roles in detoxification mechanisms have been studied, little information is available regarding freshwater rotifer CYPs and their functions. Here, we used genomic sequences and RNA-seq databases to identify 31 CYP genes in the freshwater rotifer Brachionus calyciflorus. The 31 Bc-CYP genes with a few tandem duplications were clustered into CYP 2, 3, 4, mitochondrial, and 46 clans with two marine rotifers Brachionus plicatilis and Brachionus koreanus. To understand the molecular responses of these 31 Bc-CYP genes, we also examined their expression patterns in response to benzo[α]pyrene (B[α]P). Three Bc-CYP genes (Bc-CYP3044B3, Bc-CYP3049B4, Bc-CYP3049B6) were significantly upregulated (P<0.05) in response to B[α]P, suggesting that these CYP genes can be involved in detoxification in response to B[α]P exposure. These genes might be useful as biomarkers of B[α]P exposure in B. calyciflorus. Overall, our findings expand the repertoire of known CYPs and shed light on their potential roles in xenobiotic detoxification in rotifers.}, } @article {pmid29122853, year = {2018}, author = {Phadke, SS and Maclean, CJ and Zhao, SY and Mueller, EA and Michelotti, LA and Norman, KL and Kumar, A and James, TY}, title = {Genome-Wide Screen for Saccharomyces cerevisiae Genes Contributing to Opportunistic Pathogenicity in an Invertebrate Model Host.}, journal = {G3 (Bethesda, Md.)}, volume = {8}, number = {1}, pages = {63-78}, pmid = {29122853}, issn = {2160-1836}, support = {R21 AI105167/AI/NIAID NIH HHS/United States ; R21 AI114837/AI/NIAID NIH HHS/United States ; }, mesh = {Alleles ; Animals ; Cell Wall/chemistry/metabolism ; Gene Ontology ; *Genome, Fungal ; Genome-Wide Association Study ; Genotype ; Host-Pathogen Interactions/*genetics/immunology ; Immunity, Innate ; Larva/immunology/microbiology ; Mitochondria/chemistry/metabolism ; Molecular Sequence Annotation ; Moths/immunology/*microbiology ; Mutation ; Phenotype ; Quantitative Trait Loci ; Saccharomyces cerevisiae/*genetics/growth & development/*pathogenicity ; Tyrosine/metabolism ; Virulence ; }, abstract = {Environmental opportunistic pathogens can exploit vulnerable hosts through expression of traits selected for in their natural environments. Pathogenicity is itself a complicated trait underpinned by multiple complex traits, such as thermotolerance, morphology, and stress response. The baker's yeast, Saccharomyces cerevisiae, is a species with broad environmental tolerance that has been increasingly reported as an opportunistic pathogen of humans. Here we leveraged the genetic resources available in yeast and a model insect species, the greater waxmoth Galleria mellonella, to provide a genome-wide analysis of pathogenicity factors. Using serial passaging experiments of genetically marked wild-type strains, a hybrid strain was identified as the most fit genotype across all replicates. To dissect the genetic basis for pathogenicity in the hybrid isolate, bulk segregant analysis was performed which revealed eight quantitative trait loci significantly differing between the two bulks with alleles from both parents contributing to pathogenicity. A second passaging experiment with a library of deletion mutants for most yeast genes identified a large number of mutations whose relative fitness differed in vivovs.in vitro, including mutations in genes controlling cell wall integrity, mitochondrial function, and tyrosine metabolism. Yeast is presumably subjected to a massive assault by the innate insect immune system that leads to melanization of the host and to a large bottleneck in yeast population size. Our data support that resistance to the innate immune response of the insect is key to survival in the host and identifies shared genetic mechanisms between S. cerevisiae and other opportunistic fungal pathogens.}, } @article {pmid29118632, year = {2017}, author = {Fiemapong, ARN and Masse, PSM and Tamesse, JL and Golovatch, SI and VandenSpiegel, D}, title = {The millipede genus Stemmiulus Gervais, 1844 in Cameroon, with descriptions of three new species (Diplopoda, Stemmiulida, Stemmiulidae).}, journal = {ZooKeys}, volume = {}, number = {708}, pages = {11-23}, pmid = {29118632}, issn = {1313-2989}, abstract = {The large pantropical millipede genus Stemmiulus, which currently encompasses more than 150 species, i.e. the bulk of the species diversity of the family Stemmiulidae and entire order Stemmiulida, is shown to comprise seven species in Cameroon, including three new ones: S. ongot Nzoko Fiemapong & VandenSpiegel, sp. n., S. uncus Nzoko Fiemapong & VandenSpiegel, sp. n., and S. mbalmayoensis Nzoko Fiemapong & VandenSpiegel, sp. n. In addition, S. beroni Mauriès, 1989, previously known only from the type locality in Nigeria, is recorded from Cameroon for the first time, also being redescribed based on new samples. A key is given to all species of the genus encountered in the country, based on male gonopodal conformation, except for S. camerunensis (Silvestri, 1916), which was described only from female and juvenile material.}, } @article {pmid29116122, year = {2017}, author = {Rodriguez, A and Zhang, H and Klaminder, J and Brodin, T and Andersson, M}, title = {ToxId: an efficient algorithm to solve occlusions when tracking multiple animals.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {14774}, pmid = {29116122}, issn = {2045-2322}, mesh = {*Algorithms ; *Animal Migration ; Animals ; Behavior, Animal ; Datasets as Topic ; }, abstract = {Video analysis of animal behaviour is widely used in fields such as ecology, ecotoxicology, and evolutionary research. However, when tracking multiple animals, occlusion and crossing are problematic, especially when the identity of each individual needs to be preserved. We present a new algorithm, ToxId, which preserves the identity of multiple animals by linking trajectory segments using their intensity histogram and Hu-moments. We verify the performance and accuracy of our algorithm using video sequences with different animals and experimental conditions. The results show that our algorithm achieves state-of-the-art accuracy using an efficient approach without the need of learning processes, complex feature maps or knowledge of the animal shape. ToxId is also computationally efficient, has low memory requirements, and operates without accessing future or past frames.}, } @article {pmid29113561, year = {2017}, author = {Rahman, MA and LaPierre, N and Rangwala, H and Barbara, D}, title = {Metagenome sequence clustering with hash-based canopies.}, journal = {Journal of bioinformatics and computational biology}, volume = {15}, number = {6}, pages = {1740006}, doi = {10.1142/S0219720017400066}, pmid = {29113561}, issn = {1757-6334}, mesh = {*Algorithms ; *Biodiversity ; Cluster Analysis ; Databases, Factual ; Gastrointestinal Microbiome/genetics ; Humans ; Liver Cirrhosis/microbiology ; *Metagenome ; Metagenomics/*methods ; Microbiota ; Phylogeny ; RNA, Ribosomal, 16S ; RNA, Ribosomal, 18S ; Sequence Analysis, RNA/methods ; Soil Microbiology ; }, abstract = {Metagenomics is the collective sequencing of co-existing microbial communities which are ubiquitous across various clinical and ecological environments. Due to the large volume and random short sequences (reads) obtained from community sequences, analysis of diversity, abundance and functions of different organisms within these communities are challenging tasks. We present a fast and scalable clustering algorithm for analyzing large-scale metagenome sequence data. Our approach achieves efficiency by partitioning the large number of sequence reads into groups (called canopies) using hashing. These canopies are then refined by using state-of-the-art sequence clustering algorithms. This canopy-clustering (CC) algorithm can be used as a pre-processing phase for computationally expensive clustering algorithms. We use and compare three hashing schemes for canopy construction with five popular and state-of-the-art sequence clustering methods. We evaluate our clustering algorithm on synthetic and real-world 16S and whole metagenome benchmarks. We demonstrate the ability of our proposed approach to determine meaningful Operational Taxonomic Units (OTU) and observe significant speedup with regards to run time when compared to different clustering algorithms. We also make our source code publicly available on Github. [a].}, } @article {pmid29111567, year = {2018}, author = {Weinstein, BG}, title = {A computer vision for animal ecology.}, journal = {The Journal of animal ecology}, volume = {87}, number = {3}, pages = {533-545}, doi = {10.1111/1365-2656.12780}, pmid = {29111567}, issn = {1365-2656}, mesh = {Animals ; Ecology/*methods ; Image Interpretation, Computer-Assisted/*methods ; }, abstract = {A central goal of animal ecology is to observe species in the natural world. The cost and challenge of data collection often limit the breadth and scope of ecological study. Ecologists often use image capture to bolster data collection in time and space. However, the ability to process these images remains a bottleneck. Computer vision can greatly increase the efficiency, repeatability and accuracy of image review. Computer vision uses image features, such as colour, shape and texture to infer image content. I provide a brief primer on ecological computer vision to outline its goals, tools and applications to animal ecology. I reviewed 187 existing applications of computer vision and divided articles into ecological description, counting and identity tasks. I discuss recommendations for enhancing the collaboration between ecologists and computer scientists and highlight areas for future growth of automated image analysis.}, } @article {pmid29110111, year = {2017}, author = {Goleiji, E and Hosseini, SM and Khorasani, N and Monavari, SM}, title = {Forest fire risk assessment-an integrated approach based on multicriteria evaluation.}, journal = {Environmental monitoring and assessment}, volume = {189}, number = {12}, pages = {612}, pmid = {29110111}, issn = {1573-2959}, mesh = {Disasters ; Ecology ; Environmental Monitoring/methods ; Fires/statistics & numerical data ; *Forests ; Fuzzy Logic ; Geographic Information Systems ; Iran ; Risk Assessment/methods ; Trees ; Wildfires/*statistics & numerical data ; }, abstract = {The present study deals with application of the weighted linear combination method for zoning of forest fire risk in Dohezar and Sehezar region of Mazandaran province in northern Iran. In this study, the effective criteria for fires were identified by the Delphi method, and these included ecological and socioeconomic parameters. In this regard, the first step comprised of digital layers; the required data were provided from databases, related centers, and field data collected in the region. Then, the map of criteria was digitized in a geographic information system, and all criteria and indexes were normalized by fuzzy logic. After that, the geographic information system (GIS 10.3) was integrated with the Weighted Linear Combination and the Analytical Network Process, to produce zonation of the forest fire risk map in the Dohezar and Sehezar region. In order to analyze accuracy of the evaluation, the results obtained from the study were compared to records of former fire incidents in the region. This was done using the Kappa coefficient test and a receiver operating characteristic curve. The model showing estimations for forest fire risk explained that the prepared map had accuracy of 90% determined by the Kappa coefficient test and the value of 0.924 by receiver operating characteristic. These results showed that the prepared map had high accuracy and efficacy.}, } @article {pmid29109478, year = {2018}, author = {Kolinko, S and Wu, YW and Tachea, F and Denzel, E and Hiras, J and Gabriel, R and Bäcker, N and Chan, LJG and Eichorst, SA and Frey, D and Chen, Q and Azadi, P and Adams, PD and Pray, TR and Tanjore, D and Petzold, CJ and Gladden, JM and Simmons, BA and Singer, SW}, title = {A bacterial pioneer produces cellulase complexes that persist through community succession.}, journal = {Nature microbiology}, volume = {3}, number = {1}, pages = {99-107}, pmid = {29109478}, issn = {2058-5276}, support = {S10 OD018530/OD/NIH HHS/United States ; }, mesh = {Bacteria/*classification/*enzymology/metabolism ; Bacterial Proteins/analysis/isolation & purification ; Biological Evolution ; Cellulase/*analysis/isolation & purification ; Cellulose/*metabolism ; Composting ; Genome, Bacterial/genetics ; Glycoside Hydrolases/analysis/isolation & purification ; Glycosylation ; Heterotrophic Processes ; Metagenomics ; Microbial Consortia/*physiology ; Models, Biological ; Multienzyme Complexes/*analysis/isolation & purification ; *Phylogeny ; Soil Microbiology ; }, abstract = {Cultivation of microbial consortia provides low-complexity communities that can serve as tractable models to understand community dynamics. Time-resolved metagenomics demonstrated that an aerobic cellulolytic consortium cultivated from compost exhibited community dynamics consistent with the definition of an endogenous heterotrophic succession. The genome of the proposed pioneer population, 'Candidatus Reconcilibacillus cellulovorans', possessed a gene cluster containing multidomain glycoside hydrolases (GHs). Purification of the soluble cellulase activity from a 300litre cultivation of this consortium revealed that ~70% of the activity arose from the 'Ca. Reconcilibacillus cellulovorans' multidomain GHs assembled into cellulase complexes through glycosylation. These remarkably stable complexes have supramolecular structures for enzymatic cellulose hydrolysis that are distinct from cellulosomes. The persistence of these complexes during cultivation indicates that they may be active through multiple cultivations of this consortium and act as public goods that sustain the community. The provision of extracellular GHs as public goods may influence microbial community dynamics in native biomass-deconstructing communities relevant to agriculture, human health and biotechnology.}, } @article {pmid29109410, year = {2017}, author = {Sánchez-Marañón, M and Miralles, I and Aguirre-Garrido, JF and Anguita-Maeso, M and Millán, V and Ortega, R and García-Salcedo, JA and Martínez-Abarca, F and Soriano, M}, title = {Changes in the soil bacterial community along a pedogenic gradient.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {14593}, pmid = {29109410}, issn = {2045-2322}, mesh = {Altitude ; Bacteria/genetics ; Computational Biology ; Plants ; RNA, Bacterial ; RNA, Ribosomal, 16S ; Soil/*chemistry/*classification ; *Soil Microbiology ; Spain ; }, abstract = {Current research on the influence of environmental and physicochemical factors in shaping the soil bacterial structure has seldom been approached from a pedological perspective. We studied the bacterial communities of eight soils selected along a pedogenic gradient at the local scale in a Mediterranean calcareous mountain (Sierra de María, SE Spain). The results showed that the relative abundance of Acidobacteria, Canditate division WPS-1, and Armatimonadetes decreased whereas that of Actinobacteria, Bacteroidetes, and Proteobacteria increased from the less-developed soils (Leptosol) to more-developed soils (Luvisol). This bacterial distribution pattern was also positively correlated with soil-quality parameters such as organic C, water-stable aggregates, porosity, moisture, and acidity. In addition, at a lower taxonomic level, the abundance of Acidobacteria Gp4, Armatimonadetes_gp4, Solirubrobacter, Microvirga, Terrimonas, and Nocardioides paralleled soil development and quality. Therefore, our work indicates that the composition of bacterial populations changes with pedogenesis, which could be considered a factor influencing the communities according to the environmental and physicochemical conditions during the soil formation.}, } @article {pmid29107052, year = {2018}, author = {Seelye, A and Mattek, N and Sharma, N and Riley, T and Austin, J and Wild, K and Dodge, HH and Lore, E and Kaye, J}, title = {Weekly observations of online survey metadata obtained through home computer use allow for detection of changes in everyday cognition before transition to mild cognitive impairment.}, journal = {Alzheimer's & dementia : the journal of the Alzheimer's Association}, volume = {14}, number = {2}, pages = {187-194}, pmid = {29107052}, issn = {1552-5279}, support = {P30 AG024978/AG/NIA NIH HHS/United States ; U2C AG054397/AG/NIA NIH HHS/United States ; R01 AG024059/AG/NIA NIH HHS/United States ; P30 AG008017/AG/NIA NIH HHS/United States ; T32 AG023477/AG/NIA NIH HHS/United States ; R01 AG042191/AG/NIA NIH HHS/United States ; }, mesh = {Activities of Daily Living/*psychology ; Aged ; Aged, 80 and over ; Cognitive Dysfunction/*diagnosis/*psychology ; *Computers ; Cross-Sectional Studies ; Female ; Follow-Up Studies ; Humans ; Male ; Metadata/*statistics & numerical data ; Neuropsychological Tests ; *Online Systems ; Psychiatric Status Rating Scales ; }, abstract = {INTRODUCTION: Subtle changes in instrumental activities of daily living often accompany the onset of mild cognitive impairment (MCI) but are difficult to measure using conventional tests.

METHODS: Weekly online survey metadata metrics, annual neuropsychological tests, and an instrumental activity of daily living questionnaire were examined in 110 healthy older adults with intact cognition (mean age = 85 years) followed up for up to 3.6 years; 29 transitioned to MCI during study follow-up.

RESULTS: In the baseline period, incident MCI participants completed their weekly surveys 1.4 hours later in the day than stable cognitively intact participants, P = .03, d = 0.47. Significant associations were found between earlier survey start time of day and higher memory (r = -0.34; P < .001) and visuospatial test scores (r = -0.37; P < .0001). Longitudinally, incident MCI participants showed an increase in survey completion time by 3 seconds per month for more than the year before diagnosis compared with stable cognitively intact participants (β = 0.12, SE = 0.04, t = 2.8; P = .006).

DISCUSSION: Weekly online survey metadata allowed for detection of changes in everyday cognition before transition to MCI.}, } @article {pmid29105663, year = {2018}, author = {Preston, KL and Kowalczyk, WJ and Phillips, KA and Jobes, ML and Vahabzadeh, M and Lin, JL and Mezghanni, M and Epstein, DH}, title = {Exacerbated Craving in the Presence of Stress and Drug Cues in Drug-Dependent Patients.}, journal = {Neuropsychopharmacology : official publication of the American College of Neuropsychopharmacology}, volume = {43}, number = {4}, pages = {859-867}, pmid = {29105663}, issn = {1740-634X}, mesh = {Adult ; Craving/*physiology ; *Cues ; Female ; Humans ; Male ; Middle Aged ; Opioid-Related Disorders/diagnosis/epidemiology/*psychology ; Random Allocation ; Self Report ; Stress, Psychological/diagnosis/epidemiology/*psychology ; Substance-Related Disorders/diagnosis/epidemiology/psychology ; }, abstract = {In addiction, risk factors for craving and use include stress and drug-related cues. Stress and cues have additive or more-than-additive effects on drug seeking in laboratory animals, but, surprisingly, seem to compete with one another (ie, exert less-than-additive effects) in human laboratory studies of craving. We sought heretofore elusive evidence that human drug users could show additive (or more-than-additive) effects of stress and cues on craving, using ecological momentary assessment (EMA). Outpatients (N=182) maintained on daily buprenorphine or methadone provided self-reports of stress, craving, mood, and behavior on electronic diaries for up to 16 weeks. In three randomly prompted entries (RPs) per day, participants reported the severity of stress and craving and whether they had seen or been offered opioids, cocaine, cannabis, methamphetamine, alcohol, or tobacco. In random-effects models controlling for between-person differences, we tested effects of momentary drug-cue exposure and stress (and their interaction) on momentary ratings of cocaine and heroin craving. For cocaine craving, the Stress × Cue interaction term had a positive mean effect across participants (M=0.019; CL95 0.001-0.036), denoting a more-than-additive effect. For heroin, the mean was not significantly greater than 0, but the confidence interval was predominantly positive (M=0.019; CL95 -0.007-0.044), suggesting at least an additive effect. Heterogeneity was substantial; qualitatively, the Stress × Cue effect appeared additive for most participants, more than additive for a sizeable minority, and competitive in very few. In the field, unlike in human laboratory studies to date, craving for cocaine and heroin is greater with the combination of drug cues and stress than with either alone. For a substantial minority of users, the combined effect may be more than additive.}, } @article {pmid29098814, year = {2017}, author = {Sun, HB and Jiang, SY and Sun, H and Zhou, Y and Zhu, WT}, title = {[Cultural regionalization for Notopterygium incisum based on 3S technology platform Ⅱ. Evaluation for quality suitability for N. incisum based on collocated Cokriging].}, journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica}, volume = {42}, number = {14}, pages = {2633-2638}, doi = {10.19540/j.cnki.cjcmm.20170614.008}, pmid = {29098814}, issn = {1001-5302}, mesh = {Apiaceae/*chemistry ; *Crop Production ; Drugs, Chinese Herbal/*standards ; Ecology ; Geographic Information Systems ; Medicine, Chinese Traditional ; Plant Roots ; Plants, Medicinal/*chemistry ; Rhizome ; Spatial Analysis ; }, abstract = {Quality characteristics based on active substance are focused for in the cultivation of traditional Chinese medicine(TCM) plants due to their economic values. However, ecological and quality suitability are not always a coincidence, which makes traditional cultural regionalization for TCM cultivation based on ecological suitability have great limitations in practical applications. A regionalization method integrated GIS and medicinal plants quality have been analyzed by using field quality data of Notopterygii Rhizoma et Radix as a case study. Spatial interpolation based on medicine quality by Cokriging method is reasonable, and the predicted values of interpolation are correlated with measured values significantly, which shows that cultural regionalization for TCM cultivation based on spatial quality suitability is possible theoretically. The results indicate that the most suitable areas for quality suitability were mainly distributed in Sichuan province (29.42%), while the spatial distribution of quality suitability and ecological suitability was not coincidence. The cultivation regionalization of TCM plants based on quality suitability is helpful to high quality and quantity cultivation of those TCM plants which spatial distribution of geoherbalism and ecological suitability is separated.}, } @article {pmid29097776, year = {2017}, author = {Iquebal, MA and Jaiswal, S and Mahato, AK and Jayaswal, PK and Angadi, UB and Kumar, N and Sharma, N and Singh, AK and Srivastav, M and Prakash, J and Singh, SK and Khan, K and Mishra, RK and Rajan, S and Bajpai, A and Sandhya, BS and Nischita, P and Ravishankar, KV and Dinesh, MR and Rai, A and Kumar, D and Sharma, TR and Singh, NK}, title = {MiSNPDb: a web-based genomic resources of tropical ecology fruit mango (Mangifera indica L.) for phylogeography and varietal differentiation.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {14968}, pmid = {29097776}, issn = {2045-2322}, mesh = {Databases, Genetic ; Fruit/genetics ; Genome, Plant ; Genomics ; Internet ; Mangifera/*genetics ; *Phylogeny ; Phylogeography ; *Polymorphism, Single Nucleotide ; }, abstract = {Mango is one of the most important fruits of tropical ecological region of the world, well known for its nutritive value, aroma and taste. Its world production is >45MT worth >200 billion US dollars. Genomic resources are required for improvement in productivity and management of mango germplasm. There is no web-based genomic resources available for mango. Hence rapid and cost-effective high throughput putative marker discovery is required to develop such resources. RAD-based marker discovery can cater this urgent need till whole genome sequence of mango becomes available. Using a panel of 84 mango varieties, a total of 28.6 Gb data was generated by ddRAD-Seq approach on Illumina HiSeq 2000 platform. A total of 1.25 million SNPs were discovered. Phylogenetic tree using 749 common SNPs across these varieties revealed three major lineages which was compared with geographical locations. A web genomic resources MiSNPDb, available at http://webtom.cabgrid.res.in/mangosnps/ is based on 3-tier architecture, developed using PHP, MySQL and Javascript. This web genomic resources can be of immense use in the development of high density linkage map, QTL discovery, varietal differentiation, traceability, genome finishing and SNP chip development for future GWAS in genomic selection program. We report here world's first web-based genomic resources for genetic improvement and germplasm management of mango.}, } @article {pmid29097090, year = {2018}, author = {Morris, DH and Gostic, KM and Pompei, S and Bedford, T and Łuksza, M and Neher, RA and Grenfell, BT and Lässig, M and McCauley, JW}, title = {Predictive Modeling of Influenza Shows the Promise of Applied Evolutionary Biology.}, journal = {Trends in microbiology}, volume = {26}, number = {2}, pages = {102-118}, pmid = {29097090}, issn = {1878-4380}, support = {MC_U117512723/MRC_/Medical Research Council/United Kingdom ; P2C HD047879/HD/NICHD NIH HHS/United States ; R01 AI127893/AI/NIAID NIH HHS/United States ; P01 CA087497/CA/NCI NIH HHS/United States ; F31 AI134017/AI/NIAID NIH HHS/United States ; /WT_/Wellcome Trust/United Kingdom ; FC001030/MRC_/Medical Research Council/United Kingdom ; FC001030/CRUK_/Cancer Research UK/United Kingdom ; FC001030/ARC_/Arthritis Research UK/United Kingdom ; R35 GM119774/GM/NIGMS NIH HHS/United States ; FC001030/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Antigens, Viral/genetics/immunology ; *Biological Evolution ; Decision Support Techniques ; Disease Outbreaks ; *Forecasting ; Hemagglutination Inhibition Tests/methods ; Humans ; *Influenza Vaccines/immunology ; *Influenza, Human/epidemiology/genetics/prevention & control/virology ; Orthomyxoviridae/genetics/immunology ; Public Health ; Seasons ; Vaccination ; World Health Organization ; }, abstract = {Seasonal influenza is controlled through vaccination campaigns. Evolution of influenza virus antigens means that vaccines must be updated to match novel strains, and vaccine effectiveness depends on the ability of scientists to predict nearly a year in advance which influenza variants will dominate in upcoming seasons. In this review, we highlight a promising new surveillance tool: predictive models. Based on data-sharing and close collaboration between the World Health Organization and academic scientists, these models use surveillance data to make quantitative predictions regarding influenza evolution. Predictive models demonstrate the potential of applied evolutionary biology to improve public health and disease control. We review the state of influenza predictive modeling and discuss next steps and recommendations to ensure that these models deliver upon their considerable biomedical promise.}, } @article {pmid29096650, year = {2017}, author = {Coombes, E and Jones, A and Cooper, A and Page, A}, title = {Does home neighbourhood supportiveness influence the location more than volume of adolescent's physical activity? An observational study using global positioning systems.}, journal = {The international journal of behavioral nutrition and physical activity}, volume = {14}, number = {1}, pages = {149}, pmid = {29096650}, issn = {1479-5868}, support = {//British Heart Foundation/United Kingdom ; MR/K023187/1/MRC_/Medical Research Council/United Kingdom ; //Department of Health/United Kingdom ; //Cancer Research UK/United Kingdom ; G1001164/MRC_/Medical Research Council/United Kingdom ; //Wellcome Trust/United Kingdom ; }, mesh = {Accelerometry ; Adolescent ; *Adolescent Behavior ; Cities ; Environment ; *Exercise ; Female ; *Geographic Information Systems ; Humans ; Male ; *Residence Characteristics ; Schools ; United Kingdom ; }, abstract = {BACKGROUND: Environmental characteristics of home neighbourhoods are hypothesised to be associated with residents' physical activity levels, yet many studies report only weak or equivocal associations. We theorise that this may be because neighbourhood characteristics influence the location of activity more than the volume. Using a sample of UK adolescents, we examine the role of home neighbourhood supportiveness for physical activity, both in terms of volume of activity undertaken and a measure of proximity to home at which activity takes place.

METHODS: Data were analysed from 967 adolescents living in and around the city of Bristol, UK. Each participant wore an accelerometer and a GPS device for 7 days during school term time. These data were integrated into a Geographical Information System containing information on the participants' home neighbourhoods and measures of environmental supportiveness. We then identified the amount of out-of-school activity of different intensities that adolescents undertook inside their home neighbourhood and examined how this related to home neighbourhood supportiveness.

RESULTS: We found that living in a less supportive neighbourhood did not negatively impact the volume of physical activity that adolescents undertook. Indeed these participants recorded similar amounts of activity (e.g. 20.5 mins per day of moderate activity at weekends) as those in more supportive neighbourhoods (18.6 mins per day). However, the amount of activity adolescents undertook inside their home neighbourhood did differ according to supportiveness; those living in less supportive locations had lower odds of recording activity inside their home neighbourhood. This was observed across all intensities of activity including sedentary, light, moderate, and vigorous.

CONCLUSIONS: Our findings suggest that the supportiveness of the neighbourhood around home may have a greater influence on the location of physical activity than the volume undertaken. This finding is at odds with the premise of the socio-ecological models of physical activity that have driven this research field for the last two decades, and has implications for future research, as by simply measuring volumes of activity we may be underestimating the impact of the environment on physical activity behaviours.}, } @article {pmid29095369, year = {2019}, author = {Vest, JR and Menachemi, N}, title = {A population ecology perspective on the functioning and future of health information organizations.}, journal = {Health care management review}, volume = {44}, number = {4}, pages = {344-355}, doi = {10.1097/HMR.0000000000000185}, pmid = {29095369}, issn = {1550-5030}, mesh = {*Commerce ; *Efficiency, Organizational ; Electronic Health Records ; *Health Information Exchange ; Humans ; Interviews as Topic ; Models, Theoretical ; Qualitative Research ; }, abstract = {BACKGROUND: Increasingly, health care providers need to exchange information to meet policy expectations and business needs. A variety of health information organizations (HIOs) provide services to facilitate health information exchange (HIE). However, the future of these organizations is unclear.

PURPOSE: The aim of this study was to explore the environmental context, potential futures, and survivability of community HIOs, enterprise HIEs, and electronic health record vendor-mediated exchange using the population ecology theory.

APPROACH: Qualitative interviews with 33 key informants representing each type of HIE organization were analyzed using template analysis.

RESULTS: Community HIOs, enterprise HIEs, and electronic health record vendors exhibited a high degree of competition for resources, especially in the area of exchange infrastructure services. Competition resulted in closures in some areas. In response to environmental pressures, each organizational type was endeavoring to differentiate its services and unique use case, as well as pursing symbiotic relationships or attempting resource partitioning.

CONCLUSION: HIOs compete for similar resources and are reacting to environmental pressures to better position themselves for continued survival and success. Our ecological research perspective helps move the discourse away from situation of a single exchange organization type toward a view of the broader dynamics and relationships of all organizations involved in facilitating HIE activities.

PRACTICE IMPLICATIONS: HIOs are attempting to partition the environment and differentiate services. HIE options should not be construed as an "either/or" decision, but one where multiple and complementary participation may be required.}, } @article {pmid29094429, year = {2018}, author = {Maeda, E and Ishihara, O and Tomio, J and Sato, A and Terada, Y and Kobayashi, Y and Murata, K}, title = {Cesarean section rates and local resources for perinatal care in Japan: A nationwide ecological study using the national database of health insurance claims.}, journal = {The journal of obstetrics and gynaecology research}, volume = {44}, number = {2}, pages = {208-216}, doi = {10.1111/jog.13518}, pmid = {29094429}, issn = {1447-0756}, mesh = {Adult ; Cesarean Section/*statistics & numerical data ; Databases, Factual ; Female ; Humans ; Infant, Newborn ; Insurance, Health ; Japan ; *Perinatal Care ; Pregnancy ; Pregnancy Outcome ; }, abstract = {AIM: High cesarean section (CS) rates in middle and high-income countries are partly attributable to provider factors, such as staffing patterns and fear of litigation. However, the relationship between CS rates and healthcare resources in the community is poorly understood. Official data on CS rates has been particularly limited in Japan. In this study, we examined nationwide CS statistics and evaluated the association with local resources for perinatal care.

METHODS: We used accumulated data for CS registered in the Japan National Database of health insurance claims in 2013 and calculated crude and age-standardized CS rates at national and prefectural levels. We analyzed the ecological associations with supply of obstetricians and institution and scale of obstetric facilities using multiple regression models.

RESULTS: There were 190 361 cesarean deliveries in 2013, giving an overall CS rate of 18.5% (elective CS rates 11.0%), which varied by prefecture from 14.0% to 25.6%. In multiple regression analyses, the areal number of obstetricians (standardized regression coefficient [β] = -0.58), the proportion of births at small-scale institutions (β = 0.36) and the number of beds at neonatal intensive care units per birth (β = -0.20) were significantly associated with the age-standardized elective CS rate after adjusting for socioeconomic factors (R[2] for the model = 0.40).

CONCLUSIONS: Higher elective CS rates might be associated with limited or unconsolidated medical resources. Policymakers should be aware of regional differences and the possible effects of perinatal care resources on CS rates.}, } @article {pmid29094363, year = {2018}, author = {Glynou, K and Nam, B and Thines, M and Maciá-Vicente, JG}, title = {Facultative root-colonizing fungi dominate endophytic assemblages in roots of nonmycorrhizal Microthlaspi species.}, journal = {The New phytologist}, volume = {217}, number = {3}, pages = {1190-1202}, doi = {10.1111/nph.14873}, pmid = {29094363}, issn = {1469-8137}, mesh = {Ascomycota/*physiology ; Biodiversity ; Databases, Genetic ; Endophytes/*physiology ; Microbiota ; Molecular Sequence Annotation ; Mycorrhizae/*physiology ; Sequence Analysis, DNA ; }, abstract = {There is increasing knowledge on the diversity of root-endophytic fungi, but limited information on their lifestyles and dependence on hosts hampers our understanding of their ecological functions. We compared diversity and biogeographical patterns of cultivable and noncultivable root endophytes to assess whether their occurrence is determined by distinct ecological factors. The endophytic diversity in roots of nonmycorrhizal Microthlaspi spp. growing across Europe was assessed using high-throughput sequencing (HTS) and compared with a previous dataset based on cultivation of endophytes from the same root samples. HTS revealed a large fungal richness undetected by cultivation, but which largely comprised taxa with restricted distributions and/or low representation of sequence reads. Both datasets coincided in a consistent high representation of widespread endophytes within orders Pleosporales, Hypocreales and Helotiales, as well as similar associations of community structure with spatial and environmental conditions. Likewise, distributions of particular endophytes inferred by HTS agreed with cultivation data in suggesting individual ecological preferences. Our findings support that Microthlaspi spp. roots are colonized mostly by saprotrophic and likely facultative endophytes, and that differential niche preferences and distribution ranges among fungi importantly drive the assembly of root-endophytic communities.}, } @article {pmid29092546, year = {2017}, author = {Qian, K and Zhang, Z and Baird, A and Schuller, B}, title = {Active learning for bird sound classification via a kernel-based extreme learning machine.}, journal = {The Journal of the Acoustical Society of America}, volume = {142}, number = {4}, pages = {1796}, doi = {10.1121/1.5004570}, pmid = {29092546}, issn = {1520-8524}, mesh = {*Acoustics ; Animals ; Birds/*classification/*physiology ; Databases, Factual ; Pattern Recognition, Automated/*methods ; *Signal Processing, Computer-Assisted ; *Supervised Machine Learning ; Support Vector Machine ; Vocalization, Animal/*classification ; }, abstract = {In recent years, research fields, including ecology, bioacoustics, signal processing, and machine learning, have made bird sound recognition a part of their focus. This has led to significant advancements within the field of ornithology, such as improved understanding of evolution, local biodiversity, mating rituals, and even the implications and realities associated to climate change. The volume of unlabeled bird sound data is now overwhelming, and comparatively little exploration is being made into methods for how best to handle them. In this study, two active learning (AL) methods are proposed, sparse-instance-based active learning (SI-AL), and least-confidence-score-based active learning (LCS-AL), both effectively reducing the need for expert human annotation. To both of these AL paradigms, a kernel-based extreme learning machine (KELM) is then integrated, and a comparison is made to the conventional support vector machine (SVM). Experimental results demonstrate that, when the classifier capacity is improved from an unweighted average recall of 60%-80%, KELM can outperform SVM even when a limited proportion of human annotations are used from the pool of data in both cases of SI-AL (minimum 34.5% vs minimum 59.0%) and LCS-AL (minimum 17.3% vs minimum 28.4%).}, } @article {pmid29091614, year = {2017}, author = {Zhou, W and Wang, G and Li, C and Xu, Z and Cao, W and Shen, F}, title = {Retrieval of phytoplankton cell size from chlorophyll a specific absorption and scattering spectra of phytoplankton.}, journal = {Applied optics}, volume = {56}, number = {30}, pages = {8362-8371}, doi = {10.1364/AO.56.008362}, pmid = {29091614}, issn = {1539-4522}, mesh = {Cell Count ; *Cell Size ; Chlorophyll/*analysis ; Chlorophyll A ; Chromatography, High Pressure Liquid ; Datasets as Topic ; Densitometry/methods ; Phytoplankton/chemistry/*cytology ; Remote Sensing Technology ; Species Specificity ; }, abstract = {Phytoplankton cell size is an important property that affects diverse ecological and biogeochemical processes, and analysis of the absorption and scattering spectra of phytoplankton can provide important information about phytoplankton size. In this study, an inversion method for extracting quantitative phytoplankton cell size data from these spectra was developed. This inversion method requires two inputs: chlorophyll a specific absorption and scattering spectra of phytoplankton. The average equivalent-volume spherical diameter (ESDv) was calculated as the single size approximation for the log-normal particle size distribution (PSD) of the algal suspension. The performance of this method for retrieving cell size was assessed using the datasets from cultures of 12 phytoplankton species. The estimations of a(λ) and b(λ) for the phytoplankton population using ESDv had mean error values of 5.8%-6.9% and 7.0%-10.6%, respectively, compared to the a(λ) and b(λ) for the phytoplankton populations using the log-normal PSD. The estimated values of CiESDv were in good agreement with the measurements, with r[2]=0.88 and relative root mean square error (NRMSE)=25.3%, and relatively good performances were also found for the retrieval of ESDv with r[2]=0.78 and NRMSE=23.9%.}, } @article {pmid29090545, year = {2017}, author = {Tang, C and Wen, J and Zhang, W and Su, JS and Xie, CX and Zhang, Y}, title = {[Potential distribution of the traditional Tibetan herb Pterocephalus hookeri by Maxent model].}, journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica}, volume = {42}, number = {10}, pages = {1871-1876}, doi = {10.19540/j.cnki.cjcmm.20170222.018}, pmid = {29090545}, issn = {1001-5302}, mesh = {Caprifoliaceae/*growth & development ; China ; *Climate ; *Ecology ; Geographic Information Systems ; Plant Dispersal ; Plants, Medicinal/*growth & development ; Soil ; Tibet ; }, abstract = {In order to study the ecology suitability of Pterocephalus hookeri, and provide a reference for GAP planting location and regional development, the Maxent model and GIS technology were used to investigate ecology suitability regions for P. hookeri based on the distribution points collected from Chinese virtual herbarium, the references and field trips. The potential distribution areas mainly concentrated in the eastern Tibet, western Sichuan, southern Qinghai, northwest Yunnan, and southern Gansu. There were 7 major environmental factors to have obvious influence on ecology suitability distributions of P. hookeri, including altitude (contribution rate of 62%), precipitation of warmest quarter (contribution rate of 14.4%), coefficient of variation of precipitation seasonality (contribution rate of 7.2%), mean temperature of driest quarter (contribution rate of 3.5%), the electrical conductivity of top and sub-soil (contribution rate of 3%), the total exchangeable bases in the top- and subsoil (contribution rate of 2.4%) and SD of temperature seasonality (contribution rate of 2.2%). The study of the ecological suitability regionalization of P. hookeri based on Maxent model can provide scientific basis for the selection of artificial planting base and GAP planting location.}, } @article {pmid29089486, year = {2017}, author = {Cheng, J and Demeulemeester, J and Wedge, DC and Vollan, HKM and Pitt, JJ and Russnes, HG and Pandey, BP and Nilsen, G and Nord, S and Bignell, GR and White, KP and Børresen-Dale, AL and Campbell, PJ and Kristensen, VN and Stratton, MR and Lingjærde, OC and Moreau, Y and Van Loo, P}, title = {Pan-cancer analysis of homozygous deletions in primary tumours uncovers rare tumour suppressors.}, journal = {Nature communications}, volume = {8}, number = {1}, pages = {1221}, pmid = {29089486}, issn = {2041-1723}, support = {//Wellcome Trust/United Kingdom ; T32 GM007197/GM/NIGMS NIH HHS/United States ; FC001202//Cancer Research UK/United Kingdom ; FC001202//Medical Research Council/United Kingdom ; FC001202//Wellcome Trust/United Kingdom ; }, mesh = {Alleles ; Chromosome Fragile Sites/genetics ; *Gene Deletion ; Gene Dosage ; *Genes, Tumor Suppressor ; Genome, Human ; Homozygote ; Humans ; Neoplasms/*genetics ; Ploidies ; Telomere/metabolism ; }, abstract = {Homozygous deletions are rare in cancers and often target tumour suppressor genes. Here, we build a compendium of 2218 primary tumours across 12 human cancer types and systematically screen for homozygous deletions, aiming to identify rare tumour suppressors. Our analysis defines 96 genomic regions recurrently targeted by homozygous deletions. These recurrent homozygous deletions occur either over tumour suppressors or over fragile sites, regions of increased genomic instability. We construct a statistical model that separates fragile sites from regions showing signatures of positive selection for homozygous deletions and identify candidate tumour suppressors within those regions. We find 16 established tumour suppressors and propose 27 candidate tumour suppressors. Several of these genes (including MGMT, RAD17, and USP44) show prior evidence of a tumour suppressive function. Other candidate tumour suppressors, such as MAFTRR, KIAA1551, and IGF2BP2, are novel. Our study demonstrates how rare tumour suppressors can be identified through copy number meta-analysis.}, } @article {pmid29087435, year = {2018}, author = {Piccolo, BD and Wankhade, UD and Chintapalli, SV and Bhattacharyya, S and Chunqiao, L and Shankar, K}, title = {Dynamic assessment of microbial ecology (DAME): a web app for interactive analysis and visualization of microbial sequencing data.}, journal = {Bioinformatics (Oxford, England)}, volume = {34}, number = {6}, pages = {1050-1052}, pmid = {29087435}, issn = {1367-4811}, support = {UL1 TR001449/TR/NCATS NIH HHS/United States ; }, mesh = {*Data Interpretation, Statistical ; *Ecosystem ; Microbiological Techniques ; Microbiology ; Programming Languages ; Sequence Analysis ; *Software ; }, abstract = {SUMMARY: Dynamic assessment of microbial ecology (DAME) is a Shiny-based web application for interactive analysis and visualization of microbial sequencing data. DAME provides researchers not familiar with R programming the ability to access the most current R functions utilized for ecology and gene sequencing data analyses. Currently, DAME supports group comparisons of several ecological estimates of α-diversity and β-diversity, along with differential abundance analysis of individual taxa. Using the Shiny framework, the user has complete control of all aspects of the data analysis, including sample/experimental group selection and filtering, estimate selection, statistical methods and visualization parameters. Furthermore, graphical and tabular outputs are supported by R packages using D3.js and are fully interactive.

DAME was implemented in R but can be modified by Hypertext Markup Language (HTML), Cascading Style Sheets (CSS), and JavaScript. It is freely available on the web at https://acnc-shinyapps.shinyapps.io/DAME/. Local installation and source code are available through Github (https://github.com/bdpiccolo/ACNC-DAME). Any system with R can launch DAME locally provided the shiny package is installed.

CONTACT: bdpiccolo@uams.edu.}, } @article {pmid29086695, year = {2018}, author = {Fasano, F and Mitolo, M and Gardini, S and Venneri, A and Caffarra, P and Pazzaglia, F}, title = {Combining Structural Magnetic Resonance Imaging and Visuospatial Tests to Classify Mild Cognitive Impairment.}, journal = {Current Alzheimer research}, volume = {15}, number = {3}, pages = {237-246}, doi = {10.2174/1567205014666171030112339}, pmid = {29086695}, issn = {1875-5828}, mesh = {Age Factors ; Aged ; Brain/*diagnostic imaging ; Cognitive Dysfunction/*classification/*diagnostic imaging/psychology ; Female ; Humans ; Image Interpretation, Computer-Assisted ; *Magnetic Resonance Imaging ; Male ; Mental Status Schedule ; Middle Aged ; Neuropsychological Tests ; Photic Stimulation ; Recognition, Psychology ; Space Perception/*physiology ; }, abstract = {BACKGROUND: Recently, efforts have been made to combine complementary perspectives in the assessment of Alzheimer type dementia. Of particular interest is the definition of the fingerprints of an early stage of the disease known as Mild Cognitive Impairment or prodromal Alzheimer's Disease. Machine learning approaches have been shown to be extremely suitable for the implementation of such a combination.

METHODS: In the present pilot study we combined the machine learning approach with structural magnetic resonance imaging and cognitive test assessments to classify a small cohort of 11 healthy participants and 11 patients experiencing Mild Cognitive Impairment. Cognitive assessment included a battery of standardised tests and a battery of experimental visuospatial memory tests. Correct classification was achieved in 100% of the participants, suggesting that the combination of neuroimaging with more complex cognitive tests is suitable for early detection of Alzheimer Disease.

RESULTS: In particular, the results highlighted the importance of the experimental visuospatial memory test battery in the efficiency of classification, suggesting that the high-level brain computational framework underpinning the participant's performance in these ecological tests may represent a "natural filter" in the exploration of cognitive patterns of information able to identify early signs of the disease.}, } @article {pmid29084216, year = {2017}, author = {Lau, MSY and Gibson, GJ and Adrakey, H and McClelland, A and Riley, S and Zelner, J and Streftaris, G and Funk, S and Metcalf, J and Dalziel, BD and Grenfell, BT}, title = {A mechanistic spatio-temporal framework for modelling individual-to-individual transmission-With an application to the 2014-2015 West Africa Ebola outbreak.}, journal = {PLoS computational biology}, volume = {13}, number = {10}, pages = {e1005798}, pmid = {29084216}, issn = {1553-7358}, support = {MR/K021680/1/MRC_/Medical Research Council/United Kingdom ; P2C HD047879/HD/NICHD NIH HHS/United States ; }, mesh = {Africa, Western/epidemiology ; Computer Simulation ; Disease Outbreaks/*statistics & numerical data ; Disease Transmission, Infectious/*statistics & numerical data ; Geographic Information Systems/statistics & numerical data ; Hemorrhagic Fever, Ebola/*epidemiology/*transmission ; Humans ; *Models, Statistical ; Prevalence ; Proportional Hazards Models ; Risk Assessment/methods ; *Spatio-Temporal Analysis ; }, abstract = {In recent years there has been growing availability of individual-level spatio-temporal disease data, particularly due to the use of modern communicating devices with GPS tracking functionality. These detailed data have been proven useful for inferring disease transmission to a more refined level than previously. However, there remains a lack of statistically sound frameworks to model the underlying transmission dynamic in a mechanistic manner. Such a development is particularly crucial for enabling a general epidemic predictive framework at the individual level. In this paper we propose a new statistical framework for mechanistically modelling individual-to-individual disease transmission in a landscape with heterogeneous population density. Our methodology is first tested using simulated datasets, validating our inferential machinery. The methodology is subsequently applied to data that describes a regional Ebola outbreak in Western Africa (2014-2015). Our results show that the methods are able to obtain estimates of key epidemiological parameters that are broadly consistent with the literature, while revealing a significantly shorter distance of transmission. More importantly, in contrast to existing approaches, we are able to perform a more general model prediction that takes into account the susceptible population. Finally, our results show that, given reasonable scenarios, the framework can be an effective surrogate for susceptible-explicit individual models which are often computationally challenging.}, } @article {pmid29079680, year = {2017}, author = {Song, H and Qi, L and Zhang, T and Wang, HY}, title = {Understanding microRNA Regulation Involved in the Metamorphosis of the Veined Rapa Whelk (Rapana venosa).}, journal = {G3 (Bethesda, Md.)}, volume = {7}, number = {12}, pages = {3999-4008}, pmid = {29079680}, issn = {2160-1836}, mesh = {Animals ; China ; Gene Expression Regulation/genetics ; Gene Ontology ; High-Throughput Nucleotide Sequencing ; Larva/genetics/growth & development ; Metamorphosis, Biological/*genetics ; MicroRNAs/*genetics ; Primulaceae/*genetics/growth & development ; Transcriptome/*genetics ; }, abstract = {The veined rapa whelk (Rapana venosa) is widely consumed in China. Nevertheless, it preys on oceanic bivalves, thereby reducing this resource worldwide. Its larval metamorphosis comprises a transition from pelagic to benthic form, which involves considerable physiological and structural changes and has vital roles in its natural populations and commercial breeding. Thus, understanding the endogenous microRNAs (miRNAs) that drive metamorphosis is of great interest. This is the first study to use high-throughput sequencing to examine the alterations in miRNA expression that occur during metamorphosis in a marine gastropod. A total of 195 differentially expressed miRNAs were obtained. Sixty-five of these were expressed during the transition from precompetent to competent larvae. Thirty-three of these were upregulated and the others were downregulated. Another 123 miRNAs were expressed during the transition from competent to postlarvae. Ninety-six of these were upregulated and the remaining 27 were downregulated. The expression of miR-276-y, miR-100-x, miR-183-x, and miR-263-x showed a >100-fold change during development, while the miR-242-x and novel-m0052-3p expression levels changed over 3000-fold. Putative target gene coexpression, gene ontology, and pathway analyses suggest that these miRNAs play important parts in cell proliferation, migration, apoptosis, metabolic regulation, and energy absorption. Twenty miRNAs and their target genes involved in ingestion, digestion, cytoskeleton, cell adhesion, and apoptosis were identified. Nine of them were analyzed with real-time polymerase chain reaction (PCR), which showed an inverse correlation between the miRNAs and their relative expression levels. Our data elucidate the role of miRNAs in R. venosa metamorphic transition and serve as a solid basis for further investigations into regulatory mechanisms of gastropod metamorphosis.}, } @article {pmid29079085, year = {2018}, author = {Furlan, E and Torresan, S and Critto, A and Marcomini, A}, title = {Spatially explicit risk approach for multi-hazard assessment and management in marine environment: The case study of the Adriatic Sea.}, journal = {The Science of the total environment}, volume = {618}, number = {}, pages = {1008-1023}, doi = {10.1016/j.scitotenv.2017.09.076}, pmid = {29079085}, issn = {1879-1026}, mesh = {Animals ; *Climate Change ; Conservation of Natural Resources ; *Ecosystem ; *Environmental Monitoring ; Humans ; Marine Biology ; *Oceans and Seas ; Risk Assessment ; Spatial Analysis ; }, abstract = {In the last few decades the health of marine ecosystems has been progressively endangered by the anthropogenic presence. Natural and human-made pressures, as well as climate change effects, are posing increasing threats on marine areas, triggering alteration of biological, chemical and physical processes. Planning of marine areas has become a challenge for decision makers involved in the design of sustainable management options. In order to address threats posed by climate drivers in combination with local to regional anthropogenic pressures affecting marine ecosystems and activities, a multi-hazard assessment methodology was developed and applied to the Adriatic Sea for the reference scenario 2000-2015. Through a four-stages process based on the consecutive analysis of hazard, exposure, vulnerability and risk the methodology allows a semi-quantitative evaluation of the relative risk from anthropogenic and natural sources to multiple endpoints, thus supporting the identification and ranking of areas and targets more likely to be at risk. Resulting output showed that the higher relative hazard scores are linked to exogenic pressures (e.g. sea surface temperature variation) while the lower ones resulted from endogenic and more localized stressors (e.g. abrasion, nutrient input). Relatively very high scores were observed for vulnerability over the whole case study for almost all the considered pressures, showing seagrasses meadows, maërl and coral beds as the most susceptible targets. The approach outlined in this study provides planners and decision makers a quick-screening tool to evaluate progress towards attaining a good environmental status and to identify marine areas where management actions and adaptation strategies would be best targeted. Moreover, by focusing on risks induced by land-based drivers, resulting output can support the design of infrastructures for reducing pressures on the sea, contributing to improve the land-sea interface management.}, } @article {pmid29077895, year = {2018}, author = {Springer, MS and Gatesy, J}, title = {Pinniped Diphyly and Bat Triphyly: More Homology Errors Drive Conflicts in the Mammalian Tree.}, journal = {The Journal of heredity}, volume = {109}, number = {3}, pages = {297-307}, doi = {10.1093/jhered/esx089}, pmid = {29077895}, issn = {1465-7333}, mesh = {Animals ; Caniformia/*genetics ; Carnivora/genetics ; Chiroptera/*genetics ; Databases, Genetic ; Datasets as Topic ; Exons ; Likelihood Functions ; *Phylogeny ; Sequence Alignment/methods/statistics & numerical data ; }, abstract = {Homology is perhaps the most central concept of phylogenetic biology. At difficult to resolve polytomies that are deep in the Tree of Life, a few homology errors in phylogenomic data can drive spurious phylogenetic results. Feijoo and Parada (2017) assembled three phylogenomic data sets for mammals and reported methodological discrepancies and unexpected results that contradict the monophyly of well-established clades in Pinnipedia and Yangochiroptera. Examination of Feijoo and Parada's (2017) data sets reveals extensive homology errors (paralogous sequences, alignments of different exons to each other) and cross-contamination of sequences from different species. These problems predictably result in distorted estimates of gene trees, species trees, bootstrap support, and branch lengths. Correction of these errors resulted in robust support for conventional relationships in Pinnipedia and Yangochiroptera. Phylogenomic data sets are not immune to the problems of homology errors in sequence alignments. Rather, sequence alignments underlie all inferences in molecular phylogenetics and evolution and should be spot-checked for obvious errors via manual inspection of alignments and gene trees.}, } @article {pmid29073028, year = {2017}, author = {Greenhill, SJ and Wu, CH and Hua, X and Dunn, M and Levinson, SC and Gray, RD}, title = {Evolutionary dynamics of language systems.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {114}, number = {42}, pages = {E8822-E8829}, pmid = {29073028}, issn = {1091-6490}, support = {//Medical Research Council/United Kingdom ; ANR00310//Cancer Research UK/United Kingdom ; }, mesh = {Bayes Theorem ; *Biological Evolution ; Databases, Factual ; Humans ; *Language ; Linguistics/methods ; Monte Carlo Method ; Oceania ; Papua New Guinea ; Phylogeny ; Vocabulary ; }, abstract = {Understanding how and why language subsystems differ in their evolutionary dynamics is a fundamental question for historical and comparative linguistics. One key dynamic is the rate of language change. While it is commonly thought that the rapid rate of change hampers the reconstruction of deep language relationships beyond 6,000-10,000 y, there are suggestions that grammatical structures might retain more signal over time than other subsystems, such as basic vocabulary. In this study, we use a Dirichlet process mixture model to infer the rates of change in lexical and grammatical data from 81 Austronesian languages. We show that, on average, most grammatical features actually change faster than items of basic vocabulary. The grammatical data show less schismogenesis, higher rates of homoplasy, and more bursts of contact-induced change than the basic vocabulary data. However, there is a core of grammatical and lexical features that are highly stable. These findings suggest that different subsystems of language have differing dynamics and that careful, nuanced models of language change will be needed to extract deeper signal from the noise of parallel evolution, areal readaptation, and contact.}, } @article {pmid29068761, year = {2018}, author = {Perkovic, S and Orquin, JL}, title = {Implicit Statistical Learning in Real-World Environments Leads to Ecologically Rational Decision Making.}, journal = {Psychological science}, volume = {29}, number = {1}, pages = {34-44}, doi = {10.1177/0956797617733831}, pmid = {29068761}, issn = {1467-9280}, mesh = {Adolescent ; Adult ; Aged ; Aged, 80 and over ; *Data Interpretation, Statistical ; *Decision Making ; Female ; Food Preferences ; Food, Organic ; Health Knowledge, Attitudes, Practice ; Humans ; *Learning ; Male ; Middle Aged ; Young Adult ; }, abstract = {Ecological rationality results from matching decision strategies to appropriate environmental structures, but how does the matching happen? We propose that people learn the statistical structure of the environment through observation and use this learned structure to guide ecologically rational behavior. We tested this hypothesis in the context of organic foods. In Study 1, we found that products from healthful food categories are more likely to be organic than products from nonhealthful food categories. In Study 2, we found that consumers' perceptions of the healthfulness and prevalence of organic products in many food categories are accurate. Finally, in Study 3, we found that people perceive organic products as more healthful than nonorganic products when the statistical structure justifies this inference. Our findings suggest that people believe organic foods are more healthful than nonorganic foods and use an organic-food cue to guide their behavior because organic foods are, on average, 30% more healthful.}, } @article {pmid29063475, year = {2017}, author = {Yang, RN and Li, DZ and Yu, G and Yi, SC and Zhang, Y and Kong, DX and Wang, MQ}, title = {Structural Transformation Detection Contributes to Screening of Behaviorally Active Compounds: Dynamic Binding Process Analysis of DhelOBP21 from Dastarcus helophoroides.}, journal = {Journal of chemical ecology}, volume = {43}, number = {11-12}, pages = {1033-1045}, pmid = {29063475}, issn = {1573-1561}, support = {2017YFD0600101//the National Key Research and Development Program/ ; 31230015//the National Natural Science Foundation of China/ ; 2662015PY139//Fundamental Research Funds for the Central Universities/ ; }, mesh = {Animals ; Behavior, Animal/drug effects ; Bicyclic Monoterpenes ; Binding Sites ; Bridged Bicyclo Compounds/chemistry/metabolism/pharmacology ; Circular Dichroism ; Coleoptera/*metabolism ; Insect Proteins/chemistry/genetics/*metabolism ; Molecular Dynamics Simulation ; Monoterpenes/chemistry/metabolism/pharmacology ; Polycyclic Sesquiterpenes ; RNA Interference ; RNA, Double-Stranded/metabolism ; Receptors, Odorant/chemistry/genetics/*metabolism ; Recombinant Proteins/biosynthesis/chemistry/isolation & purification ; Sesquiterpenes/chemistry/metabolism/pharmacology ; Spectrometry, Fluorescence ; }, abstract = {In light of reverse chemical ecology, the fluorescence competitive binding assays of functional odorant binding proteins (OBPs) is a recent advanced approach for screening behaviorally active compounds of insects. Previous research on Dastareus helophoroides identified a minus-C OBP, DhelOBP21, which preferably binds to several ligands. In this study, only (+)-β-pinene proved attractive to unmated adult beetles. To obtain a more in-depth explanation of the lack of behavioral activity of other ligands we selected compounds with high (camphor) and low (β-caryophyllene) binding affinities. The structural transformation of OBPs was investigated using well-established approaches for studying binding processes, such as fluorescent quenching assays, circular dichroism, and molecular dynamics. The dynamic binding process revealed that the flexibility of DhelOBP21 seems conducive to binding specific ligands, as opposed to broad substrate binding. The compound (+)-β-pinene and DhelOBP21 formed a stable complex through a secondary structural transformation of DhelOBP21, in which its amino-terminus transformed from random coil to an α-helix to cover the binding pocket. On the other hand, camphor could not efficiently induce a stable structural transformation, and its high binding affinities were due to strong hydrogen-bonding, compromising the structure of the protein. The other compound, β-caryophyllene, only collided with DhelOBP21 and could not be positioned in the binding pocket. Studying structural transformation of these proteins through examining the dynamic binding process rather than using approaches that just measure binding affinities such as fluorescence competitive binding assays can provide a more efficient and reliable approach for screening behaviorally active compounds.}, } @article {pmid29061847, year = {2017}, author = {Viborg, AH and Katayama, T and Arakawa, T and Abou Hachem, M and Lo Leggio, L and Kitaoka, M and Svensson, B and Fushinobu, S}, title = {Discovery of α-l-arabinopyranosidases from human gut microbiome expands the diversity within glycoside hydrolase family 42.}, journal = {The Journal of biological chemistry}, volume = {292}, number = {51}, pages = {21092-21101}, pmid = {29061847}, issn = {1083-351X}, mesh = {Amino Acid Substitution ; Bacterial Proteins/chemistry/genetics/*metabolism ; Bifidobacterium animalis/*enzymology/isolation & purification ; Carbohydrate Conformation ; Catalytic Domain ; Computational Biology ; Crystallography, X-Ray ; Disaccharides/chemistry/*metabolism ; *Gastrointestinal Microbiome ; Ginsenosides/chemistry/metabolism ; Glycoside Hydrolases/chemistry/genetics/*metabolism ; Glycosides/chemistry/*metabolism ; Humans ; Ligands ; Models, Molecular ; Molecular Docking Simulation ; Mutation ; Phylogeny ; Protein Conformation ; Protein Multimerization ; Recombinant Proteins/chemistry/metabolism ; Stereoisomerism ; Substrate Specificity ; }, abstract = {Enzymes of the glycoside hydrolase family 42 (GH42) are widespread in bacteria of the human gut microbiome and play fundamental roles in the decomposition of both milk and plant oligosaccharides. All GH42 enzymes characterized so far have β-galactosidase activity. Here, we report the existence of a GH42 subfamily that is exclusively specific for α-l-arabinopyranoside and describe the first representative of this subfamily. We found that this enzyme (BlArap42B) from a probiotic Bifidobacterium species cannot hydrolyze β-galactosides. However, BlArap42B effectively hydrolyzed paeonolide and ginsenoside Rb2, plant glycosides containing an aromatic aglycone conjugated to α-l-arabinopyranosyl-(1,6)-β-d-glucopyranoside. Paeonolide, a natural glycoside from the roots of the plant genus Paeonia, is not hydrolyzed by classical GH42 β-galactosidases. X-ray crystallography revealed a unique Trp[345]-X12-Trp[358] sequence motif at the BlArap42B active site, as compared with a Phe-X12-His motif in classical GH42 β-galactosidases. This analysis also indicated that the C6 position of galactose is blocked by the aromatic side chains, hence allowing accommodation only of Arap lacking this carbon. Automated docking of paeonolide revealed that it can fit into the BlArap42B active site. The Glcp moiety of paeonolide stacks onto the aromatic ring of the Trp[252] at subsite +1 and C4-OH is hydrogen bonded with Asp[249] Moreover, the aglycone stacks against Phe[421] from the neighboring monomer in the BlArap42B trimer, forming a proposed subsite +2. These results further support the notion that evolution of metabolic specialization can be tracked at the structural level in key enzymes facilitating degradation of specific glycans in an ecological niche.}, } @article {pmid29058981, year = {2018}, author = {Short, AEZ and Dikow, T and Moreau, CS}, title = {Entomological Collections in the Age of Big Data.}, journal = {Annual review of entomology}, volume = {63}, number = {}, pages = {513-530}, doi = {10.1146/annurev-ento-031616-035536}, pmid = {29058981}, issn = {1545-4487}, mesh = {Animals ; Big Data ; *Collections as Topic ; Entomology/*trends ; Genomics ; Informatics ; *Insecta ; Museums/*trends ; }, abstract = {With a million described species and more than half a billion preserved specimens, the large scale of insect collections is unequaled by those of any other group. Advances in genomics, collection digitization, and imaging have begun to more fully harness the power that such large data stores can provide. These new approaches and technologies have transformed how entomological collections are managed and utilized. While genomic research has fundamentally changed the way many specimens are collected and curated, advances in technology have shown promise for extracting sequence data from the vast holdings already in museums. Efforts to mainstream specimen digitization have taken root and have accelerated traditional taxonomic studies as well as distribution modeling and global change research. Emerging imaging technologies such as microcomputed tomography and confocal laser scanning microscopy are changing how morphology can be investigated. This review provides an overview of how the realization of big data has transformed our field and what may lie in store.}, } @article {pmid29058217, year = {2017}, author = {Jiang, X and Hu, X}, title = {Data Analysis for Gut Microbiota and Health.}, journal = {Advances in experimental medicine and biology}, volume = {1028}, number = {}, pages = {79-87}, doi = {10.1007/978-981-10-6041-0_5}, pmid = {29058217}, issn = {0065-2598}, mesh = {*Data Mining ; *Gastrointestinal Microbiome ; Health ; Humans ; Statistics as Topic ; }, abstract = {In recent years, data mining and analysis of high-throughput sequencing of microbiomes and metagenomic data enable researchers to discover biological knowledge by characterizing the composition and variation of species across environmental samples and to accumulate a huge amount of data, making it feasible to infer the complex principle of species interactions. The interactions of microbes in a microbial community play an important role in microbial ecological system. Data mining provides diverse approachs to identify the correlations between disease and microbes and how microbial species coexist and interact in a host-associated or natural environment. This is not only important to advance basic microbiology science and other related fields but also important to understand the impacts of microbial communities on human health and diseases.}, } @article {pmid29056410, year = {2018}, author = {Landrigan, PJ and Fuller, R and Acosta, NJR and Adeyi, O and Arnold, R and Basu, NN and Baldé, AB and Bertollini, R and Bose-O'Reilly, S and Boufford, JI and Breysse, PN and Chiles, T and Mahidol, C and Coll-Seck, AM and Cropper, ML and Fobil, J and Fuster, V and Greenstone, M and Haines, A and Hanrahan, D and Hunter, D and Khare, M and Krupnick, A and Lanphear, B and Lohani, B and Martin, K and Mathiasen, KV and McTeer, MA and Murray, CJL and Ndahimananjara, JD and Perera, F and Potočnik, J and Preker, AS and Ramesh, J and Rockström, J and Salinas, C and Samson, LD and Sandilya, K and Sly, PD and Smith, KR and Steiner, A and Stewart, RB and Suk, WA and van Schayck, OCP and Yadama, GN and Yumkella, K and Zhong, M}, title = {The Lancet Commission on pollution and health.}, journal = {Lancet (London, England)}, volume = {391}, number = {10119}, pages = {462-512}, doi = {10.1016/S0140-6736(17)32345-0}, pmid = {29056410}, issn = {1474-547X}, mesh = {Adolescent ; Adult ; Age Distribution ; Aged ; Air Pollutants/adverse effects ; Child ; Child, Preschool ; Chronic Disease/epidemiology/prevention & control ; Conservation of Natural Resources ; Cost of Illness ; Environmental Health/economics/legislation & jurisprudence/*standards ; Environmental Pollution/*adverse effects/prevention & control ; Female ; Global Health/*standards/statistics & numerical data ; Health Policy ; Health Status Disparities ; Humans ; Infant ; Infant, Newborn ; International Cooperation ; Male ; Middle Aged ; Mortality, Premature ; Noncommunicable Diseases/epidemiology ; Occupational Health/standards ; Poverty ; Residence Characteristics ; Soil Pollutants/adverse effects ; Water Pollutants/adverse effects ; World Health Organization ; Young Adult ; }, } @article {pmid29053868, year = {2017}, author = {Soranno, PA and Bacon, LC and Beauchene, M and Bednar, KE and Bissell, EG and Boudreau, CK and Boyer, MG and Bremigan, MT and Carpenter, SR and Carr, JW and Cheruvelil, KS and Christel, ST and Claucherty, M and Collins, SM and Conroy, JD and Downing, JA and Dukett, J and Fergus, CE and Filstrup, CT and Funk, C and Gonzalez, MJ and Green, LT and Gries, C and Halfman, JD and Hamilton, SK and Hanson, PC and Henry, EN and Herron, EM and Hockings, C and Jackson, JR and Jacobson-Hedin, K and Janus, LL and Jones, WW and Jones, JR and Keson, CM and King, KBS and Kishbaugh, SA and Lapierre, JF and Lathrop, B and Latimore, JA and Lee, Y and Lottig, NR and Lynch, JA and Matthews, LJ and McDowell, WH and Moore, KEB and Neff, BP and Nelson, SJ and Oliver, SK and Pace, ML and Pierson, DC and Poisson, AC and Pollard, AI and Post, DM and Reyes, PO and Rosenberry, DO and Roy, KM and Rudstam, LG and Sarnelle, O and Schuldt, NJ and Scott, CE and Skaff, NK and Smith, NJ and Spinelli, NR and Stachelek, JJ and Stanley, EH and Stoddard, JL and Stopyak, SB and Stow, CA and Tallant, JM and Tan, PN and Thorpe, AP and Vanni, MJ and Wagner, T and Watkins, G and Weathers, KC and Webster, KE and White, JD and Wilmes, MK and Yuan, S}, title = {LAGOS-NE: a multi-scaled geospatial and temporal database of lake ecological context and water quality for thousands of US lakes.}, journal = {GigaScience}, volume = {6}, number = {12}, pages = {1-22}, pmid = {29053868}, issn = {2047-217X}, mesh = {*Databases, Factual ; Lakes/*chemistry ; United States ; *Water Quality ; }, abstract = {Understanding the factors that affect water quality and the ecological services provided by freshwater ecosystems is an urgent global environmental issue. Predicting how water quality will respond to global changes not only requires water quality data, but also information about the ecological context of individual water bodies across broad spatial extents. Because lake water quality is usually sampled in limited geographic regions, often for limited time periods, assessing the environmental controls of water quality requires compilation of many data sets across broad regions and across time into an integrated database. LAGOS-NE accomplishes this goal for lakes in the northeastern-most 17 US states.LAGOS-NE contains data for 51 101 lakes and reservoirs larger than 4 ha in 17 lake-rich US states. The database includes 3 data modules for: lake location and physical characteristics for all lakes; ecological context (i.e., the land use, geologic, climatic, and hydrologic setting of lakes) for all lakes; and in situ measurements of lake water quality for a subset of the lakes from the past 3 decades for approximately 2600-12 000 lakes depending on the variable. The database contains approximately 150 000 measures of total phosphorus, 200 000 measures of chlorophyll, and 900 000 measures of Secchi depth. The water quality data were compiled from 87 lake water quality data sets from federal, state, tribal, and non-profit agencies, university researchers, and citizen scientists. This database is one of the largest and most comprehensive databases of its type because it includes both in situ measurements and ecological context data. Because ecological context can be used to study a variety of other questions about lakes, streams, and wetlands, this database can also be used as the foundation for other studies of freshwaters at broad spatial and ecological scales.}, } @article {pmid29051992, year = {2017}, author = {Leist, M and Ghallab, A and Graepel, R and Marchan, R and Hassan, R and Bennekou, SH and Limonciel, A and Vinken, M and Schildknecht, S and Waldmann, T and Danen, E and van Ravenzwaay, B and Kamp, H and Gardner, I and Godoy, P and Bois, FY and Braeuning, A and Reif, R and Oesch, F and Drasdo, D and Höhme, S and Schwarz, M and Hartung, T and Braunbeck, T and Beltman, J and Vrieling, H and Sanz, F and Forsby, A and Gadaleta, D and Fisher, C and Kelm, J and Fluri, D and Ecker, G and Zdrazil, B and Terron, A and Jennings, P and van der Burg, B and Dooley, S and Meijer, AH and Willighagen, E and Martens, M and Evelo, C and Mombelli, E and Taboureau, O and Mantovani, A and Hardy, B and Koch, B and Escher, S and van Thriel, C and Cadenas, C and Kroese, D and van de Water, B and Hengstler, JG}, title = {Adverse outcome pathways: opportunities, limitations and open questions.}, journal = {Archives of toxicology}, volume = {91}, number = {11}, pages = {3477-3505}, doi = {10.1007/s00204-017-2045-3}, pmid = {29051992}, issn = {1432-0738}, mesh = {*Adverse Outcome Pathways ; Animals ; Ecotoxicology/history/*methods ; History, 21st Century ; Humans ; Mice, Inbred C57BL ; Quality Control ; Risk Assessment/methods ; Systems Biology ; Toxicokinetics ; Vinyl Compounds/adverse effects ; }, abstract = {Adverse outcome pathways (AOPs) are a recent toxicological construct that connects, in a formalized, transparent and quality-controlled way, mechanistic information to apical endpoints for regulatory purposes. AOP links a molecular initiating event (MIE) to the adverse outcome (AO) via key events (KE), in a way specified by key event relationships (KER). Although this approach to formalize mechanistic toxicological information only started in 2010, over 200 AOPs have already been established. At this stage, new requirements arise, such as the need for harmonization and re-assessment, for continuous updating, as well as for alerting about pitfalls, misuses and limits of applicability. In this review, the history of the AOP concept and its most prominent strengths are discussed, including the advantages of a formalized approach, the systematic collection of weight of evidence, the linkage of mechanisms to apical end points, the examination of the plausibility of epidemiological data, the identification of critical knowledge gaps and the design of mechanistic test methods. To prepare the ground for a broadened and appropriate use of AOPs, some widespread misconceptions are explained. Moreover, potential weaknesses and shortcomings of the current AOP rule set are addressed (1) to facilitate the discussion on its further evolution and (2) to better define appropriate vs. less suitable application areas. Exemplary toxicological studies are presented to discuss the linearity assumptions of AOP, the management of event modifiers and compensatory mechanisms, and whether a separation of toxicodynamics from toxicokinetics including metabolism is possible in the framework of pathway plasticity. Suggestions on how to compromise between different needs of AOP stakeholders have been added. A clear definition of open questions and limitations is provided to encourage further progress in the field.}, } @article {pmid29050881, year = {2017}, author = {Kvas, S and Rahn, J and Engel, K and Neufeld, JD and Villeneuve, PJ and Trevors, JT and Lee, H and Scroggins, RP and Beaudette, LA}, title = {Development of a microbial test suite and data integration method for assessing microbial health of contaminated soil.}, journal = {Journal of microbiological methods}, volume = {143}, number = {}, pages = {66-77}, doi = {10.1016/j.mimet.2017.10.004}, pmid = {29050881}, issn = {1872-8359}, mesh = {Biota/*drug effects ; Canada ; *Data Interpretation, Statistical ; *Environmental Pollution ; Forests ; Metagenomics/methods ; Microbiological Techniques/*methods ; Petroleum/analysis ; *Soil Microbiology ; Soil Pollutants/analysis ; }, abstract = {There is no standard methodology or guideline for assessing soil microbial health for the purposes of contaminant risk assessments. Here we propose a laboratory-based test suite and novel data integration method for evaluating soil microbial health using site-specific contaminated and reference soil. The test suite encompasses experiments for evaluating microbial biomass, activity, and diversity. The results from the tests are then integrated so that a Soil Microbial Health Score (SMHS) may be assigned. This test suite and data integration method was tested on soils from 3 different contaminated sites in Canada. The soil microbial health of a petroleum hydrocarbon (PHC) contaminated site was found to be 'Mildly Impacted' and 'Moderately Impacted' for two soil horizons at a boreal forest site. The soil microbial health of the mixed metal/PHC and mixed metal sites were both found to be 'Not Impacted'. Continued use of this test suite and data integration method will help create guidelines for assessing soil microbial health in ecological risk assessments.}, } @article {pmid29049301, year = {2017}, author = {Heckenhauer, J and Abu Salim, K and Chase, MW and Dexter, KG and Pennington, RT and Tan, S and Kaye, ME and Samuel, R}, title = {Plant DNA barcodes and assessment of phylogenetic community structure of a tropical mixed dipterocarp forest in Brunei Darussalam (Borneo).}, journal = {PloS one}, volume = {12}, number = {10}, pages = {e0185861}, pmid = {29049301}, issn = {1932-6203}, support = {P 26548/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Borneo ; DNA Barcoding, Taxonomic/*methods ; DNA, Plant/*genetics ; Databases, Genetic ; *Forests ; Likelihood Functions ; *Phylogeny ; Plants/classification/*genetics ; }, abstract = {DNA barcoding is a fast and reliable tool to assess and monitor biodiversity and, via community phylogenetics, to investigate ecological and evolutionary processes that may be responsible for the community structure of forests. In this study, DNA barcodes for the two widely used plastid coding regions rbcL and matK are used to contribute to identification of morphologically undetermined individuals, as well as to investigate phylogenetic structure of tree communities in 70 subplots (10 × 10m) of a 25-ha forest-dynamics plot in Brunei (Borneo, Southeast Asia). The combined matrix (rbcL + matK) comprised 555 haplotypes (from ≥154 genera, 68 families and 25 orders sensu APG, Angiosperm Phylogeny Group, 2016), making a substantial contribution to tree barcode sequences from Southeast Asia. Barcode sequences were used to reconstruct phylogenetic relationships using maximum likelihood, both with and without constraining the topology of taxonomic orders to match that proposed by the Angiosperm Phylogeny Group. A third phylogenetic tree was reconstructed using the program Phylomatic to investigate the influence of phylogenetic resolution on results. Detection of non-random patterns of community assembly was determined by net relatedness index (NRI) and nearest taxon index (NTI). In most cases, community assembly was either random or phylogenetically clustered, which likely indicates the importance to community structure of habitat filtering based on phylogenetically correlated traits in determining community structure. Different phylogenetic trees gave similar overall results, but the Phylomatic tree produced greater variation across plots for NRI and NTI values, presumably due to noise introduced by using an unresolved phylogenetic tree. Our results suggest that using a DNA barcode tree has benefits over the traditionally used Phylomatic approach by increasing precision and accuracy and allowing the incorporation of taxonomically unidentified individuals into analyses.}, } @article {pmid29049284, year = {2017}, author = {Handel, A}, title = {Learning infectious disease epidemiology in a modern framework.}, journal = {PLoS computational biology}, volume = {13}, number = {10}, pages = {e1005642}, pmid = {29049284}, issn = {1553-7358}, support = {U19 AI117891/AI/NIAID NIH HHS/United States ; U19 AI117891//NIH/International ; }, mesh = {Communicable Diseases/*epidemiology ; *Computational Biology ; Computer Graphics ; Humans ; *Models, Theoretical ; Software ; User-Computer Interface ; }, } @article {pmid29048395, year = {2017}, author = {Scott-Fordsmand, JJ and Peijnenburg, WJGM and Semenzin, E and Nowack, B and Hunt, N and Hristozov, D and Marcomini, A and Irfan, MA and Jiménez, AS and Landsiedel, R and Tran, L and Oomen, AG and Bos, PMJ and Hund-Rinke, K}, title = {Environmental Risk Assessment Strategy for Nanomaterials.}, journal = {International journal of environmental research and public health}, volume = {14}, number = {10}, pages = {}, pmid = {29048395}, issn = {1660-4601}, mesh = {Environmental Exposure/*analysis ; Environmental Pollutants/*adverse effects ; Humans ; Nanostructures/*adverse effects ; Risk Assessment/*methods ; }, abstract = {An Environmental Risk Assessment (ERA) for nanomaterials (NMs) is outlined in this paper. Contrary to other recent papers on the subject, the main data requirements, models and advancement within each of the four risk assessment domains are described, i.e., in the: (i) materials, (ii) release, fate and exposure, (iii) hazard and (iv) risk characterisation domains. The material, which is obviously the foundation for any risk assessment, should be described according to the legislatively required characterisation data. Characterisation data will also be used at various levels within the ERA, e.g., exposure modelling. The release, fate and exposure data and models cover the input for environmental distribution models in order to identify the potential (PES) and relevant exposure scenarios (RES) and, subsequently, the possible release routes, both with regard to which compartment(s) NMs are distributed in line with the factors determining the fate within environmental compartment. The initial outcome in the risk characterisation will be a generic Predicted Environmental Concentration (PEC), but a refined PEC can be obtained by applying specific exposure models for relevant media. The hazard information covers a variety of representative, relevant and reliable organisms and/or functions, relevant for the RES and enabling a hazard characterisation. The initial outcome will be hazard characterisation in test systems allowing estimating a Predicted No-Effect concentration (PNEC), either based on uncertainty factors or on a NM adapted version of the Species Sensitivity Distributions approach. The risk characterisation will either be based on a deterministic risk ratio approach (i.e., PEC/PNEC) or an overlay of probability distributions, i.e., exposure and hazard distributions, using the nano relevant models.}, } @article {pmid29046278, year = {2017}, author = {Morgan, C and Webb, RT and Carr, MJ and Kontopantelis, E and Green, J and Chew-Graham, CA and Kapur, N and Ashcroft, DM}, title = {Incidence, clinical management, and mortality risk following self harm among children and adolescents: cohort study in primary care.}, journal = {BMJ (Clinical research ed.)}, volume = {359}, number = {}, pages = {j4351}, pmid = {29046278}, issn = {1756-1833}, support = {MR/K006665/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Adolescent ; Child ; Databases, Factual ; Female ; Humans ; Incidence ; Male ; Mental Health Services/statistics & numerical data ; *Patient Care Management/methods/organization & administration/statistics & numerical data ; *Primary Health Care/methods/statistics & numerical data ; Proportional Hazards Models ; Psychotropic Drugs/*therapeutic use ; Risk Assessment ; Risk Factors ; *Self-Injurious Behavior/diagnosis/mortality/psychology/therapy ; Sex Factors ; Suicide/statistics & numerical data ; United Kingdom/epidemiology ; *Suicide Prevention ; }, abstract = {Objectives To examine temporal trends in sex and age specific incidence of self harm in children and adolescents, clinical management patterns, and risk of cause specific mortality following an index self harm episode at a young age.Design Population based cohort study.Setting UK Clinical Practice Research Datalink-electronic health records from 647 general practices, with practice level deprivation measured ecologically using the index of multiple deprivation. Patients from eligible English practices were linked to hospital episode statistics (HES) and Office for National Statistics (ONS) mortality records.Participants For the descriptive analytical phases we examined data pertaining to 16 912 patients aged 10-19 who harmed themselves during 2001-14. For analysis of cause specific mortality following self harm, 8638 patients eligible for HES and ONS linkage were matched by age, sex, and general practice with up to 20 unaffected children and adolescents (n=170 274).Main outcome measures In the first phase, temporal trends in sex and age specific annual incidence were examined. In the second phase, clinical management was assessed according to the likelihood of referral to mental health services and psychotropic drug prescribing. In the third phase, relative risks of all cause mortality, unnatural death (including suicide and accidental death), and fatal acute alcohol or drug poisoning were estimated as hazard ratios derived from stratified Cox proportional hazards models for the self harm cohort versus the matched unaffected comparison cohort.Results The annual incidence of self harm was observed to increase in girls (37.4 per 10 000) compared with boys (12.3 per 10 000), and a sharp 68% increase occurred among girls aged 13-16, from 45.9 per 10 000 in 2011 to 77.0 per 10 000 in 2014. Referrals within 12 months of the index self harm episode were 23% less likely for young patients registered at the most socially deprived practices, even though incidences were considerably higher in these localities. Children and adolescents who harmed themselves were approximately nine times more likely to die unnaturally during follow-up, with especially noticeable increases in risks of suicide (deprivation adjusted hazard ratio 17.5, 95% confidence interval 7.6 to 40.5) and fatal acute alcohol or drug poisoning (34.3, 10.2 to 115.7).Conclusions Gaining a better understanding of the mechanisms responsible for the recent apparent increase in the incidence of self harm among early-mid teenage girls, and coordinated initiatives to tackle health inequalities in the provision of services to distressed children and adolescents, represent urgent priorities for multiple public agencies.}, } @article {pmid29043354, year = {2017}, author = {Cázarez-García, D and Ramírez Loustalot-Laclette, M and Ann Markow, T and Winkler, R}, title = {Lipidomic profiles of Drosophila melanogaster and cactophilic fly species: models of human metabolic diseases.}, journal = {Integrative biology : quantitative biosciences from nano to macro}, volume = {9}, number = {11}, pages = {885-891}, doi = {10.1039/c7ib00155j}, pmid = {29043354}, issn = {1757-9708}, mesh = {Animals ; Data Mining ; Disease Models, Animal ; Drosophila ; Drosophila melanogaster/*metabolism ; Ecology ; Female ; Genetic Predisposition to Disease ; Lipids/*analysis ; Male ; Metabolic Diseases/*metabolism ; Metabolic Syndrome/metabolism ; Species Specificity ; }, abstract = {The metabolic syndrome (MetS) is associated with serious diseases and represents an important threat for global public health. The common fruit fly (Drosophila melanogaster) has served as a model organism to study physiological processes of the MetS, because central metabolic pathways are conserved among species, and because the flies are easy to cultivate in a laboratory. In nature, D. melanogaster is a fruit generalist, feeding on diets rich in simple carbohydrates. Other Drosophilids, however, have specialized on distinct resources. Drosophila mojavensis, for example, is endemic to the Sonoran Desert, where it feeds on necrotic cacti which are low in carbohydrates. Its close relative Drosophila arizonae is cactophilic as well, but is also found breeding in fruits containing simple sugars. Previous studies have shown that high-sugar diets negatively affect the larval development of D. mojavensis and increase their triglyceride content, compared to D. melanogaster. More general metabolic profiles, in response to these different diets, however, have yet to be produced for any of the species. In addition, because D. arizonae appears somewhat intermediate between D. melanogaster and D. mojavensis in its development times and survival under the above mentioned diets, its general metabolic profiles are also of interest. Thus, in the present study we ask to what extent the general metabolism of these three different Drosophila species is affected by diets of distinct protein-sugar ratios. To obtain an un-biased view on possibly novel phenomena, we combined untargeted metabolomics with Random Forest data mining.}, } @article {pmid29042301, year = {2017}, author = {Simeonov, PL}, title = {Towards a first implementation of the WLIMES approach in living system studies advancing the diagnostics and therapy in augmented personalized medicine.}, journal = {Bio Systems}, volume = {162}, number = {}, pages = {177-204}, doi = {10.1016/j.biosystems.2017.10.001}, pmid = {29042301}, issn = {1872-8324}, mesh = {*Algorithms ; Computational Biology/*methods ; Computer Simulation ; Humans ; *Models, Biological ; Precision Medicine/*methods ; }, abstract = {The goal of this paper is to advance an extensible theory of living systems using an approach to biomathematics and biocomputation that suitably addresses self-organized, self-referential and anticipatory systems with multi-temporal multi-agents. Our first step is to provide foundations for modelling of emergent and evolving dynamic multi-level organic complexes and their sustentative processes in artificial and natural life systems. Main applications are in life sciences, medicine, ecology and astrobiology, as well as robotics, industrial automation, man-machine interface and creative design. Since 2011 over 100 scientists from a number of disciplines have been exploring a substantial set of theoretical frameworks for a comprehensive theory of life known as Integral Biomathics. That effort identified the need for a robust core model of organisms as dynamic wholes, using advanced and adequately computable mathematics. The work described here for that core combines the advantages of a situation and context aware multivalent computational logic for active self-organizing networks, Wandering Logic Intelligence (WLI), and a multi-scale dynamic category theory, Memory Evolutive Systems (MES), hence WLIMES. This is presented to the modeller via a formal augmented reality language as a first step towards practical modelling and simulation of multi-level living systems. Initial work focuses on the design and implementation of this visual language and calculus (VLC) and its graphical user interface. The results will be integrated within the current methodology and practices of theoretical biology and (personalized) medicine to deepen and to enhance the holistic understanding of life.}, } @article {pmid29042107, year = {2018}, author = {Arcangeli, A and Campana, I and Angeletti, D and Atzori, F and Azzolin, M and Carosso, L and Di Miccoli, V and Giacoletti, A and Gregorietti, M and Luperini, C and Paraboschi, M and Pellegrino, G and Ramazio, M and Sarà, G and Crosti, R}, title = {Amount, composition, and spatial distribution of floating macro litter along fixed trans-border transects in the Mediterranean basin.}, journal = {Marine pollution bulletin}, volume = {129}, number = {2}, pages = {545-554}, doi = {10.1016/j.marpolbul.2017.10.028}, pmid = {29042107}, issn = {1879-3363}, mesh = {Environmental Monitoring/*methods ; Geographic Information Systems ; Mediterranean Region ; Mediterranean Sea ; Plastics/*analysis ; Seasons ; Spatial Analysis ; Waste Products/*analysis ; Water Pollutants, Chemical/*analysis ; }, abstract = {Marine litter is a major source of pollution in the Mediterranean basin, but despite legislative requirements, scant information is available for the ongoing assessment of this threat. Using higher size classes as proxy for litter distribution, this study gave a synoptic estimation of the amount, composition, and distribution of floating macro-litter in the Mediterranean. The average amount of macro-litter was in a range of 2-5items/km[2], with the highest in the Adriatic basin. Seasonal patterns were present in almost all study areas and were significant in the Ligurian Sea, Sardinian-Balearic basin, and Central Tyrrhenian Sea. Plastic accounted for >80% of litter in all areas and seasons, with the highest proportion in the Adriatic Sea, Ligurian Sea, and Sicilian-Sardinian Channels; in the Bonifacio Strait, Tyrrhenian Sea, and Sardinian-Balearic basin, litter composition was instead more diverse. Spatial analysis suggested an almost homogeneous distribution of litter without evident regular aggregation zones.}, } @article {pmid29040362, year = {2019}, author = {Ma, S and Song, Q and Tao, H and Harrison, A and Wang, S and Liu, W and Lin, S and Zhang, Z and Ai, Y and He, H}, title = {Prediction of protein-protein interactions between fungus (Magnaporthe grisea) and rice (Oryza sativa L.).}, journal = {Briefings in bioinformatics}, volume = {20}, number = {2}, pages = {448-456}, doi = {10.1093/bib/bbx132}, pmid = {29040362}, issn = {1477-4054}, mesh = {Computational Biology/*methods ; Fungal Proteins/genetics/*metabolism ; *Gene Regulatory Networks ; Magnaporthe/*metabolism/pathogenicity ; Oryza/*metabolism/microbiology ; Plant Proteins/genetics/*metabolism ; *Protein Interaction Maps ; }, abstract = {Rice blast disease caused by the fungus Magnaporthe grisea (M. grisea) is one of the most serious diseases for the cultivated rice Oryza sativa (O. sativa). A key factor causing rice blast disease and defense might be protein-protein interactions (PPIs) between rice and fungus. In this research, we have developed a computational pipeline to predict PPIs between blast fungus and rice. After cross-prediction by interolog-based and domain-based method, we achieved 532 potential PPIs between 27 fungus proteins and 236 rice proteins. Accuracy of jackknife test, 10-fold cross-validation test and independent test for these PPIs were 90.43, 93.85 and 84.67%, respectively, by using support vector machine classification method. Meanwhile, the pathogenic genes of blast fungus were enriched in the predicted PPIs network when compared with 1000 random interaction networks. The rice regulatory network was downloaded and divided into 228 subnetworks with over six nodes, and the top seven subnetworks affected by blast fungus through PPIs were investigated. The results indicated that 34 upregulated and 12 downregulated master regulators in rice interacting with the fungus proteins in response to the infection of blast fungus. The common master regulators in rice in response to the infection of M. grisea, Xanthomonas oryzae pv.oryzae and rice stripe virus were analyzed. The ubiquitin proteasome pathway was the common pathway in rice regulated by these three pathogens, while apoptosis signaling pathway was induced by fungus and bacteria. In summary, the results in this article provide insight into the process of blast fungus infection.}, } @article {pmid29040319, year = {2017}, author = {Deuel, NR and Conner, LM and Miller, KV and Chamberlain, MJ and Cherry, MJ and Tannenbaum, LV}, title = {Habitat selection and diurnal refugia of gray foxes in southwestern Georgia, USA.}, journal = {PloS one}, volume = {12}, number = {10}, pages = {e0186402}, pmid = {29040319}, issn = {1932-6203}, mesh = {Agriculture ; Animals ; Circadian Rhythm/*physiology ; Ecosystem ; Female ; Forests ; Foxes/*physiology/psychology ; Geographic Information Systems ; Georgia ; Human Activities ; Humans ; Male ; Predatory Behavior/*physiology ; *Refugium ; Transportation ; }, abstract = {Understanding habitat selection of gray foxes (Urocyon cinereoargenteus) is essential to evaluate their potential response to changes in land use and predator communities. Few studies have evaluated temporal habitat selection or explicitly identified habitats used by gray foxes for diurnal refugia. We used GPS collars to obtain location data for 34 gray foxes (20 males and 14 females) from February 2014 to December 2015 to evaluate temporal (seasonal and diel) habitat selection and selection of diurnal refugia in southwestern Georgia, USA. We analyzed habitat selection at 2 levels, selection of a core area within the home range and selection of locations within the home range. Habitat selection was non-random (P < 0.001) but consistent among seasons, between day and night, and between sexes (P > 0.05). Hardwoods, human use (i.e., areas associated with regular human activity such as buildings, lawns, parking areas, etc.), and roads were selected (P < 0.05), whereas pine dominated stands were used randomly (P > 0.05). Selection of habitats for diurnal refugia did not vary seasonally or by sex (P > 0.05), with foxes selecting (P < 0.05) areas near hardwood forests, roads, agriculture, human use, pastures/food plots, and shrub scrub habitats. Gray foxes were observed on the ground while resting, and we found no evidence of gray foxes diurnally resting in trees. Our results suggest that on our study area, gray foxes are an edge species that prefer forests with a hardwood component in areas near human use and roads.}, } @article {pmid29039783, year = {2017}, author = {Sun, H and Xia, B and Wang, X and Gao, F and Zhou, Y}, title = {Quantitative Phosphoproteomic Analysis Provides Insight into the Response to Short-Term Drought Stress in Ammopiptanthus mongolicus Roots.}, journal = {International journal of molecular sciences}, volume = {18}, number = {10}, pages = {}, pmid = {29039783}, issn = {1422-0067}, mesh = {Amino Acid Motifs ; Amino Acid Sequence ; Computational Biology/methods ; *Droughts ; Fabaceae/*metabolism ; Phosphoproteins/chemistry/*metabolism ; Plant Proteins/chemistry/*metabolism ; Plant Roots/*metabolism ; Protein Interaction Mapping ; Protein Interaction Maps ; *Proteome ; *Proteomics/methods ; *Stress, Physiological ; Tandem Mass Spectrometry ; }, abstract = {Drought is one of the major abiotic stresses that negatively affects plant growth and development. Ammopiptanthus mongolicus is an ecologically important shrub in the mid-Asia desert region and used as a model for abiotic tolerance research in trees. Protein phosphorylation participates in the regulation of various biological processes, however, phosphorylation events associated with drought stress signaling and response in plants is still limited. Here, we conducted a quantitative phosphoproteomic analysis of the response of A. mongolicus roots to short-term drought stress. Data are available via the iProx database with project ID IPX0000971000. In total, 7841 phosphorylation sites were found from the 2019 identified phosphopeptides, corresponding to 1060 phosphoproteins. Drought stress results in significant changes in the abundance of 103 phosphopeptides, corresponding to 90 differentially-phosphorylated phosphoproteins (DPPs). Motif-x analysis identified two motifs, including [pSP] and [RXXpS], from these DPPs. Functional enrichment and protein-protein interaction analysis showed that the DPPs were mainly involved in signal transduction and transcriptional regulation, osmotic adjustment, stress response and defense, RNA splicing and transport, protein synthesis, folding and degradation, and epigenetic regulation. These drought-corresponsive phosphoproteins, and the related signaling and metabolic pathways probably play important roles in drought stress signaling and response in A. mongolicus roots. Our results provide new information for understanding the molecular mechanism of the abiotic stress response in plants at the posttranslational level.}, } @article {pmid29039289, year = {2018}, author = {Bunting, B and Corry, C and O'Neill, S and Moore, A}, title = {Death by suicide at the Ward level in Northern Ireland.}, journal = {Psychological medicine}, volume = {48}, number = {8}, pages = {1375-1380}, doi = {10.1017/S0033291717003026}, pmid = {29039289}, issn = {1469-8978}, mesh = {Adolescent ; Adult ; Bayes Theorem ; *Cause of Death ; Databases, Factual ; Female ; Geography ; Humans ; Male ; Middle Aged ; Northern Ireland/epidemiology ; Poisson Distribution ; Risk Factors ; Suicide/*statistics & numerical data ; Young Adult ; }, abstract = {BACKGROUND: Deaths from suicide, as recorded within the Northern Ireland Coroner's Office for the years 2005-2011 inclusive, were analysed in terms of standardised mortality ratios (SMRs), within Wards and Local Government Districts (LGDs). The aim of the study is to examine factors relating to the ecological context of the area within which the person resided at time of death. Area deprivation, religious composition and age structure are examined in terms of SMRs, while controlling for the number of individuals living within a designated area.

METHODS: Random-intercept Poisson regression models were used in conjunction with empirical Bayes prediction to examine area effects.

RESULTS: Considerable variation occurs between the numbers of recorded deaths within each area. A strong association is shown between deprivation and the number of deaths by suicide within an area. There was considerable variation at the LGD level in terms of the number of deaths, but once the nested nature of Wards was taken into account and adjusted for level of deprivation, the variation between LGD was no longer statistically significant. When adjusted for the number of individuals within each age group, the number of deaths in the younger and middle-aged groups did not show a statistical difference (0.05 level), nor did the religious composition of the area in terms of the number of recorded deaths.

CONCLUSIONS: Based on SMRs, using empirical Bayes prediction, area effects were shown to be substantial, especially in urban locations where there are high rates of deprivation.}, } @article {pmid29039012, year = {2018}, author = {Yang, K and Wen, X and Sablok, G}, title = {Method for the Large-Scale Identification of phasiRNAs in Brachypodium distachyon.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1667}, number = {}, pages = {187-194}, doi = {10.1007/978-1-4939-7278-4_14}, pmid = {29039012}, issn = {1940-6029}, mesh = {Brachypodium/*genetics ; Databases, Nucleic Acid ; *Gene Expression Regulation, Plant ; Genetic Loci ; Genomics/methods ; MicroRNAs/*genetics ; RNA, Plant/*genetics ; RNA, Small Interfering/*genetics ; }, abstract = {Postranscriptional regulation has been widely shown to be regulated by several classes of small non-coding RNAs; most abundantly, microRNAs, which have been shown to be the first dominant class and has been widely characterized as post-transcriptional regulators. In addition to microRNAs, triggered by miRNAs, transcripts called as PHAS (or TAS) generate abundant class of small RNAs in 21-nt manner, which is a pattern formed by DICER-LIKE 4 (DCL4) processing. Although PHAS can be identified by aligning transcripts to reported PHAS in other species, the most sensitive and accurate way to discovery them is by mapping of the smallRNAs taking into account the transcript coordinates. Here, we describe a workflow that can be used for the identification PHAS and corresponding phasiRNAs in Brachypodium distachyon using publically availabe smallRNAs datasets.}, } @article {pmid29038553, year = {2017}, author = {Staples, P and Torous, J and Barnett, I and Carlson, K and Sandoval, L and Keshavan, M and Onnela, JP}, title = {A comparison of passive and active estimates of sleep in a cohort with schizophrenia.}, journal = {NPJ schizophrenia}, volume = {3}, number = {1}, pages = {37}, pmid = {29038553}, issn = {2334-265X}, support = {DP2 MH103909/MH/NIMH NIH HHS/United States ; T15 LM007092/LM/NLM NIH HHS/United States ; }, abstract = {UNLABELLED: Sleep abnormalities are considered an important feature of schizophrenia, yet convenient and reliable sleep monitoring remains a challenge. Smartphones offer a novel solution to capture both self-reported and objective measures of sleep in schizophrenia. In this three-month observational study, 17 subjects with a diagnosis of schizophrenia currently in treatment downloaded Beiwe, a platform for digital phenotyping, on their personal Apple or Android smartphones. Subjects were given tri-weekly ecological momentary assessments (EMAs) on their own smartphones, and passive data including accelerometer, GPS, screen use, and anonymized call and text message logs was continuously collected. We compare the in-clinic assessment of sleep quality, assessed with the Pittsburgh Sleep Questionnaire Inventory (PSQI), to EMAs, as well as sleep estimates based on passively collected accelerometer data. EMAs and passive data classified 85% (11/13) of subjects as exhibiting high or low sleep quality compared to the in-clinic assessments among subjects who completed at least one in-person PSQI. Phone-based accelerometer data used to infer sleep duration was moderately correlated with subject self-assessment of sleep duration (r = 0.69, 95% CI 0.23-0.90). Active and passive phone data predicts concurrent PSQI scores for all subjects with mean average error of 0.75 and future PSQI scores with a mean average error of 1.9, with scores ranging from 0-14. These results suggest sleep monitoring via personal smartphones is feasible for subjects with schizophrenia in a scalable and affordable manner.

PATIENT MONITORING: SMARTPHONES CAN TRACK SCHIZOPHRENIA-RELATED SLEEP ABNORMALITIES: Smartphones may one-day offer accessible, clinically-useful insights into schizophrenia patients' sleep quality. Despite the clinical relevance of sleep to disease severity, monitoring technologies still evade convenience and reliability. In search of a preferential method, a group of Harvard University researchers led by Patrick Staples investigated the validity of data collected via patients' own mobile phones. The team, with a cohort of 17 schizophrenia patients, compared the quality of data produced by smartphone sensors and smartphone-delivered questionnaires to that of an in-clinic evaluation. The results significantly showed that smartphone monitoring could generate information that approached the accuracy of in-clinic assessments. The team noted some areas for improvement; however, this study provides convincing justifications for further research into this non-invasive, low-cost, scalable method to monitor the sleep quality of schizophrenic patients.}, } @article {pmid29038424, year = {2017}, author = {Corander, J and Fraser, C and Gutmann, MU and Arnold, B and Hanage, WP and Bentley, SD and Lipsitch, M and Croucher, NJ}, title = {Frequency-dependent selection in vaccine-associated pneumococcal population dynamics.}, journal = {Nature ecology & evolution}, volume = {1}, number = {12}, pages = {1950-1960}, pmid = {29038424}, issn = {2397-334X}, support = {/WT_/Wellcome Trust/United Kingdom ; R01 AI048935/AI/NIAID NIH HHS/United States ; R01 AI106786/AI/NIAID NIH HHS/United States ; }, mesh = {Bacterial Proteins/*genetics/metabolism ; Pneumococcal Vaccines/immunology ; Population Dynamics ; *Selection, Genetic ; Streptococcus pneumoniae/*genetics/immunology ; }, abstract = {Many bacterial species are composed of multiple lineages distinguished by extensive variation in gene content. These often cocirculate in the same habitat, but the evolutionary and ecological processes that shape these complex populations are poorly understood. Addressing these questions is particularly important for Streptococcus pneumoniae, a nasopharyngeal commensal and respiratory pathogen, because the changes in population structure associated with the recent introduction of partial-coverage vaccines have substantially reduced pneumococcal disease. Here we show that pneumococcal lineages from multiple populations each have a distinct combination of intermediate-frequency genes. Functional analysis suggested that these loci may be subject to negative frequency-dependent selection (NFDS) through interactions with other bacteria, hosts or mobile elements. Correspondingly, these genes had similar frequencies in four populations with dissimilar lineage compositions. These frequencies were maintained following substantial alterations in lineage prevalences once vaccination programmes began. Fitting a multilocus NFDS model of post-vaccine population dynamics to three genomic datasets using Approximate Bayesian Computation generated reproducible estimates of the influence of NFDS on pneumococcal evolution, the strength of which varied between loci. Simulations replicated the stable frequency of lineages unperturbed by vaccination, patterns of serotype switching and clonal replacement. This framework highlights how bacterial ecology affects the impact of clinical interventions.}, } @article {pmid29036401, year = {2017}, author = {Santos-Garcia, D and Silva, FJ and Morin, S and Dettner, K and Kuechler, SM}, title = {The All-Rounder Sodalis: A New Bacteriome-Associated Endosymbiont of the Lygaeoid Bug Henestaris halophilus (Heteroptera: Henestarinae) and a Critical Examination of Its Evolution.}, journal = {Genome biology and evolution}, volume = {9}, number = {10}, pages = {2893-2910}, pmid = {29036401}, issn = {1759-6653}, mesh = {Animals ; DNA, Bacterial ; Databases, Factual ; Enterobacteriaceae/*classification/genetics/*physiology/ultrastructure ; *Evolution, Molecular ; Genome Size ; Genome, Bacterial ; Heteroptera/*microbiology ; Metabolic Networks and Pathways ; *Phylogeny ; Pseudogenes ; Sequence Analysis, DNA ; *Symbiosis ; }, abstract = {Hemipteran insects are well-known in their ability to establish symbiotic relationships with bacteria. Among them, heteropteran insects present an array of symbiotic systems, ranging from the most common gut crypt symbiosis to the more restricted bacteriome-associated endosymbiosis, which have only been detected in members of the superfamily Lygaeoidea and the family Cimicidae so far. Genomic data of heteropteran endosymbionts are scarce and have merely been analyzed from the Wolbachia endosymbiont in bed bug and a few gut crypt-associated symbionts in pentatomoid bugs. In this study, we present the first detailed genomic analysis of a bacteriome-associated endosymbiont of a phytophagous heteropteran, present in the seed bug Henestaris halophilus (Hemiptera: Heteroptera: Lygaeoidea). Using phylogenomics and genomics approaches, we have assigned the newly characterized endosymbiont to the Sodalis genus, named as Candidatus Sodalis baculum sp. nov. strain kilmister. In addition, our findings support the reunification of the Sodalis genus, currently divided into six different genera. We have also conducted comparative analyses between 15 Sodalis species that present different genome sizes and symbiotic relationships. These analyses suggest that Ca. Sodalis baculum is a mutualistic endosymbiont capable of supplying the amino acids tyrosine, lysine, and some cofactors to its host. It has a small genome with pseudogenes but no mobile elements, which indicates middle-stage reductive evolution. Most of the genes in Ca. Sodalis baculum are likely to be evolving under purifying selection with several signals pointing to the retention of the lysine/tyrosine biosynthetic pathways compared with other Sodalis.}, } @article {pmid29036168, year = {2017}, author = {Abadi, S and Yan, WX and Amar, D and Mayrose, I}, title = {A machine learning approach for predicting CRISPR-Cas9 cleavage efficiencies and patterns underlying its mechanism of action.}, journal = {PLoS computational biology}, volume = {13}, number = {10}, pages = {e1005807}, pmid = {29036168}, issn = {1553-7358}, support = {T32 GM007753/GM/NIGMS NIH HHS/United States ; }, mesh = {Algorithms ; CRISPR-Cas Systems/*genetics ; Computational Biology/*methods ; Gene Editing/*methods ; Humans ; *Machine Learning ; RNA, Guide, CRISPR-Cas Systems/genetics ; ROC Curve ; }, abstract = {The adaptation of the CRISPR-Cas9 system as a genome editing technique has generated much excitement in recent years owing to its ability to manipulate targeted genes and genomic regions that are complementary to a programmed single guide RNA (sgRNA). However, the efficacy of a specific sgRNA is not uniquely defined by exact sequence homology to the target site, thus unintended off-targets might additionally be cleaved. Current methods for sgRNA design are mainly concerned with predicting off-targets for a given sgRNA using basic sequence features and employ elementary rules for ranking possible sgRNAs. Here, we introduce CRISTA (CRISPR Target Assessment), a novel algorithm within the machine learning framework that determines the propensity of a genomic site to be cleaved by a given sgRNA. We show that the predictions made with CRISTA are more accurate than other available methodologies. We further demonstrate that the occurrence of bulges is not a rare phenomenon and should be accounted for in the prediction process. Beyond predicting cleavage efficiencies, the learning process provides inferences regarding patterns that underlie the mechanism of action of the CRISPR-Cas9 system. We discover that attributes that describe the spatial structure and rigidity of the entire genomic site as well as those surrounding the PAM region are a major component of the prediction capabilities.}, } @article {pmid29034954, year = {2018}, author = {Verhoeven, KJF and Verbon, EH and van Gurp, TP and Oplaat, C and Ferreira de Carvalho, J and Morse, AM and Stahl, M and Macel, M and McIntyre, LM}, title = {Intergenerational environmental effects: functional signals in offspring transcriptomes and metabolomes after parental jasmonic acid treatment in apomictic dandelion.}, journal = {The New phytologist}, volume = {217}, number = {2}, pages = {871-882}, pmid = {29034954}, issn = {1469-8137}, support = {U24 DK097209/DK/NIDDK NIH HHS/United States ; }, mesh = {Apomixis/drug effects/*genetics ; Cluster Analysis ; Cyclopentanes/*pharmacology ; *Environment ; Gene Expression Regulation, Plant/drug effects ; Gene Ontology ; Metabolome/drug effects/*genetics ; Metabolomics ; Oxylipins/*pharmacology ; Phenols/metabolism ; Plant Leaves/drug effects/metabolism ; Taraxacum/drug effects/*genetics/*metabolism ; Transcriptome/drug effects/*genetics ; }, abstract = {Parental environments can influence offspring traits. However, the magnitude of the impact of parental environments on offspring molecular phenotypes is poorly understood. Here, we test the direct effects and intergenerational effects of jasmonic acid (JA) treatment, which is involved in herbivory-induced defense signaling, on transcriptomes and metabolomes in apomictic common dandelion (Taraxacum officinale). In a full factorial crossed design with parental and offspring JA and control treatments, we performed leaf RNA-seq gene expression analysis, LC-MS metabolomics and total phenolics assays in offspring plants. Expression analysis, leveraged by a de novo assembled transcriptome, revealed an induced response to JA exposure that is consistent with known JA effects. The intergenerational effect of treatment was considerable: 307 of 858 detected JA-responsive transcripts were affected by parental JA treatment. In terms of the numbers of metabolites affected, the magnitude of the chemical response to parental JA exposure was c. 10% of the direct JA treatment response. Transcriptome and metabolome analyses both identified the phosphatidylinositol signaling pathway as a target of intergenerational JA effects. Our results highlight that parental environments can have substantial effects in offspring generations. Transcriptome and metabolome assays provide a basis for zooming in on the potential mechanisms of inherited JA effects.}, } @article {pmid29032927, year = {2017}, author = {Costi, LR and Iwamoto, HM and Neves, DCO and Caldas, CAM}, title = {Mortality from systemic erythematosus lupus in Brazil: evaluation of causes according to the government health database.}, journal = {Revista brasileira de reumatologia}, volume = {57}, number = {6}, pages = {574-582}, doi = {10.1016/j.rbre.2017.09.001}, pmid = {29032927}, issn = {2255-5021}, mesh = {Adolescent ; Adult ; Aged ; Aged, 80 and over ; Brazil/epidemiology ; *Cause of Death ; Databases, Factual ; Female ; Humans ; Lupus Erythematosus, Systemic/*mortality ; Male ; Middle Aged ; National Health Programs/statistics & numerical data ; Risk Factors ; Young Adult ; }, abstract = {OBJECTIVE: To characterize the causes of mortality in patients with systemic lupus erythematosus (SLE) in Brazil between 2002 and 2011.

METHODS: An exploratory ecological study of a time series using data from the Mortality Information System of DATASUS, the Department of the Unified Health System (Brazil's National Health System).

RESULTS: Brazil's SLE mortality rate was 4.76 deaths/10[5] inhabitants. The mortality rate was higher in the Midwest, North and Southeast regions than in the country as a whole. There were 6.3% fewer and 4.2% more deaths than expected in the Northeast and Southeast regions, respectively. The mean age at death was 40.7±18 years, and 45.61% of deaths occurred between the ages of 20 and 39. Incidence was highest in women (90.7%) and whites (49.2%). Disorders of the musculoskeletal system and connective tissue were mentioned as an underlying cause of death in 77.5% of cases, and diseases of the circulatory system and infectious and parasitic diseases were also noted in fewer cases. SLE was mentioned as an underlying cause of death in 77% of cases, with no difference between the Brazilian regions (p=0.2058). The main SLE-related causes of death were, sequentially, diseases of the respiratory and circulatory systems and infectious and parasitic diseases.

CONCLUSIONS: This study identified a need for greater control of risk factors for cardiovascular diseases and a better understanding of the pathogenesis of atherosclerosis in SLE. Infectious causes are still frequent, and management should be improved, especially in the early stages of the disease.}, } @article {pmid29030749, year = {2017}, author = {Tang, N and Chow, SM and Ibrahim, JG and Zhu, H}, title = {Bayesian Sensitivity Analysis of a Nonlinear Dynamic Factor Analysis Model with Nonparametric Prior and Possible Nonignorable Missingness.}, journal = {Psychometrika}, volume = {82}, number = {4}, pages = {875-903}, pmid = {29030749}, issn = {1860-0980}, support = {R01 GM105004/GM/NIGMS NIH HHS/United States ; R01 MH086633/MH/NIMH NIH HHS/United States ; R01GM105004//National Institute of General Medical Sciences (US)/ ; SES-1357666//National Science Foundation (US)/ ; }, mesh = {Algorithms ; *Bayes Theorem ; Computer Simulation ; Data Interpretation, Statistical ; Ecological Momentary Assessment ; Emotions ; *Factor Analysis, Statistical ; Female ; Humans ; Male ; *Nonlinear Dynamics ; *Statistics, Nonparametric ; Young Adult ; }, abstract = {Many psychological concepts are unobserved and usually represented as latent factors apprehended through multiple observed indicators. When multiple-subject multivariate time series data are available, dynamic factor analysis models with random effects offer one way of modeling patterns of within- and between-person variations by combining factor analysis and time series analysis at the factor level. Using the Dirichlet process (DP) as a nonparametric prior for individual-specific time series parameters further allows the distributional forms of these parameters to deviate from commonly imposed (e.g., normal or other symmetric) functional forms, arising as a result of these parameters' restricted ranges. Given the complexity of such models, a thorough sensitivity analysis is critical but computationally prohibitive. We propose a Bayesian local influence method that allows for simultaneous sensitivity analysis of multiple modeling components within a single fitting of the model of choice. Five illustrations and an empirical example are provided to demonstrate the utility of the proposed approach in facilitating the detection of outlying cases and common sources of misspecification in dynamic factor analysis models, as well as identification of modeling components that are sensitive to changes in the DP prior specification.}, } @article {pmid29030651, year = {2017}, author = {Golka, K and Ickstadt, K and Selinski, S and Hengstler, JG and Wilhelm, M}, title = {Third symposium on Environmental Toxicology in North Rhine-Westphalia, Germany: Interdisciplinary Research Activities in Toxicology, Statistics, Hygiene and Medicine : Meeting report on a symposium held in Dortmund May 7-8, 2015.}, journal = {Archives of toxicology}, volume = {91}, number = {11}, pages = {3711-3715}, doi = {10.1007/s00204-017-2093-8}, pmid = {29030651}, issn = {1432-0738}, mesh = {Data Interpretation, Statistical ; *Ecotoxicology ; Environmental Exposure/*adverse effects ; Environmental Pollutants/toxicity ; Germany ; Humans ; *Interdisciplinary Research ; Public Health ; }, } @article {pmid29027998, year = {2018}, author = {Arkhipova, K and Skvortsov, T and Quinn, JP and McGrath, JW and Allen, CC and Dutilh, BE and McElarney, Y and Kulakov, LA}, title = {Temporal dynamics of uncultured viruses: a new dimension in viral diversity.}, journal = {The ISME journal}, volume = {12}, number = {1}, pages = {199-211}, pmid = {29027998}, issn = {1751-7370}, mesh = {Bacteria/isolation & purification ; Bacteriophages/genetics/isolation & purification ; Biodiversity ; Ecosystem ; *Genome, Viral ; Lakes/microbiology/virology ; Metagenomics ; Viruses/*genetics/isolation & purification ; }, abstract = {Recent work has vastly expanded the known viral genomic sequence space, but the seasonal dynamics of viral populations at the genome level remain unexplored. Here we followed the viral community in a freshwater lake for 1 year using genome-resolved viral metagenomics, combined with detailed analyses of the viral community structure, associated bacterial populations and environmental variables. We reconstructed 8950 complete and partial viral genomes, the majority of which were not persistent in the lake throughout the year, but instead continuously succeeded each other. Temporal analysis of 732 viral genus-level clusters demonstrated that one-fifth were undetectable at specific periods of the year. Based on host predictions for a subset of reconstructed viral genomes, we for the first time reveal three distinct patterns of host-pathogen dynamics, where the viruses may peak before, during or after the peak in their host's abundance, providing new possibilities for modelling of their interactions. Time series metagenomics opens up a new dimension in viral profiling, which is essential to understand the full scale of viral diversity and evolution, and the ecological roles of these important factors in the global ecosystem.}, } @article {pmid29027593, year = {2018}, author = {Niu, X and Wendt, A and Li, Z and Agarwal, A and Xue, L and Gonzales, M and Brantley, SL}, title = {Detecting the effects of coal mining, acid rain, and natural gas extraction in Appalachian basin streams in Pennsylvania (USA) through analysis of barium and sulfate concentrations.}, journal = {Environmental geochemistry and health}, volume = {40}, number = {2}, pages = {865-885}, pmid = {29027593}, issn = {1573-2983}, support = {OCE-11-40159//National Science Foundation/ ; DMS-1505256//National Science Foundation/ ; }, mesh = {*Acid Rain ; Appalachian Region ; Barium/*analysis ; *Coal Mining ; Datasets as Topic ; Geology ; Human Activities ; Humans ; *Hydraulic Fracking ; *Natural Gas ; Pennsylvania ; *Rivers ; Sulfates/*analysis ; Time Factors ; Water Pollutants, Chemical/*analysis ; }, abstract = {To understand how extraction of different energy sources impacts water resources requires assessment of how water chemistry has changed in comparison with the background values of pristine streams. With such understanding, we can develop better water quality standards and ecological interpretations. However, determination of pristine background chemistry is difficult in areas with heavy human impact. To learn to do this, we compiled a master dataset of sulfate and barium concentrations ([SO4], [Ba]) in Pennsylvania (PA, USA) streams from publically available sources. These elements were chosen because they can represent contamination related to oil/gas and coal, respectively. We applied changepoint analysis (i.e., likelihood ratio test) to identify pristine streams, which we defined as streams with a low variability in concentrations as measured over years. From these pristine streams, we estimated the baseline concentrations for major bedrock types in PA. Overall, we found that 48,471 data values are available for [SO4] from 1904 to 2014 and 3243 data for [Ba] from 1963 to 2014. Statewide [SO4] baseline was estimated to be 15.8 ± 9.6 mg/L, but values range from 12.4 to 26.7 mg/L for different bedrock types. The statewide [Ba] baseline is 27.7 ± 10.6 µg/L and values range from 25.8 to 38.7 µg/L. Results show that most increases in [SO4] from the baseline occurred in areas with intensive coal mining activities, confirming previous studies. Sulfate inputs from acid rain were also documented. Slight increases in [Ba] since 2007 and higher [Ba] in areas with higher densities of gas wells when compared to other areas could document impacts from shale gas development, the prevalence of basin brines, or decreases in acid rain and its coupled effects on [Ba] related to barite solubility. The largest impacts on PA stream [Ba] and [SO4] are related to releases from coal mining or burning rather than oil and gas development.}, } @article {pmid29024978, year = {2018}, author = {Vandormael, A and Dobra, A and Bärnighausen, T and de Oliveira, T and Tanser, F}, title = {Incidence rate estimation, periodic testing and the limitations of the mid-point imputation approach.}, journal = {International journal of epidemiology}, volume = {47}, number = {1}, pages = {236-245}, pmid = {29024978}, issn = {1464-3685}, support = {/WT_/Wellcome Trust/United Kingdom ; R01 AI124389/AI/NIAID NIH HHS/United States ; R01 HD084233/HD/NICHD NIH HHS/United States ; D43 TW009775/TW/FIC NIH HHS/United States ; }, mesh = {Algorithms ; Bias ; *Cohort Studies ; *Epidemiologic Methods ; HIV Infections/epidemiology ; Humans ; Incidence ; *Models, Statistical ; }, abstract = {BACKGROUND: It is common to use the mid-point between the latest-negative and earliest-positive test dates as the date of the infection event. However, the accuracy of the mid-point method has yet to be systematically quantified for incidence studies once participants start to miss their scheduled test dates.

METHODS: We used a simulation-based approach to generate an infectious disease epidemic for an incidence cohort with a high (80-100%), moderate (60-79.9%), low (40-59.9%) and poor (30-39.9%) testing rate. Next, we imputed a mid-point and random-point value between the participant's latest-negative and earliest-positive test dates. We then compared the incidence rate derived from these imputed values with the true incidence rate generated from the simulation model.

RESULTS: The mid-point incidence rate estimates erroneously declined towards the end of the observation period once the testing rate dropped below 80%. This decline was in error of approximately 9%, 27% and 41% for a moderate, low and poor testing rate, respectively. The random-point method did not introduce any systematic bias in the incidence rate estimate, even for testing rates as low as 30%.

CONCLUSIONS: The mid-point assumption of the infection date is unjustified and should not be used to calculate the incidence rate once participants start to miss the scheduled test dates. Under these conditions, we show an artefactual decline in the incidence rate towards the end of the observation period. Alternatively, the single random-point method is straightforward to implement and produces estimates very close to the true incidence rate.}, } @article {pmid29023519, year = {2017}, author = {Pfaff, CT and Eichenberg, D and Liebergesell, M and König-Ries, B and Wirth, C}, title = {Essential Annotation Schema for Ecology (EASE)-A framework supporting the efficient data annotation and faceted navigation in ecology.}, journal = {PloS one}, volume = {12}, number = {10}, pages = {e0186170}, pmid = {29023519}, issn = {1932-6203}, mesh = {Data Curation/*methods ; *Ecology ; Internet ; Vocabulary, Controlled ; }, abstract = {Ecology has become a data intensive science over the last decades which often relies on the reuse of data in cross-experimental analyses. However, finding data which qualifies for the reuse in a specific context can be challenging. It requires good quality metadata and annotations as well as efficient search strategies. To date, full text search (often on the metadata only) is the most widely used search strategy although it is known to be inaccurate. Faceted navigation is providing a filter mechanism which is based on fine granular metadata, categorizing search objects along numeric and categorical parameters relevant for their discovery. Selecting from these parameters during a full text search creates a system of filters which allows to refine and improve the results towards more relevance. We developed a framework for the efficient annotation and faceted navigation in ecology. It consists of an XML schema for storing the annotation of search objects and is accompanied by a vocabulary focused on ecology to support the annotation process. The framework consolidates ideas which originate from widely accepted metadata standards, textbooks, scientific literature, and vocabularies as well as from expert knowledge contributed by researchers from ecology and adjacent disciplines.}, } @article {pmid29023475, year = {2017}, author = {Wang, D and Li, L and Wu, G and Vasseur, L and Yang, G and Huang, P}, title = {De novo transcriptome sequencing of Isaria cateniannulata and comparative analysis of gene expression in response to heat and cold stresses.}, journal = {PloS one}, volume = {12}, number = {10}, pages = {e0186040}, pmid = {29023475}, issn = {1932-6203}, mesh = {Cold-Shock Response/*genetics ; Gene Expression Profiling ; *Gene Expression Regulation, Fungal ; Gene Ontology ; Heat-Shock Response/*genetics ; Hypocreales/genetics/*physiology ; Reverse Transcriptase Polymerase Chain Reaction ; }, abstract = {Isaria cateniannulata is a very important and virulent entomopathogenic fungus that infects many insect pest species. Although I. cateniannulata is commonly exposed to extreme environmental temperature conditions, little is known about its molecular response mechanism to temperature stress. Here, we sequenced and de novo assembled the transcriptome of I. cateniannulata in response to high and low temperature stresses using Illumina RNA-Seq technology. Our assembly encompassed 17,514 unigenes (mean length = 1,197 bp), in which 11,445 unigenes (65.34%) showed significant similarities to known sequences in NCBI non-redundant protein sequences (Nr) database. Using digital gene expression analysis, 4,483 differentially expressed genes (DEGs) were identified after heat treatment, including 2,905 up-regulated genes and 1,578 down-regulated genes. Under cold stress, 1,927 DEGs were identified, including 1,245 up-regulated genes and 682 down-regulated genes. The expression patterns of 18 randomly selected candidate DEGs resulting from quantitative real-time PCR (qRT-PCR) were consistent with their transcriptome analysis results. Although DEGs were involved in many pathways, we focused on the genes that were involved in endocytosis: In heat stress, the pathway of clathrin-dependent endocytosis (CDE) was active; however at low temperature stresses, the pathway of clathrin-independent endocytosis (CIE) was active. Besides, four categories of DEGs acting as temperature sensors were observed, including cell-wall-major-components-metabolism-related (CWMCMR) genes, heat shock protein (Hsp) genes, intracellular-compatible-solutes-metabolism-related (ICSMR) genes and glutathione S-transferase (GST). These results enhance our understanding of the molecular mechanisms of I. cateniannulata in response to temperature stresses and provide a valuable resource for the future investigations.}, } @article {pmid29020945, year = {2017}, author = {Liang, J and Chen, X and Deng, G and Pan, Z and Zhang, H and Li, Q and Yang, K and Long, H and Yu, M}, title = {Dehydration induced transcriptomic responses in two Tibetan hulless barley (Hordeum vulgare var. nudum) accessions distinguished by drought tolerance.}, journal = {BMC genomics}, volume = {18}, number = {1}, pages = {775}, pmid = {29020945}, issn = {1471-2164}, mesh = {Down-Regulation ; *Droughts ; Endoplasmic Reticulum/metabolism ; *Gene Expression Profiling ; Gene Ontology ; Genotype ; Hordeum/cytology/*genetics/physiology ; Phenotype ; Plant Proteins/genetics/metabolism ; Stress, Physiological/genetics ; Water/*metabolism ; }, abstract = {BACKGROUND: The harsh environment on the Qinghai-Tibetan Plateau gives Tibetan hulless barley (Hordeum vulgare var. nudum) great ability to resist adversities such as drought, salinity, and low temperature, and makes it a good subject for the analysis of drought tolerance mechanism. To elucidate the specific gene networks and pathways that contribute to its drought tolerance, and for identifying new candidate genes for breeding purposes, we performed a transcriptomic analysis using two accessions of Tibetan hulless barley, namely Z772 (drought-tolerant) and Z013 (drought-sensitive).

RESULTS: There were more up-regulated genes of Z772 than Z013 under both mild (5439-VS-2604) and severe (7203-VS-3359) dehydration treatments. Under mild dehydration stress, the pathways exclusively enriched in drought-tolerance genotype Z772 included Protein processing in endoplasmic reticulum, tricarboxylic acid (TCA) cycle, Wax biosynthesis, and Spliceosome. Under severe dehydration stress, the pathways that were mainly enriched in Z772 included Carbon fixation in photosynthetic organisms, Pyruvate metabolism, Porphyrin and chlorophyll metabolism. The main differentially expressed genes (DEGs) in response to dehydration stress and genes whose expression was different between tolerant and sensitive genotypes were presented in this study, respectively. The candidate genes for drought tolerance were selected based on their expression patterns.

CONCLUSIONS: The RNA-Seq data obtained in this study provided an initial overview on global gene expression patterns and networks that related to dehydration shock in Tibetan hulless barley. Furthermore, these data provided pathways and a targeted set of candidate genes that might be essential for deep analyzing the molecular mechanisms of plant tolerance to drought stress.}, } @article {pmid29020939, year = {2017}, author = {Silva-Marrero, JI and Sáez, A and Caballero-Solares, A and Viegas, I and Almajano, MP and Fernández, F and Baanante, IV and Metón, I}, title = {A transcriptomic approach to study the effect of long-term starvation and diet composition on the expression of mitochondrial oxidative phosphorylation genes in gilthead sea bream (Sparus aurata).}, journal = {BMC genomics}, volume = {18}, number = {1}, pages = {768}, pmid = {29020939}, issn = {1471-2164}, mesh = {Animals ; *Diet ; *Gene Expression Profiling ; Gene Ontology ; Genes, Mitochondrial/*genetics ; Molecular Sequence Annotation ; *Oxidative Phosphorylation ; Sea Bream/*genetics ; Starvation/*genetics ; Time Factors ; }, abstract = {BACKGROUND: The impact of nutritional status and diet composition on mitochondrial oxidative phosphorylation (OXPHOS) in fish remains largely unknown. To identify biomarkers of interest in nutritional studies, herein we obtained a deep-coverage transcriptome by 454 pyrosequencing of liver and skeletal muscle cDNA normalised libraries from long-term starved gilthead sea bream (Sparus aurata) and fish fed different diets.

RESULTS: After clean-up of high-throughput deep sequencing reads, 699,991 and 555,031 high-quality reads allowed de novo assembly of liver and skeletal muscle sequences, respectively (average length: 374 and 441 bp; total megabases: 262 and 245 Mbp). An additional incremental assembly was completed by integrating data from both tissues (hybrid assembly). Assembly of hybrid, liver and skeletal muscle transcriptomes yielded, respectively, 19,530, 11,545 and 10,599 isotigs (average length: 1330, 1208 and 1390 bp, respectively) that were grouped into 15,954, 10,033 and 9189 isogroups. Following annotation, hybrid transcriptomic data were used to construct an oligonucleotide microarray to analyse nutritional regulation of the expression of 129 genes involved in OXPHOS in S. aurata. Starvation upregulated cytochrome c oxidase components and other key OXPHOS genes in the liver, which exhibited higher sensitive to food deprivation than the skeletal muscle. However, diet composition affected OXPHOS in the skeletal muscle to a greater extent than in the liver: most of genes upregulated under starvation presented higher expression among fish fed a high carbohydrate/low protein diet.

CONCLUSIONS: Our findings indicate that the expression of coenzyme Q-binding protein (COQ10), cytochrome c oxidase subunit 6A2 (COX6A2) and ADP/ATP translocase 3 (SLC25A6) in the liver, and cytochrome c oxidase subunit 5B isoform 1 (COX5B1) in the liver and the skeletal muscle, are sensitive markers of the nutritional condition that may be relevant to assess the effect of changes in the feeding regime and diet composition on fish farming.}, } @article {pmid29020062, year = {2017}, author = {Silva, R and Afán, I and Gil, JA and Bustamante, J}, title = {Seasonal and circadian biases in bird tracking with solar GPS-tags.}, journal = {PloS one}, volume = {12}, number = {10}, pages = {e0185344}, pmid = {29020062}, issn = {1932-6203}, mesh = {Analysis of Variance ; Animals ; Bias ; Birds/*physiology ; Circadian Rhythm/*physiology ; *Geographic Information Systems ; Linear Models ; *Seasons ; *Sunlight ; }, abstract = {Global Positioning System (GPS) tags are nowadays widely used in wildlife tracking. This geolocation technique can suffer from fix loss biases due to poor satellite GPS geometry, that result in tracking data gaps leading to wrong research conclusions. In addition, new solar-powered GPS tags deployed on birds can suffer from a new "battery drain bias" currently ignored in movement ecology analyses. We use a GPS tracking dataset of bearded vultures (Gypaetus barbatus), tracked for several years with solar GPS tags, to evaluate the causes and triggers of fix and data retrieval loss biases. We compare two models of solar GPS tags using different data retrieval systems (Argos vs GSM-GPRS), and programmed with different duty cycles. Neither of the models was able to accomplish the duty cycle programed initially. Fix and data retrieval loss rates were always greater than expected, and showed non-random gaps in GPS locations. Number of fixes per month of tracking was a bad criterion to identify tags with smaller biases. Fix-loss rates were four times higher due to battery drain than due to poor GPS satellite geometry. Both tag models were biased due to the uneven solar energy available for the recharge of the tag throughout the annual cycle, resulting in greater fix-loss rates in winter compared to summer. In addition, we suggest that the bias found along the diurnal cycle is linked to a complex three-factor interaction of bird flight behavior, topography and fix interval. More fixes were lost when vultures were perching compared to flying, in rugged versus flat topography. But long fix-intervals caused greater loss of fixes in dynamic (flying) versus static situations (perching). To conclude, we emphasize the importance of evaluating fix-loss bias in current tracking projects, and deploying GPS tags that allow remote duty cycle updates so that the most appropriate fix and data retrieval intervals can be selected.}, } @article {pmid29019936, year = {2017}, author = {Geisler-Lee, J and Liu, X and Rang, W and Raveendiran, J and Szubryt, MB and Gibson, DJ and Geisler, M and Cheng, Q}, title = {Image-Based Analysis to Dissect Vertical Distribution and Horizontal Asymmetry of Conspecific Root System Interactions in Response to Planting Densities, Nutrients and Root Exudates in Arabidopsis thaliana.}, journal = {Plants (Basel, Switzerland)}, volume = {6}, number = {4}, pages = {}, pmid = {29019936}, issn = {2223-7747}, abstract = {Intraspecific competition is an important plant interaction that has been studied extensively aboveground, but less so belowground, due to the difficulties in accessing the root system experimentally. Recent in vivo and in situ automatic imaging advances help understand root system architecture. In this study, a portable imaging platform and a scalable transplant technique were applied to test intraspecific competition in Arabidopsis thaliana. A single green fluorescent protein labeled plant was placed in the center of a grid of different planting densities of neighboring unlabeled plants or empty spaces, into which different treatments were made to the media. The root system of the central plant showed changes in the vertical distribution with increasing neighbor density, becoming more positively kurtotic, and developing an increasing negative skew with time. Horizontal root distribution was initially asymmetric, but became more evenly circular with time, and mean direction was not affected by the presence of adjacent empty spaces as initially hypothesized. To date, this is the first study to analyze the patterns of both vertical and horizontal growth in conspecific root systems. We present a portable imaging platform with simplicity, accessibility, and scalability, to capture the dynamic interactions of plant root systems.}, } @article {pmid29017124, year = {2018}, author = {Fukushima, T and Komatsu, E and Arai, H and Kamiya, K and Onda, Y}, title = {Shifts of radiocesium vertical profiles in sediments and their modelling in Japanese lakes.}, journal = {The Science of the total environment}, volume = {615}, number = {}, pages = {741-750}, doi = {10.1016/j.scitotenv.2017.09.286}, pmid = {29017124}, issn = {1879-1026}, abstract = {Vertical profiles of radiocesium concentrations were measured in sediment cores collected at various times after the 2011 Fukushima nuclear accident in five Japanese lakes (Hinuma, Kasumigaura, Kitaura, Onogawa and Sohara) with different morphological and trophic characteristics in order to investigate the sedimentation-diffusion processes. In lakes where sediments had high porosities and experienced considerable wave action due to shallowness, we observed rapid penetration of radiocesium to a certain depth just after the accident, followed by downward movement of the peak depths. In contrast, gradual downward transfers of distinct peaks were found in other types of lakes. A one-dimensional differential sediment model with water-sediments interaction processes was constructed to describe the vertical shift of radiocesium profiles. Our proposed submodels relating to the length scales of the mixing using wind-induced stress and porosity of sediments were constructed based on one measurement of the vertical distribution of radiocesium in three lakes (Hinuma, Kasumigaura and Sohara). This model was then validated using samples from those lakes in different years, as well as from two other lakes. Good agreement was obtained. We discuss our findings, the limits of model application, and future research targets.}, } @article {pmid29016661, year = {2017}, author = {Yan, YW and Zou, B and Zhu, T and Hozzein, WN and Quan, ZX}, title = {Modified RNA-seq method for microbial community and diversity analysis using rRNA in different types of environmental samples.}, journal = {PloS one}, volume = {12}, number = {10}, pages = {e0186161}, pmid = {29016661}, issn = {1932-6203}, mesh = {Archaea/classification/*genetics ; Bacteria/classification/*genetics ; Datasets as Topic ; Drinking Water/microbiology ; Fungi/classification/*genetics ; Gene Library ; High-Throughput Nucleotide Sequencing ; *Metagenome ; Microbial Consortia/genetics ; *Phylogeny ; Plant Leaves/microbiology ; RNA, Ribosomal, 16S/*genetics ; Reverse Transcription ; Sequence Analysis, DNA/*methods ; Wetlands ; }, abstract = {RNA-seq-based SSU (small subunit) rRNA (ribosomal RNA) analysis has provided a better understanding of potentially active microbial community within environments. However, for RNA-seq library construction, high quantities of purified RNA are typically required. We propose a modified RNA-seq method for SSU rRNA-based microbial community analysis that depends on the direct ligation of a 5' adaptor to RNA before reverse-transcription. The method requires only a low-input quantity of RNA (10-100 ng) and does not require a DNA removal step. The method was initially tested on three mock communities synthesized with enriched SSU rRNA of archaeal, bacterial and fungal isolates at different ratios, and was subsequently used for environmental samples of high or low biomass. For high-biomass salt-marsh sediments, enriched SSU rRNA and total nucleic acid-derived RNA-seq datasets revealed highly consistent community compositions for all of the SSU rRNA sequences, and as much as 46.4%-59.5% of 16S rRNA sequences were suitable for OTU (operational taxonomic unit)-based community and diversity analyses with complete coverage of V1-V2 regions. OTU-based community structures for the two datasets were also highly consistent with those determined by all of the 16S rRNA reads. For low-biomass samples, total nucleic acid-derived RNA-seq datasets were analyzed, and highly active bacterial taxa were also identified by the OTU-based method, notably including members of the previously underestimated genus Nitrospira and phylum Acidobacteria in tap water, members of the phylum Actinobacteria on a shower curtain, and members of the phylum Cyanobacteria on leaf surfaces. More than half of the bacterial 16S rRNA sequences covered the complete region of primer 8F, and non-coverage rates as high as 38.7% were obtained for phylum-unclassified sequences, providing many opportunities to identify novel bacterial taxa. This modified RNA-seq method will provide a better snapshot of diverse microbial communities, most notably by OTU-based analysis, even communities with low-biomass samples.}, } @article {pmid28993676, year = {2017}, author = {Ji, S and Wang, Z and Wang, J and Fan, H and Wang, Y and Liu, Z}, title = {Properties analysis of transcription factor gene TasMYB36 from Trichoderma asperellum CBS433.97 and its heterogeneous transfomation to improve antifungal ability of Populus.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {12801}, pmid = {28993676}, issn = {2045-2322}, mesh = {Alternaria/physiology ; Amino Acid Sequence ; Antifungal Agents/*metabolism ; Base Sequence ; Computational Biology ; Fermentation ; Fungal Proteins/chemistry/*genetics ; Gene Expression Regulation, Fungal ; *Genes, Fungal ; Phylogeny ; Populus/*physiology ; Promoter Regions, Genetic ; Signal Transduction ; Stress, Physiological/genetics ; Transcription Factors/chemistry/*genetics ; Transcription, Genetic ; *Transformation, Genetic ; Trichoderma/*genetics ; }, abstract = {The transcription of TasMYB36 in the biocontrol species T. asperellum was upregulated in four different pathogenic fermentation broths, suggesting that TasMYB36 plays an important role in the response to biotic stresses. Seventy-nine MYB transcription factors that were homologous to TasMYB36 from six sequenced Trichoderma genomes were analyzed. They were distributed in fourteen clades in the phylogenetic tree. The 79 MYBs contained 113 DNA binding domains, and their amino acid sequences were conserved and were different to those in plants. The promoters of 79 MYBs contained 1374 cis-regulators related to the stress response, such as GCR1 (17.5%) and GCN4 (15.5%). Subsequently, TasMYB36 was integrated into the genome of Populus davidiana × P. alba var. pyramidalis (PdPap poplar), and after co-culture of the transformants (PdPap-TasMYB36s) with Alternaria alternate, the transcription of genes in the jasmonic acid (JA) and salicylic acid (SA) hormone signaling pathways were upregulated; the POD, SOD and CAT activities were enhanced; and the reactive oxygen content was reduced in PdPap-TasMYB36s. The disease spots area on PdPap-TasMYB36s leaves infected by A. alternate were average 0.63% (PdPap-Con: 24.7%). In summary, TasMYB36 of T. asperellum CBS433.97 is an important defense response gene that upregulates other stress response genes and could improve resistance to biotic stresses.}, } @article {pmid28989970, year = {2017}, author = {Silva, BSO and Coutinho, FH and Gregoracci, GB and Leomil, L and de Oliveira, LS and Fróes, A and Tschoeke, D and Soares, AC and Cabral, AS and Ward, ND and Richey, JE and Krusche, AV and Yager, PL and de Rezende, CE and Thompson, CC and Thompson, FL}, title = {Virioplankton Assemblage Structure in the Lower River and Ocean Continuum of the Amazon.}, journal = {mSphere}, volume = {2}, number = {5}, pages = {}, pmid = {28989970}, issn = {2379-5042}, abstract = {The Amazon River watershed and its associated plume comprise a vast continental and oceanic area. The microbial activities along this continuum contribute substantially to global carbon and nutrient cycling, and yet there is a dearth of information on the diversity, abundance, and possible roles of viruses in this globally important river. The aim of this study was to elucidate the diversity and structure of virus assemblages of the Amazon River-ocean continuum. Environmental viral DNA sequences were obtained for 12 locations along the river's lower reach (n = 5) and plume (n = 7). Sequence assembly yielded 29,358 scaffolds, encoding 82,546 viral proteins, with 15 new complete viral genomes. Despite the spatial connectivity mediated by the river, virome analyses and physical-chemical water parameters clearly distinguished river and plume ecosystems. Bacteriophages were ubiquitous in the continuum and were more abundant in the transition region. Eukaryotic viruses occurred mostly in the river, while the plume had more viruses of autotrophic organisms (Prochlorococcus, Synechococcus) and heterotrophic bacteria (Pelagibacter). The viral families Microviridae and Myoviridae were the most abundant and occurred throughout the continuum. The major functions of the genes in the continuum involved viral structures and life cycles, and viruses from plume locations and Tapajós River showed the highest levels of functional diversity. The distribution patterns of the viral assemblages were defined not only by the occurrence of possible hosts but also by water physical and chemical parameters, especially salinity. The findings presented here help to improve understanding of the possible roles of viruses in the organic matter cycle along the river-ocean continuum. IMPORTANCE The Amazon River forms a vast plume in the Atlantic Ocean that can extend for more than 1,000 km. Microbial communities promote a globally relevant carbon sink system in the plume. Despite the importance of viruses for the global carbon cycle, the diversity and the possible roles of viruses in the Amazon are poorly understood. The present work assesses, for the first time, the abundance and diversity of viruses simultaneously in the river and ocean in order to elucidate their possible roles. DNA sequence assembly yielded 29,358 scaffolds, encoding 82,546 viral proteins, with 15 new complete viral genomes from the 12 river and ocean locations. Viral diversity was clearly distinguished by river and ocean. Bacteriophages were the most abundant and occurred throughout the continuum. Viruses that infect eukaryotes were more abundant in the river, whereas phages appeared to have strong control over the host prokaryotic populations in the plume.}, } @article {pmid28988169, year = {2017}, author = {Du, Z and Xu, L and Zhang, W and Zhang, D and Yu, S and Hao, Y}, title = {Predicting the hand, foot, and mouth disease incidence using search engine query data and climate variables: an ecological study in Guangdong, China.}, journal = {BMJ open}, volume = {7}, number = {10}, pages = {e016263}, pmid = {28988169}, issn = {2044-6055}, mesh = {China/epidemiology ; Climate ; Data Collection/*methods ; Female ; Foot/virology ; Foot Diseases/epidemiology/etiology/virology ; Hand/virology ; Hand, Foot and Mouth Disease/epidemiology/*etiology ; Humans ; Incidence ; Informatics ; Male ; *Models, Biological ; Models, Theoretical ; Morbidity ; Mouth/virology ; Mouth Diseases/epidemiology/*etiology/virology ; Population Surveillance ; Risk Factors ; Search Engine ; *Seasons ; Skin Diseases/epidemiology/*etiology/virology ; *Temperature ; }, abstract = {OBJECTIVES: Hand, foot, and mouth disease (HFMD) has caused a substantial burden in China, especially in Guangdong Province. Based on the enhanced surveillance system, we aimed to explore whether the addition of temperate and search engine query data improves the risk prediction of HFMD.

DESIGN: Ecological study.

SETTING AND PARTICIPANTS: Information on the confirmed cases of HFMD, climate parameters and search engine query logs was collected. A total of 1.36 million HFMD cases were identified from the surveillance system during 2011-2014. Analyses were conducted at aggregate level and no confidential information was involved.

OUTCOME MEASURES: A seasonal autoregressive integrated moving average (ARIMA) model with external variables (ARIMAX) was used to predict the HFMD incidence from 2011 to 2014, taking into account temperature and search engine query data (Baidu Index, BDI). Statistics of goodness-of-fit and precision of prediction were used to compare models (1) based on surveillance data only, and with the addition of (2) temperature, (3) BDI, and (4) both temperature and BDI.

RESULTS: A high correlation between HFMD incidence and BDI (r=0.794, p<0.001) or temperature (r=0.657, p<0.001) was observed using both time series plot and correlation matrix. A linear effect of BDI (without lag) and non-linear effect of temperature (1 week lag) on HFMD incidence were found in a distributed lag non-linear model. Compared with the model based on surveillance data only, the ARIMAX model including BDI reached the best goodness-of-fit with an Akaike information criterion (AIC) value of -345.332, whereas the model including both BDI and temperature had the most accurate prediction in terms of the mean absolute percentage error (MAPE) of 101.745%.

CONCLUSIONS: An ARIMAX model incorporating search engine query data significantly improved the prediction of HFMD. Further studies are warranted to examine whether including search engine query data also improves the prediction of other infectious diseases in other settings.}, } @article {pmid28986822, year = {2018}, author = {Gonzalez, JP and Souris, M and Valdivia-Granda, W}, title = {Global Spread of Hemorrhagic Fever Viruses: Predicting Pandemics.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1604}, number = {}, pages = {3-31}, pmid = {28986822}, issn = {1940-6029}, mesh = {Communicable Diseases/epidemiology/genetics/transmission ; Geographic Information Systems ; Global Health ; Hemorrhagic Fevers, Viral/*epidemiology/genetics/*transmission ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; }, abstract = {As successive epidemics have swept the world, the scientific community has quickly learned from them about the emergence and transmission of communicable diseases. Epidemics usually occur when health systems are unprepared. During an unexpected epidemic, health authorities engage in damage control, fear drives action, and the desire to understand the threat is greatest. As humanity recovers, policy-makers seek scientific expertise to improve their "preparedness" to face future events.Global spread of disease is exemplified by the spread of yellow fever from Africa to the Americas, by the spread of dengue fever through transcontinental migration of mosquitos, by the relentless influenza virus pandemics, and, most recently, by the unexpected emergence of Ebola virus, spread by motorbike and long haul carriers. Other pathogens that are remarkable for their epidemic expansions include the arenavirus hemorrhagic fevers and hantavirus diseases carried by rodents over great geographic distances and the arthropod-borne viruses (West Nile, chikungunya and Zika) enabled by ecology and vector adaptations. Did we learn from the past epidemics? Are we prepared for the worst?The ultimate goal is to develop a resilient global health infrastructure. Besides acquiring treatments, vaccines, and other preventive medicine, bio-surveillance is critical to preventing disease emergence and to counteracting its spread. So far, only the western hemisphere has a large and established monitoring system; however, diseases continue to emerge sporadically, in particular in Southeast Asia and South America, illuminating the imperfections of our surveillance. Epidemics destabilize fragile governments, ravage the most vulnerable populations, and threaten the global community.Pandemic risk calculations employ new technologies like computerized maintenance of geographical and historical datasets, Geographic Information Systems (GIS), Next Generation sequencing, and Metagenomics to trace the molecular changes in pathogens during their emergence, and mathematical models to assess risk. Predictions help to pinpoint the hot spots of emergence, the populations at risk, and the pathogens under genetic evolution. Preparedness anticipates the risks, the needs of the population, the capacities of infrastructure, the sources of emergency funding, and finally, the international partnerships needed to manage a disaster before it occurs. At present, the world is in an intermediate phase of trying to reduce health disparities despite exponential population growth, political conflicts, migration, global trade, urbanization, and major environmental changes due to global warming. For the sake of humanity, we must focus on developing the necessary capacities for health surveillance, epidemic preparedness, and pandemic response.}, } @article {pmid28986516, year = {2018}, author = {Hofstede, SN and van Bodegom-Vos, L and Kringos, DS and Steyerberg, E and Marang-van de Mheen, PJ}, title = {Mortality, readmission and length of stay have different relationships using hospital-level versus patient-level data: an example of the ecological fallacy affecting hospital performance indicators.}, journal = {BMJ quality & safety}, volume = {27}, number = {6}, pages = {474-483}, doi = {10.1136/bmjqs-2017-006776}, pmid = {28986516}, issn = {2044-5423}, mesh = {Adult ; Aged ; Aged, 80 and over ; Databases, Factual ; Diagnosis-Related Groups ; Female ; *Hospital Mortality ; Humans ; *Length of Stay ; Logistic Models ; Male ; Middle Aged ; Netherlands/epidemiology ; *Patient Readmission ; *Quality Indicators, Health Care ; Registries ; }, abstract = {BACKGROUND: Ecological fallacy refers to an erroneous inference about individuals on the basis of findings for the group to which those individuals belong. Suppose analysis of a large database shows that hospitals with a high proportion of long length of stay (LOS) patients also have higher than average in-hospital mortality. This may prompt efforts to reduce mortality among patients with long LOS. But patients with long LOS may not be the ones at higher risk of death. It may be that hospitals with higher mortality (regardless of LOS) also have more long LOS patients-either because of quality problems on both counts or because of unaccounted differences in case mix. To provide more insight how the ecological fallacy influences the evaluation of hospital performance indicators, we assessed whether hospital-level associations between in-hospital mortality, readmission and long LOS reflect patient-level associations.

METHODS: Patient admissions from the Dutch National Medical Registration (2007-2012) for specific diseases (stroke, colorectal carcinoma, heart failure, acute myocardial infarction and hip/knee replacements in patients with osteoarthritis) were analysed, as well as all admissions. Logistic regression analysis was used to assess patient-level associations. Pearson correlation coefficients were used to quantify hospital-level associations.

RESULTS: Overall, we observed 2.2% in-hospital mortality, 8.1% readmissions and a mean LOS of 5.9 days among 8 478 884 admissions in 95 hospitals. Of the 10 disease-specific associations tested, 2 were reversed at hospital-level, 3 were consistent and 5 were only significant at either hospital-level or patient-level. A reversed association was found for stroke: patients with long LOS had 58% lower in-hospital mortality (OR 0.42 (95% CI 0.40 to 0.44)), whereas the hospital-level association was reversed (r=0.30, p<0.01). Similar negative patient-level associations were found for each hospital, but LOS varied across hospitals, thereby resulting in a positive hospital-level association. A similar effect was found for long LOS and readmission in patients with heart failure.

CONCLUSIONS: Hospital-level associations did not reflect the same patient-level associations in 7 of 10 associations, and were even reversed in 2 associations. Ecological fallacy thus potentially influences interpretation of hospital performance when patient-level associations are not taken into account.}, } @article {pmid28986112, year = {2018}, author = {Vonk, JA and Smulders, FOH and Christianen, MJA and Govers, LL}, title = {Seagrass leaf element content: A global overview.}, journal = {Marine pollution bulletin}, volume = {134}, number = {}, pages = {123-133}, doi = {10.1016/j.marpolbul.2017.09.066}, pmid = {28986112}, issn = {1879-3363}, mesh = {Alismatales/*chemistry ; Aquatic Organisms ; Databases, Factual ; Nitrogen/analysis ; Phosphorus/analysis ; Plant Leaves/*chemistry ; Species Specificity ; Trace Elements/*analysis ; Zosteraceae/*chemistry ; }, abstract = {Knowledge on the role of seagrass leaf elements and in particular micronutrients and their ranges is limited. We present a global database, consisting of 1126 unique leaf values for ten elements, obtained from literature and unpublished data, spanning 25 different seagrass species from 28 countries. The overall order of average element values in seagrass leaves was Na>K>Ca>Mg>S>Fe>Al>Si>Mn>Zn. Although we observed differences in leaf element content between seagrass families, high intraspecific variation indicated that leaf element content was more strongly determined by environmental factors than by evolutionary history. Early successional species had high leaf Al and Fe content. In addition, seagrass leaf element content also showed correlations with macronutrients (N and P), indicating that productivity also depends on other elements. Expected genomes of additional seagrass species in combination with experiments manipulating (micro)nutrients and environmental drivers might enable us to unravel the importance of various elements to sustain productive and flourishing meadows.}, } @article {pmid28984136, year = {2017}, author = {Deng, B and Ni, X and Zhai, Z and Tang, T and Tan, C and Yan, Y and Deng, J and Yin, Y}, title = {New Quantitative Structure-Activity Relationship Model for Angiotensin-Converting Enzyme Inhibitory Dipeptides Based on Integrated Descriptors.}, journal = {Journal of agricultural and food chemistry}, volume = {65}, number = {44}, pages = {9774-9781}, doi = {10.1021/acs.jafc.7b03367}, pmid = {28984136}, issn = {1520-5118}, mesh = {Angiotensin-Converting Enzyme Inhibitors/*chemistry ; Databases, Factual ; Dipeptides/*chemistry ; Hydrophobic and Hydrophilic Interactions ; Peptidyl-Dipeptidase A/*chemistry ; Quantitative Structure-Activity Relationship ; }, abstract = {Angiotensin-converting enzyme (ACE) inhibitory peptides derived from food proteins have been widely reported for hypertension treatment. In this paper, a benchmark data set containing 141 unique ACE inhibitory dipeptides was constructed through database mining, and a quantitative structure-activity relationships (QSAR) study was carried out to predict half-inhibitory concentration (IC50) of ACE activity. Sixteen descriptors were tested and the model generated by G-scale descriptor showed the best predictive performance with the coefficient of determination (R[2]) and cross-validated R[2] (Q[2]) of 0.6692 and 0.6220, respectively. For most other descriptors, R[2] were ranging from 0.52 to 0.68 and Q[2] were ranging from 0.48 to 0.61. A complex model combining all 16 descriptors was carried out and variable selection was performed in order to further improve the prediction performance. The quality of model using integrated descriptors (R[2] 0.7340 ± 0.0038, Q[2] 0.7151 ± 0.0019) was better than that of G-scale. An in-depth study of variable importance showed that the most correlated properties to ACE inhibitory activity were hydrophobicity, steric, and electronic properties and C-terminal amino acids contribute more than N-terminal amino acids. Five novel predicted ACE-inhibitory peptides were synthesized, and their IC50 values were validated through in vitro experiments. The results indicated that the constructed model could give a reliable prediction of ACE-inhibitory activity of peptides, and it may be useful in the design of novel ACE-inhibitory peptides.}, } @article {pmid28981192, year = {2018}, author = {Harden, JW and Hugelius, G and Ahlström, A and Blankinship, JC and Bond-Lamberty, B and Lawrence, CR and Loisel, J and Malhotra, A and Jackson, RB and Ogle, S and Phillips, C and Ryals, R and Todd-Brown, K and Vargas, R and Vergara, SE and Cotrufo, MF and Keiluweit, M and Heckman, KA and Crow, SE and Silver, WL and DeLonge, M and Nave, LE}, title = {Networking our science to characterize the state, vulnerabilities, and management opportunities of soil organic matter.}, journal = {Global change biology}, volume = {24}, number = {2}, pages = {e705-e718}, doi = {10.1111/gcb.13896}, pmid = {28981192}, issn = {1365-2486}, mesh = {Agriculture ; Carbon/*chemistry ; Carbon Cycle ; *Carbon Sequestration ; Climate ; Climate Change ; Databases, Factual ; *Ecosystem ; *International Cooperation ; Models, Theoretical ; Soil/*chemistry ; }, abstract = {Soil organic matter (SOM) supports the Earth's ability to sustain terrestrial ecosystems, provide food and fiber, and retains the largest pool of actively cycling carbon. Over 75% of the soil organic carbon (SOC) in the top meter of soil is directly affected by human land use. Large land areas have lost SOC as a result of land use practices, yet there are compensatory opportunities to enhance productivity and SOC storage in degraded lands through improved management practices. Large areas with and without intentional management are also being subjected to rapid changes in climate, making many SOC stocks vulnerable to losses by decomposition or disturbance. In order to quantify potential SOC losses or sequestration at field, regional, and global scales, measurements for detecting changes in SOC are needed. Such measurements and soil-management best practices should be based on well established and emerging scientific understanding of processes of C stabilization and destabilization over various timescales, soil types, and spatial scales. As newly engaged members of the International Soil Carbon Network, we have identified gaps in data, modeling, and communication that underscore the need for an open, shared network to frame and guide the study of SOM and SOC and their management for sustained production and climate regulation.}, } @article {pmid28980401, year = {2017}, author = {Stone, GN and White, SC and Csóka, G and Melika, G and Mutun, S and Pénzes, Z and Sadeghi, SE and Schönrogge, K and Tavakoli, M and Nicholls, JA}, title = {Tournament ABC analysis of the western Palaearctic population history of an oak gall wasp, Synergus umbraculus.}, journal = {Molecular ecology}, volume = {26}, number = {23}, pages = {6685-6703}, doi = {10.1111/mec.14372}, pmid = {28980401}, issn = {1365-294X}, mesh = {Animals ; Asia ; *Bayes Theorem ; Europe ; Genetic Markers ; Genetic Variation ; *Genetics, Population ; Middle East ; *Models, Genetic ; Mutation Rate ; Phylogeny ; Phylogeography ; Quercus ; Refugium ; Wasps/*genetics ; }, abstract = {Approximate Bayesian computation (ABC) is a powerful and widely used approach in inference of population history. However, the computational effort required to discriminate among alternative historical scenarios often limits the set that is compared to those considered more likely a priori. While often justifiable, this approach will fail to consider unexpected but well-supported population histories. We used a hierarchical tournament approach, in which subsets of scenarios are compared in a first round of ABC analyses and the winners are compared in a second analysis, to reconstruct the population history of an oak gall wasp, Synergus umbraculus (Hymenoptera, Cynipidae) across the Western Palaearctic. We used 4,233 bp of sequence data across seven loci to explore the relationships between four putative Pleistocene refuge populations in Iberia, Italy, the Balkans and Western Asia. We compared support for 148 alternative scenarios in eight pools, each pool comprising all possible rearrangements of four populations over a given topology of relationships, with or without founding of one population by admixture and with or without an unsampled "ghost" population. We found very little support for the directional "out of the east" scenario previously inferred for other gall wasp community members. Instead, the best-supported models identified Iberia as the first-regional population to diverge from the others in the late Pleistocene, followed by divergence between the Balkans and Western Asia, and founding of the Italian population through late Pleistocene admixture from Iberia and the Balkans. We compare these results with what is known for other members of the oak gall community, and consider the strengths and weaknesses of using a tournament approach to explore phylogeographic model space.}, } @article {pmid28977518, year = {2018}, author = {Lu, K and Li, T and He, J and Chang, W and Zhang, R and Liu, M and Yu, M and Fan, Y and Ma, J and Sun, W and Qu, C and Liu, L and Li, N and Liang, Y and Wang, R and Qian, W and Tang, Z and Xu, X and Lei, B and Zhang, K and Li, J}, title = {qPrimerDB: a thermodynamics-based gene-specific qPCR primer database for 147 organisms.}, journal = {Nucleic acids research}, volume = {46}, number = {D1}, pages = {D1229-D1236}, pmid = {28977518}, issn = {1362-4962}, mesh = {Animals ; DNA Primers/*genetics ; *Databases, Nucleic Acid ; Humans ; Internet ; Mice ; *Real-Time Polymerase Chain Reaction ; Reproducibility of Results ; Thermodynamics ; User-Computer Interface ; Workflow ; }, abstract = {Real-time quantitative polymerase chain reaction (qPCR) is one of the most important methods for analyzing the expression patterns of target genes. However, successful qPCR experiments rely heavily on the use of high-quality primers. Various qPCR primer databases have been developed to address this issue, but these databases target only a few important organisms. Here, we developed the qPrimerDB database, founded on an automatic gene-specific qPCR primer design and thermodynamics-based validation workflow. The qPrimerDB database is the most comprehensive qPCR primer database available to date, with a web front-end providing gene-specific and pre-computed primer pairs across 147 important organisms, including human, mouse, zebrafish, yeast, thale cress, rice and maize. In this database, we provide 3331426 of the best primer pairs for each gene, based on primer pair coverage, as well as 47760359 alternative gene-specific primer pairs, which can be conveniently batch downloaded. The specificity and efficiency was validated for qPCR primer pairs for 66 randomly selected genes, in six different organisms, through qPCR assays and gel electrophoresis. The qPrimerDB database represents a valuable, timesaving resource for gene expression analysis. This resource, which will be routinely updated, is publically accessible at http://biodb.swu.edu.cn/qprimerdb.}, } @article {pmid28976607, year = {2018}, author = {Doucette, WJ and Shunthirasingham, C and Dettenmaier, EM and Zaleski, RT and Fantke, P and Arnot, JA}, title = {A review of measured bioaccumulation data on terrestrial plants for organic chemicals: Metrics, variability, and the need for standardized measurement protocols.}, journal = {Environmental toxicology and chemistry}, volume = {37}, number = {1}, pages = {21-33}, doi = {10.1002/etc.3992}, pmid = {28976607}, issn = {1552-8618}, mesh = {Databases as Topic ; Humans ; Kinetics ; Organic Chemicals/*metabolism ; Plant Roots/chemistry ; Plant Transpiration ; Plants/*metabolism ; Reference Standards ; }, abstract = {Quantifying the transfer of organic chemicals from the environment into terrestrial plants is essential for assessing human and ecological risks, using plants as environmental contamination biomonitors, and predicting phytoremediation effectiveness. Experimental data describing chemical uptake by plants are often expressed as ratios of chemical concentrations in the plant compartments of interest (e.g., leaves, shoots, roots, xylem sap) to those in the exposure medium (e.g., soil, soil porewater, hydroponic solution, air). These ratios are generally referred to as "bioconcentration factors" but have also been named for the specific plant compartment sampled, such as "root concentration factors," "leaf concentration factors," or "transpiration stream (xylem sap) concentrations factors." We reviewed over 350 articles to develop a database with 7049 entries of measured bioaccumulation data for 310 organic chemicals and 112 terrestrial plant species. Various experimental approaches have been used; therefore, interstudy comparisons and data-quality evaluations are difficult. Key exposure and plant growth conditions were often missing, and units were often unclear or not reported. The lack of comparable high-confidence data also limits model evaluation and development. Standard test protocols or, at a minimum, standard reporting guidelines for the measurement of plant uptake data are recommended to generate comparable, high-quality data that will improve mechanistic understanding of organic chemical uptake by plants. Environ Toxicol Chem 2018;37:21-33. © 2017 SETAC.}, } @article {pmid28975220, year = {2017}, author = {Filippidis, FT and Laverty, AA and Hone, T and Been, JV and Millett, C}, title = {Association of Cigarette Price Differentials With Infant Mortality in 23 European Union Countries.}, journal = {JAMA pediatrics}, volume = {171}, number = {11}, pages = {1100-1106}, pmid = {28975220}, issn = {2168-6211}, support = {RP_2014-04-032/DH_/Department of Health/United Kingdom ; }, mesh = {*Commerce ; Europe/epidemiology ; European Union/*economics ; Humans ; Infant ; *Infant Mortality ; Linear Models ; Longitudinal Studies ; Taxes ; Tobacco Products/adverse effects/*economics ; }, abstract = {IMPORTANCE: Raising the price of cigarettes by increasing taxation has been associated with improved perinatal and child health outcomes. Transnational tobacco companies have sought to undermine tobacco tax policy by adopting pricing strategies that maintain the availability of budget cigarettes.

OBJECTIVE: To assess associations between median cigarette prices, cigarette price differentials, and infant mortality across the European Union.

A longitudinal, ecological study was conducted from January 1, 2004, to December 31, 2014, of infant populations in 23 countries (comprising 276 subnational regions) within the European Union.

INTERVENTIONS: Median cigarette prices and the differential between these and minimum cigarette prices were obtained from Euromonitor International. Pricing differentials were calculated as the proportions (%) obtained by dividing the difference between median and minimum cigarette price by median price. Prices were adjusted for inflation.

MAIN OUTCOMES AND MEASURES: Annual infant mortality rates. Associations were assessed using linear fixed-effect panel regression models adjusted for smoke-free policies, gross domestic product, unemployment rate, education, maternal age, and underlining temporal trends.

RESULTS: Among the 53 704 641 live births during the study period, an increase of €1 (US $1.18) per pack in the median cigarette price was associated with a decline of 0.23 deaths per 1000 live births in the same year (95% CI, -0.37 to -0.09) and a decline of 0.16 deaths per 1000 live births the following year (95% CI, -0.30 to -0.03). An increase of 10% in the price differential between median-priced and minimum-priced cigarettes was associated with an increase of 0.07 deaths per 1000 live births (95% CI, 0.01-0.13) the following year. Cigarette price increases across 23 European countries between 2004 and 2014 were associated with 9208 (95% CI, 8601-9814) fewer infant deaths; 3195 (95% CI, 3017-3372) infant deaths could have been avoided had there been no cost differential between the median-priced and minimum-priced cigarettes during this period.

CONCLUSIONS AND RELEVANCE: Higher cigarette prices were associated with reduced infant mortality, while increased cigarette price differentials were associated with higher infant mortality in the European Union. Combined with other evidence, this research suggests that legislators should implement tobacco tax and price control measures that eliminate budget cigarettes.}, } @article {pmid28974262, year = {2017}, author = {Ghenassia, A and Beuscart, JB and Ficheur, G and Occelli, F and Babykina, E and Chazard, E and Genin, M}, title = {A generic method for improving the spatial interoperability of medical and ecological databases.}, journal = {International journal of health geographics}, volume = {16}, number = {1}, pages = {36}, pmid = {28974262}, issn = {1476-072X}, mesh = {Birth Rate/*trends ; Databases, Factual/*standards/trends ; *Ecological and Environmental Phenomena ; France/epidemiology ; *Geographic Mapping ; Humans ; *Spatial Analysis ; }, abstract = {BACKGROUND: The availability of big data in healthcare and the intensive development of data reuse and georeferencing have opened up perspectives for health spatial analysis. However, fine-scale spatial studies of ecological and medical databases are limited by the change of support problem and thus a lack of spatial unit interoperability. The use of spatial disaggregation methods to solve this problem introduces errors into the spatial estimations. Here, we present a generic, two-step method for merging medical and ecological databases that avoids the use of spatial disaggregation methods, while maximizing the spatial resolution.

METHODS: Firstly, a mapping table is created after one or more transition matrices have been defined. The latter link the spatial units of the original databases to the spatial units of the final database. Secondly, the mapping table is validated by (1) comparing the covariates contained in the two original databases, and (2) checking the spatial validity with a spatial continuity criterion and a spatial resolution index.

RESULTS: We used our novel method to merge a medical database (the French national diagnosis-related group database, containing 5644 spatial units) with an ecological database (produced by the French National Institute of Statistics and Economic Studies, and containing with 36,594 spatial units). The mapping table yielded 5632 final spatial units. The mapping table's validity was evaluated by comparing the number of births in the medical database and the ecological databases in each final spatial unit. The median [interquartile range] relative difference was 2.3% [0; 5.7]. The spatial continuity criterion was low (2.4%), and the spatial resolution index was greater than for most French administrative areas.

CONCLUSIONS: Our innovative approach improves interoperability between medical and ecological databases and facilitates fine-scale spatial analyses. We have shown that disaggregation models and large aggregation techniques are not necessarily the best ways to tackle the change of support problem.}, } @article {pmid28973034, year = {2017}, author = {Tenan, S and Pedrini, P and Bragalanti, N and Groff, C and Sutherland, C}, title = {Data integration for inference about spatial processes: A model-based approach to test and account for data inconsistency.}, journal = {PloS one}, volume = {12}, number = {10}, pages = {e0185588}, pmid = {28973034}, issn = {1932-6203}, mesh = {Animals ; Conservation of Natural Resources ; *Data Interpretation, Statistical ; Italy ; *Models, Theoretical ; Population Density ; *Ursidae ; }, abstract = {Recently-developed methods that integrate multiple data sources arising from the same ecological processes have typically utilized structured data from well-defined sampling protocols (e.g., capture-recapture and telemetry). Despite this new methodological focus, the value of opportunistic data for improving inference about spatial ecological processes is unclear and, perhaps more importantly, no procedures are available to formally test whether parameter estimates are consistent across data sources and whether they are suitable for integration. Using data collected on the reintroduced brown bear population in the Italian Alps, a population of conservation importance, we combined data from three sources: traditional spatial capture-recapture data, telemetry data, and opportunistic data. We developed a fully integrated spatial capture-recapture (SCR) model that included a model-based test for data consistency to first compare model estimates using different combinations of data, and then, by acknowledging data-type differences, evaluate parameter consistency. We demonstrate that opportunistic data lend itself naturally to integration within the SCR framework and highlight the value of opportunistic data for improving inference about space use and population size. This is particularly relevant in studies of rare or elusive species, where the number of spatial encounters is usually small and where additional observations are of high value. In addition, our results highlight the importance of testing and accounting for inconsistencies in spatial information from structured and unstructured data so as to avoid the risk of spurious or averaged estimates of space use and consequently, of population size. Our work supports the use of a single modeling framework to combine spatially-referenced data while also accounting for parameter consistency.}, } @article {pmid28972978, year = {2017}, author = {Knapp, J and Damy, S and Brillaud, J and Tissot, JD and Navion, J and Mélior, R and Afonso, E and Hormaz, V and Gottstein, B and Umhang, G and Casulli, A and Dadeau, F and Millon, L and Raoul, F}, title = {EWET: Data collection and interface for the genetic analysis of Echinococcus multilocularis based on EmsB microsatellite.}, journal = {PloS one}, volume = {12}, number = {10}, pages = {e0183849}, pmid = {28972978}, issn = {1932-6203}, mesh = {Animals ; Base Sequence ; Calibration ; Databases, Genetic ; Echinococcus multilocularis/*genetics ; Genes, Helminth ; Genetic Markers ; Genetic Variation ; Microsatellite Repeats/*genetics ; }, abstract = {Evolution and dispersion history on Earth of organisms can best be studied through biological markers in molecular epidemiological studies. The biological diversity of the cestode Echinococcus multilocularis was investigated in different cladistic approaches. First the morphological aspects were explored in connection with its ecology. More recently, molecular aspects were investigated to better understand the nature of the variations observed among isolates. The study of the tandemly repeated multilocus microsatellite EmsB allowed us to attain a high genetic diversity level where other classic markers have failed. Since 2006, EmsB data have been collected on specimens from various endemic foci of the parasite in Europe (in historic and newly endemic areas), Asia (China, Japan and Kyrgyzstan), and North America (Canada and Alaska). Biological data on the isolates and metadata were also recorded (e.g. host, geographical location, EmsB analysis, citation in the literature). In order to make available the data set of 1,166 isolates from classic and aberrant domestic and wild animal hosts (larval lesions and adult worms) and from human origin, an open web access interface, developed in PHP, and connected to a PostgreSQL database, was developed in the EmsB Website for the Echinococcus Typing (EWET) project. It allows researchers to access data collection, perform genetic analyses online (e.g. defining the genetic distance between their own samples and the samples in the database), consult distribution maps of EmsB profiles, and record and share their new EmsB genotyping data. In order to standardize the EmsB analyses performed in the different laboratories throughout the world, a calibrator was developed. The final aim of this project was to gather and arrange available data to permit to better understand the dispersion and transmission patterns of the parasite among definitive and intermediate hosts, in order to organize control strategies on the ground.}, } @article {pmid28972575, year = {2017}, author = {Tedesco, PA and Beauchard, O and Bigorne, R and Blanchet, S and Buisson, L and Conti, L and Cornu, JF and Dias, MS and Grenouillet, G and Hugueny, B and Jézéquel, C and Leprieur, F and Brosse, S and Oberdorff, T}, title = {A global database on freshwater fish species occurrence in drainage basins.}, journal = {Scientific data}, volume = {4}, number = {}, pages = {170141}, pmid = {28972575}, issn = {2052-4463}, mesh = {Animals ; Biodiversity ; Databases, Factual ; Ecosystem ; *Fishes ; Fresh Water ; }, abstract = {A growing interest is devoted to global-scale approaches in ecology and evolution that examine patterns and determinants of species diversity and the threats resulting from global change. These analyses obviously require global datasets of species distribution. Freshwater systems house a disproportionately high fraction of the global fish diversity considering the small proportion of the earth's surface that they occupy, and are one of the most threatened habitats on Earth. Here we provide complete species lists for 3119 drainage basins covering more than 80% of the Earth surface using 14953 fish species inhabiting permanently or occasionally freshwater systems. The database results from an extensive survey of native and non-native freshwater fish species distribution based on 1436 published papers, books, grey literature and web-based sources. Alone or in combination with further datasets on species biological and ecological characteristics and their evolutionary history, this database represents a highly valuable source of information for further studies on freshwater macroecology, macroevolution, biogeography and conservation.}, } @article {pmid28971623, year = {2017}, author = {Goldbogen, JA and Cade, DE and Boersma, AT and Calambokidis, J and Kahane-Rapport, SR and Segre, PS and Stimpert, AK and Friedlaender, AS}, title = {Using Digital Tags With Integrated Video and Inertial Sensors to Study Moving Morphology and Associated Function in Large Aquatic Vertebrates.}, journal = {Anatomical record (Hoboken, N.J. : 2007)}, volume = {300}, number = {11}, pages = {1935-1941}, doi = {10.1002/ar.23650}, pmid = {28971623}, issn = {1932-8494}, mesh = {Animals ; Biomechanical Phenomena ; Environment ; Feeding Behavior/physiology ; Geographic Information Systems/*instrumentation ; Oceans and Seas ; Orientation ; Remote Sensing Technology/instrumentation/methods ; Respiration ; Swimming/*physiology ; Video Recording/*instrumentation/methods ; Whales/*anatomy & histology/physiology ; }, abstract = {The anatomy of large cetaceans has been well documented, mostly through dissection of dead specimens. However, the difficulty of studying the world's largest animals in their natural environment means the functions of anatomical structures must be inferred. Recently, non-invasive tracking devices have been developed that measure body position and orientation, thereby enabling the detailed reconstruction of underwater trajectories. The addition of cameras to the whale-borne tags allows the sensor data to be matched with real-time observations of how whales use their morphological structures, such as flukes, flippers, feeding apparatuses, and blowholes for the physiological functions of locomotion, feeding, and breathing. Here, we describe a new tag design with integrated video and inertial sensors and how it can be used to provide insights to the function of whale anatomy. This technology has the potential to facilitate a wide range of discoveries and comparative studies, but many challenges remain to increase the resolution and applicability of the data. Anat Rec, 300:1935-1941, 2017. © 2017 Wiley Periodicals, Inc.}, } @article {pmid28962629, year = {2017}, author = {Soltész, Z and Erdélyi, K and Bakonyi, T and Barna, M and Szentpáli-Gavallér, K and Solt, S and Horváth, É and Palatitz, P and Kotymán, L and Dán, Á and Papp, L and Harnos, A and Fehérvári, P}, title = {West Nile virus host-vector-pathogen interactions in a colonial raptor.}, journal = {Parasites & vectors}, volume = {10}, number = {1}, pages = {449}, pmid = {28962629}, issn = {1756-3305}, mesh = {Animals ; Antibodies, Viral/blood ; Bird Diseases/blood/transmission/*virology ; Culex/physiology/*virology ; Falconiformes/blood/*virology ; Feeding Behavior ; Female ; Host-Pathogen Interactions ; Insect Vectors/physiology/*virology ; Male ; Seroepidemiologic Studies ; West Nile Fever/transmission/*veterinary/virology ; West Nile virus/genetics/isolation & purification/*physiology ; }, abstract = {BACKGROUND: Avian host species have different roles in the amplification and maintenance of West Nile virus (WNV), therefore identifying key taxa is vital in understanding WNV epidemics. Here, we present a comprehensive case study conducted on red-footed falcons, where host-vector, vector-virus and host-virus interactions were simultaneously studied to evaluate host species contribution to WNV circulation qualitatively.

RESULTS: Mosquitoes were trapped inside red-footed falcon nest-boxes by a method originally developed for the capture of blackflies and midges. We showed that this approach is also efficient for trapping mosquitoes and that the number of trapped vectors is a function of host attraction. Brood size and nestling age had a positive effect on the number of attracted Culex pipiens individuals while the blood-feeding success rate of both dominant Culex species (Culex pipiens and Culex modestus) markedly decreased after the nestlings reached 14 days of age. Using RT-PCR, we showed that WNV was present in these mosquitoes with 4.2% (CI: 0.9-7.5%) prevalence. We did not detect WNV in any of the nestling blood samples. However, a relatively high seroprevalence (25.4% CI: 18.8-33.2%) was detected with an enzyme-linked immunoabsorbent assay (ELISA). Using the ELISA OD ratios as a proxy to antibody titers, we showed that older seropositive nestlings have lower antibody levels than their younger conspecifics and that hatching order negatively influences antibody levels in broods with seropositive nestlings.

CONCLUSIONS: Red-footed falcons in the studied system are exposed to a local sylvatic WNV circulation, and the risk of infection is higher for younger nestlings. However, the lack of individuals with viremia and the high WNV seroprevalence, indicate that either host has a very short viremic period or that a large percentage of nestlings in the population receive maternal antibodies. This latter assumption is supported by the age and hatching order dependence of antibody levels found for seropositive nestlings. Considering the temporal pattern in mosquito feeding success, maternal immunity may be effective in protecting progeny against WNV infection despite the short antibody half-life measured in various other species. We conclude that red-footed falcons seem to have low WNV host competence and are unlikely to be effective virus reservoirs in the studied region.}, } @article {pmid28960889, year = {2018}, author = {Zhao, M and Wang, T and Stewart, MJ and Bose, U and Suwansa-Ard, S and Storey, KB and Cummins, SF}, title = {eSnail: A transcriptome-based molecular resource of the central nervous system for terrestrial gastropods.}, journal = {Molecular ecology resources}, volume = {18}, number = {1}, pages = {147-158}, doi = {10.1111/1755-0998.12722}, pmid = {28960889}, issn = {1755-0998}, mesh = {Animals ; Central Nervous System/*physiology ; Data Mining ; *Databases, Genetic ; Gastropoda/*genetics ; Internet ; Microsatellite Repeats ; Molecular Sequence Annotation ; Polymorphism, Single Nucleotide ; Sequence Analysis, RNA ; *Transcriptome ; }, abstract = {To expand on emerging terrestrial gastropod molecular resources, we have undertaken transcriptome-based sequencing of the central nervous system (CNS) from six ecologically invasive terrestrial gastropods. Focusing on snail species Cochlicella acuta and Helix aspersa and reticulated slugs Deroceras invadens, Deroceras reticulatum, Lehmannia nyctelia and Milax gagates, we obtained a total of 367,869,636 high-quality reads and compared them with existing CNS transcript resources for the invasive Mediterranean snail, Theba pisana. In total, we obtained 419,289 unique transcripts (unigenes) from 1,410,569 assembled contigs, with blast search analysis of multiple protein databases leading to the annotation of 124,268 unigenes, of which 92,544 mapped to ncbi nonredundant protein databases. We found that these transcriptomes have representatives in most biological functions, based on comparison of gene ontology, kegg pathway and protein family contents, demonstrating a high range of transcripts responsible for regulating metabolic activities and molecular functions occurring within the CNS. To provide an accessible genetic resource, we also demonstrate the presence of 66,687 microsatellites and 304,693 single-nucleotide variants, which can be used for the design of potentially thousands of unique primers for functional screening. An online "eSnail" database with a user-friendly web interface was implemented to query all the information obtained herein (http://soft.bioinfo-minzhao.org/esnail). We demonstrate the usefulness of the database through the mining of molluscan neuropeptides. As the most comprehensive CNS transcriptome resource for terrestrial gastropods, eSnail may serve as a useful gateway for researchers to explore gastropod CNS function for multiple purposes, including for the development of biocontrol approaches.}, } @article {pmid28958130, year = {2018}, author = {Martin, RW and Waits, ER and Nietch, CT}, title = {Empirically-based modeling and mapping to consider the co-occurrence of ecological receptors and stressors.}, journal = {The Science of the total environment}, volume = {613-614}, number = {}, pages = {1228-1239}, pmid = {28958130}, issn = {1879-1026}, support = {EPA999999//Intramural EPA/United States ; }, mesh = {Animals ; Bayes Theorem ; Ecology ; Environmental Monitoring/*methods ; Fishes ; *Geographic Information Systems ; Models, Theoretical ; Ohio ; Rivers/chemistry ; Software ; }, abstract = {Part of the ecological risk assessment process involves examining the potential for environmental stressors and ecological receptors to co-occur across a landscape. In this study, we introduce a Bayesian joint modeling framework for use in evaluating and mapping the co-occurrence of stressors and receptors using empirical data, open-source statistical software, and Geographic Information Systems tools and data. To illustrate the approach, we apply the framework to bioassessment data on stream fishes and nutrients collected from a watershed in southwestern Ohio. The results highlighted the joint model's ability to parse and exploit statistical dependencies in order to provide empirical insight into the potential environmental and ecotoxicological interactions influencing co-occurrence. We also demonstrate how probabilistic predictions can be generated and mapped to visualize spatial patterns in co-occurrences. For practitioners, we believe that this data-driven approach to modeling and mapping co-occurrence can lead to more quantitatively transparent and robust assessments of ecological risk.}, } @article {pmid28957517, year = {2017}, author = {Charbonneau, D and Poff, C and Nguyen, H and Shin, MC and Kierstead, K and Dornhaus, A}, title = {Who Are the "Lazy" Ants? The Function of Inactivity in Social Insects and a Possible Role of Constraint: Inactive Ants Are Corpulent and May Be Young and/or Selfish.}, journal = {Integrative and comparative biology}, volume = {57}, number = {3}, pages = {649-667}, doi = {10.1093/icb/icx029}, pmid = {28957517}, issn = {1557-7023}, mesh = {Animals ; Ants/anatomy & histology/*physiology ; Behavior, Animal/*physiology ; Biological Evolution ; Body Size ; Social Behavior ; }, abstract = {Social insect colonies are commonly thought of as highly organized and efficient complex systems, yet high levels of worker inactivity are common. Although consistently inactive workers have been documented across many species, very little is known about the potential function or costs associated with this behavior. Here we ask what distinguishes these "lazy" individuals from their nestmates. We obtained a large set of behavioral and morphological data about individuals, and tested for consistency with the following evolutionary hypotheses: that inactivity results from constraint caused by worker (a) immaturity or (b) senescence; that (c) inactive workers are reproducing; that inactive workers perform a cryptic task such as (d) acting as communication hubs or (e) food stores; and that (f) inactive workers represent the "slow-paced" end of inter-worker variation in "pace-of-life." We show that inactive workers walk more slowly, have small spatial fidelity zones near the nest center, are more corpulent, are isolated in colony interaction networks, have the smallest behavioral repertoires, and are more likely to have oocytes than other workers. These results are consistent with the hypotheses that inactive workers are immature and/or storing food for the colony; they suggest that workers are not inactive as a consequence of senescence, and that they are not acting as communication hubs. The hypotheses listed above are not mutually exclusive, and likely form a "syndrome" of behaviors common to inactive social insect workers. Their simultaneous contribution to inactivity may explain the difficulty in finding a simple answer to this deceptively simple question.}, } @article {pmid28957328, year = {2017}, author = {Bauer, M and Graf, IR and Ngampruetikorn, V and Stephens, GJ and Frey, E}, title = {Exploiting ecology in drug pulse sequences in favour of population reduction.}, journal = {PLoS computational biology}, volume = {13}, number = {9}, pages = {e1005747}, pmid = {28957328}, issn = {1553-7358}, mesh = {Animals ; *Anti-Bacterial Agents/pharmacology/therapeutic use ; Bacteria/*drug effects ; *Bacterial Infections/drug therapy/microbiology ; Caenorhabditis elegans ; Computational Biology ; Ecology ; *Models, Biological ; *Population Dynamics ; }, abstract = {A deterministic population dynamics model involving birth and death for a two-species system, comprising a wild-type and more resistant species competing via logistic growth, is subjected to two distinct stress environments designed to mimic those that would typically be induced by temporal variation in the concentration of a drug (antibiotic or chemotherapeutic) as it permeates through the population and is progressively degraded. Different treatment regimes, involving single or periodical doses, are evaluated in terms of the minimal population size (a measure of the extinction probability), and the population composition (a measure of the selection pressure for resistance or tolerance during the treatment). We show that there exist timescales over which the low-stress regime is as effective as the high-stress regime, due to the competition between the two species. For multiple periodic treatments, competition can ensure that the minimal population size is attained during the first pulse when the high-stress regime is short, which implies that a single short pulse can be more effective than a more protracted regime. Our results suggest that when the duration of the high-stress environment is restricted, a treatment with one or multiple shorter pulses can produce better outcomes than a single long treatment. If ecological competition is to be exploited for treatments, it is crucial to determine these timescales, and estimate for the minimal population threshold that suffices for extinction. These parameters can be quantified by experiment.}, } @article {pmid28954146, year = {2017}, author = {Souza, ER and Meira, KC and Ribeiro, AP and Santos, JD and Guimarães, RM and Borges, LF and Oliveira, LVE and Simões, TC}, title = {Homicides among women in the different Brazilian regions in the last 35 years: an analysis of age-period-birth cohort effects.}, journal = {Ciencia & saude coletiva}, volume = {22}, number = {9}, pages = {2949-2962}, doi = {10.1590/1413-81232017229.12392017}, pmid = {28954146}, issn = {1678-4561}, mesh = {Adolescent ; Adult ; Age Factors ; Aged ; Brazil/epidemiology ; Child ; Cohort Effect ; Female ; Health Information Systems/statistics & numerical data ; Homicide/*statistics & numerical data ; Humans ; Middle Aged ; Mortality/*trends ; Violence/*statistics & numerical data ; Young Adult ; }, abstract = {The aim of this study is to estimate the effects of age-period-birth cohort (APC) on female homicides. This is an ecological study which analyzed the violence-related death records of women aged 10 years and older, in the Brazilian geographic regions, between 1980 and 2014. Data on mortality were extracted from the Mortality Information System. The trend analysis was conducted using negative binomial regression and APC effects were analyzed using estimable functions. The average mortality rate for the period was 5.13 deaths per 100,000 women, with the highest rates observed in the Central-West (7.98 deaths), followed by the Southeast (4.78 deaths), North (4.77 deaths), Northeast (4.05 deaths) and South (3.82 deaths) regions. All regions presented a decrease in the risk of death in the period from 2010 to 2014, except for the Northeast region (RR = 1.06, 95% CI 1.02 to 1.10). There was a progressive increase in the homicide risk for women born from 1955 to 1959 in all Brazilian regions. Younger women are at higher risk of dying from homicides in all Brazilian geographic regions. The upward trend of homicide mortality rates according to birth cohort was significant and the highest risk was observed in women born between 2000 and 2004.}, } @article {pmid28948429, year = {2017}, author = {Rachwał, M and Wawer, M and Magiera, T and Steinnes, E}, title = {Integration of soil magnetometry and geochemistry for assessment of human health risk from metallurgical slag dumps.}, journal = {Environmental science and pollution research international}, volume = {24}, number = {34}, pages = {26410-26423}, pmid = {28948429}, issn = {1614-7499}, support = {Pol-Nor/199338/45/2013//National Centre for R&D under the Norwegian Financial mechanism/ ; }, mesh = {Agriculture ; Environmental Monitoring/*methods ; Geographic Information Systems ; Humans ; Industrial Waste/*analysis ; Magnetometry ; *Metallurgy ; Metals, Heavy/*analysis ; Poland ; Risk Assessment ; Soil/*chemistry ; Soil Pollutants/*analysis ; Trace Elements/analysis ; Waste Disposal Facilities ; }, abstract = {The main objective of the study was an assessment of the pollution level of agricultural land located close to dumps of industrial waste remaining after former Zn and Pb ore processing in Poland. The integrated geophysical-geochemical methods were applied for assessment of soil quality with respect to trace element pollution. Additionally, human health risk induced by the contaminated arable soil and dusting slag heap was estimated. The investigations pointed out that soils in the vicinity of the metallurgical slag dump in Piekary were heavily polluted. Spatial distribution of magnetic susceptibility corresponding well with distribution of the content of potentially toxic elements indicated the local "pollution hotspots." Proper geophysical and geochemical data interpretation supported by statistical factor analysis enabled identification of three different sources of pollution including metallurgical slug dump as a main source, but also traffic pollution influencing the area located along the busy road and relatively strong influence of the geochemical background. Computed health hazard index revealed no adverse health effect to the farmers cultivating arable soil, but in the direct vicinity of dusting, slag dump health risk occurred, caused mostly by very toxic elements as As and Tl. In the future, investigation should be focused on contribution of different sources to the heavy metal pollution in soil-crop system in this area. It should be highlighted that a site-specific approach should be taken in order to redevelop this kind of area in order to reduce ecological and human health threat. The study proved the integrated two-stage geophysical-geochemical method to be a feasible, reliable, and cost-effective tool for identification of the extent of soil pollution and areas at risk.}, } @article {pmid28948095, year = {2017}, author = {Kerkvliet, J and de Boer, T and Schilthuizen, M and Kraaijeveld, K}, title = {Candidate genes for shell colour polymorphism in Cepaea nemoralis.}, journal = {PeerJ}, volume = {5}, number = {}, pages = {e3715}, pmid = {28948095}, issn = {2167-8359}, abstract = {The characteristic ground colour and banding patterns on shells of the land snail Cepaea nemoralis form a classic study system for genetics and adaptation as it varies widely between individuals. We use RNAseq analysis to identify candidate genes underlying this polymorphism. We sequenced cDNA from the foot and the mantle (the shell-producing tissue) of four individuals of two phenotypes and produced a de novo transcriptome of 147,397 contigs. Differential expression analysis identified a set of 1,961 transcripts that were upregulated in mantle tissue. Sequence variant analysis resulted in a set of 2,592 transcripts with single nucleotide polymorphisms (SNPs) that differed consistently between the phenotypes. Inspection of the overlap between the differential expression analysis and SNP analysis yielded a set of 197 candidate transcripts, of which 38 were annotated. Four of these transcripts are thought to be involved in production of the shell's nacreous layer. Comparison with morph-associated Restriction-site Associated DNA (RAD)-tags from a published study yielded eight transcripts that were annotated as metallothionein, a protein that is thought to inhibit the production of melanin in melanocytes. These results thus provide an excellent starting point for the elucidation of the genetic regulation of the Cepaea nemoralis shell colour polymorphism.}, } @article {pmid28947293, year = {2018}, author = {Wang, DM and Morgan, FC and Besaw, RJ and Schmults, CD}, title = {An ecological study of skin biopsies and skin cancer treatment procedures in the United States Medicare population, 2000 to 2015.}, journal = {Journal of the American Academy of Dermatology}, volume = {78}, number = {1}, pages = {47-53}, doi = {10.1016/j.jaad.2017.09.031}, pmid = {28947293}, issn = {1097-6787}, mesh = {Adult ; Age Factors ; Aged ; Biopsy, Needle ; Carcinoma, Basal Cell/epidemiology/pathology/surgery ; Carcinoma, Squamous Cell/epidemiology/pathology/surgery ; Databases, Factual ; Dermatologic Surgical Procedures/economics/methods/*statistics & numerical data ; Female ; Humans ; Immunohistochemistry ; Insurance Claim Review ; Male ; Medicare/economics/*statistics & numerical data ; Melanoma/epidemiology/pathology/surgery ; Middle Aged ; Retrospective Studies ; Risk Assessment ; Sex Factors ; Skin Neoplasms/epidemiology/*pathology/*surgery ; Socioeconomic Factors ; Survival Analysis ; United States ; }, abstract = {BACKGROUND: Analyses of skin cancer procedures adjusted for population changes are needed.

OBJECTIVE: To describe trends in skin cancer-related biopsies and procedures in Medicare beneficiaries.

METHODS: An ecological study of Medicare claims for skin biopsies and skin cancer procedures in 2000 to 2015.

RESULTS: Biopsies increased 142%, and skin cancer procedures increased 56%. Mohs micrographic surgery (MMS) utilization increased on the head/neck, hands/feet, and genitalia (increasing from 11% to 27% of all treatment procedures) but was low on the trunk/extremities (increasing from 1% to 4%). Adjusted for increased Medicare enrollment (+36%) between 2000 and 2015, the number of biopsies and MMS procedures performed per 1000 beneficiaries increased (from 56 to 99 and from 5 to 15, respectively), whereas the number of excisions and destructions changed minimally (from 18 to 16 and from 19 to 18, respectively). Growth in biopsies and MMS procedures slowed between each time period studied: 4.3 additional biopsies per year and 0.9 additional MMS procedures per year per 1000 beneficiaries between 2000 and 2007, 2.2 and 0.5 more between 2008 and 2011, and 0.5 and 0.3 more between 2012 and 2015, respectively.

LIMITATIONS: Medicare claims-level data do not provide patient-level or nonsurgical treatment information.

CONCLUSIONS: The increased number of skin cancer procedures performed was largely the result of Medicare population growth over time. MMS utilization increased primarily on high- and medium-risk and functionally and cosmetically significant locations where tissue sparing and maximizing cure are critical.}, } @article {pmid28945876, year = {2018}, author = {Cadena, CD and Zapata, F and Jiménez, I}, title = {Issues and Perspectives in Species Delimitation using Phenotypic Data: Atlantean Evolution in Darwin's Finches.}, journal = {Systematic biology}, volume = {67}, number = {2}, pages = {181-194}, doi = {10.1093/sysbio/syx071}, pmid = {28945876}, issn = {1076-836X}, mesh = {Animals ; Biodiversity ; Data Interpretation, Statistical ; Finches/genetics/*physiology ; *Models, Biological ; Phenotype ; *Phylogeny ; Species Specificity ; }, abstract = {Progress in the development and use of methods for species delimitation employing phenotypic data lags behind conceptual and practical advances in molecular genetic approaches. The basic evolutionary model underlying the use of phenotypic data to delimit species assumes random mating and quantitative polygenic traits, so that phenotypic distributions within a species should be approximately normal for individuals of the same sex and age. Accordingly, two or more distinct normal distributions of phenotypic traits suggest the existence of multiple species. In light of this model, we show that analytical approaches employed in taxonomic studies using phenotypic data are often compromised by three issues: 1) reliance on graphical analyses that convey little information on phenotype frequencies; 2) exclusion of characters potentially important for species delimitation following reduction of data dimensionality; and 3) use of measures of central tendency to evaluate phenotypic distinctiveness. We outline approaches to overcome these issues based on statistical developments related to normal mixture models (NMMs) and illustrate them empirically with a reanalysis of morphological data recently used to claim that there are no morphologically distinct species of Darwin's ground-finches (Geospiza). We found negligible support for this claim relative to taxonomic hypotheses recognizing multiple species. Although species limits among ground-finches merit further assessments using additional sources of information, our results bear implications for other areas of inquiry including speciation research: because ground-finches have likely speciated and are not trapped in a process of "Sisyphean" evolution as recently argued, they remain useful models to understand the evolutionary forces involved in speciation. Our work underscores the importance of statistical approaches grounded on appropriate evolutionary models for species delimitation. We discuss how NMMs offer new perspectives in the kind of inferences available to systematists, with significant repercussions on ideas about the phenotypic structure of biodiversity.}, } @article {pmid28944780, year = {2017}, author = {Ostrander, EA and Wayne, RK and Freedman, AH and Davis, BW}, title = {Demographic history, selection and functional diversity of the canine genome.}, journal = {Nature reviews. Genetics}, volume = {18}, number = {12}, pages = {705-720}, pmid = {28944780}, issn = {1471-0064}, mesh = {Animals ; Behavior, Animal ; Dog Diseases/genetics ; Dogs/anatomy & histology/classification/*genetics/physiology ; Domestication ; Neoplasms/genetics/veterinary ; *Polymorphism, Single Nucleotide ; Selection, Genetic ; Selective Breeding ; *Whole Genome Sequencing ; }, abstract = {The domestic dog represents one of the most dramatic long-term evolutionary experiments undertaken by humans. From a large wolf-like progenitor, unparalleled diversity in phenotype and behaviour has developed in dogs, providing a model for understanding the developmental and genomic mechanisms of diversification. We discuss pattern and process in domestication, beginning with general findings about early domestication and problems in documenting selection at the genomic level. Furthermore, we summarize genotype-phenotype studies based first on single nucleotide polymorphism (SNP) genotyping and then with whole-genome data and show how an understanding of evolution informs topics as different as human history, adaptive and deleterious variation, morphological development, ageing, cancer and behaviour.}, } @article {pmid28944516, year = {2017}, author = {Roy, AL}, title = {Innovation or Violation? Leveraging Mobile Technology to Conduct Socially Responsible Community Research.}, journal = {American journal of community psychology}, volume = {60}, number = {3-4}, pages = {385-390}, doi = {10.1002/ajcp.12187}, pmid = {28944516}, issn = {1573-2770}, mesh = {Adolescent ; Chicago ; Data Collection/*ethics ; *Ecological Momentary Assessment ; *Ethics, Research ; Ethnicity ; *Geographic Information Systems ; Humans ; Inventions ; Minority Groups ; Poverty ; Privacy ; Psychology/*ethics ; *Smartphone ; }, abstract = {Mobile technology is increasingly being used to measure individuals' moods, thoughts, and behaviors in real time. Current examples include the use of smartphones to collect ecological momentary assessments (EMAs; assessments delivered "in the moment"); wearable technology to passively collect objective measures of participants' movement, physical activity, sleep, and physiological response; and smartphones and wearable devices with global positioning system (GPS) capabilities to collect precise information about where participants spend their time. Although advances in mobile technology offer exciting opportunities for measuring and modeling individuals' experiences in their natural environments, they also introduce new ethical issues. Drawing on lessons learned while collecting GPS coordinates and EMAs measuring mood, companionship, and health-risk behavior with a sample of low-income, predominantly racial/ethnic minority youth living in Chicago, this manuscript discusses ethical challenges specific to the methodology (e.g., unanticipated access to personal information) and broader concerns related to data conceptualization and interpretation (e.g., the ethics of "monitoring" low-income youth of color). While encouraging researchers to embrace innovations offered by mobile technology, this discussion highlights some of the many ethical issues that also need to be considered.}, } @article {pmid28943998, year = {2017}, author = {Melton, ED and Sorokin, DY and Overmars, L and Lapidus, AL and Pillay, M and Ivanova, N and Del Rio, TG and Kyrpides, NC and Woyke, T and Muyzer, G}, title = {Draft genome sequence of Dethiobacter alkaliphilus strain AHT1[T], a gram-positive sulfidogenic polyextremophile.}, journal = {Standards in genomic sciences}, volume = {12}, number = {}, pages = {57}, pmid = {28943998}, issn = {1944-3277}, support = {322551/ERC_/European Research Council/International ; }, abstract = {Dethiobacter alkaliphilus strain AHT1[T] is an anaerobic, sulfidogenic, moderately salt-tolerant alkaliphilic chemolithotroph isolated from hypersaline soda lake sediments in northeastern Mongolia. It is a Gram-positive bacterium with low GC content, within the phylum Firmicutes. Here we report its draft genome sequence, which consists of 34 contigs with a total sequence length of 3.12 Mbp. D. alkaliphilus strain AHT1[T] was sequenced by the Joint Genome Institute (JGI) as part of the Community Science Program due to its relevance to bioremediation and biotechnological applications.}, } @article {pmid28941033, year = {2018}, author = {Campana, MG}, title = {BaitsTools: Software for hybridization capture bait design.}, journal = {Molecular ecology resources}, volume = {18}, number = {2}, pages = {356-361}, doi = {10.1111/1755-0998.12721}, pmid = {28941033}, issn = {1755-0998}, mesh = {Computational Biology/*methods ; Nucleic Acid Hybridization/*methods ; Oligonucleotide Probes/*genetics ; *Software ; }, abstract = {Nucleic acid hybridization capture is a principal technology in molecular ecology and genomics. Bait design, however, is a nontrivial task and few resources currently exist to automate the process. Here, I present baitstools, an open-source, user-friendly software package to facilitate the design of nucleic acid baits for hybridization capture.}, } @article {pmid28938869, year = {2017}, author = {Athrey, G and Cosme, LV and Popkin-Hall, Z and Pathikonda, S and Takken, W and Slotman, MA}, title = {Chemosensory gene expression in olfactory organs of the anthropophilic Anopheles coluzzii and zoophilic Anopheles quadriannulatus.}, journal = {BMC genomics}, volume = {18}, number = {1}, pages = {751}, pmid = {28938869}, issn = {1471-2164}, support = {R01 AI085079/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Anopheles/*genetics/physiology ; *Gene Expression Profiling ; Gene Ontology ; Receptors, Cell Surface/genetics ; Smell/*genetics ; }, abstract = {BACKGROUND: Anopheles (An.) coluzzii, one of Africa's primary malaria vectors, is highly anthropophilic. This human host preference contributes greatly to its ability to transmit malaria. In contrast, the closely related An. quadriannulatus prefers to feed on bovids and is not thought to contribute to malaria transmission. The diverged preference for host odor profiles between these sibling species is likely reflected in chemosensory gene expression levels in the olfactory organs. Therefore, we compared the transcriptomes of the antennae and maxillary palps between An. coluzzii and An. quadriannulatus, focusing on the major chemosensory gene families.

RESULTS: While chemosensory gene expression is strongly correlated between the two species, various chemosensory genes show significantly enhanced expression in one of the species. In the antennae of An. coluzzii the expression of six olfactory receptors (Ors) and seven ionotropic receptors (Irs) is considerably enhanced, whereas 11 Ors and 3 Irs are upregulated in An. quadriannulatus. In the maxillary palps, leaving aside Irs with very low level of expression, one Ir is strongly enhanced in each species. In addition, we find divergence in odorant binding protein (Obp) gene expression, with several highly expressed Obps being enhanced in the antennae and palps of An. coluzzii. Finally, the expression of several gustatory receptors (Grs) in the palps appears to be species-specific, including a homolog of a sugar-sensing Drosophila Gr.

CONCLUSIONS: A considerable number of Ors and Irs are differentially expressed between these two closely related species with diverging host preference. These chemosensory genes could play a role in the human host preference of the malaria vector An. coluzzii. Additionally, divergence in Obp expression between the two species suggests a possible role of these odor carrier proteins in determining host preference. Finally, divergence in chemosensory expression in the palps may point towards a possible role for the maxillary palps in host differentiation.}, } @article {pmid28934485, year = {2017}, author = {Gouy, A and Daub, JT and Excoffier, L}, title = {Detecting gene subnetworks under selection in biological pathways.}, journal = {Nucleic acids research}, volume = {45}, number = {16}, pages = {e149}, pmid = {28934485}, issn = {1362-4962}, mesh = {Adaptation, Physiological/genetics ; Altitude ; Computational Biology/methods ; *Gene Regulatory Networks ; Humans ; Metabolic Networks and Pathways/genetics ; *Selection, Genetic ; Signal Transduction/genetics ; *Software ; }, abstract = {Advances in high throughput sequencing technologies have created a gap between data production and functional data analysis. Indeed, phenotypes result from interactions between numerous genes, but traditional methods treat loci independently, missing important knowledge brought by network-level emerging properties. Therefore, detecting selection acting on multiple genes affecting the evolution of complex traits remains challenging. In this context, gene network analysis provides a powerful framework to study the evolution of adaptive traits and facilitates the interpretation of genome-wide data. We developed a method to analyse gene networks that is suitable to evidence polygenic selection. The general idea is to search biological pathways for subnetworks of genes that directly interact with each other and that present unusual evolutionary features. Subnetwork search is a typical combinatorial optimization problem that we solve using a simulated annealing approach. We have applied our methodology to find signals of adaptation to high-altitude in human populations. We show that this adaptation has a clear polygenic basis and is influenced by many genetic components. Our approach, implemented in the R package signet, improves on gene-level classical tests for selection by identifying both new candidate genes and new biological processes involved in adaptation to altitude.}, } @article {pmid28934274, year = {2017}, author = {Wang, J and Tiyip, T and Ding, J and Zhang, D and Liu, W and Wang, F and Tashpolat, N}, title = {Desert soil clay content estimation using reflectance spectroscopy preprocessed by fractional derivative.}, journal = {PloS one}, volume = {12}, number = {9}, pages = {e0184836}, pmid = {28934274}, issn = {1932-6203}, mesh = {*Algorithms ; Aluminum Silicates/*chemistry ; Calibration ; China ; Clay ; Datasets as Topic ; *Desert Climate ; Lakes ; Least-Squares Analysis ; Models, Theoretical ; Soil/*chemistry ; Spectrum Analysis/*methods ; }, abstract = {Effective pretreatment of spectral reflectance is vital to model accuracy in soil parameter estimation. However, the classic integer derivative has some disadvantages, including spectral information loss and the introduction of high-frequency noise. In this paper, the fractional order derivative algorithm was applied to the pretreatment and partial least squares regression (PLSR) was used to assess the clay content of desert soils. Overall, 103 soil samples were collected from the Ebinur Lake basin in the Xinjiang Uighur Autonomous Region of China, and used as data sets for calibration and validation. Following laboratory measurements of spectral reflectance and clay content, the raw spectral reflectance and absorbance data were treated using the fractional derivative order from the 0.0 to the 2.0 order (order interval: 0.2). The ratio of performance to deviation (RPD), determinant coefficients of calibration ([Formula: see text]), root mean square errors of calibration (RMSEC), determinant coefficients of prediction ([Formula: see text]), and root mean square errors of prediction (RMSEP) were applied to assess the performance of predicting models. The results showed that models built on the fractional derivative order performed better than when using the classic integer derivative. Comparison of the predictive effects of 22 models for estimating clay content, calibrated by PLSR, showed that those models based on the fractional derivative 1.8 order of spectral reflectance ([Formula: see text] = 0.907, RMSEC = 0.425%, [Formula: see text] = 0.916, RMSEP = 0.364%, and RPD = 2.484 ≥ 2.000) and absorbance ([Formula: see text] = 0.888, RMSEC = 0.446%, [Formula: see text] = 0.918, RMSEP = 0.383% and RPD = 2.511 ≥ 2.000) were most effective. Furthermore, they performed well in quantitative estimations of the clay content of soils in the study area.}, } @article {pmid28931422, year = {2017}, author = {Djokic-Petrovic, M and Cvjetkovic, V and Yang, J and Zivanovic, M and Wild, DJ}, title = {PIBAS FedSPARQL: a web-based platform for integration and exploration of bioinformatics datasets.}, journal = {Journal of biomedical semantics}, volume = {8}, number = {1}, pages = {42}, pmid = {28931422}, issn = {2041-1480}, mesh = {*Computational Biology ; Data Mining/*methods ; Databases, Factual ; *Internet ; *Software ; User-Computer Interface ; }, abstract = {BACKGROUND: There are a huge variety of data sources relevant to chemical, biological and pharmacological research, but these data sources are highly siloed and cannot be queried together in a straightforward way. Semantic technologies offer the ability to create links and mappings across datasets and manage them as a single, linked network so that searching can be carried out across datasets, independently of the source. We have developed an application called PIBAS FedSPARQL that uses semantic technologies to allow researchers to carry out such searching across a vast array of data sources.

RESULTS: PIBAS FedSPARQL is a web-based query builder and result set visualizer of bioinformatics data. As an advanced feature, our system can detect similar data items identified by different Uniform Resource Identifiers (URIs), using a text-mining algorithm based on the processing of named entities to be used in Vector Space Model and Cosine Similarity Measures. According to our knowledge, PIBAS FedSPARQL was unique among the systems that we found in that it allows detecting of similar data items. As a query builder, our system allows researchers to intuitively construct and run Federated SPARQL queries across multiple data sources, including global initiatives, such as Bio2RDF, Chem2Bio2RDF, EMBL-EBI, and one local initiative called CPCTAS, as well as additional user-specified data source. From the input topic, subtopic, template and keyword, a corresponding initial Federated SPARQL query is created and executed. Based on the data obtained, end users have the ability to choose the most appropriate data sources in their area of interest and exploit their Resource Description Framework (RDF) structure, which allows users to select certain properties of data to enhance query results.

CONCLUSIONS: The developed system is flexible and allows intuitive creation and execution of queries for an extensive range of bioinformatics topics. Also, the novel "similar data items detection" algorithm can be particularly useful for suggesting new data sources and cost optimization for new experiments. PIBAS FedSPARQL can be expanded with new topics, subtopics and templates on demand, rendering information retrieval more robust.}, } @article {pmid28931084, year = {2017}, author = {Conte-Grand, C and Britz, R and Dahanukar, N and Raghavan, R and Pethiyagoda, R and Tan, HH and Hadiaty, RK and Yaakob, NS and Rüber, L}, title = {Barcoding snakeheads (Teleostei, Channidae) revisited: Discovering greater species diversity and resolving perpetuated taxonomic confusions.}, journal = {PloS one}, volume = {12}, number = {9}, pages = {e0184017}, pmid = {28931084}, issn = {1932-6203}, mesh = {Animals ; *Biodiversity ; DNA/chemistry/*metabolism ; *DNA Barcoding, Taxonomic ; Databases, Genetic ; Fishes/classification/*genetics ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {Snakehead fishes of the family Channidae are predatory freshwater teleosts from Africa and Asia comprising 38 valid species. Snakeheads are important food fishes (aquaculture, live food trade) and have been introduced widely with several species becoming highly invasive. A channid barcode library was recently assembled by Serrao and co-workers to better detect and identify potential and established invasive snakehead species outside their native range. Comparing our own recent phylogenetic results of this taxonomically confusing group with those previously reported revealed several inconsistencies that prompted us to expand and improve on previous studies. By generating 343 novel snakehead coxI sequences and combining them with an additional 434 coxI sequences from GenBank we highlight several problems with previous efforts towards the assembly of a snakehead reference barcode library. We found that 16.3% of the channid coxI sequences deposited in GenBank are based on misidentifications. With the inclusion of our own data we were, however, able to solve these cases of perpetuated taxonomic confusion. Different species delimitation approaches we employed (BIN, GMYC, and PTP) were congruent in suggesting a potentially much higher species diversity within snakeheads than currently recognized. In total, 90 BINs were recovered and within a total of 15 currently recognized species multiple BINs were identified. This higher species diversity is mostly due to either the incorporation of undescribed, narrow range, endemics from the Eastern Himalaya biodiversity hotspot or the incorporation of several widespread species characterized by deep genetic splits between geographically well-defined lineages. In the latter case, over-lumping in the past has deflated the actual species numbers. Further integrative approaches are clearly needed for providing a better taxonomic understanding of snakehead diversity, new species descriptions and taxonomic revisions of the group.}, } @article {pmid28931057, year = {2017}, author = {Ungaro, A and Pech, N and Martin, JF and McCairns, RJS and Mévy, JP and Chappaz, R and Gilles, A}, title = {Challenges and advances for transcriptome assembly in non-model species.}, journal = {PloS one}, volume = {12}, number = {9}, pages = {e0185020}, pmid = {28931057}, issn = {1932-6203}, mesh = {Animals ; Computational Biology/*methods ; Contig Mapping ; Fishes/*genetics ; *Gene Expression Profiling ; Genome ; Genomics ; High-Throughput Nucleotide Sequencing/methods ; Models, Statistical ; Molecular Sequence Annotation ; Quercus/*genetics ; Sequence Analysis, DNA/*methods ; *Transcriptome ; Zebrafish/*genetics ; }, abstract = {Analyses of high-throughput transcriptome sequences of non-model organisms are based on two main approaches: de novo assembly and genome-guided assembly using mapping to assign reads prior to assembly. Given the limits of mapping reads to a reference when it is highly divergent, as is frequently the case for non-model species, we evaluate whether using blastn would outperform mapping methods for read assignment in such situations (>15% divergence). We demonstrate its high performance by using simulated reads of lengths corresponding to those generated by the most common sequencing platforms, and over a realistic range of genetic divergence (0% to 30% divergence). Here we focus on gene identification and not on resolving the whole set of transcripts (i.e. the complete transcriptome). For simulated datasets, the transcriptome-guided assembly based on blastn recovers 94.8% of genes irrespective of read length at 0% divergence; however, assignment rate of reads is negatively correlated with both increasing divergence level and reducing read lengths. Nevertheless, we still observe 92.6% of recovered genes at 30% divergence irrespective of read length. This analysis also produces a categorization of genes relative to their assignment, and suggests guidelines for data processing prior to analyses of comparative transcriptomics and gene expression to minimize potential inferential bias associated with incorrect transcript assignment. We also compare the performances of de novo assembly alone vs in combination with a transcriptome-guided assembly based on blastn both via simulation and empirically, using data from a cyprinid fish species and from an oak species. For any simulated scenario, the transcriptome-guided assembly using blastn outperforms the de novo approach alone, including when the divergence level is beyond the reach of traditional mapping methods. Combining de novo assembly and a related reference transcriptome for read assignment also addresses the bias/error in contigs caused by the dependence on a related reference alone. Empirical data corroborate these findings when assembling transcriptomes from the two non-model organisms: Parachondrostoma toxostoma (fish) and Quercus pubescens (plant). For the fish species, out of the 31,944 genes known from D. rerio, the guided and de novo assemblies recover respectively 20,605 and 20,032 genes but the performance of the guided assembly approach is much higher for both the contiguity and completeness metrics. For the oak, out of the 29,971 genes known from Vitis vinifera, the transcriptome-guided and de novo assemblies display similar performance, but the new guided approach detects 16,326 genes where the de novo assembly only detects 9,385 genes.}, } @article {pmid28926627, year = {2017}, author = {Afonso, AS and Garla, R and Hazin, FHV}, title = {Tiger sharks can connect equatorial habitats and fisheries across the Atlantic Ocean basin.}, journal = {PloS one}, volume = {12}, number = {9}, pages = {e0184763}, pmid = {28926627}, issn = {1932-6203}, mesh = {Animals ; Atlantic Ocean ; Behavior, Animal ; Body Size ; *Ecosystem ; Female ; Fisheries ; Geographic Information Systems ; Male ; Sharks/*physiology ; }, abstract = {Increasing our knowledge about the spatial ecology of apex predators and their interactions with diverse habitats and fisheries is necessary for understanding the trophic mechanisms that underlie several aspects of marine ecosystem dynamics and for guiding informed management policies. A preliminary assessment of tiger shark (Galeocerdo cuvier) population structure off the oceanic insular system of Fernando de Noronha (FEN) and the large-scale movements performed by this species in the equatorial Atlantic Ocean was conducted using longline and handline fishing gear and satellite telemetry. A total of 25 sharks measuring 175-372 cm in total length (TL) were sampled. Most sharks were likely immature females ranging between 200 and 260 cm TL, with few individuals < 200 cm TL being caught. This contrasts greatly with the tiger shark size-distribution previously reported for coastal waters off the Brazilian mainland, where most individuals measured < 200 cm TL. Also, the movements of 8 individuals measuring 202-310 cm TL were assessed with satellite transmitters for a combined total of 757 days (mean = 94.6 days∙shark-1; SD = 65.6). These sharks exhibited a considerable variability in their horizontal movements, with three sharks showing a mostly resident behavior around FEN during the extent of the respective tracks, two sharks traveling west to the South American continent, and two sharks moving mostly along the middle of the oceanic basin, one of which ending up in the northern hemisphere. Moreover, one shark traveled east to the African continent, where it was eventually caught by fishers from Ivory Coast in less than 474 days at liberty. The present results suggest that young tiger sharks measuring < 200 cm TL make little use of insular oceanic habitats from the western South Atlantic Ocean, which agrees with a previously-hypothesized ontogenetic habitat shift from coastal to oceanic habitats experienced by juveniles of this species in this region. In addition, this study adds evidence that tiger sharks are able to connect marine trophic webs from the neritic provinces of the eastern and western margins of the Atlantic Ocean across the equatorial basin and that they may experience mortality induced by remote fisheries. All this information is extremely relevant for understanding the energetic balance of marine ecosystems as much as the exposure of this species to fishing pressure in this yet poorly-known region.}, } @article {pmid28923966, year = {2017}, author = {Cardoso, D and Särkinen, T and Alexander, S and Amorim, AM and Bittrich, V and Celis, M and Daly, DC and Fiaschi, P and Funk, VA and Giacomin, LL and Goldenberg, R and Heiden, G and Iganci, J and Kelloff, CL and Knapp, S and Cavalcante de Lima, H and Machado, AFP and Dos Santos, RM and Mello-Silva, R and Michelangeli, FA and Mitchell, J and Moonlight, P and de Moraes, PLR and Mori, SA and Nunes, TS and Pennington, TD and Pirani, JR and Prance, GT and de Queiroz, LP and Rapini, A and Riina, R and Rincon, CAV and Roque, N and Shimizu, G and Sobral, M and Stehmann, JR and Stevens, WD and Taylor, CM and Trovó, M and van den Berg, C and van der Werff, H and Viana, PL and Zartman, CE and Forzza, RC}, title = {Amazon plant diversity revealed by a taxonomically verified species list.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {114}, number = {40}, pages = {10695-10700}, pmid = {28923966}, issn = {1091-6490}, mesh = {*Biodiversity ; Brazil ; *Databases, Factual ; Plants/*classification ; *Rainforest ; }, abstract = {Recent debates on the number of plant species in the vast lowland rain forests of the Amazon have been based largely on model estimates, neglecting published checklists based on verified voucher data. Here we collate taxonomically verified checklists to present a list of seed plant species from lowland Amazon rain forests. Our list comprises 14,003 species, of which 6,727 are trees. These figures are similar to estimates derived from nonparametric ecological models, but they contrast strongly with predictions of much higher tree diversity derived from parametric models. Based on the known proportion of tree species in neotropical lowland rain forest communities as measured in complete plot censuses, and on overall estimates of seed plant diversity in Brazil and in the neotropics in general, it is more likely that tree diversity in the Amazon is closer to the lower estimates derived from nonparametric models. Much remains unknown about Amazonian plant diversity, but this taxonomically verified dataset provides a valid starting point for macroecological and evolutionary studies aimed at understanding the origin, evolution, and ecology of the exceptional biodiversity of Amazonian forests.}, } @article {pmid28923917, year = {2017}, author = {Ripple, WJ and Wolf, C and Newsome, TM and Hoffmann, M and Wirsing, AJ and McCauley, DJ}, title = {Extinction risk is most acute for the world's largest and smallest vertebrates.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {114}, number = {40}, pages = {10678-10683}, pmid = {28923917}, issn = {1091-6490}, mesh = {Animals ; *Biological Evolution ; Body Size/*physiology ; *Databases, Factual ; *Extinction, Biological ; *Models, Biological ; Vertebrates/*physiology ; }, abstract = {Extinction risk in vertebrates has been linked to large body size, but this putative relationship has only been explored for select taxa, with variable results. Using a newly assembled and taxonomically expansive database, we analyzed the relationships between extinction risk and body mass (27,647 species) and between extinction risk and range size (21,294 species) for vertebrates across six main classes. We found that the probability of being threatened was positively and significantly related to body mass for birds, cartilaginous fishes, and mammals. Bimodal relationships were evident for amphibians, reptiles, and bony fishes. Most importantly, a bimodal relationship was found across all vertebrates such that extinction risk changes around a body mass breakpoint of 0.035 kg, indicating that the lightest and heaviest vertebrates have elevated extinction risk. We also found range size to be an important predictor of the probability of being threatened, with strong negative relationships across nearly all taxa. A review of the drivers of extinction risk revealed that the heaviest vertebrates are most threatened by direct killing by humans. By contrast, the lightest vertebrates are most threatened by habitat loss and modification stemming especially from pollution, agricultural cropping, and logging. Our results offer insight into halting the ongoing wave of vertebrate extinctions by revealing the vulnerability of large and small taxa, and identifying size-specific threats. Moreover, they indicate that, without intervention, anthropogenic activities will soon precipitate a double truncation of the size distribution of the world's vertebrates, fundamentally reordering the structure of life on our planet.}, } @article {pmid28922513, year = {2018}, author = {Gray, S and Voinov, A and Paolisso, M and Jordan, R and BenDor, T and Bommel, P and Glynn, P and Hedelin, B and Hubacek, K and Introne, J and Kolagani, N and Laursen, B and Prell, C and Schmitt Olabisi, L and Singer, A and Sterling, E and Zellner, M}, title = {Purpose, processes, partnerships, and products: four Ps to advance participatory socio-environmental modeling.}, journal = {Ecological applications : a publication of the Ecological Society of America}, volume = {28}, number = {1}, pages = {46-61}, doi = {10.1002/eap.1627}, pmid = {28922513}, issn = {1051-0761}, mesh = {Animals ; Cameroon ; *Community Participation ; *Conservation of Natural Resources ; Environment ; Geographic Information Systems ; Humans ; India ; *Models, Theoretical ; Social Environment ; Zambia ; }, abstract = {Including stakeholders in environmental model building and analysis is an increasingly popular approach to understanding ecological change. This is because stakeholders often hold valuable knowledge about socio-environmental dynamics and collaborative forms of modeling produce important boundary objects used to collectively reason about environmental problems. Although the number of participatory modeling (PM) case studies and the number of researchers adopting these approaches has grown in recent years, the lack of standardized reporting and limited reproducibility have prevented PM's establishment and advancement as a cohesive field of study. We suggest a four-dimensional framework (4P) that includes reporting on dimensions of (1) the Purpose for selecting a PM approach (the why); (2) the Process by which the public was involved in model building or evaluation (the how); (3) the Partnerships formed (the who); and (4) the Products that resulted from these efforts (the what). We highlight four case studies that use common PM software-based approaches (fuzzy cognitive mapping, agent-based modeling, system dynamics, and participatory geospatial modeling) to understand human-environment interactions and the consequences of ecological changes, including bushmeat hunting in Tanzania and Cameroon, agricultural production and deforestation in Zambia, and groundwater management in India. We demonstrate how standardizing communication about PM case studies can lead to innovation and new insights about model-based reasoning in support of ecological policy development. We suggest that our 4P framework and reporting approach provides a way for new hypotheses to be identified and tested in the growing field of PM.}, } @article {pmid28921927, year = {2018}, author = {Bayerl, H and Kraus, RHS and Nowak, C and Foerster, DW and Fickel, J and Kuehn, R}, title = {Fast and cost-effective single nucleotide polymorphism (SNP) detection in the absence of a reference genome using semideep next-generation Random Amplicon Sequencing (RAMseq).}, journal = {Molecular ecology resources}, volume = {18}, number = {1}, pages = {107-117}, doi = {10.1111/1755-0998.12717}, pmid = {28921927}, issn = {1755-0998}, mesh = {Animals ; Computational Biology/*methods ; Cost-Benefit Analysis ; Genomics/*methods ; High-Throughput Nucleotide Sequencing/*methods ; Otters/*classification/*genetics ; *Polymorphism, Single Nucleotide ; Time Factors ; }, abstract = {Biodiversity has suffered a dramatic global decline during the past decades, and monitoring tools are urgently needed providing data for the development and evaluation of conservation efforts both on a species and on a genetic level. However, in wild species, the assessment of genetic diversity is often hampered by the lack of suitable genetic markers. In this article, we present Random Amplicon Sequencing (RAMseq), a novel approach for fast and cost-effective detection of single nucleotide polymorphisms (SNPs) in nonmodel species by semideep sequencing of random amplicons. By applying RAMseq to the Eurasian otter (Lutra lutra), we identified 238 putative SNPs after quality filtering of all candidate loci and were able to validate 32 of 77 loci tested. In a second step, we evaluated the genotyping performance of these SNP loci in noninvasive samples, one of the most challenging genotyping applications, by comparing it with genotyping results of the same faecal samples at microsatellite markers. We compared (i) polymerase chain reaction (PCR) success rate, (ii) genotyping errors and (iii) Mendelian inheritance (population parameters). SNPs produced a significantly higher PCR success rate (75.5% vs. 65.1%) and lower mean allelic error rate (8.8% vs. 13.3%) than microsatellites, but showed a higher allelic dropout rate (29.7% vs. 19.8%). Genotyping results showed no deviations from Mendelian inheritance in any of the SNP loci. Hence, RAMseq appears to be a valuable tool for the detection of genetic markers in nonmodel species, which is a common challenge in conservation genetic studies.}, } @article {pmid28921901, year = {2018}, author = {Li, YL and Liu, JX}, title = {StructureSelector: A web-based software to select and visualize the optimal number of clusters using multiple methods.}, journal = {Molecular ecology resources}, volume = {18}, number = {1}, pages = {176-177}, doi = {10.1111/1755-0998.12719}, pmid = {28921901}, issn = {1755-0998}, mesh = {*Cluster Analysis ; Computational Biology/*methods ; *Genetic Variation ; Genetics, Population/*methods ; *Internet ; *Software ; }, abstract = {Inferences of population genetic structure are of great importance to the fields of ecology and evolutionary biology. The program structure has been widely used to infer population genetic structure. However, previous studies demonstrated that uneven sampling often leads to wrong inferences on hierarchical structure. The most widely used ΔK method tends to identify the uppermost hierarchy of population structure. Recently, four alternative statistics (medmedk, medmeak, maxmedk and maxmeak) were proposed, which appear to be more accurate than the previously used methods for both even and uneven sampling data. However, the lack of easy-to-use software limits the use of these appealing new estimators. Here, we developed a web-based user-friendly software structureselector to calculate the four appealing alternative statistics together with the commonly used Ln Pr(X|K) and ΔK statistics. structureselector accepts the result files of structure, admixture or faststructure as input files. It reports the "best" K for each estimator, and the results are available as HTML or tab separated tables. The program can also generate graphical representations for specific K, which can be easily downloaded from the server. The software is freely available at http://lmme.qdio.ac.cn/StructureSelector/.}, } @article {pmid28921829, year = {2018}, author = {Fisher, RA and Koven, CD and Anderegg, WRL and Christoffersen, BO and Dietze, MC and Farrior, CE and Holm, JA and Hurtt, GC and Knox, RG and Lawrence, PJ and Lichstein, JW and Longo, M and Matheny, AM and Medvigy, D and Muller-Landau, HC and Powell, TL and Serbin, SP and Sato, H and Shuman, JK and Smith, B and Trugman, AT and Viskari, T and Verbeeck, H and Weng, E and Xu, C and Xu, X and Zhang, T and Moorcroft, PR}, title = {Vegetation demographics in Earth System Models: A review of progress and priorities.}, journal = {Global change biology}, volume = {24}, number = {1}, pages = {35-54}, doi = {10.1111/gcb.13910}, pmid = {28921829}, issn = {1365-2486}, mesh = {*Earth, Planet ; *Ecosystem ; *Models, Biological ; *Plants ; Population Dynamics ; Uncertainty ; }, abstract = {Numerous current efforts seek to improve the representation of ecosystem ecology and vegetation demographic processes within Earth System Models (ESMs). These developments are widely viewed as an important step in developing greater realism in predictions of future ecosystem states and fluxes. Increased realism, however, leads to increased model complexity, with new features raising a suite of ecological questions that require empirical constraints. Here, we review the developments that permit the representation of plant demographics in ESMs, and identify issues raised by these developments that highlight important gaps in ecological understanding. These issues inevitably translate into uncertainty in model projections but also allow models to be applied to new processes and questions concerning the dynamics of real-world ecosystems. We argue that stronger and more innovative connections to data, across the range of scales considered, are required to address these gaps in understanding. The development of first-generation land surface models as a unifying framework for ecophysiological understanding stimulated much research into plant physiological traits and gas exchange. Constraining predictions at ecologically relevant spatial and temporal scales will require a similar investment of effort and intensified inter-disciplinary communication.}, } @article {pmid28920370, year = {2016}, author = {Jiang, SY and Sun, HB and Qin, JH and Zhu, WT and Sun, H}, title = {[Functional production regionalization for Fritillariae Cirrhosae Bulbus based on growth and quality suitability assessment].}, journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica}, volume = {41}, number = {17}, pages = {3194-3201}, doi = {10.4268/cjcmm20161713}, pmid = {28920370}, issn = {1001-5302}, mesh = {China ; Ecology ; Fritillaria/*growth & development ; Geographic Information Systems ; Plants, Medicinal/growth & development ; }, abstract = {The major contributing factors for growth of endangered medicinal plants of Fritillariae Cirrhosae Bulbus were screened on the GIS platform by using the MaxEnt model, and spatial distribution data of the medicine quality suitability were generated by geostatistics interpolation based on reported measured data of ecology and quality suitability assessment. On this basis, a functional production cultivation regionalization with high feasibility and operability were formatted for protection, wild monitoring, and cultivation of this plant by fuzzy superposition of spatial suitability data of ecology and quality, as well as integrated with land use and cover data. Therefore, a novel assessment and regionalization method were presented for ecology, growth and quality suitability of the Chinese traditional medicinal plants. This method is expected to overcome shortage of traditional regionalization methods difficult to distinguish the contribution of ecological factors and quality factors, which provide an innovative theory and methodology for regionalization, and is helpful to practical application of wild resource protection, monitoring, and commercialization cultivation for traditional Chinese medicinal plants.}, } @article {pmid28920369, year = {2016}, author = {Liu, X and Yang, YF and Song, HP and Zhang, XB and Huang, LQ and Wu, HZ}, title = {[Cultural regionalization for Coptis chinensis based on 3S technology platform Ⅰ. Study on growth suitability for Coptis chinensis based on ecological factors analysis by Maxent and ArcGIS model].}, journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica}, volume = {41}, number = {17}, pages = {3186-3193}, doi = {10.4268/cjcmm20161712}, pmid = {28920369}, issn = {1001-5302}, mesh = {Alkaloids/analysis ; China ; Coptis/chemistry/*growth & development ; Ecology ; Ecosystem ; Geographic Information Systems ; Rhizome/chemistry/growth & development ; }, abstract = {At the urgent request of Coptis chinensis planting,growth suitability as assessment indicators for C. chinensis cultivation was proposed and analyzed in this paper , based on chemical quality determination and ecological fators analysis by Maxent and ArcGIS model. Its potential distribution areas at differernt suitability grade and regionalization map were formulated based on statistical theory and growth suitability theory. The results showed that the most suitable habitats is some parts of Chongqing and Hubei province, such as Shizhu, Lichuan, Wulong, Wuxi, Enshi. There are seven ecological factor is the main ecological factors affect the growth of Coptidis Rhizoma, including altitude, precipitation in February and September and the rise of precipitation and altitude is conducive to the accumulation of total alkaloid content in C. chinensis. Therefore, The results of the study not only illustrates the most suitable for the surroundings of Coptidis Rhizoma, also helpful to further research and practice of cultivation regionalization, wild resource monitoring and large-scale cultivation of traditional Chinese medicine plants.}, } @article {pmid28920368, year = {2016}, author = {Miao, Q and Yuan, YJ and Luo, GM and Wei, CH and Rao, YQ and Gong, YH and Zhang, L and Shao, J and Dong, YK}, title = {[Study on ecological suitability of Gardenia jasminoides based on ArcGIS and Maxent model].}, journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica}, volume = {41}, number = {17}, pages = {3181-3185}, doi = {10.4268/cjcmm20161711}, pmid = {28920368}, issn = {1001-5302}, mesh = {China ; Climate ; Ecology ; Gardenia/*growth & development ; Geographic Information Systems ; }, abstract = {The application of ArcGIS and Maxent modelto analyze the ecological suitability of Gardenia jasminoides.Taking 85 batches of Gardenia as the basis of analysis, the selection of ecological factors for the growth of Gardenia. The results showed that the average precipitation in April, the average precipitation in November and the average precipitation in August were the most important factors affecting the growth of Gardenia. The relative concentration of Gardenia suitable growth region,north to the south of Shaanxi province, south of Henan, central Anhui, south to the north of Hainan province, west to central Sichuan province, east of Zhejiang coastal area, northeast of Taiwan.}, } @article {pmid28920367, year = {2016}, author = {Lu, YY and Yang, YM and Ma, XH and Zhang, XB and Zhu, SD and Jin, L}, title = {[Ecology suitability study of Chinese materia medica Gentianae Macrophyllae Radix].}, journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica}, volume = {41}, number = {17}, pages = {3176-3180}, doi = {10.4268/cjcmm20161710}, pmid = {28920367}, issn = {1001-5302}, mesh = {Altitude ; China ; Climate ; Ecology ; Gentiana/*growth & development ; Geographic Information Systems ; }, abstract = {This paper is aimed to predict ecology suitability distribution of Gentianae Macrophyllae Radix and search the main ecological factors affecting the suitability distribution. The 313 distribution information about G. macrophylla, 186 distribution information about G. straminea, 343 distribution information about G. dauricaand 131 distribution information about G. crasicaulis were collected though investigation and network sharing platform data . The ecology suitable distribution factors for production Gentianae Macrophyllae Radix was analyzed respectively by the software of ArcGIS and MaxEnt with 55 environmental factors. The result of MaxEnt prediction was very well (AUC was above 0.9). The results of predominant factors analysis showed that precipitation and altitude were all the major factors impacting the ecology suitable of Getiana Macrophylla Radix production. G. macrophylla ecology suitable region was mainly concentrated in south of Gansu, Shanxi, central of Shaanxi and east of Qinghai provinces. G. straminea ecology suitable region was mainly concentrated in southwest of Gansu, east of Qinghai, north and northwest of Sichuan, east of Xizang province. G. daurica ecology suitable region was mainly concentrated in south and southwest of Gansu, east of Qinghai, Shanxi and north of Shaanxi province. G. crasicaulis ecology suitable region was mainly concentrated in Sichuan and north of Yunnan, east of Xizang, south of Gansu and east of Qinghai province. The ecological suitability distribution result of Gentianae Macrophyllae Radix was consistent with each species actual distribution. The study could provide reference for the collection and protection of wild resources, meanwhile, provide the basis for the selection of cultivation area of Gentiana Macrophylla Radix.}, } @article {pmid28920366, year = {2016}, author = {Shao, Y and Ye, D and Ouyang, Z and Huang, LQ and Peng, HS and Zhang, XB and Zhu, SD and Yu, YF and Jiang, FR}, title = {[Habitat suitability and quality division of Mentha haplocalyx].}, journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica}, volume = {41}, number = {17}, pages = {3169-3175}, doi = {10.4268/cjcmm20161709}, pmid = {28920366}, issn = {1001-5302}, mesh = {China ; Climate ; *Ecosystem ; Geographic Information Systems ; Mentha/*growth & development ; Temperature ; }, abstract = {In this study, ecological factors, occurrence records, the essential oil components content were used to predict the potential geographical distribution and quality division of Mentha haplocalyx in China based on the MaxEnt modeling and geographic information system(GIS). The AUC of ROC curve was above 0.950,indicating that the predictive results with the maximum model were highly precise. The results showed that the main environmental factors determining the potential distribution were annual average precipitation (the contribution rate, 45.87%), mean temperature of wettest quarter (11.92%), mean temperature of warmest quarter (7.84%), average monthly precipitation of May (6.80%), standard deviation of seasonal temperature variation (4.42%), mean temperature of the coldest quarter (3.47%) and altitude (2.92%). The environmental variables in the highly potential areas were determined as annual average precipitation around [530,1 465] mm, mean temperature of wettest quarter around [24.5,29] ℃, mean temperature of the warmest quarter around [25.5,29] ℃, average monthly precipitation of May around [67,133] mm, standard deviation of temperature seasonal change around [8 333,9 643], mean temperature of the coldest quarter around [1.7,8.3] ℃ and the altitude around [0,165] mm. The best quality distribution of M. haplocalyx was mainly located in Jiangsu, Anhui, Shandong, Zhejiang and Heilongjiang. The zoning results basically coincide with the actual situation. The quality division of M. haplocalyx can be used for providing a scientific basis for selection of artificial planting base and guidance of its production.}, } @article {pmid28920364, year = {2016}, author = {Shi, ZW and Ma, CJ and Kang, CZ and Wang, L and Zhang, ZH and Chen, JF and Zhang, XB and Liu, DH}, title = {[Ecological suitability regionalization for Gastrodia elata in Zhaotong based on Maxent and ArcGIS].}, journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica}, volume = {41}, number = {17}, pages = {3155-3163}, doi = {10.4268/cjcmm20161707}, pmid = {28920364}, issn = {1001-5302}, mesh = {China ; Climate ; Ecology ; Gastrodia/*growth & development ; Geographic Information Systems ; Soil ; }, abstract = {In this paper, the potential distribution information and ecological suitability regionalization for Gastrodia elata in Zhaotong were studied based on the climate, terrain, soil and vegetation factors analysis by Maxent and ArcGIS. The results showed that the highly potential distribution (suitability index>0.6) mainly located in Zhaotong, Yunnan province（Zhenxiong,Yiliang and Daguan county, with an area of 2 872 km[2]）, and Bijie, Guizhou province （Hezhang,Bijie,Weining county, 1 251 km[2]）. The AUC of ROC curve was above 0.99, indicating that the predictive results with the Maxent model were highly precise. The main ecological factors determining the potential distribution were the altitude, average rainfall in November, average rainfall in October, vegetation types, average rainfall in March, average rainfall in April,soil types,isothermal characteristic and average rainfall in June. The environmental variables in the highly potential areas were determined as altitude around 1 450-2 200 m,annual average temperature around 18.0-20.4 ℃,annual average precipitation around 900 mm,yellow soil or yellow brown soil,and acid sandy loam or slightly acidic sandy loam.The results will provide valuable references for plantation regionalization and the siting for imitation wild planting of G. elata in Zhaotong.}, } @article {pmid28920363, year = {2016}, author = {Zhang, Y and Wang, J and Zhang, J and Peng, WF and Xu, XL and Fang, QM}, title = {[Study on suitable distribution areas of Grifola umbellate in Sichuan province based on remote sensing and GIS].}, journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica}, volume = {41}, number = {17}, pages = {3148-3154}, doi = {10.4268/cjcmm20161706}, pmid = {28920363}, issn = {1001-5302}, mesh = {China ; Climate ; Geographic Information Systems ; Grifola/*growth & development ; Remote Sensing Technology ; Soil ; }, abstract = {Grifola umbellate is the important medicinal materials in China which has a very high medicinal value. This study analyzedthe suitable distribution areasof G. umbellate and provided scientific basis for determining G. umbellate planting regions and planning production distribution reasonably. The suitable distribution areas of G. umbellate in Sichuan province was researched based on TM, ETM+, and DEM data,the key ecological factors that affect the growth of G. umbellate were extracted, including elevation, slope, aspect, average annual temperature,average annual precipitation,forest information,soil information, following remote sensing and GIS techniques, combining field researchdata. The results showed that the G. umbellate resources in Sichuan province were mainly distributed in Pingwu, Beichuan, Licountry, Yanyuan, Xichang, Dechang, Yanbian, Miyi, Huidong, Panzhihua and so on, the suitability distribution areas is 276.214 4 km[2] approximately and accounting for more than 0.143 3% of the total area.According to the related document information and the field investigation, showed that the suitability distribution based on RS and GIS were corresponded with the actual distribution areas of G. umbellate.}, } @article {pmid28920361, year = {2016}, author = {Lu, YY and Zhang, XB and Yang, YM and Ma, XH and Zhu, TT and Yu, XH and Jin, L}, title = {[Quality regionalization study on Gentianae Macrophyllae Radix].}, journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica}, volume = {41}, number = {17}, pages = {3132-3138}, doi = {10.4268/cjcmm20161704}, pmid = {28920361}, issn = {1001-5302}, mesh = {China ; Gentiana/*growth & development ; Geographic Information Systems ; Principal Component Analysis ; }, abstract = {The 79 samples of Gentianae Macrophyllae Radix were collected based on the distributed information by document literature. Based on sample information, and using the regression model of Gentianae Macrophyllae Radix index component and environmental factors, and combined with the prediction results of ecological suitability by MaxEnt and principal component analysis results of index component, the space distribution of Gentianae Macrophyllae Radix was estimated with the spatial analysis function of ArcGIS. The results showed that it had a higher comprehensive quality in south of Shaanxi, south of Gansu, middle of Sichuan and southeast of Xizang. The study results were coinciding with the producing regions of Gentianae Macrophyllae Radix. It can provide reference for Gentianae Macrophyllae Radix resource conservation, development and utilization.}, } @article {pmid28920360, year = {2016}, author = {Wang, HQ and Wang, Q and Ma, L and Ding, R and Di, TY and An, W and Zhang, XB and Wang, YH}, title = {[Production regionalization study of Lycii Fructus].}, journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica}, volume = {41}, number = {17}, pages = {3127-3131}, doi = {10.4268/cjcmm20161703}, pmid = {28920360}, issn = {1001-5302}, mesh = {China ; Climate ; Ecosystem ; Geographic Information Systems ; Lycium/*growth & development ; Soil ; }, abstract = {The distribution information of Lycii Fructus was collected by interview investigation and field survey, and 46 related environmental factors were collected, some kinds of functional chemical constituents the of Lycii Fructus were analyzed. Integrated climate, topography and other related ecological factors, the habitat suitability study was conducted based on Arc geographic information system(ArcGIS),and maximum entropy model. The AUC of ROC curve was both above 0.95, indicating that the predictive results with the maximum model were highly precise. The results showed that 5 major ecological factors had obvious influence on ecology suitability distributions of Lycii Fructus, including soil pH, soil subclass, vegetation type and in August the average temperature et al. It is suitable for the living habits of the Lycii Fructus, dry, cool weather, more hardy, drought-resistant, alkali soil, which is suitable for distribution in the northern temperate plains. In addition, the ecological suitability regionalization based on the chemical constituents of Lycii Fructus also provides a new suitable distribution area other than the traditional distribution area, which provides a scientific basis for the reasonable introduction of Lycii Fructus.}, } @article {pmid28918527, year = {2018}, author = {Sun, Z and Li, S and Yu, Y and Chen, H and Ommati, MM and Manthari, RK and Niu, R and Wang, J}, title = {Alterations in epididymal proteomics and antioxidant activity of mice exposed to fluoride.}, journal = {Archives of toxicology}, volume = {92}, number = {1}, pages = {169-180}, doi = {10.1007/s00204-017-2054-2}, pmid = {28918527}, issn = {1432-0738}, support = {31372497//National Natural Science Foundation of China (CN)/ ; 31201965//National Natural Science Foundation of China/ ; TYIT201408//Program for the Top Young Innovative Talents of Shanxi Agricultural University/ ; }, mesh = {Animals ; Antioxidants/analysis/*metabolism ; Enzymes/genetics/metabolism ; Epididymis/*drug effects/*metabolism ; Gene Expression Regulation, Enzymologic/drug effects ; Gene Ontology ; Glutathione/metabolism ; Male ; Mice, Inbred ICR ; Proteins/analysis/*metabolism ; Proteomics/methods ; Sodium Fluoride/*toxicity ; }, abstract = {It is well known that high fluoride results in low fertility. Epididymis is the important place for spermatozoa maturation, which is essential for successful fertilization. In the previous studies, fluoride was reported to damage the epididymal structure of mouse and rabbit. However, the mechanism underlying sodium fluoride (NaF)-induced epididymal toxicity has not yet been well elucidated. The aim of this study is to explore the global protein alterations in epididymis of mice exposed to NaF using the iTRAQ technique. Results showed that 211 proteins were differentially expressed in both 25 and 100 mg/L NaF groups. Some of them have been proved to be important for reproduction, such as low-density lipoprotein receptor-related protein 2 (Lrp2), cytochrome c, testis-specific (Cyct), sorbitol dehydrogenase (Sord), glutathione S-transferases (GSTs), acrosin, beta-defensin 126, cysteine-rich secretory protein (Crisp) 1, and Crisp2. Gene ontology (GO) analysis suggested cellular process, organelle and catalytic activity account for high percent and number of differentially expressed proteins. 171 pathways were found after the Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, among which the representative maps, such as ribosome, focal adhesion, and phagosome, were involved. Different functional categories post-translational modification, protein turnover, chaperones; translation, ribosomal structure and biogenesis; cytoskeleton; energy production and conversion are implicated in the Cluster of Orthologous Groups (COG) of proteins analysis. Subsequently, the effect of NaF on the antioxidant activity in epididymis, especially glutathione and glutathione-related enzymes, was evaluated. Results exhibited high fluoride caused low total antioxidant capacity (T-AOC), high methane dicarboxylic aldehyde (MDA), decreased reduced glutathione (GSH), and the glutathione-related enzymes [GSH peroxidase (GPx), GSH reductase (GR), and GSH S-transferase (GST)] changes in activity, protein, and mRNA expressions. In summary, NaF decreased the antioxidant activity of epididymis, especially glutathione and glutathione-related enzymes, as well as iTRAQ results, providing new explanations for the low sperm quality induced by fluoride.}, } @article {pmid28918485, year = {2018}, author = {Yang, P and Chen, Y and Wu, H and Fang, W and Liang, Q and Zheng, Y and Olsson, S and Zhang, D and Zhou, J and Wang, Z and Zheng, W}, title = {The 5-oxoprolinase is required for conidiation, sexual reproduction, virulence and deoxynivalenol production of Fusarium graminearum.}, journal = {Current genetics}, volume = {64}, number = {1}, pages = {285-301}, pmid = {28918485}, issn = {1432-0983}, support = {No.31670142//The National Natural Science Foundation of China/ ; 2016M590587//The China Postdoctoral Science Foundation/ ; }, mesh = {Biological Evolution ; Cell Wall/genetics/metabolism ; Computational Biology/methods ; Fungal Proteins/genetics/metabolism ; Fusarium/pathogenicity/*physiology ; Genetic Complementation Test ; Mutation ; Phylogeny ; Protein Transport ; Pyroglutamate Hydrolase/genetics/*metabolism ; *Spores, Fungal ; Trichothecenes/*biosynthesis ; Virulence/genetics ; Virulence Factors/genetics/metabolism ; }, abstract = {In eukaryotic organisms, the 5-oxoprolinase is one of the six key enzymes in the γ-glutamyl cycle that is involved in the biosynthetic pathway of glutathione (GSH, an antioxidative tripeptide counteracting the oxidative stress). To date, little is known about the biological functions of the 5-oxoprolinase in filamentous phytopathogenic fungi. In this study, we investigated the 5-oxoprolinase in Fusarium graminearum for the first time. In F. graminearum, two paralogous genes (FgOXP1 and FgOXP2) were identified to encode the 5-oxoprolinase while only one homologous gene encoding the 5-oxoprolinase could be found in other filamentous phytopathogenic fungi or Saccharomyces cerevisiae. Deletion of FgOXP1 or FgOXP2 in F. graminearum led to significant defects in its virulence on wheat. This is likely caused by an observed decreased deoxynivalenol (DON, a mycotoxin) production in the gene deletion mutant strains as DON is one of the best characterized virulence factors of F. graminearum. The FgOXP2 deletion mutant strains were also defective in conidiation and sexual reproduction while the FgOXP1 deletion mutant strains were normal for those phenotypes. Double deletion of FgOXP1 and FgOXP2 led to more severe defects in conidiation, DON production and virulence on plants, suggesting that both FgOXP1 and FgOXP2 play a role in fungal development and plant colonization. Although transformation of MoOXP1into ΔFgoxp1 was able to complement ΔFgoxp1, transformation of MoOXP1 into ΔFgoxp2 failed to restore its defects in sexual development, DON production and pathogenicity. Taken together, these results suggest that FgOXP1 and FgOXP2 are likely to have been functionally diversified and play significant roles in fungal development and full virulence in F. graminearum.}, } @article {pmid28915911, year = {2017}, author = {Noë, B and Turner, LD and Linden, DEJ and Allen, SM and Maio, GR and Whitaker, RM}, title = {Timing rather than user traits mediates mood sampling on smartphones.}, journal = {BMC research notes}, volume = {10}, number = {1}, pages = {481}, pmid = {28915911}, issn = {1756-0500}, support = {/WT_/Wellcome Trust/United Kingdom ; MR/L010305/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Adult ; Affect/*physiology ; Ecological Momentary Assessment/*standards ; Female ; Humans ; Male ; Middle Aged ; *Mobile Applications ; Research Design/*standards ; Smartphone ; Time Factors ; Young Adult ; }, abstract = {OBJECTIVE: Recent years have seen an increasing number of studies using smartphones to sample participants' mood states. Moods are usually collected by asking participants for their current mood or for a recollection of their mood states over a specific period of time. The current study investigates the reasons to favour collecting mood through current or daily mood surveys and outlines design recommendations for mood sampling using smartphones based on these findings. These recommendations are also relevant to more general smartphone sampling procedures.

RESULTS: N=64 participants completed a series of surveys at the beginning and end of the study providing information such as gender, personality, or smartphone addiction score. Through a smartphone application, they reported their current mood 3 times and daily mood once per day for 8 weeks. We found that none of the examined intrinsic individual qualities had an effect on matches of current and daily mood reports. However timing played a significant role: the last followed by the first reported current mood of the day were more likely to match the daily mood. Current mood surveys should be preferred for a higher sampling accuracy, while daily mood surveys are more suitable if compliance is more important.}, } @article {pmid28914350, year = {2018}, author = {Coron, C and Costa, M and Leman, H and Smadi, C}, title = {A stochastic model for speciation by mating preferences.}, journal = {Journal of mathematical biology}, volume = {76}, number = {6}, pages = {1421-1463}, pmid = {28914350}, issn = {1432-1416}, mesh = {Animal Migration ; Animals ; Biological Evolution ; Computational Biology ; Conservation of Natural Resources ; Extinction, Biological ; Female ; *Genetic Speciation ; Genetics, Population/statistics & numerical data ; Genotype ; Male ; Mathematical Concepts ; *Mating Preference, Animal ; *Models, Biological ; Reproduction ; Reproductive Isolation ; Stochastic Processes ; }, abstract = {Mechanisms leading to speciation are a major focus in evolutionary biology. In this paper, we present and study a stochastic model of population where individuals, with type a or A, are equivalent from ecological, demographical and spatial points of view, and differ only by their mating preference: two individuals with the same genotype have a higher probability to mate and produce a viable offspring. The population is subdivided in several patches and individuals may migrate between them. We show that mating preferences by themselves, even if they are very small, are enough to entail reproductive isolation between patches, and we provide the time needed for this isolation to occur as a function of the carrying capacity. Our results rely on a fine study of the stochastic process and of its deterministic limit in large population, which is given by a system of coupled nonlinear differential equations. Besides, we propose several generalisations of our model, and prove that our findings are robust for those generalisations.}, } @article {pmid28911174, year = {2017}, author = {Hirst, CE and Major, AT and Ayers, KL and Brown, RJ and Mariette, M and Sackton, TB and Smith, CA}, title = {Sex Reversal and Comparative Data Undermine the W Chromosome and Support Z-linked DMRT1 as the Regulator of Gonadal Sex Differentiation in Birds.}, journal = {Endocrinology}, volume = {158}, number = {9}, pages = {2970-2987}, doi = {10.1210/en.2017-00316}, pmid = {28911174}, issn = {1945-7170}, mesh = {Animals ; *Birds/embryology/genetics ; Chick Embryo ; Chickens ; Embryonic Development ; Female ; Feminization/embryology/genetics ; Finches/embryology/genetics ; Gene Expression Regulation, Developmental ; Gonads ; Male ; Sex Chromosomes/*genetics ; Sex Determination Processes/*genetics ; Sex Differentiation/*genetics ; Transcription Factors/*physiology ; }, abstract = {The exact genetic mechanism regulating avian gonadal sex differentiation has not been completely resolved. The most likely scenario involves a dosage mechanism, whereby the Z-linked DMRT1 gene triggers testis development. However, the possibility still exists that the female-specific W chromosome may harbor an ovarian determining factor. In this study, we provide evidence that the universal gene regulating gonadal sex differentiation in birds is Z-linked DMRT1 and not a W-linked (ovarian) factor. Three candidate W-linked ovarian determinants are HINTW, female-expressed transcript 1 (FET1), and female-associated factor (FAF). To test the association of these genes with ovarian differentiation in the chicken, we examined their expression following experimentally induced female-to-male sex reversal using the aromatase inhibitor fadrozole (FAD). Administration of FAD on day 3 of embryogenesis induced a significant loss of aromatase enzyme activity in female gonads and masculinization. However, expression levels of HINTW, FAF, and FET1 were unaltered after experimental masculinization. Furthermore, comparative analysis showed that FAF and FET1 expression could not be detected in zebra finch gonads. Additionally, an antibody raised against the predicted HINTW protein failed to detect it endogenously. These data do not support a universal role for these genes or for the W sex chromosome in ovarian development in birds. We found that DMRT1 (but not the recently identified Z-linked HEMGN gene) is male upregulated in embryonic zebra finch and emu gonads, as in the chicken. As chicken, zebra finch, and emu exemplify the major evolutionary clades of birds, we propose that Z-linked DMRT1, and not the W sex chromosome, regulates gonadal sex differentiation in birds.}, } @article {pmid28910352, year = {2017}, author = {Zieliński, B and Plichta, A and Misztal, K and Spurek, P and Brzychczy-Włoch, M and Ochońska, D}, title = {Deep learning approach to bacterial colony classification.}, journal = {PloS one}, volume = {12}, number = {9}, pages = {e0184554}, pmid = {28910352}, issn = {1932-6203}, mesh = {Bacteria/*classification ; Databases, Factual ; Machine Learning ; *Neural Networks, Computer ; Support Vector Machine ; }, abstract = {In microbiology it is diagnostically useful to recognize various genera and species of bacteria. It can be achieved using computer-aided methods, which make the recognition processes more automatic and thus significantly reduce the time necessary for the classification. Moreover, in case of diagnostic uncertainty (the misleading similarity in shape or structure of bacterial cells), such methods can minimize the risk of incorrect recognition. In this article, we apply the state of the art method for texture analysis to classify genera and species of bacteria. This method uses deep Convolutional Neural Networks to obtain image descriptors, which are then encoded and classified with Support Vector Machine or Random Forest. To evaluate this approach and to make it comparable with other approaches, we provide a new dataset of images. DIBaS dataset (Digital Image of Bacterial Species) contains 660 images with 33 different genera and species of bacteria.}, } @article {pmid28905305, year = {2018}, author = {Hou, SI and Cao, X}, title = {A Systematic Review of Promising Strategies of Faith-Based Cancer Education and Lifestyle Interventions Among Racial/Ethnic Minority Groups.}, journal = {Journal of cancer education : the official journal of the American Association for Cancer Education}, volume = {33}, number = {6}, pages = {1161-1175}, pmid = {28905305}, issn = {1543-0154}, mesh = {*Early Detection of Cancer ; Ethnicity ; Health Education/*methods ; Humans ; *Life Style ; Minority Groups ; Neoplasms/*prevention & control ; *Religion and Medicine ; }, abstract = {Church-based interventions have been used to reach racial/ethnic minorities. In order to develop effective programs, we conducted a comprehensive systematic review of faith-based cancer prevention studies (2005~2016) to examine characteristics and promising strategies. Combination terms "church or faith-based or religion," "intervention or program," and "cancer education or lifestyle" were used in searching the five major databases: CINAHL; ERIC; Health Technology Assessments; MEDLINE; and PsycInfo. A total of 20 studies met study criteria. CDC's Community Guide was used to analyze and review group interventions. Analyses were organized by two racial groups: African American (AA) and Latino/Hispanic American groups. Results showed most studies reviewed focused on breast cancer alone or in combination with other cancers. Studies of Latino/Hispanic groups targeted more on uninsured, Medicare, or Medicaid individuals, whereas AA studies generally did not include specific insurance criteria. The sample sizes of the AA studies were generally larger. The majority of these studies reviewed used pre-post, posttest only with control group, or quasi-experience designs. The Health Belief Model was the most commonly used theory in both groups. Community-based participatory research and empowerment/ecological frameworks were also used frequently in the Latino/Hispanic studies. Small media and group education were the top two most popular intervention strategies in both groups. Although one-on-one strategy was used in some Latino studies, neither group used reducing client out-of-pocket costs strategy. Client reminders could also be used more in both groups as well. Current review showed church-based cancer education programs were effective in changing knowledge, but not always screening utilization. Results show faith-based cancer educational interventions are promising. To maximize intervention impact, future studies might consider using stronger study designs, incorporating a variety of proven effective strategies, including those frequently used evidence-based strategies, as well as exploring promising strategies among specific target groups.}, } @article {pmid28904348, year = {2017}, author = {Liu, S and Hao, H and Lu, X and Zhao, X and Wang, Y and Zhang, Y and Xie, Z and Wang, R}, title = {Transcriptome profiling of genes involved in induced systemic salt tolerance conferred by Bacillus amyloliquefaciens FZB42 in Arabidopsis thaliana.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {10795}, pmid = {28904348}, issn = {2045-2322}, mesh = {Arabidopsis/*microbiology/*physiology ; *Bacillus amyloliquefaciens ; Computational Biology/methods ; Energy Metabolism ; *Gene Expression Profiling ; Gene Expression Regulation, Plant ; High-Throughput Nucleotide Sequencing ; Molecular Sequence Annotation ; Plant Development/genetics ; Reproducibility of Results ; Salinity ; Salt Tolerance/*genetics ; Soil/chemistry ; Stress, Physiological/genetics ; *Transcriptome ; }, abstract = {Plant growth-promoting Bacillus amyloliquefaciens FZB42 induces systemic salt tolerance in Arabidopsis and enhances the fresh and dry weight. However, the underlying molecular mechanism that allows plants to respond to FZB42 and exhibit salt tolerance is largely unknown. Therefore, we performed large-scale transcriptome sequencing of Arabidopsis shoot tissues grown under salt stress with or without FZB42 inoculation by using Illumina sequencing to identify the key genes and pathways with important roles during this interaction. In total, 1461 genes were differentially expressed (FZB42-inoculated versus non-inoculated samples) at 0 mM NaCl, of which 953 were upregulated and 508 downregulated, while 1288 genes were differentially expressed at 100 mM NaCl, of which 1024 were upregulated and 264 were downregulated. Transcripts associated with photosynthesis, auxin-related, SOS scavenging, Na[+] translocation, and osmoprotectant synthesis, such as trehalose and proline, were differentially expressed by FZB42 inoculation, which reduced the susceptibility to salt and facilitated salt adaptation. Meanwhile, etr1-3, eto1, jar1-1, and abi4-102 hormone-related mutants demonstrated that FZB42 might induce plant salt tolerance via activating plants ET/JA signaling but not ABA-dependent pathway. The results here characterize the plant transcriptome under salt stress with plant growth-promoting bacteria inoculation, thereby providing insights into the molecular mechanisms responsible for induced salt tolerance.}, } @article {pmid28902868, year = {2017}, author = {Hücker, SM and Ardern, Z and Goldberg, T and Schafferhans, A and Bernhofer, M and Vestergaard, G and Nelson, CW and Schloter, M and Rost, B and Scherer, S and Neuhaus, K}, title = {Discovery of numerous novel small genes in the intergenic regions of the Escherichia coli O157:H7 Sakai genome.}, journal = {PloS one}, volume = {12}, number = {9}, pages = {e0184119}, pmid = {28902868}, issn = {1932-6203}, mesh = {Conserved Sequence ; DNA, Bacterial/genetics ; DNA, Intergenic/*genetics ; Escherichia coli O157/*genetics ; *Genes, Bacterial ; Genetic Association Studies ; *Genome, Bacterial ; High-Throughput Nucleotide Sequencing ; Open Reading Frames/genetics ; RNA, Bacterial/genetics ; Transcriptome ; }, abstract = {In the past, short protein-coding genes were often disregarded by genome annotation pipelines. Transcriptome sequencing (RNAseq) signals outside of annotated genes have usually been interpreted to indicate either ncRNA or pervasive transcription. Therefore, in addition to the transcriptome, the translatome (RIBOseq) of the enteric pathogen Escherichia coli O157:H7 strain Sakai was determined at two optimal growth conditions and a severe stress condition combining low temperature and high osmotic pressure. All intergenic open reading frames potentially encoding a protein of ≥ 30 amino acids were investigated with regard to coverage by transcription and translation signals and their translatability expressed by the ribosomal coverage value. This led to discovery of 465 unique, putative novel genes not yet annotated in this E. coli strain, which are evenly distributed over both DNA strands of the genome. For 255 of the novel genes, annotated homologs in other bacteria were found, and a machine-learning algorithm, trained on small protein-coding E. coli genes, predicted that 89% of these translated open reading frames represent bona fide genes. The remaining 210 putative novel genes without annotated homologs were compared to the 255 novel genes with homologs and to 250 short annotated genes of this E. coli strain. All three groups turned out to be similar with respect to their translatability distribution, fractions of differentially regulated genes, secondary structure composition, and the distribution of evolutionary constraint, suggesting that both novel groups represent legitimate genes. However, the machine-learning algorithm only recognized a small fraction of the 210 genes without annotated homologs. It is possible that these genes represent a novel group of genes, which have unusual features dissimilar to the genes of the machine-learning algorithm training set.}, } @article {pmid28900256, year = {2017}, author = {Blasi, B and Tafer, H and Kustor, C and Poyntner, C and Lopandic, K and Sterflinger, K}, title = {Genomic and transcriptomic analysis of the toluene degrading black yeast Cladophialophora immunda.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {11436}, pmid = {28900256}, issn = {2045-2322}, support = {P 25119/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Ascomycota/classification/*genetics/*metabolism ; Computational Biology/methods ; Evolution, Molecular ; *Gene Expression Profiling/methods ; Gene Transfer, Horizontal ; Genes, Fungal ; Genome, Fungal ; *Genomics/methods ; Metabolic Networks and Pathways ; Molecular Sequence Annotation ; Phylogeny ; Secondary Metabolism/genetics ; Toluene/*metabolism ; }, abstract = {Cladophialophora immunda is an ascomycotal species belonging to the group of the black yeasts. These fungi have a thick and melanized cell wall and other physiological adaptations that allows them to cope with several extreme physical and chemical conditions. Member of the group can colonize some of the most extremophilic environments on Earth. Cladophialophora immunda together with a few other species of the order Chaetothyriales show a special association with hydrocarbon polluted environments. The finding that the fungus is able to completely mineralize toluene makes it an interesting candidate for bioremediation purposes. The present study is the first transcriptomic investigation of a fungus grown in presence of toluene as sole carbon and energy source. We could observe the activation of genes involved in toluene degradatation and several stress response mechanisms which allowed the fungus to survive the toluene exposure. The thorough comparative genomics analysis allowed us to identify several events of horizontal gene transfer between bacteria and Cladophialophora immunda and unveil toluene degradation steps that were previously reported in bacteria. The work presented here aims to give new insights into the ecology of Cladophialophora immunda and its adaptation strategies to hydrocarbon polluted environments.}, } @article {pmid28900198, year = {2017}, author = {Wu, X and Zhang, H and Chen, J and Shang, S and Yan, J and Chen, Y and Tang, X and Zhang, H}, title = {Analysis and comparison of the wolf microbiome under different environmental factors using three different data of Next Generation Sequencing.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {11332}, pmid = {28900198}, issn = {2045-2322}, mesh = {Animals ; Biodiversity ; Computational Biology/methods ; Dogs ; *Environment ; Feces/microbiology ; Gastrointestinal Microbiome ; High-Throughput Nucleotide Sequencing ; Metagenome ; Metagenomics/methods ; *Microbiota ; Phylogeny ; *Wolves ; }, abstract = {Next Generation Sequencing has been widely used to characterize the prevalence of fecal bacteria in many different species. In this study, we attempted to employ a low-cost and high-throughput sequencing model to discern information pertaining to the wolf microbiota. It is hoped that this model will allow researchers to elucidate potential protective factors in relation to endangered wolf species. We propose three high-throughput sequencing models to reveal information pertaining to the micro-ecology of the wolf. Our analyses advised that, among the three models, more than 100,000 sequences are more appropriate to retrieve the communities' richness and diversity of micro-ecology. In addition, the top five wolf microbiome OTUs (99%) were members of the following five phyla: Bacteroidetes, Fusobacteria, Firmicutes, Proteobacteria, and Actinobacteria. While Alloprevotella, Clostridium_sensu_stricto_1, Anaerobiospirillum, Faecalibactreium and Streptococcus were shared by all samples, their relative abundances were differentially represented between domestic dogs and other wolves. Our findings suggest that altitude, human interference, age, and climate all contribute towards the micro-ecology of the wolf. Specifically, we observed that genera Succinivibrio and Turicibacter are significantly related to altitude and human interference (including hunting practices).}, } @article {pmid28899362, year = {2017}, author = {Cha, S and Hong, ST and Lee, YH and Lee, KH and Cho, DS and Lee, J and Chai, JY and Elhag, MS and Khaled, SGA and Elnimeiri, MKM and Siddig, NAA and Abdelrazig, H and Awadelkareem, S and Elshafie, ATE and Ismail, HAHA and Amin, M}, title = {Nationwide cross-sectional survey of schistosomiasis and soil-transmitted helminthiasis in Sudan: study protocol.}, journal = {BMC public health}, volume = {17}, number = {1}, pages = {703}, pmid = {28899362}, issn = {1471-2458}, mesh = {Adolescent ; Child ; Cross-Sectional Studies ; Feces/parasitology ; Female ; Health Surveys ; Helminthiasis/*epidemiology/prevention & control ; Humans ; Male ; Prevalence ; Schistosomiasis/*epidemiology/prevention & control ; Schools ; Soil/parasitology ; Students/statistics & numerical data ; Sudan/epidemiology ; Urine/parasitology ; }, abstract = {BACKGROUND: Schistosomiasis and soil-transmitted helminthiasis (STHs) are target neglected tropical diseases (NTDs) of preventive chemotherapy, but the control and elimination of these diseases have been impeded due to resource constraints. Few reports have described study protocol to draw on when conducting a nationwide survey. We present a detailed methodological description of the integrated mapping of schistosomiasis and STHs on the basis of our experiences, hoping that this protocol can be applied to future surveys in similar settings. In addition to determining the ecological zones requiring mass drug administration interventions, we aim to provide precise estimates of the prevalence of these diseases.

METHODS: A school-based cross-sectional design will be applied for the nationwide survey across Sudan. The survey is designed to cover all districts in every state. We have divided each district into 3 different ecological zones depending on proximity to bodies of water. We will employ a probability-proportional-to-size sampling method for schools and systematic sampling for student selection to provide adequate data regarding the prevalence for schistosomiasis and STHs in Sudan at the state level. A total of 108,660 students will be selected from 1811 schools across Sudan. After the survey is completed, 391 ecological zones will be mapped out. To carry out the survey, 655 staff members were recruited. The feces and urine samples are microscopically examined by the Kato-Katz method and the sediment smears for helminth eggs respectively. For quality control, a minimum of 10% of the slides will be rechecked by the federal supervisors in each state and also 5% of the smears are validated again within one day by independent supervisors.

DISCUSSION: This nationwide mapping is expected to generate important epidemiological information and indicators about schistosomiasis and STHs that will be useful for monitoring and evaluating the control program. The mapping data will also be used for overviewing the status and policy formulation and updates to the control strategies. This paper, which describes a feasible and practical study protocol, is to be shared with the global health community, especially those who are planning to perform nationwide mapping of NTDs by feces or urine sampling.}, } @article {pmid28893992, year = {2017}, author = {Davis, TH}, title = {Profile of Daniel H. Janzen.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {114}, number = {39}, pages = {10300-10302}, pmid = {28893992}, issn = {1091-6490}, mesh = {Acacia/*physiology ; *Conservation of Natural Resources ; Databases, Factual ; *Ecology ; Forests ; History, 20th Century ; Symbiosis/*physiology ; }, } @article {pmid28893204, year = {2017}, author = {Wang, X and Jin, Y}, title = {Predicted networks of protein-protein interactions in Stegodyphus mimosarum by cross-species comparisons.}, journal = {BMC genomics}, volume = {18}, number = {1}, pages = {716}, pmid = {28893204}, issn = {1471-2164}, mesh = {Animals ; Arachnida/genetics/*metabolism ; Arthropod Proteins/genetics/*metabolism ; Databases, Protein ; Gene Ontology ; *Protein Interaction Mapping ; RNA Splicing ; Species Specificity ; }, abstract = {BACKGROUND: Stegodyphus mimosarum is a candidate model organism belonging to the class Arachnida in the phylum Arthropoda. Studies on the biology of S. mimosarum over the past several decades have consisted of behavioral research and comparison of gene sequences based on the assembled genome sequence. Given the lack of systematic protein analyses and the rich source of information in the genome, we predicted the relationships of proteins in S. mimosarum by bioinformatics comparison with genome-wide proteins from select model organisms using gene mapping.

RESULTS: The protein-protein interactions (PPIs) of 11 organisms were integrated from four databases (BioGrid, InAct, MINT, and DIP). Here, we present comprehensive prediction and analysis of 3810 proteins in S. mimosarum with regard to interactions between proteins using PPI data of organisms. Interestingly, a portion of the protein interactions conserved among Saccharomyces cerevisiae, Homo sapiens, Arabidopsis thaliana, and Drosophila melanogaster were found to be associated with RNA splicing. In addition, overlap of predicted PPIs in reference organisms, Gene Ontology, and topology models in S. mimosarum are also reported.

CONCLUSIONS: Addition of Stegodyphus, a spider representative of interactomic research, provides the possibility of obtaining deeper insights into the evolution of PPI networks among different animal species. This work largely supports the utility of the "stratus clouds" model for predicted PPIs, providing a roadmap for integrative systems biology in S. mimosarum.}, } @article {pmid28892487, year = {2017}, author = {Ereskovsky, AV and Richter, DJ and Lavrov, DV and Schippers, KJ and Nichols, SA}, title = {Transcriptome sequencing and delimitation of sympatric Oscarella species (O. carmela and O. pearsei sp. nov) from California, USA.}, journal = {PloS one}, volume = {12}, number = {9}, pages = {e0183002}, pmid = {28892487}, issn = {1932-6203}, mesh = {Animals ; California ; Computational Biology/methods ; DNA Barcoding, Taxonomic ; Gene Expression Profiling ; Genome, Mitochondrial ; *High-Throughput Nucleotide Sequencing ; Phylogeny ; Porifera/classification/*genetics ; Sympatry/*genetics ; *Transcriptome ; }, abstract = {The homoscleromorph sponge Oscarella carmela, first described from central California, USA is shown to represent two superficially similar but both morphologically and phylogenetically distinct species that are co-distributed. We here describe a new species as Oscarella pearsei, sp. nov. and re-describe Oscarella carmela; the original description was based upon material from both species. Further, we correct the identification of published genomic/transcriptomic resources that were originally attributed to O. carmela, and present new Illumina-sequenced transcriptome assemblies for each of these species, and the mitochondrial genome sequence for O. pearsei sp. nov. Using SSU and LSU ribosomal DNA and the mitochondrial genome, we report the phylogenetic relationships of these species relative to other Oscarella species, and find strong support for the placement of O. pearsei sp. nov. in a distinct clade within genus Oscarella defined by the presence of spherulous cells that contain paracrystalline inclusions; O. carmela lacks this cell type. Oscarella pearsei sp. nov and O. carmela can be tentatively distinguished based upon gross morphological differences such as color, surface texture and extent of mucus production, but can be more reliably identified using mitochondrial and nuclear barcode sequencing, ultrastructural characteristics of cells in the mesohyl, and the morphology of the follicle epithelium which surrounds the developing embryo in reproductively active individuals.}, } @article {pmid28889179, year = {2018}, author = {Unger, J and Skarbit, N and Gál, T}, title = {Evaluation of outdoor human thermal sensation of local climate zones based on long-term database.}, journal = {International journal of biometeorology}, volume = {62}, number = {2}, pages = {183-193}, pmid = {28889179}, issn = {1432-1254}, support = {OTKA K-111768//Országos Tudományos Kutatási Alapprogramok/ ; OTKA K-111768//Országos Tudományos Kutatási Alapprogramok/ ; OTKA K-111768//Országos Tudományos Kutatási Alapprogramok/ ; ÚNKP-16-4//Emberi Eroforrások Minisztériuma/ ; }, mesh = {Cities ; *Climate ; Databases, Factual ; Humans ; Hungary ; Seasons ; Temperature ; *Thermosensing ; }, abstract = {This study gives a comprehensive picture on the diurnal and seasonal general outdoor human thermal sensation levels in different urban quarters based on long-term (almost 3 years) data series from urban and rural areas of Szeged, Hungary. It is supplemented with a case study dealing with an extreme heat wave period which is more and more frequent in the last decades in the study area. The intra-urban comparison is based on a thermal aspect classification of the surface, namely, the local climate zone (LCZ) system, on an urban meteorological station network and on the utilization of the physiologically equivalent temperature (PET) comfort index with categories calibrated to the local population. The selected stations represent sunlit areas well inside the LCZ areas. The results show that the seasonal and annual average magnitudes of the thermal load exerted by LCZs in the afternoon and evening follow their LCZ numbers. It is perfectly in line with the LCZ concept originally concentrating only on air temperature (T air) differences between the zones. Our results justified the subdivision of urban areas into LCZs and give significant support to the application possibilities of the LCZ concept as a broader term covering different thermal phenomena.}, } @article {pmid28886108, year = {2017}, author = {Lorant, A and Pedersen, S and Holst, I and Hufford, MB and Winter, K and Piperno, D and Ross-Ibarra, J}, title = {The potential role of genetic assimilation during maize domestication.}, journal = {PloS one}, volume = {12}, number = {9}, pages = {e0184202}, pmid = {28886108}, issn = {1932-6203}, mesh = {Computational Biology/methods ; Crops, Agricultural ; *Domestication ; Environment ; Gene Expression Profiling ; Gene Ontology ; *Selection, Genetic ; Zea mays/*genetics ; }, abstract = {Domestication research has largely focused on identification of morphological and genetic differences between extant populations of crops and their wild relatives. Little attention has been paid to the potential effects of environment despite substantial known changes in climate from the time of domestication to modern day. In recent research, the exposure of teosinte (i.e., wild maize) to environments similar to the time of domestication, resulted in a plastic induction of domesticated phenotypes in teosinte. These results suggest that early agriculturalists may have selected for genetic mechanisms that cemented domestication phenotypes initially induced by a plastic response of teosinte to environment, a process known as genetic assimilation. To better understand this phenomenon and the potential role of environment in maize domestication, we examined differential gene expression in maize (Zea mays ssp. mays) and teosinte (Zea mays ssp. parviglumis) between past and present conditions. We identified a gene set of over 2000 loci showing a change in expression across environmental conditions in teosinte and invariance in maize. In fact, overall we observed both greater plasticity in gene expression and more substantial changes in co-expressionnal networks in teosinte across environments when compared to maize. While these results suggest genetic assimilation played at least some role in domestication, genes showing expression patterns consistent with assimilation are not significantly enriched for previously identified domestication candidates, indicating assimilation did not have a genome-wide effect.}, } @article {pmid28886010, year = {2017}, author = {Joshi, J and Couzin, ID and Levin, SA and Guttal, V}, title = {Mobility can promote the evolution of cooperation via emergent self-assortment dynamics.}, journal = {PLoS computational biology}, volume = {13}, number = {9}, pages = {e1005732}, pmid = {28886010}, issn = {1553-7358}, mesh = {Animals ; *Biological Evolution ; Cell Movement ; Computational Biology ; *Cooperative Behavior ; Locomotion ; *Models, Biological ; Selection, Genetic ; }, abstract = {The evolution of costly cooperation, where cooperators pay a personal cost to benefit others, requires that cooperators interact more frequently with other cooperators. This condition, called positive assortment, is known to occur in spatially-structured viscous populations, where individuals typically have low mobility and limited dispersal. However many social organisms across taxa, from cells and bacteria, to birds, fish and ungulates, are mobile, and live in populations with considerable inter-group mixing. In the absence of information regarding others' traits or conditional strategies, such mixing may inhibit assortment and limit the potential for cooperation to evolve. Here we employ spatially-explicit individual-based evolutionary simulations to incorporate costs and benefits of two coevolving costly traits: cooperative and local cohesive tendencies. We demonstrate that, despite possessing no information about others' traits or payoffs, mobility (via self-propulsion or environmental forcing) facilitates assortment of cooperators via a dynamically evolving difference in the cohesive tendencies of cooperators and defectors. We show analytically that this assortment can also be viewed in a multilevel selection framework, where selection for cooperation among emergent groups can overcome selection against cooperators within the groups. As a result of these dynamics, we find an oscillatory pattern of cooperation and defection that maintains cooperation even in the absence of well known mechanisms such as kin interactions, reciprocity, local dispersal or conditional strategies that require information on others' strategies or payoffs. Our results offer insights into differential adhesion based mechanisms for positive assortment and reveal the possibility of cooperative aggregations in dynamic fission-fusion populations.}, } @article {pmid28884018, year = {2017}, author = {Wu, CG and Chen, H and Guo, F and Yadav, VK and Mcilwain, SJ and Rowse, M and Choudhary, A and Lin, Z and Li, Y and Gu, T and Zheng, A and Xu, Q and Lee, W and Resch, E and Johnson, B and Day, J and Ge, Y and Ong, IM and Burkard, ME and Ivarsson, Y and Xing, Y}, title = {PP2A-B' holoenzyme substrate recognition, regulation and role in cytokinesis.}, journal = {Cell discovery}, volume = {3}, number = {}, pages = {17027}, pmid = {28884018}, issn = {2056-5968}, support = {R01 GM117058/GM/NIGMS NIH HHS/United States ; P30 CA014520/CA/NCI NIH HHS/United States ; T32 CA157322/CA/NCI NIH HHS/United States ; S10 OD018475/OD/NIH HHS/United States ; R01 GM096060/GM/NIGMS NIH HHS/United States ; }, abstract = {Protein phosphatase 2A (PP2A) is a major Ser/Thr phosphatase; it forms diverse heterotrimeric holoenzymes that counteract kinase actions. Using a peptidome that tiles the disordered regions of the human proteome, we identified proteins containing [LMFI]xx[ILV]xEx motifs that serve as interaction sites for B'-family PP2A regulatory subunits and holoenzymes. The B'-binding motifs have important roles in substrate recognition and in competitive inhibition of substrate binding. With more than 100 novel ligands identified, we confirmed that the recently identified LxxIxEx B'α-binding motifs serve as common binding sites for B' subunits with minor variations, and that S/T phosphorylation or D/E residues at positions 2, 7, 8 and 9 of the motifs reinforce interactions. Hundreds of proteins in the human proteome harbor intrinsic or phosphorylation-responsive B'-interaction motifs, and localize at distinct cellular organelles, such as midbody, predicting kinase-facilitated recruitment of PP2A-B' holoenzymes for tight spatiotemporal control of phosphorylation at mitosis and cytokinesis. Moroever, Polo-like kinase 1-mediated phosphorylation of Cyk4/RACGAP1, a centralspindlin component at the midbody, facilitates binding of both RhoA guanine nucleotide exchange factor (epithelial cell transforming sequence 2 (Ect2)) and PP2A-B' that in turn dephosphorylates Cyk4 and disrupts Ect2 binding. This feedback signaling loop precisely controls RhoA activation and specifies a restricted region for cleavage furrow ingression. Our results provide a framework for further investigation of diverse signaling circuits formed by PP2A-B' holoenzymes in various cellular processes.}, } @article {pmid28881939, year = {2017}, author = {Brainerd, EL and Blob, RW and Hedrick, TL and Creamer, AT and Müller, UK}, title = {Data Management Rubric for Video Data in Organismal Biology.}, journal = {Integrative and comparative biology}, volume = {57}, number = {1}, pages = {33-47}, pmid = {28881939}, issn = {1557-7023}, mesh = {Animals ; Biology/*methods/standards ; *Databases, Factual ; Video Recording/*standards ; }, abstract = {Standards-based data management facilitates data preservation, discoverability, and access for effective data reuse within research groups and across communities of researchers. Data sharing requires community consensus on standards for data management, such as storage and formats for digital data preservation, metadata (i.e., contextual data about the data) that should be recorded and stored, and data access. Video imaging is a valuable tool for measuring time-varying phenotypes in organismal biology, with particular application for research in functional morphology, comparative biomechanics, and animal behavior. The raw data are the videos, but videos alone are not sufficient for scientific analysis. Nearly endless videos of animals can be found on YouTube and elsewhere on the web, but these videos have little value for scientific analysis because essential metadata such as true frame rate, spatial calibration, genus and species, weight, age, etc. of organisms, are generally unknown. We have embarked on a project to build community consensus on video data management and metadata standards for organismal biology research. We collected input from colleagues at early stages, organized an open workshop, "Establishing Standards for Video Data Management," at the Society for Integrative and Comparative Biology meeting in January 2017, and then collected two more rounds of input on revised versions of the standards. The result we present here is a rubric consisting of nine standards for video data management, with three levels within each standard: good, better, and best practices. The nine standards are: (1) data storage; (2) video file formats; (3) metadata linkage; (4) video data and metadata access; (5) contact information and acceptable use; (6) camera settings; (7) organism(s); (8) recording conditions; and (9) subject matter/topic. The first four standards address data preservation and interoperability for sharing, whereas standards 5-9 establish minimum metadata standards for organismal biology video, and suggest additional metadata that may be useful for some studies. This rubric was developed with substantial input from researchers and students, but still should be viewed as a living document that should be further refined and updated as technology and research practices change. The audience for these standards includes researchers, journals, and granting agencies, and also the developers and curators of databases that may contribute to video data sharing efforts. We offer this project as an example of building community consensus for data management, preservation, and sharing standards, which may be useful for future efforts by the organismal biology research community.}, } @article {pmid28881167, year = {2018}, author = {Belibasakis, GN and Curtis, MA and Hajishengallis, G and Zaura, E}, title = {Meeting report: The 12[th] European oral microbiology workshop (EOMW) in Stockholm, Sweden.}, journal = {Virulence}, volume = {9}, number = {1}, pages = {64-69}, pmid = {28881167}, issn = {2150-5608}, mesh = {Anti-Infective Agents/therapeutic use ; Computational Biology ; Dysbiosis ; Host-Pathogen Interactions ; Humans ; Microbiota ; Mouth/*microbiology ; Mouth Diseases/*microbiology/therapy ; Nanotechnology ; Phage Therapy ; Tooth Diseases/*microbiology/therapy ; }, } @article {pmid28877168, year = {2017}, author = {Saunders, MI and Bode, M and Atkinson, S and Klein, CJ and Metaxas, A and Beher, J and Beger, M and Mills, M and Giakoumi, S and Tulloch, V and Possingham, HP}, title = {Simple rules can guide whether land- or ocean-based conservation will best benefit marine ecosystems.}, journal = {PLoS biology}, volume = {15}, number = {9}, pages = {e2001886}, pmid = {28877168}, issn = {1545-7885}, mesh = {Algorithms ; *Aquatic Organisms ; Conservation of Natural Resources/*economics ; Cost-Benefit Analysis/*methods ; Decision Support Techniques ; *Ecosystem ; Queensland ; Water Pollution/*economics ; }, abstract = {Coastal marine ecosystems can be managed by actions undertaken both on the land and in the ocean. Quantifying and comparing the costs and benefits of actions in both realms is therefore necessary for efficient management. Here, we quantify the link between terrestrial sediment runoff and a downstream coastal marine ecosystem and contrast the cost-effectiveness of marine- and land-based conservation actions. We use a dynamic land- and sea-scape model to determine whether limited funds should be directed to 1 of 4 alternative conservation actions-protection on land, protection in the ocean, restoration on land, or restoration in the ocean-to maximise the extent of light-dependent marine benthic habitats across decadal timescales. We apply the model to a case study for a seagrass meadow in Australia. We find that marine restoration is the most cost-effective action over decadal timescales in this system, based on a conservative estimate of the rate at which seagrass can expand into a new habitat. The optimal decision will vary in different social-ecological contexts, but some basic information can guide optimal investments to counteract land- and ocean-based stressors: (1) marine restoration should be prioritised if the rates of marine ecosystem decline and expansion are similar and low; (2) marine protection should take precedence if the rate of marine ecosystem decline is high or if the adjacent catchment is relatively intact and has a low rate of vegetation decline; (3) land-based actions are optimal when the ratio of marine ecosystem expansion to decline is greater than 1:1.4, with terrestrial restoration typically the most cost-effective action; and (4) land protection should be prioritised if the catchment is relatively intact but the rate of vegetation decline is high. These rules of thumb illustrate how cost-effective conservation outcomes for connected land-ocean systems can proceed without complex modelling.}, } @article {pmid28877031, year = {2017}, author = {Zhang, G and Feenstra, B and Bacelis, J and Liu, X and Muglia, LM and Juodakis, J and Miller, DE and Litterman, N and Jiang, PP and Russell, L and Hinds, DA and Hu, Y and Weirauch, MT and Chen, X and Chavan, AR and Wagner, GP and Pavličev, M and Nnamani, MC and Maziarz, J and Karjalainen, MK and Rämet, M and Sengpiel, V and Geller, F and Boyd, HA and Palotie, A and Momany, A and Bedell, B and Ryckman, KK and Huusko, JM and Forney, CR and Kottyan, LC and Hallman, M and Teramo, K and Nohr, EA and Davey Smith, G and Melbye, M and Jacobsson, B and Muglia, LJ}, title = {Genetic Associations with Gestational Duration and Spontaneous Preterm Birth.}, journal = {The New England journal of medicine}, volume = {377}, number = {12}, pages = {1156-1167}, pmid = {28877031}, issn = {1533-4406}, support = {U01 HG004446/HG/NHGRI NIH HHS/United States ; R01 DK107502/DK/NIDDK NIH HHS/United States ; MC_UU_12013/1/MRC_/Medical Research Council/United Kingdom ; U01 NS047537/NS/NINDS NIH HHS/United States ; N01ES75558/ES/NIEHS NIH HHS/United States ; T32 GM108540/GM/NIGMS NIH HHS/United States ; P30 AR070549/AR/NIAMS NIH HHS/United States ; U01 HG004423/HG/NHGRI NIH HHS/United States ; EP-C-15-003/EPA/EPA/United States ; /WT_/Wellcome Trust/United Kingdom ; }, mesh = {Adenylyl Cyclases/genetics ; Datasets as Topic ; Female ; *Genetic Predisposition to Disease ; *Genetic Variation ; Genome-Wide Association Study ; *Gestational Age ; Humans ; Peptide Elongation Factors/*genetics ; Phenotype ; Polymorphism, Single Nucleotide ; Pregnancy ; Premature Birth/*genetics ; Receptor, Angiotensin, Type 2/*genetics ; Regression Analysis ; Trans-Activators/*genetics ; Wnt4 Protein/genetics ; ras Proteins/genetics ; }, abstract = {BACKGROUND: Despite evidence that genetic factors contribute to the duration of gestation and the risk of preterm birth, robust associations with genetic variants have not been identified. We used large data sets that included the gestational duration to determine possible genetic associations.

METHODS: We performed a genomewide association study in a discovery set of samples obtained from 43,568 women of European ancestry using gestational duration as a continuous trait and term or preterm (<37 weeks) birth as a dichotomous outcome. We used samples from three Nordic data sets (involving a total of 8643 women) to test for replication of genomic loci that had significant genomewide association (P<5.0×10[-8]) or an association with suggestive significance (P<1.0×10[-6]) in the discovery set.

RESULTS: In the discovery and replication data sets, four loci (EBF1, EEFSEC, AGTR2, and WNT4) were significantly associated with gestational duration. Functional analysis showed that an implicated variant in WNT4 alters the binding of the estrogen receptor. The association between variants in ADCY5 and RAP2C and gestational duration had suggestive significance in the discovery set and significant evidence of association in the replication sets; these variants also showed genomewide significance in a joint analysis. Common variants in EBF1, EEFSEC, and AGTR2 showed association with preterm birth with genomewide significance. An analysis of mother-infant dyads suggested that these variants act at the level of the maternal genome.

CONCLUSIONS: In this genomewide association study, we found that variants at the EBF1, EEFSEC, AGTR2, WNT4, ADCY5, and RAP2C loci were associated with gestational duration and variants at the EBF1, EEFSEC, and AGTR2 loci with preterm birth. Previously established roles of these genes in uterine development, maternal nutrition, and vascular control support their mechanistic involvement. (Funded by the March of Dimes and others.).}, } @article {pmid28875229, year = {2018}, author = {Harrigan, KM and Moore, PA}, title = {Scaling to the Organism: An Innovative Model of Dynamic Exposure Hotspots in Stream Systems.}, journal = {Archives of environmental contamination and toxicology}, volume = {74}, number = {3}, pages = {372-394}, doi = {10.1007/s00244-017-0444-3}, pmid = {28875229}, issn = {1432-0703}, mesh = {Dopamine/analysis ; Ecosystem ; Ecotoxicology/*methods ; Environmental Exposure/*analysis ; Geographic Information Systems ; Groundwater/chemistry ; Models, Theoretical ; Rivers/chemistry ; Water Pollutants, Chemical/*analysis/toxicity ; Water Quality ; }, abstract = {In flowing systems, fluctuations in the frequency, magnitude, and duration of exposure occurs due to turbulence and geomorphology, causing spatial and temporal variations in chemical exposure at the scale of the organism. Spatial models representing toxicant distribution at the appropriate scales of stream organisms are noticeably missing from the literature. To characterize the fine scale distribution of pollutants in freshwater streams at the scale of a benthic organism, nine artificial stream habitats were created (riffle, pool, run, bend, woody debris) with either sand or gravel substrate. Dopamine was released as a chemical tracer, mimicking a groundwater source, and measurements were recorded with a microelectrode and Epsilon electrochemical recording system. Proxies for the frequency, magnitude, and duration of chemical exposure were extracted. Geographic information systems and an inverse distance weight interpolation technique were used to predict spatially the chemical distribution throughout the habitats. Spatial and temporal variations of exposure were exhibited within and across habitats, indicating that the frequency, magnitude, and duration of exposure is influenced by the organism's location within a habitat and the habitat it resides in. The run and pool with sand substrate contained the greatest frequency, magnitude, and duration of exposure, suggesting a more detrimental exposure compared to other habitats. Differences in peak heights within and across habitats are orders of magnitude in value. Spatial and temporal fluctuations of fine scale exposure need to be considered in both ecotoxicology and water quality modeling to represent and understand the exposure of pollutants impacting benthic organisms.}, } @article {pmid28874710, year = {2017}, author = {Hu, M and Qu, X and Pan, L and Fu, C and Jia, P and Liu, Q and Wang, Y}, title = {Effects of toxic Microcystis aeruginosa on the silver carp Hypophthalmichtys molitrix revealed by hepatic RNA-seq and miRNA-seq.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {10456}, pmid = {28874710}, issn = {2045-2322}, mesh = {Animals ; Bacterial Toxins ; Carps/*genetics/*microbiology ; Computational Biology/methods ; Fish Diseases/*genetics/*microbiology ; Gene Expression Profiling ; Gene Expression Regulation ; High-Throughput Nucleotide Sequencing ; Liver/*metabolism ; MicroRNAs/genetics ; Microcystis/*physiology ; Molecular Sequence Annotation ; Sequence Analysis, RNA ; Transcriptome ; }, abstract = {High-throughput sequencing was applied to analyze the effects of toxic Microcystis aeruginosa on the silver carp Hypophthalmichthys molitrix. Silver carps were exposed to two cyanobacteria species (toxic and non-toxic) for RNA-seq and miRNA-seq analysis. RNA-seq revealed that the liver tissue contained 105,379 unigenes. Of these genes, 143 were significantly differentiated, 82 were markedly up-regulated, and 61 were remarkably down-regulated. GO term enrichment analysis indicated that 35 of the 154 enriched GO terms were significantly enriched. KEGG pathway enrichment analysis demonstrated that 17 of the 118 enriched KEGG pathways were significantly enriched. A considerable number of disease/immune-associated GO terms and significantly enriched KEGG pathways were also observed. The sequence length determined by miRNA-seq was mainly distributed in 20-23 bp and composed of 882,620 unique small RNAs, and 53% of these RNAs were annotated to miRNAs. As confirmed, 272 known miRNAs were differentially expressed, 453 novel miRNAs were predicted, 112 miRNAs were well matched with 7,623 target genes, and 203 novel miRNAs were matched with 15,453 target genes. qPCR also indicated that Steap4, Cyp7a1, CABZ01088134.1, and PPP1R3G were significantly differentially expressed and might play major roles in the toxic, detoxifying, and antitoxic mechanisms of microcystin in fish.}, } @article {pmid28874057, year = {2018}, author = {Lorusso, JS and Sviderskiy, OA and Labunskyy, VM}, title = {Emerging Omics Approaches in Aging Research.}, journal = {Antioxidants & redox signaling}, volume = {29}, number = {10}, pages = {985-1002}, pmid = {28874057}, issn = {1557-7716}, support = {R00 AG040191/AG/NIA NIH HHS/United States ; R01 AG058713/AG/NIA NIH HHS/United States ; R56 AG054566/AG/NIA NIH HHS/United States ; K99 AG040191/AG/NIA NIH HHS/United States ; }, mesh = {Aging/*genetics/metabolism ; Animals ; *Biomedical Research ; *Computational Biology ; Humans ; }, abstract = {SIGNIFICANCE: Aging is a complex trait that is influenced by a combination of genetic and environmental factors. Although many cellular and physiological changes have been described to occur with aging, the precise molecular causes of aging remain unknown. Given the biological complexity and heterogeneity of the aging process, understanding the mechanisms that underlie aging requires integration of data about age-dependent changes that occur at the molecular, cellular, tissue, and organismal levels. Recent Advances: The development of high-throughput technologies such as next-generation sequencing, proteomics, metabolomics, and automated imaging techniques provides researchers with new opportunities to understand the mechanisms of aging. Using these methods, millions of biological molecules can be simultaneously monitored during the aging process with high accuracy and specificity.

CRITICAL ISSUES: Although the ability to produce big data has drastically increased over the years, integration and interpreting of high-throughput data to infer regulatory relationships between biological factors and identify causes of aging remain the major challenges. In this review, we describe recent advances and survey emerging omics approaches in aging research. We then discuss their limitations and emphasize the need for the further development of methods for the integration of different types of data.

FUTURE DIRECTIONS: Combining omics approaches and novel methods for single-cell analysis with systems biology tools would allow building interaction networks and investigate how these networks are perturbed with aging and disease states. Together, these studies are expected to provide a better understanding of the aging process and could provide insights into the pathophysiology of many age-associated human diseases. Antioxid. Redox Signal. 29, 985-1002.}, } @article {pmid28873966, year = {2017}, author = {Ahn, DH and Shin, SC and Kim, BM and Kang, S and Kim, JH and Ahn, I and Park, J and Park, H}, title = {Draft genome of the Antarctic dragonfish, Parachaenichthys charcoti.}, journal = {GigaScience}, volume = {6}, number = {8}, pages = {1-6}, pmid = {28873966}, issn = {2047-217X}, mesh = {Animals ; Antarctic Regions ; Computational Biology/methods ; Evolution, Molecular ; Fishes/classification/*genetics ; Gene Library ; Genetic Variation ; *Genome ; Genome Size ; *Genomics/methods ; High-Throughput Nucleotide Sequencing ; Molecular Sequence Annotation ; Phylogeny ; }, abstract = {The Antarctic bathydraconid dragonfish, Parachaenichthys charcoti, is an Antarctic notothenioid teleost endemic to the Southern Ocean. The Southern Ocean has cooled to -1.8ºC over the past 30 million years, and the seawater had retained this cold temperature and isolated oceanic environment because of the Antarctic Circumpolar Current. Notothenioids dominate Antarctic fish, making up 90% of the biomass, and all notothenioids have undergone molecular and ecological diversification to survive in this cold environment. Therefore, they are considered an attractive Antarctic fish model for evolutionary and ancestral genomic studies. Bathydraconidae is a speciose family of the Notothenioidei, the dominant taxonomic component of Antarctic teleosts. To understand the process of evolution of Antarctic fish, we select a typical Antarctic bathydraconid dragonfish, P. charcoti. Here, we have sequenced, de novo assembled, and annotated a comprehensive genome from P. charcoti. The draft genome of P. charcoti is 709 Mb in size. The N50 contig length is 6145 bp, and its N50 scaffold length 178 362 kb. The genome of P. charcoti is predicted to contain 32 712 genes, 18 455 of which have been assigned preliminary functions. A total of 8951 orthologous groups common to 7 species of fish were identified, while 333 genes were identified in P. charcoti only; 2519 orthologous groups were also identified in both P. charcoti and N. coriiceps, another Antarctic fish. Four gene ontology terms were statistically overrepresented among the 333 genes unique to P. charcoti, according to gene ontology enrichment analysis. The draft P. charcoti genome will broaden our understanding of the evolution of Antarctic fish in their extreme environment. It will provide a basis for further investigating the unusual characteristics of Antarctic fishes.}, } @article {pmid28873455, year = {2017}, author = {Chen, L and Zhang, YH and Wang, S and Zhang, Y and Huang, T and Cai, YD}, title = {Prediction and analysis of essential genes using the enrichments of gene ontology and KEGG pathways.}, journal = {PloS one}, volume = {12}, number = {9}, pages = {e0184129}, pmid = {28873455}, issn = {1932-6203}, mesh = {*Gene Ontology ; *Genes, Essential ; Reproducibility of Results ; Signal Transduction/*genetics ; Support Vector Machine ; }, abstract = {Identifying essential genes in a given organism is important for research on their fundamental roles in organism survival. Furthermore, if possible, uncovering the links between core functions or pathways with these essential genes will further help us obtain deep insight into the key roles of these genes. In this study, we investigated the essential and non-essential genes reported in a previous study and extracted gene ontology (GO) terms and biological pathways that are important for the determination of essential genes. Through the enrichment theory of GO and KEGG pathways, we encoded each essential/non-essential gene into a vector in which each component represented the relationship between the gene and one GO term or KEGG pathway. To analyze these relationships, the maximum relevance minimum redundancy (mRMR) was adopted. Then, the incremental feature selection (IFS) and support vector machine (SVM) were employed to extract important GO terms and KEGG pathways. A prediction model was built simultaneously using the extracted GO terms and KEGG pathways, which yielded nearly perfect performance, with a Matthews correlation coefficient of 0.951, for distinguishing essential and non-essential genes. To fully investigate the key factors influencing the fundamental roles of essential genes, the 21 most important GO terms and three KEGG pathways were analyzed in detail. In addition, several genes was provided in this study, which were predicted to be essential genes by our prediction model. We suggest that this study provides more functional and pathway information on the essential genes and provides a new way to investigate related problems.}, } @article {pmid28873454, year = {2017}, author = {Müller, M and Seifert, S and Lübbe, T and Leuschner, C and Finkeldey, R}, title = {De novo transcriptome assembly and analysis of differential gene expression in response to drought in European beech.}, journal = {PloS one}, volume = {12}, number = {9}, pages = {e0184167}, pmid = {28873454}, issn = {1932-6203}, mesh = {*Droughts ; Fagus/*genetics/*physiology ; *Gene Expression Profiling ; *Gene Expression Regulation, Plant ; Gene Ontology ; Genotype ; Microsatellite Repeats/genetics ; Molecular Sequence Annotation ; Plant Stomata/physiology ; RNA, Messenger/genetics/metabolism ; Real-Time Polymerase Chain Reaction ; Sequence Analysis, RNA ; Stress, Physiological/genetics ; Transcriptome/*genetics ; }, abstract = {Despite the ecological and economic importance of European beech (Fagus sylvatica L.) genomic resources of this species are still limited. This hampers an understanding of the molecular basis of adaptation to stress. Since beech will most likely be threatened by the consequences of climate change, an understanding of adaptive processes to climate change-related drought stress is of major importance. Here, we used RNA-seq to provide the first drought stress-related transcriptome of beech. In a drought stress trial with beech saplings, 50 samples were taken for RNA extraction at five points in time during a soil desiccation experiment. De novo transcriptome assembly and analysis of differential gene expression revealed 44,335 contigs, and 662 differentially expressed genes between the stress and normally watered control group. Gene expression was specific to the different time points, and only five genes were significantly differentially expressed between the stress and control group on all five sampling days. GO term enrichment showed that mostly genes involved in lipid- and homeostasis-related processes were upregulated, whereas genes involved in oxidative stress response were downregulated in the stressed seedlings. This study gives first insights into the genomic drought stress response of European beech, and provides new genetic resources for adaptation research in this species.}, } @article {pmid28873438, year = {2017}, author = {Musacchia, F and Vasilev, F and Borra, M and Biffali, E and Sanges, R and Santella, L and Chun, JT}, title = {De novo assembly of a transcriptome from the eggs and early embryos of Astropecten aranciacus.}, journal = {PloS one}, volume = {12}, number = {9}, pages = {e0184090}, pmid = {28873438}, issn = {1932-6203}, mesh = {Animals ; Calcium Signaling/genetics ; Cyclin-Dependent Kinases/metabolism ; Cyclins/metabolism ; Databases, Nucleic Acid ; Electron Transport Complex IV/chemistry/genetics ; Embryo, Nonmammalian/*metabolism ; Gene Expression Profiling ; Gene Expression Regulation, Developmental ; Gene Ontology ; Molecular Sequence Annotation ; Ovum/*metabolism ; Phylogeny ; RNA, Messenger/genetics/metabolism ; Real-Time Polymerase Chain Reaction ; Reproducibility of Results ; Starfish/*genetics/*metabolism ; Transcriptome/*genetics ; }, abstract = {Starfish have been instrumental in many fields of biological and ecological research. Oocytes of Astropecten aranciacus, a common species native to the Mediterranean Sea and the East Atlantic, have long been used as an experimental model to study meiotic maturation, fertilization, intracellular Ca2+ signaling, and cell cycle controls. However, investigation of the underlying molecular mechanisms has often been hampered by the overall lack of DNA or protein sequences for the species. In this study, we have assembled a transcriptome for this species from the oocytes, eggs, zygotes, and early embryos, which are known to have the highest RNA sequence complexity. Annotation of the transcriptome identified over 32,000 transcripts including the ones that encode 13 distinct cyclins and as many cyclin-dependent kinases (CDK), as well as the expected components of intracellular Ca2+ signaling toolkit. Although the mRNAs of cyclin and CDK families did not undergo significant abundance changes through the stages from oocyte to early embryo, as judged by real-time PCR, the transcript encoding Mos, a negative regulator of mitotic cell cycle, was drastically reduced during the period of rapid cleavages. Molecular phylogenetic analysis using the homologous amino acid sequences of cytochrome oxidase subunit I from A. aranciacus and 30 other starfish species indicated that Paxillosida, to which A. aranciacus belongs, is not likely to be the most basal order in Asteroidea. Taken together, the first transcriptome we assembled in this species is expected to enable us to perform comparative studies and to design gene-specific molecular tools with which to tackle long-standing biological questions.}, } @article {pmid28872632, year = {2017}, author = {Oliveira, BF and São-Pedro, VA and Santos-Barrera, G and Penone, C and Costa, GC}, title = {AmphiBIO, a global database for amphibian ecological traits.}, journal = {Scientific data}, volume = {4}, number = {}, pages = {170123}, pmid = {28872632}, issn = {2052-4463}, mesh = {*Amphibians ; Animals ; Databases, Factual ; Ecosystem ; Phylogeny ; }, abstract = {Current ecological and evolutionary research are increasingly moving from species- to trait-based approaches because traits provide a stronger link to organism's function and fitness. Trait databases covering a large number of species are becoming available, but such data remains scarce for certain groups. Amphibians are among the most diverse vertebrate groups on Earth, and constitute an abundant component of major terrestrial and freshwater ecosystems. They are also facing rapid population declines worldwide, which is likely to affect trait composition in local communities, thereby impacting ecosystem processes and services. In this context, we introduce AmphiBIO, a comprehensive database of natural history traits for amphibians worldwide. The database releases information on 17 traits related to ecology, morphology and reproduction features of amphibians. We compiled data from more than 1,500 literature sources, and for more than 6,500 species of all orders (Anura, Caudata and Gymnophiona), 61 families and 531 genera. This database has the potential to allow unprecedented large-scale analyses in ecology, evolution, and conservation of amphibians.}, } @article {pmid28867099, year = {2018}, author = {Machackova, M and Giertlova, A and Porubska, J and Roe, M and Ramos, C and Finglas, P}, title = {EuroFIR Guideline on calculation of nutrient content of foods for food business operators.}, journal = {Food chemistry}, volume = {238}, number = {}, pages = {35-41}, doi = {10.1016/j.foodchem.2017.03.103}, pmid = {28867099}, issn = {1873-7072}, support = {BBS/E/F/00041903/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Czech Republic ; Databases, Factual ; *Food ; Food Analysis ; Food Labeling ; Humans ; Nutritive Value ; }, abstract = {This paper presents a Guideline for calculating nutrient content of foods by calculation methods for food business operators and presents data on compliance between calculated values and analytically determined values. In the EU, calculation methods are legally valid to determine the nutrient values of foods for nutrition labelling (Regulation (EU) No 1169/2011). However, neither a specific calculation method nor rules for use of retention factors are defined. EuroFIR AISBL (European Food Information Resource) has introduced a Recipe Calculation Guideline based on the EuroFIR harmonized procedure for recipe calculation. The aim is to provide food businesses with a step-by-step tool for calculating nutrient content of foods for the purpose of nutrition declaration. The development of this Guideline and use in the Czech Republic is described and future application to other Member States is discussed. Limitations of calculation methods and the importance of high quality food composition data are discussed.}, } @article {pmid28866609, year = {2017}, author = {Odgerel, CO and Takahashi, K and Sorahan, T and Driscoll, T and Fitzmaurice, C and Yoko-O, M and Sawanyawisuth, K and Furuya, S and Tanaka, F and Horie, S and Zandwijk, NV and Takala, J}, title = {Estimation of the global burden of mesothelioma deaths from incomplete national mortality data.}, journal = {Occupational and environmental medicine}, volume = {74}, number = {12}, pages = {851-858}, pmid = {28866609}, issn = {1470-7926}, mesh = {Asbestos/*adverse effects ; Databases, Factual ; Environmental Exposure/*adverse effects ; Female ; *Global Health ; Humans ; Lung Neoplasms/*mortality ; Male ; Mesothelioma/*mortality ; Mesothelioma, Malignant ; World Health Organization ; }, abstract = {BACKGROUND: Mesothelioma is increasingly recognised as a global health issue and the assessment of its global burden is warranted.

OBJECTIVES: To descriptively analyse national mortality data and to use reported and estimated data to calculate the global burden of mesothelioma deaths.

METHODS: For the study period of 1994 to 2014, we grouped 230 countries into 59 countries with quality mesothelioma mortality data suitable to be used for reference rates, 45 countries with poor quality data and 126 countries with no data, based on the availability of data in the WHO Mortality Database. To estimate global deaths, we extrapolated the gender-specific and age-specific mortality rates of the countries with quality data to all other countries.

RESULTS: The global numbers and rates of mesothelioma deaths have increased over time. The 59 countries with quality data recorded 15 011 mesothelioma deaths per year over the 3 most recent years with available data (equivalent to 9.9 deaths per million per year). From these reference data, we extrapolated the global mesothelioma deaths to be 38 400 per year, based on extrapolations for asbestos use.

CONCLUSIONS: Although the validity of our extrapolation method depends on the adequate identification of quality mesothelioma data and appropriate adjustment for other variables, our estimates can be updated, refined and verified because they are based on commonly accessible data and are derived using a straightforward algorithm. Our estimates are within the range of previously reported values but higher than the most recently reported values.}, } @article {pmid28863140, year = {2017}, author = {Mota-Vargas, C and Galindo-González, J and Rojas-Soto, OR}, title = {Crumble analysis of the historic sympatric distribution between Dendrortyx macroura and D. barbatus (Aves: Galliformes).}, journal = {PloS one}, volume = {12}, number = {9}, pages = {e0183996}, pmid = {28863140}, issn = {1932-6203}, mesh = {Algorithms ; Animals ; Biodiversity ; DNA, Mitochondrial/genetics ; Galliformes/*classification ; *Genetic Variation ; Geographic Information Systems ; Geography ; Mexico ; Models, Statistical ; Phylogeny ; ROC Curve ; Rivers ; Software ; Species Specificity ; *Sympatry ; }, abstract = {In Mexico, the Long-tailed Wood-Partridge (Dendrortyx macroura) is distributed in the mountains of the Trans-Mexican Volcanic Belt, Sierra Madre del Sur and Sierra Norte de Oaxaca; while the Bearded Wood-Partridge (D. barbatus) is distributed in the Sierra Madre Oriental (SMO). There is a controversial overlap in distribution (sympatry) between these two species (on the Cofre de Perote and Pico de Orizaba volcanoes, SMO and Sierra Norte de Oaxaca), based on the ambiguity and current lack of information regarding the distribution of these two species. In order to disentangle the possible presence of both species in the area of sympatry, we conducted a crumble analysis of the historic knowledge regarding the geographic distribution of both species, based on a review of scientific literature, database records, the specimen examination (in ornithological collections), field work and a reconstruction of the distribution range based on Ecological Niche Modeling. Our results support the presence of only one of these two species in the overlapping area, rejecting the existence of such an area of sympatry between the two species. We discuss alternative hypotheses that could explain the historically reported distribution pattern: 1) an error in the single existing historical record; 2) a possible local extinction of the species and 3) the past existence of interspecific competition that has since been resolved under the principle of competitive exclusion. We propose that the Santo Domingo River in northern Oaxaca and western slope of the Sierra Madre Oriental, mark the distribution limits between these species.}, } @article {pmid28860532, year = {2017}, author = {Subramanian, A and Sarkar, RR}, title = {Revealing the mystery of metabolic adaptations using a genome scale model of Leishmania infantum.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {10262}, pmid = {28860532}, issn = {2045-2322}, mesh = {*Adaptation, Biological ; Computational Biology ; *Energy Metabolism ; *Genome, Protozoan ; *Genomics/methods ; Intracellular Space/metabolism ; Leishmania infantum/*genetics/*metabolism ; Leishmaniasis, Visceral/*parasitology ; Life Cycle Stages ; Metabolic Networks and Pathways ; Metabolome ; Metabolomics ; Mitochondria/metabolism ; }, abstract = {Human macrophage phagolysosome and sandfly midgut provide antagonistic ecological niches for Leishmania parasites to survive and proliferate. Parasites optimize their metabolism to utilize the available inadequate resources by adapting to those environments. Lately, a number of metabolomics studies have revived the interest to understand metabolic strategies utilized by the Leishmania parasite for optimal survival within its hosts. For the first time, we propose a reconstructed genome-scale metabolic model for Leishmania infantum JPCM5, the analyses of which not only captures observations reported by metabolomics studies in other Leishmania species but also divulges novel features of the L. infantum metabolome. Our results indicate that Leishmania metabolism is organized in such a way that the parasite can select appropriate alternatives to compensate for limited external substrates. A dynamic non-essential amino acid motif exists within the network that promotes a restricted redistribution of resources to yield required essential metabolites. Further, subcellular compartments regulate this metabolic re-routing by reinforcing the physiological coupling of specific reactions. This unique metabolic organization is robust against accidental errors and provides a wide array of choices for the parasite to achieve optimal survival.}, } @article {pmid28860451, year = {2017}, author = {Zhang, H and Hollander, J and Hansson, LA}, title = {Bi-directional plasticity: Rotifer prey adjust spine length to different predator regimes.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {10254}, pmid = {28860451}, issn = {2045-2322}, mesh = {Algorithms ; Analysis of Variance ; Animals ; Databases, Factual ; *Models, Theoretical ; *Predatory Behavior ; Rotifera/*anatomy & histology ; Spine/*anatomy & histology ; }, abstract = {Numerous prey organisms, including many rotifers, exhibit inducible defensive plasticity, such as spines, in response to predators. Here, we test the hypothesis that prey modify their defence response to different predator sizes with a bi-directional adjustment in spine length. First, we show experimentally, that large-sized predators induce a reduction in prey spine length. Second, we conducted a complementary field monitoring study showing that the spine length of the prey rotifer Keratella cochlearis changed in opposite directions, in response to the shift in dominance between small-sized and large-sized predators. Third, in order to test the generality of our novel findings, we conducted a meta-analysis covering a wide array of rotifer prey taxa, strengthening the conclusions from our experimental and field studies. Hence, by combining evidence from experiments and studies in the field with a meta-analysis, we, for the first time, demonstrate that rotifer prey distinguish between predators and adjust their protective spine length accordingly, i.e. rapidly adjust spine length to escape either below or above the dominant predator's gape size window. In a broader perspective, our conclusions advance our knowledge on observed spatial and temporal variations in protective morphologies among prey organisms.}, } @article {pmid28858225, year = {2017}, author = {Demoury, C and De Smedt, T and De Schutter, H and Sonck, M and Van Damme, N and Bollaerts, K and Molenberghs, G and Van Bladel, L and Van Nieuwenhuyse, A}, title = {Thyroid Cancer Incidence around the Belgian Nuclear Sites, 2000-2014.}, journal = {International journal of environmental research and public health}, volume = {14}, number = {9}, pages = {}, pmid = {28858225}, issn = {1660-4601}, mesh = {Adolescent ; Adult ; Age Factors ; Aged ; Aged, 80 and over ; Belgium/epidemiology ; Child ; Child, Preschool ; Female ; Geography ; Humans ; Incidence ; Infant ; Infant, Newborn ; Male ; Middle Aged ; *Nuclear Power Plants ; Sex Factors ; Thyroid Neoplasms/*epidemiology/etiology ; Young Adult ; }, abstract = {The present study investigates whether there is an excess incidence of thyroid cancer among people living in the vicinity of the nuclear sites in Belgium. Adjusted Rate Ratios were obtained from Poisson regressions for proximity areas of varying sizes. In addition, focused hypothesis tests and generalized additive models were performed to test the hypothesis of a gradient in thyroid cancer incidence with increasing levels of surrogate exposures. Residential proximity to the nuclear site, prevailing dominant winds frequency from the site, and simulated radioactive discharges were used as surrogate exposures. No excess incidence of thyroid cancer was observed around the nuclear power plants of Doel or Tihange. In contrast, increases in thyroid cancer incidence were found around the nuclear sites of Mol-Dessel and Fleurus; risk ratios were borderline not significant. For Mol-Dessel, there was evidence for a gradient in thyroid cancer incidence with increased proximity, prevailing winds, and simulated radioactive discharges. For Fleurus, a gradient was observed with increasing prevailing winds and, to a lesser extent, with increasing simulated radioactive discharges. This study strengthens earlier findings and suggests increased incidences in thyroid cancer around two of the four Belgian nuclear sites. Further analyses will be performed at a more detailed geographical level.}, } @article {pmid28854615, year = {2017}, author = {Mak, SST and Gopalakrishnan, S and Carøe, C and Geng, C and Liu, S and Sinding, MS and Kuderna, LFK and Zhang, W and Fu, S and Vieira, FG and Germonpré, M and Bocherens, H and Fedorov, S and Petersen, B and Sicheritz-Pontén, T and Marques-Bonet, T and Zhang, G and Jiang, H and Gilbert, MTP}, title = {Comparative performance of the BGISEQ-500 vs Illumina HiSeq2500 sequencing platforms for palaeogenomic sequencing.}, journal = {GigaScience}, volume = {6}, number = {8}, pages = {1-13}, pmid = {28854615}, issn = {2047-217X}, support = {681396/ERC_/European Research Council/International ; U01 MH106874/MH/NIMH NIH HHS/United States ; }, mesh = {Animals ; Base Composition ; DNA/chemistry ; DNA, Mitochondrial/chemistry ; Genomics/*methods/*standards ; High-Throughput Nucleotide Sequencing/*methods/*standards ; Reproducibility of Results ; Sequence Analysis, DNA ; }, abstract = {Ancient DNA research has been revolutionized following development of next-generation sequencing platforms. Although a number of such platforms have been applied to ancient DNA samples, the Illumina series are the dominant choice today, mainly because of high production capacities and short read production. Recently a potentially attractive alternative platform for palaeogenomic data generation has been developed, the BGISEQ-500, whose sequence output are comparable with the Illumina series. In this study, we modified the standard BGISEQ-500 library preparation specifically for use on degraded DNA, then directly compared the sequencing performance and data quality of the BGISEQ-500 to the Illumina HiSeq2500 platform on DNA extracted from 8 historic and ancient dog and wolf samples. The data generated were largely comparable between sequencing platforms, with no statistically significant difference observed for parameters including level (P = 0.371) and average sequence length (P = 0718) of endogenous nuclear DNA, sequence GC content (P = 0.311), double-stranded DNA damage rate (v. 0.309), and sequence clonality (P = 0.093). Small significant differences were found in single-strand DNA damage rate (δS; slightly lower for the BGISEQ-500, P = 0.011) and the background rate of difference from the reference genome (θ; slightly higher for BGISEQ-500, P = 0.012). This may result from the differences in amplification cycles used to polymerase chain reaction-amplify the libraries. A significant difference was also observed in the mitochondrial DNA percentages recovered (P = 0.018), although we believe this is likely a stochastic effect relating to the extremely low levels of mitochondria that were sequenced from 3 of the samples with overall very low levels of endogenous DNA. Although we acknowledge that our analyses were limited to animal material, our observations suggest that the BGISEQ-500 holds the potential to represent a valid and potentially valuable alternative platform for palaeogenomic data generation that is worthy of future exploration by those interested in the sequencing and analysis of degraded DNA.}, } @article {pmid28852870, year = {2017}, author = {Tumolo, BB and Flinn, MB}, title = {Top-down effects of an invasive omnivore: detection in long-term monitoring of large-river reservoir chlorophyll-a.}, journal = {Oecologia}, volume = {185}, number = {2}, pages = {293-303}, pmid = {28852870}, issn = {1432-1939}, support = {F13AP00999//U.S. Fish and Wildlife Service/ ; }, mesh = {Animals ; Carps/*physiology ; Chlorophyll/*analysis ; Chlorophyll A ; Databases, Factual ; *Food Chain ; *Introduced Species ; Kentucky ; *Lakes ; Phytoplankton/chemistry/growth & development ; *Rivers ; }, abstract = {Invasive species are capable of altering ecosystems through the consumption of basal resources. However, quantifying the effects of invasive species in large ecosystems is challenging. Measuring changes in basal resources (i.e., phytoplankton) at an ecosystem scale is an important and potentially translatable response vital to the understanding of how introduced species influence ecosystems. In this study, we analyzed patterns of early summer chlorophyll-a in a large-river reservoir in response to invasion of silver carp (Hypophthalmichthys molitrix). We used 25 years of ecological data from a 30-km reach of Kentucky Lake collected before and after silver carp establishment. We found significant decreases in chlorophyll-a within certain reservoir habitats since establishment of silver carp. Additionally, environmental and biological drivers of phytoplankton production showed no significant differences before and after invasion. These results suggest seasonal, and habitat-specific consumptive effects of invasive silver carp on an important basal food web resource. Further, our results convey the utility of long-term quantitative biological and physiochemical data in understanding ecosystem responses to elements of global change (i.e., species invasions). Importantly, the observed changes in the basal food web resource of Kentucky Lake may apply to other ecosystems facing invasion by silver carp (e.g., Laurentian Great Lakes). Our study offers insight into the mechanisms by which silver carp may influence ecosystems and furthers our understanding of invasive omnivores.}, } @article {pmid28846157, year = {2017}, author = {Meincke, R and Pokladnikova, J and Straznicka, J and Meyboom, RHB and Niedrig, D and Russmann, S and Jahodar, L}, title = {Allergy-like immediate reactions with herbal medicines in children: A retrospective study using data from VigiBase[®].}, journal = {Pediatric allergy and immunology : official publication of the European Society of Pediatric Allergy and Immunology}, volume = {28}, number = {7}, pages = {668-674}, doi = {10.1111/pai.12778}, pmid = {28846157}, issn = {1399-3038}, mesh = {Adolescent ; Child ; Child, Preschool ; Databases, Factual ; Drug Hypersensitivity/*epidemiology ; Drug-Related Side Effects and Adverse Reactions/*epidemiology ; Female ; Herbal Medicine/*statistics & numerical data ; Humans ; Infant ; Male ; Retrospective Studies ; }, abstract = {BACKGROUND: The use of herbal medicines in children and the general population is continually on the rise with an overall herbal lifetime and current use ranging between 0.8%-85.5% and 2.2%-8.9%, respectively. Although acute hypersensitivity reactions are generally considered to be rare, little knowledge exists on the frequency and type of these reactions especially in specific populations like children.

OBJECTIVES: To assess the patterns of acute hypersensitivity reactions to herbal medicines reported to the WHO global individual case safety report (ICSR) database VigiBase[®] in children.

STUDY DESIGN: From the original VigiBase[®] extract for the time between 1968 and 2014, we included all reports with adverse drug reactions (ADR) associated with herbal medicines in children where WHO-ART reaction terms were indicative of acute hypersensitivity reactions.

RESULTS: VigiBase[®] contained 2646 ICSRs with 14 860 distinct adverse reactions reported in association with herbal medicine in children. Among those, 79 cases with 107 allergy-like reactions met our inclusion criteria. The most commonly reported WHO-ART terms were urticaria or rash/rash erythematous (59.8%), and allergic reaction (8.4%). The most frequently reported suspected herbal medicines were mixed herbal products (51.4%), Hedera helix (15.0%), and Echinacea purpurea (5.6%). Most frequent routes of administration were oral (75.9%), topical (8.9%), and rectal (3.8%). Over 30% of cases were reported in the age group from 7 to 12 years. The majority of reports were received from Germany (29.1%), Thailand (21.5%), and Australia (11.4%).

CONCLUSION: VigiBase[®] contains a considerable number of acute hypersensitivity reactions in children associated with herbal medicines, including life-threatening reactions such as anaphylactic shock.}, } @article {pmid28843532, year = {2018}, author = {Ainsworth, S and Petras, D and Engmark, M and Süssmuth, RD and Whiteley, G and Albulescu, LO and Kazandjian, TD and Wagstaff, SC and Rowley, P and Wüster, W and Dorrestein, PC and Arias, AS and Gutiérrez, JM and Harrison, RA and Casewell, NR and Calvete, JJ}, title = {The medical threat of mamba envenoming in sub-Saharan Africa revealed by genus-wide analysis of venom composition, toxicity and antivenomics profiling of available antivenoms.}, journal = {Journal of proteomics}, volume = {172}, number = {}, pages = {173-189}, doi = {10.1016/j.jprot.2017.08.016}, pmid = {28843532}, issn = {1876-7737}, support = {BB/F012675/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; MC_PC_17167/MRC_/Medical Research Council/United Kingdom ; MR/L01839X/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Africa South of the Sahara ; Animals ; Antivenins/*immunology ; *Dendroaspis ; Diet ; Elapid Venoms/*chemistry/immunology/toxicity ; Elapidae ; Humans ; Phylogeny ; Species Specificity ; Transcriptome ; }, abstract = {UNLABELLED: Mambas (genus Dendroaspis) are among the most feared of the medically important elapid snakes found in sub-Saharan Africa, but many facets of their biology, including the diversity of venom composition, remain relatively understudied. Here, we present a reconstruction of mamba phylogeny, alongside genus-wide venom gland transcriptomic and high-resolution top-down venomic analyses. Whereas the green mambas, D. viridis, D. angusticeps, D. j. jamesoni and D. j. kaimosae, express 3FTx-predominant venoms, black mamba (D. polylepis) venom is dominated by dendrotoxins I and K. The divergent terrestrial ecology of D. polylepis compared to the arboreal niche occupied by all other mambas makes it plausible that this major difference in venom composition is due to dietary variation. The pattern of intrageneric venom variability across Dendroaspis represented a valuable opportunity to investigate, in a genus-wide context, the variant toxicity of the venom, and the degree of paraspecific cross-reactivity between antivenoms and mamba venoms. To this end, the immunological profiles of the five mamba venoms were assessed against a panel of commercial antivenoms generated for the sub-Saharan Africa market. This study provides a genus-wide overview of which available antivenoms may be more efficacious in neutralising human envenomings caused by mambas, irrespective of the species responsible. The information gathered in this study lays the foundations for rationalising the notably different potency and pharmacological profiles of Dendroaspis venoms at locus resolution. This understanding will allow selection and design of toxin immunogens with a view to generating a safer and more efficacious pan-specific antivenom against any mamba envenomation.

BIOLOGICAL SIGNIFICANCE: The mambas (genus Dendroaspis) comprise five especially notorious medically important venomous snakes endemic to sub-Saharan Africa. Their highly potent venoms comprise a high diversity of pharmacologically active peptides, including extremely rapid-acting neurotoxins. Previous studies on mamba venoms have focused on the biochemical and pharmacological characterisation of their most relevant toxins to rationalize the common neurological and neuromuscular symptoms of envenomings caused by these species, but there has been little work on overall venom composition or comparisons between them. Only very recently an overview of the composition of the venom of two Dendroaspis species, D. angusticeps and D. polylepis, has been unveiled through venomics approaches. Here we present the first genus-wide transcriptomic-proteomic analysis of mamba venom composition. The transcriptomic analyses described in this paper have contributed 29 (D. polylepis), 23 (D. angusticeps), 40 (D. viridis), 25 (D. j. jamesoni) and 21 (D. j. kaimosae), novel full-length toxin sequences to the non-redundant Dendroaspis sequence database. The mamba genus-wide venomic analysis demonstrated that major D. polylepis venom components are Kunitz-fold family toxins. This feature is unique in relation to the relatively conserved three-finger toxin (3FTx)-dominated venom compositions of the green mambas. Venom variation was interpreted in the context of dietary variation due to the divergent terrestrial ecology of D. polylepis compared to the arboreal niche occupied by all other mambas. Additionally, the degree of cross-reactivity conservation of mamba venoms was assessed by antivenomics against a panel of commercial antivenoms generated for the sub-Saharan Africa market. This study provides a genus-wide overview to infer which available antivenoms may be capable of neutralising human envenomings caused by mambas, irrespective of the species responsible. The information gathered in this study lays the foundations for rationalising the pharmacological profiles of mamba venoms at locus resolution. This understanding will contribute to the generation of a safer and more efficacious pan-Dendroaspis therapeutic antivenom against any mamba envenomation.}, } @article {pmid28841836, year = {2017}, author = {Liu, M and Koh, H and Kurtz, ZD and Battaglia, T and PeBenito, A and Li, H and Nazzal, L and Blaser, MJ}, title = {Oxalobacter formigenes-associated host features and microbial community structures examined using the American Gut Project.}, journal = {Microbiome}, volume = {5}, number = {1}, pages = {108}, pmid = {28841836}, issn = {2049-2618}, support = {P30 CA016087/CA/NCI NIH HHS/United States ; R01 DK090989/DK/NIDDK NIH HHS/United States ; R01 DK110014/DK/NIDDK NIH HHS/United States ; U01 AI122285/AI/NIAID NIH HHS/United States ; U54 DK083908/DK/NIDDK NIH HHS/United States ; }, mesh = {Adult ; Data Mining ; Feces/*microbiology ; Female ; Gastrointestinal Microbiome/genetics/*physiology ; Homeostasis ; Humans ; Male ; Nephrolithiasis/etiology/microbiology ; Oxalates/metabolism ; Oxalobacter formigenes/classification/genetics/isolation & purification/*physiology ; Phylogeny ; Statistics as Topic ; Systems Biology/methods ; United States ; }, abstract = {BACKGROUND: Increasing evidence shows the importance of the commensal microbe Oxalobacter formigenes in regulating host oxalate homeostasis, with effects against calcium oxalate kidney stone formation, and other oxalate-associated pathological conditions. However, limited understanding of O. formigenes in humans poses difficulties for designing targeted experiments to assess its definitive effects and sustainable interventions in clinical settings. We exploited the large-scale dataset from the American Gut Project (AGP) to study O. formigenes colonization in the human gastrointestinal (GI) tract and to explore O. formigenes-associated ecology and the underlying host-microbe relationships.

RESULTS: In >8000 AGP samples, we detected two dominant, co-colonizing O. formigenes operational taxonomic units (OTUs) in fecal specimens. Multivariate analysis suggested that O. formigenes abundance was associated with particular host demographic and clinical features, including age, sex, race, geographical location, BMI, and antibiotic history. Furthermore, we found that O. formigenes presence was an indicator of altered host gut microbiota structure, including higher community diversity, global network connectivity, and stronger resilience to simulated disturbances.

CONCLUSIONS: Through this study, we identified O. formigenes colonizing patterns in the human GI tract, potential underlying host-microbe relationships, and associated microbial community structures. These insights suggest hypotheses to be tested in future experiments. Additionally, we proposed a systematic framework to study any bacterial taxa of interest to computational biologists, using large-scale public data to yield novel biological insights.}, } @article {pmid28839161, year = {2017}, author = {Cai, L and Zhou, G and Tian, RM and Tong, H and Zhang, W and Sun, J and Ding, W and Wong, YH and Xie, JY and Qiu, JW and Liu, S and Huang, H and Qian, PY}, title = {Metagenomic analysis reveals a green sulfur bacterium as a potential coral symbiont.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {9320}, pmid = {28839161}, issn = {2045-2322}, mesh = {Animals ; Anthozoa/*microbiology ; Caribbean Region ; Chlorobi/*classification/genetics/*physiology ; Cluster Analysis ; Computational Biology ; Metabolic Networks and Pathways/genetics ; Metagenomics ; Phylogeny ; *Symbiosis ; Whole Genome Sequencing ; }, abstract = {Coral reefs are ecologically significant habitats. Coral-algal symbiosis confers ecological success on coral reefs and coral-microbial symbiosis is also vital to coral reefs. However, current understanding of coral-microbial symbiosis on a genomic scale is largely unknown. Here we report a potential microbial symbiont in corals revealed by metagenomics-based genomic study. Microbial cells in coral were enriched for metagenomic analysis and a high-quality draft genome of "Candidatus Prosthecochloris korallensis" was recovered by metagenome assembly and genome binning. Phylogenetic analysis shows "Ca. P. korallensis" belongs to the Prosthecochloris clade and is clustered with two Prosthecochloris clones derived from Caribbean corals. Genomic analysis reveals "Ca. P. korallensis" has potentially important ecological functions including anoxygenic photosynthesis, carbon fixation via the reductive tricarboxylic acid (rTCA) cycle, nitrogen fixation, and sulfur oxidization. Core metabolic pathway analysis suggests "Ca. P. korallensis" is a green sulfur bacterium capable of photoautotrophy or mixotrophy. Potential host-microbial interaction reveals a symbiotic relationship: "Ca. P. korallensis" might provide organic and nitrogenous nutrients to its host and detoxify sulfide for the host; the host might provide "Ca. P. korallensis" with an anaerobic environment for survival, carbon dioxide and acetate for growth, and hydrogen sulfide as an electron donor for photosynthesis.}, } @article {pmid28838894, year = {2017}, author = {Diniz, CSG and Pellini, ACG and Ribeiro, AG and Tedardi, MV and Miranda, MJ and Touso, MM and Baquero, OS and Santos, PCD and Chiaravalloti-Neto, F}, title = {Breast cancer mortality and associated factors in São Paulo State, Brazil: an ecological analysis.}, journal = {BMJ open}, volume = {7}, number = {8}, pages = {e016395}, pmid = {28838894}, issn = {2044-6055}, mesh = {Adolescent ; Adult ; Aged ; Brazil/epidemiology ; Breast Neoplasms/*mortality ; Databases, Factual ; Demography ; Female ; *Health Care Sector ; Humans ; Linear Models ; *Mammography ; Middle Aged ; *Parity ; *Private Sector ; Socioeconomic Factors ; Young Adult ; }, abstract = {OBJECTIVE: Identify the factors associated with the age-standardised breast cancer mortality rate in the municipalities of State of São Paulo (SSP), Brazil, in the period from 2006 to 2012.

DESIGN: Ecological study of the breast cancer mortality rate standardised by age, as the dependent variable, having each of the 645 municipalities in the SSP as the unit of analysis.

SETTINGS: The female resident population aged 15 years or older, by age group and municipality, in 2009 (mid-term), obtained from public dataset (Informatics Department of the Unified Health System).

PARTICIPANTS: Women 15 years or older who died of breast cancer in the SSP were selected for the calculation of the breast cancer mortality rate, according to the municipality and age group, from 2006 to 2012.

MAIN OUTCOME MEASURES: Mortality rates for each municipality calculated by the direct standardisation method, using the age structure of the population of SSP in 2009 as the standard.

RESULTS: In the final linear regression model, breast cancer mortality, in the municipal level, was directly associated with rates of nulliparity (p<0.0001), mammography (p<0.0001) and private healthcare (p=0.006).

CONCLUSIONS: The findings that mammography ratio was associated, in the municipal level, with increased mortality add to the evidence of a probable overestimation of benefits and underestimation of risks associated with this form of screening. The same paradoxical trend of increased mortality with screening was found in recent individual-level studies, indicating the need to expand informed choice for patients, primary prevention actions and individualised screening. Additional studies should be conducted to explore if there is a causality link in this association.}, } @article {pmid28836041, year = {2017}, author = {Detsch, F and Otte, I and Appelhans, T and Nauss, T}, title = {A glimpse at short-term controls of evapotranspiration along the southern slopes of Kilimanjaro.}, journal = {Environmental monitoring and assessment}, volume = {189}, number = {9}, pages = {465}, pmid = {28836041}, issn = {1573-2959}, mesh = {*Altitude ; *Climate Change ; *Ecosystem ; Environmental Monitoring/*methods ; Rain ; Seasons ; Soil ; Tanzania ; Water/*analysis ; }, abstract = {Future climate characteristics of the southern Kilimanjaro region, Tanzania, are mainly determined by local land-use and global climate change. Reinforcing increasing dryness throughout the twentieth century, ongoing land transformation processes emphasize the need for a proper understanding of the regional-scale water budget and possible implications on related ecosystem functioning and services. Here, we present an analysis of scintillometer-based evapotranspiration (ET) covering seven distinct habitat types across a massive climate gradient from the colline savanna woodlands to the upper-mountain Helichrysum zone (940 to 3960 m.a.s.l.). Random forest-based mean variable importance indicates an outstanding significance of net radiation (R net) on the observed ET across all elevation levels. Accordingly, topography and frequent cloud/fog events have a dampening effect at high elevations, whereas no such constraints affect the energy and moisture-rich submontane coffee/grassland level. By contrast, long-term moisture availability is likely to impose restrictions upon evapotranspirative net water loss in savanna, which particularly applies to the pronounced dry season. At plot scale, ET can thereby be approximated reasonably using R net, soil heat flux, and to a lesser degree, vapor pressure deficit and rainfall as predictor variables (R [2] 0.59 to 1.00). While multivariate regression based on pooled meteorological data from all plots proves itself useful for predicting hourly ET rates across a broader range of ecosystems (R [2] = 0.71), additional gains in explained variance can be achieved when vegetation characteristics as seen from the NDVI are considered (R [2] = 0.87). To sum up, our results indicate that valuable insights into land cover-specific ET dynamics, including underlying drivers, may be derived even from explicitly short-term measurements in an ecologically highly diverse landscape.}, } @article {pmid28835646, year = {2017}, author = {Ren, CG and Kong, CC and Yan, K and Zhang, H and Luo, YM and Xie, ZH}, title = {Elucidation of the molecular responses to waterlogging in Sesbania cannabina roots by transcriptome profiling.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {9256}, pmid = {28835646}, issn = {2045-2322}, mesh = {Adaptation, Biological ; Computational Biology/methods ; Energy Metabolism ; *Floods ; *Gene Expression Profiling ; *Gene Expression Regulation, Plant ; High-Throughput Nucleotide Sequencing ; Metabolic Networks and Pathways ; Molecular Sequence Annotation ; Plant Development/genetics ; Plant Roots/*genetics ; Sequence Analysis, DNA ; Sesbania/*genetics/metabolism ; Stress, Physiological ; *Transcriptome ; }, abstract = {Sesbania cannabina, a multipurpose leguminous crop, is highly resistant to waterlogging stress. However, the scant genomic resources in the genus Sesbania have greatly hindered further exploration of the mechanisms underlying its waterlogging tolerance. Here, the genetic basis of flooding tolerance in S. cannabina was examined by transcriptome-wide gene expression changes using RNA-Seq in seedlings exposed to short-term (3 h) and long-term (27 h) waterlogging. After de- novo assembly, 213990 unigenes were identified, of which 145162 (79.6%) were annotated. Gene Ontology and pathway enrichment analyses revealed that the glycolysis and fermentation pathways were stimulated to produce ATP under hypoxic stress conditions. Energy-consuming biosynthetic processes were dramatically repressed by short and long term waterlogging, while amino acid metabolism was greatly induced to maintain ATP levels. The expression pattern of 10 unigenes involved in phenylpropanoid biosynthesis, glycolysis, and amino acid metabolism revealed by qRT-PCR confirmed the RNA-Seq data. The present study is a large-scale assessment of genomic resources of Sesbania and provides guidelines for probing the molecular mechanisms underlying S. cannabina waterlogging tolerance.}, } @article {pmid28833890, year = {2017}, author = {Scales, KL and Hazen, EL and Maxwell, SM and Dewar, H and Kohin, S and Jacox, MG and Edwards, CA and Briscoe, DK and Crowder, LB and Lewison, RL and Bograd, SJ}, title = {Fit to predict? Eco-informatics for predicting the catchability of a pelagic fish in near real time.}, journal = {Ecological applications : a publication of the Ecological Society of America}, volume = {27}, number = {8}, pages = {2313-2329}, doi = {10.1002/eap.1610}, pmid = {28833890}, issn = {1051-0761}, mesh = {Animals ; California ; Computational Biology ; Ecology ; *Fisheries ; *Fishes ; Models, Biological ; Pacific Ocean ; Remote Sensing Technology/*methods ; }, abstract = {The ocean is a dynamic environment inhabited by a diverse array of highly migratory species, many of which are under direct exploitation in targeted fisheries. The timescales of variability in the marine realm coupled with the extreme mobility of ocean-wandering species such as tuna and billfish complicates fisheries management. Developing eco-informatics solutions that allow for near real-time prediction of the distributions of highly mobile marine species is an important step towards the maturation of dynamic ocean management and ecological forecasting. Using 25 yr (1990-2014) of NOAA fisheries' observer data from the California drift gillnet fishery, we model relative probability of occurrence (presence-absence) and catchability (total catch per gillnet set) of broadbill swordfish Xiphias gladius in the California Current System. Using freely available environmental data sets and open source software, we explore the physical drivers of regional swordfish distribution. Comparing models built upon remotely sensed data sets with those built upon a data-assimilative configuration of the Regional Ocean Modelling System (ROMS), we explore trade-offs in model construction, and address how physical data can affect predictive performance and operational capacity. Swordfish catchability was found to be highest in deeper waters (>1,500 m) with surface temperatures in the 14-20°C range, isothermal layer depth (ILD) of 20-40 m, positive sea surface height (SSH) anomalies, and during the new moon (<20% lunar illumination). We observed a greater influence of mesoscale variability (SSH, wind speed, isothermal layer depth, eddy kinetic energy) in driving swordfish catchability (total catch) than was evident in predicting the relative probability of presence (presence-absence), confirming the utility of generating spatiotemporally dynamic predictions. Data-assimilative ROMS circumvent the limitations of satellite remote sensing in providing physical data fields for species distribution models (e.g., cloud cover, variable resolution, subsurface data), and facilitate broad-scale prediction of dynamic species distributions in near real time.}, } @article {pmid28830116, year = {2017}, author = {Chen, MY and Liang, D and Zhang, P}, title = {Phylogenomic Resolution of the Phylogeny of Laurasiatherian Mammals: Exploring Phylogenetic Signals within Coding and Noncoding Sequences.}, journal = {Genome biology and evolution}, volume = {9}, number = {8}, pages = {1998-2012}, pmid = {28830116}, issn = {1759-6653}, mesh = {Animals ; Chiroptera/genetics ; Databases, Genetic ; Eutheria/*genetics ; Evolution, Molecular ; Introns ; *Phylogeny ; }, abstract = {The interordinal relationships of Laurasiatherian mammals are currently one of the most controversial questions in mammalian phylogenetics. Previous studies mainly relied on coding sequences (CDS) and seldom used noncoding sequences. Here, by data mining public genome data, we compiled an intron data set of 3,638 genes (all introns from a protein-coding gene are considered as a gene) (19,055,073 bp) and a CDS data set of 10,259 genes (20,994,285 bp), covering all major lineages of Laurasiatheria (except Pholidota). We found that the intron data contained stronger and more congruent phylogenetic signals than the CDS data. In agreement with this observation, concatenation and species-tree analyses of the intron data set yielded well-resolved and identical phylogenies, whereas the CDS data set produced weakly supported and incongruent results. Further analyses showed that the phylogeny inferred from the intron data is highly robust to data subsampling and change in outgroup, but the CDS data produced unstable results under the same conditions. Interestingly, gene tree statistical results showed that the most frequently observed gene tree topologies for the CDS and intron data are identical, suggesting that the major phylogenetic signal within the CDS data is actually congruent with that within the intron data. Our final result of Laurasiatheria phylogeny is (Eulipotyphla,((Chiroptera, Perissodactyla),(Carnivora, Cetartiodactyla))), favoring a close relationship between Chiroptera and Perissodactyla. Our study 1) provides a well-supported phylogenetic framework for Laurasiatheria, representing a step towards ending the long-standing "hard" polytomy and 2) argues that intron within genome data is a promising data resource for resolving rapid radiation events across the tree of life.}, } @article {pmid28827531, year = {2017}, author = {Parker, J and Helmstetter, AJ and Devey, D and Wilkinson, T and Papadopulos, AST}, title = {Field-based species identification of closely-related plants using real-time nanopore sequencing.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {8345}, pmid = {28827531}, issn = {2045-2322}, mesh = {Arabidopsis/*classification/*genetics ; Arabidopsis Proteins/*metabolism ; Computational Biology/*methods ; DNA, Plant/analysis/genetics ; *Genome, Plant ; High-Throughput Nucleotide Sequencing/*methods ; *Nanopores ; Sequence Analysis, DNA/methods ; }, abstract = {Advances in DNA sequencing and informatics have revolutionised biology over the past four decades, but technological limitations have left many applications unexplored. Recently, portable, real-time, nanopore sequencing (RTnS) has become available. This offers opportunities to rapidly collect and analyse genomic data anywhere. However, generation of datasets from large, complex genomes has been constrained to laboratories. The portability and long DNA sequences of RTnS offer great potential for field-based species identification, but the feasibility and accuracy of these technologies for this purpose have not been assessed. Here, we show that a field-based RTnS analysis of closely-related plant species (Arabidopsis spp.) has many advantages over laboratory-based high-throughput sequencing (HTS) methods for species level identification and phylogenomics. Samples were collected and sequenced in a single day by RTnS using a portable, "al fresco" laboratory. Our analyses demonstrate that correctly identifying unknown reads from matches to a reference database with RTnS reads enables rapid and confident species identification. Individually annotated RTnS reads can be used to infer the evolutionary relationships of A. thaliana. Furthermore, hybrid genome assembly with RTnS and HTS reads substantially improved upon a genome assembled from HTS reads alone. Field-based RTnS makes real-time, rapid specimen identification and genome wide analyses possible.}, } @article {pmid28827332, year = {2017}, author = {McManamay, RA and Surendran Nair, S and DeRolph, CR and Ruddell, BL and Morton, AM and Stewart, RN and Troia, MJ and Tran, L and Kim, H and Bhaduri, BL}, title = {US cities can manage national hydrology and biodiversity using local infrastructure policy.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {114}, number = {36}, pages = {9581-9586}, pmid = {28827332}, issn = {1091-6490}, mesh = {Animals ; Aquatic Organisms ; *Biodiversity ; Cities ; Conservation of Natural Resources/legislation & jurisprudence ; Ecosystem ; Environment ; *Environmental Policy/legislation & jurisprudence ; Humans ; *Hydrology/legislation & jurisprudence ; Rivers ; United States ; }, abstract = {Cities are concentrations of sociopolitical power and prime architects of land transformation, while also serving as consumption hubs of "hard" water and energy infrastructures. These infrastructures extend well outside metropolitan boundaries and impact distal river ecosystems. We used a comprehensive model to quantify the roles of anthropogenic stressors on hydrologic alteration and biodiversity in US streams and isolate the impacts stemming from hard infrastructure developments in cities. Across the contiguous United States, cities' hard infrastructures have significantly altered at least 7% of streams, which influence habitats for over 60% of North America's fish, mussel, and crayfish species. Additionally, city infrastructures have contributed to local extinctions in 260 species and currently influence 970 indigenous species, 27% of which are in jeopardy. We find that ecosystem impacts do not scale with city size but are instead proportionate to infrastructure decisions. For example, Atlanta's impacts by hard infrastructures extend across four major river basins, 12,500 stream km, and contribute to 100 local extinctions of aquatic species. In contrast, Las Vegas, a similar size city, impacts <1,000 stream km, leading to only seven local extinctions. So, cities have local policy choices that can reduce future impacts to regional aquatic ecosystems as they grow. By coordinating policy and communication between hard infrastructure sectors, local city governments and utilities can directly improve environmental quality in a significant fraction of the nation's streams reaching far beyond their city boundaries.}, } @article {pmid28826396, year = {2017}, author = {Liu, AL and Xie, HJ and Xie, HY and Liu, J and Yin, J and Hu, JS and Peng, CY}, title = {Association between fat mass and obesity associated (FTO) gene rs9939609 A/T polymorphism and polycystic ovary syndrome: a systematic review and meta-analysis.}, journal = {BMC medical genetics}, volume = {18}, number = {1}, pages = {89}, pmid = {28826396}, issn = {1471-2350}, mesh = {Adiposity/*genetics ; Alleles ; Alpha-Ketoglutarate-Dependent Dioxygenase FTO/*genetics ; Asian People/genetics ; Body Mass Index ; Databases, Factual ; Female ; Genetic Predisposition to Disease ; Humans ; Obesity/complications/*genetics ; Polycystic Ovary Syndrome/complications/*genetics ; Polymorphism, Single Nucleotide ; Risk Factors ; Sensitivity and Specificity ; White People/genetics ; }, abstract = {BACKGROUND: Up to now, numerous case-control studies have reported the associations between fat mass and obesity associated (FTO) gene rs9939609 A/T polymorphism and polycystic ovary syndrome (PCOS), however, without a consistent result. Hence we performed current systematic review and meta-analysis to clarify the controversial results.

METHODS: Case-control studies reporting the relationship of rs9939609 A/T polymorphism and PCOS published before April 2015 were searched in Pubmed database without language restriction. Data was analyzed by Review Manager 5.2.

RESULTS: A total of five studies involving 5010 PCOS patients and 5300 controls were included for further meta-analysis. The results of meta-analysis showed that the FTO gene rs9939609 A/T polymorphism was significantly different between PCOS group and control group in different gene models (For AA + AT vs. TT: OR = 1.41, 95% CI = 1.28-1.55, P < 0.00001. For AA vs. AT + TT: OR = 1.54, 95% CI = 1.25-1.89, P < 0.0001. For AA vs. TT: OR = 1.74, 95% CI = 1.38-2.18, P < 0.00001. For A vs. T: OR = 1.36, 95% CI = 1.25-1.47, P < 0.00001, respectively) suggesting that A allele was a risk factor for PCOS susceptibility. Furthermore, subgroup analysis in Asian and Caucasian ethnicities also found significant association between rs9939609 A/T polymorphism and PCOS (In Asian subgroup: OR = 1.43, 95% CI = 1.29-1.59, P < 0.0001. In Caucasian subgroup: OR = 1.33, 95% CI = 1.08-1.64, P = 0.008) CONCLUSION: This meta-analysis suggests that rs9939609 A/T polymorphism of FTO gene is associated with PCOS risk, and that A allele is a risk factor for PCOS susceptibility simultaneously.}, } @article {pmid28823550, year = {2017}, author = {Song, D and Gao, Z and Zhang, H and Xu, F and Zheng, X and Ai, J and Hu, X and Huang, G and Zhang, H}, title = {GIS-based health assessment of the marine ecosystem in Laizhou Bay, China.}, journal = {Marine pollution bulletin}, volume = {125}, number = {1-2}, pages = {242-249}, doi = {10.1016/j.marpolbul.2017.08.027}, pmid = {28823550}, issn = {1879-3363}, mesh = {Bays ; China ; Ecosystem ; Environmental Monitoring/*methods ; Eutrophication ; *Geographic Information Systems ; Geologic Sediments ; Metals, Heavy/analysis ; Water Pollutants, Chemical/analysis ; Water Pollution/analysis ; }, abstract = {According to 2014-2016 monitoring data, an assessment index system including water quality, depositional environment and ecosystem was built to evaluate the health statue of marine ecosystem in the Laizhou Bay using analytic hierarchy process (AHP) method. The results, spatialized in ArcGIS software, show: while the comprehensive ecological health index is 0.62, the ecological environmental quality in the Laizhou Bay is in a sub-healthy state; the unhealthy area is mainly concentrated in southwestern inshore region, and impacted by serious environmental problems, such as water eutrophication and heavy metal pollution; the northwestern and southeastern inshore regions are in a sub-healthy state, while the eastern inshore and northern areas are in the healthiest state. The land-based pollutants that discharge into the sea may be the leading factors that are causing ecological environment deterioration in the Laizhou Bay, and the reclamation work ongoing around the port has exacerbated the ecological risk.}, } @article {pmid28823476, year = {2017}, author = {Jünemann, S and Kleinbölting, N and Jaenicke, S and Henke, C and Hassa, J and Nelkner, J and Stolze, Y and Albaum, SP and Schlüter, A and Goesmann, A and Sczyrba, A and Stoye, J}, title = {Bioinformatics for NGS-based metagenomics and the application to biogas research.}, journal = {Journal of biotechnology}, volume = {261}, number = {}, pages = {10-23}, doi = {10.1016/j.jbiotec.2017.08.012}, pmid = {28823476}, issn = {1873-4863}, mesh = {Anaerobiosis ; Biofuels/*microbiology ; Computational Biology/*methods ; High-Throughput Nucleotide Sequencing/*methods ; Metagenome/*genetics ; Metagenomics/*methods ; }, abstract = {Metagenomics has proven to be one of the most important research fields for microbial ecology during the last decade. Starting from 16S rRNA marker gene analysis for the characterization of community compositions to whole metagenome shotgun sequencing which additionally allows for functional analysis, metagenomics has been applied in a wide spectrum of research areas. The cost reduction paired with the increase in the amount of data due to the advent of next-generation sequencing led to a rapidly growing demand for bioinformatic software in metagenomics. By now, a large number of tools that can be used to analyze metagenomic datasets has been developed. The Bielefeld-Gießen center for microbial bioinformatics as part of the German Network for Bioinformatics Infrastructure bundles and imparts expert knowledge in the analysis of metagenomic datasets, especially in research on microbial communities involved in anaerobic digestion residing in biogas reactors. In this review, we give an overview of the field of metagenomics, introduce into important bioinformatic tools and possible workflows, accompanied by application examples of biogas surveys successfully conducted at the Center for Biotechnology of Bielefeld University.}, } @article {pmid28822180, year = {2017}, author = {Tian, L and Zhou, WZ and He, WH and Lun, D and Liu, DH}, title = {[Habitat areas extracting of Poria cocos in Anhui based on "3S" technologies].}, journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica}, volume = {42}, number = {12}, pages = {2276-2283}, doi = {10.19540/j.cnki.cjcmm.2017.0107}, pmid = {28822180}, issn = {1001-5302}, mesh = {China ; *Ecosystem ; Geographic Information Systems ; Wolfiporia/*growth & development ; }, abstract = {"Adversity" is one primary element that impacts the pharmacology components of authentic Chinese herbal medicine. Knowledge about "adversity" is a precondition of yield estimation, quality monitoring, location selection and the geo-herbalism protection. Used 3S(GIS, RS and GPS) technology to combine multi-source key ecological factors of "Anling", and used parasitic relationships between organisms to extracting its suitable region for the first time. Results showed that the "Anling" were mainly distributed in Dabie coteau. Suitable area amount to 36.8 km[2], Yuexi, Shucheng, Jinzhai and Qianshan which account for about 93.55% of whole congenial region. The first three accounts for about 80.82%. It was Yuexi that account for 1/3 above especially. Field investigation verify accuracy of extraction about 91.67%, which has confirmed it is feasible that using the relationship between parasitic host and parasitic to extract native environment of parasitic traditional medicine based on 3S technology.}, } @article {pmid28820884, year = {2017}, author = {Bik, HM}, title = {Let's rise up to unite taxonomy and technology.}, journal = {PLoS biology}, volume = {15}, number = {8}, pages = {e2002231}, pmid = {28820884}, issn = {1545-7885}, mesh = {*Classification ; Computational Biology ; Technology ; }, abstract = {What do you think of when you think of taxonomy? An 18th century gentlemen in breeches? Or perhaps botany drawings hung on the walls of a boutique hotel? Such old-fashioned conceptions to the contrary, taxonomy is alive today although constantly struggling for survival and recognition. The scientific community is losing valuable resources as taxonomy experts age and retire, and funding for morphological studies and species descriptions remains stagnant. At the same time, organismal knowledge (morphology, ecology, physiology) has never been more important: genomic studies are becoming more taxon focused, the scientific community is recognizing the limitations of traditional "model" organisms, and taxonomic expertise is desperately needed to fight against global biodiversity declines resulting from human impacts. There has never been a better time for a taxonomic renaissance.}, } @article {pmid28820667, year = {2018}, author = {Eisenberg, ME and Mehus, CJ and Saewyc, EM and Corliss, HL and Gower, AL and Sullivan, R and Porta, CM}, title = {Helping Young People Stay Afloat: A Qualitative Study of Community Resources and Supports for LGBTQ Adolescents in the United States and Canada.}, journal = {Journal of homosexuality}, volume = {65}, number = {8}, pages = {969-989}, pmid = {28820667}, issn = {1540-3602}, support = {R01 HD078470/HD/NICHD NIH HHS/United States ; }, mesh = {Adolescent ; British Columbia ; Community Networks ; Female ; Humans ; Male ; Massachusetts ; Minnesota ; Qualitative Research ; *Sexual and Gender Minorities ; *Social Support ; Young Adult ; }, abstract = {LGBTQ youth are at increased risk of poor health outcomes. This qualitative study gathered data from LGBTQ adolescents regarding their communities and describes the resources they draw on for support. We conducted 66 go-along interviews with diverse LGBTQ adolescents (mean age = 16.6) in Minnesota, Massachusetts, and British Columbia in 2014-2015, in which interviewers accompanied participants in their communities to better understand those contexts. Their responses were systematically organized and coded for common themes, reflecting levels of the social ecological model. Participants described resources at each level, emphasizing organizational, community, and social factors such as LGBTQ youth organizations and events, media presence, and visibility of LGBTQ adults. Numerous resources were identified, and representative themes were highly consistent across locations, genders, orientations, racial/ethnic groups, and city size. Findings suggest new avenues for research with LGBTQ youth and many opportunities for communities to create and expand resources and supports for this population.}, } @article {pmid28817593, year = {2017}, author = {Warren, RJ and King, JR and Tarsa, C and Haas, B and Henderson, J}, title = {A systematic review of context bias in invasion biology.}, journal = {PloS one}, volume = {12}, number = {8}, pages = {e0182502}, pmid = {28817593}, issn = {1932-6203}, mesh = {Animals ; Bias ; Data Interpretation, Statistical ; Ecology/methods/*standards ; Ecosystem ; Introduced Species/*statistics & numerical data ; }, abstract = {The language that scientists use to frame biological invasions may reveal inherent bias-including how data are interpreted. A frequent critique of invasion biology is the use of value-laden language that may indicate context bias. Here we use a systematic study of language and interpretation in papers drawn from invasion biology to evaluate whether there is a link between the framing of papers and the interpretation of results. We also examine any trends in context bias in biological invasion research. We examined 651 peer-reviewed invasive species competition studies and implemented a rigorous systematic review to examine bias in the presentation and interpretation of native and invasive competition in invasion biology. We predicted that bias in the presentation of invasive species is increasing, as suggested by several authors, and that bias against invasive species would result in misinterpreting their competitive dominance in correlational observational studies compared to causative experimental studies. We indeed found evidence of bias in the presentation and interpretation of invasive species research; authors often introduced research with invasive species in a negative context and study results were interpreted against invasive species more in correlational studies. However, we also found a distinct decrease in those biases since the mid-2000s. Given that there have been several waves of criticism from scientists both inside and outside invasion biology, our evidence suggests that the subdiscipline has somewhat self-corrected apparent biases.}, } @article {pmid28815142, year = {2017}, author = {Tao, S and Zeng, N and Wu, X and Li, X and Zhu, W and Cui, L and Zhang, GQ}, title = {A Data Capture Framework for Large-scale Interventional Studies with Survey Workflow Management.}, journal = {AMIA Joint Summits on Translational Science proceedings. AMIA Joint Summits on Translational Science}, volume = {2017}, number = {}, pages = {278-286}, pmid = {28815142}, issn = {2153-4063}, abstract = {Capturing high-quality survey data is an arduous process for large-scale and extensive interventional studies. This paper presents the architecture, interface design, and an innovative form generation engine of a system called RE- Form: Refactorized Electronic Web Forms. REForm provides researchers the capability to design and manage surveys and the flexibility to organize them in a customizable workflow. REForm has been designed, implemented, pilot-tested and deployed for an NCI-funded interventional study IMPACT. It enables IMPACT to design and conduct a baseline survey of 95 questions with 662 options, a post-intervention survey of 82 questions with 574 options, six Ecological Momentary Assessment (EMA) surveys including four questions and 26 options each, and a follow-up survey con- taining 15 questions and 125 options. Feedback designed in the post-intervention survey showed that more than 94 percent of IMPACT participants highly endorsed the design and usability of the surveys created using REForm.}, } @article {pmid28813471, year = {2017}, author = {Ruan, J and Cheng, J and Zhang, T and Jiang, H}, title = {Mitochondrial genome evolution in the Saccharomyces sensu stricto complex.}, journal = {PloS one}, volume = {12}, number = {8}, pages = {e0183035}, pmid = {28813471}, issn = {1932-6203}, mesh = {Computational Biology/methods ; DNA, Intergenic ; *Evolution, Molecular ; Gene Order ; Genes, Mitochondrial ; *Genome, Mitochondrial ; Genomics/methods ; Introns ; Molecular Sequence Annotation ; Open Reading Frames ; Phylogeny ; Saccharomyces/classification/*genetics ; }, abstract = {Exploring the evolutionary patterns of mitochondrial genomes is important for our understanding of the Saccharomyces sensu stricto (SSS) group, which is a model system for genomic evolution and ecological analysis. In this study, we first obtained the complete mitochondrial sequences of two important species, Saccharomyces mikatae and Saccharomyces kudriavzevii. We then compared the mitochondrial genomes in the SSS group with those of close relatives, and found that the non-coding regions evolved rapidly, including dramatic expansion of intergenic regions, fast evolution of introns and almost 20-fold higher rearrangement rates than those of the nuclear genomes. However, the coding regions, and especially the protein-coding genes, are more conserved than those in the nuclear genomes of the SSS group. The different evolutionary patterns of coding and non-coding regions in the mitochondrial and nuclear genomes may be related to the origin of the aerobic fermentation lifestyle in this group. Our analysis thus provides novel insights into the evolution of mitochondrial genomes.}, } @article {pmid28813450, year = {2017}, author = {Chen, H and Peng, S and Dai, L and Zou, Q and Yi, B and Yang, X and Ma, ZS}, title = {Oral microbial community assembly under the influence of periodontitis.}, journal = {PloS one}, volume = {12}, number = {8}, pages = {e0182259}, pmid = {28813450}, issn = {1932-6203}, mesh = {Algorithms ; *Biodiversity ; Case-Control Studies ; Datasets as Topic ; Humans ; Metagenome ; Metagenomics/methods ; *Microbiota ; Models, Theoretical ; Mouth Mucosa/*microbiology ; Periodontitis/*microbiology ; }, abstract = {Several ecological hypotheses (e.g., specific plaque, non-specific plaque and keystone pathogen) regarding the etiology of periodontitis have been proposed since the 1990s, most of which have been centered on the concept of dysbiosis associated with periodontitis. Nevertheless, none of the existing hypotheses have presented mechanistic interpretations on how and why dysbiosis actually occurs. Hubbell's neutral theory of biodiversity offers a powerful null model to test hypothesis regarding the mechanism of community assembly and diversity maintenance from the metagenomic sequencing data, which can help to understand the forces that shape the community dynamics such as dysbiosis. Here we reanalyze the dataset from Abusleme et al.'s comparative study of the oral microbial communities from periodontitis patients and healthy individuals. Our study demonstrates that 14 out of 61 communities (23%) passed the neutrality test, a percentage significantly higher than the previous reported neutrality rate of 1% in human microbiome (Li & Ma 2016, Scientific Reports). This suggests that, while the niche selection may play a predominant role in the assembly and diversity maintenance in oral microbiome, the effect of neutral dynamics may not be ignored. However, no statistically significant differences in the neutrality passing rates were detected between the periodontitis and healthy treatments with Fisher's exact probability test and multiple testing corrections, suggesting that the mechanism of community assembly is robust against disturbances such as periodontitis. In addition, our study confirmed previous finding that periodontitis patients exhibited higher biodiversity. These findings suggest that while periodontitis may significantly change the community composition measured by diversity (i.e., the exhibition or 'phenotype' of community assembly), it does not seem to cause the 'mutation' of the 'genotype" (mechanism) of community assembly. We argue that the 'phenotypic' changes explain the observed link (not necessarily causal) between periodontitis and community dysbiosis, which is certainly worthy of further investigation.}, } @article {pmid28812670, year = {2017}, author = {Strassburg, BBN and Brooks, T and Feltran-Barbieri, R and Iribarrem, A and Crouzeilles, R and Loyola, R and Latawiec, AE and Oliveira Filho, FJB and Scaramuzza, CAM and Scarano, FR and Soares-Filho, B and Balmford, A}, title = {Moment of truth for the Cerrado hotspot.}, journal = {Nature ecology & evolution}, volume = {1}, number = {4}, pages = {99}, doi = {10.1038/s41559-017-0099}, pmid = {28812670}, issn = {2397-334X}, } @article {pmid28812652, year = {2017}, author = {Mahé, F and de Vargas, C and Bass, D and Czech, L and Stamatakis, A and Lara, E and Singer, D and Mayor, J and Bunge, J and Sernaker, S and Siemensmeyer, T and Trautmann, I and Romac, S and Berney, C and Kozlov, A and Mitchell, EAD and Seppey, CVW and Egge, E and Lentendu, G and Wirth, R and Trueba, G and Dunthorn, M}, title = {Parasites dominate hyperdiverse soil protist communities in Neotropical rainforests.}, journal = {Nature ecology & evolution}, volume = {1}, number = {4}, pages = {91}, doi = {10.1038/s41559-017-0091}, pmid = {28812652}, issn = {2397-334X}, abstract = {High animal and plant richness in tropical rainforest communities has long intrigued naturalists. It is unknown if similar hyperdiversity patterns are reflected at the microbial scale with unicellular eukaryotes (protists). Here we show, using environmental metabarcoding of soil samples and a phylogeny-aware cleaning step, that protist communities in Neotropical rainforests are hyperdiverse and dominated by the parasitic Apicomplexa, which infect arthropods and other animals. These host-specific parasites potentially contribute to the high animal diversity in the forests by reducing population growth in a density-dependent manner. By contrast, too few operational taxonomic units (OTUs) of Oomycota were found to broadly drive high tropical tree diversity in a host-specific manner under the Janzen-Connell model. Extremely high OTU diversity and high heterogeneity between samples within the same forests suggest that protists, not arthropods, are the most diverse eukaryotes in tropical rainforests. Our data show that protists play a large role in tropical terrestrial ecosystems long viewed as being dominated by macroorganisms.}, } @article {pmid28812558, year = {2017}, author = {Gibbons, SM}, title = {Microbial community ecology: Function over phylogeny.}, journal = {Nature ecology & evolution}, volume = {1}, number = {1}, pages = {32}, doi = {10.1038/s41559-016-0032}, pmid = {28812558}, issn = {2397-334X}, } @article {pmid28811564, year = {2017}, author = {Zhang, A and Huang, R and Chen, L and Xiong, L and He, L and Li, Y and Liao, L and Zhu, Z and Wang, Y}, title = {Computational identification of Y-linked markers and genes in the grass carp genome by using a pool-and-sequence method.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {8213}, pmid = {28811564}, issn = {2045-2322}, mesh = {Animals ; Carps/*genetics ; Computational Biology/methods ; Evolution, Molecular ; Female ; *Genes, Y-Linked ; *Genome ; *Genomics/methods ; High-Throughput Nucleotide Sequencing ; Male ; Molecular Sequence Annotation ; Phylogeny ; Repetitive Sequences, Nucleic Acid ; Sex Chromosomes ; Sex Ratio ; }, abstract = {The molecular analysis of sex in vertebrates is important, as it has the potential to provide vital information for theoretical and applied research alike. Teleost fish are the ancient vertebrates that present a broad sex chromosome system but lack differentiated sex chromosomes in most species. Hence understanding the sex in fish would not only illuminate the sex determination evolution in vertebrates but also shed light on fish farming. In the present study, we used grass carp as a teleost fish model, studied the Y chromosome by using a pool-and-sequence strategy in combination with fragment-ratio method. In total, we identified five Y-linked scaffolds (totaling 347 Kb) and six Y-specific sequences that could be used as sex-specific markers, demonstrating the suitability of NGS-based re-sequencing of pooled DNAs for the identification of sex markers in fish. Moreover, 14 putative Y-linked genes were described for the first time. All the genes, except for un-y1, un-y2, and ubq-y, showed high similarity to their female homologs. RT-PCR revealed that ubq-y was only expressed in the male hypothalamus and pituitary. These findings provided an abundant resource for the Y chromosome of grass carp, and may help elucidate sex chromosome evolution in cyprinid fish.}, } @article {pmid28810934, year = {2017}, author = {Soares, S and Brochado, S and Barros, H and Fraga, S}, title = {Does Cyberbullying Prevalence Among Adolescents Relate With Country Socioeconomic and Development Indicators? An Ecological Study of 31 Countries.}, journal = {Violence and victims}, volume = {32}, number = {5}, pages = {771-790}, doi = {10.1891/0886-6708.VV-D-15-00139}, pmid = {28810934}, issn = {0886-6708}, mesh = {Adolescent ; Bullying/*statistics & numerical data ; Crime Victims ; Databases, Factual ; Developed Countries/economics/statistics & numerical data ; Developing Countries/economics/statistics & numerical data ; Female ; Global Health ; Humans ; *Internet ; Male ; Prevalence ; Socioeconomic Factors ; Surveys and Questionnaires ; United Nations ; }, abstract = {BACKGROUND: In addition to individual characteristics, it is also important to evaluate how the environment may influence the dynamics of cyberbullying. We aim to study the correlation between cyberbullying prevalence among adolescents and selected country-level indicators.

METHODS: We used two different data sources: data from a previously published literature review, to identify information on cyberbullying prevalence across countries, and data from the World Bank databases, to extract information on country-level indicators. A correlation matrix was used to present the association between the selected country-level indicators and the prevalence of cyberbullying.

RESULTS: We observed a statistically significant negative correlation between cyberbullying victimization (cybervictims and cyberbully-victims, respectively) and gross domestic product (r = -.474 and -.842), gross national income (r = -.485 and -.758), enrollment in secondary (r = -.446 and -.898) and tertiary education (r = -.222 and -.881), the number of secure Internet servers (r = -.118 and -.794), and the number of Internet users (r = -.190 and -.818).

CONCLUSIONS: A country's educational level seems to be an important contributor to the occurrence of cyberbullying.}, } @article {pmid28810700, year = {2017}, author = {Modave, E and MacDonald, AJ and Sarre, SD}, title = {A single mini-barcode test to screen for Australian mammalian predators from environmental samples.}, journal = {GigaScience}, volume = {6}, number = {8}, pages = {1-13}, pmid = {28810700}, issn = {2047-217X}, mesh = {Animals ; Australia ; Computational Biology/methods ; DNA Barcoding, Taxonomic/*methods ; DNA Primers ; *Genetic Markers ; Mammals/*genetics ; RNA, Ribosomal ; Real-Time Polymerase Chain Reaction ; Sensitivity and Specificity ; Species Specificity ; }, abstract = {Identification of species from trace samples is now possible through the comparison of diagnostic DNA fragments against reference DNA sequence databases. DNA detection of animals from non-invasive samples, such as predator faeces (scats) that contain traces of DNA from their species of origin, has proved to be a valuable tool for the management of elusive wildlife. However, application of this approach can be limited by the availability of appropriate genetic markers. Scat DNA is often degraded, meaning that longer DNA sequences, including standard DNA barcoding markers, are difficult to recover. Instead, targeted short diagnostic markers are required to serve as diagnostic mini-barcodes. The mitochondrial genome is a useful source of such trace DNA markers because it provides good resolution at the species level and occurs in high copy numbers per cell. We developed a mini-barcode based on a short (178 bp) fragment of the conserved 12S ribosomal ribonucleic acid mitochondrial gene sequence, with the goal of discriminating amongst the scats of large mammalian predators of Australia. We tested the sensitivity and specificity of our primers and can accurately detect and discriminate amongst quolls, cats, dogs, foxes, and devils from trace DNA samples. Our approach provides a cost-effective, time-efficient, and non-invasive tool that enables identification of all 8 medium-large mammal predators in Australia, including native and introduced species, using a single test. With modification, this approach is likely to be of broad applicability elsewhere.}, } @article {pmid28808547, year = {2017}, author = {Springer, A and Fichtel, C and Al-Ghalith, GA and Koch, F and Amato, KR and Clayton, JB and Knights, D and Kappeler, PM}, title = {Patterns of seasonality and group membership characterize the gut microbiota in a longitudinal study of wild Verreaux's sifakas (Propithecus verreauxi).}, journal = {Ecology and evolution}, volume = {7}, number = {15}, pages = {5732-5745}, pmid = {28808547}, issn = {2045-7758}, support = {T32 DA007097/DA/NIDA NIH HHS/United States ; }, abstract = {The intestinal microbiota plays a major role in host development, metabolism, and health. To date, few longitudinal studies have investigated the causes and consequences of microbiota variation in wildlife, although such studies provide a comparative context for interpreting the adaptive significance of findings from studies on humans or captive animals. Here, we investigate the impact of seasonality, diet, group membership, sex, age, and reproductive state on gut microbiota composition in a wild population of group-living, frugi-folivorous primates, Verreaux's sifakas (Propithecus verreauxi). We repeatedly sampled 32 individually recognizable animals from eight adjacent groups over the course of two different climatic seasons. We used high-throughput sequencing of the 16S rRNA gene to determine the microbiota composition of 187 fecal samples. We demonstrate a clear pattern of seasonal variation in the intestinal microbiota, especially affecting the Firmicutes-Bacteroidetes ratio, which may be driven by seasonal differences in diet. The relative abundances of certain polysaccharide-fermenting taxa, for example, Lachnospiraceae, were correlated with fruit and fiber consumption. Additionally, group membership influenced microbiota composition independent of season, but further studies are needed to determine whether this pattern is driven by group divergences in diet, social contacts, or genetic factors. In accordance with findings in other wild mammals and primates with seasonally fluctuating food availability, we demonstrate seasonal variation in the microbiota of wild Verreaux's sifakas, which may be driven by food availability. This study adds to mounting evidence that variation in the intestinal microbiota may play an important role in the ability of primates to cope with seasonal variation in food availability.}, } @article {pmid28803376, year = {2017}, author = {Chen, CY and Wang, Q}, title = {Debris flow-induced topographic changes: effects of recurrent debris flow initiation.}, journal = {Environmental monitoring and assessment}, volume = {189}, number = {9}, pages = {449}, pmid = {28803376}, issn = {1573-2959}, mesh = {*Environmental Monitoring ; Geographic Information Systems ; Hydrology ; Landslides ; Rivers/*chemistry ; Taiwan ; *Water Movements ; Water Pollutants/*analysis ; }, abstract = {Chushui Creek in Shengmu Village, Nantou County, Taiwan, was analyzed for recurrent debris flow using numerical modeling and geographic information system (GIS) spatial analysis. The two-dimensional water flood and mudflow simulation program FLO-2D were used to simulate debris flow induced by rainfall during typhoon Herb in 1996 and Mindulle in 2004. Changes in topographic characteristics after the debris flows were simulated for the initiation of hydrological characteristics, magnitude, and affected area. Changes in topographic characteristics included those in elevation, slope, aspect, stream power index (SPI), topographic wetness index (TWI), and hypsometric curve integral (HI), all of which were analyzed using GIS spatial analysis. The results show that the SPI and peak discharge in the basin increased after a recurrence of debris flow. The TWI was higher in 2003 than in 2004 and indicated higher potential of landslide initiation when the slope of the basin was steeper. The HI revealed that the basin was in its mature stage and was shifting toward the old stage. Numerical simulation demonstrated that the parameters' mean depth, maximum depth, affected area, mean flow rate, maximum flow rate, and peak flow discharge were increased after recurrent debris flow, and peak discharge occurred quickly.}, } @article {pmid28802139, year = {2017}, author = {Gómez-Canela, C and Prats, E and Tauler, R and Raldúa, D}, title = {Analysis of neurobehavioural data by chemometric methods in ecotoxicological studies.}, journal = {Ecotoxicology and environmental safety}, volume = {145}, number = {}, pages = {583-590}, doi = {10.1016/j.ecoenv.2017.08.013}, pmid = {28802139}, issn = {1090-2414}, mesh = {Analysis of Variance ; Animals ; Behavior, Animal/*drug effects ; Chlorpyrifos/metabolism/toxicity ; Ecotoxicology/*methods/statistics & numerical data ; Environmental Pollutants/metabolism/*toxicity ; Motor Activity/*drug effects ; Nicotine/metabolism/toxicity ; Principal Component Analysis ; Zebrafish/*metabolism ; }, abstract = {Incorporation of chemometric tools in behavioural data management workflows allows for the early identification of most relevant endpoints complementarily to statistical confirmatory approaches. In this work, the effects of two model neurotoxicants, chlorpyrifos (CPF) and nicotine, exposures on behavioural profiles of adult zebrafish at three different times (2, 6 and 24h) were evaluated using open field test (OFT) paradigm experiments. Two chemometric methods like Principal Component Analysis (PCA) and Analysis of Variance-Simultaneous Component Analysis (ASCA) have been used to interpret the changes observed in the obtained behavioural data. A decreased of the locomotor activity, an anxiolytic effect and an altered exploratory behaviour were the most affected behavioural endpoints in the CPF exposures. However, an increase of the locomotor activity and an anxiogenic effect were observed in the nicotine exposures. Finally, an excellent correlation between the ASCA results and the results obtained using traditional statistical procedures for both compounds were encountered.}, } @article {pmid28800376, year = {2018}, author = {van der Valk, J and Bieback, K and Buta, C and Cochrane, B and Dirks, WG and Fu, J and Hickman, JJ and Hohensee, C and Kolar, R and Liebsch, M and Pistollato, F and Schulz, M and Thieme, D and Weber, T and Wiest, J and Winkler, S and Gstraunthaler, G}, title = {Fetal Bovine Serum (FBS): Past - Present - Future.}, journal = {ALTEX}, volume = {35}, number = {1}, pages = {99-118}, doi = {10.14573/altex.1705101}, pmid = {28800376}, issn = {1868-8551}, mesh = {*Animal Testing Alternatives ; Animal Welfare ; Animals ; Cattle ; Cell Culture Techniques/methods ; Cell Differentiation ; *Culture Media, Serum-Free ; Databases, Factual ; Education ; *Fetal Blood ; Humans ; }, abstract = {The supplementation of culture medium with fetal bovine serum (FBS, also referred to as "fetal calf serum") is still common practice in cell culture applications. Due to a number of disadvantages in terms of quality and reproducibility of in vitro data, animal welfare concerns, and in light of recent cases of fraudulent marketing, the search for alternatives and the development of serum-free medium formulations has gained global attention. Here, we report on the 3rd Workshop on FBS, Serum Alternatives and Serum-free Media, where regulatory aspects, the serum dilemma, alternatives to FBS, case-studies of serum-free in vitro applications, and the establishment of serum-free databases were discussed. The whole process of obtaining blood from a living calf fetus to using the FBS produced from it for scientific purposes is de facto not yet legally regulated despite the existing EU-Directive 2010/63/EU on the use of animals for scientific purposes. Together with the above-mentioned challenges, several strategies have been developed to reduce or replace FBS in cell culture media in terms of the 3Rs (Refinement, Reduction, Replacement). Most recently, releasates of activated human donor thrombocytes (human platelet lysates) have been shown to be one of the most promising serum alternatives when chemically-defined media are not yet an option. Additionally, new developments in cell-based assay techniques, advanced organ-on-chip and microphysiological systems are covered in this report. Chemically-defined serum-free media are shown to be the ultimate goal for the majority of culture systems, and examples are discussed.}, } @article {pmid28798083, year = {2017}, author = {McLachlan, S and Page, KE and Lee, SM and Loguinov, A and Valore, E and Hui, ST and Jung, G and Zhou, J and Lusis, AJ and Fuqua, B and Ganz, T and Nemeth, E and Vulpe, CD}, title = {Hamp1 mRNA and plasma hepcidin levels are influenced by sex and strain but do not predict tissue iron levels in inbred mice.}, journal = {American journal of physiology. Gastrointestinal and liver physiology}, volume = {313}, number = {5}, pages = {G511-G523}, pmid = {28798083}, issn = {1522-1547}, support = {F32 CA094588/CA/NCI NIH HHS/United States ; R01 DK065029/DK/NIDDK NIH HHS/United States ; R01 DK107309/DK/NIDDK NIH HHS/United States ; R01 GM083198/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Diet ; Female ; Hepcidins/*biosynthesis/genetics ; Iron/*metabolism ; Iron, Dietary/pharmacology ; Male ; Mice ; Mice, Inbred Strains ; RNA, Messenger/*biosynthesis ; Sex Characteristics ; Species Specificity ; Tissue Distribution ; Transferrin/metabolism ; }, abstract = {Iron homeostasis is tightly regulated, and the peptide hormone hepcidin is considered to be a principal regulator of iron metabolism. Previous studies in a limited number of mouse strains found equivocal sex- and strain-dependent differences in mRNA and serum levels of hepcidin and reported conflicting data on the relationship between hepcidin (Hamp1) mRNA levels and iron status. Our aim was to clarify the relationships between strain, sex, and hepcidin expression by examining multiple tissues and the effects of different dietary conditions in multiple inbred strains. Two studies were done: first, Hamp1 mRNA, liver iron, and plasma diferric transferrin levels were measured in 14 inbred strains on a control diet; and second, Hamp1 mRNA and plasma hepcidin levels in both sexes and iron levels in the heart, kidneys, liver, pancreas, and spleen in males were measured in nine inbred/recombinant inbred strains raised on an iron-sufficient or high-iron diet. Both sex and strain have a significant effect on both hepcidin mRNA (primarily a sex effect) and plasma hepcidin levels (primarily a strain effect). However, liver iron and diferric transferrin levels are not predictors of Hamp1 mRNA levels in mice fed iron-sufficient or high-iron diets, nor are the Hamp1 mRNA and plasma hepcidin levels good predictors of tissue iron levels, at least in males. We also measured plasma erythroferrone, performed RNA-sequencing analysis of liver samples from six inbred strains fed the iron-sufficient, low-iron, or high-iron diets, and explored differences in gene expression between the strains with the highest and lowest hepcidin levels.NEW & NOTEWORTHY Both sex and strain have a significant effect on both hepcidin mRNA (primarily a sex effect) and plasma hepcidin levels (primarily a strain effect). Liver iron and diferric transferrin levels are not predictors of Hamp1 mRNA levels in mice, nor are the Hamp1 mRNA and plasma hepcidin levels good predictors of tissue iron levels, at least in males.}, } @article {pmid28798017, year = {2017}, author = {Thompson, MP and Zhao, X and Bekelis, K and Gottlieb, DJ and Fonarow, GC and Schulte, PJ and Xian, Y and Lytle, BL and Schwamm, LH and Smith, EE and Reeves, MJ}, title = {Regional Variation in 30-Day Ischemic Stroke Outcomes for Medicare Beneficiaries Treated in Get With The Guidelines-Stroke Hospitals.}, journal = {Circulation. Cardiovascular quality and outcomes}, volume = {10}, number = {8}, pages = {}, doi = {10.1161/CIRCOUTCOMES.117.003604}, pmid = {28798017}, issn = {1941-7705}, mesh = {Administrative Claims, Healthcare ; Aged ; Brain Ischemia/diagnosis/ethnology/mortality/*therapy ; Databases, Factual ; Fee-for-Service Plans/standards ; Female ; Guideline Adherence/*standards ; Health Resources/standards/statistics & numerical data ; Healthcare Disparities/*standards ; Hospitals/*standards ; Humans ; Insurance Benefits/*standards ; Male ; Medicare/*standards ; Patient Readmission/standards ; Practice Guidelines as Topic/*standards ; Process Assessment, Health Care/*standards ; Quality Indicators, Health Care/*standards ; Registries ; Risk Factors ; Stroke/diagnosis/ethnology/mortality/*therapy ; Time Factors ; Treatment Outcome ; United States/epidemiology ; }, abstract = {BACKGROUND: We explored regional variation in 30-day ischemic stroke mortality and readmission rates and the extent to which regional differences in patients, hospitals, healthcare resources, and a quality of care composite care measure explain the observed variation.

METHODS AND RESULTS: This ecological analysis aggregated patient and hospital characteristics from the Get With The Guidelines-Stroke registry (2007-2011), healthcare resource data from the Dartmouth Atlas of Health Care (2006), and Medicare fee-for-service data on 30-day mortality and readmissions (2007-2011) to the hospital referral region (HRR) level. We used linear regression to estimate adjusted HRR-level 30-day outcomes, to identify HRR-level characteristics associated with 30-day outcomes, and to describe which characteristics explained variation in 30-day outcomes. The mean adjusted HRR-level 30-day mortality and readmission rates were 10.3% (SD=1.1%) and 13.1% (SD=1.1%), respectively; a modest, negative correlation (r=-0.17; P=0.003) was found between one another. Demographics explained more variation in readmissions than mortality (25% versus 6%), but after accounting for demographics, comorbidities accounted for more variation in mortality compared with readmission rates (17% versus 7%). The combination of hospital characteristics and healthcare resources explained 11% and 16% of the variance in mortality and readmission rates, beyond patient characteristics. Most of the regional variation in mortality (65%) and readmission (50%) rates remained unexplained.

CONCLUSIONS: Thirty-day mortality and readmission rates vary substantially across HRRs and exhibit an inverse relationship. While regional variation in 30-day outcomes were explained by patient and hospital factors differently, much of the regional variation in both outcomes remains unexplained.}, } @article {pmid28796213, year = {2017}, author = {Schwalm, CR and Anderegg, WRL and Michalak, AM and Fisher, JB and Biondi, F and Koch, G and Litvak, M and Ogle, K and Shaw, JD and Wolf, A and Huntzinger, DN and Schaefer, K and Cook, R and Wei, Y and Fang, Y and Hayes, D and Huang, M and Jain, A and Tian, H}, title = {Global patterns of drought recovery.}, journal = {Nature}, volume = {548}, number = {7666}, pages = {202-205}, pmid = {28796213}, issn = {1476-4687}, mesh = {Biodiversity ; Carbon Dioxide/analysis ; Carbon Sequestration ; Droughts/history/*statistics & numerical data ; *Ecosystem ; Global Warming ; History, 20th Century ; History, 21st Century ; *Internationality ; Rain ; Soil/chemistry ; *Spatio-Temporal Analysis ; Temperature ; Time Factors ; Tropical Climate ; Wildfires ; }, abstract = {Drought, a recurring phenomenon with major impacts on both human and natural systems, is the most widespread climatic extreme that negatively affects the land carbon sink. Although twentieth-century trends in drought regimes are ambiguous, across many regions more frequent and severe droughts are expected in the twenty-first century. Recovery time-how long an ecosystem requires to revert to its pre-drought functional state-is a critical metric of drought impact. Yet the factors influencing drought recovery and its spatiotemporal patterns at the global scale are largely unknown. Here we analyse three independent datasets of gross primary productivity and show that, across diverse ecosystems, drought recovery times are strongly associated with climate and carbon cycle dynamics, with biodiversity and CO2 fertilization as secondary factors. Our analysis also provides two key insights into the spatiotemporal patterns of drought recovery time: first, that recovery is longest in the tropics and high northern latitudes (both vulnerable areas of Earth's climate system) and second, that drought impacts (assessed using the area of ecosystems actively recovering and time to recovery) have increased over the twentieth century. If droughts become more frequent, as expected, the time between droughts may become shorter than drought recovery time, leading to permanently damaged ecosystems and widespread degradation of the land carbon sink.}, } @article {pmid28795407, year = {2018}, author = {Mihaljevic, JR and Hoye, BJ and Johnson, PTJ}, title = {Parasite metacommunities: Evaluating the roles of host community composition and environmental gradients in structuring symbiont communities within amphibians.}, journal = {The Journal of animal ecology}, volume = {87}, number = {2}, pages = {354-368}, pmid = {28795407}, issn = {1365-2656}, support = {R01 GM109499/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Anura/*microbiology ; *Biodiversity ; California ; Host Microbial Interactions/*physiology ; *Models, Biological ; Population Density ; Snails/microbiology ; Wetlands ; }, abstract = {Ecologists increasingly report the structures of metacommunities for free-living species, yet far less is known about the composition of symbiont communities through space and time. Understanding the drivers of symbiont community patterns has implications ranging from emerging infectious disease to managing host microbiomes. Using symbiont communities from amphibian hosts sampled from wetlands of California, USA, we quantified the effects of spatial structure, habitat filtering and host community components on symbiont occupancy and overall metacommunity structure. We built upon a statistical method to describe metacommunity structure that accounts for imperfect detection in survey data-detection error-corrected elements of metacommunity structure-by adding an analysis to identify covariates of community turnover. We applied our model to a metacommunity of eight parasite taxa observed in 3,571 Pacific chorus frogs (Pseudacris regilla) surveyed from 174 wetlands over 5 years. Symbiont metacommunity structure varied across years, showing nested structure in 3 years and random structure in 2 years. Species turnover was most consistently influenced by spatial and host community components. Occupancy generally increased in more southeastern wetlands, and snail (intermediate host) community composition had strong effects on most symbiont taxa. We have used sophisticated but accessible statistical methods to reveal that spatial components-which influence colonization-and host community composition-which mediates transmission-both drive symbiont community composition in this system. These methods allow us to associate broad patterns of community turnover to local, species-level effects, ultimately improving our understanding of spatial community dynamics.}, } @article {pmid28790328, year = {2017}, author = {Gao, B and Li, X and Zhang, D and Liang, Y and Yang, H and Chen, M and Zhang, Y and Zhang, J and Wood, AJ}, title = {Desiccation tolerance in bryophytes: The dehydration and rehydration transcriptomes in the desiccation-tolerant bryophyte Bryum argenteum.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {7571}, pmid = {28790328}, issn = {2045-2322}, mesh = {Bryopsida/*genetics/*physiology ; Computational Biology ; *Dehydration ; *Fluid Therapy ; *Gene Expression Profiling ; Molecular Sequence Annotation ; Plant Proteins/biosynthesis/genetics ; Sequence Analysis, RNA ; }, abstract = {The desiccation tolerant bryophyte Bryum argenteum is an important component of desert biological soil crusts (BSCs) and is emerging as a model system for studying vegetative desiccation tolerance. Here we present and analyze the hydration-dehydration-rehydration transcriptomes in B. argenteum to establish a desiccation-tolerance transcriptomic atlas. B. argenteum gametophores representing five different hydration stages (hydrated (H0), dehydrated for 2 h (D2), 24 h (D24), then rehydrated for 2 h (R2) and 48 h (R48)), were sampled for transcriptome analyses. Illumina high throughput RNA-Seq technology was employed and generated more than 488.46 million reads. An in-house de novo transcriptome assembly optimization pipeline based on Trinity assembler was developed to obtain a reference Hydration-Dehydration-Rehydration (H-D-R) transcriptome comprising of 76,206 transcripts, with an N50 of 2,016 bp and average length of 1,222 bp. Comprehensive transcription factor (TF) annotation discovered 978 TFs in 62 families, among which 404 TFs within 40 families were differentially expressed upon dehydration-rehydration. Pfam term enrichment analysis revealed 172 protein families/domains were significantly associated with the H-D-R cycle and confirmed early rehydration (i.e. the R2 stage) as exhibiting the maximum stress-induced changes in gene expression.}, } @article {pmid28789971, year = {2017}, author = {Wills, LP}, title = {The use of high-throughput screening techniques to evaluate mitochondrial toxicity.}, journal = {Toxicology}, volume = {391}, number = {}, pages = {34-41}, doi = {10.1016/j.tox.2017.07.020}, pmid = {28789971}, issn = {1879-3185}, mesh = {Animals ; Biomarkers/metabolism ; Cells, Cultured ; Computational Biology ; Databases, Protein ; Dose-Response Relationship, Drug ; Ecotoxicology/*methods ; Environmental Exposure/adverse effects ; Environmental Pollutants/*toxicity ; *High-Throughput Screening Assays ; Humans ; Mitochondria/*drug effects/metabolism/pathology ; Risk Assessment ; Structure-Activity Relationship ; Time Factors ; }, abstract = {Toxicologists and chemical regulators depend on accurate and effective methods to evaluate and predict the toxicity of thousands of current and future compounds. Robust high-throughput screening (HTS) experiments have the potential to efficiently test large numbers of chemical compounds for effects on biological pathways. HTS assays can be utilized to examine chemical toxicity across multiple mechanisms of action, experimental models, concentrations, and lengths of exposure. Many agricultural, industrial, and pharmaceutical chemicals classified as harmful to human and environmental health exert their effects through the mechanism of mitochondrial toxicity. Mitochondrial toxicants are compounds that cause a decrease in the number of mitochondria within a cell, and/or decrease the ability of mitochondria to perform normal functions including producing adenosine triphosphate (ATP) and maintaining cellular homeostasis. Mitochondrial dysfunction can lead to apoptosis, necrosis, altered metabolism, muscle weakness, neurodegeneration, decreased organ function, and eventually disease or death of the whole organism. The development of HTS techniques to identify mitochondrial toxicants will provide extensive databases with essential connections between mechanistic mitochondrial toxicity and chemical structure. Computational and bioinformatics approaches can be used to evaluate compound databases for specific chemical structures associated with toxicity, with the goal of developing quantitative structure-activity relationship (QSAR) models and mitochondrial toxicophores. Ultimately these predictive models will facilitate the identification of mitochondrial liabilities in consumer products, industrial compounds, pharmaceuticals and environmental hazards.}, } @article {pmid28789649, year = {2017}, author = {George, MA and Jin, A and Brussoni, M and Lalonde, CE and McCormick, R}, title = {Intentional injury among the indigenous and total populations in British Columbia, Canada: trends over time and ecological analyses of risk.}, journal = {International journal for equity in health}, volume = {16}, number = {1}, pages = {141}, pmid = {28789649}, issn = {1475-9276}, support = {AHR # 81043//CIHR/Canada ; }, mesh = {Adolescent ; Adult ; Aged ; Aged, 80 and over ; British Columbia/epidemiology ; Child ; Child, Preschool ; Databases, Factual ; Female ; *Health Status Disparities ; Hospitalization/*statistics & numerical data ; Humans ; Indians, North American/*psychology/statistics & numerical data ; Infant ; Infant, Newborn ; Insurance, Health ; Male ; Middle Aged ; Risk Factors ; Self-Injurious Behavior/*epidemiology/ethnology/therapy ; Young Adult ; }, abstract = {BACKGROUND: Our objective was to explore intentional injury disparity between Indigenous populations and the total population in the province of British Columbia (BC), Canada. We focus on hospitalizations, including both self-inflicted injuries and injuries inflicted by others.

METHODS: We used data from BC's universal health care insurance plan, 1991 to 2010, linked to Vital Statistics databases. Indigenous people were identified through the insurance premium group, and birth and death records. Place of residence was identified through postal code. We calculated crude hospitalization incidence rates and the Standardized Relative Risk (SRR) of hospitalization, standardized by gender, 5-year age group, and Health Service Delivery Area (HSDA). With HSDA populations as the units of observation, linear regression was used to test hypothesized associations of Indigenous ethnicity, geographic, and socio-economic characteristics with SRR of injury.

RESULTS: During the period 1991-2010, the crude rate of hospitalization for intentional injuries was 8.4 per 10,000 person-years (95% confidence interval (CI): 8.3 to 8.5) for the total BC population, compared to 45.3 per 10,000 (95% CI: 44.5 to 46.1) for the Indigenous population. For both populations, risk declined over the period for injuries self-inflicted and inflicted by others. The linear regression model predicts that the off-reserve Indigenous population will have SRR of intentional injury 3.98 greater, and the on-reserve Indigenous population 4.17, greater than the total population. The final model was an excellent fit (R[2] = 0.912, F = 177.632, p < 0.001), and found that three variables - occupational risk, high school diploma, and university degree - each provide independent effects when interacting multiplicatively with Indigenous ethnicity.

CONCLUSIONS: The observation of substantially declining rates of intentional injury for both the Indigenous and total BC populations is off-set by the high disparity in risk between the two populations, which will likely continue until Canada reduces disparity with respect to discriminatory practices, and physical, social, and economic conditions.}, } @article {pmid28786958, year = {2017}, author = {Koua, D and Kuhn-Nentwig, L}, title = {Spider Neurotoxins, Short Linear Cationic Peptides and Venom Protein Classification Improved by an Automated Competition between Exhaustive Profile HMM Classifiers.}, journal = {Toxins}, volume = {9}, number = {8}, pages = {}, pmid = {28786958}, issn = {2072-6651}, mesh = {Animals ; Arthropod Proteins/*classification ; Databases, Protein ; Neurotoxins/*classification ; Peptides/*classification ; Proteomics ; Spider Venoms/*classification ; Spiders ; }, abstract = {Spider venoms are rich cocktails of bioactive peptides, proteins, and enzymes that are being intensively investigated over the years. In order to provide a better comprehension of that richness, we propose a three-level family classification system for spider venom components. This classification is supported by an exhaustive set of 219 new profile hidden Markov models (HMMs) able to attribute a given peptide to its precise peptide type, family, and group. The proposed classification has the advantages of being totally independent from variable spider taxonomic names and can easily evolve. In addition to the new classifiers, we introduce and demonstrate the efficiency of hmmcompete, a new standalone tool that monitors HMM-based family classification and, after post-processing the result, reports the best classifier when multiple models produce significant scores towards given peptide queries. The combined used of hmmcompete and the new spider venom component-specific classifiers demonstrated 96% sensitivity to properly classify all known spider toxins from the UniProtKB database. These tools are timely regarding the important classification needs caused by the increasing number of peptides and proteins generated by transcriptomic projects.}, } @article {pmid28786955, year = {2017}, author = {Arafat, Y and Wei, X and Jiang, Y and Chen, T and Saqib, HSA and Lin, S and Lin, W}, title = {Spatial Distribution Patterns of Root-Associated Bacterial Communities Mediated by Root Exudates in Different Aged Ratooning Tea Monoculture Systems.}, journal = {International journal of molecular sciences}, volume = {18}, number = {8}, pages = {}, pmid = {28786955}, issn = {1422-0067}, mesh = {Bacteria/*classification/genetics ; Biodiversity ; Chromatography, High Pressure Liquid ; Cluster Analysis ; Computational Biology/methods ; *Exudates and Transudates ; High-Throughput Nucleotide Sequencing ; Metagenome ; Metagenomics/methods ; Plant Roots/*chemistry/*microbiology ; *Rhizosphere ; Soil/chemistry ; Soil Microbiology ; Spectrometry, Mass, Electrospray Ionization ; *Tea ; }, abstract = {Positive plant-soil feedback depends on beneficial interactions between roots and microbes for nutrient acquisition; growth promotion; and disease suppression. Recent pyrosequencing approaches have provided insight into the rhizosphere bacterial communities in various cropping systems. However; there is a scarcity of information about the influence of root exudates on the composition of root-associated bacterial communities in ratooning tea monocropping systems of different ages. In Southeastern China; tea cropping systems provide the unique natural experimental environment to compare the distribution of bacterial communities in different rhizo-compartments. High performance liquid chromatography-electrospray ionization-mass spectrometry (HPLC-ESI-MS) was performed to identify and quantify the allelochemicals in root exudates. A high-throughput sequence was used to determine the structural dynamics of the root-associated bacterial communities. Although soil physiochemical properties showed no significant differences in nutrients; long-term tea cultivation resulted in the accumulation of catechin-containing compounds in the rhizosphere and a lowering of pH. Moreover; distinct distribution patterns of bacterial taxa were observed in all three rhizo-compartments of two-year and 30-year monoculture tea; mediated strongly by soil pH and catechin-containing compounds. These results will help to explore the reasons why soil quality and fertility are disturbed in continuous ratooning tea monocropping systems; and to clarify the associated problems.}, } @article {pmid28783905, year = {2017}, author = {Destrieux, D and Laurent, F and Budzinski, H and Pedelucq, J and Vervier, P and Gerino, M}, title = {Drug residues in urban water: A database for ecotoxicological risk management.}, journal = {The Science of the total environment}, volume = {609}, number = {}, pages = {927-941}, doi = {10.1016/j.scitotenv.2017.07.043}, pmid = {28783905}, issn = {1879-1026}, mesh = {Cities ; *Databases, Factual ; Drug Residues/*analysis ; *Ecotoxicology ; *Environmental Monitoring ; Risk Assessment ; Rivers ; Water Pollutants, Chemical/*analysis ; }, abstract = {Human-use drug residues (DR) are only partially eliminated by waste water treatment plants (WWTPs), so that residual amounts can reach natural waters and cause environmental hazards. In order to properly manage these hazards in the aquatic environment, a database is made available that integrates the concentration ranges for DR, which cause adverse effects for aquatic organisms, and the temporal variations of the ecotoxicological risks. To implement this database for the ecotoxicological risk assessment (ERA database), the required information for each DR is the predicted no effect concentrations (PNECs), along with the predicted environmental concentrations (PECs). The risk assessment is based on the ratio between the PNECs and the PECs. Adverse effect data or PNECs have been found in the publicly available literature for 45 substances. These ecotoxicity test data have been extracted from 125 different sources. This ERA database contains 1157 adverse effect data and 287 PNECs. The efficiency of this ERA database was tested with a data set coming from a simultaneous survey of WWTPs and the natural environment. In this data set, 26 DR were searched for in two WWTPs and in the river. On five sampling dates, concentrations measured in the river for 10 DR could pose environmental problems of which 7 were measured only downstream of WWTP outlets. From scientific literature and measurements, data implementation with unit homogenisation in a single database facilitates the actual ecotoxicological risk assessment, and may be useful for further risk coming from data arising from the future field survey. Moreover, the accumulation of a large ecotoxicity data set in a single database should not only improve knowledge of higher risk molecules but also supply an objective tool to help the rapid and efficient evaluation of the risk.}, } @article {pmid28783637, year = {2018}, author = {Gramazio, CC and Huang, J and Laidlaw, DH}, title = {An Analysis of Automated Visual Analysis Classification: Interactive Visualization Task Inference of Cancer Genomics Domain Experts.}, journal = {IEEE transactions on visualization and computer graphics}, volume = {24}, number = {8}, pages = {2270-2283}, doi = {10.1109/TVCG.2017.2734659}, pmid = {28783637}, issn = {1941-0506}, mesh = {Algorithms ; *Computer Graphics/classification ; Data Interpretation, Statistical ; Expert Systems ; Genomics/*methods/statistics & numerical data ; Humans ; Neoplasms/*genetics ; Online Systems ; Pattern Recognition, Automated/classification/methods/statistics & numerical data ; User-Computer Interface ; }, abstract = {We show how mouse interaction log classification can help visualization toolsmiths understand how their tools are used "in the wild" through an evaluation of MAGI - a cancer genomics visualization tool. Our primary contribution is an evaluation of twelve visual analysis task classifiers, which compares predictions to task inferences made by pairs of genomics and visualization experts. Our evaluation uses common classifiers that are accessible to most visualization evaluators: -nearest neighbors, linear support vector machines, and random forests. By comparing classifier predictions to visual analysis task inferences made by experts, we show that simple automated task classification can have up to 73 percent accuracy and can separate meaningful logs from "junk" logs with up to 91 percent accuracy. Our second contribution is an exploration of common MAGI interaction trends using classification predictions, which expands current knowledge about ecological cancer genomics visualization tasks. Our third contribution is a discussion of how automated task classification can inform iterative tool design. These contributions suggest that mouse interaction log analysis is a viable method for (1) evaluating task requirements of client-side-focused tools, (2) allowing researchers to study experts on larger scales than is typically possible with in-lab observation, and (3) highlighting potential tool evaluation bias.}, } @article {pmid28783034, year = {2017}, author = {Reiczigel, J and Rozsa, L}, title = {Do small samples underestimate mean abundance? It depends on what type of bias we consider.}, journal = {Folia parasitologica}, volume = {64}, number = {}, pages = {}, doi = {10.14411/fp.2017.025}, pmid = {28783034}, issn = {0015-5683}, mesh = {Animals ; Bias ; Humans ; Parasites/*growth & development ; Parasitic Diseases/*parasitology ; Parasitology/*methods ; Sample Size ; }, abstract = {Former authors claimed that, due to parasites' aggregated distribution, small samples underestimate the true population mean abundance. Here we show that this claim is false or true, depending on what is meant by 'underestimate' or, mathematically speaking, how we define 'bias'. The 'how often' and 'on average' views lead to different conclusions because sample mean abundance itself exhibits an aggregated distribution: most often it falls slightly below the true population mean, while sometimes greatly exceeds it. Since the several small negative deviations are compensated by a few greater positive ones, the average of sample means approximates the true population mean.}, } @article {pmid28782807, year = {2017}, author = {Cline, LC and Song, Z and Al-Ghalith, GA and Knights, D and Kennedy, PG}, title = {Moving beyond de novo clustering in fungal community ecology.}, journal = {The New phytologist}, volume = {216}, number = {3}, pages = {629-634}, doi = {10.1111/nph.14752}, pmid = {28782807}, issn = {1469-8137}, mesh = {Algorithms ; Cluster Analysis ; Ecology ; Forests ; Fungi/*classification ; High-Throughput Nucleotide Sequencing ; *Mycobiome ; Plant Leaves/microbiology ; Soil Microbiology ; Wood/microbiology ; }, } @article {pmid28780265, year = {2017}, author = {Hu, R and Zheng, X and Xin, J and Sun, Z and Zheng, T}, title = {Selective enhancement and verification of woody biomass digestibility as a denitrification carbon source.}, journal = {Bioresource technology}, volume = {244}, number = {Pt 1}, pages = {313-319}, doi = {10.1016/j.biortech.2017.07.162}, pmid = {28780265}, issn = {1873-2976}, mesh = {*Biomass ; Carbon ; *Denitrification ; Nitrates ; Wood ; }, abstract = {The denitrification efficiency of woody biomass as carbon source is low because of its poor carbon availability. In this study, representative poplar sawdust was pretreated with lime and peracetic acid to enhance the biomass digestibility to different degrees; sawdust was then mixed with soil to investigate its denitrification efficiency. Under controllable conditions (25-95°C, 12-24h, varying dosages), sawdust digestibility (characterized by reducing sugar yield) was selectively enhanced 1.0-21.8 times over that of the raw sawdust (28.8mgeq.glucoseg[-1] dry biomass). This increase was mainly attributed to the removal of lignin from the biomass. As a carbon source, the sawdust (digestibility enhanced by 5.4 times) increased the nitrate removal rate by 4.7 times, without N2O emission. However, the sawdust with high digestibility (12.6 or 18.0 times), despite releasing more dissolved organic carbon (DOC), did not exhibit further increase in denitrification efficiency, and emitted N2O.}, } @article {pmid28777822, year = {2017}, author = {Demšar, U and Çöltekin, A}, title = {Quantifying gaze and mouse interactions on spatial visual interfaces with a new movement analytics methodology.}, journal = {PloS one}, volume = {12}, number = {8}, pages = {e0181818}, pmid = {28777822}, issn = {1932-6203}, mesh = {Adult ; Attention ; Diagnosis, Computer-Assisted/*methods ; Eye Movement Measurements/*instrumentation ; Eye Movements/*physiology ; Female ; Fixation, Ocular/*physiology ; Humans ; Male ; Middle Aged ; Spatial Processing/*physiology ; *User-Computer Interface ; Visual Perception/*physiology ; }, abstract = {Eye movements provide insights into what people pay attention to, and therefore are commonly included in a variety of human-computer interaction studies. Eye movement recording devices (eye trackers) produce gaze trajectories, that is, sequences of gaze location on the screen. Despite recent technological developments that enabled more affordable hardware, gaze data are still costly and time consuming to collect, therefore some propose using mouse movements instead. These are easy to collect automatically and on a large scale. If and how these two movement types are linked, however, is less clear and highly debated. We address this problem in two ways. First, we introduce a new movement analytics methodology to quantify the level of dynamic interaction between the gaze and the mouse pointer on the screen. Our method uses volumetric representation of movement, the space-time densities, which allows us to calculate interaction levels between two physically different types of movement. We describe the method and compare the results with existing dynamic interaction methods from movement ecology. The sensitivity to method parameters is evaluated on simulated trajectories where we can control interaction levels. Second, we perform an experiment with eye and mouse tracking to generate real data with real levels of interaction, to apply and test our new methodology on a real case. Further, as our experiment tasks mimics route-tracing when using a map, it is more than a data collection exercise and it simultaneously allows us to investigate the actual connection between the eye and the mouse. We find that there seem to be natural coupling when eyes are not under conscious control, but that this coupling breaks down when instructed to move them intentionally. Based on these observations, we tentatively suggest that for natural tracing tasks, mouse tracking could potentially provide similar information as eye-tracking and therefore be used as a proxy for attention. However, more research is needed to confirm this.}, } @article {pmid28776963, year = {2017}, author = {Pina-Martins, F and Silva, DN and Fino, J and Paulo, OS}, title = {Structure_threader: An improved method for automation and parallelization of programs structure, fastStructure and MavericK on multicore CPU systems.}, journal = {Molecular ecology resources}, volume = {17}, number = {6}, pages = {e268-e274}, doi = {10.1111/1755-0998.12702}, pmid = {28776963}, issn = {1755-0998}, mesh = {*Cluster Analysis ; Computational Biology/*methods ; Genotyping Techniques/methods ; *Software ; }, abstract = {Structure_threader is a program to parallelize multiple runs of genetic clustering software that does not make use of multithreading technology (structure, fastStructure and MavericK) on multicore computers. Our approach was benchmarked across multiple systems and displayed great speed improvements relative to the single-threaded implementation, scaling very close to linearly with the number of physical cores used. Structure_threader was compared to previous software written for the same task-ParallelStructure and StrAuto and was proven to be the faster (up to 25% faster) wrapper under all tested scenarios. Furthermore, Structure_threader can perform several automatic and convenient operations, assisting the user in assessing the most biologically likely value of 'K' via implementations such as the "Evanno," or "Thermodynamic Integration" tests and automatically draw the "meanQ" plots (static or interactive) for each value of K (or even combined plots). Structure_threader is written in python 3 and licensed under the GPLv3. It can be downloaded free of charge at https://github.com/StuntsPT/Structure_threader.}, } @article {pmid28776912, year = {2017}, author = {Wringe, BF and Stanley, RRE and Jeffery, NW and Anderson, EC and Bradbury, IR}, title = {hybriddetective: A workflow and package to facilitate the detection of hybridization using genomic data in r.}, journal = {Molecular ecology resources}, volume = {17}, number = {6}, pages = {e275-e284}, doi = {10.1111/1755-0998.12704}, pmid = {28776912}, issn = {1755-0998}, mesh = {Biostatistics/*methods ; *Chimera ; Computational Biology/*methods ; Genomics/*methods ; Workflow ; }, abstract = {The ability to detect and characterize hybridization in nature has long been of interest to many fields of biology and often has direct implications for wildlife management and conservation. The capacity to identify the presence of hybridization, and quantify the numbers of individuals belonging to different hybrid classes, permits inference on the magnitude of, and timescale over which, hybridization has been or is occurring. Here, we present an r package and associated workflow developed for the detection, with estimates of efficiency and accuracy, of multigenerational hybrid individuals using genetic or genomic data in conjunction with the program newhybrids. This package includes functions for the identification and testing of diagnostic panels of markers, the simulation of multigenerational hybrids, and the quantification and visualization of the efficiency and accuracy with which hybrids can be detected. Overall, this package delivers a streamlined hybrid analysis platform, providing improvements in speed, ease of use and repeatability over current ad hoc approaches. The latest version of the package and associated documentation are available on GitHub (https://github.com/bwringe/hybriddetective).}, } @article {pmid28776031, year = {2017}, author = {vonHoldt, BM and Shuldiner, E and Koch, IJ and Kartzinel, RY and Hogan, A and Brubaker, L and Wanser, S and Stahler, D and Wynne, CDL and Ostrander, EA and Sinsheimer, JS and Udell, MAR}, title = {Structural variants in genes associated with human Williams-Beuren syndrome underlie stereotypical hypersociability in domestic dogs.}, journal = {Science advances}, volume = {3}, number = {7}, pages = {e1700398}, pmid = {28776031}, issn = {2375-2548}, support = {R01 GM086887/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; *Behavior, Animal ; Computational Biology/methods ; Dog Diseases/*genetics/*psychology ; Dogs ; Genetic Association Studies ; Genetic Predisposition to Disease ; *Genetic Variation ; Humans ; Molecular Sequence Annotation ; Polymerase Chain Reaction ; Polymorphism, Single Nucleotide ; Reproducibility of Results ; Social Behavior ; *Stereotyped Behavior ; Williams Syndrome/*veterinary ; }, abstract = {Although considerable progress has been made in understanding the genetic basis of morphologic traits (for example, body size and coat color) in dogs and wolves, the genetic basis of their behavioral divergence is poorly understood. An integrative approach using both behavioral and genetic data is required to understand the molecular underpinnings of the various behavioral characteristics associated with domestication. We analyze a 5-Mb genomic region on chromosome 6 previously found to be under positive selection in domestic dog breeds. Deletion of this region in humans is linked to Williams-Beuren syndrome (WBS), a multisystem congenital disorder characterized by hypersocial behavior. We associate quantitative data on behavioral phenotypes symptomatic of WBS in humans with structural changes in the WBS locus in dogs. We find that hypersociability, a central feature of WBS, is also a core element of domestication that distinguishes dogs from wolves. We provide evidence that structural variants in GTF2I and GTF2IRD1, genes previously implicated in the behavioral phenotype of patients with WBS and contained within the WBS locus, contribute to extreme sociability in dogs. This finding suggests that there are commonalities in the genetic architecture of WBS and canine tameness and that directional selection may have targeted a unique set of linked behavioral genes of large phenotypic effect, allowing for rapid behavioral divergence of dogs and wolves, facilitating coexistence with humans.}, } @article {pmid28775335, year = {2017}, author = {Pilon, AC and Valli, M and Dametto, AC and Pinto, MEF and Freire, RT and Castro-Gamboa, I and Andricopulo, AD and Bolzani, VS}, title = {NuBBEDB: an updated database to uncover chemical and biological information from Brazilian biodiversity.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {7215}, pmid = {28775335}, issn = {2045-2322}, mesh = {Biochemistry ; *Biodiversity ; Biological Products ; Brazil ; *Databases, Factual ; Drug Discovery ; Humans ; Pharmacology ; Web Browser ; }, abstract = {The intrinsic value of biodiversity extends beyond species diversity, genetic heritage, ecosystem variability and ecological services, such as climate regulation, water quality, nutrient cycling and the provision of reproductive habitats it is also an inexhaustible source of molecules and products beneficial to human well-being. To uncover the chemistry of Brazilian natural products, the Nuclei of Bioassays, Ecophysiology and Biosynthesis of Natural Products Database (NuBBEDB) was created as the first natural product library from Brazilian biodiversity. Since its launch in 2013, the NuBBEDB has proven to be an important resource for new drug design and dereplication studies. Consequently, continuous efforts have been made to expand its contents and include a greater diversity of natural sources to establish it as a comprehensive compendium of available biogeochemical information about Brazilian biodiversity. The content in the NuBBEDB is freely accessible online (https://nubbe.iq.unesp.br/portal/nubbedb.html) and provides validated multidisciplinary information, chemical descriptors, species sources, geographic locations, spectroscopic data (NMR) and pharmacological properties. Herein, we report the latest advancements concerning the interface, content and functionality of the NuBBEDB. We also present a preliminary study on the current profile of the compounds present in Brazilian territory.}, } @article {pmid28774957, year = {2018}, author = {Jansen, LA and Mahadevan, D and Appelbaum, PS and Klein, WMP and Weinstein, ND and Mori, M and Degnin, C and Sulmasy, DP}, title = {Perceptions of control and unrealistic optimism in early-phase cancer trials.}, journal = {Journal of medical ethics}, volume = {44}, number = {2}, pages = {121-127}, doi = {10.1136/medethics-2016-103724}, pmid = {28774957}, issn = {1473-4257}, mesh = {Aged ; Clinical Trials as Topic/*ethics/*psychology ; Comprehension ; Female ; Humans ; Informed Consent/*ethics/*psychology ; Male ; Middle Aged ; Neoplasms/*psychology ; *Optimism ; Patient Selection/*ethics ; Perception ; Risk Assessment ; Surveys and Questionnaires ; }, abstract = {PURPOSE: Recent research has found unrealistic optimism (UO) among patient-subjects in early-phase oncology trials. Our aim was to investigate the cognitive and motivational factors that evoke this bias in this context. We expected perceptions of control to be a strong correlate of unrealistic optimism.

METHODS: A study of patient-subjects enrolled in early-phase oncology trials was conducted at two sites in the USA. Respondents completed questionnaires designed to assess unrealistic optimism and several risk attribute variables that have been found to evoke the bias in other contexts.

RESULTS: One hundred and seventy-one patient-subjects agreed to be interviewed for our study. Significant levels of perceived controllability were found with respect to all nine research-related questions. Perceptions of control were found to predict unrealistic optimism. Two other risk attribute variables, awareness of indicators (p=0.024) and mental image (p=0.022), were correlated with unrealistic optimism. However, in multivariate regression analysis, awareness and mental image dropped out of the model and perceived controllability was the only factor independently associated with unrealistic optimism (p<0.0001).

CONCLUSION: Patient-subjects reported that they can, at least partially, control the benefits they receive from participating in an early-phase oncology trial. This sense of control may underlie unrealistic optimism about benefiting personally from trial participation. Effective interventions to counteract unrealistic optimism may need to address the psychological factors that give rise to distorted risk/benefit processing.}, } @article {pmid28771471, year = {2017}, author = {Deck, J and Gaither, MR and Ewing, R and Bird, CE and Davies, N and Meyer, C and Riginos, C and Toonen, RJ and Crandall, ED}, title = {The Genomic Observatories Metadatabase (GeOMe): A new repository for field and sampling event metadata associated with genetic samples.}, journal = {PLoS biology}, volume = {15}, number = {8}, pages = {e2002925}, pmid = {28771471}, issn = {1545-7885}, mesh = {*Biodiversity ; *Databases, Nucleic Acid ; *Metadata ; *Metagenomics ; }, abstract = {The Genomic Observatories Metadatabase (GeOMe, http://www.geome-db.org/) is an open access repository for geographic and ecological metadata associated with biosamples and genetic data. Whereas public databases have served as vital repositories for nucleotide sequences, they do not accession all the metadata required for ecological or evolutionary analyses. GeOMe fills this need, providing a user-friendly, web-based interface for both data contributors and data recipients. The interface allows data contributors to create a customized yet standard-compliant spreadsheet that captures the temporal and geospatial context of each biosample. These metadata are then validated and permanently linked to archived genetic data stored in the National Center for Biotechnology Information's (NCBI's) Sequence Read Archive (SRA) via unique persistent identifiers. By linking ecologically and evolutionarily relevant metadata with publicly archived sequence data in a structured manner, GeOMe sets a gold standard for data management in biodiversity science.}, } @article {pmid28767522, year = {2017}, author = {Kenefick, RW and Heavens, KR and Luippold, AJ and Charkoudian, N and Schwartz, SA and Cheuvront, SN}, title = {Effect of Physical Load on Aerobic Exercise Performance during Heat Stress.}, journal = {Medicine and science in sports and exercise}, volume = {49}, number = {12}, pages = {2570-2577}, doi = {10.1249/MSS.0000000000001392}, pmid = {28767522}, issn = {1530-0315}, mesh = {Athletic Performance/*physiology ; Body Mass Index ; Body Temperature/physiology ; *Decision Support Techniques ; Exercise Test/methods ; Female ; Heart Rate/physiology ; Heat Stress Disorders/physiopathology ; *Hot Temperature ; Humans ; Male ; Military Personnel ; Nomograms ; Oxygen Consumption/physiology ; Running/*physiology ; Skin Temperature/physiology ; Weight-Bearing/*physiology ; Young Adult ; }, abstract = {PURPOSE: This study aimed to investigate the effect of increasing external loads on 5-km treadmill time trial (TT) performance in 20°C and 40°C environmental conditions and to construct an ecologically relevant performance prediction decision aid.

METHODS: Twenty-six male and four female volunteers (age, 23.5 ± 6.9 yr; weight, 76.0 ± 8.9 kg; height, 1.75 ± 0.07 m; V˙O2peak, 50.7 ± 4.5 mL·kg·min) participated in a counterbalanced, mixed-model design, with each subject assigned to a load group (20%, 30%, or 50% body mass (BM); n = 10 per group). Volunteers performed three, self-paced 5-km familiarization TT (treadmill) without external load. Each volunteer then performed a 5-km TT in each environment with loads of either 20% (n = 10), 30% (n = 10), or 50% (n = 10) of BM.

RESULTS: 1) Loads of (20%, 30%, and 50% of BM) impaired 5-km TT performance compared with that when unloaded (P < 0.05); 2) the time penalties of the 20% and 30% load were <50% load (P < 0.05); 3) in all trials, the addition of heat exposure reduced 5-km TT performance beyond the penalty of load itself (P < 0.05); and 4) the combination of heat and 50% load resulted in a substantial penalty such that continuous work was not sustainable for all of the volunteers.

CONCLUSIONS: Relative to prediction models using fixed or constant workload exercise trials, an ecologically valid decision aid was developed from self-paced data, in which pace (km·h) can be predicted for individual levels of heat, load, or heat + load in combination.}, } @article {pmid28766908, year = {2018}, author = {Kissling, WD and Ahumada, JA and Bowser, A and Fernandez, M and Fernández, N and García, EA and Guralnick, RP and Isaac, NJB and Kelling, S and Los, W and McRae, L and Mihoub, JB and Obst, M and Santamaria, M and Skidmore, AK and Williams, KJ and Agosti, D and Amariles, D and Arvanitidis, C and Bastin, L and De Leo, F and Egloff, W and Elith, J and Hobern, D and Martin, D and Pereira, HM and Pesole, G and Peterseil, J and Saarenmaa, H and Schigel, D and Schmeller, DS and Segata, N and Turak, E and Uhlir, PF and Wee, B and Hardisty, AR}, title = {Building essential biodiversity variables (EBVs) of species distribution and abundance at a global scale.}, journal = {Biological reviews of the Cambridge Philosophical Society}, volume = {93}, number = {1}, pages = {600-625}, doi = {10.1111/brv.12359}, pmid = {28766908}, issn = {1469-185X}, mesh = {Animal Distribution/*physiology ; Animals ; *Biodiversity ; Environmental Monitoring/*methods ; Models, Biological ; }, abstract = {Much biodiversity data is collected worldwide, but it remains challenging to assemble the scattered knowledge for assessing biodiversity status and trends. The concept of Essential Biodiversity Variables (EBVs) was introduced to structure biodiversity monitoring globally, and to harmonize and standardize biodiversity data from disparate sources to capture a minimum set of critical variables required to study, report and manage biodiversity change. Here, we assess the challenges of a 'Big Data' approach to building global EBV data products across taxa and spatiotemporal scales, focusing on species distribution and abundance. The majority of currently available data on species distributions derives from incidentally reported observations or from surveys where presence-only or presence-absence data are sampled repeatedly with standardized protocols. Most abundance data come from opportunistic population counts or from population time series using standardized protocols (e.g. repeated surveys of the same population from single or multiple sites). Enormous complexity exists in integrating these heterogeneous, multi-source data sets across space, time, taxa and different sampling methods. Integration of such data into global EBV data products requires correcting biases introduced by imperfect detection and varying sampling effort, dealing with different spatial resolution and extents, harmonizing measurement units from different data sources or sampling methods, applying statistical tools and models for spatial inter- or extrapolation, and quantifying sources of uncertainty and errors in data and models. To support the development of EBVs by the Group on Earth Observations Biodiversity Observation Network (GEO BON), we identify 11 key workflow steps that will operationalize the process of building EBV data products within and across research infrastructures worldwide. These workflow steps take multiple sequential activities into account, including identification and aggregation of various raw data sources, data quality control, taxonomic name matching and statistical modelling of integrated data. We illustrate these steps with concrete examples from existing citizen science and professional monitoring projects, including eBird, the Tropical Ecology Assessment and Monitoring network, the Living Planet Index and the Baltic Sea zooplankton monitoring. The identified workflow steps are applicable to both terrestrial and aquatic systems and a broad range of spatial, temporal and taxonomic scales. They depend on clear, findable and accessible metadata, and we provide an overview of current data and metadata standards. Several challenges remain to be solved for building global EBV data products: (i) developing tools and models for combining heterogeneous, multi-source data sets and filling data gaps in geographic, temporal and taxonomic coverage, (ii) integrating emerging methods and technologies for data collection such as citizen science, sensor networks, DNA-based techniques and satellite remote sensing, (iii) solving major technical issues related to data product structure, data storage, execution of workflows and the production process/cycle as well as approaching technical interoperability among research infrastructures, (iv) allowing semantic interoperability by developing and adopting standards and tools for capturing consistent data and metadata, and (v) ensuring legal interoperability by endorsing open data or data that are free from restrictions on use, modification and sharing. Addressing these challenges is critical for biodiversity research and for assessing progress towards conservation policy targets and sustainable development goals.}, } @article {pmid28763495, year = {2017}, author = {Koroiva, R and Pepinelli, M and Rodrigues, ME and Roque, FO and Lorenz-Lemke, AP and Kvist, S}, title = {DNA barcoding of odonates from the Upper Plata basin: Database creation and genetic diversity estimation.}, journal = {PloS one}, volume = {12}, number = {8}, pages = {e0182283}, pmid = {28763495}, issn = {1932-6203}, mesh = {Animals ; *Biodiversity ; Brazil ; *DNA Barcoding, Taxonomic ; *Databases, Genetic ; Electron Transport Complex IV/*genetics ; *Genetic Variation ; Geography ; Odonata/*genetics ; Phylogeny ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {We present a DNA barcoding study of Neotropical odonates from the Upper Plata basin, Brazil. A total of 38 species were collected in a transition region of "Cerrado" and Atlantic Forest, both regarded as biological hotspots, and 130 cytochrome c oxidase subunit I (COI) barcodes were generated for the collected specimens. The distinct gap between intraspecific (0-2%) and interspecific variation (15% and above) in COI, and resulting separation of Barcode Index Numbers (BIN), allowed for successful identification of specimens in 94% of cases. The 6% fail rate was due to a shared BIN between two separate nominal species. DNA barcoding, based on COI, thus seems to be a reliable and efficient tool for identifying Neotropical odonate specimens down to the species level. These results underscore the utility of DNA barcoding to aid specimen identification in diverse biological hotspots, areas that require urgent action regarding taxonomic surveys and biodiversity conservation.}, } @article {pmid28761145, year = {2017}, author = {Tessler, M and Neumann, JS and Afshinnekoo, E and Pineda, M and Hersch, R and Velho, LFM and Segovia, BT and Lansac-Toha, FA and Lemke, M and DeSalle, R and Mason, CE and Brugler, MR}, title = {Large-scale differences in microbial biodiversity discovery between 16S amplicon and shotgun sequencing.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {6589}, pmid = {28761145}, issn = {2045-2322}, mesh = {Bacteria/*classification/genetics/growth & development ; *Biodiversity ; Biota ; Computational Biology ; DNA, Bacterial/genetics ; High-Throughput Nucleotide Sequencing/*methods ; *Metagenomics ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, DNA/*methods ; *Water Microbiology ; }, abstract = {Modern metagenomic environmental DNA studies are almost completely reliant on next-generation sequencing, making evaluations of these methods critical. We compare two next-generation sequencing techniques - amplicon and shotgun - on water samples across four of Brazil's major river floodplain systems (Amazon, Araguaia, Paraná, and Pantanal). Less than 50% of phyla identified via amplicon sequencing were recovered from shotgun sequencing, clearly challenging the dogma that mid-depth shotgun recovers more diversity than amplicon-based approaches. Amplicon sequencing also revealed ~27% more families. Overall the amplicon data were more robust across both biodiversity and community ecology analyses at different taxonomic scales. Our work doubles the sampling size in similar environmental studies, and novelly integrates environmental data (e.g., pH, temperature, nutrients) from each site, revealing divergent correlations depending on which data are used. While myriad variants on NGS techniques and bioinformatic pipelines are available, our results point to core differences that have not been highlighted in any studies to date. Given the low number of taxa identified when coupling shotgun data with clade-based taxonomic algorithms, previous studies that quantified biodiversity using such bioinformatic tools should be viewed cautiously or re-analyzed. Nonetheless, shotgun has complementary advantages that should be weighed when designing projects.}, } @article {pmid28759717, year = {2017}, author = {Kienzler, A and Barron, MG and Belanger, SE and Beasley, A and Embry, MR}, title = {Mode of Action (MOA) Assignment Classifications for Ecotoxicology: An Evaluation of Approaches.}, journal = {Environmental science & technology}, volume = {51}, number = {17}, pages = {10203-10211}, doi = {10.1021/acs.est.7b02337}, pmid = {28759717}, issn = {1520-5851}, mesh = {Databases, Factual ; *Ecotoxicology ; *Quantitative Structure-Activity Relationship ; Risk Assessment ; United States ; United States Environmental Protection Agency ; }, abstract = {The mode of toxic action (MOA) is recognized as a key determinant of chemical toxicity and as an alternative to chemical class-based predictive toxicity modeling. However, MOA classification has never been standardized in ecotoxicology, and a comprehensive comparison of classification tools and approaches has never been reported. Here we critically evaluate three MOA classification methodologies using an aquatic toxicity data set of 3448 chemicals, compare the approaches, and assess utility and limitations in screening and early tier assessments. The comparisons focused on three commonly used tools: Verhaar prediction of toxicity MOA, the U.S. Environmental Protection Agency (EPA) ASsessment Tool for Evaluating Risk (ASTER) QSAR (quantitative structure activity relationship) application, and the EPA Mode of Action and Toxicity (MOAtox) database. Of the 3448 MOAs predicted using the Verhaar scheme, 1165 were classified by ASTER, and 802 were available in MOAtox. Of the subset of 432 chemicals with MOA assignments for each of the three schemes, 42% had complete concordance in MOA classification, and there was no agreement for 7% of the chemicals. The research shows the potential for large differences in MOA classification between the five broad groups of the Verhaar scheme and the more mechanism-based assignments of ASTER and MOAtox. Harmonization of classification schemes is needed to use MOA classification in chemical hazard and risk assessment more broadly.}, } @article {pmid28755311, year = {2017}, author = {Manandhar, P and Zhang, G and Lama, A and Liu, F and Hu, Y}, title = {Sphingomonas montana sp. nov., isolated from a soil sample from the Tanggula Mountain in the Qinghai Tibetan Plateau.}, journal = {Antonie van Leeuwenhoek}, volume = {110}, number = {12}, pages = {1659-1668}, doi = {10.1007/s10482-017-0915-6}, pmid = {28755311}, issn = {1572-9699}, mesh = {Computational Biology/methods ; *Environment ; Genome, Bacterial ; Genomics/methods ; Metabolomics/methods ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Soil Microbiology ; Sphingomonas/chemistry/*classification/*genetics/isolation & purification ; Tibet ; Whole Genome Sequencing ; }, abstract = {An orange pigmented, Gram-staining negative, aerobic, motile, rod-shaped bacterium isolated from a soil from the Tanggula Mountain, China was studied using a polyphasic approach. Based on 16S rRNA gene sequence similarity, strain W16RD[T] was found to be closely related to Sphingomonas prati DSM 103336[T] (99%), Sphingomonas fennica DSM 13665[T] (97.21%), followed by Sphingomonas laterariae DSM 25432[T] (96.44%), Sphingomonas haloaromaticamans CGMCC 1.10206 [T] (96.36%) and Sphingomonas formosensis DSM 24164[T] (96.06%). The strain was found to be catalase and oxidase positive and was found to grow optimally at temperatures of 20-25 °C, pH 8 and tolerated NaCl concentration up to 1% (w/v). The major fatty acids identified were summed feature eight comprising C18:1 ω 7c and/or C18:1 ω 6c (39.2%), summed feature three comprising of C16:1 ω7c and/or C16:1 ω6c (36.7%) and C16:0 (7.0%). The polar lipids detected were phosphatidylcholine, sphingoglycolipid, phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol, phosphatidyldimethylethanolamine, phosphatidylmonomethylethanolamine, and three unidentified lipids. The strain possessed ubiquinone-10 (Q-10) as the predominant respiratory quinone. Along with other distinguishing characteristics, we also describe the draft genome of strain W16RD[T]. The final assembled draft genome sequence is 3,722,743 bp with 3390 coding and 48 RNA (45 tRNA and 3 rRNA) genes. The DNA G+C content of the genomic DNA was determined to be 67%. The DNA-DNA relatedness value between the strain W16RD[T] and its closest phylogenetic relatives S. prati DSM 103336[T], S. fennica DSM 13665[T], S. laterariae DSM 25432[T], and S. haloaromaticamans CGMCC 1.10206[T] were 52.17, 47.60, 20.93 and 17.09% respectively. The strain W16RD[T] could be distinguished genotypically and phenotypically from the recognized species belonging to the genus Sphingomonas and thus represents a novel species, for which the name Sphingomonas montana sp. nov. is proposed. The type strain is W16RD[T] (=CGMCC 1.15646[T] = DSM 103337[T]).}, } @article {pmid28751502, year = {2017}, author = {Neale, DB and McGuire, PE and Wheeler, NC and Stevens, KA and Crepeau, MW and Cardeno, C and Zimin, AV and Puiu, D and Pertea, GM and Sezen, UU and Casola, C and Koralewski, TE and Paul, R and Gonzalez-Ibeas, D and Zaman, S and Cronn, R and Yandell, M and Holt, C and Langley, CH and Yorke, JA and Salzberg, SL and Wegrzyn, JL}, title = {The Douglas-Fir Genome Sequence Reveals Specialization of the Photosynthetic Apparatus in Pinaceae.}, journal = {G3 (Bethesda, Md.)}, volume = {7}, number = {9}, pages = {3157-3167}, pmid = {28751502}, issn = {2160-1836}, mesh = {Adaptation, Biological/genetics ; Computational Biology ; Evolution, Molecular ; Gene Duplication ; Gene Regulatory Networks ; *Genome, Plant ; Genomics ; Molecular Sequence Annotation ; Multigene Family ; Photosynthesis/*genetics ; Phylogeny ; Pinaceae/classification/*genetics/*metabolism ; Proteomics/methods ; Pseudotsuga/classification/*genetics/*metabolism ; Repetitive Sequences, Nucleic Acid ; *Whole Genome Sequencing ; }, abstract = {A reference genome sequence for Pseudotsuga menziesii var. menziesii (Mirb.) Franco (Coastal Douglas-fir) is reported, thus providing a reference sequence for a third genus of the family Pinaceae. The contiguity and quality of the genome assembly far exceeds that of other conifer reference genome sequences (contig N50 = 44,136 bp and scaffold N50 = 340,704 bp). Incremental improvements in sequencing and assembly technologies are in part responsible for the higher quality reference genome, but it may also be due to a slightly lower exact repeat content in Douglas-fir vs. pine and spruce. Comparative genome annotation with angiosperm species reveals gene-family expansion and contraction in Douglas-fir and other conifers which may account for some of the major morphological and physiological differences between the two major plant groups. Notable differences in the size of the NDH-complex gene family and genes underlying the functional basis of shade tolerance/intolerance were observed. This reference genome sequence not only provides an important resource for Douglas-fir breeders and geneticists but also sheds additional light on the evolutionary processes that have led to the divergence of modern angiosperms from the more ancient gymnosperms.}, } @article {pmid28749934, year = {2017}, author = {Martiniano, R and Cassidy, LM and Ó'Maoldúin, R and McLaughlin, R and Silva, NM and Manco, L and Fidalgo, D and Pereira, T and Coelho, MJ and Serra, M and Burger, J and Parreira, R and Moran, E and Valera, AC and Porfirio, E and Boaventura, R and Silva, AM and Bradley, DG}, title = {The population genomics of archaeological transition in west Iberia: Investigation of ancient substructure using imputation and haplotype-based methods.}, journal = {PLoS genetics}, volume = {13}, number = {7}, pages = {e1006852}, pmid = {28749934}, issn = {1553-7404}, mesh = {Archaeology ; Chromosomes, Human, Y/genetics ; Databases, Genetic ; Europe ; Female ; Genetic Variation ; Genetics, Population/*methods ; Genome, Human ; Genomics/*methods ; Genotype ; *Haplotypes ; Humans ; Male ; Portugal ; Sequence Analysis, DNA ; }, abstract = {We analyse new genomic data (0.05-2.95x) from 14 ancient individuals from Portugal distributed from the Middle Neolithic (4200-3500 BC) to the Middle Bronze Age (1740-1430 BC) and impute genomewide diploid genotypes in these together with published ancient Eurasians. While discontinuity is evident in the transition to agriculture across the region, sensitive haplotype-based analyses suggest a significant degree of local hunter-gatherer contribution to later Iberian Neolithic populations. A more subtle genetic influx is also apparent in the Bronze Age, detectable from analyses including haplotype sharing with both ancient and modern genomes, D-statistics and Y-chromosome lineages. However, the limited nature of this introgression contrasts with the major Steppe migration turnovers within third Millennium northern Europe and echoes the survival of non-Indo-European language in Iberia. Changes in genomic estimates of individual height across Europe are also associated with these major cultural transitions, and ancestral components continue to correlate with modern differences in stature.}, } @article {pmid28748955, year = {2017}, author = {McDaid, AF and Joshi, PK and Porcu, E and Komljenovic, A and Li, H and Sorrentino, V and Litovchenko, M and Bevers, RPJ and Rüeger, S and Reymond, A and Bochud, M and Deplancke, B and Williams, RW and Robinson-Rechavi, M and Paccaud, F and Rousson, V and Auwerx, J and Wilson, JF and Kutalik, Z}, title = {Bayesian association scan reveals loci associated with human lifespan and linked biomarkers.}, journal = {Nature communications}, volume = {8}, number = {}, pages = {15842}, pmid = {28748955}, issn = {2041-1723}, support = {MC_QA137853/MRC_/Medical Research Council/United Kingdom ; R01 AG043930/AG/NIA NIH HHS/United States ; }, mesh = {Aged ; Aged, 80 and over ; Arylsulfotransferase/genetics ; Bayes Theorem ; Biomarkers/analysis ; Disease/genetics ; Female ; Genome-Wide Association Study ; Humans ; Longevity/*genetics ; Male ; Nerve Tissue Proteins/genetics ; *Polymorphism, Single Nucleotide ; RNA-Binding Proteins/genetics ; Receptors, Nicotinic/genetics ; United Kingdom ; White People/genetics ; }, abstract = {The enormous variation in human lifespan is in part due to a myriad of sequence variants, only a few of which have been revealed to date. Since many life-shortening events are related to diseases, we developed a Mendelian randomization-based method combining 58 disease-related GWA studies to derive longevity priors for all HapMap SNPs. A Bayesian association scan, informed by these priors, for parental age of death in the UK Biobank study (n=116,279) revealed 16 independent SNPs with significant Bayes factor at a 5% false discovery rate (FDR). Eleven of them replicate (5% FDR) in five independent longevity studies combined; all but three are depleted of the life-shortening alleles in older Biobank participants. Further analysis revealed that brain expression levels of nearby genes (RBM6, SULT1A1 and CHRNA5) might be causally implicated in longevity. Gene expression and caloric restriction experiments in model organisms confirm the conserved role for RBM6 and SULT1A1 in modulating lifespan.}, } @article {pmid28747480, year = {2017}, author = {Votier, SC and Fayet, AL and Bearhop, S and Bodey, TW and Clark, BL and Grecian, J and Guilford, T and Hamer, KC and Jeglinski, JWE and Morgan, G and Wakefield, E and Patrick, SC}, title = {Effects of age and reproductive status on individual foraging site fidelity in a long-lived marine predator.}, journal = {Proceedings. Biological sciences}, volume = {284}, number = {1859}, pages = {}, pmid = {28747480}, issn = {1471-2954}, mesh = {*Age Factors ; Animals ; *Appetitive Behavior ; Birds/*physiology ; Ecology ; Feeding Behavior ; Geographic Information Systems ; *Reproduction ; }, abstract = {Individual foraging specializations, where individuals use a small component of the population niche width, are widespread in nature with important ecological and evolutionary implications. In long-lived animals, foraging ability develops with age, but we know little about the ontogeny of individuality in foraging. Here we use precision global positioning system (GPS) loggers to examine how individual foraging site fidelity (IFSF), a common component of foraging specialization, varies between breeders, failed breeders and immatures in a long-lived marine predator-the northern gannet Morus bassanus Breeders (aged 5+) showed strong IFSF: they had similar routes and were faithful to distal points during successive trips. However, centrally placed immatures (aged 2-3) were far more exploratory and lacked route or foraging site fidelity. Failed breeders were intermediate: some with strong fidelity, others being more exploratory. Individual foraging specializations were previously thought to arise as a function of heritable phenotypic differences or via social transmission. Our results instead suggest a third alternative-in long-lived species foraging sites are learned during exploratory behaviours early in life, which become canalized with age and experience, and refined where possible-the exploration-refinement foraging hypothesis. We speculate similar patterns may be present in other long-lived species and moreover that long periods of immaturity may be a consequence of such memory-based individual foraging strategies.}, } @article {pmid28746735, year = {2018}, author = {Orsini, L and Brown, JB and Shams Solari, O and Li, D and He, S and Podicheti, R and Stoiber, MH and Spanier, KI and Gilbert, D and Jansen, M and Rusch, DB and Pfrender, ME and Colbourne, JK and Frilander, MJ and Kvist, J and Decaestecker, E and De Schamphelaere, KAC and De Meester, L}, title = {Early transcriptional response pathways in Daphnia magna are coordinated in networks of crustacean-specific genes.}, journal = {Molecular ecology}, volume = {27}, number = {4}, pages = {886-897}, pmid = {28746735}, issn = {1365-294X}, support = {R00 HG006698/HG/NHGRI NIH HHS/United States ; R24 GM078274/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Conserved Sequence ; Daphnia/*genetics ; Gene Expression Regulation ; *Gene Regulatory Networks ; Genome ; Genotype ; Multigene Family ; *Transcription, Genetic ; }, abstract = {Natural habitats are exposed to an increasing number of environmental stressors that cause important ecological consequences. However, the multifarious nature of environmental change, the strength and the relative timing of each stressor largely limit our understanding of biological responses to environmental change. In particular, early response to unpredictable environmental change, critical to survival and fitness in later life stages, is largely uncharacterized. Here, we characterize the early transcriptional response of the keystone species Daphnia magna to twelve environmental perturbations, including biotic and abiotic stressors. We first perform a differential expression analysis aimed at identifying differential regulation of individual genes in response to stress. This preliminary analysis revealed that a few individual genes were responsive to environmental perturbations and they were modulated in a stressor and genotype-specific manner. Given the limited number of differentially regulated genes, we were unable to identify pathways involved in stress response. Hence, to gain a better understanding of the genetic and functional foundation of tolerance to multiple environmental stressors, we leveraged the correlative nature of networks and performed a weighted gene co-expression network analysis. We discovered that approximately one-third of the Daphnia genes, enriched for metabolism, cell signalling and general stress response, drives transcriptional early response to environmental stress and it is shared among genetic backgrounds. This initial response is followed by a genotype- and/or condition-specific transcriptional response with a strong genotype-by-environment interaction. Intriguingly, genotype- and condition-specific transcriptional response is found in genes not conserved beyond crustaceans, suggesting niche-specific adaptation.}, } @article {pmid28743947, year = {2017}, author = {Santos, CD and Hanssen, F and Muñoz, AR and Onrubia, A and Wikelski, M and May, R and Silva, JP}, title = {Match between soaring modes of black kites and the fine-scale distribution of updrafts.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {6421}, pmid = {28743947}, issn = {2045-2322}, mesh = {Animals ; Falconiformes/*physiology ; Flight, Animal/*physiology ; Geographic Information Systems ; Models, Biological ; Spain ; }, abstract = {Understanding how soaring birds use updrafts at small spatial scales is important to identify ecological constraints of movement, and may help to prevent conflicts between wind-energy development and the conservation of wildlife. We combined high-frequency GPS animal tracking and fine-spatial-scale uplift modelling to establish a link between flight behaviour of soaring birds and the distribution of updrafts. We caught 21 black kites (Milvus migrans) and GPS-tracked them while flying over the Tarifa region, on the Spanish side of the Strait of Gibraltar. This region has a diverse topography and land cover, favouring a heterogeneous updraft spatial distribution. Bird tracks were segmented and classified into flight modes from motion parameters. Thermal and orographic uplift velocities were modelled from publically available remote-sensing and meteorological data. We found that birds perform circular soaring in areas of higher predicted thermal uplift and linear soaring in areas of higher predicted orographic uplift velocity. We show that updraft maps produced from publically available data can be used to predict where soaring birds will concentrate their flight paths and how they will behave in flight. We recommend the use of this methodological approach to improve environmental impact assessments of new wind-energy installations.}, } @article {pmid28743891, year = {2017}, author = {Shankar, V and Agans, R and Paliy, O}, title = {Advantages of phylogenetic distance based constrained ordination analyses for the examination of microbial communities.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {6481}, pmid = {28743891}, issn = {2045-2322}, mesh = {Bacteroides/genetics ; Clostridioides difficile/pathogenicity ; Clostridium/genetics ; Clostridium Infections/microbiology/therapy ; Data Interpretation, Statistical ; Fecal Microbiota Transplantation ; Gastrointestinal Microbiome ; Humans ; Microbiota/genetics/*physiology ; *Phylogeny ; }, abstract = {Recently developed high throughput molecular techniques such as massively parallel sequencing and phylogenetic microarrays generate vast datasets providing insights into microbial community structure and function. Because of the high dimensionality of these datasets, multivariate ordination analyses are often employed to examine such data. Here, we show how the use of phylogenetic distance based redundancy analysis provides ecological interpretation of microbial community differences. We also extend the previously developed method of principal response curves to incorporate phylogenetic distance measure, and we demonstrate the improved ability of this approach to provide ecologically relevant insights into temporal alterations of microbial communities.}, } @article {pmid28743591, year = {2017}, author = {Diepenbroek, M and Schindler, U and Huber, R and Pesant, S and Stocker, M and Felden, J and Buss, M and Weinrebe, M}, title = {Terminology supported archiving and publication of environmental science data in PANGAEA.}, journal = {Journal of biotechnology}, volume = {261}, number = {}, pages = {177-186}, doi = {10.1016/j.jbiotec.2017.07.016}, pmid = {28743591}, issn = {1873-4863}, mesh = {*Computational Biology ; *Ecology ; Publishing ; *Semantics ; *Terminology as Topic ; *Vocabulary, Controlled ; }, abstract = {Exemplified on the information system PANGAEA, we describe the application of terminologies for archiving and publishing environmental science data. A terminology catalogue (TC) was embedded into the system, with interfaces allowing to replicate and to manually work on terminologies. For data ingest and archiving, we show how the TC can improve structuring and harmonizing lineage and content descriptions of data sets. Key is the conceptualization of measurement and observation types (parameters) and methods, for which we have implemented a basic syntax and rule set. For data access and dissemination, we have improved findability of data through enrichment of metadata with TC terms. Semantic annotations, e.g. adding term concepts (including synonyms and hierarchies) or mapped terms of different terminologies, facilitate comprehensive data retrievals. The PANGAEA thesaurus of classifying terms, which is part of the TC is used as an umbrella vocabulary that links the various domains and allows drill downs and side drills with various facets. Furthermore, we describe how TC terms can be linked to nominal data values. This improves data harmonization and facilitates structural transformation of heterogeneous data sets to a common schema. Technical developments are complemented by work on the metadata content. Over the last 20 years, more than 100 new parameters have been defined on average per week. Recently, PANGAEA has increasingly been submitting new terms to various terminology services. Matching terms from terminology services with our parameter or method strings is supported programmatically. However, the process ultimately needs manual input by domain experts. The quality of terminology services is an additional limiting factor, and varies with respect to content, editorial, interoperability, and sustainability. Good quality terminology services are the building blocks for the conceptualization of parameters and methods. In our view, they are essential for data interoperability and arguably the most difficult hurdle for data integration. In summary, the application of terminologies has a mutual positive effect for terminology services and information systems such as PANGAEA. On both sides, the application of terminologies improves content, reliability and interoperability.}, } @article {pmid28741358, year = {2017}, author = {Blank-Landeshammer, B and Kollipara, L and Biß, K and Pfenninger, M and Malchow, S and Shuvaev, K and Zahedi, RP and Sickmann, A}, title = {Combining De Novo Peptide Sequencing Algorithms, A Synergistic Approach to Boost Both Identifications and Confidence in Bottom-up Proteomics.}, journal = {Journal of proteome research}, volume = {16}, number = {9}, pages = {3209-3218}, doi = {10.1021/acs.jproteome.7b00198}, pmid = {28741358}, issn = {1535-3907}, mesh = {*Algorithms ; Amino Acid Sequence ; Animals ; Cell Line ; Chromatography, Liquid ; Databases, Protein ; HeLa Cells ; Humans ; Mice ; Myoblasts/chemistry/metabolism ; Peptides/*analysis ; Proteolysis ; Proteomics/instrumentation/*methods ; Saccharomyces cerevisiae/chemistry/metabolism ; Sequence Analysis, Protein/*methods ; Snails/chemistry/metabolism ; Tandem Mass Spectrometry ; Trypsin/chemistry ; }, abstract = {Complex mass spectrometry based proteomics data sets are mostly analyzed by protein database searches. While this approach performs considerably well for sequenced organisms, direct inference of peptide sequences from tandem mass spectra, i.e., de novo peptide sequencing, oftentimes is the only way to obtain information when protein databases are absent. However, available algorithms suffer from drawbacks such as lack of validation and often high rates of false positive hits (FP). Here we present a simple method of combining results from commonly available de novo peptide sequencing algorithms, which in conjunction with minor tweaks in data acquisition ensues lower empirical FDR compared to the analysis using single algorithms. Results were validated using state-of-the art database search algorithms as well specifically synthesized reference peptides. Thus, we could increase the number of PSMs meeting a stringent FDR of 5% more than 3-fold compared to the single best de novo sequencing algorithm alone, accounting for an average of 11 120 PSMs (combined) instead of 3476 PSMs (alone) in triplicate 2 h LC-MS runs of tryptic HeLa digestion.}, } @article {pmid28738805, year = {2017}, author = {Wong, MS and Ho, HC and Yang, L and Shi, W and Yang, J and Chan, TC}, title = {Spatial variability of excess mortality during prolonged dust events in a high-density city: a time-stratified spatial regression approach.}, journal = {International journal of health geographics}, volume = {16}, number = {1}, pages = {26}, pmid = {28738805}, issn = {1476-072X}, mesh = {Aged ; Aged, 80 and over ; Air Pollution/*analysis ; Cities/*epidemiology ; Dust/*analysis ; Environmental Monitoring/methods ; Female ; *Geographic Mapping ; Hong Kong/epidemiology ; Humans ; Male ; Mortality/*trends ; Socioeconomic Factors ; *Spatial Regression ; Time Factors ; }, abstract = {BACKGROUND: Dust events have long been recognized to be associated with a higher mortality risk. However, no study has investigated how prolonged dust events affect the spatial variability of mortality across districts in a downwind city.

METHODS: In this study, we applied a spatial regression approach to estimate the district-level mortality during two extreme dust events in Hong Kong. We compared spatial and non-spatial models to evaluate the ability of each regression to estimate mortality. We also compared prolonged dust events with non-dust events to determine the influences of community factors on mortality across the city.

RESULTS: The density of a built environment (estimated by the sky view factor) had positive association with excess mortality in each district, while socioeconomic deprivation contributed by lower income and lower education induced higher mortality impact in each territory planning unit during a prolonged dust event. Based on the model comparison, spatial error modelling with the 1st order of queen contiguity consistently outperformed other models. The high-risk areas with higher increase in mortality were located in an urban high-density environment with higher socioeconomic deprivation.

CONCLUSION: Our model design shows the ability to predict spatial variability of mortality risk during an extreme weather event that is not able to be estimated based on traditional time-series analysis or ecological studies. Our spatial protocol can be used for public health surveillance, sustainable planning and disaster preparation when relevant data are available.}, } @article {pmid28734268, year = {2017}, author = {Grzywacz, A and Wyborska, D and Piwczyński, M}, title = {DNA barcoding allows identification of European Fanniidae (Diptera) of forensic interest.}, journal = {Forensic science international}, volume = {278}, number = {}, pages = {106-114}, doi = {10.1016/j.forsciint.2017.06.023}, pmid = {28734268}, issn = {1872-6283}, mesh = {Animals ; *DNA Barcoding, Taxonomic ; DNA, Mitochondrial/genetics ; Databases, Genetic ; Diptera/*genetics ; Electron Transport Complex IV/*genetics ; Forensic Sciences ; Polymerase Chain Reaction ; }, abstract = {In forensic entomology practice, species identification is a prerequisite for any further analysis of collected material. Although morphology-based taxonomy may be hindered by a range of factors, these are not obstacles for a molecular identification approach, so-called DNA barcoding. The Fanniidae are a dipteran family that is attracted to and breeds in decomposing animal carrion and dead human bodies. However, morphological identification of fanniids, both at adult and immature stages, is considered to be difficult, particularly for non-experts. We investigated the usefulness of molecular taxonomy methods as an alternative/supplement for morphology-based identification in European Fanniidae of forensic interest. The material used in this study was collected from various regions in Asia, Europe and North America. We sequenced a barcode region of the mitochondrial cytochrome c oxidase subunit I (COI) in 27 species. For 13 species, including some taxa breeding in dead bodies, this study describes COI sequences for the first time. Our analysis revealed that both mini-barcode and full-length COI barcode sequences give very high specimen identification success. Despite the large number of COI barcode sequences referring to Fanniidae in the BOLD and GenBank databases, previous identification of forensically relevant Fanniidae was hindered by uneven taxonomic sampling. The majority of available sequences refer to species that are not of medico-legal interest, and many species of forensic interest are unrepresented or represented only by a single sequence. Because of erroneous data that are present in depository databases, DNA barcoding must be used with caution and cannot be considered to be the sole alternative to other identification methods. Wolbachia infections in the examined material did not disrupt specimen identification. The obtained results will facilitate precise identification of European Fanniidae of forensic interest, badly preserved material with degraded DNA, as well as matching of unidentified females and immature stages to already described specimens.}, } @article {pmid28729527, year = {2017}, author = {Guo, X and Yu, C and Luo, L and Wan, H and Li, Y and Wang, J and Cheng, T and Pan, H and Zhang, Q}, title = {Comparative transcriptome analysis of the floral transition in Rosa chinensis 'Old Blush' and R. odorata var. gigantea.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {6068}, pmid = {28729527}, issn = {2045-2322}, mesh = {Computational Biology/methods ; Gene Expression Profiling ; *Gene Expression Regulation, Plant ; Gene Ontology ; Genes, Plant ; Genomics/methods ; Molecular Sequence Annotation ; Phylogeny ; Reproducibility of Results ; Rosa/classification/*genetics/metabolism/*microbiology ; *Transcriptome ; }, abstract = {The floral transition is a crucial developmental event, but little is known about the underlying regulatory networks in seasonally and continuously flowering roses. In this study, we compared the genetic basis of flowering in two rose species, Rosa chinensis 'Old Blush', which flowers continuously, and R. odorata var. gigantea, which blooms in early spring. Gene ontology (GO) terms related to methylation, light reaction, and starch metabolism were enriched in R. odorata var. gigantea and terms associated with sugar metabolism were enriched in R. chinensis 'Old Blush' during the floral transition. A MapMan analysis revealed that genes involved in hormone signaling mediate the floral transition in both taxa. Furthermore, differentially expressed genes (DEGs) involved in vernalization, photoperiod, gibberellin (GA), and starch metabolism pathways converged on integrators, e.g., LFY, AGL24, SOC1, CAL, and COLs, to regulate the floral transition in R. odorata var. gigantea, while DEGs related to photoperiod, sugar metabolism, and GA pathways, including COL16, LFY, AGL11, 6PGDH, GASA4, and BAM, modulated the floral transition in R. chinensis 'Old Blush.' Our analysis of the genes underlying the floral transition in roses with different patterns of flowering provides a basis for further functional studies.}, } @article {pmid28723902, year = {2017}, author = {Igea, J and Miller, EF and Papadopulos, AST and Tanentzap, AJ}, title = {Seed size and its rate of evolution correlate with species diversification across angiosperms.}, journal = {PLoS biology}, volume = {15}, number = {7}, pages = {e2002792}, pmid = {28723902}, issn = {1545-7885}, support = {/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Adaptation, Biological ; Bayes Theorem ; Biodiversity ; *Biological Evolution ; Botany/methods ; Databases, Factual ; Genetic Speciation ; Genome Size ; Genome, Plant ; Magnoliopsida/classification/genetics/*growth & development/physiology ; *Models, Biological ; *Phylogeny ; Reproductive Isolation ; Seeds/classification/genetics/*growth & development/physiology ; Species Specificity ; Time Factors ; }, abstract = {Species diversity varies greatly across the different taxonomic groups that comprise the Tree of Life (ToL). This imbalance is particularly conspicuous within angiosperms, but is largely unexplained. Seed mass is one trait that may help clarify why some lineages diversify more than others because it confers adaptation to different environments, which can subsequently influence speciation and extinction. The rate at which seed mass changes across the angiosperm phylogeny may also be linked to diversification by increasing reproductive isolation and allowing access to novel ecological niches. However, the magnitude and direction of the association between seed mass and diversification has not been assessed across the angiosperm phylogeny. Here, we show that absolute seed size and the rate of change in seed size are both associated with variation in diversification rates. Based on the largest available angiosperm phylogenetic tree, we found that smaller-seeded plants had higher rates of diversification, possibly due to improved colonisation potential. The rate of phenotypic change in seed size was also strongly positively correlated with speciation rates, providing rare, large-scale evidence that rapid morphological change is associated with species divergence. Our study now reveals that variation in morphological traits and, importantly, the rate at which they evolve can contribute to explaining the extremely uneven distribution of diversity across the ToL.}, } @article {pmid28723310, year = {2017}, author = {Olcoń, K and Kim, Y and Gulbas, LE}, title = {Sense of Belonging and Youth Suicidal Behaviors: What Do Communities and Schools Have to Do with It?.}, journal = {Social work in public health}, volume = {32}, number = {7}, pages = {432-442}, doi = {10.1080/19371918.2017.1344602}, pmid = {28723310}, issn = {1937-190X}, mesh = {Adolescent ; Adolescent Behavior ; Bullying ; *Community Networks ; Female ; Humans ; Male ; Risk-Taking ; Safety ; *Schools ; *Social Identification ; Students/*psychology ; *Suicidal Ideation ; Surveys and Questionnaires ; Texas ; Young Adult ; }, abstract = {Situating Thomas Joiner's concept of belonging within an ecological perspective, this study examined the associations between school and community belonging and suicidal ideation and attempts among high school students. The study used data from the 2013 Texas Youth Risk Behavior Survey (N = 2,560). Results demonstrated that community belonging reduced the odds of youth suicidal behaviors. School bullying, feeling unsafe at school, and being threatened or injured at a school increased the odds of suicidal behaviors. Findings suggest that fostering safe and inclusive environments and strengthening youth's experiences of school and community belonging may reduce suicidal behaviors in high school youth.}, } @article {pmid28721523, year = {2017}, author = {Messika, I and Garrido, M and Kedem, H and China, V and Gavish, Y and Dong, Q and Fuqua, C and Clay, K and Hawlena, H}, title = {From endosymbionts to host communities: factors determining the reproductive success of arthropod vectors.}, journal = {Oecologia}, volume = {184}, number = {4}, pages = {859-871}, pmid = {28721523}, issn = {1432-1939}, support = {2012063//United States - Israel Binational Science Foundation/International ; FP7-293713//Marie Curie Career Integration Grant/International ; 1391/15//Israel Science Foundation/International ; }, mesh = {Animals ; *Arthropod Vectors ; Female ; *Flea Infestations ; *Reproduction ; Rodentia ; Selection, Genetic ; Siphonaptera ; Symbiosis ; }, abstract = {Elucidating the factors determining reproductive success has challenged scientists since Darwin, but the exact pathways that shape the evolution of life history traits by connecting extrinsic (e.g., landscape structure) and intrinsic (e.g., female's age and endosymbionts) factors and reproductive success have rarely been studied. Here we collected female fleas from wild rodents in plots differing in their densities and proportions of the most dominant rodent species. We then combined path analysis and model selection approaches to explore the network of effects, ranging from micro to macroscales, determining the reproductive success of these fleas. Our results suggest that female reproductive success is directly and positively associated with their infection by Mycoplasma bacteria and their own body mass, and with the rodent species size and total density. In addition, we found evidence for indirect effects of rodent sex and rodent community diversity on female reproductive success. These results highlight the importance of exploring interrelated factors across organization scales while studying the reproductive success of wild organisms, and they have implications for the control of vector-borne diseases.}, } @article {pmid28711676, year = {2017}, author = {Stupica, D and Lusa, L and Klevišar, MN and Terzić, S and Pirš, M and Premru, MM and Strle, F}, title = {Should we consider faecal colonisation with extended-spectrum β-lactamase-producing Enterobacteriaceae in empirical therapy of community-onset sepsis?.}, journal = {International journal of antimicrobial agents}, volume = {50}, number = {4}, pages = {564-571}, doi = {10.1016/j.ijantimicag.2017.06.019}, pmid = {28711676}, issn = {1872-7913}, mesh = {Aged ; Aged, 80 and over ; Anti-Bacterial Agents/*therapeutic use ; Bacteremia/drug therapy/microbiology/mortality ; Community-Acquired Infections/*drug therapy/microbiology/mortality ; Enterobacteriaceae/*drug effects/metabolism ; Enterobacteriaceae Infections/*drug therapy/microbiology/mortality ; Feces/*microbiology ; Female ; Humans ; Male ; Retrospective Studies ; Urinary Tract Infections/drug therapy/microbiology ; beta-Lactam Resistance/*genetics ; beta-Lactamase Inhibitors/*therapeutic use ; beta-Lactamases/*metabolism ; beta-Lactams/therapeutic use ; }, abstract = {In patients colonised with extended-spectrum β-lactamase-producing Enterobacteriaceae (ESBL-E), the preference for carbapenems (CRBs) over non-CRB antibiotics for empirical therapy of sepsis is questionable from an ecologic perspective. Moreover, how well colonisation predicts an ESBL-E aetiology of infection has been poorly investigated. The purpose of this retrospective observational study was to determine the positive predictive value (PPV) of ESBL-E faecal colonisation for ESBL-E sepsis aetiology and the impact of empirical therapy on treatment outcome. The study included 653 ESBL-E carriers with community-onset sepsis hospitalised at a single medical centre during a 5-year period. The PPV of ESBL-E colonisation for ESBL-E sepsis aetiology was significantly higher (62.6%) when sepsis originated from a urinary tract infection (UTI) than from a respiratory tract infection (24.5%), other known origins (27.1%) or an unidentified origin (21.4%). Among the 653 patients, 177 (27.1%) received CRBs empirically and 476 received non-CRBs, predominantly β-lactam/β-lactamase inhibitor combinations. Although univariate analysis suggested a higher 30-day mortality in the non-CRB versus CRB group (26.7% vs. 19.2%; OR = 1.53; P = 0.049), the estimated association was much smaller and was not significant (OR = 1.11, 95% CI 0.66-1.87; P = 0.68) in the multiple regression analysis adjusted for age, sex, Charlson comorbidity index, and severity, origin or aetiology of sepsis. The subgroup of 240 patients with unidentified sepsis aetiology also did not benefit from empirical CRB treatment. In non-critically ill ESBL-E carriers with community-onset sepsis, CRB-sparing empirical therapy seems appropriate, particularly if sepsis originates from a site other than a UTI.}, } @article {pmid28710428, year = {2017}, author = {Kiedrzyńska, E and Urbaniak, M and Kiedrzyński, M and Jóźwik, A and Bednarek, A and Gągała, I and Zalewski, M}, title = {The use of a hybrid Sequential Biofiltration System for the improvement of nutrient removal and PCB control in municipal wastewater.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {5477}, pmid = {28710428}, issn = {2045-2322}, abstract = {This article aims to evaluate the efficiency of an innovative hybrid Sequential Biofiltration System (SBS) for removing phosphorus and nitrogen and polychlorinated biphenyls (PCBs) from original municipal wastewater produced by a Wastewater Treatment Plant under authentic operating conditions. The hybrid SBS was constructed with two barriers, a geochemical (filtration beds with limestone, coal and sawdust) and a biological barrier (wetlands with Glyceria, Acorus, Typha, Phragmites), operating in parallel. Significant differences were found between inflow and outflow from the SBS with regard to wastewater contaminant concentrations, the efficiency of removal being 16% (max. 93%) for Total Phosphorus (TP), 25% (max. 93%) for Soluble Reactive Phosphorus (SRP), 15% (max. 97%) for Total Nitrogen (TN), 17% (max. 98%) for NO3[-]N, and 21% for PCB equivalency (PCB EQ). In the case of PCB EQ concentration, the highest efficiency of 43% was obtained using beds with macrophytes. The SBS removed a significant load of TP (0.415 kg), TN (3.136 kg), and PCB EQ (0.223 g) per square meter per year. The use of low-cost hybrid SBSs as a post-treatment step for wastewater treatment was found to be an effective ecohydrological biotechnology that may be used for reducing point source pollution and improving water quality.}, } @article {pmid28704402, year = {2017}, author = {Plourde, BT and Burgess, TL and Eskew, EA and Roth, TM and Stephenson, N and Foley, JE}, title = {Are disease reservoirs special? Taxonomic and life history characteristics.}, journal = {PloS one}, volume = {12}, number = {7}, pages = {e0180716}, pmid = {28704402}, issn = {1932-6203}, mesh = {Animals ; Birds/classification ; Chiroptera/classification ; Databases, Factual ; Disease Reservoirs/*classification ; Humans ; Life History Traits ; Mammals/classification ; }, abstract = {Pathogens that spill over between species cause a significant human and animal health burden. Here, we describe characteristics of animal reservoirs that are required for pathogen spillover. We assembled and analyzed a database of 330 disease systems in which a pathogen spills over from a reservoir of one or more species. Three-quarters of reservoirs included wildlife, and 84% included mammals. Further, 65% of pathogens depended on a community of reservoir hosts, rather than a single species, for persistence. Among mammals, the most frequently identified reservoir hosts were rodents, artiodactyls, and carnivores. The distribution among orders of mammalian species identified as reservoirs did not differ from that expected by chance. Among disease systems with high priority pathogens and epidemic potential, we found birds, primates, and bats to be overrepresented. We also analyzed the life history traits of mammalian reservoir hosts and compared them to mammals as a whole. Reservoir species had faster life history characteristics than mammals overall, exhibiting traits associated with greater reproductive output rather than long-term survival. Thus, we find that in many respects, reservoirs of spillover pathogens are indeed special. The described patterns provide a useful resource for studying and managing emerging infectious diseases.}, } @article {pmid28704398, year = {2017}, author = {Bukhari, SA and Saul, MC and Seward, CH and Zhang, H and Bensky, M and James, N and Zhao, SD and Chandrasekaran, S and Stubbs, L and Bell, AM}, title = {Temporal dynamics of neurogenomic plasticity in response to social interactions in male threespined sticklebacks.}, journal = {PLoS genetics}, volume = {13}, number = {7}, pages = {e1006840}, pmid = {28704398}, issn = {1553-7404}, support = {R01 GM082937/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Behavior, Animal/*physiology ; Biological Evolution ; Cerebrum/physiology ; Chromatin/genetics ; Diencephalon/physiology ; Epigenomics ; Genome ; Neuronal Plasticity/*genetics ; Sequence Analysis, RNA ; Smegmamorpha/*genetics/physiology ; *Social Behavior ; Transcription Factors/genetics ; *Transcription, Genetic ; }, abstract = {Animals exhibit dramatic immediate behavioral plasticity in response to social interactions, and brief social interactions can shape the future social landscape. However, the molecular mechanisms contributing to behavioral plasticity are unclear. Here, we show that the genome dynamically responds to social interactions with multiple waves of transcription associated with distinct molecular functions in the brain of male threespined sticklebacks, a species famous for its behavioral repertoire and evolution. Some biological functions (e.g., hormone activity) peaked soon after a brief territorial challenge and then declined, while others (e.g., immune response) peaked hours afterwards. We identify transcription factors that are predicted to coordinate waves of transcription associated with different components of behavioral plasticity. Next, using H3K27Ac as a marker of chromatin accessibility, we show that a brief territorial intrusion was sufficient to cause rapid and dramatic changes in the epigenome. Finally, we integrate the time course brain gene expression data with a transcriptional regulatory network, and link gene expression to changes in chromatin accessibility. This study reveals rapid and dramatic epigenomic plasticity in response to a brief, highly consequential social interaction.}, } @article {pmid28704168, year = {2017}, author = {Kaprelian, J and Berg, RL and Barnes, KL and Marlenga, B}, title = {Integrating Agricultural Injury Prevention with Rural Pediatrics: A Pilot Assessment.}, journal = {Journal of agromedicine}, volume = {22}, number = {4}, pages = {416-419}, doi = {10.1080/1059924X.2017.1354114}, pmid = {28704168}, issn = {1545-0813}, mesh = {Adult ; Agricultural Workers' Diseases/*prevention & control/psychology ; *Agriculture ; Child ; Child, Preschool ; Female ; Humans ; Interviews as Topic ; Male ; Middle Aged ; *Occupational Health ; Pediatrics ; Physicians/*psychology ; Pilot Projects ; Rural Health ; Workforce ; Wounds and Injuries/*prevention & control/psychology ; }, abstract = {BACKGROUND: Childhood agricultural injuries are an important public health problem. Pediatricians are a trusted source of expertise in children's health and safety and could serve as a sphere of influence to augment child agricultural injury prevention efforts. The purpose of this pilot study was to begin to explore the perspectives of pediatricians in a large rural health clinic about addressing child agricultural injury prevention within their practice.

METHODS: Structured interviews were conducted with nine pediatricians who maintain a clinical practice of at least 2 days a week and care for newborns through adolescents. Detailed interviewer notes were reviewed and summarized.

RESULTS: Rural pediatricians readily acknowledge substantial numbers of farm children in their practice. In general, these providers: (1) recognize farming environments as a safety risk and see agricultural injury prevention as an important topic to be addressed with their patients, (2) are comfortable discussing the topic, but seldom actually initiate such conversations, and (3) doubt farm parents would be receptive to integrating agricultural injury prevention into a rural pediatric practice.

CONCLUSION: While rural pediatricians recognize child safety risks in farm environments, they are reluctant to actually initiate this conversation with parents. Future research should explore both pediatricians' hesitancy to discuss agricultural injury prevention and farm parents' readiness for integrating the topic into pediatric primary care visits. Such would help to assess the viability of pediatricians as a sphere of influence for augmenting child agricultural injury prevention efforts.}, } @article {pmid28701505, year = {2017}, author = {Gibb, R and Shoji, A and Fayet, AL and Perrins, CM and Guilford, T and Freeman, R}, title = {Remotely sensed wind speed predicts soaring behaviour in a wide-ranging pelagic seabird.}, journal = {Journal of the Royal Society, Interface}, volume = {14}, number = {132}, pages = {}, pmid = {28701505}, issn = {1742-5662}, mesh = {Animal Migration ; Animals ; Behavior, Animal/*physiology ; Charadriiformes/*physiology ; Flight, Animal/*physiology ; Geographic Information Systems ; Oceans and Seas ; *Wind ; }, abstract = {Global wind patterns affect flight strategies in many birds, including pelagic seabirds, many of which use wind-powered soaring to reduce energy costs during at-sea foraging trips and migration. Such long-distance movement patterns are underpinned by local interactions between wind conditions and flight behaviour, but these fine-scale relationships are far less well understood. Here we show that remotely sensed ocean wind speed and direction are highly significant predictors of soaring behaviour in a migratory pelagic seabird, the Manx shearwater (Puffinus puffinus). We used high-frequency GPS tracking data (10 Hz) and statistical behaviour state classification to identify two energetic modes in at-sea flight, corresponding to flap-like and soar-like flight. We show that soaring is significantly more likely to occur in tailwinds and crosswinds above a wind speed threshold of around 8 m s[-1], suggesting that these conditions enable birds to reduce metabolic costs by preferentially soaring over flapping. Our results suggest a behavioural mechanism by which wind conditions may shape foraging and migration ecology in pelagic seabirds, and thus indicate that shifts in wind patterns driven by climate change could impact this and other species. They also emphasize the emerging potential of high-frequency GPS biologgers to provide detailed quantitative insights into fine-scale flight behaviour in free-living animals.}, } @article {pmid28701376, year = {2017}, author = {Brand, P and Saleh, N and Pan, H and Li, C and Kapheim, KM and Ramírez, SR}, title = {The Nuclear and Mitochondrial Genomes of the Facultatively Eusocial Orchid Bee Euglossa dilemma.}, journal = {G3 (Bethesda, Md.)}, volume = {7}, number = {9}, pages = {2891-2898}, pmid = {28701376}, issn = {2160-1836}, support = {S10 OD018174/OD/NIH HHS/United States ; S10 RR027303/RR/NCRR NIH HHS/United States ; S10 RR029668/RR/NCRR NIH HHS/United States ; }, mesh = {Animals ; Bees/classification/*genetics ; Computational Biology/methods ; Gene Order ; *Genome ; *Genome, Mitochondrial ; *Genomics/methods ; Molecular Sequence Annotation ; Phylogeny ; Sequence Analysis, DNA ; Whole Genome Sequencing ; }, abstract = {Bees provide indispensable pollination services to both agricultural crops and wild plant populations, and several species of bees have become important models for the study of learning and memory, plant-insect interactions, and social behavior. Orchid bees (Apidae: Euglossini) are especially important to the fields of pollination ecology, evolution, and species conservation. Here we report the nuclear and mitochondrial genome sequences of the orchid bee Euglossa dilemma Bembé & Eltz. E. dilemma was selected because it is widely distributed, highly abundant, and it was recently naturalized in the southeastern United States. We provide a high-quality assembly of the 3.3 Gb genome, and an official gene set of 15,904 gene annotations. We find high conservation of gene synteny with the honey bee throughout 80 MY of divergence time. This genomic resource represents the first draft genome of the orchid bee genus Euglossa, and the first draft orchid bee mitochondrial genome, thus representing a valuable resource to the research community.}, } @article {pmid28701187, year = {2017}, author = {Khelik, K and Lagesen, K and Sandve, GK and Rognes, T and Nederbragt, AJ}, title = {NucDiff: in-depth characterization and annotation of differences between two sets of DNA sequences.}, journal = {BMC bioinformatics}, volume = {18}, number = {1}, pages = {338}, pmid = {28701187}, issn = {1471-2105}, mesh = {Base Sequence ; DNA/*chemistry ; Genomics ; Internet ; Sequence Alignment ; *User-Computer Interface ; }, abstract = {BACKGROUND: Comparing sets of sequences is a situation frequently encountered in bioinformatics, examples being comparing an assembly to a reference genome, or two genomes to each other. The purpose of the comparison is usually to find where the two sets differ, e.g. to find where a subsequence is repeated or deleted, or where insertions have been introduced. Such comparisons can be done using whole-genome alignments. Several tools for making such alignments exist, but none of them 1) provides detailed information about the types and locations of all differences between the two sets of sequences, 2) enables visualisation of alignment results at different levels of detail, and 3) carefully takes genomic repeats into consideration.

RESULTS: We here present NucDiff, a tool aimed at locating and categorizing differences between two sets of closely related DNA sequences. NucDiff is able to deal with very fragmented genomes, repeated sequences, and various local differences and structural rearrangements. NucDiff determines differences by a rigorous analysis of alignment results obtained by the NUCmer, delta-filter and show-snps programs in the MUMmer sequence alignment package. All differences found are categorized according to a carefully defined classification scheme covering all possible differences between two sequences. Information about the differences is made available as GFF3 files, thus enabling visualisation using genome browsers as well as usage of the results as a component in an analysis pipeline. NucDiff was tested with varying parameters for the alignment step and compared with existing alternatives, called QUAST and dnadiff.

CONCLUSIONS: We have developed a whole genome alignment difference classification scheme together with the program NucDiff for finding such differences. The proposed classification scheme is comprehensive and can be used by other tools. NucDiff performs comparably to QUAST and dnadiff but gives much more detailed results that can easily be visualized. NucDiff is freely available on https://github.com/uio-cels/NucDiff under the MPL license.}, } @article {pmid28699746, year = {2017}, author = {Luciano, P and Imperatore, C and Senese, M and Aiello, A and Casertano, M and Guo, YW and Menna, M}, title = {Assignment of the Absolute Configuration of Phosphoeleganin via Synthesis of Model Compounds.}, journal = {Journal of natural products}, volume = {80}, number = {7}, pages = {2118-2123}, doi = {10.1021/acs.jnatprod.7b00397}, pmid = {28699746}, issn = {1520-6025}, mesh = {Databases, Factual ; Marine Biology ; Models, Chemical ; Molecular Structure ; Nuclear Magnetic Resonance, Biomolecular ; Polyketides/chemical synthesis/*chemistry/pharmacology ; Protein Tyrosine Phosphatase, Non-Receptor Type 1/*antagonists & inhibitors ; Stereoisomerism ; }, abstract = {The full absolute configuration assignment of phosphoeleganin (1), a recently discovered marine-derived phosphorylated polyketide with protein tyrosine phosphatase 1B inhibitory activity, was achieved. It was based on the synthesis of model diasteroisomeric compounds of the C-8-C-12 segment portion of phosphoeleganin, chiral derivatization methods, and application of the universal NMR database concept.}, } @article {pmid28693474, year = {2017}, author = {van der Walt, AJ and van Goethem, MW and Ramond, JB and Makhalanyane, TP and Reva, O and Cowan, DA}, title = {Assembling metagenomes, one community at a time.}, journal = {BMC genomics}, volume = {18}, number = {1}, pages = {521}, pmid = {28693474}, issn = {1471-2164}, mesh = {Benchmarking ; Databases, Genetic ; Environment ; Metagenomics/*methods ; }, abstract = {BACKGROUND: Metagenomics allows unprecedented access to uncultured environmental microorganisms. The analysis of metagenomic sequences facilitates gene prediction and annotation, and enables the assembly of draft genomes, including uncultured members of a community. However, while several platforms have been developed for this critical step, there is currently no clear framework for the assembly of metagenomic sequence data.

RESULTS: To assist with selection of an appropriate metagenome assembler we evaluated the capabilities of nine prominent assembly tools on nine publicly-available environmental metagenomes, as well as three simulated datasets. Overall, we found that SPAdes provided the largest contigs and highest N50 values across 6 of the 9 environmental datasets, followed by MEGAHIT and metaSPAdes. MEGAHIT emerged as a computationally inexpensive alternative to SPAdes, assembling the most complex dataset using less than 500 GB of RAM and within 10 hours.

CONCLUSIONS: We found that assembler choice ultimately depends on the scientific question, the available resources and the bioinformatic competence of the researcher. We provide a concise workflow for the selection of the best assembly tool.}, } @article {pmid28692652, year = {2017}, author = {Xu, EG and Mager, EM and Grosell, M and Stieglitz, JD and Hazard, ES and Hardiman, G and Schlenk, D}, title = {Developmental transcriptomic analyses for mechanistic insights into critical pathways involved in embryogenesis of pelagic mahi-mahi (Coryphaena hippurus).}, journal = {PloS one}, volume = {12}, number = {7}, pages = {e0180454}, pmid = {28692652}, issn = {1932-6203}, mesh = {Animals ; *Ecosystem ; Embryo, Nonmammalian/metabolism ; Embryonic Development/*genetics ; Gene Expression Profiling/*methods ; Gene Expression Regulation, Developmental ; Gene Ontology ; Larva/genetics ; Perciformes/*embryology/*genetics ; Sequence Analysis, RNA ; Signal Transduction/*genetics ; Takifugu/embryology/genetics ; }, abstract = {Mahi-mahi (Coryphaena hippurus) is a commercially and ecologically important species of fish occurring in tropical and temperate waters worldwide. Understanding early life events is crucial for predicting effects of environmental stress, which is largely restricted by a lack of genetic resources regarding expression of early developmental genes and regulation of pathways. The need for anchoring developmental stages to transcriptional activities is highlighted by increasing evidence on the impacts of recurrent worldwide oil spills in this sensitive species during early development. By means of high throughput sequencing, we characterized the developmental transcriptome of mahi-mahi at three critical developmental stages, from pharyngula embryonic stage (24 hpf) to 48 hpf yolk-sac larva (transition 1), and to 96 hpf free-swimming larva (transition 2). With comparative analysis by multiple bioinformatic tools, a larger number of significantly altered genes and more diverse gene ontology terms were observed during transition 2 than transition 1. Cellular and tissue development terms were more significantly enriched in transition 1, while metabolism related terms were more enriched in transition 2, indicating a switch progressing from general embryonic development to metabolism during the two transitions. Special focus was given on the most significant common canonical pathways (e.g. calcium signaling, glutamate receptor signaling, cAMP response element-binding protein signaling, cardiac β-adrenergic signaling, etc.) and expression of developmental genes (e.g. collagens, myosin, notch, glutamate metabotropic receptor etc.), which were associated with morphological changes of nervous, muscular, and cardiovascular system. These data will provide an important basis for understanding embryonic development and identifying molecular mechanisms of abnormal development in fish species.}, } @article {pmid28688976, year = {2017}, author = {Balado, M and Benzekri, H and Labella, AM and Claros, MG and Manchado, M and Borrego, JJ and Osorio, CR and Lemos, ML}, title = {Genomic analysis of the marine fish pathogen Photobacterium damselae subsp. piscicida: Insertion sequences proliferation is associated with chromosomal reorganisations and rampant gene decay.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {54}, number = {}, pages = {221-229}, doi = {10.1016/j.meegid.2017.07.007}, pmid = {28688976}, issn = {1567-7257}, mesh = {Animals ; Chromosomes, Bacterial ; Computational Biology ; Fish Diseases/*microbiology ; Genes, Bacterial ; Genetic Linkage ; *Genome, Bacterial ; *Genomics/methods ; Molecular Sequence Annotation ; Mutagenesis, Insertional ; Photobacterium/*classification/*genetics ; Sequence Analysis, DNA ; Whole Genome Sequencing ; }, abstract = {Photobacterium damselae subsp. piscicida (Pdp) is an intracellular fish pathogen that causes photobacteriosis, a disease proven deadly in farmed fish worldwide. This work focuses on the analysis of genome sequences, chromosomes structure and gene contents of two strains from Sparus aurata (DI21) and Solea senegalensis (L091106-03H), isolated on the Spanish Atlantic coast. The comparative genomic analysis revealed that DI21 and L091106-03H share 98% of their genomes, including two virulence plasmids: pPHDP70 encoding siderophore piscibactin synthesis and pPHDP10 encoding the apoptotic toxin AIP56. Both genomes harbour a surprisingly large number of IS elements accounting for 12-17% of the total genome, representing an IS density of 0.15 elements per kb, one of the highest IS density values in a bacterial pathogen. This massive proliferation of ISs is responsible for the generation of a high number of pseudogenes that caused extensive loss of biological functions. Pseudogene formation is one of the main features of Pdp genome that explains most of the ecological and phenotypic differences with respect to its sibling subspecies P. damselae subsp. damselae and to other Vibrionaceae. Evidence was also found proving the existence of two chromosomal configurations depending on the origin of the strains: an European and an Asian/American types of genome organisation, reinforcing the idea of the existence of two geographically-linked clonal lineages in Pdp. In short, our study suggests that the host-dependent lifestyle of Pdp allowed massive IS proliferation and gene decay processes, which are major evolutionary forces in the shaping of the Pdp genome.}, } @article {pmid28686565, year = {2017}, author = {Marco, D}, title = {Integration of Ecology and Environmental Metagenomics Conceptual and Methodological Frameworks.}, journal = {Current issues in molecular biology}, volume = {24}, number = {}, pages = {1-16}, doi = {10.21775/cimb.024.001}, pmid = {28686565}, issn = {1467-3045}, mesh = {*Biodiversity ; Computational Biology/*methods ; Ecology/*methods ; Ecosystem ; Environment ; Humans ; Metagenomics/*methods ; Models, Theoretical ; }, abstract = {Although from its origin metagenomics was concerned with composition of communities of microbial OTUs (Operational Taxonomic Units) living in a given habitat and their diversity and functional heterogeneity (concepts already well rooted in ecology), the new field was more 'environmentally' than 'ecologically' oriented. Probably by circumstantial reasons, metagenomics and ecology followed rather independent trajectories and conceptual and methodological gaps appeared. Recently, calls for the need of integrating the theoretical basis and methodologies coming from metagenomics (and other meta-omics) and ecology have been made. Here I will address some of the principles and methods of field ecology that, although useful in the context of environmental metagenomic studies, have been rather disregarded. In particular, I will emphasize the contribution of some well established concepts and methods of field ecology to a an appropriate field sampling and experimental design of environmental metagenomic studies.}, } @article {pmid28683838, year = {2017}, author = {de Muinck, EJ and Trosvik, P and Gilfillan, GD and Hov, JR and Sundaram, AYM}, title = {A novel ultra high-throughput 16S rRNA gene amplicon sequencing library preparation method for the Illumina HiSeq platform.}, journal = {Microbiome}, volume = {5}, number = {1}, pages = {68}, pmid = {28683838}, issn = {2049-2618}, mesh = {Bacteria/genetics ; Computational Biology ; DNA Barcoding, Taxonomic ; *Gene Library ; High-Throughput Nucleotide Sequencing/economics/instrumentation/*methods ; Metagenomics ; Polymerase Chain Reaction/methods ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, DNA/instrumentation/methods ; }, abstract = {BACKGROUND: Advances in sequencing technologies and bioinformatics have made the analysis of microbial communities almost routine. Nonetheless, the need remains to improve on the techniques used for gathering such data, including increasing throughput while lowering cost and benchmarking the techniques so that potential sources of bias can be better characterized.

METHODS: We present a triple-index amplicon sequencing strategy to sequence large numbers of samples at significantly lower c ost and in a shorter timeframe compared to existing methods. The design employs a two-stage PCR protocol, incorpo rating three barcodes to each sample, with the possibility to add a fourth-index. It also includes heterogeneity spacers to overcome low complexity issues faced when sequencing amplicons on Illumina platforms.

RESULTS: The library preparation method was extensively benchmarked through analysis of a mock community in order to assess biases introduced by sample indexing, number of PCR cycles, and template concentration. We further evaluated the method through re-sequencing of a standardized environmental sample. Finally, we evaluated our protocol on a set of fecal samples from a small cohort of healthy adults, demonstrating good performance in a realistic experimental setting. Between-sample variation was mainly related to batch effects, such as DNA extraction, while sample indexing was also a significant source of bias. PCR cycle number strongly influenced chimera formation and affected relative abundance estimates of species with high GC content. Libraries were sequenced using the Illumina HiSeq and MiSeq platforms to demonstrate that this protocol is highly scalable to sequence thousands of samples at a very low cost.

CONCLUSIONS: Here, we provide the most comprehensive study of performance and bias inherent to a 16S rRNA gene amplicon sequencing method to date. Triple-indexing greatly reduces the number of long custom DNA oligos required for library preparation, while the inclusion of variable length heterogeneity spacers minimizes the need for PhiX spike-in. This design results in a significant cost reduction of highly multiplexed amplicon sequencing. The biases we characterize highlight the need for highly standardized protocols. Reassuringly, we find that the biological signal is a far stronger structuring factor than the various sources of bias.}, } @article {pmid28683828, year = {2017}, author = {Ren, J and Ahlgren, NA and Lu, YY and Fuhrman, JA and Sun, F}, title = {VirFinder: a novel k-mer based tool for identifying viral sequences from assembled metagenomic data.}, journal = {Microbiome}, volume = {5}, number = {1}, pages = {69}, pmid = {28683828}, issn = {2049-2618}, support = {R01 GM120624/GM/NIGMS NIH HHS/United States ; }, mesh = {Computational Biology/methods ; DNA, Viral/*genetics ; Gastrointestinal Microbiome ; *Genome, Viral ; Humans ; Liver Cirrhosis/virology ; Machine Learning ; Metagenome ; Metagenomics/*methods ; Phylogeny ; Sequence Analysis, DNA ; *Software ; }, abstract = {BACKGROUND: Identifying viral sequences in mixed metagenomes containing both viral and host contigs is a critical first step in analyzing the viral component of samples. Current tools for distinguishing prokaryotic virus and host contigs primarily use gene-based similarity approaches. Such approaches can significantly limit results especially for short contigs that have few predicted proteins or lack proteins with similarity to previously known viruses.

METHODS: We have developed VirFinder, the first k-mer frequency based, machine learning method for virus contig identification that entirely avoids gene-based similarity searches. VirFinder instead identifies viral sequences based on our empirical observation that viruses and hosts have discernibly different k-mer signatures. VirFinder's performance in correctly identifying viral sequences was tested by training its machine learning model on sequences from host and viral genomes sequenced before 1 January 2014 and evaluating on sequences obtained after 1 January 2014.

RESULTS: VirFinder had significantly better rates of identifying true viral contigs (true positive rates (TPRs)) than VirSorter, the current state-of-the-art gene-based virus classification tool, when evaluated with either contigs subsampled from complete genomes or assembled from a simulated human gut metagenome. For example, for contigs subsampled from complete genomes, VirFinder had 78-, 2.4-, and 1.8-fold higher TPRs than VirSorter for 1, 3, and 5 kb contigs, respectively, at the same false positive rates as VirSorter (0, 0.003, and 0.006, respectively), thus VirFinder works considerably better for small contigs than VirSorter. VirFinder furthermore identified several recently sequenced virus genomes (after 1 January 2014) that VirSorter did not and that have no nucleotide similarity to previously sequenced viruses, demonstrating VirFinder's potential advantage in identifying novel viral sequences. Application of VirFinder to a set of human gut metagenomes from healthy and liver cirrhosis patients reveals higher viral diversity in healthy individuals than cirrhosis patients. We also identified contig bins containing crAssphage-like contigs with higher abundance in healthy patients and a putative Veillonella genus prophage associated with cirrhosis patients.

CONCLUSIONS: This innovative k-mer based tool complements gene-based approaches and will significantly improve prokaryotic viral sequence identification, especially for metagenomic-based studies of viral ecology.}, } @article {pmid28683113, year = {2017}, author = {Li, F and Ma, S and Li, Y and Tan, H and Hou, X and Ren, G and Cai, K}, title = {Impact of the Three Gorges project on ecological environment changes and snail distribution in Dongting Lake area.}, journal = {PLoS neglected tropical diseases}, volume = {11}, number = {7}, pages = {e0005661}, pmid = {28683113}, issn = {1935-2735}, mesh = {Animal Distribution/*physiology ; Animals ; China ; Databases, Factual ; *Ecosystem ; Environmental Monitoring/*methods ; Host-Parasite Interactions ; *Power Plants ; Schistosoma japonicum/physiology ; Snails/parasitology/*physiology ; }, abstract = {BACKGROUND: The Three Gorges Dam (TGD) is a remarkable, far-reaching project in China. This study was conducted to assess the impact of TGD on changes in the ecological environment, snail distribution and schistosomiasis transmission in Dongting Lake area.

METHODS: Hydrological data were collected from 12 monitoring sites in Hunan section of Yangtze River before and after TGD was established. Data on snail distribution and human schistosomiasis infection were also collected. Correlation analyses were performed to detect the significance of snail distribution to changes in ecological environmental factors and human schistosomiasis infection.

FINDINGS: A series of ecological environmental factors have changed in Dongting Lake area following the operation of TGD. Volume of annual runoff discharged into Dongting Lake declined by 20.85%. Annual sediment volume discharged into the lake and the mean lake sedimentation rate decreased by 73.9% and 32.2%, respectively. From 2003 to 2015, occurrence rate of frames with living snails and mean density of living snails decreased overall by 82.43% and 94.35%, respectively, with annual decrements being 13.49% and 21.29%. Moreover, human infection rate of schistosomiasis had decreased from 3.38% in 2003 to 0.44% in 2015, with a reduction of 86.98%. Correlation analyses showed that mean density of living snails was significantly associated with water level (r = 0.588, p<0.001), as well as the mean elevation range of the bottomland (r = 0.374, p = 0.025) and infection rate of schistosomiasis (r = 0.865, p<0.001).

CONCLUSION: Ecological environmental changes caused by the TGD were associated with distribution of snails, and might further affect the transmission and prevalence of schistosomiasis. Risk of schistosomiasis transmission still exists in Dongting Lake area and long-term monitoring is required.}, } @article {pmid28681587, year = {2017}, author = {Zhang, AL and Sun, XY and Yin, Q and Zeng, JH and Zhang, Z and Li, JQ and Zhang, H}, title = {Functional characterization of the promoter of carbonyl reductase 1 gene in porcine endometrial cells.}, journal = {Journal of Zhejiang University. Science. B}, volume = {18}, number = {7}, pages = {626-634}, pmid = {28681587}, issn = {1862-1783}, mesh = {Animals ; Binding Sites ; Carbonyl Reductase (NADPH)/*metabolism ; Catalysis ; Chromatin Immunoprecipitation ; Cloning, Molecular ; Computational Biology ; Endometrium/*cytology/metabolism ; Epithelial Cells/metabolism ; Female ; Inflammation ; NF-kappa B/*metabolism ; Pregnancy ; *Promoter Regions, Genetic ; RNA, Small Interfering/metabolism ; Swine ; Transcription Factors/metabolism ; }, abstract = {Prostaglandins (PGs) play a critical role in porcine reproduction, of which prostaglandin E2 (PGE2) and prostaglandin F2α (PGF2α) exert antiluteolytic and luteolysis actions, respectively. As a rate-limiting enzyme, carbonyl reductase 1 (CBR1) catalyzes the conversion of PGE2 to PGF2α. A high ratio of PGE2:PGF2α is beneficial to the establishment and maintenance of porcine pregnancy. PG is essential for the establishment of pregnancy which resembles the proinflammatory response and nuclear factor κB (NF-κB) is involved in the process. Bioinformatic analysis has shown that NF-κB is a possible factor bound to two cis-regulatory elements in CBR1 promoter. In this study, we cloned the 2997 bp (-2875/+122) of the promoter, and constructed six 5'-deleted dual-luciferase reporter recombinant vectors. In endometrial cells, the region of P2 (-1640/+7) exhibited the greatest transcriptional activity at driving luciferase expression, but not significantly different from that of P1 (-2089/+7). The activity of P1, P2, and P3 (-1019/+7) was highly significantly higher than that of others (P<0.01), suggesting that two positive regulatory elements were likely present in the regions of -1640/-1019 and -1019/-647. The results also showed that the -1640/-647 region was indispensable for the promoter. The results of chromatin immunoprecipitation (ChIP) demonstrated that the NF-κB subunit p65 binds to one site around -1545/-1531. Using four reference genes, we found that the over-expression of p65 enhanced the expression of CBR1 (P<0.05) in porcine endometrial epithelial cells, while knockdown of the p65 did not down-regulate the CBR1 expression. These results indicated that NF-κB (p65) could bind to the special element of CBR1 gene promoter in porcine endometrial epithelial cells in vitro. The binding site of NF-κB was a positive regulator for the CBR1 gene promoter, but was not necessary for the basic expression.}, } @article {pmid28678841, year = {2017}, author = {Wang, L and Zheng, H and Zhao, H and Robinson, BE}, title = {Nitrogen balance dynamics during 2000-2010 in the Yangtze River Basin croplands, with special reference to the relative contributions of cropland area and synthetic fertilizer N application rate changes.}, journal = {PloS one}, volume = {12}, number = {7}, pages = {e0180613}, pmid = {28678841}, issn = {1932-6203}, mesh = {China ; *Crops, Agricultural ; Fertilizers/*analysis ; Geographic Information Systems ; Nitrogen/*analysis ; Rivers ; Uncertainty ; }, abstract = {With the increases of cropland area and fertilizer nitrogen (N) application rate, general N balance characteristics in regional agroecosystems have been widely documented. However, few studies have quantitatively analyzed the drivers of spatial changes in the N budget. We constructed a mass balance model of the N budget at the soil surface using a database of county-level agricultural statistics to analyze N input, output, and proportional contribution of various factors to the overall N input changes in croplands during 2000-2010 in the Yangtze River Basin, the largest basin and the main agricultural production region in China. Over the period investigated, N input increased by 9%. Of this 87% was from fertilizer N input. In the upper and middle reaches of the basin, the increased synthetic fertilizer N application rate accounted for 84% and 76% of the N input increase, respectively, mainly due to increased N input in the cropland that previously had low synthetic fertilizer N application rate. In lower reaches of the basin, mainly due to urbanization, the decrease in cropland area and synthetic fertilizer N application rate nearly equally contributed to decreases in N input. Quantifying spatial N inputs can provide critical managerial information needed to optimize synthetic fertilizer N application rate and monitor the impacts of urbanization on agricultural production, helping to decrease agricultural environment risk and maintain sustainable agricultural production in different areas.}, } @article {pmid28676843, year = {2017}, author = {Wu, C and Qin, X and Li, P and Pan, T and Ren, W and Li, N and Peng, Y}, title = {Transcriptomic Analysis on Responses of Murine Lungs to Pasteurella multocida Infection.}, journal = {Frontiers in cellular and infection microbiology}, volume = {7}, number = {}, pages = {251}, pmid = {28676843}, issn = {2235-2988}, mesh = {Animals ; Bacterial Proteins/genetics ; Cell Proliferation ; Chemokines/metabolism ; Cytokines/metabolism ; Disease Models, Animal ; *Gene Expression Profiling ; Gene Expression Regulation ; Gene Ontology ; Genes, Bacterial/genetics ; Interferon-gamma/genetics/metabolism ; Interleukin-17/genetics/metabolism ; Lung/*microbiology/pathology ; Mice ; Pasteurella Infections/immunology/*microbiology/mortality ; Pasteurella multocida/*genetics/immunology/*pathogenicity ; RNA, Bacterial ; Up-Regulation ; }, abstract = {Pasteurella multocida infection in cattle causes serious epidemic diseases and leads to great economic losses in livestock industry; however, little is known about the interaction between host and P. multocida in the lungs. To explore a fully insight into the host responses in the lungs during P. multocida infection, a mouse model of Pasteurella pneumonia was established by intraperitoneal infection, and then transcriptomic analysis of infected lungs was performed. P. multocida localized and grew in murine lungs, and induced inflammation in the lungs, as well as mice death. With transcriptomic analysis, approximately 10[7] clean reads were acquired. 4236 differently expressed genes (DEGs) were detected during P. multocida infection, of which 1924 DEGs were up-regulated. By gene ontology (GO) and Kyoto encyclopedia of genes and genomes (KEGG) enrichments, 5,303 GO enrichments and 116 KEGG pathways were significantly enriched in the context of P. multocida infection. Interestingly, genes related to immune responses, such as pattern recognition receptors (PRRs), chemokines and inflammatory cytokines, were significantly up-regulated, suggesting the key roles of these genes in P. multocida infection. Transcriptomic data showed that IFN-γ/IL-17-related genes were increased, which were validated by qRT-PCR, ELISA, and immunoblotting. Our study characterized the transcriptomic profile of the lungs in mice upon Pasteurella infection, and our findings could provide valuable information with respect to better understanding the responses in mice during P. multocida infection.}, } @article {pmid28675770, year = {2017}, author = {Lalla, RV and Treister, N and Sollecito, T and Schmidt, B and Patton, LL and Mohammadi, K and Hodges, JS and Brennan, MT and , }, title = {Oral complications at 6 months after radiation therapy for head and neck cancer.}, journal = {Oral diseases}, volume = {23}, number = {8}, pages = {1134-1143}, pmid = {28675770}, issn = {1601-0825}, support = {U01 DE022939/DE/NIDCR NIH HHS/United States ; }, mesh = {Aged ; Carcinoma, Squamous Cell/*radiotherapy ; Female ; Head and Neck Neoplasms/*radiotherapy ; Humans ; Longitudinal Studies ; Male ; Middle Aged ; Mouth/physiopathology/radiation effects ; Oral Hygiene ; Pain/etiology ; Prospective Studies ; Quality of Life ; Radiation Injuries/*etiology ; Radiotherapy, Intensity-Modulated/*adverse effects ; Saliva/*radiation effects ; Stomatitis/*etiology ; Time Factors ; }, abstract = {OBJECTIVE: To examine oral complications 6 months after modern radiation therapy (RT) for head and neck cancer (HNC).

METHODS: Prospective multicenter cohort study of patients with HNC receiving intensity-modulated radiation therapy or more advanced RT. Stimulated whole salivary flow, maximal mouth opening, oral mucositis, oral pain, oral health-related quality of life (OH-QOL), and oral hygiene practices were measured in 372 subjects pre-RT and 216 subjects at 6 months from the start of RT.

RESULTS: Mean stimulated whole salivary flow declined from 1.09 to 0.47 ml/min at 6 months (p < .0001). Mean maximal mouth opening reduced from 45.58 to 42.53 mm at 6 months (p < .0001). 8.1% of subjects had some oral mucositis at 6 months, including 3.8% with oral ulceration. Mean overall pain score was unchanged. OH-QOL was reduced at 6 months, with changes related to dry mouth, sticky saliva, swallowing solid foods, and sense of taste (p ≤ .0001). At 6 months, there was greater frequency of using dental floss and greater proportion using supplemental fluoride (p < .0001).

CONCLUSIONS: Despite advances in RT techniques, patients with HNC experience oral complications 6 months after RT, with resulting negative impacts on oral function and quality of life.}, } @article {pmid28673253, year = {2017}, author = {Wedemeyer, A and Kliemann, L and Srivastav, A and Schielke, C and Reusch, TB and Rosenstiel, P}, title = {An improved filtering algorithm for big read datasets and its application to single-cell assembly.}, journal = {BMC bioinformatics}, volume = {18}, number = {1}, pages = {324}, pmid = {28673253}, issn = {1471-2105}, mesh = {*Algorithms ; Bacteria/genetics ; *Datasets as Topic ; Metagenomics ; Sequence Analysis, DNA/*methods ; *Single-Cell Analysis ; }, abstract = {BACKGROUND: For single-cell or metagenomic sequencing projects, it is necessary to sequence with a very high mean coverage in order to make sure that all parts of the sample DNA get covered by the reads produced. This leads to huge datasets with lots of redundant data. A filtering of this data prior to assembly is advisable. Brown et al. (2012) presented the algorithm Diginorm for this purpose, which filters reads based on the abundance of their k-mers.

METHODS: We present Bignorm, a faster and quality-conscious read filtering algorithm. An important new algorithmic feature is the use of phred quality scores together with a detailed analysis of the k-mer counts to decide which reads to keep.

RESULTS: We qualify and recommend parameters for our new read filtering algorithm. Guided by these parameters, we remove in terms of median 97.15% of the reads while keeping the mean phred score of the filtered dataset high. Using the SDAdes assembler, we produce assemblies of high quality from these filtered datasets in a fraction of the time needed for an assembly from the datasets filtered with Diginorm.

CONCLUSIONS: We conclude that read filtering is a practical and efficient method for reducing read data and for speeding up the assembly process. This applies not only for single cell assembly, as shown in this paper, but also to other projects with high mean coverage datasets like metagenomic sequencing projects. Our Bignorm algorithm allows assemblies of competitive quality in comparison to Diginorm, while being much faster. Bignorm is available for download at https://git.informatik.uni-kiel.de/axw/Bignorm .}, } @article {pmid28673048, year = {2018}, author = {Barido-Sottani, J and Bošková, V and Plessis, LD and Kühnert, D and Magnus, C and Mitov, V and Müller, NF and PecErska, J and Rasmussen, DA and Zhang, C and Drummond, AJ and Heath, TA and Pybus, OG and Vaughan, TG and Stadler, T}, title = {Taming the BEAST-A Community Teaching Material Resource for BEAST 2.}, journal = {Systematic biology}, volume = {67}, number = {1}, pages = {170-174}, pmid = {28673048}, issn = {1076-836X}, mesh = {Algorithms ; Computational Biology/*education/*methods ; *Phylogeny ; *Software ; *Teaching Materials ; }, abstract = {Phylogenetics and phylodynamics are central topics in modern evolutionary biology. Phylogenetic methods reconstruct the evolutionary relationships among organisms, whereas phylodynamic approaches reveal the underlying diversification processes that lead to the observed relationships. These two fields have many practical applications in disciplines as diverse as epidemiology, developmental biology, palaeontology, ecology, and linguistics. The combination of increasingly large genetic data sets and increases in computing power is facilitating the development of more sophisticated phylogenetic and phylodynamic methods. Big data sets allow us to answer complex questions. However, since the required analyses are highly specific to the particular data set and question, a black-box method is not sufficient anymore. Instead, biologists are required to be actively involved with modeling decisions during data analysis. The modular design of the Bayesian phylogenetic software package BEAST 2 enables, and in fact enforces, this involvement. At the same time, the modular design enables computational biology groups to develop new methods at a rapid rate. A thorough understanding of the models and algorithms used by inference software is a critical prerequisite for successful hypothesis formulation and assessment. In particular, there is a need for more readily available resources aimed at helping interested scientists equip themselves with the skills to confidently use cutting-edge phylogenetic analysis software. These resources will also benefit researchers who do not have access to similar courses or training at their home institutions. Here, we introduce the "Taming the Beast" (https://taming-the-beast.github.io/) resource, which was developed as part of a workshop series bearing the same name, to facilitate the usage of the Bayesian phylogenetic software package BEAST 2.}, } @article {pmid28672848, year = {2017}, author = {Lin, F and Li, F and Wang, C and Wang, J and Yang, Y and Yang, L and Li, Y}, title = {Mechanism Exploration of Arylpiperazine Derivatives Targeting the 5-HT2A Receptor by In Silico Methods.}, journal = {Molecules (Basel, Switzerland)}, volume = {22}, number = {7}, pages = {}, pmid = {28672848}, issn = {1420-3049}, mesh = {Binding Sites ; Catalytic Domain ; Computational Biology/*methods ; Computer Simulation ; Drug Design ; Humans ; Models, Molecular ; Molecular Conformation ; Molecular Docking Simulation ; Molecular Dynamics Simulation ; Piperazines/chemistry/*pharmacology ; Quantitative Structure-Activity Relationship ; Receptor, Serotonin, 5-HT2B/chemistry/*metabolism ; Serotonin 5-HT2 Receptor Antagonists/chemistry/*pharmacology ; }, abstract = {As a G-protein coupled receptor, the 5-hydroxytryptamine 2A (5-HT2A) receptor is known for its critical role in the cognitive, behavioural and physiological functions, and thus is a primary molecular target to treat psychiatric diseases, including especially depression. With purpose to explore the structural traits affecting the inhibitory activity, currently a dataset of 109 arylpiperazine derivatives as promising 5-HT2A antagonists was built, based on which the ligand-based three-dimensional quantitative structure-activity relationship (3D-QSAR) study by using both comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) approaches was carried out. The resultant optimal CoMSIA model displays proper validity and predictability with cross-validated correlation coefficient Q[2] = 0.587, non-cross-validated correlation coefficient R[2]ncv = 0.900 and predicted correlation coefficient for the test set of compounds R[2]pre = 0.897, respectively. Besides, molecular docking was also conducted to investigate the binding mode between these ligands and the active site of the 5-HT2A receptor. Meanwhile, as a docking supplementary tool to study the antagonists' conformation in the binding cavity, molecular dynamics (MD) simulation was also performed, providing further elucidation about the changes in the ligand-receptor complex. Lastly, some new molecules were also newly-designed based on the above results that are potential arylpiperazine antagonists of 5-HT2A receptor. We hope that the present models and derived information may be of help for facilitating the optimization and design of novel potent antagonists as antidepressant drugs as well as exploring the interaction mechanism of 5-HT2A antagonists.}, } @article {pmid28672244, year = {2017}, author = {Buosi, A and Sfriso, A}, title = {Macrophyte assemblage composition as a simple tool to assess global change in coastal areas. Freshwater impacts and climatic changes.}, journal = {The Science of the total environment}, volume = {605-606}, number = {}, pages = {559-568}, doi = {10.1016/j.scitotenv.2017.06.196}, pmid = {28672244}, issn = {1879-1026}, abstract = {Macrophyte assemblages are one of the most sensitive biological communities to assess anthropogenic impacts and climate changes. Community composition responds very quickly to environmental changes driving towards a predictable composition. The increase or decrease of the trophic status (i.e. nutrient concentrations, suspended particulate matter, Chlorophyll-a) and temperature are the most important factors responsible for the replacement of taxa of high ecological value (sensitive taxa) with opportunistic species. A qualitative and quantitative study of macrophytes in 4 areas along the coasts of the Northern Adriatic Sea, from Venice (Italy) to Savudrija (Croatia) and the analysis of river outflows in this region during one year (May 2012-April 2013) provided information about their spatial variability. The coasts of the Veneto Region and Friuli-Venezia Giulia, which are affected by significant freshwater inputs, showed a strong biodiversity reduction or a dominance of thionitrophilic taxa. No seagrasses colonized these areas. On the other hand, the coasts of Croatia had negligible fresh water inputs and macrophyte communities were dominated by sensitive taxa such as the seagrass Cymodocea nodosa and some species belonging to genus Cystoseira.}, } @article {pmid28672160, year = {2017}, author = {Hayward, A}, title = {Origin of the retroviruses: when, where, and how?.}, journal = {Current opinion in virology}, volume = {25}, number = {}, pages = {23-27}, pmid = {28672160}, issn = {1879-6265}, support = {BB/N020146/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; Computational Biology ; Endogenous Retroviruses/classification/*genetics/*physiology ; *Evolution, Molecular ; Genomics ; Humans ; Mice ; Phylogeny ; Primates/virology ; Proviruses/genetics ; Recombination, Genetic ; *Virus Integration ; }, abstract = {Retroviruses are a virus family of considerable medical and veterinary importance. Additionally, it is now clear that endogenous retroviruses (ERVs) comprise significant portions of vertebrate genomes. Until recently, very little was known about the deep evolutionary origins of retroviruses. However, advances in genomics and bioinformatics have opened the way for great strides in understanding. Recent research employing a wide variety of bioinformatic approaches has demonstrated that retroviruses evolved during the early Palaeozoic Era, between 460 and 550 million years ago, providing the oldest inferred date estimate for any virus group. This finding presents an important framework to investigate the evolutionary transitions that led to the emergence of the retroviruses, offering potential insights into the infectious origins of a major group of pathogenic viruses.}, } @article {pmid28671290, year = {2017}, author = {Saouter, E and Aschberger, K and Fantke, P and Hauschild, MZ and Kienzler, A and Paini, A and Pant, R and Radovnikovic, A and Secchi, M and Sala, S}, title = {Improving substance information in USEtox[®] , part 2: Data for estimating fate and ecosystem exposure factors.}, journal = {Environmental toxicology and chemistry}, volume = {36}, number = {12}, pages = {3463-3470}, doi = {10.1002/etc.3903}, pmid = {28671290}, issn = {1552-8618}, mesh = {Databases, Factual ; Ecosystem ; Ecotoxicology/*methods ; Environmental Pollutants/*analysis/toxicity ; Fresh Water/chemistry ; Hazardous Substances/*analysis/toxicity ; Humans ; Models, Theoretical ; Risk Assessment ; Water Pollutants/analysis/toxicity ; }, abstract = {The scientific consensus model USEtox[®] has been developed since 2003 under the auspices of the United Nations Environment Programme-Society of Environmental Toxicology and Chemistry Life Cycle Initiative as a harmonized approach for characterizing human and freshwater toxicity in life cycle assessment and other comparative assessment frameworks. Using physicochemical substance properties, USEtox quantifies potential human toxicity and freshwater ecotoxicity impacts by combining environmental fate, exposure, and toxicity effects information, considering multimedia fate and multipathway exposure processes. The main source to obtain substance properties for USEtox 1.01 and 2.0 is the Estimation Program Interface (EPI Suite™) from the US Environmental Protection Agency. However, since the development of the original USEtox substance databases, new chemical regulations have been enforced in Europe, such as the Registration, Evaluation, Authorisation and Restriction of Chemicals (REACH) and the Plant Protection Products regulations. These regulations require that a chemical risk assessment for humans and the environment is performed before a chemical is placed on the European market. Consequently, additional physicochemical property data and new toxicological endpoints are now available for thousands of chemical substances. The aim of the present study was to explore the extent to which the new available data can be used as input for USEtox-especially for application in environmental footprint studies-and to discuss how this would influence the quantification of fate and exposure factors. Initial results show that the choice of data source and the parameters selected can greatly influence fate and exposure factors, leading to potentially different rankings and relative contributions of substances to overall human toxicity and ecotoxicity impacts. Moreover, it is crucial to discuss the relevance of the exposure factor for freshwater ecotoxicity impacts, particularly for persistent highly adsorbing and bioaccumulating substances. Environ Toxicol Chem 2017;36:3463-3470. © 2017 The Authors. Environmental Toxicology and Chemistry Published by Wiley Periodicals, Inc. on behalf of SETAC.}, } @article {pmid28666129, year = {2017}, author = {Ceuppens, S and De Coninck, D and Bottledoorn, N and Van Nieuwerburgh, F and Uyttendaele, M}, title = {Microbial community profiling of fresh basil and pitfalls in taxonomic assignment of enterobacterial pathogenic species based upon 16S rRNA amplicon sequencing.}, journal = {International journal of food microbiology}, volume = {257}, number = {}, pages = {148-156}, doi = {10.1016/j.ijfoodmicro.2017.06.016}, pmid = {28666129}, issn = {1879-3460}, mesh = {Algorithms ; Computational Biology ; Databases, Factual ; Foodborne Diseases/microbiology ; High-Throughput Nucleotide Sequencing ; Humans ; Molecular Typing ; Ocimum basilicum/*microbiology ; RNA, Ribosomal, 16S/*genetics ; Real-Time Polymerase Chain Reaction ; Salmonella enterica/classification/*genetics/*isolation & purification ; }, abstract = {Application of 16S rRNA (gene) amplicon sequencing on food samples is increasingly applied for assessing microbial diversity but may as unintended advantage also enable simultaneous detection of any human pathogens without a priori definition. In the present study high-throughput next-generation sequencing (NGS) of the V1-V2-V3 regions of the 16S rRNA gene was applied to identify the bacteria present on fresh basil leaves. However, results were strongly impacted by variations in the bioinformatics analysis pipelines (MEGAN, SILVAngs, QIIME and MG-RAST), including the database choice (Greengenes, RDP and M5RNA) and the annotation algorithm (best hit, representative hit and lowest common ancestor). The use of pipelines with default parameters will lead to discrepancies. The estimate of microbial diversity of fresh basil using 16S rRNA (gene) amplicon sequencing is thus indicative but subject to biases. Salmonella enterica was detected at low frequencies, between 0.1% and 0.4% of bacterial sequences, corresponding with 37 to 166 reads. However, this result was dependent upon the pipeline used: Salmonella was detected by MEGAN, SILVAngs and MG-RAST, but not by QIIME. Confirmation of Salmonella sequences by real-time PCR was unsuccessful. It was shown that taxonomic resolution obtained from the short (500bp) sequence reads of the 16S rRNA gene containing the hypervariable regions V1-V3 cannot allow distinction of Salmonella with closely related enterobacterial species. In conclusion 16S amplicon sequencing, getting the status of standard method in microbial ecology studies of foods, needs expertise on both bioinformatics and microbiology for analysis of results. It is a powerful tool to estimate bacterial diversity but amenable to biases. Limitations concerning taxonomic resolution for some bacterial species or its inability to detect sub-dominant (pathogenic) species should be acknowledged in order to avoid overinterpretation of results.}, } @article {pmid28662636, year = {2017}, author = {Cobo-Simón, M and Tamames, J}, title = {Relating genomic characteristics to environmental preferences and ubiquity in different microbial taxa.}, journal = {BMC genomics}, volume = {18}, number = {1}, pages = {499}, pmid = {28662636}, issn = {1471-2164}, mesh = {Databases, Genetic ; *Environment ; *Genomics ; *Microbiology ; }, abstract = {BACKGROUND: Despite the important role that microorganisms play in environmental processes, the low percentage of cultured microbes (5%) has limited, until now, our knowledge of their ecological strategies. However, the development of high-throughput sequencing has generated a huge amount of genomic and metagenomic data without the need of culturing that can be used to study ecological questions. This study aims to estimate the functional capabilities, genomic sizes and 16S copy number of different taxa in relation to their ubiquity and their environmental preferences.

RESULTS: To achieve this goal, we compiled data regarding the presence of each prokaryotic genera in diverse environments. Then, genomic characteristics such as genome size, 16S rRNA gene copy number, and functional content of the genomes were related to their ubiquity and different environmental preferences of the corresponding taxa. The results showed clear correlations between genomic characteristics and environmental conditions.

CONCLUSIONS: Ubiquity and adaptation were linked to genome size, while 16S copy number was not directly related to ubiquity. We observed that different combinations of these two characteristics delineate the different environments. Besides, the analysis of functional classes showed some clear signatures linked to particular environments.}, } @article {pmid28662530, year = {2017}, author = {Sgamma, T and Lockie-Williams, C and Kreuzer, M and Williams, S and Scheyhing, U and Koch, E and Slater, A and Howard, C}, title = {DNA Barcoding for Industrial Quality Assurance.}, journal = {Planta medica}, volume = {83}, number = {14-15}, pages = {1117-1129}, doi = {10.1055/s-0043-113448}, pmid = {28662530}, issn = {1439-0221}, mesh = {Computational Biology ; DNA Barcoding, Taxonomic/*methods ; European Union ; Herbal Medicine/*standards ; High-Throughput Nucleotide Sequencing ; Plants, Medicinal/*classification ; Quality Control ; Sequence Analysis, DNA ; }, abstract = {DNA barcoding methods originally developed for the identification of plant specimens have been applied to the authentication of herbal drug materials for industrial quality assurance. These methods are intended to be complementary to current morphological and chemical methods of identification. The adoption of these methods by industry will be accelerated by the introduction of DNA-based identification techniques into regulatory standards and monographs. The introduction of DNA methods into the British Pharmacopoeia is described, along with a reference standard for use as a positive control for DNA extraction and polymerase chain reaction (PCR). A general troubleshooting chart is provided to guide the user through the problems that may be encountered during this process. Nevertheless, the nature of the plant materials and the demands of industrial quality control procedures mean that conventional DNA barcoding is not the method of choice for industrial quality control. The design of DNA barcode-targeted quantitative PCR and high resolution melt curve tests is one strategy for developing rapid, robust, and reliable protocols for high-throughput screening of raw materials. The development of authentication tests for wild-harvested Rhodiola rosea L. is used as a case study to exemplify these relatively simple tests. By way of contrast, the application of next-generation sequencing to create a complete profile of all the biological entities in a mixed herbal drug is described and its potential for industrial quality assurance discussed.}, } @article {pmid28662106, year = {2017}, author = {Kropáčková, L and Pechmanová, H and Vinkler, M and Svobodová, J and Velová, H and Těšičký, M and Martin, JF and Kreisinger, J}, title = {Variation between the oral and faecal microbiota in a free-living passerine bird, the great tit (Parus major).}, journal = {PloS one}, volume = {12}, number = {6}, pages = {e0179945}, pmid = {28662106}, issn = {1932-6203}, mesh = {Animals ; Computational Biology ; Feces/*microbiology ; *Microbiota ; Mouth/*microbiology ; Passeriformes/*microbiology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The gastrointestinal tract of vertebrates is inhabited by diverse bacterial communities that induce marked effects on the host physiology and health status. The composition of the gastrointestinal microbiota is characterized by pronounced taxonomic and functional variability among different regions of the vertebrate gastrointestinal tract. Despite the relatively solid knowledge on the among-region variations of the gastrointestinal microbiota in model mammalian species, there are only a few studies concerning among-region variations of the gastrointestinal microbiota in free-living non-mammalian vertebrate taxa. We used Illumina MiSeq sequencing of bacterial 16S rRNA amplicons to compare the diversity as well as taxonomic composition of bacterial communities in proximal vs. distal parts of the gastrointestinal tract (represented by oral swabs and faecal samples, respectively) in a wild passerine bird, the great tit (Parus major). The diversity of the oral microbiota was significantly higher compared to the faecal microbiota, whereas interindividual variation was higher in faecal than in oral samples. We also observed a pronounced difference in taxonomic content between the oral and faecal microbiota. Bacteria belonging to the phyla Proteobacteria, Firmicutes and Actinobacteria typically dominated in both oral and faecal samples. A high abundance of bacteria belonging to Tenericutes was observed only in faecal samples. Surprisingly, we found only a slight correlation between the faecal and oral microbiota at the within-individual level, suggesting that the microbial composition in these body sites is shaped by independent regulatory processes. Given the independence of these two communities at the individual level, we propose that simultaneous sampling of the faecal and oral microbiota will extend our understanding of host vs. microbiota interactions in wild populations.}, } @article {pmid28659170, year = {2017}, author = {Parmakelis, A and Kotsakiozi, P and Kontos, CK and Adamopoulos, PG and Scorilas, A}, title = {The transcriptome of a "sleeping" invader: de novo assembly and annotation of the transcriptome of aestivating Cornu aspersum.}, journal = {BMC genomics}, volume = {18}, number = {1}, pages = {491}, pmid = {28659170}, issn = {1471-2164}, mesh = {Animals ; *Gene Expression Profiling ; Gene Ontology ; Helix, Snails/*genetics ; Microsatellite Repeats/genetics ; *Molecular Sequence Annotation ; }, abstract = {BACKGROUND: Cornu aspersum is a quite intriguing species from the point of view of ecology and evolution and its potential use in medical and environmental applications. It is a species of economic importance since it is farmed and used for culinary purposes. However, the genomic tools that would allow a thorough insight into the ecology, evolution, nutritional and medical properties of this highly adaptable organism, are missing. In this work, using next-generation sequencing (NGS) techniques we assessed a significant portion of the transcriptome of this non-model organism.

RESULTS: Out of the 9445 de novo assembled contigs, 2886 (30.6%) returned significant hits and for 2261 (24%) of them Gene Ontology (GO) terms associated to the hits were retrieved. A high percentage of the contigs (69.4%) produced no BLASTx hits. The GO terms were grouped to reflect biological processes, molecular functions and cellular components. Certain GO terms were dominant in all groups. After scanning the assembled transcriptome for microsatellites (simple sequence repeats, SSRs), a total of 563 SSRs were recovered. Among the identified SSRs, trinucleotide repeats were the predominant followed by tetranucleotide and dinucleotide repeats.

CONCLUSION: The annotation success of the transcriptome of C. aspersum was relatively low. This is probably due to the very limited number of annotated reference genomes existing for mollusc species, especially terrestrial ones. Several biological processes being active in the aestivating species were revealed through the association of the transcripts to enzymes relating to the pathways. The genomic tools provided herein will eventually aid in the study of the global genomic diversity of the species and the investigation of aspects of the ecology, evolution, behavior, nutritional and medical properties of this highly adaptable organism.}, } @article {pmid28654871, year = {2017}, author = {Mennis, J and Mason, M and Ambrus, A and Way, T and Henry, K}, title = {The spatial accuracy of geographic ecological momentary assessment (GEMA): Error and bias due to subject and environmental characteristics.}, journal = {Drug and alcohol dependence}, volume = {178}, number = {}, pages = {188-193}, doi = {10.1016/j.drugalcdep.2017.05.019}, pmid = {28654871}, issn = {1879-0046}, mesh = {Adolescent ; Bias ; Ecological Momentary Assessment/*standards ; *Environment ; Female ; Geographic Information Systems/standards ; Humans ; Male ; Residence Characteristics ; Substance-Related Disorders/diagnosis/*epidemiology/*psychology ; }, abstract = {BACKGROUND: Geographic ecological momentary assessment (GEMA) combines ecological momentary assessment (EMA) with global positioning systems (GPS) and geographic information systems (GIS). This study evaluates the spatial accuracy of GEMA location data and bias due to subject and environmental data characteristics.

METHODS: Using data for 72 subjects enrolled in a study of urban adolescent substance use, we compared the GPS-based location of EMA responses in which the subject indicated they were at home to the geocoded home address. We calculated the percentage of EMA locations within a sixteenth, eighth, quarter, and half miles from the home, and the percentage within the same tract and block group as the home. We investigated if the accuracy measures were associated with subject demographics, substance use, and emotional dysregulation, as well as environmental characteristics of the home neighborhood.

RESULTS: Half of all subjects had more than 88% of their EMA locations within a half mile, 72% within a quarter mile, 55% within an eighth mile, 50% within a sixteenth of a mile, 83% in the correct tract, and 71% in the correct block group. There were no significant associations with subject or environmental characteristics.

CONCLUSIONS: Results support the use of GEMA for analyzing subjects' exposures to urban environments. Researchers should be aware of the issue of spatial accuracy inherent in GEMA, and interpret results accordingly. Understanding spatial accuracy is particularly relevant for the development of 'ecological momentary interventions' (EMI), which may depend on accurate location information, though issues of privacy protection remain a concern.}, } @article {pmid28651532, year = {2017}, author = {Nakamura, T and Nakamura, A and Mukuda, K and Harada, M and Kotani, K}, title = {Potential accessibility scores for hospital care in a province of Japan: GIS-based ecological study of the two-step floating catchment area method and the number of neighborhood hospitals.}, journal = {BMC health services research}, volume = {17}, number = {1}, pages = {438}, pmid = {28651532}, issn = {1472-6963}, mesh = {Catchment Area, Health ; Geographic Information Systems ; *Health Services Accessibility ; Hospitals/statistics & numerical data/*supply & distribution ; Japan ; Primary Health Care ; Spatial Analysis ; }, abstract = {BACKGROUND: For achieving equity of the accessibility to primary healthcare, measuring potential geographical accessibility is essential. The provider-to-population ratio is the most frequently used measure. However, it is difficult to be used in closer region because it does not take into consideration the people and health services beyond its boundary. In order to overcome this problem, we measured the potential access to hospital, using both distance measures and the enhanced two-step floating catchment area (E2SFCA) method. The aim of this study was to compare the number of hospitals in the neighborhood and the E2SFCA score with regard to the amount and equity for access to hospitals.

METHODS: This descriptive study used publicly available data from 2010. The E2SFCA score and number of neighborhood hospitals were obtained from Tochigi province in Japan using a geographic information system. Dataset of four measures by each census tract was obtained. The measures were E2SFCA score, number of hospitals within the 5 km range, number of hospitals within the 10 km range, and number of hospitals within the 15 km range. Correlation and disparity analyses with the Lorenz curve and Gini coefficient were performed.

RESULTS: The measures were obtained in a smaller area than municipality considering adjacent areas using a geographical approach. The E2SFCA score was 5.3 [3.2-7.3] hospitals/million (median [quantile range]), compared to 5.6 hospitals/million in total for the given district. The median number of hospitals within the 5 km, 10 km, and 15 km ranges were 1, 39, and 47, respectively. There was no hospital within the 5 km range in one third of the blocks. Both the number of hospitals within the 10 km range and those within the 15 km range were well correlated. Regional difference became smaller as the distance to count the number of hospitals increased. The gap between small number of hospitals and the high E2SFCA score indicated the location of community hospital in depopulated areas.

CONCLUSIONS: The E2SFCA method is superior for analyzing spatial access to hospital, because it provides information in the closer sub-regions. Regional differences were hardly seen in access to hospital beyond the 10 km range. Further studies in other regions and countries are needed for precise assessment.}, } @article {pmid28650185, year = {2017}, author = {Kubiak, SP and Brenner, HJ and Bybee, D and Campbell, R and Cummings, CE and Darcy, KM and Fedock, G and Goodman-Williams, R}, title = {Sexual misconduct in prison: What factors affect whether incarcerated women will report abuses committed by prison staff?.}, journal = {Law and human behavior}, volume = {41}, number = {4}, pages = {361-374}, doi = {10.1037/lhb0000239}, pmid = {28650185}, issn = {1573-661X}, mesh = {Adult ; Age Distribution ; Crime Victims/*psychology ; Databases, Factual ; Female ; Humans ; Logistic Models ; Male ; Michigan ; Middle Aged ; Prisoners/*psychology ; Prisons ; Probability ; Rape/*psychology ; Sexual Behavior ; Whistleblowing/*psychology ; Young Adult ; }, abstract = {More than 80,000 prisoners each year are sexually victimized during incarceration, but only about 8% report victimization to correctional authorities. Complicating reporting is the fact that half of the perpetrators are staff members. Given the restrictive and highly regulated prison environment, studies that examine reporting behaviors are difficult to conduct and to date information available relied on those who have reported or hypothetical victimization studies. This study uses an ecological framework and archival data from a class action lawsuit of sexual misconduct to determine predictors of reporting. Relying on a subsample of 179 women, chosen because they have all experienced at least 1 penetration offense, we use bivariate and multivariable mixed effects logistic regression analyses to examine individual, assault, and context-level predictors of reporting on 397 incidents of staff sexual misconduct. The final model revealed that that 6 predictors (age at time of assault, physical injury, multiple incidents, perpetrator with multiple victims, the year the abuse began, and the number of years women have left on their sentence) account for 58% of the variance in reporting. Disclosure to inmate peers and/or family and friends was significant in the bivariate results. These findings indicate the need for stronger and more systematic implementation of Prison Rape Elimination Act guidelines and remedies that create and enforce sanctions, including termination, for staff violating policy and state law. (PsycINFO Database Record}, } @article {pmid28648476, year = {2017}, author = {Fondi, M and Fani, R}, title = {Constraint-based metabolic modelling of marine microbes and communities.}, journal = {Marine genomics}, volume = {34}, number = {}, pages = {1-10}, doi = {10.1016/j.margen.2017.06.003}, pmid = {28648476}, issn = {1876-7478}, mesh = {Aquatic Organisms/genetics/metabolism ; Archaea/*genetics/*metabolism ; Bacteria/*genetics/*metabolism ; Biotechnology ; Computational Biology ; Microbiology ; *Models, Biological ; }, abstract = {Constraint-based metabolic modelling (CBMM) consists in the use of computational methods and tools to perform genome-scale simulations and predict metabolic features at the whole cellular level. This approach is rapidly expanding in microbiology, as it combines reliable predictive abilities with conceptually and technically simple frameworks. Among the possible outcomes of CBMM, the capability to i) guide a focused planning of metabolic engineering experiments and ii) provide a system-level understanding of (single or community-level) microbial metabolic circuits also represent primary aims in present-day marine microbiology. In this work we briefly introduce the theoretical formulation behind CBMM and then review the most recent and effective case studies of CBMM of marine microbes and communities. Also, the emerging challenges and possibilities in the use of such methodologies in the context of marine microbiology/biotechnology are discussed. As the potential applications of CBMM have a very broad range, the topics presented in this review span over a large plethora of fields such as ecology, biotechnology and evolution.}, } @article {pmid28647495, year = {2017}, author = {Gámez, M and López, I and Rodríguez, C and Varga, Z and Garay, J}, title = {Ecological monitoring in a discrete-time prey-predator model.}, journal = {Journal of theoretical biology}, volume = {429}, number = {}, pages = {52-60}, doi = {10.1016/j.jtbi.2017.06.025}, pmid = {28647495}, issn = {1095-8541}, mesh = {Animals ; Ecological Parameter Monitoring/*methods ; *Ecosystem ; Environmental Monitoring/methods ; *Models, Biological ; Population Dynamics ; *Predatory Behavior ; Time Factors ; }, abstract = {The paper is aimed at the methodological development of ecological monitoring in discrete-time dynamic models. In earlier papers, in the framework of continuous-time models, we have shown how a systems-theoretical methodology can be applied to the monitoring of the state process of a system of interacting populations, also estimating certain abiotic environmental changes such as pollution, climatic or seasonal changes. In practice, however, there may be good reasons to use discrete-time models. (For instance, there may be discrete cycles in the development of the populations, or observations can be made only at discrete time steps.) Therefore the present paper is devoted to the development of the monitoring methodology in the framework of discrete-time models of population ecology. By monitoring we mean that, observing only certain component(s) of the system, we reconstruct the whole state process. This may be necessary, e.g., when in a complex ecosystem the observation of the densities of certain species is impossible, or too expensive. For the first presentation of the offered methodology, we have chosen a discrete-time version of the classical Lotka-Volterra prey-predator model. This is a minimal but not trivial system where the methodology can still be presented. We also show how this methodology can be applied to estimate the effect of an abiotic environmental change, using a component of the population system as an environmental indicator. Although this approach is illustrated in a simplest possible case, it can be easily extended to larger ecosystems with several interacting populations and different types of abiotic environmental effects.}, } @article {pmid28646401, year = {2018}, author = {Peeters, D}, title = {A standardized set of 3-D objects for virtual reality research and applications.}, journal = {Behavior research methods}, volume = {50}, number = {3}, pages = {1047-1054}, pmid = {28646401}, issn = {1554-3528}, mesh = {Databases, Factual ; Humans ; Imaging, Three-Dimensional/*methods ; Photic Stimulation/methods ; Recognition, Psychology ; *Research Design ; *Virtual Reality ; }, abstract = {The use of immersive virtual reality as a research tool is rapidly increasing in numerous scientific disciplines. By combining ecological validity with strict experimental control, immersive virtual reality provides the potential to develop and test scientific theories in rich environments that closely resemble everyday settings. This article introduces the first standardized database of colored three-dimensional (3-D) objects that can be used in virtual reality and augmented reality research and applications. The 147 objects have been normed for name agreement, image agreement, familiarity, visual complexity, and corresponding lexical characteristics of the modal object names. The availability of standardized 3-D objects for virtual reality research is important, because reaching valid theoretical conclusions hinges critically on the use of well-controlled experimental stimuli. Sharing standardized 3-D objects across different virtual reality labs will allow for science to move forward more quickly.}, } @article {pmid28646139, year = {2017}, author = {Zhang, DY and Kumar, M and Xu, L and Wan, Q and Huang, YH and Xu, ZL and He, XL and Ma, JB and Pandey, GK and Shao, HB}, title = {Genome-wide identification of Major Intrinsic Proteins in Glycine soja and characterization of GmTIP2;1 function under salt and water stress.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {4106}, pmid = {28646139}, issn = {2045-2322}, mesh = {Adaptation, Biological/genetics ; Amino Acid Motifs ; Amino Acid Sequence ; Aquaporins/chemistry/*genetics/metabolism ; Computational Biology/methods ; Droughts ; *Gene Expression Regulation, Plant ; *Genome-Wide Association Study ; Multigene Family ; Organ Specificity ; Promoter Regions, Genetic ; Saccharomyces cerevisiae/genetics/metabolism ; *Salinity ; Glycine max/*genetics/*metabolism ; *Stress, Physiological/genetics ; *Water ; }, abstract = {In different plant species, aquaporins (AQPs) facilitate water movement by regulating root hydraulic conductivity under diverse stress conditions such as salt and water stresses. To improve survival and yield of crop plants, a detailed understanding of stress responses is imperative and required. We used Glycine soja genome as a tool to study AQPs, considering it shows abundant genetic diversity and higher salt environment tolerance features and identified 62 Gs AQP genes. Additionally, this study identifies major aquaporins responsive to salt and drought stresses in soybean and elucidates their mode of action through yeast two-hybrid assay and BiFC. Under stress condition, the expression analysis of AQPs in roots and leaves of two contrasting ecotypes of soybean revealed diverse expression patterns suggesting complex regulation at transcriptional level. Based on expression analysis, we identify GmTIP2;1 as a potential candidate involved in salinity and drought responses. The overexpression of GmTIP2;1 in Saccharomyces cerevisiae as well as in-planta enhanced salt and drought tolerance. We identified that GmTIP2;1 forms homodimers as well as interacts with GmTIP1;7 and GmTIP1;8. This study augments our knowledge of stress responsive pathways and also establishes GmTIP2;1 as a new stress responsive gene in imparting salt stress tolerance in soybean.}, } @article {pmid28645885, year = {2017}, author = {van Ravenzwaay, B and Jiang, X and Luechtefeld, T and Hartung, T}, title = {The Threshold of Toxicological Concern for prenatal developmental toxicity in rats and rabbits.}, journal = {Regulatory toxicology and pharmacology : RTP}, volume = {88}, number = {}, pages = {157-172}, pmid = {28645885}, issn = {1096-0295}, support = {T32 ES007141/ES/NIEHS NIH HHS/United States ; }, mesh = {Agrochemicals/*toxicity ; Animals ; Databases, Factual ; Female ; Fetal Development/*drug effects ; Fetus/*drug effects ; No-Observed-Adverse-Effect Level ; Rabbits ; Rats ; Risk Assessment ; Toxicity Tests ; }, abstract = {The Threshold Toxicological Concern (TTC) is based on the concept that in absence of experimental data reasonable assurance of safety can be given if exposure is sufficiently low. Using the REACH database the low 5th percentile of the NO(A)EL distribution, for prenatal developmental toxicity (OECD guideline 414) was determined. For rats, (434 NO(A)ELs values) for maternal toxicity, this value was 10 mg/kg-bw/day. For developmental toxicity (469 NO(A)ELs): 13 mg/kg-bw/day. For rabbits, (100 NO(A)ELs), the value for maternal toxicity was 4 mg/kg-bw/day, for developmental toxicity, (112 NO(A)EL values): 10 mg/kg-bw/day. The maternal organism may thus be slightly more sensitive than the fetus. Combining REACH- (industrial chemicals) and published BASF-data (mostly agrochemicals), 537 unique compounds with NO(A)EL values for developmental toxicity in rats and 150 in rabbits were evaluated. The low 5th percentile NO(A)EL for developmental toxicity in rats was 10 mg/kg-bw/day and 9.5 mg/kg-bw/day for rabbits. Using an assessment factor of 100, a TTC value for developmental toxicity of 100 μg/kg-bw/day for rats and 95 μg/kg-bw/day for rabbits is calculated. These values could serve as guidance whether or not to perform an animal experiment, if exposure is sufficiently low. In emergency situations this value may be useful for a first tier risk assessment.}, } @article {pmid28644890, year = {2017}, author = {Hargreaves-Allen, VA and Mourato, S and Milner-Gulland, EJ}, title = {Drivers of coral reef marine protected area performance.}, journal = {PloS one}, volume = {12}, number = {6}, pages = {e0179394}, pmid = {28644890}, issn = {1932-6203}, mesh = {*Conservation of Natural Resources ; *Coral Reefs ; Datasets as Topic ; Internationality ; Multivariate Analysis ; Regression Analysis ; Time Factors ; }, abstract = {Coral reefs are severely threatened and a principal strategy for their conservation is marine protected areas (MPAs). However the drivers of MPA performance are complex and there are likely to be trade-offs between different types of performance (e.g. conservation or welfare related outcomes). We compiled a global dataset from expert knowledge for 76 coral reef MPAs in 33 countries and identified a set of performance measures reflecting ecological and socio-economic outcomes, achievement of aims and reduction of threats, using spatial or temporal comparisons wherever possible. We wanted to test the extent to which distinct types of performance occurred simultaneously, understood as win-win outcomes. Although certain performance measures were correlated, most were not, suggesting trade-offs that limit the usefulness of composite performance scores. Hypotheses were generated as to the impact of MPA features, aims, location, management and contextual variables on MPA performance from the literature. A multivariate analysis was used to test hypotheses as to the relative importance of these "drivers" on eight uncorrelated performance measures. The analysis supported some hypotheses (e.g. benefit provision for the local community improved performance), but not others (e.g. higher overall budget and more research activity did not). Factors endogenous to the MPA (such as size of the no-take area) were generally more significant drivers of performance than exogenous ones (such as national GDP). Different types of performance were associated with different drivers, exposing the trade-offs inherent in management decisions. The study suggests that managers are able to influence MPA performance in spite of external threats and could inform adaptive management by providing an approach to test for the effects of MPA features and management actions in different contexts and so to inform decisions for allocation of effort or funds to achieve specific goals.}, } @article {pmid28643787, year = {2017}, author = {Martinez-Hernandez, F and Fornas, O and Lluesma Gomez, M and Bolduc, B and de la Cruz Peña, MJ and Martínez, JM and Anton, J and Gasol, JM and Rosselli, R and Rodriguez-Valera, F and Sullivan, MB and Acinas, SG and Martinez-Garcia, M}, title = {Single-virus genomics reveals hidden cosmopolitan and abundant viruses.}, journal = {Nature communications}, volume = {8}, number = {}, pages = {15892}, pmid = {28643787}, issn = {2041-1723}, mesh = {Atlantic Ocean ; Biodiversity ; Data Mining/methods ; Flow Cytometry/methods ; Genome, Viral ; Genomics/*methods ; Mediterranean Sea ; Metagenome ; Polymorphism, Single Nucleotide ; Proteomics/methods ; Seawater/*virology ; Viruses/*genetics/isolation & purification ; }, abstract = {Microbes drive ecosystems under constraints imposed by viruses. However, a lack of virus genome information hinders our ability to answer fundamental, biological questions concerning microbial communities. Here we apply single-virus genomics (SVGs) to assess whether portions of marine viral communities are missed by current techniques. The majority of the here-identified 44 viral single-amplified genomes (vSAGs) are more abundant in global ocean virome data sets than published metagenome-assembled viral genomes or isolates. This indicates that vSAGs likely best represent the dsDNA viral populations dominating the oceans. Species-specific recruitment patterns and virome simulation data suggest that vSAGs are highly microdiverse and that microdiversity hinders the metagenomic assembly, which could explain why their genomes have not been identified before. Altogether, SVGs enable the discovery of some of the likely most abundant and ecologically relevant marine viral species, such as vSAG 37-F6, which were overlooked by other methodologies.}, } @article {pmid28642608, year = {2017}, author = {Vizzini, S and Martínez-Crego, B and Andolina, C and Massa-Gallucci, A and Connell, SD and Gambi, MC}, title = {Ocean acidification as a driver of community simplification via the collapse of higher-order and rise of lower-order consumers.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {4018}, pmid = {28642608}, issn = {2045-2322}, abstract = {Increasing oceanic uptake of CO2 is predicted to drive ecological change as both a resource (i.e. CO2 enrichment on primary producers) and stressor (i.e. lower pH on consumers). We use the natural ecological complexity of a CO2 vent (i.e. a seagrass system) to assess the potential validity of conceptual models developed from laboratory and mesocosm research. Our observations suggest that the stressor-effect of CO2 enrichment combined with its resource-effect drives simplified food web structure of lower trophic diversity and shorter length. The transfer of CO2 enrichment from plants to herbivores through consumption (apparent resource-effect) was not compensated by predation, because carnivores failed to contain herbivore outbreaks. Instead, these higher-order consumers collapsed (apparent stressor-effect on carnivores) suggesting limited trophic propagation to predator populations. The dominance of primary producers and their lower-order consumers along with the loss of carnivores reflects the duality of intensifying ocean acidification acting both as resource-effect (i.e. bottom-up control) and stressor-effect (i.e. top-down control) to simplify community and trophic structure and function. This shifting balance between the propagation of resource enrichment and its consumption across trophic levels provides new insights into how the trophic dynamics might stabilize against or propagate future environmental change.}, } @article {pmid28641609, year = {2018}, author = {Dubad, M and Winsper, C and Meyer, C and Livanou, M and Marwaha, S}, title = {A systematic review of the psychometric properties, usability and clinical impacts of mobile mood-monitoring applications in young people.}, journal = {Psychological medicine}, volume = {48}, number = {2}, pages = {208-228}, doi = {10.1017/S0033291717001659}, pmid = {28641609}, issn = {1469-8978}, mesh = {Adolescent ; Adult ; *Affect ; Child ; *Diagnosis, Computer-Assisted/instrumentation/standards/statistics & numerical data ; Female ; Humans ; Male ; Mental Disorders/*diagnosis ; *Mobile Applications ; Psychometrics/*instrumentation ; Young Adult ; }, abstract = {BACKGROUND: Mobile mood-monitoring applications are increasingly used by mental health providers, widely advocated within research, and a potentially effective method to engage young people. However, little is known about their efficacy and usability in young populations.

METHOD: A systematic review addressing three research questions focused on young people: (1) what are the psychometric properties of mobile mood-monitoring applications; (2) what is their usability; and (3) what are their positive and negative clinical impacts? Findings were synthesised narratively, study quality assessed and compared with evidence from adult studies.

RESULTS: We reviewed 25 articles. Studies on the psychometric properties of mobile mood-monitoring applications were sparse, but indicate questionable to excellent internal consistency, moderate concurrent validity and good usability. Participation rates ranged from 30% to 99% across studies, and appeared to be affected by methodological factors (e.g. payments) and individual characteristics (e.g. IQ score). Mobile mood-monitoring applications are positively perceived by youth, may reduce depressive symptoms by increasing emotional awareness, and could aid in the detection of mental health and substance use problems. There was very limited evidence on potential negative impacts.

CONCLUSIONS: Evidence for the use of mood-monitoring applications in youth is promising but limited due to a lack of high-quality studies. Future work should explicate the effects of mobile mood-monitoring applications on effective self-regulation, clinical outcomes across disorders and young people's engagement with mental health services. Potential negative impacts in this population should also be investigated, as the adult literature suggests that application use could potentially increase negativity and depression symptoms.}, } @article {pmid28640806, year = {2017}, author = {Wilson, G and Bryan, J and Cranston, K and Kitzes, J and Nederbragt, L and Teal, TK}, title = {Good enough practices in scientific computing.}, journal = {PLoS computational biology}, volume = {13}, number = {6}, pages = {e1005510}, pmid = {28640806}, issn = {1553-7358}, mesh = {Computer Security/*standards ; *Computing Methodologies ; *Data Accuracy ; Documentation/standards ; Guidelines as Topic ; Research/*standards ; Science/*standards ; Software/*standards ; }, abstract = {Computers are now essential in all branches of science, but most researchers are never taught the equivalent of basic lab skills for research computing. As a result, data can get lost, analyses can take much longer than necessary, and researchers are limited in how effectively they can work with software and data. Computing workflows need to follow the same practices as lab projects and notebooks, with organized data, documented steps, and the project structured for reproducibility, but researchers new to computing often don't know where to start. This paper presents a set of good computing practices that every researcher can adopt, regardless of their current level of computational skill. These practices, which encompass data management, programming, collaborating with colleagues, organizing projects, tracking work, and writing manuscripts, are drawn from a wide variety of published sources from our daily lives and from our work with volunteer organizations that have delivered workshops to over 11,000 people since 2010.}, } @article {pmid28637269, year = {2017}, author = {Zhao, H and Zhao, S and , and Fei, B and Liu, H and Yang, H and Dai, H and Wang, D and Jin, W and Tang, F and Gao, Q and Xun, H and Wang, Y and Qi, L and Yue, X and Lin, S and Gu, L and Li, L and Zhu, T and Wei, Q and Su, Z and Wan, TBWA and Ofori, DA and Muthike, GM and Mengesha, YM and de Castro E Silva, RM and Beraldo, AL and Gao, Z and Liu, X and Jiang, Z}, title = {Announcing the Genome Atlas of Bamboo and Rattan (GABR) project: promoting research in evolution and in economically and ecologically beneficial plants.}, journal = {GigaScience}, volume = {6}, number = {7}, pages = {1-7}, pmid = {28637269}, issn = {2047-217X}, mesh = {Calamus/*genetics ; *Databases, Genetic ; Evolution, Molecular ; *Genome, Plant ; Molecular Sequence Annotation ; *Plant Breeding ; Sasa/*genetics ; }, abstract = {Bamboo and rattan are widely grown for manufacturing, horticulture, and agroforestry. Bamboo and rattan production might help reduce poverty, boost economic growth, mitigate climate change, and protect the natural environment. Despite progress in research, sufficient molecular and genomic resources to study these species are lacking. We launched the Genome Atlas of Bamboo and Rattan (GABR) project, a comprehensive, coordinated international effort to accelerate understanding of bamboo and rattan genetics through genome analysis. GABR includes 2 core subprojects: Bamboo-T1K (Transcriptomes of 1000 Bamboos) and Rattan-G5 (Genomes of 5 Rattans), and several other subprojects. Here we describe the organization, directions, and status of GABR.}, } @article {pmid28637218, year = {2017}, author = {Ruan, MB and Guo, X and Wang, B and Yang, YL and Li, WQ and Yu, XL and Zhang, P and Peng, M}, title = {Genome-wide characterization and expression analysis enables identification of abiotic stress-responsive MYB transcription factors in cassava (Manihot esculenta).}, journal = {Journal of experimental botany}, volume = {68}, number = {13}, pages = {3657-3672}, doi = {10.1093/jxb/erx202}, pmid = {28637218}, issn = {1460-2431}, mesh = {Computational Biology ; Gene Expression Profiling ; *Gene Expression Regulation, Plant ; *Genome, Plant ; Manihot/*genetics ; Plant Leaves/metabolism ; Plant Proteins/*genetics/metabolism ; Plant Roots/metabolism ; Transcription Factors/*genetics/metabolism ; }, abstract = {The myeloblastosis (MYB) transcription factor superfamily is the largest transcription factor family in plants, playing different roles during stress response. However, abiotic stress-responsive MYB transcription factors have not been systematically studied in cassava (Manihot esculenta), an important tropical tuber root crop. In this study, we used a genome-wide transcriptome analysis to predict 299 putative MeMYB genes in the cassava genome. Under drought and cold stresses, many MeMYB genes exhibited different expression patterns in cassava leaves, indicating that these genes might play a role in abiotic stress responses. We found that several stress-responsive MeMYB genes responded to abscisic acid (ABA) in cassava leaves. We characterize four MeMYBs, namely MeMYB1, MeMYB2, MeMYB4, and MeMYB9, as R2R3-MYB transcription factors. Furthermore, RNAi-driven repression of MeMYB2 resulted in drought and cold tolerance in transgenic cassava. Gene expression assays in wild-type and MeMYB2-RNAi cassava plants revealed that MeMYB2 may affect other MeMYBs as well as MeWRKYs under drought and cold stress, suggesting crosstalk between MYB and WRKY family genes under stress conditions in cassava.}, } @article {pmid28636817, year = {2017}, author = {Bejarano, AC and Raimondo, S and Barron, MG}, title = {Framework for Optimizing Selection of Interspecies Correlation Estimation Models to Address Species Diversity and Toxicity Gaps in an Aquatic Database.}, journal = {Environmental science & technology}, volume = {51}, number = {14}, pages = {8158-8165}, pmid = {28636817}, issn = {1520-5851}, support = {EPA999999//Intramural EPA/United States ; EPA999999//Intramural EPA/ ; }, mesh = {*Databases, Factual ; Risk Assessment ; *Species Specificity ; Uncertainty ; Water Pollutants, Chemical/*toxicity ; }, abstract = {The Chemical Aquatic Fate and Effects (CAFE) database is a tool that facilitates assessments of accidental chemical releases into aquatic environments. CAFE contains aquatic toxicity data used in the development of species sensitivity distributions (SSDs) and the estimation of hazard concentrations (HCs). For many chemicals, gaps in species diversity and toxicity data limit the development of SSDs, which may be filled with Interspecies Correlation Estimation (ICE) models. Optimization of ICE model selection and integration ICE-predicted values into CAFE required a multistep process that involved the use of different types of data to assess their influence on SSDs and HC estimates. Results from multiple analyses showed that SSDs supplemented with ICE-predicted values generally produced HC5 estimates that were within a 3-fold difference of estimates from measured SSDs (58%-82% of comparisons), but that were often more conservative (63%-76% of comparisons) and had lower uncertainty (90% of comparisons). ICE SSDs did not substantially underpredict toxicity (<10% of comparisons) when compared to estimates from measured SSD. The incorporation of ICE-predicted values into CAFE allowed the development of >800 new SSDs, increased diversity in SSDs by an average of 34 species, and augmented data for priority chemicals involved in accidental chemical releases.}, } @article {pmid28634367, year = {2017}, author = {Gao, X and Wang, C and Dai, W and Ren, S and Tao, F and He, X and Han, G and Wang, W}, title = {Proteomic analysis reveals large amounts of decomposition enzymes and major metabolic pathways involved in algicidal process of Trametes versicolor F21a.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {3907}, pmid = {28634367}, issn = {2045-2322}, mesh = {*Antibiosis ; Biomass ; Chlorophyll/metabolism ; Chromatography, Liquid ; Computational Biology/methods ; Cyanobacteria ; Fungal Proteins/*metabolism ; Metabolic Networks and Pathways ; *Proteome ; *Proteomics/methods ; Tandem Mass Spectrometry ; Trametes/*metabolism ; }, abstract = {A recent algicidal mode indicates that fungal mycelia can wrap and eliminate almost all co-cultivated algal cells within a short time span. However, the underlying molecular mechanism is rarely understood. We applied proteomic analysis to investigate the algicidal process of Trametes versicolor F21a and identified 3,754 fungal proteins. Of these, 30 fungal enzymes with endo- or exoglycosidase activities such as β-1,3-glucanase, α-galactosidase, α-glucosidase, alginate lyase and chondroitin lyase were significantly up-regulated. These proteins belong to Glycoside Hydrolases, Auxiliary Activities, Carbohydrate Esterases and Polysaccharide Lyases, suggesting that these enzymes may degrade lipopolysaccharides, peptidoglycans and alginic acid of algal cells. Additionally, peptidase, exonuclease, manganese peroxidase and cytochrome c peroxidase, which decompose proteins and DNA or convert other small molecules of algal cells, could be other major decomposition enzymes. Gene Ontology and KEGG pathway enrichment analysis demonstrated that pyruvate metabolism and tricarboxylic acid cycle pathways play a critical role in response to adverse environment via increasing energy production to synthesize lytic enzymes or uptake molecules. Carbon metabolism, selenocompound metabolism, sulfur assimilation and metabolism, as well as several amino acid biosynthesis pathways could play vital roles in the synthesis of nutrients required by fungal mycelia.}, } @article {pmid28634330, year = {2017}, author = {Shoji, J and Mitamura, H and Ichikawa, K and Kinoshita, H and Arai, N}, title = {Increase in predation risk and trophic level induced by nocturnal visits of piscivorous fishes in a temperate seagrass bed.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {3895}, pmid = {28634330}, issn = {2045-2322}, mesh = {Animals ; Ecosystem ; Environment ; *Fishes ; Food Chain ; *Predatory Behavior ; }, abstract = {The majority of surveys on food webs of aquatic ecosystems have been conducted during the day owning to difficulties in sampling animals at night. In this study, to examine diurnal changes in predator-prey interactions in a temperate seagrass Zostera marina bed, a quantitative day/night survey of fish, the dominant animal community, coupled with acoustic telemetry of their predators, was conducted. The number of species, abundance, and biomass of piscivorous predators and mean trophic level during the night were significantly higher than those in the day in all seasons. Analysis of the stomach contents of 182 piscivorous predators showed that no fish predation occurred during the day whereas predation occurred during the night in winter, spring, and summer. Acoustic telemetry demonstrated nocturnal visits by dominant piscivorous fish species (rockfishes and conger eel) to the seagrass bed. We conclude that the nocturnal visits by piscivorous fishes increased the predation risk and trophic level in the fish nursery. The ecological functions of seagrass beds should be reevaluated accounting for day/night changes in food webs; these areas serve as nurseries for juvenile and small-sized fishes during the day and as foraging grounds for predators during the night.}, } @article {pmid28632891, year = {2018}, author = {Huggins, R and Stoklosa, J and Roach, C and Yip, P}, title = {Estimating the size of an open population using sparse capture-recapture data.}, journal = {Biometrics}, volume = {74}, number = {1}, pages = {280-288}, doi = {10.1111/biom.12718}, pmid = {28632891}, issn = {1541-0420}, mesh = {Animals ; Biometry/*methods ; Computer Simulation ; *Data Interpretation, Statistical ; *Linear Models ; Models, Statistical ; Population Density ; }, abstract = {Sparse capture-recapture data from open populations are difficult to analyze using currently available frequentist statistical methods. However, in closed capture-recapture experiments, the Chao sparse estimator (Chao, 1989, Biometrics 45, 427-438) may be used to estimate population sizes when there are few recaptures. Here, we extend the Chao (1989) closed population size estimator to the open population setting by using linear regression and extrapolation techniques. We conduct a small simulation study and apply the models to several sparse capture-recapture data sets.}, } @article {pmid28630932, year = {2017}, author = {Deveson, IW and Holleley, CE and Blackburn, J and Marshall Graves, JA and Mattick, JS and Waters, PD and Georges, A}, title = {Differential intron retention in Jumonji chromatin modifier genes is implicated in reptile temperature-dependent sex determination.}, journal = {Science advances}, volume = {3}, number = {6}, pages = {e1700731}, pmid = {28630932}, issn = {2375-2548}, mesh = {Animals ; Biomarkers ; Chromatin/*genetics ; Computational Biology/methods ; Female ; Gene Expression Profiling ; Gene Expression Regulation, Developmental ; *Genes, Modifier ; *Introns ; Male ; Models, Genetic ; Reptiles/*genetics ; Sex Determination Processes/*genetics ; *Temperature ; Transcriptome ; }, abstract = {In many vertebrates, sex of offspring is determined by external environmental cues rather than by sex chromosomes. In reptiles, for instance, temperature-dependent sex determination (TSD) is common. Despite decades of work, the mechanism by which temperature is converted into a sex-determining signal remains mysterious. This is partly because it is difficult to distinguish the primary molecular events of TSD from the confounding downstream signatures of sexual differentiation. We use the Australian central bearded dragon, in which chromosomal sex determination is overridden at high temperatures to produce sex-reversed female offspring, as a unique model to identify TSD-specific features of the transcriptome. We show that an intron is retained in mature transcripts from each of two Jumonji family genes, JARID2 and JMJD3, in female dragons that have been sex-reversed by temperature but not in normal chromosomal females or males. JARID2 is a component of the master chromatin modifier Polycomb Repressive Complex 2, and the mammalian sex-determining factor SRY is directly regulated by an independent but closely related Jumonji family member. We propose that the perturbation of JARID2/JMJD3 function by intron retention alters the epigenetic landscape to override chromosomal sex-determining cues, triggering sex reversal at extreme temperatures. Sex reversal may then facilitate a transition from genetic sex determination to TSD, with JARID2/JMJD3 intron retention preserved as the decisive regulatory signal. Significantly, we also observe sex-associated differential retention of the equivalent introns in JARID2/JMJD3 transcripts expressed in embryonic gonads from TSD alligators and turtles, indicative of a reptile-wide mechanism controlling TSD.}, } @article {pmid28630911, year = {2017}, author = {Elgvin, TO and Trier, CN and Tørresen, OK and Hagen, IJ and Lien, S and Nederbragt, AJ and Ravinet, M and Jensen, H and Sætre, GP}, title = {The genomic mosaicism of hybrid speciation.}, journal = {Science advances}, volume = {3}, number = {6}, pages = {e1602996}, pmid = {28630911}, issn = {2375-2548}, mesh = {Animals ; Chromosomes ; DNA, Mitochondrial ; Evolution, Molecular ; Gene Ontology ; *Genetic Speciation ; Genetics, Population ; *Genome ; *Genomics/methods ; *Hybridization, Genetic ; Male ; *Mosaicism ; Phylogeny ; Reproductive Isolation ; Sparrows ; }, abstract = {Hybridization is widespread in nature and, in some instances, can result in the formation of a new hybrid species. We investigate the genetic foundation of this poorly understood process through whole-genome analysis of the hybrid Italian sparrow and its progenitors. We find overall balanced yet heterogeneous levels of contribution from each parent species throughout the hybrid genome and identify areas of novel divergence in the hybrid species exhibiting signals consistent with balancing selection. High-divergence areas are disproportionately located on the Z chromosome and overrepresented in gene networks relating to key traits separating the focal species, which are likely involved in reproductive barriers and/or species-specific adaptations. Of special interest are genes and functional groups known to affect body patterning, beak morphology, and the immune system, which are important features of diversification and fitness. We show that a combination of mosaic parental inheritance and novel divergence within the hybrid lineage has facilitated the origin and maintenance of an avian hybrid species.}, } @article {pmid28630352, year = {2017}, author = {Meslin, C and Cherwin, TS and Plakke, MS and Hill, J and Small, BS and Goetz, BJ and Wheat, CW and Morehouse, NI and Clark, NL}, title = {Structural complexity and molecular heterogeneity of a butterfly ejaculate reflect a complex history of selection.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {114}, number = {27}, pages = {E5406-E5413}, pmid = {28630352}, issn = {1091-6490}, support = {U54 HG008540/HG/NHGRI NIH HHS/United States ; }, mesh = {Animals ; Biological Evolution ; Butterflies/*physiology ; Computational Biology ; Evolution, Molecular ; Female ; Fertility ; Hemolymph ; Longevity ; Male ; Mass Spectrometry ; Peptides/chemistry ; Phylogeny ; Semen/*chemistry ; Sexual Behavior, Animal ; Spermatogonia/*chemistry ; Spermatozoa/*chemistry ; }, abstract = {Male ejaculates are often structurally complex, and this complexity is likely to influence key reproductive interactions between males and females. However, despite its potential evolutionary significance, the molecular underpinnings of ejaculate structural complexity have received little empirical attention. To address this knowledge gap, we sought to understand the biochemical and functional properties of the structurally complex ejaculates of Pieris rapae butterflies. Males in this species produce large ejaculates called spermatophores composed of an outer envelope, an inner matrix, and a bolus of sperm. Females are thought to benefit from the nutrition contained in the soluble inner matrix through increases in longevity and fecundity. However, the indigestible outer envelope of the spermatophore delays female remating, allowing males to monopolize paternity for longer. Here, we show that these two nonsperm-containing spermatophore regions, the inner matrix and the outer envelope, differ in their protein composition and functional properties. We also reveal how these divergent protein mixtures are separately stored in the male reproductive tract and sequentially transferred to the female reproductive tract during spermatophore assembly. Intriguingly, we discovered large quantities of female-derived proteases in both spermatophore regions shortly after mating, which may contribute to spermatophore digestion and hence, female control over remating rate. Finally, we report evidence of past selection on these spermatophore proteins and female proteases, indicating a complex evolutionary history. Our findings illustrate how structural complexity of ejaculates may allow functionally and/or spatially associated suites of proteins to respond rapidly to divergent selective pressures, such as sexual conflict or reproductive cooperation.}, } @article {pmid28630326, year = {2017}, author = {Kim, J and Farré, M and Auvil, L and Capitanu, B and Larkin, DM and Ma, J and Lewin, HA}, title = {Reconstruction and evolutionary history of eutherian chromosomes.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {114}, number = {27}, pages = {E5379-E5388}, pmid = {28630326}, issn = {1091-6490}, support = {R01 HG007352/HG/NHGRI NIH HHS/United States ; BB/K008226/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/J010170/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Algorithms ; Animals ; Cell Lineage ; Chromosome Breakpoints ; Chromosomes/*ultrastructure ; Computational Biology/methods ; Eutheria/*genetics ; *Evolution, Molecular ; Gene Rearrangement ; Genome ; Genome, Human ; Humans ; In Situ Hybridization, Fluorescence ; Phylogeny ; Software ; Synteny ; }, abstract = {Whole-genome assemblies of 19 placental mammals and two outgroup species were used to reconstruct the order and orientation of syntenic fragments in chromosomes of the eutherian ancestor and six other descendant ancestors leading to human. For ancestral chromosome reconstructions, we developed an algorithm (DESCHRAMBLER) that probabilistically determines the adjacencies of syntenic fragments using chromosome-scale and fragmented genome assemblies. The reconstructed chromosomes of the eutherian, boreoeutherian, and euarchontoglires ancestor each included >80% of the entire length of the human genome, whereas reconstructed chromosomes of the most recent common ancestor of simians, catarrhini, great apes, and humans and chimpanzees included >90% of human genome sequence. These high-coverage reconstructions permitted reliable identification of chromosomal rearrangements over ∼105 My of eutherian evolution. Orangutan was found to have eight chromosomes that were completely conserved in homologous sequence order and orientation with the eutherian ancestor, the largest number for any species. Ruminant artiodactyls had the highest frequency of intrachromosomal rearrangements, and interchromosomal rearrangements dominated in murid rodents. A total of 162 chromosomal breakpoints in evolution of the eutherian ancestral genome to the human genome were identified; however, the rate of rearrangements was significantly lower (0.80/My) during the first ∼60 My of eutherian evolution, then increased to greater than 2.0/My along the five primate lineages studied. Our results significantly expand knowledge of eutherian genome evolution and will facilitate greater understanding of the role of chromosome rearrangements in adaptation, speciation, and the etiology of inherited and spontaneously occurring diseases.}, } @article {pmid28626126, year = {2017}, author = {Toyoda, H and Mori, K}, title = {[Conduct of Occupational Health During Major Disasters: A Comparison of Literature on Occupational Health Issues in the World Trade Center Terrorist Attack and the Fukushima Nuclear Power Plant Accident].}, journal = {Journal of UOEH}, volume = {39}, number = {2}, pages = {153-159}, doi = {10.7888/juoeh.39.153}, pmid = {28626126}, issn = {0387-821X}, mesh = {Databases, Factual ; *Disasters ; *Fukushima Nuclear Accident ; Humans ; Occupational Diseases ; *Occupational Health ; *September 11 Terrorist Attacks ; }, abstract = {Workers who respond to large-scale disasters can be exposed to health hazards that do not exist in routine work. It is assumed that learning from past cases is effective for preparing for and responding to such problems, but published information is still insufficient. Accordingly, we conducted a literature review about the health issues and occupational health activities at the World Trade Center (WTC) terrorist attack and at the Fukushima Nuclear Power Plant accident to investigate how occupational health activities during disasters should be conducted. Seven studies about the WTC attack were extracted and categorized into the following topics: "in relation to emergency systems including occupational health management"; "in relation to improvement and prevention of health effects and occupational hygiene"; and "in relation to care systems aimed at mitigating health effects." Studies about the Fukushima Nuclear Power Plant accident have been used in a previous review. We conclude that, to prevent health effects in workers who respond to large-scale disasters, it is necessary to incorporate occupational health regulations into the national response plan, and to develop practical support functions that enable support to continue for an extended period, training systems for workers with opportunities to report accidents, and care systems to mitigate the health effects.}, } @article {pmid28623391, year = {2017}, author = {Piché-Choquette, S and Khdhiri, M and Constant, P}, title = {Survey of High-Affinity H2-Oxidizing Bacteria in Soil Reveals Their Vast Diversity Yet Underrepresentation in Genomic Databases.}, journal = {Microbial ecology}, volume = {74}, number = {4}, pages = {771-775}, pmid = {28623391}, issn = {1432-184X}, mesh = {Bacteria/*classification/*genetics/isolation & purification ; *Databases, Genetic ; Genes, Bacterial ; *Microbiota ; Oxidation-Reduction ; Phylogeny ; *Soil Microbiology ; }, abstract = {While high-affinity H2-oxidizing bacteria (HA-HOB) serve as the main sink of atmospheric H2, the ecology of this specialist functional group is rather unknown due to its recent discovery. The main purpose of our study is to provide the first extensive survey of HA-HOB in farmland, larch, and poplar soils exposed to 0.5 and 10,000 ppmv H2. Using qPCR and qRT-PCR assays along with PCR amplicon high-throughput sequencing of hhyL gene encoding for the large subunit of high-affinity [NiFe]-hydrogenases (HAH), we found that hhyL gene expression ratio explained better variation in measured H2 oxidation rates than HA-HOB species richness. Carbon, nitrogen, pH, and bacterial species richness appeared as the most important drivers of HA-HOB community structure. Our study also highlights the need to cultivate HA-HOB due to the huge gap in current genomic databases.}, } @article {pmid28623252, year = {2017}, author = {Fischer, S and Spielau, T and Clemens, S}, title = {Natural variation in Arabidopsis thaliana Cd responses and the detection of quantitative trait loci affecting Cd tolerance.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {3693}, pmid = {28623252}, issn = {2045-2322}, mesh = {Adaptation, Biological/*genetics ; Arabidopsis/*drug effects/*physiology ; Cadmium/*metabolism/toxicity ; Chromosome Mapping ; Computational Biology/methods ; Gene Expression Profiling ; Gene Ontology ; Genetic Association Studies ; Heavy Metal Poisoning ; Phenotype ; *Quantitative Trait Loci ; *Quantitative Trait, Heritable ; }, abstract = {Metal tolerance is often a result of metal storage or distribution. Thus, with the goal of advancing the molecular understanding of such metal homeostatic mechanisms, natural variation of metal tolerance in Arabidopsis thaliana was investigated. Substantial variation exists in tolerance of excess copper (Cu), zinc (Zn) and cadmium (Cd). Two accessions, Col-0 and Bur-0, and a recombinant inbred line (RIL) population derived from these parents were chosen for further analysis of Cd and Zn tolerance variation, which is evident at different plant ages in various experimental systems and appears to be genetically linked. Three QTLs, explaining in total nearly 50% of the variation in Cd tolerance, were mapped. The one obvious candidate gene in the mapped intervals, HMA3, is unlikely to contribute to the variation. In order to identify additional candidate genes the Cd responses of Col-0 and Bur-0 were compared at the transcriptome level. The sustained common Cd response of the two accessions was dominated by processes implicated in plant pathogen defense. Accession-specific differences suggested a more efficient activation of acclimative responses as underlying the higher Cd tolerance of Bur-0. The second hypothesis derived from the physiological characterization of the accessions is a reduced Cd accumulation in Bur-0.}, } @article {pmid28622351, year = {2017}, author = {Lanzén, A and Lekang, K and Jonassen, I and Thompson, EM and Troedsson, C}, title = {DNA extraction replicates improve diversity and compositional dissimilarity in metabarcoding of eukaryotes in marine sediments.}, journal = {PloS one}, volume = {12}, number = {6}, pages = {e0179443}, pmid = {28622351}, issn = {1932-6203}, mesh = {*Aquatic Organisms/chemistry/genetics ; *Biodiversity ; DNA Barcoding, Taxonomic/*methods ; *DNA, Ribosomal/chemistry/genetics/isolation & purification ; *Eukaryota/chemistry/genetics ; RNA, Ribosomal/*genetics ; }, abstract = {Human impact on marine benthic communities has traditionally been assessed using visible morphological traits and has focused on the macrobenthos, whereas the ecologically important organisms of the meio- and microbenthos have received less attention. DNA metabarcoding offers an alternative to this approach and enables a larger fraction of the biodiversity in marine sediments to be monitored in a cost-efficient manner. Although this methodology remains poorly standardised and challenged by biases inherent to rRNA copy number variation, DNA extraction, PCR, and limitations related to taxonomic identification, it has been shown to be semi-quantitative and useful for comparing taxon abundances between samples. Here, we evaluate the effect of replicating genomic DNA extraction in order to counteract small scale spatial heterogeneity and improve diversity and community structure estimates in metabarcoding-based monitoring. For this purpose, we used ten technical replicates from three different marine sediment samples. The effect of sequence depth was also assessed, and in silico pooling of DNA extraction replicates carried out in order to maintain the number of reads constant. Our analyses demonstrated that both sequencing depth and DNA extraction replicates could improve diversity estimates as well as the ability to separate samples with different characteristics. We could not identify a "sufficient" replicate number or sequence depth, where further improvements had a less significant effect. Based on these results, we consider replication an attractive alternative to directly increasing the amount of sample used for DNA extraction and strongly recommend it for future metabarcoding studies and routine assessments of sediment biodiversity.}, } @article {pmid28620687, year = {2017}, author = {Ma, L and Zhang, W and Zhu, Y and Zhang, G and Zhang, H and Zhang, Q and Zhang, L and Yuan, C and Zhang, C}, title = {Identification and characterization of a biosynthetic gene cluster for tryptophan dimers in deep sea-derived Streptomyces sp. SCSIO 03032.}, journal = {Applied microbiology and biotechnology}, volume = {101}, number = {15}, pages = {6123-6136}, doi = {10.1007/s00253-017-8375-5}, pmid = {28620687}, issn = {1432-0614}, mesh = {Bacterial Proteins/genetics/metabolism ; Biosynthetic Pathways/genetics ; Cloning, Molecular ; Computational Biology ; *Multigene Family ; Open Reading Frames ; Oxygenases/genetics/metabolism ; Seawater/*microbiology ; Streptomyces/*genetics/isolation & purification/metabolism ; Tryptophan/*biosynthesis/genetics ; }, abstract = {Tryptophan dimers (TDs) are an important class of natural products with diverse bioactivities and share conserved biosynthetic pathways. We report the identification of a partial gene cluster (spm) responsible for the biosynthesis of a class of unusual TDs with non-planar skeletons including spiroindimicins (SPMs), indimicins (IDMs), and lynamicins (LNMs) from the deep-sea derived Streptomyces sp. SCSIO 03032. Bioinformatics analysis, targeted gene disruptions, and heterologous expression studies confirmed the involvement of the spm gene cluster in the biosynthesis of SPM/IDM/LNMs, and revealed the indispensable roles for the halogenase/reductase pair SpmHF, the amino acid oxidase SpmO, and the chromopyrrolic acid (CPA) synthase SpmD, as well as the positive regulator SpmR and the putative transporter SpmA. However, the spm gene cluster was unable to confer a heterologous host the ability to produce SPM/IDM/LNMs. In addition, the P450 enzyme SpmP and the monooxygenase SpmX2 were found to be non-relevant to the biosynthesis of SPM/IDM/LNMs. Sequence alignment and structure modeling suggested the lack of key conserved amino acid residues in the substrate-binding pocket of SpmP. Furthermore, feeding experiments in the non-producing ΔspmO mutant revealed several biosynthetic precursors en route to SPMs, indicating that key enzymes responsible for the biosynthesis of SPMs should be encoded by genes outside of the identified spm gene cluster. Finally, the biosynthetic pathways of SPM/IDM/LNMs are proposed to lay a basis for further insights into their intriguing biosynthetic machinery.}, } @article {pmid28620233, year = {2017}, author = {Dohrmann, M and Wörheide, G}, title = {Dating early animal evolution using phylogenomic data.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {3599}, pmid = {28620233}, issn = {2045-2322}, mesh = {Animals ; Computational Biology/*methods ; *Evolution, Molecular ; *Fossils ; *Genetic Speciation ; *Phylogeny ; Time ; }, abstract = {Information about the geological timeframe during which animals radiated into their major subclades is crucial to understanding early animal ecology and evolution. Unfortunately, the pre-Cambrian fossil record is sparse and its interpretation controversial. Relaxed molecular-clock methods provide an alternative means of estimating the timing of cladogenesis deep in the metazoan tree of life. So far, thorough molecular clock studies focusing specifically on Metazoa as a whole have been based on relatively small datasets or incomplete representation of the main non-bilaterian lineages (such as sponges and ctenophores), which are fundamental for understanding early metazoan evolution. Here, we use a previously published phylogenomic dataset that includes a fair sampling of all relevant groups to estimate the timing of early animal evolution with Bayesian relaxed-clock methods. According to our results, all non-bilaterian phyla, as well as total-group Bilateria, evolved in an ancient radiation during a geologically relatively short time span, before the onset of long-term global glaciations ("Snowball Earth"; ~720-635 Ma). Importantly, this result appears robust to alterations of a number of important analytical variables, such as models of among-lineage rate variation and sets of fossil calibrations used.}, } @article {pmid28620214, year = {2017}, author = {Millán-Aguiñaga, N and Chavarria, KL and Ugalde, JA and Letzel, AC and Rouse, GW and Jensen, PR}, title = {Phylogenomic Insight into Salinispora (Bacteria, Actinobacteria) Species Designations.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {3564}, pmid = {28620214}, issn = {2045-2322}, support = {R01 GM085770/GM/NIGMS NIH HHS/United States ; U19 TW007401/TW/FIC NIH HHS/United States ; }, mesh = {Actinobacteria/*genetics ; Biodiversity ; Computational Biology/methods ; Environmental Microbiology ; *Genome, Bacterial ; *Genomics/methods ; *Phylogeny ; Quantitative Trait, Heritable ; Recombination, Genetic ; }, abstract = {Bacteria represent the most genetically diverse kingdom of life. While great progress has been made in describing this diversity, it remains difficult to identify the phylogenetic and ecological characteristics that delineate groups of bacteria that possess species-like properties. One major challenge associated with species delineations is that not all shared genes have the same evolutionary history, and thus the choice of loci can have a major impact on phylogenetic reconstruction. Sequencing the genomes of large numbers of closely related strains provides new opportunities to distinguish ancestral from acquired alleles and assess the effects of recombination on phylogenetic inference. Here we analyzed the genomes of 119 strains of the marine actinomycete genus Salinispora, which is currently comprised of three named species that share 99% 16S rRNA gene sequence identity. While 63% of the core genome showed evidence of recombination, this had no effect on species-level phylogenomic resolution. Recombination did however blur intra-species relationships and biogeographic resolution. The genome-wide average nucleotide identity provided a new perspective on Salinispora diversity, revealing as many as seven new species. Patterns of orthologous group distributions reveal a genetic basis to delineation the candidate taxa and insight into the levels of genetic cohesion associated with bacterial species.}, } @article {pmid28620188, year = {2017}, author = {He, S and Guo, L and Niu, M and Miao, F and Jiao, S and Hu, T and Long, M}, title = {Ecological diversity and co-occurrence patterns of bacterial community through soil profile in response to long-term switchgrass cultivation.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {3608}, pmid = {28620188}, issn = {2045-2322}, mesh = {*Bacteria/classification/genetics ; Biodiversity ; Computational Biology/methods ; *Microbiota ; *Panicum ; *Soil Microbiology ; }, abstract = {Switchgrass (Panicum virgatum L.) is a cellulosic biofuel feedstock and their effects on bacterial communities in deep soils remain poorly understood. To reveal the responses of bacterial communities to long-term switchgrass cultivation through the soil profile, we examined the shift of soil microbial communities with depth profiles of 0-60 cm in five-year switchgrass cultivation and fallow plots. The Illumina sequencing of the 16S rRNA gene showed that switchgrass cultivation significantly increased microbial OTU richness, rather than microbial Shannon diversity; however, there was no significant difference in the structure of microbial communities between switchgrass cultivation and fallow soils. Both switchgrass cultivation and fallow soils exhibited significant negative vertical spatial decay of microbial similarity, indicating that more vertical depth distant soils had more dissimilar communities. Specifically, switchgrass cultivation soils showed more beta-diversity variations across soil depth profile. Through network analysis, more connections and closer relationships of microbial taxa were observed in soils under switchgrass cultivation, suggesting that microbial co-occurrence patterns were substantially influenced by switchgrass cultivation. Overall, our study suggested that five-year switchgrass cultivation could generated more beta-diversity variations across soil depth and more complex inter-relationships of microbial taxa, although did not significantly shape the structure of soil microbial community.}, } @article {pmid28618056, year = {2017}, author = {Saouter, E and Aschberger, K and Fantke, P and Hauschild, MZ and Bopp, SK and Kienzler, A and Paini, A and Pant, R and Secchi, M and Sala, S}, title = {Improving substance information in USEtox[®] , part 1: Discussion on data and approaches for estimating freshwater ecotoxicity effect factors.}, journal = {Environmental toxicology and chemistry}, volume = {36}, number = {12}, pages = {3450-3462}, doi = {10.1002/etc.3889}, pmid = {28618056}, issn = {1552-8618}, mesh = {Databases, Factual ; Ecotoxicology/*methods ; Environmental Pollutants/*analysis/toxicity ; Fresh Water/*chemistry ; Hazardous Substances/*analysis/toxicity ; Humans ; Models, Theoretical ; Risk Assessment ; Water Pollutants, Chemical/analysis/toxicity ; }, abstract = {The scientific consensus model USEtox[®] is recommended by the European Commission as the reference model to characterize life cycle chemical emissions in terms of their potential human toxicity and freshwater aquatic ecotoxicity impacts in the context of the International Reference Life Cycle Data System Handbook and the Environmental Footprint pilot phase looking at products (PEF) and organizations (OEF). Consequently, this model has been systematically used within the PEF/OEF pilot phase by 25 European Union industry sectors, which manufacture a wide variety of consumer products. This testing phase has raised some questions regarding the derivation of and the data used for the chemical-specific freshwater ecotoxicity effect factor in USEtox. For calculating the potential freshwater aquatic ecotoxicity impacts, USEtox bases the effect factor on the chronic hazard concentration (HC50) value for a chemical calculated as the arithmetic mean of all logarithmized geometric means of species-specific chronic median lethal (or effect) concentrations (L[E]C50). We investigated the dependency of the USEtox effect factor on the selection of ecotoxicological data source and toxicological endpoints, and we found that both influence the ecotoxicity ranking of chemicals and may hence influence the conclusions of a PEF/OEF study. We furthermore compared the average measure (HC50) with other types of ecotoxicity effect indicators, such as the lowest species EC50 or no-observable-effect concentration, frequently used in regulatory risk assessment, and demonstrated how they may also influence the ecotoxicity ranking of chemicals. We acknowledge that these indicators represent different aspects of a chemical's ecotoxicity potential and discuss their pros and cons for a comparative chemical assessment as performed in life cycle assessment and in particular within the PEF/OEF context. Environ Toxicol Chem 2017;36:3450-3462. © 2017 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals, Inc. on behalf of SETAC.}, } @article {pmid28614384, year = {2017}, author = {Feng, B and Guo, Q and Zheng, K and Qin, Y and Du, Y}, title = {Antennal transcriptome analysis of the piercing moth Oraesia emarginata (Lepidoptera: Noctuidae).}, journal = {PloS one}, volume = {12}, number = {6}, pages = {e0179433}, pmid = {28614384}, issn = {1932-6203}, mesh = {Amino Acid Sequence ; Animals ; Arthropod Antennae/*metabolism ; Female ; Gene Expression Profiling/*methods ; Gene Ontology ; Insect Proteins/classification/*genetics ; Male ; Moths/*genetics ; Olfactory Cortex/metabolism ; Phylogeny ; Receptors, Odorant/classification/genetics ; Receptors, Pheromone/classification/genetics ; Reverse Transcriptase Polymerase Chain Reaction ; Sequence Homology, Amino Acid ; Smell/genetics ; }, abstract = {The piercing fruit moth Oraesia emarginata is an economically significant pest; however, our understanding of its olfactory mechanisms in infestation is limited. The present study conducted antennal transcriptome analysis of olfactory genes using real-time quantitative reverse transcription PCR analysis (RT-qPCR). We identified a total of 104 candidate chemosensory genes from several gene families, including 35 olfactory receptors (ORs), 41 odorant-binding proteins, 20 chemosensory proteins, 6 ionotropic receptors, and 2 sensory neuron membrane proteins. Seven candidate pheromone receptors (PRs) and 3 candidate pheromone-binding proteins (PBPs) for sex pheromone recognition were found. OemaOR29 and OemaPBP1 had the highest fragments per kb per million fragments (FPKM) values in all ORs and OBPs, respectively. Eighteen olfactory genes were upregulated in females, including 5 candidate PRs, and 20 olfactory genes were upregulated in males, including 2 candidate PRs (OemaOR29 and 4) and 2 PBPs (OemaPBP1 and 3). These genes may have roles in mediating sex-specific behaviors. Most candidate olfactory genes of sex pheromone recognition (except OemaOR29 and OemaPBP3) in O. emarginata were not clustered with those of studied noctuid species (type I pheromone). In addition, OemaOR29 was belonged to cluster PRIII, which comprise proteins that recognize type II pheromones instead of type I pheromones. The structure and function of olfactory genes that encode sex pheromones in O. emarginata might thus differ from those of other studied noctuids. The findings of the present study may help explain the molecular mechanism underlying olfaction and the evolution of olfactory genes encoding sex pheromones in O. emarginata.}, } @article {pmid28611409, year = {2017}, author = {Harter, J and El-Hadidi, M and Huson, DH and Kappler, A and Behrens, S}, title = {Soil biochar amendment affects the diversity of nosZ transcripts: Implications for N2O formation.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {3338}, pmid = {28611409}, issn = {2045-2322}, abstract = {Microbial nitrogen transformation processes such as denitrification represent major sources of the potent greenhouse gas nitrous oxide (N2O). Soil biochar amendment has been shown to significantly decrease N2O emissions in various soils. However, the effect of biochar on the structure and function of microbial communities that actively perform nitrogen redox transformations has not been studied in detail yet. To analyse the community composition of actively denitrifying and N2O-reducing microbial communities, we collected RNA samples at different time points from a soil microcosm experiment conducted under denitrifying conditions and performed Illumina amplicon sequencing targeting nirK, typical nosZ and atypical nosZ mRNA transcripts. Within 10 days, biochar significantly increased the diversity of nirK and typical nosZ transcripts and resulted in taxonomic shifts among the typical nosZ-expressing microbial community. Furthermore, biochar addition led to a significant increase in transcript production among microbial species that are specialized on direct N2O reduction from the environment. Our results point towards a potential coupling of biochar-induced N2O emission reduction and an increase in microbial N2O reduction activity among specific groups of typical and atypical N2O reducers. However, experiments with other soils and biochars will be required to verify the transferability of these findings to other soil-biochar systems.}, } @article {pmid28610561, year = {2017}, author = {Massoudi, B and Blanker, MH and van Valen, E and Wouters, H and Bockting, CLH and Burger, H}, title = {Blended care vs. usual care in the treatment of depressive symptoms and disorders in general practice [BLENDING]: study protocol of a non-inferiority randomized trial.}, journal = {BMC psychiatry}, volume = {17}, number = {1}, pages = {218}, pmid = {28610561}, issn = {1471-244X}, mesh = {Adult ; Cost-Benefit Analysis ; Depressive Disorder/psychology/*therapy ; Female ; General Practice ; Humans ; *Internet ; Male ; Netherlands ; Remission Induction ; Research Design ; *Therapy, Computer-Assisted ; }, abstract = {BACKGROUND: The majority of patients with depressive disorders are treated by general practitioners (GPs) and are prescribed antidepressant medication. Patients prefer psychological treatments but they are under-used, mainly due to time constraints and limited accessibility. A promising approach to deliver psychological treatment is blended care, i.e. guided online treatment. However, the cost-effectiveness of blended care formatted as an online psychological treatment supported by the patients' own GP or general practice mental health worker (MHW) in routine primary care is unknown. We aim to demonstrate non-inferiority of blended care compared with usual care in patients with depressive symptoms or a depressive disorder in general practice. Additionally, we will explore the real-time course over the day of emotions and affect, and events within individuals during treatment.

METHODS: This is a pragmatic non-inferiority trial including 300 patients with depressive symptoms, recruited by collaborating GPs and MHWs. After inclusion, participants are randomized to either blended care or usual care in routine general practice. Blended care consists of the 'Act and Feel' treatment: an eight-week web-based program based on behavioral activation with integrated monitoring of depressive symptomatology and automatized feedback. GPs or their MHWs coach the participants through regular face-to-face or telephonic consultations with at least three sessions. Depressive symptomatology, health status, functional impairment, treatment satisfaction, daily activities and resource use are assessed during a follow-up period of 12 months. During treatment, real-time fluctuations in emotions and affect, and daily events will be rated using ecological momentary assessment. The primary outcome is the reduction of depressive symptoms from baseline to three months follow-up. We will conduct intention-to-treat analyses and supplementary per-protocol analyses.

DISCUSSION: This trial will show whether blended care might be an appropriate treatment strategy for patients with depressive symptoms and depressive disorder in general practice.

TRIAL REGISTRATION: Netherlands Trial Register: NTR4757; 25 August 2014. http://www.trialregister.nl/trialreg/admin/rctview.asp?TC=4757 . (Archived by WebCite® at http://www.webcitation.org/6mnXNMGef).}, } @article {pmid28610022, year = {2017}, author = {Zaitzev, A}, title = {Two new species of fungus gnats (Diptera: Mycetophilidae) from Kunashir Island, Kuril Islands.}, journal = {Zootaxa}, volume = {4250}, number = {3}, pages = {296-300}, doi = {10.11646/zootaxa.42450.3.6}, pmid = {28610022}, issn = {1175-5334}, mesh = {Animals ; Ceratopogonidae ; *Diptera ; Fungi ; Islands ; }, abstract = {Two new species of Mycetophilidae (Diptera), Clastobasis subalternans sp. n. and Phthinia kurilensis sp. n. are described from Kunashir I. (South Kuril Is.). Their relationships with other species of Clastobasis Skuse and Phthinia Winnertz are briefly discussed.}, } @article {pmid28603714, year = {2017}, author = {Gall, T and Valkanas, E and Bello, C and Markello, T and Adams, C and Bone, WP and Brandt, AJ and Brazill, JM and Carmichael, L and Davids, M and Davis, J and Diaz-Perez, Z and Draper, D and Elson, J and Flynn, ED and Godfrey, R and Groden, C and Hsieh, CK and Fischer, R and Golas, GA and Guzman, J and Huang, Y and Kane, MS and Lee, E and Li, C and Links, AE and Maduro, V and Malicdan, MCV and Malik, FS and Nehrebecky, M and Park, J and Pemberton, P and Schaffer, K and Simeonov, D and Sincan, M and Smedley, D and Valivullah, Z and Wahl, C and Washington, N and Wolfe, LA and Xu, K and Zhu, Y and Gahl, WA and Tifft, CJ and Toro, C and Adams, DR and He, M and Robinson, PN and Haendel, MA and Zhai, RG and Boerkoel, CF}, title = {Defining Disease, Diagnosis, and Translational Medicine within a Homeostatic Perturbation Paradigm: The National Institutes of Health Undiagnosed Diseases Program Experience.}, journal = {Frontiers in medicine}, volume = {4}, number = {}, pages = {62}, pmid = {28603714}, issn = {2296-858X}, support = {HHSN268201300038C/HL/NHLBI NIH HHS/United States ; HHSN268201300036C/HL/NHLBI NIH HHS/United States ; HHSN268201400033C/HL/NHLBI NIH HHS/United States ; R21 GM119018/GM/NIGMS NIH HHS/United States ; HHSN268201600043C/HL/NHLBI NIH HHS/United States ; F32 HG000215/HG/NHGRI NIH HHS/United States ; R24 OD011883/OD/NIH HHS/United States ; Z01 HG000215/ImNIH/Intramural NIH HHS/United States ; }, abstract = {Traditionally, the use of genomic information for personalized medical decisions relies on prior discovery and validation of genotype-phenotype associations. This approach constrains care for patients presenting with undescribed problems. The National Institutes of Health (NIH) Undiagnosed Diseases Program (UDP) hypothesized that defining disease as maladaptation to an ecological niche allows delineation of a logical framework to diagnose and evaluate such patients. Herein, we present the philosophical bases, methodologies, and processes implemented by the NIH UDP. The NIH UDP incorporated use of the Human Phenotype Ontology, developed a genomic alignment strategy cognizant of parental genotypes, pursued agnostic biochemical analyses, implemented functional validation, and established virtual villages of global experts. This systematic approach provided a foundation for the diagnostic or non-diagnostic answers provided to patients and serves as a paradigm for scalable translational research.}, } @article {pmid28602241, year = {2017}, author = {Giles, KL and McCornack, BP and Royer, TA and Elliott, NC}, title = {Incorporating biological control into IPM decision making.}, journal = {Current opinion in insect science}, volume = {20}, number = {}, pages = {84-89}, doi = {10.1016/j.cois.2017.03.009}, pmid = {28602241}, issn = {2214-5753}, mesh = {Animals ; Crop Production/methods ; *Decision Support Techniques ; Ecology ; Pest Control/methods ; Pest Control, Biological/*methods ; Plants ; }, abstract = {Of the many ways biological control can be incorporated into Integrated Pest Management (IPM) programs, natural enemy thresholds are arguably most easily adopted by stakeholders. Integration of natural enemy thresholds into IPM programs requires ecological and cost/benefit crop production data, threshold model validation, and an understanding of the socioeconomic factors that influence stakeholder decisions about biological control. These thresholds are more likely to be utilized by stakeholders when integrated into dynamic web-based IPM decision support systems that summarize pest management data and push site-specific biological control management recommendations to decision-makers. We highlight recent literature on topics related to natural enemy thresholds and how findings may allow pest suppression services to be incorporated into advanced IPM programs.}, } @article {pmid28598891, year = {2017}, author = {Chang, HY and Murimi, I and Daubresse, M and Qato, DM and Emery, SL and Alexander, GC}, title = {Effect of Direct-to-Consumer Advertising on Statin Use in the United States.}, journal = {Medical care}, volume = {55}, number = {8}, pages = {759-764}, pmid = {28598891}, issn = {1537-1948}, support = {R01 HL107345/HL/NHLBI NIH HHS/United States ; }, mesh = {Adolescent ; Adult ; Commerce ; *Community Participation ; Databases, Factual ; *Direct-to-Consumer Advertising ; Female ; Humans ; Hydroxymethylglutaryl-CoA Reductase Inhibitors/*therapeutic use ; Male ; Middle Aged ; United States ; Young Adult ; }, abstract = {IMPORTANCE: The value of direct-to-consumer advertising (DTCA) of prescription drugs is widely debated, as is the effect of DTCA on prescription sales and health care utilization.

OBJECTIVE: We examined the association between DTCA intensity for statin medications and prescription sales and cholesterol-related health care utilization.

We conducted an ecological study for 75 designated market areas from 2005 to 2009 in the United States using linked data regarding televised DTCA volume, non-DTCA marketing and promotion, retail, mail order and long-term care prescription drug sales, prescription drug and ambulatory care health care utilization, and contextual factors such as health care density and socioeconomic status. Main outcomes and measures were volume of sales, number of dispensed prescriptions, and high cholesterol-related outpatient visits. Analyses were conducted in 2016.

RESULTS: The intensity of rosuvastatin and atorvastatin ad exposures per household varied substantially across designated market areas. After adjustment for socioeconomic, demographic, and clinical characteristics, each 100-unit increase in advertisement viewership was associated with a 2.22% [95% confidence interval (CI), 0.30%-4.19%] increase in statin sales. Similar patterns were observed between DTCA and statin dispensing among the commercially insured. DTCA was associated with increases in high cholesterol-related outpatient visits among adults 18-45 years of age (3.15% increase in visits per 100-unit increase in viewership, 95% CI, 0.98%-5.37%) but not among those 46-65 years of age (0.51%, 95% CI, -1.49% to 2.55%).

CONCLUSION: DTCA for statins is associated with increases in statin utilization and hyperlipidemia-related outpatient visits, especially for young adults.}, } @article {pmid28596537, year = {2017}, author = {Wu, ZZ and Qu, MQ and Pu, XH and Cui, Y and Xiao, WY and Zhao, HX and Bin, SY and Lin, JT}, title = {Transcriptome sequencing of Tessaratoma papillosa antennae to identify and analyze expression patterns of putative olfaction genes.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {3070}, pmid = {28596537}, issn = {2045-2322}, mesh = {Amino Acid Sequence ; Animals ; Arthropod Antennae/*metabolism ; Binding Sites ; Computational Biology/methods ; Data Curation ; Gene Expression Profiling ; *Gene Expression Regulation ; Heteroptera/*genetics ; High-Throughput Nucleotide Sequencing ; Insect Proteins/chemistry/genetics/metabolism ; Olfactory Perception/*genetics ; Phylogeny ; Protein Binding ; *Transcriptome ; }, abstract = {Studies on insect olfaction have increased our understanding of insect's chemosensory system and chemical ecology, and have improved pest control strategies based on insect behavior. In this study, we assembled the antennal transcriptomes of the lychee giant stink bug, Tessaratoma papillosa, by using next generation sequencing to identify the major olfaction gene families in this species. In total, 59 odorant receptors, 14 ionotropic receptors (8 antennal IRs), and 33 odorant binding proteins (28 classic OBPs and 5 plus-C OBPs) were identified from the male and female antennal transcriptomes. Analyses of tissue expression profiles revealed that all 59 OR transcripts, 2 of the 8 antennal IRs, and 6 of the 33 OBPs were primarily expressed in the antennae, suggesting their putative role in olfaction. The sex-biased expression patterns of these antenna-predominant genes suggested that they may have important functions in the reproductive behavior of these insects. This is the first report that provides a comprehensive resource to future studies on olfaction in the lychee giant stink bug.}, } @article {pmid28595568, year = {2017}, author = {He, L and Zhang, A and Pei, Y and Chu, P and Li, Y and Huang, R and Liao, L and Zhu, Z and Wang, Y}, title = {Differences in responses of grass carp to different types of grass carp reovirus (GCRV) and the mechanism of hemorrhage revealed by transcriptome sequencing.}, journal = {BMC genomics}, volume = {18}, number = {1}, pages = {452}, pmid = {28595568}, issn = {1471-2164}, mesh = {Animals ; Blood Coagulation/genetics ; Carps/*genetics/*virology ; Fish Diseases/*genetics/physiopathology/*virology ; Gene Dosage/genetics ; *Gene Expression Profiling ; Gene Ontology ; Hemorrhage/genetics/physiopathology/*veterinary/virology ; Reoviridae/*physiology ; }, abstract = {BACKGROUND: Grass carp is an important farmed fish in China that is affected by serious disease, especially hemorrhagic disease caused by grass carp reovirus (GCRV). The mechanism underlying the hemorrhagic symptoms in infected fish remains to be elucidated. Although GCRV can be divided into three distinct subtypes, differences in the pathogenesis and host immune responses to the different subtypes are still unclear. The aim of this study was to provide a comprehensive insight into the grass carp response to different GCRV subtypes and to elucidate the mechanism underlying the hemorrhagic symptoms.

RESULTS: Following infection of grass carp, GCRV-I was associated with a long latent period and low mortality (42.5%), while GCRV-II was associated with a short latent period and high mortality (81.4%). The relative copy number of GCRV-I remained consistent or decreased slightly throughout the first 7 days post-infection, whereas a marked increase in GCRV-II high copy number was detected at 5 days post-infection. Transcriptome sequencing revealed 211 differentially expressed genes (DEGs) in Group I (66 up-regulated, 145 down-regulated) and 670 (386 up-regulated, 284 down-regulated) in Group II. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis showed significant enrichment in the terms or pathways involved in immune responses and correlating with blood or platelets. Most of the DEGs in Group I were also present in Group II, although the expression profiles differed, with most DEGs showing mild changes in Group I, while marked changes were observed in Group II, especially the interferon-related genes. Many of the genes involved in the complement pathway and coagulation cascades were significantly up-regulated at 7 days post-infection in Group II, suggesting activation of these pathways.

CONCLUSION: GCRV-I is associated with low virulence and a long latent period prior to the induction of a mild host immune response, whereas GCRV-II is associated with high virulence, a short latent period and stimulates a strong and extensive host immune response. The complement and coagulation pathways are significantly activated at 7 days post-infection, leading to the endothelial cell and blood cell damage that result in hemorrhagic symptoms.}, } @article {pmid28594931, year = {2017}, author = {Xue, H and Cao, S and Li, H and Zhang, J and Niu, J and Chen, L and Zhang, F and Zhao, D}, title = {De novo transcriptome assembly and quantification reveal differentially expressed genes between soft-seed and hard-seed pomegranate (Punica granatum L.).}, journal = {PloS one}, volume = {12}, number = {6}, pages = {e0178809}, pmid = {28594931}, issn = {1932-6203}, mesh = {Computational Biology ; Gene Expression Profiling/*methods ; Gene Expression Regulation, Plant/genetics ; Lythraceae/*genetics ; Reverse Transcriptase Polymerase Chain Reaction ; }, abstract = {Pomegranate (Punica granatum L.) belongs to Punicaceae, and is valued for its social, ecological, economic, and aesthetic values, as well as more recently for its health benefits. The 'Tunisia' variety has softer seeds and big arils that are easily swallowed. It is a widely popular fruit; however, the molecular mechanisms of the formation of hard and soft seeds is not yet clear. We conducted a de novo assembly of the seed transcriptome in P. granatum L. and revealed differential gene expression between the soft-seed and hard-seed pomegranate varieties. A total of 35.1 Gb of data were acquired in this study, including 280,881,106 raw reads. Additionally, de novo transcriptome assembly generated 132,287 transcripts and 105,743 representative unigenes; approximately 13,805 unigenes (37.7%) were longer than 1,000 bp. Using bioinformatics annotation libraries, a total of 76,806 unigenes were annotated and, among the high-quality reads, 72.63% had at least one significant match to an existing gene model. Gene expression and differentially expressed genes were analyzed. The seed formation of the two pomegranate cultivars involves lignin biosynthesis and metabolism, including some genes encoding laccase and peroxidase, WRKY, MYB, and NAC transcription factors. In the hard-seed pomegranate, lignin-related genes and cellulose synthesis-related genes were highly expressed; in soft-seed pomegranates, expression of genes related to flavonoids and programmed cell death was slightly higher. We validated selection of the identified genes using qRT-PCR. This is the first transcriptome analysis of P. granatum L. This transcription sequencing greatly enriched the pomegranate molecular database, and the high-quality SSRs generated in this study will aid the gene cloning from pomegranate in the future. It provides important insights into the molecular mechanisms underlying the formation of soft seeds in pomegranate.}, } @article {pmid28594574, year = {2017}, author = {Lipner, EM and Knox, D and French, J and Rudman, J and Strong, M and Crooks, JL}, title = {A Geospatial Epidemiologic Analysis of Nontuberculous Mycobacterial Infection: An Ecological Study in Colorado.}, journal = {Annals of the American Thoracic Society}, volume = {14}, number = {10}, pages = {1523-1532}, pmid = {28594574}, issn = {2325-6621}, support = {R01 CA157528/CA/NCI NIH HHS/United States ; T15 LM009451/LM/NLM NIH HHS/United States ; }, mesh = {Aged ; Aged, 80 and over ; Bayes Theorem ; Colorado/epidemiology ; Databases, Factual ; Environmental Exposure ; Female ; Humans ; Middle Aged ; Multivariate Analysis ; Mycobacterium Infections, Nontuberculous/*epidemiology ; Nontuberculous Mycobacteria/*isolation & purification ; Risk Factors ; Socioeconomic Factors ; Soil ; *Water Supply ; }, abstract = {RATIONALE: Nontuberculous mycobacteria (NTM) are ubiquitous environmental microorganisms. Infection is thought to result primarily from exposure to soil and/or water sources. NTM disease prevalence varies greatly by geographic region, but the geospatial factors influencing this variation remain unclear.

OBJECTIVES: To identify sociodemographic and environmental ecological risk factors associated with NTM infection and disease in Colorado.

METHODS: We conducted an ecological study, combining data from patients with a diagnosis of NTM disease from National Jewish Health's electronic medical record database and ZIP code-level sociodemographic and environmental exposure data obtained from the U.S. Geological Survey, the U.S. Department of Agriculture, and the U.S. Census Bureau. We used spatial scan methods to identify high-risk clusters of NTM disease in Colorado. Ecological risk factors for disease were assessed using Bayesian generalized linear models assuming Poisson-distributed discrete responses (case counts by ZIP code) with the log link function.

RESULTS: We identified two statistically significant high-risk clusters of disease. The primary cluster included ZIP codes in urban regions of Denver and Aurora, as well as regions south of Denver, on the east side of the Continental Divide. The secondary cluster was located on the west side of the Continental Divide in rural and mountainous regions. After adjustment for sociodemographic, drive time, and soil variables, we identified three watershed areas with relative risks of 12.2, 4.6, and 4.2 for slowly growing NTM infections compared with the mean disease risk for all watersheds in Colorado. This study population carries with it inherent limitations that may introduce bias. The lack of complete capture of NTM cases in Colorado may be related to factors such as disease severity, education and income levels, and insurance status.

CONCLUSIONS: Our findings provide evidence that water derived from particular watersheds may be an important source of NTM exposure in Colorado. The watershed with the greatest risk of NTM disease contains the Dillon Reservoir. This reservoir is also the main water supply for major cities located in the two watersheds with the second and third highest disease risk in the state, suggesting an important possible source of infection.}, } @article {pmid28593561, year = {2017}, author = {Mogaji, KA and Lim, HS}, title = {Application of a GIS-/remote sensing-based approach for predicting groundwater potential zones using a multi-criteria data mining methodology.}, journal = {Environmental monitoring and assessment}, volume = {189}, number = {7}, pages = {321}, pmid = {28593561}, issn = {1573-2959}, mesh = {*Data Mining ; Environmental Monitoring/*methods ; *Geographic Information Systems ; Groundwater/*analysis ; Hydrology ; Malaysia ; Models, Theoretical ; *Remote Sensing Technology ; }, abstract = {This study integrates the application of Dempster-Shafer-driven evidential belief function (DS-EBF) methodology with remote sensing and geographic information system techniques to analyze surface and subsurface data sets for the spatial prediction of groundwater potential in Perak Province, Malaysia. The study used additional data obtained from the records of the groundwater yield rate of approximately 28 bore well locations. The processed surface and subsurface data produced sets of groundwater potential conditioning factors (GPCFs) from which multiple surface hydrologic and subsurface hydrogeologic parameter thematic maps were generated. The bore well location inventories were partitioned randomly into a ratio of 70% (19 wells) for model training to 30% (9 wells) for model testing. Application results of the DS-EBF relationship model algorithms of the surface- and subsurface-based GPCF thematic maps and the bore well locations produced two groundwater potential prediction (GPP) maps based on surface hydrologic and subsurface hydrogeologic characteristics which established that more than 60% of the study area falling within the moderate-high groundwater potential zones and less than 35% falling within the low potential zones. The estimated uncertainty values within the range of 0 to 17% for the predicted potential zones were quantified using the uncertainty algorithm of the model. The validation results of the GPP maps using relative operating characteristic curve method yielded 80 and 68% success rates and 89 and 53% prediction rates for the subsurface hydrogeologic factor (SUHF)- and surface hydrologic factor (SHF)-based GPP maps, respectively. The study results revealed that the SUHF-based GPP map accurately delineated groundwater potential zones better than the SHF-based GPP map. However, significant information on the low degree of uncertainty of the predicted potential zones established the suitability of the two GPP maps for future development of groundwater resources in the area. The overall results proved the efficacy of the data mining model and the geospatial technology in groundwater potential mapping.}, } @article {pmid28593441, year = {2017}, author = {Preston, KL and Kowalczyk, WJ and Phillips, KA and Jobes, ML and Vahabzadeh, M and Lin, JL and Mezghanni, M and Epstein, DH}, title = {Context and craving during stressful events in the daily lives of drug-dependent patients.}, journal = {Psychopharmacology}, volume = {234}, number = {17}, pages = {2631-2642}, pmid = {28593441}, issn = {1432-2072}, support = {ZIA DA000499-10//Intramural NIH HHS/United States ; ZIA DA000536-10//Intramural NIH HHS/United States ; Z01 DA000499//NIH NIDA Intramural Research Program/ ; }, mesh = {Adult ; Affect ; Buprenorphine/therapeutic use ; Craving/*physiology ; Female ; Humans ; Male ; Methadone/therapeutic use ; Middle Aged ; Narcotics/therapeutic use ; *Opiate Substitution Treatment ; Opioid-Related Disorders/drug therapy/*psychology ; Outpatients ; Smartphone ; Stress, Psychological/*psychology ; }, abstract = {RATIONALE: Knowing how stress manifests in the lives of people with substance-use disorders could help inform mobile "just in time" treatment.

OBJECTIVES: The purpose of this paper is to examine discrete episodes of stress, as distinct from the fluctuations in background stress assessed in most EMA studies.

METHODS: For up to 16 weeks, outpatients on opioid-agonist treatment carried smartphones on which they initiated an entry whenever they experienced a stressful event (SE) and when randomly prompted (RP) three times daily. Participants reported the severity of stress and craving and the context of the report (location, activities, companions). Decomposition of covariance was used to separate within-person from between-person effects; r effect sizes below are within-person.

RESULTS: Participants (158 of 182; 87%) made 1787 stress-event entries. Craving for opioids increased with stress severity (r effect = 0.50). Stress events tended to occur in social company (with acquaintances, 0.63, friends, 0.17, or on the phone, 0.41) rather than with family (spouse, -0.14; child, -0.18), and in places with more overall activity (bars, 0.32; outside, 0.28; walking, 0.28) and more likelihood of unexpected experiences (with strangers, 0.17). Being on the internet was slightly protective (-0.22). Our prior finding that being at the workplace protects against background stress in our participants was partly supported in these stressful-event data.

CONCLUSIONS: The contexts of specific stressful events differ from those we have seen in prior studies of ongoing background stress. However, both are associated with drug craving.}, } @article {pmid28592898, year = {2017}, author = {Li, J and Xu, B and Yang, X and Qin, Z and Zhao, L and Jin, Y and Zhao, F and Guo, J}, title = {Historical grassland desertification changes in the Horqin Sandy Land, Northern China (1985-2013).}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {3009}, pmid = {28592898}, issn = {2045-2322}, abstract = {Since rural reforms in the 1980s, both the state and local governments of China have devoted great efforts to combating desertification through a number of eco-environmental restoration campaigns, resulting in burgeoning contention at all levels of government and sparking public concern. Monitoring and accurately assessing the statuses and trends of grassland desertification are important for developing effective restoration strategies. The Horqin Sandy Land (HSL), a very typical desertified grassland (DG) with better hydrothermal conditions among sandy lands in north China, was recently selected (1985-2013) to assess the spatiotemporal dynamic performances of grassland desertification before and after implementing restoration projects. Landsat images (TM/ETM+/OLI), field investigations and expert review were integrated to form a classification scheme for the HSL. Then, spectral mixture analysis and the decision-tree method were used to extract bare-sand ratios and vegetation cover fraction dynamics. A favourable phenomenon of DG was seen to be reversed in an accelerated pace during 2001-2013, despite challenge from both climatic and anthropogenic factors. However, overexploitation of grassland (especially for farming) and ground water for irrigation has led to remarkable decreases in the ground water level in recent decades, which should be highly concerning regarding the formulation of restoration campaigns in the sandy land.}, } @article {pmid28592872, year = {2017}, author = {Hu, YW and Wu, XM and Ren, SS and Cao, L and Nie, P and Chang, MX}, title = {NOD1 deficiency impairs CD44a/Lck as well as PI3K/Akt pathway.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {2979}, pmid = {28592872}, issn = {2045-2322}, mesh = {Animals ; Animals, Genetically Modified ; Base Sequence ; CRISPR-Associated Protein 9/metabolism ; Computational Biology/methods ; Gene Expression ; Gene Expression Profiling ; Gene Knockout Techniques ; Genes, MHC Class I ; Histocompatibility Antigens Class II/genetics ; Hyaluronan Receptors/genetics/*metabolism ; Immune System/immunology/metabolism ; Larva ; Models, Biological ; Nod1 Signaling Adaptor Protein/*deficiency ; Phosphatidylinositol 3-Kinases/*metabolism ; Proto-Oncogene Proteins c-akt/*metabolism ; *Signal Transduction ; Zebrafish ; RNA, Guide, CRISPR-Cas Systems ; }, abstract = {Pattern recognition receptors (PRRs) are crucial for host defense and tissue homeostasis against infecting pathogens. PRRs are highly conserved cross species, suggesting their key roles in fundamental biological processes. Though much have been learned for NOD1 receptor in the innate and adaptive immune responses, the roles of NOD1 during embryonic and larval stages remain poorly understood. Here, we report that NOD1 is necessary for the modulation of PI3K-Akt pathway and larval survival in zebrafish. Transcriptome analysis revealed that the significantly enriched pathways in NOD1 [-/-] zebrafish larvae were mainly involved in metabolism and immune system processes. Biochemical analysis demonstrated that NOD1 was required for the expression of CD44a that, in turn, activated the PI3K-Akt pathway during larval development. Conversely, over-expression of CD44a in NOD1-deficient zebrafish restored the modulation of the PI3K-Akt pathway and improved larval survival. Collectively, our work indicates that NOD1 plays a previously undetected protective role in larval survival through CD44a-mediated activation of the PI3K-Akt signaling.}, } @article {pmid28592651, year = {2017}, author = {Cubillos, FA and Brice, C and Molinet, J and Tisné, S and Abarca, V and Tapia, SM and Oporto, C and García, V and Liti, G and Martínez, C}, title = {Identification of Nitrogen Consumption Genetic Variants in Yeast Through QTL Mapping and Bulk Segregant RNA-Seq Analyses.}, journal = {G3 (Bethesda, Md.)}, volume = {7}, number = {6}, pages = {1693-1705}, pmid = {28592651}, issn = {2160-1836}, mesh = {*Chromosome Mapping ; Computational Biology/methods ; Fermentation ; Gene Expression Profiling ; *Genetic Association Studies ; *Genetic Variation ; Genome, Fungal ; Genomics/methods ; High-Throughput Nucleotide Sequencing ; Nitrogen/*metabolism ; Polymorphism, Single Nucleotide ; *Quantitative Trait Loci ; Reproducibility of Results ; Saccharomyces cerevisiae/genetics/metabolism ; Sequence Analysis, RNA ; Yeasts/*genetics/*metabolism ; }, abstract = {Saccharomyces cerevisiae is responsible for wine must fermentation. In this process, nitrogen represents a limiting nutrient and its scarcity results in important economic losses for the wine industry. Yeast isolates use different strategies to grow in poor nitrogen environments and their genomic plasticity enables adaptation to multiple habitats through improvements in nitrogen consumption. Here, we used a highly recombinant S. cerevisiae multi-parent population (SGRP-4X) derived from the intercross of four parental strains of different origins to identify new genetic variants responsible for nitrogen consumption differences during wine fermentation. Analysis of 165 fully sequenced F12 segregants allowed us to map 26 QTL in narrow intervals for 14 amino acid sources and ammonium, the majority of which represent genomic regions previously unmapped for these traits. To complement this strategy, we performed Bulk segregant RNA-seq (BSR-seq) analysis in segregants exhibiting extremely high and low ammonium consumption levels. This identified several QTL overlapping differentially expressed genes and refined the gene candidate search. Based on these approaches, we were able to validate ARO1, PDC1, CPS1, ASI2, LYP1, and ALP1 allelic variants underlying nitrogen consumption differences between strains, providing evidence of many genes with small phenotypic effects. Altogether, these variants significantly shape yeast nitrogen consumption with important implications for evolution, ecological, and quantitative genomics.}, } @article {pmid28592647, year = {2017}, author = {King, EG and Long, AD}, title = {The Beavis Effect in Next-Generation Mapping Panels in Drosophila melanogaster.}, journal = {G3 (Bethesda, Md.)}, volume = {7}, number = {6}, pages = {1643-1652}, pmid = {28592647}, issn = {2160-1836}, support = {F32 GM099382/GM/NIGMS NIH HHS/United States ; R01 GM115562/GM/NIGMS NIH HHS/United States ; R01 GM117135/GM/NIGMS NIH HHS/United States ; R01 OD010974/OD/NIH HHS/United States ; }, mesh = {Algorithms ; Animals ; *Chromosome Mapping ; Computer Simulation ; Databases, Genetic ; Drosophila melanogaster/*genetics ; Genetic Association Studies ; Genetic Variation ; Genetics, Population ; *Genome-Wide Association Study ; Models, Genetic ; Phenotype ; *Quantitative Trait Loci ; Quantitative Trait, Heritable ; Reproducibility of Results ; Web Browser ; }, abstract = {A major goal in the analysis of complex traits is to partition the observed genetic variation in a trait into components due to individual loci and perhaps variants within those loci. However, in both QTL mapping and genetic association studies, the estimated percent variation attributable to a QTL is upwardly biased conditional on it being discovered. This bias was first described in two-way QTL mapping experiments by William Beavis, and has been referred to extensively as "the Beavis effect." The Beavis effect is likely to occur in multiparent population (MPP) panels as well as collections of sequenced lines used for genome-wide association studies (GWAS). However, the strength of the Beavis effect is unknown-and often implicitly assumed to be negligible-when "hits" are obtained from an association panel consisting of hundreds of inbred lines tested across millions of SNPs, or in multiparent mapping populations where mapping involves fitting a complex statistical model with several d.f. at thousands of genetic intervals. To estimate the size of the effect in more complex panels, we performed simulations of both biallelic and multiallelic QTL in two major Drosophila melanogaster mapping panels, the GWAS-based Drosophila Genetic Reference Panel (DGRP), and the MPP the Drosophila Synthetic Population Resource (DSPR). Our results show that overestimation is determined most strongly by sample size and is only minimally impacted by the mapping design. When < 100, 200, 500, and 1000 lines are employed, the variance attributable to hits is inflated by factors of 6, 3, 1.5, and 1.1, respectively, for a QTL that truly contributes 5% to the variation in the trait. This overestimation indicates that QTL could be difficult to validate in follow-up replication experiments where additional individuals are examined. Further, QTL could be difficult to cross-validate between the two Drosophila resources. We provide guidelines for: (1) the sample sizes necessary to accurately estimate the percent variance to an identified QTL, (2) the conditions under which one is likely to replicate a mapped QTL in a second study using the same mapping population, and (3) the conditions under which a QTL mapped in one mapping panel is likely to replicate in the other (DGRP and DSPR).}, } @article {pmid28591181, year = {2017}, author = {Hernández-Pliego, J and Rodríguez, C and Dell'Omo, G and Bustamante, J}, title = {Combined use of tri-axial accelerometers and GPS reveals the flexible foraging strategy of a bird in relation to weather conditions.}, journal = {PloS one}, volume = {12}, number = {6}, pages = {e0177892}, pmid = {28591181}, issn = {1932-6203}, mesh = {Accelerometry ; Animal Migration/*physiology ; Animals ; Birds/*physiology ; Energy Metabolism/physiology ; Flight, Animal/*physiology ; Geographic Information Systems ; *Weather ; }, abstract = {Tri-axial accelerometry has proved to be a useful technique to study animal behavior with little direct observation, and also an effective way to measure energy expenditure, allowing a refreshing revisit to optimal foraging theory. This theory predicts that individuals should gain the most energy for the lowest cost in terms of time and energy when foraging, in order to maximize their fitness. However, during a foraging trip, central-place foragers could face different trade-offs during the commuting and searching parts of the trip, influencing behavioral decisions. Using the lesser kestrel (Falco naumanni) as an example we study the time and energy costs of different behaviors during the commuting and searching parts of a foraging trip. Lesser kestrels are small insectivorous falcons that behave as central-place foragers during the breeding season. They can commute by adopting either time-saving flapping flights or energy-saving soaring-gliding flights, and capture prey by using either time-saving active hovering flights or energy-saving perch-hunting. We tracked 6 lesser kestrels using GPS and tri-axial accelerometers during the breeding season. Our results indicate that males devoted more time and energy to flight behaviors than females in agreement with being the sex responsible for food provisioning to the nest. During the commuting flights, kestrels replaced flapping with soaring-gliding flights as solar radiation increased and thermal updrafts got stronger. In the searching part, they replaced perch-hunting with hovering as wind speed increased and they experienced a stronger lift. But also, they increased the use of hovering as air temperature increased, which has a positive influence on the activity level of the preferred prey (large grasshoppers). Kestrels maintained a constant energy expenditure per foraging trip, although flight and hunting strategies changed dramatically with weather conditions, suggesting a fixed energy budget per trip to which they adjusted their commuting and searching strategies in response to weather conditions.}, } @article {pmid28590455, year = {2017}, author = {Lötsch, J and Thrun, M and Lerch, F and Brunkhorst, R and Schiffmann, S and Thomas, D and Tegder, I and Geisslinger, G and Ultsch, A}, title = {Machine-Learned Data Structures of Lipid Marker Serum Concentrations in Multiple Sclerosis Patients Differ from Those in Healthy Subjects.}, journal = {International journal of molecular sciences}, volume = {18}, number = {6}, pages = {}, pmid = {28590455}, issn = {1422-0067}, mesh = {Biomarkers ; Case-Control Studies ; Ceramides/blood ; Eicosanoids/blood ; Humans ; Informatics/methods ; *Lipid Metabolism ; Lipids/*blood ; Lysophospholipids/blood ; *Machine Learning ; Multiple Sclerosis/*blood ; }, abstract = {Lipid metabolism has been suggested to be a major pathophysiological mechanism of multiple sclerosis (MS). With the increasing knowledge about lipid signaling, acquired data become increasingly complex making bioinformatics necessary in lipid research. We used unsupervised machine-learning to analyze lipid marker serum concentrations, pursuing the hypothesis that for the most relevant markers the emerging data structures will coincide with the diagnosis of MS. Machine learning was implemented as emergent self-organizing feature maps (ESOM) combined with the U*-matrix visualization technique. The data space consisted of serum concentrations of three main classes of lipid markers comprising eicosanoids (d = 11 markers), ceramides (d = 10), and lyosophosphatidic acids (d = 6). They were analyzed in cohorts of MS patients (n = 102) and healthy subjects (n = 301). Clear data structures in the high-dimensional data space were observed in eicosanoid and ceramides serum concentrations whereas no clear structure could be found in lysophosphatidic acid concentrations. With ceramide concentrations, the structures that had emerged from unsupervised machine-learning almost completely overlapped with the known grouping of MS patients versus healthy subjects. This was only partly provided by eicosanoid serum concentrations. Thus, unsupervised machine-learning identified distinct data structures of bioactive lipid serum concentrations. These structures could be superimposed with the known grouping of MS patients versus healthy subjects, which was almost completely possible with ceramides. Therefore, based on the present analysis, ceramides are first-line candidates for further exploration as drug-gable targets or biomarkers in MS.}, } @article {pmid28587157, year = {2017}, author = {Jiang, C and Zhang, SB and Zhang, QZ}, title = {Adaptive Estimation of Multiple Fading Factors for GPS/INS Integrated Navigation Systems.}, journal = {Sensors (Basel, Switzerland)}, volume = {17}, number = {6}, pages = {}, pmid = {28587157}, issn = {1424-8220}, abstract = {The Kalman filter has been widely applied in the field of dynamic navigation and positioning. However, its performance will be degraded in the presence of significant model errors and uncertain interferences. In the literature, the fading filter was proposed to control the influences of the model errors, and the H-infinity filter can be adopted to address the uncertainties by minimizing the estimation error in the worst case. In this paper, a new multiple fading factor, suitable for the Global Positioning System (GPS) and the Inertial Navigation System (INS) integrated navigation system, is proposed based on the optimization of the filter, and a comprehensive filtering algorithm is constructed by integrating the advantages of the H-infinity filter and the proposed multiple fading filter. Measurement data of the GPS/INS integrated navigation system are collected under actual conditions. Stability and robustness of the proposed filtering algorithm are tested with various experiments and contrastive analysis are performed with the measurement data. Results demonstrate that both the filter divergence and the influences of outliers are restrained effectively with the proposed filtering algorithm, and precision of the filtering results are improved simultaneously.}, } @article {pmid28586475, year = {2017}, author = {York Cornwell, E and Cagney, KA}, title = {Aging in Activity Space: Results From Smartphone-Based GPS-Tracking of Urban Seniors.}, journal = {The journals of gerontology. Series B, Psychological sciences and social sciences}, volume = {72}, number = {5}, pages = {864-875}, pmid = {28586475}, issn = {1758-5368}, support = {R01 AG050605/AG/NIA NIH HHS/United States ; }, mesh = {Age Factors ; Aged ; Aged, 80 and over ; Aging/*psychology ; Female ; Geographic Information Systems/*statistics & numerical data ; Humans ; Male ; Middle Aged ; New York City ; Personal Satisfaction ; *Residence Characteristics ; Sex Factors ; Smartphone/*statistics & numerical data ; Social Environment ; Urban Population/*statistics & numerical data ; Utilization Review ; }, abstract = {OBJECTIVES: Prior research emphasizes the importance of the residential neighborhood context during later life but little attention has been afforded to other areas that older adults encounter as they move beyond their residential environments for daily activities and social interactions. This study examines the predominance of the residential context within older adults' everyday lives.

METHOD: We provided 60 older adults in four New York City neighborhoods with iPhones, which captured Global Positioning Systems (GPS) locations at 5-min intervals over 1 week (n = 55,561) and 17 ecological momentary assessments (EMAs) over 4 days (n = 757) to assess real-time activities.

RESULTS: Older adults in our sample spent nearly 40% of their time outside of their residential tracts and they visited 28 other tracts, on average. Exercising, shopping, socializing, and social activities were especially likely to take place outside of residential tracts. Differences in residential and nonresidential poverty exposure vary across gender, race/ethnicity, education, car ownership, and residential areas.

DISCUSSION: Measuring activity space, rather than relying on residential tracts, allows examination of the social environments that are relevant for older adults' everyday lives. Variation in characteristics of activity spaces may be an underexplored source of differences in health and well-being during later life.}, } @article {pmid28585533, year = {2017}, author = {Zhou, J and Deng, Y and Shen, L and Wen, C and Yan, Q and Ning, D and Qin, Y and Xue, K and Wu, L and He, Z and Voordeckers, JW and Van Nostrand, JD and Buzzard, V and Michaletz, ST and Enquist, BJ and Weiser, MD and Kaspari, M and Waide, R and Yang, Y and Brown, JH}, title = {Correspondence: Reply to 'Analytical flaws in a continental-scale forest soil microbial diversity study'.}, journal = {Nature communications}, volume = {8}, number = {}, pages = {15583}, pmid = {28585533}, issn = {2041-1723}, mesh = {Bacteria/classification/isolation & purification ; *Biodiversity ; *Data Interpretation, Statistical ; Fungi/classification/isolation & purification ; North America ; Soil ; *Soil Microbiology ; *Temperature ; }, } @article {pmid28584342, year = {2017}, author = {Hampton, SE and Jones, MB and Wasser, LA and Schildhauer, MP and Supp, SR and Brun, J and Hernandez, RR and Boettiger, C and Collins, SL and Gross, LJ and Fernández, DS and Budden, A and White, EP and Teal, TK and Labou, SG and Aukema, JE}, title = {Skills and Knowledge for Data-Intensive Environmental Research.}, journal = {Bioscience}, volume = {67}, number = {6}, pages = {546-557}, pmid = {28584342}, issn = {0006-3568}, abstract = {The scale and magnitude of complex and pressing environmental issues lend urgency to the need for integrative and reproducible analysis and synthesis, facilitated by data-intensive research approaches. However, the recent pace of technological change has been such that appropriate skills to accomplish data-intensive research are lacking among environmental scientists, who more than ever need greater access to training and mentorship in computational skills. Here, we provide a roadmap for raising data competencies of current and next-generation environmental researchers by describing the concepts and skills needed for effectively engaging with the heterogeneous, distributed, and rapidly growing volumes of available data. We articulate five key skills: (1) data management and processing, (2) analysis, (3) software skills for science, (4) visualization, and (5) communication methods for collaboration and dissemination. We provide an overview of the current suite of training initiatives available to environmental scientists and models for closing the skill-transfer gap.}, } @article {pmid28574420, year = {2017}, author = {Maat, DS and Biggs, T and Evans, C and van Bleijswijk, JDL and van der Wel, NN and Dutilh, BE and Brussaard, CPD}, title = {Characterization and Temperature Dependence of Arctic Micromonas polaris Viruses.}, journal = {Viruses}, volume = {9}, number = {6}, pages = {}, pmid = {28574420}, issn = {1999-4915}, mesh = {Arctic Regions ; Chlorophyta/*virology ; DNA, Viral/genetics ; Phycodnaviridae/genetics/*physiology/*radiation effects ; Temperature ; Virus Replication/*radiation effects ; }, abstract = {Global climate change-induced warming of the Artic seas is predicted to shift the phytoplankton community towards dominance of smaller-sized species due to global warming. Yet, little is known about their viral mortality agents despite the ecological importance of viruses regulating phytoplankton host dynamics and diversity. Here we report the isolation and basic characterization of four prasinoviruses infectious to the common Arctic picophytoplankter Micromonas. We furthermore assessed how temperature influenced viral infectivity and production. Phylogenetic analysis indicated that the putative double-stranded DNA (dsDNA) Micromonas polaris viruses (MpoVs) are prasinoviruses (Phycodnaviridae) of approximately 120 nm in particle size. One MpoV showed intrinsic differences to the other three viruses, i.e., larger genome size (205 ± 2 vs. 191 ± 3 Kb), broader host range, and longer latent period (39 vs. 18 h). Temperature increase shortened the latent periods (up to 50%), increased the burst size (up to 40%), and affected viral infectivity. However, the variability in response to temperature was high for the different viruses and host strains assessed, likely affecting the Arctic picoeukaryote community structure both in the short term (seasonal cycles) and long term (global warming).}, } @article {pmid28570562, year = {2017}, author = {Nagaya, N and Mizumoto, N and Abe, MS and Dobata, S and Sato, R and Fujisawa, R}, title = {Anomalous diffusion on the servosphere: A potential tool for detecting inherent organismal movement patterns.}, journal = {PloS one}, volume = {12}, number = {6}, pages = {e0177480}, pmid = {28570562}, issn = {1932-6203}, mesh = {Animals ; Diffusion ; Insecta/*physiology ; *Locomotion ; }, abstract = {Tracking animal movements such as walking is an essential task for understanding how and why animals move in an environment and respond to external stimuli. Different methods that implemented image analysis and a data logger such as GPS have been used in laboratory experiments and in field studies, respectively. Recently, animal movement patterns without stimuli have attracted an increasing attention in search for common innate characteristics underlying all of their movements. However, it is difficult to track the movements in a vast and homogeneous environment without stimuli because of space constraints in laboratories or environmental heterogeneity in the field, hindering our understanding of inherent movement patterns. Here, we applied an omnidirectional treadmill mechanism, or a servosphere, as a tool for tracking two-dimensional movements of small animals that can provide both a homogenous environment and a virtual infinite space for walking. To validate the use of our tracking system for assessment of the free-walking behavior, we compared walking patterns of individual pillbugs (Armadillidium vulgare) on the servosphere with that in two types of experimental flat arenas. Our results revealed that the walking patterns on the servosphere showed similar diffusive characteristics to those observed in the large arena simulating an open space, and we demonstrated that our mechanism provides more robust measurements of diffusive properties compared to a small arena with enclosure. Moreover, we showed that anomalous diffusion properties, including Lévy walk, can be detected from the free-walking behavior on our tracking system. Thus, our novel tracking system is useful to measure inherent movement patterns, which will contribute to the studies of movement ecology, ethology, and behavioral sciences.}, } @article {pmid28569825, year = {2017}, author = {Cernansky, R}, title = {Biodiversity moves beyond counting species.}, journal = {Nature}, volume = {546}, number = {7656}, pages = {22-24}, doi = {10.1038/546022a}, pmid = {28569825}, issn = {1476-4687}, mesh = {Animals ; Anthozoa/anatomy & histology/physiology ; Bias ; *Biodiversity ; Body Size ; Climate Change ; Conservation of Natural Resources/*methods ; Coral Reefs ; Databases, Factual ; Ecology/*methods ; Environmental Policy/trends ; Fishes/anatomy & histology/physiology ; Forests ; *Models, Biological ; Nitrogen Fixation/physiology ; *Phenotype ; Photosynthesis/physiology ; Policy Making ; Soil Microbiology ; Species Specificity ; }, } @article {pmid28562826, year = {2017}, author = {Mormul, RP and Mormul, TDS and Santos, GMB and Santana, ARA}, title = {Looking for attitudes related to amphibian species decline: how are peer-reviewed publications of education activities compared to ecological research?.}, journal = {Anais da Academia Brasileira de Ciencias}, volume = {89}, number = {1 Suppl 0}, pages = {491-496}, doi = {10.1590/0001-3765201720160463}, pmid = {28562826}, issn = {1678-2690}, mesh = {*Amphibians ; Animals ; *Bibliometrics ; Databases, Bibliographic ; Ecology/statistics & numerical data ; Extinction, Biological ; Humans ; *Peer Review, Research/trends ; Periodicals as Topic ; }, abstract = {Biodiversity decline has been the focus of discussions in the last decade, especially on the amphibian species decline. After a scientometric analysis using international databases, we found that the number of peer-reviewed articles considering education practices related to the theme increased along with the number of ecological researches. However, the increase in ecological researches is much higher than the increase in publications of education practices. Studies suggest that conservation attitudes are important and that education practices are an important tool for improving human perceptions on this subject. In this sense, increase the publication of projects and programs results related to local education practices in international journals could help the dissemination of efficient methods for conservation, as well as facilitating access to information internationally, since species decline, especially for amphibians, is a global concern. Then, we suggest that educational practices, at least when related to conservation, should follow a more standardized protocol, and be published in international journals, as the efficiency of such practices should be evaluated and methods once published could help other nations to improve their ecological literacy.}, } @article {pmid28562172, year = {2017}, author = {Rădulescu, AR and Hannon, ER}, title = {Applying fMRI complexity analyses to the single subject: a case study for proposed neurodiagnostics.}, journal = {Neurocase}, volume = {23}, number = {2}, pages = {120-137}, doi = {10.1080/13554794.2017.1316410}, pmid = {28562172}, issn = {1465-3656}, mesh = {Acoustic Stimulation ; Brain/*diagnostic imaging ; *Brain Mapping ; Datasets as Topic ; Humans ; Image Processing, Computer-Assisted ; Magnetic Resonance Imaging/*methods ; Neural Pathways/*diagnostic imaging/physiology ; Nonlinear Dynamics ; Oxygen/blood ; Photic Stimulation ; Stress, Psychological/*diagnostic imaging ; Systems Analysis ; Time Factors ; }, abstract = {Nonlinear dynamic tools have been statistically validated at the group level to identify subtle differences in system wide regulation of brain meso-circuits, often increasing clinical sensitivity over conventional analyses alone. We explored the feasibility of extracting information at the single-subject level, illustrating two pairs of healthy individuals with psychological differences in stress reactivity. We applied statistical and nonlinear dynamic tools to capture key characteristics of the prefrontal-limbic loop. We compared single subject results with statistical results for the larger group. We concluded that complexity analyses may identify important differences at the single-subject level, supporting their potential towards neurodiagnostic applications.}, } @article {pmid28560604, year = {2017}, author = {Yun, J and Deng, Y and Zhang, H}, title = {Anthropogenic protection alters the microbiome in intertidal mangrove wetlands in Hainan Island.}, journal = {Applied microbiology and biotechnology}, volume = {101}, number = {15}, pages = {6241-6252}, doi = {10.1007/s00253-017-8342-1}, pmid = {28560604}, issn = {1432-0614}, mesh = {China ; Computational Biology ; High-Throughput Nucleotide Sequencing ; Islands ; Microbiota/genetics/*physiology ; Plant Roots/microbiology ; Proteobacteria/genetics/isolation & purification ; *Soil Microbiology ; Verrucomicrobia/genetics/isolation & purification ; *Wetlands ; }, abstract = {Intertidal mangrove wetlands are of great economic and ecological importance. The regular influence of tides has led to the microbial communities in these wetlands differing significantly from those in other habitats. In this study, we investigated the microbiomes of the two largest mangrove wetlands in Hainan Island, China, which have different levels of anthropogenic protection. Soil samples were collected from the root zone of 13 mangrove species. The microbial composition, including key functional groups, was assessed using Illumina sequencing. Bioinformatics analysis showed that there was a significant difference in the microbiomes between the protected Bamen Bay and the unprotected Dongzhai Bay. The overall microbiome was assigned into 78 phyla and Proteobacteria was the most abundant phylum at both sites. In the protected wetland, there were fewer marine-related microbial communities, such as sulfate-reducing bacteria, and more terrestrial-related communities, such as Verrucomicrobia methanotrophs. We also observed distinct microbial compositions among the different mangrove species at the protected site. Our data suggest that the different microbiomes of the two mangrove wetlands are the result of a complex interaction of the different environmental variables at the two sites.}, } @article {pmid28559162, year = {2017}, author = {Wang, Q and Zhao, XJ and Wang, ZW and Liu, L and Wei, YX and Han, X and Zeng, J and Liao, WJ}, title = {Identification of Cronobacter species by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry with an optimized analysis method.}, journal = {Journal of microbiological methods}, volume = {139}, number = {}, pages = {172-180}, doi = {10.1016/j.mimet.2017.05.016}, pmid = {28559162}, issn = {1872-8359}, mesh = {Bacterial Typing Techniques/*methods ; Cluster Analysis ; Cronobacter/classification/genetics/*isolation & purification ; DNA, Bacterial/genetics ; Databases, Genetic ; Food Microbiology ; Humans ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Software ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/*methods ; Statistics as Topic/methods ; }, abstract = {Rapid and precise identification of Cronobacter species is important for foodborne pathogen detection, however, commercial biochemical methods can only identify Cronobacter strains to genus level in most cases. To evaluate the power of mass spectrometry based on matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF MS) for Cronobacter species identification, 51 Cronobacter strains (eight reference and 43 wild strains) were identified by both MALDI-TOF MS and 16S rRNA gene sequencing. Biotyper RTC provided by Bruker identified all eight reference and 43 wild strains as Cronobacter species, which demonstrated the power of MALDI-TOF MS to identify Cronobacter strains to genus level. However, using the Bruker's database (6903 main spectra products) and Biotyper software, the MALDI-TOF MS analysis could not identify the investigated strains to species level. When MALDI-TOF MS analysis was performed using the combined in-house Cronobacter database and Bruker's database, bin setting, and unweighted pair group method with arithmetic mean (UPGMA) clustering, all the 51 strains were clearly identified into six Cronobacter species and the identification accuracy increased from 60% to 100%. We demonstrated that MALDI-TOF MS was reliable and easy-to-use for Cronobacter species identification and highlighted the importance of establishing a reliable database and improving the current data analysis methods by integrating the bin setting and UPGMA clustering.}, } @article {pmid28555474, year = {2017}, author = {Mlacha, YP and Chaki, PP and Malishee, AD and Mwakalinga, VM and Govella, NJ and Limwagu, AJ and Paliga, JM and Msellemu, DF and Mageni, ZD and Terlouw, DJ and Killeen, GF and Dongus, S}, title = {Fine scale mapping of malaria infection clusters by using routinely collected health facility data in urban Dar es Salaam, Tanzania.}, journal = {Geospatial health}, volume = {12}, number = {1}, pages = {494}, doi = {10.4081/gh.2017.494}, pmid = {28555474}, issn = {1970-7096}, support = {096358/Z/11/Z//Wellcome Trust/United Kingdom ; }, mesh = {Geographic Information Systems ; Health Facilities/*statistics & numerical data ; Humans ; Malaria/*epidemiology/*transmission ; Prevalence ; Tanzania/epidemiology ; }, abstract = {This study investigated whether passively collected routine health facility data can be used for mapping spatial heterogeneities in malaria transmission at the level of local government housing cluster administrative units in Dar es Salaam, Tanzania. From June 2012 to January 2013, residential locations of patients tested for malaria at a public health facility were traced based on their local leaders' names and geo-referencing the point locations of these leaders' houses. Geographic information systems (GIS) were used to visualise the spatial distribution of malaria infection rates. Spatial scan statistics was deployed to detect spatial clustering of high infection rates. Among 2407 patients tested for malaria, 46.6% (1121) could be traced to their 411 different residential housing clusters. One small spatially aggregated cluster of neighbourhoods with high prevalence was identified. While the home residence housing cluster leader was unambiguously identified for 73.8% (240/325) of malaria-positive patients, only 42.3% (881/2082) of those with negative test results were successfully traced. It was concluded that recording simple points of reference during routine health facility visits can be used for mapping malaria infection burden on very fine geographic scales, potentially offering a feasible approach to rational geographic targeting of malaria control interventions. However, in order to tap the full potential of this approach, it would be necessary to optimise patient tracing success and eliminate biases by blinding personnel to test results.}, } @article {pmid28554882, year = {2017}, author = {Kuate Defo, B and Mbanya, JC and Tardif, JC and Ekundayo, O and Perreault, S and Potvin, L and Cote, R and Kengne, AP and Choukem, SP and Assah, F and Kingue, S and Richard, L and Pongou, R and Frohlich, K and Saji, J and Fournier, P and Sobngwi, E and Ridde, V and Dubé, MP and De Denus, S and Mbacham, W and Lafrance, JP and Nsagha, DS and Mampuya, W and Dzudie, A and Cloutier, L and Zarowsky, C and Tanya, A and Ndom, P and Hatem, M and Rey, E and Roy, L and Borgès Da Silva, R and Dagenais, C and Todem, D and Weladji, R and Mbanya, D and Emami, E and Njoumemi, Z and Monnais, L and Dubois, CA}, title = {Diagnosis, Prevalence, Awareness, Treatment, Prevention, and Control of Hypertension in Cameroon: Protocol for a Systematic Review and Meta-Analysis of Clinic-Based and Community-Based Studies.}, journal = {JMIR research protocols}, volume = {6}, number = {5}, pages = {e102}, pmid = {28554882}, issn = {1929-0748}, abstract = {BACKGROUND: Hypertension holds a unique place in population health and health care because it is the leading cause of cardiovascular disease and the most common noncommunicable condition seen in primary care worldwide. Without effective prevention and control, raised blood pressure significantly increases the risk of stroke, myocardial infarction, chronic kidney disease, heart failure, dementia, renal failure, and blindness. There is an urgent need for stakeholders-including individuals and families-across the health system, researchers, and decision makers to work collaboratively for improving prevention, screening and detection, diagnosis and evaluation, awareness, treatment and medication adherence, management, and control for people with or at high risk for hypertension. Meeting this need will help reduce the burden of hypertension-related disease, prevent complications, and reduce the need for hospitalization, costly interventions, and premature deaths.

OBJECTIVE: This review aims to synthesize evidence on the epidemiological landscape and control of hypertension in Cameroon, and to identify elements that could potentially inform interventions to combat hypertension in this setting and elsewhere in sub-Saharan Africa.

METHODS: The full search process will involve several steps, including selecting relevant databases, keywords, and Medical Subject Headings (MeSH); searching for relevant studies from the selected databases; searching OpenGrey and the Grey Literature Report for gray literature; hand searching in Google Scholar; and soliciting missed publications (if any) from relevant authors. We will select qualitative, quantitative, or mixed-methods studies with data on the epidemiology and control of hypertension in Cameroon. We will include published literature in French or English from electronic databases up to December 31, 2016, and involving adults aged 18 years or older. Both facility and population-based studies on hypertension will be included. Two reviewers of the team will independently search, screen, extract data, and assess the quality of selected studies using suitable tools. Selected studies will be analyzed by narrative synthesis, meta-analysis, or both, depending on the nature of the data retrieved in line with the review objectives.

RESULTS: This review is part of an ongoing research program on disease prevention and control in the context of the dual burden of communicable and noncommunicable diseases in Africa. The first results are expected in 2017.

CONCLUSIONS: This review will provide a comprehensive assessment of the burden of hypertension and control measures that have been designed and implemented in Cameroon. Findings will form the knowledge base relevant to stakeholders across the health system and researchers who are involved in hypertension prevention and control in the community and clinic settings in Cameroon, as a yardstick for similar African countries.

TRIAL REGISTRATION: PROSPERO registration number: CRD42017054950; http://www.crd.york.ac.uk/PROSPERO/ display_record.asp?ID=CRD42017054950 (Archived by WebCite at http://www.webcitation.org/6qYSjt9Jc).}, } @article {pmid28552183, year = {2017}, author = {Padilla, O and Rosas, P and Moreno, W and Toulkeridis, T}, title = {Modeling of the ecological niches of the anopheles spp in Ecuador by the use of geo-informatic tools.}, journal = {Spatial and spatio-temporal epidemiology}, volume = {21}, number = {}, pages = {1-11}, doi = {10.1016/j.sste.2016.12.001}, pmid = {28552183}, issn = {1877-5853}, mesh = {Animals ; Anopheles/*growth & development ; Ecology/*statistics & numerical data ; *Ecosystem ; Ecuador ; Geographic Information Systems ; Geography ; *Insect Vectors ; Logistic Models ; Malaria/*transmission ; }, abstract = {Ecuador in the northwestern edge of South America is struggling by vector-borne diseases with an endemic-epidemic behavior leading to an enormous public health problem. Malaria, which has a cyclicality in its dynamics, is closely related to climatic, ecological and socio-economic phenomena. The main objective of this research has been to compare three different prediction species models, the so-called Maxent, logistic regression and multi criteria evaluation with fuzzy logic, in order to determine the model which best describes the ecological niche of the Anopheles spp species, which transmits malaria within Ecuador. After performing a detailed data collection and data processing, we applied the mentioned models and validated them with a statistical analysis in order to discover that the Maxent model has been the model that best defines the distribution of Anopheles spp within the territory. The determined sites, which are of high strategic value and important for the increasing national development, will now be able to initiate preventive countermeasures based on this study.}, } @article {pmid28547864, year = {2017}, author = {Meyer, F and Karch, A and Schlinkmann, KM and Dreesman, J and Horn, J and Rübsamen, N and Sudradjat, H and Schubert, R and Mikolajczyk, R}, title = {Sociodemographic determinants of spatial disparities in early childhood caries: An ecological analysis in Braunschweig, Germany.}, journal = {Community dentistry and oral epidemiology}, volume = {45}, number = {5}, pages = {442-448}, doi = {10.1111/cdoe.12308}, pmid = {28547864}, issn = {1600-0528}, mesh = {Child ; Child, Preschool ; DMF Index ; Dental Care for Children/*statistics & numerical data ; Dental Caries/*epidemiology ; Female ; Finite Element Analysis ; Germany/epidemiology ; *Health Status Disparities ; Humans ; Longitudinal Studies ; Male ; Risk Factors ; }, abstract = {OBJECTIVES: To identify spatial disparities in dental caries experience (measured by dmft (decayed missing filled teeth) index) of children in the city of Braunschweig and to evaluate whether these disparities can be explained by sociodemographic characteristics.

METHODS: We examined the dental health of children aged 3-6 years visiting a daycare centre (DCC) in the metropolitan area of Braunschweig between 2009 and 2014 by combining data on dental health from the annual visits of the local health service with aggregated data on sociodemographic factors for Braunschweig's city districts. We assessed longitudinal patterns of change in average dmft index at district level from 2009 to 2014 using a finite mixture model. We analysed spatial autocorrelation of the district's average dmft indices by Moran's I to identify spatial clusters. With a spatial lag model, we evaluated whether sociodemographic risk factors (data from 2012) were associated with high dmft scores (data from 2014) and whether spatial disparities remained after adjusting for these sociodemographic characteristics.

RESULTS: The average dmft index decreased slightly (β=-0.048; P<.03; CI 95% [-0.079; -0.017]) from 2009 to 2014. The finite mixture model resulted in four different groups of trajectories over time. While three groups showed a decrease in dmft score, one group showed an increase from 2009 to 2014. Moran's I test statistic showed strong evidence for spatial clustering (Moran's I 0.30, P=.002). A cluster of districts with high dmft values was identified in the centre of the city. The spatial lag model showed that both the proportion of unemployed persons (aged 16-65) and the proportion of persons with migration background were associated with the dmft values at district level. After adjusting for these, no further spatial heterogeneity was observed.

CONCLUSION: We identified regional clusters for poor dental health in a German city and showed that these clusters can be explained by sociodemographic characteristics. The findings support the need of targeted interventions and prevention measures in regions with less favourable sociodemographic characteristics.}, } @article {pmid28545077, year = {2017}, author = {Andreadis, KM and Das, N and Stampoulis, D and Ines, A and Fisher, JB and Granger, S and Kawata, J and Han, E and Behrangi, A}, title = {The Regional Hydrologic Extremes Assessment System: A software framework for hydrologic modeling and data assimilation.}, journal = {PloS one}, volume = {12}, number = {5}, pages = {e0176506}, pmid = {28545077}, issn = {1932-6203}, mesh = {Databases, Factual ; Environmental Monitoring/*methods ; Hydrology ; *Models, Theoretical ; *Software ; }, abstract = {The Regional Hydrologic Extremes Assessment System (RHEAS) is a prototype software framework for hydrologic modeling and data assimilation that automates the deployment of water resources nowcasting and forecasting applications. A spatially-enabled database is a key component of the software that can ingest a suite of satellite and model datasets while facilitating the interfacing with Geographic Information System (GIS) applications. The datasets ingested are obtained from numerous space-borne sensors and represent multiple components of the water cycle. The object-oriented design of the software allows for modularity and extensibility, showcased here with the coupling of the core hydrologic model with a crop growth model. RHEAS can exploit multi-threading to scale with increasing number of processors, while the database allows delivery of data products and associated uncertainty through a variety of GIS platforms. A set of three example implementations of RHEAS in the United States and Kenya are described to demonstrate the different features of the system in real-world applications.}, } @article {pmid28544559, year = {2017}, author = {Anslan, S and Bahram, M and Hiiesalu, I and Tedersoo, L}, title = {PipeCraft: Flexible open-source toolkit for bioinformatics analysis of custom high-throughput amplicon sequencing data.}, journal = {Molecular ecology resources}, volume = {17}, number = {6}, pages = {e234-e240}, doi = {10.1111/1755-0998.12692}, pmid = {28544559}, issn = {1755-0998}, mesh = {Computational Biology/*methods ; Computer Graphics ; High-Throughput Nucleotide Sequencing/*methods ; *Software ; }, abstract = {High-throughput sequencing methods have become a routine analysis tool in environmental sciences as well as in public and private sector. These methods provide vast amount of data, which need to be analysed in several steps. Although the bioinformatics may be applied using several public tools, many analytical pipelines allow too few options for the optimal analysis for more complicated or customized designs. Here, we introduce PipeCraft, a flexible and handy bioinformatics pipeline with a user-friendly graphical interface that links several public tools for analysing amplicon sequencing data. Users are able to customize the pipeline by selecting the most suitable tools and options to process raw sequences from Illumina, Pacific Biosciences, Ion Torrent and Roche 454 sequencing platforms. We described the design and options of PipeCraft and evaluated its performance by analysing the data sets from three different sequencing platforms. We demonstrated that PipeCraft is able to process large data sets within 24 hr. The graphical user interface and the automated links between various bioinformatics tools enable easy customization of the workflow. All analytical steps and options are recorded in log files and are easily traceable.}, } @article {pmid28542200, year = {2017}, author = {Dallas, T and Park, AW and Drake, JM}, title = {Predicting cryptic links in host-parasite networks.}, journal = {PLoS computational biology}, volume = {13}, number = {5}, pages = {e1005557}, pmid = {28542200}, issn = {1553-7358}, mesh = {Algorithms ; Animals ; Computational Biology ; Computer Simulation ; Host-Parasite Interactions/*physiology ; Mammals/parasitology ; *Models, Biological ; Parasitic Diseases, Animal/parasitology ; }, abstract = {Networks are a way to represent interactions among one (e.g., social networks) or more (e.g., plant-pollinator networks) classes of nodes. The ability to predict likely, but unobserved, interactions has generated a great deal of interest, and is sometimes referred to as the link prediction problem. However, most studies of link prediction have focused on social networks, and have assumed a completely censused network. In biological networks, it is unlikely that all interactions are censused, and ignoring incomplete detection of interactions may lead to biased or incorrect conclusions. Previous attempts to predict network interactions have relied on known properties of network structure, making the approach sensitive to observation errors. This is an obvious shortcoming, as networks are dynamic, and sometimes not well sampled, leading to incomplete detection of links. Here, we develop an algorithm to predict missing links based on conditional probability estimation and associated, node-level features. We validate this algorithm on simulated data, and then apply it to a desert small mammal host-parasite network. Our approach achieves high accuracy on simulated and observed data, providing a simple method to accurately predict missing links in networks without relying on prior knowledge about network structure.}, } @article {pmid28541699, year = {2017}, author = {Iwasaki, A and Shiota, I and Sumimoto, S and Matsubara, T and Sato, T and Suenaga, K}, title = {Kohamamides A, B, and C, Cyclic Depsipeptides from an Okeania sp. Marine Cyanobacterium.}, journal = {Journal of natural products}, volume = {80}, number = {6}, pages = {1948-1952}, doi = {10.1021/acs.jnatprod.7b00256}, pmid = {28541699}, issn = {1520-6025}, mesh = {Cyanobacteria/*chemistry ; Depsipeptides/chemistry/*isolation & purification ; Drug Screening Assays, Antitumor ; HL-60 Cells ; Humans ; Leucine/chemistry ; Marine Biology ; Molecular Structure ; Nuclear Magnetic Resonance, Biomolecular ; Peptides, Cyclic/chemistry ; Proline/chemistry ; Structure-Activity Relationship ; }, abstract = {Kohamamides A, B, and C (1-3), new cyclic depsipeptides that belong to the kulolide superfamily, were isolated from an Okeania sp. marine cyanobacterium. Their structures were elucidated by spectroscopic analyses and degradation reactions. Kohamamide B (2) exhibited moderate cytotoxicity against HL60 cells. Although many natural products in the kulolide superfamily have been isolated from cyanobacteria collected in various parts of the world, kohamamides 1-3 are the first members to be isolated from the East Asian marine environment. In addition, unlike other members of this superfamily, kohamamides 1-3 contain a Leu residue adjacent to the Pro residue, rather than another lipophilic amino acid.}, } @article {pmid28539606, year = {2017}, author = {Wei, X and Gong, H and Yu, J and Liu, P and Wang, L and Zhang, Y and Zhang, X}, title = {SesameFG: an integrated database for the functional genomics of sesame.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {2342}, pmid = {28539606}, issn = {2045-2322}, mesh = {*Databases, Genetic ; Gene Expression Profiling ; Gene Expression Regulation, Plant ; Genes, Plant/genetics ; Genome, Plant/*genetics ; Genomics/*methods/statistics & numerical data ; Genotype ; Internet ; Microsatellite Repeats/genetics ; Phenotype ; Polymorphism, Single Nucleotide ; Sesamum/classification/*genetics ; }, abstract = {Sesame (Sesamum indicum L.) has high oil content, a small diploid genome and a short growth period, making it an attractive species for genetic studies on oilseed crops. With the advancement of next-generation sequencing technology, genomics and functional genomics research of sesame has developed quickly in the last few years, and large amounts of data have been generated. However, these results are distributed in many different publications, and there is a lack of integration. To promote functional genomics research of sesame, we collected genetic information combined with comprehensive phenotypic information and integrated them in the web-based database named SesameFG. The current version of SesameFG contains phenotypic information on agronomic traits of 705 sesame accessions, de novo assembled genomes of three sesame varieties, massive numbers of identified SNPs, gene expression profiles of five tissues, gene families, candidate genes for the important agronomic traits and genomic-SSR markers. All phenotypic and genotypic information in SesameFG is available for online queries and can be downloaded freely. SesameFG provides useful search functions and data mining tools, including Genome Browser and local BLAST services. SesameFG is freely accessible at http://ncgr.ac.cn/SesameFG/. SesameFG provides valuable resources and tools for functional genomics research and the molecular breeding of sesame.}, } @article {pmid28535257, year = {2017}, author = {Cole, NC and An, R and Lee, SY and Donovan, SM}, title = {Correlates of picky eating and food neophobia in young children: a systematic review and meta-analysis.}, journal = {Nutrition reviews}, volume = {75}, number = {7}, pages = {516-532}, doi = {10.1093/nutrit/nux024}, pmid = {28535257}, issn = {1753-4887}, mesh = {Child Behavior/psychology ; Child, Preschool ; *Choice Behavior ; Databases, Factual ; Diet/psychology ; Eating/*psychology ; Food Preferences/*psychology ; Health Behavior ; Humans ; Parent-Child Relations ; Parents/psychology ; Randomized Controlled Trials as Topic ; }, abstract = {Picky eating behavior is prevalent among toddlers and may negatively impact their growth and development. This article summarizes the correlates of picky eating and food neophobia in young children, which were identified using a socio-ecological framework. A literature search was conducted in 4 electronic databases. Inclusion criteria were English-language peer-reviewed publications that investigated correlate(s) of picky eating or food neophobia in children aged ≤30 months. Correlates were categorized into 4 levels: cell, child, clan (family), and community/country. Thirty-two studies, which examined 89 correlates, were identified from the keyword searches of the databases and manual searches of the reference lists of included articles. The most examined correlates were characteristics related to the child (sex, weight, and dietary intake) and parent (feeding beliefs and practices). A meta-analysis estimated the prevalence of picky eating to be 22%. Each additional month of a child's age was associated with a 0.06 U increase in the Children's Eating Behavior Questionnaire food fussiness score. This review highlights the importance of investigating child-parent dyads and bidirectional feeding interactions and draws attention to the lack of picky eating research at the level of the cell and the community/country.}, } @article {pmid28533770, year = {2017}, author = {Belda, I and Zarraonaindia, I and Perisin, M and Palacios, A and Acedo, A}, title = {From Vineyard Soil to Wine Fermentation: Microbiome Approximations to Explain the "terroir" Concept.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {821}, pmid = {28533770}, issn = {1664-302X}, abstract = {Wine originally emerged as a serendipitous mix of chemistry and biology, where microorganisms played a decisive role. From these ancient fermentations to the current monitored industrial processes, winegrowers and winemakers have been continuously changing their practices according to scientific knowledge and advances. A new enology direction is emerging and aiming to blend the complexity of spontaneous fermentations with industrial safety of monitored fermentations. In this context, wines with distinctive autochthonous peculiarities have a great acceptance among consumers, causing important economic returns. The concept of terroir, far from being a rural term, conceals a wide range of analytical parameters that are the basis of the knowledge-based enology trend. In this sense, the biological aspect of soils has been underestimated for years, when actually it contains a great microbial diversity. This soil-associated microbiota has been described as determinant, not only for the chemistry and nutritional properties of soils, but also for health, yield, and quality of the grapevine. Additionally, recent works describe the soil microbiome as the reservoir of the grapevine associated microbiota, and as a contributor to the final sensory properties of wines. To understand the crucial roles of microorganisms on the entire wine making process, we must understand their ecological niches, population dynamics, and relationships between 'microbiome- vine health' and 'microbiome-wine metabolome.' These are critical steps for designing precision enology practices. For that purpose, current metagenomic techniques are expanding from laboratories, to the food industry. This review focuses on the current knowledge about vine and wine microbiomes, with emphasis on their biological roles and the technical basis of next-generation sequencing pipelines. An overview of molecular and informatics tools is included and new directions are proposed, highlighting the importance of -omics technologies in wine research and industry.}, } @article {pmid28524860, year = {2017}, author = {Wang, S and Loreau, M and Arnoldi, JF and Fang, J and Rahman, KA and Tao, S and de Mazancourt, C}, title = {An invariability-area relationship sheds new light on the spatial scaling of ecological stability.}, journal = {Nature communications}, volume = {8}, number = {}, pages = {15211}, pmid = {28524860}, issn = {2041-1723}, mesh = {Animals ; Biomass ; Birds/*physiology ; Databases as Topic ; *Ecosystem ; Internationality ; *Models, Biological ; }, abstract = {The spatial scaling of stability is key to understanding ecological sustainability across scales and the sensitivity of ecosystems to habitat destruction. Here we propose the invariability-area relationship (IAR) as a novel approach to investigate the spatial scaling of stability. The shape and slope of IAR are largely determined by patterns of spatial synchrony across scales. When synchrony decays exponentially with distance, IARs exhibit three phases, characterized by steeper increases in invariability at both small and large scales. Such triphasic IARs are observed for primary productivity from plot to continental scales. When synchrony decays as a power law with distance, IARs are quasilinear on a log-log scale. Such quasilinear IARs are observed for North American bird biomass at both species and community levels. The IAR provides a quantitative tool to predict the effects of habitat loss on population and ecosystem stability and to detect regime shifts in spatial ecological systems, which are goals of relevance to conservation and policy.}, } @article {pmid28516934, year = {2017}, author = {Griffin, E}, title = {Rescue old data before it's too late.}, journal = {Nature}, volume = {545}, number = {7654}, pages = {267}, doi = {10.1038/545267a}, pmid = {28516934}, issn = {1476-4687}, mesh = {*Analog-Digital Conversion ; Animals ; Astronomy/*history ; Birds ; Ecology/*history ; Extinction, Biological ; History, 20th Century ; History, 21st Century ; Information Dissemination/*methods ; Information Storage and Retrieval/economics/*trends ; *Knowledge ; Metadata ; Ozone/analysis ; Photography/*history ; *Records/economics ; Time Factors ; Weather ; }, } @article {pmid28507230, year = {2017}, author = {Christodoulides, P and Hirata, Y and Domínguez-Hüttinger, E and Danby, SG and Cork, MJ and Williams, HC and Aihara, K and Tanaka, RJ}, title = {Computational design of treatment strategies for proactive therapy on atopic dermatitis using optimal control theory.}, journal = {Philosophical transactions. Series A, Mathematical, physical, and engineering sciences}, volume = {375}, number = {2096}, pages = {}, pmid = {28507230}, issn = {1364-503X}, support = {NC/P00217X/1/NC3RS_/National Centre for the Replacement, Refinement and Reduction of Animals in Research/United Kingdom ; }, mesh = {Administration, Cutaneous ; Algorithms ; Anti-Inflammatory Agents/*administration & dosage ; Computer Simulation ; Dermatitis, Atopic/*diagnostic imaging/pathology/*physiopathology ; Dermatologic Agents/administration & dosage ; Dose-Response Relationship, Drug ; Drug Administration Schedule ; Drug Monitoring/methods ; Drug Therapy, Computer-Assisted/*methods ; Humans ; *Models, Biological ; Skin/drug effects/*physiopathology ; Treatment Outcome ; }, abstract = {Atopic dermatitis (AD) is a common chronic skin disease characterized by recurrent skin inflammation and a weak skin barrier, and is known to be a precursor to other allergic diseases such as asthma. AD affects up to 25% of children worldwide and the incidence continues to rise. There is still uncertainty about the optimal treatment strategy in terms of choice of treatment, potency, duration and frequency. This study aims to develop a computational method to design optimal treatment strategies for the clinically recommended 'proactive therapy' for AD. Proactive therapy aims to prevent recurrent flares once the disease has been brought under initial control. Typically, this is done by using an anti-inflammatory treatment such as a potent topical corticosteroid intensively for a few weeks to 'get control', followed by intermittent weekly treatment to suppress subclinical inflammation to 'keep control'. Using a hybrid mathematical model of AD pathogenesis that we recently proposed, we computationally derived the optimal treatment strategies for individual virtual patient cohorts, by recursively solving optimal control problems using a differential evolution algorithm. Our simulation results suggest that such an approach can inform the design of optimal individualized treatment schedules that include application of topical corticosteroids and emollients, based on the disease status of patients observed on their weekly hospital visits. We demonstrate the potential and the gaps of our approach to be applied to clinical settings.This article is part of the themed issue 'Mathematical methods in medicine: neuroscience, cardiology and pathology'.}, } @article {pmid28505840, year = {2017}, author = {Wilsenach, J and Landi, P and Hui, C}, title = {Evolutionary fields can explain patterns of high-dimensional complexity in ecology.}, journal = {Physical review. E}, volume = {95}, number = {4-1}, pages = {042401}, doi = {10.1103/PhysRevE.95.042401}, pmid = {28505840}, issn = {2470-0053}, mesh = {Animals ; *Biological Evolution ; *Ecological and Environmental Phenomena ; England ; Foxes ; *Models, Biological ; Nonlinear Dynamics ; Predatory Behavior ; Rabbits ; }, abstract = {One of the properties that make ecological systems so unique is the range of complex behavioral patterns that can be exhibited by even the simplest communities with only a few species. Much of this complexity is commonly attributed to stochastic factors that have very high-degrees of freedom. Orthodox study of the evolution of these simple networks has generally been limited in its ability to explain complexity, since it restricts evolutionary adaptation to an inertia-free process with few degrees of freedom in which only gradual, moderately complex behaviors are possible. We propose a model inspired by particle-mediated field phenomena in classical physics in combination with fundamental concepts in adaptation, which suggests that small but high-dimensional chaotic dynamics near to the adaptive trait optimum could help explain complex properties shared by most ecological datasets, such as aperiodicity and pink, fractal noise spectra. By examining a simple predator-prey model and appealing to real ecological data, we show that this type of complexity could be easily confused for or confounded by stochasticity, especially when spurred on or amplified by stochastic factors that share variational and spectral properties with the underlying dynamics.}, } @article {pmid28505134, year = {2017}, author = {Yang, Y and Cai, L and Ma, R and Xu, Y and Tong, Y and Huang, Y and Jiao, N and Zhang, R}, title = {A Novel Roseosiphophage Isolated from the Oligotrophic South China Sea.}, journal = {Viruses}, volume = {9}, number = {5}, pages = {}, pmid = {28505134}, issn = {1999-4915}, mesh = {Base Composition ; Base Sequence ; Capsid/chemistry ; China ; DNA, Viral/analysis/genetics ; Databases, Nucleic Acid ; Genes, Viral/genetics ; Genome, Viral ; Host Specificity ; Host-Parasite Interactions/physiology ; Microscopy, Electron, Transmission ; *Phylogeny ; Podoviridae/*classification/*genetics/*isolation & purification/physiology ; Roseobacter/*virology ; Seawater/*virology ; Sequence Analysis, DNA ; Viral Proteins/genetics ; Virus Latency ; }, abstract = {The Roseobacter clade is abundant and widespread in marine environments and plays an important role in oceanic biogeochemical cycling. In this present study, a lytic siphophage (labeled vB_DshS-R5C) infecting the strain type of Dinoroseobacter shibae named DFL12[T], which is part of the Roseobacter clade, was isolated from the oligotrophic South China Sea. Phage R5C showed a narrow host range, short latent period and low burst size. The genome length of phage R5C was 77, 874 bp with a G+C content of 61.5%. Genomic comparisons detected no genome matches in the GenBank database and phylogenetic analysis based on DNA polymerase I revealed phylogenetic features that were distinct to other phages, suggesting the novelty of R5C. Several auxiliary metabolic genes (e.g., phoH gene, heat shock protein and queuosine biosynthesis genes) were identified in the R5C genome that may be beneficial to the host and/or offer a competitive advantage for the phage. Among siphophages infecting the Roseobacter clade (roseosiphophages), four gene transfer agent-like genes were commonly located with close proximity to structural genes, suggesting that their function may be related to the tail of siphoviruses. The isolation and characterization of R5C demonstrated the high genomic and physiological diversity of roseophages as well as improved our understanding of host-phage interactions and the ecology of the marine Roseobacter.}, } @article {pmid28504821, year = {2018}, author = {Warton, DI}, title = {Why you cannot transform your way out of trouble for small counts.}, journal = {Biometrics}, volume = {74}, number = {1}, pages = {362-368}, doi = {10.1111/biom.12728}, pmid = {28504821}, issn = {1541-0420}, mesh = {*Data Interpretation, Statistical ; Ecology ; Linear Models ; *Models, Statistical ; Multivariate Analysis ; }, abstract = {While data transformation is a common strategy to satisfy linear modeling assumptions, a theoretical result is used to show that transformation cannot reasonably be expected to stabilize variances for small counts. Under broad assumptions, as counts get smaller, it is shown that the variance becomes proportional to the mean under monotonic transformations g(·) that satisfy g(0)=0, excepting a few pathological cases. A suggested rule-of-thumb is that if many predicted counts are less than one then data transformation cannot reasonably be expected to stabilize variances, even for a well-chosen transformation. This result has clear implications for the analysis of counts as often implemented in the applied sciences, but particularly for multivariate analysis in ecology. Multivariate discrete data are often collected in ecology, typically with a large proportion of zeros, and it is currently widespread to use methods of analysis that do not account for differences in variance across observations nor across responses. Simulations demonstrate that failure to account for the mean-variance relationship can have particularly severe consequences in this context, and also in the univariate context if the sampling design is unbalanced.}, } @article {pmid28504449, year = {2017}, author = {Taber, ED and Hutchinson, ML and Smithwick, EAH and Blanford, JI}, title = {A decade of colonization: the spread of the Asian tiger mosquito in Pennsylvania and implications for disease risk.}, journal = {Journal of vector ecology : journal of the Society for Vector Ecology}, volume = {42}, number = {1}, pages = {3-12}, doi = {10.1111/jvec.12234}, pmid = {28504449}, issn = {1948-7134}, mesh = {*Aedes/virology ; *Animal Distribution ; Animals ; Chikungunya Fever/transmission ; Dengue/transmission ; Geographic Information Systems ; Humans ; *Introduced Species ; *Mosquito Vectors/virology ; Pennsylvania ; West Nile Fever/transmission ; }, abstract = {In recent decades, the Asian tiger mosquito expanded its geographic range throughout the northeastern United States, including Pennsylvania. The establishment of Aedes albopictus in novel areas raises significant public health concerns, since this species is a highly competent vector of several arboviruses, including chikungunya, West Nile, and dengue. In this study, we used geographic information systems (GIS) to examine a decade of colonization by Ae. albopictus throughout Pennsylvania between 2001 and 2010. We examined the spatial and temporal distribution of Ae. albopictus using spatial statistical analysis and examined the risk of dengue virus transmission using a model that captures the probability of transmission. Our findings show that since 2001, the Ae. albopictus population in Pennsylvania has increased, becoming established and expanding in range throughout much of the state. Since 2010, imported cases of dengue fever have been recorded in Pennsylvania. Imported cases of dengue, in combination with summer temperatures conducive for virus transmission, raise the risk of local disease transmission.}, } @article {pmid28504275, year = {2017}, author = {Wollenberg Valero, KC and Garcia-Porta, J and Rodríguez, A and Arias, M and Shah, A and Randrianiaina, RD and Brown, JL and Glaw, F and Amat, F and Künzel, S and Metzler, D and Isokpehi, RD and Vences, M}, title = {Transcriptomic and macroevolutionary evidence for phenotypic uncoupling between frog life history phases.}, journal = {Nature communications}, volume = {8}, number = {}, pages = {15213}, pmid = {28504275}, issn = {2041-1723}, mesh = {Animals ; Datasets as Topic ; Gene Expression Profiling ; Gene Expression Regulation, Developmental/physiology ; *Genetic Speciation ; Larva/genetics ; Metamorphosis, Biological/*physiology ; *Phenotype ; Phylogeny ; Transcriptome/*physiology ; Xenopus laevis/*physiology ; }, abstract = {Anuran amphibians undergo major morphological transitions during development, but the contribution of their markedly different life-history phases to macroevolution has rarely been analysed. Here we generate testable predictions for coupling versus uncoupling of phenotypic evolution of tadpole and adult life-history phases, and for the underlying expression of genes related to morphological feature formation. We test these predictions by combining evidence from gene expression in two distantly related frogs, Xenopus laevis and Mantidactylus betsileanus, with patterns of morphological evolution in the entire radiation of Madagascan mantellid frogs. Genes linked to morphological structure formation are expressed in a highly phase-specific pattern, suggesting uncoupling of phenotypic evolution across life-history phases. This gene expression pattern agrees with uncoupled rates of trait evolution among life-history phases in the mantellids, which we show to have undergone an adaptive radiation. Our results validate a prevalence of uncoupling in the evolution of tadpole and adult phenotypes of frogs.}, } @article {pmid28502716, year = {2017}, author = {Ahn, SJ and Martin, R and Rao, S and Choi, MY}, title = {Neuropeptides predicted from the transcriptome analysis of the gray garden slug Deroceras reticulatum.}, journal = {Peptides}, volume = {93}, number = {}, pages = {51-65}, doi = {10.1016/j.peptides.2017.05.005}, pmid = {28502716}, issn = {1873-5169}, mesh = {Animals ; Gastropoda/*genetics ; Gene Expression Profiling ; Gene Ontology ; Genome-Wide Association Study ; High-Throughput Nucleotide Sequencing ; Invertebrate Hormones/genetics ; Neuropeptides/chemistry/*genetics ; RNA/genetics ; Sequence Analysis, Protein ; Signal Transduction ; Transcriptome/*genetics ; }, abstract = {The gray garden slug, Deroceras reticulatum (Gastropoda: Pulmonata), is one of the most common terrestrial molluscs. Research for this slug has focused mainly on its ecology, biology, and management due to the severe damage it causes on a wide range of vegetables and field crops. However, little is known about neuropeptides and hormonal signalings. This study, therefore, aimed to establish the transcriptome of D. reticulatum and to identify a comprehensive repertoire of neuropeptides in this slug. Illumina high-throughput sequencing of the whole body transcriptome of D. reticulatum generated a total of 5.9 billion raw paired-end reads. De novo assembly by Trinity resulted in 143,575 transcripts and further filtration selected 120,553 unigenes. Gene Ontology (GO) terms were assigned to 30,588 unigenes, composed of biological processes (36.9%), cellular components (30.2%) and molecular functions (32.9%). Functional annotation by BLASTx revealed 39,987 unigenes with hits, which were further categorized into important functional groups based on sequence abundance. Neuropeptides, ion channels, ribosomal proteins, G protein-coupled receptors, detoxification, immunity and cytoskeleton-related sequences were dominant among the transcripts. BLAST searches and PCR amplification were used to identify 65 putative neuropeptide precursor genes from the D. reticulatum transcriptome, which include achatin, AKH, allatostatin A, B and C, allatotropin, APGWamide, CCAP, cerebrin, conopressin, cysteine-knot protein hormones (bursicon alpha/beta and GPA2/GPB5), elevenin, FCAP, FFamide, FVamide (enterin, fulicin, MIP and PRQFVamide), GGNG, GnRH, insulin, NdWFamide, NKY, PKYMDT, PRXamide (myomodulin, pleurin and sCAP), RFamide (CCK/SK, FMRFamide, FxRIamide, LFRFamide, luqin and NPF), and tachykinin. Over 330 putative peptides were encoded by these precursors. Comparative analysis among different molluscan species clearly revealed that, while D. reticulatum neuropeptide sequences are conserved in Mollusca, there are also some unique features distinct from other members of this species. This is the first transcriptome-wide report of neuropeptides in terrestrial slugs. Our results provide comprehensive transcriptome data of the gray garden slug, with a more detailed focus on the rich repertoire of putative neuropeptide sequences, laying the foundation for molecular studies in this terrestrial slug pest.}, } @article {pmid28500331, year = {2017}, author = {Wang, K and Hong, W and Jiao, H and Zhao, H}, title = {Transcriptome sequencing and phylogenetic analysis of four species of luminescent beetles.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {1814}, pmid = {28500331}, issn = {2045-2322}, mesh = {Animals ; Coleoptera/*classification/*genetics ; Computational Biology/methods ; Gene Expression Profiling ; Genome, Mitochondrial ; *High-Throughput Nucleotide Sequencing ; Luminescence ; Molecular Sequence Annotation ; Phenotype ; *Phylogeny ; *Transcriptome ; Whole Genome Sequencing ; }, abstract = {The evolution of bioluminescence has prompted scientific attention to illuminate phylogenetic relationships of luminescent beetles. However, genomic resources are virtually lacking in rhagophthalmids (Rhagophthalmidae) and their related firefly beetles lampyrids (Lampyridae). Here, we employed the Illumina Hiseq 2000 platform and sequenced the whole-body transcriptomes of the four luminescent beetles: one rhagophthalmid (Rhagophthalmus sp.) and three fireflies (Asymmetricata circumdata, Aquatica ficta, and Pyrocoelia pectoralis). We obtained 55.4, 43.4, 38.6, and 36.7 million clean reads for the four species, respectively. All reads were assembled into contigs from which unigenes were derived. All unigenes were annotated by publicly available databases, and a total of 4325 orthologous genes were identified. Using multiple phylogenetic approaches, our transcriptome data confirmed the distinctiveness of Rhagophthalmidae from Lampyridae, which was also supported by our mitogenome analysis using three newly determined mitogenome sequences and 12 previously published ones. Together, this study is the first report of whole transcriptome sequencing data in Rhagophthalmidae and Lampyridae species, representing a valuable genomic resource for studying the origin and evolution of some remarkable traits in these beetles such as bioluminescence. Moreover, our transcriptome and mitogenome data provide useful phylogenetic information that could be of importance in future studies of phylogenetic inference.}, } @article {pmid28500319, year = {2017}, author = {Chiu, CY and Chan, YL and Tsai, YS and Chen, SA and Wang, CJ and Chen, KF and Chung, IF}, title = {Airway Microbial Diversity is Inversely Associated with Mite-Sensitized Rhinitis and Asthma in Early Childhood.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {1820}, pmid = {28500319}, issn = {2045-2322}, mesh = {Allergens/immunology ; Animals ; Asthma/diagnosis/epidemiology/*etiology ; Biodiversity ; Case-Control Studies ; Child, Preschool ; Disease Susceptibility ; Female ; Humans ; Immunization ; Male ; *Microbiota ; Mites/*immunology ; Respiratory Mucosa/*microbiology ; Rhinitis, Allergic/diagnosis/epidemiology/*etiology ; }, abstract = {Microbiota plays an important role in regulating immune responses associated with atopic diseases. We sought to evaluate relationships among airway microbiota, serum IgE levels, allergic sensitization and their relevance to rhinitis and asthma. Microbial characterization was performed using Illumina-based 16S rRNA gene sequencing of 87 throat swabs collected from children with asthma (n = 32) and rhinitis (n = 23), and from healthy controls (n = 32). Data analysis was performed using QIIME (Quantitative Insights Into Microbial Ecology) v1.8. Significantly higher abundance of Proteobacteria was found in children with rhinitis than in the healthy controls (20.1% vs. 16.1%, P = 0.009). Bacterial species richness (Chao1 index) and diversity (Shannon index) were significantly reduced in children with mite sensitization but not in those with food or IgE sensitization. Compared with healthy children without mite sensitization, the mite-sensitized children with rhinitis and asthma showed significantly lower Chao1 and Shannon indices. Moraxella and Leptotrichia species were significantly found in the interaction of mite sensitization with rhinitis and asthma respectively. Airway microbial diversity appears to be inversely associated with sensitization to house dust mites. A modulation between airway dysbiosis and responses to allergens may potentially cause susceptibility to rhinitis and asthma in early childhood.}, } @article {pmid28500287, year = {2017}, author = {Akmatov, MK and Koch, N and Vital, M and Ahrens, W and Flesch-Janys, D and Fricke, J and Gatzemeier, A and Greiser, H and Günther, K and Illig, T and Kaaks, R and Krone, B and Kühn, A and Linseisen, J and Meisinger, C and Michels, K and Moebus, S and Nieters, A and Obi, N and Schultze, A and Six-Merker, J and Pieper, DH and Pessler, F}, title = {Determination of nasal and oropharyngeal microbiomes in a multicenter population-based study - findings from Pretest 1 of the German National Cohort.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {1855}, pmid = {28500287}, issn = {2045-2322}, mesh = {Cohort Studies ; Germany/epidemiology ; Humans ; *Microbiota ; Nasal Cavity/*microbiology ; Oropharynx/*microbiology ; *Public Health Surveillance ; }, abstract = {We examined acceptability, preference and feasibility of collecting nasal and oropharyngeal swabs, followed by microbiome analysis, in a population-based study with 524 participants. Anterior nasal and oropharyngeal swabs were collected by certified personnel. In addition, participants self-collected nasal swabs at home four weeks later. Four swab types were compared regarding (1) participants' satisfaction and acceptance and (2) detection of microbial community structures based on deep sequencing of the 16 S rRNA gene V1-V2 variable regions. All swabbing methods were highly accepted. Microbial community structure analysis revealed 846 phylotypes, 46 of which were unique to oropharynx and 164 unique to nares. The calcium alginate tipped swab was found unsuitable for microbiome determinations. Among the remaining three swab types, there were no differences in oropharyngeal microbiomes detected and only marginal differences in nasal microbiomes. Microbial community structures did not differ between staff-collected and self-collected nasal swabs. These results suggest (1) that nasal and oropharyngeal swabbing are highly feasible methods for human population-based studies that include the characterization of microbial community structures in these important ecological niches, and (2) that self-collection of nasal swabs at home can be used to reduce cost and resources needed, particularly when serial measurements are to be taken.}, } @article {pmid28500020, year = {2017}, author = {Bidargaddi, N and Musiat, P and Winsall, M and Vogl, G and Blake, V and Quinn, S and Orlowski, S and Antezana, G and Schrader, G}, title = {Efficacy of a Web-Based Guided Recommendation Service for a Curated List of Readily Available Mental Health and Well-Being Mobile Apps for Young People: Randomized Controlled Trial.}, journal = {Journal of medical Internet research}, volume = {19}, number = {5}, pages = {e141}, pmid = {28500020}, issn = {1438-8871}, mesh = {Adolescent ; Adult ; Cell Phone/*statistics & numerical data ; Female ; Humans ; Internet/*statistics & numerical data ; Male ; Mental Health/*statistics & numerical data ; Mobile Applications/*statistics & numerical data ; Young Adult ; }, abstract = {BACKGROUND: Mental disorders are highly prevalent for the people who are aged between 16 and 25 years and can permanently disrupt the development of these individuals. Easily available mobile health (mHealth) apps for mobile phones have great potential for the prevention and early intervention of mental disorders in young adults, but interventions are required that can help individuals to both identify high-quality mobile apps and use them to change health and lifestyle behavior.

OBJECTIVES: The study aimed to assess the efficacy of a Web-based self-guided app recommendation service ("The Toolbox") in improving the well-being of young Australians aged between 16 and 25 years. The intervention was developed in collaboration with young adults and consists of a curated list of 46 readily available health and well-being apps, assessed and rated by professionals and young people. Participants are guided by an interactive quiz and subsequently receive recommendations for particular apps to download and use based on their personal goals.

METHODS: The study was a waitlist, parallel-arm, randomized controlled trial. Our primary outcome measure was change in well-being as measured by the Mental Health Continuum-Short Form (MHC-SF). We also employed ecological momentary assessments (EMAs) to track mood, energy, rest, and sleep. Participants were recruited from the general Australian population, via several Web-based and community strategies. The study was conducted through a Web-based platform consisting of a landing Web page and capabilities to administer study measures at different time points. Web-based measurements were self-assessed at baseline and 4 weeks, and EMAs were collected repeatedly at regular weekly intervals or ad hoc when participants interacted with the study platform. Primary outcomes were analyzed using linear mixed-models and intention-to-treat (ITT) analysis.

RESULTS: A total of 387 participants completed baseline scores and were randomized into the trial. Results demonstrated no significant effect of "The Toolbox" intervention on participant well-being at 4 weeks compared with the control group (P=.66). There were also no significant differences between the intervention and control groups at 4 weeks on any of the subscales of the MHC-SF (psychological: P=.95, social: P=.42, emotional: P=.95). Repeat engagement with the study platform resulted in a significant difference in mood, energy, rest, and sleep trajectories between intervention and control groups as measured by EMAs (P<.01).

CONCLUSIONS: This was the first study to assess the effectiveness of a Web-based well-being intervention in a sample of young adults. The design of the intervention utilized expert rating of existing apps and end-user codesign approaches resulting in an app recommendation service. Our finding suggests that recommended readily available mental health and well-being apps may not lead to improvements in the well-being of a nonclinical sample of young people, but might halt a decline in mood, energy, rest, and sleep.

TRIAL REGISTRATION: Australian New Zealand Clinical Trials Registry (ANZCTR): ACTRN12614000710628; https://www.anzctr.org.au/Trial/Registration/TrialReview.aspx?id=366145 (Archived by WebCite at http://www.webcitation.org/ 6pWDsnKme).}, } @article {pmid28494123, year = {2017}, author = {Schueller, SM and Aguilera, A and Mohr, DC}, title = {Ecological momentary interventions for depression and anxiety.}, journal = {Depression and anxiety}, volume = {34}, number = {6}, pages = {540-545}, doi = {10.1002/da.22649}, pmid = {28494123}, issn = {1520-6394}, support = {K08 MH102336/MH/NIMH NIH HHS/United States ; P20 MH090318/MH/NIMH NIH HHS/United States ; R01 MH100482/MH/NIMH NIH HHS/United States ; R01 MH095753/MH/NIMH NIH HHS/United States ; K23 MH094442/MH/NIMH NIH HHS/United States ; }, mesh = {Anxiety/*therapy ; Depression/*therapy ; *Ecological Momentary Assessment ; Humans ; Therapy, Computer-Assisted/*methods ; }, abstract = {Ecological momentary interventions (EMIs) are becoming more popular and more powerful resources for the treatment and prevention of depression and anxiety due to advances in technological capacity and analytic sophistication. Previous work has demonstrated that EMIs can be effective at reducing symptoms of depression and anxiety as well as related outcomes of stress and at increasing positive psychological functioning. In this review, we highlight the differences between EMIs and other forms of treatment due to the nature of EMIs to be deeply integrated into the fabric of people's day-to-day lives. EMIs require unique considerations in their design, deployment, and evaluation. Furthermore, given that EMIs have been advanced by changes in technologies and that the use of behavioral intervention technologies for mental health has been increasing, we discuss how technologies and analytics might usher in a new era of EMIs. Future EMIs might reduce user burden and increase intervention personalization and sophistication by leveraging digital sensors and advances in natural language processing and machine learning. Thus, although current EMIs are effective, the EMIs of the future might be more engaging, responsive, and adaptable to different people and different contexts.}, } @article {pmid28492778, year = {2017}, author = {Soares, MLM and Amaral, NACD and Zacarias, ACP and Ribeiro, LKNP}, title = {Sociodemographic, clinical and epidemiological aspects of Tuberculosis treatment abandonment in Pernambuco, Brazil, 2001-2014.}, journal = {Epidemiologia e servicos de saude : revista do Sistema Unico de Saude do Brasil}, volume = {26}, number = {2}, pages = {369-378}, doi = {10.5123/S1679-49742017000200014}, pmid = {28492778}, issn = {2237-9622}, mesh = {Adolescent ; Adult ; Aged ; Aged, 80 and over ; Antitubercular Agents/*administration & dosage ; Brazil ; Child ; Child, Preschool ; Educational Status ; Female ; Humans ; Infant ; Infant, Newborn ; Information Systems ; Male ; Medication Adherence/*statistics & numerical data ; Middle Aged ; Tuberculosis/*drug therapy ; Tuberculosis, Pulmonary/*drug therapy ; Young Adult ; }, abstract = {OBJECTIVE: to describe abandonment rates according to sociodemographic, clinical and epidemiological characteristics of new tuberculosis cases being treated in Pernambuco State, Brazil.

METHODS: this is a descriptive ecological study using data from the Information System for Notifiable Diseases from 2001 to 2014; the abandonment rate was calculated by the Regional Administration on Health (GERES).

RESULTS: of the 57,015 new cases, 6,474 (11.3%) abandoned treatment, although abandonment decreased from 16.4% (2001) to 9.3% (2014); the abandonment rate in GERES I Recife, III Palmares, IV Caruaru, VIII Petrolina and IX Ouricuri was still >5% in 2014; the rate was higher in males (11.9%), people aged 20-39 (12.7%), people with incomplete elementary school (12.1%), black-skinned people (13.7%), institutionalized people (12.5%) and those with pulmonary + extrapulmonary tuberculosis (14.1%).

CONCLUSION: despite the decrease, the abandonment rate remained high; males, adults with low education level, black-skinned people, institutionalized patients and patients with pulmonary + extrapulmonary tuberculosis seemed more prone to abandoning treatment.}, } @article {pmid28492366, year = {2017}, author = {Luzzatto-Knaan, T and Garg, N and Wang, M and Glukhov, E and Peng, Y and Ackermann, G and Amir, A and Duggan, BM and Ryazanov, S and Gerwick, L and Knight, R and Alexandrov, T and Bandeira, N and Gerwick, WH and Dorrestein, PC}, title = {Digitizing mass spectrometry data to explore the chemical diversity and distribution of marine cyanobacteria and algae.}, journal = {eLife}, volume = {6}, number = {}, pages = {}, pmid = {28492366}, issn = {2050-084X}, support = {R01 GM107550/GM/NIGMS NIH HHS/United States ; }, mesh = {Aquatic Organisms/chemistry/classification ; *Biodiversity ; Computational Biology/methods ; Cyanobacteria/*chemistry/*classification ; Mass Spectrometry ; Metabolomics/*methods ; Microalgae/*chemistry/*classification ; }, abstract = {Natural product screening programs have uncovered molecules from diverse natural sources with various biological activities and unique structures. However, much is yet underexplored and additional information is hidden in these exceptional collections. We applied untargeted mass spectrometry approaches to capture the chemical space and dispersal patterns of metabolites from an in-house library of marine cyanobacterial and algal collections. Remarkably, 86% of the metabolomics signals detected were not found in other available datasets of similar nature, supporting the hypothesis that marine cyanobacteria and algae possess distinctive metabolomes. The data were plotted onto a world map representing eight major sampling sites, and revealed potential geographic locations with high chemical diversity. We demonstrate the use of these inventories as a tool to explore the diversity and distribution of natural products. Finally, we utilized this tool to guide the isolation of a new cyclic lipopeptide, yuvalamide A, from a marine cyanobacterium.}, } @article {pmid28491101, year = {2017}, author = {Olanrewaju, OE and Adepoju, KA}, title = {Geospatial Assessment of Cholera in a Rapidly Urbanizing Environment.}, journal = {Journal of environmental and public health}, volume = {2017}, number = {}, pages = {6847376}, pmid = {28491101}, issn = {1687-9813}, mesh = {Cholera/*epidemiology/microbiology ; *Environment ; Geographic Information Systems ; Incidence ; Nigeria/epidemiology ; Risk Factors ; *Socioeconomic Factors ; Spatial Analysis ; Urbanization ; }, abstract = {This study mapped out and investigated the spatial relationship between cholera incidences and environmental risk factors in the study area. The study area was stratified into eight zones. Water samples from each zone were collected and analyzed to determine the colony forming units. GIS layers including housing density, digitized roads, rivers, buildings, and cholera incidence data from hospital archives were also collected and analyzed using ArcGIS 10.1. It was observed that there was an association between the ERFs (p < 0.001). Similarly, 18 out of the 44 waste dump sites, seven out of 18 markets, and two out of 36 abattoirs were found near the historical cholera cases. Similarly, 4 (21.1%) locations were traced to be predominantly close to rivers and waste dump site. All the historical cholera cases were found adjoining to roads and buildings. Highest CFU count was found in the wells and streams of areas with a cluster of all the environmental risk factors and high housing density. This study revealed that waste dump sites and market had the highest predisposing attribute while the least was abattoir. The uniqueness of the study lies in the combination of mapping and microbial analyses to identify and assess the pattern of cholera risk and also to provide clear information for development of strategies for environmental supervision.}, } @article {pmid28490601, year = {2017}, author = {Mizumoto, N and Abe, MS and Dobata, S}, title = {Optimizing mating encounters by sexually dimorphic movements.}, journal = {Journal of the Royal Society, Interface}, volume = {14}, number = {130}, pages = {}, pmid = {28490601}, issn = {1742-5662}, mesh = {Animals ; *Models, Biological ; Movement/*physiology ; Sexual Behavior, Animal/*physiology ; }, abstract = {All organisms with sexual reproduction undergo a process of mating, which essentially involves the encounter of two individuals belonging to different sexes. During mate search, both sexes should mutually optimize their encounters, thus raising a question of how they achieve this. Here, we show that a population with sexually dimorphic movement patterns achieves the highest individual mating success under a limited lifespan. Extensive simulations found and analytical approximations corroborated the existence of conditions under which sexual dimorphism in the movement patterns (i.e. how diffusively they move) is advantageous over sexual monomorphism. Mutual searchers with limited lifespans need to balance the speed and accuracy of finding their mates, and dimorphic movements can solve this trade-off. We further demonstrate that the sexual dimorphism can evolve from an initial sexually monomorphic population. Our results emphasize the importance of considering mutual optimization in problems of random search.}, } @article {pmid28489896, year = {2017}, author = {Richardson, TO and Liechti, JI and Stroeymeyt, N and Bonhoeffer, S and Keller, L}, title = {Short-term activity cycles impede information transmission in ant colonies.}, journal = {PLoS computational biology}, volume = {13}, number = {5}, pages = {e1005527}, pmid = {28489896}, issn = {1553-7358}, mesh = {Activity Cycles/*physiology ; *Animal Communication ; Animals ; Ants/*physiology ; Computational Biology ; *Models, Biological ; *Periodicity ; }, abstract = {Rhythmical activity patterns are ubiquitous in nature. We study an oscillatory biological system: collective activity cycles in ant colonies. Ant colonies have become model systems for research on biological networks because the interactions between the component parts are visible to the naked eye, and because the time-ordered contact network formed by these interactions serves as the substrate for the distribution of information and other resources throughout the colony. To understand how the collective activity cycles influence the contact network transport properties, we used an automated tracking system to record the movement of all the individuals within nine different ant colonies. From these trajectories we extracted over two million ant-to-ant interactions. Time-series analysis of the temporal fluctuations of the overall colony interaction and movement rates revealed that both the period and amplitude of the activity cycles exhibit a diurnal cycle, in which daytime cycles are faster and of greater amplitude than night cycles. Using epidemiology-derived models of transmission over networks, we compared the transmission properties of the observed periodic contact networks with those of synthetic aperiodic networks. These simulations revealed that contrary to some predictions, regularly-oscillating contact networks should impede information transmission. Further, we provide a mechanistic explanation for this effect, and present evidence in support of it.}, } @article {pmid28488328, year = {2017}, author = {Sauvage, C and Rau, A and Aichholz, C and Chadoeuf, J and Sarah, G and Ruiz, M and Santoni, S and Causse, M and David, J and Glémin, S}, title = {Domestication rewired gene expression and nucleotide diversity patterns in tomato.}, journal = {The Plant journal : for cell and molecular biology}, volume = {91}, number = {4}, pages = {631-645}, doi = {10.1111/tpj.13592}, pmid = {28488328}, issn = {1365-313X}, mesh = {Domestication ; *Epigenesis, Genetic ; Gene Ontology ; *Genetic Variation ; Genetics, Population ; Genome, Plant/*genetics ; Solanum lycopersicum/*genetics ; Phenotype ; Sequence Analysis, RNA ; *Transcriptome ; }, abstract = {Plant domestication has led to considerable phenotypic modifications from wild species to modern varieties. However, although changes in key traits have been well documented, less is known about the underlying molecular mechanisms, such as the reduction of molecular diversity or global gene co-expression patterns. In this study, we used a combination of gene expression and population genetics in wild and crop tomato to decipher the footprints of domestication. We found a set of 1729 differentially expressed genes (DEG) between the two genetic groups, belonging to 17 clusters of co-expressed DEG, suggesting that domestication affected not only individual genes but also regulatory networks. Five co-expression clusters were enriched in functional terms involving carbohydrate metabolism or epigenetic regulation of gene expression. We detected differences in nucleotide diversity between the crop and wild groups specific to DEG. Our study provides an extensive profiling of the rewiring of gene co-expression induced by the domestication syndrome in one of the main crop species.}, } @article {pmid28485370, year = {2017}, author = {Vogel, H and Shukla, SP and Engl, T and Weiss, B and Fischer, R and Steiger, S and Heckel, DG and Kaltenpoth, M and Vilcinskas, A}, title = {The digestive and defensive basis of carcass utilization by the burying beetle and its microbiota.}, journal = {Nature communications}, volume = {8}, number = {}, pages = {15186}, pmid = {28485370}, issn = {2041-1723}, mesh = {Anal Canal/microbiology ; Animals ; Antimicrobial Cationic Peptides/metabolism ; Coleoptera/*microbiology ; *Digestion ; Female ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/anatomy & histology/*microbiology/physiology ; Gene Expression Profiling ; Gene Expression Regulation ; Gene Ontology ; Immunity, Innate/genetics ; Inactivation, Metabolic/genetics ; Male ; Muramidase/metabolism ; Phylogeny ; RNA, Messenger/genetics/metabolism ; Transcriptome/genetics ; Yarrowia/isolation & purification/metabolism ; }, abstract = {Insects that use ephemeral resources must rapidly digest nutrients and simultaneously protect them from competitors. Here we use burying beetles (Nicrophorus vespilloides), which feed their offspring on vertebrate carrion, to investigate the digestive and defensive basis of carrion utilization. We characterize gene expression and microbiota composition in the gut, anal secretions, and on carcasses used by the beetles. We find a strict functional compartmentalization of the gut involving differential expression of immune effectors (antimicrobial peptides and lysozymes), as well as digestive and detoxifying enzymes. A distinct microbial community composed of Firmicutes, Proteobacteria and a clade of ascomycetous yeasts (genus Yarrowia) is present in larval and adult guts, and is transmitted to the carcass via anal secretions, where the yeasts express extracellular digestive enzymes and produce antimicrobial compounds. Our results provide evidence of potential metabolic cooperation between the host and its microbiota for digestion, detoxification and defence that extends from the beetle's gut to its nutritional resource.}, } @article {pmid28481971, year = {2018}, author = {Niu, SY and Yang, J and McDermaid, A and Zhao, J and Kang, Y and Ma, Q}, title = {Bioinformatics tools for quantitative and functional metagenome and metatranscriptome data analysis in microbes.}, journal = {Briefings in bioinformatics}, volume = {19}, number = {6}, pages = {1415-1429}, doi = {10.1093/bib/bbx051}, pmid = {28481971}, issn = {1477-4054}, mesh = {*Computational Biology ; *Metagenome ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; *Transcriptome ; }, abstract = {Metagenomic and metatranscriptomic sequencing approaches are more frequently being used to link microbiota to important diseases and ecological changes. Many analyses have been used to compare the taxonomic and functional profiles of microbiota across habitats or individuals. While a large portion of metagenomic analyses focus on species-level profiling, some studies use strain-level metagenomic analyses to investigate the relationship between specific strains and certain circumstances. Metatranscriptomic analysis provides another important insight into activities of genes by examining gene expression levels of microbiota. Hence, combining metagenomic and metatranscriptomic analyses will help understand the activity or enrichment of a given gene set, such as drug-resistant genes among microbiome samples. Here, we summarize existing bioinformatics tools of metagenomic and metatranscriptomic data analysis, the purpose of which is to assist researchers in deciding the appropriate tools for their microbiome studies. Additionally, we propose an Integrated Meta-Function mapping pipeline to incorporate various reference databases and accelerate functional gene mapping procedures for both metagenomic and metatranscriptomic analyses.}, } @article {pmid28476675, year = {2017}, author = {Luo, K and Li, Y and Ai, K and Xia, L and Zhang, J and Hu, W and Gao, W and Guo, L and Qi, Z and Yuan, H and Xu, Q}, title = {Bioinformatics and expression analysis of finTRIM genes in grass carp, Ctenopharyngodon idella.}, journal = {Fish & shellfish immunology}, volume = {66}, number = {}, pages = {217-223}, doi = {10.1016/j.fsi.2017.05.004}, pmid = {28476675}, issn = {1095-9947}, mesh = {Animals ; Carps/*genetics/metabolism ; *Computational Biology ; Fish Proteins/*genetics/metabolism ; Gene Expression Profiling/veterinary ; Gene Expression Regulation/*immunology ; Phylogeny ; Sequence Analysis, DNA/veterinary ; Tripartite Motif Proteins/*genetics/metabolism ; }, abstract = {The tripartite motifs (TRIMs) constitute a large family of proteins containing a Really Interesting New Gene (RING) domain, a B-box domain and coiled-coil region followed by different C-terminal domains. TRIM proteins play multiple roles in various cellular processes, including cell growth, differentiation, apoptosis and antiviral immunity. Fish novel large multigene TRIM genes (finTRIM/ftr) appear only in teleosts and play a vital role in antiviral responses. Phylogenetic analysis revealed the existence of different subsets of novel fish TRIM 14 genes (finTRIM14/ftr14), ftr51, ftr67, ftr72, ftr82, ftr83, and ftr99 in grass carp (Ctenopharyngodon idella), suggesting lineage-specific diversification events. Therefore, the number of finTRIM genes varies greatly among species. The ftr genes in grass carp, which are closely related to zebrafish and possess various evolutionary branches, have evolved faster than human TRIMs. The predicted protein domains were almost identical RING zinc finger domains, with the exception of ftr72, the B-box domain (excluding ftr67, ftr82, ftr83), and the B30.2 domain, which evolved under positive selection (with the exception of ftr67, and ftr72). The genes were predominantly expressed in the spleen, gill and head kidney. These findings indicate that the ftr genes in grass carp are involved diverse cellular processes, including innate immune responses.}, } @article {pmid28476613, year = {2017}, author = {Sparham, SJ and Kwong, JC and Valcanis, M and Easton, M and Trott, DJ and Seemann, T and Stinear, TP and Howden, BP}, title = {Emergence of multidrug resistance in locally-acquired human infections with Salmonella Typhimurium in Australia owing to a new clade harbouring blaCTX-M-9.}, journal = {International journal of antimicrobial agents}, volume = {50}, number = {1}, pages = {101-105}, doi = {10.1016/j.ijantimicag.2017.02.014}, pmid = {28476613}, issn = {1872-7913}, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; Australia ; Cattle ; Cephalosporins/*pharmacology ; Computational Biology ; *Drug Resistance, Multiple, Bacterial ; Escherichia coli Proteins/*metabolism ; Humans ; Molecular Epidemiology ; Phylogeny ; Salmonella Infections/epidemiology/*microbiology ; Salmonella Infections, Animal/epidemiology/*microbiology ; Salmonella typhimurium/classification/*drug effects/enzymology/genetics ; Whole Genome Sequencing ; beta-Lactamases/*metabolism ; }, abstract = {Antimicrobial resistance in non-typhoidal Salmonella is a critical problem globally, with the emergence of resistance to third-generation cephalosporins (3GCs) a particular concern. The aim of this study was to use whole-genome sequencing (WGS) to characterise recently identified human and non-human isolates of 3GC-resistant Salmonella enterica subsp. enterica serovar Typhimurium from Australia. The Illumina NextSeq sequencing platform was used to determine the genome sequences of 78 S. Typhimurium definitive type 44 isolated in Australia between 1992 and 2016, including 31 3GC-resistant isolates. Phylogenetic and bioinformatics analyses were subsequently performed using a number of in silico tools. We report the emergence of 3GC resistance in locally-acquired Australian S. Typhimurium for the first time. Phenotypically resistant isolates of human and animal origin were geographically restricted and were found by WGS all to be closely related and to carry blaCTX-M-9. Dairy cattle were the suspected source based on geographical clustering of animal isolates, which were predominantly bovine in origin. In conclusion, locally-acquired human cases of S. Typhimurium carrying blaCTX-M-9 were identified that appear to be of bovine origin, raising concerns regarding the human impact of off-label use of ceftiofur in cattle.}, } @article {pmid28473709, year = {2017}, author = {Wang, J and Li, Y and Yang, Y and Chen, X and Du, J and Zheng, Q and Liang, Z and Wang, Y}, title = {A New Strategy for Deleting Animal drugs from Traditional Chinese Medicines based on Modified Yimusake Formula.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {1504}, pmid = {28473709}, issn = {2045-2322}, mesh = {Animals ; Catalytic Domain ; Computational Biology ; Drug Delivery Systems ; Drugs, Chinese Herbal/*chemistry ; Humans ; Hydrogen Bonding ; Ligands ; *Medicine, Chinese Traditional ; Molecular Conformation ; Molecular Dynamics Simulation ; Phytochemicals/analysis/chemistry ; Reproducibility of Results ; }, abstract = {Traditional Chinese medicine (TCM), such as Uyghur Medicine (UM) has been used in clinical treatment for many years. TCM is featured as multiple targets and complex mechanisms of action, which is normally a combination of medicinal herbs and sometimes even contains certain rare animal medicinal ingredients. A question arises as to whether these animal materials can be removed replaced from TCM applications due to their valuable rare resources or animal ethics. Here, we select a classical UM Yimusake formula, which contains 3 animal drugs and other 8 herbs, and has got wealthy experience and remarkable achievements in treating erectile dysfunction (ED) in China. The active components, drug targets and therapeutic mechanisms have been comprehensively analyzed by systems-pharmacology methods. Additionally, to validate the inhibitory effects of all candidate compounds on their related targets, in vitro experiments, computational analysis and molecular dynamics simulations were performed. The results show that the modified, original and three animal materials display very similar mechanisms for an effective treatment of ED, indicating that it is quite possible to remove these three animal drugs from the original formula while still keep its efficiency. This work provides a new attempt for deleting animal materials from TCM, which should be important for optimization of traditional medicines.}, } @article {pmid28472072, year = {2017}, author = {Olesen, SW and Duvallet, C and Alm, EJ}, title = {dbOTU3: A new implementation of distribution-based OTU calling.}, journal = {PloS one}, volume = {12}, number = {5}, pages = {e0176335}, pmid = {28472072}, issn = {1932-6203}, mesh = {Algorithms ; *Phylogeny ; }, abstract = {Distribution-based operational taxonomic unit-calling (dbOTU) improves on other approaches by incorporating information about the input sequences' distribution across samples. Previous implementations of dbOTU presented challenges for users. Here we introduce and evaluate a new implementation of dbOTU that is faster and more user-friendly. We show that this new implementation has theoretical and practical improvements over previous implementations of dbOTU, making the algorithm more accessible to microbial ecology and biomedical researchers.}, } @article {pmid28466792, year = {2017}, author = {Mustafin, ZS and Lashin, SA and Matushkin, YG and Gunbin, KV and Afonnikov, DA}, title = {Orthoscape: a cytoscape application for grouping and visualization KEGG based gene networks by taxonomy and homology principles.}, journal = {BMC bioinformatics}, volume = {18}, number = {Suppl 1}, pages = {1427}, pmid = {28466792}, issn = {1471-2105}, mesh = {Computational Biology/*methods ; *Computer Graphics ; Databases, Genetic ; Evolution, Molecular ; *Gene Regulatory Networks ; Humans ; *Sequence Homology, Nucleic Acid ; *Software ; }, abstract = {BACKGROUND: There are many available software tools for visualization and analysis of biological networks. Among them, Cytoscape (http://cytoscape.org/) is one of the most comprehensive packages, with many plugins and applications which extends its functionality by providing analysis of protein-protein interaction, gene regulatory and gene co-expression networks, metabolic, signaling, neural as well as ecological-type networks including food webs, communities networks etc. Nevertheless, only three plugins tagged 'network evolution' found in Cytoscape official app store and in literature. We have developed a new Cytoscape 3.0 application Orthoscape aimed to facilitate evolutionary analysis of gene networks and visualize the results.

RESULTS: Orthoscape aids in analysis of evolutionary information available for gene sets and networks by highlighting: (1) the orthology relationships between genes; (2) the evolutionary origin of gene network components; (3) the evolutionary pressure mode (diversifying or stabilizing, negative or positive selection) of orthologous groups in general and/or branch-oriented mode. The distinctive feature of Orthoscape is the ability to control all data analysis steps via user-friendly interface.

CONCLUSION: Orthoscape allows its users to analyze gene networks or separated gene sets in the context of evolution. At each step of data analysis, Orthoscape also provides for convenient visualization and data manipulation.}, } @article {pmid28463399, year = {2017}, author = {Höhna, S and Landis, MJ and Heath, TA}, title = {Phylogenetic Inference Using RevBayes.}, journal = {Current protocols in bioinformatics}, volume = {57}, number = {}, pages = {6.16.1-6.16.34}, doi = {10.1002/cpbi.22}, pmid = {28463399}, issn = {1934-340X}, mesh = {Bayes Theorem ; Computational Biology/*methods ; Likelihood Functions ; Models, Genetic ; *Models, Statistical ; *Phylogeny ; *Software ; }, abstract = {Bayesian phylogenetic inference aims to estimate the evolutionary relationships among different lineages (species, populations, gene families, viral strains, etc.) in a model-based statistical framework that uses the likelihood function for parameter estimates. In recent years, evolutionary models for Bayesian analysis have grown in number and complexity. RevBayes uses a probabilistic-graphical model framework and an interactive scripting language for model specification to accommodate and exploit model diversity and complexity within a single software package. In this unit we describe how to specify standard phylogenetic models and perform Bayesian phylogenetic analyses in RevBayes. The protocols focus on the basic analysis of inferring a phylogeny from single and multiple loci, describe a hypothesis-testing approach, and point to advanced topics. Thus, this unit is a starting point to illustrate the power and potential of Bayesian inference under complex phylogenetic models in RevBayes. © 2017 by John Wiley & Sons, Inc.}, } @article {pmid28461482, year = {2017}, author = {Alroy, J}, title = {Effects of habitat disturbance on tropical forest biodiversity.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {114}, number = {23}, pages = {6056-6061}, pmid = {28461482}, issn = {1091-6490}, mesh = {Animals ; Biodiversity ; Conservation of Natural Resources/*methods/*trends ; Databases, Factual ; Ecology ; Ecosystem ; Extinction, Biological ; Forests ; Rainforest ; Trees ; Tropical Climate ; }, abstract = {It is widely expected that habitat destruction in the tropics will cause a mass extinction in coming years, but the potential magnitude of the loss is unclear. Existing literature has focused on estimating global extinction rates indirectly or on quantifying effects only at local and regional scales. This paper directly predicts global losses in 11 groups of organisms that would ensue from disturbance of all remaining tropical forest habitats. The results are based on applying a highly accurate method of estimating species richness to 875 ecological samples. About 41% of the tree and animal species in this dataset are absent from disturbed habitats, even though most samples do still represent forests of some kind. The individual figures are 30% for trees and 8-65% for 10 animal groups. Local communities are more robust to disturbance because losses are partially balanced out by gains resulting from homogenization.}, } @article {pmid28460257, year = {2017}, author = {Ali, N and Haque, M and Venturino, E and Chakravarty, S}, title = {Dynamics of a three species ratio-dependent food chain model with intra-specific competition within the top predator.}, journal = {Computers in biology and medicine}, volume = {85}, number = {}, pages = {63-74}, doi = {10.1016/j.compbiomed.2017.04.007}, pmid = {28460257}, issn = {1879-0534}, mesh = {Algorithms ; Animals ; Computational Biology ; Computer Simulation ; *Food Chain ; *Models, Biological ; }, abstract = {In this paper, a ratio-dependent food chain model has been considered. The total population has been divided into three classes, namely prey, predator and top-predator population. We have also incorporated intra-specific competition of predators in the model. We have studied the boundedness, dissipativeness and permanence of the solutions of the system and analyzed the existence of various equilibrium points and stability of the system at those equilibrium points. The system exhibits Bogdanov-Takens bifurcation, saddle-node bifurcation, Hopf bifurcation for suitable choice of the relevant parameters. The results of extensive numerical simulation are provided to support the validity of the theoretical findings. The ecological implications of our analytical and numerical findings are discussed.}, } @article {pmid28459977, year = {2017}, author = {Simovski, B and Vodák, D and Gundersen, S and Domanska, D and Azab, A and Holden, L and Holden, M and Grytten, I and Rand, K and Drabløs, F and Johansen, M and Mora, A and Lund-Andersen, C and Fromm, B and Eskeland, R and Gabrielsen, OS and Ferkingstad, E and Nakken, S and Bengtsen, M and Nederbragt, AJ and Thorarensen, HS and Akse, JA and Glad, I and Hovig, E and Sandve, GK}, title = {GSuite HyperBrowser: integrative analysis of dataset collections across the genome and epigenome.}, journal = {GigaScience}, volume = {6}, number = {7}, pages = {1-12}, pmid = {28459977}, issn = {2047-217X}, mesh = {Datasets as Topic/*standards ; *Epigenesis, Genetic ; Epigenomics/*methods/standards ; *Genome, Human ; Humans ; *Software ; Whole Genome Sequencing/*methods/standards ; }, abstract = {BACKGROUND: Recent large-scale undertakings such as ENCODE and Roadmap Epigenomics have generated experimental data mapped to the human reference genome (as genomic tracks) representing a variety of functional elements across a large number of cell types. Despite the high potential value of these publicly available data for a broad variety of investigations, little attention has been given to the analytical methodology necessary for their widespread utilisation.

FINDINGS: We here present a first principled treatment of the analysis of collections of genomic tracks. We have developed novel computational and statistical methodology to permit comparative and confirmatory analyses across multiple and disparate data sources. We delineate a set of generic questions that are useful across a broad range of investigations and discuss the implications of choosing different statistical measures and null models. Examples include contrasting analyses across different tissues or diseases. The methodology has been implemented in a comprehensive open-source software system, the GSuite HyperBrowser. To make the functionality accessible to biologists, and to facilitate reproducible analysis, we have also developed a web-based interface providing an expertly guided and customizable way of utilizing the methodology. With this system, many novel biological questions can flexibly be posed and rapidly answered.

CONCLUSIONS: Through a combination of streamlined data acquisition, interoperable representation of dataset collections, and customizable statistical analysis with guided setup and interpretation, the GSuite HyperBrowser represents a first comprehensive solution for integrative analysis of track collections across the genome and epigenome. The software is available at: https://hyperbrowser.uio.no.}, } @article {pmid28458014, year = {2017}, author = {Cicconardi, F and Marcatili, P and Arthofer, W and Schlick-Steiner, BC and Steiner, FM}, title = {Positive diversifying selection is a pervasive adaptive force throughout the Drosophila radiation.}, journal = {Molecular phylogenetics and evolution}, volume = {112}, number = {}, pages = {230-243}, doi = {10.1016/j.ympev.2017.04.023}, pmid = {28458014}, issn = {1095-9513}, support = {P 23949/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Animals ; Base Sequence ; *Biological Evolution ; DNA, Mitochondrial/genetics ; Drosophila/*genetics ; Evolution, Molecular ; Gene Ontology ; *Genetic Variation ; Genome, Mitochondrial ; Longevity ; Phylogeny ; *Selection, Genetic ; Species Specificity ; Stress, Physiological ; Temperature ; Transcriptome/genetics ; }, abstract = {The growing genomic information on non-model organisms eases exploring the evolutionary history of biodiversity. This is particularly true for Drosophila flies, in which the number of sequenced species doubled recently. Because of its outstanding diversity of species, Drosophila has become one of the most important systems to study adaptive radiation. In this study, we performed a genome-wide analysis of positive diversifying selection on more than 2000 single-copy orthologous groups in 25 species using a recent method of increased accuracy for detecting positive diversifying selection. Adopting this novel approach enabled us to find a consistent selection signal throughout the genus Drosophila, and a total of 1342 single-copy orthologous groups were identified with a putative signal of positive diversifying selection, corresponding to 1.9% of all loci. Specifically, in lineages leading to D. grimshawi, a strong putative signal of positive diversifying selection was found related to cell, morphological, neuronal, and sensorial development and function. A recurrent signal of positive diversifying selection was found on genes related to aging and lifespan, suggesting that selection had shaped lifespan diversity in Drosophila, including extreme longevity. Our study, one of the largest and most comprehensive ones on genome-wide positive diversifying selection to date, shows that positive diversifying selection has promoted species-specific differentiation among evolutionary lineages throughout the Drosophila radiation. Acting on the same biological processes via different routes, positive diversifying selection has promoted diversity of functions and adaptive divergence.}, } @article {pmid28455605, year = {2017}, author = {Ferrás, C and García, Y and Aguilera, A and Rocha, Á}, title = {How Can Geography and Mobile Phones Contribute to Psychotherapy?.}, journal = {Journal of medical systems}, volume = {41}, number = {6}, pages = {92}, pmid = {28455605}, issn = {1573-689X}, support = {K23 MH094442/MH/NIMH NIH HHS/United States ; }, mesh = {*Cell Phone ; Geography ; Humans ; Internet ; Mental Health ; Psychotherapy ; }, abstract = {Interdisciplinary relationships between Geography and Psychotherapy are an opportunity for innovation. Indeed, scientific works found on bibliographic databases and concerning this theme are scarce. Geographical sub-fields, such as the Geography of Emotions or Psychoanalytical Geography have started to emerge, theorizing about and interpreting feelings, emotions, moods, sufferings, of the chronically ill or diversified social groups and sites. But a less theoretical and more practical approach, in the sense of proposing, predicting and intervening, is lacking; as well as research into the possibilities offered by communication technologies and mobile phones. In the present work, we present the results of a review of the most relevant scientific works published internationally; we reflect on the contributions of Geography and mobile phones to psychosocial therapies and define the orientation and questions that should be posed in future research, from the point of view of geography and regarding psychotherapy. We conclude that the production of georeferenced data via mobile phones concerning the daily lives of people opens great possibilities for cognitive behavioural therapy and mental health. They allow for the development of personalized mood maps that locate the places where a person experiences greater or lesser stress on a daily basis; they allow for a cartography of emotions, a cognitive cartography of the places we access physically or through the Internet, of our feelings and psychosocial experiences. They open the door to the possibility of offering personalized psychotherapy treatments focusing on the ecological-environmental analysis of the places frequented by the person on a daily basis.}, } @article {pmid28453624, year = {2017}, author = {Levy Karin, E and Shkedy, D and Ashkenazy, H and Cartwright, RA and Pupko, T}, title = {Inferring Rates and Length-Distributions of Indels Using Approximate Bayesian Computation.}, journal = {Genome biology and evolution}, volume = {9}, number = {5}, pages = {1280-1294}, pmid = {28453624}, issn = {1759-6653}, mesh = {Algorithms ; *Bayes Theorem ; Computational Biology/methods ; Computer Simulation ; Evolution, Molecular ; Humans ; *INDEL Mutation ; Models, Genetic ; *Models, Statistical ; Mutation Rate ; Software ; }, abstract = {The most common evolutionary events at the molecular level are single-base substitutions, as well as insertions and deletions (indels) of short DNA segments. A large body of research has been devoted to develop probabilistic substitution models and to infer their parameters using likelihood and Bayesian approaches. In contrast, relatively little has been done to model indel dynamics, probably due to the difficulty in writing explicit likelihood functions. Here, we contribute to the effort of modeling indel dynamics by presenting SpartaABC, an approximate Bayesian computation (ABC) approach to infer indel parameters from sequence data (either aligned or unaligned). SpartaABC circumvents the need to use an explicit likelihood function by extracting summary statistics from simulated sequences. First, summary statistics are extracted from the input sequence data. Second, SpartaABC samples indel parameters from a prior distribution and uses them to simulate sequences. Third, it computes summary statistics from the simulated sets of sequences. By computing a distance between the summary statistics extracted from the input and each simulation, SpartaABC can provide an approximation to the posterior distribution of indel parameters as well as point estimates. We study the performance of our methodology and show that it provides accurate estimates of indel parameters in simulations. We next demonstrate the utility of SpartaABC by studying the impact of alignment errors on the inference of positive selection. A C ++ program implementing SpartaABC is freely available in http://spartaabc.tau.ac.il.}, } @article {pmid28449317, year = {2017}, author = {Shirk, AJ and Landguth, EL and Cushman, SA}, title = {A comparison of individual-based genetic distance metrics for landscape genetics.}, journal = {Molecular ecology resources}, volume = {17}, number = {6}, pages = {1308-1317}, doi = {10.1111/1755-0998.12684}, pmid = {28449317}, issn = {1755-0998}, mesh = {Biostatistics/methods ; Computational Biology/*methods ; Computer Simulation ; *Genetic Variation ; Genetics, Population/*methods ; Models, Genetic ; }, abstract = {A major aim of landscape genetics is to understand how landscapes resist gene flow and thereby influence population genetic structure. An empirical understanding of this process provides a wealth of information that can be used to guide conservation and management of species in fragmented landscapes and also to predict how landscape change may affect population viability. Statistical approaches to infer the true model among competing alternatives are based on the strength of the relationship between pairwise genetic distances and landscape distances among sampled individuals in a population. A variety of methods have been devised to quantify individual genetic distances, but no study has yet compared their relative performance when used for model selection in landscape genetics. In this study, we used population genetic simulations to assess the accuracy of 16 individual-based genetic distance metrics under varying sample sizes and degree of population genetic structure. We found most metrics performed well when sample size and genetic structure was high. However, it was much more challenging to infer the true model when sample size and genetic structure was low. Under these conditions, we found genetic distance metrics based on principal components analysis were the most accurate (although several other metrics performed similarly), but only when they were derived from multiple principal components axes (the optimal number varied depending on the degree of population genetic structure). Our results provide guidance for which genetic distance metrics maximize model selection accuracy and thereby better inform conservation and management decisions based upon landscape genetic analysis.}, } @article {pmid28449274, year = {2017}, author = {Morinière, J and Hendrich, L and Balke, M and Beermann, AJ and König, T and Hess, M and Koch, S and Müller, R and Leese, F and Hebert, PDN and Hausmann, A and Schubart, CD and Haszprunar, G}, title = {A DNA barcode library for Germany's mayflies, stoneflies and caddisflies (Ephemeroptera, Plecoptera and Trichoptera).}, journal = {Molecular ecology resources}, volume = {17}, number = {6}, pages = {1293-1307}, doi = {10.1111/1755-0998.12683}, pmid = {28449274}, issn = {1755-0998}, mesh = {Animals ; DNA Barcoding, Taxonomic/*methods ; *Databases, Genetic ; Ephemeroptera/*classification/*genetics ; Germany ; Holometabola/*classification/*genetics ; }, abstract = {Mayflies, stoneflies and caddisflies (Ephemeroptera, Plecoptera and Trichoptera) are prominent representatives of aquatic macroinvertebrates, commonly used as indicator organisms for water quality and ecosystem assessments. However, unambiguous morphological identification of EPT species, especially their immature life stages, is a challenging, yet fundamental task. A comprehensive DNA barcode library based upon taxonomically well-curated specimens is needed to overcome the problematic identification. Once available, this library will support the implementation of fast, cost-efficient and reliable DNA-based identifications and assessments of ecological status. This study represents a major step towards a DNA barcode reference library as it covers for two-thirds of Germany's EPT species including 2,613 individuals belonging to 363 identified species. As such, it provides coverage for 38 of 44 families (86%) and practically all major bioindicator species. DNA barcode compliant sequences (≥500 bp) were recovered from 98.74% of the analysed specimens. Whereas most species (325, i.e., 89.53%) were unambiguously assigned to a single Barcode Index Number (BIN) by its COI sequence, 38 species (18 Ephemeroptera, nine Plecoptera and 11 Trichoptera) were assigned to a total of 89 BINs. Most of these additional BINs formed nearest neighbour clusters, reflecting the discrimination of geographical subclades of a currently recognized species. BIN sharing was uncommon, involving only two species pairs of Ephemeroptera. Interestingly, both maximum pairwise and nearest neighbour distances were substantially higher for Ephemeroptera compared to Plecoptera and Trichoptera, possibly indicating older speciation events, stronger positive selection or faster rate of molecular evolution.}, } @article {pmid28447371, year = {2017}, author = {Cavaliere, M and Feng, S and Soyer, OS and Jiménez, JI}, title = {Cooperation in microbial communities and their biotechnological applications.}, journal = {Environmental microbiology}, volume = {19}, number = {8}, pages = {2949-2963}, pmid = {28447371}, issn = {1462-2920}, support = {BB/M017982/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/M018040/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/M009769/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/K003240/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {*Biological Evolution ; Biotechnology ; Ecology ; Microbial Consortia/*physiology ; Microbial Interactions/*physiology ; *Models, Biological ; }, abstract = {Microbial communities are increasingly utilized in biotechnology. Efficiency and productivity in many of these applications depends on the presence of cooperative interactions between members of the community. Two key processes underlying these interactions are the production of public goods and metabolic cross-feeding, which can be understood in the general framework of ecological and evolutionary (eco-evo) dynamics. In this review, we illustrate the relevance of cooperative interactions in microbial biotechnological processes, discuss their mechanistic origins and analyse their evolutionary resilience. Cooperative behaviours can be damaged by the emergence of 'cheating' cells that benefit from the cooperative interactions but do not contribute to them. Despite this, cooperative interactions can be stabilized by spatial segregation, by the presence of feedbacks between the evolutionary dynamics and the ecology of the community, by the role of regulatory systems coupled to the environmental conditions and by the action of horizontal gene transfer. Cooperative interactions enrich microbial communities with a higher degree of robustness against environmental stress and can facilitate the evolution of more complex traits. Therefore, the evolutionary resilience of microbial communities and their ability to constraint detrimental mutants should be considered to design robust biotechnological applications.}, } @article {pmid28444848, year = {2018}, author = {Parsons, MH and Apfelbach, R and Banks, PB and Cameron, EZ and Dickman, CR and Frank, ASK and Jones, ME and McGregor, IS and McLean, S and Müller-Schwarze, D and Sparrow, EE and Blumstein, DT}, title = {Biologically meaningful scents: a framework for understanding predator-prey research across disciplines.}, journal = {Biological reviews of the Cambridge Philosophical Society}, volume = {93}, number = {1}, pages = {98-114}, doi = {10.1111/brv.12334}, pmid = {28444848}, issn = {1469-185X}, mesh = {*Animal Communication ; Animals ; *Odorants ; *Predatory Behavior ; *Research ; }, abstract = {Fear of predation is a universal motivator. Because predators hunt using stealth and surprise, there is a widespread ability among prey to assess risk from chemical information - scents - in their environment. Consequently, scents often act as particularly strong modulators of memory and emotions. Recent advances in ecological research and analytical technology are leading to novel ways to use this chemical information to create effective attractants, repellents and anti-anxiolytic compounds for wildlife managers, conservation biologists and health practitioners. However, there is extensive variation in the design, results, and interpretation of studies of olfactory-based risk discrimination. To understand the highly variable literature in this area, we adopt a multi-disciplinary approach and synthesize the latest findings from neurobiology, chemical ecology, and ethology to propose a contemporary framework that accounts for such disparate factors as the time-limited stability of chemicals, highly canalized mechanisms that influence prey responses, and the context within which these scents are detected (e.g. availability of alternative resources, perceived shelter, and ambient physical parameters). This framework helps to account for the wide range of reported responses by prey to predator scents, and explains, paradoxically, how the same individual predator scent can be interpreted as either safe or dangerous to a prey animal depending on how, when and where the cue was deposited. We provide a hypothetical example to illustrate the most common factors that influence how a predator scent (from dingoes, Canis dingo) may both attract and repel the same target organism (kangaroos, Macropus spp.). This framework identifies the catalysts that enable dynamic scents, odours or odorants to be used as attractants as well as deterrents. Because effective scent tools often relate to traumatic memories (fear and/or anxiety) that cause future avoidance, this information may also guide the development of appeasement, enrichment and anti-anxiolytic compounds, and help explain the observed variation in post-traumatic-related behaviours (including post-traumatic stress disorder, PTSD) among diverse terrestrial taxa, including humans.}, } @article {pmid28444603, year = {2017}, author = {Singh, H and Savita, and Sharma, R and Sinha, S and Kumar, M and Kumar, P and Verma, A and Sharma, SK}, title = {Physiological functioning of Lagerstroemia speciosa L. under heavy roadside traffic: an approach to screen potential species for abatement of urban air pollution.}, journal = {3 Biotech}, volume = {7}, number = {1}, pages = {61}, pmid = {28444603}, issn = {2190-572X}, abstract = {The mitigation potential of avenue tree species needs a sound understanding, especially for landscape planning or planting tree species on roadside, especially in city limits where there is huge traffic due to more number of vehicles. A preliminary study was conducted to investigate the impact of heavy traffic movement and pollution thereof on physiological functioning of Lagerstroemia speciosa trees planted on roadside in terms of carbon absorption, mitigation potential and adaptive behavior. Trees on roadside exhibited reduced carbon assimilation (36.7 ± 2.4%) and transpiration rate (42.14 ± 2.9%), decreased stomatal conductance (66.85 ± 3.87%), increased stomatal resistance (212.2 ± 11.25%), more leaf thickness (40.54 ± 3.25) and water use efficiency (9.4 ± 0.87%), and changes in lead (179.31 ± 10.24%) and proline (15.61 ± 1.92%) concentration in leaf tissues when compared to less traffic area (FRI campus). The impacts were also witnessed in the form of enhanced vapour pressure deficit of air (63.18 ± 4.94%) and leaf (45.72 ± 3.25%), and air temperature (3.2 ± 0.16%) and leaf temperature (9.0 ± 0.82%) along roadside trees. It was inferred that heavy traffic movements interrupt the physiological functioning of trees due to alteration in the surrounding environment as compared to non-traffic areas. The present study provides baseline information to further explore and identify the potential avenue tree species having significant mitigation potential and adaptive efficiency to heavy traffic movements for improving urban environment.}, } @article {pmid28444223, year = {2017}, author = {Gokhman, D and Kelman, G and Amartely, A and Gershon, G and Tsur, S and Carmel, L}, title = {Gene ORGANizer: linking genes to the organs they affect.}, journal = {Nucleic acids research}, volume = {45}, number = {W1}, pages = {W138-W145}, pmid = {28444223}, issn = {1362-4962}, mesh = {Chromosomes, Human, X/chemistry ; *Databases, Genetic ; Female ; *Genetic Association Studies ; *Genome, Human ; Genomic Imprinting ; Genotype ; Humans ; Male ; Metabolic Networks and Pathways/genetics ; Organ Specificity/genetics ; Phenotype ; *Software ; }, abstract = {One of the biggest challenges in studying how genes work is understanding their effect on the physiology and anatomy of the body. Existing tools try to address this using indirect features, such as expression levels and biochemical pathways. Here, we present Gene ORGANizer (geneorganizer.huji.ac.il), a phenotype-based tool that directly links human genes to the body parts they affect. It is built upon an exhaustive curated database that links >7000 genes to ∼150 anatomical parts using >150 000 gene-organ associations. The tool offers user-friendly platforms to analyze the anatomical effects of individual genes, and identify trends within groups of genes. We demonstrate how Gene ORGANizer can be used to make new discoveries, showing that chromosome X is enriched with genes affecting facial features, that positive selection targets genes with more constrained phenotypic effects, and more. We expect Gene ORGANizer to be useful in a variety of evolutionary, medical and molecular studies aimed at understanding the phenotypic effects of genes.}, } @article {pmid28444190, year = {2017}, author = {Maffei, VJ and Kim, S and Blanchard, E and Luo, M and Jazwinski, SM and Taylor, CM and Welsh, DA}, title = {Biological Aging and the Human Gut Microbiota.}, journal = {The journals of gerontology. Series A, Biological sciences and medical sciences}, volume = {72}, number = {11}, pages = {1474-1482}, pmid = {28444190}, issn = {1758-535X}, support = {P60 AA009803/AA/NIAAA NIH HHS/United States ; T32 AA007577/AA/NIAAA NIH HHS/United States ; K01 AG027905/AG/NIA NIH HHS/United States ; P01 AG022064/AG/NIA NIH HHS/United States ; R24 AA019661/AA/NIAAA NIH HHS/United States ; P01 HL076100/HL/NHLBI NIH HHS/United States ; P20 GM103629/GM/NIGMS NIH HHS/United States ; }, mesh = {Adult ; Aged ; Aging/*physiology ; Algorithms ; Computational Biology/methods ; Female ; Gastrointestinal Microbiome/*physiology ; High-Throughput Nucleotide Sequencing ; Humans ; Male ; Metagenomics/*methods ; Middle Aged ; Phylogeny ; RNA, Ribosomal, 16S/*genetics ; }, abstract = {The human gastrointestinal microbiota plays a key homeostatic role in normal functioning of physiologic processes commonly undermined by aging. We used a previously validated 34-item frailty index (FI34) to identify changes in gut microbiota community structure associated with biological age of community-dwelling adults. Stool 16S rRNA cDNA libraries from 85 subjects ranging in age (43-79) and FI34 score (0-0.365) were deep sequenced, denoised, and clustered using DADA2. Subject biological age but not chronological age correlated with a decrease in stool microbial diversity. Specific microbial genera were differentially abundant in the lower, middle, and upper 33rd percentiles of biological age. Using Sparse Inverse Covariance Estimation for Ecological Association and Statistical Inference (SPIEC-EASI) and Weighted Gene Co-Expression Network Analysis (WGCNA), we identified modules of coabundant microbial genera that distinguished biological from chronological aging. A biological age-associated module composed of Eggerthella, Ruminococcus, and Coprobacillus genera was robust to correction for subject age, sex, body mass index, antibiotic usage, and other confounders. Subject FI34 score positively correlated with the abundance of this module, which exhibited a distinct inferred metagenome as predicted by Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt). We conclude that increasing biological age in community-dwelling adults is associated with gastrointestinal dysbiosis.}, } @article {pmid28442452, year = {2017}, author = {Byrd-Bredbenner, C and Martin-Biggers, J and Koenings, M and Quick, V and Hongu, N and Worobey, J}, title = {HomeStyles, A Web-Based Childhood Obesity Prevention Program for Families With Preschool Children: Protocol for a Randomized Controlled Trial.}, journal = {JMIR research protocols}, volume = {6}, number = {4}, pages = {e73}, pmid = {28442452}, issn = {1929-0748}, abstract = {BACKGROUND: The home environment is where young children spend most of their time, and is critically important to supporting behaviors that promote health and prevent obesity. However, the home environment and lifestyle patterns remain understudied, and few interventions have investigated parent-led makeovers designed to create home environments that are supportive of optimal child health and healthy child weights.

OBJECTIVE: The aim of the HomeStyles randomized controlled trial (RCT) is to determine whether the Web-based HomeStyles intervention enables and motivates parents to shape the weight-related aspects of their home environments and lifestyle behavioral practices (diet, exercise, and sleep) to be more supportive of their preschool children's optimal health and weight.

METHODS: A rigorous RCT utilizing an experimental group and an attention control group, receiving a bona fide contemporaneous treatment equal in nonspecific treatment effects and differing only in subject matter content, will test the effect of HomeStyles on a diverse sample of families with preschool children. This intervention is based on social cognitive theory and uses a social ecological framework, and will assess: intrapersonal characteristics (dietary intake, physical activity level, and sleep) of parents and children; family interpersonal or social characteristics related to diet, physical activity, media use, and parental values and self-efficacy for obesity-preventive practices; and home environment food availability, physical activity space and supports in and near the home, and media availability and controls in the home.

RESULTS: Enrollment for this study has been completed and statistical data analyses are currently underway.

CONCLUSIONS: This paper describes the HomeStyles intervention with regards to: rationale, the intervention's logic model, sample eligibility criteria and recruitment, experimental group and attention control intervention content, study design, instruments, data management, and planned analyses.}, } @article {pmid28441962, year = {2017}, author = {Westergaard, RP and Genz, A and Panico, K and Surkan, PJ and Keruly, J and Hutton, HE and Chang, LW and Kirk, GD}, title = {Acceptability of a mobile health intervention to enhance HIV care coordination for patients with substance use disorders.}, journal = {Addiction science & clinical practice}, volume = {12}, number = {1}, pages = {11}, pmid = {28441962}, issn = {1940-0640}, support = {K23 DA032306/DA/NIDA NIH HHS/United States ; }, mesh = {Adult ; Anti-Retroviral Agents/administration & dosage/*therapeutic use ; Female ; HIV Infections/*drug therapy/*epidemiology ; Health Behavior ; Humans ; Male ; Medication Adherence ; Mental Disorders/epidemiology ; Middle Aged ; *Mobile Applications ; Motivation ; Patient Navigation/*methods ; Pilot Projects ; Reminder Systems ; Socioeconomic Factors ; Substance-Related Disorders/*epidemiology ; Viral Load ; }, abstract = {BACKGROUND: Persons living with HIV and substance use disorders face barriers to sustained engagement in medical care, leading to suboptimal antiretroviral treatment outcomes. Innovative mobile technology tools such as customizable smartphone applications have the potential to enhance existing care coordination programs, but have not been rigorously studied.

METHODS: We developed and implemented a two-component intervention consisting of peer health navigation supported by a smartphone application conducting ecologic momentary assessment (EMA) of barriers to care and medication adherence. Patients with a history of antiretroviral treatment failure and substance use were recruited to participate in the 9-month pilot intervention. Three peer health navigators were trained to provide social and logistical support while participants re-engaged in HIV care. We assessed the acceptability of the intervention components using qualitative analysis of in-depth interviews conducted with study participants and peer navigators.

RESULTS: Of 19 patients enrolled in the study, 17 participated for at least 2 months and 15 completed the entire 9-month study protocol. The acceptability of the peer navigation intervention was rated favorably by all participants interviewed, who felt that peer support was instrumental in helping them re-engage in HIV care. Participants also responded favorably to the smartphone application, but described its usefulness mostly as providing reminders to take medications and attend appointments, rather than as a facilitator of patient navigation.

CONCLUSIONS: Peer health navigation and smartphone-based EMA are acceptable approaches to facilitating engagement in HIV care for drug using populations. Future studies to evaluate the efficacy of this approach for improving long-term retention in care and antiretroviral treatment outcomes are warranted. ClinicalTrials.gov Identifier NCT01941108; registered on September 4, 2013.}, } @article {pmid28439121, year = {2017}, author = {Mukherjee, A and Chettri, B and Langpoklakpam, JS and Basak, P and Prasad, A and Mukherjee, AK and Bhattacharyya, M and Singh, AK and Chattopadhyay, D}, title = {Bioinformatic Approaches Including Predictive Metagenomic Profiling Reveal Characteristics of Bacterial Response to Petroleum Hydrocarbon Contamination in Diverse Environments.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {1108}, pmid = {28439121}, issn = {2045-2322}, mesh = {Bacteria/classification/*drug effects ; Biota/*drug effects ; Cluster Analysis ; Computational Biology/*methods ; DNA, Ribosomal/chemistry/genetics ; *Environmental Microbiology ; Environmental Pollutants/*metabolism ; Metagenomics/*methods ; Petroleum/*metabolism ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Microbial remediation of oil polluted habitats remains one of the foremost methods for restoration of petroleum hydrocarbon contaminated environments. The development of effective bioremediation strategies however, require an extensive understanding of the resident microbiome of these habitats. Recent developments such as high-throughput sequencing has greatly facilitated the advancement of microbial ecological studies in oil polluted habitats. However, effective interpretation of biological characteristics from these large datasets remain a considerable challenge. In this study, we have implemented recently developed bioinformatic tools for analyzing 65 16S rRNA datasets from 12 diverse hydrocarbon polluted habitats to decipher metagenomic characteristics of the resident bacterial communities. Using metagenomes predicted from 16S rRNA gene sequences through PICRUSt, we have comprehensively described phylogenetic and functional compositions of these habitats and additionally inferred a multitude of metagenomic features including 255 taxa and 414 functional modules which can be used as biomarkers for effective distinction between the 12 oil polluted sites. Additionally, we show that significantly over-represented taxa often contribute to either or both, hydrocarbon degradation and additional important functions. Our findings reveal significant differences between hydrocarbon contaminated sites and establishes the importance of endemic factors in addition to petroleum hydrocarbons as driving factors for sculpting hydrocarbon contaminated bacteriomes.}, } @article {pmid28438702, year = {2017}, author = {Hennequin, S and Rouhan, G and Salino, A and Duan, YF and Lepeigneux, MC and Guillou, M and Ansell, S and Almeida, TE and Zhang, LB and Schneider, H}, title = {Global phylogeny and biogeography of the fern genus Ctenitis (Dryopteridaceae), with a focus on the Indian Ocean region.}, journal = {Molecular phylogenetics and evolution}, volume = {112}, number = {}, pages = {277-289}, doi = {10.1016/j.ympev.2017.04.012}, pmid = {28438702}, issn = {1095-9513}, mesh = {Africa ; Databases as Topic ; Dryopteridaceae/*classification ; Indian Ocean ; Islands ; Likelihood Functions ; *Phylogeny ; *Phylogeography ; Time Factors ; }, abstract = {The diverse and pantropical genus Ctenitis, in the Dryopteridaceae, has been largely ignored in phylogenetic studies until now. In this study, we fill in this gap by reconstructing the first comprehensive phylogeny of the genus including 53 species currently recognized in the genus Ctenitis, among which seven species formerly were assigned to the genus Pseudotectaria and one to Heterogonium. Special emphasis was given to the sampling of species occurring in the African-Indian Ocean region. The presented results include reconstruction of a biogeographic scenario based on estimated divergence times and ancestral area reconstruction. Our findings confirm the inclusion, within Ctenitis, of the Indian Ocean species formerly placed in Pseudotectaria and Heterogonium. The crown group divergence was estimated to date back to the Oligocene or Early Miocene. The biogeographical scenario indicates an initial divergence of the Asian-Pacific ranges and the neotropical ranges, and a subsequent colonization of the Afro-Madagascan region by a lineage with neotropical ancestors. The Afro-Madagascan lineage splits into a lineage endemic to the Mascarene islands and a lineage occurring in Madagascar, the Comoros and Africa. The range expansion towards Africa and Madagascar was estimated to date back to the late Miocene, whereas the estimated ages for the onset of the diversification of the Mascarene diversity is consistent with the ages of these young, volcanic islands. The absence of any extant species of Ctenitis with a multi-continental distribution range and the rarity of inter-island dispersal and speciation in the Indian Ocean region suggest a limited contribution of long distance dispersal to the biogeographical history of this fern genus, versus a high contribution of local speciation.}, } @article {pmid28437440, year = {2017}, author = {Gandy, LM and Gumm, J and Fertig, B and Thessen, A and Kennish, MJ and Chavan, S and Marchionni, L and Xia, X and Shankrit, S and Fertig, EJ}, title = {Synthesizer: Expediting synthesis studies from context-free data with information retrieval techniques.}, journal = {PloS one}, volume = {12}, number = {4}, pages = {e0175860}, pmid = {28437440}, issn = {1932-6203}, support = {P30 CA006973/CA/NCI NIH HHS/United States ; R01 CA200859/CA/NCI NIH HHS/United States ; }, mesh = {Algorithms ; *Database Management Systems ; Databases, Factual ; Information Storage and Retrieval/*methods ; *Software ; }, abstract = {Scientists have unprecedented access to a wide variety of high-quality datasets. These datasets, which are often independently curated, commonly use unstructured spreadsheets to store their data. Standardized annotations are essential to perform synthesis studies across investigators, but are often not used in practice. Therefore, accurately combining records in spreadsheets from differing studies requires tedious and error-prone human curation. These efforts result in a significant time and cost barrier to synthesis research. We propose an information retrieval inspired algorithm, Synthesize, that merges unstructured data automatically based on both column labels and values. Application of the Synthesize algorithm to cancer and ecological datasets had high accuracy (on the order of 85-100%). We further implement Synthesize in an open source web application, Synthesizer (https://github.com/lisagandy/synthesizer). The software accepts input as spreadsheets in comma separated value (CSV) format, visualizes the merged data, and outputs the results as a new spreadsheet. Synthesizer includes an easy to use graphical user interface, which enables the user to finish combining data and obtain perfect accuracy. Future work will allow detection of units to automatically merge continuous data and application of the algorithm to other data formats, including databases.}, } @article {pmid28430166, year = {2017}, author = {Torres-Barceló, C and Kaltz, O and Froissart, R and Gandon, S and Ginet, N and Ansaldi, M}, title = {"French Phage Network"-Second Meeting Report.}, journal = {Viruses}, volume = {9}, number = {4}, pages = {}, pmid = {28430166}, issn = {1999-4915}, mesh = {Bacteriophages/*genetics/*physiology ; Biomedical Research/*organization & administration ; *Community Networks ; France ; Intersectoral Collaboration ; }, abstract = {The study of bacteriophages (viruses of bacteria) includes a variety of approaches, such as structural biology, genetics, ecology, and evolution, with increasingly important implications for therapeutic and industrial uses. Researchers working with phages in France have recently established a network to facilitate the exchange on complementary approaches, but also to engage new collaborations. Here, we provide a summary of the topics presented during the second meeting of the French Phage Network that took place in Marseille in November 2016.}, } @article {pmid28425128, year = {2017}, author = {Karimi, A and Tulloch, AIT and Brown, G and Hockings, M}, title = {Understanding the effects of different social data on selecting priority conservation areas.}, journal = {Conservation biology : the journal of the Society for Conservation Biology}, volume = {31}, number = {6}, pages = {1439-1449}, doi = {10.1111/cobi.12947}, pmid = {28425128}, issn = {1523-1739}, mesh = {Agriculture ; Community Participation ; *Conservation of Natural Resources ; Forestry ; *Geographic Information Systems ; Queensland ; *Social Values ; Urbanization ; }, abstract = {Conservation success is contingent on assessing social and environmental factors so that cost-effective implementation of strategies and actions can be placed in a broad social-ecological context. Until now, the focus has been on how to include spatially explicit social data in conservation planning, whereas the value of different kinds of social data has received limited attention. In a regional systematic conservation planning case study in Australia, we examined the spatial concurrence of a range of spatially explicit social values and land-use preferences collected using a public participation geographic information system and biological data. We used Zonation to integrate the social data with the biological data in a series of spatial-prioritization scenarios to determine the effect of the different types of social data on spatial prioritization compared with biological data alone. The type of social data (i.e., conservation opportunities or constraints) significantly affected spatial prioritization outcomes. The integration of social values and land-use preferences under different scenarios was highly variable and generated spatial prioritizations 1.2-51% different from those based on biological data alone. The inclusion of conservation-compatible values and preferences added relatively few new areas to conservation priorities, whereas including noncompatible economic values and development preferences as costs significantly changed conservation priority areas (48.2% and 47.4%, respectively). Based on our results, a multifaceted conservation prioritization approach that combines spatially explicit social data with biological data can help conservation planners identify the type of social data to collect for more effective and feasible conservation actions.}, } @article {pmid28424342, year = {2017}, author = {Farine, DR and Strandburg-Peshkin, A and Couzin, ID and Berger-Wolf, TY and Crofoot, MC}, title = {Individual variation in local interaction rules can explain emergent patterns of spatial organization in wild baboons.}, journal = {Proceedings. Biological sciences}, volume = {284}, number = {1853}, pages = {}, pmid = {28424342}, issn = {1471-2954}, mesh = {Algorithms ; Animals ; *Behavior, Animal ; Female ; Geographic Information Systems ; Kenya ; Male ; Models, Theoretical ; Papio/physiology/*psychology ; *Social Behavior ; }, abstract = {Researchers have long noted that individuals occupy consistent spatial positions within animal groups. However, an individual's position depends not only on its own behaviour, but also on the behaviour of others. Theoretical models of collective motion suggest that global patterns of spatial assortment can arise from individual variation in local interaction rules. However, this prediction remains untested. Using high-resolution GPS tracking of members of a wild baboon troop, we identify consistent inter-individual differences in within-group spatial positioning. We then apply an algorithm that identifies what number of conspecific group members best predicts the future location of each individual (we call this the individual's neighbourhood size) while the troop is moving. We find clear variation in the most predictive neighbourhood size, and this variation relates to individuals' propensity to be found near the centre of their group. Using simulations, we show that having different neighbourhood sizes is a simple candidate mechanism capable of linking variation in local individual interaction rules-in this case how many conspecifics an individual interacts with-to global patterns of spatial organization, consistent with the patterns we observe in wild primates and a range of other organisms.}, } @article {pmid28423967, year = {2018}, author = {Xia, JH and Li, HL and Zhang, Y and Meng, ZN and Lin, HR}, title = {Identifying selectively important amino acid positions associated with alternative habitat environments in fish mitochondrial genomes.}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {29}, number = {4}, pages = {511-524}, doi = {10.1080/24701394.2017.1315567}, pmid = {28423967}, issn = {2470-1408}, mesh = {*Adaptation, Physiological ; Amino Acids/chemistry/genetics/metabolism ; Animals ; Bayes Theorem ; Databases, Factual ; Ecosystem ; Fish Proteins/*genetics ; Fresh Water ; *Genome, Mitochondrial ; Mitochondrial Proteins/*genetics ; Salinity ; Seawater ; *Selection, Genetic ; Tilapia/*genetics/growth & development/metabolism ; }, abstract = {Fish species inhabitating seawater (SW) or freshwater (FW) habitats have to develop genetic adaptations to alternative environment factors, especially salinity. Functional consequences of the protein variations associated with habitat environments in fish mitochondrial genomes have not yet received much attention. We analyzed 829 complete fish mitochondrial genomes and compared the amino acid differences of 13 mitochondrial protein families between FW and SW fish groups. We identified 47 specificity determining sites (SDS) that associated with FW or SW environments from 12 mitochondrial protein families. Thirty-two (68%) of the SDS sites are hydrophobic, 13 (28%) are neutral, and the remaining sites are acidic or basic. Seven of those SDS from ND1, ND2 and ND5 were scored as probably damaging to the protein structures. Furthermore, phylogenetic tree based Bayes Empirical Bayes analysis also detected 63 positive sites associated with alternative habitat environments across ten mtDNA proteins. These signatures could be important for studying mitochondrial genetic variation relevant to fish physiology and ecology.}, } @article {pmid28423635, year = {2017}, author = {Annaratone, L and Simonetti, M and Wernersson, E and Marchiò, C and Garnerone, S and Scalzo, MS and Bienko, M and Chiarle, R and Sapino, A and Crosetto, N}, title = {Quantification of HER2 and estrogen receptor heterogeneity in breast cancer by single-molecule RNA fluorescence in situ hybridization.}, journal = {Oncotarget}, volume = {8}, number = {12}, pages = {18680-18698}, pmid = {28423635}, issn = {1949-2553}, mesh = {Adult ; Aged ; Area Under Curve ; Biomarkers, Tumor/*analysis ; Breast Neoplasms/classification/*pathology ; Female ; Humans ; Image Interpretation, Computer-Assisted ; Immunohistochemistry ; In Situ Hybridization, Fluorescence/*methods ; Middle Aged ; Multiplex Polymerase Chain Reaction ; RNA/analysis ; ROC Curve ; Real-Time Polymerase Chain Reaction ; Receptor, ErbB-2/analysis/*biosynthesis ; Receptors, Estrogen/analysis/*biosynthesis ; Sensitivity and Specificity ; }, abstract = {Intra-tumor heterogeneity is a pervasive property of human cancers that poses a major clinical challenge. Here, we describe the characterization, at the transcriptional level, of the intra-tumor topography of two prominent breast cancer biomarkers and drug targets, epidermal growth factor receptor 2 (HER2) and estrogen receptor 1 (ER) in 49 archival breast cancer samples. We developed a protocol for single-molecule RNA FISH in formalin-fixed, paraffin-embedded tissue sections (FFPE-smFISH), which enabled us to simultaneously detect and perform absolute quantification of HER2 and ER mature transcripts in single cells and multiple tumor regions. We benchmarked our method with standard diagnostic techniques, demonstrating that FFPE-smFISH is able to correctly classify breast cancers into well-established molecular subgroups. By counting transcripts in thousands of single cells, we identified different expression modes and levels of inter-cellular variability. In samples expressing both HER2 and ER, many cells co-expressed both genes, although expression levels were typically uncorrelated. Finally, we applied diversity metrics from the field of ecology to assess the intra-tumor topography of HER2 and ER gene expression, revealing that the spatial distribution of these key biomarkers can vary substantially even among breast cancers of the same subtype. Our results demonstrate that FFPE-smFISH is a reliable diagnostic assay and a powerful method for quantification of intra-tumor transcriptional heterogeneity of selected biomarkers in clinical samples.}, } @article {pmid28420407, year = {2017}, author = {Risueño, J and Muñoz, C and Pérez-Cutillas, P and Goyena, E and Gonzálvez, M and Ortuño, M and Bernal, LJ and Ortiz, J and Alten, B and Berriatua, E}, title = {Understanding Phlebotomus perniciosus abundance in south-east Spain: assessing the role of environmental and anthropic factors.}, journal = {Parasites & vectors}, volume = {10}, number = {1}, pages = {189}, pmid = {28420407}, issn = {1756-3305}, mesh = {*Animal Distribution ; Animal Husbandry ; Animals ; *Climate ; Dogs ; *Environment ; Geographic Information Systems ; Humidity ; Leishmania infantum/isolation & purification ; Leishmaniasis/epidemiology/parasitology ; Phlebotomus/parasitology/*physiology ; Population Density ; Regression Analysis ; Sheep ; Spain ; Temperature ; }, abstract = {BACKGROUND: Leishmaniosis is associated with Phlebotomus sand fly vector density, but our knowledge of the environmental framework that regulates highly overdispersed vector abundance distributions is limited. We used a standardized sampling procedure in the bioclimatically diverse Murcia Region in Spain and multilevel regression models for count data to estimate P. perniciosus abundance in relation to environmental and anthropic factors.

METHODS: Twenty-five dog and sheep premises were sampled for sand flies using adhesive and light-attraction traps, from late May to early October 2015. Temperature, relative humidity and other animal- and premise-related data recorded on site and other environmental data were extracted from digital databases using a geographical information system. The relationship between sand fly abundance and explanatory variables was analysed using binomial regression models.

RESULTS: The total number of sand flies captured, mostly with light-attraction traps, was 3,644 specimens, including 80% P. perniciosus, the main L. infantum vector in Spain. Abundance varied between and within zones and was positively associated with increasing altitude from 0 to 900 m above sea level, except from 500 to 700 m where it was low. Populations peaked in July and especially during a 3-day heat wave when relative humidity and wind speed plummeted. Regression models indicated that climate and not land use or soil characteristics have the greatest impact on this species density on a large geographical scale. In contrast, micro-environmental factors such as animal building characteristics and husbandry practices affect sand fly population size on a smaller scale.

CONCLUSIONS: A standardised sampling procedure and statistical analysis for highly overdispersed distributions allow reliable estimation of P. perniciosus abundance and identification of environmental drivers. While climatic variables have the greatest impact at macro-environmental scale, anthropic factors may be determinant at a micro-geographical scale. These finding may be used to elaborate predictive distribution maps useful for vector and pathogen control programs.}, } @article {pmid28420173, year = {2017}, author = {Zhou, A and Ma, H and Liu, E and Jiang, T and Feng, S and Gong, S and Wang, J}, title = {Transcriptome Sequencing of Dianthus spiculifolius and Analysis of the Genes Involved in Responses to Combined Cold and Drought Stress.}, journal = {International journal of molecular sciences}, volume = {18}, number = {4}, pages = {}, pmid = {28420173}, issn = {1422-0067}, mesh = {Cluster Analysis ; *Cold Temperature ; Computational Biology/methods ; Dianthus/*physiology ; *Droughts ; Gene Expression Profiling ; *Gene Expression Regulation, Plant ; High-Throughput Nucleotide Sequencing ; Molecular Sequence Annotation ; Phenotype ; Protein Interaction Mapping ; Stress, Physiological/*genetics ; *Transcriptome ; }, abstract = {Dianthus spiculifolius, a perennial herbaceous flower and a member of the Caryophyllaceae family, has strong resistance to cold and drought stresses. To explore the transcriptional responses of D. spiculifolius to individual and combined stresses, we performed transcriptome sequencing of seedlings under normal conditions or subjected to cold treatment (CT), simulated drought treatment (DT), or their combination (CTDT). After de novo assembly of the obtained reads, 112,015 unigenes were generated. Analysis of differentially expressed genes (DEGs) showed that 2026, 940, and 2346 genes were up-regulated and 1468, 707, and 1759 were down-regulated in CT, DT, and CTDT samples, respectively. Among all the DEGs, 182 up-regulated and 116 down-regulated genes were identified in all the treatment groups. Analysis of metabolic pathways and regulatory networks associated with the DEGs revealed overlaps and cross-talk between cold and drought stress response pathways. The expression profiles of the selected DEGs in CT, DT, and CTDT samples were characterized and confirmed by quantitative RT-PCR. These DEGs and metabolic pathways may play important roles in the response of D. spiculifolius to the combined stress. Functional characterization of these genes and pathways will provide new targets for enhancement of plant stress tolerance through genetic manipulation.}, } @article {pmid28419550, year = {2017}, author = {Klegarth, AR and Hollocher, H and Jones-Engel, L and Shaw, E and Lee, BPY and Feeney, T and Holmes, D and Laguea, D and Fuentes, A}, title = {Urban primate ranging patterns: GPS-collar deployments for Macaca fascicularis and M. sylvanus.}, journal = {American journal of primatology}, volume = {79}, number = {5}, pages = {}, doi = {10.1002/ajp.22633}, pmid = {28419550}, issn = {1098-2345}, mesh = {*Animal Distribution ; Animals ; Cities ; *Ethology/instrumentation ; Female ; *Geographic Information Systems ; Gibraltar ; Homing Behavior ; Macaca/*physiology ; Macaca fascicularis/physiology ; Male ; Seasons ; Singapore ; }, abstract = {The global increase in urbanization is leading to heavier interface between humans and wildlife. Within these anthropogenic landscapes, little is known about ranging patterns, particularly with regard to urban primates. Here we present the results of the first long-term deployment of multiple GPS collars on two species of macaques to investigate the impacts of urbanization on urban primate ranging patterns in Singapore and Gibraltar. Collars data acquisition were excellent with respect to the amount, quality, and accuracy of data collected; however, remote connectivity and drop-off functionality was poor across all deployments. Analyses highlighted high variability in ranging patterns between individuals within each species that aligned with access to human food resources and patterns of tourism. Individuals from troops with less access to human food had much larger home, core, and day ranges relative to those with regular provisioning or raiding opportunities. Almost no temporal range overlap was observed between any focal individuals at either site and spatial overlap was low for all but two troops at each site. We found no relationship between anthropogenic schedules and changes in ranging patterns. Significant seasonal variation existed for daily path length and day range size for both the Singapore long-tailed and the Gibraltar Barbary macaques, with long-tailed macaques increasing their range during the equatorial monsoon season and Barbary macaques increasing their range during drier, summer months. This study highlights how the behavioral plasticity found within the genus Macaca is reflected in ranging pattern variability within urban environments.}, } @article {pmid28416268, year = {2017}, author = {Chan, YE and Bai, YM and Hsu, JW and Huang, KL and Su, TP and Li, CT and Lin, WC and Pan, TL and Chen, TJ and Tsai, SJ and Chen, MH}, title = {Post-traumatic Stress Disorder and Risk of Parkinson Disease: A Nationwide Longitudinal Study.}, journal = {The American journal of geriatric psychiatry : official journal of the American Association for Geriatric Psychiatry}, volume = {25}, number = {8}, pages = {917-923}, doi = {10.1016/j.jagp.2017.03.012}, pmid = {28416268}, issn = {1545-7214}, mesh = {Aged ; Aged, 80 and over ; Comorbidity ; Databases, Factual/statistics & numerical data ; Female ; Follow-Up Studies ; Humans ; Longitudinal Studies ; Male ; Middle Aged ; National Health Programs/statistics & numerical data ; Parkinson Disease/*epidemiology ; Risk ; Stress Disorders, Post-Traumatic/*epidemiology ; Taiwan/epidemiology ; }, abstract = {OBJECTIVE: Increasing evidence has suggested a relationship between post-traumatic stress disorder (PTSD) and neurodegenerative disorder, such as Alzheimer disease. The association between PTSD and Parkinson disease (PD), however, remains unclear.

METHOD: Using the Taiwan National Health Insurance Research Database, 7,280 subjects (1,456 patients aged ≥45 years with PTSD and 5,824 age-/sex-matched individuals without PTSD) were enrolled between 2002 and 2009 and followed to the end of 2011. Subjects who developed PD during the follow-up period were identified.

RESULTS: An increased risk of developing PD was found in patients with PTSD (Wald χ[2] = 12.061, hazard ratio [HR]: 3.46, 95% confidence interval [CI]: 1.72-6.96) compared with individuals without PTSD, after adjusting for demographic data and medical and psychiatric comorbidities. The sensitivity tests after excluding the first year observation (Wald χ[2] = 7.948, HR: 3.01, 95% CI: 1.40-6.46) and the first 3-year observation (Wald χ[2] = 5.099, HR: 3.07, 95% CI: 1.16-8.15) were consistent.

CONCLUSIONS: Patients with PTSD had an elevated risk of developing PD in later life. Further studies would be required to clarify the exact pathophysiology between PTSD and PD and to investigate whether the prompt intervention for PTSD may reduce this risk.}, } @article {pmid28414047, year = {2018}, author = {Hewitt, BM and Yap, MH and Hodson-Tole, EF and Kennerley, AJ and Sharp, PS and Grant, RA}, title = {A novel automated rodent tracker (ART), demonstrated in a mouse model of amyotrophic lateral sclerosis.}, journal = {Journal of neuroscience methods}, volume = {300}, number = {}, pages = {147-156}, doi = {10.1016/j.jneumeth.2017.04.006}, pmid = {28414047}, issn = {1872-678X}, mesh = {Amyotrophic Lateral Sclerosis/*physiopathology ; Animals ; Behavior, Animal/*physiology ; Disease Models, Animal ; Female ; Image Interpretation, Computer-Assisted/*standards ; Image Processing, Computer-Assisted/*standards ; Locomotion/*physiology ; Mice ; Mice, Inbred C57BL ; Software/*standards ; Superoxide Dismutase-1/genetics ; Video Recording ; }, abstract = {BACKGROUND: Generating quantitative metrics of rodent locomotion and general behaviours from video footage is important in behavioural neuroscience studies. However, there is not yet a free software system that can process large amounts of video data with minimal user interventions.

NEW METHOD: Here we propose a new, automated rodent tracker (ART) that uses a simple rule-based system to quickly and robustly track rodent nose and body points, with minimal user input. Tracked points can then be used to identify behaviours, approximate body size and provide locomotion metrics, such as speed and distance.

RESULTS: ART was demonstrated here on video recordings of a SOD1 mouse model, of amyotrophic lateral sclerosis, aged 30, 60, 90 and 120days. Results showed a robust decline in locomotion speeds, as well as a reduction in object exploration and forward movement, with an increase in the time spent still. Body size approximations (centroid width), showed a significant decrease from P30.

ART performed to a very similar accuracy as manual tracking and Ethovision (a commercially available alternative), with average differences in coordinate points of 0.6 and 0.8mm, respectively. However, it required much less user intervention than Ethovision (6 as opposed to 30 mouse clicks) and worked robustly over more videos.

CONCLUSIONS: ART provides an open-source option for behavioural analysis of rodents, performing to the same standards as commercially available software. It can be considered a validated, and accessible, alternative for researchers for whom non-invasive quantification of natural rodent behaviour is desirable.}, } @article {pmid28410430, year = {2017}, author = {Mitaka, Y and Kobayashi, K and Matsuura, K}, title = {Caste-, sex-, and age-dependent expression of immune-related genes in a Japanese subterranean termite, Reticulitermes speratus.}, journal = {PloS one}, volume = {12}, number = {4}, pages = {e0175417}, pmid = {28410430}, issn = {1932-6203}, mesh = {Age Factors ; Animals ; Databases, Genetic ; Female ; *Gene Expression Regulation ; Immunity, Innate/*genetics ; Insect Proteins/*genetics/*immunology ; Isoptera/*genetics/*immunology ; Japan ; Male ; Pheromones/metabolism ; RNA/chemistry/isolation & purification/metabolism ; Sequence Analysis, RNA ; Sex Factors ; }, abstract = {Insects protect themselves from microbial infections through innate immune responses, including pathogen recognition, phagocytosis, the activation of proteolytic cascades, and the synthesis of antimicrobial peptides. Termites, eusocial insects inhabiting microbe-rich wood, live in closely-related family groups that are susceptible to shared pathogen infections. To resist pathogenic infection, termite families have evolved diverse immune adaptations at both individual and societal levels, and a strategy of trade-offs between reproduction and immunity has been suggested. Although termite immune-inducible genes have been identified, few studies have investigated the differential expression of these genes between reproductive and neuter castes, and between sexes in each caste. In this study, we compared the expression levels of immune-related genes among castes, sexes, and ages in a Japanese subterranean termite, Reticulitermes speratus. Using RNA-seq, we found 197 immune-related genes, including 40 pattern recognition proteins, 97 signalling proteins, 60 effectors. Among these genes, 174 showed differential expression among castes. Comparing expression levels between males and females in each caste, we found sexually dimorphic expression of immune-related genes not only in reproductive castes, but also in neuter castes. Moreover, we identified age-related differential expression of 162 genes in male and/or female reproductives. In addition, although R. speratus is known to use the antibacterial peptide C-type lysozyme as an egg recognition pheromone, we determined that R. speratus has not only C-type, but also P-type and I-type lysozymes, as well as other termite species. Our transcriptomic analyses revealed immune response plasticity among all castes, and sex-biased expression of immune genes even in neuter castes, suggesting a sexual division of labor in the immune system of R. speratus. This study heightens the understanding of the evolution of antimicrobial strategies in eusocial insects, and of sexual roles in insect societies as a whole.}, } @article {pmid28399263, year = {2017}, author = {Baak-Baak, CM and Moo-Llanes, DA and Cigarroa-Toledo, N and Puerto, FI and Machain-Williams, C and Reyes-Solis, G and Nakazawa, YJ and Ulloa-Garcia, A and Garcia-Rejon, JE}, title = {Ecological Niche Model for Predicting Distribution of Disease-Vector Mosquitoes in Yucatán State, México.}, journal = {Journal of medical entomology}, volume = {54}, number = {4}, pages = {854-861}, pmid = {28399263}, issn = {1938-2928}, support = {CC999999//Intramural CDC HHS/United States ; }, mesh = {Aedes/growth & development/*physiology ; *Animal Distribution ; Animals ; Culex/growth & development/*physiology ; Geographic Information Systems ; Larva/physiology ; Mexico ; Models, Biological ; Mosquito Vectors/*physiology ; }, abstract = {The majority of the Yucatán State, México, presents subtropical climate that is suitable for many species of mosquitoes that are known to be vectors of diseases, including those from the genera Aedes and Culex. The objective of this study is to identify the geographic distribution of five species from these two genera and estimate the human population at risk of coming in contact with them. We compiled distributional data for Aedes aegypti (L.), Aedes (Howardina) cozumelensis (Diaz Najera), Culex coronator Dyar and Knab, Culex quinquefasciatus Say, and Culex thriambus Dyar from several entomological studies in Yucatán between March 2010 and September 2014. Based on these data, we constructed ecological niche models to predict the spatial distribution of each species using the MaxEnt algorithm. Our models identified areas with suitable environments for Ae. aegypti in most of Yucatán. A similar percentage of urban (97.1%) and rural (96.5%) populations were contained in areas of highest suitability for Ae. aegypti, and no spatial pattern was found (Moran's I = 0.33, P = 0.38); however, we found an association of abundance of immature forms of this species with annual mean temperature (r = 0.19, P ≤ 0.001) and annual precipitation (r = 0.21, P ≤ 0.001). Aedes cozumelensis is also distributed in most areas of the Yucatán State; Cx. quinquefasciatus, Cx. coronator, and Cx. thriambus are restricted to the northwest. The information generated in this study can inform decision-making to address control measures in priority areas with presence of these vectors.}, } @article {pmid28398567, year = {2018}, author = {Chavali, AK and Rhee, SY}, title = {Bioinformatics tools for the identification of gene clusters that biosynthesize specialized metabolites.}, journal = {Briefings in bioinformatics}, volume = {19}, number = {5}, pages = {1022-1034}, pmid = {28398567}, issn = {1477-4054}, support = {U01 GM110699/GM/NIGMS NIH HHS/United States ; }, mesh = {Algorithms ; Animals ; Bacteria/genetics/metabolism ; Biosynthetic Pathways/*genetics ; Computational Biology/*methods ; Fungi/genetics/metabolism ; Humans ; Models, Genetic ; *Multigene Family ; Plants/genetics/metabolism ; Software ; }, abstract = {Specialized metabolites (also called natural products or secondary metabolites) derived from bacteria, fungi, marine organisms and plants constitute an important source of antibiotics, anti-cancer agents, insecticides, immunosuppressants and herbicides. Many specialized metabolites in bacteria and fungi are biosynthesized via metabolic pathways whose enzymes are encoded by clustered genes on a chromosome. Metabolic gene clusters comprise a group of physically co-localized genes that together encode enzymes for the biosynthesis of a specific metabolite. Although metabolic gene clusters are generally not known to occur outside of microbes, several plant metabolic gene clusters have been discovered in recent years. The discovery of novel metabolic pathways is being enabled by the increasing availability of high-quality genome sequencing coupled with the development of powerful computational toolkits to identify metabolic gene clusters. To provide a comprehensive overview of various bioinformatics methods for detecting gene clusters, we compare and contrast key aspects of algorithmic logic behind several computational tools, including 'NP.searcher', 'ClustScan', 'CLUSEAN', 'antiSMASH', 'SMURF', 'MIDDAS-M', 'ClusterFinder', 'CASSIS/SMIPS' and 'C-Hunter' among others. We also review additional tools such as 'NRPSpredictor' and 'SBSPKS' that can infer substrate specificity for previously identified gene clusters. The continual development of bioinformatics methods to predict gene clusters will help shed light on how organisms assemble multi-step metabolic pathways for adaptation to various ecological niches.}, } @article {pmid28398468, year = {2017}, author = {Saary, P and Forslund, K and Bork, P and Hildebrand, F}, title = {RTK: efficient rarefaction analysis of large datasets.}, journal = {Bioinformatics (Oxford, England)}, volume = {33}, number = {16}, pages = {2594-2595}, pmid = {28398468}, issn = {1367-4811}, mesh = {Computational Biology/*methods ; Environment ; *Microbiota ; *Software ; }, abstract = {MOTIVATION: The rapidly expanding microbiomics field is generating increasingly larger datasets, characterizing the microbiota in diverse environments. Although classical numerical ecology methods provide a robust statistical framework for their analysis, software currently available is inadequate for large datasets and some computationally intensive tasks, like rarefaction and associated analysis.

RESULTS: Here we present a software package for rarefaction analysis of large count matrices, as well as estimation and visualization of diversity, richness and evenness. Our software is designed for ease of use, operating at least 7x faster than existing solutions, despite requiring 10x less memory.

C ++ and R source code (GPL v.2) as well as binaries are available from https://github.com/hildebra/Rarefaction and from CRAN (https://cran.r-project.org/).

CONTACT: bork@embl.de or falk.hildebrand@embl.de.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, } @article {pmid28396152, year = {2017}, author = {Wallace, S and Williams, JH}, title = {Evolutionary origins of pectin methylesterase genes associated with novel aspects of angiosperm pollen tube walls.}, journal = {Biochemical and biophysical research communications}, volume = {487}, number = {3}, pages = {509-516}, doi = {10.1016/j.bbrc.2017.04.027}, pmid = {28396152}, issn = {1090-2104}, mesh = {Amino Acid Sequence ; Carboxylic Ester Hydrolases/*genetics/metabolism ; Computational Biology ; Magnoliopsida/enzymology/*genetics ; Phylogeny ; Pollen Tube/enzymology/*genetics/growth & development ; }, abstract = {The early evolution of angiosperms was marked by a number of innovations of the reproductive cycle including an accelerated fertilization process involving faster transport of sperm to the egg via a pollen tube. Fast pollen tube growth rates in angiosperms are accompanied by a hard shank-soft tip pollen tube morphology. A critical actor in that morphology is the wall-embedded enzyme pectin methylesterase (PME), which in type II PMEs is accompanied by a co-transcribed inhibitor, PMEI. PMEs convert the esterified pectic tip wall to a stiffer state in the subapical flank by pectin de-esterification. It is hypothesized that rapid and precise targeting of PME activity was gained with the origin of type II genes, which are derived and have only expanded since the origin of vascular plants. Pollen-active PMEs have yet to be reported in early-divergent angiosperms or gymnosperms. Gene expression studies in Nymphaea odorata found transcripts from four type II VGD1-like and 16 type I AtPPME1-like homologs that were more abundant in pollen and pollen tubes than in vegetative tissues. The near full-length coding sequence of one type II PME (NoPMEII-1) included at least one PMEI domain. The identification of possible VGD1 homologs in an early-diverging angiosperm suggests that the refined control of PMEs that mediate de-esterification of pectins near pollen tube tips is a conserved feature across angiosperms. The recruitment of type II PMEs into a pollen tube elongation role in angiosperms may represent a key evolutionary step in the development of faster growing pollen tubes.}, } @article {pmid28388919, year = {2017}, author = {Naude, CE and Durao, S and Harper, A and Volmink, J}, title = {Scope and quality of Cochrane reviews of nutrition interventions: a cross-sectional study.}, journal = {Nutrition journal}, volume = {16}, number = {1}, pages = {22}, pmid = {28388919}, issn = {1475-2891}, mesh = {Databases, Factual ; *Dietary Supplements ; Humans ; Micronutrients/*administration & dosage ; Observational Studies as Topic ; Randomized Controlled Trials as Topic ; Review Literature as Topic ; Treatment Outcome ; }, abstract = {BACKGROUND: All countries face significant challenges from complex manifestations of malnutrition, which affects one in three people globally. Systematic reviews provide ready-to-use syntheses of quality-appraised evidence to inform decision-making for actions. To enhance the utility and quality of future Cochrane nutrition evidence, we described the scope and quality of all nutrition systematic reviews in the Cochrane Database of Systematic Reviews (CDSR).

METHODS: We screened all active CDSR records (31 July 2015) to identify reviews and protocols using pre-specified eligibility criteria and definitions. Duplicate, independent data extraction included criteria for inclusion of studies in completed reviews (PICOS). We assessed methodological quality (AMSTAR), use of GRADE, mapped reviews against 2013 Global Burden of Disease data, and categorised the paradigm (medical, lifestyle and socio-ecological) of the review question. We analysed our results using descriptive statistics.

RESULTS: We screened 8484 records, and included 470 (8%) completed reviews (in 45 Cochrane Review Groups (CRGs)) and 169 (7%) protocols (in 41 CRGs) published by 47 of 53 CRGs with reviews. Most completed reviews were produced by the Pregnancy and Childbirth (n = 73), Neonatal (n = 64), Metabolic and Endocrine Disorders (n = 33), Developmental, Psychosocial and Learning Problems (n = 26), Kidney and Transplant (n = 18) and Heart (n = 18) CRGs. Only 27% (n = 129) of reviews had searches for new studies in 2013 or thereafter. Supplementation/supplement interventions were most common (50%; n = 235; majority with micronutrients; 73%, n = 173), followed by food interventions (20%; n = 95). All reviews included randomised controlled trials; about 5% included other designs; 25% used GRADE; the median AMSTAR score was 9 (interquartile range: 7 to 10), 51% were high (AMSTAR 9-11) and 49% moderate (AMSTAR 5-8) quality. More than 80% framed questions using a medical paradigm. For top causes of years-of-life-lost, most reviews addressed preterm birth, diabetes and ischaemic heart disease; for leading risk factors for disability-adjusted-life-years, most targeted childhood undernutrition and high body mass index.

CONCLUSIONS: Nutrition reviews comprised 8% of active CDSR records, were widely distributed across nearly all CRGs and reflected the double nutrition burden. This analysis presents a comprehensive description of the scope and quality of Cochrane nutrition reviews, and identifies gaps for future activities to support actions to address the nutrition burden, in line with the current nutrition agenda and impetus.}, } @article {pmid28387809, year = {2018}, author = {Gkoutos, GV and Schofield, PN and Hoehndorf, R}, title = {The anatomy of phenotype ontologies: principles, properties and applications.}, journal = {Briefings in bioinformatics}, volume = {19}, number = {5}, pages = {1008-1021}, pmid = {28387809}, issn = {1477-4054}, mesh = {Animals ; Animals, Domestic ; Biodiversity ; Biological Evolution ; Biological Ontologies/*statistics & numerical data ; Computational Biology/methods ; Ecology ; Gene Ontology/statistics & numerical data ; Humans ; *Phenotype ; Semantic Web ; }, abstract = {The past decade has seen an explosion in the collection of genotype data in domains as diverse as medicine, ecology, livestock and plant breeding. Along with this comes the challenge of dealing with the related phenotype data, which is not only large but also highly multidimensional. Computational analysis of phenotypes has therefore become critical for our ability to understand the biological meaning of genomic data in the biological sciences. At the heart of computational phenotype analysis are the phenotype ontologies. A large number of these ontologies have been developed across many domains, and we are now at a point where the knowledge captured in the structure of these ontologies can be used for the integration and analysis of large interrelated data sets. The Phenotype And Trait Ontology framework provides a method for formal definitions of phenotypes and associated data sets and has proved to be key to our ability to develop methods for the integration and analysis of phenotype data. Here, we describe the development and products of the ontological approach to phenotype capture, the formal content of phenotype ontologies and how their content can be used computationally.}, } @article {pmid28387705, year = {2017}, author = {Fox, MA and Brewer, LE and Martin, L}, title = {An Overview of Literature Topics Related to Current Concepts, Methods, Tools, and Applications for Cumulative Risk Assessment (2007-2016).}, journal = {International journal of environmental research and public health}, volume = {14}, number = {4}, pages = {}, pmid = {28387705}, issn = {1660-4601}, mesh = {Ecosystem ; Ecotoxicology/*methods ; Environmental Exposure/*adverse effects/statistics & numerical data ; Genetic Markers ; Geographic Information Systems ; Health Status ; Humans ; Risk Assessment/*methods ; }, abstract = {Cumulative risk assessments (CRAs) address combined risks from exposures to multiple chemical and nonchemical stressors and may focus on vulnerable communities or populations. Significant contributions have been made to the development of concepts, methods, and applications for CRA over the past decade. Work in both human health and ecological cumulative risk has advanced in two different contexts. The first context is the effects of chemical mixtures that share common modes of action, or that cause common adverse outcomes. In this context two primary models are used for predicting mixture effects, dose addition or response addition. The second context is evaluating the combined effects of chemical and nonchemical (e.g., radiation, biological, nutritional, economic, psychological, habitat alteration, land-use change, global climate change, and natural disasters) stressors. CRA can be adapted to address risk in many contexts, and this adaptability is reflected in the range in disciplinary perspectives in the published literature. This article presents the results of a literature search and discusses a range of selected work with the intention to give a broad overview of relevant topics and provide a starting point for researchers interested in CRA applications.}, } @article {pmid28386109, year = {2017}, author = {Toro, N and Villadas, PJ and Molina-Sánchez, MD and Navarro-Gómez, P and Vinardell, JM and Cuesta-Berrio, L and Rodríguez-Carvajal, MA}, title = {The underlying process of early ecological and genetic differentiation in a facultative mutualistic Sinorhizobium meliloti population.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {675}, pmid = {28386109}, issn = {2045-2322}, mesh = {Computational Biology/methods ; *Ecological and Environmental Phenomena ; *Evolution, Molecular ; Gene Flow ; Genetic Drift ; *Genetic Variation ; Genome, Bacterial ; Genome-Wide Association Study ; Genomics ; Phylogeny ; Polymorphism, Single Nucleotide ; Sinorhizobium meliloti/*genetics ; Symbiosis ; }, abstract = {The question of how genotypic and ecological units arise and spread in natural microbial populations remains controversial in the field of evolutionary biology. Here, we investigated the early stages of ecological and genetic differentiation in a highly clonal sympatric Sinorhizobium meliloti population. Whole-genome sequencing revealed that a large DNA region of the symbiotic plasmid pSymB was replaced in some isolates with a similar synteny block carrying densely clustered SNPs and displaying gene acquisition and loss. Two different versions of this genomic island of differentiation (GID) generated by multiple genetic exchanges over time appear to have arisen recently, through recombination in a particular clade within this population. In addition, these isolates display resistance to phages from the same geographic region, probably due to the modification of surface components by the acquired genes. Our results suggest that an underlying process of early ecological and genetic differentiation in S. meliloti is primarily triggered by acquisition of genes that confer resistance to soil phages within particular large genomic DNA regions prone to recombination.}, } @article {pmid28384412, year = {2017}, author = {Nascimento, MM and Zaura, E and Mira, A and Takahashi, N and Ten Cate, JM}, title = {Second Era of OMICS in Caries Research: Moving Past the Phase of Disillusionment.}, journal = {Journal of dental research}, volume = {96}, number = {7}, pages = {733-740}, pmid = {28384412}, issn = {1544-0591}, support = {K23 DE023579/DE/NIDCR NIH HHS/United States ; }, mesh = {Biofilms ; Computational Biology/*methods ; Dental Caries/*microbiology/*prevention & control ; *Dental Research ; Diffusion of Innovation ; Genomics/methods ; Humans ; *Metabolome ; Metabolomics/methods ; Metagenome ; *Microbiota ; Proteomics/methods ; }, abstract = {Novel approaches using OMICS techniques enable a collective assessment of multiple related biological units, including genes, gene expression, proteins, and metabolites. In the past decade, next-generation sequencing (NGS) technologies were improved by longer sequence reads and the development of genome databases and user-friendly pipelines for data analysis, all accessible at lower cost. This has generated an outburst of high-throughput data. The application of OMICS has provided more depth to existing hypotheses as well as new insights in the etiology of dental caries. For example, the determination of complete bacterial microbiomes of oral samples rather than selected species, together with oral metatranscriptome and metabolome analyses, supports the viewpoint of dysbiosis of the supragingival biofilms. In addition, metabolome studies have been instrumental in disclosing the contributions of major pathways for central carbon and amino acid metabolisms to biofilm pH homeostasis. New, often noncultured, oral streptococci have been identified, and their phenotypic characterization has revealed candidates for probiotic therapy. Although findings from OMICS research have been greatly informative, problems related to study design, data quality, integration, and reproducibility still need to be addressed. Also, the emergence and continuous updates of these computationally demanding technologies require expertise in advanced bioinformatics for reliable interpretation of data. Despite the obstacles cited above, OMICS research is expected to encourage the discovery of novel caries biomarkers and the development of next-generation diagnostics and therapies for caries control. These observations apply equally to the study of other oral diseases.}, } @article {pmid28379556, year = {2017}, author = {Benson, L and Ram, N and Almeida, DM and Zautra, AJ and Ong, AD}, title = {Fusing Biodiversity Metrics into Investigations of Daily Life: Illustrations and Recommendations With Emodiversity.}, journal = {The journals of gerontology. Series B, Psychological sciences and social sciences}, volume = {73}, number = {1}, pages = {75-86}, pmid = {28379556}, issn = {1758-5368}, support = {R01 HD076994/HD/NICHD NIH HHS/United States ; R01 AG026006/AG/NIA NIH HHS/United States ; UL1 TR002014/TR/NCATS NIH HHS/United States ; R24 HD041025/HD/NICHD NIH HHS/United States ; UL1 TR000127/TR/NCATS NIH HHS/United States ; }, mesh = {*Activities of Daily Living/psychology ; Adult ; Age Factors ; Aged ; Aging/*psychology ; *Data Interpretation, Statistical ; *Emotions ; Female ; Humans ; Individuality ; Male ; Middle Aged ; Models, Statistical ; Psychological Tests ; Reproducibility of Results ; }, abstract = {OBJECTIVES: Functionalist emotion and ecological systems theories suggest emodiversity-the variety and relative abundance of individuals' emotion experiences-is beneficial for psychological and physical health and may change with age. This paper examines and provides recommendations for operationalization of diversity-type intraindividual variability (IIV) constructs using intensive longitudinal data, and demonstrates the utility of emodiversity by examining its links to physical health moderated by mean levels of emotion and age.

METHOD: Using data from a daily diary study of 138 adults (age 40 to 65 years), we consider how item selection, response scale, choice of diversity index, and number of occasions enable/constrain mapping to theory, measurement reliability, and empirical inquiry.

RESULTS: Item selection and response scale had limited influence on rank-order differences in diversity. Reliable measurement (r ≥ .8) required a minimum of 6 to 12 occasions depending on choice of index, theoretical conception, study design, and distribution of diversity scores. The empirical findings suggest mean level of negative affect, rather than age, moderates the relation between negative emodiversity and health.

DISCUSSION: This study provides recommendations for the calculation of diversity-type IIV constructs and illustrates the potential for study of emodiversity to contribute to understanding of successful aging.}, } @article {pmid28378191, year = {2017}, author = {D'Anatro, A and Giorello, F and Feijoo, M and Lessa, EP}, title = {Testing for the Occurrence of Selective Episodes During the Divergence of Otophysan Fishes: Insights from Mitogenomics.}, journal = {Journal of molecular evolution}, volume = {84}, number = {4}, pages = {162-173}, pmid = {28378191}, issn = {1432-1432}, mesh = {Adaptation, Biological/genetics ; Animals ; Biodiversity ; Biological Evolution ; Computer Simulation ; Databases, Nucleic Acid ; Evolution, Molecular ; Fishes/*genetics ; Genetic Speciation ; Genome, Mitochondrial/*genetics ; Phylogeny ; Selection, Genetic/genetics ; }, abstract = {How natural selection shapes biodiversity constitutes a topic of renewed interest during the last few decades. The division Otophysi comprises approximately two-thirds of freshwater fish diversity and probably underwent an extensive adaptive radiation derived from a single invasion of the supercontinent Pangaea, giving place to the evolution of the main five Otophysan lineages during a short period of time. Little is known about the factors involved in the processes that lead to lineage diversification among this group of fishes and identifying directional selection acting over protein-coding genes could offer clues about the processes acting on species diversification. The main objective of this study was to explore the otophysan mitochondrial genome evolution, in order to account for the possible signatures of selective events in this lineage, and to explore for the functional connotations of these molecular substitutions. Mainly, three different approaches were used: the "ω-based" BS-REL and MEME methods, implemented in the DATAMONKEY web server, and analysis of selection on amino acid properties, implemented in the software TreeSAAP. We found evidence of selective episodes along several branches of the evolutionary history of othophysan fishes. Analyses carried out using the BS-REL algorithm suggest episodic diversifying selection at basal branches of the otophysan lineage, which was also supported by analyses implemented in MEME and TreeSAAP. These results suggest that throughout the Siluriformes radiation, an important number of adaptive changes occurred in their mitochondrial genome. The metabolic consequences and ecological correlates of these molecular substitutions should be addressed in future studies.}, } @article {pmid28375177, year = {2017}, author = {Forberger, S and Bammann, K and Bauer, J and Boll, S and Bolte, G and Brand, T and Hein, A and Koppelin, F and Lippke, S and Meyer, J and Pischke, CR and Voelcker-Rehage, C and Zeeb, H}, title = {How to Tackle Key Challenges in the Promotion of Physical Activity among Older Adults (65+): The AEQUIPA Network Approach.}, journal = {International journal of environmental research and public health}, volume = {14}, number = {4}, pages = {}, pmid = {28375177}, issn = {1660-4601}, mesh = {Aged ; *Exercise ; Health Promotion/*methods/*organization & administration/standards ; Humans ; Patient Care Team ; *Public Health ; }, abstract = {The paper introduces the theoretical framework and methods/instruments used by the Physical Activity and Health Equity: Primary Prevention for Healthy Ageing (AEQUIPA) prevention research network as an interdisciplinary approach to tackle key challenges in the promotion of physical activity among older people (65+). Drawing on the social-ecological model, the AEQUIPA network developed an interdisciplinary methodological design including quantitative/qualitative studies and systematic reviews, while combining expertise from diverse fields: public health, psychology, urban planning, sports sciences, health technology and geriatrics. AEQUIPA tackles key challenges when promoting physical activity (PA) in older adults: tailoring of interventions, fostering community readiness and participation, strengthening intersectoral collaboration, using new technological devices and evaluating intervention generated inequalities. AEQUIPA aims to strengthen the evidence base for age-specific preventive PA interventions and to yield new insights into the explanatory power of individual and contextual factors. Currently, the empirical work is still underway. First experiences indicate that thenetwork has achieved a strong regional linkage with communities, local stakeholders and individuals. However, involving inactive persons and individuals from minority groups remained challenging. A review of existing PA intervention studies among the elderly revealed the potential to assess equity effects. The results will add to the theoretical and methodological discussion on evidence-based age-specific PA interventions and will contribute to the discussion about European and national health targets.}, } @article {pmid28374945, year = {2017}, author = {Pelletier, J and Siampale, A and Legendre, P and Jantz, P and Laporte, NT and Goetz, SJ}, title = {Human and natural controls of the variation in aboveground tree biomass in African dry tropical forests.}, journal = {Ecological applications : a publication of the Ecological Society of America}, volume = {27}, number = {5}, pages = {1578-1593}, doi = {10.1002/eap.1550}, pmid = {28374945}, issn = {1051-0761}, mesh = {Biodiversity ; *Biomass ; Conservation of Natural Resources/*methods ; Environment ; *Forests ; Human Activities ; Trees/*physiology ; Zambia ; }, abstract = {Understanding the anthropogenic and natural controls that affect the patterns, distribution, and dynamics of terrestrial carbon is crucial to meeting climate change mitigation objectives. We assessed the human and natural controls over aboveground tree biomass density in African dry tropical forests, using Zambia's first nationwide forest inventory. We identified predictors that best explain the variation in biomass density, contrasted anthropogenic and natural sites at different spatial scales, and compared sites with different stand structure characteristics and species composition. In addition, we evaluated the effects of different management and conservation practices on biomass density. Variation in biomass density was mostly determined by biotic processes, linked with both species richness and dominance (evenness), and to a lesser extent, by land use, environmental controls, and spatial structure. Biomass density was negatively associated with tree species evenness and positively associated with species richness for both natural and human-modified sites. Human influence variables (including distance to roads, distance to town, fire occurrence, and the population on site) did not explain substantial variation in biomass density in comparison to biodiversity variables. The relationship of human activities to biomass density in managed sites appears to be mediated by effects on species diversity and stand structure characteristics, with lower values in human-modified sites for all metrics tested. Small contrasts in carbon density between human-modified and natural forest sites signal the potential to maintain carbon in the landscape inside but also outside forestlands in this region. Biodiversity is positively related to biomass density in both human and natural sites, demonstrating potential synergies between biodiversity conservation and climate change mitigation. This is the first evidence of positive outcomes of protected areas and participatory forest management on carbon storage at national scale in Zambia. This research shows that understanding controls over biomass density can provide policy relevant inputs for carbon management and on ecological processes affecting carbon storage.}, } @article {pmid28370881, year = {2017}, author = {Moore, RC and Swendsen, J and Depp, CA}, title = {Applications for self-administered mobile cognitive assessments in clinical research: A systematic review.}, journal = {International journal of methods in psychiatric research}, volume = {26}, number = {4}, pages = {}, pmid = {28370881}, issn = {1557-0657}, support = {K23 MH107260/MH/NIMH NIH HHS/United States ; L30 MH104725/MH/NIMH NIH HHS/United States ; R01 MH100417/MH/NIMH NIH HHS/United States ; }, mesh = {Adolescent ; Adult ; Aged ; Aged, 80 and over ; Cognitive Dysfunction/*diagnosis ; Diagnosis, Computer-Assisted/*standards/statistics & numerical data ; Humans ; Middle Aged ; *Mobile Applications ; Young Adult ; }, abstract = {Frequent, brief and repeated self-administered mobile assessments of cognitive function, conducted in everyday life settings, are a promising complementary tool to traditional assessment approaches. Mobile cognitive assessments promote patient-centered care and might enhance capacity to inform individual-level outcomes over time (i.e. detecting subtle declines in cognitive function), as well as in assessing cognition and its correlates in the naturalistic environment. The goal of this systematic review was to assess the feasibility and psychometric properties of mobile cognitive assessments. Through a comprehensive search, we identified 12 articles using self-administered, mobile phone-based cognitive assessments. Studies sampled participants between 1 and 6 times per day for 1-14 days. Samples ranged in age from 14 to 83 years old and were generally healthy populations without cognitive impairment. Working memory was the most frequently-assessed cognitive domain (n = 7), followed by attention/reaction time (n = 4). Seven studies reported adherence, with mean adherence rates of 79.2%. In addition to positive evidence of feasibility, there was general support for high levels of between- and within-person reliability and construct validity. While research has only begun to explore the utility of mobile cognitive assessments, studies to-date indicate they may be a promising complementary tool to traditional assessment methods with potential to improve clinical care and research.}, } @article {pmid28369655, year = {2017}, author = {Reddy, S and Kimball, RT and Pandey, A and Hosner, PA and Braun, MJ and Hackett, SJ and Han, KL and Harshman, J and Huddleston, CJ and Kingston, S and Marks, BD and Miglia, KJ and Moore, WS and Sheldon, FH and Witt, CC and Yuri, T and Braun, EL}, title = {Why Do Phylogenomic Data Sets Yield Conflicting Trees? Data Type Influences the Avian Tree of Life more than Taxon Sampling.}, journal = {Systematic biology}, volume = {66}, number = {5}, pages = {857-879}, doi = {10.1093/sysbio/syx041}, pmid = {28369655}, issn = {1076-836X}, mesh = {Animals ; Birds/*classification ; Classification/*methods ; *Datasets as Topic ; Genome/genetics ; Genomics ; Models, Biological ; *Phylogeny ; }, abstract = {Phylogenomics, the use of large-scale data matrices in phylogenetic analyses, has been viewed as the ultimate solution to the problem of resolving difficult nodes in the tree of life. However, it has become clear that analyses of these large genomic data sets can also result in conflicting estimates of phylogeny. Here, we use the early divergences in Neoaves, the largest clade of extant birds, as a "model system" to understand the basis for incongruence among phylogenomic trees. We were motivated by the observation that trees from two recent avian phylogenomic studies exhibit conflicts. Those studies used different strategies: 1) collecting many characters [$\sim$ 42 mega base pairs (Mbp) of sequence data] from 48 birds, sometimes including only one taxon for each major clade; and 2) collecting fewer characters ($\sim$ 0.4 Mbp) from 198 birds, selected to subdivide long branches. However, the studies also used different data types: the taxon-poor data matrix comprised 68% non-coding sequences whereas coding exons dominated the taxon-rich data matrix. This difference raises the question of whether the primary reason for incongruence is the number of sites, the number of taxa, or the data type. To test among these alternative hypotheses we assembled a novel, large-scale data matrix comprising 90% non-coding sequences from 235 bird species. Although increased taxon sampling appeared to have a positive impact on phylogenetic analyses the most important variable was data type. Indeed, by analyzing different subsets of the taxa in our data matrix we found that increased taxon sampling actually resulted in increased congruence with the tree from the previous taxon-poor study (which had a majority of non-coding data) instead of the taxon-rich study (which largely used coding data). We suggest that the observed differences in the estimates of topology for these studies reflect data-type effects due to violations of the models used in phylogenetic analyses, some of which may be difficult to detect. If incongruence among trees estimated using phylogenomic methods largely reflects problems with model fit developing more "biologically-realistic" models is likely to be critical for efforts to reconstruct the tree of life. [Birds; coding exons; GTR model; model fit; Neoaves; non-coding DNA; phylogenomics; taxon sampling.].}, } @article {pmid28369576, year = {2017}, author = {Li, C and Hou, Y and Xu, J and Zhang, A and Liu, Z and Qi, F and Yang, Z and Chen, K and Liu, S and Huang, H and Wang, Q and Dong, J and Wu, CI and Lu, X}, title = {A Direct Test of Selection in Cell Populations Using the Diversity in Gene Expression within Tumors.}, journal = {Molecular biology and evolution}, volume = {34}, number = {7}, pages = {1730-1742}, doi = {10.1093/molbev/msx115}, pmid = {28369576}, issn = {1537-1719}, mesh = {DNA Copy Number Variations/genetics ; Databases, Nucleic Acid ; Evolution, Molecular ; Gene Expression ; Gene Expression Regulation, Neoplastic/*genetics ; Genetic Drift ; Genetic Variation/genetics ; Humans ; Neoplasms/*genetics ; Selection, Genetic/genetics ; Sequence Analysis, DNA/methods ; Transcriptome/*genetics ; }, abstract = {Although intratumor diversity driven by selection has been the prevailing view in cancer biology, recent population genetic analyses have been unable to reject the neutral interpretation. As the power to reject neutrality in tumors is often low, it will be desirable to have an alternative means to test selection directly. Here, we utilize gene expression data as a surrogate for functional significance in intra- and intertumor comparisons. The expression divergence between samples known to be driven by selection (e.g., between tumor and normal tissues) is always higher than the divergence between normal samples, which should be close to the neutral level of divergence. In contrast, the expression differentiation between regions of the same tumor, being lower than the neutral divergence, is incompatible with the hypothesis of selectively driven divergence. To further test the hypothesis of neutral evolution, we select a hepatocellular carcinoma tumor that has large intratumor SNV and CNV (single nucleotide variation and copy number variation, respectively) diversity. This tumor enables us to calibrate the level of expression divergence against that of genetic divergence. We observe that intratumor divergence in gene expression profile lags far behind genetic divergence, indicating insufficient phenotypic differences for selection to operate. All these expression analyses corroborate that natural selection does not operate effectively within tumors, supporting recent interpretations of within-tumor diversity. As the expected level of genetic diversity, hence the potential for drug resistance, would be much higher under neutrality than under selection, the issue is of both theoretical and clinical significance.}, } @article {pmid28369202, year = {2018}, author = {O'Brien, JJ and Gunawardena, HP and Qaqish, BF}, title = {Row versus column correlations: avoiding the ecological fallacy in RNA/protein expression studies.}, journal = {Briefings in bioinformatics}, volume = {19}, number = {5}, pages = {946-953}, pmid = {28369202}, issn = {1477-4054}, support = {T32 CA106209/CA/NCI NIH HHS/United States ; }, mesh = {Bias ; Computational Biology/methods ; Computer Simulation ; Data Interpretation, Statistical ; Humans ; Models, Biological ; Models, Statistical ; Proteins/*genetics/*metabolism ; Proteomics/*statistics & numerical data ; RNA/*genetics/*metabolism ; Transcription, Genetic ; }, abstract = {Biomedical researchers are often interested in computing the correlation between RNA and protein abundance. However, correlations can be computed between rows of a data matrix or between columns, and the results are not the same. The belief that these two types of correlation are estimating the same phenomenon is a special case of a well-known logical error called the ecological fallacy. In this article, we review different uses of correlation found in the literature, explain the differences between row and column correlations and argue that one of them has an undesirable interpretation in most applications. Through simulation studies and theoretical derivations, we show that the commonly used Pearson's coefficient, computed from protein and transcript data from a single sample, is only loosely related to the biological correlation that most researchers will be interested in studying. Beyond our basic exploration of the ecological fallacy, we examine how correlations are affected by relative quantification proteomics data and common normalization procedures, finding that double normalization is capable of completely masking true correlative relationships. We conclude with guidelines for properly identifying and computing consistent correlation coefficients.}, } @article {pmid28369087, year = {2017}, author = {Pocock, MJ and Tweddle, JC and Savage, J and Robinson, LD and Roy, HE}, title = {The diversity and evolution of ecological and environmental citizen science.}, journal = {PloS one}, volume = {12}, number = {4}, pages = {e0172579}, pmid = {28369087}, issn = {1932-6203}, mesh = {Data Collection ; Data Interpretation, Statistical ; *Ecology/statistics & numerical data/trends ; Humans ; Internet ; Statistics as Topic ; *Volunteers ; }, abstract = {Citizen science-the involvement of volunteers in data collection, analysis and interpretation-simultaneously supports research and public engagement with science, and its profile is rapidly rising. Citizen science represents a diverse range of approaches, but until now this diversity has not been quantitatively explored. We conducted a systematic internet search and discovered 509 environmental and ecological citizen science projects. We scored each project for 32 attributes based on publicly obtainable information and used multiple factor analysis to summarise this variation to assess citizen science approaches. We found that projects varied according to their methodological approach from 'mass participation' (e.g. easy participation by anyone anywhere) to 'systematic monitoring' (e.g. trained volunteers repeatedly sampling at specific locations). They also varied in complexity from approaches that are 'simple' to those that are 'elaborate' (e.g. provide lots of support to gather rich, detailed datasets). There was a separate cluster of entirely computer-based projects but, in general, we found that the range of citizen science projects in ecology and the environment showed continuous variation and cannot be neatly categorised into distinct types of activity. While the diversity of projects begun in each time period (pre 1990, 1990-99, 2000-09 and 2010-13) has not increased, we found that projects tended to have become increasingly different from each other as time progressed (possibly due to changing opportunities, including technological innovation). Most projects were still active so consequently we found that the overall diversity of active projects (available for participation) increased as time progressed. Overall, understanding the landscape of citizen science in ecology and the environment (and its change over time) is valuable because it informs the comparative evaluation of the 'success' of different citizen science approaches. Comparative evaluation provides an evidence-base to inform the future development of citizen science activities.}, } @article {pmid28368823, year = {2017}, author = {Terrier, P and Le Carre, J and Connaissa, ML and Leger, B and Luthi, F}, title = {Monitoring of Gait Quality in Patients With Chronic Pain of Lower Limbs.}, journal = {IEEE transactions on neural systems and rehabilitation engineering : a publication of the IEEE Engineering in Medicine and Biology Society}, volume = {25}, number = {10}, pages = {1843-1852}, doi = {10.1109/TNSRE.2017.2688485}, pmid = {28368823}, issn = {1558-0210}, mesh = {Accelerometry ; Adult ; Aged ; Chronic Pain/*physiopathology ; Databases, Factual ; Female ; *Gait ; Gait Disorders, Neurologic/*physiopathology/rehabilitation ; Healthy Volunteers ; Humans ; Lower Extremity/*physiopathology ; Male ; Middle Aged ; Monitoring, Ambulatory/methods ; Musculoskeletal Pain/*physiopathology ; Reproducibility of Results ; Young Adult ; }, abstract = {Severe injuries of lower extremities often lead to chronic pain and reduced walking abilities. We postulated that measuring free-living gait can provide further information about walking ability in complement to clinical evaluations. We sought to validate a method that characterizes free gaits with a wearable sensor. Over one week, 81 healthy controls (HC) and 66 chronic lower limb pain patients (CLLPP) hospitalized for multidisciplinary rehabilitation wore a simple accelerometer (Actigraph). In the acceleration signals, steady 1-min walks detected numbered 7,835 (5,085 in CLLPP and 2,750 in HC). Five gait quality measures were assessed: movement intensity, cadence, stride regularity, and short-term and long-term local dynamic stability. Gait quality variables differed significantly between CLLPP and HC (4%-26%). Intraclass correlation coefficients revealed moderate to high repeatability (0.71-0.91), which suggests that seven days of measurement are sufficient to assess average gait patterns. Regression analyses showed significant association (R[2] = 0.44) between the gait quality variables and a clinical evaluation of walking ability, i.e., the 6-min walk test. Overall, the results show that the method is easy to implement, valid (high concurrent validity), and reliable to assess walking abilities ecologically.}, } @article {pmid28365723, year = {2017}, author = {Li, T and Pan, GQ and Vossbrinck, CR and Xu, JS and Li, CF and Chen, J and Long, MX and Yang, M and Xu, XF and Xu, C and Debrunner-Vossbrinck, BA and Zhou, ZY}, title = {SilkPathDB: a comprehensive resource for the study of silkworm pathogens.}, journal = {Database : the journal of biological databases and curation}, volume = {2017}, number = {1}, pages = {}, pmid = {28365723}, issn = {1758-0463}, mesh = {Animals ; Bacteria/*genetics ; Bombyx/*genetics/*microbiology ; *Databases, Genetic ; Fungi/*genetics ; *Genome ; Insect Viruses/*genetics ; Microsporidia/*genetics ; }, abstract = {UNLABELLED: Silkworm pathogens have been heavily impeding the development of sericultural industry and play important roles in lepidopteran ecology, and some of which are used as biological insecticides. Rapid advances in studies on the omics of silkworm pathogens have produced a large amount of data, which need to be brought together centrally in a coherent and systematic manner. This will facilitate the reuse of these data for further analysis. We have collected genomic data for 86 silkworm pathogens from 4 taxa (fungi, microsporidia, bacteria and viruses) and from 4 lepidopteran hosts, and developed the open-access Silkworm Pathogen Database (SilkPathDB) to make this information readily available. The implementation of SilkPathDB involves integrating Drupal and GBrowse as a graphic interface for a Chado relational database which houses all of the datasets involved. The genomes have been assembled and annotated for comparative purposes and allow the search and analysis of homologous sequences, transposable elements, protein subcellular locations, including secreted proteins, and gene ontology. We believe that the SilkPathDB will aid researchers in the identification of silkworm parasites, understanding the mechanisms of silkworm infections, and the developmental ecology of silkworm parasites (gene expression) and their hosts.

DATABASE URL: http://silkpathdb.swu.edu.cn.}, } @article {pmid28358919, year = {2017}, author = {Rocabert, C and Knibbe, C and Consuegra, J and Schneider, D and Beslon, G}, title = {Beware batch culture: Seasonality and niche construction predicted to favor bacterial adaptive diversification.}, journal = {PLoS computational biology}, volume = {13}, number = {3}, pages = {e1005459}, pmid = {28358919}, issn = {1553-7358}, mesh = {*Adaptation, Physiological ; *Bacterial Physiological Phenomena ; Batch Cell Culture Techniques/methods ; Biological Evolution ; Computational Biology ; Computer Simulation ; Ecotype ; Escherichia coli/genetics/physiology ; Microbiota ; Models, Biological ; Seasons ; Sympatry ; }, abstract = {Metabolic cross-feeding interactions between microbial strains are common in nature, and emerge during evolution experiments in the laboratory, even in homogeneous environments providing a single carbon source. In sympatry, when the environment is well-mixed, the reasons why emerging cross-feeding interactions may sometimes become stable and lead to monophyletic genotypic clusters occupying specific niches, named ecotypes, remain unclear. As an alternative to evolution experiments in the laboratory, we developed Evo2Sim, a multi-scale model of in silico experimental evolution, equipped with the whole tool case of experimental setups, competition assays, phylogenetic analysis, and, most importantly, allowing for evolvable ecological interactions. Digital organisms with an evolvable genome structure encoding an evolvable metabolic network evolved for tens of thousands of generations in environments mimicking the dynamics of real controlled environments, including chemostat or batch culture providing a single limiting resource. We show here that the evolution of stable cross-feeding interactions requires seasonal batch conditions. In this case, adaptive diversification events result in two stably co-existing ecotypes, with one feeding on the primary resource and the other on by-products. We show that the regularity of serial transfers is essential for the maintenance of the polymorphism, as it allows for at least two stable seasons and thus two temporal niches. A first season is externally generated by the transfer into fresh medium, while a second one is internally generated by niche construction as the provided nutrient is replaced by secreted by-products derived from bacterial growth. In chemostat conditions, even if cross-feeding interactions emerge, they are not stable on the long-term because fitter mutants eventually invade the whole population. We also show that the long-term evolution of the two stable ecotypes leads to character displacement, at the level of the metabolic network but also of the genome structure. This difference of genome structure between both ecotypes impacts the stability of the cross-feeding interaction, when the population is propagated in chemostat conditions. This study shows the crucial role played by seasonality in temporal niche partitioning and in promoting cross-feeding subgroups into stable ecotypes, a premise to sympatric speciation.}, } @article {pmid28357592, year = {2017}, author = {Maksimović, MŽ and Marinković, JM and Vlajinac, HD and Maksimović, JM and Tomanić, MS and Radak, DJ}, title = {Awareness and knowledge of cardiovascular disease risk factors among medical students.}, journal = {Wiener klinische Wochenschrift}, volume = {129}, number = {13-14}, pages = {458-463}, pmid = {28357592}, issn = {1613-7671}, mesh = {Adolescent ; Adult ; *Awareness ; Cardiovascular Diseases/*etiology/prevention & control/*psychology ; Cross-Sectional Studies ; Curriculum ; *Education, Medical ; Female ; Health Behavior ; *Health Knowledge, Attitudes, Practice ; Humans ; Male ; Metabolic Syndrome/etiology/prevention & control/psychology ; *Risk Factors ; Serbia ; Students, Medical/*psychology ; Surveys and Questionnaires ; Young Adult ; }, abstract = {BACKGROUND: The aim of this study was to assess the knowledge and attitude of medical students in relation to cardiovascular disease (CVD) risk factors as well as to assess the impact of medical education on their knowledge and recognition of the importance of implementation of preventive measures.

METHODS: This cross-sectional study included 514 students in the second year of studying at the Faculty of Medicine in Belgrade, Serbia (younger students response rate 79.57%) and 511 students in the last year of education (older students response rate 90.21%). For data collection, an anonymous self-administered questionnaire was used, which included two types of questions about CVD risk factors and questions about the student's attitude.

RESULTS: Older students knew significantly more about CVD risk factors than students who were at the beginning of their medical studies; however, more than half of the older students did not know the correct answers about CVD risk factors. The only exceptions were questions about "bad" and "good" cholesterol, metabolic syndrome (MSy) and lipid lowering therapy in high risk subjects. Physical inactivity, obesity, type 2 diabetes, smoking and hypertension were not ranked highly enough as important CVD risk factors. Compared groups of students did not significantly differ in attitude scores. The majority of them recognized CVD as the leading cause of death, had normal weight and knew their own blood pressure.

CONCLUSION: Knowledge of medical students from Belgrade about CVD risk factors should be improved.}, } @article {pmid28356154, year = {2017}, author = {Ballenghien, M and Faivre, N and Galtier, N}, title = {Patterns of cross-contamination in a multispecies population genomic project: detection, quantification, impact, and solutions.}, journal = {BMC biology}, volume = {15}, number = {1}, pages = {25}, pmid = {28356154}, issn = {1741-7007}, mesh = {*DNA Contamination ; Databases, Genetic ; Electron Transport Complex IV/genetics ; *Genetics, Population ; *Genomics ; Metagenomics ; Polymorphism, Single Nucleotide/genetics ; Probability ; Species Specificity ; }, abstract = {BACKGROUND: Contamination is a well-known but often neglected problem in molecular biology. Here, we investigated the prevalence of cross-contamination among 446 samples from 116 distinct species of animals, which were processed in the same laboratory and subjected to subcontracted transcriptome sequencing.

RESULTS: Using cytochrome oxidase 1 as a barcode, we identified a minimum of 782 events of between-species contamination, with approximately 80% of our samples being affected. An analysis of laboratory metadata revealed a strong effect of the sequencing center: nearly all the detected events of between-species contamination involved species that were sent the same day to the same company. We introduce new methods to address the amount of within-species, between-individual contamination, and to correct for this problem when calling genotypes from base read counts.

CONCLUSIONS: We report evidence for pervasive within-species contamination in this data set, and show that classical population genomic statistics, such as synonymous diversity, the ratio of non-synonymous to synonymous diversity, inbreeding coefficient FIT, and Tajima's D, are sensitive to this problem to various extents. Control analyses suggest that our published results are probably robust to the problem of contamination. Recommendations on how to prevent or avoid contamination in large-scale population genomics/molecular ecology are provided based on this analysis.}, } @article {pmid28355278, year = {2017}, author = {Pither, J and Botta, A and Maity, C and Ghosh, S}, title = {Analysis using national databases reveals a positive association between dietary polyunsaturated fatty acids with TV watching and diabetes in European females.}, journal = {PloS one}, volume = {12}, number = {3}, pages = {e0173084}, pmid = {28355278}, issn = {1932-6203}, mesh = {Adolescent ; Adult ; Child ; Cross-Sectional Studies ; Databases, Factual ; Diabetes Mellitus/*epidemiology/etiology/metabolism/physiopathology ; Diet ; Europe/epidemiology ; Fatty Acids, Unsaturated/administration & dosage/*adverse effects ; Female ; Humans ; Motor Activity ; Obesity/*epidemiology/etiology/metabolism/physiopathology ; Prevalence ; Prospective Studies ; *Sedentary Behavior ; Television ; }, abstract = {In recent years, dietary polyunsaturated fatty acids (PUFA) have increased in parallel to sedentary behavior and diabetes across the world. To test any putative association between dietary PUFA and sedentary behavior or diabetes in females, we obtained country-specific, cross-sectional data on sedentary activity and diabetes prevalence from European Cardiovascular Statistics 2012. Age and gender-specific, nutritional data from each country were obtained from nutritional surveys as well. Socioeconomic (GDP), physical environment (urbanization index) and climatic confounders were accounted for each country. Upon analysis, we found a strong, positive association between sedentary lifestyle in 11-yr old girls (> = 2 hours of TV/ weekday) and dietary PUFA across 21 European countries. Further, a weak association of dietary PUFA and a strong relationship of per-capita GDP was established with elevated fasting blood glucose [(> = 7.0 mmol/L; or on medication] among 25+ year old adult females across 23 countries in Europe. In summary, we present novel ecological evidence that dietary PUFA is strongly associated with sedentary behavior among pre-teen girls and weakly associated with diabetes among adult women across Europe. In the latter group, per-capita GDP was a significant predictor for diabetes as well. Therefore, we recommend that prospective randomized controlled trials (RCTs) be implemented to evaluate if ubiquitous presence of dietary PUFA and low socioeconomic status are possible confounders when intervening to treat/prevent sedentary lifestyle or diabetes in female subjects in Western nations.}, } @article {pmid28353449, year = {2017}, author = {Acevedo-Mendoza, WF and Buitrago Gómez, DP and Atehortua-Otero, MÁ and Páez, MÁ and Jiménez-Rincón, M and Lagos-Grisales, GJ and Rodríguez-Morales, AJ}, title = {Influence of socio-economic inequality measured by the Gini coefficient on meningitis incidence caused by Mycobacterium tuberculosis and Haemophilus influenzae in Colombia, 2008-2011.}, journal = {Le infezioni in medicina}, volume = {25}, number = {1}, pages = {8-12}, pmid = {28353449}, issn = {2532-8689}, mesh = {Algorithms ; Colombia/epidemiology ; Developing Countries ; Haemophilus influenzae/*isolation & purification ; Healthcare Disparities/*statistics & numerical data ; Humans ; Image Interpretation, Computer-Assisted ; Incidence ; Meningitis, Haemophilus/*complications/diagnosis/epidemiology/microbiology ; Models, Statistical ; Mycobacterium tuberculosis/*isolation & purification ; Poverty ; Reproducibility of Results ; Retrospective Studies ; Risk Factors ; *Socioeconomic Factors ; Tuberculosis, Meningeal/*complications/diagnosis/epidemiology/microbiology ; }, abstract = {Bacterial meningitis is an important cause of infectious neurological morbidity and mortality. Its incidence has decreased with the introduction of vaccination programmes against preventable agents. However, low-income and middle-income countries with poor access to health care still have a significant burden of the disease. Thus, the relationship between the Gini coefficient and H. influenzae and M. tuberculosis meningitis incidence in Colombia, during 2008-2011, was assessed. In this ecological study, the Gini coefficient was obtained from the Colombian Department of Statistics, incidence rates were calculated (cases/1,000,000 pop) and linear regressions were performed using the Gini coefficient, to assess the relationship between the latter and the incidence of meningitis. It was observed that when inequality increases in the Colombian departments, the incidence of meningitis also increases, with a significant association in the models (p<0.01) for both M. tuberculosis (r[2]=0.2382; p<0.001) and H. influenzae (r[2]=0.2509; p<0.001). This research suggests that high Gini coefficient values influence the incidence of Mycobacterium tuberculosis and Haemophilus influenzae meningitis, showing that social inequality is critical to disease occurrence. Early detection, supervised treatment, vaccination coverage, access to health care are efficient control strategies.}, } @article {pmid28350876, year = {2017}, author = {Zou, B and Li, J and Zhou, Q and Quan, ZX}, title = {MIPE: A metagenome-based community structure explorer and SSU primer evaluation tool.}, journal = {PloS one}, volume = {12}, number = {3}, pages = {e0174609}, pmid = {28350876}, issn = {1932-6203}, mesh = {Algorithms ; Computational Biology/*methods ; DNA Primers ; Metagenome/*genetics ; Metagenomics/*methods ; Microbiota/*genetics ; Polymerase Chain Reaction/methods ; RNA, Ribosomal/*genetics ; Reproducibility of Results ; Software ; }, abstract = {An understanding of microbial community structure is an important issue in the field of molecular ecology. The traditional molecular method involves amplification of small subunit ribosomal RNA (SSU rRNA) genes by polymerase chain reaction (PCR). However, PCR-based amplicon approaches are affected by primer bias and chimeras. With the development of high-throughput sequencing technology, unbiased SSU rRNA gene sequences can be mined from shotgun sequencing-based metagenomic or metatranscriptomic datasets to obtain a reflection of the microbial community structure in specific types of environment and to evaluate SSU primers. However, the use of short reads obtained through next-generation sequencing for primer evaluation has not been well resolved. The software MIPE (MIcrobiota metagenome Primer Explorer) was developed to adapt numerous short reads from metagenomes and metatranscriptomes. Using metagenomic or metatranscriptomic datasets as input, MIPE extracts and aligns rRNA to reveal detailed information on microbial composition and evaluate SSU rRNA primers. A mock dataset, a real Metagenomics Rapid Annotation using Subsystem Technology (MG-RAST) test dataset, two PrimerProspector test datasets and a real metatranscriptomic dataset were used to validate MIPE. The software calls Mothur (v1.33.3) and the SILVA database (v119) for the alignment and classification of rRNA genes from a metagenome or metatranscriptome. MIPE can effectively extract shotgun rRNA reads from a metagenome or metatranscriptome and is capable of classifying these sequences and exhibiting sensitivity to different SSU rRNA PCR primers. Therefore, MIPE can be used to guide primer design for specific environmental samples.}, } @article {pmid28350863, year = {2017}, author = {Marrotte, RR and Bowman, J}, title = {The relationship between least-cost and resistance distance.}, journal = {PloS one}, volume = {12}, number = {3}, pages = {e0174212}, pmid = {28350863}, issn = {1932-6203}, mesh = {Algorithms ; Animals ; Computational Biology/*methods ; Computer Simulation ; Ecology/methods ; *Ecosystem ; Evolution, Molecular ; Gene Flow/*genetics ; Genetics, Population/methods ; *Models, Genetic ; }, abstract = {Least-cost modelling and circuit theory are common analogs used in ecology and evolution to model gene flow or animal movement across landscapes. Least-cost modelling estimates the least-cost distance, whereas circuit theory estimates resistance distance. The bias added in choosing one method over the other has not been well documented. We designed an experiment to test whether both methods were linearly related. We also tested the sensitivity of these metrics to variation in Euclidean distance, spatial autocorrelation, the number of pixels representing the landscape, and data aggregation. We found that least-cost and resistance distance were not linearly related unless a transformation was applied. Resistance distance was less sensitive to the number of pixels representing a landscape and was also less sensitive than least-cost distance to the Euclidean distance between nodes. Spatial autocorrelation did not affect either method or the relationship between methods. Resistance distance was more sensitive to aggregation in any form compared to least-cost distance. Therefore, the metric used to infer movement or gene flow and the manipulations applied to the data used to calculate these metrics may govern findings.}, } @article {pmid28343863, year = {2017}, author = {Hiloidhari, M and Baruah, DC and Singh, A and Kataki, S and Medhi, K and Kumari, S and Ramachandra, TV and Jenkins, BM and Thakur, IS}, title = {Emerging role of Geographical Information System (GIS), Life Cycle Assessment (LCA) and spatial LCA (GIS-LCA) in sustainable bioenergy planning.}, journal = {Bioresource technology}, volume = {242}, number = {}, pages = {218-226}, doi = {10.1016/j.biortech.2017.03.079}, pmid = {28343863}, issn = {1873-2976}, mesh = {*Biofuels ; Biomass ; *Ecosystem ; Environment ; *Geographic Information Systems ; }, abstract = {Sustainability of a bioenergy project depends on precise assessment of biomass resource, planning of cost-effective logistics and evaluation of possible environmental implications. In this context, this paper reviews the role and applications of geo-spatial tool such as Geographical Information System (GIS) for precise agro-residue resource assessment, biomass logistic and power plant design. Further, application of Life Cycle Assessment (LCA) in understanding the potential impact of agro-residue bioenergy generation on different ecosystem services has also been reviewed and limitations associated with LCA variability and uncertainty were discussed. Usefulness of integration of GIS into LCA (i.e. spatial LCA) to overcome the limitations of conventional LCA and to produce a holistic evaluation of the environmental benefits and concerns of bioenergy is also reviewed. Application of GIS, LCA and spatial LCA can help alleviate the challenges faced by ambitious bioenergy projects by addressing both economics and environmental goals.}, } @article {pmid28339946, year = {2017}, author = {Park, SH and Perrotta, A and Hanning, I and Diaz-Sanchez, S and Pendleton, S and Alm, E and Ricke, SC}, title = {Pasture flock chicken cecal microbiome responses to prebiotics and plum fiber feed amendments.}, journal = {Poultry science}, volume = {96}, number = {6}, pages = {1820-1830}, doi = {10.3382/ps/pew441}, pmid = {28339946}, issn = {1525-3171}, mesh = {Animal Feed/analysis ; Animals ; Bacteria/genetics/isolation & purification ; Cecum/microbiology ; Chickens/*microbiology ; Diet/veterinary ; Dietary Fiber/*administration & dosage ; Dietary Supplements ; *Microbiota ; Oligosaccharides/administration & dosage/*pharmacology ; Prebiotics/*administration & dosage ; *Prunus domestica ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {When prebiotics and other fermentation substrates are delivered to animals as feed supplements, the typical goal is to improve weight gain and feed conversion. In this work, we examined pasture flock chicken cecal contents using next generation sequencing (NGS) to identify and understand the composition of the microbiome when prebiotics and fermentation substrates were supplemented. We generated 16S rRNA sequencing data for 120 separate cecal samples from groups of chickens receiving one of 3 prebiotics or fiber feed additives. The data indicated that respective feed additives enrich for specific bacterial community members and modulate the diversity of the microbiome. We applied synthetic learning in microbial ecology (SLiME) analysis to interpret 16S rRNA microbial community data and identify specific bacterial operational taxonomic units (OTU) that are predictive of the particular feed additives used in these experiments. The results suggest that feed can influence microbiome composition in a predictable way, and thus diet may have indirect effects on weight gain and feed conversion through the microbiome.}, } @article {pmid28337822, year = {2017}, author = {Berney, C and Ciuprina, A and Bender, S and Brodie, J and Edgcomb, V and Kim, E and Rajan, J and Parfrey, LW and Adl, S and Audic, S and Bass, D and Caron, DA and Cochrane, G and Czech, L and Dunthorn, M and Geisen, S and Glöckner, FO and Mahé, F and Quast, C and Kaye, JZ and Simpson, AGB and Stamatakis, A and Del Campo, J and Yilmaz, P and de Vargas, C}, title = {UniEuk: Time to Speak a Common Language in Protistology!.}, journal = {The Journal of eukaryotic microbiology}, volume = {64}, number = {3}, pages = {407-411}, pmid = {28337822}, issn = {1550-7408}, mesh = {Animals ; Bacteria/classification ; Biodiversity ; *Classification ; Databases, Nucleic Acid ; Ecosystem ; Environment ; Eukaryota/*classification/cytology/genetics/physiology ; Eukaryotic Cells ; Fungi/classification ; Phylogeny ; }, abstract = {Universal taxonomic frameworks have been critical tools to structure the fields of botany, zoology, mycology, and bacteriology as well as their large research communities. Animals, plants, and fungi have relatively solid, stable morpho-taxonomies built over the last three centuries, while bacteria have been classified for the last three decades under a coherent molecular taxonomic framework. By contrast, no such common language exists for microbial eukaryotes, even though environmental '-omics' surveys suggest that protists make up most of the organismal and genetic complexity of our planet's ecosystems! With the current deluge of eukaryotic meta-omics data, we urgently need to build up a universal eukaryotic taxonomy bridging the protist -omics age to the fragile, centuries-old body of classical knowledge that has effectively linked protist taxa to morphological, physiological, and ecological information. UniEuk is an open, inclusive, community-based and expert-driven international initiative to build a flexible, adaptive universal taxonomic framework for eukaryotes. It unites three complementary modules, EukRef, EukBank, and EukMap, which use phylogenetic markers, environmental metabarcoding surveys, and expert knowledge to inform the taxonomic framework. The UniEuk taxonomy is directly implemented in the European Nucleotide Archive at EMBL-EBI, ensuring its broad use and long-term preservation as a reference taxonomy for eukaryotes.}, } @article {pmid28337585, year = {2017}, author = {Spix, C and Grosche, B and Bleher, M and Kaatsch, P and Scholz-Kreisel, P and Blettner, M}, title = {Background gamma radiation and childhood cancer in Germany: an ecological study.}, journal = {Radiation and environmental biophysics}, volume = {56}, number = {2}, pages = {127-138}, pmid = {28337585}, issn = {1432-2099}, mesh = {Adolescent ; Background Radiation/*adverse effects ; Female ; Gamma Rays/*adverse effects ; Germany/epidemiology ; Humans ; Incidence ; Male ; Neoplasms, Radiation-Induced/*epidemiology/etiology ; }, abstract = {The relationship of low-dose background gamma radiation and childhood leukaemia was investigated in a number of studies. Results from these studies are inconclusive. Therefore, in the present study 25 years of German childhood cancer data were analyzed using interpolated background annual gamma dose rate per community in an ecological study. The main question was leukaemia; as exploratory questions we investigate central nervous system (CNS) tumours, thyroid carcinomas and diagnoses less likely to be related to radiation. A Poisson regression model was applied and a fractional polynomial model building procedure. As the main sensitivity analysis a community deprivation index was included as a potential confounder. It was found that outdoor background gamma annual dose rates in Germany range roughly from 0.5-1.5 mSv/a with an average of 0.817 mSv/a. No association of annual ambient gamma dose rates with leukaemia incidence was found. Amongst the exploratory analyses, a strong association was found with CNS tumour incidence [rate ratio for 1.5 vs 0.5 mSv/a: 1.35; 95% confidence interval (1.17, 1.57)]. The community level deprivation index was not a confounder. It is concluded that the present study did not confirm an association of annual outdoor ambient gamma dose rate and childhood leukaemia, corresponding to some studies and contrasting others. An association with CNS incidence was found in the exploratory analyses. As this is an ecological study no causal interpretation is possible.}, } @article {pmid28337523, year = {2017}, author = {Petit, M- and Bryère, J and Maravic, M and Pallaro, F and Marcelli, C}, title = {Hip fracture incidence and social deprivation: results from a French ecological study.}, journal = {Osteoporosis international : a journal established as result of cooperation between the European Foundation for Osteoporosis and the National Osteoporosis Foundation of the USA}, volume = {28}, number = {7}, pages = {2045-2051}, pmid = {28337523}, issn = {1433-2965}, mesh = {Adult ; Age Distribution ; Aged ; Databases, Factual ; Female ; France/epidemiology ; Health Status Disparities ; Hip Fractures/*epidemiology ; Humans ; Incidence ; Male ; Middle Aged ; Osteoporotic Fractures/*epidemiology ; Risk Factors ; Sex Distribution ; *Social Class ; Socioeconomic Factors ; }, abstract = {UNLABELLED: The association between socioeconomic status (SES) and hip fracture (HF) incidence was analyzed in France in 2008. In men and women, a decrease in HF incidence was observed as the social deprivation index increased. This result may be partly due to the protective effect of increasing body weight against HF.

INTRODUCTION: Regional variations in hip fracture (HF) incidence exist worldwide. Reasons for these variations remain unknown. As regional variations have also been observed for socioeconomic status, we analyzed the association between socioeconomic deprivation (SED) and HF incidence in France in 2008.

METHODS: From the French Hospital National Database, we selected all HF encoded as primary diagnosis in persons aged 30 years and over. The recently published French version of the European Deprivation Index (EDI) was used for SED analysis, and an EDI score was measured for the year 2007 in each French local municipality. The EDI score was categorized in quintiles. Poisson regression was performed to examine the association between HF incidence and EDI adjusted for age and sex. The population attributable fraction (PAF) was measured to calculate the proportion of excess cases of HF associated with social affluence.

RESULTS: In 2008, 83,538 HF were reported in France of which 59,143 were included in this study. Among them, 44,401 fractures occurred in women (75%) and 14,742 in men (25%). In both men and women, there was a decrease in the HF incidence with increasing SED index. In Poisson regression, the interaction of age class and sex was significant (p < 0.0001) and the EDI in quintiles was significantly associated with the incidence of HF (p < 0.0001). A higher number of people living in affluent residential areas corresponded to a higher risk of HF. The risk of HF is 2.42 times higher for those living in the most affluent group compared to those living in the most underprivileged group. The value of the PAF was calculated at 27.1%.

CONCLUSION: Social disparities in HF incidence exist in France with the most deprived municipalities having the lowest incidence. Prior knowledge demonstrates the strong relationships between body weight and HF risk as well as between body weight and the SED. The link found in our study between EDI and HF incidence as well as regional and temporal variations in HF incidence may be partly due to the protective effect of increased body weight against HF.}, } @article {pmid28336967, year = {2017}, author = {Lv, C and Wu, X and Wang, X and Su, J and Zeng, H and Zhao, J and Lin, S and Liu, R and Li, H and Li, X and Zhang, W}, title = {The gene expression profiles in response to 102 traditional Chinese medicine (TCM) components: a general template for research on TCMs.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {352}, pmid = {28336967}, issn = {2045-2322}, mesh = {Benzophenanthridines/isolation & purification/pharmacology ; Cell Line, Tumor ; Databases, Factual ; Drugs, Chinese Herbal/pharmacology ; Humans ; *Medicine, Chinese Traditional ; *Transcriptome ; Zanthoxylum/chemistry ; }, abstract = {Traditional Chinese medicines (TCMs) have important therapeutic value in long-term clinical practice. However, because TCMs contain diverse ingredients and have complex effects on the human body, the molecular mechanisms of TCMs are poorly understood. In this work, we determined the gene expression profiles of cells in response to TCM components to investigate TCM activities at the molecular and cellular levels. MCF7 cells were separately treated with 102 different molecules from TCMs, and their gene expression profiles were compared with the Connectivity Map (CMAP). To demonstrate the reliability and utility of our approach, we used nitidine chloride (NC) from the root of Zanthoxylum nitidum, a topoisomerase I/II inhibitor and α-adrenoreceptor antagonist, as an example to study the molecular function of TCMs using CMAP data as references. We successfully applied this approach to the four ingredients in Danshen and analyzed the synergistic mechanism of TCM components. The results demonstrate that our newly generated TCM data and related methods are valuable in the analysis and discovery of the molecular actions of TCM components. This is the first work to establish gene expression profiles for the study of TCM components and serves as a template for general TCM research.}, } @article {pmid28334223, year = {2017}, author = {Rabosky, DL and Mitchell, JS and Chang, J}, title = {Is BAMM Flawed? Theoretical and Practical Concerns in the Analysis of Multi-Rate Diversification Models.}, journal = {Systematic biology}, volume = {66}, number = {4}, pages = {477-498}, pmid = {28334223}, issn = {1076-836X}, mesh = {Bayes Theorem ; Biodiversity ; Classification/*methods ; Data Interpretation, Statistical ; Likelihood Functions ; *Models, Biological ; *Phylogeny ; Software ; }, abstract = {Bayesian analysis of macroevolutionary mixtures (BAMM) is a statistical framework that uses reversible jump Markov chain Monte Carlo to infer complex macroevolutionary dynamics of diversification and phenotypic evolution on phylogenetic trees. A recent article by Moore et al. (MEA) reported a number of theoretical and practical concerns with BAMM. Major claims from MEA are that (i) BAMM's likelihood function is incorrect, because it does not account for unobserved rate shifts; (ii) the posterior distribution on the number of rate shifts is overly sensitive to the prior; and (iii) diversification rate estimates from BAMM are unreliable. Here, we show that these and other conclusions from MEA are generally incorrect or unjustified. We first demonstrate that MEA's numerical assessment of the BAMM likelihood is compromised by their use of an invalid likelihood function. We then show that "unobserved rate shifts" appear to be irrelevant for biologically plausible parameterizations of the diversification process. We find that the purportedly extreme prior sensitivity reported by MEA cannot be replicated with standard usage of BAMM v2.5, or with any other version when conventional Bayesian model selection is performed. Finally, we demonstrate that BAMM performs very well at estimating diversification rate variation across the ${\sim} $20% of simulated trees in MEA's data set for which it is theoretically possible to infer rate shifts with confidence. Due to ascertainment bias, the remaining 80% of their purportedly variable-rate phylogenies are statistically indistinguishable from those produced by a constant-rate birth-death process and were thus poorly suited for the summary statistics used in their performance assessment. We demonstrate that inferences about diversification rates have been accurate and consistent across all major previous releases of the BAMM software. We recognize an acute need to address the theoretical foundations of rate-shift models for phylogenetic trees, and we expect BAMM and other modeling frameworks to improve in response to mathematical and computational innovations. However, we remain optimistic that that the imperfect tools currently available to comparative biologists have provided and will continue to provide important insights into the diversification of life on Earth.}, } @article {pmid28331552, year = {2017}, author = {Robledo-Abad, C and Althaus, HJ and Berndes, G and Bolwig, S and Corbera, E and Creutzig, F and Garcia-Ulloa, J and Geddes, A and Gregg, JS and Haberl, H and Hanger, S and Harper, RJ and Hunsberger, C and Larsen, RK and Lauk, C and Leitner, S and Lilliestam, J and Lotze-Campen, H and Muys, B and Nordborg, M and Ölund, M and Orlowsky, B and Popp, A and Portugal-Pereira, J and Reinhard, J and Scheiffle, L and Smith, P}, title = {Bioenergy production and sustainable development: science base for policymaking remains limited.}, journal = {Global change biology. Bioenergy}, volume = {9}, number = {3}, pages = {541-556}, pmid = {28331552}, issn = {1757-1693}, abstract = {The possibility of using bioenergy as a climate change mitigation measure has sparked a discussion of whether and how bioenergy production contributes to sustainable development. We undertook a systematic review of the scientific literature to illuminate this relationship and found a limited scientific basis for policymaking. Our results indicate that knowledge on the sustainable development impacts of bioenergy production is concentrated in a few well-studied countries, focuses on environmental and economic impacts, and mostly relates to dedicated agricultural biomass plantations. The scope and methodological approaches in studies differ widely and only a small share of the studies sufficiently reports on context and/or baseline conditions, which makes it difficult to get a general understanding of the attribution of impacts. Nevertheless, we identified regional patterns of positive or negative impacts for all categories - environmental, economic, institutional, social and technological. In general, economic and technological impacts were more frequently reported as positive, while social and environmental impacts were more frequently reported as negative (with the exception of impacts on direct substitution of GHG emission from fossil fuel). More focused and transparent research is needed to validate these patterns and develop a strong science underpinning for establishing policies and governance agreements that prevent/mitigate negative and promote positive impacts from bioenergy production.}, } @article {pmid28330463, year = {2017}, author = {Yang, M and You, W and Wu, S and Fan, Z and Xu, B and Zhu, M and Li, X and Xiao, Y}, title = {Global transcriptome analysis of Huperzia serrata and identification of critical genes involved in the biosynthesis of huperzine A.}, journal = {BMC genomics}, volume = {18}, number = {1}, pages = {245}, pmid = {28330463}, issn = {1471-2164}, mesh = {Alkaloids/*biosynthesis/metabolism ; Computational Biology/methods ; Databases, Genetic ; *Gene Expression Profiling ; *Gene Expression Regulation, Plant ; Gene Ontology ; High-Throughput Nucleotide Sequencing ; Huperzia/classification/*genetics/*metabolism ; Metabolic Networks and Pathways ; Molecular Sequence Annotation ; Phylogeny ; Reproducibility of Results ; Sesquiterpenes ; *Transcriptome ; }, abstract = {BACKGROUND: Huperzia serrata (H. serrata) is an economically important traditional Chinese herb with the notably medicinal value. As a representative member of the Lycopodiaceae family, the H. serrata produces various types of effectively bioactive lycopodium alkaloids, especially the huperzine A (HupA) which is a promising drug for Alzheimer's disease. Despite their medicinal importance, the public genomic and transcriptomic resources are very limited and the biosynthesis of HupA is largely unknown. Previous studies on comparison of 454-ESTs from H. serrata and Phlegmariurus carinatus predicted putative genes involved in lycopodium alkaloid biosynthesis, such as lysine decarboxylase like (LDC-like) protein and some CYP450s. However, these gene annotations were not carried out with further biochemical characterizations. To understand the biosynthesis of HupA and its regulation in H. serrata, a global transcriptome analysis on H. Serrata tissues was performed.

RESULTS: In this study, we used the Illumina Highseq4000 platform to generate a substantial RNA sequencing dataset of H. serrata. A total of 40.1 Gb clean data was generated from four different tissues: root, stem, leaf, and sporangia and assembled into 181,141 unigenes. The total length, average length, N50 and GC content of unigenes were 219,520,611 bp, 1,211 bp, 2,488 bp and 42.51%, respectively. Among them, 105,516 unigenes (58.25%) were annotated by seven public databases (NR, NT, Swiss-Prot, KEGG, COG, Interpro, GO), and 54 GO terms and 3,391 transcription factors (TFs) were functionally classified, respectively. KEGG pathway analysis revealed that 72,230 unigenes were classified into 21 functional pathways. Three types of candidate enzymes, LDC, CAO and PKS, responsible for the biosynthesis of precursors of HupA were all identified in the transcripts. Four hundred and fifty-seven CYP450 genes in H. serrata were also analyzed and compared with tissue-specific gene expression. Moreover, two key classes of CYP450 genes BBE and SLS, with 23 members in total, for modification of the lycopodium alkaloid scaffold in the late two stages of biosynthesis of HupA were further evaluated.

CONCLUSION: This study is the first report of global transcriptome analysis on all tissues of H. serrata, and critical genes involved in the biosynthesis of precursors and scaffold modifications of HupA were discovered and predicted. The transcriptome data from this work not only could provide an important resource for further investigating on metabolic pathways in H. serrata, but also shed light on synthetic biology study of HupA.}, } @article {pmid28327946, year = {2017}, author = {Xu, J and Bian, C and Chen, K and Liu, G and Jiang, Y and Luo, Q and You, X and Peng, W and Li, J and Huang, Y and Yi, Y and Dong, C and Deng, H and Zhang, S and Zhang, H and Shi, Q and Xu, P}, title = {Draft genome of the Northern snakehead, Channa argus.}, journal = {GigaScience}, volume = {6}, number = {4}, pages = {1-5}, pmid = {28327946}, issn = {2047-217X}, mesh = {Animals ; Computational Biology/methods ; *Genome ; Genome Size ; *Genomics/methods ; Molecular Sequence Annotation ; Multigene Family ; Perciformes/classification/*genetics ; Phylogeny ; Repetitive Sequences, Nucleic Acid ; Sequence Analysis, DNA ; Whole Genome Sequencing ; }, abstract = {The Northern snakehead (Channa argus), a member of the Channidae family of the Perciformes, is an economically important freshwater fish native to East Asia. In North America, it has become notorious as an intentionally released invasive species. Its ability to breathe air with gills and migrate short distances over land makes it a good model for bimodal breath research. Therefore, recent research has focused on the identification of relevant candidate genes. Here, we performed whole genome sequencing of C. argus to construct its draft genome, aiming to offer useful information for further functional studies and identification of target genes related to its unusual facultative air breathing. Findings: We assembled the C. argus genome with a total of 140.3 Gb of raw reads, which were sequenced using the Illumina HiSeq2000 platform. The final draft genome assembly was approximately 615.3 Mb, with a contig N50 of 81.4 kb and scaffold N50 of 4.5 Mb. The identified repeat sequences account for 18.9% of the whole genome. The 19 877 protein-coding genes were predicted from the genome assembly, with an average of 10.5 exons per gene. Conclusion: We generated a high-quality draft genome of C. argus, which will provide a valuable genetic resource for further biomedical investigations of this economically important teleost fish.}, } @article {pmid28327943, year = {2017}, author = {Liu, K and Xu, D and Li, J and Bian, C and Duan, J and Zhou, Y and Zhang, M and You, X and You, Y and Chen, J and Yu, H and Xu, G and Fang, DA and Qiang, J and Jiang, S and He, J and Xu, J and Shi, Q and Zhang, Z and Xu, P}, title = {Whole genome sequencing of Chinese clearhead icefish, Protosalanx hyalocranius.}, journal = {GigaScience}, volume = {6}, number = {4}, pages = {1-6}, pmid = {28327943}, issn = {2047-217X}, mesh = {Animals ; Computational Biology/methods ; *Genome ; *Genomics/methods ; High-Throughput Nucleotide Sequencing ; Molecular Sequence Annotation ; Osmeriformes/classification/*genetics ; Phenotype ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {Chinese clearhead icefish, Protosalanx hyalocranius , is a representative icefish species with economic importance and special appearance. Due to its great economic value in China, the fish was introduced into Lake Dianchi and several other lakes from the Lake Taihu half a century ago. Similar to the Sinocyclocheilus cavefish, the clearhead icefish has certain cavefish-like traits, such as transparent body and nearly scaleless skin. Here, we provide the whole genome sequence of this surface-dwelling fish and generated a draft genome assembly, aiming at exploring molecular mechanisms for the biological interests. A total of 252.1 Gb of raw reads were sequenced. Subsequently, a novel draft genome assembly was generated, with the scaffold N50 reaching 1.163 Mb. The genome completeness was estimated to be 98.39 % by using the CEGMA evaluation. Finally, we annotated 19 884 protein-coding genes and observed that repeat sequences account for 24.43 % of the genome assembly. We report the first draft genome of the Chinese clearhead icefish. The genome assembly will provide a solid foundation for further molecular breeding and germplasm resource protection in Chinese clearhead icefish, as well as other icefishes. It is also a valuable genetic resource for revealing the molecular mechanisms for the cavefish-like characters.}, } @article {pmid28327792, year = {2017}, author = {Romero-Alvarez, D and Escobar, LE}, title = {Vegetation loss and the 2016 Oropouche fever outbreak in Peru.}, journal = {Memorias do Instituto Oswaldo Cruz}, volume = {112}, number = {4}, pages = {292-298}, pmid = {28327792}, issn = {1678-8060}, mesh = {Arbovirus Infections/*epidemiology/*transmission ; *Disease Outbreaks ; *Ecosystem ; Geographic Information Systems ; Humans ; Peru/epidemiology ; Risk Factors ; }, abstract = {BACKGROUND: Oropouche virus causes Oropouche fever, an arboviral disease transmitted mainly by midges of the genus Culicoides and Culex mosquitoes. Clinical presentation of Oropouche fever in humans includes fever, headache, rash, myalgia, and in rare cases spontaneous bleeding and aseptic meningitis. Landscape change has been proposed as a driver of Oropouche fever emergence.

OBJECTIVE: To investigate the landscape epidemiology of the Oropouche fever outbreak that began in April 2016 in Cusco, Peru.

METHODS: We used information of vegetation and multivariate spatial analyses including ecological niche modeling. Vegetation was characterised using16-day composite enhanced vegetation index (EVI) images at 500 m spatial resolution from the MODIS sensor carried by the Terra satellite.

FINDINGS: Cases were distributed across seven Peruvian districts in two provinces. La Concepcion was the province with most of the affected districts. EVI time series across 2000 to 2016 suggested a decline in the vegetation in sites with Oropouche fever cases before the epidemic. Our ecological niche modeling suggests that other areas in Junin, Apurimac, and Madre de Dios departments are at risk of Oropouche fever occurrence.

MAIN CONCLUSIONS: Our results may provide a guide for future fieldwork to test hypotheses regarding Oropouche fever emergence and habitat loss in tropical Latin America.}, } @article {pmid28322330, year = {2017}, author = {Xiang, X and Wang, R and Wang, H and Gong, L and Man, B and Xu, Y}, title = {Distribution of Bathyarchaeota Communities Across Different Terrestrial Settings and Their Potential Ecological Functions.}, journal = {Scientific reports}, volume = {7}, number = {}, pages = {45028}, pmid = {28322330}, issn = {2045-2322}, mesh = {Archaea/*classification/*genetics ; *Biodiversity ; Computational Biology/methods ; *Ecosystem ; Environment ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {High abundance and widespread distribution of the archaeal phylum Bathyarchaeota in marine environment have been recognized recently, but knowledge about Bathyarchaeota in terrestrial settings and their correlation with environmental parameters is fairly limited. Here we reported the abundance of Bathyarchaeota members across different ecosystems and their correlation with environmental factors by constructing 16S rRNA clone libraries of peat from the Dajiuhu Peatland, coupling with bioinformatics analysis of 16S rRNA data available to date in NCBI database. In total, 1456 Bathyarchaeota sequences from 28 sites were subjected to UniFrac analysis based on phylogenetic distance and multivariate regression tree analysis of taxonomy. Both phylogenetic and taxon-based approaches showed that salinity, total organic carbon and temperature significantly influenced the distribution of Bathyarchaeota across different terrestrial habitats. By applying the ecological concept of 'indicator species', we identify 9 indicator groups among the 6 habitats with the most in the estuary sediments. Network analysis showed that members of Bathyarchaeota formed the "backbone" of archaeal community and often co-occurred with Methanomicrobia. These results suggest that Bathyarchaeota may play an important ecological role within archaeal communities via a potential symbiotic association with Methanomicrobia. Our results shed light on understanding of the biogeography, potential functions of Bathyarchaeota and environment conditions that influence Bathyarchaea distribution in terrestrial settings.}, } @article {pmid28320978, year = {2017}, author = {Kajiki, S and Izumi, H and Hayashida, K and Kusumoto, A and Nagata, T and Mori, K}, title = {A randomized controlled trial of the effect of participatory ergonomic low back pain training on workplace improvement.}, journal = {Journal of occupational health}, volume = {59}, number = {3}, pages = {256-266}, pmid = {28320978}, issn = {1348-9585}, mesh = {Adult ; Ergonomics/*methods ; Female ; Health Education/*methods ; Health Promotion/methods ; Humans ; Japan ; Low Back Pain/*prevention & control ; Male ; Manufacturing Industry ; Middle Aged ; Occupational Diseases/*prevention & control ; Occupational Health ; Regression Analysis ; Safety Management/methods ; Workplace ; Young Adult ; }, abstract = {OBJECTIVES: This study aimed to determine the effects of participatory workplace improvement (PWI) -based provision of ergonomic training and ergonomic action checklists (ACLs) to on-site managers on workplace improvement activities for low back pain (LBP).

METHODS: A randomized controlled trial (RCT) was conducted at a manufacturing company in Japan. Teams entered in the study were randomly assigned to a control and an intervention group. A total of three interventional training sessions on methods of ergonomics were provided to on-site managers in the intervention group, with 1-month intervals between sessions. Ergonomic ACLs were provided at the same time. After completion of the training sessions, each team then provided a report of improvements each month for the next 10 months. Two people in charge of safety and health chose two major objectives of the implemented activities from the five categories. The reported number of improvements was analyzed using a Poisson regression model.

RESULTS: In the intervention group, although the incident rate ratio (IRR) of PWIs in countermeasures for the LBP category was significantly elevated after the training sessions, the IRR of improvements decreased over time during the 10-month follow-up period. No significant difference was observed in the IRR of total PWIs in either the control or intervention group.

CONCLUSIONS: PWI-based provision of ergonomic training sessions and ergonomics ACLs to on-site managers was shown to be effective for workplace improvement activities targeted at LBP. However, because the effects decrease over time, efforts should be made to maintain the effects through regular interventions.}, } @article {pmid28320440, year = {2017}, author = {Huettmann, F and Magnuson, EE and Hueffer, K}, title = {Ecological niche modeling of rabies in the changing Arctic of Alaska.}, journal = {Acta veterinaria Scandinavica}, volume = {59}, number = {1}, pages = {18}, pmid = {28320440}, issn = {1751-0147}, support = {RL5 GM118990/GM/NIGMS NIH HHS/United States ; TL4 GM118992/GM/NIGMS NIH HHS/United States ; UL1 GM118991/GM/NIGMS NIH HHS/United States ; }, mesh = {Alaska/epidemiology ; Algorithms ; Animals ; Arctic Regions/epidemiology ; *Climate Change ; Environment ; Geographic Information Systems ; Humans ; Machine Learning ; Models, Theoretical ; Rabies/*epidemiology/veterinary/virology ; Rabies virus/*physiology ; }, abstract = {BACKGROUND: Rabies is a disease of global significance including in the circumpolar Arctic. In Alaska enzootic rabies persist in northern and western coastal areas. Only sporadic cases have occurred in areas outside of the regions considered enzootic for the virus, such as the interior of the state and urbanized regions.

RESULTS: Here we examine the distribution of diagnosed rabies cases in Alaska, explicit in space and time. We use a geographic information system (GIS), 20 environmental data layers and provide a quantitative non-parsimonious estimate of the predicted ecological niche, based on data mining, machine learning and open access data. We identify ecological correlates and possible drivers that determine the ecological niche of rabies virus in Alaska. More specifically, our models show that rabies cases are closely associated with human infrastructure, and reveal an ecological niche in remote northern wilderness areas. Furthermore a model utilizing climate modeling suggests a reduction of the current ecological niche for detection of rabies virus in Alaska, a state that is disproportionately affected by a changing climate.

CONCLUSIONS: Our results may help to better inform public health decisions in the future and guide further studies on individual drivers of rabies distribution in the Arctic.}, } @article {pmid28318412, year = {2017}, author = {Xiao, B and Cui, LQ and Ding, C and Wang, H}, title = {Effects of Lithium and 2,4-Dichlorophenol on Zebrafish: Circadian Rhythm Disorder and Molecular Effects.}, journal = {Zebrafish}, volume = {14}, number = {3}, pages = {209-215}, doi = {10.1089/zeb.2016.1389}, pmid = {28318412}, issn = {1557-8542}, mesh = {Animals ; Anthelmintics/pharmacology ; Chlorophenols/*toxicity ; Chronobiology Disorders/*genetics/pathology ; Circadian Rhythm/*drug effects ; Gene Expression Profiling ; Gene Expression Regulation, Developmental/*drug effects ; Gene Ontology ; Larva/drug effects/metabolism ; Lithium/*toxicity ; RNA, Messenger/metabolism ; Signal Transduction/drug effects ; Water Pollutants/*toxicity ; Zebrafish/growth & development/*physiology ; Zebrafish Proteins/genetics/metabolism ; }, abstract = {The aim of this study was to investigate lithium and 2,4-dichlorophenol (2,4-DCP)-induced circadian rhythm disorder and their genome-wide effects in zebrafish. Zebrafish larvae were exposed to 250 ppm LiCl (n = 40) or 20 ppm 2,4-DCP. RNA was subsequently extracted and determined quantitatively. The mRNA levels of circadian clock-related genes, including clock1a, bmal1b, per2, and per1b, were determined. Microarray datasets were generated and the differentially expressed genes (DEGs) were identified. The mRNA levels of some upregulated and downregulated DEGs were examined by quantitative real-time polymerase chain reaction (RT-PCR). Finally, gene ontology (GO) enrichment analysis was applied to determine the roles of the DEGs. The mRNA expression levels of circadian rhythm-related genes in the daily cycle were significantly affected after incubation of zebrafish with LiCl and 2,4-DCP. Many genes were differentially expressed during the light phase (97 h) and RT-PCR validation tests revealed that the expression patterns of DEGs were in accordance with those obtained by microarray analysis. GO functional enrichment analysis showed that the DEGs in LiCl- and 2,4-DCP-treated groups were associated with signal transduction and development. Collectively, our findings indicate that LiCl and 2,4-DCP could affect signal transduction pathways and immune response, thereby inducing circadian rhythm disorder.}, } @article {pmid28317909, year = {2017}, author = {Gibaldi, A and Canessa, A and Sabatini, SP}, title = {The Active Side of Stereopsis: Fixation Strategy and Adaptation to Natural Environments.}, journal = {Scientific reports}, volume = {7}, number = {}, pages = {44800}, pmid = {28317909}, issn = {2045-2322}, mesh = {*Depth Perception ; Environment ; Eye Movements ; Humans ; *Vision Disparity ; Vision, Binocular ; }, abstract = {Depth perception in near viewing strongly relies on the interpretation of binocular retinal disparity to obtain stereopsis. Statistical regularities of retinal disparities have been claimed to greatly impact on the neural mechanisms that underlie binocular vision, both to facilitate perceptual decisions and to reduce computational load. In this paper, we designed a novel and unconventional approach in order to assess the role of fixation strategy in conditioning the statistics of retinal disparity. We integrated accurate realistic three-dimensional models of natural scenes with binocular eye movement recording, to obtain accurate ground-truth statistics of retinal disparity experienced by a subject in near viewing. Our results evidence how the organization of human binocular visual system is finely adapted to the disparity statistics characterizing actual fixations, thus revealing a novel role of the active fixation strategy over the binocular visual functionality. This suggests an ecological explanation for the intrinsic preference of stereopsis for a close central object surrounded by a far background, as an early binocular aspect of the figure-ground segregation process.}, } @article {pmid28306748, year = {2017}, author = {Koen, EL and Tosa, MI and Nielsen, CK and Schauber, EM}, title = {Does landscape connectivity shape local and global social network structure in white-tailed deer?.}, journal = {PloS one}, volume = {12}, number = {3}, pages = {e0173570}, pmid = {28306748}, issn = {1932-6203}, mesh = {Animals ; *Behavior, Animal ; *Deer ; *Ecosystem ; Female ; Geographic Information Systems ; }, abstract = {Intraspecific social behavior can be influenced by both intrinsic and extrinsic factors. While much research has focused on how characteristics of individuals influence their roles in social networks, we were interested in the role that landscape structure plays in animal sociality at both individual (local) and population (global) levels. We used female white-tailed deer (Odocoileus virginianus) in Illinois, USA, to investigate the potential effect of landscape on social network structure by weighting the edges of seasonal social networks with association rate (based on proximity inferred from GPS collar data). At the local level, we found that sociality among female deer in neighboring social groups (n = 36) was mainly explained by their home range overlap, with two exceptions: 1) during fawning in an area of mixed forest and grassland, deer whose home ranges had low forest connectivity were more social than expected; and 2) during the rut in an area of intensive agriculture, deer inhabiting home ranges with high amount and connectedness of agriculture were more social than expected. At the global scale, we found that deer populations (n = 7) in areas with highly connected forest-agriculture edge, a high proportion of agriculture, and a low proportion of forest tended to have higher weighted network closeness, although low sample size precluded statistical significance. This result implies that infectious disease could spread faster in deer populations inhabiting such landscapes. Our work advances the general understanding of animal social networks, demonstrating how landscape features can underlie differences in social behavior both within and among wildlife social networks.}, } @article {pmid28306623, year = {2017}, author = {Chen, YH and Wei, HT and Bai, YM and Hsu, JW and Huang, KL and Su, TP and Li, CT and Lin, WC and Wu, YH and Pan, TL and Chen, TJ and Tsai, SJ and Chen, MH}, title = {Risk of Epilepsy in Individuals With Posttraumatic Stress Disorder: A Nationwide Longitudinal Study.}, journal = {Psychosomatic medicine}, volume = {79}, number = {6}, pages = {664-669}, doi = {10.1097/PSY.0000000000000463}, pmid = {28306623}, issn = {1534-7796}, mesh = {Adult ; Aged ; Aged, 80 and over ; Comorbidity ; Databases, Factual ; Epilepsy/*epidemiology ; Female ; Follow-Up Studies ; Humans ; Male ; Middle Aged ; Stress Disorders, Post-Traumatic/*epidemiology ; Taiwan ; Young Adult ; }, abstract = {OBJECTIVE: Several cross-sectional studies have reported a relationship between posttraumatic stress disorder (PTSD) and epilepsy. However, the temporal association between PTSD and epilepsy has rarely been investigated. We hypothesized that the risk of developing epilepsy later in life would be higher in patients with PTSD than in those without PTSD.

METHODS: Using the Taiwan National Health Insurance Research Database, 6425 individuals with PTSD and 24,980 age-/sex-matched controls were enrolled between 2002 and 2009 in our study and followed up to the end of 2011. Those who developed epilepsy during the follow-up period were identified.

RESULTS: Individuals with PTSD had a higher incidence of developing epilepsy (2.65 versus 0.33 per 1000 person-years, p < .001), with an earlier onset of epilepsy (37.53 years [15.80 years] versus 48.11 years [23.97 years], p = .002) than did the controls. Individuals with PTSD had an elevated risk of developing epilepsy (hazard ratio [HR] = 3.72, 95% confidence interval [CI] = 2.27-6.11) during the follow-up after adjustment for demographic data and medical and psychiatric comorbidities. Sensitivity analyses after excluding the observation in the first year (HR = 2.53, 95% CI = 1.44-4.47) and the first 3 years (HR = 2.14, 95% CI = 1.15-4.01) revealed consistent results.

CONCLUSIONS: These results supported a temporal association between PTSD and the development of epilepsy. Further studies are warranted to investigate the underlying pathophysiological pathways that explain the longitudinal association of PTSD with subsequent epilepsy.}, } @article {pmid28304300, year = {2017}, author = {Czaja, SJ and Loewenstein, DA and Sabbag, SA and Curiel, RE and Crocco, E and Harvey, PD}, title = {A Novel Method for Direct Assessment of Everyday Competence Among Older Adults.}, journal = {Journal of Alzheimer's disease : JAD}, volume = {57}, number = {4}, pages = {1229-1238}, pmid = {28304300}, issn = {1875-8908}, support = {R01 AG047649/AG/NIA NIH HHS/United States ; }, mesh = {*Activities of Daily Living ; Aged ; Aged, 80 and over ; Cognitive Dysfunction/*diagnosis ; Diagnosis, Computer-Assisted/*methods ; Feasibility Studies ; Female ; Geriatric Assessment/*methods ; Humans ; Male ; Middle Aged ; Neuropsychological Tests ; Reproducibility of Results ; }, abstract = {BACKGROUND: Recent findings indicate that impairments in functional performance do occur among individuals diagnosed with mild cognitive impairment (MCI). Most assessment strategies for everyday competence are associated with challenges with reliability, are typically in paper and pencil format, or require in-person administration by a trained professional.

OBJECTIVE: This paper reports on a novel technology-based assessment battery of everyday competence that includes ecologically valid simulations of daily activities important to independence.

METHODS: The sample included 85 non-cognitively impaired older adults aged 65+ and 62 older adults diagnosed with amnestic MCI (aMCI). Participants completed standard measures of cognitive abilities and the computerized battery of everyday tasks, which included simulations of a doctor's visit; and medication and financial management tasks.

RESULTS: The older adults with aMCI performed significantly poorer on all three tasks in the everyday task battery. Performance on these measures were also moderately correlated with standard measures of cognitive abilities and showed good test-retest reliability.

CONCLUSIONS: The results show that it is feasible to use a technology-based assessment battery of everyday tasks with both non-cognitively impaired older adults and older adults with MCI. The use of this type of battery can overcome many of the logistic constraints associated with current functional assessment protocols.}, } @article {pmid28302067, year = {2017}, author = {, and Abdelrahman, H and ElHady, M and Alcivar-Warren, A and Allen, S and Al-Tobasei, R and Bao, L and Beck, B and Blackburn, H and Bosworth, B and Buchanan, J and Chappell, J and Daniels, W and Dong, S and Dunham, R and Durland, E and Elaswad, A and Gomez-Chiarri, M and Gosh, K and Guo, X and Hackett, P and Hanson, T and Hedgecock, D and Howard, T and Holland, L and Jackson, M and Jin, Y and Khalil, K and Kocher, T and Leeds, T and Li, N and Lindsey, L and Liu, S and Liu, Z and Martin, K and Novriadi, R and Odin, R and Palti, Y and Peatman, E and Proestou, D and Qin, G and Reading, B and Rexroad, C and Roberts, S and Salem, M and Severin, A and Shi, H and Shoemaker, C and Stiles, S and Tan, S and Tang, KF and Thongda, W and Tiersch, T and Tomasso, J and Prabowo, WT and Vallejo, R and van der Steen, H and Vo, K and Waldbieser, G and Wang, H and Wang, X and Xiang, J and Yang, Y and Yant, R and Yuan, Z and Zeng, Q and Zhou, T}, title = {Erratum to: Aquaculture genomics, genetics and breeding in the United States: current status, challenges, and priorities for future research.}, journal = {BMC genomics}, volume = {18}, number = {1}, pages = {235}, pmid = {28302067}, issn = {1471-2164}, } @article {pmid28296954, year = {2017}, author = {Tripathi, P and Behera, MD and Roy, PS}, title = {Optimized grid representation of plant species richness in India-Utility of an existing national database in integrated ecological analysis.}, journal = {PloS one}, volume = {12}, number = {3}, pages = {e0173774}, pmid = {28296954}, issn = {1932-6203}, mesh = {*Biodiversity ; *Databases, Factual ; *Ecology ; India ; Plants/*classification ; }, abstract = {Data on the distribution of plant species at spatial (grid) scales are required as input for integrative analysis along with related climate, environment, topography and soil data. Although the world's scientific community is increasingly generating data on plant species at various spatial grids and statistically interpolating and extrapolating the available information, data on plant diversity from the Asian continent are scant. Such data are unavailable for India, the mainland of which has part of three of the world's 36 biodiversity hotspots. Although sufficient field sampling is always impossible and impractical, it is essential to utilize fully any available database by adjudging the sampling sufficiency at a given scale. In this work, we used an exhaustive database of the plant species of the Indian mainland that was sufficient in terms of sampling vegetation types. We transformed the data, obtained the distribution at the 1° and 2° spatial grid levels and evaluated the sampling sufficiency at acceptable threshold limits (60% to 80%). The greatest species richness values recorded in the 0.04 ha quadrant, 1° grid and 2° grid were 59, 623 and 1244, respectively. Clench model was significantly (p value < 0.001) fitted using the plant species data at both the grid levels with a very high coefficient of determination (>0.95). At an acceptable threshold limit of 70%, almost all the grids at the 2° level and more than 80% of the grids at the 1° level were found to be sufficiently sampled. Sampling sufficiency was observed to be highly scale-dependent as a greater number of 2° grids attained asymptotic behaviour following the species-area curve. Grid-level sampling insufficiency was attributed to lower numbers of sampling quadrats in forests with poor approachability, which coincided with the world biodiversity hotspots', suggesting that additional sampling was required. We prescribe the use of the 1° and 2° spatial grids with sufficient sampling for any ecological analysis in conjunction with other data and thereby offer grid-level plant species richness data for the Indian mainland for the first time.}, } @article {pmid28296881, year = {2017}, author = {Radhakrishnan, S and Literman, R and Neuwald, J and Severin, A and Valenzuela, N}, title = {Transcriptomic responses to environmental temperature by turtles with temperature-dependent and genotypic sex determination assessed by RNAseq inform the genetic architecture of embryonic gonadal development.}, journal = {PloS one}, volume = {12}, number = {3}, pages = {e0172044}, pmid = {28296881}, issn = {1932-6203}, mesh = {Animals ; Female ; Genotype ; Gonads/*growth & development ; Male ; *Sex Determination Processes ; *Temperature ; *Transcriptome ; Turtles/embryology/genetics/*physiology ; }, abstract = {Vertebrate sexual fate is decided primarily by the individual's genotype (GSD), by the environmental temperature during development (TSD), or both. Turtles exhibit TSD and GSD, making them ideal to study the evolution of sex determination. Here we analyze temperature-specific gonadal transcriptomes (RNA-sequencing validated by qPCR) of painted turtles (Chrysemys picta TSD) before and during the thermosensitive period, and at equivalent stages in soft-shell turtles (Apalone spinifera-GSD), to test whether TSD's and GSD's transcriptional circuitry is identical but deployed differently between mechanisms. Our data show that most elements of the mammalian urogenital network are active during turtle gonadogenesis, but their transcription is generally more thermoresponsive in TSD than GSD, and concordant with their sex-specific function in mammals [e.g., upregulation of Amh, Ar, Esr1, Fog2, Gata4, Igf1r, Insr, and Lhx9 at male-producing temperature, and of β-catenin, Foxl2, Aromatase (Cyp19a1), Fst, Nf-kb, Crabp2 at female-producing temperature in Chrysemys]. Notably, antagonistic elements in gonadogenesis (e.g., β-catenin and Insr) were thermosensitive only in TSD early-embryos. Cirbp showed warm-temperature upregulation in both turtles disputing its purported key TSD role. Genes that may convert thermal inputs into sex-specific development (e.g., signaling and hormonal pathways, RNA-binding and heat-shock) were differentially regulated. Jak-Stat, Nf-κB, retinoic-acid, Wnt, and Mapk-signaling (not Akt and Ras-signaling) potentially mediate TSD thermosensitivity. Numerous species-specific ncRNAs (including Xist) were differentially-expressed, mostly upregulated at colder temperatures, as were unannotated loci that constitute novel TSD candidates. Cirbp showed warm-temperature upregulation in both turtles. Consistent transcription between turtles and alligator revealed putatively-critical reptilian TSD elements for male (Sf1, Amh, Amhr2) and female (Crabp2 and Hspb1) gonadogenesis. In conclusion, while preliminary, our data helps illuminate the regulation and evolution of vertebrate sex determination, and contribute genomic resources to guide further research into this fundamental biological process.}, } @article {pmid28294342, year = {2017}, author = {Zeng, L and Zhang, N and Zhang, Q and Endress, PK and Huang, J and Ma, H}, title = {Resolution of deep eudicot phylogeny and their temporal diversification using nuclear genes from transcriptomic and genomic datasets.}, journal = {The New phytologist}, volume = {214}, number = {3}, pages = {1338-1354}, doi = {10.1111/nph.14503}, pmid = {28294342}, issn = {1469-8137}, mesh = {Cell Nucleus/*genetics ; Codon/genetics ; *Databases, Genetic ; *Genes, Plant ; *Genetic Variation ; Magnoliopsida/*genetics ; *Phylogeny ; Polyploidy ; Sequence Analysis, RNA ; Time Factors ; Transcriptome/*genetics ; }, abstract = {Explosive diversification is widespread in eukaryotes, making it difficult to resolve phylogenetic relationships. Eudicots contain c. 75% of extant flowering plants, are important for human livelihood and terrestrial ecosystems, and have probably experienced explosive diversifications. The eudicot phylogenetic relationships, especially among those of the Pentapetalae, remain unresolved. Here, we present a highly supported eudicot phylogeny and diversification rate shifts using 31 newly generated transcriptomes and 88 other datasets covering 70% of eudicot orders. A highly supported eudicot phylogeny divided Pentapetalae into two groups: one with rosids, Saxifragales, Vitales and Santalales; the other containing asterids, Caryophyllales and Dilleniaceae, with uncertainty for Berberidopsidales. Molecular clock analysis estimated that crown eudicots originated c. 146 Ma, considerably earlier than earliest tricolpate pollen fossils and most other molecular clock estimates, and Pentapetalae sequentially diverged into eight major lineages within c. 15 Myr. Two identified increases of diversification rate are located in the stems leading to Pentapetalae and asterids, and lagged behind the gamma hexaploidization. The nuclear genes from newly generated transcriptomes revealed a well-resolved eudicot phylogeny, sequential separation of major core eudicot lineages and temporal mode of diversifications, providing new insights into the evolutionary trend of morphologies and contributions to the diversification of eudicots.}, } @article {pmid28288926, year = {2017}, author = {Rabelo, ÉML and Miranda, RRC and Furtado, LFV and Redondo, RAF and Tennessen, JA and Blouin, MS}, title = {Development of new microsatellites for the hookworm Ancylostoma caninum and analysis of genetic diversity in Brazilian populations.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {51}, number = {}, pages = {24-27}, doi = {10.1016/j.meegid.2017.03.008}, pmid = {28288926}, issn = {1567-7257}, mesh = {Ancylostoma/*genetics ; Ancylostomiasis/parasitology ; Animals ; Brazil ; DNA, Helminth/*genetics ; Databases, Genetic ; Dogs ; *Genetic Loci ; *Genetic Variation ; Genetics, Population ; Heterozygote ; Humans ; *Microsatellite Repeats ; }, abstract = {Considering the great efforts towards formulating a vaccine against hookworms, and the concerns about the spread of drug resistance through hookworm populations, it is justified to study the molecular diversity and population genetic structure of these nematodes. This work had the aim to develop microsatellite markers to investigate the genetic structure and the molecular diversity of Brazilian populations of Ancylostoma caninum. Seven microsatellites markers were successfully used to characterize five Brazilian populations. These findings may contribute to a better comprehension of the ecology, patterns of transmission, drug resistances and development of immunotherapeutic strategies in hookworms.}, } @article {pmid28283029, year = {2017}, author = {Weil, T and De Filippo, C and Albanese, D and Donati, C and Pindo, M and Pavarini, L and Carotenuto, F and Pasqui, M and Poto, L and Gabrieli, J and Barbante, C and Sattler, B and Cavalieri, D and Miglietta, F}, title = {Legal immigrants: invasion of alien microbial communities during winter occurring desert dust storms.}, journal = {Microbiome}, volume = {5}, number = {1}, pages = {32}, pmid = {28283029}, issn = {2049-2618}, mesh = {Africa, Northern ; *Air Microbiology ; Bacteria/classification/genetics/*isolation & purification/pathogenicity ; Biodiversity ; Climate Change ; *Desert Climate ; Dust/*analysis ; Ecosystem ; Global Warming ; Italy ; Metagenomics ; Microbial Consortia ; *Microbiota ; Public Health ; Seasons ; Silicon Dioxide ; *Wind ; }, abstract = {BACKGROUND: A critical aspect regarding the global dispersion of pathogenic microorganisms is associated with atmospheric movement of soil particles. Especially, desert dust storms can transport alien microorganisms over continental scales and can deposit them in sensitive sink habitats. In winter 2014, the largest ever recorded Saharan dust event in Italy was efficiently deposited on the Dolomite Alps and was sealed between dust-free snow. This provided us the unique opportunity to overcome difficulties in separating dust associated from "domestic" microbes and thus, to determine with high precision microorganisms transported exclusively by desert dust.

RESULTS: Our metagenomic analysis revealed that sandstorms can move not only fractions but rather large parts of entire microbial communities far away from their area of origin and that this microbiota contains several of the most stress-resistant organisms on Earth, including highly destructive fungal and bacterial pathogens. In particular, we provide first evidence that winter-occurring dust depositions can favor a rapid microbial contamination of sensitive sink habitats after snowmelt.

CONCLUSIONS: Airborne microbial depositions accompanying extreme meteorological events represent a realistic threat for ecosystem and public health. Therefore, monitoring the spread and persistence of storm-travelling alien microbes is a priority while considering future trajectories of climatic anomalies as well as anthropogenically driven changes in land use in the source regions.}, } @article {pmid28278238, year = {2017}, author = {Marshall, N and Adger, N and Attwood, S and Brown, K and Crissman, C and Cvitanovic, C and De Young, C and Gooch, M and James, C and Jessen, S and Johnson, D and Marshall, P and Park, S and Wachenfeld, D and Wrigley, D}, title = {Empirically derived guidance for social scientists to influence environmental policy.}, journal = {PloS one}, volume = {12}, number = {3}, pages = {e0171950}, pmid = {28278238}, issn = {1932-6203}, mesh = {*Conservation of Natural Resources ; *Decision Making ; *Decision Support Techniques ; Ecosystem ; *Environmental Policy ; Humans ; *Policy Making ; *Social Sciences ; Surveys and Questionnaires ; Workforce ; }, abstract = {Failure to stem trends of ecological disruption and associated loss of ecosystem services worldwide is partly due to the inadequate integration of the human dimension into environmental decision-making. Decision-makers need knowledge of the human dimension of resource systems and of the social consequences of decision-making if environmental management is to be effective and adaptive. Social scientists have a central role to play, but little guidance exists to help them influence decision-making processes. We distil 348 years of cumulative experience shared by 31 environmental experts across three continents into advice for social scientists seeking to increase their influence in the environmental policy arena. Results focus on the importance of process, engagement, empathy and acumen and reveal the importance of understanding and actively participating in policy processes through co-producing knowledge and building trust. The insights gained during this research might empower a science-driven cultural change in science-policy relations for the routine integration of the human dimension in environmental decision making; ultimately for an improved outlook for earth's ecosystems and the billions of people that depend on them.}, } @article {pmid28276176, year = {2017}, author = {Barrigón, ML and Berrouiguet, S and Carballo, JJ and Bonal-Giménez, C and Fernández-Navarro, P and Pfang, B and Delgado-Gómez, D and Courtet, P and Aroca, F and Lopez-Castroman, J and Artés-Rodríguez, A and Baca-García, E and , }, title = {User profiles of an electronic mental health tool for ecological momentary assessment: MEmind.}, journal = {International journal of methods in psychiatric research}, volume = {26}, number = {1}, pages = {}, pmid = {28276176}, issn = {1557-0657}, mesh = {Adult ; Ecological Momentary Assessment/*standards ; Female ; Humans ; Internet ; Male ; *Medical Informatics Applications ; Mental Disorders/*diagnosis ; Middle Aged ; *Suicide ; }, abstract = {Ecological momentary assessment (EMA) is gaining importance in psychiatry. This article assesses the characteristics of patients who used a new electronic EMA tool: the MEmind Wellness Tracker. Over one year, 13811 adult outpatients in our Psychiatry Department were asked to use MEmind. We collected information about socio-demographic data, psychiatric diagnoses, illness severity, stressful life events and suicidal thoughts/behavior. We compared active users (N = 2838) and non-active users (N = 10,973) of MEmind and performed a Random Forest analysis to assess which variables could predict its use. Univariate analyses revealed that MEmind-users were younger (42.2 ± 13.5 years versus 48.5 ± 16.3 years; χ[2] = 18.85; P < 0.001) and more frequently diagnosed with anxiety related disorders (57.9% versus 46.7%; χ[2] = 105.92; P = 0.000) than non-active users. They were more likely to report thoughts about death and suicide (up to 24% of active users expressed wish for death) and had experienced more stressful life events than non-active users (57% versus 48.5%; χ[2] = 64.65; P < 0.001). In the Random Forest analysis, 31 variables showed mean decrease accuracy values higher than zero with a 95% confidence interval (CI), including sex, age, suicidal thoughts, life threatening events and several diagnoses. In the light of these results, strategies to improve EMA and e-Mental Health adherence are discussed.}, } @article {pmid28273915, year = {2017}, author = {Rodríguez, JP and Fernández-Gracia, J and Thums, M and Hindell, MA and Sequeira, AM and Meekan, MG and Costa, DP and Guinet, C and Harcourt, RG and McMahon, CR and Muelbert, M and Duarte, CM and Eguíluz, VM}, title = {Big data analyses reveal patterns and drivers of the movements of southern elephant seals.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {112}, pmid = {28273915}, issn = {2045-2322}, support = {U54 GM088558/GM/NIGMS NIH HHS/United States ; }, mesh = {*Animal Migration ; Animals ; Data Mining ; Ecosystem ; *Feeding Behavior ; Locomotion ; Seals, Earless/*physiology ; Spatial Analysis ; }, abstract = {The growing number of large databases of animal tracking provides an opportunity for analyses of movement patterns at the scales of populations and even species. We used analytical approaches, developed to cope with "big data", that require no 'a priori' assumptions about the behaviour of the target agents, to analyse a pooled tracking dataset of 272 elephant seals (Mirounga leonina) in the Southern Ocean, that was comprised of >500,000 location estimates collected over more than a decade. Our analyses showed that the displacements of these seals were described by a truncated power law distribution across several spatial and temporal scales, with a clear signature of directed movement. This pattern was evident when analysing the aggregated tracks despite a wide diversity of individual trajectories. We also identified marine provinces that described the migratory and foraging habitats of these seals. Our analysis provides evidence for the presence of intrinsic drivers of movement, such as memory, that cannot be detected using common models of movement behaviour. These results highlight the potential for "big data" techniques to provide new insights into movement behaviour when applied to large datasets of animal tracking.}, } @article {pmid28273342, year = {2017}, author = {Price, DC and Bhattacharya, D}, title = {Robust Dinoflagellata phylogeny inferred from public transcriptome databases.}, journal = {Journal of phycology}, volume = {53}, number = {3}, pages = {725-729}, doi = {10.1111/jpy.12529}, pmid = {28273342}, issn = {1529-8817}, mesh = {Databases, Nucleic Acid ; Dinoflagellida/*classification/*genetics ; *Phylogeny ; *Transcriptome ; }, abstract = {Dinoflagellates are dominant members of the plankton and play key roles in ocean ecosystems as primary producers, predators, parasites, coral photobionts, and causative agents of algal blooms that produce toxins harmful to humans and commercial fisheries. These unicellular protists exhibit remarkable trophic and morphological diversity and include species with some of the largest reported nuclear genomes. Despite their high ecological and economic importance, comprehensive genome (or transcriptome) based dinoflagellate trees of life are few in number. To address this issue, we used recently generated public sequencing data, including from the Moore Microbial Eukaryote Transcriptome Sequencing Project, to identify dinoflagellate-specific ortholog groups. These orthologs were combined to create a broadly sampled and highly resolved phylogeny of dinoflagellates. Our results emphasize the scope and utility of public sequencing databases in creating broad and robust phylogenies for large and complex taxonomic lineages, while also providing unique insights into the evolution of thecate dinoflagellates.}, } @article {pmid28271383, year = {2017}, author = {Li, W and Yao, Z and Zhang, X and Huang, F and Lin, W and Lin, X}, title = {Global protein expression profile response of planktonic Aeromonas hydrophila exposed to chlortetracycline.}, journal = {World journal of microbiology & biotechnology}, volume = {33}, number = {4}, pages = {68}, pmid = {28271383}, issn = {1573-0972}, mesh = {Aeromonas hydrophila/drug effects/genetics/*metabolism ; Anti-Bacterial Agents/*pharmacology ; Bacterial Proteins/genetics/*metabolism ; Chlortetracycline/*pharmacology ; Computational Biology/methods ; Drug Resistance, Bacterial ; Gene Expression Regulation, Bacterial/drug effects ; Metabolic Networks and Pathways/drug effects ; Plankton/drug effects/genetics/metabolism ; Proteomics/*methods ; }, abstract = {The antibiotics resistance phenomena of Aeromonas hydrophila has become serious economic and public health problems for the world aquaculture industry and human health care. In this study, to investigate the instinct antibiotics adaptive mechanism of this pathogen, iTRAQ (Isobaric Tags for Relative and Absolute Quantitation) based quantitative proteomics technologies were performed to compare the differential expression of A. hydrophila in planktonic status in response to chlortetracycline (CTC) stress and then identified total 1552 proteins including 285 altered proteins with 90 increasing and 195 decreasing abundance proteins. The following bioinformatics analysis showed that many metabolic metabolism pathways such as carbon metabolism, pyruvate metabolism, and glycolysis/gluconeogenesis were trend to down-regulated whereas β-Lactam resistance, RNA degradation, and amino acids biosynthesis processes were more likely to increase in CTC stress. The related pyruvate metabolism and β-Lactam resistance processes in mRNA level were further measured using the q-PCR method. Thus, an understanding of the behaviors of A. hydrophila in response to CTC would be helpful to reveal the antibiotics adaptive mechanism and for the development of novel antibiotics therapy.}, } @article {pmid28267368, year = {2017}, author = {Banky, M and Ryan, HK and Clark, R and Olver, J and Williams, G}, title = {Do clinical tests of spasticity accurately reflect muscle function during walking: A systematic review.}, journal = {Brain injury}, volume = {31}, number = {4}, pages = {440-455}, doi = {10.1080/02699052.2016.1271455}, pmid = {28267368}, issn = {1362-301X}, mesh = {Databases, Factual ; Diagnostic Tests, Routine/methods ; Humans ; Muscle Spasticity/*diagnosis/*physiopathology ; Muscle, Skeletal/*physiology ; Prospective Studies ; Range of Motion, Articular/*physiology ; Walking/*physiology ; }, abstract = {OBJECTIVE: The aim of this systematic review was to establish the ecological validity of clinical tests of lower limb spasticity by determining whether the range of motion (ROM) and speed of limb movement during the assessment accurately replicate muscle function and joint biomechanics during walking.

METHODS: An electronic search of ten databases was performed to identify all relevant articles. The reference lists of all included articles were also searched. Identification of relevant articles, data extraction and quality assessment were performed independently by two reviewers.

RESULTS: Seventeen studies were included in the review. The Modified Ashworth Scale was the most commonly used clinical measure of lower limb spasticity. The ROM and speed of assessment were poorly reported for clinical scales of lower limb spasticity, making it difficult to draw conclusions regarding the relevance of these scales to walking performance.

CONCLUSIONS: The ecological validity of the clinical scales of spasticity could not be determined as studies did not adequately report their testing procedure. Further research into the ecological validity of clinical scales of spasticity is required in order to better understand the impact that spasticity has on functional activities such as walking.}, } @article {pmid28264718, year = {2017}, author = {Sosef, MS and Dauby, G and Blach-Overgaard, A and van der Burgt, X and Catarino, L and Damen, T and Deblauwe, V and Dessein, S and Dransfield, J and Droissart, V and Duarte, MC and Engledow, H and Fadeur, G and Figueira, R and Gereau, RE and Hardy, OJ and Harris, DJ and de Heij, J and Janssens, S and Klomberg, Y and Ley, AC and Mackinder, BA and Meerts, P and van de Poel, JL and Sonké, B and Stévart, T and Stoffelen, P and Svenning, JC and Sepulchre, P and Zaiss, R and Wieringa, JJ and Couvreur, TL}, title = {Exploring the floristic diversity of tropical Africa.}, journal = {BMC biology}, volume = {15}, number = {1}, pages = {15}, pmid = {28264718}, issn = {1741-7007}, mesh = {Africa ; *Biodiversity ; Databases as Topic ; Flowers/*physiology ; Forests ; Geography ; Species Specificity ; Time Factors ; Trees/growth & development ; *Tropical Climate ; }, abstract = {BACKGROUND: Understanding the patterns of biodiversity distribution and what influences them is a fundamental pre-requisite for effective conservation and sustainable utilisation of biodiversity. Such knowledge is increasingly urgent as biodiversity responds to the ongoing effects of global climate change. Nowhere is this more acute than in species-rich tropical Africa, where so little is known about plant diversity and its distribution. In this paper, we use RAINBIO - one of the largest mega-databases of tropical African vascular plant species distributions ever compiled - to address questions about plant and growth form diversity across tropical Africa.

RESULTS: The filtered RAINBIO dataset contains 609,776 georeferenced records representing 22,577 species. Growth form data are recorded for 97% of all species. Records are well distributed, but heterogeneous across the continent. Overall, tropical Africa remains poorly sampled. When using sampling units (SU) of 0.5°, just 21 reach appropriate collection density and sampling completeness, and the average number of records per species per SU is only 1.84. Species richness (observed and estimated) and endemism figures per country are provided. Benin, Cameroon, Gabon, Ivory Coast and Liberia appear as the botanically best-explored countries, but none are optimally explored. Forests in the region contain 15,387 vascular plant species, of which 3013 are trees, representing 5-7% of the estimated world's tropical tree flora. The central African forests have the highest endemism rate across Africa, with approximately 30% of species being endemic.

CONCLUSIONS: The botanical exploration of tropical Africa is far from complete, underlining the need for intensified inventories and digitization. We propose priority target areas for future sampling efforts, mainly focused on Tanzania, Atlantic Central Africa and West Africa. The observed number of tree species for African forests is smaller than those estimated from global tree data, suggesting that a significant number of species are yet to be discovered. Our data provide a solid basis for a more sustainable management and improved conservation of tropical Africa's unique flora, and is important for achieving Objective 1 of the Global Strategy for Plant Conservation 2011-2020. In turn, RAINBIO provides a solid basis for a more sustainable management and improved conservation of tropical Africa's unique flora.}, } @article {pmid28264006, year = {2017}, author = {Farmer, NA and Heyman, WD and Karnauskas, M and Kobara, S and Smart, TI and Ballenger, JC and Reichert, MJ and Wyanski, DM and Tishler, MS and Lindeman, KC and Lowerre-Barbieri, SK and Switzer, TS and Solomon, JJ and McCain, K and Marhefka, M and Sedberry, GR}, title = {Timing and locations of reef fish spawning off the southeastern United States.}, journal = {PloS one}, volume = {12}, number = {3}, pages = {e0172968}, pmid = {28264006}, issn = {1932-6203}, mesh = {Animals ; Biodiversity ; *Coral Reefs ; Databases, Factual ; *Ecosystem ; *Fishes ; Geography ; Models, Theoretical ; Reproducibility of Results ; Seasons ; Southeastern United States ; }, abstract = {Managed reef fish in the Atlantic Ocean of the southeastern United States (SEUS) support a multi-billion dollar industry. There is a broad interest in locating and protecting spawning fish from harvest, to enhance productivity and reduce the potential for overfishing. We assessed spatiotemporal cues for spawning for six species from four reef fish families, using data on individual spawning condition collected by over three decades of regional fishery-independent reef fish surveys, combined with a series of predictors derived from bathymetric features. We quantified the size of spawning areas used by reef fish across many years and identified several multispecies spawning locations. We quantitatively identified cues for peak spawning and generated predictive maps for Gray Triggerfish (Balistes capriscus), White Grunt (Haemulon plumierii), Red Snapper (Lutjanus campechanus), Vermilion Snapper (Rhomboplites aurorubens), Black Sea Bass (Centropristis striata), and Scamp (Mycteroperca phenax). For example, Red Snapper peak spawning was predicted in 24.7-29.0°C water prior to the new moon at locations with high curvature in the 24-30 m depth range off northeast Florida during June and July. External validation using scientific and fishery-dependent data collections strongly supported the predictive utility of our models. We identified locations where reconfiguration or expansion of existing marine protected areas would protect spawning reef fish. We recommend increased sampling off southern Florida (south of 27° N), during winter months, and in high-relief, high current habitats to improve our understanding of timing and location of reef fish spawning off the southeastern United States.}, } @article {pmid28262894, year = {2017}, author = {Tratnyek, PG and Bylaska, EJ and Weber, EJ}, title = {In silico environmental chemical science: properties and processes from statistical and computational modelling.}, journal = {Environmental science. Processes & impacts}, volume = {19}, number = {3}, pages = {188-202}, doi = {10.1039/c7em00053g}, pmid = {28262894}, issn = {2050-7895}, mesh = {*Computational Biology ; *Computer Simulation ; Ecology/*methods/statistics & numerical data ; *Environmental Pollutants/chemistry/toxicity ; Humans ; *Models, Statistical ; Quantitative Structure-Activity Relationship ; }, abstract = {Quantitative structure-activity relationships (QSARs) have long been used in the environmental sciences. More recently, molecular modeling and chemoinformatic methods have become widespread. These methods have the potential to expand and accelerate advances in environmental chemistry because they complement observational and experimental data with "in silico" results and analysis. The opportunities and challenges that arise at the intersection between statistical and theoretical in silico methods are most apparent in the context of properties that determine the environmental fate and effects of chemical contaminants (degradation rate constants, partition coefficients, toxicities, etc.). The main example of this is the calibration of QSARs using descriptor variable data calculated from molecular modeling, which can make QSARs more useful for predicting property data that are unavailable, but also can make them more powerful tools for diagnosis of fate determining pathways and mechanisms. Emerging opportunities for "in silico environmental chemical science" are to move beyond the calculation of specific chemical properties using statistical models and toward more fully in silico models, prediction of transformation pathways and products, incorporation of environmental factors into model predictions, integration of databases and predictive models into more comprehensive and efficient tools for exposure assessment, and extending the applicability of all the above from chemicals to biologicals and materials.}, } @article {pmid28262809, year = {2017}, author = {Muto-Fujita, A and Takemoto, K and Kanaya, S and Nakazato, T and Tokimatsu, T and Matsumoto, N and Kono, M and Chubachi, Y and Ozaki, K and Kotera, M}, title = {Data integration aids understanding of butterfly-host plant networks.}, journal = {Scientific reports}, volume = {7}, number = {}, pages = {43368}, pmid = {28262809}, issn = {2045-2322}, mesh = {Animals ; Butterflies/*physiology ; Chemotactic Factors/analysis ; Computational Biology/*methods ; *Feeding Behavior ; Insect Repellents/analysis ; Phytochemicals/analysis ; Plants/chemistry/*parasitology ; }, abstract = {Although host-plant selection is a central topic in ecology, its general underpinnings are poorly understood. Here, we performed a case study focusing on the publicly available data on Japanese butterflies. A combined statistical analysis of plant-herbivore relationships and taxonomy revealed that some butterfly subfamilies in different families feed on the same plant families, and the occurrence of this phenomenon more than just by chance, thus indicating the independent acquisition of adaptive phenotypes to the same hosts. We consequently integrated plant-herbivore and plant-compound relationship data and conducted a statistical analysis to identify compounds unique to host plants of specific butterfly families. Some of the identified plant compounds are known to attract certain butterfly groups while repelling others. The additional incorporation of insect-compound relationship data revealed potential metabolic processes that are related to host plant selection. Our results demonstrate that data integration enables the computational detection of compounds putatively involved in particular interspecies interactions and that further data enrichment and integration of genomic and transcriptomic data facilitates the unveiling of the molecular mechanisms involved in host plant selection.}, } @article {pmid28261716, year = {2017}, author = {Waseem, H and Williams, MR and Stedtfeld, T and Chai, B and Stedtfeld, RD and Cole, JR and Tiedje, JM and Hashsham, SA}, title = {Virulence factor activity relationships (VFARs): a bioinformatics perspective.}, journal = {Environmental science. Processes & impacts}, volume = {19}, number = {3}, pages = {247-260}, pmid = {28261716}, issn = {2050-7895}, support = {P42 ES004911/ES/NIEHS NIH HHS/United States ; }, mesh = {Bacteria/classification/genetics/pathogenicity ; *Computational Biology/methods/trends ; *Databases, Factual ; Disease Outbreaks/prevention & control ; Drug Resistance, Microbial/genetics ; *Models, Theoretical ; Quantitative Structure-Activity Relationship ; Risk Assessment ; Virulence ; *Virulence Factors/genetics/metabolism ; Viruses/classification/genetics/pathogenicity ; Water Microbiology/*standards ; }, abstract = {Virulence factor activity relationships (VFARs) - a concept loosely based on quantitative structure-activity relationships (QSARs) for chemicals was proposed as a predictive tool for ranking risks due to microorganisms relevant to water safety. A rapid increase in sequencing capabilities and bioinformatics tools has significantly increased the potential for VFAR-based analyses. This review summarizes more than 20 bioinformatics databases and tools, developed over the last decade, along with their virulence and antimicrobial resistance prediction capabilities. With the number of bacterial whole genome sequences exceeding 241 000 and metagenomic analysis projects exceeding 13 000 and the ability to add additional genome sequences for few hundred dollars, it is evident that further development of VFARs is not limited by the availability of information at least at the genomic level. However, additional information related to co-occurrence, treatment response, modulation of virulence due to environmental and other factors, and economic impact must be gathered and incorporated in a manner that also addresses the associated uncertainties. Of the bioinformatics tools, a majority are either designed exclusively for virulence/resistance determination or equipped with a dedicated module. The remaining have the potential to be employed for evaluating virulence. This review focusing broadly on omics technologies and tools supports the notion that these tools are now sufficiently developed to allow the application of VFAR approaches combined with additional engineering and economic analyses to rank and prioritize organisms important to a given niche. Knowledge gaps do exist but can be filled with focused experimental and theoretical analyses that were unimaginable a decade ago. Further developments should consider the integration of the measurement of activity, risk, and uncertainty to improve the current capabilities.}, } @article {pmid28256589, year = {2017}, author = {Cicconardi, F and Di Marino, D and Olimpieri, PP and Arthofer, W and Schlick-Steiner, BC and Steiner, FM}, title = {Chemosensory adaptations of the mountain fly Drosophila nigrosparsa (Insecta: Diptera) through genomics' and structural biology's lenses.}, journal = {Scientific reports}, volume = {7}, number = {}, pages = {43770}, pmid = {28256589}, issn = {2045-2322}, support = {P 23949/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Adaptation, Physiological/genetics ; Animals ; Drosophila/*genetics ; Drosophila Proteins/classification/*genetics ; Genomic Library ; Genomics/*methods ; Models, Molecular ; Multigene Family/genetics ; Phylogeny ; Protein Conformation ; Receptors, Cell Surface/classification/*genetics ; Receptors, Ionotropic Glutamate/chemistry/classification/*genetics ; Receptors, Odorant/chemistry/classification/*genetics ; Sequence Analysis, DNA/methods ; }, abstract = {Chemoreception is essential for survival. Some chemicals signal the presence of nutrients or toxins, others the proximity of mating partners, competitors, or predators. Chemical signal transduction has therefore been studied in multiple organisms. In Drosophila species, a number of odorant receptor genes and various other types of chemoreceptors were found. Three main gene families encode for membrane receptors and one for globular proteins that shuttle compounds with different degrees of affinity and specificity towards receptors. By sequencing the genome of Drosophila nigrosparsa, a habitat specialist restricted to montane/alpine environment, and combining genomics and structural biology techniques, we characterised odorant, gustatory, ionotropic receptors and odorant binding proteins, annotating 189 loci and modelling the protein structure of two ionotropic receptors and one odorant binding protein. We hypothesise that the D. nigrosparsa genome experienced gene loss and various evolutionary pressures (diversifying positive selection, relaxation, and pseudogenisation), as well as structural modification in the geometry and electrostatic potential of the two ionotropic receptor binding sites. We discuss possible trajectories in chemosensory adaptation processes, possibly enhancing compound affinity and mediating the evolution of more specialized food, and a fine-tuned mechanism of adaptation.}, } @article {pmid28254474, year = {2017}, author = {Dornburg, A and Townsend, JP and Brooks, W and Spriggs, E and Eytan, RI and Moore, JA and Wainwright, PC and Lemmon, A and Lemmon, EM and Near, TJ}, title = {New insights on the sister lineage of percomorph fishes with an anchored hybrid enrichment dataset.}, journal = {Molecular phylogenetics and evolution}, volume = {110}, number = {}, pages = {27-38}, doi = {10.1016/j.ympev.2017.02.017}, pmid = {28254474}, issn = {1095-9513}, mesh = {Amino Acids/genetics ; Animals ; Base Composition/genetics ; *Databases, Genetic ; Fishes/*classification/*genetics ; Genomics ; *Hybridization, Genetic ; Likelihood Functions ; Nucleotides/genetics ; *Phylogeny ; Species Specificity ; }, abstract = {Percomorph fishes represent over 17,100 species, including several model organisms and species of economic importance. Despite continuous advances in the resolution of the percomorph Tree of Life, resolution of the sister lineage to Percomorpha remains inconsistent but restricted to a small number of candidate lineages. Here we use an anchored hybrid enrichment (AHE) dataset of 132 loci with over 99,000 base pairs to identify the sister lineage of percomorph fishes. Initial analyses of this dataset failed to recover a strongly supported sister clade to Percomorpha, however, scrutiny of the AHE dataset revealed a bias towards high GC content at fast-evolving codon partitions (GC bias). By combining several existing approaches aimed at mitigating the impacts of convergence in GC bias, including RY coding and analyses of amino acids, we consistently recovered a strongly supported clade comprised of Holocentridae (squirrelfishes), Berycidae (Alfonsinos), Melamphaidae (bigscale fishes), Cetomimidae (flabby whalefishes), and Rondeletiidae (redmouth whalefishes) as the sister lineage to Percomorpha. Additionally, implementing phylogenetic informativeness (PI) based metrics as a filtration method yielded this same topology, suggesting PI based approaches will preferentially filter these fast-evolving regions and act in a manner consistent with other phylogenetic approaches aimed at mitigating GC bias. Our results provide a new perspective on a key issue for studies investigating the evolutionary history of more than one quarter of all living species of vertebrates.}, } @article {pmid28253837, year = {2017}, author = {Rieder, V and Blank-Landeshammer, B and Stuhr, M and Schell, T and Biß, K and Kollipara, L and Meyer, A and Pfenninger, M and Westphal, H and Sickmann, A and Rahnenführer, J}, title = {DISMS2: A flexible algorithm for direct proteome- wide distance calculation of LC-MS/MS runs.}, journal = {BMC bioinformatics}, volume = {18}, number = {1}, pages = {148}, pmid = {28253837}, issn = {1471-2105}, mesh = {*Algorithms ; Amino Acid Sequence ; Chromatography, Liquid/*methods ; Databases, Protein ; Humans ; Peptides/*analysis ; Proteome/*chemistry ; Proteomics/*methods ; Tandem Mass Spectrometry/*methods ; }, abstract = {BACKGROUND: The classification of samples on a molecular level has manifold applications, from patient classification regarding cancer treatment to phylogenetics for identifying evolutionary relationships between species. Modern methods employ the alignment of DNA or amino acid sequences, mostly not genome-wide but only on selected parts of the genome. Recently proteomics-based approaches have become popular. An established method for the identification of peptides and proteins is liquid chromatography-tandem mass spectrometry (LC-MS/MS). First, protein sequences from MS/MS spectra are identified by means of database searches, given samples with known genome-wide sequence information, then sequence based methods are applied. Alternatively, de novo peptide sequencing algorithms annotate MS/MS spectra and deduce peptide/protein information without a database. A newer approach independent of additional information is to directly compare unidentified tandem mass spectra. The challenge then is to compute the distance between pairwise MS/MS runs consisting of thousands of spectra.

METHODS: We present DISMS2, a new algorithm to calculate proteome-wide distances directly from MS/MS data, extending the algorithm compareMS2, an approach that also uses a spectral comparison pipeline.

RESULTS: Our new more flexible algorithm, DISMS2, allows for the choice of the spectrum distance measure and includes different spectra preprocessing and filtering steps that can be tailored to specific situations by parameter optimization.

CONCLUSIONS: DISMS2 performs well for samples from species with and without database annotation and thus has clear advantages over methods that are purely based on database search.}, } @article {pmid28249694, year = {2017}, author = {Rosselló-Móra, R and Trujillo, ME and Sutcliffe, IC}, title = {Introducing a Digital Protologue: A timely move towards a database-driven systematics of Archaea and Bacteria.}, journal = {Systematic and applied microbiology}, volume = {40}, number = {3}, pages = {121-122}, doi = {10.1016/j.syapm.2017.02.001}, pmid = {28249694}, issn = {1618-0984}, mesh = {Archaea/*classification ; Bacteria/*classification ; *Databases, Factual ; Phylogeny ; }, } @article {pmid28249569, year = {2017}, author = {Doublet, V and Poeschl, Y and Gogol-Döring, A and Alaux, C and Annoscia, D and Aurori, C and Barribeau, SM and Bedoya-Reina, OC and Brown, MJ and Bull, JC and Flenniken, ML and Galbraith, DA and Genersch, E and Gisder, S and Grosse, I and Holt, HL and Hultmark, D and Lattorff, HM and Le Conte, Y and Manfredini, F and McMahon, DP and Moritz, RF and Nazzi, F and Niño, EL and Nowick, K and van Rij, RP and Paxton, RJ and Grozinger, CM}, title = {Unity in defence: honeybee workers exhibit conserved molecular responses to diverse pathogens.}, journal = {BMC genomics}, volume = {18}, number = {1}, pages = {207}, pmid = {28249569}, issn = {1471-2164}, support = {//Wellcome Trust/United Kingdom ; BB/I000100/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/I000151/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/I025220/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; Bees/*genetics/microbiology/parasitology/virology ; Databases, Genetic ; Evolution, Molecular ; Gene Expression Regulation ; Gene Regulatory Networks ; Host-Pathogen Interactions/*genetics ; Immunity, Innate/genetics ; Molecular Sequence Annotation ; Nosema/physiology ; RNA Viruses/physiology ; Varroidae/physiology ; }, abstract = {BACKGROUND: Organisms typically face infection by diverse pathogens, and hosts are thought to have developed specific responses to each type of pathogen they encounter. The advent of transcriptomics now makes it possible to test this hypothesis and compare host gene expression responses to multiple pathogens at a genome-wide scale. Here, we performed a meta-analysis of multiple published and new transcriptomes using a newly developed bioinformatics approach that filters genes based on their expression profile across datasets. Thereby, we identified common and unique molecular responses of a model host species, the honey bee (Apis mellifera), to its major pathogens and parasites: the Microsporidia Nosema apis and Nosema ceranae, RNA viruses, and the ectoparasitic mite Varroa destructor, which transmits viruses.

RESULTS: We identified a common suite of genes and conserved molecular pathways that respond to all investigated pathogens, a result that suggests a commonality in response mechanisms to diverse pathogens. We found that genes differentially expressed after infection exhibit a higher evolutionary rate than non-differentially expressed genes. Using our new bioinformatics approach, we unveiled additional pathogen-specific responses of honey bees; we found that apoptosis appeared to be an important response following microsporidian infection, while genes from the immune signalling pathways, Toll and Imd, were differentially expressed after Varroa/virus infection. Finally, we applied our bioinformatics approach and generated a gene co-expression network to identify highly connected (hub) genes that may represent important mediators and regulators of anti-pathogen responses.

CONCLUSIONS: Our meta-analysis generated a comprehensive overview of the host metabolic and other biological processes that mediate interactions between insects and their pathogens. We identified key host genes and pathways that respond to phylogenetically diverse pathogens, representing an important source for future functional studies as well as offering new routes to identify or generate pathogen resilient honey bee stocks. The statistical and bioinformatics approaches that were developed for this study are broadly applicable to synthesize information across transcriptomic datasets. These approaches will likely have utility in addressing a variety of biological questions.}, } @article {pmid28248969, year = {2017}, author = {Asare-Kyei, D and Renaud, FG and Kloos, J and Walz, Y and Rhyner, J}, title = {Development and validation of risk profiles of West African rural communities facing multiple natural hazards.}, journal = {PloS one}, volume = {12}, number = {3}, pages = {e0171921}, pmid = {28248969}, issn = {1932-6203}, mesh = {Africa, Western ; *Climate Change ; *Disasters ; Female ; *Geographic Information Systems ; Humans ; Male ; Risk Factors ; *Rural Population ; Socioeconomic Factors ; }, abstract = {West Africa has been described as a hotspot of climate change. The reliance on rain-fed agriculture by over 65% of the population means that vulnerability to climatic hazards such as droughts, rainstorms and floods will continue. Yet, the vulnerability and risk levels faced by different rural social-ecological systems (SES) affected by multiple hazards are poorly understood. To fill this gap, this study quantifies risk and vulnerability of rural communities to drought and floods. Risk is assessed using an indicator-based approach. A stepwise methodology is followed that combines participatory approaches with statistical, remote sensing and Geographic Information System techniques to develop community level vulnerability indices in three watersheds (Dano, Burkina Faso; Dassari, Benin; Vea, Ghana). The results show varying levels of risk profiles across the three watersheds. Statistically significant high levels of mean risk in the Dano area of Burkina Faso are found whilst communities in the Dassari area of Benin show low mean risk. The high risk in the Dano area results from, among other factors, underlying high exposure to droughts and rainstorms, longer dry season duration, low caloric intake per capita, and poor local institutions. The study introduces the concept of community impact score (CIS) to validate the indicator-based risk and vulnerability modelling. The CIS measures the cumulative impact of the occurrence of multiple hazards over five years. 65.3% of the variance in observed impact of hazards/CIS was explained by the risk models and communities with high simulated disaster risk generally follow areas with high observed disaster impacts. Results from this study will help disaster managers to better understand disaster risk and develop appropriate, inclusive and well integrated mitigation and adaptation plans at the local level. It fulfills the increasing need to balance global/regional assessments with community level assessments where major decisions against risk are actually taken and implemented.}, } @article {pmid28245064, year = {2017}, author = {Iversen, CM and McCormack, ML and Powell, AS and Blackwood, CB and Freschet, GT and Kattge, J and Roumet, C and Stover, DB and Soudzilovskaia, NA and Valverde-Barrantes, OJ and van Bodegom, PM and Violle, C}, title = {A global Fine-Root Ecology Database to address below-ground challenges in plant ecology.}, journal = {The New phytologist}, volume = {215}, number = {1}, pages = {15-26}, doi = {10.1111/nph.14486}, pmid = {28245064}, issn = {1469-8137}, mesh = {*Databases, Factual ; Ecology/methods ; Ecosystem ; Plant Roots/anatomy & histology/*physiology ; }, abstract = {Variation and tradeoffs within and among plant traits are increasingly being harnessed by empiricists and modelers to understand and predict ecosystem processes under changing environmental conditions. While fine roots play an important role in ecosystem functioning, fine-root traits are underrepresented in global trait databases. This has hindered efforts to analyze fine-root trait variation and link it with plant function and environmental conditions at a global scale. This Viewpoint addresses the need for a centralized fine-root trait database, and introduces the Fine-Root Ecology Database (FRED, http://roots.ornl.gov) which so far includes > 70 000 observations encompassing a broad range of root traits and also includes associated environmental data. FRED represents a critical step toward improving our understanding of below-ground plant ecology. For example, FRED facilitates the quantification of variation in fine-root traits across root orders, species, biomes, and environmental gradients while also providing a platform for assessments of covariation among root, leaf, and wood traits, the role of fine roots in ecosystem functioning, and the representation of fine roots in terrestrial biosphere models. Continued input of observations into FRED to fill gaps in trait coverage will improve our understanding of changes in fine-root traits across space and time.}, } @article {pmid28242596, year = {2017}, author = {Lan, Y and Hu, JT and Zhang, YJ}, title = {Research progress of stoichiogenomics.}, journal = {Yi chuan = Hereditas}, volume = {39}, number = {2}, pages = {89-97}, doi = {10.16288/j.yczz.16-343}, pmid = {28242596}, issn = {0253-9772}, mesh = {Computational Biology ; *Genomics ; Nucleic Acids/*analysis ; Proteins/*analysis ; Selection, Genetic ; }, abstract = {Stoichiogenomics is a newly arisen research field, which concerns the element usage biases of biological macromolecules at genome, transcriptome, proteome, metabonome levels. Different biological macromolecules have different element compositions and contents. When the supply of some elements was constrained, natural selection might bias the usage of the monomers (amino acid or nucleotide) to reduce constrained element costs in the synthesis of biological macromolecules. This field is flourishing with the intensive applications of high throughput sequencing and assembly technologies, more and more available metagenomic and metatranscriptomic data, and the applications of new analysis strategies. As a newly emerged cross discipline field, stoichiogenomics integrates stoichiometry, ecology, evolutionary biology, genomics and bioinformatics to provide a whole new perspective for investigating the interactions of the macromolecular evolution and ecosystem, and data mining in the post genomic era. In this review, we summarize the latest research progress of stoichiogenomics from the aspect of the element usage biases in proteins and nucleic acids. Furthermore, new research directions are discussed to provide some valuable references for the research and application of stoichiogenomics.}, } @article {pmid28241869, year = {2017}, author = {Thunders, M and Cavanagh, J and Li, Y}, title = {De novo transcriptome assembly, functional annotation and differential gene expression analysis of juvenile and adult E. fetida, a model oligochaete used in ecotoxicological studies.}, journal = {Biological research}, volume = {50}, number = {1}, pages = {7}, pmid = {28241869}, issn = {0717-6287}, mesh = {Animals ; *Ecotoxicology ; Environmental Exposure ; Gene Expression Profiling/*methods ; Gene Ontology ; Oligochaeta/drug effects/*genetics ; Sequence Analysis, RNA/methods ; Software ; Soil Pollutants/toxicity ; Toxicogenetics/methods ; *Transcriptome ; }, abstract = {BACKGROUND: Earthworms are sensitive to toxic chemicals present in the soil and so are useful indicator organisms for soil health. Eisenia fetida are commonly used in ecotoxicological studies; therefore the assembly of a baseline transcriptome is important for subsequent analyses exploring the impact of toxin exposure on genome wide gene expression.

RESULTS: This paper reports on the de novo transcriptome assembly of E. fetida using Trinity, a freely available software tool. Trinotate was used to carry out functional annotation of the Trinity generated transcriptome file and the transdecoder generated peptide sequence file along with BLASTX, BLASTP and HMMER searches and were loaded into a Sqlite3 database. To identify differentially expressed transcripts; each of the original sequence files were aligned to the de novo assembled transcriptome using Bowtie and then RSEM was used to estimate expression values based on the alignment. EdgeR was used to calculate differential expression between the two conditions, with an FDR corrected P value cut off of 0.001, this returned six significantly differentially expressed genes. Initial BLASTX hits of these putative genes included hits with annelid ferritin and lysozyme proteins, as well as fungal NADH cytochrome b5 reductase and senescence associated proteins. At a cut off of P = 0.01 there were a further 26 differentially expressed genes.

CONCLUSION: These data have been made publicly available, and to our knowledge represent the most comprehensive available transcriptome for E. fetida assembled from RNA sequencing data. This provides important groundwork for subsequent ecotoxicogenomic studies exploring the impact of the environment on global gene expression in E. fetida and other earthworm species.}, } @article {pmid28241131, year = {2017}, author = {Lisney, TJ and Yopak, KE and Camilieri-Asch, V and Collin, SP}, title = {Ontogenetic Shifts in Brain Organization in the Bluespotted Stingray Neotrygon kuhlii (Chondrichthyes: Dasyatidae).}, journal = {Brain, behavior and evolution}, volume = {89}, number = {2}, pages = {68-83}, doi = {10.1159/000455223}, pmid = {28241131}, issn = {1421-9743}, mesh = {Animals ; *Biological Ontologies ; Brain/*anatomy & histology ; Computer Graphics ; Female ; Linear Models ; Male ; Skates, Fish/*anatomy & histology ; Species Specificity ; }, abstract = {Fishes exhibit lifelong neurogenesis and continual brain growth. One consequence of this continual growth is that the nervous system has the potential to respond with enhanced plasticity to changes in ecological conditions that occur during ontogeny. The life histories of many teleost fishes are composed of a series of distinct stages that are characterized by shifts in diet, habitat, and behavior. In many cases, these shifts correlate with changes in overall brain growth and brain organization, possibly reflecting the relative importance of different senses and locomotor performance imposed by the new ecological niches they encounter throughout life. Chondrichthyan (cartilaginous) fishes also undergo ontogenetic shifts in habitat, movement patterns, diet, and behavior, but very little is known about any corresponding shifts in the size and organization of their brains. Here, we investigated postparturition ontogenetic changes in brain-body size scaling, the allometric scaling of seven major brain areas (olfactory bulbs, telencephalon, diencephalon, optic tectum, tegmentum, cerebellum, and medulla oblongata) relative to the rest of the brain, and cerebellar foliation in a chondrichthyan, i.e., the bluespotted stingray Neotrygon kuhlii. We also investigated the unusual morphological asymmetry of the cerebellum in this and other batoids. As in teleosts, the brain continues to grow throughout life, with a period of rapid initial growth relative to body size, before slowing considerably at the onset of sexual maturity. The olfactory bulbs and the cerebellum scale with positive allometry relative to the rest of the brain, whereas the other five brain areas scale with varying degrees of negative allometry. None of the major brain areas showed the stage-specific differences in rates of growth often found in teleosts. Cerebellar foliation also increases at a faster rate than overall brain growth. We speculate that changes in the olfactory bulbs and cerebellum could reflect increased olfactory and locomotor capabilities, which may be associated with ontogenetic shifts in diet, habitat use, and activity patterns, as well as shifts in behavior that occur with the onset of sexual maturity. The frequency distributions of the three cerebellar morphologies exhibited in this species best fit a 2:1:1 (right-sided:left-sided:intermediate) distribution, mirroring previous findings for another stingray species.}, } @article {pmid28228535, year = {2017}, author = {Schläpfer, P and Zhang, P and Wang, C and Kim, T and Banf, M and Chae, L and Dreher, K and Chavali, AK and Nilo-Poyanco, R and Bernard, T and Kahn, D and Rhee, SY}, title = {Genome-Wide Prediction of Metabolic Enzymes, Pathways, and Gene Clusters in Plants.}, journal = {Plant physiology}, volume = {173}, number = {4}, pages = {2041-2059}, pmid = {28228535}, issn = {1532-2548}, support = {U01 GM110699/GM/NIGMS NIH HHS/United States ; }, mesh = {Biosynthetic Pathways/genetics ; Computational Biology/methods ; Evolution, Molecular ; Gene Duplication ; Gene Expression Regulation, Plant ; Genome, Plant/*genetics ; Metabolic Networks and Pathways/*genetics ; Models, Genetic ; Multigene Family/*genetics ; Plant Proteins/genetics/metabolism ; Plants/enzymology/*genetics/metabolism ; Species Specificity ; }, abstract = {Plant metabolism underpins many traits of ecological and agronomic importance. Plants produce numerous compounds to cope with their environments but the biosynthetic pathways for most of these compounds have not yet been elucidated. To engineer and improve metabolic traits, we need comprehensive and accurate knowledge of the organization and regulation of plant metabolism at the genome scale. Here, we present a computational pipeline to identify metabolic enzymes, pathways, and gene clusters from a sequenced genome. Using this pipeline, we generated metabolic pathway databases for 22 species and identified metabolic gene clusters from 18 species. This unified resource can be used to conduct a wide array of comparative studies of plant metabolism. Using the resource, we discovered a widespread occurrence of metabolic gene clusters in plants: 11,969 clusters from 18 species. The prevalence of metabolic gene clusters offers an intriguing possibility of an untapped source for uncovering new metabolite biosynthesis pathways. For example, more than 1,700 clusters contain enzymes that could generate a specialized metabolite scaffold (signature enzymes) and enzymes that modify the scaffold (tailoring enzymes). In four species with sufficient gene expression data, we identified 43 highly coexpressed clusters that contain signature and tailoring enzymes, of which eight were characterized previously to be functional pathways. Finally, we identified patterns of genome organization that implicate local gene duplication and, to a lesser extent, single gene transposition as having played roles in the evolution of plant metabolic gene clusters.}, } @article {pmid28228130, year = {2017}, author = {Guo, X and Yu, C and Luo, L and Wan, H and Zhen, N and Xu, T and Tan, J and Pan, H and Zhang, Q}, title = {Transcriptome of the floral transition in Rosa chinensis 'Old Blush'.}, journal = {BMC genomics}, volume = {18}, number = {1}, pages = {199}, pmid = {28228130}, issn = {1471-2164}, mesh = {Carbohydrate Metabolism ; Cluster Analysis ; Computational Biology/methods ; Flowers/*genetics ; Gene Expression Profiling ; *Gene Expression Regulation, Plant ; Gene Ontology ; Metabolic Networks and Pathways ; Models, Biological ; Molecular Sequence Annotation ; Plant Growth Regulators/metabolism ; Rosa/*genetics/metabolism ; *Transcriptome ; }, abstract = {BACKGROUND: The floral transition plays a vital role in the life of ornamental plants. Despite progress in model plants, the molecular mechanisms of flowering regulation remain unknown in perennial plants. Rosa chinensis 'Old Blush' is a unique plant that can flower continuously year-round. In this study, gene expression profiles associated with the flowering transition were comprehensively analyzed during floral transition in the rose.

RESULTS: According to the transcriptomic profiles, 85,663 unigenes and 1,637 differentially expressed genes (DEGs) were identified, among which 32 unigenes were involved in the circadian clock, sugar metabolism, hormone, and autonomous pathways. A hypothetical model for the regulation of floral transition was proposed in which the candidate genes function synergistically the floral transition process. Hormone contents and biosynthesis and metabolism genes fluctuated during the rose floral transition process. Gibberellins (GAs) inhibited rose floral transition, the content of GAs gradually decreased and GA2ox and SCL13 were upregulated from vegetative (VM) meristem to floral meristem (FM). Auxin plays an affirmative part in mediating floral transition, auxin content and auxin-related gene expression levels were gradually upregulated during the floral transition of the rose. However, ABA content and ABA signal genes were gradually downregulated, suggesting that ABA passively regulates the rose floral transition by participating in sugar signaling. Furthermore, sugar content and sugar metabolism genes increased during floral transition in the rose, which may be a further florigenic signal that activates floral transition. Additionally, FRI, FY, DRM1, ELIP, COP1, CO, and COL16 are involved in the circadian clock and autonomous pathway, respectively, and they play a positively activating role in regulating floral transition. Overall, physiological changes associated with genes involved in the circadian clock or autonomous pathway collectively regulated the rose floral transition.

CONCLUSIONS: Our results summarize a valuable collective of gene expression profiles characterizing the rose floral transition. The DEGs are candidates for functional analyses of genes affecting the floral transition in the rose, which is a precious resource that reveals the molecular mechanism of mediating floral transition in other perennial plants.}, } @article {pmid28225056, year = {2017}, author = {Han, Y and Wan, H and Cheng, T and Wang, J and Yang, W and Pan, H and Zhang, Q}, title = {Comparative RNA-seq analysis of transcriptome dynamics during petal development in Rosa chinensis.}, journal = {Scientific reports}, volume = {7}, number = {}, pages = {43382}, pmid = {28225056}, issn = {2045-2322}, mesh = {Anthocyanins/biosynthesis/genetics ; Flowers/*genetics/growth & development/metabolism ; Gene Expression Profiling ; Gene Expression Regulation, Developmental ; *Gene Expression Regulation, Plant ; Gene Ontology ; *Genome, Plant ; High-Throughput Nucleotide Sequencing ; Molecular Sequence Annotation ; Plant Breeding ; Plant Growth Regulators/biosynthesis/genetics ; Plant Proteins/*genetics/metabolism ; RNA, Plant/*genetics/metabolism ; Rosa/*genetics/growth & development/metabolism ; Transcription Factors/genetics/metabolism ; Transcriptome ; }, abstract = {The developmental process that produces the ornate petals of the China rose (Rosa chinensis) is complex and is thought to depend on the balanced expression of a functionally diverse array of genes; however, the molecular basis of rose petal development is largely unknown. Here, petal growth of the R. chinensis cultivar 'Old Blush' was divided into four developmental stages, and RNA-seq technology was used to analyse the dynamic changes in transcription that occur as development progresses. In total, 598 million clean reads and 61,456 successfully annotated unigenes were obtained. Differentially expressed gene (DEG) analysis comparing the transcriptomes of the developmental stages resulted in the identification of several potential candidate genes involved in petal development. DEGs involved in anthocyanin biosynthesis, petal expansion, and phytohormone pathways were considered in depth, in addition to several candidate transcription factors. These results lay a foundation for future studies on the regulatory mechanisms underlying rose petal development and may be used in molecular breeding programs aimed at generating ornamental rose lines with desirable traits.}, } @article {pmid28222171, year = {2017}, author = {Hotti, H and Gopalacharyulu, P and Seppänen-Laakso, T and Rischer, H}, title = {Metabolite profiling of the carnivorous pitcher plants Darlingtonia and Sarracenia.}, journal = {PloS one}, volume = {12}, number = {2}, pages = {e0171078}, pmid = {28222171}, issn = {1932-6203}, mesh = {Alkaloids/*analysis ; Data Mining ; Gas Chromatography-Mass Spectrometry ; Genes, Plant ; *Metabolomics ; Phylogeny ; Piperidines/*analysis ; Plant Proteins/genetics ; Polyketide Synthases/genetics ; Sarraceniaceae/chemistry/classification/genetics/*metabolism ; Species Specificity ; Transcriptome ; }, abstract = {Sarraceniaceae is a New World carnivorous plant family comprising three genera: Darlingtonia, Heliamphora, and Sarracenia. The plants occur in nutrient-poor environments and have developed insectivorous capability in order to supplement their nutrient uptake. Sarracenia flava contains the alkaloid coniine, otherwise only found in Conium maculatum, in which its biosynthesis has been studied, and several Aloe species. Its ecological role and biosynthetic origin in S. flava is speculative. The aim of the current research was to investigate the occurrence of coniine in Sarracenia and Darlingtonia and to identify common constituents of both genera, unique compounds for individual variants and floral scent chemicals. In this comprehensive metabolic profiling study, we looked for compound patterns that are associated with the taxonomy of Sarracenia species. In total, 57 different Sarracenia and D. californica accessions were used for metabolite content screening by gas chromatography-mass spectrometry. The resulting high-dimensional data were studied using a data mining approach. The two genera are characterized by a large number of metabolites and huge chemical diversity between different species. By applying feature selection for clustering and by integrating new biochemical data with existing phylogenetic data, we were able to demonstrate that the chemical composition of the species can be explained by their known classification. Although transcriptome analysis did not reveal a candidate gene for coniine biosynthesis, the use of a sensitive selected ion monitoring method enabled the detection of coniine in eight Sarracenia species, showing that it is more widespread in this genus than previously believed.}, } @article {pmid29749204, year = {2017}, author = {Liang, BB and Shi, PJ and Wang, W and Tang, X and Zhou, WX and Jing, Y}, title = {[Integrated assessment of ecosystem quality of arid inland river basin based on RS and GIS: A case study on Shiyang River Basin, Northwest China].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {28}, number = {1}, pages = {199-209}, doi = {10.13287/j.1001-9332.201701.019}, pmid = {29749204}, issn = {1001-9332}, mesh = {China ; *Conservation of Natural Resources ; *Ecosystem ; Environmental Monitoring ; *Geographic Information Systems ; Rivers ; }, abstract = {The Shiyang River Basin is an important ecological area of the Eastern Hexi Corridor, and is one of the most prominent areas of water conflict and ecological environment problems. An assessment of ecosystem quality in the Shiyang River Basin can provide a reference for ecological protection in arid inland basin. Based on the concept of ecosystem quality and the statistical yearbook, remotely sensed and land cover data, an evaluation index was established with consideration of three aspects of ecosystem (i.e., productivity, stability and bearing capacity). Kruskal-Wallis (Φ[2]) test and entropy method were applied to determine the weights of evaluation index. With the assistance of RS, GIS and SPSS software, a comprehensive evaluation and change analysis of ecosystem quality and corresponding index were conducted for various ecosystem types in the Shiyang River Basin in 2000, 2005, 2010 and 2015. Results showed that the average ecosystem quality of the Shiyang River Basin was 57.76, and presented an obvious decrease with a magnitude of 0.72 per year du-ring 2000-2015. The spatial pattern of ecosystem quality was that the upstream was better than the midstream, and the midstream was superior to the downstream. The mean values of production capacity, stability and carrying capacity of ecosystem were 67.52, 45.37, and 58.53, respectively. Production capacity and stability had increased slightly, while carrying capacity gradually decreased. Considering various ecosystem types, the highest quality was detected for forest ecosystem with average annual value of 78.12, and this ecosystem presented the lowest decreasing magnitude of 0.28 per year; for grassland, farmland and urban ecosystems, the average annual value was 62.45, 58.76 and 50.29, respectively; the quality of wetland ecosystem was the lowest, and suffered the largest decline with an average rate of 0.98 per year.}, } @article {pmid29932619, year = {2016}, author = {Zhang, Q and Zeng, FL and Zhang, DF and Xie, CX and Chen, SL}, title = {[Ecology suitability regions and ecological characteristics of Panax notoginseng (Burk.) F.H. Chen based on maximum entropy model].}, journal = {Yao xue xue bao = Acta pharmaceutica Sinica}, volume = {51}, number = {10}, pages = {1629-1637}, pmid = {29932619}, issn = {0513-4870}, mesh = {Altitude ; Biodiversity ; China ; *Climate ; *Ecology ; Entropy ; Geographic Information Systems ; Models, Theoretical ; Panax notoginseng/*growth & development ; Soil ; Temperature ; }, abstract = {The ecology suitability and ecological characteristics of Panax notoginseng (Burk.) F. H. Chen were studied to provide a reference for its artificial introduction and cultivation. The maximum entropy model (MaxEnt) and geographic information system (GIS) were used to investigate the global ecology suitability regions for Panax notoginseng (Burk.) F. H. Chen based on its 67 distribution points collected from global biodiversity information facility (GBIF), Chinese virtual herbarium(CVH) and the related references. The results showed that the possible ecological suitable regions of Panax notoginseng (Burk.) F. H. Chen were located in Yunnan, Guangxi, Guangdong, Guizhou, Hainan, Sichuan, Fujian and Chongqing provinces. The areas with ecological similarity higher than 60% were about 89 571.3 square kilometers in total, mainly distributing in Yunnan and Guangxi provinces and small portion was located in Guangdong and Guizhou provinces. The areas with ecological similarity between 40% and 60% were about 155 172 square kilometers, mainly in Yunnan,Guangxi, Guangdong, Guizhou, Hainan, Sichuan provinces. The distribution areas were about 329 952.8 square kilometers with ecological similarity between 20% and 40%, mainly in Yunnan, Guangxi, Guangdong, Guizhou, Hainan, Sichuan, Fujian and Chongqing. The climate factors mainly affecting the distribution of Panax notoginseng (Burk.) F. H. Chen were precipitation of warmest quarter, SD of temperature seasonality, altitude, isothermality, coefficient of variation of precipitation seasonality, mean temperature of monthly, precipitation of driest month, reference bulk density of soil and soil texture.}, } @article {pmid29737714, year = {2016}, author = {Li, J}, title = {[Dilemma of null hypothesis in ecological hypothesis's experiment test.].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {27}, number = {6}, pages = {2031-2038}, doi = {10.13287/j.1001-9332.201606.025}, pmid = {29737714}, issn = {1001-9332}, mesh = {Data Interpretation, Statistical ; Ecology/*methods ; *Models, Statistical ; Research Design ; }, abstract = {Experimental test is one of the major test methods of ecological hypothesis, though there are many arguments due to null hypothesis. Quinn and Dunham (1983) analyzed the hypothesis deduction model from Platt (1964) and thus stated that there is no null hypothesis in ecology that can be strictly tested by experiments. Fisher's falsificationism and Neyman-Pearson (N-P)'s non-decisivity inhibit statistical null hypothesis from being strictly tested. Moreover, since the null hypothesis H0(α=1, β=0) and alternative hypothesis H1'(α'=1, β'=0) in ecological progresses are diffe-rent from classic physics, the ecological null hypothesis can neither be strictly tested experimentally. These dilemmas of null hypothesis could be relieved via the reduction of P value, careful selection of null hypothesis, non-centralization of non-null hypothesis, and two-tailed test. However, the statistical null hypothesis significance testing (NHST) should not to be equivalent to the causality logistical test in ecological hypothesis. Hence, the findings and conclusions about methodological studies and experimental tests based on NHST are not always logically reliable.}, } @article {pmid29737680, year = {2016}, author = {Yang, HJ and Li, XY and Liu, LJ and Ma, JL and Wang, J}, title = {[Estimation of net primary productivity in arid region based on coupling model.].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {27}, number = {6}, pages = {1750-1758}, doi = {10.13287/j.1001-9332.201606.008}, pmid = {29737680}, issn = {1001-9332}, mesh = {Climate ; *Ecosystem ; Geographic Information Systems ; *Models, Theoretical ; Remote Sensing Technology ; *Rivers ; }, abstract = {Net primary productivity (NPP), as the base for the research of matter recycling and energy flow in terrestrial ecosystem, is sensitive to the changes of environment and climate in arid region, and also is an important indicator of eco-environmental characteristics. Based on remote sensing (RS) and geographic information system (GIS), using meteorological data, eddy cova-riance data, Landsat 8 and MODIS data, this study coupled SEBAL model and light utility efficiency model to estimate the NPP of vegetation in Manas River Watershed, and the spatial pattern of NPP and the relationships between NPP and terrain factors (elevation and slope) were analyzed. Results showed that the estimated result of NPP in Manas River Watershed by coupling model was reasonable and could actually reflect the NPP of vegetation. The total annual NPP of vegetation and the mean annual NPP in Manas River Watershed in 2013 were 7066.72 Tg C·a[-1] and 278.06 g C·m[-2]·a[-1] respectively. With the variation of geomorphic type and land cover, the NPP changed remarkably from south to north in a trend of increase-decrease-increase-decrease pattern. The temporal variations of NPP were also obvious, with the NPP in July and August accounting for 52.2% of total annual NPP. With the increase of the elevation and slope, the mean annual NPP decreased as a whole with fluctuations induced by different land covers and environmental factors.}, } @article {pmid29726205, year = {2016}, author = {Yang, D and Fan, DY and Xie, ZQ and Zhang, AY and Xiong, GM and Zhao, CM and Xu, WT}, title = {[Research progress on the mechanisms and influence factors of nitrogen retention and transformation in riparian ecosystems.].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {27}, number = {3}, pages = {973-980}, doi = {10.13287/j.1001-9332.201603.040}, pmid = {29726205}, issn = {1001-9332}, mesh = {Agriculture ; Atmosphere ; Denitrification ; *Ecosystem ; Environmental Monitoring ; Geographic Information Systems ; Models, Theoretical ; Nitrates ; Nitrogen/*analysis ; *Nitrogen Cycle ; Plants ; Rivers ; Soil ; Wetlands ; }, abstract = {Riparian zone, the ecological transition buffer between terrestrial and aquatic ecosystems (rivers, lakes, reservoirs, wetlands, and other specific water bodies) with unique eco-hydrological and biogeochemical processes, is the last ecological barrier to prevent ammonium, nitrate and other non-point nitrogen pollutants from adjacent water bodies. Based on a summary of current progress of related studies, we found there were two major mechanisms underpinning the nitrogen retention/removal by the riparian ecosystems: 1) the relative locations of nitrogen in the soil-plant-atmosphere continuum system could be altered by riparian vegetation; 2) nitrogen could also be denitrified and then removed permanently by microorganisms in riparian soil. However, which process is more critical for the nitrogen removal remains elusive. Due to large variances of hydro-dynamic, vegetation, microbial, and soil substrate properties in nitrogen retention and transformation with various watersheds, it's difficult to identify which factor is the most important one driving nitrogen cycle in the riparian ecosystems. It is also found that the limitation of study methods, paucity of data at large spatial and temporal scale, and no consensus on the riparian width, are the three major reasons leading to large variances of the results among studies. In conclusion, it is suggested that further efforts should be focused on: 1) the detailed analysis on the successive environmental factors with long-term; 2) the application of a comprehensive method combining mathematical models, geographic information system, remote sensing and quantified technique (such as the coupled technique of the isotopic tracer and gas exchange measurement); 3) the implementation of studies at large temporal and spatial scales. It is sure that, these efforts can help to optimize the nitrogen removal pathways in the riparian ecosystems and provide scientific basis for ecosystem management.}, } @article {pmid29726174, year = {2016}, author = {Hu, RB and Fang, X and Xiang, WH and Jiang, F and Lei, PF and Zhao, LJ and Zhu, WJ and Deng, XW}, title = {[Spatial heterogeneity and influencing factors of soil phosphorus concentration in a mid-subtropical Choerospondias axillaris deciduous broad-leaved forest, China.].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {27}, number = {3}, pages = {705-715}, doi = {10.13287/j.1001-9332.201603.013}, pmid = {29726174}, issn = {1001-9332}, mesh = {Carbon/analysis ; China ; *Forests ; Fractals ; Geographic Information Systems ; Nitrogen/analysis ; Phosphorus/*analysis ; Soil/*chemistry ; Spatial Analysis ; }, abstract = {In order to investigate spatial variations in soil phosphorus (P) concentration and the influencing factors, one permanent plot of 1 hm[2] was established and stand structure was surveyed in Choerospondias axillaries deciduous broadleaved forest in Dashanchong Forest Park in Changsha County, Hunan Province, China. Soil samples were collected with equidistant grid point sampling method and soil P concentration and its spatial variation were analyzed by using geo-statistics and geographical information system (GIS) techniques. The results showed that the variations of total P and available P concentrations in humus layer and in the soil profile at depth of 0-10, 10-20 and 20-30 cm were moderate and the available P showed higher variability in a specific soil layer compared with total P. Concentrations of total P and available P in soil decreased, while the variations increased with the increase in soil depth. The total P and available P showed high spatial autocorrelation, primarily resulted from the structural factors. The spatial heterogeneity of available P was stronger than that of total P, and the spatial autocorrelation ranges of total P and available P varied from 92.80 to 168.90 m and from 79.43 to 106.20 m in different soil layers, respectively. At the same soil depth, fractal dimensions of total P were higher than that of available P, with more complex spatial pattern, while available P showed stronger spatial correlation with stronger spatial structure. In humus layer and soil depths of 0-10, 10-20 and 20-30 cm, the spatial variation pattern of total P and available P concentrations showed an apparent belt-shaped and spot massive gradient change. The high value appeared at low elevation and valley position, and the low value appeared in the high elevation and ridge area. The total P and available P concentrations showed significantly negative correlation with elevation and litter, but the relationship with convexity, species, numbers and soil pH was not significant. The total P and available P exhibited significant positive correlations with soil organic carbon (SOC), total nitrogen concentration, indicating the leaching characteristics of soil P. Its spatial variability was affected by many interactive factors.}, } @article {pmid29046592, year = {2016}, author = {Bell, AM and Bukhari, SA and Sanogo, YO}, title = {Natural variation in brain gene expression profiles of aggressive and nonaggressive individual sticklebacks.}, journal = {Behaviour}, volume = {153}, number = {13-14}, pages = {1723-1743}, pmid = {29046592}, issn = {0005-7959}, support = {R01 GM082937/GM/NIGMS NIH HHS/United States ; }, abstract = {Within many species, some individuals are consistently more aggressive than others. We examine whether there are differences in brain gene expression between aggressive versus nonaggressive behavioural types of individuals within a natural population of male three-spined sticklebacks (Gasterosteus aculeatus). We compared gene expression profiles of aggressive male sticklebacks to nonaggressive males in four regions of the brain (brainstem, cerebellum, diencephalon and telencephalon). Relatively few genes were differentially expressed between behavioural types in telencephalon, cerebellum and diencephalon, but hundreds of genes were differentially expressed in brainstem, a brain area involved in detecting threats. Six genes that were differentially expressed in response to a territorial intrusion in a previous study were also differentially expressed between behavioural types in this study, implying primarily non-shared but some shared molecular mechanisms. Our findings offer new insights into the molecular causes and correlates of behavioural plasticity and individual variation in behaviour.}, } @article {pmid29201264, year = {2015}, author = {Rangachari, P and Mehta, R and Rethemeyer, RK and Ferrang, C and Dennis, C and Redd, V}, title = {Short or Long End of the Lever? Associations between Provider Communication of the "Asthma-Action Plan" and Outpatient Revisits for Pediatric Asthma.}, journal = {Journal of hospital administration}, volume = {4}, number = {5}, pages = {26-39}, pmid = {29201264}, issn = {1927-6990}, support = {R03 HS019785/HS/AHRQ HHS/United States ; }, abstract = {BACKGROUND: At the Children's Hospital of Georgia (CHOG), we found that outpatient revisits for pediatric asthma were significantly above national norms. According to the NIH, costly hospital revisits for asthma can be prevented through guidelines-based self-management of asthma, central to which, is the use of a written Asthma-Action Plan (AAP).

PURPOSE: The asthma services literature has emphasized the role of the healthcare provider in promoting asthma self-management using the AAP, to prevent hospital revisits. On the other hand, the asthma policy literature has emphasized the need for community-based interventions to promote asthma self-management. A gap remains in understanding the extent of leverage that healthcare providers may have in preventing hospital revisits for asthma, through effective communication of AAP in the outpatient setting. Our study sought to address this gap.

METHODS: We conducted a 6-month intervention to implement "patient-and-family-centered communication of the AAP" in CHOG outpatient clinics, based on the "change-management" theoretical framework. Provider communication of AAP was assessed through a survey of "Parent Understanding of the Child's AAP." A quasi-experimental approach was used to measure outpatient revisits for pediatric asthma, pre- and post-intervention.

RESULTS: Survey results showed that provider communication of the AAP was unanimously perceived highly positively by parents of pediatric asthma patients, across various metrics of patient-centered care. However, there were no statistically significant differences in outpatient "revisit behavior" for pediatric asthma between pre- and post-intervention periods after controlling for several demographic variables. Additionally, revisits remained significantly above national norms.

CONCLUSIONS: Results suggest limited potential of "effective provider communication of AAP," in reducing outpatient revisits for pediatric asthma; and indicate need for broader community-based interventions to address patient life variables impacting self-management and hospital revisits for pediatric asthma. Findings suggest need for a revised "socio-ecological" theoretical framework, and also provide insight into various policy, research, and practice implications for asthma management and control.}, } @article {pmid28616464, year = {2015}, author = {Binot, A and Duboz, R and Promburom, P and Phimpraphai, W and Cappelle, J and Lajaunie, C and Goutard, FL and Pinyopummintr, T and Figuié, M and Roger, FL}, title = {A framework to promote collective action within the One Health community of practice: Using participatory modelling to enable interdisciplinary, cross-sectoral and multi-level integration.}, journal = {One health (Amsterdam, Netherlands)}, volume = {1}, number = {}, pages = {44-48}, pmid = {28616464}, issn = {2352-7714}, abstract = {As Southeast Asia (SEA) is characterized by high human and domestic animal densities, growing intensification of trade, drastic land use changes and biodiversity erosion, this region appears to be a hotspot to study complex dynamics of zoonoses emergence and health issues at the Animal-Human-Environment interface. Zoonotic diseases and environmental health issues can have devastating socioeconomic and wellbeing impacts. Assessing and managing the related risks implies to take into account ecological and social dynamics at play, in link with epidemiological patterns. The implementation of a One Health (OH) approach in this context calls for improved integration among disciplines and improved cross-sectoral collaboration, involving stakeholders at different levels. For sure, such integration is not achieved spontaneously, implies methodological guidelines and has transaction costs. We explore pathways for implementing such collaboration in SEA context, highlighting the main challenges to be faced by researchers and other target groups involved in OH actions. On this basis, we propose a conceptual framework of OH integration. Throughout 3 components (field-based data management, professional training workshops and higher education), we suggest to develop a new culture of networking involving actors from various disciplines, sectors and levels (from the municipality to the Ministries) through a participatory modelling process, fostering synergies and cooperation. This framework could stimulate long-term dialogue process, based on the combination of case studies implementation and capacity building. It aims for implementing both institutional OH dynamics (multi-stakeholders and cross-sectoral) and research approaches promoting systems thinking and involving social sciences to follow-up and strengthen collective action.}, } @article {pmid28286935, year = {2008}, author = {Kobayashi, K and Ishizu, H and Arioka, S and Padilla Cabrera, J and Hoshi, M and Matsumoto, M}, title = {Erratum to Production of diploid and triploid offspring by inbreeding of the triploid planarian Dugesia ryukyuensis.}, journal = {Chromosoma}, volume = {117}, number = {3}, pages = {303}, doi = {10.1007/s00412-008-0156-6}, pmid = {28286935}, issn = {1432-0886}, } @article {pmid28219347, year = {2017}, author = {, and Abdelrahman, H and ElHady, M and Alcivar-Warren, A and Allen, S and Al-Tobasei, R and Bao, L and Beck, B and Blackburn, H and Bosworth, B and Buchanan, J and Chappell, J and Daniels, W and Dong, S and Dunham, R and Durland, E and Elaswad, A and Gomez-Chiarri, M and Gosh, K and Guo, X and Hackett, P and Hanson, T and Hedgecock, D and Howard, T and Holland, L and Jackson, M and Jin, Y and Khalil, K and Kocher, T and Leeds, T and Li, N and Lindsey, L and Liu, S and Liu, Z and Martin, K and Novriadi, R and Odin, R and Palti, Y and Peatman, E and Proestou, D and Qin, G and Reading, B and Rexroad, C and Roberts, S and Salem, M and Severin, A and Shi, H and Shoemaker, C and Stiles, S and Tan, S and Tang, KF and Thongda, W and Tiersch, T and Tomasso, J and Prabowo, WT and Vallejo, R and van der Steen, H and Vo, K and Waldbieser, G and Wang, H and Wang, X and Xiang, J and Yang, Y and Yant, R and Yuan, Z and Zeng, Q and Zhou, T}, title = {Aquaculture genomics, genetics and breeding in the United States: current status, challenges, and priorities for future research.}, journal = {BMC genomics}, volume = {18}, number = {1}, pages = {191}, pmid = {28219347}, issn = {1471-2164}, mesh = {Animals ; Aquaculture/*methods ; Breeding/*methods ; Chromosome Mapping ; Genetic Variation ; Genomics/*methods ; United States ; }, abstract = {Advancing the production efficiency and profitability of aquaculture is dependent upon the ability to utilize a diverse array of genetic resources. The ultimate goals of aquaculture genomics, genetics and breeding research are to enhance aquaculture production efficiency, sustainability, product quality, and profitability in support of the commercial sector and for the benefit of consumers. In order to achieve these goals, it is important to understand the genomic structure and organization of aquaculture species, and their genomic and phenomic variations, as well as the genetic basis of traits and their interrelationships. In addition, it is also important to understand the mechanisms of regulation and evolutionary conservation at the levels of genome, transcriptome, proteome, epigenome, and systems biology. With genomic information and information between the genomes and phenomes, technologies for marker/causal mutation-assisted selection, genome selection, and genome editing can be developed for applications in aquaculture. A set of genomic tools and resources must be made available including reference genome sequences and their annotations (including coding and non-coding regulatory elements), genome-wide polymorphic markers, efficient genotyping platforms, high-density and high-resolution linkage maps, and transcriptome resources including non-coding transcripts. Genomic and genetic control of important performance and production traits, such as disease resistance, feed conversion efficiency, growth rate, processing yield, behaviour, reproductive characteristics, and tolerance to environmental stressors like low dissolved oxygen, high or low water temperature and salinity, must be understood. QTL need to be identified, validated across strains, lines and populations, and their mechanisms of control understood. Causal gene(s) need to be identified. Genetic and epigenetic regulation of important aquaculture traits need to be determined, and technologies for marker-assisted selection, causal gene/mutation-assisted selection, genome selection, and genome editing using CRISPR and other technologies must be developed, demonstrated with applicability, and application to aquaculture industries.Major progress has been made in aquaculture genomics for dozens of fish and shellfish species including the development of genetic linkage maps, physical maps, microarrays, single nucleotide polymorphism (SNP) arrays, transcriptome databases and various stages of genome reference sequences. This paper provides a general review of the current status, challenges and future research needs of aquaculture genomics, genetics, and breeding, with a focus on major aquaculture species in the United States: catfish, rainbow trout, Atlantic salmon, tilapia, striped bass, oysters, and shrimp. While the overall research priorities and the practical goals are similar across various aquaculture species, the current status in each species should dictate the next priority areas within the species. This paper is an output of the USDA Workshop for Aquaculture Genomics, Genetics, and Breeding held in late March 2016 in Auburn, Alabama, with participants from all parts of the United States.}, } @article {pmid28219339, year = {2017}, author = {He, L and Zhang, A and Chu, P and Li, Y and Huang, R and Liao, L and Zhu, Z and Wang, Y}, title = {Deep Illumina sequencing reveals conserved and novel microRNAs in grass carp in response to grass carp reovirus infection.}, journal = {BMC genomics}, volume = {18}, number = {1}, pages = {195}, pmid = {28219339}, issn = {1471-2164}, mesh = {Animals ; Carps/*genetics/*virology ; *Conserved Sequence ; Fish Diseases/virology ; Gene Expression Profiling ; Gene Ontology ; *High-Throughput Nucleotide Sequencing ; MicroRNAs/*genetics ; Reoviridae/*physiology ; *Sequence Analysis, RNA ; }, abstract = {BACKGROUND: The grass carp hemorrhagic disease caused by the grass carp reovirus (GCRV) is a major disease that hampers the development of grass carp aquaculture. The mechanism underlying GCRV pathogenesis and hemorrhagic symptoms is still unknown. MicroRNAs (miRNAs) are key regulators involved in various biological processes. The aim of this study was to identify conserved and novel miRNAs in grass carp in response to GCRV infection, as well as attempt to reveal the mechanism underlying GCRV pathogenesis and hemorrhagic symptoms.

RESULTS: Grass carp were infected with GCRV, and spleen samples were collected at 0 (control), 1, 3, 5, 7, and 9 days post-infection (dpi). These samples were used to construct and sequence small RNA libraries. A total of 1208 miRNAs were identified, of which 278 were known miRNAs and 930 were novel miRNAs. Thirty-six miRNAs were identified to exhibit differential expression when compared with the control, and 536 target genes were predicted for the 36 miRNAs. GO and KEGG enrichment analyses of these target genes showed that many of the significantly enriched terms were associated with immune response, blood coagulation, hemostasis, and complement and coagulation cascades, especially the GO term "blood coagulation" and pathway "complement and coagulation cascades." Ten representative target genes involved in "complement and coagulation cascades" were selected for qPCR analysis, and the results showed that the expression patterns of these target genes were significantly upregulated at 7 dpi, suggesting that the pathway "complement and coagulation cascades" was strongly activated.

CONCLUSION: Conserved and novel miRNAs in response to GCRV infection were identified in grass carp, of which 278 were known miRNAs and 930 were novel miRNAs. Many of the target genes involved in immune response, blood coagulation, hemostasis, and complement and coagulation cascades. Strong activation of the pathway "complement and coagulation cascades" may have led to endothelial-cell and blood-cell damage and hemorrhagic symptoms. The present study provides a new insight into understanding the mechanism underlying GCRV pathogenesis and hemorrhagic symptoms.}, } @article {pmid28212831, year = {2017}, author = {Chen, P and Jing, X and Liao, B and Zhu, Y and Xu, J and Liu, R and Zhao, Y and Li, X}, title = {BioNano Genome Map Resource for Oryza sativa ssp. japonica and indica and Its Application in Rice Genome Sequence Correction and Gap Filling.}, journal = {Molecular plant}, volume = {10}, number = {6}, pages = {895-898}, doi = {10.1016/j.molp.2017.02.003}, pmid = {28212831}, issn = {1752-9867}, mesh = {Base Sequence ; *Chromosome Mapping ; Computational Biology ; *Genome, Plant ; *Nanotechnology ; Oryza/*genetics ; }, } @article {pmid28211247, year = {2017}, author = {Narum, S and Chambers, K}, title = {Editorial 2017.}, journal = {Molecular ecology resources}, volume = {17}, number = {2}, pages = {129-137}, doi = {10.1111/1755-0998.12651}, pmid = {28211247}, issn = {1755-0998}, mesh = {Computational Biology/*methods ; Ecology/*methods ; *Editorial Policies ; Molecular Biology/*methods ; *Periodicals as Topic ; }, } @article {pmid28208714, year = {2017}, author = {Chen, Y and Peng, HM and Wang, X and Li, BQ and Long, MY and Tian, SP}, title = {Biodegradation Mechanisms of Patulin in Candida guilliermondii: An iTRAQ-Based Proteomic Analysis.}, journal = {Toxins}, volume = {9}, number = {2}, pages = {}, pmid = {28208714}, issn = {2072-6651}, mesh = {*Biodegradation, Environmental ; Candida/classification/genetics/growth & development/*metabolism ; Chromatography, Liquid ; Computational Biology ; Databases, Protein ; *Food Microbiology ; Fungal Proteins/genetics/metabolism ; Furans/metabolism ; Gene Expression Regulation, Enzymologic ; Gene Expression Regulation, Fungal ; Inactivation, Metabolic ; Microbial Viability ; Oxidoreductases/genetics/metabolism ; Patulin/*metabolism ; *Peptide Mapping ; Proteomics/*methods ; *Tandem Mass Spectrometry ; Time Factors ; }, abstract = {Patulin, a potent mycotoxin, contaminates fruits and derived products worldwide, and is a serious health concern. Several yeast strains have shown the ability to effectively degrade patulin. However, the mechanisms of its biodegradation still remain unclear at this time. In the present study, biodegradation and involved mechanisms of patulin by an antagonistic yeast Candida guilliermondii were investigated. The results indicated that C. guilliermondii was capable of not only multiplying to a high population in medium containing patulin, but also effectively reducing patulin content in culture medium. Degradation of patulin by C. guilliermondii was dependent on the yeast cell viability, and mainly occurred inside cells. E-ascladiol was the main degradation product of patulin. An iTRAQ-based proteomic analysis revealed that the responses of C. guilliermondii to patulin were complex. A total of 30 differential proteins involved in 10 biological processes were identified, and more than two-thirds of the differential proteins were down-accumulated. Notably, a short-chain dehydrogenase (gi|190348612) was markedly induced by patulin at both the protein and mRNA levels. Our findings will provide a foundation to help enable the commercial development of an enzyme formulation for the detoxification of patulin in fruit-derived products.}, } @article {pmid28206610, year = {2017}, author = {Stel, VS and Brück, K and Fraser, S and Zoccali, C and Massy, ZA and Jager, KJ}, title = {International differences in chronic kidney disease prevalence: a key public health and epidemiologic research issue.}, journal = {Nephrology, dialysis, transplantation : official publication of the European Dialysis and Transplant Association - European Renal Association}, volume = {32}, number = {suppl_2}, pages = {ii129-ii135}, doi = {10.1093/ndt/gfw420}, pmid = {28206610}, issn = {1460-2385}, mesh = {Disease Progression ; Europe/epidemiology ; Humans ; Life Style ; Prevalence ; Public Health ; Renal Insufficiency, Chronic/*epidemiology/etiology ; Risk Factors ; }, abstract = {In this narrative review, we studied the association of risk factors for chronic kidney disease (CKD) and CKD prevalence at an ecological level and describe potential reasons for international differences in estimated CKD prevalence across European countries. We found substantial variation in risk factors for CKD such as in the prevalence of diabetes mellitus, obesity, raised blood pressure, physical inactivity, current smoking and salt intake per day. In general, the countries with a higher CKD prevalence also had a higher average score on CKD risk factors, and vice versa. There was no association between cardiovascular mortality rates and CKD prevalence. In countries with a high CKD prevalence, the prevention of noncommunicable diseases may be considered important, and, therefore, all five national response systems (e.g. an operational national policy, strategy or action plan to reduce physical inactivity and/or promote physical activity) have been implemented. Furthermore, both the heterogeneity in study methods to assess CKD prevalence as well as the international differences in the implementation of lifestyle measures will contribute to the observed variation in CKD prevalence. A robust public health approach to reduce risk factors in order to prevent CKD and reduce CKD progression risk is needed and will have co-benefits for other noncommunicable diseases.}, } @article {pmid28205556, year = {2017}, author = {Rashid, I and Nagpure, NS and Srivastava, P and Kumar, R and Pathak, AK and Singh, M and Kushwaha, B}, title = {HRGFish: A database of hypoxia responsive genes in fishes.}, journal = {Scientific reports}, volume = {7}, number = {}, pages = {42346}, pmid = {28205556}, issn = {2045-2322}, mesh = {Animals ; DNA Primers/metabolism ; *Databases, Genetic ; Fishes/*genetics ; Hypoxia/*genetics ; Internet ; Response Elements ; Sequence Alignment ; User-Computer Interface ; }, abstract = {Several studies have highlighted the changes in the gene expression due to the hypoxia response in fishes, but the systematic organization of the information and the analytical platform for such genes are lacking. In the present study, an attempt was made to develop a database of hypoxia responsive genes in fishes (HRGFish), integrated with analytical tools, using LAMPP technology. Genes reported in hypoxia response for fishes were compiled through literature survey and the database presently covers 818 gene sequences and 35 gene types from 38 fishes. The upstream fragments (3,000 bp), covered in this database, enables to compute CG dinucleotides frequencies, motif finding of the hypoxia response element, identification of CpG island and mapping with the reference promoter of zebrafish. The database also includes functional annotation of genes and provides tools for analyzing sequences and designing primers for selected gene fragments. This may be the first database on the hypoxia response genes in fishes that provides a workbench to the scientific community involved in studying the evolution and ecological adaptation of the fish species in relation to hypoxia.}, } @article {pmid28202810, year = {2017}, author = {Esteban, N and Mortimer, JA and Hays, GC}, title = {How numbers of nesting sea turtles can be overestimated by nearly a factor of two.}, journal = {Proceedings. Biological sciences}, volume = {284}, number = {1849}, pages = {}, pmid = {28202810}, issn = {1471-2954}, mesh = {Animals ; *Conservation of Natural Resources ; Ecosystem ; Endangered Species ; Female ; Geographic Information Systems ; Indian Ocean ; Nesting Behavior ; *Turtles ; }, abstract = {Estimating the absolute number of individuals in populations and their fecundity is central to understanding the ecosystem role of species and their population dynamics as well as allowing informed conservation management for endangered species. Estimates of abundance and fecundity are often difficult to obtain for rare or cryptic species. Yet, in addition, here we show for a charismatic group, sea turtles, that are neither cryptic nor rare and whose nesting is easy to observe, that the traditional approach of direct observations of nesting has likely led to a gross overestimation of the number of individuals in populations and underestimation of their fecundity. We use high-resolution GPS satellite tags to track female green turtles throughout their nesting season in the Chagos Archipelago (Indian Ocean) and assess when and where they nested. For individual turtles, nest locations were often spread over several tens of kilometres of coastline. Assessed by satellite observations, a mean of 6.0 clutches (range 2-9, s.d. = 2.2) was laid by individuals, about twice as many as previously assumed, a finding also reported in other species and ocean basins. Taken together, these findings suggest that the actual number of nesting turtles may be almost 50% less than previously assumed.}, } @article {pmid28199395, year = {2017}, author = {Fruzangohar, M and Ebrahimie, E and Adelson, DL}, title = {A novel hypothesis-unbiased method for Gene Ontology enrichment based on transcriptome data.}, journal = {PloS one}, volume = {12}, number = {2}, pages = {e0170486}, pmid = {28199395}, issn = {1932-6203}, mesh = {Alzheimer Disease/*genetics/metabolism ; *Databases, Nucleic Acid ; *Gene Expression Regulation, Bacterial ; *Gene Ontology ; Humans ; Salmonella enteritidis/*genetics/metabolism ; *Transcriptome ; }, abstract = {Gene Ontology (GO) classification of statistically significantly differentially expressed genes is commonly used to interpret transcriptomics data as a part of functional genomic analysis. In this approach, all significantly expressed genes contribute equally to the final GO classification regardless of their actual expression levels. Gene expression levels can significantly affect protein production and hence should be reflected in GO term enrichment. Genes with low expression levels can also participate in GO term enrichment through cumulative effects. In this report, we have introduced a new GO enrichment method that is suitable for multiple samples and time series experiments that uses a statistical outlier test to detect GO categories with special patterns of variation that can potentially identify candidate biological mechanisms. To demonstrate the value of our approach, we have performed two case studies. Whole transcriptome expression profiles of Salmonella enteritidis and Alzheimer's disease (AD) were analysed in order to determine GO term enrichment across the entire transcriptome instead of a subset of differentially expressed genes used in traditional GO analysis. Our result highlights the key role of inflammation related functional groups in AD pathology as granulocyte colony-stimulating factor receptor binding, neuromedin U binding, and interleukin were remarkably upregulated in AD brain when all using all of the gene expression data in the transcriptome. Mitochondrial components and the molybdopterin synthase complex were identified as potential key cellular components involved in AD pathology.}, } @article {pmid28198676, year = {2017}, author = {Zhu, Y and Chen, L and Zhang, C and Hao, P and Jing, X and Li, X}, title = {Global transcriptome analysis reveals extensive gene remodeling, alternative splicing and differential transcription profiles in non-seed vascular plant Selaginella moellendorffii.}, journal = {BMC genomics}, volume = {18}, number = {Suppl 1}, pages = {1042}, pmid = {28198676}, issn = {1471-2164}, mesh = {*Alternative Splicing ; Computational Biology/methods ; *Gene Expression Profiling ; Gene Expression Regulation, Developmental ; *Gene Expression Regulation, Plant ; Gene Regulatory Networks ; High-Throughput Nucleotide Sequencing ; Metabolic Networks and Pathways ; Molecular Sequence Annotation ; Organ Specificity/genetics ; Phenotype ; Selaginellaceae/*genetics/metabolism ; *Transcriptome ; }, abstract = {BACKGROUND: Selaginella moellendorffii, a lycophyte, is a model plant to study the early evolution and development of vascular plants. As the first and only sequenced lycophyte to date, the genome of S. moellendorffii revealed many conserved genes and pathways, as well as specialized genes different from flowering plants. Despite the progress made, little is known about long noncoding RNAs (lncRNA) and the alternative splicing (AS) of coding genes in S. moellendorffii. Its coding gene models have not been fully validated with transcriptome data. Furthermore, it remains important to understand whether the regulatory mechanisms similar to flowering plants are used, and how they operate in a non-seed primitive vascular plant.

RESULTS: RNA-sequencing (RNA-seq) was performed for three S. moellendorffii tissues, root, stem, and leaf, by constructing strand-specific RNA-seq libraries from RNA purified using RiboMinus isolation protocol. A total of 176 million reads (44 Gbp) were obtained from three tissue types, and were mapped to S. moellendorffii genome. By comparing with 22,285 existing gene models of S. moellendorffii, we identified 7930 high-confidence novel coding genes (a 35.6% increase), and for the first time reported 4422 lncRNAs in a lycophyte. Further, we refined 2461 (11.0%) of existing gene models, and identified 11,030 AS events (for 5957 coding genes) revealed for the first time for lycophytes. Tissue-specific gene expression with functional implication was analyzed, and 1031, 554, and 269 coding genes, and 174, 39, and 17 lncRNAs were identified in root, stem, and leaf tissues, respectively. The expression of critical genes for vascular development stages, i.e. formation of provascular cells, xylem specification and differentiation, and phloem specification and differentiation, was compared in S. moellendorffii tissues, indicating a less complex regulatory mechanism in lycophytes than in flowering plants. The results were further strengthened by the evolutionary trend of seven transcription factor families related to vascular development, which was observed among four representative species of seed and non-seed vascular plants, and nonvascular land and aquatic plants.

CONCLUSIONS: The deep RNA-seq study of S. moellendorffii discovered extensive new gene contents, including novel coding genes, lncRNAs, AS events, and refined gene models. Compared to flowering vascular plants, S. moellendorffii displayed a less complexity in both gene structure, alternative splicing, and regulatory elements of vascular development. The study offered important insight into the evolution of vascular plants, and the regulation mechanism of vascular development in a non-seed plant.}, } @article {pmid28196453, year = {2017}, author = {Gramigna, V and Pellegrino, G and Cerasa, A and Cutini, S and Vasta, R and Olivadese, G and Martino, I and Quattrone, A}, title = {Near-Infrared Spectroscopy in Gait Disorders: Is It Time to Begin?.}, journal = {Neurorehabilitation and neural repair}, volume = {31}, number = {5}, pages = {402-412}, doi = {10.1177/1545968317693304}, pmid = {28196453}, issn = {1552-6844}, mesh = {Databases, Bibliographic/statistics & numerical data ; Gait Disorders, Neurologic/*diagnostic imaging/*metabolism ; Humans ; Image Processing, Computer-Assisted ; Oxyhemoglobins/*metabolism ; *Spectroscopy, Near-Infrared ; }, abstract = {Walking is a complex motor behavior with a special relevance in clinical neurology. Many neurological diseases, such as Parkinson's disease and stroke, are characterized by gait disorders whose neurofunctional correlates are poorly investigated. Indeed, the analysis of real walking with the standard neuroimaging techniques poses strong challenges, and only a few studies on motor imagery or walking observation have been performed so far. Functional near-infrared spectroscopy (fNIRS) is becoming an important research tool to assess functional activity in neurological populations or for special tasks, such as walking, because it allows investigating brain hemodynamic activity in an ecological setting, without strong immobility constraints. A systematic review following PRISMA guidelines was conducted on the fNIRS-based examination of gait disorders. Twelve of the initial yield of 489 articles have been included in this review. The lesson learnt from these studies suggest that oxy-hemoglobin levels within the prefrontal and premotor cortices are more sensitive to compensation strategies reflecting postural control and restoration of gait disorders. Although this field of study is in its relative infancy, the evidence provided encourages the translation of fNIRS in clinical practice, as it offers a unique opportunity to explore in depth the activity of the cortical motor system during real walking in neurological patients. We also discuss to what extent fNIRS may be applied for assessing the effectiveness of rehabilitation programs.}, } @article {pmid28195957, year = {2017}, author = {Chevignard, M and Kerrouche, B and Krasny-Pacini, A and Mariller, A and Pineau-Chardon, E and Notteghem, P and Prodhomme, J and Le Gall, D and Roulin, JL and Fournet, N and Roy, A}, title = {Ecological Assessment of Everyday Executive Functioning at Home and at School Following Childhood Traumatic Brain Injury Using the BRIEF Questionnaire.}, journal = {The Journal of head trauma rehabilitation}, volume = {32}, number = {6}, pages = {E1-E12}, doi = {10.1097/HTR.0000000000000295}, pmid = {28195957}, issn = {1550-509X}, mesh = {Adolescent ; Brain Injuries, Traumatic/diagnosis/*rehabilitation ; Child ; Child, Preschool ; Cohort Studies ; Databases, Factual ; Executive Function/*physiology ; Female ; Humans ; Injury Severity Score ; Male ; Memory Disorders/*diagnosis/epidemiology ; Monitoring, Physiologic/*methods ; Neuropsychological Tests ; Parents ; Regression Analysis ; Schools ; *Surveys and Questionnaires ; }, abstract = {OBJECTIVES: To describe dysexecutive symptoms in children with traumatic brain injury (TBI) using the Behavior Rating Inventory of Executive Function (BRIEF); to compare parent- and teacher-ratings, to analyze the differential impairment in the BRIEF subscales, and factors influencing outcome.

PARTICIPANTS: Children aged 5 to 18 years 11 months, referred to a rehabilitation department following TBI.

OUTCOME MEASURES: Parent- and teacher reports of the BRIEF.

RESULTS: A total of 194 patients participated in the study: mild (n = 13), moderate (n = 12), severe (n = 169); mean 4.92 (standard deviation = 3.94) years post-injury. According to parent ratings (n = 193), all BRIEF subscales and indices were significantly elevated (23.8%-48% in the clinical range). The Working Memory subscale score was significantly higher than all other subscales. Results of teacher ratings (n = 28) indicated similar significantly elevated scores in all subscales (39.3%-57.2% in the clinical range). No significant difference was found between parent and teacher ratings, which were significantly correlated. Regression analyses indicated that, in children with severe TBI, parental BRIEF overall and metacognition indices were significantly predicted by younger age at injury and older age at assessment, whereas no significant predictor of behavioral regulation index was identified.

DISCUSSION AND CONCLUSION: This study highlights significant executive dysfunction in everyday life several years after childhood TBI, evident in home and school environments.}, } @article {pmid28185104, year = {2017}, author = {Olsson, SB and , }, title = {New Frontiers for Chemical Ecology: Reaffirming a Commitment to the Göteborg Resolution : Guest Editorial: *The Bengaluru Consortium.}, journal = {Journal of chemical ecology}, volume = {43}, number = {1}, pages = {2-3}, pmid = {28185104}, issn = {1573-1561}, mesh = {Biodiversity ; Databases, Factual ; *Ecology/education ; Humans ; India ; Public Policy ; }, } @article {pmid28181519, year = {2017}, author = {Lee, CR and Svardal, H and Farlow, A and Exposito-Alonso, M and Ding, W and Novikova, P and Alonso-Blanco, C and Weigel, D and Nordborg, M}, title = {On the post-glacial spread of human commensal Arabidopsis thaliana.}, journal = {Nature communications}, volume = {8}, number = {}, pages = {14458}, pmid = {28181519}, issn = {2041-1723}, support = {W 1225/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Adaptation, Physiological/genetics ; Arabidopsis/genetics/*physiology ; Base Pairing/genetics ; Chromosomes, Plant/genetics ; Flowers/physiology ; Gene Ontology ; Genome, Plant ; Geography ; Haplotypes/genetics ; Humans ; Hybridization, Genetic ; *Ice Cover ; Polymorphism, Single Nucleotide/genetics ; }, abstract = {Recent work has shown that Arabidopsis thaliana contains genetic groups originating from different ice age refugia, with one particular group comprising over 95% of the current worldwide population. In Europe, relicts of other groups can be found in local populations along the Mediterranean Sea. Here we provide evidence that these 'relicts' occupied post-glacial Eurasia first and were later replaced by the invading 'non-relicts', which expanded through the east-west axis of Eurasia, leaving traces of admixture in the north and south of the species range. The non-relict expansion was likely associated with human activity and led to a demographic replacement similar to what occurred in humans. Introgressed genomic regions from relicts are associated with flowering time and enriched for genes associated with environmental conditions, such as root cap development or metal ion trans-membrane transport, which suggest that admixture with locally adapted relicts helped the non-relicts colonize new habitats.}, } @article {pmid28179014, year = {2017}, author = {Plantinga, A and Zhan, X and Zhao, N and Chen, J and Jenq, RR and Wu, MC}, title = {MiRKAT-S: a community-level test of association between the microbiota and survival times.}, journal = {Microbiome}, volume = {5}, number = {1}, pages = {17}, pmid = {28179014}, issn = {2049-2618}, support = {R01 HG007508/HG/NHGRI NIH HHS/United States ; R01 HL124112/HL/NHLBI NIH HHS/United States ; S10 OD020069/OD/NIH HHS/United States ; U10 CA180819/CA/NCI NIH HHS/United States ; }, mesh = {Blood Transfusion/*mortality ; Bone Marrow Transplantation/*mortality ; Computer Simulation ; Data Interpretation, Statistical ; Gastrointestinal Microbiome/*genetics ; Gastrointestinal Tract/*microbiology ; Graft vs Host Disease/*mortality ; Humans ; *Models, Theoretical ; RNA, Ribosomal, 16S/genetics ; *Survival Analysis ; Transfusion Reaction/*mortality ; Treatment Outcome ; }, abstract = {BACKGROUND: Community-level analysis of the human microbiota has culminated in the discovery of relationships between overall shifts in the microbiota and a wide range of diseases and conditions. However, existing work has primarily focused on analysis of relatively simple dichotomous or quantitative outcomes, for example, disease status or biomarker levels. Recently, there is also considerable interest in the relationship between the microbiota and censored survival outcomes, such as in clinical trials. How to conduct community-level analysis with censored survival outcomes is unclear, since standard dissimilarity-based tests cannot accommodate censored survival times and no alternative methods exist.

METHODS: We develop a new approach, MiRKAT-S, for community-level analysis of microbiome data with censored survival times. MiRKAT-S uses ecologically informative distance metrics, such as the UniFrac distances, to generate matrices of pairwise distances between individuals' taxonomic profiles. The distance matrices are transformed into kernel (similarity) matrices, which are used to compare similarity in the microbiota to similarity in survival times between individuals.

RESULTS: Simulation studies using synthetic microbial communities demonstrate correct control of type I error and adequate power. We also apply MiRKAT-S to examine the relationship between the gut microbiota and survival after allogeneic blood or bone marrow transplant.

CONCLUSIONS: We present MiRKAT-S, a method that facilitates community-level analysis of the association between the microbiota and survival outcomes and therefore provides a new approach to analysis of microbiome data arising from clinical trials.}, } @article {pmid28176868, year = {2017}, author = {Yergeau, E and Michel, C and Tremblay, J and Niemi, A and King, TL and Wyglinski, J and Lee, K and Greer, CW}, title = {Metagenomic survey of the taxonomic and functional microbial communities of seawater and sea ice from the Canadian Arctic.}, journal = {Scientific reports}, volume = {7}, number = {}, pages = {42242}, pmid = {28176868}, issn = {2045-2322}, mesh = {Arctic Regions ; Canada ; Databases, Genetic ; Geography ; Ice Cover/*microbiology ; Metagenomics/*methods ; Microbiota/*genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Seawater/*microbiology ; }, abstract = {Climate change has resulted in an accelerated decline of Arctic sea ice since 2001 resulting in primary production increases and prolongation of the ice-free season within the Northwest Passage. The taxonomic and functional microbial community composition of the seawater and sea ice of the Canadian Arctic is not very well known. Bacterial communities from the bottom layer of sea ice cores and surface water from 23 locations around Cornwallis Island, NU, Canada, were extensively screened. The bacterial 16S rRNA gene was sequenced for all samples while shotgun metagenomics was performed on selected samples. Bacterial community composition showed large variation throughout the sampling area both for sea ice and seawater. Seawater and sea ice samples harbored significantly distinct microbial communities, both at different taxonomic levels and at the functional level. A key difference between the two sample types was the dominance of algae in sea ice samples, as visualized by the higher relative abundance of algae and photosynthesis-related genes in the metagenomic datasets and the higher chl a concentrations. The relative abundance of various OTUs and functional genes were significantly correlated with multiple environmental parameters, highlighting many potential environmental drivers and ecological strategies.}, } @article {pmid28174619, year = {2017}, author = {Jiao, JY and Carro, L and Liu, L and Gao, XY and Zhang, XT and Hozzein, WN and Lapidus, A and Huntemann, M and Reddy, TBK and Varghese, N and Hadjithomas, M and Ivanova, NN and Göker, M and Pillay, M and Eisen, JA and Woyke, T and Klenk, HP and Kyrpides, NC and Li, WJ}, title = {Complete genome sequence of Jiangella gansuensis strain YIM 002[T] (DSM 44835[T]), the type species of the genus Jiangella and source of new antibiotic compounds.}, journal = {Standards in genomic sciences}, volume = {12}, number = {}, pages = {21}, pmid = {28174619}, issn = {1944-3277}, abstract = {Jiangella gansuensis strain YIM 002[T] is the type strain of the type species of the genus Jiangella, which is at the present time composed of five species, and was isolated from desert soil sample in Gansu Province (China). The five strains of this genus are clustered in a monophyletic group when closer actinobacterial genera are used to infer a 16S rRNA gene sequence phylogeny. The study of this genome is part of the GenomicEncyclopedia ofBacteria andArchaea project, and here we describe the complete genome sequence and annotation of this taxon. The genome of J. gansuensis strain YIM 002[T] contains a single scaffold of size 5,585,780 bp, which involves 149 pseudogenes, 4905 protein-coding genes and 50 RNA genes, including 2520 hypothetical proteins and 4 rRNA genes. From the investigation of genome sizes of Jiangella species, J. gansuensis shows a smaller size, which indicates this strain might have discarded too much genetic information to adapt to desert environment. Seven new compounds from this bacterium have recently been described; however, its potential should be higher, as secondary metabolite gene cluster analysis predicted 60 gene clusters, including the potential to produce the pristinamycin.}, } @article {pmid28172542, year = {2017}, author = {Davydov, II and Robinson-Rechavi, M and Salamin, N}, title = {State aggregation for fast likelihood computations in molecular evolution.}, journal = {Bioinformatics (Oxford, England)}, volume = {33}, number = {3}, pages = {354-362}, pmid = {28172542}, issn = {1367-4811}, mesh = {Algorithms ; Computational Biology/*methods ; *Evolution, Molecular ; Markov Chains ; *Models, Genetic ; Probability ; Sensitivity and Specificity ; *Software ; }, abstract = {MOTIVATION: Codon models are widely used to identify the signature of selection at the molecular level and to test for changes in selective pressure during the evolution of genes encoding proteins. The large size of the state space of the Markov processes used to model codon evolution makes it difficult to use these models with large biological datasets. We propose here to use state aggregation to reduce the state space of codon models and, thus, improve the computational performance of likelihood estimation on these models.

RESULTS: We show that this heuristic speeds up the computations of the M0 and branch-site models up to 6.8 times. We also show through simulations that state aggregation does not introduce a detectable bias. We analyzed a real dataset and show that aggregation provides highly correlated predictions compared to the full likelihood computations. Finally, state aggregation is a very general approach and can be applied to any continuous-time Markov process-based model with large state space, such as amino acid and coevolution models. We therefore discuss different ways to apply state aggregation to Markov models used in phylogenetics.

The heuristic is implemented in the godon package (https://bitbucket.org/Davydov/godon) and in a version of FastCodeML (https://gitlab.isb-sib.ch/phylo/fastcodeml).

CONTACT: nicolas.salamin@unil.ch

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, } @article {pmid28168565, year = {2017}, author = {Rosselló-Móra, R and Trujillo, ME and Sutcliffe, IC}, title = {Introducing a digital protologue: a timely move towards a database-driven systematics of archaea and bacteria.}, journal = {Antonie van Leeuwenhoek}, volume = {110}, number = {4}, pages = {455-456}, doi = {10.1007/s10482-017-0841-7}, pmid = {28168565}, issn = {1572-9699}, mesh = {Archaea/*classification/genetics ; Bacteria/*classification/genetics ; Classification/*methods ; Databases as Topic ; Phylogeny ; }, } @article {pmid28166306, year = {2017}, author = {Forstner, AJ and Hecker, J and Hofmann, A and Maaser, A and Reinbold, CS and Mühleisen, TW and Leber, M and Strohmaier, J and Degenhardt, F and Treutlein, J and Mattheisen, M and Schumacher, J and Streit, F and Meier, S and Herms, S and Hoffmann, P and Lacour, A and Witt, SH and Reif, A and Müller-Myhsok, B and Lucae, S and Maier, W and Schwarz, M and Vedder, H and Kammerer-Ciernioch, J and Pfennig, A and Bauer, M and Hautzinger, M and Moebus, S and Schenk, LM and Fischer, SB and Sivalingam, S and Czerski, PM and Hauser, J and Lissowska, J and Szeszenia-Dabrowska, N and Brennan, P and McKay, JD and Wright, A and Mitchell, PB and Fullerton, JM and Schofield, PR and Montgomery, GW and Medland, SE and Gordon, SD and Martin, NG and Krasnov, V and Chuchalin, A and Babadjanova, G and Pantelejeva, G and Abramova, LI and Tiganov, AS and Polonikov, A and Khusnutdinova, E and Alda, M and Cruceanu, C and Rouleau, GA and Turecki, G and Laprise, C and Rivas, F and Mayoral, F and Kogevinas, M and Grigoroiu-Serbanescu, M and Becker, T and Schulze, TG and Rietschel, M and Cichon, S and Fier, H and Nöthen, MM}, title = {Identification of shared risk loci and pathways for bipolar disorder and schizophrenia.}, journal = {PloS one}, volume = {12}, number = {2}, pages = {e0171595}, pmid = {28166306}, issn = {1932-6203}, support = {001/WHO_/World Health Organization/International ; }, mesh = {Bipolar Disorder/*genetics/*metabolism ; Genetic Linkage ; *Genetic Predisposition to Disease ; Genome-Wide Association Study ; Humans ; Linkage Disequilibrium ; Polymorphism, Single Nucleotide ; *Quantitative Trait Loci ; Risk ; Schizophrenia/*genetics/*metabolism ; *Signal Transduction ; }, abstract = {Bipolar disorder (BD) is a highly heritable neuropsychiatric disease characterized by recurrent episodes of mania and depression. BD shows substantial clinical and genetic overlap with other psychiatric disorders, in particular schizophrenia (SCZ). The genes underlying this etiological overlap remain largely unknown. A recent SCZ genome wide association study (GWAS) by the Psychiatric Genomics Consortium identified 128 independent genome-wide significant single nucleotide polymorphisms (SNPs). The present study investigated whether these SCZ-associated SNPs also contribute to BD development through the performance of association testing in a large BD GWAS dataset (9747 patients, 14278 controls). After re-imputation and correction for sample overlap, 22 of 107 investigated SCZ SNPs showed nominal association with BD. The number of shared SCZ-BD SNPs was significantly higher than expected (p = 1.46x10-8). This provides further evidence that SCZ-associated loci contribute to the development of BD. Two SNPs remained significant after Bonferroni correction. The most strongly associated SNP was located near TRANK1, which is a reported genome-wide significant risk gene for BD. Pathway analyses for all shared SCZ-BD SNPs revealed 25 nominally enriched gene-sets, which showed partial overlap in terms of the underlying genes. The enriched gene-sets included calcium- and glutamate signaling, neuropathic pain signaling in dorsal horn neurons, and calmodulin binding. The present data provide further insights into shared risk loci and disease-associated pathways for BD and SCZ. This may suggest new research directions for the treatment and prevention of these two major psychiatric disorders.}, } @article {pmid28164331, year = {2017}, author = {Wilson, AW and Hosaka, K and Mueller, GM}, title = {Evolution of ectomycorrhizas as a driver of diversification and biogeographic patterns in the model mycorrhizal mushroom genus Laccaria.}, journal = {The New phytologist}, volume = {213}, number = {4}, pages = {1862-1873}, pmid = {28164331}, issn = {1469-8137}, mesh = {*Biodiversity ; *Biological Evolution ; Carbon Isotopes ; Databases as Topic ; Laccaria/*physiology ; *Models, Biological ; Mycorrhizae/*physiology ; Nitrogen Isotopes ; *Phylogeography ; Species Specificity ; }, abstract = {A systematic and evolutionary ecology study of the model ectomycorrhizal (ECM) genus Laccaria was performed using herbarium material and field collections from over 30 countries covering its known geographic range. A four-gene (nrITS, 28S, RPB2, EF1α) nucleotide sequence dataset consisting of 232 Laccaria specimens was analyzed phylogenetically. The resulting Global Laccaria dataset was used for molecular dating and estimating diversification rates in the genus. Stable isotope analysis of carbon and nitrogen was used to evaluate the origin of Laccaria's ECM ecology. In all, 116 Laccaria molecular species were identified, resulting in a near 50% increase in its known diversity, including the new species described herein: Laccaria ambigua. Molecular dating indicates that the most recent common ancestor to Laccaria existed in the early Paleocene (56-66 million yr ago), probably in Australasia. At this time, Laccaria split into two lineages: one represented by the new species L. ambigua, and the other reflecting a large shift in diversification that resulted in the remainder of Laccaria. L. ambigua shows a different isotopic profile than all other Laccaria species. Isotopes and diversification results suggest that the evolution of the ECM ecology was a key innovation in the evolution of Laccaria. Diversification shifts associated with Laccaria's dispersal to the northern hemisphere are attributed to adaptations to new ecological niches.}, } @article {pmid28161492, year = {2017}, author = {Lim, SL and D'Agui, HM and Enright, NJ and He, T}, title = {Characterization of Leaf Transcriptome in Banksia hookeriana.}, journal = {Genomics, proteomics & bioinformatics}, volume = {15}, number = {1}, pages = {49-56}, pmid = {28161492}, issn = {2210-3244}, mesh = {Contig Mapping ; Databases, Protein ; Microsatellite Repeats ; Plant Leaves/genetics/metabolism ; Polymorphism, Single Nucleotide ; Proteaceae/*genetics/metabolism ; RNA, Plant/chemistry/isolation & purification/metabolism ; Sequence Analysis, RNA ; *Transcriptome ; }, abstract = {Banksia is a significant element in vegetation of southwestern Australia, a biodiversity hotspot with global significance. In particular, Banksia hookeriana represents a species with significant economic and ecological importance in the region. For better conservation and management, we reported an overview of transcriptome of B. hookeriana using RNA-seq and de novo assembly. We have generated a total of 202.7 million reads (18.91 billion of nucleotides) from four leaf samples in four plants of B. hookeriana, and assembled 59,063 unigenes (average size=1098bp) through de novotranscriptome assembly. Among them, 39,686 unigenes were annotated against the Swiss-Prot, Clusters of Orthologous Groups (COG), and NCBI non-redundant (NR) protein databases. We showed that there was approximately one single nucleotide polymorphism (SNP) per 5.6-7.1kb in the transcriptome, and the ratio of transitional to transversional polymorphisms was approximately 1.82. We compared unigenes of B. hookeriana to those of Arabidopsis thaliana and Nelumbo nucifera through sequence homology, Gene Ontology (GO) annotation, and KEGG pathway analyses. The comparative analysis revealed that unigenes of B. hookeriana were closely related to those of N. nucifera. B. hookeriana, N. nucifera, and A. thaliana shared similar GO annotations but different distributions in KEGG pathways, indicating that B. hookeriana has adapted to dry-Mediterranean type shrublands via regulating expression of specific genes. In total 1927 potential simple sequence repeat (SSR) markers were discovered, which could be used in the genotype and genetic diversity studies of the Banksia genus. Our results provide valuable sequence resource for further study in Banksia.}, } @article {pmid28160078, year = {2017}, author = {Hu, X and Zhu, M and Liang, Z and Kumar, D and Chen, F and Zhu, L and Kuang, S and Xue, R and Cao, G and Gong, C}, title = {Proteomic analysis of BmN cell lipid rafts reveals roles in Bombyx mori nucleopolyhedrovirus infection.}, journal = {Molecular genetics and genomics : MGG}, volume = {292}, number = {2}, pages = {465-474}, pmid = {28160078}, issn = {1617-4623}, mesh = {Animals ; Bombyx/*genetics/*virology ; Cell Line ; Cholesterol/chemistry ; Computational Biology ; Gene Expression Profiling ; HSP90 Heat-Shock Proteins/chemistry ; Insect Proteins/chemistry ; Lipids/chemistry ; Mass Spectrometry ; Membrane Microdomains/*chemistry ; Molecular Sequence Annotation ; Nucleopolyhedroviruses/*physiology ; Proteomics ; }, abstract = {The mechanism of how Bombyx mori nucleopolyhedrovirus (BmNPV) enters cells is unknown. The primary components of membrane lipid rafts are proteins and cholesterol, and membrane lipid rafts are thought to be an active region for host-viral interactions. However, whether they contribute to the entry of BmNPV into silkworm cells remains unclear. In this study, we explored the membrane protein components of lipid rafts from BmN cells with mass spectrometry (MS). Proteins and cholesterol were investigated after establishing infection with BmNPV in BmN cells. In total, 222 proteins were identified in the lipid rafts, and Gene Ontology (GO) annotation analysis showed that more than 10% of these proteins had binding and catalytic functions. We then identified proteins that potentially interact between lipid rafts and BmNPV virions using the Virus Overlay Protein Blot Assay (VOPBA). A total of 65 proteins were analyzed with MS, and 7 were predicted to be binding proteins involved in BmNPV cellular invasion, including actin, kinesin light chain-like isoform X2, annexin B13, heat-shock protein 90, barrier-to-autointegration factor B-like and serine/arginine-rich splicing factor 1 A-like. When the cholesterol of the lipid rafts from the membrane was depleted by methyl-β-cyclodextrin (MβCD), BmNPV entry into BmN cells was blocked. However, supplying cholesterol into the medium rescued the BmNPV infection ability. These results show that membrane lipid rafts may be the active regions for the entry of BmNPV into cells, and the components of membrane lipid rafts may be candidate targets for improving the resistance of the silkworm to BmNPV.}, } @article {pmid28158396, year = {2017}, author = {Iwayama, K and Aisaka, Y and Kutsuna, N and Nagano, AJ}, title = {FIT: statistical modeling tool for transcriptome dynamics under fluctuating field conditions.}, journal = {Bioinformatics (Oxford, England)}, volume = {33}, number = {11}, pages = {1672-1680}, pmid = {28158396}, issn = {1367-4811}, mesh = {Computational Biology/*methods ; Gene Expression Regulation, Plant ; *Models, Genetic ; *Models, Statistical ; Oryza/genetics ; *Software ; *Transcriptome ; }, abstract = {MOTIVATION: Considerable attention has been given to the quantification of environmental effects on organisms. In natural conditions, environmental factors are continuously changing in a complex manner. To reveal the effects of such environmental variations on organisms, transcriptome data in field environments have been collected and analyzed. Nagano et al. proposed a model that describes the relationship between transcriptomic variation and environmental conditions and demonstrated the capability to predict transcriptome variation in rice plants. However, the computational cost of parameter optimization has prevented its wide application.

RESULTS: : We propose a new statistical model and efficient parameter optimization based on the previous study. We developed and released FIT, an R package that offers functions for parameter optimization and transcriptome prediction. The proposed method achieves comparable or better prediction performance within a shorter computational time than the previous method. The package will facilitate the study of the environmental effects on transcriptomic variation in field conditions.

Freely available from CRAN (https://cran.r-project.org/web/packages/FIT/).

CONTACT: : anagano@agr.ryukoku.ac.jp.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, } @article {pmid28158222, year = {2017}, author = {Song, H and Wang, P and Li, C and Han, S and Zhao, C and Xia, H and Bi, Y and Guo, B and Zhang, X and Wang, X}, title = {Comparative analysis of NBS-LRR genes and their response to Aspergillus flavus in Arachis.}, journal = {PloS one}, volume = {12}, number = {2}, pages = {e0171181}, pmid = {28158222}, issn = {1932-6203}, mesh = {Arachis/genetics/*metabolism/*microbiology ; Aspergillus flavus/*pathogenicity ; Computational Biology ; Multigene Family/genetics ; Phylogeny ; Plant Proteins/genetics/*metabolism ; }, abstract = {Studies have demonstrated that nucleotide-binding site-leucine-rich repeat (NBS-LRR) genes respond to pathogen attack in plants. Characterization of NBS-LRR genes in peanut is not well documented. The newly released whole genome sequences of Arachis duranensis and Arachis ipaënsis have allowed a global analysis of this important gene family in peanut to be conducted. In this study, we identified 393 (AdNBS) and 437 (AiNBS) NBS-LRR genes from A. duranensis and A. ipaënsis, respectively, using bioinformatics approaches. Full-length sequences of 278 AdNBS and 303 AiNBS were identified. Fifty-one orthologous, four AdNBS paralogous, and six AiNBS paralogous gene pairs were predicted. All paralogous gene pairs were located in the same chromosomes, indicating that tandem duplication was the most likely mechanism forming these paralogs. The paralogs mainly underwent purifying selection, but most LRR 8 domains underwent positive selection. More gene clusters were found in A. ipaënsis than in A. duranensis, possibly owing to tandem duplication events occurring more frequently in A. ipaënsis. The expression profile of NBS-LRR genes was different between A. duranensis and A. hypogaea after Aspergillus flavus infection. The up-regulated expression of NBS-LRR in A. duranensis was continuous, while these genes responded to the pathogen temporally in A. hypogaea.}, } @article {pmid28155666, year = {2016}, author = {Xie, C and Goi, CL and Huson, DH and Little, PF and Williams, RB}, title = {RiboTagger: fast and unbiased 16S/18S profiling using whole community shotgun metagenomic or metatranscriptome surveys.}, journal = {BMC bioinformatics}, volume = {17}, number = {Suppl 19}, pages = {508}, pmid = {28155666}, issn = {1471-2105}, mesh = {Bacteria/*genetics ; Computational Biology/methods ; DNA, Ribosomal/genetics ; High-Throughput Nucleotide Sequencing/methods ; *Metagenome ; Metagenomics ; RNA, Ribosomal, 16S/*genetics ; RNA, Ribosomal, 18S/*genetics ; Sequence Analysis, DNA/*methods ; *Software ; *Transcriptome ; }, abstract = {BACKGROUND: Taxonomic profiling of microbial communities is often performed using small subunit ribosomal RNA (SSU) amplicon sequencing (16S or 18S), while environmental shotgun sequencing is often focused on functional analysis. Large shotgun datasets contain a significant number of SSU sequences and these can be exploited to perform an unbiased SSU--based taxonomic analysis.

RESULTS: Here we present a new program called RiboTagger that identifies and extracts taxonomically informative ribotags located in a specified variable region of the SSU gene in a high-throughput fashion.

CONCLUSIONS: RiboTagger permits fast recovery of SSU-RNA sequences from shotgun nucleic acid surveys of complex microbial communities. The program targets all three domains of life, exhibits high sensitivity and specificity and is substantially faster than comparable programs.}, } @article {pmid28155108, year = {2017}, author = {Maher, JP and Rhodes, RE and Dzubur, E and Huh, J and Intille, S and Dunton, GF}, title = {Momentary assessment of physical activity intention-behavior coupling in adults.}, journal = {Translational behavioral medicine}, volume = {7}, number = {4}, pages = {709-718}, pmid = {28155108}, issn = {1613-9860}, support = {118283-MRSGT-10-012-01-CPPB//American Cancer Society/International ; }, mesh = {Accelerometry ; Adult ; Ecological Momentary Assessment ; Exercise/*psychology ; Female ; Health Behavior ; Humans ; *Intention ; Longitudinal Studies ; Male ; Reminder Systems ; Surveys and Questionnaires ; Time Factors ; }, abstract = {Research attempting to elucidate physical activity (PA) intention-behavior relations has focused on differences in long-term behavior forecasting between people. However, regular PA requires a repeated performance on a daily or within-daily basis. An empirical case study application is presented using intensive longitudinal data from a study of PA in adults to (a) describe the extent to which short-term intention-behavior coupling occurs and (b) explore time-varying predictors of intention formation and short-term intention-behavior coupling. Adults (n = 116) participated in three 4-day waves of ecological momentary assessment (EMA). Each day, participants received EMA questionnaires assessing short-term PA intentions and wore accelerometers to assess whether they engaged in ≥10 min of moderate-to-vigorous physical activity (MVPA) in the 3-hour period after each EMA prompt. Concurrent affective states and contexts were also assessed through EMA. Participants reported having short-term intentions to engage in PA in 41% of EMA prompts. However, participants only engaged in ≥10 min of MVPA following 16% of the prompts that short-term PA intentions were reported indicating an intention-behavior gap of 84%. Odds of intentions followed by PA were greater on occasions when individuals reported higher levels of positive affect than was typical for them. This study is the first to take an EMA approach to describe short-term intention-behavior coupling in adults. Results suggest that adults have difficulty translating intentions into behavior at the momentary level, more so than over longer timescales, and that positive affect may be a key to successfully translating intentions into behavior.}, } @article {pmid28149178, year = {2017}, author = {El-Sheikh, MA and Thomas, J and Alfarhan, AH and Alatar, AA and Mayandy, S and Hennekens, SM and Schaminėe, JH and Mucina, L and Alansari, AM}, title = {SaudiVeg ecoinformatics: Aims, current status and perspectives.}, journal = {Saudi journal of biological sciences}, volume = {24}, number = {2}, pages = {389-398}, pmid = {28149178}, issn = {1319-562X}, abstract = {During the last decade many electronic databases of vegetation plots were established in many countries around the world. These databases contain valuable phytosociological information assisting both governmental and NGO (Non-governmental organizations) agencies to formulate strategies and on-ground plans to manage and protect nature resources. This paper provides an account on aims, current status and perspectives of building of a vegetation database for the Central Region (Najd) of Saudi Arabia - the founding element of the Saudi Vegetation Database (SVD). The data stored by the database are sample plots (vegetation relevés) collected according to the field techniques of the Braun-Blanquet approach (lists of taxa accompanied by semi-quantitative cover assessment), and are accompanied by general vegetation characteristics such as vegetation layering and cover, information on life-form of the recorded species, geographical coordinates, altitude, soil typology, topography and many more. More than 2900 vegetation-plot records (relevés) have so far been collected in the Najd region; of these more than 2000 have already been stored using the Turboveg database platform. These field records cover many habitats such as depressions, wadis (dry river beds), agricultural lands, sand dunes, sabkhas, and ruderal habitats. The ecological information collected in the database is currently the largest set of vegetation data collated into a database in the Middle East. These data are of great importance for biodiversity studies in Saudi Arabia, since the region is recording a loss of biodiversity at a fast rate due to environmental problems such as global warming and land-use changes. We envisage that this database would catalyze further data collection on vegetation of the entire Arabian Peninsula, and shall serve as one of the most important datasets for classification and mapping of the vegetation of the Kingdom of Saudi Arabia.}, } @article {pmid28146475, year = {2017}, author = {Cooney, CR and Bright, JA and Capp, EJR and Chira, AM and Hughes, EC and Moody, CJA and Nouri, LO and Varley, ZK and Thomas, GH}, title = {Mega-evolutionary dynamics of the adaptive radiation of birds.}, journal = {Nature}, volume = {542}, number = {7641}, pages = {344-347}, pmid = {28146475}, issn = {1476-4687}, support = {615709/ERC_/European Research Council/International ; }, mesh = {Animals ; Beak/*anatomy & histology ; *Biological Evolution ; Birds/*physiology ; Crowdsourcing ; Datasets as Topic ; Female ; Male ; Phenotype ; Phylogeny ; }, abstract = {The origin and expansion of biological diversity is regulated by both developmental trajectories and limits on available ecological niches. As lineages diversify, an early and often rapid phase of species and trait proliferation gives way to evolutionary slow-downs as new species pack into ever more densely occupied regions of ecological niche space. Small clades such as Darwin's finches demonstrate that natural selection is the driving force of adaptive radiations, but how microevolutionary processes scale up to shape the expansion of phenotypic diversity over much longer evolutionary timescales is unclear. Here we address this problem on a global scale by analysing a crowdsourced dataset of three-dimensional scanned bill morphology from more than 2,000 species. We find that bill diversity expanded early in extant avian evolutionary history, before transitioning to a phase dominated by packing of morphological space. However, this early phenotypic diversification is decoupled from temporal variation in evolutionary rate: rates of bill evolution vary among lineages but are comparatively stable through time. We find that rare, but major, discontinuities in phenotype emerge from rapid increases in rate along single branches, sometimes leading to depauperate clades with unusual bill morphologies. Despite these jumps between groups, the major axes of within-group bill-shape evolution are remarkably consistent across birds. We reveal that macroevolutionary processes underlying global-scale adaptive radiations support Darwinian and Simpsonian ideas of microevolution within adaptive zones and accelerated evolution between distinct adaptive peaks.}, } @article {pmid28143977, year = {2017}, author = {Hérivaux, A and Dugé de Bernonville, T and Roux, C and Clastre, M and Courdavault, V and Gastebois, A and Bouchara, JP and James, TY and Latgé, JP and Martin, F and Papon, N}, title = {The Identification of Phytohormone Receptor Homologs in Early Diverging Fungi Suggests a Role for Plant Sensing in Land Colonization by Fungi.}, journal = {mBio}, volume = {8}, number = {1}, pages = {}, pmid = {28143977}, issn = {2150-7511}, mesh = {Computational Biology ; *Evolution, Molecular ; Fungi/*genetics ; Histidine Kinase/*genetics ; Plant Growth Regulators/*metabolism ; Plants/*chemistry ; Receptors, Cell Surface/*genetics ; }, abstract = {Histidine kinases (HKs) are among the most prominent sensing proteins studied in the kingdom Fungi. Their distribution and biological functions in early diverging fungi (EDF), however, remain elusive. We have taken advantage of recent genomic resources to elucidate whether relationships between the occurrence of specific HKs in some EDF and their respective habitat/lifestyle could be established. This led to the unexpected discovery of fungal HKs that share a high degree of similarity with receptors for plant hormones (ethylene and cytokinin). Importantly, these phytohormone receptor homologs are found not only in EDF that behave as plant root symbionts or endophytes but also in EDF species that colonize decaying plant material. We hypothesize that these particular sensing proteins promoted the interaction of EDF with plants, leading to the conquest of land by these ancestral fungi.}, } @article {pmid28143409, year = {2017}, author = {Singh, R and Lawal, HM and Schilde, C and Glöckner, G and Barton, GJ and Schaap, P and Cole, C}, title = {Improved annotation with de novo transcriptome assembly in four social amoeba species.}, journal = {BMC genomics}, volume = {18}, number = {1}, pages = {120}, pmid = {28143409}, issn = {1471-2164}, support = {BB/K000799/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; 100293/Z/12/Z//Wellcome Trust/United Kingdom ; 098439/Z/12/Z//Wellcome Trust/United Kingdom ; }, mesh = {Amoeba/classification/*genetics ; Cloning, Molecular ; Computational Biology/methods ; *Gene Expression Profiling ; Genome ; Genomics/methods ; High-Throughput Nucleotide Sequencing ; *Molecular Sequence Annotation ; Reproducibility of Results ; *Transcriptome ; }, abstract = {BACKGROUND: Annotation of gene models and transcripts is a fundamental step in genome sequencing projects. Often this is performed with automated prediction pipelines, which can miss complex and atypical genes or transcripts. RNA sequencing (RNA-seq) data can aid the annotation with empirical data. Here we present de novo transcriptome assemblies generated from RNA-seq data in four Dictyostelid species: D. discoideum, P. pallidum, D. fasciculatum and D. lacteum. The assemblies were incorporated with existing gene models to determine corrections and improvement on a whole-genome scale. This is the first time this has been performed in these eukaryotic species.

RESULTS: An initial de novo transcriptome assembly was generated by Trinity for each species and then refined with Program to Assemble Spliced Alignments (PASA). The completeness and quality were assessed with the Benchmarking Universal Single-Copy Orthologs (BUSCO) and Transrate tools at each stage of the assemblies. The final datasets of 11,315-12,849 transcripts contained 5,610-7,712 updates and corrections to >50% of existing gene models including changes to hundreds or thousands of protein products. Putative novel genes are also identified and alternative splice isoforms were observed for the first time in P. pallidum, D. lacteum and D. fasciculatum.

CONCLUSIONS: In taking a whole transcriptome approach to genome annotation with empirical data we have been able to enrich the annotations of four existing genome sequencing projects. In doing so we have identified updates to the majority of the gene annotations across all four species under study and found putative novel genes and transcripts which could be worthy for follow-up. The new transcriptome data we present here will be a valuable resource for genome curators in the Dictyostelia and we propose this effective methodology for use in other genome annotation projects.}, } @article {pmid28143394, year = {2017}, author = {Wu, J and Zhao, HB and Yu, D and Xu, X}, title = {Transcriptome profiling of the floating-leaved aquatic plant Nymphoides peltata in response to flooding stress.}, journal = {BMC genomics}, volume = {18}, number = {1}, pages = {119}, pmid = {28143394}, issn = {1471-2164}, mesh = {Adaptation, Biological/genetics ; Computational Biology/methods ; Floods ; *Gene Expression Profiling ; *Gene Expression Regulation, Plant ; Gene Ontology ; High-Throughput Nucleotide Sequencing ; Molecular Sequence Annotation ; Plant Leaves/*genetics ; Reproducibility of Results ; Stress, Physiological/*genetics ; Tracheophyta/*genetics ; *Transcriptome ; }, abstract = {BACKGROUND: Waterlogging or flooding is one of the most challenging abiotic stresses experienced by plants. Unlike many flooding-tolerant plants, floating-leaved aquatic plants respond actively to flooding stress by fast growth and elongation of its petioles to make leaves re-floating. However, the molecular mechanisms of this plant group responding to flood have not been investigated before. Here, we investigated the genetic basis of this adaptive response by characterizing the petiole transcriptomes of a floating-leaved species Nymphoides peltata under normal and flooding conditions.

RESULTS: Clean reads under normal and flooding conditions with pooled sampling strategy were assembled into 124,302 unigenes. A total of 8883 unigenes were revealed to be differentially expressed between normal and flooding conditions. Among them, top ranked differentially expressed genes were mainly involved in antioxidant process, photosynthesis process and carbohydrate metabolism, including the glycolysis and a modified tricarboxylic acid cycle - alanine metabolism. Eight selected unigenes with significantly differentiated expression changes between normal and flooding conditions were validated by qRT-PCR.

CONCLUSIONS: Among these processes, antioxidant process and glycolysis are commonly induced by waterlogging or flooding environment in plants, whereas photosynthesis and alanine metabolism are rarely occurred in other flooding-tolerant plants, suggesting the significant contributions of the two processes in the active response of N. peltata to flooding stress. Our results provide a valuable genomic resource for future studies on N. peltata and deepen our understanding of the genetic basis underlying the response to flooding stress in aquatic plants.}, } @article {pmid28143393, year = {2017}, author = {Chen, CK and Yu, CP and Li, SC and Wu, SM and Lu, MJ and Chen, YH and Chen, DR and Ng, CS and Ting, CT and Li, WH}, title = {Identification and evolutionary analysis of long non-coding RNAs in zebra finch.}, journal = {BMC genomics}, volume = {18}, number = {1}, pages = {117}, pmid = {28143393}, issn = {1471-2164}, mesh = {Animals ; Cluster Analysis ; Computational Biology/methods ; *Evolution, Molecular ; Finches/*genetics ; Gene Expression Profiling ; Genomics/methods ; RNA, Long Noncoding/*genetics ; *Transcriptome ; }, abstract = {BACKGROUND: Long non-coding RNAs (lncRNAs) are important in various biological processes, but very few studies on lncRNA have been conducted in birds. To identify IncRNAs expressed during feather development, we analyzed single-stranded RNA-seq (ssRNA-seq) data from the anterior and posterior dorsal regions during zebra finch (Taeniopygia guttata) embryonic development. Using published transcriptomic data, we further analyzed the evolutionary conservation of IncRNAs in birds and amniotes.

RESULTS: A total of 1,081 lncRNAs, including 965 intergenic lncRNAs (lincRNAs), 59 intronic lncRNAs, and 57 antisense lncRNAs (lncNATs), were identified using our newly developed pipeline. These avian IncRNAs share similar characteristics with lncRNAs in mammals, such as shorter transcript length, lower exon number, lower average expression level and less sequence conservation than mRNAs. However, the proportion of lncRNAs overlapping with transposable elements in birds is much lower than that in mammals. We predicted the functions of IncRNAs based on the enriched functions of co-expressed protein-coding genes. Clusters of lncRNAs associated with natal down development were identified. The sequences and expression levels of candidate lncRNAs that shared conserved sequences among birds were validated by qPCR in both zebra finch and chicken. Finally, we identified three highly conserved lncRNAs that may be associated with natal down development.

CONCLUSIONS: Our study provides the first systematical identification of avian lncRNAs using ssRNA-seq analysis and offers a resource of embryonically expressed lncRNAs in zebra finch. We also predicted the biological function of identified lncRNAs.}, } @article {pmid28142011, year = {2017}, author = {Suzuki, E and Mitsuhashi, T and Tsuda, T and Yamamoto, E}, title = {A typology of four notions of confounding in epidemiology.}, journal = {Journal of epidemiology}, volume = {27}, number = {2}, pages = {49-55}, pmid = {28142011}, issn = {1349-9092}, mesh = {Bias ; Computer Graphics ; *Confounding Factors, Epidemiologic ; *Epidemiologic Methods ; Health Services Needs and Demand ; Humans ; }, abstract = {Confounding is a major concern in epidemiology. Despite its significance, the different notions of confounding have not been fully appreciated in the literature, leading to confusion of causal concepts in epidemiology. In this article, we aim to highlight the importance of differentiating between the subtly different notions of confounding from the perspective of counterfactual reasoning. By using a simple example, we illustrate the significance of considering the distribution of response types to distinguish causation from association, highlighting that confounding depends not only on the population chosen as the target of inference, but also on the notions of confounding in distribution and confounding in measure. This point has been relatively underappreciated, partly because some literature on the concept of confounding has only used the exposed and unexposed groups as the target populations, while it would be helpful to use the total population as the target population. Moreover, to clarify a further distinction between confounding "in expectation" and "realized" confounding, we illustrate the usefulness of examining the distribution of exposure status in the target population. To grasp the explicit distinction between confounding in expectation and realized confounding, we need to understand the mechanism that generates exposure events, not the product of that mechanism. Finally, we graphically illustrate this point, highlighting the usefulness of directed acyclic graphs in examining the presence of confounding in distribution, in the notion of confounding in expectation.}, } @article {pmid28132776, year = {2017}, author = {Maya-Manzano, JM and Sadyś, M and Tormo-Molina, R and Fernández-Rodríguez, S and Oteros, J and Silva-Palacios, I and Gonzalo-Garijo, A}, title = {Relationships between airborne pollen grains, wind direction and land cover using GIS and circular statistics.}, journal = {The Science of the total environment}, volume = {584-585}, number = {}, pages = {603-613}, doi = {10.1016/j.scitotenv.2017.01.085}, pmid = {28132776}, issn = {1879-1026}, mesh = {*Allergens ; Environmental Monitoring ; Geographic Information Systems ; *Pollen ; Seasons ; Spain ; *Wind ; }, abstract = {Airborne bio-aerosol content (mainly pollen and spores) depends on the surrounding vegetation and weather conditions, particularly wind direction. In order to understand this issue, maps of the main land cover in influence areas of 10km in radius surrounding pollen traps were created. Atmospheric content of the most abundant 14 pollen types was analysed in relation to the predominant wind directions measured in three localities of SW of Iberian Peninsula, from March 2011 to March 2014. Three Hirst type traps were used for aerobiological monitoring. The surface area for each land cover category was calculated and wind direction analysis was approached by using circular statistics. This method could be helpful for estimating the potential risk of exposure to various pollen types. Thus, the main land cover was different for each monitoring location, being irrigated crops, pastures and hardwood forests the main categories among 11 types described. Comparison of the pollen content with the predominant winds and land cover shows that the atmospheric pollen concentration is related to some source areas identified in the inventory. The study found that some pollen types (e.g. Plantago, Fraxinus-Phillyrea, Alnus) come from local sources but other pollen types (e.g. Quercus) are mostly coming from longer distances. As main conclusions, airborne particle concentrations can be effectively split by addressing wind with circular statistics. By combining circular statistics and GIS method with aerobiological data, we have created a useful tool for understanding pollen origin. Some pollen loads can be explained by immediate surrounding landscape and observed wind patterns for most of the time. However, other factors like medium or long-distance transport or even pollen trap location within a city, may occasionally affect the pollen load recorded using an air sampler.}, } @article {pmid28132643, year = {2017}, author = {Marra, NJ and Richards, VP and Early, A and Bogdanowicz, SM and Pavinski Bitar, PD and Stanhope, MJ and Shivji, MS}, title = {Comparative transcriptomics of elasmobranchs and teleosts highlight important processes in adaptive immunity and regional endothermy.}, journal = {BMC genomics}, volume = {18}, number = {1}, pages = {87}, pmid = {28132643}, issn = {1471-2164}, mesh = {Adaptive Immunity/*genetics ; Animals ; Computational Biology/methods ; Elasmobranchii/*genetics/*immunology ; Gene Expression Profiling/methods ; Gene Ontology ; Genome ; Genomics/methods ; Immunity ; Molecular Sequence Annotation ; Selection, Genetic ; *Transcriptome ; }, abstract = {BACKGROUND: Comparative genomic and/or transcriptomic analyses involving elasmobranchs remain limited, with genome level comparisons of the elasmobranch immune system to that of higher vertebrates, non-existent. This paper reports a comparative RNA-seq analysis of heart tissue from seven species, including four elasmobranchs and three teleosts, focusing on immunity, but concomitantly seeking to identify genetic similarities shared by the two lamnid sharks and the single billfish in our study, which could be linked to convergent evolution of regional endothermy.

RESULTS: Across seven species, we identified an average of 10,877 Swiss-Prot annotated genes from an average of 32,474 open reading frames within each species' heart transcriptome. About half of these genes were shared between all species while the remainder included functional differences between our groups of interest (elasmobranch vs. teleost and endotherms vs. ectotherms) as revealed by Gene Ontology (GO) and selection analyses. A repeatedly represented functional category, in both the uniquely expressed elasmobranch genes (total of 259) and the elasmobranch GO enrichment results, involved antibody-mediated immunity, either in the recruitment of immune cells (Fc receptors) or in antigen presentation, including such terms as "antigen processing and presentation of exogenous peptide antigen via MHC class II", and such genes as MHC class II, HLA-DPB1. Molecular adaptation analyses identified three genes in elasmobranchs with a history of positive selection, including legumain (LGMN), a gene with roles in both innate and adaptive immunity including producing antigens for presentation by MHC class II. Comparisons between the endothermic and ectothermic species revealed an enrichment of GO terms associated with cardiac muscle contraction in endotherms, with 19 genes expressed solely in endotherms, several of which have significant roles in lipid and fat metabolism.

CONCLUSIONS: This collective comparative evidence provides the first multi-taxa transcriptomic-based perspective on differences between elasmobranchs and teleosts, and suggests various unique features associated with the adaptive immune system of elasmobranchs, pointing in particular to the potential importance of MHC Class II. This in turn suggests that expanded comparative work involving additional tissues, as well as genome sequencing of multiple elasmobranch species would be productive in elucidating the regulatory and genome architectural hallmarks of elasmobranchs.}, } @article {pmid28129330, year = {2017}, author = {Prigent, S and Frioux, C and Dittami, SM and Thiele, S and Larhlimi, A and Collet, G and Gutknecht, F and Got, J and Eveillard, D and Bourdon, J and Plewniak, F and Tonon, T and Siegel, A}, title = {Meneco, a Topology-Based Gap-Filling Tool Applicable to Degraded Genome-Wide Metabolic Networks.}, journal = {PLoS computational biology}, volume = {13}, number = {1}, pages = {e1005276}, pmid = {28129330}, issn = {1553-7358}, mesh = {Algorithms ; Databases, Genetic ; Escherichia coli/genetics/metabolism ; Genome/genetics ; Genomics/*methods ; Metabolic Networks and Pathways/*genetics ; Metabolome/*genetics ; *Software ; Transcriptome/*genetics ; }, abstract = {Increasing amounts of sequence data are becoming available for a wide range of non-model organisms. Investigating and modelling the metabolic behaviour of those organisms is highly relevant to understand their biology and ecology. As sequences are often incomplete and poorly annotated, draft networks of their metabolism largely suffer from incompleteness. Appropriate gap-filling methods to identify and add missing reactions are therefore required to address this issue. However, current tools rely on phenotypic or taxonomic information, or are very sensitive to the stoichiometric balance of metabolic reactions, especially concerning the co-factors. This type of information is often not available or at least prone to errors for newly-explored organisms. Here we introduce Meneco, a tool dedicated to the topological gap-filling of genome-scale draft metabolic networks. Meneco reformulates gap-filling as a qualitative combinatorial optimization problem, omitting constraints raised by the stoichiometry of a metabolic network considered in other methods, and solves this problem using Answer Set Programming. Run on several artificial test sets gathering 10,800 degraded Escherichia coli networks Meneco was able to efficiently identify essential reactions missing in networks at high degradation rates, outperforming the stoichiometry-based tools in scalability. To demonstrate the utility of Meneco we applied it to two case studies. Its application to recent metabolic networks reconstructed for the brown algal model Ectocarpus siliculosus and an associated bacterium Candidatus Phaeomarinobacter ectocarpi revealed several candidate metabolic pathways for algal-bacterial interactions. Then Meneco was used to reconstruct, from transcriptomic and metabolomic data, the first metabolic network for the microalga Euglena mutabilis. These two case studies show that Meneco is a versatile tool to complete draft genome-scale metabolic networks produced from heterogeneous data, and to suggest relevant reactions that explain the metabolic capacity of a biological system.}, } @article {pmid28127901, year = {2017}, author = {Mouden, S and Sarmiento, KF and Klinkhamer, PG and Leiss, KA}, title = {Integrated pest management in western flower thrips: past, present and future.}, journal = {Pest management science}, volume = {73}, number = {5}, pages = {813-822}, pmid = {28127901}, issn = {1526-4998}, mesh = {Animals ; Behavior, Animal/drug effects ; Computational Biology ; Insect Control/*methods ; Mechanical Phenomena ; Pest Control, Biological ; *Thysanoptera/genetics/metabolism ; }, abstract = {Western flower thrips (WFT) is one of the most economically important pest insects of many crops worldwide. Recent EU legislation has caused a dramatic shift in pest management strategies, pushing for tactics that are less reliable on chemicals. The development of alternative strategies is therefore an issue of increasing urgency. This paper reviews the main control tactics in integrated pest management (IPM) of WFT, with the focus on biological control and host plant resistance as areas of major progress. Knowledge gaps are identified and innovative approaches emphasised, highlighting the advances in 'omics' technologies. Successful programmes are most likely generated when preventive and therapeutic strategies with mutually beneficial, cost-effective and environmentally sound foundations are incorporated. © 2017 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.}, } @article {pmid28126703, year = {2017}, author = {Berrouiguet, S and Barrigón, ML and Brandt, SA and Nitzburg, GC and Ovejero, S and Alvarez-Garcia, R and Carballo, J and Walter, M and Billot, R and Lenca, P and Delgado-Gomez, D and Ropars, J and de la Calle Gonzalez, I and Courtet, P and Baca-García, E}, title = {Ecological Assessment of Clinicians' Antipsychotic Prescription Habits in Psychiatric Inpatients: A Novel Web- and Mobile Phone-Based Prototype for a Dynamic Clinical Decision Support System.}, journal = {Journal of medical Internet research}, volume = {19}, number = {1}, pages = {e25}, pmid = {28126703}, issn = {1438-8871}, mesh = {Adolescent ; Adult ; Aged ; Antipsychotic Agents/*therapeutic use ; *Cell Phone ; *Decision Support Systems, Clinical ; Drug Prescriptions ; *Electronic Prescribing ; Feasibility Studies ; Female ; Humans ; Inpatients ; *Internet ; Male ; Middle Aged ; Pilot Projects ; Practice Patterns, Physicians' ; Psychotic Disorders/*drug therapy ; Young Adult ; }, abstract = {BACKGROUND: Electronic prescribing devices with clinical decision support systems (CDSSs) hold the potential to significantly improve pharmacological treatment management.

OBJECTIVE: The aim of our study was to develop a novel Web- and mobile phone-based application to provide a dynamic CDSS by monitoring and analyzing practitioners' antipsychotic prescription habits and simultaneously linking these data to inpatients' symptom changes.

METHODS: We recruited 353 psychiatric inpatients whose symptom levels and prescribed medications were inputted into the MEmind application. We standardized all medications in the MEmind database using the Anatomical Therapeutic Chemical (ATC) classification system and the defined daily dose (DDD). For each patient, MEmind calculated an average for the daily dose prescribed for antipsychotics (using the N05A ATC code), prescribed daily dose (PDD), and the PDD to DDD ratio.

RESULTS: MEmind results found that antipsychotics were used by 61.5% (217/353) of inpatients, with the largest proportion being patients with schizophrenia spectrum disorders (33.4%, 118/353). Of the 217 patients, 137 (63.2%, 137/217) were administered pharmacological monotherapy and 80 (36.8%, 80/217) were administered polytherapy. Antipsychotics were used mostly in schizophrenia spectrum and related psychotic disorders, but they were also prescribed in other nonpsychotic diagnoses. Notably, we observed polypharmacy going against current antipsychotics guidelines.

CONCLUSIONS: MEmind data indicated that antipsychotic polypharmacy and off-label use in inpatient units is commonly practiced. MEmind holds the potential to create a dynamic CDSS that provides real-time tracking of prescription practices and symptom change. Such feedback can help practitioners determine a maximally therapeutic drug treatment while avoiding unproductive overprescription and off-label use.}, } @article {pmid28123115, year = {2017}, author = {Sanderson, MJ and Nicolae, M and McMahon, MM}, title = {Homology-Aware Phylogenomics at Gigabase Scales.}, journal = {Systematic biology}, volume = {66}, number = {4}, pages = {590-603}, pmid = {28123115}, issn = {1076-836X}, mesh = {Classification/*methods ; Gene Transfer, Horizontal/genetics ; *Genomics ; Oryza/classification/genetics ; *Phylogeny ; }, abstract = {Obstacles to inferring species trees from whole genome data sets range from algorithmic and data management challenges to the wholesale discordance in evolutionary history found in different parts of a genome. Recent work that builds trees directly from genomes by parsing them into sets of small $k$-mer strings holds promise to streamline and simplify these efforts, but existing approaches do not account well for gene tree discordance. We describe a "seed and extend" protocol that finds nearly exact matching sets of orthologous $k$-mers and extends them to construct data sets that can properly account for genomic heterogeneity. Exploiting an efficient suffix array data structure, sets of whole genomes can be parsed and converted into phylogenetic data matrices rapidly, with contiguous blocks of $k$-mers from the same chromosome, gene, or scaffold concatenated as needed. Phylogenetic trees constructed from highly curated rice genome data and a diverse set of six other eukaryotic whole genome, transcriptome, and organellar genome data sets recovered trees nearly identical to published phylogenomic analyses, in a small fraction of the time, and requiring many fewer parameter choices. Our method's ability to retain local homology information was demonstrated by using it to characterize gene tree discordance across the rice genome, and by its robustness to the high rate of interchromosomal gene transfer found in several rice species.}, } @article {pmid28122988, year = {2017}, author = {Kaliniene, L and Šimoliūnas, E and Truncaitė, L and Zajančkauskaitė, A and Nainys, J and Kaupinis, A and Valius, M and Meškys, R}, title = {Molecular Analysis of Arthrobacter Myovirus vB_ArtM-ArV1: We Blame It on the Tail.}, journal = {Journal of virology}, volume = {91}, number = {8}, pages = {}, pmid = {28122988}, issn = {1098-5514}, mesh = {Arthrobacter/*virology ; Bacteriophages/*genetics/*isolation & purification/ultrastructure ; Base Composition ; Computational Biology ; DNA, Viral/chemistry/genetics ; Gene Order ; Genome, Viral ; Microscopy, Electron, Transmission ; Myoviridae/*genetics/*isolation & purification/ultrastructure ; Open Reading Frames ; Phylogeny ; Sequence Analysis, DNA ; *Soil Microbiology ; Viral Tail Proteins/genetics ; Virion/ultrastructure ; }, abstract = {This is the first report on a myophage that infects Arthrobacter A novel virus, vB_ArtM-ArV1 (ArV1), was isolated from soil using Arthrobacter sp. strain 68b for phage propagation. Transmission electron microscopy showed its resemblance to members of the family Myoviridae: ArV1 has an isometric head (∼74 nm in diameter) and a contractile, nonflexible tail (∼192 nm). Phylogenetic and comparative sequence analyses, however, revealed that ArV1 has more genes in common with phages from the family Siphoviridae than it does with any myovirus characterized to date. The genome of ArV1 is a linear, circularly permuted, double-stranded DNA molecule (71,200 bp) with a GC content of 61.6%. The genome includes 101 open reading frames (ORFs) yet contains no tRNA genes. More than 50% of ArV1 genes encode unique proteins that either have no reliable identity to database entries or have homologues only in Arthrobacter phages, both sipho- and myoviruses. Using bioinformatics approaches, 13 ArV1 structural genes were identified, including those coding for head, tail, tail fiber, and baseplate proteins. A further 6 ArV1 ORFs were annotated as encoding putative structural proteins based on the results of proteomic analysis. Phylogenetic analysis based on the alignment of four conserved virion proteins revealed that Arthrobacter myophages form a discrete clade that seems to occupy a position somewhat intermediate between myo- and siphoviruses. Thus, the data presented here will help to advance our understanding of genetic diversity and evolution of phages that constitute the order CaudoviralesIMPORTANCE Bacteriophages, which likely originated in the early Precambrian Era, represent the most numerous population on the planet. Approximately 95% of known phages are tailed viruses that comprise three families: Podoviridae (with short tails), Siphoviridae (with long noncontractile tails), and Myoviridae (with contractile tails). Based on the current hypothesis, myophages, which may have evolved from siphophages, are thought to have first emerged among Gram-negative bacteria, whereas they emerged only later among Gram-positive bacteria. The results of the molecular characterization of myophage vB_ArtM-ArV1 presented here conform to the aforementioned hypothesis, since, at a glance, bacteriophage vB_ArtM-ArV1 appears to be a siphovirus that possesses a seemingly functional contractile tail. Our work demonstrates that such "chimeric" myophages are of cosmopolitan nature and are likely characteristic of the ecologically important soil bacterial genus Arthrobacter.}, } @article {pmid28122127, year = {2017}, author = {Klimešová, J and Danihelka, J and Chrtek, J and de Bello, F and Herben, T}, title = {CLO-PLA: a database of clonal and bud-bank traits of the Central European flora.}, journal = {Ecology}, volume = {98}, number = {4}, pages = {1179}, doi = {10.1002/ecy.1745}, pmid = {28122127}, issn = {0012-9658}, mesh = {*Databases, Genetic ; Ecology ; Ecosystem ; Europe ; Phylogeny ; Plants/classification/*genetics ; }, abstract = {This dataset presents comprehensive and easy-to-use information on 29 functional traits of clonal growth, bud banks, and lifespan of members of the Central European flora. The source data were compiled from a number of published sources (see the reference file) and the authors' own observations or studies. In total, 2,909 species are included (2,745 herbs and 164 woody species), out of which 1,532 (i.e., 52.7% of total) are classified as possessing clonal growth organs (1,480, i.e., 53.9%, if woody plants are excluded). This provides a unique, and largely unexplored, set of traits of clonal growth that can be used in studies on comparative plant ecology, plant evolution, community assembly, and ecosystem functioning across the large flora of Central Europe. It can be directly imported into a number of programs and packages that perform trait-based and phylogenetic analyses aimed to answer a variety of open and pressing ecological questions.}, } @article {pmid28118393, year = {2017}, author = {Mahardja, B and Farruggia, MJ and Schreier, B and Sommer, T}, title = {Evidence of a Shift in the Littoral Fish Community of the Sacramento-San Joaquin Delta.}, journal = {PloS one}, volume = {12}, number = {1}, pages = {e0170683}, pmid = {28118393}, issn = {1932-6203}, mesh = {Animals ; Biodiversity ; Biomass ; *Biota ; California ; Datasets as Topic ; Ecological Parameter Monitoring ; *Ecosystem ; *Estuaries ; *Fishes ; Food Chain ; Introduced Species ; Population Dynamics ; Time Factors ; Zooplankton ; }, abstract = {Many estuarine and freshwater ecosystems worldwide have undergone substantial changes due to multiple anthropogenic stressors. Over the past two decades, the Sacramento-San Joaquin Delta (Delta) in California, USA, saw a severe decline in pelagic fishes, a shift in zooplankton community composition, and a rapid expansion of invasive aquatic vegetation. To evaluate whether major changes have also occurred in the littoral fish community, we analyzed a beach seine survey dataset collected from 1995 to 2015 from 26 sites within the Delta. We examined changes in the Delta fish community at three different ecological scales (species, community, and biomass), using clustering analyses, trend tests, and change-point analyses. We found that the annual catch per effort for many introduced species and some native species have increased since 1995, while few experienced a decline. We also observed a steady pattern of change over time in annual fish community composition, driven primarily by a steady increase in non-native Centrarchid species. Lastly, we found that littoral fish biomass has essentially doubled over the 21-year study period, with Mississippi Silverside Menidia audens and fishes in the Centrarchidae family driving most of this increase. The changes in the catch per effort, fish community composition, and biomass per volume indicate that a shift has occurred in the Delta littoral fish community and that the same factors affecting the Delta's pelagic food web may have been a key driver of change.}, } @article {pmid28115381, year = {2017}, author = {Zhang, X and Liu, X and Liang, Y and Guo, X and Xiao, Y and Ma, L and Miao, B and Liu, H and Peng, D and Huang, W and Zhang, Y and Yin, H}, title = {Adaptive Evolution of Extreme Acidophile Sulfobacillus thermosulfidooxidans Potentially Driven by Horizontal Gene Transfer and Gene Loss.}, journal = {Applied and environmental microbiology}, volume = {83}, number = {7}, pages = {}, pmid = {28115381}, issn = {1098-5336}, mesh = {Clostridiales/*genetics ; Computational Biology ; *Evolution, Molecular ; *Gene Deletion ; *Gene Transfer, Horizontal ; *Genetic Variation ; Genome, Bacterial ; Genomics ; Metabolic Networks and Pathways ; Models, Genetic ; Phylogeny ; Stress, Physiological ; }, abstract = {Recent phylogenomic analysis has suggested that three strains isolated from different copper mine tailings around the world were taxonomically affiliated with Sulfobacillusthermosulfidooxidans Here, we present a detailed investigation of their genomic features, particularly with respect to metabolic potentials and stress tolerance mechanisms. Comprehensive analysis of the Sulfobacillus genomes identified a core set of essential genes with specialized biological functions in the survival of acidophiles in their habitats, despite differences in their metabolic pathways. The Sulfobacillus strains also showed evidence for stress management, thereby enabling them to efficiently respond to harsh environments. Further analysis of metabolic profiles provided novel insights into the presence of genomic streamlining, highlighting the importance of gene loss as a main mechanism that potentially contributes to cellular economization. Another important evolutionary force, especially in larger genomes, is gene acquisition via horizontal gene transfer (HGT), which might play a crucial role in the recruitment of novel functionalities. Also, a successful integration of genes acquired from archaeal donors appears to be an effective way of enhancing the adaptive capacity to cope with environmental changes. Taken together, the findings of this study significantly expand the spectrum of HGT and genome reduction in shaping the evolutionary history of Sulfobacillus strains.IMPORTANCE Horizontal gene transfer (HGT) and gene loss are recognized as major driving forces that contribute to the adaptive evolution of microbial genomes, although their relative importance remains elusive. The findings of this study suggest that highly frequent gene turnovers within microorganisms via HGT were necessary to incur additional novel functionalities to increase the capacity of acidophiles to adapt to changing environments. Evidence also reveals a fascinating phenomenon of potential cross-kingdom HGT. Furthermore, genome streamlining may be a critical force in driving the evolution of microbial genomes. Taken together, this study provides insights into the importance of both HGT and gene loss in the evolution and diversification of bacterial genomes.}, } @article {pmid28112432, year = {2017}, author = {Van Regenmortel, T and Nys, C and Janssen, CR and Lofts, S and De Schamphelaere, KAC}, title = {Comparison of four methods for bioavailability-based risk assessment of mixtures of Cu, Zn, and Ni in freshwater.}, journal = {Environmental toxicology and chemistry}, volume = {36}, number = {8}, pages = {2123-2138}, doi = {10.1002/etc.3746}, pmid = {28112432}, issn = {1552-8618}, mesh = {Aquatic Organisms/drug effects ; Biological Availability ; Copper/chemistry/*toxicity ; Databases, Factual ; Dose-Response Relationship, Drug ; Environmental Monitoring/*methods/statistics & numerical data ; Fresh Water/*chemistry ; Models, Theoretical ; Nickel/chemistry/*toxicity ; Risk Assessment ; Rivers/chemistry ; Species Specificity ; Water Pollutants, Chemical/chemistry/*toxicity ; Zinc/chemistry/*toxicity ; }, abstract = {Although chemical risk assessment is still mainly conducted on a substance-by-substance basis, organisms in the environment are typically exposed to mixtures of substances. Risk assessment procedures should therefore be adapted to fit these situations. Four mixture risk assessment methodologies were compared for risk estimations of mixtures of copper (Cu), zinc (Zn), and nickel (Ni). The results showed that use of the log-normal species sensitivity distribution (SSD) instead of the best-fit distribution and sampling species sensitivities independently for each metal instead of using interspecies correlations in metal sensitivity had little impact on risk estimates. Across 4 different monitoring datasets, between 0% and 52% of the target water samples were estimated to be at risk, but only between 0% and 15% of the target water samples were at risk because of the mixture of metals and not any single metal individually. When a natural baseline database was examined, it was estimated that 10% of the target water samples were at risk because of single metals or their mixtures; when the most conservative method was used (concentration addition [CA] applied directly to the SSD, i.e., CASSD). However, the issue of metal mixture risk at geochemical baseline concentrations became relatively small (2% of target water samples) when a theoretically more correct method was used (CA applied to individual dose response curves, i.e., CADRC). Finally, across the 4 monitoring datasets, the following order of conservatism for the 4 methods was shown (from most to least conservative, with ranges of median margin of safety [MoS] relative to CASSD): CASSD > CADRC (MoS = 1.17-1.25) > IADRC (independent action (IA) applied to individual dose-response curves; MoS = 1.38-1.60) > IASSD (MoS = 1.48-1.72). Therefore, it is suggested that these 4 methods can be used in a general tiered scheme for the risk assessment of metal mixtures in a regulatory context. In this scheme, the CASSD method could serve as a first (conservative) tier to identify situations with likely no potential risk at all, regardless of the method used (the sum toxic unit expressed relative to the 5% hazardous concentration [SumTUHC5 ] < 1) and the IASSD method to identify situations of potential risk, also regardless of the method used (the multisubstance potentially affected fraction of species using the IASSD method [msPAFIA,SSD ] > 0.05). The CADRC and IADRC methods could be used for site-specific assessment for situations that fall in between (SumTUHC5 > 1 and msPAFIA,SSD < 0.05). Environ Toxicol Chem 2017;36:2123-2138. © 2017 SETAC.}, } @article {pmid28111366, year = {2017}, author = {Chao, YT and Yen, SH and Yeh, JH and Chen, WC and Shih, MC}, title = {Orchidstra 2.0-A Transcriptomics Resource for the Orchid Family.}, journal = {Plant & cell physiology}, volume = {58}, number = {1}, pages = {e9}, doi = {10.1093/pcp/pcw220}, pmid = {28111366}, issn = {1471-9053}, mesh = {Computational Biology/methods ; *Databases, Genetic ; *Gene Expression Regulation, Developmental ; *Gene Expression Regulation, Plant ; Gene Ontology ; Internet ; Orchidaceae/classification/genetics ; Plant Proteins/genetics ; Reproducibility of Results ; Sequence Analysis, RNA ; Species Specificity ; Transcriptome/*genetics ; }, abstract = {Orchidaceae, the orchid family, encompasses more than 25,000 species and five subfamilies. Due to their beautiful and exotic flowers, distinct biological and ecological features, orchids have aroused wide interest among both researchers and the general public. We constructed the Orchidstra database, a resource for orchid transcriptome assembly and gene annotations. The Orchistra database has been under active development since 2013. To accommodate the increasing amount of orchid transcriptome data and house more comprehensive information, Orchidstra 2.0 has been built with a new database system to store the annotations of 510,947 protein-coding genes and 161,826 noncoding transcripts, covering 18 orchid species belonging to 12 genera in five subfamilies of Orchidaceae. We have improved the N50 size of protein-coding genes, provided new functional annotations (including protein-coding gene annotations, protein domain/family information, pathways analysis, Gene Ontology term assignments, orthologous genes across orchid species, cross-links to the database of model species, and miRNA information), and improved the user interface with better website performance. We also provide new database functionalities for database searching and sequence retrieval. Moreover, the Orchidstra 2.0 database incorporates detailed RNA-Seq gene expression data from various tissues and developmental stages in different orchid species. The database will be useful for gene prediction and gene family studies, and for exploring gene expression in orchid species. The Orchidstra 2.0 database is freely accessible at http://orchidstra2.abrc.sinica.edu.tw.}, } @article {pmid28111203, year = {2017}, author = {Manor, O and Borenstein, E}, title = {Systematic Characterization and Analysis of the Taxonomic Drivers of Functional Shifts in the Human Microbiome.}, journal = {Cell host & microbe}, volume = {21}, number = {2}, pages = {254-267}, pmid = {28111203}, issn = {1934-6069}, support = {DP2 AT007802/AT/NCCIH NIH HHS/United States ; }, mesh = {Actinobacteria/classification ; Bacteroides/classification ; Communicable Diseases/microbiology ; *Computational Biology ; Databases, Genetic ; Diabetes Mellitus, Type 2/microbiology ; Firmicutes/classification ; Genome, Microbial ; Humans ; Metagenomics ; *Microbiota ; Phylogeny ; Proteobacteria/classification ; *Software ; }, abstract = {Comparative analyses of the human microbiome have identified both taxonomic and functional shifts that are associated with numerous diseases. To date, however, microbiome taxonomy and function have mostly been studied independently and the taxonomic drivers of functional imbalances have not been systematically identified. Here, we present FishTaco, an analytical and computational framework that integrates taxonomic and functional comparative analyses to accurately quantify taxon-level contributions to disease-associated functional shifts. Applying FishTaco to several large-scale metagenomic cohorts, we show that shifts in the microbiome's functional capacity can be traced back to specific taxa. Furthermore, the set of taxa driving functional shifts and their contribution levels vary markedly between functions. We additionally find that similar functional imbalances in different diseases are driven by both disease-specific and shared taxa. Such integrated analysis of microbiome ecological and functional dynamics can inform future microbiome-based therapy, pinpointing putative intervention targets for manipulating the microbiome's functional capacity.}, } @article {pmid28107341, year = {2017}, author = {Rodriguez-Brenes, IA and Hofacre, A and Fan, H and Wodarz, D}, title = {Complex Dynamics of Virus Spread from Low Infection Multiplicities: Implications for the Spread of Oncolytic Viruses.}, journal = {PLoS computational biology}, volume = {13}, number = {1}, pages = {e1005241}, pmid = {28107341}, issn = {1553-7358}, support = {U01 CA187956/CA/NCI NIH HHS/United States ; }, mesh = {Computational Biology ; HEK293 Cells ; Host-Pathogen Interactions/*physiology ; Humans ; *Models, Biological ; Oncolytic Viruses/*chemistry/metabolism/*pathogenicity ; Virus Replication/*physiology ; }, abstract = {While virus growth dynamics have been well-characterized in several infections, data are typically collected once the virus population becomes easily detectable. Earlier dynamics, however, remain less understood. We recently reported unusual early dynamics in an experimental system using adenovirus infection of human embryonic kidney (293) cells. Under identical experimental conditions, inoculation at low infection multiplicities resulted in either robust spread, or in limited spread that eventually stalled, with both outcomes occurring with approximately equal frequencies. The reasons underlying these observations have not been understood. Here, we present further experimental data showing that inhibition of interferon-induced antiviral states in cells results in a significant increase in the percentage of robust infections that are observed, implicating a race between virus replication and the spread of the anti-viral state as a central mechanism. Analysis of a variety of computational models, however, reveals that this alone cannot explain the simultaneous occurrence of both viral growth outcomes under identical conditions, and that additional biological mechanisms have to be invoked to explain the data. One such mechanism is the ability of the virus to overcome the antiviral state through multiple infection of cells. If this is included in the model, two outcomes of viral spread are found to be simultaneously stable, depending on initial conditions. In stochastic versions of such models, the system can go by chance to either state from identical initial conditions, with the relative frequency of the outcomes depending on the strength of the interferon-based anti-viral response, consistent with the experiments. This demonstrates considerable complexity during the early phase of the infection that can influence the ability of a virus to become successfully established. Implications for the initial dynamics of oncolytic virus spread through tumors are discussed.}, } @article {pmid28105701, year = {2017}, author = {Hotaling, S and Finn, DS and Joseph Giersch, J and Weisrock, DW and Jacobsen, D}, title = {Climate change and alpine stream biology: progress, challenges, and opportunities for the future.}, journal = {Biological reviews of the Cambridge Philosophical Society}, volume = {92}, number = {4}, pages = {2024-2045}, doi = {10.1111/brv.12319}, pmid = {28105701}, issn = {1469-185X}, mesh = {*Altitude ; Animals ; *Biodiversity ; *Climate Change ; Databases, Factual ; Genomics ; *Rivers ; }, abstract = {In alpine regions worldwide, climate change is dramatically altering ecosystems and affecting biodiversity in many ways. For streams, receding alpine glaciers and snowfields, paired with altered precipitation regimes, are driving shifts in hydrology, species distributions, basal resources, and threatening the very existence of some habitats and biota. Alpine streams harbour substantial species and genetic diversity due to significant habitat insularity and environmental heterogeneity. Climate change is expected to affect alpine stream biodiversity across many levels of biological resolution from micro- to macroscopic organisms and genes to communities. Herein, we describe the current state of alpine stream biology from an organism-focused perspective. We begin by reviewing seven standard and emerging approaches that combine to form the current state of the discipline. We follow with a call for increased synthesis across existing approaches to improve understanding of how these imperiled ecosystems are responding to rapid environmental change. We then take a forward-looking viewpoint on how alpine stream biologists can make better use of existing data sets through temporal comparisons, integrate remote sensing and geographic information system (GIS) technologies, and apply genomic tools to refine knowledge of underlying evolutionary processes. We conclude with comments about the future of biodiversity conservation in alpine streams to confront the daunting challenge of mitigating the effects of rapid environmental change in these sentinel ecosystems.}, } @article {pmid28101707, year = {2017}, author = {Liu, X and Shi, J and Bo, T and Meng, Y and Zhan, X and Zhang, M and Zhang, Y}, title = {Distributions and ecological risk assessment of estrogens and bisphenol A in an arid and semiarid area in northwest China.}, journal = {Environmental science and pollution research international}, volume = {24}, number = {8}, pages = {7216-7225}, pmid = {28101707}, issn = {1614-7499}, mesh = {Benzhydryl Compounds/*analysis ; China ; *Environmental Monitoring ; Estrogens/*analysis ; Geologic Sediments/*chemistry ; Phenols/*analysis ; Rivers/*chemistry ; Water Pollutants, Chemical/*analysis ; }, abstract = {Free estrogens (estrone, E1; 17β-estradiol, 17β-E2; estriol, E3; and 17α-ethinylestradiol, EE2), their corresponding sulfate and glucuronide conjugates, and bisphenol A (BPA) were investigated in water and sediments in the Fen River catchment, an arid and semiarid area in northwest China. E1 and BPA were frequently detected in the wet and dry sampling seasons. In addition to the sulfate conjugates, other conjugated estrogens were not detected in water and sediments. The concentrations of these compounds in water generally increased from upstream to downstream. The concentrations in water samples of most sites were higher in the wet season than those in the dry season, but concentrations in sediments of most sites were higher in the dry season than those in the wet season. The distributions of these compounds in sediments were positively correlated with the total organic carbon (TOC) contents of sediments (0.3 < R [2] < 0.6, p < 0.01) and concentrations in water (0.25 < R [2] < 0.50, p < 0.01). In this catchment, E1 was the main contributor to endocrine disrupting risk. The surface water in most of the tributaries and the sewage in the drainage channels were at risk. The pore waters of sediments were at risk at most sampling sites.}, } @article {pmid28100185, year = {2017}, author = {Tørresen, OK and Star, B and Jentoft, S and Reinar, WB and Grove, H and Miller, JR and Walenz, BP and Knight, J and Ekholm, JM and Peluso, P and Edvardsen, RB and Tooming-Klunderud, A and Skage, M and Lien, S and Jakobsen, KS and Nederbragt, AJ}, title = {An improved genome assembly uncovers prolific tandem repeats in Atlantic cod.}, journal = {BMC genomics}, volume = {18}, number = {1}, pages = {95}, pmid = {28100185}, issn = {1471-2164}, mesh = {Animals ; Gadus morhua/*genetics ; Genomics/*methods ; Heterozygote ; Molecular Sequence Annotation ; Promoter Regions, Genetic ; Sequence Analysis, DNA ; Tandem Repeat Sequences/*genetics ; }, abstract = {BACKGROUND: The first Atlantic cod (Gadus morhua) genome assembly published in 2011 was one of the early genome assemblies exclusively based on high-throughput 454 pyrosequencing. Since then, rapid advances in sequencing technologies have led to a multitude of assemblies generated for complex genomes, although many of these are of a fragmented nature with a significant fraction of bases in gaps. The development of long-read sequencing and improved software now enable the generation of more contiguous genome assemblies.

RESULTS: By combining data from Illumina, 454 and the longer PacBio sequencing technologies, as well as integrating the results of multiple assembly programs, we have created a substantially improved version of the Atlantic cod genome assembly. The sequence contiguity of this assembly is increased fifty-fold and the proportion of gap-bases has been reduced fifteen-fold. Compared to other vertebrates, the assembly contains an unusual high density of tandem repeats (TRs). Indeed, retrospective analyses reveal that gaps in the first genome assembly were largely associated with these TRs. We show that 21% of the TRs across the assembly, 19% in the promoter regions and 12% in the coding sequences are heterozygous in the sequenced individual.

CONCLUSIONS: The inclusion of PacBio reads combined with the use of multiple assembly programs drastically improved the Atlantic cod genome assembly by successfully resolving long TRs. The high frequency of heterozygous TRs within or in the vicinity of genes in the genome indicate a considerable standing genomic variation in Atlantic cod populations, which is likely of evolutionary importance.}, } @article {pmid28097055, year = {2017}, author = {Beisser, D and Graupner, N and Bock, C and Wodniok, S and Grossmann, L and Vos, M and Sures, B and Rahmann, S and Boenigk, J}, title = {Comprehensive transcriptome analysis provides new insights into nutritional strategies and phylogenetic relationships of chrysophytes.}, journal = {PeerJ}, volume = {5}, number = {}, pages = {e2832}, pmid = {28097055}, issn = {2167-8359}, abstract = {BACKGROUND: Chrysophytes are protist model species in ecology and ecophysiology and important grazers of bacteria-sized microorganisms and primary producers. However, they have not yet been investigated in detail at the molecular level, and no genomic and only little transcriptomic information is available. Chrysophytes exhibit different trophic modes: while phototrophic chrysophytes perform only photosynthesis, mixotrophs can gain carbon from bacterial food as well as from photosynthesis, and heterotrophs solely feed on bacteria-sized microorganisms. Recent phylogenies and megasystematics demonstrate an immense complexity of eukaryotic diversity with numerous transitions between phototrophic and heterotrophic organisms. The question we aim to answer is how the diverse nutritional strategies, accompanied or brought about by a reduction of the plasmid and size reduction in heterotrophic strains, affect physiology and molecular processes.

RESULTS: We sequenced the mRNA of 18 chrysophyte strains on the Illumina HiSeq platform and analysed the transcriptomes to determine relations between the trophic mode (mixotrophic vs. heterotrophic) and gene expression. We observed an enrichment of genes for photosynthesis, porphyrin and chlorophyll metabolism for phototrophic and mixotrophic strains that can perform photosynthesis. Genes involved in nutrient absorption, environmental information processing and various transporters (e.g., monosaccharide, peptide, lipid transporters) were present or highly expressed only in heterotrophic strains that have to sense, digest and absorb bacterial food. We furthermore present a transcriptome-based alignment-free phylogeny construction approach using transcripts assembled from short reads to determine the evolutionary relationships between the strains and the possible influence of nutritional strategies on the reconstructed phylogeny. We discuss the resulting phylogenies in comparison to those from established approaches based on ribosomal RNA and orthologous genes. Finally, we make functionally annotated reference transcriptomes of each strain available to the community, significantly enhancing publicly available data on Chrysophyceae.

CONCLUSIONS: Our study is the first comprehensive transcriptomic characterisation of a diverse set of Chrysophyceaen strains. In addition, we showcase the possibility of inferring phylogenies from assembled transcriptomes using an alignment-free approach. The raw and functionally annotated data we provide will prove beneficial for further examination of the diversity within this taxon. Our molecular characterisation of different trophic modes presents a first such example.}, } @article {pmid28095883, year = {2017}, author = {Gleeson, J and Lederman, R and Herrman, H and Koval, P and Eleftheriadis, D and Bendall, S and Cotton, SM and Alvarez-Jimenez, M}, title = {Moderated online social therapy for carers of young people recovering from first-episode psychosis: study protocol for a randomised controlled trial.}, journal = {Trials}, volume = {18}, number = {1}, pages = {27}, pmid = {28095883}, issn = {1745-6215}, mesh = {Adaptation, Psychological ; Adolescent ; Adult ; Caregivers/*psychology ; Clinical Protocols ; Female ; Humans ; *Internet ; Male ; Mental Health ; Patient Education as Topic ; *Peer Group ; Psychotherapy, Group/*methods ; Psychotic Disorders/diagnosis/psychology/*therapy ; Remission Induction ; Research Design ; Single-Blind Method ; *Social Support ; Stress, Psychological/diagnosis/etiology/psychology/*therapy ; Therapy, Computer-Assisted/*methods ; Time Factors ; Treatment Outcome ; Young Adult ; }, abstract = {BACKGROUND: First-episode psychosis most often has its onset during late adolescence. In caring for the young person, families endure high levels of stress and depression. Meanwhile, the social networks of families often erode. Our group has previously shown that family cognitive behaviour therapy (CBT) leads to significantly improved perceived stress compared with specialist first-episode treatment as usual; however, there are well-known barriers to the dissemination of effective family interventions. To address this, we have developed a novel online intervention entitled 'Altitudes' that fully integrates purpose-built online social networking, expert and peer moderation, and evidence-based psychoeducation within a single application. The primary aim of this trial is to evaluate the effectiveness of Altitudes in reducing stress in carers over a 6-month period.

METHODS/DESIGN: We describe here a single-blinded cluster randomised controlled trial (cRCT) with permutated blocks. The clusters comprise individual families. The two treatment conditions include Altitudes plus Specialist Treatment as Usual (STAU) and STAU alone. Altitudes involves participation in our novel online programme whereas STAU comprises specialist family work at the Early Psychosis Prevention and Intervention Centre (EPPIC), Melbourne, Australia. We aim to recruit 160 family members of young, 15-27 year-old, patients registered for treatment for first-episode psychosis (FEP) at EPPIC. The design includes two assessment time points, namely, baseline and 6-month follow-up. The study is due for completion within 2 years including an 18-month recruitment period and a 6-month treatment phase. The primary outcome is carers' perceived stress at 6 months. Secondary outcome measures include a biomarker of stress, depressive symptoms, worry, substance use, loneliness, social support, satisfaction with life, and a range of measures that tap into coping resources. We seek to gain a dynamic picture of carer stress through our Smartphone Ecological Momentary Assessment (SEMA) tool.

DISCUSSION: This is the first randomised controlled trial designed to evaluate an online intervention for carers of young people recovering from FEP. It has the potential to produce evidence in support of a highly novel, accessible, and cost-effective intervention to reduce stress in carers who are providing support to young people at a critical phase in their recovery from psychosis.

TRIAL REGISTRATION: Australian New Zealand Clinical Trial Registry, identifier: ACTRN12616000968471 . Retrospectively registered on 22 July 2016.}, } @article {pmid28095778, year = {2017}, author = {Bosi, E and Fondi, M and Orlandini, V and Perrin, E and Maida, I and de Pascale, D and Tutino, ML and Parrilli, E and Lo Giudice, A and Filloux, A and Fani, R}, title = {The pangenome of (Antarctic) Pseudoalteromonas bacteria: evolutionary and functional insights.}, journal = {BMC genomics}, volume = {18}, number = {1}, pages = {93}, pmid = {28095778}, issn = {1471-2164}, support = {MR/J006874/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Antarctic Regions ; Anti-Bacterial Agents/metabolism ; Bacterial Proteins/genetics/metabolism ; Cold Temperature ; Databases, Genetic ; *Evolution, Molecular ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Membrane Transport Proteins/genetics/metabolism ; Phylogeny ; Pseudoalteromonas/classification/*genetics ; Secondary Metabolism/genetics ; }, abstract = {BACKGROUND: Pseudoalteromonas is a genus of ubiquitous marine bacteria used as model organisms to study the biological mechanisms involved in the adaptation to cold conditions. A remarkable feature shared by these bacteria is their ability to produce secondary metabolites with a strong antimicrobial and antitumor activity. Despite their biotechnological relevance, representatives of this genus are still lacking (with few exceptions) an extensive genomic characterization, including features involved in the evolution of secondary metabolites production. Indeed, biotechnological applications would greatly benefit from such analysis.

RESULTS: Here, we analyzed the genomes of 38 strains belonging to different Pseudoalteromonas species and isolated from diverse ecological niches, including extreme ones (i.e. Antarctica). These sequences were used to reconstruct the largest Pseudoalteromonas pangenome computed so far, including also the two main groups of Pseudoalteromonas strains (pigmented and not pigmented strains). The downstream analyses were conducted to describe the genomic diversity, both at genus and group levels. This allowed highlighting a remarkable genomic heterogeneity, even for closely related strains. We drafted all the main evolutionary steps that led to the current structure and gene content of Pseudoalteromonas representatives. These, most likely, included an extensive genome reduction and a strong contribution of Horizontal Gene Transfer (HGT), which affected biotechnologically relevant gene sets and occurred in a strain-specific fashion. Furthermore, this study also identified the genomic determinants related to some of the most interesting features of the Pseudoalteromonas representatives, such as the production of secondary metabolites, the adaptation to cold temperatures and the resistance to abiotic compounds.

CONCLUSIONS: This study poses the bases for a comprehensive understanding of the evolutionary trajectories followed in time by this peculiar bacterial genus and for a focused exploitation of their biotechnological potential.}, } @article {pmid28094805, year = {2017}, author = {Byrne, SL and Erthmann, PØ and Agerbirk, N and Bak, S and Hauser, TP and Nagy, I and Paina, C and Asp, T}, title = {The genome sequence of Barbarea vulgaris facilitates the study of ecological biochemistry.}, journal = {Scientific reports}, volume = {7}, number = {}, pages = {40728}, pmid = {28094805}, issn = {2045-2322}, mesh = {Barbarea/chemistry/classification/*genetics/metabolism ; Computational Biology/methods ; Disease Resistance/genetics ; Genetic Variation ; *Genome, Plant ; *Genomics/methods ; Glucosinolates/metabolism ; Metabolome ; Metabolomics/methods ; Molecular Sequence Annotation ; Phylogeny ; Plant Proteins/genetics/metabolism ; Quantitative Trait Loci ; Quantitative Trait, Heritable ; Whole Genome Sequencing ; }, abstract = {The genus Barbarea has emerged as a model for evolution and ecology of plant defense compounds, due to its unusual glucosinolate profile and production of saponins, unique to the Brassicaceae. One species, B. vulgaris, includes two 'types', G-type and P-type that differ in trichome density, and their glucosinolate and saponin profiles. A key difference is the stereochemistry of hydroxylation of their common phenethylglucosinolate backbone, leading to epimeric glucobarbarins. Here we report a draft genome sequence of the G-type, and re-sequencing of the P-type for comparison. This enables us to identify candidate genes underlying glucosinolate diversity, trichome density, and study the genetics of biochemical variation for glucosinolate and saponins. B. vulgaris is resistant to the diamondback moth, and may be exploited for "dead-end" trap cropping where glucosinolates stimulate oviposition and saponins deter larvae to the extent that they die. The B. vulgaris genome will promote the study of mechanisms in ecological biochemistry to benefit crop resistance breeding.}, } @article {pmid28090215, year = {2016}, author = {Jäntschi, L and Bálint, D and Bolboacă, SD}, title = {Multiple Linear Regressions by Maximizing the Likelihood under Assumption of Generalized Gauss-Laplace Distribution of the Error.}, journal = {Computational and mathematical methods in medicine}, volume = {2016}, number = {}, pages = {8578156}, pmid = {28090215}, issn = {1748-6718}, mesh = {Algorithms ; Computer Simulation ; *Data Interpretation, Statistical ; Databases, Factual ; Ecology/methods ; Hormones/chemistry ; *Likelihood Functions ; *Linear Models ; Models, Chemical ; Models, Statistical ; Organic Chemicals/chemistry ; Regression Analysis ; Reproducibility of Results ; }, abstract = {Multiple linear regression analysis is widely used to link an outcome with predictors for better understanding of the behaviour of the outcome of interest. Usually, under the assumption that the errors follow a normal distribution, the coefficients of the model are estimated by minimizing the sum of squared deviations. A new approach based on maximum likelihood estimation is proposed for finding the coefficients on linear models with two predictors without any constrictive assumptions on the distribution of the errors. The algorithm was developed, implemented, and tested as proof-of-concept using fourteen sets of compounds by investigating the link between activity/property (as outcome) and structural feature information incorporated by molecular descriptors (as predictors). The results on real data demonstrated that in all investigated cases the power of the error is significantly different by the convenient value of two when the Gauss-Laplace distribution was used to relax the constrictive assumption of the normal distribution of the error. Therefore, the Gauss-Laplace distribution of the error could not be rejected while the hypothesis that the power of the error from Gauss-Laplace distribution is normal distributed also failed to be rejected.}, } @article {pmid28088402, year = {2017}, author = {Wang, N and Hosner, PA and Liang, B and Braun, EL and Kimball, RT}, title = {Historical relationships of three enigmatic phasianid genera (Aves: Galliformes) inferred using phylogenomic and mitogenomic data.}, journal = {Molecular phylogenetics and evolution}, volume = {109}, number = {}, pages = {217-225}, doi = {10.1016/j.ympev.2017.01.006}, pmid = {28088402}, issn = {1095-9513}, mesh = {Animals ; Base Sequence ; Cell Nucleus/genetics ; DNA, Mitochondrial/genetics ; *Databases, Genetic ; Galliformes/*classification/*genetics ; *Genome, Mitochondrial ; *Genomics ; *Phylogeny ; Species Specificity ; }, abstract = {The phylogeny of the Phasianidae (pheasants, partridges, and allies) has been studied extensively. However, these studies have largely ignored three enigmatic genera because of scarce DNA source material and limited overlapping phylogenetic data: blood pheasants (Ithaginis), snow partridges (Lerwa), and long-billed partridges (Rhizothera). Thus, phylogenetic positions of these three genera remain uncertain in what is otherwise a well-resolved phylogeny. Previous studies using different data types place Lerwa and Ithaginis in similar positions, but the absence of overlapping data means the relationship between them could not be inferred. Rhizothera was originally described in the genus Perdix (true partridges), although a partial cytochrome b (CYB) sequence suggests it is sister to Pucrasia (koklass pheasant). To identify robust relationships among Ithaginis, Lerwa, Rhizothera, and their phasianid relatives, we used 3692 ultra-conserved element (UCE) loci and complete mitogenomes from 19 species including previously hypothesized relatives of the three focal genera and representatives from all major phasianid clades. We used DNA extracted from historical specimen toepads for species that lacked fresh tissue in museum collections. Maximum likelihood and multispecies coalescent UCE analyses strongly supported Lerwa sister to a large clade which included Ithaginis at its base, and also including turkey, grouse, typical pheasants, tragopans, Pucrasia, and Perdix. Rhizothera was also in this clade, sister to a diverse group comprising Perdix, typical pheasants, Pucrasia, turkey and grouse. Mitogenomic genealogies differed from UCEs topologies, supporting a sister relationship between Ithaginis and Lerwa rather than a grade. The position of Rhizothera using mitogenomes depended on analytical choices. Unpartitioned and codon-based analyses placed Rhizothera sister to a tragopan clade, whereas a partitioned DNA model of the mitogenome was congruent with UCE results. In all mitogenome analyses, Pucrasia was sister to a clade including Perdix and the typical pheasants with high support, in contrast to UCEs and published nuclear intron data. Due to the strong support and consistent topology provided by all UCE analyses, we have identified phylogenetic relationships of these three enigmatic, poorly-studied, phasianid taxa.}, } @article {pmid28087779, year = {2017}, author = {Graves, JL and Hertweck, KL and Phillips, MA and Han, MV and Cabral, LG and Barter, TT and Greer, LF and Burke, MK and Mueller, LD and Rose, MR}, title = {Genomics of Parallel Experimental Evolution in Drosophila.}, journal = {Molecular biology and evolution}, volume = {34}, number = {4}, pages = {831-842}, pmid = {28087779}, issn = {1537-1719}, mesh = {Adaptation, Physiological/*genetics ; Alleles ; Animals ; Biological Evolution ; Databases, Nucleic Acid ; Drosophila/genetics ; Drosophila melanogaster/genetics ; Evolution, Molecular ; Gene Frequency/genetics ; Genetic Fitness/genetics ; Genetic Variation/genetics ; Genomics/*methods ; Linkage Disequilibrium/genetics ; Models, Animal ; Models, Genetic ; Polymorphism, Single Nucleotide/genetics ; Selection, Genetic/*genetics ; }, abstract = {What are the genomic foundations of adaptation in sexual populations? We address this question using fitness-character and whole-genome sequence data from 30 Drosophila laboratory populations. These 30 populations are part of a nearly 40-year laboratory radiation featuring 3 selection regimes, each shared by 10 populations for up to 837 generations, with moderately large effective population sizes. Each of 3 sets of the 10 populations that shared a selection regime consists of 5 populations that have long been maintained under that selection regime, paired with 5 populations that had only recently been subjected to that selection regime. We find a high degree of evolutionary parallelism in fitness phenotypes when most-recent selection regimes are shared, as in previous studies from our laboratory. We also find genomic parallelism with respect to the frequencies of single-nucleotide polymorphisms, transposable elements, insertions, and structural variants, which was expected. Entirely unexpected was a high degree of parallelism for linkage disequilibrium. The evolutionary genetic changes among these sexual populations are rapid and genomically extensive. This pattern may be due to segregating functional genetic variation that is abundantly maintained genome-wide by selection, variation that responds immediately to changes of selection regime.}, } @article {pmid28086860, year = {2017}, author = {Brockmöller, T and Ling, Z and Li, D and Gaquerel, E and Baldwin, IT and Xu, S}, title = {Nicotiana attenuata Data Hub (NaDH): an integrative platform for exploring genomic, transcriptomic and metabolomic data in wild tobacco.}, journal = {BMC genomics}, volume = {18}, number = {1}, pages = {79}, pmid = {28086860}, issn = {1471-2164}, mesh = {Computational Biology/*methods ; *Databases, Genetic ; Gene Expression Profiling ; Gene Expression Regulation ; Genomics/*methods ; *Metabolome ; Metabolomics/*methods ; Phylogeny ; Nicotiana/classification/*genetics/*metabolism ; *Transcriptome ; }, abstract = {BACKGROUND: Nicotiana attenuata (coyote tobacco) is an ecological model for studying plant-environment interactions and plant gene function under real-world conditions. During the last decade, large amounts of genomic, transcriptomic and metabolomic data have been generated with this plant which has provided new insights into how native plants interact with herbivores, pollinators and microbes. However, an integrative and open access platform that allows for the efficient mining of these -omics data remained unavailable until now.

DESCRIPTION: We present the Nicotiana attenuata Data Hub (NaDH) as a centralized platform for integrating and visualizing genomic, phylogenomic, transcriptomic and metabolomic data in N. attenuata. The NaDH currently hosts collections of predicted protein coding sequences of 11 plant species, including two recently sequenced Nicotiana species, and their functional annotations, 222 microarray datasets from 10 different experiments, a transcriptomic atlas based on 20 RNA-seq expression profiles and a metabolomic atlas based on 895 metabolite spectra analyzed by mass spectrometry. We implemented several visualization tools, including a modified version of the Electronic Fluorescent Pictograph (eFP) browser, co-expression networks and the Interactive Tree Of Life (iTOL) for studying gene expression divergence among duplicated homologous. In addition, the NaDH allows researchers to query phylogenetic trees of 16,305 gene families and provides tools for analyzing their evolutionary history. Furthermore, we also implemented tools to identify co-expressed genes and metabolites, which can be used for predicting the functions of genes. Using the transcription factor NaMYB8 as an example, we illustrate that the tools and data in NaDH can facilitate identification of candidate genes involved in the biosynthesis of specialized metabolites.

CONCLUSION: The NaDH provides interactive visualization and data analysis tools that integrate the expression and evolutionary history of genes in Nicotiana, which can facilitate rapid gene discovery and comparative genomic analysis. Because N. attenuata shares many genome-wide features with other Nicotiana species including cultivated tobacco, and hence NaDH can be a resource for exploring the function and evolution of genes in Nicotiana species in general. The NaDH can be accessed at: http://nadh.ice.mpg.de/ .}, } @article {pmid28079128, year = {2017}, author = {Jing, G and Sun, Z and Wang, H and Gong, Y and Huang, S and Ning, K and Xu, J and Su, X}, title = {Parallel-META 3: Comprehensive taxonomical and functional analysis platform for efficient comparison of microbial communities.}, journal = {Scientific reports}, volume = {7}, number = {}, pages = {40371}, pmid = {28079128}, issn = {2045-2322}, support = {R34 AA021502/AA/NIAAA NIH HHS/United States ; }, mesh = {Adult ; Base Sequence ; Biodiversity ; Biomarkers/metabolism ; Child ; Computer Simulation ; Databases, Genetic ; Humans ; *Metagenome ; Metagenomics ; Microbiota/*genetics ; RNA, Ribosomal, 16S/genetics ; Time Factors ; }, abstract = {The number of metagenomes is increasing rapidly. However, current methods for metagenomic analysis are limited by their capability for in-depth data mining among a large number of microbiome each of which carries a complex community structure. Moreover, the complexity of configuring and operating computational pipeline also hinders efficient data processing for the end users. In this work we introduce Parallel-META 3, a comprehensive and fully automatic computational toolkit for rapid data mining among metagenomic datasets, with advanced features including 16S rRNA extraction for shotgun sequences, 16S rRNA copy number calibration, 16S rRNA based functional prediction, diversity statistics, bio-marker selection, interaction network construction, vector-graph-based visualization and parallel computing. Application of Parallel-META 3 on 5,337 samples with 1,117,555,208 sequences from diverse studies and platforms showed it could produce similar results as QIIME and PICRUSt with much faster speed and lower memory usage, which demonstrates its ability to unravel the taxonomical and functional dynamics patterns across large datasets and elucidate ecological links between microbiome and the environment. Parallel-META 3 is implemented in C/C++ and R, and integrated into an executive package for rapid installation and easy access under Linux and Mac OS X. Both binary and source code packages are available at http://bioinfo.single-cell.cn/parallel-meta.html.}, } @article {pmid28076687, year = {2017}, author = {Paidipati, CP and Brawner, B and Eiraldi, R and Deatrick, JA}, title = {Parent and Family Processes Related to ADHD Management in Ethnically Diverse Youth.}, journal = {Journal of the American Psychiatric Nurses Association}, volume = {23}, number = {2}, pages = {90-112}, pmid = {28076687}, issn = {1532-5725}, support = {T32 NR007100/NR/NINR NIH HHS/United States ; }, mesh = {Adolescent ; Attention Deficit Disorder with Hyperactivity/*diagnosis/*therapy ; Databases, Factual ; *Ethnicity ; Family ; Female ; *Healthcare Disparities ; Humans ; Male ; *Parents ; *Racial Groups ; United States ; }, abstract = {BACKGROUND: Previous research has shown major disparities in attention deficit hyperactivity disorder (ADHD) for diverse youth across America. We do not fully understand, however, how parent and family processes are related to the identification, care-seeking approaches, treatment preferences, and engagement with care systems and services for youth with ADHD.

OBJECTIVES: The present study aimed to explore parent and family processes related to the management of ADHD in racially and ethnically diverse youth.

DESIGN: This integrative review was structured with the methodology proposed by Whittemore and Knafl.

RESULTS: Three major electronic databases yielded a final sample of 32 articles (24 quantitative, 6 qualitative, and 2 mixed methods). Nine themes emerged within three overarching meta-themes.

CONCLUSIONS: Understanding the unique perspectives of families from diverse backgrounds is essential for clinicians, researchers, and policymakers, who are dedicated to understanding racial and ethnic perspectives and developing ecologically appropriate and family-based interventions for youth with ADHD.}, } @article {pmid28075417, year = {2017}, author = {Soares Teles, A and Rocha, A and José da Silva E Silva, F and Correia Lopes, J and O'Sullivan, D and Van de Ven, P and Endler, M}, title = {Enriching Mental Health Mobile Assessment and Intervention with Situation Awareness.}, journal = {Sensors (Basel, Switzerland)}, volume = {17}, number = {1}, pages = {}, pmid = {28075417}, issn = {1424-8220}, mesh = {Awareness ; Humans ; Mental Disorders ; *Mental Health ; Mobile Applications ; }, abstract = {Current mobile devices allow the execution of sophisticated applications with the capacity for identifying the user situation, which can be helpful in treatments of mental disorders. In this paper, we present SituMan, a solution that provides situation awareness to MoodBuster, an ecological momentary assessment and intervention mobile application used to request self-assessments from patients in depression treatments. SituMan has a fuzzy inference engine to identify patient situations using context data gathered from the sensors embedded in mobile devices. Situations are specified jointly by the patient and mental health professional, and they can represent the patient's daily routine (e.g., "studying", "at work", "working out"). MoodBuster requests mental status self-assessments from patients at adequate moments using situation awareness. In addition, SituMan saves and displays patient situations in a summary, delivering them for consultation by mental health professionals. A first experimental evaluation was performed to assess the user satisfaction with the approaches to define and identify situations. This experiment showed that SituMan was well evaluated in both criteria. A second experiment was performed to assess the accuracy of the fuzzy engine to infer situations. Results from the second experiment showed that the fuzzy inference engine has a good accuracy to identify situations.}, } @article {pmid28075219, year = {2017}, author = {Poncet, F and Swaine, B and Dutil, E and Chevignard, M and Pradat-Diehl, P}, title = {How do assessments of activities of daily living address executive functions: A scoping review.}, journal = {Neuropsychological rehabilitation}, volume = {27}, number = {5}, pages = {618-666}, doi = {10.1080/09602011.2016.1268171}, pmid = {28075219}, issn = {1464-0694}, mesh = {Activities of Daily Living/*psychology ; *Brain Injuries/complications/diagnosis/psychology ; Cognition Disorders/diagnosis/*etiology ; Databases, Bibliographic/statistics & numerical data ; Executive Function/*physiology ; Humans ; Neuropsychological Tests ; }, abstract = {UNLABELLED: Executive functions (EF) allow persons to adapt to situations arising in daily life and can be affected following acquired brain injury (ABI). Measuring the impact of EF impairments on the accomplishment of activities of daily living (ADL) requires specific assessment tools, but choosing the right tool may be difficult.

PURPOSE: To conduct a scoping review on how assessments of ADL address EF and EF impairments in persons with ABI.

METHOD: A scoping review of literature (peer-reviewed and grey literature) published until August 2014 was conducted. Using a systematic procedure, literature was selected, results were charted, and tools were analysed with respect to their goals, underlying models, psychometric properties and applicability. The analysis also included how tools considered components of EF according to Lezak's model.

RESULTS: 12 tools, developed either to assess EF in ADL, independence in ADL considering EF or ADL capacities, were identified and analysed according to multiple criteria.

CONCLUSIONS: This review provides important information about existing tools to assist in tool selection and clinical decision-making related to ABI and EF.}, } @article {pmid28073087, year = {2017}, author = {Degen, B and Blanc-Jolivet, C and Stierand, K and Gillet, E}, title = {A nearest neighbour approach by genetic distance to the assignment of individual trees to geographic origin.}, journal = {Forensic science international. Genetics}, volume = {27}, number = {}, pages = {132-141}, doi = {10.1016/j.fsigen.2016.12.011}, pmid = {28073087}, issn = {1878-0326}, mesh = {Cluster Analysis ; Computational Biology/*methods ; Conservation of Natural Resources ; Genotype ; Likelihood Functions ; Meliaceae/genetics ; *Polymorphism, Single Nucleotide ; Trees/*genetics ; }, abstract = {During the past decade, the use of DNA for forensic applications has been extensively implemented for plant and animal species, as well as in humans. Tracing back the geographical origin of an individual usually requires genetic assignment analysis. These approaches are based on reference samples that are grouped into populations or other aggregates and intend to identify the most likely group of origin. Often this grouping does not have a biological but rather a historical or political justification, such as "country of origin". In this paper, we present a new nearest neighbour approach to individual assignment or classification within a given but potentially imperfect grouping of reference samples. This method, which is based on the genetic distance between individuals, functions better in many cases than commonly used methods. We demonstrate the operation of our assignment method using two data sets. One set is simulated for a large number of trees distributed in a 120km by 120km landscape with individual genotypes at 150 SNPs, and the other set comprises experimental data of 1221 individuals of the African tropical tree species Entandrophragma cylindricum (Sapelli) genotyped at 61 SNPs. Judging by the level of correct self-assignment, our approach outperformed the commonly used frequency and Bayesian approaches by 15% for the simulated data set and by 5-7% for the Sapelli data set. Our new approach is less sensitive to overlapping sources of genetic differentiation, such as genetic differences among closely-related species, phylogeographic lineages and isolation by distance, and thus operates better even for suboptimal grouping of individuals.}, } @article {pmid28070515, year = {2016}, author = {Voronina, OL and Kunda, MS and Ryzhova, NN and Aksenova, EI and Semenov, AN and Romanova, YM and Gintsburg, AL}, title = {Burkholderia contaminans Biofilm Regulating Operon and Its Distribution in Bacterial Genomes.}, journal = {BioMed research international}, volume = {2016}, number = {}, pages = {6560534}, pmid = {28070515}, issn = {2314-6141}, mesh = {Achromobacter ; *Biofilms ; Burkholderia Infections/microbiology ; Burkholderia cepacia complex/*genetics/*metabolism ; Computational Biology ; Cystic Fibrosis/complications/microbiology ; DNA, Ribosomal/genetics ; Gene Expression Regulation, Bacterial ; Gene Transfer Techniques ; Genome ; *Genome, Bacterial ; Histidine Kinase/genetics ; Humans ; Lung Diseases/*microbiology ; Mutagenesis ; *Operon ; Phylogeny ; Sequence Analysis, DNA ; Signal Transduction ; Transcription, Genetic ; }, abstract = {Biofilm formation by Burkholderia spp. is a principal cause of lung chronic infections in cystic fibrosis patients. A "lacking biofilm production" (LBP) strain B. contaminans GIMC4587:Bct370-19 has been obtained by insertion modification of clinical strain with plasposon mutagenesis. It has an interrupted transcriptional response regulator (RR) gene. The focus of our investigation was a two-component signal transduction system determination, including this RR. B. contaminans clinical and LBP strains were analyzed by whole genome sequencing and bioinformatics resources. A four-component operon (BiofilmReg) has a key role in biofilm formation. The relative location (i.e., by being separated by another gene) of RR and histidine kinase genes is unique in BiofilmReg. Orthologs were found in other members of the Burkholderiales order. Phylogenetic analysis of strains containing BiofilmReg operons demonstrated evidence for earlier inheritance of a three-component operon. During further evolution one lineage acquired a fourth gene, whereas others lost the third component of the operon. Mutations in sensor domains have created biodiversity which is advantageous for adaptation to various ecological niches. Different species Burkholderia and Achromobacter strains all demonstrated similar BiofilmReg operon structure. Therefore, there may be an opportunity to develop a common drug which is effective for treating all these causative agents.}, } @article {pmid28070210, year = {2016}, author = {Fang, J and Liu, H and Liu, H and Zhang, L and Liu, J}, title = {Localized Patch-Based Fuzzy Active Contours for Image Segmentation.}, journal = {Computational and mathematical methods in medicine}, volume = {2016}, number = {}, pages = {1064692}, pmid = {28070210}, issn = {1748-6718}, mesh = {Algorithms ; Computer Simulation ; Diagnostic Imaging/*methods ; Fuzzy Logic ; Humans ; Image Interpretation, Computer-Assisted/*methods ; Image Processing, Computer-Assisted/*methods ; Models, Statistical ; Pattern Recognition, Automated/*methods ; Reproducibility of Results ; }, abstract = {This paper presents a novel fuzzy region-based active contour model for image segmentation. By incorporating local patch-energy functional along each pixel of the evolving curve into the fuzziness of the energy, we construct a patch-based energy function without the regurgitation term. Its purpose is not only to make the active contour evolve very stably without the periodical initialization during the evolution but also to reduce the effect of noise. In particular, in order to reject local minimal of the energy functional, we utilize a direct method to calculate the energy alterations instead of solving the Euler-Lagrange equation of the underlying problem. Compared with other fuzzy active contour models, experimental results on synthetic and real images show the advantages of the proposed method in terms of computational efficiency and accuracy.}, } @article {pmid28068355, year = {2017}, author = {Li, Y and Wang, J and Lin, F and Yang, Y and Chen, SS}, title = {A Methodology for Cancer Therapeutics by Systems Pharmacology-Based Analysis: A Case Study on Breast Cancer-Related Traditional Chinese Medicines.}, journal = {PloS one}, volume = {12}, number = {1}, pages = {e0169363}, pmid = {28068355}, issn = {1932-6203}, mesh = {Algorithms ; *Antineoplastic Agents/pharmacology/therapeutic use ; Biological Availability ; *Breast Neoplasms/drug therapy ; Databases, Factual ; *Drugs, Chinese Herbal/pharmacology/therapeutic use ; Humans ; *Medicine, Chinese Traditional ; *Models, Biological ; Reproducibility of Results ; }, abstract = {Breast cancer is the most common carcinoma in women. Comprehensive therapy on breast cancer including surgical operation, chemotherapy, radiotherapy, endocrinotherapy, etc. could help, but still has serious side effect and resistance against anticancer drugs. Complementary and alternative medicine (CAM) may avoid these problems, in which traditional Chinese medicine (TCM) has been highlighted. In this section, to analyze the mechanism through which TCM act on breast cancer, we have built a virtual model consisting of the construction of database, oral bioavailability prediction, drug-likeness evaluation, target prediction, network construction. The 20 commonly employed herbs for the treatment of breast cancer were used as a database to carry out research. As a result, 150 ingredient compounds were screened out as active molecules for the herbs, with 33 target proteins predicted. Our analysis indicates that these herbs 1) takes a 'Jun-Chen-Zuo-Shi" as rule of prescription, 2) which function mainly through perturbing three pathways involving the epidermal growth factor receptor, estrogen receptor, and inflammatory pathways, to 3) display the breast cancer-related anti-estrogen, anti-inflammatory, regulation of cell metabolism and proliferation activities. To sum it up, by providing a novel in silico strategy for investigation of the botanical drugs, this work may be of some help for understanding the action mechanisms of herbal medicines and for discovery of new drugs from plants.}, } @article {pmid28068284, year = {2016}, author = {Harizanova, SN and Mateva, NG and Tarnovska, TC}, title = {Adaptation and Validation of a Burnout Inventory in a Survey of the Staff of a Correctional Institution in Bulgaria.}, journal = {Folia medica}, volume = {58}, number = {4}, pages = {282-288}, doi = {10.1515/folmed-2016-0038}, pmid = {28068284}, issn = {0204-8043}, mesh = {Adult ; Bulgaria ; Burnout, Professional/*diagnosis ; Humans ; Male ; Pilot Projects ; Police/*psychology ; *Prisons ; Reproducibility of Results ; Severity of Illness Index ; Surveys and Questionnaires ; }, abstract = {BACKGROUND: Burnout syndrome is a phenomenon that seems to be studied globally in relation to all types of populations. The staff in the system of correctional institutions in Bulgaria, however, is oddly left out of this tendency. There is no standardized model in Bulgaria that can be used to detect possible susceptibility to professional burnout. The methods available at present only register the irreversible changes that have already set in the functioning of the individual. V. Boyko's method for burnout assessment allows clinicians to use individual approach to patients and affords easy comparability of results with data from other psychodiagnostic instruments. Adaptation of the assessment instruments to fit the specificities of a study population (linguistic, ethno-cultural, etc.) is obligatory so that the instrument could be correctly used and yield valid results. Validation is one of the most frequently used technique to achieve this.

AIM: The aim of the present study was to adapt and validate V. Boyko's burnout inventory for diagnosing burnout and assessment of the severity of the burnout syndrome in correctional officers.

MATERIALS AND METHODS: We conducted a pilot study with 50 officers working in the Plovdiv Regional Correction Facility by test-retest survey performed at an interval of 2 to 4 months. All participants completed the adapted questionnaire translated into Bulgarian voluntarily and anonymously. Statistical analysis was performed using SPSS v.17.

RESULTS: We found a mild-to-strong statistically significant correlation (P<0.01) across all subscales between the most frequently used questionnaire for assessing the burnout syndrome, the Maslach Burnout Inventory, and the tool we propose here. The high Cronbach's α coefficient (α=0.94) and Spearman-Brown coefficient (rsb=0.86), and the low mean between-item correlation (r=0.30) demonstrated the instrument's good reliability and validity.

CONCLUSION: With the validation herein presented we offer a highly reliable Bulgarian variant of Boyko's method for burnout assessment and research.}, } @article {pmid28067598, year = {2017}, author = {Coray, DS and Wheeler, NE and Heinemann, JA and Gardner, PP}, title = {Why so narrow: Distribution of anti-sense regulated, type I toxin-antitoxin systems compared with type II and type III systems.}, journal = {RNA biology}, volume = {14}, number = {3}, pages = {275-280}, pmid = {28067598}, issn = {1555-8584}, mesh = {Antitoxins/*genetics ; Bacterial Toxins/*genetics ; Databases, Genetic ; *Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal ; Interspersed Repetitive Sequences ; Multigene Family ; Operon ; Phylogeny ; RNA, Antisense/*genetics ; }, abstract = {Toxin-antitoxin (TA) systems are gene modules that appear to be horizontally mobile across a wide range of prokaryotes. It has been proposed that type I TA systems, with an antisense RNA-antitoxin, are less mobile than other TAs that rely on direct toxin-antitoxin binding but no direct comparisons have been made. We searched for type I, II and III toxin families using iterative searches with profile hidden Markov models across phyla and replicons. The distribution of type I toxin families were comparatively narrow, but these patterns weakened with recently discovered families. We discuss how the function and phenotypes of TA systems as well as biases in our search methods may account for differences in their distribution.}, } @article {pmid28065496, year = {2017}, author = {Moore, RC and Kaufmann, CN and Rooney, AS and Moore, DJ and Eyler, LT and Granholm, E and Woods, SP and Swendsen, J and Heaton, RK and Scott, JC and Depp, CA}, title = {Feasibility and Acceptability of Ecological Momentary Assessment of Daily Functioning Among Older Adults with HIV.}, journal = {The American journal of geriatric psychiatry : official journal of the American Association for Geriatric Psychiatry}, volume = {25}, number = {8}, pages = {829-840}, pmid = {28065496}, issn = {1545-7214}, support = {T32 MH019934/MH/NIMH NIH HHS/United States ; K23 MH107260/MH/NIMH NIH HHS/United States ; L30 MH104725/MH/NIMH NIH HHS/United States ; IK2 CX000772/CX/CSRD VA/United States ; P30 MH062512/MH/NIMH NIH HHS/United States ; }, mesh = {*Activities of Daily Living/psychology ; Aged ; Aging/physiology/psychology ; *Ecological Momentary Assessment ; Feasibility Studies ; Female ; *HIV Infections/physiopathology/psychology ; Humans ; Male ; *Medical Informatics Applications ; Middle Aged ; *Mobile Applications ; *Patient Acceptance of Health Care ; Smartphone ; }, abstract = {OBJECTIVE: This study aimed to examine the feasibility, acceptability, and initial validity of using smartphone-based ecological momentary assessment (EMA) to assess daily functioning and other behavioral factors among older HIV+ adults.

METHODS: Twenty older HIV+ adults (mean age: 59 years) completed laboratory-based neurobehavioral and functional assessments then completed EMA surveys via smartphones five times per day for one week.

RESULTS: Excellent EMA adherence (86.4%) was found, and participants rated their experience with EMA methods positively. Time-use data indicated participants were spending 74% of their waking-sampled time at home, 63% of their time alone, and 32% of their time engaged in passive leisure activities (e.g., watching TV). Better neurocognitive and functional capacity abilities were correlated with less time spent in passive leisure activities. Lastly, mood and cognitive symptom data collected via EMA were significantly associated with scores from laboratory-based assessments of these same constructs.

CONCLUSIONS: EMA via smartphones is a feasible and acceptable data collection method among older HIV+ adults and appears to be a promising mobile tool to assess daily functioning behaviors in HIV. These preliminary findings indicate older HIV+ adults are spending a considerable amount of time at home, alone, and engaged in passive leisure activities, primarily watching TV. EMA may contribute to future research examining functional disability among the growing population of older HIV+ adults.}, } @article {pmid28061884, year = {2017}, author = {Bennett, DJ and Sutton, MD and Turvey, ST}, title = {treeman: an R package for efficient and intuitive manipulation of phylogenetic trees.}, journal = {BMC research notes}, volume = {10}, number = {1}, pages = {30}, pmid = {28061884}, issn = {1756-0500}, mesh = {Algorithms ; Computational Biology/*methods ; Computer Simulation ; Ecology ; Models, Statistical ; *Phylogeny ; *Software ; }, abstract = {BACKGROUND: Phylogenetic trees are hierarchical structures used for representing the inter-relationships between biological entities. They are the most common tool for representing evolution and are essential to a range of fields across the life sciences. The manipulation of phylogenetic trees-in terms of adding or removing tips-is often performed by researchers not just for reasons of management but also for performing simulations in order to understand the processes of evolution. Despite this, the most common programming language among biologists, R, has few class structures well suited to these tasks.

RESULTS: We present an R package that contains a new class, called TreeMan, for representing the phylogenetic tree. This class has a list structure allowing phylogenetic trees to be manipulated more efficiently. Computational running times are reduced because of the ready ability to vectorise and parallelise methods. Development is also improved due to fewer lines of code being required for performing manipulation processes.

CONCLUSIONS: We present three use cases-pinning missing taxa to a supertree, simulating evolution with a tree-growth model and detecting significant phylogenetic turnover-that demonstrate the new package's speed and simplicity.}, } @article {pmid28061392, year = {2017}, author = {Byrnes, HF and Miller, BA and Morrison, CN and Wiebe, DJ and Woychik, M and Wiehe, SE}, title = {Association of environmental indicators with teen alcohol use and problem behavior: Teens' observations vs. objectively-measured indicators.}, journal = {Health & place}, volume = {43}, number = {}, pages = {151-157}, pmid = {28061392}, issn = {1873-2054}, support = {R01 HD078415/HD/NICHD NIH HHS/United States ; }, mesh = {Adolescent ; Adolescent Behavior/*psychology ; Commerce ; *Environment Design ; Female ; Geographic Information Systems/instrumentation ; Humans ; Male ; Problem Behavior/*psychology ; Residence Characteristics ; Risk-Taking ; Smartphone/statistics & numerical data ; Underage Drinking/*psychology ; }, abstract = {UNLABELLED: Most prior studies use objectively measured data (e.g., census-based indicators) to assess contextual risks. However, teens' observations might be more important for their risk behavior.

OBJECTIVES: 1) determine relationships between observed and objective indicators of contextual risks 2) determine relations of observed and objective indicators with teen alcohol use and problem behavior. Teens aged 14-16 (N=170) carried GPS-enabled smartphones for one month, with locations documented. Ecological momentary assessment (EMA) measured teens' observations via texts regarding risk behaviors and environmental observations. Objective indicators of alcohol outlets and disorganization were spatially joined to EMAs based on teens' location at the time of the texts. Observed and objective disorganization, and objective indicators of alcohol outlets were related to alcohol use. Observed disorganization was related to problem behavior, while objective indicators were unrelated. Findings suggest the importance of considering teens' observations of contextual risk for understanding influences on risk behavior and suggest future directions for research and prevention strategies.}, } @article {pmid28061024, year = {2017}, author = {Warren, A and Patterson, DJ and Dunthorn, M and Clamp, JC and Achilles-Day, UEM and Aescht, E and Al-Farraj, SA and Al-Quraishy, S and Al-Rasheid, K and Carr, M and Day, JG and Dellinger, M and El-Serehy, HA and Fan, Y and Gao, F and Gao, S and Gong, J and Gupta, R and Hu, X and Kamra, K and Langlois, G and Lin, X and Lipscomb, D and Lobban, CS and Luporini, P and Lynn, DH and Ma, H and Macek, M and Mackenzie-Dodds, J and Makhija, S and Mansergh, RI and Martín-Cereceda, M and McMiller, N and Montagnes, DJS and Nikolaeva, S and Ong'ondo, GO and Pérez-Uz, B and Purushothaman, J and Quintela-Alonso, P and Rotterová, J and Santoferrara, L and Shao, C and Shen, Z and Shi, X and Song, W and Stoeck, T and La Terza, A and Vallesi, A and Wang, M and Weisse, T and Wiackowski, K and Wu, L and Xu, K and Yi, Z and Zufall, R and Agatha, S}, title = {Beyond the "Code": A Guide to the Description and Documentation of Biodiversity in Ciliated Protists (Alveolata, Ciliophora).}, journal = {The Journal of eukaryotic microbiology}, volume = {64}, number = {4}, pages = {539-554}, pmid = {28061024}, issn = {1550-7408}, mesh = {Biodiversity ; Ciliophora/*classification/genetics ; *Databases, Factual ; Internet ; Phylogeny ; }, abstract = {Recent advances in molecular technology have revolutionized research on all aspects of the biology of organisms, including ciliates, and created unprecedented opportunities for pursuing a more integrative approach to investigations of biodiversity. However, this goal is complicated by large gaps and inconsistencies that still exist in the foundation of basic information about biodiversity of ciliates. The present paper reviews issues relating to the taxonomy of ciliates and presents specific recommendations for best practice in the observation and documentation of their biodiversity. This effort stems from a workshop that explored ways to implement six Grand Challenges proposed by the International Research Coordination Network for Biodiversity of Ciliates (IRCN-BC). As part of its commitment to strengthening the knowledge base that supports research on biodiversity of ciliates, the IRCN-BC proposes to populate The Ciliate Guide, an online database, with biodiversity-related data and metadata to create a resource that will facilitate accurate taxonomic identifications and promote sharing of data.}, } @article {pmid28058797, year = {2017}, author = {Reeves, RM and Hardelid, P and Gilbert, R and Warburton, F and Ellis, J and Pebody, RG}, title = {Estimating the burden of respiratory syncytial virus (RSV) on respiratory hospital admissions in children less than five years of age in England, 2007-2012.}, journal = {Influenza and other respiratory viruses}, volume = {11}, number = {2}, pages = {122-129}, pmid = {28058797}, issn = {1750-2659}, support = {/BHF_/British Heart Foundation/United Kingdom ; MR/K006584/1/MRC_/Medical Research Council/United Kingdom ; /ARC_/Arthritis Research UK/United Kingdom ; /CSO_/Chief Scientist Office/United Kingdom ; /CRUK_/Cancer Research UK/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; PDF-2013-06-004/DH_/Department of Health/United Kingdom ; }, mesh = {Bronchiolitis/epidemiology ; Bronchitis/epidemiology ; Child, Preschool ; *Cost of Illness ; England/epidemiology ; Female ; Hospitalization/*statistics & numerical data ; Humans ; Infant ; Male ; Pneumonia, Viral/epidemiology ; Respiratory Syncytial Virus Infections/complications/economics/*epidemiology/virology ; Respiratory Syncytial Virus Vaccines/administration & dosage ; Respiratory Syncytial Virus, Human/*isolation & purification ; Respiratory Tract Infections/economics/epidemiology/virology ; }, abstract = {BACKGROUND: Respiratory syncytial virus (RSV) is a leading cause of hospital admission in young children. With several RSV vaccines candidates undergoing clinical trials, recent estimates of RSV burden are required to provide a baseline for vaccine impact studies.

OBJECTIVES: To estimate the number of RSV-associated hospital admissions in children aged <5 years in England over a 5-year period from 2007 using ecological time series modelling of national hospital administrative data.

PATIENTS/METHODS: Multiple linear regression modelling of weekly time series of laboratory surveillance data and Hospital Episode Statistics (HES) data was used to estimate the number of hospital admissions due to major respiratory pathogens including RSV in children <5 years of age in England from mid-2007 to mid-2012, stratified by age group (<6 months, 6-11 months, 1-4 years) and primary diagnosis: bronchiolitis, pneumonia, unspecified lower respiratory tract infection (LRTI), bronchitis and upper respiratory tract infection (URTI).

RESULTS: On average, 33 561 (95% confidence interval 30 429-38 489) RSV-associated hospital admissions in children <5 years of age occurred annually from 2007 to 2012. Average annual admission rates were 35.1 (95% CI: 32.9-38.9) per 1000 children aged <1 year and 5.31 (95% CI: 4.5-6.6) per 1000 children aged 1-4 years. About 84% (95% CI: 81-91%) of RSV-associated admissions were for LRTI. The diagnosis-specific burden of RSV-associated admissions differed significantly by age group.

CONCLUSIONS: RSV remains a significant cause of hospital admissions in young children in England. Individual-level analysis of RSV-associated admissions is required to fully describe the burden by age and risk group and identify optimal prevention strategies.}, } @article {pmid28057696, year = {2017}, author = {Fritz, H and Tarraf, W and Saleh, DJ and Cutchin, MP}, title = {Using a Smartphone-Based Ecological Momentary Assessment Protocol With Community Dwelling Older African Americans.}, journal = {The journals of gerontology. Series B, Psychological sciences and social sciences}, volume = {72}, number = {5}, pages = {876-887}, pmid = {28057696}, issn = {1758-5368}, support = {P30 ES020957/ES/NIEHS NIH HHS/United States ; }, mesh = {Black or African American/*psychology/*statistics & numerical data ; Aged ; Aged, 80 and over ; Female ; Geographic Information Systems/*statistics & numerical data ; Humans ; *Independent Living ; Male ; Michigan ; Middle Aged ; *Residence Characteristics ; Smartphone/*statistics & numerical data ; Utilization Review/statistics & numerical data ; }, abstract = {OBJECTIVES: Little is known about the feasibility of smartphone-based Ecological Momentary Assessment (EMA) approaches to collect psychosocial data from older populations, especially disadvantaged older populations. In response to this gap, this report provides evidence of the feasibility and utility of a smartphone-based EMA approach for real-time assessment with older African Americans. In addition, we share lessons learned about how to improve utility.

METHODS: Ninety-seven older African Americans ages 55 and older (range: 55-95 years) used an Android smartphone loaded with an EMA application to provide data about their everyday activities and stress four times per day for seven consecutive days.

RESULTS: Exit interviews early in the study suggested enhancements to the EMA interface. Adherence was demonstrated with response completion rates of 92-98% on EMA measures and no participant attrition based on the EMA protocol.

DISCUSSION: Our findings suggest using a smartphone-based EMA approach for data collection is feasible and has utility with older African Americans. We most likely enhanced adherence by testing, training, monitoring, and adapting the EMA protocol using input from older adults early in the EMA design process.}, } @article {pmid28057476, year = {2017}, author = {Bonnevialle, P}, title = {Operative treatment of early infection after internal fixation of limb fractures (exclusive of severe open fractures).}, journal = {Orthopaedics & traumatology, surgery & research : OTSR}, volume = {103}, number = {1S}, pages = {S67-S73}, doi = {10.1016/j.otsr.2016.06.019}, pmid = {28057476}, issn = {1877-0568}, mesh = {Anti-Bacterial Agents/therapeutic use ; Decision Support Techniques ; Femoral Fractures/surgery ; Fracture Fixation, Internal/*adverse effects/methods ; *Fracture Healing ; Fractures, Bone/*surgery ; Humans ; Humeral Fractures/surgery ; Surgical Wound Infection/drug therapy/microbiology/*surgery ; Wound Closure Techniques ; }, abstract = {Early infection after open reduction and internal fixation (ORIF) of a limb bone is defined as bacteriologically documented, deep and/or superficial surgical-site infection (SSI) diagnosed within 6months after the surgical procedure. This interval is arbitrarily considered sufficient to obtain fracture healing. The treatment of early infection after ORIF should be decided by a multidisciplinary team. The principles are the same as for revision arthroplasty. Superficial SSIs should be differentiated from deep SSIs, based on the results of bacteriological specimens collected using flawless technique. A turning point in the local microbial ecology occurs around the third or fourth week, when a biofilm develops around metallic implants. This biofilm protects the bacteria. The treatment relies on both non-operative and operative measures, which are selected based on the time to occurrence of the infection, condition of the soft tissues, and stage of bone healing. Both the surgical strategy and the antibiotic regimen should be determined during a multidisciplinary discussion. When treating superficial SSIs after ORIF, soft-tissue management is the main challenge. The treatment differs according to whether the hardware is covered or exposed. Defects in the skin and/or fascia can be managed using reliable reconstructive surgery techniques, either immediately or after a brief period of vacuum-assisted closure. In deep SSIs, deciding whether to leave or to remove the hardware is difficult. If the hardware is removed, the fracture site can be stabilised provisionally using either external fixation or a cement rod. Once infection control is achieved, several measures can be taken to stimulate bone healing before the end of the classical 6-month interval. If the hardware was removed, then internal fixation must be performed once the infection is eradicated.}, } @article {pmid28055003, year = {2017}, author = {Mauri, A and Strona, G and San-Miguel-Ayanz, J}, title = {EU-Forest, a high-resolution tree occurrence dataset for Europe.}, journal = {Scientific data}, volume = {4}, number = {}, pages = {160123}, pmid = {28055003}, issn = {2052-4463}, mesh = {Biodiversity ; Conservation of Natural Resources ; Databases, Factual ; Ecosystem ; Europe ; Forests ; *Trees ; }, abstract = {We present EU-Forest, a dataset that integrates and extends by almost one order of magnitude the publicly available information on European tree species distribution. The core of our dataset (~96% of the occurrence records) came from an unpublished, large database harmonising forest plot surveys from National Forest Inventories on an INSPIRE-compliant 1 km×1 km grid. These new data can potentially benefit several disciplines, including forestry, biodiversity conservation, palaeoecology, plant ecology, the bioeconomy, and pest management.}, } @article {pmid28051123, year = {2017}, author = {Adams, MP and Collier, CJ and Uthicke, S and Ow, YX and Langlois, L and O'Brien, KR}, title = {Model fit versus biological relevance: Evaluating photosynthesis-temperature models for three tropical seagrass species.}, journal = {Scientific reports}, volume = {7}, number = {}, pages = {39930}, pmid = {28051123}, issn = {2045-2322}, mesh = {Alismatales/*physiology ; Data Interpretation, Statistical ; *Models, Biological ; *Photosynthesis ; Reproducibility of Results ; *Temperature ; Tropical Climate ; }, abstract = {When several models can describe a biological process, the equation that best fits the data is typically considered the best. However, models are most useful when they also possess biologically-meaningful parameters. In particular, model parameters should be stable, physically interpretable, and transferable to other contexts, e.g. for direct indication of system state, or usage in other model types. As an example of implementing these recommended requirements for model parameters, we evaluated twelve published empirical models for temperature-dependent tropical seagrass photosynthesis, based on two criteria: (1) goodness of fit, and (2) how easily biologically-meaningful parameters can be obtained. All models were formulated in terms of parameters characterising the thermal optimum (Topt) for maximum photosynthetic rate (Pmax). These parameters indicate the upper thermal limits of seagrass photosynthetic capacity, and hence can be used to assess the vulnerability of seagrass to temperature change. Our study exemplifies an approach to model selection which optimises the usefulness of empirical models for both modellers and ecologists alike.}, } @article {pmid28050840, year = {2017}, author = {Decou, R and Serk, H and Ménard, D and Pesquet, E}, title = {Analysis of Lignin Composition and Distribution Using Fluorescence Laser Confocal Microspectroscopy.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1544}, number = {}, pages = {233-247}, doi = {10.1007/978-1-4939-6722-3_17}, pmid = {28050840}, issn = {1940-6029}, mesh = {Computational Biology/methods ; Image Processing, Computer-Assisted ; Lignin/*chemistry/*metabolism ; *Microscopy, Confocal/methods ; Software ; *Tissue Distribution ; Wood/chemistry/metabolism ; Xylem/chemistry/metabolism ; }, abstract = {Lignin is a polyphenolic polymer specifically accumulating in the cell walls of xylem cells in higher vascular plants. Far from being homogeneous, the lignification of xylem cell walls varies in deposition site, quantity, composition and macromolecular conformation depending on the cell wall compartment, cell type, cell developmental stage and plant species. Here, we describe how confocal microspectroscopy methods using lignin autofluorescence can be used to evaluate the relative lignin amounts, its spatial distribution and composition at the cellular and sub-cellular levels in both isolated cells and histological cross-sections of plant tissues.}, } @article {pmid28045977, year = {2017}, author = {McRae, L and Deinet, S and Freeman, R}, title = {The Diversity-Weighted Living Planet Index: Controlling for Taxonomic Bias in a Global Biodiversity Indicator.}, journal = {PloS one}, volume = {12}, number = {1}, pages = {e0169156}, pmid = {28045977}, issn = {1932-6203}, mesh = {Animals ; *Biodiversity ; Conservation of Natural Resources/*methods ; Databases, Factual ; *Earth, Planet ; Ecosystem ; *Fresh Water ; Geography ; International Cooperation ; *Marine Biology ; Science ; Species Specificity ; Time Factors ; Vertebrates ; }, abstract = {As threats to species continue to increase, precise and unbiased measures of the impact these pressures are having on global biodiversity are urgently needed. Some existing indicators of the status and trends of biodiversity largely rely on publicly available data from the scientific and grey literature, and are therefore prone to biases introduced through over-representation of well-studied groups and regions in monitoring schemes. This can give misleading estimates of biodiversity trends. Here, we report on an approach to tackle taxonomic and geographic bias in one such indicator (Living Planet Index) by accounting for the estimated number of species within biogeographical realms, and the relative diversity of species within them. Based on a proportionally weighted index, we estimate a global population decline in vertebrate species between 1970 and 2012 of 58% rather than 20% from an index with no proportional weighting. From this data set, comprising 14,152 populations of 3,706 species from 3,095 data sources, we also find that freshwater populations have declined by 81%, marine populations by 36%, and terrestrial populations by 38% when using proportional weighting (compared to trends of -46%, +12% and +15% respectively). These results not only show starker declines than previously estimated, but suggests that those species for which there is poorer data coverage may be declining more rapidly.}, } @article {pmid28045906, year = {2017}, author = {Torres, LG and Orben, RA and Tolkova, I and Thompson, DR}, title = {Classification of Animal Movement Behavior through Residence in Space and Time.}, journal = {PloS one}, volume = {12}, number = {1}, pages = {e0168513}, pmid = {28045906}, issn = {1932-6203}, mesh = {Animals ; *Behavior, Animal ; Birds/*physiology ; *Ecosystem ; Geographic Information Systems ; *Locomotion ; New Zealand ; Spatio-Temporal Analysis ; Time Factors ; }, abstract = {Identification and classification of behavior states in animal movement data can be complex, temporally biased, time-intensive, scale-dependent, and unstandardized across studies and taxa. Large movement datasets are increasingly common and there is a need for efficient methods of data exploration that adjust to the individual variability of each track. We present the Residence in Space and Time (RST) method to classify behavior patterns in movement data based on the concept that behavior states can be partitioned by the amount of space and time occupied in an area of constant scale. Using normalized values of Residence Time and Residence Distance within a constant search radius, RST is able to differentiate behavior patterns that are time-intensive (e.g., rest), time & distance-intensive (e.g., area restricted search), and transit (short time and distance). We use grey-headed albatross (Thalassarche chrysostoma) GPS tracks to demonstrate RST's ability to classify behavior patterns and adjust to the inherent scale and individuality of each track. Next, we evaluate RST's ability to discriminate between behavior states relative to other classical movement metrics. We then temporally sub-sample albatross track data to illustrate RST's response to less resolved data. Finally, we evaluate RST's performance using datasets from four taxa with diverse ecology, functional scales, ecosystems, and data-types. We conclude that RST is a robust, rapid, and flexible method for detailed exploratory analysis and meta-analyses of behavioral states in animal movement data based on its ability to integrate distance and time measurements into one descriptive metric of behavior groupings. Given the increasing amount of animal movement data collected, it is timely and useful to implement a consistent metric of behavior classification to enable efficient and comparative analyses. Overall, the application of RST to objectively explore and compare behavior patterns in movement data can enhance our fine- and broad- scale understanding of animal movement ecology.}, } @article {pmid28040838, year = {2017}, author = {Adriaenssens, EM and Krupovic, M and Knezevic, P and Ackermann, HW and Barylski, J and Brister, JR and Clokie, MR and Duffy, S and Dutilh, BE and Edwards, RA and Enault, F and Jang, HB and Klumpp, J and Kropinski, AM and Lavigne, R and Poranen, MM and Prangishvili, D and Rumnieks, J and Sullivan, MB and Wittmann, J and Oksanen, HM and Gillis, A and Kuhn, JH}, title = {Taxonomy of prokaryotic viruses: 2016 update from the ICTV bacterial and archaeal viruses subcommittee.}, journal = {Archives of virology}, volume = {162}, number = {4}, pages = {1153-1157}, doi = {10.1007/s00705-016-3173-4}, pmid = {28040838}, issn = {1432-8798}, mesh = {Viruses/*classification/genetics ; }, } @article {pmid28040499, year = {2017}, author = {Ultsch, A and Lötsch, J}, title = {Machine-learned cluster identification in high-dimensional data.}, journal = {Journal of biomedical informatics}, volume = {66}, number = {}, pages = {95-104}, pmid = {28040499}, issn = {1532-0480}, mesh = {*Algorithms ; *Cluster Analysis ; Computational Biology ; *Machine Learning ; }, abstract = {BACKGROUND: High-dimensional biomedical data are frequently clustered to identify subgroup structures pointing at distinct disease subtypes. It is crucial that the used cluster algorithm works correctly. However, by imposing a predefined shape on the clusters, classical algorithms occasionally suggest a cluster structure in homogenously distributed data or assign data points to incorrect clusters. We analyzed whether this can be avoided by using emergent self-organizing feature maps (ESOM).

METHODS: Data sets with different degrees of complexity were submitted to ESOM analysis with large numbers of neurons, using an interactive R-based bioinformatics tool. On top of the trained ESOM the distance structure in the high dimensional feature space was visualized in the form of a so-called U-matrix. Clustering results were compared with those provided by classical common cluster algorithms including single linkage, Ward and k-means.

RESULTS: Ward clustering imposed cluster structures on cluster-less "golf ball", "cuboid" and "S-shaped" data sets that contained no structure at all (random data). Ward clustering also imposed structures on permuted real world data sets. By contrast, the ESOM/U-matrix approach correctly found that these data contain no cluster structure. However, ESOM/U-matrix was correct in identifying clusters in biomedical data truly containing subgroups. It was always correct in cluster structure identification in further canonical artificial data. Using intentionally simple data sets, it is shown that popular clustering algorithms typically used for biomedical data sets may fail to cluster data correctly, suggesting that they are also likely to perform erroneously on high dimensional biomedical data.

CONCLUSIONS: The present analyses emphasized that generally established classical hierarchical clustering algorithms carry a considerable tendency to produce erroneous results. By contrast, unsupervised machine-learned analysis of cluster structures, applied using the ESOM/U-matrix method, is a viable, unbiased method to identify true clusters in the high-dimensional space of complex data.}, } @article {pmid28039930, year = {2017}, author = {Muthuramalingam, M and Wang, Y and Li, Y and Mahalingam, R}, title = {Interacting protein partners of Arabidopsis RNA-binding protein AtRBP45b.}, journal = {Plant biology (Stuttgart, Germany)}, volume = {19}, number = {3}, pages = {327-334}, doi = {10.1111/plb.12540}, pmid = {28039930}, issn = {1438-8677}, mesh = {Arabidopsis/genetics/metabolism ; Arabidopsis Proteins/genetics/*metabolism ; Cell Nucleus/metabolism ; Databases, Factual ; Fluorescence Resonance Energy Transfer ; Genetic Complementation Test ; Green Fluorescent Proteins/genetics ; Mutation ; Promoter Regions, Genetic ; Protein Domains ; Protein Interaction Mapping/*methods ; RNA Stability ; RNA-Binding Proteins/genetics/*metabolism ; Two-Hybrid System Techniques ; }, abstract = {RNA binding proteins, important players in post-transcriptional gene regulation, usually exist in ribonuclear complexes. However, even in model systems like Arabidopsis characterisation of RBP associated proteins is limited. In this study, we investigated the interacting proteins of the Arabidopsis AtRBP45b, which is involved in stress signalling. In vivo localisation of AtRBP45b was conducted using 35S-GFP. FLAG-tagged AtRBP45b under control of the 35S promoter in the Atrbp45b-1 mutant background was used to pull down AtRBP45b interacting proteins. Yeast two-hybrid analysis, fluorescence energy resonance transfer assays were used to confirm the veracity of the AtRBP45b interacting proteins. In planta GFP-tagging indicated AtRBP45b is localised to the nucleus and the cytosol. AtRBP45b protein has a N-terminal proline-rich region and a C-terminal glutamine-rich domain that are usually involved in protein-protein interactions. Co-immunoprecipitation followed by mass spectrometry-based protein sequencing led to identification of 30 proteins that interacted with AtRBP45b. Using information from interactome databases (BIOGRID, INTACT and STRING), pull-down assays and localisation data, 12 putative interacting proteins were selected for yeast two-hybrid analysis. Cap-binding protein (CBP20, At5g44200) and polyA-binding protein (PAB8, At1g49760) were shown to interact with AtRBP45b. Based on its interacting partners we speculate that AtRBP45b may play an important role in RNA metabolism, especially in aspects related to mRNA stability and translation initiation during stress conditions in plants.}, } @article {pmid28036324, year = {2016}, author = {Gudelj, I and Kinnersley, M and Rashkov, P and Schmidt, K and Rosenzweig, F}, title = {Stability of Cross-Feeding Polymorphisms in Microbial Communities.}, journal = {PLoS computational biology}, volume = {12}, number = {12}, pages = {e1005269}, pmid = {28036324}, issn = {1553-7358}, support = {R01 HG003328/HG/NHGRI NIH HHS/United States ; BB/J010340/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Computational Biology ; *Environment ; Escherichia coli/metabolism/physiology ; Glucose/metabolism ; Metabolism/*physiology ; Microbial Consortia/*physiology ; *Models, Biological ; }, abstract = {Cross-feeding, a relationship wherein one organism consumes metabolites excreted by another, is a ubiquitous feature of natural and clinically-relevant microbial communities and could be a key factor promoting diversity in extreme and/or nutrient-poor environments. However, it remains unclear how readily cross-feeding interactions form, and therefore our ability to predict their emergence is limited. In this paper we developed a mathematical model parameterized using data from the biochemistry and ecology of an E. coli cross-feeding laboratory system. The model accurately captures short-term dynamics of the two competitors that have been observed empirically and we use it to systematically explore the stability of cross-feeding interactions for a range of environmental conditions. We find that our simple system can display complex dynamics including multi-stable behavior separated by a critical point. Therefore whether cross-feeding interactions form depends on the complex interplay between density and frequency of the competitors as well as on the concentration of resources in the environment. Moreover, we find that subtly different environmental conditions can lead to dramatically different results regarding the establishment of cross-feeding, which could explain the apparently unpredictable between-population differences in experimental outcomes. We argue that mathematical models are essential tools for disentangling the complexities of cross-feeding interactions.}, } @article {pmid28035749, year = {2017}, author = {Symonová, R and Majtánová, Z and Arias-Rodriguez, L and Mořkovský, L and Kořínková, T and Cavin, L and Pokorná, MJ and Doležálková, M and Flajšhans, M and Normandeau, E and Ráb, P and Meyer, A and Bernatchez, L}, title = {Genome Compositional Organization in Gars Shows More Similarities to Mammals than to Other Ray-Finned Fish.}, journal = {Journal of experimental zoology. Part B, Molecular and developmental evolution}, volume = {328}, number = {7}, pages = {607-619}, doi = {10.1002/jez.b.22719}, pmid = {28035749}, issn = {1552-5015}, mesh = {Animals ; Computational Biology ; Fishes/*genetics ; *Genome ; Genomics ; Karyotype ; Mammals/*genetics ; *Phylogeny ; Time Factors ; }, abstract = {Genomic GC content can vary locally, and GC-rich regions are usually associated with increased DNA thermostability in thermophilic prokaryotes and warm-blooded eukaryotes. Among vertebrates, fish and amphibians appeared to possess a distinctly less heterogeneous AT/GC organization in their genomes, whereas cytogenetically detectable GC heterogeneity has so far only been documented in mammals and birds. The subject of our study is the gar, an ancient "living fossil" of a basal ray-finned fish lineage, known from the Cretaceous period. We carried out cytogenomic analysis in two gar genera (Atractosteus and Lepisosteus) uncovering a GC chromosomal pattern uncharacteristic for fish. Bioinformatic analysis of the spotted gar (Lepisosteus oculatus) confirmed a GC compartmentalization on GC profiles of linkage groups. This indicates a rather mammalian mode of compositional organization on gar chromosomes. Gars are thus the only analyzed extant ray-finned fishes with a GC compartmentalized genome. Since gars are cold-blooded anamniotes, our results contradict the generally accepted hypothesis that the phylogenomic onset of GC compartmentalization occurred near the origin of amniotes. Ecophysiological findings of other authors indicate a metabolic similarity of gars with mammals. We hypothesize that gars might have undergone convergent evolution with the tetrapod lineages leading to mammals on both metabolic and genomic levels. Their metabolic adaptations might have left footprints in their compositional genome evolution, as proposed by the metabolic rate hypothesis. The genome organization described here in gars sheds new light on the compositional genome evolution in vertebrates generally and contributes to better understanding of the complexities of the mechanisms involved in this process.}, } @article {pmid28030541, year = {2016}, author = {Kryuchkova-Mostacci, N and Robinson-Rechavi, M}, title = {Tissue-Specificity of Gene Expression Diverges Slowly between Orthologs, and Rapidly between Paralogs.}, journal = {PLoS computational biology}, volume = {12}, number = {12}, pages = {e1005274}, pmid = {28030541}, issn = {1553-7358}, mesh = {Animals ; Anura ; Computational Biology ; *Evolution, Molecular ; Gene Expression/*genetics ; Humans ; Mice ; *Models, Genetic ; Organ Specificity/*genetics ; }, abstract = {The ortholog conjecture implies that functional similarity between orthologous genes is higher than between paralogs. It has been supported using levels of expression and Gene Ontology term analysis, although the evidence was rather weak and there were also conflicting reports. In this study on 12 species we provide strong evidence of high conservation in tissue-specificity between orthologs, in contrast to low conservation between within-species paralogs. This allows us to shed a new light on the evolution of gene expression patterns. While there have been several studies of the correlation of expression between species, little is known about the evolution of tissue-specificity itself. Ortholog tissue-specificity is strongly conserved between all tetrapod species, with the lowest Pearson correlation between mouse and frog at r = 0.66. Tissue-specificity correlation decreases strongly with divergence time. Paralogs in human show much lower conservation, even for recent Primate-specific paralogs. When both paralogs from ancient whole genome duplication tissue-specific paralogs are tissue-specific, it is often to different tissues, while other tissue-specific paralogs are mostly specific to the same tissue. The same patterns are observed using human or mouse as focal species, and are robust to choices of datasets and of thresholds. Our results support the following model of evolution: in the absence of duplication, tissue-specificity evolves slowly, and tissue-specific genes do not change their main tissue of expression; after small-scale duplication the less expressed paralog loses the ancestral specificity, leading to an immediate difference between paralogs; over time, both paralogs become more broadly expressed, but remain poorly correlated. Finally, there is a small number of paralog pairs which stay tissue-specific with the same main tissue of expression, for at least 300 million years.}, } @article {pmid28028941, year = {2017}, author = {Wang, J}, title = {The computer program structure for assigning individuals to populations: easy to use but easier to misuse.}, journal = {Molecular ecology resources}, volume = {17}, number = {5}, pages = {981-990}, doi = {10.1111/1755-0998.12650}, pmid = {28028941}, issn = {1755-0998}, mesh = {Computational Biology/*methods ; Diagnostic Errors ; Genetics, Population/*methods ; Humans ; Molecular Biology/*methods ; *Software ; }, abstract = {The computer program Structure implements a Bayesian method, based on a population genetics model, to assign individuals to their source populations using genetic marker data. It is widely applied in the fields of ecology, evolutionary biology, human genetics and conservation biology for detecting hidden genetic structures, inferring the most likely number of populations (K), assigning individuals to source populations and estimating admixture and migration rates. Recently, several simulation studies repeatedly concluded that the program yields erroneous inferences when samples from different populations are highly unbalanced in size. Analysing both simulated and empirical data sets, this study confirms that Structure indeed yields poor individual assignments to source populations and gives frequently incorrect estimates of K when sampling is unbalanced. However, this poor performance is mainly caused by the adoption of the default ancestry prior, which assumes all source populations contribute equally to the pooled sample of individuals. When the alternative ancestry prior, which allows for unequal representations of the source populations by the sample, is adopted, accurate individual assignments could be obtained even if sampling is highly unbalanced. The alternative prior also improves the inference of K by two estimators, albeit the improvement is not as much as that in individual assignments to populations. For the difficult case of many populations and unbalanced sampling, a rarely used parameter combination of the alternative ancestry prior, an initial ALPHA value much smaller than the default and the uncorrelated allele frequency model is required for Structure to yield accurate inferences. I conclude that Structure is easy to use but is easier to misuse because of its complicated genetic model and many parameter (prior) options which may not be obvious to choose, and suggest using multiple plausible models (parameters) and K estimators in conducting comparative and exploratory Structure analysis.}, } @article {pmid28028483, year = {2016}, author = {Baldridge, E and Harris, DJ and Xiao, X and White, EP}, title = {An extensive comparison of species-abundance distribution models.}, journal = {PeerJ}, volume = {4}, number = {}, pages = {e2823}, pmid = {28028483}, issn = {2167-8359}, abstract = {A number of different models have been proposed as descriptions of the species-abundance distribution (SAD). Most evaluations of these models use only one or two models, focus on only a single ecosystem or taxonomic group, or fail to use appropriate statistical methods. We use likelihood and AIC to compare the fit of four of the most widely used models to data on over 16,000 communities from a diverse array of taxonomic groups and ecosystems. Across all datasets combined the log-series, Poisson lognormal, and negative binomial all yield similar overall fits to the data. Therefore, when correcting for differences in the number of parameters the log-series generally provides the best fit to data. Within individual datasets some other distributions performed nearly as well as the log-series even after correcting for the number of parameters. The Zipf distribution is generally a poor characterization of the SAD.}, } @article {pmid28027588, year = {2017}, author = {Pacifici, K and Reich, BJ and Miller, DA and Gardner, B and Stauffer, G and Singh, S and McKerrow, A and Collazo, JA}, title = {Integrating multiple data sources in species distribution modeling: a framework for data fusion.}, journal = {Ecology}, volume = {98}, number = {3}, pages = {840-850}, doi = {10.1002/ecy.1710}, pmid = {28027588}, issn = {0012-9658}, mesh = {Ecology ; Information Storage and Retrieval ; *Models, Theoretical ; *Spatial Analysis ; }, abstract = {The last decade has seen a dramatic increase in the use of species distribution models (SDMs) to characterize patterns of species' occurrence and abundance. Efforts to parameterize SDMs often create a tension between the quality and quantity of data available to fit models. Estimation methods that integrate both standardized and non-standardized data types offer a potential solution to the tradeoff between data quality and quantity. Recently several authors have developed approaches for jointly modeling two sources of data (one of high quality and one of lesser quality). We extend their work by allowing for explicit spatial autocorrelation in occurrence and detection error using a Multivariate Conditional Autoregressive (MVCAR) model and develop three models that share information in a less direct manner resulting in more robust performance when the auxiliary data is of lesser quality. We describe these three new approaches ("Shared," "Correlation," "Covariates") for combining data sources and show their use in a case study of the Brown-headed Nuthatch in the Southeastern U.S. and through simulations. All three of the approaches which used the second data source improved out-of-sample predictions relative to a single data source ("Single"). When information in the second data source is of high quality, the Shared model performs the best, but the Correlation and Covariates model also perform well. When the information quality in the second data source is of lesser quality, the Correlation and Covariates model performed better suggesting they are robust alternatives when little is known about auxiliary data collected opportunistically or through citizen scientists. Methods that allow for both data types to be used will maximize the useful information available for estimating species distributions.}, } @article {pmid28026905, year = {2017}, author = {Rajabi, M and Pilesjö, P and Bazmani, A and Mansourian, A}, title = {Identification of Visceral Leishmaniasis-Susceptible Areas using Spatial Modelling in Southern Caucasus.}, journal = {Zoonoses and public health}, volume = {64}, number = {7}, pages = {e5-e22}, doi = {10.1111/zph.12325}, pmid = {28026905}, issn = {1863-2378}, mesh = {Azerbaijan/epidemiology ; Geographic Information Systems ; Geographic Mapping ; Humans ; Incidence ; Iran/epidemiology ; Leishmaniasis, Visceral/*epidemiology ; *Models, Biological ; Prevalence ; }, abstract = {This study explores the application of spatial modelling techniques to generate susceptibility maps for a neglected zoonotic disease, visceral leishmaniasis (VL), in an endemic area in southern Caucasus that includes Iran, Armenia and Azerbaijan. The social and physical environment of southern Caucasus has been mainly characterized by the presence of several factors that are strongly associated with VL, which has caused a significant number of infections during the past decade. Three popular spatial modelling techniques, consisting of the weights of evidence, logistic regression and fuzzy logic methods, were evaluated and trained using a study area in north-western Iran where an inventory of highly infected areas and high-quality evidential factors was available. Model performance was assessed using the receiver-operating characteristic (ROC) approach. According to the results of these assessments, the fuzzy logic method with γ = 0.5 was chosen for the prediction of VL incidence in southern Caucasus. The susceptibility map generated using the fuzzy logic method indicated that VL followed a spatial pattern at the conjunction of the three countries, which suggests that the prevalence of VL in southern Caucasus is socio-ecologically dependent.}, } @article {pmid28026709, year = {2016}, author = {Terashima, M and Kephart, G}, title = {Misclassification errors from postal code-based geocoding to assign census geography in Nova Scotia, Canada.}, journal = {Canadian journal of public health = Revue canadienne de sante publique}, volume = {107}, number = {4-5}, pages = {e424-e430}, pmid = {28026709}, issn = {1920-7476}, mesh = {*Censuses ; Geographic Information Systems/*standards ; *Geographic Mapping ; Humans ; Nova Scotia ; Reproducibility of Results ; Rural Population ; Urban Population ; }, abstract = {OBJECTIVES: Postal codes are often the only available geographic identifiers in many sources of health data in Canada. In order to conduct geographic analyses, postal codes are routinely geocoded to census geography to link to ecological data. Despite common use of this method, the extent of geographic misclassification errors is poorly understood. We estimated misclassification errors in the geocoding of postal codes to assign census geography in Nova Scotia, Canada.

METHODS: We examined differences between counts and match rates for postal-code geocoded and actual locations of buildings in Nova Scotia at two census administrative area levels: dissemination areas (DAs) and census subdivisions (CSDs). Actual locations were based on the data collected by the provincial government containing actual latitude/longitude of buildings. Variation in misclassification by rurality, using Statistics Canada's classification, was also assessed.

RESULTS: Outside two urban areas (Halifax Metro and Sydney) which had <10% differences in counts, many DAs had >30% differences. Match rates showed similar patterns, with the vast majority of non-urban DAs having <40% match rates. Even in major urban areas, 10% of DAs had large misclassification errors. Misclassification errors at the CSD level were still too great to estimate counts or rates without further area aggregation.

CONCLUSION: Routine use of postal code geocoding should be replaced with geocoding of location information using additional identifiers such as civic addresses or latitude and longitude. If data holders did this in-house before providing data to researchers, the accuracy and capacity of geographic analysis would be enhanced while protecting confidentiality.}, } @article {pmid28025338, year = {2016}, author = {Ankenbrand, MJ and Weber, L and Becker, D and Förster, F and Bemm, F}, title = {TBro: visualization and management of de novo transcriptomes.}, journal = {Database : the journal of biological databases and curation}, volume = {2016}, number = {}, pages = {}, pmid = {28025338}, issn = {1758-0463}, mesh = {Animals ; *Databases, Genetic ; *Gene Expression Profiling ; *Genome, Human ; Humans ; Oligonucleotide Array Sequence Analysis ; *Transcriptome ; *User-Computer Interface ; }, abstract = {RNA sequencing (RNA-seq) has become a powerful tool to understand molecular mechanisms and/or developmental programs. It provides a fast, reliable and cost-effective method to access sets of expressed elements in a qualitative and quantitative manner. Especially for non-model organisms and in absence of a reference genome, RNA-seq data is used to reconstruct and quantify transcriptomes at the same time. Even SNPs, InDels, and alternative splicing events are predicted directly from the data without having a reference genome at hand. A key challenge, especially for non-computational personnal, is the management of the resulting datasets, consisting of different data types and formats. Here, we present TBro, a flexible de novo transcriptome browser, tackling this challenge. TBro aggregates sequences, their annotation, expression levels as well as differential testing results. It provides an easy-to-use interface to mine the aggregated data and generate publication-ready visualizations. Additionally, it supports users with an intuitive cart system, that helps collecting and analysing biological meaningful sets of transcripts. TBro's modular architecture allows easy extension of its functionalities in the future. Especially, the integration of new data types such as proteomic quantifications or array-based gene expression data is straightforward. Thus, TBro is a fully featured yet flexible transcriptome browser that supports approaching complex biological questions and enhances collaboration of numerous researchers. DATABASE URL: : tbro.carnivorom.com.}, } @article {pmid28025179, year = {2018}, author = {Finotello, F and Mastrorilli, E and Di Camillo, B}, title = {Measuring the diversity of the human microbiota with targeted next-generation sequencing.}, journal = {Briefings in bioinformatics}, volume = {19}, number = {4}, pages = {679-692}, doi = {10.1093/bib/bbw119}, pmid = {28025179}, issn = {1477-4054}, support = {T 974/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Bacteria/*classification/*genetics/isolation & purification ; Computational Biology/*methods ; DNA, Bacterial/genetics ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Metagenome ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/*genetics ; }, abstract = {The human microbiota is a complex ecological community of commensal, symbiotic and pathogenic microorganisms harboured by the human body. Next-generation sequencing (NGS) technologies, in particular targeted amplicon sequencing of the 16S ribosomal RNA gene (16S-seq), are enabling the identification and quantification of human-resident microorganisms at unprecedented resolution, providing novel insights into the role of the microbiota in health and disease. Once microbial abundances are quantified through NGS data analysis, diversity indices provide valuable mathematical tools to describe the ecological complexity of a single sample or to detect species differences between samples. However, diversity is not a determined physical quantity for which a consensus definition and unit of measure have been established, and several diversity indices are currently available. Furthermore, they were originally developed for macroecology and their robustness to the possible bias introduced by sequencing has not been characterized so far. To assist the reader with the selection and interpretation of diversity measures, we review a panel of broadly used indices, describing their mathematical formulations, purposes and properties, and characterize their behaviour and criticalities in dependence of the data features using simulated data as ground truth. In addition, we make available an R package, DiversitySeq, which implements in a unified framework the full panel of diversity indices and a simulator of 16S-seq data, and thus represents a valuable resource for the analysis of diversity from NGS count data and for the benchmarking of computational methods for 16S-seq.}, } @article {pmid28025117, year = {2017}, author = {Peng, JS and Wang, YJ and Ding, G and Ma, HL and Zhang, YJ and Gong, JM}, title = {A Pivotal Role of Cell Wall in Cadmium Accumulation in the Crassulaceae hyperaccumulator Sedum plumbizincicola.}, journal = {Molecular plant}, volume = {10}, number = {5}, pages = {771-774}, doi = {10.1016/j.molp.2016.12.007}, pmid = {28025117}, issn = {1752-9867}, mesh = {Cadmium/*metabolism ; Cell Wall/*metabolism ; Gene Expression Regulation, Plant ; Gene Ontology ; Sedum/*cytology/genetics/*metabolism/physiology ; Transcriptome/genetics ; }, } @article {pmid28018027, year = {2017}, author = {Widdig, A and Muniz, L and Minkner, M and Barth, Y and Bley, S and Ruiz-Lambides, A and Junge, O and Mundry, R and Kulik, L}, title = {Low incidence of inbreeding in a long-lived primate population isolated for 75 years.}, journal = {Behavioral ecology and sociobiology}, volume = {71}, number = {1}, pages = {18}, pmid = {28018027}, issn = {0340-5443}, support = {P40 OD012217/OD/NIH HHS/United States ; }, abstract = {ABSTRACT: When close relatives mate, offspring are expected to suffer fitness consequences due to inbreeding depression. Inbreeding has previously been quantified in two ways: using a sufficiently large panel of markers or deep and complete pedigrees over several generations. However, the application of both approaches is still limited by the challenge of compiling such data for species with long generation times, such as primates. Here, we assess inbreeding in rhesus macaques living on Cayo Santiago (Puerto Rico), a population genetically isolated since 1938, but descendant of a large set of presumably unrelated founders. Using comprehensive genetic data, we calculated inbreeding coefficients (F) for 2669 individuals with complete three generation pedigrees and 609 individuals with complete four generation pedigrees. We found that 0.79 and 7.39% of individuals had an F > 0 when using data from three and four generation pedigrees, respectively. No evidence of an increase in inbreeding over the study period (up to 23 years) was found. Furthermore, the observed mean relatedness of breeding pairs differed significantly from the distribution of parental relatedness expected as simulated based on previous reproductive data, suggesting that kin generally avoid breeding with each other. Finally, inbreeding was not a predictor of early mortality measured as survival until weaning and sexual maturation, respectively. Our results remain consistent with three estimators of inbreeding (standardized heterozygosity, internal relatedness, and homozygosity by loci) using up to 42 highly polymorphic microsatellites for the same set of individuals. Together, our results demonstrate that close inbreeding may not be prevalent even in populations isolated over long periods when mechanisms of inbreeding avoidance can operate.

SIGNIFICANCE STATEMENT: When close relatives mate, offspring may suffer from such inbreeding, e.g., via lower survival and/or fertility. Using (i) a large panel of genetic markers and (ii) complete three or four generation pedigrees, respectively, we show that incidences of inbreeding in a long-lived primate population are rare, even after genetic isolation for 75 years. Moreover, our simulations suggest that kin in our population generally avoid breeding with each other. Finally, the few inbred individuals detected in our large sample did not suffer from lower survival. Given that many animal species face dramatic habitat loss combined with critical population declines, our study provides important implications for conservation biology in general and for population management in particular.}, } @article {pmid28017855, year = {2017}, author = {Marki, PZ and Jønsson, KA and Irestedt, M and Nguyen, JMT and Rahbek, C and Fjeldså, J}, title = {Supermatrix phylogeny and biogeography of the Australasian Meliphagides radiation (Aves: Passeriformes).}, journal = {Molecular phylogenetics and evolution}, volume = {107}, number = {}, pages = {516-529}, doi = {10.1016/j.ympev.2016.12.021}, pmid = {28017855}, issn = {1095-9513}, mesh = {Animals ; Base Sequence ; Bayes Theorem ; Calibration ; Databases, Genetic ; Evolution, Molecular ; Passeriformes/*classification/genetics ; *Phylogeny ; *Phylogeography ; Time Factors ; }, abstract = {With nearly 300 species, the infraorder Meliphagides represents one of the largest and most conspicuous Australasian bird radiations. Although the group has been the focus of a number of recent phylogenetic studies, a comprehensive species-level phylogenetic hypothesis is still lacking. This has impeded the assessment of broad-scale evolutionary, biogeographic and ecological hypotheses. In the present study, we use a supermatrix approach including five mitochondrial and four nuclear markers to infer a time-calibrated phylogeny of the Meliphagides. Our phylogeny, which includes 286 of the 289 (99%) currently recognized species, is largely congruent with previous estimates. However, the addition of 60 newly sequenced species reveals some novel relationships. Our biogeographic analyses suggest an Australian origin for the group in the early Oligocene (31.3Mya, 95% HPD 25.2-38.2Mya). In addition, we find that dispersal events out of Australia have been numerous and frequent, particularly to New Guinea, which has also been the source of multiple back-colonizations to the Australian mainland. The phylogeny provides an important framework for studying a wide variety of macroecological and macroevolutionary themes, including character evolution, origin and timing of diversification, biogeographic patterns and species responses to climate change.}, } @article {pmid28012955, year = {2017}, author = {Raheem, DC and Breugelmans, K and Wade, CM and Naggs, FC and Backeljau, T}, title = {Exploring the shell-based taxonomy of the Sri Lankan land snail Corilla H. and A. Adams, 1855 (Pulmonata: Corillidae) using mitochondrial DNA.}, journal = {Molecular phylogenetics and evolution}, volume = {107}, number = {}, pages = {609-618}, doi = {10.1016/j.ympev.2016.12.020}, pmid = {28012955}, issn = {1095-9513}, mesh = {Animal Shells/*anatomy & histology ; Animals ; Base Sequence ; Bayes Theorem ; DNA, Mitochondrial/*genetics ; Databases, Genetic ; Geography ; Phylogeny ; Snails/*anatomy & histology/*classification/genetics ; Sri Lanka ; }, abstract = {The land-snail genus Corilla is endemic to Sri Lanka and India's Western Ghats. The ten extant Sri Lankan species belong to two distinct shell forms that are associated respectively with lowland and montane rainforest. We here present the first molecular phylogenetic analysis for Corilla. Our dataset includes nine nominal Sri Lankan species and is based on three mitochondrial genes (CO1, ND1 and 16S). Although the deeper nodes in the trees are not fully resolved, the results do suggest speciation in Corilla has involved repeated, ecologically-driven convergence in shell form. The mtDNA data agree with the current shell-based taxonomy for C. adamsi, C. beddomeae, C. carabinata, C. humberti and C. colletti, consistently supporting the first four as monophyletic, and supporting the last also as monophyletic in nearly all analyses. Corilla adamsi, C. beddomeae and C. colletti may each contain at least one additional, previously undescribed species. The relationship between northern and eastern C. odontophora couldn't be reliably resolved, but our results suggest that they are distinct species and that there is further species-level or intraspecific (geographical) differentiation within eastern C. odontophora. The current, morphologically-defined species limits of the three remaining nominal species, C. gudei, C. erronea and C. fryae, are inconsistent with the mtDNA sequence data. Northern and southern C. gudei appear to be distinct species: the sister taxon of southern C. gudei is C. humberti, and most analyses showed that the sister taxon of northern C. gudei is the lowland C. carabinata. Corilla erronea and C. fryae constitute a well supported clade in which both nominal species are paraphyletic. While most intra-clade CO1 p-distances are moderate to relatively large, the phylogenetic structuring within the clade does not seem to correspond to any obvious morphological, elevational or geographical patterns. These results are difficult to interpret, and further detailed study is needed before the taxonomic status of C. erronea and C. fryae can be resolved.}, } @article {pmid28004657, year = {2016}, author = {Peters, MK and Hemp, A and Appelhans, T and Behler, C and Classen, A and Detsch, F and Ensslin, A and Ferger, SW and Frederiksen, SB and Gebert, F and Haas, M and Helbig-Bonitz, M and Hemp, C and Kindeketa, WJ and Mwangomo, E and Ngereza, C and Otte, I and Röder, J and Rutten, G and Schellenberger Costa, D and Tardanico, J and Zancolli, G and Deckert, J and Eardley, CD and Peters, RS and Rödel, MO and Schleuning, M and Ssymank, A and Kakengi, V and Zhang, J and Böhning-Gaese, K and Brandl, R and Kalko, EK and Kleyer, M and Nauss, T and Tschapka, M and Fischer, M and Steffan-Dewenter, I}, title = {Predictors of elevational biodiversity gradients change from single taxa to the multi-taxa community level.}, journal = {Nature communications}, volume = {7}, number = {}, pages = {13736}, pmid = {28004657}, issn = {2041-1723}, mesh = {Altitude ; Animals ; *Biodiversity ; Ecosystem ; Geography ; Models, Biological ; Phylogeny ; Plants/classification ; Species Specificity ; Tanzania ; Temperature ; }, abstract = {The factors determining gradients of biodiversity are a fundamental yet unresolved topic in ecology. While diversity gradients have been analysed for numerous single taxa, progress towards general explanatory models has been hampered by limitations in the phylogenetic coverage of past studies. By parallel sampling of 25 major plant and animal taxa along a 3.7 km elevational gradient on Mt. Kilimanjaro, we quantify cross-taxon consensus in diversity gradients and evaluate predictors of diversity from single taxa to a multi-taxa community level. While single taxa show complex distribution patterns and respond to different environmental factors, scaling up diversity to the community level leads to an unambiguous support for temperature as the main predictor of species richness in both plants and animals. Our findings illuminate the influence of taxonomic coverage for models of diversity gradients and point to the importance of temperature for diversification and species coexistence in plant and animal communities.}, } @article {pmid28004348, year = {2017}, author = {Demirkesen, AC and Evrendilek, F}, title = {Compositing climate change vulnerability of a Mediterranean region using spatiotemporally dynamic proxies for ecological and socioeconomic impacts and stabilities.}, journal = {Environmental monitoring and assessment}, volume = {189}, number = {1}, pages = {29}, pmid = {28004348}, issn = {1573-2959}, mesh = {*Climate Change ; Ecology ; *Ecosystem ; Environmental Monitoring/*methods ; Geographic Information Systems ; Mediterranean Region ; Temperature ; Turkey ; }, abstract = {The study presents a new methodology to quantify spatiotemporal dynamics of climate change vulnerability at a regional scale adopting a new conceptual model of vulnerability as a function of climate change impacts, ecological stability, and socioeconomic stability. Spatiotemporal trends of equally weighted proxy variables for the three vulnerability components were generated to develop a composite climate change vulnerability index (CCVI) for a Mediterranean region of Turkey combining Landsat time series data, digital elevation model (DEM)-derived data, ordinary kriging, and geographical information system. Climate change impact was based on spatiotemporal trends of August land surface temperature (LST) between 1987 and 2016. Ecological stability was based on DEM, slope, aspect, and spatiotemporal trends of normalized difference vegetation index (NDVI), while socioeconomic stability was quantified as a function of spatiotemporal trends of land cover, population density, per capita gross domestic product, and illiteracy. The zones ranked on the five classes of no-to-extreme vulnerability were identified where highly and moderately vulnerable lands covered 0.02% (12 km[2]) and 11.8% (6374 km[2]) of the study region, respectively, mostly occurring in the interior central part. The adoption of this composite CCVI approach is expected to lead to spatiotemporally dynamic policy recommendations towards sustainability and tailor preventive and mitigative measures to locally specific characteristics of coupled ecological-socioeconomic systems.}, } @article {pmid28002776, year = {2017}, author = {Fernandes, JP and Freire, M and Guiomar, N and Gil, A}, title = {Using modeling tools for implementing feasible land use and nature conservation governance systems in small islands - The Pico Island (Azores) case-study.}, journal = {Journal of environmental management}, volume = {189}, number = {}, pages = {1-13}, doi = {10.1016/j.jenvman.2016.12.034}, pmid = {28002776}, issn = {1095-8630}, mesh = {Azores ; Conservation of Natural Resources/economics/*methods ; Decision Support Techniques ; Environmental Policy ; Government ; *Models, Theoretical ; }, abstract = {The present study deals with the development of systematic conservation planning as management instrument in small oceanic islands, ensuring open systems of governance, and able to integrate an informed and involved participation of the stakeholders. Marxan software was used to define management areas according a set of alternative land use scenarios considering different conservation and management paradigms. Modeled conservation zones were interpreted and compared with the existing protected areas allowing more fused information for future trade-outs and stakeholder's involvement. The results, allowing the identification of Target Management Units (TMU) based on the consideration of different development scenarios proved to be consistent with a feasible development of evaluation approaches able to support sound governance systems. Moreover, the detailed geographic identification of TMU seems to be able to support participated policies towards a more sustainable management of the entire island.}, } @article {pmid28002598, year = {2016}, author = {Santos, DN and Nunes, CF and Setotaw, TA and Pio, R and Pasqual, M and Cançado, GM}, title = {Molecular characterization and population structure study of cambuci: strategy for conservation and genetic improvement.}, journal = {Genetics and molecular research : GMR}, volume = {15}, number = {4}, pages = {}, doi = {10.4238/gmr15049134}, pmid = {28002598}, issn = {1676-5680}, mesh = {Bayes Theorem ; Brazil ; Cluster Analysis ; Conservation of Natural Resources ; DNA, Plant/*genetics ; Databases, Genetic ; Endangered Species ; *Genetic Variation ; *Microsatellite Repeats ; Myrtaceae/classification/*genetics ; Principal Component Analysis ; }, abstract = {Cambuci (Campomanesia phaea) belongs to the Myrtaceae family and is native to the Atlantic Forest of Brazil. It has ecological and social appeal but is exposed to problems associated with environmental degradation and expansion of agricultural activities in the region. Comprehensive studies on this species are rare, making its conservation and genetic improvement difficult. Thus, it is important to develop research activities to understand the current situation of the species as well as to make recommendations for its conservation and use. This study was performed to characterize the cambuci accessions found in the germplasm bank of Coordenadoria de Assistência Técnica Integral using inter-simple sequence repeat markers, with the goal of understanding the plant's population structure. The results showed the existence of some level of genetic diversity among the cambuci accessions that could be exploited for the genetic improvement of the species. Principal coordinate analysis and discriminant analysis clustered the 80 accessions into three groups, whereas Bayesian model-based clustering analysis clustered them into two groups. The formation of two cluster groups and the high membership coefficients within the groups pointed out the importance of further collection to cover more areas and more genetic variability within the species. The study also showed the lack of conservation activities; therefore, more attention from the appropriate organizations is needed to plan and implement natural and ex situ conservation activities.}, } @article {pmid28002495, year = {2016}, author = {Hinton, JW and Proctor, C and Kelly, MJ and van Manen, FT and Vaughan, MR and Chamberlain, MJ}, title = {Space Use and Habitat Selection by Resident and Transient Red Wolves (Canis rufus).}, journal = {PloS one}, volume = {11}, number = {12}, pages = {e0167603}, pmid = {28002495}, issn = {1932-6203}, mesh = {Animals ; *Ecosystem ; Geographic Information Systems ; Homing Behavior/*physiology ; Population Dynamics ; Telemetry ; Wolves ; }, abstract = {Recovery of large carnivores remains a challenge because complex spatial dynamics that facilitate population persistence are poorly understood. In particular, recovery of the critically endangered red wolf (Canis rufus) has been challenging because of its vulnerability to extinction via human-caused mortality and hybridization with coyotes (Canis latrans). Therefore, understanding red wolf space use and habitat selection is important to assist recovery because key aspects of wolf ecology such as interspecific competition, foraging, and habitat selection are well-known to influence population dynamics and persistence. During 2009-2011, we used global positioning system (GPS) radio-telemetry to quantify space use and 3rd-order habitat selection for resident and transient red wolves on the Albemarle Peninsula of eastern North Carolina. The Albemarle Peninsula was a predominantly agricultural landscape in which red wolves maintained spatially stable home ranges that varied between 25 km2 and 190 km2. Conversely, transient red wolves did not maintain home ranges and traversed areas between 122 km2 and 681 km2. Space use by transient red wolves was not spatially stable and exhibited shifting patterns until residency was achieved by individual wolves. Habitat selection was similar between resident and transient red wolves in which agricultural habitats were selected over forested habitats. However, transients showed stronger selection for edges and roads than resident red wolves. Behaviors of transient wolves are rarely reported in studies of space use and habitat selection because of technological limitations to observed extensive space use and because they do not contribute reproductively to populations. Transients in our study comprised displaced red wolves and younger dispersers that competed for limited space and mating opportunities. Therefore, our results suggest that transiency is likely an important life-history strategy for red wolves that facilitates metapopulation dynamics through short- and long-distance movements and eventual replacement of breeding residents lost to mortality.}, } @article {pmid28000753, year = {2016}, author = {Lai, S and Wardrop, NA and Huang, Z and Bosco, C and Sun, J and Bird, T and Wesolowski, A and Zhou, S and Zhang, Q and Zheng, C and Li, Z and Tatem, AJ and Yu, H}, title = {Plasmodium falciparum malaria importation from Africa to China and its mortality: an analysis of driving factors.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {39524}, pmid = {28000753}, issn = {2045-2322}, support = {/WT_/Wellcome Trust/United Kingdom ; U19 AI051915/AI/NIAID NIH HHS/United States ; U19 AI089674/AI/NIAID NIH HHS/United States ; 106866/Z/15/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Adult ; Africa/epidemiology ; China/epidemiology ; Databases, Factual ; Female ; Geography ; Humans ; Malaria, Falciparum/*epidemiology/*mortality/*transmission ; Male ; Middle Aged ; *Plasmodium falciparum ; Prevalence ; Public Health ; Risk Factors ; Travel ; }, abstract = {Plasmodium falciparum malaria importation from Africa to China is rising with increasing Chinese overseas investment and international travel. Identifying networks and drivers of this phenomenon as well as the contributors to high case-fatality rate is a growing public health concern to enable efficient response. From 2011-2015, 8653 P. falciparum cases leading to 98 deaths (11.3 per 1000 cases) were imported from 41 sub-Saharan countries into China, with most cases (91.3%) occurring in labour-related Chinese travellers. Four strongly connected groupings of origin African countries with destination Chinese provinces were identified, and the number of imported cases was significantly associated with the volume of air passengers to China (P = 0.006), parasite prevalence in Africa (P < 0.001), and the amount of official development assistance from China (P < 0.001) with investment in resource extraction having the strongest relationship with parasite importation. Risk factors for deaths from imported cases were related to the capacity of malaria diagnosis and diverse socioeconomic factors. The spatial heterogeneity uncovered, principal drivers explored, and risk factors for mortality found in the rising rates of P. falciparum malaria importation to China can serve to refine malaria elimination strategies and the management of cases, and high risk groups and regions should be targeted.}, } @article {pmid27999361, year = {2016}, author = {Jiang, C and Zhang, SB and Zhang, QZ}, title = {A New Adaptive H-Infinity Filtering Algorithm for the GPS/INS Integrated Navigation.}, journal = {Sensors (Basel, Switzerland)}, volume = {16}, number = {12}, pages = {}, pmid = {27999361}, issn = {1424-8220}, abstract = {The Kalman filter is an optimal estimator with numerous applications in technology, especially in systems with Gaussian distributed noise. Moreover, the adaptive Kalman filtering algorithms, based on the Kalman filter, can control the influence of dynamic model errors. In contrast to the adaptive Kalman filtering algorithms, the H-infinity filter is able to address the interference of the stochastic model by minimization of the worst-case estimation error. In this paper, a novel adaptive H-infinity filtering algorithm, which integrates the adaptive Kalman filter and the H-infinity filter in order to perform a comprehensive filtering algorithm, is presented. In the proposed algorithm, a robust estimation method is employed to control the influence of outliers. In order to verify the proposed algorithm, experiments with real data of the Global Positioning System (GPS) and Inertial Navigation System (INS) integrated navigation, were conducted. The experimental results have shown that the proposed algorithm has multiple advantages compared to the other filtering algorithms.}, } @article {pmid27997742, year = {2017}, author = {Donnelly, K and Cottrell, J and Ennos, RA and Vendramin, GG and A'Hara, S and King, S and Perry, A and Wachowiak, W and Cavers, S}, title = {Reconstructing the plant mitochondrial genome for marker discovery: a case study using Pinus.}, journal = {Molecular ecology resources}, volume = {17}, number = {5}, pages = {943-954}, doi = {10.1111/1755-0998.12646}, pmid = {27997742}, issn = {1755-0998}, mesh = {Computational Biology ; DNA, Mitochondrial/chemistry/genetics ; DNA, Plant/chemistry/genetics ; Europe ; *Genome, Mitochondrial ; Haplotypes ; Mitochondria/*genetics ; Pinus/classification/*genetics ; Polymorphism, Single Nucleotide ; Sequence Analysis, DNA ; Whole Genome Sequencing ; }, abstract = {Whole-genome-shotgun (WGS) sequencing of total genomic DNA was used to recover ~1 Mbp of novel mitochondrial (mtDNA) sequence from Pinus sylvestris (L.) and three members of the closely related Pinus mugo species complex. DNA was extracted from megagametophyte tissue from six mother trees from locations across Europe, and 100-bp paired-end sequencing was performed on the Illumina HiSeq platform. Candidate mtDNA sequences were identified by their size and coverage characteristics, and by comparison with published plant mitochondrial genomes. Novel variants were identified, and primers targeting these loci were trialled on a set of 28 individuals from across Europe. In total, 31 SNP loci were successfully resequenced, characterizing 15 unique haplotypes. This approach offers a cost-effective means of developing marker resources for mitochondrial genomes in other plant species where reference sequences are unavailable.}, } @article {pmid27992952, year = {2017}, author = {Ryan, EM and Ogle, K and Peltier, D and Walker, AP and De Kauwe, MG and Medlyn, BE and Williams, DG and Parton, W and Asao, S and Guenet, B and Harper, AB and Lu, X and Luus, KA and Zaehle, S and Shu, S and Werner, C and Xia, J and Pendall, E}, title = {Gross primary production responses to warming, elevated CO2 , and irrigation: quantifying the drivers of ecosystem physiology in a semiarid grassland.}, journal = {Global change biology}, volume = {23}, number = {8}, pages = {3092-3106}, doi = {10.1111/gcb.13602}, pmid = {27992952}, issn = {1365-2486}, mesh = {*Carbon Cycle ; Carbon Dioxide ; Climate ; *Ecosystem ; *Grassland ; Wyoming ; }, abstract = {Determining whether the terrestrial biosphere will be a source or sink of carbon (C) under a future climate of elevated CO2 (eCO2) and warming requires accurate quantification of gross primary production (GPP), the largest flux of C in the global C cycle. We evaluated 6 years (2007-2012) of flux-derived GPP data from the Prairie Heating and CO2 Enrichment (PHACE) experiment, situated in a grassland in Wyoming, USA. The GPP data were used to calibrate a light response model whose basic formulation has been successfully used in a variety of ecosystems. The model was extended by modeling maximum photosynthetic rate (Amax) and light-use efficiency (Q) as functions of soil water, air temperature, vapor pressure deficit, vegetation greenness, and nitrogen at current and antecedent (past) timescales. The model fits the observed GPP well (R[2] = 0.79), which was confirmed by other model performance checks that compared different variants of the model (e.g. with and without antecedent effects). Stimulation of cumulative 6-year GPP by warming (29%, P = 0.02) and eCO2 (26%, P = 0.07) was primarily driven by enhanced C uptake during spring (129%, P = 0.001) and fall (124%, P = 0.001), respectively, which was consistent across years. Antecedent air temperature (Tairant) and vapor pressure deficit (VPDant) effects on Amax (over the past 3-4 days and 1-3 days, respectively) were the most significant predictors of temporal variability in GPP among most treatments. The importance of VPDant suggests that atmospheric drought is important for predicting GPP under current and future climate; we highlight the need for experimental studies to identify the mechanisms underlying such antecedent effects. Finally, posterior estimates of cumulative GPP under control and eCO2 treatments were tested as a benchmark against 12 terrestrial biosphere models (TBMs). The narrow uncertainties of these data-driven GPP estimates suggest that they could be useful semi-independent data streams for validating TBMs.}, } @article {pmid27991706, year = {2017}, author = {Zajączkowska, U and Grabowska, K and Kokot, G and Kruk, M}, title = {On the benefits of living in clumps: a case study on Polytrichastrum formosum.}, journal = {Plant biology (Stuttgart, Germany)}, volume = {19}, number = {2}, pages = {156-164}, doi = {10.1111/plb.12532}, pmid = {27991706}, issn = {1438-8677}, mesh = {Biomechanical Phenomena ; Bryophyta/anatomy & histology/*physiology ; Ecology ; Models, Theoretical ; Plant Leaves/anatomy & histology/physiology ; Plant Stems/anatomy & histology/physiology ; Water/*physiology ; }, abstract = {The study concerns the mechanics and water relationships of clumps of a species of endohydric moss, Polytrichastrum formosum. Anatomical and morphological studies were done using optical and scanning electron microscopy. Experiments on waterdrop capture and their distribution to adjacent shoots within a moss clump were performed with the experimental set-up for the droplet collision phenomena and ultra-high speed camera. The mechanical strength of the moss clump was tested on an electromechanical testing machine. During the process of moss clump wetting, the falling water drops were captured by the apical stem part or leaves, then flowed down while adhering to the gametophore and never lost their surface continuity. In places of contact with another leaf, the water drop stops there and joins the leaves, enabling their hydration. Mathematical analysis of anatomical images showed that moss stems have different zones with varying cell lumen and cell wall/cell radius ratios, suggesting the occurrence of a periodic component structure. Our study provides evidence that the reaction of mosses to mechanical forces depends on the size of the clump, and that small groups are clearly stronger than larger groups. The clump structure of mosses acts as a net for falling rain droplets. Clumps of Polytrichastrum having overlapping leaves, at the time of loading formed a structure similar to a lattice. The observed reaction of mosses to mechanical forces indicates that this phenomenon appears to be analogous to the 'size effect on structural strength' that is of great importance for various fields of engineering.}, } @article {pmid27991489, year = {2016}, author = {Cao, X and Liu, J and Chen, J and Zheng, G and Kuntner, M and Agnarsson, I}, title = {Rapid dissemination of taxonomic discoveries based on DNA barcoding and morphology.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {37066}, pmid = {27991489}, issn = {2045-2322}, mesh = {Animals ; Biodiversity ; China ; Classification/*methods ; *DNA Barcoding, Taxonomic ; DNA, Mitochondrial/genetics ; Datasets as Topic ; Electron Transport Complex IV/genetics ; Female ; Gene Library ; Genitalia/anatomy & histology ; *Information Dissemination ; Male ; Sequence Analysis, DNA ; Species Specificity ; Spiders/anatomy & histology/*classification/genetics ; Taiwan ; }, abstract = {The taxonomic impediment is characterized by dwindling classical taxonomic expertise, and slow pace of revisionary work, thus more rapid taxonomic assessments are needed. Here we pair rapid DNA barcoding methods with swift assessment of morphology in an effort to gauge diversity, establish species limits, and rapidly disseminate taxonomic information prior to completion of formal taxonomic revisions. We focus on a poorly studied, but diverse spider genus, Pseudopoda, from East Asia. We augmented the standard barcoding locus (COI) with nuclear DNA sequence data (ITS2) and analyzed congruence among datasets and species delimitation methods for a total of 572 individuals representing 23 described species and many potentially new species. Our results suggest that a combination of CO1 + ITS2 fragments identify and diagnose species better than the mitochondrial barcodes alone, and that certain tree based methods yield considerably higher diversity estimates than the distance-based approaches and morphology. Combined, through an extensive field survey, we detect a twofold increase in species diversity in the surveyed area, at 42-45, with most species representing short range endemics. Our study demonstrates the power of biodiversity assessments and swift dissemination of taxonomic data through rapid inventory, and through a combination of morphological and multi-locus DNA barcoding diagnoses of diverse arthropod lineages.}, } @article {pmid27986083, year = {2016}, author = {Narayanasamy, S and Jarosz, Y and Muller, EE and Heintz-Buschart, A and Herold, M and Kaysen, A and Laczny, CC and Pinel, N and May, P and Wilmes, P}, title = {IMP: a pipeline for reproducible reference-independent integrated metagenomic and metatranscriptomic analyses.}, journal = {Genome biology}, volume = {17}, number = {1}, pages = {260}, pmid = {27986083}, issn = {1474-760X}, mesh = {Algorithms ; Computational Biology ; Genomics ; Metagenome/*genetics ; Microbiota/*genetics ; *Software ; Transcriptome/*genetics ; Workflow ; }, abstract = {Existing workflows for the analysis of multi-omic microbiome datasets are lab-specific and often result in sub-optimal data usage. Here we present IMP, a reproducible and modular pipeline for the integrated and reference-independent analysis of coupled metagenomic and metatranscriptomic data. IMP incorporates robust read preprocessing, iterative co-assembly, analyses of microbial community structure and function, automated binning, as well as genomic signature-based visualizations. The IMP-based data integration strategy enhances data usage, output volume, and output quality as demonstrated using relevant use-cases. Finally, IMP is encapsulated within a user-friendly implementation using Python and Docker. IMP is available at http://r3lab.uni.lu/web/imp/ (MIT license).}, } @article {pmid27984661, year = {2017}, author = {Gibb, H and Dunn, RR and Sanders, NJ and Grossman, BF and Photakis, M and Abril, S and Agosti, D and Andersen, AN and Angulo, E and Armbrecht, I and Arnan, X and Baccaro, FB and Bishop, TR and Boulay, R and Brühl, C and Castracani, C and Cerda, X and Del Toro, I and Delsinne, T and Diaz, M and Donoso, DA and Ellison, AM and Enriquez, ML and Fayle, TM and Feener, DH and Fisher, BL and Fisher, RN and Fitzpatrick, MC and Gómez, C and Gotelli, NJ and Gove, A and Grasso, DA and Groc, S and Guenard, B and Gunawardene, N and Heterick, B and Hoffmann, B and Janda, M and Jenkins, C and Kaspari, M and Klimes, P and Lach, L and Laeger, T and Lattke, J and Leponce, M and Lessard, JP and Longino, J and Lucky, A and Luke, SH and Majer, J and McGlynn, TP and Menke, S and Mezger, D and Mori, A and Moses, J and Munyai, TC and Pacheco, R and Paknia, O and Pearce-Duvet, J and Pfeiffer, M and Philpott, SM and Resasco, J and Retana, J and Silva, RR and Sorger, MD and Souza, J and Suarez, A and Tista, M and Vasconcelos, HL and Vonshak, M and Weiser, MD and Yates, M and Parr, CL}, title = {A global database of ant species abundances.}, journal = {Ecology}, volume = {98}, number = {3}, pages = {883-884}, doi = {10.1002/ecy.1682}, pmid = {27984661}, issn = {0012-9658}, mesh = {Animals ; Ants/classification/*physiology ; *Databases, Factual ; *Ecology ; Ecosystem ; }, abstract = {What forces structure ecological assemblages? A key limitation to general insights about assemblage structure is the availability of data that are collected at a small spatial grain (local assemblages) and a large spatial extent (global coverage). Here, we present published and unpublished data from 51 ,388 ant abundance and occurrence records of more than 2,693 species and 7,953 morphospecies from local assemblages collected at 4,212 locations around the world. Ants were selected because they are diverse and abundant globally, comprise a large fraction of animal biomass in most terrestrial communities, and are key contributors to a range of ecosystem functions. Data were collected between 1949 and 2014, and include, for each geo-referenced sampling site, both the identity of the ants collected and details of sampling design, habitat type, and degree of disturbance. The aim of compiling this data set was to provide comprehensive species abundance data in order to test relationships between assemblage structure and environmental and biogeographic factors. Data were collected using a variety of standardized methods, such as pitfall and Winkler traps, and will be valuable for studies investigating large-scale forces structuring local assemblages. Understanding such relationships is particularly critical under current rates of global change. We encourage authors holding additional data on systematically collected ant assemblages, especially those in dry and cold, and remote areas, to contact us and contribute their data to this growing data set.}, } @article {pmid27981576, year = {2017}, author = {Marchand, P and Garel, M and Bourgoin, G and Duparc, A and Dubray, D and Maillard, D and Loison, A}, title = {Combining familiarity and landscape features helps break down the barriers between movements and home ranges in a non-territorial large herbivore.}, journal = {The Journal of animal ecology}, volume = {86}, number = {2}, pages = {371-383}, doi = {10.1111/1365-2656.12616}, pmid = {27981576}, issn = {1365-2656}, mesh = {*Animal Distribution ; Animals ; Ecosystem ; Female ; France ; Geographic Information Systems ; *Homing Behavior ; Male ; Memory ; *Movement ; Recognition, Psychology ; Sheep/*physiology ; }, abstract = {Recent advances in animal ecology have enabled identification of certain mechanisms that lead to the emergence of territories and home ranges from movements considered as unbounded. Among them, memory and familiarity have been identified as key parameters in cognitive maps driving animal navigation, but have been only recently used in empirical analyses of animal movements. At the same time, the influence of landscape features on movements of numerous species and on space division in territorial animals has been highlighted. Despite their potential as exocentric information in cognitive maps and as boundaries for home ranges, few studies have investigated their role in the design of home ranges of non-territorial species. Using step selection analyses, we assessed the relative contribution of habitat characteristics, familiarity preferences and linear landscape features in movement step selection of 60 GPS-collared Mediterranean mouflon Ovis gmelini musimon × Ovis sp. monitored in southern France. Then, we evaluated the influence of these movement-impeding landscape features on the design of home ranges by testing for a non-random distribution of these behavioural barriers within sections of space differentially used by mouflon. We reveal that familiarity and landscape features are key determinants of movements, relegating to a lower level certain habitat constraints (e.g. food/cover trade-off) that we had previously identified as important for this species. Mouflon generally avoid crossing both anthropogenic (i.e. roads, tracks and hiking trails) and natural landscape features (i.e. ridges, talwegs and forest edges) while moving in the opposite direction, preferentially toward familiar areas. These specific behaviours largely depend on the relative position of each movement step regarding distance to the landscape features or level of familiarity in the surroundings. We also revealed cascading consequences on the design of home ranges in which most landscape features were excluded from cores and relegated to the peripheral areas. These results provide crucial information on landscape connectivity in a context of marked habitat fragmentation. They also call for more research on the role of landscape features in the emergence of home ranges in non-territorial species using recent methodological developments bridging the gap between movements and space use patterns.}, } @article {pmid27978605, year = {2017}, author = {Winkler, M and Escobar García, P and Gattringer, A and Sonnleitner, M and Hülber, K and Schönswetter, P and Schneeweiss, GM}, title = {A novel method to infer the origin of polyploids from Amplified Fragment Length Polymorphism data reveals that the alpine polyploid complex of Senecio carniolicus (Asteraceae) evolved mainly via autopolyploidy.}, journal = {Molecular ecology resources}, volume = {17}, number = {5}, pages = {877-892}, doi = {10.1111/1755-0998.12641}, pmid = {27978605}, issn = {1755-0998}, mesh = {Amplified Fragment Length Polymorphism Analysis/*methods ; Asteraceae/*genetics ; Computational Biology/*methods ; DNA, Plant/genetics ; Europe ; Evolution, Molecular ; *Polyploidy ; }, abstract = {Despite its evolutionary and ecological relevance, the mode of polyploid origin has been notoriously difficult to be reconstructed from molecular data. Here, we present a method to identify the putative parents of polyploids and thus to infer the mode of their origin (auto- vs. allopolyploidy) from Amplified Fragment Length Polymorphism (AFLP) data. To this end, we use Cohen's d of distances between in silico polyploids, generated within a priori defined scenarios of origin from a priori delimited putative parental entities (e.g. taxa, genetic lineages), and natural polyploids. Simulations show that the discriminatory power of the proposed method increases mainly with increasing divergence between the lower-ploid putative ancestors and less so with increasing delay of polyploidization relative to the time of divergence. We apply the new method to the Senecio carniolicus aggregate, distributed in the European Alps and comprising two diploid, one tetraploid and one hexaploid species. In the eastern part of its distribution, the S. carniolicus aggregate was inferred to comprise an autopolyploid series, whereas for western populations of the tetraploid species, an allopolyploid origin involving the two diploid species was the most likely scenario. Although this suggests that the tetraploid species has two independent origins, other evidence (ribotype distribution, morphology) is consistent with the hypothesis of an autopolyploid origin with subsequent introgression by the second diploid species. Altogether, identifying the best among alternative scenarios using Cohen's d can be straightforward, but particular scenarios, such as allopolyploid origin vs. autopolyploid origin with subsequent introgression, remain difficult to be distinguished.}, } @article {pmid27977685, year = {2016}, author = {Beaudoin, G and Rafanoharana, S and Boissière, M and Wijaya, A and Wardhana, W}, title = {Completing the Picture: Importance of Considering Participatory Mapping for REDD+ Measurement, Reporting and Verification (MRV).}, journal = {PloS one}, volume = {11}, number = {12}, pages = {e0166592}, pmid = {27977685}, issn = {1932-6203}, mesh = {Conservation of Natural Resources/*methods ; *Ecosystem ; Environmental Monitoring/*methods ; *Forests ; *Geographic Information Systems ; Indonesia ; }, abstract = {Remote sensing has been widely used for mapping land cover and is considered key to monitoring changes in forest areas in the REDD+ Measurement, Reporting and Verification (MRV) system. But Remote Sensing as a desk study cannot capture the whole picture; it also requires ground checking. Therefore, complementing remote sensing analysis using participatory mapping can help provide information for an initial forest cover assessment, gain better understanding of how local land use might affect changes, and provide a way to engage local communities in REDD+. Our study looked at the potential of participatory mapping in providing complementary information for remotely sensed maps. The research sites were located in different ecological and socio-economic contexts in the provinces of Papua, West Kalimantan and Central Java, Indonesia. Twenty-one maps of land cover and land use were drawn with local community participation during focus group discussions in seven villages. These maps, covering a total of 270,000ha, were used to add information to maps developed using remote sensing, adding 39 land covers to the eight from our initial desk assessment. They also provided additional information on drivers of land use and land cover change, resource areas, territory claims and land status, which we were able to correlate to understand changes in forest cover. Incorporating participatory mapping in the REDD+ MRV protocol would help with initial remotely sensed land classifications, stratify an area for ground checks and measurement plots, and add other valuable social data not visible at the RS scale. Ultimately, it would provide a forum for local communities to discuss REDD+ activities and develop a better understanding of REDD+.}, } @article {pmid27977667, year = {2016}, author = {Subramanian, R and Graham, AL and Grenfell, BT and Arinaminpathy, N}, title = {Universal or Specific? A Modeling-Based Comparison of Broad-Spectrum Influenza Vaccines against Conventional, Strain-Matched Vaccines.}, journal = {PLoS computational biology}, volume = {12}, number = {12}, pages = {e1005204}, pmid = {27977667}, issn = {1553-7358}, support = {MR/K010174/1/MRC_/Medical Research Council/United Kingdom ; P2C HD047879/HD/NICHD NIH HHS/United States ; }, mesh = {Computational Biology ; Humans ; Influenza A virus/immunology ; Influenza Vaccines/*immunology ; *Influenza, Human/epidemiology/immunology/prevention & control/virology ; *Models, Immunological ; *Models, Statistical ; *Pandemics/prevention & control/statistics & numerical data ; Vaccination/*statistics & numerical data ; }, abstract = {Despite the availability of vaccines, influenza remains a major public health challenge. A key reason is the virus capacity for immune escape: ongoing evolution allows the continual circulation of seasonal influenza, while novel influenza viruses invade the human population to cause a pandemic every few decades. Current vaccines have to be updated continually to keep up to date with this antigenic change, but emerging 'universal' vaccines-targeting more conserved components of the influenza virus-offer the potential to act across all influenza A strains and subtypes. Influenza vaccination programmes around the world are steadily increasing in their population coverage. In future, how might intensive, routine immunization with novel vaccines compare against similar mass programmes utilizing conventional vaccines? Specifically, how might novel and conventional vaccines compare, in terms of cumulative incidence and rates of antigenic evolution of seasonal influenza? What are their potential implications for the impact of pandemic emergence? Here we present a new mathematical model, capturing both transmission dynamics and antigenic evolution of influenza in a simple framework, to explore these questions. We find that, even when matched by per-dose efficacy, universal vaccines could dampen population-level transmission over several seasons to a greater extent than conventional vaccines. Moreover, by lowering opportunities for cross-protective immunity in the population, conventional vaccines could allow the increased spread of a novel pandemic strain. Conversely, universal vaccines could mitigate both seasonal and pandemic spread. However, where it is not possible to maintain annual, intensive vaccination coverage, the duration and breadth of immunity raised by universal vaccines are critical determinants of their performance relative to conventional vaccines. In future, conventional and novel vaccines are likely to play complementary roles in vaccination strategies against influenza: in this context, our results suggest important characteristics to monitor during the clinical development of emerging vaccine technologies.}, } @article {pmid27976822, year = {2017}, author = {Pang, C and Radomyski, A and Subramanian, V and Nadimi-Goki, M and Marcomini, A and Linkov, I}, title = {Multi-criteria decision analysis applied to harmful algal bloom management: A case study.}, journal = {Integrated environmental assessment and management}, volume = {13}, number = {4}, pages = {631-639}, doi = {10.1002/ieam.1882}, pmid = {27976822}, issn = {1551-3793}, mesh = {*Decision Support Techniques ; *Ecosystem ; Environmental Monitoring/*methods ; *Harmful Algal Bloom ; *Lakes ; Water Pollution/*prevention & control ; }, abstract = {Harmful algal blooms (HABs) have received greater attention in recent years due to an increase in the frequency of outbreaks and a growing potential for blooms to exact considerable economic losses and negatively impact ecosystem health. Human activity has been shown to intensify HAB outbreaks through increased eutrophication, elevated local air and water temperatures, disturbance of the thermal stratification of lakes, and modification of local hydrology. With the advent of new remediation technologies and a better understanding of the ecological factors affecting HABs, mitigating the adverse effects of HABs has become more feasible than ever before but still requires balancing mitigation efficiency, environmental impacts, costs, and stakeholder needs. In the present paper, we discuss potential HAB management solutions and propose using a Multi-Criteria Decision Analysis (MCDA) framework to analyze the perspectives and priorities of various stakeholders as they pertain to 4 major considerations for HAB mitigation: human health, environmental impact, social impact, and technical feasibility. A hypothetical case study of an HAB-affected lake is used to demonstrate how stakeholders may prioritize HAB management alternatives within the MCDA framework. Integr Environ Assess Manag 2017;13:631-639. © 2016 SETAC.}, } @article {pmid27976627, year = {2016}, author = {Wayland, MT and Chubb, JC}, title = {A new R package and web application for detecting bilateral asymmetry in parasitic infections.}, journal = {Folia parasitologica}, volume = {63}, number = {}, pages = {}, doi = {10.14411/fp.2016.039}, pmid = {27976627}, issn = {0015-5683}, mesh = {Animals ; Data Interpretation, Statistical ; Fish Diseases/*parasitology/pathology ; Metacercariae/physiology ; Perches/parasitology ; *Software ; Trematoda/*physiology ; Trematode Infections/*parasitology/*pathology ; }, abstract = {When parasites invade paired structures of their host non-randomly, the resulting asymmetry may have both pathological and ecological significance. To facilitate the detection and visualisation of asymmetric infections we have developed a free software tool, Analysis of Symmetry of Parasitic Infections (ASPI). This tool has been implemented as an R package (https://cran.r-project.org/package=aspi) and a web application (https://wayland.shinyapps.io/aspi). ASPI can detect both consistent bias towards one side, and inconsistent bias in which the left side is favoured in some hosts and the right in others. Application of ASPI is demonstrated using previously unpublished data on the distribution of metacercariae of species of Diplostomum von Nordmann, 1832 in the eyes of ruffe Gymnocephalus cernua (Linnaeus). Invasion of the lenses appeared to be random, with the proportion of metacercariae in the left and right lenses showing the pattern expected by chance. However, analysis of counts of metacercariae from the humors, choroid and retina revealed asymmetry between eyes in 38% of host fish.}, } @article {pmid27976458, year = {2017}, author = {Liang, W and Lü, Y and Zhang, W and Li, S and Jin, Z and Ciais, P and Fu, B and Wang, S and Yan, J and Li, J and Su, H}, title = {Grassland gross carbon dioxide uptake based on an improved model tree ensemble approach considering human interventions: global estimation and covariation with climate.}, journal = {Global change biology}, volume = {23}, number = {7}, pages = {2720-2742}, doi = {10.1111/gcb.13592}, pmid = {27976458}, issn = {1365-2486}, mesh = {*Carbon Cycle ; *Carbon Dioxide ; Climate ; Climate Change ; Ecosystem ; *Grassland ; *Trees ; }, abstract = {Grassland ecosystems act as a crucial role in the global carbon cycle and provide vital ecosystem services for many species. However, these low-productivity and water-limited ecosystems are sensitive and vulnerable to climate perturbations and human intervention, the latter of which is often not considered due to lack of spatial information regarding the grassland management. Here by the application of a model tree ensemble (MTE-GRASS) trained on local eddy covariance data and using as predictors gridded climate and management intensity field (grazing and cutting), we first provide an estimate of global grassland gross primary production (GPP). GPP from our study compares well (modeling efficiency NSE = 0.85 spatial; NSE between 0.69 and 0.94 interannual) with that from flux measurement. Global grassland GPP was on average 11 ± 0.31 Pg C yr[-1] and exhibited significantly increasing trend at both annual and seasonal scales, with an annual increase of 0.023 Pg C (0.2%) from 1982 to 2011. Meanwhile, we found that at both annual and seasonal scale, the trend (except for northern summer) and interannual variability of the GPP are primarily driven by arid/semiarid ecosystems, the latter of which is due to the larger variation in precipitation. Grasslands in arid/semiarid regions have a stronger (33 g C m[-2] yr[-1] /100 mm) and faster (0- to 1-month time lag) response to precipitation than those in other regions. Although globally spatial gradients (71%) and interannual changes (51%) in GPP were mainly driven by precipitation, where most regions with arid/semiarid climate zone, temperature and radiation together shared half of GPP variability, which is mainly distributed in the high-latitude or cold regions. Our findings and the results of other studies suggest the overwhelming importance of arid/semiarid regions as a control on grassland ecosystems carbon cycle. Similarly, under the projected future climate change, grassland ecosystems in these regions will be potentially greatly influenced.}, } @article {pmid27973614, year = {2016}, author = {Davis, SE and Maftei, M and Mallory, ML}, title = {Migratory Connectivity at High Latitudes: Sabine's Gulls (Xema sabini) from a Colony in the Canadian High Arctic Migrate to Different Oceans.}, journal = {PloS one}, volume = {11}, number = {12}, pages = {e0166043}, pmid = {27973614}, issn = {1932-6203}, mesh = {*Animal Migration ; Animals ; Arctic Regions ; Atlantic Ocean ; Canada ; Charadriiformes/*physiology ; Ecosystem ; Female ; Geographic Information Systems ; Geography ; Male ; Namibia ; Pacific Ocean ; Peru ; Seasons ; South Africa ; }, abstract = {The world's Arctic latitudes are some of the most recently colonized by birds, and an understanding of the migratory connectivity of circumpolar species offers insights into the mechanisms of range expansion and speciation. Migratory divides exist for many birds, however for many taxa it is unclear where such boundaries lie, and to what extent these affect the connectivity of species breeding across their ranges. Sabine's gulls (Xema sabini) have a patchy, circumpolar breeding distribution and overwinter in two ecologically similar areas in different ocean basins: the Humboldt Current off the coast of Peru in the Pacific, and the Benguela Current off the coasts of South Africa and Namibia in the Atlantic. We used geolocators to track Sabine's gulls breeding at a colony in the Canadian High Arctic to determine their migratory pathways and wintering sites. Our study provides evidence that birds from this breeding site disperse to both the Pacific and Atlantic oceans during the non-breeding season, which suggests that a migratory divide for this species exists in the Nearctic. Remarkably, members of one mated pair wintered in opposite oceans. Our results ultimately suggest that colonization of favorable breeding habitat may be one of the strongest drivers of range expansion in the High Arctic.}, } @article {pmid27973538, year = {2016}, author = {Gonzáles-Andrés, C and F M Lopes, P and Cortés, J and Sánchez-Lizaso, JL and Pennino, MG}, title = {Abundance and Distribution Patterns of Thunnus albacares in Isla del Coco National Park through Predictive Habitat Suitability Models.}, journal = {PloS one}, volume = {11}, number = {12}, pages = {e0168212}, pmid = {27973538}, issn = {1932-6203}, mesh = {*Animal Distribution ; Animals ; Bayes Theorem ; Chlorophyll/chemistry ; Chlorophyll A ; Climate Change ; Costa Rica ; *Ecosystem ; Fisheries ; Geographic Information Systems ; Temperature ; *Tuna ; Weather ; }, abstract = {Information on the distribution and habitat preferences of ecologically and commercially important species is essential for their management and protection. This is especially important as climate change, pollution, and overfishing change the structure and functioning of pelagic ecosystems. In this study, we used Bayesian hierarchical spatial-temporal models to map the Essential Fish Habitats of the Yellowfin tuna (Thunnus albacares) in the waters around Isla del Coco National Park, Pacific Costa Rica, based on independent underwater observations from 1993 to 2013. We assessed if observed changes in the distribution and abundance of this species are related with habitat characteristics, fishing intensity or more extreme climatic events, including the El Niño Southern Oscillation, and changes on the average sea surface temperature. Yellowfin tuna showed a decreasing abundance trend in the sampled period, whereas higher abundances were found in shallow and warmer waters, with high concentration of chlorophyll-a, and in surrounding seamounts. In addition, El Niño Southern Oscillation events did not seem to affect Yellowfin tuna distribution and abundance. Understanding the habitat preferences of this species, using approaches as the one developed here, may help design integrated programs for more efficient management of vulnerable species.}, } @article {pmid27973530, year = {2016}, author = {Doughty, CE and Wolf, A}, title = {Detecting 3D Vegetation Structure with the Galileo Space Probe: Can a Distant Probe Detect Vegetation Structure on Earth?.}, journal = {PloS one}, volume = {11}, number = {12}, pages = {e0167188}, pmid = {27973530}, issn = {1932-6203}, mesh = {Anisotropy ; *Earth, Planet ; Exobiology ; Extraterrestrial Environment ; Forests ; Image Processing, Computer-Assisted ; Imaging, Three-Dimensional ; Models, Theoretical ; Photosynthesis ; *Plants ; *Spacecraft ; }, abstract = {Sagan et al. (1993) used the Galileo space probe data and first principles to find evidence of life on Earth. Here we ask whether Sagan et al. (1993) could also have detected whether life on Earth had three-dimensional structure, based on the Galileo space probe data. We reanalyse the data from this probe to see if structured vegetation could have been detected in regions with abundant photosynthetic pigments through the anisotropy of reflected shortwave radiation. We compare changing brightness of the Amazon forest (a region where Sagan et al. (1993) noted a red edge in the reflectance spectrum, indicative of photosynthesis) as the planet rotates to a common model of reflectance anisotropy and found measured increase of surface reflectance of 0.019 ± 0.003 versus a 0.007 predicted from only anisotropic effects. We hypothesize the difference was due to minor cloud contamination. However, the Galileo dataset had only a small change in phase angle (sun-satellite position) which reduced the observed anisotropy signal and we demonstrate that theoretically if the probe had a variable phase angle between 0-20°, there would have been a much larger predicted change in surface reflectance of 0.1 and under such a scenario three-dimensional vegetation structure on Earth could possibly have been detected. These results suggest that anisotropic effects may be useful to help determine whether exoplanets have three-dimensional vegetation structure in the future, but that further comparisons between empirical and theoretical results are first necessary.}, } @article {pmid27973357, year = {2016}, author = {Abushandi, E}, title = {Flood prevention dams for arid regions at a micro-scale sub-catchment, case study: Tabuk, Saudi Arabia.}, journal = {Water science and technology : a journal of the International Association on Water Pollution Research}, volume = {74}, number = {11}, pages = {2523-2533}, doi = {10.2166/wst.2016.341}, pmid = {27973357}, issn = {0273-1223}, mesh = {Cities ; Desert Climate ; *Floods ; Geographic Information Systems ; Hydrology ; *Models, Theoretical ; Saudi Arabia ; Urbanization ; }, abstract = {Unexpected flash flooding is one of the periodic hydrological problems affecting the city of Tabuk in Saudi Arabia. The region has high potential for floods as it suffers high rainfall intensity in a short time and also has high urbanization rates and topographic complexity. Constructing flood prevention dams is one option to solve this problem. A cost-effective design requires a detailed feasibility study and analysis for the selection of suitable sites. The aim of this study was to develop a method for selecting a suitable site for flood protection dams in the Abu Saba'a district, the most affected part of the city of Tabuk during the flash flood in January 2013. Spatial analysis was applied using Landsat Thematic Mapper images and Shuttle Radar Topography Mission digital elevation model to select a site in the Abu Saba'a area. A simple model using ArcGIS was built including all suggested parameters. The results showed the best site for a dam was 2 km distance backfrom the area, where all parameter values matched. The results showed that the dynamic properties of land cover can affect site selection. It is therefore suggested that more field and hydrological data should be gathered for greater accuracy.}, } @article {pmid27964752, year = {2016}, author = {Abascal, F and Corvelo, A and Cruz, F and Villanueva-Cañas, JL and Vlasova, A and Marcet-Houben, M and Martínez-Cruz, B and Cheng, JY and Prieto, P and Quesada, V and Quilez, J and Li, G and García, F and Rubio-Camarillo, M and Frias, L and Ribeca, P and Capella-Gutiérrez, S and Rodríguez, JM and Câmara, F and Lowy, E and Cozzuto, L and Erb, I and Tress, ML and Rodriguez-Ales, JL and Ruiz-Orera, J and Reverter, F and Casas-Marce, M and Soriano, L and Arango, JR and Derdak, S and Galán, B and Blanc, J and Gut, M and Lorente-Galdos, B and Andrés-Nieto, M and López-Otín, C and Valencia, A and Gut, I and García, JL and Guigó, R and Murphy, WJ and Ruiz-Herrera, A and Marques-Bonet, T and Roma, G and Notredame, C and Mailund, T and Albà, MM and Gabaldón, T and Alioto, T and Godoy, JA}, title = {Extreme genomic erosion after recurrent demographic bottlenecks in the highly endangered Iberian lynx.}, journal = {Genome biology}, volume = {17}, number = {1}, pages = {251}, pmid = {27964752}, issn = {1474-760X}, mesh = {Animals ; Endangered Species ; Genetic Variation ; *Genetics, Population ; *Genome ; High-Throughput Nucleotide Sequencing ; Lynx/*genetics ; Molecular Sequence Annotation ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: Genomic studies of endangered species provide insights into their evolution and demographic history, reveal patterns of genomic erosion that might limit their viability, and offer tools for their effective conservation. The Iberian lynx (Lynx pardinus) is the most endangered felid and a unique example of a species on the brink of extinction.

RESULTS: We generate the first annotated draft of the Iberian lynx genome and carry out genome-based analyses of lynx demography, evolution, and population genetics. We identify a series of severe population bottlenecks in the history of the Iberian lynx that predate its known demographic decline during the 20th century and have greatly impacted its genome evolution. We observe drastically reduced rates of weak-to-strong substitutions associated with GC-biased gene conversion and increased rates of fixation of transposable elements. We also find multiple signatures of genetic erosion in the two remnant Iberian lynx populations, including a high frequency of potentially deleterious variants and substitutions, as well as the lowest genome-wide genetic diversity reported so far in any species.

CONCLUSIONS: The genomic features observed in the Iberian lynx genome may hamper short- and long-term viability through reduced fitness and adaptive potential. The knowledge and resources developed in this study will boost the research on felid evolution and conservation genomics and will benefit the ongoing conservation and management of this emblematic species.}, } @article {pmid27941947, year = {2016}, author = {Cardoso, JM and Anjo, SI and Fonseca, L and Egas, C and Manadas, B and Abrantes, I}, title = {Bursaphelenchus xylophilus and B. mucronatus secretomes: a comparative proteomic analysis.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {39007}, pmid = {27941947}, issn = {2045-2322}, mesh = {Animals ; Gene Ontology ; Nematoda/*genetics/*metabolism ; Oxidative Stress ; Proteomics ; Transcriptome ; }, abstract = {The pinewood nematode, Bursaphelenchus xylophilus, recognized as a worldwide major forest pest, is a migratory endoparasitic nematode with capacity to feed on pine tissues and also on fungi colonizing the trees. Bursaphelenchus mucronatus, the closest related species, differs from B. xylophilus on its pathogenicity, making this nematode a good candidate for comparative analyses. Secretome profiles of B. xylophilus and B. mucronatus were obtained and proteomic differences were evaluated by quantitative SWATH-MS. From the 681 proteins initially identified, 422 were quantified and compared between B. xylophilus and B. mucronatus secretomes and from these, 243 proteins were found differentially regulated: 158 and 85 proteins were increased in B. xylophilus and B. mucronatus secretomes, respectively. While increased proteins in B. xylophilus secretome revealed a strong enrichment in proteins with peptidase activity, the increased proteins in B. mucronatus secretome were mainly related to oxidative stress responses. The changes in peptidases were evaluated at the transcription level by RT-qPCR, revealing a correlation between the mRNA levels of four cysteine peptidases with secretion levels. The analysis presented expands our knowledge about molecular basis of B. xylophilus and B. mucronatus hosts interaction and supports the hypothesis of a key role of secreted peptidases in B. xylophilus pathogenicity.}, } @article {pmid27940071, year = {2017}, author = {Šumberová, K and Ducháček, M}, title = {Analysis of plant soil seed banks and seed dispersal vectors: Its potential and limits for forensic investigations.}, journal = {Forensic science international}, volume = {270}, number = {}, pages = {121-128}, doi = {10.1016/j.forsciint.2016.11.030}, pmid = {27940071}, issn = {1872-6283}, mesh = {Botany ; Databases as Topic ; Ecosystem ; Europe ; Forensic Sciences ; Geography ; *Seed Bank ; *Seed Dispersal ; *Seeds ; *Soil ; }, abstract = {Plant seeds exhibit many species-specific traits, thus potentially being especially helpful for forensic investigations. Seeds of a broad range of plant species occur in soil seed banks of various habitats and may become attached in large quantities to moving objects. Although plant seeds are now routinely used as trace evidence in forensic practice, only scant information has been published on this topic in the scientific literature. Thus, the standard methods remain unknown to specialists in such botanical subjects as plant ecology and plant geography. These specialists, if made aware of the forensic uses of seeds, could help in development of new, more sophisticated approaches. We aim to bridge the gap between forensic analysts and botanists. Therefore, we explore the available literature and compare it with our own experiences to reveal both the potential and limits of soil seed bank and seed dispersal analysis in forensic investigations. We demonstrate that habitat-specific and thus relatively rare species are of the greatest forensic value. Overall species composition, in terms of species presence/absence and relative abundance can also provide important information. In particular, the ecological profiles of seeds found on any moving object can help us identify the types of environments through which the object had travelled. We discuss the applicability of this approach to various European environments, with the ability to compare seed samples with georeferenced vegetation databases being particularly promising for forensic investigations. We also explore the forensic limitations of soil seed bank and seed dispersal vector analyses.}, } @article {pmid27939775, year = {2017}, author = {Ocampo-Melgar, A and Bautista, S and Edward deSteiguer, J and Orr, BJ}, title = {Potential of an outranking multi-criteria approach to support the participatory assessment of land management actions.}, journal = {Journal of environmental management}, volume = {195}, number = {Pt 1}, pages = {70-77}, doi = {10.1016/j.jenvman.2016.11.041}, pmid = {27939775}, issn = {1095-8630}, mesh = {Arizona ; Conservation of Natural Resources ; *Decision Support Techniques ; }, abstract = {We evaluated the potential of an outranking Multi-Criteria Decision Analysis approach for assisting in the participatory assessment of dryland management actions implemented in the San Simon watershed, in southeastern Arizona, USA. We compared an outranking-facilitated assessment of actions with a simple and direct (baseline) ranking of the same actions by the participating stakeholders in terms of: 1) internal homogeneity of each assessment approach, (2) similarity of individual assessments between methods, and (3) effects of the use of implicit/explicit assessment criteria. The actions assessed combined various management approaches, including livestock management (rotation, resting), vegetation management (grass seeding, brush control), and hydraulic structures (dams, dykes). The outranking-facilitated assessment discriminated better between actions and reduced the variability of results between individual stakeholders as compared with the direct ranking of actions. In general, the two assessments significantly differed in the relative preference of the five management actions assessed, yet both assessments identified rotational grazing combined with vegetation management (grass seeding and brush control) as the most preferred management action in the study area. The comparative analysis revealed inconsistencies between the use of implicit and explicit assessment criteria. Our findings highlight the opportunities offered by outranking approaches to help capture, structure, and make explicit stakeholder perspectives in the framework of a participatory environmental assessment process, which may facilitate the understanding of the multiple preferences involved. The outranking integration process, which resembles a voting procedure, proved simple and transparent, with potential for contributing to stakeholder engagement and trust in participatory assessment.}, } @article {pmid27939716, year = {2016}, author = {Dunn, RR and Beasley, DE}, title = {Democratizing evolutionary biology, lessons from insects.}, journal = {Current opinion in insect science}, volume = {18}, number = {}, pages = {89-92}, doi = {10.1016/j.cois.2016.10.005}, pmid = {27939716}, issn = {2214-5753}, mesh = {Animals ; Biology/*trends ; *Community Participation ; Computational Biology/trends ; Humans ; *Insecta ; Research/*trends ; }, abstract = {The engagement of the public in the scientific process is an old practice. Yet with recent advances in technology, the role of the citizen scientist in studying evolutionary processes has increased. Insects provide ideal models for understanding these evolutionary processes at large scales. This review highlights how insect-based citizen science has led to the expansion of specimen collections and reframed research questions in light of new observations and unexpected discoveries. Given the rapid expansion of human-modified (and inhabited) environments, the degree to which the public can participate in insect-based citizen science will allow us to track and monitor evolutionary trends at a global scale.}, } @article {pmid27935587, year = {2017}, author = {Schmidt, TS and Matias Rodrigues, JF and von Mering, C}, title = {A family of interaction-adjusted indices of community similarity.}, journal = {The ISME journal}, volume = {11}, number = {3}, pages = {791-807}, pmid = {27935587}, issn = {1751-7370}, support = {242870/ERC_/European Research Council/International ; }, mesh = {Bacteria/*classification ; *Biota ; Computational Biology/*methods ; Humans ; Models, Biological ; Oceans and Seas ; Phylogeny ; Soil Microbiology ; Water Microbiology ; }, abstract = {Interactions between taxa are essential drivers of ecological community structure and dynamics, but they are not taken into account by traditional indices of β diversity. In this study, we propose a novel family of indices that quantify community similarity in the context of taxa interaction networks. Using publicly available datasets, we assessed the performance of two specific indices that are Taxa INteraction-Adjusted (TINA, based on taxa co-occurrence networks), and Phylogenetic INteraction-Adjusted (PINA, based on phylogenetic similarities). TINA and PINA outperformed traditional indices when partitioning human-associated microbial communities according to habitat, even for extremely downsampled datasets, and when organising ocean micro-eukaryotic plankton diversity according to geographical and physicochemical gradients. We argue that interaction-adjusted indices capture novel aspects of diversity outside the scope of traditional approaches, highlighting the biological significance of ecological association networks in the interpretation of community similarity.}, } @article {pmid27932923, year = {2016}, author = {Vattakaven, T and George, RM and Balasubramanian, D and Réjou-Méchain, M and Muthusankar, G and Ramesh, BR and Prabhakar, R}, title = {India Biodiversity Portal: An integrated, interactive and participatory biodiversity informatics platform.}, journal = {Biodiversity data journal}, volume = {}, number = {4}, pages = {e10279}, pmid = {27932923}, issn = {1314-2828}, abstract = {BACKGROUND: This paper describes a growing biodiversity platform, launched in 2008, which organizes knowledge on the biodiversity of India. The main objective and originality of the India Biodiversity Portal (IBP) is to aggregate curated biodiversity data of different kinds (e.g. distribution maps, temporal distribution or life history) in an integrated platform where amateurs and experts can easily interact.

NEW INFORMATION: Since its launch, the platform has seen an exceptional increase in both user activity and biodiversity data. Currently the portal has descriptions of over 20,400 species, and has aggregated approximately 1,280,000 observations covering more than 30,000 species, which already constitutes a unique source of information for scientists and stakeholders in conservation. Over 8500 users have registered on the portal. The amount of data generated and to be generated in the next few years by this portal will certainly help the effective implementation of biodiversity conservation and management in one of the most ecologically diverse countries in the world.}, } @article {pmid27932852, year = {2016}, author = {Watson, RA and Mills, R and Buckley, CL and Kouvaris, K and Jackson, A and Powers, ST and Cox, C and Tudge, S and Davies, A and Kounios, L and Power, D}, title = {Evolutionary Connectionism: Algorithmic Principles Underlying the Evolution of Biological Organisation in Evo-Devo, Evo-Eco and Evolutionary Transitions.}, journal = {Evolutionary biology}, volume = {43}, number = {4}, pages = {553-581}, pmid = {27932852}, issn = {0071-3260}, abstract = {The mechanisms of variation, selection and inheritance, on which evolution by natural selection depends, are not fixed over evolutionary time. Current evolutionary biology is increasingly focussed on understanding how the evolution of developmental organisations modifies the distribution of phenotypic variation, the evolution of ecological relationships modifies the selective environment, and the evolution of reproductive relationships modifies the heritability of the evolutionary unit. The major transitions in evolution, in particular, involve radical changes in developmental, ecological and reproductive organisations that instantiate variation, selection and inheritance at a higher level of biological organisation. However, current evolutionary theory is poorly equipped to describe how these organisations change over evolutionary time and especially how that results in adaptive complexes at successive scales of organisation (the key problem is that evolution is self-referential, i.e. the products of evolution change the parameters of the evolutionary process). Here we first reinterpret the central open questions in these domains from a perspective that emphasises the common underlying themes. We then synthesise the findings from a developing body of work that is building a new theoretical approach to these questions by converting well-understood theory and results from models of cognitive learning. Specifically, connectionist models of memory and learning demonstrate how simple incremental mechanisms, adjusting the relationships between individually-simple components, can produce organisations that exhibit complex system-level behaviours and improve the adaptive capabilities of the system. We use the term "evolutionary connectionism" to recognise that, by functionally equivalent processes, natural selection acting on the relationships within and between evolutionary entities can result in organisations that produce complex system-level behaviours in evolutionary systems and modify the adaptive capabilities of natural selection over time. We review the evidence supporting the functional equivalences between the domains of learning and of evolution, and discuss the potential for this to resolve conceptual problems in our understanding of the evolution of developmental, ecological and reproductive organisations and, in particular, the major evolutionary transitions.}, } @article {pmid27925167, year = {2017}, author = {Harnos, A and Lang, Z and Petrás, D and Bush, SE and Szabó, K and Rózsa, L}, title = {Size matters for lice on birds: Coevolutionary allometry of host and parasite body size.}, journal = {Evolution; international journal of organic evolution}, volume = {71}, number = {2}, pages = {421-431}, doi = {10.1111/evo.13147}, pmid = {27925167}, issn = {1558-5646}, mesh = {Amblycera/*physiology ; Animals ; *Biological Evolution ; Bird Diseases/parasitology ; Birds/*parasitology ; *Body Size ; Female ; *Host-Parasite Interactions ; Ischnocera/*physiology ; Lice Infestations/parasitology/veterinary ; Male ; }, abstract = {Body size is one of the most fundamental characteristics of all organisms. It influences physiology, morphology, behavior, and even interspecific interactions such as those between parasites and their hosts. Host body size influences the magnitude and variability of parasite size according to Harrison's rule (HR: positive relationship between host and parasite body sizes) and Poulin's Increasing Variance Hypothesis (PIVH: positive relationship between host body size and the variability of parasite body size). We analyzed parasite-host body size allometry for 581 species of avian lice (∼15% of known diversity) and their hosts. We applied phylogenetic generalized least squares (PGLS) methods to account for phylogenetic nonindependence controlling for host and parasite phylogenies separately and variance heterogeneity. We tested HR and PIVH for the major families of avian lice (Ricinidae, Menoponidae, Philopteridae), and for distinct ecological guilds within Philopteridae. Our data indicate that most families and guilds of avian lice follow both HR and PIVH; however, ricinids did not follow PIVH and the "body lice" guild of philopterid lice did not follow HR or PIVH. We discuss mathematical and ecological factors that may be responsible for these patterns, and we discuss the potential pervasiveness of these relationships among all parasites on Earth.}, } @article {pmid27924593, year = {2017}, author = {Lawley, B and Tannock, GW}, title = {Analysis of 16S rRNA Gene Amplicon Sequences Using the QIIME Software Package.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1537}, number = {}, pages = {153-163}, doi = {10.1007/978-1-4939-6685-1_9}, pmid = {27924593}, issn = {1940-6029}, mesh = {Algorithms ; Biodiversity ; *Computational Biology/methods ; *High-Throughput Nucleotide Sequencing ; *Metagenomics/methods ; RNA, Ribosomal, 16S/*genetics ; *Software ; Web Browser ; }, abstract = {The study of microbial ecology has undergone a paradigm shift in recent years, with rapid advances in molecular and bioinformatic tools allowing researchers with wide-ranging interests and backgrounds access to community profiling methods. While these advances have undoubtedly led to exciting new understanding of many systems, the array of protocols available and the idiosyncrasies of particular approaches can lead to confusion or, at worst, erroneous interpretation of results. Here, we describe a workflow from raw 16S rRNA gene amplicon sequence data, generated on an Illumina MiSeq instrument, to microbial community taxonomy profiles and basic diversity measures. The workflow can be adapted to input from major sequence platforms and uses freely available open source software that can be implemented on a range of operating systems.}, } @article {pmid27921217, year = {2017}, author = {Parkinson, J and Garfinkel, S and Critchley, H and Dienes, Z and Seth, AK}, title = {Don't make me angry, you wouldn't like me when I'm angry: Volitional choices to act or inhibit are modulated by subliminal perception of emotional faces.}, journal = {Cognitive, affective & behavioral neuroscience}, volume = {17}, number = {2}, pages = {252-268}, pmid = {27921217}, issn = {1531-135X}, mesh = {Adolescent ; *Anger ; Brain/physiology ; *Choice Behavior/physiology ; Discrimination, Psychological ; Electroencephalography ; Evoked Potentials ; *Facial Recognition/physiology ; Fear ; Female ; Happiness ; Humans ; *Inhibition, Psychological ; Male ; *Motor Activity/physiology ; Psychological Tests ; Reaction Time ; *Social Perception ; Subliminal Stimulation ; Volition/physiology ; Young Adult ; }, abstract = {Volitional action and self-control-feelings of acting according to one's own intentions and in being control of one's own actions-are fundamental aspects of human conscious experience. However, it is unknown whether high-level cognitive control mechanisms are affected by socially salient but nonconscious emotional cues. In this study, we manipulated free choice decisions to act or withhold an action by subliminally presenting emotional faces: In a novel version of the Go/NoGo paradigm, participants made speeded button-press responses to Go targets, withheld responses to NoGo targets, and made spontaneous, free choices to execute or withhold the response for Choice targets. Before each target, we presented emotional faces, backwards masked to render them nonconscious. In Intentional trials, subliminal angry faces made participants more likely to voluntarily withhold the action, whereas fearful and happy faces had no effects. In a second experiment, the faces were made supraliminal, which eliminated the effects of angry faces on volitional choices. A third experiment measured neural correlates of the effects of subliminal angry faces on intentional choice using EEG. After replicating the behavioural results found in Experiment 1, we identified a frontal-midline theta component-associated with cognitive control processes-which is present for volitional decisions, and is modulated by subliminal angry faces. This suggests a mechanism whereby subliminally presented "threat" stimuli affect conscious control processes. In summary, nonconscious perception of angry faces increases choices to inhibit, and subliminal influences on volitional action are deep seated and ecologically embedded.}, } @article {pmid27919075, year = {2016}, author = {Gossner, MM and Lewinsohn, TM and Kahl, T and Grassein, F and Boch, S and Prati, D and Birkhofer, K and Renner, SC and Sikorski, J and Wubet, T and Arndt, H and Baumgartner, V and Blaser, S and Blüthgen, N and Börschig, C and Buscot, F and Diekötter, T and Jorge, LR and Jung, K and Keyel, AC and Klein, AM and Klemmer, S and Krauss, J and Lange, M and Müller, J and Overmann, J and Pašalić, E and Penone, C and Perović, DJ and Purschke, O and Schall, P and Socher, SA and Sonnemann, I and Tschapka, M and Tscharntke, T and Türke, M and Venter, PC and Weiner, CN and Werner, M and Wolters, V and Wurst, S and Westphal, C and Fischer, M and Weisser, WW and Allan, E}, title = {Land-use intensification causes multitrophic homogenization of grassland communities.}, journal = {Nature}, volume = {540}, number = {7632}, pages = {266-269}, pmid = {27919075}, issn = {1476-4687}, mesh = {*Agriculture ; Animals ; Arthropods ; *Biodiversity ; Birds ; Bryopsida ; Chiroptera ; Conservation of Natural Resources ; Datasets as Topic ; Food Chain ; Fungi ; Germany ; *Grassland ; *Human Activities ; Lichens ; Plants ; Soil Microbiology ; Species Specificity ; }, abstract = {Land-use intensification is a major driver of biodiversity loss. Alongside reductions in local species diversity, biotic homogenization at larger spatial scales is of great concern for conservation. Biotic homogenization means a decrease in β-diversity (the compositional dissimilarity between sites). Most studies have investigated losses in local (α)-diversity and neglected biodiversity loss at larger spatial scales. Studies addressing β-diversity have focused on single or a few organism groups (for example, ref. 4), and it is thus unknown whether land-use intensification homogenizes communities at different trophic levels, above- and belowground. Here we show that even moderate increases in local land-use intensity (LUI) cause biotic homogenization across microbial, plant and animal groups, both above- and belowground, and that this is largely independent of changes in α-diversity. We analysed a unique grassland biodiversity dataset, with abundances of more than 4,000 species belonging to 12 trophic groups. LUI, and, in particular, high mowing intensity, had consistent effects on β-diversity across groups, causing a homogenization of soil microbial, fungal pathogen, plant and arthropod communities. These effects were nonlinear and the strongest declines in β-diversity occurred in the transition from extensively managed to intermediate intensity grassland. LUI tended to reduce local α-diversity in aboveground groups, whereas the α-diversity increased in belowground groups. Correlations between the β-diversity of different groups, particularly between plants and their consumers, became weaker at high LUI. This suggests a loss of specialist species and is further evidence for biotic homogenization. The consistently negative effects of LUI on landscape-scale biodiversity underscore the high value of extensively managed grasslands for conserving multitrophic biodiversity and ecosystem service provision. Indeed, biotic homogenization rather than local diversity loss could prove to be the most substantial consequence of land-use intensification.}, } @article {pmid27917964, year = {2016}, author = {Seid, MA and Yoseph, LW and Befekadu, UW and Muhammed, A and Fikre, TZ}, title = {Communication for the development of pastoralism.}, journal = {Revue scientifique et technique (International Office of Epizootics)}, volume = {35}, number = {2}, pages = {639-648}, doi = {10.20506/rst.35.2.2545}, pmid = {27917964}, issn = {0253-1933}, mesh = {Africa, Central ; Animal Husbandry/economics/*methods/standards ; Animals ; Cell Phone/statistics & numerical data ; *Communication ; Cultural Competency ; Geographic Information Systems ; Humans ; Internet/trends ; Mali ; Population Groups ; Refugees ; Socioeconomic Factors ; Transients and Migrants ; Wireless Technology ; }, abstract = {Communication is vital for the socio-economic and cultural development of pastoralists. If used constructively, communication can help to create a favourable environment for change and modernisation. This paper tries to uncover trends in communication as part of pastoral development, emphasising both indigenous and current methods of communication and prevailing constraints. This study reveals that pastoral development interventions in the past have often failed to achieve their goals, due to the centralised, 'top-down' approaches adopted and to reliance on external strategies and channels which ignored the indigenous knowledge and communications systems of pastoralists. Pastoralists have their own well-established communications systems for sharing information on climatic conditions and ecology, as well as economic, social and political issues. Modern communication technologies, especially radio and mobile telephones, are increasingly being used by pastoralists to access current regional information. However, pastoral development in the communications area is currently constrained by the failure of various development agencies and stakeholders to use participatory approaches, and by poor infrastructure and weak capacity. The authors therefore call for the adoption of more participatory and integrated approaches towards communication, the expansion of infrastructure and building of capacity.}, } @article {pmid27915291, year = {2016}, author = {Brbić, M and Piškorec, M and Vidulin, V and Kriško, A and Šmuc, T and Supek, F}, title = {The landscape of microbial phenotypic traits and associated genes.}, journal = {Nucleic acids research}, volume = {44}, number = {21}, pages = {10074-10090}, pmid = {27915291}, issn = {1362-4962}, mesh = {Archaea/*genetics ; Bacteria/*genetics ; Codon ; Computational Biology/methods ; Data Mining ; *Databases, Genetic ; Genes, Archaeal ; Genes, Bacterial ; Genome, Archaeal ; Genome, Bacterial ; Metagenome ; Molecular Sequence Annotation ; Multifactorial Inheritance ; *Phenotype ; Reproducibility of Results ; }, abstract = {Bacteria and Archaea display a variety of phenotypic traits and can adapt to diverse ecological niches. However, systematic annotation of prokaryotic phenotypes is lacking. We have therefore developed ProTraits, a resource containing ∼545 000 novel phenotype inferences, spanning 424 traits assigned to 3046 bacterial and archaeal species. These annotations were assigned by a computational pipeline that associates microbes with phenotypes by text-mining the scientific literature and the broader World Wide Web, while also being able to define novel concepts from unstructured text. Moreover, the ProTraits pipeline assigns phenotypes by drawing extensively on comparative genomics, capturing patterns in gene repertoires, codon usage biases, proteome composition and co-occurrence in metagenomes. Notably, we find that gene synteny is highly predictive of many phenotypes, and highlight examples of gene neighborhoods associated with spore-forming ability. A global analysis of trait interrelatedness outlined clusters in the microbial phenotype network, suggesting common genetic underpinnings. Our extended set of phenotype annotations allows detection of 57 088 high confidence gene-trait links, which recover many known associations involving sporulation, flagella, catalase activity, aerobicity, photosynthesis and other traits. Over 99% of the commonly occurring gene families are involved in genetic interactions conditional on at least one phenotype, suggesting that epistasis has a major role in shaping microbial gene content.}, } @article {pmid27915182, year = {2017}, author = {Chicas, SD and Omine, K and Ford, JB and Sugimura, K and Yoshida, K}, title = {Using spatial metrics and surveys for the assessment of trans-boundary deforestation in protected areas of the Maya Mountain Massif: Belize-Guatemala border.}, journal = {Journal of environmental management}, volume = {187}, number = {}, pages = {320-329}, doi = {10.1016/j.jenvman.2016.11.063}, pmid = {27915182}, issn = {1095-8630}, mesh = {Belize ; *Conservation of Natural Resources ; Ecology ; *Environmental Monitoring ; Forestry/*statistics & numerical data ; *Geographic Information Systems ; Guatemala ; Humans ; }, abstract = {Understanding the trans-boundary deforestation history and patterns in protected areas along the Belize-Guatemala border is of regional and global importance. To assess deforestation history and patterns in our study area along a section of the Belize-Guatemala border, we incorporated multi-temporal deforestation rate analysis and spatial metrics with survey results. This multi-faceted approach provides spatial analysis with relevant insights from local stakeholders to better understand historic deforestation dynamics, spatial characteristics and human perspectives regarding the underlying causes thereof. During the study period 1991-2014, forest cover declined in Belize's protected areas: Vaca Forest Reserve 97.88%-87.62%, Chiquibul National Park 99.36%-92.12%, Caracol Archeological Reserve 99.47%-78.10% and Colombia River Forest Reserve 89.22%-78.38% respectively. A comparison of deforestation rates and spatial metrics indices indicated that between time periods 1991-1995 and 2012-2014 deforestation and fragmentation increased in protected areas. The major underlying causes, drivers, impacts, and barriers to bi-national collaboration and solutions of deforestation along the Belize-Guatemala border were identified by community leaders and stakeholders. The Mann-Whitney U test identified significant differences between leaders and stakeholders regarding the ranking of challenges faced by management organizations in the Maya Mountain Massif, except for the lack of assessment and quantification of deforestation (LD, SH: 18.67, 23.25, U = 148, p > 0.05). The survey results indicated that failure to integrate buffer communities, coordinate among managing organizations and establish strong bi-national collaboration has resulted in continued ecological and environmental degradation. The information provided by this research should aid managing organizations in their continued aim to implement effective deforestation mitigation strategies.}, } @article {pmid27914076, year = {2017}, author = {Collins, C and Didelot, X}, title = {Reconstructing the Ancestral Relationships Between Bacterial Pathogen Genomes.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1535}, number = {}, pages = {109-137}, doi = {10.1007/978-1-4939-6673-8_8}, pmid = {27914076}, issn = {1940-6029}, mesh = {Bacteria/*classification/*genetics ; Bacterial Infections/microbiology ; Computational Biology/methods ; Evolution, Molecular ; Genetics, Population ; *Genome, Bacterial ; *Genomics/methods ; Models, Statistical ; *Phylogeny ; Recombination, Genetic ; Software ; Web Browser ; }, abstract = {Following recent developments in DNA sequencing technology, it is now possible to sequence hundreds of whole genomes from bacterial isolates at relatively low cost. Analyzing this growing wealth of genomic data in terms of ancestral relationships can reveal many interesting aspects of the evolution, ecology, and epidemiology of bacterial pathogens. However, reconstructing the ancestry of a sample of bacteria remains challenging, especially for the majority of species where recombination is frequent. Here, we review and describe the computational techniques currently available to infer ancestral relationships, including phylogenetic methods that either ignore or account for the effect of recombination, as well as model-based and model-free phylogeny-independent approaches.}, } @article {pmid27912246, year = {2017}, author = {Rosenheim, JA and Gratton, C}, title = {Ecoinformatics (Big Data) for Agricultural Entomology: Pitfalls, Progress, and Promise.}, journal = {Annual review of entomology}, volume = {62}, number = {}, pages = {399-417}, doi = {10.1146/annurev-ento-031616-035444}, pmid = {27912246}, issn = {1545-4487}, mesh = {Agriculture/methods ; *Computational Biology ; Ecology/*methods ; Entomology/*methods ; }, abstract = {Ecoinformatics, as defined in this review, is the use of preexisting data sets to address questions in ecology. We provide the first review of ecoinformatics methods in agricultural entomology. Ecoinformatics methods have been used to address the full range of questions studied by agricultural entomologists, enabled by the special opportunities associated with data sets, nearly all of which have been observational, that are larger and more diverse and that embrace larger spatial and temporal scales than most experimental studies do. We argue that ecoinformatics research methods and traditional, experimental research methods have strengths and weaknesses that are largely complementary. We address the important interpretational challenges associated with observational data sets, highlight common pitfalls, and propose some best practices for researchers using these methods. Ecoinformatics methods hold great promise as a vehicle for capitalizing on the explosion of data emanating from farmers, researchers, and the public, as novel sampling and sensing techniques are developed and digital data sharing becomes more widespread.}, } @article {pmid27912242, year = {2017}, author = {Freedman, AH and Wayne, RK}, title = {Deciphering the Origin of Dogs: From Fossils to Genomes.}, journal = {Annual review of animal biosciences}, volume = {5}, number = {}, pages = {281-307}, doi = {10.1146/annurev-animal-022114-110937}, pmid = {27912242}, issn = {2165-8110}, mesh = {Animals ; Biological Evolution ; Dogs/*genetics/physiology ; *Fossils ; *Genome ; Wolves/genetics/physiology ; }, abstract = {Understanding the timing and geographic context of dog origins is a crucial component for understanding human history, as well as the evolutionary context in which the morphological and behavioral divergence of dogs from wolves occurred. A substantial challenge to understanding domestication is that dogs have experienced a complicated demographic history. An initial severe bottleneck was associated with domestication followed by postdivergence gene flow between dogs and wolves, as well as population expansions, contractions, and replacements. In addition, because the domestication of dogs occurred in the relatively recent past, much of the observed polymorphism may be shared between dogs and wolves, limiting the power to distinguish between alternative models of dog history. Greater insight into the domestication process will require explicit tests of alternative models of domestication through the joint analysis of whole genomes from modern lineages and ancient wolves and dogs from across Eurasia.}, } @article {pmid27912008, year = {2016}, author = {Senior, AM and Grueber, CE and Kamiya, T and Lagisz, M and O'Dwyer, K and Santos, ES and Nakagawa, S}, title = {Heterogeneity in ecological and evolutionary meta-analyses: its magnitude and implications.}, journal = {Ecology}, volume = {97}, number = {12}, pages = {3293-3299}, doi = {10.1002/ecy.1591}, pmid = {27912008}, issn = {0012-9658}, mesh = {Bias ; *Biological Evolution ; Data Interpretation, Statistical ; Ecology/*methods ; *Meta-Analysis as Topic ; Models, Statistical ; Research Design ; }, abstract = {Meta-analysis is the gold standard for synthesis in ecology and evolution. Together with estimating overall effect magnitudes, meta-analyses estimate differences between effect sizes via heterogeneity statistics. It is widely hypothesized that heterogeneity will be present in ecological/evolutionary meta-analyses due to the system-specific nature of biological phenomena. Despite driving recommended best practices, the generality of heterogeneity in ecological data has never been systematically reviewed. We reviewed 700 studies, finding 325 that used formal meta-analysis, of which total heterogeneity was reported in fewer than 40%. We used second-order meta-analysis to collate heterogeneity statistics from 86 studies. Our analysis revealed that the median and mean heterogeneity, expressed as I[2] , are 84.67% and 91.69%, respectively. These estimates are well above "high" heterogeneity (i.e., 75%), based on widely adopted benchmarks. We encourage reporting heterogeneity in the forms of I[2] and the estimated variance components (e.g., τ[2]) as standard practice. These statistics provide vital insights in to the degree to which effect sizes vary, and provide the statistical support for the exploration of predictors of effect-size magnitude. Along with standard meta-regression techniques that fit moderator variables, multi-level models now allow partitioning of heterogeneity among correlated (e.g., phylogenetic) structures that exist within data.}, } @article {pmid27911775, year = {2016}, author = {Diekert, FK and Richter, A and Rivrud, IM and Mysterud, A}, title = {How constraints affect the hunter's decision to shoot a deer.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {113}, number = {50}, pages = {14450-14455}, pmid = {27911775}, issn = {1091-6490}, mesh = {Animals ; Animals, Wild ; *Conservation of Natural Resources/legislation & jurisprudence/statistics & numerical data ; Databases, Factual ; Decision Making ; *Deer ; Ecosystem ; Female ; *Firearms ; Humans ; Male ; Models, Psychological ; Norway ; Recreation ; Red Meat ; Seasons ; Social Conditions ; }, abstract = {Hunting is the predominant way of controlling many wildlife populations devoid of large carnivores. It subjects animals to mortality rates that far exceed natural rates and that differ markedly in which age, sex, or size classes are removed relative to those of natural predators. To explain the emerging selection pattern we develop behavioral microfoundations for a hunting model, emphasizing in particular the constraints given by the formal and informal norms, rules, and regulations that govern the hunter's choice. We show how a shorter remaining season, competition among hunters, lower sighting probabilities, and higher costs all lead to lower reservation values, i.e., an increased likelihood of shooting a particular animal. Using a unique dataset on seen and shot deer from Norway, we test and confirm the theoretical predictions in a recreational and meat-motivated hunting system. To achieve sustainability, future wildlife management should account for this predictable selection pressure.}, } @article {pmid27911324, year = {2017}, author = {Shen, L and Liao, L and Chen, C and Guo, Y and Song, D and Wang, Y and Chen, Y and Zhang, K and Ying, M and Li, S and Liu, Q and Ni, J}, title = {Proteomics Analysis of Blood Serums from Alzheimer's Disease Patients Using iTRAQ Labeling Technology.}, journal = {Journal of Alzheimer's disease : JAD}, volume = {56}, number = {1}, pages = {361-378}, doi = {10.3233/JAD-160913}, pmid = {27911324}, issn = {1875-8908}, mesh = {Adipokines ; Alzheimer Disease/*blood/diagnostic imaging ; Asian People/ethnology ; Biomarkers/*blood ; Calcium-Binding Proteins/blood ; Calgranulin A/blood ; Calgranulin B/blood ; Carrier Proteins/blood ; Case-Control Studies ; Computational Biology ; Enzyme-Linked Immunosorbent Assay ; Female ; Glycoproteins/blood ; Humans ; Male ; Positron-Emission Tomography ; Protein Interaction Maps ; Proteomics/*methods ; S100 Calcium Binding Protein beta Subunit/blood ; Thrombospondin 1/blood ; beta-Thromboglobulin/metabolism ; }, abstract = {Alzheimer' disease (AD) is the most common form of dementia affecting up to 6% of the population over the age of 65. In order to discover differentially expressed proteins that might serve as potential biomarkers, the serums from AD patients and healthy controls were compared and analyzed using the proteomics approach of isobaric tagging for relative and absolute quantitation (iTRAQ). For the first time, AD biomarkers in serums are investigated in the Han Chinese population using iTRAQ labeled proteomics strategy. Twenty-two differentially expressed proteins were identified and out of which nine proteins were further validated with more sample test. Another three proteins that have been reported in the literature to be potentially associated with AD were also investigated for alteration in expression level. Functions of those proteins were mainly related to the following processes: amyloid-β (Aβ) metabolism, cholesterol transport, complement and coagulation cascades, immune response, inflammation, hemostasis, hyaluronan metabolism, and oxidative stress. These results support current views on the molecular mechanism of AD. For the first time, differential expression of zinc-alpha-2-glycoprotein (AZGP1), fibulin-1 (FBLN1), platelet basic protein (PPBP), thrombospondin-1 (THBS1), S100 calcium-binding protein A8 (S100A8), and S100 calcium-binding protein A9 (S100A9) were detected in the serums of AD patients compared with healthy controls. These proteins might play a role in AD pathophysiology and serve as potential biomarkers for AD diagnosis. Specifically, our results strengthened the crucial role of Aβ metabolism and blood coagulation in AD pathogenesis and proteins related to these two processes may be used as peripheral blood biomarkers for AD.}, } @article {pmid27908575, year = {2017}, author = {Akiyama, YB and Iseri, E and Kataoka, T and Tanaka, M and Katsukoshi, K and Moki, H and Naito, R and Hem, R and Okada, T}, title = {Discrimination of Mediterranean mussel (Mytilus galloprovincialis) feces in deposited materials by fecal morphology.}, journal = {Marine pollution bulletin}, volume = {115}, number = {1-2}, pages = {67-74}, doi = {10.1016/j.marpolbul.2016.11.040}, pmid = {27908575}, issn = {1879-3363}, mesh = {Animals ; DNA, Mitochondrial/genetics ; *Feces ; *Mytilus/genetics ; }, abstract = {In the present study, we determined the common morphological characteristics of the feces of Mytilus galloprovincialis to develop a method for visually discriminating the feces of this mussel in deposited materials. This method can be used to assess the effect of mussel feces on benthic environments. The accuracy of visual morphology-based discrimination of mussel feces in deposited materials was confirmed by DNA analysis. Eighty-nine percent of mussel feces shared five common morphological characteristics. Of the 372 animal species investigated, only four species shared all five of these characteristics. More than 96% of the samples were visually identified as M. galloprovincialis feces on the basis of morphology of the particles containing the appropriate mitochondrial DNA. These results suggest that mussel feces can be discriminated with high accuracy on the basis of their morphological characteristics. Thus, our method can be used to quantitatively assess the effect of mussel feces on local benthic environments.}, } @article {pmid27905871, year = {2016}, author = {Dornburg, A and Fisk, JN and Tamagnan, J and Townsend, JP}, title = {PhyInformR: phylogenetic experimental design and phylogenomic data exploration in R.}, journal = {BMC evolutionary biology}, volume = {16}, number = {1}, pages = {262}, pmid = {27905871}, issn = {1471-2148}, support = {UL1 TR001863/TR/NCATS NIH HHS/United States ; }, mesh = {Bayes Theorem ; Computational Biology/*methods ; Genome ; Genomics ; *Phylogeny ; Research Design ; *Software ; }, abstract = {BACKGROUND: Analyses of phylogenetic informativeness represent an important step in screening potential or existing datasets for their proclivity toward convergent or parallel evolution of molecular sites. However, while new theory has been developed from which to predict the utility of sequence data, adoption of these advances have been stymied by a lack of software enabling application of advances in theory, especially for large next-generation sequence data sets. Moreover, there are no theoretical barriers to application of the phylogenetic informativeness or the calculation of quartet internode resolution probabilities in a Bayesian setting that more robustly accounts for uncertainty, yet there is no software with which a computationally intensive Bayesian approach to experimental design could be implemented.

RESULTS: We introduce PhyInformR, an open source software package that performs rapid calculation of phylogenetic information content using the latest advances in phylogenetic informativeness based theory. These advances include modifications that incorporate uneven branch lengths and any model of nucleotide substitution to provide assessments of the phylogenetic utility of any given dataset or dataset partition. PhyInformR provides new tools for data visualization and routines optimized for rapid statistical calculations, including approaches making use of Bayesian posterior distributions and parallel processing. By implementing the computation on user hardware, PhyInformR increases the potential power users can apply toward screening datasets for phylogenetic/genomic information content by orders of magnitude.

CONCLUSIONS: PhyInformR provides a means to implement diverse substitution models and specify uneven branch lengths for phylogenetic informativeness or calculations providing quartet based probabilities of resolution, produce novel visualizations, and facilitate analyses of next-generation sequence datasets while incorporating phylogenetic uncertainty through the use parallel processing. As an open source program, PhyInformR is fully customizable and expandable, thereby allowing for advanced methodologies to be readily integrated into local bioinformatics pipelines. Software is available through CRAN and a package containing the software, a detailed manual, and additional sample data is also provided freely through github: https://github.com/carolinafishes/PhyInformR .}, } @article {pmid27905533, year = {2016}, author = {Di Franco, A and Thiriet, P and Di Carlo, G and Dimitriadis, C and Francour, P and Gutiérrez, NL and Jeudy de Grissac, A and Koutsoubas, D and Milazzo, M and Otero, MD and Piante, C and Plass-Johnson, J and Sainz-Trapaga, S and Santarossa, L and Tudela, S and Guidetti, P}, title = {Five key attributes can increase marine protected areas performance for small-scale fisheries management.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {38135}, pmid = {27905533}, issn = {2045-2322}, mesh = {Algorithms ; Animals ; Conservation of Natural Resources/economics/*methods/statistics & numerical data ; Databases, Factual ; Ecosystem ; Factor Analysis, Statistical ; Fisheries/economics/*organization & administration/statistics & numerical data ; Fishes ; Mediterranean Sea ; Socioeconomic Factors ; }, abstract = {Marine protected areas (MPAs) have largely proven to be effective tools for conserving marine ecosystem, while socio-economic benefits generated by MPAs to fisheries are still under debate. Many MPAs embed a no-take zone, aiming to preserve natural populations and ecosystems, within a buffer zone where potentially sustainable activities are allowed. Small-scale fisheries (SSF) within buffer zones can be highly beneficial by promoting local socio-economies. However, guidelines to successfully manage SSFs within MPAs, ensuring both conservation and fisheries goals, and reaching a win-win scenario, are largely unavailable. From the peer-reviewed literature, grey-literature and interviews, we assembled a unique database of ecological, social and economic attributes of SSF in 25 Mediterranean MPAs. Using random forest with Boruta algorithm we identified a set of attributes determining successful SSFs management within MPAs. We show that fish stocks are healthier, fishermen incomes are higher and the social acceptance of management practices is fostered if five attributes are present (i.e. high MPA enforcement, presence of a management plan, fishermen engagement in MPA management, fishermen representative in the MPA board, and promotion of sustainable fishing). These findings are pivotal to Mediterranean coastal communities so they can achieve conservation goals while allowing for profitable exploitation of fisheries resources.}, } @article {pmid27905442, year = {2016}, author = {Crowther, TW and Todd-Brown, KE and Rowe, CW and Wieder, WR and Carey, JC and Machmuller, MB and Snoek, BL and Fang, S and Zhou, G and Allison, SD and Blair, JM and Bridgham, SD and Burton, AJ and Carrillo, Y and Reich, PB and Clark, JS and Classen, AT and Dijkstra, FA and Elberling, B and Emmett, BA and Estiarte, M and Frey, SD and Guo, J and Harte, J and Jiang, L and Johnson, BR and Kröel-Dulay, G and Larsen, KS and Laudon, H and Lavallee, JM and Luo, Y and Lupascu, M and Ma, LN and Marhan, S and Michelsen, A and Mohan, J and Niu, S and Pendall, E and Peñuelas, J and Pfeifer-Meister, L and Poll, C and Reinsch, S and Reynolds, LL and Schmidt, IK and Sistla, S and Sokol, NW and Templer, PH and Treseder, KK and Welker, JM and Bradford, MA}, title = {Quantifying global soil carbon losses in response to warming.}, journal = {Nature}, volume = {540}, number = {7631}, pages = {104-108}, pmid = {27905442}, issn = {1476-4687}, mesh = {Atmosphere/*chemistry ; Carbon/*analysis ; *Carbon Cycle ; Databases, Factual ; Ecosystem ; Feedback ; *Geography ; *Global Warming ; Models, Statistical ; Reproducibility of Results ; Soil/*chemistry ; Temperature ; }, abstract = {The majority of the Earth's terrestrial carbon is stored in the soil. If anthropogenic warming stimulates the loss of this carbon to the atmosphere, it could drive further planetary warming. Despite evidence that warming enhances carbon fluxes to and from the soil, the net global balance between these responses remains uncertain. Here we present a comprehensive analysis of warming-induced changes in soil carbon stocks by assembling data from 49 field experiments located across North America, Europe and Asia. We find that the effects of warming are contingent on the size of the initial soil carbon stock, with considerable losses occurring in high-latitude areas. By extrapolating this empirical relationship to the global scale, we provide estimates of soil carbon sensitivity to warming that may help to constrain Earth system model projections. Our empirical relationship suggests that global soil carbon stocks in the upper soil horizons will fall by 30 ± 30 petagrams of carbon to 203 ± 161 petagrams of carbon under one degree of warming, depending on the rate at which the effects of warming are realized. Under the conservative assumption that the response of soil carbon to warming occurs within a year, a business-as-usual climate scenario would drive the loss of 55 ± 50 petagrams of carbon from the upper soil horizons by 2050. This value is around 12-17 per cent of the expected anthropogenic emissions over this period. Despite the considerable uncertainty in our estimates, the direction of the global soil carbon response is consistent across all scenarios. This provides strong empirical support for the idea that rising temperatures will stimulate the net loss of soil carbon to the atmosphere, driving a positive land carbon-climate feedback that could accelerate climate change.}, } @article {pmid27901244, year = {2016}, author = {Martins, DF and Felzemburg, RD and Dias, AB and Costa, TM and Santos, PN}, title = {Trends in mortality from ill-defined causes among the elderly in Brazil, 1979-2013: ecological study.}, journal = {Sao Paulo medical journal = Revista paulista de medicina}, volume = {134}, number = {5}, pages = {437-445}, pmid = {27901244}, issn = {1806-9460}, mesh = {Age Factors ; Aged ; Aged, 80 and over ; Brazil/epidemiology ; Cause of Death/*trends ; Death Certificates ; Delivery of Health Care ; Female ; Health Information Systems ; Humans ; Linear Models ; Male ; Middle Aged ; Mortality/*trends ; Sex Distribution ; Sex Factors ; Spatio-Temporal Analysis ; Time Factors ; }, abstract = {CONTEXT AND OBJECTIVE:: Mortality measurements are traditionally used as health indicators and are useful in describing a population's health situation through reporting injuries that lead to death. The aim here was to analyze the temporal trend of proportional mortality from ill-defined causes (IDCs) among the elderly in Brazil from 1979 to 2013.

DESIGN AND SETTING:: Ecological study using data from the Mortality Information System of the Brazilian Ministry of Health.

METHODS:: The proportional mortality from IDCs among the elderly was calculated for each year of the study series (1979 to 2013) in Brazil, and the data were disaggregated according to sex and to the five geographical regions and states. To analyze time trends, simple linear regression coefficients were calculated.

RESULTS:: During the study period, there were 2,646,194 deaths from IDCs among the elderly, with a decreasing trend (ß -0.545; confidence interval, CI: -0.616 to -0.475; P < 0.000) for both males and females. This reduction was also observed in the macroregions and states, except for Amapá. The states in the northeastern region reported an average reduction of 80%.

CONCLUSIONS:: Mortality from IDCs among the elderly has decreased continuously since 1985, but at different rates among the different regions and states. Actions aimed at improving data records on death certificates need to be strengthened in order to continue the trend observed.}, } @article {pmid27901077, year = {2016}, author = {Alves, JA and Dias, MP and Méndez, V and Katrínardóttir, B and Gunnarsson, TG}, title = {Very rapid long-distance sea crossing by a migratory bird.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {38154}, pmid = {27901077}, issn = {2045-2322}, mesh = {Africa, Western ; Animal Migration/*physiology ; Animals ; Charadriiformes/*physiology ; Female ; Flight, Animal/*physiology ; Geographic Information Systems ; Geography ; Iceland ; Male ; Oceans and Seas ; Risk Factors ; Weather ; *Wind ; }, abstract = {Landbirds undertaking within-continent migrations have the possibility to stop en route, but most long-distance migrants must also undertake large non-stop sea crossings, the length of which can vary greatly. For shorebirds migrating from Iceland to West Africa, the shortest route would involve one of the longest continuous sea crossings while alternative, mostly overland, routes are available. Using geolocators to track the migration of Icelandic whimbrels (Numenius phaeopus), we show that they can complete a round-trip of 11,000 km making two non-stop sea crossings and flying at speeds of up to 24 m s(−1); one of the fastest recorded for shorebirds flying over the ocean. Although wind support could reduce flight energetic costs, whimbrels faced headwinds up to twice their ground speed, indicating that unfavourable and potentially fatal weather conditions are not uncommon. Such apparently high risk migrations might be more common than previously thought, with potential fitness gains outweighing the costs.}, } @article {pmid27901016, year = {2017}, author = {Mendez, WM and Eftim, S and Cohen, J and Warren, I and Cowden, J and Lee, JS and Sams, R}, title = {Relationships between arsenic concentrations in drinking water and lung and bladder cancer incidence in U.S. counties.}, journal = {Journal of exposure science & environmental epidemiology}, volume = {27}, number = {3}, pages = {235-243}, pmid = {27901016}, issn = {1559-064X}, mesh = {Aged ; Aged, 80 and over ; Arsenic/*adverse effects/analysis ; Databases, Factual ; Drinking Water/*adverse effects/analysis/chemistry ; Environmental Exposure/adverse effects/analysis ; Environmental Monitoring ; Female ; Humans ; Incidence ; Lung Neoplasms/*chemically induced/*epidemiology ; Male ; Middle Aged ; Regression Analysis ; SEER Program ; Sex Distribution ; United States/epidemiology ; Urinary Bladder Neoplasms/*chemically induced/*epidemiology ; }, abstract = {Increased risks of lung and bladder cancer have been observed in populations exposed to high levels of inorganic arsenic. However, studies at lower exposures (i.e., less than 100 μg/l in water) have shown inconsistent results. We therefore conducted an ecological analysis of the association between historical drinking water arsenic concentrations and lung and bladder cancer incidence in U.S. counties. We used drinking water arsenic concentrations measured by the U.S. Geological Survey and state agencies in the 1980s and 1990s as proxies for historical exposures in counties where public groundwater systems and private wells are important sources of drinking water. Relationships between arsenic levels and cancer incidence in 2006-2010 were explored by Poisson regression analyses, adjusted for groundwater dependence and important demographic covariates. The median and 95th percentile county mean arsenic concentrations were 1.5 and 15.4 μg/l, respectively. Water arsenic concentrations were significant and positively associated with female and male bladder cancer, and with female lung cancer. Our findings support an association between low water arsenic concentrations and lung and bladder cancer incidence in the United States. However, the limitations of the ecological study design suggest caution in interpreting these results.}, } @article {pmid27899581, year = {2017}, author = {Clima, R and Preste, R and Calabrese, C and Diroma, MA and Santorsola, M and Scioscia, G and Simone, D and Shen, L and Gasparre, G and Attimonelli, M}, title = {HmtDB 2016: data update, a better performing query system and human mitochondrial DNA haplogroup predictor.}, journal = {Nucleic acids research}, volume = {45}, number = {D1}, pages = {D698-D706}, pmid = {27899581}, issn = {1362-4962}, support = {15-1144/AICR_/Worldwide Cancer Research/United Kingdom ; }, mesh = {*DNA, Mitochondrial ; *Databases, Nucleic Acid ; *Genome, Mitochondrial ; Genomics/*methods ; *Haplotypes ; Humans ; Mitochondria/*genetics ; Search Engine ; Software ; Web Browser ; }, abstract = {The HmtDB resource hosts a database of human mitochondrial genome sequences from individuals with healthy and disease phenotypes. The database is intended to support both population geneticists as well as clinicians undertaking the task to assess the pathogenicity of specific mtDNA mutations. The wide application of next-generation sequencing (NGS) has provided an enormous volume of high-resolution data at a low price, increasing the availability of human mitochondrial sequencing data, which called for a cogent and significant expansion of HmtDB data content that has more than tripled in the current release. We here describe additional novel features, including: (i) a complete, user-friendly restyling of the web interface, (ii) links to the command-line stand-alone and web versions of the MToolBox package, an up-to-date tool to reconstruct and analyze human mitochondrial DNA from NGS data and (iii) the implementation of the Reconstructed Sapiens Reference Sequence (RSRS) as mitochondrial reference sequence. The overall update renders HmtDB an even more handy and useful resource as it enables a more rapid data access, processing and analysis. HmtDB is accessible at http://www.hmtdb.uniba.it/.}, } @article {pmid27899569, year = {2017}, author = {Lakin, SM and Dean, C and Noyes, NR and Dettenwanger, A and Ross, AS and Doster, E and Rovira, P and Abdo, Z and Jones, KL and Ruiz, J and Belk, KE and Morley, PS and Boucher, C}, title = {MEGARes: an antimicrobial resistance database for high throughput sequencing.}, journal = {Nucleic acids research}, volume = {45}, number = {D1}, pages = {D574-D580}, pmid = {27899569}, issn = {1362-4962}, support = {T32 OD012201/OD/NIH HHS/United States ; }, mesh = {Computational Biology/methods ; *Databases, Genetic ; *Drug Resistance, Microbial ; *High-Throughput Nucleotide Sequencing ; Metagenome ; Metagenomics/methods ; Web Browser ; }, abstract = {Antimicrobial resistance has become an imminent concern for public health. As methods for detection and characterization of antimicrobial resistance move from targeted culture and polymerase chain reaction to high throughput metagenomics, appropriate resources for the analysis of large-scale data are required. Currently, antimicrobial resistance databases are tailored to smaller-scale, functional profiling of genes using highly descriptive annotations. Such characteristics do not facilitate the analysis of large-scale, ecological sequence datasets such as those produced with the use of metagenomics for surveillance. In order to overcome these limitations, we present MEGARes (https://megares.meglab.org), a hand-curated antimicrobial resistance database and annotation structure that provides a foundation for the development of high throughput acyclical classifiers and hierarchical statistical analysis of big data. MEGARes can be browsed as a stand-alone resource through the website or can be easily integrated into sequence analysis pipelines through download. Also via the website, we provide documentation for AmrPlusPlus, a user-friendly Galaxy pipeline for the analysis of high throughput sequencing data that is pre-packaged for use with the MEGARes database.}, } @article {pmid27896728, year = {2017}, author = {Whelan, S and Morrison, DA}, title = {Inferring Trees.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1525}, number = {}, pages = {349-377}, doi = {10.1007/978-1-4939-6622-6_14}, pmid = {27896728}, issn = {1940-6029}, mesh = {*Algorithms ; Bayes Theorem ; Computational Biology/*methods ; Evolution, Molecular ; Likelihood Functions ; Models, Genetic ; Phylogeny ; }, abstract = {Molecular evolution can reveal the relationship between sets of homologous sequences and the patterns of change that occur during their evolution. An important aspect of these studies is the inference of a phylogenetic tree, which explicitly describes evolutionary relationships between homologous sequences. This chapter provides an introduction to evolutionary trees and how to infer them from sequence data using some commonly used inferential methodology. It focuses on statistical methods for inferring trees and how to assess the confidence one should have in any resulting tree, with a particular emphasis on the underlying assumptions of the methods and how they might affect the tree estimate. There is also some discussion of the underlying algorithms used to perform tree search and recommendations regarding the performance of different algorithms. Finally, there are a few practical guidelines, including how to combine multiple software packages to improve inference, and a comparison between Bayesian and Maximum likelihood phylogenetics.}, } @article {pmid27895801, year = {2016}, author = {Sakai, S and Izumi, H and Yoshiura, Y and Nakayama, Y and Yamaguchi, T and Harada, Y and Koi, C and Kurata, H and Morimoto, Y}, title = {In vitro evaluation of a combination treatment involving anticancer agents and an aurora kinase B inhibitor.}, journal = {Oncology letters}, volume = {12}, number = {5}, pages = {4263-4269}, pmid = {27895801}, issn = {1792-1074}, abstract = {Aurora kinase B (AURKB) inhibitors are regarded as potential molecular-targeting drugs for cancer therapy. The present study evaluated the cytotoxic effect of a combination of AZD1152-hQPA, an AURKB inhibitor, and various anticancer agents on the HeLa human cervical cancer cell line, as well as its cisplatin-resistant equivalent HCP4 cell line. It was demonstrated that AZD1152-hQPA had an antagonistic effect on the cytotoxicity of cisplatin, etoposide and doxorubicin, but had a synergistic effect on that of all-trans-retinoic acid (ATRA), Am80 and TAC-101, when tested on HeLa cells. Cisplatin, etoposide and doxorubicin were shown to increase the cellular expression of AURKB, while ATRA, Am80 and TAC-101 downregulated its expression. These results suggested that AURKB expression is regulated by these anticancer agents at the transcriptional level, and that the level of expression of AURKB may influence the cytotoxic effect of AZD1152-hQPA. Therefore, when using anticancer agents, decreasing the expression of AURKB using a molecular-targeting drug may be an optimal therapeutic strategy.}, } @article {pmid27895628, year = {2016}, author = {Morris, MM and Haggerty, JM and Papudeshi, BN and Vega, AA and Edwards, MS and Dinsdale, EA}, title = {Nearshore Pelagic Microbial Community Abundance Affects Recruitment Success of Giant Kelp, Macrocystis pyrifera.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {1800}, pmid = {27895628}, issn = {1664-302X}, abstract = {Marine microbes mediate key ecological processes in kelp forest ecosystems and interact with macroalgae. Pelagic and biofilm-associated microbes interact with macroalgal propagules at multiple stages of recruitment, yet these interactions have not been described for Macrocystis pyrifera. Here we investigate the influence of microbes from coastal environments on recruitment of giant kelp, M. pyrifera. Through repeated laboratory experiments, we tested the effects of altered pelagic microbial abundance on the settlement and development of the microscopic propagules of M. pyrifera during recruitment. M. pyrifera zoospores were reared in laboratory microcosms exposed to environmental microbial communities from seawater during the complete haploid stages of the kelp recruitment cycle, including zoospore release, followed by zoospore settlement, to gametophyte germination and development. We altered the microbial abundance states differentially in three independent experiments with repeated trials, where microbes were (a) present or absent in seawater, (b) altered in community composition, and (c) altered in abundance. Within the third experiment, we also tested the effect of nearshore versus offshore microbial communities on the macroalgal propagules. Distinct pelagic microbial communities were collected from two southern California temperate environments reflecting contrasting intensity of human influence, the nearshore Point Loma kelp forest and the offshore Santa Catalina Island kelp forest. The Point Loma kelp forest is a high impacted coastal region adjacent to the populous San Diego Bay; whereas the kelp forest at Catalina Island is a low impacted region of the Channel Islands, 40 km offshore the southern California coast, and is adjacent to a marine protected area. Kelp gametophytes reared with nearshore Point Loma microbes showed lower survival, growth, and deteriorated morphology compared to gametophytes with the offshore Catalina Island microbial community, and these effects were magnified under high microbial abundances. Reducing abundance of Point Loma microbes restored M. pyrifera propagule success. Yet an intermediate microbial abundance was optimal for kelp propagules reared with Catalina Island microbes, suggesting that microbes also have a beneficial influence on kelp. Our study shows that pelagic microbes from nearshore and offshore environments are differentially influencing kelp propagule success, which has significant implications for kelp recruitment and kelp forest ecosystem health.}, } @article {pmid27894252, year = {2016}, author = {Zhang, W and Guo, Y and Li, J and Huang, L and Kazitsa, EG and Wu, H}, title = {Transcriptome analysis reveals the genetic basis underlying the seasonal development of keratinized nuptial spines in Leptobrachium boringii.}, journal = {BMC genomics}, volume = {17}, number = {1}, pages = {978}, pmid = {27894252}, issn = {1471-2164}, mesh = {Animals ; Anura/*genetics/metabolism ; Breeding ; Computational Biology/methods ; *Gene Expression Profiling ; Gene Ontology ; High-Throughput Nucleotide Sequencing ; Molecular Sequence Annotation ; Organ Specificity/genetics ; Phenotype ; *Seasons ; *Transcriptome ; }, abstract = {BACKGROUND: The expression of sexually selected traits often varies with populations' breeding cycles in many animals. The elucidation of mechanisms underlying the expression of such traits is a research topic in evolutionary biology; however, the genetic basis of the seasonal development of their expression remains unknown. Male Leptobrachium boringii develop keratinized nuptial spines on their upper jaw during the breeding season that fall off when the breeding season ends. To illuminate the genetic basis for the expression of this trait and its seasonal development, we assessed the de novo transcriptome for L. boringii using brain, testis and upper jaw skin and compared gene expression profiles of these tissues between two critical periods of the spine growth cycle.

RESULTS: We identified 94,900 unigenes in our transcriptome. Among them, 2,131 genes were differentially expressed between the breeding period when the spines developed and the post-breeding period when the spines were sloughed. An increased number of differentially expressed genes (DEGs) were identified in the upper jaw skin compared with the testis and brain. In the upper jaw skin, DEGs were mainly enriched in cytosolic part, peptidase inhibitor activity and peptidase regulator activity based on GO enrichment analysis and in glycolysis/gluconeogenesis, ribosome biogenesis in eukaryotes and retinol metabolism based on KEGG enrichment analysis. In the other two tissues, DEGs were primarily involved in the cell cycle, DNA replication and melatonin production. Specifically, insulin/insulin-like growth factor and sex steroid hormone-related DEGs were identified in the upper jaw skin, indicating . The expression variation of IGF2 and estrogen-related genes may be the main factors regulating the seasonal development of the spines.

CONCLUSIONS: Our study provides a list of potential genes involved in the regulation of seasonal development of nuptial spines in L. boringii. This is the first transcriptome survey of seasonally developed sexually selected traits for non-model amphibian species, and candidate genes provided here may provide valuable information for further studies of L. boringii.}, } @article {pmid27890772, year = {2017}, author = {Wippermann, A and Rupp, O and Brinkrolf, K and Hoffrogge, R and Noll, T}, title = {Integrative analysis of DNA methylation and gene expression in butyrate-treated CHO cells.}, journal = {Journal of biotechnology}, volume = {257}, number = {}, pages = {150-161}, doi = {10.1016/j.jbiotec.2016.11.020}, pmid = {27890772}, issn = {1873-4863}, mesh = {Animals ; Apoptosis/drug effects ; Butyrates/*pharmacology ; CHO Cells/*drug effects ; Cell Cycle/drug effects ; Cell Division/drug effects ; Cricetulus ; *DNA Methylation ; Epigenesis, Genetic ; *Gene Expression ; Gene Expression Profiling ; Gene Ontology ; Genome ; Molecular Sequence Data ; Proteins/metabolism ; Transcription Factors ; Whole Genome Sequencing ; }, abstract = {The cellular mechanisms responsible for the versatile properties of CHO cells as the major production cell line for biopharmaceutical molecules are not entirely understood yet, although several 'omics' data facilitate the understanding of CHO cells and their reactions to environmental conditions. However, genome-wide studies of epigenetic processes such as DNA methylation are still limited. To prove the applicability and usefulness of integrating DNA methylation and gene expression data in a biotechnological context, we exemplarily analyzed the time course of cellular reactions upon butyrate addition in antibody-producing CHO cells by whole-genome bisulfite sequencing and CHO-specific cDNA microarrays. Gene expression and DNA methylation analyses showed that pathways known to be affected by butyrate, including cell cycle and apoptosis, as well as pathways potentially involved in butyrate-induced hyperproductivity such as central energy metabolism and protein biosynthesis were affected. Differentially methylated regions were furthermore found to contain binding-site motifs of specific transcription factors and were hypothesized to represent regulatory regions closely connected to the cellular response to butyrate. Generally, our experiment underlines the benefit of integrating DNA methylation and gene expression data, as it provided potential novel candidate genes for rational cell line development and allowed for new insights into the butyrate effect on CHO cells.}, } @article {pmid27889953, year = {2017}, author = {Hampton, SE and Galloway, AW and Powers, SM and Ozersky, T and Woo, KH and Batt, RD and Labou, SG and O'Reilly, CM and Sharma, S and Lottig, NR and Stanley, EH and North, RL and Stockwell, JD and Adrian, R and Weyhenmeyer, GA and Arvola, L and Baulch, HM and Bertani, I and Bowman, LL and Carey, CC and Catalan, J and Colom-Montero, W and Domine, LM and Felip, M and Granados, I and Gries, C and Grossart, HP and Haberman, J and Haldna, M and Hayden, B and Higgins, SN and Jolley, JC and Kahilainen, KK and Kaup, E and Kehoe, MJ and MacIntyre, S and Mackay, AW and Mariash, HL and McKay, RM and Nixdorf, B and Nõges, P and Nõges, T and Palmer, M and Pierson, DC and Post, DM and Pruett, MJ and Rautio, M and Read, JS and Roberts, SL and Rücker, J and Sadro, S and Silow, EA and Smith, DE and Sterner, RW and Swann, GE and Timofeyev, MA and Toro, M and Twiss, MR and Vogt, RJ and Watson, SB and Whiteford, EJ and Xenopoulos, MA}, title = {Ecology under lake ice.}, journal = {Ecology letters}, volume = {20}, number = {1}, pages = {98-111}, doi = {10.1111/ele.12699}, pmid = {27889953}, issn = {1461-0248}, mesh = {*Ecosystem ; *Ice Cover ; *Lakes ; Plankton/*physiology ; Seasons ; }, abstract = {Winter conditions are rapidly changing in temperate ecosystems, particularly for those that experience periods of snow and ice cover. Relatively little is known of winter ecology in these systems, due to a historical research focus on summer 'growing seasons'. We executed the first global quantitative synthesis on under-ice lake ecology, including 36 abiotic and biotic variables from 42 research groups and 101 lakes, examining seasonal differences and connections as well as how seasonal differences vary with geophysical factors. Plankton were more abundant under ice than expected; mean winter values were 43.2% of summer values for chlorophyll a, 15.8% of summer phytoplankton biovolume and 25.3% of summer zooplankton density. Dissolved nitrogen concentrations were typically higher during winter, and these differences were exaggerated in smaller lakes. Lake size also influenced winter-summer patterns for dissolved organic carbon (DOC), with higher winter DOC in smaller lakes. At coarse levels of taxonomic aggregation, phytoplankton and zooplankton community composition showed few systematic differences between seasons, although literature suggests that seasonal differences are frequently lake-specific, species-specific, or occur at the level of functional group. Within the subset of lakes that had longer time series, winter influenced the subsequent summer for some nutrient variables and zooplankton biomass.}, } @article {pmid27887731, year = {2017}, author = {Khodami, S and Surif, M and W O, WM and Daryanabard, R}, title = {Assessment of heavy metal pollution in surface sediments of the Bayan Lepas area, Penang, Malaysia.}, journal = {Marine pollution bulletin}, volume = {114}, number = {1}, pages = {615-622}, doi = {10.1016/j.marpolbul.2016.09.038}, pmid = {27887731}, issn = {1879-3363}, mesh = {Ecology ; Environmental Monitoring/*methods ; Geographic Information Systems ; Geologic Sediments/*chemistry ; Malaysia ; Metals, Heavy/*analysis ; Models, Theoretical ; Risk Assessment ; Rivers/chemistry ; Seasons ; Seawater/chemistry ; Water Pollutants, Chemical/*analysis ; }, abstract = {This study aimed to evaluate the spatial and temporal distribution of heavy metals (Cd, Cr, Cu, Co, Fe, Pb, Ni, V, and Zn) in the sediments of Bayan Lepas Free Industrial Zone of Penang, Malaysia. Ten sampling stations were selected and sediment samples were collected during low tide (2012-2013). Metals were analyzed and the spatial distribution of metals were evaluated based on GIS mapping. According to interim sediment quality guidelines (ISQG), metal contents ranged from below low level to above high level at different stations. Based on the geoaccumulation index (Igeo) of sediment, sampling stations were categorized from unpolluted to strongly polluted. The enrichment factor (EF) of metals in the sediment varied between no enrichment to extremely high enrichment. The potential ecological risk index (RI) indicated Bayan Lepas FIZ was at low risk.}, } @article {pmid27887570, year = {2016}, author = {Shaw, GT and Pao, YY and Wang, D}, title = {MetaMIS: a metagenomic microbial interaction simulator based on microbial community profiles.}, journal = {BMC bioinformatics}, volume = {17}, number = {1}, pages = {488}, pmid = {27887570}, issn = {1471-2105}, mesh = {*Algorithms ; Bacteria/*classification/*genetics ; Computational Biology/*methods ; Ecology ; Feces/*microbiology ; Female ; Humans ; Male ; Metagenome/*genetics ; Microbial Interactions ; Microbiota/*genetics ; Software ; }, abstract = {BACKGROUND: The complexity and dynamics of microbial communities are major factors in the ecology of a system. With the NGS technique, metagenomics data provides a new way to explore microbial interactions. Lotka-Volterra models, which have been widely used to infer animal interactions in dynamic systems, have recently been applied to the analysis of metagenomic data.

RESULTS: In this paper, we present the Lotka-Volterra model based tool, the Metagenomic Microbial Interacticon Simulator (MetaMIS), which is designed to analyze the time series data of microbial community profiles. MetaMIS first infers underlying microbial interactions from abundance tables for operational taxonomic units (OTUs) and then interprets interaction networks using the Lotka-Volterra model. We also embed a Bray-Curtis dissimilarity method in MetaMIS in order to evaluate the similarity to biological reality. MetaMIS is designed to tolerate a high level of missing data, and can estimate interaction information without the influence of rare microbes. For each interaction network, MetaMIS systematically examines interaction patterns (such as mutualism or competition) and refines the biotic role within microbes. As a case study, we collect a human male fecal microbiome and show that Micrococcaceae, a relatively low abundance OTU, is highly connected with 13 dominant OTUs and seems to play a critical role. MetaMIS is able to organize multiple interaction networks into a consensus network for comparative studies; thus we as a case study have also identified a consensus interaction network between female and male fecal microbiomes.

CONCLUSIONS: MetaMIS provides an efficient and user-friendly platform that may reveal new insights into metagenomics data. MetaMIS is freely available at: https://sourceforge.net/projects/metamis/ .}, } @article {pmid27885171, year = {2016}, author = {Poyatos, R and Granda, V and Molowny-Horas, R and Mencuccini, M and Steppe, K and Martínez-Vilalta, J}, title = {SAPFLUXNET: towards a global database of sap flow measurements.}, journal = {Tree physiology}, volume = {36}, number = {12}, pages = {1449-1455}, doi = {10.1093/treephys/tpw110}, pmid = {27885171}, issn = {1758-4469}, mesh = {*Databases, Factual ; Droughts ; Ecosystem ; *Plant Transpiration ; Water/metabolism ; }, abstract = {Plant transpiration is the main evaporative flux from terrestrial ecosystems; it controls land surface energy balance, determines catchment hydrological responses and influences regional and global climate. Transpiration regulation by plants is a key (and still not completely understood) process that underlies vegetation drought responses and land evaporative fluxes under global change scenarios. Thermometric methods of sap flow measurement have now been widely used to quantify whole-plant and stand transpiration in forests, shrublands and orchards around the world. A large body of research has applied sap flow methods to analyse seasonal and diurnal patterns of transpiration and to quantify their responses to hydroclimatic variability, but syntheses of sap flow data at regional to global scales are extremely rare. Here we present the SAPFLUXNET initiative, aimed at building the first global database of plant-level sap flow measurements. A preliminary metadata survey launched in December 2015 showed an encouraging response by the sap flow community, with sap flow data sets from field studies representing >160 species and >120 globally distributed sites. The main goal of SAPFLUXNET is to analyse the ecological factors driving plant- and stand-level transpiration. SAPFLUXNET will open promising research avenues at an unprecedented global scope, namely: (i) exploring the spatio-temporal variability of plant transpiration and its relationship with plant and stand attributes, (ii) summarizing physiological regulation of transpiration by means of few water-use traits, usable for land surface models, (iii) improving our understanding of the coordination between gas exchange and plant-level traits (e.g., hydraulics) and (iv) analysing the ecological factors controlling stand transpiration and evapotranspiration partitioning. Finally, SAPFLUXNET can provide a benchmark to test models of physiological controls of transpiration, contributing to improve the accuracy of individual water stress responses, a key element to obtain robust predictions of vegetation responses to climate change.}, } @article {pmid27881233, year = {2017}, author = {Cho, H and Gonzalez, R and Lavaysse, LM and Pence, S and Fulford, D and Gard, DE}, title = {Do people with schizophrenia experience more negative emotion and less positive emotion in their daily lives? A meta-analysis of experience sampling studies.}, journal = {Schizophrenia research}, volume = {183}, number = {}, pages = {49-55}, doi = {10.1016/j.schres.2016.11.016}, pmid = {27881233}, issn = {1573-2509}, mesh = {*Activities of Daily Living ; Affective Symptoms/*etiology/psychology ; Databases, Bibliographic/statistics & numerical data ; Humans ; Schizophrenia/*complications ; *Schizophrenic Psychology ; }, abstract = {Research on emotion experience in response to valenced stimuli has consistently shown that people with schizophrenia have the capacity to experience emotion. Specifically, people with schizophrenia report similar experiences to both positive and negative emotion-eliciting stimuli as individuals without the disorder. However, it is less clear if people with schizophrenia experience similar levels of positive emotion and negative emotion outside of standardized laboratory contexts, as in their daily lives. One reliable method for assessing emotion experience in schizophrenia has been the Experience Sampling Method (ESM), or Ecological Momentary Assessment (EMA). Using the PRISMA guidelines for meta-analysis, we reviewed the literature for all studies that included people with and without schizophrenia, and that included a positive or negative emotion assessment during participants' daily lives. The current study is a meta-analysis of 12 EMA studies of emotion experience, which included a total of 619 people with schizophrenia and 730 healthy controls. Results indicate that people with schizophrenia consistently report more negative and less positive emotion than healthy control participants. These findings differ from laboratory-based studies, which may be due to several factors, including environmental differences, effects of the disorder that appear more clearly in daily life, or additional concerns, such as depression, which has been shown to be related to negative emotion in schizophrenia. Importantly, these findings are in line with questionnaire-based measures of emotion experience, lending some support for their use in research and clinical settings.}, } @article {pmid27879674, year = {2016}, author = {Liu, Y and Han, S and Ding, X and Li, X and Zhang, L and Li, W and Xu, H and Li, Z and Qi, L}, title = {Transcriptome Analysis of mRNA and miRNA in Somatic Embryos of Larix leptolepis Subjected to Hydrogen Treatment.}, journal = {International journal of molecular sciences}, volume = {17}, number = {11}, pages = {}, pmid = {27879674}, issn = {1422-0067}, mesh = {Cell Cycle/drug effects ; Cell Cycle Proteins/genetics/metabolism ; Databases, Genetic ; Gene Expression Profiling ; Gene Expression Regulation, Developmental ; *Gene Expression Regulation, Plant ; Gene Library ; Gene Regulatory Networks/drug effects ; Hydrogen/*pharmacology ; Larix/*drug effects/genetics/growth & development/metabolism ; MicroRNAs/*genetics/metabolism ; Plant Proteins/genetics/metabolism ; Plant Somatic Embryogenesis Techniques ; RNA, Messenger/*genetics/metabolism ; Reactive Oxygen Species/metabolism ; Seeds/*drug effects/genetics/growth & development/metabolism ; *Transcriptome ; }, abstract = {Hydrogen is a therapeutic antioxidant that has been used extensively in clinical trials. It also acts as a bioactive molecule that can alleviate abiotic stress in plants. However, the biological effects of hydrogen in somatic embryos and the underlying molecular basis remain largely unknown. In this study, the morphological and physiological influence of exogenous H2 treatment during somatic embryogenesis was characterized in Larix leptolepis Gordon. The results showed that exposure to hydrogen increased the proportions of active pro-embryogenic cells and normal somatic embryos. We sequenced mRNA and microRNA (miRNA) libraries to identify global transcriptome changes at different time points during H2 treatment of larch pro-embryogenic masses (PEMs). A total of 45,393 mRNAs and 315 miRNAs were obtained. Among them, 4253 genes and 96 miRNAs were differentially expressed in the hydrogen-treated libraries compared with the control. Further, a large number of the differentially expressed mRNAs and miRNAs were related to reactive oxygen species (ROS) homeostasis and cell cycle regulation. We also identified 4399 potential target genes for 285 of the miRNAs. The differential expression data and the mRNA-miRNA interaction network described here provide new insights into the molecular mechanisms that determine the performance of PEMs exposed to H2 during somatic embryogenesis.}, } @article {pmid27878652, year = {2017}, author = {Hu, L and He, H and Zhu, C and Peng, X and Fu, J and He, X and Chen, X and Ouyang, L and Bian, J and Liu, S}, title = {Genome-wide identification and phylogenetic analysis of the chalcone synthase gene family in rice.}, journal = {Journal of plant research}, volume = {130}, number = {1}, pages = {95-105}, pmid = {27878652}, issn = {1618-0860}, mesh = {Acyltransferases/*genetics ; Chromosome Mapping ; Databases, Nucleic Acid ; Gene Expression Regulation, Plant ; Genome, Plant/*genetics ; Introns/genetics ; *Multigene Family ; Oryza/*enzymology/genetics ; Phylogeny ; Plant Proteins/genetics ; Promoter Regions, Genetic/genetics ; Sequence Alignment ; Sequence Analysis, DNA ; }, abstract = {The enzymes of the chalcone synthase family are also known as type III polyketide synthases (PKS), and produce a series of secondary metabolites in bacteria, fungi and plants. In a number of plants, genes encoding PKS comprise a large multigene family. Currently, detailed reports on rice (Oryza sativa) PKS (OsPKS) family genes and tissue expression profiling are limited. Here, 27 candidate OsPKS genes were identified in the rice genome,and 23 gene structures were confirmed by EST and cDNA sequencing; phylogenetic analysis has indicated that these 23 OsPKS members could be clustered into three groups (I-III). Comparative analysis has shown OsPKS08 and OsPKS26 could be classified with the CHS genes of other species. Two members OsPKS10 and OsPKS21 were grouped into anther specific chalcone synthase-like (ASCL) clade. Intron/exon structure analysis revealed that nearly all of the OsPKS members contained one phase-1 intron at a conserved Cys. Analysis of chromosomal localization and genome distribution showed that some of the members were distributed on a chromosome as a cluster. Expression data exhibited widespread distribution of the rice OsPKS gene family within plant tissues, suggesting functional diversification of the OsPKS genes. Our results will contribute to future study of the complexity of the OsPKS gene family in rice.}, } @article {pmid27876269, year = {2017}, author = {Shpiegel, S and Cascardi, M and Dineen, M}, title = {A Social Ecology Analysis of Childbirth Among Females Emancipating From Foster Care.}, journal = {The Journal of adolescent health : official publication of the Society for Adolescent Medicine}, volume = {60}, number = {5}, pages = {563-569}, doi = {10.1016/j.jadohealth.2016.09.013}, pmid = {27876269}, issn = {1879-1972}, mesh = {Adolescent ; Age Factors ; Birth Rate/*ethnology ; Child Welfare/statistics & numerical data ; Databases, Factual ; Female ; Foster Home Care/*statistics & numerical data ; Humans ; Multivariate Analysis ; Pregnancy ; Pregnancy in Adolescence/ethnology/*prevention & control ; Prospective Studies ; Risk Factors ; Self Report ; *Social Environment ; United States/epidemiology ; Young Adult ; }, abstract = {PURPOSE: No research has examined childbirth from a national perspective among females emancipating from foster care. The present study fills this gap by: (1) documenting the rates of initial and repeat births among females ages 17 and 19 in a national prospective study and (2) identifying risk and protective factors at age 17 that predict childbirth between ages 17 and 19.

METHODS: This study used data from the National Youth in Transition Database and Adoption and Foster Care Analysis and Reporting System to identify risk and protective factors associated with childbirth in a national sample of transition-age female youth (N = 3,474).

RESULTS: The cumulative rate of childbirth by age 19 was 21%, with higher rates reported between ages 17 and 19 (17%; n = 602) compared with age 17 or earlier (9%; n = 313). In logistic regression analysis, black race and Hispanic ethnicity, placement with relatives, runaway status, trial home visit placement, early emancipation from foster care, and lifetime incarceration histories were associated with increased likelihood of childbirth. In contrast, school enrollment and employment skills were associated with decreased likelihood of childbirth. The multivariate odds of childbirth between ages 17 and 19 increased 10-fold if youth already had a child by age 17.

CONCLUSIONS: Sexual health and pregnancy prevention programs should specifically target youths who already have children. Increased attention should be paid to adolescents placed with biological families and those with histories of criminal involvement.}, } @article {pmid27875986, year = {2016}, author = {Zhang, L and Lu, Y and Xiang, M and Shang, Q and Gao, X}, title = {The retardant effect of 2-Tridecanone, mediated by Cytochrome P450, on the Development of Cotton bollworm, Helicoverpa armigera.}, journal = {BMC genomics}, volume = {17}, number = {1}, pages = {954}, pmid = {27875986}, issn = {1471-2164}, mesh = {Animals ; Computational Biology/methods ; Cytochrome P-450 Enzyme System/chemistry/classification/*genetics/metabolism ; Gene Expression Profiling ; Gene Expression Regulation, Developmental/drug effects ; Genes, Insect ; Gossypium/*parasitology ; High-Throughput Nucleotide Sequencing ; Hormones/metabolism ; Ketones/*pharmacology ; Larva ; Moths/*drug effects/*genetics/metabolism ; Phylogeny ; RNA Interference ; Transcriptome ; }, abstract = {BACKGROUND: Plant allelochemicals act as toxins, inhibitors of digestion, and deterrents that affect the fecundity of insects. These compounds have attracted significant research attention in recent decades, and much is known about the effects of these xenobiotic plant secondary metabolites on insect development. To date, although ecological interactions between xenobiotic plant secondary chemicals that retard insect growth have been observed in many species, it remains unclear how particular allelochemicals influence insect development in a life stage-dependent manner.

RESULTS: We found that 2-tridecanone can affect insect development; this effect appears similar to the symptoms induced by the physiological imbalance between juvenile and molting hormones in cotton bollworm. We later detected that a decrease in the concentration of 20-hydroxyecdysone occurred alongside the observed symptoms. We next identified the transcriptome of Helicoverpa armigera and eightdigital gene expression libraries for shading light on how 2-tridecanone retarded the development of cotton bollworm. The expression of CYP314A1, CYP315A1, CYP18A1, CYP307A1, and CYP306A1 (unigenes 16487, 15409, 40026, 41217, 35643, 16953, 8199, 13311, and 13036) were found to be induced by 2-tridecanone; these are known to be related to the biosynthesis or metabolism of 20-hydroxyecdysone. Expression analysis and RNA interference studies established that the retardant effect of 2-tridecanone on the development of cotton bollworm is mediated by P450 genes.

CONCLUSIONS: The candidate P450 gene approach described and exploited here is useful for identifying potential causal genes for the influence of plant allelochemicals on insect development.}, } @article {pmid27875147, year = {2017}, author = {Song, H and Lee, J and Kim, TJ and Lee, KH and Kim, B and Seo, J}, title = {GazeDx: Interactive Visual Analytics Framework for Comparative Gaze Analysis with Volumetric Medical Images.}, journal = {IEEE transactions on visualization and computer graphics}, volume = {23}, number = {1}, pages = {311-320}, doi = {10.1109/TVCG.2016.2598796}, pmid = {27875147}, issn = {1941-0506}, mesh = {Algorithms ; Eye Movements/*physiology ; Humans ; *Imaging, Three-Dimensional ; Medical Informatics/*methods ; Radiography, Abdominal ; Radiography, Thoracic ; Radiologists ; Tomography, X-Ray Computed ; User-Computer Interface ; }, abstract = {We present an interactive visual analytics framework, GazeDx (abbr. of GazeDiagnosis), for the comparative analysis of gaze data from multiple readers examining volumetric images while integrating important contextual information with the gaze data. Gaze pattern comparison is essential to understanding how radiologists examine medical images, and to identifying factors influencing the examination. Most prior work depended upon comparisons with manually juxtaposed static images of gaze tracking results. Comparative gaze analysis with volumetric images is more challenging due to the additional cognitive load on 3D perception. A recent study proposed a visualization design based on direct volume rendering (DVR) for visualizing gaze patterns in volumetric images; however, effective and comprehensive gaze pattern comparison is still challenging due to a lack of interactive visualization tools for comparative gaze analysis. We take the challenge with GazeDx while integrating crucial contextual information such as pupil size and windowing into the analysis process for more in-depth and ecologically valid findings. Among the interactive visualization components in GazeDx, a context-embedded interactive scatterplot is especially designed to help users examine abstract gaze data in diverse contexts by embedding medical imaging representations well known to radiologists in it. We present the results from two case studies with two experienced radiologists, where they compared the gaze patterns of 14 radiologists reading two patients' volumetric CT images.}, } @article {pmid27872593, year = {2016}, author = {Cvetkovic, A and Cvetkovic, D and Stojic, V and Zdravkovic, N}, title = {Length of Hospital Stay and Bed Occupancy Rates in Former Yugoslav Republics 1989-2015.}, journal = {Frontiers in pharmacology}, volume = {7}, number = {}, pages = {417}, pmid = {27872593}, issn = {1663-9812}, } @article {pmid27870609, year = {2017}, author = {Matsuda, T and Komaki, F}, title = {Time Series Decomposition into Oscillation Components and Phase Estimation.}, journal = {Neural computation}, volume = {29}, number = {2}, pages = {332-367}, doi = {10.1162/NECO_a_00916}, pmid = {27870609}, issn = {1530-888X}, abstract = {Many time series are naturally considered as a superposition of several oscillation components. For example, electroencephalogram (EEG) time series include oscillation components such as alpha, beta, and gamma. We propose a method for decomposing time series into such oscillation components using state-space models. Based on the concept of random frequency modulation, gaussian linear state-space models for oscillation components are developed. In this model, the frequency of an oscillator fluctuates by noise. Time series decomposition is accomplished by this model like the Bayesian seasonal adjustment method. Since the model parameters are estimated from data by the empirical Bayes' method, the amplitudes and the frequencies of oscillation components are determined in a data-driven manner. Also, the appropriate number of oscillation components is determined with the Akaike information criterion (AIC). In this way, the proposed method provides a natural decomposition of the given time series into oscillation components. In neuroscience, the phase of neural time series plays an important role in neural information processing. The proposed method can be used to estimate the phase of each oscillation component and has several advantages over a conventional method based on the Hilbert transform. Thus, the proposed method enables an investigation of the phase dynamics of time series. Numerical results show that the proposed method succeeds in extracting intermittent oscillations like ripples and detecting the phase reset phenomena. We apply the proposed method to real data from various fields such as astronomy, ecology, tidology, and neuroscience.}, } @article {pmid27869966, year = {2016}, author = {Böhm, AW and Costa, CD and Neves, RG and Flores, TR and Nunes, BP}, title = {Dengue incidence trend in Brazil, 2002-2012.}, journal = {Epidemiologia e servicos de saude : revista do Sistema Unico de Saude do Brasil}, volume = {25}, number = {4}, pages = {725-733}, doi = {10.5123/S1679-49742016000400006}, pmid = {27869966}, issn = {2237-9622}, mesh = {Age Distribution ; Brazil/epidemiology ; Dengue/*epidemiology ; Humans ; Incidence ; Information Systems ; Public Policy ; }, abstract = {OBJECTIVE: to analyze dengue incidence trend in Brazil from 2002 to 2012.

METHODS: this was an ecological study with data of the Information System for Notifiable Diseases (Sinan); the incidence rate was calculated by age groups, states and macroregions, through Prais-Winsten regression.

RESULTS: dengue incidence rates in Brazil, in 2002 and 2012, were of 401.6 and 301.5 per 100,000 inhabitants, respectively; annual increment rates were stable (21.4%; 95%CI -19.8;83.7) in most of the states, except for Alagoas (38.9%; 95%CI 5.1;83.5) and Tocantins (50.4%; 95%CI 12.6;100.7); the North Region was the only region to present increase trend in the incidence of dengue.

CONCLUSION: although rates have remained stable in most of the states, they are still high in Brazil; broader public policies focusing on new dengue control strategies are necessary.}, } @article {pmid27869957, year = {2016}, author = {Souza, ML}, title = {Mental disorders record on the Brazilian primary health care information system, 2014.}, journal = {Epidemiologia e servicos de saude : revista do Sistema Unico de Saude do Brasil}, volume = {25}, number = {2}, pages = {405-410}, doi = {10.5123/S1679-49742016000200018}, pmid = {27869957}, issn = {2237-9622}, mesh = {Brazil/epidemiology ; Cities/epidemiology ; Health Information Systems/*statistics & numerical data ; Humans ; Mental Disorders/*epidemiology ; Primary Health Care/*statistics & numerical data ; }, abstract = {OBJECTIVE: to describe the occurrence of the recording of mental disorders (MD) in primary health care (PHC) services in Brazilian municipalities and to analyze associated factors.

METHODS: an ecological study was conducted using PHC Information System secondary data for the year 2014; the magnitude of the occurrence of MD recording was assessed through indicators developed for this purpose; bivariate analysis was used.

RESULTS: 15,216 MD cases were recorded in 42 (0.8%) municipalities, corresponding to 16.9 MD cases/100,000 inhabitants for Brazil, with significant variations between the country's macro-regions; MD recording in PHC was most frequent in the Southeast and Southern macro-regions (p=0.001), in state capital cities (p<0.001), in municipalities with more than 200,000 inhabitants (p<0.001), those with PHC coverage greater than 75% (p=0.005) and those with Psychosocial Care Centers (p=0.001).

CONCLUSION: recording of MD in PHC is incipient, unequally distributed and possibly dependent on local initiatives.}, } @article {pmid27866743, year = {2017}, author = {Tsai, WP and Huang, SP and Cheng, ST and Shao, KT and Chang, FJ}, title = {A data-mining framework for exploring the multi-relation between fish species and water quality through self-organizing map.}, journal = {The Science of the total environment}, volume = {579}, number = {}, pages = {474-483}, doi = {10.1016/j.scitotenv.2016.11.071}, pmid = {27866743}, issn = {1879-1026}, mesh = {Algorithms ; Animals ; Biological Oxygen Demand Analysis ; *Data Mining ; Ecosystem ; Environmental Monitoring/*methods ; *Fishes ; Neural Networks, Computer ; Phosphorus/analysis ; Taiwan ; Water Pollutants, Chemical/*analysis ; Water Pollution, Chemical/*statistics & numerical data ; }, abstract = {The steep slopes of rivers can easily lead to large variations in river water quality during typhoon seasons in Taiwan, which may poses significant impacts on riverine eco-hydrological environments. This study aims to investigate the relationship between fish communities and water quality by using artificial neural networks (ANNs) for comprehending the upstream eco-hydrological system in northern Taiwan. We collected a total of 276 heterogeneous datasets with 8 water quality parameters and 25 fish species from 10 sampling sites. The self-organizing feature map (SOM) was used to cluster, analyze and visualize the heterogeneous datasets. Furthermore, the structuring index (SI) was adopted to determine the relative importance of each input variable of the SOM and identify the indicator factors. The clustering results showed that the SOM could suitably reflect the spatial characteristics of fishery sampling sites. Besides, the patterns of water quality parameters and fish species could be distinguishably (visually) classified into three eco-water quality groups: 1) typical upstream freshwater fishes that depended the most on dissolved oxygen (DO); 2) typical middle-lower reach riverine freshwater fishes that depended the most on total phosphorus (TP) and ammonia nitrogen; and 3) low lands or pond (reservoirs) freshwater fishes that depended the most on water temperature, suspended solids and chemical oxygen demand. According to the results of the SI, the representative indicators of water quality parameters and fish species consisted of DO, TP and Onychostoma barbatulum. This grouping result suggested that the methodology can be used as a guiding reference to comprehensively relate ecology to water quality. Our methods offer a cost-effective alternative to more traditional methods for identifying key water quality factors relating to fish species. In addition, visualizing the constructed topological maps of the SOM could produce detailed inter-relation between water quality and the fish species of stream habitat units.}, } @article {pmid27861486, year = {2016}, author = {Toju, H and Kishida, O and Katayama, N and Takagi, K}, title = {Networks Depicting the Fine-Scale Co-Occurrences of Fungi in Soil Horizons.}, journal = {PloS one}, volume = {11}, number = {11}, pages = {e0165987}, pmid = {27861486}, issn = {1932-6203}, mesh = {Biodiversity ; Computational Biology/methods ; DNA Barcoding, Taxonomic ; DNA, Ribosomal Spacer ; Ecosystem ; *Fungi/classification/genetics ; Japan ; Metagenome ; Metagenomics/methods ; *Soil Microbiology ; }, abstract = {Fungi in soil play pivotal roles in nutrient cycling, pest controls, and plant community succession in terrestrial ecosystems. Despite the ecosystem functions provided by soil fungi, our knowledge of the assembly processes of belowground fungi has been limited. In particular, we still have limited knowledge of how diverse functional groups of fungi interact with each other in facilitative and competitive ways in soil. Based on the high-throughput sequencing data of fungi in a cool-temperate forest in northern Japan, we analyzed how taxonomically and functionally diverse fungi showed correlated fine-scale distributions in soil. By uncovering pairs of fungi that frequently co-occurred in the same soil samples, networks depicting fine-scale co-occurrences of fungi were inferred at the O (organic matter) and A (surface soil) horizons. The results then led to the working hypothesis that mycorrhizal, endophytic, saprotrophic, and pathogenic fungi could form compartmentalized (modular) networks of facilitative, antagonistic, and/or competitive interactions in belowground ecosystems. Overall, this study provides a research basis for further understanding how interspecific interactions, along with sharing of niches among fungi, drive the dynamics of poorly explored biospheres in soil.}, } @article {pmid27860289, year = {2017}, author = {Lowry, DB and Hoban, S and Kelley, JL and Lotterhos, KE and Reed, LK and Antolin, MF and Storfer, A}, title = {Breaking RAD: an evaluation of the utility of restriction site-associated DNA sequencing for genome scans of adaptation.}, journal = {Molecular ecology resources}, volume = {17}, number = {2}, pages = {142-152}, pmid = {27860289}, issn = {1755-0998}, support = {R01 GM098856/GM/NIGMS NIH HHS/United States ; }, mesh = {*Adaptation, Biological ; Computational Biology/*methods ; DNA/chemistry/genetics/metabolism ; DNA Restriction Enzymes/*metabolism ; *Genetic Variation ; Genetics, Population/*methods ; Genomics/*methods ; Linkage Disequilibrium ; Sequence Analysis, DNA/*methods ; }, abstract = {Understanding how and why populations evolve is of fundamental importance to molecular ecology. Restriction site-associated DNA sequencing (RADseq), a popular reduced representation method, has ushered in a new era of genome-scale research for assessing population structure, hybridization, demographic history, phylogeography and migration. RADseq has also been widely used to conduct genome scans to detect loci involved in adaptive divergence among natural populations. Here, we examine the capacity of those RADseq-based genome scan studies to detect loci involved in local adaptation. To understand what proportion of the genome is missed by RADseq studies, we developed a simple model using different numbers of RAD-tags, genome sizes and extents of linkage disequilibrium (length of haplotype blocks). Under the best-case modelling scenario, we found that RADseq using six- or eight-base pair cutting restriction enzymes would fail to sample many regions of the genome, especially for species with short linkage disequilibrium. We then surveyed recent studies that have used RADseq for genome scans and found that the median density of markers across these studies was 4.08 RAD-tag markers per megabase (one marker per 245 kb). The length of linkage disequilibrium for many species is one to three orders of magnitude less than density of the typical recent RADseq study. Thus, we conclude that genome scans based on RADseq data alone, while useful for studies of neutral genetic variation and genetic population structure, will likely miss many loci under selection in studies of local adaptation.}, } @article {pmid27859171, year = {2016}, author = {Wang, Y and Pederson, N and Ellison, AM and Buckley, HL and Case, BS and Liang, E and Julio Camarero, J}, title = {Increased stem density and competition may diminish the positive effects of warming at alpine treeline.}, journal = {Ecology}, volume = {97}, number = {7}, pages = {1668-1679}, doi = {10.1890/15-1264.1}, pmid = {27859171}, issn = {0012-9658}, mesh = {Abies/*physiology ; Environmental Monitoring ; *Forests ; *Global Warming ; Plant Stems/*physiology ; Trees/physiology ; }, abstract = {The most widespread response to global warming among alpine treeline ecotones is not an upward shift, but an increase in tree density. However, the impact of increasing density on interactions among trees at treeline is not well understood. Here, we test if treeline densification induced by climatic warming leads to increasing intraspecific competition. We mapped and measured the size and age of Smith fir trees growing in two treelines located in the southeastern Tibetan Plateau. We used spatial point-pattern and codispersion analyses to describe the spatial association and covariation among seedlings, juveniles, and adults grouped in 30-yr age classes from the 1860s to the present. Effects of competition on tree height and regeneration were inferred from bivariate mark-correlations. Since the 1950s, a rapid densification occurred at both sites in response to climatic warming. Competition between adults and juveniles or seedlings at small scales intensified as density increased. Encroachment negatively affected height growth and further reduced recruitment around mature trees. We infer that tree recruitment at the studied treelines was more cold-limited prior to 1950 and shifted to a less temperature-constrained regime in response to climatic warming. Therefore, the ongoing densification and encroachment of alpine treelines could alter the way climate drives their transitions toward subalpine forests.}, } @article {pmid27856652, year = {2017}, author = {Xiang, Y and Huang, CH and Hu, Y and Wen, J and Li, S and Yi, T and Chen, H and Xiang, J and Ma, H}, title = {Evolution of Rosaceae Fruit Types Based on Nuclear Phylogeny in the Context of Geological Times and Genome Duplication.}, journal = {Molecular biology and evolution}, volume = {34}, number = {2}, pages = {262-281}, pmid = {27856652}, issn = {1537-1719}, mesh = {Biological Evolution ; Databases, Chemical ; Evolution, Molecular ; Fruit/genetics ; *Gene Duplication ; Genome, Plant ; Genomics ; Malus/genetics ; Phylogeny ; Plant Proteins/genetics ; Rosaceae/*genetics ; Seeds/genetics ; Transcriptome ; }, abstract = {Fruits are the defining feature of angiosperms, likely have contributed to angiosperm successes by protecting and dispersing seeds, and provide foods to humans and other animals, with many morphological types and important ecological and agricultural implications. Rosaceae is a family with ∼3000 species and an extraordinary spectrum of distinct fruits, including fleshy peach, apple, and strawberry prized by their consumers, as well as dry achenetum and follicetum with features facilitating seed dispersal, excellent for studying fruit evolution. To address Rosaceae fruit evolution and other questions, we generated 125 new transcriptomic and genomic datasets and identified hundreds of nuclear genes to reconstruct a well-resolved Rosaceae phylogeny with highly supported monophyly of all subfamilies and tribes. Molecular clock analysis revealed an estimated age of ∼101.6 Ma for crown Rosaceae and divergence times of tribes and genera, providing a geological and climate context for fruit evolution. Phylogenomic analysis yielded strong evidence for numerous whole genome duplications (WGDs), supporting the hypothesis that the apple tribe had a WGD and revealing another one shared by fleshy fruit-bearing members of this tribe, with moderate support for WGDs in the peach tribe and other groups. Ancestral character reconstruction for fruit types supports independent origins of fleshy fruits from dry-fruit ancestors, including the evolution of drupes (e.g., peach) and pomes (e.g., apple) from follicetum, and drupetum (raspberry and blackberry) from achenetum. We propose that WGDs and environmental factors, including animals, contributed to the evolution of the many fruits in Rosaceae, which provide a foundation for understanding fruit evolution.}, } @article {pmid27855648, year = {2016}, author = {Nock, CJ and Baten, A and Barkla, BJ and Furtado, A and Henry, RJ and King, GJ}, title = {Genome and transcriptome sequencing characterises the gene space of Macadamia integrifolia (Proteaceae).}, journal = {BMC genomics}, volume = {17}, number = {1}, pages = {937}, pmid = {27855648}, issn = {1471-2164}, mesh = {Computational Biology/methods ; Gene Ontology ; *Genome, Plant ; *Genomics/methods ; Glycosides/biosynthesis ; High-Throughput Nucleotide Sequencing ; Macadamia/*genetics/metabolism ; Molecular Sequence Annotation ; Multigene Family ; *Transcriptome ; }, abstract = {BACKGROUND: The large Gondwanan plant family Proteaceae is an early-diverging eudicot lineage renowned for its morphological, taxonomic and ecological diversity. Macadamia is the most economically important Proteaceae crop and represents an ancient rainforest-restricted lineage. The family is a focus for studies of adaptive radiation due to remarkable species diversification in Mediterranean-climate biodiversity hotspots, and numerous evolutionary transitions between biomes. Despite a long history of research, comparative analyses in the Proteaceae and macadamia breeding programs are restricted by a paucity of genetic information. To address this, we sequenced the genome and transcriptome of the widely grown Macadamia integrifolia cultivar 741.

RESULTS: Over 95 gigabases of DNA and RNA-seq sequence data were de novo assembled and annotated. The draft assembly has a total length of 518 Mb and spans approximately 79% of the estimated genome size. Following annotation, 35,337 protein-coding genes were predicted of which over 90% were expressed in at least one of the leaf, shoot or flower tissues examined. Gene family comparisons with five other eudicot species revealed 13,689 clusters containing macadamia genes and 1005 macadamia-specific clusters, and provides evidence for linage-specific expansion of gene families involved in pathogen recognition, plant defense and monoterpene synthesis. Cyanogenesis is an important defense strategy in the Proteaceae, and a detailed analysis of macadamia gene homologues potentially involved in cyanogenic glycoside biosynthesis revealed several highly expressed candidate genes.

CONCLUSIONS: The gene space of macadamia provides a foundation for comparative genomics, gene discovery and the acceleration of molecular-assisted breeding. This study presents the first available genomic resources for the large basal eudicot family Proteaceae, access to most macadamia genes and opportunities to uncover the genetic basis of traits of importance for adaptation and crop improvement.}, } @article {pmid27851814, year = {2016}, author = {Coetzer, W and Moodley, D and Gerber, A}, title = {Eliciting and Representing High-Level Knowledge Requirements to Discover Ecological Knowledge in Flower-Visiting Data.}, journal = {PloS one}, volume = {11}, number = {11}, pages = {e0166559}, pmid = {27851814}, issn = {1932-6203}, mesh = {Animals ; Bayes Theorem ; Behavior, Animal ; Biodiversity ; *Ecosystem ; Flowers/*physiology ; Insecta/*physiology ; *Knowledge ; Pollen/physiology ; Probability ; Reproducibility of Results ; }, abstract = {Observations of individual organisms (data) can be combined with expert ecological knowledge of species, especially causal knowledge, to model and extract from flower-visiting data useful information about behavioral interactions between insect and plant organisms, such as nectar foraging and pollen transfer. We describe and evaluate a method to elicit and represent such expert causal knowledge of behavioral ecology, and discuss the potential for wider application of this method to the design of knowledge-based systems for knowledge discovery in biodiversity and ecosystem informatics.}, } @article {pmid27851756, year = {2016}, author = {Iwanowicz, DD and Vandergast, AG and Cornman, RS and Adams, CR and Kohn, JR and Fisher, RN and Brehme, CS}, title = {Metabarcoding of Fecal Samples to Determine Herbivore Diets: A Case Study of the Endangered Pacific Pocket Mouse.}, journal = {PloS one}, volume = {11}, number = {11}, pages = {e0165366}, pmid = {27851756}, issn = {1932-6203}, mesh = {Animals ; California ; Computer Simulation ; DNA Barcoding, Taxonomic/*methods ; Databases, Genetic ; *Diet ; *Endangered Species ; Extinction, Biological ; Feces/*chemistry ; Herbivory/*physiology ; Rodentia/*genetics ; Seasons ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {Understanding the diet of an endangered species illuminates the animal's ecology, habitat requirements, and conservation needs. However, direct observation of diet can be difficult, particularly for small, nocturnal animals such as the Pacific pocket mouse (Heteromyidae: Perognathus longimembris pacificus). Very little is known of the dietary habits of this federally endangered rodent, hindering management and restoration efforts. We used a metabarcoding approach to identify source plants in fecal samples (N = 52) from the three remaining populations known. The internal transcribed spacers (ITS) of the nuclear ribosomal loci were sequenced following the Illumina MiSeq amplicon strategy and processed reads were mapped to reference databases. We evaluated a range of threshold mapping criteria and found the best-performing setting generally recovered two distinct mock communities in proportions similar to expectation. We tested our method on captive animals fed a known diet and recovered almost all plant sources, but found substantial heterogeneity among fecal pellets collected from the same individual at the same time. Observed richness did not increase with pooling of pellets from the same individual. In field-collected samples, we identified 4-14 plant genera in individual samples and 74 genera overall, but over 50 percent of reads mapped to just six species in five genera. We simulated the effects of sequencing error, variable read length, and chimera formation to infer taxon-specific rates of misassignment for the local flora, which were generally low with some exceptions. Richness at the species and genus levels did not reach a clear asymptote, suggesting that diet breadth remained underestimated in the current pool of samples. Large numbers of scat samples are therefore needed to make inferences about diet and resource selection in future studies of the Pacific pocket mouse. We conclude that our minimally invasive method is promising for determining herbivore diets given a library of sequences from local plants.}, } @article {pmid27842607, year = {2016}, author = {Hoehndorf, R and Alshahrani, M and Gkoutos, GV and Gosline, G and Groom, Q and Hamann, T and Kattge, J and de Oliveira, SM and Schmidt, M and Sierra, S and Smets, E and Vos, RA and Weiland, C}, title = {The flora phenotype ontology (FLOPO): tool for integrating morphological traits and phenotypes of vascular plants.}, journal = {Journal of biomedical semantics}, volume = {7}, number = {1}, pages = {65}, pmid = {27842607}, issn = {2041-1480}, support = {BB/J004464/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {*Biological Ontologies ; *Phenotype ; Plants/*anatomy & histology/genetics ; }, abstract = {BACKGROUND: The systematic analysis of a large number of comparable plant trait data can support investigations into phylogenetics and ecological adaptation, with broad applications in evolutionary biology, agriculture, conservation, and the functioning of ecosystems. Floras, i.e., books collecting the information on all known plant species found within a region, are a potentially rich source of such plant trait data. Floras describe plant traits with a focus on morphology and other traits relevant for species identification in addition to other characteristics of plant species, such as ecological affinities, distribution, economic value, health applications, traditional uses, and so on. However, a key limitation in systematically analyzing information in Floras is the lack of a standardized vocabulary for the described traits as well as the difficulties in extracting structured information from free text.

RESULTS: We have developed the Flora Phenotype Ontology (FLOPO), an ontology for describing traits of plant species found in Floras. We used the Plant Ontology (PO) and the Phenotype And Trait Ontology (PATO) to extract entity-quality relationships from digitized taxon descriptions in Floras, and used a formal ontological approach based on phenotype description patterns and automated reasoning to generate the FLOPO. The resulting ontology consists of 25,407 classes and is based on the PO and PATO. The classified ontology closely follows the structure of Plant Ontology in that the primary axis of classification is the observed plant anatomical structure, and more specific traits are then classified based on parthood and subclass relations between anatomical structures as well as subclass relations between phenotypic qualities.

CONCLUSIONS: The FLOPO is primarily intended as a framework based on which plant traits can be integrated computationally across all species and higher taxa of flowering plants. Importantly, it is not intended to replace established vocabularies or ontologies, but rather serve as an overarching framework based on which different application- and domain-specific ontologies, thesauri and vocabularies of phenotypes observed in flowering plants can be integrated.}, } @article {pmid27836278, year = {2017}, author = {Pająk, M and Halecki, W and Gąsiorek, M}, title = {Accumulative response of Scots pine (Pinus sylvestris L.) and silver birch (Betula pendula Roth) to heavy metals enhanced by Pb-Zn ore mining and processing plants: Explicitly spatial considerations of ordinary kriging based on a GIS approach.}, journal = {Chemosphere}, volume = {168}, number = {}, pages = {851-859}, doi = {10.1016/j.chemosphere.2016.10.125}, pmid = {27836278}, issn = {1879-1298}, mesh = {*Algorithms ; Betula/drug effects/*metabolism ; Environmental Monitoring/methods ; Environmental Pollution ; *Geographic Information Systems ; Lead/*toxicity ; Metallurgy ; Metals, Heavy/*toxicity ; *Mining ; Pinus sylvestris/drug effects/*metabolism ; Plant Leaves/drug effects/metabolism ; Poland ; Soil Pollutants/analysis ; Zinc/*toxicity ; }, abstract = {Plants have an accumulative response to heavy metals present in soils or deposited from airborne sources of emissions. Therefore, their tissues are very often used in studies of heavy metal contamination originating from different sources as a bioindicator of environmental pollution. This research was undertaken to examine accumulation capacities of Pb, Zn, Cd, Cu and Cr in washed and unwashed needles of Scots pine (Pinus sylvestris L.) and leaves of silver birch (Betula pendula Roth) growing in a contaminated area. We collected needles of Scots pine and leaves of silver birch in an area around a sedimentation pond and metallurgic plant processing Pb and Zn ores near Olkusz, Poland. Concentrations of heavy metals, which have been linked with exposure to emissions, were determined from foliar samples collected at 33 sites. These sites were established at various distances (0.5-3.6 km) from the pond and metallurgic plant so as to identify the predominant accumulative response of plants. Spatial gradients for Pb and Zn were calculated using an ordinary kriging interpolation algorithm. A spatial pattern was identified by a GIS method to visualize maps over the Pb-Zn ore mining area. The accumulation of Zn (R[2] = 0.74, p < 0.05) and Pb (R[2] = 0.85, p < 0.01) in plant tissues correlated with soil concentrations. This tendency was not found in the case of Cu, Cd and Cr.}, } @article {pmid27835832, year = {2017}, author = {Jeong, CB and Kim, HS and Kang, HM and Lee, YH and Zhou, B and Choe, J and Lee, JS}, title = {Genome-wide identification of ATP-binding cassette (ABC) transporters and conservation of their xenobiotic transporter function in the monogonont rotifer (Brachionus koreanus).}, journal = {Comparative biochemistry and physiology. Part D, Genomics & proteomics}, volume = {21}, number = {}, pages = {17-26}, doi = {10.1016/j.cbd.2016.10.003}, pmid = {27835832}, issn = {1878-0407}, mesh = {ATP-Binding Cassette Transporters/*genetics ; Adenosine Triphosphate/metabolism ; Animals ; Cells, Cultured ; Computational Biology ; *Gene Expression Profiling ; Genome/*genetics ; Phylogeny ; Rotifera/drug effects/*genetics ; Xenobiotics/*pharmacology ; }, abstract = {The ATP-binding cassette (ABC) transporter family is one of the largest gene family in animals, and members of this family are known to be involved in various biological processes due to their ability to transport a wide range of substrates across membranes using ATP cleavage-derived energy. We identified 61 ABC transporters in the genome of the monogonont rotifer Brachionus koreanus, and classified these into eight distinct subfamilies (A-H) by phylogenetic analysis. ABC transporters in the rotifer B. koreanus are comprised of 11 ABCA genes, 19 ABCB genes, 14 ABCC genes, 3 ABCD genes, 1 ABCE gene, 3 ABCF genes, 8 ABCG genes, and 2 ABCH genes. Extensive gene duplication and loss events in synteny were observed in several subfamilies. In particular, massive gene duplications of P-glycoproteins (P-gps), multidrug resistance proteins (MRPs), and Bk-Abcg-like proteins were observed. The ability of these B. koreanus proteins to function as multixenobiotic resistance (MXR) ABC transporters was validated using specific fluorescence substrates/inhibitors. The ABC transporter superfamily members identified in this study will be useful in future toxicological studies, and will facilitate comparative studies of the evolution of the ABC transporter superfamily in invertebrates.}, } @article {pmid27835646, year = {2016}, author = {Snir, S and vonHoldt, BM and Pellegrini, M}, title = {A Statistical Framework to Identify Deviation from Time Linearity in Epigenetic Aging.}, journal = {PLoS computational biology}, volume = {12}, number = {11}, pages = {e1005183}, pmid = {27835646}, issn = {1553-7358}, mesh = {Adolescent ; Adult ; Aged ; Aged, 80 and over ; Aging/*genetics ; Animals ; Biological Clocks/*genetics ; Child ; Child, Preschool ; Computer Simulation ; CpG Islands/*genetics ; DNA/*genetics ; DNA Methylation/*genetics ; Data Interpretation, Statistical ; Epigenesis, Genetic/*genetics ; Female ; Humans ; Infant ; Infant, Newborn ; Male ; Middle Aged ; Models, Genetic ; Models, Statistical ; Sequence Analysis, DNA/methods ; Young Adult ; }, abstract = {In multiple studies DNA methylation has proven to be an accurate biomarker of age. To develop these biomarkers, the methylation of multiple CpG sites is typically linearly combined to predict chronological age. By contrast, in this study we apply the Universal PaceMaker (UPM) model to investigate changes in DNA methylation during aging. The UPM was initially developed to study rate acceleration/deceleration in sequence evolution. Rather than identifying which linear combinations of sites predicts age, the UPM models the rates of change of multiple CpG sites, as well as their starting methylation levels, and estimates the age of each individual to optimize the model fit. We refer to the estimated age as the "epigenetic age", which is in contrast to the known chronological age of each individual. We construct a statistical framework and devise an algorithm to determine whether a genomic pacemaker is in effect (i.e rates of change vary with age). The decision is made by comparing two competing likelihood based models, the molecular clock (MC) and UPM. For the molecular clock model, we use the known chronological age of each individual and fit the methylation rates at multiple sites, and express the problem as a linear least squares and solve it in polynomial time. For the UPM case, the search space is larger as we are fitting both the epigenetic age of each individual as well as the rates for each site, yet we succeed to reduce the problem to the space of individuals and polynomial in the more significant space-the methylated sites. We first tested our algorithm on simulated data to elucidate the factors affecting the identification of the pacemaker model. We find that, provided with enough data, our algorithm is capable of identifying a pacemaker even when a weak signal is present in the data. Based on these results, we applied our method to DNA methylation data from human blood from individuals of various ages. Although the improvement in variance across sites between the UPM and MC was small, the results suggest that the existence of a pacemaker is highly significant. The PaceMaker results also suggest a decay in the rate of change in DNA methylation with age.}, } @article {pmid27833422, year = {2016}, author = {Sanguila, MB and Cobb, KA and Siler, CD and Diesmos, AC and Alcala, AC and Brown, RM}, title = {The amphibians and reptiles of Mindanao Island, southern Philippines, II: the herpetofauna of northeast Mindanao and adjacent islands.}, journal = {ZooKeys}, volume = {}, number = {624}, pages = {1-132}, pmid = {27833422}, issn = {1313-2989}, abstract = {We summarize all available amphibian and reptile species distribution data from the northeast Mindanao faunal region, including small islands associated with this subcenter of endemic vertebrate biodiversity. Together with all publicly available historical information from biodiversity repositories, we present new data from several major herpetological surveys, including recently conducted inventories on four major mountains of northeast Mindanao, and adjacent islands of Camiguin Sur, Dinagat, and Siargao. We present species accounts for all taxa, comment on unresolved taxonomic problems, and provide revisions to outdated IUCN conservation status assessments in cases where our new data significantly alter earlier classification status summaries. Together, our comprehensive analysis of this fauna suggests that the greater Mindanao faunal region possesses distinct subcenters of amphibian and reptile species diversity, and that until this area is revisited and its fauna and actually studied, with on-the-ground field work including targeted surveys of species distributions coupled to the study their natural history, our understanding of the diversity and conservation status of southern Philippine herpetological fauna will remain incomplete. Nevertheless, the northeast Mindanao geographical area (Caraga Region) appears to have the highest herpetological species diversity (at least 126 species) of any comparably-sized Philippine faunal subregion.}, } @article {pmid27829354, year = {2016}, author = {Wu, Q and Wu, J and Li, SS and Zhang, HJ and Feng, CY and Yin, DD and Wu, RY and Wang, LS}, title = {Transcriptome sequencing and metabolite analysis for revealing the blue flower formation in waterlily.}, journal = {BMC genomics}, volume = {17}, number = {1}, pages = {897}, pmid = {27829354}, issn = {1471-2164}, mesh = {Computational Biology/methods ; Flowers/*genetics/*metabolism ; Gene Expression Profiling ; *Metabolome ; Metabolomics ; Nymphaea/*genetics/*metabolism ; Phenotype ; *Transcriptome ; }, abstract = {BACKGROUND: Waterlily (Nymphaea spp.), a perennial herbaceous aquatic plant, is divided into two ecological groups: hardy waterlily and tropical waterlily. Although the hardy waterlily has no attractive blue flower cultivar, its adaptability is stronger than tropical waterlily because it can survive a cold winter. Thus, breeding hardy waterlily with real blue flowers has become an important target for breeders. Molecular breeding may be a useful way. However, molecular studies on waterlily are limited due to the lack of sequence data.

RESULTS: In this study, six cDNA libraries generated from the petals of two different coloring stages of blue tropical waterlily cultivar Nymphaea 'King of Siam' were sequenced using the Illumina HiSeq™ 2500 platform. Each library produced no less than 5.65 Gb clean reads. Subsequently, de novo assembly generated 112,485 unigenes, including 26,206 unigenes annotated to seven public protein databases. Then, 127 unigenes could be identified as putative homologues of color-related genes in other species, including 28 up-regulated and 5 down-regulated unigenes. In petals, 16 flavonoids (4 anthocyanins and 12 flavonols) were detected in different contents during the color development due to the different expression levels of color-related genes, and four flavonols were detected in waterlily for the first time. Furthermore, UA3GTs were selected as the most important candidates involved in the flavonoid metabolic pathway, UA3GTs induced blue petal color formation in Nymphaea 'King of Siam'.

CONCLUSIONS: This study will improve our understanding of the molecular mechanism of blue flowers in waterlily and provide the basis for molecular breeding of blue hardy waterlily cultivars.}, } @article {pmid27829306, year = {2016}, author = {Xu, J}, title = {Fungal DNA barcoding.}, journal = {Genome}, volume = {59}, number = {11}, pages = {913-932}, doi = {10.1139/gen-2016-0046}, pmid = {27829306}, issn = {1480-3321}, mesh = {Animals ; Biodiversity ; *DNA Barcoding, Taxonomic/methods/standards ; DNA, Fungal ; DNA, Intergenic ; Databases, Nucleic Acid/standards ; Environmental Microbiology ; Food Microbiology ; Fungi/*classification/*genetics/metabolism ; Gastrointestinal Microbiome ; Humans ; Metagenome ; Metagenomics/methods ; Microbiota ; Mouth/microbiology ; Research ; Sequence Analysis, DNA/methods ; Soil Microbiology ; }, abstract = {Fungi are ubiquitous in both natural and human-made environments. They play important roles in the health of plants, animals, and humans, and in broad ecosystem functions. Thus, having an efficient species-level identification system could significantly enhance our ability to treat fungal diseases and to monitor the spatial and temporal patterns of fungal distributions and migrations. DNA barcoding is a potent approach for rapid identification of fungal specimens, generating novel species hypothesis, and guiding biodiversity and ecological studies. In this mini-review, I briefly summarize (i) the history of DNA sequence-based fungal identification; (ii) the emergence of the ITS region as the consensus primary fungal barcode; (iii) the use of the ITS barcodes to address a variety of issues on fungal diversity from local to global scales, including generating a large number of species hypothesis; and (iv) the problems with the ITS barcode region and the approaches to overcome these problems. Similar to DNA barcoding research on plants and animals, significant progress has been achieved over the last few years in terms of both the questions being addressed and the foundations being laid for future research endeavors. However, significant challenges remain. I suggest three broad areas of research to enhance the usefulness of fungal DNA barcoding to meet the current and future challenges: (i) develop a common set of primers and technologies that allow the amplification and sequencing of all fungi at both the primary and secondary barcode loci; (ii) compile a centralized reference database that includes all recognized fungal species as well as species hypothesis, and allows regular updates from the research community; and (iii) establish a consensus set of new species recognition criteria based on barcode DNA sequences that can be applied across the fungal kingdom.}, } @article {pmid27827946, year = {2016}, author = {Mahara, G and Wang, C and Yang, K and Chen, S and Guo, J and Gao, Q and Wang, W and Wang, Q and Guo, X}, title = {The Association between Environmental Factors and Scarlet Fever Incidence in Beijing Region: Using GIS and Spatial Regression Models.}, journal = {International journal of environmental research and public health}, volume = {13}, number = {11}, pages = {}, pmid = {27827946}, issn = {1660-4601}, mesh = {Adolescent ; Air Pollutants/*toxicity ; Beijing/epidemiology ; Child ; Child, Preschool ; Female ; Geographic Information Systems ; Humans ; Incidence ; Male ; Models, Theoretical ; Risk Factors ; Scarlet Fever/*epidemiology/etiology ; Spatial Analysis ; Spatial Regression ; *Weather ; }, abstract = {(1) Background: Evidence regarding scarlet fever and its relationship with meteorological, including air pollution factors, is not very available. This study aimed to examine the relationship between ambient air pollutants and meteorological factors with scarlet fever occurrence in Beijing, China. (2) Methods: A retrospective ecological study was carried out to distinguish the epidemic characteristics of scarlet fever incidence in Beijing districts from 2013 to 2014. Daily incidence and corresponding air pollutant and meteorological data were used to develop the model. Global Moran's I statistic and Anselin's local Moran's I (LISA) were applied to detect the spatial autocorrelation (spatial dependency) and clusters of scarlet fever incidence. The spatial lag model (SLM) and spatial error model (SEM) including ordinary least squares (OLS) models were then applied to probe the association between scarlet fever incidence and meteorological including air pollution factors. (3) Results: Among the 5491 cases, more than half (62%) were male, and more than one-third (37.8%) were female, with the annual average incidence rate 14.64 per 100,000 population. Spatial autocorrelation analysis exhibited the existence of spatial dependence; therefore, we applied spatial regression models. After comparing the values of R-square, log-likelihood and the Akaike information criterion (AIC) among the three models, the OLS model (R[2] = 0.0741, log likelihood = -1819.69, AIC = 3665.38), SLM (R[2] = 0.0786, log likelihood = -1819.04, AIC = 3665.08) and SEM (R[2] = 0.0743, log likelihood = -1819.67, AIC = 3665.36), identified that the spatial lag model (SLM) was best for model fit for the regression model. There was a positive significant association between nitrogen oxide (p = 0.027), rainfall (p = 0.036) and sunshine hour (p = 0.048), while the relative humidity (p = 0.034) had an adverse association with scarlet fever incidence in SLM. (4) Conclusions: Our findings indicated that meteorological, as well as air pollutant factors may increase the incidence of scarlet fever; these findings may help to guide scarlet fever control programs and targeting the intervention.}, } @article {pmid27824041, year = {2016}, author = {Hoshino, A and Jayakumar, V and Nitasaka, E and Toyoda, A and Noguchi, H and Itoh, T and Shin-I, T and Minakuchi, Y and Koda, Y and Nagano, AJ and Yasugi, M and Honjo, MN and Kudoh, H and Seki, M and Kamiya, A and Shiraki, T and Carninci, P and Asamizu, E and Nishide, H and Tanaka, S and Park, KI and Morita, Y and Yokoyama, K and Uchiyama, I and Tanaka, Y and Tabata, S and Shinozaki, K and Hayashizaki, Y and Kohara, Y and Suzuki, Y and Sugano, S and Fujiyama, A and Iida, S and Sakakibara, Y}, title = {Genome sequence and analysis of the Japanese morning glory Ipomoea nil.}, journal = {Nature communications}, volume = {7}, number = {}, pages = {13295}, pmid = {27824041}, issn = {2041-1723}, mesh = {Base Sequence ; Brassinosteroids/biosynthesis ; DNA Transposable Elements/genetics ; Evolution, Molecular ; Genes, Plant ; *Genome, Plant ; Ipomoea nil/*genetics ; Molecular Sequence Annotation ; Reproducibility of Results ; *Sequence Analysis, DNA ; Transposases/metabolism ; }, abstract = {Ipomoea is the largest genus in the family Convolvulaceae. Ipomoea nil (Japanese morning glory) has been utilized as a model plant to study the genetic basis of floricultural traits, with over 1,500 mutant lines. In the present study, we have utilized second- and third-generation-sequencing platforms, and have reported a draft genome of I. nil with a scaffold N50 of 2.88 Mb (contig N50 of 1.87 Mb), covering 98% of the 750 Mb genome. Scaffolds covering 91.42% of the assembly are anchored to 15 pseudo-chromosomes. The draft genome has enabled the identification and cataloguing of the Tpn1 family transposons, known as the major mutagen of I. nil, and analysing the dwarf gene, CONTRACTED, located on the genetic map published in 1956. Comparative genomics has suggested that a whole genome duplication in Convolvulaceae, distinct from the recent Solanaceae event, has occurred after the divergence of the two sister families.}, } @article {pmid27822515, year = {2016}, author = {Kopylova, E and Navas-Molina, JA and Mercier, C and Xu, ZZ and Mahé, F and He, Y and Zhou, HW and Rognes, T and Caporaso, JG and Knight, R}, title = {Open-Source Sequence Clustering Methods Improve the State Of the Art.}, journal = {mSystems}, volume = {1}, number = {1}, pages = {}, pmid = {27822515}, issn = {2379-5077}, abstract = {Sequence clustering is a common early step in amplicon-based microbial community analysis, when raw sequencing reads are clustered into operational taxonomic units (OTUs) to reduce the run time of subsequent analysis steps. Here, we evaluated the performance of recently released state-of-the-art open-source clustering software products, namely, OTUCLUST, Swarm, SUMACLUST, and SortMeRNA, against current principal options (UCLUST and USEARCH) in QIIME, hierarchical clustering methods in mothur, and USEARCH's most recent clustering algorithm, UPARSE. All the latest open-source tools showed promising results, reporting up to 60% fewer spurious OTUs than UCLUST, indicating that the underlying clustering algorithm can vastly reduce the number of these derived OTUs. Furthermore, we observed that stringent quality filtering, such as is done in UPARSE, can cause a significant underestimation of species abundance and diversity, leading to incorrect biological results. Swarm, SUMACLUST, and SortMeRNA have been included in the QIIME 1.9.0 release. IMPORTANCE Massive collections of next-generation sequencing data call for fast, accurate, and easily accessible bioinformatics algorithms to perform sequence clustering. A comprehensive benchmark is presented, including open-source tools and the popular USEARCH suite. Simulated, mock, and environmental communities were used to analyze sensitivity, selectivity, species diversity (alpha and beta), and taxonomic composition. The results demonstrate that recent clustering algorithms can significantly improve accuracy and preserve estimated diversity without the application of aggressive filtering. Moreover, these tools are all open source, apply multiple levels of multithreading, and scale to the demands of modern next-generation sequencing data, which is essential for the analysis of massive multidisciplinary studies such as the Earth Microbiome Project (EMP) (J. A. Gilbert, J. K. Jansson, and R. Knight, BMC Biol 12:69, 2014, http://dx.doi.org/10.1186/s12915-014-0069-1).}, } @article {pmid27821178, year = {2016}, author = {Auffray, C and Balling, R and Barroso, I and Bencze, L and Benson, M and Bergeron, J and Bernal-Delgado, E and Blomberg, N and Bock, C and Conesa, A and Del Signore, S and Delogne, C and Devilee, P and Di Meglio, A and Eijkemans, M and Flicek, P and Graf, N and Grimm, V and Guchelaar, HJ and Guo, YK and Gut, IG and Hanbury, A and Hanif, S and Hilgers, RD and Honrado, Á and Hose, DR and Houwing-Duistermaat, J and Hubbard, T and Janacek, SH and Karanikas, H and Kievits, T and Kohler, M and Kremer, A and Lanfear, J and Lengauer, T and Maes, E and Meert, T and Müller, W and Nickel, D and Oledzki, P and Pedersen, B and Petkovic, M and Pliakos, K and Rattray, M and I Màs, JR and Schneider, R and Sengstag, T and Serra-Picamal, X and Spek, W and Vaas, LA and van Batenburg, O and Vandelaer, M and Varnai, P and Villoslada, P and Vizcaíno, JA and Wubbe, JP and Zanetti, G}, title = {Erratum to: Making sense of big data in health research: towards an EU action plan.}, journal = {Genome medicine}, volume = {8}, number = {1}, pages = {118}, pmid = {27821178}, issn = {1756-994X}, } @article {pmid27820840, year = {2016}, author = {Huang, A and Sang, Y and Sun, W and Fu, Y and Yang, Z}, title = {Transcriptomic Analysis of Responses to Imbalanced Carbon: Nitrogen Availabilities in Rice Seedlings.}, journal = {PloS one}, volume = {11}, number = {11}, pages = {e0165732}, pmid = {27820840}, issn = {1932-6203}, mesh = {Carbon/*pharmacology ; Cyclopentanes/metabolism ; Dose-Response Relationship, Drug ; *Gene Expression Profiling ; Gene Expression Regulation, Plant/drug effects ; Gene Ontology ; Nitrogen/*pharmacology ; Oryza/cytology/*drug effects/*genetics ; Oxylipins/metabolism ; Seedlings/cytology/*drug effects/*genetics ; Signal Transduction/drug effects ; }, abstract = {The internal C:N balance must be tightly controlled for the normal growth and development of plants. However, the underlying mechanisms, by which plants sense and balance the intracellular C:N status correspondingly to exogenous C:N availabilities remain elusive. In this study, we use comparative gene expression analysis to identify genes that are responsive to imbalanced C:N treatments in the aerial parts of rice seedlings. Transcripts of rice seedlings treated with four C:N availabilities (1:1, 1:60, 60:1 and 60:60) were compared and two groups of genes were classified: high C:low N responsive genes and low C:high N responsive genes. Our analysis identified several functional correlated genes including chalcone synthase (CHS), chlorophyll a-b binding protein (CAB) and other genes that are implicated in C:N balancing mechanism, such as alternative oxidase 1B (OsAOX1B), malate dehydrogenase (OsMDH) and lysine and histidine specific transporter 1 (OsLHT1). Additionally, six jasmonate synthetic genes and key regulatory genes involved in abiotic and biotic stresses, such as OsMYB4, autoinhibited calcium ATPase 3 (OsACA3) and pleiotropic drug resistance 9 (OsPDR9), were differentially expressed under high C:low N treatment. Gene ontology analysis showed that high C:low N up-regulated genes were primarily enriched in fatty acid biosynthesis and defense responses. Coexpression network analysis of these genes identified eight jasmonate ZIM domain protein (OsJAZ) genes and several defense response related regulators, suggesting that high C:low N status may act as a stress condition, which induces defense responses mediated by jasmonate signaling pathway. Our transcriptome analysis shed new light on the C:N balancing mechanisms and revealed several important regulators of C:N status in rice seedlings.}, } @article {pmid27819370, year = {2016}, author = {Zhou, Y and Li, W and Wang, M and Zhang, X and Zhang, H and Tong, X and Xiao, Y}, title = {Competitive profiling of celastrol targets in human cervical cancer HeLa cells via quantitative chemical proteomics.}, journal = {Molecular bioSystems}, volume = {13}, number = {1}, pages = {83-91}, doi = {10.1039/c6mb00691d}, pmid = {27819370}, issn = {1742-2051}, mesh = {Biomarkers ; Carrier Proteins/*antagonists & inhibitors/*metabolism ; Cell Proliferation/drug effects ; Computational Biology/methods ; Female ; HeLa Cells ; Humans ; Pentacyclic Triterpenes ; Protein Binding ; Protein Processing, Post-Translational/drug effects ; *Proteome ; *Proteomics/methods ; Triterpenes/*pharmacology ; Uterine Cervical Neoplasms/*metabolism ; }, abstract = {Celastrol, isolated from the traditional Chinese medicinal herb Tripterygium wilfordii Hook. f. (Thunder God's Vine), has been used to treat cancer, chronic inflammatory, autoimmune and other human diseases. However, to date, the protein targets and the mechanism of action of celastrol have remained elusive. In this study, we find that celastrol can react with protein thiols in a unique covalent and reversible manner, while protein denaturing disrupts the interaction. Through a competitive chemoproteomics approach utilizing a cysteine-targeting activity-based probe, we report the proteome-wide quantitative profiling of cellular targets of celastrol in human cervical cancer HeLa cells. Representative targets are further validated via in vitro binding experiments and/or enzymatic activity assays. Bioinformatics analysis results suggest that celastrol exerts its numerous therapeutic effects through interaction with promiscuous proteins involved in various biological processes and cellular pathways.}, } @article {pmid27815830, year = {2016}, author = {Aliani, H and Kafaky, SB and Saffari, A and Monavari, SM}, title = {Determining an appropriate method for the purpose of land allocation for ecotourism development (case study: Taleghan County, Iran).}, journal = {Environmental monitoring and assessment}, volume = {188}, number = {11}, pages = {651}, doi = {10.1007/s10661-016-5651-2}, pmid = {27815830}, issn = {1573-2959}, mesh = {*Conservation of Natural Resources ; *Environment ; Environmental Monitoring/methods ; Fuzzy Logic ; Geographic Information Systems ; Humans ; Iran ; Models, Theoretical ; *Recreation ; *Travel ; }, abstract = {Appropriate management and planning of suitable areas for the development of ecotourism activities can play an important role in ensuring proper use of the environment. Due to the complexity of nature, applying different tools and models-particularly multi-criteria methods-can be useful in order to achieve these goals. In this study, to indicate suitable areas (land allocation) for ecotourism activities in Taleghan county, weighted linear combination (WLC) using geographical information system (GIS), fuzzy logic, and analytical network process (ANP) were used. To compare the applicability of each of these methods in achieving the goal, the results were compared with the previous model presented by Makhdoum. The results showed that the WLC and ANP methods are more efficient than the Makhdoum model in allocating lands for recreational areas and ecotourism purposes since concomitant use of fuzzy logic and ANP for ranking and weighing the criteria provides us with more flexible and logical conditions. Furthermore, the mentioned method makes it possible to involve ecological, economic, and social criteria simultaneously in the evaluation process in order to allocate land for ecotourism purposes.}, } @article {pmid27815201, year = {2016}, author = {Pardo, BG and Álvarez-Dios, JA and Cao, A and Ramilo, A and Gómez-Tato, A and Planas, JV and Villalba, A and Martínez, P}, title = {Construction of an Ostrea edulis database from genomic and expressed sequence tags (ESTs) obtained from Bonamia ostreae infected haemocytes: Development of an immune-enriched oligo-microarray.}, journal = {Fish & shellfish immunology}, volume = {59}, number = {}, pages = {331-344}, doi = {10.1016/j.fsi.2016.10.047}, pmid = {27815201}, issn = {1095-9947}, mesh = {Animals ; *Databases, Genetic ; Expressed Sequence Tags ; *Genome ; Haplosporida/*immunology ; Hemocytes/immunology/metabolism/parasitology ; *Immunity, Innate ; *Oligonucleotide Array Sequence Analysis ; Ostrea/*genetics/immunology/*parasitology ; Sequence Analysis, DNA ; Sequence Analysis, RNA ; Transcriptome ; }, abstract = {The flat oyster, Ostrea edulis, is one of the main farmed oysters, not only in Europe but also in the United States and Canada. Bonamiosis due to the parasite Bonamia ostreae has been associated with high mortality episodes in this species. This parasite is an intracellular protozoan that infects haemocytes, the main cells involved in oyster defence. Due to the economical and ecological importance of flat oyster, genomic data are badly needed for genetic improvement of the species, but they are still very scarce. The objective of this study is to develop a sequence database, OedulisDB, with new genomic and transcriptomic resources, providing new data and convenient tools to improve our knowledge of the oyster's immune mechanisms. Transcriptomic and genomic sequences were obtained using 454 pyrosequencing and compiled into an O. edulis database, OedulisDB, consisting of two sets of 10,318 and 7159 unique sequences that represent the oyster's genome (WG) and de novo haemocyte transcriptome (HT), respectively. The flat oyster transcriptome was obtained from two strains (naïve and tolerant) challenged with B. ostreae, and from their corresponding non-challenged controls. Approximately 78.5% of 5619 HT unique sequences were successfully annotated by Blast search using public databases. A total of 984 sequences were identified as being related to immune response and several key immune genes were identified for the first time in flat oyster. Additionally, transcriptome information was used to design and validate the first oligo-microarray in flat oyster enriched with immune sequences from haemocytes. Our transcriptomic and genomic sequencing and subsequent annotation have largely increased the scarce resources available for this economically important species and have enabled us to develop an OedulisDB database and accompanying tools for gene expression analysis. This study represents the first attempt to characterize in depth the O. edulis haemocyte transcriptome in response to B. ostreae through massively sequencing and has aided to improve our knowledge of the immune mechanisms of flat oyster. The validated oligo-microarray and the establishment of a reference transcriptome will be useful for large-scale gene expression studies in this species.}, } @article {pmid27814692, year = {2016}, author = {Schilde, C and Lawal, HM and Noegel, AA and Eichinger, L and Schaap, P and Glöckner, G}, title = {A set of genes conserved in sequence and expression traces back the establishment of multicellularity in social amoebae.}, journal = {BMC genomics}, volume = {17}, number = {1}, pages = {871}, pmid = {27814692}, issn = {1471-2164}, mesh = {Amoeba/classification/*genetics ; Conserved Sequence ; *Evolution, Molecular ; *Gene Expression ; Gene Expression Profiling ; Gene Knockout Techniques ; Gene Ontology ; Genome ; Mutation ; Phylogeny ; }, abstract = {BACKGROUND: The developmental cycle of Dictyostelid amoebae represents an early form of multicellularity with cell type differentiation. Mutant studies in the model Dictyostelium discoideum revealed that its developmental program integrates the actions of genes involved in signal transduction, adhesion, motility, autophagy and cell wall and matrix biosynthesis. However, due to functional redundancy and fail safe options not required in the laboratory, this single organism approach cannot capture all essential genes. To understand how multicellular organisms evolved, it is essential to recognize both the conserved core features of their developmental programs and the gene modifications that instigated phenotypic innovation. For complex organisms, such as animals, this is not within easy reach, but it is feasible for less complex forms, such as the Dictyostelid social amoebas.

RESULTS: We compared global profiles of gene expression during the development of four social amoebae species that represent 600 mya of Dictyostelia evolution, and identified orthologous conserved genes with similar developmental up-regulation of expression using three different methods. For validation, we disrupted five genes of this core set and examined the phenotypic consequences.

CONCLUSION: At least 71 of the developmentally regulated genes that were identified with all methods were likely to be already present in the last ancestor of all Dictyostelia. The lack of phenotypic changes in null mutants indicates that even highly conserved genes either participate in functionally redundant pathways or are necessary for developmental progression under adverse, non-standard laboratory conditions. Both mechanisms provide robustness to the developmental program, but impose a limit on the information that can be obtained from deleting single genes.}, } @article {pmid27812946, year = {2017}, author = {Vesztrocy, AW and Dessimoz, C}, title = {A Gene Ontology Tutorial in Python.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1446}, number = {}, pages = {221-229}, doi = {10.1007/978-1-4939-3743-1_16}, pmid = {27812946}, issn = {1940-6029}, support = {//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; *Gene Ontology ; Humans ; Internet ; Molecular Sequence Annotation/*methods ; Semantics ; *Software ; }, abstract = {This chapter is a tutorial on using Gene Ontology resources in the Python programming language. This entails querying the Gene Ontology graph, retrieving Gene Ontology annotations, performing gene enrichment analyses, and computing basic semantic similarity between GO terms. An interactive version of the tutorial, including solutions, is available at http://gohandbook.org .}, } @article {pmid27812944, year = {2017}, author = {Gaudet, P and Dessimoz, C}, title = {Gene Ontology: Pitfalls, Biases, and Remedies.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1446}, number = {}, pages = {189-205}, doi = {10.1007/978-1-4939-3743-1_14}, pmid = {27812944}, issn = {1940-6029}, support = {//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; Data Mining/*methods ; Databases, Genetic ; *Gene Ontology ; Humans ; Molecular Sequence Annotation/*methods ; Proteins/genetics ; Species Specificity ; }, abstract = {The Gene Ontology (GO) is a formidable resource, but there are several considerations about it that are essential to understand the data and interpret it correctly. The GO is sufficiently simple that it can be used without deep understanding of its structure or how it is developed, which is both a strength and a weakness. In this chapter, we discuss some common misinterpretations of the ontology and the annotations. A better understanding of the pitfalls and the biases in the GO should help users make the most of this very rich resource. We also review some of the misconceptions and misleading assumptions commonly made about GO, including the effect of data incompleteness, the importance of annotation qualifiers, and the transitivity or lack thereof associated with different ontology relations. We also discuss several biases that can confound aggregate analyses such as gene enrichment analyses. For each of these pitfalls and biases, we suggest remedies and best practices.}, } @article {pmid27812933, year = {2017}, author = {Gaudet, P and Škunca, N and Hu, JC and Dessimoz, C}, title = {Primer on the Gene Ontology.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1446}, number = {}, pages = {25-37}, pmid = {27812933}, issn = {1940-6029}, support = {U24 GM088849/GM/NIGMS NIH HHS/United States ; R01 GM089636/GM/NIGMS NIH HHS/United States ; U41 HG002273/HG/NHGRI NIH HHS/United States ; //Biotechnology and Biological Sciences Research Council/United Kingdom ; R01 HG002273/HG/NHGRI NIH HHS/United States ; P41 HG002273/HG/NHGRI NIH HHS/United States ; }, mesh = {Animals ; Computational Biology/*methods ; DNA/genetics ; Databases, Genetic ; *Gene Ontology ; Humans ; Internet ; Proteins/genetics ; RNA/genetics ; }, abstract = {The Gene Ontology (GO) project is the largest resource for cataloguing gene function. The combination of solid conceptual underpinnings and a practical set of features have made the GO a widely adopted resource in the research community and an essential resource for data analysis. In this chapter, we provide a concise primer for all users of the GO. We briefly introduce the structure of the ontology and explain how to interpret annotations associated with the GO.}, } @article {pmid27812351, year = {2016}, author = {Wei, ST and Lacap-Bugler, DC and Lau, MC and Caruso, T and Rao, S and de Los Rios, A and Archer, SK and Chiu, JM and Higgins, C and Van Nostrand, JD and Zhou, J and Hopkins, DW and Pointing, SB}, title = {Taxonomic and Functional Diversity of Soil and Hypolithic Microbial Communities in Miers Valley, McMurdo Dry Valleys, Antarctica.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {1642}, pmid = {27812351}, issn = {1664-302X}, abstract = {The McMurdo Dry Valleys of Antarctica are an extreme polar desert. Mineral soils support subsurface microbial communities and translucent rocks support development of hypolithic communities on ventral surfaces in soil contact. Despite significant research attention, relatively little is known about taxonomic and functional diversity or their inter-relationships. Here we report a combined diversity and functional interrogation for soil and hypoliths of the Miers Valley in the McMurdo Dry Valleys of Antarctica. The study employed 16S rRNA fingerprinting and high throughput sequencing combined with the GeoChip functional microarray. The soil community was revealed as a highly diverse reservoir of bacterial diversity dominated by actinobacteria. Hypolithic communities were less diverse and dominated by cyanobacteria. Major differences in putative functionality were that soil communities displayed greater diversity in stress tolerance and recalcitrant substrate utilization pathways, whilst hypolithic communities supported greater diversity of nutrient limitation adaptation pathways. A relatively high level of functional redundancy in both soil and hypoliths may indicate adaptation of these communities to fluctuating environmental conditions.}, } @article {pmid27812126, year = {2016}, author = {Kallio, A}, title = {Properties of Fixed-Fixed Models and Alternatives in Presence-Absence Data Analysis.}, journal = {PloS one}, volume = {11}, number = {11}, pages = {e0165456}, pmid = {27812126}, issn = {1932-6203}, mesh = {*Data Interpretation, Statistical ; *Ecological and Environmental Phenomena ; Models, Statistical ; Stochastic Processes ; }, abstract = {Assessing the significance of patterns in presence-absence data is an important question in ecological data analysis, e.g., when studying nestedness. Significance testing can be performed with the commonly used fixed-fixed models, which preserve the row and column sums while permuting the data. The manuscript considers the properties of fixed-fixed models and points out how their strict constraints can lead to limited randomizability. The manuscript considers the question of relaxing row and column sun constraints of the fixed-fixed models. The Rasch models are presented as an alternative with relaxed constraints and sound statistical properties. Models are compared on presence-absence data and surprisingly the fixed-fixed models are observed to produce unreasonably optimistic measures of statistical significance, giving interesting insight into practical effects of limited randomizability.}, } @article {pmid27809776, year = {2016}, author = {Liu, Z and Ji, Z and Wang, G and Chao, T and Hou, L and Wang, J}, title = {Genome-wide analysis reveals signatures of selection for important traits in domestic sheep from different ecoregions.}, journal = {BMC genomics}, volume = {17}, number = {1}, pages = {863}, pmid = {27809776}, issn = {1471-2164}, mesh = {Animals ; Breeding ; Evolution, Molecular ; Gene Ontology ; Genetics, Population ; *Genome ; *Genome-Wide Association Study ; *Genomics/methods ; High-Throughput Nucleotide Sequencing ; Mutation ; Phenotype ; Polymorphism, Single Nucleotide ; *Quantitative Trait, Heritable ; Reproduction/genetics ; *Selection, Genetic ; Sheep, Domestic/*genetics ; }, abstract = {BACKGROUND: Throughout a long period of adaptation and selection, sheep have thrived in a diverse range of ecological environments. Mongolian sheep is the common ancestor of the Chinese short fat-tailed sheep. Migration to different ecoregions leads to changes in selection pressures and results in microevolution. Mongolian sheep and its subspecies differ in a number of important traits, especially reproductive traits. Genome-wide intraspecific variation is required to dissect the genetic basis of these traits.

RESULTS: This research resequenced 3 short fat-tailed sheep breeds with a 43.2-fold coverage of the sheep genome. We report more than 17 million single nucleotide polymorphisms and 2.9 million indels and identify 143 genomic regions with reduced pooled heterozygosity or increased genetic distance to each other breed that represent likely targets for selection during the migration. These regions harbor genes related to developmental processes, cellular processes, multicellular organismal processes, biological regulation, metabolic processes, reproduction, localization, growth and various components of the stress responses. Furthermore, we examined the haplotype diversity of 3 genomic regions involved in reproduction and found significant differences in TSHR and PRL gene regions among 8 sheep breeds.

CONCLUSIONS: Our results provide useful genomic information for identifying genes or causal mutations associated with important economic traits in sheep and for understanding the genetic basis of adaptation to different ecological environments.}, } @article {pmid27642037, year = {2017}, author = {Brookie, KL and Mainvil, LA and Carr, AC and Vissers, MCM and Conner, TS}, title = {The development and effectiveness of an ecological momentary intervention to increase daily fruit and vegetable consumption in low-consuming young adults.}, journal = {Appetite}, volume = {108}, number = {}, pages = {32-41}, doi = {10.1016/j.appet.2016.09.015}, pmid = {27642037}, issn = {1095-8304}, mesh = {Adolescent ; Adult ; Ascorbic Acid/blood ; Biomarkers/blood ; Carotenoids/blood ; Cell Phone ; *Choice Behavior ; *Diet, Healthy ; Female ; Focus Groups ; *Fruit ; Humans ; Male ; New Zealand ; *Patient Compliance ; *Patient Education as Topic ; *Reminder Systems ; Self Report ; *Vegetables ; Young Adult ; }, abstract = {OBJECTIVES: To develop and test the effectiveness of a mobile-phone based ecological momentary intervention (EMI) to increase fruit and vegetable (FV) consumption in low-consuming young adults.

METHODS: A two-week randomised controlled trial of low-FV consuming young adults ages 18-25 years (n = 171) compared three conditions: ecological momentary intervention (EMI), fruit and vegetable intervention (FVI), and a diet-as-usual control (ANZCTRN12615000183583). Participants in the EMI condition were sent two targeted text messages a day for 13 days and were asked to increase daily FV consumption to at least five servings. These messages were designed, using the Health Action Process Approach, to address salient beliefs identified as effective in a preliminary focus group investigation. Participants in the FVI condition were provided two servings of FV a day (carrots, kiwifruit or oranges, and apples) to eat in addition to their current diet. Control participants ate their normal diet. Participants reported their daily servings of FV each evening during the study using a smartphone-delivered survey. Blood samples testing plasma vitamin C and total carotenoids were taken pre- and post-intervention as an objective biomarker of FV intake.

RESULTS: Participants in the EMI and FVI conditions reported higher daily servings of FV - approximately +1 serving per day more compared to control (EMI = 3.7 servings/day; FVI = 3.7 servings/day; Control = 2.8 servings/day) and approximately +1.2 servings compared to baseline. Increases in objective biomarkers for the experimental conditions supported the validity of self-reported FV consumption.

CONCLUSIONS: Our results provide initial proof of concept that EMI strategies (with minor financial assistance) are as effective as giving FV in increasing FV consumption in educated, low-consuming young adults.}, } @article {pmid27068275, year = {2016}, author = {Cundy, AB and Bardos, RP and Puschenreiter, M and Mench, M and Bert, V and Friesl-Hanl, W and Müller, I and Li, XN and Weyens, N and Witters, N and Vangronsveld, J}, title = {Brownfields to green fields: Realising wider benefits from practical contaminant phytomanagement strategies.}, journal = {Journal of environmental management}, volume = {184}, number = {Pt 1}, pages = {67-77}, doi = {10.1016/j.jenvman.2016.03.028}, pmid = {27068275}, issn = {1095-8630}, mesh = {*Biodegradation, Environmental ; Decision Support Techniques ; *Environmental Pollution ; Europe ; Metals, Heavy/analysis ; Plants ; Risk Management/methods ; Soil Microbiology ; Soil Pollutants/analysis ; Trace Elements/analysis ; }, abstract = {Gentle remediation options (GROs) are risk management strategies or technologies involving plant (phyto-), fungi (myco-), and/or bacteria-based methods that result in a net gain (or at least no gross reduction) in soil function as well as effective risk management. GRO strategies can be customised along contaminant linkages, and can generate a range of wider economic, environmental and societal benefits in contaminated land management (and in brownfields management more widely). The application of GROs as practical on-site remedial solutions is still limited however, particularly in Europe and at trace element (typically metal and metalloid) contaminated sites. This paper discusses challenges to the practical adoption of GROs in contaminated land management, and outlines the decision support tools and best practice guidance developed in the European Commission FP7-funded GREENLAND project aimed at overcoming these challenges. The GREENLAND guidance promotes a refocus from phytoremediation to wider GROs- or phyto-management based approaches which place realisation of wider benefits at the core of site design, and where gentle remediation technologies can be applied as part of integrated, mixed, site risk management solutions or as part of "holding strategies" for vacant sites. The combination of GROs with renewables, both in terms of biomass generation but also with green technologies such as wind and solar power, can provide a range of economic and other benefits and can potentially support the return of low-level contaminated sites to productive usage, while combining GROs with urban design and landscape architecture, and integrating GRO strategies with sustainable urban drainage systems and community gardens/parkland (particularly for health and leisure benefits), has large potential for triggering GRO application and in realising wider benefits in urban and suburban systems. Quantifying these wider benefits and value (above standard economic returns) will be important in leveraging funding for GRO application and soft site end-use more widely at vacant or underutilized sites.}, } @article {pmid27808112, year = {2016}, author = {Wu, N and Song, YL and Wang, B and Zhang, XY and Zhang, XJ and Wang, YL and Cheng, YY and Chen, DD and Xia, XQ and Lu, YS and Zhang, YA}, title = {Fish gut-liver immunity during homeostasis or inflammation revealed by integrative transcriptome and proteome studies.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {36048}, pmid = {27808112}, issn = {2045-2322}, mesh = {Animals ; Bile/metabolism ; Fishes/genetics/*immunology ; Gastrointestinal Tract/*immunology ; Gene Expression Regulation ; Gene Library ; Gene Ontology ; *Homeostasis ; *Immunity, Mucosal ; Inflammation/*genetics/immunology/metabolism ; Liver/*immunology ; Mucus/metabolism ; Protein Domains ; Proteome/*metabolism ; RNA, Messenger/genetics/metabolism ; Transcriptome/*genetics ; }, abstract = {The gut-associated lymphoid tissue, connected with liver via bile and blood, constructs a local immune environment of both defense and tolerance. The gut-liver immunity has been well-studied in mammals, yet in fish remains largely unknown, even though enteritis as well as liver and gallbladder syndrome emerged as a limitation in aquaculture. In this study, we performed integrative bioinformatic analysis for both transcriptomic (gut and liver) and proteomic (intestinal mucus and bile) data, in both healthy and infected tilapias. We found more categories of immune transcripts in gut than liver, as well as more adaptive immune in gut meanwhile more innate in liver. Interestingly reduced differential immune transcripts between gut and liver upon inflammation were also revealed. In addition, more immune proteins in bile than intestinal mucus were identified. And bile probably providing immune effectors to intestinal mucus upon inflammation was deduced. Specifically, many key immune transcripts in gut or liver as well as key immune proteins in mucus or bile were demonstrated. Accordingly, we proposed a hypothesized profile of fish gut-liver immunity, during either homeostasis or inflammation. Current data suggested that fish gut and liver may collaborate immunologically while keep homeostasis using own strategies, including potential unique mechanisms.}, } @article {pmid27807419, year = {2016}, author = {Vasiljevic, D and Mihailovic, N and Radovanovic, S}, title = {Socioeconomic Patterns of Tobacco Use-An Example from the Balkans.}, journal = {Frontiers in pharmacology}, volume = {7}, number = {}, pages = {372}, pmid = {27807419}, issn = {1663-9812}, } @article {pmid27799338, year = {2016}, author = {Gonzalez-Ibeas, D and Martinez-Garcia, PJ and Famula, RA and Delfino-Mix, A and Stevens, KA and Loopstra, CA and Langley, CH and Neale, DB and Wegrzyn, JL}, title = {Assessing the Gene Content of the Megagenome: Sugar Pine (Pinus lambertiana).}, journal = {G3 (Bethesda, Md.)}, volume = {6}, number = {12}, pages = {3787-3802}, pmid = {27799338}, issn = {2160-1836}, mesh = {Computational Biology/methods ; Gene Expression Profiling ; Gene Expression Regulation, Plant ; *Genes, Plant ; Genetic Variation ; *Genome, Plant ; *Genomics/methods ; High-Throughput Nucleotide Sequencing ; MicroRNAs/genetics ; Molecular Sequence Annotation ; Multigene Family ; Pinus/*genetics ; Ribonuclease III/genetics ; Transcriptome ; }, abstract = {Sugar pine (Pinus lambertiana Douglas) is within the subgenus Strobus with an estimated genome size of 31 Gbp. Transcriptomic resources are of particular interest in conifers due to the challenges presented in their megagenomes for gene identification. In this study, we present the first comprehensive survey of the P. lambertiana transcriptome through deep sequencing of a variety of tissue types to generate more than 2.5 billion short reads. Third generation, long reads generated through PacBio Iso-Seq have been included for the first time in conifers to combat the challenges associated with de novo transcriptome assembly. A technology comparison is provided here to contribute to the otherwise scarce comparisons of second and third generation transcriptome sequencing approaches in plant species. In addition, the transcriptome reference was essential for gene model identification and quality assessment in the parallel project responsible for sequencing and assembly of the entire genome. In this study, the transcriptomic data were also used to address questions surrounding lineage-specific Dicer-like proteins in conifers. These proteins play a role in the control of transposable element proliferation and the related genome expansion in conifers.}, } @article {pmid27802837, year = {2016}, author = {Kim, S and Cho, YS and Kim, HM and Chung, O and Kim, H and Jho, S and Seomun, H and Kim, J and Bang, WY and Kim, C and An, J and Bae, CH and Bhak, Y and Jeon, S and Yoon, H and Kim, Y and Jun, J and Lee, H and Cho, S and Uphyrkina, O and Kostyria, A and Goodrich, J and Miquelle, D and Roelke, M and Lewis, J and Yurchenko, A and Bankevich, A and Cho, J and Lee, S and Edwards, JS and Weber, JA and Cook, J and Kim, S and Lee, H and Manica, A and Lee, I and O'Brien, SJ and Bhak, J and Yeo, JH}, title = {Comparison of carnivore, omnivore, and herbivore mammalian genomes with a new leopard assembly.}, journal = {Genome biology}, volume = {17}, number = {1}, pages = {211}, pmid = {27802837}, issn = {1474-760X}, support = {R01 HG006876/HG/NHGRI NIH HHS/United States ; }, mesh = {Adaptation, Physiological/genetics ; Animals ; Biological Evolution ; Cats ; *Genetic Variation ; *Genome ; Herbivory/genetics ; Mammals/genetics ; Molecular Sequence Annotation ; Panthera/*genetics ; Phylogeny ; *Sequence Analysis, DNA ; }, abstract = {BACKGROUND: There are three main dietary groups in mammals: carnivores, omnivores, and herbivores. Currently, there is limited comparative genomics insight into the evolution of dietary specializations in mammals. Due to recent advances in sequencing technologies, we were able to perform in-depth whole genome analyses of representatives of these three dietary groups.

RESULTS: We investigated the evolution of carnivory by comparing 18 representative genomes from across Mammalia with carnivorous, omnivorous, and herbivorous dietary specializations, focusing on Felidae (domestic cat, tiger, lion, cheetah, and leopard), Hominidae, and Bovidae genomes. We generated a new high-quality leopard genome assembly, as well as two wild Amur leopard whole genomes. In addition to a clear contraction in gene families for starch and sucrose metabolism, the carnivore genomes showed evidence of shared evolutionary adaptations in genes associated with diet, muscle strength, agility, and other traits responsible for successful hunting and meat consumption. Additionally, an analysis of highly conserved regions at the family level revealed molecular signatures of dietary adaptation in each of Felidae, Hominidae, and Bovidae. However, unlike carnivores, omnivores and herbivores showed fewer shared adaptive signatures, indicating that carnivores are under strong selective pressure related to diet. Finally, felids showed recent reductions in genetic diversity associated with decreased population sizes, which may be due to the inflexible nature of their strict diet, highlighting their vulnerability and critical conservation status.

CONCLUSIONS: Our study provides a large-scale family level comparative genomic analysis to address genomic changes associated with dietary specialization. Our genomic analyses also provide useful resources for diet-related genetic and health research.}, } @article {pmid27802151, year = {2016}, author = {Clemente, CJ and Cooper, CE and Withers, PC and Freakley, C and Singh, S and Terrill, P}, title = {The private life of echidnas: using accelerometry and GPS to examine field biomechanics and assess the ecological impact of a widespread, semi-fossorial monotreme.}, journal = {The Journal of experimental biology}, volume = {219}, number = {Pt 20}, pages = {3271-3283}, doi = {10.1242/jeb.143867}, pmid = {27802151}, issn = {1477-9145}, mesh = {*Accelerometry ; Animals ; Biomechanical Phenomena ; Body Weight ; *Ecosystem ; *Geographic Information Systems ; Seasons ; Species Specificity ; Tachyglossidae/*physiology ; Walking/physiology ; }, abstract = {The short-beaked echidna (Tachyglossus aculeatus) is a monotreme and therefore provides a unique combination of phylogenetic history, morphological differentiation and ecological specialisation for a mammal. The echidna has a unique appendicular skeleton, a highly specialised myrmecophagous lifestyle and a mode of locomotion that is neither typically mammalian nor reptilian, but has aspects of both lineages. We therefore were interested in the interactions of locomotor biomechanics, ecology and movements for wild, free-living short-beaked echidnas. To assess locomotion in its complex natural environment, we attached both GPS and accelerometer loggers to the back of echidnas in both spring and summer. We found that the locomotor biomechanics of echidnas is unique, with lower stride length and stride frequency than reported for similar-sized mammals. Speed modulation is primarily accomplished through changes in stride frequency, with a mean of 1.39 Hz and a maximum of 2.31 Hz. Daily activity period was linked to ambient air temperature, which restricted daytime activity during the hotter summer months. Echidnas had longer activity periods and longer digging bouts in spring compared with summer. In summer, echidnas had higher walking speeds than in spring, perhaps because of the shorter time suitable for activity. Echidnas spent, on average, 12% of their time digging, which indicates their potential to excavate up to 204 m[3] of soil a year. This information highlights the important contribution towards ecosystem health, via bioturbation, of this widespread Australian monotreme.}, } @article {pmid27801969, year = {2017}, author = {Stucki, S and Orozco-terWengel, P and Forester, BR and Duruz, S and Colli, L and Masembe, C and Negrini, R and Landguth, E and Jones, MR and , and Bruford, MW and Taberlet, P and Joost, S}, title = {High performance computation of landscape genomic models including local indicators of spatial association.}, journal = {Molecular ecology resources}, volume = {17}, number = {5}, pages = {1072-1089}, doi = {10.1111/1755-0998.12629}, pmid = {27801969}, issn = {1755-0998}, mesh = {Adaptation, Biological ; Animals ; *Biota ; Cattle ; Computational Biology/*methods ; *Ecosystem ; *Environmental Exposure ; Genetics, Population ; Genomics/*methods ; Genotype ; Selection, Genetic ; }, abstract = {With the increasing availability of both molecular and topo-climatic data, the main challenges facing landscape genomics - that is the combination of landscape ecology with population genomics - include processing large numbers of models and distinguishing between selection and demographic processes (e.g. population structure). Several methods address the latter, either by estimating a null model of population history or by simultaneously inferring environmental and demographic effects. Here we present samβada, an approach designed to study signatures of local adaptation, with special emphasis on high performance computing of large-scale genetic and environmental data sets. samβada identifies candidate loci using genotype-environment associations while also incorporating multivariate analyses to assess the effect of many environmental predictor variables. This enables the inclusion of explanatory variables representing population structure into the models to lower the occurrences of spurious genotype-environment associations. In addition, samβada calculates local indicators of spatial association for candidate loci to provide information on whether similar genotypes tend to cluster in space, which constitutes a useful indication of the possible kinship between individuals. To test the usefulness of this approach, we carried out a simulation study and analysed a data set from Ugandan cattle to detect signatures of local adaptation with samβada, bayenv, lfmm and an FST outlier method (FDIST approach in arlequin) and compare their results. samβada - an open source software for Windows, Linux and Mac OS X available at http://lasig.epfl.ch/sambada - outperforms other approaches and better suits whole-genome sequence data processing.}, } @article {pmid27799466, year = {2017}, author = {Paez-Espino, D and Chen, IA and Palaniappan, K and Ratner, A and Chu, K and Szeto, E and Pillay, M and Huang, J and Markowitz, VM and Nielsen, T and Huntemann, M and K Reddy, TB and Pavlopoulos, GA and Sullivan, MB and Campbell, BJ and Chen, F and McMahon, K and Hallam, SJ and Denef, V and Cavicchioli, R and Caffrey, SM and Streit, WR and Webster, J and Handley, KM and Salekdeh, GH and Tsesmetzis, N and Setubal, JC and Pope, PB and Liu, WT and Rivers, AR and Ivanova, NN and Kyrpides, NC}, title = {IMG/VR: a database of cultured and uncultured DNA Viruses and retroviruses.}, journal = {Nucleic acids research}, volume = {45}, number = {D1}, pages = {D457-D465}, pmid = {27799466}, issn = {1362-4962}, mesh = {DNA Viruses/*genetics ; *Databases, Genetic ; Environmental Microbiology ; *Genome, Viral ; Genomics/*methods ; Host-Pathogen Interactions ; Metagenome ; Metagenomics/*methods ; Retroviridae/*genetics ; Sequence Analysis, DNA ; *Software ; }, abstract = {Viruses represent the most abundant life forms on the planet. Recent experimental and computational improvements have led to a dramatic increase in the number of viral genome sequences identified primarily from metagenomic samples. As a result of the expanding catalog of metagenomic viral sequences, there exists a need for a comprehensive computational platform integrating all these sequences with associated metadata and analytical tools. Here we present IMG/VR (https://img.jgi.doe.gov/vr/), the largest publicly available database of 3908 isolate reference DNA viruses with 264 413 computationally identified viral contigs from >6000 ecologically diverse metagenomic samples. Approximately half of the viral contigs are grouped into genetically distinct quasi-species clusters. Microbial hosts are predicted for 20 000 viral sequences, revealing nine microbial phyla previously unreported to be infected by viruses. Viral sequences can be queried using a variety of associated metadata, including habitat type and geographic location of the samples, or taxonomic classification according to hallmark viral genes. IMG/VR has a user-friendly interface that allows users to interrogate all integrated data and interact by comparing with external sequences, thus serving as an essential resource in the viral genomics community.}, } @article {pmid27627550, year = {2016}, author = {Ahn, HS and Kim, HJ and Kim, KH and Lee, YS and Han, SJ and Kim, Y and Ko, MJ and Brito, JP}, title = {Thyroid Cancer Screening in South Korea Increases Detection of Papillary Cancers with No Impact on Other Subtypes or Thyroid Cancer Mortality.}, journal = {Thyroid : official journal of the American Thyroid Association}, volume = {26}, number = {11}, pages = {1535-1540}, doi = {10.1089/thy.2016.0075}, pmid = {27627550}, issn = {1557-9077}, mesh = {Adult ; Aged ; Aged, 80 and over ; *Asymptomatic Diseases/epidemiology ; Carcinoma, Papillary/*diagnosis/epidemiology/mortality ; Cohort Studies ; Cross-Sectional Studies ; *Early Detection of Cancer ; Female ; Health Care Surveys ; Humans ; Incidence ; Male ; Middle Aged ; Prevalence ; Republic of Korea/epidemiology ; Self Report ; Sex Factors ; Thyroid Cancer, Papillary ; Thyroid Neoplasms/*diagnosis/epidemiology/mortality ; Young Adult ; }, abstract = {BACKGROUND: The incidence of thyroid cancer has increased worldwide. The country where the incidence has increased most is South Korea. The goal of this study is to understand the magnitude of association between opportunistic thyroid cancer screening and thyroid cancer incidence, thyroid cancer subtype, and disease-specific mortality.

METHODS: We used the 2010 Korea Community Health Survey, which queried 226,873 individuals if they had been screened for thyroid cancer in the last two years. Thyroid cancer incidence data from 2008 to 2010 were obtained from the Korea Cancer registry data, and mortality data from 2007-2010 were obtained from the Statistics Korea database. The ecological association between thyroid screening and thyroid cancer incidence and mortality by age and sex were examined across Korea's 16 administrative regions by general linear regression models.

RESULTS: Between 2008 and 2010, the incidence of thyroid cancer was 64.1 per 100,000 individuals: the incidence in females was 107.3 and in males was 21.1. There was a strong positive correlation between regional thyroid cancer screening and regional thyroid cancer incidence (r = 0.77, [95% confidence interval 0.70-0.82]). The magnitude of correlation was higher for females (r = 0.88 [CI 0.83-0.92]) than in males (r = 0.76 [CI 0.67-0.84]) in any age group. Thyroid screening was only associated with increased detection of papillary thyroid cancer (r = 0.74 [CI 0.59-0.88]); and not associated with mortality (r = -0.08 [CI -0.59-0.63]) due to thyroid cancer.

CONCLUSIONS: The magnitude of association between thyroid cancer screening in South Korea and the incidence of thyroid cancer strongly suggests that screening is the most important driver of the epidemic of thyroid cancer, particularly among females. Thyroid cancer screening, however, was only associated with the increase of one tumor histology, papillary thyroid cancer, and it did not have any association with thyroid cancer mortality. The extent to which opportunistic thyroid cancer screening is converting thousands of asymptomatic persons to cancer patients without any known benefit to them needs to be examined carefully.}, } @article {pmid27458204, year = {2016}, author = {Chakraborty, M and Baldwin-Brown, JG and Long, AD and Emerson, JJ}, title = {Contiguous and accurate de novo assembly of metazoan genomes with modest long read coverage.}, journal = {Nucleic acids research}, volume = {44}, number = {19}, pages = {e147}, pmid = {27458204}, issn = {1362-4962}, support = {R01 GM115562/GM/NIGMS NIH HHS/United States ; R01 OD010974/OD/NIH HHS/United States ; }, mesh = {Animals ; Cell Line ; Computational Biology/methods ; Drosophila melanogaster/genetics ; *Genome ; Genomics/*methods ; High-Throughput Nucleotide Sequencing ; Humans ; Sequence Analysis, DNA ; }, abstract = {Genome assemblies that are accurate, complete and contiguous are essential for identifying important structural and functional elements of genomes and for identifying genetic variation. Nevertheless, most recent genome assemblies remain incomplete and fragmented. While long molecule sequencing promises to deliver more complete genome assemblies with fewer gaps, concerns about error rates, low yields, stringent DNA requirements and uncertainty about best practices may discourage many investigators from adopting this technology. Here, in conjunction with the platinum standard Drosophila melanogaster reference genome, we analyze recently published long molecule sequencing data to identify what governs completeness and contiguity of genome assemblies. We also present a hybrid meta-assembly approach that achieves remarkable assembly contiguity for both Drosophila and human assemblies with only modest long molecule sequencing coverage. Our results motivate a set of preliminary best practices for obtaining accurate and contiguous assemblies, a 'missing manual' that guides key decisions in building high quality de novo genome assemblies, from DNA isolation to polishing the assembly.}, } @article {pmid27798064, year = {2017}, author = {Lucas, R and Groeneveld, J and Harms, H and Johst, K and Frank, K and Kleinsteuber, S}, title = {A critical evaluation of ecological indices for the comparative analysis of microbial communities based on molecular datasets.}, journal = {FEMS microbiology ecology}, volume = {93}, number = {1}, pages = {}, doi = {10.1093/femsec/fiw209}, pmid = {27798064}, issn = {1574-6941}, mesh = {Bacteria/classification/genetics/*isolation & purification ; *Biodiversity ; Data Interpretation, Statistical ; Databases, Genetic ; Ecology ; Ecosystem ; }, abstract = {In times of global change and intensified resource exploitation, advanced knowledge of ecophysiological processes in natural and engineered systems driven by complex microbial communities is crucial for both safeguarding environmental processes and optimising rational control of biotechnological processes. To gain such knowledge, high-throughput molecular techniques are routinely employed to investigate microbial community composition and dynamics within a wide range of natural or engineered environments. However, for molecular dataset analyses no consensus about a generally applicable alpha diversity concept and no appropriate benchmarking of corresponding statistical indices exist yet. To overcome this, we listed criteria for the appropriateness of an index for such analyses and systematically scrutinised commonly employed ecological indices describing diversity, evenness and richness based on artificial and real molecular datasets. We identified appropriate indices warranting interstudy comparability and intuitive interpretability. The unified diversity concept based on 'effective numbers of types' provides the mathematical framework for describing community composition. Additionally, the Bray-Curtis dissimilarity as a beta-diversity index was found to reflect compositional changes. The employed statistical procedure is presented comprising commented R-scripts and example datasets for user-friendly trial application.}, } @article {pmid27796990, year = {2017}, author = {Toy, S and Kántor, N}, title = {Evaluation of human thermal comfort ranges in urban climate of winter cities on the example of Erzurum city.}, journal = {Environmental science and pollution research international}, volume = {24}, number = {2}, pages = {1811-1820}, pmid = {27796990}, issn = {1614-7499}, mesh = {Adaptation, Physiological ; *Cities ; Clothing ; Cold Climate ; Energy Metabolism ; Humans ; *Seasons ; Software ; Surveys and Questionnaires ; *Temperature ; Thermosensing ; Turkey ; *Weather ; }, abstract = {Human thermal comfort conditions can be evaluated using various indices based on simple empirical approaches or more complex and reliable human-biometeorological approaches. The latter is based on the energy balance model of the human body, and their calculation is supplemented with computer software. Facilitating the interpretation of results, the generally applied indices express the effects of thermal environment in the well-known temperature unit, just like in the case of the widely used index, the physiologically equivalent temperature (PET). Several studies adopting PET index for characterizing thermal components of climate preferred to organize the resulted PET values into thermal sensation categories in order to demonstrate the spatial and/or temporal characteristics of human thermal comfort conditions. The most general applied PET ranges were derived by Central European researchers, and they are valid for assumed values of internal heat production of light activity and thermal resistance of clothing representing a light business suit. Based on the example of Erzurum city, the present work demonstrates that in a city with harsh winter, the original PET ranges show almost purely discomfort and they seem to be less applicable regarding cold climate conditions. Taking into account 34-year climate data of Erzurum, the annual distribution of PET is presented together with the impact of application of different PET categorization systems, including 8°- and 7°-wide PET intervals. The demonstrated prior analyses lack any questionnaire filed surveys in Erzurum. Thus, as a next step, detailed field investigations would be required with the aim of definition of new PET categorization systems which are relevant for local residents who are adapted to this climatic background, and for tourists who may perform various kinds of winter activities in Erzurum and therefore may perceive the thermal environment more comfortable.}, } @article {pmid27796355, year = {2016}, author = {Tan, SY and Tan, IK and Tan, MF and Dutta, A and Choo, SW}, title = {Evolutionary study of Yersinia genomes deciphers emergence of human pathogenic species.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {36116}, pmid = {27796355}, issn = {2045-2322}, mesh = {Adhesins, Bacterial/chemistry/genetics ; Bacterial Outer Membrane Proteins/chemistry/genetics ; CRISPR-Cas Systems/genetics ; *Evolution, Molecular ; *Genome, Bacterial ; Humans ; Phylogeny ; Plasmids/genetics/metabolism ; Virulence/genetics ; Yersinia/classification/*genetics/pathogenicity ; Yersinia Infections/microbiology/pathology ; }, abstract = {On record, there are 17 species in the Yersinia genus, of which three are known to be pathogenic to human. While the chromosomal and pYV (or pCD1) plasmid-borne virulence genes as well as pathogenesis of these three species are well studied, their genomic evolution is poorly understood. Our study aims to predict the key evolutionary events that led to the emergence of pathogenic Yersinia species by analyzing gene gain-and-loss, virulence genes, and "Clustered regularly-interspaced short palindromic repeats". Our results suggest that the most recent ancestor shared by the human pathogenic Yersinia was most probably an environmental species that had adapted to the human body. This might have led to ecological specialization that diverged Yersinia into ecotypes and distinct lineages based on differential gene gain-and-loss in different niches. Our data also suggest that Y. pseudotuberculosis group might be the donor of the ail virulence gene to Y. enterocolitica. Hence, we postulate that evolution of human pathogenic Yersinia might not be totally in parallel, but instead, there were lateral gene transfer events. Furthermore, the presence of virulence genes seems to be important for the positive selection of virulence plasmid. Our studies provide better insights into the evolutionary biology of these bacteria.}, } @article {pmid27796084, year = {2017}, author = {Rousset, F and Gouy, A and Martinez-Almoyna, C and Courtiol, A}, title = {The summary-likelihood method and its implementation in the Infusion package.}, journal = {Molecular ecology resources}, volume = {17}, number = {1}, pages = {110-119}, doi = {10.1111/1755-0998.12627}, pmid = {27796084}, issn = {1755-0998}, mesh = {Biostatistics/*methods ; Computational Biology/*methods ; *Computer Simulation ; Population Density ; *Software ; }, abstract = {In recent years, simulation methods such as approximate Bayesian computation have extensively been used to infer parameters of population genetic models where the likelihood is intractable. We describe an alternative approach, summary likelihood, that provides a likelihood-based analysis of the information retained in the summary statistics whose distribution is simulated. We provide an automated implementation as a standard R package, Infusion, and we test the method, in particular for a scenario of inference of population-size change from genetic data. We show that the method provides confidence intervals with controlled coverage independently of a prior distribution on parameters, in contrast to approximate Bayesian computation. We expect the method to be applicable for at least six-parameter models and discuss possible modifications for higher-dimensional inference problems.}, } @article {pmid27796069, year = {2017}, author = {Yashima, AS and Innan, H}, title = {varver: a database of microsatellite variation in vertebrates.}, journal = {Molecular ecology resources}, volume = {17}, number = {4}, pages = {824-833}, doi = {10.1111/1755-0998.12625}, pmid = {27796069}, issn = {1755-0998}, mesh = {Animals ; *Databases, Nucleic Acid ; Genetic Variation ; Genetics, Population ; *Microsatellite Repeats ; Vertebrates/*classification ; }, abstract = {Understanding how genetic variation is maintained within a species is important in ecology, evolution, conservation and population genetics. Tremendous efforts have been made to evaluate the patterns of genetic variation in natural populations of various species. For this purpose, microsatellites have played a major role since the 1990s. Here we describe a comprehensive database, varver (Variation in Vertebrates) that provides complete information regarding microsatellite variation in natural populations of vertebrates. For each species, varver includes basic information of the species, a list of publications reporting the microsatellite variation, and tables of genetic variation within and between populations (heterozygosity and FST). The geographic location and rough sampling range are also shown for each sampled population. The database should be useful for researchers interested in not only specific species but also comparing multiple species. We discuss the utility of microsatellite data, particularly for meta-analyses that involve multiple microsatellite loci from various species. We show that in such analyses, it is extremely important to correct for biases caused by differences in mutation rate, mainly due to repeat unit and number.}, } @article {pmid27793827, year = {2017}, author = {Hermans, SM and Buckley, HL and Case, BS and Curran-Cournane, F and Taylor, M and Lear, G}, title = {Bacteria as Emerging Indicators of Soil Condition.}, journal = {Applied and environmental microbiology}, volume = {83}, number = {1}, pages = {}, pmid = {27793827}, issn = {1098-5336}, mesh = {Bacteria/*classification/genetics/isolation & purification/*metabolism ; Biodiversity ; Carbon/metabolism ; Climate ; Ecosystem ; Hydrogen-Ion Concentration ; Microbial Consortia/*genetics/physiology ; Nitrogen/metabolism ; Phosphorus/metabolism ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Soil/*chemistry ; *Soil Microbiology ; }, abstract = {UNLABELLED: Bacterial communities are important for the health and productivity of soil ecosystems and have great potential as novel indicators of environmental perturbations. To assess how they are affected by anthropogenic activity and to determine their ability to provide alternative metrics of environmental health, we sought to define which soil variables bacteria respond to across multiple soil types and land uses. We determined, through 16S rRNA gene amplicon sequencing, the composition of bacterial communities in soil samples from 110 natural or human-impacted sites, located up to 300 km apart. Overall, soil bacterial communities varied more in response to changing soil environments than in response to changes in climate or increasing geographic distance. We identified strong correlations between the relative abundances of members of Pirellulaceae and soil pH, members of Gaiellaceae and carbon-to-nitrogen ratios, members of Bradyrhizobium and the levels of Olsen P (a measure of plant available phosphorus), and members of Chitinophagaceae and aluminum concentrations. These relationships between specific soil attributes and individual soil taxa not only highlight ecological characteristics of these organisms but also demonstrate the ability of key bacterial taxonomic groups to reflect the impact of specific anthropogenic activities, even in comparisons of samples across large geographic areas and diverse soil types. Overall, we provide strong evidence that there is scope to use relative taxon abundances as biological indicators of soil condition.

IMPORTANCE: The impact of land use change and management on soil microbial community composition remains poorly understood. Therefore, we explored the relationship between a wide range of soil factors and soil bacterial community composition. We included variables related to anthropogenic activity and collected samples across a large spatial scale to interrogate the complex relationships between various bacterial community attributes and soil condition. We provide evidence of strong relationships between individual taxa and specific soil attributes even across large spatial scales and soil and land use types. Collectively, we were able to demonstrate the largely untapped potential of microorganisms to indicate the condition of soil and thereby influence the way that we monitor the effects of anthropogenic activity on soil ecosystems into the future.}, } @article {pmid27704185, year = {2016}, author = {Lofrano, G and Libralato, G and Carotenuto, M and Guida, M and Inglese, M and Siciliano, A and Meriç, S}, title = {Emerging Concern from Short-Term Textile Leaching: A Preliminary Ecotoxicological Survey.}, journal = {Bulletin of environmental contamination and toxicology}, volume = {97}, number = {5}, pages = {646-652}, doi = {10.1007/s00128-016-1937-x}, pmid = {27704185}, issn = {1432-0800}, mesh = {Animals ; Biodegradation, Environmental ; Chlorophyta/*drug effects/growth & development ; Coloring Agents/*toxicity ; Cotton Fiber ; Daphnia/*drug effects/growth & development ; Ecotoxicology ; Lepidium sativum/*drug effects/growth & development ; *Surveys and Questionnaires ; *Textile Industry ; Time Factors ; Wastewater/chemistry/*toxicity ; Water Pollutants, Chemical/*toxicity ; }, abstract = {Textile dyes and their residues gained growing attention worldwide. Textile industry is a strong water consumer potentially releasing xenobiotics from washing and rinsing procedures during finishing processes. On a decentralised basis, also final consumers generate textile waste streams. Thus, a procedure simulating home washing with tap water screened cotton textiles leachates (n = 28) considering physico-chemical (COD, BOD5, and UV absorbance) and ecotoxicological data (Daphnia magna, Pseudokirchneriella subcapitata and Lepidium sativum). Results evidenced that: (i) leachates presented low biodegradability levels; (ii) toxicity in more than half leachates presented slight acute or acute effects; (iii) the remaining leachates presented "no effect" suggesting the use of green dyes/additives, and/or well established finishing processes; (iv) no specific correlations were found between traditional physico-chemical and ecotoxicological data. Further investigations will be necessary to identify textile residues, and their potential interactions with simulated human sweat in order to evidence potential adverse effects on human health.}, } @article {pmid27664055, year = {2016}, author = {Kothari, A and Charrier, M and Wu, YW and Malfatti, S and Zhou, CE and Singer, SW and Dugan, L and Mukhopadhyay, A}, title = {Transcriptomic analysis of the highly efficient oil-degrading bacterium Acinetobacter venetianus RAG-1 reveals genes important in dodecane uptake and utilization.}, journal = {FEMS microbiology letters}, volume = {363}, number = {20}, pages = {}, pmid = {27664055}, issn = {1574-6968}, mesh = {Acetates/metabolism ; Acinetobacter/*genetics/*metabolism ; Alkanes/*metabolism ; Biodegradation, Environmental ; Biological Transport/*genetics ; DNA, Bacterial/genetics ; Dodecanol/*metabolism ; Fimbriae, Bacterial/*genetics ; Gene Expression Profiling ; Membrane Transport Proteins/*genetics ; Petroleum Pollution ; Sequence Analysis, DNA ; }, abstract = {The hydrocarbonoclastic bacterium Acinetobacter venetianus RAG-1 has attracted substantial attention due to its powerful oil-degrading capabilities and its potential to play an important ecological role in the cleanup of alkanes. In this study, we compare the transcriptome of the strain RAG-1 grown in dodecane, the corresponding alkanol (dodecanol), and sodium acetate for the characterization of genes involved in dodecane uptake and utilization. Comparison of the transcriptional responses of RAG-1 grown on dodecane led to the identification of 1074 genes that were differentially expressed relative to sodium acetate. Of these, 622 genes were upregulated when grown in dodecane. The highly upregulated genes were involved in alkane catabolism, along with stress response. Our data suggest AlkMb to be primarily involved in dodecane oxidation. Transcriptional response of RAG-1 grown on dodecane relative to dodecanol also led to the identification of permease, outer membrane protein and thin fimbriae coding genes potentially involved in dodecane uptake. This study provides the first model for key genes involved in alkane uptake and metabolism in A. venetianus RAG-1.}, } @article {pmid27592864, year = {2016}, author = {Adams, DC and Collyer, ML}, title = {On the comparison of the strength of morphological integration across morphometric datasets.}, journal = {Evolution; international journal of organic evolution}, volume = {70}, number = {11}, pages = {2623-2631}, doi = {10.1111/evo.13045}, pmid = {27592864}, issn = {1558-5646}, mesh = {*Algorithms ; Animals ; Body Size/*genetics ; Datasets as Topic/*statistics & numerical data ; Evolution, Molecular ; *Genetic Variation ; Least-Squares Analysis ; Lizards/anatomy & histology/genetics ; *Models, Genetic ; }, abstract = {Evolutionary morphologists frequently wish to understand the extent to which organisms are integrated, and whether the strength of morphological integration among subsets of phenotypic variables differ among taxa or other groups. However, comparisons of the strength of integration across datasets are difficult, in part because the summary measures that characterize these patterns (RV coefficient and rPLS) are dependent both on sample size and on the number of variables. As a solution to this issue, we propose a standardized test statistic (a z-score) for measuring the degree of morphological integration between sets of variables. The approach is based on a partial least squares analysis of trait covariation, and its permutation-based sampling distribution. Under the null hypothesis of a random association of variables, the method displays a constant expected value and confidence intervals for datasets of differing sample sizes and variable number, thereby providing a consistent measure of integration suitable for comparisons across datasets. A two-sample test is also proposed to statistically determine whether levels of integration differ between datasets, and an empirical example examining cranial shape integration in Mediterranean wall lizards illustrates its use. Some extensions of the procedure are also discussed.}, } @article {pmid27794488, year = {2016}, author = {Khuntikeo, N and Sithithaworn, P and Loilom, W and Namwat, N and Yongvanit, P and Thinkhamrop, B and Kiatsopit, N and Andrews, RH and Petney, TN}, title = {Changing patterns of prevalence in Opisthorchis viverrini sensu lato infection in children and adolescents in northeast Thailand.}, journal = {Acta tropica}, volume = {164}, number = {}, pages = {469-472}, doi = {10.1016/j.actatropica.2016.10.017}, pmid = {27794488}, issn = {1873-6254}, mesh = {Adolescent ; Adult ; Age Factors ; Animals ; Bile Duct Neoplasms/epidemiology ; Child ; Child, Preschool ; Cholangiocarcinoma/*epidemiology ; Humans ; Incidence ; Infant ; Infant, Newborn ; Male ; Middle Aged ; Opisthorchiasis/*epidemiology ; Opisthorchis ; Prevalence ; Risk Factors ; Thailand/epidemiology ; Young Adult ; }, abstract = {Infection with the liver fluke Opisthorchis viverrini sensu lato (s.l.), a group 1 carcinogen, is the most important risk factor for developing cholangiocarcinoma (CCA) in Southeast Asia. Cholangiocarcinoma is a fatal disease with the world's highest incidence being found in northeast Thailand. Liver fluke infection occurs through eating raw or partially cooked cyprinid fish containing metacercariae and, therefore, the control of O. viverrini s.l. infection should lead to a reduction in CCA incidence. In this report, we review and analyze the age-prevalence profile data of O. viverrini to reveal temporal changes in patterns of prevalence pre- and post-control programs in Thailand. The profiles of O. viverrini prevalence have transformed from high prevalence in school children prior to 1983 to low prevalences after 1994. This pattern strongly suggests the influence of the health education program on the likelihood of school children becoming infected. In conjunction with current developments in health and socioeconomic conditions, we predict that the incidence of CCA will be reduced with time as the population cohorts that experienced the education programs reach the age at which CCA is most likely to develop, i.e. >50 years. The lessons learned in Thailand may be applicable to other areas endemic for human liver flukes.}, } @article {pmid27720605, year = {2016}, author = {Vadiati, M and Asghari-Moghaddam, A and Nakhaei, M and Adamowski, J and Akbarzadeh, AH}, title = {A fuzzy-logic based decision-making approach for identification of groundwater quality based on groundwater quality indices.}, journal = {Journal of environmental management}, volume = {184}, number = {Pt 2}, pages = {255-270}, doi = {10.1016/j.jenvman.2016.09.082}, pmid = {27720605}, issn = {1095-8630}, mesh = {*Decision Support Techniques ; *Fuzzy Logic ; *Groundwater ; Hydrology/methods ; Iran ; Models, Theoretical ; *Water Quality ; }, abstract = {Due to inherent uncertainties in measurement and analysis, groundwater quality assessment is a difficult task. Artificial intelligence techniques, specifically fuzzy inference systems, have proven useful in evaluating groundwater quality in uncertain and complex hydrogeological systems. In the present study, a Mamdani fuzzy-logic-based decision-making approach was developed to assess groundwater quality based on relevant indices. In an effort to develop a set of new hybrid fuzzy indices for groundwater quality assessment, a Mamdani fuzzy inference model was developed with widely-accepted groundwater quality indices: the Groundwater Quality Index (GQI), the Water Quality Index (WQI), and the Ground Water Quality Index (GWQI). In an effort to present generalized hybrid fuzzy indices a significant effort was made to employ well-known groundwater quality index acceptability ranges as fuzzy model output ranges rather than employing expert knowledge in the fuzzification of output parameters. The proposed approach was evaluated for its ability to assess the drinking water quality of 49 samples collected seasonally from groundwater resources in Iran's Sarab Plain during 2013-2014. Input membership functions were defined as "desirable", "acceptable" and "unacceptable" based on expert knowledge and the standard and permissible limits prescribed by the World Health Organization. Output data were categorized into multiple categories based on the GQI (5 categories), WQI (5 categories), and GWQI (3 categories). Given the potential of fuzzy models to minimize uncertainties, hybrid fuzzy-based indices produce significantly more accurate assessments of groundwater quality than traditional indices. The developed models' accuracy was assessed and a comparison of the performance indices demonstrated the Fuzzy Groundwater Quality Index model to be more accurate than both the Fuzzy Water Quality Index and Fuzzy Ground Water Quality Index models. This suggests that the new hybrid fuzzy indices developed in this research are reliable and flexible when used in groundwater quality assessment for drinking purposes.}, } @article {pmid27494948, year = {2016}, author = {Bachman, PM and Huizinga, KM and Jensen, PD and Mueller, G and Tan, J and Uffman, JP and Levine, SL}, title = {Ecological risk assessment for DvSnf7 RNA: A plant-incorporated protectant with targeted activity against western corn rootworm.}, journal = {Regulatory toxicology and pharmacology : RTP}, volume = {81}, number = {}, pages = {77-88}, doi = {10.1016/j.yrtph.2016.08.001}, pmid = {27494948}, issn = {1096-0295}, mesh = {Animals ; Coleoptera/*genetics/pathogenicity ; Computational Biology ; Computer Simulation ; Crops, Agricultural/genetics/parasitology/*toxicity ; Databases, Genetic ; Environmental Exposure ; *Food Safety ; Food, Genetically Modified/parasitology/*toxicity ; Gene Expression Regulation, Plant ; Host-Pathogen Interactions ; Humans ; No-Observed-Adverse-Effect Level ; Pest Control, Biological/*methods ; Plants, Genetically Modified/genetics/parasitology/*toxicity ; RNA Interference ; RNA, Double-Stranded/genetics/*toxicity ; Risk Assessment ; Species Specificity ; Time Factors ; Toxicity Tests/*methods ; Zea mays/genetics/parasitology/*toxicity ; }, abstract = {MON 87411 maize, which expresses DvSnf7 RNA, was developed to provide an additional mode of action to confer protection against corn rootworm (Diabrotica spp.). A critical step in the registration of a genetically engineered crop with an insecticidal trait is performing an ecological risk assessment to evaluate the potential for adverse ecological effects. For MON 87411, an assessment plan was developed that met specific protection goals by characterizing the routes and levels of exposure, and testing representative functional taxa that would be directly or indirectly exposed in the environment. The potential for toxicity of DvSnf7 RNA was evaluated with a harmonized battery of non-target organisms (NTOs) that included invertebrate predators, parasitoids, pollinators, soil biota as well as aquatic and terrestrial vertebrate species. Laboratory tests evaluated ecologically relevant endpoints such as survival, growth, development, and reproduction and were of sufficient duration to assess the potential for adverse effects. No adverse effects were observed with any species tested at, or above, the maximum expected environmental concentration (MEEC). All margins of exposure for NTOs were >10-fold the MEEC. Therefore, it is reasonable to conclude that exposure to DvSnf7 RNA, both directly and indirectly, is safe for NTOs at the expected field exposure levels.}, } @article {pmid27457111, year = {2016}, author = {Price, JR and Guran, LA and Gregory, WT and McDonagh, MS}, title = {Nitrofurantoin vs other prophylactic agents in reducing recurrent urinary tract infections in adult women: a systematic review and meta-analysis.}, journal = {American journal of obstetrics and gynecology}, volume = {215}, number = {5}, pages = {548-560}, doi = {10.1016/j.ajog.2016.07.040}, pmid = {27457111}, issn = {1097-6868}, mesh = {Adult ; Anti-Bacterial Agents/*therapeutic use ; Anti-Infective Agents, Urinary/*therapeutic use ; Cefaclor/therapeutic use ; Estriol/therapeutic use ; Female ; Humans ; Nitrofurantoin/*therapeutic use ; Norfloxacin/therapeutic use ; Recurrence ; Secondary Prevention ; Trimethoprim/therapeutic use ; Trimethoprim, Sulfamethoxazole Drug Combination/therapeutic use ; Urinary Tract Infections/*prevention & control ; }, abstract = {BACKGROUND: The clinical and financial burden from bladder infections is significant. Daily antibiotic use is the recommended strategy for recurrent urinary tract infection prevention. Increasing antibiotic resistance rates, however, require immediate identification of innovative alternative prophylactic therapies. This systematic review aims to provide guidance on gaps in evidence to guide future research.

OBJECTIVE: The objective of this review was to provide current pooled estimates of randomized control trials comparing the effects of nitrofurantoin vs other agents in reducing recurrent urinary tract infections in adult, nonpregnant women and assess relative adverse side effects.

DATA SOURCES: Data sources included the following: MEDLINE, Jan. 1, 1946, to Jan. 31, 2015; Cochrane Central Register of Controlled Trials the Cochrane Database of Systematic Reviews, and web sites of the National Institute for Clinical Excellence, and the National Guideline Clearinghouse from 2000 to 2015. Randomized control trials of women with recurrent urinary tract infections comparing nitrofurantoin with any other treatment were included.

STUDY DESIGN: A protocol for the study was developed a priori. Published guidance was followed for assessment of study quality. All meta-analyses were performed using random-effects models with Stats Direct Software. Dual review was used for all decisions and data abstraction.

RESULTS: Twelve randomized control trials involving 1063 patients were included. One study that had a serious flaw was rated poor in quality, one study rated good, and the remainder fair. No significant differences in prophylactic antibiotic treatment with nitrofurantoin and norfloxacin, trimethoprim, sulfamethoxazole/trimethoprim, methamine hippurate, estriol, or cefaclor were found in clinical or microbiological cure in adult nonpregnant women with recurrent urinary tract infections (9 randomized control trials, 673 patients, relative risk ratio, 1.06; 95% confidence interval, 0.89-1.27; I[2], 65%; and 12 randomized control trials, 1063 patients, relative risk ratio, 1.06; 95% confidence interval, 0.90-1.26; I[2], 76%, respectively). Duration of prophylaxis also did not have a significant impact on outcomes. There was a statistically significant difference in overall adverse effects, with nitrofurantoin resulting in greater risk than other prophylactic treatments (10 randomized control trials, 948 patients, relative risk ratio, 2.17; 95% confidence interval, 1.34-3.50; I[2], 61%). Overall, the majority of nitrofurantoin adverse effects were gastrointestinal, with a significant difference for withdrawals (12 randomized control trials, 1063 patients, relative risk ratio, 2.14; 95% confidence interval, 1.28-3.56; I[2], 8%).

CONCLUSION: Nitrofurantoin had similar efficacy but a greater risk of adverse events than other prophylactic treatments. Balancing the risks of adverse events, particularly gastrointestinal symptoms, with potential benefits of decreasing collateral ecological damage should be considered if selecting nitrofurantoin.}, } @article {pmid27784950, year = {2016}, author = {Rao, S and Chan, OW and Lacap-Bugler, DC and Pointing, SB}, title = {Radiation-Tolerant Bacteria Isolated from High Altitude Soil in Tibet.}, journal = {Indian journal of microbiology}, volume = {56}, number = {4}, pages = {508-512}, pmid = {27784950}, issn = {0046-8991}, abstract = {This study reports the identification of ionising radiation tolerant bacteria from a high elevation arid region of central Tibet. Nineteen isolates were isolated from soil exposed to ionising radiation at doses from 0 to 15 kGy. Isolates were phylogenetically characterised using 16S rRNA gene sequences. Most isolates comprised taxa from the Actinobacteria, Cyanobacteria, Firmicutes and proteobacteria and these survived doses up to 5 kGy. The Firmicutes and Deinococci also survived doses up to 10 kGy, and the highest dose of 15 kGy was survived only by the Deinococci. No altitude-related pattern was discernible within the range 4638-5240 m, instead culturable bacterial estimates for irradiated soil were strongly influenced by the abundance of Deinococci. We conclude that the relatively high UV exposure in Tibet has contributed to the high diversity of radiation tolerant soil bacteria. In addition, the strong association between desiccation-tolerance and radiation tolerance pathways suggests the arid environment may also have selected in favour of radiation tolerant taxa.}, } @article {pmid27784643, year = {2016}, author = {Xiao, B and Chen, TM and Zhong, Y}, title = {Possible molecular mechanism underlying cadmium-induced circadian rhythms disruption in zebrafish.}, journal = {Biochemical and biophysical research communications}, volume = {481}, number = {3-4}, pages = {201-205}, doi = {10.1016/j.bbrc.2016.10.081}, pmid = {27784643}, issn = {1090-2104}, mesh = {Animals ; Cadmium/*toxicity ; Circadian Rhythm/*drug effects/genetics ; Gene Expression Profiling ; Gene Expression Regulation/drug effects ; Gene Ontology ; RNA, Messenger/genetics/metabolism ; Reproducibility of Results ; Signal Transduction/drug effects/genetics ; Zebrafish/genetics/*physiology ; }, abstract = {This study was aimed to explore the mechanisms underlying cadmium-induced circadian rhythms disruption. Two groups of zebrafish larvae treated with or without 5 ppm CdCl2 were incubated in a photoperiod of 14-h light/10-h dark conditions. The mRNA levels of clock1a, bmal1b, per2 and per1b in two groups were determined. Microarray data were generated in two group of samples. Differential expression of genes were identified and the changes in expression level for some genes were validated by RT-PCR. Finally, Gene Ontology functional and KEGG pathway enrichment analysis of differentially expressed genes (DEGs) were performed. In comparison with normal group, the mRNA levels of clock1a, bmal1b, and per2 were significantly changed and varied over the circadian cycle in CdCl2-treated group. DEGs were obtained from the light (84 h, ZT12) and dark (88 h, ZT16) phase. In addition, G-protein coupled receptor protein signaling pathway and immune response were both enriched by DEGs in both groups. While, proteolysis and amino acid metabolism were found associated with DEGs in light phase, and Neuroactive ligand-receptor interaction and oxidation-reduction process were significantly enriched by DEGs in dark phase. Besides, the expression pattern of genes including hsp70l and or115-11 obtained by RT-PCR were consistent with those obtained by microarray analysis. As a consequence, cadmium could make significant effects on circadian rhythms through immune response and G protein-coupled receptor signaling pathway. Besides, between the dark and the light phase, the mechanism by which cadmium inducing disruption of circadian rhythms were different to some extent.}, } @article {pmid27784001, year = {2017}, author = {Park, K and Park, S and Jeon, MJ and Choi, J and Kim, JW and Cho, YJ and Jang, WS and Keum, YS and Lee, IJ}, title = {Clinical application of 3D-printed-step-bolus in post-total-mastectomy electron conformal therapy.}, journal = {Oncotarget}, volume = {8}, number = {15}, pages = {25660-25668}, pmid = {27784001}, issn = {1949-2553}, mesh = {Aged ; Breast Neoplasms/pathology/*radiotherapy/surgery ; Female ; Humans ; Mastectomy ; Middle Aged ; Neoplasm Staging ; Postoperative Care ; Radiometry ; Radiotherapy Dosage ; Radiotherapy Planning, Computer-Assisted ; Radiotherapy, Conformal/*methods ; Treatment Outcome ; Tumor Burden ; }, abstract = {The 3D-printed boluses were used during the radiation therapy of the chest wall in six patients with breast cancer after modified radical mastectomy (MRM). We measured the in-vivo skin doses while both conventional and 3D-printed boluses were placed on the chest wall and compared the mean doses delivered to the ipsilateral lung and the heart. The homogeneity and conformity of the dose distribution in the chest wall for both types of boluses were also evaluated. The uniformity index on the chest skin was improved when the 3D-printed boluses were used, with the overall average skin dose being closer to the prescribed one in the former case (-0.47% versus -4.43%). On comparing the dose-volume histogram (DVH), it was found that the 3D-printed boluses resulted in a reduction in the mean dose to the ipsilateral lung by up to 20%. The precision of dose delivery was improved by 3% with the 3D-printed boluses; in contrast, the conventional step bolus resulted in a precision level of 5%. In conclusion, the use of the 3D-printed boluses resulted in better dose homogeneity and conformity to the chest wall as well as the sparing of the normal organs, especially the lung. This suggested that their routine use on the chest wall as a therapeutic approach during post-mastectomy radiation therapy offers numerous advantages over conventional step boluses.}, } @article {pmid27783616, year = {2016}, author = {Deguen, S and Kihal, W and Jeanjean, M and Padilla, C and Zmirou-Navier, D}, title = {Neighborhood Deprivation and Risk of Congenital Heart Defects, Neural Tube Defects and Orofacial Clefts: A Systematic Review and Meta-Analysis.}, journal = {PloS one}, volume = {11}, number = {10}, pages = {e0159039}, pmid = {27783616}, issn = {1932-6203}, mesh = {Databases, Factual ; Female ; Heart Defects, Congenital/*etiology ; Humans ; Mouth Abnormalities/*etiology ; Neural Tube Defects/*etiology ; Odds Ratio ; Pregnancy ; Residence Characteristics ; Risk Factors ; Socioeconomic Factors ; }, abstract = {BACKGROUND: We conducted this systematic review and meta-analysis to address the open question of a possible association between the socioeconomic level of the neighborhoods in which pregnant women live and the risk of Congenital Heart Defects (CHDs), Neural Tube Defects (NTDs) and OroFacial Clefts (OFCs).

METHODS: We searched MEDLINE from its inception to December 20th, 2015 for case-control, cohort and ecological studies assessing the association between neighborhood socioeconomic level and the risk of CHDs, NTDs and the specific phenotypes Cleft Lip with or without Cleft Palate (CLP) and Cleft Palate (CP). Study-specific risk estimates were pooled according to random-effect and fixed-effect models.

RESULTS: Out of 245 references, a total of seven case-control studies, two cohort studies and two ecological studies were assessed in the systematic review; all studies were enrolled in the meta-analysis with the exception of the two cohort studies. No significant association has been revealed between CHDs or NTDs and neighborhood deprivation index. For CLP phenotype subgroups, we found a significantly higher rate in deprived neighborhoods (Odds Ratios (OR) = 1.22, 95% CI: 1.10, 1.36) whereas this was not significant for CP phenotype subgroups (OR = 1.20, 95%CI: 0.89, 1.61).

CONCLUSION: In spite of the small number of epidemiological studies included in the present literature review, our findings suggest that neighborhood socioeconomic level where mothers live is associated only with an increased risk of CLP phenotype subgroups. This finding has methodological limitations that impede the formulation of firm conclusions, and further investigations should confirm this association.}, } @article {pmid27783349, year = {2016}, author = {Rapinel, S and Hubert-Moy, L and Clément, B and Maltby, E}, title = {Mapping wetland functions using Earth observation data and multi-criteria analysis.}, journal = {Environmental monitoring and assessment}, volume = {188}, number = {11}, pages = {641}, pmid = {27783349}, issn = {1573-2959}, mesh = {Ecosystem ; Environmental Monitoring/*methods ; Geographic Information Systems ; Radar ; *Wetlands ; }, abstract = {Wetland functional assessment is commonly conducted based on field observations, and thus, is generally limited to small areas. However, there is often a need for wetland managers to obtain information on wetland functional performance over larger areas. For this purpose, we are proposing a new field-based functional assessment procedure in which wetland functions are evaluated and classified into hydrogeomorphic units according to a multi-criteria analysis approach. Wetland-related geographic information system layers derived from Earth observation data (LiDAR, multispectral and radar data) are used in this study for a large-scale functional evaluation. These include maps of a hydrogeomorphic units, ditches, vegetation, annual flood duration, biomass, meadows management, and wetland boundaries. To demonstrate the feasibility of this approach, a 132 km[2] international long-term ecological research site located in the west of France was assessed. Four wetland functions were evaluated: flood peak attenuation, low water attenuation, denitrification, and habitat. A spatial distribution map of the individual wetland functions was generated, and the intensity levels of the functions were highlighted. Antagonisms between functions within individual hydrogeomorphic units were also identified. Mapping of hydrological, biogeochemical, and ecological wetland functions over large areas can provide an efficient tool for policy makers and other stakeholders including water authorities, nature conservation agencies, and farmers. Specifically, this tool has the potential to provide a mapping of ecosystem services, conservation management priorities, and possible improvements in water resources management.}, } @article {pmid27781170, year = {2016}, author = {Rognes, T and Flouri, T and Nichols, B and Quince, C and Mahé, F}, title = {VSEARCH: a versatile open source tool for metagenomics.}, journal = {PeerJ}, volume = {4}, number = {}, pages = {e2584}, pmid = {27781170}, issn = {2167-8359}, support = {MR/L015080/1/MRC_/Medical Research Council/United Kingdom ; MR/M50161X/1/MRC_/Medical Research Council/United Kingdom ; }, abstract = {BACKGROUND: VSEARCH is an open source and free of charge multithreaded 64-bit tool for processing and preparing metagenomics, genomics and population genomics nucleotide sequence data. It is designed as an alternative to the widely used USEARCH tool (Edgar, 2010) for which the source code is not publicly available, algorithm details are only rudimentarily described, and only a memory-confined 32-bit version is freely available for academic use.

METHODS: When searching nucleotide sequences, VSEARCH uses a fast heuristic based on words shared by the query and target sequences in order to quickly identify similar sequences, a similar strategy is probably used in USEARCH. VSEARCH then performs optimal global sequence alignment of the query against potential target sequences, using full dynamic programming instead of the seed-and-extend heuristic used by USEARCH. Pairwise alignments are computed in parallel using vectorisation and multiple threads.

RESULTS: VSEARCH includes most commands for analysing nucleotide sequences available in USEARCH version 7 and several of those available in USEARCH version 8, including searching (exact or based on global alignment), clustering by similarity (using length pre-sorting, abundance pre-sorting or a user-defined order), chimera detection (reference-based or de novo), dereplication (full length or prefix), pairwise alignment, reverse complementation, sorting, and subsampling. VSEARCH also includes commands for FASTQ file processing, i.e., format detection, filtering, read quality statistics, and merging of paired reads. Furthermore, VSEARCH extends functionality with several new commands and improvements, including shuffling, rereplication, masking of low-complexity sequences with the well-known DUST algorithm, a choice among different similarity definitions, and FASTQ file format conversion. VSEARCH is here shown to be more accurate than USEARCH when performing searching, clustering, chimera detection and subsampling, while on a par with USEARCH for paired-ends read merging. VSEARCH is slower than USEARCH when performing clustering and chimera detection, but significantly faster when performing paired-end reads merging and dereplication. VSEARCH is available at https://github.com/torognes/vsearch under either the BSD 2-clause license or the GNU General Public License version 3.0.

DISCUSSION: VSEARCH has been shown to be a fast, accurate and full-fledged alternative to USEARCH. A free and open-source versatile tool for sequence analysis is now available to the metagenomics community.}, } @article {pmid27339259, year = {2016}, author = {Coutinho, FH and Dutilh, BE and Thompson, CC and Thompson, FL}, title = {Proposal of fifteen new species of Parasynechococcus based on genomic, physiological and ecological features.}, journal = {Archives of microbiology}, volume = {198}, number = {10}, pages = {973-986}, doi = {10.1007/s00203-016-1256-y}, pmid = {27339259}, issn = {1432-072X}, mesh = {Cyanobacteria/*classification/genetics/physiology ; Genome, Bacterial/genetics ; Genomics ; Nucleic Acid Hybridization ; Oceans and Seas ; Phylogeny ; *Water Microbiology ; }, abstract = {Members of the recently proposed genus Parasynechococcus (Cyanobacteria) are extremely abundant throughout the global ocean and contribute significantly to global primary productivity. However, the taxonomy of these organisms remains poorly characterized. The aim of this study was to propose a new taxonomic framework for Parasynechococcus based on a genomic taxonomy approach that incorporates genomic, physiological and ecological data. Through in silico DNA-DNA hybridization, average amino acid identity, dinucleotide signatures and phylogenetic reconstruction, a total of 15 species of Parasynechococcus could be delineated. Each species was then described on the basis of their gene content, light and nutrient utilization strategies, geographical distribution patterns throughout the oceans and response to environmental parameters.}, } @article {pmid26932464, year = {2016}, author = {Winkworth-Lawrence, C and Lange, K}, title = {Antibiotic Resistance Genes in Freshwater Biofilms May Reflect Influences from High-Intensity Agriculture.}, journal = {Microbial ecology}, volume = {72}, number = {4}, pages = {763-772}, pmid = {26932464}, issn = {1432-184X}, mesh = {Agriculture/methods ; Animals ; Animals, Domestic/microbiology ; Anti-Bacterial Agents/*pharmacology ; Antiporters/genetics ; Bacteria/*drug effects/*genetics ; Biofilms/*growth & development ; Databases, Factual ; Drug Resistance, Bacterial/*genetics ; Fresh Water/*microbiology ; Genes, Bacterial/genetics ; Humans ; Interspersed Repetitive Sequences/genetics ; Methyltransferases/genetics ; Microbial Sensitivity Tests ; New Zealand ; Tetracycline Resistance/genetics ; }, abstract = {Antibiotic resistance is a major public health concern with growing evidence of environmental gene reservoirs, especially in freshwater. However, the presence of antibiotic resistance genes in freshwater, in addition to the wide spectrum of land use contaminants like nitrogen and phosphate, that waterways are subjected to is inconclusive. Using molecular analyses, freshwater benthic rock biofilms were screened for genes conferring resistance to antibiotics used in both humans and farmed animals (aacA-aphD to aminoglycosides; mecA to ß-lactams; ermA and ermB to macrolides; tetA, tetB, tetK, and tetM to tetracyclines; vanA and vanB to glycopeptides). We detected widespread low levels of antibiotic resistance genes from 20 waterways across southern New Zealand throughout the year (1.3 % overall detection rate; 480 samples from three rocks per site, 20 sites, eight occasions; July 2010-May 2011). Three of the ten genes, ermB, tetK, and tetM, were detected in 62 of the 4800 individual screens; representatives confirmed using Sanger sequencing. No distinction could be made between human and agricultural land use contamination sources based on gene presence distribution alone. However, land use pressures are suggested by moderate correlations between antibiotic resistance genes and high-intensity farming in winter. The detection of antibiotic resistance genes at several sites not subject to known agricultural pressures suggests human sources of resistance, like waterway contamination resulting from unsatisfactory toilet facilities at recreational sites.}, } @article {pmid27779179, year = {2016}, author = {Margalida, A and Pérez-García, JM and Afonso, I and Moreno-Opo, R}, title = {Spatial and temporal movements in Pyrenean bearded vultures (Gypaetus barbatus): Integrating movement ecology into conservation practice.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {35746}, pmid = {27779179}, issn = {2045-2322}, mesh = {Animal Migration/*physiology ; Animals ; Birds ; Endangered Species ; Falconiformes/*physiology ; Female ; France ; Geographic Information Systems ; Geography ; Homing Behavior/*physiology ; Male ; Movement/physiology ; Sex Factors ; Spain ; *Territoriality ; }, abstract = {Understanding the movement of threatened species is important if we are to optimize management and conservation actions. Here, we describe the age and sex specific spatial and temporal ranging patterns of 19 bearded vultures Gypaetus barbatus tracked with GPS technology. Our findings suggest that spatial asymmetries are a consequence of breeding status and age-classes. Territorial individuals exploited home ranges of about 50 km[2], while non-territorial birds used areas of around 10 000 km[2] (with no seasonal differences). Mean daily movements differed between territorial (23.8 km) and non-territorial birds (46.1 km), and differences were also found between sexes in non-territorial birds. Daily maximum distances travelled per day also differed between territorial (8.2 km) and non-territorial individuals (26.5 km). Territorial females moved greater distances (12 km) than males (6.6 km). Taking into account high-use core areas (K20), Supplementary Feeding Sites (SFS) do not seem to play an important role in the use of space by bearded vultures. For non-territorial and territorial individuals, 54% and 46% of their home ranges (K90), respectively, were outside protected areas. Our findings will help develop guidelines for establishing priority areas based on spatial use, and also optimize management and conservation actions for this threatened species.}, } @article {pmid27776516, year = {2016}, author = {Larocca, A and Moro Visconti, R and Marconi, M}, title = {Malaria diagnosis and mapping with m-Health and geographic information systems (GIS): evidence from Uganda.}, journal = {Malaria journal}, volume = {15}, number = {1}, pages = {520}, pmid = {27776516}, issn = {1475-2875}, mesh = {Adolescent ; Adult ; Aged ; Aged, 80 and over ; Child ; Child, Preschool ; Diagnostic Tests, Routine/*methods ; Female ; Geographic Information Systems ; Humans ; Infant ; Infant, Newborn ; Malaria, Falciparum/*diagnosis/*epidemiology ; Male ; Middle Aged ; Plasmodium falciparum/*isolation & purification ; Telemedicine/*methods ; *Topography, Medical ; Uganda/epidemiology ; Young Adult ; }, abstract = {BACKGROUND: Rural populations experience several barriers to accessing clinical facilities for malaria diagnosis. Increasing penetration of ICT and mobile-phones and subsequent m-Health applications can contribute overcoming such obstacles.

METHODS: GIS is used to evaluate the feasibility of m-Health technologies as part of anti-malaria strategies. This study investigates where in Uganda: (1) malaria affects the largest number of people; (2) the application of m-Health protocol based on the mobile network has the highest potential impact.

RESULTS: About 75% of the population affected by Plasmodium falciparum malaria have scarce access to healthcare facilities. The introduction of m-Health technologies should be based on the 2G protocol, as 3G mobile network coverage is still limited. The western border and the central-Southeast are the regions where m-Health could reach the largest percentage of the remote population. Six districts (Arua, Apac, Lira, Kamuli, Iganga, and Mubende) could have the largest benefit because they account for about 28% of the remote population affected by falciparum malaria with access to the 2G mobile network.

CONCLUSIONS: The application of m-Health technologies could improve access to medical services for distant populations. Affordable remote malaria diagnosis could help to decongest health facilities, reducing costs and contagion. The combination of m-Health and GIS could provide real-time and geo-localized data transmission, improving anti-malarial strategies in Uganda. Scalability to other countries and diseases looks promising.}, } @article {pmid27776492, year = {2016}, author = {Kasumovic, MM and Chen, Z and Wilkins, MR}, title = {Australian black field crickets show changes in neural gene expression associated with socially-induced morphological, life-history, and behavioral plasticity.}, journal = {BMC genomics}, volume = {17}, number = {1}, pages = {827}, pmid = {27776492}, issn = {1471-2164}, mesh = {Animals ; *Behavior, Animal ; Biological Evolution ; Cluster Analysis ; Computational Biology/methods ; Female ; *Gene Expression ; Gene Expression Profiling ; Gene Ontology ; Gryllidae/*anatomy & histology/*physiology ; Male ; Molecular Sequence Annotation ; Neurons/*metabolism ; Phenotype ; Quantitative Trait, Heritable ; Sex Factors ; }, abstract = {BACKGROUND: Ecological and evolutionary model organisms have provided extensive insight into the ecological triggers, adaptive benefits, and evolution of life-history driven developmental plasticity. Despite this, we still have a poor understanding of the underlying genetic changes that occur during shifts towards different developmental trajectories. The goal of this study is to determine whether we can identify underlying gene expression patterns that can describe the different life-history trajectories individuals follow in response to social cues of competition. To do this, we use the Australian black field cricket (Teleogryllus commodus), a species with sex-specific developmental trajectories moderated by the density and quality of calls heard during immaturity. In this study, we manipulated the social information males and females could hear by rearing individuals in either calling or silent treatments. We next used RNA-Seq to develop a reference transcriptome to study changes in brain gene expression at two points prior to sexual maturation.

RESULTS: We show accelerated development in both sexes when exposed to calling; changes were also seen in growth, lifespan, and reproductive effort. Functional relationships between genes and phenotypes were apparent from ontological enrichment analysis. We demonstrate that increased investment towards traits such as growth and reproductive effort were often associated with the expression of a greater number of genes with similar effect, thus providing a suite of candidate genes for future research in this and other invertebrate organisms.

CONCLUSIONS: Our results provide interesting insight into the genomic underpinnings of developmental plasticity and highlight the potential of a genomic exploration of other evolutionary theories such as condition dependence and sex-specific developmental strategies.}, } @article {pmid27642032, year = {2016}, author = {Schlaich, AE and Klaassen, RH and Bouten, W and Bretagnolle, V and Koks, BJ and Villers, A and Both, C}, title = {How individual Montagu's Harriers cope with Moreau's Paradox during the Sahelian winter.}, journal = {The Journal of animal ecology}, volume = {85}, number = {6}, pages = {1491-1501}, doi = {10.1111/1365-2656.12583}, pmid = {27642032}, issn = {1365-2656}, mesh = {*Animal Migration ; Animals ; *Climate Change ; *Ecosystem ; Falconiformes/*physiology ; Female ; *Food Chain ; Geographic Information Systems ; Grasshoppers/physiology ; Male ; Seasons ; Senegal ; }, abstract = {Hundreds of millions of Afro-Palaearctic migrants winter in the Sahel, a semi-arid belt south of the Sahara desert, where they experience deteriorating ecological conditions during their overwintering stay and have to prepare for spring migration when conditions are worst. This well-known phenomenon was first described by R.E. Moreau and is known ever since as Moreau's Paradox. However, empirical evidence of the deteriorating seasonal ecological conditions is limited and little is known on how birds respond. Montagu's Harriers Circus pygargus spend 6 months of the year in their wintering areas in the Sahel. Within the wintering season, birds move gradually to the south, visiting several distinct sites to which they are site-faithful in consecutive years. At the last wintering site, birds find themselves at the southern edge of the Sahelian zone and have no other options than facing deteriorating conditions. We tracked 36 Montagu's Harriers with GPS trackers to study their habitat use and behaviour during winter and collected data on the abundance of their main prey, grasshoppers, in Senegal. Since grasshopper abundance was positively related to vegetation greenness (measured as normalized difference vegetation index, NDVI), we used NDVI values as a proxy for prey abundance in areas where no field data were collected. Prey abundance (grasshopper counts and vegetation greenness) at wintering sites of Montagu's Harriers decreased during the wintering period. Montagu's Harriers responded to decreasing food availability by increasing their flight time during the second half of the winter. Individuals increased flight time more in areas with stronger declines in NDVI values, suggesting that lower food abundance required more intense foraging to achieve energy requirements. The apparent consequence was that Montagu's Harriers departed later in spring when their final wintering site had lower NDVI values and presumably lower food abundance and consequently arrived later at their breeding site. Our results confirmed the suggestions Moreau made 40 years ago: the late wintering period might be a bottleneck during the annual cycle with possible carry-over effects to the breeding season. Ongoing climate change with less rainfall in the Sahel region paired with increased human pressure on natural and agricultural habitats resulting in degradation and desertification is likely to make this period more demanding, which may negatively impact populations of migratory birds using the Sahel.}, } @article {pmid27775436, year = {2016}, author = {Sangion, A and Gramatica, P}, title = {Ecotoxicity interspecies QAAR models from Daphnia toxicity of pharmaceuticals and personal care products.}, journal = {SAR and QSAR in environmental research}, volume = {27}, number = {10}, pages = {781-798}, doi = {10.1080/1062936X.2016.1233139}, pmid = {27775436}, issn = {1029-046X}, mesh = {Animals ; Computational Biology ; Cosmetics/*toxicity ; Cyprinidae ; Daphnia/*drug effects ; *Drug-Related Side Effects and Adverse Reactions ; Environmental Pollutants/*toxicity ; Models, Statistical ; Oncorhynchus mykiss ; *Quantitative Structure-Activity Relationship ; }, abstract = {Pharmaceutical and Personal Care Products (PPCPs) became a class of contaminants of emerging concern because are ubiquitously detected in surface water and soil, where they can affect wildlife. Ecotoxicological data are only available for a few PPCPs, thus modelling approaches are essential tools to maximize the information contained in the existing data. In silico methods may be helpful in filling data gaps for the toxicity of PPCPs towards various ecological indicator organisms. The good correlation between toxicity toward Daphnia magna and those on two fish species (Pimephales promelas and Oncorhynchus mykiss), improved by the addition of one theoretical molecular descriptor, allowed us to develop predictive models to investigate the relationship between toxicities in different species. The aim of this work is to propose quantitative activity-activity relationship (QAAR) models, developed in QSARINS and validated for their external predictivity. Such models can be used to predict the toxicity of PPCPs to a particular species using available experimental toxicity data from a different species, thus reducing the tests on organisms of higher trophic level. Similarly, good QAAR models, implemented by molecular descriptors to improve the quality, are proposed here for fish interspecies. We also comment on the relevance of autocorrelation descriptors in improving all studied interspecies correlations.}, } @article {pmid27771879, year = {2017}, author = {Dai, W and Dong, J and Yan, W and Xu, J}, title = {Study on each phase characteristics of the whole coal life cycle and their ecological risk assessment-a case of coal in China.}, journal = {Environmental science and pollution research international}, volume = {24}, number = {2}, pages = {1296-1305}, pmid = {27771879}, issn = {1614-7499}, mesh = {China ; *Coal/toxicity ; *Coal Mining ; Environmental Monitoring ; *Environmental Pollutants/toxicity ; *Industrial Waste ; Mercury ; Metals, Heavy/analysis ; Refuse Disposal ; Risk Assessment ; Soil/chemistry ; }, abstract = {The paper divided the whole coal life cycle, explained each phase characteristics, and took coal mine in China as a study case to assess the ecological risk in coal utilization phase. The main conclusions are as follows: (1) the whole coal life cycle is divided into coal mining, processing, transportation, utilization, and waste disposal. (2) The key points of production organization and characteristics in the five phases have great differences. The coal mining phase is characterized by the damage of the key ecological factors (water, soil, atmosphere, vegetation, etc.) damaged while the coal processing phase by discharging waste. The characteristics in coal transportation phase mainly performance as escaping and migration of atmospheric pollutants. In coal utilization phase, the main characteristics are aggravation of greenhouse effect. The main characteristics of waste disposal phase are accumulation of negative ecological effects on the land. (3) The ecological risk of soil heavy metals is serious in coal utilization phase. The potential ecological hazard coefficients of Pb and As in coal, residue and ash are all lower than 40, presenting low environmental impact on soil; the potential ecological risk coefficients of Cd are higher than 60, nearly half of their potential ecological risk coefficients are higher than 160, which presents high environmental pollution impact on soil; Hg's potential ecological risk coefficients are higher than 320, presenting the highest environmental pollution impact on soil; the comprehensive pollution indexes in coal, residue, and ash are relatively high, which means the pollution hazard potential to soil environment is high. (4) The ecological risk of the atmospheric solid suspended matter is relatively strong in coal utilization phase. The ecological risk of Cd and As in primary flue gas is both lower than net flue gas. The geoaccumulation indexes of Cd and Hg in primary flue gas and net flue gas are both higher than 5, presenting the very strong ecological risk; 50 % of the geoaccumulation index values of As are between 3 and 4, which has also presenting a strong ecological risk while Pb does not present the ecological risk characterization.}, } @article {pmid27771778, year = {2016}, author = {Huang, B and Zhang, L and Tang, X and Zhang, G and Li, L}, title = {Genome-Wide Analysis of Alternative Splicing Provides Insights into Stress Adaptation of the Pacific Oyster.}, journal = {Marine biotechnology (New York, N.Y.)}, volume = {18}, number = {5}, pages = {598-609}, pmid = {27771778}, issn = {1436-2236}, mesh = {Adaptation, Physiological ; *Alternative Splicing ; Animals ; Base Sequence ; Chaperonin 60/*genetics/metabolism ; Crassostrea/*genetics/metabolism ; Exons ; Gene Ontology ; *Genome ; HSP90 Heat-Shock Proteins/*genetics/metabolism ; High-Throughput Nucleotide Sequencing ; Introns ; Molecular Sequence Annotation ; Salinity ; Stress, Physiological ; Temperature ; *Transcriptome ; }, abstract = {Alternative splicing (AS) is thought to enhance transcriptome diversity dramatically and play an important role in stress adaptation. While well studied in vertebrates, AS remains poorly understood in invertebrates. Here, we used high-throughput RNA-sequencing data to perform a genome-wide survey of AS in the Pacific oyster (Crassostrea gigas), an economically important mollusk that is cultivated worldwide. This analysis identified 8223 AS events corresponding to 4480 genes in the Pacific oyster, suggesting that about 16 % of oyster multiexonic genes undergo AS. We observed that a majority of the identified AS events were related to skipped exons (37.8 %). Then Gene Ontology analysis was conducted to analyze the function of the genes that undergo AS and the genes that produce more than five AS isoforms. After that, the expression of AS isoforms facing temperature, salinity, and air exposure challenge were examined. To validate our bioinformatic-predicted results and examine whether AS affects stress adaptation, we selected heat-shock protein 60 (HSP60) and HSP90 genes, both of which experience AS, for reverse transcription PCR (RT-PCR). We also performed quantitative real-time PCR (qRT-PCR) to determine the relative expression of each AS isoform among different stress adapted populations. Our study indicates that AS events are likely complex in the Pacific oyster and may be related to stress adaptation. These results will complement the predicted gene database of C. gigas and provide an invaluable resource for future functional genomic studies on molluscs.}, } @article {pmid27771142, year = {2016}, author = {Suzuki, E and Tsuda, T and Mitsuhashi, T and Mansournia, MA and Yamamoto, E}, title = {Errors in causal inference: an organizational schema for systematic error and random error.}, journal = {Annals of epidemiology}, volume = {26}, number = {11}, pages = {788-793.e1}, doi = {10.1016/j.annepidem.2016.09.008}, pmid = {27771142}, issn = {1873-2585}, mesh = {*Confounding Factors, Epidemiologic ; *Epidemiologic Methods ; Humans ; Medical Errors ; Models, Statistical ; *Selection Bias ; }, abstract = {PURPOSE: To provide an organizational schema for systematic error and random error in estimating causal measures, aimed at clarifying the concept of errors from the perspective of causal inference.

METHODS: We propose to divide systematic error into structural error and analytic error. With regard to random error, our schema shows its four major sources: nondeterministic counterfactuals, sampling variability, a mechanism that generates exposure events and measurement variability.

RESULTS: Structural error is defined from the perspective of counterfactual reasoning and divided into nonexchangeability bias (which comprises confounding bias and selection bias) and measurement bias. Directed acyclic graphs are useful to illustrate this kind of error. Nonexchangeability bias implies a lack of "exchangeability" between the selected exposed and unexposed groups. A lack of exchangeability is not a primary concern of measurement bias, justifying its separation from confounding bias and selection bias. Many forms of analytic errors result from the small-sample properties of the estimator used and vanish asymptotically. Analytic error also results from wrong (misspecified) statistical models and inappropriate statistical methods.

CONCLUSIONS: Our organizational schema is helpful for understanding the relationship between systematic error and random error from a previously less investigated aspect, enabling us to better understand the relationship between accuracy, validity, and precision.}, } @article {pmid27693333, year = {2017}, author = {Chimbari, MJ}, title = {Lessons from implementation of ecohealth projects in Southern Africa: A principal investigator's perspective.}, journal = {Acta tropica}, volume = {175}, number = {}, pages = {9-19}, doi = {10.1016/j.actatropica.2016.09.028}, pmid = {27693333}, issn = {1873-6254}, mesh = {Africa, Southern ; *Environment ; *Health Status ; Humans ; Leadership ; Research/*organization & administration ; Research Personnel/*organization & administration ; *Social Environment ; }, abstract = {Ecohealth projects are designed to garner ownership among all stakeholders, such as researchers, communities, local leadership and policy makers. Ideally, designs should ensure that implementation goes smoothly and that findings from studies benefit the stakeholders, particularly bringing changes to the communities researched. Paradoxically, the process is fraught with challenges associated with implementation. Notwithstanding these challenges, evidence from projects implemented in southern Africa justify the need to invest in the subject of ecohealth. This paper describes and discusses a principal investigator's experience of leading ecohealth projects in Zimbabwe between 2002 and 2005, in Botswana between 2010 and 2014 and in South Africa (ongoing). The discourse is centred on issues of project management and leadership, transdisciplinarity, students' involvement, data management, community engagement, dissemination of research findings and the role of institutions in project management and implementation. The paper concludes that the ecohealth approach is valuable and should be encouraged making the following recommendations; 1) principal investigators must have a good understanding of socio-ecological systems, have excellent project management and writing skills, 2) more than one PI should be involved in the day-to-day running of the project in order to avoid disruption of project activities in the event that the PI leaves the project before it ends, 3) researchers should be trained in ecohealth principles and methodologies at the time of building the research teams, 4) full proposals should be developed with active participation of communities and stakeholders in order to develop a shared vision, 5) involvement of postdoctoral fellows and dedicated researchers with postgraduate students should be encouraged to avoid situations where some objectives are not fully addressed because of the narrow nature of students' work; and 6) citizen science should be encouraged to empower communities and ensure that certain activities continue after project termination.}, } @article {pmid27667388, year = {2017}, author = {Yang, X and Zhang, Z and Gu, T and Dong, M and Peng, Q and Bai, L and Li, Y}, title = {Quantitative proteomics reveals ecological fitness cost of multi-herbicide resistant barnyardgrass (Echinochloa crus-galli L.).}, journal = {Journal of proteomics}, volume = {150}, number = {}, pages = {160-169}, doi = {10.1016/j.jprot.2016.09.009}, pmid = {27667388}, issn = {1876-7737}, mesh = {Echinochloa/*drug effects/genetics/growth & development/*metabolism ; Ecology ; *Environment ; Gene Ontology ; Genetic Fitness/drug effects ; *Herbicide Resistance/genetics ; Herbicides/pharmacology ; Photosynthesis/drug effects/genetics ; Proteomics/*methods ; }, abstract = {UNLABELLED: Barnyardgrass (Echinochloa crus-galli) is one of the top 15 herbicide-resistant weeds around the world that interferes with rice growth, resulting in major losses of rice yield. Thus, multi-herbicide resistance in barnyardgrass presents a major threat, with the underlying mechanisms that contribute to resistance requiring elucidation. In an attempt to characterize this multi-herbicide resistance at the proteomic level, comparative analysis of resistant and susceptible barnyardgrasses was performed using iTRAQ, both with and without quinclorac, bispyribac-sodium and penoxsulam herbicidal treatment. A total of 1342 protein species were identified from 2248 unique peptides by searching the UniProt database and conducting data analysis. Approximately 904 protein species with 4774 Gene Ontology (GO) terms were grouped into the categories of biological process, cellular component and molecular function. Among these, 688 protein species were annotated into 1583 KEGG pathways, with 980 protein species relating to metabolism and 93 relating to environmental information processing. A total of 292 protein species showed more than a 1.2-fold change in abundance in the resistant biotype relative to the susceptible biotype. Furthermore, herbicide treatment resulted in 157 protein species that showed more than a 1.2-fold change in the resistant biotype. Moreover, physiological analyses demonstrated an ecological fitness cost in the resistant biotype.

SIGNIFICANCE: While some studies have shown a fitness cost to be associated with an altered ecological interaction, our understanding of the fitness costs associated with herbicide resistance are limited. Herein, physiological and proteomic analysis demonstrates herbicide resistance associated ecological fitness cost and potential mechanisms of herbicide-resistance in resistant biotypes of E. crus-galli. The results presented herein have revealed differences in ecological adaptation between resistant and susceptible biotypes in E. crus-galli and provide a fundamental basis enabling the development of new strategies for weed control. Lastly, this is the first large-scale proteomics study to examine herbicide stress responses in different barnyardgrass biotypes.}, } @article {pmid27623794, year = {2016}, author = {Schmitz, C and Fritsch, L and Fischer, R and Schillberg, S and Rasche, S}, title = {Statistical experimental designs for the production of secondary metabolites in plant cell suspension cultures.}, journal = {Biotechnology letters}, volume = {38}, number = {12}, pages = {2007-2014}, doi = {10.1007/s10529-016-2206-0}, pmid = {27623794}, issn = {1573-6776}, mesh = {Cell Culture Techniques/*methods ; Data Interpretation, Statistical ; Plant Cells/*metabolism ; Research Design ; }, abstract = {Statistical experimental designs, also known as the "design of experiments" (DoE) approach, are widely used to improve not only technical processes but also to answer questions in the agricultural, medical and social sciences. Although many articles have been published about the application of DoE in these fields, few studies have addressed the use of DoE in the plant sciences, particularly in the context of plant cell suspension cultures (PCSCs). Compounds derived from PCSCs can be developed as pharmaceuticals, chemical feedstocks and cosmetic ingredients, and statistical experimental designs can be used to improve the productivity of the cells and the yield and/or quality of the target compounds in a cost efficient manner. In this article, we summarize recent findings concerning the application of statistical approaches to improve the performance of PCSCs and discuss the potential future applications of this approach.}, } @article {pmid27554794, year = {2016}, author = {Jansen, HA and Nguyen, TV and Hoang, TA}, title = {Exploring risk factors associated with intimate partner violence in Vietnam: results from a cross-sectional national survey.}, journal = {International journal of public health}, volume = {61}, number = {8}, pages = {923-934}, pmid = {27554794}, issn = {1661-8564}, mesh = {Adolescent ; Adult ; Cross-Sectional Studies ; Databases, Factual ; Female ; Humans ; *Intimate Partner Violence ; Male ; Middle Aged ; Risk Factors ; Surveys and Questionnaires ; Vietnam ; Young Adult ; }, abstract = {OBJECTIVES: Empirical evidence documents that some risk factors for intimate partner violence (IPV) are similar across contexts, while others differ considerably. In Vietnam, there was a need to investigate risk factors for IPV to support evidence-based policy and programming.

METHODS: Using the dataset gathered in the 2010 National Study on Domestic Violence against Women, forty variables were explored in logistic regression analysis, including socio-demographic characteristics of women and their husbands, other experiences with violence, husband's behaviours, family support, and context-specific variables such as the sex of their children.

RESULTS: Fifteen independent factors remained strongly associated with IPV. Significant risk was associated with husbands' behaviour that supports male power (extra-marital relationships; fighting with other men) and alcohol use. Violence experienced in childhood increased the likelihood of women experiencing and of men perpetrating IPV. Notable was further the association with women's higher financial contribution to the household and lack of association with not having sons.

CONCLUSIONS: The findings support theories describing how underlying gender and power imbalance are fundamental causes of IPV and indicate the need for context-specific interventions.}, } @article {pmid27548044, year = {2016}, author = {Ultsch, A and Kringel, D and Kalso, E and Mogil, JS and Lötsch, J}, title = {A data science approach to candidate gene selection of pain regarded as a process of learning and neural plasticity.}, journal = {Pain}, volume = {157}, number = {12}, pages = {2747-2757}, doi = {10.1097/j.pain.0000000000000694}, pmid = {27548044}, issn = {1872-6623}, mesh = {Databases, Factual/*statistics & numerical data ; Genetic Predisposition to Disease/*genetics ; Genomics ; Humans ; Learning/*physiology ; Machine Learning ; Neuronal Plasticity/*genetics ; Pain/*genetics ; }, abstract = {The increasing availability of "big data" enables novel research approaches to chronic pain while also requiring novel techniques for data mining and knowledge discovery. We used machine learning to combine the knowledge about n = 535 genes identified empirically as relevant to pain with the knowledge about the functions of thousands of genes. Starting from an accepted description of chronic pain as displaying systemic features described by the terms "learning" and "neuronal plasticity," a functional genomics analysis proposed that among the functions of the 535 "pain genes," the biological processes "learning or memory" (P = 8.6 × 10) and "nervous system development" (P = 2.4 × 10) are statistically significantly overrepresented as compared with the annotations to these processes expected by chance. After establishing that the hypothesized biological processes were among important functional genomics features of pain, a subset of n = 34 pain genes were found to be annotated with both Gene Ontology terms. Published empirical evidence supporting their involvement in chronic pain was identified for almost all these genes, including 1 gene identified in March 2016 as being involved in pain. By contrast, such evidence was virtually absent in a randomly selected set of 34 other human genes. Hence, the present computational functional genomics-based method can be used for candidate gene selection, providing an alternative to established methods.}, } @article {pmid27765035, year = {2016}, author = {Hardisty, AR and Bacall, F and Beard, N and Balcázar-Vargas, MP and Balech, B and Barcza, Z and Bourlat, SJ and De Giovanni, R and de Jong, Y and De Leo, F and Dobor, L and Donvito, G and Fellows, D and Guerra, AF and Ferreira, N and Fetyukova, Y and Fosso, B and Giddy, J and Goble, C and Güntsch, A and Haines, R and Ernst, VH and Hettling, H and Hidy, D and Horváth, F and Ittzés, D and Ittzés, P and Jones, A and Kottmann, R and Kulawik, R and Leidenberger, S and Lyytikäinen-Saarenmaa, P and Mathew, C and Morrison, N and Nenadic, A and de la Hidalga, AN and Obst, M and Oostermeijer, G and Paymal, E and Pesole, G and Pinto, S and Poigné, A and Fernandez, FQ and Santamaria, M and Saarenmaa, H and Sipos, G and Sylla, KH and Tähtinen, M and Vicario, S and Vos, RA and Williams, AR and Yilmaz, P}, title = {BioVeL: a virtual laboratory for data analysis and modelling in biodiversity science and ecology.}, journal = {BMC ecology}, volume = {16}, number = {1}, pages = {49}, pmid = {27765035}, issn = {1472-6785}, mesh = {*Biodiversity ; Ecology/instrumentation/*methods ; Internet ; Models, Biological ; Software ; Workflow ; }, abstract = {BACKGROUND: Making forecasts about biodiversity and giving support to policy relies increasingly on large collections of data held electronically, and on substantial computational capability and capacity to analyse, model, simulate and predict using such data. However, the physically distributed nature of data resources and of expertise in advanced analytical tools creates many challenges for the modern scientist. Across the wider biological sciences, presenting such capabilities on the Internet (as "Web services") and using scientific workflow systems to compose them for particular tasks is a practical way to carry out robust "in silico" science. However, use of this approach in biodiversity science and ecology has thus far been quite limited.

RESULTS: BioVeL is a virtual laboratory for data analysis and modelling in biodiversity science and ecology, freely accessible via the Internet. BioVeL includes functions for accessing and analysing data through curated Web services; for performing complex in silico analysis through exposure of R programs, workflows, and batch processing functions; for on-line collaboration through sharing of workflows and workflow runs; for experiment documentation through reproducibility and repeatability; and for computational support via seamless connections to supporting computing infrastructures. We developed and improved more than 60 Web services with significant potential in many different kinds of data analysis and modelling tasks. We composed reusable workflows using these Web services, also incorporating R programs. Deploying these tools into an easy-to-use and accessible 'virtual laboratory', free via the Internet, we applied the workflows in several diverse case studies. We opened the virtual laboratory for public use and through a programme of external engagement we actively encouraged scientists and third party application and tool developers to try out the services and contribute to the activity.

CONCLUSIONS: Our work shows we can deliver an operational, scalable and flexible Internet-based virtual laboratory to meet new demands for data processing and analysis in biodiversity science and ecology. In particular, we have successfully integrated existing and popular tools and practices from different scientific disciplines to be used in biodiversity and ecological research.}, } @article {pmid27764088, year = {2016}, author = {Hart, EM and Barmby, P and LeBauer, D and Michonneau, F and Mount, S and Mulrooney, P and Poisot, T and Woo, KH and Zimmerman, NB and Hollister, JW}, title = {Ten Simple Rules for Digital Data Storage.}, journal = {PLoS computational biology}, volume = {12}, number = {10}, pages = {e1005097}, pmid = {27764088}, issn = {1553-7358}, mesh = {Databases, Factual/trends ; Humans ; Information Storage and Retrieval/*standards ; }, } @article {pmid27762445, year = {2017}, author = {Malukiewicz, J and Hepp, CM and Guschanski, K and Stone, AC}, title = {Phylogeny of the jacchus group of Callithrix marmosets based on complete mitochondrial genomes.}, journal = {American journal of physical anthropology}, volume = {162}, number = {1}, pages = {157-169}, doi = {10.1002/ajpa.23105}, pmid = {27762445}, issn = {1096-8644}, mesh = {Animals ; Callithrix/*classification/*genetics ; DNA, Mitochondrial/*genetics ; Evolution, Molecular ; Female ; Genome, Mitochondrial/*genetics ; Male ; Phylogeny ; }, abstract = {OBJECTIVES: Two subgroups make up the marmoset genus Callithrix. The "aurita" group is composed of two species, whereas evolutionary relationships among the four species of the "jacchus" group remain unclear. To uncover these relationships, we first sequenced mitochondrial genomes for C. kuhlii and C. penicillata to complement data available for congeners. We then constructed a phylogenetic tree based on mtDNA heavy chain protein coding genes from several primates to untangle species relationships and estimate divergence times of the jacchus group.

MATERIALS AND METHODS: MtDNA genomes of C. kuhlii and C. penicillata were Sanger sequenced. These Callithrix mitogenomes were combined with other publically available primate mtDNA genomes. Phylogenies were produced using maximum likelihood and Bayesian inference. Finally, divergence times within the jacchus group of marmosets were estimated with Bayesian inference.

RESULTS: In our phylogenetic tree, C. geoffroyi was the sister to all other jacchus group species, followed by C. kuhlii, while C. jacchus and C. penicillata diverged most recently. Bayesian inference showed that C. jacchus and C. penicillata diverged approximately 0.70 MYA and that the jacchus group radiated approximately 1.30 MYA.

DISCUSSION: Callithrix nuclear and mtDNA phylogenies frequently result in polytomies and paraphyly. Here, we present a well-supported phylogenetic tree based on mitochondrial genome sequences, which facilitates the understanding of the divergence of the jacchus marmosets. Our results demonstrate how mitochondrial genomes can enrich Callithrix phylogenetic studies by alleviating some of the difficulties faced by previous mtDNA studies and allow formulation of hypotheses to test further under larger genomic-scale analyses.}, } @article {pmid27762175, year = {2017}, author = {Dallas, T and Park, AW and Drake, JM}, title = {Predictability of helminth parasite host range using information on geography, host traits and parasite community structure.}, journal = {Parasitology}, volume = {144}, number = {2}, pages = {200-205}, doi = {10.1017/S0031182016001608}, pmid = {27762175}, issn = {1469-8161}, mesh = {Animal Distribution ; Animals ; Databases, Factual ; Ecosystem ; Fish Diseases/epidemiology/parasitology ; Fishes ; Helminthiasis, Animal/epidemiology/parasitology ; Helminths/*physiology ; Host-Parasite Interactions ; Life Cycle Stages ; Models, Biological ; Species Specificity ; }, abstract = {Host-parasite associations are complex interactions dependent on aspects of hosts (e.g. traits, phylogeny or coevolutionary history), parasites (e.g. traits and parasite interactions) and geography (e.g. latitude). Predicting the permissive host set or the subset of the host community that a parasite can infect is a central goal of parasite ecology. Here we develop models that accurately predict the permissive host set of 562 helminth parasites in five different parasite taxonomic groups. We developed predictive models using host traits, host taxonomy, geographic covariates, and parasite community composition, finding that models trained on parasite community variables were more accurate than any other covariate group, even though parasite community covariates only captured a quarter of the variance in parasite community composition. This suggests that it is possible to predict the permissive host set for a given parasite, and that parasite community structure is an important predictor, potentially because parasite communities are interacting non-random assemblages.}, } @article {pmid27762069, year = {2017}, author = {Amato, KR}, title = {An introduction to microbiome analysis for human biology applications.}, journal = {American journal of human biology : the official journal of the Human Biology Council}, volume = {29}, number = {1}, pages = {}, doi = {10.1002/ajhb.22931}, pmid = {27762069}, issn = {1520-6300}, mesh = {Computational Biology/methods ; *Gastrointestinal Microbiome ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Microbiological Techniques/*methods ; Polymerase Chain Reaction/methods ; }, abstract = {Research examining the gut microbiota is currently exploding, and results are providing new perspectives on human biology. Factors such as host diet and physiology influence the composition and function of the gut microbiota, which in turn affects human nutrition, health, and behavior via interactions with metabolism, the immune system, and the brain. These findings represent an exciting new twist on familiar topics, and as a result, gut microbiome research is likely to provide insight into unresolved biological mechanisms driving human health. However, much remains to be learned about the broader ecological and evolutionary contexts within which gut microbes and humans are affecting each other. Here, I outline the procedures for generating data describing the gut microbiota with the goal of facilitating the wider integration of microbiome analyses into studies of human biology. I describe the steps involved in sample collection, DNA extraction, PCR amplification, high-throughput sequencing, and bioinformatics. While this review serves only as an introduction to these topics, it provides sufficient resources for researchers interested in launching new microbiome initiatives. As knowledge of these methods spreads, microbiome analysis should become a standard tool in the arsenal of human biology research.}, } @article {pmid27760996, year = {2016}, author = {Song, K and Li, L and Zhang, G}, title = {Coverage recommendation for genotyping analysis of highly heterologous species using next-generation sequencing technology.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {35736}, pmid = {27760996}, issn = {2045-2322}, mesh = {Animals ; Computational Biology/*methods ; Crassostrea/*classification/*genetics ; Genetic Variation ; Genotyping Techniques/*methods ; High-Throughput Nucleotide Sequencing/*methods ; Polymorphism, Single Nucleotide ; }, abstract = {Next-generation sequencing (NGS) technology is being applied to an increasing number of non-model species and has been used as the primary approach for accurate genotyping in genetic and evolutionary studies. However, inferring genotypes from sequencing data is challenging, particularly for organisms with a high degree of heterozygosity. This is because genotype calls from sequencing data are often inaccurate due to low sequencing coverage, and if this is not accounted for, genotype uncertainty can lead to serious bias in downstream analyses, such as quantitative trait locus mapping and genome-wide association studies. Here, we used high-coverage reference data sets from Crassostrea gigas to simulate sequencing data with different coverage, and we evaluate the influence of genotype calling rate and accuracy as a function of coverage. Having initially identified the appropriate parameter settings for filtering to ensure genotype accuracy, we used two different single-nucleotide polymorphism (SNP) calling pipelines, single-sample and multi-sample. We found that a coverage of 15× was suitable for obtaining sufficient numbers of SNPs with high accuracy. Our work provides guidelines for the selection of sequence coverage when using NGS to investigate species with a high degree of heterozygosity and rapid decay of linkage disequilibrium.}, } @article {pmid27760854, year = {2016}, author = {Hibbett, D and Abarenkov, K and Kõljalg, U and Öpik, M and Chai, B and Cole, J and Wang, Q and Crous, P and Robert, V and Helgason, T and Herr, JR and Kirk, P and Lueschow, S and O'Donnell, K and Nilsson, RH and Oono, R and Schoch, C and Smyth, C and Walker, DM and Porras-Alfaro, A and Taylor, JW and Geiser, DM}, title = {Sequence-based classification and identification of Fungi.}, journal = {Mycologia}, volume = {108}, number = {6}, pages = {1049-1068}, doi = {10.3852/16-130}, pmid = {27760854}, issn = {0027-5514}, mesh = {Archaea/classification/genetics ; Bacteria/classification/genetics ; Fungi/*classification/*genetics ; Metagenomics/*methods ; *Phylogeny ; }, abstract = {Fungal taxonomy and ecology have been revolutionized by the application of molecular methods and both have increasing connections to genomics and functional biology. However, data streams from traditional specimen- and culture-based systematics are not yet fully integrated with those from metagenomic and metatranscriptomic studies, which limits understanding of the taxonomic diversity and metabolic properties of fungal communities. This article reviews current resources, needs, and opportunities for sequence-based classification and identification (SBCI) in fungi as well as related efforts in prokaryotes. To realize the full potential of fungal SBCI it will be necessary to make advances in multiple areas. Improvements in sequencing methods, including long-read and single-cell technologies, will empower fungal molecular ecologists to look beyond ITS and current shotgun metagenomics approaches. Data quality and accessibility will be enhanced by attention to data and metadata standards and rigorous enforcement of policies for deposition of data and workflows. Taxonomic communities will need to develop best practices for molecular characterization in their focal clades, while also contributing to globally useful datasets including ITS. Changes to nomenclatural rules are needed to enable validPUBLICation of sequence-based taxon descriptions. Finally, cultural shifts are necessary to promote adoption of SBCI and to accord professional credit to individuals who contribute to community resources.}, } @article {pmid27760794, year = {2016}, author = {Crava, CM and Ramasamy, S and Ometto, L and Anfora, G and Rota-Stabelli, O}, title = {Evolutionary Insights into Taste Perception of the Invasive Pest Drosophila suzukii.}, journal = {G3 (Bethesda, Md.)}, volume = {6}, number = {12}, pages = {4185-4196}, pmid = {27760794}, issn = {2160-1836}, mesh = {Animals ; *Biological Evolution ; Computational Biology/methods ; Drosophila/classification/*physiology ; Drosophila Proteins/genetics ; Gene Duplication ; Gene Expression Regulation ; Genome, Insect ; Genomics/methods ; Molecular Sequence Annotation ; Phylogeny ; Selection, Genetic ; Taste Perception/*genetics ; }, abstract = {Chemosensory perception allows insects to interact with the environment by perceiving odorant or tastant molecules; genes encoding chemoreceptors are the molecular interface between the environment and the insect, and play a central role in mediating its chemosensory behavior. Here, we explore how the evolution of these genes in the emerging pest Drosophila suzukii correlates with the peculiar ecology of this species. We annotated approximately 130 genes coding for gustatory receptors (GRs) and divergent ionotropic receptors (dIRs) in D. suzukii and in its close relative D. biarmipes We then analyzed the evolution, in terms of size, of each gene family as well of the molecular evolution of the genes in a 14 Drosophila species phylogenetic framework. We show that the overall evolution of GRs parallels that of dIRs not only in D. suzukii, but also in all other analyzed Drosophila Our results reveal an unprecedented burst of gene family size in the lineage leading to the suzukii subgroup, as well as genomic changes that characterize D. suzukii, particularly duplications and strong signs of positive selection in the putative bitter-taste receptor GR59d. Expression studies of duplicate genes in D. suzukii support a spatio-temporal subfunctionalization of the duplicate isoforms. Our results suggest that D. suzukii is not characterized by gene loss, as observed in other specialist Drosophila species, but rather by a dramatic acceleration of gene gains, compatible with a highly generalist feeding behavior. Overall, our analyses provide candidate taste receptors specific for D. suzukii that may correlate with its specific behavior, and which may be tested in functional studies to ultimately enhance its control in the field.}, } @article {pmid27760558, year = {2016}, author = {Debelius, J and Song, SJ and Vazquez-Baeza, Y and Xu, ZZ and Gonzalez, A and Knight, R}, title = {Tiny microbes, enormous impacts: what matters in gut microbiome studies?.}, journal = {Genome biology}, volume = {17}, number = {1}, pages = {217}, pmid = {27760558}, issn = {1474-760X}, support = {P01 DK078669/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; *Data Interpretation, Statistical ; Gastrointestinal Microbiome/*genetics ; Humans ; Mice ; Research Design ; *Sample Size ; }, abstract = {Many factors affect the microbiomes of humans, mice, and other mammals, but substantial challenges remain in determining which of these factors are of practical importance. Considering the relative effect sizes of both biological and technical covariates can help improve study design and the quality of biological conclusions. Care must be taken to avoid technical bias that can lead to incorrect biological conclusions. The presentation of quantitative effect sizes in addition to P values will improve our ability to perform meta-analysis and to evaluate potentially relevant biological effects. A better consideration of effect size and statistical power will lead to more robust biological conclusions in microbiome studies.}, } @article {pmid27755713, year = {2016}, author = {Williams, PJ and Hooten, MB}, title = {Combining statistical inference and decisions in ecology.}, journal = {Ecological applications : a publication of the Ecological Society of America}, volume = {26}, number = {6}, pages = {1930-1942}, doi = {10.1890/15-1593.1}, pmid = {27755713}, issn = {1051-0761}, mesh = {*Data Interpretation, Statistical ; Ecology/*methods ; *Models, Biological ; }, abstract = {Statistical decision theory (SDT) is a sub-field of decision theory that formally incorporates statistical investigation into a decision-theoretic framework to account for uncertainties in a decision problem. SDT provides a unifying analysis of three types of information: statistical results from a data set, knowledge of the consequences of potential choices (i.e., loss), and prior beliefs about a system. SDT links the theoretical development of a large body of statistical methods, including point estimation, hypothesis testing, and confidence interval estimation. The theory and application of SDT have mainly been developed and published in the fields of mathematics, statistics, operations research, and other decision sciences, but have had limited exposure in ecology. Thus, we provide an introduction to SDT for ecologists and describe its utility for linking the conventionally separate tasks of statistical investigation and decision making in a single framework. We describe the basic framework of both Bayesian and frequentist SDT, its traditional use in statistics, and discuss its application to decision problems that occur in ecology. We demonstrate SDT with two types of decisions: Bayesian point estimation and an applied management problem of selecting a prescribed fire rotation for managing a grassland bird species. Central to SDT, and decision theory in general, are loss functions. Thus, we also provide basic guidance and references for constructing loss functions for an SDT problem.}, } @article {pmid27755581, year = {2016}, author = {Shi, G and Peng, C and Wang, M and Shi, S and Yang, Y and Chu, J and Zhang, J and Lin, G and Shen, Y and Zhu, Q}, title = {The Spatial and Temporal Distribution of Dissolved Organic Carbon Exported from Three Chinese Rivers to the China Sea.}, journal = {PloS one}, volume = {11}, number = {10}, pages = {e0165039}, pmid = {27755581}, issn = {1932-6203}, mesh = {Carbon/*analysis ; China ; Databases, Factual ; Ecosystem ; Environmental Monitoring ; Oceans and Seas ; Rain ; Rivers/*chemistry ; Seasons ; Temperature ; }, abstract = {The lateral transport of dissolved organic carbon (DOC) plays an important role in linking the carbon cycles of terrestrial and aquatic ecosystems. Neglecting the lateral flow of dissolved organic carbon can lead to an underestimation of the organic carbon budget of terrestrial ecosystems. It is thus necessary to integrate DOC concentrations and flux into carbon cycle models, particularly with regard to the development of models that are intended to directly link terrestrial and ocean carbon cycles. However, to achieve this goal, more accurate information is needed to better understand and predict DOC dynamics. In this study, we compiled an inclusive database of available data collected from the Yangtze River, Yellow River and Pearl River in China. The database is collected based on online literature survey and analysed by statistic method. Overall, our results revealed a positive correlation between DOC flux and discharge in all three rivers, whereas the DOC concentration was more strongly correlated with the regional net primary productivity (NPP). We estimated the total DOC flux exported by the three rivers into the China Sea to be approximately 2.73 Tg yr-1. Specifically, the annual flux of DOC from the Yangtze River, Yellow River and Pearl River was estimated to be 1.85 Tg yr-1, 0.06 Tg yr-1 and 0.82 Tg yr-1, respectively, and the average annual DOC concentrations were estimated to be 2.24 ± 0.53 mg L-1, 2.70 ± 0.38 mg L-1 and 1.51 ± 0.09 mg L-1, respectively. Seasonal variations in DOC concentrations are greatly influenced by the interaction between temperature and precipitation. NPP is significantly and positively related to the DOC concentration in the Yangtze River and the Pearl River. In addition, differences in climate and the productivity of the vegetation may influence both the flux and concentrations of DOC transported by the rivers and thus potentially affect estuarine geochemistry.}, } @article {pmid27754599, year = {2017}, author = {Sandoval-Castillo, J and Attard, CR and Marri, S and Brauer, CJ and Möller, LM and Beheregaray, LB}, title = {swinger: a user-friendly computer program to establish captive breeding groups that minimize relatedness without pedigree information.}, journal = {Molecular ecology resources}, volume = {17}, number = {2}, pages = {278-287}, doi = {10.1111/1755-0998.12609}, pmid = {27754599}, issn = {1755-0998}, mesh = {*Breeding ; Computational Biology/*methods ; Genotype ; Genotyping Techniques/*methods ; Internet ; Microsatellite Repeats ; Pedigree ; Polymorphism, Single Nucleotide ; *Software ; }, abstract = {Captive breeding programmes are often a necessity for the continued persistence of a population or species. They typically have the goal of maintaining genetic diversity and minimizing inbreeding. However, most captive breeding programmes have been based on the assumption that the founding breeders are unrelated and outbred, even though in situ anthropogenic impacts often mean these founders may have high relatedness and substantial inbreeding. In addition, polygamous group-breeding species in captivity often have uncertain pedigrees, making it difficult to select the group composition for subsequent breeding. Molecular-based estimates of relatedness and inbreeding may instead be used to select breeding groups (≥two individuals) that minimize relatedness and filter out inbred individuals. swinger constructs breeding groups based on molecular estimates of relatedness and inbreeding. The number of possible combinations of breeding groups quickly becomes intractable by hand. swinger was designed to overcome this major issue in ex situ conservation biology. The user can specify parameters within swinger to reach breeding solutions that suit the mating system of the target species and available resources. We provide evidence of the efficiency of the software with an empirical example and using simulations. The only data required are a typical molecular marker data set, such as a microsatellite or SNP data set, from which estimates of inbreeding and pairwise relatedness may be obtained. Such molecular data sets are becoming easier to gather from non-model organisms with next-generation sequencing technology. swinger is an open-source software with a user-friendly interface and is available at http://www.molecularecology.flinders.edu.au/molecular-ecology-lab/software/swinger/swinger/ and https://github.com/Yuma248/Swinger.}, } @article {pmid27747959, year = {2016}, author = {Grossmann, L and Beisser, D and Bock, C and Chatzinotas, A and Jensen, M and Preisfeld, A and Psenner, R and Rahmann, S and Wodniok, S and Boenigk, J}, title = {Trade-off between taxon diversity and functional diversity in European lake ecosystems.}, journal = {Molecular ecology}, volume = {25}, number = {23}, pages = {5876-5888}, doi = {10.1111/mec.13878}, pmid = {27747959}, issn = {1365-294X}, mesh = {*Biodiversity ; Chlorophyta/classification ; Ciliophora/classification ; Diatoms/classification ; *Ecosystem ; Germany ; Italy ; *Lakes ; Romania ; Spain ; Transcriptome ; }, abstract = {Inferring ecosystem functioning and ecosystem services through inspections of the species inventory is a major aspect of ecological field studies. Ecosystem functions are often stable despite considerable species turnover. Using metatranscriptome analyses, we analyse a thus-far unparalleled freshwater data set which comprises 21 mainland European freshwater lakes from the Sierra Nevada (Spain) to the Carpathian Mountains (Romania) and from northern Germany to the Apennines (Italy) and covers an altitudinal range from 38 m above sea level (a.s.l) to 3110 m a.s.l. The dominant taxa were Chlorophyta and streptophytic algae, Ciliophora, Bacillariophyta and Chrysophyta. Metatranscriptomics provided insights into differences in community composition and into functional diversity via the relative share of taxa to the overall read abundance of distinct functional genes on the ecosystem level. The dominant metabolic pathways in terms of the fraction of expressed sequences in the cDNA libraries were affiliated with primary metabolism, specifically oxidative phosphorylation, photosynthesis and the TCA cycle. Our analyses indicate that community composition is a good first proxy for the analysis of ecosystem functions. However, differential gene regulation modifies the relative importance of taxa in distinct pathways. Whereas taxon composition varies considerably between lakes, the relative importance of distinct metabolic pathways is much more stable, indicating that ecosystem functioning is buffered against shifts in community composition through a functional redundancy of taxa.}, } @article {pmid27740737, year = {2017}, author = {Xu, Z and Yang, Y and Huang, B}, title = {A teaching approach from the exhaustive search method to the Needleman-Wunsch algorithm.}, journal = {Biochemistry and molecular biology education : a bimonthly publication of the International Union of Biochemistry and Molecular Biology}, volume = {45}, number = {3}, pages = {194-204}, doi = {10.1002/bmb.21027}, pmid = {27740737}, issn = {1539-3429}, mesh = {*Algorithms ; Computational Biology/*education ; Humans ; Sequence Alignment/*methods ; }, abstract = {The Needleman-Wunsch algorithm has become one of the core algorithms in bioinformatics; however, this programming requires more suitable explanations for students with different major backgrounds. In supposing sample sequences and using a simple store system, the connection between the exhaustive search method and the Needleman-Wunsch algorithm was analyzed to more thoroughly explain this algorithm. The present study could benefit the teaching and learning of the Needleman-Wunsch algorithm. © 2016 by The International Union of Biochemistry and Molecular Biology, 45(3):194-204, 2017.}, } @article {pmid27736016, year = {2017}, author = {Parobek, CM and Archer, FI and DePrenger-Levin, ME and Hoban, SM and Liggins, L and Strand, AE}, title = {skelesim: an extensible, general framework for population genetic simulation in R.}, journal = {Molecular ecology resources}, volume = {17}, number = {1}, pages = {101-109}, pmid = {27736016}, issn = {1755-0998}, support = {F30 AI109979/AI/NIAID NIH HHS/United States ; T32 GM007092/GM/NIGMS NIH HHS/United States ; T32 GM008719/GM/NIGMS NIH HHS/United States ; }, mesh = {Biostatistics ; Computational Biology/*methods ; *Computer Simulation ; Ecosystem ; Genetics, Population/*methods ; Software ; }, abstract = {Simulations are a key tool in molecular ecology for inference and forecasting, as well as for evaluating new methods. Due to growing computational power and a diversity of software with different capabilities, simulations are becoming increasingly powerful and useful. However, the widespread use of simulations by geneticists and ecologists is hindered by difficulties in understanding these softwares' complex capabilities, composing code and input files, a daunting bioinformatics barrier and a steep conceptual learning curve. skelesim (an R package) guides users in choosing appropriate simulations, setting parameters, calculating genetic summary statistics and organizing data output, in a reproducible pipeline within the R environment. skelesim is designed to be an extensible framework that can 'wrap' around any simulation software (inside or outside the R environment) and be extended to calculate and graph any genetic summary statistics. Currently, skelesim implements coalescent and forward-time models available in the fastsimcoal2 and rmetasim simulation engines to produce null distributions for multiple population genetic statistics and marker types, under a variety of demographic conditions. skelesim is intended to make simulations easier while still allowing full model complexity to ensure that simulations play a fundamental role in molecular ecology investigations. skelesim can also serve as a teaching tool: demonstrating the outcomes of stochastic population genetic processes; teaching general concepts of simulations; and providing an introduction to the R environment with a user-friendly graphical user interface (using shiny).}, } @article {pmid27734962, year = {2016}, author = {Tsai, KJ and Lu, MJ and Yang, KJ and Li, M and Teng, Y and Chen, S and Ku, MS and Li, WH}, title = {Assembling the Setaria italica L. Beauv. genome into nine chromosomes and insights into regions affecting growth and drought tolerance.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {35076}, pmid = {27734962}, issn = {2045-2322}, mesh = {Chromosome Mapping/methods ; Chromosomes, Plant/*genetics ; Droughts ; Gene Ontology ; Genome, Plant/*genetics ; Genomics/methods ; Molecular Sequence Annotation/methods ; Pennisetum/genetics ; Plant Proteins/genetics ; Sequence Analysis, DNA/methods ; Setaria Plant/*genetics ; }, abstract = {The diploid C4 plant foxtail millet (Setaria italica L. Beauv.) is an important crop in many parts of Africa and Asia for the vast consumption of its grain and ability to grow in harsh environments, but remains understudied in terms of complete genomic architecture. To date, there have been only two genome assembly and annotation efforts with neither assembly reaching over 86% of the estimated genome size. We have combined de novo assembly with custom reference-guided improvements on a popular cultivar of foxtail millet and have achieved a genome assembly of 477 Mbp in length, which represents over 97% of the estimated 490 Mbp. The assembly anchors over 98% of the predicted genes to the nine assembled nuclear chromosomes and contains more functional annotation gene models than previous assemblies. Our annotation has identified a large number of unique gene ontology terms related to metabolic activities, a region of chromosome 9 with several growth factor proteins, and regions syntenic with pearl millet or maize genomic regions that have been previously shown to affect growth. The new assembly and annotation for this important species can be used for detailed investigation and future innovations in growth for millet and other grains.}, } @article {pmid27729382, year = {2016}, author = {Chou, HH and Chiou, MJ and Liang, FW and Chen, LH and Lu, TH and Li, CY}, title = {Association of maternal chronic disease with risk of congenital heart disease in offspring.}, journal = {CMAJ : Canadian Medical Association journal = journal de l'Association medicale canadienne}, volume = {188}, number = {17-18}, pages = {E438-E446}, pmid = {27729382}, issn = {1488-2329}, mesh = {Adult ; Anemia/*epidemiology ; Chronic Disease ; Cohort Studies ; Connective Tissue Diseases/*epidemiology ; Databases, Factual ; Diabetes Mellitus, Type 1/epidemiology ; Diabetes Mellitus, Type 2/epidemiology ; Epilepsy/*epidemiology ; Female ; Heart Defects, Congenital/*epidemiology ; Humans ; Hypertension/*epidemiology ; Infant, Newborn ; Logistic Models ; Mood Disorders/*epidemiology ; Multivariate Analysis ; Odds Ratio ; Pregnancy ; Pregnancy Complications/*epidemiology ; Pregnancy Complications, Cardiovascular/epidemiology ; Pregnancy Complications, Hematologic/epidemiology ; Pregnancy in Diabetics/*epidemiology ; Prevalence ; Risk Factors ; Taiwan/epidemiology ; }, abstract = {BACKGROUND: Information about known risk factors for congenital heart disease is scarce. In this population-based study, we aimed to investigate the relation between maternal chronic disease and congenital heart disease in offspring.

METHODS: The study cohort consisted of 1 387 650 live births from 2004 to 2010. We identified chronic disease in mothers and mild and severe forms of congenital heart disease in their offspring from Taiwan's National Health Insurance medical claims. We used multivariable logistic regression analysis to assess the associations of all cases and specific types of congenital heart disease with various maternal chronic diseases.

RESULTS: For mothers with the following chronic diseases, the overall prevalence of congenital heart disease in their children was significantly higher than for mothers without these diseases: diabetes mellitus type 1 (adjusted odds ratio [OR] 2.32, 95% confidence interval [CI] 1.66-3.25), diabetes mellitus type 2 (adjusted OR 2.85, 95% CI 2.60-3.12), hypertension (adjusted OR 1.87, 95% CI 1.69-2.07), congenital heart defects (adjusted OR 3.05, 95% CI 2.45-3.80), anemia (adjusted OR 1.31, 95% CI 1.25-1.38), connective tissue disorders (adjusted OR 1.39, 95% CI 1.19-1.62), epilepsy (adjusted OR 1.37, 95% CI 1.08-1.74) and mood disorders (adjusted OR 1.25, 95% CI 1.11-1.41). The same pattern held for mild forms of congenital heart disease. A higher prevalence of severe congenital heart disease was seen only among offspring of mothers with congenital heart defects or type 2 diabetes.

INTERPRETATION: The children of women with several kinds of chronic disease appear to be at risk for congenital heart disease. Preconception counselling and optimum treatment of pregnant women with chronic disease would seem prudent.}, } @article {pmid27729074, year = {2016}, author = {Ulicsni, V and Svanberg, I and Molnár, Z}, title = {Folk knowledge of invertebrates in Central Europe - folk taxonomy, nomenclature, medicinal and other uses, folklore, and nature conservation.}, journal = {Journal of ethnobiology and ethnomedicine}, volume = {12}, number = {1}, pages = {47}, pmid = {27729074}, issn = {1746-4269}, mesh = {Animals ; *Conservation of Natural Resources ; Europe ; *Folklore ; Humans ; Invertebrates ; *Knowledge ; *Medicine, Traditional ; Terminology as Topic ; }, abstract = {BACKGROUND: There is scarce information about European folk knowledge of wild invertebrate fauna. We have documented such folk knowledge in three regions, in Romania, Slovakia and Croatia. We provide a list of folk taxa, and discuss folk biological classification and nomenclature, salient features, uses, related proverbs and sayings, and conservation.

METHODS: We collected data among Hungarian-speaking people practising small-scale, traditional agriculture. We studied "all" invertebrate species (species groups) potentially occurring in the vicinity of the settlements. We used photos, held semi-structured interviews, and conducted picture sorting.

RESULTS: We documented 208 invertebrate folk taxa. Many species were known which have, to our knowledge, no economic significance. 36 % of the species were known to at least half of the informants. Knowledge reliability was high, although informants were sometimes prone to exaggeration. 93 % of folk taxa had their own individual names, and 90 % of the taxa were embedded in the folk taxonomy. Twenty four species were of direct use to humans (4 medicinal, 5 consumed, 11 as bait, 2 as playthings). Completely new was the discovery that the honey stomachs of black-coloured carpenter bees (Xylocopa violacea, X. valga) were consumed. 30 taxa were associated with a proverb or used for weather forecasting, or predicting harvests. Conscious ideas about conserving invertebrates only occurred with a few taxa, but informants would generally refrain from harming firebugs (Pyrrhocoris apterus), field crickets (Gryllus campestris) and most butterflies. We did not find any mythical creatures among invertebrate folk taxa. Almost every invertebrate species was regarded as basically harmful. Where possible, they were destroyed or at least regarded as worth eradicating. However, we could find no evidence to suggest any invertebrate species had suffered population loss as a result of conscious destruction. Sometimes knowledge pertaining to the taxa could have more general relevance, and be regarded as folk wisdom concerning the functioning of nature as a whole.

CONCLUSIONS: The high number of known invertebrate folk taxa suggests that it would be worth conducting further investigations in other areas of Europe.}, } @article {pmid27725734, year = {2016}, author = {Friedemann, G and Leshem, Y and Kerem, L and Shacham, B and Bar-Massada, A and McClain, KM and Bohrer, G and Izhaki, I}, title = {Multidimensional differentiation in foraging resource use during breeding of two sympatric top predators.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {35031}, pmid = {27725734}, issn = {2045-2322}, mesh = {Animals ; Breeding ; Eagles/*physiology ; Ecology ; Feeding Behavior ; Geographic Information Systems ; Hawks/*physiology ; Predatory Behavior ; Species Specificity ; Sympatry ; }, abstract = {Ecologically-similar species were found to develop specific strategies to partition their resources, leading to niche differentiation and divergence, in order to avoid interspecific competition. Our study determines multi-dimensional differentiation of two sympatric top-predators, long-legged buzzards (LLB) and short-toed eagles (STE), which recently became sympatric during their breeding season in the Judean Foothills, Israel. By combining information from comprehensive diet and movement analyses we found four dimensions of differentiation: (1) Geographic foraging area: LLB tended to forage relatively close to their nests (2.35 ± 0.62 km), while STE forage far from their nest (13.03 ± 2.20 km); (2) Foraging-habitat type: LLBs forage at low natural vegetation, avoiding cultivated fields, whereas STEs forage in cultivated fields, avoiding low natural vegetation; (3) Diurnal dynamics of foraging: LLBs are uniformly active during daytime, whereas STEs activity peaks in the early afternoon; and (4) Food-niche: while both species largely rely on reptiles (47.8% and 76.3% for LLB and STE, respectively), LLB had a more diverse diet and consumed significantly higher percentages of lizards, while STE consumed significantly higher percentages of snakes. Our results suggest that this multidimensional differentiation allows the spatial coexistence of these two dense populations in the study area.}, } @article {pmid27725348, year = {2016}, author = {Ikegami, K and Nozawa, H and Michii, S and Sugano, R and Ando, H and Hasegawa, M and Kitamura, H and Ogami, A}, title = {[Investigation of the working behavior of part-time occupational physicians using practical recording sheets].}, journal = {Sangyo eiseigaku zasshi = Journal of occupational health}, volume = {58}, number = {6}, pages = {251-259}, doi = {10.1539/sangyoeisei.E15004}, pmid = {27725348}, issn = {1349-533X}, mesh = {Behavior ; Databases as Topic ; Humans ; Industry/statistics & numerical data ; *Occupational Health Physicians ; Occupational Health Services/*statistics & numerical data ; *Personnel Staffing and Scheduling ; Work/*statistics & numerical data ; Workforce ; }, abstract = {OBJECTIVES: We investigated the working behavior of part-time occupational physicians using practical recording sheets to clarify issues of occupational physicians' activities according to industrial groups or size of business.

METHODS: We collected 561 recording sheets in 96 industries from 11 part-time occupational physicians as collaborators, who volunteered to be a part of this research. We collected a variety of information from the practical recording sheets, including the industry in which each occupational physician was employed, the annual number of times of work attendance, occupational physician-conducted workplace patrol, and employee health management. We investigated their annual practices regarding work environment management, work management, health management, and general occupational health management. In addition, we analyzed the differences between the secondary and tertiary industry groups and between the group of offices employing 100 people or fewer (≤100 group) and 101 people and above (≥101 group) in each industry group.

RESULTS: The median work attendance by all occupational physicians was four times a year; the tertiary industry group had a significantly lower rate of work attendance than the secondary industry group. The occupational physicians' participation in risk assessment, mental health measures or overwork prevention, and the formulation of the occupational health management system and the annual plan were significantly lower in the tertiary industry group than in the secondary industry group. We observed that for the annual number of times of work attendance, occupational physician-conducted workplace patrol was significantly lower in the ≤100 group than in the ≥101 group in each industry group.

CONCLUSIONS: These findings show that occupational physicians' activities have not been conducted enough in tertiary industries and small-sized offices employing ≤100 people. It would be necessary to evaluate how to provide occupational health service or appropriate occupational physicians' activities for small-sized offices or tertiary industries. Thereafter, it would likely be beneficial to construct a system to support the activities of part-time occupational physicians as well as the activity of occupational health at workplaces.}, } @article {pmid27723830, year = {2016}, author = {Tahden, M and Manitz, J and Baumgardt, K and Fell, G and Kneib, T and Hegasy, G}, title = {Epidemiological and Ecological Characterization of the EHEC O104:H4 Outbreak in Hamburg, Germany, 2011.}, journal = {PloS one}, volume = {11}, number = {10}, pages = {e0164508}, pmid = {27723830}, issn = {1932-6203}, mesh = {Adolescent ; Adult ; Age Factors ; Aged ; Aged, 80 and over ; Child ; Child, Preschool ; Disease Outbreaks ; Escherichia coli Infections/*epidemiology ; *Escherichia coli O104 ; Female ; Germany/epidemiology ; Hemolytic-Uremic Syndrome/*epidemiology ; Humans ; Infant ; Infant, Newborn ; Male ; Middle Aged ; *Models, Biological ; Sex Factors ; Socioeconomic Factors ; *Software ; }, abstract = {In 2011, a large outbreak of entero-hemorrhagic E. coli (EHEC) and hemolytic uremic syndrome (HUS) occurred in Germany. The City of Hamburg was the first focus of the epidemic and had the highest incidences among all 16 Federal States of Germany. In this article, we present epidemiological characteristics of the Hamburg notification data. Evaluating the epicurves retrospectively, we found that the first epidemiological signal of the outbreak, which was in form of a HUS case cluster, was received by local health authorities when already 99 EHEC and 48 HUS patients had experienced their first symptoms. However, only two EHEC and seven HUS patients had been notified. Middle-aged women had the highest risk for contracting the infection in Hamburg. Furthermore, we studied timeliness of case notification in the course of the outbreak. To analyze the spatial distribution of EHEC/HUS incidences in 100 districts of Hamburg, we mapped cases' residential addresses using geographic information software. We then conducted an ecological study in order to find a statistical model identifying associations between local socio-economic factors and EHEC/HUS incidences in the epidemic. We employed a Bayesian Poisson model with covariates characterizing the Hamburg districts as well as incorporating structured and unstructured spatial effects. The Deviance Information Criterion was used for stepwise variable selection. We applied different modeling approaches by using primary data, transformed data, and preselected subsets of transformed data in order to identify socio-economic factors characterizing districts where EHEC/HUS outbreak cases had their residence.}, } @article {pmid27720470, year = {2017}, author = {Hailei, W and Ping, L and Ying, W and Lei, L and Jianming, Y}, title = {Metagenomic insight into the bioaugmentation mechanism of Phanerochaete chrysosporium in an activated sludge system treating coking wastewater.}, journal = {Journal of hazardous materials}, volume = {321}, number = {}, pages = {820-829}, doi = {10.1016/j.jhazmat.2016.09.072}, pmid = {27720470}, issn = {1873-3336}, mesh = {Bacteria/metabolism ; Biological Oxygen Demand Analysis ; Biomass ; Bioreactors/microbiology ; Coke/*analysis ; Computational Biology ; Kinetics ; Metagenomics ; Phanerochaete/*genetics/*metabolism ; Phenols/chemistry ; Proteobacteria/metabolism ; Sewage/*analysis ; Wastewater/*analysis ; Water Microbiology ; }, abstract = {Phanerochaete chrysosporium was seeded to a sequencing batch reactor treating phenol wastewater. Compared to the contrast reactor (R1), the bioaugmented reactor (R2) exhibits better performance in sludge settling ability, as well as biomass and phenol removal, even though the added fungus is not persistently surviving in the reactor. Bioaugmentation improved bacterial population, growing up to 10,000 times higher than that of eukaryotes. Metagenomic sequencing results show the bioaugmentation finally increases bacterial and eukaryotic richness, but reduces their community diversity. In contrast to R1, bacterial distribution in R2 is more concentrated in Proteobacteria. The relative abundances of filamentous fungi, yeast and microalgae in R2 are all higher than those in R1 at different treatment phases, and two reactors are finally dominated by different protozoan and metazoan. In conclusion, P. chrysosporium improves reactor performances by influencing microbial community structure, and this phenomenon might be attributed to the ecological competition in sludge and toxicity reduction of phenol wastewater. The novelty of this study emphasizes why a species which is not persistently active in bioreactor still plays a crucial role in enhancing reactor performance. Results obtained here impact the conventional criteria for selection of bioaugmentation microbes used in activated sludge systems.}, } @article {pmid27716053, year = {2016}, author = {Peterson, BF and Scharf, ME}, title = {Metatranscriptome analysis reveals bacterial symbiont contributions to lower termite physiology and potential immune functions.}, journal = {BMC genomics}, volume = {17}, number = {1}, pages = {772}, pmid = {27716053}, issn = {1471-2164}, mesh = {Amidohydrolases/genetics/metabolism ; Animals ; Antibiosis ; Bacteria/*genetics ; Computational Biology/methods ; Fungi/physiology ; Gene Expression Profiling ; Genes, rRNA ; Glutathione Transferase/metabolism ; Isoptera/*immunology/metabolism/*microbiology ; *Metagenome ; *Metagenomics/methods ; Oxidative Stress ; Reactive Oxygen Species/metabolism ; Reproducibility of Results ; *Symbiosis ; *Transcriptome ; }, abstract = {BACKGROUND: Symbioses throughout the animal kingdom are known to extend physiological and ecological capabilities to hosts. Insect-microbe associations are extremely common and are often related to novel niche exploitation, fitness advantages, and even speciation events. These phenomena include expansions in host diet, detoxification of insecticides and toxins, and increased defense against pathogens. However, dissecting the contributions of individual groups of symbionts at the molecular level is often underexplored due to methodological and analytical limitations. Termites are one of the best studied systems for physiological collaborations between host and symbiota; however, most work in lower termites (those with bacterial and protist symbionts) focuses on the eukaryotic members of this symbiotic consortium. Here we present a metatranscriptomic analysis which provides novel insights into bacterial contributions to the holobiont of the eastern subterranean termite, Reticulitermes flavipes, in the presence and absence of a fungal pathogen.

RESULTS: Using a customized ribodepletion strategy, a metatranscriptome assembly was obtained representing the host termite as well as bacterial and protist symbiota. Sequence data provide new insights into biosynthesis, catabolism, and transport of major organic molecules and ions by the gut consortium, and corroborate previous findings suggesting that bacteria play direct roles in nitrogen fixation, amino acid biosynthesis, and lignocellulose digestion. With regard to fungal pathogen challenge, a total of 563 differentially expressed candidate host and symbiont contigs were identified (162 up- and 401 downregulated; α/FDR = 0.05) including an upregulated bacterial amidohydrolase.

CONCLUSIONS: This study presents the most complete bacterial metatranscriptome from a lower termite and provides a framework on which to build a more complete model of termite-symbiont interactions including, but not limited to, digestion and pathogen defense.}, } @article {pmid27716042, year = {2016}, author = {Hess, M and Wildhagen, H and Junker, LV and Ensminger, I}, title = {Erratum to: Transcriptome responses to temperature, water availability and photoperiod are conserved among mature trees of two divergent Douglas-fir provenances from a coastal and an interior habitat.}, journal = {BMC genomics}, volume = {17}, number = {1}, pages = {780}, pmid = {27716042}, issn = {1471-2164}, } @article {pmid27709843, year = {2016}, author = {Kim, YS and Choi, YJ}, title = {The Ecology of Medical Care in Korea.}, journal = {Journal of Korean medical science}, volume = {31}, number = {11}, pages = {1684-1688}, pmid = {27709843}, issn = {1598-6357}, mesh = {Adolescent ; Adult ; Aged ; Ambulatory Care ; Databases, Factual ; Delivery of Health Care/*statistics & numerical data ; Emergency Service, Hospital ; Female ; Health Services Research ; Hospitalization ; Humans ; Male ; Middle Aged ; Republic of Korea ; Young Adult ; }, abstract = {This study aimed to describe the ecology of medical care in Korea. Using the yearly data of 2012 derived from the Korea Health Panel, we estimated the numbers of people per 1,000 residents aged 18 and over who had any health problem and/or any medical care at a variety of care settings, such as clinics, hospitals, and tertiary hospitals, in an average month. There was a total of 11,518 persons in the study population. While the number of those who had any health problem in an average month was estimated to be 939 per 1,000 persons, the estimated numbers of ambulatory care users were 333 at clinics, 101 at hospital outpatient departments, 35 at tertiary hospital outpatient departments, and 38 for Korean Oriental medical providers. The number of people who used emergency care at least once was 7 per 1,000 persons in an average month. The numbers of people hospitalized in clinics and hospitals were 3 and 8, respectively, while 3 persons were admitted to tertiary hospitals. There was a gap between the number of people experiencing any health problem and that of those having any medical care, and primary care comprised a large share of people's medical care experiences. It was noteworthy that more patients received ambulatory care at tertiary hospitals in Korea than in other countries. We hope that discussion about care delivery system reform and further studies will be encouraged.}, } @article {pmid27709807, year = {2017}, author = {De Filippis, F and Parente, E and Ercolini, D}, title = {Metagenomics insights into food fermentations.}, journal = {Microbial biotechnology}, volume = {10}, number = {1}, pages = {91-102}, pmid = {27709807}, issn = {1751-7915}, mesh = {Computational Biology ; *Fermentation ; *Food Microbiology ; Gene Expression Profiling ; High-Throughput Nucleotide Sequencing ; *Metagenomics ; *Microbial Consortia ; }, abstract = {This review describes the recent advances in the study of food microbial ecology, with a focus on food fermentations. High-throughput sequencing (HTS) technologies have been widely applied to the study of food microbial consortia and the different applications of HTS technologies were exploited in order to monitor microbial dynamics in food fermentative processes. Phylobiomics was the most explored application in the past decade. Metagenomics and metatranscriptomics, although still underexploited, promise to uncover the functionality of complex microbial consortia. The new knowledge acquired will help to understand how to make a profitable use of microbial genetic resources and modulate key activities of beneficial microbes in order to ensure process efficiency, product quality and safety.}, } @article {pmid27708022, year = {2016}, author = {Greenville, AC and Emery, NJ}, title = {Gathering lots of data on a small budget.}, journal = {Science (New York, N.Y.)}, volume = {353}, number = {6306}, pages = {1360-1361}, doi = {10.1126/science.aag3057}, pmid = {27708022}, issn = {1095-9203}, mesh = {Animals ; Budgets ; Data Collection/economics/*instrumentation ; Environmental Monitoring/economics/*instrumentation ; Geographic Information Systems/*instrumentation ; Microcomputers/*economics ; Remote Sensing Technology/economics/*instrumentation ; Software ; }, } @article {pmid27706173, year = {2016}, author = {Harris, LW and Davies, TJ}, title = {A Complete Fossil-Calibrated Phylogeny of Seed Plant Families as a Tool for Comparative Analyses: Testing the 'Time for Speciation' Hypothesis.}, journal = {PloS one}, volume = {11}, number = {10}, pages = {e0162907}, pmid = {27706173}, issn = {1932-6203}, mesh = {Bayes Theorem ; Biological Evolution ; DNA, Plant/chemistry/metabolism ; Databases, Genetic ; *Fossils ; Linear Models ; Models, Theoretical ; Phylogeny ; Plants/*classification/genetics ; Seeds/genetics ; }, abstract = {Explaining the uneven distribution of species richness across the branches of the tree of life has been a major challenge for evolutionary biologists. Advances in phylogenetic reconstruction, allowing the generation of large, well-sampled, phylogenetic trees have provided an opportunity to contrast competing hypotheses. Here, we present a new time-calibrated phylogeny of seed plant families using Bayesian methods and 26 fossil calibrations. While there are various published phylogenetic trees for plants which have a greater density of species sampling, we are still a long way from generating a complete phylogeny for all ~300,000+ plants. Our phylogeny samples all seed plant families and is a useful tool for comparative analyses. We use this new phylogenetic hypothesis to contrast two alternative explanations for differences in species richness among higher taxa: time for speciation versus ecological limits. We calculated net diversification rate for each clade in the phylogeny and assessed the relationship between clade age and species richness. We then fit models of speciation and extinction to individual branches in the tree to identify major rate-shifts. Our data suggest that the majority of lineages are diversifying very slowly while a few lineages, distributed throughout the tree, are diversifying rapidly. Diversification is unrelated to clade age, no matter the age range of the clades being examined, contrary to both the assumption of an unbounded lineage increase through time, and the paradigm of fixed ecological limits. These findings are consistent with the idea that ecology plays a role in diversification, but rather than imposing a fixed limit, it may have variable effects on per lineage diversification rates through time.}, } @article {pmid27702488, year = {2016}, author = {Adesioye, FA and Makhalanyane, TP and Biely, P and Cowan, DA}, title = {Phylogeny, classification and metagenomic bioprospecting of microbial acetyl xylan esterases.}, journal = {Enzyme and microbial technology}, volume = {93-94}, number = {}, pages = {79-91}, doi = {10.1016/j.enzmictec.2016.07.001}, pmid = {27702488}, issn = {1879-0909}, mesh = {Acetylesterase/*classification/*genetics/metabolism ; Bioprospecting ; Data Mining ; Databases, Protein ; Extremophiles/enzymology/genetics ; Lignin/chemistry/metabolism ; Metagenomics ; Phylogeny ; Substrate Specificity ; Xylans/chemistry/metabolism ; }, abstract = {Acetyl xylan esterases (AcXEs), also termed xylan deacetylases, are broad specificity Carbohydrate-Active Enzymes (CAZymes) that hydrolyse ester bonds to liberate acetic acid from acetylated hemicellulose (typically polymeric xylan and xylooligosaccharides). They belong to eight families within the Carbohydrate Esterase (CE) class of the CAZy database. AcXE classification is largely based on sequence-dependent phylogenetic relationships, supported in some instances with substrate specificity data. However, some sequence-based predictions of AcXE-encoding gene identity have proved to be functionally incorrect. Such ambiguities can lead to mis-assignment of genes and enzymes during sequence data-mining, reinforcing the necessity for the experimental confirmation of the functional properties of putative AcXE-encoding gene products. Although one-third of all characterized CEs within CAZy families 1-7 and 16 are AcXEs, there is a need to expand the sequence database in order to strengthen the link between AcXE gene sequence and specificity. Currently, most AcXEs are derived from a limited range of (mostly microbial) sources and have been identified via culture-based bioprospecting methods, restricting current knowledge of AcXEs to data from relatively few microbial species. More recently, the successful identification of AcXEs via genome and metagenome mining has emphasised the huge potential of culture-independent bioprospecting strategies. We note, however, that the functional metagenomics approach is still hampered by screening bottlenecks. The most relevant recent reviews of AcXEs have focused primarily on the biochemical and functional properties of these enzymes. In this review, we focus on AcXE phylogeny, classification and the future of metagenomic bioprospecting for novel AcXEs.}, } @article {pmid27702481, year = {2016}, author = {Tan, Z and Ma, H and Li, Q and Pu, L and Cao, Y and Qu, X and Zhu, C and Ying, H}, title = {Biosynthesis of optically pure chiral alcohols by a substrate coupled and biphasic system with a short-chain dehydrogenase from Streptomyces griseus.}, journal = {Enzyme and microbial technology}, volume = {93-94}, number = {}, pages = {191-199}, doi = {10.1016/j.enzmictec.2016.08.015}, pmid = {27702481}, issn = {1879-0909}, mesh = {Alcohol Oxidoreductases/chemistry/genetics/*metabolism ; Alcohols/chemistry/*metabolism ; Amino Acid Sequence ; Bacterial Proteins/chemistry/genetics/*metabolism ; Biocatalysis ; Data Mining ; Enzyme Stability ; Genome, Bacterial ; Kinetics ; Recombinant Proteins/chemistry/genetics/metabolism ; Sequence Homology, Amino Acid ; Stereoisomerism ; Streptomyces griseus/*enzymology/genetics ; Substrate Specificity ; }, abstract = {The increasing demand for biocatalysts in synthesizing enantiomerically pure chiral alcohols results from the outstanding characteristics of enzymes in reaction, economic, ecological issues. Many carbonyl reductases for producing chiral alcohols have been reported but there is still a lack of good catalytic efficacies. Herein, five carbonyl reductases from different Streptomyces were discovered by the strategy of genome mining. These reductases were overexpressed, and we chose SgCR for further study as it owned better enzyme activity. This protein was purified to apparent homogeneity, and its amino acid sequence was analyzed in comparison with that of the reported SDRs. The biocatalytic properties of SgCR were investigated, and this enzyme was confirmed to have the ability to convert various prochiral ketones into highly optically active alcohols. SgCR exhibited the highest activity towards ethyl 4-chloro-3-oxobutanoate (COBE) and the corresponding product ethyl (S)-4-chloro-3-hydroxybutanoate ((S)-CHBE) was obtained with high yield and excellent e.e. value by optimizing the biphasic system. Eventually, using isopropanol as the co-substrate for NADH recycling in the substrate-coupled reaction, the yield and enantioselectivity of (S)-CHBE were obtained at the values of 90% and 99%, respectively. These results indicate that SgCR is a promising boicatalyst for the synthesis of chiral alcohols in industry.}, } @article {pmid27699597, year = {2017}, author = {Hatsu, I and Hade, E and Campa, A}, title = {Food Security Status is Related to Mental Health Quality of Life Among Persons Living with HIV.}, journal = {AIDS and behavior}, volume = {21}, number = {3}, pages = {745-753}, pmid = {27699597}, issn = {1573-3254}, support = {R01 DA023405/DA/NIDA NIH HHS/United States ; U01 DA040381/DA/NIDA NIH HHS/United States ; U01 MD017423/MD/NIMHD NIH HHS/United States ; UL1 TR001070/TR/NCATS NIH HHS/United States ; }, mesh = {Adult ; Aged ; CD4 Lymphocyte Count ; Cost of Illness ; Cross-Sectional Studies ; Female ; Food Assistance ; Food Supply/*statistics & numerical data ; HIV Infections/*epidemiology/*psychology ; Humans ; Male ; Middle Aged ; Quality of Life/*psychology ; Socioeconomic Factors ; Surveys and Questionnaires ; Young Adult ; }, abstract = {This study evaluated the association between health related quality of life and food security among persons living with HIV (PLHIV). We studied 167 PLHIV who completed questionnaires assessing food security, disease symptomatology, and several domains of the SF-36 health related quality of life survey. HIV disease state was assessed from medical records. Associations between independent and outcome variables were determined through linear regression models. Compared to food security, very low food security was significantly associated with lower mental component summary scores, [average difference -4.98 (95 % CI -9.85, -0.10)]; mental health, [average difference -5.44 (95 % CI -10.08, -0.81)]; and general health, [average difference -5.13 (95 % CI -9.65, -0.65)] after adjusting for covariates. About a fourth of participants experienced severe food insecurity, which negatively influenced their mental health and general wellbeing. The inclusion of resources for food assistance in HIV treatment programs may help ameliorate mental health challenges faced by PLHIV.}, } @article {pmid27698620, year = {2016}, author = {Bik, EM}, title = {The Hoops, Hopes, and Hypes of Human Microbiome Research.}, journal = {The Yale journal of biology and medicine}, volume = {89}, number = {3}, pages = {363-373}, pmid = {27698620}, issn = {1551-4056}, mesh = {Autistic Disorder/genetics ; Computational Biology/methods ; Humans ; Inflammatory Bowel Diseases/genetics ; Microbiota/*genetics ; }, abstract = {Recent developments in sequencing methods and bioinformatics analysis tools have greatly enabled the culture-independent analysis of complex microbial communities associated with environmental samples, plants, and animals. This has led to a spectacular increase in the number of studies on both membership and functionalities of these hitherto invisible worlds, in particular those of the human microbiome. The wide variety in available microbiome tools and platforms can be overwhelming, and making sound conclusions from scientific research can be challenging. Here, I will review 1) the methodological and analytic hoops a good microbiome study has to jump through, including DNA extraction and choice of bioinformatics tools, 2) the hopes this field has generated for diseases such as autism and inflammatory bowel diseases, and 3) some of the hypes that it has created, e.g., by confusing correlation and causation, and the recent pseudoscientific commercialization of microbiome research.}, } @article {pmid27698612, year = {2016}, author = {Smith, BC and Zolnik, CP and Usyk, M and Chen, Z and Kaiser, K and Nucci-Sack, A and Peake, K and Diaz, A and Viswanathan, S and Strickler, HD and Schlecht, NF and Burk, RD}, title = {Distinct Ecological Niche of Anal, Oral, and Cervical Mucosal Microbiomes in Adolescent Women.}, journal = {The Yale journal of biology and medicine}, volume = {89}, number = {3}, pages = {277-284}, pmid = {27698612}, issn = {1551-4056}, support = {K12 GM102779/GM/NIGMS NIH HHS/United States ; R01 AI072204/AI/NIAID NIH HHS/United States ; }, mesh = {Adolescent ; Adult ; Anal Canal/*microbiology ; Cervix Mucus/*microbiology ; Child ; Computational Biology ; Female ; Humans ; Microbiota/physiology ; Mouth/*microbiology ; Sequence Analysis, DNA ; Young Adult ; }, abstract = {Human body sites represent ecological niches for microorganisms, each providing variations in microbial exposure, nutrient availability, microbial competition, and host immunological responses. In this study, we investigated the oral, anal, and cervical microbiomes from the same 20 sexually active adolescent females, using culture-independent, next-generation sequencing. DNA from each sample was amplified for the bacterial 16S rRNA gene and sequenced on an Illumina platform using paired-end reads. Across the three anatomical niches, we found significant differences in bacterial community composition and diversity. Overall anal samples were dominated with Prevotella and Bacteriodes, oral samples with Streptococcus and Prevotella, and cervical samples with Lactobacillus. The microbiomes of a few cervical samples clustered with anal samples in weighted principal coordinate analyses, due in part to a higher proportion of Prevotella in those samples. Additionally, cervical samples had the lowest alpha diversity. Our results demonstrate the occurrence of distinct microbial communities across body sites within the same individual.}, } @article {pmid27695919, year = {2016}, author = {Lötsch, J and Ultsch, A}, title = {A machine-learned computational functional genomics-based approach to drug classification.}, journal = {European journal of clinical pharmacology}, volume = {72}, number = {12}, pages = {1449-1461}, pmid = {27695919}, issn = {1432-1041}, mesh = {Analgesics/*classification ; Databases, Factual ; Drug Discovery ; Gene Ontology ; *Genomics ; Humans ; Machine Learning ; Pharmaceutical Preparations/*classification ; }, abstract = {OBJECTIVE: The public accessibility of "big data" about the molecular targets of drugs and the biological functions of genes allows novel data science-based approaches to pharmacology that link drugs directly with their effects on pathophysiologic processes. This provides a phenotypic path to drug discovery and repurposing. This paper compares the performance of a functional genomics-based criterion to the traditional drug target-based classification.

METHODS: Knowledge discovery in the DrugBank and Gene Ontology databases allowed the construction of a "drug target versus biological process" matrix as a combination of "drug versus genes" and "genes versus biological processes" matrices. As a canonical example, such matrices were constructed for classical analgesic drugs. These matrices were projected onto a toroid grid of 50 × 82 artificial neurons using a self-organizing map (SOM). The distance, respectively, cluster structure of the high-dimensional feature space of the matrices was visualized on top of this SOM using a U-matrix.

RESULTS: The cluster structure emerging on the U-matrix provided a correct classification of the analgesics into two main classes of opioid and non-opioid analgesics. The classification was flawless with both the functional genomics and the traditional target-based criterion. The functional genomics approach inherently included the drugs' modulatory effects on biological processes. The main pharmacological actions known from pharmacological science were captures, e.g., actions on lipid signaling for non-opioid analgesics that comprised many NSAIDs and actions on neuronal signal transmission for opioid analgesics.

CONCLUSIONS: Using machine-learned techniques for computational drug classification in a comparative assessment, a functional genomics-based criterion was found to be similarly suitable for drug classification as the traditional target-based criterion. This supports a utility of functional genomics-based approaches to computational system pharmacology for drug discovery and repurposing.}, } @article {pmid27694967, year = {2016}, author = {Zhou, X and Zhao, M and Zhou, L and Yang, G and Huang, L and Yan, C and Huang, Q and Ye, L and Zhang, X and Guo, L and Ke, X and Guo, J}, title = {Regionalization of Habitat Suitability of Masson's Pine based on geographic information system and Fuzzy Matter-Element Model.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {34716}, pmid = {27694967}, issn = {2045-2322}, mesh = {China ; Ecology ; *Ecosystem ; Fuzzy Logic ; *Geographic Information Systems ; Geography ; *Models, Theoretical ; Pinus/*growth & development ; }, abstract = {Pine needles have been widely used in the development of anti-hypertensive and anti-hyperlipidemic agents and health food. However, the widespread distribution of this tree poses great obstacles to the quality control and efficacy evaluation. To facilitate the effective and rational exploitation of Masson's pine (Pinus massoniana Lamb), as well as ensure effective development of Masson's pine needles as a medicinal agent, we investigated the spatial distribution of habitat suitability and evaluated the optimal ranges of ecological factors of P. massoniana with 280 samples collected from 12 provinces in China through the evaluation of four constituents known to be effective medicinally. The results of habitat suitability evaluation were also verified by Root Mean Square Error (RMSE). Finally, five ecological factors were chosen in the establishment of a habitat suitability evaluation system. The most suitable areas for P. massoniana growth were mainly concentrated in the middle and lower reaches of the Yangtze River basin, such as Sichuan, Guizhou, and Jiangxi provinces, while the best quality needles were from Guizhou, Sichuan, and the junction area of Chongqing, Hunan, and Hubei provinces. This information revealed that suitable areas for effective constituent accumulation of Masson's pine needles accounted for only 7.41% of its distribution area.}, } @article {pmid27694115, year = {2016}, author = {Lind, AL and Smith, TD and Saterlee, T and Calvo, AM and Rokas, A}, title = {Regulation of Secondary Metabolism by the Velvet Complex Is Temperature-Responsive in Aspergillus.}, journal = {G3 (Bethesda, Md.)}, volume = {6}, number = {12}, pages = {4023-4033}, pmid = {27694115}, issn = {2160-1836}, support = {T15 LM007450/LM/NLM NIH HHS/United States ; }, mesh = {Aspergillus/*genetics/*metabolism ; Cluster Analysis ; Fungal Proteins/genetics/metabolism ; Gene Expression Profiling ; *Gene Expression Regulation, Fungal ; Multigene Family ; *Secondary Metabolism ; *Temperature ; }, abstract = {Sensing and responding to environmental cues is critical to the lifestyle of filamentous fungi. How environmental variation influences fungi to produce a wide diversity of ecologically important secondary metabolites (SMs) is not well understood. To address this question, we first examined changes in global gene expression of the opportunistic human pathogen, Aspergillus fumigatus, after exposure to different temperature conditions. We found that 11 of the 37 SM gene clusters in A. fumigatus were expressed at higher levels at 30° than at 37°. We next investigated the role of the light-responsive Velvet complex in environment-dependent gene expression by examining temperature-dependent transcription profiles in the absence of two key members of the Velvet protein complex, VeA and LaeA We found that the 11 temperature-regulated SM gene clusters required VeA at 37° and LaeA at both 30 and 37° for wild-type levels of expression. Interestingly, four SM gene clusters were regulated by VeA at 37° but not at 30°, and two additional ones were regulated by VeA at both temperatures but were substantially less so at 30°, indicating that the role of VeA and, more generally of the Velvet complex, in the regulation of certain SM gene clusters is temperature-dependent. Our findings support the hypothesis that fungal secondary metabolism is regulated by an intertwined network of transcriptional regulators responsive to multiple environmental factors.}, } @article {pmid27693307, year = {2016}, author = {Maldonado-Gómez, MX and Martínez, I and Bottacini, F and O'Callaghan, A and Ventura, M and van Sinderen, D and Hillmann, B and Vangay, P and Knights, D and Hutkins, RW and Walter, J}, title = {Stable Engraftment of Bifidobacterium longum AH1206 in the Human Gut Depends on Individualized Features of the Resident Microbiome.}, journal = {Cell host & microbe}, volume = {20}, number = {4}, pages = {515-526}, doi = {10.1016/j.chom.2016.09.001}, pmid = {27693307}, issn = {1934-6069}, mesh = {Administration, Oral ; Bifidobacterium longum/*growth & development ; *Carrier State ; *Gastrointestinal Microbiome ; Humans ; *Microbiota ; Probiotics/*administration & dosage ; Time Factors ; }, abstract = {Live bacteria (such as probiotics) have long been used to modulate gut microbiota and human physiology, but their colonization is mostly transient. Conceptual understanding of the ecological principles as they apply to exogenously introduced microbes in gut ecosystems is lacking. We find that, when orally administered to humans, Bifidobacterium longum AH1206 stably persists in the gut of 30% of individuals for at least 6 months without causing gastrointestinal symptoms or impacting the composition of the resident gut microbiota. AH1206 engraftment was associated with low abundance of resident B. longum and underrepresentation of specific carbohydrate utilization genes in the pre-treatment microbiome. Thus, phylogenetic limiting and resource availability are two factors that control the niche opportunity for AH1206 colonization. These findings suggest that bacterial species and functional genes absent in the gut microbiome of individual humans can be reestablished, providing opportunities for precise and personalized microbiome reconstitution.}, } @article {pmid27692516, year = {2016}, author = {Santos, ARD and Antonio Alvares Soares Ribeiro, C and de Oliveira Peluzio, TM and Esteves Peluzio, JB and de Queiroz, VT and Figueira Branco, ER and Lorenzon, AS and Domingues, GF and Marcatti, GE and de Castro, NLM and Teixeira, TR and Dos Santos, GMADA and Santos Mota, PH and Ferreira da Silva, S and Vargas, R and de Carvalho, JR and Macedo, LL and da Silva Araújo, C and de Almeida, SLH}, title = {Geotechnology and landscape ecology applied to the selection of potential forest fragments for seed harvesting.}, journal = {Journal of environmental management}, volume = {183}, number = {Pt 3}, pages = {1050-1063}, doi = {10.1016/j.jenvman.2016.09.073}, pmid = {27692516}, issn = {1095-8630}, mesh = {Biodiversity ; Brazil ; Conservation of Natural Resources/*methods ; *Decision Support Techniques ; Ecology/methods ; Forestry/*methods ; *Forests ; *Seeds ; Trees ; }, abstract = {The Atlantic Forest biome is recognized for its biodiversity and is one of the most threatened biomes on the planet, with forest fragmentation increasing due to uncontrolled land use, land occupation, and population growth. The most serious aspect of the forest fragmentation process is the edge effect and the loss of biodiversity. In this context, the aim of this study was to evaluate the dynamics of forest fragmentation and select potential forest fragments with a higher degree of conservation for seed harvesting in the Itapemirim river basin, Espírito Santo State, Brazil. Image classification techniques, forest landscape ecology, and multi-criteria analysis were used to evaluate the evolution of forest fragmentation to develop the landscape metric indexes, and to select potential forest fragments for seed harvesting for the years 1985 and 2013. According to the results, there was a reduction of 2.55% of the occupancy of the fragments in the basin between the years 1985 and 2013. For the years 1985 and 2013, forest fragment units 2 and 3 were spatialized with a high potential for seed harvesting, representing 6.99% and 16.01% of the total fragments, respectively. The methodology used in this study has the potential to be used to support decisions for the selection of potential fragments for seed harvesting because selecting fragments in different environments by their spatial attributes provides a greater degree of conservation, contributing to the protection and conscious management of the forests. The proposed methodology can be adapted to other areas and different biomes of the world.}, } @article {pmid27687493, year = {2016}, author = {Fernandes-da-Silva, J and Castagna, C and Teixeira, AS and Carminatti, LJ and Guglielmo, LG}, title = {The peak velocity derived from the Carminatti Test is related to physical match performance in young soccer players.}, journal = {Journal of sports sciences}, volume = {34}, number = {24}, pages = {2238-2245}, doi = {10.1080/02640414.2016.1209307}, pmid = {27687493}, issn = {1466-447X}, mesh = {Adolescent ; *Athletic Performance ; *Exercise Test ; Geographic Information Systems ; Humans ; Male ; Physical Endurance ; Physical Fitness ; *Running ; *Soccer ; }, abstract = {The aim of this study was to examine the relationship between the peak velocity derived from the Carminatti Test (T-CAR) (PVT-CAR) and physical match performance in young soccer players. Thirty-three youth soccer players were recruited from 2 non-professional clubs. Friendly matches and small-sided game were performed. Physical match demands were assessed using Global Positioning System (GPS) technology. On a separate occasion, the players were submitted to the T-CAR. Players were categorised into 3 groups based on their T-CAR performance: Low (PVT-CAR ≤ P33), Intermediate (P33 > PVT-CAR < P66) and High (PVT-CAR ≥ P66). The PVT-CAR (15.5 ± 0.7 km·h[-1]) was significantly related to high-intensity activities (HIA; r = 0.78, P < 0.001), high-intensity running (HIR; r = 0.66, P < 0.001), sprinting (r = 0.62, P < 0.001) and total distance (TD) covered (r = 0.47, P < 0.01) during friendly matches. The PVT-CAR was strongly correlated with the amount of HIA (r = 0.81, P < 0.001), HIR (r = 0.85, P < 0.001) and TD covered (r = 0.81, P < 0.001) during small-sided game. No significant correlation was observed between the PVT-CAR and distance of sprinting (r = 0.49, P = 0.067) during small-side game. Furthermore, players in the High group covered significantly more TD (10%) and did more HIA (42%), sprinting (31%) and HIR (25%) during friendly matches compared to the players classified as having Low performance on the T-CAR. These differences still remained after adjusting for chronological age (CA), maturity and body size. In conclusion, the current study gives empirical support to the ecological and construct validity of this novel field test (T-CAR) as an indicator of match-related physical performance in young soccer players during pubertal years.}, } @article {pmid27672114, year = {2016}, author = {Shen, XX and Zhou, X and Kominek, J and Kurtzman, CP and Hittinger, CT and Rokas, A}, title = {Reconstructing the Backbone of the Saccharomycotina Yeast Phylogeny Using Genome-Scale Data.}, journal = {G3 (Bethesda, Md.)}, volume = {6}, number = {12}, pages = {3927-3939}, pmid = {27672114}, issn = {2160-1836}, support = {R21 AI105619/AI/NIAID NIH HHS/United States ; }, mesh = {Ascomycota/*classification/*genetics ; Computational Biology/methods ; Genetic Markers ; *Genome, Fungal ; *Genomics/methods ; *Phylogeny ; Workflow ; }, abstract = {Understanding the phylogenetic relationships among the yeasts of the subphylum Saccharomycotina is a prerequisite for understanding the evolution of their metabolisms and ecological lifestyles. In the last two decades, the use of rDNA and multilocus data sets has greatly advanced our understanding of the yeast phylogeny, but many deep relationships remain unsupported. In contrast, phylogenomic analyses have involved relatively few taxa and lineages that were often selected with limited considerations for covering the breadth of yeast biodiversity. Here we used genome sequence data from 86 publicly available yeast genomes representing nine of the 11 known major lineages and 10 nonyeast fungal outgroups to generate a 1233-gene, 96-taxon data matrix. Species phylogenies reconstructed using two different methods (concatenation and coalescence) and two data matrices (amino acids or the first two codon positions) yielded identical and highly supported relationships between the nine major lineages. Aside from the lineage comprised by the family Pichiaceae, all other lineages were monophyletic. Most interrelationships among yeast species were robust across the two methods and data matrices. However, eight of the 93 internodes conflicted between analyses or data sets, including the placements of: the clade defined by species that have reassigned the CUG codon to encode serine, instead of leucine; the clade defined by a whole genome duplication; and the species Ascoidea rubescens These phylogenomic analyses provide a robust roadmap for future comparative work across the yeast subphylum in the disciplines of taxonomy, molecular genetics, evolutionary biology, ecology, and biotechnology. To further this end, we have also provided a BLAST server to query the 86 Saccharomycotina genomes, which can be found at http://y1000plus.org/blast.}, } @article {pmid27668852, year = {2017}, author = {Mo, W and Wang, Y and Zhang, Y and Zhuang, D}, title = {Impacts of road network expansion on landscape ecological risk in a megacity, China: A case study of Beijing.}, journal = {The Science of the total environment}, volume = {574}, number = {}, pages = {1000-1011}, doi = {10.1016/j.scitotenv.2016.09.048}, pmid = {27668852}, issn = {1879-1026}, mesh = {Beijing ; Cities ; *Conservation of Natural Resources ; Ecology ; *Ecosystem ; Geographic Information Systems ; Risk Assessment ; *Transportation ; }, abstract = {Road networks affect the spatial structure of urban landscapes, and with continuous expansion, it will also exert more widespread influences on the regional ecological environment. With the support of geographic information system (GIS) technology, based on the application of various spatial analysis methods, this study analyzed the spatiotemporal changes of road networks and landscape ecological risk in the research area of Beijing to explore the impacts of road network expansion on ecological risk in the urban landscape. The results showed the following: 1) In the dynamic processes of change in the overall landscape pattern, the changing differences in landscape indices of various landscape types were obvious and were primarily related to land-use type. 2) For the changes in a time series, the expansion of the road kernel area was consistent with the extension of the sub-low-risk area in the urban center, but some differences were observed during different stages of development. 3) For the spatial position, the expanding changes in the road kernel area were consistent with the grade changes of the urban central ecological risk, primarily because both had a certain spatial correlation with the expressways. 4) The influence of road network expansion on the ecological risk in the study area had obvious spatial differences, which may be closely associated with the distribution of ecosystem types.}, } @article {pmid27655556, year = {2016}, author = {Knörlein, BJ and Baier, DB and Gatesy, SM and Laurence-Chasen, JD and Brainerd, EL}, title = {Validation of XMALab software for marker-based XROMM.}, journal = {The Journal of experimental biology}, volume = {219}, number = {Pt 23}, pages = {3701-3711}, doi = {10.1242/jeb.145383}, pmid = {27655556}, issn = {1477-9145}, mesh = {Animals ; Bone and Bones/*diagnostic imaging ; Dimensional Measurement Accuracy ; Fluoroscopy/instrumentation/methods ; Imaging, Three-Dimensional/*methods ; Movement/*physiology ; Reproducibility of Results ; *Software ; Swine ; Swine, Miniature ; Tomography, X-Ray Computed/methods ; Video Recording/methods ; X-Rays ; }, abstract = {Marker-based XROMM requires software tools for: (1) correcting fluoroscope distortion; (2) calibrating X-ray cameras; (3) tracking radio-opaque markers; and (4) calculating rigid body motion. In this paper we describe and validate XMALab, a new open-source software package for marker-based XROMM (C++ source and compiled versions on Bitbucket). Most marker-based XROMM studies to date have used XrayProject in MATLAB. XrayProject can produce results with excellent accuracy and precision, but it is somewhat cumbersome to use and requires a MATLAB license. We have designed XMALab to accelerate the XROMM process and to make it more accessible to new users. Features include the four XROMM steps (listed above) in one cohesive user interface, real-time plot windows for detecting errors, and integration with an online data management system, XMAPortal. Accuracy and precision of XMALab when tracking markers in a machined object are ±0.010 and ±0.043 mm, respectively. Mean precision for nine users tracking markers in a tutorial dataset of minipig feeding was ±0.062 mm in XMALab and ±0.14 mm in XrayProject. Reproducibility of 3D point locations across nine users was 10-fold greater in XMALab than in XrayProject, and six degree-of-freedom bone motions calculated with a joint coordinate system were 3- to 6-fold more reproducible in XMALab. XMALab is also suitable for tracking white or black markers in standard light videos with optional checkerboard calibration. We expect XMALab to increase both the quality and quantity of animal motion data available for comparative biomechanics research.}, } @article {pmid27654921, year = {2016}, author = {Roux, S and Brum, JR and Dutilh, BE and Sunagawa, S and Duhaime, MB and Loy, A and Poulos, BT and Solonenko, N and Lara, E and Poulain, J and Pesant, S and Kandels-Lewis, S and Dimier, C and Picheral, M and Searson, S and Cruaud, C and Alberti, A and Duarte, CM and Gasol, JM and Vaqué, D and , and Bork, P and Acinas, SG and Wincker, P and Sullivan, MB}, title = {Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses.}, journal = {Nature}, volume = {537}, number = {7622}, pages = {689-693}, pmid = {27654921}, issn = {1476-4687}, support = {P 25111/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {DNA, Viral/analysis ; Datasets as Topic ; Ecology ; *Ecosystem ; Expeditions ; Genes, Viral ; *Genome, Viral ; Geographic Mapping ; Metagenome ; *Metagenomics ; Nitrogen Cycle ; Oceans and Seas ; Seawater/*virology ; Sulfur/metabolism ; Viruses/*genetics/*isolation & purification/metabolism ; }, abstract = {Ocean microbes drive biogeochemical cycling on a global scale. However, this cycling is constrained by viruses that affect community composition, metabolic activity, and evolutionary trajectories. Owing to challenges with the sampling and cultivation of viruses, genome-level viral diversity remains poorly described and grossly understudied, with less than 1% of observed surface-ocean viruses known. Here we assemble complete genomes and large genomic fragments from both surface- and deep-ocean viruses sampled during the Tara Oceans and Malaspina research expeditions, and analyse the resulting 'global ocean virome' dataset to present a global map of abundant, double-stranded DNA viruses complete with genomic and ecological contexts. A total of 15,222 epipelagic and mesopelagic viral populations were identified, comprising 867 viral clusters (defined as approximately genus-level groups). This roughly triples the number of known ocean viral populations and doubles the number of candidate bacterial and archaeal virus genera, providing a near-complete sampling of epipelagic communities at both the population and viral-cluster level. We found that 38 of the 867 viral clusters were locally or globally abundant, together accounting for nearly half of the viral populations in any global ocean virome sample. While two-thirds of these clusters represent newly described viruses lacking any cultivated representative, most could be computationally linked to dominant, ecologically relevant microbial hosts. Moreover, we identified 243 viral-encoded auxiliary metabolic genes, of which only 95 were previously known. Deeper analyses of four of these auxiliary metabolic genes (dsrC, soxYZ, P-II (also known as glnB) and amoC) revealed that abundant viruses may directly manipulate sulfur and nitrogen cycling throughout the epipelagic ocean. This viral catalog and functional analyses provide a necessary foundation for the meaningful integration of viruses into ecosystem models where they act as key players in nutrient cycling and trophic networks.}, } @article {pmid27654914, year = {2016}, author = {Malaspinas, AS and Westaway, MC and Muller, C and Sousa, VC and Lao, O and Alves, I and Bergström, A and Athanasiadis, G and Cheng, JY and Crawford, JE and Heupink, TH and Macholdt, E and Peischl, S and Rasmussen, S and Schiffels, S and Subramanian, S and Wright, JL and Albrechtsen, A and Barbieri, C and Dupanloup, I and Eriksson, A and Margaryan, A and Moltke, I and Pugach, I and Korneliussen, TS and Levkivskyi, IP and Moreno-Mayar, JV and Ni, S and Racimo, F and Sikora, M and Xue, Y and Aghakhanian, FA and Brucato, N and Brunak, S and Campos, PF and Clark, W and Ellingvåg, S and Fourmile, G and Gerbault, P and Injie, D and Koki, G and Leavesley, M and Logan, B and Lynch, A and Matisoo-Smith, EA and McAllister, PJ and Mentzer, AJ and Metspalu, M and Migliano, AB and Murgha, L and Phipps, ME and Pomat, W and Reynolds, D and Ricaut, FX and Siba, P and Thomas, MG and Wales, T and Wall, CM and Oppenheimer, SJ and Tyler-Smith, C and Durbin, R and Dortch, J and Manica, A and Schierup, MH and Foley, RA and Lahr, MM and Bowern, C and Wall, JD and Mailund, T and Stoneking, M and Nielsen, R and Sandhu, MS and Excoffier, L and Lambert, DM and Willerslev, E}, title = {A genomic history of Aboriginal Australia.}, journal = {Nature}, volume = {538}, number = {7624}, pages = {207-214}, pmid = {27654914}, issn = {1476-4687}, support = {154717/SNSF_/Swiss National Science Foundation/Switzerland ; 100719/WT_/Wellcome Trust/United Kingdom ; 143393/SNSF_/Swiss National Science Foundation/Switzerland ; 098051/WT_/Wellcome Trust/United Kingdom ; 090532/WT_/Wellcome Trust/United Kingdom ; BB/H005854/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; 106289/WT_/Wellcome Trust/United Kingdom ; 647787/ERC_/European Research Council/International ; }, mesh = {Africa/ethnology ; Australia ; Datasets as Topic ; Desert Climate ; Gene Flow ; Genetics, Population ; Genome, Human/*genetics ; *Genomics ; History, Ancient ; Human Migration/history ; Humans ; Language ; New Guinea ; *Phylogeny ; Population Dynamics ; Racial Groups/*genetics ; Tasmania ; }, abstract = {The population history of Aboriginal Australians remains largely uncharacterized. Here we generate high-coverage genomes for 83 Aboriginal Australians (speakers of Pama-Nyungan languages) and 25 Papuans from the New Guinea Highlands. We find that Papuan and Aboriginal Australian ancestors diversified 25-40 thousand years ago (kya), suggesting pre-Holocene population structure in the ancient continent of Sahul (Australia, New Guinea and Tasmania). However, all of the studied Aboriginal Australians descend from a single founding population that differentiated ~10-32 kya. We infer a population expansion in northeast Australia during the Holocene epoch (past 10,000 years) associated with limited gene flow from this region to the rest of Australia, consistent with the spread of the Pama-Nyungan languages. We estimate that Aboriginal Australians and Papuans diverged from Eurasians 51-72 kya, following a single out-of-Africa dispersal, and subsequently admixed with archaic populations. Finally, we report evidence of selection in Aboriginal Australians potentially associated with living in the desert.}, } @article {pmid27654912, year = {2016}, author = {Mallick, S and Li, H and Lipson, M and Mathieson, I and Gymrek, M and Racimo, F and Zhao, M and Chennagiri, N and Nordenfelt, S and Tandon, A and Skoglund, P and Lazaridis, I and Sankararaman, S and Fu, Q and Rohland, N and Renaud, G and Erlich, Y and Willems, T and Gallo, C and Spence, JP and Song, YS and Poletti, G and Balloux, F and van Driem, G and de Knijff, P and Romero, IG and Jha, AR and Behar, DM and Bravi, CM and Capelli, C and Hervig, T and Moreno-Estrada, A and Posukh, OL and Balanovska, E and Balanovsky, O and Karachanak-Yankova, S and Sahakyan, H and Toncheva, D and Yepiskoposyan, L and Tyler-Smith, C and Xue, Y and Abdullah, MS and Ruiz-Linares, A and Beall, CM and Di Rienzo, A and Jeong, C and Starikovskaya, EB and Metspalu, E and Parik, J and Villems, R and Henn, BM and Hodoglugil, U and Mahley, R and Sajantila, A and Stamatoyannopoulos, G and Wee, JT and Khusainova, R and Khusnutdinova, E and Litvinov, S and Ayodo, G and Comas, D and Hammer, MF and Kivisild, T and Klitz, W and Winkler, CA and Labuda, D and Bamshad, M and Jorde, LB and Tishkoff, SA and Watkins, WS and Metspalu, M and Dryomov, S and Sukernik, R and Singh, L and Thangaraj, K and Pääbo, S and Kelso, J and Patterson, N and Reich, D}, title = {The Simons Genome Diversity Project: 300 genomes from 142 diverse populations.}, journal = {Nature}, volume = {538}, number = {7624}, pages = {201-206}, pmid = {27654912}, issn = {1476-4687}, support = {R01 GM100233/GM/NIGMS NIH HHS/United States ; R01 DK104339/DK/NIDDK NIH HHS/United States ; R01 HG006399/HG/NHGRI NIH HHS/United States ; R01 GM059290/GM/NIGMS NIH HHS/United States ; R01 GM113657/GM/NIGMS NIH HHS/United States ; /WT_/Wellcome Trust/United Kingdom ; R00 GM111744/GM/NIGMS NIH HHS/United States ; R01 GM094402/GM/NIGMS NIH HHS/United States ; UL1 TR001067/TR/NCATS NIH HHS/United States ; DP1 ES022577/ES/NIEHS NIH HHS/United States ; }, mesh = {Animals ; Australia ; Black People/genetics ; Datasets as Topic ; Genetic Variation/*genetics ; Genetics, Population ; Genome, Human/*genetics ; *Genomics ; History, Ancient ; Human Migration/history ; Humans ; *Mutation Rate ; Neanderthals/genetics ; New Guinea ; *Phylogeny ; Racial Groups/*genetics ; Sequence Analysis, DNA ; Species Specificity ; Time Factors ; }, abstract = {Here we report the Simons Genome Diversity Project data set: high quality genomes from 300 individuals from 142 diverse populations. These genomes include at least 5.8 million base pairs that are not present in the human reference genome. Our analysis reveals key features of the landscape of human genome variation, including that the rate of accumulation of mutations has accelerated by about 5% in non-Africans compared to Africans since divergence. We show that the ancestors of some pairs of present-day human populations were substantially separated by 100,000 years ago, well before the archaeologically attested onset of behavioural modernity. We also demonstrate that indigenous Australians, New Guineans and Andamanese do not derive substantial ancestry from an early dispersal of modern humans; instead, their modern human ancestry is consistent with coming from the same source as that of other non-Africans.}, } @article {pmid27651433, year = {2016}, author = {Akinkugbe, AA and Sharma, S and Ohrbach, R and Slade, GD and Poole, C}, title = {Response to Letter to the Editor, "Directed Acyclic Graphs for Oral Disease Research".}, journal = {Journal of dental research}, volume = {95}, number = {11}, pages = {1315}, pmid = {27651433}, issn = {1544-0591}, support = {T32 DE023526/DE/NIDCR NIH HHS/United States ; T90 DE021986/DE/NIDCR NIH HHS/United States ; }, mesh = {*Confounding Factors, Epidemiologic ; *Data Interpretation, Statistical ; Humans ; Mouth Diseases ; }, } @article {pmid27651028, year = {2016}, author = {Powell, JT and Pons, JC and Chertow, M}, title = {Waste Informatics: Establishing Characteristics of Contemporary U.S. Landfill Quantities and Practices.}, journal = {Environmental science & technology}, volume = {50}, number = {20}, pages = {10877-10884}, doi = {10.1021/acs.est.6b02848}, pmid = {27651028}, issn = {1520-5851}, abstract = {Waste generation is expected to increase in most countries for many decades with landfill disposal still the dominant solid waste management method[1-3]. Yet, operational characteristics of landfills are often poorly understood with comparative statistics substantially lacking. Here, we call for a more formal waste informatics to organize and standardize waste management knowledge at multiple spatial scales through analysis of recently reported data from 1232 U.S. landfills and other high resolution data sets. We create the first known estimate of available U.S. municipal waste stocks (8.5 billion tonnes) and go on to resolve these stocks at the county level, reflecting prospective urban mining opportunities. Our analysis of disposal rates and landfill capacities reveals that more than half of U.S. states have more than 25 years of life remaining. We also estimate the gross energy potential of landfill gas in the U.S. (338 billion MJ/yr) by examining 922 operational methane collection systems and demonstrate that the greatest energy recovery opportunities lie at landfills with existing collection systems and energy conversion infrastructure. Finally, we found that the number of landfills reaching the federally defined 30-year postclosure care period will more than triple in the coming two decades, with 264 sites expected by the year 2044, highlighting the need to develop and standardize metrics carefully to define and standardize when it is appropriate to end or scale back long-term landfill monitoring.}, } @article {pmid27649991, year = {2016}, author = {Lei, Y and Wang, Y and Ahola, V and Luo, S and Xu, C and Wang, R}, title = {RNA sequencing reveals differential thermal regulation mechanisms between sexes of Glanville fritillary butterfly in the Tianshan Mountains, China.}, journal = {Molecular biology reports}, volume = {43}, number = {12}, pages = {1423-1433}, pmid = {27649991}, issn = {1573-4978}, mesh = {Adaptation, Physiological ; Animals ; Butterflies/*genetics/metabolism ; China ; Female ; Gene Expression Regulation ; Gene Ontology ; Genes, Insect ; Male ; Metabolic Networks and Pathways ; Sequence Analysis, RNA ; Sex Characteristics ; Temperature ; *Transcriptome ; }, abstract = {The Glanville fritillary butterfly (Melitaea cinxia; Nymphalidae) has been extensively studied as a model species in metapopulation ecology. We investigated in the earlier studies that female butterflies exhibit higher thermal tolerance than males in the Tianshan Mountains of China. We aim to understand the molecular mechanism of differences of thermal responses between sexes. We used RNA-seq approach and performed de novo assembly of transcriptome to compare the gene expression patterns between two sexes after heat stress. All the reads were assembled into 84,376 transcripts and 72,701 unigenes. The number of differential expressed genes (DEGs) between control and heat shock samples was 175 and 268 for males and females, respectively. Heat shock proteins genes (hsps) were up-regulated in response to heat stress in both males and females. Most of the up-regulated hsps showed higher fold changes in males than in females. Females expressed more ribosomal subunit protein genes, transcriptional elongation factor genes, and methionine-rich storage protein genes, participating in protein synthesis. It indicated that protein synthesis is needed for females to replace the damaged proteins due to heat shock. In addition, aspartate decarboxylase might contribute to thermal tolerance in females. These differences in gene expression may at least partly explain the response to high temperature stress, and the fact that females exhibit higher thermal tolerance.}, } @article {pmid27645228, year = {2016}, author = {Devictor, V and Bensaude-Vincent, B}, title = {From ecological records to big data: the invention of global biodiversity.}, journal = {History and philosophy of the life sciences}, volume = {38}, number = {4}, pages = {13}, doi = {10.1007/s40656-016-0113-2}, pmid = {27645228}, issn = {0391-9714}, mesh = {*Biodiversity ; Conservation of Natural Resources/*history ; Data Collection ; Databases, Factual/*history ; Ecology/*history ; History, 20th Century ; History, 21st Century ; }, abstract = {This paper is a critical assessment of the epistemological impact of the systematic quantification of nature with the accumulation of big datasets on the practice and orientation of ecological science. We examine the contents of big databases and argue that it is not just accumulated information; records are translated into digital data in a process that changes their meanings. In order to better understand what is at stake in the 'datafication' process, we explore the context for the emergence and quantification of biodiversity in the 1980s, along with the concept of the global environment. In tracing the origin and development of the global biodiversity information facility (GBIF) we describe big data biodiversity projects as a techno-political construction dedicated to monitoring a new object: the global diversity. We argue that, biodiversity big data became a powerful driver behind the invention of the concept of the global environment, and a way to embed ecological science in the political agenda.}, } @article {pmid27640952, year = {2017}, author = {Calió, MF and Lepis, KB and Pirani, JR and Struwe, L}, title = {Phylogeny of Helieae (Gentianaceae): Resolving taxonomic chaos in a Neotropical clade.}, journal = {Molecular phylogenetics and evolution}, volume = {106}, number = {}, pages = {192-208}, doi = {10.1016/j.ympev.2016.09.013}, pmid = {27640952}, issn = {1095-9513}, mesh = {Bayes Theorem ; DNA, Plant/chemistry/isolation & purification/metabolism ; Databases, Genetic ; Flowers/genetics ; Gentianaceae/*classification/genetics ; Phylogeny ; Plastids/genetics ; RNA, Ribosomal, 5S/classification/genetics/metabolism ; Sequence Alignment ; Sequence Analysis, DNA ; }, abstract = {The monophyletic and Neotropical tribe Helieae of the worldwide family Gentianaceae (Gentianales, Asterids, Angiospermae) is well known for its problematic generic classifications. An initial phylogenetic analysis of Helieae shed light onto the relationships between genera, and indicated that traditional generic limits did not correspond to monophyletic groups. In order to obtain a more thorough understanding of generic relationships within the group, we enhanced sampling within the so-called Symbolanthus clade and performed phylogenetic analyses from DNA sequences from one plastid region (matK) and two nuclear regions (ITS and 5S-NTS), plus 112 morphological characters, which were analyzed separately and in combination, using parsimony and Bayesian approaches. A total of 83 individuals representing 20 genera and 51 species of Helieae were sampled; 13 species were included in this study solely based on their morphological characters. Ancestral character reconstructions were performed to identify potential synapomorphies of clades and patterns of homoplasy in the morphological dataset. Our results demonstrate that Prepusa is sister to the remainder of Helieae. Furthermore, the Macrocarpaea clade, the Irlbachia clade and the Symbolanthus clade were also recovered. Within the Symbolanthus clade, our results confirm that Calolisianthus and Chelonanthus are not monophyletic, and also contest the monophyly of Irlbachia as currently circumscribed. Specifically, two species of Calolisianthus group with the type species of Chelonanthus, while the other Calolisianthus species are more closely related to Tetrapollinia and Symbolanthus. Moreover, the green-white-flowered Chelonanthus species and Adenolisianthus are undoubtedly related to Helia and several analyses support Irlbachia pratensis as more closely related to the lineage including the type species of Chelonanthus described above The addition of new characters and taxa led to higher confidence in the relative position of some clades, as well as provided further support for a new generic circumscription of Calolisianthus, Chelonanthus, and Helia. Even though several morphological characters traditionally used in the taxonomy of the group were shown to be homoplasious, most clades can be diagnosed by a combination of morphological character states.}, } @article {pmid27640153, year = {2016}, author = {Carriger, JF and Martin, TM and Barron, MG}, title = {A Bayesian network model for predicting aquatic toxicity mode of action using two dimensional theoretical molecular descriptors.}, journal = {Aquatic toxicology (Amsterdam, Netherlands)}, volume = {180}, number = {}, pages = {11-24}, doi = {10.1016/j.aquatox.2016.09.006}, pmid = {27640153}, issn = {1879-1514}, mesh = {Animals ; Bayes Theorem ; Computational Biology ; Databases, Factual ; Ecotoxicology/*methods ; Markov Chains ; *Models, Biological ; *Models, Chemical ; Reproducibility of Results ; Water Pollutants, Chemical/*toxicity ; }, abstract = {The mode of toxic action (MoA) has been recognized as a key determinant of chemical toxicity, but development of predictive MoA classification models in aquatic toxicology has been limited. We developed a Bayesian network model to classify aquatic toxicity MoA using a recently published dataset containing over one thousand chemicals with MoA assignments for aquatic animal toxicity. Two dimensional theoretical chemical descriptors were generated for each chemical using the Toxicity Estimation Software Tool. The model was developed through augmented Markov blanket discovery from the dataset of 1098 chemicals with the MoA broad classifications as a target node. From cross validation, the overall precision for the model was 80.2%. The best precision was for the AChEI MoA (93.5%) where 257 chemicals out of 275 were correctly classified. Model precision was poorest for the reactivity MoA (48.5%) where 48 out of 99 reactive chemicals were correctly classified. Narcosis represented the largest class within the MoA dataset and had a precision and reliability of 80.0%, reflecting the global precision across all of the MoAs. False negatives for narcosis most often fell into electron transport inhibition, neurotoxicity or reactivity MoAs. False negatives for all other MoAs were most often narcosis. A probabilistic sensitivity analysis was undertaken for each MoA to examine the sensitivity to individual and multiple descriptor findings. The results show that the Markov blanket of a structurally complex dataset can simplify analysis and interpretation by identifying a subset of the key chemical descriptors associated with broad aquatic toxicity MoAs, and by providing a computational chemistry-based network classification model with reasonable prediction accuracy.}, } @article {pmid27639256, year = {2017}, author = {Weinstock, MA and Lott, JP and Wang, Q and Titus, LJ and Onega, T and Nelson, HD and Pearson, L and Piepkorn, M and Barnhill, RL and Elmore, JG and Tosteson, ANA}, title = {Skin biopsy utilization and melanoma incidence among Medicare beneficiaries.}, journal = {The British journal of dermatology}, volume = {176}, number = {4}, pages = {949-954}, pmid = {27639256}, issn = {1365-2133}, support = {K05 CA104699/CA/NCI NIH HHS/United States ; P30 CA023108/CA/NCI NIH HHS/United States ; R01 CA151306/CA/NCI NIH HHS/United States ; }, mesh = {Age Distribution ; Aged ; Aged, 80 and over ; Biopsy/statistics & numerical data ; Cross-Sectional Studies ; Female ; Humans ; Incidence ; Male ; Medicare/statistics & numerical data ; Melanoma/epidemiology/*pathology ; Regression Analysis ; Risk Factors ; Skin/*pathology ; Skin Neoplasms/epidemiology/*pathology ; United States/epidemiology ; }, abstract = {BACKGROUND: Melanoma incidence has increased in recent decades in the U.S.A. Uncertainty remains regarding how much of this increase is attributable to greater melanoma screening activities, potential detection bias and overdiagnosis.

OBJECTIVES: To use a cross-sectional ecological analysis to evaluate the relationship between skin biopsy and melanoma incidence rates over a more recent time period than prior reports.

METHODS: Examination of the association of biopsy rates and melanoma incidence (invasive and in situ) in SEER-Medicare data (including 10 states) for 2002-2009.

RESULTS: The skin biopsy rate increased by approximately 50% (6% per year) throughout this 8-year period, from 7012 biopsies per 100 000 persons in 2002 to 10 528 biopsies per 100 000 persons in 2009. The overall melanoma incidence rate increased approximately 4% (< 1% per year) over the same time period. The incidence of melanoma in situ increased approximately 10% (1% per year), while the incidence of invasive melanoma increased from 2002 to 2005 then decreased from 2006 to 2009. Regression models estimated that, on average, for every 1000 skin biopsies performed, an additional 5·2 (95% confidence interval 4·1-6·3) cases of melanoma in situ were diagnosed and 8·1 (95% confidence interval 6·7-9·5) cases of invasive melanoma were diagnosed. When considering individual states, some demonstrated a positive association between biopsy rate and invasive melanoma incidence, others an inverse association, and still others a more complex pattern.

CONCLUSIONS: Increased skin biopsies over time are associated with increased diagnosis of in situ melanoma, but the association with invasive melanoma is more complex.}, } @article {pmid27639030, year = {2016}, author = {Fu, B and Wang, X and Feng, X and Yu, X and Tong, J}, title = {Comparative transcriptomic analyses of two bighead carp (Hypophthalmichthys nobilis) groups with different growth rates.}, journal = {Comparative biochemistry and physiology. Part D, Genomics & proteomics}, volume = {20}, number = {}, pages = {111-117}, doi = {10.1016/j.cbd.2016.08.006}, pmid = {27639030}, issn = {1878-0407}, mesh = {Animals ; Computational Biology ; Cyprinidae/classification/*genetics/*growth & development ; *Gene Expression Profiling ; Genome/genetics ; High-Throughput Nucleotide Sequencing/*methods ; Microsatellite Repeats/*genetics ; Molecular Sequence Annotation ; Phylogeny ; Polymorphism, Single Nucleotide/*genetics ; Transcriptome/*genetics ; }, abstract = {Growth is one of the most important and desired economic traits for aquaculture species, and identification of loci controlling growth is a difficult task without genomic sequences. In this study, the liver transcriptomes of two groups (F and S) of bighead carp (Hypophthalmichthys nobilis) within a full-sib family with significant differences in growth rate were sequenced. Following de novo assembly of the combined reads from the two groups, a total of 410 differentially expressed genes were identified. Functional annotation and analysis of these genes indicated that some of these were involved in regulation of glucose levels and lipid metabolism, particularly fatty acid oxidation and transport. In addition to the differences on expression levels between the two groups, we also identified many non-synonymous coding single-nucleotide polymorphisms (SNPs) that were specific to each group, including SNPs from 4 genes involved in the lipid metabolism process (GO: 0006629). These differences in gene expression and DNA sequences may in part comprise the genetic background for the regulation of early growth rate in bighead carp.}, } @article {pmid27633232, year = {2017}, author = {Tremblay, S and Gagnon, JF and Lafond, D and Hodgetts, HM and Doiron, M and Jeuniaux, PPJMH}, title = {A cognitive prosthesis for complex decision-making.}, journal = {Applied ergonomics}, volume = {58}, number = {}, pages = {349-360}, doi = {10.1016/j.apergo.2016.07.009}, pmid = {27633232}, issn = {1872-9126}, mesh = {Artificial Intelligence ; *Cognition ; Computer Simulation ; Data Display ; *Decision Making ; *Decision Support Techniques ; Female ; Humans ; Knowledge ; Learning ; Male ; }, abstract = {While simple heuristics can be ecologically rational and effective in naturalistic decision making contexts, complex situations require analytical decision making strategies, hypothesis-testing and learning. Sub-optimal decision strategies - using simplified as opposed to analytic decision rules - have been reported in domains such as healthcare, military operational planning, and government policy making. We investigate the potential of a computational toolkit called "IMAGE" to improve decision-making by developing structural knowledge and increasing understanding of complex situations. IMAGE is tested within the context of a complex military convoy management task through (a) interactive simulations, and (b) visualization and knowledge representation capabilities. We assess the usefulness of two versions of IMAGE (desktop and immersive) compared to a baseline. Results suggest that the prosthesis helped analysts in making better decisions, but failed to increase their structural knowledge about the situation once the cognitive prosthesis is removed.}, } @article {pmid27630050, year = {2016}, author = {Haddadderafshi, N and Pósa, TB and Péter, G and Gáspár, L and Ladányi, M and Hrotkó, K and Lukács, N and Halász, K}, title = {Characterization of community structure of culturable endophytic fungi in sweet cherry composite trees and their growth-retarding effect against pathogens.}, journal = {Acta biologica Hungarica}, volume = {67}, number = {3}, pages = {269-285}, doi = {10.1556/018.67.2016.3.5}, pmid = {27630050}, issn = {0236-5383}, mesh = {Ascomycota/*growth & development ; Biodiversity ; Crosses, Genetic ; Ecosystem ; Endophytes/classification/*growth & development/isolation & purification/physiology ; Fungi/classification/*growth & development/isolation & purification ; Host-Pathogen Interactions ; Phylogeny ; Plant Diseases/microbiology/*prevention & control ; Plant Leaves/microbiology ; Plant Roots/microbiology ; Prunus/*microbiology ; Prunus avium/*microbiology ; Symbiosis ; }, abstract = {Endophytic fungi have the potential to protect their host plants in stress situations. Characterizing the ecology and complex interaction between these endophytes and their host plants is therefore of great practical importance, particularly in horticultural plants. Among horticultural plants, fruit trees form a special category because of their longevity and because they are composites of rootstock and scion, which often belong to different plant species. Here we present the first characterization of culturable endophytic fungal community of sweet cherry. Samples from the Hungarian cultivar 'Petrus' grafted on 11 different rootstocks were collected in autumn and in spring in a bearing orchard and the dependence of colonization rate and endophyte diversity on rootstock, organ and season was analysed. On the basis of their ITS sequences 26 fungal operational taxonomic units were identified at least down to the genus level. The dominant genus, comprising more than 50% of all isolates, was Alternaria, followed by different Fusarium and Epicoccum species. We observed some organ-specificity amongst endophytes, and organs showed more sizeable differences in colonization rates and endophyte diversity than rootstocks. Most dynamic endophyte populations, strongly influenced by environmental conditions and crop management, were observed in leaves. The potential of selected endophytes to confer protection against Monilinia laxa was also analysed and 7 isolates were found to inhibit the growth of this pathogen in vitro.}, } @article {pmid27621130, year = {2017}, author = {Lopes-Lima, M and Froufe, E and Do, VT and Ghamizi, M and Mock, KE and Kebapçı, Ü and Klishko, O and Kovitvadhi, S and Kovitvadhi, U and Paulo, OS and Pfeiffer, JM and Raley, M and Riccardi, N and Şereflişan, H and Sousa, R and Teixeira, A and Varandas, S and Wu, X and Zanatta, DT and Zieritz, A and Bogan, AE}, title = {Phylogeny of the most species-rich freshwater bivalve family (Bivalvia: Unionida: Unionidae): Defining modern subfamilies and tribes.}, journal = {Molecular phylogenetics and evolution}, volume = {106}, number = {}, pages = {174-191}, doi = {10.1016/j.ympev.2016.08.021}, pmid = {27621130}, issn = {1095-9513}, mesh = {Animals ; Bayes Theorem ; Biological Evolution ; Bivalvia/*classification/genetics ; Cytochromes c/classification/genetics/metabolism ; DNA/chemistry/isolation & purification/metabolism ; Databases, Genetic ; Likelihood Functions ; Phylogeny ; RNA, Ribosomal, 28S/classification/genetics/metabolism ; Sequence Analysis, DNA ; }, abstract = {Freshwater mussels of the order Unionida are key elements of freshwater habitats and are responsible for important ecological functions and services. Unfortunately, these bivalves are among the most threatened freshwater taxa in the world. However, conservation planning and management are hindered by taxonomic problems and a lack of detailed ecological data. This highlights the urgent need for advances in the areas of systematics and evolutionary relationships within the Unionida. This study presents the most comprehensive phylogeny to date of the larger Unionida family, i.e., the Unionidae. The phylogeny is based on a combined dataset of 1032bp (COI+28S) of 70 species in 46 genera, with 7 of this genera being sequenced for the first time. The resulting phylogeny divided the Unionidae into 6 supported subfamilies and 18 tribes, three of which are here named for the first time (i.e., Chamberlainiini nomen novum, Cristariini nomen novum and Lanceolariini nomen novum). Molecular analyses were complemented by investigations of selected morphological, anatomical and behavioral characters used in traditional phylogenetic studies. No single morphological, anatomical or behavioral character was diagnostic at the subfamily level and few were useful at the tribe level. However, within subfamilies, many tribes can be recognized based on a subset of these characters. The geographical distribution of each of the subfamilies and tribes is also presented. The present study provides important advances in the systematics of these extraordinary taxa with implications for future ecological and conservation studies.}, } @article {pmid27619155, year = {2016}, author = {Boakes, EH and Gliozzo, G and Seymour, V and Harvey, M and Smith, C and Roy, DB and Haklay, M}, title = {Patterns of contribution to citizen science biodiversity projects increase understanding of volunteers' recording behaviour.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {33051}, pmid = {27619155}, issn = {2045-2322}, mesh = {*Biodiversity ; *Classification ; *Databases, Factual ; Female ; Humans ; Male ; United Kingdom ; *Volunteers ; }, abstract = {The often opportunistic nature of biological recording via citizen science leads to taxonomic, spatial and temporal biases which add uncertainty to biodiversity estimates. However, such biases may also give valuable insight into volunteers' recording behaviour. Using Greater London as a case-study we examined the composition of three citizen science datasets - from Greenspace Information for Greater London CIC, iSpot and iRecord - with respect to recorder contribution and spatial and taxonomic biases, i.e. when, where and what volunteers record. We found most volunteers contributed few records and were active for just one day. Each dataset had its own taxonomic and spatial signature suggesting that volunteers' personal recording preferences may attract them towards particular schemes. There were also patterns across datasets: species' abundance and ease of identification were positively associated with number of records, as was plant height. We found clear hotspots of recording activity, the 10 most popular sites containing open water. We note that biases are accrued as part of the recording process (e.g. species' detectability) as well as from volunteer preferences. An increased understanding of volunteer behaviour gained from analysing the composition of records could thus enhance the fit between volunteers' interests and the needs of scientific projects.}, } @article {pmid27617417, year = {2017}, author = {Wringe, BF and Stanley, RR and Jeffery, NW and Anderson, EC and Bradbury, IR}, title = {parallelnewhybrid: an R package for the parallelization of hybrid detection using newhybrids.}, journal = {Molecular ecology resources}, volume = {17}, number = {1}, pages = {91-95}, doi = {10.1111/1755-0998.12597}, pmid = {27617417}, issn = {1755-0998}, mesh = {Biostatistics/*methods ; Chimera/*genetics ; Computational Biology/*methods ; Genetics, Population/*methods ; *Software ; }, abstract = {Hybridization among populations and species is a central theme in many areas of biology, and the study of hybridization has direct applicability to testing hypotheses about evolution, speciation and genetic recombination, as well as having conservation, legal and regulatory implications. Yet, despite being a topic of considerable interest, the identification of hybrid individuals, and quantification of the (un)certainty surrounding the identifications, remains difficult. Unlike other programs that exist to identify hybrids based on genotypic information, newhybrids is able to assign individuals to specific hybrid classes (e.g. F1 , F2) because it makes use of patterns of gene inheritance within each locus, rather than just the proportions of gene inheritance within each individual. For each comparison and set of markers, multiple independent runs of each data set should be used to develop an estimate of the hybrid class assignment accuracy. The necessity of analysing multiple simulated data sets, constructed from large genomewide data sets, presents significant computational challenges. To address these challenges, we present parallelnewhybrid, an r package designed to decrease user burden when undertaking multiple newhybrids analyses. parallelnewhybrid does so by taking advantage of the parallel computational capabilities inherent in modern computers to efficiently and automatically execute separate newhybrids runs in parallel. We show that parallelization of analyses using this package affords users several-fold reductions in time over a traditional serial analysis. parallelnewhybrid consists of an example data set, a readme and three operating system-specific functions to execute parallel newhybrids analyses on each of a computer's c cores. parallelnewhybrid is freely available on the long-term software hosting site github (www.github.com/bwringe/parallelnewhybrid).}, } @article {pmid27617329, year = {2016}, author = {Li, T and Bai, F and Han, P and Zhang, Y}, title = {Non-Point Source Pollutant Load Variation in Rapid Urbanization Areas by Remote Sensing, Gis and the L-THIA Model: A Case in Bao'an District, Shenzhen, China.}, journal = {Environmental management}, volume = {58}, number = {5}, pages = {873-888}, pmid = {27617329}, issn = {1432-1009}, mesh = {Biological Oxygen Demand Analysis ; China ; Cities ; Environmental Monitoring/*methods ; Environmental Pollution/*analysis ; Geographic Information Systems ; Hydrology ; *Models, Theoretical ; Nitrogen/analysis ; Phosphorus/analysis ; Population Dynamics ; *Remote Sensing Technology ; Spatio-Temporal Analysis ; *Urbanization ; }, abstract = {Urban sprawl is a major driving force that alters local and regional hydrology and increases non-point source pollution. Using the Bao'an District in Shenzhen, China, a typical rapid urbanization area, as the study area and land-use change maps from 1988 to 2014 that were obtained by remote sensing, the contributions of different land-use types to NPS pollutant production were assessed with a localized long-term hydrologic impact assessment (L-THIA) model. The results show that the non-point source pollution load changed significantly both in terms of magnitude and spatial distribution. The loads of chemical oxygen demand, total suspended substances, total nitrogen and total phosphorus were affected by the interactions between event mean concentration and the magnitude of changes in land-use acreages and the spatial distribution. From 1988 to 2014, the loads of chemical oxygen demand, suspended substances and total phosphorus showed clearly increasing trends with rates of 132.48 %, 32.52 % and 38.76 %, respectively, while the load of total nitrogen decreased by 71.52 %. The immigrant population ratio was selected as an indicator to represent the level of rapid urbanization and industrialization in the study area, and a comparison analysis of the indicator with the four non-point source loads demonstrated that the chemical oxygen demand, total phosphorus and total nitrogen loads are linearly related to the immigrant population ratio. The results provide useful information for environmental improvement and city management in the study area.}, } @article {pmid27617057, year = {2016}, author = {Melton, ED and Sorokin, DY and Overmars, L and Chertkov, O and Clum, A and Pillay, M and Ivanova, N and Shapiro, N and Kyrpides, NC and Woyke, T and Lapidus, AL and Muyzer, G}, title = {Complete genome sequence of Desulfurivibrio alkaliphilus strain AHT2(T), a haloalkaliphilic sulfidogen from Egyptian hypersaline alkaline lakes.}, journal = {Standards in genomic sciences}, volume = {11}, number = {1}, pages = {67}, pmid = {27617057}, issn = {1944-3277}, support = {322551/ERC_/European Research Council/International ; }, abstract = {Desulfurivibrio alkaliphilus strain AHT2(T) is a strictly anaerobic sulfidogenic haloalkaliphile isolated from a composite sediment sample of eight hypersaline alkaline lakes in the Wadi al Natrun valley in the Egyptian Libyan Desert. D. alkaliphilus AHT2(T) is Gram-negative and belongs to the family Desulfobulbaceae within the Deltaproteobacteria. Here we report its genome sequence, which contains a 3.10 Mbp chromosome. D. alkaliphilus AHT2(T) is adapted to survive under highly alkaline and moderately saline conditions and therefore, is relevant to the biotechnology industry and life under extreme conditions. For these reasons, D. alkaliphilus AHT2(T) was sequenced by the DOE Joint Genome Institute as part of the Community Science Program.}, } @article {pmid27614957, year = {2015}, author = {Bennett-Martin, P and Visaggi, CC and Hawthorne, TL}, title = {Mapping marine debris across coastal communities in Belize: developing a baseline for understanding the distribution of litter on beaches using geographic information systems.}, journal = {Environmental monitoring and assessment}, volume = {188}, number = {10}, pages = {557}, pmid = {27614957}, issn = {1573-2959}, mesh = {Bathing Beaches/*statistics & numerical data ; Belize ; Caribbean Region ; Ecosystem ; Environmental Monitoring/*methods ; Geographic Information Systems ; Humans ; Plastics/*analysis ; Waste Products/*analysis ; }, abstract = {Monitoring of marine debris (also known as marine litter) is an essential step in the process to eradicate ecological dangers in marine ecosystems caused by humans. This study examines marine debris in the Caribbean country of Belize using geographic information systems (GIS) to develop (1) a detailed data library for use on handheld Global Positioning System (GPS) units and tablets with mobile mapping applications for deployment in the field and (2) a freely available, online mapping portal to share data with Belizeans to encourage future citizen science efforts. Four diverse communities were targeted ranging from larger more populated towns, to smaller villages across central and southern Belize: San Pedro, Caye Caulker, Punta Gorda, and Monkey River. Fieldwork was conducted over 1 month, during which data points were collected in 50-m surveys followed by debris cleanup and removal. Features in our database included material, quantity, item, brand, and condition. Over 6000 pieces of debris were recorded in GIS for further analysis, and 299 gal of debris were removed from the shores of Belize. The most abundant form of debris observed was plastic (commonly bottles) across all locations; plastic comprised 77.6 % of all debris items observed. Through GIS, a detailed snapshot understanding of debris patterns across multiple settings in Belize was documented. Ongoing collaborations with local organizations in Belize have demonstrated significant interest and utility for such GIS approaches in analyzing and managing marine debris. The data, methodology, visual representations, and online mapping platform resulting from this research are a first step in directly supporting local Belizean community advocacy and policy, while contributing to larger institutional strategies for addressing marine debris issues in the Caribbean.}, } @article {pmid27614455, year = {2016}, author = {Joffard, N and Buatois, B and Schatz, B}, title = {Integrative taxonomy of the fly orchid group: insights from chemical ecology.}, journal = {Die Naturwissenschaften}, volume = {103}, number = {9-10}, pages = {77}, pmid = {27614455}, issn = {1432-1904}, mesh = {Classification/*methods ; Datasets as Topic ; Flowers/*chemistry ; Gas Chromatography-Mass Spectrometry ; Hydrocarbons/*analysis/chemistry ; Orchidaceae/*chemistry/*classification ; Species Specificity ; }, abstract = {Several authors have recently stressed the need to develop an integrative approach in taxonomy, but studies applying such an approach to Mediterranean orchids are scarce. In sexually deceptive orchids from the taxonomically difficult genus Ophrys, pollination is specific and performed by male insects attracted to the flowers by sex pheromone-mimicking floral scents. Floral compounds are therefore of primary importance for reproductive isolation and species delimitations in this genus. In the fly orchid group, molecular, morphological, and ecological characters have been extensively studied, but a comprehensive survey of floral scents is still lacking. In the present study, the blends of floral compounds of its three members, Ophrys insectifera, Ophrys aymoninii, and Ophrys subinsectifera, were extracted and analyzed by gas chromatography-mass spectrometry. A total of 107 compounds were found, with a majority of saturated and unsaturated hydrocarbons. Significant differentiation, both qualitative and quantitative, was found among the three taxa. This result, pooled with those from the literature, forms a comprehensive and congruent dataset that allows us to elucidate the taxonomic rank of the three members of the fly orchid group.}, } @article {pmid27614083, year = {2017}, author = {Yoshida, K and Makino, T and Kitano, J}, title = {Accumulation of Deleterious Mutations on the Neo-Y Chromosome of Japan Sea Stickleback (Gasterosteus nipponicus).}, journal = {The Journal of heredity}, volume = {108}, number = {1}, pages = {63-68}, doi = {10.1093/jhered/esw054}, pmid = {27614083}, issn = {1465-7333}, mesh = {Animals ; Female ; Gene Ontology ; Male ; Open Reading Frames ; Polymorphism, Single Nucleotide ; *Sequence Deletion ; Smegmamorpha/*genetics ; *Y Chromosome ; }, abstract = {Degeneration of Y chromosomes is a common evolutionary path of XY sex chromosome systems. Recent genomic studies in flies and plants have revealed that even young neo-sex chromosomes with the age of a few million years show signs of Y degeneration, such as the accumulation of nonsense and frameshift mutations. However, it remains unclear whether neo-Y chromosomes also show rapid degeneration in fishes, which often have homomorphic sex chromosomes. Here, we investigated whether a neo-Y chromosome of Japan Sea stickleback (Gasterosteus nipponicus), which was formed by a Y-autosome fusion within the last 2 million years, accumulates deleterious mutations. Our previous genomic analyses did not detect excess nonsense and frameshift mutations on the Japan Sea stickleback neo-Y. In the present study, we found that the nonrecombining region of the neo-Y near the fusion end has accumulated nonsynonymous mutations altering amino acids of evolutionarily highly conserved residues. Enrichment of gene ontology terms related to protein phosphorylation and cellular protein modification process was found in the genes with potentially deleterious mutations on the neo-Y. These results suggest that the neo-Y of the Japan Sea stickleback has already accumulated mutations that may impair protein functions.}, } @article {pmid27604225, year = {2016}, author = {Huang, CH and Zhang, C and Liu, M and Hu, Y and Gao, T and Qi, J and Ma, H}, title = {Multiple Polyploidization Events across Asteraceae with Two Nested Events in the Early History Revealed by Nuclear Phylogenomics.}, journal = {Molecular biology and evolution}, volume = {33}, number = {11}, pages = {2820-2835}, pmid = {27604225}, issn = {1537-1719}, mesh = {Asteraceae/*genetics ; Biodiversity ; Biological Evolution ; Databases, Nucleic Acid ; Evolution, Molecular ; *Gene Duplication ; Genetic Variation ; Genome, Plant ; Models, Genetic ; Phylogeny ; Polyploidy ; Selection, Genetic ; Sequence Analysis, DNA/methods ; Transcriptome ; }, abstract = {Biodiversity results from multiple evolutionary mechanisms, including genetic variation and natural selection. Whole-genome duplications (WGDs), or polyploidizations, provide opportunities for large-scale genetic modifications. Many evolutionarily successful lineages, including angiosperms and vertebrates, are ancient polyploids, suggesting that WGDs are a driving force in evolution. However, this hypothesis is challenged by the observed lower speciation and higher extinction rates of recently formed polyploids than diploids. Asteraceae includes about 10% of angiosperm species, is thus undoubtedly one of the most successful lineages and paleopolyploidization was suggested early in this family using a small number of datasets. Here, we used genes from 64 new transcriptome datasets and others to reconstruct a robust Asteraceae phylogeny, covering 73 species from 18 tribes in six subfamilies. We estimated their divergence times and further identified multiple potential ancient WGDs within several tribes and shared by the Heliantheae alliance, core Asteraceae (Asteroideae-Mutisioideae), and also with the sister family Calyceraceae. For two of the WGD events, there were subsequent great increases in biodiversity; the older one proceeded the divergence of at least 10 subfamilies within 10 My, with great variation in morphology and physiology, whereas the other was followed by extremely high species richness in the Heliantheae alliance clade. Our results provide different evidence for several WGDs in Asteraceae and reveal distinct association among WGD events, dramatic changes in environment and species radiations, providing a possible scenario for polyploids to overcome the disadvantages of WGDs and to evolve into lineages with high biodiversity.}, } @article {pmid27603265, year = {2016}, author = {Ankenbrand, MJ and Keller, A}, title = {bcgTree: automatized phylogenetic tree building from bacterial core genomes.}, journal = {Genome}, volume = {59}, number = {10}, pages = {783-791}, doi = {10.1139/gen-2015-0175}, pmid = {27603265}, issn = {1480-3321}, mesh = {Bacteria/*classification/*genetics ; Computational Biology/*methods ; *Genome, Bacterial ; Lactobacillus/classification/genetics ; Markov Chains ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Reproducibility of Results ; *Software ; Web Browser ; Workflow ; }, abstract = {The need for multi-gene analyses in scientific fields such as phylogenetics and DNA barcoding has increased in recent years. In particular, these approaches are increasingly important for differentiating bacterial species, where reliance on the standard 16S rDNA marker can result in poor resolution. Additionally, the assembly of bacterial genomes has become a standard task due to advances in next-generation sequencing technologies. We created a bioinformatic pipeline, bcgTree, which uses assembled bacterial genomes either from databases or own sequencing results from the user to reconstruct their phylogenetic history. The pipeline automatically extracts 107 essential single-copy core genes, found in a majority of bacteria, using hidden Markov models and performs a partitioned maximum-likelihood analysis. Here, we describe the workflow of bcgTree and, as a proof-of-concept, its usefulness in resolving the phylogeny of 293 publically available bacterial strains of the genus Lactobacillus. We also evaluate its performance in both low- and high-level taxonomy test sets. The tool is freely available at github (https://github.com/iimog/bcgTree) and our institutional homepage (http://www.dna-analytics.biozentrum.uni-wuerzburg.de).}, } @article {pmid27603019, year = {2016}, author = {Costanzo, LD and Ghosh, S and Zardecki, C and Burley, SK}, title = {Using the Tools and Resources of the RCSB Protein Data Bank.}, journal = {Current protocols in bioinformatics}, volume = {55}, number = {}, pages = {1.9.1-1.9.35}, doi = {10.1002/cpbi.13}, pmid = {27603019}, issn = {1934-340X}, support = {R01 GM133198/GM/NIGMS NIH HHS/United States ; }, mesh = {Computational Biology/*methods ; *Databases, Protein ; Humans ; Proteins/chemistry ; }, abstract = {The Protein Data Bank (PDB) archive is the worldwide repository of experimentally determined three-dimensional structures of large biological molecules found in all three kingdoms of life. Atomic-level structures of these proteins, nucleic acids, and complex assemblies thereof are central to research and education in molecular, cellular, and organismal biology, biochemistry, biophysics, materials science, bioengineering, ecology, and medicine. Several types of information are associated with each PDB archival entry, including atomic coordinates, primary experimental data, polymer sequence(s), and summary metadata. The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) serves as the U.S. data center for the PDB, distributing archival data and supporting both simple and complex queries that return results. These data can be freely downloaded, analyzed, and visualized using RCSB PDB tools and resources to gain a deeper understanding of fundamental biological processes, molecular evolution, human health and disease, and drug discovery. © 2016 by John Wiley & Sons, Inc.}, } @article {pmid27601374, year = {2017}, author = {Luu, K and Bazin, E and Blum, MG}, title = {pcadapt: an R package to perform genome scans for selection based on principal component analysis.}, journal = {Molecular ecology resources}, volume = {17}, number = {1}, pages = {67-77}, doi = {10.1111/1755-0998.12592}, pmid = {27601374}, issn = {1755-0998}, mesh = {*Adaptation, Biological ; Biostatistics/*methods ; Computational Biology/*methods ; Genetics, Population/*methods ; Principal Component Analysis ; *Selection, Genetic ; *Software ; }, abstract = {The R package pcadapt performs genome scans to detect genes under selection based on population genomic data. It assumes that candidate markers are outliers with respect to how they are related to population structure. Because population structure is ascertained with principal component analysis, the package is fast and works with large-scale data. It can handle missing data and pooled sequencing data. By contrast to population-based approaches, the package handle admixed individuals and does not require grouping individuals into populations. Since its first release, pcadapt has evolved in terms of both statistical approach and software implementation. We present results obtained with robust Mahalanobis distance, which is a new statistic for genome scans available in the 2.0 and later versions of the package. When hierarchical population structure occurs, Mahalanobis distance is more powerful than the communality statistic that was implemented in the first version of the package. Using simulated data, we compare pcadapt to other computer programs for genome scans (BayeScan, hapflk, OutFLANK, sNMF). We find that the proportion of false discoveries is around a nominal false discovery rate set at 10% with the exception of BayeScan that generates 40% of false discoveries. We also find that the power of BayeScan is severely impacted by the presence of admixed individuals whereas pcadapt is not impacted. Last, we find that pcadapt and hapflk are the most powerful in scenarios of population divergence and range expansion. Because pcadapt handles next-generation sequencing data, it is a valuable tool for data analysis in molecular ecology.}, } @article {pmid27598992, year = {2016}, author = {Xu, J and He, Q and Ma, Z and Li, T and Zhang, X and Debrunner-Vossbrinck, BA and Zhou, Z and Vossbrinck, CR}, title = {The Genome of Nosema sp. Isolate YNPr: A Comparative Analysis of Genome Evolution within the Nosema/Vairimorpha Clade.}, journal = {PloS one}, volume = {11}, number = {9}, pages = {e0162336}, pmid = {27598992}, issn = {1932-6203}, mesh = {Animals ; Base Composition ; Base Sequence ; Bees/microbiology ; Biological Evolution ; Butterflies/microbiology ; DNA Transposable Elements ; DNA, Fungal/*genetics ; DNA, Ribosomal/*genetics ; Gene Ontology ; Genetic Drift ; Genome Size ; *Genome, Fungal ; High-Throughput Nucleotide Sequencing ; Microsporidia/classification/*genetics ; Molecular Sequence Annotation ; Nosema/classification/*genetics ; Sequence Alignment ; Species Specificity ; Synteny ; }, abstract = {The microsporidian parasite designated here as Nosema sp. Isolate YNPr was isolated from the cabbage butterfly Pieris rapae collected in Honghe Prefecture, Yunnan Province, China. The genome was sequenced by Illumina sequencing and compared to those of two related members of the Nosema/Vairimorpha clade, Nosema ceranae and Nosema apis. Based upon assembly statistics, the Nosema sp. YNPr genome is 3.36 x 106bp with a G+C content of 23.18% and 2,075 protein coding sequences. An "ACCCTT" motif is present approximately 50-bp upstream of the start codon, as reported from other members of the clade and from Encephalitozoon cuniculi, a sister taxon. Comparative small subunit ribosomal DNA (SSU rDNA) analysis as well as genome-wide phylogenetic analysis confirms a closer relationship between N. ceranae and Nosema sp. YNPr than between the two honeybee parasites N. ceranae and N. apis. The more closely related N. ceranae and Nosema sp. YNPr show similarities in a number of structural characteristics such as gene synteny, gene length, gene number, transposon composition and gene reduction. Based on transposable element content of the assemblies, the transposon content of Nosema sp. YNPr is 4.8%, that of N. ceranae is 3.7%, and that of N. apis is 2.5%, with large differences in the types of transposons present among these 3 species. Gene function annotation indicates that the number of genes participating in most metabolic activities is similar in all three species. However, the number of genes in the transcription, general function, and cysteine protease categories is greater in N. apis than in the other two species. Our studies further characterize the evolution of the Nosema/Vairimorpha clade of microsporidia. These organisms maintain variable but very reduced genomes. We are interested in understanding the effects of genetic drift versus natural selection on genome size in the microsporidia and in developing a testable hypothesis for further studies on the genomic ecology of this group.}, } @article {pmid27598635, year = {2016}, author = {Almeida, TS and Fook, SM and França, FO and Monteiro, TM and Silva, EL and Gomes, LC and Farias, AM}, title = {Spatial distribution of scorpions according to the socioeconomic conditions in Campina Grande,State of Paraíba, Brazil.}, journal = {Revista da Sociedade Brasileira de Medicina Tropical}, volume = {49}, number = {4}, pages = {477-485}, doi = {10.1590/0037-8682-0128-2016}, pmid = {27598635}, issn = {1678-9849}, mesh = {Adolescent ; Adult ; Aged ; Animals ; Brazil/epidemiology ; Child ; Child, Preschool ; Female ; Geographic Information Systems ; Geographic Mapping ; Humans ; Incidence ; Infant ; Infant, Newborn ; Male ; Middle Aged ; Population Density ; Scorpion Stings/*epidemiology ; *Scorpions ; Socioeconomic Factors ; Young Adult ; }, abstract = {INTRODUCTION: Due to its frequency and morbidity, such as that caused by scorpions have achieved public health importance in certain regions of the world. The present exploratory ecological study aimed to characterize the epidemiological profile and spatial distribution of scorpion stings in Campina Grande, State of Paraíba in Northeastern Brazil.

METHODS: Geographical information system techniques were used to record the scorpion stings, and Google Earth software, Track Maker, and ArcGIS 10 Esri were used as geocoding databases. The Moran test was used to evaluate spatial correlation, and the Pearson chi-square test was used to analyze associations between scorpion stings and socioeconomic variables.

RESULTS: The study evaluated 1,466 scorpion stings. Envenomations were more frequent among women (n = 908, 61.9%), and most patients were aged 13-28 years (n = 428, 29.2%). The Southern region of the city had the largest number of registered cases (n = 548, 37.4%), followed by the Western region (n = 510, 34.8%).

CONCLUSIONS: Spatial analysis of scorpionism revealed an irregular occurrence in Campina Grande. Further, no association was observed between the socioeconomic factors analyzed and the geographic location of the scorpion envenomations. Detection of spatial areas with an increased risk of scorpionism can help prioritize adoption of preventive measures in these regions to reduce the associated incidence and morbidity.}, } @article {pmid27598186, year = {2016}, author = {Kim, JH and Gu, D and Sohn, W and Kil, SH and Kim, H and Lee, DK}, title = {Neighborhood Landscape Spatial Patterns and Land Surface Temperature: An Empirical Study on Single-Family Residential Areas in Austin, Texas.}, journal = {International journal of environmental research and public health}, volume = {13}, number = {9}, pages = {}, pmid = {27598186}, issn = {1660-4601}, mesh = {Cities ; *Environment ; Environmental Monitoring/*methods ; Geographic Information Systems ; Models, Theoretical ; *Residence Characteristics ; *Temperature ; Texas ; Urbanization ; }, abstract = {Rapid urbanization has accelerated land use and land cover changes, and generated the urban heat island effect (UHI). Previous studies have reported positive effects of neighborhood landscapes on mitigating urban surface temperatures. However, the influence of neighborhood landscape spatial patterns on enhancing cooling effects has not yet been fully investigated. The main objective of this study was to assess the relationships between neighborhood landscape spatial patterns and land surface temperatures (LST) by using multi-regression models considering spatial autocorrelation issues. To measure the influence of neighborhood landscape spatial patterns on LST, this study analyzed neighborhood environments of 15,862 single-family houses in Austin, Texas, USA. Using aerial photos, geographic information systems (GIS), and remote sensing, FRAGSTATS was employed to calculate values of several landscape indices used to measure neighborhood landscape spatial patterns. After controlling for the spatial autocorrelation effect, results showed that larger and better-connected landscape spatial patterns were positively correlated with lower LST values in neighborhoods, while more fragmented and isolated neighborhood landscape patterns were negatively related to the reduction of LST.}, } @article {pmid27591249, year = {2016}, author = {Mykles, DL and Burnett, KG and Durica, DS and Stillman, JH}, title = {Tapping the Power of Crustacean Transcriptomics to Address Grand Challenges in Comparative Biology: An Introduction to the Symposium.}, journal = {Integrative and comparative biology}, volume = {56}, number = {6}, pages = {1047-1054}, doi = {10.1093/icb/icw116}, pmid = {27591249}, issn = {1557-7023}, mesh = {Animals ; Computational Biology/*trends ; Congresses as Topic ; Crustacea/*genetics ; Transcriptome/genetics ; }, abstract = {Crustaceans, and decapods in particular (i.e., crabs, shrimp, and lobsters), are a diverse and ecologically and commercially important group of organisms. Understanding responses to abiotic and biotic factors is critical for developing best practices in aquaculture and assessing the effects of changing environments on the biology of these important animals. A relatively small number of decapod crustacean species have been intensively studied at the molecular level; the availability, experimental tractability, and economic relevance factor into the selection of a particular species as a model. Transcriptomics, using high-throughput next generation sequencing (NGS, coupled with RNA sequencing or RNA-seq) is revolutionizing crustacean biology. The 11 symposium papers in this volume illustrate how RNA-seq is being used to study stress response, molting and limb regeneration, immunity and disease, reproduction and development, neurobiology, and ecology and evolution. This symposium occurred on the 10th anniversary of the symposium, "Genomic and Proteomic Approaches to Crustacean Biology", held at the Society for Integrative and Comparative Biology 2006 meeting. Two participants in the 2006 symposium, the late Paul Gross and David Towle, were recognized as leaders who pioneered the use of molecular techniques that would ultimately foster the transcriptomics research reviewed in this volume. RNA-seq is a powerful tool for hypothesis-driven research, as well as an engine for discovery. It has eclipsed the technologies available in 2006, such as microarrays, expressed sequence tags, and subtractive hybridization screening, as the millions of "reads" from NGS enable researchers to de novo assemble a comprehensive transcriptome without a complete genome sequence. The symposium series concludes with a policy paper that gives an overview of the resources available and makes recommendations for developing better tools for functional annotation and pathway and network analysis in organisms in which the genome is not available or is incomplete.}, } @article {pmid27584861, year = {2016}, author = {Janzen, DH and Hallwachs, W}, title = {DNA barcoding the Lepidoptera inventory of a large complex tropical conserved wildland, Area de Conservacion Guanacaste, northwestern Costa Rica.}, journal = {Genome}, volume = {59}, number = {9}, pages = {641-660}, doi = {10.1139/gen-2016-0005}, pmid = {27584861}, issn = {1480-3321}, mesh = {Animals ; Biodiversity ; Cluster Analysis ; Conservation of Natural Resources ; Costa Rica ; *DNA Barcoding, Taxonomic ; Lepidoptera/*classification/*genetics ; Tropical Climate ; }, abstract = {The 37-year ongoing inventory of the estimated 15 000 species of Lepidoptera living in the 125 000 terrestrial hectares of Area de Conservacion Guanacaste, northwestern Costa Rica, has DNA barcode documented 11 000+ species, and the simultaneous inventory of at least 6000+ species of wild-caught caterpillars, plus 2700+ species of parasitoids. The inventory began with Victorian methodologies and species-level perceptions, but it was transformed in 2004 by the full application of DNA barcoding for specimen identification and species discovery. This tropical inventory of an extraordinarily species-rich and complex multidimensional trophic web has relied upon the sequencing services provided by the Canadian Centre for DNA Barcoding, and the informatics support from BOLD, the Barcode of Life Data Systems, major tools developed by the Centre for Biodiversity Genomics at the Biodiversity Institute of Ontario, and available to all through couriers and the internet. As biodiversity information flows from these many thousands of undescribed and often look-alike species through their transformations to usable product, we see that DNA barcoding, firmly married to our centuries-old morphology-, ecology-, microgeography-, and behavior-based ways of taxonomizing the wild world, has made possible what was impossible before 2004. We can now work with all the species that we find, as recognizable species-level units of biology. In this essay, we touch on some of the details of the mechanics of actually using DNA barcoding in an inventory.}, } @article {pmid27579737, year = {2016}, author = {Ferreira, FR and Nascimento, LF}, title = {Mortality due to cutaneous melanoma in south region of Brazil: a spatial approach.}, journal = {Anais brasileiros de dermatologia}, volume = {91}, number = {4}, pages = {437-441}, pmid = {27579737}, issn = {1806-4841}, mesh = {Brazil/epidemiology ; Cluster Analysis ; Female ; Geographic Information Systems ; Humans ; Incidence ; Male ; Melanoma/*mortality ; Reference Values ; Sex Distribution ; Sex Factors ; Skin Neoplasms/*mortality ; Spatial Analysis ; }, abstract = {BACKGROUND: Cutaneous melanoma is a skin cancer with low incidence but high mortality rates. The South region of Brazil has the highest death rates by melanoma per 100,000 inhabitants of the country. Little is known about the spatial distribution of this malignancy in southern Brazil.

OBJECTIVES: Identify the spatial patterns of deaths from cutaneous melanoma in South region of Brazil, using geoprocessing tools.

METHODS: This is an ecological and exploratory study of death information by cutaneous melanoma obtained from portal Datasus, for Brazil's southern region, from January 2008 to December 2012. Deaths were separated by gender and rates per 100,000 inhabitants were calculated and used to compile thematic maps, Moran maps and Kernel maps, using TerraView software. It was adopted an alpha = 5%.

RESULTS: There were data on 2378 deaths from cutaneous melanoma in the study period. High rates were identified in the northern and littoral regions of Rio Grande do Sul; the northeast of Santa Catarina; and west of Paraná - for the total population, with minor differences detected and indicated regarding gender. The global Moran index presented p-values of 0.03, 0.04 and 0.03, respectively, for male, female and overall deaths. All the micro-regions that showed high priority for intervention were detected in the Rio Grande do Sul.

CONCLUSION: Spatial clusters of micro-regions with high death rates from cutaneous melanoma in South region of Brazil were identified, serving as an important tool for health managers.}, } @article {pmid27573208, year = {2016}, author = {Ye, C and Hill, CM and Wu, S and Ruan, J and Ma, ZS}, title = {DBG2OLC: Efficient Assembly of Large Genomes Using Long Erroneous Reads of the Third Generation Sequencing Technologies.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {31900}, pmid = {27573208}, issn = {2045-2322}, mesh = {Computational Biology/*methods ; Genomics/*methods ; High-Throughput Nucleotide Sequencing/*methods ; Sequence Analysis, DNA/*methods ; }, abstract = {The highly anticipated transition from next generation sequencing (NGS) to third generation sequencing (3GS) has been difficult primarily due to high error rates and excessive sequencing cost. The high error rates make the assembly of long erroneous reads of large genomes challenging because existing software solutions are often overwhelmed by error correction tasks. Here we report a hybrid assembly approach that simultaneously utilizes NGS and 3GS data to address both issues. We gain advantages from three general and basic design principles: (i) Compact representation of the long reads leads to efficient alignments. (ii) Base-level errors can be skipped; structural errors need to be detected and corrected. (iii) Structurally correct 3GS reads are assembled and polished. In our implementation, preassembled NGS contigs are used to derive the compact representation of the long reads, motivating an algorithmic conversion from a de Bruijn graph to an overlap graph, the two major assembly paradigms. Moreover, since NGS and 3GS data can compensate for each other, our hybrid assembly approach reduces both of their sequencing requirements. Experiments show that our software is able to assemble mammalian-sized genomes orders of magnitude more quickly than existing methods without consuming a lot of memory, while saving about half of the sequencing cost.}, } @article {pmid27573121, year = {2016}, author = {Nelson, MB and Chase, AB and Martiny, JB and Stocker, R and Nguyen, J and Lloyd, K and Oshiro, RT and Kearns, DB and Schneider, JP and Ringel, PD and Basler, M and Olson, CA and Vuong, HE and Hsiao, EY and Roller, BR and Ackermann, M and Smillie, C and Chien, D and Alm, E and Jermy, AJ}, title = {The Microbial Olympics 2016.}, journal = {Nature microbiology}, volume = {1}, number = {8}, pages = {16122}, pmid = {27573121}, issn = {2058-5276}, support = {DP5 OD017924/OD/NIH HHS/United States ; F31 MH090749/MH/NIMH NIH HHS/United States ; T32 GM087237/GM/NIGMS NIH HHS/United States ; }, mesh = {*Bacteria/genetics/growth & development/metabolism ; *Bacterial Physiological Phenomena ; Humans ; Zika Virus/pathogenicity ; }, abstract = {Following the success of the inaugural games, the Microbial Olympics return with a new series of events and microbial competitors. The games may have moved to a new hosting venue, but the dedication to training, fitness, competition (and yes, education and humour) lives on.}, } @article {pmid27572284, year = {2016}, author = {Aubert, AH and Thrun, MC and Breuer, L and Ultsch, A}, title = {Knowledge discovery from high-frequency stream nitrate concentrations: hydrology and biology contributions.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {31536}, pmid = {27572284}, issn = {2045-2322}, mesh = {*Databases, Factual ; *Environmental Monitoring ; Nitrates/*analysis ; Rivers/*chemistry ; }, abstract = {High-frequency, in-situ monitoring provides large environmental datasets. These datasets will likely bring new insights in landscape functioning and process scale understanding. However, tailoring data analysis methods is necessary. Here, we detach our analysis from the usual temporal analysis performed in hydrology to determine if it is possible to infer general rules regarding hydrochemistry from available large datasets. We combined a 2-year in-stream nitrate concentration time series (time resolution of 15 min) with concurrent hydrological, meteorological and soil moisture data. We removed the low-frequency variations through low-pass filtering, which suppressed seasonality. We then analyzed the high-frequency variability component using Pareto Density Estimation, which to our knowledge has not been applied to hydrology. The resulting distribution of nitrate concentrations revealed three normally distributed modes: low, medium and high. Studying the environmental conditions for each mode revealed the main control of nitrate concentration: the saturation state of the riparian zone. We found low nitrate concentrations under conditions of hydrological connectivity and dominant denitrifying biological processes, and we found high nitrate concentrations under hydrological recession conditions and dominant nitrifying biological processes. These results generalize our understanding of hydro-biogeochemical nitrate flux controls and bring useful information to the development of nitrogen process-based models at the landscape scale.}, } @article {pmid27565341, year = {2016}, author = {Nayfach, S and Pollard, KS}, title = {Toward Accurate and Quantitative Comparative Metagenomics.}, journal = {Cell}, volume = {166}, number = {5}, pages = {1103-1116}, pmid = {27565341}, issn = {1097-4172}, support = {R21 AI108953/AI/NIAID NIH HHS/United States ; T32 GM067547/GM/NIGMS NIH HHS/United States ; }, mesh = {Classification ; Computational Biology ; Humans ; *Metagenome ; Metagenomics/*standards ; Microbiota/*genetics ; Models, Statistical ; }, abstract = {Shotgun metagenomics and computational analysis are used to compare the taxonomic and functional profiles of microbial communities. Leveraging this approach to understand roles of microbes in human biology and other environments requires quantitative data summaries whose values are comparable across samples and studies. Comparability is currently hampered by the use of abundance statistics that do not estimate a meaningful parameter of the microbial community and biases introduced by experimental protocols and data-cleaning approaches. Addressing these challenges, along with improving study design, data access, metadata standardization, and analysis tools, will enable accurate comparative metagenomics. We envision a future in which microbiome studies are replicable and new metagenomes are easily and rapidly integrated with existing data. Only then can the potential of metagenomics for predictive ecological modeling, well-powered association studies, and effective microbiome medicine be fully realized.}, } @article {pmid27565139, year = {2016}, author = {Hess, M and Wildhagen, H and Junker, LV and Ensminger, I}, title = {Transcriptome responses to temperature, water availability and photoperiod are conserved among mature trees of two divergent Douglas-fir provenances from a coastal and an interior habitat.}, journal = {BMC genomics}, volume = {17}, number = {1}, pages = {682}, pmid = {27565139}, issn = {1471-2164}, mesh = {Abies/drug effects/*genetics/*physiology ; Adaptation, Physiological/drug effects/genetics ; Conserved Sequence ; Dose-Response Relationship, Drug ; *Ecosystem ; *Gene Expression Profiling ; Gene Ontology ; Molecular Sequence Annotation ; *Photoperiod ; Sequence Analysis, RNA ; *Temperature ; Water/*pharmacology ; }, abstract = {BACKGROUND: Local adaptation and phenotypic plasticity are important components of plant responses to variations in environmental conditions. While local adaptation has been widely studied in trees, little is known about plasticity of gene expression in adult trees in response to ever changing environmental conditions in natural habitats. Here we investigate plasticity of gene expression in needle tissue between two Douglas-fir provenances represented by 25 adult trees using deep RNA sequencing (RNA-Seq).

RESULTS: Using linear mixed models we investigated the effect of temperature, soil water availability and photoperiod on the abundance of 59189 detected transcripts. Expression of more than 80 % of all identified transcripts revealed a response to variations in environmental conditions in the field. GO term overrepresentation analysis revealed gene expression responses to temperature, soil water availability and photoperiod that are highly conserved among many plant taxa. However, expression differences between the two Douglas-fir provenances were rather small compared to the expression differences observed between individual trees. Although the effect of environment on global transcript expression was high, the observed genotype by environment (GxE) interaction of gene expression was surprisingly low, since only 21 of all detected transcripts showed a GxE interaction.

CONCLUSIONS: The majority of the transcriptome responses in plant leaf tissue is driven by variations in environmental conditions. The small variation between individuals and populations suggests strong conservation of this response within Douglas-fir. Therefore we conclude that plastic transcriptome responses to variations in environmental conditions are only weakly affected by local adaptation in Douglas-fir.}, } @article {pmid27559000, year = {2016}, author = {Basak, SC and Vracko, M and Witzmann, FA}, title = {Mathematical Nanotoxicoproteomics: Quantitative Characterization of Effects of Multi-walled Carbon Nanotubes (MWCNT) and TiO2 Nanobelts (TiO2-NB) on Protein Expression Patterns in Human Intestinal Cells.}, journal = {Current computer-aided drug design}, volume = {12}, number = {4}, pages = {259-264}, doi = {10.2174/1573409912666160824145722}, pmid = {27559000}, issn = {1875-6697}, mesh = {Biomarkers/metabolism ; Caco-2 Cells ; Colon/*drug effects/metabolism ; Data Mining ; Databases, Protein ; HT29 Cells ; Humans ; Informatics ; Models, Biological ; Nanoparticles/*toxicity ; *Nanotechnology ; Nanotubes, Carbon/*toxicity ; Proteins/*metabolism ; *Proteomics ; Risk Assessment ; Time Factors ; Titanium/*toxicity ; Toxicology/*methods ; }, abstract = {BACKGROUND: Various applications of nanosubstances in industrial and consumer goods sectors are growing rapidly because of their useful chemical and physical properties.

OBJECTIVES: Assessment of hazard posed by exposure to nanosubstances is essential for the protection of human and ecological health.

METHODS: We analyzed the proteomics patterns of Caco-2/HT29-MTX cells in co-culture exposed for three and twenty four hours to two kinds of nanoparticles: multi-walled carbon nanotubes (MWCNT) and TiO2 nanobelts (TiO2-NB). For each nanosubstance cells were exposed to two concentrations of the material before carrying out proteomics analyses: 10 μg and 100 μg. In each case over 3000 proteins were identified. A mathematically based similarity index, which measures the changes in abundances of cellular proteins that are highly affected by exposure to the nanosubstances, was used to characterize toxic effects of the nanomaterials.

RESULTS: We identified 8 and 25 proteins, which are most highly affected by MWCNT and TiO2-NB, respectively. These proteins may be responsible for specific response of cells to the nanoparticles. Further 14 reported proteins are affected by either of the two nanoparticles and they are probably related to nonspecific toxic response of the cells.

CONCLUSION: The similarity methods proposed in this paper may be useful in the management and visualization of the large amount of data generated by proteomics technologies.}, } @article {pmid27558710, year = {2016}, author = {Kirchner, TR and Shiffman, S}, title = {Spatio-temporal determinants of mental health and well-being: advances in geographically-explicit ecological momentary assessment (GEMA).}, journal = {Social psychiatry and psychiatric epidemiology}, volume = {51}, number = {9}, pages = {1211-1223}, pmid = {27558710}, issn = {1433-9285}, support = {R01 DA034734/DA/NIDA NIH HHS/United States ; R01 DA040930/DA/NIDA NIH HHS/United States ; }, mesh = {*Ecological Momentary Assessment ; *Geographic Information Systems ; Humans ; Mental Disorders/epidemiology ; *Mental Health ; Residence Characteristics/statistics & numerical data ; Resilience, Psychological ; Risk ; *Spatio-Temporal Analysis ; Telemedicine ; }, abstract = {PURPOSE: Overview of geographically explicit momentary assessment research, applied to the study of mental health and well-being, which allows for cross-validation, extension, and enrichment of research on place and health.

METHODS: Building on the historical foundations of both ecological momentary assessment and geographic momentary assessment research, this review explores their emerging synergy into a more generalized and powerful research framework.

RESULTS: Geographically explicit momentary assessment methods are rapidly advancing across a number of complimentary literatures that intersect but have not yet converged. Key contributions from these areas reveal tremendous potential for transdisciplinary and translational science.

CONCLUSIONS: Mobile communication devices are revolutionizing research on mental health and well-being by physically linking momentary experience sampling to objective measures of socio-ecological context in time and place. Methodological standards are not well-established and will be required for transdisciplinary collaboration and scientific inference moving forward.}, } @article {pmid27557578, year = {2016}, author = {Carter, JM and Gibbs, M and Breuker, CJ}, title = {Studying Oogenesis in a Non-model Organism Using Transcriptomics: Assembling, Annotating, and Analyzing Your Data.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1457}, number = {}, pages = {129-143}, doi = {10.1007/978-1-4939-3795-0_10}, pmid = {27557578}, issn = {1940-6029}, mesh = {Computational Biology/*methods ; Databases, Nucleic Acid ; *Gene Expression Profiling/methods ; Gene Ontology ; Molecular Sequence Annotation ; Oogenesis/*genetics ; Quality Control ; Software ; *Transcriptome ; Web Browser ; Workflow ; }, abstract = {This chapter provides a guide to processing and analyzing RNA-Seq data in a non-model organism. This approach was implemented for studying oogenesis in the Speckled Wood Butterfly Pararge aegeria. We focus in particular on how to perform a more informative primary annotation of your non-model organism by implementing our multi-BLAST annotation strategy. We also provide a general guide to other essential steps in the next-generation sequencing analysis workflow. Before undertaking these methods, we recommend you familiarize yourself with command line usage and fundamental concepts of database handling. Most of the operations in the primary annotation pipeline can be performed in Galaxy (or equivalent standalone versions of the tools) and through the use of common database operations (e.g. to remove duplicates) but other equivalent programs and/or custom scripts can be implemented for further automation.}, } @article {pmid27556474, year = {2016}, author = {Karamage, F and Zhang, C and Kayiranga, A and Shao, H and Fang, X and Ndayisaba, F and Nahayo, L and Mupenzi, C and Tian, G}, title = {USLE-Based Assessment of Soil Erosion by Water in the Nyabarongo River Catchment, Rwanda.}, journal = {International journal of environmental research and public health}, volume = {13}, number = {8}, pages = {}, pmid = {27556474}, issn = {1660-4601}, mesh = {*Conservation of Natural Resources ; Ecosystem ; Environmental Monitoring/methods ; Geographic Information Systems ; Remote Sensing Technology ; Rwanda ; *Soil ; Uganda ; *Water Movements ; }, abstract = {Soil erosion has become a serious problem in recent decades due to unhalted trends of unsustainable land use practices. Assessment of soil erosion is a prominent tool in planning and conservation of soil and water resource ecosystems. The Universal Soil Loss Equation (USLE) was applied to Nyabarongo River Catchment that drains about 8413.75 km[2] (33%) of the total Rwanda coverage and a small part of the Southern Uganda (about 64.50 km[2]) using Geographic Information Systems (GIS) and Remote Sensing technologies. The estimated total annual actual soil loss was approximately estimated at 409 million tons with a mean erosion rate of 490 t·ha(-1)·y(-1) (i.e., 32.67 mm·y(-1)). The cropland that occupied 74.85% of the total catchment presented a mean erosion rate of 618 t·ha(-1)·y(-1) (i.e., 41.20 mm·y(-1)) and was responsible for 95.8% of total annual soil loss. Emergency soil erosion control is required with a priority accorded to cropland area of 173,244 ha, which is extremely exposed to actual soil erosion rate of 2222 t·ha(-1)·y(-1) (i.e., 148.13 mm·y(-1)) and contributed to 96.2% of the total extreme soil loss in the catchment. According to this study, terracing cultivation method could reduce the current erosion rate in cropland areas by about 78%. Therefore, the present study suggests the catchment management by constructing check dams, terracing, agroforestry and reforestation of highly exposed areas as suitable measures for erosion and water pollution control within the Nyabarongo River Catchment and in other regions facing the same problems.}, } @article {pmid27555220, year = {2016}, author = {Zhao, K and Jurdak, R}, title = {Understanding the spatiotemporal pattern of grazing cattle movement.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {31967}, pmid = {27555220}, issn = {2045-2322}, mesh = {Algorithms ; Animals ; Behavior, Animal ; Cattle ; Entropy ; Geographic Information Systems ; Movement/*physiology ; }, abstract = {Understanding the drivers of animal movement is significant for ecology and biology. Yet researchers have so far been unable to fully understand these drivers, largely due to low data resolution. In this study, we analyse a high-frequency movement dataset for a group of grazing cattle and investigate their spatiotemporal patterns using a simple two-state 'stop-and-move' mobility model. We find that the dispersal kernel in the moving state is best described by a mixture exponential distribution, indicating the hierarchical nature of the movement. On the other hand, the waiting time appears to be scale-invariant below a certain cut-off and is best described by a truncated power-law distribution, suggesting that the non-moving state is governed by time-varying dynamics. We explore possible explanations for the observed phenomena, covering factors that can play a role in the generation of mobility patterns, such as the context of grazing environment, the intrinsic decision-making mechanism or the energy status of different activities. In particular, we propose a new hypothesis that the underlying movement pattern can be attributed to the most probable observable energy status under the maximum entropy configuration. These results are not only valuable for modelling cattle movement but also provide new insights for understanding the underlying biological basis of grazing behaviour.}, } @article {pmid27554344, year = {2016}, author = {Igai, K and Itakura, M and Nishijima, S and Tsurumaru, H and Suda, W and Tsutaya, T and Tomitsuka, E and Tadokoro, K and Baba, J and Odani, S and Natsuhara, K and Morita, A and Yoneda, M and Greenhill, AR and Horwood, PF and Inoue, J and Ohkuma, M and Hongoh, Y and Yamamoto, T and Siba, PM and Hattori, M and Minamisawa, K and Umezaki, M}, title = {Nitrogen fixation and nifH diversity in human gut microbiota.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {31942}, pmid = {27554344}, issn = {2045-2322}, mesh = {Acetylene/chemistry/metabolism ; Adult ; Bacterial Proteins/classification/genetics/*metabolism ; Clostridiales/enzymology/genetics/isolation & purification ; Databases, Factual ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Humans ; Klebsiella/enzymology/genetics/isolation & purification ; Male ; Metagenomics ; Nitrogen/chemistry/*metabolism ; Nitrogen Fixation ; Nitrogen Isotopes/metabolism ; Oxidoreductases/classification/genetics/*metabolism ; Phylogeny ; RNA, Bacterial/chemistry/isolation & purification/metabolism ; Sequence Analysis, DNA ; Young Adult ; }, abstract = {It has been hypothesized that nitrogen fixation occurs in the human gut. However, whether the gut microbiota truly has this potential remains unclear. We investigated the nitrogen-fixing activity and diversity of the nitrogenase reductase (NifH) genes in the faecal microbiota of humans, focusing on Papua New Guinean and Japanese individuals with low to high habitual nitrogen intake. A (15)N2 incorporation assay showed significant enrichment of (15)N in all faecal samples, irrespective of the host nitrogen intake, which was also supported by an acetylene reduction assay. The fixed nitrogen corresponded to 0.01% of the standard nitrogen requirement for humans, although our data implied that the contribution in the gut in vivo might be higher than this value. The nifH genes recovered in cloning and metagenomic analyses were classified in two clusters: one comprising sequences almost identical to Klebsiella sequences and the other related to sequences of Clostridiales members. These results are consistent with an analysis of databases of faecal metagenomes from other human populations. Collectively, the human gut microbiota has a potential for nitrogen fixation, which may be attributable to Klebsiella and Clostridiales strains, although no evidence was found that the nitrogen-fixing activity substantially contributes to the host nitrogen balance.}, } @article {pmid27549737, year = {2016}, author = {Mark, K and Cornejo, C and Keller, C and Flück, D and Scheidegger, C}, title = {Barcoding lichen-forming fungi using 454 pyrosequencing is challenged by artifactual and biological sequence variation.}, journal = {Genome}, volume = {59}, number = {9}, pages = {685-704}, doi = {10.1139/gen-2015-0189}, pmid = {27549737}, issn = {1480-3321}, mesh = {Biodiversity ; Biological Evolution ; Computational Biology ; Consensus Sequence ; *DNA Barcoding, Taxonomic ; *Genetic Variation ; *High-Throughput Nucleotide Sequencing/instrumentation/methods ; Lichens/*classification/*genetics ; Molecular Typing/instrumentation/methods ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {Although lichens (lichen-forming fungi) play an important role in the ecological integrity of many vulnerable landscapes, only a minority of lichen-forming fungi have been barcoded out of the currently accepted ∼18 000 species. Regular Sanger sequencing can be problematic when analyzing lichens since saprophytic, endophytic, and parasitic fungi live intimately admixed, resulting in low-quality sequencing reads. Here, high-throughput, long-read 454 pyrosequencing in a GS FLX+ System was tested to barcode the fungal partner of 100 epiphytic lichen species from Switzerland using fungal-specific primers when amplifying the full internal transcribed spacer region (ITS). The present study shows the potential of DNA barcoding using pyrosequencing, in that the expected lichen fungus was successfully sequenced for all samples except one. Alignment solutions such as BLAST were found to be largely adequate for the generated long reads. In addition, the NCBI nucleotide database-currently the most complete database for lichen-forming fungi-can be used as a reference database when identifying common species, since the majority of analyzed lichens were identified correctly to the species or at least to the genus level. However, several issues were encountered, including a high sequencing error rate, multiple ITS versions in a genome (incomplete concerted evolution), and in some samples the presence of mixed lichen-forming fungi (possible lichen chimeras).}, } @article {pmid27548952, year = {2016}, author = {Li, YJ and Zhang, LY and Wu, YW and Li, CL and Yang, TX and Tang, J}, title = {[GIS Spatial Distribution and Ecological Risk Assessment of Heavy Metals in Surface Sediments of Shallow Lakes in Jiangsu Province].}, journal = {Huan jing ke xue= Huanjing kexue}, volume = {37}, number = {4}, pages = {1321-1329}, pmid = {27548952}, issn = {0250-3301}, mesh = {China ; *Environmental Monitoring ; Geographic Information Systems ; Geologic Sediments/*chemistry ; Geology ; Lakes/*chemistry ; Metals, Heavy/*analysis ; Risk Assessment ; Soil ; Water Pollutants, Chemical/*analysis ; }, abstract = {To understand pollution of heavy metals in surface sediments of shallow lakes, surface sediments samples of 11 lakes in Jiangsu province were collected to determine the content of six heavy metals including As, Cr, Cu, Pb, Zn and Ni. GIS was used to analyze the spatial distribution of heavy metals, and geological accumulation index (Igeo), modified contamination index (mCd) pollution load index (PLI) and potential ecological risk index (RI) were used to evaluate heavy metal contamination in the sediments. The results showed that: in the lakes' surface sediments, the average content of As, Cu, Zn, Cr, Pb, Ni in multiples of soil background of Jiangsu province were 1.74-3.85, 0.65-2.66, 0.48-3.56, 0.43-1.52, 0.02-1.49 and 0.12-1.42. According to the evaluation results of Igeo and RI, As, which had high degree of enrichment and great potential ecological risk, was the main pollutant, followed by Cu, and pollution of the rest of heavy metals was relatively light. Combining the results of several evaluation methods, in surface sediments of Sanjiu Lake, Gaoyou Lake and Shaobo Lake, these heavy metals had the most serious pollution, the maximum pollution loading and moderate potential ecological risk; in surface sediments of Gehu Lake, Baima Lake and Hongze Lake, some regions were polluted by certain metals, the overall trend of pollution was aggravating, the pollution loading was large, and the potential ecological risk reached moderate; in the other 5 lakes, the risk of sediments polluted by heavy metals, as well as the pollution loading, was small, and the overall was not polluted.}, } @article {pmid27548162, year = {2016}, author = {Alkhalili, RN and Bernfur, K and Dishisha, T and Mamo, G and Schelin, J and Canbäck, B and Emanuelsson, C and Hatti-Kaul, R}, title = {Antimicrobial Protein Candidates from the Thermophilic Geobacillus sp. Strain ZGt-1: Production, Proteomics, and Bioinformatics Analysis.}, journal = {International journal of molecular sciences}, volume = {17}, number = {8}, pages = {}, pmid = {27548162}, issn = {1422-0067}, mesh = {Anti-Infective Agents/chemistry/metabolism ; Bacterial Proteins/chemistry/metabolism ; Computational Biology/*methods ; Geobacillus/*metabolism ; Hot Temperature ; Proteomics/*methods ; }, abstract = {A thermophilic bacterial strain, Geobacillus sp. ZGt-1, isolated from Zara hot spring in Jordan, was capable of inhibiting the growth of the thermophilic G. stearothermophilus and the mesophilic Bacillus subtilis and Salmonella typhimurium on a solid cultivation medium. Antibacterial activity was not observed when ZGt-1 was cultivated in a liquid medium; however, immobilization of the cells in agar beads that were subjected to sequential batch cultivation in the liquid medium at 60 °C showed increasing antibacterial activity up to 14 cycles. The antibacterial activity was lost on protease treatment of the culture supernatant. Concentration of the protein fraction by ammonium sulphate precipitation followed by denaturing polyacrylamide gel electrophoresis separation and analysis of the gel for antibacterial activity against G. stearothermophilus showed a distinct inhibition zone in 15-20 kDa range, suggesting that the active molecule(s) are resistant to denaturation by SDS. Mass spectrometric analysis of the protein bands around the active region resulted in identification of 22 proteins with molecular weight in the range of interest, three of which were new and are here proposed as potential antimicrobial protein candidates by in silico analysis of their amino acid sequences. Mass spectrometric analysis also indicated the presence of partial sequences of antimicrobial enzymes, amidase, and dd-carboxypeptidase.}, } @article {pmid27542380, year = {2017}, author = {Scholtissek, A and Ullrich, SR and Mühling, M and Schlömann, M and Paul, CE and Tischler, D}, title = {A thermophilic-like ene-reductase originating from an acidophilic iron oxidizer.}, journal = {Applied microbiology and biotechnology}, volume = {101}, number = {2}, pages = {609-619}, doi = {10.1007/s00253-016-7782-3}, pmid = {27542380}, issn = {1432-0614}, mesh = {Betaproteobacteria/*enzymology/*genetics ; Cloning, Molecular ; Coenzymes/analysis ; Computational Biology ; Escherichia coli/genetics/metabolism ; Gene Expression ; *Genome, Bacterial ; Hydrogen-Ion Concentration ; Kinetics ; Maleimides/metabolism ; Oxidoreductases/genetics/*isolation & purification/*metabolism ; Recombinant Proteins/genetics/isolation & purification/metabolism ; Succinimides/metabolism ; Temperature ; }, abstract = {Ene-reductases originating from extremophiles are gaining importance in the field of biocatalysis due to higher-stability properties. The genome of the acidophilic iron-oxidizing bacterium "Ferrovum" sp. JA12 was found to harbor a thermophilic-like ene-reductase (FOYE-1). The foye-1 gene was ligated into a pET16bp expression vector system, and the enzyme was produced in Escherichia coli BL21 (DE3; pLysS) cells in yields of 10 mg L[-1]. FOYE-1 showed remarkable activity and rates on N-phenylmaleimide and N-phenyl-2-methylmaleimide (up to 89 U mg[-1], >97 % conversion, 95 % (R)-selective) with both nicotinamide cofactors, NADPH and NADH. The catalytic efficiency with NADPH was 27 times higher compared to NADH. At the temperature maximum (50 °C) and pH optimum (6.5), activity was almost doubled to 160 U mg[-1]. These findings accomplish FOYE-1 for a valuable biocatalyst in the synthesis of succinimides. The appearance of a thermophilic-like ene-reductase in an acidic habitat is discussed with respect to its phylogenetic placement and to the genomic neighborhood of the encoding gene, awarding FOYE-1 a putative involvement in a quorum-sensing process.}, } @article {pmid27540160, year = {2016}, author = {Yoshida, S and Hiraga, K and Takehana, T and Taniguchi, I and Yamaji, H and Maeda, Y and Toyohara, K and Miyamoto, K and Kimura, Y and Oda, K}, title = {Response to Comment on "A bacterium that degrades and assimilates poly(ethylene terephthalate)".}, journal = {Science (New York, N.Y.)}, volume = {353}, number = {6301}, pages = {759}, doi = {10.1126/science.aaf8625}, pmid = {27540160}, issn = {1095-9203}, mesh = {Betaproteobacteria/*enzymology ; Plastics/*metabolism ; Polyethylene Terephthalates/*metabolism ; }, abstract = {Yang et al suggest that the use of low-crystallinity poly(ethylene terephthalate) (PET) exaggerates our results. However, the primary focus of our study was identifying an organism capable of the biological degradation and assimilation of PET, regardless of its crystallinity. We provide additional PET depolymerization data that further support several other lines of data showing PET assimilation by growing cells of Ideonella sakaiensis.}, } @article {pmid27539327, year = {2017}, author = {Schweitzer, P and Husky, M and Allard, M and Amieva, H and Pérès, K and Foubert-Samier, A and Dartigues, JF and Swendsen, J}, title = {Feasibility and validity of mobile cognitive testing in the investigation of age-related cognitive decline.}, journal = {International journal of methods in psychiatric research}, volume = {26}, number = {3}, pages = {}, pmid = {27539327}, issn = {1557-0657}, mesh = {Aged ; Aged, 80 and over ; *Cognitive Aging ; Cognitive Dysfunction/*diagnosis ; Diagnosis, Computer-Assisted/*standards ; Feasibility Studies ; Female ; Humans ; Male ; *Medical Informatics Applications ; *Mobile Applications ; Reproducibility of Results ; }, abstract = {Mobile cognitive testing may be used to help characterize subtle deficits at the earliest stages of cognitive decline. Despite growing interest in this approach, comprehensive information concerning its feasibility and validity has been lacking in elderly samples. Over a one-week period, this study applied mobile cognitive tests of semantic memory, episodic memory and executive functioning in a cohort of 114 elderly non-demented community residents. While the study acceptance rate was moderate (66%), the majority of recruited individuals met minimal compliance thresholds and responded to an average of 82% of the repeated daily assessments. Missing data did not increase over the course of the study, but practice effects were observed for several test scores. However, even when controlling for practice effects, traditional neuropsychological tests were significantly associated with mobile cognitive test scores. In particular, the Isaacs Set Test was associated with mobile assessments of semantic memory (γ = 0.084, t = 5.598, p < 0.001), the Grober and Buschke with mobile assessments of episodic memory (γ = 0.069, t = 3.156, p < 0.01, and the Weschler symbol coding with mobile assessments of executive functioning (γ = 0.168, t = 4.562, p < 0.001). Mobile cognitive testing in the elderly may provide complementary and potentially more sensitive data relative to traditional neuropsychological assessment. Copyright © 2016 John Wiley & Sons, Ltd.}, } @article {pmid27538504, year = {2016}, author = {Gao, W and Hedeker, D and Mermelstein, R and Xie, H}, title = {A scalable approach to measuring the impact of nonignorable nonresponse with an EMA application.}, journal = {Statistics in medicine}, volume = {35}, number = {30}, pages = {5579-5602}, pmid = {27538504}, issn = {1097-0258}, support = {P01 CA098262/CA/NCI NIH HHS/United States ; R01 CA178061/CA/NCI NIH HHS/United States ; }, mesh = {*Data Interpretation, Statistical ; *Models, Statistical ; }, abstract = {There is often a need to assess the dependence of standard analyses on the strong untestable assumption of ignorable missingness. To tackle this problem, past research developed simple sensitivity index measures assuming a linear impact of nonignorability and missingness in outcomes only. These restrictions limit their applicability for studies with missingness in both outcome and covariates. Nonignorable missingness in this setting poses significant new analytic challenges and calls for more general and flexible methods that are also computationally tractable even for large datasets. In this paper, we relax the restrictions of extant linear sensitivity index methods and develop nonlinear sensitivity indices that maintain computational simplicity and perform equally well when the impact of nonignorability is locally linear. On the other hand, they can substantially improve the effectiveness of local sensitivity analysis when regression outcomes and covariates are subject to concurrent missingness. In this situation, the local linear sensitivity analysis fails to detect the impact of nonignorability while the proposed nonlinear sensitivity measures can. Because the new sensitivity indices avoid fitting complicated nonignorable models, they are computationally tractable (i.e., scalable) for use in large datasets. We develop general formula for nonlinear sensitivity index measures, and evaluate the new measures in simulated data and a real dataset collected using the ecological momentary assessment method. Copyright © 2016 John Wiley & Sons, Ltd.}, } @article {pmid27535769, year = {2017}, author = {Crocker-Buque, T and Edelstein, M and Mounier-Jack, S}, title = {Interventions to reduce inequalities in vaccine uptake in children and adolescents aged <19 years: a systematic review.}, journal = {Journal of epidemiology and community health}, volume = {71}, number = {1}, pages = {87-97}, pmid = {27535769}, issn = {1470-2738}, mesh = {Adolescent ; Child ; Child, Preschool ; Ethnicity ; Humans ; Immunization Programs/organization & administration ; Infant ; Infant, Newborn ; Reminder Systems ; Socioeconomic Factors ; Text Messaging ; Vaccines/*administration & dosage ; }, abstract = {BACKGROUND: In high-income countries, substantial differences exist in vaccine uptake relating to socioeconomic status, gender, ethnic group, geographic location and religious belief. This paper updates a 2009 systematic review on effective interventions to decrease vaccine uptake inequalities in light of new technologies applied to vaccination and new vaccine programmes (eg, human papillomavirus in adolescents).

METHODS: We searched MEDLINE, Embase, ASSIA, The Campbell Collaboration, CINAHL, The Cochrane Database of Systematic Reviews, Eppi Centre, Eric and PsychINFO for intervention, cohort or ecological studies conducted at primary/community care level in children and young people from birth to 19 years in OECD countries, with vaccine uptake or coverage as outcomes, published between 2008 and 2015.

RESULTS: The 41 included studies evaluated complex multicomponent interventions (n=16), reminder/recall systems (n=18), outreach programmes (n=3) or computer-based interventions (n=2). Complex, locally designed interventions demonstrated the best evidence for effectiveness in reducing inequalities in deprived, urban, ethnically diverse communities. There is some evidence that postal and telephone reminders are effective, however, evidence remains mixed for text-message reminders, although these may be more effective in adolescents. Interventions that escalated in intensity appeared particularly effective. Computer-based interventions were not effective. Few studies targeted an inequality specifically, although several reported differential effects by the ethnic group.

CONCLUSIONS: Locally designed, multicomponent interventions should be used in urban, ethnically diverse, deprived populations. Some evidence is emerging for text-message reminders, particularly in adolescents. Further research should be conducted in the UK and Europe with a focus on reducing specific inequalities.}, } @article {pmid27530250, year = {2016}, author = {Tu, Q and Lin, L}, title = {Gene content dissimilarity for subclassification of highly similar microbial strains.}, journal = {BMC genomics}, volume = {17}, number = {}, pages = {647}, pmid = {27530250}, issn = {1471-2164}, mesh = {Cluster Analysis ; Computational Biology/methods ; *DNA Barcoding, Taxonomic ; Databases, Nucleic Acid ; Enterobacteriaceae/classification/genetics ; *Genome, Microbial ; *Metagenome ; *Metagenomics/methods ; RNA, Ribosomal, 16S/genetics ; }, abstract = {BACKGROUND: Identification and classification of highly similar microbial strains is a challenging issue in microbiology, ecology and evolutionary biology. Among various available approaches, gene content analysis is also at the core of microbial taxonomy. However, no threshold has been determined for grouping microorgnisms to different taxonomic levels, and it is still not clear that to what extent genomic fluidity should occur to form a microbial taxonomic group.

RESULTS: By taking advantage of the eggNOG database for orthologous groups, we calculated gene content dissimilarity among different microbial strains based on the orthologous gene profiles and tested the possibility of applying gene content dissimilarity as a quantitative index in classifying microbial taxonomic groups, as well as its potential application in subclassification of highly similar microbial strains. Evaluation of gene content dissimilarity to completed microbial genomes at different taxonomic levels suggested that cutoffs of 0.2 and 0.4 can be respectively used for species and family delineation, and that 0.2 gene content dissimilarity cutoff approximately corresponded to 98 % 16S rRNA gene identity and 94 % ANI for microbial species delineation. Furthermore, application of gene content dissimilarity to highly similar microbial strains suggested it as an effective approach in classifying closely related microorganisms into subgroups.

CONCLUSIONS: This approach is especially useful in identifying pathogens from commensals in clinical microbiology. It also provides novel insights into how genomic fluidity is linked with microbial taxonomy.}, } @article {pmid27523267, year = {2016}, author = {Hristozov, D and Gottardo, S and Semenzin, E and Oomen, A and Bos, P and Peijnenburg, W and van Tongeren, M and Nowack, B and Hunt, N and Brunelli, A and Scott-Fordsmand, JJ and Tran, L and Marcomini, A}, title = {Frameworks and tools for risk assessment of manufactured nanomaterials.}, journal = {Environment international}, volume = {95}, number = {}, pages = {36-53}, doi = {10.1016/j.envint.2016.07.016}, pmid = {27523267}, issn = {1873-6750}, mesh = {Computer Simulation ; Environment ; Environmental Health ; Humans ; Nanostructures/*adverse effects ; Nanotechnology ; Risk Assessment/*methods ; Risk Management ; }, abstract = {Commercialization of nanotechnologies entails a regulatory requirement for understanding their environmental, health and safety (EHS) risks. Today we face challenges to assess these risks, which emerge from uncertainties around the interactions of manufactured nanomaterials (MNs) with humans and the environment. In order to reduce these uncertainties, it is necessary to generate sound scientific data on hazard and exposure by means of relevant frameworks and tools. The development of such approaches to facilitate the risk assessment (RA) of MNs has become a dynamic area of research. The aim of this paper was to review and critically analyse these approaches against a set of relevant criteria. The analysis concluded that none of the reviewed frameworks were able to fulfill all evaluation criteria. Many of the existing modelling tools are designed to provide screening-level assessments rather than to support regulatory RA and risk management. Nevertheless, there is a tendency towards developing more quantitative, higher-tier models, capable of incorporating uncertainty into their analyses. There is also a trend towards developing validated experimental protocols for material identification and hazard testing, reproducible across laboratories. These tools could enable a shift from a costly case-by-case RA of MNs towards a targeted, flexible and efficient process, based on grouping and read-across strategies and compliant with the 3R (Replacement, Reduction, Refinement) principles. In order to facilitate this process, it is important to transform the current efforts on developing databases and computational models into creating an integrated data and tools infrastructure to support the risk assessment and management of MNs.}, } @article {pmid27516337, year = {2016}, author = {Delgado-Serrano, L and Restrepo, S and Bustos, JR and Zambrano, MM and Anzola, JM}, title = {Mycofier: a new machine learning-based classifier for fungal ITS sequences.}, journal = {BMC research notes}, volume = {9}, number = {1}, pages = {402}, pmid = {27516337}, issn = {1756-0500}, mesh = {Base Sequence ; Bayes Theorem ; DNA, Ribosomal Spacer/*genetics ; Databases, Genetic ; Fungi/*genetics ; *Machine Learning ; Models, Genetic ; *Software ; }, abstract = {BACKGROUND: The taxonomic and phylogenetic classification based on sequence analysis of the ITS1 genomic region has become a crucial component of fungal ecology and diversity studies. Nowadays, there is no accurate alignment-free classification tool for fungal ITS1 sequences for large environmental surveys. This study describes the development of a machine learning-based classifier for the taxonomical assignment of fungal ITS1 sequences at the genus level.

RESULTS: A fungal ITS1 sequence database was built using curated data. Training and test sets were generated from it. A Naïve Bayesian classifier was built using features from the primary sequence with an accuracy of 87 % in the classification at the genus level.

CONCLUSIONS: The final model was based on a Naïve Bayes algorithm using ITS1 sequences from 510 fungal genera. This classifier, denoted as Mycofier, provides similar classification accuracy compared to BLASTN, but the database used for the classification contains curated data and the tool, independent of alignment, is more efficient and contributes to the field, given the lack of an accurate classification tool for large data from fungal ITS1 sequences. The software and source code for Mycofier are freely available at https://github.com/ldelgado-serrano/mycofier.git .}, } @article {pmid27516060, year = {2017}, author = {Bakitas, M and Dionne-Odom, JN and Jackson, L and Frost, J and Bishop, MF and Li, Z}, title = {"There were more decisions and more options than just yes or no": Evaluating a decision aid for advanced cancer patients and their family caregivers.}, journal = {Palliative & supportive care}, volume = {15}, number = {1}, pages = {44-56}, doi = {10.1017/S1478951516000596}, pmid = {27516060}, issn = {1478-9523}, support = {R01 NR011871/NR/NINR NIH HHS/United States ; K99 NR015903/NR/NINR NIH HHS/United States ; R25 CA047888/CA/NCI NIH HHS/United States ; }, mesh = {Aged ; Caregivers/*psychology ; *Decision Making ; *Decision Support Techniques ; Female ; Humans ; Male ; Middle Aged ; Neoplasms/*psychology/*therapy ; Palliative Care/methods/psychology ; Prospective Studies ; Randomized Controlled Trials as Topic ; }, abstract = {OBJECTIVE: Few decision aids are available for patients with a serious illness who face many treatment and end-of-life decisions. We evaluated the Looking Ahead: Choices for Medical Care When You're Seriously Ill® patient decision aid (PtDA), one component of an early palliative care clinical trial.

METHOD: Our participants included individuals with advanced cancer and their caregivers who had participated in the ENABLE (Educate, Nurture, Advise, Before Life Ends) early palliative care telehealth randomized controlled trial (RCT) conducted in a National Cancer Institute-designated cancer center, a U.S. Department of Veterans Affairs medical center, and affiliated outreach clinics in rural New England. ENABLE included six weekly patient and three weekly family caregiver structured sessions. Participants watched the Looking Ahead PtDA prior to session 3, which covered content on decision making and advance care planning. Nurse coaches employed semistructured interviews to obtain feedback from consecutive patient and caregiver participants approximately one week after viewing the Looking Ahead PtDA program (booklet and DVD).

RESULTS: Between April 1, 2011, and October 31, 2012, 57 patients (mean age = 64), 42% of whom had lung and 23% gastrointestinal cancer, and 20 caregivers (mean age = 59), 80% of whom were spouses, completed the PtDA evaluation. Participants reported a high degree of satisfaction with the PtDA format, as well as with its length and clarity. They found the format of using patient interviews "validating." The key themes were: (1) "the earlier the better" to view the PtDA; (2) feeling empowered, aware of different options, and an urgency to participate in advance care planning.

SIGNIFICANCE OF RESULTS: The Looking Ahead PtDA was well received and helped patients with a serious illness realize the importance of prospective decision making in guiding their treatment pathways. We found that this PtDA can help seriously ill patients prior to the end of life to understand and discuss future healthcare decision making. However, systems to routinely provide PtDAs to seriously ill patients are yet not well developed.}, } @article {pmid27515514, year = {2016}, author = {Ni, Y and Li, J and Panagiotou, G}, title = {COMAN: a web server for comprehensive metatranscriptomics analysis.}, journal = {BMC genomics}, volume = {17}, number = {1}, pages = {622}, pmid = {27515514}, issn = {1471-2164}, mesh = {Computational Biology/*methods/statistics & numerical data ; High-Throughput Nucleotide Sequencing ; Humans ; Internet ; Metagenomics/*methods/statistics & numerical data ; Microbiota/*genetics ; Sequence Analysis, RNA ; *Software ; *Transcriptome ; }, abstract = {BACKGROUND: Microbiota-oriented studies based on metagenomic or metatranscriptomic sequencing have revolutionised our understanding on microbial ecology and the roles of both clinical and environmental microbes. The analysis of massive metatranscriptomic data requires extensive computational resources, a collection of bioinformatics tools and expertise in programming.

RESULTS: We developed COMAN (Comprehensive Metatranscriptomics Analysis), a web-based tool dedicated to automatically and comprehensively analysing metatranscriptomic data. COMAN pipeline includes quality control of raw reads, removal of reads derived from non-coding RNA, followed by functional annotation, comparative statistical analysis, pathway enrichment analysis, co-expression network analysis and high-quality visualisation. The essential data generated by COMAN are also provided in tabular format for additional analysis and integration with other software. The web server has an easy-to-use interface and detailed instructions, and is freely available at http://sbb.hku.hk/COMAN/ CONCLUSIONS: COMAN is an integrated web server dedicated to comprehensive functional analysis of metatranscriptomic data, translating massive amount of reads to data tables and high-standard figures. It is expected to facilitate the researchers with less expertise in bioinformatics in answering microbiota-related biological questions and to increase the accessibility and interpretation of microbiota RNA-Seq data.}, } @article {pmid27513576, year = {2016}, author = {Busch, DS and McElhany, P}, title = {Estimates of the Direct Effect of Seawater pH on the Survival Rate of Species Groups in the California Current Ecosystem.}, journal = {PloS one}, volume = {11}, number = {8}, pages = {e0160669}, pmid = {27513576}, issn = {1932-6203}, mesh = {Animals ; Biodiversity ; California ; Carbon Dioxide/analysis ; Databases, Factual ; Environmental Monitoring ; Hydrogen-Ion Concentration ; Seawater/*chemistry ; Species Specificity ; *Water Movements ; }, abstract = {Ocean acidification (OA) has the potential to restructure ecosystems due to variation in species sensitivity to the projected changes in ocean carbon chemistry. Ecological models can be forced with scenarios of OA to help scientists, managers, and other stakeholders understand how ecosystems might change. We present a novel methodology for developing estimates of species sensitivity to OA that are regionally specific, and applied the method to the California Current ecosystem. To do so, we built a database of all published literature on the sensitivity of temperate species to decreased pH. This database contains 393 papers on 285 species and 89 multi-species groups from temperate waters around the world. Research on urchins and oysters and on adult life stages dominates the literature. Almost a third of the temperate species studied to date occur in the California Current. However, most laboratory experiments use control pH conditions that are too high to represent average current chemistry conditions in the portion of the California Current water column where the majority of the species live. We developed estimates of sensitivity to OA for functional groups in the ecosystem, which can represent single species or taxonomically diverse groups of hundreds of species. We based these estimates on the amount of available evidence derived from published studies on species sensitivity, how well this evidence could inform species sensitivity in the California Current ecosystem, and the agreement of the available evidence for a species/species group. This approach is similar to that taken by the Intergovernmental Panel on Climate Change to characterize certainty when summarizing scientific findings. Most functional groups (26 of 34) responded negatively to OA conditions, but when uncertainty in sensitivity was considered, only 11 groups had relationships that were consistently negative. Thus, incorporating certainty about the sensitivity of species and functional groups to OA is an important part of developing robust scenarios for ecosystem projections.}, } @article {pmid27509003, year = {2017}, author = {El-Atem, N and Irvine, KM and Valery, PC and Wojcik, K and Horsfall, L and Johnson, T and Janda, M and McPhail, SM and Powell, EE}, title = {Identifying areas of need relative to liver disease: geographic clustering within a health service district.}, journal = {Australian health review : a publication of the Australian Hospital Association}, volume = {41}, number = {4}, pages = {407-418}, doi = {10.1071/AH15225}, pmid = {27509003}, issn = {0156-5788}, mesh = {Adult ; Aged ; Australia/epidemiology ; Catchment Area, Health/*statistics & numerical data ; China/ethnology ; Databases, Factual ; Female ; Geography ; Health Services Accessibility/*statistics & numerical data ; Health Services Needs and Demand/*statistics & numerical data ; Humans ; Linear Models ; *Liver Diseases/epidemiology/therapy ; Male ; Middle Aged ; Queensland/epidemiology ; Sex Distribution ; Small-Area Analysis ; Tertiary Care Centers ; Travel/statistics & numerical data ; Vietnam/ethnology ; }, abstract = {Background Many people with chronic liver disease (CLD) are not detected until they present to hospital with advanced disease, when opportunities for intervention are reduced and morbidity is high. In order to build capacity and liver expertise in the community, it is important to focus liver healthcare resources in high-prevalence disease areas and specific populations with an identified need. The aim of the present study was to examine the geographic location of people seen in a tertiary hospital hepatology clinic, as well as ethnic and sociodemographic characteristics of these geographic areas. Methods The geographic locations of hepatology out-patients were identified via the out-patient scheduling database and grouped into statistical area (SA) regions for demographic analysis using data compiled by the Australian Bureau of Statistics. Results During the 3-month study period, 943 individuals from 71 SA Level 3 regions attended clinic. Nine SA Level 3 regions accounted for 55% of the entire patient cohort. Geographic clustering was seen especially for people living with chronic hepatitis B virus. There was a wide spectrum of socioeconomic advantage and disadvantage in areas with high liver disease prevalence. Conclusions The geographic area from which people living with CLD travel to access liver health care is extensive. However, the greatest demand for tertiary liver disease speciality care is clustered within specific geographic areas. Outreach programs targeted to these areas may enhance liver disease-specific health service resourcing. What is known about the topic? The demand for tertiary hospital clinical services in CLD is rising. However, there is limited knowledge about the geographic areas from which people living with CLD travel to access liver services, or the ethnic, socioeconomic and education characteristics of these areas. What does this paper add? The present study demonstrates that a substantial proportion of people living with CLD and accessing tertiary hospital liver services are clustered within specific geographic areas. The most striking geographic clustering was seen for people living with chronic hepatitis B, in regions with a relatively high proportion of people born in Vietnam and China. In addition to ethnicity, the data show an apparent ecological association between liver disease and both socioeconomic and educational and/or occupational disadvantage. What are the implications for practitioners? Identifying where demand for clinical services arises is an important step for service planning and preparing for potential outreach programs to optimise community-based care. It is likely that outreach programs to engage and enhance primary care services in geographic areas from which the greatest demand for tertiary liver disease speciality care arises would yield greater relative return on investment than non-targeted outreach programs.}, } @article {pmid27507286, year = {2018}, author = {White, SR and Muniz-Terrera, G and Matthews, FE}, title = {Sample size and classification error for Bayesian change-point models with unlabelled sub-groups and incomplete follow-up.}, journal = {Statistical methods in medical research}, volume = {27}, number = {5}, pages = {1476-1497}, pmid = {27507286}, issn = {1477-0334}, support = {MC_U105292687/MRC_/Medical Research Council/United Kingdom ; MC_UU_00002/12/MRC_/Medical Research Council/United Kingdom ; }, mesh = {*Bayes Theorem ; Cognitive Dysfunction/diagnosis/epidemiology ; Data Interpretation, Statistical ; Humans ; Markov Chains ; *Models, Statistical ; Monte Carlo Method ; Neuropsychological Tests ; *Sample Size ; }, abstract = {Many medical (and ecological) processes involve the change of shape, whereby one trajectory changes into another trajectory at a specific time point. There has been little investigation into the study design needed to investigate these models. We consider the class of fixed effect change-point models with an underlying shape comprised two joined linear segments, also known as broken-stick models. We extend this model to include two sub-groups with different trajectories at the change-point, a change and no change class, and also include a missingness model to account for individuals with incomplete follow-up. Through a simulation study, we consider the relationship of sample size to the estimates of the underlying shape, the existence of a change-point, and the classification-error of sub-group labels. We use a Bayesian framework to account for the missing labels, and the analysis of each simulation is performed using standard Markov chain Monte Carlo techniques. Our simulation study is inspired by cognitive decline as measured by the Mini-Mental State Examination, where our extended model is appropriate due to the commonly observed mixture of individuals within studies who do or do not exhibit accelerated decline. We find that even for studies of modest size (n = 500, with 50 individuals observed past the change-point) in the fixed effect setting, a change-point can be detected and reliably estimated across a range of observation-errors.}, } @article {pmid27507121, year = {2016}, author = {Raia, P and Carotenuto, F and Mondanaro, A and Castiglione, S and Passaro, F and Saggese, F and Melchionna, M and Serio, C and Alessio, L and Silvestro, D and Fortelius, M}, title = {Progress to extinction: increased specialisation causes the demise of animal clades.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {30965}, pmid = {27507121}, issn = {2045-2322}, mesh = {Animals ; Biodiversity ; Biological Evolution ; Databases, Factual ; *Extinction, Biological ; Fossils ; *Genetic Speciation ; Markov Chains ; *Models, Biological ; Paleontology ; Sympatry ; }, abstract = {Animal clades tend to follow a predictable path of waxing and waning during their existence, regardless of their total species richness or geographic coverage. Clades begin small and undifferentiated, then expand to a peak in diversity and range, only to shift into a rarely broken decline towards extinction. While this trajectory is now well documented and broadly recognised, the reasons underlying it remain obscure. In particular, it is unknown why clade extinction is universal and occurs with such surprising regularity. Current explanations for paleontological extinctions call on the growing costs of biological interactions, geological accidents, evolutionary traps, and mass extinctions. While these are effective causes of extinction, they mainly apply to species, not clades. Although mass extinctions is the undeniable cause for the demise of a sizeable number of major taxa, we show here that clades escaping them go extinct because of the widespread tendency of evolution to produce increasingly specialised, sympatric, and geographically restricted species over time.}, } @article {pmid27506228, year = {2019}, author = {Rosen, T and Bloemen, EM and LoFaso, VM and Clark, S and Flomenbaum, NE and Breckman, R and Markarian, A and Riffin, C and Lachs, MS and Pillemer, K}, title = {Acute Precipitants of Physical Elder Abuse: Qualitative Analysis of Legal Records From Highly Adjudicated Cases.}, journal = {Journal of interpersonal violence}, volume = {34}, number = {12}, pages = {2599-2623}, pmid = {27506228}, issn = {1552-6518}, support = {K24 AG022399/AG/NIA NIH HHS/United States ; P30 AG022845/AG/NIA NIH HHS/United States ; R03 AG048109/AG/NIA NIH HHS/United States ; }, mesh = {Adolescent ; Adult ; Aged ; Databases, Factual ; *Elder Abuse/legislation & jurisprudence ; Female ; Humans ; *Law Enforcement ; Male ; Middle Aged ; Narration ; *Physical Abuse/legislation & jurisprudence ; Risk Factors ; Substance-Related Disorders ; Young Adult ; }, abstract = {Elder abuse is a common phenomenon with potentially devastating consequences for older adults. Although researchers have begun to identify predisposing risk factors for elder abuse victims and abusers, little is known about the acute precipitants that lead to escalation to physical violence. We analyzed legal records from highly adjudicated cases to describe these acute precipitants for physical elder abuse. In collaboration with a large, urban district attorney's office, we qualitatively evaluated legal records from 87 successfully prosecuted physical elder abuse cases from 2003 to 2015. We transcribed and analyzed narratives of the events surrounding physical abuse within victim statements, police reports, and prosecutor records. We identified major themes using content analysis. We identified 10 categories of acute precipitants that commonly triggered physical elder abuse, including victim attempting to prevent the abuser from entering or demanding that he or she leave, victim threatening or attempting to leave/escape, threat or perception that the victim would involve the authorities, conflict about a romantic relationship, presence during/intervention in ongoing family violence, issues in multi-generational child rearing, conflict about the abuser's substance abuse, confrontation about financial exploitation, dispute over theft/destruction of property, and disputes over minor household issues. Common acute precipitants of physical elder abuse may be identified. Improved understanding of these acute precipitants for escalation to physical violence and their contribution to elder abuse may assist in the development of prevention and management strategies.}, } @article {pmid27501943, year = {2016}, author = {Sojo, V and Dessimoz, C and Pomiankowski, A and Lane, N}, title = {Membrane Proteins Are Dramatically Less Conserved than Water-Soluble Proteins across the Tree of Life.}, journal = {Molecular biology and evolution}, volume = {33}, number = {11}, pages = {2874-2884}, pmid = {27501943}, issn = {1537-1719}, support = {BB/L018241/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Adaptation, Biological ; Archaea/genetics ; Bacteria/genetics ; Biological Evolution ; Databases, Protein ; Eukaryota/genetics ; Evolution, Molecular ; Homeostasis ; Membrane Proteins/*genetics/metabolism ; Phylogeny ; Prokaryotic Cells ; Proteins/*genetics/metabolism ; Sequence Analysis, Protein/*methods ; Solubility ; Water/metabolism ; }, abstract = {Membrane proteins are crucial in transport, signaling, bioenergetics, catalysis, and as drug targets. Here, we show that membrane proteins have dramatically fewer detectable orthologs than water-soluble proteins, less than half in most species analyzed. This sparse distribution could reflect rapid divergence or gene loss. We find that both mechanisms operate. First, membrane proteins evolve faster than water-soluble proteins, particularly in their exterior-facing portions. Second, we demonstrate that predicted ancestral membrane proteins are preferentially lost compared with water-soluble proteins in closely related species of archaea and bacteria. These patterns are consistent across the whole tree of life, and in each of the three domains of archaea, bacteria, and eukaryotes. Our findings point to a fundamental evolutionary principle: membrane proteins evolve faster due to stronger adaptive selection in changing environments, whereas cytosolic proteins are under more stringent purifying selection in the homeostatic interior of the cell. This effect should be strongest in prokaryotes, weaker in unicellular eukaryotes (with intracellular membranes), and weakest in multicellular eukaryotes (with extracellular homeostasis). We demonstrate that this is indeed the case. Similarly, we show that extracellular water-soluble proteins exhibit an even stronger pattern of low homology than membrane proteins. These striking differences in conservation of membrane proteins versus water-soluble proteins have important implications for evolution and medicine.}, } @article {pmid27499266, year = {2016}, author = {Star, B and Tørresen, OK and Nederbragt, AJ and Jakobsen, KS and Pampoulie, C and Jentoft, S}, title = {Genomic characterization of the Atlantic cod sex-locus.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {31235}, pmid = {27499266}, issn = {2045-2322}, mesh = {Animals ; Databases, Protein ; Female ; Gadus morhua/*genetics ; *Gene Expression Profiling ; Genetic Linkage ; *Genetic Loci ; Genome ; Genotype ; Male ; Polymorphism, Single Nucleotide ; Sequence Analysis, DNA ; *Sex Chromosomes ; *Sex Determination Processes ; }, abstract = {A variety of sex determination mechanisms can be observed in evolutionary divergent teleosts. Sex determination is genetic in Atlantic cod (Gadus morhua), however the genomic location or size of its sex-locus is unknown. Here, we characterize the sex-locus of Atlantic cod using whole genome sequence (WGS) data of 227 wild-caught specimens. Analyzing more than 55 million polymorphic loci, we identify 166 loci that are associated with sex. These loci are located in six distinct regions on five different linkage groups (LG) in the genome. The largest of these regions, an approximately 55 Kb region on LG11, contains the majority of genotypes that segregate closely according to a XX-XY system. Genotypes in this region can be used genetically determine sex, whereas those in the other regions are inconsistently sex-linked. The identified region on LG11 and its surrounding genes have no clear sequence homology with genes or regulatory elements associated with sex-determination or differentiation in other species. The functionality of this sex-locus therefore remains unknown. The WGS strategy used here proved adequate for detecting the small regions associated with sex in this species. Our results highlight the evolutionary flexibility in genomic architecture underlying teleost sex-determination and allow practical applications to genetically sex Atlantic cod.}, } @article {pmid27494625, year = {2016}, author = {Leontaridou, M and Gabbert, S and Van Ierland, EC and Worth, AP and Landsiedel, R}, title = {Evaluation of non-animal methods for assessing skin sensitisation hazard: A Bayesian Value-of-Information analysis.}, journal = {Alternatives to laboratory animals : ATLA}, volume = {44}, number = {3}, pages = {255-269}, doi = {10.1177/026119291604400309}, pmid = {27494625}, issn = {0261-1929}, mesh = {Animal Testing Alternatives/*methods ; Animals ; Bayes Theorem ; Cosmetics/*toxicity ; Databases, Factual ; *Dermatitis, Contact ; Dermatologic Agents/*toxicity ; }, abstract = {This paper offers a Bayesian Value-of-Information (VOI) analysis for guiding the development of non-animal testing strategies, balancing information gains from testing with the expected social gains and costs from the adoption of regulatory decisions. Testing is assumed to have value, if, and only if, the information revealed from testing triggers a welfare-improving decision on the use (or non-use) of a substance. As an illustration, our VOI model is applied to a set of five individual non-animal prediction methods used for skin sensitisation hazard assessment, seven battery combinations of these methods, and 236 sequential 2-test and 3-test strategies. Their expected values are quantified and compared to the expected value of the local lymph node assay (LLNA) as the animal method. We find that battery and sequential combinations of non-animal prediction methods reveal a significantly higher expected value than the LLNA. This holds for the entire range of prior beliefs. Furthermore, our results illustrate that the testing strategy with the highest expected value does not necessarily have to follow the order of key events in the sensitisation adverse outcome pathway (AOP).}, } @article {pmid27494607, year = {2016}, author = {Han, JC and Huang, Y and Li, Z and Zhao, C and Cheng, G and Huang, P}, title = {Groundwater level prediction using a SOM-aided stepwise cluster inference model.}, journal = {Journal of environmental management}, volume = {182}, number = {}, pages = {308-321}, doi = {10.1016/j.jenvman.2016.07.069}, pmid = {27494607}, issn = {1095-8630}, mesh = {*Agriculture ; China ; Droughts ; Environmental Monitoring ; Geographic Information Systems ; *Groundwater ; Humans ; *Models, Theoretical ; *Water Supply ; }, abstract = {Accurate groundwater level (GWL) prediction can contribute to sustaining reliable water supply to domestic, agricultural and industrial uses as well as ecological services, especially in arid and semi-arid areas. In this paper, a regional GWL modeling framework was first presented through coupling both spatial and temporal clustering techniques. Specifically, the self-organizing map (SOM) was applied to identify spatially homogeneous clusters of GWL piezometers, while GWL time series forecasting was performed through developing a stepwise cluster multisite inference model with various predictors including climate conditions, well extractions, surface runoffs, reservoir operations and GWL measurements at previous steps. The proposed modeling approach was then demonstrated by a case of an arid irrigation district in the western Hexi Corridor, northwest China. Spatial clustering analysis identified 6 regionally representative central piezometers out of 30, for which sensitivity and uncertainty analysis were carried out regarding GWL predictions. As the stepwise cluster tree provided uncertain predictions, we added an AR(1) error model to the mean prediction to forecast GWL 1 month ahead. Model performance indicators suggest that the modeling system is a useful tool to aid decision-making for informed groundwater resource management in arid areas, and would have a great potential to extend its applications to more areas or regions in the future.}, } @article {pmid27494028, year = {2016}, author = {Sousa, LL and López-Castejón, F and Gilabert, J and Relvas, P and Couto, A and Queiroz, N and Caldas, R and Dias, PS and Dias, H and Faria, M and Ferreira, F and Ferreira, AS and Fortuna, J and Gomes, RJ and Loureiro, B and Martins, R and Madureira, L and Neiva, J and Oliveira, M and Pereira, J and Pinto, J and Py, F and Queirós, H and Silva, D and Sujit, PB and Zolich, A and Johansen, TA and de Sousa, JB and Rajan, K}, title = {Integrated Monitoring of Mola mola Behaviour in Space and Time.}, journal = {PloS one}, volume = {11}, number = {8}, pages = {e0160404}, pmid = {27494028}, issn = {1932-6203}, mesh = {Animals ; Behavior, Animal ; Environmental Monitoring/methods ; Geographic Information Systems ; Marine Biology/*methods ; Portugal ; Remote Sensing Technology/*methods ; Robotics/instrumentation/methods ; Satellite Communications ; *Tetraodontiformes ; Zooplankton ; }, abstract = {Over the last decade, ocean sunfish movements have been monitored worldwide using various satellite tracking methods. This study reports the near-real time monitoring of fine-scale (< 10 m) behaviour of sunfish. The study was conducted in southern Portugal in May 2014 and involved satellite tags and underwater and surface robotic vehicles to measure both the movements and the contextual environment of the fish. A total of four individuals were tracked using custom-made GPS satellite tags providing geolocation estimates of fine-scale resolution. These accurate positions further informed sunfish areas of restricted search (ARS), which were directly correlated to steep thermal frontal zones. Simultaneously, and for two different occasions, an Autonomous Underwater Vehicle (AUV) video-recorded the path of the tracked fish and detected buoyant particles in the water column. Importantly, the densities of these particles were also directly correlated to steep thermal gradients. Thus, both sunfish foraging behaviour (ARS) and possibly prey densities, were found to be influenced by analogous environmental conditions. In addition, the dynamic structure of the water transited by the tracked individuals was described by a Lagrangian modelling approach. The model informed the distribution of zooplankton in the region, both horizontally and in the water column, and the resultant simulated densities positively correlated with sunfish ARS behaviour estimator (rs = 0.184, p<0.001). The model also revealed that tracked fish opportunistically displace with respect to subsurface current flow. Thus, we show how physical forcing and current structure provide a rationale for a predator's fine-scale behaviour observed over a two weeks in May 2014.}, } @article {pmid27493068, year = {2016}, author = {Woodroffe, R and Donnelly, CA and Ham, C and Jackson, SY and Moyes, K and Chapman, K and Stratton, NG and Cartwright, SJ}, title = {Badgers prefer cattle pasture but avoid cattle: implications for bovine tuberculosis control.}, journal = {Ecology letters}, volume = {19}, number = {10}, pages = {1201-1208}, doi = {10.1111/ele.12654}, pmid = {27493068}, issn = {1461-0248}, support = {MR/K010174/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Animal Identification Systems ; Animals ; *Behavior, Animal ; Cattle ; Contact Tracing/veterinary ; Disease Reservoirs/*veterinary ; Geographic Information Systems ; Mustelidae/*microbiology ; Mycobacterium bovis/*physiology ; Tuberculosis, Bovine/*prevention & control/transmission ; }, abstract = {Effective management of infectious disease relies upon understanding mechanisms of pathogen transmission. In particular, while models of disease dynamics usually assume transmission through direct contact, transmission through environmental contamination can cause different dynamics. We used Global Positioning System (GPS) collars and proximity-sensing contact-collars to explore opportunities for transmission of Mycobacterium bovis [causal agent of bovine tuberculosis] between cattle and badgers (Meles meles). Cattle pasture was badgers' most preferred habitat. Nevertheless, although collared cattle spent 2914 collar-nights in the home ranges of contact-collared badgers, and 5380 collar-nights in the home ranges of GPS-collared badgers, we detected no direct contacts between the two species. Simultaneous GPS-tracking revealed that badgers preferred land > 50 m from cattle. Very infrequent direct contact indicates that badger-to-cattle and cattle-to-badger M. bovis transmission may typically occur through contamination of the two species' shared environment. This information should help to inform tuberculosis control by guiding both modelling and farm management.}, } @article {pmid27492876, year = {2016}, author = {Cavaliere, M and Yang, G and Danos, V and Dakos, V}, title = {Detecting the Collapse of Cooperation in Evolving Networks.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {30845}, pmid = {27492876}, issn = {2045-2322}, mesh = {Area Under Curve ; *Cooperative Behavior ; Game Theory ; Humans ; *Models, Theoretical ; ROC Curve ; }, abstract = {The sustainability of biological, social, economic and ecological communities is often determined by the outcome of social conflicts between cooperative and selfish individuals (cheaters). Cheaters avoid the cost of contributing to the community and can occasionally spread in the population leading to the complete collapse of cooperation. Although such collapse often unfolds unexpectedly, it is unclear whether one can detect the risk of cheater's invasions and loss of cooperation in an evolving community. Here, we combine dynamical networks and evolutionary game theory to study the abrupt loss of cooperation with tools for studying critical transitions. We estimate the risk of cooperation collapse following the introduction of a single cheater under gradually changing conditions. We observe an increase in the average time it takes for cheaters to be eliminated from the community as the risk of collapse increases. We argue that such slow system response resembles slowing down in recovery rates prior to a critical transition. In addition, we show how changes in community structure reflect the risk of cooperation collapse. We find that these changes strongly depend on the mechanism that governs how cheaters evolve in the community. Our results highlight novel directions for detecting abrupt transitions in evolving networks.}, } @article {pmid27489210, year = {2016}, author = {Sanchez-Flores, A and Peñaloza, F and Carpinteyro-Ponce, J and Nazario-Yepiz, N and Abreu-Goodger, C and Machado, CA and Markow, TA}, title = {Genome Evolution in Three Species of Cactophilic Drosophila.}, journal = {G3 (Bethesda, Md.)}, volume = {6}, number = {10}, pages = {3097-3105}, pmid = {27489210}, issn = {2160-1836}, mesh = {Animals ; Chromosome Inversion ; Chromosomes, Insect ; Computational Biology/methods ; Drosophila/*genetics ; *Evolution, Molecular ; Gene Ontology ; *Genome, Insect ; *Genomics/methods ; High-Throughput Nucleotide Sequencing ; Molecular Sequence Annotation ; Selection, Genetic ; Species Specificity ; }, abstract = {We report genomes of two species of cactophilic Drosophila: Drosophila arizonae and D. navojoa These two are the closest relatives of D. mojavensis, forming the D. mojavensis cluster. D. mojavensis and D. arizonae diverged from D. navojoa ∼5.8 Mya, while the split between D. arizonae and D. mojavensis is more recent, at 1.5 Mya. Together the three genomes provide opportunities to examine genomic changes associated with speciation and host shifts in this ecologically defined group of flies. The three species are also separated by fixed inversion differences in three of their six chromosomes. While the levels of nucleotide divergence in the colinear chromosomes are significantly lower than in the inverted chromosomes, consistent with a past role of the inversions in preventing gene flow, the patterns differ among the inverted chromosomes when the locations of nucleotides inside or outside of the inversions are considered. For Muller element E, there is greater divergence external to the inversion breakpoints. For Muller A, the divergence is slightly higher inside the inversions, while for Muller B, the breakpoints and hence the difference in substitutions in relation to the inversions could not be determined. The differences among the inverted chromosomes, especially once the breakpoints are clearly established, could aid in dating the origins of the inversions.}, } @article {pmid27489002, year = {2016}, author = {Nakka, P and Raphael, BJ and Ramachandran, S}, title = {Gene and Network Analysis of Common Variants Reveals Novel Associations in Multiple Complex Diseases.}, journal = {Genetics}, volume = {204}, number = {2}, pages = {783-798}, pmid = {27489002}, issn = {1943-2631}, support = {R01 CA180776/CA/NCI NIH HHS/United States ; R01 GM118652/GM/NIGMS NIH HHS/United States ; R01 HG007069/HG/NHGRI NIH HHS/United States ; }, mesh = {Data Interpretation, Statistical ; *Epistasis, Genetic ; Gene Regulatory Networks/*genetics ; *Genetic Predisposition to Disease ; Genome-Wide Association Study/*statistics & numerical data ; Genotype ; Humans ; Phenotype ; Polymorphism, Single Nucleotide/genetics ; }, abstract = {Genome-wide association (GWA) studies typically lack power to detect genotypes significantly associated with complex diseases, where different causal mutations of small effect may be present across cases. A common, tractable approach for identifying genomic elements associated with complex traits is to evaluate combinations of variants in known pathways or gene sets with shared biological function. Such gene-set analyses require the computation of gene-level P-values or gene scores; these gene scores are also useful when generating hypotheses for experimental validation. However, commonly used methods for generating GWA gene scores are computationally inefficient, biased by gene length, imprecise, or have low true positive rate (TPR) at low false positive rates (FPR), leading to erroneous hypotheses for functional validation. Here we introduce a new method, PEGASUS, for analytically calculating gene scores. PEGASUS produces gene scores with as much as 10 orders of magnitude higher numerical precision than competing methods. In simulation, PEGASUS outperforms existing methods, achieving up to 30% higher TPR when the FPR is fixed at 1%. We use gene scores from PEGASUS as input to HotNet2 to identify networks of interacting genes associated with multiple complex diseases and traits; this is the first application of HotNet2 to common variation. In ulcerative colitis and waist-hip ratio, we discover networks that include genes previously associated with these phenotypes, as well as novel candidate genes. In contrast, existing methods fail to identify these networks. We also identify networks for attention-deficit/hyperactivity disorder, in which GWA studies have yet to identify any significant SNPs.}, } @article {pmid27488501, year = {2017}, author = {Rothstein, AP and McLaughlin, R and Acevedo-Gutiérrez, A and Schwarz, D}, title = {wisepair: a computer program for individual matching in genetic tracking studies.}, journal = {Molecular ecology resources}, volume = {17}, number = {2}, pages = {267-277}, doi = {10.1111/1755-0998.12590}, pmid = {27488501}, issn = {1755-0998}, mesh = {Animals ; Anura/classification/genetics ; Computational Biology/*methods ; Genotype ; Genotyping Techniques/*methods ; Otters/classification/genetics ; Phoca/classification/genetics ; Sequence Homology ; *Software ; }, abstract = {Individual-based data sets tracking organisms over space and time are fundamental to answering broad questions in ecology and evolution. A 'permanent' genetic tag circumvents a need to invasively mark or tag animals, especially if there are little phenotypic differences among individuals. However, genetic tracking of individuals does not come without its limits; correctly matching genotypes and error rates associated with laboratory work can make it difficult to parse out matched individuals. In addition, defining a sampling design that effectively matches individuals in the wild can be a challenge for researchers. Here, we combine the two objectives of defining sampling design and reducing genotyping error through an efficient Python-based computer-modelling program, wisepair. We describe the methods used to develop the computer program and assess its effectiveness through three empirical data sets, with and without reference genotypes. Our results show that wisepair outperformed similar genotype matching programs using previously published from reference genotype data of diurnal poison frogs (Allobates femoralis) and without-reference (faecal) genotype sample data sets of harbour seals (Phoca vitulina) and Eurasian otters (Lutra lutra). In addition, due to limited sampling effort in the harbour seal data, we present optimal sampling designs for future projects. wisepair allows for minimal sacrifice in the available methods as it incorporates sample rerun error data, allelic pairwise comparisons and probabilistic simulations to determine matching thresholds. Our program is the lone tool available to researchers to define parameters a priori for genetic tracking studies.}, } @article {pmid27488343, year = {2016}, author = {Johansson, EW and Selling, KE and Nsona, H and Mappin, B and Gething, PW and Petzold, M and Peterson, SS and Hildenwall, H}, title = {Integrated paediatric fever management and antibiotic over-treatment in Malawi health facilities: data mining a national facility census.}, journal = {Malaria journal}, volume = {15}, number = {1}, pages = {396}, pmid = {27488343}, issn = {1475-2875}, support = {//Medical Research Council/United Kingdom ; }, mesh = {Adolescent ; Adult ; Aged ; Anti-Bacterial Agents/*therapeutic use ; Censuses ; Child ; Child, Preschool ; Data Mining ; *Delivery of Health Care, Integrated ; Diagnostic Tests, Routine/*statistics & numerical data ; *Drug Utilization ; Female ; Fever/*diagnosis/*drug therapy ; *Health Services Research ; Humans ; Infant ; Malaria/diagnosis/drug therapy ; Malawi ; Male ; Middle Aged ; Young Adult ; }, abstract = {BACKGROUND: There are growing concerns about irrational antibiotic prescription practices in the era of test-based malaria case management. This study assessed integrated paediatric fever management using malaria rapid diagnostic tests (RDT) and Integrated Management of Childhood Illness (IMCI) guidelines, including the relationship between RDT-negative results and antibiotic over-treatment in Malawi health facilities in 2013-2014.

METHODS: A Malawi national facility census included 1981 observed sick children aged 2-59 months with fever complaints. Weighted frequencies were tabulated for other complaints, assessments and prescriptions for RDT-confirmed malaria, IMCI-classified non-severe pneumonia, and clinical diarrhoea. Classification trees using model-based recursive partitioning estimated the association between RDT results and antibiotic over-treatment and learned the influence of 38 other input variables at patient-, provider- and facility-levels.

RESULTS: Among 1981 clients, 72 % were tested or referred for malaria diagnosis and 85 % with RDT-confirmed malaria were prescribed first-line anti-malarials. Twenty-eight percent with IMCI-pneumonia were not prescribed antibiotics (under-treatment) and 59 % 'without antibiotic need' were prescribed antibiotics (over-treatment). Few clients had respiratory rates counted to identify antibiotic need for IMCI-pneumonia (18 %). RDT-negative children had 16.8 (95 % CI 8.6-32.7) times higher antibiotic over-treatment odds compared to RDT-positive cases conditioned by cough or difficult breathing complaints.

CONCLUSIONS: Integrated paediatric fever management was sub-optimal for completed assessments and antibiotic targeting despite common compliance to malaria treatment guidelines. RDT-negative results were strongly associated with antibiotic over-treatment conditioned by cough or difficult breathing complaints. A shift from malaria-focused 'test and treat' strategies toward 'IMCI with testing' is needed to improve quality fever care and rational use of both anti-malarials and antibiotics in line with recent global commitments to combat resistance.}, } @article {pmid27488180, year = {2016}, author = {Yang, W and Rosenstiel, PC and Schulenburg, H}, title = {ABSSeq: a new RNA-Seq analysis method based on modelling absolute expression differences.}, journal = {BMC genomics}, volume = {17}, number = {}, pages = {541}, pmid = {27488180}, issn = {1471-2164}, mesh = {Computational Biology/methods ; Computer Simulation ; Gene Expression Profiling/*methods ; *Gene Expression Regulation ; ROC Curve ; Sequence Analysis, RNA/*methods ; *Software ; Transcriptome ; }, abstract = {BACKGROUND: The recent advances in next generation sequencing technology have made the sequencing of RNA (i.e., RNA-Seq) an extemely popular approach for gene expression analysis. Identification of significant differential expression represents a crucial initial step in these analyses, on which most subsequent inferences of biological functions are built. Yet, for identification of these subsequently analysed genes, most studies use an additional minimal threshold of differential expression that is not captured by the applied statistical procedures.

RESULTS: Here we introduce a new analysis approach, ABSSeq, which uses a negative binomal distribution to model absolute expression differences between conditions, taking into account variations across genes and samples as well as magnitude of differences. In comparison to alternative methods, ABSSeq shows higher performance on controling type I error rate and at least a similar ability to correctly identify differentially expressed genes.

CONCLUSIONS: ABSSeq specifically considers the overall magnitude of expression differences, which enhances the power in detecting truly differentially expressed genes by reducing false positives at both very low and high expression level. In addition, ABSSeq offers to calculate shrinkage of fold change to facilitate gene ranking and effective outlier detection.}, } @article {pmid27485510, year = {2016}, author = {Chrismas, NA and Barker, G and Anesio, AM and Sánchez-Baracaldo, P}, title = {Genomic mechanisms for cold tolerance and production of exopolysaccharides in the Arctic cyanobacterium Phormidesmis priestleyi BC1401.}, journal = {BMC genomics}, volume = {17}, number = {}, pages = {533}, pmid = {27485510}, issn = {1471-2164}, mesh = {Adaptation, Biological/*genetics ; Amino Acid Sequence ; Arctic Regions ; *Cold Temperature ; Computational Biology/methods ; Cyanobacteria/*physiology ; Gene Order ; *Genome, Bacterial ; *Genomics/methods ; Phylogeny ; Polysaccharides, Bacterial/*biosynthesis ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: Cyanobacteria are major primary producers in extreme cold ecosystems. Many lineages of cyanobacteria thrive in these harsh environments, but it is not fully understood how they survive in these conditions and whether they have evolved specific mechanisms of cold adaptation. Phormidesmis priestleyi is a cyanobacterium found throughout the cold biosphere (Arctic, Antarctic and alpine habitats). Genome sequencing of P. priestleyi BC1401, an isolate from a cryoconite hole on the Greenland Ice Sheet, has allowed for the examination of genes involved in cold shock response and production of extracellular polymeric substances (EPS). EPSs likely enable cyanobacteria to buffer the effects of extreme cold and by identifying mechanisms for EPS production in P. priestleyi BC1401 this study lays the way for investigating transcription and regulation of EPS production in an ecologically important cold tolerant cyanobacterium.

RESULTS: We sequenced the draft genome of P. priestleyi BC1401 and implemented a new de Bruijn graph visualisation approach combined with BLAST analysis to separate cyanobacterial contigs from a simple metagenome generated from non-axenic cultures. Comparison of known cold adaptation genes in P. priestleyi BC1401 with three relatives from other environments revealed no clear differences between lineages. Genes involved in EPS biosynthesis were identified from the Wzy- and ABC-dependent pathways. The numbers of genes involved in cell wall and membrane biogenesis in P. priestleyi BC1401 were typical relative to the genome size. A gene cluster implicated in biofilm formation was found homologous to the Wps system, although the intracellular signalling pathways by which this could be regulated remain unclear.

CONCLUSIONS: Results show that the genomic characteristics and complement of known cold shock genes in P. priestleyi BC1401 are comparable to related lineages from a wide variety of habitats, although as yet uncharacterised cold shock genes in this organism may still exist. EPS production by P. priestleyi BC1401 likely contributes to its ability to survive efficiently in cold environments, yet this mechanism is widely distributed throughout the cyanobacterial phylum. Discovering how these EPS related mechanisms are regulated may help explain why P. priestleyi BC1401 is so successful in cold environments where related lineages are not.}, } @article {pmid27485508, year = {2016}, author = {Allen, HK and Bayles, DO and Looft, T and Trachsel, J and Bass, BE and Alt, DP and Bearson, SM and Nicholson, T and Casey, TA}, title = {Pipeline for amplifying and analyzing amplicons of the V1-V3 region of the 16S rRNA gene.}, journal = {BMC research notes}, volume = {9}, number = {}, pages = {380}, pmid = {27485508}, issn = {1756-0500}, mesh = {Computational Biology/methods ; DNA, Archaeal/*genetics ; DNA, Bacterial/*genetics ; Data Mining ; High-Throughput Nucleotide Sequencing ; *Metagenome ; Microbial Consortia/*genetics ; Molecular Sequence Annotation ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, DNA/*methods ; }, abstract = {BACKGROUND: Profiling of 16S rRNA gene sequences is an important tool for testing hypotheses in complex microbial communities, and analysis methods must be updated and validated as sequencing technologies advance. In host-associated bacterial communities, the V1-V3 region of the 16S rRNA gene is a valuable region to profile because it provides a useful level of taxonomic resolution; however, use of Illumina MiSeq data for experiments targeting this region needs validation.

RESULTS: Using a MiSeq machine and the version 3 (300 × 2) chemistry, we sequenced the V1-V3 region of the 16S rRNA gene within a mock community. Nineteen bacteria and one archaeon comprised the mock community, and 12 replicate amplifications of the community were performed and sequenced. Sequencing the large fragment (490 bp) that encompasses V1-V3 yielded a higher error rate (3.6 %) than has been reported when using smaller fragment sizes. This higher error rate was due to a large number of sequences that occurred only one or two times among all mock community samples. Removing sequences that occurred one time among all samples (singletons) reduced the error rate to 1.4 %. Diversity estimates of the mock community containing all sequences were inflated, whereas estimates following singleton removal more closely reflected the actual mock community membership. A higher percentage of the sequences could be taxonomically assigned after singleton and doubleton sequences were removed, and the assignments reflected the membership of the input DNA.

CONCLUSIONS: Sequencing the V1-V3 region of the 16S rRNA gene on the MiSeq platform may require additional sequence curation in silico, and improved error rates and diversity estimates show that removing low-frequency sequences is reasonable. When datasets have a high number of singletons, these singletons can be removed from the analysis without losing statistical power while reducing error and improving microbiota assessment.}, } @article {pmid27484342, year = {2016}, author = {Puente-Sánchez, F and Olsson, S and Aguilera, A}, title = {Comparative Transcriptomic Analysis of the Response of Dunaliella acidophila (Chlorophyta) to Short-Term Cadmium and Chronic Natural Metal-Rich Water Exposures.}, journal = {Microbial ecology}, volume = {72}, number = {3}, pages = {595-607}, pmid = {27484342}, issn = {1432-184X}, mesh = {Base Sequence ; Cadmium/*metabolism/toxicity ; Chlorophyta/*genetics/*metabolism ; Drug Tolerance/genetics ; Gene Expression Regulation, Plant ; Gene Ontology ; Genes, Plant ; Metals, Heavy/*metabolism/toxicity ; Oxidative Stress ; Photosynthesis ; Reactive Oxygen Species/metabolism ; Stress, Physiological/genetics ; Transcriptome/*genetics ; Water/chemistry/*metabolism ; }, abstract = {Heavy metals are toxic compounds known to cause multiple and severe cellular damage. However, acidophilic extremophiles are able to cope with very high concentrations of heavy metals. This study investigated the stress response under natural environmental heavy metal concentrations in an acidophilic Dunaliella acidophila. We employed Illumina sequencing for a de novo transcriptome assembly and to identify changes in response to high cadmium concentrations and natural metal-rich water. The photosynthetic performance was also estimated by pulse amplitude-modulated (PAM) fluorescence. Transcriptomic analysis highlights a number of processes mainly related to a high constitutive expression of genes involved in oxidative stress and response to reactive oxygen species (ROS), even in the absence of heavy metals. Photosynthetic activity seems to be unaltered under short-term exposition to Cd and chronic exposure to natural metal-rich water, probably due to an increase in the synthesis of structural photosynthetic components preserving their functional integrity. An overrepresentation of Gene Ontology (GO) terms related to metabolic activities, transcription, and proteosomal catabolic process was observed when D. acidophila grew under chronic exposure to natural metal-rich water. GO terms involved in carbohydrate metabolic process, reticulum endoplasmic and Golgi bodies, were also specifically overrepresented in natural metal-rich water library suggesting an endoplasmic reticulum stress response.}, } @article {pmid27481793, year = {2016}, author = {Zhou, X and Frandsen, PB and Holzenthal, RW and Beet, CR and Bennett, KR and Blahnik, RJ and Bonada, N and Cartwright, D and Chuluunbat, S and Cocks, GV and Collins, GE and deWaard, J and Dean, J and Flint, OS and Hausmann, A and Hendrich, L and Hess, M and Hogg, ID and Kondratieff, BC and Malicky, H and Milton, MA and Morinière, J and Morse, JC and Mwangi, FN and Pauls, SU and Gonzalez, MR and Rinne, A and Robinson, JL and Salokannel, J and Shackleton, M and Smith, B and Stamatakis, A and StClair, R and Thomas, JA and Zamora-Muñoz, C and Ziesmann, T and Kjer, KM}, title = {The Trichoptera barcode initiative: a strategy for generating a species-level Tree of Life.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {371}, number = {1702}, pages = {}, pmid = {27481793}, issn = {1471-2970}, support = {P 23687/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Animals ; Biodiversity ; *DNA Barcoding, Taxonomic ; Haplotypes ; Insecta/*classification/genetics ; *Phylogeny ; Sequence Analysis, DNA ; }, abstract = {DNA barcoding was intended as a means to provide species-level identifications through associating DNA sequences from unknown specimens to those from curated reference specimens. Although barcodes were not designed for phylogenetics, they can be beneficial to the completion of the Tree of Life. The barcode database for Trichoptera is relatively comprehensive, with data from every family, approximately two-thirds of the genera, and one-third of the described species. Most Trichoptera, as with most of life's species, have never been subjected to any formal phylogenetic analysis. Here, we present a phylogeny with over 16 000 unique haplotypes as a working hypothesis that can be updated as our estimates improve. We suggest a strategy of implementing constrained tree searches, which allow larger datasets to dictate the backbone phylogeny, while the barcode data fill out the tips of the tree. We also discuss how this phylogeny could be used to focus taxonomic attention on ambiguous species boundaries and hidden biodiversity. We suggest that systematists continue to differentiate between 'Barcode Index Numbers' (BINs) and 'species' that have been formally described. Each has utility, but they are not synonyms. We highlight examples of integrative taxonomy, using both barcodes and morphology for species description.This article is part of the themed issue 'From DNA barcodes to biomes'.}, } @article {pmid27481789, year = {2016}, author = {La Salle, J and Williams, KJ and Moritz, C}, title = {Biodiversity analysis in the digital era.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {371}, number = {1702}, pages = {}, pmid = {27481789}, issn = {1471-2970}, mesh = {Australia ; *Biodiversity ; Classification/*methods ; *Computational Biology ; *DNA Barcoding, Taxonomic ; Phylogeny ; }, abstract = {This paper explores what the virtual biodiversity e-infrastructure will look like as it takes advantage of advances in 'Big Data' biodiversity informatics and e-research infrastructure, which allow integration of various taxon-level data types (genome, morphology, distribution and species interactions) within a phylogenetic and environmental framework. By overcoming the data scaling problem in ecology, this integrative framework will provide richer information and fast learning to enable a deeper understanding of biodiversity evolution and dynamics in a rapidly changing world. The Atlas of Living Australia is used as one example of the advantages of progressing towards this future. Living in this future will require the adoption of new ways of integrating scientific knowledge into societal decision making.This article is part of the themed issue 'From DNA barcodes to biomes'.}, } @article {pmid27480660, year = {2016}, author = {Durvasula, A and Hoffman, PJ and Kent, TV and Liu, C and Kono, TJ and Morrell, PL and Ross-Ibarra, J}, title = {angsd-wrapper: utilities for analysing next-generation sequencing data.}, journal = {Molecular ecology resources}, volume = {16}, number = {6}, pages = {1449-1454}, doi = {10.1111/1755-0998.12578}, pmid = {27480660}, issn = {1755-0998}, mesh = {Computational Biology/*methods ; Genetic Variation ; Genetics, Population/*methods ; *High-Throughput Nucleotide Sequencing ; Sequence Analysis, DNA/*methods ; Software ; Zea mays/classification/genetics ; }, abstract = {High-throughput sequencing has changed many aspects of population genetics, molecular ecology and related fields, affecting both experimental design and data analysis. The software package angsd allows users to perform a number of population genetic analyses on high-throughput sequencing data. angsd uses probabilistic approaches which can directly make use of genotype likelihoods; thus, SNP calling is not required for comparative analyses. This takes advantage of all the sequencing data and produces more accurate results for samples with low sequencing depth. Here, we present angsd-wrapper, a set of wrapper scripts that provides a user-friendly interface for running angsd and visualizing results. angsd-wrapper supports multiple types of analyses including estimates of nucleotide sequence diversity neutrality tests, principal component analysis, estimation of admixture proportions for individual samples and calculation of statistics that quantify recent introgression. angsd-wrapper also provides interactive graphing of angsd results to enhance data exploration. We demonstrate the usefulness of angsd-wrapper by analysing resequencing data from populations of wild and domesticated Zea. angsd-wrapper is freely available from https://github.com/mojaveazure/angsd-wrapper.}, } @article {pmid27475032, year = {2016}, author = {Kolmodin MacDonell, K and Naar, S and Gibson-Scipio, W and Lam, P and Secord, E}, title = {The Detroit Young Adult Asthma Project: Pilot of a Technology-Based Medication Adherence Intervention for African-American Emerging Adults.}, journal = {The Journal of adolescent health : official publication of the Society for Adolescent Medicine}, volume = {59}, number = {4}, pages = {465-471}, pmid = {27475032}, issn = {1879-1972}, support = {R34 HL107664/HL/NHLBI NIH HHS/United States ; }, mesh = {Adolescent ; Adult ; Black or African American/*statistics & numerical data ; Asthma/*drug therapy ; Feasibility Studies ; Female ; Humans ; Male ; Medication Adherence/*statistics & numerical data ; Motivational Interviewing/*methods ; Pilot Projects ; *Reminder Systems/instrumentation ; Self Report ; Text Messaging ; Young Adult ; }, abstract = {PURPOSE: To conduct a randomized controlled pilot of a multicomponent, technology-based intervention promoting adherence to controller medication in African-American emerging adults with asthma. The intervention consisted of two computer-delivered sessions based on motivational interviewing combined with text messaged reminders between sessions.

METHODS: Participants (N = 49) were 18-29 years old, African-American, with persistent asthma requiring controller medication. Participants had to report poor medication adherence and asthma control. Youth were randomized to receive the intervention or an attention control. Data were collected through computer-delivered self-report questionnaires at baseline, 1, and 3 months. Ecological Momentary Assessment via two-way text messaging was also used to collect "real-time" data on medication use and asthma control.

RESULTS: The intervention was feasible and acceptable to the target population, as evidenced by high retention rates and satisfaction scores. Changes in study outcomes from pre- to postintervention favored the intervention, particularly for decrease in asthma symptoms, t (42) = 2.22, p < .05 (Cohen's d = .071).

CONCLUSIONS: Results suggest that the intervention is feasible and effective. However, findings are preliminary and should be replicated with a larger sample and more sophisticated data analyses.}, } @article {pmid27470284, year = {2016}, author = {Wang, P and Li, Y and Nie, H and Zhang, X and Shao, Q and Hou, X and Xu, W and Hong, W and Xu, A}, title = {The changes of gene expression profiling between segmental vitiligo, generalized vitiligo and healthy individual.}, journal = {Journal of dermatological science}, volume = {84}, number = {1}, pages = {40-49}, doi = {10.1016/j.jdermsci.2016.07.006}, pmid = {27470284}, issn = {1873-569X}, mesh = {Adolescent ; Adult ; Apoptosis ; Autophagy ; Case-Control Studies ; Cluster Analysis ; Computational Biology ; Cytokines/metabolism ; Female ; Gene Expression Profiling ; *Gene Expression Regulation ; Genetic Predisposition to Disease ; Glycolysis ; Humans ; Immune System ; Male ; Melanocytes/cytology ; Oxidation-Reduction ; Purines/chemistry ; Pyrimidines/chemistry ; Reactive Oxygen Species/metabolism ; Sphingolipids/chemistry ; *Transcriptome ; Vitiligo/*genetics ; Young Adult ; }, abstract = {BACKGROUND: Vitiligo is a common acquired depigmentation skin disease characterized by loss or dysfunction of melanocytes within the skin lesion, but its pathologenesis is far from lucid. The gene expression profiling of segmental vitiligo (SV) and generalized vitiligo (GV) need further investigation.

OBJECTIVE: To better understanding the common and distinct factors, especially in the view of gene expression profile, which were involved in the diseases development and maintenance of segmental vitiligo (SV) and generalized vitiligo (GV).

METHODS: Peripheral bloods were collected from SV, GV and healthy individual (HI), followed by leukocytes separation and total RNA extraction. The high-throughput whole genome expression microarrays were used to assay the gene expression profiles between HI, SV and GV. Bioinformatics tools were employed to annotated the biological function of differently expressed genes. Quantitative PCR assay was used to validate the gene expression of array.

RESULTS: Compared to HI, 239 over-expressed genes and 175 down-expressed genes detected in SV, 688 over-expressed genes and 560 down-expressed genes were found in GV, following the criteria of log2 (fold change)≥0.585 and P value<0.05. In these differently expressed genes, 60 over-expressed genes and 60 down-expressed genes had similar tendency in SV and GV. Compared to SV, 223 genes were up regulated and 129 genes were down regulated in GV. In the SV with HI as control, the differently expressed genes were mainly involved in the adaptive immune response, cytokine-cytokine receptor interaction, chemokine signaling, focal adhesion and sphingolipid metabolism. The differently expressed genes between GV and HI were mainly involved in the innate immune, autophagy, apoptosis, melanocyte biology, ubiquitin mediated proteolysis and tyrosine metabolism, which was different from SV. While the differently expressed genes between SV and GV were mainly involved in the metabolism pathway of purine, pyrimidine, glycolysis and sphingolipid.

CONCLUSIONS: Above results suggested that they not only shared part bio-process and signal pathway, but more important, they utilized different biological mechanism in their pathogenesis and maintenance. Our results provide a comprehensive view on the gene expression profiling change between SV and GV especially in the side of leukocytes, and may facilitate the future study on their molecular mechanism and theraputic targets.}, } @article {pmid27468941, year = {2017}, author = {Larson, L and Johnson, DE and Wilson, M and Wilson, K and Louhaichi, M and Williams, J}, title = {Spatial occupancy patterns and activity of arid rangeland cattle grazing small riparian pastures.}, journal = {Animal science journal = Nihon chikusan Gakkaiho}, volume = {88}, number = {3}, pages = {553-558}, doi = {10.1111/asj.12670}, pmid = {27468941}, issn = {1740-0929}, mesh = {Animals ; *Behavior, Animal ; Cattle/*physiology/*psychology ; Geographic Information Systems ; Herbivory/*physiology ; Locomotion/*physiology ; Oregon ; Rivers ; Time Factors ; }, abstract = {The spatial occupancy patterns and activity of cattle grazing three riparian pastures was investigated in northeastern Oregon using Global Positioning System (GPS) collars logging at 1-sec intervals. Cattle consistently selected plant communities as grazing areas that had forage in sufficient volume to meet their requirements and favored communities as resting areas that were dry and open. Cattle were stationary for more than 50% of the time in each pasture and consistently rested between dark and 04:00 hours. Interaction with stream channels was found to be 1-2% of total occupancy time and occurred on less than 10% of channel length. Cattle were indifferent or avoided channel areas relative to their area and, when in this zone, they spent most of their time moving not resting. Cattle did not prefer the stream bank zone and spent only 2% of their time in that zone. When occupied, the stream bank zone was used as a travel corridor to gain access to water or cross the channel to access other pasture areas. These results are in contrast with the general belief that cattle are a primary occupant of the stream bank/channel area; additional research is needed to define factors influencing cattle occupancy.}, } @article {pmid27464261, year = {2016}, author = {Mikulic-Petkovsek, M and Stampar, F and Veberic, R and Sircelj, H}, title = {Wild Prunus Fruit Species as a Rich Source of Bioactive Compounds.}, journal = {Journal of food science}, volume = {81}, number = {8}, pages = {C1928-37}, doi = {10.1111/1750-3841.13398}, pmid = {27464261}, issn = {1750-3841}, mesh = {Acids/analysis ; Anthocyanins/analysis/pharmacology ; Antioxidants/analysis/*pharmacology ; Carbohydrates/analysis ; Chromatography, High Pressure Liquid ; Flavonols/analysis/*pharmacology ; Fruit/*chemistry ; Glucosides/analysis/pharmacology ; Humans ; Phenols/analysis/*pharmacology ; Plant Extracts/chemistry/*pharmacology ; Prunus/*chemistry ; }, abstract = {Sugars, organic acids, carotenoids, tocopherols, chlorophylls, and phenolic compounds were quantified in fruit of 4 wild growing Prunus species (wild cherry, bird cherry, blackthorn, and mahaleb cherry) using HPLC-DAD-MSn. In wild Prunus, the major sugars were glucose and fructose, whereas malic and citric acids dominated among organic acids. The most abundant classes of phenolic compounds in the analyzed fruit species were anthocyanins, flavonols, derivatives of cinnamic acids, and flavanols. Two major groups of anthocyanins measured in Prunus fruits were cyanidin-3-rutinoside and cyanidin-3-glucoside. Flavonols were represented by 19 derivatives of quercetin, 10 derivatives of kaempferol, and 2 derivatives of isorhamnetin. The highest total flavonol content was measured in mahaleb cherry and bird cherry, followed by blackthorn and wild cherry fruit. Total phenolic content varied from 2373 (wild cherry) to 11053 mg GAE per kg (bird cherry) and ferric reducing antioxidant power antioxidant activity from 7.26 to 31.54 mM trolox equivalents per kg fruits.}, } @article {pmid27461508, year = {2017}, author = {Paradis, E and Gosselin, T and Goudet, J and Jombart, T and Schliep, K}, title = {Linking genomics and population genetics with R.}, journal = {Molecular ecology resources}, volume = {17}, number = {1}, pages = {54-66}, doi = {10.1111/1755-0998.12577}, pmid = {27461508}, issn = {1755-0998}, support = {MR/K010174/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Biostatistics/*methods ; Computational Biology/*methods ; Genetics, Population/*methods ; Genomics/*methods ; Haplotypes ; Linkage Disequilibrium ; Polymorphism, Single Nucleotide ; *Software ; }, abstract = {Population genetics and genomics have developed and been treated as independent fields of study despite having common roots. The continuous progress of sequencing technologies is contributing to (re-)connect these two disciplines. We review the challenges faced by data analysts and software developers when handling very big genetic data sets collected on many individuals. We then expose how r, as a computing language and development environment, proposes some solutions to meet these challenges. We focus on some specific issues that are often encountered in practice: handling and analysing single-nucleotide polymorphism data, handling and reading variant call format files, analysing haplotypes and linkage disequilibrium and performing multivariate analyses. We illustrate these implementations with some analyses of three recently published data sets that contain between 60 000 and 1 000 000 loci. We conclude with some perspectives on future developments of r software for population genomics.}, } @article {pmid27460381, year = {2016}, author = {Leray, M and Knowlton, N}, title = {Visualizing Patterns of Marine Eukaryotic Diversity from Metabarcoding Data Using QIIME.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1452}, number = {}, pages = {219-235}, doi = {10.1007/978-1-4939-3774-5_15}, pmid = {27460381}, issn = {1940-6029}, mesh = {Biodiversity ; Computational Biology/methods ; High-Throughput Nucleotide Sequencing ; Humans ; Microbiota/genetics ; Principal Component Analysis ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA/*methods ; }, abstract = {PCR amplification followed by deep sequencing of homologous gene regions is increasingly used to characterize the diversity and taxonomic composition of marine eukaryotic communities. This approach may generate millions of sequences for hundreds of samples simultaneously. Therefore, tools that researchers can use to visualize complex patterns of diversity for these massive datasets are essential. Efforts by microbiologists to understand the Earth and human microbiomes using high-throughput sequencing of the 16S rRNA gene has led to the development of several user-friendly, open-source software packages that can be similarly used to analyze eukaryotic datasets. Quantitative Insights Into Microbial Ecology (QIIME) offers some of the most helpful data visualization tools. Here, we describe functionalities to import OTU tables generated with any molecular marker (e.g., 18S, COI, ITS) and associated metadata into QIIME. We then present a range of analytical tools implemented within QIIME that can be used to obtain insights about patterns of alpha and beta diversity for marine eukaryotes.}, } @article {pmid27457242, year = {2017}, author = {Miller, TR and Lawrence, BA and Carlson, NN and Hendrie, D and Randall, S and Rockett, IR and Spicer, RS}, title = {Perils of police action: a cautionary tale from US data sets.}, journal = {Injury prevention : journal of the International Society for Child and Adolescent Injury Prevention}, volume = {23}, number = {1}, pages = {27-32}, doi = {10.1136/injuryprev-2016-042023}, pmid = {27457242}, issn = {1475-5785}, mesh = {Adolescent ; Adult ; *Cause of Death/trends ; Datasets as Topic ; Ethnicity/*statistics & numerical data ; Female ; Humans ; *Law Enforcement ; Male ; Middle Aged ; Models, Theoretical ; *Police ; Racism/statistics & numerical data ; Social Justice/statistics & numerical data ; United States/epidemiology ; Violence/*statistics & numerical data ; Young Adult ; }, abstract = {OBJECTIVE: To count and characterise injuries resulting from legal intervention by US law enforcement personnel and injury ratios per 10 000 arrests or police stops, thus expanding discussion of excessive force by police beyond fatalities.

DESIGN: Ecological.

POPULATION: Those injured during US legal police intervention as recorded in 2012 Vital Statistics mortality census, 2012 Healthcare Cost and Utilization Project nationwide inpatient and emergency department samples, and two 2015 newspaper censuses of deaths.

EXPOSURE: 2012 and 2014 arrests from Federal Bureau of Investigation data adjusted for non-reporting jurisdictions; street stops and traffic stops that involved vehicle or occupant searches, without arrest, from the 2011 Police Public Contact Survey (PPCS), with the percentage breakdown by race computed from pooled 2005, 2008 and 2011 PPCS surveys due to small case counts.

RESULTS: US police killed or injured an estimated 55 400 people in 2012 (95% CI 47 050 to 63 740 for cases coded as police involved). Blacks, Native Americans and Hispanics had higher stop/arrest rates per 10 000 population than white non-Hispanics and Asians. On average, an estimated 1 in 291 stops/arrests resulted in hospital-treated injury or death of a suspect or bystander. Ratios of admitted and fatal injury due to legal police intervention per 10 000 stops/arrests did not differ significantly between racial/ethnic groups. Ratios rose with age, and were higher for men than women.

CONCLUSIONS: Healthcare administrative data sets can inform public debate about injuries resulting from legal police intervention. Excess per capita death rates among blacks and youth at police hands are reflections of excess exposure. International Classification of Diseases legal intervention coding needs revision.}, } @article {pmid27456675, year = {2016}, author = {Bosompem, C and Stemn, E and Fei-Baffoe, B}, title = {Multi-criteria GIS-based siting of transfer station for municipal solid waste: The case of Kumasi Metropolitan Area, Ghana.}, journal = {Waste management & research : the journal of the International Solid Wastes and Public Cleansing Association, ISWA}, volume = {34}, number = {10}, pages = {1054-1063}, doi = {10.1177/0734242X16658363}, pmid = {27456675}, issn = {1096-3669}, mesh = {Databases, Factual ; *Decision Support Techniques ; *Geographic Information Systems ; Ghana ; Humans ; Population Density ; Refuse Disposal/*methods ; Waste Disposal Facilities ; }, abstract = {The increase in the quantity of municipal solid waste generated as a result of population growth in most urban areas has resulted in the difficulty of locating suitable land areas to be used as landfills. To curb this, waste transfer stations are used. The Kumasi Metropolitan Area, even though it has an engineered landfill, is faced with the problem of waste collection from the generation centres to the final disposal site. Thus in this study, multi-criteria decision analysis incorporated into a geographic information system was used to determine potential waste transfer station sites. The key result established 11 sites located within six different sub-metros. This result can be used by decision makers for site selection of the waste transfer stations after taking into account other relevant ecological and economic factors.}, } @article {pmid27454666, year = {2017}, author = {Rutschmann, S and Detering, H and Simon, S and Fredslund, J and Monaghan, MT}, title = {discomark: nuclear marker discovery from orthologous sequences using draft genome data.}, journal = {Molecular ecology resources}, volume = {17}, number = {2}, pages = {257-266}, doi = {10.1111/1755-0998.12576}, pmid = {27454666}, issn = {1755-0998}, mesh = {Animals ; Computational Biology/*methods ; Ephemeroptera/classification/genetics ; *Genetic Markers ; Genomics/*methods ; High-Throughput Nucleotide Sequencing ; *Phylogeny ; Sequence Analysis, DNA/*methods ; *Software ; }, abstract = {High-throughput sequencing has laid the foundation for fast and cost-effective development of phylogenetic markers. Here we present the program discomark, which streamlines the development of nuclear DNA (nDNA) markers from whole-genome (or whole-transcriptome) sequencing data, combining local alignment, alignment trimming, reference mapping and primer design based on multiple sequence alignments to design primer pairs from input orthologous sequences. To demonstrate the suitability of discomark, we designed markers for two groups of species, one consisting of closely related species and one group of distantly related species. For the closely related members of the species complex of Cloeon dipterum s.l. (Insecta, Ephemeroptera), the program discovered a total of 78 markers. Among these, we selected eight markers for amplification and Sanger sequencing. The exon sequence alignments (2526 base pairs) were used to reconstruct a well-supported phylogeny and to infer clearly structured haplotype networks. For the distantly related species, we designed primers for the insect order Ephemeroptera, using available genomic data from four sequenced species. We developed primer pairs for 23 markers that are designed to amplify across several families. The discomark program will enhance the development of new nDNA markers by providing a streamlined, automated approach to perform genome-scale scans for phylogenetic markers. The program is written in Python, released under a public licence (GNU GPL version 2), and together with a manual and example data set available at: https://github.com/hdetering/discomark.}, } @article {pmid27450239, year = {2016}, author = {Ip, JC and Leung, PT and Ho, KK and Qiu, JW and Leung, KM}, title = {De novo transcriptome assembly of the marine gastropod Reishia clavigera for supporting toxic mechanism studies.}, journal = {Aquatic toxicology (Amsterdam, Netherlands)}, volume = {178}, number = {}, pages = {39-48}, doi = {10.1016/j.aquatox.2016.07.006}, pmid = {27450239}, issn = {1879-1514}, mesh = {Animals ; Ecotoxicology/*methods ; Female ; Gastropoda/*drug effects/genetics ; Gene Ontology ; Gonads/drug effects ; Male ; Molecular Sequence Annotation ; Organ Specificity ; Organotin Compounds/*toxicity ; Transcriptome/*drug effects ; Water Pollutants, Chemical/*toxicity ; }, abstract = {The intertidal whelk Reishia clavigera is commonly used as a biomonitor of chemical contamination in the marine environment along Western Pacific region, and as a model for mechanistic studies of organotin-mediated imposex development. However, limited genomic resources of R. clavigera have restricted its role for the investigation of molecular mechanisms of such endocrine disruptions. This study, therefore, aimed to establish tissue-specific transcriptomes of the digestive gland, gonad, head ganglia, penis and the remaining body part of the male and female R. clavigera. By combining the results, a global transcriptome was obtained. A total of 578,134,720 high-quality filtered reads were obtained using Illumina sequencing. The R. clavigera transcriptome comprised of 38,466 transcripts and 32,798 unigenes with predicted open reading frames. The average length of transcripts was 1,709bp with N50 of 2,236bp. Based on sequence similarity searches against public databases, 28,657 transcripts and 24,403 unigenes had at least one BLAST hit. There were 17,530 transcripts and 14,897 unigenes annotated with at least one Gene Ontology (GO) term. Moreover, 5,776 transcripts and 5,137 unigenes were associated with 333 Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathways. The numbers of unigenes were similar among the five target tissues and between sexes, but tissue-specific expression profiles were revealed by multivariate analyses. Based on the functional annotation, putative steroid hormone-associated unigenes were identified. In particular, we highlighted the presence of steroid hormone receptor homologues that could be the targets for mechanistic studies of the organotin-mediated imposex development in marine gastropods. This newly generated transcriptome assembly of R. clavigera provides a valuable molecular resource for ecotoxicological and environmental genomic studies.}, } @article {pmid27448048, year = {2016}, author = {Navarro, J and Grémillet, D and Afán, I and Ramírez, F and Bouten, W and Forero, MG}, title = {Feathered Detectives: Real-Time GPS Tracking of Scavenging Gulls Pinpoints Illegal Waste Dumping.}, journal = {PloS one}, volume = {11}, number = {7}, pages = {e0159974}, pmid = {27448048}, issn = {1932-6203}, mesh = {Animals ; *Charadriiformes ; Crime ; Environmental Monitoring ; *Geographic Information Systems ; Humans ; Spain ; Spatial Analysis ; *Waste Disposal Facilities ; Waste Management ; }, abstract = {Urban waste impacts human and environmental health, and waste management has become one of the major challenges of humanity. Concurrently with new directives due to manage this human by-product, illegal dumping has become one of the most lucrative activities of organized crime. Beyond economic fraud, illegal waste disposal strongly enhances uncontrolled dissemination of human pathogens, pollutants and invasive species. Here, we demonstrate the potential of novel real-time GPS tracking of scavenging species to detect environmental crime. Specifically, we were able to detect illegal activities at an officially closed dump, which was visited recurrently by 5 of 19 GPS-tracked yellow-legged gulls (Larus michahellis). In comparison with conventional land-based surveys, GPS tracking allows a much wider and cost-efficient spatiotemporal coverage, even of the most hazardous sites, while GPS data accessibility through the internet enables rapid intervention. Our results suggest that multi-species guilds of feathered detectives equipped with GPS and cameras could help fight illegal dumping at continental scales. We encourage further experimental studies, to infer waste detection thresholds in gulls and other scavenging species exploiting human waste dumps.}, } @article {pmid27447649, year = {2016}, author = {Baten, A and Ngangbam, AK and Waters, DL and Benkendorff, K}, title = {Transcriptome of the Australian Mollusc Dicathais orbita Provides Insights into the Biosynthesis of Indoles and Choline Esters.}, journal = {Marine drugs}, volume = {14}, number = {7}, pages = {}, pmid = {27447649}, issn = {1660-3397}, mesh = {Animals ; Australia ; Biosynthetic Pathways/*genetics ; Choline/*metabolism ; Databases, Genetic ; Esters/*metabolism ; Gastropoda/*genetics/metabolism ; Indoles/*metabolism ; Molecular Sequence Annotation/methods ; Mollusca/*genetics/metabolism ; Peroxidases/metabolism ; Transcriptome/*genetics ; }, abstract = {Dicathais orbita is a mollusc of the Muricidae family and is well known for the production of the expensive dye Tyrian purple and its brominated precursors that have anticancer properties, in addition to choline esters with muscle-relaxing properties. However, the biosynthetic pathways that produce these secondary metabolites in D. orbita are not known. Illumina HiSeq 2000 transcriptome sequencing of hypobranchial glands, prostate glands, albumen glands, capsule glands, and mantle and foot tissues of D. orbita generated over 201 million high quality reads that were de novo assembled into 219,437 contigs. Annotation with reference to the Nr, Swiss-Prot and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases identified candidate-coding regions in 76,152 of these contigs, with transcripts for many enzymes in various metabolic pathways associated with secondary metabolite biosynthesis represented. This study revealed that D. orbita expresses a number of genes associated with indole, sulfur and histidine metabolism pathways that are relevant to Tyrian purple precursor biosynthesis, and many of which were not found in the fully annotated genomes of three other molluscs in the KEGG database. However, there were no matches to known bromoperoxidase enzymes within the D. orbita transcripts. These transcriptome data provide a significant molecular resource for gastropod research in general and Tyrian purple producing Muricidae in particular.}, } @article {pmid27442429, year = {2016}, author = {Crespo, BG and Wallhead, PJ and Logares, R and Pedrós-Alió, C}, title = {Probing the Rare Biosphere of the North-West Mediterranean Sea: An Experiment with High Sequencing Effort.}, journal = {PloS one}, volume = {11}, number = {7}, pages = {e0159195}, pmid = {27442429}, issn = {1932-6203}, mesh = {Bacteria/isolation & purification ; Base Sequence ; *Biodiversity ; Databases, Genetic ; High-Throughput Nucleotide Sequencing/*methods ; Mediterranean Sea ; Species Specificity ; }, abstract = {High-throughput sequencing (HTS) techniques have suggested the existence of a wealth of species with very low relative abundance: the rare biosphere. We attempted to exhaustively map this rare biosphere in two water samples by performing an exceptionally deep pyrosequencing analysis (~500,000 final reads per sample). Species data were derived by a 97% identity criterion and various parametric distributions were fitted to the observed counts. Using the best-fitting Sichel distribution we estimate a total species richness of 1,568-1,669 (95% Credible Interval) and 5,027-5,196 for surface and deep water samples respectively, implying that 84-89% of the total richness in those two samples was sequenced, and we predict that a quadrupling of the present sequencing effort would suffice to observe 90% of the total richness in both samples. Comparing the HTS results with a culturing approach we found that most of the cultured taxa were not obtained by HTS, despite the high sequencing effort. Culturing therefore remains a useful tool for uncovering marine bacterial diversity, in addition to its other uses for studying the ecology of marine bacteria.}, } @article {pmid27442252, year = {2016}, author = {Bohlen, J and Šlechtová, V and Šlechta, V and Šlechtová, V and Sember, A and Ráb, P}, title = {A Ploidy Difference Represents an Impassable Barrier for Hybridisation in Animals. Is There an Exception among Botiid Loaches (Teleostei: Botiidae)?.}, journal = {PloS one}, volume = {11}, number = {7}, pages = {e0159311}, pmid = {27442252}, issn = {1932-6203}, mesh = {Animals ; China ; Chromosomes/genetics ; Cypriniformes/anatomy & histology/*genetics ; Cytochromes b/genetics ; Databases, Genetic ; Geography ; *Hybridization, Genetic ; Karyotyping ; Phylogeny ; Pigmentation/genetics ; *Ploidies ; Rivers ; Sequence Analysis, DNA ; }, abstract = {One of the most efficient mechanisms to keep animal lineages separate is a difference in ploidy level (number of whole genome copies), since hybrid offspring from parents with different ploidy level are functionally sterile. In the freshwater fish family Botiidae, ploidy difference has been held responsible for the separation of its two subfamilies, the evolutionary tetraploid Botiinae and the diploid Leptobotiinae. Diploid and tetraploid species coexist in the upper Yangtze, the Pearl River and the Red River basins in China. Interestingly, the species 'Botia' zebra from the Pearl River basin combines a number of morphological characters that otherwise are found in the diploid genus Leptobotia with morphological characters of the tetraploid genus Sinibotia, therefore the aim of the present study is to test weather 'B.' zebra is the result of a hybridisation event between species from different subfamilies with different ploidy level. A closer morphological examination indeed demonstrates a high similarity of 'B.' zebra to two co-occurring species, the diploid Leptobotia guilinensis and the tetraploid Sinibotia pulchra. These two species thus could have been the potential parental species in case of a hybrid origin of 'B.' zebra. The morphologic analysis further reveals that 'B.' zebra bears even the diagnostic characters of the genera Leptobotia (Leptobotiinae) and Sinibotia (Botiinae). In contrast, a comparison of six allozyme loci between 'B.' zebra, L. guilinensis and S. pulchra showed only similarities between 'B.' zebra and S. pulchra, not between 'B.' zebra and L. guilinensis. Six specimens of 'B.' zebra that were cytogenetically analysed were tetraploid with 4n = 100. The composition of the karyotype (18% metacentric, 18% submetacentric, 36% subtelocentric and 28% acrocentric chromosomes) differs from those of L. guilinensis (12%, 24%, 20% and 44%) and S. pulchra (20%, 26%, 28% and 26%), and cannot be obtained by any combination of genomes from L. guilinensis and S. pulchra. Phylogenetic reconstructions based on sequence data of the mitochondrial cytochrome b gene and the nuclear RAG-1 gene invariably places 'Botia' zebra as sister species to S. pulchra, while L. guilinensis is only distantly related. The presented combination of genetic data demonstrates that 'B.' zebra is not the result of a hybridisation, but a species of tetraploid genus Sinibotia with a striking morphological evolution towards an enormous similarity with a co-occurring, but not directly related species. The complete lack of knowledge of the ecology of these species, their main predators or their ecological interactions hampers any conclusion regarding the evolutionary advantage of such adaptation.}, } @article {pmid27442123, year = {2016}, author = {Sayadi, A and Immonen, E and Bayram, H and Arnqvist, G}, title = {The De Novo Transcriptome and Its Functional Annotation in the Seed Beetle Callosobruchus maculatus.}, journal = {PloS one}, volume = {11}, number = {7}, pages = {e0158565}, pmid = {27442123}, issn = {1932-6203}, mesh = {Animals ; Coleoptera/*genetics ; Gene Ontology ; Genes, Insect ; Larva/genetics ; *Molecular Sequence Annotation ; Pupa/genetics ; Seeds/*parasitology ; Sequence Analysis, RNA ; Statistics as Topic ; Transcriptome/*genetics ; }, abstract = {Despite their unparalleled biodiversity, the genomic resources available for beetles (Coleoptera) remain relatively scarce. We present an integrative and high quality annotated transcriptome of the beetle Callosobruchus maculatus, an important and cosmopolitan agricultural pest as well as an emerging model species in ecology and evolutionary biology. Using Illumina sequencing technology, we sequenced 492 million read pairs generated from 51 samples of different developmental stages (larvae, pupae and adults) of C. maculatus. Reads were de novo assembled using the Trinity software, into a single combined assembly as well as into three separate assemblies based on data from the different developmental stages. The combined assembly generated 218,192 transcripts and 145,883 putative genes. Putative genes were annotated with the Blast2GO software and the Trinotate pipeline. In total, 33,216 putative genes were successfully annotated using Blastx against the Nr (non-redundant) database and 13,382 were assigned to 34,100 Gene Ontology (GO) terms. We classified 5,475 putative genes into Clusters of Orthologous Groups (COG) and 116 metabolic pathways maps were predicted based on the annotation. Our analyses suggested that the transcriptional specificity increases with ontogeny. For example, out of 33,216 annotated putative genes, 51 were only expressed in larvae, 63 only in pupae and 171 only in adults. Our study illustrates the importance of including samples from several developmental stages when the aim is to provide an integrative and high quality annotated transcriptome. Our results will represent an invaluable resource for those working with the ecology, evolution and pest control of C. maculatus, as well for comparative studies of the transcriptomics and genomics of beetles more generally.}, } @article {pmid27441565, year = {2016}, author = {Subramaniam, A and Ptacek, T and Lobashevsky, E and Cliver, S and Lefkowitz, EJ and Morrow, CD and Biggio, JR and Edwards, RK}, title = {Midtrimester Cervicovaginal Microbiota: Identification of Microbial Variations Associated with Puerperal Infection at Term.}, journal = {American journal of perinatology}, volume = {33}, number = {12}, pages = {1165-1175}, pmid = {27441565}, issn = {1098-8785}, support = {P30 AI027767/AI/NIAID NIH HHS/United States ; P30 AR050948/AR/NIAMS NIH HHS/United States ; UL1 TR000165/TR/NCATS NIH HHS/United States ; }, mesh = {Adolescent ; Adult ; Bacteria/*isolation & purification ; Cervix Uteri/*microbiology ; Female ; Humans ; *Microbiota ; Obesity/epidemiology ; Pregnancy ; Pregnancy Trimester, Second ; Proteobacteria/isolation & purification ; Puerperal Infection/*epidemiology ; Vagina/*microbiology ; Young Adult ; }, abstract = {Objective This study aims to evaluate differences in the midtrimester cervicovaginal microbiota between women who developed puerperal infections at term and those who did not, and whether obesity modulates this relationship. Methods Previously, cervicovaginal swabs were collected at 21 to 25 weeks gestation (stored at -80°C). Samples were identified from Black women with normal vaginal flora (Nugent score: 0-2) delivering term singletons. Patients were in one of four equally sized groups (total n = 120) characterized by absence or presence of puerperal infection and maternal obesity. Samples were thawed, DNA extracted, and polymerase chain reaction with primers targeting the 16S rDNA V4 region was used to prepare an amplicon library sequenced and analyzed using Quantitative Insights into Microbial Ecology (QIIME) suite. Microbiota differences were assessed using permutation-based anodis over three β-diversity measures; Kruskal-Wallis test was used for taxa level analysis. Results After quality control measures, 113 samples were analyzed. Overall, there was significant clustering by puerperal infection (p = 0.03), but not by obesity (p > 0.05). Detailed taxa level analysis revealed approximately 66% less Proteobacteria phylum and 400% more BVAB1 genera in the second-trimester microbiota of women who had puerperal infections at term (p < 0.05). Conclusion Women who develop puerperal infections at term have a significantly altered midtrimester cervicovaginal microbiome with less Proteobacteria and greater BVAB1. This finding may represent a potential method to identify women at an increased risk of puerperal infection.}, } @article {pmid27436009, year = {2016}, author = {Lenz, TL and Spirin, V and Jordan, DM and Sunyaev, SR}, title = {Excess of Deleterious Mutations around HLA Genes Reveals Evolutionary Cost of Balancing Selection.}, journal = {Molecular biology and evolution}, volume = {33}, number = {10}, pages = {2555-2564}, pmid = {27436009}, issn = {1537-1719}, support = {R01 GM078598/GM/NIGMS NIH HHS/United States ; R01 MH101244/MH/NIMH NIH HHS/United States ; }, mesh = {Alleles ; Biological Evolution ; Computer Simulation ; Databases, Genetic ; Evolution, Molecular ; Gene Frequency/genetics ; Genetic Variation ; Genome, Human ; HLA Antigens/*genetics ; Haplotypes/genetics ; Humans ; Major Histocompatibility Complex/*genetics ; Polymorphism, Genetic/genetics ; *Selection, Genetic ; *Sequence Deletion ; }, abstract = {Deleterious mutations are expected to evolve under negative selection and are usually purged from the population. However, deleterious alleles segregate in the human population and some disease-associated variants are maintained at considerable frequencies. Here, we test the hypothesis that balancing selection may counteract purifying selection in neighboring regions and thus maintain deleterious variants at higher frequency than expected from their detrimental fitness effect. We first show in realistic simulations that balancing selection reduces the density of polymorphic sites surrounding a locus under balancing selection, but at the same time markedly increases the population frequency of the remaining variants, including even substantially deleterious alleles. To test the predictions of our simulations empirically, we then use whole-exome sequencing data from 6,500 human individuals and focus on the most established example for balancing selection in the human genome, the major histocompatibility complex (MHC). Our analysis shows an elevated frequency of putatively deleterious coding variants in nonhuman leukocyte antigen (non-HLA) genes localized in the MHC region. The mean frequency of these variants declined with physical distance from the classical HLA genes, indicating dependency on genetic linkage. These results reveal an indirect cost of the genetic diversity maintained by balancing selection, which has hitherto been perceived as mostly advantageous, and have implications both for the evolution of recombination and also for the epidemiology of various MHC-associated diseases.}, } @article {pmid27435114, year = {2016}, author = {Song, Y and Zhang, Z and Tan, X and Jiang, Y and Gao, J and Lin, L and Wang, Z and Ren, J and Wang, X and Qin, L and Cheng, W and Qi, J and Kuai, B}, title = {Association of the molecular regulation of ear leaf senescence/stress response and photosynthesis/metabolism with heterosis at the reproductive stage in maize.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {29843}, pmid = {27435114}, issn = {2045-2322}, mesh = {Gene Expression Profiling/methods ; Gene Expression Regulation, Plant ; Gene Ontology ; Genes, Plant/genetics ; Hybrid Vigor/*genetics ; Hybridization, Genetic ; Phenotype ; Photosynthesis/*genetics ; Plant Breeding/methods ; Plant Leaves/*genetics ; Plant Proteins/genetics/metabolism ; Reproduction/genetics ; Time Factors ; Zea mays/*genetics/metabolism ; }, abstract = {Maize exhibits a wide range of heterotic traits, but the molecular basis of heterosis at the reproductive stage has seldom been exploited. Leaf senescence is a degenerative process which affects crop yield and quality. In this study, we observed significantly delayed ear leaf senescence in the reciprocal hybrids of B73/Mo17 and Zheng58/Chang7-2 after silking, and all the hybrids displayed larger leaf areas and higher stems with higher yields. Our time-course transcriptome analysis identified 2,826 differentially expressed genes (DEGs) between two parental lines (PP-DEGs) and 2,328 DEGs between parental lines and the hybrid (PH-DEGs) after silking. Notably, several senescence promoting genes (ZmNYE1, ZmORE1, ZmWRKY53 and ZmPIFs) exhibited underdominant expression patterns in the hybrid, whereas putative photosynthesis and carbon-fixation (ZmPEPC)-associated, starch biosynthetic (ZmAPS1, ZmAPL), gibberellin biosynthetic genes (ZmGA20OX, ZmGA3OX) expressed overdominantly. We also identified 86 transcription factors from PH-DEGs, some of which were known to regulate senescence, stress and metabolic processes. Collectively, we demonstrate a molecular association of the regulations of both ear leaf senescence/stress response and photosynthesis/metabolism with heterosis at the late developmental stage. This finding not only extends our understanding to the molecular basis of maize heterosis but also provides basic information for molecular breeding.}, } @article {pmid27434438, year = {2016}, author = {Dai, J and Wang, X and Ayala, FJ}, title = {Medical Informatics and the "Three Long, One Short" Problem of Large Urban Hospitals in China.}, journal = {JAMA}, volume = {316}, number = {3}, pages = {269-270}, doi = {10.1001/jama.2016.5487}, pmid = {27434438}, issn = {1538-3598}, mesh = {China ; Crowding ; Health Care Reform ; Health Expenditures ; Hospitals, Urban/*organization & administration ; Humans ; Medical Informatics/*trends ; *Patient Satisfaction ; Quality of Health Care ; Tertiary Care Centers/organization & administration ; *Waiting Lists ; }, } @article {pmid27434208, year = {2016}, author = {Rodríguez-Rey, M and Herrando-Pérez, S and Brook, BW and Saltré, F and Alroy, J and Beeton, N and Bird, MI and Cooper, A and Gillespie, R and Jacobs, Z and Johnson, CN and Miller, GH and Prideaux, GJ and Roberts, RG and Turney, CS and Bradshaw, CJ}, title = {A comprehensive database of quality-rated fossil ages for Sahul's Quaternary vertebrates.}, journal = {Scientific data}, volume = {3}, number = {}, pages = {160053}, pmid = {27434208}, issn = {2052-4463}, mesh = {Animals ; Biological Evolution ; *Databases, Factual ; *Fossils ; *Vertebrates ; }, abstract = {The study of palaeo-chronologies using fossil data provides evidence for past ecological and evolutionary processes, and is therefore useful for predicting patterns and impacts of future environmental change. However, the robustness of inferences made from fossil ages relies heavily on both the quantity and quality of available data. We compiled Quaternary non-human vertebrate fossil ages from Sahul published up to 2013. This, the FosSahul database, includes 9,302 fossil records from 363 deposits, for a total of 478 species within 215 genera, of which 27 are from extinct and extant megafaunal species (2,559 records). We also provide a rating of reliability of individual absolute age based on the dating protocols and association between the dated materials and the fossil remains. Our proposed rating system identified 2,422 records with high-quality ages (i.e., a reduction of 74%). There are many applications of the database, including disentangling the confounding influences of hypothetical extinction drivers, better spatial distribution estimates of species relative to palaeo-climates, and potentially identifying new areas for fossil discovery.}, } @article {pmid27433888, year = {2016}, author = {Hewson, CM and Thorup, K and Pearce-Higgins, JW and Atkinson, PW}, title = {Population decline is linked to migration route in the Common Cuckoo.}, journal = {Nature communications}, volume = {7}, number = {}, pages = {12296}, pmid = {27433888}, issn = {2041-1723}, mesh = {Africa, Northern ; *Animal Migration ; Animals ; Birds/*physiology ; Breeding/statistics & numerical data ; *Conservation of Natural Resources ; Desert Climate/*adverse effects ; Geographic Information Systems ; Male ; Population Dynamics/*statistics & numerical data ; Time Factors ; United Kingdom ; }, abstract = {Migratory species are in rapid decline globally. Although most mortality in long-distance migrant birds is thought to occur during migration, evidence of conditions on migration affecting breeding population sizes has been completely lacking. We addressed this by tracking 42 male Common Cuckoos from the rapidly declining UK population during 56 autumn migrations in 2011-14. Uniquely, the birds use two distinct routes to reach the same wintering grounds, allowing assessment of survival during migration independently of origin and destination. Mortality up to completion of the Sahara crossing (the major ecological barrier encountered in both routes) is higher for birds using the shorter route. The proportion of birds using this route strongly correlates with population decline across nine local breeding populations. Knowledge of variability in migratory behaviour and performance linked to robust population change data may therefore be necessary to understand population declines of migratory species and efficiently target conservation resources.}, } @article {pmid27432731, year = {2016}, author = {Radomyski, A and Giubilato, E and Ciffroy, P and Critto, A and Brochot, C and Marcomini, A}, title = {Modelling ecological and human exposure to POPs in Venice lagoon - Part II: Quantitative uncertainty and sensitivity analysis in coupled exposure models.}, journal = {The Science of the total environment}, volume = {569-570}, number = {}, pages = {1635-1649}, doi = {10.1016/j.scitotenv.2016.07.057}, pmid = {27432731}, issn = {1879-1026}, mesh = {*Environmental Exposure ; Environmental Monitoring/*methods ; Food Chain ; Humans ; Italy ; Models, Theoretical ; Polychlorinated Biphenyls/*analysis ; Polychlorinated Dibenzodioxins/*analysis ; Sensitivity and Specificity ; Uncertainty ; Water Pollutants, Chemical/*analysis ; }, abstract = {The study is focused on applying uncertainty and sensitivity analysis to support the application and evaluation of large exposure models where a significant number of parameters and complex exposure scenarios might be involved. The recently developed MERLIN-Expo exposure modelling tool was applied to probabilistically assess the ecological and human exposure to PCB 126 and 2,3,7,8-TCDD in the Venice lagoon (Italy). The 'Phytoplankton', 'Aquatic Invertebrate', 'Fish', 'Human intake' and PBPK models available in MERLIN-Expo library were integrated to create a specific food web to dynamically simulate bioaccumulation in various aquatic species and in the human body over individual lifetimes from 1932 until 1998. MERLIN-Expo is a high tier exposure modelling tool allowing propagation of uncertainty on the model predictions through Monte Carlo simulation. Uncertainty in model output can be further apportioned between parameters by applying built-in sensitivity analysis tools. In this study, uncertainty has been extensively addressed in the distribution functions to describe the data input and the effect on model results by applying sensitivity analysis techniques (screening Morris method, regression analysis, and variance-based method EFAST). In the exposure scenario developed for the Lagoon of Venice, the concentrations of 2,3,7,8-TCDD and PCB 126 in human blood turned out to be mainly influenced by a combination of parameters (half-lives of the chemicals, body weight variability, lipid fraction, food assimilation efficiency), physiological processes (uptake/elimination rates), environmental exposure concentrations (sediment, water, food) and eating behaviours (amount of food eaten). In conclusion, this case study demonstrated feasibility of MERLIN-Expo to be successfully employed in integrated, high tier exposure assessment.}, } @article {pmid27427948, year = {2016}, author = {Sun, Z and Plikus, MV and Komarova, NL}, title = {Near Equilibrium Calculus of Stem Cells in Application to the Airway Epithelium Lineage.}, journal = {PLoS computational biology}, volume = {12}, number = {7}, pages = {e1004990}, pmid = {27427948}, issn = {1553-7358}, support = {R01 AR067273/AR/NIAMS NIH HHS/United States ; U01 CA187956/CA/NCI NIH HHS/United States ; }, mesh = {Animals ; Cell Lineage ; Computational Biology ; Epithelial Cells/*cytology ; Homeostasis/*physiology ; Mice ; *Models, Biological ; Signal Transduction ; Stem Cells/*cytology ; Stochastic Processes ; }, abstract = {Homeostatic maintenance of tissues is orchestrated by well tuned networks of cellular signaling. Such networks regulate, in a stochastic manner, fates of all cells within the respective lineages. Processes such as symmetric and asymmetric divisions, differentiation, de-differentiation, and death have to be controlled in a dynamic fashion, such that the cell population is maintained at a stable equilibrium, has a sufficiently low level of stochastic variation, and is capable of responding efficiently to external damage. Cellular lineages in real tissues may consist of a number of different cell types, connected by hierarchical relationships, albeit not necessarily linear, and engaged in a number of different processes. Here we develop a general mathematical methodology for near equilibrium studies of arbitrarily complex hierarchical cell populations, under regulation by a control network. This methodology allows us to (1) determine stability properties of the network, (2) calculate the stochastic variance, and (3) predict how different control mechanisms affect stability and robustness of the system. We demonstrate the versatility of this tool by using the example of the airway epithelium lineage. Recent research shows that airway epithelium stem cells divide mostly asymmetrically, while the so-called secretory cells divide predominantly symmetrically. It further provides quantitative data on the recovery dynamics of the airway epithelium, which can include secretory cell de-differentiation. Using our new methodology, we demonstrate that while a number of regulatory networks can be compatible with the observed recovery behavior, the observed division patterns of cells are the most optimal from the viewpoint of homeostatic lineage stability and minimizing the variation of the cell population size. This not only explains the observed yet poorly understood features of airway tissue architecture, but also helps to deduce the information on the still largely hypothetical regulatory mechanisms governing tissue turnover, and lends insight into how different control loops influence the stability and variance properties of cell populations.}, } @article {pmid27426920, year = {2016}, author = {Nilse, L and Avci, D and Heisterkamp, P and Serang, O and Lemberg, MK and Schilling, O}, title = {Yeast membrane proteomics using leucine metabolic labelling: Bioinformatic data processing and exemplary application to the ER-intramembrane protease Ypf1.}, journal = {Biochimica et biophysica acta}, volume = {1864}, number = {10}, pages = {1363-1371}, doi = {10.1016/j.bbapap.2016.07.002}, pmid = {27426920}, issn = {0006-3002}, mesh = {Computational Biology/methods ; Endoplasmic Reticulum/*metabolism ; Fungal Proteins/metabolism ; Isotope Labeling/methods ; Leucine/*metabolism ; Membrane Proteins/*metabolism ; Membranes/*metabolism ; Peptide Hydrolases/*metabolism ; Peptide Mapping/methods ; Peptides/metabolism ; Proteome/*metabolism ; Proteomics/methods ; Yeasts/*metabolism ; }, abstract = {We describe in detail the usage of leucine metabolic labelling in yeast in order to monitor quantitative proteome alterations, e.g. upon removal of a protease. Since laboratory yeast strains are typically leucine auxotroph, metabolic labelling with trideuterated leucine (d3-leucine) is a straightforward, cost-effective, and ubiquitously applicable strategy for quantitative proteomic studies, similar to the widely used arginine/lysine metabolic labelling method for mammalian cells. We showcase the usage of advanced peptide quantification using the FeatureFinderMultiplex algorithm (part of the OpenMS software package) for robust and reliable quantification. Furthermore, we present an OpenMS bioinformatics data analysis workflow that combines accurate quantification with high proteome coverage. In order to enable visualization, peptide-mapping, and sharing of quantitative proteomic data, especially for membrane-spanning and cell-surface proteins, we further developed the web-application Proteator (http://proteator.appspot.com). Due to its simplicity and robustness, we expect metabolic leucine labelling in yeast to be of great interest to the research community. As an exemplary application, we show the identification of the copper transporter Ctr1 as a putative substrate of the ER-intramembrane protease Ypf1 by yeast membrane proteomics using d3-leucine isotopic labelling.}, } @article {pmid27422487, year = {2016}, author = {Martino, ME and Bayjanov, JR and Caffrey, BE and Wels, M and Joncour, P and Hughes, S and Gillet, B and Kleerebezem, M and van Hijum, SA and Leulier, F}, title = {Nomadic lifestyle of Lactobacillus plantarum revealed by comparative genomics of 54 strains isolated from different habitats.}, journal = {Environmental microbiology}, volume = {18}, number = {12}, pages = {4974-4989}, doi = {10.1111/1462-2920.13455}, pmid = {27422487}, issn = {1462-2920}, mesh = {Adaptation, Physiological/*genetics ; Base Sequence ; Biological Evolution ; Comparative Genomic Hybridization ; DNA, Bacterial/genetics ; Ecosystem ; Environment ; Genome, Bacterial/*genetics ; Genomics ; High-Throughput Nucleotide Sequencing ; Lactobacillus plantarum/*genetics/*isolation & purification/physiology ; Phenotype ; Sequence Analysis, DNA ; }, abstract = {The ability of bacteria to adapt to diverse environmental conditions is well-known. The process of bacterial adaptation to a niche has been linked to large changes in the genome content, showing that many bacterial genomes reflect the constraints imposed by their habitat. However, some highly versatile bacteria are found in diverse habitats that almost share nothing in common. Lactobacillus plantarum is a lactic acid bacterium that is found in a large variety of habitat. With the aim of unravelling the link between evolution and ecological versatility of L. plantarum, we analysed the genomes of 54 L. plantarum strains isolated from different environments. Comparative genome analysis identified a high level of genomic diversity and plasticity among the strains analysed. Phylogenomic and functional divergence studies coupled with gene-trait matching analyses revealed a mixed distribution of the strains, which was uncoupled from their environmental origin. Our findings revealed the absence of specific genomic signatures marking adaptations of L. plantarum towards the diverse habitats it is associated with. This suggests fundamentally similar trends of genome evolution in L. plantarum, which occur in a manner that is apparently uncoupled from ecological constraint and reflects the nomadic lifestyle of this species.}, } @article {pmid27420028, year = {2017}, author = {Bolduc, B and Youens-Clark, K and Roux, S and Hurwitz, BL and Sullivan, MB}, title = {iVirus: facilitating new insights in viral ecology with software and community data sets imbedded in a cyberinfrastructure.}, journal = {The ISME journal}, volume = {11}, number = {1}, pages = {7-14}, pmid = {27420028}, issn = {1751-7370}, mesh = {*Databases, Genetic ; Environmental Microbiology ; Internet ; Metagenome ; Open Reading Frames ; Software ; Viruses/classification/genetics/*isolation & purification ; }, abstract = {Microbes affect nutrient and energy transformations throughout the world's ecosystems, yet they do so under viral constraints. In complex communities, viral metagenome (virome) sequencing is transforming our ability to quantify viral diversity and impacts. Although some bottlenecks, for example, few reference genomes and nonquantitative viromics, have been overcome, the void of centralized data sets and specialized tools now prevents viromics from being broadly applied to answer fundamental ecological questions. Here we present iVirus, a community resource that leverages the CyVerse cyberinfrastructure to provide access to viromic tools and data sets. The iVirus Data Commons contains both raw and processed data from 1866 samples and 73 projects derived from global ocean expeditions, as well as existing and legacy public repositories. Through the CyVerse Discovery Environment, users can interrogate these data sets using existing analytical tools (software applications known as 'Apps') for assembly, open reading frame prediction and annotation, as well as several new Apps specifically developed for analyzing viromes. Because Apps are web based and powered by CyVerse supercomputing resources, they enable scalable analyses for a broad user base. Finally, a use-case scenario documents how to apply these advances toward new data. This growing iVirus resource should help researchers utilize viromics as yet another tool to elucidate viral roles in nature.}, } @article {pmid27418020, year = {2016}, author = {Connelly, K and Stein, KF and Chaudry, B and Trabold, N}, title = {Development of an Ecological Momentary Assessment Mobile App for a Low-Literacy, Mexican American Population to Collect Disordered Eating Behaviors.}, journal = {JMIR public health and surveillance}, volume = {2}, number = {2}, pages = {e31}, pmid = {27418020}, issn = {2369-2960}, abstract = {BACKGROUND: Ecological momentary assessment (EMA) is a popular method for understanding population health in which participants report their experiences while in naturally occurring contexts in order to increase the reliability and ecological validity of the collected data (as compared to retrospective recall). EMA studies, however, have relied primarily on text-based questionnaires, effectively eliminating low-literacy populations from the samples.

OBJECTIVE: To provide a case study of design of an EMA mobile app for a low-literacy population. In particular, we present the design process and final design of an EMA mobile app for low literate, Mexican American women to record unhealthy eating and weight control behaviors (UEWCBs).

METHODS: An iterative, user-centered design process was employed to develop the mobile app. An existing EMA protocol to measure UEWCBs in college-enrolled Mexican American women was used as the starting point for the application. The app utilizes an icon interface, with optional audio prompts, that is culturally sensitive and usable by a low-literacy population. A total of 41 women participated over the course of 4 phases of the design process, which included 2 interview and task-based phases (n=8, n=11), focus groups (n=15), and a 5-day, in situ deployment (n=7).

RESULTS: Participants' mental models of UEWCBs differed substantially from prevailing definitions found in the literature, prompting a major reorganization of the app interface. Differences in health literacy and numeracy were better identified with the Newest Vital Sign tool, as compared with the Short Assessment of Health Literacy tool. Participants had difficulty imagining scenarios in the interviews to practice recording a specific UEWCB; instead, usability was best tested in situ. Participants were able to use the EMA mobile app over the course of 5 days to record UEWCBs.

CONCLUSIONS: Results suggest that the iterative, user-centered design process was essential for designing the app to be made usable by the target population. Simply taking the protocol designed for a higher-literacy population and replacing words with icons and/or audio would have been unsuccessful with this population.}, } @article {pmid27417145, year = {2017}, author = {Jombart, T and Archer, F and Schliep, K and Kamvar, Z and Harris, R and Paradis, E and Goudet, J and Lapp, H}, title = {apex: phylogenetics with multiple genes.}, journal = {Molecular ecology resources}, volume = {17}, number = {1}, pages = {19-26}, pmid = {27417145}, issn = {1755-0998}, mesh = {Computational Biology/*methods ; *Genes ; *Genetic Variation ; Molecular Biology/*methods ; *Phylogeny ; *Sequence Homology ; *Software ; }, abstract = {Genetic sequences of multiple genes are becoming increasingly common for a wide range of organisms including viruses, bacteria and eukaryotes. While such data may sometimes be treated as a single locus, in practice, a number of biological and statistical phenomena can lead to phylogenetic incongruence. In such cases, different loci should, at least as a preliminary step, be examined and analysed separately. The r software has become a popular platform for phylogenetics, with several packages implementing distance-based, parsimony and likelihood-based phylogenetic reconstruction, and an even greater number of packages implementing phylogenetic comparative methods. Unfortunately, basic data structures and tools for analysing multiple genes have so far been lacking, thereby limiting potential for investigating phylogenetic incongruence. In this study, we introduce the new r package apex to fill this gap. apex implements new object classes, which extend existing standards for storing DNA and amino acid sequences, and provides a number of convenient tools for handling, visualizing and analysing these data. In this study, we introduce the main features of the package and illustrate its functionalities through the analysis of a simple data set.}, } @article {pmid27416036, year = {2016}, author = {Ahonen, L and Cowley, B and Torniainen, J and Ukkonen, A and Vihavainen, A and Puolamäki, K}, title = {Cognitive Collaboration Found in Cardiac Physiology: Study in Classroom Environment.}, journal = {PloS one}, volume = {11}, number = {7}, pages = {e0159178}, pmid = {27416036}, issn = {1932-6203}, mesh = {Adolescent ; Adult ; Cognition/*physiology ; *Cooperative Behavior ; Efficiency ; Electrocardiography ; Female ; Heart Rate/*physiology ; Humans ; Informatics/education ; Interpersonal Relations ; Male ; Problem Solving/physiology ; Software Design ; Students/*psychology ; Workload ; Young Adult ; }, abstract = {It is known that periods of intense social interaction result in shared patterns in collaborators' physiological signals. However, applied quantitative research on collaboration is hindered due to scarcity of objective metrics of teamwork effectiveness. Indeed, especially in the domain of productive, ecologically-valid activity such as programming, there is a lack of evidence for the most effective, affordable and reliable measures of collaboration quality. In this study we investigate synchrony in physiological signals between collaborating computer science students performing pair-programming exercises in a class room environment. We recorded electrocardiography over the course of a 60 minute programming session, using lightweight physiological sensors. We employ correlation of heart-rate variability features to study social psychophysiological compliance of the collaborating students. We found evident physiological compliance in collaborating dyads' heart-rate variability signals. Furthermore, dyads' self-reported workload was associated with the physiological compliance. Our results show viability of a novel approach to field measurement using lightweight devices in an uncontrolled environment, and suggest that self-reported collaboration quality can be assessed via physiological signals.}, } @article {pmid27414263, year = {2016}, author = {Pigott, DM and Millear, AI and Earl, L and Morozoff, C and Han, BA and Shearer, FM and Weiss, DJ and Brady, OJ and Kraemer, MU and Moyes, CL and Bhatt, S and Gething, PW and Golding, N and Hay, SI}, title = {Updates to the zoonotic niche map of Ebola virus disease in Africa.}, journal = {eLife}, volume = {5}, number = {}, pages = {}, pmid = {27414263}, issn = {2050-084X}, support = {//Wellcome Trust/United Kingdom ; 095066//Wellcome Trust/United Kingdom ; U01 GM110744/GM/NIGMS NIH HHS/United States ; //Medical Research Council/United Kingdom ; }, mesh = {Africa/epidemiology ; Animal Distribution/physiology ; Animals ; Chiroptera/*virology ; Databases, Factual ; *Disease Outbreaks ; Disease Reservoirs/*virology ; Ebolavirus/pathogenicity/physiology ; Epidemiological Monitoring ; Hemorrhagic Fever, Ebola/*epidemiology/prevention & control/transmission ; Humans ; *Maps as Topic ; Zoonoses/*epidemiology/prevention & control/transmission ; }, abstract = {As the outbreak of Ebola virus disease (EVD) in West Africa is now contained, attention is turning from control to future outbreak prediction and prevention. Building on a previously published zoonotic niche map (Pigott et al., 2014), this study incorporates new human and animal occurrence data and expands upon the way in which potential bat EVD reservoir species are incorporated. This update demonstrates the potential for incorporating and updating data used to generate the predicted suitability map. A new data portal for sharing such maps is discussed. This output represents the most up-to-date estimate of the extent of EVD zoonotic risk in Africa. These maps can assist in strengthening surveillance and response capacity to contain viral haemorrhagic fevers.}, } @article {pmid27411240, year = {2016}, author = {Hunsicker, ME and Kappel, CV and Selkoe, KA and Halpern, BS and Scarborough, C and Mease, L and Amrhein, A}, title = {Characterizing driver-response relationships in marine pelagic ecosystems for improved ocean management.}, journal = {Ecological applications : a publication of the Ecological Society of America}, volume = {26}, number = {3}, pages = {651-663}, doi = {10.1890/14-2200}, pmid = {27411240}, issn = {1051-0761}, mesh = {Animals ; Biomass ; Databases, Factual ; *Ecosystem ; Marine Biology/*methods ; *Models, Biological ; *Oceans and Seas ; Population Density ; }, abstract = {Scientists and resource managers often use methods and tools that assume ecosystem components respond linearly to environmental drivers and human stressors. However, a growing body of literature demonstrates that many relationships are-non-linear, where small changes in a driver prompt a disproportionately large ecological response. We aim to provide a comprehensive assessment of the relationships between drivers and ecosystem components to identify where and when non-linearities are likely to occur. We focused our analyses on one of the best-studied marine systems, pelagic ecosystems, which allowed us to apply robust statistical techniques on a large pool of previously published studies. In this synthesis, we (1) conduct a wide literature review on single driver-response relationships in pelagic systems, (2) use statistical models to identify the degree of non-linearity in these relationships, and (3) assess whether general patterns exist in the strengths and shapes of non-linear relationships across drivers. Overall we found that non-linearities are common in pelagic ecosystems, comprising at least 52% of all driver-response relation- ships. This is likely an underestimate, as papers with higher quality data and analytical approaches reported non-linear relationships at a higher frequency (on average 11% more). Consequently, in the absence of evidence for a linear relationship, it is safer to assume a relationship is non-linear. Strong non-linearities can lead to greater ecological and socioeconomic consequences if they are unknown (and/or unanticipated), but if known they may provide clear thresholds to inform management targets. In pelagic systems, strongly non-linear relationships are often driven by climate and trophodynamic variables but are also associated with local stressors, such as overfishing and pollution, that can be more easily controlled by managers. Even when marine resource managers cannot influence ecosystem change, they can use information about threshold responses to guide how other stressors are managed and to adapt to new ocean conditions. As methods to detect and reduce uncertainty around threshold values improve, managers will be able to better understand and account for ubiquitous non-linear relationships.}, } @article {pmid27411058, year = {2016}, author = {Iandiorio, MJ and Fair, JM and Chatzipanagiotou, S and Ioannidis, A and Trikka-Graphakos, E and Charalampaki, N and Sereti, C and Tegos, GP and Hoogesteijn, AL and Rivas, AL}, title = {Preventing Data Ambiguity in Infectious Diseases with Four-Dimensional and Personalized Evaluations.}, journal = {PloS one}, volume = {11}, number = {7}, pages = {e0159001}, pmid = {27411058}, issn = {1932-6203}, mesh = {Animals ; Communicable Diseases/*diagnosis/immunology/microbiology/virology ; Diagnostic Errors/prevention & control ; Dogs ; Humans ; Leukocytes/cytology ; Medical Informatics/*methods ; Pilot Projects ; Spatio-Temporal Analysis ; }, abstract = {BACKGROUND: Diagnostic errors can occur, in infectious diseases, when anti-microbial immune responses involve several temporal scales. When responses span from nanosecond to week and larger temporal scales, any pre-selected temporal scale is likely to miss some (faster or slower) responses. Hoping to prevent diagnostic errors, a pilot study was conducted to evaluate a four-dimensional (4D) method that captures the complexity and dynamics of infectious diseases.

METHODS: Leukocyte-microbial-temporal data were explored in canine and human (bacterial and/or viral) infections, with: (i) a non-structured approach, which measures leukocytes or microbes in isolation; and (ii) a structured method that assesses numerous combinations of interacting variables. Four alternatives of the structured method were tested: (i) a noise-reduction oriented version, which generates a single (one data point-wide) line of observations; (ii) a version that measures complex, three-dimensional (3D) data interactions; (iii) a non-numerical version that displays temporal data directionality (arrows that connect pairs of consecutive observations); and (iv) a full 4D (single line-, complexity-, directionality-based) version.

RESULTS: In all studies, the non-structured approach revealed non-interpretable (ambiguous) data: observations numerically similar expressed different biological conditions, such as recovery and lack of recovery from infections. Ambiguity was also found when the data were structured as single lines. In contrast, two or more data subsets were distinguished and ambiguity was avoided when the data were structured as complex, 3D, single lines and, in addition, temporal data directionality was determined. The 4D method detected, even within one day, changes in immune profiles that occurred after antibiotics were prescribed.

CONCLUSIONS: Infectious disease data may be ambiguous. Four-dimensional methods may prevent ambiguity, providing earlier, in vivo, dynamic, complex, and personalized information that facilitates both diagnostics and selection or evaluation of anti-microbial therapies.}, } @article {pmid27400974, year = {2016}, author = {Havird, JC and Santos, SR}, title = {Here We Are, But Where Do We Go? A Systematic Review of Crustacean Transcriptomic Studies from 2014-2015.}, journal = {Integrative and comparative biology}, volume = {56}, number = {6}, pages = {1055-1066}, pmid = {27400974}, issn = {1557-7023}, support = {F32 GM116361/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Biological Evolution ; Computational Biology/history/standards/*trends ; Crustacea/*genetics ; History, 21st Century ; Software ; Transcriptome/*genetics ; Venoms/metabolism ; }, abstract = {Despite their economic, ecological, and experimental importance, genomic resources remain scarce for crustaceans. In lieu of genomes, many researchers have taken advantage of technological advancements to instead sequence and assemble crustacean transcriptomes de novo However, there is little consensus on what standard operating procedures are, or should be, for the field. Here, we systematically reviewed 53 studies published during 2014-2015 that utilized transcriptomic resources from this taxonomic group in an effort to identify commonalities as well as potential weaknesses that have applicability beyond just crustaceans. In general, these studies utilized RNA-Seq data, both novel and publicly available, to characterize transcriptomes and/or identify differentially expressed genes (DEGs) between treatments. Although the software suite Trinity was popular in assembly pipelines and other programs were also commonly employed, many studies failed to report crucial details regarding bioinformatic methodologies, including read mappers and the utilized parameters in identifying and characterizing DEGs. Annotation percentages for assembled transcriptomic contigs were low, averaging 32% overall. While other metrics, such as numbers of contigs and DEGs reported, correlated with the number of sequence reads utilized per sample, these did reach apparent saturation with increasing sequencing depth. Most disturbingly, a number of studies (55%) reported DEGs based on non-replicated experimental designs and single biological replicates for each treatment. Given this, we suggest future RNA-Seq experiments targeting transcriptome characterization conduct deeper (i.e., 50-100 M reads) sequencing while those examining differential expression instead focus more on increased biological replicates at shallower (i.e., ∼10-20 M reads/sample) sequencing depths. Moreover, the community must avoid submitting for review, or accepting for publication, non-replicated differential expression studies. Finally, mining the ever growing publicly available transcriptomic data from crustaceans will allow future studies to focus on hypothesis-driven research instead of continuing to simply characterize transcriptomes. As an example of this, we utilized neurotoxin sequences from the recently described remipede venom gland transcriptome in conjunction with publicly available crustacean transcriptomic data to derive preliminary results and hypotheses regarding the evolution of venom in crustaceans.}, } @article {pmid27396978, year = {2016}, author = {May, DH and Timmins-Schiffman, E and Mikan, MP and Harvey, HR and Borenstein, E and Nunn, BL and Noble, WS}, title = {An Alignment-Free "Metapeptide" Strategy for Metaproteomic Characterization of Microbiome Samples Using Shotgun Metagenomic Sequencing.}, journal = {Journal of proteome research}, volume = {15}, number = {8}, pages = {2697-2705}, pmid = {27396978}, issn = {1535-3907}, support = {P41 GM103533/GM/NIGMS NIH HHS/United States ; }, mesh = {Aquatic Organisms/*chemistry/genetics ; Biodiversity ; Databases, Protein ; Metagenomics/*methods ; *Microbiota/genetics ; Peptides/*analysis ; Proteomics/*methods ; Sequence Analysis, DNA ; Specimen Handling ; Tandem Mass Spectrometry ; }, abstract = {In principle, tandem mass spectrometry can be used to detect and quantify the peptides present in a microbiome sample, enabling functional and taxonomic insight into microbiome metabolic activity. However, the phylogenetic diversity constituting a particular microbiome is often unknown, and many of the organisms present may not have assembled genomes. In ocean microbiome samples, with particularly diverse and uncultured bacterial communities, it is difficult to construct protein databases that contain the bulk of the peptides in the sample without losing detection sensitivity due to the overwhelming number of candidate peptides for each tandem mass spectrum. We describe a method for deriving "metapeptides" (short amino acid sequences that may be represented in multiple organisms) from shotgun metagenomic sequencing of microbiome samples. In two ocean microbiome samples, we constructed site-specific metapeptide databases to detect more than one and a half times as many peptides as by searching against predicted genes from an assembled metagenome and roughly three times as many peptides as by searching against the NCBI environmental proteome database. The increased peptide yield has the potential to enrich the taxonomic and functional characterization of sample metaproteomes.}, } @article {pmid27394051, year = {2016}, author = {Fängström, K and Bokström, P and Dahlberg, A and Calam, R and Lucas, S and Sarkadi, A}, title = {In My Shoes - Validation of a computer assisted approach for interviewing children.}, journal = {Child abuse & neglect}, volume = {58}, number = {}, pages = {160-172}, doi = {10.1016/j.chiabu.2016.06.022}, pmid = {27394051}, issn = {1873-7757}, mesh = {Child Abuse/diagnosis ; Child, Preschool ; Diagnosis, Computer-Assisted/*methods ; Female ; Forensic Psychiatry/*methods ; Humans ; Interview, Psychological/*methods ; Male ; *Mental Recall ; Observer Variation ; Surveys and Questionnaires ; }, abstract = {Interviewing young children presents a challenge because they tend to provide incomplete accounts and are easily misled. Therefore there is a need for techniques to improve young children's recall, while maintaining accuracy and increasing completeness. The computer-assisted interview In My Shoes (IMS) is an aid that potentially offers a way for young children to provide accounts of their experiences. This study examined the validity of IMS, by comparing it with a forensic best practice interview approach using a real-life clinical situation to ensure high ecological validity. Children were randomly assigned to either method and both accuracy and completeness of statements made by 4- and 5-year-olds (N=54) regarding a video-documented health check-up were assessed. The In My Shoes interviews were as good as best practice interviews on all accuracy measures for both age groups, except for object accuracy that was better in the forensic interview condition. Events description completeness was similar in both interview conditions; however, IMS interviews generated more complete statements about people present at the visit. The findings suggest that the IMS approach yields comparable results to a best practice interview, and it can be used as an alternative aid in child interviews.}, } @article {pmid27392936, year = {2017}, author = {Huang, YJ and Erb-Downward, JR and Dickson, RP and Curtis, JL and Huffnagle, GB and Han, MK}, title = {Understanding the role of the microbiome in chronic obstructive pulmonary disease: principles, challenges, and future directions.}, journal = {Translational research : the journal of laboratory and clinical medicine}, volume = {179}, number = {}, pages = {71-83}, pmid = {27392936}, issn = {1878-1810}, support = {UL1 TR000433/TR/NCATS NIH HHS/United States ; T32 HL007749/HL/NHLBI NIH HHS/United States ; K23 HL105572/HL/NHLBI NIH HHS/United States ; K23 HL130641/HL/NHLBI NIH HHS/United States ; L30 HL120241/HL/NHLBI NIH HHS/United States ; I01 CX000911/CX/CSRD VA/United States ; }, mesh = {Animals ; Computational Biology ; High-Throughput Nucleotide Sequencing ; Humans ; Inflammation/pathology ; Lung/microbiology/pathology ; *Microbiota ; Pulmonary Disease, Chronic Obstructive/*microbiology ; }, abstract = {In the past several years, advances in sequencing platforms and bioinformatics have transformed our understanding of the relationship between microbial ecology and human health. Both the normal and diseased lung are host to hundreds of bacterial genera, blurring the lines between "colonization" and "infection". However, whereas in health the respiratory microbiome is determined primarily by the dynamic balance of immigration and elimination, in chronic disease conditions become much more favorable for the reproduction of resident bacteria. Recent studies demonstrate that the microbiota of the chronic obstructive pulmonary disease (COPD) lung differ from the healthy lung although significant intrasubject and intersubject heterogeneity are still present with variation impacted by factors such as disease stage and inhaled medications. Changes in the relative abundance of specific bacterial taxa during COPD exacerbations have also been noted although further longitudinal analyses are needed to ascertain the malleability and resilience of this ecological system and its role in the occurrence and frequency of exacerbations. Whether patients with a "frequent exacerbator" phenotype possess specific or greater alterations in their airway microbiome that predispose them to recurrent exacerbations as compared with nonfrequent exacerbators needs to be determined. Although recent data suggest that the presence of bacteria has the potential to influence the host immune response, a key challenge in the next few years will be to continue to move beyond descriptive studies to define the clinical relevance of differences in lung microbiota associated with COPD.}, } @article {pmid27392085, year = {2017}, author = {Llorens-Marès, T and Liu, Z and Allen, LZ and Rusch, DB and Craig, MT and Dupont, CL and Bryant, DA and Casamayor, EO}, title = {Speciation and ecological success in dimly lit waters: horizontal gene transfer in a green sulfur bacteria bloom unveiled by metagenomic assembly.}, journal = {The ISME journal}, volume = {11}, number = {1}, pages = {201-211}, pmid = {27392085}, issn = {1751-7370}, mesh = {Bacterial Proteins/metabolism ; Bacteriochlorophylls/metabolism ; Chlorobium/classification/genetics/isolation & purification/*metabolism ; Ecosystem ; *Gene Transfer, Horizontal ; Lakes/*microbiology ; Metagenomics ; Photosynthesis ; RNA, Ribosomal, 16S/genetics ; Spain ; Sulfur/*metabolism ; }, abstract = {A natural planktonic bloom of a brown-pigmented photosynthetic green sulfur bacteria (GSB) from the disphotic zone of karstic Lake Banyoles (NE Spain) was studied as a natural enrichment culture from which a nearly complete genome was obtained after metagenomic assembly. We showed in situ a case where horizontal gene transfer (HGT) explained the ecological success of a natural population unveiling ecosystem-specific adaptations. The uncultured brown-pigmented GSB was 99.7% identical in the 16S rRNA gene sequence to its green-pigmented cultured counterpart Chlorobium luteolum DSM 273[T]. Several differences were detected for ferrous iron acquisition potential, ATP synthesis and gas vesicle formation, although the most striking trait was related to pigment biosynthesis strategy. Chl. luteolum DSM 273[T] synthesizes bacteriochlorophyll (BChl) c, whereas Chl. luteolum CIII incorporated by HGT a 18-kbp cluster with the genes needed for BChl e and specific carotenoids biosynthesis that provided ecophysiological advantages to successfully colonize the dimly lit waters. We also genomically characterized what we believe to be the first described GSB phage, which based on the metagenomic coverage was likely in an active state of lytic infection. Overall, we observed spread HGT and we unveiled clear evidence for virus-mediated HGT in a natural population of photosynthetic GSB.}, } @article {pmid27391016, year = {2016}, author = {Kirby, KR and Gray, RD and Greenhill, SJ and Jordan, FM and Gomes-Ng, S and Bibiko, HJ and Blasi, DE and Botero, CA and Bowern, C and Ember, CR and Leehr, D and Low, BS and McCarter, J and Divale, W and Gavin, MC}, title = {D-PLACE: A Global Database of Cultural, Linguistic and Environmental Diversity.}, journal = {PloS one}, volume = {11}, number = {7}, pages = {e0158391}, pmid = {27391016}, issn = {1932-6203}, mesh = {*Cultural Diversity ; *Databases, Factual ; Female ; Humans ; *Language ; Male ; }, abstract = {From the foods we eat and the houses we construct, to our religious practices and political organization, to who we can marry and the types of games we teach our children, the diversity of cultural practices in the world is astounding. Yet, our ability to visualize and understand this diversity is limited by the ways it has been documented and shared: on a culture-by-culture basis, in locally-told stories or difficult-to-access repositories. In this paper we introduce D-PLACE, the Database of Places, Language, Culture, and Environment. This expandable and open-access database (accessible at https://d-place.org) brings together a dispersed corpus of information on the geography, language, culture, and environment of over 1400 human societies. We aim to enable researchers to investigate the extent to which patterns in cultural diversity are shaped by different forces, including shared history, demographics, migration/diffusion, cultural innovations, and environmental and ecological conditions. We detail how D-PLACE helps to overcome four common barriers to understanding these forces: i) location of relevant cultural data, (ii) linking data from distinct sources using diverse ethnonyms, (iii) variable time and place foci for data, and (iv) spatial and historical dependencies among cultural groups that present challenges for analysis. D-PLACE facilitates the visualisation of relationships among cultural groups and between people and their environments, with results downloadable as tables, on a map, or on a linguistic tree. We also describe how D-PLACE can be used for exploratory, predictive, and evolutionary analyses of cultural diversity by a range of users, from members of the worldwide public interested in contrasting their own cultural practices with those of other societies, to researchers using large-scale computational phylogenetic analyses to study cultural evolution. In summary, we hope that D-PLACE will enable new lines of investigation into the major drivers of cultural change and global patterns of cultural diversity.}, } @article {pmid27386165, year = {2016}, author = {Jovelin, R and Cutter, AD}, title = {Hitting two birds with one stone: The unforeseen consequences of nested gene knockouts in Caenorhabditis elegans.}, journal = {Worm}, volume = {5}, number = {2}, pages = {e1156835}, pmid = {27386165}, issn = {2162-4046}, abstract = {Nested genes represent an intriguing form of non-random genomic organization in which the boundaries of one gene are fully contained within another, longer host gene. The C. elegans genome contains over 10,000 nested genes, 92% of which are ncRNAs, which occur inside 16% of the protein coding gene complement. Host genes are longer than non-host coding genes, owing to their longer and more numerous introns. Indel alleles are available for nearly all of these host genes that simultaneously alter the nested gene, raising the possibility of nested gene disruption contributing to phenotypes that might be attributed to the host gene. Such dual-knockouts could represent a source of misinterpretation about host gene function. Dual-knockouts might also provide a novel source of synthetic phenotypes that reveal the functional effects of ncRNA genes, whereby the host gene disruption acts as a perturbed genetic background to help unmask ncRNA phenotypes.}, } @article {pmid27383682, year = {2016}, author = {Hiraoka, S and Yang, CC and Iwasaki, W}, title = {Metagenomics and Bioinformatics in Microbial Ecology: Current Status and Beyond.}, journal = {Microbes and environments}, volume = {31}, number = {3}, pages = {204-212}, pmid = {27383682}, issn = {1347-4405}, mesh = {*Biota ; Computational Biology/*methods ; *Environmental Microbiology ; Metagenomics/*methods ; }, abstract = {Metagenomic approaches are now commonly used in microbial ecology to study microbial communities in more detail, including many strains that cannot be cultivated in the laboratory. Bioinformatic analyses make it possible to mine huge metagenomic datasets and discover general patterns that govern microbial ecosystems. However, the findings of typical metagenomic and bioinformatic analyses still do not completely describe the ecology and evolution of microbes in their environments. Most analyses still depend on straightforward sequence similarity searches against reference databases. We herein review the current state of metagenomics and bioinformatics in microbial ecology and discuss future directions for the field. New techniques will allow us to go beyond routine analyses and broaden our knowledge of microbial ecosystems. We need to enrich reference databases, promote platforms that enable meta- or comprehensive analyses of diverse metagenomic datasets, devise methods that utilize long-read sequence information, and develop more powerful bioinformatic methods to analyze data from diverse perspectives.}, } @article {pmid27380513, year = {2018}, author = {Bollaerts, K and Simons, K and Van Bladel, L and De Smedt, T and Sonck, M and Fierens, S and Poffijn, A and Geraets, D and Gosselin, P and Van Oyen, H and Francart, J and Van Nieuwenhuyse, A}, title = {Childhood leukaemia near nuclear sites in Belgium, 2002-2008.}, journal = {European journal of cancer prevention : the official journal of the European Cancer Prevention Organisation (ECP)}, volume = {27}, number = {2}, pages = {184-191}, pmid = {27380513}, issn = {1473-5709}, mesh = {Adolescent ; Age Factors ; Belgium/epidemiology ; Child ; Child, Preschool ; Environmental Exposure/*adverse effects ; Female ; Humans ; Incidence ; Infant ; Infant, Newborn ; Leukemia/*epidemiology/etiology ; Leukemia, Radiation-Induced/*epidemiology/etiology ; Male ; *Nuclear Power Plants ; Sex Factors ; Thyroid Neoplasms/*epidemiology ; }, abstract = {This paper describes an ecological study investigating whether there is an excess incidence of acute leukaemia among children aged 0-14 years living in the vicinity of the nuclear sites in Belgium. Poisson regression modelling was carried out for proximity areas of varying sizes. In addition, the hypothesis of a gradient in leukaemia incidence with increasing levels of surrogate exposures was explored by means of focused hypothesis tests and generalized additive models. For the surrogate exposures, three proxies were used, that is, residential proximity to the nuclear site, prevailing winds and simulated radioactive discharges, on the basis of mathematical dispersion modelling. No excess incidence of acute leukaemia was observed around the nuclear power plants of Doel or Tihange nor around the nuclear site of Fleurus, which is a major manufacturer of radioactive isotopes in Europe. Around the site of Mol-Dessel, however, two- to three-fold increased leukaemia incidence rates were found in children aged 0-14 years living in the 0-5, 0-10 and the 0-15 km proximity areas. For this site, there was evidence for a gradient in leukaemia incidence with increased proximity, prevailing winds and simulated radioactive discharges, suggesting a potential link with the site that needs further investigation. An increased incidence of acute leukaemia in children aged 0-14 years was observed around one nuclear site that hosted reprocessing activities in the past and where nuclear research activities and radioactive waste treatment are ongoing.}, } @article {pmid27376994, year = {2016}, author = {Evangeliou, N and Hamburger, T and Talerko, N and Zibtsev, S and Bondar, Y and Stohl, A and Balkanski, Y and Mousseau, TA and Møller, AP}, title = {Reconstructing the Chernobyl Nuclear Power Plant (CNPP) accident 30 years after. A unique database of air concentration and deposition measurements over Europe.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {216}, number = {}, pages = {408-418}, doi = {10.1016/j.envpol.2016.05.030}, pmid = {27376994}, issn = {1873-6424}, mesh = {Air Pollutants, Radioactive/analysis ; Cesium Radioisotopes/analysis ; *Chernobyl Nuclear Accident ; *Databases, Factual ; Europe ; Half-Life ; *Nuclear Power Plants ; Soil Pollutants, Radioactive/analysis ; }, abstract = {30 years after the Chernobyl Nuclear Power Plant (CNPP) accident, its radioactive releases still remain of great interest mainly due to the long half-lives of many radionuclides emitted. Observations from the terrestrial environment, which hosts radionuclides for many years after initial deposition, are important for health and environmental assessments. Furthermore, such measurements are the basis for validation of atmospheric transport models and can be used for constraining the still not accurately known source terms. However, although the "Atlas of cesium deposition on Europe after the Chernobyl accident" (hereafter referred to as "Atlas") has been published since 1998, less than 1% of the direct observations of (137)Cs deposition has been made publicly available. The remaining ones are neither accessible nor traceable to specific data providers and a large fraction of these data might have been lost entirely. The present paper is an effort to rescue some of the data collected over the years following the CNPP accident and make them publicly available. The database includes surface air activity concentrations and deposition observations for (131)I, (134)Cs and (137)Cs measured and provided by Former Soviet Union authorities the years that followed the accident. Using the same interpolation tool as the official authorities, we have reconstructed a deposition map of (137)Cs based on about 3% of the data used to create the Atlas map. The reconstructed deposition map is very similar to the official one, but it has the advantage that it is based exclusively on documented data sources, which are all made available within this publication. In contrast to the official map, our deposition map is therefore reproducible and all underlying data can be used also for other purposes. The efficacy of the database was proved using simulated activity concentrations and deposition of (137)Cs from a Langrangian and a Euleurian transport model.}, } @article {pmid27374152, year = {2016}, author = {Baringou, S and Rouault, JD and Koken, M and Hardivillier, Y and Hurtado, L and Leignel, V}, title = {Diversity of cytosolic HSP70 Heat Shock Protein from decapods and their phylogenetic placement within Arthropoda.}, journal = {Gene}, volume = {591}, number = {1}, pages = {97-107}, doi = {10.1016/j.gene.2016.06.061}, pmid = {27374152}, issn = {1879-0038}, mesh = {Amino Acid Sequence ; Animals ; Cytosol/*metabolism ; Databases, Protein ; Decapoda/*genetics ; *Genetic Variation ; HSP70 Heat-Shock Proteins/*genetics ; Introns/genetics ; *Phylogeny ; Protein Structure, Secondary ; }, abstract = {The 70kDa heat shock proteins (HSP70) are considered the most conserved members of the HSP family. These proteins are primordial to the cell, because of their implications in many cellular pathways (e. g., development, immunity) and also because they minimize the effects of multiple stresses (e. g., temperature, pollutants, salinity, radiations). In the cytosol, two ubiquitous HSP70s with either a constitutive (HSC70) or an inducible (HSP70) expression pattern are found in all metazoan species, encoded by 5 or 6 genes (Drosophila melanogaster or yeast and human respectively). The cytosolic HSP70 protein family is considered a major actor in environmental adaptation, and widely used in ecology as an important biomarker of environmental stress. Nevertheless, the diversity of cytosolic HSP70 remains unclear amongst the Athropoda phylum, especially within decapods. Using 122 new and 311 available sequences, we carried out analyses of the overall cytosolic HSP70 diversity in arthropods (with a focus on decapods) and inferred molecular phylogenies. Overall structural and phylogenetic analyses showed a surprisingly high diversity in cytosolic HSP70 and revealed the existence of several unrecognised groups. All crustacean HSP70 sequences present signature motifs and molecular weights characteristic of non-organellar HSP70, with multiple specific substitutions in the protein sequence. The cytosolic HSP70 family in arthropods appears to be constituted of at least three distinct groups (annotated as A, B and C), which comprise several subdivisions, including both constitutive and inducible forms. Group A is constituted by several classes of Arthropods, while group B and C seem to be specific to Malacostraca and Hexapoda/Chelicerata, respectively. The HSP70 organization appeared much more complex than previously suggested, and far beyond a simple differentiation according to their expression pattern (HSC70 versus HSP70). This study proposes a new classification of cytosolic HSP70 and an evolutionary model of the distinct forms amongst the Arthropoda phylum. The observed differences between HSP70 groups will probably have to be linked to distinct interactions with co-chaperones or other co-factors.}, } @article {pmid27372411, year = {2016}, author = {Yang, W and Dierking, K and Rosenstiel, PC and Schulenburg, H}, title = {GATA transcription factor as a likely key regulator of the Caenorhabditis elegans innate immune response against gut pathogens.}, journal = {Zoology (Jena, Germany)}, volume = {119}, number = {4}, pages = {244-253}, doi = {10.1016/j.zool.2016.05.013}, pmid = {27372411}, issn = {1873-2720}, mesh = {Amino Acid Sequence ; Animals ; Caenorhabditis elegans/*immunology/metabolism ; Caenorhabditis elegans Proteins/genetics/*metabolism ; Databases, Factual ; GATA Transcription Factors/genetics/*metabolism ; Gastrointestinal Tract/immunology/*microbiology ; Gene Expression Regulation/immunology ; Immunity, Innate/*physiology ; Signal Transduction ; }, abstract = {Invertebrate defence against pathogens exclusively relies on components of the innate immune system. Comprehensive information has been collected over the last years on the molecular components of invertebrate immunity and the involved signalling processes, especially for the main invertebrate model species, the fruitfly Drosophila melanogaster and the nematode Caenorhabditis elegans. Yet, the exact regulation of general and specific defences is still not well understood. In the current study, we take advantage of a recently established database, WormExp, which combines all available gene expression studies for C. elegans, in order to explore commonalities and differences in the regulation of nematode immune defence against a large variety of pathogens versus food microbes. We identified significant overlaps in the transcriptional response towards microbes, especially pathogenic bacteria. We also found that the GATA motif is overrepresented in many microbe-induced gene sets and in targets of other previously identified regulators of worm immunity. Moreover, the activated targets of one of the known C. elegans GATA transcription factors, ELT-2, are significantly enriched in the gene sets, which are differentially regulated by gut-infecting pathogens. These findings strongly suggest that GATA transcription factors and particularly ELT-2 play a central role in regulating the C. elegans immune response against gut pathogens. More specific responses to distinct pathogens may be mediated by additional transcription factors, either acting alone or jointly with GATA transcription factors. Taken together, our analysis of the worm's transcriptional response to microbes provides a new perspective on the C. elegans immune system, which we propose to be coordinated by GATA transcription factor ELT-2 in the gut.}, } @article {pmid27372218, year = {2016}, author = {Mennis, J and Mason, M and Light, J and Rusby, J and Westling, E and Way, T and Zahakaris, N and Flay, B}, title = {Does substance use moderate the association of neighborhood disadvantage with perceived stress and safety in the activity spaces of urban youth?.}, journal = {Drug and alcohol dependence}, volume = {165}, number = {}, pages = {288-292}, doi = {10.1016/j.drugalcdep.2016.06.019}, pmid = {27372218}, issn = {1879-0046}, support = {R01 DA031724/DA/NIDA NIH HHS/United States ; }, mesh = {Adolescent ; Female ; Follow-Up Studies ; *Geographic Information Systems/trends ; Humans ; Longitudinal Studies ; Male ; Peer Group ; Perception ; *Residence Characteristics ; *Safety ; Stress, Psychological/diagnosis/epidemiology/*psychology ; Substance-Related Disorders/diagnosis/epidemiology/*psychology ; *Urban Population ; }, abstract = {BACKGROUND: This study investigates the association of activity space-based exposure to neighborhood disadvantage with momentary perceived stress and safety, and the moderation of substance use on those associations, among a sample of 139 urban, primarily African American, adolescents.

METHOD: Geospatial technologies are integrated with Ecological Momentary Assessment (EMA) to capture exposure to neighborhood disadvantage and perceived stress and safety in the activity space. A relative neighborhood disadvantage measure for each subject is calculated by conditioning the neighborhood disadvantage observed at the EMA location on that of the home neighborhood. Generalized estimating equations (GEE) are used to model the effect of relative neighborhood disadvantage on momentary perceived stress and safety, and the extent to which substance use moderates those associations.

RESULTS: Relative neighborhood disadvantage is significantly associated with higher perceived stress, lower perceived safety, and greater substance use involvement. The association of relative neighborhood disadvantage with stress is significantly stronger among those with greater substance use involvement.

CONCLUSION: This research highlights the value of integrating geospatial technologies with EMA and developing personalized measures of environmental exposure for investigating neighborhood effects on substance use, and suggests substance use intervention strategies aimed at neighborhood conditions. Future research should seek to disentangle the causal pathways of influence and selection that relate neighborhood environment, stress, and substance use, while also accounting for the role of gender and family and peer social contexts.}, } @article {pmid27367425, year = {2016}, author = {de Souza, EN and Boerder, K and Matwin, S and Worm, B}, title = {Improving Fishing Pattern Detection from Satellite AIS Using Data Mining and Machine Learning.}, journal = {PloS one}, volume = {11}, number = {7}, pages = {e0158248}, pmid = {27367425}, issn = {1932-6203}, mesh = {Animals ; Data Mining/*methods ; Fisheries/*statistics & numerical data ; *Machine Learning ; Pattern Recognition, Automated/*methods ; *Spacecraft ; }, abstract = {A key challenge in contemporary ecology and conservation is the accurate tracking of the spatial distribution of various human impacts, such as fishing. While coastal fisheries in national waters are closely monitored in some countries, existing maps of fishing effort elsewhere are fraught with uncertainty, especially in remote areas and the High Seas. Better understanding of the behavior of the global fishing fleets is required in order to prioritize and enforce fisheries management and conservation measures worldwide. Satellite-based Automatic Information Systems (S-AIS) are now commonly installed on most ocean-going vessels and have been proposed as a novel tool to explore the movements of fishing fleets in near real time. Here we present approaches to identify fishing activity from S-AIS data for three dominant fishing gear types: trawl, longline and purse seine. Using a large dataset containing worldwide fishing vessel tracks from 2011-2015, we developed three methods to detect and map fishing activities: for trawlers we produced a Hidden Markov Model (HMM) using vessel speed as observation variable. For longliners we have designed a Data Mining (DM) approach using an algorithm inspired from studies on animal movement. For purse seiners a multi-layered filtering strategy based on vessel speed and operation time was implemented. Validation against expert-labeled datasets showed average detection accuracies of 83% for trawler and longliner, and 97% for purse seiner. Our study represents the first comprehensive approach to detect and identify potential fishing behavior for three major gear types operating on a global scale. We hope that this work will enable new efforts to assess the spatial and temporal distribution of global fishing effort and make global fisheries activities transparent to ocean scientists, managers and the public.}, } @article {pmid27363730, year = {2016}, author = {de Sousa-Uva, M and Antunes, L and Nunes, B and Rodrigues, AP and Simões, JA and Ribeiro, RT and Boavida, JM and Matias-Dias, C}, title = {Trends in diabetes incidence from 1992 to 2015 and projections for 2024: A Portuguese General Practitioner's Network study.}, journal = {Primary care diabetes}, volume = {10}, number = {5}, pages = {329-333}, doi = {10.1016/j.pcd.2016.05.003}, pmid = {27363730}, issn = {1878-0210}, mesh = {Adolescent ; Adult ; Age Distribution ; Aged ; Child ; Child, Preschool ; Databases, Factual ; Diabetes Mellitus/diagnosis/*epidemiology ; Female ; Forecasting ; General Practice/*trends ; Humans ; Incidence ; Infant ; Infant, Newborn ; Male ; Middle Aged ; Portugal/epidemiology ; Sex Distribution ; Time Factors ; Young Adult ; }, abstract = {BACKGROUND: Diabetes is known as a major cause of morbidity and mortality worldwide. Portugal is known as the European country with the highest prevalence of this disease. While diabetes prevalence data is updated annually in Portugal, the General Practitioner's (GP) Sentinel Network represents the only data source on diabetes incidence. This study describes the trends in Diabetes incidence, between 1992 and 2015, and estimate projections for the future incidence rates in Portugal until 2024.

METHODS: An ecological time-series study was conducted using data from GP Sentinel Network between 1992 and 2015. Family doctors reported all new cases of Diabetes in their patients' lists. Annual trends were estimated through Poisson regression models as well as the future incidence rates (until 2024), sex and age group stratified. Incidence rate projections were adjusted to the distribution of the resident Portuguese population given Statistics Portugal projections.

RESULTS: The average increase in Diabetes incidence rate was in total 4.29% (CI95% 3.80-4.80) per year under study. Until 1998-2000, the annual incidence rate was higher in women, and from 1998-2000 to 2013-2015 turn out to be higher in men. The incidence rate projected for 2022-2024 was 972.77/10(5) inhabitants in total, and 846.74/10(5) and 1114.42/10(5), respectively, in women and men.

CONCLUSIONS: This is the first study in Portugal to estimate diabetes incidence rate projections. The disturbing reported projections seem realistic if things continue as in the past. Actually, effective public health policies will need to be undertaken to minimize this alarming future scenario.}, } @article {pmid27362222, year = {2016}, author = {Thackeray, SJ and Henrys, PA and Hemming, D and Bell, JR and Botham, MS and Burthe, S and Helaouet, P and Johns, DG and Jones, ID and Leech, DI and Mackay, EB and Massimino, D and Atkinson, S and Bacon, PJ and Brereton, TM and Carvalho, L and Clutton-Brock, TH and Duck, C and Edwards, M and Elliott, JM and Hall, SJ and Harrington, R and Pearce-Higgins, JW and Høye, TT and Kruuk, LE and Pemberton, JM and Sparks, TH and Thompson, PM and White, I and Winfield, IJ and Wanless, S}, title = {Phenological sensitivity to climate across taxa and trophic levels.}, journal = {Nature}, volume = {535}, number = {7611}, pages = {241-245}, doi = {10.1038/nature18608}, pmid = {27362222}, issn = {1476-4687}, support = {//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; Aquatic Organisms ; Climate ; Climate Change/*statistics & numerical data ; Datasets as Topic ; *Ecosystem ; Forecasting ; Rain ; Seasons ; Species Specificity ; Temperature ; Time Factors ; United Kingdom ; }, abstract = {Differences in phenological responses to climate change among species can desynchronise ecological interactions and thereby threaten ecosystem function. To assess these threats, we must quantify the relative impact of climate change on species at different trophic levels. Here, we apply a Climate Sensitivity Profile approach to 10,003 terrestrial and aquatic phenological data sets, spatially matched to temperature and precipitation data, to quantify variation in climate sensitivity. The direction, magnitude and timing of climate sensitivity varied markedly among organisms within taxonomic and trophic groups. Despite this variability, we detected systematic variation in the direction and magnitude of phenological climate sensitivity. Secondary consumers showed consistently lower climate sensitivity than other groups. We used mid-century climate change projections to estimate that the timing of phenological events could change more for primary consumers than for species in other trophic levels (6.2 versus 2.5-2.9 days earlier on average), with substantial taxonomic variation (1.1-14.8 days earlier on average).}, } @article {pmid27358393, year = {2016}, author = {Bálint, M and Bahram, M and Eren, AM and Faust, K and Fuhrman, JA and Lindahl, B and O'Hara, RB and Öpik, M and Sogin, ML and Unterseher, M and Tedersoo, L}, title = {Millions of reads, thousands of taxa: microbial community structure and associations analyzed via marker genes.}, journal = {FEMS microbiology reviews}, volume = {40}, number = {5}, pages = {686-700}, doi = {10.1093/femsre/fuw017}, pmid = {27358393}, issn = {1574-6976}, mesh = {Archaea/classification/*genetics ; Bacteria/classification/*genetics ; Biodiversity ; Data Interpretation, Statistical ; Fungi/classification/*genetics ; Genetic Markers/*genetics ; High-Throughput Nucleotide Sequencing/methods ; Microbiota/*genetics ; Sequence Analysis, DNA/methods ; }, abstract = {With high-throughput sequencing (HTS), we are able to explore the hidden world of microscopic organisms to an unpre-cedented level. The fast development of molecular technology and statistical methods means that microbial ecologists must keep their toolkits updated. Here, we review and evaluate some of the more widely adopted and emerging techniques for analysis of diversity and community composition, and the inference of species interactions from co-occurrence data generated by HTS of marker genes. We emphasize the importance of observational biases and statistical properties of the data and methods. The aim of the review is to critically discuss the advantages and disadvantages of established and emerging statistical methods, and to contribute to the integration of HTS-based marker gene data into community ecology.}, } @article {pmid27357964, year = {2016}, author = {Lewis, C and Darnell, D and Kerns, S and Monroe-DeVita, M and Landes, SJ and Lyon, AR and Stanick, C and Dorsey, S and Locke, J and Marriott, B and Puspitasari, A and Dorsey, C and Hendricks, K and Pierson, A and Fizur, P and Comtois, KA and Palinkas, LA and Chamberlain, P and Aarons, GA and Green, AE and Ehrhart, MG and Trott, EM and Willging, CE and Fernandez, ME and Woolf, NH and Liang, SL and Heredia, NI and Kegler, M and Risendal, B and Dwyer, A and Young, V and Campbell, D and Carvalho, M and Kellar-Guenther, Y and Damschroder, LJ and Lowery, JC and Ono, SS and Carlson, KF and Cottrell, EK and O’Neil, ME and Lovejoy, TL and Arch, JJ and Mitchell, JL and Lewis, CC and Marriott, BR and Scott, K and Coldiron, JS and Bruns, EJ and Hook, AN and Graham, BC and Jordan, K and Hanson, RF and Moreland, A and Saunders, BE and Resnick, HS and Stirman, SW and Gutner, CA and Gamarra, J and Vogt, D and Suvak, M and Wachen, JS and Dondanville, K and Yarvis, JS and Mintz, J and Peterson, AL and Borah, EV and Litz, BT and Molino, A and McCaughan, SY and Resick, PA and Pandhi, N and Jacobson, N and Serrano, N and Hernandez, A and Schreiter, EZ and Wietfeldt, N and Karp, Z and Pullmann, MD and Lucenko, B and Pavelle, B and Uomoto, JA and Negrete, A and Cevasco, M and Kerns, SEU and Franks, RP and Bory, C and Miech, EJ and Damush, TM and Satterfield, J and Satre, D and Wamsley, M and Yuan, P and O’Sullivan, P and Best, H and Velasquez, S and Barnett, M and Brookman-Frazee, L and Regan, J and Stadnick, N and Hamilton, A and Lau, A and Regan, J and Hamilton, A and Stadnick, N and Barnett, M and Lau, A and Brookman-Frazee, L and Stadnick, N and Lau, A and Barnett, M and Regan, J and Roesch, S and Brookman-Frazee, L and Powell, BJ and Waltz, TJ and Chinman, MJ and Damschroder, L and Smith, JL and Matthieu, MM and Proctor, EK and Kirchner, JE and Waltz, TJ and Powell, BJ and Chinman, MJ and Damschroder, LJ and Smith, JL and Matthieu, MJ and Proctor, EK and Kirchner, JE and Matthieu, MM and Rosen, CS and Waltz, TJ and Powell, BJ and Chinman, MJ and Damschroder, LJ and Smith, JL and Proctor, EK and Kirchner, JE and Walker, SC and Bishop, AS and Lockhart, M and Rodriguez, AL and Manfredi, L and Nevedal, A and Rosenthal, J and Blonigen, DM and Mauricio, AM and Dishion, TD and Rudo-Stern, J and Smith, JD and Locke, J and Wolk, CB and Harker, C and Olsen, A and Shingledecker, T and Barg, F and Mandell, D and Beidas, RS and Hansen, MC and Aranda, MP and Torres-Vigil, I and Hartzler, B and Steinfeld, B and Gildred, T and Harlin, Z and Shephard, F and Ditty, MS and Doyle, A and Bickel, JA and Cristaudo, K and Fox, D and Combs, S and Lischner, DH and Van Dorn, RA and Tueller, SJ and Hinde, JM and Karuntzos, GT and Monroe-DeVita, M and Peterson, R and Darnell, D and Berliner, L and Dorsey, S and Murray, LK and Botanov, Y and Kikuta, B and Chen, T and Navarro-Haro, M and DuBose, A and Korslund, KE and Linehan, MM and Harker, CM and Karp, EA and Edmunds, SR and Ibañez, LV and Stone, WL and Andrews, JH and Johnides, BD and Hausman, EM and Hawley, KM and Prusaczyk, B and Ramsey, A and Baumann, A and Colditz, G and Proctor, EK and Botanov, Y and Kikuta, B and Chen, T and Navarro-Haro, M and DuBose, A and Korslund, KE and Linehan, MM and Harker, CM and Karp, EA and Edmunds, SR and Ibañez, LV and Stone, WL and Choy-Brown, M and Andrews, JH and Johnides, BD and Hausman, EM and Hawley, KM and Prusaczyk, B and Ramsey, A and Baumann, A and Colditz, G and Proctor, EK and Meza, RD and Dorsey, S and Wiltsey-Stirman, S and Sedlar, G and Lucid, L and Dorsey, C and Marriott, B and Zounlome, N and Lewis, C and Gutner, CA and Monson, CM and Shields, N and Mastlej, M and Landy, MSH and Lane, J and Stirman, SW and Finn, NK and Torres, EM and Ehrhart, MG and Aarons, GA and Malte, CA and Lott, A and Saxon, AJ and Boyd, M and Scott, K and Lewis, CC and Pierce, JD and Lorthios-Guilledroit, A and Richard, L and Filiatrault, J and Hallgren, K and Crotwell, S and Muñoz, R and Gius, B and Ladd, B and McCrady, B and Epstein, E and Clapp, JD and Ruderman, DE and Barwick, M and Barac, R and Zlotkin, S and Salim, L and Davidson, M and Bunger, AC and Powell, BJ and Robertson, HA and Botsko, C and Landes, SJ and Smith, BN and Rodriguez, AL and Trent, LR and Matthieu, MM and Powell, BJ and Proctor, EK and Harned, MS and Navarro-Haro, M and Korslund, KE and Chen, T and DuBose, A and Ivanoff, A and Linehan, MM and Garcia, AR and Kim, M and Palinkas, LA and Snowden, L and Landsverk, J and Sweetland, AC and Fernandes, MJ and Santos, E and Duarte, C and Kritski, A and Krawczyk, N and Nelligan, C and Wainberg, ML and Aarons, GA and Sommerfeld, DH and Chi, B and Ezeanolue, E and Sturke, R and Kline, L and Guay, L and Siberry, G and Bennett, IM and Beidas, R and Gold, R and Mao, J and Powers, D and Vredevoogd, M and Unutzer, J and Schroeder, J and Volpe, L and Steffen, J and Dorsey, S and Pullmann, MD and Kerns, SEU and Jungbluth, N and Berliner, L and Thompson, K and Segell, E and McGee-Vincent, P and Liu, N and Walser, R and Runnals, J and Shaw, RK and Landes, SJ and Rosen, C and Schmidt, J and Calhoun, P and Varkovitzky, RL and Landes, SJ and Drahota, A and Martinez, JI and Brikho, B and Meza, R and Stahmer, AC and Aarons, GA and Williamson, A and Rubin, RM and Powell, BJ and Hurford, MO and Weaver, SL and Beidas, RS and Mandell, DS and Evans, AC and Powell, BJ and Beidas, RS and Rubin, RM and Stewart, RE and Wolk, CB and Matlin, SL and Weaver, S and Hurford, MO and Evans, AC and Hadley, TR and Mandell, DS and Gerke, DR and Prusaczyk, B and Baumann, A and Lewis, EM and Proctor, EK and McWilliam, J and Brown, J and Tucker, M and Conte, KP and Lyon, AR and Boyd, M and Melvin, A and Lewis, CC and Liu, F and Jungbluth, N and Kotte, A and Hill, KA and Mah, AC and Korathu-Larson, PA and Au, JR and Izmirian, S and Keir, S and Nakamura, BJ and Higa-McMillan, CK and Cooper, BR and Funaiole, A and Dizon, E and Hawkins, EJ and Malte, CA and Hagedorn, HJ and Berger, D and Frank, A and Lott, A and Achtmeyer, CE and Mariano, AJ and Saxon, AJ and Wolitzky-Taylor, K and Rawson, R and Ries, R and Roy-Byrne, P and Craske, M and Simmons, D and Torrente, C and Nathanson, L and Carroll, G and Smith, JD and Brown, K and Ramos, K and Thornton, N and Dishion, TJ and Stormshak, EA and Shaw, DS and Wilson, MN and Choy-Brown, M and Tiderington, E and Smith, BT and Padgett, DK and Rubin, RM and Ray, ML and Wandersman, A and Lamont, A and Hannah, G and Alia, KA and Hurford, MO and Evans, AC and Saldana, L and Schaper, H and Campbell, M and Chamberlain, P and Shapiro, VB and Kim, BKE and Fleming, JL and LeBuffe, PA and Landes, SJ and Lewis, CC and Rodriguez, AL and Marriott, BR and Comtois, KA and Lewis, CC and Stanick, C and Weiner, BJ and Halko, H and Dorsey, C}, title = {Proceedings of the 3rd Biennial Conference of the Society for Implementation Research Collaboration (SIRC) 2015: advancing efficient methodologies through community partnerships and team science : Seattle, WA, USA. 24-26 September 2015.}, journal = {Implementation science : IS}, volume = {11 Suppl 1}, number = {Suppl 1}, pages = {85}, doi = {10.1186/s13012-016-0428-0}, pmid = {27357964}, issn = {1748-5908}, support = {K01 MH100199/MH/NIMH NIH HHS/United States ; K23 MH099179/MH/NIMH NIH HHS/United States ; R01 MH097748/MH/NIMH NIH HHS/United States ; T32 MH096724/MH/NIMH NIH HHS/United States ; }, abstract = {Introduction to the 3rd Biennial Conference of the Society for Implementation Research Collaboration: advancing efficient methodologies through team science and community partnerships Cara Lewis, Doyanne Darnell, Suzanne Kerns, Maria Monroe-DeVita, Sara J. Landes, Aaron R. Lyon, Cameo Stanick, Shannon Dorsey, Jill Locke, Brigid Marriott, Ajeng Puspitasari, Caitlin Dorsey, Karin Hendricks, Andria Pierson, Phil Fizur, Katherine A. Comtois A1: A behavioral economic perspective on adoption, implementation, and sustainment of evidence-based interventions Lawrence A. Palinkas A2: Towards making scale up of evidence-based practices in child welfare systems more efficient and affordable Patricia Chamberlain A3: Mixed method examination of strategic leadership for evidence-based practice implementation Gregory A. Aarons, Amy E. Green, Mark. G. Ehrhart, Elise M. Trott, Cathleen E. Willging A4: Implementing practice change in Federally Qualified Health Centers: Learning from leaders’ experiences Maria E. Fernandez, Nicholas H. Woolf, Shuting (Lily) Liang, Natalia I. Heredia, Michelle Kegler, Betsy Risendal, Andrea Dwyer, Vicki Young, Dayna Campbell, Michelle Carvalho, Yvonne Kellar-Guenther A3: Mixed method examination of strategic leadership for evidence-based practice implementation Gregory A. Aarons, Amy E. Green, Mark. G. Ehrhart, Elise M. Trott, Cathleen E. Willging A4: Implementing practice change in Federally Qualified Health Centers: Learning from leaders’ experiences Maria E. Fernandez, Nicholas H. Woolf, Shuting (Lily) Liang, Natalia I. Heredia, Michelle Kegler, Betsy Risendal, Andrea Dwyer, Vicki Young, Dayna Campbell, Michelle Carvalho, Yvonne Kellar-Guenther A5: Efficient synthesis: Using qualitative comparative analysis and the Consolidated Framework for Implementation Research across diverse studies Laura J. Damschroder, Julie C. Lowery A6: Establishing a veterans engagement group to empower patients and inform Veterans Affairs (VA) health services research Sarah S. Ono, Kathleen F. Carlson, Erika K. Cottrell, Maya E. O’Neil, Travis L. Lovejoy A7: Building patient-practitioner partnerships in community oncology settings to implement behavioral interventions for anxious and depressed cancer survivors Joanna J. Arch, Jill L. Mitchell A8: Tailoring a Cognitive Behavioral Therapy implementation protocol using mixed methods, conjoint analysis, and implementation teams Cara C. Lewis, Brigid R. Marriott, Kelli Scott A9: Wraparound Structured Assessment and Review (WrapSTAR): An efficient, yet comprehensive approach to Wraparound implementation evaluation Jennifer Schurer Coldiron, Eric J. Bruns, Alyssa N. Hook A10: Improving the efficiency of standardized patient assessment of clinician fidelity: A comparison of automated actor-based and manual clinician-based ratings Benjamin C. Graham, Katelin Jordan A11: Measuring fidelity on the cheap Rochelle F. Hanson, Angela Moreland, Benjamin E. Saunders, Heidi S. Resnick A12: Leveraging routine clinical materials to assess fidelity to an evidence-based psychotherapy Shannon Wiltsey Stirman, Cassidy A. Gutner, Jennifer Gamarra, Dawne Vogt, Michael Suvak, Jennifer Schuster Wachen, Katherine Dondanville, Jeffrey S. Yarvis, Jim Mintz, Alan L. Peterson, Elisa V. Borah, Brett T. Litz, Alma Molino, Stacey Young McCaughanPatricia A. Resick A13: The video vignette survey: An efficient process for gathering diverse community opinions to inform an intervention Nancy Pandhi, Nora Jacobson, Neftali Serrano, Armando Hernandez, Elizabeth Zeidler- Schreiter, Natalie Wietfeldt, Zaher Karp A14: Using integrated administrative data to evaluate implementation of a behavioral health and trauma screening for children and youth in foster care Michael D. Pullmann, Barbara Lucenko, Bridget Pavelle, Jacqueline A. Uomoto, Andrea Negrete, Molly Cevasco, Suzanne E. U. Kerns A15: Intermediary organizations as a vehicle to promote efficiency and speed of implementation Robert P. Franks, Christopher Bory A16: Applying the Consolidated Framework for Implementation Research constructs directly to qualitative data: The power of implementation science in action Edward J. Miech, Teresa M. Damush A17: Efficient and effective scaling-up, screening, brief interventions, and referrals to treatment (SBIRT) training: a snowball implementation model Jason Satterfield, Derek Satre, Maria Wamsley, Patrick Yuan, Patricia O’Sullivan A18: Matching models of implementation to system needs and capacities: addressing the human factor Helen Best, Susan Velasquez A19: Agency characteristics that facilitate efficient and successful implementation efforts Miya Barnett, Lauren Brookman-Frazee, Jennifer Regan, Nicole Stadnick, Alison Hamilton, Anna Lau A20: Rapid assessment process: Application to the Prevention and Early Intervention transformation in Los Angeles County Jennifer Regan, Alison Hamilton, Nicole Stadnick, Miya Barnett, Anna Lau, Lauren Brookman-Frazee A21: The development of the Evidence-Based Practice-Concordant Care Assessment: An assessment tool to examine treatment strategies across practices Nicole Stadnick, Anna Lau, Miya Barnett, Jennifer Regan, Scott Roesch, Lauren Brookman-Frazee A22: Refining a compilation of discrete implementation strategies and determining their importance and feasibility Byron J. Powell, Thomas J. Waltz, Matthew J. Chinman, Laura Damschroder, Jeffrey L. Smith, Monica M. Matthieu, Enola K. Proctor, JoAnn E. Kirchner A23: Structuring complex recommendations: Methods and general findings Thomas J. Waltz, Byron J. Powell, Matthew J. Chinman, Laura J. Damschroder, Jeffrey L. Smith, Monica J. Matthieu, Enola K. Proctor, JoAnn E. Kirchner A24: Implementing prolonged exposure for post-traumatic stress disorder in the Department of Veterans Affairs: Expert recommendations from the Expert Recommendations for Implementing Change (ERIC) project Monica M. Matthieu, Craig S. Rosen, Thomas J. Waltz, Byron J. Powell, Matthew J. Chinman, Laura J. Damschroder, Jeffrey L. Smith, Enola K. Proctor, JoAnn E. Kirchner A25: When readiness is a luxury: Co-designing a risk assessment and quality assurance process with violence prevention frontline workers in Seattle, WA Sarah C. Walker, Asia S. Bishop, Mariko Lockhart A26: Implementation potential of structured recidivism risk assessments with justice- involved veterans: Qualitative perspectives from providers Allison L. Rodriguez, Luisa Manfredi, Andrea Nevedal, Joel Rosenthal, Daniel M. Blonigen A27: Developing empirically informed readiness measures for providers and agencies for the Family Check-Up using a mixed methods approach Anne M. Mauricio, Thomas D. Dishion, Jenna Rudo-Stern, Justin D. Smith A28: Pebbles, rocks, and boulders: The implementation of a school-based social engagement intervention for children with autism Jill Locke, Courtney Benjamin Wolk, Colleen Harker, Anne Olsen, Travis Shingledecker, Frances Barg, David Mandell, Rinad S. Beidas A29: Problem Solving Teletherapy (PST.Net): A stakeholder analysis examining the feasibility and acceptability of teletherapy in community based aging services Marissa C. Hansen, Maria P. Aranda, Isabel Torres-Vigil A30: A case of collaborative intervention design eventuating in behavior therapy sustainment and diffusion Bryan Hartzler A31: Implementation of suicide risk prevention in an integrated delivery system: Mental health specialty services Bradley Steinfeld, Tory Gildred, Zandrea Harlin, Fredric Shephard A32: Implementation team, checklist, evaluation, and feedback (ICED): A step-by-step approach to Dialectical Behavior Therapy program implementation Matthew S. Ditty, Andrea Doyle, John A. Bickel III, Katharine Cristaudo A33: The challenges in implementing muliple evidence-based practices in a community mental health setting Dan Fox, Sonia Combs A34: Using electronic health record technology to promote and support evidence-based practice assessment and treatment intervention David H. Lischner A35: Are existing frameworks adequate for measuring implementation outcomes? Results from a new simulation methodology Richard A. Van Dorn, Stephen J. Tueller, Jesse M. Hinde, Georgia T. Karuntzos A36: Taking global local: Evaluating training of Washington State clinicians in a modularized cogntive behavioral therapy approach designed for low-resource settings Maria Monroe-DeVita, Roselyn Peterson, Doyanne Darnell, Lucy Berliner, Shannon Dorsey, Laura K. Murray A37: Attitudes toward evidence-based practices across therapeutic orientations Yevgeny Botanov, Beverly Kikuta, Tianying Chen, Marivi Navarro-Haro, Anthony DuBose, Kathryn E. Korslund, Marsha M. Linehan A38: Predicting the use of an evidence-based intervention for autism in birth-to-three programs Colleen M. Harker, Elizabeth A. Karp, Sarah R. Edmunds, Lisa V. Ibañez, Wendy L. Stone A39: Supervision practices and improved fidelity across evidence-based practices: A literature review Mimi Choy-Brown A40: Beyond symptom tracking: clinician perceptions of a hybrid measurement feedback system for monitoring treatment fidelity and client progress Jack H. Andrews, Benjamin D. Johnides, Estee M. Hausman, Kristin M. Hawley A41: A guideline decision support tool: From creation to implementation Beth Prusaczyk, Alex Ramsey, Ana Baumann, Graham Colditz, Enola K. Proctor A42: Dabblers, bedazzlers, or total makeovers: Clinician modification of a common elements cognitive behavioral therapy approach Rosemary D. Meza, Shannon Dorsey, Shannon Wiltsey-Stirman, Georganna Sedlar, Leah Lucid A43: Characterization of context and its role in implementation: The impact of structure, infrastructure, and metastructure Caitlin Dorsey, Brigid Marriott, Nelson Zounlome, Cara Lewis A44: Effects of consultation method on implementation of cognitive processing therapy for post-traumatic stress disorder Cassidy A. Gutner, Candice M. Monson, Norman Shields, Marta Mastlej, Meredith SH Landy, Jeanine Lane, Shannon Wiltsey Stirman A45: Cross-validation of the Implementation Leadership Scale factor structure in child welfare service organizations Natalie K. Finn, Elisa M. Torres, Mark. G. Ehrhart, Gregory A. Aarons A46: Sustainability of integrated smoking cessation care in Veterans Affairs posttraumatic stress disorder clinics: A qualitative analysis of focus group data from learning collaborative participants Carol A. Malte, Aline Lott, Andrew J. Saxon A47: Key characteristics of effective mental health trainers: The creation of the Measure of Effective Attributes of Trainers (MEAT) Meredith Boyd, Kelli Scott, Cara C. Lewis A48: Coaching to improve teacher implementation of evidence-based practices (EBPs) Jennifer D. Pierce A49: Factors influencing the implementation of peer-led health promotion programs targeting seniors: A literature review Agathe Lorthios-Guilledroit, Lucie Richard, Johanne Filiatrault A50: Developing treatment fidelity rating systems for psychotherapy research: Recommendations and lessons learned Kevin Hallgren, Shirley Crotwell, Rosa Muñoz, Becky Gius, Benjamin Ladd, Barbara McCrady, Elizabeth Epstein A51: Rapid translation of alcohol prevention science John D. Clapp, Danielle E. Ruderman A52: Factors implicated in successful implementation: evidence to inform improved implementation from high and low-income countries Melanie Barwick, Raluca Barac, Stanley Zlotkin, Laila Salim, Marnie Davidson A53: Tracking implementation strategies prospectively: A practical approach Alicia C. Bunger, Byron J. Powell, Hillary A. Robertson A54: Trained but not implementing: the need for effective implementation planning tools Christopher Botsko A55: Evidence, context, and facilitation variables related to implementation of Dialectical Behavior Therapy: Qualitative results from a mixed methods inquiry in the Department of Veterans Affairs Sara J. Landes, Brandy N. Smith, Allison L. Rodriguez, Lindsay R. Trent, Monica M. Matthieu A56: Learning from implementation as usual in children’s mental health Byron J. Powell, Enola K. Proctor A57: Rates and predictors of implementation after Dialectical Behavior Therapy Intensive Training Melanie S. Harned, Marivi Navarro-Haro, Kathryn E. Korslund, Tianying Chen, Anthony DuBose, André Ivanoff, Marsha M. Linehan A58: Socio-contextual determinants of research evidence use in public-youth systems of care Antonio R. Garcia, Minseop Kim, Lawrence A. Palinkas, Lonnie Snowden, John Landsverk A59: Community resource mapping to integrate evidence-based depression treatment in primary care in Brazil: A pilot project Annika C. Sweetland, Maria Jose Fernandes, Edilson Santos, Cristiane Duarte, Afrânio Kritski, Noa Krawczyk, Caitlin Nelligan, Milton L. Wainberg A60: The use of concept mapping to efficiently identify determinants of implementation in the National Institute of Health--President’s Emergent Plan for AIDS Relief Prevention of Mother to Child HIV Transmission Implementation Science Alliance Gregory A. Aarons, David H. Sommerfeld, Benjamin Chi, Echezona Ezeanolue, Rachel Sturke, Lydia Kline, Laura Guay, George Siberry A61: Longitudinal remote consultation for implementing collaborative care for depression Ian M. Bennett, Rinad Beidas, Rachel Gold, Johnny Mao, Diane Powers, Mindy Vredevoogd, Jurgen Unutzer A62: Integrating a peer coach model to support program implementation and ensure long- term sustainability of the Incredible Years in community-based settings Jennifer Schroeder, Lane Volpe, Julie Steffen A63: Efficient sustainability: Existing community based supervisors as evidence-based treatment supports Shannon Dorsey, Michael D Pullmann, Suzanne E. U. Kerns, Nathaniel Jungbluth, Lucy Berliner, Kelly Thompson, Eliza Segell A64: Establishment of a national practice-based implementation network to accelerate adoption of evidence-based and best practices Pearl McGee-Vincent, Nancy Liu, Robyn Walser, Jennifer Runnals, R. Keith Shaw, Sara J. Landes, Craig Rosen, Janet Schmidt, Patrick Calhoun A65: Facilitation as a mechanism of implementation in a practice-based implementation network: Improving care in a Department of Veterans Affairs post-traumatic stress disorder outpatient clinic Ruth L. Varkovitzky, Sara J. Landes A66: The ACT SMART Toolkit: An implementation strategy for community-based organizations providing services to children with autism spectrum disorder Amy Drahota, Jonathan I. Martinez, Brigitte Brikho, Rosemary Meza, Aubyn C. Stahmer, Gregory A. Aarons A67: Supporting Policy In Health with Research: An intervention trial (SPIRIT) - protocol and early findings Anna Williamson A68: From evidence based practice initiatives to infrastructure: Lessons learned from a public behavioral health system’s efforts to promote evidence based practices Ronnie M. Rubin, Byron J. Powell, Matthew O. Hurford, Shawna L. Weaver, Rinad S. Beidas, David S. Mandell, Arthur C. Evans A69: Applying the policy ecology model to Philadelphia’s behavioral health transformation efforts Byron J. Powell, Rinad S. Beidas, Ronnie M. Rubin, Rebecca E. Stewart, Courtney Benjamin Wolk, Samantha L. Matlin, Shawna Weaver, Matthew O. Hurford, Arthur C. Evans, Trevor R. Hadley, David S. Mandell A70: A model for providing methodological expertise to advance dissemination and implementation of health discoveries in Clinical and Translational Science Award institutions Donald R. Gerke, Beth Prusaczyk, Ana Baumann, Ericka M. Lewis, Enola K. Proctor A71: Establishing a research agenda for the Triple P Implementation Framework Jenna McWilliam, Jacquie Brown, Michelle Tucker A72: Cheap and fast, but what is “best?”: Examining implementation outcomes across sites in a state-wide scaled-up evidence-based walking program, Walk With Ease Kathleen P Conte A73: Measurement feedback systems in mental health: Initial review of capabilities and characteristics Aaron R. Lyon, Meredith Boyd, Abigail Melvin, Cara C. Lewis, Freda Liu, Nathaniel Jungbluth A74: A qualitative investigation of case managers’ attitudes toward implementation of a measurement feedback system in a public mental health system for youth Amelia Kotte, Kaitlin A. Hill, Albert C. Mah, Priya A. Korathu-Larson, Janelle R. Au, Sonia Izmirian, Scott Keir, Brad J. Nakamura, Charmaine K. Higa-McMillan A75: Multiple pathways to sustainability: Using Qualitative Comparative Analysis to uncover the necessary and sufficient conditions for successful community-based implementation Brittany Rhoades Cooper, Angie Funaiole, Eleanor Dizon A76: Prescribers’ perspectives on opioids and benzodiazepines and medication alerts to reduce co-prescribing of these medications Eric J. Hawkins, Carol A. Malte, Hildi J. Hagedorn, Douglas Berger, Anissa Frank, Aline Lott, Carol E. Achtmeyer, Anthony J. Mariano, Andrew J. Saxon A77: Adaptation of Coordinated Anxiety Learning and Management for comorbid anxiety and substance use disorders: Delivery of evidence-based treatment for anxiety in addictions treatment centers Kate Wolitzky-Taylor, Richard Rawson, Richard Ries, Peter Roy-Byrne, Michelle Craske A78: Opportunities and challenges of measuring program implementation with online surveys Dena Simmons, Catalina Torrente, Lori Nathanson, Grace Carroll A79: Observational assessment of fidelity to a family-centered prevention program: Effectiveness and efficiency Justin D. Smith, Kimbree Brown, Karina Ramos, Nicole Thornton, Thomas J. Dishion, Elizabeth A. Stormshak, Daniel S. Shaw, Melvin N. Wilson A80: Strategies and challenges in housing first fidelity: A multistate qualitative analysis Mimi Choy-Brown, Emmy Tiderington, Bikki Tran Smith, Deborah K. Padgett A81: Procurement and contracting as an implementation strategy: Getting To Outcomes® contracting Ronnie M. Rubin, Marilyn L. Ray, Abraham Wandersman, Andrea Lamont, Gordon Hannah, Kassandra A. Alia, Matthew O. Hurford, Arthur C. Evans A82: Web-based feedback to aid successful implementation: The interactive Stages of Implementation Completion (SIC)[TM] tool Lisa Saldana, Holle Schaper, Mark Campbell, Patricia Chamberlain A83: Efficient methodologies for monitoring fidelity in routine implementation: Lessons from the Allentown Social Emotional Learning Initiative Valerie B. Shapiro, B.K. Elizabeth Kim, Jennifer L. Fleming, Paul A. LeBuffe A84: The Society for Implementation Research Collaboration (SIRC) implementation development workshop: Results from a new methodology for enhancing implementation science proposals Sara J. Landes, Cara C. Lewis, Allison L. Rodriguez, Brigid R. Marriott, Katherine Anne Comtois A85: An update on the Society for Implementation Research Collaboration (SIRC) Instrument Review Project}, } @article {pmid27357258, year = {2016}, author = {MacMillan, HA and Knee, JM and Dennis, AB and Udaka, H and Marshall, KE and Merritt, TJ and Sinclair, BJ}, title = {Cold acclimation wholly reorganizes the Drosophila melanogaster transcriptome and metabolome.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {28999}, pmid = {27357258}, issn = {2045-2322}, mesh = {Acclimatization/genetics/*physiology ; Animals ; *Cold Temperature ; Drosophila melanogaster/genetics/metabolism/*physiology ; Gene Expression Regulation ; Gene Ontology ; Genes, Insect ; High-Throughput Nucleotide Sequencing ; Insect Proteins/genetics/physiology ; Metabolic Networks and Pathways/genetics ; *Metabolome ; Models, Biological ; RNA, Messenger/biosynthesis ; Thermotolerance/genetics ; *Transcriptome ; }, abstract = {Cold tolerance is a key determinant of insect distribution and abundance, and thermal acclimation can strongly influence organismal stress tolerance phenotypes, particularly in small ectotherms like Drosophila. However, there is limited understanding of the molecular and biochemical mechanisms that confer such impressive plasticity. Here, we use high-throughput mRNA sequencing (RNA-seq) and liquid chromatography - mass spectrometry (LC-MS) to compare the transcriptomes and metabolomes of D. melanogaster acclimated as adults to warm (rearing) (21.5 °C) or cold conditions (6 °C). Cold acclimation improved cold tolerance and led to extensive biological reorganization: almost one third of the transcriptome and nearly half of the metabolome were differentially regulated. There was overlap in the metabolic pathways identified via transcriptomics and metabolomics, with proline and glutathione metabolism being the most strongly-supported metabolic pathways associated with increased cold tolerance. We discuss several new targets in the study of insect cold tolerance (e.g. dopamine signaling and Na(+)-driven transport), but many previously identified candidate genes and pathways (e.g. heat shock proteins, Ca(2+) signaling, and ROS detoxification) were also identified in the present study, and our results are thus consistent with and extend the current understanding of the mechanisms of insect chilling tolerance.}, } @article {pmid27355758, year = {2017}, author = {Müller, N and de Zwart, D and Hauschild, M and Kijko, G and Fantke, P}, title = {Exploring REACH as a potential data source for characterizing ecotoxicity in life cycle assessment.}, journal = {Environmental toxicology and chemistry}, volume = {36}, number = {2}, pages = {492-500}, doi = {10.1002/etc.3542}, pmid = {27355758}, issn = {1552-8618}, mesh = {Aquatic Organisms/drug effects ; Ecotoxicology/*methods ; Europe ; Information Storage and Retrieval ; Lethal Dose 50 ; Life Cycle Stages/*drug effects ; *Models, Theoretical ; Risk Assessment ; Water Pollutants, Chemical/chemistry/*toxicity ; }, abstract = {Toxicity models in life cycle impact assessment (LCIA) currently only characterize a small fraction of marketed substances, mostly because of limitations in the underlying ecotoxicity data. One approach to improve the current data situation in LCIA is to identify new data sources, such as the European Registration, Evaluation, Authorisation, and Restriction of Chemicals (REACH) database. The present study explored REACH as a potential data source for LCIA based on matching reported ecotoxicity data for substances that are currently also included in the United Nations Environment Programme/Society for Environmental Toxicology and Chemistry (UNEP/SETAC) scientific consensus model USEtox for characterizing toxicity impacts. Data are evaluated with respect to number of data points, reported reliability, and test duration, and are compared with data listed in USEtox at the level of hazardous concentration for 50% of the covered species per substance. The results emphasize differences between data available via REACH and in USEtox. The comparison of ecotoxicity data from REACH and USEtox shows potential for using REACH ecotoxicity data in LCIA toxicity characterization, but also highlights issues related to compliance of submitted data with REACH requirements as well as different assumptions underlying regulatory risk assessment under REACH versus data needed for LCIA. Thus, further research is required to address data quality, pre-processing, and applicability, before considering data submitted under REACH as a data source for use in LCIA, and also to explore additionally available data sources, published studies, and reports. Environ Toxicol Chem 2017;36:492-500. © 2016 SETAC.}, } @article {pmid27350093, year = {2016}, author = {Barrett, M and Fitzhenry, K and O'Flaherty, V and Dore, W and Keaveney, S and Cormican, M and Rowan, N and Clifford, E}, title = {Detection, fate and inactivation of pathogenic norovirus employing settlement and UV treatment in wastewater treatment facilities.}, journal = {The Science of the total environment}, volume = {568}, number = {}, pages = {1026-1036}, doi = {10.1016/j.scitotenv.2016.06.067}, pmid = {27350093}, issn = {1879-1026}, mesh = {Bacteriophages/physiology ; Disinfection/*methods ; Norovirus/isolation & purification/*physiology ; *Ultraviolet Rays ; Virus Inactivation ; Waste Disposal, Fluid/*methods ; Wastewater/*virology ; *Water Microbiology ; }, abstract = {It is accepted that discharged wastewaters can be a significant source of pathogenic viruses in receiving water bodies contributing to pollution and may in turn enter the human food chain and pose a risk to human health, thus norovirus (NoV) is often a predominant cause of gastroenteritis globally. Working with NoV poses particular challenges as it cannot be readily identified and detection by molecular methods does not assess infectivity. It has been proposed that the infectivity of NoV may be modelled through the use of an alternative virus; F-specific RNA (FRNA) bacteriophages; GA genotype and other FRNA bacteriophages have been used as a surrogate in studies of NoV inactivation. This study investigated the efficiency of novel pulsed ultraviolet irradiation and low pressure ultraviolet irradiation as a potential pathogen inactivation system for NoV and FRNA bacteriophage (GA) in secondary treated wastewaters. The role of UV dose and the impact of suspended solids concentration on removal efficiency were also examined. The study also investigated the role of settlement processes in wastewater treatment plants in removing NoV. While NoV inactivation could not be determined it was found that at a maximum UV dose of 6.9J/cm(2) (6900mJ/cm(2)) an average 2.4 log removal of FRNA bacteriophage (GA) was observed; indicating the potential need for high UV doses to remove NoV if FRNA bacteriophage prove a suitable indicator for NoV. The study found that increasing concentrations of suspended solids impacted on PUV efficiency however, it appears the extent of the impact may be site specific. Furthermore, the study found that settlement processes can play a significant role in the removal of FRNA bacteriophage, thus potentially NoV.}, } @article {pmid27349087, year = {2016}, author = {Deacy, W and Leacock, W and Armstrong, JB and Stanford, JA}, title = {Kodiak brown bears surf the salmon red wave: direct evidence from GPS collared individuals.}, journal = {Ecology}, volume = {97}, number = {5}, pages = {1091-1098}, doi = {10.1890/15-1060.1}, pmid = {27349087}, issn = {0012-9658}, mesh = {Alaska ; Animal Identification Systems/*instrumentation ; Animal Migration/*physiology ; Animals ; Feeding Behavior/*physiology ; Geographic Information Systems ; Salmon/*physiology ; Time Factors ; Ursidae/*physiology ; }, abstract = {A key constraint faced by consumers is achieving a positive energy balance in the face of temporal variation in foraging opportunities. Recent work has shown that spatial heterogeneity in resource phenology can buffer mobile consumers from this constraint by allowing them to track changes in resource availability across space. For example, salmon populations spawn asynchronously across watersheds, causing high-quality foraging opportunities to propagate across the landscape, prolonging the availability of salmon at the regional scale. However, we know little about how individual consumers integrate across phenological variation or the benefits they receive by doing so. Here, we present direct evidence that individual brown bears track spatial variation in salmon phenology. Data from 40 GPS collared brown bears show that bears visited multiple spawning sites in synchrony with the order of spawning phenology. The number of sites used was correlated with the number of days a bear exploited salmon, suggesting the phenological variation in the study area influenced bear access to salmon, a resource which strongly influences bear fitness. Fisheries managers attempting to maximize harvest while maintaining ecosystem function should strive to protect the population diversity that underlies the phenological variation used by wildlife consumers.}, } @article {pmid27341199, year = {2016}, author = {Leimar, O and Dall, SR and Hammerstein, P and McNamara, JM}, title = {Genes as Cues of Relatedness and Social Evolution in Heterogeneous Environments.}, journal = {PLoS computational biology}, volume = {12}, number = {6}, pages = {e1005006}, pmid = {27341199}, issn = {1553-7358}, mesh = {*Biological Evolution ; Computational Biology ; *Cues ; Ecosystem ; Genetic Linkage/*genetics ; *Models, Genetic ; Polymorphism, Genetic/*genetics ; *Social Behavior ; }, abstract = {There are many situations where relatives interact while at the same time there is genetic polymorphism in traits influencing survival and reproduction. Examples include cheater-cooperator polymorphism and polymorphic microbial pathogens. Environmental heterogeneity, favoring different traits in nearby habitats, with dispersal between them, is one general reason to expect polymorphism. Currently, there is no formal framework of social evolution that encompasses genetic polymorphism. We develop such a framework, thus integrating theories of social evolution into the evolutionary ecology of heterogeneous environments. We allow for adaptively maintained genetic polymorphism by applying the concept of genetic cues. We analyze a model of social evolution in a two-habitat situation with limited dispersal between habitats, in which the average relatedness at the time of helping and other benefits of helping can differ between habitats. An important result from the analysis is that alleles at a polymorphic locus play the role of genetic cues, in the sense that the presence of a cue allele contains statistical information for an organism about its current environment, including information about relatedness. We show that epistatic modifiers of the cue polymorphism can evolve to make optimal use of the information in the genetic cue, in analogy with a Bayesian decision maker. Another important result is that the genetic linkage between a cue locus and modifier loci influences the evolutionary interest of modifiers, with tighter linkage leading to greater divergence between social traits induced by different cue alleles, and this can be understood in terms of genetic conflict.}, } @article {pmid27340043, year = {2016}, author = {Jovic, D and Marinkovic, J and Vukovic, D}, title = {Association between body mass index and prevalence of multimorbidity: a cross-sectional study.}, journal = {Public health}, volume = {139}, number = {}, pages = {103-111}, doi = {10.1016/j.puhe.2016.05.014}, pmid = {27340043}, issn = {1476-5616}, mesh = {Adult ; Aged ; *Body Mass Index ; Chronic Disease ; Comorbidity ; Cross-Sectional Studies ; Female ; Health Surveys ; Humans ; Male ; Middle Aged ; Obesity/*epidemiology ; Overweight/*epidemiology ; Prevalence ; Serbia/epidemiology ; Sex Distribution ; Young Adult ; }, abstract = {OBJECTIVES: To explore the prevalence of multimorbidity in Serbia according to sex and body mass index (BMI) categories, and to examine the association between BMI and multimorbidity. In addition, this study examined the relationships between the main demographic and socio-economic characteristics of the population (age, settlement, education) and multimorbidity.

STUDY DESIGN: Secondary analysis of data from the 2013 Serbian National Health Survey.

METHODS: This study analyzed data from 13,103 participants aged ≥20 years with BMI data. The associations between BMI, age, education and multimorbidity were analyzed by multivariate logistic regression.

RESULTS: The overall prevalence of multimorbidity was higher than the overall prevalence of a single disease (26.9% vs 20.7%). The proportion of participants who reported two or more chronic diseases increased with each BMI category in both sexes, reaching the highest values in obese category III. Odds ratios (ORs) for the prevalence in all morbidity groups increased gradually with BMI category, and the highest OR values were found in obese category III. Males of obese category III were seven times more likely to have multimorbidity [OR 7.2, 95% confidence interval (CI) 4.2-12.6] than males of normal weight, whereas females of obese category III were nine and a half times more likely to have multimorbidity (OR 9.5, 95% CI 4.0-22.4) than females of normal weight. In the multivariable analysis, age (both sexes), low and middle level of education (males), and rural settlement and low level of education (females) were found to be predictors of multimorbidity.

CONCLUSIONS: This study found positive associations between obesity and multimorbidity and between overweight and multimorbidity. Recognizing these associations is of great importance from both clinical and public health perspectives because this could lead to an integrated approach for patients.}, } @article {pmid27338147, year = {2016}, author = {Auffray, C and Balling, R and Barroso, I and Bencze, L and Benson, M and Bergeron, J and Bernal-Delgado, E and Blomberg, N and Bock, C and Conesa, A and Del Signore, S and Delogne, C and Devilee, P and Di Meglio, A and Eijkemans, M and Flicek, P and Graf, N and Grimm, V and Guchelaar, HJ and Guo, YK and Gut, IG and Hanbury, A and Hanif, S and Hilgers, RD and Honrado, Á and Hose, DR and Houwing-Duistermaat, J and Hubbard, T and Janacek, SH and Karanikas, H and Kievits, T and Kohler, M and Kremer, A and Lanfear, J and Lengauer, T and Maes, E and Meert, T and Müller, W and Nickel, D and Oledzki, P and Pedersen, B and Petkovic, M and Pliakos, K and Rattray, M and I Màs, JR and Schneider, R and Sengstag, T and Serra-Picamal, X and Spek, W and Vaas, LA and van Batenburg, O and Vandelaer, M and Varnai, P and Villoslada, P and Vizcaíno, JA and Wubbe, JP and Zanetti, G}, title = {Making sense of big data in health research: Towards an EU action plan.}, journal = {Genome medicine}, volume = {8}, number = {1}, pages = {71}, pmid = {27338147}, issn = {1756-994X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Biomedical Research/*legislation & jurisprudence/standards ; Databases, Factual/legislation & jurisprudence/*standards ; European Union/*organization & administration ; Health Plan Implementation ; Humans ; Information Dissemination/legislation & jurisprudence ; }, abstract = {Medicine and healthcare are undergoing profound changes. Whole-genome sequencing and high-resolution imaging technologies are key drivers of this rapid and crucial transformation. Technological innovation combined with automation and miniaturization has triggered an explosion in data production that will soon reach exabyte proportions. How are we going to deal with this exponential increase in data production? The potential of "big data" for improving health is enormous but, at the same time, we face a wide range of challenges to overcome urgently. Europe is very proud of its cultural diversity; however, exploitation of the data made available through advances in genomic medicine, imaging, and a wide range of mobile health applications or connected devices is hampered by numerous historical, technical, legal, and political barriers. European health systems and databases are diverse and fragmented. There is a lack of harmonization of data formats, processing, analysis, and data transfer, which leads to incompatibilities and lost opportunities. Legal frameworks for data sharing are evolving. Clinicians, researchers, and citizens need improved methods, tools, and training to generate, analyze, and query data effectively. Addressing these barriers will contribute to creating the European Single Market for health, which will improve health and healthcare for all Europeans.}, } @article {pmid27336738, year = {2016}, author = {Izquierdo, EJ and Beer, RD}, title = {The whole worm: brain-body-environment models of C. elegans.}, journal = {Current opinion in neurobiology}, volume = {40}, number = {}, pages = {23-30}, doi = {10.1016/j.conb.2016.06.005}, pmid = {27336738}, issn = {1873-6882}, mesh = {Animals ; Behavior, Animal/physiology ; Brain/physiology ; Caenorhabditis elegans/*physiology ; Humans ; Models, Animal ; *Models, Neurological ; Optogenetics ; }, abstract = {Brain, body and environment are in continuous dynamical interaction, and it is becoming increasingly clear that an animal's behavior must be understood as a product not only of its nervous system, but also of the ongoing feedback of this neural activity through the biomechanics of its body and the ecology of its environment. Modeling has an essential integrative role to play in such an understanding. But successful whole-animal modeling requires an animal for which detailed behavioral, biomechanical and neural information is available and a modeling methodology which can gracefully cope with the constantly changing balance of known and unknown biological constraints. Here we review recent progress on both optogenetic techniques for imaging and manipulating neural activity and neuromechanical modeling in the nematode worm Caenorhabditis elegans. This work demonstrates both the feasibility and challenges of whole-animal modeling.}, } @article {pmid27336696, year = {2016}, author = {Wang, J and Xue, DX and Zhang, BD and Li, YL and Liu, BJ and Liu, JX}, title = {Genome-Wide SNP Discovery, Genotyping and Their Preliminary Applications for Population Genetic Inference in Spotted Sea Bass (Lateolabrax maculatus).}, journal = {PloS one}, volume = {11}, number = {6}, pages = {e0157809}, pmid = {27336696}, issn = {1932-6203}, mesh = {Animals ; Bass/*genetics ; Cluster Analysis ; Computational Biology/methods ; Gene Ontology ; *Genetic Variation ; *Genetics, Population ; *Genome-Wide Association Study ; *Genotype ; Molecular Sequence Annotation ; *Polymorphism, Single Nucleotide ; }, abstract = {Next-generation sequencing and the collection of genome-wide single-nucleotide polymorphisms (SNPs) allow identifying fine-scale population genetic structure and genomic regions under selection. The spotted sea bass (Lateolabrax maculatus) is a non-model species of ecological and commercial importance and widely distributed in northwestern Pacific. A total of 22 648 SNPs was discovered across the genome of L. maculatus by paired-end sequencing of restriction-site associated DNA (RAD-PE) for 30 individuals from two populations. The nucleotide diversity (π) for each population was 0.0028±0.0001 in Dandong and 0.0018±0.0001 in Beihai, respectively. Shallow but significant genetic differentiation was detected between the two populations analyzed by using both the whole data set (FST = 0.0550, P < 0.001) and the putatively neutral SNPs (FST = 0.0347, P < 0.001). However, the two populations were highly differentiated based on the putatively adaptive SNPs (FST = 0.6929, P < 0.001). Moreover, a total of 356 SNPs representing 298 unique loci were detected as outliers putatively under divergent selection by FST-based outlier tests as implemented in BAYESCAN and LOSITAN. Functional annotation of the contigs containing putatively adaptive SNPs yielded hits for 22 of 55 (40%) significant BLASTX matches. Candidate genes for local selection constituted a wide array of functions, including binding, catalytic and metabolic activities, etc. The analyses with the SNPs developed in the present study highlighted the importance of genome-wide genetic variation for inference of population structure and local adaptation in L. maculatus.}, } @article {pmid27336619, year = {2016}, author = {Den Uyl, PA and Richardson, LL and Jain, S and Dick, GJ}, title = {Unraveling the Physiological Roles of the Cyanobacterium Geitlerinema sp. BBD and Other Black Band Disease Community Members through Genomic Analysis of a Mixed Culture.}, journal = {PloS one}, volume = {11}, number = {6}, pages = {e0157953}, pmid = {27336619}, issn = {1932-6203}, mesh = {Animal Diseases/*microbiology ; Animals ; Anthozoa/*microbiology ; Computational Biology ; Cyanobacteria/classification/*genetics/metabolism ; Energy Metabolism ; Fermentation ; *Genome, Bacterial ; *Genomics/methods ; Heterotrophic Processes ; High-Throughput Nucleotide Sequencing ; Inactivation, Metabolic/genetics ; Molecular Sequence Annotation ; Operon ; Photosynthesis ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sulfides/metabolism ; }, abstract = {Black band disease (BBD) is a cyanobacterial-dominated polymicrobial mat that propagates on and migrates across coral surfaces, necrotizing coral tissue. Culture-based laboratory studies have investigated cyanobacteria and heterotrophic bacteria isolated from BBD, but the metabolic potential of various BBD microbial community members and interactions between them remain poorly understood. Here we report genomic insights into the physiological and metabolic potential of the BBD-associated cyanobacterium Geitlerinema sp. BBD 1991 and six associated bacteria that were also present in the non-axenic culture. The essentially complete genome of Geitlerinema sp. BBD 1991 contains a sulfide quinone oxidoreductase gene for oxidation of sulfide, suggesting a mechanism for tolerating the sulfidic conditions of BBD mats. Although the operon for biosynthesis of the cyanotoxin microcystin was surprisingly absent, potential relics were identified. Genomic evidence for mixed-acid fermentation indicates a strategy for energy metabolism under the anaerobic conditions present in BBD during darkness. Fermentation products may supply carbon to BBD heterotrophic bacteria. Among the six associated bacteria in the culture, two are closely related to organisms found in culture-independent studies of diseased corals. Their metabolic pathways for carbon and sulfur cycling, energy metabolism, and mechanisms for resisting coral defenses suggest adaptations to the coral surface environment and biogeochemical roles within the BBD mat. Polysulfide reductases were identified in a Flammeovirgaceae genome (Bacteroidetes) and the sox pathway for sulfur oxidation was found in the genome of a Rhodospirillales bacterium (Alphaproteobacteria), revealing mechanisms for sulfur cycling, which influences virulence of BBD. Each genomic bin possessed a pathway for conserving energy from glycerol degradation, reflecting adaptations to the glycerol-rich coral environment. The presence of genes for detoxification of reactive oxygen species and resistance to antibiotics suggest mechanisms for combating coral defense strategies. This study builds upon previous research on BBD and provides new insights into BBD disease etiology.}, } @article {pmid27336462, year = {2016}, author = {Clare, EL and Chain, FJ and Littlefair, JE and Cristescu, ME}, title = {The effects of parameter choice on defining molecular operational taxonomic units and resulting ecological analyses of metabarcoding data.}, journal = {Genome}, volume = {59}, number = {11}, pages = {981-990}, doi = {10.1139/gen-2015-0184}, pmid = {27336462}, issn = {1480-3321}, mesh = {*Biodiversity ; Computational Biology/methods ; *DNA Barcoding, Taxonomic/methods ; Ecology ; *Ecosystem ; Electron Transport Complex IV/genetics ; High-Throughput Nucleotide Sequencing ; }, abstract = {The combination of DNA barcoding and high-throughput (next-generation) sequencing (metabarcoding) provides many promises but also serious challenges. Generating a reliable comparable estimate of biodiversity remains a central challenge to the application of the technology. Many approaches have been used to turn millions of sequences into distinct taxonomic units. However, the extent to which these methods impact the outcome of simple ecological analyses is not well understood. Here we performed a simple analysis of dietary overlap by skinks and shrews on Ile Aux Aigrettes, Mauritius. We used a combination of filtering thresholds and clustering algorithms on a COI metabarcoding dataset and demonstrate that all bioinformatics parameters will have interacting effects on molecular operational taxonomic unit (MOTU) recovery rates. These effects generated estimates covering two orders of magnitude. However, the effect on a simple ecological analysis was not large and, despite the wide variation in estimates of niche overlap, the same ecological conclusion was drawn in most cases. We advise that a conservative clustering programme coupled with larger sequence divergences to define a cluster, the removal of singletons, rigorous length filtering, and stringent match criteria for Molecular Identifier tags are preferable to avoid MOTU inflation and that the same parameters be used in all comparative analyses.}, } @article {pmid27334820, year = {2016}, author = {Amarante, CF and Tassinari, Wde S and Luque, JL and Pereira, MJ}, title = {Parasite abundance and its determinants in fishes from Brazil: an eco-epidemiological approach.}, journal = {Revista brasileira de parasitologia veterinaria = Brazilian journal of veterinary parasitology : Orgao Oficial do Colegio Brasileiro de Parasitologia Veterinaria}, volume = {25}, number = {2}, pages = {196-201}, doi = {10.1590/S1984-29612016033}, pmid = {27334820}, issn = {1984-2961}, mesh = {Animals ; Brazil ; Databases, Factual ; Ecosystem ; Female ; Fishes/*parasitology ; Parasites/*isolation & purification ; }, abstract = {The variability in parasite abundance has an ecological basis; however, from an epidemiological point of view, the contribution of factors inherent to the host to the variability in parasite abundance remains an open question. A database consisting of 3,746 specimens of 73 fish species was used to verify the relation between the distribution of parasite abundance in fishes and a set of biotic factors inherent to the hosts. Classical and mixed Poisson regression models were constructed. Prevalence ratios (PR) and their respective 95% confidence intervals were estimated. The parasite abundance was significantly higher in female hosts, nonschooling species, species from benthopelagic and pelagic habitats, and fishes with greater body length. Overall, these results suggest that the variability in the abundance of infection is an attribute of the parasite species. Although the results are biologically plausible, important gaps may still exist and should be explored to better understand the variations in parasite abundance, which has great relevance in epidemiological studies. We reinforce the importance of choosing the statistical model most appropriate for the nature of the data to avoid spurious results, especially when the autocorrelation in the data is not taken into account.}, } @article {pmid27332714, year = {2016}, author = {Pylro, VS and Oliveira, FS and Morais, DK and Cuadros-Orellana, S and Pais, FS and Medeiros, JD and Geraldo, JA and Gilbert, J and Volpini, AC and Fernandes, GR}, title = {ZIKV - CDB: A Collaborative Database to Guide Research Linking SncRNAs and ZIKA Virus Disease Symptoms.}, journal = {PLoS neglected tropical diseases}, volume = {10}, number = {6}, pages = {e0004817}, pmid = {27332714}, issn = {1935-2735}, mesh = {*Databases, Factual ; *Genome, Viral ; Humans ; MicroRNAs/*genetics ; Phylogeny ; RNA, Viral/*genetics ; Zika Virus/*genetics ; Zika Virus Infection/pathology/*virology ; }, abstract = {BACKGROUND: In early 2015, a ZIKA Virus (ZIKV) infection outbreak was recognized in northeast Brazil, where concerns over its possible links with infant microcephaly have been discussed. Providing a causal link between ZIKV infection and birth defects is still a challenge. MicroRNAs (miRNAs) are small noncoding RNAs (sncRNAs) that regulate post-transcriptional gene expression by translational repression, and play important roles in viral pathogenesis and brain development. The potential for flavivirus-mediated miRNA signalling dysfunction in brain-tissue development provides a compelling hypothesis to test the perceived link between ZIKV and microcephaly.

Here, we applied in silico analyses to provide novel insights to understand how Congenital ZIKA Syndrome symptoms may be related to an imbalance in miRNAs function. Moreover, following World Health Organization (WHO) recommendations, we have assembled a database to help target investigations of the possible relationship between ZIKV symptoms and miRNA-mediated human gene expression.

CONCLUSIONS/SIGNIFICANCE: We have computationally predicted both miRNAs encoded by ZIKV able to target genes in the human genome and cellular (human) miRNAs capable of interacting with ZIKV genomes. Our results represent a step forward in the ZIKV studies, providing new insights to support research in this field and identify potential targets for therapy.}, } @article {pmid27332491, year = {2016}, author = {Lee, JH and Park, HA and Song, TM}, title = {Development and Evaluation of a Low Fertility Ontology for Analyzing Social Data in Korea.}, journal = {Studies in health technology and informatics}, volume = {225}, number = {}, pages = {1076-1077}, pmid = {27332491}, issn = {1879-8365}, mesh = {Data Mining/methods ; *Fertility ; Humans ; Republic of Korea ; Social Media/statistics & numerical data ; *Terminology as Topic ; *Vocabulary, Controlled ; }, abstract = {The purpose of this study is to develop a low fertility ontology for collecting and analyzing social data. A low fertility ontology was developed according to Ontology Development 101 and formally represented using Protégé. The content coverage of the ontology was evaluated using 1,387 narratives posted by the public and 63 narratives posted by public servants. Six super-classes of the ontology were developed based on Bronfenbrenner's ecological system theory with an individual in the center and environmental systems impacting their as surroundings. In total, 568 unique concepts were extracted from the narratives. Out of these concepts, 424(74.6%) concepts were lexically or semantically mapped, 67(11.8%) were either broadly or narrowly mapped to the ontology concepts. Remaining 77(13.6%) concepts were not mapped to any of the ontology concepts. This ontology can be used as a framework to understand low fertility problems using social data in Korea.}, } @article {pmid27329779, year = {2017}, author = {Pan, J and Del Campo, J and Keeling, PJ}, title = {Reference Tree and Environmental Sequence Diversity of Labyrinthulomycetes.}, journal = {The Journal of eukaryotic microbiology}, volume = {64}, number = {1}, pages = {88-96}, doi = {10.1111/jeu.12342}, pmid = {27329779}, issn = {1550-7408}, mesh = {Base Sequence ; Biodiversity ; DNA, Ribosomal/genetics ; Databases, Nucleic Acid ; Environment ; High-Throughput Nucleotide Sequencing/methods ; Oceans and Seas ; Phylogeny ; RNA, Ribosomal, 18S/genetics ; Sequence Analysis, DNA ; Stramenopiles/*classification/genetics/isolation & purification ; }, abstract = {Labyrinthulomycetes are heterotrophic stramenopiles that are ubiquitous in a wide range of both marine and freshwater habitats and play important roles in decomposition of organic matter. The diversity and taxonomy of Labyrinthulomycetes has been studied for many years, but we nevertheless lack both a comprehensive reference database and up-to-date phylogeny including all known diversity, which hinders many global insights into their ecological distribution and the relative importance of various subgroups in different environments. Here, we present a curated reference database and a phylogenetic tree of Labyrinthulomycetes small subunit ribosomal RNA (SSU or 18S rRNA) data. Based on this created reference database, we analyzed high-throughput environmental sequencing data, revealing many previously unknown environmental clades and exploring the ecological distribution of various subgroups. Particularly, a number of newly identified environmental clades that are widespread in the open ocean. Comparing the manually curated reference database to existing tools for identification of environmental sequences (e.g. PR2 or SILVA databases) suggests that the curated database provides a higher degree of specificity and a lower frequency of misidentification. The phylogenetic framework and database will be a useful tool for future ecological and evolutionary studies.}, } @article {pmid27329207, year = {2016}, author = {Tangherlini, M and Dell'Anno, A and Zeigler Allen, L and Riccioni, G and Corinaldesi, C}, title = {Assessing viral taxonomic composition in benthic marine ecosystems: reliability and efficiency of different bioinformatic tools for viral metagenomic analyses.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {28428}, pmid = {27329207}, issn = {2045-2322}, mesh = {Computational Biology/*methods ; Databases, Nucleic Acid ; Ecosystem ; Metagenomics/*methods ; Oceans and Seas ; Phylogeny ; Viruses/*classification/genetics ; Water Microbiology ; }, abstract = {In benthic deep-sea ecosystems, which represent the largest biome on Earth, viruses have a recognised key ecological role, but their diversity is still largely unknown. Identifying the taxonomic composition of viruses is crucial for understanding virus-host interactions, their role in food web functioning and evolutionary processes. Here, we compared the performance of various bioinformatic tools (BLAST, MG-RAST, NBC, VMGAP, MetaVir, VIROME) for analysing the viral taxonomic composition in simulated viromes and viral metagenomes from different benthic deep-sea ecosystems. The analyses of simulated viromes indicate that all the BLAST tools, followed by MetaVir and VMGAP, are more reliable in the affiliation of viral sequences and strains. When analysing the environmental viromes, tBLASTx, MetaVir, VMGAP and VIROME showed a similar efficiency of sequence annotation; however, MetaVir and tBLASTx identified a higher number of viral strains. These latter tools also identified a wider range of viral families than the others, providing a wider view of viral taxonomic diversity in benthic deep-sea ecosystems. Our findings highlight strengths and weaknesses of available bioinformatic tools for investigating the taxonomic diversity of viruses in benthic ecosystems in order to improve our comprehension of viral diversity in the oceans and its relationships with host diversity and ecosystem functioning.}, } @article {pmid27328409, year = {2016}, author = {Davies, CH and Coughlan, A and Hallegraeff, G and Ajani, P and Armbrecht, L and Atkins, N and Bonham, P and Brett, S and Brinkman, R and Burford, M and Clementson, L and Coad, P and Coman, F and Davies, D and Dela-Cruz, J and Devlin, M and Edgar, S and Eriksen, R and Furnas, M and Hassler, C and Hill, D and Holmes, M and Ingleton, T and Jameson, I and Leterme, SC and Lønborg, C and McLaughlin, J and McEnnulty, F and McKinnon, AD and Miller, M and Murray, S and Nayar, S and Patten, R and Pausina, SA and Pritchard, T and Proctor, R and Purcell-Meyerink, D and Raes, E and Rissik, D and Ruszczyk, J and Slotwinski, A and Swadling, KM and Tattersall, K and Thompson, P and Thomson, P and Tonks, M and Trull, TW and Uribe-Palomino, J and Waite, AM and Yauwenas, R and Zammit, A and Richardson, AJ}, title = {A database of marine phytoplankton abundance, biomass and species composition in Australian waters.}, journal = {Scientific data}, volume = {3}, number = {}, pages = {160043}, pmid = {27328409}, issn = {2052-4463}, mesh = {Australia ; Biomass ; Climate Change ; *Databases, Factual ; Ecosystem ; Eutrophication ; *Phytoplankton ; }, abstract = {There have been many individual phytoplankton datasets collected across Australia since the mid 1900s, but most are unavailable to the research community. We have searched archives, contacted researchers, and scanned the primary and grey literature to collate 3,621,847 records of marine phytoplankton species from Australian waters from 1844 to the present. Many of these are small datasets collected for local questions, but combined they provide over 170 years of data on phytoplankton communities in Australian waters. Units and taxonomy have been standardised, obviously erroneous data removed, and all metadata included. We have lodged this dataset with the Australian Ocean Data Network (http://portal.aodn.org.au/) allowing public access. The Australian Phytoplankton Database will be invaluable for global change studies, as it allows analysis of ecological indicators of climate change and eutrophication (e.g., changes in distribution; diatom:dinoflagellate ratios). In addition, the standardised conversion of abundance records to biomass provides modellers with quantifiable data to initialise and validate ecosystem models of lower marine trophic levels.}, } @article {pmid27323880, year = {2016}, author = {Power, DA and Watson, RA and Szathmáry, E and Mills, R and Powers, ST and Doncaster, CP and Czapp, B}, title = {Erratum to: What can ecosystems learn? Expanding evolutionary ecology with learning theory.}, journal = {Biology direct}, volume = {11}, number = {1}, pages = {29}, pmid = {27323880}, issn = {1745-6150}, } @article {pmid27322652, year = {2016}, author = {Bell, KL and de Vere, N and Keller, A and Richardson, RT and Gous, A and Burgess, KS and Brosi, BJ}, title = {Pollen DNA barcoding: current applications and future prospects.}, journal = {Genome}, volume = {59}, number = {9}, pages = {629-640}, doi = {10.1139/gen-2015-0200}, pmid = {27322652}, issn = {1480-3321}, mesh = {Allergens/genetics/immunology ; Biodiversity ; Computational Biology/methods ; *DNA Barcoding, Taxonomic ; *DNA, Plant ; Databases, Genetic ; Food Quality ; Genetic Markers ; High-Throughput Nucleotide Sequencing/methods ; Metagenomics/methods ; Plants/*classification/*genetics ; Pollen/*genetics ; }, abstract = {Identification of the species origin of pollen has many applications, including assessment of plant-pollinator networks, reconstruction of ancient plant communities, product authentication, allergen monitoring, and forensics. Such applications, however, have previously been limited by microscopy-based identification of pollen, which is slow, has low taxonomic resolution, and has few expert practitioners. One alternative is pollen DNA barcoding, which could overcome these issues. Recent studies demonstrate that both chloroplast and nuclear barcoding markers can be amplified from pollen. These recent validations of pollen metabarcoding indicate that now is the time for researchers in various fields to consider applying these methods to their research programs. In this paper, we review the nascent field of pollen DNA barcoding and discuss potential new applications of this technology, highlighting existing limitations and future research developments that will improve its utility in a wide range of applications.}, } @article {pmid27314840, year = {2016}, author = {Germerodt, S and Bohl, K and Lück, A and Pande, S and Schröter, A and Kaleta, C and Schuster, S and Kost, C}, title = {Pervasive Selection for Cooperative Cross-Feeding in Bacterial Communities.}, journal = {PLoS computational biology}, volume = {12}, number = {6}, pages = {e1004986}, pmid = {27314840}, issn = {1553-7358}, mesh = {Amino Acids/metabolism ; Bacteria/*genetics/*metabolism ; Computational Biology ; Computer Simulation ; Genotype ; Microbial Consortia/*physiology ; Microbial Interactions/*physiology ; }, abstract = {Bacterial communities are taxonomically highly diverse, yet the mechanisms that maintain this diversity remain poorly understood. We hypothesized that an obligate and mutual exchange of metabolites, as is very common among bacterial cells, could stabilize different genotypes within microbial communities. To test this, we developed a cellular automaton to model interactions among six empirically characterized genotypes that differ in their ability and propensity to produce amino acids. By systematically varying intrinsic (i.e. benefit-to-cost ratio) and extrinsic parameters (i.e. metabolite diffusion level, environmental amino acid availability), we show that obligate cross-feeding of essential metabolites is selected for under a broad range of conditions. In spatially structured environments, positive assortment among cross-feeders resulted in the formation of cooperative clusters, which limited exploitation by non-producing auxotrophs, yet allowed them to persist at the clusters' periphery. Strikingly, cross-feeding helped to maintain genotypic diversity within populations, while amino acid supplementation to the environment decoupled obligate interactions and favored auxotrophic cells that saved amino acid production costs over metabolically autonomous prototrophs. Together, our results suggest that spatially structured environments and limited nutrient availabilities should facilitate the evolution of metabolic interactions, which can help to maintain genotypic diversity within natural microbial populations.}, } @article {pmid27314158, year = {2016}, author = {Geiger, MF and Astrin, JJ and Borsch, T and Burkhardt, U and Grobe, P and Hand, R and Hausmann, A and Hohberg, K and Krogmann, L and Lutz, M and Monje, C and Misof, B and Morinière, J and Müller, K and Pietsch, S and Quandt, D and Rulik, B and Scholler, M and Traunspurger, W and Haszprunar, G and Wägele, W}, title = {How to tackle the molecular species inventory for an industrialized nation-lessons from the first phase of the German Barcode of Life initiative GBOL (2012-2015).}, journal = {Genome}, volume = {59}, number = {9}, pages = {661-670}, doi = {10.1139/gen-2015-0185}, pmid = {27314158}, issn = {1480-3321}, mesh = {Animals ; *Biodiversity ; *DNA Barcoding, Taxonomic ; *Databases, Genetic ; Developed Countries ; Germany ; Guideline Adherence ; Humans ; International Cooperation ; Libraries ; Reproducibility of Results ; }, abstract = {Biodiversity loss is mainly driven by human activity. While concern grows over the fate of hot spots of biodiversity, contemporary species losses still prevail in industrialized nations. Therefore, strategies were formulated to halt or reverse the loss, driven by evidence for its value for ecosystem services. Maintenance of the latter through conservation depends on correctly identified species. To this aim, the German Federal Ministry of Education and Research is funding the GBOL project, a consortium of natural history collections, botanic gardens, and universities working on a barcode reference database for the country's fauna and flora. Several noticeable findings could be useful for future campaigns: (i) validating taxon lists to serve as a taxonomic backbone is time-consuming, but without alternative; (ii) offering financial incentives to taxonomic experts, often citizen scientists, is indispensable; (iii) completion of the libraries for widespread species enables analyses of environmental samples, but the process may not hold pace with technological advancements; (iv) discoveries of new species are among the best stories for the media; (v) a commitment to common data standards and repositories is needed, as well as transboundary cooperation between nations; (vi) after validation, all data should be published online via the BOLD to make them searchable for external users and to allow cross-checking with data from other countries.}, } @article {pmid27312700, year = {2016}, author = {Ortseifen, V and Stolze, Y and Maus, I and Sczyrba, A and Bremges, A and Albaum, SP and Jaenicke, S and Fracowiak, J and Pühler, A and Schlüter, A}, title = {An integrated metagenome and -proteome analysis of the microbial community residing in a biogas production plant.}, journal = {Journal of biotechnology}, volume = {231}, number = {}, pages = {268-279}, doi = {10.1016/j.jbiotec.2016.06.014}, pmid = {27312700}, issn = {1873-4863}, mesh = {Biofuels/*microbiology ; Bioreactors/*microbiology ; Databases, Protein ; Electrophoresis, Gel, Two-Dimensional ; Metagenome/*genetics ; Microbial Consortia/*genetics ; Proteome/*analysis/genetics ; }, abstract = {To study the metaproteome of a biogas-producing microbial community, fermentation samples were taken from an agricultural biogas plant for microbial cell and protein extraction and corresponding metagenome analyses. Based on metagenome sequence data, taxonomic community profiling was performed to elucidate the composition of bacterial and archaeal sub-communities. The community's cytosolic metaproteome was represented in a 2D-PAGE approach. Metaproteome databases for protein identification were compiled based on the assembled metagenome sequence dataset for the biogas plant analyzed and non-corresponding biogas metagenomes. Protein identification results revealed that the corresponding biogas protein database facilitated the highest identification rate followed by other biogas-specific databases, whereas common public databases yielded insufficient identification rates. Proteins of the biogas microbiome identified as highly abundant were assigned to the pathways involved in methanogenesis, transport and carbon metabolism. Moreover, the integrated metagenome/-proteome approach enabled the examination of genetic-context information for genes encoding identified proteins by studying neighboring genes on the corresponding contig. Exemplarily, this approach led to the identification of a Methanoculleus sp. contig encoding 16 methanogenesis-related gene products, three of which were also detected as abundant proteins within the community's metaproteome. Thus, metagenome contigs provide additional information on the genetic environment of identified abundant proteins.}, } @article {pmid27311470, year = {2016}, author = {Roy, K and Kar, S}, title = {In Silico Models for Ecotoxicity of Pharmaceuticals.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1425}, number = {}, pages = {237-304}, pmid = {27311470}, issn = {1940-6029}, mesh = {Computational Biology/*methods ; Computer Simulation ; Environmental Pollutants/*toxicity ; Humans ; Models, Molecular ; Quantitative Structure-Activity Relationship ; Toxicity Tests ; }, abstract = {Pharmaceuticals and their active metabolites are one of the significantly emerging environmental toxicants. The major routes of entry of pharmaceuticals into the environment are industries, hospitals, or direct disposal of unwanted or expired drugs made by the patient. The most important and distinct features of pharmaceuticals are that they are deliberately designed to have an explicit mode of action and designed to exert an effect on humans and other living systems. This distinctive feature makes pharmaceuticals and their metabolites different from other chemicals, and this necessitates the evaluation of the direct effects of pharmaceuticals in various environmental compartments as well as to living systems. In this background, the alarming situation of ecotoxicity of diverse pharmaceuticals have forced government and nongovernment regulatory authorities to recommend the application of in silico methods to provide quick information about the risk assessment and fate properties of pharmaceuticals as well as their ecological and indirect human health effects. This chapter aims to offer information regarding occurrence of pharmaceuticals in the environment, their persistence, environmental fate, and toxicity as well as application of in silico methods to provide information about the basic risk management and fate prediction of pharmaceuticals in the environment. Brief ideas about toxicity endpoints, available ecotoxicity databases, and expert systems employed for rapid toxicity predictions of ecotoxicity of pharmaceuticals are also discussed.}, } @article {pmid27310720, year = {2016}, author = {Fahner, NA and Shokralla, S and Baird, DJ and Hajibabaei, M}, title = {Large-Scale Monitoring of Plants through Environmental DNA Metabarcoding of Soil: Recovery, Resolution, and Annotation of Four DNA Markers.}, journal = {PloS one}, volume = {11}, number = {6}, pages = {e0157505}, pmid = {27310720}, issn = {1932-6203}, mesh = {Alberta ; DNA Barcoding, Taxonomic ; DNA, Intergenic/*genetics ; DNA, Plant/*genetics ; Databases, Genetic ; Ecosystem ; Genetic Markers ; High-Throughput Nucleotide Sequencing ; *Metagenome ; Molecular Sequence Annotation ; *Phylogeny ; Plants/classification/*genetics ; Pollen/genetics ; Ribulose-Bisphosphate Carboxylase/*genetics ; Seeds/genetics ; Soil/chemistry ; }, abstract = {In a rapidly changing world we need methods to efficiently assess biodiversity in order to monitor ecosystem trends. Ecological monitoring often uses plant community composition to infer quality of sites but conventional aboveground surveys only capture a snapshot of the actively growing plant diversity. Environmental DNA (eDNA) extracted from soil samples, however, can include taxa represented by both active and dormant tissues, seeds, pollen, and detritus. Analysis of this eDNA through DNA metabarcoding provides a more comprehensive view of plant diversity at a site from a single assessment but it is not clear which DNA markers are best used to capture this diversity. Sequence recovery, annotation, and sequence resolution among taxa were evaluated for four established DNA markers (matK, rbcL, ITS2, and the trnL P6 loop) in silico using database sequences and in situ using high throughput sequencing of 35 soil samples from a remote boreal wetland. Overall, ITS2 and rbcL are recommended for DNA metabarcoding of vascular plants from eDNA when not using customized or geographically restricted reference databases. We describe a new framework for evaluating DNA metabarcodes and, contrary to existing assumptions, we found that full length DNA barcode regions could outperform shorter markers for surveying plant diversity from soil samples. By using current DNA barcoding markers rbcL and ITS2 for plant metabarcoding, we can take advantage of existing resources such as the growing DNA barcode database. Our work establishes the value of standard DNA barcodes for soil plant eDNA analysis in ecological investigations and biomonitoring programs and supports the collaborative development of DNA barcoding and metabarcoding.}, } @article {pmid27309073, year = {2016}, author = {Śmietanka, K and Bocian, Ł and Meissner, W and Ziętek-Barszcz, A and Żółkoś, K}, title = {Assessment of the Potential Distance of Dispersal of High Pathogenicity Avian Influenza Virus by Wild Mallards.}, journal = {Avian diseases}, volume = {60}, number = {1 Suppl}, pages = {316-321}, doi = {10.1637/11080-040715-RegR}, pmid = {27309073}, issn = {1938-4351}, mesh = {*Animal Distribution ; Animals ; Animals, Wild/virology ; Anseriformes/*virology ; Geographic Information Systems ; Influenza A virus/genetics/isolation & purification/pathogenicity/*physiology ; Influenza in Birds/*virology ; Seasons ; Virulence ; }, abstract = {This work presents the results of studies aimed at assessing the median and maximum distances covered by wild mallards (Anas platyrhynchos; n = 38), hypothetically infected with the high pathogenicity avian influenza virus (HPAIV) during spring migrations, using GPS-GSM tracking and published data on the susceptibility to HPAIV infection and duration of shedding. The model was based on the assumptions that the birds shed virus in the absence of clinical signs during infectious periods (IP) that were assumed to last 1 day (IP1), 4 days (IP4), and 8 days (IP8) and that each day of migration is a hypothetical day of the onset of IP. Using the haversine formula over a sliding timeframe corresponding to each IP, distances were estimated for each duck that undertook migration and then the maximum distance (Dmax) was selected. Ten mallards undertook spring migrations but, due to the loss of signal in the GPS-GSM devices, only three ducks were observed during autumn migrations. The following ranges of Dmax values were calculated for spring migrations: 124-382 km for IP1 (median 210 km), 208-632 km for IP4 (median 342 km), and 213-687 km for IP8 (median 370 km). The present study provides information that can be used as a data source to perform risk assessment related to the contribution of wild mallards in the dispersal of HPAIV over considerable distances.}, } @article {pmid27309051, year = {2016}, author = {Chang, CF and King, CC and Wan, CH and Chang, YC and Chan, TC and David Lee, CC and Chou, PH and Li, ZR and Li, YT and Tseng, TJ and Lee, PF and Chang, CH}, title = {Lessons from the Largest Epidemic of Avian Influenza Viruses in Taiwan, 2015.}, journal = {Avian diseases}, volume = {60}, number = {1 Suppl}, pages = {156-171}, doi = {10.1637/11168-051915-Reg}, pmid = {27309051}, issn = {1938-4351}, mesh = {Animals ; Animals, Wild/virology ; Chickens ; Disease Outbreaks ; Ducks ; Geese ; Influenza A virus/classification/genetics/*isolation & purification ; Influenza in Birds/*epidemiology/virology ; Phylogeny ; Poultry Diseases/*epidemiology/virology ; Taiwan/epidemiology ; }, abstract = {The largest epidemic of avian influenza (AI) in history attacked poultry and wild birds throughout Taiwan starting January 6, 2015. This study analyzed surveillance results, epidemiologic characteristics, and viral sequences by using government-released information, with the intention to provide recommendations to minimize future pandemic influenza. The H5 clade 2.3.4.4 highly pathogenic AI viruses (HPAIVs) had not been detected in Taiwan before 2015. During this epidemic, four types of etiologic agents were identified: the three novel subtypes H5N2, H5N8, and H5N3 clade 2.3.4.4 HPAIVs and one endemic chicken H5N2 subtype (Mexican-like lineage) of low pathogenic AI viruses. Cocirculation of mixed subtypes also occurred, with H5N2 clade 2.3.4.4 HPAIVs accompanied by the H5N8 and H5N3 subtypes or old H5N2 viruses in the same farm. More than 90% of domestic geese died from this AI epidemic; geese were affected the most at the early outbreaks. The epidemic peaked in mid-January for all three novel H5 subtypes. Spatial epidemiology found that most affected areas were located in southwestern coastal areas. In terrestrial poultry (mostly chickens), different geographic distributions of AI virus subtypes were detected, with hot spots of H5N2 clade 2.3.4.4 vs. past-endemic old H5N2 viruses in Changhwa (P = 0.03) and Yunlin (P = 0.007) counties, respectively, of central Taiwan. Phylogenetic and sequence analyses of all the early 10 Taiwan H5 clade 2.3.4.4 isolates covering the three subtypes showed that they were very different from the HA of the past local H5 viruses from domestic ducks (75%-80%) and chickens (70%-75%). However, they had the highest sequence identity percentages (99.53%-100%), with the HA of A/crane/Kagoshima/KU13/2014(H5N8) isolated on December 7, 2014, in Japan being higher than those of recent American and Korean H5 HPAIVs [A/Northern pintail/Washington/40964/2014 (H5N2) and A/gyrfalcon/Washington/41088-6/2014 (H5N8): 99.02%-99.54% and A/Baikal teal/Korea/Donglim3/2014 (H5N8): 98.61%-99.08%], implying a likely common ancestor of these H5 clade 2.3.4.4 viruses. The multiple subtypes of H5 clade 2.3.4.4 HPAIVs imply high viral reassortment. We recommend establishing an integrated surveillance system, involving clinical, virologic, and serologic surveillance in poultry and wild birds, swine and other mammals prevalent on multiple-animal mixed-type traditional farms, and high-risk human populations, as a crucially important step to minimize future pandemic influenza.}, } @article {pmid27309010, year = {2016}, author = {Mu, Y and Wu, F and Zhao, Q and Ji, R and Qie, Y and Zhou, Y and Hu, Y and Pang, C and Hristozov, D and Giesy, JP and Xing, B}, title = {Predicting toxic potencies of metal oxide nanoparticles by means of nano-QSARs.}, journal = {Nanotoxicology}, volume = {10}, number = {9}, pages = {1207-1214}, doi = {10.1080/17435390.2016.1202352}, pmid = {27309010}, issn = {1743-5404}, mesh = {Computer Simulation ; Escherichia coli/drug effects ; Humans ; Metal Nanoparticles/*chemistry/*toxicity ; *Models, Theoretical ; Nanoparticles/*chemistry/*toxicity ; Oxides ; Predictive Value of Tests ; Quantitative Structure-Activity Relationship ; Tissue Distribution ; }, abstract = {BACKGROUND: The enormous physicochemical and structural diversity of metal oxide nanoparticles (MeONPs) poses significant challenges to the testing of their biological uptake, biodistribution, and effects that can be used to develop understanding of key nano-bio modes of action. This has generated considerable uncertainties in the assessment of their human health and environmental risks and has raised concerns about the adequacy of their regulation. In order to surpass the extremely resource intensive case-by-case testing, intelligent strategies combining testing methods and non-testing predictive modeling should be developed.

METHODS: The quantitative structure-activity relationship (QSARs) in silico tools can be instrumental in understanding properties that affect the potencies of MeONPs and in predicting toxic responses and thresholds of effects.

RESULTS: The present study proposes a predictive nano-QSAR model for predicting the cytotoxicity of MeONPs. The model was applied to test the relationships between 26 physicochemical properties of 51 MeONPs and their cytotoxic effects in Escherichia coli. The two parameters, enthalpy of formation of a gaseous cation (▵Hme+) and polarization force (Z/r), were elucidated to make a significant contribution for the toxic effect of these MeONPs. The study also proposed the mechanisms of toxic potency in E. coli through the model, which indicated that the MeONPs as well as their released metal ions could collectively induce DNA damage and cell apoptosis.

SIGNIFICANCE: These findings may provide an alternative method for prioritizing current and future MeONPs for potential in vivo testing, virtual prescreening and for designing environmentally benign nanomaterials.}, } @article {pmid27307276, year = {2016}, author = {Zhou, J and Lai, L and Guan, T and Cai, W and Gao, N and Zhang, X and Yang, D and Cong, Z and Zheng, Y}, title = {Comparison modeling for alpine vegetation distribution in an arid area.}, journal = {Environmental monitoring and assessment}, volume = {188}, number = {7}, pages = {408}, pmid = {27307276}, issn = {1573-2959}, mesh = {*Altitude ; China ; Ecology ; Environmental Monitoring/*methods ; *Forests ; Geographic Information Systems ; *Models, Theoretical ; *Plants ; Random Allocation ; Rivers ; }, abstract = {Mapping and modeling vegetation distribution are fundamental topics in vegetation ecology. With the rise of powerful new statistical techniques and GIS tools, the development of predictive vegetation distribution models has increased rapidly. However, modeling alpine vegetation with high accuracy in arid areas is still a challenge because of the complexity and heterogeneity of the environment. Here, we used a set of 70 variables from ASTER GDEM, WorldClim, and Landsat-8 OLI (land surface albedo and spectral vegetation indices) data with decision tree (DT), maximum likelihood classification (MLC), and random forest (RF) models to discriminate the eight vegetation groups and 19 vegetation formations in the upper reaches of the Heihe River Basin in the Qilian Mountains, northwest China. The combination of variables clearly discriminated vegetation groups but failed to discriminate vegetation formations. Different variable combinations performed differently in each type of model, but the most consistently important parameter in alpine vegetation modeling was elevation. The best RF model was more accurate for vegetation modeling compared with the DT and MLC models for this alpine region, with an overall accuracy of 75 % and a kappa coefficient of 0.64 verified against field point data and an overall accuracy of 65 % and a kappa of 0.52 verified against vegetation map data. The accuracy of regional vegetation modeling differed depending on the variable combinations and models, resulting in different classifications for specific vegetation groups.}, } @article {pmid27306515, year = {2016}, author = {Brindefalk, B and Ekman, M and Ininbergs, K and Dupont, CL and Yooseph, S and Pinhassi, J and Bergman, B}, title = {Distribution and expression of microbial rhodopsins in the Baltic Sea and adjacent waters.}, journal = {Environmental microbiology}, volume = {18}, number = {12}, pages = {4442-4455}, doi = {10.1111/1462-2920.13407}, pmid = {27306515}, issn = {1462-2920}, mesh = {Adaptation, Physiological/genetics ; Bacteria/*genetics/*metabolism ; Gene Expression Regulation, Bacterial/physiology ; Light ; *Oceans and Seas ; Phylogeny ; Phytoplankton/metabolism ; Rhodopsins, Microbial/*chemistry/*genetics ; *Water Microbiology ; }, abstract = {Rhodopsins are light-driven ion-pumping membrane proteins found in many organisms and are proposed to be of global importance for oceanic microbial energy generation. Several studies have focused on marine environments, with less exploration of rhodopsins in brackish waters. We investigated microbial rhodopsins in the Baltic Sea using size-fractionated metagenomic and metatranscriptomic datasets collected along a salinity gradient spanning from ∼0 to 35 PSU. The normalised genomic abundance of rhodopsins in Bacteria, as well as rhodopsin gene expression, was highest in the smallest size fraction (0.1-0.8 μm), relative to the medium (0.8-3.0 μm) and large (>3.0 μm) size fractions. The abundance of rhodopsins in the two smaller size fractions displayed a positive correlation with salinity. Proteobacteria and Bacteroidetes rhodopsins were the most abundant while Actinobacteria rhodopsins, or actinorhodopsins, were common at lower salinities. Phylogenetic analysis indicated that rhodopsins have adapted independently to the marine-brackish transition on multiple occasions, giving rise to green light-adapted variants from ancestral blue light-adapted ones. A notable diversity of viral-like rhodopsins was also detected in the dataset and potentially linked with eukaryotic phytoplankton blooms. Finally, a new clade of likely proton-pumping rhodopsin with non-canonical amino acids in the spectral tuning and proton accepting site was identified.}, } @article {pmid27296707, year = {2016}, author = {Buyuktimkin, B and Saier, MH}, title = {Comparative analyses of transport proteins encoded within the genomes of Leptospira species.}, journal = {Microbial pathogenesis}, volume = {98}, number = {}, pages = {118-131}, pmid = {27296707}, issn = {1096-1208}, support = {R01 GM077402/GM/NIGMS NIH HHS/United States ; }, mesh = {*Computational Biology ; *Genetic Variation ; *Genome, Bacterial ; Humans ; Leptospira/classification/*genetics/pathogenicity ; Membrane Transport Proteins/analysis/*genetics ; Virulence Factors/analysis/*genetics ; }, abstract = {Select species of the bacterial genus Leptospira are causative agents of leptospirosis, an emerging global zoonosis affecting nearly one million people worldwide annually. We examined two Leptospira pathogens, Leptospira interrogans serovar Lai str. 56601 and Leptospira borgpetersenii serovar Hardjo-bovis str. L550, as well as the free-living leptospiral saprophyte, Leptospira biflexa serovar Patoc str. 'Patoc 1 (Ames)'. The transport proteins of these leptospires were identified and compared using bioinformatics to gain an appreciation for which proteins may be related to pathogenesis and saprophytism. L. biflexa possesses a disproportionately high number of secondary carriers for metabolite uptake and environmental adaptability as well as an increased number of inorganic cation transporters providing ionic homeostasis and effective osmoregulation in a rapidly changing environment. L. interrogans and L. borgpetersenii possess far fewer transporters, but those that they all have are remarkably similar, with near-equivalent representation in most transporter families. These two Leptospira pathogens also possess intact sphingomyelinases, holins, and virulence-related outer membrane porins. These virulence-related factors, in conjunction with decreased transporter substrate versatility, indicate that pathogenicity arose in Leptospira correlating to progressively narrowing ecological niches and the emergence of a limited set of proteins responsible for host invasion. The variability of host tropism and mortality rates by infectious leptospires suggests that small differences in individual sets of proteins play important physiological and pathological roles.}, } @article {pmid27296526, year = {2016}, author = {Rideout, JR and Chase, JH and Bolyen, E and Ackermann, G and González, A and Knight, R and Caporaso, JG}, title = {Keemei: cloud-based validation of tabular bioinformatics file formats in Google Sheets.}, journal = {GigaScience}, volume = {5}, number = {}, pages = {27}, pmid = {27296526}, issn = {2047-217X}, mesh = {Cloud Computing ; Computational Biology/*methods ; Humans ; Information Storage and Retrieval ; Software ; User-Computer Interface ; }, abstract = {BACKGROUND: Bioinformatics software often requires human-generated tabular text files as input and has specific requirements for how those data are formatted. Users frequently manage these data in spreadsheet programs, which is convenient for researchers who are compiling the requisite information because the spreadsheet programs can easily be used on different platforms including laptops and tablets, and because they provide a familiar interface. It is increasingly common for many different researchers to be involved in compiling these data, including study coordinators, clinicians, lab technicians and bioinformaticians. As a result, many research groups are shifting toward using cloud-based spreadsheet programs, such as Google Sheets, which support the concurrent editing of a single spreadsheet by different users working on different platforms. Most of the researchers who enter data are not familiar with the formatting requirements of the bioinformatics programs that will be used, so validating and correcting file formats is often a bottleneck prior to beginning bioinformatics analysis.

MAIN TEXT: We present Keemei, a Google Sheets Add-on, for validating tabular files used in bioinformatics analyses. Keemei is available free of charge from Google's Chrome Web Store. Keemei can be installed and run on any web browser supported by Google Sheets. Keemei currently supports the validation of two widely used tabular bioinformatics formats, the Quantitative Insights into Microbial Ecology (QIIME) sample metadata mapping file format and the Spatially Referenced Genetic Data (SRGD) format, but is designed to easily support the addition of others.

CONCLUSIONS: Keemei will save researchers time and frustration by providing a convenient interface for tabular bioinformatics file format validation. By allowing everyone involved with data entry for a project to easily validate their data, it will reduce the validation and formatting bottlenecks that are commonly encountered when human-generated data files are first used with a bioinformatics system. Simplifying the validation of essential tabular data files, such as sample metadata, will reduce common errors and thereby improve the quality and reliability of research outcomes.}, } @article {pmid27292778, year = {2016}, author = {Farine, DR and Strandburg-Peshkin, A and Berger-Wolf, T and Ziebart, B and Brugere, I and Li, J and Crofoot, MC}, title = {Both Nearest Neighbours and Long-term Affiliates Predict Individual Locations During Collective Movement in Wild Baboons.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {27704}, pmid = {27292778}, issn = {2045-2322}, support = {T32 HG003284/HG/NHGRI NIH HHS/United States ; BB/L006081/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; Behavior, Animal ; Female ; Geographic Information Systems ; Male ; Movement ; Papio/*physiology ; *Social Behavior ; Social Dominance ; }, abstract = {In many animal societies, groups of individuals form stable social units that are shaped by well-delineated dominance hierarchies and a range of affiliative relationships. How do socially complex groups maintain cohesion and achieve collective movement? Using high-resolution GPS tracking of members of a wild baboon troop, we test whether collective movement in stable social groups is governed by interactions among local neighbours (commonly found in groups with largely anonymous memberships), social affiliates, and/or by individuals paying attention to global group structure. We construct candidate movement prediction models and evaluate their ability to predict the future trajectory of focal individuals. We find that baboon movements are best predicted by 4 to 6 neighbours. While these are generally individuals' nearest neighbours, we find that baboons have distinct preferences for particular neighbours, and that these social affiliates best predict individual location at longer time scales (>10 minutes). Our results support existing theoretical and empirical studies highlighting the importance of local rules in driving collective outcomes, such as collective departures, in primates. We extend previous studies by elucidating the rules that maintain cohesion in baboons 'on the move', as well as the different temporal scales of social interactions that are at play.}, } @article {pmid27292122, year = {2017}, author = {Horn, RL and Ramaraj, T and Devitt, NP and Schilkey, FD and Cowley, DE}, title = {De novo assembly of a tadpole shrimp (Triops newberryi) transcriptome and preliminary differential gene expression analysis.}, journal = {Molecular ecology resources}, volume = {17}, number = {2}, pages = {161-171}, pmid = {27292122}, issn = {1755-0998}, support = {P20 GM103451/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Computational Biology ; Crustacea/*genetics/*growth & development ; Environmental Exposure ; *Gene Expression Profiling ; High-Throughput Nucleotide Sequencing ; Water ; }, abstract = {Next-generation sequencing techniques, such as RNA sequencing, have provided a wealth of genomic information for nonmodel species. Transcriptomic information can be used to quantify the patterns of gene expression, which can identify how environmental differences invoke organismal stress responses and provide a gauge in predicting species adaptability. In our study, we used RNA sequencing to characterize the first transcriptome from a naupliar tadpole shrimp (Triops newberryi) to identify the genes expressed during the early life history stages and which could be important for future genomic studies. RNA was extracted from naupliar T. newberryi that were reared in a laboratory-controlled setting and in two different water types, a native and a non-native condition. A total of six replicates, three per condition, were sequenced with the Illumina Hi-Seq 2000 achieving 365 M 50-nt reads. High-quality reads were produced and de novo assembly was used to construct a T. newberryi transcriptome that was approximately 24.8 M base pairs. More than 10 000 peptides were predicted from the assembly, and genes were sorted into gene ontology categories. The use of different water conditions allowed for a preliminary differential gene expression analysis in order to compare the changes in gene expression between conditions. There were 299 differentially expressed genes between water conditions that might serve as a focal point for future genomic studies of Triops acclimation to different environments. The Triops transcriptome could serve as vital genomic information for additional studies on Branchiopod crustaceans.}, } @article {pmid27288885, year = {2017}, author = {Mora-Márquez, F and García-Olivares, V and Emerson, BC and López de Heredia, U}, title = {ddradseqtools: a software package for in silico simulation and testing of double-digest RADseq experiments.}, journal = {Molecular ecology resources}, volume = {17}, number = {2}, pages = {230-246}, doi = {10.1111/1755-0998.12550}, pmid = {27288885}, issn = {1755-0998}, mesh = {Computational Biology/*methods ; DNA/chemistry/metabolism ; DNA Restriction Enzymes/metabolism ; High-Throughput Nucleotide Sequencing/*methods ; *Software ; }, abstract = {Double-digested RADseq (ddRADseq) is a NGS methodology that generates reads from thousands of loci targeted by restriction enzyme cut sites, across multiple individuals. To be statistically sound and economically optimal, a ddRADseq experiment has a preliminary design stage that needs to consider issues related to the selection of enzymes, particular features of the genome of the focal species, possible modifications to the library construction protocol, coverage needed to minimize missing data, and the potential sources of error that may impact upon the coverage. We present ddradseqtools, a software package to help ddRADseq experimental design by (i) the generation of in silico double-digested fragments; (ii) the construction of modified ddRADseq libraries using adapters with either one or two indexes and degenerate base regions (DBRs) to quantify PCR duplicates; and (iii) the initial steps of the bioinformatics preprocessing of reads. ddradseqtools generates single-end (SE) or paired-end (PE) reads that may bear SNPs and/or indels. The effect of allele dropout and PCR duplicates on coverage is also simulated. The resulting output files can be submitted to pipelines of alignment and variant calling, to allow the fine-tuning of parameters. The software was validated with specific tests for the correct operability of the program. The correspondence between in silico settings and parameters from ddRADseq in vitro experiments was assessed to provide guidelines for the reliable performance of the software. ddradseqtools is cost-efficient in terms of execution time, and can be run on computers with standard CPU and RAM configuration.}, } @article {pmid27283948, year = {2016}, author = {Behr, AA and Liu, KZ and Liu-Fang, G and Nakka, P and Ramachandran, S}, title = {pong: fast analysis and visualization of latent clusters in population genetic data.}, journal = {Bioinformatics (Oxford, England)}, volume = {32}, number = {18}, pages = {2817-2823}, pmid = {27283948}, issn = {1367-4811}, mesh = {Algorithms ; Cluster Analysis ; Computer Graphics ; *Data Mining ; Genetics, Population ; Humans ; *Population Groups ; Programming Languages ; Protein Conformation ; *Software ; }, abstract = {MOTIVATION: A series of methods in population genetics use multilocus genotype data to assign individuals membership in latent clusters. These methods belong to a broad class of mixed-membership models, such as latent Dirichlet allocation used to analyze text corpora. Inference from mixed-membership models can produce different output matrices when repeatedly applied to the same inputs, and the number of latent clusters is a parameter that is often varied in the analysis pipeline. For these reasons, quantifying, visualizing, and annotating the output from mixed-membership models are bottlenecks for investigators across multiple disciplines from ecology to text data mining.

RESULTS: We introduce pong, a network-graphical approach for analyzing and visualizing membership in latent clusters with a native interactive D3.js visualization. pong leverages efficient algorithms for solving the Assignment Problem to dramatically reduce runtime while increasing accuracy compared with other methods that process output from mixed-membership models. We apply pong to 225 705 unlinked genome-wide single-nucleotide variants from 2426 unrelated individuals in the 1000 Genomes Project, and identify previously overlooked aspects of global human population structure. We show that pong outpaces current solutions by more than an order of magnitude in runtime while providing a customizable and interactive visualization of population structure that is more accurate than those produced by current tools.

pong is freely available and can be installed using the Python package management system pip. pong's source code is available at https://github.com/abehr/pong

CONTACT: aaron_behr@alumni.brown.edu or sramachandran@brown.edu

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, } @article {pmid27279224, year = {2016}, author = {Bashan, A and Gibson, TE and Friedman, J and Carey, VJ and Weiss, ST and Hohmann, EL and Liu, YY}, title = {Universality of human microbial dynamics.}, journal = {Nature}, volume = {534}, number = {7606}, pages = {259-262}, pmid = {27279224}, issn = {1476-4687}, support = {R01 HL091528/HL/NHLBI NIH HHS/United States ; }, mesh = {Clostridioides difficile/physiology ; Clostridium Infections/microbiology ; Computer Simulation ; Cross-Sectional Studies ; Datasets as Topic ; *Ecosystem ; Environment ; Fecal Microbiota Transplantation ; Gastrointestinal Microbiome/physiology ; Healthy Volunteers ; Humans ; Intestines/microbiology ; Metagenomics ; Microbiota/*physiology ; Mouth/microbiology ; Organ Specificity ; Skin/microbiology ; Species Specificity ; }, abstract = {Human-associated microbial communities have a crucial role in determining our health and well-being, and this has led to the continuing development of microbiome-based therapies such as faecal microbiota transplantation. These microbial communities are very complex, dynamic and highly personalized ecosystems, exhibiting a high degree of inter-individual variability in both species assemblages and abundance profiles. It is not known whether the underlying ecological dynamics of these communities, which can be parameterized by growth rates, and intra- and inter-species interactions in population dynamics models, are largely host-independent (that is, universal) or host-specific. If the inter-individual variability reflects host-specific dynamics due to differences in host lifestyle, physiology or genetics, then generic microbiome manipulations may have unintended consequences, rendering them ineffective or even detrimental. Alternatively, microbial ecosystems of different subjects may exhibit universal dynamics, with the inter-individual variability mainly originating from differences in the sets of colonizing species. Here we develop a new computational method to characterize human microbial dynamics. By applying this method to cross-sectional data from two large-scale metagenomic studies--the Human Microbiome Project and the Student Microbiome Project--we show that gut and mouth microbiomes display pronounced universal dynamics, whereas communities associated with certain skin sites are probably shaped by differences in the host environment. Notably, the universality of gut microbial dynamics is not observed in subjects with recurrent Clostridium difficile infection but is observed in the same set of subjects after faecal microbiota transplantation. These results fundamentally improve our understanding of the processes that shape human microbial ecosystems, and pave the way to designing general microbiome-based therapies.}, } @article {pmid27278626, year = {2016}, author = {Wen, M and Lin, X and Xie, M and Wang, Y and Shen, X and Liufu, Z and Wu, CI and Shi, S and Tang, T}, title = {Small RNA transcriptomes of mangroves evolve adaptively in extreme environments.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {27551}, pmid = {27278626}, issn = {2045-2322}, mesh = {Arabidopsis ; Biological Evolution ; Cluster Analysis ; Computational Biology ; Expressed Sequence Tags ; Gene Expression Regulation, Plant ; Gene Library ; High-Throughput Nucleotide Sequencing ; MicroRNAs/genetics ; RNA, Plant/genetics ; RNA, Small Interfering/*genetics ; Rhizophoraceae/*genetics ; Sequence Analysis, RNA ; Stress, Physiological ; Temperature ; *Transcriptome ; }, abstract = {MicroRNAs (miRNAs) and endogenous small interfering RNAs (siRNAs) are key players in plant stress responses. Here, we present the sRNA transcriptomes of mangroves Bruguiera gymnorrhiza and Kandelia candel. Comparative computational analyses and target predictions revealed that mangroves exhibit distinct sRNA regulatory networks that differ from those of glycophytes. A total of 32 known and three novel miRNA families were identified. Conserved and mangrove-specific miRNA targets were predicted; the latter were widely involved in stress responses. The known miRNAs showed differential expression between the mangroves and glycophytes, reminiscent of the adaptive stress-responsive changes in Arabidopsis. B. gymnorrhiza possessed highly abundant but less conserved TAS3 trans-acting siRNAs (tasiRNAs) in addition to tasiR-ARFs, with expanded potential targets. Our results indicate that the evolutionary alteration of sRNA expression levels and the rewiring of sRNA-regulatory networks are important mechanisms underlying stress adaptation. We also identified sRNAs that are involved in salt and/or drought tolerance and nutrient homeostasis as possible contributors to mangrove success in stressful environments.}, } @article {pmid27275583, year = {2016}, author = {Wang, T and Hamann, A and Spittlehouse, D and Carroll, C}, title = {Locally Downscaled and Spatially Customizable Climate Data for Historical and Future Periods for North America.}, journal = {PloS one}, volume = {11}, number = {6}, pages = {e0156720}, pmid = {27275583}, issn = {1932-6203}, mesh = {*Climate ; History, 20th Century ; History, 21st Century ; *Models, Theoretical ; North America ; *Software ; }, abstract = {Large volumes of gridded climate data have become available in recent years including interpolated historical data from weather stations and future predictions from general circulation models. These datasets, however, are at various spatial resolutions that need to be converted to scales meaningful for applications such as climate change risk and impact assessments or sample-based ecological research. Extracting climate data for specific locations from large datasets is not a trivial task and typically requires advanced GIS and data management skills. In this study, we developed a software package, ClimateNA, that facilitates this task and provides a user-friendly interface suitable for resource managers and decision makers as well as scientists. The software locally downscales historical and future monthly climate data layers into scale-free point estimates of climate values for the entire North American continent. The software also calculates a large number of biologically relevant climate variables that are usually derived from daily weather data. ClimateNA covers 1) 104 years of historical data (1901-2014) in monthly, annual, decadal and 30-year time steps; 2) three paleoclimatic periods (Last Glacial Maximum, Mid Holocene and Last Millennium); 3) three future periods (2020s, 2050s and 2080s); and 4) annual time-series of model projections for 2011-2100. Multiple general circulation models (GCMs) were included for both paleo and future periods, and two representative concentration pathways (RCP4.5 and 8.5) were chosen for future climate data.}, } @article {pmid27272017, year = {2016}, author = {Koch, C and Jeschke, JM and Overbeck, GE and Kollmann, J}, title = {Setting Priorities for Monitoring and Managing Non-native Plants: Toward a Practical Approach.}, journal = {Environmental management}, volume = {58}, number = {3}, pages = {465-475}, pmid = {27272017}, issn = {1432-1009}, mesh = {Brazil ; Conservation of Natural Resources/*methods ; Databases, Factual ; Environmental Monitoring/*methods ; *Grassland ; *Introduced Species ; Poaceae/*growth & development ; Risk Assessment ; }, abstract = {Land managers face the challenge to set priorities in monitoring and managing non-native plant species, as resources are limited and not all non-natives become invasive. Existing frameworks that have been proposed to rank non-native species require extensive information on their distribution, abundance, and impact. This information is difficult to obtain and often not available for many species and regions. National watch or priority lists are helpful, but it is questionable whether they provide sufficient information for environmental management on a regional scale. We therefore propose a decision tree that ranks species based on more simple albeit robust information, but still provides reliable management recommendations. To test the decision tree, we collected and evaluated distribution data from non-native plants in highland grasslands of Southern Brazil. We compared the results with a national list from the Brazilian Invasive Species Database for the state to discuss advantages and disadvantages of the different approaches on a regional scale. Out of 38 non-native species found, only four were also present on the national list. If management would solely rely on this list, many species that were identified as spreading based on the decision tree would go unnoticed. With the suggested scheme, it is possible to assign species to active management, to monitoring, or further evaluation. While national lists are certainly important, management on a regional scale should employ additional tools that adequately consider the actual risk of non-natives to become invasive.}, } @article {pmid27271207, year = {2016}, author = {Vivaldo, G and Masi, E and Pandolfi, C and Mancuso, S and Caldarelli, G}, title = {Networks of plants: how to measure similarity in vegetable species.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {27077}, pmid = {27271207}, issn = {2045-2322}, mesh = {Asteraceae/anatomy & histology/physiology ; Brassicaceae/anatomy & histology/physiology ; Cyperaceae/anatomy & histology/physiology ; Datasets as Topic ; Ecosystem ; Fabaceae/anatomy & histology/physiology ; Fruit/anatomy & histology/*physiology ; Plant Dispersal/*physiology ; Poaceae/anatomy & histology/physiology ; Rosaceae/anatomy & histology/physiology ; Systems Biology/*statistics & numerical data ; Vegetables/anatomy & histology/*physiology ; }, abstract = {Despite the common misconception of nearly static organisms, plants do interact continuously with the environment and with each other. It is fair to assume that during their evolution they developed particular features to overcome similar problems and to exploit possibilities from environment. In this paper we introduce various quantitative measures based on recent advancements in complex network theory that allow to measure the effective similarities of various species. By using this approach on the similarity in fruit-typology ecological traits we obtain a clear plant classification in a way similar to traditional taxonomic classification. This result is not trivial, since a similar analysis done on the basis of diaspore morphological properties do not provide any clear parameter to classify plants species. Complex network theory can then be used in order to determine which feature amongst many can be used to distinguish scope and possibly evolution of plants. Future uses of this approach range from functional classification to quantitative determination of plant communities in nature.}, } @article {pmid27271123, year = {2017}, author = {Fakhrzadeh, A and Spörndly-Nees, E and Ekstedt, E and Holm, L and Luengo Hendriks, CL}, title = {New computerized staging method to analyze mink testicular tissue in environmental research.}, journal = {Environmental toxicology and chemistry}, volume = {36}, number = {1}, pages = {156-164}, doi = {10.1002/etc.3517}, pmid = {27271123}, issn = {1552-8618}, mesh = {Acrosome/*drug effects/pathology ; Animals ; Ecotoxicology/*methods ; Endocrine Disruptors/toxicity ; Environmental Pollutants/toxicity ; Humans ; Image Interpretation, Computer-Assisted/*methods ; Immunohistochemistry ; Male ; *Mink ; Reproducibility of Results ; Reproduction/*drug effects ; Sensitivity and Specificity ; Testis/*drug effects/pathology ; }, abstract = {Histopathology of testicular tissue is considered to be the most sensitive tool to detect adverse effects on male reproduction. When assessing tissue damage, seminiferous epithelium needs to be classified into different stages to detect certain cell damages; but stage identification is a demanding task. The authors present a method to identify the 12 stages in mink testicular tissue. The staging system uses Gata-4 immunohistochemistry to visualize acrosome development and proved to be both intraobserver-reproducible and interobserver-reproducible with a substantial agreement of 83.6% (kappa = 0.81) and 70.5% (kappa = 0.67), respectively. To further advance and objectify this method, they present a computerized staging system that identifies these 12 stages. This program has an agreement of 52.8% (kappa 0.47) with the consensus staging by 2 investigators. The authors propose a pooling of the stages into 5 groups based on morphology, stage transition, and toxicologically important endpoints. The computerized program then reached a substantial agreement of 76.7% (kappa = 0.69). The computerized staging tool uses local ternary patterns to describe the texture of the tubules and a support vector machine classifier to learn which textures correspond to which stages. The results have the potential to modernize the tedious staging process required in toxicological evaluation of testicular tissue, especially if combined with whole-slide imaging and automated tubular segmentation. Environ Toxicol Chem 2017;36:156-164. © 2016 The Authors. Environmental Toxicology and Chemistry Published by Wiley Periodicals, Inc. on behalf of SETAC.}, } @article {pmid27267926, year = {2016}, author = {Sempéré, G and Philippe, F and Dereeper, A and Ruiz, M and Sarah, G and Larmande, P}, title = {Gigwa-Genotype investigator for genome-wide analyses.}, journal = {GigaScience}, volume = {5}, number = {}, pages = {25}, pmid = {27267926}, issn = {2047-217X}, mesh = {Computational Biology/*methods ; Databases, Genetic ; Genetic Variation ; Genome-Wide Association Study/*methods ; Genotype ; Information Storage and Retrieval ; Internet ; Sequence Analysis, DNA/*methods ; Software ; User-Computer Interface ; }, abstract = {BACKGROUND: Exploring the structure of genomes and analyzing their evolution is essential to understanding the ecological adaptation of organisms. However, with the large amounts of data being produced by next-generation sequencing, computational challenges arise in terms of storage, search, sharing, analysis and visualization. This is particularly true with regards to studies of genomic variation, which are currently lacking scalable and user-friendly data exploration solutions.

DESCRIPTION: Here we present Gigwa, a web-based tool that provides an easy and intuitive way to explore large amounts of genotyping data by filtering it not only on the basis of variant features, including functional annotations, but also on genotype patterns. The data storage relies on MongoDB, which offers good scalability properties. Gigwa can handle multiple databases and may be deployed in either single- or multi-user mode. In addition, it provides a wide range of popular export formats.

CONCLUSIONS: The Gigwa application is suitable for managing large amounts of genomic variation data. Its user-friendly web interface makes such processing widely accessible. It can either be simply deployed on a workstation or be used to provide a shared data portal for a given community of researchers.}, } @article {pmid27267057, year = {2016}, author = {Ge, Y and Wang, Y and Liu, Y and Tan, Y and Ren, X and Zhang, X and Hyde, KD and Liu, Y and Liu, Z}, title = {Comparative genomic and transcriptomic analyses of the Fuzhuan brick tea-fermentation fungus Aspergillus cristatus.}, journal = {BMC genomics}, volume = {17}, number = {}, pages = {428}, pmid = {27267057}, issn = {1471-2164}, mesh = {Aspergillus/classification/*genetics/metabolism/ultrastructure ; Biological Evolution ; Computational Biology/methods ; Fermentation ; Fungal Proteins/genetics ; Gene Expression Profiling ; Gene Expression Regulation, Fungal ; *Genome, Fungal ; *Genomics/methods ; High-Throughput Nucleotide Sequencing ; MAP Kinase Signaling System ; Molecular Sequence Annotation ; Multigene Family ; Phylogeny ; Quantitative Trait Loci ; Tea/metabolism/*microbiology ; *Transcriptome ; }, abstract = {BACKGROUND: Aspergillus cristatus is the dominant fungus involved in the fermentation of Chinese Fuzhuan brick tea. Aspergillus cristatus is a homothallic fungus that undergoes a sexual stage without asexual conidiation when cultured in hypotonic medium. The asexual stage is induced by a high salt concentration, which completely inhibits sexual development. The taxon is therefore appropriate for investigating the mechanisms of asexual and sexual reproduction in fungi. In this study, de novo genome sequencing and analysis of transcriptomes during culture under high- and low-osmolarity conditions were performed. These analyses facilitated investigation of the evolution of mating-type genes, which determine the mode of sexual reproduction, in A. cristatus, the response of the high-osmolarity glycerol (HOG) pathway to osmotic stimulation, and the detection of mycotoxins and evaluation of the relationship with the location of the encoding genes.

RESULTS: The A. cristatus genome comprised 27.9 Mb and included 68 scaffolds, from which 10,136 protein-coding gene models were predicted. A phylogenetic analysis suggested a considerable phylogenetic distance between A. cristatus and A. nidulans. Comparison of the mating-type gene loci among Aspergillus species indicated that the mode in A. cristatus differs from those in other Aspergillus species. The components of the HOG pathway were conserved in the genome of A. cristatus. Differential gene expression analysis in A. cristatus using RNA-Seq demonstrated that the expression of most genes in the HOG pathway was unaffected by osmotic pressure. No gene clusters associated with the production of carcinogens were detected.

CONCLUSIONS: A model of the mating-type locus in A. cristatus is reported for the first time. Aspergillus cristatus has evolved various mechanisms to cope with high osmotic stress. As a fungus associated with Fuzhuan tea, it is considered to be safe under low- and high-osmolarity conditions.}, } @article {pmid27266845, year = {2016}, author = {Probert, WJ and Shea, K and Fonnesbeck, CJ and Runge, MC and Carpenter, TE and Dürr, S and Garner, MG and Harvey, N and Stevenson, MA and Webb, CT and Werkman, M and Tildesley, MJ and Ferrari, MJ}, title = {Decision-making for foot-and-mouth disease control: Objectives matter.}, journal = {Epidemics}, volume = {15}, number = {}, pages = {10-19}, pmid = {27266845}, issn = {1878-0067}, support = {BB/K010972/4/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; R01 GM105247/GM/NIGMS NIH HHS/United States ; BB/K010972/3/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; *Decision Support Techniques ; Disease Outbreaks/*prevention & control ; Foot-and-Mouth Disease/*prevention & control/*transmission ; }, abstract = {Formal decision-analytic methods can be used to frame disease control problems, the first step of which is to define a clear and specific objective. We demonstrate the imperative of framing clearly-defined management objectives in finding optimal control actions for control of disease outbreaks. We illustrate an analysis that can be applied rapidly at the start of an outbreak when there are multiple stakeholders involved with potentially multiple objectives, and when there are also multiple disease models upon which to compare control actions. The output of our analysis frames subsequent discourse between policy-makers, modellers and other stakeholders, by highlighting areas of discord among different management objectives and also among different models used in the analysis. We illustrate this approach in the context of a hypothetical foot-and-mouth disease (FMD) outbreak in Cumbria, UK using outputs from five rigorously-studied simulation models of FMD spread. We present both relative rankings and relative performance of controls within each model and across a range of objectives. Results illustrate how control actions change across both the base metric used to measure management success and across the statistic used to rank control actions according to said metric. This work represents a first step towards reconciling the extensive modelling work on disease control problems with frameworks for structured decision making.}, } @article {pmid27266017, year = {2016}, author = {Dudov, SV}, title = {[Modeling of species distribution using topography and remote sensing data, with vascular plants of the Tukuringra Range low mountain belt (Zeya state Nature Reserve, Amur Region) as a case study].}, journal = {Zhurnal obshchei biologii}, volume = {77}, number = {2}, pages = {122-134}, pmid = {27266017}, issn = {0044-4596}, mesh = {Altitude ; Embryophyta/*growth & development ; Geographic Information Systems ; *Models, Theoretical ; Phylogeny ; Population Dynamics ; Russia ; *Satellite Imagery ; }, abstract = {On the basis of maximum entropy method embedded in MaxEnt software, the cartographic models are designed for spatial distribution of 63 species of vascular plants inhabiting low mountain belt of the Tukuringra Range. Initial data for modeling were actual points of a species occurrence, data on remote sensing (multispectral space snapshots by Landsat), and a digital topographic model. It is found out that the structure of factors contributing to the model is related to species ecological amplitude. The distribution of stenotopic species is determined, mainly, by the topography, which thermal and humidity conditions of habitats are associated with. To the models for eurytopic species, variables formed on the basis of remote sensing contribute significantly, those variables encompassing the parameters of the soil-vegetable cover. In course of the obtained models analyzing, three principal groups of species are revealed that have similar distribution pattern. Species of the first group are restricted in their distribution by the slopes of the. River Zeya and River Giluy gorges. Species of the second group are associated with the southern macroslope of the range and with southern slopes of large rivers' valleys. The third group incorporates those species that are distributed over the whole territory under study.}, } @article {pmid27259333, year = {2016}, author = {Wu, Q and Liu, L and Miron, A and Klímová, B and Wan, D and Kuča, K}, title = {The antioxidant, immunomodulatory, and anti-inflammatory activities of Spirulina: an overview.}, journal = {Archives of toxicology}, volume = {90}, number = {8}, pages = {1817-1840}, doi = {10.1007/s00204-016-1744-5}, pmid = {27259333}, issn = {1432-0738}, mesh = {Animals ; Anti-Inflammatory Agents/isolation & purification/*pharmacology/therapeutic use ; Antioxidants/isolation & purification/*pharmacology/therapeutic use ; Clinical Trials as Topic ; Dietary Supplements ; Humans ; Immunologic Factors/isolation & purification/*pharmacology/therapeutic use ; Lipid Peroxidation/drug effects ; Oxidative Stress/drug effects ; Spirulina/*chemistry ; }, abstract = {Spirulina is a species of filamentous cyanobacteria that has long been used as a food supplement. In particular, Spirulina platensis and Spirulina maxima are the most important. Thanks to a high protein and vitamin content, Spirulina is used as a nutraceutical food supplement, although its other potential health benefits have attracted much attention. Oxidative stress and dysfunctional immunity cause many diseases in humans, including atherosclerosis, cardiac hypertrophy, heart failure, and hypertension. Thus, the antioxidant, immunomodulatory, and anti-inflammatory activities of these microalgae may play an important role in human health. Here, we discuss the antioxidant, immunomodulatory, and anti-inflammatory activities of Spirulina in both animals and humans, along with the underlying mechanisms. In addition, its commercial and regulatory status in different countries is discussed as well. Spirulina activates cellular antioxidant enzymes, inhibits lipid peroxidation and DNA damage, scavenges free radicals, and increases the activity of superoxide dismutase and catalase. Notably, there appears to be a threshold level above which Spirulina will taper off the antioxidant activity. Clinical trials show that Spirulina prevents skeletal muscle damage under conditions of exercise-induced oxidative stress and can stimulate the production of antibodies and up- or downregulate the expression of cytokine-encoding genes to induce immunomodulatory and anti-inflammatory responses. The molecular mechanism(s) by which Spirulina induces these activities is unclear, but phycocyanin and β-carotene are important molecules. Moreover, Spirulina effectively regulates the ERK1/2, JNK, p38, and IκB pathways. This review provides new insight into the potential therapeutic applications of Spirulina and may provide new ideas for future studies.}, } @article {pmid27257812, year = {2016}, author = {Wong-Ng, J and Melbinger, A and Celani, A and Vergassola, M}, title = {The Role of Adaptation in Bacterial Speed Races.}, journal = {PLoS computational biology}, volume = {12}, number = {6}, pages = {e1004974}, pmid = {27257812}, issn = {1553-7358}, mesh = {Adaptation, Physiological/*physiology ; Aspartic Acid ; Chemotactic Factors/metabolism ; Chemotaxis/*physiology ; Computational Biology ; Escherichia coli/*physiology ; *Models, Biological ; Serine ; }, abstract = {Evolution of biological sensory systems is driven by the need for efficient responses to environmental stimuli. A paradigm among prokaryotes is the chemotaxis system, which allows bacteria to navigate gradients of chemoattractants by biasing their run-and-tumble motion. A notable feature of chemotaxis is adaptation: after the application of a step stimulus, the bacterial running time relaxes to its pre-stimulus level. The response to the amino acid aspartate is precisely adapted whilst the response to serine is not, in spite of the same pathway processing the signals preferentially sensed by the two receptors Tar and Tsr, respectively. While the chemotaxis pathway in E. coli is well characterized, the role of adaptation, its functional significance and the ecological conditions where chemotaxis is selected, are largely unknown. Here, we investigate the role of adaptation in the climbing of gradients by E. coli. We first present theoretical arguments that highlight the mechanisms that control the efficiency of the chemotactic up-gradient motion. We discuss then the limitations of linear response theory, which motivate our subsequent experimental investigation of E. coli speed races in gradients of aspartate, serine and combinations thereof. By using microfluidic techniques, we engineer controlled gradients and demonstrate that bacterial fronts progress faster in equal-magnitude gradients of serine than aspartate. The effect is observed over an extended range of concentrations and is not due to differences in swimming velocities. We then show that adding a constant background of serine to gradients of aspartate breaks the adaptation to aspartate, which results in a sped-up progression of the fronts and directly illustrate the role of adaptation in chemotactic gradient-climbing.}, } @article {pmid27257671, year = {2016}, author = {Larkin, DJ and Jacobi, SK and Hipp, AL and Kramer, AT}, title = {Keeping All the PIECES: Phylogenetically Informed Ex Situ Conservation of Endangered Species.}, journal = {PloS one}, volume = {11}, number = {6}, pages = {e0156973}, pmid = {27257671}, issn = {1932-6203}, mesh = {Conservation of Natural Resources/methods/statistics & numerical data ; Decision Support Techniques ; Endangered Species/*statistics & numerical data ; Magnoliopsida/classification ; North America ; Phylogeny ; Plants/*classification ; }, abstract = {Ex situ conservation in germplasm and living collections is a major focus of global plant conservation strategies. Prioritizing species for ex situ collection is a necessary component of this effort for which sound strategies are needed. Phylogenetic considerations can play an important role in prioritization. Collections that are more phylogenetically diverse are likely to encompass more ecological and trait variation, and thus provide stronger conservation insurance and richer resources for future restoration efforts. However, phylogenetic criteria need to be weighed against other, potentially competing objectives. We used ex situ collection and threat rank data for North American angiosperms to investigate gaps in ex situ coverage and phylogenetic diversity of collections and to develop a flexible framework for prioritizing species across multiple objectives. We found that ex situ coverage of 18,766 North American angiosperm taxa was low with respect to the most vulnerable taxa: just 43% of vulnerable to critically imperiled taxa were in ex situ collections, far short of a year-2020 goal of 75%. In addition, species held in ex situ collections were phylogenetically clustered (P < 0.001), i.e., collections comprised less phylogenetic diversity than would be expected had species been drawn at random. These patterns support incorporating phylogenetic considerations into ex situ prioritization in a manner balanced with other criteria, such as vulnerability. To meet this need, we present the 'PIECES' index (Phylogenetically Informed Ex situ Conservation of Endangered Species). PIECES integrates phylogenetic considerations into a flexible framework for prioritizing species across competing objectives using multi-criteria decision analysis. Applying PIECES to prioritizing ex situ conservation of North American angiosperms, we show strong return on investment across multiple objectives, some of which are negatively correlated with each other. A spreadsheet-based decision support tool for North American angiosperms is provided; this tool can be customized to align with different conservation objectives.}, } @article {pmid27255409, year = {2016}, author = {Livernois, A and Hardy, K and Domaschenz, R and Papanicolaou, A and Georges, A and Sarre, SD and Rao, S and Ezaz, T and Deakin, JE}, title = {Identification of interleukin genes in Pogona vitticeps using a de novo transcriptome assembly from RNA-seq data.}, journal = {Immunogenetics}, volume = {68}, number = {9}, pages = {719-731}, pmid = {27255409}, issn = {1432-1211}, mesh = {Amino Acid Sequence ; Animals ; Computational Biology/*methods ; Gene Expression Profiling ; High-Throughput Nucleotide Sequencing/*methods ; Interleukins/*genetics ; Lizards/*genetics ; Sequence Analysis, RNA/*methods ; Sequence Homology, Amino Acid ; Software ; Transcriptome/*genetics ; }, abstract = {Interleukins are a group of cytokines with complex immunomodulatory functions that are important for regulating immunity in vertebrate species. Reptiles and mammals last shared a common ancestor more than 350 million years ago, so it is not surprising that low sequence identity has prevented divergent interleukin genes from being identified in the central bearded dragon lizard, Pogona vitticeps, in its genome assembly. To determine the complete nucleotide sequences of key interleukin genes, we constructed full-length transcripts, using the Trinity platform, from short paired-end read RNA sequences from stimulated spleen cells. De novo transcript reconstruction and analysis allowed us to identify interleukin genes that are missing from the published P. vitticeps assembly. Identification of key cytokines in P. vitticeps will provide insight into the essential molecular mechanisms and evolution of interleukin gene families and allow for characterization of the immune response in a lizard for comparison with mammals.}, } @article {pmid27253902, year = {2016}, author = {Balbinot, AD and Horta, RL and da Costa, JS and Araújo, RB and Poletto, S and Teixeira, MB}, title = {Hospitalization due to drug use did not change after a decade of the Psychiatric Reform.}, journal = {Revista de saude publica}, volume = {50}, number = {}, pages = {26}, pmid = {27253902}, issn = {1518-8787}, mesh = {Adolescent ; Brazil ; Female ; Hospitalization/*trends ; Hospitals, Psychiatric/*statistics & numerical data ; Humans ; Length of Stay ; Male ; Mental Disorders/*physiopathology ; Primary Health Care ; Sex Factors ; Substance-Related Disorders/*physiopathology ; }, abstract = {OBJECTIVE: To investigate whether the psychiatric hospitalization rates due to use of psychoactive substances and average time of hospitalization suffered any changes after the first decade of effective implementation of the psychiatric reform in Brazil.

METHODS: This article examines the evolution of hospitalizations due to disorders arising from the use of alcohol or other substances in the state of Santa Catarina, Southern Brazil, from 2000 to 2012. This is an ecological, time-series study, which uses data from admissions obtained by the Informatics Service of the Brazilian Unified Health System. Hospitalization rates by 100,000 inhabitants and average time of occupancy of beds were estimated. Coefficients of variation of these rates were estimated by Poisson Regression.

RESULTS: The total and male hospitalization rates did not vary (p = 0.056 and p = 0.244, respectively). We observed an increase of 3.0% for the female sex (p = 0.049). We did not observe any significant variation for occupancy time of beds.

CONCLUSIONS: The deployment of services triggered by the Brazilian psychiatric reform was not accompanied by a reduction of hospitalization rates or mean occupancy time of hospitalized patients during this first decade of implementation of the reform.}, } @article {pmid27251219, year = {2016}, author = {Wang, Z and Du, X}, title = {Monitoring Natural World Heritage Sites: optimization of the monitoring system in Bogda with GIS-based multi-criteria decision analysis.}, journal = {Environmental monitoring and assessment}, volume = {188}, number = {7}, pages = {384}, pmid = {27251219}, issn = {1573-2959}, mesh = {China ; *Conservation of Natural Resources ; *Decision Support Techniques ; Environmental Monitoring/*methods ; Forests ; *Geographic Information Systems ; History ; }, abstract = {Natural World Heritage Sites (NWHSs) are invaluable treasure due to the uniqueness of each site. Proper monitoring and management can guarantee their protection from multiple threats. In this study, geographic information system (GIS)-based multi-criteria decision analysis (GIS-MCDA) was used to assess criteria layers acquired from the data available in the literature. A conceptual model for determining the priority area for monitoring in Bogda, China, was created based on outstanding universal values (OUV) and expert knowledge. Weights were assigned to each layer using the analytic hierarchy process (AHP) based on group decisions, encompassing three experts: one being a heritage site expert, another a forest ranger, and the other a heritage site manager. Subsequently, evaluation layers and constraint layers were used to generate a priority map and to determine the feasibility of monitoring in Bogda. Finally, a monitoring suitability map of Bogda was obtained by referencing priority and feasibility maps.The high-priority monitoring area is located in the montane forest belt, which exhibits high biodiversity and is the main tourist area of Bogda. The northern buffer zone of Bogda comprises the concentrated feasible monitoring areas, and the area closest to roads and monitoring facilities is highly feasible for NWHS monitoring. The suitability of an area in terms of monitoring is largely determined by the monitoring priority in that particular area. The majority of planned monitoring facilities are well distributed in both suitable and less suitable areas. Analysis results indicate that the protection of Bogda will be more scientifically based due to its effective and all-around planned monitoring system proposed by the declaration text of Xinjiang Tianshan, which is the essential file submitted to World Heritage Centre to inscribe as a NWHS.}, } @article {pmid27250093, year = {2016}, author = {Yin, N and Zhang, Z and Wang, L and Qian, K}, title = {Variations in organic carbon, aggregation, and enzyme activities of gangue-fly ash-reconstructed soils with sludge and arbuscular mycorrhizal fungi during 6-year reclamation.}, journal = {Environmental science and pollution research international}, volume = {23}, number = {17}, pages = {17840-17849}, pmid = {27250093}, issn = {1614-7499}, mesh = {Biomass ; Carbon/analysis ; Coal Ash ; Environmental Restoration and Remediation/*methods ; Lolium ; Mining ; Mycorrhizae/*physiology ; Nitrogen/analysis ; Sewage ; Soil/*chemistry ; *Soil Microbiology ; Soil Pollutants/*analysis ; }, abstract = {Mining activities can cause drastic disturbances in soil properties, which adversely affect the nutrient cycling and soil environment. As a result, many efforts have been made to explore suitable reclamation strategies that can be applied to accelerate ecology restoration. In this study, we reconstructed mine soils with fly ash, gangue, sludge, planted ryegrass, and inoculated arbuscular mycorrhizal fungi (AMF) in Pangzhuang mine of Xuzhou during 2009 to 2015. The soil aggregation process, enzyme activities (i.e., invertase, urease and acid phosphatase activities), soil organic carbon (SOC) as well as other soil nutrients such as nitrogen, phosphorus, and potassium contents of the reconstructed mine soils were monitored during 6-year reclamation. The integrated application of sludge and AMF led to a promising reclamation performance of mining areas, in which soil aggregate stability, enzyme activities, SOC, and ryegrass biomass were effectively enhanced. The micro-aggregates (< 0.25 mm) decreased with the increase of macro-aggregates (> 0.25 mm) during the reclamation, indicating that macro-aggregates were gradually formed from micro-aggregates during the pedogenesis of reconstructed mine soils. The correlation analysis shows that SOC contents in aggregate fraction of 0.25∼0.5 mm were correlated with aggregate distribution and enzyme activities. Enzyme activities, however, were not significantly correlated with aggregate distribution. The outcomes from the present study could enrich our understanding on soil property changes in pedogenesis process of reconstructed mine soils, and meanwhile, the employment of sludge combined with AMF is suggested to be an effective alternative for the mine soil reclamation.}, } @article {pmid27247405, year = {2016}, author = {Bakker, KM and Martinez-Bakker, ME and Helm, B and Stevenson, TJ}, title = {Digital epidemiology reveals global childhood disease seasonality and the effects of immunization.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {113}, number = {24}, pages = {6689-6694}, pmid = {27247405}, issn = {1091-6490}, mesh = {Adolescent ; *Chickenpox/epidemiology/prevention & control/transmission ; Child ; Child, Preschool ; *Databases, Factual ; Female ; *Herpesvirus 3, Human ; Humans ; *Immunization ; Infant ; Infant, Newborn ; Male ; *Models, Biological ; *Seasons ; Viral Vaccines/*administration & dosage ; }, abstract = {Public health surveillance systems are important for tracking disease dynamics. In recent years, social and real-time digital data sources have provided new means of studying disease transmission. Such affordable and accessible data have the potential to offer new insights into disease epidemiology at national and international scales. We used the extensive information repository Google Trends to examine the digital epidemiology of a common childhood disease, chicken pox, caused by varicella zoster virus (VZV), over an 11-y period. We (i) report robust seasonal information-seeking behavior for chicken pox using Google data from 36 countries, (ii) validate Google data using clinical chicken pox cases, (iii) demonstrate that Google data can be used to identify recurrent seasonal outbreaks and forecast their magnitude and seasonal timing, and (iv) reveal that VZV immunization significantly dampened seasonal cycles in information-seeking behavior. Our findings provide strong evidence that VZV transmission is seasonal and that seasonal peaks show remarkable latitudinal variation. We attribute the dampened seasonal cycles in chicken pox information-seeking behavior to VZV vaccine-induced reduction of seasonal transmission. These data and the methodological approaches provide a way to track the global burden of childhood disease and illustrate population-level effects of immunization. The global latitudinal patterns in outbreak seasonality could direct future studies of environmental and physiological drivers of disease transmission.}, } @article {pmid27246226, year = {2016}, author = {Nadimi, M and Stefani, FO and Hijri, M}, title = {The large (134.9 kb) mitochondrial genome of the glomeromycete Funneliformis mosseae.}, journal = {Mycorrhiza}, volume = {26}, number = {7}, pages = {747-755}, pmid = {27246226}, issn = {1432-1890}, mesh = {Computational Biology ; DNA, Fungal/*genetics ; DNA, Mitochondrial/genetics ; Genome, Fungal/*genetics ; Genome, Mitochondrial/*genetics ; Glomeromycota/*genetics ; Phylogeny ; }, abstract = {Funneliformis mosseae is among the most ecologically and economically important glomeromycete species and occurs both in natural and disturbed areas in a wide range of habitats and climates. In this study, we report the sequencing of the complete mitochondrial (mt) genome of F. mosseae isolate FL299 using 454 pyrosequencing and Illumina HiSeq technologies. This mt genome is a full-length circular chromosome of 134,925 bp, placing it among the largest mitochondrial DNAs (mtDNAs) in the fungal kingdom. A comparative analysis with publically available arbuscular mycorrhizal fungal mtDNAs revealed that the mtDNA of F. mosseae FL299 contained a very large number of insertions contributing to its expansion. The gene synteny was completely reshuffled compared to previously published glomeromycotan mtDNAs and several genes were oriented in an anti-sense direction. Furthermore, the presence of different types of introns and insertions in rnl (14 introns) made this gene very distinctive in Glomeromycota. The presence of alternative genetic codes in both initiation (GUG) and termination (UGA) codons was another new feature in this mtDNA compared to previously published glomeromycotan mt genomes. The phylogenetic analysis inferred from the analysis of 14 protein mt genes confirmed the position of the Glomeromycota clade as a sister group of Mortierellomycotina. This mt genome is the largest observed so far in Glomeromycota and the first mt genome within the Funneliformis clade, providing new opportunities to better understand their evolution and to develop molecular markers.}, } @article {pmid27243207, year = {2016}, author = {Foote, AD and Vijay, N and Ávila-Arcos, MC and Baird, RW and Durban, JW and Fumagalli, M and Gibbs, RA and Hanson, MB and Korneliussen, TS and Martin, MD and Robertson, KM and Sousa, VC and Vieira, FG and Vinař, T and Wade, P and Worley, KC and Excoffier, L and Morin, PA and Gilbert, MTP and Wolf, JBW}, title = {Genome-culture coevolution promotes rapid divergence of killer whale ecotypes.}, journal = {Nature communications}, volume = {7}, number = {}, pages = {11693}, pmid = {27243207}, issn = {2041-1723}, mesh = {Adaptation, Biological/genetics ; Animals ; Biopsy ; *Ecotype ; *Evolution, Molecular ; Female ; Gene-Environment Interaction ; Genetic Drift ; *Genetic Speciation ; Genetic Variation/genetics ; Genetics, Population/methods ; Genome ; Genomics/methods ; Male ; Phylogeny ; Reproductive Isolation ; Selection, Genetic/*genetics ; Skin ; Sympatry/genetics ; Whale, Killer/*physiology ; }, abstract = {Analysing population genomic data from killer whale ecotypes, which we estimate have globally radiated within less than 250,000 years, we show that genetic structuring including the segregation of potentially functional alleles is associated with socially inherited ecological niche. Reconstruction of ancestral demographic history revealed bottlenecks during founder events, likely promoting ecological divergence and genetic drift resulting in a wide range of genome-wide differentiation between pairs of allopatric and sympatric ecotypes. Functional enrichment analyses provided evidence for regional genomic divergence associated with habitat, dietary preferences and post-zygotic reproductive isolation. Our findings are consistent with expansion of small founder groups into novel niches by an initial plastic behavioural response, perpetuated by social learning imposing an altered natural selection regime. The study constitutes an important step towards an understanding of the complex interaction between demographic history, culture, ecological adaptation and evolution at the genomic level.}, } @article {pmid27242883, year = {2016}, author = {Klisz, M and Koprowski, M and Ukalska, J and Nabais, C}, title = {Does the Genotype Have a Significant Effect on the Formation of Intra-Annual Density Fluctuations? A Case Study Using Larix decidua from Northern Poland.}, journal = {Frontiers in plant science}, volume = {7}, number = {}, pages = {691}, pmid = {27242883}, issn = {1664-462X}, abstract = {Intra-annual density fluctuations (IADFs) can imprint environmental conditions within the growing season and most of the research on IADFs has been focused on their climatic signal. However, to our knowledge, the genetic influence on the frequency and type of IADFs has not been evaluated. To understand if the genotype can affect the formation of IADFs we have used a common garden experiment using eight families of Larix decidua established in two neighboring forest stands in northern Poland. Four types of IADFs were identified using X-ray density profiles: latewood-like cells within earlywood (IADF-type E), latewood-like cells in the transition from early- to latewood (IADF type E+), earlywood-like cells within latewood (IADF-type L), and earlywood-like cells in the border zone between the previous and present annual ring (IADF-type L+). The influence of explanatory variables i.e., families, sites, and years on identified density fluctuations was analyzed using generalized estimating equations (GEE). We hypothesized that trees from different families will differ in terms of frequency and type of IADFs because each family will react to precipitation and temperature in a different way, depending on the origin of those trees. The most frequent fluctuation was E+ and L types on both sites. The most important factors in the formation of IADFs were the site and year, the last one reflecting the variable climatic conditions, with no significant effect of the family. However, the relation between the formation of IADFs and selected climate parameters was different between families. Although, our results did not give a significant effect of the genotype on the formation of IADFs, the different sensitivity to climatic parameters among different families indicate that there is a genetic influence.}, } @article {pmid27239817, year = {2016}, author = {Nsoesie, EO and Kraemer, MU and Golding, N and Pigott, DM and Brady, OJ and Moyes, CL and Johansson, MA and Gething, PW and Velayudhan, R and Khan, K and Hay, SI and Brownstein, JS}, title = {Global distribution and environmental suitability for chikungunya virus, 1952 to 2015.}, journal = {Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin}, volume = {21}, number = {20}, pages = {}, pmid = {27239817}, issn = {1560-7917}, support = {R01 LM010812/LM/NLM NIH HHS/United States ; K01 ES025438/ES/NIEHS NIH HHS/United States ; U54 GM088558/GM/NIGMS NIH HHS/United States ; /WT_/Wellcome Trust/United Kingdom ; 001/WHO_/World Health Organization/International ; }, mesh = {Aedes/*virology ; Animals ; Chikungunya Fever/prevention & control/*transmission/virology ; *Chikungunya virus ; Geography ; *Global Health ; Humans ; Insect Vectors/*virology ; Sentinel Surveillance ; }, abstract = {Chikungunya fever is an acute febrile illness caused by the chikungunya virus (CHIKV), which is transmitted to humans by Aedes mosquitoes. Although chikungunya fever is rarely fatal, patients can experience debilitating symptoms that last from months to years. Here we comprehensively assess the global distribution of chikungunya and produce high-resolution maps, using an established modelling framework that combines a comprehensive occurrence database with bespoke environmental correlates, including up-to-date Aedes distribution maps. This enables estimation of the current total population-at-risk of CHIKV transmission and identification of areas where the virus may spread to in the future. We identified 94 countries with good evidence for current CHIKV presence and a set of countries in the New and Old World with potential for future CHIKV establishment, demonstrated by high environmental suitability for transmission and in some cases previous sporadic reports. Aedes aegypti presence was identified as one of the major contributing factors to CHIKV transmission but significant geographical heterogeneity exists. We estimated 1.3 billion people are living in areas at-risk of CHIKV transmission. These maps provide a baseline for identifying areas where prevention and control efforts should be prioritised and can be used to guide estimation of the global burden of CHIKV.}, } @article {pmid27239043, year = {2016}, author = {Nnamani, MC and Ganguly, S and Erkenbrack, EM and Lynch, VJ and Mizoue, LS and Tong, Y and Darling, HL and Fuxreiter, M and Meiler, J and Wagner, GP}, title = {A Derived Allosteric Switch Underlies the Evolution of Conditional Cooperativity between HOXA11 and FOXO1.}, journal = {Cell reports}, volume = {15}, number = {10}, pages = {2097-2108}, doi = {10.1016/j.celrep.2016.04.088}, pmid = {27239043}, issn = {2211-1247}, mesh = {Allosteric Regulation ; Amino Acid Sequence ; Amino Acid Substitution ; Animals ; *Biological Evolution ; CREB-Binding Protein/chemistry/metabolism ; DNA-Activated Protein Kinase/metabolism ; Forkhead Box Protein O1/*metabolism ; HeLa Cells ; Homeodomain Proteins/chemistry/*metabolism ; Humans ; Intrinsically Disordered Proteins/chemistry ; Mice ; Models, Biological ; Models, Molecular ; Phosphorylation ; Protein Binding ; Protein Domains ; Protein Structure, Secondary ; Transcriptional Activation/genetics ; }, abstract = {Transcription factors (TFs) play multiple roles in development. Given this multifunctionality, it has been assumed that TFs are evolutionarily highly constrained. Here, we investigate the molecular mechanisms for the origin of a derived functional interaction between two TFs, HOXA11 and FOXO1. We have previously shown that the regulatory role of HOXA11 in mammalian endometrial stromal cells requires interaction with FOXO1, and that the physical interaction between these proteins evolved before their functional cooperativity. Here, we demonstrate that the derived functional cooperativity between HOXA11 and FOXO1 is due to derived allosteric regulation of HOXA11 by FOXO1. This study shows that TF function can evolve through changes affecting the functional output of a pre-existing protein complex.}, } @article {pmid27238575, year = {2017}, author = {Binder, SB and Baker, CK}, title = {Culture, local capacity, and outside aid: a community perspective on disaster response after the 2009 tsunami in American Sāmoa.}, journal = {Disasters}, volume = {41}, number = {2}, pages = {282-305}, doi = {10.1111/disa.12203}, pmid = {27238575}, issn = {1467-7717}, mesh = {American Samoa ; *Community Networks ; *Cultural Characteristics ; *Disasters ; Female ; Focus Groups ; Humans ; *International Cooperation ; Male ; Qualitative Research ; Relief Work/*organization & administration ; *Tsunamis ; }, abstract = {Research on diverse cultural contexts has indicated that aid organisations often fail to leverage local, culturally-grounded resources and capacities in disaster-affected communities. Case-study methodology was employed to explore the relationship between local and external disaster response efforts in American Sāmoa following the earthquake and tsunami on 29 September 2009 in the southern Pacific Ocean, with a specific focus on the role of culture in defining that relationship. Interview and focus group data from 37 participants, along with observational data, suggested that the local response to the event was swift and grounded in Samoan cultural systems and norms. External aid was viewed as helpful in some respects, although, on the whole, it was seen as a disruption to village hierarchies, social networks, and local response efforts. The study discusses the implications for the role of outside aid in diverse cultural contexts, and makes suggestions for improving the ecological fit of post-disaster interventions.}, } @article {pmid27235550, year = {2016}, author = {Stervander, M and Alström, P and Olsson, U and Ottosson, U and Hansson, B and Bensch, S}, title = {Multiple instances of paraphyletic species and cryptic taxa revealed by mitochondrial and nuclear RAD data for Calandrella larks (Aves: Alaudidae).}, journal = {Molecular phylogenetics and evolution}, volume = {102}, number = {}, pages = {233-245}, doi = {10.1016/j.ympev.2016.05.032}, pmid = {27235550}, issn = {1095-9513}, mesh = {Animals ; Cell Nucleus/*genetics ; Cytochromes b/chemistry/genetics/metabolism ; DNA/chemistry/isolation & purification/metabolism ; DNA, Mitochondrial/chemistry/genetics/metabolism ; Databases, Genetic ; Genetic Variation ; Mitochondria/*genetics/metabolism ; Passeriformes/*classification/genetics ; Phylogeny ; Phylogeography ; Polymorphism, Single Nucleotide ; Sequence Analysis, DNA ; }, abstract = {The avian genus Calandrella (larks) was recently suggested to be non-monophyletic, and was divided into two genera, of which Calandrella sensu stricto comprises 4-5 species in Eurasia and Africa. We analysed mitochondrial cytochrome b (cytb) and nuclear Restriction-site Associated DNA (RAD) sequences from all species, and for cytb we studied 21 of the 22 recognised subspecies, with the aim to clarify the phylogenetic relationships within the genus and to compare large-scale nuclear sequence patterns with a widely used mitochondrial marker. Cytb indicated deep splits among the currently recognised species, although it failed to support the interrelationships among most of these. It also revealed unexpected deep divergences within C. brachydactyla, C. blanfordi/C. erlangeri, C. cinerea, and C. acutirostris. It also suggested that both C. brachydactyla and C. blanfordi, as presently circumscribed, are paraphyletic. In contrast, most of the many subspecies of C. brachydactyla and C. cinerea were unsupported by cytb, although two populations of C. cinerea were found to be genetically distinct. The RAD data corroborated the cytb tree (for the smaller number of taxa analysed) and recovered strongly supported interspecific relationships. However, coalescence analyses of the RAD data, analysed in SNAPP both with and without an outgroup, received equally strong support for two conflicting topologies. We suggest that the tree rooted with an outgroup - which is not recommended for SNAPP - is more trustworthy, and suggest that the reliability of analyses performed without any outgroup species should be thoroughly evaluated. We also demonstrate that degraded museum samples can be phylogenetically informative in RAD analyses following careful bioinformatic treatment. We note that the genus Calandrella is in need of taxonomic revision.}, } @article {pmid27229931, year = {2016}, author = {Phuong, MA and Mahardika, GN and Alfaro, ME}, title = {Dietary breadth is positively correlated with venom complexity in cone snails.}, journal = {BMC genomics}, volume = {17}, number = {}, pages = {401}, pmid = {27229931}, issn = {1471-2164}, support = {S10 RR027303/RR/NCRR NIH HHS/United States ; S10 RR029668/RR/NCRR NIH HHS/United States ; }, mesh = {*Animal Feed ; Animals ; Cluster Analysis ; Computational Biology/methods ; *Conus Snail/genetics/metabolism ; Gene Expression ; Gene Expression Profiling ; High-Throughput Nucleotide Sequencing ; Peptides/genetics ; Phylogeny ; Transcriptome ; *Venoms/chemistry ; }, abstract = {BACKGROUND: Although diet is believed to be a major factor underlying the evolution of venom, few comparative studies examine both venom composition and diet across a radiation of venomous species. Cone snails within the family, Conidae, comprise more than 700 species of carnivorous marine snails that capture their prey by using a cocktail of venomous neurotoxins (conotoxins or conopeptides). Venom composition across species has been previously hypothesized to be shaped by (a) prey taxonomic class (i.e., worms, molluscs, or fish) and (b) dietary breadth. We tested these hypotheses under a comparative phylogenetic framework using ecological data from past studies in conjunction with venom duct transcriptomes sequenced from 12 phylogenetically disparate cone snail species, including 10 vermivores (worm-eating), one molluscivore, and one generalist.

RESULTS: We discovered 2223 unique conotoxin precursor peptides that encoded 1864 unique mature toxins across all species, >90 % of which are new to this study. In addition, we identified two novel gene superfamilies and 16 novel cysteine frameworks. Each species exhibited unique venom profiles, with venom composition and expression patterns among species dominated by a restricted set of gene superfamilies and mature toxins. In contrast with the dominant paradigm for interpreting Conidae venom evolution, prey taxonomic class did not predict venom composition patterns among species. We also found a significant positive relationship between dietary breadth and measures of conotoxin complexity.

CONCLUSIONS: The poor performance of prey taxonomic class in predicting venom components suggests that cone snails have either evolved species-specific expression patterns likely as a consequence of the rapid evolution of conotoxin genes, or that traditional means of categorizing prey type (i.e., worms, mollusc, or fish) and conotoxins (i.e., by gene superfamily) do not accurately encapsulate evolutionary dynamics between diet and venom composition. We also show that species with more generalized diets tend to have more complex venoms and utilize a greater number of venom genes for prey capture. Whether this increased gene diversity confers an increased capacity for evolutionary change remains to be tested. Overall, our results corroborate the key role of diet in influencing patterns of venom evolution in cone snails and other venomous radiations.}, } @article {pmid27225275, year = {2016}, author = {Liu, H and Sun, M and Du, D and Pan, H and Cheng, T and Wang, J and Zhang, Q and Gao, Y}, title = {Whole-transcriptome analysis of differentially expressed genes in the ray florets and disc florets of Chrysanthemum morifolium.}, journal = {BMC genomics}, volume = {17}, number = {}, pages = {398}, pmid = {27225275}, issn = {1471-2164}, mesh = {Chrysanthemum/genetics/*growth & development ; Flowers/genetics/growth & development ; Gene Expression Profiling/*methods ; Gene Expression Regulation, Plant ; Gene Ontology ; Gene Regulatory Networks ; Molecular Sequence Annotation ; Plant Breeding ; Plant Leaves/genetics/growth & development ; Plant Proteins/*genetics ; Sequence Analysis, RNA/*methods ; }, abstract = {BACKGROUND: Chrysanthemum morifolium is one of the most important global cut flower and pot plants, and has been cultivated worldwide. However, limited genomic resources are available and the molecular mechanisms involved in the two morphologically distinct floret developmental cycles in chrysanthemum remain unclear.

RESULTS: The transcriptomes of chrysanthemum ray florets, disc florets and leaves were sequenced using Illumina paired-end sequencing technology. In total, 16.9 G reads were assembled into 93,138 unigenes with an average length of 738 bp, of which 44,364 unigenes showed similarity to known proteins in the Swissprot or NCBI non-redundant protein databases. Additionally, 26,320, 22,304 and 13,949 unigenes were assigned to 54 gene ontology (GO) categories, 25 EuKaryotic Orthologous Groups (KOG) categories, and 280 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, respectively. A total of 1863 differentially expressed genes (DEGs) (1210 up-regulated and 653 down-regulated) were identified between ray florets and disc florets, including genes encoding transcription factors and protein kinases. GO and KEGG pathway enrichment analyses were performed on the DEGs to identify differences in the biological processes and pathways between ray florets and disc florets. The important regulatory genes controlling flower development and flower organ determination, as well as important functional genes in the anthocyanin biosynthetic pathway, were identified, of which two leucoanthocyanidin dioxygenase-encoding genes showed specific expression in ray florets. Lastly, reverse transcription quantitative PCR was conducted to validate the DEGs identified in our study.

CONCLUSIONS: Comparative transcriptome analysis revealed significant differences in patterns of gene expression and signaling pathways between ray florets and disc florets in Chrysanthemum morifolium. This study provided the first step to understanding the molecular mechanism of the differential development of ray florets and disc florets in chrysanthemum, and also provided valuable genomic resources for candidate genes applicable for the breeding of novel varieties in chrysanthemum.}, } @article {pmid27224050, year = {2016}, author = {Gove, B and Williams, LJ and Beresford, AE and Roddis, P and Campbell, C and Teuten, E and Langston, RH and Bradbury, RB}, title = {Reconciling Biodiversity Conservation and Widespread Deployment of Renewable Energy Technologies in the UK.}, journal = {PloS one}, volume = {11}, number = {5}, pages = {e0150956}, pmid = {27224050}, issn = {1932-6203}, mesh = {*Biodiversity ; *Conservation of Natural Resources ; Ecology ; *Renewable Energy ; Solar Energy ; United Kingdom ; Water Movements ; Wind ; }, abstract = {Renewable energy will potentially make an important contribution towards the dual aims of meeting carbon emission reduction targets and future energy demand. However, some technologies have considerable potential to impact on the biodiversity of the environments in which they are placed. In this study, an assessment was undertaken of the realistic deployment potential of a range of renewable energy technologies in the UK, considering constraints imposed by biodiversity conservation priorities. We focused on those energy sources that have the potential to make important energy contributions but which might conflict with biodiversity conservation objectives. These included field-scale solar, bioenergy crops, wind energy (both onshore and offshore), wave and tidal stream energy. The spatially-explicit analysis considered the potential opportunity available for each technology, at various levels of ecological risk. The resultant maps highlight the energy resource available, physical and policy constraints to deployment, and ecological sensitivity (based on the distribution of protected areas and sensitive species). If the technologies are restricted to areas which currently appear not to have significant ecological constraints, the total potential energy output from these energy sources was estimated to be in the region of 5,547 TWh/yr. This would be sufficient to meet projected energy demand in the UK, and help to achieve carbon reduction targets. However, we highlight two important caveats. First, further ecological monitoring and surveillance is required to improve understanding of wildlife distributions and therefore potential impacts of utilising these energy sources. This is likely to reduce the total energy available, especially at sea. Second, some of the technologies under investigation are currently not deployed commercially. Consequently this potential energy will only be available if continued effort is put into developing these energy sources/technologies, to enable realisation of their full potential.}, } @article {pmid27221643, year = {2016}, author = {Giannakopoulos, A and Tsokana, CN and Pervanidou, D and Papadopoulos, E and Papaspyropoulos, K and Spyrou, V and Rodi Burriel, A and Vakali, A and Hadjichristodoulou, C and Billinis, C}, title = {Environmental parameters as risk factors for human and canine Leishmania infection in Thessaly, Central Greece.}, journal = {Parasitology}, volume = {143}, number = {9}, pages = {1179-1186}, doi = {10.1017/S0031182016000378}, pmid = {27221643}, issn = {1469-8161}, mesh = {Adolescent ; Adult ; Aged ; Aged, 80 and over ; Animals ; Child ; Child, Preschool ; Climate ; Computer Simulation ; Dog Diseases/*epidemiology/parasitology ; Dogs ; *Environment ; Female ; Geographic Information Systems ; Greece/epidemiology ; Humans ; Infant ; Leishmaniasis/*epidemiology ; Male ; Middle Aged ; Models, Biological ; Population Density ; Risk Factors ; Young Adult ; }, abstract = {Thessaly, Central Greece, is an endemic area for leishmaniasis with higher incidence rate during the last years. We herein investigated the geographical distribution of human leishmaniasis cases and Leishmania infected dogs in relation to environmental parameters to identify high-risk areas. All the human leishmaniasis cases (n = 82) reported to Hellenic Centre for Disease Control and Prevention from 2007 to 2014 and 85 Leishmania polymerase chain reaction positive dogs were included in this study. To analyse the data geographical information system (GIS) together with the Ecological Niche Model (ENM) were used. The most important findings of the study were: (i) Central plain of Thessaly together with the coast line and the western and eastern lowlands were identified as high-risk geographical areas. (ii) The highest percentage of the high-risk areas was found in low altitude (<200 m above sea level) and in irrigated and cultivated agricultural areas. (iii) A total of 20% of the human settlements was found in high-risk areas. (iv) The maximum temperature of the warmest month contributes the highest per cent to define both environmental niche profiles for humans and dogs. (v) The ENM could be a useful tool for the epidemiological study of leishmaniasis. Spatial analysis may allow the design of entomological studies and identify target population in order to implement preventive measures.}, } @article {pmid27221127, year = {2016}, author = {Mandic, S and Williams, J and Moore, A and Hopkins, D and Flaherty, C and Wilson, G and García Bengoechea, E and Spence, JC}, title = {Built Environment and Active Transport to School (BEATS) Study: protocol for a cross-sectional study.}, journal = {BMJ open}, volume = {6}, number = {5}, pages = {e011196}, pmid = {27221127}, issn = {2044-6055}, mesh = {Accelerometry ; Adolescent ; Anthropometry ; *Bicycling ; Body Weight ; Cross-Sectional Studies ; *Environment Design ; Faculty ; Female ; Focus Groups ; Geographic Information Systems ; Geographic Mapping ; Humans ; Interviews as Topic ; Male ; New Zealand ; Parents/psychology ; Perception ; Research Design ; Residence Characteristics ; Safety ; Schools/organization & administration ; Students/psychology ; Surveys and Questionnaires ; Transportation/*methods ; *Walking ; }, abstract = {INTRODUCTION: Active transport to school (ATS) is a convenient way to increase physical activity and undertake an environmentally sustainable travel practice. The Built Environment and Active Transport to School (BEATS) Study examines ATS in adolescents in Dunedin, New Zealand, using ecological models for active transport that account for individual, social, environmental and policy factors. The study objectives are to: (1) understand the reasons behind adolescents and their parents' choice of transport mode to school; (2) examine the interaction between the transport choices, built environment, physical activity and weight status in adolescents; and (3) identify policies that promote or hinder ATS in adolescents.

METHODS AND ANALYSIS: The study will use a mixed-method approach incorporating both quantitative (surveys, anthropometry, accelerometers, Geographic Information System (GIS) analysis, mapping) and qualitative methods (focus groups, interviews) to gather data from students, parents, teachers and school principals. The core data will include accelerometer-measured physical activity, anthropometry, GIS measures of the built environment and the use of maps indicating route to school (students)/work (parents) and perceived safe/unsafe areas along the route. To provide comprehensive data for understanding how to change the infrastructure to support ATS, the study will also examine complementary variables such as individual, family and social factors, including student and parental perceptions of walking and cycling to school, parental perceptions of different modes of transport to school, perceptions of the neighbourhood environment, route to school (students)/work (parents), perceptions of driving, use of information communication technology, reasons for choosing a particular school and student and parental physical activity habits, screen time and weight status. The study has achieved a 100% school recruitment rate (12 secondary schools).

ETHICS AND DISSEMINATION: The study has been approved by the University of Otago Ethics Committee. The results will be actively disseminated through reports and presentations to stakeholders, symposiums and scientific publications.}, } @article {pmid27220098, year = {2016}, author = {Klaus, VH and Hölzel, N and Prati, D and Schmitt, B and Schöning, I and Schrumpf, M and Solly, EF and Hänsel, F and Fischer, M and Kleinebecker, T}, title = {Plant diversity moderates drought stress in grasslands: Implications from a large real-world study on (13)C natural abundances.}, journal = {The Science of the total environment}, volume = {566-567}, number = {}, pages = {215-222}, doi = {10.1016/j.scitotenv.2016.05.008}, pmid = {27220098}, issn = {1879-1026}, mesh = {*Agriculture ; *Biodiversity ; *Droughts ; Fertilizers/*analysis ; Germany ; *Grassland ; *Plants ; }, abstract = {Land-use change and intensification play a key role in the current biodiversity crisis. The resulting species loss can have severe effects on ecosystem functions and services, thereby increasing ecosystem vulnerability to climate change. We explored whether land-use intensification (i.e. fertilization intensity), plant diversity and other potentially confounding environmental factors may be significantly related to water use (i.e. drought stress) of grassland plants. Drought stress was assessed using δ(13)C abundances in aboveground plant biomass of 150 grassland plots across a gradient of land-use intensity. Under water shortage, plants are forced to increasingly take up the heavier (13)C due to closing stomata leading to an enrichment of (13)C in biomass. Plants were sampled at the community level and for single species, which belong to three different functional groups (one grass, one herb, two legumes). Results show that plant diversity was significantly related to the δ(13)C signal in community, grass and legume biomass indicating that drought stress was lower under higher diversity, although this relation was not significant for the herb species under study. Fertilization, in turn, mostly increased drought stress as indicated by more positive δ(13)C values. This effect was mostly indirect by decreasing plant diversity. In line with these results, we found similar patterns in the δ(13)C signal of the organic matter in the topsoil, indicating a long history of these processes. Our study provided strong indication for a positive biodiversity-ecosystem functioning relationship with reduced drought stress at higher plant diversity. However, it also underlined a negative reinforcing situation: as land-use intensification decreases plant diversity in grasslands, this might subsequently increases drought sensitivity. Vice-versa, enhancing plant diversity in species-poor agricultural grasslands may moderate negative effects of future climate change.}, } @article {pmid27208996, year = {2016}, author = {Pezdevšek Malovrh, Š and Kurttila, M and Hujala, T and Kärkkäinen, L and Leban, V and Lindstad, BH and Peters, DM and Rhodius, R and Solberg, B and Wirth, K and Zadnik Stirn, L and Krč, J}, title = {Decision support framework for evaluating the operational environment of forest bioenergy production and use: Case of four European countries.}, journal = {Journal of environmental management}, volume = {180}, number = {}, pages = {68-81}, doi = {10.1016/j.jenvman.2016.05.021}, pmid = {27208996}, issn = {1095-8630}, mesh = {*Biofuels ; Decision Making ; *Decision Support Techniques ; Environmental Policy ; Finland ; Forestry/*methods ; *Forests ; Germany ; Humans ; Norway ; Policy Making ; Slovenia ; }, abstract = {Complex policy-making situations around bioenergy production and use require examination of the operational environment of the society and a participatory approach. This paper presents and demonstrates a three-phase decision-making framework for analysing the operational environment of strategies related to increased forest bioenergy targets. The framework is based on SWOT (strengths, weaknesses, opportunities and threats) analysis and the Simple Multi-Attribute Rating Technique (SMART). Stakeholders of four case countries (Finland, Germany, Norway and Slovenia) defined the factors that affect the operational environments, classified in four pre-set categories (Forest Characteristics and Management, Policy Framework, Technology and Science, and Consumers and Society). The stakeholders participated in weighting of SWOT items for two future scenarios with SMART technique. The first scenario reflected the current 2020 targets (the Business-as-Usual scenario), and the second scenario contained a further increase in the targets (the Increase scenario). This framework can be applied to various problems of environmental management and also to other fields where public decision-making is combined with stakeholders' engagement. The case results show that the greatest differences between the scenarios appear in Germany, indicating a notably negative outlook for the Increase scenario, while the smallest differences were found in Finland. Policy Framework was a highly rated category across the countries, mainly with respect to weaknesses and threats. Intensified forest bioenergy harvesting and utilization has potentially wide country-specific impacts which need to be anticipated and considered in national policies and public dialogue.}, } @article {pmid27206631, year = {2016}, author = {Wysocki, WP and Ruiz-Sanchez, E and Yin, Y and Duvall, MR}, title = {The floral transcriptomes of four bamboo species (Bambusoideae; Poaceae): support for common ancestry among woody bamboos.}, journal = {BMC genomics}, volume = {17}, number = {}, pages = {384}, pmid = {27206631}, issn = {1471-2164}, mesh = {Computational Biology/methods ; Evolution, Molecular ; Gene Expression Profiling ; Gene Expression Regulation, Plant ; High-Throughput Nucleotide Sequencing ; Phylogeny ; Poaceae/classification/*genetics ; *Transcriptome ; }, abstract = {BACKGROUND: Next-generation sequencing now allows for total RNA extracts to be sequenced in non-model organisms such as bamboos, an economically and ecologically important group of grasses. Bamboos are divided into three lineages, two of which are woody perennials with bisexual flowers, which undergo gregarious monocarpy. The third lineage, which are herbaceous perennials, possesses unisexual flowers that undergo annual flowering events.

RESULTS: Transcriptomes were assembled using both reference-based and de novo methods. These two methods were tested by characterizing transcriptome content using sequence alignment to previously characterized reference proteomes and by identifying Pfam domains. Because of the striking differences in floral morphology and phenology between the herbaceous and woody bamboo lineages, MADS-box genes, transcription factors that control floral development and timing, were characterized and analyzed in this study. Transcripts were identified using phylogenetic methods and categorized as A, B, C, D or E-class genes, which control floral development, or SOC or SVP-like genes, which control the timing of flowering events. Putative nuclear orthologues were also identified in bamboos to use as phylogenetic markers.

CONCLUSIONS: Instances of gene copies exhibiting topological patterns that correspond to shared phenotypes were observed in several gene families including floral development and timing genes. Alignments and phylogenetic trees were generated for 3,878 genes and for all genes in a concatenated analysis. Both the concatenated analysis and those of 2,412 separate gene trees supported monophyly among the woody bamboos, which is incongruent with previous phylogenetic studies using plastid markers.}, } @article {pmid27206349, year = {2016}, author = {Luo, Y and Hu, JY and Li, L and Luo, YL and Wang, PF and Song, BH}, title = {Genome-wide analysis of gene expression reveals gene regulatory networks that regulate chasmogamous and cleistogamous flowering in Pseudostellaria heterophylla (Caryophyllaceae).}, journal = {BMC genomics}, volume = {17}, number = {}, pages = {382}, pmid = {27206349}, issn = {1471-2164}, mesh = {Caryophyllaceae/*genetics ; Computational Biology/methods ; Environment ; Flowers/*genetics ; Gene Expression Profiling ; *Gene Expression Regulation, Plant ; *Gene Regulatory Networks ; *Genome-Wide Association Study ; High-Throughput Nucleotide Sequencing ; Models, Biological ; Molecular Sequence Annotation ; Phenotype ; Reproducibility of Results ; Transcriptome ; }, abstract = {BACKGROUND: Pseudostellaria heterophylla produces both closed (cleistogamous, CL) and open (chasmogamous, CH) flowers on the same individual but in different seasons. The production of CH and CL flowers might be in response to environmental changes. To better understand the molecular mechanisms of CH and CL flowering, we compared the transcriptome of the two types of flowers to examine differential gene expression patterns, and to identify gene regulatory networks that control CH and CL flowering.

RESULTS: Using RNA sequencing, we identified homologues of 428 Arabidopsis genes involved in regulating flowering processes and estimated the differential gene expression patterns between CH and CL flowers. Some of these genes involved in gene regulatory networks of flowering processes showed significantly differential expression patterns between CH and CL flowers. In addition, we identified another 396 differentially expressed transcripts between CH and CL flowers. Some are involved in environmental stress responses and flavonoid biosynthesis.

CONCLUSIONS: We propose how the differential expression of key members of three gene regulatory modules may explain CH and CL flowering. Future research is needed to investigate how the environment impinges on these flowering pathways to regulate CH and CL flowering in P. heterophylla.}, } @article {pmid27199028, year = {2016}, author = {Malapi-Wight, M and Demers, JE and Veltri, D and Marra, RE and Crouch, JA}, title = {LAMP Detection Assays for Boxwood Blight Pathogens: A Comparative Genomics Approach.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {26140}, pmid = {27199028}, issn = {2045-2322}, mesh = {Ascomycota/classification/genetics/*isolation & purification ; Buxus/*microbiology ; Computational Biology ; Genomics ; Nucleic Acid Amplification Techniques/*methods ; Plant Diseases/*microbiology ; Sensitivity and Specificity ; }, abstract = {Rapid and accurate molecular diagnostic tools are critical to efforts to minimize the impact and spread of emergent pathogens. The identification of diagnostic markers for novel pathogens presents several challenges, especially in the absence of information about population diversity and where genetic resources are limited. The objective of this study was to use comparative genomics datasets to find unique target regions suitable for the diagnosis of two fungal species causing a newly emergent blight disease of boxwood. Candidate marker regions for loop-mediated isothermal amplification (LAMP) assays were identified from draft genomes of Calonectria henricotiae and C. pseudonaviculata, as well as three related species not associated with this disease. To increase the probability of identifying unique targets, we used three approaches to mine genome datasets, based on (i) unique regions, (ii) polymorphisms, and (iii) presence/absence of regions across datasets. From a pool of candidate markers, we demonstrate LAMP assay specificity by testing related fungal species, common boxwood pathogens, and environmental samples containing 445 diverse fungal taxa. This comparative-genomics-based approach to the development of LAMP diagnostic assays is the first of its kind for fungi and could be easily applied to diagnostic marker development for other newly emergent plant pathogens.}, } @article {pmid27196065, year = {2016}, author = {Díez, B and Nylander, JA and Ininbergs, K and Dupont, CL and Allen, AE and Yooseph, S and Rusch, DB and Bergman, B}, title = {Metagenomic Analysis of the Indian Ocean Picocyanobacterial Community: Structure, Potential Function and Evolution.}, journal = {PloS one}, volume = {11}, number = {5}, pages = {e0155757}, pmid = {27196065}, issn = {1932-6203}, mesh = {Biological Evolution ; Chlorophyll/chemistry ; Chlorophyll A ; Cyanobacteria/*genetics ; Ecosystem ; Genome, Bacterial ; Indian Ocean ; Likelihood Functions ; *Metagenome ; Metagenomics ; Phycobilisomes/genetics ; Phylogeny ; Prochlorococcus/*genetics ; Seawater/microbiology ; Synechococcus/*genetics ; Temperature ; }, abstract = {Unicellular cyanobacteria are ubiquitous photoautotrophic microbes that contribute substantially to global primary production. Picocyanobacteria such as Synechococcus and Prochlorococcus depend on chlorophyll a-binding protein complexes to capture light energy. In addition, Synechococcus has accessory pigments organized into phycobilisomes, and Prochlorococcus contains chlorophyll b. Across a surface water transect spanning the sparsely studied tropical Indian Ocean, we examined Synechococcus and Prochlorococcus occurrence, taxonomy and habitat preference in an evolutionary context. Shotgun sequencing of size fractionated microbial communities from 0.1 μm to 20 μm and subsequent phylogenetic analysis indicated that cyanobacteria account for up to 15% of annotated reads, with the genera Prochlorococcus and Synechococcus comprising 90% of the cyanobacterial reads, even in the largest size fraction (3.0-20 mm). Phylogenetic analyses of cyanobacterial light-harvesting genes (chl-binding pcb/isiA, allophycocyanin (apcAB), phycocyanin (cpcAB) and phycoerythin (cpeAB)) mostly identified picocyanobacteria clades comprised of overlapping sequences obtained from Indian Ocean, Atlantic and/or Pacific Oceans samples. Habitat reconstructions coupled with phylogenetic analysis of the Indian Ocean samples suggested that large Synechococcus-like ancestors in coastal waters expanded their ecological niche towards open oligotrophic waters in the Indian Ocean through lineage diversification and associated streamlining of genomes (e.g. loss of phycobilisomes and acquisition of Chl b); resulting in contemporary small celled Prochlorococcus. Comparative metagenomic analysis with picocyanobacteria populations in other oceans suggests that this evolutionary scenario may be globally important.}, } @article {pmid27195106, year = {2016}, author = {Bissett, A and Fitzgerald, A and Court, L and Meintjes, T and Mele, PM and Reith, F and Dennis, PG and Breed, MF and Brown, B and Brown, MV and Brugger, J and Byrne, M and Caddy-Retalic, S and Carmody, B and Coates, DJ and Correa, C and Ferrari, BC and Gupta, VV and Hamonts, K and Haslem, A and Hugenholtz, P and Karan, M and Koval, J and Lowe, AJ and Macdonald, S and McGrath, L and Martin, D and Morgan, M and North, KI and Paungfoo-Lonhienne, C and Pendall, E and Phillips, L and Pirzl, R and Powell, JR and Ragan, MA and Schmidt, S and Seymour, N and Snape, I and Stephen, JR and Stevens, M and Tinning, M and Williams, K and Yeoh, YK and Zammit, CM and Young, A}, title = {Introducing BASE: the Biomes of Australian Soil Environments soil microbial diversity database.}, journal = {GigaScience}, volume = {5}, number = {}, pages = {21}, pmid = {27195106}, issn = {2047-217X}, mesh = {Archaea/classification/genetics ; Australia ; Bacteria/classification/genetics ; Biodiversity ; *Databases, Factual ; Fungi/classification/genetics ; Metagenomics ; Phylogeny ; Sequence Analysis, DNA/*methods ; *Soil Microbiology ; }, abstract = {BACKGROUND: Microbial inhabitants of soils are important to ecosystem and planetary functions, yet there are large gaps in our knowledge of their diversity and ecology. The 'Biomes of Australian Soil Environments' (BASE) project has generated a database of microbial diversity with associated metadata across extensive environmental gradients at continental scale. As the characterisation of microbes rapidly expands, the BASE database provides an evolving platform for interrogating and integrating microbial diversity and function.

FINDINGS: BASE currently provides amplicon sequences and associated contextual data for over 900 sites encompassing all Australian states and territories, a wide variety of bioregions, vegetation and land-use types. Amplicons target bacteria, archaea and general and fungal-specific eukaryotes. The growing database will soon include metagenomics data. Data are provided in both raw sequence (FASTQ) and analysed OTU table formats and are accessed via the project's data portal, which provides a user-friendly search tool to quickly identify samples of interest. Processed data can be visually interrogated and intersected with other Australian diversity and environmental data using tools developed by the 'Atlas of Living Australia'.

CONCLUSIONS: Developed within an open data framework, the BASE project is the first Australian soil microbial diversity database. The database will grow and link to other global efforts to explore microbial, plant, animal, and marine biodiversity. Its design and open access nature ensures that BASE will evolve as a valuable tool for documenting an often overlooked component of biodiversity and the many microbe-driven processes that are essential to sustain soil function and ecosystem services.}, } @article {pmid27194808, year = {2016}, author = {Song, H and Yu, ZL and Sun, LN and Xue, DX and Zhang, T and Wang, HY}, title = {Transcriptomic Analysis of Differentially Expressed Genes During Larval Development of Rapana venosa by Digital Gene Expression Profiling.}, journal = {G3 (Bethesda, Md.)}, volume = {6}, number = {7}, pages = {2181-2193}, pmid = {27194808}, issn = {2160-1836}, mesh = {Animals ; Apoptosis ; Digestive System/growth & development/metabolism ; Gastropoda/*genetics/growth & development ; Gene Expression Profiling ; *Gene Expression Regulation, Developmental ; *Gene Library ; Gene Ontology ; High-Throughput Nucleotide Sequencing ; Immune System/growth & development/metabolism ; Larva/*genetics/growth & development ; Molecular Sequence Annotation ; Nervous System/growth & development/metabolism ; Shellfish ; *Transcriptome ; }, abstract = {During the life cycle of shellfish, larval development, especially metamorphosis, has a vital influence on the dynamics, distribution, and recruitment of natural populations, as well as seed breeding. Rapana venosa, a carnivorous gastropod, is an important commercial shellfish in China, and is an ecological invader in the United States, Argentina, and France. However, information about the mechanism of its early development is still limited, because research in this area has long suffered from a lack of genomic resources. In this study, 15 digital gene expression (DGE) libraries from five developmental stages of R. venosa were constructed and sequenced on the IIIumina Hi-Sequation 2500 platform. Bioinformaticsanalysis identified numerous differentially and specifically expressed genes, which revealed that genes associated with growth, nervous system, digestive system, immune system, and apoptosis participate in important developmental processes. The functional analysis of differentially expressed genes was further implemented by gene ontology, and Kyoto encyclopedia of genes and genomes enrichment. DGE profiling provided a general picture of the transcriptomic activities during the early development of R. venosa, which may provide interesting hints for further study. Our data represent the first comparative transcriptomic information available for the early development of R. venosa, which is a prerequisite for a better understanding of the physiological traits controlling development.}, } @article {pmid27191204, year = {2016}, author = {Vansteelandt, K and Verbeke, G}, title = {A Mixed Model to Disentangle Variance and Serial Autocorrelation in Affective Instability Using Ecological Momentary Assessment Data.}, journal = {Multivariate behavioral research}, volume = {51}, number = {4}, pages = {446-465}, doi = {10.1080/00273171.2016.1159177}, pmid = {27191204}, issn = {1532-7906}, mesh = {*Affect ; *Analysis of Variance ; Anorexia Nervosa/diagnosis/psychology ; Binge-Eating Disorder/diagnosis/psychology ; Bulimia Nervosa/diagnosis/psychology ; *Data Interpretation, Statistical ; Datasets as Topic ; *Ecological Momentary Assessment ; Humans ; *Linear Models ; Time Factors ; }, abstract = {Affective instability, the tendency to experience emotions that fluctuate frequently and intensively over time, is a core feature of several mental disorders including borderline personality disorder. Currently, affect is often measured with Ecological Momentary Assessment protocols, which yield the possibility to quantify the instability of affect over time. A number of linear mixed models are proposed to examine (diagnostic) group differences in affective instability. The models contribute to the existing literature by estimating simultaneously both the variance and serial dependency component of affective instability when observations are unequally spaced in time with the serial autocorrelation (or emotional inertia) declining as a function of the time interval between observations. In addition, the models can eliminate systematic trends, take between subject differences into account and test for (diagnostic) group differences in serial autocorrelation, short-term as well as long-term affective variability. The usefulness of the models is illustrated in a study on diagnostic group differences in affective instability in the domain of eating disorders. Limitations of the model are that they pertain to group (and not individual) differences and do not focus explicitly on circadian rhythms or cycles in affect.}, } @article {pmid27189567, year = {2016}, author = {Wisecaver, JH and Alexander, WG and King, SB and Hittinger, CT and Rokas, A}, title = {Dynamic Evolution of Nitric Oxide Detoxifying Flavohemoglobins, a Family of Single-Protein Metabolic Modules in Bacteria and Eukaryotes.}, journal = {Molecular biology and evolution}, volume = {33}, number = {8}, pages = {1979-1987}, doi = {10.1093/molbev/msw073}, pmid = {27189567}, issn = {1537-1719}, mesh = {Adaptation, Biological/genetics ; Amino Acid Sequence ; Bacteria/*genetics/*metabolism ; Bacterial Proteins/*genetics/*metabolism ; Biological Evolution ; Computational Biology ; Databases, Nucleic Acid ; Dihydropteridine Reductase/genetics/metabolism ; Escherichia coli Proteins/genetics/metabolism ; Eukaryota/*genetics/*metabolism ; Evolution, Molecular ; Fungi/genetics ; Gene Duplication ; Gene Transfer, Horizontal ; Hemeproteins/*genetics/*metabolism ; NADH, NADPH Oxidoreductases/genetics/metabolism ; Nitric Oxide/*metabolism ; Phylogeny ; }, abstract = {Due to their functional independence, proteins that comprise standalone metabolic units, which we name single-protein metabolic modules, may be particularly prone to gene duplication (GD) and horizontal gene transfer (HGT). Flavohemoglobins (flavoHbs) are prime examples of single-protein metabolic modules, detoxifying nitric oxide (NO), a ubiquitous toxin whose antimicrobial properties many life forms exploit, to nitrate, a common source of nitrogen for organisms. FlavoHbs appear widespread in bacteria and have been identified in a handful of microbial eukaryotes, but how the distribution of this ecologically and biomedically important protein family evolved remains unknown. Reconstruction of the evolutionary history of 3,318 flavoHb protein sequences covering the family's known diversity showed evidence of recurrent HGT at multiple evolutionary scales including intrabacterial HGT, as well as HGT from bacteria to eukaryotes. One of the most striking examples of HGT is the acquisition of a flavoHb by the dandruff- and eczema-causing fungus Malassezia from Corynebacterium Actinobacteria, a transfer that growth experiments show is capable of mediating NO resistance in fungi. Other flavoHbs arose via GD; for example, many filamentous fungi possess two flavoHbs that are differentially targeted to the cytosol and mitochondria, likely conferring protection against external and internal sources of NO, respectively. Because single-protein metabolic modules such as flavoHb function independently, readily undergo GD and HGT, and are frequently involved in organismal defense and competition, we suggest that they represent "plug-and-play" proteins for ecological arms races.}, } @article {pmid27189561, year = {2016}, author = {Robinson, O and Dylus, D and Dessimoz, C}, title = {Phylo.io: Interactive Viewing and Comparison of Large Phylogenetic Trees on the Web.}, journal = {Molecular biology and evolution}, volume = {33}, number = {8}, pages = {2163-2166}, pmid = {27189561}, issn = {1537-1719}, support = {BB/M015009/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Biological Evolution ; Computational Biology/*methods ; Computer Graphics ; Evolution, Molecular ; *Internet ; Phylogeny ; Software ; }, abstract = {Phylogenetic trees are pervasively used to depict evolutionary relationships. Increasingly, researchers need to visualize large trees and compare multiple large trees inferred for the same set of taxa (reflecting uncertainty in the tree inference or genuine discordance among the loci analyzed). Existing tree visualization tools are however not well suited to these tasks. In particular, side-by-side comparison of trees can prove challenging beyond a few dozen taxa. Here, we introduce Phylo.io, a web application to visualize and compare phylogenetic trees side-by-side. Its distinctive features are: highlighting of similarities and differences between two trees, automatic identification of the best matching rooting and leaf order, scalability to large trees, high usability, multiplatform support via standard HTML5 implementation, and possibility to store and share visualizations. The tool can be freely accessed at http://phylo.io and can easily be embedded in other web servers. The code for the associated JavaScript library is available at https://github.com/DessimozLab/phylo-io under an MIT open source license.}, } @article {pmid27189481, year = {2016}, author = {Pasquier, J and Cabau, C and Nguyen, T and Jouanno, E and Severac, D and Braasch, I and Journot, L and Pontarotti, P and Klopp, C and Postlethwait, JH and Guiguen, Y and Bobe, J}, title = {Gene evolution and gene expression after whole genome duplication in fish: the PhyloFish database.}, journal = {BMC genomics}, volume = {17}, number = {}, pages = {368}, pmid = {27189481}, issn = {1471-2164}, support = {R01 OD011116/OD/NIH HHS/United States ; R24 OD011199/OD/NIH HHS/United States ; }, mesh = {Animals ; Computational Biology/methods ; *Databases, Nucleic Acid ; *Evolution, Molecular ; Fishes/classification/*genetics ; *Gene Duplication ; *Gene Expression ; Gene Expression Profiling ; *Genome ; Phylogeny ; Transcriptome ; Web Browser ; }, abstract = {With more than 30,000 species, ray-finned fish represent approximately half of vertebrates. The evolution of ray-finned fish was impacted by several whole genome duplication (WGD) events including a teleost-specific WGD event (TGD) that occurred at the root of the teleost lineage about 350 million years ago (Mya) and more recent WGD events in salmonids, carps, suckers and others. In plants and animals, WGD events are associated with adaptive radiations and evolutionary innovations. WGD-spurred innovation may be especially relevant in the case of teleost fish, which colonized a wide diversity of habitats on earth, including many extreme environments. Fish biodiversity, the use of fish models for human medicine and ecological studies, and the importance of fish in human nutrition, fuel an important need for the characterization of gene expression repertoires and corresponding evolutionary histories of ray-finned fish genes. To this aim, we performed transcriptome analyses and developed the PhyloFish database to provide (i) de novo assembled gene repertoires in 23 different ray-finned fish species including two holosteans (i.e. a group that diverged from teleosts before TGD) and 21 teleosts (including six salmonids), and (ii) gene expression levels in ten different tissues and organs (and embryos for many) in the same species. This resource was generated using a common deep RNA sequencing protocol to obtain the most exhaustive gene repertoire possible in each species that allows between-species comparisons to study the evolution of gene expression in different lineages. The PhyloFish database described here can be accessed and searched using RNAbrowse, a simple and efficient solution to give access to RNA-seq de novo assembled transcripts.}, } @article {pmid27187689, year = {2016}, author = {Morgan-Richards, M and Hills, SF and Biggs, PJ and Trewick, SA}, title = {Sticky Genomes: Using NGS Evidence to Test Hybrid Speciation Hypotheses.}, journal = {PloS one}, volume = {11}, number = {5}, pages = {e0154911}, pmid = {27187689}, issn = {1932-6203}, mesh = {Animals ; Biological Evolution ; Cluster Analysis ; Computational Biology/methods ; *Genome, Insect ; *Genomics ; *High-Throughput Nucleotide Sequencing ; *Hybridization, Genetic ; Insecta/*genetics ; Polymorphism, Single Nucleotide ; }, abstract = {Hypotheses of hybrid origin are common. Here we use next generation sequencing to test a hybrid hypothesis for a non-model insect with a large genome. We compared a putative hybrid triploid stick insect species (Acanthoxyla geisovii) with its putative paternal diploid taxon (Clitarchus hookeri), a relationship that provides clear predictions for the relative genetic diversity within each genome. The parental taxon is expected to have comparatively low allelic diversity that is nested within the diversity of the hybrid daughter genome. The scale of genome sequencing required was conveniently achieved by extracting mRNA and sequencing cDNA to examine expressed allelic diversity. This allowed us to test hybrid-progenitor relationships among non-model organisms with large genomes and different ploidy levels. Examination of thousands of independent loci avoids potential problems produced by the silencing of parts of one or other of the parental genomes, a phenomenon sometimes associated with the process of stabilisation of a hybrid genome. Transcript assembles were assessed for evidence of paralogs and/or alternative splice variants before proceeding. Comparison of transcript assemblies was not an appropriate measure of genetic variability, but by mapping reads back to clusters derived from each species we determined levels of allelic diversity. We found greater cDNA sequence diversity among alleles in the putative hybrid species (Acanthoxyla geisovii) than the non-hybrid. The allelic diversity within the putative paternal species (Clitachus hookeri) nested within the hybrid-daughter genome, supports the current view of a hybrid-progenitor relationship for these stick insect species. Next generation sequencing technology provides opportunities for testing evolutionary hypotheses with non-model organisms, including, as here, genomes that are large due to polyploidy.}, } @article {pmid27185348, year = {2016}, author = {Roberts, WM and Fealy, RM and Doody, DG and Jordan, P and Daly, K}, title = {Estimating the effects of land use at different scales on high ecological status in Irish rivers.}, journal = {The Science of the total environment}, volume = {572}, number = {}, pages = {618-625}, doi = {10.1016/j.scitotenv.2016.04.011}, pmid = {27185348}, issn = {1879-1026}, mesh = {Agriculture ; Ecosystem ; Environment ; Environmental Monitoring/*methods ; Forests ; Geographic Information Systems ; Grassland ; Ireland ; Rain ; *Rivers ; }, abstract = {High ecological status at river sites is an indicator of minimal disturbance from anthropogenic activities and the presence of ecologically important species and communities. However, a lack of clarity on what factors cause sites to lose high ecological status is limiting the ability to maintain the quality of these sites. Examination of ecological status records at 508 high status river sites throughout the Republic of Ireland revealed that 337 had fallen below high status at some point between 2001 and 2012 due to changes in invertebrate communities. A geographical information system was used to characterise land use and environmental variables in the catchment, riparian and reach areas upstream of the sites. The relationships between these variables at the three spatial scales and whether or not river sites had maintained high ecological status were then estimated by multiple logistic regression and propensity modelling. The results indicated that grassland at either catchment or riparian scales had a greater negative impact on high ecological status than at the reach scale. This effect appeared to be strongest for upland, steeply sloping rivers that are subject to high rainfall, possibly due to the presence of sensitive biota and/or a greater potential for erosion. These results highlighted the need for better management of grassland upstream of the high status sites, with a focus on river alterations and critical source areas of nutrients, sediments and pesticides that are hydrologically connected to the river. Sustainable management practices and land use planning in those areas will need to be considered carefully if the aim of maintaining high ecological status at river sites is to be achieved.}, } @article {pmid27183224, year = {2016}, author = {Portman, ME and Shabtay-Yanai, A and Zanzuri, A}, title = {Incorporation of Socio-Economic Features' Ranking in Multicriteria Analysis Based on Ecosystem Services for Marine Protected Area Planning.}, journal = {PloS one}, volume = {11}, number = {5}, pages = {e0154473}, pmid = {27183224}, issn = {1932-6203}, mesh = {Algorithms ; *City Planning ; *Conservation of Natural Resources ; *Decision Support Techniques ; *Ecosystem ; Environment ; Geography ; Humans ; *Marine Biology ; }, abstract = {Developed decades ago for spatial choice problems related to zoning in the urban planning field, multicriteria analysis (MCA) has more recently been applied to environmental conflicts and presented in several documented cases for the creation of protected area management plans. Its application is considered here for the development of zoning as part of a proposed marine protected area management plan. The case study incorporates specially-explicit conservation features while considering stakeholder preferences, expert opinion and characteristics of data quality. It involves the weighting of criteria using a modified analytical hierarchy process. Experts ranked physical attributes which include socio-economically valued physical features. The parameters used for the ranking of (physical) attributes important for socio-economic reasons are derived from the field of ecosystem services assessment. Inclusion of these feature values results in protection that emphasizes those areas closest to shore, most likely because of accessibility and familiarity parameters and because of data biases. Therefore, other spatial conservation prioritization methods should be considered to supplement the MCA and efforts should be made to improve data about ecosystem service values farther from shore. Otherwise, the MCA method allows incorporation of expert and stakeholder preferences and ecosystem services values while maintaining the advantages of simplicity and clarity.}, } @article {pmid27182792, year = {2016}, author = {Close, ME and Abraham, P and Humphries, B and Lilburne, L and Cuthill, T and Wilson, S}, title = {Predicting groundwater redox status on a regional scale using linear discriminant analysis.}, journal = {Journal of contaminant hydrology}, volume = {191}, number = {}, pages = {19-32}, doi = {10.1016/j.jconhyd.2016.04.006}, pmid = {27182792}, issn = {1873-6009}, mesh = {Denitrification ; Discriminant Analysis ; Environmental Monitoring/methods ; Geographic Information Systems ; Geology ; Groundwater/*chemistry ; Hydrology/*methods ; Models, Theoretical ; New Zealand ; Nitrates/analysis/chemistry ; Oxidation-Reduction ; Soil/chemistry ; Water Wells ; }, abstract = {Reducing conditions are necessary for denitrification, thus the groundwater redox status can be used to identify subsurface zones where potentially significant nitrate reduction can occur. Groundwater chemistry in two contrasting regions of New Zealand was classified with respect to redox status and related to mappable factors, such as geology, topography and soil characteristics using discriminant analysis. Redox assignment was carried out for water sampled from 568 and 2223 wells in the Waikato and Canterbury regions, respectively. For the Waikato region 64% of wells sampled indicated oxic conditions in the water; 18% indicated reduced conditions and 18% had attributes indicating both reducing and oxic conditions termed "mixed". In Canterbury 84% of wells indicated oxic conditions; 10% were mixed; and only 5% indicated reduced conditions. The analysis was performed over three different well depths, <25m, 25 to 100 and >100m. For both regions, the percentage of oxidised groundwater decreased with increasing well depth. Linear discriminant analysis was used to develop models to differentiate between the three redox states. Models were derived for each depth and region using 67% of the data, and then subsequently validated on the remaining 33%. The average agreement between predicted and measured redox status was 63% and 70% for the Waikato and Canterbury regions, respectively. The models were incorporated into GIS and the prediction of redox status was extended over the whole region, excluding mountainous land. This knowledge improves spatial prediction of reduced groundwater zones, and therefore, when combined with groundwater flow paths, improves estimates of denitrification.}, } @article {pmid27178754, year = {2016}, author = {Giubilato, E and Radomyski, A and Critto, A and Ciffroy, P and Brochot, C and Pizzol, L and Marcomini, A}, title = {Modelling ecological and human exposure to POPs in Venice lagoon. Part I - Application of MERLIN-Expo tool for integrated exposure assessment.}, journal = {The Science of the total environment}, volume = {565}, number = {}, pages = {961-976}, doi = {10.1016/j.scitotenv.2016.04.146}, pmid = {27178754}, issn = {1879-1026}, mesh = {*Environmental Exposure ; Environmental Monitoring/*methods ; Food Chain ; Humans ; Italy ; Models, Theoretical ; Polychlorinated Biphenyls/*analysis ; Polychlorinated Dibenzodioxins/*analysis ; Water Pollutants, Chemical/*analysis ; }, } @article {pmid27177244, year = {2016}, author = {Borremans, B and Hens, N and Beutels, P and Leirs, H and Reijniers, J}, title = {Estimating Time of Infection Using Prior Serological and Individual Information Can Greatly Improve Incidence Estimation of Human and Wildlife Infections.}, journal = {PLoS computational biology}, volume = {12}, number = {5}, pages = {e1004882}, pmid = {27177244}, issn = {1553-7358}, mesh = {Animals ; Animals, Wild ; Bayes Theorem ; Computational Biology ; Computer Simulation ; Humans ; Incidence ; Infections/*epidemiology/immunology/*veterinary ; Mice ; Models, Biological ; Models, Statistical ; Seroconversion ; Time Factors ; }, abstract = {Diseases of humans and wildlife are typically tracked and studied through incidence, the number of new infections per time unit. Estimating incidence is not without difficulties, as asymptomatic infections, low sampling intervals and low sample sizes can introduce large estimation errors. After infection, biomarkers such as antibodies or pathogens often change predictably over time, and this temporal pattern can contain information about the time since infection that could improve incidence estimation. Antibody level and avidity have been used to estimate time since infection and to recreate incidence, but the errors on these estimates using currently existing methods are generally large. Using a semi-parametric model in a Bayesian framework, we introduce a method that allows the use of multiple sources of information (such as antibody level, pathogen presence in different organs, individual age, season) for estimating individual time since infection. When sufficient background data are available, this method can greatly improve incidence estimation, which we show using arenavirus infection in multimammate mice as a test case. The method performs well, especially compared to the situation in which seroconversion events between sampling sessions are the main data source. The possibility to implement several sources of information allows the use of data that are in many cases already available, which means that existing incidence data can be improved without the need for additional sampling efforts or laboratory assays.}, } @article {pmid27177237, year = {2016}, author = {Holden, PA and Gardea-Torresdey, JL and Klaessig, F and Turco, RF and Mortimer, M and Hund-Rinke, K and Cohen Hubal, EA and Avery, D and Barceló, D and Behra, R and Cohen, Y and Deydier-Stephan, L and Ferguson, PL and Fernandes, TF and Herr Harthorn, B and Henderson, WM and Hoke, RA and Hristozov, D and Johnston, JM and Kane, AB and Kapustka, L and Keller, AA and Lenihan, HS and Lovell, W and Murphy, CJ and Nisbet, RM and Petersen, EJ and Salinas, ER and Scheringer, M and Sharma, M and Speed, DE and Sultan, Y and Westerhoff, P and White, JC and Wiesner, MR and Wong, EM and Xing, B and Steele Horan, M and Godwin, HA and Nel, AE}, title = {Considerations of Environmentally Relevant Test Conditions for Improved Evaluation of Ecological Hazards of Engineered Nanomaterials.}, journal = {Environmental science & technology}, volume = {50}, number = {12}, pages = {6124-6145}, pmid = {27177237}, issn = {1520-5851}, support = {9999-NIST//Intramural NIST DOC/United States ; P42 ES013660/ES/NIEHS NIH HHS/United States ; }, mesh = {*Ecology ; Ecosystem ; Ecotoxicology ; Environment ; Humans ; *Nanostructures ; }, abstract = {Engineered nanomaterials (ENMs) are increasingly entering the environment with uncertain consequences including potential ecological effects. Various research communities view differently whether ecotoxicological testing of ENMs should be conducted using environmentally relevant concentrations-where observing outcomes is difficult-versus higher ENM doses, where responses are observable. What exposure conditions are typically used in assessing ENM hazards to populations? What conditions are used to test ecosystem-scale hazards? What is known regarding actual ENMs in the environment, via measurements or modeling simulations? How should exposure conditions, ENM transformation, dose, and body burden be used in interpreting biological and computational findings for assessing risks? These questions were addressed in the context of this critical review. As a result, three main recommendations emerged. First, researchers should improve ecotoxicology of ENMs by choosing test end points, duration, and study conditions-including ENM test concentrations-that align with realistic exposure scenarios. Second, testing should proceed via tiers with iterative feedback that informs experiments at other levels of biological organization. Finally, environmental realism in ENM hazard assessments should involve greater coordination among ENM quantitative analysts, exposure modelers, and ecotoxicologists, across government, industry, and academia.}, } @article {pmid27174430, year = {2016}, author = {Guilbert, A and Simons, K and Hoebeke, L and Packeu, A and Hendrickx, M and De Cremer, K and Buyl, R and Coomans, D and Van Nieuwenhuyse, A}, title = {Short-Term Effect of Pollen and Spore Exposure on Allergy Morbidity in the Brussels-Capital Region.}, journal = {EcoHealth}, volume = {13}, number = {2}, pages = {303-315}, pmid = {27174430}, issn = {1612-9210}, mesh = {Adult ; Aged ; *Allergens ; Belgium ; Europe ; Female ; Humans ; Male ; Middle Aged ; Poaceae ; *Pollen ; Rhinitis, Allergic, Seasonal/*epidemiology ; Young Adult ; }, abstract = {Belgium is among the European countries that are the most affected by allergic rhinitis. Pollen grains and fungal spores represent important triggers of symptoms. However, few studies have investigated their real link with disease morbidity over several years. Based on aeroallergen counts and health insurance datasets, the relationship between daily changes in pollen, fungal spore concentrations and daily changes in reimbursable systemic antihistamine sales has been investigated between 2005 and 2011 in the Brussels-Capital Region. A Generalized Linear Model was used and adjusted for air pollution, meteorological conditions, flu, seasonal component and day of the week. We observed an augmentation in drug sales despite no significant increase in allergen levels in the long term. The relative risk of buying allergy medications associated with an interquartile augmentation in pollen distributions increased significantly for Poaceae, Betula, Carpinus, Fraxinus and Quercus. Poaceae affected the widest age group and led to the highest increase of risk which reached 1.13 (95% CI [1.11-1.14]) among the 19- to 39-year-old men. Betula showed the second most consistent relationship across age groups. Clear identification of the provoking agents may improve disease management by customizing prevention programmes. This work also opens several research perspectives related to impact of climate modification or subpopulation sensitivity.}, } @article {pmid27170620, year = {2016}, author = {Han, BA and Drake, JM}, title = {Future directions in analytics for infectious disease intelligence: Toward an integrated warning system for emerging pathogens.}, journal = {EMBO reports}, volume = {17}, number = {6}, pages = {785-789}, pmid = {27170620}, issn = {1469-3178}, support = {U01 GM110744/GM/NIGMS NIH HHS/United States ; }, mesh = {Communicable Disease Control/methods/*trends ; Communicable Diseases, Emerging/economics/*prevention & control ; *Decision Support Systems, Clinical ; Disease Outbreaks/*prevention & control ; Earthquakes ; Global Warming ; Humans ; Risk ; Tsunamis ; }, abstract = {Anticipating the emergence of infectious diseases would be more effective in reducing their toll, rather than reacting to an outbreak. Machine learning and simulation tools that use environmental, epidemiological and molecular data could help manage and analyse the flow or risks, and inform appropriate actions by public health authorities. [Image: see text]}, } @article {pmid27170415, year = {2017}, author = {Bosomworth, K and Owen, C and Curnin, S}, title = {Addressing challenges for future strategic-level emergency management: reframing, networking, and capacity-building.}, journal = {Disasters}, volume = {41}, number = {2}, pages = {306-323}, doi = {10.1111/disa.12196}, pmid = {27170415}, issn = {1467-7717}, mesh = {Australia ; Capacity Building ; Community Networks/organization & administration ; Disaster Planning/*organization & administration ; Humans ; }, abstract = {The mounting frequency and intensity of natural hazards, alongside growing interdependencies between social-technical and ecological systems, are placing increased pressure on emergency management. This is particularly true at the strategic level of emergency management, which involves planning for and managing non-routine, high-consequence events. Drawing on the literature, a survey, and interviews and workshops with Australia's senior emergency managers, this paper presents an analysis of five core challenges that these pressures are creating for strategic-level emergency management. It argues that emphasising 'emergency management' as a primary adaptation strategy is a retrograde step that ignores the importance of addressing socio-political drivers of vulnerabilities. Three key suggestions are presented that could assist the country's strategic-level emergency management in tackling these challenges: (i) reframe emergency management as a component of disaster risk reduction rather than them being one and the same; (ii) adopt a network governance approach; and (iii) further develop the capacities of strategic-level emergency managers.}, } @article {pmid27169596, year = {2016}, author = {Blaxter, M and Danchin, A and Savakis, B and Fukami-Kobayashi, K and Kurokawa, K and Sugano, S and Roberts, RJ and Salzberg, SL and Wu, CI}, title = {Reminder to deposit DNA sequences.}, journal = {Science (New York, N.Y.)}, volume = {352}, number = {6287}, pages = {780}, doi = {10.1126/science.aaf7672}, pmid = {27169596}, issn = {1095-9203}, mesh = {*Base Sequence ; DNA/*genetics ; Databases, Nucleic Acid/*standards ; Humans ; Publications/standards ; }, } @article {pmid27168574, year = {2016}, author = {Nemeth, C and Anders, S and Strouse, R and Grome, A and Crandall, B and Pamplin, J and Salinas, J and Mann-Salinas, E}, title = {Developing a Cognitive and Communications Tool for Burn Intensive Care Unit Clinicians.}, journal = {Military medicine}, volume = {181}, number = {5 Suppl}, pages = {205-213}, doi = {10.7205/MILMED-D-15-00173}, pmid = {27168574}, issn = {1930-613X}, mesh = {Burn Units/organization & administration ; Burns/*therapy ; Humans ; Intensive Care Units/organization & administration ; *Interdisciplinary Communication ; Machine Learning ; Medical Informatics/instrumentation/standards ; Software ; Surveys and Questionnaires ; *Systems Analysis ; Task Performance and Analysis ; User-Computer Interface ; }, abstract = {BACKGROUND: Burn Intensive Care Unit (BICU) work is necessarily complex and depends on clinician actions, resources, and variable patient responses to interventions. Clinicians use large volumes of data that are condensed in time, but separated across resources, to care for patients. Correctly designed health information technology (IT) systems may help clinicians to treat these patients more efficiently, accurately, and reliably. We report on a 3-year project to design and develop an ecologically valid IT system for use in a military BICU.

METHODS: We use a mixed methods Cognitive Systems Engineering approach for research and development. Observations, interviews, artifact analysis, survey, and thematic analysis methods were used to reveal underlying factors that mold the work environment and affect clinician decisions that may affect patient outcomes. Participatory design and prototyping methods have been used to develop solutions.

RESULTS: We developed 39 requirements for the IT system and used them to create three use cases to help developers better understand how the system might support clinician work to develop interface prototypes. We also incorporated data mining functions that offer the potential to aid clinicians by recognizing patterns recognition of clinically significant events, such as incipient sepsis. The gaps between information sources and accurate, reliable, and efficient clinical decision that we have identified will enable us to create scenarios to evaluate prototype systems with BICU clinicians, to develop increasingly improved designs, and to measure outcomes.

CONCLUSION: The link from data to analyses, requirements, prototypes, and their evaluation ensures that the solution will reflect and support work in the BICU as it actually occurs, improving staff efficiency and patient care quality.}, } @article {pmid27164179, year = {2016}, author = {Orsini, L and Gilbert, D and Podicheti, R and Jansen, M and Brown, JB and Solari, OS and Spanier, KI and Colbourne, JK and Rusch, DB and Decaestecker, E and Asselman, J and De Schamphelaere, KA and Ebert, D and Haag, CR and Kvist, J and Laforsch, C and Petrusek, A and Beckerman, AP and Little, TJ and Chaturvedi, A and Pfrender, ME and De Meester, L and Frilander, MJ}, title = {Daphnia magna transcriptome by RNA-Seq across 12 environmental stressors.}, journal = {Scientific data}, volume = {3}, number = {}, pages = {160030}, pmid = {27164179}, issn = {2052-4463}, support = {R24 GM078274/GM/NIGMS NIH HHS/United States ; R24-GM078274/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Base Sequence ; Daphnia/*genetics ; Databases, Genetic ; Gene-Environment Interaction ; *Genome ; RNA/genetics ; *Transcriptome ; }, abstract = {The full exploration of gene-environment interactions requires model organisms with well-characterized ecological interactions in their natural environment, manipulability in the laboratory and genomic tools. The waterflea Daphnia magna is an established ecological and toxicological model species, central to the food webs of freshwater lentic habitats and sentinel for water quality. Its tractability and cyclic parthenogenetic life-cycle are ideal to investigate links between genes and the environment. Capitalizing on this unique model system, the STRESSFLEA consortium generated a comprehensive RNA-Seq data set by exposing two inbred genotypes of D. magna and a recombinant cross of these genotypes to a range of environmental perturbations. Gene models were constructed from the transcriptome data and mapped onto the draft genome of D. magna using EvidentialGene. The transcriptome data generated here, together with the available draft genome sequence of D. magna and a high-density genetic map will be a key asset for future investigations in environmental genomics.}, } @article {pmid27164171, year = {2017}, author = {Holden, RJ and Valdez, RS and Schubert, CC and Thompson, MJ and Hundt, AS}, title = {Macroergonomic factors in the patient work system: examining the context of patients with chronic illness.}, journal = {Ergonomics}, volume = {60}, number = {1}, pages = {26-43}, pmid = {27164171}, issn = {1366-5847}, support = {K01 AG044439/AG/NIA NIH HHS/United States ; KL2 TR000446/TR/NCATS NIH HHS/United States ; UL1 TR000427/TR/NCATS NIH HHS/United States ; UL1 TR000445/TR/NCATS NIH HHS/United States ; }, mesh = {Adult ; Aged ; Aged, 80 and over ; Asthma/*therapy ; Chronic Disease ; Ergonomics ; Female ; Heart Failure/*therapy ; Humans ; Male ; Middle Aged ; Pulmonary Disease, Chronic Obstructive/*therapy ; Qualitative Research ; *Self Care ; *Work ; Young Adult ; }, abstract = {Human factors/ergonomics recognises work as embedded in and shaped by levels of social, physical and organisational context. This study investigates the contextual or macroergonomic factors present in the health-related work performed by patients. We performed a secondary content analysis of findings from three studies of the work of chronically ill patients and their informal caregivers. Our resulting consolidated macroergonomic patient work system model identified 17 factors across physical, social and organisational domains and household and community levels. These factors are illustrated with examples from the three studies and discussed as having positive, negative or varying effects on health and health behaviour. We present three brief case studies to illustrate how macroergonomic factors combine across domains and levels to shape performance in expected and unexpected ways. Findings demonstrate not only the importance of context for patients' health-related activities but also specific factors to consider in future research, design and policy efforts. Practitioner Summary: Health-related activities of patients are embedded in and shaped by levels of social, physical and organisational context. This paper combined findings from three studies to specify 17 contextual or macroergonomic factors in home- and community-based work systems of chronically ill patients. These factors have research, design and policy implications.}, } @article {pmid27163938, year = {2016}, author = {Chaudhary, VB and Rúa, MA and Antoninka, A and Bever, JD and Cannon, J and Craig, A and Duchicela, J and Frame, A and Gardes, M and Gehring, C and Ha, M and Hart, M and Hopkins, J and Ji, B and Johnson, NC and Kaonongbua, W and Karst, J and Koide, RT and Lamit, LJ and Meadow, J and Milligan, BG and Moore, JC and Pendergast, TH and Piculell, B and Ramsby, B and Simard, S and Shrestha, S and Umbanhowar, J and Viechtbauer, W and Walters, L and Wilson, GW and Zee, PC and Hoeksema, JD}, title = {MycoDB, a global database of plant response to mycorrhizal fungi.}, journal = {Scientific data}, volume = {3}, number = {}, pages = {160028}, pmid = {27163938}, issn = {2052-4463}, mesh = {Biomass ; *Databases, Factual ; *Mycorrhizae ; Phylogeny ; *Plants/microbiology ; *Symbiosis ; }, abstract = {Plants form belowground associations with mycorrhizal fungi in one of the most common symbioses on Earth. However, few large-scale generalizations exist for the structure and function of mycorrhizal symbioses, as the nature of this relationship varies from mutualistic to parasitic and is largely context-dependent. We announce the public release of MycoDB, a database of 4,010 studies (from 438 unique publications) to aid in multi-factor meta-analyses elucidating the ecological and evolutionary context in which mycorrhizal fungi alter plant productivity. Over 10 years with nearly 80 collaborators, we compiled data on the response of plant biomass to mycorrhizal fungal inoculation, including meta-analysis metrics and 24 additional explanatory variables that describe the biotic and abiotic context of each study. We also include phylogenetic trees for all plants and fungi in the database. To our knowledge, MycoDB is the largest ecological meta-analysis database. We aim to share these data to highlight significant gaps in mycorrhizal research and encourage synthesis to explore the ecological and evolutionary generalities that govern mycorrhizal functioning in ecosystems.}, } @article {pmid27163567, year = {2016}, author = {Duarte-Cunha, M and Almeida, AS and Cunha, GM and Souza-Santos, R}, title = {Geographic weighted regression: applicability to epidemiological studies of leprosy.}, journal = {Revista da Sociedade Brasileira de Medicina Tropical}, volume = {49}, number = {1}, pages = {74-82}, doi = {10.1590/0037-8682-0307-2015}, pmid = {27163567}, issn = {1678-9849}, mesh = {Brazil/epidemiology ; Epidemiologic Studies ; Geographic Information Systems ; *Geography, Medical ; Humans ; Leprosy/*epidemiology ; Prevalence ; Risk Factors ; }, abstract = {INTRODUCTION: Geographic information systems (GIS) enable public health data to be analyzed in terms of geographical variability and the relationship between risk factors and diseases. This study discusses the application of the geographic weighted regression (GWR) model to health data to improve the understanding of spatially varying social and clinical factors that potentially impact leprosy prevalence.

METHODS: This ecological study used data from leprosy case records from 1998-2006, aggregated by neighborhood in the Duque de Caxias municipality in the State of Rio de Janeiro, Brazil. In the GWR model, the associations between the log of the leprosy detection rate and social and clinical factors were analyzed.

RESULTS: Maps of the estimated coefficients by neighborhood confirmed the heterogeneous spatial relationships between the leprosy detection rates and the predictors. The proportion of households with piped water was associated with higher detection rates, mainly in the northeast of the municipality. Indeterminate forms were strongly associated with higher detections rates in the south, where access to health services was more established.

CONCLUSIONS: GWR proved a useful tool for epidemiological analysis of leprosy in a local area, such as Duque de Caxias. Epidemiological analysis using the maps of the GWR model offered the advantage of visualizing the problem in sub-regions and identifying any spatial dependence in the local study area.}, } @article {pmid27161395, year = {2016}, author = {Zampieri, E and Chiapello, M and Daghino, S and Bonfante, P and Mello, A}, title = {Soil metaproteomics reveals an inter-kingdom stress response to the presence of black truffles.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {25773}, pmid = {27161395}, issn = {2045-2322}, mesh = {Ascomycota/*physiology ; Fungal Proteins/isolation & purification ; Gene Ontology ; *Metagenomics ; *Proteomics ; *Soil Microbiology ; *Stress, Physiological ; }, abstract = {For some truffle species of the Tuber genus, the symbiotic phase is often associated with the presence of an area of scant vegetation, commonly known as the brûlé, around the host tree. Previous metagenomics studies have identified the microorganisms present inside and outside the brûlé of a Tuber melanosporum truffle-ground, but the molecular mechanisms that operate in this ecological niche remain to be clarified. To elucidate the metabolic pathways present in the brûlé, we conducted a metaproteomics analysis on the soil of a characterized truffle-ground and cross-referenced the resulting proteins with a database we constructed, incorporating the metagenomics data for the organisms previously identified in this soil. The soil inside the brûlé contained a larger number of proteins and, surprisingly, more proteins from plants, compared with the soil outside the brûlé. In addition, Fisher's Exact Tests detected more biological processes inside the brûlé; these processes were related to responses to multiple types of stress. Thus, although the brûlé has a reduced diversity of plant and microbial species, the organisms in the brûlé show strong metabolic activity. Also, the combination of metagenomics and metaproteomics provides a powerful tool to reveal soil functioning.}, } @article {pmid27158095, year = {2016}, author = {Mimee, M and Citorik, RJ and Lu, TK}, title = {Microbiome therapeutics - Advances and challenges.}, journal = {Advanced drug delivery reviews}, volume = {105}, number = {Pt A}, pages = {44-54}, pmid = {27158095}, issn = {1872-8294}, support = {P30 DK043351/DK/NIDDK NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; R01 EB017755/EB/NIBIB NIH HHS/United States ; P50 GM098792/GM/NIGMS NIH HHS/United States ; DP2 OD008435/OD/NIH HHS/United States ; }, mesh = {Animals ; Anti-Infective Agents/therapeutic use ; Bioengineering ; Humans ; *Microbiota ; Probiotics/therapeutic use ; }, abstract = {The microbial community that lives on and in the human body exerts a major impact on human health, from metabolism to immunity. In order to leverage the close associations between microbes and their host, development of therapeutics targeting the microbiota has surged in recent years. Here, we discuss current additive and subtractive strategies to manipulate the microbiota, focusing on bacteria engineered to produce therapeutic payloads, consortia of natural organisms and selective antimicrobials. Further, we present challenges faced by the community in the development of microbiome therapeutics, including designing microbial therapies that are adapted for specific geographies in the body, stable colonization with microbial therapies, discovery of clinically relevant biosensors, robustness of engineered synthetic gene circuits and addressing safety and biocontainment concerns. Moving forward, collaboration between basic and applied researchers and clinicians to address these challenges will poise the field to herald an age of next-generation, cellular therapies that draw on novel findings in basic research to inform directed augmentation of the human microbiota.}, } @article {pmid27157636, year = {2016}, author = {Ren, W and Yin, J and Chen, S and Duan, J and Liu, G and Li, T and Li, N and Peng, Y and Tan, B and Yin, Y}, title = {Proteome analysis for the global proteins in the jejunum tissues of enterotoxigenic Escherichia coli -infected piglets.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {25640}, pmid = {27157636}, issn = {2045-2322}, mesh = {Animals ; Animals, Newborn ; Diarrhea/immunology/microbiology ; Disease Resistance ; Enterotoxigenic Escherichia coli/*physiology ; Escherichia coli Infections/immunology/metabolism/microbiology ; Gene Ontology ; Jejunum/immunology/*metabolism/microbiology ; Proteome/*metabolism ; Proteomics/*methods ; Sus scrofa/immunology/*microbiology ; }, abstract = {Enterotoxigenic Escherichia coli (ETEC) is a common cause of diarrhea in humans and livestock. In this study, isobaric tags for relative and absolute quantitation (iTRAQ) combined with multidimensional liquid chromatography (LC) and MS analysis was used for screening the differentially expressed proteins in piglet jejunum after ETEC infection. Totally 1,897 proteins were identified with quantitative information in piglet jejunum. We identified 92 differentially expressed proteins in ETEC-induced diarrhea, of which 30 were up regulated and 62 down regulated. Most of the differentially expressed proteins were involved in intestinal function of binding, metabolic process, catalytic activity and immune responses. The inhibition of intestinal immune responses in the jejunum in ETEC-induced diarrhea was also validated by immunobloting and RT-PCR. Our study is the first attempt to analyze the protein profile of ETEC-infected piglets by quantitative proteomics, and our findings could provide valuable information with respect to better understanding the host response to ETEC infection.}, } @article {pmid27154469, year = {2016}, author = {Ning, C and Qin, R and Chen, D and Björn, LO and Li, S}, title = {Application of in-house virtual protein database performed in genomic-proteomic combined research on heavy-metal stressed onion roots.}, journal = {Biotechnology letters}, volume = {38}, number = {8}, pages = {1293-1300}, doi = {10.1007/s10529-016-2114-3}, pmid = {27154469}, issn = {1573-6776}, mesh = {*Databases, Protein ; Genomics/*methods ; Metals, Heavy/*toxicity ; Onions/*drug effects/metabolism ; Plant Roots/*drug effects/metabolism ; Proteomics/*methods ; }, abstract = {OBJECTIVES: To establish an in-house virtual protein database that can be employed in proteomic research on non-model plants.

RESULTS: A total of 87,430 unigenes were obtained through transcriptome sequencing from onion roots. Of these, 24,305 unigenes were annotated and their nucleotide sequences of coding regions were translated into amino acid sequences. The corresponding 24,305 amino acid sequences were considered as an in-house virtual protein database. Thirty-two protein spots with significant differential abundance were selected. Their MS data were submitted to a restriction enzyme map which was converted from the in-house virtual protein database. A total of 27 proteins were finally matched.

CONCLUSIONS: The in-house protein database is a feasible and innovative strategy for proteomic research on non-model plants.}, } @article {pmid27154210, year = {2016}, author = {Carvalho-Sobrinho, JG and Alverson, WS and Alcantara, S and Queiroz, LP and Mota, AC and Baum, DA}, title = {Revisiting the phylogeny of Bombacoideae (Malvaceae): Novel relationships, morphologically cohesive clades, and a new tribal classification based on multilocus phylogenetic analyses.}, journal = {Molecular phylogenetics and evolution}, volume = {101}, number = {}, pages = {56-74}, doi = {10.1016/j.ympev.2016.05.006}, pmid = {27154210}, issn = {1095-9513}, mesh = {Bayes Theorem ; Databases, Genetic ; *Genetic Loci ; Malvaceae/anatomy & histology/*classification/*genetics ; *Phylogeny ; Quantitative Trait, Heritable ; Seeds/anatomy & histology ; }, abstract = {Bombacoideae (Malvaceae) is a clade of deciduous trees with a marked dominance in many forests, especially in the Neotropics. The historical lack of a well-resolved phylogenetic framework for Bombacoideae hinders studies in this ecologically important group. We reexamined phylogenetic relationships in this clade based on a matrix of 6465 nuclear (ETS, ITS) and plastid (matK, trnL-trnF, trnS-trnG) DNA characters. We used maximum parsimony, maximum likelihood, and Bayesian inference to infer relationships among 108 species (∼70% of the total number of known species). We analyzed the evolution of selected morphological traits: trunk or branch prickles, calyx shape, endocarp type, seed shape, and seed number per fruit, using ML reconstructions of their ancestral states to identify possible synapomorphies for major clades. Novel phylogenetic relationships emerged from our analyses, including three major lineages marked by fruit or seed traits: the winged-seed clade (Bernoullia, Gyranthera, and Huberodendron), the spongy endocarp clade (Adansonia, Aguiaria, Catostemma, Cavanillesia, and Scleronema), and the Kapok clade (Bombax, Ceiba, Eriotheca, Neobuchia, Pachira, Pseudobombax, Rhodognaphalon, and Spirotheca). The Kapok clade, the most diverse lineage of the subfamily, includes sister relationships (i) between Pseudobombax and "Pochota fendleri" a historically incertae sedis taxon, and (ii) between the Paleotropical genera Bombax and Rhodognaphalon, implying just two bombacoid dispersals to the Old World, the other one involving Adansonia. This new phylogenetic framework offers new insights and a promising avenue for further evolutionary studies. In view of this information, we present a new tribal classification of the subfamily, accompanied by an identification key.}, } @article {pmid27153797, year = {2016}, author = {Fabian, E and Bordag, N and Herold, M and Kamp, H and Krennrich, G and Looser, R and Ma-Hock, L and Mellert, W and Montoya, G and Peter, E and Prokudin, A and Spitzer, M and Strauss, V and Walk, T and Zbranek, R and van Ravenzwaay, B}, title = {Metabolite profiles of rats in repeated dose toxicological studies after oral and inhalative exposure.}, journal = {Toxicology letters}, volume = {255}, number = {}, pages = {11-23}, doi = {10.1016/j.toxlet.2016.05.003}, pmid = {27153797}, issn = {1879-3169}, mesh = {Administration, Inhalation ; Administration, Oral ; Aniline Compounds/administration & dosage/pharmacokinetics/*toxicity ; Animals ; Benzene Derivatives/administration & dosage/pharmacokinetics/*toxicity ; Chloroform/administration & dosage/pharmacokinetics/*toxicity ; Databases, Factual ; Dimethylformamide/administration & dosage/pharmacokinetics/*toxicity ; Dose-Response Relationship, Drug ; Drug Administration Schedule ; Ethylene Glycols/administration & dosage/pharmacokinetics/*toxicity ; Female ; Furans/administration & dosage/pharmacokinetics/*toxicity ; Inhalation Exposure ; Male ; *Metabolome ; *Metabolomics ; Principal Component Analysis ; Rats, Wistar ; Risk Assessment ; *Toxicity Tests ; }, abstract = {The MetaMap(®)-Tox database contains plasma-metabolome and toxicity data of rats obtained from oral administration of 550 reference compounds following a standardized adapted OECD 407 protocol. Here, metabolic profiles for aniline (A), chloroform (CL), ethylbenzene (EB), 2-methoxyethanol (ME), N,N-dimethylformamide (DMF) and tetrahydrofurane (THF), dosed inhalatively for six hours/day, five days a week for 4 weeks were compared to oral dosing performed daily for 4 weeks. To investigate if the oral and inhalative metabolome would be comparable statistical analyses were performed. Best correlations for metabolome changes via both routes of exposure were observed for toxicants that induced profound metabolome changes. e.g. CL and ME. Liver and testes were correctly identified as target organs. In contrast, route of exposure dependent differences in metabolic profiles were noted for low profile strength e.g. female rats dosed inhalatively with A or THF. Taken together, the current investigations demonstrate that plasma metabolome changes are generally comparable for systemic effects after oral and inhalation exposure. Differences may result from kinetics and first pass effects. For compounds inducing only weak changes, the differences between both routes of exposure are visible in the metabolome.}, } @article {pmid27153622, year = {2016}, author = {Peng, Y and Yang, L and Li, H and Zou, Y and Deng, L and Wu, A and Du, X and Wang, D and Shu, Y and Jiang, T}, title = {PREDAC-H3: a user-friendly platform for antigenic surveillance of human influenza a(H3N2) virus based on hemagglutinin sequences.}, journal = {Bioinformatics (Oxford, England)}, volume = {32}, number = {16}, pages = {2526-2527}, doi = {10.1093/bioinformatics/btw185}, pmid = {27153622}, issn = {1367-4811}, mesh = {Antigenic Variation ; Antigens, Viral ; Computational Biology/*methods ; DNA, Viral ; *Epidemiological Monitoring ; Hemagglutinin Glycoproteins, Influenza Virus ; *Hemagglutinins ; Humans ; *Influenza A Virus, H3N2 Subtype ; Influenza A virus ; Influenza, Human/*epidemiology ; *Sequence Analysis, DNA ; }, abstract = {MOTIVATION: Timely surveillance of the antigenic dynamics of the influenza virus is critical for accurate selection of vaccine strains, which is important for effective prevention of viral spread and infection.

RESULTS: Here, we provide a computational platform, called PREDAC-H3, for antigenic surveillance of human influenza A(H3N2) virus based on the sequence of surface protein hemagglutinin (HA). PREDAC-H3 not only determines the antigenic variants and antigenic cluster (grouped for similar antigenicity) to which the virus belongs, based on HA sequences, but also allows visualization of the spatial distribution and temporal dynamics of antigenic clusters of viruses isolated from around the world, thus assisting in antigenic surveillance of human influenza A(H3N2) virus.

It is publicly available from: http://biocloud.hnu.edu.cn/influ411/html/index.php

CONTACTS: : yshu@cnic.org.cn or taijiao@moon.ibp.ac.cn.}, } @article {pmid27151089, year = {2016}, author = {Kohno, A and Musa, G and Nik Farid, ND and Abdul Aziz, N and Nakayama, T and Dahlui, M}, title = {Issues in healthcare services in Malaysia as experienced by Japanese retirees.}, journal = {BMC health services research}, volume = {16}, number = {}, pages = {167}, pmid = {27151089}, issn = {1472-6963}, mesh = {Aged ; Attitude to Health ; Communication Barriers ; Delivery of Health Care/standards ; Emigrants and Immigrants/*psychology ; Emigration and Immigration/statistics & numerical data ; Female ; Focus Groups ; Health Services Accessibility/standards ; Health Services for the Aged/*standards ; Humans ; Japan/ethnology ; Malaysia/epidemiology ; Male ; Middle Aged ; Personal Satisfaction ; Retirement/*psychology/statistics & numerical data ; Trust ; }, abstract = {BACKGROUND: Worldwide, international retirement migration is growing in its popularity and Japanese retirees choose Malaysia as their most preferred destination. This study examines the pertinent issues related to healthcare services as experienced by Japanese retirees in this country.

METHODS AND RESULTS: From January to March 2015, we conducted focus group discussions with 30 Japanese retirees who live in Kuala Lumpur and Ipoh. Guided by the social-ecological model, we discovered seven pertinent themes: 'language barriers','healthcare decisions', 'medical check-ups','healthcare insurance', 'nursing and palliative care', 'trust and distrust of healthcare services', and 'word-of-mouth information'.

DISCUSSION: We identified seven pertinent issues related to healthcare services among Japanese retirees in Malaysia, of which four are especially important. These issues are explained as integrated themes within the social-ecological model. Language barriers prohibit them from having difficulty accessing to healthcare in Malaysia, but lack of will to improve their language skills exist among them. For that reason, they rely heavily on word-of-mouth information when seeking for healthcare. As a consequence, some develop feelings of trust and distrust of healthcare services. In addition, we have identified the needs for provide nursing and palliative care among Japanese retirees in Malaysia.

CONCLUSION: Based on the magnitude of the discussion, we concluded that there are four crucial healthcare issues among Japanese retirees; 'language barriers', 'trust and distrust of healthcare services', 'word-of-mouth information' and 'nursing and palliative care'. We propose that further dialogue by healthcare stakeholders should be carried out to improve further the healthcare service provisions for Japanese retirees in Malaysia.}, } @article {pmid27147762, year = {2016}, author = {Murguía-Peniche, T and Illescas-Zárate, D and Chico-Barba, G and Bhutta, ZA}, title = {An ecological study of stillbirths in Mexico from 2000 to 2013.}, journal = {Bulletin of the World Health Organization}, volume = {94}, number = {5}, pages = {322-330A}, pmid = {27147762}, issn = {1564-0604}, mesh = {Adolescent ; Adult ; Databases, Factual ; Delivery of Health Care ; *Demography ; Female ; *Gestational Age ; Humans ; Infant, Newborn ; Male ; Mexico/epidemiology ; Stillbirth/*epidemiology ; Young Adult ; }, abstract = {OBJECTIVE: To examine trends in the rate of stillbirths at or after 21 weeks' gestation in Mexico from 2000 to 2013, identify factors associated with stillbirths and estimate subnational variability in stillbirth rates and the proportion of deaths occurring intrapartum.

METHODS: This population-based, ecological study involved data from a national database on 263 475 stillbirths in 29 Mexican states and maternal sociodemographic factors. Subnational variability in the stillbirth rate in 2012 was investigated and stillbirths in 2013 were categorized as intrapartum or antepartum according to the fetus' skin condition.

FINDINGS: The national stillbirth rate declined from 9.2 to 7.2 per 1000 births between 2000 and 2013 (i.e. -1.9% per year). The prevalence of stillbirths varied 3.9-fold between states. Stillbirths were associated, in particular, with: residence in Mexico City (odds ratio, OR: 1.71; 95% confidence interval, CI: 1.68-1.73) or central Mexico (OR: 1.36; 95% CI: 1.34-1.38); maternal education of 9 years or less (OR:1.10; 95% CI: 1.08-1.11) or 10 to 12 years (OR: 1.16; 95% CI: 1.14-1.18); mothers younger than 15 years (OR: 1.64; 95% CI: 1.55-1.72) or older than 34 years (OR: 1.68; 95% CI: 1.66-1.70); and male fetal sex (OR: 1.20; 95% CI: 1.19-1.21). Overall, 51% (7348/14 344) of fetal deaths occurred intrapartum.

CONCLUSION: In Mexico, the total stillbirth rate declined between 2000 and 2013, however geographical variations were observed. Stillbirths were associated with sociodemographic factors. The proportion of intrapartum stillbirths was relatively high, suggesting that health system performance could be improved, especially at places of delivery.}, } @article {pmid27147245, year = {2016}, author = {Rämä, T and Davey, ML and Nordén, J and Halvorsen, R and Blaalid, R and Mathiassen, GH and Alsos, IG and Kauserud, H}, title = {Fungi Sailing the Arctic Ocean: Speciose Communities in North Atlantic Driftwood as Revealed by High-Throughput Amplicon Sequencing.}, journal = {Microbial ecology}, volume = {72}, number = {2}, pages = {295-304}, pmid = {27147245}, issn = {1432-184X}, mesh = {Adaptation, Physiological ; Ascomycota/*classification/isolation & purification ; Basidiomycota/*classification/isolation & purification ; Biodiversity ; Computational Biology ; DNA, Fungal/genetics ; Ecosystem ; Multivariate Analysis ; Oceans and Seas ; Sequence Analysis, DNA ; Species Specificity ; *Water Microbiology ; Wood/*microbiology ; }, abstract = {High amounts of driftwood sail across the oceans and provide habitat for organisms tolerating the rough and saline environment. Fungi have adapted to the extremely cold and saline conditions which driftwood faces in the high north. For the first time, we applied high-throughput sequencing to fungi residing in driftwood to reveal their taxonomic richness, community composition, and ecology in the North Atlantic. Using pyrosequencing of ITS2 amplicons obtained from 49 marine logs, we found 807 fungal operational taxonomic units (OTUs) based on clustering at 97 % sequence similarity cut-off level. The phylum Ascomycota comprised 74 % of the OTUs and 20 % belonged to Basidiomycota. The richness of basidiomycetes decreased with prolonged submersion in the sea, supporting the general view of ascomycetes being more extremotolerant. However, more than one fourth of the fungal OTUs remained unassigned to any fungal class, emphasising the need for better DNA reference data from the marine habitat. Different fungal communities were detected in coniferous and deciduous logs. Our results highlight that driftwood hosts a considerably higher fungal diversity than currently known. The driftwood fungal community is not a terrestrial relic but a speciose assemblage of fungi adapted to the stressful marine environment and different kinds of wooden substrates found in it.}, } @article {pmid27145698, year = {2016}, author = {Wang, C and Tang, Y and Chen, J}, title = {Plant phenological synchrony increases under rapid within-spring warming.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {25460}, pmid = {27145698}, issn = {2045-2322}, mesh = {Analysis of Variance ; Arctic Regions ; Climate Change ; Datasets as Topic ; Ecology ; Europe ; Flowers/*physiology ; *Models, Statistical ; Plant Development/*physiology ; Plant Leaves/*physiology ; Seasons ; *Spatio-Temporal Analysis ; Temperature ; }, abstract = {Phenological synchrony influences many ecological processes. Recent climate change has altered the synchrony of phenology, but little is known about the underlying mechanisms. Here using in situ phenological records from Europe, we found that the standard deviation (SD, as a measure of synchrony) of first leafing day (FLD) and the SD of first flowering day (FFD) among local plants were significantly smaller in the years and/or in the regions with a more rapid within-spring warming speed (WWS, the linear slope of the daily mean temperature against the days during spring, in (o)C/day) with correlation coefficients of -0.75 and -0.48 for FLD and -0.55 and -0.23 for FFD. We further found that the SDs of temperature sensitivity of local plants were smaller under the rapid WWS conditions with correlation coefficients of -0.46 and -0.33 for FLD and FFD respectively. This study provides the first evidence that the within-season rate of change of the temperature but not the magnitude determines plant phenological synchrony. It implies that temporally, the asymmetric seasonal climatic warming may decrease the synchrony via increasing WWS, especially in arctic regions; spatially, plants in coastal and low latitude areas with low WWS would have more diverse spring phenological traits.}, } @article {pmid27144589, year = {2016}, author = {Xu, M and He, C and Liu, Z and Dou, Y}, title = {How Did Urban Land Expand in China between 1992 and 2015? A Multi-Scale Landscape Analysis.}, journal = {PloS one}, volume = {11}, number = {5}, pages = {e0154839}, pmid = {27144589}, issn = {1932-6203}, mesh = {China ; Conservation of Natural Resources/*statistics & numerical data ; Environmental Monitoring/methods ; Geographic Information Systems/*statistics & numerical data ; Light ; Temperature ; Urbanization ; }, abstract = {Effective and timely quantification of the spatiotemporal pattern of urban expansion in China is important for the assessment of its environmental effects. However, the dynamics of the most recent urban expansions in China since 2012 have not yet been adequately explained due to a lack of current information. In this paper, our objective was to quantify spatiotemporal patterns of urban expansion in China between 1992 and 2015. First, we extracted information on urban expansion in China between 1992 and 2015 by integrating nighttime light data, vegetation index data, and land surface temperature data. Then we analyzed the spatiotemporal patterns of urban expansion at the national and regional scales, as well as at that of urban agglomerations. We found that China experienced a rapid and large-scale process of urban expansion between 1992 and 2015, with urban land increasing from 1.22 × 104 km2 to 7.29 × 104 km2, increasing in size nearly fivefold and with an average annual growth rate of 8.10%, almost 2.5 times as rapid as the global average. We also found that urban land in China expanded mainly by occupying 3.31 × 104 km2 of cropland, which comprised 54.67% of the total area of expanded urban land. Among the three modes of growth-infilling, edge expansion, and leapfrog-edge expansion was the main cause of cropland loss. Cropland loss resulting from edge expansion of urban land totalled 2.51 × 104 km2, accounting for over 75% of total cropland loss. We suggest that effective future management with respect to edge expansion of urban land is needed to protect cropland in China.}, } @article {pmid27144000, year = {2016}, author = {Sun, Y and Huang, Y and Li, X and Baldwin, CC and Zhou, Z and Yan, Z and Crandall, KA and Zhang, Y and Zhao, X and Wang, M and Wong, A and Fang, C and Zhang, X and Huang, H and Lopez, JV and Kilfoyle, K and Zhang, Y and Ortí, G and Venkatesh, B and Shi, Q}, title = {Fish-T1K (Transcriptomes of 1,000 Fishes) Project: large-scale transcriptome data for fish evolution studies.}, journal = {GigaScience}, volume = {5}, number = {}, pages = {18}, pmid = {27144000}, issn = {2047-217X}, mesh = {Animals ; Databases, Genetic ; *Evolution, Molecular ; Fishes/classification/*genetics ; Gene Expression Profiling/*methods/statistics & numerical data ; Geography ; International Cooperation ; Research/organization & administration/statistics & numerical data ; Sequence Analysis, RNA/methods/statistics & numerical data ; Species Specificity ; *Transcriptome ; }, abstract = {Ray-finned fishes (Actinopterygii) represent more than 50 % of extant vertebrates and are of great evolutionary, ecologic and economic significance, but they are relatively underrepresented in 'omics studies. Increased availability of transcriptome data for these species will allow researchers to better understand changes in gene expression, and to carry out functional analyses. An international project known as the "Transcriptomes of 1,000 Fishes" (Fish-T1K) project has been established to generate RNA-seq transcriptome sequences for 1,000 diverse species of ray-finned fishes. The first phase of this project has produced transcriptomes from more than 180 ray-finned fishes, representing 142 species and covering 51 orders and 109 families. Here we provide an overview of the goals of this project and the work done so far.}, } @article {pmid27144499, year = {2016}, author = {Del Signore, A and Hendriks, AJ and Lenders, HJ and Leuven, RS and Breure, AM}, title = {Development and application of the SSD approach in scientific case studies for ecological risk assessment.}, journal = {Environmental toxicology and chemistry}, volume = {35}, number = {9}, pages = {2149-2161}, doi = {10.1002/etc.3474}, pmid = {27144499}, issn = {1552-8618}, mesh = {Animals ; Databases, Factual ; Ecosystem ; Ecotoxicology/*methods/*statistics & numerical data ; Environmental Pollutants/*toxicity ; *Research Design ; Risk Assessment ; Species Specificity ; }, abstract = {Species sensitivity distributions (SSDs) are used in ecological risk assessment for extrapolation of the results of toxicity tests with single species to a toxicity threshold considered protective of ecosystem structure and functioning. The attention to and importance of the SSD approach has increased in scientific and regulatory communities since the 1990s. Discussion and criticism have been triggered on the concept of the approach as well as its technical aspects (e.g., distribution type, number of toxicity endpoints). Various questions remain unanswered, especially with regard to different endpoints, statistical methods, and protectiveness of threshold levels, for example. In the present literature review (covering the period 2002-2013), case studies are explored in which the SSD approach was applied, as well as how endpoint types, species choice, and data availability affect SSDs. How statistical methods may be used to construct reliable SSDs and whether the lower 5th percentile hazard concentrations (HC5s) from a generic SSD can be protective for a specific local community are also investigated. It is shown that estimated protective concentrations were determined by taxonomic groups rather than the statistical method used to construct the distribution. Based on comparisons between semifield and laboratory-based SSDs, the output from a laboratory SSD was protective of semifield communities in the majority of studies. Environ Toxicol Chem 2016;35:2149-2161. © 2016 SETAC.}, } @article {pmid27142449, year = {2016}, author = {Herraiz, FJ and Blanca, J and Ziarsolo, P and Gramazio, P and Plazas, M and Anderson, GJ and Prohens, J and Vilanova, S}, title = {The first de novo transcriptome of pepino (Solanum muricatum): assembly, comprehensive analysis and comparison with the closely related species S. caripense, potato and tomato.}, journal = {BMC genomics}, volume = {17}, number = {}, pages = {321}, pmid = {27142449}, issn = {1471-2164}, mesh = {Evolution, Molecular ; Flowers/genetics ; Gene Expression Profiling/*methods ; Gene Ontology ; Genetic Variation ; High-Throughput Nucleotide Sequencing/*methods ; Solanum lycopersicum/*genetics ; Molecular Sequence Annotation ; Phylogeny ; Plant Leaves/genetics ; Plant Proteins/genetics ; Sequence Analysis, RNA/*methods ; Solanum/*classification/genetics ; Solanum tuberosum/genetics ; }, abstract = {BACKGROUND: Solanum sect. Basarthrum is phylogenetically very close to potatoes (Solanum sect. Petota) and tomatoes (Solanum sect. Lycopersicon), two groups with great economic importance, and for which Solanum sect. Basarthrum represents a tertiary gene pool for breeding. This section includes the important regional cultigen, the pepino (Solanum muricatum), and several wild species. Among the wild species, S. caripense is prominent due to its major involvement in the origin of pepino and its wide geographical distribution. Despite the value of the pepino as an emerging crop, and the potential for gene transfer from both the pepino and S. caripense to potatoes and tomatoes, there has been virtually no genomic study of these species.

RESULTS: Using Illumina HiSeq 2000, RNA-Seq was performed with a pool of three tissues (young leaf, flowers in pre-anthesis and mature fruits) from S. muricatum and S. caripense, generating almost 111,000,000 reads among the two species. A high quality de novo transcriptome was assembled from S. muricatum clean reads resulting in 75,832 unigenes with an average length of 704 bp. These unigenes were functionally annotated based on similarity of public databases. We used Blast2GO, to conduct an exhaustive study of the gene ontology, including GO terms, EC numbers and KEGG pathways. Pepino unigenes were compared to both potato and tomato genomes in order to determine their estimated relative position, and to infer gene prediction models. Candidate genes related to traits of interest in other Solanaceae were evaluated by presence or absence and compared with S. caripense transcripts. In addition, by studying five genes, the phylogeny of pepino and five other members of the family, Solanaceae, were studied. The comparison of S. caripense reads against S. muricatum assembled transcripts resulted in thousands of intra- and interspecific nucleotide-level variants. In addition, more than 1000 SSRs were identified in the pepino transcriptome.

CONCLUSIONS: This study represents the first genomic resource for the pepino. We suggest that the data will be useful not only for improvement of the pepino, but also for potato and tomato breeding and gene transfer. The high quality of the transcriptome presented here also facilitates comparative studies in the genus Solanum. The accurate transcript annotation will enable us to figure out the gene function of particular traits of interest. The high number of markers (SSR and nucleotide-level variants) obtained will be useful for breeding programs, as well as studies of synteny, diversity evolution, and phylogeny.}, } @article {pmid27140965, year = {2016}, author = {Jovelin, R and Krizus, A and Taghizada, B and Gray, JC and Phillips, PC and Claycomb, JM and Cutter, AD}, title = {Comparative genomic analysis of upstream miRNA regulatory motifs in Caenorhabditis.}, journal = {RNA (New York, N.Y.)}, volume = {22}, number = {7}, pages = {968-978}, pmid = {27140965}, issn = {1469-9001}, support = {R01 GM096008/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Caenorhabditis/*genetics ; Gene Expression Regulation ; MicroRNAs/*genetics ; Phylogeny ; RNA, Helminth/*genetics ; *Regulatory Sequences, Nucleic Acid ; }, abstract = {MicroRNAs (miRNAs) comprise a class of short noncoding RNA molecules that play diverse developmental and physiological roles by controlling mRNA abundance and protein output of the vast majority of transcripts. Despite the importance of miRNAs in regulating gene function, we still lack a complete understanding of how miRNAs themselves are transcriptionally regulated. To fill this gap, we predicted regulatory sequences by searching for abundant short motifs located upstream of miRNAs in eight species of Caenorhabditis nematodes. We identified three conserved motifs across the Caenorhabditis phylogeny that show clear signatures of purifying selection from comparative genomics, patterns of nucleotide changes in motifs of orthologous miRNAs, and correlation between motif incidence and miRNA expression. We then validated our predictions with transgenic green fluorescent protein reporters and site-directed mutagenesis for a subset of motifs located in an enhancer region upstream of let-7 We demonstrate that a CT-dinucleotide motif is sufficient for proper expression of GFP in the seam cells of adult C. elegans, and that two other motifs play incremental roles in combination with the CT-rich motif. Thus, functional tests of sequence motifs identified through analysis of molecular evolutionary signatures provide a powerful path for efficiently characterizing the transcriptional regulation of miRNA genes.}, } @article {pmid27138046, year = {2016}, author = {Lan, Y and Rosen, G and Hershberg, R}, title = {Marker genes that are less conserved in their sequences are useful for predicting genome-wide similarity levels between closely related prokaryotic strains.}, journal = {Microbiome}, volume = {4}, number = {1}, pages = {18}, pmid = {27138046}, issn = {2049-2618}, mesh = {Archaea/*classification/*genetics ; Bacteria/*classification/*genetics ; Base Sequence ; Conserved Sequence/genetics ; Databases, Genetic ; Genes, Essential/*genetics ; Genetic Markers/genetics ; Genome, Archaeal/genetics ; Genome, Bacterial/genetics ; Phylogeny ; RNA, Ribosomal, 16S/*genetics ; Sequence Alignment ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: The 16s rRNA gene is so far the most widely used marker for taxonomical classification and separation of prokaryotes. Since it is universally conserved among prokaryotes, it is possible to use this gene to classify a broad range of prokaryotic organisms. At the same time, it has often been noted that the 16s rRNA gene is too conserved to separate between prokaryotes at finer taxonomic levels.

RESULTS: In this paper, we examine how well levels of similarity of 16s rRNA and 73 additional universal or nearly universal marker genes correlate with genome-wide levels of gene sequence similarity. We demonstrate that the percent identity of 16s rRNA predicts genome-wide levels of similarity very well for distantly related prokaryotes, but not for closely related ones. In closely related prokaryotes, we find that there are many other marker genes for which levels of similarity are much more predictive of genome-wide levels of gene sequence similarity. Finally, we show that the identities of the markers that are most useful for predicting genome-wide levels of similarity within closely related prokaryotic lineages vary greatly between lineages. However, the most useful markers are always those that are least conserved in their sequences within each lineage.

CONCLUSIONS: Our results show that by choosing markers that are less conserved in their sequences within a lineage of interest, it is possible to better predict genome-wide gene sequence similarity between closely related prokaryotes than is possible using the 16s rRNA gene. We point readers towards a database we have created (POGO-DB) that can be used to easily establish which markers show lowest levels of sequence conservation within different prokaryotic lineages.}, } @article {pmid27137446, year = {2016}, author = {Wang, XY and He, J and Yang, K and Liang, S}, title = {Applications of Spatial Technology in Schistosomiasis Control Programme in The People's Republic of China.}, journal = {Advances in parasitology}, volume = {92}, number = {}, pages = {143-163}, doi = {10.1016/bs.apar.2016.02.020}, pmid = {27137446}, issn = {2163-6079}, mesh = {Animals ; China/epidemiology ; Geographic Information Systems ; Geography ; Humans ; Remote Sensing Technology ; Schistosoma/*physiology ; Schistosomiasis/epidemiology/parasitology/*prevention & control ; Spatio-Temporal Analysis ; }, abstract = {Schistosomiasis, as the important parasitic disease, has caused serious threats to human health globally. The People's Republic of China has acquired significant achievements based on large-scale interventions and innovational technology. The spatial technology was introduced in 1980s and widely used in the study and control of schistosomiasis in The People's Republic of China. This chapter reviews the progress and application of spatial technology in schistosomiasis control by analysing the spatiotemporal pattern of and the impact of ecological changes on schistosomiasis transmission, which have provided the information to design and select the control strategy, and assisted the establishment of the monitoring and early warning system in The People's Republic of China, especially in the marshland and mountainous regions.}, } @article {pmid27130172, year = {2017}, author = {Anikin, A and Persson, T}, title = {Nonlinguistic vocalizations from online amateur videos for emotion research: A validated corpus.}, journal = {Behavior research methods}, volume = {49}, number = {2}, pages = {758-771}, doi = {10.3758/s13428-016-0736-y}, pmid = {27130172}, issn = {1554-3528}, mesh = {Adult ; *Databases, Factual ; *Emotions ; Female ; Humans ; *Internet ; Language ; Male ; *Nonverbal Communication ; *Psychoacoustics ; Recognition, Psychology ; *Videotape Recording ; *Voice ; }, abstract = {This study introduces a corpus of 260 naturalistic human nonlinguistic vocalizations representing nine emotions: amusement, anger, disgust, effort, fear, joy, pain, pleasure, and sadness. The recognition accuracy in a rating task varied greatly per emotion, from <40% for joy and pain, to >70% for amusement, pleasure, fear, and sadness. In contrast, the raters' linguistic-cultural group had no effect on recognition accuracy: The predominantly English-language corpus was classified with similar accuracies by participants from Brazil, Russia, Sweden, and the UK/USA. Supervised random forest models classified the sounds as accurately as the human raters. The best acoustic predictors of emotion were pitch, harmonicity, and the spacing and regularity of syllables. This corpus of ecologically valid emotional vocalizations can be filtered to include only sounds with high recognition rates, in order to study reactions to emotional stimuli of known perceptual types (reception side), or can be used in its entirety to study the association between affective states and vocal expressions (production side).}, } @article {pmid27128031, year = {2016}, author = {Lin, Q and Luo, W and Wan, S and Gao, Z}, title = {De Novo Transcriptome Analysis of Two Seahorse Species (Hippocampus erectus and H. mohnikei) and the Development of Molecular Markers for Population Genetics.}, journal = {PloS one}, volume = {11}, number = {4}, pages = {e0154096}, pmid = {27128031}, issn = {1932-6203}, mesh = {Animals ; *Gene Expression Profiling ; Gene Ontology ; Genetic Variation ; Genetics, Population ; High-Throughput Nucleotide Sequencing ; Metabolic Networks and Pathways ; Microsatellite Repeats ; Molecular Sequence Annotation ; Smegmamorpha/*genetics/metabolism ; Transcriptome ; }, abstract = {Seahorse conservation has been performed utilizing various strategies for many decades, and the deeper understanding of genomic information is necessary to more efficiently protect the germplasm resources of seahorse species. However, little genetic information about seahorses currently exists in the public databases. In this study, high-throughput RNA sequencing for two seahorse species, Hippocampus erectus and H. mohnikei, was carried out, and de novo assembly generated 37,506 unigenes for H. erectus and 36,113 unigenes for H. mohnikei. Among them, 17,338 (46.23%) unigenes for H. erectus and 17,900 (49.57%) for H. mohnikei were successfully annotated based on the information available from the public databases. Through comparing the unigenes of two seahorse species, 7,802 candidate orthologous genes were identified and 5,268 genes among them could be annotated. In addition, gene ontology analysis of two species was similarly performed on biological processes, cellular components, and molecular functions. Twenty-four and twenty-one unigenes in H. erectus and H. mohnikei were annotated in the biosynthesis of unsaturated fatty acids pathways, and both seahorses lacked the Δ12 and Δ15 desaturases. Total of 8,992 and 9,116 SSR loci were obtained from H. erectus and H. mohnikei unigenes, respectively. Dozens of SSR were developed and then applied to assess the population genetic diversity, as well as cross-amplified in a related species, H. trimaculatus. The HO and HE values of the tested populations for H. erectus, H. mohnikei, and H. trimaculatus were medium. These resources would facilitate the conservation of the species through a better understanding of the genomics and comparative genome analysis within the Hippocampus genus.}, } @article {pmid27126702, year = {2016}, author = {Solbakken, MH and Tørresen, OK and Nederbragt, AJ and Seppola, M and Gregers, TF and Jakobsen, KS and Jentoft, S}, title = {Evolutionary redesign of the Atlantic cod (Gadus morhua L.) Toll-like receptor repertoire by gene losses and expansions.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {25211}, pmid = {27126702}, issn = {2045-2322}, mesh = {Animals ; *Evolution, Molecular ; Gadus morhua/*genetics ; Gene Expression Profiling ; Gene Expression Regulation, Developmental ; Selection, Genetic ; Toll-Like Receptors/*genetics ; }, abstract = {Genome sequencing of the teleost Atlantic cod demonstrated loss of the Major Histocompatibility Complex (MHC) class II, an extreme gene expansion of MHC class I and gene expansions and losses in the innate pattern recognition receptor (PRR) family of Toll-like receptors (TLR). In a comparative genomic setting, using an improved version of the genome, we characterize PRRs in Atlantic cod with emphasis on TLRs demonstrating the loss of TLR1/6, TLR2 and TLR5 and expansion of TLR7, TLR8, TLR9, TLR22 and TLR25. We find that Atlantic cod TLR expansions are strongly influenced by diversifying selection likely to increase the detectable ligand repertoire through neo- and subfunctionalization. Using RNAseq we find that Atlantic cod TLRs display likely tissue or developmental stage-specific expression patterns. In a broader perspective, a comprehensive vertebrate TLR phylogeny reveals that the Atlantic cod TLR repertoire is extreme with regards to losses and expansions compared to other teleosts. In addition we identify a substantial shift in TLR repertoires following the evolutionary transition from an aquatic vertebrate (fish) to a terrestrial (tetrapod) life style. Collectively, our findings provide new insight into the function and evolution of TLRs in Atlantic cod as well as the evolutionary history of vertebrate innate immunity.}, } @article {pmid27126235, year = {2016}, author = {Salnikova, LE and Khadzhieva, MB and Kolobkov, DS}, title = {Biological findings from the PheWAS catalog: focus on connective tissue-related disorders (pelvic floor dysfunction, abdominal hernia, varicose veins and hemorrhoids).}, journal = {Human genetics}, volume = {135}, number = {7}, pages = {779-795}, pmid = {27126235}, issn = {1432-1203}, mesh = {Connective Tissue/pathology ; Databases, Factual ; Genetic Predisposition to Disease ; Hemorrhoids/epidemiology/*genetics/physiopathology ; Hernia, Abdominal/epidemiology/*genetics/physiopathology ; Humans ; Pelvic Floor Disorders/epidemiology/*genetics/physiopathology ; Phenotype ; Risk Factors ; Varicose Veins/epidemiology/*genetics/physiopathology ; }, abstract = {Pelvic floor dysfunction, specifically genital prolapse (GP) and stress urinary inconsistency (SUI) presumably co-occur with other connective tissue disorders such as hernia, hemorrhoids, and varicose veins. Observations on non-random coexistence of these disorders have never been summarized in a meta-analysis. The performed meta-analysis demonstrated that varicose veins and hernia are associated with GP. Disease connections on the molecular level may be partially based on shared genetic susceptibility. A unique opportunity to estimate shared genetic susceptibility to disorders is provided by a PheWAS (phenome-wide association study) designed to utilize GWAS data concurrently to many phenotypes. We searched the PheWAS Catalog, which includes the results of the PheWAS study with P value < 0.05, for genes associated with GP, SUI, abdominal hernia, varicose veins and hemorrhoids. We found pronounced signals for the associations of the SLC2A9 gene with SUI (P = 6.0e-05) and the MYH9 gene with varicose veins of lower extremity (P = 0.0001) and hemorrhoids (P = 0.0007). The comparison of the PheWAS Catalog and the NHGRI Catalog data revealed enrichment of genes associated with bone mineral density in GP and with activated partial thromboplastin time in varicose veins of lower extremity. In cross-phenotype associations, genes responsible for peripheral nerve functions seem to predominate. This study not only established novel biologically plausible associations that may warrant further studies but also exemplified an effective use of the PheWAS Catalog data.}, } @article {pmid27126040, year = {2016}, author = {Zhernakova, A and Kurilshikov, A and Bonder, MJ and Tigchelaar, EF and Schirmer, M and Vatanen, T and Mujagic, Z and Vila, AV and Falony, G and Vieira-Silva, S and Wang, J and Imhann, F and Brandsma, E and Jankipersadsing, SA and Joossens, M and Cenit, MC and Deelen, P and Swertz, MA and , and Weersma, RK and Feskens, EJ and Netea, MG and Gevers, D and Jonkers, D and Franke, L and Aulchenko, YS and Huttenhower, C and Raes, J and Hofker, MH and Xavier, RJ and Wijmenga, C and Fu, J}, title = {Population-based metagenomics analysis reveals markers for gut microbiome composition and diversity.}, journal = {Science (New York, N.Y.)}, volume = {352}, number = {6285}, pages = {565-569}, pmid = {27126040}, issn = {1095-9203}, support = {310372/ERC_/European Research Council/International ; 322698/ERC_/European Research Council/International ; P30 DK043351/DK/NIDDK NIH HHS/United States ; }, mesh = {Bacteria/*classification/genetics/isolation & purification ; Chromogranin A/analysis/metabolism ; Diet ; Enteroendocrine Cells/metabolism ; Feces/chemistry/microbiology ; Gastrointestinal Microbiome/*genetics ; Gastrointestinal Tract/*microbiology ; Genetic Markers ; High-Throughput Nucleotide Sequencing ; Humans ; Metagenomics ; Netherlands ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Deep sequencing of the gut microbiomes of 1135 participants from a Dutch population-based cohort shows relations between the microbiome and 126 exogenous and intrinsic host factors, including 31 intrinsic factors, 12 diseases, 19 drug groups, 4 smoking categories, and 60 dietary factors. These factors collectively explain 18.7% of the variation seen in the interindividual distance of microbial composition. We could associate 110 factors to 125 species and observed that fecal chromogranin A (CgA), a protein secreted by enteroendocrine cells, was exclusively associated with 61 microbial species whose abundance collectively accounted for 53% of microbial composition. Low CgA concentrations were seen in individuals with a more diverse microbiome. These results are an important step toward a better understanding of environment-diet-microbe-host interactions.}, } @article {pmid27125885, year = {2016}, author = {Lee, HG and Jo, J and Hong, HH and Kim, KK and Park, JK and Cho, SJ and Park, C}, title = {State-of-the-art housekeeping proteins for quantitative western blotting: Revisiting the first draft of the human proteome.}, journal = {Proteomics}, volume = {16}, number = {13}, pages = {1863-1867}, doi = {10.1002/pmic.201500344}, pmid = {27125885}, issn = {1615-9861}, mesh = {Blotting, Western/*methods ; Chromatography, Liquid/methods ; Databases, Protein ; Humans ; Protein Interaction Maps ; Proteome/*analysis/metabolism ; Proteomics/*methods ; Tandem Mass Spectrometry/methods ; }, abstract = {Western blotting (WB) analysis is the most popular and widely used methodology for protein detection and characterization over recent decades. In accordance with the advancement of the technologies for the acquisition of WB signals, a quantitative value is used to present the abundance of target proteins in a complex sample, thereby requiring the use of specific proteins as internal references that represent total proteins. Heretofore, proteins encoded by housekeeping genes such as GAPDH, β-tubulin and β-actin have been commonly used as loading controls without any hesitation because their mRNA expression levels tend to be high and constant in many different cells and tissues. Experimentally, however, some of the housekeeping reference proteins are often displayed with inconsistent expression levels in both homogeneous and heterogeneous tissues, and, in terms of mRNA levels, they have a weak correlation to the abundance of proteins. To estimate accurate, reliable, and reproducible protein quantifications, it is crucial to define appropriate reference controls. For this paper, we explored the recently released large-scale, human proteomic database ProteomicsDB including 16 857 liquid chromatography tandem-mass-spectrometry data from 27 human tissues, and suggest 20 ubiquitously- and constitutively-expressed, putative internal-reference controls for the quantification of differential protein expressions. Intriguingly, the most commonly used, known housekeeping genes were entirely excluded in our newly defined candidates. Although the applications of the candidates under many different biological conditions and in other organisms are yet to be empirically verified, we propose reliable, potential loading controls for a WB analysis in this paper.}, } @article {pmid27124399, year = {2016}, author = {Tandon, D and Haque, MM and Mande, SS}, title = {Inferring Intra-Community Microbial Interaction Patterns from Metagenomic Datasets Using Associative Rule Mining Techniques.}, journal = {PloS one}, volume = {11}, number = {4}, pages = {e0154493}, pmid = {27124399}, issn = {1932-6203}, mesh = {Algorithms ; Data Mining/*methods ; Databases, Genetic ; Gastrointestinal Microbiome ; Humans ; *Metagenome ; *Microbial Interactions ; Web Browser ; }, abstract = {The nature of inter-microbial metabolic interactions defines the stability of microbial communities residing in any ecological niche. Deciphering these interaction patterns is crucial for understanding the mode/mechanism(s) through which an individual microbial community transitions from one state to another (e.g. from a healthy to a diseased state). Statistical correlation techniques have been traditionally employed for mining microbial interaction patterns from taxonomic abundance data corresponding to a given microbial community. In spite of their efficiency, these correlation techniques can capture only 'pair-wise interactions'. Moreover, their emphasis on statistical significance can potentially result in missing out on several interactions that are relevant from a biological standpoint. This study explores the applicability of one of the earliest association rule mining algorithm i.e. the 'Apriori algorithm' for deriving 'microbial association rules' from the taxonomic profile of given microbial community. The classical Apriori approach derives association rules by analysing patterns of co-occurrence/co-exclusion between various '(subsets of) features/items' across various samples. Using real-world microbiome data, the efficiency/utility of this rule mining approach in deciphering multiple (biologically meaningful) association patterns between 'subsets/subgroups' of microbes (constituting microbiome samples) is demonstrated. As an example, association rules derived from publicly available gut microbiome datasets indicate an association between a group of microbes (Faecalibacterium, Dorea, and Blautia) that are known to have mutualistic metabolic associations among themselves. Application of the rule mining approach on gut microbiomes (sourced from the Human Microbiome Project) further indicated similar microbial association patterns in gut microbiomes irrespective of the gender of the subjects. A Linux implementation of the Association Rule Mining (ARM) software (customised for deriving 'microbial association rules' from microbiome data) is freely available for download from the following link: http://metagenomics.atc.tcs.com/arm.}, } @article {pmid27119084, year = {2016}, author = {Franta, Z and Vogel, H and Lehmann, R and Rupp, O and Goesmann, A and Vilcinskas, A}, title = {Next Generation Sequencing Identifies Five Major Classes of Potentially Therapeutic Enzymes Secreted by Lucilia sericata Medical Maggots.}, journal = {BioMed research international}, volume = {2016}, number = {}, pages = {8285428}, pmid = {27119084}, issn = {2314-6141}, mesh = {Animals ; Cluster Analysis ; Contig Mapping ; Databases, Factual ; Debridement/methods ; Diptera/*enzymology ; Enzymes/genetics/*isolation & purification ; Gene Expression Profiling ; Insect Proteins/genetics/*isolation & purification ; Intestines/enzymology ; Larva/enzymology ; Peptide Hydrolases/chemistry ; Proteolysis ; Pseudomonas aeruginosa ; Real-Time Polymerase Chain Reaction ; Reverse Transcriptase Polymerase Chain Reaction ; Salivary Glands/enzymology ; Sequence Analysis, RNA ; Staphylococcus aureus ; Transcriptome ; Wound Healing ; }, abstract = {Lucilia sericata larvae are used as an alternative treatment for recalcitrant and chronic wounds. Their excretions/secretions contain molecules that facilitate tissue debridement, disinfect, or accelerate wound healing and have therefore been recognized as a potential source of novel therapeutic compounds. Among the substances present in excretions/secretions various peptidase activities promoting the wound healing processes have been detected but the peptidases responsible for these activities remain mostly unidentified. To explore these enzymes we applied next generation sequencing to analyze the transcriptomes of different maggot tissues (salivary glands, gut, and crop) associated with the production of excretions/secretions and/or with digestion as well as the rest of the larval body. As a result we obtained more than 123.8 million paired-end reads, which were assembled de novo using Trinity and Oases assemblers, yielding 41,421 contigs with an N50 contig length of 2.22 kb and a total length of 67.79 Mb. BLASTp analysis against the MEROPS database identified 1729 contigs in 577 clusters encoding five peptidase classes (serine, cysteine, aspartic, threonine, and metallopeptidases), which were assigned to 26 clans, 48 families, and 185 peptidase species. The individual enzymes were differentially expressed among maggot tissues and included peptidase activities related to the therapeutic effects of maggot excretions/secretions.}, } @article {pmid27117388, year = {2016}, author = {Yu, CP and Lin, JJ and Li, WH}, title = {Positional distribution of transcription factor binding sites in Arabidopsis thaliana.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {25164}, pmid = {27117388}, issn = {2045-2322}, mesh = {Arabidopsis/*genetics/metabolism ; Arabidopsis Proteins/genetics/metabolism ; Binding Sites ; Chromatin Immunoprecipitation ; Computational Biology/*methods ; DNA, Plant/chemistry/*metabolism ; Oligonucleotide Array Sequence Analysis ; Promoter Regions, Genetic ; Sequence Analysis, DNA ; Transcription Factors/chemistry/*metabolism ; Transcription Initiation Site ; }, abstract = {Binding of a transcription factor (TF) to its DNA binding sites (TFBSs) is a critical step to initiate the transcription of its target genes. It is therefore interesting to know where the TFBSs of a gene are likely to locate in the promoter region. Here we studied the positional distribution of TFBSs in Arabidopsis thaliana, for which many known TFBSs are now available. We developed a method to identify the locations of TFBSs in the promoter sequences of genes in A. thaliana. We found that the distribution is nearly bell-shaped with a peak at 50 base pairs (bp) upstream of the transcription start site (TSS) and 86% of the TFBSs are in the region from -1,000 bp to +200 bp with respect to the TSS. Our distribution was supported by chromatin immunoprecipitation sequencing and microarray data and DNase I hypersensitive site sequencing data. When TF families were considered separately, differences in positional preference were observed between TF families. Our study of the positional distribution of TFBSs seems to be the first in a plant.}, } @article {pmid27109483, year = {2016}, author = {Pylro, VS and Morais, DK and Kalks, KH and Roesch, LF and Hirsch, PR and Tótola, MR and Yotoko, K}, title = {Misguided phylogenetic comparisons using DGGE excised bands may contaminate public sequence databases.}, journal = {Journal of microbiological methods}, volume = {126}, number = {}, pages = {18-23}, doi = {10.1016/j.mimet.2016.04.012}, pmid = {27109483}, issn = {1872-8359}, mesh = {Bacteria/classification/*genetics/isolation & purification ; Databases, Nucleic Acid/*standards ; *Denaturing Gradient Gel Electrophoresis/methods ; Genes, rRNA ; *Phylogeny ; Polymerase Chain Reaction/methods ; RNA, Ribosomal, 16S/*genetics ; }, abstract = {Controversy surrounding bacterial phylogenies has become one of the most important challenges for microbial ecology. Comparative analyses with nucleotide databases and phylogenetic reconstruction of the amplified 16S rRNA genes from DGGE (Denaturing Gradient Gel Electrophoresis) excised bands have been used by several researchers for the identification of organisms in complex samples. Here, we individually analyzed DGGE-excised 16S rRNA gene bands from 10 certified bacterial strains of different species, and demonstrated that this kind of approach can deliver erroneous outcomes to researchers, besides causing/emphasizing errors in public databases.}, } @article {pmid27100086, year = {2016}, author = {Le, HT and Angotzi, AR and Ebbesson, LO and Karlsen, Ø and Rønnestad, I}, title = {The Ontogeny and Brain Distribution Dynamics of the Appetite Regulators NPY, CART and pOX in Larval Atlantic Cod (Gadus morhua L.).}, journal = {PloS one}, volume = {11}, number = {4}, pages = {e0153743}, pmid = {27100086}, issn = {1932-6203}, mesh = {Animals ; Appetite Regulation/*physiology ; Brain/cytology/*metabolism ; Fish Proteins/genetics/*metabolism ; Gadus morhua/*physiology ; Gene Expression Regulation, Developmental ; Gene Ontology ; In Situ Hybridization, Fluorescence ; Larva/cytology/*physiology ; Nerve Tissue Proteins/genetics/*metabolism ; Neuropeptides/genetics/*metabolism ; }, abstract = {Similar to many marine teleost species, Atlantic cod undergo remarkable physiological changes during the early life stages with concurrent and profound changes in feeding biology and ecology. In contrast to the digestive system, very little is known about the ontogeny and the localization of the centers that control appetite and feed ingestion in the developing brain of fish. We examined the expression patterns of three appetite regulating factors (orexigenic: neuropeptide Y, NPY; prepro-orexin, pOX and anorexigenic: cocaine- and amphetamine-regulated transcript, CART) in discrete brain regions of developing Atlantic cod using chromogenic and double fluorescent in situ hybridization. Differential temporal and spatial expression patterns for each appetite regulator were found from first feeding (4 days post hatch; dph) to juvenile stage (76 dph). Neurons expressing NPY mRNA were detected in the telencephalon (highest expression), diencephalon, and optic tectum from 4 dph onward. CART mRNA expression had a wider distribution along the anterior-posterior brain axis, including both telencephalon and diencephalon from 4 dph. From 46 dph, CART transcripts were also detected in the olfactory bulb, region of the nucleus of medial longitudinal fascicle, optic tectum and midbrain tegmentum. At 4 and 20 dph, pOX mRNA expression was exclusively found in the preoptic region, but extended to the hypothalamus at 46 and 76 dph. Co-expression of both CART and pOX genes were also observed in several hypothalamic neurons throughout larval development. Our results show that both orexigenic and anorexigenic factors are present in the telencephalon, diencephalon and mesencephalon in cod larvae. The telencephalon mostly contains key factors of hunger control (NPY), while the diencephalon, and particularly the hypothalamus may have a more complex role in modulating the multifunctional control of appetite in this species. As the larvae develop, the overall progression in temporal and spatial complexity of NPY, CART and pOX mRNAs expression might be correlated to the maturation of appetite control regulation. These observations suggest that teleost larvae continue to develop the regulatory networks underlying appetite control after onset of exogenous feeding.}, } @article {pmid27099553, year = {2016}, author = {Leidenberger, S and Käck, M and Karlsson, B and Kindvall, O}, title = {The Analysis Portal and the Swedish LifeWatch e-infrastructure for biodiversity research.}, journal = {Biodiversity data journal}, volume = {}, number = {4}, pages = {e7644}, pmid = {27099553}, issn = {1314-2828}, abstract = {BACKGROUND: During the last years, more and more online portals were generated and are now available for ecologists to run advanced models with extensive data sets. Some examples are the Biodiversity Virtual e-Laboratory (BioVel) Portal (https://portal.biovel.eu) for ecological niche modelling and the Mobyle SNAP Workbench (https://snap.hpc.ncsu.edu) for evolutionary and population genetics analysis. Such portals have the main goal to facilitate the run of advanced models, through access to large-capacity computers or servers. In this study, we present the Analysis Portal (www.analysisportal.se), which is a part of the Swedish LifeWatch e-infrastructure for biodiversity research that combines a variety of Swedish web services to perform different kinds of dataprocessing.

NEW INFORMATION: For the first time, the Swedish Analysis Portal for integrated analysis of species occurrence data is described in detail. It was launched in 2013 and today, over 60 Million Swedish species observation records can be assessed, visualized and analyzed via the portal. Datasets can be assembled using sophisticated filtering tools, and combined with environmental and climatic data from a wide range of providers. Different validation tools, for example the official Swedish taxon concept database Dyntaxa, ensure high data quality. Results can be downloaded in different formats as maps, tables, diagrams and reports.}, } @article {pmid27094624, year = {2016}, author = {Varela-Silva, MI and Bogin, B and Sobral, JA and Dickinson, F and Monserrat-Revillo, S and , }, title = {Deep data science to prevent and treat growth faltering in Maya children.}, journal = {European journal of clinical nutrition}, volume = {70}, number = {6}, pages = {679-680}, pmid = {27094624}, issn = {1476-5640}, mesh = {Adolescent ; Adolescent Development ; Body Height ; Body Weight ; Central America/epidemiology ; Child ; Child Development ; Child, Preschool ; Cognitive Dysfunction/prevention & control/therapy ; Databases, Factual ; Female ; Growth Disorders/epidemiology/*prevention & control/*therapy ; Guatemala/epidemiology ; Humans ; Longitudinal Studies ; Male ; Mexico/epidemiology ; Rural Population ; United States ; }, abstract = {The Maya people are descended from the indigenous inhabitants of southern Mexico, Guatemala and adjacent regions of Central America. In Guatemala, 50% of infants and children are stunted (very low height-for-age), and some rural Maya regions have >70% children stunted. A large, longitudinal, intergenerational database was created to (1) provide deep data to prevent and treat somatic growth faltering and impaired neurocognitive development, (2) detect key dependencies and predictive relations between highly complex, time-varying, and interacting biological and cultural variables and (3) identify targeted multifactorial intervention strategies for field testing and validation. Contributions to this database included data from the Universidad del Valle de Guatemala Longitudinal Study of Child and Adolescent Development, child growth and intergenerational studies among the Maya in Mexico and studies about Maya migrants in the United States.}, } @article {pmid27093907, year = {2016}, author = {Ackerman, JT and Eagles-Smith, CA and Herzog, MP and Hartman, CA and Peterson, SH and Evers, DC and Jackson, AK and Elliott, JE and Vander Pol, SS and Bryan, CE}, title = {Avian mercury exposure and toxicological risk across western North America: A synthesis.}, journal = {The Science of the total environment}, volume = {568}, number = {}, pages = {749-769}, pmid = {27093907}, issn = {1879-1026}, support = {9999-NIST//Intramural NIST DOC/United States ; }, mesh = {Animals ; Birds/*blood/classification ; Canada ; Databases, Factual ; Environmental Monitoring/*methods ; Environmental Pollutants/*analysis/pharmacokinetics/*toxicity ; Geographic Information Systems ; Methylmercury Compounds/*analysis/pharmacokinetics/*toxicity ; Midwestern United States ; Models, Biological ; Northwestern United States ; Risk Assessment ; Southwestern United States ; Species Specificity ; Tissue Distribution ; }, abstract = {Methylmercury contamination of the environment is an important issue globally, and birds are useful bioindicators for mercury monitoring programs. The available data on mercury contamination of birds in western North America were synthesized. Original data from multiple databases were obtained and a literature review was conducted to obtain additional mercury concentrations. In total, 29219 original bird mercury concentrations from 225 species were compiled, and an additional 1712 mean mercury concentrations, representing 19998 individuals and 176 species, from 200 publications were obtained. To make mercury data comparable across bird tissues, published equations of tissue mercury correlations were used to convert all mercury concentrations into blood-equivalent mercury concentrations. Blood-equivalent mercury concentrations differed among species, foraging guilds, habitat types, locations, and ecoregions. Piscivores and carnivores exhibited the greatest mercury concentrations, whereas herbivores and granivores exhibited the lowest mercury concentrations. Bird mercury concentrations were greatest in ocean and salt marsh habitats and lowest in terrestrial habitats. Bird mercury concentrations were above toxicity benchmarks in many areas throughout western North America, and multiple hotspots were identified. Additionally, published toxicity benchmarks established in multiple tissues were summarized and translated into a common blood-equivalent mercury concentration. Overall, 66% of birds sampled in western North American exceeded a blood-equivalent mercury concentration of 0.2 μg/g wet weight (ww; above background levels), which is the lowest-observed effect level, 28% exceeded 1.0 μg/g ww (moderate risk), 8% exceeded 3.0 μg/g ww (high risk), and 4% exceeded 4.0 μg/g ww (severe risk). Mercury monitoring programs should sample bird tissues, such as adult blood and eggs, that are most-easily translated into tissues with well-developed toxicity benchmarks and that are directly relevant to bird reproduction. Results indicate that mercury contamination of birds is prevalent in many areas throughout western North America, and large-scale ecological attributes are important factors influencing bird mercury concentrations.}, } @article {pmid27091919, year = {2016}, author = {Kmetty, Z and Bozsonyi, K and Zonda, T}, title = {[Ecological study of the Hungarian suicide data using complex statistical methods].}, journal = {Psychiatria Hungarica : A Magyar Pszichiatriai Tarsasag tudomanyos folyoirata}, volume = {31}, number = {1}, pages = {5-14}, pmid = {27091919}, issn = {0237-7896}, mesh = {Adult ; Aged ; Alcohol Drinking/epidemiology/psychology ; Antidepressive Agents/*therapeutic use ; Data Interpretation, Statistical ; Divorce/psychology/statistics & numerical data ; Female ; Humans ; Hungary/epidemiology ; Male ; Middle Aged ; Research Design ; Risk Factors ; *Social Environment ; Suicide/*psychology/*statistics & numerical data/trends ; Unemployment/psychology/statistics & numerical data ; Suicide Prevention ; }, abstract = {UNLABELLED: Problem posing:According to a number of psychiatrists, the decrease in the number of suicides can almost exclusively be ascribed to the increasing use of new antidepressants (ADs). Several ecological studies have been carried out to lend support to this claim; unfortunately, many of these started out from either methodologically or statistically flawed assumptions. The purpose of the current study is to demonstrate the examined relationships using complex time-series techniques on our national sample.

METHOD: When investigating the relationships between our time series, first we ensured their stationarity using several methods. We used two methods for the analysis involving several independent variables.

RESULTS: The models fitting our data showed somewhat mixed results. When using dynamic regression to ensure stationarity, the residuals of the suicide and AD time series showed a significant negative correlation. At the same time, when using the more robust technique of time series differentiation, the stationary time series showed no significant relationship between the use of antidepressants and suicide rates. Moreover, those regression models in which several independent variables were entered to control for the AD data showed no significant relationship between the variables either. A further detail is provided by the fact that according to our calculations, suicide rates are not Granger caused by the amount of antidepressants sold. However, the vagueness of ecological models is well demonstrated by the fact that even those sociological variables (number of divorces, alcohol consumption) failed to show a significant relationship with suicides here, which are usually significant in analyses using micro data.}, } @article {pmid27089125, year = {2016}, author = {Dreger, S and Krille, L and Maier, W and Pokora, R and Blettner, M and Zeeb, H}, title = {Regional Deprivation and Non-Cancer Related Computed Tomography Use in Pediatric Patients in Germany: Cross-Sectional Analysis of Cohort Data.}, journal = {PloS one}, volume = {11}, number = {4}, pages = {e0153644}, pmid = {27089125}, issn = {1932-6203}, support = {001/WHO_/World Health Organization/International ; }, mesh = {Adolescent ; Child ; Child, Preschool ; Cross-Sectional Studies ; Female ; Germany/epidemiology ; *Healthcare Disparities ; Humans ; Infant ; Infant, Newborn ; Male ; Neoplasms/epidemiology/*pathology ; Retrospective Studies ; *Social Class ; Socioeconomic Factors ; Tomography, X-Ray Computed/*statistics & numerical data ; }, abstract = {BACKGROUND: Conflicting findings were observed in recent studies assessing the association between patients' area-level socio-economic status and the received number of computed tomography (CT) examinations in children. The aim was to investigate the association between area-level socio-economic status and variation in CT examination practice for pediatric patients in Germany.

METHODS: Data from Radiology Information Systems for children aged 0 to < 15 years without cancer who had at least one CT examination between 2001 and 2010 were extracted in 20 hospitals across Germany. The small-area German Index of Multiple Deprivation (GIMD) was used to assess regional deprivation. The GIMD scores were classified into least, medium and most deprived areas and linked with the patient's last known postal code. A multinomial logistic regression model was used to assess the association between patients' CT numbers and regional deprivation adjusting for age, sex, and location of residence (urban/rural).

RESULTS: A total of 37,810 pediatric patients received 59,571 CT scans during the study period. 27,287 (72%) children received only one CT, while n = 885 (2.3%) received six or more. Increasing numbers of CT examinations in non-cancer patients were significantly associated with higher regional deprivation, which increased, although CI overlap, for higher CT categories: '2-3 CT' odds ratio (OR) = 1.45, 95%CI: 1.40-1.50; '4-5 CT' OR = 1.48, 95%CI: 1.38-1.59; '6+CT' OR = 1.54, 95%CI: 1.41-1.69. In addition, male sex, higher age categories, and specific body regions were positively associated with increased numbers of CT examinations.

CONCLUSION: We observed a positive association between regional deprivation and CT numbers in non-cancer pediatric patients. Limitations of the ecological approach and the lack of differentiation of CT details have to be acknowledged. More information on CT indications is necessary for a full assessment of this finding. In addition, further work on ways to assess socio-economic status more accurately may be required.}, } @article {pmid27088604, year = {2016}, author = {Lien, S and Koop, BF and Sandve, SR and Miller, JR and Kent, MP and Nome, T and Hvidsten, TR and Leong, JS and Minkley, DR and Zimin, A and Grammes, F and Grove, H and Gjuvsland, A and Walenz, B and Hermansen, RA and von Schalburg, K and Rondeau, EB and Di Genova, A and Samy, JK and Olav Vik, J and Vigeland, MD and Caler, L and Grimholt, U and Jentoft, S and Våge, DI and de Jong, P and Moen, T and Baranski, M and Palti, Y and Smith, DR and Yorke, JA and Nederbragt, AJ and Tooming-Klunderud, A and Jakobsen, KS and Jiang, X and Fan, D and Hu, Y and Liberles, DA and Vidal, R and Iturra, P and Jones, SJ and Jonassen, I and Maass, A and Omholt, SW and Davidson, WS}, title = {The Atlantic salmon genome provides insights into rediploidization.}, journal = {Nature}, volume = {533}, number = {7602}, pages = {200-205}, pmid = {27088604}, issn = {1476-4687}, mesh = {Animals ; DNA Transposable Elements/genetics ; *Diploidy ; *Evolution, Molecular ; Female ; Gene Duplication/*genetics ; Genes, Duplicate/*genetics ; Genome/*genetics ; Genomics ; Male ; Models, Genetic ; Mutagenesis/genetics ; Phylogeny ; Reference Standards ; Salmo salar/classification/*genetics ; Sequence Homology ; }, abstract = {The whole-genome duplication 80 million years ago of the common ancestor of salmonids (salmonid-specific fourth vertebrate whole-genome duplication, Ss4R) provides unique opportunities to learn about the evolutionary fate of a duplicated vertebrate genome in 70 extant lineages. Here we present a high-quality genome assembly for Atlantic salmon (Salmo salar), and show that large genomic reorganizations, coinciding with bursts of transposon-mediated repeat expansions, were crucial for the post-Ss4R rediploidization process. Comparisons of duplicate gene expression patterns across a wide range of tissues with orthologous genes from a pre-Ss4R outgroup unexpectedly demonstrate far more instances of neofunctionalization than subfunctionalization. Surprisingly, we find that genes that were retained as duplicates after the teleost-specific whole-genome duplication 320 million years ago were not more likely to be retained after the Ss4R, and that the duplicate retention was not influenced to a great extent by the nature of the predicted protein interactions of the gene products. Finally, we demonstrate that the Atlantic salmon assembly can serve as a reference sequence for the study of other salmonids for a range of purposes.}, } @article {pmid27085583, year = {2016}, author = {Li, M and Tan, X and Sui, Y and Jiao, S and Wu, Z and You, F}, title = {Conserved elements in the nanos3 3'UTR of olive flounder are responsible for the selective retention of RNA in germ cells.}, journal = {Comparative biochemistry and physiology. Part B, Biochemistry & molecular biology}, volume = {198}, number = {}, pages = {66-72}, doi = {10.1016/j.cbpb.2016.04.002}, pmid = {27085583}, issn = {1879-1107}, mesh = {3' Untranslated Regions/*genetics ; Animals ; Base Sequence ; Computational Biology ; *Conserved Sequence ; Female ; Fish Proteins/*genetics ; Flounder/*genetics ; Germ Cells/*metabolism ; Male ; RNA Stability ; RNA-Binding Proteins/*genetics ; }, abstract = {In teleost fish, primordial germ cells (PGCs) are specified very early during embryogenesis and migrate to the site that gonads are formed. A previous study indicated that nanos3 is specifically expressed in PGCs, and the 3' untranslated region (UTR) of nanos3 is responsible for the localization of mRNA in these cells. In this study, we aimed to investigate the functional regions of nanos3 3'UTR in olive flounder using truncated and mutated nanos3 3'UTRs fused to chimeric RNAs and microinjected into fertilized zebrafish eggs. The results indicated that a 68-bp functional element in the nanos3 3'UTR of olive flounder played important roles in the protection and degradation of RNA. Within this element, a U-rich region was identified to be responsible for the protection of RNA in PGCs and two GCAC sites for the degradation of RNA in somatic cells. The first GCAC was located adjacently to the U-rich region and the second GCAC within the U-rich region. Overall, we concluded that the two GCACs were the binding sites of miR-430, a microRNA that suppresses translation, whereas the U-rich region was the binding site of Dnd, a protein that antagonizes the miR-430-mediated silencing of mRNA.}, } @article {pmid27085184, year = {2016}, author = {Bickhart, DM and Xu, L and Hutchison, JL and Cole, JB and Null, DJ and Schroeder, SG and Song, J and Garcia, JF and Sonstegard, TS and Van Tassell, CP and Schnabel, RD and Taylor, JF and Lewin, HA and Liu, GE}, title = {Diversity and population-genetic properties of copy number variations and multicopy genes in cattle.}, journal = {DNA research : an international journal for rapid publication of reports on genes and genomes}, volume = {23}, number = {3}, pages = {253-262}, pmid = {27085184}, issn = {1756-1663}, mesh = {Animals ; Breeding ; Cattle/*genetics ; *DNA Copy Number Variations ; Gene Duplication ; *Genome ; *Multigene Family ; *Polymorphism, Genetic ; }, abstract = {The diversity and population genetics of copy number variation (CNV) in domesticated animals are not well understood. In this study, we analysed 75 genomes of major taurine and indicine cattle breeds (including Angus, Brahman, Gir, Holstein, Jersey, Limousin, Nelore, and Romagnola), sequenced to 11-fold coverage to identify 1,853 non-redundant CNV regions. Supported by high validation rates in array comparative genomic hybridization (CGH) and qPCR experiments, these CNV regions accounted for 3.1% (87.5 Mb) of the cattle reference genome, representing a significant increase over previous estimates of the area of the genome that is copy number variable (∼2%). Further population genetics and evolutionary genomics analyses based on these CNVs revealed the population structures of the cattle taurine and indicine breeds and uncovered potential diversely selected CNVs near important functional genes, including AOX1, ASZ1, GAT, GLYAT, and KRTAP9-1 Additionally, 121 CNV gene regions were found to be either breed specific or differentially variable across breeds, such as RICTOR in dairy breeds and PNPLA3 in beef breeds. In contrast, clusters of the PRP and PAG genes were found to be duplicated in all sequenced animals, suggesting that subfunctionalization, neofunctionalization, or overdominance play roles in diversifying those fertility-related genes. These CNV results provide a new glimpse into the diverse selection histories of cattle breeds and a basis for correlating structural variation with complex traits in the future.}, } @article {pmid27082742, year = {2016}, author = {Schulze, J and Frank, K and Priess, JA and Meyer, MA}, title = {Assessing Regional-Scale Impacts of Short Rotation Coppices on Ecosystem Services by Modeling Land-Use Decisions.}, journal = {PloS one}, volume = {11}, number = {4}, pages = {e0153862}, pmid = {27082742}, issn = {1932-6203}, mesh = {Agriculture/*methods ; Biodiversity ; Biofuels/supply & distribution ; Biomass ; Computer Simulation ; Conservation of Natural Resources/*economics ; Decision Support Techniques ; Ecology ; Ecosystem ; Germany ; Models, Economic ; Regression Analysis ; Soil ; Spatial Analysis ; }, abstract = {Meeting the world's growing energy demand through bioenergy production involves extensive land-use change which could have severe environmental and social impacts. Second generation bioenergy feedstocks offer a possible solution to this problem. They have the potential to reduce land-use conflicts between food and bioenergy production as they can be grown on low quality land not suitable for food production. However, a comprehensive impact assessment that considers multiple ecosystem services (ESS) and biodiversity is needed to identify the environmentally best feedstock option, as trade-offs are inherent. In this study, we simulate the spatial distribution of short rotation coppices (SRCs) in the landscape of the Mulde watershed in Central Germany by modeling profit-maximizing farmers under different economic and policy-driven scenarios using a spatially explicit economic simulation model. This allows to derive general insights and a mechanistic understanding of regional-scale impacts on multiple ESS in the absence of large-scale implementation. The modeled distribution of SRCs, required to meet the regional demand of combined heat and power (CHP) plants for solid biomass, had little or no effect on the provided ESS. In the policy-driven scenario, placing SRCs on low or high quality soils to provide ecological focus areas, as required within the Common Agricultural Policy in the EU, had little effect on ESS. Only a substantial increase in the SRC production area, beyond the regional demand of CHP plants, had a relevant effect, namely a negative impact on food production as well as a positive impact on biodiversity and regulating ESS. Beneficial impacts occurred for single ESS. However, the number of sites with balanced ESS supply hardly increased due to larger shares of SRCs in the landscape. Regression analyses showed that the occurrence of sites with balanced ESS supply was more strongly driven by biophysical factors than by the SRC share in the landscape. This indicates that SRCs negligibly affect trade-offs between individual ESS. Coupling spatially explicit economic simulation models with environmental and ESS assessment models can contribute to a comprehensive impact assessment of bioenergy feedstocks that have not yet been planted.}, } @article {pmid27074898, year = {2016}, author = {Leo, SS and Gonzalez, A and Millien, V}, title = {Multi-taxa integrated landscape genetics for zoonotic infectious diseases: deciphering variables influencing disease emergence.}, journal = {Genome}, volume = {59}, number = {5}, pages = {349-361}, doi = {10.1139/gen-2016-0039}, pmid = {27074898}, issn = {1480-3321}, mesh = {Animals ; Communicable Diseases, Emerging/epidemiology/*genetics/transmission ; Ecology ; Environment ; *Gene Flow ; Genetic Variation ; Genetics, Population/*methods ; Geographic Information Systems ; Host-Parasite Interactions ; Host-Pathogen Interactions ; *Models, Genetic ; Molecular Epidemiology ; Species Specificity ; Zoonoses/epidemiology/*genetics/transmission ; }, abstract = {Zoonotic disease transmission systems involve sets of species interacting with each other and their environment. This complexity impedes development of disease monitoring and control programs that require reliable identification of spatial and biotic variables and mechanisms facilitating disease emergence. To overcome this difficulty, we propose a framework that simultaneously examines all species involved in disease emergence by integrating concepts and methods from population genetics, landscape ecology, and spatial statistics. Multi-taxa integrated landscape genetics (MTILG) can reveal how interspecific interactions and landscape variables influence disease emergence patterns. We test the potential of our MTILG-based framework by modelling the emergence of a disease system across multiple species dispersal, interspecific interaction, and landscape scenarios. Our simulations showed that both interspecific-dependent dispersal patterns and landscape characteristics significantly influenced disease spread. Using our framework, we were able to detect statistically similar inter-population genetic differences and highly correlated spatial genetic patterns that imply species-dependent dispersal. Additionally, species that were assigned coupled-dispersal patterns were affected to the same degree by similar landscape variables. This study underlines the importance of an integrated approach to investigating emergence of disease systems. MTILG is a robust approach for such studies and can identify potential avenues for targeted disease management strategies.}, } @article {pmid27073838, year = {2016}, author = {Aubert, AH and Breuer, L}, title = {New Seasonal Shift in In-Stream Diurnal Nitrate Cycles Identified by Mining High-Frequency Data.}, journal = {PloS one}, volume = {11}, number = {4}, pages = {e0153138}, pmid = {27073838}, issn = {1932-6203}, mesh = {Agriculture ; Data Mining ; *Environmental Monitoring ; Germany ; Nitrates/*analysis ; *Periodicity ; Rivers/*chemistry ; *Seasons ; Water/*analysis ; }, abstract = {The recent development of in-situ monitoring devices, such as UV-spectrometers, makes the study of short-term stream chemistry variation relevant, especially the study of diurnal cycles, which are not yet fully understood. Our study is based on high-frequency data from an agricultural catchment (Studienlandschaft Schwingbachtal, Germany). We propose a novel approach, i.e. the combination of cluster analysis and Linear Discriminant Analysis, to mine from these data nitrate behavior patterns. As a result, we observe a seasonality of nitrate diurnal cycles, that differs from the most common cycle seasonality described in the literature, i.e. pre-dawn peaks in spring. Our cycles appear in summer and the maximum and minimum shift to a later time in late summer/autumn. This is observed both for water- and energy-limited years, thus potentially stressing the role of evapotranspiration. This concluding hypothesis on the role of evapotranspiration on nitrate stream concentration, which was obtained through data mining, broadens the perspective on the diurnal cycling of stream nitrate concentrations.}, } @article {pmid27072404, year = {2016}, author = {Ouwehand, J and Both, C}, title = {Alternate non-stop migration strategies of pied flycatchers to cross the Sahara desert.}, journal = {Biology letters}, volume = {12}, number = {4}, pages = {}, pmid = {27072404}, issn = {1744-957X}, mesh = {Africa, Northern ; *Animal Migration ; Animals ; Female ; *Flight, Animal ; Geographic Information Systems ; Male ; Passeriformes/*physiology ; Seasons ; Time Factors ; }, abstract = {Each year more than two billion songbirds cross the Sahara, but how they perform this formidable task is largely unknown. Using geolocation tracks from 27 pied flycatchers, a nocturnally migrating passerine, we show that most birds made diurnal flights in both autumn and spring. These diurnal flights were estimated to be part of non-stop flights of mostly 40-60 h. In spring, birds flew across the Sahara, while autumn migration probably circumpassed part of the desert, through a long oversea flight. Our data contradict claims that passerines cross the Sahara by intermittent flight and daytime resting. The frequent occurrence of long non-stop flights to cross the desert shows migrants' physiological abilities and poses the question why this would not be the general migration strategy to cross the Sahara.}, } @article {pmid27067833, year = {2016}, author = {Davis, JA and Ross, JRM and Bezalel, S and Sim, L and Bonnema, A and Ichikawa, G and Heim, WA and Schiff, K and Eagles-Smith, CA and Ackerman, JT}, title = {Hg concentrations in fish from coastal waters of California and Western North America.}, journal = {The Science of the total environment}, volume = {568}, number = {}, pages = {1146-1156}, doi = {10.1016/j.scitotenv.2016.03.093}, pmid = {27067833}, issn = {1879-1026}, mesh = {Animals ; California ; Environmental Monitoring ; Fishes/*metabolism ; Mercury/*metabolism ; Pacific States ; Water Pollutants, Chemical/*metabolism ; }, abstract = {The State of California conducted an extensive and systematic survey of mercury (Hg) in fish from the California coast in 2009 and 2010. The California survey sampled 3483 fish representing 46 species at 68 locations, and demonstrated that methylHg in fish presents a widespread exposure risk to fish consumers. Most of the locations sampled (37 of 68) had a species with an average concentration above 0.3μg/gwet weight (ww), and 10 locations an average above 1.0μg/gww. The recent and robust dataset from California provided a basis for a broader examination of spatial and temporal patterns in fish Hg in coastal waters of Western North America. There is a striking lack of data in publicly accessible databases on Hg and other contaminants in coastal fish. An assessment of the raw data from these databases suggested the presence of relatively high concentrations along the California coast and in Puget Sound, and relatively low concentrations along the coasts of Alaska and Oregon, and the outer coast of Washington. The dataset suggests that Hg concentrations of public health concern can be observed at any location on the coast of Western North America where long-lived predator species are sampled. Output from a linear mixed-effects model resembled the spatial pattern observed for the raw data and suggested, based on the limited dataset, a lack of trend in fish Hg over the nearly 30-year period covered by the dataset. Expanded and continued monitoring, accompanied by rigorous data management procedures, would be of great value in characterizing methylHg exposure, and tracking changes in contamination of coastal fish in response to possible increases in atmospheric Hg emissions in Asia, climate change, and terrestrial Hg control efforts in coastal watersheds.}, } @article {pmid27067409, year = {2016}, author = {Whiteside, MD and Laing, CR and Manji, A and Kruczkiewicz, P and Taboada, EN and Gannon, VP}, title = {SuperPhy: predictive genomics for the bacterial pathogen Escherichia coli.}, journal = {BMC microbiology}, volume = {16}, number = {}, pages = {65}, pmid = {27067409}, issn = {1471-2180}, mesh = {Databases, Nucleic Acid ; Drug Resistance, Bacterial ; Escherichia coli/*genetics ; *Genome, Bacterial ; Genomics/*methods ; Phenotype ; Sequence Analysis, DNA ; Software ; Virulence Factors/genetics ; }, abstract = {BACKGROUND: Predictive genomics is the translation of raw genome sequence data into a phenotypic assessment of the organism. For bacterial pathogens, these phenotypes can range from environmental survivability, to the severity of human disease. Significant progress has been made in the development of generic tools for genomic analyses that are broadly applicable to all microorganisms; however, a fundamental missing component is the ability to analyze genomic data in the context of organism-specific phenotypic knowledge, which has been accumulated from decades of research and can provide a meaningful interpretation of genome sequence data.

RESULTS: In this study, we present SuperPhy, an online predictive genomics platform (http://lfz.corefacility.ca/superphy/) for Escherichia coli. The platform integrates the analytical tools and genome sequence data for all publicly available E. coli genomes and facilitates the upload of new genome sequences from users under public or private settings. SuperPhy provides real-time analyses of thousands of genome sequences with results that are understandable and useful to a wide community, including those in the fields of clinical medicine, epidemiology, ecology, and evolution. SuperPhy includes identification of: 1) virulence and antimicrobial resistance determinants 2) statistical associations between genotypes, biomarkers, geospatial distribution, host, source, and phylogenetic clade; 3) the identification of biomarkers for groups of genomes on the based presence/absence of specific genomic regions and single-nucleotide polymorphisms and 4) in silico Shiga-toxin subtype.

CONCLUSIONS: SuperPhy is a predictive genomics platform that attempts to provide an essential link between the vast amounts of genome information currently being generated and phenotypic knowledge in an organism-specific context.}, } @article {pmid27064667, year = {2016}, author = {Vander Mijnsbrugge, K and Turcsán, A and Maes, J and Duchêne, N and Meeus, S and Steppe, K and Steenackers, M}, title = {Repeated Summer Drought and Re-watering during the First Growing Year of Oak (Quercus petraea) Delay Autumn Senescence and Bud Burst in the Following Spring.}, journal = {Frontiers in plant science}, volume = {7}, number = {}, pages = {419}, pmid = {27064667}, issn = {1664-462X}, abstract = {Climate change predicts harsher summer droughts for mid-latitudes in Europe. To enhance our understanding of the putative impacts on forest regeneration, we studied the response of oak seedlings (Quercus petraea) to water deficit. Potted seedlings originating from three locally sourced provenances were subjected to two successive drought periods during the first growing season each followed by a plentiful re-watering. Here, we describe survival and phenological responses after the second drought treatment, applying general linear mixed modeling. From the 441 drought treated seedlings 189 subsisted with higher chances of survival among smaller plants and among single plants per pot compared to doubles. Remarkably, survival was independent of the provenance, although relatively more plants had died off in two provenances compared to the third one with mean plant height being higher in one provenance and standard deviation of plant height being higher in the other. Timing of leaf senescence was clearly delayed after the severe drought treatment followed by re-watering, with two seedlings per pot showing a lesser retardation compared to single plants. This delay can be interpreted as a compensation time in which plants recover before entering the subsequent developmental process of leaf senescence, although it renders seedlings more vulnerable to early autumn frosts because of the delayed hardening of the shoots. Onset of bud flush in the subsequent spring still showed a significant but small delay in the drought treated group, independent of the number of seedlings per pot, and can be considered as an after effect of the delayed senescence. In both phenological models significant differences among the three provenances were detected independent from the treatment. The only provenance that is believed to be local of origin, displayed the earliest leaf senescence and the latest flushing, suggesting an adaptation to the local maritime climate. This provenance also displayed the highest standard deviation of plant height, which can be interpreted as an adaptation to variable and unpredictable weather conditions, favoring smaller plants in drought-prone summers and higher plants in more normal growing seasons.}, } @article {pmid27064176, year = {2016}, author = {Adams, RH and Blackmon, H and Reyes-Velasco, J and Schield, DR and Card, DC and Andrew, AL and Waynewood, N and Castoe, TA}, title = {Microsatellite landscape evolutionary dynamics across 450 million years of vertebrate genome evolution.}, journal = {Genome}, volume = {59}, number = {5}, pages = {295-310}, doi = {10.1139/gen-2015-0124}, pmid = {27064176}, issn = {1480-3321}, mesh = {Animals ; Biological Evolution ; Databases, Nucleic Acid ; *Evolution, Molecular ; Genome ; Genomics/methods ; *Microsatellite Repeats ; Phylogeny ; Tandem Repeat Sequences ; Vertebrates/classification/*genetics ; }, abstract = {The evolutionary dynamics of simple sequence repeats (SSRs or microsatellites) across the vertebrate tree of life remain largely undocumented and poorly understood. In this study, we analyzed patterns of genomic microsatellite abundance and evolution across 71 vertebrate genomes. The highest abundances of microsatellites exist in the genomes of ray-finned fishes, squamate reptiles, and mammals, while crocodilian, turtle, and avian genomes exhibit reduced microsatellite landscapes. We used comparative methods to infer evolutionary rates of change in microsatellite abundance across vertebrates and to highlight particular lineages that have experienced unusually high or low rates of change in genomic microsatellite abundance. Overall, most variation in microsatellite content, abundance, and evolutionary rate is observed among major lineages of reptiles, yet we found that several deeply divergent clades (i.e., squamate reptiles and mammals) contained relatively similar genomic microsatellite compositions. Archosauromorph reptiles (turtles, crocodilians, and birds) exhibit reduced genomic microsatellite content and the slowest rates of microsatellite evolution, in contrast to squamate reptile genomes that have among the highest rates of microsatellite evolution. Substantial branch-specific shifts in SSR content in primates, monotremes, rodents, snakes, and fish are also evident. Collectively, our results support multiple major shifts in microsatellite genomic landscapes among vertebrates.}, } @article {pmid27064124, year = {2016}, author = {Mamykina, L and Jiang, S and Collins, SA and Twohig, B and Hirsh, J and Hripcsak, G and Stanley Hum, R and Kaufman, DR}, title = {Revealing structures in narratives: A mixed-methods approach to studying interdisciplinary handoff in critical care.}, journal = {Journal of biomedical informatics}, volume = {62}, number = {}, pages = {117-124}, doi = {10.1016/j.jbi.2016.03.025}, pmid = {27064124}, issn = {1532-0480}, mesh = {Communication ; Continuity of Patient Care ; *Critical Care ; Humans ; *Narration ; *Patient Handoff ; }, abstract = {OBJECTIVE: To examine a novel mixed-methods approach for studying patterns of clinical communication that could inform future informatics solutions, with a specific focus on handoff within interdisciplinary teams.

MATERIALS AND METHODS: Researchers observed, recorded, and transcribed verbal handoff discussions of different members of critical care teams. The transcripts were coded qualitatively, and then analyzed quantitatively for emerging structural patterns using categorical cluster analysis, and for degree of shared mental models (SMM) using the modified Pyramid method.

RESULTS: An empirical study using the proposed mixed-methods approach suggested emerging patterns of communication among clinicians. For example, the temporal focus of handoff was often determined by the role of the clinician giving the handoff; the clinical content of handoff was consistent between clinicians, but varied between patients. The SMM index ranged from 0.065 (with the maximum possible overlap score of 1) to 0.007 with a median of 0.026; the overlap was higher in statements concerned with patient presentation (23.6% of these had overlap) and referring to the past (24% overlapped). This calculated SMM index was correlated with the assessment of coherence within the participating teams by independent physicians (r=0.63, p=0.038).

CONCLUSIONS: The proposed novel mixed-methods approach helped to reveal emerging patterns in content and structure of handoff communication and highlight differences due to the clinical context, and to the different priorities of clinicians on interdisciplinary patient care teams. The approach for calculating SMM is more ecologically sensitive as it relies on naturally occurring discourse and less intrusive than traditional ways of assessing SMM, and takes initial steps toward establishing empirical foundation for the design of electronic tools to support handoff in interdisciplinary teams.}, } @article {pmid27062682, year = {2016}, author = {LaFreniere, LS and Newman, MG}, title = {A BRIEF ECOLOGICAL MOMENTARY INTERVENTION FOR GENERALIZED ANXIETY DISORDER: A RANDOMIZED CONTROLLED TRIAL OF THE WORRY OUTCOME JOURNAL.}, journal = {Depression and anxiety}, volume = {33}, number = {9}, pages = {829-839}, doi = {10.1002/da.22507}, pmid = {27062682}, issn = {1520-6394}, mesh = {Adult ; Anxiety Disorders/diagnosis/psychology/*therapy ; Cognitive Behavioral Therapy/*methods ; Female ; Humans ; Male ; Psychotherapy, Brief/*methods ; Self Care/psychology ; Self Disclosure ; Stress Disorders, Traumatic, Acute ; Students/psychology ; Surveys and Questionnaires ; *Text Messaging ; Therapy, Computer-Assisted/*methods ; Treatment Outcome ; Writing ; Young Adult ; }, abstract = {BACKGROUND: The efficacy of many cognitive behavioral component interventions has not been examined, with worry outcome monitoring among them.

METHODS: To address this issue, 51 participants with clinical levels of generalized anxiety disorder were randomly assigned to a treatment or control condition for 10 days. The treatment condition consisted of a brief ecological momentary intervention termed the Worry Outcome Journal (WOJ). WOJ participants recorded worries and tracked their outcomes, rating worry distress, interference, and expected outcome probabilities. Thought log (TL) control participants completed a record of their everyday thoughts and rated associated distress. All participants made four entries on paper each day when randomly prompted by text message. They then entered their paper contents online each night. After 30 days they reviewed their contents electronically and completed follow-up measures.

RESULTS: Primary results revealed significant reductions in worry for WOJ users compared to TL users at postintervention. A marginally significant difference was found at 20-day follow-up and treatment gains were maintained. Secondary analyses showed no harmful increases in worry beliefs for WOJ users, as well as preliminary evidence for decreases in beliefs about the uncontrollability of thoughts in both groups.

CONCLUSION: The WOJ may be a viable therapist-independent treatment for reducing worry, even after only 10 days of use.}, } @article {pmid27062589, year = {2016}, author = {Ficetola, GF and Taberlet, P and Coissac, E}, title = {How to limit false positives in environmental DNA and metabarcoding?.}, journal = {Molecular ecology resources}, volume = {16}, number = {3}, pages = {604-607}, doi = {10.1111/1755-0998.12508}, pmid = {27062589}, issn = {1755-0998}, mesh = {Computational Biology ; DNA/genetics ; Ecology ; *Ecosystem ; *Environment ; }, abstract = {Environmental DNA (eDNA) and metabarcoding are boosting our ability to acquire data on species distribution in a variety of ecosystems. Nevertheless, as most of sampling approaches, eDNA is not perfect. It can fail to detect species that are actually present, and even false positives are possible: a species may be apparently detected in areas where it is actually absent. Controlling false positives remains a main challenge for eDNA analyses: in this issue of Molecular Ecology Resources, Lahoz-Monfort et al. () test the performance of multiple statistical modelling approaches to estimate the rate of detection and false positives from eDNA data. Here, we discuss the importance of controlling for false detection from early steps of eDNA analyses (laboratory, bioinformatics), to improve the quality of results and allow an efficient use of the site occupancy-detection modelling (SODM) framework for limiting false presences in eDNA analysis.}, } @article {pmid27062588, year = {2016}, author = {Gilbert, KJ}, title = {Identifying the number of population clusters with structure: problems and solutions.}, journal = {Molecular ecology resources}, volume = {16}, number = {3}, pages = {601-603}, doi = {10.1111/1755-0998.12521}, pmid = {27062588}, issn = {1755-0998}, mesh = {*Cluster Analysis ; Computational Biology/*methods ; Genetics, Population/*methods ; Sequence Analysis, DNA/*methods ; }, abstract = {The program structure has been used extensively to understand and visualize population genetic structure. It is one of the most commonly used clustering algorithms, cited over 11,500 times in Web of Science since its introduction in 2000. The method estimates ancestry proportions to assign individuals to clusters, and post hoc analyses of results may indicate the most likely number of clusters, or populations, on the landscape. However, as has been shown in this issue of Molecular Ecology Resources by Puechmaille (), when sampling is uneven across populations or across hierarchical levels of population structure, these post hoc analyses can be inaccurate and identify an incorrect number of population clusters. To solve this problem, Puechmaille () presents strategies for subsampling and new analysis methods that are robust to uneven sampling to improve inferences of the number of population clusters.}, } @article {pmid27061206, year = {2016}, author = {Contina, A and Bridge, ES and Kelly, JF}, title = {Exploring novel candidate genes from the Mouse Genome Informatics database: Potential implications for avian migration research.}, journal = {Integrative zoology}, volume = {11}, number = {4}, pages = {240-249}, doi = {10.1111/1749-4877.12199}, pmid = {27061206}, issn = {1749-4877}, mesh = {*Animal Migration ; Animals ; *Databases, Genetic ; *Genome ; Mice/*genetics ; Microsatellite Repeats ; Phenotype ; Research ; Songbirds/*genetics/physiology ; }, abstract = {To search for genes associated with migratory phenotypes in songbirds, we selected candidate genes through annotations from the Mouse Genome Informatics database and assembled an extensive candidate-gene library. Then, we implemented a next-generation sequencing approach to obtain DNA sequences from the Painted Bunting genome. We focused on those sequences that were conserved across avian species and that aligned with candidate genes in our mouse library. We genotyped short sequence repeats from the following candidate genes: ADRA1d, ANKRD17, CISH and MYH7. We studied the possible correlations between allelic variations occurring in these novel candidate migration genes and avian migratory phenotypes available from the published literature. We found that allele variation at MYH7 correlated with a calculated index of speed of migration (km/day) across 11 species of songbirds. We highlight the potential of the Mouse Genome Informatics database in providing new candidate genes that might play a crucial role in regulating migration in birds and possibly in other taxa. Our research effort shows the benefits and limitations of working with extensive genomic datasets and offers a snapshot of the challenges related to cross-species validation in behavioral and molecular ecology studies.}, } @article {pmid27060758, year = {2016}, author = {Veselinović, JB and Veselinović, AM and Toropova, AP and Toropov, AA}, title = {The Monte Carlo technique as a tool to predict LOAEL.}, journal = {European journal of medicinal chemistry}, volume = {116}, number = {}, pages = {71-75}, doi = {10.1016/j.ejmech.2016.03.075}, pmid = {27060758}, issn = {1768-3254}, mesh = {*Computational Biology ; *Monte Carlo Method ; Organic Chemicals/*adverse effects/*chemistry ; *Quantitative Structure-Activity Relationship ; Software ; }, abstract = {Quantitative structure - activity relationships (QSARs) for the Lowest Observed Adverse Effect Level (LOAEL) for a large set of organic compounds (n = 341) are suggested. The molecular structures of these compounds are represented by Simplified Molecular Input-Line Entry Systems (SMILES). A criteria for the estimation quality of split into the "visible" training set (used for developing a model) and "invisible" external validation set is suggested. The correlation between the above criterion and the predictive potential of developed QSAR model (root-mean-square error for "invisible" validation set) has been detected. One-variable models are built up for several different splits into the "visible" training set and "invisible" validation set. The statistical quality of these models is quite good. Mechanistic interpretation and the domain of applicability for these models are defined according to probabilistic point of view. The methodology for defining applicability domain in QSAR modeling with SMILES notation based optimal descriptors is presented.}, } @article {pmid27058254, year = {2016}, author = {Evans, SR}, title = {Gauging the Purported Costs of Public Data Archiving for Long-Term Population Studies.}, journal = {PLoS biology}, volume = {14}, number = {4}, pages = {e1002432}, pmid = {27058254}, issn = {1545-7885}, mesh = {Costs and Cost Analysis ; Information Storage and Retrieval/*economics ; }, abstract = {It was recently proposed that long-term population studies be exempted from the expectation that authors publicly archive the primary data underlying published articles. Such studies are valuable to many areas of ecological and evolutionary biological research, and multiple risks to their viability were anticipated as a result of public data archiving (PDA), ultimately all stemming from independent reuse of archived data. However, empirical assessment was missing, making it difficult to determine whether such fears are realistic. I addressed this by surveying data packages from long-term population studies archived in the Dryad Digital Repository. I found no evidence that PDA results in reuse of data by independent parties, suggesting the purported costs of PDA for long-term population studies have been overstated.}, } @article {pmid27055028, year = {2016}, author = {Hoffmann, H and Zhao, G and Asseng, S and Bindi, M and Biernath, C and Constantin, J and Coucheney, E and Dechow, R and Doro, L and Eckersten, H and Gaiser, T and Grosz, B and Heinlein, F and Kassie, BT and Kersebaum, KC and Klein, C and Kuhnert, M and Lewan, E and Moriondo, M and Nendel, C and Priesack, E and Raynal, H and Roggero, PP and Rötter, RP and Siebert, S and Specka, X and Tao, F and Teixeira, E and Trombi, G and Wallach, D and Weihermüller, L and Yeluripati, J and Ewert, F}, title = {Impact of Spatial Soil and Climate Input Data Aggregation on Regional Yield Simulations.}, journal = {PloS one}, volume = {11}, number = {4}, pages = {e0151782}, pmid = {27055028}, issn = {1932-6203}, support = {BB/K009265/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/N004922/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Agriculture/*methods ; *Climate Change ; *Computer Simulation ; Crops, Agricultural/*growth & development ; Databases, Factual ; Oryza/growth & development ; Soil/*chemistry ; Triticum/growth & development ; Water ; Zea mays/growth & development ; }, abstract = {We show the error in water-limited yields simulated by crop models which is associated with spatially aggregated soil and climate input data. Crop simulations at large scales (regional, national, continental) frequently use input data of low resolution. Therefore, climate and soil data are often generated via averaging and sampling by area majority. This may bias simulated yields at large scales, varying largely across models. Thus, we evaluated the error associated with spatially aggregated soil and climate data for 14 crop models. Yields of winter wheat and silage maize were simulated under water-limited production conditions. We calculated this error from crop yields simulated at spatial resolutions from 1 to 100 km for the state of North Rhine-Westphalia, Germany. Most models showed yields biased by <15% when aggregating only soil data. The relative mean absolute error (rMAE) of most models using aggregated soil data was in the range or larger than the inter-annual or inter-model variability in yields. This error increased further when both climate and soil data were aggregated. Distinct error patterns indicate that the rMAE may be estimated from few soil variables. Illustrating the range of these aggregation effects across models, this study is a first step towards an ex-ante assessment of aggregation errors in large-scale simulations.}, } @article {pmid27050459, year = {2016}, author = {Rodriguez, KA and Li, K and Nevo, E and Buffenstein, R}, title = {Mechanisms regulating proteostasis are involved in sympatric speciation of the blind mole rat, Spalax galili.}, journal = {Autophagy}, volume = {12}, number = {4}, pages = {703-704}, doi = {10.1080/15548627.2016.1143592}, pmid = {27050459}, issn = {1554-8635}, support = {K99 AG049940/AG/NIA NIH HHS/United States ; }, mesh = {Animals ; Gene Expression Regulation ; Gene Ontology ; *Genetic Speciation ; *Homeostasis ; Proteins/*metabolism ; Proteolysis ; Spalax/*metabolism ; *Sympatry ; }, abstract = {Genome-wide analysis demonstrates extensive genomic adaptive complexes involved in sympatric speciation between blind mole rats (Spalax galili) in abutting populations living in basalt and chalk soils. Among the gene ontology (GO) enrichment, musculature and metabolism stood out in basalt dwellers while nutrition and neurogenetics were highlighted in chalk residents. Measurements of mechanisms regulating protein homeostasis inspired by these GO terms suggest that at the proteomic level there is also a habitat/soil-type driven divergence with the basalt residents exhibiting higher proteasome activity whereas elevated levels of markers of autophagy are evident in the chalk inhabitants.}, } @article {pmid27045776, year = {2016}, author = {Kurczy, ME and Forsberg, EM and Thorgersen, MP and Poole, FL and Benton, HP and Ivanisevic, J and Tran, ML and Wall, JD and Elias, DA and Adams, MW and Siuzdak, G}, title = {Global Isotope Metabolomics Reveals Adaptive Strategies for Nitrogen Assimilation.}, journal = {ACS chemical biology}, volume = {11}, number = {6}, pages = {1677-1685}, pmid = {27045776}, issn = {1554-8937}, support = {R01 GM114368/GM/NIGMS NIH HHS/United States ; R01 GMH4368//National Institutes of Health/International ; P01 AG043376/AG/NIA NIH HHS/United States ; }, mesh = {Amino Acids/metabolism ; Ammonia/*metabolism ; Computational Biology ; Denitrification ; Metabolomics ; Nitrates/*metabolism ; *Nitrogen Fixation ; Nitrogen Radioisotopes ; Nucleotides/biosynthesis ; Pseudomonas/*metabolism ; Purines/biosynthesis/metabolism ; Pyrimidines/biosynthesis/metabolism ; }, abstract = {Nitrogen cycling is a microbial metabolic process essential for global ecological/agricultural balance. To investigate the link between the well-established ammonium and the alternative nitrate assimilation metabolic pathways, global isotope metabolomics was employed to examine three nitrate reducing bacteria using (15)NO3 as a nitrogen source. In contrast to a control (Pseudomonas stutzeri RCH2), the results show that two of the isolates from Oak Ridge, Tennessee (Pseudomonas N2A2 and N2E2) utilize nitrate and ammonia for assimilation concurrently with differential labeling observed across multiple classes of metabolites including amino acids and nucleotides. The data reveal that the N2A2 and N2E2 strains conserve nitrogen-containing metabolites, indicating that the nitrate assimilation pathway is a conservation mechanism for the assimilation of nitrogen. Co-utilization of nitrate and ammonia is likely an adaption to manage higher levels of nitrite since the denitrification pathways utilized by the N2A2 and N2E2 strains from the Oak Ridge site are predisposed to the accumulation of the toxic nitrite. The use of global isotope metabolomics allowed for this adaptive strategy to be investigated, which would otherwise not have been possible to decipher.}, } @article {pmid27045523, year = {2016}, author = {Ndeffo-Mbah, ML and Durham, DP and Skrip, LA and Nsoesie, EO and Brownstein, JS and Fish, D and Galvani, AP}, title = {Evaluating the effectiveness of localized control strategies to curtail chikungunya.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {23997}, pmid = {27045523}, issn = {2045-2322}, support = {S10 RR029676/RR/NCRR NIH HHS/United States ; U01 GM087719/GM/NIGMS NIH HHS/United States ; U01-GM087719/GM/NIGMS NIH HHS/United States ; RR19895/RR/NCRR NIH HHS/United States ; S10 RR019895/RR/NCRR NIH HHS/United States ; U01-GM105627/GM/NIGMS NIH HHS/United States ; RR029676-01/RR/NCRR NIH HHS/United States ; T32 AI007404/AI/NIAID NIH HHS/United States ; U01 GM105627/GM/NIGMS NIH HHS/United States ; }, mesh = {Aedes/virology ; Algorithms ; Animals ; Chikungunya Fever/*prevention & control/*transmission ; *Chikungunya virus ; *Communicable Disease Control ; Disease Outbreaks ; Geography ; Humans ; Insect Vectors/virology ; *Mosquito Control ; Program Evaluation ; Residence Characteristics ; South America ; Vaccines ; }, abstract = {Chikungunya, a re-emerging arbovirus transmitted to humans by Aedes aegypti and Ae. albopictus mosquitoes, causes debilitating disease characterized by an acute febrile phase and chronic joint pain. Chikungunya has recently spread to the island of St. Martin and subsequently throughout the Americas. The disease is now affecting 42 countries and territories throughout the Americas. While chikungunya is mainly a tropical disease, the recent introduction and subsequent spread of Ae. albopictus into temperate regions has increased the threat of chikungunya outbreaks beyond the tropics. Given that there are currently no vaccines or treatments for chikungunya, vector control remains the primary measure to curtail transmission. To investigate the effectiveness of a containment strategy that combines disease surveillance, localized vector control and transmission reduction measures, we developed a model of chikungunya transmission dynamics within a large residential neighborhood, explicitly accounting for human and mosquito movement. Our findings indicate that prompt targeted vector control efforts combined with measures to reduce transmission from symptomatic cases to mosquitoes may be highly effective approaches for controlling outbreaks of chikungunya, provided that sufficient detection of chikungunya cases can be achieved.}, } @article {pmid27044302, year = {2016}, author = {Crawford, DL and Oleksiak, MF}, title = {Ecological population genomics in the marine environment.}, journal = {Briefings in functional genomics}, volume = {15}, number = {5}, pages = {342-351}, doi = {10.1093/bfgp/elw008}, pmid = {27044302}, issn = {2041-2657}, mesh = {Animals ; Computational Biology/*methods ; *Environment ; *Genetic Variation ; *Genetics, Population ; Genomics/*methods ; *Marine Biology ; Sequence Analysis, DNA ; }, abstract = {Marine species live in a wide diversity of environments and yet, because of their pelagic life stages, are thought to be well-connected: they have high migration rates that inhibit significant population structure. Recent innovations in sequencing technologies now provide information on nucleotide polymorphisms at thousands to tens of thousands of loci based on whole genomes, reduced representative portions of genomes (0.1-1%) or a majority of expressed mRNAs. Data from these genomic approaches are used to define and quantify single-nucleotide polymorphisms (SNPs). These SNP data tend to agree with data from older technologies (allozymes or microsatellites), which support well-connected populations with few genetic differences among populations. However, these studies also find few percentages of SNPs (1-5%) that readily distinguish genetic differences among populations on relatively small geographic scales. The magnitudes of the genetic differences (FST values) suggest that hundreds of loci with significant differences are due to positive selective pressures. Thus, these data suggest that natural selection is effectively altering allele frequencies at 100s of loci in marine populations. In this manuscript, we provide examples of these studies, the strengths and weaknesses of different genomic approaches as well as important technical aspects associated with genomic approaches.}, } @article {pmid27044277, year = {2017}, author = {Scherer, EA and Huang, L and Shrier, LA}, title = {Application of Correlated Time-to-Event Models to Ecological Momentary Assessment Data.}, journal = {Psychometrika}, volume = {82}, number = {1}, pages = {233-244}, pmid = {27044277}, issn = {1860-0980}, support = {P30 DA029926/DA/NIDA NIH HHS/United States ; R21 MH072533/MH/NIMH NIH HHS/United States ; }, mesh = {Adolescent ; *Data Interpretation, Statistical ; *Depression ; *Ecological Momentary Assessment ; Female ; Humans ; Male ; *Models, Statistical ; Proportional Hazards Models ; *Psychometrics ; *Risk-Taking ; *Sexual Behavior ; Unsafe Sex ; }, abstract = {Ecological momentary assessment data consist of in-the-moment sampling several times per day aimed at capturing phenomena that are highly variable. When research questions are focused on the association between a construct measured repeatedly and an event that occurs sporadically over time interspersed between repeated measures, the data consist of correlated observed or censored times to an event. In such a case, specialized time-to-event models that account for correlated observations are required to properly assess the relationships under study. In the current study, we apply two time-to-event analysis techniques, proportional hazards, and accelerated failure time modeling, to data from a study of affective states and sexual behavior in depressed adolescents and illustrate differing interpretations from the models.}, } @article {pmid27043913, year = {2016}, author = {Ruktanonchai, NW and DeLeenheer, P and Tatem, AJ and Alegana, VA and Caughlin, TT and Zu Erbach-Schoenberg, E and Lourenço, C and Ruktanonchai, CW and Smith, DL}, title = {Identifying Malaria Transmission Foci for Elimination Using Human Mobility Data.}, journal = {PLoS computational biology}, volume = {12}, number = {4}, pages = {e1004846}, pmid = {27043913}, issn = {1553-7358}, support = {/WT_/Wellcome Trust/United Kingdom ; U19 AI089674/AI/NIAID NIH HHS/United States ; U19AI089674/AI/NIAID NIH HHS/United States ; }, mesh = {Cell Phone/statistics & numerical data ; Computational Biology ; Data Interpretation, Statistical ; Human Migration ; Humans ; Malaria/*epidemiology/prevention & control/*transmission ; *Models, Biological ; Namibia/epidemiology ; Prevalence ; }, abstract = {Humans move frequently and tend to carry parasites among areas with endemic malaria and into areas where local transmission is unsustainable. Human-mediated parasite mobility can thus sustain parasite populations in areas where they would otherwise be absent. Data describing human mobility and malaria epidemiology can help classify landscapes into parasite demographic sources and sinks, ecological concepts that have parallels in malaria control discussions of transmission foci. By linking transmission to parasite flow, it is possible to stratify landscapes for malaria control and elimination, as sources are disproportionately important to the regional persistence of malaria parasites. Here, we identify putative malaria sources and sinks for pre-elimination Namibia using malaria parasite rate (PR) maps and call data records from mobile phones, using a steady-state analysis of a malaria transmission model to infer where infections most likely occurred. We also examined how the landscape of transmission and burden changed from the pre-elimination setting by comparing the location and extent of predicted pre-elimination transmission foci with modeled incidence for 2009. This comparison suggests that while transmission was spatially focal pre-elimination, the spatial distribution of cases changed as burden declined. The changing spatial distribution of burden could be due to importation, with cases focused around importation hotspots, or due to heterogeneous application of elimination effort. While this framework is an important step towards understanding progressive changes in malaria distribution and the role of subnational transmission dynamics in a policy-relevant way, future work should account for international parasite movement, utilize real time surveillance data, and relax the steady state assumption required by the presented model.}, } @article {pmid27043882, year = {2016}, author = {Altenhoff, AM and Boeckmann, B and Capella-Gutierrez, S and Dalquen, DA and DeLuca, T and Forslund, K and Huerta-Cepas, J and Linard, B and Pereira, C and Pryszcz, LP and Schreiber, F and da Silva, AS and Szklarczyk, D and Train, CM and Bork, P and Lecompte, O and von Mering, C and Xenarios, I and Sjölander, K and Jensen, LJ and Martin, MJ and Muffato, M and , and Gabaldón, T and Lewis, SE and Thomas, PD and Sonnhammer, E and Dessimoz, C}, title = {Standardized benchmarking in the quest for orthologs.}, journal = {Nature methods}, volume = {13}, number = {5}, pages = {425-430}, pmid = {27043882}, issn = {1548-7105}, support = {BB/L018241/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; R24 OD011883/OD/NIH HHS/United States ; WT095908/WT_/Wellcome Trust/United Kingdom ; //Wellcome Trust/United Kingdom ; U41 HG007822/HG/NHGRI NIH HHS/United States ; 310325/ERC_/European Research Council/International ; U41 HG002273/HG/NHGRI NIH HHS/United States ; }, mesh = {Archaea/classification/genetics ; Bacteria/classification/genetics ; Computational Biology/methods/*standards ; Databases, Genetic ; Eukaryota/classification/genetics ; Gene Ontology ; Genomics/methods/*standards ; Models, Genetic ; *Phylogeny ; Proteomics/methods/*standards ; Sequence Analysis, Protein ; Sequence Homology ; Species Specificity ; }, abstract = {Achieving high accuracy in orthology inference is essential for many comparative, evolutionary and functional genomic analyses, yet the true evolutionary history of genes is generally unknown and orthologs are used for very different applications across phyla, requiring different precision-recall trade-offs. As a result, it is difficult to assess the performance of orthology inference methods. Here, we present a community effort to establish standards and an automated web-based service to facilitate orthology benchmarking. Using this service, we characterize 15 well-established inference methods and resources on a battery of 20 different benchmarks. Standardized benchmarking provides a way for users to identify the most effective methods for the problem at hand, sets a minimum requirement for new tools and resources, and guides the development of more accurate orthology inference methods.}, } @article {pmid27037819, year = {2016}, author = {Buckley, HL and Case, BS and Zimmerman, JK and Thompson, J and Myers, JA and Ellison, AM}, title = {Using codispersion analysis to quantify and understand spatial patterns in species-environment relationships.}, journal = {The New phytologist}, volume = {211}, number = {2}, pages = {735-749}, doi = {10.1111/nph.13934}, pmid = {27037819}, issn = {1469-8137}, mesh = {Computer Simulation ; *Ecosystem ; Models, Theoretical ; Species Specificity ; }, abstract = {The analysis of spatial patterns in species-environment relationships can provide new insights into the niche requirements and potential co-occurrence of species, but species abundance and environmental data are routinely collected at different spatial scales. Here, we investigate the use of codispersion analysis to measure and assess the scale, directionality and significance of complex relationships between plants and their environment in large forest plots. We applied codispersion analysis to both simulated and field data on spatially located tree species basal area and environmental variables. The significance of the observed bivariate spatial associations between the basal area of key species and underlying environmental variables was tested using three null models. Codispersion analysis reliably detected directionality (anisotropy) in bivariate species-environment relationships and identified relevant scales of effects. Null model-based significance tests applied to codispersion analyses of forest plot data enabled us to infer the extent to which environmental conditions, tree sizes and/or tree spatial positions underpinned the observed basal area-environment relationships, or whether relationships were a result of other unmeasured factors. Codispersion analysis, combined with appropriate null models, can be used to infer hypothesized ecological processes from spatial patterns, allowing us to start disentangling the possible drivers of plant species-environment relationships.}, } @article {pmid27037501, year = {2016}, author = {Lohman, BK and Weber, JN and Bolnick, DI}, title = {Evaluation of TagSeq, a reliable low-cost alternative for RNAseq.}, journal = {Molecular ecology resources}, volume = {16}, number = {6}, pages = {1315-1321}, doi = {10.1111/1755-0998.12529}, pmid = {27037501}, issn = {1755-0998}, mesh = {Computational Biology/*methods ; Costs and Cost Analysis ; Gene Expression Profiling/economics/*methods ; High-Throughput Nucleotide Sequencing/economics/*methods ; }, abstract = {RNAseq is a relatively new tool for ecological genetics that offers researchers insight into changes in gene expression in response to a myriad of natural or experimental conditions. However, standard RNAseq methods (e.g., Illumina TruSeq[®] or NEBNext[®]) can be cost prohibitive, especially when study designs require large sample sizes. Consequently, RNAseq is often underused as a method, or is applied to small sample sizes that confer poor statistical power. Low cost RNAseq methods could therefore enable far greater and more powerful applications of transcriptomics in ecological genetics and beyond. Standard mRNAseq is costly partly because one sequences portions of the full length of all transcripts. Such whole-mRNA data are redundant for estimates of relative gene expression. TagSeq is an alternative method that focuses sequencing effort on mRNAs' 3' end, reducing the necessary sequencing depth per sample, and thus cost. We present a revised TagSeq library construction procedure, and compare its performance against NEBNext[®] , the 'gold-standard' whole mRNAseq method. We built both TagSeq and NEBNext[®] libraries from the same biological samples, each spiked with control RNAs. We found that TagSeq measured the control RNA distribution more accurately than NEBNext[®] , for a fraction of the cost per sample (~10%). The higher accuracy of TagSeq was particularly apparent for transcripts of moderate to low abundance. Technical replicates of TagSeq libraries are highly correlated, and were correlated with NEBNext[®] results. Overall, we show that our modified TagSeq protocol is an efficient alternative to traditional whole mRNAseq, offering researchers comparable data at greatly reduced cost.}, } @article {pmid27036942, year = {2016}, author = {Ahn, S and Jung, J and Jang, IA and Madsen, EL and Park, W}, title = {Role of Glyoxylate Shunt in Oxidative Stress Response.}, journal = {The Journal of biological chemistry}, volume = {291}, number = {22}, pages = {11928-11938}, pmid = {27036942}, issn = {1083-351X}, mesh = {Acetates/metabolism ; Biofilms/growth & development ; Computational Biology ; *Gene Expression Regulation, Bacterial ; Genome, Bacterial ; Glyoxylates/*metabolism ; Isocitrate Lyase/genetics/*metabolism ; Malate Synthase/genetics/*metabolism ; Metabolic Networks and Pathways ; *Oxidative Stress ; Oxygen Consumption ; Pseudomonas aeruginosa/genetics/growth & development/*metabolism ; Transcriptome ; }, abstract = {The glyoxylate shunt (GS) is a two-step metabolic pathway (isocitrate lyase, aceA; and malate synthase, glcB) that serves as an alternative to the tricarboxylic acid cycle. The GS bypasses the carbon dioxide-producing steps of the tricarboxylic acid cycle and is essential for acetate and fatty acid metabolism in bacteria. GS can be up-regulated under conditions of oxidative stress, antibiotic stress, and host infection, which implies that it plays important but poorly explored roles in stress defense and pathogenesis. In many bacterial species, including Pseudomonas aeruginosa, aceA and glcB are not in an operon, unlike in Escherichia coli In P. aeruginosa, we explored relationships between GS genes and growth, transcription profiles, and biofilm formation. Contrary to our expectations, deletion of aceA in P. aeruginosa improved cell growth under conditions of oxidative and antibiotic stress. Transcriptome data suggested that aceA mutants underwent a metabolic shift toward aerobic denitrification; this was supported by additional evidence, including up-regulation of denitrification-related genes, decreased oxygen consumption without lowering ATP yield, increased production of denitrification intermediates (NO and N2O), and increased cyanide resistance. The aceA mutants also produced a thicker exopolysaccharide layer; that is, a phenotype consistent with aerobic denitrification. A bioinformatic survey across known bacterial genomes showed that only microorganisms capable of aerobic metabolism possess the glyoxylate shunt. This trend is consistent with the hypothesis that the GS plays a previously unrecognized role in allowing bacteria to tolerate oxidative stress.}, } @article {pmid27030726, year = {2016}, author = {Hurwitz, BL and U'Ren, JM and Youens-Clark, K}, title = {Computational prospecting the great viral unknown.}, journal = {FEMS microbiology letters}, volume = {363}, number = {10}, pages = {}, doi = {10.1093/femsle/fnw077}, pmid = {27030726}, issn = {1574-6968}, mesh = {Bacteria/genetics ; Bacteriophages/*genetics/physiology ; Computational Biology ; DNA, Viral/genetics ; Gene Transfer, Horizontal ; *Genome, Viral ; Host-Pathogen Interactions/genetics ; Humans ; Metagenome ; *Metagenomics ; Skin/virology ; }, abstract = {Bacteriophages play an important role in host-driven biological processes by controlling bacterial population size, horizontally transferring genes between hosts and expressing host-derived genes to alter host metabolism. Metagenomics provides the genetic basis for understanding the interplay between uncultured bacteria, their phage and the environment. In particular, viral metagenomes (viromes) are providing new insight into phage-encoded host genes (i.e. auxiliary metabolic genes; AMGs) that reprogram host metabolism during infection. Yet, despite deep sequencing efforts of viral communities, the majority of sequences have no match to known proteins. Reference-independent computational techniques, such as protein clustering, contig spectra and ecological profiling are overcoming these barriers to examine both the known and unknown components of viromes. As the field of viral metagenomics progresses, a critical assessment of tools is required as the majority of algorithms have been developed for analyzing bacteria. The aim of this paper is to offer an overview of current computational methodologies for virome analysis and to provide an example of reference-independent approaches using human skin viromes. Additionally, we present methods to carefully validate AMGs from host contamination. Despite computational challenges, these new methods offer novel insights into the diversity and functional roles of phages in diverse environments.}, } @article {pmid27030297, year = {2016}, author = {Lee, J and Kim, KM and Yang, EC and Miller, KA and Boo, SM and Bhattacharya, D and Yoon, HS}, title = {Reconstructing the complex evolutionary history of mobile plasmids in red algal genomes.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {23744}, pmid = {27030297}, issn = {2045-2322}, mesh = {DNA Copy Number Variations ; DNA, Mitochondrial/*genetics ; DNA, Plant/*genetics ; *Evolution, Molecular ; Gene Ontology ; Gene Transfer, Horizontal ; *Genome, Plastid ; Molecular Sequence Annotation ; Open Reading Frames ; Phylogeny ; Plasmids/chemistry/*metabolism ; Plastids/genetics ; Rhodophyta/classification/*genetics ; }, abstract = {The integration of foreign DNA into algal and plant plastid genomes is a rare event, with only a few known examples of horizontal gene transfer (HGT). Plasmids, which are well-studied drivers of HGT in prokaryotes, have been reported previously in red algae (Rhodophyta). However, the distribution of these mobile DNA elements and their sites of integration into the plastid (ptDNA), mitochondrial (mtDNA), and nuclear genomes of Rhodophyta remain unknown. Here we reconstructed the complex evolutionary history of plasmid-derived DNAs in red algae. Comparative analysis of 21 rhodophyte ptDNAs, including new genome data for 5 species, turned up 22 plasmid-derived open reading frames (ORFs) that showed syntenic and copy number variation among species, but were conserved within different individuals in three lineages. Several plasmid-derived homologs were found not only in ptDNA but also in mtDNA and in the nuclear genome of green plants, stramenopiles, and rhizarians. Phylogenetic and plasmid-derived ORF analyses showed that the majority of plasmid DNAs originated within red algae, whereas others were derived from cyanobacteria, other bacteria, and viruses. Our results elucidate the evolution of plasmid DNAs in red algae and suggest that they spread as parasitic genetic elements. This hypothesis is consistent with their sporadic distribution within Rhodophyta.}, } @article {pmid27029774, year = {2016}, author = {Vancheri, F and Backlund, L and Strender, LE and Godman, B and Wettermark, B}, title = {Time trends in statin utilisation and coronary mortality in Western European countries.}, journal = {BMJ open}, volume = {6}, number = {3}, pages = {e010500}, pmid = {27029774}, issn = {2044-6055}, mesh = {Coronary Artery Disease/*drug therapy/*mortality ; Databases, Factual ; Europe ; Humans ; Hydroxymethylglutaryl-CoA Reductase Inhibitors/*therapeutic use ; Risk Assessment ; }, abstract = {OBJECTIVES: To determine whether there is a relation between statin utilisation and coronary heart disease (CHD) mortality in populations with different levels of coronary risk, and whether the relation changes over time.

DESIGN: Ecological study using national databases of dispensed medicines and mortality rates.

SETTING: Western European countries with similar public health systems.

MAIN OUTCOME MEASURES: Population CHD mortality rates (rate/100,000) as a proxy for population coronary risk level, and statin utilisation expressed as Defined Daily Dose per one Thousand Inhabitants per Day (DDD/TID), in each country, for each year between 2000 and 2012. Spearman's correlation coefficients between CHD mortality and statin utilisation were calculated. Linear regression analysis was used to assess the relation between changes in CHD mortality and statin utilisation over the years.

RESULTS: 12 countries were included in the study. There was a wide range of CHD mortality reduction between the years 2000 and 2012 (from 25.9% in Italy to 57.9% in Denmark) and statin utilisation increase (from 121% in Belgium to 1263% in Denmark). No statistically significant relations were found between CHD mortality rates and statin utilisation, nor between changes in CHD and changes in statin utilisation in the countries over the years 2000 and 2012.

CONCLUSIONS: Among the Western European countries studied, the large increase in statin utilisation between 2000 and 2012 was not associated with CHD mortality, nor with its rate of change over the years. Factors different from the individual coronary risk, such as population ageing, health authority programmes, guidelines, media attention and pharmaceutical industry marketing, may have influenced the large increase in statin utilisation. These need to be re-examined with a greater emphasis on prevention strategies.}, } @article {pmid27029554, year = {2016}, author = {Speth, DR and In 't Zandt, MH and Guerrero-Cruz, S and Dutilh, BE and Jetten, MS}, title = {Genome-based microbial ecology of anammox granules in a full-scale wastewater treatment system.}, journal = {Nature communications}, volume = {7}, number = {}, pages = {11172}, pmid = {27029554}, issn = {2041-1723}, mesh = {Ammonium Compounds/analysis ; Bacteria/classification/*genetics/metabolism ; Biodegradation, Environmental ; Bioreactors/microbiology ; Denitrification ; *Genome, Bacterial ; Metagenomics ; Nitrites/metabolism ; Phylogeny ; Sewage/chemistry/microbiology ; *Wastewater ; Water Purification/*methods ; }, abstract = {Partial-nitritation anammox (PNA) is a novel wastewater treatment procedure for energy-efficient ammonium removal. Here we use genome-resolved metagenomics to build a genome-based ecological model of the microbial community in a full-scale PNA reactor. Sludge from the bioreactor examined here is used to seed reactors in wastewater treatment plants around the world; however, the role of most of its microbial community in ammonium removal remains unknown. Our analysis yielded 23 near-complete draft genomes that together represent the majority of the microbial community. We assign these genomes to distinct anaerobic and aerobic microbial communities. In the aerobic community, nitrifying organisms and heterotrophs predominate. In the anaerobic community, widespread potential for partial denitrification suggests a nitrite loop increases treatment efficiency. Of our genomes, 19 have no previously cultivated or sequenced close relatives and six belong to bacterial phyla without any cultivated members, including the most complete Omnitrophica (formerly OP3) genome to date.}, } @article {pmid27025964, year = {2016}, author = {Li, C and Lim, KM and Chng, KR and Nagarajan, N}, title = {Predicting microbial interactions through computational approaches.}, journal = {Methods (San Diego, Calif.)}, volume = {102}, number = {}, pages = {12-19}, doi = {10.1016/j.ymeth.2016.02.019}, pmid = {27025964}, issn = {1095-9130}, mesh = {*Computer Simulation ; Data Mining/methods ; Metagenomics/*methods ; *Microbial Interactions ; }, abstract = {Microorganisms play a vital role in various ecosystems and characterizing interactions between them is an essential step towards understanding the organization and function of microbial communities. Computational prediction has recently become a widely used approach to investigate microbial interactions. We provide a thorough review of emerging computational methods organized by the type of data they employ. We highlight three major challenges in inferring interactions using metagenomic survey data and discuss the underlying assumptions and mathematics of interaction inference algorithms. In addition, we review interaction prediction methods relying on metabolic pathways, which are increasingly used to reveal mechanisms of interactions. Furthermore, we also emphasize the importance of mining the scientific literature for microbial interactions - a largely overlooked data source for experimentally validated interactions.}, } @article {pmid27023900, year = {2016}, author = {Madin, JS and Anderson, KD and Andreasen, MH and Bridge, TC and Cairns, SD and Connolly, SR and Darling, ES and Diaz, M and Falster, DS and Franklin, EC and Gates, RD and Harmer, A and Hoogenboom, MO and Huang, D and Keith, SA and Kosnik, MA and Kuo, CY and Lough, JM and Lovelock, CE and Luiz, O and Martinelli, J and Mizerek, T and Pandolfi, JM and Pochon, X and Pratchett, MS and Putnam, HM and Roberts, TE and Stat, M and Wallace, CC and Widman, E and Baird, AH}, title = {The Coral Trait Database, a curated database of trait information for coral species from the global oceans.}, journal = {Scientific data}, volume = {3}, number = {}, pages = {160017}, pmid = {27023900}, issn = {2052-4463}, mesh = {Animals ; *Anthozoa ; Coral Reefs ; *Databases, Factual ; Ecosystem ; Oceans and Seas ; Phylogeny ; }, abstract = {Trait-based approaches advance ecological and evolutionary research because traits provide a strong link to an organism's function and fitness. Trait-based research might lead to a deeper understanding of the functions of, and services provided by, ecosystems, thereby improving management, which is vital in the current era of rapid environmental change. Coral reef scientists have long collected trait data for corals; however, these are difficult to access and often under-utilized in addressing large-scale questions. We present the Coral Trait Database initiative that aims to bring together physiological, morphological, ecological, phylogenetic and biogeographic trait information into a single repository. The database houses species- and individual-level data from published field and experimental studies alongside contextual data that provide important framing for analyses. In this data descriptor, we release data for 56 traits for 1547 species, and present a collaborative platform on which other trait data are being actively federated. Our overall goal is for the Coral Trait Database to become an open-source, community-led data clearinghouse that accelerates coral reef research.}, } @article {pmid27022408, year = {2016}, author = {Kiware, SS and Russell, TL and Mtema, ZJ and Malishee, AD and Chaki, P and Lwetoijera, D and Chanda, J and Chinula, D and Majambere, S and Gimnig, JE and Smith, TA and Killeen, GF}, title = {A generic schema and data collection forms applicable to diverse entomological studies of mosquitoes.}, journal = {Source code for biology and medicine}, volume = {11}, number = {}, pages = {4}, pmid = {27022408}, issn = {1751-0473}, support = {/WT_/Wellcome Trust/United Kingdom ; 107599/WT_/Wellcome Trust/United Kingdom ; }, abstract = {BACKGROUND: Standardized schemas, databases, and public data repositories are needed for the studies of malaria vectors that encompass a remarkably diverse array of designs and rapidly generate large data volumes, often in resource-limited tropical settings lacking specialized software or informatics support.

RESULTS: Data from the majority of mosquito studies conformed to a generic schema, with data collection forms recording the experimental design, sorting of collections, details of sample pooling or subdivision, and additional observations. Generically applicable forms with standardized attribute definitions enabled rigorous, consistent data and sample management with generic software and minimal expertise. Forms use now includes 20 experiments, 8 projects, and 15 users at 3 research and control institutes in 3 African countries, resulting in 11 peer-reviewed publications.

CONCLUSION: We have designed generic data schema that can be used to develop paper or electronic based data collection forms depending on the availability of resources. We have developed paper-based data collection forms that can be used to collect data from majority of entomological studies across multiple study areas using standardized data formats. Data recorded on these forms with standardized formats can be entered and linked with any relational database software. These informatics tools are recommended because they ensure that medical entomologists save time, improve data quality, and data collected and shared across multiple studies is in standardized formats hence increasing research outputs.}, } @article {pmid27020245, year = {2016}, author = {Jacquiod, S and Stenbæk, J and Santos, SS and Winding, A and Sørensen, SJ and Priemé, A}, title = {Metagenomes provide valuable comparative information on soil microeukaryotes.}, journal = {Research in microbiology}, volume = {167}, number = {5}, pages = {436-450}, doi = {10.1016/j.resmic.2016.03.003}, pmid = {27020245}, issn = {1769-7123}, mesh = {*Biodiversity ; Computational Biology/*methods ; Eukaryota/*classification/*genetics ; *Metagenome ; *Phylogeny ; *Soil Microbiology ; }, abstract = {Despite the critical ecological roles of microeukaryotes in terrestrial ecosystems, most descriptive studies of soil microbes published so far focused only on specific groups. Meanwhile, the fast development of metagenome sequencing leads to considerable data accumulation in public repositories, providing microbiologists with substantial amounts of accessible information. We took advantage of public metagenomes in order to investigate microeukaryote communities in a well characterized grassland soil. The data gathered allowed the evaluation of several factors impacting the community structure, including the DNA extraction method, the database choice and also the annotation procedure. While most studies on soil microeukaryotes are based on sequencing of PCR-amplified taxonomic markers (18S rRNA genes, ITS regions), this work represents, to our knowledge, the first report based solely on metagenomic microeukaryote DNA. Choosing the correct annotation procedure and reference database has proven to be crucial, as it considerably limits the risk of wrong assignments. In addition, a significant and pronounced effect of the DNA extraction method on the taxonomical structure of soil microeukaryotes has been identified. Our analyses suggest that publicly available metagenome data can provide valuable information on soil microeukaryotes for comparative purposes when handled appropriately, complementing the current view provided by ribosomal amplicon sequencing methods.}, } @article {pmid27019346, year = {2016}, author = {Piwczyński, M and Pabijan, M and Grzywacz, A and Glinkowski, W and Bereś, PK and Buszko, J}, title = {High regional genetic diversity and lack of host-specificity in Ostrinia nubilalis (Lepidoptera: Crambidae) as revealed by mtDNA variation.}, journal = {Bulletin of entomological research}, volume = {106}, number = {4}, pages = {512-521}, doi = {10.1017/S0007485316000195}, pmid = {27019346}, issn = {1475-2670}, mesh = {Animals ; Bayes Theorem ; DNA, Mitochondrial/chemistry ; Databases, Nucleic Acid ; Feeding Behavior ; Genetic Variation ; Moths/*genetics/physiology ; Phylogeny ; Poland ; Sequence Analysis, DNA ; }, abstract = {The European corn borer (Ostrinia nubilalis) infests a wide array of host plants and is considered one of the most serious pests of maize in Europe. Recent studies suggest that individuals feeding on maize in Europe should be referred to O. nubilalis (sensu nov.), while those infesting dicots as Ostrinia scapulalis (sensu nov.). We test if the clear genetic distinctiveness among individuals of O. nubilalis living on maize vs. dicots is tracked by mitochondrial DNA (mtDNA). We used fragments of COI and COII genes of 32 individuals traditionally recognized as O. nubilalis collected on three host plants, maize, mugwort and hop, growing in different parts of Poland. In addition, we reconstructed the mtDNA phylogeny of Ostrinia species based on our data and sequences retrieved from GenBank to assess host and/or biogeographic patterns. We also compared haplotype variation found in Poland (east-central Europe) with other regions (Anatolia, Eastern Europe, Balkans, Far East, North America). Our study showed high mtDNA diversity of O. nubilalis in Poland in comparison with other regions and revealed rare haplotypes likely of Asian origin. We did not find distinct mtDNA haplotypes in larvae feeding on maize vs. dicotyledonous plants. Phylogenetic analyses showed an apparent lack of mtDNA divergence among putatively distinct lineages belonging to the O. nubilalis group as identical haplotypes are shared by Asian and European individuals. We argue that human-mediated dispersal, hybridization and sporadic host jumps are likely responsible for the lack of a geographic pattern in mtDNA variation.}, } @article {pmid27014872, year = {2016}, author = {Moura, MR and Villalobos, F and Costa, GC and Garcia, PC}, title = {Disentangling the Role of Climate, Topography and Vegetation in Species Richness Gradients.}, journal = {PloS one}, volume = {11}, number = {3}, pages = {e0152468}, pmid = {27014872}, issn = {1932-6203}, mesh = {Amphibians ; Animals ; *Biodiversity ; Biomass ; Birds ; Chiroptera ; *Climate ; Databases, Factual ; Ecology ; Forests ; *Geography ; Mammals ; Models, Theoretical ; Plants ; Population Dynamics ; *Temperature ; }, abstract = {Environmental gradients (EG) related to climate, topography and vegetation are among the most important drivers of broad scale patterns of species richness. However, these different EG do not necessarily drive species richness in similar ways, potentially presenting synergistic associations when driving species richness. Understanding the synergism among EG allows us to address key questions arising from the effects of global climate and land use changes on biodiversity. Herein, we use variation partitioning (also know as commonality analysis) to disentangle unique and shared contributions of different EG in explaining species richness of Neotropical vertebrates. We use three broad sets of predictors to represent the environmental variability in (i) climate (annual mean temperature, temperature annual range, annual precipitation and precipitation range), (ii) topography (mean elevation, range and coefficient of variation of elevation), and (iii) vegetation (land cover diversity, standard deviation and range of forest canopy height). The shared contribution between two types of EG is used to quantify synergistic processes operating among EG, offering new perspectives on the causal relationships driving species richness. To account for spatially structured processes, we use Spatial EigenVector Mapping models. We perform analyses across groups with distinct dispersal abilities (amphibians, non-volant mammals, bats and birds) and discuss the influence of vagility on the partitioning results. Our findings indicate that broad scale patterns of vertebrate richness are mainly affected by the synergism between climate and vegetation, followed by the unique contribution of climate. Climatic factors were relatively more important in explaining species richness of good dispersers. Most of the variation in vegetation that explains vertebrate richness is climatically structured, supporting the productivity hypothesis. Further, the weak synergism between topography and vegetation urges caution when using topographic complexity as a surrogate of habitat (vegetation) heterogeneity.}, } @article {pmid27011368, year = {2016}, author = {Roberts, TE and Bridge, TC and Caley, MJ and Baird, AH}, title = {The Point Count Transect Method for Estimates of Biodiversity on Coral Reefs: Improving the Sampling of Rare Species.}, journal = {PloS one}, volume = {11}, number = {3}, pages = {e0152335}, pmid = {27011368}, issn = {1932-6203}, mesh = {Animals ; Anthozoa ; Australia ; *Biodiversity ; Biota ; *Coral Reefs ; Data Collection ; *Data Interpretation, Statistical ; Ecology ; Geography ; Population Density ; Time Factors ; }, abstract = {Understanding patterns in species richness and diversity over environmental gradients (such as altitude and depth) is an enduring component of ecology. As most biological communities feature few common and many rare species, quantifying the presence and abundance of rare species is a crucial requirement for analysis of these patterns. Coral reefs present specific challenges for data collection, with limitations on time and site accessibility making efficiency crucial. Many commonly used methods, such as line intercept transects (LIT), are poorly suited to questions requiring the detection of rare events or species. Here, an alternative method for surveying reef-building corals is presented; the point count transect (PCT). The PCT consists of a count of coral colonies at a series of sample stations, located at regular intervals along a transect. In contrast the LIT records the proportion of each species occurring under a transect tape of a given length. The same site was surveyed using PCT and LIT to compare species richness estimates between the methods. The total number of species increased faster per individual sampled and unit of time invested using PCT. Furthermore, 41 of the 44 additional species recorded by the PCT occurred ≤ 3 times, demonstrating the increased capacity of PCT to detect rare species. PCT provides a more accurate estimate of local-scale species richness than the LIT, and is an efficient alternative method for surveying reef corals to address questions associated with alpha-diversity, and rare or incidental events.}, } @article {pmid27008340, year = {2017}, author = {Kim, D and Brown, Z and Anderson, R and Mutero, C and Miranda, ML and Wiener, J and Kramer, R}, title = {The Value of Information in Decision-Analytic Modeling for Malaria Vector Control in East Africa.}, journal = {Risk analysis : an official publication of the Society for Risk Analysis}, volume = {37}, number = {2}, pages = {231-244}, pmid = {27008340}, issn = {1539-6924}, support = {R01 AI088009/AI/NIAID NIH HHS/United States ; }, mesh = {Africa, Eastern ; Animals ; Costs and Cost Analysis ; *Decision Support Techniques ; Global Health ; Humans ; Malaria/*prevention & control ; Models, Theoretical ; Mosquito Control/economics/*methods ; Resource Allocation ; Uncertainty ; }, abstract = {Decision analysis tools and mathematical modeling are increasingly emphasized in malaria control programs worldwide to improve resource allocation and address ongoing challenges with sustainability. However, such tools require substantial scientific evidence, which is costly to acquire. The value of information (VOI) has been proposed as a metric for gauging the value of reduced model uncertainty. We apply this concept to an evidenced-based Malaria Decision Analysis Support Tool (MDAST) designed for application in East Africa. In developing MDAST, substantial gaps in the scientific evidence base were identified regarding insecticide resistance in malaria vector control and the effectiveness of alternative mosquito control approaches, including larviciding. We identify four entomological parameters in the model (two for insecticide resistance and two for larviciding) that involve high levels of uncertainty and to which outputs in MDAST are sensitive. We estimate and compare a VOI for combinations of these parameters in evaluating three policy alternatives relative to a status quo policy. We find having perfect information on the uncertain parameters could improve program net benefits by up to 5-21%, with the highest VOI associated with jointly eliminating uncertainty about reproductive speed of malaria-transmitting mosquitoes and initial efficacy of larviciding at reducing the emergence of new adult mosquitoes. Future research on parameter uncertainty in decision analysis of malaria control policy should investigate the VOI with respect to other aspects of malaria transmission (such as antimalarial resistance), the costs of reducing uncertainty in these parameters, and the extent to which imperfect information about these parameters can improve payoffs.}, } @article {pmid27007388, year = {2016}, author = {Guo, B and Chen, Z and Guo, J and Liu, F and Chen, C and Liu, K}, title = {Analysis of the Nonlinear Trends and Non-Stationary Oscillations of Regional Precipitation in Xinjiang, Northwestern China, Using Ensemble Empirical Mode Decomposition.}, journal = {International journal of environmental research and public health}, volume = {13}, number = {3}, pages = {}, pmid = {27007388}, issn = {1660-4601}, mesh = {China ; *Climate Change ; Empirical Research ; Geographic Information Systems ; Models, Theoretical ; *Rain ; *Snow ; *Water Supply ; }, abstract = {Changes in precipitation could have crucial influences on the regional water resources in arid regions such as Xinjiang. It is necessary to understand the intrinsic multi-scale variations of precipitation in different parts of Xinjiang in the context of climate change. In this study, based on precipitation data from 53 meteorological stations in Xinjiang during 1960-2012, we investigated the intrinsic multi-scale characteristics of precipitation variability using an adaptive method named ensemble empirical mode decomposition (EEMD). Obvious non-linear upward trends in precipitation were found in the north, south, east and the entire Xinjiang. Changes in precipitation in Xinjiang exhibited significant inter-annual scale (quasi-2 and quasi-6 years) and inter-decadal scale (quasi-12 and quasi-23 years). Moreover, the 2-3-year quasi-periodic fluctuation was dominant in regional precipitation and the inter-annual variation had a considerable effect on the regional-scale precipitation variation in Xinjiang. We also found that there were distinctive spatial differences in variation trends and turning points of precipitation in Xinjiang. The results of this study indicated that compared to traditional decomposition methods, the EEMD method, without using any a priori determined basis functions, could effectively extract the reliable multi-scale fluctuations and reveal the intrinsic oscillation properties of climate elements.}, } @article {pmid27006271, year = {2017}, author = {Perez, AL and Gauthier, AM and Ferracini, T and Cowan, DM and Kingsbury, T and Panko, J}, title = {The challenge of predicting problematic chemicals using a decision analysis tool: Triclosan as a case study.}, journal = {Integrated environmental assessment and management}, volume = {13}, number = {1}, pages = {198-207}, doi = {10.1002/ieam.1778}, pmid = {27006271}, issn = {1551-3793}, mesh = {*Decision Support Techniques ; Environmental Monitoring/*methods ; Environmental Pollutants/*toxicity ; Environmental Pollution/*statistics & numerical data ; Risk Assessment/methods ; Triclosan/*toxicity ; }, abstract = {Manufacturers lack a reliable means for determining whether a chemical will be targeted for deselection from their supply chain. In this analysis, 3 methods for determining whether a specific chemical (triclosan) would meet the criteria necessary for being targeted for deselection are presented. The methods included a list-based approach, use of a commercially available chemical assessment software tool run in 2 modes, and a public interest evaluation. Our results indicated that triclosan was included on only 6 of the lists reviewed, none of which were particularly influential in chemical selection decisions. The results from the chemical assessment tool evaluations indicated that human and ecological toxicity for triclosan is low and received scores indicating that the chemical would be considered of low concern. However, triclosan's peak public interest tracked several years in advance of increased regulatory scrutiny of this chemical suggesting that public pressure may have been influential in deselection decisions. Key data gaps and toxicity endpoints not yet regulated such as endocrine disruption potential or phototoxicity, but that are important to estimate the trajectory for deselection of a chemical, are discussed. Integr Environ Assess Manag 2017;13:198-207. © 2016 SETAC.}, } @article {pmid27004596, year = {2016}, author = {das Nair, R and Martin, KJ and Lincoln, NB}, title = {Memory rehabilitation for people with multiple sclerosis.}, journal = {The Cochrane database of systematic reviews}, volume = {3}, number = {}, pages = {CD008754}, doi = {10.1002/14651858.CD008754.pub3}, pmid = {27004596}, issn = {1469-493X}, mesh = {Audiovisual Aids ; Humans ; Memory Disorders/etiology/*rehabilitation ; Multiple Sclerosis/*complications ; Randomized Controlled Trials as Topic ; Therapy, Computer-Assisted/methods ; }, abstract = {BACKGROUND: This is an update of the Cochrane review 'Memory rehabilitation for people with multiple sclerosis' (first published in the Cochrane Library 14 March 2012, Issue 3). Impairments in cognitive function, particularly memory, are common in people with multiple sclerosis (MS) and can potentially affect their ability to complete functional activities. There is evidence from single-case or small group studies that memory rehabilitation can be beneficial for people with MS, but findings from randomised controlled trials (RCTs) and systematic reviews have been inconclusive.

OBJECTIVES: To determine whether people with MS who received memory rehabilitation showed: 1. better outcomes in their memory functions compared to those given no treatment or receiving a placebo control; and 2. better functional abilities, in terms of activities of daily living, mood, and quality of life, than those who received no treatment or a placebo.

SEARCH METHODS: We searched the Trials Specialised Register of the Cochrane Multiple Sclerosis and Rare Diseases of the CNS Group (2 June 2015) and the following electronic databases: The NIHR Clinical Research Network Portfolio database (NIHR CRN) (from 2010 to June 2015), The Allied and Complementary Medicine Database (AMED) (2010 to June 2015), British Nursing Index (BNI) (2010 to June 2015), PsycINFO (2011 to June 2015), and CAB Abstracts (2010 to June 2015). Start dates for the electronic databases coincided with the last search for the previous review. We handsearched relevant journals and reference lists.

SELECTION CRITERIA: We selected RCTs or quasi-randomised trials of memory rehabilitation or cognitive rehabilitation for people with MS in which a memory rehabilitation treatment group was compared to a control group. Selection was conducted independently first and then confirmed through group discussion. We excluded studies that included participants whose memory deficits were the result of conditions other than MS unless we could identify a subgroup of participants with MS with separate results.

DATA COLLECTION AND ANALYSIS: Three review authors were involved in this update in terms of study selection, quality assessment, and data extraction. We contacted investigators of primary studies for further information where required. We conducted data analysis and synthesis in accordance with the Cochrane Handbook for Systematic Reviews of Interventions (Higgins 2011). We performed a 'best evidence' synthesis based on the methodological quality of the primary studies included.

MAIN RESULTS: We added seven studies during this update, bringing the total to 15 studies, involving 989 participants. The interventions involved various memory retraining techniques, such as computerised programmes and training on internal and external memory aids. Control groups varied in format from assessment-only groups, discussion and games, non-specific cognitive retraining, and attention or visuospatial training. The risk of bias of the included studies was generally low, but we found eight studies to have high risk of bias related to certain aspects of their methodology.We found significant effect of intervention on objective assessments of memory in both the immediate and long-term follow-ups: standardised mean difference (SMD) 0.23 (95% confidence interval (CI) 0.05 to 0.41) and SMD 0.26 (95% CI 0.03 to 0.49), respectively. We also found significant effect of intervention for quality of life in the immediate follow-up (SMD 0.23 (95% CI 0.05 to 0.41)). These findings showed that the intervention group performed significantly better than the control group. We also found a significant difference for activities of daily living (ADL) in the long-term follow-up (SMD -0.33 (95% CI -0.63 to -0.03)), showing that the control groups had significantly less difficulty completing ADLs than the intervention groups. We found no significant effects, either immediate or long-term, on subjective reports of memory problems (SMD 0.04 (95% CI -0.19 to 0.27) and SMD 0.04 (95% CI -0.19 to 0.27)); on mood (SMD 0.02 (95% CI -0.16 to 0.20) and SMD -0.01 (95% CI -0.21 to 0.20)); and on immediate follow-up for ADL (SMD -0.13 (95% CI -0.60 to 0.33)) and in the long term for quality of life (SMD 0.16 (95% CI -0.03 to 0.36)). We could not complete a sensitivity analysis of intention-to-treat in comparison with per-protocol analysis, due to insufficient information from the included papers. However, a sensitivity analysis of high- versus low-risk studies suggested that while quality of the trials did not affect most outcomes, differences were seen in the objective memory outcomes (both at immediate and long term) and quality of life (immediate) outcome, with studies with higher risk of bias inflating the overall effect size estimates for these outcomes, and the test of overall effect changing from being statistically significant to not significant when studies at high risk of bias were excluded. This suggests that lower-quality studies may have positively influenced the outcomes.

AUTHORS' CONCLUSIONS: There is some evidence to support the effectiveness of memory rehabilitation on memory function, as well as on quality of life. However, the evidence is limited and does not extend to subjective reports of memory functioning or mood. Furthermore, the objective measures used are not ecologically valid measures, and thus potentially limit generalisability of these findings into daily life. Further robust RCTs of high methodological quality and better quality of reporting, using ecologically valid outcome assessments, are still needed.}, } @article {pmid27003359, year = {2016}, author = {Zeng, YQ and Dai, Z and Lu, F and Lu, Z and Liu, X and Chen, C and Qu, P and Li, D and Hua, Z and Qu, Y and Zou, C}, title = {Emodin via colonic irrigation modulates gut microbiota and reduces uremic toxins in rats with chronic kidney disease.}, journal = {Oncotarget}, volume = {7}, number = {14}, pages = {17468-17478}, pmid = {27003359}, issn = {1949-2553}, mesh = {Animals ; Emodin/*administration & dosage ; Gastrointestinal Microbiome/*drug effects ; Indican/*blood ; Male ; Microbiota/*drug effects ; Random Allocation ; Rats ; Rats, Sprague-Dawley ; Renal Insufficiency, Chronic/blood/*drug therapy/*microbiology ; Therapeutic Irrigation/methods ; Urea/*blood ; }, abstract = {Gut microbiota plays a dual role in chronic kidney disease (CKD) and is closely linked to production of uremic toxins. Strategies of reducing uremic toxins by targeting gut microbiota are emerging. It is known that Chinese medicine rhubarb enema can reduce uremic toxins and improve renal function. However, it remains unknown which ingredient or mechanism mediates its effect. Here we utilized a rat CKD model of 5/6 nephrectomy to evaluate the effect of emodin, a main ingredient of rhubarb, on gut microbiota and uremic toxins in CKD. Emodin was administered via colonic irrigation at 5ml (1mg/day) for four weeks. We found that emodin via colonic irrigation (ECI) altered levels of two important uremic toxins, urea and indoxyl sulfate (IS), and changed gut microbiota in rats with CKD. ECI remarkably reduced urea and IS and improved renal function. Pyrosequencing and Real-Time qPCR analyses revealed that ECI resumed the microbial balance from an abnormal status in CKD. We also demonstrated that ten genera were positively correlated with Urea while four genera exhibited the negative correlation. Moreover, three genera were positively correlated with IS. Therefore, emodin altered the gut microbiota structure. It reduced the number of harmful bacteria, such as Clostridium spp. that is positively correlated with both urea and IS, but augmented the number of beneficial bacteria, including Lactobacillus spp. that is negatively correlated with urea. Thus, changes in gut microbiota induced by emodin via colonic irrigation are closely associated with reduction in uremic toxins and mitigation of renal injury.}, } @article {pmid27000052, year = {2016}, author = {Akinkugbe, AA and Sharma, S and Ohrbach, R and Slade, GD and Poole, C}, title = {Directed Acyclic Graphs for Oral Disease Research.}, journal = {Journal of dental research}, volume = {95}, number = {8}, pages = {853-859}, pmid = {27000052}, issn = {1544-0591}, support = {T32 DE023526/DE/NIDCR NIH HHS/United States ; T90 DE021986/DE/NIDCR NIH HHS/United States ; U01 DE017018/DE/NIDCR NIH HHS/United States ; }, mesh = {Causality ; *Confounding Factors, Epidemiologic ; Data Interpretation, Statistical ; Dental Research/*methods ; Facial Injuries/complications ; Humans ; Mouth Diseases/*etiology ; Stomatognathic Diseases/etiology ; Temporomandibular Joint Disorders/etiology ; }, abstract = {Directed acyclic graphs (DAGs) are nonparametric graphical tools used to depict causal relations in the epidemiologic assessment of exposure-outcome associations. Although their use in dental research was first advocated in 2002, DAGs have yet to be widely adopted in this field. DAGs help identify threats to causal inference such as confounders, bias due to subject selection, and inappropriate handling of missing data. DAGs can also inform the data analysis strategy based on relations among variables depicted on it. This article uses the example of a study of temporomandibular disorders (TMDs), investigating causal effects of facial injury on subsequent risk of TMD. We illustrate how DAGs can be used to identify 1) potential confounders, 2) mediators and the consequences of attempt to estimate direct causal effects, 3) colliders and the consequences of conditioning on colliders, and 4) variables that are simultaneously mediators and confounders and the consequences of adjustment for such variables. For example, one DAG shows that statistical adjustment for the pressure pain threshold would necessarily bias the causal relation between facial injury and TMD. Finally, we discuss the usefulness of DAGs during study design, subject selection, and choosing variables to be measured in a study.}, } @article {pmid26999359, year = {2016}, author = {Suchan, T and Pitteloud, C and Gerasimova, NS and Kostikova, A and Schmid, S and Arrigo, N and Pajkovic, M and Ronikier, M and Alvarez, N}, title = {Hybridization Capture Using RAD Probes (hyRAD), a New Tool for Performing Genomic Analyses on Collection Specimens.}, journal = {PloS one}, volume = {11}, number = {3}, pages = {e0151651}, pmid = {26999359}, issn = {1932-6203}, mesh = {Animals ; Butterflies/genetics ; Computational Biology ; DNA/genetics ; Data Accuracy ; Gene Library ; Genetic Loci ; Genomics/*methods ; Grasshoppers/genetics ; Nucleic Acid Hybridization/*methods ; Polymorphism, Single Nucleotide/genetics ; Restriction Mapping ; Sequence Analysis, DNA ; *Specimen Handling ; }, abstract = {In the recent years, many protocols aimed at reproducibly sequencing reduced-genome subsets in non-model organisms have been published. Among them, RAD-sequencing is one of the most widely used. It relies on digesting DNA with specific restriction enzymes and performing size selection on the resulting fragments. Despite its acknowledged utility, this method is of limited use with degraded DNA samples, such as those isolated from museum specimens, as these samples are less likely to harbor fragments long enough to comprise two restriction sites making possible ligation of the adapter sequences (in the case of double-digest RAD) or performing size selection of the resulting fragments (in the case of single-digest RAD). Here, we address these limitations by presenting a novel method called hybridization RAD (hyRAD). In this approach, biotinylated RAD fragments, covering a random fraction of the genome, are used as baits for capturing homologous fragments from genomic shotgun sequencing libraries. This simple and cost-effective approach allows sequencing of orthologous loci even from highly degraded DNA samples, opening new avenues of research in the field of museum genomics. Not relying on the restriction site presence, it improves among-sample loci coverage. In a trial study, hyRAD allowed us to obtain a large set of orthologous loci from fresh and museum samples from a non-model butterfly species, with a high proportion of single nucleotide polymorphisms present in all eight analyzed specimens, including 58-year-old museum samples. The utility of the method was further validated using 49 museum and fresh samples of a Palearctic grasshopper species for which the spatial genetic structure was previously assessed using mtDNA amplicons. The application of the method is eventually discussed in a wider context. As it does not rely on the restriction site presence, it is therefore not sensitive to among-sample loci polymorphisms in the restriction sites that usually causes loci dropout. This should enable the application of hyRAD to analyses at broader evolutionary scales.}, } @article {pmid26996522, year = {2016}, author = {Jackson, A and Evers, DC and Eagles-Smith, CA and Ackerman, JT and Willacker, JJ and Elliott, JE and Lepak, JM and Vander Pol, SS and Bryan, CE}, title = {Mercury risk to avian piscivores across western United States and Canada.}, journal = {The Science of the total environment}, volume = {568}, number = {}, pages = {685-696}, pmid = {26996522}, issn = {1879-1026}, support = {9999-NIST//Intramural NIST DOC/United States ; }, mesh = {Animals ; Birds/*blood/growth & development ; Canada ; Databases, Factual ; Environmental Exposure/*analysis/prevention & control ; Environmental Monitoring ; Fishes/*blood/growth & development ; Food Chain ; Liver/chemistry ; Mercury/*analysis/blood ; Northwestern United States ; Ovum/chemistry ; Risk Assessment ; Water Pollutants, Chemical/*analysis/blood ; }, abstract = {The widespread distribution of mercury (Hg) threatens wildlife health, particularly piscivorous birds. Western North America is a diverse region that provides critical habitat to many piscivorous bird species, and also has a well-documented history of mercury contamination from legacy mining and atmospheric deposition. The diversity of landscapes in the west limits the distribution of avian piscivore species, complicating broad comparisons across the region. Mercury risk to avian piscivores was evaluated across the western United States and Canada using a suite of avian piscivore species representing a variety of foraging strategies that together occur broadly across the region. Prey fish Hg concentrations were size-adjusted to the preferred size class of the diet for each avian piscivore (Bald Eagle=36cm, Osprey=30cm, Common and Yellow-billed Loon=15cm, Western and Clark's Grebe=6cm, and Belted Kingfisher=5cm) across each species breeding range. Using a combination of field and lab-based studies on Hg effect in a variety of species, wet weight blood estimates were grouped into five relative risk categories including: background (<0.5μg/g), low (0.5-1μg/g), moderate (1-2μg/g), high (2-3μg/g), and extra high (>3μg/g). These risk categories were used to estimate potential mercury risk to avian piscivores across the west at a 1degree-by-1degree grid cell resolution. Avian piscivores foraging on larger-sized fish generally were at a higher relative risk to Hg. Habitats with a relatively high risk included wetland complexes (e.g., prairie pothole in Saskatchewan), river deltas (e.g., San Francisco Bay, Puget Sound, Columbia River), and arid lands (Great Basin and central Arizona). These results indicate that more intensive avian piscivore sampling is needed across Western North America to generate a more robust assessment of exposure risk.}, } @article {pmid26994606, year = {2016}, author = {Young, C and Laurent, O and Chung, JH and Wu, J}, title = {Geographic Distribution of Healthy Resources and Adverse Pregnancy Outcomes.}, journal = {Maternal and child health journal}, volume = {20}, number = {8}, pages = {1673-1679}, pmid = {26994606}, issn = {1573-6628}, mesh = {California/epidemiology ; Commerce ; Diabetes, Gestational/*epidemiology ; Female ; Food Supply ; Geographic Information Systems ; Geographic Mapping ; Humans ; Incidence ; Los Angeles ; Pre-Eclampsia/*epidemiology ; Pregnancy ; Pregnancy Outcome/*epidemiology ; Registries ; Residence Characteristics ; Risk Factors ; }, abstract = {Objective To determine the risk of gestational diabetes (GDM) and preeclampsia associated with various community resources. Methods An ecological study was performed in Los Angeles and Orange counties in California. Fast food restaurants, supermarkets, grocery stores, gyms, health clubs and green space were identified using Google © Maps Extractor and through the Southern California Association of Government. California Birth Certificate data was used to identify cases of GDM and preeclampsia. Unadjusted and adjusted risk ratios were calculated using negative binomial regression. Results There were 9692 cases of GDM and 6288 cases of preeclampsia corresponding to incidences of 2.5 and 1.4 % respectively. The adjusted risk of GDM was reduced in zip codes with greater concentration of grocery stores [relative risk (RR) 0.95, 95 % confidence interval (CI) 0.92-0.99] and supermarkets (RR 0.94, 95 % CI 0.90-0.98). There were no significant relationships between preeclampsia and the concentration of fast food restaurants, grocery store, supermarkets or the amount of green space. Conclusion The distribution of community resources has a significant association with the risk of developing GDM but not preeclampsia.}, } @article {pmid26991208, year = {2016}, author = {Pardo, A and García, FM and Valladares, F and Pulido, F}, title = {Simulated herbivory does not constrain phenotypic plasticity to shade through ontogeny in a relict tree.}, journal = {Plant biology (Stuttgart, Germany)}, volume = {18}, number = {4}, pages = {618-626}, doi = {10.1111/plb.12447}, pmid = {26991208}, issn = {1438-8677}, mesh = {*Biological Ontologies ; Ecology ; *Herbivory ; Light ; Models, Biological ; Phenotype ; Plant Leaves/physiology/radiation effects ; Plant Roots/physiology/radiation effects ; Plant Shoots/physiology/radiation effects ; Seedlings/physiology/radiation effects ; Stress, Physiological ; Trees/*physiology/radiation effects ; }, abstract = {Ecological limits to phenotypic plasticity (PP), induced by simultaneous biotic and abiotic factors, can prevent organisms from exhibiting optimal plasticity, and in turn lead to decreased fitness. Herbivory is an important biotic stressor and may limit plant functional responses to challenging environmental conditions such as shading. In this study we investigated whether plant functional responses and PP to shade are constrained by herbivory, and whether such constraints are due to direct effects based on resource limitation by considering ontogeny. We used as a model system the relict tree Prunus lusitanica and implemented an indoor experiment to quantify the response of saplings of different ages to shade and herbivory. We measured five functional traits and quantitatively calculated PP. Results showed that herbivory did not constrain functional responses or PP to shade except for shoot:root ratio (SR), which, despite showing a high PP in damaged saplings, decreased under shade instead of increasing. Damaged saplings of older age did not exhibit reduced constraints on functional responses to shade and generally presented a lower PP than damaged saplings of younger age. Our findings suggest that herbivory-mediated constraints on plant plasticity to shade may not be as widespread as previously thought. Nonetheless, the negative effect of herbivory on SR plastic expression to shade could be detrimental for plant fitness. Finally, our results suggest a secondary role of direct effects (resource-based) on P. lusitanica plasticity limitation. Further studies should quantify plant resources in order to gain a better understanding of this seldom-explored subject.}, } @article {pmid26989475, year = {2016}, author = {Boyer, S and Case, BS and Lefort, MC and Waterhouse, BR and Wratten, SD}, title = {Can ecosystem-scale translocations mitigate the impact of climate change on terrestrial biodiversity? Promises, pitfalls, and possibilities: Ecosystem-scale translocations.}, journal = {F1000Research}, volume = {5}, number = {}, pages = {146}, pmid = {26989475}, issn = {2046-1402}, abstract = {Because ecological interactions are the first components of the ecosystem to be impacted by climate change, future forms of threatened-species and ecosystem management should aim at conserving complete, functioning communities rather than single charismatic species. A possible way forward is the deployment of ecosystem-scale translocation (EST), where above- and below-ground elements of a functioning terrestrial ecosystem (including vegetation and topsoil) are carefully collected and moved together. Small-scale attempts at such practice have been made for the purpose of ecological restoration. By moving larger subsets of functioning ecosystems from climatically unstable regions to more stable ones, EST could provide a practical means to conserve mature and complex ecosystems threatened by climate change. However, there are a number of challenges associated with EST in the context of climate change mitigation, in particular the choice of donor and receptor sites. With the aim of fostering discussion and debate about the EST concept, we 1) outline the possible promises and pitfalls of EST in mitigating the impact of climate change on terrestrial biodiversity and 2) use a GIS-based approach to illustrate how potential source and receptor sites, where EST could be trialed and evaluated globally, could be identified.}, } @article {pmid26989149, year = {2016}, author = {Rimet, F and Chaumeil, P and Keck, F and Kermarrec, L and Vasselon, V and Kahlert, M and Franc, A and Bouchez, A}, title = {R-Syst::diatom: an open-access and curated barcode database for diatoms and freshwater monitoring.}, journal = {Database : the journal of biological databases and curation}, volume = {2016}, number = {}, pages = {}, pmid = {26989149}, issn = {1758-0463}, mesh = {*Access to Information ; Base Sequence ; *DNA Barcoding, Taxonomic ; *Data Curation ; *Databases, Genetic ; Diatoms/*classification/genetics ; *Environmental Monitoring ; *Fresh Water ; Phenotype ; Phylogeny ; Statistics as Topic ; }, abstract = {Diatoms are micro-algal indicators of freshwater pollution. Current standardized methodologies are based on microscopic determinations, which is time consuming and prone to identification uncertainties. The use of DNA-barcoding has been proposed as a way to avoid these flaws. Combining barcoding with next-generation sequencing enables collection of a large quantity of barcodes from natural samples. These barcodes are identified as certain diatom taxa by comparing the sequences to a reference barcoding library using algorithms. Proof of concept was recently demonstrated for synthetic and natural communities and underlined the importance of the quality of this reference library. We present an open-access and curated reference barcoding database for diatoms, called R-Syst::diatom, developed in the framework of R-Syst, the network of systematic supported by INRA (French National Institute for Agricultural Research), see http://www.rsyst.inra.fr/en. R-Syst::diatom links DNA-barcodes to their taxonomical identifications, and is dedicated to identify barcodes from natural samples. The data come from two sources, a culture collection of freshwater algae maintained in INRA in which new strains are regularly deposited and barcoded and from the NCBI (National Center for Biotechnology Information) nucleotide database. Two kinds of barcodes were chosen to support the database: 18S (18S ribosomal RNA) and rbcL (Ribulose-1,5-bisphosphate carboxylase/oxygenase), because of their efficiency. Data are curated using innovative (Declic) and classical bioinformatic tools (Blast, classical phylogenies) and up-to-date taxonomy (Catalogues and peer reviewed papers). Every 6 months R-Syst::diatom is updated. The database is available through the R-Syst microalgae website (http://www.rsyst.inra.fr/) and a platform dedicated to next-generation sequencing data analysis, virtual_BiodiversityL@b (https://galaxy-pgtp.pierroton.inra.fr/). We present here the content of the library regarding the number of barcodes and diatom taxa. In addition to these information, morphological features (e.g. biovolumes, chloroplasts…), life-forms (mobility, colony-type) or ecological features (taxa preferenda to pollution) are indicated in R-Syst::diatom. Database URL: http://www.rsyst.inra.fr/.}, } @article {pmid26981637, year = {2016}, author = {Li, X and Niu, X and Wang, B and Gao, P and Liu, Y}, title = {Driving Forces of Dynamic Changes in Soil Erosion in the Dahei Mountain Ecological Restoration Area of Northern China Based on GIS and RS.}, journal = {PloS one}, volume = {11}, number = {3}, pages = {e0142331}, pmid = {26981637}, issn = {1932-6203}, mesh = {*Conservation of Natural Resources ; *Ecosystem ; *Geographic Information Systems ; *Remote Sensing Technology ; *Soil ; }, abstract = {Dynamic change in soil erosion is an important focus of regional ecological restoration research. Here, the dynamic changes of soil erosion and its driving forces in the Dahei Mountain ecological restoration area of northern China were analyzed by LANDSAT TM remote sensing captured via geographic information system (GIS) technologies during three typical periods in 2004, 2008 and 2013. The results showed the following: (1) a decrease in intensive erosion and moderate erosion areas, as well as an increase in light erosion areas, was observed during two periods: one from 2004 to 2008 and the other from 2008 to 2013. (2) Between 2004 and 2008, the variation in the range of slight erosion was the largest (24.28%), followed by light erosion and intensive erosion; between 2008 and 2013, the variation in the range of intensive erosion area was the largest (9.89%), followed by slight erosion and moderate erosion. (3) Socioeconomic impact, accompanied by natural environmental factors, was the main driving force underlying the change in soil erosion within the ecological restoration area. In particular, the socioeconomic factors of per capita forest area and land reclamation rate, as well as the natural environmental factor of terrain slope, significantly influenced soil erosion changes within the ecological restoration area.}, } @article {pmid26980341, year = {2016}, author = {Rovatsos, M and Vukić, J and Kratochvíl, L}, title = {Mammalian X homolog acts as sex chromosome in lacertid lizards.}, journal = {Heredity}, volume = {117}, number = {1}, pages = {8-13}, pmid = {26980341}, issn = {1365-2540}, mesh = {Animals ; Chromosome Mapping ; Computational Biology/methods ; *Evolution, Molecular ; Female ; Gene Dosage ; Gene Expression Profiling ; High-Throughput Nucleotide Sequencing ; Humans ; Lizards/*genetics ; Male ; Mammals/*genetics ; *Sex Chromosomes ; Transcriptome ; }, abstract = {Among amniotes, squamate reptiles are especially variable in their mechanisms of sex determination; however, based largely on cytogenetic data, some lineages possess highly evolutionary stable sex chromosomes. The still very limited knowledge of the genetic content of squamate sex chromosomes precludes a reliable reconstruction of the evolutionary history of sex determination in this group and consequently in all amniotes. Female heterogamety with a degenerated W chromosome typifies the lizards of the family Lacertidae, the widely distributed Old World clade including several hundreds of species. From the liver transcriptome of the lacertid Takydromus sexlineatus female, we selected candidates for Z-specific genes as the loci lacking single-nucleotide polymorphisms. We validated the candidate genes through the comparison of the copy numbers in the female and male genomes of T. sexlineatus and another lacertid species, Lacerta agilis, by quantitative PCR that also proved to be a reliable technique for the molecular sexing of the studied species. We suggest that this novel approach is effective for the detection of Z-specific and X-specific genes in lineages with degenerated W, respectively Y chromosomes. The analyzed gene content of the Z chromosome revealed that lacertid sex chromosomes are not homologous with those of other reptiles including birds, but instead the genes have orthologs in the X-conserved region shared by viviparous mammals. It is possible that this part of the vertebrate genome was independently co-opted for the function of sex chromosomes in viviparous mammals and lacertids because of its content of genes involved in gonad differentiation.}, } @article {pmid26979952, year = {2016}, author = {van der Plas, F and Manning, P and Soliveres, S and Allan, E and Scherer-Lorenzen, M and Verheyen, K and Wirth, C and Zavala, MA and Ampoorter, E and Baeten, L and Barbaro, L and Bauhus, J and Benavides, R and Benneter, A and Bonal, D and Bouriaud, O and Bruelheide, H and Bussotti, F and Carnol, M and Castagneyrol, B and Charbonnier, Y and Coomes, DA and Coppi, A and Bastias, CC and Dawud, SM and De Wandeler, H and Domisch, T and Finér, L and Gessler, A and Granier, A and Grossiord, C and Guyot, V and Hättenschwiler, S and Jactel, H and Jaroszewicz, B and Joly, FX and Jucker, T and Koricheva, J and Milligan, H and Mueller, S and Muys, B and Nguyen, D and Pollastrini, M and Ratcliffe, S and Raulund-Rasmussen, K and Selvi, F and Stenlid, J and Valladares, F and Vesterdal, L and Zielínski, D and Fischer, M}, title = {Biotic homogenization can decrease landscape-scale forest multifunctionality.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {113}, number = {13}, pages = {3557-3562}, pmid = {26979952}, issn = {1091-6490}, mesh = {*Biodiversity ; Computer Simulation ; Databases, Factual ; Ecosystem ; Europe ; Forestry ; *Forests ; Models, Biological ; Trees ; }, abstract = {Many experiments have shown that local biodiversity loss impairs the ability of ecosystems to maintain multiple ecosystem functions at high levels (multifunctionality). In contrast, the role of biodiversity in driving ecosystem multifunctionality at landscape scales remains unresolved. We used a comprehensive pan-European dataset, including 16 ecosystem functions measured in 209 forest plots across six European countries, and performed simulations to investigate how local plot-scale richness of tree species (α-diversity) and their turnover between plots (β-diversity) are related to landscape-scale multifunctionality. After accounting for variation in environmental conditions, we found that relationships between α-diversity and landscape-scale multifunctionality varied from positive to negative depending on the multifunctionality metric used. In contrast, when significant, relationships between β-diversity and landscape-scale multifunctionality were always positive, because a high spatial turnover in species composition was closely related to a high spatial turnover in functions that were supported at high levels. Our findings have major implications for forest management and indicate that biotic homogenization can have previously unrecognized and negative consequences for large-scale ecosystem multifunctionality.}, } @article {pmid26977807, year = {2016}, author = {Nicolas, G and Robinson, TP and Wint, GR and Conchedda, G and Cinardi, G and Gilbert, M}, title = {Using Random Forest to Improve the Downscaling of Global Livestock Census Data.}, journal = {PloS one}, volume = {11}, number = {3}, pages = {e0150424}, pmid = {26977807}, issn = {1932-6203}, mesh = {Animals ; *Databases, Factual ; *Livestock ; *Models, Theoretical ; }, abstract = {Large scale, high-resolution global data on farm animal distributions are essential for spatially explicit assessments of the epidemiological, environmental and socio-economic impacts of the livestock sector. This has been the major motivation behind the development of the Gridded Livestock of the World (GLW) database, which has been extensively used since its first publication in 2007. The database relies on a downscaling methodology whereby census counts of animals in sub-national administrative units are redistributed at the level of grid cells as a function of a series of spatial covariates. The recent upgrade of GLW1 to GLW2 involved automating the processing, improvement of input data, and downscaling at a spatial resolution of 1 km per cell (5 km per cell in the earlier version). The underlying statistical methodology, however, remained unchanged. In this paper, we evaluate new methods to downscale census data with a higher accuracy and increased processing efficiency. Two main factors were evaluated, based on sample census datasets of cattle in Africa and chickens in Asia. First, we implemented and evaluated Random Forest models (RF) instead of stratified regressions. Second, we investigated whether models that predicted the number of animals per rural person (per capita) could provide better downscaled estimates than the previous approach that predicted absolute densities (animals per km2). RF models consistently provided better predictions than the stratified regressions for both continents and species. The benefit of per capita over absolute density models varied according to the species and continent. In addition, different technical options were evaluated to reduce the processing time while maintaining their predictive power. Future GLW runs (GLW 3.0) will apply the new RF methodology with optimized modelling options. The potential benefit of per capita models will need to be further investigated with a better distinction between rural and agricultural populations.}, } @article {pmid26976729, year = {2016}, author = {McCluskey, K and Alvarez, A and Bennett, R and Bokati, D and Boundy-Mills, K and Brown, D and Bull, CT and Coffey, M and Dreaden, T and Duke, C and Dye, G and Ehmke, E and Eversole, K and Fenstermacher, K and Geiser, D and Glaeser, JA and Greene, S and Gribble, L and Griffith, MP and Hanser, K and Humber, R and Johnson, BW and Kermode, A and Krichevsky, M and Laudon, M and Leach, J and Leslie, J and May, M and Melcher, U and Nobles, D and Fonseca, NR and Robinson, S and Ryan, M and Scott, J and Silflow, C and Vidaver, A and Webb, KM and Wertz, JE and Yentsch, S and Zehr, S}, title = {The U.S. Culture Collection Network Lays the Foundation for Progress in Preservation of Valuable Microbial Resources.}, journal = {Phytopathology}, volume = {106}, number = {6}, pages = {532-540}, doi = {10.1094/PHYTO-02-16-0074-RVW}, pmid = {26976729}, issn = {0031-949X}, mesh = {Agriculture ; Bacteria/classification/*genetics ; Databases, Factual/legislation & jurisprudence ; Genomics/*organization & administration ; Microbiology/*organization & administration ; United States ; United States Department of Agriculture/organization & administration ; }, abstract = {The U.S. Culture Collection Network was formed in 2012 by a group of culture collection scientists and stakeholders in order to continue the progress established previously through efforts of an ad hoc group. The network is supported by a Research Coordination Network grant from the U.S. National Science Foundation (NSF) and has the goals of promoting interaction among collections, encouraging the adoption of best practices, and protecting endangered or orphaned collections. After prior meetings to discuss best practices, shared data, and synergy with genome programs, the network held a meeting at the U.S. Department of Agriculture (USDA)-Agricultural Research Service (ARS) National Center for Genetic Resources Preservation (NCGRP) in Fort Collins, Colorado in October 2015 specifically to discuss collections that are vulnerable because of changes in funding programs, or are at risk of loss because of retirement or lack of funding. The meeting allowed collection curators who had already backed up their resources at the USDA NCGRP to visit the site, and brought collection owners, managers, and stakeholders together. Eight formal collections have established off-site backups with the USDA-ARS, ensuring that key material will be preserved for future research. All of the collections with backup at the NCGRP are public distributing collections including U.S. NSF-supported genetic stock centers, USDA-ARS collections, and university-supported collections. Facing the retirement of several pioneering researchers, the community discussed the value of preserving personal research collections and agreed that a mechanism to preserve these valuable collections was essential to any future national culture collection system. Additional input from curators of plant and animal collections emphasized that collections of every kind face similar challenges in developing long-range plans for sustainability.}, } @article {pmid26974148, year = {2016}, author = {Kuchta, SR and Brown, AD and Converse, PE and Highton, R}, title = {Multilocus Phylogeography and Species Delimitation in the Cumberland Plateau Salamander, Plethodon kentucki: Incongruence among Data Sets and Methods.}, journal = {PloS one}, volume = {11}, number = {3}, pages = {e0150022}, pmid = {26974148}, issn = {1932-6203}, mesh = {Animals ; DNA, Mitochondrial/*genetics ; *Databases, Genetic ; *Genetic Variation ; *Models, Genetic ; Phylogeography ; Urodela/*genetics ; }, abstract = {Species are a fundamental unit of biodiversity, yet can be challenging to delimit objectively. This is particularly true of species complexes characterized by high levels of population genetic structure, hybridization between genetic groups, isolation by distance, and limited phenotypic variation. Previous work on the Cumberland Plateau Salamander, Plethodon kentucki, suggested that it might constitute a species complex despite occupying a relatively small geographic range. To examine this hypothesis, we sampled 135 individuals from 43 populations, and used four mitochondrial loci and five nuclear loci (5693 base pairs) to quantify phylogeographic structure and probe for cryptic species diversity. Rates of evolution for each locus were inferred using the multidistribute package, and time calibrated gene trees and species trees were inferred using BEAST 2 and *BEAST 2, respectively. Because the parameter space relevant for species delimitation is large and complex, and all methods make simplifying assumptions that may lead them to fail, we conducted an array of analyses. Our assumption was that strongly supported species would be congruent across methods. Putative species were first delimited using a Bayesian implementation of the GMYC model (bGMYC), Geneland, and Brownie. We then validated these species using the genealogical sorting index and BPP. We found substantial phylogeographic diversity using mtDNA, including four divergent clades and an inferred common ancestor at 14.9 myr (95% HPD: 10.8-19.7 myr). By contrast, this diversity was not corroborated by nuclear sequence data, which exhibited low levels of variation and weak phylogeographic structure. Species trees estimated a far younger root than did the mtDNA data, closer to 1.0 myr old. Mutually exclusive putative species were identified by the different approaches. Possible causes of data set discordance, and the problem of species delimitation in complexes with high levels of population structure and introgressive hybridization, are discussed.}, } @article {pmid26973148, year = {2016}, author = {Chen, MH and Lan, WH and Bai, YM and Huang, KL and Su, TP and Tsai, SJ and Li, CT and Lin, WC and Chang, WH and Pan, TL and Chen, TJ and Hsu, JW}, title = {Influence of Relative Age on Diagnosis and Treatment of Attention-Deficit Hyperactivity Disorder in Taiwanese Children.}, journal = {The Journal of pediatrics}, volume = {172}, number = {}, pages = {162-167.e1}, doi = {10.1016/j.jpeds.2016.02.012}, pmid = {26973148}, issn = {1097-6833}, mesh = {Adolescent ; Age Factors ; Attention Deficit Disorder with Hyperactivity/*diagnosis/therapy ; Child ; Child, Preschool ; Databases, Factual ; Female ; Humans ; Logistic Models ; Male ; Risk ; Taiwan ; }, abstract = {OBJECTIVE: To determine the potential influence of relative age on the diagnosis and treatment of attention-deficit hyperactivity disorder (ADHD), especially in reference to an Asian country.

STUDY DESIGN: A total of 378 881 subjects aged 4-17 years during the study period (September 1, 1997 to August 31, 2011) were enrolled in our study from the Taiwan National Health Insurance Research Database. Logistic regression analysis was used to examine the likelihood of receiving ADHD diagnosis and treatment for those who were born in August (the youngest) compared with those who were born in September (the oldest).

RESULTS: Both boys and girls born in August had a higher risk of being diagnosed with ADHD (OR 1.63, 95% CI 1.45-1.84; OR 1.71, 95% CI 1.36-2.15) and receiving ADHD medication (OR 1.76, 95% CI 1.53-2.02; OR 1.65, 95% CI 1.26-2.18) than those born in September. Sensitivity tests conducted over different periods revealed consistent findings.

CONCLUSIONS: Relative age, as an indicator of neurocognitive maturity, is crucial in the risk of being diagnosed with ADHD and receiving ADHD medication among children and adolescents. Our findings emphasize the importance of considering the age of a child within a grade when diagnosing ADHD and prescribing medication for treating ADHD.}, } @article {pmid26971522, year = {2016}, author = {Ebinger, MR and Haroldson, MA and van Manen, FT and Costello, CM and Bjornlie, DD and Thompson, DJ and Gunther, KA and Fortin, JK and Teisberg, JE and Pils, SR and White, PJ and Cain, SL and Cross, PC}, title = {Detecting grizzly bear use of ungulate carcasses using global positioning system telemetry and activity data.}, journal = {Oecologia}, volume = {181}, number = {3}, pages = {695-708}, pmid = {26971522}, issn = {1432-1939}, mesh = {Animals ; Ecosystem ; *Geographic Information Systems ; Predatory Behavior ; Telemetry ; *Ursidae ; }, abstract = {Global positioning system (GPS) wildlife collars have revolutionized wildlife research. Studies of predation by free-ranging carnivores have particularly benefited from the application of location clustering algorithms to determine when and where predation events occur. These studies have changed our understanding of large carnivore behavior, but the gains have concentrated on obligate carnivores. Facultative carnivores, such as grizzly/brown bears (Ursus arctos), exhibit a variety of behaviors that can lead to the formation of GPS clusters. We combined clustering techniques with field site investigations of grizzly bear GPS locations (n = 732 site investigations; 2004-2011) to produce 174 GPS clusters where documented behavior was partitioned into five classes (large-biomass carcass, small-biomass carcass, old carcass, non-carcass activity, and resting). We used multinomial logistic regression to predict the probability of clusters belonging to each class. Two cross-validation methods-leaving out individual clusters, or leaving out individual bears-showed that correct prediction of bear visitation to large-biomass carcasses was 78-88 %, whereas the false-positive rate was 18-24 %. As a case study, we applied our predictive model to a GPS data set of 266 bear-years in the Greater Yellowstone Ecosystem (2002-2011) and examined trends in carcass visitation during fall hyperphagia (September-October). We identified 1997 spatial GPS clusters, of which 347 were predicted to be large-biomass carcasses. We used the clustered data to develop a carcass visitation index, which varied annually, but more than doubled during the study period. Our study demonstrates the effectiveness and utility of identifying GPS clusters associated with carcass visitation by a facultative carnivore.}, } @article {pmid26970666, year = {2016}, author = {Juggins, S and Kelly, M and Allott, T and Kelly-Quinn, M and Monteith, D}, title = {A Water Framework Directive-compatible metric for assessing acidification in UK and Irish rivers using diatoms.}, journal = {The Science of the total environment}, volume = {568}, number = {}, pages = {671-678}, doi = {10.1016/j.scitotenv.2016.02.163}, pmid = {26970666}, issn = {1879-1026}, mesh = {Calcium/analysis ; Conservation of Water Resources/legislation & jurisprudence/*methods ; Databases, Factual ; Diatoms/*classification/isolation & purification ; Environmental Monitoring/legislation & jurisprudence/*methods ; Hydrogen-Ion Concentration ; Ireland ; Models, Theoretical ; Predictive Value of Tests ; Reference Values ; Rivers/*chemistry ; United Kingdom ; Water Pollutants, Chemical/*analysis ; }, abstract = {Freshwater acidification continues to be a major problem affecting large areas of Europe, and while there is evidence for chemical recovery, similar evidence for biological recovery of freshwaters is sparse. The need for a methodology to identify waterbodies impacted acidification and to assess the extent of biological recovery is relevant to the EU Water Framework Directive, which requires methods to quantify differences in biology between impacted and unimpacted or reference sites. This study presents a new WFD-compliant metric based on diatoms (Diatom Acidification Metric: DAM) for assessing the acidification status of rivers. A database of 558 benthic diatom samples and associated water chemistry data was assembled. Diatom taxa were assigned to one of 5 indicator classes on the basis of their pH optimum, assessed using Gaussian logistic regression, and these indicator values used to calculate a DAM score for each site using weighted averaging. Reference sites were selected on the basis of their acid neutralising capacity (ANC) and calcium concentration, and a regression model developed to predict expected DAM for each site using pH and total organic carbon (TOC) concentration. Site-specific DAM scores were used to calculate ecological quality ratios ranging from ≥1, where the diatom assemblage showed no impact, to (theoretically) 0, when the diatom assemblage was indicative of major anthropogenic activities. The boundary between 'high' and 'good' status was defined as the 25th percentile of Ecological Quality Ratios (EQRs) of all reference sites. The boundary between 'good' and 'moderate' status was set at the point at which nutrient-sensitive and nutrient-tolerant taxa were present in equal relative abundance. The methodology was evaluated using long-term data from 11 sites from the UK Uplands Waters Monitoring Network and is shown to perform well in discriminating naturally acid from acidified sites.}, } @article {pmid26967526, year = {2016}, author = {Daume, S and Galaz, V}, title = {"Anyone Know What Species This Is?" - Twitter Conversations as Embryonic Citizen Science Communities.}, journal = {PloS one}, volume = {11}, number = {3}, pages = {e0151387}, pmid = {26967526}, issn = {1932-6203}, mesh = {*Classification ; *Communication ; Quality Control ; *Residence Characteristics ; Science/*methods ; *Social Media ; Time Factors ; }, abstract = {Social media like blogs, micro-blogs or social networks are increasingly being investigated and employed to detect and predict trends for not only social and physical phenomena, but also to capture environmental information. Here we argue that opportunistic biodiversity observations published through Twitter represent one promising and until now unexplored example of such data mining. As we elaborate, it can contribute to real-time information to traditional ecological monitoring programmes including those sourced via citizen science activities. Using Twitter data collected for a generic assessment of social media data in ecological monitoring we investigated a sample of what we denote biodiversity observations with species determination requests (N = 191). These entail images posted as messages on the micro-blog service Twitter. As we show, these frequently trigger conversations leading to taxonomic determinations of those observations. All analysed Tweets were posted with species determination requests, which generated replies for 64% of Tweets, 86% of those contained at least one suggested determination, of which 76% were assessed as correct. All posted observations included or linked to images with the overall image quality categorised as satisfactory or better for 81% of the sample and leading to taxonomic determinations at the species level in 71% of provided determinations. We claim that the original message authors and conversation participants can be viewed as implicit or embryonic citizen science communities which have to offer valuable contributions both as an opportunistic data source in ecological monitoring as well as potential active contributors to citizen science programmes.}, } @article {pmid26965627, year = {2016}, author = {Yoshida, S and Hiraga, K and Takehana, T and Taniguchi, I and Yamaji, H and Maeda, Y and Toyohara, K and Miyamoto, K and Kimura, Y and Oda, K}, title = {A bacterium that degrades and assimilates poly(ethylene terephthalate).}, journal = {Science (New York, N.Y.)}, volume = {351}, number = {6278}, pages = {1196-1199}, doi = {10.1126/science.aad6359}, pmid = {26965627}, issn = {1095-9203}, mesh = {Amino Acid Sequence ; Betaproteobacteria/*enzymology ; Environmental Restoration and Remediation ; Enzymes/classification/genetics/metabolism ; Hydrolysis ; Microbial Consortia ; Molecular Sequence Data ; Phthalic Acids/metabolism ; Phylogeny ; Plastics/*metabolism ; Polyethylene Terephthalates/*metabolism ; Recycling ; }, abstract = {Poly(ethylene terephthalate) (PET) is used extensively worldwide in plastic products, and its accumulation in the environment has become a global concern. Because the ability to enzymatically degrade PET has been thought to be limited to a few fungal species, biodegradation is not yet a viable remediation or recycling strategy. By screening natural microbial communities exposed to PET in the environment, we isolated a novel bacterium, Ideonella sakaiensis 201-F6, that is able to use PET as its major energy and carbon source. When grown on PET, this strain produces two enzymes capable of hydrolyzing PET and the reaction intermediate, mono(2-hydroxyethyl) terephthalic acid. Both enzymes are required to enzymatically convert PET efficiently into its two environmentally benign monomers, terephthalic acid and ethylene glycol.}, } @article {pmid26965054, year = {2016}, author = {Sauvage, T and Schmidt, WE and Suda, S and Fredericq, S}, title = {A metabarcoding framework for facilitated survey of endolithic phototrophs with tufA.}, journal = {BMC ecology}, volume = {16}, number = {}, pages = {8}, pmid = {26965054}, issn = {1472-6785}, mesh = {Chlorophyta/classification/*genetics ; Cyanobacteria/genetics ; *DNA Barcoding, Taxonomic/methods ; DNA Primers ; DNA, Plant ; Databases, Nucleic Acid ; Peptide Elongation Factor Tu/*genetics ; *Phototrophic Processes ; Rhodophyta/classification/*genetics ; }, abstract = {BACKGROUND: In spite of their ecological importance as primary producers and microbioeroders of marine calcium carbonate (CaCO3) substrata, endolithic phototrophs spanning both prokaryotic (the cyanobacteria) and eukaryotic algae lack established molecular resources for their facilitated survey with high throughput sequencing. Here, the development of a metabarcoding framework for the elongation factor EF-Ttu (tufA) was tested on four Illumina-sequenced marine CaCO3 microfloras for the characterization of their endolithic phototrophs, especially the abundant bioeroding Ostreobium spp. (Ulvophyceae). The framework consists of novel tufA degenerate primers and a comprehensive database enabling Operational Taxonomic Unit (OTU) identification at multiple taxonomic ranks with percent identity thresholds determined herein.

RESULTS: The newly established tufA database comprises 4057 non-redundant sequences (from 1339 eukaryotic and prokaryotic phototrophs, and 2718 prokaryotic heterotrophs) including 27 classes in 10 phyla of phototrophic diversity summarized from data mining on GenBank(®), our barcoding of >150 clones produced from coral reef microfloras, and >300 eukaryotic phototrophs (>230 Ulvophyceae including >100 'Ostreobium' spp., and >70 Florideophyceae, Phaeophyceae and miscellaneous taxa). Illumina metabarcoding with the newly designed primers resulted in 802 robust OTUs including 618 phototrophs and 184 heterotrophs (77 and 23% of OTUs, respectively). Phototrophic OTUs belonged to 14 classes of phototrophs found in seven phyla, and represented ~98% of all reads. The phylogenetic profiles of coral reef microfloras showed few OTUs in large abundance (proportion of reads) for the Chlorophyta (Ulvophyceae, i.e. Ostreobium and Phaeophila), the Rhodophyta (Florideophyceae) and Haptophyta (Coccolithophyceae), and a large diversity (richness) of OTUs in lower abundance for the Cyanophyta (Cyanophyceae) and the Ochrophyta (the diatoms, 'Bacillariophyta'). The bioerosive 'Ostreobium' spp. represented four families in a large clade of subordinal divergence, i.e. the Ostreobidineae, and a fifth, phylogenetically remote family in the suborder Halimedineae (provisionally assigned as the 'Pseudostreobiaceae'). Together they harbor 85-95 delimited cryptic species of endolithic microsiphons.

CONCLUSIONS: The novel degenerate primers allowed for amplification of endolithic phototrophs across a wide phylogenetic breadth as well as their recovery in very large proportions of reads (overall 98%) and diversity (overall 77% of OTUs). The established companion tufA database and determined identity thresholds allow for OTU identification at multiple taxonomic ranks to facilitate the monitoring of phototrophic assemblages via metabarcoding, especially endolithic communities rich in bioeroding Ulvophyceae, such as those harboring 'Ostreobium' spp., Phaeophila spp. and associated algal diversity.}, } @article {pmid26963526, year = {2016}, author = {Sakamoto, T}, title = {Computational Research on Mobile Pastoralism Using Agent-Based Modeling and Satellite Imagery.}, journal = {PloS one}, volume = {11}, number = {3}, pages = {e0151157}, pmid = {26963526}, issn = {1932-6203}, mesh = {*Agriculture/methods ; Environment ; *Geographic Information Systems ; *Natural Resources ; Nigeria ; Satellite Imagery/*methods ; Seasons ; *Systems Analysis ; }, abstract = {Dryland pastoralism has long attracted considerable attention from researchers in diverse fields. However, rigorous formal study is made difficult by the high level of mobility of pastoralists as well as by the sizable spatio-temporal variability of their environment. This article presents a new computational approach for studying mobile pastoralism that overcomes these issues. Combining multi-temporal satellite images and agent-based modeling allows a comprehensive examination of pastoral resource access over a realistic dryland landscape with unpredictable ecological dynamics. The article demonstrates the analytical potential of this approach through its application to mobile pastoralism in northeast Nigeria. Employing more than 100 satellite images of the area, extensive simulations are conducted under a wide array of circumstances, including different land-use constraints. The simulation results reveal complex dependencies of pastoral resource access on these circumstances along with persistent patterns of seasonal land use observed at the macro level.}, } @article {pmid26963257, year = {2016}, author = {Masquillier, C and Wouters, E and Mortelmans, D and van Wyk, B and Hausler, H and Van Damme, W}, title = {HIV/AIDS Competent Households: Interaction between a Health-Enabling Environment and Community-Based Treatment Adherence Support for People Living with HIV/AIDS in South Africa.}, journal = {PloS one}, volume = {11}, number = {3}, pages = {e0151379}, pmid = {26963257}, issn = {1932-6203}, mesh = {*Acquired Immunodeficiency Syndrome/epidemiology/therapy ; *Community Networks ; *Family Characteristics ; Female ; Humans ; Male ; *Medication Adherence ; South Africa/epidemiology ; }, abstract = {In the context of severe human resource shortages in HIV care, task-shifting and especially community-based support are increasingly being cited as potential means of providing durable care to chronic HIV patients. Socio-ecological theory clearly stipulates that-in all social interventions-the interrelatedness and interdependency between individuals and their immediate social contexts should be taken into account. People living with HIV/AIDS (PLWHA) seldom live in isolation, yet community-based interventions for supporting chronic HIV patients have largely ignored the social contexts in which they are implemented. Research is thus required to investigate such community-based support within its context. The aim of this study is to address this research gap by examining the way in which HIV/AIDS competence in the household hampers or facilitates community-based treatment adherence support. The data was analyzed carefully in accordance with the Grounded Theory procedures, using Nvivo 10. More specifically, we analyzed field notes from participatory observations conducted during 48 community-based treatment adherence support sessions in townships on the outskirts of Cape Town, transcripts of 32 audio-recorded in-depth interviews with PLWHA and transcripts of 4 focus group discussions with 36 community health workers (CHWs). Despite the fact that the CHWs try to present themselves as not being openly associated with HIV/AIDS services, results show that the presence of a CHW is often seen as a marker of the disease. Depending on the HIV/AIDS competence in the household, this association can challenge the patient's hybrid identity management and his/her attempt to regulate the interference of the household in the disease management. The results deepen our understanding of how the degree of HIV/AIDS competence present in a PLWHA's household affects the manner in which the CHW can perform his or her job and the associated benefits for the patient and his/her household members. In this respect, a household with a high level of HIV/AIDS competence will be more receptive to treatment adherence support, as the patient is more likely to allow interaction between the CHW and the household. In contrast, in a household which exhibits limited characteristics of HIV/AIDS competence, interaction with the treatment adherence supporter may be difficult in the beginning. In such a situation, visits from the CHW threaten the hybrid identity management. If the CHW handles this situation cautiously and the patient-acting as a gate keeper-allows interaction, the CHW may be able to help the household develop towards HIV/AIDS competence. This would have a more added value compared to a household which was more HIV/AIDS competent from the outset. This study indicates that pre-existing dynamics in a patient's social environment, such as the HIV/AIDS competence of the household, should be taken into account when designing community-based treatment adherence programs in order to provide long-term quality care, treatment and support in the context of human resource shortages.}, } @article {pmid26960569, year = {2016}, author = {Drebes, J and Künz, M and Windshügel, B and Kikhney, AG and Müller, IB and Eberle, RJ and Oberthür, D and Cang, H and Svergun, DI and Perbandt, M and Betzel, C and Wrenger, C}, title = {Structure of ThiM from Vitamin B1 biosynthetic pathway of Staphylococcus aureus - Insights into a novel pro-drug approach addressing MRSA infections.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {22871}, pmid = {26960569}, issn = {2045-2322}, mesh = {Anti-Bacterial Agents/*chemistry ; Biosynthetic Pathways ; Catalytic Domain ; Databases, Chemical ; Methicillin Resistance ; Models, Molecular ; Phosphotransferases (Alcohol Group Acceptor)/*chemistry ; Prodrugs/*chemistry ; Staphylococcus aureus/*enzymology ; Thiamine/*biosynthesis ; Thiazoles/*chemistry ; }, abstract = {Infections caused by the methicillin-resistant Staphylococcus aureus (MRSA) are today known to be a substantial threat for global health. Emerging multi-drug resistant bacteria have created a substantial need to identify and discover new drug targets and to develop novel strategies to treat bacterial infections. A promising and so far untapped antibiotic target is the biosynthesis of vitamin B1 (thiamin). Thiamin in its activated form, thiamin pyrophosphate, is an essential co-factor for all organisms. Therefore, thiamin analogous compounds, when introduced into the vitamin B1 biosynthetic pathway and further converted into non-functional co-factors by the bacterium can function as pro-drugs which thus block various co-factor dependent pathways. We characterized one of the key enzymes within the S. aureus vitamin B1 biosynthetic pathway, 5-(hydroxyethyl)-4-methylthiazole kinase (SaThiM; EC 2.7.1.50), a potential target for pro-drug compounds and analyzed the native structure of SaThiM and complexes with the natural substrate 5-(hydroxyethyl)-4-methylthiazole (THZ) and two selected substrate analogues.}, } @article {pmid26959950, year = {2016}, author = {Rezende, LF and Arenque-Musa, BC and Moura, MS and Aidar, ST and Von Randow, C and Menezes, RS and Ometto, JP}, title = {Calibration of the maximum carboxylation velocity (Vcmax) using data mining techniques and ecophysiological data from the Brazilian semiarid region, for use in Dynamic Global Vegetation Models.}, journal = {Brazilian journal of biology = Revista brasleira de biologia}, volume = {76}, number = {2}, pages = {341-351}, doi = {10.1590/1519-6984.14414}, pmid = {26959950}, issn = {1678-4375}, mesh = {Biodiversity ; Brazil ; *Caesalpinia/growth & development/physiology ; Calibration ; Data Mining/methods ; Ecological and Environmental Phenomena ; *Forests ; Global Warming ; Linear Models ; Models, Biological ; Trees/*classification ; }, abstract = {The semiarid region of northeastern Brazil, the Caatinga, is extremely important due to its biodiversity and endemism. Measurements of plant physiology are crucial to the calibration of Dynamic Global Vegetation Models (DGVMs) that are currently used to simulate the responses of vegetation in face of global changes. In a field work realized in an area of preserved Caatinga forest located in Petrolina, Pernambuco, measurements of carbon assimilation (in response to light and CO2) were performed on 11 individuals of Poincianella microphylla, a native species that is abundant in this region. These data were used to calibrate the maximum carboxylation velocity (Vcmax) used in the INLAND model. The calibration techniques used were Multiple Linear Regression (MLR), and data mining techniques as the Classification And Regression Tree (CART) and K-MEANS. The results were compared to the UNCALIBRATED model. It was found that simulated Gross Primary Productivity (GPP) reached 72% of observed GPP when using the calibrated Vcmax values, whereas the UNCALIBRATED approach accounted for 42% of observed GPP. Thus, this work shows the benefits of calibrating DGVMs using field ecophysiological measurements, especially in areas where field data is scarce or non-existent, such as in the Caatinga.}, } @article {pmid26954353, year = {2016}, author = {Langhans, SD and Lienert, J}, title = {Four Common Simplifications of Multi-Criteria Decision Analysis do not hold for River Rehabilitation.}, journal = {PloS one}, volume = {11}, number = {3}, pages = {e0150695}, pmid = {26954353}, issn = {1932-6203}, mesh = {Algorithms ; Biodiversity ; *Decision Support Techniques ; *Ecosystem ; Humans ; Models, Theoretical ; *Rivers ; }, abstract = {River rehabilitation aims at alleviating negative effects of human impacts such as loss of biodiversity and reduction of ecosystem services. Such interventions entail difficult trade-offs between different ecological and often socio-economic objectives. Multi-Criteria Decision Analysis (MCDA) is a very suitable approach that helps assessing the current ecological state and prioritizing river rehabilitation measures in a standardized way, based on stakeholder or expert preferences. Applications of MCDA in river rehabilitation projects are often simplified, i.e. using a limited number of objectives and indicators, assuming linear value functions, aggregating individual indicator assessments additively, and/or assuming risk neutrality of experts. Here, we demonstrate an implementation of MCDA expert preference assessments to river rehabilitation and provide ample material for other applications. To test whether the above simplifications reflect common expert opinion, we carried out very detailed interviews with five river ecologists and a hydraulic engineer. We defined essential objectives and measurable quality indicators (attributes), elicited the experts´ preferences for objectives on a standardized scale (value functions) and their risk attitude, and identified suitable aggregation methods. The experts recommended an extensive objectives hierarchy including between 54 and 93 essential objectives and between 37 to 61 essential attributes. For 81% of these, they defined non-linear value functions and in 76% recommended multiplicative aggregation. The experts were risk averse or risk prone (but never risk neutral), depending on the current ecological state of the river, and the experts´ personal importance of objectives. We conclude that the four commonly applied simplifications clearly do not reflect the opinion of river rehabilitation experts. The optimal level of model complexity, however, remains highly case-study specific depending on data and resource availability, the context, and the complexity of the decision problem.}, } @article {pmid26952077, year = {2017}, author = {Garnham-Lee, KP and Falconer, CL and Sherar, LB and Taylor, IM}, title = {Evidence of moderation effects in predicting active transport to school.}, journal = {Journal of public health (Oxford, England)}, volume = {39}, number = {1}, pages = {153-162}, pmid = {26952077}, issn = {1741-3850}, mesh = {Child ; *Exercise ; Female ; Geographic Information Systems ; Humans ; Male ; *Schools ; Self Report ; *Transportation ; United Kingdom ; }, abstract = {BACKGROUND: Distance from home to school is an important influence on the decision to use active transport (AT); however, ecological perspectives would suggest this relationship may be moderated by individual, interpersonal and environmental factors. This study investigates whether (i) gender, (ii) biological maturation, (iii) perceived family support for physical activity (PA) and (iv) multiple deprivation moderate the relationship between distance to school and AT.

METHODS: A total of 611 children (11-12 years old, 334 females) were recruited from schools in Leicestershire, UK. Gender, family support for PA, and AT were self-reported. Home and school postcodes were used to determine multiple deprivation and distance to school (km). Predicted age at peak height velocity was used to indicate biological maturation.

RESULTS: Logistic regressions revealed the main effects explained 40.2% of the variance in AT; however; distance to school was the only significant predictor. Further analyses revealed that distance to school had a greater negative impact on the use of AT in late-maturing (OR: 3.60, CI: 1.45-8.96), less deprived (OR: 3.54, CI: 1.17-10.72) and children with low family support of PA (OR: 0.26, CI: 0.11-0.61).

CONCLUSIONS: This study provides evidence that, although distance to school might be the strongest predictor of AT, this relationship is complex.}, } @article {pmid26951682, year = {2016}, author = {Moran, MA and Kujawinski, EB and Stubbins, A and Fatland, R and Aluwihare, LI and Buchan, A and Crump, BC and Dorrestein, PC and Dyhrman, ST and Hess, NJ and Howe, B and Longnecker, K and Medeiros, PM and Niggemann, J and Obernosterer, I and Repeta, DJ and Waldbauer, JR}, title = {Deciphering ocean carbon in a changing world.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {113}, number = {12}, pages = {3143-3151}, pmid = {26951682}, issn = {1091-6490}, mesh = {Carbon/*chemistry/metabolism ; *Carbon Cycle ; Ecosystem ; Geology/*methods ; Information Science ; Marine Biology/*methods ; Microbiota ; Oceans and Seas ; Organic Chemicals/analysis ; Phytoplankton/metabolism ; Seawater/*analysis ; Solubility ; Water Movements ; }, abstract = {Dissolved organic matter (DOM) in the oceans is one of the largest pools of reduced carbon on Earth, comparable in size to the atmospheric CO2 reservoir. A vast number of compounds are present in DOM, and they play important roles in all major element cycles, contribute to the storage of atmospheric CO2 in the ocean, support marine ecosystems, and facilitate interactions between organisms. At the heart of the DOM cycle lie molecular-level relationships between the individual compounds in DOM and the members of the ocean microbiome that produce and consume them. In the past, these connections have eluded clear definition because of the sheer numerical complexity of both DOM molecules and microorganisms. Emerging tools in analytical chemistry, microbiology, and informatics are breaking down the barriers to a fuller appreciation of these connections. Here we highlight questions being addressed using recent methodological and technological developments in those fields and consider how these advances are transforming our understanding of some of the most important reactions of the marine carbon cycle.}, } @article {pmid26951112, year = {2016}, author = {Sangwan, N and Xia, F and Gilbert, JA}, title = {Recovering complete and draft population genomes from metagenome datasets.}, journal = {Microbiome}, volume = {4}, number = {}, pages = {8}, pmid = {26951112}, issn = {2049-2618}, mesh = {Contig Mapping ; Datasets as Topic ; *Genome, Microbial ; *Metagenome ; Metagenomics/*methods ; Sequence Analysis, DNA ; }, abstract = {Assembly of metagenomic sequence data into microbial genomes is of fundamental value to improving our understanding of microbial ecology and metabolism by elucidating the functional potential of hard-to-culture microorganisms. Here, we provide a synthesis of available methods to bin metagenomic contigs into species-level groups and highlight how genetic diversity, sequencing depth, and coverage influence binning success. Despite the computational cost on application to deeply sequenced complex metagenomes (e.g., soil), covarying patterns of contig coverage across multiple datasets significantly improves the binning process. We also discuss and compare current genome validation methods and reveal how these methods tackle the problem of chimeric genome bins i.e., sequences from multiple species. Finally, we explore how population genome assembly can be used to uncover biogeographic trends and to characterize the effect of in situ functional constraints on the genome-wide evolution.}, } @article {pmid26950417, year = {2016}, author = {Cartenì, F and Bonanomi, G and Giannino, F and Incerti, G and Vincenot, CE and Chiusano, ML and Mazzoleni, S}, title = {Self-DNA inhibitory effects: Underlying mechanisms and ecological implications.}, journal = {Plant signaling & behavior}, volume = {11}, number = {4}, pages = {e1158381}, pmid = {26950417}, issn = {1559-2324}, mesh = {DNA, Plant/*metabolism ; *Ecosystem ; Feedback ; Plants/metabolism ; Soil ; }, abstract = {DNA is usually known as the molecule that carries the instructions necessary for cell functioning and genetic inheritance. A recent discovery reported a new functional role for extracellular DNA. After fragmentation, either by natural or artificial decomposition, small DNA molecules (between ∼50 and ∼2000 bp) exert a species specific inhibitory effect on individuals of the same species. Evidence shows that such effect occurs for a wide range of organisms, suggesting a general biological process. In this paper we explore the possible molecular mechanisms behind those findings and discuss the ecological implications, specifically those related to plant species coexistence.}, } @article {pmid26950402, year = {2016}, author = {Jun, YW and Park, H and Lee, YK and Kaang, BK and Lee, JA and Jang, DJ}, title = {D-AKAP1a is a signal-anchored protein in the mitochondrial outer membrane.}, journal = {FEBS letters}, volume = {590}, number = {7}, pages = {954-961}, doi = {10.1002/1873-3468.12123}, pmid = {26950402}, issn = {1873-3468}, mesh = {A Kinase Anchor Proteins/chemistry/genetics/*metabolism ; Amino Acid Substitution ; Animals ; Biomarkers/metabolism ; Computational Biology ; Cyclic AMP/*metabolism ; Endoplasmic Reticulum ; Golgi Apparatus/metabolism ; Green Fluorescent Proteins/genetics/metabolism ; HEK293 Cells ; Humans ; Hydrophobic and Hydrophilic Interactions ; Mice ; Microscopy, Confocal ; Microscopy, Fluorescence ; Mitochondrial Membranes/*metabolism ; *Models, Molecular ; Mutation ; Protein Structure, Tertiary ; Protein Transport ; Recombinant Fusion Proteins/chemistry/metabolism ; *Second Messenger Systems ; }, abstract = {Dual A-kinase anchoring protein 1a (D-AKAP1a, AKAP1) regulates cAMP signaling in mitochondria. However, it is not clear how D-AKAP1a is associated with mitochondria. In this study, we show that D-AKAP1a is a transmembrane protein in the mitochondrial outer membrane (MOM). We revealed that the N-terminus of D-AKAP1a is exposed to the intermembrane space of mitochondria and that its C-terminus is located on the cytoplasmic side of the MOM. Moderate hydrophobicity and the positively charged flanking residues of the transmembrane domain of D-AKAP1a were important for targeting. Taken together, D-AKAP1a can be classified as a signal-anchored protein in the MOM. Our topological study provides valuable information about the molecular and cellular mechanisms of mitochondrial targeting of AKAP1.}, } @article {pmid26946832, year = {2015}, author = {Shang, ZH and Wei, HY and Gu, W and Mao, YJ and Zhu, LN and Sang, MJ}, title = {[Potential Ecological Suitability Regionalization Analysis of Angelica sinensis Based on GIS and Fuzzy Matter Element Model].}, journal = {Zhong yao cai = Zhongyaocai = Journal of Chinese medicinal materials}, volume = {38}, number = {7}, pages = {1370-1374}, pmid = {26946832}, issn = {1001-4454}, mesh = {Altitude ; Angelica sinensis/*growth & development ; China ; Climate ; *Ecosystem ; Geographic Information Systems ; *Models, Theoretical ; Plants, Medicinal/growth & development ; Soil ; Temperature ; Tibet ; }, abstract = {OBJECTIVE: To study the potential ecological suitability regionalization of Angelica sinensis, for protecting wild resources and selecting cultivation location and designing rational production layout.

METHODS: Based on fuzzy matter element model, the relationship of fuzzy membership function between ferulic acid content and 14 ecological factors, including climate, topography and soil,were established. Then information entropy theory was used to determine the relative importance of each environmental factor, and thus to determine the most limiting habitat criteria. Finally, the probable spatial distribution of Angelica sinensis across ten provinces in Western China was determined based on GIS spatial analysis of habitat conditions. Meanwhile, the optimal index range of ecological factors was quantified.

RESULTS: It was showed that the percentage of moderately and highly suitable habitats for Angelica sinensis in the study area was 9. 64%, its area was 306,768. 01 km2. The moderately and highly suitable habitats were mainly located in the southeast of Gansu ind Tibet,the north of Sichuan and the northwest of Yunnan. The results also showed that six dominant ecological factors controlling the distribution of Angelica sinensis. These six dominant features were as follows: (1) mean temperature of wettest quarter, (2) altitude, (3) precipitation of growth, (4) annual relative humidity, (5) average temperature of growth period, and (6) annual)recipitation.

CONCLUSION: The habitat suitability assessment model based on GIS and fuzzy matter element model theory can accurately valuate the habitat suitability of Angelica sinensis, quantify the area of suitable habitat and analyze the spatial distribution. This informaion is of value to provide insight for choosing the most suitable cultivation sites,as well as the habitat protection zones.}, } @article {pmid26945783, year = {2016}, author = {Rosenzweig, BK and Pease, JB and Besansky, NJ and Hahn, MW}, title = {Powerful methods for detecting introgressed regions from population genomic data.}, journal = {Molecular ecology}, volume = {25}, number = {11}, pages = {2387-2397}, pmid = {26945783}, issn = {1365-294X}, support = {R01 AI076584/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Anopheles/*genetics ; Chromosome Inversion ; Computer Simulation ; *Evolution, Molecular ; Genetic Speciation ; *Genetics, Population ; Genomics/*methods ; Hybridization, Genetic ; *Models, Genetic ; Models, Statistical ; X Chromosome/genetics ; }, abstract = {Understanding the types and functions of genes that are able to cross species boundaries-and those that are not-is an important step in understanding the forces maintaining species as largely independent lineages across the remainder of the genome. With large next-generation sequencing data sets we are now able to ask whether introgression has occurred across the genome, and multiple methods have been proposed to detect the signature of such events. Here, we introduce a new summary statistic that can be used to test for introgression, RNDmin , that makes use of the minimum pairwise sequence distance between two population samples relative to divergence to an outgroup. We find that our method offers a modest increase in power over other, related tests, but that all such tests have high power to detect introgressed loci when migration is recent and strong. RNDmin is robust to variation in the mutation rate, and remains reliable even when estimates of the divergence time between sister species are inaccurate. We apply RNDmin to population genomic data from the African mosquitoes Anopheles quadriannulatus and A. arabiensis, identifying three novel candidate regions for introgression. Interestingly, one of the introgressed loci is on the X chromosome, but outside of an inversion separating these two species. Our results suggest that significant, but rare, sharing of alleles is occurring between species that diverged more than 1 million years ago, and that application of these methods to additional systems are likely to reveal similar results.}, } @article {pmid26944260, year = {2016}, author = {Lightfoot, JW and Chauhan, VM and Aylott, JW and Rödelsperger, C}, title = {Comparative transcriptomics of the nematode gut identifies global shifts in feeding mode and pathogen susceptibility.}, journal = {BMC research notes}, volume = {9}, number = {}, pages = {142}, pmid = {26944260}, issn = {1756-0500}, mesh = {Animals ; Base Sequence ; Caenorhabditis elegans/*genetics/microbiology ; Conserved Sequence ; Escherichia coli/growth & development ; Feeding Behavior/physiology ; Gastrointestinal Tract/*metabolism ; Gene Expression Profiling ; Gene Expression Regulation ; Gene Ontology ; *Genes, Helminth ; Hedgehog Proteins/genetics ; High-Throughput Nucleotide Sequencing ; Host-Pathogen Interactions/*genetics ; Molecular Sequence Annotation ; Molecular Sequence Data ; Nematoda/*genetics/microbiology ; Signal Transduction ; Species Specificity ; *Transcriptome ; }, abstract = {BACKGROUND: The nematode Pristionchus pacificus has been established as a model for comparative studies using the well known Caenorhabditis elegans as a reference. Despite their relatedness, previous studies have revealed highly divergent development and a number of morphological differences including the lack of a pharyngal structure, the grinder, used to physically lyse the ingested bacteria in C. elegans.

RESULTS: To complement current knowledge about developmental and ecological differences with a better understanding of their feeding modes, we have sequenced the intestinal transcriptomes of both nematodes. In total, we found 464 intestine-enriched genes in P. pacificus and 724 in C. elegans, of which the majority (66%) has been identified by previous studies. Interestingly, only 15 genes could be identified with shared intestinal enrichment in both species, of which three genes are Hedgehog signaling molecules supporting a highly conserved role of this pathway for intestinal development across all metazoa. At the level of gene families, we find similar divergent trends with only five families displaying significant intestinal enrichment in both species. We compared our data with transcriptomic responses to various pathogens. Strikingly, C. elegans intestine-enriched genes showed highly significant overlaps with pathogen response genes whereas this was not the case for P. pacificus, indicating shifts in pathogen susceptibility that might be explained by altered feeding modes.

CONCLUSIONS: Our study reveals first insights into the evolution of feeding systems and the associated changes in intestinal gene expression that might have facilitated nematodes of the P. pacificus lineage to colonize new environments. These findings deepen our understanding about how morphological and genomic diversity is created during the course of evolution.}, } @article {pmid26942286, year = {2016}, author = {Broadaway, KA and Cutler, DJ and Duncan, R and Moore, JL and Ware, EB and Jhun, MA and Bielak, LF and Zhao, W and Smith, JA and Peyser, PA and Kardia, SLR and Ghosh, D and Epstein, MP}, title = {A Statistical Approach for Testing Cross-Phenotype Effects of Rare Variants.}, journal = {American journal of human genetics}, volume = {98}, number = {3}, pages = {525-540}, pmid = {26942286}, issn = {1537-6605}, support = {R56 MH071537/MH/NIMH NIH HHS/United States ; R01 MH071537/MH/NIMH NIH HHS/United States ; R01 AR060893/AR/NIAMS NIH HHS/United States ; GM117946/GM/NIGMS NIH HHS/United States ; R01 HL086694/HL/NHLBI NIH HHS/United States ; R01 HL119443/HL/NHLBI NIH HHS/United States ; R01 GM117946/GM/NIGMS NIH HHS/United States ; HG007508/HG/NHGRI NIH HHS/United States ; R01 HG007508/HG/NHGRI NIH HHS/United States ; MH071537/MH/NIMH NIH HHS/United States ; HL086694/HL/NHLBI NIH HHS/United States ; HL119443/HL/NHLBI NIH HHS/United States ; AR060893/AR/NIAMS NIH HHS/United States ; }, mesh = {Blood Pressure ; Body Mass Index ; Cardiovascular System/metabolism ; Cholesterol, HDL/blood ; Databases, Genetic ; Exome ; Genetic Association Studies ; *Genetic Variation ; Genome, Human ; Genotype ; Humans ; *Models, Genetic ; Multivariate Analysis ; Oligonucleotide Array Sequence Analysis ; *Phenotype ; }, abstract = {Increasing empirical evidence suggests that many genetic variants influence multiple distinct phenotypes. When cross-phenotype effects exist, multivariate association methods that consider pleiotropy are often more powerful than univariate methods that model each phenotype separately. Although several statistical approaches exist for testing cross-phenotype effects for common variants, there is a lack of similar tests for gene-based analysis of rare variants. In order to fill this important gap, we introduce a statistical method for cross-phenotype analysis of rare variants using a nonparametric distance-covariance approach that compares similarity in multivariate phenotypes to similarity in rare-variant genotypes across a gene. The approach can accommodate both binary and continuous phenotypes and further can adjust for covariates. Our approach yields a closed-form test whose significance can be evaluated analytically, thereby improving computational efficiency and permitting application on a genome-wide scale. We use simulated data to demonstrate that our method, which we refer to as the Gene Association with Multiple Traits (GAMuT) test, provides increased power over competing approaches. We also illustrate our approach using exome-chip data from the Genetic Epidemiology Network of Arteriopathy.}, } @article {pmid26941760, year = {2016}, author = {Turcsán, A and Steppe, K and Sárközi, E and Erdélyi, É and Missoorten, M and Mees, G and Mijnsbrugge, KV}, title = {Early Summer Drought Stress During the First Growing Year Stimulates Extra Shoot Growth in Oak Seedlings (Quercus petraea).}, journal = {Frontiers in plant science}, volume = {7}, number = {}, pages = {193}, pmid = {26941760}, issn = {1664-462X}, abstract = {More severe summer droughts are predicted for mid-latitudes in Europe. To evaluate the impact on forest ecosystems and more specifically on forest regeneration, we studied the response to summer drought in oak seedlings (Quercus petraea). Acorns were collected from different mother trees in three stands in Belgium, sown in pots and grown in non-heated greenhouse conditions. We imposed drought on the seedlings in early summer by first watering the pots to saturation and then stopping any watering. Weight of the pots and stomatal conductance were regularly measured. Re-watering followed this drought period of 5 weeks. Height of the seedlings and apical bud development were observed. Stomatal resistance increased toward the end of the experiment in the drought-treated group and was restored after re-watering. The seedlings from the drought treatment displayed a higher probability to produce additional shoot growth after re-watering (p ≤ 0.05). A higher competition for water (two plants per pot) increased this chance. Although this chance was also higher for smaller seedlings, the actual length of the extra growth after re-watering was higher for larger seedlings (p ≤ 0.01). Both in the drought-treated and in the control group the autochthonous provenance growing on a xeric site produced less extra shoots compared to the two other provenances. Finally, stressed plants showed less developed apical buds compared to the control group after re-watering, suggesting a phenological effect on the growth cycle of oaks (p ≤ 0.0001). The higher chance for an extra shoot growth after the drought period can be considered as a compensation for the induced growth arrest during the drought period.}, } @article {pmid26938459, year = {2016}, author = {Wille, M and Muradrasoli, S and Nilsson, A and Järhult, JD}, title = {High Prevalence and Putative Lineage Maintenance of Avian Coronaviruses in Scandinavian Waterfowl.}, journal = {PloS one}, volume = {11}, number = {3}, pages = {e0150198}, pmid = {26938459}, issn = {1932-6203}, mesh = {Algorithms ; Animals ; Biodiversity ; Birds/*virology ; Charadriiformes/virology ; Coronavirus/*classification/genetics ; Coronavirus Infections/*epidemiology/*virology ; DNA-Directed RNA Polymerases/genetics ; Databases, Factual ; Ducks/virology ; Geese/virology ; Genetic Variation ; Molecular Epidemiology ; Phylogeny ; Prevalence ; RNA, Viral/genetics ; Sweden ; }, abstract = {Coronaviruses (CoVs) are found in a wide variety of wild and domestic animals, and constitute a risk for zoonotic and emerging infectious disease. In poultry, the genetic diversity, evolution, distribution and taxonomy of some coronaviruses have been well described, but little is known about the features of CoVs in wild birds. In this study we screened 764 samples from 22 avian species of the orders Anseriformes and Charadriiformes in Sweden collected in 2006/2007 for CoV, with an overall CoV prevalence of 18.7%, which is higher than many other wild bird surveys. The highest prevalence was found in the diving ducks--mainly Greater Scaup (Aythya marila; 51.5%)--and the dabbling duck Mallard (Anas platyrhynchos; 19.2%). Sequences from two of the Greater Scaup CoV fell into an infrequently detected lineage, shared only with a Tufted Duck (Aythya fuligula) CoV. Coronavirus sequences from Mallards in this study were highly similar to CoV sequences from the sample species and location in 2011, suggesting long-term maintenance in this population. A single Black-headed Gull represented the only positive sample from the order Charadriiformes. Globally, Anas species represent the largest fraction of avian CoV sequences, and there seems to be no host species, geographical or temporal structure. To better understand the eitiology, epidemiology and ecology of these viruses more systematic surveillance of wild birds and subsequent sequencing of detected CoV is imperative.}, } @article {pmid26938243, year = {2016}, author = {Karcher, MD and Palacios, JA and Bedford, T and Suchard, MA and Minin, VN}, title = {Quantifying and Mitigating the Effect of Preferential Sampling on Phylodynamic Inference.}, journal = {PLoS computational biology}, volume = {12}, number = {3}, pages = {e1004789}, pmid = {26938243}, issn = {1553-7358}, support = {R01 AI107034/AI/NIAID NIH HHS/United States ; R01 LM012080/LM/NLM NIH HHS/United States ; U54 GM111274/GM/NIGMS NIH HHS/United States ; }, mesh = {Biological Evolution ; Computer Simulation ; Data Interpretation, Statistical ; Genetic Variation/genetics ; *Genetics, Population ; Hemagglutinins/*genetics ; Influenza A Virus, H3N2 Subtype/*genetics ; *Models, Genetic ; *Models, Statistical ; Phylogeny ; Sample Size ; }, abstract = {Phylodynamics seeks to estimate effective population size fluctuations from molecular sequences of individuals sampled from a population of interest. One way to accomplish this task formulates an observed sequence data likelihood exploiting a coalescent model for the sampled individuals' genealogy and then integrating over all possible genealogies via Monte Carlo or, less efficiently, by conditioning on one genealogy estimated from the sequence data. However, when analyzing sequences sampled serially through time, current methods implicitly assume either that sampling times are fixed deterministically by the data collection protocol or that their distribution does not depend on the size of the population. Through simulation, we first show that, when sampling times do probabilistically depend on effective population size, estimation methods may be systematically biased. To correct for this deficiency, we propose a new model that explicitly accounts for preferential sampling by modeling the sampling times as an inhomogeneous Poisson process dependent on effective population size. We demonstrate that in the presence of preferential sampling our new model not only reduces bias, but also improves estimation precision. Finally, we compare the performance of the currently used phylodynamic methods with our proposed model through clinically-relevant, seasonal human influenza examples.}, } @article {pmid26934343, year = {2016}, author = {Lester, LA and Gutierrez Ramirez, M and Kneidel, AH and Heckscher, CM}, title = {Use of a Florida Gulf Coast Barrier Island by Spring Trans-Gulf Migrants and the Projected Effects of Sea Level Rise on Habitat Availability.}, journal = {PloS one}, volume = {11}, number = {3}, pages = {e0148975}, pmid = {26934343}, issn = {1932-6203}, mesh = {*Animal Migration ; Animals ; *Climate Change ; *Ecosystem ; Florida ; Geographic Information Systems ; Gulf of Mexico ; Islands ; Oceans and Seas ; Seasons ; Songbirds/*physiology ; }, abstract = {Barrier islands on the north coast of the Gulf of Mexico are an internationally important coastal resource. Each spring hundreds of thousands of Nearctic-Neotropical songbirds crossing the Gulf of Mexico during spring migration use these islands because they provide the first landfall for individuals following a trans-Gulf migratory route. The effects of climate change, particularly sea level rise, may negatively impact habitat availability for migrants on barrier islands. Our objectives were (1) to confirm the use of St. George Island, Florida by trans-Gulf migrants and (2) to determine whether forested stopover habitat will be available for migrants on St. George Island following sea level rise. We used avian transect data, geographic information systems, remote sensing, and simulation modelling to investigate the potential effects of three different sea level rise scenarios (0.28 m, 0.82 m, and 2 m) on habitat availability for trans-Gulf migrants. We found considerable use of the island by spring trans-Gulf migrants. Migrants were most abundant in areas with low elevation, high canopy height, and high coverage of forests and scrub/shrub. A substantial percentage of forest (44%) will be lost by 2100 assuming moderate sea level rise (0.82 m). Thus, as sea level rise progresses, less forests will be available for migrants during stopover. Many migratory bird species' populations are declining, and degradation of barrier island stopover habitat may further increase the cost of migration for many individuals. To preserve this coastal resource, conservation and wise management of migratory stopover areas, especially near ecological barriers like the Gulf of Mexico, will be essential as sea levels rise.}, } @article {pmid26932765, year = {2016}, author = {Rampelli, S and Soverini, M and Turroni, S and Quercia, S and Biagi, E and Brigidi, P and Candela, M}, title = {ViromeScan: a new tool for metagenomic viral community profiling.}, journal = {BMC genomics}, volume = {17}, number = {}, pages = {165}, pmid = {26932765}, issn = {1471-2164}, mesh = {Computational Biology ; DNA, Viral ; *Genome, Viral ; High-Throughput Nucleotide Sequencing ; Humans ; Metagenomics/*methods ; *Microbiota ; RNA, Viral/isolation & purification ; Sequence Analysis, DNA ; *Software ; Viruses/*classification/isolation & purification ; }, abstract = {BACKGROUND: Bioinformatics tools available for metagenomic sequencing analysis are principally devoted to the identification of microorganisms populating an ecological niche, but they usually do not consider viruses. Only some software have been designed to profile the viral sequences, however they are not efficient in the characterization of viruses in the context of complex communities, like the intestinal microbiota, containing bacteria, archeabacteria, eukaryotic microorganisms and viruses. In any case, a comprehensive description of the host-microbiota interactions can not ignore the profile of eukaryotic viruses within the virome, as viruses are definitely critical for the regulation of the host immunophenotype.

RESULTS: ViromeScan is an innovative metagenomic analysis tool that characterizes the taxonomy of the virome directly from raw data of next-generation sequencing. The tool uses hierarchical databases for eukaryotic viruses to unambiguously assign reads to viral species more accurately and >1000 fold faster than other existing approaches. We validated ViromeScan on synthetic microbial communities and applied it on metagenomic samples of the Human Microbiome Project, providing a sensitive eukaryotic virome profiling of different human body sites.

CONCLUSIONS: ViromeScan allows the user to explore and taxonomically characterize the virome from metagenomic reads, efficiently denoising samples from reads of other microorganisms. This implies that users can fully characterize the microbiome, including bacteria and viruses, by shotgun metagenomic sequencing followed by different bioinformatic pipelines.}, } @article {pmid26932459, year = {2016}, author = {Plotnick, RE and Smith, FA and Lyons, SK}, title = {The fossil record of the sixth extinction.}, journal = {Ecology letters}, volume = {19}, number = {5}, pages = {546-553}, doi = {10.1111/ele.12589}, pmid = {26932459}, issn = {1461-0248}, mesh = {Animals ; Bias ; Body Size ; Data Interpretation, Statistical ; *Extinction, Biological ; *Fossils ; Homing Behavior ; }, abstract = {Comparing the magnitude of the current biodiversity crisis with those in the fossil record is difficult without an understanding of differential preservation. Integrating data from palaeontological databases with information on IUCN status, ecology and life history characteristics of contemporary mammals, we demonstrate that only a small and biased fraction of threatened species (< 9%) have a fossil record, compared with 20% of non-threatened species. We find strong taphonomic biases related to body size and geographic range. Modern species with a fossil record tend to be large and widespread and were described in the 19(th) century. The expected magnitude of the current extinction based only on species with a fossil record is about half of that of one based on all modern species; values for genera are similar. The record of ancient extinctions may be similarly biased, with many species having originated and gone extinct without leaving a tangible record.}, } @article {pmid26930056, year = {2016}, author = {Ma, L and Li, ZQ and Bian, L and Cai, XM and Luo, ZX and Zhang, YJ and Chen, ZM}, title = {Identification and Comparative Study of Chemosensory Genes Related to Host Selection by Legs Transcriptome Analysis in the Tea Geometrid Ectropis obliqua.}, journal = {PloS one}, volume = {11}, number = {3}, pages = {e0149591}, pmid = {26930056}, issn = {1932-6203}, mesh = {Amino Acid Sequence ; Animals ; Female ; Gene Expression Profiling ; Gene Ontology ; Insect Proteins/chemistry/genetics ; Male ; Molecular Sequence Data ; Moths/anatomy & histology/chemistry/*genetics/*physiology ; Plants/*parasitology ; Receptors, Odorant/chemistry/genetics ; Sequence Alignment ; Taste ; *Transcriptome ; }, abstract = {Host selection by female moths is fundamental to the survival of their larvae. Detecting and perceiving the non-volatile chemicals of the plant surface involved in gustatory detection determine the host preference. In many lepidopteran species, tarsal chemosensilla are sensitive to non-volatile chemicals and responsible for taste detection. The tea geometrid Ectropis obliqua is one devastating chewing pest selectively feeding on limited plants, requiring the specialized sensors to forage certain host for oviposition. In present study, we revealed the distribution of chemosensilla in the ventral side of female fifth tarsomere in E. obliqua. To investigate its molecular mechanism of gustatory perception, we performed HiSeq 2500 sequencing of the male- and female- legs transcriptome and identified 24 candidate odorant binding proteins (OBPs), 21 chemosensory proteins (CSPs), 2 sensory neuron membrane proteins (SNMPs), 3 gustatory receptors (GRs) and 4 odorant receptors (ORs). Several leg-specific or enriched chemosensory genes were screened by tissue expression analysis, and clustered with functionally validated genes from other moths, suggesting the potential involvement in taste sensation or other physiological processes. The RPKM value analysis revealed that 9 EoblOBPs showed sex discrepancy in the leg expression, 8 being up-regulated in female and only 1 being over expressed in male. These female-biased EoblOBPs indicated an ecological adaption related with host-seeking and oviposition behaviors. Our work will provide basic knowledge for further studies on the molecular mechanism of gustatory perception, and enlighten a host-selection-based control strategy of insect pests.}, } @article {pmid26929361, year = {2016}, author = {Malviya, S and Scalco, E and Audic, S and Vincent, F and Veluchamy, A and Poulain, J and Wincker, P and Iudicone, D and de Vargas, C and Bittner, L and Zingone, A and Bowler, C}, title = {Insights into global diatom distribution and diversity in the world's ocean.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {113}, number = {11}, pages = {E1516-25}, pmid = {26929361}, issn = {1091-6490}, mesh = {Aquatic Organisms ; *Biodiversity ; DNA, Ribosomal ; Databases, Factual ; Diatoms/classification/*genetics ; Ecosystem ; Microscopy/methods ; *Oceans and Seas ; Phytoplankton ; Reproducibility of Results ; }, abstract = {Diatoms (Bacillariophyta) constitute one of the most diverse and ecologically important groups of phytoplankton. They are considered to be particularly important in nutrient-rich coastal ecosystems and at high latitudes, but considerably less so in the oligotrophic open ocean. The Tara Oceans circumnavigation collected samples from a wide range of oceanic regions using a standardized sampling procedure. Here, a total of ∼12 million diatom V9-18S ribosomal DNA (rDNA) ribotypes, derived from 293 size-fractionated plankton communities collected at 46 sampling sites across the global ocean euphotic zone, have been analyzed to explore diatom global diversity and community composition. We provide a new estimate of diversity of marine planktonic diatoms at 4,748 operational taxonomic units (OTUs). Based on the total assigned ribotypes, Chaetoceros was the most abundant and diverse genus, followed by Fragilariopsis, Thalassiosira, and Corethron We found only a few cosmopolitan ribotypes displaying an even distribution across stations and high abundance, many of which could not be assigned with confidence to any known genus. Three distinct communities from South Pacific, Mediterranean, and Southern Ocean waters were identified that share a substantial percentage of ribotypes within them. Sudden drops in diversity were observed at Cape Agulhas, which separates the Indian and Atlantic Oceans, and across the Drake Passage between the Atlantic and Southern Oceans, indicating the importance of these ocean circulation choke points in constraining diatom distribution and diversity. We also observed high diatom diversity in the open ocean, suggesting that diatoms may be more relevant in these oceanic systems than generally considered.}, } @article {pmid26927852, year = {2016}, author = {Massey, NC and Garrod, G and Wiebe, A and Henry, AJ and Huang, Z and Moyes, CL and Sinka, ME}, title = {A global bionomic database for the dominant vectors of human malaria.}, journal = {Scientific data}, volume = {3}, number = {}, pages = {160014}, pmid = {26927852}, issn = {2052-4463}, mesh = {Animals ; *Anopheles/physiology ; *Databases, Factual ; Humans ; *Insect Vectors ; Malaria/epidemiology/*transmission ; }, abstract = {Anopheles mosquitoes were first recognised as the transmitters of human malaria in the late 19th Century and have been subject to a huge amount of research ever since. Yet there is still much that is unknown regarding the ecology, behaviour (collectively 'bionomics') and sometimes even the identity of many of the world's most prominent disease vectors, much less the within-species variation in their bionomics. Whilst malaria elimination remains an ambitious goal, it is becoming increasingly clear that knowledge of vector behaviour is needed to effectively target control measures. A database of bionomics data for the dominant vector species of malaria worldwide has been compiled from published peer-reviewed literature. The data identification and collation processes are described, together with the geo-positioning and quality control methods. This is the only such dataset in existence and provides a valuable resource to researchers and policy makers in this field.}, } @article {pmid26924127, year = {2016}, author = {Hua, J and Vijver, MG and Chen, G and Richardson, MK and Peijnenburg, WJ}, title = {Dose metrics assessment for differently shaped and sized metal-based nanoparticles.}, journal = {Environmental toxicology and chemistry}, volume = {35}, number = {10}, pages = {2466-2473}, doi = {10.1002/etc.3414}, pmid = {26924127}, issn = {1552-8618}, mesh = {Animals ; Cell Line ; Copper/chemistry ; Daphnia/drug effects/metabolism ; Databases, Factual ; Ions/chemistry/metabolism ; Lethal Dose 50 ; Metal Nanoparticles/*chemistry/toxicity ; Metals/*chemistry ; Particle Size ; Silver/chemistry ; Surface Properties ; Toxicity Tests ; Zebrafish/growth & development/metabolism ; Zinc Oxide/chemistry ; }, abstract = {The mean primary diameter (d) of nanoparticles (NPs) is commonly used as the best basis to assess the dose metric for expressing the toxicity of spherical NPs. However, d bears no relevance for nonspherical NPs. In the present study, the mean surface area to volume ratio, applicable to both spherical and nonspherical NPs, was used to replace d given the aim of obtaining the best dose metric (volume, surface area, or number) of differently shaped metallic NPs in vivo (9 organisms) and in vitro (6 mammalian cell lines). The slope of the curves obtained by relating the total particle number of NPs at various effect concentrations to the mean surface area to volume ratio was subsequently used to deduce the best dose metric. For the majority of the organisms studied, it was found that NP volume is the most appropriate dose metric, independent of the composition of the NPs tested. For 3 organisms exposed to Ag NPs, however, surface area was found to be the best dose metric. It is therefore concluded that the optimum dose metric depends on organism and NP properties. Environ Toxicol Chem 2016;35:2466-2473. © 2016 SETAC.}, } @article {pmid26923884, year = {2016}, author = {Carr, MJ and Ashcroft, DM and Kontopantelis, E and Awenat, Y and Cooper, J and Chew-Graham, C and Kapur, N and Webb, RT}, title = {The epidemiology of self-harm in a UK-wide primary care patient cohort, 2001-2013.}, journal = {BMC psychiatry}, volume = {16}, number = {}, pages = {53}, pmid = {26923884}, issn = {1471-244X}, support = {MC_PC_13042/MRC_/Medical Research Council/United Kingdom ; MR/K006665/1/MRC_/Medical Research Council/United Kingdom ; WMCLAHRC-2014-1/DH_/Department of Health/United Kingdom ; }, mesh = {Adolescent ; Adult ; Age Distribution ; Cohort Studies ; Female ; Humans ; Incidence ; Longitudinal Studies ; Male ; Middle Aged ; Primary Health Care/*statistics & numerical data ; Self-Injurious Behavior/*epidemiology ; Sex Distribution ; United Kingdom/epidemiology ; Young Adult ; }, abstract = {BACKGROUND: Most of the research conducted on people who harm themselves has been undertaken in secondary healthcare settings. Little is known about the frequency of self-harm in primary care patient populations. This is the first study to describe the epidemiology of self-harm presentations to primary care using broadly representative national data from across the United Kingdom (UK).

METHODS: Using the Clinical Practice Research Datalink (CPRD), we calculated directly standardised rates of incidence and annual presentation during 2001-2013. Rates were compared by gender and age and across the nations of the UK, and also by degree of socioeconomic deprivation measured ecologically at general practice level.

RESULTS: We found significantly elevated rates in females vs. males for incidence (rate ratio - RR, 1.45, 95 % confidence interval - CI, 1.42-1.47) and for annual presentation (RR 1.56, CI 1.54-1.58). An increasing trend over time in incidence was apparent for males (P < 0.001) but not females (P = 0.08), and both genders exhibited rising temporal trends in presentation rates (P < 0.001). We observed a decreasing gradient of risk with increasing age and markedly elevated risk for females in the youngest age group (aged 15-24 years vs. all other females: RR 3.75, CI 3.67-3.83). Increasing presentation rates over time were observed for males across all age bands (P < 0.001). We found higher rates when comparing Northern Ireland, Scotland, and Wales with England, and increasing rates of presentation over time for all four nations. We also observed higher rates with increasing levels of deprivation - most vs. least deprived male patients: RR 2.17, CI 2.10-2.25.

CONCLUSIONS: Incorporating data from primary care yields a more comprehensive quantification of the health burden of self-harm. These novel findings may be useful in informing public health programmes and the targeting of high-risk groups toward the ultimate goal of lowering risk of self-harm repetition and premature death in this population.}, } @article {pmid26923854, year = {2016}, author = {Schroeder, AL and Ankley, GT and Houck, KA and Villeneuve, DL}, title = {Environmental surveillance and monitoring--The next frontiers for high-throughput toxicology.}, journal = {Environmental toxicology and chemistry}, volume = {35}, number = {3}, pages = {513-525}, doi = {10.1002/etc.3309}, pmid = {26923854}, issn = {1552-8618}, mesh = {Animals ; Databases, Factual ; Environmental Monitoring/*methods ; Organic Chemicals/chemistry/metabolism ; Protein Interaction Maps ; Proteins/chemistry/metabolism ; *Toxicity Tests ; }, abstract = {High-throughput toxicity testing technologies along with the World Wide Web are revolutionizing both generation of and access to data regarding the biological activities that chemicals can elicit when they interact with specific proteins, genes, or other targets in the body of an organism. To date, however, most of the focus has been on the application of such data to assessment of individual chemicals. The authors suggest that environmental surveillance and monitoring represent the next frontiers for high-throughput toxicity testing. Resources already exist in curated databases of chemical-biological interactions, including highly standardized quantitative dose-response data generated from nascent high-throughput toxicity testing programs such as ToxCast and Tox21, to link chemicals detected through environmental analytical chemistry to known biological activities. The emergence of the adverse outcome pathway framework and the associated knowledge base for linking molecular-level or pathway-level perturbations of biological systems to adverse outcomes traditionally considered in risk assessment and regulatory decision-making through a series of measurable biological changes provides a critical link between activity and hazard. Furthermore, environmental samples can be directly analyzed via high-throughput toxicity testing platforms to provide an unprecedented breadth of biological activity characterization that integrates the effects of all compounds present in a mixture, whether known or not. Novel application of these chemical-biological interaction data provides an opportunity to transform scientific characterization of potential hazards associated with exposure to complex mixtures of environmental contaminants.}, } @article {pmid26921294, year = {2016}, author = {Hamaji, T and Mogi, Y and Ferris, PJ and Mori, T and Miyagishima, S and Kabeya, Y and Nishimura, Y and Toyoda, A and Noguchi, H and Fujiyama, A and Olson, BJ and Marriage, TN and Nishii, I and Umen, JG and Nozaki, H}, title = {Sequence of the Gonium pectorale Mating Locus Reveals a Complex and Dynamic History of Changes in Volvocine Algal Mating Haplotypes.}, journal = {G3 (Bethesda, Md.)}, volume = {6}, number = {5}, pages = {1179-1189}, pmid = {26921294}, issn = {2160-1836}, support = {R01 GM078376/GM/NIGMS NIH HHS/United States ; }, mesh = {Chromosome Walking ; Computational Biology ; Evolution, Molecular ; Gene Expression ; Genetic Linkage ; Genome, Plant ; Genomics/methods ; *Haplotypes ; High-Throughput Nucleotide Sequencing ; Phylogeny ; *Quantitative Trait Loci ; Reproduction/*genetics ; Sex Determination Processes/genetics ; Volvox/classification/*genetics ; }, abstract = {Sex-determining regions (SDRs) or mating-type (MT) loci in two sequenced volvocine algal species, Chlamydomonas reinhardtii and Volvox carteri, exhibit major differences in size, structure, gene content, and gametolog differentiation. Understanding the origin of these differences requires investigation of MT loci from related species. Here, we determined the sequences of the minus and plus MT haplotypes of the isogamous 16-celled volvocine alga, Gonium pectorale, which is more closely related to the multicellular V. carteri than to C. reinhardtii Compared to C. reinhardtii MT, G. pectorale MT is moderately larger in size, and has a less complex structure, with only two major syntenic blocs of collinear gametologs. However, the gametolog content of G. pectorale MT has more overlap with that of V. carteri MT than with C. reinhardtii MT, while the allelic divergence between gametologs in G. pectorale is even lower than that in C. reinhardtii Three key sex-related genes are conserved in G. pectorale MT: GpMID and GpMTD1 in MT-, and GpFUS1 in MT+. GpFUS1 protein exhibited specific localization at the plus-gametic mating structure, indicating a conserved function in fertilization. Our results suggest that the G. pectorale-V. carteri common ancestral MT experienced at least one major reformation after the split from C. reinhardtii, and that the V. carteri ancestral MT underwent a subsequent expansion and loss of recombination after the divergence from G. pectorale These data begin to polarize important changes that occurred in volvocine MT loci, and highlight the potential for discontinuous and dynamic evolution in SDRs.}, } @article {pmid26919723, year = {2016}, author = {Hu, M and Li, W and Li, L and Houston, D and Wu, J}, title = {Refining Time-Activity Classification of Human Subjects Using the Global Positioning System.}, journal = {PloS one}, volume = {11}, number = {2}, pages = {e0148875}, pmid = {26919723}, issn = {1932-6203}, mesh = {Accelerometry ; *Activities of Daily Living ; Adult ; Air Pollution/analysis ; Cities ; Environmental Exposure/analysis ; *Geographic Information Systems ; Humans ; Models, Statistical ; Spatial Analysis ; Time Factors ; Walking ; }, abstract = {BACKGROUND: Detailed spatial location information is important in accurately estimating personal exposure to air pollution. Global Position System (GPS) has been widely used in tracking personal paths and activities. Previous researchers have developed time-activity classification models based on GPS data, most of them were developed for specific regions. An adaptive model for time-location classification can be widely applied to air pollution studies that use GPS to track individual level time-activity patterns.

METHODS: Time-activity data were collected for seven days using GPS loggers and accelerometers from thirteen adult participants from Southern California under free living conditions. We developed an automated model based on random forests to classify major time-activity patterns (i.e. indoor, outdoor-static, outdoor-walking, and in-vehicle travel). Sensitivity analysis was conducted to examine the contribution of the accelerometer data and the supplemental spatial data (i.e. roadway and tax parcel data) to the accuracy of time-activity classification. Our model was evaluated using both leave-one-fold-out and leave-one-subject-out methods.

RESULTS: Maximum speeds in averaging time intervals of 7 and 5 minutes, and distance to primary highways with limited access were found to be the three most important variables in the classification model. Leave-one-fold-out cross-validation showed an overall accuracy of 99.71%. Sensitivities varied from 84.62% (outdoor walking) to 99.90% (indoor). Specificities varied from 96.33% (indoor) to 99.98% (outdoor static). The exclusion of accelerometer and ambient light sensor variables caused a slight loss in sensitivity for outdoor walking, but little loss in overall accuracy. However, leave-one-subject-out cross-validation showed considerable loss in sensitivity for outdoor static and outdoor walking conditions.

CONCLUSIONS: The random forests classification model can achieve high accuracy for the four major time-activity categories. The model also performed well with just GPS, road and tax parcel data. However, caution is warranted when generalizing the model developed from a small number of subjects to other populations.}, } @article {pmid26914768, year = {2016}, author = {Lemasson, BH and Tanner, CJ and Dimperio, E}, title = {A Sensory-Driven Trade-Off between Coordinated Motion in Social Prey and a Predator's Visual Confusion.}, journal = {PLoS computational biology}, volume = {12}, number = {2}, pages = {e1004708}, pmid = {26914768}, issn = {1553-7358}, mesh = {Adult ; Animals ; Computational Biology ; Computer Simulation ; Confusion ; Humans ; *Models, Biological ; Movement/*physiology ; Predatory Behavior/*physiology ; *Social Behavior ; }, abstract = {Social animals are capable of enhancing their awareness by paying attention to their neighbors, and prey found in groups can also confuse their predators. Both sides of these sensory benefits have long been appreciated, yet less is known of how the perception of events from the perspectives of both prey and predator can interact to influence their encounters. Here we examined how a visual sensory mechanism impacts the collective motion of prey and, subsequently, how their resulting movements influenced predator confusion and capture ability. We presented virtual prey to human players in a targeting game and measured the speed and accuracy with which participants caught designated prey. As prey paid more attention to neighbor movements their collective coordination increased, yet increases in prey coordination were positively associated with increases in the speed and accuracy of attacks. However, while attack speed was unaffected by the initial state of the prey, accuracy dropped significantly if the prey were already organized at the start of the attack, rather than in the process of self-organizing. By repeating attack scenarios and masking the targeted prey's neighbors we were able to visually isolate them and conclusively demonstrate how visual confusion impacted capture ability. Delays in capture caused by decreased coordination amongst the prey depended upon the collection motion of neighboring prey, while it was primarily the motion of the targets themselves that determined capture accuracy. Interestingly, while a complete loss of coordination in the prey (e.g., a flash expansion) caused the greatest delay in capture, such behavior had little effect on capture accuracy. Lastly, while increases in collective coordination in prey enhanced personal risk, traveling in coordinated groups was still better than appearing alone. These findings demonstrate a trade-off between the sensory mechanisms that can enhance the collective properties that emerge in social animals and the individual group member's predation risk during an attack.}, } @article {pmid26912171, year = {2016}, author = {Lu, L and Ren, Z and Yue, Y and Yu, X and Lu, S and Li, G and Li, H and Wei, J and Liu, J and Mu, Y and Hai, R and Yang, Y and Wei, R and Kan, B and Wang, H and Wang, J and Wang, Z and Liu, Q and Xu, J}, title = {Niche modeling predictions of the potential distribution of Marmota himalayana, the host animal of plague in Yushu County of Qinghai.}, journal = {BMC public health}, volume = {16}, number = {}, pages = {183}, pmid = {26912171}, issn = {1471-2458}, mesh = {Animals ; China/epidemiology ; Earthquakes ; *Ecosystem ; Epidemics ; Geographic Information Systems ; *Marmota/microbiology ; *Models, Biological ; Plague/*epidemiology ; Probability ; Seasons ; Soil ; Temperature ; }, abstract = {BACKGROUND: After the earthquake on 14, April 2010 at Yushu in China, a plague epidemic hosted by Himalayan marmot (Marmota himalayana) became a major public health concern during the reconstruction period. A rapid assessment of the distribution of Himalayan marmot in the area was urgent. The aims of this study were to analyze the relationship between environmental factors and the distribution of burrow systems of the marmot and to predict the distribution of marmots.

METHODS: Two types of marmot burrows (hibernation and temporary) in Yushu County were investigated from June to September in 2011. The location of every burrow was recorded with a global positioning system receiver. An ecological niche model was used to determine the relationship between the burrow occurrence data and environmental variables, such as land surface temperature (LST) in winter and summer, normalized difference vegetation index (NDVI) in winter and summer, elevation, and soil type. The predictive accuracies of the models were assessed by the area under the curve of the receiving operator curve.

RESULTS: The models for hibernation and temporary burrows both performed well. The contribution orders of the variables were LST in winter and soil type, NDVI in winter and elevation for the hibernation burrow model, and LST in summer, NDVI in summer, soil type and elevation in the temporary burrow model. There were non-linear relationships between the probability of burrow presence and LST, NDVI and elevation. LST of 14 and 23 °C, NDVI of 0.22 and 0.60, and 4100 m were inflection points. A substantially higher probability of burrow presence was observed in swamp soil and dark felty soil than in other soil types. The potential area for hibernation burrows was 5696 km(2) (37.7% of Yushu County), and the area for temporary burrows was 7711 km(2) (51.0% of Yushu County).

CONCLUSIONS: The results suggested that marmots preferred warm areas with relatively low altitudes and good vegetation conditions in Yushu County. Based on these results, the present research is useful in understanding the niche selection and distribution pattern of marmots in this region.}, } @article {pmid26909905, year = {2016}, author = {Pinto, JV and Crispim, BA and Vasconcelos, AA and Geelen, D and Grisolia, AB and Vieira, MC}, title = {Intravarietal polymorphisms reveal possible common ancestor of native Schinus terebinthifolius Raddi populations in Brazil.}, journal = {Genetics and molecular research : GMR}, volume = {15}, number = {1}, pages = {}, doi = {10.4238/gmr.15017477}, pmid = {26909905}, issn = {1676-5680}, mesh = {Anacardiaceae/classification/*genetics ; Base Sequence ; Brazil ; Chloroplasts/genetics ; DNA, Chloroplast/*genetics ; DNA, Intergenic ; Databases, Nucleic Acid ; *Haplotypes ; Hybridization, Genetic ; Molecular Sequence Data ; *Phylogeny ; Phylogeography ; *Polymorphism, Genetic ; }, abstract = {Schinus terebinthifolius Raddi is a perennial native from Atlantic forest. It is of high ecological plasticity and is used in traditional medicine. Based on promising reports concerning its bioactivity, it was included as a species of great interest for distribution through the National Health System. A number of agronomic studies to guide its crop production are therefore underway. This study examined diversity and phylogenetic relationships among native S. terebinthifolius populations from different Brazilian ecosystems: Cerrado; sandbanks; dense rainforest; and deciduous forest. The intergenic regions rpl20-5'rps12, trnH-psbA, and trnS-trnG were sequenced from cpDNA and aligned using BLASTn. There were few fragments for comparison in GenBank and so only region trnS-trnG was informative. There were variations among and within populations with intravarietal polymorphisms and three distinct haplotypes (HpSM, HpDDO, HpNE), once populations from NE (sandbanks and rainforest) clustered together. Sequences from HpSM, HpNE, and HpDDO returned greater similarity to haplotypes A (AY928398.1), B (AY928399.1), and C (AY928400.1), respectively. A network, built by median-joining among native haplotypes and 10 available on GenBank, revealed HpSM as the origin of all other haplogroups. HpDDO showed the most mutations and was closely related to haplogroups from Argentina. While this could indicate hybridization, we believe that the polymorphisms resulted from adaptation to events such as deforestation, fire, rising temperature, and seasonal drought during the transition from Atlantic forest to Cerrado. While more detailed phylogeographical studies are needed, these results indicate eligible groups for distinct climates as an important step for pre-breeding programs before field propagation.}, } @article {pmid26909427, year = {2015}, author = {Turner, TF and Krabbenhoft, TI and Collyer, ML and Krabbenhoft, CA and Edwards, MS and Sharp, ZD}, title = {Retrospective stable isotope analysis reveals ecosystem responses to river regulation over the last century.}, journal = {Ecology}, volume = {96}, number = {12}, pages = {3213-3226}, doi = {10.1890/14-1666.1}, pmid = {26909427}, issn = {0012-9658}, mesh = {Animals ; Data Interpretation, Statistical ; *Ecosystem ; Environmental Monitoring/*methods ; Fishes/metabolism/*physiology ; *Human Activities ; Isotopes ; New Mexico ; *Rivers ; Time Factors ; Water Pollution ; }, abstract = {Disruption of natural flow regimes, nutrient pollution, and other consequences of human population growth and development have impacted most major rivers of the world. Alarming losses of aquatic biodiversity coincide with human-caused river alteration, but effects of biotic homogenization on aquatic ecosystem processes are not as well documented. This is because unaltered systems for comparison are scarce, and some ecosystem-wide effects may take decades to manifest. We evaluated aquatic ecosystem responses to extensive river- floodplain engineering and nutrient addition in the Rio Grande of southwestern North America as revealed by changes in trophic structure of, and resource availability to, the fish community. Stable Isotope Analysis (SIA) was conducted on museum-preserved fishes collected over a 70-year period of intensive river management and exponential human population growth. Trophic complexity and resource heterogeneity for fish consumers (measured as "isotopic niche breadth") decreased following sediment deprivation and channelization, and these effects persist into the present. Increased nutrient inputs led to δ15N enrichment in the entire fish community at all affected sites, and a shift to autochthonous sources of carbon at the most proximal site downstream of wastewater release, probably via bottom-up transfer. Overall, retrospective SIA of apex consumers suggests radical change and functional impairment of a floodplain river ecosystem already marked by significant biodiversity loss.}, } @article {pmid26909419, year = {2015}, author = {Kendall, BE}, title = {Some directions in ecological theory.}, journal = {Ecology}, volume = {96}, number = {12}, pages = {3117-3125}, doi = {10.1890/14-2080.1}, pmid = {26909419}, issn = {0012-9658}, mesh = {Animals ; Biomass ; Causality ; Conservation of Natural Resources/*methods ; Data Interpretation, Statistical ; Ecology/education/*methods ; Ecosystem ; Extinction, Biological ; Humans ; *Models, Theoretical ; }, abstract = {The role of theory within ecology has changed dramatically in recent decades. Once primarily a source of qualitative conceptual framing, ecological theories and models are now often used to develop quantitative explanations of empirical patterns and to project future dynamics of specific ecological systems. In this essay, I recount my own experience of this transformation, in which accelerating computing power and the widespread incorporation of stochastic processes into ecological theory combined to create some novel integration of mathematical and statistical models. This stronger integration drives theory towards incorporating more biological realism, and I explore ways in which we can grapple with that realism to generate new general theoretical insights. This enhanced realism, in turn, may lead to frameworks for projecting ecological responses to anthropogenic change, which is, arguably, the central challenge for 21st-century ecology. In an era of big data and synthesis, ecologists are increasingly seeking to infer causality from observational data; but conventional biometry provides few tools for this project. This is a realm where theorists can and should play an important role, and I close by pointing towards some analytical and philosophical approaches developed in our sister discipline of economics that address this very problem. While I make no grand prognostications about the likely discoveries of ecological theory over the coming century, you will find in this essay a scattering of more or less far-fetched ideas that I, at least, think are interesting and (possibly) fruitful directions for our field.}, } @article {pmid26906946, year = {2016}, author = {Qiao, Q and Wang, Q and Han, X and Guan, Y and Sun, H and Zhong, Y and Huang, J and Zhang, T}, title = {Transcriptome sequencing of Crucihimalaya himalaica (Brassicaceae) reveals how Arabidopsis close relative adapt to the Qinghai-Tibet Plateau.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {21729}, pmid = {26906946}, issn = {2045-2322}, mesh = {Adaptation, Physiological ; Arabidopsis/*genetics/metabolism ; Evolution, Molecular ; Gene Ontology ; Genes, Plant ; Molecular Sequence Annotation ; Phylogeny ; Sequence Analysis, DNA ; Tibet ; *Transcriptome ; }, abstract = {The extreme environment of the Qinghai-Tibet Plateau (QTP) provides an ideal natural laboratory for studies on adaptive evolution. Few genome/transcriptome based studies have been conducted on how plants adapt to the environments of QTP compared to numerous studies on vertebrates. Crucihimalaya himalaica is a close relative of Arabidopsis with typical QTP distribution, and is hoped to be a new model system to study speciation and ecological adaptation in extreme environment. In this study, we de novo generated a transcriptome sequence of C. himalaica, with a total of 49,438 unigenes. Compared to five relatives, 10,487 orthogroups were shared by all six species, and 4,286 orthogroups contain putative single copy gene. Further analysis identified 487 extremely significantly positively selected genes (PSGs) in C. himalaica transcriptome. Theses PSGs were enriched in functions related to specific adaptation traits, such as response to radiation, DNA repair, nitrogen metabolism, and stabilization of membrane. These functions are responsible for the adaptation of C. himalaica to the high radiation, soil depletion and low temperature environments on QTP. Our findings indicate that C. himalaica has evolved complex strategies for adapting to the extreme environments on QTP and provide novel insights into genetic mechanisms of highland adaptation in plants.}, } @article {pmid26905627, year = {2016}, author = {Weiss, S and Van Treuren, W and Lozupone, C and Faust, K and Friedman, J and Deng, Y and Xia, LC and Xu, ZZ and Ursell, L and Alm, EJ and Birmingham, A and Cram, JA and Fuhrman, JA and Raes, J and Sun, F and Zhou, J and Knight, R}, title = {Correlation detection strategies in microbial data sets vary widely in sensitivity and precision.}, journal = {The ISME journal}, volume = {10}, number = {7}, pages = {1669-1681}, pmid = {26905627}, issn = {1751-7370}, support = {R01 HG004872/HG/NHGRI NIH HHS/United States ; U01 HG004866/HG/NHGRI NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; }, mesh = {Bacteria/*genetics ; Benchmarking/*statistics & numerical data ; Computational Biology ; Humans ; *Microbial Interactions ; *Microbiota ; Models, Statistical ; RNA, Ribosomal, 16S/genetics ; Statistics as Topic ; }, abstract = {Disruption of healthy microbial communities has been linked to numerous diseases, yet microbial interactions are little understood. This is due in part to the large number of bacteria, and the much larger number of interactions (easily in the millions), making experimental investigation very difficult at best and necessitating the nascent field of computational exploration through microbial correlation networks. We benchmark the performance of eight correlation techniques on simulated and real data in response to challenges specific to microbiome studies: fractional sampling of ribosomal RNA sequences, uneven sampling depths, rare microbes and a high proportion of zero counts. Also tested is the ability to distinguish signals from noise, and detect a range of ecological and time-series relationships. Finally, we provide specific recommendations for correlation technique usage. Although some methods perform better than others, there is still considerable need for improvement in current techniques.}, } @article {pmid26905247, year = {2015}, author = {Chatterjee, S and Chakraborty, A and Sinha, SK}, title = {Spatial distribution & physicochemical characterization of the breeding habitats of Aedes aegypti in & around Kolkata, West Bengal, India.}, journal = {The Indian journal of medical research}, volume = {142 Suppl}, number = {Suppl 1}, pages = {S79-86}, pmid = {26905247}, issn = {0971-5916}, mesh = {Aedes/growth & development/*virology ; Animals ; Dengue/epidemiology/*transmission/virology ; Dengue Virus/*pathogenicity ; Ecology ; Ecosystem ; Female ; Geographic Information Systems ; Humans ; India ; Insect Vectors/growth & development/*virology ; Water/parasitology ; }, abstract = {BACKGROUND & OBJECTIVES: Dengue infection is endemic in several areas and the dengue virus is transmitted by Aedes mosquitoes. Thus, it becomes important to understand the breeding ecology of dengue vector and characterize the physicochemical parameters of its breeding habitat. The objective of this study was to analyze the physicochemical parameters of the breeding habitat of the dengue vector and to find out the nutrient composition of the habitat in and around Kolkata, West Bengal. In addition, a geographic information system (GIS) was used to map the disease prone areas for its effective management and prevention.

METHODS: Water samples were collected from various breeding habitats of Aedes mosquitoes of Kolkata and adjoining areas and were analysed for various physicochemical properties like acidity, alkalinity, hardness, electrical conductivity, total dissolved solids, concentration of chloride (Cl -), sodium (Na +), potassium (K +), fluoride (F -) in relation to larval prevalence.

RESULTS: Parameters like water pH, total dissolved solids, total hardness, electrical conductivity, concentration of chloride, sodium and potassium were seen to vary throughout the year. Certain parameters were found to be dependent on container type, like concentration of fluoride. Significant positive correlations were seen between per dip larval density and total dissolved solids (TDS) and electrical conductivity.

Water pH, electrical conductivity, total dissolved solids were seen to play a major role in the ovipositional preferences. Container type did not seem to affect TDS. Tyres had the highest TDS in most of the cases. Nutrient composition like sodium concentration was mostly found in the coconut shells, potassium concentration also showed the same. Thus, container type and various parameters and nutrients play a major role in determining where a gravid female mosquito will lay its eggs. It was observed that by altering various chemical and physical properties of breeding habitats it was possible to control the larvae survivability.}, } @article {pmid26904042, year = {2016}, author = {Dong, Y and Li, B and Malitsky, S and Rogachev, I and Aharoni, A and Kaftan, F and Svatoš, A and Franceschi, P}, title = {Sample Preparation for Mass Spectrometry Imaging of Plant Tissues: A Review.}, journal = {Frontiers in plant science}, volume = {7}, number = {}, pages = {60}, pmid = {26904042}, issn = {1664-462X}, abstract = {Mass spectrometry imaging (MSI) is a mass spectrometry based molecular ion imaging technique. It provides the means for ascertaining the spatial distribution of a large variety of analytes directly on tissue sample surfaces without any labeling or staining agents. These advantages make it an attractive molecular histology tool in medical, pharmaceutical, and biological research. Likewise, MSI has started gaining popularity in plant sciences; yet, information regarding sample preparation methods for plant tissues is still limited. Sample preparation is a crucial step that is directly associated with the quality and authenticity of the imaging results, it therefore demands in-depth studies based on the characteristics of plant samples. In this review, a sample preparation pipeline is discussed in detail and illustrated through selected practical examples. In particular, special concerns regarding sample preparation for plant imaging are critically evaluated. Finally, the applications of MSI techniques in plants are reviewed according to different classes of plant metabolites.}, } @article {pmid26900673, year = {2016}, author = {St John, HK and Adams, ML and Masuoka, PM and Flyer-Adams, JG and Jiang, J and Rozmajzl, PJ and Stromdahl, EY and Richards, AL}, title = {Prevalence, Distribution, and Development of an Ecological Niche Model of Dermacentor variabilis Ticks Positive for Rickettsia montanensis.}, journal = {Vector borne and zoonotic diseases (Larchmont, N.Y.)}, volume = {16}, number = {4}, pages = {253-263}, doi = {10.1089/vbz.2015.1856}, pmid = {26900673}, issn = {1557-7759}, mesh = {Animals ; Arachnid Vectors/microbiology ; DNA, Bacterial/genetics ; Dermacentor/genetics/*microbiology ; Ecological and Environmental Phenomena ; Geographic Information Systems ; Humans ; Military Personnel ; Prevalence ; Real-Time Polymerase Chain Reaction ; Rickettsia/genetics/*isolation & purification ; United States ; }, abstract = {Rickettsia montanensis has long been considered a nonpathogenic member of the spotted fever group rickettsiae. However, the infection potential of R. montanensis is being revisited in light of its recent association with a case of human infection in the United States and the possibility that additional cases may have been misdiagnosed as Rocky Mountain spotted fever. To this end, DNA was extracted from American dog ticks (Dermacentor variabilis) removed from Department of Defense (DoD) personnel and their dependents at DoD medical treatment facilities (MTFs) during 2002-2012 (n = 4792). These 4792 samples were analyzed for the presence of R. montanensis (n = 36; 2.84%) and all vector DNA was confirmed to be of D. variabilis origin using a novel Dermacentor genus-specific quantitative real-time polymerase chain reaction procedure, Derm, and a novel Dermacentor species multilocus sequence typing assay. To assess the risk of R. montanensis infection, the positive and negative samples were geographically mapped utilizing MTF site locations. Tick localities were imported into a geographical information systems (GIS) program, ArcGIS, for mapping and analysis. The ecological niche modeling (ENM) program, Maxent, was used to estimate the probability of tick presence in eastern United States using locations of both R. montanensis-positive and -negative ticks, climate, and elevation data. The ENM for R. montanensis-positive D. variabilis estimated high probabilities of the positive ticks occurring in two main areas, including the northern Midwest and mid-Atlantic portions of the northeastern regions of United States, whereas the R. montanensis-negative D. variabilis tick model showed a wider estimated range. The results suggest that R. montanensis-positive and -negative D. variabilis have different ranges where humans may be at risk and are influenced by similar and different factors.}, } @article {pmid26897477, year = {2017}, author = {Bennett, KB}, title = {Ecological interface design and system safety: One facet of Rasmussen's legacy.}, journal = {Applied ergonomics}, volume = {59}, number = {Pt B}, pages = {625-636}, doi = {10.1016/j.apergo.2015.08.001}, pmid = {26897477}, issn = {1872-9126}, mesh = {Decision Making ; *Decision Support Techniques ; *Ecology ; Humans ; Safety Management/*methods ; *Systems Analysis ; *User-Computer Interface ; }, abstract = {The focus of this manuscript is on cognitive systems engineering/ecological interface design (CSE/EID) and the role that this framework may play in improving system safety. First, the decision making and problem solving literatures are reviewed with an eye towards informational needs that are required to support these activities. The utility of two of Rasmussen's analytical tools (i.e., the abstraction and aggregation hierarchies) in conducting work domain analyses to identify associated information (i.e., categories and relationships) is discussed. The importance of designing ecological displays and interfaces that span the informational categories in the abstraction hierarchy is described and concrete examples are provided. The potential role that ecological interfaces can play in providing effective decision making (i.e., preventing accidents) and problem solving (i.e., dealing with accidents) support, thereby improving the safety of our socio-technical systems, is explored.}, } @article {pmid26897111, year = {2016}, author = {Rey, G}, title = {[Death certificate data in France: Production process and main types of analyses].}, journal = {La Revue de medecine interne}, volume = {37}, number = {10}, pages = {685-693}, doi = {10.1016/j.revmed.2016.01.011}, pmid = {26897111}, issn = {1768-3122}, mesh = {*Cause of Death ; *Data Interpretation, Statistical ; Databases, Factual/standards/statistics & numerical data ; *Death Certificates ; France/epidemiology ; Humans ; Information Systems ; }, abstract = {Mortality data, by the unambiguity of their definition and understanding by all stakeholders, and completeness of registration, are a cornerstone of public health statistics in France and in most industrialized countries. This article describes the data production process, and the main types of possible analyses. Data production is composed of different stages: death certification by a medical doctor on paper or electronic (using a web application) format, data transmission to Inserm, capture and coding of information. The encoding of the information follows the WHO recommendations of the International Classification of Diseases ([ICD], 10th revision used since 2000). It is carried out using an automatic coding software, called Iris, developed in an international consortium. The coding aims, first, at assigning an ICD code to all nosologic entities encountered on the certificate, and then at selecting the underlying cause of death. The latter is the main information used for statistical analyses. Three main types of analysis emerge in the literature: the exploitation of data on the death certificate only, ecological analyses (studies of associations between variables measured across groups) and analysis from data individually linked to other databases. Many public health issues can be addressed with these various analyses. Several developments in the production process are being implemented: the deployment of electronic certification, increased automation of the death certificate information processing and durable and complete record linkage with health insurance and hospitalisation data. They could soon be deeply expanding the scope of possible uses of causes of death data.}, } @article {pmid26896844, year = {2016}, author = {Pafilis, E and Buttigieg, PL and Ferrell, B and Pereira, E and Schnetzer, J and Arvanitidis, C and Jensen, LJ}, title = {EXTRACT: interactive extraction of environment metadata and term suggestion for metagenomic sample annotation.}, journal = {Database : the journal of biological databases and curation}, volume = {2016}, number = {}, pages = {}, pmid = {26896844}, issn = {1758-0463}, mesh = {Computational Biology/*methods ; Data Mining/*methods ; Databases, Factual ; Ecology/*methods ; Genomics ; Humans ; Internet ; *Metagenomics ; Phenotype ; Programming Languages ; Sequence Alignment ; Software ; User-Computer Interface ; }, abstract = {The microbial and molecular ecology research communities have made substantial progress on developing standards for annotating samples with environment metadata. However, sample manual annotation is a highly labor intensive process and requires familiarity with the terminologies used. We have therefore developed an interactive annotation tool, EXTRACT, which helps curators identify and extract standard-compliant terms for annotation of metagenomic records and other samples. Behind its web-based user interface, the system combines published methods for named entity recognition of environment, organism, tissue and disease terms. The evaluators in the BioCreative V Interactive Annotation Task found the system to be intuitive, useful, well documented and sufficiently accurate to be helpful in spotting relevant text passages and extracting organism and environment terms. Comparison of fully manual and text-mining-assisted curation revealed that EXTRACT speeds up annotation by 15-25% and helps curators to detect terms that would otherwise have been missed. Database URL: https://extract.hcmr.gr/.}, } @article {pmid26895641, year = {2016}, author = {Bell, SM and Angrish, MM and Wood, CE and Edwards, SW}, title = {Integrating Publicly Available Data to Generate Computationally Predicted Adverse Outcome Pathways for Fatty Liver.}, journal = {Toxicological sciences : an official journal of the Society of Toxicology}, volume = {150}, number = {2}, pages = {510-520}, doi = {10.1093/toxsci/kfw017}, pmid = {26895641}, issn = {1096-0929}, mesh = {Animals ; Biomedical Research/*methods ; Computer Simulation ; *Databases, Factual ; Ecotoxicology/*methods ; Environmental Pollutants/*toxicity ; Fatty Liver/*chemically induced ; High-Throughput Screening Assays ; Humans ; Risk Assessment/*methods ; }, abstract = {Newin vitrotesting strategies make it possible to design testing batteries for large numbers of environmental chemicals. Full utilization of the results requires knowledge of the underlying biological networks and the adverse outcome pathways (AOPs) that describe the route from early molecular perturbations to an adverse outcome. Curation of a formal AOP is a time-intensive process and a rate-limiting step to designing these test batteries. Here, we describe a method for integrating publicly available data in order to generate computationally predicted AOP (cpAOP) scaffolds, which can be leveraged by domain experts to shorten the time for formal AOP development. A network-based workflow was used to facilitate the integration of multiple data types to generate cpAOPs. Edges between graph entities were identified through direct experimental or literature information, or computationally inferred using frequent itemset mining. Data from the TG-GATEs and ToxCast programs were used to channel large-scale toxicogenomics information into a cpAOP network (cpAOPnet) of over 20 000 relationships describing connections between chemical treatments, phenotypes, and perturbed pathways as measured by differential gene expression and high-throughput screening targets. The resulting fatty liver cpAOPnet is available as a resource to the community. Subnetworks of cpAOPs for a reference chemical (carbon tetrachloride, CCl4) and outcome (fatty liver) were compared with published mechanistic descriptions. In both cases, the computational approaches approximated the manually curated AOPs. The cpAOPnet can be used for accelerating expert-curated AOP development and to identify pathway targets that lack genomic markers or high-throughput screening tests. It can also facilitate identification of key events for designing test batteries and for classification and grouping of chemicals for follow up testing.}, } @article {pmid26894881, year = {2016}, author = {van Gestel, J and Nowak, MA}, title = {Phenotypic Heterogeneity and the Evolution of Bacterial Life Cycles.}, journal = {PLoS computational biology}, volume = {12}, number = {2}, pages = {e1004764}, pmid = {26894881}, issn = {1553-7358}, mesh = {Bacterial Physiological Phenomena/*genetics ; *Biological Evolution ; Computational Biology ; Computer Simulation ; *Phenotype ; }, abstract = {Most bacteria live in colonies, where they often express different cell types. The ecological significance of these cell types and their evolutionary origin are often unknown. Here, we study the evolution of cell differentiation in the context of surface colonization. We particularly focus on the evolution of a 'sticky' cell type that is required for surface attachment, but is costly to express. The sticky cells not only facilitate their own attachment, but also that of non-sticky cells. Using individual-based simulations, we show that surface colonization rapidly evolves and in most cases leads to phenotypic heterogeneity, in which sticky and non-sticky cells occur side by side on the surface. In the presence of regulation, cell differentiation leads to a remarkable set of bacterial life cycles, in which cells alternate between living in the liquid and living on the surface. The dominant life stage is formed by the surface-attached colony that shows many complex features: colonies reproduce via fission and by producing migratory propagules; cells inside the colony divide labour; and colonies can produce filaments to facilitate expansion. Overall, our model illustrates how the evolution of an adhesive cell type goes hand in hand with the evolution of complex bacterial life cycles.}, } @article {pmid26892686, year = {2016}, author = {Drew, S and Lavy, C and Gooberman-Hill, R}, title = {What factors affect patient access and engagement with clubfoot treatment in low- and middle-income countries? Meta-synthesis of existing qualitative studies using a social ecological model.}, journal = {Tropical medicine & international health : TM & IH}, volume = {21}, number = {5}, pages = {570-589}, doi = {10.1111/tmi.12684}, pmid = {26892686}, issn = {1365-3156}, mesh = {Clubfoot/economics/*surgery/therapy ; Databases, Bibliographic ; Developing Countries/economics/statistics & numerical data ; Health Services Accessibility/economics/*statistics & numerical data ; Humans ; Orthopedic Procedures/economics/*methods/statistics & numerical data ; *Patient Compliance ; Qualitative Research ; }, abstract = {OBJECTIVES: To conduct a systematic synthesis of previous research to identify factors that affect treatment-seeking for clubfoot and community-level interventions to improve engagement in low- and middle-income counties.

METHODS: A search of five databases was conducted, and articles screened using six criteria. Quality was appraised using the Critical Appraisal Skills Programme checklist. Eleven studies were identified for inclusion. Analysis was informed by a social ecological model, which specifies five inter-related factors that may affect treatment-seeking: intrapersonal, interpersonal, institutional, community or socio-cultural factors and public policy.

RESULTS: Intrapersonal barriers experienced were a lack of income and additional responsibilities. At the interpersonal level, support from fathers, the extended family and wider community affected on treatment-seeking. Institutional or organisational factors included long distances to treatment centres, insufficient information about treatments and challenges following treatment. Guardians' beliefs about the causes of clubfoot shaped behaviour. At the level of public policy, two-tiered healthcare systems made it difficult for some groups to access timely care. Interventions to address these challenges included counselling sessions, outreach clinics, brace recycling and a range of education programmes.

CONCLUSIONS: This study identifies factors that affect access and engagement with clubfoot treatment across diverse settings and strategies to address them.}, } @article {pmid26890485, year = {2016}, author = {Greischar, MA and Mideo, N and Read, AF and Bjørnstad, ON}, title = {Quantifying Transmission Investment in Malaria Parasites.}, journal = {PLoS computational biology}, volume = {12}, number = {2}, pages = {e1004718}, pmid = {26890485}, issn = {1553-7358}, support = {R01 GM089932/GM/NIGMS NIH HHS/United States ; R01GM089932/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Computational Biology ; Erythrocytes/parasitology ; Female ; Life Cycle Stages ; Malaria/*parasitology/*transmission ; Male ; Mice ; Models, Biological ; Plasmodium chabaudi/*pathogenicity/*physiology ; }, abstract = {Many microparasites infect new hosts with specialized life stages, requiring a subset of the parasite population to forgo proliferation and develop into transmission forms. Transmission stage production influences infectivity, host exploitation, and the impact of medical interventions like drug treatment. Predicting how parasites will respond to public health efforts on both epidemiological and evolutionary timescales requires understanding transmission strategies. These strategies can rarely be observed directly and must typically be inferred from infection dynamics. Using malaria as a case study, we test previously described methods for inferring transmission stage investment against simulated data generated with a model of within-host infection dynamics, where the true transmission investment is known. We show that existing methods are inadequate and potentially very misleading. The key difficulty lies in separating transmission stages produced by different generations of parasites. We develop a new approach that performs much better on simulated data. Applying this approach to real data from mice infected with a single Plasmodium chabaudi strain, we estimate that transmission investment varies from zero to 20%, with evidence for variable investment over time in some hosts, but not others. These patterns suggest that, even in experimental infections where host genetics and other environmental factors are controlled, parasites may exhibit remarkably different patterns of transmission investment.}, } @article {pmid26888263, year = {2016}, author = {Hsieh, P and Veeramah, KR and Lachance, J and Tishkoff, SA and Wall, JD and Hammer, MF and Gutenkunst, RN}, title = {Whole-genome sequence analyses of Western Central African Pygmy hunter-gatherers reveal a complex demographic history and identify candidate genes under positive natural selection.}, journal = {Genome research}, volume = {26}, number = {3}, pages = {279-290}, pmid = {26888263}, issn = {1549-5469}, support = {8DP1ES022577-04/DP/NCCDPHP CDC HHS/United States ; R01 HG005226/HG/NHGRI NIH HHS/United States ; 1R01GM113657-01/GM/NIGMS NIH HHS/United States ; P30 ES013508/ES/NIEHS NIH HHS/United States ; F32HG006648/HG/NHGRI NIH HHS/United States ; R01 GM113657/GM/NIGMS NIH HHS/United States ; F32 HG006648/HG/NHGRI NIH HHS/United States ; DP1 ES022577/ES/NIEHS NIH HHS/United States ; }, mesh = {Adaptation, Biological ; Animals ; Black People/*genetics ; Computational Biology ; Computer Simulation ; Gene Flow ; Genetic Variation ; *Genetics, Population ; *Genome ; *Genomics ; High-Throughput Nucleotide Sequencing ; Humans ; Linkage Disequilibrium ; Models, Genetic ; Models, Statistical ; Pan paniscus/*genetics ; Reproducibility of Results ; *Selection, Genetic ; }, abstract = {African Pygmies practicing a mobile hunter-gatherer lifestyle are phenotypically and genetically diverged from other anatomically modern humans, and they likely experienced strong selective pressures due to their unique lifestyle in the Central African rainforest. To identify genomic targets of adaptation, we sequenced the genomes of four Biaka Pygmies from the Central African Republic and jointly analyzed these data with the genome sequences of three Baka Pygmies from Cameroon and nine Yoruba famers. To account for the complex demographic history of these populations that includes both isolation and gene flow, we fit models using the joint allele frequency spectrum and validated them using independent approaches. Our two best-fit models both suggest ancient divergence between the ancestors of the farmers and Pygmies, 90,000 or 150,000 yr ago. We also find that bidirectional asymmetric gene flow is statistically better supported than a single pulse of unidirectional gene flow from farmers to Pygmies, as previously suggested. We then applied complementary statistics to scan the genome for evidence of selective sweeps and polygenic selection. We found that conventional statistical outlier approaches were biased toward identifying candidates in regions of high mutation or low recombination rate. To avoid this bias, we assigned P-values for candidates using whole-genome simulations incorporating demography and variation in both recombination and mutation rates. We found that genes and gene sets involved in muscle development, bone synthesis, immunity, reproduction, cell signaling and development, and energy metabolism are likely to be targets of positive natural selection in Western African Pygmies or their recent ancestors.}, } @article {pmid26886349, year = {2016}, author = {Ujiié, Y and Ishitani, Y}, title = {Evolution of a Planktonic Foraminifer during Environmental Changes in the Tropical Oceans.}, journal = {PloS one}, volume = {11}, number = {2}, pages = {e0148847}, pmid = {26886349}, issn = {1932-6203}, mesh = {Bayes Theorem ; *Biological Evolution ; Confidence Intervals ; DNA, Ribosomal/genetics ; Databases, Genetic ; Foraminifera/*genetics ; Genetic Variation ; Geography ; *Oceans and Seas ; Phylogeny ; Time Factors ; *Tropical Climate ; }, abstract = {Ecological adaptation to environmental changes is a strong driver of evolution, enabling speciation of pelagic plankton in the open ocean without the presence of effective physical barriers to gene flow. The tropical ocean environment, which plays an important role in shaping marine biodiversity, has drastically and frequently changed since the Pliocene. Nevertheless, the evolutionary history of tropical pelagic plankton has been poorly understood, as phylogeographic investigations are still in the developing state and paleontological approaches are insufficient to obtain a sequential record from the deep-sea sediments. The planktonic foraminifer Pulleniatina obliquiloculata is widely distributed in the tropical area throughout the world's oceans, and its phylogeography is well established. It is thus one of the best candidates to examine how past environmental changes may have shifted the spatial distribution and affected the diversification of tropical pelagic plankton. Such an examination requires the divergence history of the planktonic foraminifers, yet the gene marker (partial small subunit (SSU) rDNA) previously used for phylogeographic studies was not powerful enough to achieve a high accuracy in estimating the divergence times. The present study focuses on improving the precision of divergence time estimates for the splits between sibling species (genetic types) of planktonic foraminifers by increasing the number of genes as well as the number of nucleotide bases used for molecular clock estimates. We have amplified the entire coding regions of two ribosomal RNA genes (SSU rDNA and large subunit (LSU) rDNA) of three genetic types of P. obliquiloculata and two closely related species for the first time and applied them to the Bayesian relaxed clock method. The comparison of the credible intervals of the four datasets consisting either of sequences of the partial SSU rDNA, the complete SSU rDNA, LSU rDNA, or a combination of both genes (SSU+LSU) clearly demonstrated that the two-gene dataset improved the accuracy of divergence time estimates. The P. obliquiloculata lineage diverged twice, first at the end of the Pliocene (3.1 Ma) and again in the middle Pleistocene (1.4 Ma). Both timings coincided with the environmental changes, which indirectly involved geographic separation of populations. The habitat of P. obliquiloculata was expanded toward the higher latitudinal zones during the stable warm periods and subsequently placed on the steep environmental gradients following the global cooling. Different environmental conditions in the stable warm tropics and unstable higher latitudes may have triggered ecological divergence among the populations, leading to adaptive differentiation and eventually speciation. A comprehensive analysis of divergence time estimates combined with phylogeography enabled us to reveal the evolutionary history of the pelagic plankton and to find the potential paleoenvironmental events, which could have changed their biogeography and ecology.}, } @article {pmid26883901, year = {2016}, author = {Ren, X and Yang, GL and Peng, WF and Zhao, YX and Zhang, M and Chen, ZH and Wu, FA and Kantanen, J and Shen, M and Li, MH}, title = {A genome-wide association study identifies a genomic region for the polycerate phenotype in sheep (Ovis aries).}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {21111}, pmid = {26883901}, issn = {2045-2322}, mesh = {Animals ; Computational Biology/methods ; *Genome ; *Genome-Wide Association Study ; *Genomics ; Haplotypes ; Horns ; Linkage Disequilibrium ; Molecular Sequence Annotation ; *Phenotype ; Polymorphism, Single Nucleotide ; Quality Control ; Sheep/*genetics ; }, abstract = {Horns are a cranial appendage found exclusively in Bovidae, and play important roles in accessing resources and mates. In sheep (Ovies aries), horns vary from polled to six-horned, and human have been selecting polled animals in farming and breeding. Here, we conducted a genome-wide association study on 24 two-horned versus 22 four-horned phenotypes in a native Chinese breed of Sishui Fur sheep. Together with linkage disequilibrium (LD) analyses and haplotype-based association tests, we identified a genomic region comprising 132.0-133.1 Mb on chromosome 2 that contained the top 10 SNPs (including 4 significant SNPs) and 5 most significant haplotypes associated with the polycerate phenotype. In humans and mice, this genomic region contains the HOXD gene cluster and adjacent functional genes EVX2 and KIAA1715, which have a close association with the formation of limbs and genital buds. Our results provide new insights into the genetic basis underlying variable numbers of horns and represent a new resource for use in sheep genetics and breeding.}, } @article {pmid26881995, year = {2016}, author = {Hu, XG and Liu, H and Jin, Y and Sun, YQ and Li, Y and Zhao, W and El-Kassaby, YA and Wang, XR and Mao, JF}, title = {De Novo Transcriptome Assembly and Characterization for the Widespread and Stress-Tolerant Conifer Platycladus orientalis.}, journal = {PloS one}, volume = {11}, number = {2}, pages = {e0148985}, pmid = {26881995}, issn = {1932-6203}, mesh = {Adaptation, Physiological/genetics ; Alkyl and Aryl Transferases/genetics/*metabolism ; Databases, Genetic ; Gene Expression Profiling ; *Genes, Plant ; High-Throughput Nucleotide Sequencing ; Microsatellite Repeats ; Molecular Sequence Annotation ; Phylogeny ; RNA, Messenger/genetics/metabolism ; Stress, Physiological ; Tracheophyta/classification/genetics ; *Transcriptome ; }, abstract = {Platycladus orientalis, of the family Cupressaceae, is a widespread conifer throughout China and is extensively used for ecological reforestation, horticulture, and in medicine. Transcriptome assemblies are required for this ecologically important conifer for understanding genes underpinning adaptation and complex traits for breeding programs. To enrich the species' genomic resources, a de novo transcriptome sequencing was performed using Illumina paired-end sequencing. In total, 104,073,506 high quality sequence reads (approximately 10.3 Gbp) were obtained, which were assembled into 228,948 transcripts and 148,867 unigenes that were longer than 200 nt. Quality assessment using CEGMA showed that the transcriptomes obtained were mostly complete for highly conserved core eukaryotic genes. Based on similarity searches with known proteins, 62,938 (42.28% of all unigenes), 42,158 (28.32%), and 23,179 (15.57%) had homologs in the Nr, GO, and KOG databases, 25,625 (17.21%) unigenes were mapped to 322 pathways by BLASTX comparison against the KEGG database and 1,941 unigenes involved in environmental signaling and stress response were identified. We also identified 43 putative terpene synthase (TPS) functional genes loci and compared them with TPSs from other species. Additionally, 5,296 simple sequence repeats (SSRs) were identified in 4,715 unigenes, which were assigned to 142 motif types. This is the first report of a complete transcriptome analysis of P. orientalis. These resources provide a foundation for further studies of adaptation mechanisms and molecular-based breeding programs.}, } @article {pmid26881957, year = {2016}, author = {Liu, S and Molenaar, P}, title = {Testing for Granger Causality in the Frequency Domain: A Phase Resampling Method.}, journal = {Multivariate behavioral research}, volume = {51}, number = {1}, pages = {53-66}, doi = {10.1080/00273171.2015.1100528}, pmid = {26881957}, issn = {1532-7906}, mesh = {Algorithms ; Brain/physiology ; Child ; Clinical Studies as Topic ; Computer Simulation ; Data Interpretation, Statistical ; Electroencephalography/methods ; Galvanic Skin Response ; Humans ; Male ; *Multivariate Analysis ; Nonlinear Dynamics ; Normal Distribution ; Occupational Therapy ; Perceptual Disorders/physiopathology/therapy ; Signal Processing, Computer-Assisted ; }, abstract = {This article introduces phase resampling, an existing but rarely used surrogate data method for making statistical inferences of Granger causality in frequency domain time series analysis. Granger causality testing is essential for establishing causal relations among variables in multivariate dynamic processes. However, testing for Granger causality in the frequency domain is challenging due to the nonlinear relation between frequency domain measures (e.g., partial directed coherence, generalized partial directed coherence) and time domain data. Through a simulation study, we demonstrate that phase resampling is a general and robust method for making statistical inferences even with short time series. With Gaussian data, phase resampling yields satisfactory type I and type II error rates in all but one condition we examine: when a small effect size is combined with an insufficient number of data points. Violations of normality lead to slightly higher error rates but are mostly within acceptable ranges. We illustrate the utility of phase resampling with two empirical examples involving multivariate electroencephalography (EEG) and skin conductance data.}, } @article {pmid26881428, year = {2016}, author = {Vanselow, KA and Samimi, C and Breckle, SW}, title = {Preserving a Comprehensive Vegetation Knowledge Base--An Evaluation of Four Historical Soviet Vegetation Maps of the Western Pamirs (Tajikistan).}, journal = {PloS one}, volume = {11}, number = {2}, pages = {e0148930}, pmid = {26881428}, issn = {1932-6203}, mesh = {Astragalus Plant/classification ; *Ecosystem ; Forests ; *Geological Phenomena ; Humans ; Knowledge Bases ; Poaceae/*classification ; Tajikistan ; Trees/*classification ; Water Supply ; }, abstract = {We edited, redrew, and evaluated four unpublished historical vegetation maps of the Western Pamirs (Tajikistan) by the Soviet geobotanist Okmir E. Agakhanjanz. These maps cover an area of 5,188 km2 and date from 1958 to 1960. The purpose of this article is to make the historic vegetation data available to the scientific community and thus preserve a hitherto non available and up to now neglected or forgotten data source with great potential for studies on vegetation and ecosystem response to global change. The original hand-drawn maps were scanned, georeferenced, and digitized and the corresponding land cover class was assigned to each polygon. The partly differing legends were harmonized and plant names updated. Furthermore, a digital elevation model and generalized additive models were used to calculate response curves of the land cover classes and to explore vegetation-topography relationships quantitatively. In total, 2,216 polygons belonging to 13 major land cover classes were included that are characterized by 252 different plant species. As such, the presented maps provide excellent comparison data for studies on vegetation and ecosystem change in an area that is deemed to be an important water tower in Central Asia.}, } @article {pmid26880736, year = {2016}, author = {Nicholson, JM and Kellar, LC and Ahmad, S and Abid, A and Woloski, J and Hewamudalige, N and Henning, GF and Lauring, JR and Ural, SH and Yaklic, JL}, title = {US term stillbirth rates and the 39-week rule: a cause for concern?.}, journal = {American journal of obstetrics and gynecology}, volume = {214}, number = {5}, pages = {621.e1-9}, doi = {10.1016/j.ajog.2016.02.019}, pmid = {26880736}, issn = {1097-6868}, mesh = {Cesarean Section/statistics & numerical data ; Databases, Factual ; Female ; *Gestational Age ; *Health Policy ; Humans ; Labor, Induced/statistics & numerical data ; Pregnancy ; Stillbirth/*epidemiology ; Term Birth ; Time Factors ; United States/epidemiology ; }, abstract = {BACKGROUND: More than a decade ago an obstetric directive called "the 39-week rule" sought to limit "elective" delivery, via labor induction or cesarean delivery, before 39 weeks 0 days of gestation. In 2010 the 39-week rule became a formal quality measure in the United States. The progressive adherence to the 39-week rule throughout the United States has caused a well-documented, progressive reduction in the proportion of term deliveries occurring during the early-term period. Because of the known association between increasing gestational age during the term period and increasing cumulative risk of stillbirth, however, there have been published concerns that the 39-week rule-by increasing the gestational age of delivery for a substantial number of pregnancies-might increase the rate of term stillbirth within the United States. Although adherence to the 39-week rule is assumed to be beneficial, its actual impact on the US rate of term stillbirth in the years since 2010 is unknown.

OBJECTIVE: To determine whether the adoption of the 39-week rule was associated with an increased rate of term stillbirth in the United States.

STUDY DESIGN: Sequential ecological study, based on state data, of US term deliveries that occurred during a 7-year period bounded by 2007 and 2013. The patterns of the timing of both term childbirth and term stillbirth were determined for each state and for the United States as a whole.

RESULTS: A total of 46 usable datasets were obtained (45 states and the District of Columbia). During the 7-year period, there was a continuous reduction in all geographic entities in the proportion of term deliveries that occurred before 39 weeks of gestation. The overall rate of term stillbirth, when we compared 2007-2009 with 2011-2013, increased significantly (1.103/1000 vs 1.177/1000, RR 1.067, 95% confidence interval 1.038-1.096). Furthermore, during the 7-year period, the increase in the rate of US term stillbirth appeared to be continuous (estimated slope: 0.0186/1000/year, 95% confidence interval 0.002-0.035). Assuming 3.5 million term US births per year, and given 6 yearly "intervals" with this rate increase, it is possible that more than 335 additional term stillbirths occurred in the United States in 2013 as compared with 2007. In addition, during the 7-year period, there was a progressive shift in the timing of delivery from the 40th week to the 39th week. Absent this confounding factor, the magnitude of association between the adoption of the 39-week rule and the increase in rate of term stillbirth might have been greater.

CONCLUSIONS: Between 2007 and 2013 in the United States, the adoption of the 39-week rule caused a progressive reduction in the proportion of term births occurring before the 39th week of gestation. During the same interval the United States experienced a significant increase in its rate of term stillbirth. This study raises the possibility that the 39-week rule may be causing unintended harm. Additional studies of the actual impact of the adoption of the 39-week rule on major childbirth outcomes are urgently needed. Pressures to enforce the 39-week rule should be reconsidered pending the findings of such studies.}, } @article {pmid26879116, year = {2016}, author = {Glonti, K and Mackenbach, JD and Ng, J and Lakerveld, J and Oppert, JM and Bárdos, H and McKee, M and Rutter, H}, title = {Psychosocial environment: definitions, measures and associations with weight status--a systematic review.}, journal = {Obesity reviews : an official journal of the International Association for the Study of Obesity}, volume = {17 Suppl 1}, number = {}, pages = {81-95}, doi = {10.1111/obr.12383}, pmid = {26879116}, issn = {1467-789X}, mesh = {*Body Weight ; Databases, Factual ; Environment Design ; Health Behavior ; Health Status ; Humans ; Obesity/*psychology ; Risk Assessment ; *Social Environment ; Socioeconomic Factors ; }, abstract = {Socio-ecological models suggest that many elements of the social environment act as upstream determinants of obesity. This systematic review examined definitions, measures and strength of associations between the psychosocial environment and adult weight status. Studies were included if they were conducted on adults, the outcome was weight status, carried out in any developed country and investigated at least one psychosocial environmental construct. Six databases for primary studies were searched: EMBASE, MEDLINE, PsycINFO, Scopus, Web of Science and the Cochrane Library. We restricted our search to studies published in English between January 1995 and February 2015. An adapted 'Quality Assessment Tool for Quantitative Studies' was used to evaluate risk of bias of included studies. Out of 14,784 screened records, 42 articles were assessed using full text. A total of 19 studies were included. The strongest associations with weight status were found for social capital and collective efficacy, although few studies found significant associations. There was heterogeneity in the definitions and metrics of psychosocial environmental constructs. There is limited evidence that greater social capital and collective efficacy are associated with healthier weight status. The research conducted to date has not robustly identified relations. We highlight challenges to undertaking research and establishing causality in this field and provide recommendations for further research.}, } @article {pmid26879048, year = {2016}, author = {Zondag, LE and Rutherford, K and Gemmell, NJ and Wilson, MJ}, title = {Uncovering the pathways underlying whole body regeneration in a chordate model, Botrylloides leachi using de novo transcriptome analysis.}, journal = {BMC genomics}, volume = {17}, number = {}, pages = {114}, pmid = {26879048}, issn = {1471-2164}, mesh = {Animals ; Chordata/*physiology ; Computational Biology/methods ; *Gene Expression Profiling ; *Gene Expression Regulation ; High-Throughput Nucleotide Sequencing ; Phenotype ; Protein Biosynthesis ; Regeneration/*genetics ; Reproducibility of Results ; *Signal Transduction ; *Transcriptome ; }, abstract = {BACKGROUND: Regenerative capacity differs greatly between animals. In vertebrates regenerative abilities are highly limited and tissue or organ specific. However the closest related chordate to the vertebrate clade, Botrylloides leachi, can undergo whole body regeneration (WBR). Therefore, research on WBR in B. leachi has focused on pathways known to be important for regeneration in vertebrates. To obtain a comprehensive vision of this unique process we have carried out the first de novo transcriptome sequencing for multiple stages of WBR occurring in B. leachi. The identified changes in gene expression during B. leachi WBR offer novel insights into this remarkable ability to regenerate.

RESULTS: The transcriptome of B. leachi tissue undergoing WBR were analysed using differential gene expression, gene ontology and pathway analyses. We observed up-regulation in the expression of genes involved in wound healing and known developmental pathways including WNT, TGF-β and Notch, during the earliest stages of WBR. Later in WBR, the expression patterns in several pathways required for protein synthesis, biogenesis and the organisation of cellular components were up-regulated.

CONCLUSIONS: While the genes expressed early on are characteristic of a necessary wound healing response to an otherwise lethal injury, the subsequent vast increase in protein synthesis conceivably sustains the reestablishment of the tissue complexity and body axis polarity within the regenerating zooid. We have, for the first time, provided a global overview of the genes and their corresponding pathways that are modulated during WBR in B. leachi.}, } @article {pmid26877677, year = {2016}, author = {Martellos, S and Ukosich, L and Avian, M}, title = {JellyWeb: an interactive information system on Scyphozoa, Cubozoa and Staurozoa.}, journal = {ZooKeys}, volume = {}, number = {554}, pages = {1-25}, pmid = {26877677}, issn = {1313-2989}, abstract = {Identification of organisms is traditionally based on the use of "classic" identification keys, normally printed on paper. These keys have several drawbacks: they are mainly based on the systematics, requiring identification of orders, families and genera at first; they are written by experts for other experts, in a specific scientific jargon; they have a "frozen" structure (sequence of theses/antitheses); once published, they cannot be changed or updated without printing a new edition. Due to the use of computers, it is now possible to build new digital identification tools, which: 1) can be produced automatically, if the characters are stored in a database; 2) can be freed from the traditional systematics, giving priority to easy-to-observe characters, incl. those usually uncommon to the classical keys, such as ecology and distribution; 3) can be updated in real time once published on-line; 4) can be available on different media, and on mobile devices. An important feature of these new digital tools is their "collaborative" nature. They can be enriched by the contribution of several researchers, which can cooperate while maintaining rights and property of the resources and data they contribute to the system. JellyWeb, the information system on Scyphozoa, Cubozoa and Staurozoa has been developed in Trieste since 2010. The system was created with the aim of - potentially - becoming a starting point for a wide collaborative effort in developing a user-friendly worldwide digital identification system for jellyfishes.}, } @article {pmid26876925, year = {2016}, author = {Adamík, P and Emmenegger, T and Briedis, M and Gustafsson, L and Henshaw, I and Krist, M and Laaksonen, T and Liechti, F and Procházka, P and Salewski, V and Hahn, S}, title = {Barrier crossing in small avian migrants: individual tracking reveals prolonged nocturnal flights into the day as a common migratory strategy.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {21560}, pmid = {26876925}, issn = {2045-2322}, mesh = {Africa, Northern ; Animal Migration/*physiology ; Animals ; Breeding ; Flight, Animal/*physiology ; Geographic Information Systems ; Mediterranean Sea ; Songbirds/*physiology ; }, abstract = {Over decades it has been unclear how individual migratory songbirds cross large ecological barriers such as seas or deserts. By deploying light-level geolocators on four songbird species weighing only about 12 g, we found that these otherwise mainly nocturnal migrants seem to regularly extend their nocturnal flights into the day when crossing the Sahara Desert and the Mediterranean Sea. The proportion of the proposed diurnally flying birds gradually declined over the day with similar landing patterns in autumn and spring. The prolonged flights were slightly more frequent in spring than in autumn, suggesting tighter migratory schedules when returning to breeding sites. Often we found several patterns for barrier crossing for the same individual in autumn compared to the spring journey. As only a small proportion of the birds flew strictly during the night and even some individuals might have flown non-stop, we suggest that prolonged endurance flights are not an exception even in small migratory species. We emphasise an individual's ability to perform both diurnal and nocturnal migration when facing the challenge of crossing a large ecological barrier to successfully complete a migratory journey.}, } @article {pmid26875912, year = {2016}, author = {Breen, M and Villeneuve, DL and Ankley, GT and Bencic, D and Breen, MS and Watanabe, KH and Lloyd, AL and Conolly, RB}, title = {Computational model of the fathead minnow hypothalamic-pituitary-gonadal axis: Incorporating protein synthesis in improving predictability of responses to endocrine active chemicals.}, journal = {Comparative biochemistry and physiology. Toxicology & pharmacology : CBP}, volume = {183-184}, number = {}, pages = {36-45}, doi = {10.1016/j.cbpc.2016.02.002}, pmid = {26875912}, issn = {1532-0456}, mesh = {Animals ; Aromatase/chemistry/genetics/*metabolism ; Aromatase Inhibitors/administration & dosage/toxicity ; Computational Biology ; Cyprinidae/blood/growth & development/*physiology ; Dose-Response Relationship, Drug ; Endocrine Disruptors/administration & dosage/*toxicity ; Estradiol/blood ; Fadrozole/administration & dosage/toxicity ; Female ; Fish Proteins/agonists/antagonists & inhibitors/genetics/metabolism ; Gene Expression Regulation, Developmental/*drug effects ; Hypothalamo-Hypophyseal System/*drug effects/metabolism ; Male ; *Models, Biological ; Ovary/*drug effects/enzymology/metabolism ; RNA, Messenger/metabolism ; Random Allocation ; Reproducibility of Results ; Testis/drug effects/metabolism ; Toxicity Tests/methods ; Water Pollutants, Chemical/administration & dosage/toxicity ; }, abstract = {There is international concern about chemicals that alter endocrine system function in humans and/or wildlife and subsequently cause adverse effects. We previously developed a mechanistic computational model of the hypothalamic-pituitary-gonadal (HPG) axis in female fathead minnows exposed to a model aromatase inhibitor, fadrozole (FAD), to predict dose-response and time-course behaviors for apical reproductive endpoints. Initial efforts to develop a computational model describing adaptive responses to endocrine stress providing good fits to empirical plasma 17β-estradiol (E2) data in exposed fish were only partially successful, which suggests that additional regulatory biology processes need to be considered. In this study, we addressed short-comings of the previous model by incorporating additional details concerning CYP19A (aromatase) protein synthesis. Predictions based on the revised model were evaluated using plasma E2 concentrations and ovarian cytochrome P450 (CYP) 19A aromatase mRNA data from two fathead minnow time-course experiments with FAD, as well as from a third 4-day study. The extended model provides better fits to measured E2 time-course concentrations, and the model accurately predicts CYP19A mRNA fold changes and plasma E2 dose-response from the 4-d concentration-response study. This study suggests that aromatase protein synthesis is an important process in the biological system to model the effects of FAD exposure.}, } @article {pmid26875497, year = {2016}, author = {Sørhus, E and Incardona, JP and Furmanek, T and Jentoft, S and Meier, S and Edvardsen, RB}, title = {Developmental transcriptomics in Atlantic haddock: Illuminating pattern formation and organogenesis in non-model vertebrates.}, journal = {Developmental biology}, volume = {411}, number = {2}, pages = {301-313}, doi = {10.1016/j.ydbio.2016.02.012}, pmid = {26875497}, issn = {1095-564X}, mesh = {Animals ; Blastula/physiology ; Body Patterning ; Bone and Bones/embryology ; Cardiovascular System/embryology ; Computational Biology ; Eye/embryology ; Fishes/*physiology ; Gene Expression Profiling ; *Gene Expression Regulation, Developmental ; Gene Library ; Larva/physiology ; Organogenesis/genetics ; RNA, Messenger/metabolism ; Sequence Analysis, RNA ; Skull/embryology ; *Transcriptome ; }, abstract = {Gadiforms such as Atlantic haddock comprise some of the world's most economically important fisheries. Understanding the early life history of these fish is a prerequisite for predicting effects of a changing environment and increased human activities. Robust assessment of the effects of environmental impacts on the embryos of non-model vertebrates is hampered by a lack of molecular resources and detailed knowledge regarding the regulation of genes and pathways in early development. Here we used mRNA sequencing to link transcriptional changes to developmental processes in haddock, specifically, pattern formation and organogenesis. Temporal expression of key developmental genes was tightly anchored to either the appearance of visible structures or cellular processes characterised in model organisms. These findings demonstrate the high potential of developmental transcriptomics as an analytical tool for improved understanding of pathophysiological mechanisms leading to abnormal development in any vertebrate.}, } @article {pmid26874833, year = {2016}, author = {La Torre, G and Mipatrini, D}, title = {Country-level correlates of e-cigarette use in the European Union.}, journal = {International journal of public health}, volume = {61}, number = {2}, pages = {269-275}, pmid = {26874833}, issn = {1661-8564}, mesh = {Adult ; Databases, Factual ; Electronic Nicotine Delivery Systems/*statistics & numerical data ; Europe/epidemiology ; Health Status ; Humans ; Middle Aged ; Prevalence ; Smoking/*epidemiology ; Smoking Cessation/methods ; Social Class ; }, abstract = {OBJECTIVES: The aim of this study was to assess the relationship between the prevalence of e-cigarette use and country-level factors across 28 European countries.

METHODS: The study objectives were addressed in an ecological design in which both exposures and outcomes were measured at the country level. Data from the Eurobarometer Report, the Eurostat database and the WHO observatory were analyzed. Bivariate and multivariate analyses were performed considering the rates of current and ever smokers of e-cigarettes as dependent variables, and socio-economic factors, health status and policies against tobacco as independent variables.

RESULTS: Both the rate of current smokers and ever smokers of e-cigarette were positively associated to the offer of help to quit tobacco use (P < 0.01; P = 0.04) and to the raise of taxes on tobacco (P = 0.01; P = 0.01). The warn on dangers of tobacco negatively correlated with the rate of e-cigarette current smokers. The rate of current e-cigarette smokers correlated with the rate of current smokers and with national Gross Domestic Product, while the rate of ever e-cigarette smokers did not correlate with any socio-economic factor.

CONCLUSIONS: Our analysis suggests that both policy and non-policy factors are associated with the geographical variability seen in the prevalence of e-cigarette use. Policies against the consumption of conventional tobacco products may lead to an increase of e-cigarette smokers.}, } @article {pmid26871936, year = {2016}, author = {Jovic, D and Vukovic, D and Marinkovic, J}, title = {Prevalence and Patterns of Multi-Morbidity in Serbian Adults: A Cross-Sectional Study.}, journal = {PloS one}, volume = {11}, number = {2}, pages = {e0148646}, pmid = {26871936}, issn = {1932-6203}, mesh = {Adult ; Age Factors ; Aged ; Aged, 80 and over ; Cardiovascular Diseases/*epidemiology ; Comorbidity ; Cross-Sectional Studies ; Female ; Health Surveys ; Humans ; Lung Diseases/*epidemiology ; Male ; Mental Disorders/*epidemiology ; Metabolic Diseases/*epidemiology ; Middle Aged ; Musculoskeletal Diseases/*epidemiology ; Prevalence ; Serbia/epidemiology ; Sex Factors ; }, abstract = {INTRODUCTION: Like many developing countries, Serbia is facing a growing burden of chronic diseases. Within such public health issue, multi-morbidity requires a special attention.

AIMS: This study investigated the prevalence of multi-morbidity in the Serbia population and assessed the co-occurrence of chronic diseases by age and gender.

METHODS: We analyzed data from the 2013 National Health Survey, which included 13,103 individuals ≥ 20 years old. Multi-morbidity patterns were identified by exploratory factor analysis of data on self-reported chronic diseases, as well as data on measured body weight and height. The analysis was stratified by age and gender.

RESULTS: Multi-morbidity was present in nearly one-third of respondents (26.9%) and existed in all age groups, with the highest prevalence among individuals aged 65 years and older (47.2% of men and 65.0% of women). Six patterns of multi-morbidity were identified: non-communicable, cardio-metabolic, respiratory, cardiovascular, aggregate, and mechanical/mental/metabolic. The non-communicable pattern was observed in both genders but only in the 20-44 years age group, while the aggregate pattern occurred only in middle-aged men. Cardio-metabolic and respiratory patterns were present in all age groups. Cardiovascular and mechanical/mental/metabolic patterns showed similar presentation in both men and women.

CONCLUSIONS: Multi-morbidity is a common occurrence among adults in Serbia, especially in the elderly. While several patterns may be explained by underlying pathophysiologies, some require further investigation and follow-up. Recognizing the complexity of multi-morbidity in Serbia is of great importance from both clinical and preventive perspectives given that it affects one-third of the population and may require adjustment of the healthcare system to address the needs of affected individuals.}, } @article {pmid26871574, year = {2016}, author = {Pease, JB and Haak, DC and Hahn, MW and Moyle, LC}, title = {Phylogenomics Reveals Three Sources of Adaptive Variation during a Rapid Radiation.}, journal = {PLoS biology}, volume = {14}, number = {2}, pages = {e1002379}, pmid = {26871574}, issn = {1545-7885}, mesh = {*Genetic Speciation ; Genomics ; Solanum lycopersicum/*genetics ; Polymorphism, Genetic ; }, abstract = {Speciation events often occur in rapid bursts of diversification, but the ecological and genetic factors that promote these radiations are still much debated. Using whole transcriptomes from all 13 species in the ecologically and reproductively diverse wild tomato clade (Solanum sect. Lycopersicon), we infer the species phylogeny and patterns of genetic diversity in this group. Despite widespread phylogenetic discordance due to the sorting of ancestral variation, we date the origin of this radiation to approximately 2.5 million years ago and find evidence for at least three sources of adaptive genetic variation that fuel diversification. First, we detect introgression both historically between early-branching lineages and recently between individual populations, at specific loci whose functions indicate likely adaptive benefits. Second, we find evidence of lineage-specific de novo evolution for many genes, including loci involved in the production of red fruit color. Finally, using a "PhyloGWAS" approach, we detect environment-specific sorting of ancestral variation among populations that come from different species but share common environmental conditions. Estimated across the whole clade, small but substantial and approximately equal fractions of the euchromatic portion of the genome are inferred to contribute to each of these three sources of adaptive genetic variation. These results indicate that multiple genetic sources can promote rapid diversification and speciation in response to new ecological opportunity, in agreement with our emerging phylogenomic understanding of the complexity of both ancient and recent species radiations.}, } @article {pmid26870828, year = {2016}, author = {Hua, X and Goedert, JJ and Pu, A and Yu, G and Shi, J}, title = {Allergy associations with the adult fecal microbiota: Analysis of the American Gut Project.}, journal = {EBioMedicine}, volume = {3}, number = {}, pages = {172-179}, pmid = {26870828}, issn = {2352-3964}, support = {ZIA CP010214//Intramural NIH HHS/United States ; ZIA-CP-010214/CP/NCI NIH HHS/United States ; }, mesh = {Adult ; Aged ; Biodiversity ; Databases, Nucleic Acid ; Feces/*microbiology ; Female ; *Gastrointestinal Microbiome ; Humans ; Hypersensitivity/*epidemiology/*etiology ; Male ; Metagenome ; Metagenomics/methods ; Middle Aged ; Odds Ratio ; RNA, Ribosomal, 16S/genetics ; Risk ; Surveys and Questionnaires ; }, abstract = {BACKGROUND: Alteration of the gut microbial population (dysbiosis) may increase the risk for allergies and other conditions. This study sought to clarify the relationship of dysbiosis with allergies in adults.

METHODS: Publicly available American Gut Project questionnaire and fecal 16S rRNA sequence data were analyzed. Fecal microbiota richness (number of observed species) and composition (UniFrac) were used to compare adults with versus without allergy to foods (peanuts, tree nuts, shellfish, other) and non-foods (drug, bee sting, dander, asthma, seasonal, eczema). Logistic and Poisson regression models adjusted for potential confounders. Odds ratios and 95% confidence intervals (CI) were calculated for lowest vs highest richness tertile. Taxonomy associations considered 122 non-redundant taxa (of 2379 total taxa) with ≥ 0.1% mean abundance.

RESULTS: Self-reported allergy prevalence among the 1879 participants (mean age, 45.5 years; 46.9% male) was 81.5%, ranging from 2.5% for peanuts to 40.5% for seasonal. Fecal microbiota richness was markedly lower with total allergies (P = 10(-9)) and five particular allergies (P ≤ 10(-4)). Richness odds ratios were 1.7 (CI 1.3-2.2) with seasonal, 1.8 (CI 1.3-2.5) with drug, and 7.8 (CI 2.3-26.5) with peanut allergy. These allergic participants also had markedly altered microbial community composition (unweighted UniFrac, P = 10(-4) to 10(-7)). Total food and non-food allergies were significantly associated with 7 and 9 altered taxa, respectively. The dysbiosis was most marked with nut and seasonal allergies, driven by higher Bacteroidales and reduced Clostridiales taxa.

INTERPRETATION: American adults with allergies, especially to nuts and seasonal pollen, have low diversity, reduced Clostridiales, and increased Bacteroidales in their gut microbiota. This dysbiosis might be targeted to improve treatment or prevention of allergy.}, } @article {pmid26867790, year = {2016}, author = {Gilarranz, LJ and Mora, C and Bascompte, J}, title = {Anthropogenic effects are associated with a lower persistence of marine food webs.}, journal = {Nature communications}, volume = {7}, number = {}, pages = {10737}, pmid = {26867790}, issn = {2041-1723}, mesh = {Animals ; *Biomass ; Caribbean Region ; Conservation of Natural Resources ; *Ecosystem ; Fisheries ; Fishes ; *Food Chain ; Geographic Information Systems ; *Human Activities ; Humans ; Linear Models ; Models, Theoretical ; *Oceans and Seas ; Zooplankton ; }, abstract = {Marine coastal ecosystems are among the most exposed to global environmental change, with reported effects on species biomass, species richness and length of trophic chains. By combining a biologically informed food-web model with information on anthropogenic influences in 701 sites across the Caribbean region, we show that fishing effort, human density and thermal stress anomaly are associated with a decrease in local food-web persistence. The conservation status of the site, in turn, is associated with an increase in food-web persistence. Some of these associations are explained through effects on food-web structure and total community biomass. Our results unveil a hidden footprint of human activities. Even when food webs may seem healthy in terms of the presence and abundance of their constituent species, they may be losing the capacity to withstand further environmental degradation.}, } @article {pmid26867599, year = {2016}, author = {Wang, P and Zhang, B and Duan, G and Wang, Y and Hong, L and Wang, L and Guo, X and Xi, Y and Yang, H}, title = {Bioinformatics analyses of Shigella CRISPR structure and spacer classification.}, journal = {World journal of microbiology & biotechnology}, volume = {32}, number = {3}, pages = {38}, pmid = {26867599}, issn = {1573-0972}, mesh = {*Clustered Regularly Interspaced Short Palindromic Repeats ; *Computational Biology ; DNA, Bacterial/*genetics ; Shigella/*genetics ; }, abstract = {Clustered regularly interspaced short palindromic repeats (CRISPR) are inheritable genetic elements of a variety of archaea and bacteria and indicative of the bacterial ecological adaptation, conferring acquired immunity against invading foreign nucleic acids. Shigella is an important pathogen for anthroponosis. This study aimed to analyze the features of Shigella CRISPR structure and classify the spacers through bioinformatics approach. Among 107 Shigella, 434 CRISPR structure loci were identified with two to seven loci in different strains. CRISPR-Q1, CRISPR-Q4 and CRISPR-Q5 were widely distributed in Shigella strains. Comparison of the first and last repeats of CRISPR1, CRISPR2 and CRISPR3 revealed several base variants and different stem-loop structures. A total of 259 cas genes were found among these 107 Shigella strains. The cas gene deletions were discovered in 88 strains. However, there is one strain that does not contain cas gene. Intact clusters of cas genes were found in 19 strains. From comprehensive analysis of sequence signature and BLAST and CRISPRTarget score, the 708 spacers were classified into three subtypes: Type I, Type II and Type III. Of them, Type I spacer referred to those linked with one gene segment, Type II spacer linked with two or more different gene segments, and Type III spacer undefined. This study examined the diversity of CRISPR/cas system in Shigella strains, demonstrated the main features of CRISPR structure and spacer classification, which provided critical information for elucidation of the mechanisms of spacer formation and exploration of the role the spacers play in the function of the CRISPR/cas system.}, } @article {pmid26867156, year = {2016}, author = {Liu, S and Zhou, Y and Palumbo, R and Wang, JL}, title = {Dynamical correlation: A new method for quantifying synchrony with multivariate intensive longitudinal data.}, journal = {Psychological methods}, volume = {21}, number = {3}, pages = {291-308}, doi = {10.1037/met0000071}, pmid = {26867156}, issn = {1939-1463}, mesh = {Data Interpretation, Statistical ; Humans ; *Longitudinal Studies ; *Models, Statistical ; *Multivariate Analysis ; }, abstract = {In this article, we introduce dynamical correlation, a new method for quantifying synchrony between 2 variables with intensive longitudinal data. Dynamical correlation is a functional data analysis technique developed to measure the similarity of 2 curves. It has advantages over existing methods for studying synchrony, such as multilevel modeling. In particular, it is a nonparametric approach that does not require a prespecified functional form, and it places no assumption on homogeneity of the sample. Dynamical correlation can be easily estimated with irregularly spaced observations and tested to draw population-level inferences. We illustrate this flexible statistical technique with a simulation example and empirical data from an experiment examining interpersonal physiological synchrony between romantic partners. We discuss the advantages and limitations of the method, and how it can be extended and applied in psychological research. We also provide a set of R code for other researchers to estimate and test for dynamical correlation. (PsycINFO Database Record}, } @article {pmid26866806, year = {2016}, author = {Gibson, TE and Bashan, A and Cao, HT and Weiss, ST and Liu, YY}, title = {On the Origins and Control of Community Types in the Human Microbiome.}, journal = {PLoS computational biology}, volume = {12}, number = {2}, pages = {e1004688}, pmid = {26866806}, issn = {1553-7358}, support = {R01 HL091528/HL/NHLBI NIH HHS/United States ; }, mesh = {Algorithms ; Cluster Analysis ; Computational Biology ; Humans ; *Microbiota ; *Models, Biological ; }, abstract = {Microbiome-based stratification of healthy individuals into compositional categories, referred to as "enterotypes" or "community types", holds promise for drastically improving personalized medicine. Despite this potential, the existence of community types and the degree of their distinctness have been highly debated. Here we adopted a dynamic systems approach and found that heterogeneity in the interspecific interactions or the presence of strongly interacting species is sufficient to explain community types, independent of the topology of the underlying ecological network. By controlling the presence or absence of these strongly interacting species we can steer the microbial ecosystem to any desired community type. This open-loop control strategy still holds even when the community types are not distinct but appear as dense regions within a continuous gradient. This finding can be used to develop viable therapeutic strategies for shifting the microbial composition to a healthy configuration.}, } @article {pmid26865391, year = {2016}, author = {Maksimović, MŽ and Gudelj Rakić, JM and Vlajinac, HD and Vasiljević, ND and Nikić, MI and Marinković, JM}, title = {Comparison of different anthropometric measures in the adult population in Serbia as indicators of obesity: data from the National Health Survey 2013.}, journal = {Public health nutrition}, volume = {19}, number = {12}, pages = {2246-2255}, pmid = {26865391}, issn = {1475-2727}, mesh = {Adiposity ; Adult ; Aged ; Anthropometry/*methods ; Body Mass Index ; Cardiovascular Diseases ; Cross-Sectional Studies ; Female ; Health Surveys ; Humans ; Male ; Middle Aged ; Obesity/*epidemiology ; Overweight/*epidemiology ; Risk Factors ; Serbia/epidemiology ; }, abstract = {OBJECTIVE: The present study aimed to compare different indicators of obesity in the Serbian adult population.

DESIGN: Cross-sectional study. A stratified, two-stage, national-representative random sampling approach was used for the selection of the survey sample. Data sources were questionnaires created according to the European Health Interview Survey questionnaire. Measurements of weight, height and waist circumference (WC) were performed using standard procedures. Anthropometric measures included BMI, WC and waist-to-height ratio (WHtR).

SETTING: Data for the study were obtained from the 2013 National Health Survey, performed in line with the EUROSTAT recommendations for performance of the European Health Interview Survey.

SUBJECTS: Adults aged ≥20 years.

RESULTS: According to BMI, out of the whole studied population (12 460 adults of both sexes) 2·4 % were underweight, 36·4 % overweight and 22·4 % obese. Using WC and WHtR as measures of adiposity showed that 22·5 % and 42·8 % of participants were overweight and 39·8 % and 25·3 % were obese, respectively. Men and women differed significantly in all variables observed. Overweight was more frequent in men and obesity in women regardless of adiposity measure used.

CONCLUSIONS: In spite of strong correlations between BMI, WC and WHtR, substantial discrepancies between these three measures in the assessment of overweight and obesity were found, especially in some age groups. Which of these anthropometric measures should be used, or whether two or all three of them should be applied, depends on their associations with cardiovascular or some other disease of interest.}, } @article {pmid26863516, year = {2016}, author = {Zhu, H and Bouhifd, M and Donley, E and Egnash, L and Kleinstreuer, N and Kroese, ED and Liu, Z and Luechtefeld, T and Palmer, J and Pamies, D and Shen, J and Strauss, V and Wu, S and Hartung, T}, title = {Supporting read-across using biological data.}, journal = {ALTEX}, volume = {33}, number = {2}, pages = {167-182}, pmid = {26863516}, issn = {1868-8551}, support = {P30 ES005022/ES/NIEHS NIH HHS/United States ; R15 ES023148/ES/NIEHS NIH HHS/United States ; T32 ES007141/ES/NIEHS NIH HHS/United States ; }, mesh = {Animal Testing Alternatives ; Animals ; Biological Assay/*methods ; Chemical Safety/*methods ; Data Mining ; *Databases, Factual ; Hazardous Substances/*chemistry/*toxicity ; High-Throughput Screening Assays ; Molecular Structure ; Rats ; Structure-Activity Relationship ; }, abstract = {Read-across, i.e. filling toxicological data gaps by relating to similar chemicals, for which test data are available, is usually done based on chemical similarity. Besides structure and physico-chemical properties, however, biological similarity based on biological data adds extra strength to this process. In the context of developing Good Read-Across Practice guidance, a number of case studies were evaluated to demonstrate the use of biological data to enrich read-across. In the simplest case, chemically similar substances also show similar test results in relevant in vitro assays. This is a well-established method for the read-across of e.g. genotoxicity assays. Larger datasets of biological and toxicological properties of hundreds and thousands of substances become increasingly available enabling big data approaches in read-across studies. Several case studies using various big data sources are described in this paper. An example is given for the US EPA's ToxCast dataset allowing read-across for high quality uterotrophic assays for estrogenic endocrine disruption. Similarly, an example for REACH registration data enhancing read-across for acute toxicity studies is given. A different approach is taken using omics data to establish biological similarity: Examples are given for stem cell models in vitro and short-term repeated dose studies in rats in vivo to support read-across and category formation. These preliminary biological data-driven read-across studies highlight the road to the new generation of read-across approaches that can be applied in chemical safety assessment.}, } @article {pmid26861660, year = {2016}, author = {ten Hoopen, P and Amid, C and Buttigieg, PL and Pafilis, E and Bravakos, P and Cerdeño-Tárraga, AM and Gibson, R and Kahlke, T and Legaki, A and Narayana Murthy, K and Papastefanou, G and Pereira, E and Rossello, M and Luisa Toribio, A and Cochrane, G}, title = {Value, but high costs in post-deposition data curation.}, journal = {Database : the journal of biological databases and curation}, volume = {2016}, number = {}, pages = {}, pmid = {26861660}, issn = {1758-0463}, support = {BB/I02612X/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Computational Biology/*economics ; Data Collection ; Databases, Nucleic Acid/*economics ; Ecosystem ; Europe ; Geography ; Humans ; *Metagenomics ; Microbiota ; Molecular Sequence Annotation ; Semantics ; Sequence Analysis ; }, abstract = {Discoverability of sequence data in primary data archives is proportional to the richness of contextual information associated with the data. Here, we describe an exercise in the improvement of contextual information surrounding sample records associated with metagenomics sequence reads available in the European Nucleotide Archive. We outline the annotation process and summarize findings of this effort aimed at increasing usability of publicly available environmental data. Furthermore, we emphasize the benefits of such an exercise and detail its costs. We conclude that such a third party annotation approach is expensive and has value as an element of curation, but should form only part of a more sustainable submitter-driven approach. Database URL: http://www.ebi.ac.uk/ena.}, } @article {pmid26861659, year = {2016}, author = {García Morales, M and Denno, BD and Miller, DR and Miller, GL and Ben-Dov, Y and Hardy, NB}, title = {ScaleNet: a literature-based model of scale insect biology and systematics.}, journal = {Database : the journal of biological databases and curation}, volume = {2016}, number = {}, pages = {}, pmid = {26861659}, issn = {1758-0463}, mesh = {Animals ; Biodiversity ; Biological Evolution ; Biology ; Computational Biology/*methods ; *Databases, Bibliographic ; *Databases, Genetic ; Ecology ; Geography ; Hemiptera/*physiology ; Software ; }, abstract = {Scale insects (Hemiptera: Coccoidea) are small herbivorous insects found on all continents except Antarctica. They are extremely invasive, and many species are serious agricultural pests. They are also emerging models for studies of the evolution of genetic systems, endosymbiosis and plant-insect interactions. ScaleNet was launched in 1995 to provide insect identifiers, pest managers, insect systematists, evolutionary biologists and ecologists efficient access to information about scale insect biological diversity. It provides comprehensive information on scale insects taken directly from the primary literature. Currently, it draws from 23,477 articles and describes the systematics and biology of 8194 valid species. For 20 years, ScaleNet ran on the same software platform. That platform is no longer viable. Here, we present a new, open-source implementation of ScaleNet. We have normalized the data model, begun the process of correcting invalid data, upgraded the user interface, and added online administrative tools. These improvements make ScaleNet easier to use and maintain and make the ScaleNet data more accurate and extendable. Database URL: http://scalenet.info.}, } @article {pmid26861502, year = {2016}, author = {Sędzielewska Toro, K and Brachmann, A}, title = {The effector candidate repertoire of the arbuscular mycorrhizal fungus Rhizophagus clarus.}, journal = {BMC genomics}, volume = {17}, number = {}, pages = {101}, pmid = {26861502}, issn = {1471-2164}, mesh = {Cell Wall/genetics/metabolism ; Computational Biology/methods ; Enzymes/genetics/metabolism ; Fungal Proteins/chemistry/genetics/metabolism ; *Genome, Fungal ; Genomics/methods ; Glomeromycota/*classification/enzymology/*genetics/metabolism ; *Mycorrhizae ; Plant Roots/microbiology ; Protein Sorting Signals/genetics ; Symbiosis ; }, abstract = {BACKGROUND: Arbuscular mycorrhizal fungi (AMF) form an ecologically important symbiosis with more than two thirds of studied land plants. Recent studies of plant-pathogen interactions showed that effector proteins play a key role in host colonization by controlling the plant immune system. We hypothesise that also for symbiotic-plant interactions the secreted effectome of the fungus is a major component of communication and the conservation level of effector proteins between AMF species may be indicative whether they play a fundamental role.

RESULTS: In this study, we used a bioinformatics pipeline to predict and compare the effector candidate repertoire of the two AMF species, Rhizophagus irregularis and Rhizophagus clarus. Our in silico pipeline revealed a list of 220 R. irregularis candidate effector genes that create a valuable information source to elucidate the mechanism of plant infection and colonization by fungi during AMF symbiotic interaction. While most of the candidate effectors show no homologies to known domains or proteins, the candidates with homologies point to potential roles in signal transduction, cell wall modification or transcription regulation. A remarkable aspect of our work is presence of a large portion of the effector proteins involved in symbiosis, which are not unique to each fungi or plant species, but shared along the Glomeromycota phylum. For 95% of R. irregularis candidates we found homologs in a R. clarus genome draft generated by Illumina high-throughput sequencing. Interestingly, 9% of the predicted effectors are at least as conserved between the two Rhizophagus species as proteins with housekeeping functions (similarity > 90%). Therefore, we state that this group of highly conserved effector proteins between AMF species may play a fundamental role during fungus-plant interaction.

CONCLUSIONS: We hypothesise that in symbiotic interactions the secreted effectome of the fungus might be an important component of communication. Identification and functional characterization of the primary AMF effectors that regulate symbiotic development will help in understanding the mechanisms of fungus-plant interaction.}, } @article {pmid26861288, year = {2016}, author = {Xu, D and Sun, L and Liu, S and Zhang, L and Yang, H}, title = {Understanding the Heat Shock Response in the Sea Cucumber Apostichopus japonicus, Using iTRAQ-Based Proteomics.}, journal = {International journal of molecular sciences}, volume = {17}, number = {2}, pages = {150}, pmid = {26861288}, issn = {1422-0067}, mesh = {Animals ; Computational Biology/methods ; *Heat-Shock Response ; Hot Temperature ; Molecular Sequence Annotation ; *Proteome ; Proteomics/*methods ; Stichopus/genetics/*metabolism ; Stress, Physiological ; }, abstract = {The sea cucumber Apostichopus japonicus is exploited as a commercial species owing to their high nutritive and medicinal value. Recent high summer temperatures have caused high mortality rates in A. japonicus. In this study, we applied the isobaric tag for relative and absolute quantitation (iTRAQ) technique to investigate the global protein expression profile under an acute short-term (48 h) heat stress. In total, 3432 proteins were identified, and 127 proteins showed significant heat stress responses, with 61 upregulated proteins and 66 downregulated proteins. Our results suggest that heat stress influenced the expression of proteins involved in various biological processes, such as tissue protection and detoxification, lipid and amino acid metabolism, energy production and usage, transcription and translation, cell apoptosis, and cell proliferation. These findings provide a better understanding about the response and thermo-tolerance mechanisms of A. japonicus under heat stress.}, } @article {pmid26860243, year = {2016}, author = {Cunningham, JA}, title = {Addiction and eHealth.}, journal = {Addiction (Abingdon, England)}, volume = {111}, number = {3}, pages = {389-390}, doi = {10.1111/add.13243}, pmid = {26860243}, issn = {1360-0443}, mesh = {Behavior, Addictive/*rehabilitation ; Humans ; Substance-Related Disorders/*rehabilitation ; Telemedicine/*methods ; Therapy, Computer-Assisted/*methods ; }, } @article {pmid26859769, year = {2016}, author = {Grossmann, L and Jensen, M and Heider, D and Jost, S and Glücksman, E and Hartikainen, H and Mahamdallie, SS and Gardner, M and Hoffmann, D and Bass, D and Boenigk, J}, title = {Protistan community analysis: key findings of a large-scale molecular sampling.}, journal = {The ISME journal}, volume = {10}, number = {9}, pages = {2269-2279}, pmid = {26859769}, issn = {1751-7370}, mesh = {Cluster Analysis ; Computational Biology ; Ecology ; Ecosystem ; Eukaryota/*classification/genetics/isolation & purification ; }, abstract = {Protists are perhaps the most lineage-rich of microbial lifeforms, but remain largely unknown. High-throughput sequencing technologies provide opportunities to screen whole habitats in depth and enable detailed comparisons of different habitats to measure, compare and map protistan diversity. Such comparisons are often limited by low sample numbers within single studies and a lack of standardisation between studies. Here, we analysed 232 samples from 10 sampling campaigns using a standardised PCR protocol and bioinformatics pipeline. We show that protistan community patterns are highly consistent within habitat types and geographic regions, provided that sample processing is standardised. Community profiles are only weakly affected by fluctuations of the abundances of the most abundant taxa and, therefore, provide a sound basis for habitat comparison beyond random short-term fluctuations in the community composition. Further, we provide evidence that distribution patterns are not solely resulting from random processes. Distinct habitat types and distinct taxonomic groups are dominated by taxa with distinct distribution patterns that reflect their ecology with respect to dispersal and habitat colonisation. However, there is no systematic shift of the distribution pattern with taxon abundance.}, } @article {pmid26859767, year = {2016}, author = {Standage, DS and Berens, AJ and Glastad, KM and Severin, AJ and Brendel, VP and Toth, AL}, title = {Genome, transcriptome and methylome sequencing of a primitively eusocial wasp reveal a greatly reduced DNA methylation system in a social insect.}, journal = {Molecular ecology}, volume = {25}, number = {8}, pages = {1769-1784}, doi = {10.1111/mec.13578}, pmid = {26859767}, issn = {1365-294X}, mesh = {Animals ; Behavior, Animal ; *DNA Methylation ; Female ; *Genome, Insect ; Male ; *Social Behavior ; *Transcriptome ; Wasps/*genetics ; }, abstract = {Comparative genomics of social insects has been intensely pursued in recent years with the goal of providing insights into the evolution of social behaviour and its underlying genomic and epigenomic basis. However, the comparative approach has been hampered by a paucity of data on some of the most informative social forms (e.g. incipiently and primitively social) and taxa (especially members of the wasp family Vespidae) for studying social evolution. Here, we provide a draft genome of the primitively eusocial model insect Polistes dominula, accompanied by analysis of caste-related transcriptome and methylome sequence data for adult queens and workers. Polistes dominula possesses a fairly typical hymenopteran genome, but shows very low genomewide GC content and some evidence of reduced genome size. We found numerous caste-related differences in gene expression, with evidence that both conserved and novel genes are related to caste differences. Most strikingly, these -omics data reveal a major reduction in one of the major epigenetic mechanisms that has been previously suggested to be important for caste differences in social insects: DNA methylation. Along with a conspicuous loss of a key gene associated with environmentally responsive DNA methylation (the de novo DNA methyltransferase Dnmt3), these wasps have greatly reduced genomewide methylation to almost zero. In addition to providing a valuable resource for comparative analysis of social insect evolution, our integrative -omics data for this important behavioural and evolutionary model system call into question the general importance of DNA methylation in caste differences and evolution in social insects.}, } @article {pmid26856252, year = {2016}, author = {Puechmaille, SJ}, title = {The program structure does not reliably recover the correct population structure when sampling is uneven: subsampling and new estimators alleviate the problem.}, journal = {Molecular ecology resources}, volume = {16}, number = {3}, pages = {608-627}, doi = {10.1111/1755-0998.12512}, pmid = {26856252}, issn = {1755-0998}, mesh = {Computational Biology/*methods ; *Diagnostic Errors ; Genetics, Population/*methods ; *Selection Bias ; *Software ; }, abstract = {Inferences of population structure and more precisely the identification of genetically homogeneous groups of individuals are essential to the fields of ecology, evolutionary biology and conservation biology. Such population structure inferences are routinely investigated via the program structure implementing a Bayesian algorithm to identify groups of individuals at Hardy-Weinberg and linkage equilibrium. While the method is performing relatively well under various population models with even sampling between subpopulations, the robustness of the method to uneven sample size between subpopulations and/or hierarchical levels of population structure has not yet been tested despite being commonly encountered in empirical data sets. In this study, I used simulated and empirical microsatellite data sets to investigate the impact of uneven sample size between subpopulations and/or hierarchical levels of population structure on the detected population structure. The results demonstrated that uneven sampling often leads to wrong inferences on hierarchical structure and downward-biased estimates of the true number of subpopulations. Distinct subpopulations with reduced sampling tended to be merged together, while at the same time, individuals from extensively sampled subpopulations were generally split, despite belonging to the same panmictic population. Four new supervised methods to detect the number of clusters were developed and tested as part of this study and were found to outperform the existing methods using both evenly and unevenly sampled data sets. Additionally, a subsampling strategy aiming to reduce sampling unevenness between subpopulations is presented and tested. These results altogether demonstrate that when sampling evenness is accounted for, the detection of the correct population structure is greatly improved.}, } @article {pmid26851723, year = {2016}, author = {Ostroumova, E and Hatch, M and Brenner, A and Nadyrov, E and Veyalkin, I and Polyanskaya, O and Yauseyenka, V and Polyakov, S and Levin, L and Zablotska, L and Rozhko, A and Mabuchi, K}, title = {Non-thyroid cancer incidence in Belarusian residents exposed to Chernobyl fallout in childhood and adolescence: Standardized Incidence Ratio analysis, 1997-2011.}, journal = {Environmental research}, volume = {147}, number = {}, pages = {44-49}, pmid = {26851723}, issn = {1096-0953}, support = {HHSN261201300002C/CA/NCI NIH HHS/United States ; /ImNIH/Intramural NIH HHS/United States ; }, mesh = {Adolescent ; *Chernobyl Nuclear Accident ; Child ; Child, Preschool ; Cohort Studies ; Humans ; Incidence ; Infant ; Infant, Newborn ; Leukemia/*epidemiology/etiology ; Lymphoma/*epidemiology/etiology ; Neoplasms, Radiation-Induced/*epidemiology/etiology ; Republic of Belarus/epidemiology ; Risk Factors ; }, abstract = {BACKGROUND: While an increased risk of thyroid cancer from post-Chernobyl exposure to Iodine-131 (I-131) in children and adolescents has been well-documented, risks of other cancers or leukemia as a result of residence in radioactively contaminated areas remain uncertain.

METHODS: We studied non-thyroid cancer incidence in a cohort of about 12,000 individuals from Belarus exposed under age of 18 years to Chernobyl fallout (median age at the time of Chernobyl accident of 7.9 years). During 15 years of follow-up from1997 through 2011, 54 incident cancers excluding thyroid were identified in the study cohort with 142,968 person-years at risk. We performed Standardized Incidence Ratio (SIR) analysis of all solid cancers excluding thyroid (n=42), of leukemia (n=6) and of lymphoma (n=6).

RESULTS: We found no significant increase in the incidence of non-thyroid solid cancer (SIR=0.83, 95% Confidence Interval [CI]: 0.61; 1.11), lymphoma (SIR=0.66, 95% CI: 0.26; 1.33) or leukemia (SIR=1.78, 95% CI: 0.71; 3.61) in the study cohort as compared with the sex-, age- and calendar-time-specific national rates. These findings may in part reflect the relatively young age of study subjects (median attained age of 33.4 years), and long latency for some radiation-related solid cancers.

CONCLUSIONS: We found no evidence of statistically significant increases in solid cancer, lymphoma and leukemia incidence 25 years after childhood exposure in the study cohort; however, it is important to continue follow-up non-thyroid cancers in individuals exposed to low-level radiation at radiosensitive ages.}, } @article {pmid26850278, year = {2016}, author = {Dawood, T and Yang, X and Visser, EJ and Te Beek, TA and Kensche, PR and Cristescu, SM and Lee, S and Floková, K and Nguyen, D and Mariani, C and Rieu, I}, title = {A Co-Opted Hormonal Cascade Activates Dormant Adventitious Root Primordia upon Flooding in Solanum dulcamara.}, journal = {Plant physiology}, volume = {170}, number = {4}, pages = {2351-2364}, pmid = {26850278}, issn = {1532-2548}, mesh = {Abscisic Acid/metabolism ; Biological Transport/drug effects ; Ethylenes/pharmacology ; *Floods ; Gene Expression Regulation, Plant/drug effects ; Indoleacetic Acids/metabolism ; Organ Specificity/drug effects/genetics ; Plant Growth Regulators/*metabolism ; Plant Proteins/metabolism ; Plant Roots/drug effects/*metabolism ; Signal Transduction/drug effects ; Solanum/drug effects/*metabolism ; Transcriptome/drug effects/genetics ; }, abstract = {Soil flooding is a common stress factor affecting plants. To sustain root function in the hypoxic environment, flooding-tolerant plants may form new, aerenchymatous adventitious roots (ARs), originating from preformed, dormant primordia on the stem. We investigated the signaling pathway behind AR primordium reactivation in the dicot species Solanum dulcamara Transcriptome analysis indicated that flooding imposes a state of quiescence on the stem tissue, while increasing cellular activity in the AR primordia. Flooding led to ethylene accumulation in the lower stem region and subsequently to a drop in abscisic acid (ABA) level in both stem and AR primordia tissue. Whereas ABA treatment prevented activation of AR primordia by flooding, inhibition of ABA synthesis was sufficient to activate them in absence of flooding. Together, this reveals that there is a highly tissue-specific response to reduced ABA levels. The central role for ABA in the response differentiates the pathway identified here from the AR emergence pathway known from rice (Oryza sativa). Flooding and ethylene treatment also induced expression of the polar auxin transporter PIN2, and silencing of this gene or chemical inhibition of auxin transport inhibited primordium activation, even though ABA levels were reduced. Auxin treatment, however, was not sufficient for AR emergence, indicating that the auxin pathway acts in parallel with the requirement for ABA reduction. In conclusion, adaptation of S. dulcamara to wet habitats involved co-option of a hormonal signaling cascade well known to regulate shoot growth responses, to direct a root developmental program upon soil flooding.}, } @article {pmid26850162, year = {2016}, author = {Stedtfeld, RD and Williams, MR and Fakher, U and Johnson, TA and Stedtfeld, TM and Wang, F and Khalife, WT and Hughes, M and Etchebarne, BE and Tiedje, JM and Hashsham, SA}, title = {Antimicrobial resistance dashboard application for mapping environmental occurrence and resistant pathogens.}, journal = {FEMS microbiology ecology}, volume = {92}, number = {3}, pages = {}, pmid = {26850162}, issn = {1574-6941}, support = {P42 ES004911/ES/NIEHS NIH HHS/United States ; 2 P42 ES004911-22A1/ES/NIEHS NIH HHS/United States ; }, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; Bacteria/*drug effects/genetics/isolation & purification ; Bacterial Infections/microbiology/veterinary ; Bacterial Proteins/genetics ; *Databases, Factual ; *Drug Resistance, Bacterial ; Humans ; Microbial Sensitivity Tests ; Prospective Studies ; Rivers/microbiology ; Swine/microbiology ; Wastewater/microbiology ; }, abstract = {An antibiotic resistance (AR) Dashboard application is being developed regarding the occurrence of antibiotic resistance genes (ARG) and bacteria (ARB) in environmental and clinical settings. The application gathers and geospatially maps AR studies, reported occurrence and antibiograms, which can be downloaded for offline analysis. With the integration of multiple data sets, the database can be used on a regional or global scale to identify hot spots for ARGs and ARB; track and link spread and transmission, quantify environmental or human factors influencing presence and persistence of ARG harboring organisms; differentiate natural ARGs from those distributed via human or animal activity; cluster and compare ARGs connections in different environments and hosts; and identify genes that can be used as proxies to routinely monitor anthropogenic pollution. To initially populate and develop the AR Dashboard, a qPCR ARG array was tested with 30 surface waters, primary influent from three waste water treatment facilities, ten clinical isolates from a regional hospital and data from previously published studies including river, park soil and swine farm samples. Interested users are invited to download a beta version (available on iOS or Android), submit AR information using the application, and provide feedback on current and prospective functionalities.}, } @article {pmid26849107, year = {2016}, author = {Yáñez, JM and Naswa, S and López, ME and Bassini, L and Correa, K and Gilbey, J and Bernatchez, L and Norris, A and Neira, R and Lhorente, JP and Schnable, PS and Newman, S and Mileham, A and Deeb, N and Di Genova, A and Maass, A}, title = {Genomewide single nucleotide polymorphism discovery in Atlantic salmon (Salmo salar): validation in wild and farmed American and European populations.}, journal = {Molecular ecology resources}, volume = {16}, number = {4}, pages = {1002-1011}, doi = {10.1111/1755-0998.12503}, pmid = {26849107}, issn = {1755-0998}, mesh = {Americas ; Animals ; Animals, Wild ; Aquaculture ; Computational Biology/methods ; Europe ; Genetic Association Studies ; Genetics, Population/*methods ; Genotyping Techniques/*methods ; *Polymorphism, Single Nucleotide ; Salmo salar/*classification/*genetics ; Sequence Analysis, DNA ; }, abstract = {A considerable number of single nucleotide polymorphisms (SNPs) are required to elucidate genotype-phenotype associations and determine the molecular basis of important traits. In this work, we carried out de novo SNP discovery accounting for both genome duplication and genetic variation from American and European salmon populations. A total of 9 736 473 nonredundant SNPs were identified across a set of 20 fish by whole-genome sequencing. After applying six bioinformatic filtering steps, 200 K SNPs were selected to develop an Affymetrix Axiom(®) myDesign Custom Array. This array was used to genotype 480 fish representing wild and farmed salmon from Europe, North America and Chile. A total of 159 099 (79.6%) SNPs were validated as high quality based on clustering properties. A total of 151 509 validated SNPs showed a unique position in the genome. When comparing these SNPs against 238 572 markers currently available in two other Atlantic salmon arrays, only 4.6% of the SNP overlapped with the panel developed in this study. This novel high-density SNP panel will be very useful for the dissection of economically and ecologically relevant traits, enhancing breeding programmes through genomic selection as well as supporting genetic studies in both wild and farmed populations of Atlantic salmon using high-resolution genomewide information.}, } @article {pmid26848672, year = {2016}, author = {Curtis, A and Blackburn, JK and Smiley, SL and Yen, M and Camilli, A and Alam, MT and Ali, A and Morris, JG}, title = {Mapping to Support Fine Scale Epidemiological Cholera Investigations: A Case Study of Spatial Video in Haiti.}, journal = {International journal of environmental research and public health}, volume = {13}, number = {2}, pages = {187}, pmid = {26848672}, issn = {1660-4601}, support = {R01 AI097405/AI/NIAID NIH HHS/United States ; T32 AI007422/AI/NIAID NIH HHS/United States ; R01AI097405/AI/NIAID NIH HHS/United States ; }, mesh = {Cholera/*epidemiology/transmission ; *Geographic Information Systems ; *Geographic Mapping ; Haiti/epidemiology ; Humans ; *Video Recording ; }, abstract = {The cartographic challenge in many developing world environments suffering a high disease burden is a lack of granular environmental covariates suitable for modeling disease outcomes. As a result, epidemiological questions, such as how disease diffuses at intra urban scales are extremely difficult to answer. This paper presents a novel geospatial methodology, spatial video, which can be used to collect and map environmental covariates, while also supporting field epidemiology. An example of epidemic cholera in a coastal town of Haiti is used to illustrate the potential of this new method. Water risks from a 2012 spatial video collection are used to guide a 2014 survey, which concurrently included the collection of water samples, two of which resulted in positive lab results "of interest" (bacteriophage specific for clinical cholera strains) to the current cholera situation. By overlaying sample sites on 2012 water risk maps, a further fifteen proposed water sample locations are suggested. These resulted in a third spatial video survey and an additional "of interest" positive water sample. A potential spatial connection between the "of interest" water samples is suggested. The paper concludes with how spatial video can be an integral part of future fine-scale epidemiological investigations for different pathogens.}, } @article {pmid26847559, year = {2016}, author = {Kogure, Y and Sato, K and Watanuki, Y and Wanless, S and Daunt, F}, title = {European shags optimize their flight behavior according to wind conditions.}, journal = {The Journal of experimental biology}, volume = {219}, number = {Pt 3}, pages = {311-318}, doi = {10.1242/jeb.131441}, pmid = {26847559}, issn = {1477-9145}, mesh = {Accelerometry ; Animals ; Birds/*physiology ; *Flight, Animal ; Geographic Information Systems ; Male ; *Wind ; }, abstract = {Aerodynamics results in two characteristic speeds of flying birds: the minimum power speed and the maximum range speed. The minimum power speed requires the lowest rate of energy expenditure per unit time to stay airborne and the maximum range speed maximizes air distance traveled per unit of energy consumed. Therefore, if birds aim to minimize the cost of transport under a range of wind conditions, they are predicted to fly at the maximum range speed. Furthermore, take-off is predicted to be strongly affected by wind speed and direction. To investigate the effect of wind conditions on take-off and cruising flight behavior, we equipped 14 European shags Phalacrocorax aristotelis with a back-mounted GPS logger to measure position and hence ground speed, and a neck-mounted accelerometer to record wing beat frequency and strength. Local wind conditions were recorded during the deployment period. Shags always took off into the wind regardless of their intended destination and take-off duration was correlated negatively with wind speed. We combined ground speed and direction during the cruising phase with wind speed and direction to estimate air speed and direction. Whilst ground speed was highly variable, air speed was comparatively stable, although it increased significantly during strong head winds, because of stronger wing beats. The increased air speeds in head winds suggest that birds fly at the maximum range speed, not at the minimum power speed. Our study demonstrates that European shags actively adjust their flight behavior to utilize wind power to minimize the costs of take-off and cruising flight.}, } @article {pmid26845437, year = {2016}, author = {Dalziel, BD and Bjørnstad, ON and van Panhuis, WG and Burke, DS and Metcalf, CJ and Grenfell, BT}, title = {Persistent Chaos of Measles Epidemics in the Prevaccination United States Caused by a Small Change in Seasonal Transmission Patterns.}, journal = {PLoS computational biology}, volume = {12}, number = {2}, pages = {e1004655}, pmid = {26845437}, issn = {1553-7358}, support = {P2C HD047879/HD/NICHD NIH HHS/United States ; U54 GM088491/GM/NIGMS NIH HHS/United States ; 5U54GM088491/GM/NIGMS NIH HHS/United States ; }, mesh = {Computational Biology ; Epidemics/*statistics & numerical data ; Humans ; Mass Vaccination ; Measles/*epidemiology ; *Measles Vaccine ; *Models, Biological ; Stochastic Processes ; United Kingdom/epidemiology ; United States/epidemiology ; }, abstract = {Epidemics of infectious diseases often occur in predictable limit cycles. Theory suggests these cycles can be disrupted by high amplitude seasonal fluctuations in transmission rates, resulting in deterministic chaos. However, persistent deterministic chaos has never been observed, in part because sufficiently large oscillations in transmission rates are uncommon. Where they do occur, the resulting deep epidemic troughs break the chain of transmission, leading to epidemic extinction, even in large cities. Here we demonstrate a new path to locally persistent chaotic epidemics via subtle shifts in seasonal patterns of transmission, rather than through high-amplitude fluctuations in transmission rates. We base our analysis on a comparison of measles incidence in 80 major cities in the prevaccination era United States and United Kingdom. Unlike the regular limit cycles seen in the UK, measles cycles in US cities consistently exhibit spontaneous shifts in epidemic periodicity resulting in chaotic patterns. We show that these patterns were driven by small systematic differences between countries in the duration of the summer period of low transmission. This example demonstrates empirically that small perturbations in disease transmission patterns can fundamentally alter the regularity and spatiotemporal coherence of epidemics.}, } @article {pmid26845332, year = {2016}, author = {Wilder, HK and Raffel, SJ and Barbour, AG and Porcella, SF and Sturdevant, DE and Vaisvil, B and Kapatral, V and Schmitt, DP and Schwan, TG and Lopez, JE}, title = {Transcriptional Profiling the 150 kb Linear Megaplasmid of Borrelia turicatae Suggests a Role in Vector Colonization and Initiating Mammalian Infection.}, journal = {PloS one}, volume = {11}, number = {2}, pages = {e0147707}, pmid = {26845332}, issn = {1932-6203}, support = {AI091652/AI/NIAID NIH HHS/United States ; K22 AI091652/AI/NIAID NIH HHS/United States ; U54 AI065359/AI/NIAID NIH HHS/United States ; R21 AI103724/AI/NIAID NIH HHS/United States ; AI103724/AI/NIAID NIH HHS/United States ; AI065359/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Borrelia/*genetics ; Computational Biology/methods ; Contig Mapping ; Disease Models, Animal ; *Disease Vectors ; Gene Expression ; Gene Expression Profiling ; Gene Order ; Lyme Disease/microbiology ; Mice ; Molecular Sequence Annotation ; Open Reading Frames ; Plasmids/*genetics ; Ticks/microbiology ; *Transcriptome ; }, abstract = {Adaptation is key for survival as vector-borne pathogens transmit between the arthropod and vertebrate, and temperature change is an environmental signal inducing alterations in gene expression of tick-borne spirochetes. While plasmids are often associated with adaptation, complex genomes of relapsing fever spirochetes have hindered progress in understanding the mechanisms of vector colonization and transmission. We utilized recent advances in genome sequencing to generate the most complete version of the Borrelia turicatae 150 kb linear megaplasmid (lp150). Additionally, a transcriptional analysis of open reading frames (ORFs) in lp150 was conducted and identified regions that were up-regulated during in vitro cultivation at tick-like growth temperatures (22°C), relative to bacteria grown at 35°C and infected murine blood. Evaluation of the 3' end of lp150 identified a cluster of ORFs that code for putative surface lipoproteins. With a microbe's surface proteome serving important roles in pathogenesis, we confirmed the ORFs expression in vitro and in the tick compared to spirochetes infecting murine blood. Transcriptional evaluation of lp150 indicates the plasmid likely has essential roles in vector colonization and/or initiating mammalian infection. These results also provide a much needed transcriptional framework to delineate the molecular mechanisms utilized by relapsing fever spirochetes during their enzootic cycle.}, } @article {pmid26844413, year = {2016}, author = {Tsuda, T and Tokinobu, A and Yamamoto, E and Suzuki, E}, title = {The Authors Respond.}, journal = {Epidemiology (Cambridge, Mass.)}, volume = {27}, number = {3}, pages = {e21-3}, doi = {10.1097/EDE.0000000000000468}, pmid = {26844413}, issn = {1531-5487}, } @article {pmid26844190, year = {2016}, author = {Paschal, AM and Wilroy, JD and Hawley, SR}, title = {Unmet needs for dental care in children with special health care needs.}, journal = {Preventive medicine reports}, volume = {3}, number = {}, pages = {62-67}, pmid = {26844190}, issn = {2211-3355}, abstract = {OBJECTIVE: The unmet need for dental care is one of the greatest public health problems facing U.S. children. This issue is particularly concerning for children with special health care needs (CSHCN), who experience higher prevalence of unmet dental care needs. The primary purpose of this study was to investigate regional differences in unmet dental care needs for CSHCN. Using the Social Ecological Model as a framework, additional variables were analyzed for regional differences. It was hypothesized that (H1) unmet dental care needs would be high in the CSHCN population, (H2) there would be regional differences in unmet dental care needs in CSHCN, and (H3) there would be differences in specific individual, interpersonal (family), community (state), and policy level factors by region.

METHODS: Data were obtained from the 2009-2010 National Survey of CSHCN. SPSS was used for data management and analysis.

RESULTS: Each of the study hypotheses was supported for the sample of 40,242 CSHCN. The West region was more likely to have more unmet needs for preventive and specialized dental care in CSHCN than the reference region (Northeast). The South region followed the West region in unmet dental care needs. Statistically significant differences in individual, interpersonal (family), community (state) and policy factors were found by region.

CONCLUSION: Further research is recommended. Effective strategies that include policy to address unmet dental care needs at multiple levels of intervention are suggested.}, } @article {pmid26840389, year = {2016}, author = {Kawaguchi, H and Koike, S}, title = {Association between the Density of Physicians and Suicide Rates in Japan: Nationwide Ecological Study Using a Spatial Bayesian Model.}, journal = {PloS one}, volume = {11}, number = {2}, pages = {e0148288}, pmid = {26840389}, issn = {1932-6203}, mesh = {Adult ; Aged ; Aged, 80 and over ; Bayes Theorem ; Female ; Humans ; Japan ; Male ; Middle Aged ; *Models, Biological ; *Physicians ; *Suicide ; }, abstract = {BACKGROUND: Regional disparity in suicide rates is a serious problem worldwide. One possible cause is unequal distribution of the health workforce, especially psychiatrists. Research about the association between regional physician numbers and suicide rates is therefore important but studies are rare. The objective of this study was to evaluate the association between physician numbers and suicide rates in Japan, by municipality.

METHODS: The study included all the municipalities in Japan (n = 1,896). We estimated smoothed standardized mortality ratios of suicide rates for each municipality and evaluated the association between health workforce and suicide rates using a hierarchical Bayesian model accounting for spatially correlated random effects, a conditional autoregressive model. We assumed a Poisson distribution for the observed number of suicides and set the expected number of suicides as the offset variable. The explanatory variables were numbers of physicians, a binary variable for the presence of psychiatrists, and social covariates.

RESULTS: After adjustment for socioeconomic factors, suicide rates in municipalities that had at least one psychiatrist were lower than those in the other municipalities. There was, however, a positive and statistically significant association between the number of physicians and suicide rates.

CONCLUSIONS: Suicide rates in municipalities that had at least one psychiatrist were lower than those in other municipalities, but the number of physicians was positively and significantly related with suicide rates. To improve the regional disparity in suicide rates, the government should encourage psychiatrists to participate in community-based suicide prevention programs and to settle in municipalities that currently have no psychiatrists. The government and other stakeholders should also construct better networks between psychiatrists and non-psychiatrists to support sharing of information for suicide prevention.}, } @article {pmid26839740, year = {2016}, author = {Coutinho, F and Tschoeke, DA and Thompson, F and Thompson, C}, title = {Comparative genomics of Synechococcus and proposal of the new genus Parasynechococcus.}, journal = {PeerJ}, volume = {4}, number = {}, pages = {e1522}, pmid = {26839740}, issn = {2167-8359}, abstract = {Synechococcus is among the most important contributors to global primary productivity. The genomes of several strains of this taxon have been previously sequenced in an effort to understand the physiology and ecology of these highly diverse microorganisms. Here we present a comparative study of Synechococcus genomes. For that end, we developed GenTaxo, a program written in Perl to perform genomic taxonomy based on average nucleotide identity, average amino acid identity and dinucleotide signatures, which revealed that the analyzed strains are drastically distinct regarding their genomic content. Phylogenomic reconstruction indicated a division of Synechococcus in two clades (i.e. Synechococcus and the new genus Parasynechococcus), corroborating evidences that this is in fact a polyphyletic group. By clustering protein encoding genes into homologue groups we were able to trace the Pangenome and core genome of both marine and freshwater Synechococcus and determine the genotypic traits that differentiate these lineages.}, } @article {pmid26838249, year = {2016}, author = {Keramatinia, A and Hassanipour, S and Nazarzadeh, M and Wurtz, M and Monfared, AB and Khayyamzadeh, M and Bidel, Z and Mhrvar, N and Mosavi-Jarrahi, A}, title = {Correlation Between Nitrogen Dioxide as an Air Pollution Indicator and Breast Cancer: a Systematic Review and Meta- Analysis.}, journal = {Asian Pacific journal of cancer prevention : APJCP}, volume = {17}, number = {1}, pages = {419-424}, doi = {10.7314/apjcp.2016.17.1.419}, pmid = {26838249}, issn = {2476-762X}, mesh = {Aged ; Female ; Humans ; Middle Aged ; *Air Pollution/adverse effects ; *Breast Neoplasms/etiology ; Case-Control Studies ; Databases, Factual ; Incidence ; *Nitrogen Dioxide/adverse effects ; Observational Studies as Topic ; }, abstract = {BACKGROUND: The aim of this systematic review was to study the relationship between exposure to nitrogen dioxide (NO2) in the ambient air and breast cancer incidence.

MATERIALS AND METHODS: A systematic review was performed based on the MOOSE guideline for review of observational studies. We searched five online databases (PubMed, Science Direct, Google Scholar, EBSCO, and Scopus) from their conception to June 2014. A pooled estimate of the correlation between NO2 exposure and breast cancer incidence was calculated using Pearson's correlation coefficient.

RESULTS: A total of 654 titles were retrieved in the initial search of the databases. Further refinement and screening of the retrieved studies produced a total of five studies from four countries. The studies included three ecological studies (aggregate level) and two individual based studies (one prospective cohort and the other one a case-control study). The ecological studies were pooled and the meta-analysis of correlation coefficient without z transformation showed a pooled estimate of r = 0.89 with 95% CI of 0.84 to 0.95. Using z transformation, the pooled r was 1.38 with 95%CI of 1.11 to 1.59. No significant heterogeneity between studies was observed. Following a sensitivity analysis and the removal of each study from pooled analysis we did not see any significant change in the pooled estimate.

CONCLUSIONS: It was concluded that there is a tendency toward a weak association between exposure to NO2 in ambient air and breast cancer at the individual level and a significant association at the aggregate level.}, } @article {pmid26838160, year = {2016}, author = {Wang, L and Huang, L and Pan, Y and Kuča, K and Klímová, B and Wu, Q and Xie, S and Ahmad, I and Chen, D and Tao, Y and Wan, D and Liu, Z and Yuan, Z}, title = {Metabolism and Disposition of Aditoprim in Swine, Broilers, Carp and Rats.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {20370}, pmid = {26838160}, issn = {2045-2322}, mesh = {Adenosine Diphosphate/*metabolism ; Administration, Oral ; Animals ; Carps/urine ; Chickens/urine ; Chromatography, Liquid ; Liver/*chemistry ; Mass Spectrometry ; Rats/urine ; Swine/urine ; Tissue Distribution ; Trimethoprim/administration & dosage/*analogs & derivatives/pharmacokinetics/urine ; }, abstract = {Aditoprim (ADP) is a newly developed antibacterial agent in veterinary medicine. The metabolism and disposition of ADP in swine, broilers, carp and rats were investigated by using a radio tracer method combined with a radioactivity detector and a liquid chromatography/ion trap/time-of-flight mass spectrometry. After a single oral administration, more than 94% of the dose was recovered within 14 d in the four species. The urine excretion was dominant in swine and rats, making up 78% of the dose. N-monodesmethyl-ADP, N-didesmethyl-ADP, and 10 new metabolites were characterized. These metabolites were biotransformed from the process of demethylation, α-hydroxylation, N-oxidation, and NH2-glucuronidation. After an oral dose for 7 d, ADP-derived radioactivity was widely distributed in tissues, and high concentrations were especially observed in bile, liver, kidney, lung, and spleen. The radioactivity in the liver was eliminated much more slowly than in other tissues, with a half-life of 4.26, 3.38, 6.69, and 5.21 d in swine, broilers, carp, and rats, respectively. ADP, N-monodesmethyl-ADP, and N-didesmethyl-ADP were the major metabolites in edible tissues. Notably, ADP was detected with the highest concentration and the longest duration in these tissues. These findings indicated that ADP is the marker residue and the liver is the residue target tissue.}, } @article {pmid26836814, year = {2016}, author = {Benoit, JB and Adelman, ZN and Reinhardt, K and Dolan, A and Poelchau, M and Jennings, EC and Szuter, EM and Hagan, RW and Gujar, H and Shukla, JN and Zhu, F and Mohan, M and Nelson, DR and Rosendale, AJ and Derst, C and Resnik, V and Wernig, S and Menegazzi, P and Wegener, C and Peschel, N and Hendershot, JM and Blenau, W and Predel, R and Johnston, PR and Ioannidis, P and Waterhouse, RM and Nauen, R and Schorn, C and Ott, MC and Maiwald, F and Johnston, JS and Gondhalekar, AD and Scharf, ME and Peterson, BF and Raje, KR and Hottel, BA and Armisén, D and Crumière, AJJ and Refki, PN and Santos, ME and Sghaier, E and Viala, S and Khila, A and Ahn, SJ and Childers, C and Lee, CY and Lin, H and Hughes, DST and Duncan, EJ and Murali, SC and Qu, J and Dugan, S and Lee, SL and Chao, H and Dinh, H and Han, Y and Doddapaneni, H and Worley, KC and Muzny, DM and Wheeler, D and Panfilio, KA and Vargas Jentzsch, IM and Vargo, EL and Booth, W and Friedrich, M and Weirauch, MT and Anderson, MAE and Jones, JW and Mittapalli, O and Zhao, C and Zhou, JJ and Evans, JD and Attardo, GM and Robertson, HM and Zdobnov, EM and Ribeiro, JMC and Gibbs, RA and Werren, JH and Palli, SR and Schal, C and Richards, S}, title = {Unique features of a global human ectoparasite identified through sequencing of the bed bug genome.}, journal = {Nature communications}, volume = {7}, number = {}, pages = {10165}, pmid = {26836814}, issn = {2041-1723}, support = {GM070559-9/GM/NIGMS NIH HHS/United States ; R01 GM070559/GM/NIGMS NIH HHS/United States ; U54 HG003273/HG/NHGRI NIH HHS/United States ; 260986/ERC_/European Research Council/International ; UL1 TR001427/TR/NCATS NIH HHS/United States ; 616346/ERC_/European Research Council/International ; }, mesh = {Animals ; Bedbugs/*genetics ; *Ectoparasitic Infestations ; *Feeding Behavior ; Gene Transfer, Horizontal/*genetics ; Genome ; Host-Parasite Interactions/*genetics ; Humans ; Insecticide Resistance/*genetics ; *Insecticides ; Sequence Analysis, DNA ; }, abstract = {The bed bug, Cimex lectularius, has re-established itself as a ubiquitous human ectoparasite throughout much of the world during the past two decades. This global resurgence is likely linked to increased international travel and commerce in addition to widespread insecticide resistance. Analyses of the C. lectularius sequenced genome (650 Mb) and 14,220 predicted protein-coding genes provide a comprehensive representation of genes that are linked to traumatic insemination, a reduced chemosensory repertoire of genes related to obligate hematophagy, host-symbiont interactions, and several mechanisms of insecticide resistance. In addition, we document the presence of multiple putative lateral gene transfer events. Genome sequencing and annotation establish a solid foundation for future research on mechanisms of insecticide resistance, human-bed bug and symbiont-bed bug associations, and unique features of bed bug biology that contribute to the unprecedented success of C. lectularius as a human ectoparasite.}, } @article {pmid26836261, year = {2016}, author = {Kent, AG and Dupont, CL and Yooseph, S and Martiny, AC}, title = {Global biogeography of Prochlorococcus genome diversity in the surface ocean.}, journal = {The ISME journal}, volume = {10}, number = {8}, pages = {1856-1865}, pmid = {26836261}, issn = {1751-7370}, support = {T32 EB009418/EB/NIBIB NIH HHS/United States ; }, mesh = {Ecosystem ; *Genetic Variation ; Genome, Bacterial/*genetics ; *Metagenomics ; Oceans and Seas ; Phylogeny ; Prochlorococcus/classification/*genetics ; Seawater/microbiology ; }, abstract = {Prochlorococcus, the smallest known photosynthetic bacterium, is abundant in the ocean's surface layer despite large variation in environmental conditions. There are several genetically divergent lineages within Prochlorococcus and superimposed on this phylogenetic diversity is extensive gene gain and loss. The environmental role in shaping the global ocean distribution of genome diversity in Prochlorococcus is largely unknown, particularly in a framework that considers the vertical and lateral mechanisms of evolution. Here we show that Prochlorococcus field populations from a global circumnavigation harbor extensive genome diversity across the surface ocean, but this diversity is not randomly distributed. We observed a significant correspondence between phylogenetic and gene content diversity, including regional differences in both phylogenetic composition and gene content that were related to environmental factors. Several gene families were strongly associated with specific regions and environmental factors, including the identification of a set of genes related to lower nutrient and temperature regions. Metagenomic assemblies of natural Prochlorococcus genomes reinforced this association by providing linkage of genes across genomic backbones. Overall, our results show that the phylogeography in Prochlorococcus taxonomy is echoed in its genome content. Thus environmental variation shapes the functional capabilities and associated ecosystem role of the globally abundant Prochlorococcus.}, } @article {pmid26834710, year = {2015}, author = {Melendrez, MC and Becraft, ED and Wood, JM and Olsen, MT and Bryant, DA and Heidelberg, JF and Rusch, DB and Cohan, FM and Ward, DM}, title = {Recombination Does Not Hinder Formation or Detection of Ecological Species of Synechococcus Inhabiting a Hot Spring Cyanobacterial Mat.}, journal = {Frontiers in microbiology}, volume = {6}, number = {}, pages = {1540}, pmid = {26834710}, issn = {1664-302X}, abstract = {Recent studies of bacterial speciation have claimed to support the biological species concept-that reduced recombination is required for bacterial populations to diverge into species. This conclusion has been reached from the discovery that ecologically distinct clades show lower rates of recombination than that which occurs among closest relatives. However, these previous studies did not attempt to determine whether the more-rapidly recombining close relatives within the clades studied may also have diversified ecologically, without benefit of sexual isolation. Here we have measured the impact of recombination on ecological diversification within and between two ecologically distinct clades (A and B') of Synechococcus in a hot spring microbial mat in Yellowstone National Park, using a cultivation-free, multi-locus approach. Bacterial artificial chromosome (BAC) libraries were constructed from mat samples collected at 60°C and 65°C. Analysis of multiple linked loci near Synechococcus 16S rRNA genes showed little evidence of recombination between the A and B' lineages, but a record of recombination was apparent within each lineage. Recombination and mutation rates within each lineage were of similar magnitude, but recombination had a somewhat greater impact on sequence diversity than mutation, as also seen in many other bacteria and archaea. Despite recombination within the A and B' lineages, there was evidence of ecological diversification within each lineage. The algorithm Ecotype Simulation identified sequence clusters consistent with ecologically distinct populations (ecotypes), and several hypothesized ecotypes were distinct in their habitat associations and in their adaptations to different microenvironments. We conclude that sexual isolation is more likely to follow ecological divergence than to precede it. Thus, an ecology-based model of speciation appears more appropriate than the biological species concept for bacterial and archaeal diversification.}, } @article {pmid26833806, year = {2016}, author = {Starr, TN and Thornton, JW}, title = {Epistasis in protein evolution.}, journal = {Protein science : a publication of the Protein Society}, volume = {25}, number = {7}, pages = {1204-1218}, pmid = {26833806}, issn = {1469-896X}, support = {R01 GM104397/GM/NIGMS NIH HHS/United States ; T32 GM007183/GM/NIGMS NIH HHS/United States ; }, mesh = {Binding Sites ; Cell Lineage ; Computational Biology/methods ; *Epistasis, Genetic ; Evolution, Molecular ; Humans ; *Mutation ; Protein Binding ; Proteins/chemistry/*genetics/metabolism ; Selection, Genetic ; }, abstract = {The structure, function, and evolution of proteins depend on physical and genetic interactions among amino acids. Recent studies have used new strategies to explore the prevalence, biochemical mechanisms, and evolutionary implications of these interactions-called epistasis-within proteins. Here we describe an emerging picture of pervasive epistasis in which the physical and biological effects of mutations change over the course of evolution in a lineage-specific fashion. Epistasis can restrict the trajectories available to an evolving protein or open new paths to sequences and functions that would otherwise have been inaccessible. We describe two broad classes of epistatic interactions, which arise from different physical mechanisms and have different effects on evolutionary processes. Specific epistasis-in which one mutation influences the phenotypic effect of few other mutations-is caused by direct and indirect physical interactions between mutations, which nonadditively change the protein's physical properties, such as conformation, stability, or affinity for ligands. In contrast, nonspecific epistasis describes mutations that modify the effect of many others; these typically behave additively with respect to the physical properties of a protein but exhibit epistasis because of a nonlinear relationship between the physical properties and their biological effects, such as function or fitness. Both types of interaction are rampant, but specific epistasis has stronger effects on the rate and outcomes of evolution, because it imposes stricter constraints and modulates evolutionary potential more dramatically; it therefore makes evolution more contingent on low-probability historical events and leaves stronger marks on the sequences, structures, and functions of protein families.}, } @article {pmid26833403, year = {2016}, author = {Song, F and Li, J and Fan, X and Zhang, Q and Chang, W and Yang, F and Geng, G}, title = {Transcriptome analysis of Glomus mosseae/Medicago sativa mycorrhiza on atrazine stress.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {20245}, pmid = {26833403}, issn = {2045-2322}, mesh = {Atrazine/*pharmacology ; Computational Biology/methods ; *Gene Expression Profiling ; Gene Expression Regulation, Plant ; Gene Ontology ; *Glomeromycota ; Herbicides/*pharmacology ; Medicago sativa/*drug effects/*genetics ; Molecular Sequence Annotation ; *Mycorrhizae ; Plant Roots/genetics/microbiology ; Reproducibility of Results ; Stress, Physiological/*genetics ; Transcriptome ; }, abstract = {Arbuscular mycorrhizal fungi (AMF) protect host plants against diverse biotic and abiotic stresses, and promote biodegradation of various contaminants. In this study effect of Glomus mosseae/Medicago sativa mycorrhiza on atrazine degradation was investigated. It was observed that the atrazine degradation rates with any addition level in mycorrhizal treatments were all significantly higher than those in non-mycorrhizal treatments. When atrazine was applied at 20 mg kg(-1), the removal efficiency was up to 74.65%. Therefore, G. mosseae can be considered as ideal inhabitants of technical installations to facilitate phytoremediation. Furthermore, a total of 10.4 Gb was used for de novo transcriptome assembly, resulting in a comprehensive data set for the identification of genes corresponding to atrazine stress in the AM association. After comparative analysis with edgeR, a total of 2,060 differential expressed genes were identified, including 570 up-regulated genes and 1490 down-regulated genes. After excluding 'function unknown' and 'general function predictions only' genes, 172 up-regulated genes were obtained. The differentially expressed genes in AM association with and without atrazine stress were associated with molecular processes/other proteins, zinc finger protein, intracellular/extracellular enzymes, structural proteins, anti-stress/anti-disease protein, electron transport-related protein, and plant growth associated protein. Our results not only prove AMF has important ecological significance on atrazine degradation but also provide evidence for the molecular mechanisms of atrazine degradation by AMF.}, } @article {pmid26828894, year = {2016}, author = {Wilkinson, LC and Handel, CM and Van Hemert, C and Loiseau, C and Sehgal, RN}, title = {Avian malaria in a boreal resident species: long-term temporal variability, and increased prevalence in birds with avian keratin disorder.}, journal = {International journal for parasitology}, volume = {46}, number = {4}, pages = {281-290}, doi = {10.1016/j.ijpara.2015.12.008}, pmid = {26828894}, issn = {1879-0135}, mesh = {Age Factors ; Alaska/epidemiology ; Animals ; Beak/*abnormalities/growth & development ; Bird Diseases/blood/*epidemiology/parasitology ; Birds ; DNA, Protozoan/chemistry/isolation & purification ; Datasets as Topic ; Female ; Haemosporida/classification/genetics/isolation & purification ; Keratins/*metabolism ; Malaria, Avian/blood/*complications/epidemiology ; Male ; Passeriformes/blood/*parasitology ; Prevalence ; Seasons ; Sex Factors ; }, abstract = {The prevalence of vector-borne parasitic diseases is widely influenced by biological and ecological factors. Environmental conditions such as temperature and precipitation can have a marked effect on haemosporidian parasites (Plasmodium spp.) that cause malaria and those that cause other malaria-like diseases in birds. However, there have been few long-term studies monitoring haemosporidian infections in birds in northern latitudes, where weather conditions can be highly variable and the effects of climate change are becoming more pronounced. We used molecular methods to screen more than 2,000 blood samples collected from black-capped chickadees (Poecile atricapillus), a resident passerine bird. Samples were collected over a 10 year period, mostly during the non-breeding season, at seven sites in Alaska, USA. We tested for associations between Plasmodium prevalence and local environmental conditions including temperature, precipitation, site, year and season. We also evaluated the relationship between parasite prevalence and individual host factors of age, sex and presence or absence of avian keratin disorder. This disease, which causes accelerated keratin growth in the beak, provided a natural study system in which to test the interaction between disease state and malaria prevalence. Prevalence of Plasmodium infection varied by year, site, age and individual disease status but there was no support for an effect of sex or seasonal period. Significantly, birds with avian keratin disorder were 2.6 times more likely to be infected by Plasmodium than birds without the disorder. Interannual variation in the prevalence of Plasmodium infection at different sites was positively correlated with summer temperatures at the local but not statewide scale. Sequence analysis of the parasite cytochrome b gene revealed a single Plasmodium spp. lineage, P43. Our results demonstrate associations between prevalence of avian malaria and a variety of biological and ecological factors. These results also provide important baseline data that will be informative for predicting future changes in Plasmodium prevalence in the subarctic.}, } @article {pmid26828363, year = {2016}, author = {Haerter, JO and Mitarai, N and Sneppen, K}, title = {Food Web Assembly Rules for Generalized Lotka-Volterra Equations.}, journal = {PLoS computational biology}, volume = {12}, number = {2}, pages = {e1004727}, pmid = {26828363}, issn = {1553-7358}, mesh = {Animals ; Computational Biology/*methods ; Computer Simulation ; Ecosystem ; *Food Chain ; *Models, Biological ; }, abstract = {In food webs, many interacting species coexist despite the restrictions imposed by the competitive exclusion principle and apparent competition. For the generalized Lotka-Volterra equations, sustainable coexistence necessitates nonzero determinant of the interaction matrix. Here we show that this requirement is equivalent to demanding that each species be part of a non-overlapping pairing, which substantially constrains the food web structure. We demonstrate that a stable food web can always be obtained if a non-overlapping pairing exists. If it does not, the matrix rank can be used to quantify the lack of niches, corresponding to unpaired species. For the species richness at each trophic level, we derive the food web assembly rules, which specify sustainable combinations. In neighboring levels, these rules allow the higher level to avert competitive exclusion at the lower, thereby incorporating apparent competition. In agreement with data, the assembly rules predict high species numbers at intermediate levels and thinning at the top and bottom. Using comprehensive food web data, we demonstrate how omnivores or parasites with hosts at multiple trophic levels can loosen the constraints and help obtain coexistence in food webs. Hence, omnivory may be the glue that keeps communities intact even under extinction or ecological release of species.}, } @article {pmid26824732, year = {2016}, author = {Neufingerl, N and Djuwita, R and Otten-Hofman, A and Nurdiani, R and Garczarek, U and Sulaeman, A and Zock, PL and Eilander, A}, title = {Intake of essential fatty acids in Indonesian children: secondary analysis of data from a nationally representative survey.}, journal = {The British journal of nutrition}, volume = {115}, number = {4}, pages = {687-693}, doi = {10.1017/S0007114515004845}, pmid = {26824732}, issn = {1475-2662}, mesh = {Child ; *Child Nutritional Physiological Phenomena/ethnology ; Child, Preschool ; Cross-Sectional Studies ; Databases, Factual ; Deficiency Diseases/epidemiology/ethnology/*etiology ; Diet/*adverse effects/ethnology ; Dietary Fats/administration & dosage/adverse effects/analysis ; Fatty Acids, Essential/*administration & dosage/analysis/deficiency ; Female ; Food Analysis ; Humans ; Indonesia/epidemiology ; Male ; *Nutrition Policy ; Nutrition Surveys ; Patient Compliance/*ethnology ; Prevalence ; Risk ; United Nations ; }, abstract = {Essential fatty acids (EFA) such as α-linolenic acid (ALA) and linoleic acid (LA) are needed for healthy growth and development of children. Worldwide, reliable intake data of EFA are often lacking. The objective of this study was to investigate dietary intake of EFA in Indonesian children. Dietary intake data of 4-12-year-old children (n 45,821) from a nationally representative Indonesian survey were used to estimate median intake and distribution of population fatty acid intake. Missing data on individual fatty acids in the Indonesian food composition table were complemented through chemical analyses of national representative food samples and imputation of data from the US nutrient database. Nutrient adequacy ratios were calculated as a percentage of FAO/WHO intake recommendations. The medians of total fat intake of the children was 26·7 (10th-90th percentile 11·2-40·0) percentage of total daily energy (%E). Intakes of fatty acids were 4·05 (10th-90th percentile 1·83-7·22) %E for total PUFA, 3·36 (10th-90th percentile 1·14-6·29) %E for LA and 0·20 (10th-90th percentile 0·07-0·66) %E for ALA. Median intake of PUFA was 67 % and that of ALA 40 % of the minimum amounts recommended by FAO/WHO. These data indicate that a majority of Indonesian children has intakes of PUFA and specifically ALA that are lower than recommended intake levels. Total fat and LA intakes may be suboptimal for a smaller yet considerable proportion of children. Public health initiatives should provide practical guidelines to promote consumption of PUFA-rich foods.}, } @article {pmid26824289, year = {2016}, author = {Raju, KH and Sabesan, S and Rajavel, AR and Subramanian, S and Natarajan, R and Thenmozhi, V and Tyagi, BK and Jambulingam, P}, title = {A Preliminary Study to Forecast Japanese Encephalitis Vector Abundance in Paddy Growing Area, with the Aid of Radar Satellite Images.}, journal = {Vector borne and zoonotic diseases (Larchmont, N.Y.)}, volume = {16}, number = {2}, pages = {117-123}, doi = {10.1089/vbz.2014.1757}, pmid = {26824289}, issn = {1557-7759}, mesh = {Agriculture ; Animals ; Culex/*virology ; Ecosystem ; *Encephalitis Virus, Japanese ; Encephalitis, Japanese/*transmission ; Geographic Information Systems ; Insect Vectors/*virology ; Oryza ; *Radar ; Satellite Imagery/*methods ; }, abstract = {Vector mosquitoes of Japanese encephalitis (JE) breed mostly in rice fields, and human cases occur scattered over extended rural rice-growing areas. From this, one may surmise an ecological connection with the irrigation facilities and paddy cultivation. Furthermore, it has been hypothesized that a particular stage of paddy growth is a premonitory sign that can lead to a markedly increased population of the vector mosquitoes. The present study aimed to forecast the vector abundance by monitoring the paddy growth using remote sensing and geographical information systems. The abundance of the JE vector Culex tritaeniorhynchus peaked when the paddy crop was at its heading stage and dipped when the crop reached the maturing stage. A significant positive correlation was observed between paddy growth and adult density (r = 0.73, p < 0.008). The sigma naught values (σ0) derived from satellite images of paddy fields ranged from -18.3 (during transplantation stage) to approximately -10 (during the noncultivation period). A significant positive correlation was observed between σ0 and paddy growth stages (r = 0.87, p < 0.05) and adult vector density (r = 0.74, p = 0.04). The σ0 value observed during the vegetative and flowering stages of paddy growth ranged from -17.6 to -17.16, at which period the vector density started building up. This could be the spectral signature that denotes the "risk," following which a high vector abundance is expected during heading stage of the paddy.}, } @article {pmid26822217, year = {2016}, author = {Barać, N and Škrivanj, S and Bukumirić, Z and Živojinović, D and Manojlović, D and Barać, M and Petrović, R and Ćorac, A}, title = {Distribution and mobility of heavy elements in floodplain agricultural soils along the Ibar River (Southern Serbia and Northern Kosovo). Chemometric investigation of pollutant sources and ecological risk assessment.}, journal = {Environmental science and pollution research international}, volume = {23}, number = {9}, pages = {9000-9011}, pmid = {26822217}, issn = {1614-7499}, mesh = {Agriculture ; Ecology ; *Environmental Monitoring ; Industry ; Kosovo ; Metals, Heavy/*analysis ; Risk Assessment ; Rivers/chemistry ; Serbia ; Soil/chemistry ; Soil Pollutants/*analysis ; }, abstract = {This work investigates the influence of a high-magnitude flood event on heavy elements (HEs) pollution and mobility in the agricultural soils along Ibar River in Southern Serbia and Northern Kosovo. The study area was one of the most important Pb/Zn industrial regions in Europe. Soil samples (n = 50) collected before and after the floods in May 2014 were subjected to the sequential extraction procedure proposed by the Community Bureau of Reference (BCR). The results indicated that the floods significantly increased not only the pseudo total concentrations of HEs in the soil but also their mobile and potentially bioavailable amounts. Moreover, higher concentrations (both pseudo total and potentially bioavailable) were found in the agricultural soils closer to the industrial hotspots. Principal component analysis and hierarchical cluster analysis successfully grouped the analyzed elements according to their anthropogenic or natural origin. The floods significantly increased the potential ecological risk of HEs associated with Pb/Zn industrial activities in the study area. The potential ecological risk of Cd after the floods was highest and should be of special concern.}, } @article {pmid26821913, year = {2016}, author = {Ogilvie, HA and Heled, J and Xie, D and Drummond, AJ}, title = {Computational Performance and Statistical Accuracy of *BEAST and Comparisons with Other Methods.}, journal = {Systematic biology}, volume = {65}, number = {3}, pages = {381-396}, pmid = {26821913}, issn = {1076-836X}, mesh = {Bayes Theorem ; Biological Evolution ; Classification/*methods ; Data Interpretation, Statistical ; Evolution, Molecular ; Models, Genetic ; *Phylogeny ; *Software ; }, abstract = {Under the multispecies coalescent model of molecular evolution, gene trees have independent evolutionary histories within a shared species tree. In comparison, supermatrix concatenation methods assume that gene trees share a single common genealogical history, thereby equating gene coalescence with species divergence. The multispecies coalescent is supported by previous studies which found that its predicted distributions fit empirical data, and that concatenation is not a consistent estimator of the species tree. *BEAST, a fully Bayesian implementation of the multispecies coalescent, is popular but computationally intensive, so the increasing size of phylogenetic data sets is both a computational challenge and an opportunity for better systematics. Using simulation studies, we characterize the scaling behavior of *BEAST, and enable quantitative prediction of the impact increasing the number of loci has on both computational performance and statistical accuracy. Follow-up simulations over a wide range of parameters show that the statistical performance of *BEAST relative to concatenation improves both as branch length is reduced and as the number of loci is increased. Finally, using simulations based on estimated parameters from two phylogenomic data sets, we compare the performance of a range of species tree and concatenation methods to show that using *BEAST with tens of loci can be preferable to using concatenation with thousands of loci. Our results provide insight into the practicalities of Bayesian species tree estimation, the number of loci required to obtain a given level of accuracy and the situations in which supermatrix or summary methods will be outperformed by the fully Bayesian multispecies coalescent.}, } @article {pmid26820986, year = {2016}, author = {Day, T and Read, AF}, title = {Does High-Dose Antimicrobial Chemotherapy Prevent the Evolution of Resistance?.}, journal = {PLoS computational biology}, volume = {12}, number = {1}, pages = {e1004689}, pmid = {26820986}, issn = {1553-7358}, mesh = {Animals ; Anti-Infective Agents/*administration & dosage/*pharmacology ; *Biological Evolution ; Communicable Diseases/drug therapy ; Computational Biology ; Drug Resistance/*drug effects ; Drug Therapy ; Humans ; Mice ; Models, Biological ; }, abstract = {High-dose chemotherapy has long been advocated as a means of controlling drug resistance in infectious diseases but recent empirical studies have begun to challenge this view. We develop a very general framework for modeling and understanding resistance emergence based on principles from evolutionary biology. We use this framework to show how high-dose chemotherapy engenders opposing evolutionary processes involving the mutational input of resistant strains and their release from ecological competition. Whether such therapy provides the best approach for controlling resistance therefore depends on the relative strengths of these processes. These opposing processes typically lead to a unimodal relationship between drug pressure and resistance emergence. As a result, the optimal drug dose lies at either end of the therapeutic window of clinically acceptable concentrations. We illustrate our findings with a simple model that shows how a seemingly minor change in parameter values can alter the outcome from one where high-dose chemotherapy is optimal to one where using the smallest clinically effective dose is best. A review of the available empirical evidence provides broad support for these general conclusions. Our analysis opens up treatment options not currently considered as resistance management strategies, and it also simplifies the experiments required to determine the drug doses which best retard resistance emergence in patients.}, } @article {pmid26820846, year = {2016}, author = {Mair, L and Ruete, A}, title = {Explaining Spatial Variation in the Recording Effort of Citizen Science Data across Multiple Taxa.}, journal = {PloS one}, volume = {11}, number = {1}, pages = {e0147796}, pmid = {26820846}, issn = {1932-6203}, mesh = {Animal Distribution ; Animals ; Conservation of Natural Resources ; *Data Collection ; Data Interpretation, Statistical ; Humans ; Knowledge ; Observer Variation ; Sweden ; }, abstract = {The collation of citizen science data in open-access biodiversity databases makes temporally and spatially extensive species' observation data available to a wide range of users. Such data are an invaluable resource but contain inherent limitations, such as sampling bias in favour of recorder distribution, lack of survey effort assessment, and lack of coverage of the distribution of all organisms. Any technical assessment, monitoring program or scientific research applying citizen science data should therefore include an evaluation of the uncertainty of its results. We use 'ignorance' scores, i.e. spatially explicit indices of sampling bias across a study region, to further understand spatial patterns of observation behaviour for 13 reference taxonomic groups. The data is based on voluntary observations made in Sweden between 2000 and 2014. We compared the effect of six geographical variables (elevation, steepness, population density, log population density, road density and footpath density) on the ignorance scores of each group. We found substantial variation among taxonomic groups in the relative importance of different geographic variables for explaining ignorance scores. In general, road access and logged population density were consistently important variables explaining bias in sampling effort, indicating that access at a landscape-scale facilitates voluntary reporting by citizen scientists. Also, small increases in population density can produce a substantial reduction in ignorance score. However the between-taxa variation in the importance of geographic variables for explaining ignorance scores demonstrated that different taxa suffer from different spatial biases. We suggest that conservationists and researchers should use ignorance scores to acknowledge uncertainty in their analyses and conclusions, because they may simultaneously include many correlated variables that are difficult to disentangle.}, } @article {pmid26818626, year = {2016}, author = {Trucchi, E and Mazzarella, AB and Gilfillan, GD and Lorenzo, MT and Schönswetter, P and Paun, O}, title = {BsRADseq: screening DNA methylation in natural populations of non-model species.}, journal = {Molecular ecology}, volume = {25}, number = {8}, pages = {1697-1713}, pmid = {26818626}, issn = {1365-294X}, support = {Y 661/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Animals ; Caryophyllaceae/classification/*genetics ; Computational Biology ; *DNA Methylation ; *Epigenesis, Genetic ; *Genetics, Population ; Genome ; Orchidaceae/classification/*genetics ; Polymorphism, Single Nucleotide ; Sequence Analysis, DNA ; Smegmamorpha/*genetics ; }, abstract = {Epigenetic modifications are expected to occur at a much faster rate than genetic mutations, potentially causing isolated populations to stochastically drift apart, or if they are subjected to different selective regimes, to directionally diverge. A high level of genome-wide epigenetic divergence between individuals occupying distinct habitats is therefore predicted. Here, we introduce bisulfite-converted restriction site associated DNA sequencing (bsRADseq), an approach to quantify the level of DNA methylation differentiation across multiple individuals. This reduced representation method is flexible in the extent of DNA sequence interrogated. We showcase its applicability in three natural systems, each comprising individuals adapted to divergent environments: a diploid plant (Heliosperma, Caryophyllaceae), a tetraploid plant (Dactylorhiza, Orchidaceae) and an animal (Gasterosteusaculeatus, Gasterosteidae). We present a robust bioinformatic pipeline, combining tools for RAD locus assembly, SNP calling, bisulfite-converted read mapping and DNA methylation calling to analyse bsRADseq data with or without a reference genome. Importantly, our approach accurately distinguishes between SNPs and methylation polymorphism (SMPs). Although DNA methylation frequency between different positions of a genome varies widely, we find a surprisingly high consistency in the methylation profile between individuals thriving in divergent ecological conditions, particularly in Heliosperma. This constitutive stability points to significant molecular or developmental constraints acting on DNA methylation variation. Altogether, by combining the flexibility of RADseq with the accuracy of bisulfite sequencing in quantifying DNA methylation, the bsRADseq methodology and our bioinformatic pipeline open up the opportunity for genome-wide epigenetic investigations of evolutionary and ecological relevance in non-model species, independent of their genomic features.}, } @article {pmid26817767, year = {2016}, author = {Bellard, C and Genovesi, P and Jeschke, JM}, title = {Global patterns in threats to vertebrates by biological invasions.}, journal = {Proceedings. Biological sciences}, volume = {283}, number = {1823}, pages = {}, pmid = {26817767}, issn = {1471-2954}, mesh = {Animals ; Biodiversity ; Databases, Factual ; Endangered Species ; *Environmental Monitoring ; *Extinction, Biological ; Internationality ; *Introduced Species ; *Vertebrates ; }, abstract = {Biological invasions as drivers of biodiversity loss have recently been challenged. Fundamentally, we must know where species that are threatened by invasive alien species (IAS) live, and the degree to which they are threatened. We report the first study linking 1372 vertebrates threatened by more than 200 IAS from the completely revised Global Invasive Species Database. New maps of the vulnerability of threatened vertebrates to IAS permit assessments of whether IAS have a major influence on biodiversity, and if so, which taxonomic groups are threatened and where they are threatened. We found that centres of IAS-threatened vertebrates are concentrated in the Americas, India, Indonesia, Australia and New Zealand. The areas in which IAS-threatened species are located do not fully match the current hotspots of invasions, or the current hotspots of threatened species. The relative importance of biological invasions as drivers of biodiversity loss clearly varies across regions and taxa, and changes over time, with mammals from India, Indonesia, Australia and Europe are increasingly being threatened by IAS. The chytrid fungus primarily threatens amphibians, whereas invasive mammals primarily threaten other vertebrates. The differences in IAS threats between regions and taxa can help efficiently target IAS, which is essential for achieving the Strategic Plan 2020 of the Convention on Biological Diversity.}, } @article {pmid26815143, year = {2016}, author = {Zhao, P and Zhang, J and Zhao, X and Chen, G and Ma, XF}, title = {Different Sets of Post-Embryonic Development Genes Are Conserved or Lost in Two Caryophyllales Species (Reaumuria soongorica and Agriophyllum squarrosum).}, journal = {PloS one}, volume = {11}, number = {1}, pages = {e0148034}, pmid = {26815143}, issn = {1932-6203}, mesh = {Arabidopsis/genetics/growth & development ; Evolution, Molecular ; *Gene Expression Regulation, Developmental ; *Gene Expression Regulation, Plant ; Gene Ontology ; *Genes, Plant ; Magnoliopsida/*genetics/growth & development ; Multigene Family ; Transcriptome ; }, abstract = {Reaumuria soongorica and sand rice (Agriophyllum squarrosum) belong to the clade of Caryophyllales and are widely distributed in the desert regions of north China. Both plants have evolved many specific traits and adaptation strategies to cope with recurring environmental threats. However, the genetic basis that underpins their unique traits and adaptation remains unknown. In this study, the transcriptome data of R. soongorica and sand rice were compared with three other species with previously sequenced genomes (Arabidopsis thaliana, Oryza sativa, and Beta vulgaris). Four different gene sets were identified, namely, the genes conserved in both species, those lost in both species, those conserved in R. soongorica only, and those conserved in sand rice only. Gene ontology showed that post-embryonic development genes (PEDGs) were enriched in all gene sets, and different sets of PEDGs were conserved or lost in both the R. soongorica and sand rice genomes. Expression profiles of Arabidopsis orthologs further provided some clues to the function of the species-specific conserved PEDGs. Such orthologs included LEAFY PETIOLE, which could be a candidate gene involved in the development of branch priority in sand rice.}, } @article {pmid26814420, year = {2016}, author = {Salguero-Gómez, R and Jones, OR and Archer, CR and Bein, C and de Buhr, H and Farack, C and Gottschalk, F and Hartmann, A and Henning, A and Hoppe, G and Römer, G and Ruoff, T and Sommer, V and Wille, J and Voigt, J and Zeh, S and Vieregg, D and Buckley, YM and Che-Castaldo, J and Hodgson, D and Scheuerlein, A and Caswell, H and Vaupel, JW}, title = {COMADRE: a global data base of animal demography.}, journal = {The Journal of animal ecology}, volume = {85}, number = {2}, pages = {371-384}, pmid = {26814420}, issn = {1365-2656}, mesh = {Animals ; *Databases, Factual ; *Demography ; Ecology/*methods ; *Models, Biological ; }, abstract = {UNLABELLED: The open-data scientific philosophy is being widely adopted and proving to promote considerable progress in ecology and evolution. Open-data global data bases now exist on animal migration, species distribution, conservation status, etc. However, a gap exists for data on population dynamics spanning the rich diversity of the animal kingdom world-wide. This information is fundamental to our understanding of the conditions that have shaped variation in animal life histories and their relationships with the environment, as well as the determinants of invasion and extinction. Matrix population models (MPMs) are among the most widely used demographic tools by animal ecologists. MPMs project population dynamics based on the reproduction, survival and development of individuals in a population over their life cycle. The outputs from MPMs have direct biological interpretations, facilitating comparisons among animal species as different as Caenorhabditis elegans, Loxodonta africana and Homo sapiens. Thousands of animal demographic records exist in the form of MPMs, but they are dispersed throughout the literature, rendering comparative analyses difficult. Here, we introduce the COMADRE Animal Matrix Database, an open-data online repository, which in its version 1.0.0 contains data on 345 species world-wide, from 402 studies with a total of 1625 population projection matrices. COMADRE also contains ancillary information (e.g. ecoregion, taxonomy, biogeography, etc.) that facilitates interpretation of the numerous demographic metrics that can be derived from its MPMs. We provide R code to some of these examples.

SYNTHESIS: We introduce the COMADRE Animal Matrix Database, a resource for animal demography. Its open-data nature, together with its ancillary information, will facilitate comparative analysis, as will the growing availability of databases focusing on other aspects of the rich animal diversity, and tools to query and combine them. Through future frequent updates of COMADRE, and its integration with other online resources, we encourage animal ecologists to tackle global ecological and evolutionary questions with unprecedented sample size.}, } @article {pmid26812397, year = {2016}, author = {Ramachandran, A and Radhapriya, P and Jayakumar, S and Dhanya, P and Geetha, R}, title = {Critical Analysis of Forest Degradation in the Southern Eastern Ghats of India: Comparison of Satellite Imagery and Soil Quality Index.}, journal = {PloS one}, volume = {11}, number = {1}, pages = {e0147541}, pmid = {26812397}, issn = {1932-6203}, mesh = {Biodiversity ; *Environmental Monitoring ; *Forests ; India ; Principal Component Analysis ; Satellite Imagery ; Soil/*chemistry ; }, abstract = {India has one of the largest assemblages of tropical biodiversity, with its unique floristic composition of endemic species. However, current forest cover assessment is performed via satellite-based forest surveys, which have many limitations. The present study, which was performed in the Eastern Ghats, analysed the satellite-based inventory provided by forest surveys and inferred from the results that this process no longer provides adequate information for quantifying forest degradation in an empirical manner. The study analysed 21 soil properties and generated a forest soil quality index of the Eastern Ghats, using principal component analysis. Using matrix modules and geospatial technology, we compared the forest degradation status calculated from satellite-based forest surveys with the degradation status calculated from the forest soil quality index. The Forest Survey of India classified about 1.8% of the Eastern Ghats' total area as degraded forests and the remainder (98.2%) as open, dense, and very dense forests, whereas the soil quality index results found that about 42.4% of the total area is degraded, with the remainder (57.6%) being non-degraded. Our ground truth verification analyses indicate that the forest soil quality index along with the forest cover density data from the Forest Survey of India are ideal tools for evaluating forest degradation.}, } @article {pmid26812300, year = {2016}, author = {Thabet, R and Rouault, JD and Ayadi, H and Leignel, V}, title = {Structural analysis of the α subunit of Na(+)/K(+) ATPase genes in invertebrates.}, journal = {Comparative biochemistry and physiology. Part B, Biochemistry & molecular biology}, volume = {196-197}, number = {}, pages = {11-18}, doi = {10.1016/j.cbpb.2016.01.007}, pmid = {26812300}, issn = {1879-1107}, mesh = {Amino Acid Sequence ; Animals ; Biocatalysis ; Databases, Genetic ; Evolution, Molecular ; *Genomics ; Invertebrates/*enzymology/genetics/metabolism ; Phylogeny ; Protein Subunits/chemistry/*genetics/metabolism ; Sodium-Potassium-Exchanging ATPase/chemistry/*genetics/metabolism ; }, abstract = {The Na(+)/K(+) ATPase is a ubiquitous pump coordinating the transport of Na(+) and K(+) across the membrane of cells and its role is fundamental to cellular functions. It is heteromer in eukaryotes including two or three subunits (α, β and γ which is specific to the vertebrates). The catalytic functions of the enzyme have been attributed to the α subunit. Several complete α protein sequences are available, but only few gene structures were characterized. We identified the genomic sequences coding the α-subunit of the Na(+)/K(+) ATPase, from the whole-genome shotgun contigs (WGS), NCBI Genomes (chromosome), Genomic Survey Sequences (GSS) and High Throughput Genomic Sequences (HTGS) databases across distinct phyla. One copy of the α subunit gene was found in Annelida, Arthropoda, Cnidaria, Echinodermata, Hemichordata, Mollusca, Placozoa, Porifera, Platyhelminthes, Urochordata, but the nematodes seem to possess 2 to 4 copies. The number of introns varied from 0 (Platyhelminthes) to 26 (Porifera); and their localization and length are also highly variable. Molecular phylogenies (Maximum Likelihood and Maximum Parsimony methods) showed some clusters constituted by (Chordata/(Echinodermata/Hemichordata)) or (Plathelminthes/(Annelida/Mollusca)) and a basal position for Porifera. These structural analyses increase our knowledge about the evolutionary events of the α subunit genes in the invertebrates.}, } @article {pmid26812054, year = {2016}, author = {Tosas Auguet, O and Betley, JR and Stabler, RA and Patel, A and Ioannou, A and Marbach, H and Hearn, P and Aryee, A and Goldenberg, SD and Otter, JA and Desai, N and Karadag, T and Grundy, C and Gaunt, MW and Cooper, BS and Edgeworth, JD and Kypraios, T}, title = {Evidence for Community Transmission of Community-Associated but Not Health-Care-Associated Methicillin-Resistant Staphylococcus Aureus Strains Linked to Social and Material Deprivation: Spatial Analysis of Cross-sectional Data.}, journal = {PLoS medicine}, volume = {13}, number = {1}, pages = {e1001944}, pmid = {26812054}, issn = {1549-1676}, support = {/WT_/Wellcome Trust/United Kingdom ; 106698/Z/14/Z/WT_/Wellcome Trust/United Kingdom ; MR/K006924/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Adolescent ; Adult ; Aged ; Child ; Child, Preschool ; Community-Acquired Infections/diagnosis/*epidemiology/psychology ; *Cross Infection ; Cross-Sectional Studies ; Data Interpretation, Statistical ; Female ; Humans ; Infant ; Infant, Newborn ; London/epidemiology ; Male ; *Maternal Deprivation ; *Methicillin-Resistant Staphylococcus aureus/isolation & purification ; Middle Aged ; *Social Isolation/psychology ; Staphylococcal Infections/diagnosis/*epidemiology/psychology ; Young Adult ; }, abstract = {BACKGROUND: Identifying and tackling the social determinants of infectious diseases has become a public health priority following the recognition that individuals with lower socioeconomic status are disproportionately affected by infectious diseases. In many parts of the world, epidemiologically and genotypically defined community-associated (CA) methicillin-resistant Staphylococcus aureus (MRSA) strains have emerged to become frequent causes of hospital infection. The aim of this study was to use spatial models with adjustment for area-level hospital attendance to determine the transmission niche of genotypically defined CA- and health-care-associated (HA)-MRSA strains across a diverse region of South East London and to explore a potential link between MRSA carriage and markers of social and material deprivation.

METHODS AND FINDINGS: This study involved spatial analysis of cross-sectional data linked with all MRSA isolates identified by three National Health Service (NHS) microbiology laboratories between 1 November 2011 and 29 February 2012. The cohort of hospital-based NHS microbiology diagnostic services serves 867,254 usual residents in the Lambeth, Southwark, and Lewisham boroughs in South East London, United Kingdom (UK). Isolates were classified as HA- or CA-MRSA based on whole genome sequencing. All MRSA cases identified over 4 mo within the three-borough catchment area (n = 471) were mapped to small geographies and linked to area-level aggregated socioeconomic and demographic data. Disease mapping and ecological regression models were used to infer the most likely transmission niches for each MRSA genetic classification and to describe the spatial epidemiology of MRSA in relation to social determinants. Specifically, we aimed to identify demographic and socioeconomic population traits that explain cross-area extra variation in HA- and CA-MRSA relative risks following adjustment for hospital attendance data. We explored the potential for associations with the English Indices of Deprivation 2010 (including the Index of Multiple Deprivation and several deprivation domains and subdomains) and the 2011 England and Wales census demographic and socioeconomic indicators (including numbers of households by deprivation dimension) and indicators of population health. Both CA-and HA-MRSA were associated with household deprivation (CA-MRSA relative risk [RR]: 1.72 [1.03-2.94]; HA-MRSA RR: 1.57 [1.06-2.33]), which was correlated with hospital attendance (Pearson correlation coefficient [PCC] = 0.76). HA-MRSA was also associated with poor health (RR: 1.10 [1.01-1.19]) and residence in communal care homes (RR: 1.24 [1.12-1.37]), whereas CA-MRSA was linked with household overcrowding (RR: 1.58 [1.04-2.41]) and wider barriers, which represent a combined score for household overcrowding, low income, and homelessness (RR: 1.76 [1.16-2.70]). CA-MRSA was also associated with recent immigration to the UK (RR: 1.77 [1.19-2.66]). For the area-level variation in RR for CA-MRSA, 28.67% was attributable to the spatial arrangement of target geographies, compared with only 0.09% for HA-MRSA. An advantage to our study is that it provided a representative sample of usual residents receiving care in the catchment areas. A limitation is that relationships apparent in aggregated data analyses cannot be assumed to operate at the individual level.

CONCLUSIONS: There was no evidence of community transmission of HA-MRSA strains, implying that HA-MRSA cases identified in the community originate from the hospital reservoir and are maintained by frequent attendance at health care facilities. In contrast, there was a high risk of CA-MRSA in deprived areas linked with overcrowding, homelessness, low income, and recent immigration to the UK, which was not explainable by health care exposure. Furthermore, areas adjacent to these deprived areas were themselves at greater risk of CA-MRSA, indicating community transmission of CA-MRSA. This ongoing community transmission could lead to CA-MRSA becoming the dominant strain types carried by patients admitted to hospital, particularly if successful hospital-based MRSA infection control programmes are maintained. These results suggest that community infection control programmes targeting transmission of CA-MRSA will be required to control MRSA in both the community and hospital. These epidemiological changes will also have implications for effectiveness of risk-factor-based hospital admission MRSA screening programmes.}, } @article {pmid26809315, year = {2016}, author = {Schrider, DR and Hahn, MW and Begun, DJ}, title = {Parallel Evolution of Copy-Number Variation across Continents in Drosophila melanogaster.}, journal = {Molecular biology and evolution}, volume = {33}, number = {5}, pages = {1308-1316}, pmid = {26809315}, issn = {1537-1719}, support = {F32 GM105231/GM/NIGMS NIH HHS/United States ; R01 GM084056/GM/NIGMS NIH HHS/United States ; R01 GM110258/GM/NIGMS NIH HHS/United States ; }, mesh = {Adaptation, Physiological/*genetics ; Animals ; Biological Evolution ; *DNA Copy Number Variations ; Drosophila melanogaster/*genetics ; Evolution, Molecular ; Female ; Gene Frequency ; Genetic Variation ; Genetics, Population/methods ; Phylogeny ; Phylogeography/methods ; Polymorphism, Single Nucleotide ; Selection, Genetic ; }, abstract = {Genetic differentiation across populations that is maintained in the presence of gene flow is a hallmark of spatially varying selection. In Drosophila melanogaster, the latitudinal clines across the eastern coasts of Australia and North America appear to be examples of this type of selection, with recent studies showing that a substantial portion of the D. melanogaster genome exhibits allele frequency differentiation with respect to latitude on both continents. As of yet there has been no genome-wide examination of differentiated copy-number variants (CNVs) in these geographic regions, despite their potential importance for phenotypic variation in Drosophila and other taxa. Here, we present an analysis of geographic variation in CNVs in D. melanogaster. We also present the first genomic analysis of geographic variation for copy-number variation in the sister species, D. simulans, in order to investigate patterns of parallel evolution in these close relatives. In D. melanogaster we find hundreds of CNVs, many of which show parallel patterns of geographic variation on both continents, lending support to the idea that they are influenced by spatially varying selection. These findings support the idea that polymorphic CNVs contribute to local adaptation in D. melanogaster In contrast, we find very few CNVs in D. simulans that are geographically differentiated in parallel on both continents, consistent with earlier work suggesting that clinal patterns are weaker in this species.}, } @article {pmid26808374, year = {2016}, author = {Ogbunugafor, CB and Wylie, CS and Diakite, I and Weinreich, DM and Hartl, DL}, title = {Adaptive Landscape by Environment Interactions Dictate Evolutionary Dynamics in Models of Drug Resistance.}, journal = {PLoS computational biology}, volume = {12}, number = {1}, pages = {e1004710}, pmid = {26808374}, issn = {1553-7358}, support = {R01 AI106734/AI/NIAID NIH HHS/United States ; AI106734/AI/NIAID NIH HHS/United States ; }, mesh = {Antimalarials/*pharmacology ; Computational Biology/*methods ; Drug Resistance/*genetics ; Evolution, Molecular ; Humans ; Inhibitory Concentration 50 ; Malaria, Falciparum/drug therapy/parasitology ; Models, Biological ; Mutation ; Plasmodium falciparum/*drug effects/*genetics ; Proguanil/pharmacology ; Pyrimethamine/pharmacology ; Triazines/pharmacology ; }, abstract = {The adaptive landscape analogy has found practical use in recent years, as many have explored how their understanding can inform therapeutic strategies that subvert the evolution of drug resistance. A major barrier to applications of these concepts is a lack of detail concerning how the environment affects adaptive landscape topography, and consequently, the outcome of drug treatment. Here we combine empirical data, evolutionary theory, and computer simulations towards dissecting adaptive landscape by environment interactions for the evolution of drug resistance in two dimensions-drug concentration and drug type. We do so by studying the resistance mediated by Plasmodium falciparum dihydrofolate reductase (DHFR) to two related inhibitors-pyrimethamine and cycloguanil-across a breadth of drug concentrations. We first examine whether the adaptive landscapes for the two drugs are consistent with common definitions of cross-resistance. We then reconstruct all accessible pathways across the landscape, observing how their structure changes with drug environment. We offer a mechanism for non-linearity in the topography of accessible pathways by calculating of the interaction between mutation effects and drug environment, which reveals rampant patterns of epistasis. We then simulate evolution in several different drug environments to observe how these individual mutation effects (and patterns of epistasis) influence paths taken at evolutionary "forks in the road" that dictate adaptive dynamics in silico. In doing so, we reveal how classic metrics like the IC50 and minimal inhibitory concentration (MIC) are dubious proxies for understanding how evolution will occur across drug environments. We also consider how the findings reveal ambiguities in the cross-resistance concept, as subtle differences in adaptive landscape topography between otherwise equivalent drugs can drive drastically different evolutionary outcomes. Summarizing, we discuss the results with regards to their basic contribution to the study of empirical adaptive landscapes, and in terms of how they inform new models for the evolution of drug resistance.}, } @article {pmid26806325, year = {2016}, author = {Wu, Y and Guo, J and Cai, Y and Gong, X and Xiong, X and Qi, W and Pang, Q and Wang, X and Wang, Y}, title = {Genome-wide identification and characterization of Eutrema salsugineum microRNAs for salt tolerance.}, journal = {Physiologia plantarum}, volume = {157}, number = {4}, pages = {453-468}, doi = {10.1111/ppl.12419}, pmid = {26806325}, issn = {1399-3054}, mesh = {Brassicaceae/drug effects/*genetics/physiology ; *Gene Expression Regulation, Plant ; Gene Library ; Gene Ontology ; Genome, Plant/*genetics ; High-Throughput Nucleotide Sequencing ; MicroRNAs/*genetics ; Salinity ; Salt Tolerance ; Salt-Tolerant Plants ; Sodium Chloride/pharmacology ; Stress, Physiological ; }, abstract = {Eutrema salsugineum, a close relative of Arabidopsis thaliana, is a valuable halophytic model plant that has extreme tolerance to salinity. As posttranscriptional gene regulators, microRNAs (miRNAs) control gene expression and a variety of biological processes, including plant-stress responses. To identify salt-stress responsive miRNAs in E. salsugineum and reveal their possible roles in the adaptive response to salt stress, we chose the Solexa sequencing platform to screen the miRNAs in 4-week-old E. salsugineum seedlings under salt treatment. A total of 82 conserved miRNAs belonging to 27 miRNA families and 17 novel miRNAs were identified and 11 conserved miRNA families and 4 novel miRNAs showed a significant response to salt stress. To investigate the possible biological roles of miRNAs, 1060 potential targets were predicted. Moreover, 35 gene ontology (GO) categories and 1 pathway, including a few terms that were directly and indirectly related to salt stress, were significantly enriched in the salt-stress-responsive miRNAs targets. The relative expression analysis of six target genes was analyzed using quantitative real-time polymerase chain reaction (PCR) and showed a negative correlation with their corresponding miRNAs. Many stress regulatory and phytohormone regulatory cis-regulatory elements were widely present in the promoter region of the salt-responsive miRNA precursors. This study describes the large-scale characterization of E. salsugineum miRNAs and provides a useful resource for further understanding of miRNA functions in the regulation of the E. salsugineum salt-stress response.}, } @article {pmid26805925, year = {2017}, author = {Xu, XH and Lv, ZQ and Zhou, XY and Jiang, N}, title = {Drought prediction and sustainable development of the ecological environment.}, journal = {Environmental science and pollution research international}, volume = {24}, number = {35}, pages = {26974-26982}, doi = {10.1007/s11356-015-6011-4}, pmid = {26805925}, issn = {1614-7499}, mesh = {China ; Conservation of Natural Resources/*methods ; *Droughts ; Geographic Information Systems ; *Models, Theoretical ; Prognosis ; *Rain ; Seasons ; }, abstract = {In the 1990s ecological early warning research began with the aim of elucidating the effect of drought in dry regions of the world. Drought has been a prevalent natural disaster, ravaging the Yun'nan province of China for over 5 years since 2009. Due to the extensive range, depth and devastating losses, the drought has reached a once-in-a-century severity. Yun'nan province suffered particularly badly from the drought, which took its toll on both the ecological environment and the sustainable economic development of the province. We chose to study Pu'er city in Yun'nun province for this research, and analysed the drought traits of Pu'er city utilizing geographic information technology. We applied the Mann-Kendall test for trend, linear tendency estimation and percentage of precipitation anomalies, as well as using combinations of monthly data searches of meteorological reports from 1980-2010. The results showed that except for a small rise in spring precipitation, the overall rainfall of Pu'er city showed a decreasing trend. The results of this study can provide an adequate and reliable theoretical basis and technological methods for use in government decision making, and promote research into early warning ecology.}, } @article {pmid26803258, year = {2016}, author = {D'Antonio, A and Monz, C}, title = {The influence of visitor use levels on visitor spatial behavior in off-trail areas of dispersed recreation use.}, journal = {Journal of environmental management}, volume = {170}, number = {}, pages = {79-87}, doi = {10.1016/j.jenvman.2016.01.011}, pmid = {26803258}, issn = {1095-8630}, mesh = {California ; Conservation of Natural Resources/*methods ; *Geographic Information Systems ; Humans ; *Recreation ; *Spatial Behavior ; Wyoming ; }, abstract = {A variety of social and ecological factors influence the level and extent of ecological change that occurs in a park or protected area. Understanding these factors and how they are interrelated can help managers prevent undesirable ecological impacts, especially in areas without formal trails and visitor sites. This study examines the relationship between levels of visitor use and spatial patterns of visitor behavior at a variety of backcountry recreation destinations. Current assumptions in both the literature and simulation modeling efforts assume that visitor behavior either does not change with use level or that visitors are more likely to disperse at high levels of visitor use. Using visitor counts and GPS tracks of visitor behavior in locations where visitors could disperse off-trail, we found that visitors' spatial behavior does vary with visitor use level in some recreation settings, however the patterns of visitor behavior observed in this study are sometimes contrary to current generalizations. When visitor behavior does vary with use level, visitors are dispersing more at low levels of visitor use not when use level is high. Overall, these findings suggest that in certain situations the amount of visitor use at a recreation destination may be a less important driver of ecological change than visitor behavior.}, } @article {pmid26794310, year = {2016}, author = {Liu, S and Li, L and Tong, C and Zhao, Q and Lukyanov, PA and Chernikov, OV and Li, W}, title = {Quantitative proteomic analysis of the effects of a GalNAc/Man-specific lectin CSL on yeast cells by label-free LC-MS.}, journal = {International journal of biological macromolecules}, volume = {85}, number = {}, pages = {530-538}, doi = {10.1016/j.ijbiomac.2016.01.034}, pmid = {26794310}, issn = {1879-0003}, mesh = {Computational Biology/methods ; Ethanol/metabolism ; Fermentation ; Glucose/metabolism ; Lectins/*pharmacology ; *Proteome ; *Proteomics/methods ; Saccharomyces cerevisiae/metabolism ; Saccharomyces cerevisiae Proteins/metabolism ; Yeasts/*drug effects/*metabolism ; }, abstract = {A Ca(2+)-dependent GalNAc/Man-specific lectin (CSL) from Cyclina sinensis was isolated, and its stimulatory action was characterized in yeast. CSL showed a potent effect on the production of ethanol by Saccharomyces cerevisiae. In this work, the changes in the protein expression profiles of S. cerevisiae after 24h of incubation with CSL were analyzed using label-free quantitative proteomics. A total of 1410 proteins were identified, but only 117 proteins showed significant differences in normalized volume (p<0.05). Among the latter proteins, 24 proteins were up-regulated, and 93 were down-regulated. Analysis of the proteome revealed that CSL triggered changes in the concentrations of some enzymes, such as increased expression of hexokinase, glyceraldehyde 3-phosphate dehydrogenase and enolase and decreased expression of dihydrolipoamide dehydrogenase and aldehyde dehydrogenase. These results indicate that CSL can cause some changes in the metabolic pathway involved in ethanol synthesis in S. cerevisiae. These data may help us understand the stimulatory mechanism of lectin in the fermentation process.}, } @article {pmid26792236, year = {2016}, author = {Brill, JL and Belanger, SE and Chaney, JG and Dyer, SD and Raimondo, S and Barron, MG and Pittinger, CA}, title = {Development of algal interspecies correlation estimation models for chemical hazard assessment.}, journal = {Environmental toxicology and chemistry}, volume = {35}, number = {9}, pages = {2368-2378}, doi = {10.1002/etc.3375}, pmid = {26792236}, issn = {1552-8618}, mesh = {Animals ; Chlorophyta/*drug effects/growth & development ; Cyanobacteria/*drug effects/growth & development ; Diatoms/*drug effects/growth & development ; Environmental Monitoring ; Hazardous Substances/*toxicity ; *Models, Theoretical ; Sample Size ; Species Specificity ; Water Pollutants, Chemical/*toxicity ; }, abstract = {Web-based Interspecies Correlation Estimation (ICE) is an application developed to predict the acute toxicity of a chemical from 1 species to another taxon. Web-ICE models use the acute toxicity value for a surrogate species to predict effect values for other species, thus potentially filling in data gaps for a variety of environmental assessment purposes. Web-ICE has historically been dominated by aquatic and terrestrial animal prediction models. Web-ICE models for algal species were essentially absent and are addressed in the present study. A compilation of public and private sector-held algal toxicity data were compiled and reviewed for quality based on relevant aspects of individual studies. Interspecies correlations were constructed from the most commonly tested algal genera for a broad spectrum of chemicals. The ICE regressions were developed based on acute 72-h and 96-h endpoint values involving 1647 unique studies on 476 unique chemicals encompassing 40 genera and 70 species of green, blue-green, and diatom algae. Acceptance criteria for algal ICE models were established prior to evaluation of individual models and included a minimum sample size of 3, a statistically significant regression slope, and a slope estimation parameter ≥0.65. A total of 186 ICE models were possible at the genus level, with 21 meeting quality criteria; and 264 ICE models were developed at the species level, with 32 meeting quality criteria. Algal ICE models will have broad utility in screening environmental hazard assessments, data gap filling in certain regulatory scenarios, and as supplemental information to derive species sensitivity distributions. Environ Toxicol Chem 2016;35:2368-2378. Published 2016 Wiley Periodicals Inc. on behalf of SETAC. This article is a US government work and, as such, is in the public domain in the United States of America.}, } @article {pmid26790568, year = {2016}, author = {Anderson-Teixeira, KJ and Wang, MM and McGarvey, JC and LeBauer, DS}, title = {Carbon dynamics of mature and regrowth tropical forests derived from a pantropical database (TropForC-db).}, journal = {Global change biology}, volume = {22}, number = {5}, pages = {1690-1709}, doi = {10.1111/gcb.13226}, pmid = {26790568}, issn = {1365-2486}, mesh = {*Carbon Cycle ; Databases, Factual ; *Forests ; Tropical Climate ; }, abstract = {Tropical forests play a critical role in the global carbon (C) cycle, storing ~45% of terrestrial C and constituting the largest component of the terrestrial C sink. Despite their central importance to the global C cycle, their ecosystem-level C cycles are not as well-characterized as those of extra-tropical forests, and knowledge gaps hamper efforts to quantify C budgets across the tropics and to model tropical forest-climate interactions. To advance understanding of C dynamics of pantropical forests, we compiled a new database, the Tropical Forest C database (TropForC-db), which contains data on ground-based measurements of ecosystem-level C stocks and annual fluxes along with disturbance history. This database currently contains 3568 records from 845 plots in 178 geographically distinct areas, making it the largest and most comprehensive database of its type. Using TropForC-db, we characterized C stocks and fluxes for young, intermediate-aged, and mature forests. Relative to existing C budgets of extra-tropical forests, mature tropical broadleaf evergreen forests had substantially higher gross primary productivity (GPP) and ecosystem respiration (Reco), their autotropic respiration (Ra) consumed a larger proportion (~67%) of GPP, and their woody stem growth (ANPPstem) represented a smaller proportion of net primary productivity (NPP, ~32%) or GPP (~9%). In regrowth stands, aboveground biomass increased rapidly during the first 20 years following stand-clearing disturbance, with slower accumulation following agriculture and in deciduous forests, and continued to accumulate at a slower pace in forests aged 20-100 years. Most other C stocks likewise increased with stand age, while potential to describe age trends in C fluxes was generally data-limited. We expect that TropForC-db will prove useful for model evaluation and for quantifying the contribution of forests to the global C cycle. The database version associated with this publication is archived in Dryad (DOI: 10.5061/dryad.t516f) and a dynamic version is maintained at https://github.com/forc-db.}, } @article {pmid26789360, year = {2016}, author = {Bundschuh, R and Kuhn, U and Bundschuh, M and Naegele, C and Elsaesser, D and Schlechtriemen, U and Oehen, B and Hilbeck, A and Otto, M and Schulz, R and Hofmann, F}, title = {Prioritizing stream types according to their potential risk to receive crop plant material--A GIS-based procedure to assist in the risk assessment of genetically modified crops and systemic insecticide residues.}, journal = {The Science of the total environment}, volume = {547}, number = {}, pages = {226-233}, doi = {10.1016/j.scitotenv.2015.12.124}, pmid = {26789360}, issn = {1879-1026}, mesh = {*Crops, Agricultural ; Environmental Monitoring/*methods ; Geographic Information Systems ; Germany ; Insecticides/*analysis ; Pesticide Residues/analysis ; *Plants, Genetically Modified ; Risk Assessment ; Rivers/chemistry ; Water Pollutants, Chemical/*analysis ; Water Pollution, Chemical/*statistics & numerical data ; }, abstract = {Crop plant residues may enter aquatic ecosystems via wind deposition or surface runoff. In the case of genetically modified crops or crops treated with systemic pesticides, these materials may contain insecticidal Bt toxins or pesticides that potentially affect aquatic life. However, the particular exposure pattern of aquatic ecosystems (i.e., via plant material) is not properly reflected in current risk assessment schemes, which primarily focus on waterborne toxicity and not on plant material as the route of uptake. To assist in risk assessment, the present study proposes a prioritization procedure of stream types based on the freshwater network and crop-specific cultivation data using maize in Germany as a model system. To identify stream types with a high probability of receiving crop materials, we developed a formalized, criteria-based and thus transparent procedure that considers the exposure-related parameters, ecological status--an estimate of the diversity and potential vulnerability of local communities towards anthropogenic stress--and availability of uncontaminated reference sections. By applying the procedure to maize, ten stream types out of 38 are expected to be the most relevant if the ecological effects from plant-incorporated pesticides need to be evaluated. This information is an important first step to identifying habitats within these stream types with a high probability of receiving crop plant material at a more local scale, including accumulation areas. Moreover, the prioritization procedure developed in the present study may support the selection of aquatic species for ecotoxicological testing based on their probability of occurrence in stream types having a higher chance of exposure. Finally, this procedure can be adapted to any geographical region or crop of interest and is, therefore, a valuable tool for a site-specific risk assessment of crop plants carrying systemic pesticides or novel proteins, such as insecticidal Bt toxins, expressed in genetically modified crops.}, } @article {pmid26789284, year = {2016}, author = {Higashi, K and Tobe, T and Kanai, A and Uyar, E and Ishikawa, S and Suzuki, Y and Ogasawara, N and Kurokawa, K and Oshima, T}, title = {H-NS Facilitates Sequence Diversification of Horizontally Transferred DNAs during Their Integration in Host Chromosomes.}, journal = {PLoS genetics}, volume = {12}, number = {1}, pages = {e1005796}, pmid = {26789284}, issn = {1553-7404}, mesh = {Adaptation, Biological/genetics ; Chromosomes, Bacterial ; DNA-Binding Proteins/*genetics ; Escherichia coli/*genetics ; Escherichia coli Proteins/*genetics/metabolism ; Evolution, Molecular ; Fimbriae Proteins/*genetics/metabolism ; Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal/*genetics ; Phylogeny ; Promoter Regions, Genetic ; Protein Binding ; Transcription Factors/*genetics ; }, abstract = {Bacteria can acquire new traits through horizontal gene transfer. Inappropriate expression of transferred genes, however, can disrupt the physiology of the host bacteria. To reduce this risk, Escherichia coli expresses the nucleoid-associated protein, H-NS, which preferentially binds to horizontally transferred genes to control their expression. Once expression is optimized, the horizontally transferred genes may actually contribute to E. coli survival in new habitats. Therefore, we investigated whether and how H-NS contributes to this optimization process. A comparison of H-NS binding profiles on common chromosomal segments of three E. coli strains belonging to different phylogenetic groups indicated that the positions of H-NS-bound regions have been conserved in E. coli strains. The sequences of the H-NS-bound regions appear to have diverged more so than H-NS-unbound regions only when H-NS-bound regions are located upstream or in coding regions of genes. Because these regions generally contain regulatory elements for gene expression, sequence divergence in these regions may be associated with alteration of gene expression. Indeed, nucleotide substitutions in H-NS-bound regions of the ybdO promoter and coding regions have diversified the potential for H-NS-independent negative regulation among E. coli strains. The ybdO expression in these strains was still negatively regulated by H-NS, which reduced the effect of H-NS-independent regulation under normal growth conditions. Hence, we propose that, during E. coli evolution, the conservation of H-NS binding sites resulted in the diversification of the regulation of horizontally transferred genes, which may have facilitated E. coli adaptation to new ecological niches.}, } @article {pmid26787189, year = {2016}, author = {Pina-Martins, F and Vieira, BM and Seabra, SG and Batista, D and Paulo, OS}, title = {4Pipe4--A 454 data analysis pipeline for SNP detection in datasets with no reference sequence or strain information.}, journal = {BMC bioinformatics}, volume = {17}, number = {}, pages = {41}, pmid = {26787189}, issn = {1471-2105}, mesh = {Computer Simulation ; *Databases, Genetic ; Genome, Human ; Genotyping Techniques ; *High-Throughput Nucleotide Sequencing ; Humans ; Models, Molecular ; *Polymorphism, Single Nucleotide ; Reproducibility of Results ; *Software ; }, abstract = {BACKGROUND: Next-generation sequencing datasets are becoming more frequent, and their use in population studies is becoming widespread. For non-model species, without a reference genome, it is possible from a panel of individuals to identify a set of SNPs that can be used for further population genotyping. However the lack of a reference genome to which the sequenced data could be compared makes the finding of SNPs more troublesome. Additionally when the data sources (strains) are not identified (e.g. in datasets of pooled individuals), the problem of finding reliable variation in these datasets can become much more difficult due to the lack of specialized software for this specific task.

RESULTS: Here we describe 4Pipe4, a 454 data analysis pipeline particularly focused on SNP detection when no reference or strain information is available. It uses a command line interface to automatically call other programs, parse their outputs and summarize the results. The variation detection routine is built-in in the program itself. Despite being optimized for SNP mining in 454 EST data, it is flexible enough to automate the analysis of genomic data or even data from other NGS technologies. 4Pipe4 will output several HTML formatted reports with metrics on many of the most common assembly values, as well as on all the variation found. There is also a module available for finding putative SSRs in the analysed datasets.

CONCLUSIONS: This program can be especially useful for researchers that have 454 datasets of a panel of pooled individuals and want to discover and characterize SNPs for subsequent individual genotyping with customized genotyping arrays. In comparison with other SNP detection approaches, 4Pipe4 showed the best validation ratio, retrieving a smaller number of SNPs but with a considerably lower false positive rate than other methods. 4Pipe4's source code is available at https://github.com/StuntsPT/4Pipe4.}, } @article {pmid26782541, year = {2015}, author = {Jin, SB and Zhang, Y and Dong, XL and Xi, QK and Song, D and Fu, HT and Sun, DJ}, title = {Comparative transcriptome analysis of testes and ovaries for the discovery of novel genes from Amur sturgeon (Acipenser schrenckii).}, journal = {Genetics and molecular research : GMR}, volume = {14}, number = {4}, pages = {18913-18927}, doi = {10.4238/2015.December.28.40}, pmid = {26782541}, issn = {1676-5680}, mesh = {Animals ; Female ; Fish Proteins/*genetics/metabolism ; Fishes/*genetics/growth & development/metabolism ; Gene Expression Profiling ; Gene Expression Regulation, Developmental ; Gene Ontology ; Male ; Molecular Sequence Annotation ; Ovary/growth & development/*metabolism ; Polymorphism, Single Nucleotide ; Reproduction/*genetics ; *Sex Determination Processes ; Testis/growth & development/*metabolism ; *Transcriptome ; }, abstract = {Sturgeons (Acipenser schrenckii) are of high evolutionary, economic, and conservation value, and caviar isone of the most valuable animal food products in the world. The Illumina HiSeq2000 sequencing platform was used to construct testicular and ovarian transcriptomes to identify genes involved in reproduction and sex determination in A. schrenckii. A total of 122,381 and 114,527 unigenes were obtained in the testicular and ovarian transcriptomes, respectively, with average lengths of 748 and 697 bp. A total of 46,179 genes were matched to the non-redundant nr database. GO (31,266), KEGG (39,712), and COG analyses (20,126) were performed to identify potential genes and their functions. Twenty-six gene families involved in reproduction and sex determination were identified from the A. schrenckii testicular and ovarian transcriptomes based on functional annotation of non-redundant transcripts and comparisons with the published literature. Furthermore, 1309 unigenes showed significant differences between the testes and ovaries, including 782 genes that were up-regulated in the testes and 527 that were up-regulated in the ovaries. Eleven genes were involved in reproduction and sex determination mechanisms. Furthermore, 19,065 simple sequence repeats (SSRs) were identified in the expressed sequence tagged dataset, and 190,863 and 193,258 single nucleotide polymorphisms (SNPs) were obtained from the testicular and ovarian transcriptomic databases, respectively. This study provides new sequence information about A. schrenckii, which will provide a basis for the further study of reproduction and sex determination mechanisms in Acipenser species. The potential SSR and SNP markers isolated from the transcriptome may shed light on the evolution and molecular ecology of Acipenser species.}, } @article {pmid26781959, year = {2016}, author = {Mueller, AK and Chakarov, N and Heseker, H and Krüger, O}, title = {Intraguild predation leads to cascading effects on habitat choice, behaviour and reproductive performance.}, journal = {The Journal of animal ecology}, volume = {85}, number = {3}, pages = {774-784}, doi = {10.1111/1365-2656.12493}, pmid = {26781959}, issn = {1365-2656}, mesh = {Animals ; Competitive Behavior ; *Ecosystem ; Falconiformes/*physiology ; Female ; Geographic Information Systems ; Germany ; Male ; *Nesting Behavior ; Population Dynamics ; *Predatory Behavior ; Reproduction/*physiology ; Strigiformes/*physiology ; Territoriality ; }, abstract = {Intraguild predation (IGP) is a commonly recognized mechanism influencing the community structure of predators, but the complex interactions are notoriously difficult to disentangle. The mesopredator suppression hypothesis predicts that a superpredator may either simultaneously repress two mesopredators, restrain the dominant one and thereby release the subdominant mesopredator, or elicit different responses by both mesopredators. We show the outcome arising from such conditions in a three-level predator assemblage (Eurasian eagle owl Bubo bubo L., northern goshawk Accipiter gentilis L. and common buzzard Buteo buteo L.) studied over 25 years. In the second half of the study period, the eagle owl re-colonized the study area, thereby providing a natural experiment of superpredator introduction. We combined this set-up with detailed GIS analysis of habitat use and a field experiment simulating intrusion by the superpredator into territories of the subdominant mesopredator, the buzzard. Although population trends were positive for all three species in the assemblage, the proportion of failed breeding attempts increased significantly in both mesopredators after the superpredator re-colonized the area. We predicted that superpredator-induced niche shifts in the dominant mesopredator may facilitate mesopredator coexistence in superpredator-free refugia. We found significant changes in nesting habitat choice in goshawk, but not in buzzard. Since competition for enemy-free refugia and the rapid increase in population density may have constrained niche shifts of the subdominant mesopredator, we further predicted behavioural changes in response to the superpredator. The field experiment indeed showed a significant increase in aggressive response of buzzards towards eagle owl territory intrusion over the course of 10 years, probably due to phenotypic plasticity in the response towards superpredation risk. Overall, our results show that intraguild predation can be a powerful force of behavioural change, simultaneously influencing habitat use and aggressiveness in predator communities. These changes might help to buffer mesopredator populations against the negative effects of intraguild predation.}, } @article {pmid26775796, year = {2016}, author = {Guang, A and Zapata, F and Howison, M and Lawrence, CE and Dunn, CW}, title = {An Integrated Perspective on Phylogenetic Workflows.}, journal = {Trends in ecology & evolution}, volume = {31}, number = {2}, pages = {116-126}, doi = {10.1016/j.tree.2015.12.007}, pmid = {26775796}, issn = {1872-8383}, mesh = {Animals ; Computational Biology ; *Evolution, Molecular ; *Gene Flow ; *Phylogeny ; Software ; Species Specificity ; }, abstract = {Molecular phylogenetics is the study of evolutionary relationships between biological sequences, often to infer the evolutionary relationships of organisms. These studies require many analysis components, including sequence assembly, identification of homologous sequences, gene tree inference, and species tree inference. At present, each component is usually treated as a single step in a linear analysis, where the output of each component is passed as input to the next as a point estimate. Here we outline a generative model that helps clarify assumptions that are implicit to phylogenetic workflows, focusing on the assumption of low relative entropy. This perspective unifies currently disparate advances, and will help investigators evaluate which steps would benefit the most from additional computation and future methods development.}, } @article {pmid26773508, year = {2016}, author = {Brown, JE and Alfonso, B and Avila, R and Beresford, NA and Copplestone, D and Hosseini, A}, title = {A new version of the ERICA tool to facilitate impact assessments of radioactivity on wild plants and animals.}, journal = {Journal of environmental radioactivity}, volume = {153}, number = {}, pages = {141-148}, doi = {10.1016/j.jenvrad.2015.12.011}, pmid = {26773508}, issn = {1879-1700}, mesh = {Animals ; Bayes Theorem ; Databases, Factual ; Invertebrates/*metabolism ; Plants/*metabolism ; *Radiation Exposure ; Radiation Monitoring/*instrumentation/*methods ; Radioactivity ; Risk Assessment ; Software ; Vertebrates/*metabolism ; }, abstract = {A new version of the ERICA Tool (version 1.2) was released in November 2014; this constitutes the first major update of the Tool since release in 2007. The key features of the update are presented in this article. Of particular note are new transfer databases extracted from an international compilation of concentration ratios (CRwo-media) and the modification of 'extrapolation' approaches used to select transfer data in cases where information is not available. Bayesian updating approaches have been used in some cases to draw on relevant information that would otherwise have been excluded in the process of deriving CRwo-media statistics. All of these efforts have in turn led to the requirement to update Environmental Media Concentration Limits (EMCLs) used in Tier 1 assessments. Some of the significant changes with regard to EMCLs are highlighted.}, } @article {pmid26771623, year = {2016}, author = {Kim, JH and Lee, C and Sohn, W}, title = {Urban Natural Environments, Obesity, and Health-Related Quality of Life among Hispanic Children Living in Inner-City Neighborhoods.}, journal = {International journal of environmental research and public health}, volume = {13}, number = {1}, pages = {}, pmid = {26771623}, issn = {1660-4601}, mesh = {Body Mass Index ; Child ; Cities ; *Environment ; Female ; Geographic Information Systems ; *Hispanic or Latino ; Humans ; Male ; Obesity/*ethnology/etiology ; Protective Factors ; *Quality of Life ; Remote Sensing Technology ; *Residence Characteristics ; Risk Factors ; Texas/epidemiology ; *Trees ; Urban Health/*statistics & numerical data ; }, abstract = {Although a substantial body of literature has provided evidence supporting the positive effects of natural environments on well-being, little has been known about the specific spatial patterns of urban nature in promoting health-related quality of life (HRQOL) among children. This study assessed the association that the urban natural environment measured by landscape spatial patterns may have with obesity and HRQOL among Hispanic children. Ninety-two 4th and 5th grade students were recruited from Houston, Texas, and the Pediatric Quality of Life Inventory (PedsQL) was used to capture the children's HRQOL. The quality of urban natural environments was assessed by quantifying the landscape spatial patterns, using landscape indices generated by Geographic Information Systems and remote sensing. From the bivariate analyses, children's body mass index showed a significantly negative association with their HRQOL. After controlling for socio-demographic factors, the results revealed that larger and more tree areas were positively correlated with children's HRQOL. In addition, those children living in areas with tree patches further apart from each other showed higher HRQOL. This research adds to the current multi-disciplinary area of research on environment-health relationships by investigating the roles of urban greeneries and linking their spatial structures with children's HRQOL.}, } @article {pmid26768196, year = {2016}, author = {Duchesne, P and Turgeon, J}, title = {Interpreting the flock algorithm: a reply to Anderson & Barry (2015).}, journal = {Molecular ecology resources}, volume = {16}, number = {1}, pages = {13-16}, doi = {10.1111/1755-0998.12480}, pmid = {26768196}, issn = {1755-0998}, mesh = {*Cluster Analysis ; Computational Biology/*methods ; Genotyping Techniques/*methods ; *Software ; }, abstract = {Anderson & Barry (Molecular Ecology Resources, 2015, 10, 1020-1030) compared a reprogrammed version of flock (Duchesne & Turgeon , Molecular Ecology Resources, 2009, 9, 1333-1344), flockture, to a particular model of structure (Pritchard , Genetics, 2000, 155, 945-959) that they propose is equivalent to flock, a non-MCMC, non-Bayesian algorithm. They conclude that structure performs better than flockture at clustering individuals from simulated populations with very low level of differentiation (FST c. 0.008) based on 15 microsatellites or 96 SNPs. We rather consider that both algorithms failed, with proportions of correct allocations lower than 50%. The authors also noted the slightly better performance of flockture with SNPs at intermediate FST values (c. 0.02-0.04) but did not comment. Finally, we disagree with the way the processing time of each program was compared. When compared on the basis of a run leading to a clustering solution, the main output of any clustering algorithm, flock, is, as users can readily experience, much faster. In all, we feel that flock performs at least as well as structure as a clustering algorithm. Moreover, flock has two major assets: high speed and clear, well validated, rules to estimate K, the number of populations. It thus provides a valuable addition to the set of tools at the disposal of the many researchers dealing with real empirical data sets.}, } @article {pmid26763747, year = {2016}, author = {Wang, J and Zhao, Y and Ray, I and Song, M}, title = {Transcriptome responses in alfalfa associated with tolerance to intensive animal grazing.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {19438}, pmid = {26763747}, issn = {2045-2322}, mesh = {*Adaptation, Biological ; Animals ; Cell Wall/metabolism ; Computational Biology/methods ; Energy Metabolism ; Gene Expression Regulation, Plant ; Gene Ontology ; Gene-Environment Interaction ; *Herbivory ; Medicago sativa/*genetics/metabolism ; Metabolic Networks and Pathways ; Phenotype ; Polymorphism, Single Nucleotide ; Reactive Oxygen Species/metabolism ; Ribosomes/metabolism ; Selection, Genetic ; Signal Transduction ; *Transcriptome ; }, abstract = {Tolerance of alfalfa (Medicago sativa L.) to animal grazing varies widely within the species. However, the molecular mechanisms influencing the grazing tolerant phenotype remain uncharacterized. The objective of this study was to identify genes and pathways that control grazing response in alfalfa. We analyzed whole-plant de novo transcriptomes from grazing tolerant and intolerant populations of M. sativa ssp. falcata subjected to grazing by sheep. Among the Gene Ontology terms which were identified as grazing responsive in the tolerant plants and differentially enriched between the tolerant and intolerant populations (both grazed), most were associated with the ribosome and translation-related activities, cell wall processes, and response to oxygen levels. Twenty-one grazing responsive pathways were identified that also exhibited differential expression between the tolerant and intolerant populations. These pathways were associated with secondary metabolite production, primary carbohydrate metabolic pathways, shikimate derivative dependent pathways, ribosomal subunit composition, hormone signaling, wound response, cell wall formation, and anti-oxidant defense. Sequence polymorphisms were detected among several differentially expressed homologous transcripts between the tolerant and intolerant populations. These differentially responsive genes and pathways constitute potential response mechanisms for grazing tolerance in alfalfa. They also provide potential targets for molecular breeding efforts to develop grazing-tolerant cultivars of alfalfa.}, } @article {pmid26761487, year = {2016}, author = {Chao, L and Rang, CU and Proenca, AM and Chao, JU}, title = {Asymmetrical Damage Partitioning in Bacteria: A Model for the Evolution of Stochasticity, Determinism, and Genetic Assimilation.}, journal = {PLoS computational biology}, volume = {12}, number = {1}, pages = {e1004700}, pmid = {26761487}, issn = {1553-7358}, mesh = {*Biological Evolution ; Cell Polarity/*physiology ; Computational Biology ; Escherichia coli/genetics/*physiology ; Genetic Fitness ; *Models, Biological ; Selection, Genetic ; Stochastic Processes ; }, abstract = {Non-genetic phenotypic variation is common in biological organisms. The variation is potentially beneficial if the environment is changing. If the benefit is large, selection can favor the evolution of genetic assimilation, the process by which the expression of a trait is transferred from environmental to genetic control. Genetic assimilation is an important evolutionary transition, but it is poorly understood because the fitness costs and benefits of variation are often unknown. Here we show that the partitioning of damage by a mother bacterium to its two daughters can evolve through genetic assimilation. Bacterial phenotypes are also highly variable. Because gene-regulating elements can have low copy numbers, the variation is attributed to stochastic sampling. Extant Escherichia coli partition asymmetrically and deterministically more damage to the old daughter, the one receiving the mother's old pole. By modeling in silico damage partitioning in a population, we show that deterministic asymmetry is advantageous because it increases fitness variance and hence the efficiency of natural selection. However, we find that symmetrical but stochastic partitioning can be similarly beneficial. To examine why bacteria evolved deterministic asymmetry, we modeled the effect of damage anchored to the mother's old pole. While anchored damage strengthens selection for asymmetry by creating additional fitness variance, it has the opposite effect on symmetry. The difference results because anchored damage reinforces the polarization of partitioning in asymmetric bacteria. In symmetric bacteria, it dilutes the polarization. Thus, stochasticity alone may have protected early bacteria from damage, but deterministic asymmetry has evolved to be equally important in extant bacteria. We estimate that 47% of damage partitioning is deterministic in E. coli. We suggest that the evolution of deterministic asymmetry from stochasticity offers an example of Waddington's genetic assimilation. Our model is able to quantify the evolution of the assimilation because it characterizes the fitness consequences of variation.}, } @article {pmid26758516, year = {2016}, author = {Moyers, BA and Zhang, J}, title = {Evaluating Phylostratigraphic Evidence for Widespread De Novo Gene Birth in Genome Evolution.}, journal = {Molecular biology and evolution}, volume = {33}, number = {5}, pages = {1245-1256}, pmid = {26758516}, issn = {1537-1719}, support = {R01 GM103232/GM/NIGMS NIH HHS/United States ; T32 GM070449/GM/NIGMS NIH HHS/United States ; T32 HG000040/HG/NHGRI NIH HHS/United States ; }, mesh = {Animals ; *Biological Evolution ; Codon ; Computer Simulation ; Databases, Nucleic Acid ; Evolution, Molecular ; Gene Duplication ; Genomics/*methods ; Humans ; *Models, Genetic ; *Mutation ; Open Reading Frames ; Phylogeny ; Saccharomyces cerevisiae/genetics ; Saccharomyces cerevisiae Proteins/genetics ; }, abstract = {The source of genetic novelty is an area of wide interest and intense investigation. Although gene duplication is conventionally thought to dominate the production of new genes, this view was recently challenged by a proposal of widespread de novo gene origination in eukaryotic evolution. Specifically, distributions of various gene properties such as coding sequence length, expression level, codon usage, and probability of being subject to purifying selection among groups of genes with different estimated ages were reported to support a model in which new protein-coding proto-genes arise from noncoding DNA and gradually integrate into cellular networks. Here we show that the genomic patterns asserted to support widespread de novo gene origination are largely attributable to biases in gene age estimation by phylostratigraphy, because such patterns are also observed in phylostratigraphic analysis of simulated genes bearing identical ages. Furthermore, there is no evidence of purifying selection on very young de novo genes previously claimed to show such signals. Together, these findings are consistent with the prevailing view that de novo gene birth is a relatively minor contributor to new genes in genome evolution. They also illustrate the danger of using phylostratigraphy in the study of new gene origination without considering its inherent bias.}, } @article {pmid26758000, year = {2015}, author = {Barros, FC and Matijasevich, A and Maranhão, AG and Escalante, JJ and Rabello Neto, DL and Fernandes, RM and Vilella, ME and Matos, AC and Albuquerque, C and Léon, RG and Victora, CG}, title = {Cesarean sections in Brazil: will they ever stop increasing?.}, journal = {Revista panamericana de salud publica = Pan American journal of public health}, volume = {38}, number = {3}, pages = {217-225}, pmid = {26758000}, issn = {1680-5348}, support = {001/WHO_/World Health Organization/International ; }, mesh = {Brazil/epidemiology ; *Cesarean Section ; Female ; Humans ; Poverty ; Pregnancy ; Risk Factors ; White People ; }, abstract = {OBJECTIVE: To describe trends, geographic distribution, and risk factors for cesarean deliveries in Brazil in 2000-2011, and to determine if efforts to curtail rates have had a measurable impact.

METHODS: This was an observational study using nationwide information from the Department of Informatics of the Unified Health System (DATASUS). Individual level analyses were based on data regarding maternal education, age, parity, and skin color. Ecological analyses at the level of 431 health districts investigated the relationships with health facility density and poverty level.

RESULTS: Cesarean rates increased markedly, from 37.9% in 2000 to 53.9% in 2011. Preliminary results from 2012 showed a rate of 55.8%, with the richest geographic areas showing the highest rates. Rates at the municipal level varied from 9%-96%. Cesareans were more common in women with higher education, white skin color, older age, and in primi- paras. In the ecological analyses, the number of health facilities per 1 000 population was strongly and positively correlated with cesarean rates, with an increase of 16.1 percentage points (95% Confidence Interval [95%CI] = 4.3-17.8) for each facility. An increase of 1 percentage point in the poverty rate was associated with a decline of 0.5 percentage point in cesarean rates (95%CI = 0.5-0.6).

CONCLUSIONS: The strong associations with maternal education and health facility density suggest that the vast majority of cesareans are not medically indicated. A number of policies and programs have been launched to counteract this trend, but have had virtually no impact.}, } @article {pmid26757311, year = {2016}, author = {Longden, E and Read, J}, title = {Assessing and Reporting the Adverse Effects of Antipsychotic Medication: A Systematic Review of Clinical Studies, and Prospective, Retrospective, and Cross-Sectional Research.}, journal = {Clinical neuropharmacology}, volume = {39}, number = {1}, pages = {29-39}, doi = {10.1097/WNF.0000000000000117}, pmid = {26757311}, issn = {1537-162X}, mesh = {Antipsychotic Agents/*adverse effects ; Cross-Sectional Studies/statistics & numerical data ; Databases, Factual/statistics & numerical data ; Humans ; Mental Disorders/*drug therapy ; *Prospective Studies ; *Retrospective Studies ; Treatment Outcome ; }, abstract = {OBJECTIVE: Adverse effects (AEs) of antipsychotic medication have important implications for patients and prescribers in terms of well-being, treatment adherence, and quality of life. This review summarizes strategies for collecting and reporting AE data across a representative literature sample to ascertain their rigor and comprehensiveness.

METHODS: A PsycINFO search, following preferred reporting items for systematic reviews and meta-analyses statement guidelines, was conducted in English-language journals (1980 to July 2014) using the following search string: (antipsychotic* or neuroleptic*) and (subjective effect or subjective experience or subjective response or subjective mental alterations or subjective tolerability OR subjective well-being or patient perspective or self-rated effects or adverse effects or side effects). Of 7825 articles, 384 were retained that reported quantified results for AEs of typical or atypical antipsychotics among transdiagnostic adult, adolescent, and child populations. Information extracted included: types of AEs reported, how AEs were assessed, assessment duration, assessment of the global impact of antipsychotic consumption on subjective patient wellbeing, and conflict of interest due to industry sponsorship.

RESULTS: Neurological, metabolic, and sedation-related cognitive effects were reported more systematically than affective, anticholinergic, autonomic, cutaneous, hormonal, miscellaneous, and nonsedative cognitive effects. The global impact of AEs on patient well-being was poorly assessed. Cross-sectional and prospective research designs yielded more comprehensive data about AE severity and prevalence than clinical or observational retrospective studies.

CONCLUSIONS: The detection and classification of AEs can be improved through the use of standardized assessment instruments and consideration of the global impact on subjective patient wellbeing. Observational research can supplement information from clinical trials to improve the ecological validity of AE data.}, } @article {pmid26755501, year = {2016}, author = {Bertozzi Silva, J and Storms, Z and Sauvageau, D}, title = {Host receptors for bacteriophage adsorption.}, journal = {FEMS microbiology letters}, volume = {363}, number = {4}, pages = {}, doi = {10.1093/femsle/fnw002}, pmid = {26755501}, issn = {1574-6968}, mesh = {Adsorption ; Bacteria/virology ; Bacteriophages/genetics/*physiology ; Databases, Factual ; Host-Pathogen Interactions ; Humans ; Receptors, Virus/chemistry/*physiology ; Sequence Analysis, DNA ; }, abstract = {The adsorption of bacteriophages (phages) onto host cells is, in all but a few rare cases, a sine qua non condition for the onset of the infection process. Understanding the mechanisms involved and the factors affecting it is, thus, crucial for the investigation of host-phage interactions. This review provides a survey of the phage host receptors involved in recognition and adsorption and their interactions during attachment. Comprehension of the whole infection process, starting with the adsorption step, can enable and accelerate our understanding of phage ecology and the development of phage-based technologies. To assist in this effort, we have established an open-access resource--the Phage Receptor Database (PhReD)--to serve as a repository for information on known and newly identified phage receptors.}, } @article {pmid26751565, year = {2016}, author = {Hardion, L and Leriche, A and Schwoertzig, E and Millon, A}, title = {Species Distribution 2.0: An Accurate Time- and Cost-Effective Method of Prospection Using Street View Imagery.}, journal = {PloS one}, volume = {11}, number = {1}, pages = {e0146899}, pmid = {26751565}, issn = {1932-6203}, mesh = {*Biodiversity ; Climate ; *Cost-Benefit Analysis ; Data Collection ; Ecology ; Environmental Monitoring/*economics ; Geographic Information Systems/*economics ; Geography ; Linear Models ; *Poaceae ; Principal Component Analysis ; Probability ; Spain ; }, abstract = {Species occurrence data provide crucial information for biodiversity studies in the current context of global environmental changes. Such studies often rely on a limited number of occurrence data collected in the field and on pseudo-absences arbitrarily chosen within the study area, which reduces the value of these studies. To overcome this issue, we propose an alternative method of prospection using geo-located street view imagery (SVI). Following a standardised protocol of virtual prospection using both vertical (aerial photographs) and horizontal (SVI) perceptions, we have surveyed 1097 randomly selected cells across Spain (0.1x0.1 degree, i.e. 20% of Spain) for the presence of Arundo donax L. (Poaceae). In total we have detected A. donax in 345 cells, thus substantially expanding beyond the now two-centuries-old field-derived record, which described A. donax only 216 cells. Among the field occurrence cells, 81.1% were confirmed by SVI prospection to be consistent with species presence. In addition, we recorded, by SVI prospection, 752 absences, i.e. cells where A. donax was considered absent. We have also compared the outcomes of climatic niche modeling based on SVI data against those based on field data. Using generalized linear models fitted with bioclimatic predictors, we have found SVI data to provide far more compelling results in terms of niche modeling than does field data as classically used in SDM. This original, cost- and time-effective method provides the means to accurately locate highly visible taxa, reinforce absence data, and predict species distribution without long and expensive in situ prospection. At this time, the majority of available SVI data is restricted to human-disturbed environments that have road networks. However, SVI is becoming increasingly available in natural areas, which means the technique has considerable potential to become an important factor in future biodiversity studies.}, } @article {pmid26750628, year = {2016}, author = {Hauser, FE and Schott, RK and Castiglione, GM and Van Nynatten, A and Kosyakov, A and Tang, PL and Gow, DA and Chang, BS}, title = {Comparative sequence analyses of rhodopsin and RPE65 reveal patterns of selective constraint across hereditary retinal disease mutations.}, journal = {Visual neuroscience}, volume = {33}, number = {}, pages = {e002}, doi = {10.1017/S0952523815000322}, pmid = {26750628}, issn = {1469-8714}, mesh = {Animals ; Databases, Genetic ; Evolution, Molecular ; Mammals ; Phylogeny ; Retinitis Pigmentosa/*genetics ; Rhodopsin/*genetics ; Sequence Analysis/*methods ; Vertebrates ; cis-trans-Isomerases/*genetics ; }, abstract = {Retinitis pigmentosa (RP) comprises several heritable diseases that involve photoreceptor, and ultimately retinal, degeneration. Currently, mutations in over 50 genes have known links to RP. Despite advances in clinical characterization, molecular characterization of RP remains challenging due to the heterogeneous nature of causal genes, mutations, and clinical phenotypes. In this study, we compiled large datasets of two important visual genes associated with RP: rhodopsin, which initiates the phototransduction cascade, and the retinoid isomerase RPE65, which regenerates the visual cycle. We used a comparative evolutionary approach to investigate the relationship between interspecific sequence variation and pathogenic mutations that lead to degenerative retinal disease. Using codon-based likelihood methods, we estimated evolutionary rates (d N/d S) across both genes in a phylogenetic context to investigate differences between pathogenic and nonpathogenic amino acid sites. In both genes, disease-associated sites showed significantly lower evolutionary rates compared to nondisease sites, and were more likely to occur in functionally critical areas of the proteins. The nature of the dataset (e.g., vertebrate or mammalian sequences), as well as selection of pathogenic sites, affected the differences observed between pathogenic and nonpathogenic sites. Our results illustrate that these methods can serve as an intermediate step in understanding protein structure and function in a clinical context, particularly in predicting the relative pathogenicity (i.e., functional impact) of point mutations and their downstream phenotypic effects. Extensions of this approach may also contribute to current methods for predicting the deleterious effects of candidate mutations and to the identification of protein regions under strong constraint where we expect pathogenic mutations to occur.}, } @article {pmid26744948, year = {2016}, author = {Zhou, Q and Ren, Y and Xu, M and Han, N and Wang, H}, title = {Adaptation to urbanization impacts on drainage in the city of Hohhot, China.}, journal = {Water science and technology : a journal of the International Association on Water Pollution Research}, volume = {73}, number = {1}, pages = {167-175}, doi = {10.2166/wst.2015.478}, pmid = {26744948}, issn = {0273-1223}, mesh = {China ; Cities ; *City Planning ; *Drainage, Sanitary ; *Floods ; Geographic Information Systems ; Hydrology ; Models, Theoretical ; Rain ; *Urbanization ; }, abstract = {This study presents a quantitative assessment of urbanization effects on hydrological runoff and drainage network in the city of Hohhot, China. The evolution of urban spatial morphology for the historical years (1987-2010) and projected year (2020) is described by changes in geographic information system (GIS)-based land use maps and further represented in hydrological parameters in the Storm Water Management Model (SWMM) simulation. The results show the levels of service of historical drainage were too low to have dominant impacts on flood risks, and hence a significant upward trend in catchment runoff response was observed over time. Comparisons with changes in system overloading indicate that the relative increase in flood risk is greatest at the early stage of urbanization with relatively low levels of development. The proposed adaptation measures based on a cost-effective optimal approach was found feasible to significantly improve the drainage performance and mitigate the increasing flooding impacts.}, } @article {pmid26733293, year = {2016}, author = {Krupovic, M and Dutilh, BE and Adriaenssens, EM and Wittmann, J and Vogensen, FK and Sullivan, MB and Rumnieks, J and Prangishvili, D and Lavigne, R and Kropinski, AM and Klumpp, J and Gillis, A and Enault, F and Edwards, RA and Duffy, S and Clokie, MR and Barylski, J and Ackermann, HW and Kuhn, JH}, title = {Taxonomy of prokaryotic viruses: update from the ICTV bacterial and archaeal viruses subcommittee.}, journal = {Archives of virology}, volume = {161}, number = {4}, pages = {1095-1099}, doi = {10.1007/s00705-015-2728-0}, pmid = {26733293}, issn = {1432-8798}, support = {HHSN272200700016I//PHS HHS/United States ; }, mesh = {Archaea/*virology ; Archaeal Viruses/*classification ; Classification/methods ; *International Cooperation ; Phylogeny ; *Societies, Scientific ; *Terminology as Topic ; }, } @article {pmid26730727, year = {2016}, author = {Park, IJ and Hein, AM and Bobkov, YV and Reidenbach, MA and Ache, BW and Principe, JC}, title = {Neurally Encoding Time for Olfactory Navigation.}, journal = {PLoS computational biology}, volume = {12}, number = {1}, pages = {e1004682}, pmid = {26730727}, issn = {1553-7358}, support = {R21 DC011859/DC/NIDCD NIH HHS/United States ; UL1 TR001427/TR/NCATS NIH HHS/United States ; DC011859/DC/NIDCD NIH HHS/United States ; }, mesh = {Animals ; Appetitive Behavior/*physiology ; Computational Biology ; *Models, Neurological ; Odorants/*analysis ; Olfactory Receptor Neurons/*physiology ; Smell/*physiology ; }, abstract = {Accurately encoding time is one of the fundamental challenges faced by the nervous system in mediating behavior. We recently reported that some animals have a specialized population of rhythmically active neurons in their olfactory organs with the potential to peripherally encode temporal information about odor encounters. If these neurons do indeed encode the timing of odor arrivals, it should be possible to demonstrate that this capacity has some functional significance. Here we show how this sensory input can profoundly influence an animal's ability to locate the source of odor cues in realistic turbulent environments-a common task faced by species that rely on olfactory cues for navigation. Using detailed data from a turbulent plume created in the laboratory, we reconstruct the spatiotemporal behavior of a real odor field. We use recurrence theory to show that information about position relative to the source of the odor plume is embedded in the timing between odor pulses. Then, using a parameterized computational model, we show how an animal can use populations of rhythmically active neurons to capture and encode this temporal information in real time, and use it to efficiently navigate to an odor source. Our results demonstrate that the capacity to accurately encode temporal information about sensory cues may be crucial for efficient olfactory navigation. More generally, our results suggest a mechanism for extracting and encoding temporal information from the sensory environment that could have broad utility for neural information processing.}, } @article {pmid26725698, year = {2016}, author = {Wentzel, J and Müller, F and Beerlage-de Jong, N and van Gemert-Pijnen, J}, title = {Card sorting to evaluate the robustness of the information architecture of a protocol website.}, journal = {International journal of medical informatics}, volume = {86}, number = {}, pages = {71-81}, doi = {10.1016/j.ijmedinf.2015.12.003}, pmid = {26725698}, issn = {1872-8243}, mesh = {Adult ; *Clinical Protocols ; Female ; Humans ; Internet/*statistics & numerical data ; Male ; *Medical Informatics Applications ; Medical Records Systems, Computerized/*statistics & numerical data ; *Methicillin-Resistant Staphylococcus aureus ; Staphylococcal Infections/microbiology/*prevention & control/transmission ; User-Computer Interface ; }, abstract = {OBJECTIVES: A website on Methicillin-Resistant Staphylococcus Aureus, MRSA-net, was developed for Health Care Workers (HCWs) and the general public, in German and in Dutch. The website's content was based on existing protocols and its structure was based on a card sort study. A Human Centered Design approach was applied to ensure a match between user and technology. In the current study we assess whether the website's structure still matches user needs, again via a card sort study.

METHODS: An open card sort study was conducted. Randomly drawn samples of 100 on-site search queries as they were entered on the MRSA-net website (during one year of use) were used as card input. In individual sessions, the cards were sorted by each participant (18 German and 10 Dutch HCWs, and 10 German and 10 Dutch members of the general public) into piles that were meaningful to them. Each participant provided a label for every pile of cards they created. Cluster analysis was performed on the resulting sorts, creating an overview of clusters of items placed together in one pile most frequently. In addition, pile labels were qualitatively analyzed to identify the participants' mental models.

RESULTS: Cluster analysis confirmed existing categories and revealed new themes emerging from the search query samples, such as financial issues and consequences for the patient. Even though MRSA-net addresses these topics, they are not prominently covered in the menu structure. The label analysis shows that 7 of a total of 44 MRSA-net categories were not reproduced by the participants. Additional themes such as information on other pathogens and categories such as legal issues emerged.

CONCLUSIONS: This study shows that the card sort performed to create MRSA-net resulted in overall long-lasting structure and categories. New categories were identified, indicating that additional information needs emerged. Therefore, evaluating website structure should be a recurrent activity. Card sorting with ecological data as input for the cards is useful to identify changes in needs and mental models. By combining qualitative and quantitative analysis we gained insight into additional information needed by the target group, including their view on the domain and related themes. The results show differences between the four user groups in their sorts, which can mostly be explained by the groups' background. These findings confirm that HCD is a valuable approach to tailor information to the target group.}, } @article {pmid26724407, year = {2016}, author = {Lewis, LR and Liu, Y and Rozzi, R and Goffinet, B}, title = {Infraspecific variation within and across complete organellar genomes and nuclear ribosomal repeats in a moss.}, journal = {Molecular phylogenetics and evolution}, volume = {96}, number = {}, pages = {195-199}, doi = {10.1016/j.ympev.2015.12.005}, pmid = {26724407}, issn = {1095-9513}, mesh = {Bryophyta/*cytology/*genetics ; Cell Nucleus/*genetics ; DNA, Ribosomal/*genetics ; Datasets as Topic ; Evolution, Molecular ; Genome, Plant/*genetics ; Genome, Plastid/genetics ; *Genomics ; Organelles/*genetics ; Plastids/genetics ; Polymorphism, Genetic ; }, abstract = {Bryophytes (mosses, liverworts, and hornworts) are diverse and ecologically and evolutionarily significant yet genome scale data sets and analyses remain extremely sparse relative to other groups of plants, and are completely lacking at the infraspecific level. By sequencing the complete organellar genomes and nuclear ribosomal repeat from seven patches of a South American sub-Antarctic neo-endemic non-model moss, we present the first characterization of infraspecific polymorphism within and across the three genomic compartments for a bryophyte. Diversity within patches is accounted for by both intraindividual and interindividual variation for the nuclear ribosomal repeat and plastid genome, respectively. This represents the most extensive infraspecific genomic dataset generated for an early land plant lineage thus far and provides insight into relative rates of substitution between organellar genomes, including high rates of nonsynonymous to synonymous substitutions.}, } @article {pmid26719951, year = {2016}, author = {De Kauwe, MG and Lin, YS and Wright, IJ and Medlyn, BE and Crous, KY and Ellsworth, DS and Maire, V and Prentice, IC and Atkin, OK and Rogers, A and Niinemets, Ü and Serbin, SP and Meir, P and Uddling, J and Togashi, HF and Tarvainen, L and Weerasinghe, LK and Evans, BJ and Ishida, FY and Domingues, TF}, title = {A test of the 'one-point method' for estimating maximum carboxylation capacity from field-measured, light-saturated photosynthesis.}, journal = {The New phytologist}, volume = {210}, number = {3}, pages = {1130-1144}, doi = {10.1111/nph.13815}, pmid = {26719951}, issn = {1469-8137}, mesh = {Carbon Dioxide/*metabolism ; Cell Respiration ; Databases as Topic ; Kinetics ; *Light ; Photosynthesis/*radiation effects ; Plant Stomata/physiology ; Plants/*metabolism ; Temperature ; }, abstract = {Simulations of photosynthesis by terrestrial biosphere models typically need a specification of the maximum carboxylation rate (Vcmax). Estimating this parameter using A-Ci curves (net photosynthesis, A, vs intercellular CO2 concentration, Ci) is laborious, which limits availability of Vcmax data. However, many multispecies field datasets include net photosynthetic rate at saturating irradiance and at ambient atmospheric CO2 concentration (Asat) measurements, from which Vcmax can be extracted using a 'one-point method'. We used a global dataset of A-Ci curves (564 species from 46 field sites, covering a range of plant functional types) to test the validity of an alternative approach to estimate Vcmax from Asat via this 'one-point method'. If leaf respiration during the day (Rday) is known exactly, Vcmax can be estimated with an r(2) value of 0.98 and a root-mean-squared error (RMSE) of 8.19 μmol m(-2) s(-1) . However, Rday typically must be estimated. Estimating Rday as 1.5% of Vcmax, we found that Vcmax could be estimated with an r(2) of 0.95 and an RMSE of 17.1 μmol m(-2) s(-1) . The one-point method provides a robust means to expand current databases of field-measured Vcmax , giving new potential to improve vegetation models and quantify the environmental drivers of Vcmax variation.}, } @article {pmid26717555, year = {2016}, author = {Fouquier, J and Schwartz, T and Kelley, ST}, title = {Rapid assemblage of diverse environmental fungal communities on public restroom floors.}, journal = {Indoor air}, volume = {26}, number = {6}, pages = {869-879}, doi = {10.1111/ina.12279}, pmid = {26717555}, issn = {1600-0668}, mesh = {DNA, Fungal/*analysis ; Female ; Fungi/*classification/genetics/*isolation & purification ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Male ; Phylogeny ; Sequence Analysis, DNA/*methods ; Surface Properties ; *Toilet Facilities ; }, abstract = {An increasing proportion of humanity lives in urban environments where they spend most of their lives indoors. Recent molecular studies have shown that bacterial assemblages in built environments (BEs) are extremely diverse, but BE fungal diversity remains poorly understood. We applied culture-independent methods based on next-generation sequencing (NGS) of the fungal internal transcribed spacer to investigate the diversity and temporal dynamics of fungi in restrooms. Swab samples were collected weekly from three different surfaces in two public restrooms (male and female) in San Diego, CA, USA, over an 8-week period. DNA amplification and culturing methods both found that the floor samples had significantly higher fungal loads than other surfaces. NGS sequencing of floor fungal assemblages identified a total of 2550 unique phylotypes (~800 per sample), less than half of which were identifiable. Of the known fungi, the majority came from environmental sources and we found little evidence of known human skin fungi. Fungal assemblages reformed rapidly in a highly consistent manner, and the variance in the species diversity among samples was low. Overall, our study contributes to a better understanding of public restroom floor fungal communities.}, } @article {pmid26714456, year = {2015}, author = {Gharat, SA and Shaw, BP}, title = {Novel and conserved miRNAs in the halophyte Suaeda maritima identified by deep sequencing and computational predictions using the ESTs of two mangrove plants.}, journal = {BMC plant biology}, volume = {15}, number = {}, pages = {301}, pmid = {26714456}, issn = {1471-2229}, mesh = {Chenopodiaceae/*genetics/metabolism ; Computational Biology ; Expressed Sequence Tags ; Gene Expression Regulation, Plant ; High-Throughput Nucleotide Sequencing ; Malvaceae/*genetics/metabolism ; MicroRNAs/*genetics/metabolism ; Oryza/drug effects/genetics/metabolism ; RNA, Plant/*genetics/metabolism ; Rhizophoraceae/*genetics/metabolism ; *Salt Tolerance ; Salt-Tolerant Plants/genetics/metabolism ; Sodium Chloride/pharmacology ; Transcriptome ; }, abstract = {BACKGROUND: Although miRNAs are reportedly involved in the salt stress tolerance of plants, miRNA profiling in plants has largely remained restricted to glycophytes, including certain crop species that do not exhibit any tolerance to salinity. Hence, this manuscript describes the results from the miRNA profiling of the halophyte Suaeda maritima, which is used worldwide to study salt tolerance in plants.

RESULTS: A total of 134 conserved miRNAs were identified from unique sRNA reads, with 126 identified using miRBase 21.0 and an additional eight identified using the Plant Non-coding RNA Database. The presence of the precursors of seven conserved miRNAs was validated in S. maritima. In addition, 13 novel miRNAs were predicted using the ESTs of two mangrove plants, Rhizophora mangle and Heritiera littoralis, and the precursors of seven miRNAs were found in S. maritima. Most of the miRNAs considered for characterization were responsive to NaCl application, indicating their importance in the regulation of metabolic activities in plants exposed to salinity. An expression study of the novel miRNAs in plants of diverse ecological and taxonomic groups revealed that two of the miRNAs, sma-miR6 and sma-miR7, were also expressed in Oryza sativa, whereas another two, sma-miR2 and sma-miR5, were only expressed in plants growing under the influence of seawater, similar to S. maritima.

CONCLUSION: The distribution of conserved miRNAs among only 25 families indicated the possibility of identifying a greater number of miRNAs with increase in knowledge of the genomes of more halophytes. The expression of two novel miRNAs, sma-miR2 and sma-miR5, only in plants growing under the influence of seawater suggested their metabolic regulatory roles specific to saline environments, and such behavior might be mediated by alterations in the expression of certain genes, modifications of proteins leading to changes in their activity and production of secondary metabolites as revealed by the miRNA target predictions. Moreover, the auxin responsive factor targeted by sma-miR7 could also be involved in salt tolerance because the target is conserved between species. This study also indicated that the transcriptome of one species can be successfully used to computationally predict the miRNAs in other species, especially those that have similar metabolism, even if they are taxonomically separated.}, } @article {pmid26713226, year = {2015}, author = {Mahé, F and Rognes, T and Quince, C and de Vargas, C and Dunthorn, M}, title = {Swarm v2: highly-scalable and high-resolution amplicon clustering.}, journal = {PeerJ}, volume = {3}, number = {}, pages = {e1420}, pmid = {26713226}, issn = {2167-8359}, abstract = {Previously we presented Swarm v1, a novel and open source amplicon clustering program that produced fine-scale molecular operational taxonomic units (OTUs), free of arbitrary global clustering thresholds and input-order dependency. Swarm v1 worked with an initial phase that used iterative single-linkage with a local clustering threshold (d), followed by a phase that used the internal abundance structures of clusters to break chained OTUs. Here we present Swarm v2, which has two important novel features: (1) a new algorithm for d = 1 that allows the computation time of the program to scale linearly with increasing amounts of data; and (2) the new fastidious option that reduces under-grouping by grafting low abundant OTUs (e.g., singletons and doubletons) onto larger ones. Swarm v2 also directly integrates the clustering and breaking phases, dereplicates sequencing reads with d = 0, outputs OTU representatives in fasta format, and plots individual OTUs as two-dimensional networks.}, } @article {pmid26712016, year = {2016}, author = {Frelat, R and Lopez-Ridaura, S and Giller, KE and Herrero, M and Douxchamps, S and Andersson Djurfeldt, A and Erenstein, O and Henderson, B and Kassie, M and Paul, BK and Rigolot, C and Ritzema, RS and Rodriguez, D and van Asten, PJ and van Wijk, MT}, title = {Drivers of household food availability in sub-Saharan Africa based on big data from small farms.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {113}, number = {2}, pages = {458-463}, pmid = {26712016}, issn = {1091-6490}, mesh = {Africa South of the Sahara ; *Agriculture ; Crops, Agricultural/growth & development ; *Databases as Topic ; *Family Characteristics ; *Food Supply ; Geography ; Neural Networks, Computer ; }, abstract = {We calculated a simple indicator of food availability using data from 93 sites in 17 countries across contrasted agroecologies in sub-Saharan Africa (>13,000 farm households) and analyzed the drivers of variations in food availability. Crop production was the major source of energy, contributing 60% of food availability. The off-farm income contribution to food availability ranged from 12% for households without enough food available (18% of the total sample) to 27% for the 58% of households with sufficient food available. Using only three explanatory variables (household size, number of livestock, and land area), we were able to predict correctly the agricultural determined status of food availability for 72% of the households, but the relationships were strongly influenced by the degree of market access. Our analyses suggest that targeting poverty through improving market access and off-farm opportunities is a better strategy to increase food security than focusing on agricultural production and closing yield gaps. This calls for multisectoral policy harmonization, incentives, and diversification of employment sources rather than a singular focus on agricultural development. Recognizing and understanding diversity among smallholder farm households in sub-Saharan Africa is key for the design of policies that aim to improve food security.}, } @article {pmid26707943, year = {2016}, author = {Qi, Z and Wu, P and Zhang, Q and Wei, Y and Wang, Z and Qiu, M and Shao, R and Li, Y and Gao, Q}, title = {Transcriptome analysis of soiny mullet (Liza haematocheila) spleen in response to Streptococcus dysgalactiae.}, journal = {Fish & shellfish immunology}, volume = {49}, number = {}, pages = {194-204}, doi = {10.1016/j.fsi.2015.12.029}, pmid = {26707943}, issn = {1095-9947}, mesh = {Animals ; Fish Diseases/*genetics/*immunology/microbiology ; Fish Proteins/*genetics/metabolism ; Gene Expression Profiling/veterinary ; Gene Ontology ; Immune System ; Microsatellite Repeats ; Molecular Sequence Annotation ; Polymorphism, Single Nucleotide ; Sequence Analysis, DNA/veterinary ; Signal Transduction ; Smegmamorpha/*genetics/metabolism/*microbiology ; Spleen/immunology/metabolism ; Streptococcal Infections/genetics/immunology/microbiology/*veterinary ; Streptococcus/immunology ; *Transcriptome ; }, abstract = {Soiny mullet (Liza haematocheila) is becoming an economically important aquaculture mugilid species in China and other Asian countries. However, increasing incidences of bacterial pathogenic diseases has greatly hampered the production of the soiny mullet. Deeper understanding of the soiny mullet immune system and its related genes in response to bacterial infections are necessary for disease control in this species. In this study, the transcriptomic profile of spleen from soiny mullet challenged with Streptococcus dysgalactiae was analyzed by Illumina-based paired-end sequencing method. After assembly, 86,884 unique transcript fragments (unigenes) were assembled, with an average length of 991 bp. Approximately 41,795 (48.1%) unigenes were annotated in the nr NCBI database and 57.9% of the unigenes were similar to that of the Nile tilapia. A total of 24,299 unigenes were categorized into three Gene Ontology (GO) categories (molecular function, cellular component and biological process), 13,570 unigenes into 25 functional Clusters of Orthologous Groups of proteins (COG) categories, and 30,547 unigenes were grouped into 258 known pathways in the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. Following S. dysgalactiae infection, 11,461 differentially expressed unigenes were identified including 4658 up-regulated unigenes and 6803 down-regulated unigenes. Significant enrichment analysis of these differentially expressed unigenes identified major immune related pathways, including the Toll-like receptor, complement and coagulation cascades, T cell receptor signaling pathway and B cell receptor signaling pathway. In addition, 24,813 simple sequence repeats (SSRs) and 127,503 candidate single nucleotide polymorphisms (SNPs) were identified from the mullet spleen transcriptome. To this date, this study has globally analyzed the transcriptome profile from the spleen of L. haematocheila after S. dysgalactiae infection. Therefore, the results of our study contributes to better on the immune system and defense mechanisms of soiny mullet in response to bacterial infection, and provides valuable references for related studies in mugilidae species which currently lack genomic reference.}, } @article {pmid26704455, year = {2016}, author = {Mislan, KAS and Heer, JM and White, EP}, title = {Elevating The Status of Code in Ecology.}, journal = {Trends in ecology & evolution}, volume = {31}, number = {1}, pages = {4-7}, doi = {10.1016/j.tree.2015.11.006}, pmid = {26704455}, issn = {1872-8383}, mesh = {*Access to Information ; *Ecology ; *Periodicals as Topic ; Programming Languages ; Research Report ; *Software ; }, abstract = {Code is increasingly central to ecological research but often remains unpublished and insufficiently recognized. Making code available allows analyses to be more easily reproduced and can facilitate research by other scientists. We evaluate journal handling of code, discuss barriers to its publication, and suggest approaches for promoting and archiving code.}, } @article {pmid26700882, year = {2016}, author = {Pitta, DW and Indugu, N and Kumar, S and Vecchiarelli, B and Sinha, R and Baker, LD and Bhukya, B and Ferguson, JD}, title = {Metagenomic assessment of the functional potential of the rumen microbiome in Holstein dairy cows.}, journal = {Anaerobe}, volume = {38}, number = {}, pages = {50-60}, doi = {10.1016/j.anaerobe.2015.12.003}, pmid = {26700882}, issn = {1095-8274}, mesh = {Animals ; Archaea/classification/genetics ; Bacteria/classification/genetics ; Cattle ; Computational Biology/methods ; Lactation ; *Metagenome ; *Metagenomics/methods ; *Microbiota ; Phylogeny ; Rumen/*microbiology/physiology ; }, abstract = {The microbial ecology of the rumen microbiome is influenced by the diet and the physiological status of the dairy cow and can have tremendous influence on the yield and components of milk. There are significant differences in milk yields between first and subsequent lactations of dairy cows, but information on how the rumen microbiome changes as the dairy cow gets older has received little attention. We characterized the rumen microbiome of the dairy cow for phylogeny and functional pathways by lactation group and stage of lactation using a metagenomics approach. Our findings revealed that the rumen microbiome was dominated by Bacteroidetes (70%), Firmicutes (15-20%) and Proteobacteria (7%). The abundance of Firmicutes and Proteobacteria were independently influenced by diet and lactation. Bacteroidetes contributed to a majority of the metabolic functions in first lactation dairy cows while the contribution from Firmicutes and Proteobacteria increased incrementally in second and third lactation dairy cows. We found that nearly 70% of the CAZymes were oligosaccharide breaking enzymes which reflect the higher starch and fermentable sugars in the diet. The results of this study suggest that the rumen microbiome continues to evolve as the dairy cow advances in lactations and these changes may have a significant role in milk production.}, } @article {pmid26700811, year = {2016}, author = {Díaz, S and Kattge, J and Cornelissen, JH and Wright, IJ and Lavorel, S and Dray, S and Reu, B and Kleyer, M and Wirth, C and Prentice, IC and Garnier, E and Bönisch, G and Westoby, M and Poorter, H and Reich, PB and Moles, AT and Dickie, J and Gillison, AN and Zanne, AE and Chave, J and Wright, SJ and Sheremet'ev, SN and Jactel, H and Baraloto, C and Cerabolini, B and Pierce, S and Shipley, B and Kirkup, D and Casanoves, F and Joswig, JS and Günther, A and Falczuk, V and Rüger, N and Mahecha, MD and Gorné, LD}, title = {The global spectrum of plant form and function.}, journal = {Nature}, volume = {529}, number = {7585}, pages = {167-171}, pmid = {26700811}, issn = {1476-4687}, mesh = {Biodiversity ; Databases, Factual ; Genetic Variation ; Internationality ; Models, Biological ; Nitrogen/analysis ; Organ Size ; *Phenotype ; Plant Development ; Plant Leaves/anatomy & histology ; *Plant Physiological Phenomena ; Plant Stems/anatomy & histology ; Plants/*anatomy & histology/classification ; Reproduction ; Seeds/anatomy & histology ; Selection, Genetic ; Species Specificity ; }, abstract = {Earth is home to a remarkable diversity of plant forms and life histories, yet comparatively few essential trait combinations have proved evolutionarily viable in today's terrestrial biosphere. By analysing worldwide variation in six major traits critical to growth, survival and reproduction within the largest sample of vascular plant species ever compiled, we found that occupancy of six-dimensional trait space is strongly concentrated, indicating coordination and trade-offs. Three-quarters of trait variation is captured in a two-dimensional global spectrum of plant form and function. One major dimension within this plane reflects the size of whole plants and their parts; the other represents the leaf economics spectrum, which balances leaf construction costs against growth potential. The global plant trait spectrum provides a backdrop for elucidating constraints on evolution, for functionally qualifying species and ecosystems, and for improving models that predict future vegetation based on continuous variation in plant form and function.}, } @article {pmid26700742, year = {2016}, author = {Band, R and Barrowclough, C and Emsley, R and Machin, M and Wearden, AJ}, title = {Significant other behavioural responses and patient chronic fatigue syndrome symptom fluctuations in the context of daily life: An experience sampling study.}, journal = {British journal of health psychology}, volume = {21}, number = {3}, pages = {499-514}, pmid = {26700742}, issn = {2044-8287}, mesh = {Adolescent ; Adult ; Disabled Persons/psychology/statistics & numerical data ; Ecological Momentary Assessment/*statistics & numerical data ; Fatigue Syndrome, Chronic/complications/*physiopathology/*psychology ; Female ; Humans ; Male ; Middle Aged ; Severity of Illness Index ; Stress, Psychological/complications/physiopathology/psychology ; United Kingdom ; Young Adult ; }, abstract = {OBJECTIVE: Significant other responses to patients' symptoms are important for patient illness outcomes in chronic fatigue syndrome (CFS/ME); negative responses have been associated with increased patient depression, whilst increased disability and fatigue have been associated with solicitous significant other responses. The current study aimed to examine the relationship between significant other responses and patient outcomes within the context of daily life.

DESIGN: Experience Sampling Methodology (ESM).

METHOD: Twenty-three patients with CFS/ME and their significant others were recruited from specialist CFS/ME services. Sixty momentary assessments, delivered using individual San Francisco Android Smartphones, were conducted over a period of 6 days. All participants reported on affect, dyadic contact, and significant other responses to the patient. Patients reported on symptom severity, disability, and activity management strategies.

RESULTS: Negative significant other responses were associated with increased patient symptom severity and distress reported at the same momentary assessment; there was evidence of a potentially mediating role of concurrent distress on symptom severity. Patient-perceived solicitous responses were associated with reduced patient activity and disability reported at the same momentary assessment. Lagged analyses indicate that momentary associations between significant other responses and patient outcomes are largely transitory; significant other responses were not associated with any of the patient outcomes at the subsequent assessment.

CONCLUSION: The results indicate that significant other responses are important influences on the day-to-day experience of CFS/ME. Further research examining patient outcomes in association with specific significant other behavioural responses is warranted and future interventions that target such significant other behaviours may be beneficial. Statement of contribution What is already known on this subject? The existing literature has identified that significant other responses are important with respect to patient outcomes in CFS/ME. In particular, when examined cross-sectionally and longitudinally, negative and solicitous significant other responses are associated with poorer illness outcomes. This study is the first to examine the momentary associations between negative and solicitous responses, as reported by the patient and significant other, and patient-reported outcomes. An ESM paradigm was used to assess these temporal relationships within the context of participants' daily life. What does this study add? Negative responses were associated with increased momentary patient distress and symptoms. Perceived solicitousness was associated with activity limitation but less perceived disability. The impact of significant other responses on patient outcomes was found to be transitory.}, } @article {pmid26699508, year = {2016}, author = {Marsden, CD and Ortega-Del Vecchyo, D and O'Brien, DP and Taylor, JF and Ramirez, O and Vilà, C and Marques-Bonet, T and Schnabel, RD and Wayne, RK and Lohmueller, KE}, title = {Bottlenecks and selective sweeps during domestication have increased deleterious genetic variation in dogs.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {113}, number = {1}, pages = {152-157}, pmid = {26699508}, issn = {1091-6490}, mesh = {Animals ; Animals, Domestic/*genetics ; *Datasets as Topic ; Dog Diseases/*genetics ; Dogs/*genetics ; Endangered Species ; *Genetic Variation ; Genome/genetics ; Heterozygote ; Inbreeding ; Population Density ; Selection, Genetic ; Selective Breeding/*genetics ; Wolves/genetics ; }, abstract = {Population bottlenecks, inbreeding, and artificial selection can all, in principle, influence levels of deleterious genetic variation. However, the relative importance of each of these effects on genome-wide patterns of deleterious variation remains controversial. Domestic and wild canids offer a powerful system to address the role of these factors in influencing deleterious variation because their history is dominated by known bottlenecks and intense artificial selection. Here, we assess genome-wide patterns of deleterious variation in 90 whole-genome sequences from breed dogs, village dogs, and gray wolves. We find that the ratio of amino acid changing heterozygosity to silent heterozygosity is higher in dogs than in wolves and, on average, dogs have 2-3% higher genetic load than gray wolves. Multiple lines of evidence indicate this pattern is driven by less efficient natural selection due to bottlenecks associated with domestication and breed formation, rather than recent inbreeding. Further, we find regions of the genome implicated in selective sweeps are enriched for amino acid changing variants and Mendelian disease genes. To our knowledge, these results provide the first quantitative estimates of the increased burden of deleterious variants directly associated with domestication and have important implications for selective breeding programs and the conservation of rare and endangered species. Specifically, they highlight the costs associated with selective breeding and question the practice favoring the breeding of individuals that best fit breed standards. Our results also suggest that maintaining a large population size, rather than just avoiding inbreeding, is a critical factor for preventing the accumulation of deleterious variants.}, } @article {pmid26689780, year = {2015}, author = {Hernández-Pliego, J and Rodríguez, C and Bustamante, J}, title = {Why Do Kestrels Soar?.}, journal = {PloS one}, volume = {10}, number = {12}, pages = {e0145402}, pmid = {26689780}, issn = {1932-6203}, mesh = {Animals ; Ecosystem ; Energy Metabolism/physiology ; Falconiformes/*physiology ; Female ; Flight, Animal/*physiology ; Geographic Information Systems ; Male ; Predatory Behavior ; Raptors/*physiology ; Spain ; Sunlight ; }, abstract = {Individuals allocate considerable amounts of energy to movement, which ultimately affects their ability to survive and reproduce. Birds fly by flapping their wings, which is dependent on the chemical energy produced by muscle work, or use soaring-gliding flight, in which chemical energy is replaced with energy harvested from moving air masses, such as thermals. Flapping flight requires more energy than soaring-gliding flight, and this difference in the use of energy increases with body mass. However, soaring-gliding results in lower speeds than flapping, especially for small species. Birds therefore face a trade-off between energy and time costs when deciding which flight strategy to use. Raptors are a group of large birds that typically soar. As relatively light weight raptors, falcons can either soar on weak thermals or fly by flapping with low energy costs. In this paper, we study the flight behavior of the insectivorous lesser kestrel (Falco naumanni) during foraging trips and the influence of solar radiation, which we have adopted as a proxy for thermal formation, on kestrel flight variables. We tracked 35 individuals from two colonies using high frequency GPS-dataloggers over four consecutive breeding seasons. Contrary to expectations, kestrels relied heavily on thermal soaring when foraging, especially during periods of high solar radiation. This produced a circadian pattern in the kestrel flight strategy that led to a spatial segregation of foraging areas. Kestrels flapped towards foraging areas close to the colony when thermals were not available. However, as soon as thermals were formed, they soared on them towards foraging areas far from the colony, especially when they were surrounded by poor foraging habitats. This reduced the chick provisioning rate at the colony. Given that lesser kestrels have a preference for feeding on large insects, and considering the average distance they cover to capture them during foraging trips, to commute using flapping flight would result in a negative energy balance for the family group. Our results show that lesser kestrels prioritize saving energy when foraging, suggesting that kestrels are more energy than time-constrained during the breeding season.}, } @article {pmid26684963, year = {2016}, author = {Molnar, BE and Goerge, RM and Gilsanz, P and Hill, A and Subramanian, SV and Holton, JK and Duncan, DT and Beatriz, ED and Beardslee, WR}, title = {Neighborhood-level social processes and substantiated cases of child maltreatment.}, journal = {Child abuse & neglect}, volume = {51}, number = {}, pages = {41-53}, pmid = {26684963}, issn = {1873-7757}, support = {K01 HD053172/HD/NICHD NIH HHS/United States ; T32 MH017119/MH/NIMH NIH HHS/United States ; 1K01HD053172/HD/NICHD NIH HHS/United States ; }, mesh = {Adolescent ; Child ; *Child Abuse ; Child, Preschool ; Databases, Factual ; Female ; Humans ; Illinois ; Male ; *Residence Characteristics ; Social Environment ; United States ; }, abstract = {Child maltreatment is a preventable public health problem. Research has demonstrated that neighborhood structural factors (e.g. poverty, crime) can influence the proportion of a neighborhood's children who are victims of maltreatment. A newer strategy is the identification of potentially modifiable social processes at the neighborhood level that can also influence maltreatment. Toward this end, this study examines neighborhood-level data (maltreatment cases substantiated by Illinois' child protection agency, 1995-2005, social processes measured by the Project on Human Development in Chicago Neighborhoods, U.S. Census data, proportions of neighborhoods on public assistance, and crime data) that were linked across clusters of contiguous, relatively homogenous Chicago, IL census tracts with respect to racial/ethnic and socioeconomic composition. Our analysis-an ecological-level, repeated cross-sectional design utilizing random-intercept logit models-with a sensitivity analysis using spatial models to control for spatial autocorrelation-revealed consistent associations between neighborhood social processes and maltreatment. Neighborhoods higher in collective efficacy, intergenerational closure, and social networks, and lower in disorder had lower proportions of neglect, physical abuse, and sexual abuse substantiated cases, controlling for differences in structural factors. Higher collective efficacy and social network size also predicted a lower proportion of substance-exposed infants. This research indicates that strategies to mobilize neighborhood-level protective factors may decrease child maltreatment more effectively than individual and family-focused efforts alone.}, } @article {pmid26683336, year = {2015}, author = {Du, K and Yang, L and He, S}, title = {Phylogenomic analyses reveal a molecular signature linked to subterranean adaptation in rodents.}, journal = {BMC evolutionary biology}, volume = {15}, number = {}, pages = {287}, pmid = {26683336}, issn = {1471-2148}, mesh = {Adaptation, Physiological ; Animals ; *Biological Evolution ; *Ecosystem ; Evolution, Molecular ; Gene Ontology ; Genome ; Guinea Pigs ; Mice ; Mole Rats/classification/genetics/*physiology ; Open Reading Frames ; Phylogeny ; Selection, Genetic ; Transcriptome ; }, abstract = {BACKGROUND: Genome-wide signatures of convergent evolution are widely expected but rarely revealed in animals. Subterranean rodent genome and transcriptome data produced by next-generation sequencing facilitate the use of phylogenetic methods to infer non-synonymous and synonymous substitution rates within coding regions, which can reveal changes at the molecular level that are correlated with the dramatic shift from a terrestrial to subterranean habitat.

RESULTS: Our study used previously sequenced genome or transcriptome data of two subterranean rodents, the blind mole rat and naked mole rat, and their terrestrial relatives, the mouse and guinea pig, to investigate the genetic basis of rodent subterranean adaptation. An analysis of 4996 orthologous genes revealed that the substitution pace of coding sequences was significantly slower in the blind mole rat than in the mouse, and slower in the naked mole rat than in the guinea pig. The dN/dS ratio was significantly higher in the blind mole rat than in the mouse and in the naked mole rat than in the guinea pig. These patterns are most likely related to the longer generation time and lower effective population size of subterranean rodents caused by subterranean ecological constraints. We also identified some genes and gene ontology (GO) categories that might be candidates for adaptation to subterranean life.

CONCLUSIONS: Our study reveals a case of subterranean convergent evolution in rodents that is correlated with change in the pace and mode of molecular evolution observed at the genome scale. We believe that this genomic signature could have also evolved in other cases of subterranean convergence. Additionally, the genes that displayed the most radical changes in their patterns of evolution and their associated GO categories provide a strong basis for further comparative and functional studies, and potentially reveal molecular signatures of adaptation to subterranean life.}, } @article {pmid26681696, year = {2016}, author = {Huang, JP and Knowles, LL}, title = {The Species versus Subspecies Conundrum: Quantitative Delimitation from Integrating Multiple Data Types within a Single Bayesian Approach in Hercules Beetles.}, journal = {Systematic biology}, volume = {65}, number = {4}, pages = {685-699}, doi = {10.1093/sysbio/syv119}, pmid = {26681696}, issn = {1076-836X}, mesh = {Animals ; Bayes Theorem ; Classification/*methods ; Coleoptera/*classification ; Data Interpretation, Statistical ; *Phylogeny ; Species Specificity ; }, abstract = {With the recent attention and focus on quantitative methods for species delimitation, an overlooked but equally important issue regards what has actually been delimited. This study investigates the apparent arbitrariness of some taxonomic distinctions, and in particular how species and subspecies are assigned. Specifically, we use a recently developed Bayesian model-based approach to show that in the Hercules beetles (genus Dynastes) there is no statistical difference in the probability that putative taxa represent different species, irrespective of whether they were given species or subspecies designations. By considering multiple data types, as opposed to relying exclusively on genetic data alone, we also show that both previously recognized species and subspecies represent a variety of points along the speciation spectrum (i.e., previously recognized species are not systematically further along the continuum than subspecies). For example, based on evolutionary models of divergence, some taxa are statistically distinguishable on more than one axis of differentiation (e.g., along both phenotypic and genetic dimensions), whereas other taxa can only be delimited statistically from a single data type. Because both phenotypic and genetic data are analyzed in a common Bayesian framework, our study provides a framework for investigating whether disagreements in species boundaries among data types reflect (i) actual discordance with the actual history of lineage splitting, or instead (ii) differences among data types in the amount of time required for differentiation to become apparent among the delimited taxa. We discuss what the answers to these questions imply about what characters are used to delimit species, as well as the diverse processes involved in the origin and maintenance of species boundaries. With this in mind, we then reflect more generally on how quantitative methods for species delimitation are used to assign taxonomic status.}, } @article {pmid26680538, year = {2016}, author = {Cruz de Carvalho, MH and Sun, HX and Bowler, C and Chua, NH}, title = {Noncoding and coding transcriptome responses of a marine diatom to phosphate fluctuations.}, journal = {The New phytologist}, volume = {210}, number = {2}, pages = {497-510}, doi = {10.1111/nph.13787}, pmid = {26680538}, issn = {1469-8137}, mesh = {Aquatic Organisms/drug effects/*genetics/growth & development ; Diatoms/drug effects/*genetics/growth & development ; Down-Regulation/drug effects/genetics ; Gene Ontology ; Genome ; Homeostasis/drug effects ; Open Reading Frames/*genetics ; Phosphates/*pharmacology ; RNA, Messenger/genetics/metabolism ; Signal Transduction/drug effects/genetics ; Transcription Factors/metabolism ; Transcriptome/drug effects/*genetics ; Up-Regulation/drug effects/genetics ; }, abstract = {Phosphorus (P) is an essential element to all living cells, yet fluctuations in P concentrations are recurrent in the marine environment. Diatoms are amongst the most successful phytoplankton groups, adapting to and surviving periods of suboptimal conditions and resuming growth as soon as nutrient concentrations permit. A knowledge of the molecular underpinnings of diatom ecological success is, however, still very incomplete. By strand-specific RNA sequencing, we analyzed the global transcriptome changes of the diatom Phaeodactylum tricornutum in response to P fluctuations over a course of 8 d, defining five distinct physiological states. This study reports previously unidentified genes highly responsive to P stress in P. tricornutum. Our data also uncover the complexity of the P. tricornutum P-responsive sensory and signaling system that combines bacterial two-component systems with more complex pathways reminiscent of metazoans. Finally, we identify a multitude of novel long intergenic nonprotein coding RNAs (lincRNAs) specifically responsive to P depletion, suggesting putative regulatory roles in the regulation of P homeostasis. Our work provides additional molecular insights into the resilience of diatoms and their ecological success, and opens up novel routes to address and explore the function and regulatory roles of P. tricornutum lincRNAs in the context of nutrient stress.}, } @article {pmid26679359, year = {2016}, author = {Bak, SY and Qi, XS and Kelly, JA and Alexander, S and Chung, Y and Gyurdzhyan, S and Patton, LL and Lee, SP}, title = {Dosimetric distribution to tooth-bearing areas in intensity-modulated radiation therapy for head and neck cancer: a pilot study.}, journal = {Oral surgery, oral medicine, oral pathology and oral radiology}, volume = {121}, number = {1}, pages = {43-48}, doi = {10.1016/j.oooo.2015.10.007}, pmid = {26679359}, issn = {2212-4411}, mesh = {Adult ; Aged ; Aged, 80 and over ; Female ; Head and Neck Neoplasms/*radiotherapy ; Humans ; Male ; Mandible/*radiation effects ; Maxilla/*radiation effects ; Middle Aged ; Osteoradionecrosis/*etiology ; Pilot Projects ; Radiotherapy Dosage ; *Radiotherapy, Intensity-Modulated ; Retrospective Studies ; Risk Factors ; Tooth/*radiation effects ; }, abstract = {OBJECTIVES: Dosimetric distribution of intensity-modulated radiotherapy (IMRT) to tooth-bearing areas for common head and neck (H&N) cancer sites were analyzed to facilitate minimization of osteoradionecrosis (ORN) risk through preradiation dental treatment planning.

STUDY DESIGN: Fifty-four patients received IMRT with prescribed doses ranging from 6000 centigrays (cGy) (adjuvant) to 6930 cGy (primary) to treat base of tongue (BOT), tonsil, larynx, nasopharynx, and hypopharynx cancers. The average maximal radiation dose delivered was recorded in tooth-bearing areas (anteriors, premolars, and first, second, and third molars) of the maxilla and mandible.

RESULTS: All tooth-bearing areas in laryngeal cancer cases received less than 2500 cGy. Maxillary and mandibular molar regions for BOT, tonsil, and hypopharynx cancers received 5000 cGy or higher. In nasopharynx cancers, maxillary teeth received higher doses than mandibular teeth.

CONCLUSIONS: Among 5 H&N subsites, mandibular molar regions for BOT, tonsil, and hypopharynx cancers received higher IMRT doses on average, posing the greatest ORN risk.}, } @article {pmid26678263, year = {2015}, author = {Kelly, DJ and Foley, DH and Richards, AL}, title = {A Spatiotemporal Database to Track Human Scrub Typhus Using the VectorMap Application.}, journal = {PLoS neglected tropical diseases}, volume = {9}, number = {12}, pages = {e0004161}, pmid = {26678263}, issn = {1935-2735}, mesh = {*Databases, Factual ; *Epidemiologic Methods ; Global Health ; Humans ; Scrub Typhus/*epidemiology ; *Software ; Spatio-Temporal Analysis ; }, abstract = {Scrub typhus is a potentially fatal mite-borne febrile illness, primarily of the Asia-Pacific Rim. With an endemic area greater than 13 million km2 and millions of people at risk, scrub typhus remains an underreported, often misdiagnosed febrile illness. A comprehensive, updatable map of the true distribution of cases has been lacking, and therefore the true risk of disease within the very large endemic area remains unknown. The purpose of this study was to establish a database and map to track human scrub typhus. An online search using PubMed and the United States Armed Forces Pest Management Board Literature Retrieval System was performed to identify articles describing human scrub typhus cases both within and outside the traditionally accepted endemic regions. Using World Health Organization guidelines, stringent criteria were used to establish diagnoses for inclusion in the database. The preliminary screening of 181 scrub typhus publications yielded 145 publications that met the case criterion, 267 case records, and 13 serosurvey records that could be georeferenced, describing 13,739 probable or confirmed human cases in 28 countries. A map service has been established within VectorMap (www.vectormap.org) to explore the role that relative location of vectors, hosts, and the pathogen play in the transmission of mite-borne scrub typhus. The online display of scrub typhus cases in VectorMap illustrates their presence and provides an up-to-date geographic distribution of proven scrub typhus cases.}, } @article {pmid26676236, year = {2016}, author = {Zhou, J and Feng, K and Pei, Z and Meng, F and Sun, J}, title = {Multivariate analysis combined with GIS to source identification of heavy metals in soils around an abandoned industrial area, Eastern China.}, journal = {Ecotoxicology (London, England)}, volume = {25}, number = {2}, pages = {380-388}, pmid = {26676236}, issn = {1573-3017}, mesh = {China ; Environmental Monitoring/*methods ; Geographic Information Systems ; Metals, Heavy/*analysis ; Multivariate Analysis ; Soil Pollutants/*analysis ; }, abstract = {Heavy metals in soils polluted by industrial production are a meaningful topic worldwide. The purpose of this study is to understand the pollution status and spatial distribution of heavy metals in soils. The result can help decision-makers apportion possible soil heavy metals sources and formulate effective pollution control policies. In this paper, 155 soil samples (0-20 cm) were collected and analyzed for eight heavy metals (Cd, Hg, As, Cu, Pb, Cr, Zn, and Ni) from an abandoned industrial area of Tong County, located in Jiangsu Province of Eastern China. The multivariate analysis (including I(geo), Ei/RI, EF, PCA, and CA) and geostatistics (GIS) were used to assess the enrichment level and pollution level of soil heavy metals and identify their sources. The results indicated that eight heavy metals in soils had moderate variations, with CVs ranging from 19.63 to 63.34%. The pollution level of I(geo) of soil heavy metals decreased in the order of Cd~Zn > Cu > Hg~As~Pb~Cr~Ni. The enrichment level of soil heavy metals decreased in the order of Cd > Zn > Hg > Cu > Pb > Ni > As > Cr. According to the Ei, except Cd and Hg were in the significant and moderate ecological risk levels respectively, other soil heavy metals were in the clean or light ecological risk levels, the level of potential ecological risk (RI) of the whole industrial area was moderate. Finally, the source identification of soil heavy metals indicated that Cd and Zn were primarily controlled by human activities, and Hg and Cu were controlled by natural and anthropogenic sources, and As, Pb, Cr, and Ni were mainly controlled by soil parent materials.}, } @article {pmid26675011, year = {2016}, author = {Romero-Ramirez, A and Bonifácio, P and Labrune, C and Sardá, R and Amouroux, JM and Bellan, G and Duchêne, JC and Hermand, R and Karakassis, I and Dounas, C and Grémare, A}, title = {Long-term (1998-2010) large-scale comparison of the ecological quality status of gulf of lions (NW Mediterranean) benthic habitats.}, journal = {Marine pollution bulletin}, volume = {102}, number = {1}, pages = {102-113}, doi = {10.1016/j.marpolbul.2015.11.052}, pmid = {26675011}, issn = {1879-3363}, mesh = {Animals ; Aquatic Organisms/*physiology ; *Biodiversity ; Databases, Factual ; Ecology ; *Ecosystem ; Environmental Monitoring/methods ; Geologic Sediments/chemistry ; Mediterranean Sea ; *Water Quality ; }, abstract = {A comprehensive Mediterranean data set has been used to address 3 questions associated with the use of sensitivity/tolerance based biotic indices to infer the Ecological Quality status (EcoQs) of benthic habitats. Our results showed: (1) a significant effect of the reference database on derived sensitivity/tolerance measure (ES500.05) as well as associated Benthic Quality Index values and derived EcoQs; (2) a lack of correlation neither between BQI and AZTI Marine Biotic Index values nor between BQI and Multivariate-AZTI Marine Biotic Index values; (3) a lack of correlation between the values of the Benthic Habitat Quality Index (index derived from Sediment Profile Imagery) and those of either of the 3 tested biotic indices; and (4) a general agreement between the 3 tested biotic indices in describing the lack of global trend for the EcoQs of the Gulf of Lions despite the occurrence of significant changes in benthic macrofauna composition between 1998 and 2010.}, } @article {pmid26674683, year = {2016}, author = {Abbas, S and Nichol, JE and Fischer, GA}, title = {A 70-year perspective on tropical forest regeneration.}, journal = {The Science of the total environment}, volume = {544}, number = {}, pages = {544-552}, doi = {10.1016/j.scitotenv.2015.11.171}, pmid = {26674683}, issn = {1879-1026}, abstract = {Forested areas of the world decreased by 129 million hectare during the past quarter-century, and only 35 % of remainder is primary forest. Secondary forests are therefore relatively more important for biodiversity conservation, catchment protection, climate control, and the ecological services they provide. Many governments expend large resources on afforestation projects, which may not be supported by objective data on rates and pathways of natural succession in secondary forest. This paper describes a 70-year succession of tropical forest in Hong Kong under different management regimes including afforestation programs, frequent fire, and fire protection. From complete destruction of its forest during the Second World War, forest has established rapidly in areas where a shrub cover was able to colonize. The practice of afforestation as a nursery stage on degraded hillsides, for establishment of forest seedlings by natural invasion is not supported by the evidence, as when the native Pinus massoniana plantations were eliminated by disease during the 1970s, no forest or woody species were seen in the areas affected. In fact there was a reversion to grassland, which persisted there for almost three decades, until recent shrub invasion. The fastest period of forest regeneration, at 10.9% annually between 1989 and 2001, occurred when shrubland edge was greatest and forest was able to colonize across interfluves between linear-shaped riparian shrublands in valley bottoms. After 2001, succession to forest was slower, at 7.8% annually, as forest patches consolidated and edge habitats reduced. Effective forest management policies could include seeding of native shrubs extending linearly from established forest, to maximize edge length between woody species and grasslands, and planting of late successional species in areas where forest pioneers are in decline.}, } @article {pmid26673328, year = {2015}, author = {Klughammer, J and Datlinger, P and Printz, D and Sheffield, NC and Farlik, M and Hadler, J and Fritsch, G and Bock, C}, title = {Differential DNA Methylation Analysis without a Reference Genome.}, journal = {Cell reports}, volume = {13}, number = {11}, pages = {2621-2633}, pmid = {26673328}, issn = {2211-1247}, support = {I 1575/FWF_/Austrian Science Fund FWF/Austria ; I 1626/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Animals ; Blood Cells/metabolism ; Carps ; Cattle ; Chromosome Mapping ; CpG Islands ; DNA/chemistry/*metabolism ; *DNA Methylation ; *Genome ; Genomics/*methods ; High-Throughput Nucleotide Sequencing ; Humans ; Leukocytes/metabolism ; Sequence Analysis, DNA ; Software ; }, abstract = {Genome-wide DNA methylation mapping uncovers epigenetic changes associated with animal development, environmental adaptation, and species evolution. To address the lack of high-throughput methods for DNA methylation analysis in non-model organisms, we developed an integrated approach for studying DNA methylation differences independent of a reference genome. Experimentally, our method relies on an optimized 96-well protocol for reduced representation bisulfite sequencing (RRBS), which we have validated in nine species (human, mouse, rat, cow, dog, chicken, carp, sea bass, and zebrafish). Bioinformatically, we developed the RefFreeDMA software to deduce ad hoc genomes directly from RRBS reads and to pinpoint differentially methylated regions between samples or groups of individuals (http://RefFreeDMA.computational-epigenetics.org). The identified regions are interpreted using motif enrichment analysis and/or cross-mapping to annotated genomes. We validated our method by reference-free analysis of cell-type-specific DNA methylation in the blood of human, cow, and carp. In summary, we present a cost-effective method for epigenome analysis in ecology and evolution, which enables epigenome-wide association studies in natural populations and species without a reference genome.}, } @article {pmid26672334, year = {2015}, author = {Shi, L and Zhang, CC and Ming, MD and Guo, LP and Zhu, SD and Yang, HB}, title = {[Quality Suitability of Magnolia officinalis in China Based on GIS].}, journal = {Zhong yao cai = Zhongyaocai = Journal of Chinese medicinal materials}, volume = {38}, number = {4}, pages = {706-710}, pmid = {26672334}, issn = {1001-4454}, mesh = {Biphenyl Compounds/*analysis ; China ; Geographic Information Systems ; Lignans/*analysis ; Magnolia/*chemistry ; }, abstract = {OBJECTIVE: To study the quality suitability rank dividing of Magnolia officinalis on the basis of investigation on the correlation between the ratio of magnolol and honokiol in Magnoliae Officinalis Cortex and ecological factors, in order to provide scientific basis for its planting area of high-quality medicinal materials.

METHODS: Based on the samples' quality analysis of 43 sampling points of Magnolia officinalis,the relationship between the ratio of magnolol and honokiol in Magnoliae officinalis Cortex and ecological factors was analyzed by statistical analysis. The geographic information system(GIS) was applied to assess the quality suitability rank dividing of Magnolia officinalis in China.

RESULTS: There were 12 ecological factors mainly affecting the quality of Magnoliae Officinalis Cortex; The ratio of magnolol and honokiol had obvious characteristics of regional quality. Conclusion: Magnoliae Officinalis Cortex which produced in Hubei and Chongqing is dao-di herbs.}, } @article {pmid26671457, year = {2016}, author = {Stevison, LS and Woerner, AE and Kidd, JM and Kelley, JL and Veeramah, KR and McManus, KF and , and Bustamante, CD and Hammer, MF and Wall, JD}, title = {The Time Scale of Recombination Rate Evolution in Great Apes.}, journal = {Molecular biology and evolution}, volume = {33}, number = {4}, pages = {928-945}, pmid = {26671457}, issn = {1537-1719}, support = {F32 GM101744/GM/NIGMS NIH HHS/United States ; R01 GM115433/GM/NIGMS NIH HHS/United States ; F32GM101744/GM/NIGMS NIH HHS/United States ; R01_HG005226/HG/NHGRI NIH HHS/United States ; }, mesh = {Animals ; Chromosome Mapping ; Chromosomes/genetics ; *Evolution, Molecular ; Genetic Variation ; Gorilla gorilla/genetics ; Hominidae/*genetics ; Humans ; Linkage Disequilibrium/*genetics ; Pan troglodytes/genetics ; Papio/genetics ; *Recombination, Genetic ; Species Specificity ; }, abstract = {We present three linkage-disequilibrium (LD)-based recombination maps generated using whole-genome sequence data from 10 Nigerian chimpanzees, 13 bonobos, and 15 western gorillas, collected as part of the Great Ape Genome Project (Prado-Martinez J, et al. 2013. Great ape genetic diversity and population history. Nature 499:471-475). We also identified species-specific recombination hotspots in each group using a modified LDhot framework, which greatly improves statistical power to detect hotspots at varying strengths. We show that fewer hotspots are shared among chimpanzee subspecies than within human populations, further narrowing the time scale of complete hotspot turnover. Further, using species-specific PRDM9 sequences to predict potential binding sites (PBS), we show higher predicted PRDM9 binding in recombination hotspots as compared to matched cold spot regions in multiple great ape species, including at least one chimpanzee subspecies. We found that correlations between broad-scale recombination rates decline more rapidly than nucleotide divergence between species. We also compared the skew of recombination rates at centromeres and telomeres between species and show a skew from chromosome means extending as far as 10-15 Mb from chromosome ends. Further, we examined broad-scale recombination rate changes near a translocation in gorillas and found minimal differences as compared to other great ape species perhaps because the coordinates relative to the chromosome ends were unaffected. Finally, on the basis of multiple linear regression analysis, we found that various correlates of recombination rate persist throughout the African great apes including repeats, diversity, and divergence. Our study is the first to analyze within- and between-species genome-wide recombination rate variation in several close relatives.}, } @article {pmid26669414, year = {2016}, author = {Li, Q and Qin, X and Liu, J and Gui, C and Wang, B and Li, J and Ju, J}, title = {Deciphering the Biosynthetic Origin of L-allo-Isoleucine.}, journal = {Journal of the American Chemical Society}, volume = {138}, number = {1}, pages = {408-415}, doi = {10.1021/jacs.5b11380}, pmid = {26669414}, issn = {1520-5126}, mesh = {Catalysis ; Computational Biology ; Humans ; Isoleucine/*biosynthesis ; Mutagenesis, Site-Directed ; }, abstract = {The nonproteinogenic amino acid L-allo-isoleucine (L-allo-Ile) is featured in an assortment of life forms comprised of, but not limited to, bacteria, fungi, plants and mammalian systems including Homo sapiens. Despite its ubiquity and functional importance, the specific origins of this unique amino acid have eluded characterization. In this study, we describe the discovery and characterization of two enzyme pairs consisting of a pyridoxal 5'-phosphate (PLP)-linked aminotransferase and an unprecedented isomerase synergistically responsible for the biosynthesis of L-allo-Ile from L-isoleucine (L-Ile) in natural products. DsaD/DsaE from the desotamide biosynthetic pathway in Streptomyces scopuliridis SCSIO ZJ46, and MfnO/MfnH from the marformycin biosynthetic pathway in Streptomyces drozdowiczii SCSIO 10141 drive L-allo-Ile generation in each respective system. In vivo gene inactivations validated the importance of the DsaD/DsaE pair and MfnO/MfnH pair in L-allo-Ile unit biosynthesis. Inactivation of PLP-linked aminotransferases DsaD and MfnO led to significantly diminished desotamide and marformycin titers, respectively. Additionally, inactivation of the isomerase genes dsaE and mfnH completely abolished production of all L-allo-Ile-containing metabolites in both biosynthetic pathways. Notably, in vitro biochemical assays revealed that DsaD/DsaE and MfnO/MfnH each catalyze a bidirectional reaction between L-allo-Ile and L-Ile. Site-directed mutagenesis experiments revealed that the enzymatic reaction involves a PLP-linked ketimine intermediate and uses an arginine residue from the C-terminus of each isomerase to epimerize the amino acid β-position. Consequently, these data provide important new insight into the origins of L-allo-Ile in natural products with medicinal potential and illuminate new possibilities for biotool development.}, } @article {pmid26668305, year = {2016}, author = {Geiser, C and Mandáková, T and Arrigo, N and Lysak, MA and Parisod, C}, title = {Repeated Whole-Genome Duplication, Karyotype Reshuffling, and Biased Retention of Stress-Responding Genes in Buckler Mustard.}, journal = {The Plant cell}, volume = {28}, number = {1}, pages = {17-27}, pmid = {26668305}, issn = {1532-298X}, mesh = {Fluorescence ; *Gene Duplication ; Gene Ontology ; *Genes, Plant ; *Karyotype ; Models, Genetic ; Mustard Plant/*genetics ; Selection, Genetic ; Stress, Physiological/*genetics ; Transcriptome/genetics ; }, abstract = {Whole-genome duplication (WGD) is usually followed by gene loss and karyotype repatterning. Despite evidence of new adaptive traits associated with WGD, the underpinnings and evolutionary significance of such genome fractionation remain elusive. Here, we use Buckler mustard (Biscutella laevigata) to infer processes that have driven the retention of duplicated genes after recurrent WGDs. In addition to the β- and α-WGD events shared by all Brassicaceae, cytogenetic and transcriptome analyses revealed two younger WGD events that occurred at times of environmental changes in the clade of Buckler mustard (Biscutelleae): a mesopolyploidy event from the late Miocene that was followed by considerable karyotype reshuffling and chromosome number reduction and a neopolyploidy event during the Pleistocene. Although a considerable number of the older duplicates presented signatures of retention under positive selection, the majority of retained duplicates arising from the younger mesopolyploidy WGD event matched predictions of the gene balance hypothesis and showed evidence of strong purifying selection as well as enrichment in gene categories responding to abiotic stressors. Retention of large stretches of chromosomes for both genomic copies supported the hypothesis that cycles of WGD and biased fractionation shaped the genome of this stress-tolerant polypolyloid, promoting the adaptive recruitment of stress-responding genes in the face of environmental challenges.}, } @article {pmid26667220, year = {2016}, author = {Ramisetty, BC and Santhosh, RS}, title = {Horizontal gene transfer of chromosomal Type II toxin-antitoxin systems of Escherichia coli.}, journal = {FEMS microbiology letters}, volume = {363}, number = {3}, pages = {}, doi = {10.1093/femsle/fnv238}, pmid = {26667220}, issn = {1574-6968}, mesh = {Bacterial Toxins/*genetics ; Computational Biology ; Escherichia coli/*genetics ; *Gene Transfer, Horizontal ; Genetic Variation ; }, abstract = {Type II toxin-antitoxin systems (TAs) are small autoregulated bicistronic operons that encode a toxin protein with the potential to inhibit metabolic processes and an antitoxin protein to neutralize the toxin. Most of the bacterial genomes encode multiple TAs. However, the diversity and accumulation of TAs on bacterial genomes and its physiological implications are highly debated. Here we provide evidence that Escherichia coli chromosomal TAs (encoding RNase toxins) are 'acquired' DNA likely originated from heterologous DNA and are the smallest known autoregulated operons with the potential for horizontal propagation. Sequence analyses revealed that integration of TAs into the bacterial genome is unique and contributes to variations in the coding and/or regulatory regions of flanking host genome sequences. Plasmids and genomes encoding identical TAs of natural isolates are mutually exclusive. Chromosomal TAs might play significant roles in the evolution and ecology of bacteria by contributing to host genome variation and by moderation of plasmid maintenance.}, } @article {pmid26666348, year = {2015}, author = {Chandramouli, KH and Al-Aqeel, S and Ryu, T and Zhang, H and Seridi, L and Ghosheh, Y and Qian, PY and Ravasi, T}, title = {Transcriptome and proteome dynamics in larvae of the barnacle Balanus Amphitrite from the Red Sea.}, journal = {BMC genomics}, volume = {16}, number = {}, pages = {1063}, pmid = {26666348}, issn = {1471-2164}, mesh = {Animals ; Databases, Genetic ; Gene Expression Profiling/*methods ; Gene Expression Regulation, Developmental ; Indian Ocean ; Larva/genetics/metabolism ; Open Reading Frames ; Proteomics/*methods ; Sequence Analysis, DNA ; Thoracica/*genetics/*metabolism ; }, abstract = {BACKGROUND: The barnacle Balanus amphitrite is widely distributed in marine shallow and tidal waters, and has significant economic and ecological importance. Nauplii, the first larval stage of most crustaceans, are extremely abundant in the marine zooplankton. However, a lack of genome information has hindered elucidation of the molecular mechanisms of development, settlement and survival strategies in extreme marine environments. We sequenced and constructed the genome dataset for nauplii to obtain comprehensive larval genetic information. We also investigated iTRAQ-based protein expression patterns to reveal the molecular basis of nauplii development, and to gain information on larval survival strategies in the Red Sea marine environment.

RESULTS: A nauplii larval transcript dataset, containing 92,117 predicted open reading frames (ORFs), was constructed and used as a reference for the proteome analysis. Genes related to translation, oxidative phosphorylation and cytoskeletal development were highly abundant. We observed remarkable plasticity in the proteome of Red Sea larvae. The proteins associated with development, stress responses and osmoregulation showed the most significant differences between the two larval populations studied. The synergistic overexpression of heat shock and osmoregulatory proteins may facilitate larval survival in intertidal habitats or in extreme environments.

CONCLUSIONS: We presented, for the first time, comprehensive transcriptome and proteome datasets for Red Sea nauplii. The datasets provide a foundation for future investigations focused on the survival mechanisms of other crustaceans in extreme marine environments.}, } @article {pmid26662617, year = {2016}, author = {Shi, Y and Liu, X and Kok, SY and Rajarethinam, J and Liang, S and Yap, G and Chong, CS and Lee, KS and Tan, SS and Chin, CK and Lo, A and Kong, W and Ng, LC and Cook, AR}, title = {Three-Month Real-Time Dengue Forecast Models: An Early Warning System for Outbreak Alerts and Policy Decision Support in Singapore.}, journal = {Environmental health perspectives}, volume = {124}, number = {9}, pages = {1369-1375}, pmid = {26662617}, issn = {1552-9924}, mesh = {Decision Support Techniques ; Dengue/*epidemiology/*prevention & control/virology ; *Disease Outbreaks ; Forecasting ; *Health Policy ; Humans ; Incidence ; *Models, Statistical ; Public Health/*methods ; Singapore/epidemiology ; Time Factors ; }, abstract = {BACKGROUND: With its tropical rainforest climate, rapid urbanization, and changing demography and ecology, Singapore experiences endemic dengue; the last large outbreak in 2013 culminated in 22,170 cases. In the absence of a vaccine on the market, vector control is the key approach for prevention.

OBJECTIVES: We sought to forecast the evolution of dengue epidemics in Singapore to provide early warning of outbreaks and to facilitate the public health response to moderate an impending outbreak.

METHODS: We developed a set of statistical models using least absolute shrinkage and selection operator (LASSO) methods to forecast the weekly incidence of dengue notifications over a 3-month time horizon. This forecasting tool used a variety of data streams and was updated weekly, including recent case data, meteorological data, vector surveillance data, and population-based national statistics. The forecasting methodology was compared with alternative approaches that have been proposed to model dengue case data (seasonal autoregressive integrated moving average and step-down linear regression) by fielding them on the 2013 dengue epidemic, the largest on record in Singapore.

RESULTS: Operationally useful forecasts were obtained at a 3-month lag using the LASSO-derived models. Based on the mean average percentage error, the LASSO approach provided more accurate forecasts than the other methods we assessed. We demonstrate its utility in Singapore's dengue control program by providing a forecast of the 2013 outbreak for advance preparation of outbreak response.

CONCLUSIONS: Statistical models built using machine learning methods such as LASSO have the potential to markedly improve forecasting techniques for recurrent infectious disease outbreaks such as dengue.

CITATION: Shi Y, Liu X, Kok SY, Rajarethinam J, Liang S, Yap G, Chong CS, Lee KS, Tan SS, Chin CK, Lo A, Kong W, Ng LC, Cook AR. 2016. Three-month real-time dengue forecast models: an early warning system for outbreak alerts and policy decision support in Singapore. Environ Health Perspect 124:1369-1375; http://dx.doi.org/10.1289/ehp.1509981.}, } @article {pmid26662396, year = {2015}, author = {Song, H and Wang, PF and Li, TT and Xia, H and Zhao, SZ and Hou, L and Zhao, CZ}, title = {Genome-wide identification and evolutionary analysis of nucleotide-binding site-encoding resistance genes in Lotus japonicus (Fabaceae).}, journal = {Genetics and molecular research : GMR}, volume = {14}, number = {4}, pages = {16024-16040}, doi = {10.4238/2015.December.7.16}, pmid = {26662396}, issn = {1676-5680}, mesh = {Amino Acid Motifs ; Chromosome Mapping ; Codon ; Computational Biology/methods ; Conserved Sequence ; Databases, Genetic ; Disease Resistance/*genetics ; *Evolution, Molecular ; Gene Duplication ; *Genes, Plant ; *Genome-Wide Association Study ; Host-Pathogen Interactions ; Lotus/classification/*genetics ; Multigene Family ; Phylogeny ; Selection, Genetic ; }, abstract = {Nucleotide-binding site (NBS) disease resistance genes play a crucial role in plant defense responses against pathogens and insect pests. Many NBS-encoding genes have been detected in Lotus japonicus, an important forage crop in many parts of the world. However, most NBS genes identified so far in L. japonicus were only partial sequences. We identified 45 full-length NBS-encoding genes in the L. japonicus genome, and analyzed gene duplications, motifs, and the molecular phylogeny to further understand the NBS gene family. We found that gene duplication events rarely occur in L. japonicus NBS-encoding (LjNBS) genes. In addition, LjNBS genes were subjected to selection pressure, and codon usage bias was evident. We tested for purifying selection (specifically in the CC-NBS-LRR and TIR-NBS-LRR groups), and found strong purifying selection in the TIR-domain-containing sequences, indicating that the CC-NBS-LRR group is more likely to undergo expansion than the TIR-NBS-LRR group. Moreover, our results showed that both selection and mutation contributed to LjNBS codon usage bias, but mutational bias was the major influence on codon usage.}, } @article {pmid26657537, year = {2016}, author = {Edwards, RA and McNair, K and Faust, K and Raes, J and Dutilh, BE}, title = {Computational approaches to predict bacteriophage-host relationships.}, journal = {FEMS microbiology reviews}, volume = {40}, number = {2}, pages = {258-272}, pmid = {26657537}, issn = {1574-6976}, mesh = {Bacteria/*virology ; Bacteriophages/genetics/*physiology ; Genome, Viral/genetics ; Host-Pathogen Interactions/*genetics ; *Metagenomics ; }, abstract = {Metagenomics has changed the face of virus discovery by enabling the accurate identification of viral genome sequences without requiring isolation of the viruses. As a result, metagenomic virus discovery leaves the first and most fundamental question about any novel virus unanswered: What host does the virus infect? The diversity of the global virosphere and the volumes of data obtained in metagenomic sequencing projects demand computational tools for virus-host prediction. We focus on bacteriophages (phages, viruses that infect bacteria), the most abundant and diverse group of viruses found in environmental metagenomes. By analyzing 820 phages with annotated hosts, we review and assess the predictive power of in silico phage-host signals. Sequence homology approaches are the most effective at identifying known phage-host pairs. Compositional and abundance-based methods contain significant signal for phage-host classification, providing opportunities for analyzing the unknowns in viral metagenomes. Together, these computational approaches further our knowledge of the interactions between phages and their hosts. Importantly, we find that all reviewed signals significantly link phages to their hosts, illustrating how current knowledge and insights about the interaction mechanisms and ecology of coevolving phages and bacteria can be exploited to predict phage-host relationships, with potential relevance for medical and industrial applications.}, } @article {pmid26657036, year = {2016}, author = {Tao, L and Zhao, Y and Wu, Y and Wang, Q and Yuan, H and Zhao, L and Guo, W and You, X}, title = {Transcriptome profiling and digital gene expression by deep sequencing in early somatic embryogenesis of endangered medicinal Eleutherococcus senticosus Maxim.}, journal = {Gene}, volume = {578}, number = {1}, pages = {17-24}, doi = {10.1016/j.gene.2015.11.050}, pmid = {26657036}, issn = {1879-0038}, mesh = {Eleutherococcus/*embryology/genetics ; Gene Expression Profiling/*methods ; Gene Expression Regulation, Developmental ; Gene Expression Regulation, Plant ; Gene Ontology ; High-Throughput Nucleotide Sequencing/*methods ; Metabolic Networks and Pathways ; Molecular Sequence Annotation ; Plant Proteins/*genetics ; Plant Somatic Embryogenesis Techniques ; Plants, Medicinal/embryology/genetics ; Sequence Analysis, RNA/*methods ; }, abstract = {Somatic embryogenesis (SE) has been studied as a model system to understand molecular events in physiology, biochemistry, and cytology during plant embryo development. In particular, it is exceedingly difficult to access the morphological and early regulatory events in zygotic embryos. To understand the molecular mechanisms regulating early SE in Eleutherococcus senticosus Maxim., we used high-throughput RNA-Seq technology to investigate its transcriptome. We obtained 58,327,688 reads, which were assembled into 75,803 unique unigenes. To better understand their functions, the unigenes were annotated using the Clusters of Orthologous Groups, Gene Ontology, and Kyoto Encyclopedia of Genes and Genomes databases. Digital gene expression libraries revealed differences in gene expression profiles at different developmental stages (embryogenic callus, yellow embryogenic callus, global embryo). We obtained a sequencing depth of >5.6 million tags per sample and identified many differentially expressed genes at various stages of SE. The initiation of SE affected gene expression in many KEGG pathways, but predominantly that in metabolic pathways, biosynthesis of secondary metabolites, and plant hormone signal transduction. This information on the changes in the multiple pathways related to SE induction in E. senticosus Maxim. embryogenic tissue will contribute to a more comprehensive understanding of the mechanisms involved in early SE. Additionally, the differentially expressed genes may act as molecular markers and could play very important roles in the early stage of SE. The results are a comprehensive molecular biology resource for investigating SE of E. senticosus Maxim.}, } @article {pmid26656102, year = {2015}, author = {Yang, C and Pan, H and Noland, JE and Zhang, D and Zhang, Z and Liu, Y and Zhou, X}, title = {Selection of reference genes for RT-qPCR analysis in a predatory biological control agent, Coleomegilla maculata (Coleoptera: Coccinellidae).}, journal = {Scientific reports}, volume = {5}, number = {}, pages = {18201}, pmid = {26656102}, issn = {2045-2322}, mesh = {Animals ; *Biological Control Agents ; Coleoptera/*genetics ; Computational Biology ; Gene Expression Profiling ; Gene Expression Regulation ; *Genes, Insect ; RNA Stability ; Real-Time Polymerase Chain Reaction ; }, abstract = {Reverse transcriptase-quantitative polymerase chain reaction (RT-qPCR) is a reliable technique for quantifying gene expression across various biological processes, of which requires a set of suited reference genes to normalize the expression data. Coleomegilla maculata (Coleoptera: Coccinellidae), is one of the most extensively used biological control agents in the field to manage arthropod pest species. In this study, expression profiles of 16 housekeeping genes selected from C. maculata were cloned and investigated. The performance of these candidates as endogenous controls under specific experimental conditions was evaluated by dedicated algorithms, including geNorm, Normfinder, BestKeeper, and ΔCt method. In addition, RefFinder, a comprehensive platform integrating all the above-mentioned algorithms, ranked the overall stability of these candidate genes. As a result, various sets of suitable reference genes were recommended specifically for experiments involving different tissues, developmental stages, sex, and C. maculate larvae treated with dietary double stranded RNA. This study represents the critical first step to establish a standardized RT-qPCR protocol for the functional genomics research in a ladybeetle C. maculate. Furthermore, it lays the foundation for conducting ecological risk assessment of RNAi-based gene silencing biotechnologies on non-target organisms; in this case, a key predatory biological control agent.}, } @article {pmid26650184, year = {2016}, author = {Frasier, TR}, title = {A note on the use of multiple linear regression in molecular ecology.}, journal = {Molecular ecology resources}, volume = {16}, number = {2}, pages = {382-387}, doi = {10.1111/1755-0998.12499}, pmid = {26650184}, issn = {1755-0998}, mesh = {Biostatistics/*methods ; *Data Interpretation, Statistical ; Ecology/*methods ; Linear Models ; Molecular Biology/*methods ; }, abstract = {Multiple linear regression analyses (also often referred to as generalized linear models--GLMs, or generalized linear mixed models--GLMMs) are widely used in the analysis of data in molecular ecology, often to assess the relative effects of genetic characteristics on individual fitness or traits, or how environmental characteristics influence patterns of genetic differentiation. However, the coefficients resulting from multiple regression analyses are sometimes misinterpreted, which can lead to incorrect interpretations and conclusions within individual studies, and can propagate to wider-spread errors in the general understanding of a topic. The primary issue revolves around the interpretation of coefficients for independent variables when interaction terms are also included in the analyses. In this scenario, the coefficients associated with each independent variable are often interpreted as the independent effect of each predictor variable on the predicted variable. However, this interpretation is incorrect. The correct interpretation is that these coefficients represent the effect of each predictor variable on the predicted variable when all other predictor variables are zero. This difference may sound subtle, but the ramifications cannot be overstated. Here, my goals are to raise awareness of this issue, to demonstrate and emphasize the problems that can result and to provide alternative approaches for obtaining the desired information.}, } @article {pmid26649380, year = {2015}, author = {Brost, BM and Hooten, MB and Hanks, EM and Small, RJ}, title = {Animal movement constraints improve resource selection inference in the presence of telemetry error.}, journal = {Ecology}, volume = {96}, number = {10}, pages = {2590-2597}, doi = {10.1890/15-0472.1}, pmid = {26649380}, issn = {0012-9658}, mesh = {Animals ; Environmental Monitoring ; Female ; Geographic Information Systems ; Models, Biological ; Motor Activity/*physiology ; Phoca/*physiology ; *Spacecraft ; Telemetry/methods/*veterinary ; Time Factors ; }, abstract = {Multiple factors complicate the analysis of animal telemetry location data. Recent advancements address issues such as temporal autocorrelation and telemetry measurement error, but additional challenges remain. Difficulties introduced by complicated error structures or barriers to animal movement can weaken inference. We propose an approach for obtaining resource selection inference from animal location data that accounts for complicated error structures, movement constraints, and temporally autocorrelated observations. We specify a model for telemetry data observed with error conditional on unobserved true locations that reflects prior knowledge about constraints in the animal movement process. The observed telemetry data are modeled using a flexible distribution that accommodates extreme errors and complicated error structures. Although constraints to movement are often viewed as a nuisance, we use constraints to simultaneously estimate and account for telemetry error. We apply the model to simulated data, showing that it outperforms common ad hoc approaches used when confronted with measurement error and movement constraints. We then apply our framework to an Argos satellite telemetry data set on harbor seals (Phoca vitulina) in the Gulf of Alaska, a species that is constrained to move within the marine environment and adjacent coastlines.}, } @article {pmid26646954, year = {2016}, author = {Kieltyka, J and Kucybala, K and Crandall, M}, title = {Ecologic factors relating to firearm injuries and gun violence in Chicago.}, journal = {Journal of forensic and legal medicine}, volume = {37}, number = {}, pages = {87-90}, doi = {10.1016/j.jflm.2015.11.003}, pmid = {26646954}, issn = {1878-7487}, mesh = {Chicago/epidemiology ; Databases, Factual ; Firearms ; Humans ; *Rain ; Registries ; Retrospective Studies ; Risk Assessment ; Snow ; *Temperature ; Violence/*statistics & numerical data ; Wounds, Gunshot/*epidemiology ; }, abstract = {BACKGROUND: Firearm violence is a major burden on Chicago with greater than 1500 gunshot injuries occurring annually. Identifying ecologic variables related to the incidence of firearm-related injuries and crime could prove useful for developing new strategies for reducing gun-related injuries.

METHODS: The Illinois Trauma Registry (ITSR) and the Chicago Police Department's CLEAR (Citizen Law Enforcement Analysis and Reporting) dataset were retrospectively analyzed to investigate group-level factors potentially related to the incidence of gun-related injuries and crime in Chicago from 1999 through 2012. Multivariate linear regression was used to evaluate the effects of day of the week, daily maximum temperature, precipitation, and snow on the incidence of firearm-related injuries and crime.

RESULTS: A total of 18,655 gunshot wounds occurred during the study period (ITSR, 1999-2009). There were 156,866 acts of gun violence identified in the CLEAR dataset (2002-2012). Day of the week, daily maximum temperature, and precipitation were associated with differential risks of gun injury and violence. Rain decreased firearm-related injuries by 9.80% [RR: 0.902, 95% CI: 0.854-0.950] and crime by 7.00% [RR: 0.930, 95% CI: 0.910-0.950]. Gunshot wounds were 33% [RR: 1.33, 95% CI: 1.29-1.37] more frequent on Fridays and Saturdays and gun crime was 18% [RR: 1.18, 95% CI: 1.16-1.20] more common on these days. Snow was not associated with firearm-related injuries or crime.

CONCLUSIONS: Day of the week, daily maximum temperature, and rain are associated with the incidence of firearm-related injuries and crime. Understanding the effects of these variables may allow for the development of predictive models and for risk-adjusting injury and crime data.}, } @article {pmid26645667, year = {2015}, author = {Pauli, M and Chakarov, N and Rupp, O and Kalinowski, J and Goesmann, A and Sorenson, MD and Krüger, O and Hoffman, JI}, title = {De novo assembly of the dual transcriptomes of a polymorphic raptor species and its malarial parasite.}, journal = {BMC genomics}, volume = {16}, number = {}, pages = {1038}, pmid = {26645667}, issn = {1471-2164}, mesh = {Amino Acid Sequence ; Animals ; *Computational Biology/methods ; Gene Expression Regulation ; Genetic Markers ; *Genomics/methods ; Haemosporida/*genetics ; High-Throughput Nucleotide Sequencing ; Melanins/metabolism ; Metabolic Networks and Pathways ; Molecular Sequence Annotation ; Molecular Sequence Data ; *Polymorphism, Genetic ; Raptors/*genetics/metabolism/*parasitology ; Reproducibility of Results ; Sequence Alignment ; *Transcriptome ; }, abstract = {BACKGROUND: Studies of non-model species are important for understanding the molecular processes underpinning phenotypic variation under natural ecological conditions. The common buzzard (Buteo buteo; Aves: Accipitriformes) is a widespread and common Eurasian raptor with three distinct plumage morphs that differ in several fitness-related traits, including parasite infestation. To provide a genomic resource for plumage polymorphic birds in general and to search for candidate genes relating to fitness, we generated a transcriptome from a single dead buzzard specimen plus easily accessible, minimally invasive samples from live chicks.

RESULTS: We not only de novo assembled a near-complete buzzard transcriptome, but also obtained a significant fraction of the transcriptome of its malaria-like parasite, Leucocytozoon buteonis. By identifying melanogenesis-related transcripts that are differentially expressed in light ventral and dark dorsal feathers, but which are also expressed in other regions of the body, we also identified a suite of candidate genes that could be associated with fitness differences among the morphs. These include several immune-related genes, providing a plausible link between melanisation and parasite load. qPCR analysis of a subset of these genes revealed significant differences between ventral and dorsal feathers and an additional effect of morph.

CONCLUSION: This new resource provides preliminary insights into genes that could be involved in fitness differences between the buzzard colour morphs, and should facilitate future studies of raptors and their malaria-like parasites.}, } @article {pmid26645076, year = {2016}, author = {Sizo, A and Noble, BF and Bell, S}, title = {Strategic Environmental Assessment Framework for Landscape-Based, Temporal Analysis of Wetland Change in Urban Environments.}, journal = {Environmental management}, volume = {57}, number = {3}, pages = {696-710}, pmid = {26645076}, issn = {1432-1009}, mesh = {Canada ; Cities ; *City Planning ; Ecology ; Ecosystem ; *Geographic Information Systems ; *Wetlands ; }, abstract = {This paper presents and demonstrates a spatial framework for the application of strategic environmental assessment (SEA) in the context of change analysis for urban wetland environments. The proposed framework is focused on two key stages of the SEA process: scoping and environmental baseline assessment. These stages are arguably the most information-intense phases of SEA and have a significant effect on the quality of the SEA results. The study aims to meet the needs for proactive frameworks to assess and protect wetland habitat and services more efficiently, toward the goal of advancing more intelligent urban planning and development design. The proposed framework, adopting geographic information system and remote sensing tools and applications, supports the temporal evaluation of wetland change and sustainability assessment based on landscape indicator analysis. The framework was applied to a rapidly developing urban environment in the City of Saskatoon, Saskatchewan, Canada, analyzing wetland change and land-use pressures from 1985 to 2011. The SEA spatial scale was rescaled from administrative urban planning units to an ecologically meaningful area. Landscape change assessed was based on a suite of indicators that were subsequently rolled up into a single, multi-dimensional, and easy to understand and communicate index to examine the implications of land-use change for wetland sustainability. The results show that despite the recent extremely wet period in the Canadian prairie region, land-use change contributed to increasing threats to wetland sustainability.}, } @article {pmid26644778, year = {2015}, author = {Reis, S and Seto, E and Northcross, A and Quinn, NW and Convertino, M and Jones, RL and Maier, HR and Schlink, U and Steinle, S and Vieno, M and Wimberly, MC}, title = {Integrating modelling and smart sensors for environmental and human health.}, journal = {Environmental modelling & software : with environment data news}, volume = {74}, number = {}, pages = {238-246}, pmid = {26644778}, issn = {1364-8152}, support = {R21 ES024715/ES/NIEHS NIH HHS/United States ; R33 ES024715/ES/NIEHS NIH HHS/United States ; }, abstract = {Sensors are becoming ubiquitous in everyday life, generating data at an unprecedented rate and scale. However, models that assess impacts of human activities on environmental and human health, have typically been developed in contexts where data scarcity is the norm. Models are essential tools to understand processes, identify relationships, associations and causality, formalize stakeholder mental models, and to quantify the effects of prevention and interventions. They can help to explain data, as well as inform the deployment and location of sensors by identifying hotspots and areas of interest where data collection may achieve the best results. We identify a paradigm shift in how the integration of models and sensors can contribute to harnessing 'Big Data' and, more importantly, make the vital step from 'Big Data' to 'Big Information'. In this paper, we illustrate current developments and identify key research needs using human and environmental health challenges as an example.}, } @article {pmid26644569, year = {2015}, author = {Ibsen-Jensen, R and Chatterjee, K and Nowak, MA}, title = {Computational complexity of ecological and evolutionary spatial dynamics.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {112}, number = {51}, pages = {15636-15641}, pmid = {26644569}, issn = {1091-6490}, mesh = {Algorithms ; *Biological Evolution ; Computational Biology ; *Ecology ; Ecosystem ; Probability ; }, abstract = {There are deep, yet largely unexplored, connections between computer science and biology. Both disciplines examine how information proliferates in time and space. Central results in computer science describe the complexity of algorithms that solve certain classes of problems. An algorithm is deemed efficient if it can solve a problem in polynomial time, which means the running time of the algorithm is a polynomial function of the length of the input. There are classes of harder problems for which the fastest possible algorithm requires exponential time. Another criterion is the space requirement of the algorithm. There is a crucial distinction between algorithms that can find a solution, verify a solution, or list several distinct solutions in given time and space. The complexity hierarchy that is generated in this way is the foundation of theoretical computer science. Precise complexity results can be notoriously difficult. The famous question whether polynomial time equals nondeterministic polynomial time (i.e., P = NP) is one of the hardest open problems in computer science and all of mathematics. Here, we consider simple processes of ecological and evolutionary spatial dynamics. The basic question is: What is the probability that a new invader (or a new mutant) will take over a resident population? We derive precise complexity results for a variety of scenarios. We therefore show that some fundamental questions in this area cannot be answered by simple equations (assuming that P is not equal to NP).}, } @article {pmid26643685, year = {2015}, author = {Power, DA and Watson, RA and Szathmáry, E and Mills, R and Powers, ST and Doncaster, CP and Czapp, B}, title = {What can ecosystems learn? Expanding evolutionary ecology with learning theory.}, journal = {Biology direct}, volume = {10}, number = {}, pages = {69}, pmid = {26643685}, issn = {1745-6150}, mesh = {*Biological Evolution ; Ecology ; *Ecosystem ; *Models, Biological ; }, abstract = {BACKGROUND: The structure and organisation of ecological interactions within an ecosystem is modified by the evolution and coevolution of the individual species it contains. Understanding how historical conditions have shaped this architecture is vital for understanding system responses to change at scales from the microbial upwards. However, in the absence of a group selection process, the collective behaviours and ecosystem functions exhibited by the whole community cannot be organised or adapted in a Darwinian sense. A long-standing open question thus persists: Are there alternative organising principles that enable us to understand and predict how the coevolution of the component species creates and maintains complex collective behaviours exhibited by the ecosystem as a whole?

RESULTS: Here we answer this question by incorporating principles from connectionist learning, a previously unrelated discipline already using well-developed theories on how emergent behaviours arise in simple networks. Specifically, we show conditions where natural selection on ecological interactions is functionally equivalent to a simple type of connectionist learning, 'unsupervised learning', well-known in neural-network models of cognitive systems to produce many non-trivial collective behaviours. Accordingly, we find that a community can self-organise in a well-defined and non-trivial sense without selection at the community level; its organisation can be conditioned by past experience in the same sense as connectionist learning models habituate to stimuli. This conditioning drives the community to form a distributed ecological memory of multiple past states, causing the community to: a) converge to these states from any random initial composition; b) accurately restore historical compositions from small fragments; c) recover a state composition following disturbance; and d) to correctly classify ambiguous initial compositions according to their similarity to learned compositions. We examine how the formation of alternative stable states alters the community's response to changing environmental forcing, and we identify conditions under which the ecosystem exhibits hysteresis with potential for catastrophic regime shifts.

CONCLUSIONS: This work highlights the potential of connectionist theory to expand our understanding of evo-eco dynamics and collective ecological behaviours. Within this framework we find that, despite not being a Darwinian unit, ecological communities can behave like connectionist learning systems, creating internal conditions that habituate to past environmental conditions and actively recalling those conditions.}, } @article {pmid26642473, year = {2016}, author = {Furlan, N and Waldron, M and Osborne, M and Gray, AJ}, title = {Ecological Validity and Reliability of the Rugby Sevens Simulation Protocol.}, journal = {International journal of sports physiology and performance}, volume = {11}, number = {6}, pages = {749-755}, doi = {10.1123/ijspp.2015-0487}, pmid = {26642473}, issn = {1555-0273}, mesh = {Adolescent ; Adult ; Athletic Performance/physiology ; Football/*physiology ; Geographic Information Systems ; Heart Rate/*physiology ; Humans ; Lactic Acid/blood ; Male ; Movement ; Physical Exertion/*physiology ; Reproducibility of Results ; Time and Motion Studies ; Young Adult ; }, abstract = {PURPOSE: To assess the ecological validity of the Rugby Sevens Simulation Protocol (R7SP) and to evaluate its interday reliability.

METHODS: Ten male participants (20 ± 2 y, 74 ± 11 kg) completed 2 trials of the R7SP, separated by 7 d. The R7SP comprised typical running and collision activities, based on data recorded during international rugby sevens match play. Heart rate (HR) was monitored continuously during the R7SP, and the participants' movements were recorded through a 20-Hz global positioning system unit. Blood lactate and rating of perceived exertion were collected before and immediately after the 1st and 2nd halves of the R7SP.

RESULTS: The average activity profile was 117 ± 5 m/min, of which 27 ± 2 m/min was covered at high speed, with a calculated energetic demand of 1037 ± 581 J/kg, of which ~40% was expended at a rate above 19 W/kg. Mean HR was 88% ± 4% of maximal HR. Participants spent ~45% ± 27% of time above 90% of maximal HR (t >90%HRmax). There were no significant differences between trials, except for lactate between the halves of the R7SP. The majority of the measured variables demonstrated a between-trials coefficient of variation (CV%) lower than 5%. Blood lactate measurements (14-20% CV) and t >90%HRmax (26% CV) were less reliable variables. In most cases, the calculated moderate worthwhile change was higher than the CV%.

CONCLUSIONS: The R7SP replicates the activity profile and HR responses of rugby sevens match play. It is a reliable simulation protocol that can be used in a research environment to detect systematic worthwhile changes in selected performance variables.}, } @article {pmid26641818, year = {2015}, author = {Theobald, DM and Harrison-Atlas, D and Monahan, WB and Albano, CM}, title = {Ecologically-Relevant Maps of Landforms and Physiographic Diversity for Climate Adaptation Planning.}, journal = {PloS one}, volume = {10}, number = {12}, pages = {e0143619}, pmid = {26641818}, issn = {1932-6203}, mesh = {Adaptation, Biological ; Animals ; *Biodiversity ; *Climate Change ; Ecology/methods ; Environment ; Environmental Monitoring/*methods ; Environmental Policy ; Geographic Information Systems ; Maps as Topic ; *Models, Theoretical ; }, abstract = {Key to understanding the implications of climate and land use change on biodiversity and natural resources is to incorporate the physiographic platform on which changes in ecological systems unfold. Here, we advance a detailed classification and high-resolution map of physiography, built by combining landforms and lithology (soil parent material) at multiple spatial scales. We used only relatively static abiotic variables (i.e., excluded climatic and biotic factors) to prevent confounding current ecological patterns and processes with enduring landscape features, and to make the physiographic classification more interpretable for climate adaptation planning. We generated novel spatial databases for 15 landform and 269 physiographic types across the conterminous United States of America. We examined their potential use by natural resource managers by placing them within a contemporary climate change adaptation framework, and found our physiographic databases could play key roles in four of seven general adaptation strategies. We also calculated correlations with common empirical measures of biodiversity to examine the degree to which the physiographic setting explains various aspects of current biodiversity patterns. Additionally, we evaluated the relationship between landform diversity and measures of climate change to explore how changes may unfold across a geophysical template. We found landform types are particularly sensitive to spatial scale, and so we recommend using high-resolution datasets when possible, as well as generating metrics using multiple neighborhood sizes to both minimize and characterize potential unknown biases. We illustrate how our work can inform current strategies for climate change adaptation. The analytical framework and classification of landforms and parent material are easily extendable to other geographies and may be used to promote climate change adaptation in other settings.}, } @article {pmid26639410, year = {2016}, author = {Wu, Y and Chen, K and Zeng, B and Yang, M and Geng, S}, title = {Cloud-based decision framework for waste-to-energy plant site selection - A case study from China.}, journal = {Waste management (New York, N.Y.)}, volume = {48}, number = {}, pages = {593-603}, doi = {10.1016/j.wasman.2015.11.030}, pmid = {26639410}, issn = {1879-2456}, mesh = {Algorithms ; China ; *Decision Support Techniques ; Environment ; Fuzzy Logic ; Models, Statistical ; Power Plants ; Refuse Disposal/*methods ; *Uncertainty ; Waste Management/*methods ; }, abstract = {Waste-to-energy (WtE) plant site selection is crucially important during the whole life cycle. Currently, the scholars launch some research in the WtE plant site selection. However, there are still two great problems in the present methods. Firstly, the uncertainty of information is not fully described. Secondly, the correlation among criteria lacks rationality, which is mainly manifested in two aspects: one is ignoring the correlation, and the other is measuring unreasonably. Firstly cloud model is introduced to describe the fuzziness and randomness of the information fully and precisely. Secondly, the 2-order additive fuzzy measures based on the Mobius transform and correlation coefficient matrix is introduced for fuzzy measure scientifically and reasonably. Thirdly, Cloud Choquet integral (CCI) operator is constructed to evaluate the alternatives. Finally, a case from China proves the effectiveness.}, } @article {pmid26635734, year = {2015}, author = {Fistarol, GO and Coutinho, FH and Moreira, AP and Venas, T and Cánovas, A and de Paula, SE and Coutinho, R and de Moura, RL and Valentin, JL and Tenenbaum, DR and Paranhos, R and do Valle, Rde A and Vicente, AC and Amado Filho, GM and Pereira, RC and Kruger, R and Rezende, CE and Thompson, CC and Salomon, PS and Thompson, FL}, title = {Environmental and Sanitary Conditions of Guanabara Bay, Rio de Janeiro.}, journal = {Frontiers in microbiology}, volume = {6}, number = {}, pages = {1232}, pmid = {26635734}, issn = {1664-302X}, abstract = {Guanabara Bay is the second largest bay in the coast of Brazil, with an area of 384 km(2). In its surroundings live circa 16 million inhabitants, out of which 6 million live in Rio de Janeiro city, one of the largest cities of the country, and the host of the 2016 Olympic Games. Anthropogenic interference in Guanabara Bay area started early in the XVI century, but environmental impacts escalated from 1930, when this region underwent an industrialization process. Herein we present an overview of the current environmental and sanitary conditions of Guanabara Bay, a consequence of all these decades of impacts. We will focus on microbial communities, how they may affect higher trophic levels of the aquatic community and also human health. The anthropogenic impacts in the bay are flagged by heavy eutrophication and by the emergence of pathogenic microorganisms that are either carried by domestic and/or hospital waste (e.g., virus, KPC-producing bacteria, and fecal coliforms), or that proliferate in such conditions (e.g., vibrios). Antibiotic resistance genes are commonly found in metagenomes of Guanabara Bay planktonic microorganisms. Furthermore, eutrophication results in recurrent algal blooms, with signs of a shift toward flagellated, mixotrophic groups, including several potentially harmful species. A recent large-scale fish kill episode, and a long trend decrease in fish stocks also reflects the bay's degraded water quality. Although pollution of Guanabara Bay is not a recent problem, the hosting of the 2016 Olympic Games propelled the government to launch a series of plans to restore the bay's water quality. If all plans are fully implemented, the restoration of Guanabara Bay and its shores may be one of the best legacies of the Olympic Games in Rio de Janeiro.}, } @article {pmid26634550, year = {2015}, author = {Wang, JX and Sun, P and Yuan, CQ and Dai, L and Zhang, Y and Wu, B and Long, C and Sun, YH and Li, Y}, title = {Transcriptional profiles of emasculated flowers of black locust (Robinia pseudoacacia) determined using the cDNA-AFLP technique.}, journal = {Genetics and molecular research : GMR}, volume = {14}, number = {4}, pages = {15822-15838}, doi = {10.4238/2015.December.1.34}, pmid = {26634550}, issn = {1676-5680}, mesh = {*Amplified Fragment Length Polymorphism Analysis ; Computational Biology/methods ; *DNA, Complementary ; Flowers/*genetics ; Gene Expression Profiling ; Gene Expression Regulation, Plant ; High-Throughput Nucleotide Sequencing ; Molecular Sequence Annotation ; Photosynthesis/genetics ; Quantitative Trait, Heritable ; Robinia/*genetics/growth & development/metabolism ; Signal Transduction ; Stress, Physiological/genetics ; Transcription Factors/genetics/metabolism ; *Transcriptome ; }, abstract = {Black locust (Robinia pseudoacacia) is a tree in the subfamily Faboideae, native to North America, that has been naturalized and widely planted in temperate Europe and Asia. Black locust has important ecological and economic value, but its quality needs improvement. Hybridization programs are important for black locust breeding, but the low rate of fruit set after controlled pollination limits both its breeding and that of other monoclinous plant species that share this problem. In this study, we investigated gene expression in emasculated black locust flowers using the cDNA-amplified fragment length polymorphism technique to determine why the rate of fruit set is low after controlled pollination. Flowers that were emasculated after being frozen in liquid nitrogen were used as controls. Changes in the flower transcriptome were more dramatic at 5 h after emasculation than at 48 h. Injury caused by emasculation decreased the expression levels of genes associated with metabolism, growth regulation, signal transduction, and photosynthesis, and it increased the expression of genes related to stress-response metabolism, signal transduction, and promotion of senescence. The changes in the expression levels of these genes had negative effects on sugar metabolism, protein metabolism, lipid metabolism, energy metabolism, matter transport, signal transduction, osmotic regulation, pH regulation, and photosynthesis. Thus, emasculation accelerated flower senescence, resulting in low fruit set.}, } @article {pmid26633430, year = {2015}, author = {Bos, PM and Gottardo, S and Scott-Fordsmand, JJ and van Tongeren, M and Semenzin, E and Fernandes, TF and Hristozov, D and Hund-Rinke, K and Hunt, N and Irfan, MA and Landsiedel, R and Peijnenburg, WJ and Sánchez Jiménez, A and van Kesteren, PC and Oomen, AG}, title = {The MARINA Risk Assessment Strategy: A Flexible Strategy for Efficient Information Collection and Risk Assessment of Nanomaterials.}, journal = {International journal of environmental research and public health}, volume = {12}, number = {12}, pages = {15007-15021}, pmid = {26633430}, issn = {1660-4601}, mesh = {Data Collection ; Environmental Exposure/*adverse effects ; Humans ; Models, Theoretical ; Nanoparticles/*adverse effects ; Nanostructures/*adverse effects ; Risk Assessment/*methods ; Risk Management/*methods ; }, abstract = {An engineered nanomaterial (ENM) may actually consist of a population of primary particles, aggregates and agglomerates of various sizes. Furthermore, their physico-chemical characteristics may change during the various life-cycle stages. It will probably not be feasible to test all varieties of all ENMs for possible health and environmental risks. There is therefore a need to further develop the approaches for risk assessment of ENMs. Within the EU FP7 project Managing Risks of Nanoparticles (MARINA) a two-phase risk assessment strategy has been developed. In Phase 1 (Problem framing) a base set of information is considered, relevant exposure scenarios (RESs) are identified and the scope for Phase 2 (Risk assessment) is established. The relevance of an RES is indicated by information on exposure, fate/kinetics and/or hazard; these three domains are included as separate pillars that contain specific tools. Phase 2 consists of an iterative process of risk characterization, identification of data needs and integrated collection and evaluation of data on the three domains, until sufficient information is obtained to conclude on possible risks in a RES. Only data are generated that are considered to be needed for the purpose of risk assessment. A fourth pillar, risk characterization, is defined and it contains risk assessment tools. This strategy describes a flexible and efficient approach for data collection and risk assessment which is essential to ensure safety of ENMs. Further developments are needed to provide guidance and make the MARINA Risk Assessment Strategy operational. Case studies will be needed to refine the strategy.}, } @article {pmid26633360, year = {2015}, author = {Cuadrat, RR and Cury, JC and Dávila, AM}, title = {Metagenomic Analysis of Upwelling-Affected Brazilian Coastal Seawater Reveals Sequence Domains of Type I PKS and Modular NRPS.}, journal = {International journal of molecular sciences}, volume = {16}, number = {12}, pages = {28285-28295}, pmid = {26633360}, issn = {1422-0067}, mesh = {Computational Biology ; Datasets as Topic ; *Metagenomics ; Peptide Synthases/*genetics ; Phylogeny ; Polyketide Synthases/*genetics ; Seawater/*microbiology ; *Water Microbiology ; }, abstract = {Marine environments harbor a wide range of microorganisms from the three domains of life. These microorganisms have great potential to enable discovery of new enzymes and bioactive compounds for industrial use. However, only ~1% of microorganisms from the environment can currently be identified through cultured isolates, limiting the discovery of new compounds. To overcome this limitation, a metagenomics approach has been widely adopted for biodiversity studies on samples from marine environments. In this study, we screened metagenomes in order to estimate the potential for new natural compound synthesis mediated by diversity in the Polyketide Synthase (PKS) and Nonribosomal Peptide Synthetase (NRPS) genes. The samples were collected from the Praia dos Anjos (Angel's Beach) surface water-Arraial do Cabo (Rio de Janeiro state, Brazil), an environment affected by upwelling. In order to evaluate the potential for screening natural products in Arraial do Cabo samples, we used KS (keto-synthase) and C (condensation) domains (from PKS and NRPS, respectively) to build Hidden Markov Models (HMM) models. From both samples, a total of 84 KS and 46 C novel domain sequences were obtained, showing the potential of this environment for the discovery of new genes of biotechnological interest. These domains were classified by phylogenetic analysis and this was the first study conducted to screen PKS and NRPS genes in an upwelling affected sample.}, } @article {pmid26631984, year = {2015}, author = {Klein, CJ and Brown, CJ and Halpern, BS and Segan, DB and McGowan, J and Beger, M and Watson, JE}, title = {Shortfalls in the global protected area network at representing marine biodiversity.}, journal = {Scientific reports}, volume = {5}, number = {}, pages = {17539}, pmid = {26631984}, issn = {2045-2322}, mesh = {Animals ; *Biodiversity ; Conservation of Natural Resources/*methods/*statistics & numerical data ; Databases, Factual ; Ecosystem ; Fishes ; Invertebrates ; Mammals ; Oceans and Seas ; }, abstract = {The first international goal for establishing marine protected areas (MPAs) to conserve the ocean's biodiversity was set in 2002. Since 2006, the Convention on Biological Diversity (CBD) has driven MPA establishment, with 193 parties committed to protecting >10% of marine environments globally by 2020, especially 'areas of particular importance for biodiversity' (Aichi target 11). This has resulted in nearly 10 million km(2) of new MPAs, a growth of ~360% in a decade. Unlike on land, it is not known how well protected areas capture marine biodiversity, leaving a significant gap in our understanding of existing MPAs and future protection requirements. We assess the overlap of global MPAs with the ranges of 17,348 marine species (fishes, mammals, invertebrates), and find that 97.4% of species have <10% of their ranges represented in stricter conservation classes. Almost all (99.8%) of the very poorly represented species (<2% coverage) are found within exclusive economic zones, suggesting an important role for particular nations to better protect biodiversity. Our results offer strategic guidance on where MPAs should be placed to support the CBD's overall goal to avert biodiversity loss. Achieving this goal is imperative for nature and humanity, as people depend on biodiversity for important and valuable services.}, } @article {pmid26631584, year = {2016}, author = {Grande, F and Parisi, OI and Mordocco, RA and Rocca, C and Puoci, F and Scrivano, L and Quintieri, AM and Cantafio, P and Ferla, S and Brancale, A and Saturnino, C and Cerra, MC and Sinicropi, MS and Angelone, T}, title = {Quercetin derivatives as novel antihypertensive agents: Synthesis and physiological characterization.}, journal = {European journal of pharmaceutical sciences : official journal of the European Federation for Pharmaceutical Sciences}, volume = {82}, number = {}, pages = {161-170}, doi = {10.1016/j.ejps.2015.11.021}, pmid = {26631584}, issn = {1879-0720}, mesh = {Animals ; Antihypertensive Agents/chemistry/*pharmacology ; Biological Availability ; Dose-Response Relationship, Drug ; Gastric Juice/metabolism ; Heart/drug effects/physiology ; Intestinal Secretions/metabolism ; Models, Molecular ; Pancreatin/metabolism ; Pepsin A/metabolism ; Quercetin/analogs & derivatives/chemistry/*pharmacology ; Rats, Inbred SHR ; Rats, Inbred WKY ; Receptors, Adrenergic, beta-1/metabolism ; Receptors, Adrenergic, beta-2/metabolism ; }, abstract = {The antihypertensive flavonol quercetin (Q1) is endowed with a cardioprotective effect against myocardial ischemic damage. Q1 inhibits angiotensin converting enzyme activity, improves vascular relaxation, and decreases oxidative stress and gene expression. However, the clinical application of this flavonol is limited by its poor bioavailability and low stability in aqueous medium. In the aim to overcome these drawbacks and preserve the cardioprotective effects of quercetin, the present study reports on the preparation of five different Q1 analogs, in which all OH groups were replaced by hydrophobic functional moieties. Q1 derivatives have been synthesized by optimizing previously reported procedures and analyzed by spectroscopic analysis. The cardiovascular properties of the obtained compounds were also investigated in order to evaluate whether chemical modification affects their biological efficacy. The interaction with β-adrenergic receptors was evaluated by molecular docking and the cardiovascular efficacy was investigated on the ex vivo Langendorff perfused rat heart. Furthermore, the bioavailability and the antihypertensive properties of the most active derivative were evaluated by in vitro studies and in vivo administration (1month) on spontaneously hypertensive rats (SHRs), respectively. Among all studied Q1 derivatives, only the ethyl derivative reduced left ventricular pressure (at 10(-8)M÷10(-6)M doses) and improved relaxation and coronary dilation. NOSs inhibition by L-NAME abolished inotropism, lusitropism and coronary effects. Chronic administration of high doses of this compound on SHR reduced systolic and diastolic pressure. Differently, the acetyl derivative induced negative inotropism and lusitropism (at 10(-10)M and 10(-8)÷10(-6)M doses), without affecting coronary pressure. Accordingly, docking studies suggested that these compounds bind both β1/β2-adrenergic receptors. Taking into consideration all the obtained results, the replacement of OH with ethyl groups seems to improve Q1 bioavailability and stability; therefore, the ethyl derivative could represent a good candidate for clinical use in hypertension.}, } @article {pmid26627985, year = {2016}, author = {Mulder, NJ and Adebiyi, E and Alami, R and Benkahla, A and Brandful, J and Doumbia, S and Everett, D and Fadlelmola, FM and Gaboun, F and Gaseitsiwe, S and Ghazal, H and Hazelhurst, S and Hide, W and Ibrahimi, A and Jaufeerally Fakim, Y and Jongeneel, CV and Joubert, F and Kassim, S and Kayondo, J and Kumuthini, J and Lyantagaye, S and Makani, J and Mansour Alzohairy, A and Masiga, D and Moussa, A and Nash, O and Ouwe Missi Oukem-Boyer, O and Owusu-Dabo, E and Panji, S and Patterton, H and Radouani, F and Sadki, K and Seghrouchni, F and Tastan Bishop, Ö and Tiffin, N and Ulenga, N and , }, title = {H3ABioNet, a sustainable pan-African bioinformatics network for human heredity and health in Africa.}, journal = {Genome research}, volume = {26}, number = {2}, pages = {271-277}, pmid = {26627985}, issn = {1549-5469}, support = {095009/WT_/Wellcome Trust/United Kingdom ; 093727/WT_/Wellcome Trust/United Kingdom ; U24 HL135600/HL/NHLBI NIH HHS/United States ; /WT_/Wellcome Trust/United Kingdom ; U01 HG007459/HG/NHGRI NIH HHS/United States ; U41HG006941/HG/NHGRI NIH HHS/United States ; U41 HG006941/HG/NHGRI NIH HHS/United States ; }, mesh = {Africa ; Black People/*genetics ; Computational Biology ; Computer Systems ; Genetic Variation ; Genetics, Medical ; Genomics ; *Health Promotion ; Humans ; }, abstract = {The application of genomics technologies to medicine and biomedical research is increasing in popularity, made possible by new high-throughput genotyping and sequencing technologies and improved data analysis capabilities. Some of the greatest genetic diversity among humans, animals, plants, and microbiota occurs in Africa, yet genomic research outputs from the continent are limited. The Human Heredity and Health in Africa (H3Africa) initiative was established to drive the development of genomic research for human health in Africa, and through recognition of the critical role of bioinformatics in this process, spurred the establishment of H3ABioNet, a pan-African bioinformatics network for H3Africa. The limitations in bioinformatics capacity on the continent have been a major contributory factor to the lack of notable outputs in high-throughput biology research. Although pockets of high-quality bioinformatics teams have existed previously, the majority of research institutions lack experienced faculty who can train and supervise bioinformatics students. H3ABioNet aims to address this dire need, specifically in the area of human genetics and genomics, but knock-on effects are ensuring this extends to other areas of bioinformatics. Here, we describe the emergence of genomics research and the development of bioinformatics in Africa through H3ABioNet.}, } @article {pmid26625892, year = {2016}, author = {Pelikan, C and Herbold, CW and Hausmann, B and Müller, AL and Pester, M and Loy, A}, title = {Diversity analysis of sulfite- and sulfate-reducing microorganisms by multiplex dsrA and dsrB amplicon sequencing using new primers and mock community-optimized bioinformatics.}, journal = {Environmental microbiology}, volume = {18}, number = {9}, pages = {2994-3009}, doi = {10.1111/1462-2920.13139}, pmid = {26625892}, issn = {1462-2920}, mesh = {Bacteria/classification/*genetics/isolation & purification ; Bacterial Proteins/*genetics/metabolism ; Computational Biology ; DNA Primers/*genetics ; DNA, Bacterial/genetics ; Hydrogensulfite Reductase/genetics/metabolism ; Phylogeny ; Polymerase Chain Reaction ; Sulfates/*metabolism ; Sulfites/*metabolism ; }, abstract = {Genes encoding dissimilatory sulfite reductase (DsrAB) are commonly used as diagnostic markers in ecological studies of sulfite- and sulfate-reducing microorganisms. Here, we developed new high-coverage primer sets for generation of reductive bacterial-type dsrA and dsrB polymerase chain reaction (PCR) products for highly parallel amplicon sequencing and a bioinformatics workflow for processing and taxonomic classification of short dsrA and dsrB reads. We employed two diverse mock communities that consisted of 45 or 90 known dsrAB sequences derived from environmental clones to precisely evaluate the performance of individual steps of our amplicon sequencing approach on the Illumina MiSeq platform. Although PCR cycle number, gene-specific primer mismatches and stringent filtering for high-quality sequences had notable effects on the observed dsrA and dsrB community structures, recovery of most mock community sequences was generally proportional to their relative input abundances. Successful dsrA and dsrB diversity analysis in selected environmental samples further proved that the multiplex amplicon sequencing approach is adequate for monitoring spatial distribution and temporal abundance dynamics of dsrAB-containing microorganisms. Although tested for reductive bacterial-type dsrAB, this method is readily applicable for oxidative-type dsrAB of sulfur-oxidizing bacteria and also provides guidance for processing short amplicon reads of other functional genes.}, } @article {pmid26621578, year = {2016}, author = {Rowlands, G and Purkis, S and Bruckner, A}, title = {Tight coupling between coral reef morphology and mapped resilience in the Red Sea.}, journal = {Marine pollution bulletin}, volume = {105}, number = {2}, pages = {575-585}, doi = {10.1016/j.marpolbul.2015.11.027}, pmid = {26621578}, issn = {1879-3363}, mesh = {*Adaptation, Physiological ; Adolescent ; Animals ; Anthozoa/classification/*growth & development/physiology ; Climate Change ; Conservation of Natural Resources/*methods ; *Coral Reefs ; Ecosystem ; Geographic Information Systems ; Humans ; Indian Ocean ; Remote Sensing Technology ; Saudi Arabia ; }, abstract = {Lack of knowledge on the conservation value of different reef types can stymie decision making, and result in less optimal management solutions. Addressing the information gap of coral reef resilience, we produce a map-based Remote Sensed Resilience Index (RSRI) from data describing the spatial distribution of stressors, and properties of reef habitats on the Farasan Banks, Saudi Arabia. We contrast the distribution of this index among fourteen reef types, categorized on a scale of maturity that includes juvenile (poorly aggraded), mature (partially aggraded), and senile (fully aggraded) reefs. Sites with high reef resilience can be found in most detached reef types; however they are most common in mature reefs. We aim to stimulate debate on the coupling that exists between geomorphology and conservation biology, and consider how such information can be used to inform management decisions.}, } @article {pmid26620952, year = {2015}, author = {Gülci, S and Akay, AE}, title = {Assessment of ecological passages along road networks within the Mediterranean forest using GIS-based multi criteria evaluation approach.}, journal = {Environmental monitoring and assessment}, volume = {187}, number = {12}, pages = {779}, pmid = {26620952}, issn = {1573-2959}, mesh = {Accidents, Traffic/prevention & control ; Animals ; Conservation of Natural Resources/*methods ; *Construction Industry ; Deer ; Ecosystem ; Environmental Monitoring/*methods ; *Forests ; *Geographic Information Systems ; Humans ; Mediterranean Region ; Models, Theoretical ; Turkey ; }, abstract = {Major roads cause barrier effect and fragmentation on wildlife habitats that are suitable places for feeding, mating, socializing, and hiding. Due to wildlife collisions (Wc), human-wildlife conflicts result in lost lives and loss of biodiversity. Geographical information system (GIS)-based multi criteria evaluation (MCE) methods have been successfully used in short-term planning of road networks considering wild animals. Recently, wildlife passages have been effectively utilized as road engineering structures provide quick and certain solutions for traffic safety and wildlife conservation problems. GIS-based MCE methods provide decision makers with optimum location for ecological passages based on habitat suitability models (HSMs) that classify the areas based on ecological requirements of target species. In this study, ecological passages along Motorway 52 within forested areas in Mediterranean city of Osmaniye in Turkey were evaluated. Firstly, HSM coupled with nine eco-geographic decision variables were developed based on ecological requirements of roe deer (Capreolus capreolus) that were chosen as target species. Then specified decision variables were evaluated using GIS-based weighted linear combination (WLC) method to estimate movement corridors and mitigation points along the motorway. In the solution process, two linkage nodes were evaluated for eco-passages which were determined based on the least-cost movement corridor intersecting with the motorway. One of the passages was identified as a natural wildlife overpass while the other was suggested as underpass construction. The results indicated that computer-based models provide accurate and quick solutions for positioning ecological passages to reduce environmental effects of road networks on wild animals.}, } @article {pmid26618926, year = {2016}, author = {Akman, M and Carlson, JE and Holsinger, KE and Latimer, AM}, title = {Transcriptome sequencing reveals population differentiation in gene expression linked to functional traits and environmental gradients in the South African shrub Protea repens.}, journal = {The New phytologist}, volume = {210}, number = {1}, pages = {295-309}, doi = {10.1111/nph.13761}, pmid = {26618926}, issn = {1469-8137}, support = {S10RR027303/RR/NCRR NIH HHS/United States ; S10RR029668/RR/NCRR NIH HHS/United States ; }, mesh = {Carbohydrate Metabolism/genetics ; Cell Wall/metabolism ; Climate ; *Environment ; Gene Expression Profiling ; *Gene Expression Regulation, Plant ; Gene Ontology ; Gene Regulatory Networks ; Genes, Plant ; Glycolysis/genetics ; Photosynthesis/genetics ; Plant Proteins/genetics/metabolism ; Plant Stomata/anatomy & histology ; Proteaceae/*genetics ; *Quantitative Trait, Heritable ; Rain ; Seasons ; *Sequence Analysis, RNA ; Temperature ; Transcriptome/*genetics ; }, abstract = {Understanding the environmental and genetic mechanisms underlying locally adaptive trait variation across the ranges of species is a major focus of evolutionary biology. Combining transcriptome sequencing with common garden experiments on populations spanning geographical and environmental gradients holds promise for identifying such mechanisms. The South African shrub Protea repens displays diverse phenotypes in the wild along drought and temperature gradients. We grew plants from seeds collected at 19 populations spanning this species' range, and sequenced the transcriptomes of these plants to reveal gene pathways associated with adaptive trait variation. We related expression in co-expressed gene networks to trait phenotypes measured in the common garden and to source population climate. We found that expression in gene networks correlated with source-population environment and with plant traits. In particular, the activity of gene networks enriched for growth related pathways correlated strongly with source site minimum winter temperature and with leaf size, stem diameter and height in the garden. Other gene networks with enrichments for photosynthesis related genes showed associations with precipitation. Our results strongly suggest that this species displays population-level differences in gene expression that have been shaped by source population site climate, and that are reflected in trait variation along environmental gradients.}, } @article {pmid26615560, year = {2015}, author = {Reddy, CS and Jha, CS and Diwakar, PG and Dadhwal, VK}, title = {Nationwide classification of forest types of India using remote sensing and GIS.}, journal = {Environmental monitoring and assessment}, volume = {187}, number = {12}, pages = {777}, pmid = {26615560}, issn = {1573-2959}, mesh = {Carbon ; Climate ; Conservation of Natural Resources/*methods ; Environmental Monitoring/*methods ; *Forests ; *Geographic Information Systems ; India ; *Remote Sensing Technology ; Seasons ; Trees ; }, abstract = {India, a mega-diverse country, possesses a wide range of climate and vegetation types along with a varied topography. The present study has classified forest types of India based on multi-season IRS Resourcesat-2 Advanced Wide Field Sensor (AWiFS) data. The study has characterized 29 land use/land cover classes including 14 forest types and seven scrub types. Hybrid classification approach has been used for the classification of forest types. The classification of vegetation has been carried out based on the ecological rule bases followed by Champion and Seth's (1968) scheme of forest types in India. The present classification scheme has been compared with the available global and national level land cover products. The natural vegetation cover was estimated to be 29.36% of total geographical area of India. The predominant forest types of India are tropical dry deciduous and tropical moist deciduous. Of the total forest cover, tropical dry deciduous forests occupy an area of 2,17,713 km(2) (34.80%) followed by 2,07,649 km(2) (33.19%) under tropical moist deciduous forests, 48,295 km(2) (7.72%) under tropical semi-evergreen forests and 47,192 km(2) (7.54%) under tropical wet evergreen forests. The study has brought out a comprehensive vegetation cover and forest type maps based on inputs critical in defining the various categories of vegetation and forest types. This spatially explicit database will be highly useful for the studies related to changes in various forest types, carbon stocks, climate-vegetation modeling and biogeochemical cycles.}, } @article {pmid26615214, year = {2016}, author = {Guillot, G and Jónsson, H and Hinge, A and Manchih, N and Orlando, L}, title = {Accurate continuous geographic assignment from low- to high-density SNP data.}, journal = {Bioinformatics (Oxford, England)}, volume = {32}, number = {7}, pages = {1106-1108}, doi = {10.1093/bioinformatics/btv703}, pmid = {26615214}, issn = {1367-4811}, mesh = {*Data Interpretation, Statistical ; *Genotype ; *High-Throughput Nucleotide Sequencing ; Humans ; Models, Theoretical ; Monte Carlo Method ; *Polymorphism, Single Nucleotide ; }, abstract = {MOTIVATION: Large-scale genotype datasets can help track the dispersal patterns of epidemiological outbreaks and predict the geographic origins of individuals. Such genetically-based geographic assignments also show a range of possible applications in forensics for profiling both victims and criminals, and in wildlife management, where poaching hotspot areas can be located. They, however, require fast and accurate statistical methods to handle the growing amount of genetic information made available from genotype arrays and next-generation sequencing technologies.

RESULTS: We introduce a novel statistical method for geopositioning individuals of unknown origin from genotypes. Our method is based on a geostatistical model trained with a dataset of georeferenced genotypes. Statistical inference under this model can be implemented within the theoretical framework of Integrated Nested Laplace Approximation, which represents one of the major recent breakthroughs in statistics, as it does not require Monte Carlo simulations. We compare the performance of our method and an alternative method for geospatial inference, SPA in a simulation framework. We highlight the accuracy and limits of continuous spatial assignment methods at various scales by analyzing genotype datasets from a diversity of species, including Florida Scrub-jay birds Aphelocoma coerulescens, Arabidopsis thaliana and humans, representing 41-197,146 SNPs. Our method appears to be best suited for the analysis of medium-sized datasets (a few tens of thousands of loci), such as reduced-representation sequencing data that become increasingly available in ecology.

http://www2.imm.dtu.dk/∼gigu/Spasiba/

CONTACT: gilles.b.guillot@gmail.com

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, } @article {pmid26614306, year = {2015}, author = {Mousazadeh, R and Ghaffarzadeh, H and Nouri, J and Gharagozlou, A and Farahpour, M}, title = {Land use change detection and impact assessment in Anzali international coastal wetland using multi-temporal satellite images.}, journal = {Environmental monitoring and assessment}, volume = {187}, number = {12}, pages = {776}, pmid = {26614306}, issn = {1573-2959}, mesh = {Agriculture ; Conservation of Natural Resources/*methods ; Ecosystem ; Environmental Monitoring/*methods ; Geographic Information Systems ; Iran ; *Satellite Imagery ; *Wetlands ; }, abstract = {Anzali is one of the 18 Iranian wetlands of international importance listed in Ramsar Convention. This unique ecosystem in the world with high ecological diversity is highly threatened by various factors such as pollutants, sedimentation, unauthorized development of urban infrastructure, over-harvesting of wetland resources, land use changes, and invasive species. Among which, one of the most challenging destructive factors, land use change, was scrutinized in this study. For this, remotely sensed data and Geographical Information System (GIS) were used to detect land changes and corresponding impacts on the study area over a 38-year period from 1975 to 2013.. Changes in the study area were traced in five dominant land-use classes at four time intervals of 1975, 1989, 2007, and 2013. Accordingly, changes in different categories were quantified using satellite images. The methodology adopted in this study includes an integrated approach of supervised classification, zonal and object-oriented image analyses. According to the Kappa coefficient of 0.84 for the land use map of 2013, the overall accuracy of the method was estimated at 89%, which indicated that this method can be useful for monitoring and behavior analysis of other Iranian wetlands. The obtained results revealed extensive land use changes over the study period. As the results suggest, between the years 1975 to 2013, approximately 6500 ha (∼69%) rangeland area degraded. Further, urban and agricultural areas have been extended by 2982 ha (∼74%) and 2228 ha (∼6%), respectively. This could leave a negative impact on water quality of the wetland.}, } @article {pmid26613535, year = {2015}, author = {Tomata, Y and Suzuki, Y and Kawado, M and Yamada, H and Murakami, Y and Mieno, MN and Shibata, Y and Ojima, T and Hashimoto, S and Tsuji, I}, title = {Long-term impact of the 2011 Great East Japan Earthquake and tsunami on functional disability among older people: A 3-year longitudinal comparison of disability prevalence among Japanese municipalities.}, journal = {Social science & medicine (1982)}, volume = {147}, number = {}, pages = {296-299}, doi = {10.1016/j.socscimed.2015.11.016}, pmid = {26613535}, issn = {1873-5347}, mesh = {Aged ; Aged, 80 and over ; Cities/epidemiology ; Disabled Persons/*rehabilitation/statistics & numerical data ; Disasters/statistics & numerical data ; Earthquakes/*statistics & numerical data ; Health Services Accessibility/*standards/statistics & numerical data ; Humans ; Japan/epidemiology ; Longitudinal Studies ; Male ; Prevalence ; }, abstract = {It has been unclear whether the prevalence of disability is higher in an area affected by natural disaster than in other areas even if more than one year has passed since the disaster. The aim of this ecological study was to examine whether the rate of increase in disability prevalence among the older population was higher in disaster-stricken areas during the 3 years after the Great East Japan Earthquake (GEJE) and tsunami. This analysis used public Long-term Care Insurance (LTCI) data covering 1570 municipalities. "Disaster areas" were considered to be the three prefectures most affected by the earthquake and tsunami: Iwate, Miyagi, and Fukushima. The outcome measure was the number of aged people (≥65 years) with LTCI disability certification. Rates of change in disability prevalence from January 2011 to January 2014 were used as the primary outcome variable, and compared by analysis of covariance between "coastal disaster areas", "inland disaster areas" and "non-disaster areas". The mean rate of increase in disability prevalence in coastal (14.7%) and inland (10.0%) disaster areas was higher than in non-disaster areas (6.2%) (P < 0.001). During the 3 years after the earthquake, the increase of disability prevalence from before the GEJE continued to be higher in the disaster-stricken areas.}, } @article {pmid26611970, year = {2015}, author = {Kahime, K and Boussaa, S and El Mzabi, A and Boumezzough, A}, title = {Spatial relations among environmental factors and phlebotomine sand fly populations (Diptera: Psychodidae) in central and southern Morocco.}, journal = {Journal of vector ecology : journal of the Society for Vector Ecology}, volume = {40}, number = {2}, pages = {342-354}, doi = {10.1111/jvec.12173}, pmid = {26611970}, issn = {1948-7134}, mesh = {Altitude ; Animals ; Climate ; Ecosystem ; Environmental Monitoring ; Geographic Information Systems ; Insect Vectors ; Leishmaniasis, Cutaneous/transmission ; Leishmaniasis, Visceral/transmission ; Male ; Morocco ; Phlebotomus/physiology ; Principal Component Analysis ; Psychodidae/*physiology ; Soil ; }, abstract = {Phlebotomine sand flies (Diptera: Psychodidae, Phlebotominae) are of considerable public health importance because of their ability to transmit several human parasites, mainly as vectors of Leishmania spp. Over the past decade, the epidemiological situation of cutaneous leishmaniasis (CL) has significantly increased with its geographic expansion to previously free areas and the emergence of overlapping foci of cutaneous leishmaniasis and visceral leishmaniasis (VL) in several provinces of Morocco. A total of 15,313 specimens was collected during this entomological survey. The genera Phlebotomus (57.38%) and Sergentomyia (42.62%) were identified. Sergentomyia minuta (22.01%) was the most prevalent species, followed by S. fallax (18.21%), Phlebotomus perniciosus (14.35%), P. papatasi (14.06%), P. sergenti (12.85%), P. longicuspis (10.74%), P. ariasi (2.68%), S. dreyfussi (1.53%), P. alexandri (1.31%), P. bergeroti (1.14%), S. christophersi (0.62%), S. africana (0.25%), P. chabaudi (0.14%), P. chadlii (0.05%), and P. kazeruni (0.04%). We aimed to determine current distribution of leishmaniases vectors, their ecological characteristics, and the significance of the predominant species at any bioclimate stage, altitude range, and soil texture in terms of the risk of leishmaniasis transmission.}, } @article {pmid26609082, year = {2015}, author = {Spiegel, O and Leu, ST and Sih, A and Godfrey, SS and Bull, CM}, title = {When the going gets tough: behavioural type-dependent space use in the sleepy lizard changes as the season dries.}, journal = {Proceedings. Biological sciences}, volume = {282}, number = {1819}, pages = {}, pmid = {26609082}, issn = {1471-2954}, mesh = {Animals ; Bayes Theorem ; *Ecosystem ; Geographic Information Systems ; *Homing Behavior ; Lizards/*physiology ; Models, Biological ; *Seasons ; South Australia ; Spatial Analysis ; }, abstract = {Understanding space use remains a major challenge for animal ecology, with implications for species interactions, disease spread, and conservation. Behavioural type (BT) may shape the space use of individuals within animal populations. Bolder or more aggressive individuals tend to be more exploratory and disperse further. Yet, to date we have limited knowledge on how space use other than dispersal depends on BT. To address this question we studied BT-dependent space-use patterns of sleepy lizards (Tiliqua rugosa) in southern Australia. We combined high-resolution global positioning system (GPS) tracking of 72 free-ranging lizards with repeated behavioural assays, and with a survey of the spatial distributions of their food and refuge resources. Bayesian generalized linear mixed models (GLMM) showed that lizards responded to the spatial distribution of resources at the neighbourhood scale and to the intensity of space use by other conspecifics (showing apparent conspecific avoidance). BT (especially aggressiveness) affected space use by lizards and their response to ecological and social factors, in a seasonally dependent manner. Many of these effects and interactions were stronger later in the season when food became scarce and environmental conditions got tougher. For example, refuge and food availability became more important later in the season and unaggressive lizards were more responsive to these predictors. These findings highlight a commonly overlooked source of heterogeneity in animal space use and improve our mechanistic understanding of processes leading to behaviourally driven disease dynamics and social structure.}, } @article {pmid26609078, year = {2016}, author = {Stoltzfus, A and Norris, RW}, title = {On the Causes of Evolutionary Transition:Transversion Bias.}, journal = {Molecular biology and evolution}, volume = {33}, number = {3}, pages = {595-602}, pmid = {26609078}, issn = {1537-1719}, mesh = {Amino Acid Substitution ; Databases, Genetic ; *Evolution, Molecular ; Genetic Fitness ; *Models, Genetic ; Mutation ; Nucleotides ; Selection, Genetic ; }, abstract = {A pattern in which nucleotide transitions are favored several fold over transversions is common in molecular evolution. When this pattern occurs among amino acid replacements, explanations often invoke an effect of selection, on the grounds that transitions are more conservative in their effects on proteins. However, the underlying hypothesis of conservative transitions has never been tested directly. Here we assess support for this hypothesis using direct evidence: the fitness effects of mutations in actual proteins measured via individual or paired growth experiments. We assembled data from 8 published studies, ranging in size from 24 to 757 single-nucleotide mutations that change an amino acid. Every study has the statistical power to reveal significant effects of amino acid exchangeability, and most studies have the power to discern a binary conservative-vs-radical distinction. However, only one study suggests that transitions are significantly more conservative than transversions. In the combined set of 1,239 replacements (544 transitions, 695 transversions), the chance that a transition is more conservative than a transversion is 53 % (95 % confidence interval 50 to 56) compared with the null expectation of 50 %. We show that this effect is not large compared with that of most biochemical factors, and is not large enough to explain the several-fold bias observed in evolution. In short, the available data have the power to verify the "conservative transitions" hypothesis if true, but suggest instead that selection on proteins plays at best a minor role in the observed bias.}, } @article {pmid26607231, year = {2015}, author = {Trumbić, Ž and Bekaert, M and Taggart, JB and Bron, JE and Gharbi, K and Mladineo, I}, title = {Development and validation of a mixed-tissue oligonucleotide DNA microarray for Atlantic bluefin tuna, Thunnus thynnus (Linnaeus, 1758).}, journal = {BMC genomics}, volume = {16}, number = {}, pages = {1007}, pmid = {26607231}, issn = {1471-2164}, support = {G0900740/MRC_/Medical Research Council/United Kingdom ; MR/K001744/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Animals ; Chromosome Mapping ; Cluster Analysis ; Computational Biology/methods ; DNA, Complementary ; Gene Expression Profiling ; Gene Library ; Genomics ; Molecular Sequence Annotation ; *Oligonucleotide Array Sequence Analysis/methods ; Organ Specificity/genetics ; Reproducibility of Results ; Transcriptome ; Tuna/*genetics ; }, abstract = {BACKGROUND: The largest of the tuna species, Atlantic bluefin tuna (Thunnus thynnus), inhabits the North Atlantic Ocean and the Mediterranean Sea and is considered to be an endangered species, largely a consequence of overfishing. T. thynnus aquaculture, referred to as fattening or farming, is a capture based activity dependent on yearly renewal from the wild. Thus, the development of aquaculture practices independent of wild resources can provide an important contribution towards ensuring security and sustainability of this species in the longer-term. The development of such practices is today greatly assisted by large scale transcriptomic studies.

RESULTS: We have used pyrosequencing technology to sequence a mixed-tissue normalised cDNA library, derived from adult T. thynnus. A total of 976,904 raw sequence reads were assembled into 33,105 unique transcripts having a mean length of 893 bases and an N50 of 870. Of these, 33.4% showed similarity to known proteins or gene transcripts and 86.6% of them were matched to the congeneric Pacific bluefin tuna (Thunnus orientalis) genome, compared to 70.3% for the more distantly related Nile tilapia (Oreochromis niloticus) genome. Transcript sequences were used to develop a novel 15 K Agilent oligonucleotide DNA microarray for T. thynnus and comparative tissue gene expression profiles were inferred for gill, heart, liver, ovaries and testes. Functional contrasts were strongest between gills and ovaries. Gills were particularly associated with immune system, signal transduction and cell communication, while ovaries displayed signatures of glycan biosynthesis, nucleotide metabolism, transcription, translation, replication and repair.

CONCLUSIONS: Sequence data generated from a novel mixed-tissue T. thynnus cDNA library provide an important transcriptomic resource that can be further employed for study of various aspects of T. thynnus ecology and genomics, with strong applications in aquaculture. Tissue-specific gene expression profiles inferred through the use of novel oligo-microarray can serve in the design of new and more focused transcriptomic studies for future research of tuna physiology and assessment of the welfare in a production environment.}, } @article {pmid26604859, year = {2015}, author = {Al-Ghalith, GA and Knights, D}, title = {Bygiene: The New Paradigm of Bidirectional Hygiene.}, journal = {The Yale journal of biology and medicine}, volume = {88}, number = {4}, pages = {359-365}, pmid = {26604859}, issn = {1551-4056}, mesh = {Bacteria/drug effects/*pathogenicity ; Biological Evolution ; Cross Infection/*prevention & control ; Drug Resistance, Microbial ; Drug Resistance, Multiple, Bacterial ; Hospitals/*standards ; Humans ; *Hygiene ; }, abstract = {The pervasive dogma surrounding the evolution of virulence - -namely, that a pathogen's virulence decreases over time to prevent threatening its host -- is an archaic assertion that is more appropriately cast as an optimization of virulence cost and benefit. However, the prevailing attitudes underlying practices of medical hygiene and sanitization remain entrenched in these passé ideas. This is true despite the emergence of evidence linking those practices to mounting virulence and antimicrobial resistance in the hospital. It is, therefore, our position that just as the microbe has sought an optimized balance in virulence, so should we seek such an optimized balance in vigilance, complementing warfare with restoration. We call this approach "bygiene," or bidirectional hygiene.}, } @article {pmid26603831, year = {2016}, author = {Fan, F and Ding, G and Wen, X}, title = {Proteomic analyses provide new insights into the responses of Pinus massoniana seedlings to phosphorus deficiency.}, journal = {Proteomics}, volume = {16}, number = {3}, pages = {504-515}, doi = {10.1002/pmic.201500140}, pmid = {26603831}, issn = {1615-9861}, mesh = {Adaptation, Physiological ; Electrophoresis, Gel, Two-Dimensional ; Gene Expression Profiling ; *Gene Expression Regulation, Plant ; Gene Ontology ; Metabolic Networks and Pathways ; Molecular Sequence Annotation ; Phosphorus/*deficiency ; Pinus/genetics/*metabolism ; Plant Leaves/genetics/metabolism ; Plant Proteins/genetics/*metabolism ; Proteome/genetics/*metabolism ; Proteomics/methods ; Seedlings/genetics/*metabolism ; Signal Transduction ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ; Stress, Physiological ; }, abstract = {Phosphorus is an essential macronutrient for plant growth and development. Plants can respond defensively to phosphorus deficiency by modifying their morphology and metabolic pathways via the differential expression of low phosphate responsive genes. To better understand the mechanisms by which the Masson pine (Pinus massoniana) adapts to phosphorus deficiency, we conducted comparative proteomic analysis using an elite line exhibiting high tolerance to phosphorus deficiency. The selected seedlings were treated with 0.5 mM KH2PO4 (control), 0.01 mM KH2PO4 (P1), or 0.06 mM KH2PO4 (P2) for 48 days. Total protein samples were separated via 2DE. A total of 98 differentially expressed proteins, which displayed at least 1.7-fold change expression compared to the control levels (p ≤ 0.05), were identified by MALDI-TOF/TOF MS. These phosphate starvation responsive proteins were implicated in photosynthesis, defense, cellular organization, biosynthesis, energy metabolism, secondary metabolism, signal transduction etc. Therefore, these proteins might play important roles in facilitating internal phosphorus homeostasis. Additionally, the obtained data may be useful for the further characterization of gene function and may provide a foundation for a more comprehensive understanding of the adaptations of the Masson pine to phosphorus-deficient conditions.}, } @article {pmid26601886, year = {2015}, author = {Hangartner, SB and Hoffmann, AA and Smith, A and Griffin, PC}, title = {A collection of Australian Drosophila datasets on climate adaptation and species distributions.}, journal = {Scientific data}, volume = {2}, number = {}, pages = {150067}, pmid = {26601886}, issn = {2052-4463}, mesh = {*Adaptation, Physiological ; Animals ; Australia ; *Climate Change ; Datasets as Topic ; *Drosophila/physiology ; Genetics, Population ; Species Specificity ; }, abstract = {The Australian Drosophila Ecology and Evolution Resource (ADEER) collates Australian datasets on drosophilid flies, which are aimed at investigating questions around climate adaptation, species distribution limits and population genetics. Australian drosophilid species are diverse in climatic tolerance, geographic distribution and behaviour. Many species are restricted to the tropics, a few are temperate specialists, and some have broad distributions across climatic regions. Whereas some species show adaptability to climate changes through genetic and plastic changes, other species have limited adaptive capacity. This knowledge has been used to identify traits and genetic polymorphisms involved in climate change adaptation and build predictive models of responses to climate change. ADEER brings together 103 datasets from 39 studies published between 1982-2013 in a single online resource. All datasets can be downloaded freely in full, along with maps and other visualisations. These historical datasets are preserved for future studies, which will be especially useful for assessing climate-related changes over time.}, } @article {pmid26599833, year = {2016}, author = {Spasojevic, MJ and Bahlai, CA and Bradley, BA and Butterfield, BJ and Tuanmu, MN and Sistla, S and Wiederholt, R and Suding, KN}, title = {Scaling up the diversity-resilience relationship with trait databases and remote sensing data: the recovery of productivity after wildfire.}, journal = {Global change biology}, volume = {22}, number = {4}, pages = {1421-1432}, doi = {10.1111/gcb.13174}, pmid = {26599833}, issn = {1365-2486}, mesh = {*Biodiversity ; Databases, Factual ; *Fires ; Forests ; *Models, Theoretical ; Remote Sensing Technology ; United States ; }, abstract = {Understanding the mechanisms underlying ecosystem resilience - why some systems have an irreversible response to disturbances while others recover - is critical for conserving biodiversity and ecosystem function in the face of global change. Despite the widespread acceptance of a positive relationship between biodiversity and resilience, empirical evidence for this relationship remains fairly limited in scope and localized in scale. Assessing resilience at the large landscape and regional scales most relevant to land management and conservation practices has been limited by the ability to measure both diversity and resilience over large spatial scales. Here, we combined tools used in large-scale studies of biodiversity (remote sensing and trait databases) with theoretical advances developed from small-scale experiments to ask whether the functional diversity within a range of woodland and forest ecosystems influences the recovery of productivity after wildfires across the four-corner region of the United States. We additionally asked how environmental variation (topography, macroclimate) across this geographic region influences such resilience, either directly or indirectly via changes in functional diversity. Using path analysis, we found that functional diversity in regeneration traits (fire tolerance, fire resistance, resprout ability) was a stronger predictor of the recovery of productivity after wildfire than the functional diversity of seed mass or species richness. Moreover, slope, elevation, and aspect either directly or indirectly influenced the recovery of productivity, likely via their effect on microclimate, while macroclimate had no direct or indirect effects. Our study provides some of the first direct empirical evidence for functional diversity increasing resilience at large spatial scales. Our approach highlights the power of combining theory based on local-scale studies with tools used in studies at large spatial scales and trait databases to understand pressing environmental issues.}, } @article {pmid26599399, year = {2015}, author = {Lau, MS and Marion, G and Streftaris, G and Gibson, G}, title = {A Systematic Bayesian Integration of Epidemiological and Genetic Data.}, journal = {PLoS computational biology}, volume = {11}, number = {11}, pages = {e1004633}, pmid = {26599399}, issn = {1553-7358}, mesh = {Algorithms ; Animals ; *Bayes Theorem ; Computational Biology/*methods ; Computer Simulation ; Databases, Factual ; Foot-and-Mouth Disease/epidemiology ; *Models, Biological ; Molecular Epidemiology/*methods ; }, abstract = {Genetic sequence data on pathogens have great potential to inform inference of their transmission dynamics ultimately leading to better disease control. Where genetic change and disease transmission occur on comparable timescales additional information can be inferred via the joint analysis of such genetic sequence data and epidemiological observations based on clinical symptoms and diagnostic tests. Although recently introduced approaches represent substantial progress, for computational reasons they approximate genuine joint inference of disease dynamics and genetic change in the pathogen population, capturing partially the joint epidemiological-evolutionary dynamics. Improved methods are needed to fully integrate such genetic data with epidemiological observations, for achieving a more robust inference of the transmission tree and other key epidemiological parameters such as latent periods. Here, building on current literature, a novel Bayesian framework is proposed that infers simultaneously and explicitly the transmission tree and unobserved transmitted pathogen sequences. Our framework facilitates the use of realistic likelihood functions and enables systematic and genuine joint inference of the epidemiological-evolutionary process from partially observed outbreaks. Using simulated data it is shown that this approach is able to infer accurately joint epidemiological-evolutionary dynamics, even when pathogen sequences and epidemiological data are incomplete, and when sequences are available for only a fraction of exposures. These results also characterise and quantify the value of incomplete and partial sequence data, which has important implications for sampling design, and demonstrate the abilities of the introduced method to identify multiple clusters within an outbreak. The framework is used to analyse an outbreak of foot-and-mouth disease in the UK, enhancing current understanding of its transmission dynamics and evolutionary process.}, } @article {pmid26598990, year = {2016}, author = {El-Temsah, YS and Sevcu, A and Bobcikova, K and Cernik, M and Joner, EJ}, title = {DDT degradation efficiency and ecotoxicological effects of two types of nano-sized zero-valent iron (nZVI) in water and soil.}, journal = {Chemosphere}, volume = {144}, number = {}, pages = {2221-2228}, doi = {10.1016/j.chemosphere.2015.10.122}, pmid = {26598990}, issn = {1879-1298}, mesh = {Animals ; Crustacea/drug effects ; DDT/*chemistry/toxicity ; Ecotoxicology ; Environmental Restoration and Remediation ; Escherichia coli/drug effects ; Flax/drug effects ; Hordeum/drug effects ; Iron/*chemistry/toxicity ; Oligochaeta/drug effects ; Oxygen/metabolism ; Soil ; Soil Pollutants/*chemistry/toxicity ; Water Pollutants, Chemical/*chemistry/toxicity ; }, abstract = {Nano-scale zero-valent iron (nZVI) has been conceived for cost-efficient degradation of chlorinated pollutants in soil as an alternative to e.g permeable reactive barriers or excavation. Little is however known about its efficiency in degradation of the ubiquitous environmental pollutant DDT and its secondary effects on organisms. Here, two types of nZVI (type B made using precipitation with borohydride, and type T produced by gas phase reduction of iron oxides under H2) were compared for efficiency in degradation of DDT in water and in a historically (>45 years) contaminated soil (24 mg kg(-1) DDT). Further, the ecotoxicity of soil and water was tested on plants (barley and flax), earthworms (Eisenia fetida), ostracods (Heterocypris incongruens), and bacteria (Escherichia coli). Both types of nZVI effectively degraded DDT in water, but showed lower degradation of aged DDT in soil. Both types of nZVI had negative impact on the tested organisms, with nZVI-T giving least adverse effects. Negative effects were mostly due to oxidation of nZVI, resulting in O2 consumption and excess Fe(II) in water and soil.}, } @article {pmid26597459, year = {2015}, author = {Dib, L and Meyer, X and Artimo, P and Ioannidis, V and Stockinger, H and Salamin, N}, title = {Coev-web: a web platform designed to simulate and evaluate coevolving positions along a phylogenetic tree.}, journal = {BMC bioinformatics}, volume = {16}, number = {}, pages = {394}, pmid = {26597459}, issn = {1471-2105}, mesh = {Algorithms ; Amino Acids/*metabolism ; Bayes Theorem ; Computational Biology/*methods ; *Evolution, Molecular ; Humans ; *Internet ; *Phylogeny ; Sequence Analysis, DNA/*methods ; *Software ; }, abstract = {BACKGROUND: Available methods to simulate nucleotide or amino acid data typically use Markov models to simulate each position independently. These approaches are not appropriate to assess the performance of combinatorial and probabilistic methods that look for coevolving positions in nucleotide or amino acid sequences.

RESULTS: We have developed a web-based platform that gives a user-friendly access to two phylogenetic-based methods implementing the Coev model: the evaluation of coevolving scores and the simulation of coevolving positions. We have also extended the capabilities of the Coev model to allow for the generalization of the alphabet used in the Markov model, which can now analyse both nucleotide and amino acid data sets. The simulation of coevolving positions is novel and builds upon the developments of the Coev model. It allows user to simulate pairs of dependent nucleotide or amino acid positions.

CONCLUSIONS: The main focus of our paper is the new simulation method we present for coevolving positions. The implementation of this method is embedded within the web platform Coev-web that is freely accessible at http://coev.vital-it.ch/, and was tested in most modern web browsers.}, } @article {pmid26595447, year = {2016}, author = {Stang, A and Kowall, B and Rusner, C and Trabert, B and Bray, F and Schüz, J and McGlynn, KA and Kuss, O}, title = {A novel method for identifying settings for well-motivated ecologic studies of cancer.}, journal = {International journal of cancer}, volume = {138}, number = {8}, pages = {1887-1893}, pmid = {26595447}, issn = {1097-0215}, support = {001/WHO_/World Health Organization/International ; ZIA CP010126-21/ImNIH/Intramural NIH HHS/United States ; ZIA CP010128-20/ImNIH/Intramural NIH HHS/United States ; }, mesh = {*Ecosystem ; Europe/epidemiology ; Female ; Humans ; Incidence ; Male ; Neoplasms/*epidemiology/etiology ; Registries ; *Research Design ; }, abstract = {A low within-country variability and a large between-country variability in cancer incidence may indicate that ecologic factors are involved in the etiology of the disease. The aim of this study is to explore the within- and between-country variability of cancer incidence to motivate high-quality ecologic studies. We extracted age-standardized incidence rate estimates (world standard population) from 135 regions for the ten most frequent invasive cancers in Europe for non-Hispanic white populations from Cancer Incidence in Five Continents, Volume X. We fitted weighted multilevel Poisson regression models with random country effects for each cancer and sex. We estimated intraclass correlation coefficients (ICCs) and 95% confidence intervals (95% CIs). A high ICC indicates a low within- and a high between-country variability of rates. The two cancer sites with the highest ICC among men were prostate cancer (0.96, 95% CI: 0.92-0.99) and skin melanoma (0.78, 0.64-0.93). Among women, high ICCs were observed for lung cancer (0.84, 0.73-0.95) and breast cancer (0.80, 0.69-0.91). The two most prominent sex differences for ICC occurred for cancers of the head and neck (men: 0.70, 0.55-0.85, women: 0.19, 0.08-0.30) and breast cancer (men: 0.04, 0.01-0.07, women: 0.80, 0.69-0.91). ICCs were relatively low for pancreatic cancer (men: 0.23, 0.10-0.35; women: 0.13, 0.04-0.21) and leukemia (men: 0.12, 0.04-0.21; women: 0.08, 0.02-0.14). For cancers with high ICC for which systematic factors of the health care system, screening and diagnostic activities are not plausible explanations for between-country variations in incidence, cross-country sex-specific ecologic studies may be especially promising.}, } @article {pmid26592351, year = {2016}, author = {Nawaz, S and Yuan, Y}, title = {Computational pathology: Exploring the spatial dimension of tumor ecology.}, journal = {Cancer letters}, volume = {380}, number = {1}, pages = {296-303}, doi = {10.1016/j.canlet.2015.11.018}, pmid = {26592351}, issn = {1872-7980}, support = {105104//Wellcome Trust/United Kingdom ; }, mesh = {Animals ; Biopsy ; Breast Neoplasms/mortality/*pathology/therapy ; Female ; *High-Throughput Screening Assays/statistics & numerical data ; Humans ; *Image Interpretation, Computer-Assisted ; Models, Statistical ; Pathology/*methods/statistics & numerical data ; Pattern Recognition, Automated ; Phenotype ; Predictive Value of Tests ; Prognosis ; Time Factors ; *Tumor Microenvironment ; }, abstract = {Tumors are evolving ecosystems where cancer subclones and the microenvironment interact. This is analogous to interaction dynamics between species in their natural habitats, which is a prime area of study in ecology. Spatial statistics are frequently used in ecological studies to infer complex relations including predator-prey, resource dependency and co-evolution. Recently, the emerging field of computational pathology has enabled high-throughput spatial analysis by using image processing to identify different cell types and their locations within histological tumor samples. We discuss how these data may be analyzed with spatial statistics used in ecology to reveal patterns and advance our understanding of ecological interactions occurring among cancer cells and their microenvironment.}, } @article {pmid26591450, year = {2015}, author = {Hanna, C and Naughton, I and Boser, C and Holway, D}, title = {Testing the effects of ant invasions on non-ant arthropods with high-resolution taxonomic data.}, journal = {Ecological applications : a publication of the Ecological Society of America}, volume = {25}, number = {7}, pages = {1841-1850}, doi = {10.1890/14-0952.1}, pmid = {26591450}, issn = {1051-0761}, mesh = {Animals ; Ants/*physiology ; California ; Databases, Factual ; *Ecosystem ; Environmental Monitoring ; Insecta/*classification/physiology ; *Introduced Species ; Islands ; Population Dynamics ; Species Specificity ; }, abstract = {Invasions give rise to a wide range of ecological effects. Many invasions proceed without noticeable impacts on the resident biota, whereas others shift species composition and even alter ecosystem function. Ant invasions generate a broad spectrum of ecological effects, but controversy surrounds the extent of these impacts, especially with regard to how other arthropods are affected. This uncertainty in part results from the widespread use of low-resolution taxonomic data, which can mask the presence of other introduced species and make it difficult to isolate the effects of ant invasions on native species. Here, we use high-resolution taxonomic data to examine the effects of Argentine ant invasions on arthropods on Santa Cruz Island, California. We sampled arthropods in eight pairs of invaded and uninvaded plots and then collaborated with taxonomic experts to identify taxa in four focal groups: spiders, bark lice, beetles, and ants. Spiders, bark lice, and beetles made up ~40% of the 9868 non-ant arthropod individuals sampled; the majority of focal group arthropods were putatively native taxa. Although our results indicate strong negative effects of the Argentine ant on native ants, as is well documented, invaded and uninvaded plots did not differ with respect to the richness, abundance, or species composition of spiders, bark lice, and beetles. One common, introduced species of bark louse was more common in uninvaded plots than in invaded plots, and including this species into our analyses changed the relationship between bark louse richness vs. L. humile abundance from no relationship to a significant negative relationship. This case illustrates how failure to differentiate native and introduced taxa can lead to erroneous conclusions about the effects of ant invasions. Our results caution against unqualified assertions about the effects of ant invasions on non-ant arthropods, and more generally demonstrate that accurate assessments of invasion impacts depend on adequate information about species identity.}, } @article {pmid26590126, year = {2016}, author = {Kim, J and Fabris, M and Baart, G and Kim, MK and Goossens, A and Vyverman, W and Falkowski, PG and Lun, DS}, title = {Flux balance analysis of primary metabolism in the diatom Phaeodactylum tricornutum.}, journal = {The Plant journal : for cell and molecular biology}, volume = {85}, number = {1}, pages = {161-176}, doi = {10.1111/tpj.13081}, pmid = {26590126}, issn = {1365-313X}, mesh = {Biofuels ; *Computational Biology ; Computer Simulation ; Databases, Factual ; Diatoms/growth & development/*metabolism ; Genome/*genetics ; *Glycolysis ; *Metabolic Networks and Pathways ; Microalgae ; Mitochondria/metabolism ; *Models, Biological ; Photosynthesis ; Species Specificity ; }, abstract = {Diatoms (Bacillarophyceae) are photosynthetic unicellular microalgae that have risen to ecological prominence in oceans over the past 30 million years. They are of interest as potential feedstocks for sustainable biofuels. Maximizing production of these feedstocks will require genetic modifications and an understanding of algal metabolism. These processes may benefit from genome-scale models, which predict intracellular fluxes and theoretical yields, as well as the viability of knockout and knock-in transformants. Here we present a genome-scale metabolic model of a fully sequenced and transformable diatom: Phaeodactylum tricornutum. The metabolic network was constructed using the P. tricornutum genome, biochemical literature, and online bioinformatic databases. Intracellular fluxes in P. tricornutum were calculated for autotrophic, mixotrophic and heterotrophic growth conditions, as well as knockout conditions that explore the in silico role of glycolytic enzymes in the mitochondrion. The flux distribution for lower glycolysis in the mitochondrion depended on which transporters for TCA cycle metabolites were included in the model. The growth rate predictions were validated against experimental data obtained using chemostats. Two published studies on this organism were used to validate model predictions for cyclic electron flow under autotrophic conditions, and fluxes through the phosphoketolase, glycine and serine synthesis pathways under mixotrophic conditions. Several gaps in annotation were also identified. The model also explored unusual features of diatom metabolism, such as the presence of lower glycolysis pathways in the mitochondrion, as well as differences between P. tricornutum and other photosynthetic organisms.}, } @article {pmid26589994, year = {2016}, author = {Xu, J and Zhang, J}, title = {Are Human Translated Pseudogenes Functional?.}, journal = {Molecular biology and evolution}, volume = {33}, number = {3}, pages = {755-760}, pmid = {26589994}, issn = {1537-1719}, support = {R01 GM103232/GM/NIGMS NIH HHS/United States ; R01GM103232/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Computational Biology/methods ; Evolution, Molecular ; Genomics/methods ; Humans ; Molecular Sequence Data ; Open Reading Frames ; *Protein Biosynthesis ; Proteome ; Pseudogenes/*genetics ; Selection, Genetic ; *Transcription, Genetic ; Transcriptome ; }, abstract = {By definition, pseudogenes are relics of former genes that no longer possess biological functions. Operationally, they are identified based on disruptions of open reading frames (ORFs) or presumed losses of promoter activities. Intriguingly, a recent human proteomic study reported peptides encoded by 107 pseudogenes. These peptides may play currently unrecognized physiological roles. Alternatively, they may have resulted from accidental translations of pseudogene transcripts and possess no function. Comparing between human and macaque orthologs, we show that the nonsynonymous to synonymous substitution rate ratio (ω) is significantly smaller for translated pseudogenes than other pseudogenes. In particular, five of 34 translated pseudogenes amenable to evolutionary analysis have ω values significantly lower than 1, indicative of the action of purifying selection. This and other findings demonstrate that some but not all translated pseudogenes have selected functions at the protein level. Hence, neither ORF disruption nor presence of protein product disproves or proves gene functionality at the protein level.}, } @article {pmid26586809, year = {2016}, author = {Greuter, D and Loy, A and Horn, M and Rattei, T}, title = {probeBase--an online resource for rRNA-targeted oligonucleotide probes and primers: new features 2016.}, journal = {Nucleic acids research}, volume = {44}, number = {D1}, pages = {D586-9}, pmid = {26586809}, issn = {1362-4962}, support = {281633/ERC_/European Research Council/International ; I 1628/FWF_/Austrian Science Fund FWF/Austria ; I 2320/FWF_/Austrian Science Fund FWF/Austria ; P 25111/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Computer Simulation ; DNA Primers/*chemistry ; *Databases, Nucleic Acid ; Internet ; Nucleic Acid Hybridization ; Oligonucleotide Probes/*chemistry ; RNA, Ribosomal/*chemistry ; Sequence Analysis, RNA ; }, abstract = {probeBase http://www.probebase.net is a manually maintained and curated database of rRNA-targeted oligonucleotide probes and primers. Contextual information and multiple options for evaluating in silico hybridization performance against the most recent rRNA sequence databases are provided for each oligonucleotide entry, which makes probeBase an important and frequently used resource for microbiology research and diagnostics. Here we present a major update of probeBase, which was last featured in the NAR Database Issue 2007. This update describes a complete remodeling of the database architecture and environment to accommodate computationally efficient access. Improved search functions, sequence match tools and data output now extend the opportunities for finding suitable hierarchical probe sets that target an organism or taxon at different taxonomic levels. To facilitate the identification of complementary probe sets for organisms represented by short rRNA sequence reads generated by amplicon sequencing or metagenomic analysis with next generation sequencing technologies such as Illumina and IonTorrent, we introduce a novel tool that recovers surrogate near full-length rRNA sequences for short query sequences and finds matching oligonucleotides in probeBase.}, } @article {pmid26586804, year = {2016}, author = {Burns, J and Kukushkin, D and Lindblad, K and Chen, X and Jonoska, N and Landweber, LF}, title = {<mds_ies_db>: a database of ciliate genome rearrangements.}, journal = {Nucleic acids research}, volume = {44}, number = {D1}, pages = {D703-9}, pmid = {26586804}, issn = {1362-4962}, support = {GM59708/GM/NIGMS NIH HHS/United States ; GM109459/GM/NIGMS NIH HHS/United States ; R01 GM059708/GM/NIGMS NIH HHS/United States ; R01 GM109459/GM/NIGMS NIH HHS/United States ; T32 HG003284/HG/NHGRI NIH HHS/United States ; }, mesh = {*Databases, Nucleic Acid ; *Gene Rearrangement ; *Genome ; Molecular Sequence Annotation ; Oxytricha/*genetics ; Recombination, Genetic ; Tetrahymena thermophila/*genetics ; }, abstract = {Ciliated protists exhibit nuclear dimorphism through the presence of somatic macronuclei (MAC) and germline micronuclei (MIC). In some ciliates, DNA from precursor segments in the MIC genome rearranges to form transcriptionally active genes in the mature MAC genome, making these ciliates model organisms to study the process of somatic genome rearrangement. Similar broad scale, somatic rearrangement events occur in many eukaryotic cells and tumors. The (http://oxytricha.princeton.edu/mds_ies_db) is a database of genome recombination and rearrangement annotations, and it provides tools for visualization and comparative analysis of precursor and product genomes. The database currently contains annotations for two completely sequenced ciliate genomes: Oxytricha trifallax and Tetrahymena thermophila.}, } @article {pmid26582008, year = {2016}, author = {Maksimović, MŽ and Gudelj Rakić, JM and Vlajinac, HD and Vasiljević, ND and Marinković, JM}, title = {Relationship between health behaviour and body mass index in the Serbian adult population: data from National Health Survey 2013.}, journal = {International journal of public health}, volume = {61}, number = {1}, pages = {57-68}, pmid = {26582008}, issn = {1661-8564}, mesh = {Adult ; Aged ; Alcohol Drinking/adverse effects ; *Body Mass Index ; Cross-Sectional Studies ; Exercise/physiology ; Feeding Behavior/*physiology ; Female ; *Health Behavior ; Health Surveys ; Humans ; Logistic Models ; Male ; Middle Aged ; Overweight/epidemiology/*etiology ; Risk Factors ; Serbia/epidemiology ; Smoking/adverse effects ; }, abstract = {OBJECTIVES: To determine relationship between health behaviour and body mass index (BMI) in a Serbian adult population.

METHODS: Study population included adults aged 20 and more years. A stratified, two-stage national representative random sampling approach was used for the selection of the survey sample.

RESULTS: Regarding BMI, out of the 12,461 subjects of both sexes, 2.4 % were underweight, 36.5 % overweight and 22.4 % obese. Multivariate logistic regression analysis showed that both in men and women, risk factors for obesity were former smoking, irregular eating breakfast and low physical activity level, while in women only risk of obesity was associated with alcohol consumption. In both sexes, risk factors for overweight were former smoking and low physical activity level, and in women additionally those were alcohol consumption, irregular eating breakfast, always adding salt to meals and consumption of 2-4 portions of fruit daily. Smoking and irregular eating of breakfast in men were risk factors for underweight.

CONCLUSIONS: Physical activity, alcohol consumption, smoking, irregular breakfast consumption, adding salt to meals, frequency of vegetable and fruit consumption were related to BMI in adult Serbian population.}, } @article {pmid26581632, year = {2015}, author = {Chen, X and Liang, S and Cao, Y and He, T and Wang, D}, title = {Observed contrast changes in snow cover phenology in northern middle and high latitudes from 2001-2014.}, journal = {Scientific reports}, volume = {5}, number = {}, pages = {16820}, pmid = {26581632}, issn = {2045-2322}, support = {2013AA121201/AA/NIAAA NIH HHS/United States ; }, mesh = {*Altitude ; Atmosphere ; Databases as Topic ; Geography ; Seasons ; *Snow ; Spatio-Temporal Analysis ; }, abstract = {Quantifying and attributing the phenological changes in snow cover are essential for meteorological, hydrological, ecological, and societal implications. However, snow cover phenology changes have not been well documented. Evidence from multiple satellite and reanalysis data from 2001 to 2014 points out that the snow end date (De) advanced by 5.11 (±2.20) days in northern high latitudes (52-75°N) and was delayed by 3.28 (±2.59) days in northern mid-latitudes (32-52°N) at the 90% confidence level. Dominated by changes in De, snow duration days (Dd) was shorter in duration by 5.57 (±2.55) days in high latitudes and longer by 9.74 (±2.58) days in mid-latitudes. Changes in De during the spring season were consistent with the spatiotemporal pattern of land surface albedo change. Decreased land surface temperature combined with increased precipitation in mid-latitudes and significantly increased land surface temperature in high latitudes, impacted by recent Pacific surface cooling, Arctic amplification and strengthening westerlies, result in contrasting changes in the Northern Hemisphere snow cover phenology. Changes in the snow cover phenology led to contrasting anomalies of snow radiative forcing, which is dominated by De and accounts for 51% of the total shortwave flux anomalies at the top of the atmosphere.}, } @article {pmid26580327, year = {2015}, author = {Rubiano, AM and Carney, N and Chesnut, R and Puyana, JC}, title = {Global neurotrauma research challenges and opportunities.}, journal = {Nature}, volume = {527}, number = {7578}, pages = {S193-7}, pmid = {26580327}, issn = {1476-4687}, support = {R21 TW009332/TW/FIC NIH HHS/United States ; R01NS080648-01/NS/NINDS NIH HHS/United States ; R21TW009332-01A1/TW/FIC NIH HHS/United States ; R25TW009714-01/TW/FIC NIH HHS/United States ; }, mesh = {Biomedical Research/*organization & administration ; *Brain Injuries ; Developing Countries/economics ; Humans ; *Internationality ; Leadership ; }, abstract = {Traumatic injury to the brain or spinal cord is one of the most serious public health problems worldwide. The devastating impact of 'trauma', a term used to define the global burden of disease related to all injuries, is the leading cause of loss of human potential across the globe, especially in low- and middle-income countries. Enormous challenges must be met to significantly advance neurotrauma research around the world, specifically in underserved and austere environments. Neurotrauma research at the global level needs to be contextualized: different regions have their own needs and obstacles. Interventions that are not considered a priority in some regions could be a priority for others. The introduction of inexpensive and innovative interventions, including mobile technologies and e-health applications, focused on policy management improvement are essential and should be applicable to the needs of the local environment. The simple transfer of a clinical question from resource-rich environments to those of low- and middle-income countries that lack sophisticated interventions may not be the best strategy to address these countries' needs. Emphasis on promoting the design of true 'ecological' studies that include the evaluation of human factors in relation to the process of care, analytical descriptions of health systems, and how leadership is best applied in medical communities and society as a whole will become crucial.}, } @article {pmid26577458, year = {2016}, author = {Ren, X and Che, Y and Yang, K and Tao, Y}, title = {Risk perception and public acceptance toward a highly protested Waste-to-Energy facility.}, journal = {Waste management (New York, N.Y.)}, volume = {48}, number = {}, pages = {528-539}, doi = {10.1016/j.wasman.2015.10.036}, pmid = {26577458}, issn = {1879-2456}, mesh = {Adolescent ; Adult ; Attitude ; China ; Cities ; Communication ; Conservation of Natural Resources/methods ; Discriminant Analysis ; *Energy-Generating Resources ; Female ; Geographic Information Systems ; Geography ; Humans ; Incineration ; Male ; Middle Aged ; *Public Opinion ; Risk ; Social Class ; Solid Waste ; Surveys and Questionnaires ; Waste Management/*methods ; Young Adult ; }, abstract = {The application of Waste-to-Energy treatment in Municipal Solid Waste faces strong protest by local communities, especially in cities with high population densities. This study introduces insight into the public awareness, acceptance and risk perception toward Waste-to-Energy through a structured questionnaire survey around a Waste-to-Energy facility in Shanghai, China. The Dichotomous-Choice contingent valuation method was applied to study the willingness to accept of residents as an indicator of risk perception and tolerance. The factors influencing risk perception and the protest response choice were analyzed. The geographical distributions of the acceptance of Waste-to-Energy facility and protest response were explored using geographical information systems. The findings of the research indicated an encouraging vision of promoting Waste-to-Energy, considering its benefits of renewable energy and the conservation of land. A high percentage of protest willingness to accept (50.94%) was highlighted with the effect of income, opinion about Waste-to-Energy, gender and perceived impact. The fuzzy classification among people with different opinions on compensation (valid 0, positive or protest willingness to accept) revealed the existing yet rejected demand of compensation among protesters. Geographical distribution in the public attitude can also be observed. Finally significant statistical relation between knowledge and risk perception indicates the need of risk communication, as well as involving public into whole management process.}, } @article {pmid26574686, year = {2016}, author = {Mordecai, GJ and Wilfert, L and Martin, SJ and Jones, IM and Schroeder, DC}, title = {Diversity in a honey bee pathogen: first report of a third master variant of the Deformed Wing Virus quasispecies.}, journal = {The ISME journal}, volume = {10}, number = {5}, pages = {1264-1273}, pmid = {26574686}, issn = {1751-7370}, support = {BB/G02040X/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; Bayes Theorem ; Bees/*parasitology/*virology ; Computational Biology ; Evolution, Molecular ; Genome, Viral ; High-Throughput Nucleotide Sequencing ; Markov Chains ; Phylogeny ; RNA Viruses/genetics ; Varroidae/*virology ; }, abstract = {Treatment of emerging RNA viruses is hampered by the high mutation and replication rates that enable these viruses to operate as a quasispecies. Declining honey bee populations have been attributed to the ectoparasitic mite Varroa destructor and its affiliation with Deformed Wing Virus (DWV). In the current study we use next-generation sequencing to investigate the DWV quasispecies in an apiary known to suffer from overwintering colony losses. We show that the DWV species complex is made up of three master variants. Our results indicate that a new DWV Type C variant is distinct from the previously described types A and B, but together they form a distinct clade compared with other members of the Iflaviridae. The molecular clock estimation predicts that Type C diverged from the other variants ∼319 years ago. The discovery of a new master variant of DWV has important implications for the positive identification of the true pathogen within global honey bee populations.}, } @article {pmid26573879, year = {2016}, author = {Ke, JY and Cole, RM and Hamad, EM and Hsiao, YH and Cotten, BM and Powell, KA and Belury, MA}, title = {Citrus flavonoid, naringenin, increases locomotor activity and reduces diacylglycerol accumulation in skeletal muscle of obese ovariectomized mice.}, journal = {Molecular nutrition & food research}, volume = {60}, number = {2}, pages = {313-324}, pmid = {26573879}, issn = {1613-4133}, support = {P30 CA016058/CA/NCI NIH HHS/United States ; R03 CA162551/CA/NCI NIH HHS/United States ; CA162551/CA/NCI NIH HHS/United States ; }, mesh = {Animals ; Body Weight/drug effects ; Citrus/chemistry ; Dietary Supplements ; Diglycerides/*metabolism ; Energy Intake/drug effects ; Energy Metabolism/drug effects ; Female ; Flavanones/pharmacokinetics/*pharmacology ; Mice, Inbred C57BL ; Motor Activity/drug effects ; Muscle, Skeletal/*drug effects/metabolism ; Obesity/*diet therapy/etiology/metabolism ; Ovariectomy ; Postmenopause ; Tissue Distribution ; }, abstract = {SCOPE: Estrogen deficiency has been associated with central obesity, muscle loss and metabolic syndrome in postmenopausal women. This study assessed naringenin accumulation in tissues and investigated the hypothesis that naringenin reverses diet-induced metabolic disturbances in obese ovariectomized mice.

METHODS AND RESULTS: In study 1, we measured naringenin concentrations in plasma, liver, perigonadal and subcutaneous adipose tissues, and muscle of ovariectomized C57BL/6J female mice after 11 weeks of naringenin supplementation. Naringenin accumulated 5-12 times more in mice fed a 3% naringenin diet than in mice fed a 1% naringenin diet. In study 2, ovariectomized mice were fed a high-fat diet (60 kcal% fat) for 11 weeks and half of the mice were then supplemented with 3% naringenin for another 11 weeks. Dietary naringenin suppressed weight gain, lowered hyperglycemia and decreased intra-abdominal adiposity evaluated by magnetic resonance imaging. Naringenin-fed mice exhibited elevated locomotor activity monitored by infrared beam breaks, maintained muscle mass and reduced muscle diacylglycerol content. Real-time PCR analysis in muscle revealed decreased mRNA level for genes involved in de novo lipogenesis, lipolysis and triglyceride synthesis/storage.

CONCLUSION: Long-term 3% naringenin supplementation resulted in significant naringenin accumulation in plasma and tissues, associated with attenuated metabolic dysregulation and muscle loss in obese ovariectomized mice.}, } @article {pmid26569270, year = {2015}, author = {Gong, J and Yang, J and Tang, W}, title = {Spatially Explicit Landscape-Level Ecological Risks Induced by Land Use and Land Cover Change in a National Ecologically Representative Region in China.}, journal = {International journal of environmental research and public health}, volume = {12}, number = {11}, pages = {14192-14215}, pmid = {26569270}, issn = {1660-4601}, mesh = {Biodiversity ; China ; Cities ; Computer Simulation ; Conservation of Natural Resources ; Ecology/*methods ; Ecosystem ; *Environment ; Geographic Information Systems ; Humans ; *Models, Theoretical ; Risk ; Risk Assessment/methods ; }, abstract = {Land use and land cover change is driven by multiple influential factors from environmental and social dimensions in a land system. Land use practices of human decision-makers modify the landscape of the land system, possibly leading to landscape fragmentation, biodiversity loss, or environmental pollution-severe environmental or ecological impacts. While landscape-level ecological risk assessment supports the evaluation of these impacts, investigations on how these ecological risks induced by land use practices change over space and time in response to alternative policy intervention remain inadequate. In this article, we conducted spatially explicit landscape ecological risk analysis in Ezhou City, China. Our study area is a national ecologically representative region experiencing drastic land use and land cover change, and is regulated by multiple policies represented by farmland protection, ecological conservation, and urban development. We employed landscape metrics to consider the influence of potential landscape-level disturbance for the evaluation of landscape ecological risks. Using spatiotemporal simulation, we designed scenarios to examine spatiotemporal patterns in landscape ecological risks in response to policy intervention. Our study demonstrated that spatially explicit landscape ecological risk analysis combined with simulation-driven scenario analysis is of particular importance for guiding the sustainable development of ecologically vulnerable land systems.}, } @article {pmid26563467, year = {2015}, author = {Alma'abadi, AD and Gojobori, T and Mineta, K}, title = {Marine Metagenome as A Resource for Novel Enzymes.}, journal = {Genomics, proteomics & bioinformatics}, volume = {13}, number = {5}, pages = {290-295}, pmid = {26563467}, issn = {2210-3244}, mesh = {Aquatic Organisms/enzymology/genetics ; Bacteria/*enzymology/*genetics ; Computational Biology ; High-Throughput Nucleotide Sequencing/methods ; Metagenome/*genetics ; Metagenomics/*methods ; }, abstract = {More than 99% of identified prokaryotes, including many from the marine environment, cannot be cultured in the laboratory. This lack of capability restricts our knowledge of microbial genetics and community ecology. Metagenomics, the culture-independent cloning of environmental DNAs that are isolated directly from an environmental sample, has already provided a wealth of information about the uncultured microbial world. It has also facilitated the discovery of novel biocatalysts by allowing researchers to probe directly into a huge diversity of enzymes within natural microbial communities. Recent advances in these studies have led to a great interest in recruiting microbial enzymes for the development of environmentally-friendly industry. Although the metagenomics approach has many limitations, it is expected to provide not only scientific insights but also economic benefits, especially in industry. This review highlights the importance of metagenomics in mining microbial lipases, as an example, by using high-throughput techniques. In addition, we discuss challenges in the metagenomics as an important part of bioinformatics analysis in big data.}, } @article {pmid26561396, year = {2015}, author = {Bonatelli, IA and Carstens, BC and Moraes, EM}, title = {Using Next Generation RAD Sequencing to Isolate Multispecies Microsatellites for Pilosocereus (Cactaceae).}, journal = {PloS one}, volume = {10}, number = {11}, pages = {e0142602}, pmid = {26561396}, issn = {1932-6203}, mesh = {Cactaceae/*genetics ; Computational Biology ; Cost-Benefit Analysis ; DNA Primers ; DNA Restriction Enzymes/genetics ; DNA, Plant/genetics ; Genetic Markers/genetics ; Genetic Variation ; Genotype ; High-Throughput Nucleotide Sequencing/*methods ; Linkage Disequilibrium ; Microsatellite Repeats/*genetics ; Molecular Sequence Data ; Polymerase Chain Reaction ; Polymorphism, Genetic ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {Microsatellite markers (also known as SSRs, Simple Sequence Repeats) are widely used in plant science and are among the most informative molecular markers for population genetic investigations, but the development of such markers presents substantial challenges. In this report, we discuss how next generation sequencing can replace the cloning, Sanger sequencing, identification of polymorphic loci, and testing cross-amplification that were previously required to develop microsatellites. We report the development of a large set of microsatellite markers for five species of the Neotropical cactus genus Pilosocereus using a restriction-site-associated DNA sequencing (RAD-seq) on a Roche 454 platform. We identified an average of 165 microsatellites per individual, with the absolute numbers across individuals proportional to the sequence reads obtained per individual. Frequency distribution of the repeat units was similar in the five species, with shorter motifs such as di- and trinucleotide being the most abundant repeats. In addition, we provide 72 microsatellites that could be potentially amplified in the sampled species and 22 polymorphic microsatellites validated in two populations of the species Pilosocereus machrisii. Although low coverage sequencing among individuals was observed for most of the loci, which we suggest to be more related to the nature of the microsatellite markers and the possible bias inserted by the restriction enzymes than to the genome size, our work demonstrates that an NGS approach is an efficient method to isolate multispecies microsatellites even in non-model organisms.}, } @article {pmid26559506, year = {2016}, author = {Yang, W and Dierking, K and Schulenburg, H}, title = {WormExp: a web-based application for a Caenorhabditis elegans-specific gene expression enrichment analysis.}, journal = {Bioinformatics (Oxford, England)}, volume = {32}, number = {6}, pages = {943-945}, doi = {10.1093/bioinformatics/btv667}, pmid = {26559506}, issn = {1367-4811}, mesh = {Animals ; *Caenorhabditis elegans ; Databases, Factual ; Gene Expression Profiling ; Internet ; Software ; }, abstract = {MOTIVATION: A particular challenge of the current omics age is to make sense of the inferred differential expression of genes and proteins. The most common approach is to perform a gene ontology (GO) enrichment analysis, thereby relying on a database that has been extracted from a variety of organisms and that can therefore only yield reliable information on evolutionary conserved functions.

RESULTS: We here present a web-based application for a taxon-specific gene set exploration and enrichment analysis, which is expected to yield novel functional insights into newly determined gene sets. The approach is based on the complete collection of curated high-throughput gene expression data sets for the model nematode Caenorhabditis elegans, including 1786 gene sets from more than 350 studies.

WormExp is available at http://wormexp.zoologie.uni-kiel.de

CONTACTS: hschulenburg@zoologie.uni-kiel.de

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, } @article {pmid26556502, year = {2015}, author = {Roche, DG and Kruuk, LE and Lanfear, R and Binning, SA}, title = {Public Data Archiving in Ecology and Evolution: How Well Are We Doing?.}, journal = {PLoS biology}, volume = {13}, number = {11}, pages = {e1002295}, pmid = {26556502}, issn = {1545-7885}, mesh = {*Access to Information ; Animals ; *Biological Evolution ; Biology/*methods ; Data Accuracy ; Data Curation ; *Datasets as Topic/standards ; Ecology/*methods ; Guidelines as Topic ; Humans ; Internet ; *Periodicals as Topic ; Workforce ; }, abstract = {Policies that mandate public data archiving (PDA) successfully increase accessibility to data underlying scientific publications. However, is the data quality sufficient to allow reuse and reanalysis? We surveyed 100 datasets associated with nonmolecular studies in journals that commonly publish ecological and evolutionary research and have a strong PDA policy. Out of these datasets, 56% were incomplete, and 64% were archived in a way that partially or entirely prevented reuse. We suggest that cultural shifts facilitating clearer benefits to authors are necessary to achieve high-quality PDA and highlight key guidelines to help authors increase their data's reuse potential and compliance with journal data policies.}, } @article {pmid26556496, year = {2016}, author = {Gibb, GC and Condamine, FL and Kuch, M and Enk, J and Moraes-Barros, N and Superina, M and Poinar, HN and Delsuc, F}, title = {Shotgun Mitogenomics Provides a Reference Phylogenetic Framework and Timescale for Living Xenarthrans.}, journal = {Molecular biology and evolution}, volume = {33}, number = {3}, pages = {621-642}, pmid = {26556496}, issn = {1537-1719}, mesh = {Animals ; Bayes Theorem ; Biological Evolution ; Computational Biology ; *Evolution, Molecular ; *Genome, Mitochondrial ; *Genomics ; High-Throughput Nucleotide Sequencing ; *Phylogeny ; Xenarthra/*classification/*genetics ; }, abstract = {Xenarthra (armadillos, sloths, and anteaters) constitutes one of the four major clades of placental mammals. Despite their phylogenetic distinctiveness in mammals, a reference phylogeny is still lacking for the 31 described species. Here we used Illumina shotgun sequencing to assemble 33 new complete mitochondrial genomes, establishing Xenarthra as the first major placental clade to be fully sequenced at the species level for mitogenomes. The resulting data set allowed the reconstruction of a robust phylogenetic framework and timescale that are consistent with previous studies conducted at the genus level using nuclear genes. Incorporating the full species diversity of extant xenarthrans points to a number of inconsistencies in xenarthran systematics and species definition. We propose to split armadillos into two distinct families Dasypodidae (dasypodines) and Chlamyphoridae (euphractines, chlamyphorines, and tolypeutines) to better reflect their ancient divergence, estimated around 42 Ma. Species delimitation within long-nosed armadillos (genus Dasypus) appeared more complex than anticipated, with the discovery of a divergent lineage in French Guiana. Diversification analyses showed Xenarthra to be an ancient clade with a constant diversification rate through time with a species turnover driven by high but constant extinction. We also detected a significant negative correlation between speciation rate and past temperature fluctuations with an increase in speciation rate corresponding to the general cooling observed during the last 15 My. Biogeographic reconstructions identified the tropical rainforest biome of Amazonia and the Guiana Shield as the cradle of xenarthran evolutionary history with subsequent dispersions into more open and dry habitats.}, } @article {pmid26556287, year = {2015}, author = {Forstner, AJ and Hofmann, A and Maaser, A and Sumer, S and Khudayberdiev, S and Mühleisen, TW and Leber, M and Schulze, TG and Strohmaier, J and Degenhardt, F and Treutlein, J and Mattheisen, M and Schumacher, J and Breuer, R and Meier, S and Herms, S and Hoffmann, P and Lacour, A and Witt, SH and Reif, A and Müller-Myhsok, B and Lucae, S and Maier, W and Schwarz, M and Vedder, H and Kammerer-Ciernioch, J and Pfennig, A and Bauer, M and Hautzinger, M and Moebus, S and Priebe, L and Sivalingam, S and Verhaert, A and Schulz, H and Czerski, PM and Hauser, J and Lissowska, J and Szeszenia-Dabrowska, N and Brennan, P and McKay, JD and Wright, A and Mitchell, PB and Fullerton, JM and Schofield, PR and Montgomery, GW and Medland, SE and Gordon, SD and Martin, NG and Krasnov, V and Chuchalin, A and Babadjanova, G and Pantelejeva, G and Abramova, LI and Tiganov, AS and Polonikov, A and Khusnutdinova, E and Alda, M and Cruceanu, C and Rouleau, GA and Turecki, G and Laprise, C and Rivas, F and Mayoral, F and Kogevinas, M and Grigoroiu-Serbanescu, M and Propping, P and Becker, T and Rietschel, M and Cichon, S and Schratt, G and Nöthen, MM}, title = {Genome-wide analysis implicates microRNAs and their target genes in the development of bipolar disorder.}, journal = {Translational psychiatry}, volume = {5}, number = {11}, pages = {e678}, pmid = {26556287}, issn = {2158-3188}, support = {001/WHO_/World Health Organization/International ; MOP-13506/CAPMC/CIHR/Canada ; 084703/WT_/Wellcome Trust/United Kingdom ; 64410/CAPMC/CIHR/Canada ; }, mesh = {Animals ; Bipolar Disorder/*genetics ; Disease Models, Animal ; Genetic Predisposition to Disease/*genetics ; Genome-Wide Association Study/*statistics & numerical data ; Humans ; MicroRNAs/*genetics ; Rats ; Rats, Sprague-Dawley ; }, abstract = {Bipolar disorder (BD) is a severe and highly heritable neuropsychiatric disorder with a lifetime prevalence of 1%. Molecular genetic studies have identified the first BD susceptibility genes. However, the disease pathways remain largely unknown. Accumulating evidence suggests that microRNAs, a class of small noncoding RNAs, contribute to basic mechanisms underlying brain development and plasticity, suggesting their possible involvement in the pathogenesis of several psychiatric disorders, including BD. In the present study, gene-based analyses were performed for all known autosomal microRNAs using the largest genome-wide association data set of BD to date (9747 patients and 14 278 controls). Associated and brain-expressed microRNAs were then investigated in target gene and pathway analyses. Functional analyses of miR-499 and miR-708 were performed in rat hippocampal neurons. Ninety-eight of the six hundred nine investigated microRNAs showed nominally significant P-values, suggesting that BD-associated microRNAs might be enriched within known microRNA loci. After correction for multiple testing, nine microRNAs showed a significant association with BD. The most promising were miR-499, miR-708 and miR-1908. Target gene and pathway analyses revealed 18 significant canonical pathways, including brain development and neuron projection. For miR-499, four Bonferroni-corrected significant target genes were identified, including the genome-wide risk gene for psychiatric disorder CACNB2. First results of functional analyses in rat hippocampal neurons neither revealed nor excluded a major contribution of miR-499 or miR-708 to dendritic spine morphogenesis. The present results suggest that research is warranted to elucidate the precise involvement of microRNAs and their downstream pathways in BD.}, } @article {pmid26553774, year = {2016}, author = {Deshpande, V and Wang, Q and Greenfield, P and Charleston, M and Porras-Alfaro, A and Kuske, CR and Cole, JR and Midgley, DJ and Tran-Dinh, N}, title = {Fungal identification using a Bayesian classifier and the Warcup training set of internal transcribed spacer sequences.}, journal = {Mycologia}, volume = {108}, number = {1}, pages = {1-5}, doi = {10.3852/14-293}, pmid = {26553774}, issn = {0027-5514}, mesh = {Bayes Theorem ; DNA, Fungal/chemistry/genetics ; DNA, Ribosomal Spacer/chemistry/genetics ; Datasets as Topic ; Fungi/*classification/genetics ; Reproducibility of Results ; Sequence Analysis, DNA ; }, abstract = {Fungi are key organisms in many ecological processes and communities. Rapid and low cost surveys of the fungal members of a community can be undertaken by isolating and sequencing a taxonomically informative genomic region, such as the ITS (internal transcribed spacer), from DNA extracted from a metagenomic sample, and then classifying these sequences to determine which organisms are present. This paper announces the availability of the Warcup ITS training set and shows how it can be used with the Ribosomal Database Project (RDP) Bayesian Classifier to rapidly and accurately identify fungi using ITS sequences. The classifications can be down to species level and use conventional literature-based mycological nomenclature and taxonomic assignments.}, } @article {pmid26552634, year = {2016}, author = {Vogt, DJ and Vogt, KA and Gmur, SJ and Scullion, JJ and Suntana, AS and Daryanto, S and Sigurðardóttir, R}, title = {Vulnerability of tropical forest ecosystems and forest dependent communities to droughts.}, journal = {Environmental research}, volume = {144}, number = {Pt B}, pages = {27-38}, doi = {10.1016/j.envres.2015.10.022}, pmid = {26552634}, issn = {1096-0953}, support = {R24 HD042828/HD/NICHD NIH HHS/United States ; }, mesh = {*Climate Change ; Databases, Factual ; Decision Making ; *Droughts ; *Forests ; Rain ; Soil/*chemistry ; Tropical Climate ; }, abstract = {Energy captured by and flowing through a forest ecosystem can be indexed by its total Net Primary Productivity (NPP). This forest NPP can also be a reflection of its sensitivity to, and its ability to adapt to, any climate change while also being harvested by humans. However detecting and identifying the vulnerability of forest and human ecosystems to climate change requires information on whether these coupled social and ecological systems are able to maintain functionality while responding to environmental variability. To better understand what parameters might be representative of environmental variability, we compiled a metadata analysis of 96 tropical forest sites. We found that three soil textural classes (i.e., sand, sandy loam and clay) had significant but different relationships between NPP and precipitation levels. Therefore, assessing the vulnerability of forests and forest dependent communities to drought was carried out using data from those sites that had one of those three soil textural classes. For example, forests growing on soil textures of sand and clay had NPP levels decreasing as precipitation levels increased, in contrast to those forest sites that had sandy loam soils where NPP levels increased. Also, forests growing on sandy loam soil textures appeared better adapted to grow at lower precipitation levels compared to the sand and clay textured soils. In fact in our tropical database the lowest precipitation level found for the sandy loam soils was 821 mm yr(-1) compared to sand at 1739 mm yr(-1) and clay at 1771 mm yr(-1). Soil texture also determined the level of NPP reached by a forest, i.e., forest growing on sandy loam and clay reached low-medium NPP levels while higher NPP levels (i.e., medium, high) were found on sand-textured soils. Intermediate precipitation levels (>1800-3000 mm yr(-1)) were needed to grow forests at the medium and high NPP levels. Low thresholds of NPP were identified at both low (∼750 mm) and high precipitation (>3500 mm) levels. By combining data on the ratios of precipitation to the amount of biomass produced in a year with how much less precipitation input occurs during a drought year, it is possible to estimate whether productivity levels are sufficient to support forest growth and forest dependent communities following a drought. In this study, the ratios of annual precipitation inputs required to produce 1 Mg ha(-1) yr(-1) biomass by soil texture class varied across the three soil textural classes. By using a conservative estimate of 20% of productivity collected or harvested by people and 30% precipitation reduction level as triggering a drought, it was possible to estimate a potential loss of annual productivity due to a drought. In this study, the total NPP unavailable due to drought and harvest by forest dependent communities per year was 10.2 Mg ha(-1) yr(-1) for the sandy textured soils (64% of NPP still available), 8.4 Mg ha(-1) yr(-1) for the sandy loam textured soils (60% available) and 12.7 Mg ha(-1) yr(-1) for the clay textured soils (29% available). Forests growing on clay textured soils would be most vulnerable to drought triggered reductions in productivity so NPP levels would be inadequate to maintain ecosystem functions and would potentially cause a forest-to-savanna shift. Further, these forests would not be able to provide sufficient NPP to satisfy the requirements of forest dependent communities. By predicting the productivity responses of different tropical forest ecosystems to changes in precipitation patterns coupled with edaphic data, it could be possible to spatially identify where tropical forests are most vulnerable to climate change impacts and where mitigation efforts should be concentrated.}, } @article {pmid26551018, year = {2016}, author = {Morris, H and Plavcová, L and Cvecko, P and Fichtler, E and Gillingham, MA and Martínez-Cabrera, HI and McGlinn, DJ and Wheeler, E and Zheng, J and Ziemińska, K and Jansen, S}, title = {A global analysis of parenchyma tissue fractions in secondary xylem of seed plants.}, journal = {The New phytologist}, volume = {209}, number = {4}, pages = {1553-1565}, pmid = {26551018}, issn = {1469-8137}, mesh = {Climate ; Databases as Topic ; Magnoliopsida/growth & development/physiology ; Mesophyll Cells/cytology/*physiology ; Rain ; Seeds/*physiology ; Statistics, Nonparametric ; Temperature ; Tracheophyta/growth & development/physiology ; Trees/*physiology ; Wood/physiology ; Xylem/cytology/*physiology ; }, abstract = {Parenchyma is an important tissue in secondary xylem of seed plants, with functions ranging from storage to defence and with effects on the physical and mechanical properties of wood. Currently, we lack a large-scale quantitative analysis of ray parenchyma (RP) and axial parenchyma (AP) tissue fractions. Here, we use data from the literature on AP and RP fractions to investigate the potential relationships of climate and growth form with total ray and axial parenchyma fractions (RAP). We found a 29-fold variation in RAP fraction, which was more strongly related to temperature than with precipitation. Stem succulents had the highest RAP values (mean ± SD: 70.2 ± 22.0%), followed by lianas (50.1 ± 16.3%), angiosperm trees and shrubs (26.3 ± 12.4%), and conifers (7.6 ± 2.6%). Differences in RAP fraction between temperate and tropical angiosperm trees (21.1 ± 7.9% vs 36.2 ± 13.4%, respectively) are due to differences in the AP fraction, which is typically three times higher in tropical than in temperate trees, but not in RP fraction. Our results illustrate that both temperature and growth form are important drivers of RAP fractions. These findings should help pave the way to better understand the various functions of RAP in plants.}, } @article {pmid26548946, year = {2015}, author = {Pollonara, E and Luschi, P and Guilford, T and Wikelski, M and Bonadonna, F and Gagliardo, A}, title = {Olfaction and topography, but not magnetic cues, control navigation in a pelagic seabird: displacements with shearwaters in the Mediterranean Sea.}, journal = {Scientific reports}, volume = {5}, number = {}, pages = {16486}, pmid = {26548946}, issn = {2045-2322}, mesh = {Animals ; *Birds ; *Cues ; Geographic Information Systems ; Geography ; *Homing Behavior ; Mediterranean Sea ; *Olfactory Perception ; *Spatial Navigation ; }, abstract = {Pelagic seabirds wander the open oceans then return accurately to their habitual nest-sites. We investigated the effects of sensory manipulation on oceanic navigation in Scopoli's shearwaters (Calonectris diomedea) breeding at Pianosa island (Italy), by displacing them 400 km from their colony and tracking them. A recent experiment on Atlantic shearwaters (Cory's shearwater, Calonectris borealis) breeding in the Azores indicated a crucial role of olfaction over the open ocean, but left open the question of whether birds might navigate by topographical landmark cues when available. Our experiment was conducted in the Mediterranean sea, where the availability of topographical cues may provide an alternative navigational mechanism for homing. Magnetically disturbed shearwaters and control birds oriented homeward even when the coast was not visible and rapidly homed. Anosmic shearwaters oriented in a direction significantly different from the home direction when in open sea. After having approached a coastline their flight path changed from convoluted to homeward oriented, so that most of them eventually reached home. Beside confirming that magnetic cues appear unimportant for oceanic navigation by seabirds, our results support the crucial role of olfactory cues for birds' navigation and reveal that anosmic shearwaters are able to home eventually by following coastal features.}, } @article {pmid26546154, year = {2016}, author = {Nerva, L and Ciuffo, M and Vallino, M and Margaria, P and Varese, GC and Gnavi, G and Turina, M}, title = {Multiple approaches for the detection and characterization of viral and plasmid symbionts from a collection of marine fungi.}, journal = {Virus research}, volume = {219}, number = {}, pages = {22-38}, doi = {10.1016/j.virusres.2015.10.028}, pmid = {26546154}, issn = {1872-7492}, mesh = {*Aquatic Organisms ; Biological Products ; Computational Biology ; Fungal Viruses/classification/isolation & purification/*physiology/ultrastructure ; Fungi/isolation & purification/*physiology/*virology ; Genome, Viral ; High-Throughput Nucleotide Sequencing ; Phylogeny ; Plasmids/*genetics ; RNA, Viral ; *Symbiosis ; }, abstract = {The number of reported mycoviruses is increasing exponentially due to the current ability to detect mycoviruses using next-generation sequencing (NGS) approaches, with a large number of viral genomes built in-silico using data from fungal transcriptome projects. We decided to screen a collection of fungi originating from a specific marine environment (associated with the seagrass Posidonia oceanica) for the presence of mycoviruses: our findings reveal a wealth of diversity among these symbionts and this complexity will require further studies to address their specific role in this ecological niche. In specific, we identified twelve new virus species belonging to nine distinct lineages: they are members of megabirnavirus, totivirus, chrysovirus, partitivirus and five still undefined clades. We showed evidence of an endogenized virus ORF, and evidence of accumulation of dsRNA from metaviridae retroviral elements. We applied different techniques for detecting the presence of mycoviruses including (i) dsRNA extraction and cDNA cloning, (ii) small and total RNA sequencing through NGS techniques, (iii) rolling circle amplification (RCA) and total DNA extraction analyses, (iv) virus purifications and electron microscopy. We tried also to critically evaluate the intrinsic value and limitations of each of these techniques. Based on the samples we could compare directly, RNAseq analysis is superior to sRNA for de novo assembly of mycoviruses. To our knowledge this is the first report on the virome of fungi isolated from marine environment. The GenBank/eMBL/DDBJ accession numbers of the sequences reported in this paper are: KT601099-KT601110; KT601114-KT601120; KT592305; KT950836-KT950841.}, } @article {pmid26545922, year = {2016}, author = {Coffman, AJ and Hsieh, PH and Gravel, S and Gutenkunst, RN}, title = {Computationally Efficient Composite Likelihood Statistics for Demographic Inference.}, journal = {Molecular biology and evolution}, volume = {33}, number = {2}, pages = {591-593}, pmid = {26545922}, issn = {1537-1719}, support = {MOP-134855//Canadian Institutes of Health Research/Canada ; }, mesh = {Computational Biology/*methods ; *Demography ; Genetics, Population/*methods ; Humans ; *Likelihood Functions ; *Models, Genetic ; }, abstract = {Many population genetics tools employ composite likelihoods, because fully modeling genomic linkage is challenging. But traditional approaches to estimating parameter uncertainties and performing model selection require full likelihoods, so these tools have relied on computationally expensive maximum-likelihood estimation (MLE) on bootstrapped data. Here, we demonstrate that statistical theory can be applied to adjust composite likelihoods and perform robust computationally efficient statistical inference in two demographic inference tools: ∂a∂i and TRACTS. On both simulated and real data, the adjustments perform comparably to MLE bootstrapping while using orders of magnitude less computational time.}, } @article {pmid26545921, year = {2016}, author = {Nakagome, S and Alkorta-Aranburu, G and Amato, R and Howie, B and Peter, BM and Hudson, RR and Di Rienzo, A}, title = {Estimating the Ages of Selection Signals from Different Epochs in Human History.}, journal = {Molecular biology and evolution}, volume = {33}, number = {3}, pages = {657-669}, pmid = {26545921}, issn = {1537-1719}, support = {R01 GM101682/GM/NIGMS NIH HHS/United States ; P30 CA14599/CA/NCI NIH HHS/United States ; P30 CA014599/CA/NCI NIH HHS/United States ; R01 HL119577/HL/NHLBI NIH HHS/United States ; R01GM10168/GM/NIGMS NIH HHS/United States ; }, mesh = {Alleles ; Bayes Theorem ; Computational Biology/methods ; Computer Simulation ; Evolution, Molecular ; Gene Frequency ; Genetic Variation ; *Genetics, Population ; Humans ; *Models, Genetic ; Polymorphism, Single Nucleotide ; *Selection, Genetic ; Sequence Analysis, DNA ; }, abstract = {Genetic variation harbors signatures of natural selection driven by selective pressures that are often unknown. Estimating the ages of selection signals may allow reconstructing the history of environmental changes that shaped human phenotypes and diseases. We have developed an approximate Bayesian computation (ABC) approach to estimate allele ages under a model of selection on new mutations and under demographic models appropriate for human populations. We have applied it to two resequencing data sets: An ultra-high depth data set from a relatively small sample of unrelated individuals and a lower depth data set in a larger sample with transmission information. In addition to evaluating the accuracy of our method based on simulations, for each SNP, we assessed the consistency between the posterior probabilities estimated by the ABC approach and the ancient DNA record, finding good agreement between the two types of data and methods. Applying this ABC approach to data for eight single nucleotide polymorphisms (SNPs), we were able to rule out an onset of selection prior to the dispersal out-of-Africa for three of them and more recent than the spread of agriculture for an additional three SNPs.}, } @article {pmid26544687, year = {2015}, author = {Abe, MS and Shimada, M}, title = {Lévy Walks Suboptimal under Predation Risk.}, journal = {PLoS computational biology}, volume = {11}, number = {11}, pages = {e1004601}, pmid = {26544687}, issn = {1553-7358}, mesh = {Algorithms ; Animals ; Computational Biology ; Computer Simulation ; *Models, Biological ; Movement ; Predatory Behavior/*physiology ; Risk ; }, abstract = {A key challenge in movement ecology is to understand how animals move in nature. Previous studies have predicted that animals should perform a special class of random walks, called Lévy walk, to obtain more targets. However, some empirical studies did not support this hypothesis, and the relationship between search strategy and ecological factors is still unclear. We focused on ecological factors, such as predation risk, and analyzed whether Lévy walk may not be favored. It was remarkable that the ecological factors often altered an optimal search strategy from Lévy walk to Brownian walk, depending on the speed of the predator's movement, density of predators, etc. This occurred because higher target encounter rates simultaneously led searchers to higher predation risks. Our findings indicate that animals may not perform Lévy walks often, and we suggest that it is crucial to consider the ecological context for evaluating the search strategy performed by animals in the field.}, } @article {pmid26539210, year = {2015}, author = {Bruford, MW and Ginja, C and Hoffmann, I and Joost, S and Orozco-terWengel, P and Alberto, FJ and Amaral, AJ and Barbato, M and Biscarini, F and Colli, L and Costa, M and Curik, I and Duruz, S and Ferenčaković, M and Fischer, D and Fitak, R and Groeneveld, LF and Hall, SJ and Hanotte, O and Hassan, FU and Helsen, P and Iacolina, L and Kantanen, J and Leempoel, K and Lenstra, JA and Ajmone-Marsan, P and Masembe, C and Megens, HJ and Miele, M and Neuditschko, M and Nicolazzi, EL and Pompanon, F and Roosen, J and Sevane, N and Smetko, A and Štambuk, A and Streeter, I and Stucki, S and Supakorn, C and Telo Da Gama, L and Tixier-Boichard, M and Wegmann, D and Zhan, X}, title = {Prospects and challenges for the conservation of farm animal genomic resources, 2015-2025.}, journal = {Frontiers in genetics}, volume = {6}, number = {}, pages = {314}, pmid = {26539210}, issn = {1664-8021}, abstract = {Livestock conservation practice is changing rapidly in light of policy developments, climate change and diversifying market demands. The last decade has seen a step change in technology and analytical approaches available to define, manage and conserve Farm Animal Genomic Resources (FAnGR). However, these rapid changes pose challenges for FAnGR conservation in terms of technological continuity, analytical capacity and integrative methodologies needed to fully exploit new, multidimensional data. The final conference of the ESF Genomic Resources program aimed to address these interdisciplinary problems in an attempt to contribute to the agenda for research and policy development directions during the coming decade. By 2020, according to the Convention on Biodiversity's Aichi Target 13, signatories should ensure that "…the genetic diversity of …farmed and domesticated animals and of wild relatives …is maintained, and strategies have been developed and implemented for minimizing genetic erosion and safeguarding their genetic diversity." However, the real extent of genetic erosion is very difficult to measure using current data. Therefore, this challenging target demands better coverage, understanding and utilization of genomic and environmental data, the development of optimized ways to integrate these data with social and other sciences and policy analysis to enable more flexible, evidence-based models to underpin FAnGR conservation. At the conference, we attempted to identify the most important problems for effective livestock genomic resource conservation during the next decade. Twenty priority questions were identified that could be broadly categorized into challenges related to methodology, analytical approaches, data management and conservation. It should be acknowledged here that while the focus of our meeting was predominantly around genetics, genomics and animal science, many of the practical challenges facing conservation of genomic resources are societal in origin and are predicated on the value (e.g., socio-economic and cultural) of these resources to farmers, rural communities and society as a whole. The overall conclusion is that despite the fact that the livestock sector has been relatively well-organized in the application of genetic methodologies to date, there is still a large gap between the current state-of-the-art in the use of tools to characterize genomic resources and its application to many non-commercial and local breeds, hampering the consistent utilization of genetic and genomic data as indicators of genetic erosion and diversity. The livestock genomic sector therefore needs to make a concerted effort in the coming decade to enable to the democratization of the powerful tools that are now at its disposal, and to ensure that they are applied in the context of breed conservation as well as development.}, } @article {pmid26538599, year = {2016}, author = {Ison, J and Rapacki, K and Ménager, H and Kalaš, M and Rydza, E and Chmura, P and Anthon, C and Beard, N and Berka, K and Bolser, D and Booth, T and Bretaudeau, A and Brezovsky, J and Casadio, R and Cesareni, G and Coppens, F and Cornell, M and Cuccuru, G and Davidsen, K and Vedova, GD and Dogan, T and Doppelt-Azeroual, O and Emery, L and Gasteiger, E and Gatter, T and Goldberg, T and Grosjean, M and Grüning, B and Helmer-Citterich, M and Ienasescu, H and Ioannidis, V and Jespersen, MC and Jimenez, R and Juty, N and Juvan, P and Koch, M and Laibe, C and Li, JW and Licata, L and Mareuil, F and Mičetić, I and Friborg, RM and Moretti, S and Morris, C and Möller, S and Nenadic, A and Peterson, H and Profiti, G and Rice, P and Romano, P and Roncaglia, P and Saidi, R and Schafferhans, A and Schwämmle, V and Smith, C and Sperotto, MM and Stockinger, H and Vařeková, RS and Tosatto, SC and de la Torre, V and Uva, P and Via, A and Yachdav, G and Zambelli, F and Vriend, G and Rost, B and Parkinson, H and Løngreen, P and Brunak, S}, title = {Tools and data services registry: a community effort to document bioinformatics resources.}, journal = {Nucleic acids research}, volume = {44}, number = {D1}, pages = {D38-47}, pmid = {26538599}, issn = {1362-4962}, support = {U41 HG002273/HG/NHGRI NIH HHS/United States ; 5U41HG002273-14/HG/NHGRI NIH HHS/United States ; }, mesh = {*Computational Biology ; Data Curation ; *Registries ; Software ; }, abstract = {Life sciences are yielding huge data sets that underpin scientific discoveries fundamental to improvement in human health, agriculture and the environment. In support of these discoveries, a plethora of databases and tools are deployed, in technically complex and diverse implementations, across a spectrum of scientific disciplines. The corpus of documentation of these resources is fragmented across the Web, with much redundancy, and has lacked a common standard of information. The outcome is that scientists must often struggle to find, understand, compare and use the best resources for the task at hand.Here we present a community-driven curation effort, supported by ELIXIR-the European infrastructure for biological information-that aspires to a comprehensive and consistent registry of information about bioinformatics resources. The sustainable upkeep of this Tools and Data Services Registry is assured by a curation effort driven by and tailored to local needs, and shared amongst a network of engaged partners.As of November 2015, the registry includes 1785 resources, with depositions from 126 individual registrations including 52 institutional providers and 74 individuals. With community support, the registry can become a standard for dissemination of information about bioinformatics resources: we welcome everyone to join us in this common endeavour. The registry is freely available at https://bio.tools.}, } @article {pmid26536842, year = {2016}, author = {Furlan, EM and Gleeson, D and Hardy, CM and Duncan, RP}, title = {A framework for estimating the sensitivity of eDNA surveys.}, journal = {Molecular ecology resources}, volume = {16}, number = {3}, pages = {641-654}, doi = {10.1111/1755-0998.12483}, pmid = {26536842}, issn = {1755-0998}, mesh = {*Biota ; Computational Biology/*methods ; *Ecosystem ; Models, Statistical ; Sensitivity and Specificity ; Sequence Analysis, DNA/*methods ; }, abstract = {Imperfect sensitivity, or imperfect detection, is a feature of all survey methods that needs to be accounted for when interpreting survey results. Detection of environmental DNA (eDNA) is increasingly being used to infer species distributions, yet the sensitivity of the technique has not been fully evaluated. Sensitivity, or the probability of detecting target DNA given it is present at a site, will depend on both the survey method and the concentration and dispersion of target DNA molecules at a site. We present a model to estimate target DNA concentration and dispersion at survey sites and to estimate the sensitivity of an eDNA survey method. We fitted this model to data from a species-specific eDNA survey for Oriental weatherloach, Misgurnus anguillicaudatus, at three sites sampled in both autumn and spring. The concentration of target DNA molecules was similar at all three sites in autumn but much higher at two sites in spring. Our analysis showed the survey method had ≥95% sensitivity at sites where target DNA concentrations were ≥11 molecules per litre. We show how these data can be used to compare sampling schemes that differ in the number of field samples collected per site and number of PCR replicates per sample to achieve ≥95% sensitivity at a given target DNA concentration. These models allow researchers to quantify the sensitivity of eDNA survey methods to optimize the probability of detecting target species, and to compare DNA concentrations spatially and temporarily.}, } @article {pmid26536595, year = {2015}, author = {Bürgi, R and Tomatis, L and Murer, K and de Bruin, ED}, title = {Localization of Physical Activity in Primary School Children Using Accelerometry and Global Positioning System.}, journal = {PloS one}, volume = {10}, number = {11}, pages = {e0142223}, pmid = {26536595}, issn = {1932-6203}, mesh = {*Accelerometry ; Adolescent ; Child ; Female ; *Geographic Information Systems ; Humans ; Male ; *Motor Activity ; Switzerland ; }, abstract = {BACKGROUND: Ecological approaches have highlighted the importance of the built environment as a factor affecting physical activity. However, knowledge on children's activity patterns is still incomplete. Particularly, data on the spatial context of physical activity is limited, which limits the potential to design location-based interventions effectively. Using global positioning system (GPS) and accelerometry, this study aimed to identify locations where children engage in moderate-vigorous physical activity (MVPA).

METHODS: Participants included 119 children (11-14 years, 57% girls) from public schools in Winterthur, Switzerland. During a regular school week between February and April 2013, children wore an accelerometer and GPS sensor for seven consecutive days. Time-matched accelerometer and GPS data was mapped with a geographic information system and each data point was assigned to one of seven defined activity settings. Both the absolute amount of MVPA and proportion of time in MVPA were calculated for every setting. Multilevel analyses accounting for the hierarchical structure of the data were conducted to investigate any gender differences.

RESULTS: Children achieved most MVPA on streets (34.5%) and on school grounds (33.4%). The proportion children spent in MVPA was highest in recreational facilities (19.4%), at other schools (19.2%) and on streets (18.6%). Boys accumulated significantly more MVPA overall and on other school grounds (p < 0.05) and showed a significantly higher proportion of time in MVPA at own school and outside of Winterthur (p < 0.05).

CONCLUSIONS: The results indicate the importance of streets and school grounds as activity-promoting environments. The high use of streets may be an indicator for active transportation, which appears to contribute to an active lifestyle in both genders. In contrast, the school setting is more likely to encourage physical activity in boys. Recreational facilities seem to be conducive for MVPA among both genders, although infrequently visited during the week of measurement.}, } @article {pmid26530215, year = {2016}, author = {Enrico, L and Díaz, S and Westoby, M and Rice, BL}, title = {Leaf mechanical resistance in plant trait databases: comparing the results of two common measurement methods.}, journal = {Annals of botany}, volume = {117}, number = {1}, pages = {209-214}, pmid = {26530215}, issn = {1095-8290}, mesh = {Biomechanical Phenomena ; *Databases as Topic ; Linear Models ; Plant Leaves/*physiology ; *Quantitative Trait, Heritable ; Statistics, Nonparametric ; }, abstract = {BACKGROUND AND AIMS: The influence of leaf mechanical properties on local ecosystem processes, such as trophic transfer, decomposition and nutrient cycling, has resulted in a growing interest in including leaf mechanical resistance in large-scale databases of plant functional traits. 'Specific work to shear' and 'force to tear' are two properties commonly used to describe mechanical resistance (toughness or strength) of leaves. Two methodologies have been widely used to measure them across large datasets. This study aimed to assess correlations and standardization between the two methods, as measured by two widely used apparatuses, in order to inter-convert existing data in those global datasets.

METHODS: Specific work to shear (W(SS)) and force to tear (FT) were measured in leaves of 72 species from south-eastern Australia. The measurements were made including and excluding midribs. Relationships between the variables were tested by Spearman correlations and ordinary least square regressions.

KEY RESULTS: A positive and significant correlation was found between the methods, but coefficients varied according to the inclusion or exclusion of the midrib in the measurements. Equations for prediction varied according to leaf venation pattern. A positive and significant (r = 0·90, P < 0·0001) correlation was also found between W(SS) values for fresh and rehydrated leaves, which is considered to be of practical relevance.

CONCLUSIONS: In the context of broad-scale ecological hypotheses and used within the constraints recommended here, leaf mechanical resistance data obtained with both methodologies could be pooled together into a single coarser variable, using the equations provided in this paper. However, more detailed datasets of FT cannot be safely filled in with estimations based on W(SS), or vice versa. In addition, W(SS) values of green leaves can be predicted with good accuracy from W(SS) of rehydrated leaves of the same species.}, } @article {pmid26528407, year = {2015}, author = {Case, BS and Buckley, HL}, title = {Local-scale topoclimate effects on treeline elevations: a country-wide investigation of New Zealand's southern beech treelines.}, journal = {PeerJ}, volume = {3}, number = {}, pages = {e1334}, pmid = {26528407}, issn = {2167-8359}, abstract = {Although treeline elevations are limited globally by growing season temperature, at regional scales treelines frequently deviate below their climatic limit. The cause of these deviations relate to a host of climatic, disturbance, and geomorphic factors that operate at multiple scales. The ability to disentangle the relative effects of these factors is currently hampered by the lack of reliable topoclimatic data, which describe how regional climatic characteristics are modified by topographic effects in mountain areas. In this study we present an analysis of the combined effects of local- and regional-scale factors on southern beech treeline elevation variability at 28 study areas across New Zealand. We apply a mesoscale atmospheric model to generate local-scale (200 m) meteorological data at these treelines and, from these data, we derive a set of topoclimatic indices that reflect possible detrimental and ameliorative influences on tree physiological functioning. Principal components analysis of meteorological data revealed geographic structure in how study areas were situated in multivariate space along gradients of topoclimate. Random forest and conditional inference tree modelling enabled us to tease apart the relative effects of 17 explanatory factors on local-scale treeline elevation variability. Overall, modelling explained about 50% of the variation in treeline elevation variability across the 28 study areas, with local landform and topoclimatic effects generally outweighing those from regional-scale factors across the 28 study areas. Further, the nature of the relationships between treeline elevation variability and the explanatory variables were complex, frequently non-linear, and consistent with the treeline literature. To our knowledge, this is the first study where model-generated meteorological data, and derived topoclimatic indices, have been developed and applied to explain treeline variation. Our results demonstrate the potential of such an approach for ecological research in mountainous environments.}, } @article {pmid26527720, year = {2016}, author = {Moretti, S and Martin, O and Van Du Tran, T and Bridge, A and Morgat, A and Pagni, M}, title = {MetaNetX/MNXref--reconciliation of metabolites and biochemical reactions to bring together genome-scale metabolic networks.}, journal = {Nucleic acids research}, volume = {44}, number = {D1}, pages = {D523-6}, pmid = {26527720}, issn = {1362-4962}, mesh = {*Databases, Chemical ; *Genome ; Metabolic Networks and Pathways/*genetics ; Molecular Structure ; Software ; }, abstract = {MetaNetX is a repository of genome-scale metabolic networks (GSMNs) and biochemical pathways from a number of major resources imported into a common namespace of chemical compounds, reactions, cellular compartments--namely MNXref--and proteins. The MetaNetX.org website (http://www.metanetx.org/) provides access to these integrated data as well as a variety of tools that allow users to import their own GSMNs, map them to the MNXref reconciliation, and manipulate, compare, analyze, simulate (using flux balance analysis) and export the resulting GSMNs. MNXref and MetaNetX are regularly updated and freely available.}, } @article {pmid26527718, year = {2015}, author = {Wong, KC and Li, Y and Peng, C and Moses, AM and Zhang, Z}, title = {Computational learning on specificity-determining residue-nucleotide interactions.}, journal = {Nucleic acids research}, volume = {43}, number = {21}, pages = {10180-10189}, pmid = {26527718}, issn = {1362-4962}, mesh = {Binding Sites ; Computational Biology/methods ; DNA/*chemistry/metabolism ; DNA-Binding Proteins/*chemistry/metabolism ; Humans ; Machine Learning ; Models, Molecular ; Nucleotide Motifs ; Position-Specific Scoring Matrices ; Protein Binding ; Protein Structure, Tertiary ; Sequence Analysis, DNA ; Sequence Analysis, Protein/*methods ; }, abstract = {The protein-DNA interactions between transcription factors and transcription factor binding sites are essential activities in gene regulation. To decipher the binding codes, it is a long-standing challenge to understand the binding mechanism across different transcription factor DNA binding families. Past computational learning studies usually focus on learning and predicting the DNA binding residues on protein side. Taking into account both sides (protein and DNA), we propose and describe a computational study for learning the specificity-determining residue-nucleotide interactions of different known DNA-binding domain families. The proposed learning models are compared to state-of-the-art models comprehensively, demonstrating its competitive learning performance. In addition, we describe and propose two applications which demonstrate how the learnt models can provide meaningful insights into protein-DNA interactions across different DNA binding families.}, } @article {pmid26527343, year = {2016}, author = {Hou, K and Li, X and Wang, JJ and Zhang, J}, title = {An analysis of the impact on land use and ecological vulnerability of the policy of returning farmland to forest in Yan'an, China.}, journal = {Environmental science and pollution research international}, volume = {23}, number = {5}, pages = {4670-4680}, pmid = {26527343}, issn = {1614-7499}, mesh = {*Agriculture ; China ; Ecosystem ; Environmental Restoration and Remediation ; *Forests ; Geographic Information Systems ; Principal Component Analysis ; Public Policy ; }, abstract = {During the past decades, land use change has taken place around the Loess Plateau at unprecedented rates. Due to the impact of existing land use policy, great changes have taken place in the land use types in this ecologically vulnerable area. Taking eight counties in Yan'an, Shaanxi province, China, as the study area, this study analyzed the long-term (from 1997 to 2011) changes in land use and ecological vulnerability. Based on thematic mapper (TM) images of Yan'an in 1997, 2004, and 2011, the dynamic changes in land use are analyzed with the application software for remote sensing (RS) and geographic information system (GIS) since the implementation of the policy of returning farmland to forest. Combined with the land use data, the local socio-economic data, and natural resources condition, ecological vulnerability is evaluated using the spatial principal component analysis (SPCA) model in Yan'an region. Using the natural breaks classification (NBC), the evaluation results are divided into five categories: potential, slight, light, medium, and heavy. The results show that although the regional land use types changed markedly, the ecological vulnerability in the study shows greater than average optimism, and the ecological vulnerability index of the southern four counties is lower than that of the northern four counties. In 1997-2011, the eco-environmental quality gradually improved in most areas. However, it gradually deteriorated in some regions.}, } @article {pmid26522937, year = {2016}, author = {Zomorrodi, AR and Segrè, D}, title = {Synthetic Ecology of Microbes: Mathematical Models and Applications.}, journal = {Journal of molecular biology}, volume = {428}, number = {5 Pt B}, pages = {837-861}, pmid = {26522937}, issn = {1089-8638}, support = {R01 DE024468/DE/NIDCR NIH HHS/United States ; R01 GM121950/GM/NIGMS NIH HHS/United States ; 5R01GM103502/GM/NIGMS NIH HHS/United States ; R01 GM103502/GM/NIGMS NIH HHS/United States ; 5R01GM089978/GM/NIGMS NIH HHS/United States ; 5R01DE024468/DE/NIDCR NIH HHS/United States ; R01 GM089978/GM/NIGMS NIH HHS/United States ; }, mesh = {Computational Biology/methods ; *Ecosystem ; *Microbial Consortia ; *Models, Theoretical ; }, abstract = {As the indispensable role of natural microbial communities in many aspects of life on Earth is uncovered, the bottom-up engineering of synthetic microbial consortia with novel functions is becoming an attractive alternative to engineering single-species systems. Here, we summarize recent work on synthetic microbial communities with a particular emphasis on open challenges and opportunities in environmental sustainability and human health. We next provide a critical overview of mathematical approaches, ranging from phenomenological to mechanistic, to decipher the principles that govern the function, dynamics and evolution of microbial ecosystems. Finally, we present our outlook on key aspects of microbial ecosystems and synthetic ecology that require further developments, including the need for more efficient computational algorithms, a better integration of empirical methods and model-driven analysis, the importance of improving gene function annotation, and the value of a standardized library of well-characterized organisms to be used as building blocks of synthetic communities.}, } @article {pmid26522790, year = {2015}, author = {Tonk, M and Knorr, E and Cabezas-Cruz, A and Valdés, JJ and Kollewe, C and Vilcinskas, A}, title = {Tribolium castaneum defensins are primarily active against Gram-positive bacteria.}, journal = {Journal of invertebrate pathology}, volume = {132}, number = {}, pages = {208-215}, doi = {10.1016/j.jip.2015.10.009}, pmid = {26522790}, issn = {1096-0805}, mesh = {Animals ; Computational Biology ; Defensins/*physiology ; Gene Expression Regulation ; Gram-Positive Bacteria/*immunology ; Immunity, Innate ; Insect Proteins/*physiology ; Phylogeny ; Tribolium/*immunology ; }, abstract = {The red flour beetle Tribolium castaneum is a destructive insect pest of stored food and feed products, and a model organism for development, evolutionary biology and immunity. The insect innate immune system includes antimicrobial peptides (AMPs) with a wide spectrum of targets including viruses, bacteria, fungi and parasites. Defensins are an evolutionarily-conserved class of AMPs and a potential new source of antimicrobial agents. In this context, we report the antimicrobial activity, phylogenetic and structural properties of three T. castaneum defensins (Def1, Def2 and Def3) and their relevance in the immunity of T. castaneum against bacterial pathogens. All three recombinant defensins showed bactericidal activity against Micrococcus luteus and Bacillus thuringiensis serovar tolworthi, but only Def1 and Def2 showed a bacteriostatic effect against Staphylococcus epidermidis. None of the defensins showed activity against the Gram-negative bacteria Escherichia coli and Pseudomonas entomophila or against the yeast Saccharomyces cerevisiae. All three defensins were transcriptionally upregulated following a bacterial challenge, suggesting a key role in the immunity of T. castaneum against bacterial pathogens. Phylogenetic analysis showed that defensins from T. castaneum, mealworms, Udo longhorn beetle and houseflies cluster within a well-defined clade of insect defensins. We conclude that T. castaneum defensins are primarily active against Gram-positive bacteria and that other AMPs may play a more prominent role against Gram-negative species.}, } @article {pmid26522658, year = {2016}, author = {Chan, Z and Wang, Y and Cao, M and Gong, Y and Mu, Z and Wang, H and Hu, Y and Deng, X and He, XJ and Zhu, JK}, title = {RDM4 modulates cold stress resistance in Arabidopsis partially through the CBF-mediated pathway.}, journal = {The New phytologist}, volume = {209}, number = {4}, pages = {1527-1539}, pmid = {26522658}, issn = {1469-8137}, support = {R01 GM059138/GM/NIGMS NIH HHS/United States ; R01 GM070795/GM/NIGMS NIH HHS/United States ; R01GM059138/GM/NIGMS NIH HHS/United States ; }, mesh = {Arabidopsis/genetics/*physiology ; Arabidopsis Proteins/genetics/*metabolism ; Cell Membrane/metabolism ; *Cold Temperature ; Electrolytes/metabolism ; Freezing ; Gene Expression Profiling ; Gene Expression Regulation, Plant ; Gene Ontology ; Genes, Plant ; Mutation/genetics ; Oxidative Stress/genetics ; Plant Leaves/physiology ; Promoter Regions, Genetic/genetics ; Protein Binding ; RNA Polymerase II/metabolism ; Reactive Oxygen Species/metabolism ; Seedlings/metabolism ; *Stress, Physiological/genetics ; Trans-Activators/genetics/*metabolism ; Transcription Factors/genetics/*metabolism ; }, abstract = {The C-REPEAT-BINDING FACTOR (CBF) pathway has important roles in plant responses to cold stress. How the CBF genes themselves are activated after cold acclimation remains poorly understood. In this study, we characterized cold tolerance of null mutant of RNA-DIRECTED DNA METHYLATION 4 (RDM4), which encodes a protein that associates with RNA polymerases Pol V and Pol II, and is required for RNA-directed DNA methylation (RdDM) in Arabidopsis. The results showed that dysfunction of RDM4 reduced cold tolerance, as evidenced by decreased survival and increased electrolyte leakage. Mutation of RDM4 resulted in extensive transcriptomic reprogramming. CBFs and CBF regulon genes were down-regulated in rdm4 but not nrpe1 (the largest subunit of PolV) mutants, suggesting that the role of RDM4 in cold stress responses is independent of the RdDM pathway. Overexpression of RDM4 constitutively increased the expression of CBFs and regulon genes and decreased cold-induced membrane injury. A great proportion of genes affected by rdm4 overlapped with those affected by CBFs. Chromatin immunoprecipitation results suggested that RDM4 is important for Pol II occupancy at the promoters of CBF2 and CBF3. We present evidence of a considerable role for RDM4 in regulating gene expression at low temperature, including the CBF pathway in Arabidopsis.}, } @article {pmid26519912, year = {2016}, author = {Santos, J and Al-Azzawi, M and Aronson, J and Flowers, TJ}, title = {eHALOPH a Database of Salt-Tolerant Plants: Helping put Halophytes to Work.}, journal = {Plant & cell physiology}, volume = {57}, number = {1}, pages = {e10}, doi = {10.1093/pcp/pcv155}, pmid = {26519912}, issn = {1471-9053}, mesh = {Antioxidants/metabolism ; *Databases, Genetic ; Salinity ; Salt Tolerance ; Salt-Tolerant Plants/*genetics/physiology ; Sodium Chloride/metabolism ; }, abstract = {eHALOPH (http://www.sussex.ac.uk/affiliates/halophytes/) is a database of salt-tolerant plants-halophytes. Records of plant species tolerant of salt concentrations of around 80 mM sodium chloride or more have been collected, along with data on plant type, life form, ecotypes, maximum salinity tolerated, the presence or absence of salt glands, photosynthetic pathway, antioxidants, secondary metabolites, compatible solutes, habitat, economic use and whether there are publications on germination, microbial interactions and mycorrhizal status, bioremediation and of molecular data. The database eHALOPH can be used in the analysis of traits associated with tolerance and for informing choice of species that might be used for saline agriculture, bioremediation or ecological restoration and rehabilitation of degraded wetlands or other areas.}, } @article {pmid26519097, year = {2016}, author = {Coco, MI and Keller, F and Malcolm, GL}, title = {Anticipation in Real-World Scenes: The Role of Visual Context and Visual Memory.}, journal = {Cognitive science}, volume = {40}, number = {8}, pages = {1995-2024}, doi = {10.1111/cogs.12313}, pmid = {26519097}, issn = {1551-6709}, mesh = {Adult ; Attention/*physiology ; Eye Movements/physiology ; Female ; Humans ; Male ; Memory/*physiology ; Photic Stimulation ; Visual Perception/*physiology ; Young Adult ; }, abstract = {The human sentence processor is able to make rapid predictions about upcoming linguistic input. For example, upon hearing the verb eat, anticipatory eye-movements are launched toward edible objects in a visual scene (Altmann & Kamide, 1999). However, the cognitive mechanisms that underlie anticipation remain to be elucidated in ecologically valid contexts. Previous research has, in fact, mainly used clip-art scenes and object arrays, raising the possibility that anticipatory eye-movements are limited to displays containing a small number of objects in a visually impoverished context. In Experiment 1, we confirm that anticipation effects occur in real-world scenes and investigate the mechanisms that underlie such anticipation. In particular, we demonstrate that real-world scenes provide contextual information that anticipation can draw on: When the target object is not present in the scene, participants infer and fixate regions that are contextually appropriate (e.g., a table upon hearing eat). Experiment 2 investigates whether such contextual inference requires the co-presence of the scene, or whether memory representations can be utilized instead. The same real-world scenes as in Experiment 1 are presented to participants, but the scene disappears before the sentence is heard. We find that anticipation occurs even when the screen is blank, including when contextual inference is required. We conclude that anticipatory language processing is able to draw upon global scene representations (such as scene type) to make contextual inferences. These findings are compatible with theories assuming contextual guidance, but posit a challenge for theories assuming object-based visual indices.}, } @article {pmid26518717, year = {2016}, author = {Mineta, K and Gojobori, T}, title = {Databases of the marine metagenomics.}, journal = {Gene}, volume = {576}, number = {2 Pt 1}, pages = {724-728}, doi = {10.1016/j.gene.2015.10.035}, pmid = {26518717}, issn = {1879-0038}, mesh = {*Databases, Genetic ; *Marine Biology ; *Metagenomics ; }, abstract = {The metagenomic data obtained from marine environments is significantly useful for understanding marine microbial communities. In comparison with the conventional amplicon-based approach of metagenomics, the recent shotgun sequencing-based approach has become a powerful tool that provides an efficient way of grasping a diversity of the entire microbial community at a sampling point in the sea. However, this approach accelerates accumulation of the metagenome data as well as increase of data complexity. Moreover, when metagenomic approach is used for monitoring a time change of marine environments at multiple locations of the seawater, accumulation of metagenomics data will become tremendous with an enormous speed. Because this kind of situation has started becoming of reality at many marine research institutions and stations all over the world, it looks obvious that the data management and analysis will be confronted by the so-called Big Data issues such as how the database can be constructed in an efficient way and how useful knowledge should be extracted from a vast amount of the data. In this review, we summarize the outline of all the major databases of marine metagenome that are currently publically available, noting that database exclusively on marine metagenome is none but the number of metagenome databases including marine metagenome data are six, unexpectedly still small. We also extend our explanation to the databases, as reference database we call, that will be useful for constructing a marine metagenome database as well as complementing important information with the database. Then, we would point out a number of challenges to be conquered in constructing the marine metagenome database.}, } @article {pmid26518484, year = {2016}, author = {Chen, X and Yang, JR and Zhang, J}, title = {Nascent RNA folding mitigates transcription-associated mutagenesis.}, journal = {Genome research}, volume = {26}, number = {1}, pages = {50-59}, pmid = {26518484}, issn = {1549-5469}, support = {R01 GM103232/GM/NIGMS NIH HHS/United States ; R01GM103232/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acid Transport Systems, Basic/genetics/metabolism ; Computational Biology ; DNA, Fungal/genetics ; Databases, Genetic ; *Gene Expression Regulation, Fungal ; Genome-Wide Association Study ; Humans ; *Mutagenesis ; Mutation ; Polymorphism, Single Nucleotide ; *RNA Folding ; Ribonuclease H/genetics/metabolism ; Saccharomyces cerevisiae/genetics ; Saccharomyces cerevisiae Proteins/genetics/metabolism ; Sequence Analysis, DNA ; *Transcription, Genetic ; Transcriptome ; }, abstract = {Transcription is mutagenic, in part because the R-loop formed by the binding of the nascent RNA with its DNA template exposes the nontemplate DNA strand to mutagens and primes unscheduled error-prone DNA synthesis. We hypothesize that strong folding of nascent RNA weakens R-loops and hence decreases mutagenesis. By a yeast forward mutation assay, we show that strengthening RNA folding and reducing R-loop formation by synonymous changes in a reporter gene can lower mutation rate by >80%. This effect is diminished after the overexpression of the gene encoding RNase H1 that degrades the RNA in a DNA-RNA hybrid, indicating that the effect is R-loop-dependent. Analysis of genomic data of yeast mutation accumulation lines and human neutral polymorphisms confirms the generality of these findings. This mechanism for local protection of genome integrity is of special importance to highly expressed genes because of their frequent transcription and strong RNA folding, the latter also improves translational fidelity. As a result, strengthening RNA folding simultaneously curtails genotypic and phenotypic mutations.}, } @article {pmid26518480, year = {2016}, author = {Keith, N and Tucker, AE and Jackson, CE and Sung, W and Lucas Lledó, JI and Schrider, DR and Schaack, S and Dudycha, JL and Ackerman, M and Younge, AJ and Shaw, JR and Lynch, M}, title = {High mutational rates of large-scale duplication and deletion in Daphnia pulex.}, journal = {Genome research}, volume = {26}, number = {1}, pages = {60-69}, pmid = {26518480}, issn = {1549-5469}, support = {R01GM036827/GM/NIGMS NIH HHS/United States ; R01 GM101672/GM/NIGMS NIH HHS/United States ; R01ES019324/ES/NIEHS NIH HHS/United States ; R01 GM036827/GM/NIGMS NIH HHS/United States ; R01GM101672-01A1/GM/NIGMS NIH HHS/United States ; R01 ES019324/ES/NIEHS NIH HHS/United States ; }, mesh = {Animals ; DNA Copy Number Variations ; Daphnia/*genetics ; Evolution, Molecular ; Female ; *Gene Deletion ; *Gene Duplication ; Genetic Association Studies ; Genetic Variation ; Heterozygote ; Male ; *Mutation Rate ; Sequence Analysis, DNA ; }, abstract = {Knowledge of the genome-wide rate and spectrum of mutations is necessary to understand the origin of disease and the genetic variation driving all evolutionary processes. Here, we provide a genome-wide analysis of the rate and spectrum of mutations obtained in two Daphnia pulex genotypes via separate mutation-accumulation (MA) experiments. Unlike most MA studies that utilize haploid, homozygous, or self-fertilizing lines, D. pulex can be propagated ameiotically while maintaining a naturally heterozygous, diploid genome, allowing the capture of the full spectrum of genomic changes that arise in a heterozygous state. While base-substitution mutation rates are similar to those in other multicellular eukaryotes (about 4 × 10(-9) per site per generation), we find that the rates of large-scale (>100 kb) de novo copy-number variants (CNVs) are significantly elevated relative to those seen in previous MA studies. The heterozygosity maintained in this experiment allowed for estimates of gene-conversion processes. While most of the conversion tract lengths we report are similar to those generated by meiotic processes, we also find larger tract lengths that are indicative of mitotic processes. Comparison of MA lines to natural isolates reveals that a majority of large-scale CNVs in natural populations are removed by purifying selection. The mutations observed here share similarities with disease-causing, complex, large-scale CNVs, thereby demonstrating that MA studies in D. pulex serve as a system for studying the processes leading to such alterations.}, } @article {pmid26517698, year = {2016}, author = {Llewellyn, MS and McGinnity, P and Dionne, M and Letourneau, J and Thonier, F and Carvalho, GR and Creer, S and Derome, N}, title = {The biogeography of the atlantic salmon (Salmo salar) gut microbiome.}, journal = {The ISME journal}, volume = {10}, number = {5}, pages = {1280-1284}, pmid = {26517698}, issn = {1751-7370}, mesh = {Animals ; Biodiversity ; Computational Biology ; Environment ; Fresh Water ; *Gastrointestinal Microbiome ; Geography ; Intestines/*microbiology ; Life Cycle Stages ; Microbiota ; Salmo salar/*microbiology ; }, abstract = {Although understood in many vertebrate systems, the natural diversity of host-associated microbiota has been little studied in teleosts. For migratory fishes, successful exploitation of multiple habitats may affect and be affected by the composition of the intestinal microbiome. We collected 96 Salmo salar from across the Atlantic encompassing both freshwater and marine phases. Dramatic differences between environmental and gut bacterial communities were observed. Furthermore, community composition was not significantly impacted by geography. Instead life-cycle stage strongly defined both the diversity and identity of microbial assemblages in the gut, with evidence for community destabilisation in migratory phases. Mycoplasmataceae phylotypes were abundantly recovered in all life-cycle stages. Patterns of Mycoplasmataceae phylotype recruitment to the intestinal microbial community among sites and life-cycle stages support a dual role for deterministic and stochastic processes in defining the composition of the S. salar gut microbiome.}, } @article {pmid26516872, year = {2015}, author = {Oomen, AG and Bleeker, EA and Bos, PM and van Broekhuizen, F and Gottardo, S and Groenewold, M and Hristozov, D and Hund-Rinke, K and Irfan, MA and Marcomini, A and Peijnenburg, WJ and Rasmussen, K and Jiménez, AS and Scott-Fordsmand, JJ and van Tongeren, M and Wiench, K and Wohlleben, W and Landsiedel, R}, title = {Grouping and Read-Across Approaches for Risk Assessment of Nanomaterials.}, journal = {International journal of environmental research and public health}, volume = {12}, number = {10}, pages = {13415-13434}, pmid = {26516872}, issn = {1660-4601}, mesh = {Environment ; Humans ; Nanostructures/*toxicity ; Risk Assessment/methods ; Safety ; }, abstract = {Physicochemical properties of chemicals affect their exposure, toxicokinetics/fate and hazard, and for nanomaterials, the variation of these properties results in a wide variety of materials with potentially different risks. To limit the amount of testing for risk assessment, the information gathering process for nanomaterials needs to be efficient. At the same time, sufficient information to assess the safety of human health and the environment should be available for each nanomaterial. Grouping and read-across approaches can be utilised to meet these goals. This article presents different possible applications of grouping and read-across for nanomaterials within the broader perspective of the MARINA Risk Assessment Strategy (RAS), as developed in the EU FP7 project MARINA. Firstly, nanomaterials can be grouped based on limited variation in physicochemical properties to subsequently design an efficient testing strategy that covers the entire group. Secondly, knowledge about exposure, toxicokinetics/fate or hazard, for example via properties such as dissolution rate, aspect ratio, chemical (non-)activity, can be used to organise similar materials in generic groups to frame issues that need further attention, or potentially to read-across. Thirdly, when data related to specific endpoints is required, read-across can be considered, using data from a source material for the target nanomaterial. Read-across could be based on a scientifically sound justification that exposure, distribution to the target (fate/toxicokinetics) and hazard of the target material are similar to, or less than, the source material. These grouping and read-across approaches pave the way for better use of available information on nanomaterials and are flexible enough to allow future adaptations related to scientific developments.}, } @article {pmid26516623, year = {2015}, author = {Hashim, S and Yuebo, X and Saifullah, M and Nabi Jan, R and Muhetaer, A}, title = {Integrated Evaluation of Urban Water Bodies for Pollution Abatement Based on Fuzzy Multicriteria Decision Approach.}, journal = {BioMed research international}, volume = {2015}, number = {}, pages = {327280}, pmid = {26516623}, issn = {2314-6141}, mesh = {Ammonia/analysis ; Biological Oxygen Demand Analysis ; China ; Decision Making ; Decision Support Techniques ; Ecology/*methods ; Environmental Monitoring/*methods ; Fresh Water/analysis ; Fuzzy Logic ; Nitrogen/analysis ; Oxygen/chemistry ; Phosphorus/analysis ; *Rivers ; Temperature ; Urban Population ; Water Pollutants, Chemical/analysis ; Water Pollution/*analysis ; Water Quality ; }, abstract = {Today's ecology is erected with miscellaneous framework. However, numerous sources deteriorate it, such as urban rivers that directly cause the environmental pollution. For chemical pollution abatement from urban water bodies, many techniques were introduced to rehabilitate the water quality of these water bodies. In this research, Bacterial Technology (BT) was applied to urban rivers escalating the necessity to control the water pollution in different places (Xuxi River (XXU); Gankeng River (GKS); Xia Zhang River (XZY); Fenghu and Song Yang Rivers (FSR); Jiu Haogang River (JHH)) in China. For data analysis, the physiochemical parameters such as temperature, chemical oxygen demand (COD), dissolved oxygen (DO), total phosphorus (TP), and ammonia nitrogen (NH3N) were determined before and after the treatment. Multicriteria Decision Making (MCDM) method was used for relative significance of different water quality on each station, based on fuzzy analytical hierarchy process (FAHP). The overall results revealed that the pollution is exceeding at "JHH" due to the limit of "COD" as critical water quality parameter and after treatment, an abrupt recovery of the rivers compared with the average improved efficiency of nutrients was 79%, 74%, 68%, and 70% of COD, DO, TP, and NH3N, respectively. The color of the river's water changed to its original form and aquatic living organism appeared with clear effluents from them.}, } @article {pmid26514870, year = {2015}, author = {Jordán, F and Lauria, M and Scotti, M and Nguyen, TP and Praveen, P and Morine, M and Priami, C}, title = {Diversity of key players in the microbial ecosystems of the human body.}, journal = {Scientific reports}, volume = {5}, number = {}, pages = {15920}, pmid = {26514870}, issn = {2045-2322}, mesh = {Bacteria/*isolation & purification ; Databases, Factual ; Feces/microbiology ; Female ; Gastrointestinal Tract/*microbiology ; Genitalia, Female/*microbiology ; Human Body ; Humans ; Male ; Microbiota ; Models, Theoretical ; }, abstract = {Coexisting bacteria form various microbial communities in human body parts. In these ecosystems they interact in various ways and the properties of the interaction network can be related to the stability and functional diversity of the local bacterial community. In this study, we analyze the interaction network among bacterial OTUs in 11 locations of the human body. These belong to two major groups. One is the digestive system and the other is the female genital tract. In each local ecosystem we determine the key species, both the ones being in key positions in the interaction network and the ones that dominate by frequency. Beyond identifying the key players and discussing their biological relevance, we also quantify and compare the properties of the 11 networks. The interaction networks of the female genital system and the digestive system show totally different architecture. Both the topological properties and the identity of the key groups differ. Key groups represent four phyla of prokaryotes. Some groups appear in key positions in several locations, while others are assigned only to a single body part. The key groups of the digestive and the genital tracts are totally different.}, } @article {pmid26513661, year = {2015}, author = {Halleran, A and Clamons, S and Saha, M}, title = {Transcriptomic Characterization of an Infection of Mycobacterium smegmatis by the Cluster A4 Mycobacteriophage Kampy.}, journal = {PloS one}, volume = {10}, number = {10}, pages = {e0141100}, pmid = {26513661}, issn = {1932-6203}, support = {R15 HD077624/HD/NICHD NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; 1R15HD077624-01/HD/NICHD NIH HHS/United States ; }, mesh = {Computational Biology ; Gene Expression Profiling ; *Gene Expression Regulation, Viral ; Genes, Viral ; Mycobacteriophages/*genetics ; Mycobacterium smegmatis/*virology ; Open Reading Frames ; Transcription, Genetic ; *Transcriptome ; Virus Latency/genetics ; }, abstract = {The mycobacteriophages, phages that infect the genus Mycobacterium, display profound genetic diversity and widespread geographical distribution, and possess significant medical and ecological importance. However, most of the majority of functions of mycobacteriophage proteins and the identity of most genetic regulatory elements remain unknown. We characterized the gene expression profile of Kampy, a cluster A4 mycobacteriophage, during infection of its host, Mycobacterium smegmatis, using RNA-Seq and mass spectrometry. We show that mycobacteriophage Kampy transcription occurs in roughly two phases, an early phase consisting of genes for metabolism, DNA synthesis, and gene regulation, and a late phase consisting of structural genes and lysis genes. Additionally, we identify the earliest genes transcribed during infection, along with several other possible regulatory units not obvious from inspection of Kampy's genomic structure. The transcriptional profile of Kampy appears similar to that of mycobacteriophage TM4 but unlike that of mycobacteriophage Giles, a result which further expands our understanding of the diversity of mycobacteriophage gene expression programs during infection.}, } @article {pmid26511852, year = {2015}, author = {Zhu, H and Ren, X and Jin, Y and Yang, K and Che, Y}, title = {Multilevel analysis of a riverscape under rapid urbanization in the Yangtze delta plain, China: 1965-2006.}, journal = {Environmental monitoring and assessment}, volume = {187}, number = {11}, pages = {711}, pmid = {26511852}, issn = {1573-2959}, mesh = {China ; Ecology ; Environmental Monitoring/*methods ; Geographic Information Systems ; Models, Theoretical ; Multilevel Analysis ; Rivers/*chemistry ; *Urbanization ; }, abstract = {River networks are the typical hydrological characteristic of the Yangtze delta plain. They have important ecological service functions and a unique landscape, which has been significantly degraded during the past 50 years. Qingpu District in Shanghai has been used as study area to develop an integrated method for riverscape assessment in floodplain areas with a dense river network. This integrated method bridges geomorgraphy, landscape, and regional planning. Indicators of sinuosity, connectivity, and circuitry have been integrated into a three-level framework, including river, intersection, and river network level. Furthermore, this method was integrated by the geographic information system method and stepwise regression to identify the riverscape response to the changes in the use of the land. The spatial and temporal changes of the riverscape and land use were calculated for each grid (3000 m×3000 m) from 1965 to 2006. The results indicated that the riverscape had been significantly degraded during the study period in terms of sinuosity, connectivity, and circuitry reducing. The land use changed significantly with more building areas and less water regions and agricultural land. Additionally, the regression results indicated that several specific land use conversion types had had strong effects on the change in the riverscape structure. Finally, according to the assessing method, we have proposed specific planning and management recommendations based on the pressure-state-response model to protect the riverscape from the impact of rapid urbanization.}, } @article {pmid26510185, year = {2015}, author = {Ying, S and Zeng, DN and Chi, L and Tan, Y and Galzote, C and Cardona, C and Lax, S and Gilbert, J and Quan, ZX}, title = {The Influence of Age and Gender on Skin-Associated Microbial Communities in Urban and Rural Human Populations.}, journal = {PloS one}, volume = {10}, number = {10}, pages = {e0141842}, pmid = {26510185}, issn = {1932-6203}, mesh = {Adolescent ; Adult ; Age Factors ; Bacteria/classification/genetics ; Biodiversity ; Child ; Cluster Analysis ; Computational Biology ; Female ; Humans ; Male ; Metagenome ; *Microbiota ; Middle Aged ; Public Health Surveillance ; *Rural Population ; Sex Factors ; Skin/*microbiology ; *Urban Population ; Young Adult ; }, abstract = {Differences in the bacterial community structure associated with 7 skin sites in 71 healthy people over five days showed significant correlations with age, gender, physical skin parameters, and whether participants lived in urban or rural locations in the same city. While body site explained the majority of the variance in bacterial community structure, the composition of the skin-associated bacterial communities were predominantly influenced by whether the participants were living in an urban or rural environment, with a significantly greater relative abundance of Trabulsiella in urban populations. Adults maintained greater overall microbial diversity than adolescents or the elderly, while the intragroup variation among the elderly and rural populations was significantly greater. Skin-associated bacterial community structure and composition could predict whether a sample came from an urban or a rural resident ~5x greater than random.}, } @article {pmid26509157, year = {2015}, author = {Munguia-Fragozo, P and Alatorre-Jacome, O and Rico-Garcia, E and Torres-Pacheco, I and Cruz-Hernandez, A and Ocampo-Velazquez, RV and Garcia-Trejo, JF and Guevara-Gonzalez, RG}, title = {Perspective for Aquaponic Systems: "Omic" Technologies for Microbial Community Analysis.}, journal = {BioMed research international}, volume = {2015}, number = {}, pages = {480386}, pmid = {26509157}, issn = {2314-6141}, mesh = {Animals ; Aquaculture ; Bacteria/*genetics ; Computational Biology ; Hydroponics ; Metabolomics/methods ; *Metagenomics ; Proteomics/methods ; RNA, Ribosomal, 16S/genetics ; Water ; *Water Microbiology ; }, abstract = {Aquaponics is the combined production of aquaculture and hydroponics, connected by a water recirculation system. In this productive system, the microbial community is responsible for carrying out the nutrient dynamics between the components. The nutrimental transformations mainly consist in the transformation of chemical species from toxic compounds into available nutrients. In this particular field, the microbial research, the "Omic" technologies will allow a broader scope of studies about a current microbial profile inside aquaponics community, even in those species that currently are unculturable. This approach can also be useful to understand complex interactions of living components in the system. Until now, the analog studies were made to set up the microbial characterization on recirculation aquaculture systems (RAS). However, microbial community composition of aquaponics is still unknown. "Omic" technologies like metagenomic can help to reveal taxonomic diversity. The perspectives are also to begin the first attempts to sketch the functional diversity inside aquaponic systems and its ecological relationships. The knowledge of the emergent properties inside the microbial community, as well as the understanding of the biosynthesis pathways, can derive in future biotechnological applications. Thus, the aim of this review is to show potential applications of current "Omic" tools to characterize the microbial community in aquaponic systems.}, } @article {pmid26508349, year = {2015}, author = {Newey, S and Davidson, P and Nazir, S and Fairhurst, G and Verdicchio, F and Irvine, RJ and van der Wal, R}, title = {Limitations of recreational camera traps for wildlife management and conservation research: a practitioner's perspective.}, journal = {Ambio}, volume = {44 Suppl 4}, number = {Suppl 4}, pages = {624-635}, pmid = {26508349}, issn = {1654-7209}, mesh = {Animals ; *Animals, Wild ; Conservation of Natural Resources/*methods ; Data Collection/*methods ; Inventions ; Photography/*methods ; Recreation ; }, abstract = {The availability of affordable 'recreational' camera traps has dramatically increased over the last decade. We present survey results which show that many conservation practitioners use cheaper 'recreational' units for research rather than more expensive 'professional' equipment. We present our perspective of using two popular models of 'recreational' camera trap for ecological field-based studies. The models used (for >2 years) presented us with a range of practical problems at all stages of their use including deployment, operation, and data management, which collectively crippled data collection and limited opportunities for quantification of key issues arising. Our experiences demonstrate that prospective users need to have a sufficient understanding of the limitations camera trap technology poses, dimensions we communicate here. While the merits of different camera traps will be study specific, the performance of more expensive 'professional' models may prove more cost-effective in the long-term when using camera traps for research.}, } @article {pmid26505988, year = {2016}, author = {Lin, Y and Chen, Y and Xiong, W and Zhan, A}, title = {Genomewide gene-associated microsatellite markers for the model invasive ascidian, Ciona intestinalis species complex.}, journal = {Molecular ecology resources}, volume = {16}, number = {3}, pages = {784-793}, doi = {10.1111/1755-0998.12481}, pmid = {26505988}, issn = {1755-0998}, mesh = {Adaptation, Biological ; Animals ; Ciona intestinalis/*classification/*genetics ; Computational Biology ; Expressed Sequence Tags ; *Genetic Variation ; Genetics, Population ; *Genome ; *Microsatellite Repeats ; South Africa ; Spain ; }, abstract = {The vase tunicate, Ciona intestinalis species complex, has become a good model for ecological and evolutionary studies, especially those focusing on microevolution associated with rapidly changing environments. However, genomewide genetic markers are still lacking. Here, we characterized a large set of genomewide gene-associated microsatellite markers for C. intestinalis spA (=C. robusta). Bioinformatic analysis identified 4654 microsatellites from expressed sequence tags (ESTs), 2126 of which successfully assigned to chromosomes were selected for further analysis. Based on the distribution evenness on chromosomes, function annotation and suitability for primer design, we chose 545 candidate microsatellites for further characterization. After amplification validation and variation assessment, 218 loci were polymorphic in at least one of the two populations collected from the coast of Arenys de Mar, Spain (N = 24-48), and Cape Town, South Africa (N = 24-33). The number of alleles, observed heterozygosity and expected heterozygosity ranged from 2 to 11, 0 to 0.833 and 0.021 to 0.818, and from 2 to 10, 0 to 0.879 and 0.031 to 0.845 for the Spanish and African populations, respectively. When all microsatellites were tested for cross-species utility, only 60 loci (25.8%) could be successfully amplified and all loci were polymorphic in C. intestinalis spB. A high level of genomewide polymorphism is likely responsible for the low transferability. The large set of microsatellite markers characterized here is expected to provide a useful genomewide resource for ecological and evolutionary studies using C. intestinalis as a model.}, } @article {pmid26505829, year = {2016}, author = {Mordecai, GJ and Brettell, LE and Martin, SJ and Dixon, D and Jones, IM and Schroeder, DC}, title = {Superinfection exclusion and the long-term survival of honey bees in Varroa-infested colonies.}, journal = {The ISME journal}, volume = {10}, number = {5}, pages = {1182-1191}, pmid = {26505829}, issn = {1751-7370}, support = {BB/G02040X/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; Bees/*parasitology ; Computational Biology ; Contig Mapping ; Genome, Viral ; *Host-Pathogen Interactions ; *RNA, Viral ; Superinfection/*parasitology/*virology ; Varroidae/*pathogenicity/*virology ; }, abstract = {Over the past 50 years, many millions of European honey bee (Apis mellifera) colonies have died as the ectoparasitic mite, Varroa destructor, has spread around the world. Subsequent studies have indicated that the mite's association with a group of RNA viral pathogens (Deformed Wing Virus, DWV) correlates with colony death. Here, we propose a phenomenon known as superinfection exclusion that provides an explanation of how certain A. mellifera populations have survived, despite Varroa infestation and high DWV loads. Next-generation sequencing has shown that a non-lethal DWV variant 'type B' has become established in these colonies and that the lethal 'type A' DWV variant fails to persist in the bee population. We propose that this novel stable host-pathogen relationship prevents the accumulation of lethal variants, suggesting that this interaction could be exploited for the development of an effective treatment that minimises colony losses in the future.}, } @article {pmid26500288, year = {2015}, author = {Perkins, EJ and Antczak, P and Burgoon, L and Falciani, F and Garcia-Reyero, N and Gutsell, S and Hodges, G and Kienzler, A and Knapen, D and McBride, M and Willett, C}, title = {Adverse Outcome Pathways for Regulatory Applications: Examination of Four Case Studies With Different Degrees of Completeness and Scientific Confidence.}, journal = {Toxicological sciences : an official journal of the Society of Toxicology}, volume = {148}, number = {1}, pages = {14-25}, doi = {10.1093/toxsci/kfv181}, pmid = {26500288}, issn = {1096-0929}, mesh = {Animals ; Aromatase Inhibitors/toxicity ; Carcinogens, Environmental/toxicity ; Cell Membrane/drug effects/enzymology/metabolism ; Cell Proliferation/drug effects ; Computational Biology ; Congresses as Topic ; Decision Making, Organizational ; Dermatitis, Allergic Contact/etiology/immunology/metabolism/pathology ; Ecotoxicology/legislation & jurisprudence/*methods ; Environmental Pollutants/*toxicity ; *Evidence-Based Practice ; Hepatocytes/cytology/drug effects/pathology ; Humans ; *Models, Biological ; Organisation for Economic Co-Operation and Development ; Risk Assessment/methods/standards ; Skin/drug effects/immunology/metabolism/pathology ; *Toxicity Tests, Acute/standards ; *Toxicity Tests, Chronic/standards ; }, abstract = {Adverse outcome pathways (AOPs) offer a pathway-based toxicological framework to support hazard assessment and regulatory decision-making. However, little has been discussed about the scientific confidence needed, or how complete a pathway should be, before use in a specific regulatory application. Here we review four case studies to explore the degree of scientific confidence and extent of completeness (in terms of causal events) that is required for an AOP to be useful for a specific purpose in a regulatory application: (i) Membrane disruption (Narcosis) leading to respiratory failure (low confidence), (ii) Hepatocellular proliferation leading to cancer (partial pathway, moderate confidence), (iii) Covalent binding to proteins leading to skin sensitization (high confidence), and (iv) Aromatase inhibition leading to reproductive dysfunction in fish (high confidence). Partially complete AOPs with unknown molecular initiating events, such as 'Hepatocellular proliferation leading to cancer', were found to be valuable. We demonstrate that scientific confidence in these pathways can be increased though the use of unconventional information (eg, computational identification of potential initiators). AOPs at all levels of confidence can contribute to specific uses. A significant statistical or quantitative relationship between events and/or the adverse outcome relationships is a common characteristic of AOPs, both incomplete and complete, that have specific regulatory uses. For AOPs to be useful in a regulatory context they must be at least as useful as the tools that regulators currently possess, or the techniques currently employed by regulators.}, } @article {pmid26499288, year = {2016}, author = {Avitabile, V and Herold, M and Heuvelink, GB and Lewis, SL and Phillips, OL and Asner, GP and Armston, J and Ashton, PS and Banin, L and Bayol, N and Berry, NJ and Boeckx, P and de Jong, BH and DeVries, B and Girardin, CA and Kearsley, E and Lindsell, JA and Lopez-Gonzalez, G and Lucas, R and Malhi, Y and Morel, A and Mitchard, ET and Nagy, L and Qie, L and Quinones, MJ and Ryan, CM and Ferry, SJ and Sunderland, T and Laurin, GV and Gatti, RC and Valentini, R and Verbeeck, H and Wijaya, A and Willcock, S}, title = {An integrated pan-tropical biomass map using multiple reference datasets.}, journal = {Global change biology}, volume = {22}, number = {4}, pages = {1406-1420}, doi = {10.1111/gcb.13139}, pmid = {26499288}, issn = {1365-2486}, mesh = {*Biomass ; Datasets as Topic ; *Maps as Topic ; Models, Theoretical ; Trees ; Tropical Climate ; }, abstract = {We combined two existing datasets of vegetation aboveground biomass (AGB) (Proceedings of the National Academy of Sciences of the United States of America, 108, 2011, 9899; Nature Climate Change, 2, 2012, 182) into a pan-tropical AGB map at 1-km resolution using an independent reference dataset of field observations and locally calibrated high-resolution biomass maps, harmonized and upscaled to 14 477 1-km AGB estimates. Our data fusion approach uses bias removal and weighted linear averaging that incorporates and spatializes the biomass patterns indicated by the reference data. The method was applied independently in areas (strata) with homogeneous error patterns of the input (Saatchi and Baccini) maps, which were estimated from the reference data and additional covariates. Based on the fused map, we estimated AGB stock for the tropics (23.4 N-23.4 S) of 375 Pg dry mass, 9-18% lower than the Saatchi and Baccini estimates. The fused map also showed differing spatial patterns of AGB over large areas, with higher AGB density in the dense forest areas in the Congo basin, Eastern Amazon and South-East Asia, and lower values in Central America and in most dry vegetation areas of Africa than either of the input maps. The validation exercise, based on 2118 estimates from the reference dataset not used in the fusion process, showed that the fused map had a RMSE 15-21% lower than that of the input maps and, most importantly, nearly unbiased estimates (mean bias 5 Mg dry mass ha(-1) vs. 21 and 28 Mg ha(-1) for the input maps). The fusion method can be applied at any scale including the policy-relevant national level, where it can provide improved biomass estimates by integrating existing regional biomass maps as input maps and additional, country-specific reference datasets.}, } @article {pmid26497314, year = {2015}, author = {Matarashvili, I and Shvangiradze, I and Chankvetadze, L and Sidamonidze, S and Takaishvili, N and Farkas, T and Chankvetadze, B}, title = {High-performance liquid chromatographic separations of stereoisomers of chiral basic agrochemicals with polysaccharide-based chiral columns and polar organic mobile phases.}, journal = {Journal of separation science}, volume = {38}, number = {24}, pages = {4173-4179}, doi = {10.1002/jssc.201500919}, pmid = {26497314}, issn = {1615-9314}, abstract = {The separation of the stereoisomers of 23 chiral basic agrochemicals was studied on six different polysaccharide-based chiral columns in high-performance liquid chromatography with various polar organic mobile phases. Along with the successful separation of analyte stereoisomers, emphasis was placed on the effect of the chiral selector and mobile phase composition on the elution order of stereoisomers. The interesting phenomenon of reversal of enantiomer/stereoisomer elution order function of the polysaccharide backbone (cellulose or amylose), type of derivative (carbamate or benzoate), nature, and position of the substituent(s) in the phenylcarbamate moiety (methyl or chloro) and the nature of the mobile phase was observed. For several of the analytes containing two chiral centers all four stereoisomers were resolved with at least one chiral selector/mobile phase combination.}, } @article {pmid26495281, year = {2015}, author = {Abdullah, AA and Altaf-Ul-Amin, M and Ono, N and Sato, T and Sugiura, T and Morita, AH and Katsuragi, T and Muto, A and Nishioka, T and Kanaya, S}, title = {Development and mining of a volatile organic compound database.}, journal = {BioMed research international}, volume = {2015}, number = {}, pages = {139254}, pmid = {26495281}, issn = {2314-6141}, mesh = {Data Mining/*methods ; *Database Management Systems ; *Databases, Chemical ; Natural Language Processing ; Pattern Recognition, Automated/methods ; *Periodicals as Topic ; Volatile Organic Compounds/*chemistry/classification/*metabolism ; }, abstract = {Volatile organic compounds (VOCs) are small molecules that exhibit high vapor pressure under ambient conditions and have low boiling points. Although VOCs contribute only a small proportion of the total metabolites produced by living organisms, they play an important role in chemical ecology specifically in the biological interactions between organisms and ecosystems. VOCs are also important in the health care field as they are presently used as a biomarker to detect various human diseases. Information on VOCs is scattered in the literature until now; however, there is still no available database describing VOCs and their biological activities. To attain this purpose, we have developed KNApSAcK Metabolite Ecology Database, which contains the information on the relationships between VOCs and their emitting organisms. The KNApSAcK Metabolite Ecology is also linked with the KNApSAcK Core and KNApSAcK Metabolite Activity Database to provide further information on the metabolites and their biological activities. The VOC database can be accessed online.}, } @article {pmid26492521, year = {2015}, author = {Wang, Y and Kaplan, N and Newman, G and Scarpino, R}, title = {CitSci.org: A New Model for Managing, Documenting, and Sharing Citizen Science Data.}, journal = {PLoS biology}, volume = {13}, number = {10}, pages = {e1002280}, pmid = {26492521}, issn = {1545-7885}, mesh = {Access to Information ; Animals ; Biomedical Research/methods/trends ; Communication Barriers ; Data Accuracy ; *Database Management Systems ; Databases, Factual ; Humans ; *Information Dissemination ; Internet ; *Models, Theoretical ; *Research/trends ; Science/*methods ; Technology Transfer ; *Volunteers ; Workforce ; }, abstract = {Citizen science projects have the potential to advance science by increasing the volume and variety of data, as well as innovation. Yet this potential has not been fully realized, in part because citizen science data are typically not widely shared and reused. To address this and related challenges, we built CitSci.org (see www.citsci.org), a customizable platform that allows users to collect and generate diverse datasets. We hope that CitSci.org will ultimately increase discoverability and confidence in citizen science observations, encouraging scientists to use such data in their own scientific research.}, } @article {pmid26491393, year = {2015}, author = {de Jong, Y and Kouwenberg, J and Boumans, L and Hussey, C and Hyam, R and Nicolson, N and Kirk, P and Paton, A and Michel, E and Guiry, MD and Boegh, PS and Pedersen, HÆ and Enghoff, H and von Raab-Straube, E and Güntsch, A and Geoffroy, M and Müller, A and Kohlbecker, A and Berendsohn, W and Appeltans, W and Arvanitidis, C and Vanhoorne, B and Declerck, J and Vandepitte, L and Hernandez, F and Nash, R and Costello, MJ and Ouvrard, D and Bezard-Falgas, P and Bourgoin, T and Wetzel, FT and Glöckler, F and Korb, G and Ring, C and Hagedorn, G and Häuser, C and Aktaç, N and Asan, A and Ardelean, A and Borges, PA and Dhora, D and Khachatryan, H and Malicky, M and Ibrahimov, S and Tuzikov, A and De Wever, A and Moncheva, S and Spassov, N and Chobot, K and Popov, A and Boršić, I and Sfenthourakis, S and Kõljalg, U and Uotila, P and Olivier, G and Dauvin, JC and Tarkhnishvili, D and Chaladze, G and Tuerkay, M and Legakis, A and Peregovits, L and Gudmundsson, G and Ólafsson, E and Lysaght, L and Galil, BS and Raimondo, FM and Domina, G and Stoch, F and Minelli, A and Spungis, V and Budrys, E and Olenin, S and Turpel, A and Walisch, T and Krpach, V and Gambin, MT and Ungureanu, L and Karaman, G and Kleukers, RM and Stur, E and Aagaard, K and Valland, N and Moen, TL and Bogdanowicz, W and Tykarski, P and Węsławski, JM and Kędra, M and M de Frias Martins, A and Abreu, AD and Silva, R and Medvedev, S and Ryss, A and Šimić, S and Marhold, K and Stloukal, E and Tome, D and Ramos, MA and Valdés, B and Pina, F and Kullander, S and Telenius, A and Gonseth, Y and Tschudin, P and Sergeyeva, O and Vladymyrov, V and Rizun, VB and Raper, C and Lear, D and Stoev, P and Penev, L and Rubio, AC and Backeljau, T and Saarenmaa, H and Ulenberg, S}, title = {PESI - a taxonomic backbone for Europe.}, journal = {Biodiversity data journal}, volume = {}, number = {3}, pages = {e5848}, pmid = {26491393}, issn = {1314-2828}, abstract = {BACKGROUND: Reliable taxonomy underpins communication in all of biology, not least nature conservation and sustainable use of ecosystem resources. The flexibility of taxonomic interpretations, however, presents a serious challenge for end-users of taxonomic concepts. Users need standardised and continuously harmonised taxonomic reference systems, as well as high-quality and complete taxonomic data sets, but these are generally lacking for non-specialists. The solution is in dynamic, expertly curated web-based taxonomic tools. The Pan-European Species-directories Infrastructure (PESI) worked to solve this key issue by providing a taxonomic e-infrastructure for Europe. It strengthened the relevant social (expertise) and information (standards, data and technical) capacities of five major community networks on taxonomic indexing in Europe, which is essential for proper biodiversity assessment and monitoring activities. The key objectives of PESI were: 1) standardisation in taxonomic reference systems, 2) enhancement of the quality and completeness of taxonomic data sets and 3) creation of integrated access to taxonomic information.

NEW INFORMATION: This paper describes the results of PESI and its future prospects, including the involvement in major European biodiversity informatics initiatives and programs.}, } @article {pmid26490638, year = {2015}, author = {Guo, ZW and Xie, C and Yang, JR and Li, JH and Yang, JH and Zheng, L}, title = {MtiBase: a database for decoding microRNA target sites located within CDS and 5'UTR regions from CLIP-Seq and expression profile datasets.}, journal = {Database : the journal of biological databases and curation}, volume = {2015}, number = {}, pages = {}, pmid = {26490638}, issn = {1758-0463}, mesh = {5' Untranslated Regions/*genetics ; Animals ; *Databases, Nucleic Acid ; *Gene Expression Profiling ; *Gene Expression Regulation ; Humans ; Mice ; MicroRNAs/*genetics ; Molecular Sequence Annotation ; Open Reading Frames/*genetics ; Polymorphism, Single Nucleotide/genetics ; Sequence Analysis, RNA ; Statistics as Topic ; }, abstract = {MicroRNAs (miRNAs) play an important role in the regulation of gene expression. Previous studies on miRNA functions mainly focused on their target sites in the 3' untranslated regions (UTRs) of mRNAs. However, increasing evidence has revealed that miRNAs can also induce mRNA degradation and mediate translational repression via complementary interactions with the coding sequence (CDS) and 5'UTR of mRNAs. In this study, we developed a novel database, MtiBase, to facilitate the comprehensive exploration of CDS- and 5'UTR-located miRNA target sites identified from cross-linking immunoprecipitation sequencing (CLIP-Seq) datasets and to uncover their regulatory effects on mRNA stability and translation from expression profile datasets. By integrating 61 Argonaute protein-binding CLIP-Seq datasets and miRNA target sites predicted by five commonly used programs, we identified approximately 4 400 000 CDS-located and 470 000 5'UTR-located miRNA target sites. Moreover, we evaluated the regulatory effects of miRNAs on mRNA stability and translation using the data from 222 gene expression profiles, and 28 ribosome-protected fragment sequencing, and six pulsed stable isotope labeling with amino acids in culture. Finally, the effects of SNPs on the functions of miRNA target sites were systematically evaluated. Our study provides a useful tool for functional studies of miRNAs in regulating physiology and pathology. Database URL: http://mtibase.sysu.edu.cn.}, } @article {pmid26490190, year = {2015}, author = {Antweiler, RC}, title = {Evaluation of Statistical Treatments of Left-Censored Environmental Data Using Coincident Uncensored Data Sets. II. Group Comparisons.}, journal = {Environmental science & technology}, volume = {49}, number = {22}, pages = {13439-13446}, doi = {10.1021/acs.est.5b02385}, pmid = {26490190}, issn = {1520-5851}, mesh = {*Data Interpretation, Statistical ; Ecology/*statistics & numerical data ; Limit of Detection ; Probability ; United States ; }, abstract = {The main classes of statistical treatments that have been used to determine if two groups of censored environmental data arise from the same distribution are substitution methods, maximum likelihood (MLE) techniques, and nonparametric methods. These treatments along with using all instrument-generated data (IN), even those less than the detection limit, were evaluated by examining 550 data sets in which the true values of the censored data were known, and therefore "true" probabilities could be calculated and used as a yardstick for comparison. It was found that technique "quality" was strongly dependent on the degree of censoring present in the groups. For low degrees of censoring (<25% in each group), the Generalized Wilcoxon (GW) technique and substitution of √2/2 times the detection limit gave overall the best results. For moderate degrees of censoring, MLE worked best, but only if the distribution could be estimated to be normal or log-normal prior to its application; otherwise, GW was a suitable alternative. For higher degrees of censoring (each group >40% censoring), no technique provided reliable estimates of the true probability. Group size did not appear to influence the quality of the result, and no technique appeared to become better or worse than other techniques relative to group size. Finally, IN appeared to do very well relative to the other techniques regardless of censoring or group size.}, } @article {pmid26489437, year = {2015}, author = {Santos, CD and Cramer, JF and Pârâu, LG and Miranda, AC and Wikelski, M and Dechmann, DK}, title = {Personality and morphological traits affect pigeon survival from raptor attacks.}, journal = {Scientific reports}, volume = {5}, number = {}, pages = {15490}, pmid = {26489437}, issn = {2045-2322}, mesh = {Animals ; *Behavior, Animal ; Columbidae/genetics/*physiology ; Geographic Information Systems ; Humans ; Personality/*genetics/physiology ; Predatory Behavior/*physiology ; Raptors/physiology ; }, abstract = {Personality traits have recently been shown to impact fitness in different animal species, potentially making them similarly relevant drivers as morphological and life history traits along the evolutionary pathways of organisms. Predation is a major force of natural selection through its deterministic effects on individual survival, but how predation pressure has helped to shape personality trait selection, especially in free-ranging animals, remains poorly understood. We used high-precision GPS tracking to follow whole flocks of homing pigeons (Columba livia) with known personalities and morphology during homing flights where they were severely predated by raptors. This allowed us to determine how the personality and morphology traits of pigeons may affect their risk of being predated by raptors. Our survival model showed that individual pigeons, which were more tolerant to human approach, slower to escape from a confined environment, more resistant to human handling, with larger tarsi, and with lighter plumage, were more likely to be predated by raptors. We provide rare empirical evidence that the personality of prey influences their risk of being predated under free-ranging circumstances.}, } @article {pmid26487380, year = {2015}, author = {Liu, X and Zhang, L and Zhang, Z and Ma, X and Liu, J}, title = {Transcriptional response to sulfide in the Echiuran Worm Urechis unicinctus by digital gene expression analysis.}, journal = {BMC genomics}, volume = {16}, number = {}, pages = {829}, pmid = {26487380}, issn = {1471-2164}, mesh = {Animals ; Chromosome Mapping ; Databases, Protein ; Gene Expression Regulation/drug effects ; Molecular Sequence Annotation ; Polychaeta/drug effects/*genetics ; Sequence Analysis, DNA ; Sulfides/toxicity ; Transcription, Genetic/*drug effects ; Transcriptome/drug effects/*genetics ; }, abstract = {BACKGROUND: Urechis unicinctus, an echiuran worm inhabiting the U-shaped burrows in the coastal mud flats, is an important commercial and ecological invertebrate in Northeast Asian countries, which has potential applications in the study of animal evolution, coastal sediment improvement and marine drug development. Furthermore, the worm can tolerate and utilize well-known toxicant-sulfide. However, knowledge is limited on the molecular mechanism of U. unicinctus responding to sulfide due to deficiency of its genetic information.

METHODS: In this study, we performed Illumina sequencing to obtain the first Urechis unicinctus transcriptome data. Sequenced reads were assembled and then annotated using blast searches against Nr, Nt, Swiss-Prot, KEGG and COG. The clean tags from four digital gene expression (DGE) libraries were mapped to the U. unicinctus transcriptome. DGE analysis and functional annotation were then performed to reveal its response to sulfide. The expressions of 12 candidate genes were validated using quantitative real-time PCR. The results of qRT-PCR were regressed against the DGE analysis, with a correlation coefficient and p-value reported for each of them.

RESULTS: Here we first present a draft of U. unicinctus transcriptome using the Illumina HiSeq(TM) 2000 platform and 52,093 unique sequences were assembled with the average length of 738 bp and N50 of 1131 bp. About 51.6 % of the transcriptome were functionally annotated based on the databases of Nr, Nt, Swiss-Prot, KEGG and COG. Then based on the transcriptome, the digital gene expression analysis was conducted to examine the transcriptional response to sulfide during 6, 24 and 48 h exposure, and finally 1705, 1181 and 1494 tag-mapped genes were identified as differentially expressed genes in the 6-h, 24-h and 48-h libraries, then were further subjected to pathway analyses.

CONCLUSIONS: In the DGE database of U. unicinctus, the alterations in certain known sulfide-related pathways indicate similar changes in response to sulfide. For more than 80 % of the identified pathway members, this is the first report on their association with sulfide stress, among which glycolysis pathway and PIDD involving pathways were unique and discussed in details, and were thought to play important roles in the sulfide tolerance of U. unicinctus. All the results are helpful to explain the mechanism of sulfide tolerance and detoxification.}, } @article {pmid26487142, year = {2015}, author = {Yamamura, M and Santos-Neto, M and dos Santos, RA and Garcia, MC and Nogueira, Jde A and Arcêncio, RA}, title = {Epidemiological characteristics of cases of death from tuberculosis and vulnerable territories.}, journal = {Revista latino-americana de enfermagem}, volume = {23}, number = {5}, pages = {910-918}, pmid = {26487142}, issn = {1518-8345}, mesh = {Adult ; Aged ; Aged, 80 and over ; Brazil/epidemiology ; Cause of Death ; Female ; Geographic Information Systems ; Humans ; Male ; Middle Aged ; Tuberculosis/*mortality ; }, abstract = {OBJECTIVE: to characterize the differences in the clinical and epidemiological profile of cases of death that had tuberculosis as an immediate or associated cause, and to analyze the spatial distribution of the cases of death from tuberculosis within the territories of Ribeirão Preto, Brazil.

METHOD: an ecological study, in which the population consisted of 114 cases of death from tuberculosis. Bivariate analysis was carried out, as well as point density analysis, defined with the Kernel estimate.

RESULTS: of the cases of death from tuberculosis, 50 were the immediate cause and 64 an associated cause. Age (p=.008) and sector responsible for the death certificate (p=.003) were the variables that presented statistically significant associations with the cause of death. The spatial distribution, in both events, did not occur randomly, forming clusters in areas of the municipality.

CONCLUSION: the difference in the profiles of the cases of death from tuberculosis, as a basic cause and as an associated cause, was governed by the age and the sector responsible for the completion of the death certificate. The non-randomness of the spatial distribution of the cases suggests areas that are vulnerable to these events. Knowing these areas can contribute to the choice of disease control strategies.}, } @article {pmid26486362, year = {2015}, author = {Gordine, SA and Fedak, M and Boehme, L}, title = {Fishing for drifts: detecting buoyancy changes of a top marine predator using a step-wise filtering method.}, journal = {The Journal of experimental biology}, volume = {218}, number = {Pt 23}, pages = {3816-3824}, pmid = {26486362}, issn = {1477-9145}, mesh = {Animal Migration ; Animals ; Antarctic Regions ; Body Composition ; Data Interpretation, Statistical ; Diving/*physiology ; Knowledge Bases ; Seals, Earless/*physiology ; Telemetry ; }, abstract = {In southern elephant seals (Mirounga leonina), fasting- and foraging-related fluctuations in body composition are reflected by buoyancy changes. Such buoyancy changes can be monitored by measuring changes in the rate at which a seal drifts passively through the water column, i.e. when all active swimming motion ceases. Here, we present an improved knowledge-based method for detecting buoyancy changes from compressed and abstracted dive profiles received through telemetry. By step-wise filtering of the dive data, the developed algorithm identifies fragments of dives that correspond to times when animals drift. In the dive records of 11 southern elephant seals from South Georgia, this filtering method identified 0.8-2.2% of all dives as drift dives, indicating large individual variation in drift diving behaviour. The obtained drift rate time series exhibit that, at the beginning of each migration, all individuals were strongly negatively buoyant. Over the following 75-150 days, the buoyancy of all individuals peaked close to or at neutral buoyancy, indicative of a seal's foraging success. Independent verification with visually inspected detailed high-resolution dive data confirmed that this method is capable of reliably detecting buoyancy changes in the dive records of drift diving species using abstracted data. This also affirms that abstracted dive profiles convey the geometric shape of drift dives in sufficient detail for them to be identified. Further, it suggests that, using this step-wise filtering method, buoyancy changes could be detected even in old datasets with compressed dive information, for which conventional drift dive classification previously failed.}, } @article {pmid26485956, year = {2015}, author = {Willis, KJ and Seddon, AW and Long, PR and Jeffers, ES and Caithness, N and Thurston, M and Smit, MG and Hagemann, R and Macias-Fauria, M}, title = {Remote assessment of locally important ecological features across landscapes: how representative of reality?.}, journal = {Ecological applications : a publication of the Ecological Society of America}, volume = {25}, number = {5}, pages = {1290-1302}, doi = {10.1890/14-1431.1}, pmid = {26485956}, issn = {1051-0761}, mesh = {*Biodiversity ; Cities ; Databases, Factual ; Environmental Monitoring ; *Spacecraft ; Uncertainty ; }, abstract = {The local ecological footprinting tool (LEFT) uses globally available databases, modeling, and algorithms to, remotely assess locally important ecological features across landscapes based on five criteria: biodiversity (beta-diversity), vulnerability (threatened species), fragmentation, connectivity, and resilience. This approach can be applied to terrestrial landscapes at a 300-m resolution within a given target area. Input is minimal (latitude and longitude) and output is a computer-generated report and series of maps that both individually and synthetically depict the relative value of each ecological criteria. A key question for any such tool, however, is how representative is the remotely obtained output compared to what is on the ground. Here, we present the results from comparing remotely- vs. field-generated outputs from the LEFT tool on two distinct study areas for beta-diversity and distribution of threatened species (vulnerability), the two fields computed by LEFT for which such an approach is feasible. The comparison method consists of a multivariate measure of similarity between two fields based on discrete wavelet transforms, and reveals consistent agreement across a wide range of spatial scales. These results suggest that remote assessment tools such as LEFT hold great potential for determining key ecological features across landscapes and for being utilized in preplanning biodiversity assessment tools.}, } @article {pmid26484735, year = {2016}, author = {Wu, X and Holmfeldt, K and Hubalek, V and Lundin, D and Åström, M and Bertilsson, S and Dopson, M}, title = {Microbial metagenomes from three aquifers in the Fennoscandian shield terrestrial deep biosphere reveal metabolic partitioning among populations.}, journal = {The ISME journal}, volume = {10}, number = {5}, pages = {1192-1203}, pmid = {26484735}, issn = {1751-7370}, mesh = {Bacteria/*genetics ; Biodiversity ; Biological Evolution ; Biomass ; Computational Biology ; Groundwater ; *Metagenome ; Microbiota ; Phylogeny ; Principal Component Analysis ; Proteobacteria/genetics ; Sequence Analysis, DNA ; Species Specificity ; Sweden ; *Water Microbiology ; }, abstract = {Microorganisms in the terrestrial deep biosphere host up to 20% of the earth's biomass and are suggested to be sustained by the gases hydrogen and carbon dioxide. A metagenome analysis of three deep subsurface water types of contrasting age (from <20 to several thousand years) and depth (171 to 448 m) revealed phylogenetically distinct microbial community subsets that either passed or were retained by a 0.22 μm filter. Such cells of <0.22 μm would have been overlooked in previous studies relying on membrane capture. Metagenomes from the three water types were used for reconstruction of 69 distinct microbial genomes, each with >86% coverage. The populations were dominated by Proteobacteria, Candidate divisions, unclassified archaea and unclassified bacteria. The estimated genome sizes of the <0.22 μm populations were generally smaller than their phylogenetically closest relatives, suggesting that small dimensions along with a reduced genome size may be adaptations to oligotrophy. Shallow 'modern marine' water showed community members with a predominantly heterotrophic lifestyle. In contrast, the deeper, 'old saline' water adhered more closely to the current paradigm of a hydrogen-driven deep biosphere. The data were finally used to create a combined metabolic model of the deep terrestrial biosphere microbial community.}, } @article {pmid26483571, year = {2016}, author = {Radak, DJ and Tanaskovic, SZ and Vlajinac, HD and Marinkovic, JM and Maksimovic, MZ}, title = {Relationship Between Pain and CEAP C Categories of Chronic Venous Disease.}, journal = {Angiology}, volume = {67}, number = {7}, pages = {670-675}, doi = {10.1177/0003319715613179}, pmid = {26483571}, issn = {1940-1574}, mesh = {Adult ; Aged ; Chi-Square Distribution ; Chronic Disease ; Cross-Sectional Studies ; Female ; Humans ; Linear Models ; Logistic Models ; Male ; Middle Aged ; Multivariate Analysis ; Pain/*diagnosis/etiology/physiopathology ; *Pain Measurement ; Predictive Value of Tests ; Risk Factors ; Serbia ; Severity of Illness Index ; Varicose Veins/complications/*diagnosis/physiopathology ; }, abstract = {In this study, we investigated whether the occurrence and intensity of leg pain are related to C class of the clinical, etiological, anatomical, and pathophysiological (CEAP) classification for chronic venous disease (CVeD). This cross-sectional study, conducted in Serbia, included 2841 patients: 2027 (71.3%) women and 814 (28.7%) men with CVeD diagnosed by general practitioners. For the first time, the Numeric Rating Scale of 0 to 5 units was used to assess the intensity of pain. For the analysis, univariate and multivariate logistic and linear regressions were applied. Pain in the legs was reported by 90.5% of the patients. The occurrence of pain significantly (P < .001) increased with increasing C class. Of the patients who reported pain in the legs, 42.0% had moderate pain, 23.7% had moderate to severe pain, 22.8% had light pain, 11.2% had severe pain, and 0.3% had very severe pain. Severity of pain differed significantly (P < .001) according to C class. Light and moderate pain gradually decreased and severe pain gradually increased from C0 to C6 class. These associations remained significant after adjustment for age, body mass index, and family history of CVeD.}, } @article {pmid26479170, year = {2016}, author = {Subramaniam, A and Kumar, R and Cliver, SP and Zhi, D and Szychowski, JM and Abramovici, A and Biggio, JR and Lefkowitz, EJ and Morrow, C and Edwards, RK}, title = {Vaginal Microbiota in Pregnancy: Evaluation Based on Vaginal Flora, Birth Outcome, and Race.}, journal = {American journal of perinatology}, volume = {33}, number = {4}, pages = {401-408}, pmid = {26479170}, issn = {1098-8785}, support = {P30 AI027767/AI/NIAID NIH HHS/United States ; UL1TR000165/TR/NCATS NIH HHS/United States ; P30AR050948/AR/NIAMS NIH HHS/United States ; UL1 TR000165/TR/NCATS NIH HHS/United States ; 5P30AI027767/AI/NIAID NIH HHS/United States ; P30 AR050948/AR/NIAMS NIH HHS/United States ; UL1 TR001417/TR/NCATS NIH HHS/United States ; }, mesh = {Adolescent ; Adult ; Alabama ; DNA, Ribosomal/isolation & purification ; Female ; Humans ; *Microbiota ; Polymerase Chain Reaction ; Pregnancy ; Sequence Analysis, DNA ; Vagina/*microbiology ; Vaginosis, Bacterial/*diagnosis ; Young Adult ; }, abstract = {OBJECTIVE: This study aims to evaluate vaginal microbiota differences by bacterial vaginosis (BV), birth timing, and race, and to estimate parameters to power future vaginal microbiome studies.

METHODS: Previously, vaginal swabs were collected at 21 to 25 weeks (stored at -80°C), and vaginal smears evaluated for BV (Nugent criteria). In a blinded fashion, 40 samples were selected, creating 8 equal-sized groups stratified by race (black/white), BV (present/absent), and birth timing (preterm/term). Samples were thawed, DNA extracted, and prepared. Polymerase chain reaction (PCR) with primers targeting the 16S rDNA V4 region was used to prepare an amplicon library. PCR products were sequenced and analyzed using quantitative insight into microbial ecology; taxonomy was assigned using ribosomal database program classifier (threshold 0.8) against the modified Greengenes database.

RESULTS: After quality control, 97,720 sequences (mean) per sample, single-end 250 base-reads, were analyzed. BV samples had greater microbiota diversity (p < 0.05)-with BVAB1, Prevotella, and unclassified genus, Bifidobacteriaceae family (all p < 0.001) more abundant; there was minimal content of Gardnerella or Mobiluncus. Microbiota did not differ by race or birth timing, but there was an association between certain microbial clusters and preterm birth (p = 0.07). To evaluate this difference, 159 patients per group are needed.

CONCLUSIONS: There are differences in the vaginal microbiota between patients with and without BV. Larger studies should assess the relationship between microbiota composition and preterm birth.}, } @article {pmid26474753, year = {2015}, author = {Christmas, MJ and Biffin, E and Lowe, AJ}, title = {Transcriptome sequencing, annotation and polymorphism detection in the hop bush, Dodonaea viscosa.}, journal = {BMC genomics}, volume = {16}, number = {}, pages = {803}, pmid = {26474753}, issn = {1471-2164}, mesh = {Adaptation, Physiological/genetics ; Australia ; Gene Expression Profiling ; Gene Expression Regulation, Plant ; Gene Ontology ; *Genome, Plant ; Genomics ; *Molecular Sequence Annotation ; Polymorphism, Single Nucleotide/genetics ; Sapindaceae/*genetics ; Transcriptome/*genetics ; }, abstract = {BACKGROUND: The hop bush, Dodonaea viscosa, is a trans-oceanic species distributed oversix continents. It evolved in Australia where it is found over a wide range of habitat types and is an ecologically important species. Limited genomic resources are currently available for this species, thus our understanding of its evolutionary history and ecological adaptation is restricted. Here, we present a comprehensive transcriptome dataset for future genomic studies into this species.

METHODS: We performed Illumina sequencing of cDNA prepared from leaf tissue collected from seven populations of D. viscosa ssp. angustissima and spatulata distributed along an environmental gradient in South Australia. Sequenced reads were assembled to provide a transcriptome resource. Contiguous sequences (contigs) were annotated using BLAST searches against the NCBI non-redundant database and gene ontology definitions were assigned. Single nucleotide polymorphisms were detected for the establishment of a genetic marker set. A comparison between the two subspecies was also carried out.

RESULTS: Illumina sequencing returned 268,672,818 sequence reads, which were de novoassembled into 105,125 contigs. Contigs with significant BLAST alignments (E value < 1e(-5))numbered at 44,191, with 38,311 of these having their most significant hits to sequences from land plant species. Gene Ontology terms were assigned to 28,440 contigs and KEGG analysis identified 146 pathways that the gene products from 5,070 contigs are potentially involved in. The subspecies comparison identified 8,494 fixed SNP differences across 3,979 contiguous sequences, indicating a level of genetic differentiation between them. Across all samples, 248,235 SNPs were detected.

CONCLUSIONS: We have established a significant genomic data resource for D. viscosa,providing a comprehensive transcriptomic reference. Genetic differences among morphologically distinct subspecies were found. A wide range of putative gene regions were identified along with a large set of variable SNP markers, providing a basis for studies into the evolution and ecological adaptation of D. viscosa.}, } @article {pmid26473972, year = {2015}, author = {Louca, S and Doebeli, M}, title = {Calibration and analysis of genome-based models for microbial ecology.}, journal = {eLife}, volume = {4}, number = {}, pages = {e08208}, pmid = {26473972}, issn = {2050-084X}, mesh = {Acetates/metabolism ; Biological Evolution ; *Biota ; Carbon/metabolism ; Computational Biology/*methods ; Escherichia coli/*genetics/physiology ; *Genome, Bacterial ; Metabolism ; *Microbial Consortia ; Models, Biological ; Oxygen/metabolism ; }, abstract = {Microbial ecosystem modeling is complicated by the large number of unknown parameters and the lack of appropriate calibration tools. Here we present a novel computational framework for modeling microbial ecosystems, which combines genome-based model construction with statistical analysis and calibration to experimental data. Using this framework, we examined the dynamics of a community of Escherichia coli strains that emerged in laboratory evolution experiments, during which an ancestral strain diversified into two coexisting ecotypes. We constructed a microbial community model comprising the ancestral and the evolved strains, which we calibrated using separate monoculture experiments. Simulations reproduced the successional dynamics in the evolution experiments, and pathway activation patterns observed in microarray transcript profiles. Our approach yielded detailed insights into the metabolic processes that drove bacterial diversification, involving acetate cross-feeding and competition for organic carbon and oxygen. Our framework provides a missing link towards a data-driven mechanistic microbial ecology.}, } @article {pmid26473720, year = {2016}, author = {Glassman, SI and Levine, CR and DiRocco, AM and Battles, JJ and Bruns, TD}, title = {Ectomycorrhizal fungal spore bank recovery after a severe forest fire: some like it hot.}, journal = {The ISME journal}, volume = {10}, number = {5}, pages = {1228-1239}, pmid = {26473720}, issn = {1751-7370}, mesh = {Basidiomycota ; Biological Assay ; California ; Computational Biology ; Ecology ; *Fires ; Forests ; Mycorrhizae/*physiology ; Pinus/*microbiology ; Seedlings/microbiology ; *Spores, Fungal ; }, abstract = {After severe wildfires, pine recovery depends on ectomycorrhizal (ECM) fungal spores surviving and serving as partners for regenerating forest trees. We took advantage of a large, severe natural forest fire that burned our long-term study plots to test the response of ECM fungi to fire. We sampled the ECM spore bank using pine seedling bioassays and high-throughput sequencing before and after the California Rim Fire. We found that ECM spore bank fungi survived the fire and dominated the colonization of in situ and bioassay seedlings, but there were specific fire adapted fungi such as Rhizopogon olivaceotinctus that increased in abundance after the fire. The frequency of ECM fungal species colonizing pre-fire bioassay seedlings, post-fire bioassay seedlings and in situ seedlings were strongly positively correlated. However, fire reduced the ECM spore bank richness by eliminating some of the rare species, and the density of the spore bank was reduced as evidenced by a larger number of soil samples that yielded uncolonized seedlings. Our results show that although there is a reduction in ECM inoculum, the ECM spore bank community largely remains intact, even after a high-intensity fire. We used advanced techniques for data quality control with Illumina and found consistent results among varying methods. Furthermore, simple greenhouse bioassays can be used to determine which fungi will colonize after fires. Similar to plant seed banks, a specific suite of ruderal, spore bank fungi take advantage of open niche space after fires.}, } @article {pmid26471998, year = {2016}, author = {Srivastava, D and Shanker, A}, title = {Identification of Simple Sequence Repeats in Chloroplast Genomes of Magnoliids Through Bioinformatics Approach.}, journal = {Interdisciplinary sciences, computational life sciences}, volume = {8}, number = {4}, pages = {327-336}, doi = {10.1007/s12539-015-0129-4}, pmid = {26471998}, issn = {1867-1462}, mesh = {Computational Biology/*methods ; Genome, Chloroplast/*genetics ; Genome, Plant/genetics ; Microsatellite Repeats/*genetics ; Plant Proteins/genetics ; Plants/*genetics ; }, abstract = {Basal angiosperms or Magnoliids is an important clade of commercially important plants which mainly include spices and edible fruits. In this study, 17 chloroplast genome sequences belonging to clade Magnoliids were screened for the identification of chloroplast simple sequence repeats (cpSSRs). Simple sequence repeats or microsatellites are short stretches of DNA up to 1-6 base pair in length. These repeats are ubiquitous and play important role in the development of molecular markers and to study the mapping of traits of economic, medical or ecological interest. A total of 479 SSRs were detected, showing average density of 1 SSR/6.91 kb. Depending on the repeat units, the length of SSRs ranged from 12 to 24 bp for mono-, 12 to 18 bp for di-, 12 to 26 bp for tri-, 12 to 24 bp for tetra-, 15 bp for penta- and 18 bp for hexanucleotide repeats. Mononucleotide repeats were the most frequent (207, 43.21 %) followed by tetranucleotide repeats (130, 27.13 %). Penta- and hexanucleotide repeats were least frequent or absent in these chloroplast genomes.}, } @article {pmid26471066, year = {2015}, author = {Marchini, A and Galil, BS and Occhipinti-Ambrogi, A}, title = {Recommendations on standardizing lists of marine alien species: Lessons from the Mediterranean Sea.}, journal = {Marine pollution bulletin}, volume = {101}, number = {1}, pages = {267-273}, doi = {10.1016/j.marpolbul.2015.09.054}, pmid = {26471066}, issn = {1879-3363}, mesh = {Animals ; Classification ; Databases, Factual ; Environmental Monitoring/*methods/*standards/statistics & numerical data ; Government Regulation ; Introduced Species/legislation & jurisprudence/*statistics & numerical data/*trends ; Marine Biology/*methods/statistics & numerical data ; Species Specificity ; }, abstract = {Analyses of marine alien species based on national/regional datasets are of paramount importance for the success of regulation on the prevention and management of invasive alien species. Yet in the extant data systems the criteria for the inclusion of records are seldom explicit, and frequently inconsistent in their definitions, spatial and temporal frames and comprehensiveness. Agreed-upon uniform guiding principles, based on solid and transparent scientific criteria, are therefore required in order to provide policy makers with validated and comparable data. Following a meta-analysis on the records of marine alien species in the Mediterranean Sea, we recommend a judicious approach to compiling the data. Here, three categories of uncertainty were identified: species' taxonomic identification, species' actual occurrence in the area, and its status as an alien. In proposing guiding principles to standardize such datasets, we aim to encourage discourse on logical, standardized and transparent criteria to substantiate records of alien species.}, } @article {pmid26467206, year = {2015}, author = {Chen, SC and Tsai, TH and Chung, CH and Li, WH}, title = {Dynamic association rules for gene expression data analysis.}, journal = {BMC genomics}, volume = {16}, number = {}, pages = {786}, pmid = {26467206}, issn = {1471-2164}, mesh = {*Algorithms ; Animals ; Cluster Analysis ; Computational Biology ; Databases, Genetic ; Gene Expression Profiling/*statistics & numerical data ; Gene Expression Regulation/genetics ; High-Throughput Nucleotide Sequencing/*statistics & numerical data ; Mice ; Mouse Embryonic Stem Cells/metabolism ; }, abstract = {BACKGROUND: The purpose of gene expression analysis is to look for the association between regulation of gene expression levels and phenotypic variations. This association based on gene expression profile has been used to determine whether the induction/repression of genes correspond to phenotypic variations including cell regulations, clinical diagnoses and drug development. Statistical analyses on microarray data have been developed to resolve gene selection issue. However, these methods do not inform us of causality between genes and phenotypes. In this paper, we propose the dynamic association rule algorithm (DAR algorithm) which helps ones to efficiently select a subset of significant genes for subsequent analysis. The DAR algorithm is based on association rules from market basket analysis in marketing. We first propose a statistical way, based on constructing a one-sided confidence interval and hypothesis testing, to determine if an association rule is meaningful. Based on the proposed statistical method, we then developed the DAR algorithm for gene expression data analysis. The method was applied to analyze four microarray datasets and one Next Generation Sequencing (NGS) dataset: the Mice Apo A1 dataset, the whole genome expression dataset of mouse embryonic stem cells, expression profiling of the bone marrow of Leukemia patients, Microarray Quality Control (MAQC) data set and the RNA-seq dataset of a mouse genomic imprinting study. A comparison of the proposed method with the t-test on the expression profiling of the bone marrow of Leukemia patients was conducted.

RESULTS: We developed a statistical way, based on the concept of confidence interval, to determine the minimum support and minimum confidence for mining association relationships among items. With the minimum support and minimum confidence, one can find significant rules in one single step. The DAR algorithm was then developed for gene expression data analysis. Four gene expression datasets showed that the proposed DAR algorithm not only was able to identify a set of differentially expressed genes that largely agreed with that of other methods, but also provided an efficient and accurate way to find influential genes of a disease.

CONCLUSIONS: In the paper, the well-established association rule mining technique from marketing has been successfully modified to determine the minimum support and minimum confidence based on the concept of confidence interval and hypothesis testing. It can be applied to gene expression data to mine significant association rules between gene regulation and phenotype. The proposed DAR algorithm provides an efficient way to find influential genes that underlie the phenotypic variance.}, } @article {pmid26467174, year = {2016}, author = {Sabath, N and Goldberg, EE and Glick, L and Einhorn, M and Ashman, TL and Ming, R and Otto, SP and Vamosi, JC and Mayrose, I}, title = {Dioecy does not consistently accelerate or slow lineage diversification across multiple genera of angiosperms.}, journal = {The New phytologist}, volume = {209}, number = {3}, pages = {1290-1300}, doi = {10.1111/nph.13696}, pmid = {26467174}, issn = {1469-8137}, mesh = {*Biodiversity ; Computer Simulation ; Databases as Topic ; Magnoliopsida/*physiology ; *Phylogeny ; Probability ; Quantitative Trait, Heritable ; Reproduction ; }, abstract = {Dioecy, the sexual system in which male and female organs are found in separate individuals, allows greater specialization for sex-specific functions and can be advantageous under various ecological and environmental conditions. However, dioecy is rare among flowering plants. Previous studies identified contradictory trends regarding the relative diversification rates of dioecious lineages vs their nondioecious counterparts, depending on the methods and data used. We gathered detailed species-level data for dozens of genera that contain both dioecious and nondioecious species. We then applied a probabilistic approach that accounts for differential speciation, extinction, and transition rates between states to examine whether there is an association between dioecy and lineage diversification. We found a bimodal distribution, whereby dioecious lineages exhibited higher diversification in certain genera but lower diversification in others. Additional analyses did not uncover an ecological or life history trait that could explain a context-dependent effect of dioecy on diversification. Furthermore, in-depth simulations of neutral characters demonstrated that such bimodality is also found when simulating neutral characters across the observed trees. Our analyses suggest that - at least for these genera with the currently available data - dioecy neither consistently places a strong brake on diversification nor is a strong driver.}, } @article {pmid26465332, year = {2015}, author = {Dempsey, SJ and Gese, EM and Kluever, BM and Lonsinger, RC and Waits, LP}, title = {Evaluation of Scat Deposition Transects versus Radio Telemetry for Developing a Species Distribution Model for a Rare Desert Carnivore, the Kit Fox.}, journal = {PloS one}, volume = {10}, number = {10}, pages = {e0138995}, pmid = {26465332}, issn = {1932-6203}, mesh = {Animal Distribution/*physiology ; Animals ; *Conservation of Natural Resources ; Desert Climate ; Endangered Species ; Feces ; Female ; Foxes/*physiology ; Geographic Information Systems ; Male ; *Models, Statistical ; Remote Sensing Technology/*methods ; Species Specificity ; Utah ; }, abstract = {Development and evaluation of noninvasive methods for monitoring species distribution and abundance is a growing area of ecological research. While noninvasive methods have the advantage of reduced risk of negative factors associated with capture, comparisons to methods using more traditional invasive sampling is lacking. Historically kit foxes (Vulpes macrotis) occupied the desert and semi-arid regions of southwestern North America. Once the most abundant carnivore in the Great Basin Desert of Utah, the species is now considered rare. In recent decades, attempts have been made to model the environmental variables influencing kit fox distribution. Using noninvasive scat deposition surveys for determination of kit fox presence, we modeled resource selection functions to predict kit fox distribution using three popular techniques (Maxent, fixed-effects, and mixed-effects generalized linear models) and compared these with similar models developed from invasive sampling (telemetry locations from radio-collared foxes). Resource selection functions were developed using a combination of landscape variables including elevation, slope, aspect, vegetation height, and soil type. All models were tested against subsequent scat collections as a method of model validation. We demonstrate the importance of comparing multiple model types for development of resource selection functions used to predict a species distribution, and evaluating the importance of environmental variables on species distribution. All models we examined showed a large effect of elevation on kit fox presence, followed by slope and vegetation height. However, the invasive sampling method (i.e., radio-telemetry) appeared to be better at determining resource selection, and therefore may be more robust in predicting kit fox distribution. In contrast, the distribution maps created from the noninvasive sampling (i.e., scat transects) were significantly different than the invasive method, thus scat transects may be appropriate when used in an occupancy framework to predict species distribution. We concluded that while scat deposition transects may be useful for monitoring kit fox abundance and possibly occupancy, they do not appear to be appropriate for determining resource selection. On our study area, scat transects were biased to roadways, while data collected using radio-telemetry was dictated by movements of the kit foxes themselves. We recommend that future studies applying noninvasive scat sampling should consider a more robust random sampling design across the landscape (e.g., random transects or more complete road coverage) that would then provide a more accurate and unbiased depiction of resource selection useful to predict kit fox distribution.}, } @article {pmid26465139, year = {2015}, author = {Fahr, J and Abedi-Lartey, M and Esch, T and Machwitz, M and Suu-Ire, R and Wikelski, M and Dechmann, DK}, title = {Pronounced Seasonal Changes in the Movement Ecology of a Highly Gregarious Central-Place Forager, the African Straw-Coloured Fruit Bat (Eidolon helvum).}, journal = {PloS one}, volume = {10}, number = {10}, pages = {e0138985}, pmid = {26465139}, issn = {1932-6203}, mesh = {Accelerometry ; Animal Migration/*physiology ; Animals ; Chiroptera/*physiology ; Diet ; Feeding Behavior/*physiology ; Female ; Flight, Animal/*physiology ; Food Chain ; Fruit ; Geographic Information Systems ; Ghana ; Humans ; Male ; Plant Dispersal/physiology ; Remote Sensing Technology ; Seasons ; Trees ; Urbanization ; }, abstract = {BACKGROUND: Straw-coloured fruit bats (Eidolon helvum) migrate over vast distances across the African continent, probably following seasonal bursts of resource availability. This causes enormous fluctuations in population size, which in turn may influence the bats' impact on local ecosystems. We studied the movement ecology of this central-place forager with state-of-the-art GPS/acceleration loggers and concurrently monitored the seasonal fluctuation of the colony in Accra, Ghana. Habitat use on the landscape scale was assessed with remote sensing data as well as ground-truthing of foraging areas.

PRINCIPAL FINDINGS: During the wet season population low (~ 4000 individuals), bats foraged locally (3.5-36.7 km) in urban areas with low tree cover. Major food sources during this period were fruits of introduced trees. Foraging distances almost tripled (24.1-87.9 km) during the dry season population peak (~ 150,000 individuals), but this was not compensated for by reduced resting periods. Dry season foraging areas were random with regard to urban footprint and tree cover, and food consisted almost exclusively of nectar and pollen of native trees.

CONCLUSIONS AND SIGNIFICANCE: Our study suggests that straw-coloured fruit bats disperse seeds in the range of hundreds of meters up to dozens of kilometres, and pollinate trees for up to 88 km. Straw-coloured fruit bats forage over much larger distances compared to most other Old World fruit bats, thus providing vital ecosystem services across extensive landscapes. We recommend increased efforts aimed at maintaining E. helvum populations throughout Africa since their keystone role in various ecosystems is likely to increase due to the escalating loss of other seed dispersers as well as continued urbanization and habitat fragmentation.}, } @article {pmid26462237, year = {2015}, author = {Stahl, BA and Gross, JB and Speiser, DI and Oakley, TH and Patel, NH and Gould, DB and Protas, ME}, title = {A Transcriptomic Analysis of Cave, Surface, and Hybrid Isopod Crustaceans of the Species Asellus aquaticus.}, journal = {PloS one}, volume = {10}, number = {10}, pages = {e0140484}, pmid = {26462237}, issn = {1932-6203}, mesh = {Alleles ; Animals ; *Caves ; Female ; Gene Ontology ; Genetic Association Studies ; Genetic Linkage ; Genotype ; High-Throughput Nucleotide Sequencing ; *Hybridization, Genetic ; Isopoda/*genetics ; Male ; Molecular Sequence Data ; Polymorphism, Single Nucleotide/genetics ; Species Specificity ; Transcriptome/*genetics ; }, abstract = {Cave animals, compared to surface-dwelling relatives, tend to have reduced eyes and pigment, longer appendages, and enhanced mechanosensory structures. Pressing questions include how certain cave-related traits are gained and lost, and if they originate through the same or different genetic programs in independent lineages. An excellent system for exploring these questions is the isopod, Asellus aquaticus. This species includes multiple cave and surface populations that have numerous morphological differences between them. A key feature is that hybrids between cave and surface individuals are viable, which enables genetic crosses and linkage analyses. Here, we advance this system by analyzing single animal transcriptomes of Asellus aquaticus. We use high throughput sequencing of non-normalized cDNA derived from the head of a surface-dwelling male, the head of a cave-dwelling male, the head of a hybrid male (produced by crossing a surface individual with a cave individual), and a pooled sample of surface embryos and hatchlings. Assembling reads from surface and cave head RNA pools yielded an integrated transcriptome comprised of 23,984 contigs. Using this integrated assembly as a reference transcriptome, we aligned reads from surface-, cave- and hybrid- head tissue and pooled surface embryos and hatchlings. Our approach identified 742 SNPs and placed four new candidate genes to an existing linkage map for A. aquaticus. In addition, we examined SNPs for allele-specific expression differences in the hybrid individual. All of these resources will facilitate identification of genes and associated changes responsible for cave adaptation in A. aquaticus and, in concert with analyses of other species, will inform our understanding of the evolutionary processes accompanying adaptation to the subterranean environment.}, } @article {pmid26460745, year = {2015}, author = {Kramer, A and Beck, HC and Kumar, A and Kristensen, LP and Imhoff, JF and Labes, A}, title = {Proteomic Analysis of Anti-Cancerous Scopularide Production by a Marine Microascus brevicaulis Strain and Its UV Mutant.}, journal = {PloS one}, volume = {10}, number = {10}, pages = {e0140047}, pmid = {26460745}, issn = {1932-6203}, mesh = {Antineoplastic Agents/*metabolism ; Aquatic Organisms/*metabolism ; Ascomycota/growth & development/*metabolism/*radiation effects ; Depsipeptides/*biosynthesis ; Fungal Proteins/isolation & purification ; Gene Ontology ; Models, Biological ; Mutation/*genetics ; Proteome/metabolism ; Proteomics/*methods ; *Ultraviolet Rays ; }, abstract = {The marine fungus Microascus brevicaulis strain LF580 is a non-model secondary metabolite producer with high yields of the two secondary metabolites scopularides A and B, which exhibit distinct activities against tumour cell lines. A mutant strain was obtained using UV mutagenesis, showing faster growth and differences in pellet formation besides higher production levels. Here, we show the first proteome study of a marine fungus. Comparative proteomics were applied to gain deeper understanding of the regulation of production and of the physiology of the wild type strain and its mutant. For this purpose, an optimised protein extraction protocol was established. In total, 4759 proteins were identified. The central metabolic pathway of strain LF580 was mapped using the KEGG pathway analysis and GO annotation. Employing iTRAQ labelling, 318 proteins were shown to be significantly regulated in the mutant strain: 189 were down- and 129 upregulated. Proteomics are a powerful tool for the understanding of regulatory aspects: The differences on proteome level could be attributed to limited nutrient availability in the wild type strain due to a strong pellet formation. This information can be applied for optimisation on strain and process level. The linkage between nutrient limitation and pellet formation in the non-model fungus M. brevicaulis is in consensus with the knowledge on model organisms like Aspergillus niger and Penicillium chrysogenum.}, } @article {pmid26460003, year = {2015}, author = {Bhattacharyya, S and Gesteland, PH and Korgenski, K and Bjørnstad, ON and Adler, FR}, title = {Cross-immunity between strains explains the dynamical pattern of paramyxoviruses.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {112}, number = {43}, pages = {13396-13400}, pmid = {26460003}, issn = {1091-6490}, support = {K08 HS018538/HS/AHRQ HHS/United States ; }, mesh = {Cross Protection/*immunology ; Disease Outbreaks ; Humans ; Metapneumovirus/*immunology ; *Models, Immunological ; Paramyxoviridae Infections/*epidemiology/*immunology ; Prevalence ; Respiratory Syncytial Viruses/*immunology ; Respirovirus/*immunology ; Seasons ; Species Specificity ; }, abstract = {Viral respiratory tract diseases pose serious public health problems. Our ability to predict and thus, be able to prepare for outbreaks is strained by the complex factors driving the prevalence and severity of these diseases. The abundance of diseases and transmission dynamics of strains are not only affected by external factors, such as weather, but also driven by interactions among viruses mediated by human behavior and immunity. To untangle the complex out-of-phase annual and biennial pattern of three common paramyxoviruses, Respiratory Syncytial Virus (RSV), Human Parainfluenza Virus (HPIV), and Human Metapneumovirus (hMPV), we adopt a theoretical approach that integrates ecological and immunological mechanisms of disease interactions. By estimating parameters from multiyear time series of laboratory-confirmed cases from the intermountain west region of the United States and using statistical inference, we show that models of immune-mediated interactions better explain the data than those based on ecological competition by convalescence. The strength of cross-protective immunity among viruses is correlated with their genetic distance in the phylogenetic tree of the paramyxovirus family.}, } @article {pmid26459858, year = {2015}, author = {Tang, M and Chen, Z and Grover, CE and Wang, Y and Li, S and Liu, G and Ma, Z and Wendel, JF and Hua, J}, title = {Rapid evolutionary divergence of Gossypium barbadense and G. hirsutum mitochondrial genomes.}, journal = {BMC genomics}, volume = {16}, number = {}, pages = {770}, pmid = {26459858}, issn = {1471-2164}, mesh = {Base Sequence ; Computational Biology ; *Evolution, Molecular ; Gene Rearrangement ; Gene Transfer, Horizontal ; Genes, Mitochondrial ; *Genetic Variation ; *Genome, Mitochondrial ; Gossypium/*genetics ; High-Throughput Nucleotide Sequencing ; Molecular Sequence Data ; Mutation ; Phylogeny ; Pseudogenes ; RNA, Transfer/chemistry/genetics ; Sequence Alignment ; Synteny/genetics ; }, abstract = {BACKGROUND: The mitochondrial genome from upland cotton, G. hirsutum, was previously sequenced. To elucidate the evolution of mitochondrial genomic diversity within a single genus, we sequenced the mitochondrial genome from Sea Island cotton (Gossypium barbadense L.).

METHODS: Mitochondrial DNA from week-old etiolated seedlings was extracted from isolated organelles using discontinuous sucrose density gradient method. Mitochondrial genome was sequenced with Solexa using paired-end, 90 bp read. The clean reads were assembled into contigs using ABySS and finished via additional fosmid and BAC sequencing. Finally, the genome was annotated and analyzed using different softwares.

RESULTS: The G. barbadense (Sea Island cotton) mitochondrial genome was fully sequenced (677,434-bp) and compared to the mitogenome of upland cotton. The G. barbadense mitochondrial DNA contains seven more genes than that of upland cotton, with a total of 40 protein coding genes (excluding possible pseudogenes), 6 rRNA genes, and 29 tRNA genes. Of these 75 genes, atp1, mttB, nad4, nad9, rrn5, rrn18, and trnD(GTC)-cp were each represented by two identical copies. A single 64 kb repeat was largely responsible for the 9 % difference in genome size between the two mtDNAs. Comparison of genome structures between the two mitochondrial genomes revealed 8 rearranged syntenic regions and several large repeats. The largest repeat was missing from the master chromosome in G. hirsutum. Both mitochondrial genomes contain a duplicated copy of rps3 (rps3-2) in conjunction with a duplication of repeated sequences. Phylogenetic and divergence considerations suggest that a 544-bp fragment of rps3 was transferred to the nuclear genome shortly after divergence of the A- and D- genome diploid cottons.

CONCLUSION: These results highlight the insights to the evolution of structural variation between Sea Island and upland cotton mitochondrial genomes.}, } @article {pmid26458893, year = {2015}, author = {Pucholt, P and Sjödin, P and Weih, M and Rönnberg-Wästljung, AC and Berlin, S}, title = {Genome-wide transcriptional and physiological responses to drought stress in leaves and roots of two willow genotypes.}, journal = {BMC plant biology}, volume = {15}, number = {}, pages = {244}, pmid = {26458893}, issn = {1471-2229}, mesh = {Analysis of Variance ; *Droughts ; Gene Expression Profiling ; Gene Expression Regulation, Plant ; Gene Ontology ; Genes, Plant ; Genetic Association Studies ; *Genome, Plant ; Genotype ; Molecular Sequence Annotation ; Phenotype ; Plant Leaves/*genetics ; Plant Roots/*genetics ; Plant Shoots/anatomy & histology ; Salix/*genetics/*physiology ; Stress, Physiological/*genetics ; *Transcription, Genetic ; }, abstract = {BACKGROUND: Drought is a major environmental stress that can have severe impacts on plant productivity and survival. Understanding molecular mechanisms of drought responses is crucial in order to breed for drought adapted plant cultivars. The aim of the present study was to investigate phenotypic and transcriptional drought responses in two willow genotypes (520 and 592) originating from an experimental cross between S. viminalis × (S. viminalis × S. schwerinii). Willows are woody perennials in the Salicaceae plant family that are grown as bioenergy crops worldwide.

METHODS: An experiment was conducted where plants were exposed to drought and different eco-physiological parameters were assessed. RNA-seq data was furthermore generated with the Illumina technology from root tips and leaves from plants grown in drought and well-watered (WW) conditions. The RNA-seq data was assembled de novo with the Trinity assembler to create a reference gene set to which the reads were mapped in order to obtain differentially expressed genes (DEGs) between the drought and WW conditions. To investigate molecular mechanisms involved in the drought response, GO enrichment analyses were conducted. Candidate genes with a putative function in the drought response were also identified.

RESULTS: A total of 52,599 gene models were obtained and after filtering on gene expression (FPKM ≥ 1), 35,733 gene models remained, of which 24,421 contained open reading frames. A total of 5,112 unique DEGs were identified between drought and WW conditions, of which the majority were found in the root tips. Phenotypically, genotype 592 displayed less growth reduction in response to drought compared to genotype 520. At the transcriptional level, genotype 520 displayed a greater response in the leaves as more DEGs were found in genotype 520 compared to genotype 592. In contrast, the transcriptional responses in the root tips were rather similar between the two genotypes. A core set of candidate genes encoding proteins with a putative function in drought response was identified, for example MYBs and bZIPs as well as chlorophyll a/b binding proteins.

DISCUSSION: We found substantial differences in drought responses between the genotypes, both at the phenotypic and transcriptional levels. In addition to the genotypic variation in several traits, we also found indications for genotypic variation in trait plasticity, which could play a role in drought adaptation. Furthermore, the two genotypes displayed overall similar transcriptional responses in the root tips, but more variation in the leaves. It is thus possible that the observed phenotypic differences could be a result of transcriptional differences mostly at the leaf level.

CONCLUSIONS: This study has contributed to a better general understanding of drought responses in woody plants, specifically in willows, and has implications for breeding research towards more drought adapted plants.}, } @article {pmid26458227, year = {2016}, author = {Jousselin, E and Clamens, AL and Galan, M and Bernard, M and Maman, S and Gschloessl, B and Duport, G and Meseguer, AS and Calevro, F and Coeur d'acier, A}, title = {Assessment of a 16S rRNA amplicon Illumina sequencing procedure for studying the microbiome of a symbiont-rich aphid genus.}, journal = {Molecular ecology resources}, volume = {16}, number = {3}, pages = {628-640}, doi = {10.1111/1755-0998.12478}, pmid = {26458227}, issn = {1755-0998}, mesh = {Animals ; Aphids/*microbiology ; Bacteria/*classification/genetics/*isolation & purification ; Computational Biology/*methods ; High-Throughput Nucleotide Sequencing/*methods ; *Microbiota ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, DNA/methods ; Symbiosis ; }, abstract = {The bacterial communities inhabiting arthropods are generally dominated by a few endosymbionts that play an important role in the ecology of their hosts. Rather than comparing bacterial species richness across samples, ecological studies on arthropod endosymbionts often seek to identify the main bacterial strains associated with each specimen studied. The filtering out of contaminants from the results and the accurate taxonomic assignment of sequences are therefore crucial in arthropod microbiome studies. We aimed here to validate an Illumina 16S rRNA gene sequencing protocol and analytical pipeline for investigating endosymbiotic bacteria associated with aphids. Using replicate DNA samples from 12 species (Aphididae: Lachninae, Cinara) and several controls, we removed individual sequences not meeting a minimum threshold number of reads in each sample and carried out taxonomic assignment for the remaining sequences. With this approach, we show that (i) contaminants accounted for a negligible proportion of the bacteria identified in our samples; (ii) the taxonomic composition of our samples and the relative abundance of reads assigned to a taxon were very similar across PCR and DNA replicates for each aphid sample; in particular, bacterial DNA concentration had no impact on the results. Furthermore, by analysing the distribution of unique sequences across samples rather than aggregating them into operational taxonomic units (OTUs), we gained insight into the specificity of endosymbionts for their hosts. Our results confirm that Serratia symbiotica is often present in Cinara species, in addition to the primary symbiont, Buchnera aphidicola. Furthermore, our findings reveal new symbiotic associations with Erwinia- and Sodalis-related bacteria. We conclude with suggestions for generating and analysing 16S rRNA gene sequences for arthropod-endosymbiont studies.}, } @article {pmid26456470, year = {2016}, author = {Trautman, EP and Crawford, JM}, title = {Linking Biosynthetic Gene Clusters to their Metabolites via Pathway- Targeted Molecular Networking.}, journal = {Current topics in medicinal chemistry}, volume = {16}, number = {15}, pages = {1705-1716}, pmid = {26456470}, issn = {1873-4294}, support = {DP2 CA186575/CA/NCI NIH HHS/United States ; R00 GM097096/GM/NIGMS NIH HHS/United States ; 1DP2-CA186575/CA/NCI NIH HHS/United States ; R00-GM097096/GM/NIGMS NIH HHS/United States ; }, mesh = {Biological Products/*metabolism ; Biosynthetic Pathways/*genetics ; Computational Biology ; Humans ; Metabolic Networks and Pathways/*genetics ; Microbiota/genetics ; *Multigene Family ; }, abstract = {The connection of microbial biosynthetic gene clusters to the small molecule metabolites they encode is central to the discovery and characterization of new metabolic pathways with ecological and pharmacological potential. With increasing microbial genome sequence information being deposited into publicly available databases, it is clear that microbes have the coding capacity for many more biologically active small molecules than previously realized. Of increasing interest are the small molecules encoded by the human microbiome, as these metabolites likely mediate a variety of currently uncharacterized human-microbe interactions that influence health and disease. In this mini-review, we describe the ongoing biosynthetic, structural, and functional characterizations of the genotoxic colibactin pathway in gut bacteria as a thematic example of linking biosynthetic gene clusters to their metabolites. We also highlight other natural products that are produced through analogous biosynthetic logic and comment on some current disconnects between bioinformatics predictions and experimental structural characterizations. Lastly, we describe the use of pathway-targeted molecular networking as a tool to characterize secondary metabolic pathways within complex metabolomes and to aid in downstream metabolite structural elucidation efforts.}, } @article {pmid26456382, year = {2015}, author = {Link, JS and Pranovi, F and Libralato, S and Coll, M and Christensen, V and Solidoro, C and Fulton, EA}, title = {Emergent Properties Delineate Marine Ecosystem Perturbation and Recovery.}, journal = {Trends in ecology & evolution}, volume = {30}, number = {11}, pages = {649-661}, doi = {10.1016/j.tree.2015.08.011}, pmid = {26456382}, issn = {1872-8383}, mesh = {Biomass ; *Conservation of Natural Resources ; *Ecosystem ; *Food Chain ; *Marine Biology ; Models, Theoretical ; Oceans and Seas ; }, abstract = {Whether there are common and emergent patterns from marine ecosystems remains an important question because marine ecosystems provide billions of dollars of ecosystem services to the global community, but face many perturbations with significant consequences. Here, we develop cumulative trophic patterns for marine ecosystems, featuring sigmoidal cumulative biomass (cumB)-trophic level (TL) and 'hockey-stick' production (cumP)-cumB curves. The patterns have a trophodynamic theoretical basis and capitalize on emergent, fundamental, and invariant features of marine ecosystems. These patterns have strong global support, being observed in over 120 marine ecosystems. Parameters from these curves elucidate the direction and magnitude of marine ecosystem perturbation or recovery; if biomass and productivity can be monitored effectively over time, such relations may prove to be broadly useful. Curve parameters are proposed as possible ecosystem thresholds, perhaps to better manage the marine ecosystems of the world.}, } @article {pmid26455368, year = {2015}, author = {Barnard, S and Ippoliti, C and Di Flaviano, D and De Ruvo, A and Messori, S and Giovannini, A and Dalla Villa, P}, title = {Smartphone and GPS technology for free-roaming dog population surveillance - a methodological study.}, journal = {Veterinaria italiana}, volume = {51}, number = {3}, pages = {165-172}, doi = {10.12834/VetIt.233.2163.3}, pmid = {26455368}, issn = {1828-1427}, mesh = {Animals ; Dogs ; *Geographic Information Systems ; Homing Behavior ; Italy ; Population Surveillance/methods ; Records ; *Smartphone ; Urban Population ; }, abstract = {Free-roaming dogs (FRD) represent a potential threat to the quality of life in cities from an ecological, social and public health point of view. One of the most urgent concerns is the role of uncontrolled dogs as reservoirs of infectious diseases transmittable to humans and, above all, rabies. An estimate of the FRD population size and characteristics in a given area is the first step for any relevant intervention programme. Direct count methods are still prominent because of their non-invasive approach, information technologies can support such methods facilitating data collection and allowing for a more efficient data handling. This paper presents a new framework for data collection using a topological algorithm implemented as ArcScript in ESRI® ArcGIS software, which allows for a random selection of the sampling areas. It also supplies a mobile phone application for Android® operating system devices which integrates Global Positioning System (GPS) and Google MapsTM. The potential of such a framework was tested in 2 Italian regions. Coupling technological and innovative solutions associated with common counting methods facilitate data collection and transcription. It also paves the way to future applications, which could support dog population management systems.}, } @article {pmid26454874, year = {2015}, author = {Meirelles, PM and Gadelha, LM and Francini-Filho, RB and de Moura, RL and Amado-Filho, GM and Bastos, AC and Paranhos, RP and Rezende, CE and Swings, J and Siegle, E and Asp Neto, NE and Leitão, SN and Coutinho, R and Mattoso, M and Salomon, PS and Valle, RA and Pereira, RC and Kruger, RH and Thompson, C and Thompson, FL}, title = {BaMBa: towards the integrated management of Brazilian marine environmental data.}, journal = {Database : the journal of biological databases and curation}, volume = {2015}, number = {}, pages = {}, pmid = {26454874}, issn = {1758-0463}, mesh = {Animals ; *Aquatic Organisms/classification/physiology ; Biota/*physiology ; Brazil ; *Databases, Factual ; }, abstract = {A new open access database, Brazilian Marine Biodiversity (BaMBa) (https://marinebiodiversity.lncc.br), was developed in order to maintain large datasets from the Brazilian marine environment. Essentially, any environmental information can be added to BaMBa. Certified datasets obtained from integrated holistic studies, comprising physical-chemical parameters, -omics, microbiology, benthic and fish surveys can be deposited in the new database, enabling scientific, industrial and governmental policies and actions to be undertaken on marine resources. There is a significant number of databases, however BaMBa is the only integrated database resource both supported by a government initiative and exclusive for marine data. BaMBa is linked to the Information System on Brazilian Biodiversity (SiBBr, http://www.sibbr.gov.br/) and will offer opportunities for improved governance of marine resources and scientists' integration. Database URL: http://marinebiodiversity.lncc.br.}, } @article {pmid26451629, year = {2015}, author = {Ju, F and Zhang, T}, title = {Experimental Design and Bioinformatics Analysis for the Application of Metagenomics in Environmental Sciences and Biotechnology.}, journal = {Environmental science & technology}, volume = {49}, number = {21}, pages = {12628-12640}, doi = {10.1021/acs.est.5b03719}, pmid = {26451629}, issn = {1520-5851}, mesh = {Biodegradation, Environmental ; Biofuels ; Biotechnology/*methods ; Computational Biology/*methods ; Ecology/*methods ; Genome ; Metagenomics/*methods ; Microbial Consortia/genetics ; Microbial Interactions ; Research Design ; Sequence Analysis, DNA ; Waste Disposal, Fluid/methods ; }, abstract = {Recent advances in DNA sequencing technologies have prompted the widespread application of metagenomics for the investigation of novel bioresources (e.g., industrial enzymes and bioactive molecules) and unknown biohazards (e.g., pathogens and antibiotic resistance genes) in natural and engineered microbial systems across multiple disciplines. This review discusses the rigorous experimental design and sample preparation in the context of applying metagenomics in environmental sciences and biotechnology. Moreover, this review summarizes the principles, methodologies, and state-of-the-art bioinformatics procedures, tools and database resources for metagenomics applications and discusses two popular strategies (analysis of unassembled reads versus assembled contigs/draft genomes) for quantitative or qualitative insights of microbial community structure and functions. Overall, this review aims to facilitate more extensive application of metagenomics in the investigation of uncultured microorganisms, novel enzymes, microbe-environment interactions, and biohazards in biotechnological applications where microbial communities are engineered for bioenergy production, wastewater treatment, and bioremediation.}, } @article {pmid26450849, year = {2015}, author = {Ressayre, A and Glémin, S and Montalent, P and Serre-Giardi, L and Dillmann, C and Joets, J}, title = {Introns Structure Patterns of Variation in Nucleotide Composition in Arabidopsis thaliana and Rice Protein-Coding Genes.}, journal = {Genome biology and evolution}, volume = {7}, number = {10}, pages = {2913-2928}, pmid = {26450849}, issn = {1759-6653}, mesh = {Arabidopsis/*genetics/metabolism ; Base Composition ; *Codon ; DNA, Complementary/genetics/metabolism ; Databases, Genetic ; Exons ; Gene Conversion ; Genome, Plant ; *Introns ; Nucleotides/*genetics/metabolism ; Open Reading Frames ; Oryza/*genetics/metabolism ; Plant Proteins/*genetics/metabolism ; Species Specificity ; }, abstract = {Plant genomes present a continuous range of variation in nucleotide composition (G + C content). In coding regions, G + C-poor species tend to have unimodal distributions of G + C content among genes within genomes and slight 5'-3' gradients along genes. In contrast, G + C-rich species display bimodal distributions of G + C content among genes and steep 5'-3' decreasing gradients along genes. The causes of these peculiar patterns are still poorly understood. Within two species (Arabidopsis thaliana and rice), each representative of one side of the continuum, we studied the consequences of intron presence on coding region and intron G + C content at different scales. By properly taking intron structure into account, we showed that, in both species, intron presence is associated with step changes in nucleotide, codon, and amino acid composition. This suggests that introns have a barrier effect structuring G + C content along genes and that previous continuous characterizations of the 5'-3' gradients were artifactual. In external gene regions (located upstream first or downstream last introns), species-specific factors, such as GC-biased gene conversion, are shaping G + C content whereas in internal gene regions (surrounded by introns), G + C content is likely constrained to remain within a range common to both species.}, } @article {pmid26450644, year = {2016}, author = {Blanckenhorn, WU and Rohner, PT and Bernasconi, MV and Haugstetter, J and Buser, A}, title = {Is qualitative and quantitative metabarcoding of dung fauna biodiversity feasible?.}, journal = {Environmental toxicology and chemistry}, volume = {35}, number = {8}, pages = {1970-1977}, doi = {10.1002/etc.3275}, pmid = {26450644}, issn = {1552-8618}, mesh = {Animals ; *Biodiversity ; Coleoptera/classification/genetics ; Computational Biology ; *DNA Barcoding, Taxonomic ; Diptera/classification/genetics ; Environmental Monitoring/*methods ; Feasibility Studies ; *Feces ; }, abstract = {In biodiversity assessments, especially of small-bodied organisms for which taxonomic expertise is lacking, identification by genetic barcoding may be a cost-effective and efficient alternative to traditional identification of species by morphology, ecology, and behavior. The authors tested the feasibility and accuracy of such an approach using dung insects of practical relevance in ecotoxicological assessments of veterinary pharmaceutical residues in the environment. They produced 8 known mixtures that varied in absolute and relative composition of small-bodied and large-bodied species to see whether mitochondrial cytochrome c oxidase subunit 1 barcoding picks up all species qualitatively and quantitatively. As demonstrated before in other contexts, such metabarcoding of large numbers of dung insect specimens is principally possible using next-generation sequencing. The authors recovered most species in a sample (low type I error), at minimum permitting analysis of species richness. They obtained even quantitative responses reflecting the body size of the species, although the number of specimens was not well detected. The latter is problematic when calculating diversity indices. Nevertheless, the method yielded too many closely related false positives (type II error), thus generally overestimating species diversity and richness. These errors can be reduced by refining methods and data filtering, although this requires bioinformatics expertise often unavailable where such research is carried out. Identification by barcoding foremost hinges on a good reference database, which does not yet exist for dung organisms but would be worth developing for practical applications. Environ Toxicol Chem 2016;35:1970-1977. © 2015 SETAC.}, } @article {pmid26450523, year = {2016}, author = {Anderson, EC and Ng, TC}, title = {Bayesian pedigree inference with small numbers of single nucleotide polymorphisms via a factor-graph representation.}, journal = {Theoretical population biology}, volume = {107}, number = {}, pages = {39-51}, doi = {10.1016/j.tpb.2015.09.005}, pmid = {26450523}, issn = {1096-0325}, mesh = {Algorithms ; Animals ; Bayes Theorem ; Computational Biology/*methods ; Computer Simulation ; Genetic Markers/*genetics ; Genotype ; Likelihood Functions ; Markov Chains ; *Pedigree ; Polymorphism, Single Nucleotide ; Salmon/*genetics ; Siblings ; }, abstract = {We develop a computational framework for addressing pedigree inference problems using small numbers (80-400) of single nucleotide polymorphisms (SNPs). Our approach relaxes the assumptions, which are commonly made, that sampling is complete with respect to the pedigree and that there is no genotyping error. It relies on representing the inferred pedigree as a factor graph and invoking the Sum-Product algorithm to compute and store quantities that allow the joint probability of the data to be rapidly computed under a large class of rearrangements of the pedigree structure. This allows efficient MCMC sampling over the space of pedigrees, and, hence, Bayesian inference of pedigree structure. In this paper we restrict ourselves to inference of pedigrees without loops using SNPs assumed to be unlinked. We present the methodology in general for multigenerational inference, and we illustrate the method by applying it to the inference of full sibling groups in a large sample (n=1157) of Chinook salmon typed at 95 SNPs. The results show that our method provides a better point estimate and estimate of uncertainty than the currently best-available maximum-likelihood sibling reconstruction method. Extensions of this work to more complex scenarios are briefly discussed.}, } @article {pmid26442024, year = {2015}, author = {Nicholls, JA and Pennington, RT and Koenen, EJ and Hughes, CE and Hearn, J and Bunnefeld, L and Dexter, KG and Stone, GN and Kidner, CA}, title = {Using targeted enrichment of nuclear genes to increase phylogenetic resolution in the neotropical rain forest genus Inga (Leguminosae: Mimosoideae).}, journal = {Frontiers in plant science}, volume = {6}, number = {}, pages = {710}, pmid = {26442024}, issn = {1664-462X}, support = {G0900740/MRC_/Medical Research Council/United Kingdom ; MR/K001744/1/MRC_/Medical Research Council/United Kingdom ; }, abstract = {Evolutionary radiations are prominent and pervasive across many plant lineages in diverse geographical and ecological settings; in neotropical rainforests there is growing evidence suggesting that a significant fraction of species richness is the result of recent radiations. Understanding the evolutionary trajectories and mechanisms underlying these radiations demands much greater phylogenetic resolution than is currently available for these groups. The neotropical tree genus Inga (Leguminosae) is a good example, with ~300 extant species and a crown age of 2-10 MY, yet over 6 kb of plastid and nuclear DNA sequence data gives only poor phylogenetic resolution among species. Here we explore the use of larger-scale nuclear gene data obtained though targeted enrichment to increase phylogenetic resolution within Inga. Transcriptome data from three Inga species were used to select 264 nuclear loci for targeted enrichment and sequencing. Following quality control to remove probable paralogs from these sequence data, the final dataset comprised 259,313 bases from 194 loci for 24 accessions representing 22 Inga species and an outgroup (Zygia). Bayesian phylogenies reconstructed using either all loci concatenated or a gene-tree/species-tree approach yielded highly resolved phylogenies. We used coalescent approaches to show that the same targeted enrichment data also have significant power to discriminate among alternative within-species population histories within the widespread species I. umbellifera. In either application, targeted enrichment simplifies the informatics challenge of identifying orthologous loci associated with de novo genome sequencing. We conclude that targeted enrichment provides the large volumes of phylogenetically-informative sequence data required to resolve relationships within recent plant species radiations, both at the species level and for within-species phylogeographic studies.}, } @article {pmid26441345, year = {2016}, author = {Tsuda, T and Tokinobu, A and Yamamoto, E and Suzuki, E}, title = {Thyroid Cancer Detection by Ultrasound Among Residents Ages 18 Years and Younger in Fukushima, Japan: 2011 to 2014.}, journal = {Epidemiology (Cambridge, Mass.)}, volume = {27}, number = {3}, pages = {316-322}, pmid = {26441345}, issn = {1531-5487}, mesh = {Adolescent ; Biopsy, Fine-Needle ; Child ; Child, Preschool ; Early Detection of Cancer ; Female ; *Fukushima Nuclear Accident ; Humans ; Incidence ; Infant ; Infant, Newborn ; Japan/epidemiology ; Male ; Neoplasms, Radiation-Induced/diagnostic imaging/*epidemiology/pathology ; Odds Ratio ; Prevalence ; Risk Factors ; Thyroid Neoplasms/diagnostic imaging/*epidemiology/pathology ; Ultrasonography ; }, abstract = {BACKGROUND: After the Great East Japan Earthquake and Tsunami in March 2011, radioactive elements were released from the Fukushima Daiichi Nuclear Power Plant. Based on prior knowledge, concern emerged about whether an increased incidence of thyroid cancer among exposed residents would occur as a result.

METHODS: After the release, Fukushima Prefecture performed ultrasound thyroid screening on all residents ages ≤18 years. The first round of screening included 298,577 examinees, and a second round began in April 2014. We analyzed the prefecture results from the first and second round up to December 31, 2014, in comparison with the Japanese annual incidence and the incidence within a reference area in Fukushima Prefecture.

RESULTS: The highest incidence rate ratio, using a latency period of 4 years, was observed in the central middle district of the prefecture compared with the Japanese annual incidence (incidence rate ratio = 50; 95% confidence interval [CI] = 25, 90). The prevalence of thyroid cancer was 605 per million examinees (95% CI = 302, 1,082) and the prevalence odds ratio compared with the reference district in Fukushima Prefecture was 2.6 (95% CI = 0.99, 7.0). In the second screening round, even under the assumption that the rest of examinees were disease free, an incidence rate ratio of 12 has already been observed (95% CI = 5.1, 23).

CONCLUSIONS: An excess of thyroid cancer has been detected by ultrasound among children and adolescents in Fukushima Prefecture within 4 years of the release, and is unlikely to be explained by a screening surge.}, } @article {pmid26439680, year = {2016}, author = {Zhang, BD and Xue, DX and Wang, J and Li, YL and Liu, BJ and Liu, JX}, title = {Development and preliminary evaluation of a genomewide single nucleotide polymorphisms resource generated by RAD-seq for the small yellow croaker (Larimichthys polyactis).}, journal = {Molecular ecology resources}, volume = {16}, number = {3}, pages = {755-768}, doi = {10.1111/1755-0998.12476}, pmid = {26439680}, issn = {1755-0998}, mesh = {Adaptation, Biological ; Animals ; *Databases, Genetic ; Genetics, Population ; *High-Throughput Nucleotide Sequencing ; Perciformes/*genetics ; *Polymorphism, Single Nucleotide ; }, abstract = {Recent advances in high-throughput sequencing technologies have offered the possibility to generate genomewide sequence data to delineate previously unidentified genetic structure, obtain more accurate estimates of demographic parameters and to evaluate potential adaptive divergence. Here, we identified 27 556 single nucleotide polymorphisms for the small yellow croaker (Larimichthys polyactis) using restriction-site-associated DNA (RAD) sequencing of 24 individuals from two populations. Significant sources of genetic variation were identified, with an average nucleotide diversity (π) of 0.00105 ± 0.000425 across individuals, and long-term effective population size was thus estimated to range between 26 172 and 261 716. According to the results, no differentiation between the two populations was detected based on the SNP data set of top quality score per contig or neutral loci. However, the two analysed populations were highly differentiated based on SNP data set of both top FST value per contig and the outlier SNPs. Moreover, local adaptation was highlighted by an FST -based outlier tests implemented in LOSITAN and a total of 538 potentially locally selected SNPs were identified. blast2go annotation of contigs containing the outlier SNPs yielded hits for 37 (66%) of 56 significant blastx matches. Candidate genes for local adaptation constituted a wide array of biological functions, including cellular response to oxidative stress, actin filament binding, ion transmembrane transport and synapse assembly. The generated SNP resources in this study provided a valuable tool for future population genetics and genomics studies of L. polyactis.}, } @article {pmid26439491, year = {2015}, author = {Berlincourt, M and Angel, LP and Arnould, JP}, title = {Combined Use of GPS and Accelerometry Reveals Fine Scale Three-Dimensional Foraging Behaviour in the Short-Tailed Shearwater.}, journal = {PloS one}, volume = {10}, number = {10}, pages = {e0139351}, pmid = {26439491}, issn = {1932-6203}, mesh = {Accelerometry ; Animals ; Appetitive Behavior/*physiology ; Australia ; Birds/*physiology ; Ecosystem ; Feeding Behavior/*physiology ; Flight, Animal/*physiology ; Geographic Information Systems ; Telemetry ; }, abstract = {Determining the foraging behaviour of free-ranging marine animals is fundamental for assessing their habitat use and how they may respond to changes in the environment. However, despite recent advances in bio-logging technology, collecting information on both at-sea movement patterns and activity budgets still remains difficult in small pelagic seabird species due to the constraints of instrument size. The short-tailed shearwater, the most abundant seabird species in Australia (ca 23 million individuals), is a highly pelagic procellariiform. Despite its ecological importance to the region, almost nothing is known about its at-sea behaviour, in particular, its foraging activity. Using a combination of GPS and tri-axial accelerometer data-loggers, the fine scale three-dimensional foraging behaviour of 10 breeding individuals from two colonies was investigated. Five at-sea behaviours were identified: (1) resting on water, (2) flapping flight, (3) gliding flight, (4) foraging (i.e., surface foraging and diving events), and (5) taking-off. There were substantial intra- and inter- individual variations in activity patterns, with individuals spending on average 45.8% (range: 17.1-70.0%) of time at sea resting on water and 18.2% (range: 2.3-49.6%) foraging. Individuals made 76.4 ± 65.3 dives (range: 8-237) per foraging trip (mean duration 9.0 ± 1.9 s), with dives also recorded during night-time. With the continued miniaturisation of recording devices, the use of combined data-loggers could provide us with further insights into the foraging behaviour of small procellariiforms, helping to better understand interactions with their prey.}, } @article {pmid26437354, year = {2016}, author = {Pecorari, E and Mantovani, A and Franceschini, C and Bassano, D and Palmeri, L and Rampazzo, G}, title = {Analysis of the effects of meteorology on aircraft exhaust dispersion and deposition using a Lagrangian particle model.}, journal = {The Science of the total environment}, volume = {541}, number = {}, pages = {839-856}, doi = {10.1016/j.scitotenv.2015.08.147}, pmid = {26437354}, issn = {1879-1026}, mesh = {Air Pollutants/*analysis ; Air Pollution/statistics & numerical data ; *Aircraft ; Airports ; Atmosphere/chemistry ; Cities ; *Environmental Monitoring ; Europe ; Meteorology ; Models, Theoretical ; Particulate Matter/analysis ; Vehicle Emissions/*analysis ; }, abstract = {The risk of air quality degradation is of considerable concern particularly for those airports that are located near urban areas. The ability to quantitatively predict the effects of air pollutants originated by airport operations is important for assessing air quality and the related impacts on human health. Current emission regulations have focused on local air quality in the proximity of airports. However, an integrated study should consider the effects of meteorological events, at both regional and local level, that can affect the dispersion and the deposition of exhausts. Rigorous scientific studies and extensive experimental data could contribute to the analysis of the impacts of airports expansion plans. This paper is focused on the analysis of the effects of meteorology on aircraft emission for the Marco Polo Airport in Venice. This is the most important international airport in the eastern part of the Po' Valley, one of the most polluted area in Europe. Air pollution is exacerbated by meteorology that is a combination of large and local scale effects that do not allow significant dispersion. Moreover, the airport is located near Venice, a city of noteworthy cultural and architectural relevance, and nearby the lagoon that hosts several areas of outstanding ecological importance at European level (Natura 2000 sites). Dispersion and deposit of the main aircraft exhausts (NOx, HC and CO) have been evaluated by using a Lagrangian particle model. Spatial and temporal aircraft exhaust dispersion has been analyzed for LTO cycle. Aircraft taxiing resulted to be the most impacting aircraft operation especially for the airport working area and its surroundings, however occasionally peaks may be observed even at high altitudes when cruise mode starts. Mixing height can affect concentrations more significantly than the concentrations in the exhausts themselves. An increase of HC and CO concentrations (15-50%) has been observed during specific meteorological events.}, } @article {pmid26436804, year = {2015}, author = {Paiva, VH and Geraldes, P and Rodrigues, I and Melo, T and Melo, J and Ramos, JA}, title = {The Foraging Ecology of the Endangered Cape Verde Shearwater, a Sentinel Species for Marine Conservation off West Africa.}, journal = {PloS one}, volume = {10}, number = {10}, pages = {e0139390}, pmid = {26436804}, issn = {1932-6203}, mesh = {Africa, Western ; Animal Migration ; Animals ; Area Under Curve ; Atlantic Ocean ; Biodiversity ; Birds/*physiology ; *Conservation of Natural Resources ; Diet ; *Ecosystem ; *Endangered Species ; *Feeding Behavior ; Female ; Fishes ; Geographic Information Systems ; Human Activities ; Male ; Models, Theoretical ; *Nesting Behavior ; *Predatory Behavior ; Probability ; ROC Curve ; Reproduction ; Species Specificity ; }, abstract = {Large Marine Ecosystems such as the Canary Current system off West Africa sustains high abundance of small pelagic prey, which attracts marine predators. Seabirds are top predators often used as biodiversity surrogates and sentinel species of the marine ecosystem health, thus frequently informing marine conservation planning. This study presents the first data on the spatial (GPS-loggers) and trophic (stable isotope analysis) ecology of a tropical seabird-the endangered Cape Verde shearwater Calonectris edwardsii-during both the incubation and the chick-rearing periods of two consecutive years. This information was related with marine environmental predictors (species distribution models), existent areas of conservation concern for seabirds (i.e. marine Important Bird Areas; marine IBAs) and threats to the marine environment in the West African areas heavily used by the shearwaters. There was an apparent inter-annual consistency on the spatial, foraging and trophic ecology of Cape Verde shearwater, but a strong alteration on the foraging strategies of adult breeders among breeding phases (i.e. from incubation to chick-rearing). During incubation, birds mostly targeted a discrete region off West Africa, known by its enhanced productivity profile and thus also highly exploited by international industrial fishery fleets. When chick-rearing, adults exploited the comparatively less productive tropical environment within the islands of Cape Verde, at relatively close distance from their breeding colony. The species enlarged its trophic niche and increased the trophic level of their prey from incubation to chick-rearing, likely to provision their chicks with a more diversified and better quality diet. There was a high overlap between the Cape Verde shearwaters foraging areas with those of European shearwater species that overwinter in this area and known areas of megafauna bycatch off West Africa, but very little overlap with existing Marine Important Bird Areas. Further investigation on the potential nefarious effects of fisheries on seabird communities exploiting the Canary Current system off West Africa is needed. Such negative effects could be alleviated or even dissipated if the 'fisheries-conservation hotspots' identified for the region, would be legislated as Marine Protected Areas.}, } @article {pmid26436732, year = {2015}, author = {Eweleit, L and Reinhold, K and Sauer, J}, title = {Speciation Progress: A Case Study on the Bushcricket Poecilimon veluchianus.}, journal = {PloS one}, volume = {10}, number = {10}, pages = {e0139494}, pmid = {26436732}, issn = {1932-6203}, mesh = {Animal Distribution ; Animals ; DNA, Mitochondrial/genetics ; DNA, Ribosomal Spacer ; Datasets as Topic ; Evolution, Molecular ; Female ; Gene Flow ; Genetic Markers ; *Genetic Speciation ; Genetic Variation ; Greece ; Gryllidae/classification/*genetics ; Homing Behavior ; Locus Control Region ; Male ; Models, Genetic ; Reproductive Isolation ; Sequence Alignment ; Sequence Homology, Nucleic Acid ; Species Specificity ; }, abstract = {Different mechanisms such as selection or genetic drift permitted e.g. by geographical isolation can lead to differentiation of populations and could cause subsequent speciation. The two subspecies of Poecilimon veluchianus, a bushcricket endemic to central Greece, show a parapatric distribution and are partially reproductively isolated. Therefore, P. veluchianus is suitable to investigate an ongoing speciation process. We based our analysis on sequences of the internal transcribed spacer (ITS) and the mitochondrial control region (CR). The population genetic analysis based on the nuclear marker ITS revealed a barrier to gene flow within the range of Poecilimon veluchianus, which corresponds well to the described subspecies. In contrast to the results based on the nuclear ITS marker, the mitochondrial CR marker does not clearly support the separation into two subspecies with restricted gene flow and a clear contact zone. Furthermore, we could identify isolation by distance (IBD) as one important mechanism responsible for the observed genetic structure (based on the ITS marker). The population genetic analysis based on the nuclear marker ITS also suggests the existence of hybrids in the wild. Furthermore, the simultaneous lack of strong prezygotic barriers and the presence of postzygotic mating barriers, observed in previous laboratory experiments, suggest that a secondary contact after an allopatric phase is more likely than parapatric speciation.}, } @article {pmid26433722, year = {2016}, author = {Tsypik, O and Yushchuk, O and Zaburannyi, N and Flärdh, K and Walker, S and Fedorenko, V and Ostash, B}, title = {Transcriptional regulators of GntR family in Streptomyces coelicolor A3(2): analysis in silico and in vivo of YtrA subfamily.}, journal = {Folia microbiologica}, volume = {61}, number = {3}, pages = {209-220}, pmid = {26433722}, issn = {1874-9356}, mesh = {Anti-Bacterial Agents/biosynthesis ; Bacterial Proteins/*genetics/*metabolism ; Computational Biology/methods ; DNA-Binding Proteins/genetics/metabolism ; Databases, Genetic ; *Gene Expression Regulation, Bacterial ; Gene Knockout Techniques ; Genome, Bacterial ; Glucuronidase/metabolism ; *Multigene Family ; Open Reading Frames ; Phenotype ; Phylogeny ; Streptomyces coelicolor/classification/*genetics/*metabolism ; Transcription Factors/*metabolism ; *Transcription, Genetic ; }, abstract = {Transcriptional factors of the GntR family regulate numerous physiological and morphological processes in response to the nutrient state of bacterial cells. The number of GntR transcriptional factors in genomes of soil-dwelling actinomycetes is one of the highest among bacteria, reflecting both the large size of their chromosomes and the complex ecological niche that they occupy. However, very little is known about the roles of GntRs in actinomycete biology. Here, we analyzed the genome of model actinomycete, Streptomyces coelicolor A3(2), in an attempt to gain new insights into the function of GntR family. All 56 GntR proteins of M145 strain were classified into FadR, HutC, MocR, YtrA, and DevA subfamilies according to their secondary structure. We then checked for the presence of GntR orthologs in six other sequenced Streptomyces and one Kitasatospora genomes, revealing that 12 GntRs were conserved in all analyzed strains. Genomic analysis of the less studied YtrA type regulators revealed 160 sequences present in 88 members of Coriobacteridae, Rubrobacteridae, and Actinobacteridae subclasses. These proteins form seven dense clusters on the consensus phylogenetic tree and their genes are usually co-located with the genes for transport proteins. Probable operator sites were identified for orthologous groups of Sco0823 and Sco3812 proteins. All S. coelicolor YtrA-like regulatory genes (SCO0823, SCO1728, SCO3812) were analyzed at transcriptional level, knocked out, and introduced on moderate copy number plasmid in M145 strain. Also, gene SCO0824, a part of putative SCO0823 operon, was studied. Results of these experiments are discussed here.}, } @article {pmid26431771, year = {2015}, author = {Hirao, K and Nagano, AJ and Awazu, A}, title = {Noise-plasticity correlations of gene expression in the multicellular organism Arabidopsis thaliana.}, journal = {Journal of theoretical biology}, volume = {387}, number = {}, pages = {13-22}, doi = {10.1016/j.jtbi.2015.09.017}, pmid = {26431771}, issn = {1095-8541}, mesh = {Arabidopsis/drug effects/*genetics/physiology ; Circadian Rhythm/drug effects/genetics ; Databases, Genetic ; *Gene Expression Regulation, Plant/drug effects ; Genes, Plant ; Plant Growth Regulators/pharmacology ; Promoter Regions, Genetic ; }, abstract = {Gene expression levels exhibit stochastic variations among genetically identical organisms under the same environmental conditions (called gene expression "noise" or phenotype "fluctuation"). In yeast and Escherichia coli, positive correlations have been found between such gene expression noise and "plasticity" with environmental variations. To determine the universality of such correlations in both unicellular and multicellular organisms, we focused on the relationships between gene expression "noise" and "plasticity" in Arabidopsis thaliana, a multicellular model organism. In recent studies on yeast and E. coli, only some gene groups with specific properties of promoter architecture, average expression levels, and functions exhibited strong noise-plasticity correlations. However, we found strong noise-plasticity correlations for most gene groups in Arabidopsis; additionally, promoter architecture, functional essentiality of genes, and circadian rhythm appeared to have only a weak influence on the correlation strength. The differences in the characteristics of noise-plasticity correlations may result from three-dimensional chromosomal structures and/or circadian rhythm.}, } @article {pmid26426971, year = {2015}, author = {Winkler, TW and Justice, AE and Graff, M and Barata, L and Feitosa, MF and Chu, S and Czajkowski, J and Esko, T and Fall, T and Kilpeläinen, TO and Lu, Y and Mägi, R and Mihailov, E and Pers, TH and Rüeger, S and Teumer, A and Ehret, GB and Ferreira, T and Heard-Costa, NL and Karjalainen, J and Lagou, V and Mahajan, A and Neinast, MD and Prokopenko, I and Simino, J and Teslovich, TM and Jansen, R and Westra, HJ and White, CC and Absher, D and Ahluwalia, TS and Ahmad, S and Albrecht, E and Alves, AC and Bragg-Gresham, JL and de Craen, AJ and Bis, JC and Bonnefond, A and Boucher, G and Cadby, G and Cheng, YC and Chiang, CW and Delgado, G and Demirkan, A and Dueker, N and Eklund, N and Eiriksdottir, G and Eriksson, J and Feenstra, B and Fischer, K and Frau, F and Galesloot, TE and Geller, F and Goel, A and Gorski, M and Grammer, TB and Gustafsson, S and Haitjema, S and Hottenga, JJ and Huffman, JE and Jackson, AU and Jacobs, KB and Johansson, Å and Kaakinen, M and Kleber, ME and Lahti, J and Mateo Leach, I and Lehne, B and Liu, Y and Lo, KS and Lorentzon, M and Luan, J and Madden, PA and Mangino, M and McKnight, B and Medina-Gomez, C and Monda, KL and Montasser, ME and Müller, G and Müller-Nurasyid, M and Nolte, IM and Panoutsopoulou, K and Pascoe, L and Paternoster, L and Rayner, NW and Renström, F and Rizzi, F and Rose, LM and Ryan, KA and Salo, P and Sanna, S and Scharnagl, H and Shi, J and Smith, AV and Southam, L and Stančáková, A and Steinthorsdottir, V and Strawbridge, RJ and Sung, YJ and Tachmazidou, I and Tanaka, T and Thorleifsson, G and Trompet, S and Pervjakova, N and Tyrer, JP and Vandenput, L and van der Laan, SW and van der Velde, N and van Setten, J and van Vliet-Ostaptchouk, JV and Verweij, N and Vlachopoulou, E and Waite, LL and Wang, SR and Wang, Z and Wild, SH and Willenborg, C and Wilson, JF and Wong, A and Yang, J and Yengo, L and Yerges-Armstrong, LM and Yu, L and Zhang, W and Zhao, JH and Andersson, EA and Bakker, SJ and Baldassarre, D and Banasik, K and Barcella, M and Barlassina, C and Bellis, C and Benaglio, P and Blangero, J and Blüher, M and Bonnet, F and Bonnycastle, LL and Boyd, HA and Bruinenberg, M and Buchman, AS and Campbell, H and Chen, YD and Chines, PS and Claudi-Boehm, S and Cole, J and Collins, FS and de Geus, EJ and de Groot, LC and Dimitriou, M and Duan, J and Enroth, S and Eury, E and Farmaki, AE and Forouhi, NG and Friedrich, N and Gejman, PV and Gigante, B and Glorioso, N and Go, AS and Gottesman, O and Gräßler, J and Grallert, H and Grarup, N and Gu, YM and Broer, L and Ham, AC and Hansen, T and Harris, TB and Hartman, CA and Hassinen, M and Hastie, N and Hattersley, AT and Heath, AC and Henders, AK and Hernandez, D and Hillege, H and Holmen, O and Hovingh, KG and Hui, J and Husemoen, LL and Hutri-Kähönen, N and Hysi, PG and Illig, T and De Jager, PL and Jalilzadeh, S and Jørgensen, T and Jukema, JW and Juonala, M and Kanoni, S and Karaleftheri, M and Khaw, KT and Kinnunen, L and Kittner, SJ and Koenig, W and Kolcic, I and Kovacs, P and Krarup, NT and Kratzer, W and Krüger, J and Kuh, D and Kumari, M and Kyriakou, T and Langenberg, C and Lannfelt, L and Lanzani, C and Lotay, V and Launer, LJ and Leander, K and Lindström, J and Linneberg, A and Liu, YP and Lobbens, S and Luben, R and Lyssenko, V and Männistö, S and Magnusson, PK and McArdle, WL and Menni, C and Merger, S and Milani, L and Montgomery, GW and Morris, AP and Narisu, N and Nelis, M and Ong, KK and Palotie, A and Pérusse, L and Pichler, I and Pilia, MG and Pouta, A and Rheinberger, M and Ribel-Madsen, R and Richards, M and Rice, KM and Rice, TK and Rivolta, C and Salomaa, V and Sanders, AR and Sarzynski, MA and Scholtens, S and Scott, RA and Scott, WR and Sebert, S and Sengupta, S and Sennblad, B and Seufferlein, T and Silveira, A and Slagboom, PE and Smit, JH and Sparsø, TH and Stirrups, K and Stolk, RP and Stringham, HM and Swertz, MA and Swift, AJ and Syvänen, AC and Tan, ST and Thorand, B and Tönjes, A and Tremblay, A and Tsafantakis, E and van der Most, PJ and Völker, U and Vohl, MC and Vonk, JM and Waldenberger, M and Walker, RW and Wennauer, R and Widén, E and Willemsen, G and Wilsgaard, T and Wright, AF and Zillikens, MC and van Dijk, SC and van Schoor, NM and Asselbergs, FW and de Bakker, PI and Beckmann, JS and Beilby, J and Bennett, DA and Bergman, RN and Bergmann, S and Böger, CA and Boehm, BO and Boerwinkle, E and Boomsma, DI and Bornstein, SR and Bottinger, EP and Bouchard, C and Chambers, JC and Chanock, SJ and Chasman, DI and Cucca, F and Cusi, D and Dedoussis, G and Erdmann, J and Eriksson, JG and Evans, DA and de Faire, U and Farrall, M and Ferrucci, L and Ford, I and Franke, L and Franks, PW and Froguel, P and Gansevoort, RT and Gieger, C and Grönberg, H and Gudnason, V and Gyllensten, U and Hall, P and Hamsten, A and van der Harst, P and Hayward, C and Heliövaara, M and Hengstenberg, C and Hicks, AA and Hingorani, A and Hofman, A and Hu, F and Huikuri, HV and Hveem, K and James, AL and Jordan, JM and Jula, A and Kähönen, M and Kajantie, E and Kathiresan, S and Kiemeney, LA and Kivimaki, M and Knekt, PB and Koistinen, HA and Kooner, JS and Koskinen, S and Kuusisto, J and Maerz, W and Martin, NG and Laakso, M and Lakka, TA and Lehtimäki, T and Lettre, G and Levinson, DF and Lind, L and Lokki, ML and Mäntyselkä, P and Melbye, M and Metspalu, A and Mitchell, BD and Moll, FL and Murray, JC and Musk, AW and Nieminen, MS and Njølstad, I and Ohlsson, C and Oldehinkel, AJ and Oostra, BA and Palmer, LJ and Pankow, JS and Pasterkamp, G and Pedersen, NL and Pedersen, O and Penninx, BW and Perola, M and Peters, A and Polašek, O and Pramstaller, PP and Psaty, BM and Qi, L and Quertermous, T and Raitakari, OT and Rankinen, T and Rauramaa, R and Ridker, PM and Rioux, JD and Rivadeneira, F and Rotter, JI and Rudan, I and den Ruijter, HM and Saltevo, J and Sattar, N and Schunkert, H and Schwarz, PE and Shuldiner, AR and Sinisalo, J and Snieder, H and Sørensen, TI and Spector, TD and Staessen, JA and Stefania, B and Thorsteinsdottir, U and Stumvoll, M and Tardif, JC and Tremoli, E and Tuomilehto, J and Uitterlinden, AG and Uusitupa, M and Verbeek, AL and Vermeulen, SH and Viikari, JS and Vitart, V and Völzke, H and Vollenweider, P and Waeber, G and Walker, M and Wallaschofski, H and Wareham, NJ and Watkins, H and Zeggini, E and , and , and , and , and , and , and Chakravarti, A and Clegg, DJ and Cupples, LA and Gordon-Larsen, P and Jaquish, CE and Rao, DC and Abecasis, GR and Assimes, TL and Barroso, I and Berndt, SI and Boehnke, M and Deloukas, P and Fox, CS and Groop, LC and Hunter, DJ and Ingelsson, E and Kaplan, RC and McCarthy, MI and Mohlke, KL and O'Connell, JR and Schlessinger, D and Strachan, DP and Stefansson, K and van Duijn, CM and Hirschhorn, JN and Lindgren, CM and Heid, IM and North, KE and Borecki, IB and Kutalik, Z and Loos, RJ}, title = {The Influence of Age and Sex on Genetic Associations with Adult Body Size and Shape: A Large-Scale Genome-Wide Interaction Study.}, journal = {PLoS genetics}, volume = {11}, number = {10}, pages = {e1005378}, pmid = {26426971}, issn = {1553-7404}, support = {R01 DK072193/DK/NIDDK NIH HHS/United States ; U01 MH079470/MH/NIMH NIH HHS/United States ; MR/K013351/1/MRC_/Medical Research Council/United Kingdom ; RC2 MH089951/MH/NIMH NIH HHS/United States ; R01 MH061675/MH/NIMH NIH HHS/United States ; U01 HL105198/HL/NHLBI NIH HHS/United States ; R01 DK093757/DK/NIDDK NIH HHS/United States ; N01HC55020/HL/NHLBI NIH HHS/United States ; R01 HL103612/HL/NHLBI NIH HHS/United States ; 098017/WT_/Wellcome Trust/United Kingdom ; R01 MH063706/MH/NIMH NIH HHS/United States ; R01 AA007535/AA/NIAAA NIH HHS/United States ; R01 NS045012/NS/NINDS NIH HHS/United States ; P60 AR049465/AR/NIAMS NIH HHS/United States ; U01 HG004438/HG/NHGRI NIH HHS/United States ; N01AG12100/AG/NIA NIH HHS/United States ; R01 AA014041/AA/NIAAA NIH HHS/United States ; R01 MH081802/MH/NIMH NIH HHS/United States ; RF1 AG015819/AG/NIA NIH HHS/United States ; N01HG65403/HG/NHGRI NIH HHS/United States ; U01 HG004446/HG/NHGRI NIH HHS/United States ; R01 HL120393/HL/NHLBI NIH HHS/United States ; N01HC55018/HL/NHLBI NIH HHS/United States ; R01 HL036310/HL/NHLBI NIH HHS/United States ; R01 HL087647/HL/NHLBI NIH HHS/United States ; U01 HL084729/HL/NHLBI NIH HHS/United States ; UL1 RR025005/RR/NCRR NIH HHS/United States ; MC_UP_A100_1003/MRC_/Medical Research Council/United Kingdom ; U01 HL080295/HL/NHLBI NIH HHS/United States ; R01 HL087679/HL/NHLBI NIH HHS/United States ; RC2 MH089995/MH/NIMH NIH HHS/United States ; R01 HL087676/HL/NHLBI NIH HHS/United States ; P60 AR030701/AR/NIAMS NIH HHS/United States ; R01 HG002651/HG/NHGRI NIH HHS/United States ; R01 HL043851/HL/NHLBI NIH HHS/United States ; R01 HL059367/HL/NHLBI NIH HHS/United States ; R01 MD009164/MD/NIMHD NIH HHS/United States ; R01 AG030146/AG/NIA NIH HHS/United States ; HHSN268200800007C/HL/NHLBI NIH HHS/United States ; MC_UU_12015/1/MRC_/Medical Research Council/United Kingdom ; R01 HL086694/HL/NHLBI NIH HHS/United States ; U01 MH079469/MH/NIMH NIH HHS/United States ; T32 HL091823/HL/NHLBI NIH HHS/United States ; R01 DK091718/DK/NIDDK NIH HHS/United States ; R01 AG008724/AG/NIA NIH HHS/United States ; R01 AA013326/AA/NIAAA NIH HHS/United States ; G1001799/MRC_/Medical Research Council/United Kingdom ; R01 AG017917/AG/NIA NIH HHS/United States ; T32 HG000040/HG/NHGRI NIH HHS/United States ; R56 DA012854/DA/NIDA NIH HHS/United States ; R01 HL087652/HL/NHLBI NIH HHS/United States ; U01 HG004402/HG/NHGRI NIH HHS/United States ; N01HC55022/HL/NHLBI NIH HHS/United States ; R01 DK075787/DK/NIDDK NIH HHS/United States ; UL1 TR000124/TR/NCATS NIH HHS/United States ; N01HC55222/HL/NHLBI NIH HHS/United States ; G0700931/MRC_/Medical Research Council/United Kingdom ; N02HL64278/HL/NHLBI NIH HHS/United States ; R01 DK075681/DK/NIDDK NIH HHS/United States ; N01HC85086/HL/NHLBI NIH HHS/United States ; N01HC55015/HL/NHLBI NIH HHS/United States ; G0000934/MRC_/Medical Research Council/United Kingdom ; 20308/VAC_/Versus Arthritis/United Kingdom ; R01 MH067257/MH/NIMH NIH HHS/United States ; R01 AA013321/AA/NIAAA NIH HHS/United States ; R01 DK062370/DK/NIDDK NIH HHS/United States ; R01 HL105756/HL/NHLBI NIH HHS/United States ; RG/13/2/30098/BHF_/British Heart Foundation/United Kingdom ; R01 MH060870/MH/NIMH NIH HHS/United States ; R01 MH081800/MH/NIMH NIH HHS/United States ; R37 AG013196/AG/NIA NIH HHS/United States ; P30 DK046200/DK/NIDDK NIH HHS/United States ; U01 DK062418/DK/NIDDK NIH HHS/United States ; R01 AG028555/AG/NIA NIH HHS/United States ; MC_UU_12015/2/MRC_/Medical Research Council/United Kingdom ; U01 HL084756/HL/NHLBI NIH HHS/United States ; P30 DK063491/DK/NIDDK NIH HHS/United States ; R01 MH059571/MH/NIMH NIH HHS/United States ; MR/N01104X/1/MRC_/Medical Research Council/United Kingdom ; R01 MH059565/MH/NIMH NIH HHS/United States ; MC_UU_12019/1/MRC_/Medical Research Council/United Kingdom ; HHSN268201200036C/HL/NHLBI NIH HHS/United States ; P30 AG010161/AG/NIA NIH HHS/United States ; P30 DK072488/DK/NIDDK NIH HHS/United States ; U01 NS069208/NS/NINDS NIH HHS/United States ; 20109/VAC_/Versus Arthritis/United Kingdom ; G0600705/MRC_/Medical Research Council/United Kingdom ; G0401527/MRC_/Medical Research Council/United Kingdom ; R01 MH059587/MH/NIMH NIH HHS/United States ; Z01 HG000024/ImNIH/Intramural NIH HHS/United States ; G1002319/MRC_/Medical Research Council/United Kingdom ; MC_PC_U127561128/MRC_/Medical Research Council/United Kingdom ; P30 DK020541/DK/NIDDK NIH HHS/United States ; MC_U106179472/MRC_/Medical Research Council/United Kingdom ; G1000143/MRC_/Medical Research Council/United Kingdom ; N01HC55016/HL/NHLBI NIH HHS/United States ; U01 HL072515/HL/NHLBI NIH HHS/United States ; U24 MH068457/MH/NIMH NIH HHS/United States ; UM1 CA182913/CA/NCI NIH HHS/United States ; U01 CA098233/CA/NCI NIH HHS/United States ; M01 RR016500/RR/NCRR NIH HHS/United States ; MR/K002414/1/MRC_/Medical Research Council/United Kingdom ; R01 DA012854/DA/NIDA NIH HHS/United States ; 098395/WT_/Wellcome Trust/United Kingdom ; R01 MH059586/MH/NIMH NIH HHS/United States ; U01 DK062370/DK/NIDDK NIH HHS/United States ; R01 HL071981/HL/NHLBI NIH HHS/United States ; RG/10/12/28456/BHF_/British Heart Foundation/United Kingdom ; HHSN268200782096C/HL/NHLBI NIH HHS/United States ; R01 CA047988/CA/NCI NIH HHS/United States ; G0601966/MRC_/Medical Research Council/United Kingdom ; N01AG12109/AG/NIA NIH HHS/United States ; N01HC55019/HL/NHLBI NIH HHS/United States ; R01 HL080467/HL/NHLBI NIH HHS/United States ; N01HC85082/HL/NHLBI NIH HHS/United States ; U01 HG004436/HG/NHGRI NIH HHS/United States ; 14136/CRUK_/Cancer Research UK/United Kingdom ; R01 DK089256/DK/NIDDK NIH HHS/United States ; R01 AG013196/AG/NIA NIH HHS/United States ; N01HC85083/HL/NHLBI NIH HHS/United States ; N01HC25195/HL/NHLBI NIH HHS/United States ; P30 DK020572/DK/NIDDK NIH HHS/United States ; R01 MH059566/MH/NIMH NIH HHS/United States ; P60 DK020541/DK/NIDDK NIH HHS/United States ; /WT_/Wellcome Trust/United Kingdom ; R01 AG011101/AG/NIA NIH HHS/United States ; T32 AG000219/AG/NIA NIH HHS/United States ; MC_UU_12015/5/MRC_/Medical Research Council/United Kingdom ; U01 HG004423/HG/NHGRI NIH HHS/United States ; RL1 MH083268/MH/NIMH NIH HHS/United States ; R01 MH059588/MH/NIMH NIH HHS/United States ; N01HC85079/HL/NHLBI NIH HHS/United States ; 098381/WT_/Wellcome Trust/United Kingdom ; F32 AR059469/AR/NIAMS NIH HHS/United States ; R01 HL117078/HL/NHLBI NIH HHS/United States ; N01HC55021/HL/NHLBI NIH HHS/United States ; R01 AG023629/AG/NIA NIH HHS/United States ; R01 HL087641/HL/NHLBI NIH HHS/United States ; P2C HD050924/HD/NICHD NIH HHS/United States ; T32 HL007055/HL/NHLBI NIH HHS/United States ; N01HC85080/HL/NHLBI NIH HHS/United States ; R01 AG010175/AG/NIA NIH HHS/United States ; MC_U106179471/MRC_/Medical Research Council/United Kingdom ; U01 GM074518/GM/NIGMS NIH HHS/United States ; R56 AG023629/AG/NIA NIH HHS/United States ; U54 RR020278/RR/NCRR NIH HHS/United States ; R01 AG015819/AG/NIA NIH HHS/United States ; R01 MH060879/MH/NIMH NIH HHS/United States ; R01 AA013320/AA/NIAAA NIH HHS/United States ; N01HC85081/HL/NHLBI NIH HHS/United States ; R01 HL045670/HL/NHLBI NIH HHS/United States ; }, mesh = {Adult ; Age Factors ; Aged ; *Body Mass Index ; Body Size/*genetics ; Chromosome Mapping ; Female ; *Genetic Predisposition to Disease ; *Genome-Wide Association Study ; Humans ; Male ; Middle Aged ; Polymorphism, Single Nucleotide ; Sex Characteristics ; Waist-Hip Ratio ; White People ; }, abstract = {Genome-wide association studies (GWAS) have identified more than 100 genetic variants contributing to BMI, a measure of body size, or waist-to-hip ratio (adjusted for BMI, WHRadjBMI), a measure of body shape. Body size and shape change as people grow older and these changes differ substantially between men and women. To systematically screen for age- and/or sex-specific effects of genetic variants on BMI and WHRadjBMI, we performed meta-analyses of 114 studies (up to 320,485 individuals of European descent) with genome-wide chip and/or Metabochip data by the Genetic Investigation of Anthropometric Traits (GIANT) Consortium. Each study tested the association of up to ~2.8M SNPs with BMI and WHRadjBMI in four strata (men ≤50y, men >50y, women ≤50y, women >50y) and summary statistics were combined in stratum-specific meta-analyses. We then screened for variants that showed age-specific effects (G x AGE), sex-specific effects (G x SEX) or age-specific effects that differed between men and women (G x AGE x SEX). For BMI, we identified 15 loci (11 previously established for main effects, four novel) that showed significant (FDR<5%) age-specific effects, of which 11 had larger effects in younger (<50y) than in older adults (≥50y). No sex-dependent effects were identified for BMI. For WHRadjBMI, we identified 44 loci (27 previously established for main effects, 17 novel) with sex-specific effects, of which 28 showed larger effects in women than in men, five showed larger effects in men than in women, and 11 showed opposite effects between sexes. No age-dependent effects were identified for WHRadjBMI. This is the first genome-wide interaction meta-analysis to report convincing evidence of age-dependent genetic effects on BMI. In addition, we confirm the sex-specificity of genetic effects on WHRadjBMI. These results may provide further insights into the biology that underlies weight change with age or the sexually dimorphism of body shape.}, } @article {pmid26423964, year = {2015}, author = {Haag, ES and Thomas, CG}, title = {Fundamentals of Comparative Genome Analysis in Caenorhabditis Nematodes.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1327}, number = {}, pages = {11-21}, doi = {10.1007/978-1-4939-2842-2_2}, pmid = {26423964}, issn = {1940-6029}, mesh = {Animals ; Caenorhabditis/*genetics ; Computational Biology/methods ; Gene Dosage ; *Genome, Helminth ; Genomics/*methods ; Genotype ; Phylogeny ; }, abstract = {The genome of the nematode Caenorhabditis elegans was the first of any animal to be sequenced completely, and it remains the "gold standard" for completeness and annotations. Even before the C. elegans genome was completed, however, biologists began examining the generality of its features in the genomes of other Caenorhabditis species. With many such genomes now sequenced and available via WormBase, C. elegans researchers are often confronted with how to interpret comparative genomic data. In this article, we present practical approaches to addressing several common issues, including possible sources of error in homology annotations, the often complex relationships between sequence similarity, orthology, paralogy, and gene family evolution, the impact of sexual mode on genome assemblies and content, and the determination and use of synteny as a tool.}, } @article {pmid26420863, year = {2015}, author = {Semenkovich, CF and Danska, J and Darsow, T and Dunne, JL and Huttenhower, C and Insel, RA and McElvaine, AT and Ratner, RE and Shuldiner, AR and Blaser, MJ}, title = {American Diabetes Association and JDRF Research Symposium: Diabetes and the Microbiome.}, journal = {Diabetes}, volume = {64}, number = {12}, pages = {3967-3977}, pmid = {26420863}, issn = {1939-327X}, support = {M01 RR002719/RR/NCRR NIH HHS/United States ; P30 DK072488/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; *Biomedical Research/trends ; Combined Modality Therapy ; Computational Biology/trends ; Diabetes Complications/prevention & control ; Diabetes Mellitus, Type 1/complications/immunology/*microbiology/therapy ; Diabetes Mellitus, Type 2/complications/immunology/*microbiology/therapy ; *Evidence-Based Medicine ; *Gastrointestinal Microbiome/drug effects/immunology ; Humans ; Hypoglycemic Agents/adverse effects/therapeutic use ; *Models, Biological ; *Precision Medicine ; }, abstract = {From 27-29 October 2014, more than 100 people gathered in Chicago, IL, to participate in a research symposium titled "Diabetes and the Microbiome," jointly sponsored by the American Diabetes Association and JDRF. The conference brought together international scholars and trainees from multiple disciplines, including microbiology, bioinformatics, endocrinology, metabolism, and immunology, to share the current understanding of host-microbe interactions and their influences on diabetes and metabolism. Notably, this gathering was the first to assemble specialists with distinct expertise in type 1 diabetes, type 2 diabetes, immunology, and microbiology with the goal of discussing and defining potential pathophysiologies linking the microbiome and diabetes. In addition to reviewing existing evidence in the field, speakers presented their own original research to provide a comprehensive view of the current understanding of the topics under discussion.Presentations and discussions throughout the conference reflected a number of important concepts. The microbiota in any host represent a complex ecosystem with a high degree of interindividual variability. Different microbial communities, comprising bacteria, archaea, viruses, and fungi, occupy separate niches in and on the human body. Individually and collectively, these microbes provide benefits to the host-including nutrient harvest from food and protection against pathogens. They are dynamically regulated by both host genes and the environment, and they critically influence both physiology and lifelong health. The objective of the symposium was to discuss the relationship between the host and the microbiome-the combination of microbiota and their biomolecular environment and ecology-specifically with regard to metabolic and immunological systems and to define the critical research needed to understand and potentially target the microbiome in the prevention and treatment of diabetes. In this report, we present meeting highlights in the following areas: 1) relationships between diabetes and the microbiome, 2) bioinformatic tools, resources, and study design considerations, 3) microbial programming of the immune system, 4) the microbiome and energy balance, 5) interventions, and 6) limitations, unanswered questions, and resource and policy needs.}, } @article {pmid26420475, year = {2015}, author = {Liu, X and Zhao, B and Zheng, HJ and Hu, Y and Lu, G and Yang, CQ and Chen, JD and Chen, JJ and Chen, DY and Zhang, L and Zhou, Y and Wang, LJ and Guo, WZ and Bai, YL and Ruan, JX and Shangguan, XX and Mao, YB and Shan, CM and Jiang, JP and Zhu, YQ and Jin, L and Kang, H and Chen, ST and He, XL and Wang, R and Wang, YZ and Chen, J and Wang, LJ and Yu, ST and Wang, BY and Wei, J and Song, SC and Lu, XY and Gao, ZC and Gu, WY and Deng, X and Ma, D and Wang, S and Liang, WH and Fang, L and Cai, CP and Zhu, XF and Zhou, BL and Jeffrey Chen, Z and Xu, SH and Zhang, YG and Wang, SY and Zhang, TZ and Zhao, GP and Chen, XY}, title = {Gossypium barbadense genome sequence provides insight into the evolution of extra-long staple fiber and specialized metabolites.}, journal = {Scientific reports}, volume = {5}, number = {}, pages = {14139}, pmid = {26420475}, issn = {2045-2322}, mesh = {Alkyl and Aryl Transferases/genetics/metabolism ; *Biological Evolution ; Chromosomes, Plant ; Cluster Analysis ; Computational Biology/methods ; *Cotton Fiber ; Gene Expression Profiling ; Genetic Association Studies ; *Genome, Plant ; *Genomics/methods ; Gossypium/*genetics/*metabolism ; *Metabolomics/methods ; Molecular Sequence Annotation ; Phenotype ; Phylogeny ; Polyploidy ; Quantitative Trait, Heritable ; Sesquiterpenes/metabolism ; Translocation, Genetic ; Phytoalexins ; }, abstract = {Of the two cultivated species of allopolyploid cotton, Gossypium barbadense produces extra-long fibers for the production of superior textiles. We sequenced its genome (AD)2 and performed a comparative analysis. We identified three bursts of retrotransposons from 20 million years ago (Mya) and a genome-wide uneven pseudogenization peak at 11-20 Mya, which likely contributed to genomic divergences. Among the 2,483 genes preferentially expressed in fiber, a cell elongation regulator, PRE1, is strikingly At biased and fiber specific, echoing the A-genome origin of spinnable fiber. The expansion of the PRE members implies a genetic factor that underlies fiber elongation. Mature cotton fiber consists of nearly pure cellulose. G. barbadense and G. hirsutum contain 29 and 30 cellulose synthase (CesA) genes, respectively; whereas most of these genes (>25) are expressed in fiber, genes for secondary cell wall biosynthesis exhibited a delayed and higher degree of up-regulation in G. barbadense compared with G. hirsutum, conferring an extended elongation stage and highly active secondary wall deposition during extra-long fiber development. The rapid diversification of sesquiterpene synthase genes in the gossypol pathway exemplifies the chemical diversity of lineage-specific secondary metabolites. The G. barbadense genome advances our understanding of allopolyploidy, which will help improve cotton fiber quality.}, } @article {pmid26417098, year = {2015}, author = {Murray, KA and Preston, N and Allen, T and Zambrana-Torrelio, C and Hosseini, PR and Daszak, P}, title = {Global biogeography of human infectious diseases.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {112}, number = {41}, pages = {12746-12751}, pmid = {26417098}, issn = {1091-6490}, mesh = {Communicable Diseases/*epidemiology ; *Disease Outbreaks ; Humans ; Phylogeography ; }, abstract = {The distributions of most infectious agents causing disease in humans are poorly resolved or unknown. However, poorly known and unknown agents contribute to the global burden of disease and will underlie many future disease risks. Existing patterns of infectious disease co-occurrence could thus play a critical role in resolving or anticipating current and future disease threats. We analyzed the global occurrence patterns of 187 human infectious diseases across 225 countries and seven epidemiological classes (human-specific, zoonotic, vector-borne, non-vector-borne, bacterial, viral, and parasitic) to show that human infectious diseases exhibit distinct spatial grouping patterns at a global scale. We demonstrate, using outbreaks of Ebola virus as a test case, that this spatial structuring provides an untapped source of prior information that could be used to tighten the focus of a range of health-related research and management activities at early stages or in data-poor settings, including disease surveillance, outbreak responses, or optimizing pathogen discovery. In examining the correlates of these spatial patterns, among a range of geographic, epidemiological, environmental, and social factors, mammalian biodiversity was the strongest predictor of infectious disease co-occurrence overall and for six of the seven disease classes examined, giving rise to a striking congruence between global pathogeographic and "Wallacean" zoogeographic patterns. This clear biogeographic signal suggests that infectious disease assemblages remain fundamentally constrained in their distributions by ecological barriers to dispersal or establishment, despite the homogenizing forces of globalization. Pathogeography thus provides an overarching context in which other factors promoting infectious disease emergence and spread are set.}, } @article {pmid26415759, year = {2015}, author = {Accetto, T and Avguštin, G}, title = {Polysaccharide utilization locus and CAZYme genome repertoires reveal diverse ecological adaptation of Prevotella species.}, journal = {Systematic and applied microbiology}, volume = {38}, number = {7}, pages = {453-461}, doi = {10.1016/j.syapm.2015.07.007}, pmid = {26415759}, issn = {1618-0984}, mesh = {*Computational Biology ; *Genetic Loci ; *Genetic Variation ; *Metabolic Networks and Pathways ; Polysaccharides/*metabolism ; Prevotella/*enzymology/*genetics/metabolism ; }, abstract = {The results of metagenomic studies have clearly established that bacteria of the genus Prevotella represent one of the important groups found in the oral cavity and large intestine of man, and they also dominate the rumen. They belong to the Bacteroidetes, a phylum well-known for its polysaccharide degrading potential that stems from the outer membrane-localized enzyme/binding protein complexes encoded in polysaccharide utilization loci (PULs). Dozens of Prevotella species have been described, primarily from the oral cavity, and many of them occur simultaneously at the same sites, but research on their ecological adaptation has been neglected. Therefore, in this study, the repertoires of PULs and carbohydrate acting enzymes (CAZYmes) found in Prevotella genomes were analyzed and it was concluded that the Prevotella species were widely heterogeneous in this respect and displayed several distinct adaptations with regard to the number, source and nature of the substrates apparently preferred for growth.}, } @article {pmid26407889, year = {2015}, author = {Zarzycki, J and Erbilgin, O and Kerfeld, CA}, title = {Bioinformatic characterization of glycyl radical enzyme-associated bacterial microcompartments.}, journal = {Applied and environmental microbiology}, volume = {81}, number = {24}, pages = {8315-8329}, pmid = {26407889}, issn = {1098-5336}, support = {R01 AI114975/AI/NIAID NIH HHS/United States ; 1R01AI114975-01/AI/NIAID NIH HHS/United States ; }, mesh = {Alcohol Oxidoreductases/genetics/metabolism ; Aldehyde Oxidoreductases/genetics/metabolism ; Bacteria/*enzymology/genetics/*metabolism ; Choline/metabolism ; Computational Biology/*methods ; Fructose-Bisphosphate Aldolase/genetics/metabolism ; Hexosephosphates/metabolism ; Metabolic Networks and Pathways/*genetics ; Organelles/metabolism ; Propylene Glycols/metabolism ; }, abstract = {Bacterial microcompartments (BMCs) are proteinaceous organelles encapsulating enzymes that catalyze sequential reactions of metabolic pathways. BMCs are phylogenetically widespread; however, only a few BMCs have been experimentally characterized. Among them are the carboxysomes and the propanediol- and ethanolamine-utilizing microcompartments, which play diverse metabolic and ecological roles. The substrate of a BMC is defined by its signature enzyme. In catabolic BMCs, this enzyme typically generates an aldehyde. Recently, it was shown that the most prevalent signature enzymes encoded by BMC loci are glycyl radical enzymes, yet little is known about the function of these BMCs. Here we characterize the glycyl radical enzyme-associated microcompartment (GRM) loci using a combination of bioinformatic analyses and active-site and structural modeling to show that the GRMs comprise five subtypes. We predict distinct functions for the GRMs, including the degradation of choline, propanediol, and fuculose phosphate. This is the first family of BMCs for which identification of the signature enzyme is insufficient for predicting function. The distinct GRM functions are also reflected in differences in shell composition and apparently different assembly pathways. The GRMs are the counterparts of the vitamin B12-dependent propanediol- and ethanolamine-utilizing BMCs, which are frequently associated with virulence. This study provides a comprehensive foundation for experimental investigations of the diverse roles of GRMs. Understanding this plasticity of function within a single BMC family, including characterization of differences in permeability and assembly, can inform approaches to BMC bioengineering and the design of therapeutics.}, } @article {pmid26407293, year = {2015}, author = {Petric, RC and Braicu, C and Bassi, C and Pop, L and Taranu, I and Dragos, N and Dumitrascu, D and Negrini, M and Berindan-Neagoe, I}, title = {Interspecies Gene Name Extrapolation--A New Approach.}, journal = {PloS one}, volume = {10}, number = {9}, pages = {e0138751}, pmid = {26407293}, issn = {1932-6203}, mesh = {Animals ; Computational Biology/methods ; *Genes ; Humans ; Internet ; Molecular Sequence Annotation/methods ; Software ; *Terminology as Topic ; }, abstract = {The use of animal models has facilitated numerous scientific developments, especially when employing "omics" technologies to study the effects of various environmental factors on humans. Our study presents a new bioinformatics pipeline suitable when the generated microarray data from animal models does not contain the necessary human gene name annotation. We conducted single color gene expression microarray on duodenum and spleen tissue obtained from pigs which have been exposed to zearalenone and Escherichia coli contamination, either alone or combined. By performing a combination of file format modifications and data alignments using various online tools as well as a command line environment, we performed the pig to human gene name extrapolation with an average yield of 58.34%, compared to 3.64% when applying more simple methods. In conclusion, while online data analysis portals on their own are of great importance in data management and assessment, our new pipeline provided a more effective approach for a situation which can be frequently encountered by researchers in the "omics" era.}, } @article {pmid26406595, year = {2015}, author = {Lin, X and Stur, E and Ekrem, T}, title = {Exploring Genetic Divergence in a Species-Rich Insect Genus Using 2790 DNA Barcodes.}, journal = {PloS one}, volume = {10}, number = {9}, pages = {e0138993}, pmid = {26406595}, issn = {1932-6203}, mesh = {Animals ; Chironomidae/*classification/enzymology/genetics ; DNA Barcoding, Taxonomic/*standards ; Databases, Genetic ; Electron Transport Complex IV/*analysis ; Genetic Variation ; Insect Proteins/analysis ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {DNA barcoding using a fragment of the mitochondrial cytochrome c oxidase subunit 1 gene (COI) has proven to be successful for species-level identification in many animal groups. However, most studies have been focused on relatively small datasets or on large datasets of taxonomically high-ranked groups. We explore the quality of DNA barcodes to delimit species in the diverse chironomid genus Tanytarsus (Diptera: Chironomidae) by using different analytical tools. The genus Tanytarsus is the most species-rich taxon of tribe Tanytarsini (Diptera: Chironomidae) with more than 400 species worldwide, some of which can be notoriously difficult to identify to species-level using morphology. Our dataset, based on sequences generated from own material and publicly available data in BOLD, consist of 2790 DNA barcodes with a fragment length of at least 500 base pairs. A neighbor joining tree of this dataset comprises 131 well separated clusters representing 121 morphological species of Tanytarsus: 77 named, 16 unnamed and 28 unidentified theoretical species. For our geographically widespread dataset, DNA barcodes unambiguously discriminate 94.6% of the Tanytarsus species recognized through prior morphological study. Deep intraspecific divergences exist in some species complexes, and need further taxonomic studies using appropriate nuclear markers as well as morphological and ecological data to be resolved. The DNA barcodes cluster into 120-242 molecular operational taxonomic units (OTUs) depending on whether Objective Clustering, Automatic Barcode Gap Discovery (ABGD), Generalized Mixed Yule Coalescent model (GMYC), Poisson Tree Process (PTP), subjective evaluation of the neighbor joining tree or Barcode Index Numbers (BINs) are used. We suggest that a 4-5% threshold is appropriate to delineate species of Tanytarsus non-biting midges.}, } @article {pmid26405731, year = {2015}, author = {Lajeunesse, MJ}, title = {Bias and correction for the log response ratio in ecological meta-analysis.}, journal = {Ecology}, volume = {96}, number = {8}, pages = {2056-2063}, doi = {10.1890/14-2402.1}, pmid = {26405731}, issn = {0012-9658}, mesh = {Computer Simulation ; Data Interpretation, Statistical ; *Ecosystem ; Linear Models ; *Meta-Analysis as Topic ; *Models, Biological ; Monte Carlo Method ; Risk Assessment ; Sampling Studies ; }, abstract = {Ecologists widely use the log response ratio for summarizing the outcomes of studies for meta-analysis. However, little is known about the sampling distribution of this effect size estimator. Here I show with a Monte Carlo simulation that the log response ratio is biased when quantifying the outcome of studies with small sample sizes, and can yield erroneous variance estimates when the scale of study parameters are near zero. Given these challenges, I derive and compare two new estimators that help correct this small-sample bias, and update guidelines and diagnostics for assessing when the response ratio is appropriate for ecological meta-analysis. These new bias-corrected estimators retain much of the original utility of the response ratio and are aimed to improve the quality and reliability of inferences with effect sizes based on the log ratio of two means.}, } @article {pmid26400090, year = {2015}, author = {Cetin, M}, title = {Determining the bioclimatic comfort in Kastamonu City.}, journal = {Environmental monitoring and assessment}, volume = {187}, number = {10}, pages = {640}, doi = {10.1007/s10661-015-4861-3}, pmid = {26400090}, issn = {1573-2959}, mesh = {Altitude ; *Cities ; *Climate Change ; Environmental Monitoring/*methods ; Geographic Information Systems ; Humans ; Humidity ; Temperature ; Turkey ; Urbanization ; Wind ; }, abstract = {Bioclimatic comfort defines the optimal climatic conditions in which people feel healthy and dynamic. Bioclimatic comfort mapping methods are useful to urban managers and planners. For the purposes of planning, climatic conditions, as determined by bioclimatic comfort assessments, are important. Bioclimatic components such as temperature, relative humidity, and wind speeds are important in evaluating bioclimatic comfort. In this study of the climate of Kastamonu province, the most suitable areas in terms of bioclimatic comfort have been identified. In this context, climate values belonging to the province of Kastamonu are taken from a total of nine meteorological stations. Altitude (36-1050 m) between stations is noted for revealing climatic changes. The data collected from these stations, including average temperature, relative humidity, and wind speed values are transferred to geographical information system (GIS) using ArcMap 10.2.2 software. GIS maps created from the imported data has designated the most suitable comfort areas in and around the city of Kastamonu. As a result, the study shows that Kastamonu has suitable ranges for bioclimatic comfort zone. The range of bioclimatic comfort value for Kastamonu is 17.6 °C. It is between a comfort ranges which is 15-20 °C. Kastamonu City has suitable area for bioclimatic comfort.}, } @article {pmid26399714, year = {2015}, author = {Richards, AJ and Herrel, A and Bonneaud, C}, title = {htsint: a Python library for sequencing pipelines that combines data through gene set generation.}, journal = {BMC bioinformatics}, volume = {16}, number = {}, pages = {307}, pmid = {26399714}, issn = {1471-2105}, mesh = {Computational Biology/*methods ; *Databases, Genetic ; *Genome, Human ; Genomics/*methods ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; *Programming Languages ; Sequence Analysis, RNA ; *Software ; }, abstract = {BACKGROUND: Sequencing technologies provide a wealth of details in terms of genes, expression, splice variants, polymorphisms, and other features. A standard for sequencing analysis pipelines is to put genomic or transcriptomic features into a context of known functional information, but the relationships between ontology terms are often ignored. For RNA-Seq, considering genes and their genetic variants at the group level enables a convenient way to both integrate annotation data and detect small coordinated changes between experimental conditions, a known caveat of gene level analyses.

RESULTS: We introduce the high throughput data integration tool, htsint, as an extension to the commonly used gene set enrichment frameworks. The central aim of htsint is to compile annotation information from one or more taxa in order to calculate functional distances among all genes in a specified gene space. Spectral clustering is then used to partition the genes, thereby generating functional modules. The gene space can range from a targeted list of genes, like a specific pathway, all the way to an ensemble of genomes. Given a collection of gene sets and a count matrix of transcriptomic features (e.g. expression, polymorphisms), the gene sets produced by htsint can be tested for 'enrichment' or conditional differences using one of a number of commonly available packages.

CONCLUSION: The database and bundled tools to generate functional modules were designed with sequencing pipelines in mind, but the toolkit nature of htsint allows it to also be used in other areas of genomics. The software is freely available as a Python library through GitHub at https://github.com/ajrichards/htsint.}, } @article {pmid26398546, year = {2015}, author = {Blecha, KA and Alldredge, MW}, title = {Improvements on GPS Location Cluster Analysis for the Prediction of Large Carnivore Feeding Activities: Ground-Truth Detection Probability and Inclusion of Activity Sensor Measures.}, journal = {PloS one}, volume = {10}, number = {9}, pages = {e0138915}, pmid = {26398546}, issn = {1932-6203}, mesh = {Animal Distribution ; Animals ; *Carnivory ; Cluster Analysis ; Female ; Geographic Information Systems ; Male ; Puma ; Quality Improvement ; }, abstract = {Animal space use studies using GPS collar technology are increasingly incorporating behavior based analysis of spatio-temporal data in order to expand inferences of resource use. GPS location cluster analysis is one such technique applied to large carnivores to identify the timing and location of feeding events. For logistical and financial reasons, researchers often implement predictive models for identifying these events. We present two separate improvements for predictive models that future practitioners can implement. Thus far, feeding prediction models have incorporated a small range of covariates, usually limited to spatio-temporal characteristics of the GPS data. Using GPS collared cougar (Puma concolor) we include activity sensor data as an additional covariate to increase prediction performance of feeding presence/absence. Integral to the predictive modeling of feeding events is a ground-truthing component, in which GPS location clusters are visited by human observers to confirm the presence or absence of feeding remains. Failing to account for sources of ground-truthing false-absences can bias the number of predicted feeding events to be low. Thus we account for some ground-truthing error sources directly in the model with covariates and when applying model predictions. Accounting for these errors resulted in a 10% increase in the number of clusters predicted to be feeding events. Using a double-observer design, we show that the ground-truthing false-absence rate is relatively low (4%) using a search delay of 2-60 days. Overall, we provide two separate improvements to the GPS cluster analysis techniques that can be expanded upon and implemented in future studies interested in identifying feeding behaviors of large carnivores.}, } @article {pmid26398231, year = {2015}, author = {Watts, J and Sheehan, O and Greenhill, SJ and Gomes-Ng, S and Atkinson, QD and Bulbulia, J and Gray, RD}, title = {Pulotu: Database of Austronesian Supernatural Beliefs and Practices.}, journal = {PloS one}, volume = {10}, number = {9}, pages = {e0136783}, pmid = {26398231}, issn = {1932-6203}, mesh = {Cluster Analysis ; Cultural Evolution ; *Culture ; *Databases, Factual ; Ethnicity ; Humans ; Models, Theoretical ; *Religion ; *Software ; Web Browser ; }, abstract = {Scholars have debated naturalistic theories of religion for thousands of years, but only recently have scientists begun to test predictions empirically. Existing databases contain few variables on religion, and are subject to Galton's Problem because they do not sufficiently account for the non-independence of cultures or systematically differentiate the traditional states of cultures from their contemporary states. Here we present Pulotu: the first quantitative cross-cultural database purpose-built to test evolutionary hypotheses of supernatural beliefs and practices. The Pulotu database documents the remarkable diversity of the Austronesian family of cultures, which originated in Taiwan, spread west to Madagascar and east to Easter Island-a region covering over half the world's longitude. The focus of Austronesian beliefs range from localised ancestral spirits to powerful creator gods. A wide range of practices also exist, such as headhunting, elaborate tattooing, and the construction of impressive monuments. Pulotu is freely available, currently contains 116 cultures, and has 80 variables describing supernatural beliefs and practices, as well as social and physical environments. One major advantage of Pulotu is that it has separate sections on the traditional states of cultures, the post-contact history of cultures, and the contemporary states of cultures. A second major advantage is that cultures are linked to a language-based family tree, enabling the use phylogenetic methods, which can be used to address Galton's Problem by accounting for common ancestry, to infer deep prehistory, and to model patterns of trait evolution over time. We illustrate the power of phylogenetic methods by performing an ancestral state reconstruction on the Pulotu variable "headhunting", finding evidence that headhunting was practiced in proto-Austronesian culture. Quantitative cross-cultural databases explicitly linking cultures to a phylogeny have the potential to revolutionise the field of comparative religious studies in the same way that genetic databases have revolutionised the field of evolutionary biology.}, } @article {pmid26398032, year = {2015}, author = {Kumar, M and Kumar, R and Singh, PK and Singh, M and Yadav, KK and Mittal, HK}, title = {Catchment delineation and morphometric analysis using geographical information system.}, journal = {Water science and technology : a journal of the International Association on Water Pollution Research}, volume = {72}, number = {7}, pages = {1168-1175}, doi = {10.2166/wst.2015.303}, pmid = {26398032}, issn = {0273-1223}, mesh = {Conservation of Natural Resources/*methods ; Environmental Monitoring/*methods ; *Geographic Information Systems ; Hydrology ; India ; Rain ; Rivers ; *Water Movements ; Water Supply ; }, abstract = {The geographical information system (GIS) has emerged as an efficient tool in delineation of drainage patterns of watershed planning and management. The morphometric parameters of basins can address linear, areal and relief aspects. The study deals with the integrated watershed management of Baliya micro-watersheds, located in the Udaipur district of Rajasthan, India. Morphometric analysis in hydrological investigation is an important aspect and it is inevitable in the development and management of drainage basins. The determination of linear, areal and relief parameters indicate fairly good significance. The low value of the bifurcation ratio of 4.19 revealed that the drainage pattern has not been distorted by structural disturbance. The high value of the elongation ratio (0.68) compared to the circulatory ratio (0.27) indicates an elongated shape of the watershed. The high value of drainage density (5.39 km/km(2)) and stream frequency (12.32) shows that the region has impermeable subsoil material under poor vegetative cover with a low relief factor. The morphometric parameters of relief ratio (0.041) and relative relief (0.99%) show that the watershed can be treated using GIS techniques to determine the morphometric presence of dendritic drainage pattern, with a view to selecting the soil and water conservation measures and water harvesting.}, } @article {pmid26397832, year = {2015}, author = {Liu, B and Wu, H and Wang, Y and Liu, W}, title = {Main Road Extraction from ZY-3 Grayscale Imagery Based on Directional Mathematical Morphology and VGI Prior Knowledge in Urban Areas.}, journal = {PloS one}, volume = {10}, number = {9}, pages = {e0138071}, pmid = {26397832}, issn = {1932-6203}, mesh = {*Cities ; *Geographic Information Systems ; *Image Processing, Computer-Assisted ; *Satellite Communications ; }, abstract = {Main road features extracted from remotely sensed imagery play an important role in many civilian and military applications, such as updating Geographic Information System (GIS) databases, urban structure analysis, spatial data matching and road navigation. Current methods for road feature extraction from high-resolution imagery are typically based on threshold value segmentation. It is difficult however, to completely separate road features from the background. We present a new method for extracting main roads from high-resolution grayscale imagery based on directional mathematical morphology and prior knowledge obtained from the Volunteered Geographic Information found in the OpenStreetMap. The two salient steps in this strategy are: (1) using directional mathematical morphology to enhance the contrast between roads and non-roads; (2) using OpenStreetMap roads as prior knowledge to segment the remotely sensed imagery. Experiments were conducted on two ZiYuan-3 images and one QuickBird high-resolution grayscale image to compare our proposed method to other commonly used techniques for road feature extraction. The results demonstrated the validity and better performance of the proposed method for urban main road feature extraction.}, } @article {pmid26394010, year = {2016}, author = {Spencer, SJ and Tamminen, MV and Preheim, SP and Guo, MT and Briggs, AW and Brito, IL and A Weitz, D and Pitkänen, LK and Vigneault, F and Juhani Virta, MP and Alm, EJ}, title = {Massively parallel sequencing of single cells by epicPCR links functional genes with phylogenetic markers.}, journal = {The ISME journal}, volume = {10}, number = {2}, pages = {427-436}, pmid = {26394010}, issn = {1751-7370}, support = {P30 ES002109/ES/NIEHS NIH HHS/United States ; P30-ES002109/ES/NIEHS NIH HHS/United States ; }, mesh = {Bacteria/*classification/genetics/*isolation & purification ; Bacterial Proteins/genetics ; DNA, Bacterial/genetics ; High-Throughput Nucleotide Sequencing/*methods ; Lakes/*microbiology ; Metagenomics ; Molecular Sequence Data ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Many microbial communities are characterized by high genetic diversity. 16S ribosomal RNA sequencing can determine community members, and metagenomics can determine the functional diversity, but resolving the functional role of individual cells in high throughput remains an unsolved challenge. Here, we describe epicPCR (Emulsion, Paired Isolation and Concatenation PCR), a new technique that links functional genes and phylogenetic markers in uncultured single cells, providing a throughput of hundreds of thousands of cells with costs comparable to one genomic library preparation. We demonstrate the utility of our technique in a natural environment by profiling a sulfate-reducing community in a freshwater lake, revealing both known sulfate reducers and discovering new putative sulfate reducers. Our method is adaptable to any conserved genetic trait and translates genetic associations from diverse microbial samples into a sequencing library that answers targeted ecological questions. Potential applications include identifying functional community members, tracing horizontal gene transfer networks and mapping ecological interactions between microbial cells.}, } @article {pmid26391897, year = {2016}, author = {Martínez-Moreno, JM and Sánchez-González, P and Luna, M and Roig, T and Tormos, JM and Gómez, EJ}, title = {Modelling Ecological Cognitive Rehabilitation Therapies for Building Virtual Environments in Brain Injury.}, journal = {Methods of information in medicine}, volume = {55}, number = {1}, pages = {50-59}, doi = {10.3414/ME15-01-0050}, pmid = {26391897}, issn = {2511-705X}, mesh = {Activities of Daily Living ; Brain Injuries/*rehabilitation ; Cognition ; Computer Simulation ; Equipment Design ; Humans ; Models, Theoretical ; Neurological Rehabilitation/methods ; Neuropsychology/methods ; Psychometrics/methods ; Quality of Life ; Software ; Spain ; Telemedicine/*methods ; Therapy, Computer-Assisted ; User-Computer Interface ; }, abstract = {BACKGROUND: Brain Injury (BI) has become one of the most common causes of neurological disability in developed countries. Cognitive disorders result in a loss of independence and patients' quality of life. Cognitive rehabilitation aims to promote patients' skills to achieve their highest degree of personal autonomy. New technologies such as virtual reality or interactive video allow developing rehabilitation therapies based on reproducible Activities of Daily Living (ADLs), increasing the ecological validity of the therapy. However, the lack of frameworks to formalize and represent the definition of this kind of therapies can be a barrier for widespread use of interactive virtual environments in clinical routine.

OBJECTIVES: To provide neuropsychologists with a methodology and an instrument to design and evaluate cognitive rehabilitation therapeutic interventions strategies based on ADLs performed in interactive virtual environments.

METHODS: The proposed methodology is used to model therapeutic interventions during virtual ADLs considering cognitive deficit, expected abnormal interactions and therapeutic hypotheses. It allows identifying abnormal behavioural patterns and designing interventions strategies in order to achieve errorless-based rehabilitation.

RESULTS: An ADL case study ('buying bread') is defined according to the guidelines established by the ADL intervention model. This case study is developed, as a proof of principle, using interactive video technology and is used to assess the feasibility of the proposed methodology in the definition of therapeutic intervention procedures.

CONCLUSIONS: The proposed methodology provides neuropsychologists with an instrument to design and evaluate ADL-based therapeutic intervention strategies, attending to solve actual limitation of virtual scenarios, to be use for ecological rehabilitation of cognitive deficit in daily clinical practice. The developed case study proves the potential of the methodology to design therapeutic interventions strategies; however our current work is devoted to designing more experiments in order to present more evidence about its values.}, } @article {pmid26391002, year = {2016}, author = {Baddeley, AD and Hitch, GJ and Quinlan, PT and Bowes, L and Stone, R}, title = {Doors for memory: A searchable database.}, journal = {Quarterly journal of experimental psychology (2006)}, volume = {69}, number = {11}, pages = {2111-2118}, doi = {10.1080/17470218.2015.1087582}, pmid = {26391002}, issn = {1747-0226}, mesh = {Adolescent ; Databases, Factual/*statistics & numerical data ; Female ; Humans ; Male ; Photic Stimulation ; Reaction Time/physiology ; Recognition, Psychology/*physiology ; Visual Perception/*physiology ; Young Adult ; }, abstract = {The study of human long-term memory has for over 50 years been dominated by research on words. This is partly due to lack of suitable nonverbal materials. Experience in developing a clinical test suggested that door scenes can provide an ecologically relevant and sensitive alternative to the faces and geometrical figures traditionally used to study visual memory. In pursuing this line of research, we have accumulated over 2000 door scenes providing a database that is categorized on a range of variables including building type, colour, age, condition, glazing, and a range of other physical characteristics. We describe an illustrative study of recognition memory for 100 doors tested by yes/no, two-alternative, or four-alternative forced-choice paradigms. These stimuli, together with the full categorized database, are available through a dedicated website. We suggest that door scenes provide an ecologically relevant and participant-friendly source of material for studying the comparatively neglected field of visual long-term memory.}, } @article {pmid26388813, year = {2015}, author = {Reinoso Carvalho, F and Van Ee, R and Rychtarikova, M and Touhafi, A and Steenhaut, K and Persoone, D and Spence, C}, title = {Using sound-taste correspondences to enhance the subjective value of tasting experiences.}, journal = {Frontiers in psychology}, volume = {6}, number = {}, pages = {1309}, pmid = {26388813}, issn = {1664-1078}, abstract = {The soundscapes of those places where we eat and drink can influence our perception of taste. Here, we investigated whether contextual sound would enhance the subjective value of a tasting experience. The customers in a chocolate shop were invited to take part in an experiment in which they had to evaluate a chocolate's taste while listening to an auditory stimulus. Four different conditions were presented in a between-participants design. Envisioning a more ecological approach, a pre-recorded piece of popular music and the shop's own soundscape were used as the sonic stimuli. The results revealed that not only did the customers report having a significantly better tasting experience when the sounds were presented as part of the food's identity, but they were also willing to pay significantly more for the experience. The method outlined here paves a new approach to dealing with the design of multisensory tasting experiences, and gastronomic situations.}, } @article {pmid26385553, year = {2015}, author = {Lötsch, J and Niederberger, E and Ultsch, A}, title = {Computational functional genomics based analysis of pain-relevant micro-RNAs.}, journal = {Human genetics}, volume = {134}, number = {11-12}, pages = {1221-1238}, pmid = {26385553}, issn = {1432-1203}, mesh = {Data Mining ; Databases, Genetic ; Epistasis, Genetic ; Gene Expression Regulation ; Gene Regulatory Networks ; Genomics/*methods ; Humans ; MicroRNAs/*genetics ; Molecular Sequence Annotation ; Pain/*genetics ; }, abstract = {Micro-ribonucleic acids (miRNAs) play a role in pain, based on studies on models of neuropathic or inflammatory pain and clinical evidence. The present analysis made extensive use of computational biology, knowledge discovery methods, publicly available databases and data mining tools to merge results from genetic and miRNA research into an analysis of the systems biological roles of miRNAs in pain. We identified that about one-third of miRNAs detected through nociceptive research have been associated with a mere 18 regulated genes. Substituting the missing genetic information by computational data mining and based on comprehensive current empirical evidence of gene versus miRNA interactions, we have identified a total of 130 pain genes as being probably regulated by a total of 167 different miRNAs. Particularly pain-relevant roles of miRNAs include the control of gene expression at any level and regulation of interleukin-6-related pain entities. Among the miRNAs regulating pain genes are seven that are brain specific, hinting at their therapeutic utility for modulating central nervous mechanisms of pain.}, } @article {pmid26385065, year = {2015}, author = {Patalay, P and Belsky, J and Fonagy, P and Vostanis, P and Humphrey, N and Deighton, J and Wolpert, M}, title = {The Extent and Specificity of Relative Age Effects on Mental Health and Functioning in Early Adolescence.}, journal = {The Journal of adolescent health : official publication of the Society for Adolescent Medicine}, volume = {57}, number = {5}, pages = {475-481}, doi = {10.1016/j.jadohealth.2015.07.012}, pmid = {26385065}, issn = {1879-1972}, mesh = {Adolescent ; *Affective Symptoms ; Age Factors ; Child ; Databases, Factual ; England ; Female ; Humans ; Male ; *Mental Health ; Peer Group ; *Psychology, Adolescent ; Schools ; Sensitivity and Specificity ; Surveys and Questionnaires ; }, abstract = {PURPOSE: Although extensive evidence indicates that being younger within a school cohort is associated with poorer academic functioning, much less is known about such relative age effects (RAEs) for mental health--the focus of the current investigation.

METHODS: Data from 23,379 11- to 13-year-olds attending state-maintained secondary schools in England were analyzed to investigate RAEs on mental health measured using the Strengths and Difficulties Questionnaire. Participants were grouped into oldest, middle, and youngest thirds of their academic year based on their month of birth relative to their cohort. Hierarchical linear regression analysis evaluated RAEs and gender- or deprivation-related moderation of such effects.

RESULTS: Relatively younger adolescents had significantly more emotional symptoms and peer problems compared with relatively older individuals in a year group, although effect sizes were small. These effects were not moderated by gender or deprivation. Impact of mental health difficulties on other aspects of functioning was also greater among relatively younger children. Larger RAEs are observed in the younger cohort (11-12 years) compared with those in the 12- to 13-year-olds, thereby indicating that RAEs might attenuate with age.

CONCLUSIONS: Being relatively younger than classmates is associated with increased internalizing symptoms, poorer peer relationships, and higher impact of mental health difficulties on functioning at school and home. The findings support wider inclusion of relative age in understanding mental health difficulties and its inclusion as a potential risk factor in studies investigating the development of psychopathology, especially for internalizing symptoms. Possible mechanisms of the effects detected are discussed.}, } @article {pmid26379467, year = {2015}, author = {Balsamo, M and D Hondt, JL and Kisielewski, J and Todaro, MA and Tongiorgi, P and Guidi, L and Grilli, P and de Jong, Y}, title = {Fauna Europaea: Gastrotricha.}, journal = {Biodiversity data journal}, volume = {}, number = {3}, pages = {e5800}, pmid = {26379467}, issn = {1314-2828}, abstract = {Fauna Europaea provides a public web-service with an index of scientific names (including important synonyms) of all living European land and freshwater animals, their geographical distribution at country level (up to the Urals, excluding the Caucasus region), and some additional information. The Fauna Europaea project covers about 230,000 taxonomic names, including 130,000 accepted species and 14,000 accepted subspecies, which is much more than the originally projected number of 100,000 species. This represents a huge effort by more than 400 contributing specialists throughout Europe and is a unique (standard) reference suitable for many users in science, government, industry, nature conservation and education. Gastrotricha are a meiobenthic phylum composed of 813 species known so far (2 orders, 17 families) of free-living microinvertebrates commonly present and actively moving on and into sediments of aquatic ecosystems, 339 of which live in fresh and brackish waters. The Fauna Europaea database includes 214 species of Chaetonotida (4 families) plus a single species of Macrodasyida incertae sedis. This paper deals with the 224 European freshwater species known so far, 9 of which, all of Chaetonotida, have been described subsequently and will be included in the next database version. Basic information on their biology and ecology are summarized, and a list of selected, main references is given. As a general conclusion the gastrotrich fauna from Europe is the best known compared with that of other continents, but shows some important gaps of knowledge in Eastern and Southern regions.}, } @article {pmid26378959, year = {2015}, author = {Beresford, NA and Beaugelin-Seiller, K and Burgos, J and Cujic, M and Fesenko, S and Kryshev, A and Pachal, N and Real, A and Su, BS and Tagami, K and Vives i Batlle, J and Vives-Lynch, S and Wells, C and Wood, MD}, title = {Radionuclide biological half-life values for terrestrial and aquatic wildlife.}, journal = {Journal of environmental radioactivity}, volume = {150}, number = {}, pages = {270-276}, doi = {10.1016/j.jenvrad.2015.08.018}, pmid = {26378959}, issn = {1879-1700}, mesh = {Animals ; Animals, Wild/*metabolism ; Databases, Factual ; Half-Life ; *Radiation Exposure ; Radiation Monitoring/*methods ; Radioactive Pollutants/*metabolism ; Radioisotopes/*metabolism ; }, abstract = {The equilibrium concentration ratio is typically the parameter used to estimate organism activity concentrations within wildlife dose assessment tools. Whilst this is assumed to be fit for purpose, there are scenarios such as accidental or irregular, fluctuating, releases from licensed facilities when this might not be the case. In such circumstances, the concentration ratio approach may under- or over-estimate radiation exposure depending upon the time since the release. To carrying out assessments for such releases, a dynamic approach is needed. The simplest and most practical option is representing the uptake and turnover processes by first-order kinetics, for which organism- and element-specific biological half-life data are required. In this paper we describe the development of a freely available international database of radionuclide biological half-life values. The database includes 1907 entries for terrestrial, freshwater, riparian and marine organisms. Biological half-life values are reported for 52 elements across a range of wildlife groups (marine = 9, freshwater = 10, terrestrial = 7 and riparian = 3 groups). Potential applications and limitations of the database are discussed.}, } @article {pmid26378178, year = {2015}, author = {Eden, JS and Read, AJ and Duckworth, JA and Strive, T and Holmes, EC}, title = {Resolving the Origin of Rabbit Hemorrhagic Disease Virus: Insights from an Investigation of the Viral Stocks Released in Australia.}, journal = {Journal of virology}, volume = {89}, number = {23}, pages = {12217-12220}, pmid = {26378178}, issn = {1098-5514}, support = {R01 AI093804/AI/NIAID NIH HHS/United States ; R01 AI093804-01A1/AI/NIAID NIH HHS/United States ; }, mesh = {Australia ; Base Sequence ; Computational Biology ; *Evolution, Molecular ; Hemorrhagic Disease Virus, Rabbit/chemistry/*genetics ; *Models, Molecular ; Molecular Sequence Data ; *Phylogeny ; Polymorphism, Single Nucleotide/genetics ; Sequence Analysis, DNA ; }, abstract = {To resolve the evolutionary history of rabbit hemorrhagic disease virus (RHDV), we performed a genomic analysis of the viral stocks imported and released as a biocontrol measure in Australia, as well as a global phylogenetic analysis. Importantly, conflicts were identified between the sequences determined here and those previously published that may have affected evolutionary rate estimates. By removing likely erroneous sequences, we show that RHDV emerged only shortly before its initial description in China.}, } @article {pmid26377525, year = {2016}, author = {Lwin, MO and Vijaykumar, S and Lim, G and Fernando, ON and Rathnayake, VS and Foo, S}, title = {Baseline Evaluation of a Participatory Mobile Health Intervention for Dengue Prevention in Sri Lanka.}, journal = {Health education & behavior : the official publication of the Society for Public Health Education}, volume = {43}, number = {4}, pages = {471-479}, doi = {10.1177/1090198115604623}, pmid = {26377525}, issn = {1552-6127}, mesh = {Adolescent ; Adult ; Animals ; Cell Phone ; *Cell Phone Use ; Cross-Sectional Studies ; Culicidae ; Dengue/epidemiology/*prevention & control ; Female ; Health Behavior ; *Health Knowledge, Attitudes, Practice ; Health Promotion/*methods ; Humans ; Male ; Maps as Topic ; Middle Aged ; Population Surveillance ; Regression Analysis ; Social Media ; Sri Lanka/epidemiology ; Surveys and Questionnaires ; Telemedicine ; Young Adult ; }, abstract = {Challenges posed by infectious disease outbreaks have led to a range of participatory mobile phone-based innovations that use the power of crowdsourcing for disease surveillance. However, the dynamics of participatory behavior by crowds in such interventions have yet to be examined. This article reports results from a baseline evaluation of one such intervention called Mo-Buzz, a mobile-based crowdsource-driven socially mediated system developed to address gaps in dengue surveillance and education in Colombo, Sri Lanka. We conducted a 30-minute cross-sectional field survey (N = 404) among potential users of Mo-Buzz in Colombo. We examined individual, institutional, and cultural factors that influence their potential intention-to-use Mo-Buzz and assessed if these factors varied by demographic factors. Descriptive analysis revealed high perceived ease-of-use (PEOU; M = 3.81, SD = 0.44), perceived usefulness (PU; M = 4.01, SD = 0.48), and intention-to-use (PI; M = 3.91, SD = 0.46) among participants. Analysis of variance suggested participants in the 31 to 40 years age group reported highest PEOU, whereas the oldest group reported high perceived institutional efficacy (M = 3.59, SD = 0.64) and collectivistic tendencies. Significant differences (at the p < .05 level) were also found by education and income. Regression analysis demonstrated that PU, behavioral control, institutional efficacy, and collectivism were significant predictors of PI. We concluded that despite high overall PI, future adoption and use of Mo-Buzz will be shaped by a complex mix of factors at different levels of the public health ecology. Implications of study findings from theoretical and practical perspectives related to the future adoption of mobile-based participatory systems in public health are discussed and ideas for a future research agenda presented.}, } @article {pmid26375008, year = {2015}, author = {Bhatt, S and Weiss, DJ and Cameron, E and Bisanzio, D and Mappin, B and Dalrymple, U and Battle, K and Moyes, CL and Henry, A and Eckhoff, PA and Wenger, EA and Briët, O and Penny, MA and Smith, TA and Bennett, A and Yukich, J and Eisele, TP and Griffin, JT and Fergus, CA and Lynch, M and Lindgren, F and Cohen, JM and Murray, CLJ and Smith, DL and Hay, SI and Cibulskis, RE and Gething, PW}, title = {The effect of malaria control on Plasmodium falciparum in Africa between 2000 and 2015.}, journal = {Nature}, volume = {526}, number = {7572}, pages = {207-211}, pmid = {26375008}, issn = {1476-4687}, support = {MR/K00669X/1/MRC_/Medical Research Council/United Kingdom ; 095066/WT_/Wellcome Trust/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; 001/WHO_/World Health Organization/International ; G1002284/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Africa/epidemiology ; Animals ; Antimalarials/therapeutic use ; Child ; Child, Preschool ; Databases, Factual ; Drug Resistance ; Endemic Diseases/prevention & control/statistics & numerical data ; Humans ; Incidence ; Insecticide-Treated Bednets/statistics & numerical data ; Insecticides ; Malaria, Falciparum/drug therapy/*epidemiology/parasitology/*prevention & control ; Plasmodium falciparum/*drug effects ; Prevalence ; Risk Assessment ; }, abstract = {Since the year 2000, a concerted campaign against malaria has led to unprecedented levels of intervention coverage across sub-Saharan Africa. Understanding the effect of this control effort is vital to inform future control planning. However, the effect of malaria interventions across the varied epidemiological settings of Africa remains poorly understood owing to the absence of reliable surveillance data and the simplistic approaches underlying current disease estimates. Here we link a large database of malaria field surveys with detailed reconstructions of changing intervention coverage to directly evaluate trends from 2000 to 2015, and quantify the attributable effect of malaria disease control efforts. We found that Plasmodium falciparum infection prevalence in endemic Africa halved and the incidence of clinical disease fell by 40% between 2000 and 2015. We estimate that interventions have averted 663 (542-753 credible interval) million clinical cases since 2000. Insecticide-treated nets, the most widespread intervention, were by far the largest contributor (68% of cases averted). Although still below target levels, current malaria interventions have substantially reduced malaria disease incidence across the continent. Increasing access to these interventions, and maintaining their effectiveness in the face of insecticide and drug resistance, should form a cornerstone of post-2015 control strategies.}, } @article {pmid26372933, year = {2015}, author = {Litt, JS and Schmiege, SJ and Hale, JW and Buchenau, M and Sancar, F}, title = {Exploring ecological, emotional and social levers of self-rated health for urban gardeners and non-gardeners: A path analysis.}, journal = {Social science & medicine (1982)}, volume = {144}, number = {}, pages = {1-8}, pmid = {26372933}, issn = {1873-5347}, support = {K01 EH-000066-03/EH/NCEH CDC HHS/United States ; UL1 RR025780/RR/NCRR NIH HHS/United States ; K01 EH000066/EH/NCEH CDC HHS/United States ; UL1RR025780/RR/NCRR NIH HHS/United States ; UL1 TR001082/TR/NCATS NIH HHS/United States ; }, mesh = {Adult ; Cross-Sectional Studies ; Diagnostic Self Evaluation ; *Emotions ; Female ; *Gardening ; *Health Status ; Humans ; Male ; Middle Aged ; Residence Characteristics ; *Social Environment ; Surveys and Questionnaires ; Urban Population ; }, abstract = {RATIONALE: The social, emotional, and mental health benefits associated with gardening have been well documented. However, the processes underlying the relationship between garden participation and improvements in health status have not been sufficiently studied.

METHODS: Using population-based survey data (n = 469 urban residents), objective street environment data, and area-level measures, this research used a path analytic framework to examine several theoretically based constructs as mediators between gardening history and self-reported health.

RESULTS: The results showed that garden participation influenced health status indirectly through social involvement with one's community, perceived aesthetic appeal of the neighborhood, and perceived collective efficacy. Gardeners, compared to non-gardeners, reported higher ratings of neighborhood aesthetics and more involvement in social activities, whereas aesthetics and involvement were associated with higher ratings of collective efficacy and neighborhood attachment. Collective efficacy, but not neighborhood attachment, predicted self-rated health. Gardening also directly influenced improved fruit and vegetable intake. The physical and social qualities of garden participation may therefore stimulate a range of interpersonal and social responses that are supportive of positive ratings of health.

CONCLUSION: This research suggests that community planners and health professionals should aim to strengthen the social and aesthetic relationships while designing environments and policies as a way to ignite intermediate processes that may lead to improved health status.}, } @article {pmid26370435, year = {2016}, author = {Janković, J and Marinković, J and Stojisavljević, D and Erić, M and Vasiljević, N and Janković, S}, title = {Sex inequalities in cardiovascular health: a cross-sectional study.}, journal = {European journal of public health}, volume = {26}, number = {1}, pages = {152-158}, doi = {10.1093/eurpub/ckv161}, pmid = {26370435}, issn = {1464-360X}, mesh = {Adolescent ; Adult ; Age Distribution ; Aged ; Aged, 80 and over ; Blood Glucose ; Blood Pressure ; Body Mass Index ; Bosnia and Herzegovina/epidemiology ; Cardiovascular Diseases/*epidemiology ; Cholesterol/blood ; Cross-Sectional Studies ; Diet ; Exercise ; Female ; *Health Behavior ; *Health Status Disparities ; Humans ; Male ; Middle Aged ; Prevalence ; Risk Factors ; Sex Distribution ; Smoking/epidemiology ; Socioeconomic Factors ; Young Adult ; }, abstract = {BACKGROUND: The aim of this study was to determine sex differences in the prevalence of cardiovascular health (CVH) metrics according to the CVH status.

METHODS: The cross-sectional, population-based study involved 2250 women and 1920 men aged ≥18 years that participated in the 2010 National Health Survey in the Republic of Srpska, Bosnia and Herzegovina. Prevalence of CVH behaviours (smoking, body mass index, physical activity, diet), CVH factors (cholesterol, fasting blood glucose and blood pressure, plus smoking) and ideal CVH were estimated according to the American Heart Association criteria for ideal, intermediate and poor levels. Association between sex and ideal CVH categories was analyzed with multivariable logistic regression analysis across three age stratums.

RESULTS: A higher prevalence of ideal CVH metrics was seen in women for smoking status, body mass index, healthy diet score and blood pressure, and in men for physical activity and total cholesterol. Women from all age groups had better CVH behaviours (odds ratio [OR] = 1.40 for the youngest; OR = 2.05 for middle-aged; and OR = 2.03 for older-aged women), while only women from the youngest age group had better CVH factors (OR = 5.09). In line with this, ideal overall CVH prevailed in younger and middle-aged women in comparison to men of the same ages (OR = 3.01 and OR = 2.25, respectively), while disappeared in older ones.

CONCLUSIONS: Significant differences in the prevalence of CVH metrics between men and women in the Republic of Srpska should be considered in cardiovascular disease prevention.}, } @article {pmid26370116, year = {2015}, author = {Collier, CA and Almeida Neto, MS and Aretakis, GM and Santos, RE and de Oliveira, TH and Mourão, JS and Severi, W and El-Deir, AC}, title = {Integrated approach to the understanding of the degradation of an urban river: local perceptions, environmental parameters and geoprocessing.}, journal = {Journal of ethnobiology and ethnomedicine}, volume = {11}, number = {}, pages = {69}, pmid = {26370116}, issn = {1746-4269}, mesh = {Animals ; Brazil ; Conservation of Natural Resources/*methods ; Ecosystem ; Fishes ; Geographic Information Systems ; Humans ; Interdisciplinary Studies ; Knowledge ; *Rivers ; *Urbanization ; Water Pollution ; }, abstract = {BACKGROUND: The use of interdisciplinary approaches such as the proposed report provides a broad understanding of the relationship between people and the environment, revealing reliable aspects not previously considered in the study of this relationship. This study compiled evidence on the environmental degradation of an urbanized river over the past few decades, providing a diagnosis of the consequences of this process for the river, its ichthyofauna, and the local human population.

METHODS: The study was focused on the Beira Rio community on the Capibaribe River in the municipality of São Lourenço da Mata, Pernambuco, Brazil. Data were collected using geoprocessing and ethnobiological approaches, as well as environmental parameters. This research was conducted with the most experienced long-term residents in the local community, through interviews and participatory methodologies to recovering information about the river environment, its ichthyofauna and its environmental services for the last decades.

RESULTS: According to the GIS analysis, the study area was subject to an accelerated process of urbanization, with the total urban area increasing from 73 565, 98 m(2) in 1974 to 383 363, 6 m(2) in 2005. The informants perceived the urban growth, especially in the late twentieth century, being this period recognized as the phase of greatest negative changes in the river environment. The perceived decline of fish stocks was indicated by the community as one of the effects of river degradation. According to the interviews, the deterioration of the river affected the ecosystem services and the relationship of the adjacent human community with this ecosystem. The environmental data indicated that the river is suffering eutrophization and has fecal coliform concentrations 160 times higher than the maximum level permitted by Brazilian legislation.

CONCLUSIONS: The interdisciplinary approach used in this research allowed the understanding of the degradation process of an urban river and some negative effects through the integration of environmental data, GIS and the local knowledge, revealing the complementarity of obtained data and the effectiveness of implementation of this approach.}, } @article {pmid26369904, year = {2016}, author = {Raimondo, S and Lilavois, CR and Lee, L and Augspurger, T and Wang, N and Ingersoll, CG and Bauer, C and Hammer, E and Barron, MG}, title = {Assessing variability in chemical acute toxicity of unionid mussels: Influence of intra- and interlaboratory testing, life stage, and species.}, journal = {Environmental toxicology and chemistry}, volume = {35}, number = {3}, pages = {750-758}, doi = {10.1002/etc.3245}, pmid = {26369904}, issn = {1552-8618}, mesh = {Aging ; Animals ; Bivalvia/*growth & development/*metabolism ; Cladocera ; Daphnia ; Databases, Factual ; Fishes ; Fresh Water ; Larva/drug effects ; Reproducibility of Results ; Species Specificity ; Toxicity Tests, Acute/*methods ; Unionidae/*growth & development/*metabolism ; Water Pollutants, Chemical/*toxicity ; }, abstract = {The authors developed a toxicity database for unionid mussels to examine the extent of intra- and interlaboratory variability in acute toxicity tests with mussel larvae (glochidia) and juveniles; the extent of differential sensitivity of the 2 life stages; and the variation in sensitivity among commonly tested mussels (Lampsilis siliquoidea, Utterbackia imbecillis, and Villosa iris), commonly tested cladocerans (Daphnia magna and Ceriodaphnia dubia), and fish (Oncorhynchus mykiss, Pimephales promelas, and Lepomis macrochirus). The results of these analyses indicate that intralaboratory variability for median effect concentrations (EC50) averaged about 2-fold for both life stages, whereas interlaboratory variability averaged 3.6-fold for juvenile mussels and 6.3-fold for glochidia. The EC50s for juveniles and glochidia were within a factor of 2 of each other for 50% of paired records across chemicals, with juveniles more sensitive than glochidia by more than 2-fold for 33% of the comparisons made between life stages. There was a high concurrence of sensitivity of commonly tested L. siliquoidea, U. imbecillis, and V. iris to that of other mussels. However, this concurrence decreased as the taxonomic distance of the commonly tested cladocerans and fish to mussels increased. The compiled mussel database and determination of data variability will advance risk assessments by including more robust species sensitivity distributions, interspecies correlation estimates, and availability of taxon-specific empirically derived application factors for risk assessment.}, } @article {pmid26361211, year = {2015}, author = {Conner, LM and Morris, G}, title = {Impacts of Mesopredator Control on Conservation of Mesopredators and Their Prey.}, journal = {PloS one}, volume = {10}, number = {9}, pages = {e0137169}, pmid = {26361211}, issn = {1932-6203}, mesh = {Animals ; Biodiversity ; Databases, Factual ; *Ecosystem ; *Food Chain ; *Predatory Behavior ; }, abstract = {Declining large carnivore populations, increased habitat fragmentation, declining interests in fur trapping, and other anthropogenic factors can all lead to increased mesopredator populations and these may negatively impact biodiversity. Lethal mesopredator control potentially mitigates some of these effects but can be controversial, largely because impacts on mesopredator populations have not been evaluated. Estimating these impacts may reduce controversies while increasing our understanding of when lethal control may be beneficial. Therefore, we analyzed published mesopredator removal data to determine if mesopredator removal rates changed over time. Removals of medium,(e.g., raccoons (Procyon lotor) or red foxes (Vulpes vulpes), and large, i.e., bobcats (Lynx rufus) or coyotes (Canis latrans), mesopredators were consistent from year to year and over the duration of study (i.e., number removed during the first and last years of studies were similar). In contrast, removals of small mesopredators, e.g., weasels (Mustela spp.) or spotted skunks (Spilogale putorius), declined over the duration of study. Study area size, number of species targeted for removal, and duration of removal effort were poor predictors of removal rates. Our analyses suggest that: (1) control, as typically implemented, is unlikely to cause negative long-term impacts on populations of medium and large mesopredators but may negatively impact small mesopredators, (2) if mesopredator control benefits prey, recurring removals will generally be needed to maintain benefits, and (3) timing of removals will be important to achieve management goals. We suggest that mesopredator control efforts are frequently spatially structured harvests from continuously distributed populations. This may explain (1) why removal of small mesopredators declined over time; whereas, medium and large mesopredator removals remained consistent, and (2) why some prey failed to respond to mesopredator control efforts.}, } @article {pmid26359911, year = {2016}, author = {Perisin, M and Vetter, M and Gilbert, JA and Bergelson, J}, title = {16Stimator: statistical estimation of ribosomal gene copy numbers from draft genome assemblies.}, journal = {The ISME journal}, volume = {10}, number = {4}, pages = {1020-1024}, pmid = {26359911}, issn = {1751-7370}, support = {R01 GM062504/GM/NIGMS NIH HHS/United States ; }, mesh = {Arabidopsis/*microbiology ; Bacteria/genetics ; Bacteroides ; Computational Biology ; Escherichia coli ; Gene Dosage ; *Genome, Bacterial ; Phylogeny ; Plant Leaves/*genetics ; Pseudomonas aeruginosa ; RNA, Ribosomal, 16S/*genetics ; Reproducibility of Results ; Sequence Analysis, DNA/*methods ; Staphylococcus aureus ; }, abstract = {The 16S rRNA gene (16S) is an accepted marker of bacterial taxonomic diversity, even though differences in copy number obscure the relationship between amplicon and organismal abundances. Ancestral state reconstruction methods can predict 16S copy numbers through comparisons with closely related reference genomes; however, the database of closed genomes is limited. Here, we extend the reference database of 16S copy numbers to de novo assembled draft genomes by developing 16Stimator, a method to estimate 16S copy numbers when these repetitive regions collapse during assembly. Using a read depth approach, we estimate 16S copy numbers for 12 endophytic isolates from Arabidopsis thaliana and confirm estimates by qPCR. We further apply this approach to draft genomes deposited in NCBI and demonstrate accurate copy number estimation regardless of sequencing platform, with an overall median deviation of 14%. The expanded database of isolates with 16S copy number estimates increases the power of phylogenetic correction methods for determining organismal abundances from 16S amplicon surveys.}, } @article {pmid26355995, year = {2015}, author = {Sun, H and Peng, T and Zhao, Y and Du, Y and Zhang, J and Li, J and Xin, Z and Zhao, Q}, title = {Dynamic Analysis of Gene Expression in Rice Superior and Inferior Grains by RNA-Seq.}, journal = {PloS one}, volume = {10}, number = {9}, pages = {e0137168}, pmid = {26355995}, issn = {1932-6203}, mesh = {Cell Cycle/genetics ; Gene Expression Profiling ; *Gene Expression Regulation, Plant ; Gene Ontology ; Genes, Plant ; Molecular Sequence Annotation ; Organ Size/genetics ; Oryza/*genetics ; Plant Proteins/genetics/metabolism ; Seeds/*genetics ; Sequence Analysis, RNA/*methods ; Starch/metabolism ; Sucrose/metabolism ; }, abstract = {Poor grain filling of inferior grains located on lower secondary panicle branch causes great drop in rice yield and quality. Dynamic gene expression patterns between superior and inferior grains were examined from the view of the whole transcriptome by using RNA-Seq method. In total, 19,442 genes were detected during rice grain development. Genes involved in starch synthesis, grain storage and grain development were interrogated in particular in superior and inferior grains. Of the genes involved in sucrose to starch transformation process, most were expressed at lower level in inferior grains at early filling stage compared to that of superior grains. But at late filling stage, the expression of those genes was higher in inferior grains and lower in superior grains. The same trends were observed in the expression of grain storage protein genes. While, evidence that genes involved in cell cycle showed higher expression in inferior grains during whole period of grain filling indicated that cell proliferation was active till the late filling stage. In conclusion, delayed expression of most starch synthesis genes in inferior grains and low capacity of sink organ might be two important factors causing low filling rate of inferior grain at early filling stage, and shortage of carbohydrate supply was a limiting factor at late filling stage.}, } @article {pmid26352260, year = {2015}, author = {Cheng, F and Liu, C and Lin, CC and Zhao, J and Jia, P and Li, WH and Zhao, Z}, title = {A Gene Gravity Model for the Evolution of Cancer Genomes: A Study of 3,000 Cancer Genomes across 9 Cancer Types.}, journal = {PLoS computational biology}, volume = {11}, number = {9}, pages = {e1004497}, pmid = {26352260}, issn = {1553-7358}, support = {P50CA095103/CA/NCI NIH HHS/United States ; P50 CA095103/CA/NCI NIH HHS/United States ; P50CA098131/CA/NCI NIH HHS/United States ; P30 CA068485/CA/NCI NIH HHS/United States ; R01 LM011177/LM/NLM NIH HHS/United States ; P30CA068485/CA/NCI NIH HHS/United States ; R01LM011177/LM/NLM NIH HHS/United States ; P50 CA098131/CA/NCI NIH HHS/United States ; }, mesh = {Databases, Genetic ; Female ; Genome, Human/*genetics ; Genomics/*methods ; Humans ; Male ; *Models, Genetic ; Mutation/*genetics ; Neoplasms/*genetics ; }, abstract = {Cancer development and progression result from somatic evolution by an accumulation of genomic alterations. The effects of those alterations on the fitness of somatic cells lead to evolutionary adaptations such as increased cell proliferation, angiogenesis, and altered anticancer drug responses. However, there are few general mathematical models to quantitatively examine how perturbations of a single gene shape subsequent evolution of the cancer genome. In this study, we proposed the gene gravity model to study the evolution of cancer genomes by incorporating the genome-wide transcription and somatic mutation profiles of ~3,000 tumors across 9 cancer types from The Cancer Genome Atlas into a broad gene network. We found that somatic mutations of a cancer driver gene may drive cancer genome evolution by inducing mutations in other genes. This functional consequence is often generated by the combined effect of genetic and epigenetic (e.g., chromatin regulation) alterations. By quantifying cancer genome evolution using the gene gravity model, we identified six putative cancer genes (AHNAK, COL11A1, DDX3X, FAT4, STAG2, and SYNE1). The tumor genomes harboring the nonsynonymous somatic mutations in these genes had a higher mutation density at the genome level compared to the wild-type groups. Furthermore, we provided statistical evidence that hypermutation of cancer driver genes on inactive X chromosomes is a general feature in female cancer genomes. In summary, this study sheds light on the functional consequences and evolutionary characteristics of somatic mutations during tumorigenesis by propelling adaptive cancer genome evolution, which would provide new perspectives for cancer research and therapeutics.}, } @article {pmid26350795, year = {2015}, author = {Manaswini, G and Sudhakar Reddy, C}, title = {Geospatial monitoring and prioritization of forest fire incidences in Andhra Pradesh, India.}, journal = {Environmental monitoring and assessment}, volume = {187}, number = {10}, pages = {616}, pmid = {26350795}, issn = {1573-2959}, mesh = {Biodiversity ; Climate ; Conservation of Natural Resources/*methods ; Databases, Factual ; Ecology ; Environmental Monitoring/*methods ; *Fires/statistics & numerical data ; *Forests ; Incidence ; India ; Spatio-Temporal Analysis ; Trees ; }, abstract = {Forest fire has been identified as one of the key environmental issue for long-term conservation of biodiversity and has impact on global climate. Spatially multiple observations are necessary for monitoring of forest fires in tropics for understanding conservation efficacy and sustaining biodiversity in protected areas. The present work was carried out to estimate the spatial extent of forest burnt areas and fire frequency using Resourcesat Advanced Wide Field Sensor (AWiFS) data (2009, 2010, 2012, 2013 and 2014) in Andhra Pradesh, India. The spatio-temporal analysis shows that an area of 7514.10 km(2) (29.22% of total forest cover) has been affected by forest fires. Six major forest types are distributed in Andhra Pradesh, i.e. semi-evergreen, moist deciduous, dry deciduous, dry evergreen, thorn and mangroves. Of the total forest burnt area, dry deciduous forests account for >75%. District-wise analysis shows that Kurnool, Prakasam and Cuddapah have shown >100 km(2) of burnt area every year. The total forest burnt area estimate covering protected areas ranges between 6.9 and 22.3% during the study period. Spatial burnt area analysis for protected areas in 2014 indicates 37.2% of fire incidences in the Nagarjunasagar Srisailam Tiger Reserve followed by 20.2 % in the Sri Lankamalleswara Wildlife Sanctuary, 20.1% in the Sri Venkateswara Wildlife Sanctuary and 17.4% in the Gundla Brahmeswaram Wildlife Sanctuary. The analysis of cumulative fire occurrences from 2009 to 2014 has helped in delineation of conservation priority hotspots using a spatial grid cell approach. Conservation priority hotspots I and II are distributed in major parts of study area including protected areas of the Nagarjunasagar Srisailam Tiger Reserve and Gundla Brahmeswaram Wildlife Sanctuary. The spatial database generated will be useful in studies related to influence of fires on species adaptability, ecological damage assessment and conservation planning.}, } @article {pmid26348291, year = {2015}, author = {Meyer, C and Kreft, H and Guralnick, R and Jetz, W}, title = {Global priorities for an effective information basis of biodiversity distributions.}, journal = {Nature communications}, volume = {6}, number = {}, pages = {8221}, pmid = {26348291}, issn = {2041-1723}, mesh = {*Animal Distribution ; Animals ; *Biodiversity ; Conservation of Natural Resources/*methods ; Databases, Factual ; *Internationality ; Vertebrates/*classification/*physiology ; }, abstract = {Gaps in digital accessible information (DAI) on species distributions hamper prospects of safeguarding biodiversity and ecosystem services, and addressing central ecological and evolutionary questions. Achieving international targets on biodiversity knowledge requires that information gaps be identified and actions prioritized. Integrating 157 million point records and distribution maps for 21,170 terrestrial vertebrate species, we find that outside a few well-sampled regions, DAI on point occurrences provides very limited and spatially biased inventories of species. Surprisingly, many large, emerging economies are even more under-represented in global DAI than species-rich, developing countries in the tropics. Multi-model inference reveals that completeness is mainly limited by distance to researchers, locally available research funding and participation in data-sharing networks, rather than transportation infrastructure, or size and funding of Western data contributors as often assumed. Our results highlight the urgent need for integrating non-Western data sources and intensifying cooperation to more effectively address societal biodiversity information needs.}, } @article {pmid26345272, year = {2016}, author = {Greshake, B and Zehr, S and Dal Grande, F and Meiser, A and Schmitt, I and Ebersberger, I}, title = {Potential and pitfalls of eukaryotic metagenome skimming: a test case for lichens.}, journal = {Molecular ecology resources}, volume = {16}, number = {2}, pages = {511-523}, doi = {10.1111/1755-0998.12463}, pmid = {26345272}, issn = {1755-0998}, mesh = {Ascomycota/classification/genetics ; *Biota ; Chlorophyta/classification/genetics ; Computational Biology/*methods ; Computer Simulation ; Lichens/classification/*genetics ; *Metagenome ; Metagenomics/*methods ; Sequence Analysis, DNA/*methods ; }, abstract = {Whole-genome shotgun sequencing of multispecies communities using only a single library layout is commonly used to assess taxonomic and functional diversity of microbial assemblages. Here, we investigate to what extent such metagenome skimming approaches are applicable for in-depth genomic characterizations of eukaryotic communities, for example lichens. We address how to best assemble a particular eukaryotic metagenome skimming data, what pitfalls can occur, and what genome quality can be expected from these data. To facilitate a project-specific benchmarking, we introduce the concept of twin sets, simulated data resembling the outcome of a particular metagenome sequencing study. We show that the quality of genome reconstructions depends essentially on assembler choice. Individual tools, including the metagenome assemblers Omega and MetaVelvet, are surprisingly sensitive to low and uneven coverages. In combination with the routine of assembly parameter choice to optimize the assembly N50 size, these tools can preclude an entire genome from the assembly. In contrast, MIRA, an all-purpose overlap assembler, and SPAdes, a multisized de Bruijn graph assembler, facilitate a comprehensive view on the individual genomes across a wide range of coverage ratios. Testing assemblers on a real-world metagenome skimming data from the lichen Lasallia pustulata demonstrates the applicability of twin sets for guiding method selection. Furthermore, it reveals that the assembly outcome for the photobiont Trebouxia sp. falls behind the a priori expectation given the simulations. Although the underlying reasons remain still unclear, this highlights that further studies on this organism require special attention during sequence data generation and downstream analysis.}, } @article {pmid26343383, year = {2015}, author = {Jiménez, DJ and Chaves-Moreno, D and van Elsas, JD}, title = {Unveiling the metabolic potential of two soil-derived microbial consortia selected on wheat straw.}, journal = {Scientific reports}, volume = {5}, number = {}, pages = {13845}, pmid = {26343383}, issn = {2045-2322}, mesh = {Bacteria/classification/genetics/metabolism ; Biomass ; Computational Biology ; Energy Metabolism/genetics ; Gene Order ; Metagenome ; Metagenomics ; *Microbial Consortia/genetics ; Molecular Sequence Annotation ; Open Reading Frames/genetics ; RNA, Ribosomal, 16S/genetics ; *Soil Microbiology ; Triticum/*microbiology ; }, abstract = {Based on the premise that plant biomass can be efficiently degraded by mixed microbial cultures and/or enzymes, we here applied a targeted metagenomics-based approach to explore the metabolic potential of two forest soil-derived lignocellulolytic microbial consortia, denoted RWS and TWS (bred on wheat straw). Using the metagenomes of three selected batches of two experimental systems, about 1.2 Gb of sequence was generated. Comparative analyses revealed an overrepresentation of predicted carbohydrate transporters (ABC, TonB and phosphotransferases), two-component sensing systems and β-glucosidases/galactosidases in the two consortia as compared to the forest soil inoculum. Additionally, "profiling" of carbohydrate-active enzymes showed significant enrichments of several genes encoding glycosyl hydrolases of families GH2, GH43, GH92 and GH95. Sequence analyses revealed these to be most strongly affiliated to genes present on the genomes of Sphingobacterium, Bacteroides, Flavobacterium and Pedobacter spp. Assembly of the RWS and TWS metagenomes generated 16,536 and 15,902 contigs of ≥10 Kb, respectively. Thirteen contigs, containing 39 glycosyl hydrolase genes, constitute novel (hemi)cellulose utilization loci with affiliation to sequences primarily found in the Bacteroidetes. Overall, this study provides deep insight in the plant polysaccharide degrading capabilities of microbial consortia bred from forest soil, highlighting their biotechnological potential.}, } @article {pmid26343167, year = {2015}, author = {McCarty, LS}, title = {Data quality and relevance in ecotoxicity: The undocumented influences of model assumptions and modifying factors on aquatic toxicity dose metrics.}, journal = {Regulatory toxicology and pharmacology : RTP}, volume = {73}, number = {2}, pages = {552-561}, doi = {10.1016/j.yrtph.2015.08.006}, pmid = {26343167}, issn = {1096-0295}, mesh = {Databases, Factual/*standards ; Dose-Response Relationship, Drug ; Ecotoxicology/*methods ; Lethal Dose 50 ; *Models, Theoretical ; Toxicity Tests/*methods ; Water Pollutants, Chemical/*toxicity ; }, abstract = {A model-based approach using hypothetical organic chemicals examines how aquatic toxicity test results are influenced by toxicity modifying factors such as hydrophobicity, exposure duration, body size, lipid content, mode of toxic action (via Critical Body Residue differences), and metabolic degradation. Differences of up to one to three orders of magnitude were identified for modeled LC50s. Dominance of CBR by low log Kow chemicals can cause further influences. Such differences cause significant changes in the relationship between exposure- and organism-based doses and create substantial difficulties for both interpretation of test results and extrapolation to other laboratory or field exposure conditions. The resulting variability is not readily evident in toxicity testing as insufficient data are collected to validate fundamental assumptions. Consequently, results obtained with standard aquatic toxicity test protocols do not yield consistent, comparable measures of relative toxicity and are inappropriate for quantitative toxicology and risk applications. The substantial uncertainties in testing results created by such undocumented variability must also be given serious consideration in data quality and relevance assessments. Necessary improvements in aquatic toxicity testing methodology should include explicit estimation of toxicokinetics and toxicodynamics and routine validation of toxicological model assumptions.}, } @article {pmid26343035, year = {2015}, author = {Scheirs, S and Malgosa, A and Galtés, I}, title = {The use of ultraviolet light to reveal and enhance burned areas on human bone.}, journal = {Forensic science, medicine, and pathology}, volume = {11}, number = {4}, pages = {618-621}, pmid = {26343035}, issn = {1556-2891}, mesh = {Adult ; Bone and Bones/*pathology ; Burns/*pathology ; Female ; *Fires ; Forensic Anthropology/methods ; Humans ; *Ultraviolet Rays ; }, } @article {pmid26342966, year = {2015}, author = {Edwards, CJ and Cella, M and Tarrier, N and Wykes, T}, title = {Investigating the empirical support for therapeutic targets proposed by the temporal experience of pleasure model in schizophrenia: A systematic review.}, journal = {Schizophrenia research}, volume = {168}, number = {1-2}, pages = {120-144}, doi = {10.1016/j.schres.2015.08.013}, pmid = {26342966}, issn = {1573-2509}, support = {//Medical Research Council/United Kingdom ; }, mesh = {Cognition Disorders/etiology ; Databases, Bibliographic/statistics & numerical data ; *Emotions ; Executive Function ; Humans ; Models, Theoretical ; Psychiatric Status Rating Scales ; Schizophrenia/complications/*therapy ; *Schizophrenic Psychology ; }, abstract = {BACKGROUND: Anhedonia and amotivation are substantial predictors of poor functional outcomes in people with schizophrenia and often present a formidable barrier to returning to work or building relationships. The Temporal Experience of Pleasure Model proposes constructs which should be considered therapeutic targets for these symptoms in schizophrenia e.g. anticipatory pleasure, memory, executive functions, motivation and behaviours related to the activity. Recent reviews have highlighted the need for a clear evidence base to drive the development of targeted interventions.

OBJECTIVE: To review systematically the empirical evidence for each TEP model component and propose evidence-based therapeutic targets for anhedonia and amotivation in schizophrenia.

METHOD: Following PRISMA guidelines, PubMed and PsycInfo were searched using the terms "schizophrenia" and "anhedonia". Studies were included if they measured anhedonia and participants had a diagnosis of schizophrenia. The methodology, measures and main findings from each study were extracted and critically summarised for each TEP model construct.

RESULTS: 80 independent studies were reviewed and executive functions, emotional memory and the translation of motivation into actions are highlighted as key deficits with a strong evidence base in people with schizophrenia. However, there are many relationships that are unclear because the empirical work is limited by over-general tasks and measures.

CONCLUSIONS: Promising methods for research which have more ecological validity include experience sampling and behavioural tasks assessing motivation. Specific adaptations to Cognitive Remediation Therapy, Cognitive Behavioural Therapy and the utilisation of mobile technology to enhance representations and emotional memory are recommended for future development.}, } @article {pmid26340990, year = {2015}, author = {Li, K and Hong, W and Jiao, H and Wang, GD and Rodriguez, KA and Buffenstein, R and Zhao, Y and Nevo, E and Zhao, H}, title = {Sympatric speciation revealed by genome-wide divergence in the blind mole rat Spalax.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {112}, number = {38}, pages = {11905-11910}, pmid = {26340990}, issn = {1091-6490}, support = {K99 AG049940/AG/NIA NIH HHS/United States ; }, mesh = {Animals ; Bayes Theorem ; Gene Ontology ; *Genetic Speciation ; *Genetic Variation ; *Genome ; Linkage Disequilibrium/genetics ; Molecular Sequence Data ; Phylogeny ; Polymorphism, Single Nucleotide/genetics ; Population Dynamics ; Proteolysis ; Receptors, Odorant/genetics ; Sequence Analysis, DNA ; Spalax/*genetics ; Sympatry/*genetics ; }, abstract = {Sympatric speciation (SS), i.e., speciation within a freely breeding population or in contiguous populations, was first proposed by Darwin [Darwin C (1859) On the Origins of Species by Means of Natural Selection] and is still controversial despite theoretical support [Gavrilets S (2004) Fitness Landscapes and the Origin of Species (MPB-41)] and mounting empirical evidence. Speciation of subterranean mammals generally, including the genus Spalax, was considered hitherto allopatric, whereby new species arise primarily through geographic isolation. Here we show in Spalax a case of genome-wide divergence analysis in mammals, demonstrating that SS in continuous populations, with gene flow, encompasses multiple widespread genomic adaptive complexes, associated with the sharply divergent ecologies. The two abutting soil populations of S. galili in northern Israel habituate the ancestral Senonian chalk population and abutting derivative Plio-Pleistocene basalt population. Population divergence originated ∼0.2-0.4 Mya based on both nuclear and mitochondrial genome analyses. Population structure analysis displayed two distinctly divergent clusters of chalk and basalt populations. Natural selection has acted on 300+ genes across the genome, diverging Spalax chalk and basalt soil populations. Gene ontology enrichment analysis highlights strong but differential soil population adaptive complexes: in basalt, sensory perception, musculature, metabolism, and energetics, and in chalk, nutrition and neurogenetics are outstanding. Population differentiation of chemoreceptor genes suggests intersoil population's mate and habitat choice substantiating SS. Importantly, distinctions in protein degradation may also contribute to SS. Natural selection and natural genetic engineering [Shapiro JA (2011) Evolution: A View From the 21st Century] overrule gene flow, evolving divergent ecological adaptive complexes. Sharp ecological divergences abound in nature; therefore, SS appears to be an important mode of speciation as first envisaged by Darwin [Darwin C (1859) On the Origins of Species by Means of Natural Selection].}, } @article {pmid26339283, year = {2015}, author = {Chicchi Giglioli, IA and Pallavicini, F and Pedroli, E and Serino, S and Riva, G}, title = {Augmented Reality: A Brand New Challenge for the Assessment and Treatment of Psychological Disorders.}, journal = {Computational and mathematical methods in medicine}, volume = {2015}, number = {}, pages = {862942}, pmid = {26339283}, issn = {1748-6718}, mesh = {Animals ; Cockroaches ; Computer Simulation ; Diagnosis, Computer-Assisted/methods/trends ; Humans ; Mental Disorders/*diagnosis/psychology/*therapy ; Models, Psychological ; Phobic Disorders/diagnosis/therapy ; Spiders ; Therapy, Computer-Assisted/methods/trends ; *User-Computer Interface ; Virtual Reality Exposure Therapy/*methods/statistics & numerical data ; }, abstract = {Augmented Reality is a new technological system that allows introducing virtual contents in the real world in order to run in the same representation and, in real time, enhancing the user's sensory perception of reality. From another point of view, Augmented Reality can be defined as a set of techniques and tools that add information to the physical reality. To date, Augmented Reality has been used in many fields, such as medicine, entertainment, maintenance, architecture, education, and cognitive and motor rehabilitation but very few studies and applications of AR exist in clinical psychology. In the treatment of psychological disorders, Augmented Reality has given preliminary evidence to be a useful tool due to its adaptability to the patient needs and therapeutic purposes and interactivity. Another relevant factor is the quality of the user's experience in the Augmented Reality system determined from emotional engagement and sense of presence. This experience could increase the AR ecological validity in the treatment of psychological disorders. This paper reviews the recent studies on the use of Augmented Reality in the evaluation and treatment of psychological disorders, focusing on current uses of this technology and on the specific features that delineate Augmented Reality a new technique useful for psychology.}, } @article {pmid26339034, year = {2015}, author = {Hatton, IA and McCann, KS and Fryxell, JM and Davies, TJ and Smerlak, M and Sinclair, AR and Loreau, M}, title = {The predator-prey power law: Biomass scaling across terrestrial and aquatic biomes.}, journal = {Science (New York, N.Y.)}, volume = {349}, number = {6252}, pages = {aac6284}, doi = {10.1126/science.aac6284}, pmid = {26339034}, issn = {1095-9203}, mesh = {Animals ; *Biomass ; *Databases, Factual ; *Food Chain ; Invertebrates ; Mammals ; Plankton ; }, abstract = {Ecosystems exhibit surprising regularities in structure and function across terrestrial and aquatic biomes worldwide. We assembled a global data set for 2260 communities of large mammals, invertebrates, plants, and plankton. We find that predator and prey biomass follow a general scaling law with exponents consistently near ¾. This pervasive pattern implies that the structure of the biomass pyramid becomes increasingly bottom-heavy at higher biomass. Similar exponents are obtained for community production-biomass relations, suggesting conserved links between ecosystem structure and function. These exponents are similar to many body mass allometries, and yet ecosystem scaling emerges independently from individual-level scaling, which is not fully understood. These patterns suggest a greater degree of ecosystem-level organization than previously recognized and a more predictive approach to ecological theory.}, } @article {pmid26338692, year = {2015}, author = {Liu, JJ and Sturrock, RN and Sniezko, RA and Williams, H and Benton, R and Zamany, A}, title = {Transcriptome analysis of the white pine blister rust pathogen Cronartium ribicola: de novo assembly, expression profiling, and identification of candidate effectors.}, journal = {BMC genomics}, volume = {16}, number = {1}, pages = {678}, pmid = {26338692}, issn = {1471-2164}, mesh = {Basidiomycota/*genetics ; Cluster Analysis ; Computational Biology/methods ; Fungal Proteins/genetics ; *Gene Expression Profiling ; Gene Expression Regulation, Fungal ; Molecular Sequence Annotation ; Molecular Sequence Data ; Pinus/*microbiology ; Plant Diseases/*microbiology ; *Transcriptome ; }, abstract = {BACKGROUND: The fungus Cronartium ribicola (Cri) is an economically and ecologically important forest pathogen that causes white pine blister rust (WPBR) disease on five-needle pines. To cause stem cankers and kill white pine trees the fungus elaborates a life cycle with five stages of spore development on five-needle pines and the alternate host Ribes plants. To increase our understanding of molecular WP-BR interactions, here we report genome-wide transcriptional profile analysis of C. ribicola using RNA-seq.

RESULTS: cDNA libraries were constructed from aeciospore, urediniospore, and western white pine (Pinus monticola) tissues post Cri infection. Over 200 million RNA-seq 100-bp paired-end (PE) reads from rust fungal spores were de novo assembled and a reference transcriptome was generated with 17,880 transcripts that were expressed from 13,629 unigenes. A total of 734 unique proteins were predicted as a part of the Cri secretome from complete open reading frames (ORFs), and 41 % of them were Cronartium-specific. This study further identified a repertoire of candidate effectors and other pathogenicity determinants. Differentially expressed genes (DEGs) were identified to gain an understanding of molecular events important during the WPBR fungus life cycle by comparing Cri transcriptomes at different infection stages. Large-scale changes of in planta gene expression profiles were observed, revealing that multiple fungal biosynthetic pathways were enhanced during mycelium growth inside infected pine stem tissues. Conversely, many fungal genes that were up-regulated at the urediniospore stage appeared to be signalling components and transporters. The secreted fungal protein genes that were up-regulated in pine needle tissues during early infection were primarily associated with cell wall modifications, possibly to mask the rust pathogen from plant defenses.

CONCLUSION: This comprehensive transcriptome profiling substantially improves our current understanding of molecular WP-BR interactions. The repertoire of candidate effectors and other putative pathogenicity determinants identified here are valuable for future functional analysis of Cri virulence and pathogenicity.}, } @article {pmid26338071, year = {2015}, author = {Guo, S and Qiang, M and Luan, X and Xu, P and He, G and Yin, X and Xi, L and Jin, X and Shao, J and Chen, X and Fang, D and Li, B}, title = {The application of the Internet of Things to animal ecology.}, journal = {Integrative zoology}, volume = {10}, number = {6}, pages = {572-578}, doi = {10.1111/1749-4877.12162}, pmid = {26338071}, issn = {1749-4877}, mesh = {*Animal Distribution ; Animals ; Ecology/instrumentation/*methods ; Geographic Information Systems ; *Internet ; Radio Frequency Identification Device ; Remote Sensing Technology ; }, abstract = {For ecologists, understanding the reaction of animals to environmental changes is critical. Using networked sensor technology to measure wildlife and environmental parameters can provide accurate, real-time and comprehensive data for monitoring, research and conservation of wildlife. This paper reviews: (i) conventional detection technology; (ii) concepts and applications of the Internet of Things (IoT) in animal ecology; and (iii) the advantages and disadvantages of IoT. The current theoretical limits of IoT in animal ecology are also discussed. Although IoT offers a new direction in animal ecological research, it still needs to be further explored and developed as a theoretical system and applied to the appropriate scientific frameworks for understanding animal ecology.}, } @article {pmid26337864, year = {2016}, author = {Magpantay, FMG and Domenech DE Cellès, M and Rohani, P and King, AA}, title = {Pertussis immunity and epidemiology: mode and duration of vaccine-induced immunity.}, journal = {Parasitology}, volume = {143}, number = {7}, pages = {835-849}, pmid = {26337864}, issn = {1469-8161}, support = {R01 AI101155/AI/NIAID NIH HHS/United States ; U54 GM111274/GM/NIGMS NIH HHS/United States ; }, mesh = {Age Distribution ; Databases, Factual ; Humans ; Immunity/*immunology ; Incidence ; Italy/epidemiology ; *Models, Biological ; Pertussis Vaccine/*immunology ; Time Factors ; Whooping Cough/*epidemiology/*immunology/prevention & control/transmission ; }, abstract = {The resurgence of pertussis in some countries that maintain high vaccination coverage has drawn attention to gaps in our understanding of the epidemiological effects of pertussis vaccines. In particular, major questions surround the nature, degree and durability of vaccine protection. To address these questions, we used mechanistic transmission models to examine regional time series incidence data from Italy in the period immediately following the introduction of acellular pertussis (aP) vaccine. Our results concur with recent animal-challenge experiments wherein infections in aP-vaccinated individuals proved as transmissible as those in naive individuals but much less symptomatic. On the other hand, the data provide evidence for vaccine-driven reduction in susceptibility, which we quantify via a synthetic measure of vaccine impact. As to the precise nature of vaccine failure, the data do not allow us to distinguish between leakiness and waning of vaccine immunity, or some combination of these. Across the range of well-supported models, the nature and duration of vaccine protection, the age profile of incidence and the range of projected epidemiological futures differ substantially, underscoring the importance of the remaining unknowns. We identify key data gaps: sources of data that can supply the information needed to eliminate these remaining uncertainties.}, } @article {pmid26336168, year = {2015}, author = {Franz, M and McLean, E and Tung, J and Altmann, J and Alberts, SC}, title = {Self-organizing dominance hierarchies in a wild primate population.}, journal = {Proceedings. Biological sciences}, volume = {282}, number = {1814}, pages = {}, pmid = {26336168}, issn = {1471-2954}, support = {T32 GM007754/GM/NIGMS NIH HHS/United States ; P01AG031719/AG/NIA NIH HHS/United States ; R01AG034513/AG/NIA NIH HHS/United States ; }, mesh = {*Aggression ; Animals ; *Behavior, Animal ; Data Interpretation, Statistical ; Male ; Papio/*psychology ; Personality ; Social Behavior ; *Social Dominance ; }, abstract = {Linear dominance hierarchies, which are common in social animals, can profoundly influence access to limited resources, reproductive opportunities and health. In spite of their importance, the mechanisms that govern the dynamics of such hierarchies remain unclear. Two hypotheses explain how linear hierarchies might emerge and change over time. The 'prior attributes hypothesis' posits that individual differences in fighting ability directly determine dominance ranks. By contrast, the 'social dynamics hypothesis' posits that dominance ranks emerge from social self-organization dynamics such as winner and loser effects. While the prior attributes hypothesis is well supported in the literature, current support for the social dynamics hypothesis is limited to experimental studies that artificially eliminate or minimize individual differences in fighting abilities. Here, we present the first evidence supporting the social dynamics hypothesis in a wild population. Specifically, we test for winner and loser effects on male hierarchy dynamics in wild baboons, using a novel statistical approach based on the Elo rating method for cardinal rank assignment, which enables the detection of winner and loser effects in uncontrolled group settings. Our results demonstrate (i) the presence of winner and loser effects, and (ii) that individual susceptibility to such effects may have a genetic basis. Taken together, our results show that both social self-organization dynamics and prior attributes can combine to influence hierarchy dynamics even when agonistic interactions are strongly influenced by differences in individual attributes. We hypothesize that, despite variation in individual attributes, winner and loser effects exist (i) because these effects could be particularly beneficial when fighting abilities in other group members change over time, and (ii) because the coevolution of prior attributes and winner and loser effects maintains a balance of both effects.}, } @article {pmid26335547, year = {2015}, author = {Grol-Prokopczyk, H and Verdes-Tennant, E and McEniry, M and Ispány, M}, title = {Promises and Pitfalls of Anchoring Vignettes in Health Survey Research.}, journal = {Demography}, volume = {52}, number = {5}, pages = {1703-1728}, pmid = {26335547}, issn = {1533-7790}, support = {U01 AG009740/AG/NIA NIH HHS/United States ; P01 AG021079/AG/NIA NIH HHS/United States ; P30 AG017266/AG/NIA NIH HHS/United States ; R24 HD047873/HD/NICHD NIH HHS/United States ; 001/WHO_/World Health Organization/International ; U01AG009740/AG/NIA NIH HHS/United States ; P2C HD047873/HD/NICHD NIH HHS/United States ; }, mesh = {Adolescent ; Adult ; Aged ; Aged, 80 and over ; Cross-Cultural Comparison ; Female ; *Health Status ; Health Surveys/*methods/*standards ; Humans ; Male ; Mental Health ; Middle Aged ; Reproducibility of Results ; *Research Design ; Self Report/*standards ; Socioeconomic Factors ; World Health Organization ; Young Adult ; }, abstract = {Data harmonization is a topic of growing importance to demographers, who increasingly conduct domestic or international comparative research. Many self-reported survey items cannot be directly compared across demographic groups or countries because these groups differ in how they use subjective response categories. Anchoring vignettes, already appearing in numerous surveys worldwide, promise to overcome this problem. However, many anchoring vignettes have not been formally evaluated for adherence to the key measurement assumptions of vignette equivalence and response consistency. This article tests these assumptions in some of the most widely fielded anchoring vignettes in the world: the health vignettes in the World Health Organization (WHO) Study on Global AGEing and Adult Health (SAGE) and World Health Survey (WHS) (representing 10 countries; n = 52,388), as well as similar vignettes in the Health and Retirement Study (HRS) (n = 4,528). Findings are encouraging regarding adherence to response consistency, but reveal substantial violations of vignette equivalence both cross-nationally and across socioeconomic groups. That is, members of different sociocultural groups appear to interpret vignettes as depicting fundamentally different levels of health. The evaluated anchoring vignettes do not fulfill their promise of providing interpersonally comparable measures of health. Recommendations for improving future implementations of vignettes are discussed.}, } @article {pmid26335202, year = {2015}, author = {Böttger, K and Hatzikirou, H and Voss-Böhme, A and Cavalcanti-Adam, EA and Herrero, MA and Deutsch, A}, title = {An Emerging Allee Effect Is Critical for Tumor Initiation and Persistence.}, journal = {PLoS computational biology}, volume = {11}, number = {9}, pages = {e1004366}, pmid = {26335202}, issn = {1553-7358}, mesh = {Cell Count ; Cell Movement/physiology ; Cell Proliferation/physiology ; Computational Biology ; Computer Simulation ; *Models, Biological ; *Neoplastic Processes ; Tumor Microenvironment/*physiology ; }, abstract = {Tumor cells develop different strategies to cope with changing microenvironmental conditions. A prominent example is the adaptive phenotypic switching between cell migration and proliferation. While it has been shown that the migration-proliferation plasticity influences tumor spread, it remains unclear how this particular phenotypic plasticity affects overall tumor growth, in particular initiation and persistence. To address this problem, we formulate and study a mathematical model of spatio-temporal tumor dynamics which incorporates the microenvironmental influence through a local cell density dependence. Our analysis reveals that two dynamic regimes can be distinguished. If cell motility is allowed to increase with local cell density, any tumor cell population will persist in time, irrespective of its initial size. On the contrary, if cell motility is assumed to decrease with respect to local cell density, any tumor population below a certain size threshold will eventually extinguish, a fact usually termed as Allee effect in ecology. These results suggest that strategies aimed at modulating migration are worth to be explored as alternatives to those mainly focused at keeping tumor proliferation under control.}, } @article {pmid26334912, year = {2015}, author = {Ulrich, J and Dao, VA and Majumdar, U and Schmitt-Engel, C and Schwirz, J and Schultheis, D and Ströhlein, N and Troelenberg, N and Grossmann, D and Richter, T and Dönitz, J and Gerischer, L and Leboulle, G and Vilcinskas, A and Stanke, M and Bucher, G}, title = {Large scale RNAi screen in Tribolium reveals novel target genes for pest control and the proteasome as prime target.}, journal = {BMC genomics}, volume = {16}, number = {1}, pages = {674}, pmid = {26334912}, issn = {1471-2164}, mesh = {Animals ; Base Sequence ; Cluster Analysis ; Conserved Sequence ; Gene Ontology ; *Genes, Insect ; *Pest Control, Biological ; Proteasome Endopeptidase Complex/*metabolism ; *RNA Interference ; Tribolium/*genetics ; }, abstract = {BACKGROUND: Insect pest control is challenged by insecticide resistance and negative impact on ecology and health. One promising pest specific alternative is the generation of transgenic plants, which express double stranded RNAs targeting essential genes of a pest species. Upon feeding, the dsRNA induces gene silencing in the pest resulting in its death. However, the identification of efficient RNAi target genes remains a major challenge as genomic tools and breeding capacity is limited in most pest insects impeding whole-animal-high-throughput-screening.

RESULTS: We use the red flour beetle Tribolium castaneum as a screening platform in order to identify the most efficient RNAi target genes. From about 5,000 randomly screened genes of the iBeetle RNAi screen we identify 11 novel and highly efficient RNAi targets. Our data allowed us to determine GO term combinations that are predictive for efficient RNAi target genes with proteasomal genes being most predictive. Finally, we show that RNAi target genes do not appear to act synergistically and that protein sequence conservation does not correlate with the number of potential off target sites.

CONCLUSIONS: Our results will aid the identification of RNAi target genes in many pest species by providing a manageable number of excellent candidate genes to be tested and the proteasome as prime target. Further, the identified GO term combinations will help to identify efficient target genes from organ specific transcriptomes. Our off target analysis is relevant for the sequence selection used in transgenic plants.}, } @article {pmid26332837, year = {2015}, author = {Del Chierico, F and Vernocchi, P and Petrucca, A and Paci, P and Fuentes, S and Praticò, G and Capuani, G and Masotti, A and Reddel, S and Russo, A and Vallone, C and Salvatori, G and Buffone, E and Signore, F and Rigon, G and Dotta, A and Miccheli, A and de Vos, WM and Dallapiccola, B and Putignani, L}, title = {Phylogenetic and Metabolic Tracking of Gut Microbiota during Perinatal Development.}, journal = {PloS one}, volume = {10}, number = {9}, pages = {e0137347}, pmid = {26332837}, issn = {1932-6203}, mesh = {Humans ; Infant, Newborn ; Intestines/*microbiology ; Magnetic Resonance Spectroscopy ; *Microbiota ; *Phylogeny ; }, abstract = {The colonization and development of gut microbiota immediately after birth is highly variable and depends on several factors, such as delivery mode and modality of feeding during the first months of life. A cohort of 31 mother and neonate pairs, including 25 at-term caesarean (CS) and 6 vaginally (V) delivered neonates (DNs), were included in this study and 121 meconium/faecal samples were collected at days 1 through 30 following birth. Operational taxonomic units (OTUs) were assessed in 69 stool samples by phylogenetic microarray HITChip and inter- and intra-individual distributions were established by inter-OTUs correlation matrices and OTUs co-occurrence or co-exclusion networks. 1H-NMR metabolites were determined in 70 stool samples, PCA analysis was performed on 55 CS DNs samples, and metabolome/OTUs co-correlations were assessed in 45 CS samples, providing an integrated map of the early microbiota OTUs-metabolome. A microbiota "core" of OTUs was identified that was independent of delivery mode and lactation stage, suggesting highly specialized communities that act as seminal colonizers of microbial networks. Correlations among OTUs, metabolites, and OTUs-metabolites revealed metabolic profiles associated with early microbial ecological dynamics, maturation of milk components, and host physiology.}, } @article {pmid26331957, year = {2015}, author = {Humphries, GR}, title = {Estimating Regions of Oceanographic Importance for Seabirds Using A-Spatial Data.}, journal = {PloS one}, volume = {10}, number = {9}, pages = {e0137241}, pmid = {26331957}, issn = {1932-6203}, mesh = {Algorithms ; Animals ; *Birds ; Geographic Information Systems ; Machine Learning ; *Oceanography ; }, abstract = {Advances in GPS tracking technologies have allowed for rapid assessment of important oceanographic regions for seabirds. This allows us to understand seabird distributions, and the characteristics which determine the success of populations. In many cases, quality GPS tracking data may not be available; however, long term population monitoring data may exist. In this study, a method to infer important oceanographic regions for seabirds will be presented using breeding sooty shearwaters as a case study. This method combines a popular machine learning algorithm (generalized boosted regression modeling), geographic information systems, long-term ecological data and open access oceanographic datasets. Time series of chick size and harvest index data derived from a long term dataset of Maori 'muttonbirder' diaries were obtained and used as response variables in a gridded spatial model. It was found that areas of the sub-Antarctic water region best capture the variation in the chick size data. Oceanographic features including wind speed and charnock (a derived variable representing ocean surface roughness) came out as top predictor variables in these models. Previously collected GPS data demonstrates that these regions are used as "flyways" by sooty shearwaters during the breeding season. It is therefore likely that wind speeds in these flyways affect the ability of sooty shearwaters to provision for their chicks due to changes in flight dynamics. This approach was designed to utilize machine learning methodology but can also be implemented with other statistical algorithms. Furthermore, these methods can be applied to any long term time series of population data to identify important regions for a species of interest.}, } @article {pmid26328611, year = {2015}, author = {Kurth, F and Feldhahn, L and Bönn, M and Herrmann, S and Buscot, F and Tarkka, MT}, title = {Large scale transcriptome analysis reveals interplay between development of forest trees and a beneficial mycorrhiza helper bacterium.}, journal = {BMC genomics}, volume = {16}, number = {1}, pages = {658}, pmid = {26328611}, issn = {1471-2164}, mesh = {Basidiomycota/*physiology ; Down-Regulation/genetics ; *Forests ; *Gene Expression Profiling ; Gene Expression Regulation, Plant ; Gene Ontology ; Mycorrhizae/*physiology ; Plant Leaves/genetics ; Plant Roots/genetics ; Quercus/genetics/microbiology ; Streptomyces/*physiology ; Trees/*genetics/*microbiology ; Up-Regulation/genetics ; }, abstract = {BACKGROUND: Pedunculate oak, Quercus robur is an abundant forest tree species that hosts a large and diverse community of beneficial ectomycorrhizal fungi (EMFs), whereby ectomycorrhiza (EM) formation is stimulated by mycorrhiza helper bacteria such as Streptomyces sp. AcH 505. Oaks typically grow rhythmically, with alternating root flushes (RFs) and shoot flushes (SFs). We explored the poorly understood mechanisms by which oaks integrate signals induced by their beneficial microbes and endogenous rhythmic growth at the level of gene expression. To this end, we compared transcript profiles of oak microcuttings at RF and SF during interactions with AcH 505 alone and in combination with the basidiomycetous EMF Piloderma croceum.

RESULTS: The local root and distal leaf responses to the microorganisms differed substantially. More genes involved in the recognition of bacteria and fungi, defence and cell wall remodelling related transcription factors (TFs) were differentially expressed in the roots than in the leaves of oaks. In addition, interaction with AcH 505 and P. croceum affected the expression of a higher number of genes during SF than during RF, including AcH 505 elicited defence response, which was attenuated by co-inoculation with P. croceum in the roots during SF. Genes encoding leucine-rich receptor-like kinases (LRR-RLKs) and proteins (LRR-RLPs), LRR containing defence response regulators, TFs from bZIP, ERF and WRKY families, xyloglucan cell wall transglycolases/hydrolases and exordium proteins were differentially expressed in both roots and leaves of plants treated with AcH 505. Only few genes, including specific RLKs and TFs, were induced in both AcH 505 and co-inoculation treatments.

CONCLUSION: Treatment with AcH 505 induces and maintains the expression levels of signalling genes encoding candidate receptor protein kinases and TFs and leads to differential expression of cell wall modification related genes in pedunculate oak microcuttings. Local gene expression response to AcH 505 alone and in combination with P. croceum are more pronounced when roots are in resting stages, possibly due to the fact that non growing roots re-direct their activity towards plant defence rather than growth.}, } @article {pmid26323664, year = {2015}, author = {Homan, T and Di Pasquale, A and Kiche, I and Onoka, K and Hiscox, A and Mweresa, C and Mukabana, WR and Takken, W and Maire, N}, title = {Innovative tools and OpenHDS for health and demographic surveillance on Rusinga Island, Kenya.}, journal = {BMC research notes}, volume = {8}, number = {}, pages = {397}, pmid = {26323664}, issn = {1756-0500}, mesh = {*Demography ; Geographic Information Systems ; *Health Status Indicators ; Humans ; Kenya/epidemiology ; Malaria/*epidemiology ; *Population Surveillance ; }, abstract = {BACKGROUND: Health in low and middle income countries is on one hand characterized by a high burden associated with preventable communicable diseases and on the other hand considered to be under-documented due to improper basic health and demographic record-keeping. health and demographic surveillance systems (HDSSs) have provided researchers, policy makers and governments with data about local population dynamics and health related information. In order for an HDSS to deliver high quality data, effective organization of data collection and management are vital. HDSSs impose a challenging logistical process typically characterized by door to door visits, poor navigational guidance, conducting interviews recorded on paper, error prone data entry, an extensive staff and marginal data quality management possibilities.

METHODS: A large trial investigating the effect of odour-baited mosquito traps on malaria vector populations and malaria transmission on Rusinga Island, western Kenya, has deployed an HDSS. By means of computer tablets in combination with Open Data Kit and OpenHDS data collection and management software experiences with time efficiency, cost effectiveness and high data quality are illustrate. Step by step, a complete organization of the data management infrastructure is described, ranging from routine work in the field to the organization of the centralized data server.

RESULTS AND DISCUSSION: Adopting innovative technological advancements has enabled the collection of demographic and malaria data quickly and effectively, with minimal margin for errors. Real-time data quality controls integrated within the system can lead to financial savings and a time efficient work flow.

CONCLUSION: This novel method of HDSS implementation demonstrates the feasibility of integrating electronic tools in large-scale health interventions.}, } @article {pmid26317871, year = {2015}, author = {Zhu, C and Delmont, TO and Vogel, TM and Bromberg, Y}, title = {Functional Basis of Microorganism Classification.}, journal = {PLoS computational biology}, volume = {11}, number = {8}, pages = {e1004472}, pmid = {26317871}, issn = {1553-7358}, mesh = {Bacteria/*classification/genetics ; Classification/*methods ; Computational Biology/*methods ; Genome, Bacterial/*physiology ; *Software ; }, abstract = {Correctly identifying nearest "neighbors" of a given microorganism is important in industrial and clinical applications where close relationships imply similar treatment. Microbial classification based on similarity of physiological and genetic organism traits (polyphasic similarity) is experimentally difficult and, arguably, subjective. Evolutionary relatedness, inferred from phylogenetic markers, facilitates classification but does not guarantee functional identity between members of the same taxon or lack of similarity between different taxa. Using over thirteen hundred sequenced bacterial genomes, we built a novel function-based microorganism classification scheme, functional-repertoire similarity-based organism network (FuSiON; flattened to fusion). Our scheme is phenetic, based on a network of quantitatively defined organism relationships across the known prokaryotic space. It correlates significantly with the current taxonomy, but the observed discrepancies reveal both (1) the inconsistency of functional diversity levels among different taxa and (2) an (unsurprising) bias towards prioritizing, for classification purposes, relatively minor traits of particular interest to humans. Our dynamic network-based organism classification is independent of the arbitrary pairwise organism similarity cut-offs traditionally applied to establish taxonomic identity. Instead, it reveals natural, functionally defined organism groupings and is thus robust in handling organism diversity. Additionally, fusion can use organism meta-data to highlight the specific environmental factors that drive microbial diversification. Our approach provides a complementary view to cladistic assignments and holds important clues for further exploration of microbial lifestyles. Fusion is a more practical fit for biomedical, industrial, and ecological applications, as many of these rely on understanding the functional capabilities of the microbes in their environment and are less concerned with phylogenetic descent.}, } @article {pmid26317654, year = {2015}, author = {Newberry, MG and Ennis, DB and Savage, VM}, title = {Testing Foundations of Biological Scaling Theory Using Automated Measurements of Vascular Networks.}, journal = {PLoS computational biology}, volume = {11}, number = {8}, pages = {e1004455}, pmid = {26317654}, issn = {1553-7358}, mesh = {Adult ; Algorithms ; Carotid Artery Diseases/pathology ; Computational Biology/*methods ; Humans ; Magnetic Resonance Angiography/*methods ; *Models, Cardiovascular ; Prospective Studies ; Regression Analysis ; }, abstract = {Scientists have long sought to understand how vascular networks supply blood and oxygen to cells throughout the body. Recent work focuses on principles that constrain how vessel size changes through branching generations from the aorta to capillaries and uses scaling exponents to quantify these changes. Prominent scaling theories predict that combinations of these exponents explain how metabolic, growth, and other biological rates vary with body size. Nevertheless, direct measurements of individual vessel segments have been limited because existing techniques for measuring vasculature are invasive, time consuming, and technically difficult. We developed software that extracts the length, radius, and connectivity of in vivo vessels from contrast-enhanced 3D Magnetic Resonance Angiography. Using data from 20 human subjects, we calculated scaling exponents by four methods-two derived from local properties of branching junctions and two from whole-network properties. Although these methods are often used interchangeably in the literature, we do not find general agreement between these methods, particularly for vessel lengths. Measurements for length of vessels also diverge from theoretical values, but those for radius show stronger agreement. Our results demonstrate that vascular network models cannot ignore certain complexities of real vascular systems and indicate the need to discover new principles regarding vessel lengths.}, } @article {pmid26317526, year = {2018}, author = {Aubin, G and Béliveau, MF and Klinger, E}, title = {An exploration of the ecological validity of the Virtual Action Planning-Supermarket (VAP-S) with people with schizophrenia.}, journal = {Neuropsychological rehabilitation}, volume = {28}, number = {5}, pages = {689-708}, doi = {10.1080/09602011.2015.1074083}, pmid = {26317526}, issn = {1464-0694}, mesh = {*Activities of Daily Living ; Adult ; *Diagnosis, Computer-Assisted/adverse effects ; *Executive Function ; Female ; Humans ; Male ; Middle Aged ; *Psychological Tests ; Schizophrenia/*diagnosis/drug therapy ; *Schizophrenic Psychology ; Surveys and Questionnaires ; Virtual Reality ; Young Adult ; }, abstract = {People with schizophrenia often have functional limitations that affect their daily activities due to executive function deficits. One way to assess these deficits is through the use of virtual reality programmes that reproduce real-life instrumental activities of daily living (IADLs). One such programme is the Virtual Action Planning-Supermarket (VAP-S). This exploratory study aimed to examine the ecological validity of this programme, specifically, how task performance in both virtual and natural environments compares. Case studies were used and involved five participants with schizophrenia, who were familiar with grocery shopping. They were assessed during both the VAP-S shopping task and a real-life grocery shopping task using an observational assessment tool, the Perceive, Recall, Plan and Perform (PRPP) System of Task Analysis. The results show that when difficulties were present in the virtual task, difficulties were also observed in the real-life task. For some participants, greater difficulties were observed in the virtual task. These difficulties could be explained by the presence of perceptual deficits and problems remembering the required sequenced actions in the virtual task. In conclusion, performance on the VAP-S by these five participants was generally comparable to the performance in a natural environment.}, } @article {pmid26313959, year = {2015}, author = {Li, HF and Lan, YC and Fujisaki, I and Kanzaki, N and Lee, HJ and Su, NY}, title = {Termite Assemblage Pattern and Niche Partitioning in a Tropical Forest Ecosystem.}, journal = {Environmental entomology}, volume = {44}, number = {3}, pages = {546-556}, doi = {10.1093/ee/nvv038}, pmid = {26313959}, issn = {1938-2936}, mesh = {Animals ; *Ecosystem ; Forests ; Geographic Information Systems ; Isoptera/*physiology ; Taiwan ; *Tropical Climate ; }, abstract = {Termites are major plant decomposers in tropical forest ecosystems, but their cryptic nature poses an obstacle for studying their ecological roles in depth. In the current study, we quantified climatic and geographic information of 137 termite collection sites in the Kenting National Park, Taiwan, and described the ecological niches and assemblage patterns of 13 termite species of three families. Three major assemblage patterns are reported. First, the three termite families were found in most landcovering types with similar number of species, which indicated that each family played a unique role in the ecosystem. Second, average numbers of termite species were not different among collection sites, but the total number of termite species found in each landcovering type was different, which indicated that termite niche capacity in each small area was the same but some landcovering types were composed of diverse microhabitats to host more termite species. Third, termite species of every family showed distinct moisture preferences in their habitat choices. In addition to the three assemblage patterns, we found that niche size of the advanced termite family, Termitidae, was larger than that of the primitive termite families, Rhinotermitidae or Kalotermitidae. The broader choices of cellulosic materials as food sources may allow Termitidae to adapt to more diverse environments than exclusive wood feeders. Termite niche quantification could further be used to study termite pest adaption in urban areas, interspecific competition between native and invasive species, and plant decomposition processes.}, } @article {pmid26313687, year = {2015}, author = {Pang, T and Guo, L and Shim, D and Cannon, N and Tang, S and Chen, J and Xia, X and Yin, W and Carlson, JE}, title = {Characterization of the Transcriptome of the Xerophyte Ammopiptanthus mongolicus Leaves under Drought Stress by 454 Pyrosequencing.}, journal = {PloS one}, volume = {10}, number = {8}, pages = {e0136495}, pmid = {26313687}, issn = {1932-6203}, mesh = {China ; Databases, Genetic ; *Fabaceae/genetics/metabolism ; Gene Expression Regulation, Plant/*physiology ; High-Throughput Nucleotide Sequencing ; *Plant Leaves/genetics/metabolism ; *RNA, Plant/biosynthesis/genetics ; Software ; Stress, Physiological/*physiology ; Transcriptome/*physiology ; }, abstract = {BACKGROUND: Ammopiptanthus mongolicus (Maxim. Ex Kom.) Cheng f., an endangered ancient legume species, endemic to the Gobi desert in north-western China. As the only evergreen broadleaf shrub in this area, A. mongolicus plays an important role in the region's ecological-environmental stability. Despite the strong potential of A. mongolicus in providing new insights on drought tolerance, sequence information on the species in public databases remains scarce. To both learn about the role of gene expression in drought stress tolerance in A. mongolicus and to expand genomic resources for the species, transcriptome sequencing of stress-treated A. mongolicus plants was performed.

RESULTS: Using 454 pyrosequencing technology, 8,480 and 7,474 contigs were generated after de novo assembly of RNA sequences from leaves of untreated and drought-treated plants, respectively. After clustering using TGICL and CAP3 programs, a combined assembly of all reads produced a total of 11,357 putative unique transcripts (PUTs). Functional annotation and classification of the transcripts were conducted by aligning the 11,357 PUTs against the public protein databases and nucleotide database (Nt). Between control and drought-treated plants, 1,620 differentially expressed genes (DEGs) were identified, of which 1,106 were up-regulated and 514 were down-regulated. The differential expression of twenty candidate genes in metabolic pathways and transcription factors families related to stress-response were confirmed by quantitative real-time PCR. Representatives of several large gene families, such as WRKY and P5CS, were identified and verified in A. mongolicus for the first time.

CONCLUSIONS: The additional transcriptome resources, gene expression profiles, functional annotations, and candidate genes provide a more comprehensive understanding of the stress response pathways in xeric-adapted plant species such as A. mongolicus.}, } @article {pmid26312513, year = {2015}, author = {Mombelli, MA and Barreto, Mda S and de Arruda, GO and Marcon, SS}, title = {AIDS epidemic in the triple frontier: subsidies for professional practice.}, journal = {Revista brasileira de enfermagem}, volume = {68}, number = {3}, pages = {371-8, 429-37}, doi = {10.1590/0034-7167.2015680308i}, pmid = {26312513}, issn = {1984-0446}, mesh = {Acquired Immunodeficiency Syndrome/*epidemiology/nursing ; Adolescent ; Adult ; Aged ; Argentina/epidemiology ; Brazil ; Child ; Female ; Humans ; Male ; Middle Aged ; Paraguay/epidemiology ; Professional Practice ; Young Adult ; }, abstract = {OBJECTIVE: to analyze the AIDS epidemic trend from 1988 to 2012, in a tri-border area.

METHOD: Ecological time-series study with data from the Department of informatics from the Brazilian Unified Health System (SUS).

RESULTS: A total of 1427 cases of AIDS were registered, and 82.1% were aged 20-49 years and 56% in males. The relationship man/woman went from 9/1 to 1/1 and increased the number of cases among individuals with more years of education, also, people aged more than 50 years old the age group from 20 to 34 years old. The most common exposure category was heterosexual, significantly higher among women; on the other hand, drug injection use was associated with male gender.

CONCLUSION: seeking to embrace the changes in the epidemiological scenario of AIDS, nursing professionals should implement intervention strategies for people identified as the most vulnerable to HIV infection.}, } @article {pmid26311086, year = {2015}, author = {Steenberg, JW and Millward, AA and Duinker, PN and Nowak, DJ and Robinson, PJ}, title = {Neighbourhood-scale urban forest ecosystem classification.}, journal = {Journal of environmental management}, volume = {163}, number = {}, pages = {134-145}, doi = {10.1016/j.jenvman.2015.08.008}, pmid = {26311086}, issn = {1095-8630}, mesh = {Canada ; *Cities ; Cluster Analysis ; Decision Support Techniques ; Ecology/classification/*methods ; *Ecosystem ; *Forests ; Humans ; Population Density ; Residence Characteristics ; Trees ; }, abstract = {Urban forests are now recognized as essential components of sustainable cities, but there remains uncertainty concerning how to stratify and classify urban landscapes into units of ecological significance at spatial scales appropriate for management. Ecosystem classification is an approach that entails quantifying the social and ecological processes that shape ecosystem conditions into logical and relatively homogeneous management units, making the potential for ecosystem-based decision support available to urban planners. The purpose of this study is to develop and propose a framework for urban forest ecosystem classification (UFEC). The multifactor framework integrates 12 ecosystem components that characterize the biophysical landscape, built environment, and human population. This framework is then applied at the neighbourhood scale in Toronto, Canada, using hierarchical cluster analysis. The analysis used 27 spatially-explicit variables to quantify the ecosystem components in Toronto. Twelve ecosystem classes were identified in this UFEC application. Across the ecosystem classes, tree canopy cover was positively related to economic wealth, especially income. However, education levels and homeownership were occasionally inconsistent with the expected positive relationship with canopy cover. Open green space and stocking had variable relationships with economic wealth and were more closely related to population density, building intensity, and land use. The UFEC can provide ecosystem-based information for greening initiatives, tree planting, and the maintenance of the existing canopy. Moreover, its use has the potential to inform the prioritization of limited municipal resources according to ecological conditions and to concerns of social equity in the access to nature and distribution of ecosystem service supply.}, } @article {pmid26310498, year = {2015}, author = {Less, EL and McKee, P and Toomey, T and Nelson, T and Erickson, D and Xiong, S and Jones-Webb, R}, title = {Matching study areas using Google Street View: A new application for an emerging technology.}, journal = {Evaluation and program planning}, volume = {53}, number = {}, pages = {72-79}, pmid = {26310498}, issn = {1873-7870}, support = {R01 AA020496/AA/NIAAA NIH HHS/United States ; #R01AA020496/AA/NIAAA NIH HHS/United States ; }, mesh = {Crime/*statistics & numerical data ; *Geographic Information Systems ; Humans ; *Internet ; Observer Variation ; *Residence Characteristics ; Software Design ; User-Computer Interface ; }, abstract = {Google Street View (GSV) can be used as an effective tool to conduct virtual neighborhood audits. We expand on this research by exploring the utility of a GSV-based neighborhood audit to measure and match target and comparison study areas. We developed a GSV-based inventory to measure characteristics of retail alcohol stores and their surrounding neighborhoods. We assessed its reliability and assessed the utility of GSV-based audits for matching target and comparison study areas. We found that GSV-based neighborhood audits can be a useful, reliable, and cost-effective tool for matching target and comparison study areas when archival data are insufficient and primary data collection is prohibitive. We suggest that researchers focus on characteristics that are easily visible on GSV and are relatively stable over time when creating future GSV-based measuring and matching tools. Dividing the study area into small segments may also provide more accurate measurements and more precise matching.}, } @article {pmid26308326, year = {2015}, author = {McAvoy, A and Hauert, C}, title = {Asymmetric Evolutionary Games.}, journal = {PLoS computational biology}, volume = {11}, number = {8}, pages = {e1004349}, pmid = {26308326}, issn = {1553-7358}, mesh = {Animals ; Biological Evolution ; Computational Biology/*methods ; Cultural Evolution ; Ecology ; *Game Theory ; Genotype ; Humans ; *Models, Theoretical ; }, abstract = {Evolutionary game theory is a powerful framework for studying evolution in populations of interacting individuals. A common assumption in evolutionary game theory is that interactions are symmetric, which means that the players are distinguished by only their strategies. In nature, however, the microscopic interactions between players are nearly always asymmetric due to environmental effects, differing baseline characteristics, and other possible sources of heterogeneity. To model these phenomena, we introduce into evolutionary game theory two broad classes of asymmetric interactions: ecological and genotypic. Ecological asymmetry results from variation in the environments of the players, while genotypic asymmetry is a consequence of the players having differing baseline genotypes. We develop a theory of these forms of asymmetry for games in structured populations and use the classical social dilemmas, the Prisoner's Dilemma and the Snowdrift Game, for illustrations. Interestingly, asymmetric games reveal essential differences between models of genetic evolution based on reproduction and models of cultural evolution based on imitation that are not apparent in symmetric games.}, } @article {pmid26306230, year = {2015}, author = {Breitenstein, MK and Pathak, J and Simon, G}, title = {Studying the Confounding Effects of Socio-Ecological Conditions in Retrospective Clinical Research: A Use Case of Social Stress.}, journal = {AMIA Joint Summits on Translational Science proceedings. AMIA Joint Summits on Translational Science}, volume = {2015}, number = {}, pages = {41-45}, pmid = {26306230}, issn = {2153-4063}, support = {R01 GM105688/GM/NIGMS NIH HHS/United States ; }, abstract = {Socio-ecological Conditions (SECs) are important to include in clinical research models as they have been known to impact the health of patients. However, current clinical research models account for these factors only in an unsatisfyingly rudimentary way. In this study, we developed an SEC Index that captured the latent and direct effects of social stress, one of the many kinds of SEC, on patients' general health as measured by the Charlson Comorbidity Index. We demonstrated that the above SEC Index had a significant effect in a clinical model, a patient-level model with the specific clinical outcome of breast cancer prevalence. Further, we demonstrated that including the SEC Index of social stress into the clinical models significantly increased their performance. Our study demonstrated a viable approach that is interchangeable to include any SEC of interest, to more appropriately account for SECs in clinical research models.}, } @article {pmid26306203, year = {2015}, author = {Battle, KE and Guerra, CA and Golding, N and Duda, KA and Cameron, E and Howes, RE and Elyazar, IR and Baird, JK and Reiner, RC and Gething, PW and Smith, DL and Hay, SI}, title = {Global database of matched Plasmodium falciparum and P. vivax incidence and prevalence records from 1985-2013.}, journal = {Scientific data}, volume = {2}, number = {}, pages = {150012}, pmid = {26306203}, issn = {2052-4463}, support = {MR/K00669X/1/MRC_/Medical Research Council/United Kingdom ; 095066/WT_/Wellcome Trust/United Kingdom ; B9RJIXO/WT_/Wellcome Trust/United Kingdom ; 089276/WT_/Wellcome Trust/United Kingdom ; B9RZGS0/WT_/Wellcome Trust/United Kingdom ; K00669X/MRC_/Medical Research Council/United Kingdom ; UL1 TR001108/TR/NCATS NIH HHS/United States ; }, mesh = {*Databases, Factual ; Humans ; Incidence ; Malaria, Falciparum/epidemiology/parasitology ; Malaria, Vivax/epidemiology/parasitology ; *Plasmodium falciparum ; *Plasmodium vivax ; Prevalence ; }, abstract = {Measures of clinical incidence are necessary to help estimate the burden of a disease. Incidence is a metric not commonly measured in malariology because the longitudinal surveys required are costly and labour intensive. This database is an effort to collate published incidence records obtained using active case detection for Plasmodium falciparum and Plasmodium vivax malaria. The literature search methods, data abstraction procedures and data processing procedures are described here. A total of 1,680 spatio-temporally unique incidence records were collected for the database: 1,187 for P. falciparum and 493 for P. vivax. These data were gathered to model the relationship between clinical incidence and prevalence of infection and can be used for a variety of modelling exercises including the assessment of change in disease burden in relation to age and control interventions. The subset of data that have been used for such modelling exercises are described and identified.}, } @article {pmid26306174, year = {2015}, author = {Pfaff, CT and König-Ries, B and Lang, AC and Ratcliffe, S and Wirth, C and Man, X and Nadrowski, K}, title = {rBEFdata: documenting data exchange and analysis for a collaborative data management platform.}, journal = {Ecology and evolution}, volume = {5}, number = {14}, pages = {2890-2897}, pmid = {26306174}, issn = {2045-7758}, abstract = {We are witnessing a growing gap separating primary research data from derived data products presented as knowledge in publications. Although journals today more often require the underlying data products used to derive the results as a prerequisite for a publication, the important link to the primary data is lost. However, documenting the postprocessing steps of data linking, the primary data with derived data products has the potential to increase the accuracy and the reproducibility of scientific findings significantly. Here, we introduce the rBEFdata R package as companion to the collaborative data management platform BEFdata. The R package provides programmatic access to features of the platform. It allows to search for data and integrates the search with external thesauri to improve the data discovery. It allows to download and import data and metadata into R for analysis. A batched download is available as well which works along a paper proposal mechanism implemented by BEFdata. This feature of BEFdata allows to group primary data and metadata and streamlines discussions and collaborations revolving around a certain research idea. The upload functionality of the R package in combination with the paper proposal mechanism of the portal allows to attach derived data products and scripts directly from R, thus addressing major aspects of documenting data postprocessing. We present the core features of the rBEFdata R package along an ecological analysis example and further discuss the potential of postprocessing documentation for data, linking primary data with derived data products and knowledge.}, } @article {pmid26305881, year = {2015}, author = {Zhu, HR and Liu, L and Zhou, XN and Yang, GJ}, title = {Ecological Model to Predict Potential Habitats of Oncomelania hupensis, the Intermediate Host of Schistosoma japonicum in the Mountainous Regions, China.}, journal = {PLoS neglected tropical diseases}, volume = {9}, number = {8}, pages = {e0004028}, pmid = {26305881}, issn = {1935-2735}, mesh = {Animals ; China ; Disease Reservoirs/parasitology ; *Ecosystem ; Geographic Information Systems ; Humans ; Schistosoma japonicum/physiology ; Schistosomiasis japonica/parasitology/transmission ; Snails/*growth & development/parasitology ; }, abstract = {BACKGROUND: Schistosomiasis japonica is a parasitic disease that remains endemic in seven provinces in the People's Republic of China (P.R. China). One of the most important measures in the process of schistosomiasis elimination in P.R. China is control of Oncomelania hupensis, the unique intermediate host snail of Schistosoma japonicum. Compared with plains/swamp and lake regions, the hilly/mountainous regions of schistosomiasis endemic areas are more complicated, which makes the snail survey difficult to conduct precisely and efficiently. There is a pressing call to identify the snail habitats of mountainous regions in an efficient and cost-effective manner.

METHODS: Twelve out of 56 administrative villages distributed with O. hupensis in Eryuan, Yunnan Province, were randomly selected to set up the ecological model. Thirty out of the rest of 78 villages (villages selected for building model were excluded from the villages for validation) in Eryuan and 30 out of 89 villages in Midu, Yunnan Province were selected via a chessboard method for model validation, respectively. Nine-year-average Normalized Difference Vegetation Index (NDVI) and Land Surface Temperature (LST) as well as Digital Elevation Model (DEM) covering Eryuan and Midu were extracted from MODIS and ASTER satellite images, respectively. Slope, elevation and the distance from every village to its nearest stream were derived from DEM. Suitable survival environment conditions for snails were defined by comparing historical snail presence data and remote sensing derived images. According to the suitable conditions for snails, environment factors, i.e. NDVI, LST, elevation, slope and the distance from every village to its nearest stream, were integrated into an ecological niche model to predict O. hupensis potential habitats in Eryuan and Midu. The evaluation of the model was assessed by comparing the model prediction and field investigation. Then, the consistency rate of model validation was calculated in Eryuan and Midu Counties, respectively.

RESULTS: The final ecological niche model for potential O. hupensis habitats prediction comprised the following environmental factors, namely: NDVI (≥ 0.446), LST (≥ 22.70°C), elevation (≤ 2,300 m), slope (≤ 11°) and the distance to nearest stream (≤ 1,000 m). The potential O. hupensis habitats in Eryuan distributed in the Lancang River basin and O. hupensis in Midu shows a trend of clustering in the north and spotty distribution in the south. The consistency rates of the ecological niche model in Eryuan and Midu were 76.67% and 83.33%, respectively.

CONCLUSIONS: The ecological niche model integrated with NDVI, LST, elevation, slope and distance from every village to its nearest stream adequately predicted the snail habitats in the mountainous regions.}, } @article {pmid26298306, year = {2015}, author = {Wittenstrom, K and Baumann, DJ and Fluke, J and Graham, JC and James, J}, title = {The impact of drugs, infants, single mothers, and relatives on reunification: A Decision-Making Ecology approach.}, journal = {Child abuse & neglect}, volume = {49}, number = {}, pages = {86-96}, doi = {10.1016/j.chiabu.2015.06.010}, pmid = {26298306}, issn = {1873-7757}, mesh = {Child ; *Child Welfare ; Child, Preschool ; *Decision Making ; *Decision Support Techniques ; *Family ; Humans ; Infant ; Mothers ; Only Child ; Racial Groups ; Risk Factors ; Single Parent ; Socioeconomic Factors ; Substance-Related Disorders ; Texas ; }, abstract = {Using a Decision-Making Ecology (DME) approach and proportional hazards models, the study isolated four case factor profiles that interacted strongly with race and resulted in disparate reunification outcomes for African American children compared with Anglos. The four interrelated factors were drug involvement, a solo infant case, single mothers, and relative placements. A cohort of 21,763 children from the Texas Department of Family and Protective Services who were placed for the first time in care, who were under 13 and either Anglo or African American were followed for 20 months or more post entry into care. Starting with an initial model consisting of main effects only and consistent with other studies, African American children had a 12% lower hazard rate of reunification compared to Anglo children. However, when a set of case profiles involving combinations of single parents, single infants, drug involvements and kinship placements were crossed with race, the magnitude of the effect of race on hazard rates fanned out from no difference to as much as 68% that of Anglo children. The results show that racial disparities in outcomes resulting from complex, contextual decision making cannot be modeled well with simple main effects models.}, } @article {pmid26298253, year = {2015}, author = {Isigonis, P and Ciffroy, P and Zabeo, A and Semenzin, E and Critto, A and Giove, S and Marcomini, A}, title = {A Multi-Criteria Decision Analysis based methodology for quantitatively scoring the reliability and relevance of ecotoxicological data.}, journal = {The Science of the total environment}, volume = {538}, number = {}, pages = {102-116}, doi = {10.1016/j.scitotenv.2015.06.016}, pmid = {26298253}, issn = {1879-1026}, mesh = {*Decision Support Techniques ; Ecotoxicology ; Environmental Monitoring/*methods ; Fuzzy Logic ; Risk Assessment ; Water Pollutants, Chemical/*analysis ; }, abstract = {Ecotoxicological data are highly important for risk assessment processes and are used for deriving environmental quality criteria, which are enacted for assuring the good quality of waters, soils or sediments and achieving desirable environmental quality objectives. Therefore, it is of significant importance the evaluation of the reliability of available data for analysing their possible use in the aforementioned processes. The thorough analysis of currently available frameworks for the assessment of ecotoxicological data has led to the identification of significant flaws but at the same time various opportunities for improvement. In this context, a new methodology, based on Multi-Criteria Decision Analysis (MCDA) techniques, has been developed with the aim of analysing the reliability and relevance of ecotoxicological data (which are produced through laboratory biotests for individual effects), in a transparent quantitative way, through the use of expert knowledge, multiple criteria and fuzzy logic. The proposed methodology can be used for the production of weighted Species Sensitivity Weighted Distributions (SSWD), as a component of the ecological risk assessment of chemicals in aquatic systems. The MCDA aggregation methodology is described in detail and demonstrated through examples in the article and the hierarchically structured framework that is used for the evaluation and classification of ecotoxicological data is shortly discussed. The methodology is demonstrated for the aquatic compartment but it can be easily tailored to other environmental compartments (soil, air, sediments).}, } @article {pmid26296474, year = {2015}, author = {Abroi, A}, title = {A protein domain-based view of the virosphere-host relationship.}, journal = {Biochimie}, volume = {119}, number = {}, pages = {231-243}, doi = {10.1016/j.biochi.2015.08.008}, pmid = {26296474}, issn = {1638-6183}, mesh = {Animals ; Databases, Protein ; *Evolution, Molecular ; *Genome, Viral ; *Host-Pathogen Interactions ; Humans ; *Models, Genetic ; Protein Isoforms/chemistry/genetics/metabolism ; Protein Structure, Tertiary ; Structural Homology, Protein ; Viral Proteins/*chemistry/genetics/metabolism ; }, abstract = {Despite being an important and inseparable part of the biosphere, viruses are too often overlooked in several life sciences, including evolutionary biology, systems biology, and non-marine ecology. In this review, a protein domain-based view of viral proteomes, the proteomes of other organisms and the overlap between them is presented. The data show that in many viral species, viral proteins are not very well annotated with protein domains. Compared with viral proteomes, cellular proteomes are covered quite uniformly with respect to protein domains and show higher coverage. A tremendous number of virally coded domains exist; in fact, the number of protein domains in the characterised virosphere is approaching that found in Archaea, a well-accepted superkingdom. Proteins encoded by viruses contain virosphere-specific domains (i.e., not found in cellular proteomes) and/or many domains shared by viral and cellular proteomes. Virosphere-specific domains are structurally peculiar with respect to different structural measures, making them a clear source of structural and functional novelty. Viral families with RNA genomes tend to harbour more virosphere-specific domains than other viruses. Interestingly, host range preferences of different viral classes are, for the most part, not reflected by domains shared between viruses and different superkingdoms. The role of viruses in the genesis of the cellular domain repertoire is reviewed to bring them more confidently and firmly into the larger biological picture.}, } @article {pmid26296338, year = {2015}, author = {Gkarmiri, K and Finlay, RD and Alström, S and Thomas, E and Cubeta, MA and Högberg, N}, title = {Transcriptomic changes in the plant pathogenic fungus Rhizoctonia solani AG-3 in response to the antagonistic bacteria Serratia proteamaculans and Serratia plymuthica.}, journal = {BMC genomics}, volume = {16}, number = {1}, pages = {630}, pmid = {26296338}, issn = {1471-2164}, mesh = {*Antibiosis ; Fungal Proteins/*genetics ; Gene Expression Profiling/*methods ; Gene Expression Regulation, Fungal ; Gene Ontology ; RNA, Fungal/analysis ; RNA, Messenger/analysis ; Rhizoctonia/*genetics/physiology ; Rhizosphere ; Sequence Analysis, RNA/*methods ; Serratia/*physiology ; Species Specificity ; }, abstract = {BACKGROUND: Improved understanding of bacterial-fungal interactions in the rhizosphere should assist in the successful application of bacteria as biological control agents against fungal pathogens of plants, providing alternatives to chemicals in sustainable agriculture. Rhizoctonia solani is an important soil-associated fungal pathogen and its chemical treatment is not feasible or economic. The genomes of the plant-associated bacteria Serratia proteamaculans S4 and Serratia plymuthica AS13 have been sequenced, revealing genetic traits that may explain their diverse plant growth promoting activities and antagonistic interactions with R. solani. To understand the functional response of this pathogen to different bacteria and to elucidate whether the molecular mechanisms that the fungus exploits involve general stress or more specific responses, we performed a global transcriptome profiling of R. solani Rhs1AP anastomosis group 3 (AG-3) during interaction with the S4 and AS13 species of Serratia using RNA-seq.

RESULTS: Approximately 104,504 million clean 75-100 bp paired-end reads were obtained from three libraries, each in triplicate (AG3-Control, AG3-S4 and AG3-AS13). Transcriptome analysis revealed that approximately 10% of the fungal transcriptome was differentially expressed during challenge with Serratia. The numbers of S4- and AS13-specific differentially expressed genes (DEG) were 866 and 292 respectively, while there were 1035 common DEGs in the two treatment groups. Four hundred and sixty and 242 genes respectively had values of log2 fold-change > 3 and for further analyses this cut-off value was used. Functional classification of DEGs based on Gene Ontology enrichment analysis and on KEGG pathway annotations revealed a general shift in fungal gene expression in which genes related to xenobiotic degradation, toxin and antioxidant production, energy, carbohydrate and lipid metabolism and hyphal rearrangements were subjected to transcriptional regulation.

CONCLUSIONS: This RNA-seq profiling generated a novel dataset describing the functional response of the phytopathogen R. solani AG3 to the plant-associated Serratia bacteria S4 and AS13. Most genes were regulated in the same way in the presence of both bacterial isolates, but there were also some strain-specific responses. The findings in this study will be beneficial for further research on biological control and in depth exploration of bacterial-fungal interactions in the rhizosphere.}, } @article {pmid26296205, year = {2015}, author = {Brandt, EC and Petersen, JE and Grossman, JJ and Allen, GA and Benzing, DH}, title = {Relationships between Spatial Metrics and Plant Diversity in Constructed Freshwater Wetlands.}, journal = {PloS one}, volume = {10}, number = {8}, pages = {e0135917}, pmid = {26296205}, issn = {1932-6203}, mesh = {Biodiversity ; Conservation of Natural Resources ; *Fresh Water ; Geographic Information Systems ; Humans ; *Models, Statistical ; Ohio ; Photography ; Plant Development/*physiology ; Plant Dispersal/*physiology ; *Wetlands ; }, abstract = {The diversity of plant species and their distribution in space are both thought to have important effects on the function of wetland ecosystems. However, knowledge of the relationships between plant species and spatial diversity remains incomplete. In this study, we investigated relationships between spatial pattern and plant species diversity over a five year period following the initial restoration of experimental wetland ecosystems. In 2003, six identical and hydrologically-isolated 0.18 ha wetland "cells" were constructed in former farmland in northeast Ohio. The systems were subjected to planting treatments that resulted in different levels of vascular plant species diversity among cells. Plant species diversity was assessed through annual inventories. Plant spatial pattern was assessed by digitizing low-altitude aerial photographs taken at the same time as the inventories. Diversity metrics derived from the inventories were significantly related to certain spatial metrics derived from the photographs, including cover type diversity and contagion. We found that wetlands with high cover type diversity harbor higher plant species diversity than wetlands with fewer types of patches. We also found significant relationships between plant species diversity and spatial patterning of patch types, but the direction of the effect differed depending on the diversity metric used. Links between diversity and spatial pattern observed in this study suggest that high-resolution aerial imagery may provide wetland scientists with a useful tool for assessing plant diversity.}, } @article {pmid26292783, year = {2015}, author = {Adamczuk, M and Mieczan, T}, title = {Different levels of precision in studies on the alimentary tract content of omnivorous fish affect predictions of their food niche and competitive interactions.}, journal = {Comptes rendus biologies}, volume = {338}, number = {10}, pages = {678-687}, doi = {10.1016/j.crvi.2015.05.003}, pmid = {26292783}, issn = {1768-3238}, mesh = {Age Factors ; Animals ; Biodiversity ; *Competitive Behavior ; Datasets as Topic ; Ecosystem ; *Feeding Behavior ; Fishes/*physiology ; Food/*classification ; *Food Chain ; Gastrointestinal Contents/*chemistry ; Lakes ; Poland ; *Predatory Behavior ; Species Specificity ; }, abstract = {The food niche partitioning of omnivorous fish is commonly estimated on the basis of the alimentary tract content (ATC). However, since omnivorous fish utilise different ecological formations, data relating to ATC are very noisy, since an identified ATC comprises remains that can be determined according to the species level, determined only according to general food categories (i.e. higher taxonomic levels) as well as amounts of fragmented and digested remains that cannot be determined taxonomically. Thus, a variety of scales of precision can be applied during work on ATC. Up until now, there has been no evidence as to whether and how precision in ATC estimation can affect the results. This study aims at assessing how three different options of the same database influence the effectiveness and concurrency of indexes commonly used to describe the food niche of fish. The options include: (1) only general (higher than species level) food categories; (2) categories of different levels of generality; and (3) only detailed (species level) food categories. The study shows that the use of detailed (species level) food categories only, with the exclusion of general food categories, is the best method to recognise food niche partitioning and competitive interactions among fish. The food categories estimated in detail were cladocerans, and the possibility to use cladocerans as specific markers to find similarities in fish diets is discussed.}, } @article {pmid26291081, year = {2015}, author = {Groten, K and Pahari, NT and Xu, S and Miloradovic van Doorn, M and Baldwin, IT}, title = {Virus-Induced Gene Silencing Using Tobacco Rattle Virus as a Tool to Study the Interaction between Nicotiana attenuata and Rhizophagus irregularis.}, journal = {PloS one}, volume = {10}, number = {8}, pages = {e0136234}, pmid = {26291081}, issn = {1932-6203}, mesh = {Gene Expression Regulation, Fungal/genetics/physiology ; Gene Expression Regulation, Plant/genetics/physiology ; Gene Ontology ; *Gene Silencing ; Genes, Plant/genetics/physiology ; Glomeromycota/genetics/*physiology ; Mycorrhizae/genetics/*physiology ; Plant Roots/genetics/microbiology/physiology ; Plant Viruses/*genetics/physiology ; Real-Time Polymerase Chain Reaction ; Sequence Homology ; Nicotiana/genetics/*physiology ; }, abstract = {Most land plants live in a symbiotic association with arbuscular mycorrhizal fungi (AMF) that belong to the phylum Glomeromycota. Although a number of plant genes involved in the plant-AMF interactions have been identified by analyzing mutants, the ability to rapidly manipulate gene expression to study the potential functions of new candidate genes remains unrealized. We analyzed changes in gene expression of wild tobacco roots (Nicotiana attenuata) after infection with mycorrhizal fungi (Rhizophagus irregularis) by serial analysis of gene expression (SuperSAGE) combined with next generation sequencing, and established a virus-induced gene-silencing protocol to study the function of candidate genes in the interaction. From 92,434 SuperSAGE Tag sequences, 32,808 (35%) matched with our in-house Nicotiana attenuata transcriptome database and 3,698 (4%) matched to Rhizophagus genes. In total, 11,194 Tags showed a significant change in expression (p<0.05, >2-fold change) after infection. When comparing the functions of highly up-regulated annotated Tags in this study with those of two previous large-scale gene expression studies, 18 gene functions were found to be up-regulated in all three studies mainly playing roles related to phytohormone metabolism, catabolism and defense. To validate the function of identified candidate genes, we used the technique of virus-induced gene silencing (VIGS) to silence the expression of three putative N. attenuata genes: germin-like protein, indole-3-acetic acid-amido synthetase GH3.9 and, as a proof-of-principle, calcium and calmodulin-dependent protein kinase (CCaMK). The silencing of the three plant genes in roots was successful, but only CCaMK silencing had a significant effect on the interaction with R. irregularis. Interestingly, when a highly activated inoculum was used for plant inoculation, the effect of CCaMK silencing on fungal colonization was masked, probably due to trans-complementation. This study demonstrates that large-scale gene expression studies across different species induce of a core set of genes of similar functions. However, additional factors seem to influence the overall pattern of gene expression, resulting in high variability among independent studies with different hosts. We conclude that VIGS is a powerful tool with which to investigate the function of genes involved in plant-AMF interactions but that inoculum strength can strongly influence the outcome of the interaction.}, } @article {pmid27669514, year = {2014}, author = {Boričić, K and Simić, S and Vasiljević, N and Marinković, J}, title = {Risk Factors Associated with Overweight among Adolescents in Serbia.}, journal = {Zdravstveno varstvo}, volume = {53}, number = {4}, pages = {283-293}, pmid = {27669514}, issn = {0351-0026}, abstract = {INTRODUCTION: The pandemic of obesity in adolescents is one of the challenges of public health.

AIM: The aim of this study was to examine the association of overweight with demographic, socioeconomic and lifestyle factors among Serbian adolescents.

METHOD: A cross-sectional study of 2139 adolescents aged 10 to 19 years was carried out. Data used in this study were from the 2006 Health Survey. In accordance with the international sex- and age-specific Body Mass Index cut-off points, all participants were classified as being normal weight or overweight, including obese. The association between the risk factors and overweight were examined using a multivariate logistic regression model.

RESULTS: The study showed that 28.9% of boys and 17.0% of girls were overweight, while 14.5% of boys and 8.1% of girls were obese. Boys were more likely to be overweight/obese, compared with girls. Being younger (p< 0.01 for 14 to 15 years) and (p< 0.01, for 16 to 19 years), engaging in physical activities that last less than 7 hours a week, in such a manner that they breathe quickly and become sweaty, (p< 0.01) and skipping breakfast (p< 0.05) were risk factors significantly associated with overweight among adolescents. No significant association was found with wealth index.

CONCLUSION: These findings should be an integral part of further preventive interventions, especially oriented towards younger adolescents, who are physically inactive, have a habit of skipping breakfast and are boys.}, } @article {pmid26295106, year = {2013}, author = {Schmidt, C}, title = {Molecular phylogenetics of ponerine ants (Hymenoptera: Formicidae: Ponerinae).}, journal = {Zootaxa}, volume = {3647}, number = {}, pages = {201-250}, doi = {10.11646/zootaxa.3647.2.1}, pmid = {26295106}, issn = {1175-5326}, mesh = {Animals ; Ants/anatomy & histology/*classification/*genetics/physiology ; Databases, Genetic ; Ecosystem ; Phylogeny ; Phylogeography ; Social Behavior ; Species Specificity ; Time Factors ; }, abstract = {Recent molecular phylogenetic studies of ants (Hymenoptera: Formicidae) have revolutionized our understanding of how these ecologically dominant organisms diversified, but detailed phylogenies are lacking for most major ant subfamilies. I report the results of the first detailed phylogenetic study of the ant subfamily Ponerinae, a diverse cosmopolitan lineage whose properties make it an attractive model system for investigating social and ecological evolution in ants. Molecular sequence data were obtained from four nuclear genes (wingless, long-wavelength rhodopsin, rudimentary [CAD], 28S rDNA; total of ~3.3 kb) for 86 ponerine taxa, representing all three ponerine tribes, 22 of the 28 currently recognized genera, and 14 of the 18 informal subgenera of Pachycondyla, a heterogeneous grouping whose monophyly is doubtful on morphological grounds. Phylogenetic reconstructions using maximum likelihood and Bayesian inference support the monophyly of Ponerinae and tribe Platythyreini, but fail to support the monophyly of the large tribe Ponerini due to its inclusion of the unusual genus Thaumatomyrmex. Pachycondyla is inferred to be broadly non-monophyletic. Numerous novel generic and suprageneric relationships are inferred within Ponerini, which was found to consist of four major multi-generic clades (the Ponera, Pachycondyla, Plectroctena and Odontomachus genus groups) plus the single genera Hypoponera and Harpegnathos. Uncertainty remains in some regions of the phylogeny, including at the base of Ponerini, possibly reflecting rapid radiation. Divergence dating using a Bayesian relaxed clock method estimates an origin for stem Ponerinae in the upper Cretaceous, a major burst of diversification near the K/T boundary, and a rich and continual history of diversification during the Cenozoic. These results fail to support the predictions of the "dynastic-succession hypothesis" previously developed to explain the high species diversity of Ponerinae. Though model-based reconstructions of historical biogeography and trait evolution were not attempted in this study, the phylogeny suggests that ponerine evolution was marked by regionalized radiations and frequent faunal exchange between major biogeographic provinces. The reported results also imply multiple origins of cryptobiotic foraging, mass raiding behavior, and gamergate reproduction within Ponerinae, highlighting the value of the subfamily as a model for studying the incipient evolution of these and other ecological and behavioral traits.}, } @article {pmid27463848, year = {2010}, author = {Michielan, L and Pireddu, L and Floris, M and Moro, S}, title = {Support Vector Machine (SVM) as Alternative Tool to Assign Acute Aquatic Toxicity Warning Labels to Chemicals.}, journal = {Molecular informatics}, volume = {29}, number = {1-2}, pages = {51-64}, doi = {10.1002/minf.200900005}, pmid = {27463848}, issn = {1868-1743}, abstract = {Quantitative structure-activity relationship (QSAR) analysis has been frequently utilized as a computational tool for the prediction of several eco-toxicological parameters including the acute aquatic toxicity. In the present study, we describe a novel integrated strategy to describe the acute aquatic toxicity through the combination of both toxicokinetic and toxicodynamic behaviors of chemicals. In particular, a robust classification model (TOXclass) has been derived by combining Support Vector Machine (SVM) analysis with three classes of toxicokinetic-like molecular descriptors: the autocorrelation molecular electrostatic potential (autoMEP) vectors, Sterimol topological descriptors and logP(o/w) property values. TOXclass model is able to assign chemicals to different levels of acute aquatic toxicity, providing an appropriate answer to the new regulatory requirements. Moreover, we have extended the above mentioned toxicokinetic-like descriptor set with a more toxicodynamic-like descriptors, as for example HOMO and LUMO energies, to generate a valuable SVM classifier (MOAclass) for the prediction of the mode of action (MOA) of toxic chemicals. As preliminary validation of our approach, the toxicokinetic (TOXclass) and the toxicodynamic (MOAclass) models have been applied in series to inspect both aquatic toxicity hazard and mode of action of 296 chemical substances with unknown or uncertain toxicodynamic information to assess the potential ecological risk and the toxic mechanism.}, } @article {pmid26054910, year = {2016}, author = {Batista Ferrer, H and Trotter, CL and Hickman, M and Audrey, S}, title = {Barriers and facilitators to uptake of the school-based HPV vaccination programme in an ethnically diverse group of young women.}, journal = {Journal of public health (Oxford, England)}, volume = {38}, number = {3}, pages = {569-577}, pmid = {26054910}, issn = {1741-3850}, support = {/WT_/Wellcome Trust/United Kingdom ; MR/K023233/1/MRC_/Medical Research Council/United Kingdom ; /CRUK_/Cancer Research UK/United Kingdom ; /BHF_/British Heart Foundation/United Kingdom ; }, mesh = {Adolescent ; Asian People/statistics & numerical data ; Black People/statistics & numerical data ; Child ; Ethnicity/*statistics & numerical data ; Female ; *Health Services Accessibility/organization & administration/statistics & numerical data ; Humans ; Immunization Programs/organization & administration/*statistics & numerical data ; Papillomavirus Infections/ethnology/prevention & control ; Papillomavirus Vaccines/*therapeutic use ; School Health Services/*organization & administration/statistics & numerical data ; Uterine Cervical Neoplasms/ethnology/prevention & control ; White People/statistics & numerical data ; }, abstract = {BACKGROUND: To identify the barriers and facilitators to uptake of the HPV vaccine in an ethnically diverse group of young women in the south west of England.

METHODS: Three school-based vaccination sessions were observed. Twenty-three young women aged 12 to 13 years, and six key informants, were interviewed between October 2012 and July 2013. Data were analysed using thematic analysis and the Framework method for data management.

RESULTS: The priority given to preventing cervical cancer in this age group influenced whether young women received the HPV vaccine. Access could be affected by differing levels of commitment by school staff, school nurses, parents and young women to ensure parental consent forms were returned. Beliefs and values, particularly relevant to minority ethnic groups, in relation to adolescent sexual activity may affect uptake. Literacy and language difficulties undermine informed consent and may prevent vaccination.

CONCLUSIONS: The school-based HPV vaccination programme successfully reaches the majority of young women. However, responsibility for key aspects remain unresolved which can affect delivery and prevent uptake for some groups. A multi-faceted approach, targeting appropriate levels of the socio-ecological model, is required to address procedures for consent and cultural and literacy barriers faced by minority ethnic groups, increase uptake and reduce inequalities.}, } @article {pmid26290174, year = {2015}, author = {Varga, C and Pearl, DL and McEwen, SA and Sargeant, JM and Pollari, F and Guerin, MT}, title = {Area-level global and local clustering of human Salmonella Enteritidis infection rates in the city of Toronto, Canada, 2007-2009.}, journal = {BMC infectious diseases}, volume = {15}, number = {}, pages = {359}, pmid = {26290174}, issn = {1471-2334}, mesh = {Adolescent ; Adult ; Aged ; Aged, 80 and over ; Bayes Theorem ; Child ; Child, Preschool ; Cities ; Cluster Analysis ; Female ; Geographic Information Systems ; Humans ; Infant ; Infant, Newborn ; Male ; Middle Aged ; Ontario/epidemiology ; Retrospective Studies ; Risk Factors ; Salmonella Infections/*epidemiology/microbiology ; Salmonella enteritidis/*isolation & purification ; Urban Population ; Young Adult ; }, abstract = {BACKGROUND: Salmonella enterica serotype Enteritidis (S. Enteritidis) remains a major foodborne pathogen in North America yet studies examining the spatial epidemiology of salmonellosis in urban environments are lacking. Our ecological study combined a number of spatial statistical methods with a geographic information system to assess area-level heterogeneity of S. Enteritidis infection rates in the city of Toronto.

METHODS: Data on S. Enteritidis infections between January 1, 2007 and December 31, 2009 were obtained from Ontario's surveillance system, and were grouped and analyzed at the forward sortation area (FSA)-level (an area signified by the first three characters of the postal code). Incidence rates were directly standardized using the FSA-level age- and sex-based standard population. A spatial empirical Bayes method was used to smooth the standardized incidence rates (SIRs). Global clustering of FSAs with high or low non-smoothed SIRs was evaluated using the Getis-Ord G method. Local clustering of FSAs with high, low, or dissimilar non-smoothed SIRs was assessed using the Getis-Ord Gi* and the Local Moran's I methods.

RESULTS: Spatial heterogeneity of S. Enteritidis infection rates was detected across the city of Toronto. The non-smoothed FSA-level SIRs ranged from 0 to 16.9 infections per 100,000 person-years (mean = 6.6), whereas the smoothed SIRs ranged from 2.9 to 11.1 (mean = 6.3). The global Getis-Ord G method showed significant (p ≤ 0.05) maximum spatial clustering of FSAs with high SIRs at 3.3 km. The local Getis-Ord Gi* method identified eight FSAs with significantly high SIRs and one FSA with a significantly low SIR. The Local Moran's I method detected five FSAs with significantly high-high SIRs, one FSA with a significantly low-low SIR, and four significant outlier FSAs (one high-low, and three low-high).

CONCLUSIONS: Salmonella Enteritidis infection rates clustered globally at a small distance band, suggesting clustering of high SIRs in small distinct areas. This finding was supported by the local cluster analyses, where distinct FSAs with high SIRs, mainly in downtown Toronto, were detected. These areas should be evaluated by future studies to identify risk factors of disease in order to implement targeted prevention and control programs. We demonstrated the usefulness of combining several spatial statistical techniques with a geographic information system to detect geographical areas of interest for further study, and to evaluate spatial processes that influenced S. Enteritidis infection rates. Our study methodology could be applied to other foodborne disease surveillance data.}, } @article {pmid26287466, year = {2015}, author = {van Kleunen, M and Dawson, W and Essl, F and Pergl, J and Winter, M and Weber, E and Kreft, H and Weigelt, P and Kartesz, J and Nishino, M and Antonova, LA and Barcelona, JF and Cabezas, FJ and Cárdenas, D and Cárdenas-Toro, J and Castaño, N and Chacón, E and Chatelain, C and Ebel, AL and Figueiredo, E and Fuentes, N and Groom, QJ and Henderson, L and Inderjit, and Kupriyanov, A and Masciadri, S and Meerman, J and Morozova, O and Moser, D and Nickrent, DL and Patzelt, A and Pelser, PB and Baptiste, MP and Poopath, M and Schulze, M and Seebens, H and Shu, WS and Thomas, J and Velayos, M and Wieringa, JJ and Pyšek, P}, title = {Global exchange and accumulation of non-native plants.}, journal = {Nature}, volume = {525}, number = {7567}, pages = {100-103}, pmid = {26287466}, issn = {1476-4687}, mesh = {*Biodiversity ; Databases, Factual ; *Geographic Mapping ; Introduced Species/*statistics & numerical data ; North America ; Pacific Islands ; Phylogeography ; *Plants ; }, abstract = {All around the globe, humans have greatly altered the abiotic and biotic environment with ever-increasing speed. One defining feature of the Anthropocene epoch is the erosion of biogeographical barriers by human-mediated dispersal of species into new regions, where they can naturalize and cause ecological, economic and social damage. So far, no comprehensive analysis of the global accumulation and exchange of alien plant species between continents has been performed, primarily because of a lack of data. Here we bridge this knowledge gap by using a unique global database on the occurrences of naturalized alien plant species in 481 mainland and 362 island regions. In total, 13,168 plant species, corresponding to 3.9% of the extant global vascular flora, or approximately the size of the native European flora, have become naturalized somewhere on the globe as a result of human activity. North America has accumulated the largest number of naturalized species, whereas the Pacific Islands show the fastest increase in species numbers with respect to their land area. Continents in the Northern Hemisphere have been the major donors of naturalized alien species to all other continents. Our results quantify for the first time the extent of plant naturalizations worldwide, and illustrate the urgent need for globally integrated efforts to control, manage and understand the spread of alien species.}, } @article {pmid26284671, year = {2015}, author = {Medema, MH and Fischbach, MA}, title = {Computational approaches to natural product discovery.}, journal = {Nature chemical biology}, volume = {11}, number = {9}, pages = {639-648}, pmid = {26284671}, issn = {1552-4469}, support = {R01 AI101018/AI/NIAID NIH HHS/United States ; DP2 OD007290/OD/NIH HHS/United States ; R01 DK101674/DK/NIDDK NIH HHS/United States ; GM081879/GM/NIGMS NIH HHS/United States ; AI101018/AI/NIAID NIH HHS/United States ; DK101674/DK/NIDDK NIH HHS/United States ; P50 GM081879/GM/NIGMS NIH HHS/United States ; OD007290/OD/NIH HHS/United States ; }, mesh = {Algorithms ; Alkaloids/biosynthesis ; Bacteria/*genetics/metabolism ; Biological Products/chemistry/*metabolism ; Computational Biology/instrumentation/*methods ; Data Mining ; Databases, Genetic ; Fungi/*genetics/metabolism ; *Metagenome ; Multigene Family ; Peptide Biosynthesis, Nucleic Acid-Independent ; Peptides/metabolism ; Plants/*genetics/metabolism ; Polyketides/metabolism ; Polysaccharides/biosynthesis ; Terpenes/metabolism ; }, abstract = {Starting with the earliest Streptomyces genome sequences, the promise of natural product genome mining has been captivating: genomics and bioinformatics would transform compound discovery from an ad hoc pursuit to a high-throughput endeavor. Until recently, however, genome mining has advanced natural product discovery only modestly. Here, we argue that the development of algorithms to mine the continuously increasing amounts of (meta)genomic data will enable the promise of genome mining to be realized. We review computational strategies that have been developed to identify biosynthetic gene clusters in genome sequences and predict the chemical structures of their products. We then discuss networking strategies that can systematize large volumes of genetic and chemical data and connect genomic information to metabolomic and phenotypic data. Finally, we provide a vision of what natural product discovery might look like in the future, specifically considering longstanding questions in microbial ecology regarding the roles of metabolites in interspecies interactions.}, } @article {pmid26284661, year = {2015}, author = {Medema, MH and Kottmann, R and Yilmaz, P and Cummings, M and Biggins, JB and Blin, K and de Bruijn, I and Chooi, YH and Claesen, J and Coates, RC and Cruz-Morales, P and Duddela, S and Düsterhus, S and Edwards, DJ and Fewer, DP and Garg, N and Geiger, C and Gomez-Escribano, JP and Greule, A and Hadjithomas, M and Haines, AS and Helfrich, EJ and Hillwig, ML and Ishida, K and Jones, AC and Jones, CS and Jungmann, K and Kegler, C and Kim, HU and Kötter, P and Krug, D and Masschelein, J and Melnik, AV and Mantovani, SM and Monroe, EA and Moore, M and Moss, N and Nützmann, HW and Pan, G and Pati, A and Petras, D and Reen, FJ and Rosconi, F and Rui, Z and Tian, Z and Tobias, NJ and Tsunematsu, Y and Wiemann, P and Wyckoff, E and Yan, X and Yim, G and Yu, F and Xie, Y and Aigle, B and Apel, AK and Balibar, CJ and Balskus, EP and Barona-Gómez, F and Bechthold, A and Bode, HB and Borriss, R and Brady, SF and Brakhage, AA and Caffrey, P and Cheng, YQ and Clardy, J and Cox, RJ and De Mot, R and Donadio, S and Donia, MS and van der Donk, WA and Dorrestein, PC and Doyle, S and Driessen, AJ and Ehling-Schulz, M and Entian, KD and Fischbach, MA and Gerwick, L and Gerwick, WH and Gross, H and Gust, B and Hertweck, C and Höfte, M and Jensen, SE and Ju, J and Katz, L and Kaysser, L and Klassen, JL and Keller, NP and Kormanec, J and Kuipers, OP and Kuzuyama, T and Kyrpides, NC and Kwon, HJ and Lautru, S and Lavigne, R and Lee, CY and Linquan, B and Liu, X and Liu, W and Luzhetskyy, A and Mahmud, T and Mast, Y and Méndez, C and Metsä-Ketelä, M and Micklefield, J and Mitchell, DA and Moore, BS and Moreira, LM and Müller, R and Neilan, BA and Nett, M and Nielsen, J and O'Gara, F and Oikawa, H and Osbourn, A and Osburne, MS and Ostash, B and Payne, SM and Pernodet, JL and Petricek, M and Piel, J and Ploux, O and Raaijmakers, JM and Salas, JA and Schmitt, EK and Scott, B and Seipke, RF and Shen, B and Sherman, DH and Sivonen, K and Smanski, MJ and Sosio, M and Stegmann, E and Süssmuth, RD and Tahlan, K and Thomas, CM and Tang, Y and Truman, AW and Viaud, M and Walton, JD and Walsh, CT and Weber, T and van Wezel, GP and Wilkinson, B and Willey, JM and Wohlleben, W and Wright, GD and Ziemert, N and Zhang, C and Zotchev, SB and Breitling, R and Takano, E and Glöckner, FO}, title = {Minimum Information about a Biosynthetic Gene cluster.}, journal = {Nature chemical biology}, volume = {11}, number = {9}, pages = {625-631}, pmid = {26284661}, issn = {1552-4469}, support = {BB/M028860/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/J014478/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; R01 GM107550/GM/NIGMS NIH HHS/United States ; BBS/E/J/00000614/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; R01 AI113766/AI/NIAID NIH HHS/United States ; BB/M017702/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; R01 AI037027/AI/NIAID NIH HHS/United States ; T32 GM067550/GM/NIGMS NIH HHS/United States ; R01 GM123998/GM/NIGMS NIH HHS/United States ; R01 CA108874/CA/NCI NIH HHS/United States ; BB/L014130/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/E021611/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/B/07071/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; R37 AI016935/AI/NIAID NIH HHS/United States ; }, mesh = {Alkaloids/biosynthesis ; Bacteria/*genetics/metabolism ; Computational Biology/*standards ; Databases, Genetic ; Fungi/*genetics/metabolism ; Genetic Markers ; International Cooperation ; Metagenome ; *Multigene Family ; Peptide Biosynthesis, Nucleic Acid-Independent ; Peptides/metabolism ; Plants/*genetics/metabolism ; Polyketides/metabolism ; Polysaccharides/biosynthesis ; *Protein Biosynthesis ; Terminology as Topic ; Terpenes/metabolism ; }, } @article {pmid26284346, year = {2015}, author = {Gao, Y and An, T and Ji, Y and Li, G and Zhao, C}, title = {Eco-toxicity and human estrogenic exposure risks from OH-initiated photochemical transformation of four phthalates in water: A computational study.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {206}, number = {}, pages = {510-517}, doi = {10.1016/j.envpol.2015.08.006}, pmid = {26284346}, issn = {1873-6424}, mesh = {Aquatic Organisms/*drug effects ; Computational Biology ; *Ecotoxicology ; Estrogens/*analysis/toxicity ; Humans ; Hydroxyl Radical/*chemistry ; Oxidation-Reduction ; Photochemical Processes ; Phthalic Acids/chemistry/radiation effects/*toxicity ; Risk Assessment ; Structure-Activity Relationship ; Water/chemistry ; Water Pollutants, Chemical/*analysis/toxicity ; }, abstract = {Transformation products (TPs) of emerging organic contaminates (EOCs) in water are still rarely considered in environmental risk assessment, although some have been found to be concern. OH is believed as an important reactive species both in indirect phototransformation and advanced oxidation technology. Thus, eco-toxicity and human estrogenic exposure risks of four phthalates and TPs during the OH-initiated photochemical process were investigated using computational approach. Four phthalates can be degraded through OH-addition and H-transfer pathways. The OH-addition TPs were predominant for dimethyl phthalates, while H-transfer TPs were predominant for other three phthalates. Compared with phthalates, OH-addition TPs (o-OH-phthalates) were one level more toxic to aquatic organisms, and m-OH-phthalates exhibit higher estrogenic activity. Although H-transfer TPs were less harmful than OH-addition TPs, some of them still have aquatic toxicity and estrogenic activity. Therefore, more attentions should be paid to photochemical TPs and original EOCs, particularly those exhibiting high estrogenic activity to humans.}, } @article {pmid26283349, year = {2015}, author = {Wesolowski, A and Metcalf, CJ and Eagle, N and Kombich, J and Grenfell, BT and Bjørnstad, ON and Lessler, J and Tatem, AJ and Buckee, CO}, title = {Quantifying seasonal population fluxes driving rubella transmission dynamics using mobile phone data.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {112}, number = {35}, pages = {11114-11119}, pmid = {26283349}, issn = {1091-6490}, support = {106866/Z/15/Z//Wellcome Trust/United Kingdom ; P2C HD047879/HD/NICHD NIH HHS/United States ; U54 GM088558/GM/NIGMS NIH HHS/United States ; U19 AI089674/AI/NIAID NIH HHS/United States ; 1U54GM088558/GM/NIGMS NIH HHS/United States ; U19AI089674/AI/NIAID NIH HHS/United States ; //Wellcome Trust/United Kingdom ; }, mesh = {*Cell Phone ; *Data Interpretation, Statistical ; Humans ; Rubella/*transmission ; *Seasons ; }, abstract = {Changing patterns of human aggregation are thought to drive annual and multiannual outbreaks of infectious diseases, but the paucity of data about travel behavior and population flux over time has made this idea difficult to test quantitatively. Current measures of human mobility, especially in low-income settings, are often static, relying on approximate travel times, road networks, or cross-sectional surveys. Mobile phone data provide a unique source of information about human travel, but the power of these data to describe epidemiologically relevant changes in population density remains unclear. Here we quantify seasonal travel patterns using mobile phone data from nearly 15 million anonymous subscribers in Kenya. Using a rich data source of rubella incidence, we show that patterns of population travel (fluxes) inferred from mobile phone data are predictive of disease transmission and improve significantly on standard school term time and weather covariates. Further, combining seasonal and spatial data on travel from mobile phone data allows us to characterize seasonal fluctuations in risk across Kenya and produce dynamic importation risk maps for rubella. Mobile phone data therefore offer a valuable previously unidentified source of data for measuring key drivers of seasonal epidemics.}, } @article {pmid26282771, year = {2015}, author = {Jiang, YX and Liu, YS and Ying, GG and Wang, HW and Liang, YQ and Chen, XW}, title = {A new tool for assessing sediment quality based on the Weight of Evidence approach and grey TOPSIS.}, journal = {The Science of the total environment}, volume = {537}, number = {}, pages = {369-376}, doi = {10.1016/j.scitotenv.2015.08.004}, pmid = {26282771}, issn = {1879-1026}, mesh = {*Decision Support Techniques ; Environmental Monitoring/*methods ; Geologic Sediments/*chemistry ; Water Pollutants, Chemical/*analysis ; }, abstract = {Sediment is an important part of an aquatic ecosystem, so it is essential to develop an effective sediment quality assessment tool. This study aims to develop a new sediment quality assessment tool using a Weight of Evidence approach in combination with the grey TOPSIS (Technique for Order Preference by Similarity, a mathematical calculation of multi-criteria decision analysis). This tool can analyze data from chemical analyses, laboratory toxicity tests and benthic community structure analyses to generate individual results from each line of evidence, and integrate data from these three lines of evidence to obtain an overall assessment through an Excel Visual Basic for Application program. The tool can compare the relative magnitude of risks among sites and rate each site with high, moderate, or low ecological risk, thus guiding us to take pertinent measures toward polluted sediment. A case study of the sediment of Dongjiang River basin, south China, demonstrated the successful application of this tool. It proved that this assessment tool can provide a comprehensive and accurate assessment of sediment quality and efficiently discriminate risks among different sites, suggesting it is a powerful tool for environment risk assessment.}, } @article {pmid26278009, year = {2015}, author = {Price, DC and Egizi, A and Fonseca, DM}, title = {The ubiquity and ancestry of insect doublesex.}, journal = {Scientific reports}, volume = {5}, number = {}, pages = {13068}, pmid = {26278009}, issn = {2045-2322}, mesh = {Alternative Splicing ; Animals ; Base Sequence ; Databases, Genetic ; Drosophila Proteins/chemistry/classification/*genetics ; Drosophila melanogaster/*genetics ; Evolution, Molecular ; Expressed Sequence Tags ; Female ; Gene Dosage ; Male ; Phylogeny ; Protein Structure, Tertiary ; RNA, Messenger/metabolism ; Sex Differentiation ; Transcription Factors/chemistry/classification/*genetics ; }, abstract = {The doublesex (dsx) gene functions as a molecular switch at the base of the insect sex determination cascade, and triggers male or female somatic sexual differentiation in Drosophila. Having been reported from only seven current insect orders, the exact phylogenetic distribution of dsx within the largest Arthropod sub-phylum, the Hexapoda, is unknown. To understand the evolution of this integral gene relative to other arthropods, we tested for the presence of dsx within public EST and genome sequencing projects representative of all 32 hexapod orders. We find the dsx gene to be ubiquitous, with putative orthologs recovered from 30 orders. Additionally, we recovered both alternatively spliced and putative paralogous dsx transcripts from several orders of hexapods, including basal lineages, indicating the likely presence of these characteristics in the hexapod common ancestor. Of note, other arthropods such as chelicerates and crustaceans express two dsx genes, both of which are shown to lack alternative splicing. Furthermore, we discovered a large degree of length heterogeneity in the common region of dsx coding sequences within and among orders, possibly resulting from lineage-specific selective pressures inherent to each taxon. Our work serves as a valuable resource for understanding the evolution of sex determination in insects.}, } @article {pmid26276382, year = {2015}, author = {Jones, BM and Wcislo, WT and Robinson, GE}, title = {Developmental Transcriptome for a Facultatively Eusocial Bee, Megalopta genalis.}, journal = {G3 (Bethesda, Md.)}, volume = {5}, number = {10}, pages = {2127-2135}, pmid = {26276382}, issn = {2160-1836}, support = {1 OD006414/OD/NIH HHS/United States ; }, mesh = {Animals ; Bees/*genetics ; Biological Evolution ; Cluster Analysis ; Computational Biology/methods ; Gene Expression Profiling ; Molecular Sequence Annotation ; Multigene Family ; Phenotype ; *Transcriptome ; }, abstract = {Transcriptomes provide excellent foundational resources for mechanistic and evolutionary analyses of complex traits. We present a developmental transcriptome for the facultatively eusocial bee Megalopta genalis, which represents a potential transition point in the evolution of eusociality. A de novo transcriptome assembly of Megalopta genalis was generated using paired-end Illumina sequencing and the Trinity assembler. Males and females of all life stages were aligned to this transcriptome for analysis of gene expression profiles throughout development. Gene Ontology analysis indicates that stage-specific genes are involved in ion transport, cell-cell signaling, and metabolism. A number of distinct biological processes are upregulated in each life stage, and transitions between life stages involve shifts in dominant functional processes, including shifts from transcriptional regulation in embryos to metabolism in larvae, and increased lipid metabolism in adults. We expect that this transcriptome will provide a useful resource for future analyses to better understand the molecular basis of the evolution of eusociality and, more generally, phenotypic plasticity.}, } @article {pmid26273839, year = {2015}, author = {Tiedke, J and Borner, J and Beeck, H and Kwiatkowski, M and Schmidt, H and Thiel, R and Fabrizius, A and Burmester, T}, title = {Evaluating the Hypoxia Response of Ruffe and Flounder Gills by a Combined Proteome and Transcriptome Approach.}, journal = {PloS one}, volume = {10}, number = {8}, pages = {e0135911}, pmid = {26273839}, issn = {1932-6203}, mesh = {Animals ; Databases, Genetic ; Fish Proteins/*biosynthesis/genetics ; Flounder/genetics/*metabolism ; Gills/*metabolism ; Hypoxia/genetics/*metabolism ; Proteome/*biosynthesis/genetics ; Proteomics ; *Transcriptome ; }, abstract = {Hypoxia has gained ecological importance during the last decades, and it is the most dramatically increasing environmental factor in coastal areas and estuaries. The gills of fish are the prime target of hypoxia and other stresses. Here we have studied the impact of the exposure to hypoxia (1.5 mg O2/l for 48 h) on the protein expression of the gills of two estuarine fish species, the ruffe (Gymnocephalus cernua) and the European flounder (Platichthys flesus). First, we obtained the transcriptomes of mixed tissues (gills, heart and brain) from both species by Illumina next-generation sequencing. Then, the gill proteomes were investigated using two-dimensional gel electrophoresis and mass spectrometry. Quantification of the normalized proteome maps resulted in a total of 148 spots in the ruffe, of which 28 (18.8%) were significantly regulated (> 1.5-fold). In the flounder, 121 spots were found, of which 27 (22.3%) proteins were significantly regulated. The transcriptomes were used for the identification of these proteins, which was successful for 15 proteins of the ruffe and 14 of the flounder. The ruffe transcriptome dataset comprised 87,169,850 reads, resulting in an assembly of 72,108 contigs (N50 = 1,828 bp). 20,860 contigs (26.93%) had blastx hits with E < 1e-5 in the human sequences in the RefSeq database, representing 14,771 unique accession numbers. The flounder transcriptome with 78,943,030 reads assembled into 49,241 contigs (N50 = 2,106 bp). 20,127 contigs (40.87%) had a hit with human proteins, corresponding to 14,455 unique accession numbers. The regulation of selected genes was confirmed by quantitative real-time RT-PCR. Most of the regulated proteins that were identified by this approach function in the energy metabolism, while others are involved in the immune response, cell signalling and the cytoskeleton.}, } @article {pmid26271937, year = {2014}, author = {Liu, T and Pelowski, M}, title = {A new research trend in social neuroscience: Towards an interactive-brain neuroscience.}, journal = {PsyCh journal}, volume = {3}, number = {3}, pages = {177-188}, doi = {10.1002/pchj.56}, pmid = {26271937}, issn = {2046-0260}, abstract = {The ability to flexibly modulate our behaviors in social contexts and to successfully interact with other persons is a fundamental, but pivotal, requirement for human survival. Although previous social neuroscience research with single individuals has contributed greatly to our understanding of the basic mechanisms underlying social perception and social emotions, much of the dynamic nature of interactions between persons remains beyond the reach of single-brain studies. This has led to a growing argument for a shift to the simultaneous measurement of the brain activity of two or more individuals in realistic social interactions-an approach termed "hyperscanning." Although this approach offers important promise in unlocking the brain's role in truly social situations, there are multiple procedural and theoretical questions that require review and analysis. In this paper we discuss this research trend from four aspects: hyperscanning apparatus, experimental task, quantification method, and theoretical interpretation. We also give four suggestions for future research: (a) electroencephalography and near-infrared spectroscopy are useful tools by which to explore the interactive brain in more ecological settings; (b) games are an appropriate method to simulate daily life interactions; (c) transfer entropy may be an important method by which to quantify directed exchange of information between brains; and (d) more explanation is needed of the results of interbrain synchronization itself.}, } @article {pmid26271213, year = {2015}, author = {Westgate, MJ and Barton, PS and Pierson, JC and Lindenmayer, DB}, title = {Text analysis tools for identification of emerging topics and research gaps in conservation science.}, journal = {Conservation biology : the journal of the Society for Conservation Biology}, volume = {29}, number = {6}, pages = {1606-1614}, doi = {10.1111/cobi.12605}, pmid = {26271213}, issn = {1523-1739}, mesh = {Animals ; Conservation of Natural Resources/*methods ; *Data Mining ; Ecosystem ; Invertebrates/genetics ; Plants/genetics ; *Statistics as Topic ; Vertebrates/genetics ; }, abstract = {Keeping track of conceptual and methodological developments is a critical skill for research scientists, but this task is increasingly difficult due to the high rate of academic publication. As a crisis discipline, conservation science is particularly in need of tools that facilitate rapid yet insightful synthesis. We show how a common text-mining method (latent Dirichlet allocation, or topic modeling) and statistical tests familiar to ecologists (cluster analysis, regression, and network analysis) can be used to investigate trends and identify potential research gaps in the scientific literature. We tested these methods on the literature on ecological surrogates and indicators. Analysis of topic popularity within this corpus showed a strong emphasis on monitoring and management of fragmented ecosystems, while analysis of research gaps suggested a greater role for genetic surrogates and indicators. Our results show that automated text analysis methods need to be used with care, but can provide information that is complementary to that given by systematic reviews and meta-analyses, increasing scientists' capacity for research synthesis.}, } @article {pmid26269100, year = {2015}, author = {Ndhlovu, A and Hazelhurst, S and Durand, PM}, title = {Robust sequence alignment using evolutionary rates coupled with an amino acid substitution matrix.}, journal = {BMC bioinformatics}, volume = {16}, number = {}, pages = {255}, pmid = {26269100}, issn = {1471-2105}, mesh = {*Algorithms ; Amino Acid Sequence ; *Amino Acid Substitution ; Codon/genetics ; Databases, Factual ; *Evolution, Molecular ; Humans ; Molecular Sequence Data ; Protein Structure, Tertiary ; Proteins/*chemistry ; Sequence Alignment/*methods ; Sequence Analysis, Protein/*methods ; Sequence Homology, Amino Acid ; }, abstract = {BACKGROUND: Selective pressures at the DNA level shape genes into profiles consisting of patterns of rapidly evolving sites and sites withstanding change. These profiles remain detectable even when protein sequences become extensively diverged. A common task in molecular biology is to infer functional, structural or evolutionary relationships by querying a database using an algorithm. However, problems arise when sequence similarity is low. This study presents an algorithm that uses the evolutionary rate at codon sites, the dN/dS (ω) parameter, coupled to a substitution matrix as an alignment metric for detecting distantly related proteins. The algorithm, called BLOSUM-FIRE couples a newer and improved version of the original FIRE (Functional Inference using Rates of Evolution) algorithm with an amino acid substitution matrix in a dynamic scoring function. The enigmatic hepatitis B virus X protein was used as a test case for BLOSUM-FIRE and its associated database EvoDB.

RESULTS: The evolutionary rate based approach was coupled with a conventional BLOSUM substitution matrix. The two approaches are combined in a dynamic scoring function, which uses the selective pressure to score aligned residues. The dynamic scoring function is based on a coupled additive approach that scores aligned sites based on the level of conservation inferred from the ω values. Evaluation of the accuracy of this new implementation, BLOSUM-FIRE, using MAFFT alignment as reference alignments has shown that it is more accurate than its predecessor FIRE. Comparison of the alignment quality with widely used algorithms (MUSCLE, T-COFFEE, and CLUSTAL Omega) revealed that the BLOSUM-FIRE algorithm performs as well as conventional algorithms. Its main strength lies in that it provides greater potential for aligning divergent sequences and addresses the problem of low specificity inherent in the original FIRE algorithm. The utility of this algorithm is demonstrated using the Hepatitis B virus X (HBx) protein, a protein of unknown function, as a test case.

CONCLUSION: This study describes the utility of an evolutionary rate based approach coupled to the BLOSUM62 amino acid substitution matrix in inferring protein domain function. We demonstrate that such an approach is robust and performs as well as an array of conventional algorithms.}, } @article {pmid26261300, year = {2015}, author = {Bibi, F and Kiessling, W}, title = {Continuous evolutionary change in Plio-Pleistocene mammals of eastern Africa.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {112}, number = {34}, pages = {10623-10628}, pmid = {26261300}, issn = {1091-6490}, mesh = {Adaptation, Physiological ; Africa, Eastern ; Animals ; Antelopes/physiology ; *Biological Evolution ; Body Weight ; *Climate Change/history ; Databases, Factual ; Ecology ; Extinction, Biological ; Fossils ; Genetic Speciation ; History, Ancient ; Humidity ; Mammals/*physiology ; Temperature ; }, abstract = {Much debate has revolved around the question of whether the mode of evolutionary and ecological turnover in the fossil record of African mammals was continuous or pulsed, and the degree to which faunal turnover tracked changes in global climate. Here, we assembled and analyzed large specimen databases of the fossil record of eastern African Bovidae (antelopes) and Turkana Basin large mammals. Our results indicate that speciation and extinction proceeded continuously throughout the Pliocene and Pleistocene, as did increases in the relative abundance of arid-adapted bovids, and in bovid body mass. Species durations were similar among clades with different ecological attributes. Occupancy patterns were unimodal, with long and nearly symmetrical origination and extinction phases. A single origination pulse may be present at 2.0-1.75 Ma, but besides this, there is no evidence that evolutionary or ecological changes in the eastern African record tracked rapid, 100,000-y-scale changes in global climate. Rather, eastern African large mammal evolution tracked global or regional climatic trends at long (million year) time scales, while local, basin-scale changes (e.g., tectonic or hydrographic) and biotic interactions ruled at shorter timescales.}, } @article {pmid26261040, year = {2015}, author = {Baird, SJ}, title = {Exploring linkage disequilibrium.}, journal = {Molecular ecology resources}, volume = {15}, number = {5}, pages = {1017-1019}, doi = {10.1111/1755-0998.12424}, pmid = {26261040}, issn = {1755-0998}, mesh = {Computational Biology/*methods ; Genetics, Population/*methods ; *Linkage Disequilibrium ; *Software ; }, abstract = {Linkage disequilibrium (LD, association of allelic states across loci) is poorly understood by many evolutionary biologists, but as technology for multilocus sampling improves, we ignore LD at our peril. If we sample variation at 10 loci in an organism with 20 chromosomes, we can reasonably treat them as 10 'independent witnesses' of the evolutionary process. If instead, we sample variation at 1000 loci, many are bound to be close together on a chromosome. With only one or two crossovers per meiosis, associations between close neighbours decay so slowly that even LD created far in the past will not have dissipated, so we cannot treat the 1000 loci as independent witnesses (Barton). This means that as marker density on genomes increases classic analyses assuming independent loci become mired in the problem of overconfidence: if 1000 independent witnesses are assumed, and that number should be much lower, any conclusion will be overconfident. This is of special concern because our literature suffers from a strong publication bias towards confident answers, even when they turn out to be wrong (Knowles). In contrast, analyses that take into account associations across loci both control for overconfidence and can inform us about LD generating events far in the past, for example human/Neanderthal admixture (Fu et al.). With increased marker density, biologists must increase their awareness of LD and, in this issue of Molecular Ecology Resources, Kemppainen et al. () make software available that can only help in this process: LDna allows patterns of LD in a data set to be explored using tools borrowed from network analysis. This has great potential, but realizing that potential requires understanding LD.}, } @article {pmid26260630, year = {2016}, author = {Gerst, KL and Kellermann, JL and Enquist, CA and Rosemartin, AH and Denny, EG}, title = {Estimating the onset of spring from a complex phenology database: trade-offs across geographic scales.}, journal = {International journal of biometeorology}, volume = {60}, number = {3}, pages = {391-400}, pmid = {26260630}, issn = {1432-1254}, mesh = {*Databases, Factual ; Geography ; Linear Models ; Magnoliopsida/growth & development ; Plant Leaves/growth & development ; Research Design ; *Seasons ; Temperature ; Trees/*growth & development ; United States ; }, abstract = {Phenology is an important indicator of ecological response to climate change. Yet, phenological responses are highly variable among species and biogeographic regions. Recent monitoring initiatives have generated large phenological datasets comprised of observations from both professionals and volunteers. Because the observation frequency is often variable, there is uncertainty associated with estimating the timing of phenological activity. "Status monitoring" is an approach that focuses on recording observations throughout the full development of life cycle stages rather than only first dates in order to quantify uncertainty in generating phenological metrics, such as onset dates or duration. However, methods for using status data and calculating phenological metrics are not standardized. To understand how data selection criteria affect onset estimates of springtime leaf-out, we used status-based monitoring data curated by the USA National Phenology Network for 11 deciduous tree species in the eastern USA between 2009 and 2013. We asked, (1) How are estimates of the date of leaf-out onset, at the site and regional levels, influenced by different data selection criteria and methods for calculating onset, and (2) at the regional level, how does the timing of leaf-out relate to springtime minimum temperatures across latitudes and species? Results indicate that, to answer research questions at site to landscape levels, data users may need to apply more restrictive data selection criteria to increase confidence in calculating phenological metrics. However, when answering questions at the regional level, such as when investigating spatiotemporal patterns across a latitudinal gradient, there is low risk of acquiring erroneous results by maximizing sample size when using status-derived phenological data.}, } @article {pmid26260166, year = {2015}, author = {Steyaert, SM and Zedrosser, A and Rosell, F}, title = {Socio-ecological features other than sex affect habitat selection in the socially obligate monogamous Eurasian beaver.}, journal = {Oecologia}, volume = {179}, number = {4}, pages = {1023-1032}, pmid = {26260166}, issn = {1432-1939}, mesh = {Animals ; Avoidance Learning/*physiology ; *Ecosystem ; Female ; Geographic Information Systems ; Humans ; Male ; Pair Bond ; Rodentia/*growth & development/physiology ; Sex Characteristics ; Sexual Behavior, Animal/*physiology ; *Social Behavior ; Territoriality ; }, abstract = {Habitat selection is a context-dependent mechanism, in which both the internal state as well as external factors affect the behavior and decisions of an individual. This is well known for polygamous mammals, which are typically sexually dimorphic, and often express great variability in behavior and habitat selection between individuals as well between the sexes. Among monogamous mammals, however, variability in habitat selection should be explained by group characteristics and the presence of offspring rather than by sex. We evaluated this hypothesis in a socially monogamous rodent, the Eurasian beaver (Castor fiber), in a saturated Norwegian population. For the first time in this species we applied GPS tracking devices (N = 22 adult beavers, in 15 territories, 2009-2013), and used resource selection functions (i) to document population-wide habitat selection and the importance of 'territory' therein, and (ii) to evaluate which socio-ecological factors explained potential individual differences in habitat selection. We found that variation in habitat selection was stronger between territories than between years or individuals nested by territory. We identified that family size and the presence of kits, but not sex, explained individual variation in habitat selection. Adults with kits and/or larger families tended to exhibit low risk-taking behavior (avoiding human-related variables such as roads, buildings, and agricultural land), and stayed close to their main lodge (parental care). Our results show that habitat selection is a context-dependent mechanism even in a species which expresses very little behavioral and morphological dimorphism.}, } @article {pmid26258998, year = {2014}, author = {Freisthler, B and Lipperman-Kreda, S and Bersamin, M and Gruenewald, PJ}, title = {Tracking the When, Where, and With Whom of Alcohol Use: Integrating Ecological Momentary Assessment and Geospatial Data to Examine Risk for Alcohol-Related Problems.}, journal = {Alcohol research : current reviews}, volume = {36}, number = {1}, pages = {29-38}, pmid = {26258998}, issn = {2168-3492}, support = {P60 AA006282/AA/NIAAA NIH HHS/United States ; P60-AA-006282/AA/NIAAA NIH HHS/United States ; }, mesh = {*Alcohol Drinking ; *Geographic Information Systems ; Humans ; Monitoring, Ambulatory/*methods ; }, abstract = {Prevention researchers have found that drinking in different contexts is related to different alcohol problems. Where and with whom people drink affects the types of alcohol-related problems they experience. Consequently, identifying those contexts that result in the greatest number of problems provides a novel opportunity to target new prevention efforts aimed at those contexts. However, identifying these contexts poses methodological challenges to prevention research. To overcome these challenges, researchers need tools that allow them to gather detailed information about when and where people choose to drink and how contextual factors influence drinking risks. New data collection and analysis techniques, such as activity-space analysis, which examines movement through different contexts, and ecological momentary assessment, which captures microlevel contextual changes as individuals move through their days, can advance the field of alcohol studies by providing detailed information on the use of drinking contexts, particularly when combined. Data acquired through these methods allow researchers to better identify those con-texts where and conditions under which drinking and problems related to drinking occur. Use of these methods will allow prevention practitioners to target prevention efforts to those contexts that place most drinkers at risk and tailor prevention efforts to each context for specific outcomes.}, } @article {pmid26258845, year = {2015}, author = {Lenz, TL and Deutsch, AJ and Han, B and Hu, X and Okada, Y and Eyre, S and Knapp, M and Zhernakova, A and Huizinga, TW and Abecasis, G and Becker, J and Boeckxstaens, GE and Chen, WM and Franke, A and Gladman, DD and Gockel, I and Gutierrez-Achury, J and Martin, J and Nair, RP and Nöthen, MM and Onengut-Gumuscu, S and Rahman, P and Rantapää-Dahlqvist, S and Stuart, PE and Tsoi, LC and van Heel, DA and Worthington, J and Wouters, MM and Klareskog, L and Elder, JT and Gregersen, PK and Schumacher, J and Rich, SS and Wijmenga, C and Sunyaev, SR and de Bakker, PI and Raychaudhuri, S}, title = {Widespread non-additive and interaction effects within HLA loci modulate the risk of autoimmune diseases.}, journal = {Nature genetics}, volume = {47}, number = {9}, pages = {1085-1090}, pmid = {26258845}, issn = {1546-1718}, support = {1R01AR062886/AR/NIAMS NIH HHS/United States ; 1R01AR063759-01A1/AR/NIAMS NIH HHS/United States ; MANMKBRU-2012-1/DH_/Department of Health/United Kingdom ; UH2 AR067677/AR/NIAMS NIH HHS/United States ; 1UH2AR067677-01/AR/NIAMS NIH HHS/United States ; R01 AR042742/AR/NIAMS NIH HHS/United States ; G1001158/MRC_/Medical Research Council/United Kingdom ; U19 AI111224/AI/NIAID NIH HHS/United States ; R01AR065183/AR/NIAMS NIH HHS/United States ; U01 GM092691/GM/NIGMS NIH HHS/United States ; 5U01GM092691/GM/NIGMS NIH HHS/United States ; R01 AR063759/AR/NIAMS NIH HHS/United States ; R01 AR062886/AR/NIAMS NIH HHS/United States ; R01 AR065183/AR/NIAMS NIH HHS/United States ; R01 AR063611/AR/NIAMS NIH HHS/United States ; }, mesh = {Autoimmune Diseases/*genetics ; Case-Control Studies ; Epistasis, Genetic ; Genetic Association Studies ; Genetic Loci ; Genetic Predisposition to Disease ; HLA-C Antigens/*genetics ; HLA-D Antigens/*genetics ; Haplotypes ; Histocompatibility Antigens Class I/*genetics ; Humans ; Polymorphism, Single Nucleotide ; Risk Factors ; }, abstract = {Human leukocyte antigen (HLA) genes confer substantial risk for autoimmune diseases on a log-additive scale. Here we speculated that differences in autoantigen-binding repertoires between a heterozygote's two expressed HLA variants might result in additional non-additive risk effects. We tested the non-additive disease contributions of classical HLA alleles in patients and matched controls for five common autoimmune diseases: rheumatoid arthritis (ncases = 5,337), type 1 diabetes (T1D; ncases = 5,567), psoriasis vulgaris (ncases = 3,089), idiopathic achalasia (ncases = 727) and celiac disease (ncases = 11,115). In four of the five diseases, we observed highly significant, non-additive dominance effects (rheumatoid arthritis, P = 2.5 × 10(-12); T1D, P = 2.4 × 10(-10); psoriasis, P = 5.9 × 10(-6); celiac disease, P = 1.2 × 10(-87)). In three of these diseases, the non-additive dominance effects were explained by interactions between specific classical HLA alleles (rheumatoid arthritis, P = 1.8 × 10(-3); T1D, P = 8.6 × 10(-27); celiac disease, P = 6.0 × 10(-100)). These interactions generally increased disease risk and explained moderate but significant fractions of phenotypic variance (rheumatoid arthritis, 1.4%; T1D, 4.0%; celiac disease, 4.1%) beyond a simple additive model.}, } @article {pmid26257019, year = {2015}, author = {Serang, O and Käll, L}, title = {Solution to Statistical Challenges in Proteomics Is More Statistics, Not Less.}, journal = {Journal of proteome research}, volume = {14}, number = {10}, pages = {4099-4103}, doi = {10.1021/acs.jproteome.5b00568}, pmid = {26257019}, issn = {1535-3907}, mesh = {Algorithms ; *Artifacts ; Databases, Protein ; Humans ; Proteins/*isolation & purification ; Proteomics/methods/*statistics & numerical data ; *Software ; Tandem Mass Spectrometry/*statistics & numerical data ; }, abstract = {In any high-throughput scientific study, it is often essential to estimate the percent of findings that are actually incorrect. This percentage is called the false discovery rate (abbreviated "FDR"), and it is an invariant (albeit, often unknown) quantity for any well-formed study. In proteomics, it has become common practice to incorrectly conflate the protein FDR (the percent of identified proteins that are actually absent) with protein-level target-decoy, a particular method for estimating the protein-level FDR. In this manner, the challenges of one approach have been used as the basis for an argument that the field should abstain from protein-level FDR analysis altogether or even the suggestion that the very notion of a protein FDR is flawed. As we demonstrate in simple but accurate simulations, not only is the protein-level FDR an invariant concept, when analyzing large data sets, the failure to properly acknowledge it or to correct for multiple testing can result in large, unrecognized errors, whereby thousands of absent proteins (and, potentially every protein in the FASTA database being considered) can be incorrectly identified.}, } @article {pmid26254872, year = {2015}, author = {Garza, DR and Dutilh, BE}, title = {From cultured to uncultured genome sequences: metagenomics and modeling microbial ecosystems.}, journal = {Cellular and molecular life sciences : CMLS}, volume = {72}, number = {22}, pages = {4287-4308}, pmid = {26254872}, issn = {1420-9071}, mesh = {Computer Simulation ; Ecosystem ; Genome, Microbial/*genetics ; Genome, Viral/*genetics ; High-Throughput Nucleotide Sequencing/*methods ; Metagenomics/*methods ; Microbial Consortia/genetics ; Microbiological Techniques/*methods ; Models, Theoretical ; Viruses/genetics ; }, abstract = {Microorganisms and the viruses that infect them are the most numerous biological entities on Earth and enclose its greatest biodiversity and genetic reservoir. With strength in their numbers, these microscopic organisms are major players in the cycles of energy and matter that sustain all life. Scientists have only scratched the surface of this vast microbial world through culture-dependent methods. Recent developments in generating metagenomes, large random samples of nucleic acid sequences isolated directly from the environment, are providing comprehensive portraits of the composition, structure, and functioning of microbial communities. Moreover, advances in metagenomic analysis have created the possibility of obtaining complete or nearly complete genome sequences from uncultured microorganisms, providing important means to study their biology, ecology, and evolution. Here we review some of the recent developments in the field of metagenomics, focusing on the discovery of genetic novelty and on methods for obtaining uncultured genome sequences, including through the recycling of previously published datasets. Moreover we discuss how metagenomics has become a core scientific tool to characterize eco-evolutionary patterns of microbial ecosystems, thus allowing us to simultaneously discover new microbes and study their natural communities. We conclude by discussing general guidelines and challenges for modeling the interactions between uncultured microorganisms and viruses based on the information contained in their genome sequences. These models will significantly advance our understanding of the functioning of microbial ecosystems and the roles of microbes in the environment.}, } @article {pmid26252388, year = {2015}, author = {Baumann, A and Lehmann, R and Beckert, A and Vilcinskas, A and Franta, Z}, title = {Selection and Evaluation of Tissue Specific Reference Genes in Lucilia sericata during an Immune Challenge.}, journal = {PloS one}, volume = {10}, number = {8}, pages = {e0135093}, pmid = {26252388}, issn = {1932-6203}, mesh = {Actins/genetics ; Algorithms ; Animals ; Computational Biology ; DNA Primers ; Debridement ; Diptera/embryology/*genetics/*immunology ; Fat Body/metabolism ; *Gene Expression Regulation ; *Genes, Insect ; Immune System ; Intestinal Mucosa/metabolism ; Larva ; Molecular Sequence Data ; Pseudomonas aeruginosa ; RNA, Ribosomal, 18S/genetics ; RNA, Ribosomal, 28S/genetics ; Salivary Glands/metabolism ; Tissue Distribution ; Tubulin/genetics ; Wound Healing ; }, abstract = {The larvae of the common green bottle fly Lucilia sericata (Diptera: Calliphoridae) have been used for centuries to promote wound healing, but the molecular basis of their antimicrobial, debridement and healing functions remains largely unknown. The analysis of differential gene expression in specific larval tissues before and after immune challenge could be used to identify key molecular factors, but the most sensitive and reproducible method qRT-PCR requires validated reference genes. We therefore selected 10 candidate reference genes encoding products from different functional classes (18S rRNA, 28S rRNA, actin, β-tubulin, RPS3, RPLP0, EF1α, PKA, GAPDH and GST1). Two widely applied algorithms (GeNorm and Normfinder) were used to analyze reference gene candidates in different larval tissues associated with secretion, digestion, and antimicrobial activity (midgut, hindgut, salivary glands, crop and fat body). The Gram-negative bacterium Pseudomonas aeruginosa was then used to boost the larval immune system and the stability of reference gene expression was tested in comparison to three immune genes (lucimycin, defensin-1 and attacin-2), which target different pathogen classes. We observed no differential expression of the antifungal peptide lucimycin, whereas the representative targeting Gram-positive bacteria (defensin-1) was upregulated in salivary glands, crop, nerve ganglion and reached its maximum in fat body (up to 300-fold). The strongest upregulation in all immune challenged tissues (over 50,000-fold induction in the fat body) was monitored for attacin-2, the representative targeting Gram-negative bacteria. Here we identified and validated a set of reference genes that allows the accurate normalization of gene expression in specific tissues of L. sericata after immune challenge.}, } @article {pmid26252155, year = {2015}, author = {Boyce, DG and Frank, KT and Worm, B and Leggett, WC}, title = {Spatial patterns and predictors of trophic control in marine ecosystems.}, journal = {Ecology letters}, volume = {18}, number = {10}, pages = {1001-1011}, doi = {10.1111/ele.12481}, pmid = {26252155}, issn = {1461-0248}, mesh = {Animals ; Biodiversity ; Databases, Factual ; *Ecosystem ; Food Chain ; Geography ; Linear Models ; *Marine Biology ; *Models, Biological ; Multivariate Analysis ; Plankton ; Spatial Analysis ; *Temperature ; }, abstract = {A key question in ecology is under which conditions ecosystem structure tends to be controlled by resource availability vs. consumer pressure. Several hypotheses derived from theory, experiments and observational field studies have been advanced, yet a unified explanation remains elusive. Here, we identify common predictors of trophic control in a synthetic analysis of 52 observational field studies conducted within marine ecosystems across the Northern Hemisphere and published between 1951 and 2014. Spatial regression analysis of 45 candidate variables revealed temperature to be the dominant predictor, with unimodal effects on trophic control operating both directly (r(2) = 0.32; P < 0.0001) and indirectly through influences on turnover rate and quality of primary production, biodiversity and omnivory. These findings indicate that temperature is an overarching determinant of the trophic dynamics of marine ecosystems, and that variation in ocean temperature will affect the trophic structure of marine ecosystems through both direct and indirect mechanisms.}, } @article {pmid26249193, year = {2015}, author = {Novak, LL and Simpson, CL and Slagle, J and Mulvaney, SA}, title = {Technology and the Ecology of Chronic Illness in Everyday Life.}, journal = {Studies in health technology and informatics}, volume = {215}, number = {}, pages = {145-156}, pmid = {26249193}, issn = {1879-8365}, mesh = {Activities of Daily Living ; Adolescent ; Adult ; Aged ; *Anthropology, Cultural ; Anti-Asthmatic Agents/*therapeutic use ; Asthma/*drug therapy ; Data Collection/methods ; Female ; Health Behavior ; Humans ; Male ; *Medical Informatics ; Middle Aged ; Qualitative Research ; *Social Environment ; Technology Assessment, Biomedical ; Tennessee ; }, abstract = {A major challenge in the design of useful technological tools is effectively conceptualizing the context in which users engage the technology. Contextually specific research on activities of patients and their caregivers - and how those activities are supported by social and material arrangements--can result in insights for design of consumer health informatics technologies and infrastructural advancements that can better support patients outside of institutional settings. This chapter describes an ecosystem focused on activity--how activity is shaped by cultural institutions, and the negotiations that arise between actors and institutions.}, } @article {pmid26248563, year = {2015}, author = {Ankenbrand, MJ and Keller, A and Wolf, M and Schultz, J and Förster, F}, title = {ITS2 Database V: Twice as Much.}, journal = {Molecular biology and evolution}, volume = {32}, number = {11}, pages = {3030-3032}, doi = {10.1093/molbev/msv174}, pmid = {26248563}, issn = {1537-1719}, mesh = {DNA, Ribosomal Spacer/*genetics ; *Databases, Nucleic Acid ; Eukaryota/genetics ; Internet ; Nucleic Acid Conformation ; Phylogeny ; Sequence Alignment/methods ; }, abstract = {The internal transcribed spacer 2 (ITS2) is a well-established marker for phylogenetic analyses in eukaryotes. A reliable resource for reference sequences and their secondary structures is the ITS2 database (http://its2.bioapps.biozentrum.uni-wuerzburg.de/). However, the database was last updated in 2011. Here, we present a major update of the underlying data almost doubling the number of entities. This increases the number of taxa represented within all major eukaryotic clades. Moreover, additional data has been added to underrepresented groups and some new groups have been added. The broader coverage across the tree of life improves phylogenetic analyses and the capability of ITS2 as a DNA barcode.}, } @article {pmid26248105, year = {2015}, author = {Barbieri, AR and Gonçalves, CC and Cheade, Mde F and Souza, C and Tsuha, DH and Ferreira, KC and Rasi, L and Paranhos Filho, AC}, title = {Hemodialysis services: are public policies turned to guaranteeing the access?.}, journal = {Cadernos de saude publica}, volume = {31}, number = {7}, pages = {1505-1516}, doi = {10.1590/0102-311X00073514}, pmid = {26248105}, issn = {1678-4464}, mesh = {Adolescent ; Adult ; Aged ; Aged, 80 and over ; Brazil/epidemiology ; Child ; Child, Preschool ; Cross-Sectional Studies ; Female ; Health Services Accessibility ; Humans ; Infant ; Infant, Newborn ; Kidney Failure, Chronic/epidemiology/*therapy ; Male ; Middle Aged ; National Health Programs ; Prevalence ; Public Policy ; *Renal Dialysis/statistics & numerical data ; Residence Characteristics ; Socioeconomic Factors ; Young Adult ; }, abstract = {The increasing incidence of chronic renal failure in Brazil and the consequential expansion of hemodialysis as a choice for treatment in final stage have to be taken into account to guarantee access to those in need. The ecological study conducted in Mato Grosso do Sul State, Brazil, in 2012, using data from the Brazilian Health Informatics Department (DATASUS) and from the analysis of medical records in 12 clinics, identified and mapped patients on hemodialysis, the distance they travelled and the estimated number of patients. The prevalence of hemodialysis patients in Mato Grosso do Sul State, about 55 per 100,000 inhabitants, is similar to the national average. The analyses indicated concentration of patients in counties with clinics and also geographical gaps that generate displacement of over 100km for more than 16% of patients. The results point to the necessity of strengthening public policies that consider, for decision-making, the decentralization of service, the expansion of home care and the follow-up education for professionals.}, } @article {pmid26247819, year = {2015}, author = {Ferrante, E and Turgut, AE and Duéñez-Guzmán, E and Dorigo, M and Wenseleers, T}, title = {Evolution of Self-Organized Task Specialization in Robot Swarms.}, journal = {PLoS computational biology}, volume = {11}, number = {8}, pages = {e1004273}, pmid = {26247819}, issn = {1553-7358}, mesh = {Animals ; Ants/physiology ; *Artificial Intelligence ; *Biological Evolution ; Computational Biology ; *Models, Biological ; *Robotics/instrumentation/methods ; *Social Behavior ; Task Performance and Analysis ; Work ; }, abstract = {Division of labor is ubiquitous in biological systems, as evidenced by various forms of complex task specialization observed in both animal societies and multicellular organisms. Although clearly adaptive, the way in which division of labor first evolved remains enigmatic, as it requires the simultaneous co-occurrence of several complex traits to achieve the required degree of coordination. Recently, evolutionary swarm robotics has emerged as an excellent test bed to study the evolution of coordinated group-level behavior. Here we use this framework for the first time to study the evolutionary origin of behavioral task specialization among groups of identical robots. The scenario we study involves an advanced form of division of labor, common in insect societies and known as "task partitioning", whereby two sets of tasks have to be carried out in sequence by different individuals. Our results show that task partitioning is favored whenever the environment has features that, when exploited, reduce switching costs and increase the net efficiency of the group, and that an optimal mix of task specialists is achieved most readily when the behavioral repertoires aimed at carrying out the different subtasks are available as pre-adapted building blocks. Nevertheless, we also show for the first time that self-organized task specialization could be evolved entirely from scratch, starting only from basic, low-level behavioral primitives, using a nature-inspired evolutionary method known as Grammatical Evolution. Remarkably, division of labor was achieved merely by selecting on overall group performance, and without providing any prior information on how the global object retrieval task was best divided into smaller subtasks. We discuss the potential of our method for engineering adaptively behaving robot swarms and interpret our results in relation to the likely path that nature took to evolve complex sociality and task specialization.}, } @article {pmid26247465, year = {2015}, author = {Christensen, AB and Herman, JL and Elphick, MR and Kober, KM and Janies, D and Linchangco, G and Semmens, DC and Bailly, X and Vinogradov, SN and Hoogewijs, D}, title = {Phylogeny of Echinoderm Hemoglobins.}, journal = {PloS one}, volume = {10}, number = {8}, pages = {e0129668}, pmid = {26247465}, issn = {1932-6203}, mesh = {Animals ; Bayes Theorem ; Cytoglobin ; Echinodermata/chemistry/*genetics ; Globins/chemistry/*genetics ; Likelihood Functions ; Models, Molecular ; Nerve Tissue Proteins/chemistry/*genetics ; Neuroglobin ; Phylogeny ; Protein Conformation ; }, abstract = {BACKGROUND: Recent genomic information has revealed that neuroglobin and cytoglobin are the two principal lineages of vertebrate hemoglobins, with the latter encompassing the familiar myoglobin and α-globin/β-globin tetramer hemoglobin, and several minor groups. In contrast, very little is known about hemoglobins in echinoderms, a phylum of exclusively marine organisms closely related to vertebrates, beyond the presence of coelomic hemoglobins in sea cucumbers and brittle stars. We identified about 50 hemoglobins in sea urchin, starfish and sea cucumber genomes and transcriptomes, and used Bayesian inference to carry out a molecular phylogenetic analysis of their relationship to vertebrate sequences, specifically, to assess the hypothesis that the neuroglobin and cytoglobin lineages are also present in echinoderms.

RESULTS: The genome of the sea urchin Strongylocentrotus purpuratus encodes several hemoglobins, including a unique chimeric 14-domain globin, 2 androglobin isoforms and a unique single androglobin domain protein. Other strongylocentrotid genomes appear to have similar repertoires of globin genes. We carried out molecular phylogenetic analyses of 52 hemoglobins identified in sea urchin, brittle star and sea cucumber genomes and transcriptomes, using different multiple sequence alignment methods coupled with Bayesian and maximum likelihood approaches. The results demonstrate that there are two major globin lineages in echinoderms, which are related to the vertebrate neuroglobin and cytoglobin lineages. Furthermore, the brittle star and sea cucumber coelomic hemoglobins appear to have evolved independently from the cytoglobin lineage, similar to the evolution of erythroid oxygen binding globins in cyclostomes and vertebrates.

CONCLUSION: The presence of echinoderm globins related to the vertebrate neuroglobin and cytoglobin lineages suggests that the split between neuroglobins and cytoglobins occurred in the deuterostome ancestor shared by echinoderms and vertebrates.}, } @article {pmid26247102, year = {2015}, author = {Buyuktimkin, B and Saier, MH}, title = {Comparative genomic analyses of transport proteins encoded within the genomes of Leptospira species.}, journal = {Microbial pathogenesis}, volume = {88}, number = {}, pages = {52-64}, pmid = {26247102}, issn = {1096-1208}, support = {R01 GM077402/GM/NIGMS NIH HHS/United States ; R01 GM109895/GM/NIGMS NIH HHS/United States ; GM077402/GM/NIGMS NIH HHS/United States ; GM109895/GM/NIGMS NIH HHS/United States ; }, mesh = {Carrier Proteins/*genetics ; *Computational Biology ; Evolution, Molecular ; *Genome, Bacterial ; Humans ; Leptospira/*genetics ; }, abstract = {Select species of the bacterial genus Leptospira are causative agents of leptospirosis, an emerging global zoonosis affecting nearly one million people worldwide annually. We examined two Leptospira pathogens, Leptospira interrogans serovar Lai str. 56601 and Leptospira borgpetersenii serovar Hardjo-bovis str. L550, as well as the free-living leptospiral saprophyte, Leptospira biflexa serovar Patoc str. 'Patoc 1 (Ames)'. The transport proteins of these leptospires were identified and compared using bioinformatics to gain an appreciation for which proteins may be related to pathogenesis and saprophytism. L. biflexa possesses a disproportionately high number of secondary carriers for metabolite uptake and environmental adaptability as well as an increased number of inorganic cation transporters providing ionic homeostasis and effective osmoregulation in a rapidly changing environment. L. interrogans and L. borgpetersenii possess far fewer transporters, but those that they have are remarkably similar, with near-equivalent representation in most transporter families. These two Leptospira pathogens also possess intact sphingomyelinases, holins, and virulence-related outer membrane porins. These virulence-related factors, in conjunction with decreased transporter substrate versatility, indicate that pathogenicity was accompanied by progressively narrowing ecological niches and the emergence of a limited set of proteins responsible for host invasion. The variability of host tropism and mortality rates by infectious leptospires suggests that small differences in individual sets of proteins play important physiological and pathological roles.}, } @article {pmid26243266, year = {2015}, author = {Vargas, WP and Kawa, H and Sabroza, PC and Soares, VB and Honório, NA and de Almeida, AS}, title = {Association among house infestation index, dengue incidence, and sociodemographic indicators: surveillance using geographic information system.}, journal = {BMC public health}, volume = {15}, number = {}, pages = {746}, pmid = {26243266}, issn = {1471-2458}, mesh = {Aedes ; Animals ; Bayes Theorem ; Brazil/epidemiology ; Dengue/*epidemiology/*transmission ; Dengue Virus/isolation & purification ; Disease Outbreaks/*statistics & numerical data ; Geographic Information Systems ; Humans ; Incidence ; *Insect Vectors ; *Population Density ; Socioeconomic Factors ; Spatial Analysis ; }, abstract = {BACKGROUND: We identified dengue transmission areas by using the Geographic Information Systems located at local surveillance units of the Itaboraí municipality in state of Rio de Janeiro. We considered the association among the house infestation index, the disease incidence, and sociodemographic indicators during a prominent dengue outbreak in 2007 and 2008.

METHODS: In this ecological study, the Local Surveillance Units (UVLs) of the municipality were used as spatial pattern units. For the house analysis, we used the period of higher vector density that occurred previous to the larger magnitude epidemic range of dengue cases. The average dengue incidence rates calculated in this epidemic range were smoothed using the Bayesian method. The associations among the House Infestation Index (HI), the Bayesian rate of the average dengue incidence, and the sociodemographic indicators were evaluated using a Pearson's correlation coefficient. The areas that were at a higher risk of dengue occurrence were detected using a kernel density estimation with the kernel quartic function.

RESULTS: The dengue transmission pattern in Itaboraí showed that the increase in the vector density preceded the increase in incidence. The HI was positively correlated to the Bayesian dengue incidence rate (r = 0.641; p = 0.01). The higher risk areas were those that were close to the main highways. In the Kernel density estimation analysis, we observed that the regions that were at a higher risk of dengue were those that were located in the UVLs and had the highest population densities; these locations were typically located along major highways. Four nuclei were identified as epicenters of high risk.

CONCLUSIONS: The spatial analysis units used in this research, i.e., UVLs, served as a methodological resource for examining the compatibility of different information sources concerning the disease, the vector indices, and the municipal sociodemographic aspects and were arranged in distinct cartographic bases. Dengue is a multi-scale geographic phenomenon, and using the UVLs as analysis units made it possible to differentiate the dengue occurrence throughout the municipality. The methodological approach used in this research helped improve the Itaboraí municipality monitoring activities and the local territorial monitoring in other municipalities that are affected by this public health issue.}, } @article {pmid26241034, year = {2015}, author = {Taylor, SM and Loew, ER and Grace, MS}, title = {Ontogenic retinal changes in three ecologically distinct elopomorph fishes (Elopomorpha:Teleostei) correlate with light environment and behavior.}, journal = {Visual neuroscience}, volume = {32}, number = {}, pages = {E005}, doi = {10.1017/S0952523815000024}, pmid = {26241034}, issn = {1469-8714}, mesh = {Animals ; *Biological Ontologies ; *Ecology ; *Environment ; Fishes/classification ; Larva ; *Light ; *Metamorphosis, Biological ; Opsins/metabolism ; Retina/cytology/*physiology ; Retinal Cone Photoreceptor Cells/metabolism ; Retinal Rod Photoreceptor Cells/metabolism ; Species Specificity ; Visual Acuity ; }, abstract = {Unlike the mammalian retina, the teleost fish retina undergoes persistent neurogenesis from intrinsic stem cells. In marine teleosts, most cone photoreceptor genesis occurs early in the embryonic and larval stages, and rods are added primarily during and after metamorphosis. This study demonstrates a developmental paradigm in elopomorph fishes in which retinas are rod-dominated in larvae, but undergo periods of later cone genesis. Retinal characteristics were compared at different developmental stages among three ecologically distinct elopomorph fishes-ladyfish (Elops saurus), bonefish (Albula vulpes), and speckled worm eel (Myrophis punctatus). The objectives were to improve our understanding of (1) the developmental strategy in the elopomorph retina, (2) the functional architecture of the retina as it relates to ecology, and (3) how the light environment influences photoreceptor genesis. Photoreceptor morphologies, distributions, and spectral absorption were studied at larval, juvenile, and adult stages. Premetamorphic retinas in all three species are rod-dominated, but the retinas of these species undergo dramatic change over the course of development, resulting in juvenile and adult retinal characteristics that correlate closely with ecology. Adult E. saurus has high rod densities, grouped photoreceptors, a reflective tapetum, and longer-wavelength photopigments, supporting vision in turbid, low-light conditions. Adult A. vulpes has high cone densities, low rod densities, and shorter-wavelength photopigments, supporting diurnal vision in shallow, clear water. M. punctatus loses cones during metamorphosis, develops new cones after settlement, and maintains high rod but low cone densities, supporting primarily nocturnal vision. M. punctatus secondary cone genesis occurs rapidly throughout the retina, suggesting a novel mechanism of vertebrate photoreceptor genesis. Finally, in postsettlement M. punctatus, the continuous presence or absence of visible light modulates rod distribution but does not affect secondary cone genesis, suggesting some degree of developmental plasticity influenced by the light environment.}, } @article {pmid26237179, year = {2015}, author = {Ord, TJ and Klomp, DA and Garcia-Porta, J and Hagman, M}, title = {Repeated evolution of exaggerated dewlaps and other throat morphology in lizards.}, journal = {Journal of evolutionary biology}, volume = {28}, number = {11}, pages = {1948-1964}, doi = {10.1111/jeb.12709}, pmid = {26237179}, issn = {1420-9101}, mesh = {Animals ; *Biological Evolution ; Databases, Factual ; Female ; Hyoid Bone/anatomy & histology ; Lizards/*anatomy & histology/*genetics ; Male ; *Sex Characteristics ; }, abstract = {The existence of elaborate ornamental structures in males is often assumed to reflect the outcome of female mate choice for showy males. However, female mate choice appears weak in many iguanian lizards, but males still exhibit an array of ornament-like structures around the throat. We performed a phylogenetic comparative study to assess whether these structures have originated in response to male-male competition or the need for improved signal efficiency in visually difficult environments. We found little evidence for the influence of male-male competition. Instead, forest species were more likely to exhibit colourful throat appendages than species living in open habitats, suggesting selection for signal efficiency. On at least three independent occasions, throat ornamentation has become further elaborated into a large, conspicuously coloured moving dewlap. Although the function of the dewlap is convergent, the underlying hyoid apparatus has evolved very differently, revealing the same adaptive outcome has been achieved through multiple evolutionary trajectories. More generally, our findings highlight that extravagant, ornament-like morphology can evolve in males without the direct influence of female mate choice and that failure to consider alternative hypotheses for the evolution of these structures can obscure the true origins of signal diversity among closely related taxa.}, } @article {pmid26236833, year = {2015}, author = {Fleming, CH and Fagan, WF and Mueller, T and Olson, KA and Leimgruber, P and Calabrese, JM}, title = {Rigorous home range estimation with movement data: a new autocorrelated kernel density estimator.}, journal = {Ecology}, volume = {96}, number = {5}, pages = {1182-1188}, doi = {10.1890/14-2010.1}, pmid = {26236833}, issn = {0012-9658}, mesh = {Animal Distribution/*physiology ; Animals ; Antelopes/physiology ; Computer Simulation ; Data Interpretation, Statistical ; Ecosystem ; Homing Behavior/*physiology ; *Models, Biological ; Models, Statistical ; Movement ; }, abstract = {Quantifying animals' home ranges is a key problem in ecology and has important conservation and wildlife management applications. Kernel density estimation (KDE) is a workhorse technique for range delineation problems that is both statistically efficient and nonparametric. KDE assumes that the data are independent and identically distributed (IID). However, animal tracking data, which are routinely used as inputs to KDEs, are inherently autocorrelated and violate this key assumption. As we demonstrate, using realistically autocorrelated data in conventional KDEs results in grossly underestimated home ranges. We further show that the performance of conventional KDEs actually degrades as data quality improves, because autocorrelation strength increases as movement paths become more finely resolved. To remedy these flaws with the traditional KDE method, we derive an autocorrelated KDE (AKDE) from first principles to use autocorrelated data, making it perfectly suited for movement data sets. We illustrate the vastly improved performance of AKDE using analytical arguments, relocation data from Mongolian gazelles, and simulations based upon the gazelle's observed movement process. By yielding better minimum area estimates for threatened wildlife populations, we believe that future widespread use of AKDE will have significant impact on ecology and conservation biology.}, } @article {pmid26236474, year = {2015}, author = {Tedersoo, L and Ramirez, KS and Nilsson, RH and Kaljuvee, A and Kõljalg, U and Abarenkov, K}, title = {Standardizing metadata and taxonomic identification in metabarcoding studies.}, journal = {GigaScience}, volume = {4}, number = {}, pages = {34}, pmid = {26236474}, issn = {2047-217X}, mesh = {Biodiversity ; *DNA Barcoding, Taxonomic ; High-Throughput Nucleotide Sequencing ; Sequence Alignment ; }, abstract = {High-throughput sequencing-based metabarcoding studies produce vast amounts of ecological data, but a lack of consensus on standardization of metadata and how to refer to the species recovered severely hampers reanalysis and comparisons among studies. Here we propose an automated workflow covering data submission, compression, storage and public access to allow easy data retrieval and inter-study communication. Such standardized and readily accessible datasets facilitate data management, taxonomic comparisons and compilation of global metastudies.}, } @article {pmid26235829, year = {2016}, author = {Mançaneira, JF and Benedetti, JR and Zhang, L}, title = {Hospitalizations and deaths due to pertussis in children from 1996 to 2013.}, journal = {Jornal de pediatria}, volume = {92}, number = {1}, pages = {40-45}, doi = {10.1016/j.jped.2015.03.006}, pmid = {26235829}, issn = {1678-4782}, mesh = {Adolescent ; Age Distribution ; Brazil/epidemiology ; Child ; Child, Preschool ; Databases, Factual/*statistics & numerical data ; Hospitalization/economics/*statistics & numerical data ; Humans ; Incidence ; Infant ; Infant, Newborn ; Pertussis Vaccine/standards ; Whooping Cough/*mortality ; Young Adult ; }, abstract = {OBJECTIVES: To assess temporal trends of hospitalizations and deaths from pertussis in Brazilian children in the period of 1996-2013.

METHODS: This was a descriptive ecological study of temporal trends, based on the DATASUS database. The number of hospitalizations and deaths from pertussis in children up to 19 years of age from January 1996 to December 2013 was obtained. Descriptive statistics were applied for data analysis.

RESULTS: During the study period, a total of 19,047 hospital admissions from pertussis were recorded, of which 88.2% occurred in infants younger than 1 year. In the period 1996-2010, the mean annual number of admissions was 755, ranging from a maximum of 1179 in 2004 to a minimum of 400 in 2010. There was an increase of admissions in the last three consecutive years (2011, 2012, and 2013) with 1177, 2954 and 3589 hospitalizations, respectively. There were 498 deaths from pertussis throughout the study period, of which 96.8% occurred in children younger than one year. There was an increase in the number of deaths from pertussis in children in the years 2011, 2012, and 2013, with 40, 93, and 87 recorded deaths, respectively. The increase in hospitalizations and deaths from pertussis in children occurred in all regions of the country, with the highest increase observed in the Southeast, North and Northeast regions.

CONCLUSIONS: There was a substantial increase in hospitalizations and deaths from pertussis in children for three consecutive years (2011, 2012, and 2013) in all Brazilian regions. The most affected age group was that of children younger than one year.}, } @article {pmid26233048, year = {2015}, author = {Matias, L and Harris, D}, title = {A single-station method for the detection, classification and location of fin whale calls using ocean-bottom seismic stations.}, journal = {The Journal of the Acoustical Society of America}, volume = {138}, number = {1}, pages = {504-520}, doi = {10.1121/1.4922706}, pmid = {26233048}, issn = {1520-8524}, mesh = {Acoustics/*instrumentation ; Animals ; Balaenoptera/*physiology ; Datasets as Topic ; Equipment Design ; Fin Whale/*physiology ; Homing Behavior ; Marine Biology/*instrumentation ; Oceans and Seas ; Sound Localization ; *Vocalization, Animal ; }, abstract = {Passive seismic monitoring in the oceans uses long-term deployments of Ocean Bottom Seismometers (OBSs). An OBS usually records the three components of ground motion and pressure, typically at 100 Hz. This makes the OBS an ideal tool to investigate fin and blue whales that vocalize at frequencies below 45 Hz. Previous applications of OBS data to locate whale calls have relied on single channel analyses that disregard the information that is conveyed by the horizontal seismic channels. Recently, Harris, Matias, Thomas, Harwood, and Geissler [J. Acoust. Soc. Am. 134, 3522-3535 (2013)] presented a method that used all four channels recorded by one OBS to derive the range and azimuth of fin whale calls. In this work, the detection, classification, and ranging of calls using this four-channel method were further investigated, focusing on methods to increase the accuracy of range estimates to direct path arrivals. Corrections to account for the influences of the sound speed in the water layer and the velocity structure in the top strata of the seabed were considered. The single station method discussed here is best implemented when OBSs have been deployed in deep water on top of seabed strata with low P-wave velocity. These conditions maximize the ability to detect and estimate ranges to fin whale calls.}, } @article {pmid26231182, year = {2015}, author = {Church, SH and Ryan, JF and Dunn, CW}, title = {Automation and Evaluation of the SOWH Test with SOWHAT.}, journal = {Systematic biology}, volume = {64}, number = {6}, pages = {1048-1058}, pmid = {26231182}, issn = {1076-836X}, mesh = {Classification/*methods ; *Computer Simulation ; Data Interpretation, Statistical ; *Phylogeny ; Primulaceae/*classification/*genetics ; *Software ; }, abstract = {The Swofford-Olsen-Waddell-Hillis (SOWH) test evaluates statistical support for incongruent phylogenetic topologies. It is commonly applied to determine if the maximum likelihood tree in a phylogenetic analysis is significantly different than an alternative hypothesis. The SOWH test compares the observed difference in log-likelihood between two topologies to a null distribution of differences in log-likelihood generated by parametric resampling. The test is a well-established phylogenetic method for topology testing, but it is sensitive to model misspecification, it is computationally burdensome to perform, and its implementation requires the investigator to make several decisions that each have the potential to affect the outcome of the test. We analyzed the effects of multiple factors using seven data sets to which the SOWH test was previously applied. These factors include a number of sample replicates, likelihood software, the introduction of gaps to simulated data, the use of distinct models of evolution for data simulation and likelihood inference, and a suggested test correction wherein an unresolved "zero-constrained" tree is used to simulate sequence data. To facilitate these analyses and future applications of the SOWH test, we wrote SOWHAT, a program that automates the SOWH test. We find that inadequate bootstrap sampling can change the outcome of the SOWH test. The results also show that using a zero-constrained tree for data simulation can result in a wider null distribution and higher p-values, but does not change the outcome of the SOWH test for most of the data sets tested here. These results will help others implement and evaluate the SOWH test and allow us to provide recommendations for future applications of the SOWH test. SOWHAT is available for download from https://github.com/josephryan/SOWHAT.}, } @article {pmid26228545, year = {2015}, author = {Vega, FE and Brown, SM and Chen, H and Shen, E and Nair, MB and Ceja-Navarro, JA and Brodie, EL and Infante, F and Dowd, PF and Pain, A}, title = {Draft genome of the most devastating insect pest of coffee worldwide: the coffee berry borer, Hypothenemus hampei.}, journal = {Scientific reports}, volume = {5}, number = {}, pages = {12525}, pmid = {26228545}, issn = {2045-2322}, mesh = {ATP-Binding Cassette Transporters/genetics/metabolism ; Animals ; Caffeine/pharmacokinetics ; Carboxylesterase/genetics/metabolism ; Coffea ; Crops, Agricultural ; Cytochrome P-450 Enzyme System/genetics/metabolism ; Enzymes/genetics/metabolism ; Female ; Gene Transfer, Horizontal ; *Genome, Insect ; Inactivation, Metabolic ; Insect Proteins/*genetics/metabolism ; Multigene Family ; Phylogeny ; RNA, Untranslated ; Weevils/drug effects/*genetics/physiology ; }, abstract = {The coffee berry borer, Hypothenemus hampei, is the most economically important insect pest of coffee worldwide. We present an analysis of the draft genome of the coffee berry borer, the third genome for a Coleopteran species. The genome size is ca. 163 Mb with 19,222 predicted protein-coding genes. Analysis was focused on genes involved in primary digestion as well as gene families involved in detoxification of plant defense molecules and insecticides, such as carboxylesterases, cytochrome P450, gluthathione S-transferases, ATP-binding cassette transporters, and a gene that confers resistance to the insecticide dieldrin. A broad range of enzymes capable of degrading complex polysaccharides were identified. We also evaluated the pathogen defense system and found homologs to antimicrobial genes reported in the Drosophila genome. Ten cases of horizontal gene transfer were identified with evidence for expression, integration into the H. hampei genome, and phylogenetic evidence that the sequences are more closely related to bacterial rather than eukaryotic genes. The draft genome analysis broadly expands our knowledge on the biology of a devastating tropical insect pest and suggests new pest management strategies.}, } @article {pmid26227803, year = {2015}, author = {Byers, JE and Smith, RS and Pringle, JM and Clark, GF and Gribben, PE and Hewitt, CL and Inglis, GJ and Johnston, EL and Ruiz, GM and Stachowicz, JJ and Bishop, MJ}, title = {Invasion Expansion: Time since introduction best predicts global ranges of marine invaders.}, journal = {Scientific reports}, volume = {5}, number = {}, pages = {12436}, pmid = {26227803}, issn = {2045-2322}, mesh = {Animals ; Aquatic Organisms ; Australia ; Databases, Factual ; Ecosystem ; Environment ; *Introduced Species ; *Invertebrates/physiology ; Marine Biology ; New Zealand ; Ships ; Time Factors ; United States ; }, abstract = {Strategies for managing biological invasions are often based on the premise that characteristics of invading species and the invaded environment are key predictors of the invader's distribution. Yet, for either biological traits or environmental characteristics to explain distribution, adequate time must have elapsed for species to spread to all potential habitats. We compiled and analyzed a database of natural history and ecological traits of 138 coastal marine invertebrate species, the environmental conditions at sites to which they have been introduced, and their date of first introduction. We found that time since introduction explained the largest fraction (20%) of the variability in non-native range size, while traits of the species and environmental variables had significant, but minimal, influence on non-native range size. The positive relationship between time since introduction and range size indicates that non-native marine invertebrate species are not at equilibrium and are still spreading, posing a major challenge for management of coastal ecosystems.}, } @article {pmid26225933, year = {2015}, author = {Kidd, AM and Monz, C and D'Antonio, A and Manning, RE and Reigner, N and Goonan, KA and Jacobi, C}, title = {The effect of minimum impact education on visitor spatial behavior in parks and protected areas: An experimental investigation using GPS-based tracking.}, journal = {Journal of environmental management}, volume = {162}, number = {}, pages = {53-62}, doi = {10.1016/j.jenvman.2015.07.007}, pmid = {26225933}, issn = {1095-8630}, mesh = {Conservation of Natural Resources/*methods ; Ecology/*education ; Education, Nonprofessional/*methods ; Geographic Information Systems ; Humans ; Knowledge ; Maine ; Recreation/*psychology ; Spatial Analysis ; Spatial Behavior ; Travel ; }, abstract = {The unmanaged impacts of recreation and tourism can often result in unacceptable changes in resource conditions and quality of the visitor experience. Minimum impact visitor education programs aim to reduce the impacts of recreation by altering visitor behaviors. Specifically, education seeks to reduce impacts resulting from lack of knowledge both about the consequences of one's actions and impact-minimizing best practices. In this study, three different on-site minimum impact education strategies ("treatments") and a control condition were applied on the trails and summit area of Sargent Mountain in Acadia National Park, Maine. Treatment conditions were designed to encourage visitors to stay on marked trails and minimize off-trail travel. Treatments included a message delivered via personal contact, and both an ecological-based message and an amenity-based message posted on signs located alongside the trail. A control condition of current trail markings and directional signs was also assessed. The efficacy of the messaging was evaluated through the use of Global Positioning System (GPS) tracking of visitor spatial behavior on/off trails. Spatial analysis of GPS tracks revealed statistically significant differences among treatments, with the personal contact treatment yielding significantly less dispersion of visitors on the mountain summit. Results also indicate that the signs deployed in the study were ineffective at limiting off-trail use beyond what can be accomplished with trail markers and directional signs. These findings suggest that personal contact by a uniformed ranger or volunteer may be the most effective means of message delivery for on-site minimum impact education.}, } @article {pmid26224734, year = {2015}, author = {Palacios, JA and Wakeley, J and Ramachandran, S}, title = {Bayesian Nonparametric Inference of Population Size Changes from Sequential Genealogies.}, journal = {Genetics}, volume = {201}, number = {1}, pages = {281-304}, pmid = {26224734}, issn = {1943-2631}, mesh = {Bayes Theorem ; Black People/*genetics ; Computational Biology/*methods ; Genome, Human ; Human Migration ; Humans ; Markov Chains ; Models, Genetic ; *Pedigree ; Population Density ; White People/*genetics ; }, abstract = {Sophisticated inferential tools coupled with the coalescent model have recently emerged for estimating past population sizes from genomic data. Recent methods that model recombination require small sample sizes, make constraining assumptions about population size changes, and do not report measures of uncertainty for estimates. Here, we develop a Gaussian process-based Bayesian nonparametric method coupled with a sequentially Markov coalescent model that allows accurate inference of population sizes over time from a set of genealogies. In contrast to current methods, our approach considers a broad class of recombination events, including those that do not change local genealogies. We show that our method outperforms recent likelihood-based methods that rely on discretization of the parameter space. We illustrate the application of our method to multiple demographic histories, including population bottlenecks and exponential growth. In simulation, our Bayesian approach produces point estimates four times more accurate than maximum-likelihood estimation (based on the sum of absolute differences between the truth and the estimated values). Further, our method's credible intervals for population size as a function of time cover 90% of true values across multiple demographic scenarios, enabling formal hypothesis testing about population size differences over time. Using genealogies estimated with ARGweaver, we apply our method to European and Yoruban samples from the 1000 Genomes Project and confirm key known aspects of population size history over the past 150,000 years.}, } @article {pmid26224325, year = {2016}, author = {Favaro, S and Nipoti, B and Teh, YW}, title = {Rediscovery of Good-Turing estimators via Bayesian nonparametrics.}, journal = {Biometrics}, volume = {72}, number = {1}, pages = {136-145}, doi = {10.1111/biom.12366}, pmid = {26224325}, issn = {1541-0420}, mesh = {Algorithms ; *Bayes Theorem ; Computer Simulation ; Data Interpretation, Statistical ; *Expressed Sequence Tags ; *Machine Learning ; *Models, Statistical ; Pattern Recognition, Automated/*methods ; Sequence Analysis, DNA/*methods ; }, abstract = {The problem of estimating discovery probabilities originated in the context of statistical ecology, and in recent years it has become popular due to its frequent appearance in challenging applications arising in genetics, bioinformatics, linguistics, designs of experiments, machine learning, etc. A full range of statistical approaches, parametric and nonparametric as well as frequentist and Bayesian, has been proposed for estimating discovery probabilities. In this article, we investigate the relationships between the celebrated Good-Turing approach, which is a frequentist nonparametric approach developed in the 1940s, and a Bayesian nonparametric approach recently introduced in the literature. Specifically, under the assumption of a two parameter Poisson-Dirichlet prior, we show that Bayesian nonparametric estimators of discovery probabilities are asymptotically equivalent, for a large sample size, to suitably smoothed Good-Turing estimators. As a by-product of this result, we introduce and investigate a methodology for deriving exact and asymptotic credible intervals to be associated with the Bayesian nonparametric estimators of discovery probabilities. The proposed methodology is illustrated through a comprehensive simulation study and the analysis of Expressed Sequence Tags data generated by sequencing a benchmark complementary DNA library.}, } @article {pmid26220934, year = {2015}, author = {Schaefke, B and Wang, TY and Wang, CY and Li, WH}, title = {Gains and Losses of Transcription Factor Binding Sites in Saccharomyces cerevisiae and Saccharomyces paradoxus.}, journal = {Genome biology and evolution}, volume = {7}, number = {8}, pages = {2245-2257}, pmid = {26220934}, issn = {1759-6653}, mesh = {Binding Sites ; *Evolution, Molecular ; Gene Expression ; *Promoter Regions, Genetic ; Saccharomyces/*genetics/metabolism ; Saccharomyces cerevisiae/*genetics/metabolism ; Transcription Factors/*metabolism ; }, abstract = {Gene expression evolution occurs through changes in cis- or trans-regulatory elements or both. Interactions between transcription factors (TFs) and their binding sites (TFBSs) constitute one of the most important points where these two regulatory components intersect. In this study, we investigated the evolution of TFBSs in the promoter regions of different Saccharomyces strains and species. We divided the promoter of a gene into the proximal region and the distal region, which are defined, respectively, as the 200-bp region upstream of the transcription starting site and as the 200-bp region upstream of the proximal region. We found that the predicted TFBSs in the proximal promoter regions tend to be evolutionarily more conserved than those in the distal promoter regions. Additionally, Saccharomyces cerevisiae strains used in the fermentation of alcoholic drinks have experienced more TFBS losses than gains compared with strains from other environments (wild strains, laboratory strains, and clinical strains). We also showed that differences in TFBSs correlate with the cis component of gene expression evolution between species (comparing S. cerevisiae and its sister species Saccharomyces paradoxus) and within species (comparing two closely related S. cerevisiae strains).}, } @article {pmid26220359, year = {2016}, author = {Mueller, JC and Kuhl, H and Timmermann, B and Kempenaers, B}, title = {Characterization of the genome and transcriptome of the blue tit Cyanistes caeruleus: polymorphisms, sex-biased expression and selection signals.}, journal = {Molecular ecology resources}, volume = {16}, number = {2}, pages = {549-561}, doi = {10.1111/1755-0998.12450}, pmid = {26220359}, issn = {1755-0998}, mesh = {Animals ; Databases, Genetic ; Databases, Nucleic Acid ; Female ; *Gene Expression Profiling ; *Genetic Variation ; *Genome ; Internet ; Male ; Passeriformes/*genetics ; Polymorphism, Single Nucleotide ; RNA, Messenger/analysis ; Sequence Analysis, DNA ; Sex Factors ; }, abstract = {Decoding genomic sequences and determining their variation within populations has potential to reveal adaptive processes and unravel the genetic basis of ecologically relevant trait variation within a species. The blue tit Cyanistes caeruleus--a long-time ecological model species--has been used to investigate fitness consequences of variation in mating and reproductive behaviour. However, very little is known about the underlying genetic changes due to natural and sexual selection in the genome of this songbird. As a step to bridge this gap, we assembled the first draft genome of a single blue tit, mapped the transcriptome of five females and five males to this reference, identified genomewide variants and performed sex-differential expression analysis in the gonads, brain and other tissues. In the gonads, we found a high number of sex-biased genes, and of those, a similar proportion were sex-limited (genes only expressed in one sex) in males and females. However, in the brain, the proportion of female-limited genes within the female-biased gene category (82%) was substantially higher than the proportion of male-limited genes within the male-biased category (6%). This suggests a predominant on-off switching mechanism for the female-limited genes. In addition, most male-biased genes were located on the Z-chromosome, indicating incomplete dosage compensation for the male-biased genes. We called more than 500,000 SNPs from the RNA-seq data. Heterozygote detection in the single reference individual was highly congruent between DNA-seq and RNA-seq calling. Using information from these polymorphisms, we identified potential selection signals in the genome. We list candidate genes which can be used for further sequencing and detailed selection studies, including genes potentially related to meiotic drive evolution. A public genome browser of the blue tit with the described information is available at http://public-genomes-ngs.molgen.mpg.de.}, } @article {pmid26218496, year = {2015}, author = {Holt, J and Bennett, KB and Flach, JM}, title = {Emergent features and perceptual objects: re-examining fundamental principles in analogical display design.}, journal = {Ergonomics}, volume = {58}, number = {12}, pages = {1960-1973}, doi = {10.1080/00140139.2015.1049217}, pmid = {26218496}, issn = {1366-5847}, mesh = {Adult ; *Data Display ; Decision Support Techniques ; Equipment Design ; *Ergonomics ; Female ; Humans ; Male ; *Perception ; Young Adult ; }, abstract = {Two sets of design principles for analogical visual displays, based on the concepts of emergent features and perceptual objects, are described. An interpretation of previous empirical findings for three displays (bar graph, polar graphic, alphanumeric) is provided from both perspectives. A fourth display (configural coordinate) was designed using principles of ecological interface design (i.e. direct perception). An experiment was conducted to evaluate performance (accuracy and latency of state identification) with these four displays. Numerous significant effects were obtained and a clear rank ordering of performance emerged (from best to worst): configural coordinate, bar graph, alphanumeric and polar graphic. These findings are consistent with principles of design based on emergent features; they are inconsistent with principles based on perceptual objects. Some limitations of the configural coordinate display are discussed and a redesign is provided. Practitioner Summary: Principles of ecological interface design, which emphasise the quality of very specific mappings between domain, display and observer constraints, are described; these principles are applicable to the design of all analogical graphical displays.}, } @article {pmid26216993, year = {2015}, author = {Helb, DA and Tetteh, KK and Felgner, PL and Skinner, J and Hubbard, A and Arinaitwe, E and Mayanja-Kizza, H and Ssewanyana, I and Kamya, MR and Beeson, JG and Tappero, J and Smith, DL and Crompton, PD and Rosenthal, PJ and Dorsey, G and Drakeley, CJ and Greenhouse, B}, title = {Novel serologic biomarkers provide accurate estimates of recent Plasmodium falciparum exposure for individuals and communities.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {112}, number = {32}, pages = {E4438-47}, pmid = {26216993}, issn = {1091-6490}, support = {OCCU024421//PHS HHS/United States ; U19 AI089674/AI/NIAID NIH HHS/United States ; U19AI089674/AI/NIAID NIH HHS/United States ; U19 AI089686/AI/NIAID NIH HHS/United States ; //PEPFAR/United States ; }, mesh = {Antibodies, Protozoan/immunology ; Antibody Formation/immunology ; Antibody Specificity/immunology ; Antigens, Protozoan/immunology ; Biomarkers/*blood ; Child ; Child, Preschool ; Female ; Gene Ontology ; Geography ; Humans ; Incidence ; Malaria, Falciparum/*blood/epidemiology/immunology/*parasitology ; Male ; Mali/epidemiology ; Plasmodium falciparum/genetics/immunology/*physiology ; ROC Curve ; *Residence Characteristics ; Treatment Outcome ; Uganda/epidemiology ; }, abstract = {Tools to reliably measure Plasmodium falciparum (Pf) exposure in individuals and communities are needed to guide and evaluate malaria control interventions. Serologic assays can potentially produce precise exposure estimates at low cost; however, current approaches based on responses to a few characterized antigens are not designed to estimate exposure in individuals. Pf-specific antibody responses differ by antigen, suggesting that selection of antigens with defined kinetic profiles will improve estimates of Pf exposure. To identify novel serologic biomarkers of malaria exposure, we evaluated responses to 856 Pf antigens by protein microarray in 186 Ugandan children, for whom detailed Pf exposure data were available. Using data-adaptive statistical methods, we identified combinations of antibody responses that maximized information on an individual's recent exposure. Responses to three novel Pf antigens accurately classified whether an individual had been infected within the last 30, 90, or 365 d (cross-validated area under the curve = 0.86-0.93), whereas responses to six antigens accurately estimated an individual's malaria incidence in the prior year. Cross-validated incidence predictions for individuals in different communities provided accurate stratification of exposure between populations and suggest that precise estimates of community exposure can be obtained from sampling a small subset of that community. In addition, serologic incidence predictions from cross-sectional samples characterized heterogeneity within a community similarly to 1 y of continuous passive surveillance. Development of simple ELISA-based assays derived from the successful selection strategy outlined here offers the potential to generate rich epidemiologic surveillance data that will be widely accessible to malaria control programs.}, } @article {pmid26215889, year = {2015}, author = {Paillard, L and Jones, KL and Evans, AL and Berret, J and Jacquet, M and Lienhard, R and Bouzelboudjen, M and Arnemo, JM and Swenson, JE and Voordouw, MJ}, title = {Serological signature of tick-borne pathogens in Scandinavian brown bears over two decades.}, journal = {Parasites & vectors}, volume = {8}, number = {}, pages = {398}, pmid = {26215889}, issn = {1756-3305}, mesh = {Animals ; Antibodies, Bacterial/*blood ; Antibodies, Viral/*blood ; Arachnid Vectors/microbiology ; Borrelia burgdorferi/*immunology/isolation & purification ; Encephalitis Viruses, Tick-Borne/*immunology/isolation & purification ; Encephalitis, Tick-Borne/epidemiology/veterinary/virology ; Female ; Humans ; Incidence ; Ixodes/microbiology ; Lyme Disease/epidemiology/microbiology/veterinary ; Male ; Middle Aged ; Prevalence ; Scandinavian and Nordic Countries/epidemiology ; Tick-Borne Diseases/epidemiology/microbiology/*veterinary ; Ursidae/*microbiology ; }, abstract = {BACKGROUND: Anthropogenic disturbances are changing the geographic distribution of ticks and tick-borne diseases. Over the last few decades, the tick Ixodes ricinus has expanded its range and abundance considerably in northern Europe. Concurrently, the incidence of tick-borne diseases, such as Lyme borreliosis and tick-borne encephalitis, has increased in the human populations of the Scandinavian countries.

METHODS: Wildlife populations can serve as sentinels for changes in the distribution of tick-borne diseases. We used serum samples from a long-term study on the Scandinavian brown bear, Ursus arctos, and standard immunological methods to test whether exposure to Borrelia burgdorferi sensu lato, the causative agent of Lyme borreliosis, and tick-borne encephalitis virus (TBEV) had increased over time. Bears had been sampled over a period of 18 years (1995-2012) from a southern area, where Ixodes ricinus ticks are present, and a northern area where ticks are uncommon or absent.

RESULTS: Bears had high levels of IgG antibodies against B. burgdorferi sensu lato but not TBEV. Bears at the southern area had higher values of anti-Borrelia IgG antibodies than bears at the northern area. Over the duration of the study, the value of anti-Borrelia IgG antibodies increased in the southern area but not the northern area. Anti-Borrelia IgG antibodies increased with the age of the bear but declined in the oldest age classes.

CONCLUSIONS: Our study is consistent with the view that ticks and tick-borne pathogens are expanding their abundance and prevalence in Scandinavia. Long-term serological monitoring of large mammals can provide insight into how anthropogenic disturbances are changing the distribution of ticks and tick-borne diseases.}, } @article {pmid26215638, year = {2015}, author = {Wang, Y and Wu, N and Liu, J and Wu, Z and Dong, D}, title = {FusionCancer: a database of cancer fusion genes derived from RNA-seq data.}, journal = {Diagnostic pathology}, volume = {10}, number = {}, pages = {131}, pmid = {26215638}, issn = {1746-1596}, mesh = {*Databases, Genetic ; High-Throughput Nucleotide Sequencing ; Humans ; Neoplasms/*genetics ; Oncogene Fusion/*genetics ; RNA/*genetics ; }, abstract = {BACKGROUND: Fusion genes are chimeric results originated from previous separate genes with aberrant functions. The resulting protein products may lead to abnormal status of expression levels, functions and action sites, which in return may cause the abnormal proliferation of cells and cancer development.

RESULTS: With the emergence of next-generation sequencing technology, RNA-seq has spurred gene fusion discovery in various cancer types. In this work, we compiled 591 recently published RNA-seq datasets in 15 kinds of human cancer, and the gene fusion events were comprehensively identified. Based on the results, a database was developed for gene fusion in cancers (FusionCancer), with the attempt to provide a user-friendly utility for the cancer research community. A flexible query engine has been developed for the acquisition of annotated information of cancer fusion genes, which would help users to determine the chimera events leading to functional changes. FusionCancer can be accessible at the following hyperlink website: http://donglab.ecnu.edu.cn/databases/FusionCancer/

CONCLUSION: To the best of our knowledge, FusionCancer is the first comprehensive fusion gene database derived only from cancer RNA-seq data.}, } @article {pmid26205258, year = {2015}, author = {Ding, C and Chen, T and Yang, Y and Liu, S and Yan, K and Yue, X and Zhang, H and Xiang, Y and An, L and Chen, S}, title = {Molecular cloning and characterization of an S-adenosylmethionine synthetase gene from Chorispora bungeana.}, journal = {Gene}, volume = {572}, number = {2}, pages = {205-213}, doi = {10.1016/j.gene.2015.07.062}, pmid = {26205258}, issn = {1879-0038}, mesh = {Adenosine Triphosphate/metabolism ; Binding Sites ; Brassicaceae/*enzymology/genetics ; Cloning, Molecular/*methods ; Computational Biology/methods ; Flowers/genetics/metabolism ; Methionine Adenosyltransferase/chemistry/*genetics/*metabolism ; Nuclear Export Signals/genetics ; Plant Proteins/chemistry/genetics/metabolism ; Plant Roots/genetics/metabolism ; Promoter Regions, Genetic ; }, abstract = {S-adenosylmethionine synthetase (SAMS) catalyzes the formation of S-adenosylmethionine (SAM) which is a molecule essential for polyamines and ethylene biosynthesis, methylation modifications of protein, DNA and lipids. SAMS also plays an important role in abiotic stress response. Chorispora bungeana (C. bungeana) is an alpine subnival plant species which possesses strong tolerance to cold stress. Here, we cloned and characterized an S-adenosylmethionine synthetase gene, CbSAMS (C. bungeana S-adenosylmethionine synthetase), from C. bungeana, which encodes a protein of 393 amino acids containing a methionine binding motif GHPDK, an ATP binding motif GAGDQG and a phosphate binding motif GGGAFSGDK. Furthermore, an NES (nuclear export signal) peptide was identified through bioinformatics analysis. To explore the CbSAMS gene expression regulation, we isolated the promoter region of CbSAMS gene 1919bp upstream the ATG start codon, CbSAMSp, and analyzed its cis-acting elements by bioinformatics method. It was revealed that a transcription start site located at 320 bp upstream the ATG start codon and cis-acting elements related to light, ABA, auxin, ethylene, MeJA, low temperature and drought had been found in the CbSAMSp sequence. The gene expression pattern of CbSAMS was then analyzed by TR-qPCR and GUS assay method. The result showed that CbSAMS is expressed in all examined tissues including callus, roots, petioles, leaves, and flowers with a significant higher expression level in roots and flowers. Furthermore, the expression level of CbSAMS was induced by low temperature, ethylene and NaCl. Subcellular localization revealed that CbSAMS was located in the cytoplasm and nucleus but has a significant higher level in the nucleus. These results indicated a potential role of CbSAMS in abiotic stresses and plant growth in C. bungeana.}, } @article {pmid26203877, year = {2015}, author = {Prager, K}, title = {Agri-environmental collaboratives as bridging organisations in landscape management.}, journal = {Journal of environmental management}, volume = {161}, number = {}, pages = {375-384}, doi = {10.1016/j.jenvman.2015.07.027}, pmid = {26203877}, issn = {1095-8630}, mesh = {Agriculture/*organization & administration ; Conservation of Natural Resources/*economics/methods ; *Cooperative Behavior ; Ecosystem ; Financing, Government ; Germany ; Humans ; Knowledge Management ; Netherlands ; }, abstract = {In recent years, landscape and its management has become a focus of policies and academic conceptualisation. Landscape is understood as a concept of interconnected natural and human systems. Its management must take into account the dynamic interdependencies and diverging interests of various stakeholders at different levels. Bridging organisations can provide an arena for trust-building, conflict resolution, learning and collaboration between relevant stakeholders. This paper draws on two strands of literature - landscape governance and co-management of social-ecological systems - to investigate the contributions of agri-environmental collaboratives (AEC) to sustainable landscape management. Based on data from 41 interviews with key informants and AEC members in Germany and the Netherlands, six fields of contributions were identified: policy implementation and service provision; coordination and mediation; awareness raising and behaviour change; care for 'everyday' landscapes; maintenance and protection of landscapes (including species and habitats); and income generation and economic benefits. Some of the contributions evolve around the specific role of AEC as bridging organisations, but other contributions such as economic benefits emerge beyond this analytical lens. The paper therefore emphasises holistic, bottom up assessment of AEC contributions and argues that governments should support such organisations through i) funding for facilitators and ii) funding for impact monitoring and data management.}, } @article {pmid26203465, year = {2014}, author = {Lopez, D and Gunasekaran, M and Murugan, BS and Kaur, H and Abbas, KM}, title = {Spatial Big Data Analytics of Influenza Epidemic in Vellore, India.}, journal = {Proceedings : ... IEEE International Conference on Big Data. IEEE International Conference on Big Data}, volume = {2014}, number = {}, pages = {19-24}, pmid = {26203465}, support = {R01 GM109718/GM/NIGMS NIH HHS/United States ; }, abstract = {The study objective is to develop a big spatial data model to predict the epidemiological impact of influenza in Vellore, India. Large repositories of geospatial and health data provide vital statistics on surveillance and epidemiological metrics, and valuable insight into the spatiotemporal determinants of disease and health. The integration of these big data sources and analytics to assess risk factors and geospatial vulnerability can assist to develop effective prevention and control strategies for influenza epidemics and optimize allocation of limited public health resources. We used the spatial epidemiology data of the HIN1 epidemic collected at the National Informatics Center during 2009-2010 in Vellore. We developed an ecological niche model based on geographically weighted regression for predicting influenza epidemics in Vellore, India during 2013-2014. Data on rainfall, temperature, wind speed, humidity and population are included in the geographically weighted regression analysis. We inferred positive correlations for H1N1 influenza prevalence with rainfall and wind speed, and negative correlations for H1N1 influenza prevalence with temperature and humidity. We evaluated the results of the geographically weighted regression model in predicting the spatial distribution of the influenza epidemic during 2013-2014.}, } @article {pmid26202430, year = {2015}, author = {Lee, S and Barron, MG}, title = {Development of 3D-QSAR Model for Acetylcholinesterase Inhibitors Using a Combination of Fingerprint, Molecular Docking, and Structure-Based Pharmacophore Approaches.}, journal = {Toxicological sciences : an official journal of the Society of Toxicology}, volume = {148}, number = {1}, pages = {60-70}, doi = {10.1093/toxsci/kfv160}, pmid = {26202430}, issn = {1096-0929}, mesh = {Acetylcholinesterase/chemistry/metabolism ; Animals ; Artificial Intelligence ; Binding Sites ; Catalytic Domain ; Cholinesterase Inhibitors/chemistry/metabolism/*pharmacology ; Computational Biology ; Databases, Protein ; *Expert Systems ; GPI-Linked Proteins/antagonists & inhibitors/chemistry/metabolism ; Humans ; Imaging, Three-Dimensional ; Insecticides/chemistry/metabolism/*pharmacology ; Ligands ; *Models, Molecular ; Molecular Conformation ; Molecular Docking Simulation ; Nerve Tissue Proteins/*antagonists & inhibitors/chemistry/metabolism ; Nootropic Agents/chemistry/metabolism/*pharmacology ; Peptide Mapping ; Quantitative Structure-Activity Relationship ; }, abstract = {Acetylcholinesterase (AChE), a serine hydrolase vital for regulating the neurotransmitter acetylcholine in animals, has been used as a target for drugs and pesticides. With the increasing availability of AChE crystal structures, with or without ligands bound, structure-based approaches have been successfully applied to AChE inhibitors (AChEIs). The major limitation of these approaches has been the small applicability domain due to the lack of structural diversity in the training set. In this study, we developed a 3 dimensional quantitative structure-activity relationship (3D-QSAR) for inhibitory activity of 89 reversible and irreversible AChEIs including drugs and insecticides. A 3D-fingerprint descriptor encoding protein-ligand interactions was developed using molecular docking and structure-based pharmacophore to rationalize the structural requirements responsible for the activity of these compounds. The obtained 3D-QSAR model exhibited high correlation value (R(2) = 0.93) and low mean absolute error (MAE = 0.32 log units) for the training set (n = 63). The model was predictive across a range of structures as shown by the leave-one-out cross-validated correlation coefficient (Q(2) = 0.89) and external validation results (n = 26, R(2) = 0.89, and MAE = 0.38 log units). The model revealed that the compounds with high inhibition potency had proper conformation in the active site gorge and interacted with key amino acid residues, in particular Trp84 and Phe330 at the catalytic anionic site, Trp279 at the peripheral anionic site, and Gly118, Gly119, and Ala201 at the oxyanion hole. The resulting universal 3D-QSAR model provides insight into the multiple molecular interactions determining AChEI potency that may guide future chemical design and regulation of toxic AChEIs.}, } @article {pmid26200753, year = {2015}, author = {Pierneef, R and Cronje, L and Bezuidt, O and Reva, ON}, title = {Pre_GI: a global map of ontological links between horizontally transferred genomic islands in bacterial and archaeal genomes.}, journal = {Database : the journal of biological databases and curation}, volume = {2015}, number = {}, pages = {bav058}, pmid = {26200753}, issn = {1758-0463}, mesh = {Archaea/*genetics ; Bacteria/*genetics ; *Databases, Nucleic Acid ; *Gene Ontology ; *Gene Transfer, Horizontal ; *Genome, Archaeal ; *Genome, Bacterial ; }, abstract = {The Predicted Genomic Islands database (Pre_GI) is a comprehensive repository of prokaryotic genomic islands (islands, GIs) freely accessible at http://pregi.bi.up.ac.za/index.php. Pre_GI, Version 2015, catalogues 26 744 islands identified in 2407 bacterial/archaeal chromosomes and plasmids. It provides an easy-to-use interface which allows users the ability to query against the database with a variety of fields, parameters and associations. Pre_GI is constructed to be a web-resource for the analysis of ontological roads between islands and cartographic analysis of the global fluxes of mobile genetic elements through bacterial and archaeal taxonomic borders. Comparison of newly identified islands against Pre_GI presents an alternative avenue to identify their ontology, origin and relative time of acquisition. Pre_GI aims to aid research on horizontal transfer events and materials through providing data and tools for holistic investigation of migration of genes through ecological niches and taxonomic boundaries.}, } @article {pmid26199233, year = {2015}, author = {Gray, MM and Parmenter, MD and Hogan, CA and Ford, I and Cuthbert, RJ and Ryan, PG and Broman, KW and Payseur, BA}, title = {Genetics of Rapid and Extreme Size Evolution in Island Mice.}, journal = {Genetics}, volume = {201}, number = {1}, pages = {213-228}, pmid = {26199233}, issn = {1943-2631}, support = {R01 GM100426/GM/NIGMS NIH HHS/United States ; F32 GM090685/GM/NIGMS NIH HHS/United States ; T32 GM007133/GM/NIGMS NIH HHS/United States ; R01 GM100426A/GM/NIGMS NIH HHS/United States ; 1F32GM090685/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Biological Evolution ; Body Size/*genetics ; Chromosome Mapping/*methods ; Crosses, Genetic ; Female ; Islands ; Male ; Mice/*genetics/*growth & development ; *Quantitative Trait Loci ; }, abstract = {Organisms on islands provide a revealing window into the process of adaptation. Populations that colonize islands often evolve substantial differences in body size from their mainland relatives. Although the ecological drivers of this phenomenon have received considerable attention, its genetic basis remains poorly understood. We use house mice (subspecies: Mus musculus domesticus) from remote Gough Island to provide a genetic portrait of rapid and extreme size evolution. In just a few hundred generations, Gough Island mice evolved the largest body size among wild house mice from around the world. Through comparisons with a smaller-bodied wild-derived strain from the same subspecies (WSB/EiJ), we demonstrate that Gough Island mice achieve their exceptional body weight primarily by growing faster during the 6 weeks after birth. We use genetic mapping in large F(2) intercrosses between Gough Island mice and WSB/EiJ to identify 19 quantitative trait loci (QTL) responsible for the evolution of 16-week weight trajectories: 8 QTL for body weight and 11 QTL for growth rate. QTL exhibit modest effects that are mostly additive. We conclude that body size evolution on islands can be genetically complex, even when substantial size changes occur rapidly. In comparisons to published studies of laboratory strains of mice that were artificially selected for divergent body sizes, we discover that the overall genetic profile of size evolution in nature and in the laboratory is similar, but many contributing loci are distinct. Our results underscore the power of genetically characterizing the entire growth trajectory in wild populations and lay the foundation necessary for identifying the mutations responsible for extreme body size evolution in nature.}, } @article {pmid26194794, year = {2015}, author = {Sickel, W and Ankenbrand, MJ and Grimmer, G and Holzschuh, A and Härtel, S and Lanzen, J and Steffan-Dewenter, I and Keller, A}, title = {Increased efficiency in identifying mixed pollen samples by meta-barcoding with a dual-indexing approach.}, journal = {BMC ecology}, volume = {15}, number = {}, pages = {20}, pmid = {26194794}, issn = {1472-6785}, mesh = {Animals ; Bees ; *DNA Barcoding, Taxonomic ; DNA Primers/*genetics ; Databases, Factual ; *High-Throughput Nucleotide Sequencing ; Pollen/*classification ; }, abstract = {BACKGROUND: Meta-barcoding of mixed pollen samples constitutes a suitable alternative to conventional pollen identification via light microscopy. Current approaches however have limitations in practicability due to low sample throughput and/or inefficient processing methods, e.g. separate steps for amplification and sample indexing.

RESULTS: We thus developed a new primer-adapter design for high throughput sequencing with the Illumina technology that remedies these issues. It uses a dual-indexing strategy, where sample-specific combinations of forward and reverse identifiers attached to the barcode marker allow high sample throughput with a single sequencing run. It does not require further adapter ligation steps after amplification. We applied this protocol to 384 pollen samples collected by solitary bees and sequenced all samples together on a single Illumina MiSeq v2 flow cell. According to rarefaction curves, 2,000-3,000 high quality reads per sample were sufficient to assess the complete diversity of 95% of the samples. We were able to detect 650 different plant taxa in total, of which 95% were classified at the species level. Together with the laboratory protocol, we also present an update of the reference database used by the classifier software, which increases the total number of covered global plant species included in the database from 37,403 to 72,325 (93% increase).

CONCLUSIONS: This study thus offers improvements for the laboratory and bioinformatical workflow to existing approaches regarding data quantity and quality as well as processing effort and cost-effectiveness. Although only tested for pollen samples, it is furthermore applicable to other research questions requiring plant identification in mixed and challenging samples.}, } @article {pmid26194356, year = {2015}, author = {Copetti, D and Zhang, J and El Baidouri, M and Gao, D and Wang, J and Barghini, E and Cossu, RM and Angelova, A and Maldonado L, CE and Roffler, S and Ohyanagi, H and Wicker, T and Fan, C and Zuccolo, A and Chen, M and Costa de Oliveira, A and Han, B and Henry, R and Hsing, YI and Kurata, N and Wang, W and Jackson, SA and Panaud, O and Wing, RA}, title = {RiTE database: a resource database for genus-wide rice genomics and evolutionary biology.}, journal = {BMC genomics}, volume = {16}, number = {1}, pages = {538}, pmid = {26194356}, issn = {1471-2164}, mesh = {DNA Transposable Elements/genetics ; *Databases, Genetic ; *Evolution, Molecular ; *Genome, Plant ; Genomics ; Oryza/*genetics ; Software ; }, abstract = {BACKGROUND: Comparative evolutionary analysis of whole genomes requires not only accurate annotation of gene space, but also proper annotation of the repetitive fraction which is often the largest component of most if not all genomes larger than 50 kb in size.

RESULTS: Here we present the Rice TE database (RiTE-db)--a genus-wide collection of transposable elements and repeated sequences across 11 diploid species of the genus Oryza and the closely-related out-group Leersia perrieri. The database consists of more than 170,000 entries divided into three main types: (i) a classified and curated set of publicly-available repeated sequences, (ii) a set of consensus assemblies of highly-repetitive sequences obtained from genome sequencing surveys of 12 species; and (iii) a set of full-length TEs, identified and extracted from 12 whole genome assemblies.

CONCLUSIONS: This is the first report of a repeat dataset that spans the majority of repeat variability within an entire genus, and one that includes complete elements as well as unassembled repeats. The database allows sequence browsing, downloading, and similarity searches. Because of the strategy adopted, the RiTE-db opens a new path to unprecedented direct comparative studies that span the entire nuclear repeat content of 15 million years of Oryza diversity.}, } @article {pmid26192322, year = {2015}, author = {Williams, NE and Thomas, TA and Dunbar, M and Eagle, N and Dobra, A}, title = {Measures of Human Mobility Using Mobile Phone Records Enhanced with GIS Data.}, journal = {PloS one}, volume = {10}, number = {7}, pages = {e0133630}, pmid = {26192322}, issn = {1932-6203}, support = {R24HD042828/HD/NICHD NIH HHS/United States ; P2C HD042828/HD/NICHD NIH HHS/United States ; R00HD067587/HD/NICHD NIH HHS/United States ; R24 HD042828/HD/NICHD NIH HHS/United States ; R00 HD067587/HD/NICHD NIH HHS/United States ; }, mesh = {Cell Phone/*statistics & numerical data ; Geographic Information Systems/statistics & numerical data ; Geography ; Humans ; Population Dynamics/*statistics & numerical data ; Population Surveillance/*methods ; Reproducibility of Results ; Travel ; }, abstract = {In the past decade, large scale mobile phone data have become available for the study of human movement patterns. These data hold an immense promise for understanding human behavior on a vast scale, and with a precision and accuracy never before possible with censuses, surveys or other existing data collection techniques. There is already a significant body of literature that has made key inroads into understanding human mobility using this exciting new data source, and there have been several different measures of mobility used. However, existing mobile phone based mobility measures are inconsistent, inaccurate, and confounded with social characteristics of local context. New measures would best be developed immediately as they will influence future studies of mobility using mobile phone data. In this article, we do exactly this. We discuss problems with existing mobile phone based measures of mobility and describe new methods for measuring mobility that address these concerns. Our measures of mobility, which incorporate both mobile phone records and detailed GIS data, are designed to address the spatial nature of human mobility, to remain independent of social characteristics of context, and to be comparable across geographic regions and time. We also contribute a discussion of the variety of uses for these new measures in developing a better understanding of how human mobility influences micro-level human behaviors and well-being, and macro-level social organization and change.}, } @article {pmid26187747, year = {2015}, author = {Anderson, D and Ferreras, E and Trindade, M and Cowan, D}, title = {A novel bacterial Water Hypersensitivity-like protein shows in vivo protection against cold and freeze damage.}, journal = {FEMS microbiology letters}, volume = {362}, number = {15}, pages = {fnv110}, doi = {10.1093/femsle/fnv110}, pmid = {26187747}, issn = {1574-6968}, mesh = {Adaptation, Physiological/*genetics ; Amino Acid Sequence ; Antarctic Regions ; Bacterial Proteins/*genetics/*physiology ; Computational Biology ; Desiccation ; Escherichia coli/genetics ; *Freezing ; Gene Library ; *Genes, Bacterial ; *Metagenome ; Phylogeny ; Pseudomonas/genetics ; Sequence Analysis, DNA ; *Soil ; Soil Microbiology ; Stress, Physiological ; Water ; }, abstract = {Metagenomic library screening, by functional or sequence analysis, has become an established method for the identification of novel genes and gene products, including genetic elements implicated in microbial stress response and adaptation. We have identified, using a sequence-based approach, a fosmid clone from an Antarctic desert soil metagenome library containing a novel gene which codes for a protein homologous to a Water Hypersensitivity domain (WHy). The WHy domain is typically found as a component of specific LEA (Late Embryogenesis Abundant) proteins, particularly the LEA-14 (LEA-8) variants, which occur widely in plants, nematodes, bacteria and archaea and which are typically induced by exposure to stress conditions. The novel WHy-like protein (165 amino acid, 18.6 kDa) exhibits a largely invariant NPN motif at the N-terminus and has high sequence identity to genes identified in Pseudomonas genomes. Expression of this protein in Escherichia coli significantly protected the recombinant host against cold and freeze stress.}, } @article {pmid26187735, year = {2017}, author = {Augustin, NH and Mattocks, C and Faraway, JJ and Greven, S and Ness, AR}, title = {Modelling a response as a function of high-frequency count data: The association between physical activity and fat mass.}, journal = {Statistical methods in medical research}, volume = {26}, number = {5}, pages = {2210-2226}, doi = {10.1177/0962280215595832}, pmid = {26187735}, issn = {1477-0334}, support = {G9815508/MRC_/Medical Research Council/United Kingdom ; MC_PC_15018/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Accelerometry ; Adipose Tissue/*anatomy & histology ; Adult ; Child ; Data Interpretation, Statistical ; *Exercise ; Female ; Humans ; Longitudinal Studies ; Male ; *Models, Statistical ; Sex Factors ; Statistics as Topic ; Time Factors ; }, abstract = {Accelerometers are widely used in health sciences, ecology and other application areas. They quantify the intensity of physical activity as counts per epoch over a given period of time. Currently, health scientists use very lossy summaries of the accelerometer time series, some of which are based on coarse discretisation of activity levels, and make certain implicit assumptions, including linear or constant effects of physical activity. We propose the histogram as a functional summary for achieving a near lossless dimension reduction, comparability between individual time series and easy interpretability. Using the histogram as a functional summary avoids registration of accelerometer counts in time. In our novel method, a scalar response is regressed on additive multi-dimensional functional predictors, including the histogram of the high-frequency counts, and additive non-linear predictors for other continuous covariates. The method improves on the current state-of-the art, as it can deal with high-frequency time series of different lengths and missing values and yields a flexible way to model the physical activity effect with fewer assumptions. It also allows the commonly made modelling assumptions to be tested. We investigate the relationship between the response fat mass and physical activity measured by accelerometer, in data from the Avon Longitudinal Study of Parents and Children. Our method allows testing of whether the effect of physical activity varies over its intensity by gender, by time of day or by day of the week. We show that meaningful interpretation requires careful treatment of identifiability constraints in the light of the sum-to-one property of a histogram. We find that the (not necessarily causal) effect of physical activity on kg fat mass is not linear and not constant over the activity intensity.}, } @article {pmid26186694, year = {2015}, author = {Rohlfs, RV and Aguiar, VRC and Lohmueller, KE and Castro, AM and Ferreira, ACS and Almeida, VCO and Louro, ID and Nielsen, R}, title = {Fitting the Balding-Nichols model to forensic databases.}, journal = {Forensic science international. Genetics}, volume = {19}, number = {}, pages = {86-91}, doi = {10.1016/j.fsigen.2015.05.005}, pmid = {26186694}, issn = {1878-0326}, support = {R01 HG003229/HG/NHGRI NIH HHS/United States ; 2R14003229-07//PHS HHS/United States ; }, mesh = {Alleles ; *Databases, Genetic ; *Forensic Genetics ; Humans ; Likelihood Functions ; *Models, Genetic ; }, abstract = {Large forensic databases provide an opportunity to compare observed empirical rates of genotype matching with those expected under forensic genetic models. A number of researchers have taken advantage of this opportunity to validate some forensic genetic approaches, particularly to ensure that estimated rates of genotype matching between unrelated individuals are indeed slight overestimates of those observed. However, these studies have also revealed systematic error trends in genotype probability estimates. In this analysis, we investigate these error trends and show how they result from inappropriate implementation of the Balding-Nichols model in the context of database-wide matching. Specifically, we show that in addition to accounting for increased allelic matching between individuals with recent shared ancestry, studies must account for relatively decreased allelic matching between individuals with more ancient shared ancestry.}, } @article {pmid26186210, year = {2015}, author = {Pailler, S and Naidoo, R and Burgess, ND and Freeman, OE and Fisher, B}, title = {Impacts of Community-Based Natural Resource Management on Wealth, Food Security and Child Health in Tanzania.}, journal = {PloS one}, volume = {10}, number = {7}, pages = {e0133252}, pmid = {26186210}, issn = {1932-6203}, mesh = {Child ; *Child Health ; Child, Preschool ; *Conservation of Natural Resources ; Demography ; *Food Supply ; Forests ; Geographic Information Systems ; Geography ; Health Surveys ; Humans ; Models, Theoretical ; *Natural Resources ; Outcome Assessment, Health Care ; *Residence Characteristics ; Sample Size ; Tanzania ; Time Factors ; }, abstract = {Community-based natural resource management (CBNRM) is a major global strategy for enhancing conservation outcomes while also seeking to improve rural livelihoods; however, little evidence of socioeconomic outcomes exists. We present a national-level analysis that empirically estimates socioeconomic impacts of CBNRM across Tanzania, while systematically controlling for potential sources of bias. Specifically, we apply a difference-in-differences model to national-scale, cross-sectional data to estimate the impact of three different CBNRM governance regimes on wealth, food security and child health, considering differential impacts of CBNRM on wealthy and poor populations. We also explore whether or not longer-standing CBNRM efforts provide more benefits than recently-established CBNRM areas. Our results show significant improvements in household food security in CBNRM areas compared with non-CBNRM areas, but household wealth and health outcomes in children are generally not significantly different. No one CBNRM governance regime demonstrates consistently different welfare outcomes than the others. Wealthy households benefit more from CBNRM than poor households and CBNRM benefits appear to increase with longer periods of implementation. Perhaps evidence of CBNRM benefits is limited because CBNRM hasn't been around long enough to yield demonstrable outcomes. Nonetheless, achieving demonstrable benefits to rural populations will be crucial for CBNRM's future success in Tanzania.}, } @article {pmid26179447, year = {2015}, author = {Ehsan, AM and De Silva, MJ}, title = {Social capital and common mental disorder: a systematic review.}, journal = {Journal of epidemiology and community health}, volume = {69}, number = {10}, pages = {1021-1028}, doi = {10.1136/jech-2015-205868}, pmid = {26179447}, issn = {1470-2738}, support = {//Wellcome Trust/United Kingdom ; }, mesh = {Adolescent ; Adult ; Aged ; Bias ; Cross-Sectional Studies ; Databases, Bibliographic ; Health Promotion/*methods ; Humans ; Longitudinal Studies ; Mental Disorders/economics/etiology/*prevention & control ; Middle Aged ; Protective Factors ; Risk Factors ; *Social Capital ; *Social Environment ; Socioeconomic Factors ; Young Adult ; }, abstract = {OBJECTIVE: This study aims to systematically review all published quantitative studies examining the direct association between social capital and common mental disorders (CMD). Social capital has potential value for the promotion and prevention of CMD. The association between different types of social capital (individual cognitive and structural, and ecological cognitive and structural) and CMD must be explored to obtain conclusive evidence regarding the association, and to ascertain a direction of causality.

DESIGN: 10 electronic databases were searched to find studies examining the association between social capital and CMD published before July 2014. The effect estimates and sample sizes for each type of social capital were separately analysed for cross-sectional and cohort studies. From 1857 studies retrieved, 39 were selected for inclusion: 31 cross-sectional and 8 cohort studies. 39 effect estimates were found for individual level cognitive, 31 for individual level structural, 9 for ecological level cognitive and 11 for ecological level structural social capital.

MAIN RESULTS: This review provides evidence that individual cognitive social capital is protective against developing CMD. Ecological cognitive social capital is also associated with reduced risk of CMD, though the included studies were cross-sectional. For structural social capital there was overall no association at either the individual or ecological levels. Two cross-sectional studies found that in low-income settings, a mother's participation in civic activities is associated with an increased risk of CMD.

CONCLUSIONS: There is now sufficient evidence to design and evaluate individual and ecological cognitive social capital interventions to promote mental well-being and prevent CMD.}, } @article {pmid26179278, year = {2015}, author = {Gupta, RS and Naushad, S and Chokshi, C and Griffiths, E and Adeolu, M}, title = {A phylogenomic and molecular markers based analysis of the phylum Chlamydiae: proposal to divide the class Chlamydiia into two orders, Chlamydiales and Parachlamydiales ord. nov., and emended description of the class Chlamydiia.}, journal = {Antonie van Leeuwenhoek}, volume = {108}, number = {3}, pages = {765-781}, doi = {10.1007/s10482-015-0532-1}, pmid = {26179278}, issn = {1572-9699}, mesh = {Bacterial Proteins/genetics ; Chlamydiales/*classification/*genetics ; Cluster Analysis ; Computational Biology ; Conserved Sequence ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; *Genetic Variation ; Genome, Bacterial ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {The phylum Chlamydiae contains nine ecologically and genetically diverse families all placed within a single order. In this work, we have completed a comprehensive comparative analysis of 36 sequenced Chlamydiae genomes in order to identify shared molecular characteristics, namely conserved signature insertions/deletions (CSIs) and conserved signature proteins (CSPs), which can serve as distinguishing characteristics of supra-familial clusters within the phylum Chlamydiae. Our analysis has led to the identification of 32 CSIs which are specific to clusters within the phylum Chlamydiae at various phylogenetic depths. Importantly, 17 CSIs and 98 CSPs were found to be specific for the family Chlamydiaceae while another 3 CSI variants and 15 CSPs were specific for a grouping of the families Criblamydiaceae, Parachlamydiaceae, Simkaniaceae and Waddliaceae. These two clusters were also found to be distinguishable in 16S rRNA based phylogenetic trees, concatenated protein based phylogenetic trees, character compatibility based phylogenetic analyses, and on the basis of 16S rRNA gene sequence identity and average amino acid identity values. On the basis of the identified molecular characteristics, branching in phylogenetic trees, and the genetic distance between the two clusters within the phylum Chlamydiae we propose a division of the class Chlamydiia into two orders: an emended order Chlamydiales, containing the family Chlamydiaceae and the closely related Candidatus family Clavichlamydiaceae, and the novel order Parachlamydiales ord. nov. containing the families Parachlamydiaceae, Simkaniaceae and Waddliaceae and the Candidatus families Criblamydiaceae, Parilichlamydiaceae, Piscichlamydiaceae, and Rhabdochlamydiaceae. We also include a brief discussion of the reunification of the genera Chlamydia and Chlamydophila.}, } @article {pmid26175912, year = {2015}, author = {Kraemer, MU and Sinka, ME and Duda, KA and Mylne, A and Shearer, FM and Brady, OJ and Messina, JP and Barker, CM and Moore, CG and Carvalho, RG and Coelho, GE and Van Bortel, W and Hendrickx, G and Schaffner, F and Wint, GR and Elyazar, IR and Teng, HJ and Hay, SI}, title = {The global compendium of Aedes aegypti and Ae. albopictus occurrence.}, journal = {Scientific data}, volume = {2}, number = {}, pages = {150035}, pmid = {26175912}, issn = {2052-4463}, support = {089276//Wellcome Trust/United Kingdom ; 095066//Wellcome Trust/United Kingdom ; B9RZGS0//Wellcome Trust/United Kingdom ; //Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {*Aedes ; Animals ; *Chikungunya virus ; Databases, Factual ; *Dengue/epidemiology/transmission ; *Dengue Virus ; Humans ; *Insect Vectors ; }, abstract = {Aedes aegypti and Ae. albopictus are the main vectors transmitting dengue and chikungunya viruses. Despite being pathogens of global public health importance, knowledge of their vectors' global distribution remains patchy and sparse. A global geographic database of known occurrences of Ae. aegypti and Ae. albopictus between 1960 and 2014 was compiled. Herein we present the database, which comprises occurrence data linked to point or polygon locations, derived from peer-reviewed literature and unpublished studies including national entomological surveys and expert networks. We describe all data collection processes, as well as geo-positioning methods, database management and quality-control procedures. This is the first comprehensive global database of Ae. aegypti and Ae. albopictus occurrence, consisting of 19,930 and 22,137 geo-positioned occurrence records respectively. Both datasets can be used for a variety of mapping and spatial analyses of the vectors and, by inference, the diseases they transmit.}, } @article {pmid26172230, year = {2015}, author = {Gutiérrez Robledo, LM and Palloni, A and Téllez Rojo, MM and Wong, R}, title = {Introduction.}, journal = {Salud publica de Mexico}, volume = {57 Suppl 1}, number = {}, pages = {S2-5}, pmid = {26172230}, issn = {1606-7916}, mesh = {Aged ; Aged, 80 and over ; Congresses as Topic ; Databases, Factual ; Female ; Follow-Up Studies ; *Health Surveys ; Humans ; Male ; Mexico ; Middle Aged ; *Population Dynamics ; }, } @article {pmid26170056, year = {2016}, author = {Chetverikov, A and Upravitelev, P}, title = {Online versus offline: The Web as a medium for response time data collection.}, journal = {Behavior research methods}, volume = {48}, number = {3}, pages = {1086-1099}, doi = {10.3758/s13428-015-0632-x}, pmid = {26170056}, issn = {1554-3528}, mesh = {Adult ; Data Collection/*methods ; Female ; Humans ; *Internet ; Male ; *Online Systems ; Programming Languages ; Psychomotor Performance ; *Reaction Time ; Sample Size ; Software ; Young Adult ; }, abstract = {The Internet provides a convenient environment for data collection in psychology. Modern Web programming languages, such as JavaScript or Flash (ActionScript), facilitate complex experiments without the necessity of experimenter presence. Yet there is always a question of how much noise is added due to the differences between the setups used by participants and whether it is compensated for by increased ecological validity and larger sample sizes. This is especially a problem for experiments that measure response times (RTs), because they are more sensitive (and hence more susceptible to noise) than, for example, choices per se. We used a simple visual search task with different set sizes to compare laboratory performance with Web performance. The results suggest that although the locations (means) of RT distributions are different, other distribution parameters are not. Furthermore, the effect of experiment setting does not depend on set size, suggesting that task difficulty is not important in the choice of a data collection method. We also collected an additional online sample to investigate the effects of hardware and software diversity on the accuracy of RT data. We found that the high diversity of browsers, operating systems, and CPU performance may have a detrimental effect, though it can partly be compensated for by increased sample sizes and trial numbers. In sum, the findings show that Web-based experiments are an acceptable source of RT data, comparable to a common keyboard-based setup in the laboratory.}, } @article {pmid26169943, year = {2015}, author = {Tovar-Corona, JM and Castillo-Morales, A and Chen, L and Olds, BP and Clark, JM and Reynolds, SE and Pittendrigh, BR and Feil, EJ and Urrutia, AO}, title = {Alternative Splice in Alternative Lice.}, journal = {Molecular biology and evolution}, volume = {32}, number = {10}, pages = {2749-2759}, pmid = {26169943}, issn = {1537-1719}, support = {BB/I000836/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Alternative Splicing/*genetics ; Animals ; Gene Ontology ; Genes, Insect ; Humans ; Pediculus/genetics ; Phthiraptera/*genetics ; }, abstract = {Genomic and transcriptomics analyses have revealed human head and body lice to be almost genetically identical; although con-specific, they nevertheless occupy distinct ecological niches and have differing feeding patterns. Most importantly, while head lice are not known to be vector competent, body lice can transmit three serious bacterial diseases; epidemictyphus, trench fever, and relapsing fever. In order to gain insights into the molecular bases for these differences, we analyzed alternative splicing (AS) using next-generation sequencing data for one strain of head lice and one strain of body lice. We identified a total of 3,598 AS events which were head or body lice specific. Exon skipping AS events were overrepresented among both head and body lice, whereas intron retention events were underrepresented in both. However, both the enrichment of exon skipping and the underrepresentation of intron retention are significantly stronger in body lice compared with head lice. Genes containing body louse-specific AS events were found to be significantly enriched for functions associated with development of the nervous system, salivary gland, trachea, and ovarian follicle cells, as well as regulation of transcription. In contrast, no functional categories were overrepresented among genes with head louse-specific AS events. Together, our results constitute the first evidence for transcript pool differences in head and body lice, providing insights into molecular adaptations that enabled human lice to adapt to clothing, and representing a powerful illustration of the pivotal role AS can play in functional adaptation.}, } @article {pmid26163215, year = {2015}, author = {Yalkovskaya, LE and Bol'shakov, VN and Sibiryakov, PA and Borodin, AV}, title = {Phylogeography of the Siberian flying squirrel (Pteromys volans L., 1785) and the history of the formation of the modern species range: New data.}, journal = {Doklady. Biochemistry and biophysics}, volume = {462}, number = {}, pages = {181-184}, pmid = {26163215}, issn = {1608-3091}, mesh = {Animals ; Computational Biology ; Haplotypes ; *Phylogeography ; Sciuridae/*classification/genetics ; }, } @article {pmid26161499, year = {2015}, author = {Serang, O}, title = {A Fast Numerical Method for Max-Convolution and the Application to Efficient Max-Product Inference in Bayesian Networks.}, journal = {Journal of computational biology : a journal of computational molecular cell biology}, volume = {22}, number = {8}, pages = {770-783}, doi = {10.1089/cmb.2015.0013}, pmid = {26161499}, issn = {1557-8666}, mesh = {Algorithms ; *Bayes Theorem ; Computational Biology/*methods ; Markov Chains ; Models, Statistical ; }, abstract = {Observations depending on sums of random variables are common throughout many fields; however, no efficient solution is currently known for performing max-product inference on these sums of general discrete distributions (max-product inference can be used to obtain maximum a posteriori estimates). The limiting step to max-product inference is the max-convolution problem (sometimes presented in log-transformed form and denoted as "infimal convolution," "min-convolution," or "convolution on the tropical semiring"), for which no O(k log(k)) method is currently known. Presented here is an O(k log(k)) numerical method for estimating the max-convolution of two nonnegative vectors (e.g., two probability mass functions), where k is the length of the larger vector. This numerical max-convolution method is then demonstrated by performing fast max-product inference on a convolution tree, a data structure for performing fast inference given information on the sum of n discrete random variables in O(nk log(nk)log(n)) steps (where each random variable has an arbitrary prior distribution on k contiguous possible states). The numerical max-convolution method can be applied to specialized classes of hidden Markov models to reduce the runtime of computing the Viterbi path from nk(2) to nk log(k), and has potential application to the all-pairs shortest paths problem.}, } @article {pmid26158662, year = {2015}, author = {Doubravsky, K and Dohnal, M}, title = {Reconciliation of Decision-Making Heuristics Based on Decision Trees Topologies and Incomplete Fuzzy Probabilities Sets.}, journal = {PloS one}, volume = {10}, number = {7}, pages = {e0131590}, pmid = {26158662}, issn = {1932-6203}, mesh = {Algorithms ; Decision Making/*physiology ; Decision Support Techniques ; *Decision Trees ; *Fuzzy Logic ; Heuristics/*physiology ; Humans ; Models, Theoretical ; Probability ; }, abstract = {Complex decision making tasks of different natures, e.g. economics, safety engineering, ecology and biology, are based on vague, sparse, partially inconsistent and subjective knowledge. Moreover, decision making economists / engineers are usually not willing to invest too much time into study of complex formal theories. They require such decisions which can be (re)checked by human like common sense reasoning. One important problem related to realistic decision making tasks are incomplete data sets required by the chosen decision making algorithm. This paper presents a relatively simple algorithm how some missing III (input information items) can be generated using mainly decision tree topologies and integrated into incomplete data sets. The algorithm is based on an easy to understand heuristics, e.g. a longer decision tree sub-path is less probable. This heuristic can solve decision problems under total ignorance, i.e. the decision tree topology is the only information available. But in a practice, isolated information items e.g. some vaguely known probabilities (e.g. fuzzy probabilities) are usually available. It means that a realistic problem is analysed under partial ignorance. The proposed algorithm reconciles topology related heuristics and additional fuzzy sets using fuzzy linear programming. The case study, represented by a tree with six lotteries and one fuzzy probability, is presented in details.}, } @article {pmid26157601, year = {2015}, author = {Coutinho, FH and Meirelles, PM and Moreira, AP and Paranhos, RP and Dutilh, BE and Thompson, FL}, title = {Niche distribution and influence of environmental parameters in marine microbial communities: a systematic review.}, journal = {PeerJ}, volume = {3}, number = {}, pages = {e1008}, pmid = {26157601}, issn = {2167-8359}, abstract = {Associations between microorganisms occur extensively throughout Earth's oceans. Understanding how microbial communities are assembled and how the presence or absence of species is related to that of others are central goals of microbial ecology. Here, we investigate co-occurrence associations between marine prokaryotes by combining 180 new and publicly available metagenomic datasets from different oceans in a large-scale meta-analysis. A co-occurrence network was created by calculating correlation scores between the abundances of microorganisms in metagenomes. A total of 1,906 correlations amongst 297 organisms were detected, segregating them into 11 major groups that occupy distinct ecological niches. Additionally, by analyzing the oceanographic parameters measured for a selected number of sampling sites, we characterized the influence of environmental variables over each of these 11 groups. Clustering organisms into groups of taxa that have similar ecology, allowed the detection of several significant correlations that could not be observed for the taxa individually.}, } @article {pmid26156032, year = {2015}, author = {Hoen, AG and Hladish, TJ and Eggo, RM and Lenczner, M and Brownstein, JS and Meyers, LA}, title = {Epidemic Wave Dynamics Attributable to Urban Community Structure: A Theoretical Characterization of Disease Transmission in a Large Network.}, journal = {Journal of medical Internet research}, volume = {17}, number = {7}, pages = {e169}, pmid = {26156032}, issn = {1438-8871}, support = {U01 GM087719/GM/NIGMS NIH HHS/United States ; R01LM010812/LM/NLM NIH HHS/United States ; R01 LM010812/LM/NLM NIH HHS/United States ; K01 LM011985/LM/NLM NIH HHS/United States ; P20 GM104416/GM/NIGMS NIH HHS/United States ; }, mesh = {Communicable Diseases/*epidemiology/transmission ; Disease Outbreaks ; Disease Transmission, Infectious/*statistics & numerical data ; Epidemics/*statistics & numerical data ; Humans ; Models, Theoretical ; Urban Health Services/*standards ; }, abstract = {BACKGROUND: Multiple waves of transmission during infectious disease epidemics represent a major public health challenge, but the ecological and behavioral drivers of epidemic resurgence are poorly understood. In theory, community structure—aggregation into highly intraconnected and loosely interconnected social groups—within human populations may lead to punctuated outbreaks as diseases progress from one community to the next. However, this explanation has been largely overlooked in favor of temporal shifts in environmental conditions and human behavior and because of the difficulties associated with estimating large-scale contact patterns.

OBJECTIVE: The aim was to characterize naturally arising patterns of human contact that are capable of producing simulated epidemics with multiple wave structures.

METHODS: We used an extensive dataset of proximal physical contacts between users of a public Wi-Fi Internet system to evaluate the epidemiological implications of an empirical urban contact network. We characterized the modularity (community structure) of the network and then estimated epidemic dynamics under a percolation-based model of infectious disease spread on the network. We classified simulated epidemics as multiwave using a novel metric and we identified network structures that were critical to the network's ability to produce multiwave epidemics.

RESULTS: We identified robust community structure in a large, empirical urban contact network from which multiwave epidemics may emerge naturally. This pattern was fueled by a special kind of insularity in which locally popular individuals were not the ones forging contacts with more distant social groups.

CONCLUSIONS: Our results suggest that ordinary contact patterns can produce multiwave epidemics at the scale of a single urban area without the temporal shifts that are usually assumed to be responsible. Understanding the role of community structure in epidemic dynamics allows officials to anticipate epidemic resurgence without having to forecast future changes in hosts, pathogens, or the environment.}, } @article {pmid26154287, year = {2015}, author = {Holman, L and Head, ML and Lanfear, R and Jennions, MD}, title = {Evidence of Experimental Bias in the Life Sciences: Why We Need Blind Data Recording.}, journal = {PLoS biology}, volume = {13}, number = {7}, pages = {e1002190}, pmid = {26154287}, issn = {1545-7885}, mesh = {Biology/*standards/statistics & numerical data ; Data Collection/*standards/statistics & numerical data ; Data Mining ; }, abstract = {Observer bias and other "experimenter effects" occur when researchers' expectations influence study outcome. These biases are strongest when researchers expect a particular result, are measuring subjective variables, and have an incentive to produce data that confirm predictions. To minimize bias, it is good practice to work "blind," meaning that experimenters are unaware of the identity or treatment group of their subjects while conducting research. Here, using text mining and a literature review, we find evidence that blind protocols are uncommon in the life sciences and that nonblind studies tend to report higher effect sizes and more significant p-values. We discuss methods to minimize bias and urge researchers, editors, and peer reviewers to keep blind protocols in mind.}, } @article {pmid26153373, year = {2015}, author = {Yang, X and Cushman, JC and Borland, AM and Edwards, EJ and Wullschleger, SD and Tuskan, GA and Owen, NA and Griffiths, H and Smith, JA and De Paoli, HC and Weston, DJ and Cottingham, R and Hartwell, J and Davis, SC and Silvera, K and Ming, R and Schlauch, K and Abraham, P and Stewart, JR and Guo, HB and Albion, R and Ha, J and Lim, SD and Wone, BW and Yim, WC and Garcia, T and Mayer, JA and Petereit, J and Nair, SS and Casey, E and Hettich, RL and Ceusters, J and Ranjan, P and Palla, KJ and Yin, H and Reyes-García, C and Andrade, JL and Freschi, L and Beltrán, JD and Dever, LV and Boxall, SF and Waller, J and Davies, J and Bupphada, P and Kadu, N and Winter, K and Sage, RF and Aguilar, CN and Schmutz, J and Jenkins, J and Holtum, JA}, title = {A roadmap for research on crassulacean acid metabolism (CAM) to enhance sustainable food and bioenergy production in a hotter, drier world.}, journal = {The New phytologist}, volume = {207}, number = {3}, pages = {491-504}, doi = {10.1111/nph.13393}, pmid = {26153373}, issn = {1469-8137}, support = {BB/F009313/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {*Biofuels ; Carboxylic Acids/*metabolism ; *Droughts ; *Food ; *Hot Temperature ; *Research ; }, abstract = {Crassulacean acid metabolism (CAM) is a specialized mode of photosynthesis that features nocturnal CO2 uptake, facilitates increased water-use efficiency (WUE), and enables CAM plants to inhabit water-limited environments such as semi-arid deserts or seasonally dry forests. Human population growth and global climate change now present challenges for agricultural production systems to increase food, feed, forage, fiber, and fuel production. One approach to meet these challenges is to increase reliance on CAM crops, such as Agave and Opuntia, for biomass production on semi-arid, abandoned, marginal, or degraded agricultural lands. Major research efforts are now underway to assess the productivity of CAM crop species and to harness the WUE of CAM by engineering this pathway into existing food, feed, and bioenergy crops. An improved understanding of CAM has potential for high returns on research investment. To exploit the potential of CAM crops and CAM bioengineering, it will be necessary to elucidate the evolution, genomic features, and regulatory mechanisms of CAM. Field trials and predictive models will be required to assess the productivity of CAM crops, while new synthetic biology approaches need to be developed for CAM engineering. Infrastructure will be needed for CAM model systems, field trials, mutant collections, and data management.}, } @article {pmid26153115, year = {2015}, author = {Andrewin, AN and Rodriguez-Llanes, JM and Guha-Sapir, D}, title = {Determinants of the lethality of climate-related disasters in the Caribbean Community (CARICOM): a cross-country analysis.}, journal = {Scientific reports}, volume = {5}, number = {}, pages = {11972}, pmid = {26153115}, issn = {2045-2322}, mesh = {Agriculture ; Caribbean Region ; Climate ; Conservation of Natural Resources ; Databases, Factual ; *Disasters ; Floods ; Humans ; Logistic Models ; Odds Ratio ; Risk Factors ; Urban Population ; }, abstract = {Floods and storms are climate-related hazards posing high mortality risk to Caribbean Community (CARICOM) nations. However risk factors for their lethality remain untested. We conducted an ecological study investigating risk factors for flood and storm lethality in CARICOM nations for the period 1980-2012. Lethality--deaths versus no deaths per disaster event- was the outcome. We examined biophysical and social vulnerability proxies and a decadal effect as predictors. We developed our regression model via multivariate analysis using a generalized logistic regression model with quasi-binomial distribution; removal of multi-collinear variables and backward elimination. Robustness was checked through subset analysis. We found significant positive associations between lethality, percentage of total land dedicated to agriculture (odds ratio [OR] 1.032; 95% CI: 1.013-1.053) and percentage urban population (OR 1.029, 95% CI 1.003-1.057). Deaths were more likely in the 2000-2012 period versus 1980-1989 (OR 3.708, 95% CI 1.615-8.737). Robustness checks revealed similar coefficients and directions of association. Population health in CARICOM nations is being increasingly impacted by climate-related disasters connected to increasing urbanization and land use patterns. Our findings support the evidence base for setting sustainable development goals (SDG).}, } @article {pmid26148692, year = {2016}, author = {Driscoll, DA and Bode, M and Bradstock, RA and Keith, DA and Penman, TD and Price, OF}, title = {Resolving future fire management conflicts using multicriteria decision making.}, journal = {Conservation biology : the journal of the Society for Conservation Biology}, volume = {30}, number = {1}, pages = {196-205}, doi = {10.1111/cobi.12580}, pmid = {26148692}, issn = {1523-1739}, mesh = {Conservation of Natural Resources/*methods ; *Decision Support Techniques ; Ecosystem ; Fires/*prevention & control ; Models, Theoretical ; New South Wales ; Risk Assessment ; }, abstract = {Management strategies to reduce the risks to human life and property from wildfire commonly involve burning native vegetation. However, planned burning can conflict with other societal objectives such as human health and biodiversity conservation. These conflicts are likely to intensify as fire regimes change under future climates and as growing human populations encroach farther into fire-prone ecosystems. Decisions about managing fire risks are therefore complex and warrant more sophisticated approaches than are typically used. We applied a multicriteria decision making approach (MCDA) with the potential to improve fire management outcomes to the case of a highly populated, biodiverse, and flammable wildland-urban interface. We considered the effects of 22 planned burning options on 8 objectives: house protection, maximizing water quality, minimizing carbon emissions and impacts on human health, and minimizing declines of 5 distinct species types. The MCDA identified a small number of management options (burning forest adjacent to houses) that performed well for most objectives, but not for one species type (arboreal mammal) or for water quality. Although MCDA made the conflict between objectives explicit, resolution of the problem depended on the weighting assigned to each objective. Additive weighting of criteria traded off the arboreal mammal and water quality objectives for other objectives. Multiplicative weighting identified scenarios that avoided poor outcomes for any objective, which is important for avoiding potentially irreversible biodiversity losses. To distinguish reliably among management options, future work should focus on reducing uncertainty in outcomes across a range of objectives. Considering management actions that have more predictable outcomes than landscape fuel management will be important. We found that, where data were adequate, an MCDA can support decision making in the complex and often conflicted area of fire management.}, } @article {pmid26147931, year = {2015}, author = {Puncher, GN and Arrizabalaga, H and Alemany, F and Cariani, A and Oray, IK and Karakulak, FS and Basilone, G and Cuttitta, A and Mazzola, S and Tinti, F}, title = {Molecular Identification of Atlantic Bluefin Tuna (Thunnus thynnus, Scombridae) Larvae and Development of a DNA Character-Based Identification Key for Mediterranean Scombrids.}, journal = {PloS one}, volume = {10}, number = {7}, pages = {e0130407}, pmid = {26147931}, issn = {1932-6203}, mesh = {Animals ; DNA, Mitochondrial/*genetics ; Databases, Genetic ; Eggs ; Fisheries/methods ; Larva/*genetics ; Mediterranean Sea ; Mitochondria/genetics ; Sequence Alignment ; Tuna/*genetics ; }, abstract = {The Atlantic bluefin tuna, Thunnus thynnus, is a commercially important species that has been severely over-exploited in the recent past. Although the eastern Atlantic and Mediterranean stock is now showing signs of recovery, its current status remains very uncertain and as a consequence their recovery is dependent upon severe management informed by rigorous scientific research. Monitoring of early life history stages can inform decision makers about the health of the species based upon recruitment and survival rates. Misidentification of fish larvae and eggs can lead to inaccurate estimates of stock biomass and productivity which can trigger demands for increased quotas and unsound management conclusions. Herein we used a molecular approach employing mitochondrial and nuclear genes (CO1 and ITS1, respectively) to identify larvae (n = 188) collected from three spawning areas in the Mediterranean Sea by different institutions working with a regional fisheries management organization. Several techniques were used to analyze the genetic sequences (sequence alignments using search algorithms, neighbour joining trees, and a genetic character-based identification key) and an extensive comparison of the results is presented. During this process various inaccuracies in related publications and online databases were uncovered. Our results reveal important differences in the accuracy of the taxonomic identifications carried out by different ichthyoplanktologists following morphology-based methods. While less than half of larvae provided were bluefin tuna, other dominant taxa were bullet tuna (Auxis rochei), albacore (Thunnus alalunga) and little tunny (Euthynnus alletteratus). We advocate an expansion of expertise for a new generation of morphology-based taxonomists, increased dialogue between morphology-based and molecular taxonomists and increased scrutiny of public sequence databases.}, } @article {pmid26147438, year = {2015}, author = {Bradshaw, PL and Colville, JF and Linder, HP}, title = {Optimising Regionalisation Techniques: Identifying Centres of Endemism in the Extraordinarily Endemic-Rich Cape Floristic Region.}, journal = {PloS one}, volume = {10}, number = {7}, pages = {e0132538}, pmid = {26147438}, issn = {1932-6203}, mesh = {*Databases, Factual ; Plants/*classification ; South Africa ; }, abstract = {We used a very large dataset (>40% of all species) from the endemic-rich Cape Floristic Region (CFR) to explore the impact of different weighting techniques, coefficients to calculate similarity among the cells, and clustering approaches on biogeographical regionalisation. The results were used to revise the biogeographical subdivision of the CFR. We show that weighted data (down-weighting widespread species), similarity calculated using Kulczinsky's second measure, and clustering using UPGMA resulted in the optimal classification. This maximized the number of endemic species, the number of centres recognized, and operational geographic units assigned to centres of endemism (CoEs). We developed a dendrogram branch order cut-off (BOC) method to locate the optimal cut-off points on the dendrogram to define candidate clusters. Kulczinsky's second measure dendrograms were combined using consensus, identifying areas of conflict which could be due to biotic element overlap or transitional areas. Post-clustering GIS manipulation substantially enhanced the endemic composition and geographic size of candidate CoEs. Although there was broad spatial congruence with previous phytogeographic studies, our techniques allowed for the recovery of additional phytogeographic detail not previously described for the CFR.}, } @article {pmid26145151, year = {2015}, author = {Xing, MQ and Zhang, YJ and Zhou, SR and Hu, WY and Wu, XT and Ye, YJ and Wu, XX and Xiao, YP and Li, X and Xue, HW}, title = {Global Analysis Reveals the Crucial Roles of DNA Methylation during Rice Seed Development.}, journal = {Plant physiology}, volume = {168}, number = {4}, pages = {1417-1432}, pmid = {26145151}, issn = {1532-2548}, mesh = {*DNA Methylation ; DNA Transposable Elements/genetics ; Endosperm/genetics/growth & development ; *Gene Expression Profiling ; *Gene Expression Regulation, Developmental ; *Gene Expression Regulation, Plant ; Gene Ontology ; Genes, Plant/genetics ; Genome, Plant/genetics ; Oryza/*genetics/growth & development ; Plant Proteins/genetics ; Seeds/*genetics/growth & development ; }, abstract = {Seed development is an important process of reproductive development and consists of embryo and endosperm development; both comprise several key processes. To determine and investigate the functions of the dynamic DNA methylome during seed development, we profiled the DNA methylation genome wide in a series of developmental stages of rice (Oryza sativa) embryo and endosperm by methylcytosine immunoprecipitation followed by Illumina sequencing. The results showed that embryo is hypermethylated predominantly around non-transposable element (TE) genes, short DNA-TEs, and short interspersed TEs compared with endosperm, and non-TE genes have the most diverse methylation status across seed development. In addition, lowly expressed genes are significantly enriched in hypermethylated genes, but not vice versa, confirming the crucial role of DNA methylation in suppressing gene transcription. Further analysis revealed the significantly decreased methylation at early developing stages (from 2 to 3 d after pollination), indicating a predominant role of demethylation during early endosperm development and that genes with a consistent negative correlation between DNA methylation change and expression change may be potentially directly regulated by DNA methylation. Interestingly, comparative analysis of the DNA methylation profiles revealed that both rice indica and japonica subspecies showed robust fluctuant profiles of DNA methylation levels in embryo and endosperm across seed development, with the highest methylation level at 6 d after pollination (2 d after pollination of endosperm in japonica as well), indicating that a complex and finely controlled methylation pattern is closely associated with seed development regulation. The systemic characterization of the dynamic DNA methylome in developing rice seeds will help us understand the effects and mechanism of epigenetic regulation in seed development.}, } @article {pmid26144657, year = {2016}, author = {Preston, S and Jabbar, A and Gasser, RB}, title = {A perspective on genomic-guided anthelmintic discovery and repurposing using Haemonchus contortus.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {40}, number = {}, pages = {368-373}, doi = {10.1016/j.meegid.2015.06.029}, pmid = {26144657}, issn = {1567-7257}, mesh = {Animals ; Anthelmintics/*pharmacology ; Computational Biology/methods ; Drug Discovery/methods ; Drug Evaluation, Preclinical ; *Drug Repositioning/methods ; Drug Resistance ; Gene Expression Profiling ; *Genome ; *Genomics/methods ; Haemonchus/*drug effects/*genetics ; Humans ; Small Molecule Libraries ; Transcriptome ; }, abstract = {High-throughput molecular and computer technologies have become instrumental for systems biological explorations of parasites. Investigating the genomes and transcriptomes of different developmental stages of parasitic nematodes can provide insights into gene expression, regulation and function in the parasite, which is a significant step toward understanding their biology as well as host interactions and disease. This article covers aspects of a talk given at the MEEGID XII conference in Thailand in 2014. Here, we refer to recent studies of the genomes and transcriptomes of socioeconomically important parasitic nematodes of animals; provide an account of the barber's pole worm (Haemonchus contortus) and emerging drug resistance problems in this and related worms; we also propose a genomic-guided drug discovery and repurposing approach, involving the prediction of the druggable genome, prioritization of drug targets, screening of compound libraries against H. contortus and, briefly, a hit-to-lead optimization approach. We conclude by indicating prospects that molecular tool kits for nematodes provide to the scientific community for future comparative genomic, genetic, proteomic, metabolomic, evolutionary, biological, ecological and epidemiological investigations, and as a basis for biotechnological outcomes and translation.}, } @article {pmid26144560, year = {2015}, author = {Goe, M and Gaustad, G and Tomaszewski, B}, title = {System tradeoffs in siting a solar photovoltaic material recovery infrastructure.}, journal = {Journal of environmental management}, volume = {160}, number = {}, pages = {154-166}, doi = {10.1016/j.jenvman.2015.05.038}, pmid = {26144560}, issn = {1095-8630}, mesh = {Decision Support Techniques ; *Electronic Waste ; Environment ; Humans ; Models, Theoretical ; New York ; Recycling/economics ; Refuse Disposal/*methods ; Waste Disposal Facilities ; Waste Management/*methods ; }, abstract = {The consumption and disposal of rare and hazardous metals contained in electronics and emerging technologies such as photovoltaics increases the material complexity of the municipal waste stream. Developing effective waste policies and material recovery systems is required to inhibit landfilling of valuable and finite resources. This work developed a siting and waste infrastructure configuration model to inform the management and recovery of end-of-life photovoltaics. This model solves the siting and waste location-allocation problem for a New York State case study by combining multi-criteria decision methods with spatial tools, however this methodology is generalizable to any geographic area. For the case study, the results indicate that PV installations are spatially statistically significant (i.e., clustered). At least 9 sites, which are co-located with landfills and current MRFs, were 'highly' suitable for siting according to our criteria. After combining criteria in an average weighted sum, 86% of the study area was deemed unsuitable for siting while less than 5% is characterized as highly suitable. This method implicitly prioritized social and environmental concerns and therefore, these concerns accounted for the majority of siting decisions. As we increased the priority of economic criteria, the likelihood of siting near ecologically sensitive areas such as coastline or socially vulnerable areas such as urban centers increased. The sensitivity of infrastructure configurations to land use and waste policy are analyzed. The location allocation model results suggest current tip fees are insufficient to avoid landfilling of photovoltaics. Scenarios where tip fees were increased showed model results where facilities decide to adopt limited recycling technologies that bypass compositionally complex materials; a result with strong implications for global PV installations as well as other waste streams. We suggest a multi-pronged approach that lowers technology cost, imposes a minimum collection rate, and implements higher tip fees would encourage exhaustive material recovery for solar photovoltaic modules at end-of-life, beyond New York State. These results have important implications for policy makers and waste managers especially in locations where there is rapid adoption of renewable energy technologies.}, } @article {pmid26142451, year = {2015}, author = {Messina, JP and Pigott, DM and Golding, N and Duda, KA and Brownstein, JS and Weiss, DJ and Gibson, H and Robinson, TP and Gilbert, M and William Wint, GR and Nuttall, PA and Gething, PW and Myers, MF and George, DB and Hay, SI}, title = {The global distribution of Crimean-Congo hemorrhagic fever.}, journal = {Transactions of the Royal Society of Tropical Medicine and Hygiene}, volume = {109}, number = {8}, pages = {503-513}, pmid = {26142451}, issn = {1878-3503}, support = {/WT_/Wellcome Trust/United Kingdom ; 095066/WT_/Wellcome Trust/United Kingdom ; R01 LM010812/LM/NLM NIH HHS/United States ; }, mesh = {Abattoirs ; Animal Husbandry ; Animals ; Arachnid Vectors/*virology ; Disease Outbreaks/*prevention & control ; Farmers ; Geography ; *Global Health ; Hemorrhagic Fever Virus, Crimean-Congo/*pathogenicity ; Hemorrhagic Fever, Crimean/blood/prevention & control/*transmission ; Humans ; Occupational Diseases/*prevention & control/virology ; Occupational Exposure/*prevention & control ; Phylogeny ; Ticks/virology ; }, abstract = {BACKGROUND: Crimean-Congo hemorrhagic fever (CCHF) is a tick-borne infection caused by a virus (CCHFV) from the Bunyaviridae family. Domestic and wild vertebrates are asymptomatic reservoirs for the virus, putting animal handlers, slaughter-house workers and agricultural labourers at highest risk in endemic areas, with secondary transmission possible through contact with infected blood and other bodily fluids. Human infection is characterized by severe symptoms that often result in death. While it is known that CCHFV transmission is limited to Africa, Asia and Europe, definitive global extents and risk patterns within these limits have not been well described.

METHODS: We used an exhaustive database of human CCHF occurrence records and a niche modeling framework to map the global distribution of risk for human CCHF occurrence.

RESULTS: A greater proportion of shrub or grass land cover was the most important contributor to our model, which predicts highest levels of risk around the Black Sea, Turkey, and some parts of central Asia. Sub-Saharan Africa shows more focalized areas of risk throughout the Sahel and the Cape region.

CONCLUSIONS: These new risk maps provide a valuable starting point for understanding the zoonotic niche of CCHF, its extent and the risk it poses to humans.}, } @article {pmid26140928, year = {2015}, author = {Ndhlovu, A and Durand, PM and Hazelhurst, S}, title = {EvoDB: a database of evolutionary rate profiles, associated protein domains and phylogenetic trees for PFAM-A.}, journal = {Database : the journal of biological databases and curation}, volume = {2015}, number = {}, pages = {bav065}, pmid = {26140928}, issn = {1758-0463}, mesh = {*Algorithms ; *Databases, Protein ; *Evolution, Molecular ; *Phylogeny ; Protein Structure, Tertiary ; Sequence Analysis, Protein/*methods ; *Software ; }, abstract = {The evolutionary rate at codon sites across protein-coding nucleotide sequences represents a valuable tier of information for aligning sequences, inferring homology and constructing phylogenetic profiles. However, a comprehensive resource for cataloguing the evolutionary rate at codon sites and their corresponding nucleotide and protein domain sequence alignments has not been developed. To address this gap in knowledge, EvoDB (an Evolutionary rates DataBase) was compiled. Nucleotide sequences and their corresponding protein domain data including the associated seed alignments from the PFAM-A (protein family) database were used to estimate evolutionary rate (ω = dN/dS) profiles at codon sites for each entry. EvoDB contains 98.83% of the gapped nucleotide sequence alignments and 97.1% of the evolutionary rate profiles for the corresponding information in PFAM-A. As the identification of codon sites under positive selection and their position in a sequence profile is usually the most sought after information for molecular evolutionary biologists, evolutionary rate profiles were determined under the M2a model using the CODEML algorithm in the PAML (Phylogenetic Analysis by Maximum Likelihood) suite of software. Validation of nucleotide sequences against amino acid data was implemented to ensure high data quality. EvoDB is a catalogue of the evolutionary rate profiles and provides the corresponding phylogenetic trees, PFAM-A alignments and annotated accession identifier data. In addition, the database can be explored and queried using known evolutionary rate profiles to identify domains under similar evolutionary constraints and pressures. EvoDB is a resource for evolutionary, phylogenetic studies and presents a tier of information untapped by current databases.}, } @article {pmid26140212, year = {2015}, author = {Soranno, PA and Bissell, EG and Cheruvelil, KS and Christel, ST and Collins, SM and Fergus, CE and Filstrup, CT and Lapierre, JF and Lottig, NR and Oliver, SK and Scott, CE and Smith, NJ and Stopyak, S and Yuan, S and Bremigan, MT and Downing, JA and Gries, C and Henry, EN and Skaff, NK and Stanley, EH and Stow, CA and Tan, PN and Wagner, T and Webster, KE}, title = {Building a multi-scaled geospatial temporal ecology database from disparate data sources: fostering open science and data reuse.}, journal = {GigaScience}, volume = {4}, number = {}, pages = {28}, pmid = {26140212}, issn = {2047-217X}, mesh = {*Database Management Systems ; *Ecology ; *Geographic Information Systems ; }, abstract = {Although there are considerable site-based data for individual or groups of ecosystems, these datasets are widely scattered, have different data formats and conventions, and often have limited accessibility. At the broader scale, national datasets exist for a large number of geospatial features of land, water, and air that are needed to fully understand variation among these ecosystems. However, such datasets originate from different sources and have different spatial and temporal resolutions. By taking an open-science perspective and by combining site-based ecosystem datasets and national geospatial datasets, science gains the ability to ask important research questions related to grand environmental challenges that operate at broad scales. Documentation of such complicated database integration efforts, through peer-reviewed papers, is recommended to foster reproducibility and future use of the integrated database. Here, we describe the major steps, challenges, and considerations in building an integrated database of lake ecosystems, called LAGOS (LAke multi-scaled GeOSpatial and temporal database), that was developed at the sub-continental study extent of 17 US states (1,800,000 km(2)). LAGOS includes two modules: LAGOSGEO, with geospatial data on every lake with surface area larger than 4 ha in the study extent (~50,000 lakes), including climate, atmospheric deposition, land use/cover, hydrology, geology, and topography measured across a range of spatial and temporal extents; and LAGOSLIMNO, with lake water quality data compiled from ~100 individual datasets for a subset of lakes in the study extent (~10,000 lakes). Procedures for the integration of datasets included: creating a flexible database design; authoring and integrating metadata; documenting data provenance; quantifying spatial measures of geographic data; quality-controlling integrated and derived data; and extensively documenting the database. Our procedures make a large, complex, and integrated database reproducible and extensible, allowing users to ask new research questions with the existing database or through the addition of new data. The largest challenge of this task was the heterogeneity of the data, formats, and metadata. Many steps of data integration need manual input from experts in diverse fields, requiring close collaboration.}, } @article {pmid26137637, year = {2015}, author = {Novoselskaya-Dragovich, AY}, title = {[Genetics and Genomics of Wheat: Storage Proteins, Ecological Plasticity, and Immunity].}, journal = {Genetika}, volume = {51}, number = {5}, pages = {568-583}, pmid = {26137637}, issn = {0016-6758}, mesh = {*Adaptation, Physiological/genetics/immunology ; Databases, Genetic ; *Evolution, Molecular ; *Genomics ; Plant Immunity/*genetics ; *Seed Storage Proteins/genetics/immunology ; *Triticum/genetics/immunology ; }, abstract = {Recent advances in genetics and genetic research methods made it possible to explain the large polymorphism observed among storage proteins of wheat weevil (gliadins and glutenins), to determine their genetic control mechanism, and to develop a system for the identification of wheat genotypes on the basis of multiple allelism. This system has extremely high sensitivity and efficiency, which makes it possible to conduct studies to determine the purity and authenticity of wheat varieties, the dynamics of alleles diversity in time and space, the phylogenetics, etc., through the use of an extensive database on the allelic composition of gliadin loci. An investigation of the molecular structure of genes controlling the synthesis of storage proteins and their organization on chromosomes, as well as an analysis of wheat genome structure, revealed the molecular mechanisms of variability in the wheat genome and its reorganization in response to changes in environmental conditions and cultivation technologies. The multilevel genetic system of protection against pathogens and adverse environmental factors that developed in the course of wheat evolution continues to astound researchers' imagination with new resistance genes and novel types of antimicrobial peptides having been discovered and sequenced in recent years and the diversity of their structures and mechanisms of action in response to pathogens. An analysis of gene sequences involved in wheat domestication, namely, those that define ecological plasticity, i. e. the type of plant development (Vrn genes), and those responsible for spikelet traits (Q genes), which ensured the successful cultivation of wheat by humans, revealed that the basis for these features are specific mutations.}, } @article {pmid26133641, year = {2015}, author = {Tzika, AC and Ullate-Agote, A and Grbic, D and Milinkovitch, MC}, title = {Reptilian Transcriptomes v2.0: An Extensive Resource for Sauropsida Genomics and Transcriptomics.}, journal = {Genome biology and evolution}, volume = {7}, number = {6}, pages = {1827-1841}, pmid = {26133641}, issn = {1759-6653}, mesh = {Alligators and Crocodiles/genetics ; Animals ; Base Sequence ; Consensus Sequence ; *Databases, Genetic ; *Gene Expression Profiling ; Genome ; *Genomics ; Lizards/genetics ; Molecular Sequence Annotation ; Phylogeny ; Reptiles/classification/*genetics ; Snakes/genetics ; }, abstract = {Despite the availability of deep-sequencing techniques, genomic and transcriptomic data remain unevenly distributed across phylogenetic groups. For example, reptiles are poorly represented in sequence databases, hindering functional evolutionary and developmental studies in these lineages substantially more diverse than mammals. In addition, different studies use different assembly and annotation protocols, inhibiting meaningful comparisons. Here, we present the "Reptilian Transcriptomes Database 2.0," which provides extensive annotation of transcriptomes and genomes from species covering the major reptilian lineages. To this end, we sequenced normalized complementary DNA libraries of multiple adult tissues and various embryonic stages of the leopard gecko and the corn snake and gathered published reptilian sequence data sets from representatives of the four extant orders of reptiles: Squamata (snakes and lizards), the tuatara, crocodiles, and turtles. The LANE runner 2.0 software was implemented to annotate all assemblies within a single integrated pipeline. We show that this approach increases the annotation completeness of the assembled transcriptomes/genomes. We then built large concatenated protein alignments of single-copy genes and inferred phylogenetic trees that support the positions of turtles and the tuatara as sister groups of Archosauria and Squamata, respectively. The Reptilian Transcriptomes Database 2.0 resource will be updated to include selected new data sets as they become available, thus making it a reference for differential expression studies, comparative genomics and transcriptomics, linkage mapping, molecular ecology, and phylogenomic analyses involving reptiles. The database is available at www.reptilian-transcriptomes.org and can be enquired using a wwwblast server installed at the University of Geneva.}, } @article {pmid26126606, year = {2015}, author = {Becerra, MB and Becerra, BJ and Banta, JE and Safdar, N}, title = {Impact of Clostridium difficile infection among pneumonia and urinary tract infection hospitalizations: an analysis of the Nationwide Inpatient Sample.}, journal = {BMC infectious diseases}, volume = {15}, number = {}, pages = {254}, pmid = {26126606}, issn = {1471-2334}, mesh = {Adolescent ; Adult ; Aged ; *Clostridioides difficile ; Clostridium Infections/epidemiology ; Coinfection/epidemiology ; Comorbidity ; Cross Infection/epidemiology ; Databases, Factual ; Enterocolitis, Pseudomembranous/*epidemiology ; Female ; Hospital Mortality ; Hospitalization ; Hospitals, Community ; Humans ; Inpatients ; Male ; Middle Aged ; Odds Ratio ; Pneumonia/*epidemiology ; Prevalence ; Regression Analysis ; Risk Factors ; United States/epidemiology ; Urinary Tract Infections/*epidemiology ; Young Adult ; }, abstract = {BACKGROUND: Clostridium difficile infection (CDI) remains one of the major hospital acquired infections in the nation, often attributable to increased antibiotic use. Little research, however, exists on the prevalence and impact of CDI on patient and hospital outcomes among populations requiring such treatment. As such, the goal of this study was to examine the prevalence, risk factors, and impact of CDI among pneumonia and urinary tract infection (UTI) hospitalizations.

METHODS: The Nationwide Inpatient Sample (2009-2011), reflecting a 20% stratified sample of community hospitals in the United States, was used. A total of 593,038 pneumonia and 255,770 UTI discharges were included. Survey-weighted multivariable regression analyses were conducted to assess the predictors and impact of CDI among pneumonia and UTI discharges.

RESULTS: A significantly higher prevalence of CDI was present among men with UTI (13.3 per 1,000) as compared to women (11.3 per 1,000). CDI was associated with higher in-hospital mortality among discharges for pneumonia (adjusted odds ratio [aOR] for men = 3.2, women aOR = 2.8) and UTI (aOR for men = 4.1, women aOR = 3.4). Length of stay among pneumonia and UTI discharges were also double upon presence of CDI. In addition, CDI increased the total charges by at least 75% and 55% among pneumonia and UTI discharges, respectively. Patient and hospital characteristics associated with CDI included being 65 years or older, Charlson Deyo index for comorbidity of 2 or more, Medicare as the primary payer, and discharge from urban hospitals, among both pneumonia and UTI discharges.

CONCLUSION: CDI occurs frequently in hospitalizations among those discharged from hospital for pneumonia and UTI, and is associated with increased in-hospital mortality and health resource utilization. Interventions to mitigate the burden of CDI in these high-risk populations are urgently needed.}, } @article {pmid26125950, year = {2015}, author = {Ke, R and Loverdo, C and Qi, H and Sun, R and Lloyd-Smith, JO}, title = {Rational Design and Adaptive Management of Combination Therapies for Hepatitis C Virus Infection.}, journal = {PLoS computational biology}, volume = {11}, number = {6}, pages = {e1004040}, pmid = {26125950}, issn = {1553-7358}, mesh = {*Antiviral Agents/pharmacokinetics/pharmacology/therapeutic use ; Computational Biology ; Drug Resistance, Viral/drug effects/genetics ; Genetic Fitness ; *Hepacivirus/drug effects/genetics/physiology ; *Hepatitis C/drug therapy/virology ; Humans ; Medication Adherence ; *Models, Biological ; }, abstract = {Recent discoveries of direct acting antivirals against Hepatitis C virus (HCV) have raised hopes of effective treatment via combination therapies. Yet rapid evolution and high diversity of HCV populations, combined with the reality of suboptimal treatment adherence, make drug resistance a clinical and public health concern. We develop a general model incorporating viral dynamics and pharmacokinetics/ pharmacodynamics to assess how suboptimal adherence affects resistance development and clinical outcomes. We derive design principles and adaptive treatment strategies, identifying a high-risk period when missing doses is particularly risky for de novo resistance, and quantifying the number of additional doses needed to compensate when doses are missed. Using data from large-scale resistance assays, we demonstrate that the risk of resistance can be reduced substantially by applying these principles to a combination therapy of daclatasvir and asunaprevir. By providing a mechanistic framework to link patient characteristics to the risk of resistance, these findings show the potential of rational treatment design.}, } @article {pmid26124105, year = {2015}, author = {Savage, PE and Brown, S and Sakai, E and Currie, TE}, title = {Statistical universals reveal the structures and functions of human music.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {112}, number = {29}, pages = {8987-8992}, pmid = {26124105}, issn = {1091-6490}, mesh = {Databases as Topic ; Geography ; Humans ; Language ; Likelihood Functions ; Models, Theoretical ; *Music ; Phylogeny ; *Statistics as Topic ; }, abstract = {Music has been called "the universal language of mankind." Although contemporary theories of music evolution often invoke various musical universals, the existence of such universals has been disputed for decades and has never been empirically demonstrated. Here we combine a music-classification scheme with statistical analyses, including phylogenetic comparative methods, to examine a well-sampled global set of 304 music recordings. Our analyses reveal no absolute universals but strong support for many statistical universals that are consistent across all nine geographic regions sampled. These universals include 18 musical features that are common individually as well as a network of 10 features that are commonly associated with one another. They span not only features related to pitch and rhythm that are often cited as putative universals but also rarely cited domains including performance style and social context. These cross-cultural structural regularities of human music may relate to roles in facilitating group coordination and cohesion, as exemplified by the universal tendency to sing, play percussion instruments, and dance to simple, repetitive music in groups. Our findings highlight the need for scientists studying music evolution to expand the range of musical cultures and musical features under consideration. The statistical universals we identified represent important candidates for future investigation.}, } @article {pmid26123545, year = {2015}, author = {Rosser, N and Kozak, KM and Phillimore, AB and Mallet, J}, title = {Extensive range overlap between heliconiine sister species: evidence for sympatric speciation in butterflies?.}, journal = {BMC evolutionary biology}, volume = {15}, number = {}, pages = {125}, pmid = {26123545}, issn = {1471-2148}, support = {BB/G006903/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; Biodiversity ; Butterflies/anatomy & histology/*classification/*genetics ; Climate ; Computer Simulation ; Databases, Factual ; Ecology ; Genetic Speciation ; Phylogeny ; Sympatry ; Wings, Animal/anatomy & histology ; }, abstract = {BACKGROUND: Sympatric speciation is today generally viewed as plausible, and some well-supported examples exist, but its relative contribution to biodiversity remains to be established. We here quantify geographic overlap of sister species of heliconiine butterflies, and use age-range correlations and spatial simulations of the geography of speciation to infer the frequency of sympatric speciation. We also test whether shifts in mimetic wing colour pattern, host plant use and climate niche play a role in speciation, and whether such shifts are associated with sympatry.

RESULTS: Approximately a third of all heliconiine sister species pairs exhibit near complete range overlap, and analyses of the observed patterns of range overlap suggest that sympatric speciation contributes 32%-95% of speciation events. Müllerian mimicry colour patterns and host plant choice are highly labile traits that seem to be associated with speciation, but we find no association between shifts in these traits and range overlap. In contrast, climatic niches of sister species are more conserved.

CONCLUSIONS: Unlike birds and mammals, sister species of heliconiines are often sympatric and our inferences using the most recent comparative methods suggest that sympatric speciation is common. However, if sister species spread rapidly into sympatry (e.g. due to their similar climatic niches), then assumptions underlying our methods would be violated. Furthermore, although we find some evidence for the role of ecology in speciation, ecological shifts did not show the associations with range overlap expected under sympatric speciation. We delimit species of heliconiines in three different ways, based on "strict and " "relaxed" biological species concepts (BSC), as well as on a surrogate for the widely-used "diagnostic" version of the phylogenetic species concept (PSC). We show that one reason why more sympatric speciation is inferred in heliconiines than in birds may be due to a different culture of species delimitation in the two groups. To establish whether heliconiines are exceptional will require biogeographic comparative studies for a wider range of animal taxa including many more invertebrates.}, } @article {pmid26123276, year = {2015}, author = {Nobel, YR and Cox, LM and Kirigin, FF and Bokulich, NA and Yamanishi, S and Teitler, I and Chung, J and Sohn, J and Barber, CM and Goldfarb, DS and Raju, K and Abubucker, S and Zhou, Y and Ruiz, VE and Li, H and Mitreva, M and Alekseyenko, AV and Weinstock, GM and Sodergren, E and Blaser, MJ}, title = {Metabolic and metagenomic outcomes from early-life pulsed antibiotic treatment.}, journal = {Nature communications}, volume = {6}, number = {}, pages = {7486}, pmid = {26123276}, issn = {2041-1723}, support = {UL1 TR001445/TR/NCATS NIH HHS/United States ; UL1 RR029893/RR/NCRR NIH HHS/United States ; 1UL1RR029893/RR/NCRR NIH HHS/United States ; U54 HG004968/HG/NHGRI NIH HHS/United States ; TL1 RR029892/RR/NCRR NIH HHS/United States ; U54HG004968/HG/NHGRI NIH HHS/United States ; R01-DK090989/DK/NIDDK NIH HHS/United States ; R01 DK090989/DK/NIDDK NIH HHS/United States ; T32 GM088118/GM/NIGMS NIH HHS/United States ; }, mesh = {*Aging ; Amoxicillin/administration & dosage/*pharmacology ; Animals ; Anti-Bacterial Agents/administration & dosage/*pharmacology ; Drug Administration Schedule ; Drug Therapy, Combination ; Energy Metabolism/physiology ; Feces/chemistry ; Female ; Gene Expression Regulation/*drug effects ; Liver/drug effects/metabolism ; Male ; Metagenomics ; Mice ; Mice, Inbred C57BL ; Transcriptome ; Tylosin/administration & dosage/*pharmacology ; }, abstract = {Mammalian species have co-evolved with intestinal microbial communities that can shape development and adapt to environmental changes, including antibiotic perturbation or nutrient flux. In humans, especially children, microbiota disruption is common, yet the dynamic microbiome recovery from early-life antibiotics is still uncharacterized. Here we use a mouse model mimicking paediatric antibiotic use and find that therapeutic-dose pulsed antibiotic treatment (PAT) with a beta-lactam or macrolide alters both host and microbiota development. Early-life PAT accelerates total mass and bone growth, and causes progressive changes in gut microbiome diversity, population structure and metagenomic content, with microbiome effects dependent on the number of courses and class of antibiotic. Whereas control microbiota rapidly adapts to a change in diet, PAT slows the ecological progression, with delays lasting several months with previous macrolide exposure. This study identifies key markers of disturbance and recovery, which may help provide therapeutic targets for microbiota restoration following antibiotic treatment.}, } @article {pmid26121354, year = {2015}, author = {Kryuchkova-Mostacci, N and Robinson-Rechavi, M}, title = {Tissue-Specific Evolution of Protein Coding Genes in Human and Mouse.}, journal = {PloS one}, volume = {10}, number = {6}, pages = {e0131673}, pmid = {26121354}, issn = {1932-6203}, mesh = {Animals ; Databases, Nucleic Acid ; *Evolution, Molecular ; Gene Duplication ; Gene Regulatory Networks ; Genomics/methods ; Humans ; Mice ; *Open Reading Frames ; Organ Specificity/genetics ; Selection, Genetic ; }, abstract = {Protein-coding genes evolve at different rates, and the influence of different parameters, from gene size to expression level, has been extensively studied. While in yeast gene expression level is the major causal factor of gene evolutionary rate, the situation is more complex in animals. Here we investigate these relations further, especially taking in account gene expression in different organs as well as indirect correlations between parameters. We used RNA-seq data from two large datasets, covering 22 mouse tissues and 27 human tissues. Over all tissues, evolutionary rate only correlates weakly with levels and breadth of expression. The strongest explanatory factors of purifying selection are GC content, expression in many developmental stages, and expression in brain tissues. While the main component of evolutionary rate is purifying selection, we also find tissue-specific patterns for sites under neutral evolution and for positive selection. We observe fast evolution of genes expressed in testis, but also in other tissues, notably liver, which are explained by weak purifying selection rather than by positive selection.}, } @article {pmid26121293, year = {2015}, author = {Chen, BC and Luo, J and Hendryx, M}, title = {Zinc compound air releases from Toxics Release Inventory facilities and cardiovascular disease mortality rates.}, journal = {Environmental research}, volume = {142}, number = {}, pages = {96-103}, doi = {10.1016/j.envres.2015.06.022}, pmid = {26121293}, issn = {1096-0953}, mesh = {Air Pollutants/adverse effects/*analysis ; Cardiovascular Diseases/etiology/*mortality ; *Chemical Hazard Release ; *Databases, Factual ; Female ; Humans ; Male ; Mortality/trends ; Retrospective Studies ; United States ; United States Environmental Protection Agency ; Zinc Compounds/adverse effects/*analysis ; }, abstract = {BACKGROUND: Inhaled zinc has been found in association with cardiopulmonary toxicity. However, limited human epidemiologic studies are available. This study analyzed the association between covariate-adjusted cardiovascular (CVD) mortality rates and zinc compound air releases in the United States.

METHODS: We conducted an ecological analysis on the association between zinc compound air releases for 1991-2000 using the Toxics Release Inventory database and average age-adjusted CVD mortality for 2006-2010, adjusting for race/ethnicity composition and several health and socioeconomic factors. Models were estimated for males and females and for metropolitan and nonmetropolitan counties.

RESULTS: Zinc compound air releases were positively associated with increased adjusted CVD mortality rates in all four models (β=0.0085, p<0.0001 for males in nonmetropolitan counties; β=0.0093, p<0.0001 for males in metropolitan counties; β=0.0145, p<0.0001 for females in nonmetropolitan counties; and β=0.0098, p<0.0001 for females in metropolitan counties). Results were largely robust to various sensitivity analyses.

CONCLUSION: This study provides epidemiological evidence for possible CVD health impacts of inhaled zinc in the United States. Although the strongest effect was found for females in nonmetropolitan counties, the associations were consistent in nonmetropolitan or metropolitan counties for both genders.}, } @article {pmid26120139, year = {2015}, author = {McIlroy, SJ and Saunders, AM and Albertsen, M and Nierychlo, M and McIlroy, B and Hansen, AA and Karst, SM and Nielsen, JL and Nielsen, PH}, title = {MiDAS: the field guide to the microbes of activated sludge.}, journal = {Database : the journal of biological databases and curation}, volume = {2015}, number = {}, pages = {bav062}, pmid = {26120139}, issn = {1758-0463}, mesh = {*Bacteria/classification/genetics ; *Databases, Nucleic Acid ; RNA, Bacterial/*genetics ; RNA, Ribosomal, 16S/*genetics ; Sewage/*microbiology ; }, abstract = {The Microbial Database for Activated Sludge (MiDAS) field guide is a freely available online resource linking the identity of abundant and process critical microorganisms in activated sludge wastewater treatment systems to available data related to their functional importance. Phenotypic properties of some of these genera are described, but most are known only from sequence data. The MiDAS taxonomy is a manual curation of the SILVA taxonomy that proposes a name for all genus-level taxa observed to be abundant by large-scale 16 S rRNA gene amplicon sequencing of full-scale activated sludge communities. The taxonomy can be used to classify unknown sequences, and the online MiDAS field guide links the identity to the available information about their morphology, diversity, physiology and distribution. The use of a common taxonomy across the field will provide a solid foundation for the study of microbial ecology of the activated sludge process and related treatment processes. The online MiDAS field guide is a collaborative workspace intended to facilitate a better understanding of the ecology of activated sludge and related treatment processes--knowledge that will be an invaluable resource for the optimal design and operation of these systems.}, } @article {pmid26113203, year = {2015}, author = {Keum, J and Kaluarachchi, JJ}, title = {Development of a decision-making methodology to design a water quality monitoring network.}, journal = {Environmental monitoring and assessment}, volume = {187}, number = {7}, pages = {466}, pmid = {26113203}, issn = {1573-2959}, mesh = {*Decision Support Techniques ; Environmental Monitoring/*methods ; Hydrology ; *Models, Theoretical ; Rivers ; Salinity ; Southwestern United States ; Water ; *Water Quality ; Water Supply ; }, abstract = {The number of water quality monitoring stations in the USA has decreased over the past few decades. Scarcity of observations can easily produce prediction uncertainty due to unreliable model calibration. An effective water quality monitoring network is important not only for model calibration and water quality prediction but also for resources management. Redundant or improperly located monitoring stations may cause increased monitoring costs without improvement to the understanding of water quality in watersheds. In this work, a decision-making methodology is proposed to design a water quality monitoring network by providing an adequate number of monitoring stations and their approximate locations at the eight-digit hydrologic unit codes (HUC8) scale. The proposed methodology is demonstrated for an example at the Upper Colorado River Basin (UCRB), where salinity is a serious concern. The level of monitoring redundancy or scarcity is defined by an index, station ratio (SR), which represents a monitoring density based on water quality load originated within a subbasin. By comparing the number of stations from a selected target SR with the available number of stations including the actual and the potential stations, the suggested number of stations in each subbasin was decided. If monitoring stations are primarily located in the low salinity loading subbasins, the average actual SR tends to increase, and vice versa. Results indicate that the spatial distribution of monitoring locations in 2011 is concentrated on low salinity loading subbasins, and therefore, additional monitoring is required for the high salinity loading subbasins. The proposed methodology shows that the SR is a simple and a practical indicator for monitoring density.}, } @article {pmid26111519, year = {2015}, author = {Song, Y and Laskay, ÜA and Vilcins, IM and Barbour, AG and Wysocki, VH}, title = {Top-down-assisted bottom-up method for homologous protein sequencing: hemoglobin from 33 bird species.}, journal = {Journal of the American Society for Mass Spectrometry}, volume = {26}, number = {11}, pages = {1875-1884}, pmid = {26111519}, issn = {1879-1123}, support = {U54 AI065359/AI/NIAID NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Animals ; *Avian Proteins/analysis/chemistry/classification ; Birds ; *Databases, Protein ; *Hemoglobins/analysis/chemistry/classification ; Molecular Sequence Data ; Peptide Fragments/analysis/chemistry ; Sequence Analysis, Protein/*methods ; *Software ; Tandem Mass Spectrometry ; }, abstract = {Ticks are vectors for disease transmission because they are indiscriminant in their feeding on multiple vertebrate hosts, transmitting pathogens between their hosts. Identifying the hosts on which ticks have fed is important for disease prevention and intervention. We have previously shown that hemoglobin (Hb) remnants from a host on which a tick fed can be used to reveal the host's identity. For the present research, blood was collected from 33 bird species that are common in the U.S. as hosts for ticks but that have unknown Hb sequences. A top-down-assisted bottom-up mass spectrometry approach with a customized searching database, based on variability in known bird hemoglobin sequences, has been devised to facilitate fast and complete sequencing of hemoglobin from birds with unknown sequences. These hemoglobin sequences will be added to a hemoglobin database and used for tick host identification. The general approach has the potential to sequence any set of homologous proteins completely in a rapid manner. Graphical Abstract ᅟ.}, } @article {pmid26110587, year = {2015}, author = {Alkhamis, MA and Moore, BR and Perez, AM}, title = {Phylodynamics of H5N1 Highly Pathogenic Avian Influenza in Europe, 2005-2010: Potential for Molecular Surveillance of New Outbreaks.}, journal = {Viruses}, volume = {7}, number = {6}, pages = {3310-3328}, pmid = {26110587}, issn = {1999-4915}, mesh = {Animals ; Birds ; Computational Biology ; *Disease Outbreaks ; Disease Transmission, Infectious ; *Epidemiological Monitoring ; Europe/epidemiology ; Genetic Variation ; Hemagglutinin Glycoproteins, Influenza Virus/genetics ; Influenza A Virus, H5N1 Subtype/*classification/genetics/*isolation & purification ; Influenza in Birds/*epidemiology/*virology ; Molecular Epidemiology ; Neuraminidase/genetics ; *Phylogeography ; Poultry ; Russia/epidemiology ; Sequence Analysis, DNA ; Viral Proteins/genetics ; }, abstract = {Previous Bayesian phylogeographic studies of H5N1 highly pathogenic avian influenza viruses (HPAIVs) explored the origin and spread of the epidemic from China into Russia, indicating that HPAIV circulated in Russia prior to its detection there in 2005. In this study, we extend this research to explore the evolution and spread of HPAIV within Europe during the 2005-2010 epidemic, using all available sequences of the hemagglutinin (HA) and neuraminidase (NA) gene regions that were collected in Europe and Russia during the outbreak. We use discrete-trait phylodynamic models within a Bayesian statistical framework to explore the evolution of HPAIV. Our results indicate that the genetic diversity and effective population size of HPAIV peaked between mid-2005 and early 2006, followed by drastic decline in 2007, which coincides with the end of the epidemic in Europe. Our results also suggest that domestic birds were the most likely source of the spread of the virus from Russia into Europe. Additionally, estimates of viral dispersal routes indicate that Russia, Romania, and Germany were key epicenters of these outbreaks. Our study quantifies the dynamics of a major European HPAIV pandemic and substantiates the ability of phylodynamic models to improve molecular surveillance of novel AIVs.}, } @article {pmid26110276, year = {2015}, author = {Fang, J and Wang, X and Mu, S and Zhang, S and Dong, D}, title = {BGD: a database of bat genomes.}, journal = {PloS one}, volume = {10}, number = {6}, pages = {e0131296}, pmid = {26110276}, issn = {1932-6203}, mesh = {Animals ; Chiroptera/*genetics ; Computational Biology ; *Databases, Genetic ; *Genome ; Molecular Sequence Annotation ; Phylogeny ; Programming Languages ; Search Engine ; Species Specificity ; User-Computer Interface ; }, abstract = {Bats account for ~20% of mammalian species, and are the only mammals with true powered flight. For the sake of their specialized phenotypic traits, many researches have been devoted to examine the evolution of bats. Until now, some whole genome sequences of bats have been assembled and annotated, however, a uniform resource for the annotated bat genomes is still unavailable. To make the extensive data associated with the bat genomes accessible to the general biological communities, we established a Bat Genome Database (BGD). BGD is an open-access, web-available portal that integrates available data of bat genomes and genes. It hosts data from six bat species, including two megabats and four microbats. Users can query the gene annotations using efficient searching engine, and it offers browsable tracks of bat genomes. Furthermore, an easy-to-use phylogenetic analysis tool was also provided to facilitate online phylogeny study of genes. To the best of our knowledge, BGD is the first database of bat genomes. It will extend our understanding of the bat evolution and be advantageous to the bat sequences analysis. BGD is freely available at: http://donglab.ecnu.edu.cn/databases/BatGenome/.}, } @article {pmid26110266, year = {2015}, author = {Obolski, U and Stein, GY and Hadany, L}, title = {Antibiotic Restriction Might Facilitate the Emergence of Multi-drug Resistance.}, journal = {PLoS computational biology}, volume = {11}, number = {6}, pages = {e1004340}, pmid = {26110266}, issn = {1553-7358}, mesh = {*Anti-Bacterial Agents/pharmacology/therapeutic use ; *Bacterial Infections/drug therapy/epidemiology/microbiology/transmission ; Computational Biology ; Drug Resistance, Multiple, Bacterial/*drug effects ; Humans ; *Models, Biological ; }, abstract = {High antibiotic resistance frequencies have become a major public health issue. The decrease in new antibiotics' production, combined with increasing frequencies of multi-drug resistant (MDR) bacteria, cause substantial limitations in treatment options for some bacterial infections. To diminish overall resistance, and especially the occurrence of bacteria that are resistant to all antibiotics, certain drugs are deliberately scarcely used--mainly when other options are exhausted. We use a mathematical model to explore the efficiency of such antibiotic restrictions. We assume two commonly used drugs and one restricted drug. The model is examined for the mixing strategy of antibiotic prescription, in which one of the drugs is randomly assigned to each incoming patient. Data obtained from Rabin medical center, Israel, is used to estimate realistic single and double antibiotic resistance frequencies in incoming patients. We find that broad usage of the hitherto restricted drug can reduce the number of incorrectly treated patients, and reduce the spread of bacteria resistant to both common antibiotics. Such double resistant infections are often eventually treated with the restricted drug, and therefore are prone to become resistant to all three antibiotics. Thus, counterintuitively, a broader usage of a formerly restricted drug can sometimes lead to a decrease in the emergence of bacteria resistant to all drugs. We recommend re-examining restriction of specific drugs, when multiple resistance to the relevant alternative drugs already exists.}, } @article {pmid26107643, year = {2015}, author = {de Weerd, N and van Langevelde, F and van Oeveren, H and Nolet, BA and Kölzsch, A and Prins, HH and de Boer, WF}, title = {Deriving Animal Behaviour from High-Frequency GPS: Tracking Cows in Open and Forested Habitat.}, journal = {PloS one}, volume = {10}, number = {6}, pages = {e0129030}, pmid = {26107643}, issn = {1932-6203}, mesh = {Animals ; Behavior, Animal/*physiology ; Cattle ; Decision Trees ; Ecosystem ; Female ; Forests ; Geographic Information Systems/*statistics & numerical data ; Movement/*physiology ; }, abstract = {The increasing spatiotemporal accuracy of Global Navigation Satellite Systems (GNSS) tracking systems opens the possibility to infer animal behaviour from tracking data. We studied the relationship between high-frequency GNSS data and behaviour, aimed at developing an easily interpretable classification method to infer behaviour from location data. Behavioural observations were carried out during tracking of cows (Bos Taurus) fitted with high-frequency GPS (Global Positioning System) receivers. Data were obtained in an open field and forested area, and movement metrics were calculated for 1 min, 12 s and 2 s intervals. We observed four behaviour types (Foraging, Lying, Standing and Walking). We subsequently used Classification and Regression Trees to classify the simultaneously obtained GPS data as these behaviour types, based on distances and turning angles between fixes. GPS data with a 1 min interval from the open field was classified correctly for more than 70% of the samples. Data from the 12 s and 2 s interval could not be classified successfully, emphasizing that the interval should be long enough for the behaviour to be defined by its characteristic movement metrics. Data obtained in the forested area were classified with a lower accuracy (57%) than the data from the open field, due to a larger positional error of GPS locations and differences in behavioural performance influenced by the habitat type. This demonstrates the importance of understanding the relationship between behaviour and movement metrics, derived from GNSS fixes at different frequencies and in different habitats, in order to successfully infer behaviour. When spatially accurate location data can be obtained, behaviour can be inferred from high-frequency GNSS fixes by calculating simple movement metrics and using easily interpretable decision trees. This allows for the combined study of animal behaviour and habitat use based on location data, and might make it possible to detect deviations in behaviour at the individual level.}, } @article {pmid26107170, year = {2015}, author = {Wang, Z and Zhou, J and Loaiciga, H and Guo, H and Hong, S}, title = {A DPSIR model for ecological security assessment through indicator screening: a case study at Dianchi Lake in China.}, journal = {PloS one}, volume = {10}, number = {6}, pages = {e0131732}, pmid = {26107170}, issn = {1932-6203}, mesh = {Algorithms ; China ; Conservation of Natural Resources/*methods ; Cyanobacteria ; Databases, Factual ; Ecology/*methods ; Ecosystem ; Environmental Monitoring/*methods ; Eutrophication ; Human Activities ; Lakes ; Models, Theoretical ; Principal Component Analysis ; Risk ; Risk Assessment ; }, abstract = {Given the important role of lake ecosystems in social and economic development, and the current severe environmental degradation in China, a systematic diagnosis of the ecological security of lakes is essential for sustainable development. A Driving-force, Pressure, Status, Impact, and Risk (DPSIR) model, combined with data screening for lake ecological security assessment was developed to overcome the disadvantages of data selection in existing assessment methods. Correlation and principal component analysis were used to select independent and representative data. The DPSIR model was then applied to evaluate the ecological security of Dianchi Lake in China during 1988-2007 using an ecological security index. The results revealed a V-shaped trend. The application of the DPSIR model with data screening provided useful information regarding the status of the lake's ecosystem, while ensuring information efficiency and eliminating multicollinearity. The modeling approach described here is practical and operationally efficient, and provides an attractive alternative approach to assess the ecological security of lakes.}, } @article {pmid26102275, year = {2015}, author = {Morlon, H and O'Connor, TK and Bryant, JA and Charkoudian, LK and Docherty, KM and Jones, E and Kembel, SW and Green, JL and Bohannan, BJ}, title = {The Biogeography of Putative Microbial Antibiotic Production.}, journal = {PloS one}, volume = {10}, number = {6}, pages = {e0130659}, pmid = {26102275}, issn = {1932-6203}, mesh = {Actinobacteria/classification/enzymology/genetics ; Anti-Bacterial Agents/*biosynthesis ; Bacteria/classification/enzymology/*genetics ; Bacterial Proteins/*genetics ; Bayes Theorem ; Biodiversity ; Bioprospecting ; Databases, Genetic ; Ecosystem ; Fungal Proteins/*genetics ; Fungi/classification/enzymology/*genetics ; *Genes, Bacterial ; *Genes, Fungal ; Likelihood Functions ; Phylogeny ; Phylogeography ; Plants ; Polyketide Synthases/classification/genetics ; Polyketides/metabolism ; Sequence Alignment ; Sequence Homology, Nucleic Acid ; *Soil Microbiology ; }, abstract = {Understanding patterns in the distribution and abundance of functional traits across a landscape is of fundamental importance to ecology. Mapping these distributions is particularly challenging for species-rich groups with sparse trait measurement coverage, such as flowering plants, insects, and microorganisms. Here, we use likelihood-based character reconstruction to infer and analyze the spatial distribution of unmeasured traits. We apply this framework to a microbial dataset comprised of 11,732 ketosynthase alpha gene sequences extracted from 144 soil samples from three continents to document the spatial distribution of putative microbial polyketide antibiotic production. Antibiotic production is a key competitive strategy for soil microbial survival and performance. Additionally, novel antibiotic discovery is highly relevant to human health, making natural antibiotic production by soil microorganisms a major target for bioprospecting. Our comparison of trait-based biogeographical patterns to patterns based on taxonomy and phylogeny is relevant to our basic understanding of microbial biogeography as well as the pressing need for new antibiotics.}, } @article {pmid26100883, year = {2015}, author = {Edger, PP and Heidel-Fischer, HM and Bekaert, M and Rota, J and Glöckner, G and Platts, AE and Heckel, DG and Der, JP and Wafula, EK and Tang, M and Hofberger, JA and Smithson, A and Hall, JC and Blanchette, M and Bureau, TE and Wright, SI and dePamphilis, CW and Eric Schranz, M and Barker, MS and Conant, GC and Wahlberg, N and Vogel, H and Pires, JC and Wheat, CW}, title = {The butterfly plant arms-race escalated by gene and genome duplications.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {112}, number = {27}, pages = {8362-8366}, pmid = {26100883}, issn = {1091-6490}, mesh = {Animals ; Bayes Theorem ; Biodiversity ; Brassicaceae/classification/*genetics/parasitology ; Butterflies/classification/*genetics/physiology ; Evolution, Molecular ; *Gene Duplication ; Gene Expression ; Genes, Insect/genetics ; Genes, Plant/genetics ; Genetic Variation ; Genome, Insect/*genetics ; Genome, Plant/*genetics ; Host-Parasite Interactions/genetics ; Insect Proteins/genetics ; Phylogeny ; Plant Proteins/genetics ; Species Specificity ; }, abstract = {Coevolutionary interactions are thought to have spurred the evolution of key innovations and driven the diversification of much of life on Earth. However, the genetic and evolutionary basis of the innovations that facilitate such interactions remains poorly understood. We examined the coevolutionary interactions between plants (Brassicales) and butterflies (Pieridae), and uncovered evidence for an escalating evolutionary arms-race. Although gradual changes in trait complexity appear to have been facilitated by allelic turnover, key innovations are associated with gene and genome duplications. Furthermore, we show that the origins of both chemical defenses and of molecular counter adaptations were associated with shifts in diversification rates during the arms-race. These findings provide an important connection between the origins of biodiversity, coevolution, and the role of gene and genome duplications as a substrate for novel traits.}, } @article {pmid26099482, year = {2015}, author = {Bayliss, HR and Beyer, FR}, title = {Information retrieval for ecological syntheses.}, journal = {Research synthesis methods}, volume = {6}, number = {2}, pages = {136-148}, doi = {10.1002/jrsm.1120}, pmid = {26099482}, issn = {1759-2887}, mesh = {Data Accuracy ; *Data Interpretation, Statistical ; Data Mining/*methods ; Ecology/*methods ; Evidence-Based Medicine/methods ; *Meta-Analysis as Topic ; *Research Design ; *Review Literature as Topic ; }, abstract = {Research syntheses are increasingly being conducted within the fields of ecology and environmental management. Information retrieval is crucial in any synthesis in identifying data for inclusion whilst potentially reducing biases in the dataset gathered, yet the nature of ecological information provides several challenges when compared with medicine that should be considered when planning and undertaking searches. We present ten recommendations for anyone considering undertaking information retrieval for ecological research syntheses that highlight the main differences with medicine and, if adopted, may help reduce biases in the dataset retrieved, increase search efficiency and improve reporting standards. They are as follows: (1) plan for information retrieval at an early stage, (2) identify and use sources of help, (3) clearly define the question to be addressed, (4) ensure that provisions for managing, recording and reporting the search are in place, (5) select an appropriate search type, (6) identify sources to be used, (7) identify limitations of the sources, (8) ensure that the search vocabulary is appropriate, (9) identify limits and filters that can help direct the search, and (10) test the strategy to ensure that it is realistic and manageable. These recommendations may be of value for other disciplines where search infrastructures are not yet sufficiently well developed.}, } @article {pmid26099481, year = {2015}, author = {Shrier, I}, title = {How to critically read ecological meta-analyses.}, journal = {Research synthesis methods}, volume = {6}, number = {2}, pages = {134-135}, doi = {10.1002/jrsm.1150}, pmid = {26099481}, issn = {1759-2887}, mesh = {*Data Accuracy ; *Data Interpretation, Statistical ; Data Mining/*methods ; Ecology/*methods ; *Meta-Analysis as Topic ; *Research Design ; }, } @article {pmid26099480, year = {2015}, author = {Lortie, CJ and Stewart, G and Rothstein, H and Lau, J}, title = {How to critically read ecological meta-analyses.}, journal = {Research synthesis methods}, volume = {6}, number = {2}, pages = {124-133}, doi = {10.1002/jrsm.1109}, pmid = {26099480}, issn = {1759-2887}, mesh = {*Data Accuracy ; *Data Interpretation, Statistical ; Data Mining/*methods ; Ecology/*methods ; *Meta-Analysis as Topic ; Reading ; *Research Design ; }, abstract = {Meta-analysis offers ecologists a powerful tool for knowledge synthesis. Albeit a form of review, it also shares many similarities with primary empirical research. Consequently, critical reading of meta-analyses incorporates criteria from both sets of approaches particularly because ecology is a discipline that embraces heterogeneity and broad methodologies. The most important issues in critically assessing a meta-analysis initially include transparency, replicability, and clear statement of purpose by the authors. Specific to ecology, more so than other disciplines, tests of the same hypothesis are generally conducted at different study sites, have variable ecological contexts (i.e., seasonality), and use very different methods. Clear reporting and careful examination of heterogeneity in ecological meta-analyses is thus crucial. Ecologists often also test similar hypotheses with different species, and in these meta-analyses, the reader should expect exploration of phylogenetic dependencies. Finally, observational studies not only provide the substrate for potential current manipulative experiments in this discipline but also form an important body of literature historically for synthesis. Sensitivity analyses of observational versus manipulative experiments when aggregated in the same ecological meta-analysis are also frequent and appropriate. This brief conceptual review is not intended as an instrument to rate meta-analyses for ecologists but does provide the appropriate framing for those purposes and directs the reader to ongoing developments in this direction in other disciplines.}, } @article {pmid26099479, year = {2015}, author = {Craig, D}, title = {The potential for meta-analysis to support decision analysis in ecology.}, journal = {Research synthesis methods}, volume = {6}, number = {2}, pages = {122-123}, doi = {10.1002/jrsm.1154}, pmid = {26099479}, issn = {1759-2887}, mesh = {*Data Interpretation, Statistical ; *Decision Support Techniques ; Ecology/*methods ; *Meta-Analysis as Topic ; *Research Design ; }, } @article {pmid26099478, year = {2015}, author = {Mengersen, K and MacNeil, MA and Caley, MJ}, title = {The potential for meta-analysis to support decision analysis in ecology.}, journal = {Research synthesis methods}, volume = {6}, number = {2}, pages = {111-121}, doi = {10.1002/jrsm.1105}, pmid = {26099478}, issn = {1759-2887}, mesh = {*Data Interpretation, Statistical ; *Decision Support Techniques ; Ecology/*methods ; Feasibility Studies ; *Meta-Analysis as Topic ; *Research Design ; }, abstract = {Meta-analysis and decision analysis are underpinned by well-developed methods that are commonly applied to a variety of problems and disciplines. While these two fields have been closely linked in some disciplines such as medicine, comparatively little attention has been paid to the potential benefits of linking them in ecology, despite reasonable expectations that benefits would be derived from doing so. Meta-analysis combines information from multiple studies to provide more accurate parameter estimates and to reduce the uncertainty surrounding them. Decision analysis involves selecting among alternative choices using statistical information that helps to shed light on the uncertainties involved. By linking meta-analysis to decision analysis, improved decisions can be made, with quantification of the costs and benefits of alternate decisions supported by a greater density of information. Here, we briefly review concepts of both meta-analysis and decision analysis, illustrating the natural linkage between them and the benefits from explicitly linking one to the other. We discuss some examples in which this linkage has been exploited in the medical arena and how improvements in precision and reduction of structural uncertainty inherent in a meta-analysis can provide substantive improvements to decision analysis outcomes by reducing uncertainty in expected loss and maximising information from across studies. We then argue that these significant benefits could be translated to ecology, in particular to the problem of making optimal ecological decisions in the face of uncertainty.}, } @article {pmid26099477, year = {2015}, author = {Stewart, GB and Schmid, CH}, title = {Lessons from meta-analysis in ecology and evolution: the need for trans-disciplinary evidence synthesis methodologies.}, journal = {Research synthesis methods}, volume = {6}, number = {2}, pages = {109-110}, doi = {10.1002/jrsm.1152}, pmid = {26099477}, issn = {1759-2887}, mesh = {Data Interpretation, Statistical ; Ecology/*methods ; Evidence-Based Medicine/methods ; *Evolution, Molecular ; *Genetic Research ; *Interdisciplinary Communication ; *Meta-Analysis as Topic ; *Research Design ; }, } @article {pmid26098107, year = {2015}, author = {Ayanu, Y and Conrad, C and Jentsch, A and Koellner, T}, title = {Unveiling Undercover Cropland Inside Forests Using Landscape Variables: A Supplement to Remote Sensing Image Classification.}, journal = {PloS one}, volume = {10}, number = {6}, pages = {e0130079}, pmid = {26098107}, issn = {1932-6203}, mesh = {Agriculture ; Conservation of Natural Resources/methods ; Crops, Agricultural/*growth & development ; Ecosystem ; Environmental Monitoring/*methods ; Ethiopia ; Food ; Food Supply ; Forests ; *Geographic Information Systems ; Remote Sensing Technology/*methods ; Satellite Imagery/*methods ; }, abstract = {The worldwide demand for food has been increasing due to the rapidly growing global population, and agricultural lands have increased in extent to produce more food crops. The pattern of cropland varies among different regions depending on the traditional knowledge of farmers and availability of uncultivated land. Satellite images can be used to map cropland in open areas but have limitations for detecting undergrowth inside forests. Classification results are often biased and need to be supplemented with field observations. Undercover cropland inside forests in the Bale Mountains of Ethiopia was assessed using field observed percentage cover of land use/land cover classes, and topographic and location parameters. The most influential factors were identified using Boosted Regression Trees and used to map undercover cropland area. Elevation, slope, easterly aspect, distance to settlements, and distance to national park were found to be the most influential factors determining undercover cropland area. When there is very high demand for growing food crops, constrained under restricted rights for clearing forest, cultivation could take place within forests as an undercover. Further research on the impact of undercover cropland on ecosystem services and challenges in sustainable management is thus essential.}, } @article {pmid26093894, year = {2015}, author = {Sudhakar Reddy, C and Vazeed Pasha, S and Jha, CS and Dadhwal, VK}, title = {Geospatial characterization of deforestation, fragmentation and forest fires in Telangana state, India: conservation perspective.}, journal = {Environmental monitoring and assessment}, volume = {187}, number = {7}, pages = {455}, pmid = {26093894}, issn = {1573-2959}, mesh = {Biodiversity ; Conservation of Natural Resources/*methods ; Ecology ; Environmental Monitoring/*methods ; *Fires ; Forests ; Geographic Information Systems ; Geography ; India ; *Trees ; }, abstract = {Conservation of biodiversity has been put to the highest priority throughout the world. The process of identifying threatened ecosystems will search for different drivers related to biodiversity loss. The present study aimed to generate spatial information on deforestation and ecological degradation indicators of fragmentation and forest fires using systematic conceptual approach in Telangana state, India. Identification of ecosystems facing increasing vulnerability can help to safeguard the extinctions of species and useful for conservation planning. The technological advancement of satellite remote sensing and Geographical Information System has increased greatly in assessment and monitoring of ecosystem-level changes. The areas of threat were identified by creating grid cells (5 × 5 km) in Geographical Information System (GIS). Deforestation was assessed using multi-source data of 1930, 1960, 1975, 1985, 1995, 2005 and 2013. The forest cover of 40,746 km(2), 29,299 km(2), 18,652 km(2), 18,368 km(2), 18,006 km(2), 17,556 km(2) and 17,520 km(2) was estimated during 1930, 1960, 1975, 1985, 1995, 2005 and 2013, respectively. Historical evaluation of deforestation revealed that major changes had occurred in forests of Telangana and identified 1095 extinct, 397 critically endangered, 523 endangered and 311 vulnerable ecosystem grid cells. The fragmentation analysis has identified 307 ecosystem grid cells under critically endangered status. Forest burnt area information was extracted using AWiFS data of 2005 to 2014. Spatial analysis indicates total fire-affected forest in Telangana as 58.9% in a decadal period. Conservation status has been recorded depending upon values of threat for each grid, which forms the basis for conservation priority hotspots. Of existing forest, 2.1% grids had severe ecosystem collapse and had been included under the category of conservation priority hotspot-I, followed by 27.2% in conservation priority hotspot-II and 51.5% in conservation priority hotspot-III. This analysis complements assessment of ecosystems undergoing multiple threats. An integrated approach involving the deforestation and degradation indicators is useful in formulating the strategies to take appropriate conservation measures.}, } @article {pmid26089514, year = {2015}, author = {Strandburg-Peshkin, A and Farine, DR and Couzin, ID and Crofoot, MC}, title = {GROUP DECISIONS. Shared decision-making drives collective movement in wild baboons.}, journal = {Science (New York, N.Y.)}, volume = {348}, number = {6241}, pages = {1358-1361}, pmid = {26089514}, issn = {1095-9203}, support = {T32 HG003284/HG/NHGRI NIH HHS/United States ; BB/L006081/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; T32HG003284/HG/NHGRI NIH HHS/United States ; }, mesh = {Animals ; *Consensus ; *Decision Making ; Geographic Information Systems ; *Group Processes ; Leadership ; Motion ; Movement ; Papio ; }, abstract = {Conflicts of interest about where to go and what to do are a primary challenge of group living. However, it remains unclear how consensus is achieved in stable groups with stratified social relationships. Tracking wild baboons with a high-resolution global positioning system and analyzing their movements relative to one another reveals that a process of shared decision-making governs baboon movement. Rather than preferentially following dominant individuals, baboons are more likely to follow when multiple initiators agree. When conflicts arise over the direction of movement, baboons choose one direction over the other when the angle between them is large, but they compromise if it is not. These results are consistent with models of collective motion, suggesting that democratic collective action emerging from simple rules is widespread, even in complex, socially stratified societies.}, } @article {pmid26087545, year = {2015}, author = {Sun, HB and Sun, H and Jiang, SY and Zhou, Y and Cao, WL and Ji, MC and Zhy, WT and Yan, HJ}, title = {[Cultural regionalization for Notopterygium incisum based on 3S technology platform. I. Evaluation for growth suitability for N. incisum based on ecological factors analysis by Maxent and ArcGIS model].}, journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica}, volume = {40}, number = {5}, pages = {853-862}, pmid = {26087545}, issn = {1001-5302}, mesh = {Apiaceae/*growth & development ; China ; *Ecosystem ; Environment ; Geographic Information Systems ; Soil/chemistry ; Temperature ; }, abstract = {Growth suitability as assessment indicators for medicinal plants cultivation was proposed based on chemical quality determination and ecological factors analysis by Maxent and ArcGIS model. Notopterygium incisum, an endangered Chinese medicinal plant, was analyzed as a case, its potential distribution areas at different suitability grade and regionalization map were formulated based on growth suitability theory. The results showed that the most suitable habitats is Sichuan province, and more than 60% of the most suitable areawas located in the western Sichuan such as Aba and Ganzi prefectures for N. incisum. The results indicated that habitat altitude, average air temperature in September, and vegetation types were the dominant factors contributing to the grade of plant growth, precipitation and slope were the major factors contributing to notopterol accumulation in its underground parts, while isoimperatorin in its underground parts was negatively corelated with precipitation and slope of its habitat. However, slope as a factor influencing chemical components seemed to be a pseudo corelationship. Therefore, there were distinguishing differences between growth suitability and quality suitability for medicinal plants, which was helpful to further research and practice of cultivation regionalization, wild resource monitoring and large-scale cultivation of traditional Chinese medicine plants.}, } @article {pmid26087534, year = {2015}, author = {Li, ZH and Wang, YF and Yi, LT and Zhang, AH and Ren, K and Zhang, CH and Bi, YQ and Li, MH}, title = {[Ecology suitability study of Cistanche deserticola in Alxa].}, journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica}, volume = {40}, number = {5}, pages = {785-792}, pmid = {26087534}, issn = {1001-5302}, mesh = {China ; Cistanche/*growth & development ; *Ecosystem ; Environment ; Geographic Information Systems ; Rain ; Soil/chemistry ; Temperature ; }, abstract = {The distribution information of Cistanche deserticola was collected by interview investigation and field survey, and 55 related environmental factors were collected, the habitat suitability study was conducted based on geographic information system (GIS) and Maximum entropy model. The AUCs of ROC curve were both above 0.9, indicating that the predictive results with the maxent model were highly precise. The results showed that 14 major environmental factors have obvious influence on ecology suitability distributions of C. deserticola, including vegetation type et al, the suitable distribution areas are mainly concentrated in the central of Alxa Youqi, the north of Alxa Zouqi and the south-east of Ejin Banner, including Tamusu towns, Alateng towns et al, The zoning results basically coincide with the genuine producing areas, and further afford new suitable distribution areas, which can provide reference for the siting of introduction and cultivation of C. deserticola.}, } @article {pmid26087533, year = {2015}, author = {Li, ZH and Zhang, AH and Yun, XH and Zhang, CH and Zhu, SD and Zou, DZ and Bi, YQ and Li, MH}, title = {[Ecology suitability study of Lomatogonium rotatum in Inner Mongolia].}, journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica}, volume = {40}, number = {5}, pages = {778-784}, pmid = {26087533}, issn = {1001-5302}, mesh = {China ; *Ecosystem ; Environment ; Gentianaceae/*growth & development ; Geographic Information Systems ; Rain ; Temperature ; }, abstract = {The distribution information of Lomatogonium rotatum. was collected by interview investigation and field survey, and 55 related environmental factors were collected, the habitat suitability study was conducted based on geographic information system (GIS) and maximum entropy model. The AUCs of ROC curve were both above 0.99, indicating that the predictive results with the maximum model were highly precise. The results showed that 13 major environmental factors have obvious influence on ecology suitability distributions of L. rotatum, including month average temperature of February et al., the suitable distribution areas are mainly concentrated in the east-central of Inner Mongolia, including Hexigten banner, Duolun county, Zhenglan banner et al., The zoning results basically coincide with the genuine producing areas, and further afford new suitable distribution areas, which can provide reference for L. rotatum's wild nursery and the siting of introduction and cultivation.}, } @article {pmid26085291, year = {2015}, author = {Koyanagi, A and Stickley, A}, title = {The Association between Sleep Problems and Psychotic Symptoms in the General Population: A Global Perspective.}, journal = {Sleep}, volume = {38}, number = {12}, pages = {1875-1885}, pmid = {26085291}, issn = {1550-9109}, mesh = {Adult ; Aged ; Anxiety/epidemiology ; China ; Cross-Sectional Studies ; Databases, Factual ; Depression/epidemiology ; Female ; Global Health/*statistics & numerical data ; Health Surveys ; Humans ; Logistic Models ; Male ; Middle Aged ; Morocco ; Odds Ratio ; Prevalence ; Psychotic Disorders/diagnosis/*epidemiology ; Sleep Wake Disorders/diagnosis/*epidemiology ; World Health Organization ; }, abstract = {STUDY OBJECTIVES: To assess the prevalence of sleep problems and their association with psychotic symptoms using a global database.

DESIGN: Community-based cross-sectional study.

SETTING: Data were analyzed from the World Health Organization's World Health Survey (WHS), a population-based survey conducted in 70 countries between 2002 and 2004.

PATIENTS OR PARTICIPANTS: 261,547 individuals aged ≥ 18 years from 56 countries.

INTERVENTIONS: N/A.

MEASUREMENTS AND RESULTS: The presence of psychotic symptoms in the past 12 months was established using 4 questions pertaining to positive symptoms from the psychosis screening module of the Composite International Diagnostic Interview. Sleep problems referred to severe or extreme sleep problems in the past 30 days. Multivariable logistic regression was used to estimate the associations. The overall prevalence of sleep problems was 7.6% and ranged from 1.6% (China) to 18.6% (Morocco). Sleep problems were associated with significantly higher odds for at least one psychotic symptom in the vast majority of countries. In the pooled sample, after adjusting for demographic factors, alcohol consumption, smoking, and chronic medical conditions, having sleep problems resulted in an odds ratio (OR) for at least one psychotic symptom of 2.41 (95% confidence interval [CI] 2.18-2.65). This OR was 1.59 (1.40-1.81) when further adjusted for anxiety and depression.

CONCLUSIONS: A strong association between sleep problems and psychotic symptoms was observed globally. These results have clinical implications and serve as a basis for future studies to elucidate the causal association between psychotic symptoms and sleep problems.}, } @article {pmid26082544, year = {2015}, author = {Schaefer, M and Goldman, E and Bartuska, AM and Sutton-Grier, A and Lubchenco, J}, title = {Nature as capital: Advancing and incorporating ecosystem services in United States federal policies and programs.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {112}, number = {24}, pages = {7383-7389}, pmid = {26082544}, issn = {1091-6490}, mesh = {Conservation of Natural Resources/*economics/*legislation & jurisprudence ; Decision Making ; Decision Support Techniques ; Ecology/economics/legislation & jurisprudence ; *Ecosystem ; Government Agencies ; *Government Programs ; Public Policy ; United States ; }, abstract = {The concept of nature as capital is gaining visibility in policies and practices in both the public and private sectors. This change is due to an improved ability to assess and value ecosystem services, as well as to a growing recognition of the potential of an ecosystem services approach to make tradeoffs in decision making more transparent, inform efficient use of resources, enhance resilience and sustainability, and avoid unintended negative consequences of policy actions. Globally, governments, financial institutions, and corporations have begun to incorporate natural capital accounting in their policies and practices. In the United States, universities, nongovernmental organizations, and federal agencies are actively collaborating to develop and apply ecosystem services concepts to further national environmental and economic objectives. Numerous federal agencies have begun incorporating these concepts into land use planning, water resources management, and preparations for, and responses to, climate change. Going forward, well-defined policy direction will be necessary to institutionalize ecosystem services approaches in federal agencies, as well as to guide intersector and interdisciplinary collaborative research and development efforts. In addition, a new generation of decision support tools are needed to further the practical application of ecosystem services principles in policymaking and commercial activities. Improved performance metrics are needed, as are mechanisms to monitor the status of ecosystem services and assess the environmental and economic impacts of policies and programs. A greater national and international financial commitment to advancing ecosystem services and natural capital accounting would likely have broad, long-term economic and environmental benefits.}, } @article {pmid26082541, year = {2015}, author = {Reyers, B and Nel, JL and O'Farrell, PJ and Sitas, N and Nel, DC}, title = {Navigating complexity through knowledge coproduction: Mainstreaming ecosystem services into disaster risk reduction.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {112}, number = {24}, pages = {7362-7368}, pmid = {26082541}, issn = {1091-6490}, mesh = {Conservation of Natural Resources/*methods ; Decision Making ; *Disasters ; Droughts ; *Ecosystem ; Fires ; Floods ; Knowledge Bases ; Risk Reduction Behavior ; South Africa ; Tidal Waves ; }, abstract = {Achieving the policy and practice shifts needed to secure ecosystem services is hampered by the inherent complexities of ecosystem services and their management. Methods for the participatory production and exchange of knowledge offer an avenue to navigate this complexity together with the beneficiaries and managers of ecosystem services. We develop and apply a knowledge coproduction approach based on social-ecological systems research and assess its utility in generating shared knowledge and action for ecosystem services. The approach was piloted in South Africa across four case studies aimed at reducing the risk of disasters associated with floods, wildfires, storm waves, and droughts. Different configurations of stakeholders (knowledge brokers, assessment teams, implementers, and bridging agents) were involved in collaboratively designing each study, generating and exchanging knowledge, and planning for implementation. The approach proved useful in the development of shared knowledge on the sizable contribution of ecosystem services to disaster risk reduction. This knowledge was used by stakeholders to design and implement several actions to enhance ecosystem services, including new investments in ecosystem restoration, institutional changes in the private and public sector, and innovative partnerships of science, practice, and policy. By bringing together multiple disciplines, sectors, and stakeholders to jointly produce the knowledge needed to understand and manage a complex system, knowledge coproduction approaches offer an effective avenue for the improved integration of ecosystem services into decision making.}, } @article {pmid26081923, year = {2016}, author = {Griffith, SD and Shiffman, S and Li, Y and Heitjan, DF}, title = {Model-based imputation of latent cigarette counts using data from a calibration study.}, journal = {International journal of methods in psychiatric research}, volume = {25}, number = {2}, pages = {112-122}, pmid = {26081923}, issn = {1557-0657}, support = {P30 CA016520/CA/NCI NIH HHS/United States ; }, mesh = {Adult ; Calibration ; *Data Interpretation, Statistical ; Humans ; Smoking Cessation/*statistics & numerical data ; Tobacco Products/*statistics & numerical data ; }, abstract = {In addition to dichotomous measures of abstinence, smoking studies may use daily cigarette consumption as an outcome variable. These counts hold the promise of more efficient and detailed analyses than dichotomous measures, but present serious quality issues - measurement error and heaping - if obtained by retrospective recall. A doubly-coded dataset with a retrospective recall measurement (timeline followback, TLFB) and a more precise instantaneous measurement (ecological momentary assessment, EMA) serves as a calibration dataset, allowing us to predict EMA given TLFB and baseline factors. We apply this model to multiply impute precise cigarette counts for a randomized, placebo-controlled trial of bupropion with only TLFB measurements available. To account for repeated measurements on a subject, we induce correlation in the imputed counts. Finally, we analyze the imputed data in a longitudinal model that accommodates random subject effects and zero inflation. Both raw and imputed data show a significant drug effect for reducing the odds of non-abstinence and the number of cigarettes smoked among non-abstainers, but the imputed data provide efficiency gains. This method permits the analysis of daily cigarette consumption data previously deemed suspect due to reporting error and is applicable to other self-reported count data sets for which calibration samples are available. Copyright © 2015 John Wiley & Sons, Ltd.}, } @article {pmid26079130, year = {2015}, author = {Gilbert, PS and Chang, J and Pan, C and Sobel, EM and Sinsheimer, JS and Faircloth, BC and Alfaro, ME}, title = {Genome-wide ultraconserved elements exhibit higher phylogenetic informativeness than traditional gene markers in percomorph fishes.}, journal = {Molecular phylogenetics and evolution}, volume = {92}, number = {}, pages = {140-146}, pmid = {26079130}, issn = {1095-9513}, support = {T32 HG002536/HG/NHGRI NIH HHS/United States ; T32HG002536/HG/NHGRI NIH HHS/United States ; }, mesh = {Animals ; Confidence Intervals ; Conserved Sequence/*genetics ; Databases, Genetic ; Fishes/*genetics ; Genetic Loci ; Genetic Markers ; *Genome ; Linear Models ; Nucleotides/genetics ; Open Reading Frames/genetics ; *Phylogeny ; Reproducibility of Results ; }, abstract = {Ultraconserved elements (UCEs) have become popular markers in phylogenomic studies because of their cost effectiveness and their potential to resolve problematic phylogenetic relationships. Although UCE datasets typically contain a much larger number of loci and sites than more traditional datasets of PCR-amplified, single-copy, protein coding genes, a fraction of UCE sites are expected to be part of a nearly invariant core, and the relative performance of UCE datasets versus protein coding gene datasets is poorly understood. Here we use phylogenetic informativeness (PI) to compare the resolving power of multi-locus and UCE datasets in a sample of percomorph fishes with sequenced genomes (genome-enabled). We compare three data sets: UCE core regions, flanking sequence adjacent to the UCE core and a set of ten protein coding genes commonly used in fish systematics. We found the net informativeness of UCE core and flank regions to be roughly ten-fold and 100-fold more informative than that of the protein coding genes. On a per locus basis UCEs and protein coding genes exhibited similar levels of phylogenetic informativeness. Our results suggest that UCEs offer enormous potential for resolving relationships across the percomorph tree of life.}, } @article {pmid26077888, year = {2016}, author = {Gonzalez, OA and Nagarajan, R and Novak, MJ and Orraca, L and Gonzalez-Martinez, JA and Kirakodu, SS and Ebersole, JL}, title = {Immune system transcriptome in gingival tissues of young nonhuman primates.}, journal = {Journal of periodontal research}, volume = {51}, number = {2}, pages = {152-163}, pmid = {26077888}, issn = {1600-0765}, support = {UL1 TR000117/TR/NCATS NIH HHS/United States ; UL1TR000117/TR/NCATS NIH HHS/United States ; P30 GM110788/GM/NIGMS NIH HHS/United States ; P40 RR003640/RR/NCRR NIH HHS/United States ; P20GM103538/GM/NIGMS NIH HHS/United States ; P40RR03640/RR/NCRR NIH HHS/United States ; P20 GM103538/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; *Gingiva ; Immune System ; Macaca mulatta ; Oligonucleotide Array Sequence Analysis ; Periodontitis ; Transcriptome ; }, abstract = {BACKGROUND AND OBJECTIVE: Young/adolescent humans harbor many microorganisms associated with periodontal disease in adults and show substantial gingival inflammatory responses. However, younger individuals do not demonstrate the soft- and hard-tissue destruction that hallmark periodontitis.

MATERIAL AND METHODS: This study evaluated responses to the oral microbial ecology in gingival tissues from clinically healthy young Macaca mulatta (< 3 years of age) compared with older animals (5-23 years of age). RNA was isolated from the tissues and analyzed for the transcriptome using the Rhesus Macaque GeneChip (Affymetrix).

RESULTS: Global transcriptional profiling of four age groups revealed a subset of 159 genes that were differentially expressed across at least one of the age comparisons. Correlation metrics generated a relevance network abstraction of these genes. Partitioning of the relevance network revealed seven distinct communities comprising functionally related genes associated with host inflammatory and immune responses. A group of genes was identified that were selectively increased/decreased or positively/negatively correlated with gingival profiles in the animals. A principal components analysis created metagenes of expression profiles for classifying the 23 animals.

CONCLUSION: The results provide novel system-level insights into gene-expression differences in gingival tissues from healthy young animals, weighted toward host responses associated with anti-inflammatory biomolecules or those linked with T-cell regulation of responses. The combination of the regulated microenvironment may help to explain the apparent 'resistance' of younger individuals to developing periodontal disease.}, } @article {pmid26076901, year = {2015}, author = {Liu, Z and Zhu, Q and Li, J and Yu, J and Li, Y and Huang, X and Wang, W and Tan, R and Zhou, J and Liao, H}, title = {Selection and evaluation of reference genes for expression analysis of Cassi.}, journal = {Bioscience, biotechnology, and biochemistry}, volume = {79}, number = {11}, pages = {1818-1826}, doi = {10.1080/09168451.2015.1052771}, pmid = {26076901}, issn = {1347-6947}, mesh = {Cassia/*genetics ; Computational Biology ; Gene Expression Regulation, Plant/*genetics ; Plant Proteins/*biosynthesis/genetics ; Software ; Tissue Distribution/genetics ; }, abstract = {Cassia obtusifolia, belonging to legume family, is important in many fields with high pharmaceutical, economic, and ecological values. These interests of C. obtusifolia triggered in-depth and fundamental genetic and molecular research. Therefore, the stable reference gene is necessary for normalization of the gene expression studies. In this study, 10 candidate reference genes were subjected to expression analysis in 12 different tissues and under different stresses by qRT-PCR. The expression stability was evaluated using geNorm, NormFinder, and BestKeeper software. In conclusion, different suitable reference genes were selected in different tissues and under different stress. CYP1, EF1α2, ACT2, UBQ1 were the most stable reference genes in all samples. The relative expression levels of WRKY gene were detected to confirm the reliability of the selected reference genes. These results provided suitable reference genes that could be used for normalization in C. obtusifolia tissues and under different stress.}, } @article {pmid26076233, year = {2015}, author = {Anderson, DW and McKeown, AN and Thornton, JW}, title = {Intermolecular epistasis shaped the function and evolution of an ancient transcription factor and its DNA binding sites.}, journal = {eLife}, volume = {4}, number = {}, pages = {e07864}, pmid = {26076233}, issn = {2050-084X}, support = {UL1 TR000430/TR/NCATS NIH HHS/United States ; 5-T32-GM-7759-33/GM/NIGMS NIH HHS/United States ; //Howard Hughes Medical Institute/United States ; R01 GM104397/GM/NIGMS NIH HHS/United States ; NIH R01-GM104397/GM/NIGMS NIH HHS/United States ; T32 GM007759/GM/NIGMS NIH HHS/United States ; }, mesh = {Binding Sites ; Computational Biology ; DNA/*genetics/*metabolism ; *Epistasis, Genetic ; *Evolution, Molecular ; *Response Elements ; Transcription Factors/*genetics/*metabolism ; }, abstract = {Complexes of specifically interacting molecules, such as transcription factor proteins (TFs) and the DNA response elements (REs) they recognize, control most biological processes, but little is known concerning the functional and evolutionary effects of epistatic interactions across molecular interfaces. We experimentally characterized all combinations of genotypes in the joint protein-DNA sequence space defined by an historical transition in TF-RE specificity that occurred some 500 million years ago in the DNA-binding domain of an ancient steroid hormone receptor. We found that rampant epistasis within and between the two molecules was essential to specific TF-RE recognition and to the evolution of a novel TF-RE complex with unique derived specificity. Permissive and restrictive epistatic mutations across the TF-RE interface opened and closed potential evolutionary paths accessible by the other, making the evolution of each molecule contingent on its partner's history and allowing a molecular complex with novel specificity to evolve.}, } @article {pmid26074184, year = {2015}, author = {Puth, MT and Neuhäuser, M and Ruxton, GD}, title = {On the variety of methods for calculating confidence intervals by bootstrapping.}, journal = {The Journal of animal ecology}, volume = {84}, number = {4}, pages = {892-897}, doi = {10.1111/1365-2656.12382}, pmid = {26074184}, issn = {1365-2656}, mesh = {*Confidence Intervals ; *Data Interpretation, Statistical ; Ecology/*methods ; }, abstract = {Researchers often want to place a confidence interval around estimated parameter values calculated from a sample. This is commonly implemented by bootstrapping. There are several different frequently used bootstrapping methods for this purpose. Here we demonstrate that authors of recent papers frequently do not specify the method they have used and that different methods can produce markedly different confidence intervals for the same sample and parameter estimate. We encourage authors to be more explicit about the method they use (and number of bootstrap resamples used). We recommend the bias corrected and accelerated method as giving generally good performance; although researchers should be warned that coverage of bootstrap confidence intervals is characteristically less than the specified nominal level, and confidence interval evaluation by any method can be unreliable for small samples in some situations.}, } @article {pmid26073028, year = {2015}, author = {Gao, L and Hu, Y and Wang, Y and Jiang, W and He, Z and Zhu, C and Ma, R and Huang, Z}, title = {Exploring the variation of oral microbiota in supragingival plaque during and after head-and-neck radiotherapy using pyrosequencing.}, journal = {Archives of oral biology}, volume = {60}, number = {9}, pages = {1222-1230}, doi = {10.1016/j.archoralbio.2015.05.006}, pmid = {26073028}, issn = {1879-1506}, mesh = {Bacteria/*classification ; Cluster Analysis ; DNA, Bacterial/analysis ; Dental Plaque/*microbiology ; Follow-Up Studies ; Head and Neck Neoplasms/diagnostic imaging/*radiotherapy ; Humans ; Microbiota ; Mouth/*microbiology ; Polymerase Chain Reaction ; Radiation Dosage ; Radiotherapy Planning, Computer-Assisted ; Tomography, X-Ray Computed ; }, abstract = {OBJECTIVE: The aim of this article was to study the variation in oral microflora of the subgingival plaque during and after radiotherapy.

DESIGN: During and after radiotherapy, microbial samples were collected at seven time points (early stage, medium stage, and later stage of radiotherapy, and 1 month, 3 months, 6 months, and 1 year after radiotherapy) in three subjects for a total of 21 samples. Polymerase chain reaction (PCR) amplification was carried out on the 16S rDNA hypervariable V1-V3 region, and then the PCR products were determined by high-throughput pyrosequencing.

RESULTS: The rarefaction curve indicating the richness of the microflora demonstrated that the number of operational taxonomic units (OTUs) was in decline from the early stage of radiotherapy to the time point 1 month after radiotherapy and then trended upward. The Shannon diversity index declined during radiotherapy (ranging from 4.59 to 3.73), and generally rose after radiotherapy, with the lowest value of 3.5 (1 month after radiotherapy) and highest value of 4.75 (6 months after radiotherapy). A total of 120 genera were found; five genera (Actinomyces, Veillonella, Prevotella, Streptococcus, Campylobacter) were found in all subjects across all time points.

CONCLUSION: The richness and diversity of oral ecology decreased with increased radiation dose, and it was gradually restored with time.}, } @article {pmid26072503, year = {2015}, author = {Yuan, C and Lei, J and Cole, J and Sun, Y}, title = {Reconstructing 16S rRNA genes in metagenomic data.}, journal = {Bioinformatics (Oxford, England)}, volume = {31}, number = {12}, pages = {i35-43}, pmid = {26072503}, issn = {1367-4811}, mesh = {Computational Biology/*methods ; Databases, Nucleic Acid ; Genes, rRNA/*genetics ; Metagenomics/*methods ; Microbiota/*genetics ; Phylogeny ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, RNA ; }, abstract = {UNLABELLED: Metagenomic data, which contains sequenced DNA reads of uncultured microbial species from environmental samples, provide a unique opportunity to thoroughly analyze microbial species that have never been identified before. Reconstructing 16S ribosomal RNA, a phylogenetic marker gene, is usually required to analyze the composition of the metagenomic data. However, massive volume of dataset, high sequence similarity between related species, skewed microbial abundance and lack of reference genes make 16S rRNA reconstruction difficult. Generic de novo assembly tools are not optimized for assembling 16S rRNA genes. In this work, we introduce a targeted rRNA assembly tool, REAGO (REconstruct 16S ribosomal RNA Genes from metagenOmic data). It addresses the above challenges by combining secondary structure-aware homology search, zproperties of rRNA genes and de novo assembly. Our experimental results show that our tool can correctly recover more rRNA genes than several popular generic metagenomic assembly tools and specially designed rRNA construction tools.

The source code of REAGO is freely available at https://github.com/chengyuan/reago.}, } @article {pmid26072452, year = {2015}, author = {Adrion, JR and Hahn, MW and Cooper, BS}, title = {Revisiting classic clines in Drosophila melanogaster in the age of genomics.}, journal = {Trends in genetics : TIG}, volume = {31}, number = {8}, pages = {434-444}, pmid = {26072452}, issn = {0168-9525}, support = {F32 AI114176/AI/NIAID NIH HHS/United States ; T32 GM007757/GM/NIGMS NIH HHS/United States ; F32-AI114176/AI/NIAID NIH HHS/United States ; T32-GM007757/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Drosophila melanogaster/*genetics ; *Ecosystem ; Genetic Variation ; Genome, Insect ; *Genomics ; Phenotype ; }, abstract = {Adaptation to spatially varying environments has been studied for decades, but advances in sequencing technology are now enabling researchers to investigate the landscape of genetic variation underlying this adaptation genome wide. In this review we highlight some of the decades-long research on local adaptation in Drosophila melanogaster from well-studied clines in North America and Australia. We explore the evidence for parallel adaptation and identify commonalities in the genes responding to clinal selection across continents as well as discussing instances where patterns differ among clines. We also investigate recent studies utilizing whole-genome data to identify clines in D. melanogaster and several other systems. Although connecting segregating genomic variation to variation in phenotypes and fitness remains challenging, clinal genomics is poised to increase our understanding of local adaptation and the selective pressures that drive the extensive phenotypic diversity observed in nature.}, } @article {pmid26071752, year = {2015}, author = {Rochefort, CM and Buckeridge, DL and Abrahamowicz, M}, title = {Improving patient safety by optimizing the use of nursing human resources.}, journal = {Implementation science : IS}, volume = {10}, number = {}, pages = {89}, pmid = {26071752}, issn = {1748-5908}, support = {FRN 130499//Canadian Institutes of Health Research/Canada ; }, mesh = {Academic Medical Centers ; Accidental Falls/statistics & numerical data ; Canada ; Cross Infection/epidemiology ; Electronic Health Records/statistics & numerical data ; Hospital Mortality ; Humans ; Incidence ; Longitudinal Studies ; Nursing Staff, Hospital/*statistics & numerical data ; Patient Safety/*statistics & numerical data ; Personnel Staffing and Scheduling/*statistics & numerical data ; Pneumonia/epidemiology ; Quality Improvement/*organization & administration ; Quality Indicators, Health Care/*statistics & numerical data ; Regression Analysis ; Research Design ; Venous Thromboembolism/epidemiology ; }, abstract = {BACKGROUND: Recent ecological studies have suggested that inadequate nurse staffing may contribute to the incidence of adverse events in acute care hospitals. However, longitudinal studies are needed to further examine these associations and to identify the staffing patterns that are of greatest risk. The aims of this study are to determine if (a) nurse staffing levels are associated with an increased risk of adverse events, (b) the risk of adverse events in relationship to nurse staffing levels is modified by the complexity of patient requirements, and (c) optimal nurse staffing levels can be established.

METHODS/DESIGN: A dynamic cohort of all adult medical, surgical, and intensive care unit patients admitted between 2010 and 2015 to a Canadian academic health center will be followed during the inpatient and 7-day post-discharge period to assess the occurrence and frequency of adverse events in relationship to antecedent nurse staffing levels. Four potentially preventable adverse events will be measured: (a) hospital-acquired pneumonia, (b) ventilator-associated pneumonia, (c) venous thromboembolism, and (d) in-hospital fall. These events were selected for their high incidence, morbidity and mortality rates, and because they are hypothesized to be related to nurse staffing levels. Adverse events will be ascertained from electronic health record data using validated automated detection algorithms. Patient exposure to nurse staffing will be measured on every shift of the hospitalization using electronic payroll records. To examine the association between nurse staffing levels and the risk of adverse events, four Cox proportional hazards regression models will be used (one for each adverse event), while adjusting for patient characteristics and risk factors of adverse event occurrence. To determine if the association between nurse staffing levels and the occurrence of adverse events is modified by the complexity of patient requirements, interaction terms will be included in the regression models, and their significance assessed. To assess for the presence of optimal nurse staffing levels, flexible nonlinear spline functions will be fitted.

DISCUSSION: This study will likely generate evidence-based information that will assist managers in making the most effective use of scarce nursing resources and in identifying staffing patterns that minimize the risk of adverse events.}, } @article {pmid26070087, year = {2015}, author = {Wei, Y and Zhou, H and Zhang, J and Zhang, L and Geng, A and Liu, F and Zhao, G and Wang, S and Zhou, Z and Yan, X}, title = {Insight into Dominant Cellulolytic Bacteria from Two Biogas Digesters and Their Glycoside Hydrolase Genes.}, journal = {PloS one}, volume = {10}, number = {6}, pages = {e0129921}, pmid = {26070087}, issn = {1932-6203}, mesh = {Bacteria/classification/*genetics/*metabolism ; Biodiversity ; Biofuels/*microbiology ; *Biotransformation ; Computational Biology ; Gene Expression ; Genomics ; Glycoside Hydrolases/*genetics/metabolism ; Lignin/metabolism ; Metagenomics ; Multigene Family ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Diverse cellulolytic bacteria are essential for maintaining high lignocellulose degradation ability in biogas digesters. However, little was known about functional genes and gene clusters of dominant cellulolytic bacteria in biogas digesters. This is the foundation to understand lignocellulose degradation mechanisms of biogas digesters and apply these gene resource for optimizing biofuel production. A combination of metagenomic and 16S rRNA gene clone library methods was used to investigate the dominant cellulolytic bacteria and their glycoside hydrolase (GH) genes in two biogas digesters. The 16S rRNA gene analysis revealed that the dominant cellulolytic bacteria were strains closely related to Clostridium straminisolvens and an uncultured cellulolytic bacterium designated BG-1. To recover GH genes from cellulolytic bacteria in general, and BG-1 in particular, a refined assembly approach developed in this study was used to assemble GH genes from metagenomic reads; 163 GH-containing contigs ≥ 1 kb in length were obtained. Six recovered GH5 genes that were expressed in E. coli demonstrated multiple lignocellulase activities and one had high mannanase activity (1255 U/mg). Eleven fosmid clones harboring the recovered GH-containing contigs were sequenced and assembled into 10 fosmid contigs. The composition of GH genes in the 163 assembled metagenomic contigs and 10 fosmid contigs indicated that diverse GHs and lignocellulose degradation mechanisms were present in the biogas digesters. In particular, a small portion of BG-1 genome information was recovered by PhyloPythiaS analysis. The lignocellulase gene clusters in BG-1 suggested that it might use a possible novel lignocellulose degradation mechanism to efficiently degrade lignocellulose. Dominant cellulolytic bacteria of biogas digester possess diverse GH genes, not only in sequences but also in their functions, which may be applied for production of biofuel in the future.}, } @article {pmid26068858, year = {2015}, author = {Kays, R and Crofoot, MC and Jetz, W and Wikelski, M}, title = {ECOLOGY. Terrestrial animal tracking as an eye on life and planet.}, journal = {Science (New York, N.Y.)}, volume = {348}, number = {6240}, pages = {aaa2478}, doi = {10.1126/science.aaa2478}, pmid = {26068858}, issn = {1095-9203}, mesh = {*Animal Migration ; Animals ; Behavior, Animal ; Environmental Monitoring/*methods ; *Geographic Information Systems ; Movement ; Spatio-Temporal Analysis ; }, abstract = {Moving animals connect our world, spreading pollen, seeds, nutrients, and parasites as they go about the their daily lives. Recent integration of high-resolution Global Positioning System and other sensors into miniaturized tracking tags has dramatically improved our ability to describe animal movement. This has created opportunities and challenges that parallel big data transformations in other fields and has rapidly advanced animal ecology and physiology. New analytical approaches, combined with remotely sensed or modeled environmental information, have opened up a host of new questions on the causes of movement and its consequences for individuals, populations, and ecosystems. Simultaneous tracking of multiple animals is leading to new insights on species interactions and, scaled up, may enable distributed monitoring of both animals and our changing environment.}, } @article {pmid26066862, year = {2015}, author = {Leidenberger, S and Obst, M and Kulawik, R and Stelzer, K and Heyer, K and Hardisty, A and Bourlat, SJ}, title = {Evaluating the potential of ecological niche modelling as a component in marine non-indigenous species risk assessments.}, journal = {Marine pollution bulletin}, volume = {97}, number = {1-2}, pages = {470-487}, doi = {10.1016/j.marpolbul.2015.04.033}, pmid = {26066862}, issn = {1879-3363}, mesh = {Animal Distribution ; Animals ; Aquatic Organisms/*growth & development ; Biodiversity ; Ecosystem ; *Introduced Species ; *Models, Biological ; North Sea ; Risk Assessment ; Salinity ; *Ships ; }, abstract = {Marine biological invasions have increased with the development of global trading, causing the homogenization of communities and the decline of biodiversity. A main vector is ballast water exchange from shipping. This study evaluates the use of ecological niche modelling (ENM) to predict the spread of 18 non-indigenous species (NIS) along shipping routes and their potential habitat suitability (hot/cold spots) in the Baltic Sea and Northeast Atlantic. Results show that, contrary to current risk assessment methods, temperature and sea ice concentration determine habitat suitability for 61% of species, rather than salinity (11%). We show high habitat suitability for NIS in the Skagerrak and Kattegat, a transitional area for NIS entering or leaving the Baltic Sea. As many cases of NIS introduction in the marine environment are associated with shipping pathways, we explore how ENM can be used to provide valuable information on the potential spread of NIS for ballast water risk assessment.}, } @article {pmid26066834, year = {2015}, author = {Owen-Smith, N and Martin, J}, title = {Identifying Space Use at Foraging Arena Scale within the Home Ranges of Large Herbivores.}, journal = {PloS one}, volume = {10}, number = {6}, pages = {e0128821}, pmid = {26066834}, issn = {1932-6203}, mesh = {Animals ; Antelopes/physiology ; Equidae/physiology ; Feeding Behavior ; Geographic Information Systems ; Homing Behavior/*physiology ; Seasons ; }, abstract = {An intermediate spatiotemporal scale of food procurement by large herbivores is evident within annual or seasonal home ranges. It takes the form of settlement periods spanning several days or weeks during which foraging activity is confined to spatially discrete foraging arenas, separated by roaming interludes. Extended by areas occupied for other activities, these foraging arenas contribute towards generating the home range structure. We delineated and compared the foraging arenas exploited by two African large herbivores, sable antelope (a ruminant) and plains zebra (a non-ruminant), using GPS-derived movement data. We developed a novel approach to specifically delineate foraging arenas based on local change points in distance relative to adjoining clusters of locations, and compared its output with modifications of two published methods developed for home range estimation and residence time estimation respectively. We compared how these herbivore species responded to seasonal variation in food resources and how they differed in their spatial patterns of resource utilization. Sable antelope herds tended to concentrate their space use locally, while zebra herds moved more opportunistically over a wider set of foraging arenas. The amalgamated extent of the foraging arenas exploited by sable herds amounted to 12-30 km2, compared with 22-100 km2 for the zebra herds. Half-day displacement distances differed between settlement periods and roaming interludes, and zebra herds generally shifted further over 12h than sable herds. Foraging arenas of sable herds tended to be smaller than those of zebra, and were occupied for period twice as long, and hence exploited more intensively in days spent per unit area than the foraging arenas of zebra. For sable both the intensity of utilization of foraging arenas and proportion of days spent in foraging arenas relative to roaming interludes declined as food resources diminished seasonally, while zebra showed no seasonal variation in these metrics. Identifying patterns of space use at foraging arena scale helps reveal mechanisms generating the home range extent, and in turn the local population density. Thereby it helps forge links between behavioural ecology, movement ecology and population ecology.}, } @article {pmid26064571, year = {2014}, author = {Smyth, AK and Smee, E and Godfrey, SS and Crowther, M and Phalen, D}, title = {The use of body condition and haematology to detect widespread threatening processes in sleepy lizards (Tiliqua rugosa) in two agricultural environments.}, journal = {Royal Society open science}, volume = {1}, number = {4}, pages = {140257}, pmid = {26064571}, issn = {2054-5703}, abstract = {Agricultural practices, including habitat alteration and application of agricultural chemicals, can impact wildlife resulting in their decline. Determining which of these practices are contributing to declines is essential if the declines are to be reversed. In this study, the health of two geographically separated sleepy lizard (Tiliqua rugosa) populations was compared between a rangeland environment and cropping environment using linear body size index (LBSI) and haematology. Animals in the cropping site were smaller, suggesting genetic differences as the result of geographical isolation. The animals in the cropping site had a lower LBSI and many were experiencing a regenerative anaemia. The anaemia was postulated to be the cause of the low LBSI. The anaemia appeared to be the result of haemolysis and was likely to be caused by exposure to agricultural chemicals applied in the cropping site but not the rangeland site. Elevated white blood cell counts in lizards in the rangeland site suggested that they were experiencing an inflammatory disease of possible ecological significance. Together, these results demonstrate the value of combining physical and haematological parameters when studying the impact of agricultural practices on wildlife. They also show that reptiles may be useful as sentinel species for livestock and humans.}, } @article {pmid26063516, year = {2015}, author = {Roger, E and Duursma, DE and Downey, PO and Gallagher, RV and Hughes, L and Steel, J and Johnson, SB and Leishman, MR}, title = {A tool to assess potential for alien plant establishment and expansion under climate change.}, journal = {Journal of environmental management}, volume = {159}, number = {}, pages = {121-127}, doi = {10.1016/j.jenvman.2015.05.039}, pmid = {26063516}, issn = {1095-8630}, mesh = {Australia ; *Climate Change ; Databases, Factual ; *Ecosystem ; Environmental Monitoring/methods ; Forecasting ; *Introduced Species ; Plants ; *Software ; }, abstract = {Predicting the influence of climate change on the potential distribution of naturalised alien plant species is an important and challenging task. While prioritisation of management actions for alien plants under current climatic conditions has been widely adopted, very few systems explicitly incorporate the potential of future changes in climate conditions to influence the distribution of alien plant species. Here, we develop an Australia-wide screening tool to assess the potential of naturalised alien plants to establish and spread under both current and future climatic conditions. The screening tool developed uses five spatially explicit criteria to establish the likelihood of alien plant population establishment and expansion under baseline climate conditions and future climates for the decades 2035 and 2065. Alien plants are then given a threat rating according to current and future threat to enable natural resource managers to focus on those species that pose the largest potential threat now and in the future. To demonstrate the screening tool, we present results for a representative sample of approximately 10% (n = 292) of Australia's known, naturalised alien plant species. Overall, most alien plant species showed decreases in area of habitat suitability under future conditions compared to current conditions and therefore the threat rating of most alien plant species declined between current and future conditions. Use of the screening tool is intended to assist natural resource managers in assessing the threat of alien plant establishment and spread under current and future conditions and thus prioritise detailed weed risk assessments for those species that pose the greatest threat. The screening tool is associated with a searchable database for all 292 alien plant species across a range of spatial scales, available through an interactive web-based portal at http://weedfutures.net/.}, } @article {pmid26061246, year = {2015}, author = {Gimmler, A and Stoeck, T}, title = {Mining environmental high-throughput sequence data sets to identify divergent amplicon clusters for phylogenetic reconstruction and morphotype visualization.}, journal = {Environmental microbiology reports}, volume = {7}, number = {4}, pages = {679-686}, doi = {10.1111/1758-2229.12307}, pmid = {26061246}, issn = {1758-2229}, mesh = {*Biodiversity ; Cluster Analysis ; *Computational Biology ; DNA Primers/genetics ; DNA, Protozoan/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; *Environmental Microbiology ; High-Throughput Nucleotide Sequencing ; In Situ Hybridization, Fluorescence ; Molecular Sequence Data ; *Phylogeography ; Polymerase Chain Reaction ; RNA, Ribosomal, 18S/genetics ; Sequence Analysis, DNA ; }, abstract = {Environmental high-throughput sequencing (envHTS) is a very powerful tool, which in protistan ecology is predominantly used for the exploration of diversity and its geographic and local patterns. We here used a pyrosequenced V4-SSU rDNA data set from a solar saltern pond as test case to exploit such massive protistan amplicon data sets beyond this descriptive purpose. Therefore, we combined a Swarm-based blastn network including 11 579 ciliate V4 amplicons to identify divergent amplicon clusters with targeted polymerase chain reaction (PCR) primer design for full-length small subunit of the ribosomal DNA retrieval and probe design for fluorescence in situ hybridization (FISH). This powerful strategy allows to benefit from envHTS data sets to (i) reveal the phylogenetic position of the taxon behind divergent amplicons; (ii) improve phylogenetic resolution and evolutionary history of specific taxon groups; (iii) solidly assess an amplicons (species') degree of similarity to its closest described relative; (iv) visualize the morphotype behind a divergent amplicons cluster; (v) rapidly FISH screen many environmental samples for geographic/habitat distribution and abundances of the respective organism and (vi) to monitor the success of enrichment strategies in live samples for cultivation and isolation of the respective organisms.}, } @article {pmid26061064, year = {2015}, author = {Ultsch, A and Lötsch, J}, title = {Computed ABC Analysis for Rational Selection of Most Informative Variables in Multivariate Data.}, journal = {PloS one}, volume = {10}, number = {6}, pages = {e0129767}, pmid = {26061064}, issn = {1932-6203}, mesh = {*Algorithms ; *Datasets as Topic ; Multivariate Analysis ; }, abstract = {OBJECTIVE: Multivariate data sets often differ in several factors or derived statistical parameters, which have to be selected for a valid interpretation. Basing this selection on traditional statistical limits leads occasionally to the perception of losing information from a data set. This paper proposes a novel method for calculating precise limits for the selection of parameter sets.

METHODS: The algorithm is based on an ABC analysis and calculates these limits on the basis of the mathematical properties of the distribution of the analyzed items. The limits implement the aim of any ABC analysis, i.e., comparing the increase in yield to the required additional effort. In particular, the limit for set A, the "important few", is optimized in a way that both, the effort and the yield for the other sets (B and C), are minimized and the additional gain is optimized.

RESULTS: As a typical example from biomedical research, the feasibility of the ABC analysis as an objective replacement for classical subjective limits to select highly relevant variance components of pain thresholds is presented. The proposed method improved the biological interpretation of the results and increased the fraction of valid information that was obtained from the experimental data.

CONCLUSIONS: The method is applicable to many further biomedical problems including the creation of diagnostic complex biomarkers or short screening tests from comprehensive test batteries. Thus, the ABC analysis can be proposed as a mathematically valid replacement for traditional limits to maximize the information obtained from multivariate research data.}, } @article {pmid26058704, year = {2015}, author = {Semenzin, E and Lanzellotto, E and Hristozov, D and Critto, A and Zabeo, A and Giubilato, E and Marcomini, A}, title = {Species sensitivity weighted distribution for ecological risk assessment of engineered nanomaterials: the n-TiO2 case study.}, journal = {Environmental toxicology and chemistry}, volume = {34}, number = {11}, pages = {2644-2659}, doi = {10.1002/etc.3103}, pmid = {26058704}, issn = {1552-8618}, mesh = {Animals ; Bacteria/drug effects ; Ecology ; Fresh Water ; Invertebrates/drug effects/physiology ; Metal Nanoparticles/*chemistry/toxicity ; Risk Assessment ; Species Specificity ; Titanium/*chemistry ; Vertebrates/physiology ; }, abstract = {Societal concerns about the environmental risks of engineered nanomaterials (ENMs) have recently increased, but nano-ecological risk assessments are constrained by significant gaps in basic information on long-term effects and exposures, for example. An approach to the ecological risk assessment of ENMs is proposed that can operate in the context of high uncertainty. This approach further develops species sensitivity weighted distribution (SSWD) by including 3 weighting criteria (species relevance, trophic level abundance, and nanotoxicity data quality) to address nano-specific needs (n-SSWD). The application of n-SSWD is illustrated for nanoscale titanium dioxide (n-TiO2), which is available in different crystal forms; it was selected because of its widespread use in consumer products (e.g., cosmetics) and the ample availability of data from ecotoxicological studies in the literature (including endpoints for algae, invertebrates, bacteria, and vertebrates in freshwater, saltwater, and terrestrial compartments). The n-SSWD application resulted in estimation of environmental quality criteria (hazard concentration affecting 5% and 50% of the species) and ecological risk (potentially affected fraction of species), which were then compared with similar results obtained by applying the traditional species sensitivity distribution (SSD) approach to the same dataset. The n-SSWDs were also built for specific trophic levels (e.g., primary producers) and taxonomic groups (e.g., algae), which helped to identify the most sensitive organisms. These results showd that n-SSWD is a valuable risk tool, although further testing is suggested.}, } @article {pmid26058066, year = {2015}, author = {Forcino, FL and Leighton, LR and Twerdy, P and Cahill, JF}, title = {Reexamining Sample Size Requirements for Multivariate, Abundance-Based Community Research: When Resources are Limited, the Research Does Not Have to Be.}, journal = {PloS one}, volume = {10}, number = {6}, pages = {e0128379}, pmid = {26058066}, issn = {1932-6203}, mesh = {*Community-Based Participatory Research ; Databases as Topic ; *Health Resources ; Multivariate Analysis ; *Research Design ; Sample Size ; }, abstract = {Community ecologists commonly perform multivariate techniques (e.g., ordination, cluster analysis) to assess patterns and gradients of taxonomic variation. A critical requirement for a meaningful statistical analysis is accurate information on the taxa found within an ecological sample. However, oversampling (too many individuals counted per sample) also comes at a cost, particularly for ecological systems in which identification and quantification is substantially more resource consuming than the field expedition itself. In such systems, an increasingly larger sample size will eventually result in diminishing returns in improving any pattern or gradient revealed by the data, but will also lead to continually increasing costs. Here, we examine 396 datasets: 44 previously published and 352 created datasets. Using meta-analytic and simulation-based approaches, the research within the present paper seeks (1) to determine minimal sample sizes required to produce robust multivariate statistical results when conducting abundance-based, community ecology research. Furthermore, we seek (2) to determine the dataset parameters (i.e., evenness, number of taxa, number of samples) that require larger sample sizes, regardless of resource availability. We found that in the 44 previously published and the 220 created datasets with randomly chosen abundances, a conservative estimate of a sample size of 58 produced the same multivariate results as all larger sample sizes. However, this minimal number varies as a function of evenness, where increased evenness resulted in increased minimal sample sizes. Sample sizes as small as 58 individuals are sufficient for a broad range of multivariate abundance-based research. In cases when resource availability is the limiting factor for conducting a project (e.g., small university, time to conduct the research project), statistically viable results can still be obtained with less of an investment.}, } @article {pmid26056424, year = {2015}, author = {Kornobis, E and Cabellos, L and Aguilar, F and Frías-López, C and Rozas, J and Marco, J and Zardoya, R}, title = {TRUFA: A User-Friendly Web Server for de novo RNA-seq Analysis Using Cluster Computing.}, journal = {Evolutionary bioinformatics online}, volume = {11}, number = {}, pages = {97-104}, pmid = {26056424}, issn = {1176-9343}, abstract = {Application of next-generation sequencing (NGS) methods for transcriptome analysis (RNA-seq) has become increasingly accessible in recent years and are of great interest to many biological disciplines including, eg, evolutionary biology, ecology, biomedicine, and computational biology. Although virtually any research group can now obtain RNA-seq data, only a few have the bioinformatics knowledge and computation facilities required for transcriptome analysis. Here, we present TRUFA (TRanscriptome User-Friendly Analysis), an open informatics platform offering a web-based interface that generates the outputs commonly used in de novo RNA-seq analysis and comparative transcriptomics. TRUFA provides a comprehensive service that allows performing dynamically raw read cleaning, transcript assembly, annotation, and expression quantification. Due to the computationally intensive nature of such analyses, TRUFA is highly parallelized and benefits from accessing high-performance computing resources. The complete TRUFA pipeline was validated using four previously published transcriptomic data sets. TRUFA's results for the example datasets showed globally similar results when comparing with the original studies, and performed particularly better when analyzing the green tea dataset. The platform permits analyzing RNA-seq data in a fast, robust, and user-friendly manner. Accounts on TRUFA are provided freely upon request at https://trufa.ifca.es.}, } @article {pmid26054405, year = {2015}, author = {Khuntikeo, N and Chamadol, N and Yongvanit, P and Loilome, W and Namwat, N and Sithithaworn, P and Andrews, RH and Petney, TN and Promthet, S and Thinkhamrop, K and Tawarungruang, C and Thinkhamrop, B and , }, title = {Cohort profile: cholangiocarcinoma screening and care program (CASCAP).}, journal = {BMC cancer}, volume = {15}, number = {}, pages = {459}, pmid = {26054405}, issn = {1471-2407}, mesh = {Adult ; Aged ; Animals ; Cholangiocarcinoma/*diagnosis/*epidemiology/pathology ; Cohort Studies ; *Early Detection of Cancer ; Female ; Humans ; Male ; Middle Aged ; Thailand ; }, abstract = {BACKGROUND: Cholangiocarcinoma (CCA) is an extremely aggressive cancer that is usually fatal. Although globally morbidity and mortality are increasing, knowledge of the disease remains limited. The Mekong region of Southeast Asia, and particularly the northeast of Thailand, has by far the highest incidence of CCA worldwide with 135.4 per 100,000 among males and 43.0 per 100,000 among females being reported in Khon Kaen Province. Most patients are first seen during late stage disease with 5-year survival being less than 10%. Starting in 1984, control and prevention strategies have been focused on health education. Although early detection can substantially increase 5-year survival, there are currently no strategies to increase early diagnosis.

METHODS/DESIGN: The Cholangiocarcinoma Screening and Care Program (CASCAP) is a prospective cohort study comprising two cohorts- the screening and the patient cohorts. For the screening cohort, ultrasound examination will be carried out regularly at least annually to determine whether there is current bile duct and/or liver pathology so that the optimal screening program for early diagnosis can be established. This cohort is expected to include at least 150,000 individuals coming from high-risk areas for CCA. For the patient cohort, it is estimated that about 25,000 CCA patients will be included during the 5-year recruitment period. All CCA patients will be treated according to routine clinical care and followed so that effective surgical treatment can be formulated. This cohort is indeed a conventional cancer registry. Thus, CASCAP is an ongoing project in which the number of participants changes dynamically.

DISCUSSIONS: This is the first project on CCA that involves screening the at risk population at the community level. At the time of preparing this report, a total of 85,927 individuals have been enrolled in the screening cohort, 55.0% of whom have already undergone ultrasound screening, and 2661 CCA cases have been enrolled in the patient cohort. Among the participants of the screening, whose mean age was 53.8±9.8 years, 55.6% were female, 77.5% attained primary school as the highest level of education, 79.9% were farmers, 29.9%, reported having relatives with CCA, 89.1% had eaten uncooked fish, and 42.2% of those who had been tested for liver fluke were found to be infected.}, } @article {pmid26052957, year = {2014}, author = {Hansen, RA and Zeng, P and Ryan, P and Gao, J and Sonawane, K and Teeter, B and Westrich, K and Dubois, RW}, title = {Exploration of heterogeneity in distributed research network drug safety analyses.}, journal = {Research synthesis methods}, volume = {5}, number = {4}, pages = {352-370}, doi = {10.1002/jrsm.1121}, pmid = {26052957}, issn = {1759-2887}, mesh = {Adverse Drug Reaction Reporting Systems/statistics & numerical data ; Bias ; *Data Interpretation, Statistical ; Drug-Related Side Effects and Adverse Reactions/*epidemiology ; Electronic Health Records/*statistics & numerical data ; Medical Record Linkage/*methods ; *Meta-Analysis as Topic ; Outcome Assessment, Health Care/*methods ; Prevalence ; Reproducibility of Results ; Risk Assessment/methods ; Sensitivity and Specificity ; }, abstract = {Distributed data networks representing large diverse populations are an expanding focus of drug safety research. However, interpreting results is difficult when treatment effect estimates vary across datasets (i.e., heterogeneity). In a previous study, risk estimates were generated for selected drugs and potential adverse outcomes. Analyses were replicated across eight distributed data sources using an identical analytic structure. To evaluate heterogeneity of risk estimates across data sources, the estimates were combined with summary-level data characterizing the population of each data source. Meta-analysis, meta-regression, and plots of the influence on overall results versus contribution to heterogeneity were examined and used to illustrate an approach to heterogeneity assessment. Heterogeneity, as measured by the I-squared statistic, was high with variability across outcomes. Plots of the relationship between influence on overall results and contribution to heterogeneity suggest that certain datasets and characteristics were influential but there was variability dependent on the drug and outcome being assessed. Exploratory meta-regression identified many possible influential factors, but may be subject to ecological bias and false positive conclusions. Distributed data network drug safety analyses can produce heterogeneous risk estimates that may not be easily explained. Approaches illustrated here can be useful for research that is subject to similar problems with heterogeneity.}, } @article {pmid26052956, year = {2014}, author = {Yamaguchi, Y and Sakamoto, W and Goto, M and Staessen, JA and Wang, J and Gueyffier, F and Riley, RD}, title = {Meta-analysis of a continuous outcome combining individual patient data and aggregate data: a method based on simulated individual patient data.}, journal = {Research synthesis methods}, volume = {5}, number = {4}, pages = {322-351}, doi = {10.1002/jrsm.1119}, pmid = {26052956}, issn = {1759-2887}, support = {G0800808/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Bayes Theorem ; Bias ; Clinical Trials as Topic/*statistics & numerical data ; Computer Simulation ; *Data Interpretation, Statistical ; Humans ; Likelihood Functions ; *Meta-Analysis as Topic ; *Models, Statistical ; Outcome Assessment, Health Care/*methods ; *Regression Analysis ; Reproducibility of Results ; Sample Size ; Sensitivity and Specificity ; }, abstract = {When some trials provide individual patient data (IPD) and the others provide only aggregate data (AD), meta-analysis methods for combining IPD and AD are required. We propose a method that reconstructs the missing IPD for AD trials by a Bayesian sampling procedure and then applies an IPD meta-analysis model to the mixture of simulated IPD and collected IPD. The method is applicable when a treatment effect can be assumed fixed across trials. We focus on situations of a single continuous outcome and covariate and aim to estimate treatment-covariate interactions separated into within-trial and across-trial effect. An illustration with hypertension data which has similar mean covariates across trials indicates that the method substantially reduces mean square error of the pooled within-trial interaction estimate in comparison with existing approaches. A simulation study supposing there exists one IPD trial and nine AD trials suggests that the method has suitable type I error rate and approximately zero bias as long as the available IPD contains at least 10% of total patients, where the average gain in mean square error is up to about 40%. However, the method is currently restricted by the fixed effect assumption, and extension to random effects to allow heterogeneity is required.}, } @article {pmid26047160, year = {2015}, author = {Gao, P and Niu, X and Wang, B and Zheng, Y}, title = {Land use changes and its driving forces in hilly ecological restoration area based on gis and RS of northern China.}, journal = {Scientific reports}, volume = {5}, number = {}, pages = {11038}, pmid = {26047160}, issn = {2045-2322}, mesh = {Agriculture ; China ; *Conservation of Natural Resources ; Ecosystem ; Environmental Monitoring/*methods ; Forests ; Geographic Information Systems ; Remote Sensing Technology ; }, abstract = {Land use change is one of the important aspects of the regional ecological restoration research. With remote sensing (RS) image in 2003, 2007 and 2012, using geographic information system (GIS) technologies, the land use pattern changes in Yimeng Mountain ecological restoration area in China and its driving force factors were studied. Results showed that: (1) Cultivated land constituted the largest area during 10 years, and followed by forest land and grass land; cultivated land and unused land were reduced by 28.43% and 44.32%, whereas forest land, water area and land for water facilities and others were increased. (2) During 2003-2007, forest land change showed the largest, followed by unused land and grass land; however, during 2008-2012, water area and land for water facilities change showed the largest, followed by grass land and unused land. (3) Land use degree was above the average level, it was in the developing period during 2003-2007 and in the degenerating period during 2008-2012. (4) Ecological Restoration Projects can greatly change the micro topography, increase vegetation coverage, and then induce significant changes in the land use distribution, which were the main driving force factors of the land use pattern change in the ecological restoration area.}, } @article {pmid26047146, year = {2015}, author = {Singh, KS and Thual, D and Spurio, R and Cannata, N}, title = {SaDA: From Sampling to Data Analysis-An Extensible Open Source Infrastructure for Rapid, Robust and Automated Management and Analysis of Modern Ecological High-Throughput Microarray Data.}, journal = {International journal of environmental research and public health}, volume = {12}, number = {6}, pages = {6352-6366}, pmid = {26047146}, issn = {1660-4601}, mesh = {Ecology/methods ; *Environmental Microbiology ; Environmental Monitoring/methods ; Information Management/*methods ; *Microarray Analysis ; *Software ; }, abstract = {One of the most crucial characteristics of day-to-day laboratory information management is the collection, storage and retrieval of information about research subjects and environmental or biomedical samples. An efficient link between sample data and experimental results is absolutely important for the successful outcome of a collaborative project. Currently available software solutions are largely limited to large scale, expensive commercial Laboratory Information Management Systems (LIMS). Acquiring such LIMS indeed can bring laboratory information management to a higher level, but most of the times this requires a sufficient investment of money, time and technical efforts. There is a clear need for a light weighted open source system which can easily be managed on local servers and handled by individual researchers. Here we present a software named SaDA for storing, retrieving and analyzing data originated from microorganism monitoring experiments. SaDA is fully integrated in the management of environmental samples, oligonucleotide sequences, microarray data and the subsequent downstream analysis procedures. It is simple and generic software, and can be extended and customized for various environmental and biomedical studies.}, } @article {pmid26046541, year = {2015}, author = {Hofberger, JA and Ramirez, AM and Bergh, Ev and Zhu, X and Bouwmeester, HJ and Schuurink, RC and Schranz, ME}, title = {Large-Scale Evolutionary Analysis of Genes and Supergene Clusters from Terpenoid Modular Pathways Provides Insights into Metabolic Diversification in Flowering Plants.}, journal = {PloS one}, volume = {10}, number = {6}, pages = {e0128808}, pmid = {26046541}, issn = {1932-6203}, mesh = {Alkyl and Aryl Transferases/genetics/metabolism ; Biological Evolution ; Carbon-Carbon Double Bond Isomerases/genetics/metabolism ; Dimethylallyltranstransferase/genetics/metabolism ; *Genome, Plant ; Hemiterpenes ; Isoenzymes/genetics/metabolism ; Magnoliopsida/classification/*genetics/metabolism ; Metabolic Networks and Pathways/genetics ; Metabolomics ; Mevalonic Acid/metabolism ; Molecular Sequence Annotation ; *Multigene Family ; *Phylogeny ; Plant Proteins/*genetics/metabolism ; Terpenes/*metabolism ; }, abstract = {An important component of plant evolution is the plethora of pathways producing more than 200,000 biochemically diverse specialized metabolites with pharmacological, nutritional and ecological significance. To unravel dynamics underlying metabolic diversification, it is critical to determine lineage-specific gene family expansion in a phylogenomics framework. However, robust functional annotation is often only available for core enzymes catalyzing committed reaction steps within few model systems. In a genome informatics approach, we extracted information from early-draft gene-space assemblies and non-redundant transcriptomes to identify protein families involved in isoprenoid biosynthesis. Isoprenoids comprise terpenoids with various roles in plant-environment interaction, such as pollinator attraction or pathogen defense. Combining lines of evidence provided by synteny, sequence homology and Hidden-Markov-Modelling, we screened 17 genomes including 12 major crops and found evidence for 1,904 proteins associated with terpenoid biosynthesis. Our terpenoid genes set contains evidence for 840 core terpene-synthases and 338 triterpene-specific synthases. We further identified 190 prenyltransferases, 39 isopentenyl-diphosphate isomerases as well as 278 and 219 proteins involved in mevalonate and methylerithrol pathways, respectively. Assessing the impact of gene and genome duplication to lineage-specific terpenoid pathway expansion, we illustrated key events underlying terpenoid metabolic diversification within 250 million years of flowering plant radiation. By quantifying Angiosperm-wide versatility and phylogenetic relationships of pleiotropic gene families in terpenoid modular pathways, our analysis offers significant insight into evolutionary dynamics underlying diversification of plant secondary metabolism. Furthermore, our data provide a blueprint for future efforts to identify and more rapidly clone terpenoid biosynthetic genes from any plant species.}, } @article {pmid26044351, year = {2015}, author = {Jha, AR and Miles, CM and Lippert, NR and Brown, CD and White, KP and Kreitman, M}, title = {Whole-Genome Resequencing of Experimental Populations Reveals Polygenic Basis of Egg-Size Variation in Drosophila melanogaster.}, journal = {Molecular biology and evolution}, volume = {32}, number = {10}, pages = {2616-2632}, pmid = {26044351}, issn = {1537-1719}, support = {P50 GM081892/GM/NIGMS NIH HHS/United States ; T32HL094282/HL/NHLBI NIH HHS/United States ; P20GM103443/GM/NIGMS NIH HHS/United States ; T32 HL094282/HL/NHLBI NIH HHS/United States ; P20 GM103443/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Cell Size ; Crosses, Genetic ; Directed Molecular Evolution ; Drosophila melanogaster/*cytology/*genetics ; Female ; Gene Expression Regulation ; Gene Frequency/genetics ; Gene Ontology ; Genetic Association Studies ; Genetic Variation ; *Genome, Insect ; Male ; Multifactorial Inheritance/*genetics ; Ovum/*cytology ; Phenotype ; Sequence Analysis, DNA/*methods ; }, abstract = {Complete genome resequencing of populations holds great promise in deconstructing complex polygenic traits to elucidate molecular and developmental mechanisms of adaptation. Egg size is a classic adaptive trait in insects, birds, and other taxa, but its highly polygenic architecture has prevented high-resolution genetic analysis. We used replicated experimental evolution in Drosophila melanogaster and whole-genome sequencing to identify consistent signatures of polygenic egg-size adaptation. A generalized linear-mixed model revealed reproducible allele frequency differences between replicated experimental populations selected for large and small egg volumes at approximately 4,000 single nucleotide polymorphisms (SNPs). Several hundred distinct genomic regions contain clusters of these SNPs and have lower heterozygosity than the genomic background, consistent with selection acting on polymorphisms in these regions. These SNPs are also enriched among genes expressed in Drosophila ovaries and many of these genes have well-defined functions in Drosophila oogenesis. Additional genes regulating egg development, growth, and cell size show evidence of directional selection as genes regulating these biological processes are enriched for highly differentiated SNPs. Genetic crosses performed with a subset of candidate genes demonstrated that these genes influence egg size, at least in the large genetic background. These findings confirm the highly polygenic architecture of this adaptive trait, and suggest the involvement of many novel candidate genes in regulating egg size.}, } @article {pmid26042592, year = {2015}, author = {Alexander, KA and Sanderson, CE and Marathe, M and Lewis, BL and Rivers, CM and Shaman, J and Drake, JM and Lofgren, E and Dato, VM and Eisenberg, MC and Eubank, S}, title = {What factors might have led to the emergence of Ebola in West Africa?.}, journal = {PLoS neglected tropical diseases}, volume = {9}, number = {6}, pages = {e0003652}, pmid = {26042592}, issn = {1935-2735}, support = {R01 GM109718/GM/NIGMS NIH HHS/United States ; U01 GM110744/GM/NIGMS NIH HHS/United States ; U01 GM110748/GM/NIGMS NIH HHS/United States ; T15 LM007059/LM/NLM NIH HHS/United States ; R01 GM100467/GM/NIGMS NIH HHS/United States ; 5U01GM070694-11/GM/NIGMS NIH HHS/United States ; 5T15 LM007059-28/LM/NLM NIH HHS/United States ; U01 GM070694/GM/NIGMS NIH HHS/United States ; }, mesh = {Africa, Western/epidemiology ; Communicable Diseases, Emerging/*epidemiology ; Disease Outbreaks/*prevention & control ; Ebolavirus/*physiology ; Hemorrhagic Fever, Ebola/*epidemiology ; Humans ; Risk Factors ; }, abstract = {An Ebola outbreak of unprecedented scope emerged in West Africa in December 2013 and presently continues unabated in the countries of Guinea, Sierra Leone, and Liberia. Ebola is not new to Africa, and outbreaks have been confirmed as far back as 1976. The current West African Ebola outbreak is the largest ever recorded and differs dramatically from prior outbreaks in its duration, number of people affected, and geographic extent. The emergence of this deadly disease in West Africa invites many questions, foremost among these: why now, and why in West Africa? Here, we review the sociological, ecological, and environmental drivers that might have influenced the emergence of Ebola in this region of Africa and its spread throughout the region. Containment of the West African Ebola outbreak is the most pressing, immediate need. A comprehensive assessment of the drivers of Ebola emergence and sustained human-to-human transmission is also needed in order to prepare other countries for importation or emergence of this disease. Such assessment includes identification of country-level protocols and interagency policies for outbreak detection and rapid response, increased understanding of cultural and traditional risk factors within and between nations, delivery of culturally embedded public health education, and regional coordination and collaboration, particularly with governments and health ministries throughout Africa. Public health education is also urgently needed in countries outside of Africa in order to ensure that risk is properly understood and public concerns do not escalate unnecessarily. To prevent future outbreaks, coordinated, multiscale, early warning systems should be developed that make full use of these integrated assessments, partner with local communities in high-risk areas, and provide clearly defined response recommendations specific to the needs of each community.}, } @article {pmid26039741, year = {2015}, author = {North, AC and Hodgson, DJ and Price, SJ and Griffiths, AG}, title = {Anthropogenic and ecological drivers of amphibian disease (ranavirosis).}, journal = {PloS one}, volume = {10}, number = {6}, pages = {e0127037}, pmid = {26039741}, issn = {1932-6203}, mesh = {Animals ; *DNA Virus Infections/epidemiology/veterinary ; *Databases, Factual ; *Extinction, Biological ; Rana temporaria/*virology ; *Ranavirus ; United Kingdom/epidemiology ; }, abstract = {Ranaviruses are causing mass amphibian die-offs in North America, Europe and Asia, and have been implicated in the decline of common frog (Rana temporaria) populations in the UK. Despite this, we have very little understanding of the environmental drivers of disease occurrence and prevalence. Using a long term (1992-2000) dataset of public reports of amphibian mortalities, we assess a set of potential predictors of the occurrence and prevalence of Ranavirus-consistent common frog mortality events in Britain. We reveal the influence of biotic and abiotic drivers of this disease, with many of these abiotic characteristics being anthropogenic. Whilst controlling for the geographic distribution of mortality events, disease prevalence increases with increasing frog population density, presence of fish and wild newts, increasing pond depth and the use of garden chemicals. The presence of an alternative host reduces prevalence, potentially indicating a dilution effect. Ranavirosis occurrence is associated with the presence of toads, an urban setting and the use of fish care products, providing insight into the causes of emergence of disease. Links between occurrence, prevalence, pond characteristics and garden management practices provides useful management implications for reducing the impacts of Ranavirus in the wild.}, } @article {pmid26038558, year = {2015}, author = {Han, BA and Schmidt, JP and Bowden, SE and Drake, JM}, title = {Rodent reservoirs of future zoonotic diseases.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {112}, number = {22}, pages = {7039-7044}, pmid = {26038558}, issn = {1091-6490}, mesh = {Age Factors ; Animals ; Artificial Intelligence ; Computational Biology ; *Disease Reservoirs ; Forecasting/methods ; Geographic Mapping ; Geography ; Humans ; Population Density ; Public Health/*methods ; Regression Analysis ; Reproduction/physiology ; Rodentia/*growth & development ; Sexual Maturation/physiology ; Species Specificity ; Zoonoses/*transmission ; }, abstract = {The increasing frequency of zoonotic disease events underscores a need to develop forecasting tools toward a more preemptive approach to outbreak investigation. We apply machine learning to data describing the traits and zoonotic pathogen diversity of the most speciose group of mammals, the rodents, which also comprise a disproportionate number of zoonotic disease reservoirs. Our models predict reservoir status in this group with over 90% accuracy, identifying species with high probabilities of harboring undiscovered zoonotic pathogens based on trait profiles that may serve as rules of thumb to distinguish reservoirs from nonreservoir species. Key predictors of zoonotic reservoirs include biogeographical properties, such as range size, as well as intrinsic host traits associated with lifetime reproductive output. Predicted hotspots of novel rodent reservoir diversity occur in the Middle East and Central Asia and the Midwestern United States.}, } @article {pmid26038228, year = {2015}, author = {Willis, A and Bunge, J}, title = {Estimating diversity via frequency ratios.}, journal = {Biometrics}, volume = {71}, number = {4}, pages = {1042-1049}, doi = {10.1111/biom.12332}, pmid = {26038228}, issn = {1541-0420}, mesh = {*Biodiversity ; Biometry/methods ; Computer Simulation ; Databases, Genetic ; High-Throughput Nucleotide Sequencing ; *Microbial Consortia ; Nonlinear Dynamics ; Probability Theory ; }, abstract = {We wish to estimate the total number of classes in a population based on sample counts, especially in the presence of high latent diversity. Drawing on probability theory that characterizes distributions on the integers by ratios of consecutive probabilities, we construct a nonlinear regression model for the ratios of consecutive frequency counts. This allows us to predict the unobserved count and hence estimate the total diversity. We believe that this is the first approach to depart from the classical mixed Poisson model in this problem. Our method is geometrically intuitive and yields good fits to data with reasonable standard errors. It is especially well-suited to analyzing high diversity datasets derived from next-generation sequencing in microbial ecology. We demonstrate the method's performance in this context and via simulation, and we present a dataset for which our method outperforms all competitors.}, } @article {pmid26037451, year = {2015}, author = {Hernandez-Blanco, JA and Naidenko, SV and Chistopolova, MD and Lukarevskiy, VS and Kostyrya, A and Rybin, A and Sorokin, PA and Litvinov, MN and Kotlyar, AK and Miquelle, DG and Rozhnov, VV}, title = {Social structure and space use of Amur tigers (Panthera tigris altaica) in Southern Russian Far East based on GPS telemetry data.}, journal = {Integrative zoology}, volume = {10}, number = {4}, pages = {365-375}, doi = {10.1111/1749-4877.12140}, pmid = {26037451}, issn = {1749-4877}, mesh = {Animals ; Female ; Geographic Information Systems ; Homing Behavior ; Male ; Russia ; Sex Ratio ; *Social Behavior ; Telemetry ; Tigers/*psychology ; }, abstract = {To better understand the spatial structure of Amur tigers (Panthera tigris altaica) at the southern edge of their range we fitted 14 tigers (6♀♀ and 8♂♂) with 15 GPS-Argos collars between 2008 and 2011 in 2 study sites: the Ussuriskii Reserve of southern Sikhote-Alin and the Land of the Leopard National Park in southwest Primorye, Russian Far East. Fixed kernel estimates of male home ranges were larger than those of female home ranges (P < 0.05 [mean 95% fixed kernel(♀) = 401 ± 205 km(2) ; mean 95% fixed kernel(♂) = 778 ± 267 km(2)]). The home range size of females varied greatly, but on average was similar to estimates derived from earlier work further north. Low overlap of adjacent home ranges suggested that females retained exclusive territories. Real core areas of females overlapped only slightly, and remained stable over multiple years. The home ranges of adult males were smaller than those of males to the north, and in contrast to previous studies, high overlap among males indicated the absence of territoriality. Nonetheless, real core areas of males did not overlap, suggesting some spatial separation. In comparison to other tiger populations and other areas of the Russian Far East, the sex ratio in our 2 study areas was highly skewed towards males. We believe this skewed sex ratio resulted in the dissolution of territoriality of males due to an inability to defend individual females, with males resorting to scramble competition for mates. Continued monitoring of these sites to determine whether shifts in the sex ratio might result in a return to male territoriality would provide confirmation of our tentative hypothesis.}, } @article {pmid26035530, year = {2015}, author = {Rodríguez, A and Rodríguez, B and Negro, JJ}, title = {GPS tracking for mapping seabird mortality induced by light pollution.}, journal = {Scientific reports}, volume = {5}, number = {}, pages = {10670}, pmid = {26035530}, issn = {2045-2322}, mesh = {Animals ; *Birds ; *Environmental Pollution ; *Geographic Information Systems ; Geography ; *Light ; Spain ; *Spatial Analysis ; }, abstract = {Light pollution and its consequences on ecosystems are increasing worldwide. Knowledge on the threshold levels of light pollution at which significant ecological impacts emerge and the size of dark refuges to maintain natural nocturnal processes is crucial to mitigate its negative consequences. Seabird fledglings are attracted by artificial lights when they leave their nest at night, causing high mortality. We used GPS data-loggers to track the flights of Cory's shearwater Calonectris diomedea fledglings from nest-burrows to ground, and to evaluate the light pollution levels of overflown areas on Tenerife, Canary Islands, using nocturnal, high-resolution satellite imagery. Birds were grounded at locations closer than 16 km from colonies in their maiden flights, and 50% were rescued within a 3 km radius from the nest-site. Most birds left the nests in the first three hours after sunset. Rescue locations showed radiance values greater than colonies, and flight distance was positively related to light pollution levels. Breeding habitat alteration by light pollution was more severe for inland colonies. We provide scientific-based information to manage dark refuges facilitating that fledglings from inland colonies reach the sea successfully. We also offer methodological approaches useful for other critically threatened petrel species grounded by light pollution.}, } @article {pmid26034279, year = {2015}, author = {Slik, JW and Arroyo-Rodríguez, V and Aiba, S and Alvarez-Loayza, P and Alves, LF and Ashton, P and Balvanera, P and Bastian, ML and Bellingham, PJ and van den Berg, E and Bernacci, L and da Conceição Bispo, P and Blanc, L and Böhning-Gaese, K and Boeckx, P and Bongers, F and Boyle, B and Bradford, M and Brearley, FQ and Breuer-Ndoundou Hockemba, M and Bunyavejchewin, S and Calderado Leal Matos, D and Castillo-Santiago, M and Catharino, EL and Chai, SL and Chen, Y and Colwell, RK and Chazdon, RL and Clark, C and Clark, DB and Clark, DA and Culmsee, H and Damas, K and Dattaraja, HS and Dauby, G and Davidar, P and DeWalt, SJ and Doucet, JL and Duque, A and Durigan, G and Eichhorn, KA and Eisenlohr, PV and Eler, E and Ewango, C and Farwig, N and Feeley, KJ and Ferreira, L and Field, R and de Oliveira Filho, AT and Fletcher, C and Forshed, O and Franco, G and Fredriksson, G and Gillespie, T and Gillet, JF and Amarnath, G and Griffith, DM and Grogan, J and Gunatilleke, N and Harris, D and Harrison, R and Hector, A and Homeier, J and Imai, N and Itoh, A and Jansen, PA and Joly, CA and de Jong, BH and Kartawinata, K and Kearsley, E and Kelly, DL and Kenfack, D and Kessler, M and Kitayama, K and Kooyman, R and Larney, E and Laumonier, Y and Laurance, S and Laurance, WF and Lawes, MJ and Amaral, IL and Letcher, SG and Lindsell, J and Lu, X and Mansor, A and Marjokorpi, A and Martin, EH and Meilby, H and Melo, FP and Metcalfe, DJ and Medjibe, VP and Metzger, JP and Millet, J and Mohandass, D and Montero, JC and de Morisson Valeriano, M and Mugerwa, B and Nagamasu, H and Nilus, R and Ochoa-Gaona, S and Onrizal, and Page, N and Parolin, P and Parren, M and Parthasarathy, N and Paudel, E and Permana, A and Piedade, MT and Pitman, NC and Poorter, L and Poulsen, AD and Poulsen, J and Powers, J and Prasad, RC and Puyravaud, JP and Razafimahaimodison, JC and Reitsma, J and Dos Santos, JR and Roberto Spironello, W and Romero-Saltos, H and Rovero, F and Rozak, AH and Ruokolainen, K and Rutishauser, E and Saiter, F and Saner, P and Santos, BA and Santos, F and Sarker, SK and Satdichanh, M and Schmitt, CB and Schöngart, J and Schulze, M and Suganuma, MS and Sheil, D and da Silva Pinheiro, E and Sist, P and Stevart, T and Sukumar, R and Sun, IF and Sunderland, T and Suresh, HS and Suzuki, E and Tabarelli, M and Tang, J and Targhetta, N and Theilade, I and Thomas, DW and Tchouto, P and Hurtado, J and Valencia, R and van Valkenburg, JL and Van Do, T and Vasquez, R and Verbeeck, H and Adekunle, V and Vieira, SA and Webb, CO and Whitfeld, T and Wich, SA and Williams, J and Wittmann, F and Wöll, H and Yang, X and Adou Yao, CY and Yap, SL and Yoneda, T and Zahawi, RA and Zakaria, R and Zang, R and de Assis, RL and Garcia Luize, B and Venticinque, EM}, title = {An estimate of the number of tropical tree species.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {112}, number = {24}, pages = {7472-7477}, pmid = {26034279}, issn = {1091-6490}, mesh = {*Biodiversity ; Conservation of Natural Resources ; Databases, Factual ; Ecosystem ; *Forests ; Phylogeography ; Rainforest ; Species Specificity ; Statistics, Nonparametric ; *Trees/classification ; *Tropical Climate ; }, abstract = {The high species richness of tropical forests has long been recognized, yet there remains substantial uncertainty regarding the actual number of tropical tree species. Using a pantropical tree inventory database from closed canopy forests, consisting of 657,630 trees belonging to 11,371 species, we use a fitted value of Fisher's alpha and an approximate pantropical stem total to estimate the minimum number of tropical forest tree species to fall between ∼ 40,000 and ∼ 53,000, i.e., at the high end of previous estimates. Contrary to common assumption, the Indo-Pacific region was found to be as species-rich as the Neotropics, with both regions having a minimum of ∼ 19,000-25,000 tree species. Continental Africa is relatively depauperate with a minimum of ∼ 4,500-6,000 tree species. Very few species are shared among the African, American, and the Indo-Pacific regions. We provide a methodological framework for estimating species richness in trees that may help refine species richness estimates of tree-dependent taxa.}, } @article {pmid26033415, year = {2015}, author = {Pope, LC and Liggins, L and Keyse, J and Carvalho, SB and Riginos, C}, title = {Not the time or the place: the missing spatio-temporal link in publicly available genetic data.}, journal = {Molecular ecology}, volume = {24}, number = {15}, pages = {3802-3809}, doi = {10.1111/mec.13254}, pmid = {26033415}, issn = {1365-294X}, mesh = {*Bibliometrics ; *Data Curation ; *Datasets as Topic ; Editorial Policies ; Genetics/statistics & numerical data ; *Periodicals as Topic ; Spatio-Temporal Analysis ; }, abstract = {Genetic data are being generated at unprecedented rates. Policies of many journals, institutions and funding bodies aim to ensure that these data are publicly archived so that published results are reproducible. Additionally, publicly archived data can be 'repurposed' to address new questions in the future. In 2011, along with other leading journals in ecology and evolution, Molecular Ecology implemented mandatory public data archiving (the Joint Data Archiving Policy). To evaluate the effect of this policy, we assessed the genetic, spatial and temporal data archived for 419 data sets from 289 articles in Molecular Ecology from 2009 to 2013. We then determined whether archived data could be used to reproduce analyses as presented in the manuscript. We found that the journal's mandatory archiving policy has had a substantial positive impact, increasing genetic data archiving from 49 (pre-2011) to 98% (2011-present). However, 31% of publicly archived genetic data sets could not be recreated based on information supplied in either the manuscript or public archives, with incomplete data or inconsistent codes linking genetic data and metadata as the primary reasons. While the majority of articles did provide some geographic information, 40% did not provide this information as geographic coordinates. Furthermore, a large proportion of articles did not contain any information regarding date of sampling (40%). Although the inclusion of spatio-temporal data does require an increase in effort, we argue that the enduring value of publicly accessible genetic data to the molecular ecology field is greatly compromised when such metadata are not archived alongside genetic data.}, } @article {pmid26031601, year = {2016}, author = {Widdig, A and Kessler, MJ and Bercovitch, FB and Berard, JD and Duggleby, C and Nürnberg, P and Rawlins, RG and Sauermann, U and Wang, Q and Krawczak, M and Schmidtke, J}, title = {Genetic studies on the Cayo Santiago rhesus macaques: A review of 40 years of research.}, journal = {American journal of primatology}, volume = {78}, number = {1}, pages = {44-62}, doi = {10.1002/ajp.22424}, pmid = {26031601}, issn = {1098-2345}, support = {P40-RR-01293/RR/NCRR NIH HHS/United States ; P40-RR-03640/RR/NCRR NIH HHS/United States ; RR-712003/RR/NCRR NIH HHS/United States ; RR-72115/RR/NCRR NIH HHS/United States ; }, mesh = {Animals ; Genetics/*history ; History, 20th Century ; History, 21st Century ; Macaca mulatta/*genetics ; Puerto Rico ; }, abstract = {Genetic studies not only contribute substantially to our current understanding of the natural variation in behavior and health in many species, they also provide the basis of numerous in vivo models of human traits. Despite the many challenges posed by the high level of biological and social complexity, a long lifespan and difficult access in the field, genetic studies of primates are particularly rewarding because of the close evolutionary relatedness of these species to humans. The free-ranging rhesus macaque (Macaca mulatta) population on Cayo Santiago (CS), Puerto Rico, provides a unique resource in this respect because several of the abovementioned caveats are of either minor importance there, or lacking altogether, thereby allowing long-term genetic research in a primate population under constant surveillance since 1956. This review summarizes more than 40 years of genetic research carried out on CS, from early blood group typing and the genetic characterization of skeletal material via population-wide paternity testing with DNA fingerprints and short tandem repeats (STRs) to the analysis of the highly polymorphic DQB1 locus within the major histocompatibility complex (MHC). The results of the paternity studies also facilitated subsequent studies of male dominance and other factors influencing male reproductive success, of male reproductive skew, paternal kin bias, and mechanisms of paternal kin recognition. More recently, the CS macaques have been the subjects of functional genetic and gene expression analyses and have played an important role in behavioral and quantitative genetic studies. In addition, the CS colony has been used as a natural model for human adult-onset macular degeneration, glaucoma, and circadian rhythm disorder. Our review finishes off with a discussion of potential future directions of research on CS, including the transition from STRs to single nucleotide polymorphism (SNP) typing and whole genome sequencing.}, } @article {pmid26027797, year = {2015}, author = {Guo, C and Cui, H and Ni, S and Yan, Y and Qin, Q}, title = {Comprehensive identification and profiling of host miRNAs in response to Singapore grouper iridovirus (SGIV) infection in grouper (Epinephelus coioides).}, journal = {Developmental and comparative immunology}, volume = {52}, number = {2}, pages = {226-235}, doi = {10.1016/j.dci.2015.05.014}, pmid = {26027797}, issn = {1879-0089}, mesh = {Animals ; Cells, Cultured ; DNA Virus Infections/genetics/immunology/metabolism/*veterinary ; Fish Diseases/genetics/immunology/*metabolism ; Gene Ontology ; Gene Regulatory Networks ; High-Throughput Nucleotide Sequencing ; Iridovirus/immunology ; MicroRNAs/genetics/*metabolism ; Perciformes/immunology/*metabolism/virology ; Phylogeny ; Sequence Analysis, RNA ; *Transcriptome ; }, abstract = {microRNAs (miRNAs) are an evolutionarily conserved class of non-coding RNA molecules that participate in various biological processes. Employment of high-throughput screening strategies greatly prompts the investigation and profiling of miRNAs in diverse species. In recent years, grouper (Epinephelus spp.) aquaculture was severely affected by iridoviral diseases. However, knowledge regarding the host immune responses to viral infection, especially the miRNA-mediated immune regulatory roles, is rather limited. In this study, by employing Solexa deep sequencing approach, we identified 116 grouper miRNAs from grouper spleen-derived cells (GS). As expected, these miRNAs shared high sequence similarity with miRNAs identified in zebrafish (Danio rerio), pufferfish (Fugu rubripes), and other higher vertebrates. In the process of Singapore grouper iridovirus (SGIV) infection, 45 and 43 miRNAs with altered expression (>1.5-fold) were identified by miRNA microarray assays in grouper spleen tissues and GS cells, respectively. Furthermore, target prediction revealed 189 putative targets of these grouper miRNAs.}, } @article {pmid26027242, year = {2015}, author = {Kopylov, FY and Mesitskaya, DF and Nikitina, YM and Aksenova, MG and Dobrovolsky, AV and Lomakin, OV and Chernyi, OV}, title = {[Positive effect of low-activity thromboxane A synthase gene on prognosis in coronary heart disease].}, journal = {Terapevticheskii arkhiv}, volume = {87}, number = {3}, pages = {59-65}, doi = {10.17116/terarkh201587359-65}, pmid = {26027242}, issn = {0040-3660}, mesh = {Clopidogrel ; Coronary Disease/drug therapy/*genetics/metabolism ; Cytochrome P-450 CYP2C19/genetics ; Data Interpretation, Statistical ; Drug Resistance/*genetics ; Female ; Gene Frequency ; Humans ; Kaplan-Meier Estimate ; Male ; Platelet Aggregation/drug effects ; Platelet Aggregation Inhibitors/administration & dosage/*therapeutic use ; Polymorphism, Genetic ; Prognosis ; Prospective Studies ; Risk ; Thromboxane-A Synthase/*genetics/metabolism ; Ticlopidine/administration & dosage/*analogs & derivatives/therapeutic use ; }, abstract = {AIM: To analyze the influence of pharmacogenetic factors on the risk of clopidogrel resistance and cardiovascular events during 18-months follow-up.

SUBJECTS AND METHODS: Two hundred and fifty patients taking clopidogrel were examined. Platelet function was determined by optical aggregometry. Thromboxane A synthase 1 (TBS1) gene polymorphism was investigated in all the patients. The impact of TBS1 gene polymorphism on the risk of clopidogrel resistance and cardiovascular events was analyzed during 18 months of follow-up.

RESULTS: The carriage of TBS1 gene polymorphism AA was shown to affect the risk of clopidogrel resistance. Cardiovascular complications significantly less frequently occurred in TBSI gene polymorphism AA carriers during 18 months.

CONCLUSION: The carriage of a slow AA allele of the'TBS1 gene is suggested to be a clinically significant protective factor in the secondary prevention of coronary heart disease}, } @article {pmid26022532, year = {2015}, author = {Peterson, AT and Soberón, J and Krishtalka, L}, title = {A global perspective on decadal challenges and priorities in biodiversity informatics.}, journal = {BMC ecology}, volume = {15}, number = {}, pages = {15}, pmid = {26022532}, issn = {1472-6785}, mesh = {*Biodiversity ; Conservation of Natural Resources ; Ecology/*methods ; *Informatics ; Information Dissemination ; Information Management ; }, abstract = {Biodiversity informatics is a field that is growing rapidly in data infrastructure, tools, and participation by researchers worldwide from diverse disciplines and with diverse, innovative approaches. A recent 'decadal view' of the field laid out a vision that was nonetheless restricted and constrained by its European focus. Our alternative decadal view is global, i.e., it sees the worldwide scope and importance of biodiversity informatics as addressing five major, global goals: (1) mobilize existing knowledge; (2) share this knowledge and the experience of its myriad deployments globally; (3) avoid 'siloing' and reinventing the tools of knowledge deployment; (4) tackle biodiversity informatics challenges at appropriate scales; and (5) seek solutions to difficult challenges that are strategic.}, } @article {pmid26020921, year = {2015}, author = {Liu, YX and Pang, CK and Liu, Y and Sun, XB and Li, XX and Jiang, SW and Xue, F}, title = {Association between Multidrug-Resistant Tuberculosis and Risk Factors in China: Applying Partial Least Squares Path Modeling.}, journal = {PloS one}, volume = {10}, number = {5}, pages = {e0128298}, pmid = {26020921}, issn = {1932-6203}, mesh = {China/epidemiology ; Climate ; Databases, Factual ; Geography ; Humans ; Least-Squares Analysis ; Prevalence ; Risk Factors ; Tuberculosis, Multidrug-Resistant/*epidemiology ; Tuberculosis, Pulmonary/*epidemiology ; }, abstract = {BACKGROUND: Multidrug-resistant tuberculosis (MDR-TB) resulting from various factors has raised serious public health concerns worldwide. Identifying the ecological risk factors associated with MDR-TB is critical to its prevention and control. This study aimed to explore the association between the development of MDR-TB and the risk factors at the group-level (ecological risk factors) in China.

METHODS: Data on MDR-TB in 120 counties were obtained from the National Tuberculosis Information Management System, and data on risk-factor variables were extracted from the Health Statistical Yearbook, provincial databases, and the meteorological bureau of each province (municipality). Partial Least Square Path Modeling was used to detect the associations.

RESULTS: The median proportion of MDR-TB in new TB cases was 3.96% (range, 0-39.39%). Six latent factors were extracted from the ecological risk factors, which explained 27.60% of the total variance overall in the prevalence of MDR-TB. Based on the results of PLS-PM, TB prevention, health resources, health services, TB treatment, TB detection, geography and climate factors were all associated with the risk of MDR-TB, but socioeconomic factors were not significant.

CONCLUSIONS: The development of MDR-TB was influenced by TB prevention, health resources, health services, TB treatment, TB detection, geography and climate factors. Such information may help us to establish appropriate public health intervention strategies to prevent and control MDR-TB and yield benefits to the entire public health system in China.}, } @article {pmid26018831, year = {2015}, author = {Jordan, LA and Ryan, MJ}, title = {The sensory ecology of adaptive landscapes.}, journal = {Biology letters}, volume = {11}, number = {5}, pages = {20141054}, pmid = {26018831}, issn = {1744-957X}, mesh = {*Adaptation, Psychological ; Animals ; *Behavior, Animal ; Computational Biology ; *Sensation ; }, abstract = {In complex environments, behavioural plasticity depends on the ability of an animal to integrate numerous sensory stimuli. The multidimensionality of factors interacting to shape plastic behaviour means it is difficult for both organisms and researchers to predict what constitutes an adaptive response to a given set of conditions. Although researchers may be able to map the fitness pay-offs of different behavioural strategies in changing environments, there is no guarantee that the study species will be able to perceive these pay-offs. We thus risk a disconnect between our own predictions about adaptive behaviour and what is behaviourally achievable given the umwelt of the animal being studied. This may lead to erroneous conclusions about maladaptive behaviour in circumstances when the behaviour exhibited is the most adaptive possible given sensory limitations. With advances in the computational resources available to behavioural ecologists, we can now measure vast numbers of interactions among behaviours and environments to create adaptive behavioural surfaces. These surfaces have massive heuristic, predictive and analytical potential in understanding adaptive animal behaviour, but researchers using them are destined to fail if they ignore the sensory ecology of the species they study. Here, we advocate the continued use of these approaches while directly linking them to perceptual space to ensure that the topology of the generated adaptive landscape matches the perceptual reality of the animal it intends to study. Doing so will allow predictive models of animal behaviour to reflect the reality faced by the agents on adaptive surfaces, vastly improving our ability to determine what constitutes an adaptive response for the animal in question.}, } @article {pmid26011166, year = {2015}, author = {Dyer, RJ}, title = {Is there such a thing as landscape genetics?.}, journal = {Molecular ecology}, volume = {24}, number = {14}, pages = {3518-3528}, doi = {10.1111/mec.13249}, pmid = {26011166}, issn = {1365-294X}, mesh = {Data Mining ; Discriminant Analysis ; Ecology/*methods ; Genetics, Population/*methods ; Geography ; Natural Language Processing ; Terminology as Topic ; }, abstract = {For a scientific discipline to be interdisciplinary, it must satisfy two conditions; it must consist of contributions from at least two existing disciplines, and it must be able to provide insights, through this interaction, that neither progenitor discipline could address. In this study, I examine the complete body of peer-reviewed literature self-identified as landscape genetics (LG) using the statistical approaches of text mining and natural language processing. The goal here was to quantify the kinds of questions being addressed in LG studies, the ways in which questions are evaluated mechanistically, and how they are differentiated from the progenitor disciplines of landscape ecology and population genetics. I then circumscribe the main factions within published LG studies examining the extent to which emergent questions are being addressed and highlighting a deep bifurcation between existing individual- and population-based approaches. I close by providing some suggestions on where theoretical and analytical work is needed if LGs is to serve as a real bridge connecting evolution and ecology sensu lato.}, } @article {pmid26011006, year = {2016}, author = {Tan, J and Levine, SL and Bachman, PM and Jensen, PD and Mueller, GM and Uffman, JP and Meng, C and Song, Z and Richards, KB and Beevers, MH}, title = {No impact of DvSnf7 RNA on honey bee (Apis mellifera L.) adults and larvae in dietary feeding tests.}, journal = {Environmental toxicology and chemistry}, volume = {35}, number = {2}, pages = {287-294}, pmid = {26011006}, issn = {1552-8618}, mesh = {Animals ; Base Sequence ; Bees/*genetics/*physiology ; Coleoptera ; Computational Biology ; *Diet ; Environment ; *Feeding Behavior ; *Food, Genetically Modified ; Larva/genetics/physiology ; Molecular Sequence Data ; Pollination ; RNA/*adverse effects/*genetics ; RNA, Double-Stranded/adverse effects/genetics ; Risk Assessment ; Survival Analysis ; Zea mays/*genetics ; }, abstract = {The honey bee (Apis mellifera L.) is the most important managed pollinator species worldwide and plays a critical role in the pollination of a diverse range of economically important crops. This species is important to agriculture and historically has been used as a surrogate species for pollinators to evaluate the potential adverse effects for conventional, biological, and microbial pesticides, as well as for genetically engineered plants that produce pesticidal products. As part of the ecological risk assessment of MON 87411 maize, which expresses a double-stranded RNA targeting the Snf7 ortholog (DvSnf7) in western corn rootworm (Diabrotica virgifera virgifera), dietary feeding studies with honey bee larvae and adults were conducted. Based on the mode of action of the DvSnf7 RNA in western corn rootworm, the present studies were designed to be of sufficient duration to evaluate the potential for adverse effects on larval survival and development through emergence and adult survival to a significant portion of the adult stage. Testing was conducted at concentrations of DvSnf7 RNA that greatly exceeded environmentally relevant exposure levels based on expression levels in maize pollen. No adverse effects were observed in either larval or adult honey bees at these high exposure levels, providing a large margin of safety between environmental exposure levels and no-observed-adverse-effect levels.}, } @article {pmid26010543, year = {2015}, author = {Gong, L and Zhang, H and Gan, X and Zhang, L and Chen, Y and Nie, F and Shi, L and Li, M and Guo, Z and Zhang, G and Song, Y}, title = {Transcriptome Profiling of the Potato (Solanum tuberosum L.) Plant under Drought Stress and Water-Stimulus Conditions.}, journal = {PloS one}, volume = {10}, number = {5}, pages = {e0128041}, pmid = {26010543}, issn = {1932-6203}, mesh = {Droughts ; Gene Expression Profiling/*methods ; Gene Expression Regulation, Plant ; Gene Ontology ; Metabolic Networks and Pathways ; Plant Proteins/*genetics ; Sequence Analysis, DNA/methods ; Solanum tuberosum/genetics/*growth & development ; *Stress, Physiological ; Water ; }, abstract = {Drought stress can seriously affect tuberization, yield and quality of potato plant. However, the precise molecular mechanisms governing potato stolon's response to drought stress and water supply are not very well understood. In this work, a potato (Solanum tuberosum L.) variant, Ningshu 4, was subjected to severe drought stress treatment (DT) and re-watering treatment (RWT) at tuber bulking stage. Strand-specific cDNA libraries of stolon materials were constructed for paired-end transcriptome sequencing analyses and differentially expressed gene (DEG) examination. In comparison to untreated-control (CT) plants, 3189 and 1797 DEGs were identified in DT and RWT plants and 4154 solely expressed DEGs were screened out from these two comparison groups. Interestingly, 263 genes showed opposite expression patterns in DT and RWT plants. Among them, genes homologous to Protein Phosphatase 2C (PP2C), Aspartic protease in guard cell 1 (ASPG1), auxin-responsive protein, Arabidopsis pseudo response regualtor 2 (APRR2), GA stimulated transcripts in Arabidopsis 6 (GASA6), Calmodulin-like protein 19 (CML19), abscisic acid 8'-hydroxylases and calcium-transporting ATPase, et al. were related with drought-stress and water stimulus response. Sixteen DEGs involved in starch synthesis, accumulation and tuber formation exhibited significantly different expression upon re-watering. In addition, 1630, 1527 and 1596 transcription factor encoding genes were detected in CT, DT and RWT. DEGs of ERF, bHLH, MYB, NAC, WRKY, C2H2, bZIP and HD-ZIP families accounted for 50% in three comparison groups, respectively. Furthermore, characteristics of 565 gene ontology (GO) and 108 Kyoto Encyclopedia of Genes and Genomes pathways (KEGG) were analyzed with the 4154 DEGs. All these results suggest that the drought- and water-stimulus response could be implemented by the regulated expression of metabolic pathway DEGs, and these genes were involved in the endogenous hormone biosynthesis and signal transduction pathways. Our data provide more direct information for future study on the interaction between key genes involved in various metabolic pathways under drought stress in potato.}, } @article {pmid26009840, year = {2015}, author = {Campana, I and Crosti, R and Angeletti, D and Carosso, L and David, L and Di-Méglio, N and Moulins, A and Rosso, M and Tepsich, P and Arcangeli, A}, title = {Cetacean response to summer maritime traffic in the Western Mediterranean Sea.}, journal = {Marine environmental research}, volume = {109}, number = {}, pages = {1-8}, doi = {10.1016/j.marenvres.2015.05.009}, pmid = {26009840}, issn = {1879-0291}, mesh = {Animals ; Cetacea/*physiology ; *Conservation of Natural Resources ; Mediterranean Sea ; Population Density ; Seasons ; *Ships ; }, abstract = {Maritime traffic is one of many anthropogenic pressures threatening the marine environment. This study was specifically designed to investigate the relationship between vessels presence and cetacean sightings in the high sea areas of the Western Mediterranean Sea region. We recorded and compared the total number of vessels in the presence and absence of cetacean sightings using data gathered during the summer season (2009-2013) along six fixed transects repeatedly surveyed. In locations with cetacean sightings (N = 2667), nautical traffic was significantly lower, by 20%, compared to random locations where no sightings occurred (N = 1226): all cetacean species, except bottlenose dolphin, were generally observed in locations with lower vessel abundance. In different areas the species showed variable results likely influenced by a combination of biological and local environmental factors. The approach of this research helped create, for the first time, a wide vision of the different responses of animals towards a common pressure.}, } @article {pmid26008700, year = {2015}, author = {Hargreaves, KR and Clokie, MR}, title = {A Taxonomic Review of Clostridium difficile Phages and Proposal of a Novel Genus, "Phimmp04likevirus".}, journal = {Viruses}, volume = {7}, number = {5}, pages = {2534-2541}, pmid = {26008700}, issn = {1999-4915}, support = {G0700855//Medical Research Council/United Kingdom ; }, mesh = {Bacteriophages/*classification/genetics/ultrastructure ; Clostridioides difficile/*virology ; Cluster Analysis ; Computational Biology ; Myoviridae/*classification/genetics/ultrastructure ; *Phylogeny ; Sequence Homology, Amino Acid ; Viral Proteins/genetics ; }, abstract = {Currently, only three phages that infect the medically important bacterium Clostridium difficile have been discussed by the International Committee of Viral Taxonomy (ICTV). They are all myoviruses, and have been assigned to the genus "phicd119likevirus". An additional nine phages have since been described in the literature with their genome data available. The Phicd119likevirus is named after the type species: the myovirus ΦCD119 which was the first C. difficile phage to be sequenced. The two additional myoviruses, ϕCD27 and φC2, also fall into this genus based on the similarity of their genome and morphological characteristics. The other nine phages have not been assigned to this genus, and four of them do not fit the criteria for the current taxonomic grouping. We have applied protein clustering analysis to determine their phylogenetic relationships. From these results we propose an additional myoviridae genus, that we term "phiMMP04likevirus".}, } @article {pmid26006775, year = {2015}, author = {Davies, AJ and Hope, MJ}, title = {Bayesian inference-based environmental decision support systems for oil spill response strategy selection.}, journal = {Marine pollution bulletin}, volume = {96}, number = {1-2}, pages = {87-102}, doi = {10.1016/j.marpolbul.2015.05.041}, pmid = {26006775}, issn = {1879-3363}, mesh = {Bayes Theorem ; Conservation of Natural Resources/*methods ; *Decision Support Techniques ; Ecosystem ; *Environmental Policy ; Petroleum Pollution/*analysis/*prevention & control ; }, abstract = {Contingency plans are essential in guiding the response to marine oil spills. However, they are written before the pollution event occurs so must contain some degree of assumption and prediction and hence may be unsuitable for a real incident when it occurs. The use of Bayesian networks in ecology, environmental management, oil spill contingency planning and post-incident analysis is reviewed and analysed to establish their suitability for use as real-time environmental decision support systems during an oil spill response. It is demonstrated that Bayesian networks are appropriate for facilitating the re-assessment and re-validation of contingency plans following pollutant release, thus helping ensure that the optimum response strategy is adopted. This can minimise the possibility of sub-optimal response strategies causing additional environmental and socioeconomic damage beyond the original pollution event.}, } @article {pmid26006264, year = {2015}, author = {Gomar, JJ and Valls, E and Radua, J and Mareca, C and Tristany, J and del Olmo, F and Rebolleda-Gil, C and Jañez-Álvarez, M and de Álvaro, FJ and Ovejero, MR and Llorente, A and Teixidó, C and Donaire, AM and García-Laredo, E and Lazcanoiturburu, A and Granell, L and Mozo, Cde P and Pérez-Hernández, M and Moreno-Alcázar, A and Pomarol-Clotet, E and McKenna, PJ and , }, title = {A Multisite, Randomized Controlled Clinical Trial of Computerized Cognitive Remediation Therapy for Schizophrenia.}, journal = {Schizophrenia bulletin}, volume = {41}, number = {6}, pages = {1387-1396}, pmid = {26006264}, issn = {1745-1701}, mesh = {Adult ; Aged ; Cognition Disorders/etiology/*rehabilitation ; Cognitive Behavioral Therapy/*methods ; Executive Function/*physiology ; Female ; Humans ; Male ; Memory Disorders/etiology/*rehabilitation ; Middle Aged ; Schizophrenia/complications/*rehabilitation ; Therapy, Computer-Assisted/*methods ; Treatment Failure ; Young Adult ; }, abstract = {The effectiveness of cognitive remediation therapy (CRT) for the neuropsychological deficits seen in schizophrenia is supported by meta-analysis. However, a recent methodologically rigorous trial had negative findings. In this study, 130 chronic schizophrenic patients were randomly assigned to computerized CRT, an active computerized control condition (CC) or treatment as usual (TAU). Primary outcome measures were 2 ecologically valid batteries of executive function and memory, rated under blind conditions; other executive and memory tests and a measure of overall cognitive function were also employed. Carer ratings of executive and memory failures in daily life were obtained before and after treatment. Computerized CRT was found to produce improvement on the training tasks, but this did not transfer to gains on the primary outcome measures and most other neuropsychological tests in comparison to either CC or TAU conditions. Nor did the intervention result in benefits on carer ratings of daily life cognitive failures. According to this study, computerized CRT is not effective in schizophrenia. The use of both active and passive CCs suggests that nature of the control group is not an important factor influencing results.}, } @article {pmid26003982, year = {2015}, author = {Kukita, S and Gouda, M and Ikeda, S and Ishibashi, S and Furuya, T and Nakamura, K}, title = {Effects of Photoperiod and Temperature on Growth and Development in Clouded Salamander (Hynobius nebulosus) Larvae.}, journal = {Zoological science}, volume = {32}, number = {3}, pages = {266-271}, doi = {10.2108/zs140220}, pmid = {26003982}, issn = {0289-0003}, mesh = {Animals ; Larva/*growth & development ; Metamorphosis, Biological ; *Photoperiod ; *Temperature ; Urodela/*growth & development ; }, abstract = {Day length is one of the most important factors that organisms use to predict seasonal changes in their environment. Several amphibians regulate their growth and development in response to photoperiod. However, many studies have not focused on the ecological effects of the photoperiodic response on growth and development because they use tropical animals, animals from a commercial source or from unknown localities, or extreme light regimens for experiments. In the present study, we examined the effects of photoperiod on growth and development in the clouded salamander (Hynobius nebulosus) by raising larvae under different photoperiods and at different temperatures in the laboratory. The average larval period under a long-day photoperiod of L16:D8 was longer than that under L12:D12 at 15°C or 20°C, although the difference between the photoperiods was only significant for 15°C. Juveniles weighed more at metamorphosis under L16:D8 than those under L12:D12, irrespective of temperature, suggesting that a longer developmental period results in a heavier body weight. The head width of juveniles did not differ for different photoperiods at either temperature. However, the growth rate of the head width under L12:D12 was faster than that under L16:D8 at 15°C. Long day length appears to produce larger H. nebulosus juveniles in a relatively stable aquatic environment with a low population density. Thus, development may be accelerated when the day length becomes shorter as winter approaches, and larvae may have increased the growth rate of their head widths to compensate for the shorter growing period under shorter day lengths.}, } @article {pmid26001744, year = {2016}, author = {Costa, M and Hauzy, C and Loeuille, N and Méléard, S}, title = {Stochastic eco-evolutionary model of a prey-predator community.}, journal = {Journal of mathematical biology}, volume = {72}, number = {3}, pages = {573-622}, pmid = {26001744}, issn = {1432-1416}, mesh = {Adaptation, Physiological ; Animals ; *Biological Evolution ; Computational Biology ; Ecosystem ; Markov Chains ; Mathematical Concepts ; *Models, Biological ; Mutation ; Phenotype ; Population Dynamics ; *Predatory Behavior ; Selection, Genetic ; Stochastic Processes ; }, abstract = {We are interested in the impact of natural selection in a prey-predator community. We introduce an individual-based model of the community that takes into account both prey and predator phenotypes. Our aim is to understand the phenotypic coevolution of prey and predators. The community evolves as a multi-type birth and death process with mutations. We first consider the infinite particle approximation of the process without mutation. In this limit, the process can be approximated by a system of differential equations. We prove the existence of a unique globally asymptotically stable equilibrium under specific conditions on the interaction among prey individuals. When mutations are rare, the community evolves on the mutational scale according to a Markovian jump process. This process describes the successive equilibria of the prey-predator community and extends the polymorphic evolutionary sequence to a coevolutionary framework. We then assume that mutations have a small impact on phenotypes and consider the evolution of monomorphic prey and predator populations. The limit of small mutation steps leads to a system of two differential equations which is a version of the canonical equation of adaptive dynamics for the prey-predator coevolution. We illustrate these different limits with an example of prey-predator community that takes into account different prey defense mechanisms. We observe through simulations how these various prey strategies impact the community.}, } @article {pmid25999513, year = {2015}, author = {Sunagawa, S and Coelho, LP and Chaffron, S and Kultima, JR and Labadie, K and Salazar, G and Djahanschiri, B and Zeller, G and Mende, DR and Alberti, A and Cornejo-Castillo, FM and Costea, PI and Cruaud, C and d'Ovidio, F and Engelen, S and Ferrera, I and Gasol, JM and Guidi, L and Hildebrand, F and Kokoszka, F and Lepoivre, C and Lima-Mendez, G and Poulain, J and Poulos, BT and Royo-Llonch, M and Sarmento, H and Vieira-Silva, S and Dimier, C and Picheral, M and Searson, S and Kandels-Lewis, S and , and Bowler, C and de Vargas, C and Gorsky, G and Grimsley, N and Hingamp, P and Iudicone, D and Jaillon, O and Not, F and Ogata, H and Pesant, S and Speich, S and Stemmann, L and Sullivan, MB and Weissenbach, J and Wincker, P and Karsenti, E and Raes, J and Acinas, SG and Bork, P}, title = {Ocean plankton. Structure and function of the global ocean microbiome.}, journal = {Science (New York, N.Y.)}, volume = {348}, number = {6237}, pages = {1261359}, doi = {10.1126/science.1261359}, pmid = {25999513}, issn = {1095-9203}, support = {294823/ERC_/European Research Council/International ; }, mesh = {Databases, Genetic ; Ecosystem ; Gastrointestinal Tract/microbiology ; Genetic Variation ; Humans ; Metagenome ; Microbiota/*genetics ; Oceans and Seas ; Plankton/*classification/genetics/isolation & purification ; Seawater/*microbiology ; }, abstract = {Microbes are dominant drivers of biogeochemical processes, yet drawing a global picture of functional diversity, microbial community structure, and their ecological determinants remains a grand challenge. We analyzed 7.2 terabases of metagenomic data from 243 Tara Oceans samples from 68 locations in epipelagic and mesopelagic waters across the globe to generate an ocean microbial reference gene catalog with >40 million nonredundant, mostly novel sequences from viruses, prokaryotes, and picoeukaryotes. Using 139 prokaryote-enriched samples, containing >35,000 species, we show vertical stratification with epipelagic community composition mostly driven by temperature rather than other environmental factors or geography. We identify ocean microbial core functionality and reveal that >73% of its abundance is shared with the human gut microbiome despite the physicochemical differences between these two ecosystems.}, } @article {pmid25999395, year = {2015}, author = {Sanderson, MJ and McMahon, MM and Stamatakis, A and Zwickl, DJ and Steel, M}, title = {Impacts of Terraces on Phylogenetic Inference.}, journal = {Systematic biology}, volume = {64}, number = {5}, pages = {709-726}, doi = {10.1093/sysbio/syv024}, pmid = {25999395}, issn = {1076-836X}, mesh = {Classification/*methods ; Computer Simulation/*standards ; Models, Genetic ; *Phylogeny ; }, abstract = {Terraces are sets of trees with precisely the same likelihood or parsimony score, which can be induced by missing sequences in partitioned multi-locus phylogenetic data matrices. The potentially large set of trees on a terrace can be characterized by enumeration algorithms or consensus methods that exploit the pattern of partial taxon coverage in the data, independent of the sequence data themselves. Terraces can add ambiguity and complexity to phylogenetic inference, particularly in settings where inference is already challenging: data sets with many taxa and relatively few loci. In this article we present five new findings about terraces and their impacts on phylogenetic inference. First, we clarify assumptions about partitioning scheme model parameters that are necessary for the existence of terraces. Second, we explore the dependence of terrace size on partitioning scheme and indicate how to find the partitioning scheme associated with the largest terrace containing a given tree. Third, we highlight the impact of terrace size on bootstrap estimates of confidence limits in clades, and characterize the surprising result that the bootstrap proportion for a clade, as it is usually calculated, can be entirely determined by the frequency of bipartitions on a terrace, with some bipartitions receiving high support even when incorrect. Fourth, we dissect some effects of prior distributions of edge lengths on the computed posterior probabilities of clades on terraces, to understand an example in which long edges "attract" each other in Bayesian inference. Fifth, we describe how assuming relationships between edge-lengths of different loci, as an attempt to avoid terraces, can also be problematic when taxon coverage is partial, specifically when heterotachy is present. Finally, we discuss strategies for remediation of some of these problems. One promising approach finds a minimal set of taxa which, when deleted from the data matrix, reduces the size of a terrace to a single tree.}, } @article {pmid25993004, year = {2015}, author = {Grilli, J and Barabás, G and Allesina, S}, title = {Metapopulation persistence in random fragmented landscapes.}, journal = {PLoS computational biology}, volume = {11}, number = {5}, pages = {e1004251}, pmid = {25993004}, issn = {1553-7358}, mesh = {Animals ; Computational Biology ; *Ecosystem ; Extinction, Biological ; Humans ; Markov Chains ; *Models, Biological ; Population Density ; *Population Dynamics/statistics & numerical data ; }, abstract = {Habitat destruction and land use change are making the world in which natural populations live increasingly fragmented, often leading to local extinctions. Although local populations might undergo extinction, a metapopulation may still be viable as long as patches of suitable habitat are connected by dispersal, so that empty patches can be recolonized. Thus far, metapopulations models have either taken a mean-field approach, or have modeled empirically-based, realistic landscapes. Here we show that an intermediate level of complexity between these two extremes is to consider random landscapes, in which the patches of suitable habitat are randomly arranged in an area (or volume). Using methods borrowed from the mathematics of Random Geometric Graphs and Euclidean Random Matrices, we derive a simple, analytic criterion for the persistence of the metapopulation in random fragmented landscapes. Our results show how the density of patches, the variability in their value, the shape of the dispersal kernel, and the dimensionality of the landscape all contribute to determining the fate of the metapopulation. Using this framework, we derive sufficient conditions for the population to be spatially localized, such that spatially confined clusters of patches act as a source of dispersal for the whole landscape. Finally, we show that a regular arrangement of the patches is always detrimental for persistence, compared to the random arrangement of the patches. Given the strong parallel between metapopulation models and contact processes, our results are also applicable to models of disease spread on spatial networks.}, } @article {pmid25992800, year = {2015}, author = {Jalali, MA and Ierodiaconou, D and Gorfine, H and Monk, J and Rattray, A}, title = {Exploring Spatiotemporal Trends in Commercial Fishing Effort of an Abalone Fishing Zone: A GIS-Based Hotspot Model.}, journal = {PloS one}, volume = {10}, number = {5}, pages = {e0122995}, pmid = {25992800}, issn = {1932-6203}, mesh = {Animals ; Australia ; *Conservation of Natural Resources ; *Environmental Monitoring ; *Fisheries ; Fishes ; *Geographic Information Systems ; Marine Biology ; *Models, Theoretical ; Species Specificity ; }, abstract = {Assessing patterns of fisheries activity at a scale related to resource exploitation has received particular attention in recent times. However, acquiring data about the distribution and spatiotemporal allocation of catch and fishing effort in small scale benthic fisheries remains challenging. Here, we used GIS-based spatio-statistical models to investigate the footprint of commercial diving events on blacklip abalone (Haliotis rubra) stocks along the south-west coast of Victoria, Australia from 2008 to 2011. Using abalone catch data matched with GPS location we found catch per unit of fishing effort (CPUE) was not uniformly spatially and temporally distributed across the study area. Spatial autocorrelation and hotspot analysis revealed significant spatiotemporal clusters of CPUE (with distance thresholds of 100's of meters) among years, indicating the presence of CPUE hotspots focused on specific reefs. Cumulative hotspot maps indicated that certain reef complexes were consistently targeted across years but with varying intensity, however often a relatively small proportion of the full reef extent was targeted. Integrating CPUE with remotely-sensed light detection and ranging (LiDAR) derived bathymetry data using generalized additive mixed model corroborated that fishing pressure primarily coincided with shallow, rugose and complex components of reef structures. This study demonstrates that a geospatial approach is efficient in detecting patterns and trends in commercial fishing effort and its association with seafloor characteristics.}, } @article {pmid25989855, year = {2015}, author = {Fan, J and Semenzin, E and Meng, W and Giubilato, E and Zhang, Y and Critto, A and Zabeo, A and Zhou, Y and Ding, S and Wan, J and He, M and Lin, C}, title = {Ecological status classification of the Taizi River Basin, China: a comparison of integrated risk assessment approaches.}, journal = {Environmental science and pollution research international}, volume = {22}, number = {19}, pages = {14738-14754}, pmid = {25989855}, issn = {1614-7499}, mesh = {Animals ; Biological Oxygen Demand Analysis ; Biota ; China ; Polycyclic Aromatic Hydrocarbons/*analysis ; Risk Assessment/methods ; *Rivers ; Water Pollutants, Chemical/*analysis ; Water Quality ; }, abstract = {Integrated risk assessment approaches allow to achieve a sound evaluation of ecological status of river basins and to gain knowledge about the likely causes of impairment, useful for informing and supporting the decision-making process. In this paper, the integrated risk assessment (IRA) methodology developed in the EU MODELKEY project (and implemented in the MODELKEY Decision Support System) is applied to the Taizi River (China), in order to assess its Ecological and Chemical Status according to EU Water Framework Directive (WFD) requirements. The available dataset is derived by an extensive survey carried out in 2009 and 2010 across the Taizi River catchment, including the monitoring of physico-chemical (i.e. DO, EC, NH3-_N, chemical oxygen demand (COD), biological oxygen demand in 5 days (BOD5) and TP), chemical (i.e. polycyclic aromatic hydrocarbons (PAHs) and metals), biological (i.e. macroinvertebrates, fish, and algae), and hydromorphological parameters (i.e. water quantity, channel change and morphology diversity). The results show a negative trend in the ecological status from the highland to the lowland of the Taizi River Basin. Organic pollution from agriculture and domestic sources (i.e. COD and BOD5), unstable hydrological regime (i.e. water quantity shortage) and chemical pollutants from industry (i.e. PAHs and metals) are found to be the main stressors impacting the ecological status of the Taizi River Basin. The comparison between the results of the IRA methodology and those of a previous study (Leigh et al. 2012) indicates that the selection of indicators and integrating methodologies can have a relevant impact on the classification of the ecological status. The IRA methodology, which integrates information from five lines of evidence (i.e., biology, physico-chemistry, chemistry, ecotoxicology and hydromorphology) required by WFD, allows to better identify the biological communities that are potentially at risk and the stressors that are most likely responsible for the observed alterations. This knowledge can be beneficial for a more effective restoration and management of the river basin ecosystem.}, } @article {pmid25989024, year = {2015}, author = {Mittell, EA and Nakagawa, S and Hadfield, JD}, title = {Are molecular markers useful predictors of adaptive potential?.}, journal = {Ecology letters}, volume = {18}, number = {8}, pages = {772-778}, doi = {10.1111/ele.12454}, pmid = {25989024}, issn = {1461-0248}, mesh = {*Adaptation, Biological ; Databases, Genetic ; *Genetic Markers ; *Genetic Variation ; *Genetics, Population ; Linear Models ; Microsatellite Repeats ; Models, Genetic ; }, abstract = {Estimates of molecular genetic variation are often used as a cheap and simple surrogate for a population's adaptive potential, yet empirical evidence suggests they are unlikely to be a valid proxy. However, this evidence is based on molecular genetic variation poorly predicting estimates of adaptive potential rather than how well it predicts true values. As a consequence, the relationship has been systematically underestimated and the precision with which it could be measured severely overstated. By collating a large database, and using suitable statistical methods, we obtain a 95% upper bound of 0.26 for the proportion of variance in quantitative genetic variation explained by molecular diversity. The relationship is probably too weak to be useful, but this conclusion must be taken as provisional: less noisy estimates of quantitative genetic variation are required. In contrast, and perhaps surprisingly, current sampling strategies appear sufficient for characterising a population's molecular genetic variation at comparable markers.}, } @article {pmid25988396, year = {2015}, author = {Albanese, D and Fontana, P and De Filippo, C and Cavalieri, D and Donati, C}, title = {MICCA: a complete and accurate software for taxonomic profiling of metagenomic data.}, journal = {Scientific reports}, volume = {5}, number = {}, pages = {9743}, pmid = {25988396}, issn = {2045-2322}, mesh = {Algorithms ; Biodiversity ; Computational Biology/methods ; DNA Barcoding, Taxonomic/*methods ; Datasets as Topic ; Metagenomics/*methods ; Microbiota/genetics ; *Software ; }, abstract = {The introduction of high throughput sequencing technologies has triggered an increase of the number of studies in which the microbiota of environmental and human samples is characterized through the sequencing of selected marker genes. While experimental protocols have undergone a process of standardization that makes them accessible to a large community of scientist, standard and robust data analysis pipelines are still lacking. Here we introduce MICCA, a software pipeline for the processing of amplicon metagenomic datasets that efficiently combines quality filtering, clustering of Operational Taxonomic Units (OTUs), taxonomy assignment and phylogenetic tree inference. MICCA provides accurate results reaching a good compromise among modularity and usability. Moreover, we introduce a de-novo clustering algorithm specifically designed for the inference of Operational Taxonomic Units (OTUs). Tests on real and synthetic datasets shows that thanks to the optimized reads filtering process and to the new clustering algorithm, MICCA provides estimates of the number of OTUs and of other common ecological indices that are more accurate and robust than currently available pipelines. Analysis of public metagenomic datasets shows that the higher consistency of results improves our understanding of the structure of environmental and human associated microbial communities. MICCA is an open source project.}, } @article {pmid25985671, year = {2015}, author = {Wang, XJ and Zhou, Y and Yan, YB and Li, L}, title = {[Agricultural policies and farming systems: A case study of landscape changes in Shizuitou Village in the recent four decades].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {26}, number = {1}, pages = {199-206}, pmid = {25985671}, issn = {1001-9332}, mesh = {Agriculture/*legislation & jurisprudence/*methods ; China ; Conservation of Natural Resources ; Food Supply ; Geographic Information Systems ; Geography ; Humans ; *Industrial Development ; Rural Population ; }, abstract = {Agricultural policy in China's rural heartland is driving profound changes to traditional farming systems. A case study covering four decades mapped and recorded farming patterns and processes in Shizuitou Village, a rural village in northwest Shanxi. An integrated geospatial methodology from geography and anthropology was employed in the case study to record the changing dynamics of farming systems in Shizuitou Village to discover the long-term impacts of China's agricultural policies on village farming systems. Positive and negative impacts of agricultural policies on village farming systems were mapped, inventoried and evaluated using Participatory Geographic Information Systems (PGIS). The results revealed traditional polycultures are being gradually replaced by industrialized monocultures. The driving forces behind these farming changes come from a series of government agricultural policies aiming at modernization of farming systems in China. The goal of these policies was to spur rapid development of industrial agriculture under the guise of modernization but is leading to the decay of traditional farming systems in the village that maintained local food security with healthy land for hundreds of years. The paper concluded with a recommendation that in future, agricultural policy makers should strike a more reasonable balance between short-term agricultural profits and long-term farming sustainability based on the principles of ecological sustainable development under the context of global changes.}, } @article {pmid25983555, year = {2015}, author = {Oulas, A and Pavloudi, C and Polymenakou, P and Pavlopoulos, GA and Papanikolaou, N and Kotoulas, G and Arvanitidis, C and Iliopoulos, I}, title = {Metagenomics: tools and insights for analyzing next-generation sequencing data derived from biodiversity studies.}, journal = {Bioinformatics and biology insights}, volume = {9}, number = {}, pages = {75-88}, pmid = {25983555}, issn = {1177-9322}, abstract = {Advances in next-generation sequencing (NGS) have allowed significant breakthroughs in microbial ecology studies. This has led to the rapid expansion of research in the field and the establishment of "metagenomics", often defined as the analysis of DNA from microbial communities in environmental samples without prior need for culturing. Many metagenomics statistical/computational tools and databases have been developed in order to allow the exploitation of the huge influx of data. In this review article, we provide an overview of the sequencing technologies and how they are uniquely suited to various types of metagenomic studies. We focus on the currently available bioinformatics techniques, tools, and methodologies for performing each individual step of a typical metagenomic dataset analysis. We also provide future trends in the field with respect to tools and technologies currently under development. Moreover, we discuss data management, distribution, and integration tools that are capable of performing comparative metagenomic analyses of multiple datasets using well-established databases, as well as commonly used annotation standards.}, } @article {pmid25983046, year = {2015}, author = {Cooper, JD and Neuhauser, C and Dean, AM and Kerr, B}, title = {Tipping the mutation-selection balance: Limited migration increases the frequency of deleterious mutants.}, journal = {Journal of theoretical biology}, volume = {380}, number = {}, pages = {123-133}, doi = {10.1016/j.jtbi.2015.05.003}, pmid = {25983046}, issn = {1095-8541}, mesh = {Models, Theoretical ; *Mutation ; *Selection, Genetic ; Stochastic Processes ; }, abstract = {Typical mutation-selection models assume well-mixed populations, but dispersal and migration within many natural populations is spatially limited. Such limitations can lead to enhanced variation among locations as different types become clustered in different places. Such clustering weakens competition between unlike types relative to competition between like types; thus, the rate by which a fitter type displaces an inferior competitor can be affected by the spatial scale of movement. In this paper, we use a birth-death model to show that limited migration can affect asexual populations by creating competitive refugia. We use a moment closure approach to show that as population structure is introduced by limiting migration, the equilibrial frequency of deleterious mutants increases. We support and extend the model through stochastic simulation, and we use a spatially explicit cellular automaton approach to corroborate the results. We discuss the implications of these results for standing variation in structured populations and adaptive valley crossing in Wright's "shifting balance" process.}, } @article {pmid25981911, year = {2015}, author = {Rodríguez-García, MJ and Machado, V and Galián, J}, title = {Identification and characterisation of putative seminal fluid proteins from male reproductive tissue EST libraries in tiger beetles.}, journal = {BMC genomics}, volume = {16}, number = {1}, pages = {391}, pmid = {25981911}, issn = {1471-2164}, mesh = {Animals ; Coleoptera/classification/*genetics ; Computational Biology ; *Expressed Sequence Tags ; Female ; Gene Library ; Genes, Insect/*genetics ; Male ; Molecular Sequence Annotation ; Phylogeny ; RNA/chemistry/isolation & purification/metabolism ; Reverse Transcriptase Polymerase Chain Reaction ; Semen/*metabolism ; Seminal Plasma Proteins/chemistry/*genetics ; }, abstract = {BACKGROUND: The study of proteins transferred through semen can provide important information for biological questions such as adaptive evolution, the origin of new species and species richness. The objective of this study was to identify seminal fluid proteins (SFPs) that may contribute to the study of the reproductive system of tiger beetles (cicindelids), a group of more than 2,500 species distributed worldwide that occupy a great diversity of habitats.

RESULTS: Two cDNA libraries were constructed from the male gonads of Calomera littoralis and Cephalota litorea. Expressed sequence tags (ESTs) were analysed by bioinformatics approaches and 14 unigenes were selected as candidate SFPs, which were submitted to Reverse Transcription Polymerase Chain Reaction (RT-PCR) to identify patterns of tissue-specific expression. We have identified four novel putative SFPs of cicindelids, of which similarity searches did not show homologues with known function. However, two of the protein classes (immune response and hormone) predicted by Protfun are similar to SFPs reported in other insects. Searches for homology in other cicindelids showed one lineage specific SFPs (rapidly evolving proteins), only present in the closely related species C. littoralis and Lophyra flexuosa and two conserved SFP present in other tiger beetles species tested.

CONCLUSIONS: This work represents the first characterisation of putative SFPs in Adephagan species of the order Coleoptera. The results will serve as a foundation for further studies aimed to understand gene (and protein) functions and their evolutionary implications in this group of ecologically relevant beetles.}, } @article {pmid25980726, year = {2015}, author = {Xiao, Y and Xiao, Q and Ouyang, Z and Maomao, Q}, title = {Assessing changes in water flow regulation in Chongqing region, China.}, journal = {Environmental monitoring and assessment}, volume = {187}, number = {6}, pages = {362}, pmid = {25980726}, issn = {1573-2959}, mesh = {Altitude ; China ; Conservation of Natural Resources/*methods ; *Ecosystem ; Environmental Monitoring/*methods ; Geographic Information Systems ; Humans ; Models, Theoretical ; Rivers/*chemistry ; *Water Movements ; }, abstract = {Water flow regulation is an important ecosystem service that significantly impacts on ecological quality and social benefits. With the aim of improving our understanding of ecosystems and proposing strategies for optimizing ecosystem services, a geographic information system (GIS)-based approach was designed to estimate and map regulated water flow in the Chongqing region of China. In this study, we applied the integrated valuation of environmental services and tradeoffs (InVEST) model and mathematical simulations to estimate the provision of the regulated water flow across space and time in 2000, 2005, and 2010. The results indicated that this ecosystem service had improved by 2.07 % from 2000 to 2010 as a result of human activities (such as vegetation restoration) and climatic interaction. Places with positive changes mainly occurred in high mountain areas, whereas places with negative changes were mainly distributed in resettlement areas along the Yangtze River. The type of ecosystem in areas with high mountains and steep slopes was a relatively minor contributor to the total service, but this ecosystem had the higher water flow regulation capacity. Moreover, with the increase in altitude and slope, the percentage contribution of forest increased significantly from 2000 to 2010; by contrast, the percentage contribution of cropland decreased rapidly. As for the impacts, the spatial variation of water flow regulation in the Chongqing region had a significant relation with climate and human activities at the regional scale. These results provided specific information that could be used to strengthen necessary public awareness about the protection and restoration of ecosystems.}, } @article {pmid25980407, year = {2015}, author = {Levy, R and Carr, R and Kreimer, A and Freilich, S and Borenstein, E}, title = {NetCooperate: a network-based tool for inferring host-microbe and microbe-microbe cooperation.}, journal = {BMC bioinformatics}, volume = {16}, number = {1}, pages = {164}, pmid = {25980407}, issn = {1471-2105}, support = {DP2 AT007802/AT/NCCIH NIH HHS/United States ; }, mesh = {Animals ; Bacteria/classification/genetics/*metabolism ; Computational Biology/*methods ; *Host-Parasite Interactions ; Humans ; Internet ; *Metabolic Networks and Pathways ; *Microbial Interactions ; Models, Biological ; *Software ; }, abstract = {BACKGROUND: Host-microbe and microbe-microbe interactions are often governed by the complex exchange of metabolites. Such interactions play a key role in determining the way pathogenic and commensal species impact their host and in the assembly of complex microbial communities. Recently, several studies have demonstrated how such interactions are reflected in the organization of the metabolic networks of the interacting species, and introduced various graph theory-based methods to predict host-microbe and microbe-microbe interactions directly from network topology. Using these methods, such studies have revealed evolutionary and ecological processes that shape species interactions and community assembly, highlighting the potential of this reverse-ecology research paradigm.

RESULTS: NetCooperate is a web-based tool and a software package for determining host-microbe and microbe-microbe cooperative potential. It specifically calculates two previously developed and validated metrics for species interaction: the Biosynthetic Support Score which quantifies the ability of a host species to supply the nutritional requirements of a parasitic or a commensal species, and the Metabolic Complementarity Index which quantifies the complementarity of a pair of microbial organisms' niches. NetCooperate takes as input a pair of metabolic networks, and returns the pairwise metrics as well as a list of potential syntrophic metabolic compounds.

CONCLUSIONS: The Biosynthetic Support Score and Metabolic Complementarity Index provide insight into host-microbe and microbe-microbe metabolic interactions. NetCooperate determines these interaction indices from metabolic network topology, and can be used for small- or large-scale analyses. NetCooperate is provided as both a web-based tool and an open-source Python module; both are freely available online at http://elbo.gs.washington.edu/software_netcooperate.html.}, } @article {pmid25977820, year = {2015}, author = {Messina, JP and Pigott, DM and Duda, KA and Brownstein, JS and Myers, MF and George, DB and Hay, SI}, title = {A global compendium of human Crimean-Congo haemorrhagic fever virus occurrence.}, journal = {Scientific data}, volume = {2}, number = {}, pages = {150016}, pmid = {25977820}, issn = {2052-4463}, support = {095066//Wellcome Trust/United Kingdom ; R01 LM010812/LM/NLM NIH HHS/United States ; R01LM010812/LM/NLM NIH HHS/United States ; }, mesh = {*Databases, Factual ; Geographic Mapping ; *Hemorrhagic Fever Virus, Crimean-Congo/isolation & purification ; *Hemorrhagic Fever, Crimean/epidemiology/virology ; Humans ; }, abstract = {In order to map global disease risk, a geographic database of human Crimean-Congo haemorrhagic fever virus (CCHFV) occurrence was produced by surveying peer-reviewed literature and case reports, as well as informal online sources. Here we present this database, comprising occurrence data linked to geographic point or polygon locations dating from 1953 to 2013. We fully describe all data collection, geo-positioning, database management and quality-control procedures. This is the most comprehensive database of confirmed CCHF occurrence in humans to-date, containing 1,721 geo-positioned occurrences in total.}, } @article {pmid25976089, year = {2015}, author = {Le Meur, N and Gao, F and Bayat, S}, title = {Mining care trajectories using health administrative information systems: the use of state sequence analysis to assess disparities in prenatal care consumption.}, journal = {BMC health services research}, volume = {15}, number = {}, pages = {200}, pmid = {25976089}, issn = {1472-6963}, mesh = {Adolescent ; Adult ; *Data Mining ; Databases, Factual ; Employment ; Female ; France ; *Healthcare Disparities ; Humans ; *Information Systems ; Middle Aged ; Patient Discharge ; Pilot Projects ; Pregnancy ; Prenatal Care/*statistics & numerical data ; Sequence Analysis ; Young Adult ; }, abstract = {BACKGROUND: Pregnant women are a vulnerable population. Although regular follow-ups are recommended during pregnancy, not all pregnant women seek care. This pilot study wanted to assess whether the integration of data from administrative health information systems and socio-economic features allows identifying disparities in prenatal care trajectories.

METHODS: Prenatal care trajectories were extracted from the permanent sample of the French health insurance information system linked to the hospital discharge information system. The records of 2518 women who gave birth without complications in France in 2009 were analyzed. State sequence data analysis was performed to identify homogeneous groups of prenatal care trajectories. Socio-economic data were used to characterize their living environment.

RESULTS: We identified three groups of homogeneous prenatal care trajectories: (i) women with relatively high prenatal care consumption (~11%), (ii) women with no prenatal care (~21%), and (iii) women with an intermediate level of prenatal care (~66%). Analysis of the socio-economic data demonstrated the association between disparities in prenatal care trajectories and the women's living environment. Women with relatively high care consumption generally lived in socio-economically privileged areas (better education levels, employment status and housing conditions) compared with women with few or no prenatal care.

CONCLUSIONS: Although ecological, our approach demonstrates that data from health administrative information systems could be used to describe prenatal care. However, more individual variables and an improvement of the data quality are needed to efficiently monitor the content and timing of prenatal care. Moreover, state sequence analysis, which was used in this context for the first time, proves to be an interesting approach to explore care trajectories. Finally, the integration of heterogeneous sources of data, including contextual information, might help identifying areas that require health promotion actions toward vulnerable populations, such as pregnant women.}, } @article {pmid25974338, year = {2015}, author = {Hinow, P and Magal, P and Ruan, S}, title = {Special issue dedicated to the 70th birthday of Glenn F. Webb. Preface.}, journal = {Mathematical biosciences and engineering : MBE}, volume = {12}, number = {4}, pages = {i-iv}, doi = {10.3934/mbe.2015.12.4i}, pmid = {25974338}, issn = {1551-0018}, mesh = {Communicable Diseases/*history ; Computational Biology/*history ; History, 20th Century ; History, 21st Century ; Humans ; Mathematics/*history ; Microbiology/*history ; Population Dynamics/*history ; United States ; }, abstract = {This special issue is dedicated to the 70th birthday of Glenn F. Webb. The topics of the 12 articles appearing in this special issue include evolutionary dynamics of population growth, spatio-temporal dynamics in reaction-diffusion biological models, transmission dynamics of infectious diseases, modeling of antibiotic-resistant bacteria in hospitals, analysis of Prion models, age-structured models in ecology and epidemiology, modeling of immune response to infections, modeling of cancer growth, etc. These topics partially represent the broad areas of Glenn's research interest.}, } @article {pmid25971735, year = {2015}, author = {Pierre, JP and Abolt, CJ and Young, MH}, title = {Impacts from above-ground activities in the eagle ford shale play on landscapes and hydrologic flows, La Salle County, Texas.}, journal = {Environmental management}, volume = {55}, number = {6}, pages = {1262-1275}, pmid = {25971735}, issn = {1432-1009}, mesh = {Conservation of Natural Resources/*methods ; *Ecosystem ; Environmental Monitoring/*methods ; Geographic Information Systems ; Hydrology ; *Natural Resources ; *Oil and Gas Industry ; Soil ; Texas ; *Water Movements ; }, abstract = {We assess the spatial and geomorphic fragmentation from the recent Eagle Ford Shale play in La Salle County, Texas, USA. Wells and pipelines were overlaid onto base maps of land cover, soil properties, vegetation assemblages, and hydrologic units. Changes to continuity of different ecoregions and supporting landscapes were assessed using the Landscape Fragmentation Tool (a third-party ArcGIS extension) as quantified by land area and continuity of core landscape areas (i.e., those degraded by "edge effects"). Results show decreases in core areas (8.7%; ~33,290 ha) and increases in landscape patches (0.2%; ~640 ha), edges (1.8%; ~6940 ha), and perforated areas (4.2%; ~16230 ha). Pipeline construction dominates landscape disturbance, followed by drilling and injection pads (85, 15, and 0.03% of disturbed area, respectively). An increased potential for soil loss is indicated, with 51% (~5790 ha) of all disturbance regimes occurring on soils with low water-transmission rates (depth to impermeable layer less than 50 cm) and a high surface runoff potential (hydrologic soil group D). Additionally, 88% (~10,020 ha) of all disturbances occurred on soils with a wind erodibility index of approximately 19 kt/km(2)/year (0.19 kt/ha/year) or higher, resulting in an estimated potential of 2 million tons of soil loss per year. Results demonstrate that infrastructure placement is occurring on soils susceptible to erosion while reducing and splitting core areas potentially vital to ecosystem services.}, } @article {pmid25971519, year = {2015}, author = {Zhu, J and Zhou, Y and Wang, S and Wang, L and Wang, F and Liu, W and Guo, B}, title = {Multicriteria decision analysis for monitoring ecosystem service function of the Three-River Headwaters region of the Qinghai-Tibet Plateau, China.}, journal = {Environmental monitoring and assessment}, volume = {187}, number = {6}, pages = {355}, pmid = {25971519}, issn = {1573-2959}, mesh = {China ; Climate ; Conservation of Natural Resources/methods ; *Decision Support Techniques ; Ecology ; *Ecosystem ; Environment ; Environmental Monitoring/*methods ; Rivers ; Tibet ; }, abstract = {The Three-River Headwaters (TRH) region in the Qinghai-Tibet Plateau, China, is of key importance to the ecological security of China and Southeast Asia and contains some of the most sensitive and fragile ecosystems. Monitoring and evaluating the ecosystem service function and its changes in the TRH region could support decision-making for regional ecological protection and restoration programs. Referencing the concept of ecosystem service and the Millennium Ecosystem Assessment (MA) framework, this study built a system of indicators for monitoring and evaluating the ecosystem service function. Thus, combining a multicriteria decision analysis (MCDA) and weighted linear combination (WLC) with analytic hierarchy process (AHP), we applied the ecosystem service function index (ESFI) based on remote sensing data at 1-km spatial resolution to spatiotemporally monitor the changes during the period 2005-2010. The study results indicated that ESFI had a good performance for monitoring the ecosystem service function and showed an improving trend in the TRH region over the past 5 years. Ecosystem environment recovery not only reflected the changing trend of warm and wet climate but was also a response of the ecological protection project of the Key Ecological Function Zone in the TRH region.}, } @article {pmid25971280, year = {2015}, author = {Daub, JT and Dupanloup, I and Robinson-Rechavi, M and Excoffier, L}, title = {Inference of Evolutionary Forces Acting on Human Biological Pathways.}, journal = {Genome biology and evolution}, volume = {7}, number = {6}, pages = {1546-1558}, pmid = {25971280}, issn = {1759-6653}, mesh = {Black People/genetics ; Data Interpretation, Statistical ; Demography ; *Evolution, Molecular ; Gene Regulatory Networks ; Genes ; Genomics ; Humans ; Metabolic Networks and Pathways/genetics ; Multifactorial Inheritance ; Selection, Genetic ; Signal Transduction/genetics ; }, abstract = {Because natural selection is likely to act on multiple genes underlying a given phenotypic trait, we study here the potential effect of ongoing and past selection on the genetic diversity of human biological pathways. We first show that genes included in gene sets are generally under stronger selective constraints than other genes and that their evolutionary response is correlated. We then introduce a new procedure to detect selection at the pathway level based on a decomposition of the classical McDonald-Kreitman test extended to multiple genes. This new test, called 2DNS, detects outlier gene sets and takes into account past demographic effects and evolutionary constraints specific to gene sets. Selective forces acting on gene sets can be easily identified by a mere visual inspection of the position of the gene sets relative to their two-dimensional null distribution. We thus find several outlier gene sets that show signals of positive, balancing, or purifying selection but also others showing an ancient relaxation of selective constraints. The principle of the 2DNS test can also be applied to other genomic contrasts. For instance, the comparison of patterns of polymorphisms private to African and non-African populations reveals that most pathways show a higher proportion of nonsynonymous mutations in non-Africans than in Africans, potentially due to different demographic histories and selective pressures.}, } @article {pmid25965051, year = {2015}, author = {Dafforn, KA and Mayer-Pinto, M and Morris, RL and Waltham, NJ}, title = {Application of management tools to integrate ecological principles with the design of marine infrastructure.}, journal = {Journal of environmental management}, volume = {158}, number = {}, pages = {61-73}, doi = {10.1016/j.jenvman.2015.05.001}, pmid = {25965051}, issn = {1095-8630}, mesh = {*Conservation of Natural Resources ; *Decision Support Techniques ; Ecology ; *Ecosystem ; Environment Design ; Humans ; *Oceans and Seas ; }, abstract = {Globally the coastal zone is suffering the collateral damage from continuing urban development and construction, expanding resource sectors, increasing population, regulation to river flow, and on-going land change and degradation. While protection of natural coastal habitat is recommended, balancing conservation with human services is now the challenge for managers. Marine infrastructure such as seawalls, marinas and offshore platforms is increasingly used to support and provide services, but has primarily been designed for engineering purposes without consideration of the ecological consequences. Increasingly developments are seeking alternatives to hard engineering and a range of ecological solutions has begun to replace or be incorporated into marine and coastal infrastructure. But too often, hard engineering remains the primary strategy because the tools for managers to implement ecological solutions are either lacking or not supported by policy and stakeholders. Here we outline critical research needs for marine urban development and emerging strategies that seek to mitigate the impacts of marine infrastructure. We present case studies to highlight the strategic direction necessary to support management decisions internationally.}, } @article {pmid25957950, year = {2015}, author = {Bastian, FB and Chibucos, MC and Gaudet, P and Giglio, M and Holliday, GL and Huang, H and Lewis, SE and Niknejad, A and Orchard, S and Poux, S and Skunca, N and Robinson-Rechavi, M}, title = {The Confidence Information Ontology: a step towards a standard for asserting confidence in annotations.}, journal = {Database : the journal of biological databases and curation}, volume = {2015}, number = {}, pages = {bav043}, pmid = {25957950}, issn = {1758-0463}, support = {R01 GM089636/GM/NIGMS NIH HHS/United States ; U41 HG002273/HG/NHGRI NIH HHS/United States ; BB/L024179/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; 1 U41 HG006104/HG/NHGRI NIH HHS/United States ; U41 HG006104/HG/NHGRI NIH HHS/United States ; U41 HG007822/HG/NHGRI NIH HHS/United States ; }, mesh = {*Biological Ontologies ; Congresses as Topic ; Data Curation/*standards ; }, abstract = {Biocuration has become a cornerstone for analyses in biology, and to meet needs, the amount of annotations has considerably grown in recent years. However, the reliability of these annotations varies; it has thus become necessary to be able to assess the confidence in annotations. Although several resources already provide confidence information about the annotations that they produce, a standard way of providing such information has yet to be defined. This lack of standardization undermines the propagation of knowledge across resources, as well as the credibility of results from high-throughput analyses. Seeded at a workshop during the Biocuration 2012 conference, a working group has been created to address this problem. We present here the elements that were identified as essential for assessing confidence in annotations, as well as a draft ontology--the Confidence Information Ontology--to illustrate how the problems identified could be addressed. We hope that this effort will provide a home for discussing this major issue among the biocuration community. Tracker URL: https://github.com/BgeeDB/confidence-information-ontology Ontology URL: https://raw.githubusercontent.com/BgeeDB/confidence-information-ontology/master/src/ontology/cio-simple.obo}, } @article {pmid25956356, year = {2015}, author = {Zhu, Y and Xu, Y and Helseth, DL and Gulukota, K and Yang, S and Pesce, LL and Mitra, R and Müller, P and Sengupta, S and Guo, W and Silverstein, JC and Foster, I and Parsad, N and White, KP and Ji, Y}, title = {Zodiac: A Comprehensive Depiction of Genetic Interactions in Cancer by Integrating TCGA Data.}, journal = {Journal of the National Cancer Institute}, volume = {107}, number = {8}, pages = {}, pmid = {25956356}, issn = {1460-2105}, support = {R01 CA132897/CA/NCI NIH HHS/United States ; S10 RR029030-01/RR/NCRR NIH HHS/United States ; }, mesh = {Bayes Theorem ; *Databases, Genetic/trends ; *Epistasis, Genetic ; *Genomics/methods ; Humans ; Internet ; Likelihood Functions ; Neoplasms/*genetics ; *Software ; User-Computer Interface ; }, abstract = {BACKGROUND: Genetic interactions play a critical role in cancer development. Existing knowledge about cancer genetic interactions is incomplete, especially lacking evidences derived from large-scale cancer genomics data. The Cancer Genome Atlas (TCGA) produces multimodal measurements across genomics and features of thousands of tumors, which provide an unprecedented opportunity to investigate the interplays of genes in cancer.

METHODS: We introduce Zodiac, a computational tool and resource to integrate existing knowledge about cancer genetic interactions with new information contained in TCGA data. It is an evolution of existing knowledge by treating it as a prior graph, integrating it with a likelihood model derived by Bayesian graphical model based on TCGA data, and producing a posterior graph as updated and data-enhanced knowledge. In short, Zodiac realizes "Prior interaction map + TCGA data → Posterior interaction map."

RESULTS: Zodiac provides molecular interactions for about 200 million pairs of genes. All the results are generated from a big-data analysis and organized into a comprehensive database allowing customized search. In addition, Zodiac provides data processing and analysis tools that allow users to customize the prior networks and update the genetic pathways of their interest. Zodiac is publicly available at www.compgenome.org/ZODIAC.

CONCLUSIONS: Zodiac recapitulates and extends existing knowledge of molecular interactions in cancer. It can be used to explore novel gene-gene interactions, transcriptional regulation, and other types of molecular interplays in cancer.}, } @article {pmid25955479, year = {2015}, author = {Kitazumi, A and Kawahara, Y and Onda, TS and De Koeyer, D and de los Reyes, BG}, title = {Implications of miR166 and miR159 induction to the basal response mechanisms of an andigena potato (Solanum tuberosum subsp. andigena) to salinity stress, predicted from network models in Arabidopsis.}, journal = {Genome}, volume = {58}, number = {1}, pages = {13-24}, doi = {10.1139/gen-2015-0011}, pmid = {25955479}, issn = {1480-3321}, mesh = {Arabidopsis/genetics ; Computational Biology/methods ; Gene Expression Regulation, Plant ; MicroRNAs/*genetics ; Models, Genetic ; Plant Dormancy ; Plant Proteins/*genetics ; RNA, Plant/*genetics ; Salinity ; Sequence Analysis, RNA ; Solanum tuberosum/genetics/*growth & development ; *Stress, Physiological ; }, abstract = {MicroRNA (miRNA) mediated changes in gene expression by post-transcriptional modulation of major regulatory transcription factors is a potent mechanism for integrating growth and stress-related responses. Exotic plants including many traditional varieties of Andean potatoes (Solanum tuberosum subsp. andigena) are known for better adaptation to marginal environments. Stress physiological studies confirmed earlier reports on the salinity tolerance potentials of certain andigena cultivars. Guided by the hypothesis that certain miRNAs play important roles in growth modulation under suboptimal conditions, we identified and characterized salinity stress-responsive miRNA-target gene pairs in the andigena cultivar Sullu by parallel analysis of noncoding and coding RNA transcriptomes. Inverse relationships were established by the reverse co-expression between two salinity stress-regulated miRNAs (miR166, miR159) and their target transcriptional regulators HD-ZIP-Phabulosa/Phavulota and Myb101, respectively. Based on heterologous models in Arabidopsis, the miR166-HD-ZIP-Phabulosa/Phavulota network appears to be involved in modulating growth perhaps by mediating vegetative dormancy, with linkages to defense-related pathways. The miR159-Myb101 network may be important for the modulation of vegetative growth while also controlling stress-induced premature transition to reproductive phase. We postulate that the induction of miR166 and miR159 under salinity stress represents important network hubs for balancing gene expression required for basal growth adjustments.}, } @article {pmid25950956, year = {2015}, author = {Kurtz, ZD and Müller, CL and Miraldi, ER and Littman, DR and Blaser, MJ and Bonneau, RA}, title = {Sparse and compositionally robust inference of microbial ecological networks.}, journal = {PLoS computational biology}, volume = {11}, number = {5}, pages = {e1004226}, pmid = {25950956}, issn = {1553-7358}, support = {R01 DK103358-01/DK/NIDDK NIH HHS/United States ; R01 GM063270/GM/NIGMS NIH HHS/United States ; R01 GM63270/GM/NIGMS NIH HHS/United States ; R01 DK103358/DK/NIDDK NIH HHS/United States ; T32 AI007180/AI/NIAID NIH HHS/United States ; T32AI007180-30/AI/NIAID NIH HHS/United States ; R01 DK090989/DK/NIDDK NIH HHS/United States ; }, mesh = {Algorithms ; *Biota ; Computational Biology/methods ; Gastrointestinal Microbiome ; Humans ; Metagenomics/methods ; Microbiota/genetics/*physiology ; *Models, Biological ; RNA, Ribosomal, 16S/genetics ; }, abstract = {16S ribosomal RNA (rRNA) gene and other environmental sequencing techniques provide snapshots of microbial communities, revealing phylogeny and the abundances of microbial populations across diverse ecosystems. While changes in microbial community structure are demonstrably associated with certain environmental conditions (from metabolic and immunological health in mammals to ecological stability in soils and oceans), identification of underlying mechanisms requires new statistical tools, as these datasets present several technical challenges. First, the abundances of microbial operational taxonomic units (OTUs) from amplicon-based datasets are compositional. Counts are normalized to the total number of counts in the sample. Thus, microbial abundances are not independent, and traditional statistical metrics (e.g., correlation) for the detection of OTU-OTU relationships can lead to spurious results. Secondly, microbial sequencing-based studies typically measure hundreds of OTUs on only tens to hundreds of samples; thus, inference of OTU-OTU association networks is severely under-powered, and additional information (or assumptions) are required for accurate inference. Here, we present SPIEC-EASI (SParse InversE Covariance Estimation for Ecological Association Inference), a statistical method for the inference of microbial ecological networks from amplicon sequencing datasets that addresses both of these issues. SPIEC-EASI combines data transformations developed for compositional data analysis with a graphical model inference framework that assumes the underlying ecological association network is sparse. To reconstruct the network, SPIEC-EASI relies on algorithms for sparse neighborhood and inverse covariance selection. To provide a synthetic benchmark in the absence of an experimentally validated gold-standard network, SPIEC-EASI is accompanied by a set of computational tools to generate OTU count data from a set of diverse underlying network topologies. SPIEC-EASI outperforms state-of-the-art methods to recover edges and network properties on synthetic data under a variety of scenarios. SPIEC-EASI also reproducibly predicts previously unknown microbial associations using data from the American Gut project.}, } @article {pmid25950366, year = {2015}, author = {Schnall, R}, title = {Short message service use in clinical care through a simulation activity.}, journal = {The Journal of nursing education}, volume = {54}, number = {5}, pages = {290-294}, doi = {10.3928/01484834-20150417-08}, pmid = {25950366}, issn = {1938-2421}, mesh = {Adult ; Cohort Studies ; Curriculum ; *Education, Nursing, Graduate ; Female ; Humans ; Male ; Middle Aged ; Nurse Practitioners/*education ; *Simulation Training ; *Text Messaging ; }, abstract = {BACKGROUND: Research has shown that the integration of informatics competencies into nursing education especially for Doctor of Nursing Practice (DNP) students, has been inadequate. This article reports on a Short Message Service (SMS) simulation activity for incorporating informatics knowledge and skills into the DNP curriculum.

METHOD: DNP students participated in a 3-week simulated ecological momentary assessment using SMS technology. Students rated their experience through a survey and wrote a 1 page narrative describing their experience. Data were analyzed using descriptive statistics and open-ended coding.

RESULTS: This simulation activity provided information for the future delivery of care using SMS. The cost-saving potential of follow-up messaging reimbursement for providers who use SMS may be a worthwhile investment of health care payers.

CONCLUSIONS: This activity demonstrated the usefulness of SMS technology for helping patients manage their chronic health conditions. Use of SMS would be a reinforcing factor for providers in clinical care if it becomes reimbursable.}, } @article {pmid25948716, year = {2015}, author = {Pearse, WD and Cadotte, MW and Cavender-Bares, J and Ives, AR and Tucker, CM and Walker, SC and Helmus, MR}, title = {pez: phylogenetics for the environmental sciences.}, journal = {Bioinformatics (Oxford, England)}, volume = {31}, number = {17}, pages = {2888-2890}, doi = {10.1093/bioinformatics/btv277}, pmid = {25948716}, issn = {1367-4811}, mesh = {*Biodiversity ; *Databases, Genetic ; *Ecology ; Phenotype ; *Phylogeny ; *Software ; }, abstract = {UNLABELLED: pez is an R package that permits measurement, modelling and simulation of phylogenetic structure in ecological data. pez contains the first implementation of many methods in R, and aggregates existing data structures and methods into a single, coherent package.

pez is released under the GPL v3 open-source license, available on the Internet from CRAN (http://cran.r-project.org). The package is under active development, and the authors welcome contributions (see http://github.com/willpearse/pez).

CONTACT: will.pearse@gmail.com.}, } @article {pmid25946132, year = {2015}, author = {Armitage, AR and Highfield, WE and Brody, SD and Louchouarn, P}, title = {The contribution of mangrove expansion to salt marsh loss on the Texas Gulf Coast.}, journal = {PloS one}, volume = {10}, number = {5}, pages = {e0125404}, pmid = {25946132}, issn = {1932-6203}, mesh = {Avicennia/*growth & development ; *Climate Change ; *Ecosystem ; Image Interpretation, Computer-Assisted ; Poaceae/*growth & development ; *Satellite Imagery ; Seasons ; Texas ; Wetlands ; }, abstract = {Landscape-level shifts in plant species distribution and abundance can fundamentally change the ecology of an ecosystem. Such shifts are occurring within mangrove-marsh ecotones, where over the last few decades, relatively mild winters have led to mangrove expansion into areas previously occupied by salt marsh plants. On the Texas (USA) coast of the western Gulf of Mexico, most cases of mangrove expansion have been documented within specific bays or watersheds. Based on this body of relatively small-scale work and broader global patterns of mangrove expansion, we hypothesized that there has been a recent regional-level displacement of salt marshes by mangroves. We classified Landsat-5 Thematic Mapper images using artificial neural networks to quantify black mangrove (Avicennia germinans) expansion and salt marsh (Spartina alterniflora and other grass and forb species) loss over 20 years across the entire Texas coast. Between 1990 and 2010, mangrove area grew by 16.1 km(2), a 74% increase. Concurrently, salt marsh area decreased by 77.8 km(2), a 24% net loss. Only 6% of that loss was attributable to mangrove expansion; most salt marsh was lost due to conversion to tidal flats or water, likely a result of relative sea level rise. Our research confirmed that mangroves are expanding and, in some instances, displacing salt marshes at certain locations. However, this shift is not widespread when analyzed at a larger, regional level. Rather, local, relative sea level rise was indirectly implicated as another important driver causing regional-level salt marsh loss. Climate change is expected to accelerate both sea level rise and mangrove expansion; these mechanisms are likely to interact synergistically and contribute to salt marsh loss.}, } @article {pmid25945629, year = {2015}, author = {Rodrigues-Filho, JL and Degani, RM and Soares, FS and Periotto, NA and Blanco, FP and Abe, DS and Matsumura-Tundisi, T and Tundisi, JE and Tundisi, JG}, title = {Alterations in land uses based on amendments to the Brazilian Forest Law and their influences on water quality of a watershed.}, journal = {Brazilian journal of biology = Revista brasleira de biologia}, volume = {75}, number = {1}, pages = {125-134}, doi = {10.1590/1519-6984.08813}, pmid = {25945629}, issn = {1678-4375}, mesh = {Agriculture ; Brazil ; Environmental Monitoring/methods ; Forestry/*legislation & jurisprudence ; *Forests ; Geographic Information Systems ; Humans ; Nitrogen/*analysis ; Phosphorus/*analysis ; Water Pollutants, Chemical/*analysis ; *Water Quality ; }, abstract = {The amendments to the Forest Law proposed by the Brazilian government that allow partial substitution of forested areas by agricultural activities raised deep concern about the integrity of aquatic ecosystems. To assess the impacts of this alteration in land uses on the watershed, diffuse loads of total nitrogen (Nt) and total phosphorus (Pt) were estimated in Lobo Stream watershed, southeastern Brazil, based on export coefficients of the Model of Correlation between Land Use and Water Quality (MQUAL). Three scenarios were generated: scenario 1 (present scenario), with 30-meter-wide permanent preservation areas along the shore of water bodies and 50-meter-radius in springs; scenario 2, conservative, with 100-meter-wide permanent preservation areas along water bodies; and scenario 3, with the substitution of 20% of natural forest by agricultural activities. Results indicate that a suppression of 20% of forest cover would cause an increase in nutrient loads as well as in the trophic state of aquatic ecosystems of the watershed. This could result in losses of ecosystem services and compromise the quality of water and its supply for the basin. This study underlines the importance of forest cover for the maintenance of water quality in Lobo Stream watershed.}, } @article {pmid25943565, year = {2015}, author = {Hofner, B and Boccuto, L and Göker, M}, title = {Controlling false discoveries in high-dimensional situations: boosting with stability selection.}, journal = {BMC bioinformatics}, volume = {16}, number = {}, pages = {144}, pmid = {25943565}, issn = {1471-2105}, mesh = {*Algorithms ; Biomarkers/*analysis ; Case-Control Studies ; Child Development Disorders, Pervasive/genetics/*metabolism ; Computer Simulation ; *False Positive Reactions ; Gene Expression Profiling ; Humans ; *Models, Statistical ; Nonlinear Dynamics ; Phenotype ; }, abstract = {BACKGROUND: Modern biotechnologies often result in high-dimensional data sets with many more variables than observations (n≪p). These data sets pose new challenges to statistical analysis: Variable selection becomes one of the most important tasks in this setting. Similar challenges arise if in modern data sets from observational studies, e.g., in ecology, where flexible, non-linear models are fitted to high-dimensional data. We assess the recently proposed flexible framework for variable selection called stability selection. By the use of resampling procedures, stability selection adds a finite sample error control to high-dimensional variable selection procedures such as Lasso or boosting. We consider the combination of boosting and stability selection and present results from a detailed simulation study that provide insights into the usefulness of this combination. The interpretation of the used error bounds is elaborated and insights for practical data analysis are given.

RESULTS: Stability selection with boosting was able to detect influential predictors in high-dimensional settings while controlling the given error bound in various simulation scenarios. The dependence on various parameters such as the sample size, the number of truly influential variables or tuning parameters of the algorithm was investigated. The results were applied to investigate phenotype measurements in patients with autism spectrum disorders using a log-linear interaction model which was fitted by boosting. Stability selection identified five differentially expressed amino acid pathways.

CONCLUSION: Stability selection is implemented in the freely available R package stabs (http://CRAN.R-project.org/package=stabs). It proved to work well in high-dimensional settings with more predictors than observations for both, linear and additive models. The original version of stability selection, which controls the per-family error rate, is quite conservative, though, this is much less the case for its improvement, complementary pairs stability selection. Nevertheless, care should be taken to appropriately specify the error bound.}, } @article {pmid25940563, year = {2015}, author = {McTavish, EJ and Hinchliff, CE and Allman, JF and Brown, JW and Cranston, KA and Holder, MT and Rees, JA and Smith, SA}, title = {Phylesystem: a git-based data store for community-curated phylogenetic estimates.}, journal = {Bioinformatics (Oxford, England)}, volume = {31}, number = {17}, pages = {2794-2800}, pmid = {25940563}, issn = {1367-4811}, mesh = {Computational Biology/*methods ; *Databases, Factual ; Humans ; *Information Storage and Retrieval ; Internet ; *Phylogeny ; Programming Languages ; Reproducibility of Results ; *Software ; User-Computer Interface ; }, abstract = {MOTIVATION: Phylogenetic estimates from published studies can be archived using general platforms like Dryad (Vision, 2010) or TreeBASE (Sanderson et al., 1994). Such services fulfill a crucial role in ensuring transparency and reproducibility in phylogenetic research. However, digital tree data files often require some editing (e.g. rerooting) to improve the accuracy and reusability of the phylogenetic statements. Furthermore, establishing the mapping between tip labels used in a tree and taxa in a single common taxonomy dramatically improves the ability of other researchers to reuse phylogenetic estimates. As the process of curating a published phylogenetic estimate is not error-free, retaining a full record of the provenance of edits to a tree is crucial for openness, allowing editors to receive credit for their work and making errors introduced during curation easier to correct.

RESULTS: Here, we report the development of software infrastructure to support the open curation of phylogenetic data by the community of biologists. The backend of the system provides an interface for the standard database operations of creating, reading, updating and deleting records by making commits to a git repository. The record of the history of edits to a tree is preserved by git's version control features. Hosting this data store on GitHub (http://github.com/) provides open access to the data store using tools familiar to many developers. We have deployed a server running the 'phylesystem-api', which wraps the interactions with git and GitHub. The Open Tree of Life project has also developed and deployed a JavaScript application that uses the phylesystem-api and other web services to enable input and curation of published phylogenetic statements.

Source code for the web service layer is available at https://github.com/OpenTreeOfLife/phylesystem-api. The data store can be cloned from: https://github.com/OpenTreeOfLife/phylesystem. A web application that uses the phylesystem web services is deployed at http://tree.opentreeoflife.org/curator. Code for that tool is available from https://github.com/OpenTreeOfLife/opentree.

CONTACT: mtholder@gmail.com.}, } @article {pmid25938968, year = {2015}, author = {Qu, Y and Zhou, A and Zhang, X and Tang, H and Liang, M and Han, H and Zuo, Y}, title = {De Novo Transcriptome Sequencing of Low Temperature-Treated Phlox subulata and Analysis of the Genes Involved in Cold Stress.}, journal = {International journal of molecular sciences}, volume = {16}, number = {5}, pages = {9732-9748}, pmid = {25938968}, issn = {1422-0067}, mesh = {Cluster Analysis ; *Cold Temperature ; Gene Expression Profiling ; Gene Expression Regulation, Plant ; Gene Ontology ; *Genes, Plant ; Magnoliopsida/*genetics/*physiology ; Molecular Sequence Annotation ; Open Reading Frames/genetics ; Phenotype ; *Sequence Analysis, RNA ; Sequence Homology, Nucleic Acid ; Stress, Physiological/*genetics ; Transcriptome/*genetics ; Up-Regulation/genetics ; }, abstract = {Phlox subulata, a perennial herbaceous flower, can survive during the winter of northeast China, where the temperature can drop to -30 °C, suggesting that P. subulata is an ideal model for studying the molecular mechanisms of cold acclimation in plants. However, little is known about the gene expression profile of P. subulata under cold stress. Here, we examined changes in cold stress-related genes in P. subulata. We sequenced three cold-treated (CT) and control (CK) samples of P. subulata. After de novo assembly and quantitative assessment of the obtained reads, 99,174 unigenes were generated. Based on similarity searches with known proteins in public protein databases, 59,994 unigenes were functionally annotated. Among all differentially expressed genes (DEGs), 8302, 10,638 and 11,021 up-regulated genes and 9898, 17,876, and 12,358 down-regulated genes were identified after treatment at 4, 0, and -10 °C, respectively. Furthermore, 3417 up-regulated unigenes were expressed only in CT samples. Twenty major cold-related genes, including transcription factors, antioxidant enzymes, osmoregulation proteins, and Ca[2+] and ABA signaling components, were identified, and their expression levels were estimated. Overall, this is the first transcriptome sequencing of this plant species under cold stress. Studies of DEGs involved in cold-related metabolic pathways may facilitate the discovery of cold-resistance genes.}, } @article {pmid25938501, year = {2015}, author = {Gilbert, JA and Long, EF and Brooks, RP and Friedland, GH and Moll, AP and Townsend, JP and Galvani, AP and Shenoi, SV}, title = {Integrating Community-Based Interventions to Reverse the Convergent TB/HIV Epidemics in Rural South Africa.}, journal = {PloS one}, volume = {10}, number = {5}, pages = {e0126267}, pmid = {25938501}, issn = {1932-6203}, support = {1K23AI089260/AI/NIAID NIH HHS/United States ; 5U01GM105627/GM/NIGMS NIH HHS/United States ; R24 TW007988/TW/FIC NIH HHS/United States ; R01DA015612/DA/NIDA NIH HHS/United States ; U01 GM105627/GM/NIGMS NIH HHS/United States ; R24TW007988/TW/FIC NIH HHS/United States ; R01 DA015612/DA/NIDA NIH HHS/United States ; K23 AI089260/AI/NIAID NIH HHS/United States ; U01 GM087719/GM/NIGMS NIH HHS/United States ; R01 DA025932/DA/NIDA NIH HHS/United States ; P30 MH062294/MH/NIMH NIH HHS/United States ; R01DA025932/DA/NIDA NIH HHS/United States ; U01 GH000524/GH/CGH CDC HHS/United States ; 1U01GH000524-01/GH/CGH CDC HHS/United States ; 2U01GM087719/GM/NIGMS NIH HHS/United States ; }, mesh = {Adolescent ; Adult ; Anti-HIV Agents/therapeutic use ; Antitubercular Agents/therapeutic use ; HIV Infections/*drug therapy/*epidemiology ; Humans ; Middle Aged ; South Africa/epidemiology ; Tuberculosis/*drug therapy/*epidemiology ; Young Adult ; }, abstract = {The WHO recommends integrating interventions to address the devastating TB/HIV co-epidemics in South Africa, yet integration has been poorly implemented and TB/HIV control efforts need strengthening. Identifying infected individuals is particularly difficult in rural settings. We used mathematical modeling to predict the impact of community-based, integrated TB/HIV case finding and additional control strategies on South Africa's TB/HIV epidemics. We developed a model incorporating TB and HIV transmission to evaluate the effectiveness of integrating TB and HIV interventions in rural South Africa over 10 years. We modeled the impact of a novel screening program that integrates case finding for TB and HIV in the community, comparing it to status quo and recommended TB/HIV control strategies, including GeneXpert, MDR-TB treatment decentralization, improved first-line TB treatment cure rate, isoniazid preventive therapy, and expanded ART. Combining recommended interventions averted 27% of expected TB cases (95% CI 18-40%) 18% HIV (95% CI 13-24%), 60% MDR-TB (95% CI 34-83%), 69% XDR-TB (95% CI 34-90%), and 16% TB/HIV deaths (95% CI 12-29). Supplementing these interventions with annual community-based TB/HIV case finding averted a further 17% of TB cases (44% total; 95% CI 31-56%), 5% HIV (23% total; 95% CI 17-29%), 8% MDR-TB (68% total; 95% CI 40-88%), 4% XDR-TB (73% total; 95% CI 38-91%), and 8% TB/HIV deaths (24% total; 95% CI 16-39%). In addition to increasing screening frequency, we found that improving TB symptom questionnaire sensitivity, second-line TB treatment delays, default before initiating TB treatment or ART, and second-line TB drug efficacy were significantly associated with even greater reductions in TB and HIV cases. TB/HIV epidemics in South Africa were most effectively curtailed by simultaneously implementing interventions that integrated community-based TB/HIV control strategies and targeted drug-resistant TB. Strengthening existing TB and HIV treatment programs is needed to further reduce disease incidence.}, } @article {pmid25931973, year = {2015}, author = {Wilkin, P and Muasya, AM}, title = {Clarifying the Dioscoreabuchananii Benth. species complex: a new potentially extinct subspecies for South Africa.}, journal = {PhytoKeys}, volume = {}, number = {48}, pages = {51-72}, pmid = {25931973}, issn = {1314-2011}, abstract = {The Dioscoreabuchananii complex is shown to comprise three species, one of which is divided into two subspecies, based on morphological data. Two species, Dioscorearupicola Kunth and Dioscoreamultiloba Kunth, are endemic or subendemic to South Africa and of widespread occurrence in KwaZulu Natal. They differ markedly from each other in inflorescence and floral morphology and appear to be ecologically differentiated. The third species, Dioscoreabuchananii Benth., is primarily found in southeastern tropical Africa, but a small number of specimens collected in South Africa in the late 19(th) and early 20(th) centuries are placed in an endemic subspecies, Dioscoreabuchananiisubsp.undatiloba (Baker) Wilkin. The latter taxon is a high priority in terms of rediscovery and conservation. Keys, descriptions, supporting information and illustrations are provided and made available online through eMonocot biodiversity informatics tools. Three nomenclatural acts are undertaken: two names are placed in synonymy and a new combination made.}, } @article {pmid25928234, year = {2015}, author = {Anisimova, M}, title = {Darwin and Fisher meet at biotech: on the potential of computational molecular evolution in industry.}, journal = {BMC evolutionary biology}, volume = {15}, number = {}, pages = {76}, pmid = {25928234}, issn = {1471-2148}, mesh = {Animals ; Biotechnology ; Computational Biology/*methods ; *Evolution, Molecular ; *Genomics ; Humans ; Metabolome ; Proteins/genetics ; Selection, Genetic ; }, abstract = {BACKGROUND: Today computational molecular evolution is a vibrant research field that benefits from the availability of large and complex new generation sequencing data - ranging from full genomes and proteomes to microbiomes, metabolomes and epigenomes. The grounds for this progress were established long before the discovery of the DNA structure. Specifically, Darwin's theory of evolution by means of natural selection not only remains relevant today, but also provides a solid basis for computational research with a variety of applications. But a long-term progress in biology was ensured by the mathematical sciences, as exemplified by Sir R. Fisher in early 20th century. Now this is true more than ever: The data size and its complexity require biologists to work in close collaboration with experts in computational sciences, modeling and statistics.

RESULTS: Natural selection drives function conservation and adaptation to emerging pathogens or new environments; selection plays key role in immune and resistance systems. Here I focus on computational methods for evaluating selection in molecular sequences, and argue that they have a high potential for applications. Pharma and biotech industries can successfully use this potential, and should take the initiative to enhance their research and development with state of the art bioinformatics approaches.

CONCLUSIONS: This review provides a quick guide to the current computational approaches that apply the evolutionary principles of natural selection to real life problems - from drug target validation, vaccine design and protein engineering to applications in agriculture, ecology and conservation.}, } @article {pmid25923712, year = {2015}, author = {Mahmoud, SH and Alazba, AA}, title = {Hydrological response to land cover changes and human activities in arid regions using a geographic information system and remote sensing.}, journal = {PloS one}, volume = {10}, number = {4}, pages = {e0125805}, pmid = {25923712}, issn = {1932-6203}, mesh = {*Conservation of Natural Resources ; Desert Climate ; Environmental Monitoring ; *Geographic Information Systems ; *Human Activities ; Humans ; Hydrology ; *Remote Sensing Technology ; Saudi Arabia ; Soil ; Water Movements ; }, abstract = {The hydrological response to land cover changes induced by human activities in arid regions has attracted increased research interest in recent decades. The study reported herein assessed the spatial and quantitative changes in surface runoff resulting from land cover change in the Al-Baha region of Saudi Arabia between 1990 and 2000 using an ArcGIS-surface runoff model and predicted land cover and surface runoff depth in 2030 using Markov chain analysis. Land cover maps for 1990 and 2000 were derived from satellite images using ArcGIS 10.1. The findings reveal a 26% decrease in forest and shrubland area, 28% increase in irrigated cropland, 1.5% increase in sparsely vegetated land and 0.5% increase in bare soil between 1990 and 2000. Overall, land cover changes resulted in a significant decrease in runoff depth values in most of the region. The decrease in surface runoff depth ranged from 25-106 mm/year in a 7020-km2 area, whereas the increase in such depth reached only 10 mm/year in a 243-km2 area. A maximum increase of 73 mm/year was seen in a limited area. The surface runoff depth decreased to the greatest extent in the central region of the study area due to the huge transition in land cover classes associated with the construction of 25 rainwater harvesting dams. The land cover prediction revealed a greater than twofold increase in irrigated cropland during the 2000-2030 period, whereas forest and shrubland are anticipated to occupy just 225 km2 of land area by 2030, a significant decrease from the 747 km2 they occupied in 2000. Overall, changes in land cover are predicted to result in an annual increase in irrigated cropland and dramatic decline in forest area in the study area over the next few decades. The increase in surface runoff depth is likely to have significant implications for irrigation activities.}, } @article {pmid25923521, year = {2015}, author = {Ruggiero, MA and Gordon, DP and Orrell, TM and Bailly, N and Bourgoin, T and Brusca, RC and Cavalier-Smith, T and Guiry, MD and Kirk, PM}, title = {A higher level classification of all living organisms.}, journal = {PloS one}, volume = {10}, number = {4}, pages = {e0119248}, pmid = {25923521}, issn = {1932-6203}, mesh = {*Biodiversity ; Biological Evolution ; Cooperative Behavior ; Databases, Factual ; Life ; *Phylogeny ; }, abstract = {We present a consensus classification of life to embrace the more than 1.6 million species already provided by more than 3,000 taxonomists' expert opinions in a unified and coherent, hierarchically ranked system known as the Catalogue of Life (CoL). The intent of this collaborative effort is to provide a hierarchical classification serving not only the needs of the CoL's database providers but also the diverse public-domain user community, most of whom are familiar with the Linnaean conceptual system of ordering taxon relationships. This classification is neither phylogenetic nor evolutionary but instead represents a consensus view that accommodates taxonomic choices and practical compromises among diverse expert opinions, public usages, and conflicting evidence about the boundaries between taxa and the ranks of major taxa, including kingdoms. Certain key issues, some not fully resolved, are addressed in particular. Beyond its immediate use as a management tool for the CoL and ITIS (Integrated Taxonomic Information System), it is immediately valuable as a reference for taxonomic and biodiversity research, as a tool for societal communication, and as a classificatory "backbone" for biodiversity databases, museum collections, libraries, and textbooks. Such a modern comprehensive hierarchy has not previously existed at this level of specificity.}, } @article {pmid25922515, year = {2015}, author = {Ksepka, DT and Parham, JF and Allman, JF and Benton, MJ and Carrano, MT and Cranston, KA and Donoghue, PC and Head, JJ and Hermsen, EJ and Irmis, RB and Joyce, WG and Kohli, M and Lamm, KD and Leehr, D and Patané, JL and Polly, PD and Phillips, MJ and Smith, NA and Smith, ND and Van Tuinen, M and Ware, JL and Warnock, RC}, title = {The Fossil Calibration Database-A New Resource for Divergence Dating.}, journal = {Systematic biology}, volume = {64}, number = {5}, pages = {853-859}, doi = {10.1093/sysbio/syv025}, pmid = {25922515}, issn = {1076-836X}, support = {BB/G006660/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/J00538X/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Access to Information ; Calibration ; Data Interpretation, Statistical ; Databases, Factual/*standards ; *Fossils ; Internet ; *Phylogeny ; Time ; }, abstract = {Fossils provide the principal basis for temporal calibrations, which are critical to the accuracy of divergence dating analyses. Translating fossil data into minimum and maximum bounds for calibrations is the most important-often least appreciated-step of divergence dating. Properly justified calibrations require the synthesis of phylogenetic, paleontological, and geological evidence and can be difficult for nonspecialists to formulate. The dynamic nature of the fossil record (e.g., new discoveries, taxonomic revisions, updates of global or local stratigraphy) requires that calibration data be updated continually lest they become obsolete. Here, we announce the Fossil Calibration Database (http://fossilcalibrations.org), a new open-access resource providing vetted fossil calibrations to the scientific community. Calibrations accessioned into this database are based on individual fossil specimens and follow best practices for phylogenetic justification and geochronological constraint. The associated Fossil Calibration Series, a calibration-themed publication series at Palaeontologia Electronica, will serve as a key pipeline for peer-reviewed calibrations to enter the database.}, } @article {pmid25921530, year = {2015}, author = {Tapaltsyan, V and Eronen, JT and Lawing, AM and Sharir, A and Janis, C and Jernvall, J and Klein, OD}, title = {Continuously growing rodent molars result from a predictable quantitative evolutionary change over 50 million years.}, journal = {Cell reports}, volume = {11}, number = {5}, pages = {673-680}, pmid = {25921530}, issn = {2211-1247}, support = {DP2 OD007191/OD/NIH HHS/United States ; F32-DE023702/DE/NIDCR NIH HHS/United States ; F30-DE022482/DE/NIDCR NIH HHS/United States ; F32 DE023702/DE/NIDCR NIH HHS/United States ; DP2-OD007191/OD/NIH HHS/United States ; R01 DE021420/DE/NIDCR NIH HHS/United States ; F30 DE022482/DE/NIDCR NIH HHS/United States ; R01-DE021420/DE/NIDCR NIH HHS/United States ; }, mesh = {Animals ; Biological Clocks ; *Biological Evolution ; Databases, Factual ; Fossils ; Markov Chains ; Mice ; Models, Theoretical ; Molar/diagnostic imaging/*physiology ; Tomography, X-Ray Computed ; }, abstract = {The fossil record is widely informative about evolution, but fossils are not systematically used to study the evolution of stem-cell-driven renewal. Here, we examined evolution of the continuous growth (hypselodonty) of rodent molar teeth, which is fuelled by the presence of dental stem cells. We studied occurrences of 3,500 North American rodent fossils, ranging from 50 million years ago (mya) to 2 mya. We examined changes in molar height to determine whether evolution of hypselodonty shows distinct patterns in the fossil record, and we found that hypselodont taxa emerged through intermediate forms of increasing crown height. Next, we designed a Markov simulation model, which replicated molar height increases throughout the Cenozoic and, moreover, evolution of hypselodonty. Thus, by extension, the retention of the adult stem cell niche appears to be a predictable quantitative rather than a stochastic qualitative process. Our analyses predict that hypselodonty will eventually become the dominant phenotype.}, } @article {pmid25918418, year = {2015}, author = {Yu, CP and Chen, SC and Chang, YM and Liu, WY and Lin, HH and Lin, JJ and Chen, HJ and Lu, YJ and Wu, YH and Lu, MY and Lu, CH and Shih, AC and Ku, MS and Shiu, SH and Wu, SH and Li, WH}, title = {Transcriptome dynamics of developing maize leaves and genomewide prediction of cis elements and their cognate transcription factors.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {112}, number = {19}, pages = {E2477-86}, pmid = {25918418}, issn = {1091-6490}, mesh = {Amino Acid Motifs ; Arabidopsis/genetics ; Binding Sites ; Computational Biology ; Gene Expression Profiling ; Gene Expression Regulation ; *Gene Expression Regulation, Plant ; Genome, Plant ; Multigene Family ; Oryza/genetics ; Photosynthesis ; Plant Leaves/*metabolism ; Promoter Regions, Genetic ; Protein Binding ; Transcription Factors/*metabolism ; Transcription, Genetic ; *Transcriptome ; Zea mays/*genetics ; }, abstract = {Maize is a major crop and a model plant for studying C4 photosynthesis and leaf development. However, a genomewide regulatory network of leaf development is not yet available. This knowledge is useful for developing C3 crops to perform C4 photosynthesis for enhanced yields. Here, using 22 transcriptomes of developing maize leaves from dry seeds to 192 h post imbibition, we studied gene up- and down-regulation and functional transition during leaf development and inferred sets of strongly coexpressed genes. More significantly, we developed a method to predict transcription factor binding sites (TFBSs) and their cognate transcription factors (TFs) using genomic sequence and transcriptomic data. The method requires not only evolutionary conservation of candidate TFBSs and sets of strongly coexpressed genes but also that the genes in a gene set share the same Gene Ontology term so that they are involved in the same biological function. In addition, we developed another method to predict maize TF-TFBS pairs using known TF-TFBS pairs in Arabidopsis or rice. From these efforts, we predicted 1,340 novel TFBSs and 253 new TF-TFBS pairs in the maize genome, far exceeding the 30 TF-TFBS pairs currently known in maize. In most cases studied by both methods, the two methods gave similar predictions. In vitro tests of 12 predicted TF-TFBS interactions showed that our methods perform well. Our study has significantly expanded our knowledge on the regulatory network involved in maize leaf development.}, } @article {pmid25915767, year = {2015}, author = {Bruno, N and Bertamini, M and Protti, F}, title = {Selfie and the city: a world-wide, large, and ecologically valid database reveals a two-pronged side bias in naïve self-portraits.}, journal = {PloS one}, volume = {10}, number = {4}, pages = {e0124999}, pmid = {25915767}, issn = {1932-6203}, mesh = {Cheek ; Cities ; Datasets as Topic ; Emotions ; Facial Expression ; Functional Laterality ; Humans ; *Photography ; Portraits as Topic/*psychology ; }, abstract = {Self-portraits are more likely to show the artist's right than left cheek. This phenomenon may have a psychobiological basis: Self-portraitists often copy their subject from mirrors and, if they prefer to present their left cheek (more expressive due to right-lateralization of emotions) to the mirror, this would result in a right-cheek bias in the painting. We tested this hypothesis using SelfieCity (3200 selfies posted on Instagram from December 4 through 12, 2013 from New York, Sao Paulo, Berlin, Moskow, and Bangkok), which includes two selfie-taking styles: a "standard" (photograph of selfie-taker) and a "mirror" (photograph of mirror reflection of selfie-taker) style. We show that the first style reveals a left cheek bias, whereas the second reveals a right cheek bias. Thus side biases observed in a world-wide, large, and ecologically valid database of naïve self-portraits provide strong support for a role of psychobiological factors in the artistic composition of self-portraits.}, } @article {pmid25914427, year = {2014}, author = {Ulrich, W and Soliveres, S and Kryszewski, W and Maestre, FT and Gotelli, NJ}, title = {Matrix models for quantifying competitive intransitivity.}, journal = {Oikos (Copenhagen, Denmark)}, volume = {123}, number = {9}, pages = {1057-1070}, pmid = {25914427}, issn = {0030-1299}, support = {242658/ERC_/European Research Council/International ; }, abstract = {Assessing the relative importance of intransitive competition networks in nature has been difficult because it requires a large number of pairwise competition experiments linked to observed field abundances of interacting species. Here we introduce metrics and statistical tests for evaluating the contribution of intransitivity to community structure using two kinds of data: competition matrices derived from the outcomes of pairwise experimental studies (C matrices) and species abundance matrices. We use C matrices to develop patch transition matrices (P) that predict community structure in a simple Markov chain model. We propose a randomization test to evaluate the degree of intransitivity from these P matrices in combination with empirical or simulated C matrices. Benchmark tests revealed that the methods could correctly detect intransitive competition networks, even in the absence of direct measures of pairwise competitive strength. These tests represent the first tools for estimating the degree of intransitivity in competitive networks from observational datasets. They can be applied to both spatio-temporal data sampled in homogeneous environments or across environmental gradients, and to experimental measures of pairwise interactions. To illustrate the methods, we analyzed empirical data matrices on the colonization of slug carrion by necrophagous flies and their parasitoids.}, } @article {pmid25913382, year = {2015}, author = {Dettlaff, AJ and Christopher Graham, J and Holzman, J and Baumann, DJ and Fluke, JD}, title = {Development of an instrument to understand the child protective services decision-making process, with a focus on placement decisions.}, journal = {Child abuse & neglect}, volume = {49}, number = {}, pages = {24-34}, doi = {10.1016/j.chiabu.2015.04.007}, pmid = {25913382}, issn = {1873-7757}, mesh = {Adult ; Aged ; Child ; Child Abuse/prevention & control ; Child Protective Services/*methods ; *Child Welfare ; *Decision Making ; *Decision Support Techniques ; Female ; *Foster Home Care ; Humans ; Male ; Middle Aged ; Reproducibility of Results ; Risk Factors ; Social Workers ; Texas ; Young Adult ; }, abstract = {When children come to the attention of the child welfare system, they become involved in a decision-making process in which decisions are made that have a significant effect on their future and well-being. The decision to remove children from their families is particularly complex; yet surprisingly little is understood about this decision-making process. This paper presents the results of a study to develop an instrument to explore, at the caseworker level, the context of the removal decision, with the objective of understanding the influence of the individual and organizational factors on this decision, drawing from the Decision Making Ecology as the underlying rationale for obtaining the measures. The instrument was based on the development of decision-making scales used in prior decision-making studies and administered to child protection caseworkers in several states. Analyses included reliability analyses, principal components analyses, and inter-correlations among the resulting scales. For one scale regarding removal decisions, a principal components analysis resulted in the extraction of two components, jointly identified as caseworkers' decision-making orientation, described as (1) an internal reference to decision-making and (2) an external reference to decision-making. Reliability analyses demonstrated acceptable to high internal consistency for 9 of the 11 scales. Full details of the reliability analyses, principal components analyses, and inter-correlations among the seven scales are discussed, along with implications for practice and the utility of this instrument to support the understanding of decision-making in child welfare.}, } @article {pmid25913208, year = {2015}, author = {Charlop-Powers, Z and Brady, SF}, title = {phylogeo: an R package for geographic analysis and visualization of microbiome data.}, journal = {Bioinformatics (Oxford, England)}, volume = {31}, number = {17}, pages = {2909-2911}, pmid = {25913208}, issn = {1367-4811}, support = {F32 AI110029/AI/NIAID NIH HHS/United States ; U01 GM110714/GM/NIGMS NIH HHS/United States ; AI110029/AI/NIAID NIH HHS/United States ; GM077516/GM/NIGMS NIH HHS/United States ; }, mesh = {*Computer Graphics ; Data Interpretation, Statistical ; Humans ; *Metagenome ; Microbiota/*genetics ; *Phylogeny ; *Programming Languages ; Sequence Analysis, DNA/*methods ; *Software ; Web Browser ; }, abstract = {MOTIVATION: We have created an R package named phylogeo that provides a set of geographic utilities for sequencing-based microbial ecology studies. Although the geographic location of samples is an important aspect of environmental microbiology, none of the major software packages used in processing microbiome data include utilities that allow users to map and explore the spatial dimension of their data. phylogeo solves this problem by providing a set of plotting and mapping functions that can be used to visualize the geographic distribution of samples, to look at the relatedness of microbiomes using ecological distance, and to map the geographic distribution of particular sequences. By extending the popular phyloseq package and using the same data structures and command formats, phylogeo allows users to easily map and explore the geographic dimensions of their data from the R programming language.

phylogeo is documented and freely available http://zachcp.github.io/phylogeo

CONTACT: : zcharlop@rockefeller.edu.}, } @article {pmid25913195, year = {2015}, author = {Anderson, EC and Barry, PD}, title = {Interpreting the flock algorithm from a statistical perspective.}, journal = {Molecular ecology resources}, volume = {15}, number = {5}, pages = {1020-1030}, doi = {10.1111/1755-0998.12417}, pmid = {25913195}, issn = {1755-0998}, mesh = {Algorithms ; Biostatistics/methods ; *Cluster Analysis ; Computational Biology/*methods ; Genotyping Techniques/*methods ; Microsatellite Repeats ; Polymorphism, Single Nucleotide ; *Software ; }, abstract = {We show that the algorithm in the program flock (Duchesne & Turgeon 2009) can be interpreted as an estimation procedure based on a model essentially identical to the structure (Pritchard et al. 2000) model with no admixture and without correlated allele frequency priors. Rather than using MCMC, the flock algorithm searches for the maximum a posteriori estimate of this structure model via a simulated annealing algorithm with a rapid cooling schedule (namely, the exponent on the objective function →∞). We demonstrate the similarities between the two programs in a two-step approach. First, to enable rapid batch processing of many simulated data sets, we modified the source code of structure to use the flock algorithm, producing the program flockture. With simulated data, we confirmed that results obtained with flock and flockture are very similar (though flockture is some 200 times faster). Second, we simulated multiple large data sets under varying levels of population differentiation for both microsatellite and SNP genotypes. We analysed them with flockture and structure and assessed each program on its ability to cluster individuals to their correct subpopulation. We show that flockture yields results similar to structure albeit with greater variability from run to run. flockture did perform better than structure when genotypes were composed of SNPs and differentiation was moderate (FST= 0.022-0.032). When differentiation was low, structure outperformed flockture for both marker types. On large data sets like those we simulated, it appears that flock's reliance on inference rules regarding its 'plateau record' is not helpful. Interpreting flock's algorithm as a special case of the model in structure should aid in understanding the program's output and behaviour.}, } @article {pmid25908869, year = {2015}, author = {Sanguino, L and Franqueville, L and Vogel, TM and Larose, C}, title = {Linking environmental prokaryotic viruses and their host through CRISPRs.}, journal = {FEMS microbiology ecology}, volume = {91}, number = {5}, pages = {}, doi = {10.1093/femsec/fiv046}, pmid = {25908869}, issn = {1574-6941}, mesh = {Arctic Regions ; Bacteria/*genetics/isolation & purification/*virology ; Bacteriophages/*genetics ; Base Sequence ; Clustered Regularly Interspaced Short Palindromic Repeats/genetics ; Computational Biology ; Ecosystem ; Environment ; Genome, Bacterial/*genetics ; Ice Cover/microbiology/virology ; Metagenome ; Metagenomics ; Norway ; RNA, Ribosomal, 16S/genetics ; Soil Microbiology ; Virus Physiological Phenomena/*genetics ; }, abstract = {The ecological pressure that viruses place on microbial communities is not only based on predation, but also on gene transfer. In order to determine the potential impact of viruses and transduction, we need a better understanding of the dynamics of interactions between viruses and their hosts in the environment. Data on environmental viruses are scarce, and methods for tracking their interactions with prokaryotes are needed. Clustered regularly interspaced short palindromic repeats (CRISPRs), which contain viral sequences in bacterial genomes, might help document the history of virus-host interactions in the environment. In this study, a bioinformatics network linking viruses and their hosts using CRISPR sequences obtained from metagenomic data was developed and applied to metagenomes from Arctic glacial ice and soil. The application of our network approach showed that putative interactions were more commonly detected in the ice samples than the soil which would be consistent with the ice viral-bacterial interactions being more dynamic than those in soil. Further analysis of the viral sequences in the CRISPRs indicated that Ralstonia phages might be agents of transduction in the Arctic glacial ice.}, } @article {pmid25908251, year = {2015}, author = {Sadd, BM and Barribeau, SM and Bloch, G and de Graaf, DC and Dearden, P and Elsik, CG and Gadau, J and Grimmelikhuijzen, CJ and Hasselmann, M and Lozier, JD and Robertson, HM and Smagghe, G and Stolle, E and Van Vaerenbergh, M and Waterhouse, RM and Bornberg-Bauer, E and Klasberg, S and Bennett, AK and Câmara, F and Guigó, R and Hoff, K and Mariotti, M and Munoz-Torres, M and Murphy, T and Santesmasses, D and Amdam, GV and Beckers, M and Beye, M and Biewer, M and Bitondi, MM and Blaxter, ML and Bourke, AF and Brown, MJ and Buechel, SD and Cameron, R and Cappelle, K and Carolan, JC and Christiaens, O and Ciborowski, KL and Clarke, DF and Colgan, TJ and Collins, DH and Cridge, AG and Dalmay, T and Dreier, S and du Plessis, L and Duncan, E and Erler, S and Evans, J and Falcon, T and Flores, K and Freitas, FC and Fuchikawa, T and Gempe, T and Hartfelder, K and Hauser, F and Helbing, S and Humann, FC and Irvine, F and Jermiin, LS and Johnson, CE and Johnson, RM and Jones, AK and Kadowaki, T and Kidner, JH and Koch, V and Köhler, A and Kraus, FB and Lattorff, HM and Leask, M and Lockett, GA and Mallon, EB and Antonio, DS and Marxer, M and Meeus, I and Moritz, RF and Nair, A and Näpflin, K and Nissen, I and Niu, J and Nunes, FM and Oakeshott, JG and Osborne, A and Otte, M and Pinheiro, DG and Rossié, N and Rueppell, O and Santos, CG and Schmid-Hempel, R and Schmitt, BD and Schulte, C and Simões, ZL and Soares, MP and Swevers, L and Winnebeck, EC and Wolschin, F and Yu, N and Zdobnov, EM and Aqrawi, PK and Blankenburg, KP and Coyle, M and Francisco, L and Hernandez, AG and Holder, M and Hudson, ME and Jackson, L and Jayaseelan, J and Joshi, V and Kovar, C and Lee, SL and Mata, R and Mathew, T and Newsham, IF and Ngo, R and Okwuonu, G and Pham, C and Pu, LL and Saada, N and Santibanez, J and Simmons, D and Thornton, R and Venkat, A and Walden, KK and Wu, YQ and Debyser, G and Devreese, B and Asher, C and Blommaert, J and Chipman, AD and Chittka, L and Fouks, B and Liu, J and O'Neill, MP and Sumner, S and Puiu, D and Qu, J and Salzberg, SL and Scherer, SE and Muzny, DM and Richards, S and Robinson, GE and Gibbs, RA and Schmid-Hempel, P and Worley, KC}, title = {The genomes of two key bumblebee species with primitive eusocial organization.}, journal = {Genome biology}, volume = {16}, number = {1}, pages = {76}, pmid = {25908251}, issn = {1474-760X}, support = {R01 HG006677/HG/NHGRI NIH HHS/United States ; MR/K001744/1/MRC_/Medical Research Council/United Kingdom ; G0900740/MRC_/Medical Research Council/United Kingdom ; U54 HG003273/HG/NHGRI NIH HHS/United States ; BB/G00661X/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; 095831/WT_/Wellcome Trust/United Kingdom ; DP1 OD006416/OD/NIH HHS/United States ; }, mesh = {Animals ; Bee Venoms/genetics ; Bees/classification/*genetics/physiology ; *Behavior, Animal ; Chemoreceptor Cells/metabolism ; Chromosome Mapping ; Databases, Genetic ; Evolution, Molecular ; Female ; Gene Expression Regulation ; Gene Rearrangement ; *Genes, Insect ; Genomics ; Interspersed Repetitive Sequences ; Male ; Open Reading Frames ; Polymorphism, Single Nucleotide ; Selenoproteins/genetics/metabolism ; Sequence Analysis, DNA ; *Social Behavior ; Species Specificity ; Synteny ; }, abstract = {BACKGROUND: The shift from solitary to social behavior is one of the major evolutionary transitions. Primitively eusocial bumblebees are uniquely placed to illuminate the evolution of highly eusocial insect societies. Bumblebees are also invaluable natural and agricultural pollinators, and there is widespread concern over recent population declines in some species. High-quality genomic data will inform key aspects of bumblebee biology, including susceptibility to implicated population viability threats.

RESULTS: We report the high quality draft genome sequences of Bombus terrestris and Bombus impatiens, two ecologically dominant bumblebees and widely utilized study species. Comparing these new genomes to those of the highly eusocial honeybee Apis mellifera and other Hymenoptera, we identify deeply conserved similarities, as well as novelties key to the biology of these organisms. Some honeybee genome features thought to underpin advanced eusociality are also present in bumblebees, indicating an earlier evolution in the bee lineage. Xenobiotic detoxification and immune genes are similarly depauperate in bumblebees and honeybees, and multiple categories of genes linked to social organization, including development and behavior, show high conservation. Key differences identified include a bias in bumblebee chemoreception towards gustation from olfaction, and striking differences in microRNAs, potentially responsible for gene regulation underlying social and other traits.

CONCLUSIONS: These two bumblebee genomes provide a foundation for post-genomic research on these key pollinators and insect societies. Overall, gene repertoires suggest that the route to advanced eusociality in bees was mediated by many small changes in many genes and processes, and not by notable expansion or depauperation.}, } @article {pmid25903634, year = {2015}, author = {Parker, IM and Saunders, M and Bontrager, M and Weitz, AP and Hendricks, R and Magarey, R and Suiter, K and Gilbert, GS}, title = {Phylogenetic structure and host abundance drive disease pressure in communities.}, journal = {Nature}, volume = {520}, number = {7548}, pages = {542-544}, pmid = {25903634}, issn = {1476-4687}, mesh = {*Biodiversity ; California ; Databases, Factual ; *Grassland ; Introduced Species/trends ; *Phylogeny ; Plant Diseases/*statistics & numerical data ; Plants/*classification ; Population Density ; }, abstract = {Pathogens play an important part in shaping the structure and dynamics of natural communities, because species are not affected by them equally. A shared goal of ecology and epidemiology is to predict when a species is most vulnerable to disease. A leading hypothesis asserts that the impact of disease should increase with host abundance, producing a 'rare-species advantage'. However, the impact of a pathogen may be decoupled from host abundance, because most pathogens infect more than one species, leading to pathogen spillover onto closely related species. Here we show that the phylogenetic and ecological structure of the surrounding community can be important predictors of disease pressure. We found that the amount of tissue lost to disease increased with the relative abundance of a species across a grassland plant community, and that this rare-species advantage had an additional phylogenetic component: disease pressure was stronger on species with many close relatives. We used a global model of pathogen sharing as a function of relatedness between hosts, which provided a robust predictor of relative disease pressure at the local scale. In our grassland, the total amount of disease was most accurately explained not by the abundance of the focal host alone, but by the abundance of all species in the community weighted by their phylogenetic distance to the host. Furthermore, the model strongly predicted observed disease pressure for 44 novel host species we introduced experimentally to our study site, providing evidence for a mechanism to explain why phylogenetically rare species are more likely to become invasive when introduced. Our results demonstrate how the phylogenetic and ecological structure of communities can have a key role in disease dynamics, with implications for the maintenance of biodiversity, biotic resistance against introduced weeds, and the success of managed plants in agriculture and forestry.}, } @article {pmid25899440, year = {2015}, author = {Gee, PM and Paterniti, DA and Ward, D and Soederberg Miller, LM}, title = {e-Patients Perceptions of Using Personal Health Records for Self-management Support of Chronic Illness.}, journal = {Computers, informatics, nursing : CIN}, volume = {33}, number = {6}, pages = {229-237}, doi = {10.1097/CIN.0000000000000151}, pmid = {25899440}, issn = {1538-9774}, mesh = {Aged ; Chronic Disease/*therapy ; Communication ; *Electronic Health Records ; Female ; Grounded Theory ; Health Personnel ; *Health Records, Personal ; Humans ; Male ; Middle Aged ; Nursing Informatics ; Physician-Patient Relations ; Self Care/*psychology ; }, abstract = {Chronic illness self-management is largely moving from healthcare professionals and into the hands of the patient. One tool that has been promoted to facilitate self-management support of chronic illness by policymakers, health advocates, providers, and consumers is the personal health record. Little is known about how consumers effectively use personal health records for self-management support and for productive patient-provider interactions. The purpose of this study was to learn from chronically ill engaged, experienced, and educated (e-patient) adults how and why they use personal health records for self-management support and productive patient-provider interactions. Eighteen purposively selected consumers were interviewed in two communities. Qualitative description methods were used, and we used a grounded theory approach to analyzing interview data, which was digitally recorded and transcribed verbatim. We identified four major thematic categories that capture the perceptions of the chronically ill using personal health records: (1) patient engagement and health self-management, (2) access to and control over personal health data, (3) promotion of productive communication, and (4) opportunities for training and education. Knowledge gained from the e-patient personal health record users suggest that making improvements to the portal system and providing education to consumers and providers will increase the utility among the experienced users and encourage new users to embrace adoption and use.}, } @article {pmid25899045, year = {2015}, author = {Park, MK and Park, JY and Nicolas, G and Paik, HY and Kim, J and Slimani, N}, title = {Adapting a standardised international 24 h dietary recall methodology (GloboDiet software) for research and dietary surveillance in Korea.}, journal = {The British journal of nutrition}, volume = {113}, number = {11}, pages = {1810-1818}, doi = {10.1017/S0007114515000987}, pmid = {25899045}, issn = {1475-2662}, support = {001/WHO_/World Health Organization/International ; }, mesh = {Databases, Factual ; *Diet Records ; Europe ; *Feeding Behavior ; Humans ; *Mental Recall ; Nutrition Surveys/*methods/*standards ; Reference Standards ; Republic of Korea ; Software/*standards ; Surveys and Questionnaires ; }, abstract = {During the past decades, a rapid nutritional transition has been observed along with economic growth in the Republic of Korea. Since this dramatic change in diet has been frequently associated with cancer and other non-communicable diseases, dietary monitoring is essential to understand the association. Benefiting from pre-existing standardised dietary methodologies, the present study aimed to evaluate the feasibility and describe the development of a Korean version of the international computerised 24 h dietary recall method (GloboDiet software) and its complementary tools, developed at the International Agency for Research on Cancer (IARC), WHO. Following established international Standard Operating Procedures and guidelines, about seventy common and country-specific databases on foods, recipes, dietary supplements, quantification methods and coefficients were customised and translated. The main results of the present study highlight the specific adaptations made to adapt the GloboDiet software for research and dietary surveillance in Korea. New (sub-) subgroups were added into the existing common food classification, and new descriptors were added to the facets to classify and describe specific Korean foods. Quantification methods were critically evaluated and adapted considering the foods and food packages available in the Korean market. Furthermore, a picture book of foods/dishes was prepared including new pictures and food portion sizes relevant to Korean diet. The development of the Korean version of GloboDiet demonstrated that it was possible to adapt the IARC-WHO international dietary tool to an Asian context without compromising its concept of standardisation and software structure. It, thus, confirms that this international dietary methodology, used so far only in Europe, is flexible and robust enough to be customised for other regions worldwide.}, } @article {pmid25898989, year = {2015}, author = {Quick, H and Banerjee, S and Carlin, BP}, title = {Bayesian modeling and analysis for gradients in spatiotemporal processes.}, journal = {Biometrics}, volume = {71}, number = {3}, pages = {575-584}, pmid = {25898989}, issn = {1541-0420}, support = {RC1 GM092400/GM/NIGMS NIH HHS/United States ; 1-RC1-GM092400-01/GM/NIGMS NIH HHS/United States ; }, mesh = {Air Pollution/analysis/*statistics & numerical data ; *Bayes Theorem ; California ; Computer Simulation ; Data Interpretation, Statistical ; Fires/*statistics & numerical data ; Humans ; *Models, Statistical ; Particulate Matter/*analysis ; Reproducibility of Results ; Sensitivity and Specificity ; *Spatio-Temporal Analysis ; }, abstract = {Stochastic process models are widely employed for analyzing spatiotemporal datasets in various scientific disciplines including, but not limited to, environmental monitoring, ecological systems, forestry, hydrology, meteorology, and public health. After inferring on a spatiotemporal process for a given dataset, inferential interest may turn to estimating rates of change, or gradients, over space and time. This manuscript develops fully model-based inference on spatiotemporal gradients under continuous space, continuous time settings. Our contribution is to offer, within a flexible spatiotemporal process model setting, a framework to estimate arbitrary directional gradients over space at any given timepoint, temporal derivatives at any given spatial location and, finally, mixed spatiotemporal gradients that reflect rapid change in spatial gradients over time and vice-versa. We achieve such inference without compromising on rich and flexible spatiotemporal process models and use nonseparable covariance structures. We illustrate our methodology using a simulated data example and subsequently apply it to a dataset of daily PM2.5 concentrations in California, where the spatiotemporal gradient process reveals the effects of California's unique topography on pollution and detects the aftermath of a devastating series of wildfires.}, } @article {pmid25898925, year = {2016}, author = {Brown, R and Lee, H and Eskin, A and Kichaev, G and Lohmueller, KE and Reversade, B and Nelson, SF and Pasaniuc, B}, title = {Leveraging ancestry to improve causal variant identification in exome sequencing for monogenic disorders.}, journal = {European journal of human genetics : EJHG}, volume = {24}, number = {1}, pages = {113-119}, pmid = {25898925}, issn = {1476-5438}, support = {T32-HG002536/HG/NHGRI NIH HHS/United States ; T32 HG002536/HG/NHGRI NIH HHS/United States ; P30AR057230/AR/NIAMS NIH HHS/United States ; R03 CA162200/CA/NCI NIH HHS/United States ; P30 AR057230/AR/NIAMS NIH HHS/United States ; R01 GM053275/GM/NIGMS NIH HHS/United States ; R01-GM053275/GM/NIGMS NIH HHS/United States ; R03-CA162200/CA/NCI NIH HHS/United States ; }, mesh = {*Algorithms ; Computational Biology/*methods ; Computer Simulation ; *Exome ; Female ; Genetic Diseases, Inborn/diagnosis/ethnology/*genetics ; Genetic Variation ; Genome, Human ; High-Throughput Nucleotide Sequencing ; Humans ; Inheritance Patterns ; Male ; *Models, Statistical ; Pedigree ; *Polymorphism, Single Nucleotide ; Racial Groups ; Sequence Analysis, DNA ; }, abstract = {Recent breakthroughs in exome-sequencing technology have made possible the identification of many causal variants of monogenic disorders. Although extremely powerful when closely related individuals (eg, child and parents) are simultaneously sequenced, sequencing of a single case is often unsuccessful due to the large number of variants that need to be followed up for functional validation. Many approaches filter out common variants above a given frequency threshold (eg, 1%), and then prioritize the remaining variants according to their functional, structural and conservation properties. Here we present methods that leverage the genetic structure across different populations to improve filtering performance while accounting for the finite sample size of the reference panels. We show that leveraging genetic structure reduces the number of variants that need to be followed up by 16% in simulations and by up to 38% in empirical data of 20 exomes from individuals with monogenic disorders for which the causal variants are known.}, } @article {pmid25898843, year = {2015}, author = {Marras, S and Noda, T and Steffensen, JF and Svendsen, MB and Krause, J and Wilson, AD and Kurvers, RH and Herbert-Read, J and Boswell, KM and Domenici, P}, title = {Not So Fast: Swimming Behavior of Sailfish during Predator-Prey Interactions using High-Speed Video and Accelerometry.}, journal = {Integrative and comparative biology}, volume = {55}, number = {4}, pages = {719-727}, doi = {10.1093/icb/icv017}, pmid = {25898843}, issn = {1557-7023}, mesh = {Accelerometry/*veterinary ; Animals ; Biomechanical Phenomena ; Fishes/anatomy & histology/*physiology ; Predatory Behavior/*physiology ; Swimming/*physiology ; *Video Recording ; }, abstract = {Billfishes are considered among the fastest swimmers in the oceans. Despite early estimates of extremely high speeds, more recent work showed that these predators (e.g., blue marlin) spend most of their time swimming slowly, rarely exceeding 2 m s(-1). Predator-prey interactions provide a context within which one may expect maximal speeds both by predators and prey. Beyond speed, however, an important component determining the outcome of predator-prey encounters is unsteady swimming (i.e., turning and accelerating). Although large predators are faster than their small prey, the latter show higher performance in unsteady swimming. To contrast the evading behaviors of their highly maneuverable prey, sailfish and other large aquatic predators possess morphological adaptations, such as elongated bills, which can be moved more rapidly than the whole body itself, facilitating capture of the prey. Therefore, it is an open question whether such supposedly very fast swimmers do use high-speed bursts when feeding on evasive prey, in addition to using their bill for slashing prey. Here, we measured the swimming behavior of sailfish by using high-frequency accelerometry and high-speed video observations during predator-prey interactions. These measurements allowed analyses of tail beat frequencies to estimate swimming speeds. Our results suggest that sailfish burst at speeds of about 7 m s(-1) and do not exceed swimming speeds of 10 m s(-1) during predator-prey interactions. These speeds are much lower than previous estimates. In addition, the oscillations of the bill during swimming with, and without, extension of the dorsal fin (i.e., the sail) were measured. We suggest that extension of the dorsal fin may allow sailfish to improve the control of the bill and minimize its yaw, hence preventing disturbance of the prey. Therefore, sailfish, like other large predators, may rely mainly on accuracy of movement and the use of the extensions of their bodies, rather than resorting to top speeds when hunting evasive prey.}, } @article {pmid25898571, year = {2014}, author = {Liu, X and Huang, H and Yang, YF and Wu, HZ}, title = {[Analysis of effect of topographical conditions on content of total alkaloid in Coptidis Rhizoma in Chongqin, China].}, journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica}, volume = {39}, number = {24}, pages = {4748-4753}, pmid = {25898571}, issn = {1001-5302}, mesh = {Alkaloids/*analysis/metabolism ; China ; Coptis/*chemistry ; Ecology ; Environment ; Geographic Information Systems ; Geography ; Plants, Medicinal ; Rhizome/*chemistry ; }, abstract = {To study ecology suitability rank dividing of the total alkaloid content of Coptis Rhizoma for selecting artificial planting base and high-quality industrial raw material in Chongqing province. Based on the investigation of PCB and DEM data of Chongqing province, the relationship between the total alkaloid content in Coptis Rhizoma and topographical conditions was analyzed by statistical analysis. The geographic information systems (GIS)-based assessment and landscape ecological principles were applied to assess eco logy suitability areas of Coptis Rhizoma in Chongqing. slope, aspect and altitude are main topographical factors that affect the content of the total alkaloid content in Coptis Rhizoma The total alkaloid content in Coptis Rhizoma is higher in the lower altitude, shady slope and bigger slope areas. The total alkaloid content is higher in the south areas of Chongqing province and lower in the northeast. Terrain conditions of the southern region of Chongqing are most suitable for The accumulated of total alkaloid Coptis Rhizoma content.}, } @article {pmid25898407, year = {2015}, author = {Hou, K and Li, X and Zhang, J}, title = {GIS analysis of changes in ecological vulnerability using a SPCA model in the Loess plateau of Northern Shaanxi, China.}, journal = {International journal of environmental research and public health}, volume = {12}, number = {4}, pages = {4292-4305}, pmid = {25898407}, issn = {1660-4601}, mesh = {China ; Climate ; Ecological and Environmental Phenomena ; Geographic Information Systems ; *Models, Theoretical ; Principal Component Analysis ; Soil ; }, abstract = {Changes in ecological vulnerability were analyzed for Northern Shaanxi, China using a geographic information system (GIS). An evaluation model was developed using a spatial principal component analysis (SPCA) model containing land use, soil erosion, topography, climate, vegetation and social economy variables. Using this model, an ecological vulnerability index was computed for the research region. Using natural breaks classification (NBC), the evaluation results were divided into five types: potential, slight, light, medium and heavy. The results indicate that there is greater than average optimism about the conditions of the study region, and the ecological vulnerability index (EVI) of the southern eight counties is lower than that of the northern twelve counties. From 1997 to 2011, the ecological vulnerability index gradually decreased, which means that environmental security was gradually enhanced, although there are still some places that have gradually deteriorated over the past 15 years. In the study area, government and economic factors and precipitation are the main reasons for the changes in ecological vulnerability.}, } @article {pmid25896820, year = {2015}, author = {Uhde, B and Hahn, WA and Griess, VC and Knoke, T}, title = {Hybrid MCDA Methods to Integrate Multiple Ecosystem Services in Forest Management Planning: A Critical Review.}, journal = {Environmental management}, volume = {56}, number = {2}, pages = {373-388}, pmid = {25896820}, issn = {1432-1009}, mesh = {*Decision Support Techniques ; Ecosystem ; Forestry/economics/*methods/*organization & administration ; *Forests ; *Models, Theoretical ; Planning Techniques ; Uncertainty ; }, abstract = {Multi-criteria decision analysis (MCDA) is a decision aid frequently used in the field of forest management planning. It includes the evaluation of multiple criteria such as the production of timber and non-timber forest products and tangible as well as intangible values of ecosystem services (ES). Hence, it is beneficial compared to those methods that take a purely financial perspective. Accordingly, MCDA methods are increasingly popular in the wide field of sustainability assessment. Hybrid approaches allow aggregating MCDA and, potentially, other decision-making techniques to make use of their individual benefits and leading to a more holistic view of the actual consequences that come with certain decisions. This review is providing a comprehensive overview of hybrid approaches that are used in forest management planning. Today, the scientific world is facing increasing challenges regarding the evaluation of ES and the trade-offs between them, for example between provisioning and regulating services. As the preferences of multiple stakeholders are essential to improve the decision process in multi-purpose forestry, participatory and hybrid approaches turn out to be of particular importance. Accordingly, hybrid methods show great potential for becoming most relevant in future decision making. Based on the review presented here, the development of models for the use in planning processes should focus on participatory modeling and the consideration of uncertainty regarding available information.}, } @article {pmid25892924, year = {2015}, author = {Audisio, P and Alonso Zarazaga, MA and Slipinski, A and Nilsson, A and Jelínek, J and Taglianti, AV and Turco, F and Otero, C and Canepari, C and Kral, D and Liberti, G and Sama, G and Nardi, G and Löbl, I and Horak, J and Kolibac, J and Háva, J and Sapiejewski, M and Jäch, M and Bologna, MA and Biondi, M and Nikitsky, NB and Mazzoldi, P and Zahradnik, P and Wegrzynowicz, P and Constantin, R and Gerstmeier, R and Zhantiev, R and Fattorini, S and Tomaszewska, W and Rücker, WH and Vazquez-Albalate, X and Cassola, F and Angelini, F and Johnson, C and Schawaller, W and Regalin, R and Baviera, C and Rocchi, S and Cianferoni, F and Beenen, R and Schmitt, M and Sassi, D and Kippenberg, H and Zampetti, MF and Trizzino, M and Chiari, S and Carpaneto, GM and Sabatelli, S and de Jong, Y}, title = {Fauna Europaea: Coleoptera 2 (excl. series Elateriformia, Scarabaeiformia, Staphyliniformia and superfamily Curculionoidea).}, journal = {Biodiversity data journal}, volume = {}, number = {3}, pages = {e4750}, pmid = {25892924}, issn = {1314-2828}, abstract = {Fauna Europaea provides a public web-service with an index of scientific names (including synonyms) of all living European land and freshwater animals, their geographical distribution at country level (up to the Urals, excluding the Caucasus region), and some additional information. The Fauna Europaea project covers about 230,000 taxonomic names, including 130,000 accepted species and 14,000 accepted subspecies, which is much more than the originally projected number of 100,000 species. This represents a huge effort by more than 400 contributing specialists throughout Europe and is a unique (standard) reference suitable for many users in science, government, industry, nature conservation and education. Coleoptera represent a huge assemblage of holometabolous insects, including as a whole more than 200 recognized families and some 400,000 described species worldwide. Basic information is summarized on their biology, ecology, economic relevance, and estimated number of undescribed species worldwide. Little less than 30,000 species are listed from Europe. The Coleoptera 2 section of the Fauna Europaea database (Archostemata, Myxophaga, Adephaga and Polyphaga excl. the series Elateriformia, Scarabaeiformia, Staphyliniformia and the superfamily Curculionoidea) encompasses 80 families (according to the previously accepted family-level systematic framework) and approximately 13,000 species. Tabulations included a complete list of the families dealt with, the number of species in each, the names of all involved specialists, and, when possible, an estimate of the gaps in terms of total number of species at an European level. A list of some recent useful references is appended. Most families included in the Coleoptera 2 Section have been updated in the most recent release of the Fauna Europaea index, or are ready to be updated as soon as the FaEu data management environment completes its migration from Zoological Museum Amsterdam to Berlin Museum für Naturkunde.}, } @article {pmid25891686, year = {2015}, author = {Specht, A and Guru, S and Houghton, L and Keniger, L and Driver, P and Ritchie, EG and Lai, K and Treloar, A}, title = {Data management challenges in analysis and synthesis in the ecosystem sciences.}, journal = {The Science of the total environment}, volume = {534}, number = {}, pages = {144-158}, doi = {10.1016/j.scitotenv.2015.03.092}, pmid = {25891686}, issn = {1879-1026}, mesh = {Australia ; Conservation of Natural Resources/*methods ; Database Management Systems ; *Ecology ; Ecosystem ; }, abstract = {Open-data has created an unprecedented opportunity with new challenges for ecosystem scientists. Skills in data management are essential to acquire, manage, publish, access and re-use data. These skills span many disciplines and require trans-disciplinary collaboration. Science synthesis centres support analysis and synthesis through collaborative 'Working Groups' where domain specialists work together to synthesise existing information to provide insight into critical problems. The Australian Centre for Ecological Analysis and Synthesis (ACEAS) served a wide range of stakeholders, from scientists to policy-makers to managers. This paper investigates the level of sophistication in data management in the ecosystem science community through the lens of the ACEAS experience, and identifies the important factors required to enable us to benefit from this new data-world and produce innovative science. ACEAS promoted the analysis and synthesis of data to solve transdisciplinary questions, and promoted the publication of the synthesised data. To do so, it provided support in many of the key skillsets required. Analysis and synthesis in multi-disciplinary and multi-organisational teams, and publishing data were new for most. Data were difficult to discover and access, and to make ready for analysis, largely due to lack of metadata. Data use and publication were hampered by concerns about data ownership and a desire for data citation. A web portal was created to visualise geospatial datasets to maximise data interpretation. By the end of the experience there was a significant increase in appreciation of the importance of a Data Management Plan. It is extremely doubtful that the work would have occurred or data delivered without the support of the Synthesis centre, as few of the participants had the necessary networks or skills. It is argued that participation in the Centre provided an important learning opportunity, and has resulted in improved knowledge and understanding of good data management practices.}, } @article {pmid25890254, year = {2015}, author = {Shen, L and Chen, C and Yang, A and Chen, Y and Liu, Q and Ni, J}, title = {Redox proteomics identification of specifically carbonylated proteins in the hippocampi of triple transgenic Alzheimer's disease mice at its earliest pathological stage.}, journal = {Journal of proteomics}, volume = {123}, number = {}, pages = {101-113}, doi = {10.1016/j.jprot.2015.04.005}, pmid = {25890254}, issn = {1876-7737}, mesh = {Alcohol Oxidoreductases/metabolism ; Alzheimer Disease/*genetics ; Animals ; Carbon/chemistry ; Chaperonin Containing TCP-1/metabolism ; Cognition Disorders/genetics ; Computational Biology ; Disease Models, Animal ; Electrophoresis, Gel, Two-Dimensional ; Glutamate-Ammonia Ligase/metabolism ; Hippocampus/*metabolism ; Male ; Mass Spectrometry ; Mice ; Mice, Transgenic ; *Oxidation-Reduction ; Oxidative Stress ; Phosphopyruvate Hydratase/metabolism ; Protein Carbonylation ; Protein Disulfide-Isomerases/metabolism ; Protein Folding ; Protein Interaction Mapping ; Proteomics/*methods ; Signal Transduction ; }, abstract = {UNLABELLED: Alzheimer's disease (AD) is the most common cause of dementia in the elderly population. Attempts to develop therapies for the treatment of the late stage AD have been unsuccessful. Increasing evidences indicate that oxidative stress is an early event of neurodegeneration, however the pathogenic mechanism of AD remains unclarified. In the present study, slot-blot analysis was used to determine the levels of protein carbonyls in the hippocampi of 3-month-old triple transgenic AD mice (3 × Tg-AD). The increased levels of protein carbonyls were observed in the hippocampi of 3 × Tg-AD mice as compared to the non-transgenic controls (non-Tg). Using a redox-proteomic approach, twelve proteins were found to be significantly altered in the levels of protein carbonyls in the hippocampus. These proteins are crucial in energy metabolism, protein folding, cell structure, signal transduction and excitotoxicity. Immunoprecipitation and Western blot were used to validate two proteins identified by the redox proteomics. In addition, increased expression level of carbonyl reductase 1 (CBR1) was observed in the hippocampi of 3 × Tg-AD mice. These results demonstrate that significant protein carbonylation occurs early in the 3-month-old 3 × Tg-AD mice, which support the viewpoint that oxidative stress is an early event in AD progression.

BIOLOGICAL SIGNIFICANCE: In this study, we have observed increased levels of protein carbonyls in the hippocampi of 3 × Tg-AD mice before the appearance of Aβ plaques and neurofibrillary tangles (NFTs). By redox proteomics, twelve specifically carbonylated proteins were identified. Among them, alpha-enolase (ENO1) and glutamine synthetase (GS) were identified as the common targets of oxidation in the brains of 3 × Tg-AD mice, mild cognitive impairment (MCI) sufferers and AD patients. For the first time, the oxidation of t-complex protein 1 subunit epsilon (CCT5) and protein disulfide-isomerase A3 (PDIA3) were reported to be associated with AD. These results indicated that the combination of monoclonal anti-DNP antibody with digital imaging system could enhance the specificity and accuracy of redox proteomics analysis. Those data support the viewpoint that oxidative stress occurs at the early pathological stage of AD. In addition, this paper provides new information for understanding the pathological process of AD and for developing more appropriate therapies to intervene AD progression.}, } @article {pmid25889759, year = {2015}, author = {Knapen, D and Vergauwen, L and Villeneuve, DL and Ankley, GT}, title = {The potential of AOP networks for reproductive and developmental toxicity assay development.}, journal = {Reproductive toxicology (Elmsford, N.Y.)}, volume = {56}, number = {}, pages = {52-55}, doi = {10.1016/j.reprotox.2015.04.003}, pmid = {25889759}, issn = {1873-1708}, mesh = {Animal Testing Alternatives ; Animals ; Computer Simulation ; Embryonic Development/*drug effects ; Female ; Fetal Development/*drug effects ; Gene Expression Regulation, Developmental/drug effects ; Gene Regulatory Networks/drug effects ; Humans ; *Knowledge Bases ; Models, Biological ; Pregnancy ; Reproduction/*drug effects ; Risk Assessment ; Signal Transduction/drug effects ; Systems Integration ; Toxicity Tests/*methods ; }, abstract = {Historically, the prediction of reproductive and developmental toxicity has largely relied on the use of animals. The adverse outcome pathway (AOP) framework forms a basis for the development of new non-animal test methods. It also provides biological context for mechanistic information from existing assays. However, a single AOP may not capture all events that contribute to any relevant toxic effect, even in single chemical exposure scenarios. AOP networks, defined as sets of AOPs sharing at least one common element, are capable of more realistically representing potential chemical effects. They provide information on interactions between AOPs and have the potential to reveal previously unknown links between biological pathways. Analysis of these AOP networks can aid the prioritization of assay development, whether the goal is to develop a single assay with predictive utility of multiple outcomes, or development of assays that are highly specific for a particular mode of action. This paper provides a brief overview of the AOPs related to reproductive and developmental toxicity currently available in the AOP Wiki (http://aopwiki.org), and gives an example of an AOP network based on five reproductive and developmental toxicity-related AOPs for fish to illustrate how AOP networks can be used for assay development and refinement.}, } @article {pmid25887758, year = {2015}, author = {Galla, G and Vogel, H and Sharbel, TF and Barcaccia, G}, title = {De novo sequencing of the Hypericum perforatum L. flower transcriptome to identify potential genes that are related to plant reproduction sensu lato.}, journal = {BMC genomics}, volume = {16}, number = {1}, pages = {254}, pmid = {25887758}, issn = {1471-2164}, mesh = {Apomixis/genetics ; Base Sequence ; Databases, Genetic ; Flowers/genetics ; *Genes, Plant ; Genotype ; High-Throughput Nucleotide Sequencing ; Hypericum/*genetics ; Meiosis/genetics ; Molecular Sequence Data ; Plant Development/genetics ; Plant Proteins/genetics ; Plants, Medicinal/genetics ; RNA, Plant/analysis/isolation & purification/metabolism ; Reproduction, Asexual/*genetics ; Sequence Analysis, RNA ; *Transcriptome ; }, abstract = {BACKGROUND: St. John's wort (Hypericum perforatum L.) is a medicinal plant that produces important metabolites with antidepressant and anticancer activities. Recently gained biological information has shown that this species is also an attractive model system for the study of a naturally occurring form of asexual reproduction called apomixis, which allows cloning plants through seeds. In aposporic gametogenesis, one or multiple somatic cells belonging to the ovule nucellus change their fate by dividing mitotically and developing functionally unreduced embryo sacs by mimicking sexual gametogenesis. Although the introduction of apomixis into agronomically important crops could have revolutionary implications for plant breeding, the genetic control of this mechanism of seed formation is still not well understood for most of the model species investigated so far. We used Roche 454 technology to sequence the entire H. perforatum flower transcriptome of whole flower buds and single flower verticils collected from obligately sexual and unrelated highly or facultatively apomictic genotypes, which enabled us to identify RNAs that are likely exclusive to flower organs (i.e., sepals, petals, stamens and carpels) or reproductive strategies (i.e., sexual vs. apomictic).

RESULTS: Here we sequenced and annotated the flower transcriptome of H. perforatum with particular reference to reproductive organs and processes. In particular, in our study we characterized approximately 37,000 transcripts found expressed in male and/or female reproductive organs, including tissues or cells of sexual and apomictic flower buds. Ontological annotation was applied to identify major biological processes and molecular functions involved in flower development and plant reproduction. Starting from this dataset, we were able to recover and annotate a large number of transcripts related to meiosis, gametophyte/gamete formation, and embryogenesis, as well as genes that are exclusively or preferentially expressed in sexual or apomictic libraries. Real-Time RT-qPCR assays on pistils and anthers collected at different developmental stages from accessions showing alternative modes of reproduction were used to identify potential genes that are related to plant reproduction sensu lato in H. perforatum.

CONCLUSIONS: Our approach of sequencing flowers from two fully obligate sexual genotypes and two unrelated highly apomictic genotypes, in addition to different flower parts dissected from a facultatively apomictic accession, enabled us to analyze the complexity of the flower transcriptome according to its main reproductive organs as well as for alternative reproductive behaviors. Both annotation and expression data provided original results supporting the hypothesis that apomixis in H. perforatum relies upon spatial or temporal mis-expression of genes acting during female sexual reproduction. The present analyses aim to pave the way toward a better understanding of the molecular basis of flower development and plant reproduction, by identifying genes or RNAs that may differentiate or regulate the sexual and apomictic reproductive pathways in H. perforatum.}, } @article {pmid25887225, year = {2015}, author = {He, L and Pei, Y and Jiang, Y and Li, Y and Liao, L and Zhu, Z and Wang, Y}, title = {Global gene expression patterns of grass carp following compensatory growth.}, journal = {BMC genomics}, volume = {16}, number = {1}, pages = {184}, pmid = {25887225}, issn = {1471-2164}, mesh = {Animals ; Body Weight ; Carps/*genetics/*growth & development ; Computational Biology ; Fasting ; *Gene Expression Profiling ; Gene Expression Regulation ; High-Throughput Nucleotide Sequencing ; Reproducibility of Results ; *Transcriptome ; }, abstract = {BACKGROUND: Compensatory growth is accelerated compared with normal growth and occurs when growth-limiting conditions are overcome. Most animals, especially fish, are capable of compensatory growth, but the mechanisms remain unclear. Further investigation of the mechanism of compensatory growth in fish is needed to improve feeding efficiency, reduce cost, and explore growth-related genes.

RESULTS: In the study, grass carp, an important farmed fish in China, were subjected to a compensatory growth experiment followed by transcriptome analysis by RNA-sequencing. Samples of fish from starved and re-feeding conditions were compared with the control. Under starved conditions, 4061 and 1988 differentially expressed genes (DEGs) were detected in muscle and liver tissue when compared the experimental group with control group, respectively. After re-feeding, 349 and 247 DEGs were identified in muscle and liver when the two groups were compared. Moreover, when samples from experimental group in starved and re-feeding conditions were compared, 4903 and 2444 DEGs were found in muscle and liver. Most of these DEGs were involved in metabolic processes, or encoded enzymes or proteins with catalytic activity or binding functions, or involved in metabolic and biosynthetic pathways. A number of the more significant DEGs were subjected to further analysis. Under fasting conditions, many up-regulated genes were associated with protein ubiquitination or degradation, whereas many down-regulated genes were involved in the metabolism of glucose and fatty acids. Under re-feeding conditions, genes participating in muscle synthesis and fatty acid metabolism were up-regulated significantly, and genes related to protein ubiquitination or degradation were down-regulated. Moreover, Several DEGs were random selected for confirmation by real-time quantitative PCR.

CONCLUSIONS: Global gene expression patterns of grass carp during compensatory growth were determined. To our knowledge, this is a first reported for a teleost fish. The results will enhance our understanding of the mechanism of compensatory growth in teleost fish.}, } @article {pmid25885965, year = {2015}, author = {Feuillet, T and Charreire, H and Menai, M and Salze, P and Simon, C and Dugas, J and Hercberg, S and Andreeva, VA and Enaux, C and Weber, C and Oppert, JM}, title = {Spatial heterogeneity of the relationships between environmental characteristics and active commuting: towards a locally varying social ecological model.}, journal = {International journal of health geographics}, volume = {14}, number = {}, pages = {12}, pmid = {25885965}, issn = {1476-072X}, mesh = {Adolescent ; Adult ; *Environment Design ; Female ; Geographic Information Systems ; Humans ; *Locomotion ; Male ; Middle Aged ; Paris ; Regression Analysis ; Social Environment ; Spatio-Temporal Analysis ; Surveys and Questionnaires ; *Transportation ; Young Adult ; }, abstract = {BACKGROUND: According to the social ecological model of health-related behaviors, it is now well accepted that environmental factors influence habitual physical activity. Most previous studies on physical activity determinants have assumed spatial homogeneity across the study area, i.e. that the association between the environment and physical activity is the same whatever the location. The main novelty of our study was to explore geographical variation in the relationships between active commuting (walking and cycling to/from work) and residential environmental characteristics.

METHODS: 4,164 adults from the ongoing Nutrinet-Santé web-cohort, residing in and around Paris, France, were studied using a geographically weighted Poisson regression (GWPR) model. Objective environmental variables, including both the built and the socio-economic characteristics around the place of residence of individuals, were assessed by GIS-based measures. Perceived environmental factors (index including safety, aesthetics, and pollution) were reported by questionnaires.

RESULTS: Our results show that the influence of the overall neighborhood environment appeared to be more pronounced in the suburban southern part of the study area (Val-de-Marne) compared to Paris inner city, whereas more complex patterns were found elsewhere. Active commuting was positively associated with the built environment only in the southern and northeastern parts of the study area, whereas positive associations with the socio-economic environment were found only in some specific locations in the southern and northern parts of the study area. Similar local variations were observed for the perceived environmental variables.

CONCLUSIONS: These results suggest that: (i) when applied to active commuting, the social ecological conceptual framework should be locally nuanced, and (ii) local rather than global targeting of public health policies might be more efficient in promoting active commuting.}, } @article {pmid25882668, year = {2015}, author = {Rodrigues, L and Calheiros, M and Pereira, C}, title = {The decision of out-of-home placement in residential care after parental neglect: Empirically testing a psychosocial model.}, journal = {Child abuse & neglect}, volume = {49}, number = {}, pages = {35-49}, doi = {10.1016/j.chiabu.2015.03.014}, pmid = {25882668}, issn = {1873-7757}, mesh = {Adult ; Child ; Child Abuse/*prevention & control ; Child Protective Services/*methods ; *Child Welfare ; *Decision Making ; *Decision Support Techniques ; Empirical Research ; Female ; Foster Home Care ; Humans ; Infant ; Male ; Middle Aged ; *Models, Psychological ; Portugal ; Reproducibility of Results ; Social Workers ; Surveys and Questionnaires ; Young Adult ; }, abstract = {Out-of-home placement decisions in residential care are complex, ambiguous and full of uncertainty, especially in cases of parental neglect. Literature on this topic is so far unable to understand and demonstrate the source of errors involved in those decisions and still fails to focus on professional's decision making process. Therefore, this work intends to test a socio-psychological model of decision-making that is a more integrated, dualistic and ecological version of the Theory of Planned Behavior's model. It describes the process through which the decision maker takes into account personal, contextual and social factors of the Decision-Making Ecology in the definition of his/her decision threshold. One hundred and ninety-five professionals from different Children and Youth Protection Units, throughout the Portuguese territory, participated in this online study. After reading a vignette of a (psychological and physical) neglect case toward a one-year-old child, participants were presented with a group of questions that measured worker's assessment of risk, intention, attitude, subjective norm, behavior control and beliefs toward residential care placement decision, as well as worker's behavior experience, emotions and family/child-related-values involved in that decision. A set of structural equation modeling analyses have proven the good fit of the proposed model. The intention to propose a residential care placement decision was determined by cognitive, social, affective, value-laden and experience variables and the perceived risk. Altogether our model explained 61% of professional's decision toward a parental neglect case. The theoretical and practical implications of these results are discussed, namely the importance of raising awareness about the existence of these biased psychosocial determinants.}, } @article {pmid25881700, year = {2015}, author = {Huang, XQ and Li, DD and Wu, J}, title = {[Long non-coding RNAs in plants].}, journal = {Yi chuan = Hereditas}, volume = {37}, number = {4}, pages = {344-359}, doi = {10.16288/j.yczz.14-432}, pmid = {25881700}, issn = {0253-9772}, mesh = {Animals ; Computational Biology ; Humans ; Plants/classification/*genetics/metabolism ; RNA, Long Noncoding/*genetics/metabolism ; RNA, Plant/*genetics/metabolism ; }, abstract = {Long non-coding RNAs (lncRNAs), which are longer than 200 nucleotides in length, widely exist in organisms and function in a variety of biological processes. Currently, most of lncRNAs found in plants are transcribed by RNA polymerase Ⅱ and mediate gene expression through multiple mechanisms, such as target mimicry, transcription interference, histone methylation and DNA methylation, and play important roles in flowering, male sterility, nutrition metabolism, biotic and abiotic stress and other biological processes as regulators in plants. In this review, we summarize the databases, prediction methods, and possible functions of plant lncRNAs discovered in recent years.}, } @article {pmid25881271, year = {2015}, author = {Ma, Y and Xu, T and Wan, D and Ma, T and Shi, S and Liu, J and Hu, Q}, title = {The salinity tolerant poplar database (STPD): a comprehensive database for studying tree salt-tolerant adaption and poplar genomics.}, journal = {BMC genomics}, volume = {16}, number = {1}, pages = {205}, pmid = {25881271}, issn = {1471-2164}, mesh = {Adaptation, Physiological/drug effects ; *Databases, Genetic ; Gene Expression Regulation, Plant/*drug effects ; *Genome, Plant ; Genomics ; Internet ; Populus/*genetics ; Salts/*pharmacology ; Soil/chemistry ; User-Computer Interface ; }, abstract = {BACKGROUND: Soil salinity is a significant factor that impairs plant growth and agricultural productivity, and numerous efforts are underway to enhance salt tolerance of economically important plants. Populus species are widely cultivated for diverse uses. Especially, they grow in different habitats, from salty soil to mesophytic environment, and are therefore used as a model genus for elucidating physiological and molecular mechanisms of stress tolerance in woody plants.

DESCRIPTION: The Salinity Tolerant Poplar Database (STPD) is an integrative database for salt-tolerant poplar genome biology. Currently the STPD contains Populus euphratica genome and its related genetic resources. P. euphratica, with a preference of the salty habitats, has become a valuable genetic resource for the exploitation of tolerance characteristics in trees. This database contains curated data including genomic sequence, genes and gene functional information, non-coding RNA sequences, transposable elements, simple sequence repeats and single nucleotide polymorphisms information of P. euphratica, gene expression data between P. euphratica and Populus tomentosa, and whole-genome alignments between Populus trichocarpa, P. euphratica and Salix suchowensis. The STPD provides useful searching and data mining tools, including GBrowse genome browser, BLAST servers and genome alignments viewer, which can be used to browse genome regions, identify similar sequences and visualize genome alignments. Datasets within the STPD can also be downloaded to perform local searches.

CONCLUSIONS: A new Salinity Tolerant Poplar Database has been developed to assist studies of salt tolerance in trees and poplar genomics. The database will be continuously updated to incorporate new genome-wide data of related poplar species. This database will serve as an infrastructure for researches on the molecular function of genes, comparative genomics, and evolution in closely related species as well as promote advances in molecular breeding within Populus. The STPD can be accessed at http://me.lzu.edu.cn/stpd/ .}, } @article {pmid25880983, year = {2015}, author = {Berens, AJ and Hunt, JH and Toth, AL}, title = {Nourishment level affects caste-related gene expression in Polistes wasps.}, journal = {BMC genomics}, volume = {16}, number = {1}, pages = {235}, pmid = {25880983}, issn = {1471-2164}, mesh = {Animals ; Computational Biology ; *Gene Expression Regulation ; *Genome ; Insect Proteins/genetics ; Larva/genetics/growth & development ; Lipid Metabolism/genetics ; Phenotype ; Reproduction/genetics ; Sequence Analysis, RNA ; Transcriptome ; Up-Regulation ; Wasps/*genetics/growth & development ; }, abstract = {BACKGROUND: Social insects exhibit striking phenotypic plasticity in the form of distinct reproductive (queen) and non-reproductive (worker) castes, which are typically driven by differences in the environment during early development. Nutritional environment and nourishment during development has been shown to be broadly associated with caste determination across social insect taxa such as bees, wasps, and termites. In primitively social insects such as Polistes paper wasps, caste remains flexible throughout adulthood, but there is evidence that nourishment inequalities can bias caste development with workers receiving limited nourishment compared to queens. Dominance and vibrational signaling are behaviors that have also been linked to caste differences in paper wasps, suggesting that a combination of nourishment and social factors may drive caste determination. To better understand the molecular basis of nutritional effects on caste determination, we used RNA-sequencing to investigate the gene expression changes in response to proteinaceous nourishment deprivation in Polistes metricus larvae.

RESULTS: We identified 285 nourishment-responsive transcripts, many of which are related to lipid metabolism and oxidation-reduction activity. Via comparisons to previously identified caste-related genes, we found that nourishment restriction only partially biased wasp gene expression patterns toward worker caste-like traits, which supports the notion that nourishment, in conjunction with social environment, is a determinant of developmental caste bias. In addition, we conducted cross-species comparisons of nourishment-responsive genes, and uncovered largely lineage-specific gene expression changes, suggesting few shared nourishment-responsive genes across taxa.

CONCLUSION: Overall, the results from this study highlight the complex and multifactorial nature of environmental effects on the gene expression patterns underlying plastic phenotypes.}, } @article {pmid25880543, year = {2015}, author = {Wu, AC and Rifkin, SA}, title = {Aro: a machine learning approach to identifying single molecules and estimating classification error in fluorescence microscopy images.}, journal = {BMC bioinformatics}, volume = {16}, number = {}, pages = {102}, pmid = {25880543}, issn = {1471-2105}, support = {P50 GM085764/GM/NIGMS NIH HHS/United States ; R01 GM103782/GM/NIGMS NIH HHS/United States ; R01GM103782/GM/NIGMS NIH HHS/United States ; }, mesh = {Algorithms ; Animals ; Artificial Intelligence ; Caenorhabditis elegans/embryology/*metabolism ; Computational Biology ; Embryo, Nonmammalian/cytology/*metabolism ; Fluorescence ; Fluorescent Dyes/*metabolism ; Image Processing, Computer-Assisted/*methods ; In Situ Hybridization, Fluorescence ; Microscopy, Fluorescence/*methods ; Nanotechnology ; RNA, Messenger/*analysis ; *Software ; Staining and Labeling ; }, abstract = {BACKGROUND: Recent techniques for tagging and visualizing single molecules in fixed or living organisms and cell lines have been revolutionizing our understanding of the spatial and temporal dynamics of fundamental biological processes. However, fluorescence microscopy images are often noisy, and it can be difficult to distinguish a fluorescently labeled single molecule from background speckle.

RESULTS: We present a computational pipeline to distinguish the true signal of fluorescently labeled molecules from background fluorescence and noise. We test our technique using the challenging case of wide-field, epifluorescence microscope image stacks from single molecule fluorescence in situ experiments on nematode embryos where there can be substantial out-of-focus light and structured noise. The software recognizes and classifies individual mRNA spots by measuring several features of local intensity maxima and classifying them with a supervised random forest classifier. A key innovation of this software is that, by estimating the probability that each local maximum is a true spot in a statistically principled way, it makes it possible to estimate the error introduced by image classification. This can be used to assess the quality of the data and to estimate a confidence interval for the molecule count estimate, all of which are important for quantitative interpretations of the results of single-molecule experiments.

CONCLUSIONS: The software classifies spots in these images well, with >95% AUROC on realistic artificial data and outperforms other commonly used techniques on challenging real data. Its interval estimates provide a unique measure of the quality of an image and confidence in the classification.}, } @article {pmid25880385, year = {2015}, author = {Thanapongtharm, W and Linard, C and Wiriyarat, W and Chinsorn, P and Kanchanasaka, B and Xiao, X and Biradar, C and Wallace, RG and Gilbert, M}, title = {Spatial characterization of colonies of the flying fox bat, a carrier of Nipah virus in Thailand.}, journal = {BMC veterinary research}, volume = {11}, number = {}, pages = {81}, pmid = {25880385}, issn = {1746-6148}, support = {R01 AI101028/AI/NIAID NIH HHS/United States ; 1R01AI101028-01A1/AI/NIAID NIH HHS/United States ; }, mesh = {Animal Distribution ; Animals ; Chiroptera/*physiology/virology ; Disease Reservoirs ; Geographic Information Systems ; Henipavirus Infections/epidemiology/*veterinary/virology ; Humans ; Models, Biological ; Nipah Virus/*physiology ; Risk Factors ; Swine ; Swine Diseases/epidemiology/virology ; Thailand/epidemiology ; }, abstract = {BACKGROUND: A major reservoir of Nipah virus is believed to be the flying fox genus Pteropus, a fruit bat distributed across many of the world's tropical and sub-tropical areas. The emergence of the virus and its zoonotic transmission to livestock and humans have been linked to losses in the bat's habitat. Nipah has been identified in a number of indigenous flying fox populations in Thailand. While no evidence of infection in domestic pigs or people has been found to date, pig farming is an active agricultural sector in Thailand and therefore could be a potential pathway for zoonotic disease transmission from the bat reservoirs. The disease, then, represents a potential zoonotic risk. To characterize the spatial habitat of flying fox populations along Thailand's Central Plain, and to map potential contact zones between flying fox habitats, pig farms and human settlements, we conducted field observation, remote sensing, and ecological niche modeling to characterize flying fox colonies and their ecological neighborhoods. A Potential Surface Analysis was applied to map contact zones among local epizootic actors.

RESULTS: Flying fox colonies are found mainly on Thailand's Central Plain, particularly in locations surrounded by bodies of water, vegetation, and safe havens such as Buddhist temples. High-risk areas for Nipah zoonosis in pigs include the agricultural ring around the Bangkok metropolitan region where the density of pig farms is high.

CONCLUSIONS: Passive and active surveillance programs should be prioritized around Bangkok, particularly on farms with low biosecurity, close to water, and/or on which orchards are concomitantly grown. Integration of human and animal health surveillance should be pursued in these same areas. Such proactive planning would help conserve flying fox colonies and should help prevent zoonotic transmission of Nipah and other pathogens.}, } @article {pmid25880302, year = {2015}, author = {Kushwaha, SK and Manoharan, L and Meerupati, T and Hedlund, K and Ahrén, D}, title = {MetCap: a bioinformatics probe design pipeline for large-scale targeted metagenomics.}, journal = {BMC bioinformatics}, volume = {16}, number = {1}, pages = {65}, pmid = {25880302}, issn = {1471-2105}, mesh = {Computational Biology/*methods ; DNA Primers/genetics ; Ecology ; Environment ; *Metagenome ; Metagenomics/*methods ; Sequence Analysis, DNA/methods ; *Software ; Soil/*chemistry ; }, abstract = {BACKGROUND: Massive sequencing of genes from different environments has evolved metagenomics as central to enhancing the understanding of the wide diversity of micro-organisms and their roles in driving ecological processes. Reduced cost and high throughput sequencing has made large-scale projects achievable to a wider group of researchers, though complete metagenome sequencing is still a daunting task in terms of sequencing as well as the downstream bioinformatics analyses. Alternative approaches such as targeted amplicon sequencing requires custom PCR primer generation, and is not scalable to thousands of genes or gene families.

RESULTS: In this study, we are presenting a web-based tool called MetCap that circumvents the limitations of amplicon sequencing of multiple genes by designing probes that are suitable for large-scale targeted metagenomics sequencing studies. MetCap provides a novel approach to target thousands of genes and genomic regions that could be used in targeted metagenomics studies. Automatic analysis of user-defined sequences is performed, and probes specifically designed for metagenome studies are generated. To illustrate the advantage of a targeted metagenome approach, we have generated more than 400,000 probes that match more than 300,000 [corrected] publicly available sequences related to carbon degradation, and used these probes for target sequencing in a soil metagenome study. The results show high enrichment of target genes and a successful capturing of the majority of gene families. MetCap is freely available to users from: http://soilecology.biol.lu.se/metcap/ .

CONCLUSION: MetCap is facilitating probe-based target enrichment as an easy and efficient alternative tool compared to complex primer-based enrichment for large-scale investigations of metagenomes. Our results have shown efficient large-scale target enrichment through MetCap-designed probes for a soil metagenome. The web service is suitable for any targeted metagenomics project that aims to study several genes simultaneously. The novel bioinformatics approach taken by the web service will enable researchers in microbial ecology to tap into the vast diversity of microbial communities using targeted metagenomics as a cost-effective alternative to whole metagenome sequencing.}, } @article {pmid25879720, year = {2015}, author = {Suzuki, T and Miyaki, K and Song, Y and Tsutsumi, A and Kawakami, N and Shimazu, A and Takahashi, M and Inoue, A and Kurioka, S}, title = {Relationship between sickness presenteeism (WHO-HPQ) with depression and sickness absence due to mental disease in a cohort of Japanese workers.}, journal = {Journal of affective disorders}, volume = {180}, number = {}, pages = {14-20}, doi = {10.1016/j.jad.2015.03.034}, pmid = {25879720}, issn = {1573-2517}, mesh = {*Absenteeism ; Adult ; Depression/*epidemiology/psychology ; Female ; Humans ; Japan/epidemiology ; Male ; Mental Disorders/*epidemiology/psychology ; Middle Aged ; Prospective Studies ; Surveys and Questionnaires ; *Workplace ; }, abstract = {BACKGROUND: Absence due to mental disease in the workplace has become a global public health problem. We aimed to evaluate the influence of presenteeism on depression and absence due to mental disease.

METHODS: A prospective study of 1831 Japanese employees from all areas of Japan was conducted. Presenteeism and depression were measured by the validated Japanese version of the World Health Organization Health and Work Performance Questionnaire (WHO-HPQ) and the K6 scale, respectively. Absence due to mental disease across a 2-year follow up was surveyed through medical certificates obtained for work absence.

RESULTS: After adjusting for age and gender, participants with higher rates of sickness absolute and relative presenteeism (the lowest tertile of the scores) were significantly more likely to be absent due to mental disease (OR=4.40, 95% CI: 1.65-11.73, and OR=3.31, 95% CI: 1.50-7.27). Subsequently, higher rates of sickness absolute or relative presenteeism were significantly associated with higher rates of depression (K6≥13) one year later (OR=3.79, 95% CI: 2.48-5.81, and OR=2.89, 95% CI: 1.98-4.22).

LIMITATIONS: The number of females in the sample was relatively small. However, the rates of absence for females with and without mental illness did not significantly differ from those of men.

CONCLUSIONS: More sickness presenteeism scores were found to be related to higher rates of depression and absence due to mental disease in this large-scale cohort of Japanese workers. Measurement of presenteeism could be used to evaluate the risk for depression and absenteeism. Furthermore, our findings suggest that intervention to improve presenteeism would be effective in preventing depression and absence due to mental illness.}, } @article {pmid25879439, year = {2015}, author = {Bik, HM and Dove, AD and Goldstein, MC and Helm, RR and MacPherson, R and Martini, K and Warneke, A and McClain, C}, title = {Ten simple rules for effective online outreach.}, journal = {PLoS computational biology}, volume = {11}, number = {4}, pages = {e1003906}, pmid = {25879439}, issn = {1553-7358}, mesh = {Algorithms ; *Communication ; Information Dissemination/*methods ; Models, Organizational ; Online Systems ; Publishing/*organization & administration ; *Research Design ; Science/*organization & administration ; Social Media/*organization & administration ; }, } @article {pmid25875597, year = {2015}, author = {Bécares, J and García-Tarrasón, M and Villero, D and Bateman, S and Jover, L and García-Matarranz, V and Sanpera, C and Arcos, JM}, title = {Modelling terrestrial and marine foraging habitats in breeding Audouin's gulls Larus audouinii: timing matters.}, journal = {PloS one}, volume = {10}, number = {4}, pages = {e0120799}, pmid = {25875597}, issn = {1932-6203}, mesh = {Animals ; Charadriiformes/*physiology ; Feeding Behavior/*physiology ; Female ; Fisheries ; Fishes ; Food Supply ; Geographic Information Systems/instrumentation ; Human Activities ; Male ; Mediterranean Sea ; *Models, Biological ; Predatory Behavior/*physiology ; Radio Frequency Identification Device ; Seasons ; Sexual Behavior, Animal ; Spain ; Time Factors ; Waste Products ; }, abstract = {Although the breeding ecology of Audouin's gull has been widely studied, its spatial distribution patterns have received little attention. We assessed the foraging movements of 36 GPS-tracked adult Audouin's gulls breeding at the Ebro Delta (NW Mediterranean), coinciding with the incubation period (May 2011). This also coincided with a trawling moratorium northwards from the colony. We modelled the distribution of the gulls by combining these tracking data with environmental variables (including fishing activities from Vessel Monitoring System, VMS), using Maxent. The modelling range included both marine and terrestrial areas. Models were produced separately for every 2h time interval across the day, and for 2 fishing activity scenarios (workdays vs. weekends), allowing to assess the spatio-temporal distribution patterns of the gulls and the degree of association with fisheries. During workdays, gull distribution at sea fully matched with fishing activities, both trawling (daylight) and purse-seining (nightime). Gulls tended to avoid the area under trawling moratorium, confirming the high influence of fisheries on the distribution patterns of this species. On weekends, gulls made lesser use of the sea and tended to increase the use of rice fields. Overall, Audouin's gull activity was more intense during dailight hours, although birds also showed nocturnal activity, on both workdays and weekends. Nocturnal patterns at sea were more disperse during the latter, probably because these gulls are able to capture small pelagic fish at night in natural conditions, but tend to congregate around purse-seiners (which would enhance their foraging efficiency) in workdays. These results provide important insight for the management of this species. This is of particular relevance under the current scenario of European fisheries policies, since new regulations are aimed at eliminating discards, and this would likely influence Audouin's gull populations.}, } @article {pmid25869933, year = {2015}, author = {Wang, Y and Yang, L and Wu, B and Song, Z and He, S}, title = {Transcriptome analysis of the plateau fish (Triplophysa dalaica): Implications for adaptation to hypoxia in fishes.}, journal = {Gene}, volume = {565}, number = {2}, pages = {211-220}, doi = {10.1016/j.gene.2015.04.023}, pmid = {25869933}, issn = {1879-0038}, mesh = {Adaptation, Physiological/*genetics ; Animals ; Cypriniformes/*genetics ; Databases, Genetic ; Fishes/*genetics ; Gene Expression Profiling/methods ; Hypoxia/*genetics ; Microsatellite Repeats/genetics ; Phylogeny ; Polymorphism, Single Nucleotide/genetics ; Transcriptome/*genetics ; }, abstract = {Triplophysa dalaica, endemic species of Qinghai-Tibetan Plateau, is informative for understanding the genetic basis of adaptation to hypoxic conditions of high altitude habitats. Here, a comprehensive gene repertoire for this plateau fish was generated using the Illumina deep paired-end high-throughput sequencing technology. De novo assembly yielded 145, 256 unigenes with an average length of 1632 bp. Blast searches against GenBank non-redundant database annotated 74,594 (51.4%) unigenes encoding for 30,047 gene descriptions in T. dalaica. Functional annotation and classification of assembled sequences were performed using Gene Ontology (GO), clusters of euKaryotic Orthologous Groups (KOG) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis. After comparison with other fish transcriptomes, including silver carp (Hypophthalmichthys molitrix) and mud loach (Misgurnus anguillicaudatus), 2621 high-quality orthologous gene alignments were constructed among these species. 61 (2.3%) of the genes were identified as having undergone positive selection in the T. dalaica lineage. Within the positively selected genes, 13 genes were involved in hypoxia response, of which 11 were listed in HypoxiaDB. Furthermore, duplicated hif-α (hif-1αA/B and hif-2αA/B), EGLN1 and PPARA candidate genes involved in adaptation to hypoxia were identified in T. dalaica transcriptome. Branch-site model in PAML validated that hif-1αB and hif-2αA genes have undergone positive selection in T.dalaica. Finally, 37,501 simple sequence repeats (SSRs) and 19,497 high-quality single nucleotide polymorphisms (SNPs) were identified in T. dalaica. The identified SSR and SNP markers will facilitate the genetic structure, population geography and ecological studies of Triplophysa fishes.}, } @article {pmid25866281, year = {2015}, author = {Stagaman, K and Martinez, ES and Guillemin, K}, title = {Immigrants in immunology: the benefits of lax borders.}, journal = {Trends in immunology}, volume = {36}, number = {5}, pages = {286-289}, pmid = {25866281}, issn = {1471-4981}, support = {P50 GM098911/GM/NIGMS NIH HHS/United States ; 1P50GM098911/GM/NIGMS NIH HHS/United States ; }, mesh = {Allergy and Immunology/*trends ; Computational Biology ; Ecology ; Humans ; *Interdisciplinary Communication ; Microbiology ; Systems Biology ; }, abstract = {The field of immunology has a long history of illuminating fundamental biological processes of critical importance to human health. From an outsider's perspective, the questions are profoundly philosophical and the experimental approaches are elegantly precise. Yet immunology can also appear impenetrable. Here we recount the experience of two graduate students from the fields of ecology and computer science, who have immigrated into immunological terrain attracted by systems-level questions. We argue that such migrations enrich the field of immunology, and that cultural and institutional changes are needed to promote more interdisciplinary explorations.}, } @article {pmid25865627, year = {2015}, author = {Nietlisbach, P and Camenisch, G and Bucher, T and Slate, J and Keller, LF and Postma, E}, title = {A microsatellite-based linkage map for song sparrows (Melospiza melodia).}, journal = {Molecular ecology resources}, volume = {15}, number = {6}, pages = {1486-1496}, doi = {10.1111/1755-0998.12414}, pmid = {25865627}, issn = {1755-0998}, mesh = {Animals ; Canada ; *Chromosome Mapping ; Computational Biology ; Female ; Finches/genetics ; Male ; *Microsatellite Repeats ; Molecular Sequence Data ; Recombination, Genetic ; Sequence Analysis, DNA ; Sparrows/*classification/*genetics ; Synteny ; }, abstract = {Although linkage maps are important tools in evolutionary biology, their availability for wild populations is limited. The population of song sparrows (Melospiza melodia) on Mandarte Island, Canada, is among the more intensively studied wild animal populations. Its long-term pedigree data, together with extensive genetic sampling, have allowed the study of a range of questions in evolutionary biology and ecology. However, the availability of genetic markers has been limited. We here describe 191 new microsatellite loci, including 160 high-quality polymorphic autosomal, 7 Z-linked and 1 W-linked markers. We used these markers to construct a linkage map for song sparrows with a total sex-averaged map length of 1731 cM and covering 35 linkage groups, and hence, these markers cover most of the 38-40 chromosomes. Female and male map lengths did not differ significantly. We then bioinformatically mapped these loci to the zebra finch (Taeniopygia guttata) genome and found that linkage groups were conserved between song sparrows and zebra finches. Compared to the zebra finch, marker order within small linkage groups was well conserved, whereas the larger linkage groups showed some intrachromosomal rearrangements. Finally, we show that as expected, recombination frequency between linked loci explained the majority of variation in gametic phase disequilibrium. Yet, there was substantial overlap in gametic phase disequilibrium between pairs of linked and unlinked loci. Given that the microsatellites described here lie on 35 of the 38-40 chromosomes, these markers will be useful for studies in this species, as well as for comparative genomics studies with other species.}, } @article {pmid25865625, year = {2015}, author = {Mikkelsen, SS and Panzarin, V and Jonstrup, SP and Bigarré, L and Baud, M and Gray, T and Agapow, PM and Olesen, NJ}, title = {Fishpathogens.eu/noda: a free and handy online platform for Betanodavirus targeted research and data sharing.}, journal = {Journal of fish diseases}, volume = {38}, number = {8}, pages = {755-760}, doi = {10.1111/jfd.12378}, pmid = {25865625}, issn = {1365-2761}, mesh = {Animals ; Fish Diseases/*virology ; Fishes ; Information Dissemination/*methods ; Nodaviridae/*physiology ; *Online Systems/economics ; RNA Virus Infections/*veterinary/virology ; Research/trends ; }, abstract = {Viral nervous necrosis (VNN) is a severe neuropathological disease affecting a broad variety of finfish species worldwide. The causative agents of VNN are small viruses with a bi-segmented RNA genome known as betanodaviruses. At least four species with distinct but yet insufficiently characterized epidemiological features are recognized. The spread of VNN to an increasing number of host species, its wide geographic extent and its economical and ecological impacts justify the importance of collating as much molecular data as possible for tracing the origin of viral isolates and highlight the need for a freely accessible tool for epidemiological and molecular data sharing and consultation. For this purpose, we established a web-based specific database using the www.fishpathogens.eu platform, with the aim of collecting molecular and epidemiological information on VNN viruses, with relevance to their control, management and research studies.}, } @article {pmid25864941, year = {2015}, author = {Mahboubi, P and Parkes, M and Stephen, C and Chan, HM}, title = {Using expert informed GIS to locate important marine social-ecological hotspots.}, journal = {Journal of environmental management}, volume = {160}, number = {}, pages = {342-352}, doi = {10.1016/j.jenvman.2015.03.055}, pmid = {25864941}, issn = {1095-8630}, mesh = {*Biodiversity ; British Columbia ; Ecology ; *Geographic Information Systems ; Humans ; *Marine Biology ; }, abstract = {The marine environment provides significant benefits to many local communities. Pressure to develop coastal waterways worldwide creates an urgent need for tools to locate marine spaces that have important social or ecological values, and to quantify their relative importance. The primary objective of this study was to develop, apply and critically assess a tool to identify important social-ecological hotspots in the marine environment. The study was conducted in a typical coastal community in northern British Columbia, Canada. This expert-informed GIS, or xGIS, tool used a survey instrument to draw on the knowledge of local experts from a range of backgrounds with respect to a series of 12 social-ecological value attributes, such as biodiversity, cultural and economic values. We identified approximately 1500 polygons on marine maps and assigned relative values to them using a token distribution exercise. A series of spatial statistical analyses were performed to locate and quantify the relative social-ecological importance of marine spaces and the results were ultimately summarized in a single hotspot map of the entire study area. This study demonstrates the utility of xGIS as a useful tool for stakeholders and environmental managers engaged in the planning and management of marine resources at the local and regional levels.}, } @article {pmid25864439, year = {2015}, author = {Roux, J and Rosikiewicz, M and Robinson-Rechavi, M}, title = {What to compare and how: Comparative transcriptomics for Evo-Devo.}, journal = {Journal of experimental zoology. Part B, Molecular and developmental evolution}, volume = {324}, number = {4}, pages = {372-382}, pmid = {25864439}, issn = {1552-5015}, mesh = {Anatomy, Comparative ; Animals ; *Biological Evolution ; Computational Biology ; Gene Expression ; Genetic Research ; Growth and Development/*genetics ; Species Specificity ; *Transcriptome ; }, abstract = {Evolutionary developmental biology has grown historically from the capacity to relate patterns of evolution in anatomy to patterns of evolution of expression of specific genes, whether between very distantly related species, or very closely related species or populations. Scaling up such studies by taking advantage of modern transcriptomics brings promising improvements, allowing us to estimate the overall impact and molecular mechanisms of convergence, constraint or innovation in anatomy and development. But it also presents major challenges, including the computational definitions of anatomical homology and of organ function, the criteria for the comparison of developmental stages, the annotation of transcriptomics data to proper anatomical and developmental terms, and the statistical methods to compare transcriptomic data between species to highlight significant conservation or changes. In this article, we review these challenges, and the ongoing efforts to address them, which are emerging from bioinformatics work on ontologies, evolutionary statistics, and data curation, with a focus on their implementation in the context of the development of our database Bgee (http://bgee.org).}, } @article {pmid25864002, year = {2015}, author = {Ki, SJ and Ray, C and Hantush, MM}, title = {Applying a statewide geospatial leaching tool for assessing soil vulnerability ratings for agrochemicals across the contiguous United States.}, journal = {Water research}, volume = {77}, number = {}, pages = {107-118}, doi = {10.1016/j.watres.2015.03.009}, pmid = {25864002}, issn = {1879-2448}, mesh = {Agrochemicals/chemistry ; *Environmental Pollution ; Geographic Information Systems ; Groundwater/chemistry ; Hydrology ; Pesticides/*chemistry ; Risk Assessment ; Software ; Soil/classification ; United States ; Water Pollutants, Chemical/*chemistry ; Water Pollution, Chemical/*prevention & control ; }, abstract = {A large-scale leaching assessment tool not only illustrates soil (or groundwater) vulnerability in unmonitored areas, but also can identify areas of potential concern for agrochemical contamination. This study describes the methodology of how the statewide leaching tool in Hawaii modified recently for use with pesticides and volatile organic compounds can be extended to the national assessment of soil vulnerability ratings. For this study, the tool was updated by extending the soil and recharge maps to cover the lower 48 states in the United States (US). In addition, digital maps of annual pesticide use (at a national scale) as well as detailed soil properties and monthly recharge rates (at high spatial and temporal resolutions) were used to examine variations in the leaching (loads) of pesticides for the upper soil horizons. Results showed that the extended tool successfully delineated areas of high to low vulnerability to selected pesticides. The leaching potential was high for picloram, medium for simazine, and low to negligible for 2,4-D and glyphosate. The mass loadings of picloram moving below 0.5 m depth increased greatly in northwestern and central US that recorded its extensive use in agricultural crops. However, in addition to the amount of pesticide used, annual leaching load of atrazine was also affected by other factors that determined the intrinsic aquifer vulnerability such as soil and recharge properties. Spatial and temporal resolutions of digital maps had a great effect on the leaching potential of pesticides, requiring a trade-off between data availability and accuracy. Potential applications of this tool include the rapid, large-scale vulnerability assessments for emerging contaminants which are hard to quantify directly through vadose zone models due to lack of full environmental data.}, } @article {pmid25863721, year = {2015}, author = {Hinton, TG and Byrne, ME and Webster, S and Beasley, JC}, title = {Quantifying the spatial and temporal variation in dose from external exposure to radiation: a new tool for use on free-ranging wildlife.}, journal = {Journal of environmental radioactivity}, volume = {145}, number = {}, pages = {58-65}, doi = {10.1016/j.jenvrad.2015.03.027}, pmid = {25863721}, issn = {1879-1700}, mesh = {Animals ; Geographic Information Systems/*instrumentation ; Radiation Monitoring/instrumentation/*methods ; South Carolina ; *Sus scrofa ; }, abstract = {Inadequate dosimetry is often the fundamental problem in much of the controversial research dealing with radiation effects on free-ranging wildlife. Such research is difficult because of the need to measure dose from several potential pathways of exposure (i.e., internal contamination, external irradiation, and inhalation). Difficulties in quantifying external exposures can contribute significantly to the uncertainties of dose-effect relationships. Quantifying an animal's external exposure due to spatial-temporal use of habitats that can vary by orders of magnitude in radiation levels is particularly challenging. Historically, wildlife dosimetry studies have largely ignored or been unable to accurately quantify variability in external dose because of technological limitations. The difficulties of quantifying the temporal-spatial aspects of external irradiation prompted us to develop a new dosimetry instrument for field research. We merged two existing technologies [Global Positioning Systems (GPS) and electronic dosimeters] to accommodate the restrictive conditions of having a combined unit small enough to be unobtrusively worn on the neck of a free-ranging animal, and sufficiently robust to withstand harsh environmental conditions. The GPS-dosimeter quantifies the spatial and temporal variation in external dose as wildlife traverse radioactively contaminated habitats and sends, via satellites, an animal's location and short term integrated dose to the researcher at a user-defined interval. Herein we describe: (1) the GPS-dosimeters; (2) tests to compare their uniformity of response to external irradiation under laboratory conditions; (3) field tests of their durability when worn on wildlife under natural conditions; and (4) a field application of the new technology at a radioactively contaminated site. Use of coupled GPS-dosimetry will allow, for the first time, researchers to better understand the relationship of animals to their contaminated habitats and better assess animal responses to the stress of radiological exposures.}, } @article {pmid25863354, year = {2015}, author = {Iyer, R and Smith, K and Kudrle, B and Leon, A}, title = {Detection and location of OP-degrading activity: A model to integrate education and research.}, journal = {New biotechnology}, volume = {32}, number = {4}, pages = {403-411}, doi = {10.1016/j.nbt.2015.03.010}, pmid = {25863354}, issn = {1876-4347}, mesh = {Biodegradation, Environmental ; Databases as Topic ; Hydrolysis ; *Models, Theoretical ; Organophosphates/*metabolism ; *Research ; Soil ; }, abstract = {The Environmental Sampling Research Module (ESRM) is an investigative/discovery module that provides undergraduate research experiences for students as part of an interdisciplinary research-based biotechnology curriculum at the University of Houston campus. As part of the ESRM, students collect soil samples from various locations to test for the presence of organophosphorous (OP) degrading bacteria. At the end of this research project students submit a research paper on their field and laboratory activities and discuss their experimental data and observations. Students also record the date, location of collection, and the results of testing the sample for the degradation of two pesticides, methyl parathion or paraoxon, in an electronic laboratory notebook (ELN). Each collection site is recorded on a Google Maps module and the data from student research activities is made available to other undergraduate students. This data is then used to generate a microorganism database of pesticide degrading activity and promote reading, critical thinking, and analytical skills as part of the curriculum. Our sampling of agricultural sites and wastewater within and around the city of Houston has identified seven distinct genera of OP degrading organisms, including Pseudomonas, Stenotrophomonas, Exiguobacterium, Delftia, Agrobacterium, Aeromonas, and Rhizobium. Collected strains exhibit phosphotriesterase-like enzymatic activity with isolates of Pseudomonas putida and Stenotrophomonas maltophilia capable of degrading both the phosphotriester paraoxon and the phosphorothioate methyl parathion. Using this collection of OP-degrading microorganisms, undergraduate students have evaluated their potential for enhancing the removal of harmful organophosphates and their toxic metabolites from contaminated agricultural soil and adjacent bodies of water. This analytical data can potentially be utilized for environmental and industrial applications in bioremediation and ecology providing an innovative method for integrating education and research. In addition, the versatility of the ESRM itself provides for easy and rapid adaptation into varying environmental science courses with significant potential for the discovery and isolation of new and unique organisms to be used as part of ongoing research in the laboratory.}, } @article {pmid25863290, year = {2015}, author = {Ramos, AA and Weydmann, A and Cox, CJ and Canário, AV and Serrão, EA and Pearson, GA}, title = {A transcriptome resource for the copepod Calanus glacialis across a range of culture temperatures.}, journal = {Marine genomics}, volume = {23}, number = {}, pages = {27-29}, doi = {10.1016/j.margen.2015.03.014}, pmid = {25863290}, issn = {1876-7478}, mesh = {Animals ; Computational Biology ; Copepoda/*genetics ; Gene Expression Regulation/*physiology ; *Temperature ; *Transcriptome ; }, abstract = {The copepod Calanus glacialis plays a key role in the Arctic pelagic ecosystem. Despite its ecological importance and ongoing climate changes, limited knowledge at the genomic level has hindered the understanding of the molecular processes underlying environmental stress responses and ecological adaptation. Transcriptome data was generated from an experiment with C. glacialis copepodite (CV) subjected to five different temperatures. We obtained a total of 512,352 high-quality 454 pyrosequencing reads, which were assembled into 55,562 contigs distributed in 128 KEGG pathways. Functional analysis revealed numerous genes related to diverse biological functions and processes, including members of all major conserved signaling pathways. Comparative analysis of acclimated individuals to experimental temperatures has provided information about gene variations observed in several pathways (e.g. genes involved in energy, lipid and amino acid metabolism were shown to be down-regulated with increasing temperatures). These mRNA sequence resources will facilitate further studies on genomics and physiology-driven molecular processes in C. glacialis and related species.}, } @article {pmid25861871, year = {2015}, author = {Graham, JC and Dettlaff, AJ and Baumann, DJ and Fluke, JD}, title = {The Decision Making Ecology of placing a child into foster care: A structural equation model.}, journal = {Child abuse & neglect}, volume = {49}, number = {}, pages = {12-23}, doi = {10.1016/j.chiabu.2015.02.020}, pmid = {25861871}, issn = {1873-7757}, mesh = {Adult ; Aged ; Child ; *Child Welfare ; *Decision Making ; *Decision Support Techniques ; Female ; Foster Home Care/*methods ; Humans ; Male ; Middle Aged ; *Models, Theoretical ; Risk Factors ; Social Workers ; Texas ; Young Adult ; }, abstract = {The Decision Making Ecology provided a framework for empirically testing the impact of Case, Caseworker and Organizational factors on the decision to place children in out-of-home care. The structural equation model we developed fit the data extremely well, indicating a complex relationship between the variables. The main findings indicate that Case factors, even as aggregated to the worker level, were of most importance: Percent Removed was increased in part by greater average Risk being assessed and more families on a worker's caseload being Low Income. Furthermore, removal rates were increased by lower proportions of Hispanic families on the caseload, as well as lower organizational support, and a perception of manageable workload and sufficient resources. Individual factors, i.e., variables characterizing the caseworkers themselves, were not found to directly influence the placement decision, including workers' own race/ethnicity, though various orders of mediated effects were indicated, and these are detailed. Interrelationships between variables that affect case, caseworker and organizational factors are discussed along with implications for practice.}, } @article {pmid25860872, year = {2015}, author = {Lin, YL and Ma, LT and Lee, YR and Lin, SS and Wang, SY and Chang, TT and Shaw, JF and Li, WH and Chu, FH}, title = {MicroRNA-like small RNAs prediction in the development of Antrodia cinnamomea.}, journal = {PloS one}, volume = {10}, number = {4}, pages = {e0123245}, pmid = {25860872}, issn = {1932-6203}, mesh = {Antrodia/*genetics/*growth & development/metabolism ; Base Sequence ; Gene Expression Profiling ; Gene Expression Regulation, Developmental ; Gene Expression Regulation, Fungal ; Gene Ontology ; Genome, Fungal ; High-Throughput Nucleotide Sequencing ; MicroRNAs/chemistry/*genetics ; Molecular Sequence Data ; Nucleic Acid Conformation ; RNA, Fungal/chemistry/*genetics ; }, abstract = {Antrodia cinnamomea, a precious, host-specific brown-rot fungus that has been used as a folk medicine in Taiwan for centuries is known to have diverse bioactive compounds with potent pharmaceutical activity. In this study, different fermentation states of A. cinnamomea (wild-type fruiting bodies and liquid cultured mycelium) were sequenced using the next-generation sequencing (NGS) technique. A 45.58 Mb genome encoding 6,522 predicted genes was obtained. High quality reads were assembled into a total of 13,109 unigenes. Using a previously constructed pipeline to search for microRNAs (miRNAs), we then identified 4 predicted conserved miRNA and 63 novel predicted miRNA-like small RNA (milRNA) candidates. Target prediction revealed several interesting proteins involved in tri-terpenoid synthesis, mating type recognition, chemical or physical sensory protein and transporters predicted to be regulated by the miRNAs and milRNAs.}, } @article {pmid25859127, year = {2015}, author = {Mitroiu, MD and Noyes, J and Cetkovic, A and Nonveiller, G and Radchenko, A and Polaszek, A and Ronquist, F and Forshage, M and Pagliano, G and Gusenleitner, J and Bartalucci, MB and Olmi, M and Fusu, L and Madl, M and Johnson, NF and Jansta, P and Wahis, R and Soon, V and Rosa, P and Osten, T and Barbier, Y and de Jong, Y}, title = {Fauna Europaea: Hymenoptera - Apocrita (excl. Ichneumonoidea).}, journal = {Biodiversity data journal}, volume = {}, number = {3}, pages = {e4186}, pmid = {25859127}, issn = {1314-2828}, abstract = {Fauna Europaea provides a public web-service with an index of scientific names (including important synonyms) of all living European land and freshwater animals, their geographical distribution at country level (up to the Urals, excluding the Caucasus region), and some additional information. The Fauna Europaea project covers about 230,000 taxonomic names, including 130,000 accepted species and 14,000 accepted subspecies. This represents a huge effort by more than 400 contributing specialists throughout Europe and is a unique (standard) reference suitable for many users in science, government, industry, nature conservation and education. Hymenoptera is one of the four largest orders of insects, with about 130,000 described species. In the Fauna Europaea database, 'Hymenoptera - Apocrita (excluding Ichneumonoidea)' comprises 13 superfamilies, 52 families, 91 subfamilies, 38 tribes and 13,211 species. The paper includes a complete list of taxa dealt with, the number of species in each and the name of the specialist responsible for data acquisition. As a general conclusion about the European fauna of Hymenoptera, the best known countries in terms of recorded species are those from northwestern Europe, with the least known fauna probably in the more eastern and southeastern parts of Europe.}, } @article {pmid25858475, year = {2015}, author = {Costello, MJ and Vanhoorne, B and Appeltans, W}, title = {Conservation of biodiversity through taxonomy, data publication, and collaborative infrastructures.}, journal = {Conservation biology : the journal of the Society for Conservation Biology}, volume = {29}, number = {4}, pages = {1094-1099}, doi = {10.1111/cobi.12496}, pmid = {25858475}, issn = {1523-1739}, mesh = {*Biodiversity ; *Classification ; Conservation of Natural Resources/*methods ; Cooperative Behavior ; *Databases, Factual ; *Publishing ; }, abstract = {Taxonomy is the foundation of biodiversity science because it furthers discovery of new species. Globally, there have never been so many people involved in naming species new to science. The number of new marine species described per decade has never been greater. Nevertheless, it is estimated that tens of thousands of marine species, and hundreds of thousands of terrestrial species, are yet to be discovered; many of which may already be in specimen collections. However, naming species is only a first step in documenting knowledge about their biology, biogeography, and ecology. Considering the threats to biodiversity, new knowledge of existing species and discovery of undescribed species and their subsequent study are urgently required. To accelerate this research, we recommend, and cite examples of, more and better communication: use of collaborative online databases; easier access to knowledge and specimens; production of taxonomic revisions and species identification guides; engagement of nonspecialists; and international collaboration. "Data-sharing" should be abandoned in favor of mandated data publication by the conservation science community. Such a step requires support from peer reviewers, editors, journals, and conservation organizations. Online data publication infrastructures (e.g., Global Biodiversity Information Facility, Ocean Biogeographic Information System) illustrate gaps in biodiversity sampling and may provide common ground for long-term international collaboration between scientists and conservation organizations.}, } @article {pmid25854193, year = {2015}, author = {Rico, A and Van den Brink, PJ}, title = {Evaluating aquatic invertebrate vulnerability to insecticides based on intrinsic sensitivity, biological traits, and toxic mode of action.}, journal = {Environmental toxicology and chemistry}, volume = {34}, number = {8}, pages = {1907-1917}, doi = {10.1002/etc.3008}, pmid = {25854193}, issn = {1552-8618}, mesh = {Animals ; Arthropods/drug effects/physiology ; Chloride Channels/antagonists & inhibitors/metabolism ; Cholinesterases/chemistry/metabolism ; Databases, Factual ; Ecosystem ; Insecticides/*toxicity ; Invertebrates/*drug effects/physiology ; Linear Models ; Motor Activity/drug effects ; Risk Assessment ; Sodium Channels/chemistry/metabolism ; }, abstract = {In the present study, the authors evaluated the vulnerability of aquatic invertebrates to insecticides based on their intrinsic sensitivity and their population-level recovery potential. The relative sensitivity of invertebrates to 5 different classes of insecticides was calculated at the genus, family, and order levels using the acute toxicity data available in the US Environmental Protection Agency ECOTOX database. Biological trait information was linked to the calculated relative sensitivity to evaluate correlations between traits and sensitivity and to calculate a vulnerability index, which combines intrinsic sensitivity and traits describing the recovery potential of populations partially exposed to insecticides (e.g., voltinism, flying strength, occurrence in drift). The analysis shows that the relative sensitivity of arthropods depends on the insecticide mode of action. Traits such as degree of sclerotization, size, and respiration type showed good correlation to sensitivity and can be used to make predictions for invertebrate taxa without a priori sensitivity knowledge. The vulnerability analysis revealed that some of the Ephemeroptera, Plecoptera, and Trichoptera taxa were vulnerable to all insecticide classes and indicated that particular gastropod and bivalve species were potentially vulnerable. Microcrustaceans (e.g., daphnids, copepods) showed low potential vulnerability, particularly in lentic ecosystems. The methods described in the present study can be used for the selection of focal species to be included as part of ecological scenarios and higher tier risk assessments.}, } @article {pmid25849620, year = {2015}, author = {White, RL and Bennett, PM}, title = {Elevational distribution and extinction risk in birds.}, journal = {PloS one}, volume = {10}, number = {4}, pages = {e0121849}, pmid = {25849620}, issn = {1932-6203}, mesh = {Animals ; *Biodiversity ; Birds/classification/*physiology ; *Databases, Factual ; *Extinction, Biological ; Humans ; *Phylogeny ; Population Dynamics ; }, abstract = {Mountainous regions are hotspots of terrestrial biodiversity. Unlike islands, which have been the focus of extensive research on extinction dynamics, fewer studies have examined mountain ranges even though they face increasing threats from human pressures - notably habitat conversion and climate change. Limits to the taxonomic and geographical extent and resolution of previously available information have precluded an explicit assessment of the relative role of elevational distribution in determining extinction risk. We use a new global species-level avian database to quantify the influence of elevational distribution (range, maximum and midpoint) on extinction risk in birds at the global scale. We also tested this relationship within biogeographic realms, higher taxonomic levels, and across phylogenetic contrasts. Potential confounding variables (i.e. phylogenetic, distributional, morphological, life history and niche breadth) were also tested and controlled for. We show that the three measures of elevational distribution are strong negative predictors of avian extinction risk, with elevational range comparable and complementary to that of geographical range size. Extinction risk was also found to be positively associated with body weight, development and adult survival, but negatively associated with reproduction and niche breadth. The robust and consistent findings from this study demonstrate the importance of elevational distribution as a key driver of variation in extinction dynamics in birds. Our results also highlight elevational distribution as a missing criterion in current schemes for quantifying extinction risk and setting species conservation priorities in birds. Further research is recommended to test for generality across non-avian taxa, which will require an advance in our knowledge of species' current elevational ranges and increased efforts to digitise and centralise such data.}, } @article {pmid25849349, year = {2015}, author = {Lepora, NF and Pezzulo, G}, title = {Embodied choice: how action influences perceptual decision making.}, journal = {PLoS computational biology}, volume = {11}, number = {4}, pages = {e1004110}, pmid = {25849349}, issn = {1553-7358}, mesh = {Animals ; Choice Behavior/*physiology ; Decision Making/physiology ; *Decision Support Techniques ; Ecosystem ; Mice ; *Models, Neurological ; Motivation/*physiology ; Perception/*physiology ; *Task Performance and Analysis ; }, abstract = {Embodied Choice considers action performance as a proper part of the decision making process rather than merely as a means to report the decision. The central statement of embodied choice is the existence of bidirectional influences between action and decisions. This implies that for a decision expressed by an action, the action dynamics and its constraints (e.g. current trajectory and kinematics) influence the decision making process. Here we use a perceptual decision making task to compare three types of model: a serial decision-then-action model, a parallel decision-and-action model, and an embodied choice model where the action feeds back into the decision making. The embodied model incorporates two key mechanisms that together are lacking in the other models: action preparation and commitment. First, action preparation strategies alleviate delays in enacting a choice but also modify decision termination. Second, action dynamics change the prospects and create a commitment effect to the initially preferred choice. Our results show that these two mechanisms make embodied choice models better suited to combine decision and action appropriately to achieve suitably fast and accurate responses, as usually required in ecologically valid situations. Moreover, embodied choice models with these mechanisms give a better account of trajectory tracking experiments during decision making. In conclusion, the embodied choice framework offers a combined theory of decision and action that gives a clear case that embodied phenomena such as the dynamics of actions can have a causal influence on central cognition.}, } @article {pmid25848894, year = {2015}, author = {Bárta, J and Stone, JD and Pech, J and Sirová, D and Adamec, L and Campbell, MA and Štorchová, H}, title = {The transcriptome of Utricularia vulgaris, a rootless plant with minimalist genome, reveals extreme alternative splicing and only moderate sequence similarity with Utricularia gibba.}, journal = {BMC plant biology}, volume = {15}, number = {}, pages = {78}, pmid = {25848894}, issn = {1471-2229}, mesh = {Alternative Splicing/*genetics ; DNA Primers/metabolism ; Gene Ontology ; Genes, Plant ; *Genome, Plant ; Magnoliopsida/*genetics ; Molecular Sequence Annotation ; Organ Specificity/genetics ; Phylogeny ; Plant Roots/genetics ; Polymerase Chain Reaction ; *Sequence Homology, Nucleic Acid ; Transcriptome/*genetics ; }, abstract = {BACKGROUND: The species of Utricularia attract attention not only owing to their carnivorous lifestyle, but also due to an elevated substitution rate and a dynamic evolution of genome size leading to its dramatic reduction. To better understand the evolutionary dynamics of genome size and content as well as the great physiological plasticity in this mostly aquatic carnivorous genus, we analyzed the transcriptome of Utricularia vulgaris, a temperate species with well characterized physiology and ecology. We compared its transcriptome, namely gene content and overall transcript profile, with a previously described transcriptome of Utricularia gibba, a congener possessing one of the smallest angiosperm genomes.

RESULTS: We sequenced a normalized cDNA library prepared from total RNA extracted from shoots of U. vulgaris including leaves and traps, cultivated under sterile or outdoor conditions. 454 pyrosequencing resulted in more than 1,400,000 reads which were assembled into 41,407 isotigs in 19,522 isogroups. We observed high transcript variation in several isogroups explained by multiple loci and/or alternative splicing. The comparison of U. vulgaris and U. gibba transcriptomes revealed a similar distribution of GO categories among expressed genes, despite the differences in transcriptome preparation. We also found a strong correspondence in the presence or absence of root-associated genes between the U. vulgaris transcriptome and U. gibba genome, which indicated that the loss of some root-specific genes had occurred before the divergence of the two rootless species.

CONCLUSIONS: The species-rich genus Utricularia offers a unique opportunity to study adaptations related to the environment and carnivorous habit and also evolutionary processes responsible for considerable genome reduction. We show that a transcriptome may approximate the genome for gene content or gene duplication estimation. Our study is the first comparison of two global sequence data sets in Utricularia.}, } @article {pmid25847874, year = {2015}, author = {Yang, H and Li, S and Li, F and Wen, R and Xiang, J}, title = {Analysis on the expression and function of syndecan in the Pacific white shrimp Litopenaeus vannamei.}, journal = {Developmental and comparative immunology}, volume = {51}, number = {2}, pages = {278-286}, doi = {10.1016/j.dci.2015.03.013}, pmid = {25847874}, issn = {1879-0089}, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Cell Membrane/immunology/*metabolism ; Cloning, Molecular ; Computational Biology ; DNA Virus Infections/*immunology ; Hemocytes/immunology/*metabolism ; Immunity ; Molecular Sequence Data ; Penaeidae/*immunology ; RNA, Small Interfering/genetics ; Syndecans/genetics/*metabolism ; Up-Regulation ; White spot syndrome virus 1/*immunology ; }, abstract = {Syndecan is considered to be a multifunctional protein which functions as a cell surface receptor involved in cell adhesion, migration, cytoskeleton organization and differentiation. Previous bioinformatic analysis has revealed that syndecan in shrimp might interact with white spot syndrome virus (WSSV). In the present study, we experimentally studied the function of syndecan in shrimp immunity. The syndecan from Litopenaeus vannamei (LvSDC) was cloned and analyzed. The full-length cDNA of LvSDC was 1005 bp, consisting of 59 bp 5'-UTR, 253 bp 3'-UTR, and 693 bp open reading frame encoding 230 amino acids. LvSDC consisted of an extracellular domain (ED), a transmembrane domain (TM) and a cytoplasmic domain (CD). TM and CD shared high similarities with those of syndecan proteins from other species. LvSDC was ubiquitously expressed in all tested tissues, with the highest level in Oka. After WSSV challenge, the transcription level of LvSDC in Oka was apparently up-regulated. Recombinant LvSDC protein and its rabbit polyclonal antibody were prepared for detecting the location of LvSDC in hemocytes using immunocytochemistry approach. Data showed that LvSDC mainly located at the cell membrane and the cytoplasm of hemocytes. After silencing of LvSDC with siRNA, the WSSV copy numbers and mortality of shrimp after WSSV infection were both significantly decreased. These data provide useful information for understanding the immune mechanism of shrimp to WSSV infection.}, } @article {pmid25842383, year = {2015}, author = {Trapp, GS and Hickling, S and Christian, HE and Bull, F and Timperio, AF and Boruff, B and Shrestha, D and Giles-Corti, B}, title = {Individual, Social, and Environmental Correlates of Healthy and Unhealthy Eating.}, journal = {Health education & behavior : the official publication of the Society for Public Health Education}, volume = {42}, number = {6}, pages = {759-768}, doi = {10.1177/1090198115578750}, pmid = {25842383}, issn = {1552-6127}, mesh = {Adult ; Aged ; Aged, 80 and over ; Australia ; *Environment ; *Feeding Behavior/psychology ; Female ; Food Preferences ; Fruit ; Geographic Information Systems ; Health Behavior ; Humans ; Male ; Middle Aged ; Nutrition Policy ; Socioeconomic Factors ; Vegetables ; }, abstract = {BACKGROUND: Few studies use comprehensive ecological approaches considering multilevel factors to understand correlates of healthy (and unhealthy) dietary intake. The aim of this study was to examine the association between individual, social, and environmental factors on composite measures of healthy and unhealthy dietary intake in adults.

METHOD: Participants (n = 565) of the Australian RESIDential Environments (RESIDE) project self-reported dietary intake, home food availability, and behavioral and perceived social and physical environmental influences on food choices. A geographic information system measured proximity of supermarkets from each participant's home. "Healthy" and "unhealthy" eating scores were computed based on adherence to dietary guidelines. Univariate and multivariate models were constructed using linear regression.

RESULTS: After full adjustment, "healthy" eating (mean = 6.25, standard deviation [SD] = 1.95) was significantly associated with having confidence to prepare healthy meals (β = 0.34; 95% confidence interval [CI] = [0.13, 0.55]); having more healthy (β = 0.13; 95% CI = [0.09-0.16]) and fewer unhealthy (β = -0.04; 95% CI = [-0.06, -0.02]) foods available at home; and having a supermarket within 800 meters of home (β = 1.39; 95% CI = [0.37, 2.404]). "Unhealthy" eating (mean = 3.53, SD = 2.06) was associated with being male (β = 0.39; 95% CI = [0.02, 0.75]), frequently eating takeaway (β = 0.33; 95% CI = [0.21, 0.46]) and cafe or restaurant meals (β = 0.20; 95% CI = [0.06, 0.33]) and having fewer healthy (β = -0.07; 95% CI = [-0.10, -0.03]) and more unhealthy (β = 0.09; 95% CI = [0.07, 0.10]) foods available within the home.

CONCLUSION: Initiatives to improve adherence to dietary guidelines and reduce the consumption of unhealthy foods needs to be multifaceted; addressing individual factors and access to healthy food choices in both the home and neighborhood food environment. Ensuring proximity to local supermarkets, particularly in new suburban developments, appears to be an important strategy for facilitating healthy eating.}, } @article {pmid25842007, year = {2015}, author = {Imangaliyev, S and Keijser, B and Crielaard, W and Tsivtsivadze, E}, title = {Personalized microbial network inference via co-regularized spectral clustering.}, journal = {Methods (San Diego, Calif.)}, volume = {83}, number = {}, pages = {28-35}, doi = {10.1016/j.ymeth.2015.03.017}, pmid = {25842007}, issn = {1095-9130}, mesh = {Algorithms ; *Cluster Analysis ; Computational Biology/*methods ; Humans ; *Microbial Consortia ; Microbiota/*genetics ; }, abstract = {We use Human Microbiome Project (HMP) cohort (Peterson et al., 2009) to infer personalized oral microbial networks of healthy individuals. To determine clustering of individuals with similar microbial profiles, co-regularized spectral clustering algorithm is applied to the dataset. For each cluster we discovered, we compute co-occurrence relationships among the microbial species that determine microbial network per cluster of individuals. The results of our study suggest that there are several differences in microbial interactions on personalized network level in healthy oral samples acquired from various niches. Based on the results of co-regularized spectral clustering we discover two groups of individuals with different topology of their microbial interaction network. The results of microbial network inference suggest that niche-wise interactions are different in these two groups. Our study shows that healthy individuals have different microbial clusters according to their oral microbiota. Such personalized microbial networks open a better understanding of the microbial ecology of healthy oral cavities and new possibilities for future targeted medication. The scripts written in scientific Python and in Matlab, which were used for network visualization, are provided for download on the website http://learning-machines.com/.}, } @article {pmid25841066, year = {2015}, author = {Callegaro, S and Minetto, D and Pojana, G and Bilanicová, D and Libralato, G and Volpi Ghirardini, A and Hassellöv, M and Marcomini, A}, title = {Effects of alginate on stability and ecotoxicity of nano-TiO2 in artificial seawater.}, journal = {Ecotoxicology and environmental safety}, volume = {117}, number = {}, pages = {107-114}, doi = {10.1016/j.ecoenv.2015.03.030}, pmid = {25841066}, issn = {1090-2414}, mesh = {Alginates/chemistry/*toxicity ; Animals ; Artemia ; Diatoms ; Ecotoxicology/*methods ; Glucuronic Acid/chemistry/toxicity ; Hexuronic Acids/chemistry/toxicity ; Nanoparticles/*toxicity ; Seawater ; Suspensions/chemistry ; Titanium/*toxicity ; Toxicity Tests/*methods ; }, abstract = {The large-scale use of titanium dioxide nanoparticles (nano-TiO2) in consumer and industrial applications raised environmental health and safety concerns. Potentially impacted ecosystems include estuarine and coastal organisms. Results from ecotoxicological studies with nano-TiO2 dispersed in salt exposure media are difficult to interpret due to fast flocculation and sedimentation phenomena affecting the dispersion stability. The goal of this study was to investigate the stabilisation effect of alginate on uncoated nano-Ti22 in artificial seawater dispersions used in ecotoxicity bioassays. The most effective stabilisation was obtained at alginate concentration of 0.45 g/L after sonicating dispersions for 20 min (100 W). The size distribution remained constant after re-suspension, indicating that no agglomeration occurred after deposition. Ecotoxicity tests on Artemia franciscana and Phaeodactylum tricornutum did not show any adverse effects related to the presence of alginate in the exposure media, and provided evidence on possible reduced bioavailability of nano-TiO2. The suitable concentration of alginate is recommended to occur on a case-by-case basis.}, } @article {pmid25840699, year = {2015}, author = {Kozak, JP and Bennett, MG and Hayden-Lesmeister, A and Fritz, KA and Nickolotsky, A}, title = {Using Flow-Ecology Relationships to Evaluate Ecosystem Service Trade-Offs and Complementarities in the Nation's Largest River Swamp.}, journal = {Environmental management}, volume = {55}, number = {6}, pages = {1327-1342}, pmid = {25840699}, issn = {1432-1009}, mesh = {Animals ; Brachyura/growth & development ; Decision Support Techniques ; Ecology/*methods ; *Ecosystem ; Fisheries ; Hydrology ; Ictaluridae/growth & development ; Louisiana ; Models, Theoretical ; Principal Component Analysis ; Rivers/*chemistry ; *Water Movements ; *Wetlands ; }, abstract = {Large river systems are inextricably linked with social systems; consequently, management decisions must be made within a given ecological, social, and political framework that often defies objective, technical resolution. Understanding flow-ecology relationships in rivers is necessary to assess potential impacts of management decisions, but translating complex flow-ecology relationships into stakeholder-relevant information remains a struggle. The concept of ecosystem services provides a bridge between flow-ecology relationships and stakeholder-relevant data. Flow-ecology relationships were used to explore complementary and trade-off relationships among 12 ecosystem services and related variables in the Atchafalaya River Basin, Louisiana. Results from Indicators of Hydrologic Alteration were reduced to four management-relevant hydrologic variables using principal components analysis. Multiple regression was used to determine flow-ecology relationships and Pearson correlation coefficients, along with regression results, were used to determine complementary and trade-off relationships among ecosystem services and related variables that were induced by flow. Seven ecosystem service variables had significant flow-ecology relationships for at least one hydrologic variable (R (2) = 0.19-0.64). River transportation and blue crab (Callinectes sapidus) landings exhibited a complementary relationship mediated by flow; whereas transportation and crawfish landings, crawfish landings and crappie (Pomoxis spp.) abundance, and blue crab landings and blue catfish (Ictalurus furcatus) abundance exhibited trade-off relationships. Other trade-off and complementary relationships among ecosystem services and related variables, however, were not related to flow. These results give insight into potential conflicts among stakeholders, can reduce the dimensions of management decisions, and provide initial hypotheses for experimental flow modifications.}, } @article {pmid25839752, year = {2015}, author = {Andersen, Ø and Johnsen, H and De Rosa, MC and Præbel, K and Stjelja, S and Kirubakaran, TG and Pirolli, D and Jentoft, S and Fevolden, SE}, title = {Evolutionary history and adaptive significance of the polymorphic Pan I in migratory and stationary populations of Atlantic cod (Gadus morhua).}, journal = {Marine genomics}, volume = {22}, number = {}, pages = {45-54}, doi = {10.1016/j.margen.2015.03.009}, pmid = {25839752}, issn = {1876-7478}, mesh = {Animal Distribution/*physiology ; Animals ; Base Sequence ; Bayes Theorem ; Computational Biology ; *Evolution, Molecular ; Female ; Gadus morhua/*genetics/physiology ; Gene Expression Profiling ; Genetics, Population ; Linkage Disequilibrium ; Male ; Models, Genetic ; Phylogeny ; *Polymorphism, Genetic ; Rhodopsin/*genetics ; Sequence Alignment ; Species Specificity ; Synaptophysin/*genetics ; }, abstract = {The synaptophysin (SYP) family comprises integral membrane proteins involved in vesicle-trafficking events, but the physiological function of several members has been enigmatic for decades. The presynaptic SYP protein controls neurotransmitter release, while SYP-like 2 (SYPL2) contributes to maintain normal Ca(2+)-signaling in the skeletal muscles. The polymorphic pantophysin (Pan I) of Atlantic cod shows strong genetic divergence between stationary and migratory populations, which seem to be adapted to local environmental conditions. We have investigated the functional involvement of Pan I in the different ecotypes by analyzing the 1) phylogeny, 2) spatio-temporal gene expression, 3) structure-function relationship of the Pan I(A) and I(B) protein variants, and 4) linkage to rhodopsin (rho) recently proposed to be associated with different light sensitivities in Icelandic populations of Atlantic cod. We searched for SYP family genes in phylogenetic key species and identified a single syp-related gene in three invertebrate chordates, while four members, Syp, Sypl1, Sypl2 and synaptoporin (Synpr), were found in tetrapods, Comoran coelacanth and spotted gar. Teleost fish were shown to possess duplicated syp, sypl2 and synpr genes of which the sypl2b paralog is identical to Pan I. The ubiquitously expressed cod Pan I codes for a tetra-spanning membrane protein possessing five amino acid substitutions in the first intravesicular loop, but only minor structural differences were shown between the allelic variants. Despite sizable genomic distance (>2.5 Mb) between Pan I and rho, highly significant linkage disequilibrium was found by genotyping shallow and deep water juvenile settlers predominated by the Pan I(A)-rho(A) and Pan I(B)-rho(B) haplotypes, respectively. However, the predicted rhodopsin protein showed no amino acid changes, while multiple polymorphic sites in the upstream region might affect the gene expression and pigment levels in stationary and migratory cod. Alternatively, other strongly linked genes might be responsible for the sharp settling stratification of juveniles and the different vertical behavior patterns of adult Atlantic cod.}, } @article {pmid25839052, year = {2015}, author = {Wang, MC and Wang, YP and Chu, CH and Tu, TY and Shiao, AS and Chou, P}, title = {Impact of pneumococcal conjugate vaccine on pediatric tympanostomy tube insertion in partial immunized population.}, journal = {TheScientificWorldJournal}, volume = {2015}, number = {}, pages = {248678}, pmid = {25839052}, issn = {1537-744X}, mesh = {Adolescent ; Child ; Child, Preschool ; Cohort Studies ; Databases, Factual/trends ; Female ; Heptavalent Pneumococcal Conjugate Vaccine/*administration & dosage ; Humans ; Immunization/*trends ; Infant ; Infant, Newborn ; Male ; Middle Ear Ventilation/*trends ; Pneumococcal Vaccines/administration & dosage ; *Population Surveillance/methods ; Retrospective Studies ; Taiwan/epidemiology ; Vaccines, Conjugate/administration & dosage ; }, abstract = {OBJECTIVE: To investigate the impact of seven-valent pneumococcal conjugate vaccine on tube insertions in a partial immunized pediatric population.

STUDY DESIGN: Retrospective ecological study.

METHODS: This study used Taiwan National Health Insurance Research Database for the period 2000-2009. Every child under 17 years old who received tubes during this 10-year period was identified and analyzed. The tube insertion rates in different age groups and the risk to receive tubes in different birth cohorts before and after the release of the vaccine in 2005 were compared.

RESULTS: The tube insertion rates for children under 17 years of age ranged from 21.6 to 31.9 for 100,000 persons/year. The tube insertion rate of children under 2 years old decreased significantly after 2005 in period effect analysis (β = -0.074, P < 0.05, and the negative β value means a downward trend) and increased in children 2 to 9 years old throughout the study period (positive β values which mean upward trends, P < 0.05). The rate of tube insertion was lower in 2004-2005 and 2006-2007 birth cohorts than that of 2002-2003 birth cohort (RR = 0.90 and 0.21, 95% CI 0.83-0.97 and 0.19-0.23, resp.).

CONCLUSION: The seven-valent pneumococcal conjugate vaccine may reduce the risk of tube insertion for children of later birth cohorts. The vaccine may have the protective effect on tube insertions in a partial immunized pediatric population.}, } @article {pmid25831547, year = {2015}, author = {Leger, MM and Petrů, M and Žárský, V and Eme, L and Vlček, Č and Harding, T and Lang, BF and Eliáš, M and Doležal, P and Roger, AJ}, title = {An ancestral bacterial division system is widespread in eukaryotic mitochondria.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {112}, number = {33}, pages = {10239-10246}, pmid = {25831547}, issn = {1091-6490}, support = {//Canadian Institutes of Health Research/Canada ; }, mesh = {Adenosine Triphosphatases/metabolism ; Arabidopsis/genetics ; Bacteria/cytology ; Bacterial Proteins/*genetics/metabolism ; Base Sequence ; Cell Cycle Proteins/metabolism ; Cell Division ; Cytoskeletal Proteins/*genetics ; DNA, Bacterial/*genetics ; Databases, Genetic ; Dictyostelium/metabolism ; Escherichia coli Proteins/metabolism ; Evolution, Molecular ; Likelihood Functions ; Mitochondria/*metabolism ; *Mitochondrial Dynamics ; Molecular Sequence Data ; Phylogeny ; Plastids/metabolism ; Saccharomyces cerevisiae/genetics/metabolism ; }, abstract = {Bacterial division initiates at the site of a contractile Z-ring composed of polymerized FtsZ. The location of the Z-ring in the cell is controlled by a system of three mutually antagonistic proteins, MinC, MinD, and MinE. Plastid division is also known to be dependent on homologs of these proteins, derived from the ancestral cyanobacterial endosymbiont that gave rise to plastids. In contrast, the mitochondria of model systems such as Saccharomyces cerevisiae, mammals, and Arabidopsis thaliana seem to have replaced the ancestral α-proteobacterial Min-based division machinery with host-derived dynamin-related proteins that form outer contractile rings. Here, we show that the mitochondrial division system of these model organisms is the exception, rather than the rule, for eukaryotes. We describe endosymbiont-derived, bacterial-like division systems comprising FtsZ and Min proteins in diverse less-studied eukaryote protistan lineages, including jakobid and heterolobosean excavates, a malawimonad, stramenopiles, amoebozoans, a breviate, and an apusomonad. For two of these taxa, the amoebozoan Dictyostelium purpureum and the jakobid Andalucia incarcerata, we confirm a mitochondrial localization of these proteins by their heterologous expression in Saccharomyces cerevisiae. The discovery of a proteobacterial-like division system in mitochondria of diverse eukaryotic lineages suggests that it was the ancestral feature of all eukaryotic mitochondria and has been supplanted by a host-derived system multiple times in distinct eukaryote lineages.}, } @article {pmid25829116, year = {2015}, author = {Hanson, D and Gunning, C and Rose, J and McFarlane, K and Franklin, RC}, title = {Working from the inside out: a case study of Mackay Safe Community.}, journal = {Health education & behavior : the official publication of the Society for Public Health Education}, volume = {42}, number = {1 Suppl}, pages = {35S-45S}, doi = {10.1177/1090198114568305}, pmid = {25829116}, issn = {1552-6127}, mesh = {Accidents, Traffic/prevention & control ; Australia ; Community Networks/economics/*organization & administration ; Cooperative Behavior ; *Environment ; Health Promotion/economics/*organization & administration ; Humans ; Interpersonal Relations ; Occupational Health ; Politics ; *Residence Characteristics ; *Safety ; *Social Environment ; Wounds and Injuries/prevention & control ; }, abstract = {Mackay Whitsunday Safe Community (MWSC) was established in 2000 in response to high rates of injury observed in the region. MWSC assumed an ecological perspective, incorporating targeted safety promotion campaigns reinforced by supportive environments and policy. By involving the community in finding its own solutions, MWSC attempted to catalyze structural, social, and political changes that empowered the community and, ultimately, individuals within the community, to modify their environment and their behavior to reduce the risk of injury. A community network consisting of 118 members and an external support network of 50 members was established. A social network analysis conducted in 2000 and 2004 indicated that the network doubled its cohesiveness, thereby strengthening its ability to collaborate for mutual benefit. However, while MWSC was rich in social resources, human and financial resources were largely controlled by external agencies. The bridging and linking relationships that connected MWSC to its external support network were the social mechanism MWSC used to access the resources it required to run programs. These boundary-spanning relationships accessed an estimated 6.5 full-time equivalents of human resources and US$750,000 in 2004 that it used to deliver a suite of injury control and safety promotion activities, associated with a 33% reduction in injury deaths over the period 2002 to 2010. MWSC can only be understood in its ecological context. The productivity of MWSC was vulnerable to the changing policy priorities of external sponsoring agents and critically dependent on the advocacy skills of its leaders.}, } @article {pmid25828689, year = {2015}, author = {Morard, R and Darling, KF and Mahé, F and Audic, S and Ujiié, Y and Weiner, AK and André, A and Seears, HA and Wade, CM and Quillévéré, F and Douady, CJ and Escarguel, G and de Garidel-Thoron, T and Siccha, M and Kucera, M and de Vargas, C}, title = {PFR[2]: a curated database of planktonic foraminifera 18S ribosomal DNA as a resource for studies of plankton ecology, biogeography and evolution.}, journal = {Molecular ecology resources}, volume = {15}, number = {6}, pages = {1472-1485}, doi = {10.1111/1755-0998.12410}, pmid = {25828689}, issn = {1755-0998}, mesh = {*Biodiversity ; Cluster Analysis ; DNA, Protozoan/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; *Databases, Nucleic Acid ; *Ecosystem ; Foraminifera/*classification/*genetics ; Molecular Sequence Data ; *Phylogeography ; Plankton/classification/genetics ; RNA, Ribosomal, 18S/genetics ; Rhizaria ; Sequence Analysis, DNA ; }, abstract = {Planktonic foraminifera (Rhizaria) are ubiquitous marine pelagic protists producing calcareous shells with conspicuous morphology. They play an important role in the marine carbon cycle, and their exceptional fossil record serves as the basis for biochronostratigraphy and past climate reconstructions. A major worldwide sampling effort over the last two decades has resulted in the establishment of multiple large collections of cryopreserved individual planktonic foraminifera samples. Thousands of 18S rDNA partial sequences have been generated, representing all major known morphological taxa across their worldwide oceanic range. This comprehensive data coverage provides an opportunity to assess patterns of molecular ecology and evolution in a holistic way for an entire group of planktonic protists. We combined all available published and unpublished genetic data to build PFR(2), the Planktonic foraminifera Ribosomal Reference database. The first version of the database includes 3322 reference 18S rDNA sequences belonging to 32 of the 47 known morphospecies of extant planktonic foraminifera, collected from 460 oceanic stations. All sequences have been rigorously taxonomically curated using a six-rank annotation system fully resolved to the morphological species level and linked to a series of metadata. The PFR(2) website, available at http://pfr2.sb-roscoff.fr, allows downloading the entire database or specific sections, as well as the identification of new planktonic foraminiferal sequences. Its novel, fully documented curation process integrates advances in morphological and molecular taxonomy. It allows for an increase in its taxonomic resolution and assures that integrity is maintained by including a complete contingency tracking of annotations and assuring that the annotations remain internally consistent.}, } @article {pmid25825767, year = {2015}, author = {Karkar, S and Facchinelli, F and Price, DC and Weber, AP and Bhattacharya, D}, title = {Metabolic connectivity as a driver of host and endosymbiont integration.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {112}, number = {33}, pages = {10208-10215}, pmid = {25825767}, issn = {1091-6490}, mesh = {Arabidopsis/genetics/metabolism ; *Biological Evolution ; Biological Transport ; Computational Biology ; Evolution, Molecular ; Oxidation-Reduction ; Photosynthesis ; Phylogeny ; Plastids/*genetics/metabolism ; Rhodophyta/metabolism ; Symbiosis/*genetics ; }, abstract = {The origin of oxygenic photosynthesis in the Archaeplastida common ancestor was foundational for the evolution of multicellular life. It is very likely that the primary endosymbiosis that explains plastid origin relied initially on the establishment of a metabolic connection between the host cell and captured cyanobacterium. We posit that these connections were derived primarily from existing host-derived components. To test this idea, we used phylogenomic and network analysis to infer the phylogenetic origin and evolutionary history of 37 validated plastid innermost membrane (permeome) metabolite transporters from the model plant Arabidopsis thaliana. Our results show that 57% of these transporter genes are of eukaryotic origin and that the captured cyanobacterium made a relatively minor (albeit important) contribution to the process. We also tested the hypothesis that the bacterium-derived hexose-phosphate transporter UhpC might have been the primordial sugar transporter in the Archaeplastida ancestor. Bioinformatic and protein localization studies demonstrate that this protein in the extremophilic red algae Galdieria sulphuraria and Cyanidioschyzon merolae are plastid targeted. Given this protein is also localized in plastids in the glaucophyte alga Cyanophora paradoxa, we suggest it played a crucial role in early plastid endosymbiosis by connecting the endosymbiont and host carbon storage networks. In summary, our work significantly advances understanding of plastid integration and favors a host-centric view of endosymbiosis. Under this view, nuclear genes of either eukaryotic or bacterial (noncyanobacterial) origin provided key elements of the toolkit needed for establishing metabolic connections in the primordial Archaeplastida lineage.}, } @article {pmid25824671, year = {2015}, author = {Belcaid, M and Toonen, RJ}, title = {Demystifying computer science for molecular ecologists.}, journal = {Molecular ecology}, volume = {24}, number = {11}, pages = {2619-2640}, doi = {10.1111/mec.13175}, pmid = {25824671}, issn = {1365-294X}, support = {G12MD00760/MD/NIMHD NIH HHS/United States ; P20GM103516/GM/NIGMS NIH HHS/United States ; }, mesh = {Algorithms ; Artificial Intelligence ; *Computational Biology ; Computer Literacy ; Ecology/*education ; Programming Languages ; }, abstract = {In this age of data-driven science and high-throughput biology, computational thinking is becoming an increasingly important skill for tackling both new and long-standing biological questions. However, despite its obvious importance and conspicuous integration into many areas of biology, computer science is still viewed as an obscure field that has, thus far, permeated into only a few of the biology curricula across the nation. A national survey has shown that lack of computational literacy in environmental sciences is the norm rather than the exception [Valle & Berdanier (2012) Bulletin of the Ecological Society of America, 93, 373-389]. In this article, we seek to introduce a few important concepts in computer science with the aim of providing a context-specific introduction aimed at research biologists. Our goal was to help biologists understand some of the most important mainstream computational concepts to better appreciate bioinformatics methods and trade-offs that are not obvious to the uninitiated.}, } @article {pmid25819582, year = {2015}, author = {Reyes, C and Garcia-Gil, M and Elorza, JM and Mendez-Boo, L and Hermosilla, E and Javaid, MK and Cooper, C and Diez-Perez, A and Arden, NK and Bolibar, B and Ramos, R and Prieto-Alhambra, D}, title = {Socio-economic status and the risk of developing hand, hip or knee osteoarthritis: a region-wide ecological study.}, journal = {Osteoarthritis and cartilage}, volume = {23}, number = {8}, pages = {1323-1329}, doi = {10.1016/j.joca.2015.03.020}, pmid = {25819582}, issn = {1522-9653}, support = {MC_U147585824/MRC_/Medical Research Council/United Kingdom ; MC_U147585827/MRC_/Medical Research Council/United Kingdom ; MC_UP_A620_1014/MRC_/Medical Research Council/United Kingdom ; MC_UU_12011/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Adult ; Age Factors ; Alcohol Drinking/epidemiology ; Databases, Factual ; Female ; Hand/*physiopathology ; Humans ; Incidence ; Male ; Middle Aged ; Obesity/epidemiology ; Osteoarthritis, Hip/*epidemiology/physiopathology ; Osteoarthritis, Knee/*epidemiology/physiopathology ; Prevalence ; Retrospective Studies ; Risk Factors ; Sex Factors ; Smoking/epidemiology ; *Social Class ; Spain/epidemiology ; }, abstract = {OBJECTIVE: To determine the association between socio-economic status (SES) and risk of hand, hip or knee osteoarthritis (OA) at a population level.

DESIGN: Retrospective ecological study using the System for the Development of Research in Primary Care (SIDIAP) database (primary care anonymized records for >5 million people in Catalonia (Spain)). Urban residents >15 years old (2009-2012) were eligible.

OUTCOMES: Validated area-based SES deprivation index MEDEA (proportion of unemployed, temporary workers, manual workers, low educational attainment and low educational attainment among youngsters) was estimated for each area based on census data as well as incident diagnoses (ICD-10 codes) of hand, hip or knee OA (2009-2012). Zero-inflated Poisson models were fitted to study the association between MEDEA quintiles and the outcomes.

RESULTS: Compared to the least deprived, the most deprived areas were younger (43.29 (17.59) vs 46.83 (18.49), years (Mean SD), had fewer women (49.1% vs 54.8%), a higher percentage of obese (16.2% vs 8.4%), smokers (16.9% vs 11.9%) and high-risk alcohol consumption subjects (1.5% vs 1.3%). Compared to the least deprived, the most deprived areas had an excess risk of OA: age-sex-adjusted Incidence Rate Ratio (IRR) 1.26 (1.11-1.42) for hand, 1.23 (1.17-1.29) hip, and 1.51 (1.45-1.57) knee. Adjustment for obesity attenuated this association: 1.06 (0.93-1.20), 1.04 (0.99-1.09), and 1.23 (1.19-1.28) respectively.

CONCLUSIONS: Deprived areas have higher rates OA (hand, hip, knee). Their increased prevalence of obesity accounts for a 50% of the excess risk of knee OA observed. Public health interventions to reduce the prevalence of obesity in this population could reduce health inequalities.}, } @article {pmid25817433, year = {2015}, author = {Stölting, KN and Paris, M and Meier, C and Heinze, B and Castiglione, S and Bartha, D and Lexer, C}, title = {Genome-wide patterns of differentiation and spatially varying selection between postglacial recolonization lineages of Populus alba (Salicaceae), a widespread forest tree.}, journal = {The New phytologist}, volume = {207}, number = {3}, pages = {723-734}, doi = {10.1111/nph.13392}, pmid = {25817433}, issn = {1469-8137}, mesh = {*Forests ; Gene Ontology ; Genes, Plant ; Genetic Association Studies ; *Genetic Variation ; *Genome, Plant ; Hungary ; *Ice Cover ; Italy ; Microsatellite Repeats/genetics ; *Phylogeny ; Polymorphism, Single Nucleotide/genetics ; Populus/*genetics ; Reproducibility of Results ; *Selection, Genetic ; Sequence Analysis, DNA ; Trees/*genetics ; }, abstract = {Studying the divergence continuum in plants is relevant to fundamental and applied biology because of the potential to reveal functionally important genetic variation. In this context, whole-genome sequencing (WGS) provides the necessary rigour for uncovering footprints of selection. We resequenced populations of two divergent phylogeographic lineages of Populus alba (n = 48), thoroughly characterized by microsatellites (n = 317), and scanned their genomes for regions of unusually high allelic differentiation and reduced diversity using > 1.7 million single nucleotide polymorphisms (SNPs) from WGS. Results were confirmed by Sanger sequencing. On average, 9134 high-differentiation (≥ 4 standard deviations) outlier SNPs were uncovered between populations, 848 of which were shared by ≥ three replicate comparisons. Annotation revealed that 545 of these were located in 437 predicted genes. Twelve percent of differentiation outlier genome regions exhibited significantly reduced genetic diversity. Gene ontology (GO) searches were successful for 327 high-differentiation genes, and these were enriched for 63 GO terms. Our results provide a snapshot of the roles of 'hard selective sweeps' vs divergent selection of standing genetic variation in distinct postglacial recolonization lineages of P. alba. Thus, this study adds to our understanding of the mechanisms responsible for the origin of functionally relevant variation in temperate trees.}, } @article {pmid25816972, year = {2015}, author = {Pallavi, B and Shankar, KM and Abhiman, PB and Iqlas, A}, title = {Identification of putative genes involved in parasitism in the anchor worm, Lernaea cyprinacea by de novo transcriptome analysis.}, journal = {Experimental parasitology}, volume = {153}, number = {}, pages = {191-197}, doi = {10.1016/j.exppara.2015.03.014}, pmid = {25816972}, issn = {1090-2449}, mesh = {Animals ; Arthropod Proteins/*genetics/metabolism ; Carps ; Copepoda/*genetics/growth & development/physiology ; Databases, Genetic ; Female ; Fish Diseases/*parasitology ; Gene Expression ; Male ; Microsatellite Repeats ; Molecular Sequence Annotation ; *Transcriptome ; }, abstract = {There is little information on the genome sequence of Lernaea cyprinacea a major ectoparasite of freshwater fish throughout the world. We subjected the L. cyprinacea transcriptome (adult and free living stages) to Illumina HiSeq 2000 sequencing. We obtained a total of 31,671,751 (31.67 millions) reads for the adult parasitic stage and 33,840,446 (33.84 millions) for the free living stage. The reads were assembled into 50,792 contigs for the adult stage and 69,378 for the free living stage. Using the pfam database, 41.91% of the transcriptome was annotated. The transcriptome was mined for genes associated with parasitism. To examine gene expression changes associated with the parasitism of L. cyprinacea during the transit from the free living to parasitic stage, we studied the differentially expressed transcripts between the two stages. The microsatellite markers were also identified (9,843 for adult stage; 16,813 for free living stages) and this would facilitate population genetic studies in various geographical isolates of Lernaea. Our data provides the most comprehensive sequence resource available for L. cyprinacea and demonstrates that Illumina sequencing allows de novo transcriptome assembly and gene expression analysis in a species lacking genome information. The data could open new avenues for a wide array of genetic, evolutionary, biological, ecological, epidemiological studies, and a solid foundation for the development of novel interventions against L. cyprinacea.}, } @article {pmid25816114, year = {2015}, author = {Klein-Flügge, MC and Kennerley, SW and Saraiva, AC and Penny, WD and Bestmann, S}, title = {Behavioral modeling of human choices reveals dissociable effects of physical effort and temporal delay on reward devaluation.}, journal = {PLoS computational biology}, volume = {11}, number = {3}, pages = {e1004116}, pmid = {25816114}, issn = {1553-7358}, support = {086120/Z/08/Z//Wellcome Trust/United Kingdom ; 091593/Z/10///Wellcome Trust/United Kingdom ; //Wellcome Trust/United Kingdom ; 096689//Wellcome Trust/United Kingdom ; 091593//Wellcome Trust/United Kingdom ; 096689/Z/11/Z//Wellcome Trust/United Kingdom ; //Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Adult ; Choice Behavior/*physiology ; Computational Biology ; Female ; Hand Strength/physiology ; Humans ; Male ; *Models, Biological ; *Reward ; Task Performance and Analysis ; Young Adult ; }, abstract = {There has been considerable interest from the fields of biology, economics, psychology, and ecology about how decision costs decrease the value of rewarding outcomes. For example, formal descriptions of how reward value changes with increasing temporal delays allow for quantifying individual decision preferences, as in animal species populating different habitats, or normal and clinical human populations. Strikingly, it remains largely unclear how humans evaluate rewards when these are tied to energetic costs, despite the surge of interest in the neural basis of effort-guided decision-making and the prevalence of disorders showing a diminished willingness to exert effort (e.g., depression). One common assumption is that effort discounts reward in a similar way to delay. Here we challenge this assumption by formally comparing competing hypotheses about effort and delay discounting. We used a design specifically optimized to compare discounting behavior for both effort and delay over a wide range of decision costs (Experiment 1). We then additionally characterized the profile of effort discounting free of model assumptions (Experiment 2). Contrary to previous reports, in both experiments effort costs devalued reward in a manner opposite to delay, with small devaluations for lower efforts, and progressively larger devaluations for higher effort-levels (concave shape). Bayesian model comparison confirmed that delay-choices were best predicted by a hyperbolic model, with the largest reward devaluations occurring at shorter delays. In contrast, an altogether different relationship was observed for effort-choices, which were best described by a model of inverse sigmoidal shape that is initially concave. Our results provide a novel characterization of human effort discounting behavior and its first dissociation from delay discounting. This enables accurate modelling of cost-benefit decisions, a prerequisite for the investigation of the neural underpinnings of effort-guided choice and for understanding the deficits in clinical disorders characterized by behavioral inactivity.}, } @article {pmid25815976, year = {2015}, author = {Senior, AM and Charleston, MA and Lihoreau, M and Buhl, C and Raubenheimer, D and Simpson, SJ}, title = {Evolving nutritional strategies in the presence of competition: a geometric agent-based model.}, journal = {PLoS computational biology}, volume = {11}, number = {3}, pages = {e1004111}, pmid = {25815976}, issn = {1553-7358}, mesh = {Animals ; Competitive Behavior/*physiology ; Computational Biology ; Feeding Behavior/*physiology ; Female ; Insecta ; Male ; *Models, Biological ; Nutritional Physiological Phenomena/*physiology ; }, abstract = {Access to nutrients is a key factor governing development, reproduction and ultimately fitness. Within social groups, contest-competition can fundamentally affect nutrient access, potentially leading to reproductive asymmetry among individuals. Previously, agent-based models have been combined with the Geometric Framework of nutrition to provide insight into how nutrition and social interactions affect one another. Here, we expand this modelling approach by incorporating evolutionary algorithms to explore how contest-competition over nutrient acquisition might affect the evolution of animal nutritional strategies. Specifically, we model tolerance of nutrient excesses and deficits when ingesting nutritionally imbalanced foods, which we term 'nutritional latitude'; a higher degree of nutritional latitude constitutes a higher tolerance of nutritional excess and deficit. Our results indicate that a transition between two alternative strategies occurs at moderate to high levels of competition. When competition is low, individuals display a low level of nutritional latitude and regularly switch foods in search of an optimum. When food is scarce and contest-competition is intense, high nutritional latitude appears optimal, and individuals continue to consume an imbalanced food for longer periods before attempting to switch to an alternative. However, the relative balance of nutrients within available foods also strongly influences at what levels of competition, if any, transitions between these two strategies occur. Our models imply that competition combined with reproductive skew in social groups can play a role in the evolution of diet breadth. We discuss how the integration of agent-based, nutritional and evolutionary modelling may be applied in future studies to further understand the evolution of nutritional strategies across social and ecological contexts.}, } @article {pmid25815509, year = {2015}, author = {Melis, C and Herfindal, I and Dahl, F and Åhlén, PA}, title = {Individual and temporal variation in habitat association of an alien carnivore at its invasion front.}, journal = {PloS one}, volume = {10}, number = {3}, pages = {e0122492}, pmid = {25815509}, issn = {1932-6203}, mesh = {Agriculture ; Animals ; *Ecosystem ; Female ; Forests ; Geographic Information Systems ; *Introduced Species ; Male ; *Raccoon Dogs ; Seasons ; Sweden ; Wetlands ; }, abstract = {Gathering information on how invasive species utilize the habitat is important, in order to better aim actions to reduce their negative impact. We studied habitat use and selection of 55 GPS-marked raccoon dogs (30 males, 25 females) at their invasion front in Northern Sweden, with particular focus on differences between males and females, between movement states, and between seasons and times of the day. Daily movement pattern was used to classify GPS-locations into dispersing and settled. We focused on both anthropogenic and natural landscape characteristics. Since we did not have any a priori knowledge about the spatial scale of raccoon dog habitat selection, we first assessed how landscape characteristics of random points changed with distance from the GPS-location they were paired to. Because changes in habitat use became less pronounced at approximately 5 km for all variables, we focused on habitat use at two spatial scales: fine (500 m) and coarse (5 km). Habitat selection was strongest at the coarse scale, and reflected the results found for habitat use. Raccoon dogs selected agricultural areas and wetlands, lower altitudes, and shallow slopes, and avoided forests, open natural areas, and areas close to water and roads. There were no differences in habitat selection between males and females, or between movement states. This lack of sexual segregation increases the probability of encountering potential mates during dispersal, and therefore the likelihood for reproduction in new areas. The seasonal and diurnal pattern of habitat use may provide guidance for where and when to aim management efforts.}, } @article {pmid25813493, year = {2015}, author = {Huber, R and Knaden, M}, title = {Egocentric and geocentric navigation during extremely long foraging paths of desert ants.}, journal = {Journal of comparative physiology. A, Neuroethology, sensory, neural, and behavioral physiology}, volume = {201}, number = {6}, pages = {609-616}, pmid = {25813493}, issn = {1432-1351}, mesh = {Animals ; Ants/*physiology ; *Cues ; Desert Climate ; Exploratory Behavior/*physiology ; Feeding Behavior/*physiology ; Geographic Information Systems ; Homing Behavior/*physiology ; Odorants ; Orientation/*physiology ; Smell ; Time Factors ; Tunisia ; Visual Perception ; }, abstract = {Desert ants, Cataglyphis fortis, navigate individually in the salt pans of Tunisia by means of path integration. However, as path integration is error-prone, the ants in addition use visual and olfactory cues to pinpoint their nest entrance. It has been shown that the accuracy of the path integrator as well as the ants' confidence in that egocentric navigational tool decreases with increasing foraging distance. Here, we show that despite the accumulating errors, even after far-reaching foraging runs path integration provides the ants with surprisingly accurate information regarding the nest position. However, in addition, the ants take into account distant visual cues that are most probably provided by the patterns along the horizon line behind the nest entrance.}, } @article {pmid25812092, year = {2015}, author = {Al-Omari, A and Wett, B and Nopens, I and De Clippeleir, H and Han, M and Regmi, P and Bott, C and Murthy, S}, title = {Model-based evaluation of mechanisms and benefits of mainstream shortcut nitrogen removal processes.}, journal = {Water science and technology : a journal of the International Association on Water Pollution Research}, volume = {71}, number = {6}, pages = {840-847}, doi = {10.2166/wst.2015.022}, pmid = {25812092}, issn = {0273-1223}, mesh = {Ammonia/metabolism ; Bacteria/*metabolism ; Bioreactors/microbiology ; Denitrification ; Models, Theoretical ; Nitrates/metabolism ; Nitrification ; Nitrites/metabolism ; Nitrogen/*metabolism ; Oxidation-Reduction ; Waste Disposal, Fluid/*methods ; Wastewater/analysis ; Water Pollutants, Chemical/*metabolism ; }, abstract = {The main challenge in implementing shortcut nitrogen removal processes for mainstream wastewater treatment is the out-selection of nitrite oxidizing bacteria (NOB) to limit nitrate production. A model-based approach was utilized to simulate the impact of individual features of process control strategies to achieve NO(-)(2)-N shunt via NOB out-selection. Simulations were conducted using a two-step nitrogen removal model from the literature. Nitrogen shortcut removal processes from two case studies were modeled to illustrate the contribution of NOB out-selection mechanisms. The paper highlights a comparison between two control schemes; one was based on online measured ammonia and the other was based on a target ratio of 1 for ammonia vs. NOx (nitrate + nitrite) (AVN). Results indicated that the AVN controller possesses unique features to nitrify only that amount of nitrogen that can be denitrified, which promotes better management of incoming organics and bicarbonate for a more efficient NOB out-selection. Finally, the model was used in a scenario analysis, simulating hypothetical optimized performance of the pilot process. An estimated potential saving of 60% in carbon addition for nitrogen removal by implementing full-scale mainstream deammonification was predicted.}, } @article {pmid25811842, year = {2015}, author = {Visser, MD and McMahon, SM and Merow, C and Dixon, PM and Record, S and Jongejans, E}, title = {Speeding up ecological and evolutionary computations in R; essentials of high performance computing for biologists.}, journal = {PLoS computational biology}, volume = {11}, number = {3}, pages = {e1004140}, pmid = {25811842}, issn = {1553-7358}, mesh = {Cluster Analysis ; Computational Biology/*methods ; *Computing Methodologies ; Ecology/*methods ; Genetics, Population/*methods ; Humans ; }, abstract = {Computation has become a critical component of research in biology. A risk has emerged that computational and programming challenges may limit research scope, depth, and quality. We review various solutions to common computational efficiency problems in ecological and evolutionary research. Our review pulls together material that is currently scattered across many sources and emphasizes those techniques that are especially effective for typical ecological and environmental problems. We demonstrate how straightforward it can be to write efficient code and implement techniques such as profiling or parallel computing. We supply a newly developed R package (aprof) that helps to identify computational bottlenecks in R code and determine whether optimization can be effective. Our review is complemented by a practical set of examples and detailed Supporting Information material (S1-S3 Texts) that demonstrate large improvements in computational speed (ranging from 10.5 times to 14,000 times faster). By improving computational efficiency, biologists can feasibly solve more complex tasks, ask more ambitious questions, and include more sophisticated analyses in their research.}, } @article {pmid25811627, year = {2015}, author = {Giuggioli, L and McKetterick, TJ and Holderied, M}, title = {Delayed response and biosonar perception explain movement coordination in trawling bats.}, journal = {PLoS computational biology}, volume = {11}, number = {3}, pages = {e1004089}, pmid = {25811627}, issn = {1553-7358}, support = {BB/F002386/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; Appetitive Behavior/*physiology ; Chiroptera/*physiology ; Computational Biology ; Echolocation/*physiology ; England ; Models, Biological ; Spatial Behavior/*physiology ; }, abstract = {Animal coordinated movement interactions are commonly explained by assuming unspecified social forces of attraction, repulsion and alignment with parameters drawn from observed movement data. Here we propose and test a biologically realistic and quantifiable biosonar movement interaction mechanism for echolocating bats based on spatial perceptual bias, i.e. actual sound field, a reaction delay, and observed motor constraints in speed and acceleration. We found that foraging pairs of bats flying over a water surface swapped leader-follower roles and performed chases or coordinated manoeuvres by copying the heading a nearby individual has had up to 500 ms earlier. Our proposed mechanism based on the interplay between sensory-motor constraints and delayed alignment was able to recreate the observed spatial actor-reactor patterns. Remarkably, when we varied model parameters (response delay, hearing threshold and echolocation directionality) beyond those observed in nature, the spatio-temporal interaction patterns created by the model only recreated the observed interactions, i.e. chases, and best matched the observed spatial patterns for just those response delays, hearing thresholds and echolocation directionalities found to be used by bats. This supports the validity of our sensory ecology approach of movement coordination, where interacting bats localise each other by active echolocation rather than eavesdropping.}, } @article {pmid25810357, year = {2016}, author = {Bannister, R and Kennelly, P}, title = {Incorporating Stream Features into Groundwater Contouring Tools Within GIS.}, journal = {Ground water}, volume = {54}, number = {2}, pages = {286-290}, doi = {10.1111/gwat.12332}, pmid = {25810357}, issn = {1745-6584}, mesh = {Environmental Monitoring/*methods ; Geographic Information Systems ; Groundwater/*analysis ; Hydrology/*methods ; *Rivers ; *Water Supply ; }, abstract = {Hydrogeologists often are called upon to estimate surfaces from discrete, sparse data points. This estimation is often accomplished by manually drawing contours on maps using interpolation methods between points of known value while accounting for features known to influence the water table's surface. By contrast, geographic information systems (GIS) are good at creating smooth continuous surfaces from limited data points and allowing the user to represent the resulting surface resulting with contours, but these automated methods often fail to meet the expectations of many hydrogeologists because they do not include knowledge of other influences on the water table. In this study, we seek to fill this gap in the GIS-based methodology for hydrogeologists through an interactive tool that shapes an interpolated surface based on additional knowledge of the water table inferred from gaining or losing streams. The modified surface is reflected in water table contours that, for example, "V" upstream for gaining streams, and can be interactively adjusted to fit the user's expectations. By modifying not only the contours but also the associated interpolated surface, additional contours will follow the same trend, and the modified surface can be used for other analyses like calculating average gradients and flow paths. The tool leverages Esri's ArcGIS Desktop software, building upon a robust suite of mapping tools. We see this as a prototype for other tools that could be developed for hydrogeologists to account for variations in the water table inferred from local topographic trends, pumping or injection wells, and other hydrogeologic features.}, } @article {pmid25810242, year = {2015}, author = {Pollet, TV and Stulp, G and Henzi, SP and Barrett, L}, title = {Taking the aggravation out of data aggregation: A conceptual guide to dealing with statistical issues related to the pooling of individual-level observational data.}, journal = {American journal of primatology}, volume = {77}, number = {7}, pages = {727-740}, doi = {10.1002/ajp.22405}, pmid = {25810242}, issn = {1098-2345}, mesh = {Animals ; Behavior, Animal ; *Bias ; Data Collection/*methods ; *Data Interpretation, Statistical ; Meta-Analysis as Topic ; Models, Statistical ; Papio ; }, abstract = {Field data often include multiple observations taken from the same individual. In order to avoid pseudoreplication, it is commonplace to aggregate data, generating a mean score per individual, and then using these aggregated data in subsequent analyses. Aggregation, however, can generate problems of its own. Not only does it lead to a loss of information, it can also leave analyses vulnerable to the "ecological fallacy": the drawing of false inferences about individual behavior on the basis of population level ("ecological") data. It can also result in Simpson's paradox, where relationships seen at the individual level can be completely reversed when analyzed at the aggregate level. These phenomena have been documented widely in the medical and social sciences but tend to go unremarked in primatological studies that rely on observational data from the field. Here, we provide a conceptual guide that explains how and why aggregate data are vulnerable to the ecological fallacy and Simpson's paradox, illustrating these points using data on baboons. We then discuss one particular analytical approach, namely multi-level modeling, that can potentially eliminate these problems. By highlighting the issue of the ecological fallacy, and increasing awareness of how datasets are often organized into a number of different levels, we also highlight the manner in which researchers can more positively exploit the structure of their datasets, without any information loss. These analytical approaches may thus provide greater insight into behavior by permitting more thorough investigation of interactions and cross-level effects.}, } @article {pmid25808888, year = {2015}, author = {Polansky, L and Kilian, W and Wittemyer, G}, title = {Elucidating the significance of spatial memory on movement decisions by African savannah elephants using state-space models.}, journal = {Proceedings. Biological sciences}, volume = {282}, number = {1805}, pages = {}, pmid = {25808888}, issn = {1471-2954}, mesh = {Animals ; Decision Making ; Elephants/*physiology ; Female ; Geographic Information Systems ; Hippocampus/physiology ; Male ; Markov Chains ; *Models, Biological ; *Movement ; Namibia ; Seasons ; *Spatial Memory ; }, abstract = {Spatial memory facilitates resource acquisition where resources are patchy, but how it influences movement behaviour of wide-ranging species remains to be resolved. We examined African elephant spatial memory reflected in movement decisions regarding access to perennial waterholes. State-space models of movement data revealed a rapid, highly directional movement behaviour almost exclusively associated with visiting perennial water. Behavioural change point (BCP) analyses demonstrated that these goal-oriented movements were initiated on average 4.59 km, and up to 49.97 km, from the visited waterhole, with the closest waterhole accessed 90% of the time. Distances of decision points increased when switching to different waterholes, during the dry season, or for female groups relative to males, while selection of the closest waterhole decreased when switching. Overall, our analyses indicated detailed spatial knowledge over large scales, enabling elephants to minimize travel distance through highly directional movement when accessing water. We discuss the likely cognitive and socioecological mechanisms driving these spatially precise movements that are most consistent with our findings. By applying modern analytic techniques to high-resolution movement data, this study illustrates emerging approaches for studying how cognition structures animal movement behaviour in different ecological and social contexts.}, } @article {pmid25808743, year = {2015}, author = {Ma, S and Zhang, S and Yu, C and Zheng, H and Song, G and Semakula, HM and Chai, Y}, title = {Assessing Major Accident Risks to Support Land-Use Planning Using a Severity-Vulnerability Combination Method: A Case Study in Dagushan Peninsula, China.}, journal = {Risk analysis : an official publication of the Society for Risk Analysis}, volume = {35}, number = {8}, pages = {1503-1519}, doi = {10.1111/risa.12351}, pmid = {25808743}, issn = {1539-6924}, mesh = {*Accidents ; China ; *Conservation of Natural Resources ; Geographic Information Systems ; Risk Assessment ; }, abstract = {Major accident risks posed by chemical hazards have raised major social concerns in today's China. Land-use planning has been adopted by many countries as one of the essential elements for accident prevention. This article aims at proposing a method to assess major accident risks to support land-use planning in the vicinity of chemical installations. This method is based on the definition of risk by the Accidental Risk Assessment Methodology for IndustrieS (ARAMIS) project and it is an expansion application of severity and vulnerability assessment tools. The severity and vulnerability indexes from the ARAMIS methodology are employed to assess both the severity and vulnerability levels, respectively. A risk matrix is devised to support risk ranking and compatibility checking. The method consists of four main steps and is presented in geographical information-system-based maps. As an illustration, the proposed method is applied in Dagushan Peninsula, China. The case study indicated that the method could not only aid risk regulations on existing land-use planning, but also support future land-use planning by offering alternatives or influencing the plans at the development stage, and thus further enhance the roles and influence of land-use planning in the accident prevention activities in China.}, } @article {pmid25808518, year = {2015}, author = {Ju, F and Zhang, T}, title = {16S rRNA gene high-throughput sequencing data mining of microbial diversity and interactions.}, journal = {Applied microbiology and biotechnology}, volume = {99}, number = {10}, pages = {4119-4129}, doi = {10.1007/s00253-015-6536-y}, pmid = {25808518}, issn = {1432-0614}, mesh = {Bacteria/classification/genetics/*isolation & purification ; Bacterial Physiological Phenomena ; *Biodiversity ; DNA, Bacterial/genetics ; Data Mining ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, DNA/*methods ; }, abstract = {The ubiquitous occurrence of microorganisms gives rise to continuous public concerns regarding their pathogenicity and threats to human environment, as well as potential engineering benefits in biotechnology. The development and wide application of environmental biotechnology, for example in bioenergy production, wastewater treatment, bioremediation, and drinking water disinfection, have been bringing us with both environmental and economic benefits. Strikingly, extensive applications of microscopic and molecular techniques since 1990s have allowed engineers to peep into the microbiology in "black box" of engineered microbial communities in biotechnological processes, providing guidelines for process design and optimization. Recently, revolutionary advances in DNA sequencing technologies and rapidly decreasing costs are altering conventional ways of microbiology and ecology research, as it launches an era of next-generation sequencing (NGS). The principal research burdens are now transforming from traditional labor-intensive wet-lab experiments to dealing with analysis of huge and informative NGS data, which is computationally expensive and bioinformatically challenging. This study discusses state-of-the-art bioinformatics and statistical analyses of 16S ribosomal RNA (rRNA) gene high-throughput sequencing (HTS) data from prevalent NGS platforms to promote its applications in exploring microbial diversity of functional and pathogenic microorganisms, as well as their interactions in biotechnological processes.}, } @article {pmid25804868, year = {2015}, author = {Nonacs, P and Richards, MH}, title = {How (not) to review papers on inclusive fitness.}, journal = {Trends in ecology & evolution}, volume = {30}, number = {5}, pages = {235-237}, doi = {10.1016/j.tree.2015.02.007}, pmid = {25804868}, issn = {1872-8383}, mesh = {Altruism ; Animals ; *Biological Evolution ; Datasets as Topic ; *Genetic Fitness ; Humans ; Models, Genetic ; *Peer Review, Research ; Selection, Genetic ; Social Behavior ; }, } @article {pmid25804492, year = {2015}, author = {Li, J and Zhang, Y and Zhang, Y and Liu, Y and Xiang, Z and Qu, F and Yu, Z}, title = {Cloning and characterization of three suppressors of cytokine signaling (SOCS) genes from the Pacific oyster, Crassostrea gigas.}, journal = {Fish & shellfish immunology}, volume = {44}, number = {2}, pages = {525-532}, doi = {10.1016/j.fsi.2015.03.022}, pmid = {25804492}, issn = {1095-9947}, mesh = {Analysis of Variance ; Animals ; Base Sequence ; Cloning, Molecular ; Computational Biology ; Crassostrea/*genetics/*immunology ; DNA Primers/genetics ; DNA, Complementary/genetics ; Luciferases ; Molecular Sequence Data ; Pathogen-Associated Molecular Pattern Molecules/immunology ; Real-Time Polymerase Chain Reaction ; Sequence Analysis, DNA ; Suppressor of Cytokine Signaling Proteins/*genetics ; }, abstract = {Members of the suppressor of cytokine signaling (SOCS) family are crucial for the control of a variety of signal transduction pathways that are involved in the immunity, growth and development of organisms. However, in mollusks, the identity and function of SOCS proteins remain largely unclear. In the present study, three SOCS genes, CgSOCS2, CgSOCS5 and CgSOCS7, have been identified by searching and analyzing the Pacific oyster genome. Structural analysis indicated that the CgSOCS share conserved functional domains with their vertebrate counterparts. Phylogenetic analysis showed that the three SOCS genes clustered into two distinct groups, the type I and II subfamilies, indicating that these subfamilies had common ancestors. Tissue-specific expression results showed that the three genes were constitutively expressed in all examined tissues and were highly expressed in immune-related tissues, such as the hemocytes, gills and digestive gland. The expression of CgSOCS can also be induced to varying degrees in hemocytes after challenge with pathogen-associated molecular patterns (PAMPs). Moreover, dual-luciferase reporter assays showed that the over-expression of CgSOCS2 and CgSOCS7, but not CgSOC5, can activate an NF-κB reporter gene. Collectively, these results demonstrated that the CgSOCS might play an important role in the innate immune responses of the Pacific oyster.}, } @article {pmid25803814, year = {2015}, author = {Marcantonio, M and Rizzoli, A and Metz, M and Rosà, R and Marini, G and Chadwick, E and Neteler, M}, title = {Identifying the environmental conditions favouring West Nile Virus outbreaks in Europe.}, journal = {PloS one}, volume = {10}, number = {3}, pages = {e0121158}, pmid = {25803814}, issn = {1932-6203}, mesh = {Disease Outbreaks/*statistics & numerical data ; *Environment ; Europe/epidemiology ; Geographic Information Systems ; Humans ; Linear Models ; Population Dynamics ; Remote Sensing Technology/methods ; Species Specificity ; West Nile Fever/*epidemiology ; West Nile virus/*genetics ; }, abstract = {West Nile Virus (WNV) is a globally important mosquito borne virus, with significant implications for human and animal health. The emergence and spread of new lineages, and increased pathogenicity, is the cause of escalating public health concern. Pinpointing the environmental conditions that favour WNV circulation and transmission to humans is challenging, due both to the complexity of its biological cycle, and the under-diagnosis and reporting of epidemiological data. Here, we used remote sensing and GIS to enable collation of multiple types of environmental data over a continental spatial scale, in order to model annual West Nile Fever (WNF) incidence across Europe and neighbouring countries. Multi-model selection and inference were used to gain a consensus from multiple linear mixed models. Climate and landscape were key predictors of WNF outbreaks (specifically, high precipitation in late winter/early spring, high summer temperatures, summer drought, occurrence of irrigated croplands and highly fragmented forests). Identification of the environmental conditions associated with WNF outbreaks is key to enabling public health bodies to properly focus surveillance and mitigation of West Nile virus impact, but more work needs to be done to enable accurate predictions of WNF risk.}, } @article {pmid25803280, year = {2015}, author = {Reeder, TW and Townsend, TM and Mulcahy, DG and Noonan, BP and Wood, PL and Sites, JW and Wiens, JJ}, title = {Integrated analyses resolve conflicts over squamate reptile phylogeny and reveal unexpected placements for fossil taxa.}, journal = {PloS one}, volume = {10}, number = {3}, pages = {e0118199}, pmid = {25803280}, issn = {1932-6203}, mesh = {Animals ; Biological Evolution ; Databases, Factual ; Databases, Genetic ; *Fossils ; Lizards/*classification/genetics ; Phylogeny ; Snakes/*classification/genetics ; }, abstract = {Squamate reptiles (lizards and snakes) are a pivotal group whose relationships have become increasingly controversial. Squamates include >9000 species, making them the second largest group of terrestrial vertebrates. They are important medicinally and as model systems for ecological and evolutionary research. However, studies of squamate biology are hindered by uncertainty over their relationships, and some consider squamate phylogeny unresolved, given recent conflicts between molecular and morphological results. To resolve these conflicts, we expand existing morphological and molecular datasets for squamates (691 morphological characters and 46 genes, for 161 living and 49 fossil taxa, including a new set of 81 morphological characters and adding two genes from published studies) and perform integrated analyses. Our results resolve higher-level relationships as indicated by molecular analyses, and reveal hidden morphological support for the molecular hypothesis (but not vice-versa). Furthermore, we find that integrating molecular, morphological, and paleontological data leads to surprising placements for two major fossil clades (Mosasauria and Polyglyphanodontia). These results further demonstrate the importance of combining fossil and molecular information, and the potential problems of estimating the placement of fossil taxa from morphological data alone. Thus, our results caution against estimating fossil relationships without considering relevant molecular data, and against placing fossils into molecular trees (e.g. for dating analyses) without considering the possible impact of molecular data on their placement.}, } @article {pmid25800171, year = {2015}, author = {Lewandowski, E and Specht, H}, title = {Influence of volunteer and project characteristics on data quality of biological surveys.}, journal = {Conservation biology : the journal of the Society for Conservation Biology}, volume = {29}, number = {3}, pages = {713-723}, doi = {10.1111/cobi.12481}, pmid = {25800171}, issn = {1523-1739}, mesh = {Conservation of Natural Resources/*methods ; *Data Accuracy ; Datasets as Topic/*standards ; Surveys and Questionnaires/*standards ; *Volunteers ; }, abstract = {Volunteer involvement in biological surveys is becoming common in conservation and ecology, prompting questions on the quality of data collected in such surveys. In a systematic review of the peer-reviewed literature on the quality of data collected by volunteers, we examined the characteristics of volunteers (e.g., age, prior knowledge) and projects (e.g., systematic vs. opportunistic monitoring schemes) that affect data quality with regards to standardization of sampling, accuracy and precision of data collection, spatial and temporal representation of data, and sample size. Most studies (70%, n = 71) focused on the act of data collection. The majority of assessments of volunteer characteristics (58%, n = 93) examined the effect of prior knowledge and experience on quality of the data collected, often by comparing volunteers with experts or professionals, who were usually assumed to collect higher quality data. However, when both groups' data were compared with the same accuracy standard, professional data were more accurate in only 4 of 7 cases. The few studies that measured precision of volunteer and professional data did not conclusively show that professional data were less variable than volunteer data. To improve data quality, studies recommended changes to survey protocols, volunteer training, statistical analyses, and project structure (e.g., volunteer recruitment and retention).}, } @article {pmid25799512, year = {2015}, author = {Bu, N and Qu, J and Li, Z and Li, G and Zhao, H and Zhao, B and Li, B and Chen, J and Fang, C}, title = {Effects of Spartina alterniflora invasion on soil respiration in the Yangtze River estuary, China.}, journal = {PloS one}, volume = {10}, number = {3}, pages = {e0121571}, pmid = {25799512}, issn = {1932-6203}, mesh = {Carbon/analysis ; Carbon Dioxide/analysis ; Cell Respiration ; China ; Climate Change ; *Estuaries ; Hydrogen-Ion Concentration ; *Introduced Species ; Poaceae/*metabolism ; *Rivers ; Soil/*chemistry ; Wetlands ; }, abstract = {Many studies have found that plant invasion can enhance soil organic carbon (SOC) pools, by increasing net primary production (NPP) and/or decreased soil respiration. While most studies have focused on C input, little attention has been paid to plant invasion effects on soil respiration, especially in wetland ecosystems. Our study examined the effects of Spartina alterniflora invasion on soil respiration and C dynamics in the Yangtze River estuary. The estuary was originally occupied by two native plant species: Phragmites australis in the high tide zone and Scirpus mariqueter in the low tide zone. Mean soil respiration rates were 185.8 and 142.3 mg CO2 m(-2) h(-1) in S. alterniflora and P. australis stands in the high tide zone, and 159.7 and 112.0 mg CO2 m(-2) h(-1) in S. alterniflora and S. mariqueter stands in the low tide zone, respectively. Aboveground NPP (ANPP), SOC, and microbial biomass were also significantly higher in the S. alterniflora stands than in the two native plant stands. S. alterniflora invasion did not significantly change soil inorganic carbon or pH. Our results indicated that enhanced ANPP by S. alterniflora exceeded invasion-induced C loss through soil respiration. This suggests that S. alterniflora invasion into the Yangtze River estuary could strengthen the net C sink of wetlands in the context of global climate change.}, } @article {pmid25799349, year = {2016}, author = {Elbrecht, V and Leese, F}, title = {The mitochondrial genome of the Arizona Snowfly Mesocapnia arizonensis (Plecoptera, Capniidae).}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {5}, pages = {3365-3366}, doi = {10.3109/19401736.2015.1018223}, pmid = {25799349}, issn = {2470-1408}, mesh = {Animals ; Base Composition ; Codon ; Computational Biology/methods ; Genes, Mitochondrial ; Genome Size ; *Genome, Mitochondrial ; Insecta/classification/*genetics ; Open Reading Frames ; Regulatory Sequences, Nucleic Acid ; Sequence Analysis, DNA ; Whole Genome Sequencing ; }, abstract = {We assembled the mitochondrial genome of the capniid stonefly Mesocapnia arizonensis (Baumann & Gaufin, 1969) using Illumina HiSeq sequence data. The recovered mitogenome is 14,921 bp in length and includes 13 protein-coding genes, 2 ribosomal RNA genes and 22 transfer RNA genes. The control region could only be assembled partially. Gene order resembles that of basal arthropods. This is the first partial mitogenome sequence for the stonefly superfamily group Euholognatha and will be useful in future phylogenetic analyses.}, } @article {pmid25797829, year = {2015}, author = {Chaspari, T and Soldatos, C and Maragos, P}, title = {The development of the Athens Emotional States Inventory (AESI): collection, validation and automatic processing of emotionally loaded sentences.}, journal = {The world journal of biological psychiatry : the official journal of the World Federation of Societies of Biological Psychiatry}, volume = {16}, number = {5}, pages = {312-322}, doi = {10.3109/15622975.2015.1012228}, pmid = {25797829}, issn = {1814-1412}, mesh = {Adult ; Data Collection/methods ; *Databases, Factual ; Emotions/*physiology ; Greece ; Humans ; *Language ; *Natural Language Processing ; Young Adult ; }, abstract = {OBJECTIVES: The development of ecologically valid procedures for collecting reliable and unbiased emotional data towards computer interfaces with social and affective intelligence targeting patients with mental disorders.

METHODS: Following its development, presented with, the Athens Emotional States Inventory (AESI) proposes the design, recording and validation of an audiovisual database for five emotional states: anger, fear, joy, sadness and neutral. The items of the AESI consist of sentences each having content indicative of the corresponding emotion. Emotional content was assessed through a survey of 40 young participants with a questionnaire following the Latin square design. The emotional sentences that were correctly identified by 85% of the participants were recorded in a soundproof room with microphones and cameras. A preliminary validation of AESI is performed through automatic emotion recognition experiments from speech.

RESULTS: The resulting database contains 696 recorded utterances in Greek language by 20 native speakers and has a total duration of approximately 28 min. Speech classification results yield accuracy up to 75.15% for automatically recognizing the emotions in AESI.

CONCLUSIONS: These results indicate the usefulness of our approach for collecting emotional data with reliable content, balanced across classes and with reduced environmental variability.}, } @article {pmid25796906, year = {2014}, author = {Li, XF and Liu, LM and Qi, X and Zhang, JX and Zhao, TB and Wang, Y and Liu, XF and Zhou, YB}, title = {[Land use change dynamics and driving forces of the vulnerable ecological region in northwestern Shanxi Province, China].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {25}, number = {10}, pages = {2959-2967}, pmid = {25796906}, issn = {1001-9332}, mesh = {Agriculture ; China ; *Conservation of Natural Resources ; Ecology ; *Ecosystem ; Environmental Restoration and Remediation ; Forests ; Geographic Information Systems ; Grassland ; Industry ; Remote Sensing Technology ; }, abstract = {By using remote sensing and GIS technology, this paper collected land use information of 1980, 1990, 2000 and 2010 and the relevant statistical data, and analyzed the characteristics of land use change and its driving forces in northwestern Shanxi Province, the typical ecological fragile area. The results showed that there were significant changes in land use patterns in the past 30 years. During 1980-1990, 1990-2000 and 2000-2010 periods, the area of farmland decreased continuously, while the areas of grassland and woodland experienced increase-decrease-increase and decrease-increase-decrease patterns of change, respectively. The areas of industrial and resident lands increased continuously, but the water body and unused land decreased. The farmland was mainly transformed to grassland and woodland, and the areas of industrial and resident lands increased from the farmland. The lost area of water body was transformed to grassland and farmland. The decrease of unused land was due to the implementation of ecological engineering and urban ex-panding. In general, the changes of land use types were significantly higher before 2000 than after 2000. The industrial and resident lands, unused land and grassland changed drastically. The relationships between land use types and driving forces indicated that population pressure and economic development led to the changes of industrial land and farmland; policy of forestry ecological engi- neering drove the changes of woodland and grassland; the drought-characterized climate was the major cause inducing the decrease of water area and hindering the restoration of forest.}, } @article {pmid25796346, year = {2015}, author = {Drabeck, DH and Dean, AM and Jansa, SA}, title = {Why the honey badger don't care: Convergent evolution of venom-targeted nicotinic acetylcholine receptors in mammals that survive venomous snake bites.}, journal = {Toxicon : official journal of the International Society on Toxinology}, volume = {99}, number = {}, pages = {68-72}, doi = {10.1016/j.toxicon.2015.03.007}, pmid = {25796346}, issn = {1879-3150}, mesh = {Animals ; Animals, Zoo/blood/genetics/physiology ; Binding Sites ; Databases, Protein ; Drug Resistance, Multiple ; Elapid Venoms/*antagonists & inhibitors/chemistry/toxicity ; Elapidae/*physiology ; *Evolution, Molecular ; Ligands ; *Models, Molecular ; Mustelidae/blood/genetics/*physiology ; Nerve Tissue Proteins/chemistry/genetics/metabolism ; Neurotoxins/antagonists & inhibitors/chemistry/toxicity ; Phylogeny ; Predatory Behavior ; Protein Conformation ; Receptors, Nicotinic/chemistry/*genetics/metabolism ; Snake Bites/metabolism/physiopathology/*veterinary ; }, abstract = {Honey badgers (Mellivora capensis) prey upon and survive bites from venomous snakes (Family: Elapidae), but the molecular basis of their venom resistance is unknown. The muscular nicotinic cholinergic receptor (nAChR), targeted by snake α-neurotoxins, has evolved in some venom-resistant mammals to no longer bind these toxins. Through phylogenetic analysis of mammalian nAChR sequences, we show that honey badgers, hedgehogs, and pigs have independently acquired functionally equivalent amino acid replacements in the toxin-binding site of this receptor. These convergent amino acid changes impede toxin binding by introducing a positively charged amino acid in place of an uncharged aromatic residue. In venom-resistant mongooses, different replacements at these same sites are glycosylated, which is thought to disrupt binding through steric effects. Thus, it appears that resistance to snake venom α-neurotoxin has evolved at least four times among mammals through two distinct biochemical mechanisms operating at the same sites on the same receptor.}, } @article {pmid25794146, year = {2015}, author = {Reich, A and Dunn, C and Akasaka, K and Wessel, G}, title = {Phylogenomic analyses of Echinodermata support the sister groups of Asterozoa and Echinozoa.}, journal = {PloS one}, volume = {10}, number = {3}, pages = {e0119627}, pmid = {25794146}, issn = {1932-6203}, support = {R01 HD028152/HD/NICHD NIH HHS/United States ; T32 GM007601/GM/NIGMS NIH HHS/United States ; 2R01HD028152/HD/NICHD NIH HHS/United States ; 5T32 GM007601/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Computational Biology ; Echinodermata/*classification/*genetics ; Female ; *Genomics ; *Phylogeny ; Transcriptome ; }, abstract = {Echinoderms (sea urchins, sea stars, brittle stars, sea lilies and sea cucumbers) are a group of diverse organisms, second in number within deuterostome species to only the chordates. Echinoderms serve as excellent model systems for developmental biology due to their diverse developmental mechanisms, tractable laboratory use, and close phylogenetic distance to chordates. In addition, echinoderms are very well represented in the fossil record, including some larval features, making echinoderms a valuable system for studying evolutionary development. The internal relationships of Echinodermata have not been consistently supported across phylogenetic analyses, however, and this has hindered the study of other aspects of their biology. In order to test echinoderm phylogenetic relationships, we sequenced 23 de novo transcriptomes from all five clades of echinoderms. Using multiple phylogenetic methods at a variety of sampling depths we have constructed a well-supported phylogenetic tree of Echinodermata, including support for the sister groups of Asterozoa (sea stars and brittle stars) and Echinozoa (sea urchins and sea cucumbers). These results will help inform developmental and evolutionary studies specifically in echinoderms and deuterostomes in general.}, } @article {pmid25793889, year = {2015}, author = {Al Hammal, O and Alonso, D and Etienne, RS and Cornell, SJ}, title = {When can species abundance data reveal non-neutrality?.}, journal = {PLoS computational biology}, volume = {11}, number = {3}, pages = {e1004134}, pmid = {25793889}, issn = {1553-7358}, mesh = {*Biodiversity ; Computational Biology ; *Ecology ; *Forests ; *Models, Biological ; Panama ; *Population Dynamics ; }, abstract = {Species abundance distributions (SAD) are probably ecology's most well-known empirical pattern, and over the last decades many models have been proposed to explain their shape. There is no consensus over which model is correct, because the degree to which different processes can be discerned from SAD patterns has not yet been rigorously quantified. We present a power calculation to quantify our ability to detect deviations from neutrality using species abundance data. We study non-neutral stochastic community models, and show that the presence of non-neutral processes is detectable if sample size is large enough and/or the amplitude of the effect is strong enough. Our framework can be used for any candidate community model that can be simulated on a computer, and determines both the sampling effort required to distinguish between alternative processes, and a range for the strength of non-neutral processes in communities whose patterns are statistically consistent with neutral theory. We find that even data sets of the scale of the 50 Ha forest plot on Barro Colorado Island, Panama, are unlikely to be large enough to detect deviations from neutrality caused by competitive interactions alone, though the presence of multiple non-neutral processes with contrasting effects on abundance distributions may be detectable.}, } @article {pmid25792152, year = {2015}, author = {Inoue, A and Kawakami, N and Eguchi, H and Miyaki, K and Tsutsumi, A}, title = {Organizational Justice and Physiological Coronary Heart Disease Risk Factors in Japanese Employees: a Cross-Sectional Study.}, journal = {International journal of behavioral medicine}, volume = {22}, number = {6}, pages = {775-785}, pmid = {25792152}, issn = {1532-7558}, mesh = {Adult ; Cholesterol, HDL/*blood ; Cholesterol, LDL/*blood ; *Coronary Disease/blood/epidemiology/psychology ; Cross-Sectional Studies ; Female ; Humans ; Japan/epidemiology ; Life Style ; Male ; Middle Aged ; Occupational Health/statistics & numerical data ; Odds Ratio ; *Personnel Management/methods/standards ; Risk Factors ; Social Justice ; Surveys and Questionnaires ; Triglycerides/blood ; }, abstract = {BACKGROUND: Growing evidence has shown that lack of organizational justice (i.e., procedural justice and interactional justice) is associated with coronary heart disease (CHD) while biological mechanisms underlying this association have not yet been fully clarified.

PURPOSE: The purpose of the present study was to investigate the cross-sectional association of organizational justice with physiological CHD risk factors (i.e., blood pressure, high-density lipoprotein [HDL] cholesterol, low-density lipoprotein [LDL] cholesterol, and triglyceride) in Japanese employees.

METHODS: Overall, 3598 male and 901 female employees from two manufacturing companies in Japan completed self-administered questionnaires measuring organizational justice, demographic characteristics, and lifestyle factors. They completed health checkup, which included blood pressure and serum lipid measurements. Multiple logistic regression analyses and trend tests were conducted.

RESULTS: Among male employees, multiple logistic regression analyses and trend tests showed significant associations of low procedural justice and low interactional justice with high triglyceride (defined as 150 mg/dL or greater) after adjusting for demographic characteristics and lifestyle factors. Among female employees, trend tests showed significant dose-response relationship between low interactional justice and high LDL cholesterol (defined as 140 mg/dL or greater) while multiple logistic regression analysis showed only marginally significant or insignificant odds ratio of high LDL cholesterol among the low interactional justice group. Neither procedural justice nor interactional justice was associated with blood pressure or HDL cholesterol.

CONCLUSION: Organizational justice may be an important psychosocial factor associated with increased triglyceride at least among Japanese male employees.}, } @article {pmid25789874, year = {2015}, author = {Johnson, FA and Frempong-Ainguah, F and Matthews, Z and Harfoot, AJ and Nyarko, P and Baschieri, A and Gething, PW and Falkingham, J and Atkinson, PM}, title = {Evaluating the impact of the community-based health planning and services initiative on uptake of skilled birth care in Ghana.}, journal = {PloS one}, volume = {10}, number = {3}, pages = {e0120556}, pmid = {25789874}, issn = {1932-6203}, mesh = {Adolescent ; Adult ; Birthing Centers ; Community Health Planning/*statistics & numerical data ; Cross-Sectional Studies ; Databases, Factual ; Female ; Ghana ; Humans ; Infant, Newborn ; Male ; Middle Aged ; Pregnancy ; Rural Health Services/*statistics & numerical data ; Surveys and Questionnaires ; Young Adult ; }, abstract = {BACKGROUND: The Community-based Health Planning and Services (CHPS) initiative is a major government policy to improve maternal and child health and accelerate progress in the reduction of maternal mortality in Ghana. However, strategic intelligence on the impact of the initiative is lacking, given the persistant problems of patchy geographical access to care for rural women. This study investigates the impact of proximity to CHPS on facilitating uptake of skilled birth care in rural areas.

METHODS AND FINDINGS: Data from the 2003 and 2008 Demographic and Health Survey, on 4,349 births from 463 rural communities were linked to georeferenced data on health facilities, CHPS and topographic data on national road-networks. Distance to nearest health facility and CHPS was computed using the closest facility functionality in ArcGIS 10.1. Multilevel logistic regression was used to examine the effect of proximity to health facilities and CHPS on use of skilled care at birth, adjusting for relevant predictors and clustering within communities. The results show that a substantial proportion of births continue to occur in communities more than 8 km from both health facilities and CHPS. Increases in uptake of skilled birth care are more pronounced where both health facilities and CHPS compounds are within 8 km, but not in communities within 8 km of CHPS but lack access to health facilities. Where both health facilities and CHPS are within 8 km, the odds of skilled birth care is 16% higher than where there is only a health facility within 8km.

CONCLUSION: Where CHPS compounds are set up near health facilities, there is improved access to care, demonstrating the facilitatory role of CHPS in stimulating access to better care at birth, in areas where health facilities are accessible.}, } @article {pmid25786130, year = {2015}, author = {Lind, AL and Wisecaver, JH and Smith, TD and Feng, X and Calvo, AM and Rokas, A}, title = {Examining the evolution of the regulatory circuit controlling secondary metabolism and development in the fungal genus Aspergillus.}, journal = {PLoS genetics}, volume = {11}, number = {3}, pages = {e1005096}, pmid = {25786130}, issn = {1553-7404}, support = {T15 LM007450/LM/NLM NIH HHS/United States ; 2T15LM007450/LM/NLM NIH HHS/United States ; }, mesh = {Aspergillus/classification/*genetics/*metabolism ; *Biological Evolution ; Evolution, Molecular ; Genome, Fungal ; *Metabolic Networks and Pathways ; }, abstract = {Filamentous fungi produce diverse secondary metabolites (SMs) essential to their ecology and adaptation. Although each SM is typically produced by only a handful of species, global SM production is governed by widely conserved transcriptional regulators in conjunction with other cellular processes, such as development. We examined the interplay between the taxonomic narrowness of SM distribution and the broad conservation of global regulation of SM and development in Aspergillus, a diverse fungal genus whose members produce well-known SMs such as penicillin and gliotoxin. Evolutionary analysis of the 2,124 genes comprising the 262 SM pathways in four Aspergillus species showed that most SM pathways were species-specific, that the number of SM gene orthologs was significantly lower than that of orthologs in primary metabolism, and that the few conserved SM orthologs typically belonged to non-homologous SM pathways. RNA sequencing of two master transcriptional regulators of SM and development, veA and mtfA, showed that the effects of deletion of each gene, especially veA, on SM pathway regulation were similar in A. fumigatus and A. nidulans, even though the underlying genes and pathways regulated in each species differed. In contrast, examination of the role of these two regulators in development, where 94% of the underlying genes are conserved in both species showed that whereas the role of veA is conserved, mtfA regulates development in the homothallic A. nidulans but not in the heterothallic A. fumigatus. Thus, the regulation of these highly conserved developmental genes is divergent, whereas-despite minimal conservation of target genes and pathways-the global regulation of SM production is largely conserved. We suggest that the evolution of the transcriptional regulation of secondary metabolism in Aspergillus represents a novel type of regulatory circuit rewiring and hypothesize that it has been largely driven by the dramatic turnover of the target genes involved in the process.}, } @article {pmid25783854, year = {2015}, author = {Thomas, CG and Wang, W and Jovelin, R and Ghosh, R and Lomasko, T and Trinh, Q and Kruglyak, L and Stein, LD and Cutter, AD}, title = {Full-genome evolutionary histories of selfing, splitting, and selection in Caenorhabditis.}, journal = {Genome research}, volume = {25}, number = {5}, pages = {667-678}, pmid = {25783854}, issn = {1549-5469}, support = {R01 GM096008/GM/NIGMS NIH HHS/United States ; R01 HG004321/HG/NHGRI NIH HHS/United States ; GM096008/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Caenorhabditis elegans/*genetics/physiology ; *Evolution, Molecular ; *Genetic Speciation ; *Genome, Helminth ; Inbreeding ; Mutation ; *Selection, Genetic ; Self-Fertilization ; }, abstract = {The nematode Caenorhabditis briggsae is a model for comparative developmental evolution with C. elegans. Worldwide collections of C. briggsae have implicated an intriguing history of divergence among genetic groups separated by latitude, or by restricted geography, that is being exploited to dissect the genetic basis to adaptive evolution and reproductive incompatibility; yet, the genomic scope and timing of population divergence is unclear. We performed high-coverage whole-genome sequencing of 37 wild isolates of the nematode C. briggsae and applied a pairwise sequentially Markovian coalescent (PSMC) model to 703 combinations of genomic haplotypes to draw inferences about population history, the genomic scope of natural selection, and to compare with 40 wild isolates of C. elegans. We estimate that a diaspora of at least six distinct C. briggsae lineages separated from one another approximately 200,000 generations ago, including the "Temperate" and "Tropical" phylogeographic groups that dominate most samples worldwide. Moreover, an ancient population split in its history approximately 2 million generations ago, coupled with only rare gene flow among lineage groups, validates this system as a model for incipient speciation. Low versus high recombination regions of the genome give distinct signatures of population size change through time, indicative of widespread effects of selection on highly linked portions of the genome owing to extreme inbreeding by self-fertilization. Analysis of functional mutations indicates that genomic context, owing to selection that acts on long linkage blocks, is a more important driver of population variation than are the functional attributes of the individually encoded genes.}, } @article {pmid25781019, year = {2015}, author = {Tarasov, S and Génier, F}, title = {Innovative Bayesian and parsimony phylogeny of dung beetles (coleoptera, scarabaeidae, scarabaeinae) enhanced by ontology-based partitioning of morphological characters.}, journal = {PloS one}, volume = {10}, number = {3}, pages = {e0116671}, pmid = {25781019}, issn = {1932-6203}, mesh = {Animals ; Bayes Theorem ; *Biological Ontologies ; Coleoptera/*anatomy & histology/*classification ; *Phylogeny ; }, abstract = {Scarabaeine dung beetles are the dominant dung feeding group of insects and are widely used as model organisms in conservation, ecology and developmental biology. Due to the conflicts among 13 recently published phylogenies dealing with the higher-level relationships of dung beetles, the phylogeny of this lineage remains largely unresolved. In this study, we conduct rigorous phylogenetic analyses of dung beetles, based on an unprecedented taxon sample (110 taxa) and detailed investigation of morphology (205 characters). We provide the description of morphology and thoroughly illustrate the used characters. Along with parsimony, traditionally used in the analysis of morphological data, we also apply the Bayesian method with a novel approach that uses anatomy ontology for matrix partitioning. This approach allows for heterogeneity in evolutionary rates among characters from different anatomical regions. Anatomy ontology generates a number of parameter-partition schemes which we compare using Bayes factor. We also test the effect of inclusion of autapomorphies in the morphological analysis, which hitherto has not been examined. Generally, schemes with more parameters were favored in the Bayesian comparison suggesting that characters located on different body regions evolve at different rates and that partitioning of the data matrix using anatomy ontology is reasonable; however, trees from the parsimony and all the Bayesian analyses were quite consistent. The hypothesized phylogeny reveals many novel clades and provides additional support for some clades recovered in previous analyses. Our results provide a solid basis for a new classification of dung beetles, in which the taxonomic limits of the tribes Dichotomiini, Deltochilini and Coprini are restricted and many new tribes must be described. Based on the consistency of the phylogeny with biogeography, we speculate that dung beetles may have originated in the Mesozoic contrary to the traditional view pointing to a Cenozoic origin.}, } @article {pmid25777342, year = {2015}, author = {Bordes, F and Morand, S and Pilosof, S and Claude, J and Krasnov, BR and Cosson, JF and Chaval, Y and Ribas, A and Chaisiri, K and Blasdell, K and Herbreteau, V and Dupuy, S and Tran, A}, title = {Habitat fragmentation alters the properties of a host-parasite network: rodents and their helminths in South-East Asia.}, journal = {The Journal of animal ecology}, volume = {84}, number = {5}, pages = {1253-1263}, doi = {10.1111/1365-2656.12368}, pmid = {25777342}, issn = {1365-2656}, mesh = {Animals ; *Biodiversity ; Cambodia/epidemiology ; Ecosystem ; Geographic Information Systems ; Helminthiasis, Animal/*epidemiology/parasitology ; Helminths/*physiology ; *Host-Parasite Interactions ; Laos/epidemiology ; *Muridae ; Prevalence ; Rodent Diseases/*epidemiology/parasitology ; Spacecraft ; Thailand/epidemiology ; }, abstract = {1. While the effects of deforestation and habitat fragmentation on parasite prevalence or richness are well investigated, host-parasite networks are still understudied despite their importance in understanding the mechanisms of these major disturbances. Because fragmentation may negatively impact species occupancy, abundance and co-occurrence, we predict a link between spatiotemporal changes in habitat and the architecture of host-parasite networks. 2. For this, we used an extensive data set on 16 rodent species and 29 helminth species from seven localities of South-East Asia. We analysed the effects of rapid deforestation on connectance and modularity of helminth-parasite networks. We estimated both the degree of fragmentation and the rate of deforestation through the development of land uses and their changes through the last 20 to 30 years in order to take into account the dynamics of habitat fragmentation in our statistical analyses. 3. We found that rapid fragmentation does not affect helminth species richness per se but impacts host-parasite interactions as the rodent-helminth network becomes less connected and more modular. 4. Our results suggest that parasite sharing among host species may become more difficult to maintain with the increase of habitat disturbance.}, } @article {pmid25775520, year = {2015}, author = {Ruff, SE and Biddle, JF and Teske, AP and Knittel, K and Boetius, A and Ramette, A}, title = {Global dispersion and local diversification of the methane seep microbiome.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {112}, number = {13}, pages = {4015-4020}, pmid = {25775520}, issn = {1091-6490}, support = {294757/ERC_/European Research Council/International ; }, mesh = {Archaea/classification/physiology ; Biodiversity ; Databases, Genetic ; Deltaproteobacteria/classification/physiology ; Ecosystem ; Gammaproteobacteria/classification/physiology ; Geologic Sediments/*microbiology ; Hydrothermal Vents/microbiology ; Methane/*chemistry ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Seawater/*microbiology ; Sequence Analysis, DNA ; }, abstract = {Methane seeps are widespread seafloor ecosystems shaped by the emission of gas from seabed reservoirs. The microorganisms inhabiting methane seeps transform the chemical energy in methane to products that sustain rich benthic communities around the gas leaks. Despite the biogeochemical relevance of microbial methane removal at seeps, the global diversity and dispersion of seep microbiota remain unknown. Here we determined the microbial diversity and community structure of 23 globally distributed methane seeps and compared these to the microbial communities of 54 other seafloor ecosystems, including sulfate-methane transition zones, hydrothermal vents, coastal sediments, and deep-sea surface and subsurface sediments. We found that methane seep communities show moderate levels of microbial richness compared with other seafloor ecosystems and harbor distinct bacterial and archaeal taxa with cosmopolitan distribution and key biogeochemical functions. The high relative sequence abundance of ANME (anaerobic methanotrophic archaea), as well as aerobic Methylococcales, sulfate-reducing Desulfobacterales, and sulfide-oxidizing Thiotrichales, matches the most favorable microbial metabolisms at methane seeps in terms of substrate supply and distinguishes the seep microbiome from other seafloor microbiomes. The key functional taxa varied in relative sequence abundance between different seeps due to the environmental factors, sediment depth and seafloor temperature. The degree of endemism of the methane seep microbiome suggests a high local diversification in these heterogeneous but long-lived ecosystems. Our results indicate that the seep microbiome is structured according to metacommunity processes and that few cosmopolitan microbial taxa mediate the bulk of methane oxidation, with global relevance to methane emission in the ocean.}, } @article {pmid25774033, year = {2015}, author = {Camacho, A and Trefaut Rodrigues, M and Navas, C}, title = {Extreme operative temperatures are better descriptors of the thermal environment than mean temperatures.}, journal = {Journal of thermal biology}, volume = {49-50}, number = {}, pages = {106-111}, doi = {10.1016/j.jtherbio.2015.02.007}, pmid = {25774033}, issn = {0306-4565}, mesh = {Brazil ; Data Interpretation, Statistical ; *Environment ; *Temperature ; }, abstract = {In ecological studies of thermal biology the thermal environment is most frequently described using the mean or other measures of central tendency in environmental temperatures. However, this procedure may hide biologically relevant thermal variation for ectotherms, potentially misleading interpretations. Extremes of operative temperatures (EOT) can help with this problem by bracketing the thermal environment of focal animals. Within this paper, we quantify how mean operative temperatures relate to the range of simultaneously available operative temperatures (a measure of error). We also show how EOT: 1) detect more thermal differences among microsites than measures of central tendency, like the mean OT, 2) allow inferring on microsite use by ectothermic animals, and 3) clarify the relationships between field operative temperatures and temperatures measured at weather stations (WS). To do that, we explored operative temperatures measured at four sites of the Brazilian Caatingas and their correspondent nearest weather stations. We found that the daily mean OT can hide temperature ranges of 41 °C simultaneously available at our study sites. In addition, EOT detected more thermal differences among microsites than central quantiles. We also show how EOT allow inferring about microsite use of ectothermic animals in a given site. Finally, the daily maximum temperature and the daily temperature range measured at WSs predicted well the minimum available field OT at localities many kilometers away. Based on our results, we recommend the use of EOT, instead of mean OT, in thermal ecology studies.}, } @article {pmid25772004, year = {2016}, author = {Berninger, JP and LaLone, CA and Villeneuve, DL and Ankley, GT}, title = {Prioritization of pharmaceuticals for potential environmental hazard through leveraging a large-scale mammalian pharmacological dataset.}, journal = {Environmental toxicology and chemistry}, volume = {35}, number = {4}, pages = {1007-1020}, doi = {10.1002/etc.2965}, pmid = {25772004}, issn = {1552-8618}, mesh = {Animals ; Aquatic Organisms ; *Databases, Factual ; *Drug-Related Side Effects and Adverse Reactions ; Fishes ; Half-Life ; Hazardous Substances/pharmacokinetics/*toxicity ; Humans ; Mammals ; Pharmaceutical Preparations/*metabolism ; Probability ; Risk Assessment ; Species Specificity ; United States ; Water Pollutants, Chemical/pharmacokinetics/*toxicity ; }, abstract = {The potential for pharmaceuticals in the environment to cause adverse ecological effects is of increasing concern. Given the thousands of active pharmaceutical ingredients (APIs) that can enter the aquatic environment through human and/or animal (e.g., livestock) waste, a current challenge in aquatic toxicology is identifying those that pose the greatest risk. Because empirical toxicity information for aquatic species is generally lacking for pharmaceuticals, an important data source for prioritization is that generated during the mammalian drug development process. Applying concepts of species read-across, mammalian pharmacokinetic data were used to systematically prioritize APIs by estimating their potential to cause adverse biological consequences to aquatic organisms, using fish as an example. Mammalian absorption, distribution, metabolism, and excretion (ADME) data (e.g., peak plasma concentration, apparent volume of distribution, clearance rate, and half-life) were collected and curated, creating the Mammalian Pharmacokinetic Prioritization For Aquatic Species Targeting (MaPPFAST) database representing 1070 APIs. From these data, a probabilistic model and scoring system were developed and evaluated. Individual APIs and therapeutic classes were ranked based on clearly defined read-across assumptions for translating mammalian-derived ADME parameters to estimate potential hazard in fish (i.e., greatest predicted hazard associated with lowest mammalian peak plasma concentrations, total clearance and highest volume of distribution, half-life). It is anticipated that the MaPPFAST database and the associated API prioritization approach will help guide research and/or inform ecological risk assessment.}, } @article {pmid25771261, year = {2015}, author = {Feldstein, LR and Brownstein, JS and Brady, OJ and Hay, SI and Johansson, MA}, title = {Dengue on islands: a Bayesian approach to understanding the global ecology of dengue viruses.}, journal = {Transactions of the Royal Society of Tropical Medicine and Hygiene}, volume = {109}, number = {5}, pages = {303-312}, pmid = {25771261}, issn = {1878-3503}, support = {095066//Wellcome Trust/United Kingdom ; R01 LM010812/LM/NLM NIH HHS/United States ; R01LM010812/LM/NLM NIH HHS/United States ; //Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Aedes ; Animals ; *Bayes Theorem ; Climate ; Dengue/prevention & control/*transmission ; Dengue Virus/*pathogenicity ; Disease Outbreaks ; Humans ; Islands ; *Molecular Epidemiology ; Phylogeography ; }, abstract = {BACKGROUND: Transmission of dengue viruses (DENV), the most common arboviral pathogens globally, is influenced by many climatic and socioeconomic factors. However, the relative contributions of these factors on a global scale are unclear.

METHODS: We randomly selected 94 islands stratified by socioeconomic and geographic characteristics. With a Bayesian model, we assessed factors contributing to the probability of islands having a history of any dengue outbreaks and of having frequent outbreaks.

RESULTS: Minimum temperature was strongly associated with suitability for DENV transmission. Islands with a minimum monthly temperature of greater than 14.8°C (95% CI: 12.4-16.6°C) were predicted to be suitable for DENV transmission. Increased population size and precipitation were associated with increased outbreak frequency, but did not capture all of the variability. Predictions for 48 testing islands verified these findings.

CONCLUSIONS: This analysis clarified two key components of DENV ecology: minimum temperature was the most important determinant of suitability; and endemicity was more likely in areas with high precipitation and large, but not necessarily dense, populations. Wealth and connectivity, in contrast, had no discernable effects. This model adds to our knowledge of global determinants of dengue risk and provides a basis for understanding the ecology of dengue endemicity.}, } @article {pmid25769125, year = {2015}, author = {Gentes, ML and Mazerolle, MJ and Giroux, JF and Patenaude-Monette, M and Verreault, J}, title = {Tracking the sources of polybrominated diphenyl ethers in birds: foraging in waste management facilities results in higher DecaBDE exposure in males.}, journal = {Environmental research}, volume = {138}, number = {}, pages = {361-371}, doi = {10.1016/j.envres.2015.02.036}, pmid = {25769125}, issn = {1096-0953}, mesh = {Animals ; Charadriiformes/*physiology ; Environmental Pollutants/*blood ; *Feeding Behavior ; Female ; Flame Retardants/*metabolism ; Geographic Information Systems ; Male ; Polybrominated Biphenyls/*blood ; Quebec ; Refuse Disposal ; Telemetry ; *Waste Disposal Facilities ; Waste Disposal, Fluid ; }, abstract = {Differences in feeding ecology are now recognized as major determinants of inter-individual variations in contaminant profiles of free-ranging animals, but exceedingly little attention has been devoted to the role of habitat use. Marked inter-individual variations and high levels of polybrominated diphenyl ethers (PBDEs) (e.g., DecaBDE) have previously been documented in ring-billed gulls (Larus delawarensis) breeding in a colony near Montreal (QC, Canada). However, the environmental sources of these compounds, and thus the reasons causing these large inter-individual variations remain unidentified. In the present study, we used GPS-based telemetry (±5 to 10m precision) to track ring-billed gulls from this colony to reconstruct their movements at the landscape level. We related habitat use of individual gulls (n=76) to plasma concentrations (ng/g ww) and relative contributions (percentages) to Σ38PBDEs of major congeners in the internationally restricted PentaBDE and current-use DecaBDE mixtures. Male gulls that visited waste management facilities (WMFs; i.e., landfills, wastewater treatment plants and related facilities; 25% of all GPS-tracked males) exhibited greater DecaBDE (concentrations and percentages) and lower PentaBDE (percentages) relative to those that did not. In contrast, no such relationships were found in females. Moreover, in males, DecaBDE (concentrations and percentages) increased with percentages of time spent in WMFs (i.e., ~5% of total foraging time), while PentaBDE (percentages) decreased. No relationships between percentages of time spent in other habitats (i.e., urban areas, agriculture fields, and St. Lawrence River) were found in either sex. These findings suggest that animals breeding in the vicinity of WMFs as well as mobile species that only use these sites for short stopovers to forage, could be at risk of enhanced DecaBDE exposure.}, } @article {pmid25762112, year = {2015}, author = {Forster, D and Bittner, L and Karkar, S and Dunthorn, M and Romac, S and Audic, S and Lopez, P and Stoeck, T and Bapteste, E}, title = {Testing ecological theories with sequence similarity networks: marine ciliates exhibit similar geographic dispersal patterns as multicellular organisms.}, journal = {BMC biology}, volume = {13}, number = {}, pages = {16}, pmid = {25762112}, issn = {1741-7007}, mesh = {Animal Migration/*physiology ; Animals ; Base Sequence ; Ciliophora/*genetics/physiology ; DNA, Complementary/genetics ; Databases, Genetic ; *Ecosystem ; *Gene Regulatory Networks ; Genetic Variation ; *Geography ; *Models, Biological ; *Sequence Homology, Nucleic Acid ; }, abstract = {BACKGROUND: High-throughput sequencing technologies are lifting major limitations to molecular-based ecological studies of eukaryotic microbial diversity, but analyses of the resulting millions of short sequences remain a major bottleneck for these approaches. Here, we introduce the analytical and statistical framework of sequence similarity networks, increasingly used in evolutionary studies and graph theory, into the field of ecology to analyze novel pyrosequenced V4 small subunit rDNA (SSU-rDNA) sequence data sets in the context of previous studies, including SSU-rDNA Sanger sequence data from cultured ciliates and from previous environmental diversity inventories.

RESULTS: Our broadly applicable protocol quantified the progress in the description of genetic diversity of ciliates by environmental SSU-rDNA surveys, detected a fundamental historical bias in the tendency to recover already known groups in these surveys, and revealed substantial amounts of hidden microbial diversity. Moreover, network measures demonstrated that ciliates are not globally dispersed, but are structured by habitat and geographical location at intermediate geographical scale, as observed for bacteria, plants, and animals.

CONCLUSIONS: Currently available 'universal' primers used for local in-depth sequencing surveys provide little hope to exhaust the significantly higher ciliate (and most likely microbial) diversity than previously thought. Network analyses such as presented in this study offer a promising way to guide the design of novel primers and to further explore this vast and structured microbial diversity.}, } @article {pmid25759841, year = {2015}, author = {Qi, Z and Zhang, Q and Wang, Z and Zhao, W and Gao, Q}, title = {Cloning of interleukin-10 from African clawed frog (Xenopus tropicalis), with the Finding of IL-19/20 homologue in the IL-10 locus.}, journal = {Journal of immunology research}, volume = {2015}, number = {}, pages = {462138}, pmid = {25759841}, issn = {2314-7156}, mesh = {Amino Acid Sequence ; Animals ; *Cloning, Molecular ; Computational Biology ; Gene Expression ; Gene Order ; *Genetic Loci ; Interleukin-10/chemistry/*genetics ; Interleukins/chemistry/*genetics ; Models, Molecular ; Molecular Sequence Data ; Phylogeny ; Protein Conformation ; Sequence Alignment ; Sequence Analysis, DNA ; *Sequence Homology ; Xenopus/*genetics ; }, abstract = {Interleukin-10 (IL-10) is a pleiotropic cytokine that plays an important role in immune system. In the present study, the IL-10 gene of African clawed frog (Xenopus tropicalis) was first cloned, and its expression pattern and 3D structure were also analyzed. The frog IL-10 mRNA encoded 172 amino acids which possessed several conserved features found in IL-10s from other species, including five-exon/four-intron genomic structure, conserved four cysteine residues, IL-10 family motif, and six α-helices. Real-time PCR showed that frog IL-10 mRNA was ubiquitous expressed in all examined tissues, highly in some immune related tissues including kidney, spleen, and intestine and lowly in heart, stomach, and liver. The frog IL-10 mRNA was upregulated at 24 h after LPS stimulation, indicating that it plays a part in the host immune response to bacterial infection. Another IL, termed as IL-20, was identified from the frog IL-10 locus, which might be the homologue of mammalian IL-19/20 according to the analysis results of the phylogenetic tree and the sequence identities.}, } @article {pmid25759807, year = {2015}, author = {Subramoni, S and Florez Salcedo, DV and Suarez-Moreno, ZR}, title = {A bioinformatic survey of distribution, conservation, and probable functions of LuxR solo regulators in bacteria.}, journal = {Frontiers in cellular and infection microbiology}, volume = {5}, number = {}, pages = {16}, pmid = {25759807}, issn = {2235-2988}, mesh = {Amino Acid Sequence ; Bacteria/chemistry/classification/genetics/*metabolism ; Computational Biology ; Conserved Sequence ; Genome, Bacterial ; Molecular Sequence Data ; Phylogeny ; Repressor Proteins/*chemistry/genetics/*metabolism ; Trans-Activators/*chemistry/genetics/*metabolism ; }, abstract = {LuxR solo transcriptional regulators contain both an autoinducer binding domain (ABD; N-terminal) and a DNA binding Helix-Turn-Helix domain (HTH; C-terminal), but are not associated with a cognate N-acyl homoserine lactone (AHL) synthase coding gene in the same genome. Although a few LuxR solos have been characterized, their distributions as well as their role in bacterial signal perception and other processes are poorly understood. In this study we have carried out a systematic survey of distribution of all ABD containing LuxR transcriptional regulators (QS domain LuxRs) available in the InterPro database (IPR005143), and identified those lacking a cognate AHL synthase. These LuxR solos were then analyzed regarding their taxonomical distribution, predicted functions of neighboring genes and the presence of complete AHL-QS systems in the genomes that carry them. Our analyses reveal the presence of one or multiple predicted LuxR solos in many proteobacterial genomes carrying QS domain LuxRs, some of them harboring genes for one or more AHL-QS circuits. The presence of LuxR solos in bacteria occupying diverse environments suggests potential ecological functions for these proteins beyond AHL and interkingdom signaling. Based on gene context and the conservation levels of invariant amino acids of ABD, we have classified LuxR solos into functionally meaningful groups or putative orthologs. Surprisingly, putative LuxR solos were also found in a few non-proteobacterial genomes which are not known to carry AHL-QS systems. Multiple predicted LuxR solos in the same genome appeared to have different levels of conservation of invariant amino acid residues of ABD questioning their binding to AHLs. In summary, this study provides a detailed overview of distribution of LuxR solos and their probable roles in bacteria with genome sequence information.}, } @article {pmid25757729, year = {2015}, author = {Plominsky, ÁM and Delherbe, N and Mandakovic, D and Riquelme, B and González, K and Bergman, B and Mariscal, V and Vásquez, M}, title = {Intercellular transfer along the trichomes of the invasive terminal heterocyst forming cyanobacterium Cylindrospermopsis raciborskii CS-505.}, journal = {FEMS microbiology letters}, volume = {362}, number = {5}, pages = {}, doi = {10.1093/femsle/fnu009}, pmid = {25757729}, issn = {1574-6968}, mesh = {Anabaena/genetics/physiology ; Bacterial Proteins/metabolism ; Computational Biology ; Cylindrospermopsis/genetics/growth & development/*physiology/ultrastructure ; Fluoresceins/metabolism ; Gene Expression Regulation, Bacterial ; Microscopy, Electron, Transmission ; *Nitrogen Fixation ; Nitrogenase/metabolism ; Open Reading Frames ; Periplasm/metabolism ; Phenotype ; Trichomes/*growth & development/physiology ; }, abstract = {Cylindrospermopsis raciborskii CS-505 is an invasive freshwater filamentous cyanobacterium that when grown diazotrophically may develop trichomes of up to 100 vegetative cells while differentiating only two end heterocysts, the sole sites for their N2-fixation process. We examined the diazotrophic growth and intercellular transfer mechanisms in C. raciborskii CS-505. Subjecting cultures to a combined-nitrogen-free medium to elicit N2 fixation, the trichome length remained unaffected while growth rates decreased. The structures and proteins for intercellular communication showed that while a continuous periplasmic space was apparent along the trichomes, the putative septal junction sepJ gene is divided into two open reading frames and lacks several transmembrane domains unlike the situation in Anabaena, differentiating a 5-fold higher frequency of heterocysts. FRAP analyses also showed that the dyes calcein and 5-CFDA were taken up by heterocysts and vegetative cells, and that the transfer from heterocysts and 'terminal' vegetative cells showed considerably higher transfer rates than that from vegetative cells located in the middle of the trichomes. The data suggest that C. raciborskii CS-505 compensates its low-frequency heterocyst phenotype by a highly efficient transfer of the fixed nitrogen towards cells in distal parts of the trichomes (growing rapidly) while cells in central parts suffers (slow growth).}, } @article {pmid25752629, year = {2015}, author = {Wu, L and Gao, JE and Ma, XY and Li, D}, title = {Application of modified export coefficient method on the load estimation of non-point source nitrogen and phosphorus pollution of soil and water loss in semiarid regions.}, journal = {Environmental science and pollution research international}, volume = {22}, number = {14}, pages = {10647-10660}, pmid = {25752629}, issn = {1614-7499}, mesh = {China ; Databases, Factual ; *Desert Climate ; Environmental Monitoring/*methods ; Nitrogen/*analysis ; Phosphorus/*analysis ; Rain ; Rivers/chemistry ; Soil/chemistry ; Soil Pollutants/*analysis ; Water Movements ; Water Pollutants, Chemical/*analysis ; }, abstract = {Chinese Loess Plateau is considered as one of the most serious soil loss regions in the world, its annual sediment output accounts for 90 % of the total sediment loads of the Yellow River, and most of the Loess Plateau has a very typical characteristic of "soil and water flow together", and water flow in this area performs with a high sand content. Serious soil loss results in nitrogen and phosphorus loss of soil. Special processes of water and soil in the Loess Plateau lead to the loss mechanisms of water, sediment, nitrogen, and phosphorus are different from each other, which are greatly different from other areas of China. In this study, the modified export coefficient method considering the rainfall erosivity factor was proposed to simulate and evaluate non-point source (NPS) nitrogen and phosphorus loss load caused by soil and water loss in the Yanhe River basin of the hilly and gully area, Loess Plateau. The results indicate that (1) compared with the traditional export coefficient method, annual differences of NPS total nitrogen (TN) and total phosphorus (TP) load after considering the rainfall erosivity factor are obvious; it is more in line with the general law of NPS pollution formation in a watershed, and it can reflect the annual variability of NPS pollution more accurately. (2) Under the traditional and modified conditions, annual changes of NPS TN and TP load in four counties (districts) took on the similar trends from 1999 to 2008; the load emission intensity not only is closely related to rainfall intensity but also to the regional distribution of land use and other pollution sources. (3) The output structure, source composition, and contribution rate of NPS pollution load under the modified method are basically the same with the traditional method. The average output structure of TN from land use and rural life is about 66.5 and 17.1 %, the TP is about 53.8 and 32.7 %; the maximum source composition of TN (59 %) is farmland; the maximum source composition of TP (38.1 %) is rural life; the maximum contribution rates of TN and TP in Baota district are 36.26 and 39.26 %, respectively. Results may provide data support for NPS pollution prevention and control in the loess hilly and gully region and also provide scientific reference for the protection of ecological environment of the Loess Plateau in northern Shaanxi.}, } @article {pmid25745505, year = {2015}, author = {Ke, JY and Kliewer, KL and Hamad, EM and Cole, RM and Powell, KA and Andridge, RR and Straka, SR and Yee, LD and Belury, MA}, title = {The flavonoid, naringenin, decreases adipose tissue mass and attenuates ovariectomy-associated metabolic disturbances in mice.}, journal = {Nutrition & metabolism}, volume = {12}, number = {}, pages = {1}, pmid = {25745505}, issn = {1743-7075}, support = {P30 CA016058/CA/NCI NIH HHS/United States ; R03 CA162551/CA/NCI NIH HHS/United States ; }, abstract = {OBJECTIVE: Adverse metabolic changes associated with loss of ovarian function increase the risk of developing metabolic syndrome and non-alcoholic fatty liver disease (NAFLD) in postmenopausal women. Naringenin improves metabolic disturbances in vitro and in vivo. In the present study, we tested the effects of naringenin on metabolic disturbances resulting from estrogen deficiency in ovariectomized mice.

MATERIALS/METHODS: Ovariectomized C57BL/6 J female mice were fed a control diet (10% calories from fat) for 11 weeks. Mice either continued on the control diet (n = 9) or were switched to the control diet supplemented with 3% naringenin (n = 10) for the next 11 weeks. Energy expenditure was measured by indirect calorimetry and activity was monitored by infrared beam breaks. Intra-abdominal and subcutaneous adiposity was evaluated by magnetic resonance imaging (MRI). Blood biochemical measures of metabolic response included glucose, insulin, adipokines, and lipids. Lipid content in liver and muscle and expression of relevant genes in adipose tissue, liver, and muscle were quantified.

RESULTS: Ovariectomized mice fed naringenin exhibited lower fasting glucose and insulin levels compared to controls, with over 50% reduction of intra-abdominal and subcutaneous adiposity. Plasma leptin and leptin mRNA in adipose depots were also decreased in mice fed a naringenin diet. Monocyte chemoattractant protein-1 (MCP1/Ccl2) and interleukin 6 (IL-6/Il6) mRNA expression levels were significantly lower in perigonadal adipose tissue of naringenin-supplemented mice. We also observed that mice fed a naringenin diet had less hepatic lipid accumulation with corresponding alterations of hepatic gene expression associated with de novo lipogenesis, fatty acid oxidation, and gluconeogenesis.

CONCLUSION: Dietary naringenin attenuates many of the metabolic disturbances associated with ovariectomy in female mice.}, } @article {pmid25741440, year = {2015}, author = {Jarvis, ED and Mirarab, S and Aberer, AJ and Li, B and Houde, P and Li, C and Ho, SY and Faircloth, BC and Nabholz, B and Howard, JT and Suh, A and Weber, CC and da Fonseca, RR and Alfaro-Núñez, A and Narula, N and Liu, L and Burt, D and Ellegren, H and Edwards, SV and Stamatakis, A and Mindell, DP and Cracraft, J and Braun, EL and Warnow, T and Jun, W and Gilbert, MT and Zhang, G and , }, title = {Phylogenomic analyses data of the avian phylogenomics project.}, journal = {GigaScience}, volume = {4}, number = {}, pages = {4}, pmid = {25741440}, issn = {2047-217X}, support = {DP1 OD000448/OD/NIH HHS/United States ; R01 HL087216/HL/NHLBI NIH HHS/United States ; }, mesh = {Animals ; Birds/classification/*genetics ; Classification/methods ; DNA/chemistry ; DNA Transposable Elements ; Genome ; Genomics ; *Phylogeny ; Sequence Alignment ; }, abstract = {BACKGROUND: Determining the evolutionary relationships among the major lineages of extant birds has been one of the biggest challenges in systematic biology. To address this challenge, we assembled or collected the genomes of 48 avian species spanning most orders of birds, including all Neognathae and two of the five Palaeognathae orders. We used these genomes to construct a genome-scale avian phylogenetic tree and perform comparative genomic analyses.

FINDINGS: Here we present the datasets associated with the phylogenomic analyses, which include sequence alignment files consisting of nucleotides, amino acids, indels, and transposable elements, as well as tree files containing gene trees and species trees. Inferring an accurate phylogeny required generating: 1) A well annotated data set across species based on genome synteny; 2) Alignments with unaligned or incorrectly overaligned sequences filtered out; and 3) Diverse data sets, including genes and their inferred trees, indels, and transposable elements. Our total evidence nucleotide tree (TENT) data set (consisting of exons, introns, and UCEs) gave what we consider our most reliable species tree when using the concatenation-based ExaML algorithm or when using statistical binning with the coalescence-based MP-EST algorithm (which we refer to as MP-EST*). Other data sets, such as the coding sequence of some exons, revealed other properties of genome evolution, namely convergence.

CONCLUSIONS: The Avian Phylogenomics Project is the largest vertebrate phylogenomics project to date that we are aware of. The sequence, alignment, and tree data are expected to accelerate analyses in phylogenomics and other related areas.}, } @article {pmid25740996, year = {2015}, author = {Zhu, H and Hughes, J and Murcia, PR}, title = {Origins and Evolutionary Dynamics of H3N2 Canine Influenza Virus.}, journal = {Journal of virology}, volume = {89}, number = {10}, pages = {5406-5418}, pmid = {25740996}, issn = {1098-5514}, support = {G0801822//Medical Research Council/United Kingdom ; }, mesh = {Animals ; Birds ; Databases, Genetic ; Dog Diseases/*virology ; Dogs ; Evolution, Molecular ; Genome, Viral ; Host Specificity ; Humans ; Influenza A Virus, H3N2 Subtype/*genetics/isolation & purification/pathogenicity ; Influenza A Virus, H5N1 Subtype/genetics/isolation & purification/pathogenicity ; Influenza in Birds/*virology ; Influenza, Human/virology ; Mutation ; Orthomyxoviridae Infections/*veterinary/virology ; Phylogeny ; Reassortant Viruses/genetics/isolation & purification/pathogenicity ; Selection, Genetic ; Time Factors ; Viral Proteins/genetics ; }, abstract = {UNLABELLED: Influenza A viruses (IAVs) are maintained mainly in wild birds, and despite frequent spillover infections of avian IAVs into mammals, only a small number of viruses have become established in mammalian hosts. A new H3N2 canine influenza virus (CIV) of avian origin emerged in Asia in the mid-2000s and is now circulating in dog populations of China and South Korea, and possibly in Thailand. The emergence of CIV provides new opportunities for zoonotic infections and interspecies transmission. We examined 14,764 complete IAV genomes together with all CIV genomes publicly available since its first isolation until 2013. We show that CIV may have originated as early as 1999 as a result of segment reassortment among Eurasian and North American avian IAV lineages. We also identified amino acid changes that might have played a role in CIV emergence, some of which have not been previously identified in other cross-species jumps. CIV evolves at a lower rate than H3N2 human influenza viruses do, and viral phylogenies exhibit geographical structure compatible with high levels of local transmission. We detected multiple intrasubtypic and heterosubtypic reassortment events, including the acquisition of the NS segment of an H5N1 avian influenza virus that had previously been overlooked. In sum, our results provide insight into the adaptive changes required by avian viruses to establish themselves in mammals and also highlight the potential role of dogs to act as intermediate hosts in which viruses with zoonotic and/or pandemic potential could originate, particularly with an estimated dog population of ∼ 700 million.

IMPORTANCE: Influenza A viruses circulate in humans and animals. This multihost ecology has important implications, as past pandemics were caused by IAVs carrying gene segments of both human and animal origin. Adaptive evolution is central to cross-species jumps, and this is why understanding the evolutionary processes that shape influenza A virus genomes is key to elucidating the mechanisms underpinning viral emergence. An avian-origin canine influenza virus (CIV) has recently emerged in dogs and is spreading in Asia. We reconstructed the evolutionary history of CIV and show that it originated from both Eurasian and North American avian lineages. We also identified the mutations that might have been responsible for the cross-species jump. Finally, we provide evidence of multiple reassortment events between CIV and other influenza viruses (including an H5N1 avian virus). This is a cause for concern, as there is a large global dog population to which humans are highly exposed.}, } @article {pmid25740460, year = {2015}, author = {Decelle, J and Romac, S and Stern, RF and Bendif, el M and Zingone, A and Audic, S and Guiry, MD and Guillou, L and Tessier, D and Le Gall, F and Gourvil, P and Dos Santos, AL and Probert, I and Vaulot, D and de Vargas, C and Christen, R}, title = {PhytoREF: a reference database of the plastidial 16S rRNA gene of photosynthetic eukaryotes with curated taxonomy.}, journal = {Molecular ecology resources}, volume = {15}, number = {6}, pages = {1435-1445}, doi = {10.1111/1755-0998.12401}, pmid = {25740460}, issn = {1755-0998}, mesh = {Cluster Analysis ; DNA, Ribosomal/chemistry/genetics ; *Databases, Nucleic Acid ; *Eukaryota ; *Genes, rRNA ; Molecular Sequence Data ; Phylogeny ; Plastids/*genetics ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, DNA ; }, abstract = {Photosynthetic eukaryotes have a critical role as the main producers in most ecosystems of the biosphere. The ongoing environmental metabarcoding revolution opens the perspective for holistic ecosystems biological studies of these organisms, in particular the unicellular microalgae that often lack distinctive morphological characters and have complex life cycles. To interpret environmental sequences, metabarcoding necessarily relies on taxonomically curated databases containing reference sequences of the targeted gene (or barcode) from identified organisms. To date, no such reference framework exists for photosynthetic eukaryotes. In this study, we built the PhytoREF database that contains 6490 plastidial 16S rDNA reference sequences that originate from a large diversity of eukaryotes representing all known major photosynthetic lineages. We compiled 3333 amplicon sequences available from public databases and 879 sequences extracted from plastidial genomes, and generated 411 novel sequences from cultured marine microalgal strains belonging to different eukaryotic lineages. A total of 1867 environmental Sanger 16S rDNA sequences were also included in the database. Stringent quality filtering and a phylogeny-based taxonomic classification were applied for each 16S rDNA sequence. The database mainly focuses on marine microalgae, but sequences from land plants (representing half of the PhytoREF sequences) and freshwater taxa were also included to broaden the applicability of PhytoREF to different aquatic and terrestrial habitats. PhytoREF, accessible via a web interface (http://phytoref.fr), is a new resource in molecular ecology to foster the discovery, assessment and monitoring of the diversity of photosynthetic eukaryotes using high-throughput sequencing.}, } @article {pmid25739841, year = {2015}, author = {Ding, J and Lu, G and Liu, J and Zhang, Z}, title = {Evaluation of the potential for trophic transfer of roxithromycin along an experimental food chain.}, journal = {Environmental science and pollution research international}, volume = {22}, number = {14}, pages = {10592-10600}, pmid = {25739841}, issn = {1614-7499}, mesh = {Animals ; Chlorophyta/chemistry/*metabolism ; Daphnia/chemistry/*metabolism ; Data Interpretation, Statistical ; *Food Chain ; Gills/chemistry/metabolism ; Goldfish/*metabolism ; Nutritional Status ; Roxithromycin/*analysis ; Water Pollutants, Chemical/*analysis ; }, abstract = {Pharmaceuticals have been recognized as a new class of environmental pollutants in recent years. But data about their potential for transfer and biomagnification in aquatic food chains are still lacking. In this study, bioaccumulation of the macrolide antibiotic roxithromycin (ROX) was determined in an experimental aquatic food chain involving the green algae Scenedesmus obliquus, the water flea Daphnia magna and the crucian carp Carassius auratus. After 48 h of exposure, S. obliquus accumulated ROX from media, with bioconcentration factors (BCFs) of 74.6, 46.3, and 24.5 l kg(-1) at nominal exposure concentrations of 4, 20, and 100 μg l(-1), respectively. After 48 h of feeding ROX-contaminated algae, D. magna was able to accumulate ROX in all three concentration treatments, but biomagnification did not occur at this trophic level, as biomagnification factors (BMFs) varied from 0.21 to 0.29 in different concentration treatments were well below one. In tissues (muscle, gill, liver, and bile) of C. auratus fed with contaminated daphnia for 8 days, no biomagnification was observed. However, this species did accumulate a certain degree of ROX through food chain transfer, and the tissue burden was greatest in the liver > muscle > gill and lowest in the bile. This work suggests that the trophic transfer should be a matter of concern for ecological risk assessments of pharmaceutical substances in aquatic food webs.}, } @article {pmid25739651, year = {2015}, author = {Chan, C and Jayasekera, S and Kao, B and Páramo, M and von Grotthuss, M and Ranz, JM}, title = {Remodelling of a homeobox gene cluster by multiple independent gene reunions in Drosophila.}, journal = {Nature communications}, volume = {6}, number = {}, pages = {6509}, doi = {10.1038/ncomms7509}, pmid = {25739651}, issn = {2041-1723}, support = {R25-GM056647/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Animals ; Arthropods/genetics ; Chromosome Mapping ; Computational Biology ; Drosophila/*genetics ; *Evolution, Molecular ; Gene Duplication/genetics ; Gene Expression Regulation/*genetics ; Genes, Homeobox/*genetics ; In Situ Hybridization ; Likelihood Functions ; Models, Genetic ; Molecular Sequence Annotation ; Molecular Sequence Data ; Multigene Family/*genetics ; Phylogeny ; Species Specificity ; Translocation, Genetic/genetics/*physiology ; }, abstract = {Genome clustering of homeobox genes is often thought to reflect arrangements of tandem gene duplicates maintained by advantageous coordinated gene regulation. Here we analyse the chromosomal organization of the NK homeobox genes, presumed to be part of a single cluster in the Bilaterian ancestor, across 20 arthropods. We find that the ProtoNK cluster was extensively fragmented in some lineages, showing that NK clustering in Drosophila species does not reflect selectively maintained gene arrangements. More importantly, the arrangement of NK and neighbouring genes across the phylogeny supports that, in two instances within the Drosophila genus, some cluster remnants became reunited via large-scale chromosomal rearrangements. Simulated scenarios of chromosome evolution indicate that these reunion events are unlikely unless the genome neighbourhoods harbouring the participating genes tend to colocalize in the nucleus. Our results underscore how mechanisms other than tandem gene duplication can result in paralogous gene clustering during genome evolution.}, } @article {pmid25737096, year = {2015}, author = {Hart, MM and Aleklett, K and Chagnon, PL and Egan, C and Ghignone, S and Helgason, T and Lekberg, Y and Öpik, M and Pickles, BJ and Waller, L}, title = {Navigating the labyrinth: a guide to sequence-based, community ecology of arbuscular mycorrhizal fungi.}, journal = {The New phytologist}, volume = {207}, number = {1}, pages = {235-247}, doi = {10.1111/nph.13340}, pmid = {25737096}, issn = {1469-8137}, support = {BB/L026007/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Biota/*genetics ; Computational Biology ; DNA, Fungal/genetics ; Databases, Nucleic Acid ; High-Throughput Nucleotide Sequencing/*methods ; Models, Biological ; Mycorrhizae/*genetics ; Specimen Handling ; }, abstract = {Data generated from next generation sequencing (NGS) will soon comprise the majority of information about arbuscular mycorrhizal fungal (AMF) communities. Although these approaches give deeper insight, analysing NGS data involves decisions that can significantly affect results and conclusions. This is particularly true for AMF community studies, because much remains to be known about their basic biology and genetics. During a workshop in 2013, representatives from seven research groups using NGS for AMF community ecology gathered to discuss common challenges and directions for future research. Our goal was to improve the quality and accessibility of NGS data for the AMF research community. Discussions spanned sampling design, sample preservation, sequencing, bioinformatics and data archiving. With concrete examples we demonstrated how different approaches can significantly alter analysis outcomes. Failure to consider the consequences of these decisions may compound bias introduced at each step along the workflow. The products of these discussions have been summarized in this paper in order to serve as a guide for any researcher undertaking NGS sequencing of AMF communities.}, } @article {pmid25733962, year = {2015}, author = {Pape, T and Beuk, P and Pont, AC and Shatalkin, AI and Ozerov, AL and Woźnica, AJ and Merz, B and Bystrowski, C and Raper, C and Bergström, C and Kehlmaier, C and Clements, DK and Greathead, D and Kameneva, EP and Nartshuk, E and Petersen, FT and Weber, G and Bächli, G and Geller-Grimm, F and Van de Weyer, G and Tschorsnig, HP and de Jong, H and van Zuijlen, JW and Vaňhara, J and Roháček, J and Ziegler, J and Majer, J and Hůrka, K and Holston, K and Rognes, K and Greve-Jensen, L and Munari, L and de Meyer, M and Pollet, M and Speight, MC and Ebejer, MJ and Martinez, M and Carles-Tolrá, M and Földvári, M and Chvála, M and Barták, M and Evenhuis, NL and Chandler, PJ and Cerretti, P and Meier, R and Rozkosny, R and Prescher, S and Gaimari, SD and Zatwarnicki, T and Zeegers, T and Dikow, T and Korneyev, VA and Richter, VA and Michelsen, V and Tanasijtshuk, VN and Mathis, WN and Hubenov, Z and de Jong, Y}, title = {Fauna europaea: Diptera - brachycera.}, journal = {Biodiversity data journal}, volume = {}, number = {3}, pages = {e4187}, pmid = {25733962}, issn = {1314-2828}, abstract = {Fauna Europaea provides a public web-service with an index of scientific names (including important synonyms) of all extant multicellular European terrestrial and freshwater animals and their geographical distribution at the level of countries and major islands (east of the Urals and excluding the Caucasus region). The Fauna Europaea project comprises about 230,000 taxonomic names, including 130,000 accepted species and 14,000 accepted subspecies, which is much more than the originally projected number of 100,000 species. Fauna Europaea represents a huge effort by more than 400 contributing taxonomic specialists throughout Europe and is a unique (standard) reference suitable for many user communities in science, government, industry, nature conservation and education. The Diptera-Brachycera is one of the 58 Fauna Europaea major taxonomic groups, and data have been compiled by a network of 55 specialists. Within the two-winged insects (Diptera), the Brachycera constitute a monophyletic group, which is generally given rank of suborder. The Brachycera may be classified into the probably paraphyletic 'lower brachyceran grade' and the monophyletic Eremoneura. The latter contains the Empidoidea, the Apystomyioidea with a single Nearctic species, and the Cyclorrhapha, which in turn is divided into the paraphyletic 'aschizan grade' and the monophyletic Schizophora. The latter is traditionally divided into the paraphyletic 'acalyptrate grade' and the monophyletic Calyptratae. Our knowledge of the European fauna of Diptera-Brachycera varies tremendously among families, from the reasonably well known hoverflies (Syrphidae) to the extremely poorly known scuttle flies (Phoridae). There has been a steady growth in our knowledge of European Diptera for the last two centuries, with no apparent slow down, but there is a shift towards a larger fraction of the new species being found among the families of the nematoceran grade (lower Diptera), which due to a larger number of small-sized species may be considered as taxonomically more challenging. Most of Europe is highly industrialised and has a high human population density, and the more fertile habitats are extensively cultivated. This has undoubtedly increased the extinction risk for numerous species of brachyceran flies, yet with the recent re-discovery of Thyreophoracynophila (Panzer), there are no known cases of extinction at a European level. However, few national Red Lists have extensive information on Diptera. For the Diptera-Brachycera, data from 96 families containing 11,751 species are included in this paper.}, } @article {pmid25732605, year = {2015}, author = {Bengtsson-Palme, J and Hartmann, M and Eriksson, KM and Pal, C and Thorell, K and Larsson, DG and Nilsson, RH}, title = {METAXA2: improved identification and taxonomic classification of small and large subunit rRNA in metagenomic data.}, journal = {Molecular ecology resources}, volume = {15}, number = {6}, pages = {1403-1414}, doi = {10.1111/1755-0998.12399}, pmid = {25732605}, issn = {1755-0998}, mesh = {Computational Biology/*methods ; DNA, Ribosomal/chemistry/genetics ; Metagenomics/*methods ; RNA, Ribosomal/genetics ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 18S/genetics ; RNA, Ribosomal, 23S/genetics ; Sequence Analysis, DNA/*methods ; Software ; }, abstract = {The ribosomal rRNA genes are widely used as genetic markers for taxonomic identification of microbes. Particularly the small subunit (SSU; 16S/18S) rRNA gene is frequently used for species- or genus-level identification, but also the large subunit (LSU; 23S/28S) rRNA gene is employed in taxonomic assignment. The METAXA software tool is a popular utility for extracting partial rRNA sequences from large sequencing data sets and assigning them to an archaeal, bacterial, nuclear eukaryote, mitochondrial or chloroplast origin. This study describes a comprehensive update to METAXA - METAXA2 - that extends the capabilities of the tool, introducing support for the LSU rRNA gene, a greatly improved classifier allowing classification down to genus or species level, as well as enhanced support for short-read (100 bp) and paired-end sequences, among other changes. The performance of METAXA2 was compared to other commonly used taxonomic classifiers, showing that METAXA2 often outperforms previous methods in terms of making correct predictions while maintaining a low misclassification rate. METAXA2 is freely available from http://microbiology.se/software/metaxa2/.}, } @article {pmid25728797, year = {2015}, author = {Beasley, A and Belanger, SE and Otter, RR}, title = {Stepwise Information-Filtering Tool (SIFT): A method for using risk assessment metadata in a nontraditional way.}, journal = {Environmental toxicology and chemistry}, volume = {34}, number = {6}, pages = {1436-1442}, doi = {10.1002/etc.2955}, pmid = {25728797}, issn = {1552-8618}, mesh = {Databases, Factual ; Ecotoxicology/*methods ; Models, Theoretical ; Risk Assessment ; }, abstract = {Tools exist to evaluate large ecotoxicity databases for risk assessment purposes, but these tools are less useful for alternative analytical purposes. In the present study, the authors developed the Stepwise Information-Filtering Tool (SIFT), a strategic method to select relevant, reliable data from a large ecotoxicity database; demonstrated utility in a case study of chronic toxicity data for statistical endpoint comparison purposes; and evaluated SIFT by comparison with 2 existing data evaluation methods.}, } @article {pmid25728598, year = {2015}, author = {Choi, YJ and Beakes, G and Glockling, S and Kruse, J and Nam, B and Nigrelli, L and Ploch, S and Shin, HD and Shivas, RG and Telle, S and Voglmayr, H and Thines, M}, title = {Towards a universal barcode of oomycetes--a comparison of the cox1 and cox2 loci.}, journal = {Molecular ecology resources}, volume = {15}, number = {6}, pages = {1275-1288}, pmid = {25728598}, issn = {1755-0998}, support = {P 22739/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Computational Biology/*methods ; DNA Barcoding, Taxonomic/*methods ; DNA, Ribosomal Spacer/genetics ; Electron Transport Complex IV/genetics ; *Genetic Variation ; Oomycetes/*classification/*genetics ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; }, abstract = {Oomycetes are a diverse group of eukaryotes in terrestrial, limnic and marine habitats worldwide and include several devastating plant pathogens, for example Phytophthora infestans (potato late blight). The cytochrome c oxidase subunit 2 gene (cox2) has been widely used for identification, taxonomy and phylogeny of various oomycete groups. However, recently the cox1 gene was proposed as a DNA barcode marker instead, together with ITS rDNA. The cox1 locus has been used in some studies of Pythium and Phytophthora, but has rarely been used for other oomycetes, as amplification success of cox1 varies with different lineages and sample ages. To determine which out of cox1 or cox2 is best suited as a universal oomycete barcode, we compared these two genes in terms of (i) PCR efficiency for 31 representative genera, as well as for historic herbarium specimens, and (ii) sequence polymorphism, intra- and interspecific divergence. The primer sets for cox2 successfully amplified all oomycete genera tested, while cox1 failed to amplify three genera. In addition, cox2 exhibited higher PCR efficiency for historic herbarium specimens, providing easier access to barcoding-type material. Sequence data for several historic type specimens exist for cox2, but there are none for cox1. In addition, cox2 yielded higher species identification success, with higher interspecific and lower intraspecific divergences than cox1. Therefore, cox2 is suggested as a partner DNA barcode along with ITS rDNA instead of cox1. The cox2-1 spacer could be a useful marker below species level. Improved protocols and universal primers are presented for all genes to facilitate future barcoding efforts.}, } @article {pmid25728529, year = {2015}, author = {González-Tortuero, E and Rusek, J and Petrusek, A and Gießler, S and Lyras, D and Grath, S and Castro-Monzón, F and Wolinska, J}, title = {The Quantification of Representative Sequences pipeline for amplicon sequencing: case study on within-population ITS1 sequence variation in a microparasite infecting Daphnia.}, journal = {Molecular ecology resources}, volume = {15}, number = {6}, pages = {1385-1395}, doi = {10.1111/1755-0998.12396}, pmid = {25728529}, issn = {1755-0998}, mesh = {Animals ; Computational Biology/*methods ; DNA, Ribosomal Spacer/chemistry/genetics ; Daphnia/*parasitology ; *Genetic Variation ; High-Throughput Nucleotide Sequencing ; Mesomycetozoea/*classification/*genetics ; *Sequence Analysis, DNA ; Software ; }, abstract = {Next generation sequencing (NGS) platforms are replacing traditional molecular biology protocols like cloning and Sanger sequencing. However, accuracy of NGS platforms has rarely been measured when quantifying relative frequencies of genotypes or taxa within populations. Here we developed a new bioinformatic pipeline (QRS) that pools similar sequence variants and estimates their frequencies in NGS data sets from populations or communities. We tested whether the estimated frequency of representative sequences, generated by 454 amplicon sequencing, differs significantly from that obtained by Sanger sequencing of cloned PCR products. This was performed by analysing sequence variation of the highly variable first internal transcribed spacer (ITS1) of the ichthyosporean Caullerya mesnili, a microparasite of cladocerans of the genus Daphnia. This analysis also serves as a case example of the usage of this pipeline to study within-population variation. Additionally, a public Illumina data set was used to validate the pipeline on community-level data. Overall, there was a good correspondence in absolute frequencies of C. mesnili ITS1 sequences obtained from Sanger and 454 platforms. Furthermore, analyses of molecular variance (amova) revealed that population structure of C. mesnili differs across lakes and years independently of the sequencing platform. Our results support not only the usefulness of amplicon sequencing data for studies of within-population structure but also the successful application of the QRS pipeline on Illumina-generated data. The QRS pipeline is freely available together with its documentation under GNU Public Licence version 3 at http://code.google.com/p/quantification-representative-sequences.}, } @article {pmid25725222, year = {2015}, author = {Al-Ghalith, GA and Vangay, P and Knights, D}, title = {The guts of obesity: progress and challenges in linking gut microbes to obesity.}, journal = {Discovery medicine}, volume = {19}, number = {103}, pages = {81-88}, pmid = {25725222}, issn = {1944-7930}, mesh = {Animals ; Bacteria/classification ; Gastrointestinal Tract/*microbiology/pathology ; Humans ; *Microbiota ; Obesity/*microbiology ; }, abstract = {The sharp rise in prevalence of obesity in recent decades has been suggestively labeled as an "epidemic," and the lack of fully explanatory causal factors has challenged existing understandings of obesity's etiology from a purely energetic standpoint. Much recent attention has been focused on the microbial members of the human gut for insights into their role in potentially causing or promoting obesity. The human gut is home to trillions of microbes, among which hundreds of distinct species of bacteria interact to form the human gut microbiome, and numerous studies in humans and animal models have linked shifts in the gut microbiome to obesity. In this review we explore contemporary understandings of the relationship between obesity and the microbiome from a high-level ecological and functional perspective, along with a survey of recently proposed interventions. We highlight areas of consensus and areas for further study in the field.}, } @article {pmid25723815, year = {2014}, author = {Ruz, GA and Timmermann, T and Barrera, J and Goles, E}, title = {Neutral space analysis for a Boolean network model of the fission yeast cell cycle network.}, journal = {Biological research}, volume = {47}, number = {1}, pages = {64}, pmid = {25723815}, issn = {0717-6287}, mesh = {Cell Cycle/*physiology ; Cell Cycle Proteins/metabolism ; Computational Biology ; Computer Graphics ; Computer Simulation ; Cyclin-Dependent Kinases/*metabolism ; G1 Phase/physiology ; Gene Regulatory Networks/*physiology ; *Models, Biological ; Neural Networks, Computer ; Schizosaccharomyces/genetics/*physiology ; }, abstract = {BACKGROUND: Interactions between genes and their products give rise to complex circuits known as gene regulatory networks (GRN) that enable cells to process information and respond to external stimuli. Several important processes for life, depend of an accurate and context-specific regulation of gene expression, such as the cell cycle, which can be analyzed through its GRN, where deregulation can lead to cancer in animals or a directed regulation could be applied for biotechnological processes using yeast. An approach to study the robustness of GRN is through the neutral space. In this paper, we explore the neutral space of a Schizosaccharomyces pombe (fission yeast) cell cycle network through an evolution strategy to generate a neutral graph, composed of Boolean regulatory networks that share the same state sequences of the fission yeast cell cycle.

RESULTS: Through simulations it was found that in the generated neutral graph, the functional networks that are not in the wildtype connected component have in general a Hamming distance more than 3 with the wildtype, and more than 10 between the other disconnected functional networks. Significant differences were found between the functional networks in the connected component of the wildtype network and the rest of the network, not only at a topological level, but also at the state space level, where significant differences in the distribution of the basin of attraction for the G1 fixed point was found for deterministic updating schemes.

CONCLUSIONS: In general, functional networks in the wildtype network connected component, can mutate up to no more than 3 times, then they reach a point of no return where the networks leave the connected component of the wildtype. The proposed method to construct a neutral graph is general and can be used to explore the neutral space of other biologically interesting networks, and also formulate new biological hypotheses studying the functional networks in the wildtype network connected component.}, } @article {pmid25721271, year = {2016}, author = {Sharma, KK}, title = {Fungal genome sequencing: basic biology to biotechnology.}, journal = {Critical reviews in biotechnology}, volume = {36}, number = {4}, pages = {743-759}, doi = {10.3109/07388551.2015.1015959}, pmid = {25721271}, issn = {1549-7801}, mesh = {Animals ; Biotechnology ; Databases, Factual ; Food Industry ; Fungi/genetics/metabolism ; *Genome, Fungal ; Humans ; Lignin/metabolism ; Plant Diseases ; Sequence Analysis, DNA ; }, abstract = {The genome sequences provide a first glimpse into the genomic basis of the biological diversity of filamentous fungi and yeast. The genome sequence of the budding yeast, Saccharomyces cerevisiae, with a small genome size, unicellular growth, and rich history of genetic and molecular analyses was a milestone of early genomics in the 1990s. The subsequent completion of fission yeast, Schizosaccharomyces pombe and genetic model, Neurospora crassa initiated a revolution in the genomics of the fungal kingdom. In due course of time, a substantial number of fungal genomes have been sequenced and publicly released, representing the widest sampling of genomes from any eukaryotic kingdom. An ambitious genome-sequencing program provides a wealth of data on metabolic diversity within the fungal kingdom, thereby enhancing research into medical science, agriculture science, ecology, bioremediation, bioenergy, and the biotechnology industry. Fungal genomics have higher potential to positively affect human health, environmental health, and the planet's stored energy. With a significant increase in sequenced fungal genomes, the known diversity of genes encoding organic acids, antibiotics, enzymes, and their pathways has increased exponentially. Currently, over a hundred fungal genome sequences are publicly available; however, no inclusive review has been published. This review is an initiative to address the significance of the fungal genome-sequencing program and provides the road map for basic and applied research.}, } @article {pmid25720324, year = {2015}, author = {Nawaz, S and Heindl, A and Koelble, K and Yuan, Y}, title = {Beyond immune density: critical role of spatial heterogeneity in estrogen receptor-negative breast cancer.}, journal = {Modern pathology : an official journal of the United States and Canadian Academy of Pathology, Inc}, volume = {28}, number = {6}, pages = {766-777}, pmid = {25720324}, issn = {1530-0285}, support = {105104/Z/14/Z//Wellcome Trust/United Kingdom ; }, mesh = {Algorithms ; Breast Neoplasms/*immunology/mortality/*pathology ; Female ; Humans ; Image Interpretation, Computer-Assisted/*methods ; Kaplan-Meier Estimate ; Lymphocytes, Tumor-Infiltrating/*immunology ; Proportional Hazards Models ; Receptors, Estrogen/biosynthesis ; }, abstract = {The abundance of tumor-infiltrating lymphocytes has been associated with a favorable prognosis in estrogen receptor-negative breast cancer. However, a high degree of spatial heterogeneity in lymphocytic infiltration is often observed and its clinical implication remains unclear. Here we combine automated histological image processing with methods of spatial statistics used in ecological data analysis to quantify spatial heterogeneity in the distribution patterns of tumor-infiltrating lymphocytes. Hematoxylin and eosin-stained sections from two cohorts of estrogen receptor-negative breast cancer patients (discovery: n=120; validation: n=125) were processed with our automated cell classification algorithm to identify the location of lymphocytes and cancer cells. Subsequently, hotspot analysis (Getis-Ord Gi*) was applied to identify statistically significant hotspots of cancer and immune cells, defined as tumor regions with a significantly high number of cancer cells or immune cells, respectively. We found that the amount of co-localized cancer and immune hotspots weighted by tumor area, rather than number of cancer or immune hotspots, correlates with a better prognosis in estrogen receptor-negative breast cancer in univariate and multivariate analysis. Moreover, co-localization of cancer and immune hotspots further stratified patients with immune cell-rich tumors. Our study demonstrates the importance of quantifying not only the abundance of lymphocytes but also their spatial variation in the tumor specimen for which methods from other disciplines such as spatial statistics can be successfully applied.}, } @article {pmid25714592, year = {2015}, author = {Avgar, T and Baker, JA and Brown, GS and Hagens, JS and Kittle, AM and Mallon, EE and McGreer, MT and Mosser, A and Newmaster, SG and Patterson, BR and Reid, DE and Rodgers, AR and Shuter, J and Street, GM and Thompson, I and Turetsky, MJ and Wiebe, PA and Fryxell, JM}, title = {Space-use behaviour of woodland caribou based on a cognitive movement model.}, journal = {The Journal of animal ecology}, volume = {84}, number = {4}, pages = {1059-1070}, doi = {10.1111/1365-2656.12357}, pmid = {25714592}, issn = {1365-2656}, mesh = {Animals ; *Behavior, Animal ; *Cognition ; Ecosystem ; Food Chain ; Geographic Information Systems ; Models, Biological ; Ontario ; Predatory Behavior ; Reindeer/*physiology/*psychology ; Spatial Behavior ; Wolves/*physiology ; }, abstract = {Movement patterns offer a rich source of information on animal behaviour and the ecological significance of landscape attributes. This is especially useful for species occupying remote landscapes where direct behavioural observations are limited. In this study, we fit a mechanistic model of animal cognition and movement to GPS positional data of woodland caribou (Rangifer tarandus caribou; Gmelin 1788) collected over a wide range of ecological conditions. The model explicitly tracks individual animal informational state over space and time, with resulting parameter estimates that have direct cognitive and ecological meaning. Three biotic landscape attributes were hypothesized to motivate caribou movement: forage abundance (dietary digestible biomass), wolf (Canis lupus; Linnaeus, 1758) density and moose (Alces alces; Linnaeus, 1758) habitat. Wolves are the main predator of caribou in this system and moose are their primary prey. Resulting parameter estimates clearly indicated that forage abundance is an important driver of caribou movement patterns, with predator and moose avoidance often having a strong effect, but not for all individuals. From the cognitive perspective, our results support the notion that caribou rely on limited sensory inputs from their surroundings, as well as on long-term spatial memory, to make informed movement decisions. Our study demonstrates how sensory, memory and motion capacities may interact with ecological fitness covariates to influence movement decisions by free-ranging animals.}, } @article {pmid25710777, year = {2015}, author = {Zhang, R and Ding, J and Liu, C and Cai, C and Zhou, B and Zhang, T and Guo, W}, title = {Molecular evolution and phylogenetic analysis of eight COL superfamily genes in group I related to photoperiodic regulation of flowering time in wild and domesticated cotton (Gossypium) species.}, journal = {PloS one}, volume = {10}, number = {2}, pages = {e0118669}, pmid = {25710777}, issn = {1932-6203}, mesh = {Cloning, Molecular ; DNA-Binding Proteins/classification/*genetics/metabolism ; Databases, Genetic ; Evolution, Molecular ; Flowers/genetics/metabolism ; Genes, Plant ; Gossypium/*genetics/metabolism ; Photoperiod ; Phylogeny ; Plant Proteins/classification/*genetics/*metabolism ; Sequence Analysis, DNA ; }, abstract = {Flowering time is an important ecological trait that determines the transition from vegetative to reproductive growth. Flowering time in cotton is controlled by short-day photoperiods, with strict photoperiod sensitivity. As the CO-FT (CONSTANS-FLOWER LOCUS T) module regulates photoperiodic flowering in several plants, we selected eight CONSTANS genes (COL) in group I to detect their expression patterns in long-day and short-day conditions. Further, we individually cloned and sequenced their homologs from 25 different cotton accessions and one outgroup. Finally, we studied their structures, phylogenetic relationship, and molecular evolution in both coding region and three characteristic domains. All the eight COLs in group I show diurnal expression. In the orthologous and homeologous loci, each gene structure in different cotton species is highly conserved, while length variation has occurred due to insertions/deletions in intron and/or exon regions. Six genes, COL2 to COL5, COL7 and COL8, exhibit higher nucleotide diversity in the D-subgenome than in the A-subgenome. The Ks values of 98.37% in all allotetraploid cotton species examined were higher in the A-D and At-Dt comparison than in the A-At and D-Dt comparisons, and the Pearson's correlation coefficient (r) of Ks between A vs. D and At vs. Dt also showed positive, high correlations, with a correlation coefficient of at least 0.797. The nucleotide polymorphism in wild species is significantly higher compared to G. hirsutum and G. barbadense, indicating a genetic bottleneck associated with the domesticated cotton species. Three characteristic domains in eight COLs exhibit different evolutionary rates, with the CCT domain highly conserved, while the B-box and Var domain much more variable in allotetraploid species. Taken together, COL1, COL2 and COL8 endured greater selective pressures during the domestication process. The study improves our understanding of the domestication-related genes/traits during cotton evolutionary process.}, } @article {pmid25710600, year = {2015}, author = {Kourgialas, NN and Dokou, Z and Karatzas, GP}, title = {Statistical analysis and ANN modeling for predicting hydrological extremes under climate change scenarios: the example of a small Mediterranean agro-watershed.}, journal = {Journal of environmental management}, volume = {154}, number = {}, pages = {86-101}, doi = {10.1016/j.jenvman.2015.02.034}, pmid = {25710600}, issn = {1095-8630}, mesh = {*Climate Change ; Data Interpretation, Statistical ; *Fresh Water ; Greece ; Humans ; *Hydrology ; Mediterranean Region ; *Models, Theoretical ; }, abstract = {The purpose of this study was to create a modeling management tool for the simulation of extreme flow events under current and future climatic conditions. This tool is a combination of different components and can be applied in complex hydrogeological river basins, where frequent flood and drought phenomena occur. The first component is the statistical analysis of the available hydro-meteorological data. Specifically, principal components analysis was performed in order to quantify the importance of the hydro-meteorological parameters that affect the generation of extreme events. The second component is a prediction-forecasting artificial neural network (ANN) model that simulates, accurately and efficiently, river flow on an hourly basis. This model is based on a methodology that attempts to resolve a very difficult problem related to the accurate estimation of extreme flows. For this purpose, the available measurements (5 years of hourly data) were divided in two subsets: one for the dry and one for the wet periods of the hydrological year. This way, two ANNs were created, trained, tested and validated for a complex Mediterranean river basin in Crete, Greece. As part of the second management component a statistical downscaling tool was used for the creation of meteorological data according to the higher and lower emission climate change scenarios A2 and B1. These data are used as input in the ANN for the forecasting of river flow for the next two decades. The final component is the application of a meteorological index on the measured and forecasted precipitation and flow data, in order to assess the severity and duration of extreme events.}, } @article {pmid25700118, year = {2015}, author = {Barron, MG and Lilavois, CR and Martin, TM}, title = {MOAtox: A comprehensive mode of action and acute aquatic toxicity database for predictive model development.}, journal = {Aquatic toxicology (Amsterdam, Netherlands)}, volume = {161}, number = {}, pages = {102-107}, doi = {10.1016/j.aquatox.2015.02.001}, pmid = {25700118}, issn = {1879-1514}, mesh = {Animals ; *Databases, Chemical ; Fishes ; Invertebrates/drug effects ; Metals/toxicity ; *Models, Theoretical ; Pesticides ; Quantitative Structure-Activity Relationship ; Species Specificity ; Water Pollutants, Chemical/toxicity ; }, abstract = {The mode of toxic action (MOA) has been recognized as a key determinant of chemical toxicity and as an alternative to chemical class-based predictive toxicity modeling. However, the development of quantitative structure activity relationship (QSAR) and other models has been limited by the availability of comprehensive high quality MOA and toxicity databases. The current study developed a dataset of MOA assignments for 1213 chemicals that included a diversity of metals, pesticides, and other organic compounds that encompassed six broad and 31 specific MOAs. MOA assignments were made using a combination of high confidence approaches that included international consensus classifications, QSAR predictions, and weight of evidence professional judgment based on an assessment of structure and literature information. A toxicity database of 674 acute values linked to chemical MOA was developed for fish and invertebrates. Additionally, species-specific measured or high confidence estimated acute values were developed for the four aquatic species with the most reported toxicity values: rainbow trout (Oncorhynchus mykiss), fathead minnow (Pimephales promelas), bluegill (Lepomis macrochirus), and the cladoceran (Daphnia magna). Measured acute toxicity values met strict standardization and quality assurance requirements. Toxicity values for chemicals with missing species-specific data were estimated using established interspecies correlation models and procedures (Web-ICE; http://epa.gov/ceampubl/fchain/webice/), with the highest confidence values selected. The resulting dataset of MOA assignments and paired toxicity values are provided in spreadsheet format as a comprehensive standardized dataset available for predictive aquatic toxicology model development.}, } @article {pmid25691733, year = {2015}, author = {Li, C and Qiao, Z and Qi, W and Wang, Q and Yuan, Y and Yang, X and Tang, Y and Mei, B and Lv, Y and Zhao, H and Xiao, H and Song, R}, title = {Genome-wide characterization of cis-acting DNA targets reveals the transcriptional regulatory framework of opaque2 in maize.}, journal = {The Plant cell}, volume = {27}, number = {3}, pages = {532-545}, pmid = {25691733}, issn = {1532-298X}, mesh = {Base Sequence ; Binding Sites ; Chromatin Immunoprecipitation ; DNA, Plant/*genetics ; Down-Regulation/genetics ; *Gene Expression Regulation, Plant ; Gene Ontology ; Genes, Plant ; *Genome, Plant ; Molecular Sequence Data ; Mutation ; Nitrogen/metabolism ; Nucleotide Motifs/genetics ; Open Reading Frames/genetics ; Plant Proteins/*genetics/metabolism ; *Promoter Regions, Genetic ; Protein Binding ; RNA, Messenger/genetics/metabolism ; RNA, Untranslated/genetics ; Sequence Analysis, RNA ; Stress, Physiological/genetics ; *Transcription, Genetic ; Zea mays/*genetics ; Zein/genetics ; }, abstract = {Opaque2 (O2) is a transcription factor that plays important roles during maize endosperm development. Mutation of the O2 gene improves the nutritional value of maize seeds but also confers pleiotropic effects that result in reduced agronomic quality. To reveal the transcriptional regulatory framework of O2, we studied the transcriptome of o2 mutants using RNA sequencing (RNA-Seq) and determined O2 DNA binding targets using chromatin immunoprecipitation coupled to high-throughput sequencing (ChIP-Seq). The RNA-Seq analysis revealed 1605 differentially expressed genes (DEGs) and 383 differentially expressed long, noncoding RNAs. The DEGs cover a wide range of functions related to nutrient reservoir activity, nitrogen metabolism, stress resistance, etc. ChIP-Seq analysis detected 1686 O2 DNA binding sites distributed over 1143 genes. Overlay of the RNA-Seq and ChIP-Seq results revealed 35 O2-modulated target genes. We identified four O2 binding motifs; among them, TGACGTGG appears to be the most conserved and strongest. We confirmed that, except for the 16- and 18-kD zeins, O2 directly regulates expression of all other zeins. O2 directly regulates two transcription factors, genes linked to carbon and amino acid metabolism and abiotic stress resistance. We built a hierarchical regulatory model for O2 that provides an understanding of its pleiotropic biological effects.}, } @article {pmid25689585, year = {2015}, author = {Stevens, FR and Gaughan, AE and Linard, C and Tatem, AJ}, title = {Disaggregating census data for population mapping using random forests with remotely-sensed and ancillary data.}, journal = {PloS one}, volume = {10}, number = {2}, pages = {e0107042}, pmid = {25689585}, issn = {1932-6203}, mesh = {Cambodia ; *Censuses ; Datasets as Topic ; Geography ; Humans ; Kenya ; *Models, Statistical ; Population Density ; Reproducibility of Results ; *Spatial Analysis ; Vietnam ; }, abstract = {High resolution, contemporary data on human population distributions are vital for measuring impacts of population growth, monitoring human-environment interactions and for planning and policy development. Many methods are used to disaggregate census data and predict population densities for finer scale, gridded population data sets. We present a new semi-automated dasymetric modeling approach that incorporates detailed census and ancillary data in a flexible, "Random Forest" estimation technique. We outline the combination of widely available, remotely-sensed and geospatial data that contribute to the modeled dasymetric weights and then use the Random Forest model to generate a gridded prediction of population density at ~100 m spatial resolution. This prediction layer is then used as the weighting surface to perform dasymetric redistribution of the census counts at a country level. As a case study we compare the new algorithm and its products for three countries (Vietnam, Cambodia, and Kenya) with other common gridded population data production methodologies. We discuss the advantages of the new method and increases over the accuracy and flexibility of those previous approaches. Finally, we outline how this algorithm will be extended to provide freely-available gridded population data sets for Africa, Asia and Latin America.}, } @article {pmid25683807, year = {2015}, author = {Harel, A and Karkar, S and Cheng, S and Falkowski, PG and Bhattacharya, D}, title = {Deciphering primordial cyanobacterial genome functions from protein network analysis.}, journal = {Current biology : CB}, volume = {25}, number = {5}, pages = {628-634}, doi = {10.1016/j.cub.2014.12.061}, pmid = {25683807}, issn = {1879-0445}, mesh = {Bacteria, Anaerobic/*genetics ; Computational Biology ; Cyanobacteria/*genetics ; *Evolution, Molecular ; Genome, Bacterial/*genetics ; Hydrogenase/genetics ; Multigene Family/*genetics ; Oxidation-Reduction ; Photosynthesis/genetics ; Protein Interaction Maps/*genetics ; Proteomics/methods ; Species Specificity ; }, abstract = {The Great Oxidation Event (GOE) ∼2.4 billion years ago resulted from the accumulation of oxygen by the ancestors of cyanobacteria [1-3]. Cyanobacteria continue to play a significant role in primary production [4] and in regulating the global marine and limnic nitrogen cycles [5, 6]. Relatively little is known, however, about the evolutionary history and gene content of primordial cyanobacteria [7, 8]. To address these issues, we used protein similarity networks [9], containing proteomes from 48 cyanobacteria as the test group, and reference proteomes from 84 microbes representing four distinct metabolic groups from most reducing to most oxidizing: methanogens, obligate anaerobes (nonmethanogenic), facultative aerobes, and obligate aerobes. These four metabolic groups represent extant bioinformatic proxies for ancient redox chemistries, extending from an anoxic origin through the GOE and ultimately to obligate aerobes [10-13]. Analysis of the network metric degree showed a strong relationship between cyanobacteria and obligate anaerobes, from which cyanobacteria presumably arose, for core functions that include translation, photosynthesis, energy conservation, and environmental interactions. These data were used to reconstruct primordial functions in cyanobacteria that included nine gene families involved in photosynthesis, hydrogenases, and proteins involved in defense from environmental stress. The presence of 60% of these genes in both reaction center I (RC-I) and RC-II-type bacteria may be explained by selective loss of either RC in the evolutionary history of some photosynthetic lineages. Finally, the network reveals that cyanobacteria occupy a unique position among prokaryotes as a hub between anaerobes and obligate aerobes.}, } @article {pmid25682266, year = {2015}, author = {Pert, PL and Ens, EJ and Locke, J and Clarke, PA and Packer, JM and Turpin, G}, title = {An online spatial database of Australian Indigenous Biocultural Knowledge for contemporary natural and cultural resource management.}, journal = {The Science of the total environment}, volume = {534}, number = {}, pages = {110-121}, doi = {10.1016/j.scitotenv.2015.01.073}, pmid = {25682266}, issn = {1879-1026}, mesh = {Australia ; Conservation of Natural Resources/*methods ; *Databases, Factual ; Humans ; }, abstract = {With growing international calls for the enhanced involvement of Indigenous peoples and their biocultural knowledge in managing conservation and the sustainable use of physical environment, it is timely to review the available literature and develop cross-cultural approaches to the management of biocultural resources. Online spatial databases are becoming common tools for educating land managers about Indigenous Biocultural Knowledge (IBK), specifically to raise a broad awareness of issues, identify knowledge gaps and opportunities, and to promote collaboration. Here we describe a novel approach to the application of internet and spatial analysis tools that provide an overview of publically available documented Australian IBK (AIBK) and outline the processes used to develop the online resource. By funding an AIBK working group, the Australian Centre for Ecological Analysis and Synthesis (ACEAS) provided a unique opportunity to bring together cross-cultural, cross-disciplinary and trans-organizational contributors who developed these resources. Without such an intentionally collaborative process, this unique tool would not have been developed. The tool developed through this process is derived from a spatial and temporal literature review, case studies and a compilation of methods, as well as other relevant AIBK papers. The online resource illustrates the depth and breadth of documented IBK and identifies opportunities for further work, partnerships and investment for the benefit of not only Indigenous Australians, but all Australians. The database currently includes links to over 1500 publically available IBK documents, of which 568 are geo-referenced and were mapped. It is anticipated that as awareness of the online resource grows, more documents will be provided through the website to build the database. It is envisaged that this will become a well-used tool, integral to future natural and cultural resource management and maintenance.}, } @article {pmid25681255, year = {2015}, author = {Konstantinidis, KT and Rosselló-Móra, R}, title = {Classifying the uncultivated microbial majority: A place for metagenomic data in the Candidatus proposal.}, journal = {Systematic and applied microbiology}, volume = {38}, number = {4}, pages = {223-230}, doi = {10.1016/j.syapm.2015.01.001}, pmid = {25681255}, issn = {1618-0984}, mesh = {*Bacteria/classification/genetics ; *Bacteriological Techniques ; *Computational Biology ; *Metagenomics ; *Single-Cell Analysis ; }, abstract = {Microbial taxonomists have generally been reluctant to accept the valid publication of names of uncultured taxa given that only pure cultures allow for a thorough description of the genealogy, genetics and phenotype of the putative taxa to be classified. The classification of conspicuous uncultured organisms has been considered into the Candidatus provisional status, but this is only possible with organisms for which it is possible to retrieve basic data on phylogeny, morphology, ecology and some metabolic traits that unequivocally identify them. The current developments on modern sequencing techniques, and especially metagenomics, allow the recognition of discrete populations of DNA sequences in environmental samples, which can be considered to belong to individual closely related populations that may be identified as members of yet-to-be described species. The recognition of such populations of (meta)genomes allow the retrieval of valuable taxonomic information, i.e. genealogy, genome, phenotypic coherence with other populations, and ecological relevant traits. Such traits may be included in the Candidatus proposals of environmentally occurring, yet uncultured species not exhibiting exceptional morphologies, phenotypes or ecological relevancies.}, } @article {pmid25679219, year = {2015}, author = {McMahon, MM and Deepak, A and Fernández-Baca, D and Boss, D and Sanderson, MJ}, title = {STBase: one million species trees for comparative biology.}, journal = {PloS one}, volume = {10}, number = {2}, pages = {e0117987}, pmid = {25679219}, issn = {1932-6203}, mesh = {Biology/*methods ; *Databases, Genetic ; Trees/*classification/*genetics ; User-Computer Interface ; }, abstract = {Comprehensively sampled phylogenetic trees provide the most compelling foundations for strong inferences in comparative evolutionary biology. Mismatches are common, however, between the taxa for which comparative data are available and the taxa sampled by published phylogenetic analyses. Moreover, many published phylogenies are gene trees, which cannot always be adapted immediately for species level comparisons because of discordance, gene duplication, and other confounding biological processes. A new database, STBase, lets comparative biologists quickly retrieve species level phylogenetic hypotheses in response to a query list of species names. The database consists of 1 million single- and multi-locus data sets, each with a confidence set of 1000 putative species trees, computed from GenBank sequence data for 413,000 eukaryotic taxa. Two bodies of theoretical work are leveraged to aid in the assembly of multi-locus concatenated data sets for species tree construction. First, multiply labeled gene trees are pruned to conflict-free singly-labeled species-level trees that can be combined between loci. Second, impacts of missing data in multi-locus data sets are ameliorated by assembling only decisive data sets. Data sets overlapping with the user's query are ranked using a scheme that depends on user-provided weights for tree quality and for taxonomic overlap of the tree with the query. Retrieval times are independent of the size of the database, typically a few seconds. Tree quality is assessed by a real-time evaluation of bootstrap support on just the overlapping subtree. Associated sequence alignments, tree files and metadata can be downloaded for subsequent analysis. STBase provides a tool for comparative biologists interested in exploiting the most relevant sequence data available for the taxa of interest. It may also serve as a prototype for future species tree oriented databases and as a resource for assembly of larger species phylogenies from precomputed trees.}, } @article {pmid25678942, year = {2015}, author = {Gao, XY and Zhi, XY and Li, HW and Zhou, Y and Lapidus, A and Han, J and Haynes, M and Lobos, E and Huntemann, M and Pati, A and Ivanova, NN and Mavromatis, K and Tindall, BJ and Markowitz, V and Woyke, T and Klenk, HP and Kyrpides, NC and Li, WJ}, title = {Draft genome sequence of Halomonas lutea strain YIM 91125(T) (DSM 23508(T)) isolated from the alkaline Lake Ebinur in Northwest China.}, journal = {Standards in genomic sciences}, volume = {10}, number = {}, pages = {1}, pmid = {25678942}, issn = {1944-3277}, abstract = {Species of the genus Halomonas are halophilic and their flexible adaption to changes of salinity and temperature brings considerable potential biotechnology applications, such as degradation of organic pollutants and enzyme production. The type strain Halomonas lutea YIM 91125(T) was isolated from a hypersaline lake in China. The genome of strain YIM 91125(T) becomes the twelfth species sequenced in Halomonas, and the thirteenth species sequenced in Halomonadaceae. We described the features of H. lutea YIM 91125(T), together with the high quality draft genome sequence and annotation of its type strain. The 4,533,090 bp long genome of strain YIM 91125(T) with its 4,284 protein-coding and 84 RNA genes is a part of Genomic Encyclopedia of Type Strains, Phase I: the one thousand microbial genomes (KMG-I) project. From the viewpoint of comparative genomics, H. lutea has a larger genome size and more specific genes, which indicated acquisition of function bringing better adaption to its environment. DDH analysis demonstrated that H. lutea is a distinctive species, and halophilic features and nitrogen metabolism related genes were discovered in its genome.}, } @article {pmid25672962, year = {2015}, author = {Morton, J and Withers, M and Konrad, SC and Buterbaugh, C and Spence, R}, title = {Bridging the gaps: An early integrated support collaborative for at risk mothers in rural Maine.}, journal = {Work (Reading, Mass.)}, volume = {50}, number = {3}, pages = {413-423}, doi = {10.3233/WOR-151999}, pmid = {25672962}, issn = {1875-9270}, mesh = {Community Networks/*organization & administration ; Female ; Health Services Accessibility ; Healthcare Disparities ; Humans ; Infant, Newborn ; Intensive Care, Neonatal ; Maine ; Models, Organizational ; *Mothers ; *Neonatal Abstinence Syndrome/therapy ; Poverty ; *Rural Health ; *Rural Population ; *Social Support ; Social Work ; }, abstract = {BACKGROUND: The antecedents that contribute to health disparities in maternal child health populations begin before birth and extend into the early prenatal and gestational growth periods. Mothers and infants living in rural poverty in particular are at considerable risk for problems associated with reproductive health, including pregnancy complications and premature births.

OBJECTIVE: The aim of this manuscript is thus two-fold, to describe the epidemiologic makeup of the community and the intervention model of the Community Caring Collaborative.

METHODS: Innovative models of early-integrated care for high-risk mothers and children are showing promise for long-term outcomes. They foster environments that enable mothers to trust health systems while maintaining a workforce of high functioning health workers who understand the mechanisms that underpin maternal and child health disparities. The Community Caring Collaborative in Washington County, Maine developed one such model that has made inroads in bridging such gaps. This manuscript explicates a case study of how the Community Caring Collaborative came into being and why it established the Bridging model of comprehensive care. The focus of this manuscript is thus two-fold, the community and the intervention model.

RESULTS: The "bridging model" develops trust-based relationships between high-risk mothers with the health system and its multiple resources. Community members with advanced training provide the support and care linkages that are critical for family success.

CONCLUSIONS: Innovative models of collaborative care impact the health of vulnerable mothers and their children working toward a marked decrease in health related disparities.}, } @article {pmid25669144, year = {2015}, author = {Campbell, HA and Beyer, HL and Dennis, TE and Dwyer, RG and Forester, JD and Fukuda, Y and Lynch, C and Hindell, MA and Menke, N and Morales, JM and Richardson, C and Rodgers, E and Taylor, G and Watts, ME and Westcott, DA}, title = {Finding our way: On the sharing and reuse of animal telemetry data in Australasia.}, journal = {The Science of the total environment}, volume = {534}, number = {}, pages = {79-84}, doi = {10.1016/j.scitotenv.2015.01.089}, pmid = {25669144}, issn = {1879-1026}, mesh = {Animals ; Australasia ; *Biodiversity ; Ecosystem ; Environmental Monitoring/*methods ; Geographic Information Systems ; *Telemetry ; }, abstract = {The presence and movements of organisms both reflect and influence the distribution of ecological resources in space and time. The monitoring of animal movement by telemetry devices is being increasingly used to inform management of marine, freshwater and terrestrial ecosystems. Here, we brought together academics, and environmental managers to determine the extent of animal movement research in the Australasian region, and assess the opportunities and challenges in the sharing and reuse of these data. This working group was formed under the Australian Centre for Ecological Analysis and Synthesis (ACEAS), whose overall aim was to facilitate trans-organisational and transdisciplinary synthesis. We discovered that between 2000 and 2012 at least 501 peer-reviewed scientific papers were published that report animal location data collected by telemetry devices from within the Australasian region. Collectively, this involved the capture and electronic tagging of 12 656 animals. The majority of studies were undertaken to address specific management questions; rarely were these data used beyond their original intent. We estimate that approximately half (~500) of all animal telemetry projects undertaken remained unpublished, a similar proportion were not discoverable via online resources, and less than 8.8% of all animals tagged and tracked had their data stored in a discoverable and accessible manner. Animal telemetry data contain a wealth of information about how animals and species interact with each other and the landscapes they inhabit. These data are expensive and difficult to collect and can reduce survivorship of the tagged individuals, which implies an ethical obligation to make the data available to the scientific community. This is the first study to quantify the gap between telemetry devices placed on animals and findings/data published, and presents methods for improvement. Instigation of these strategies will enhance the cost-effectiveness of the research and maximise its impact on the management of natural resources.}, } @article {pmid25666700, year = {2015}, author = {Wheeler, HC and Chipperfield, JD and Roland, C and Svenning, JC}, title = {How will the greening of the Arctic affect an important prey species and disturbance agent? Vegetation effects on arctic ground squirrels.}, journal = {Oecologia}, volume = {178}, number = {3}, pages = {915-929}, pmid = {25666700}, issn = {1432-1939}, mesh = {Alaska ; Animals ; Arctic Regions ; Bayes Theorem ; *Behavior, Animal ; *Climate Change ; *Ecosystem ; *Models, Theoretical ; *Plants ; Predatory Behavior ; Sciuridae/physiology/*psychology ; }, abstract = {Increases in terrestrial primary productivity across the Arctic and northern alpine ecosystems are leading to altered vegetation composition and stature. Changes in vegetation stature may affect predator-prey interactions via changes in the prey's ability to detect predators, changes in predation pressure, predator identity and predator foraging strategy. Changes in productivity and vegetation composition may also affect herbivores via effects on forage availability and quality. We investigated if height-dependent effects of forage and non-forage vegetation determine burrowing extent and activity of arctic ground squirrels (Urocitellus parryii). We collected data on burrow networks and activity of arctic ground squirrels across long-term vegetation monitoring sites in Denali National Park and Preserve, Alaska. The implications of height-specific cover of potential forage and non-forage vegetation on burrowing behaviour and habitat suitability for arctic ground squirrels were investigated using hierarchical Bayesian modelling. Increased cover of forbs was associated with more burrows and burrow systems, and higher activity of systems, for all forb heights. No other potential forage functional group was related to burrow distribution and activity. In contrast, height-dependent negative effects of non-forage vegetation were observed, with cover over 50-cm height negatively affecting the number of burrows, systems and system activity. Our results demonstrate that increases in vegetation productivity have dual, potentially counteracting effects on arctic ground squirrels via changes in forage and vegetation stature. Importantly, increases in tall-growing woody vegetation (shrubs and trees) have clear negative effects, whereas increases in forb should benefit arctic ground squirrels.}, } @article {pmid25660540, year = {2015}, author = {Zhao, C and Escalante, LN and Chen, H and Benatti, TR and Qu, J and Chellapilla, S and Waterhouse, RM and Wheeler, D and Andersson, MN and Bao, R and Batterton, M and Behura, SK and Blankenburg, KP and Caragea, D and Carolan, JC and Coyle, M and El-Bouhssini, M and Francisco, L and Friedrich, M and Gill, N and Grace, T and Grimmelikhuijzen, CJ and Han, Y and Hauser, F and Herndon, N and Holder, M and Ioannidis, P and Jackson, L and Javaid, M and Jhangiani, SN and Johnson, AJ and Kalra, D and Korchina, V and Kovar, CL and Lara, F and Lee, SL and Liu, X and Löfstedt, C and Mata, R and Mathew, T and Muzny, DM and Nagar, S and Nazareth, LV and Okwuonu, G and Ongeri, F and Perales, L and Peterson, BF and Pu, LL and Robertson, HM and Schemerhorn, BJ and Scherer, SE and Shreve, JT and Simmons, D and Subramanyam, S and Thornton, RL and Xue, K and Weissenberger, GM and Williams, CE and Worley, KC and Zhu, D and Zhu, Y and Harris, MO and Shukle, RH and Werren, JH and Zdobnov, EM and Chen, MS and Brown, SJ and Stuart, JJ and Richards, S}, title = {A massive expansion of effector genes underlies gall-formation in the wheat pest Mayetiola destructor.}, journal = {Current biology : CB}, volume = {25}, number = {5}, pages = {613-620}, doi = {10.1016/j.cub.2014.12.057}, pmid = {25660540}, issn = {1879-0445}, support = {U54 HG003273/HG/NHGRI NIH HHS/United States ; }, mesh = {Adaptation, Biological/genetics ; Amino Acid Sequence ; Animals ; Base Sequence ; Chromosomes/*genetics ; Diptera/*genetics/metabolism ; Larva/metabolism ; Models, Genetic ; Molecular Sequence Data ; Multigene Family/*genetics ; *Phylogeny ; Plant Tumors/*genetics ; Sequence Analysis, DNA ; Sequence Homology ; Sexual Behavior, Animal/physiology ; Triticum/*parasitology ; Two-Hybrid System Techniques ; Ubiquitin-Protein Ligases/genetics ; }, abstract = {Gall-forming arthropods are highly specialized herbivores that, in combination with their hosts, produce extended phenotypes with unique morphologies [1]. Many are economically important, and others have improved our understanding of ecology and adaptive radiation [2]. However, the mechanisms that these arthropods use to induce plant galls are poorly understood. We sequenced the genome of the Hessian fly (Mayetiola destructor; Diptera: Cecidomyiidae), a plant parasitic gall midge and a pest of wheat (Triticum spp.), with the aim of identifying genic modifications that contribute to its plant-parasitic lifestyle. Among several adaptive modifications, we discovered an expansive reservoir of potential effector proteins. Nearly 5% of the 20,163 predicted gene models matched putative effector gene transcripts present in the M. destructor larval salivary gland. Another 466 putative effectors were discovered among the genes that have no sequence similarities in other organisms. The largest known arthropod gene family (family SSGP-71) was also discovered within the effector reservoir. SSGP-71 proteins lack sequence homologies to other proteins, but their structures resemble both ubiquitin E3 ligases in plants and E3-ligase-mimicking effectors in plant pathogenic bacteria. SSGP-71 proteins and wheat Skp proteins interact in vivo. Mutations in different SSGP-71 genes avoid the effector-triggered immunity that is directed by the wheat resistance genes H6 and H9. Results point to effectors as the agents responsible for arthropod-induced plant gall formation.}, } @article {pmid25660373, year = {2015}, author = {Kainer, D and Lanfear, R}, title = {The effects of partitioning on phylogenetic inference.}, journal = {Molecular biology and evolution}, volume = {32}, number = {6}, pages = {1611-1627}, doi = {10.1093/molbev/msv026}, pmid = {25660373}, issn = {1537-1719}, mesh = {Classification/*methods ; Databases, Genetic ; Empirical Research ; Evolution, Molecular ; *Models, Genetic ; *Phylogeny ; }, abstract = {Partitioning is a commonly used method in phylogenetics that aims to accommodate variation in substitution patterns among sites. Despite its popularity, there have been few systematic studies of its effects on phylogenetic inference, and there have been no studies that compare the effects of different approaches to partitioning across many empirical data sets. In this study, we applied four commonly used approaches to partitioning to each of 34 empirical data sets, and then compared the resulting tree topologies, branch-lengths, and bootstrap support estimated using each approach. We find that the choice of partitioning scheme often affects tree topology, particularly when partitioning is omitted. Most notably, we find occasional instances where the use of a suboptimal partitioning scheme produces highly supported but incorrect nodes in the tree. Branch-lengths and bootstrap support are also affected by the choice of partitioning scheme, sometimes dramatically so. We discuss the reasons for these effects and make some suggestions for best practice.}, } @article {pmid25659310, year = {2015}, author = {Wang, Z and Mao, D and Li, L and Jia, M and Dong, Z and Miao, Z and Ren, C and Song, C}, title = {Quantifying changes in multiple ecosystem services during 1992-2012 in the Sanjiang Plain of China.}, journal = {The Science of the total environment}, volume = {514}, number = {}, pages = {119-130}, doi = {10.1016/j.scitotenv.2015.01.007}, pmid = {25659310}, issn = {1879-1026}, mesh = {Agriculture ; Carbon ; China ; Conservation of Natural Resources/*methods ; *Ecosystem ; Environment ; Environmental Monitoring/*methods ; Food ; Geographic Information Systems ; Rivers ; Soil ; Water ; Wetlands ; }, abstract = {Rapid and periodic assessment of the impact of land cover changes on ecosystem services at regional levels is essential to understanding services and sustainability of ecosystems. This study focused on quantifying and assessing changes of multiple ecosystem services in the Sanjiang Plain of China as a result of land cover changes over the period of 1992-2012. This region is important for its large area of natural wetlands and intensive agriculture. The ecosystem services that were assessed for this region included its regulating services (water yield and ecosystem carbon stocks), supporting services (suitable waterbird habitats), and provisioning services (food production), and the approach to the assessment was composed of the surface energy balance algorithms for land (SEBAL), soil survey re-sampling method and an empirical waterbird habitat suitability model. This large scale and integrated investigation represents the first systematic evaluation on the status of ecosystem carbon stocks in the Sanjiang Plain in addition to the development of an effective model for analysis of waterbird habitat suitability with the use of both remote sensing and geographic information systems (GIS). More importantly, the result from this study has confirmed trade-offs between ecosystem services and negative consequences to environment in this region. The trade-offs were typically manifested by increased water yield and significantly grown food production, which is in contrast with significant losses in ecosystem carbon stocks (-14%) and suitable waterbird habitats (-23%) mainly due to the conversion of land cover from wetland to farmland. This finding implies that land use planning and policy making for this economically important region should take ecosystem service losses into account in order to preserve its natural ecosystems in the best interest of society.}, } @article {pmid25657328, year = {2015}, author = {Gamble, T and Coryell, J and Ezaz, T and Lynch, J and Scantlebury, DP and Zarkower, D}, title = {Restriction Site-Associated DNA Sequencing (RAD-seq) Reveals an Extraordinary Number of Transitions among Gecko Sex-Determining Systems.}, journal = {Molecular biology and evolution}, volume = {32}, number = {5}, pages = {1296-1309}, doi = {10.1093/molbev/msv023}, pmid = {25657328}, issn = {1537-1719}, mesh = {Animals ; *Evolution, Molecular ; Female ; High-Throughput Nucleotide Sequencing ; Lizards/*genetics/physiology ; Male ; Phylogeny ; Restriction Mapping ; Sex Chromosomes/genetics ; *Sex Determination Processes ; Snakes/genetics/physiology ; }, abstract = {Sex chromosomes have evolved many times in animals and studying these replicate evolutionary "experiments" can help broaden our understanding of the general forces driving the origin and evolution of sex chromosomes. However this plan of study has been hindered by the inability to identify the sex chromosome systems in the large number of species with cryptic, homomorphic sex chromosomes. Restriction site-associated DNA sequencing (RAD-seq) is a critical enabling technology that can identify the sex chromosome systems in many species where traditional cytogenetic methods have failed. Using newly generated RAD-seq data from 12 gecko species, along with data from the literature, we reinterpret the evolution of sex-determining systems in lizards and snakes and test the hypothesis that sex chromosomes can routinely act as evolutionary traps. We uncovered between 17 and 25 transitions among gecko sex-determining systems. This is approximately one-half to two-thirds of the total number of transitions observed among all lizards and snakes. We find support for the hypothesis that sex chromosome systems can readily become trap-like and show that adding even a small number of species from understudied clades can greatly enhance hypothesis testing in a model-based phylogenetic framework. RAD-seq will undoubtedly prove useful in evaluating other species for male or female heterogamety, particularly the majority of fish, amphibian, and reptile species that lack visibly heteromorphic sex chromosomes, and will significantly accelerate the pace of biological discovery.}, } @article {pmid25654111, year = {2015}, author = {Fengler, S and Spirer, I and Neef, M and Ecke, M and Nieselt, K and Hampp, R}, title = {A whole-genome microarray study of Arabidopsis thaliana semisolid callus cultures exposed to microgravity and nonmicrogravity related spaceflight conditions for 5 days on board of Shenzhou 8.}, journal = {BioMed research international}, volume = {2015}, number = {}, pages = {547495}, pmid = {25654111}, issn = {2314-6141}, mesh = {Arabidopsis/*genetics/physiology ; Cluster Analysis ; Gene Expression Profiling ; Gene Expression Regulation, Plant ; Gene Ontology ; Genes, Plant ; *Genome, Plant ; Oligonucleotide Array Sequence Analysis/*methods ; *Space Flight ; *Spacecraft ; Temperature ; Tissue Culture Techniques/*methods ; *Weightlessness ; }, abstract = {The Simbox mission was the first joint space project between Germany and China in November 2011. Eleven-day-old Arabidopsis thaliana wild type semisolid callus cultures were integrated into fully automated plant cultivation containers and exposed to spaceflight conditions within the Simbox hardware on board of the spacecraft Shenzhou 8. The related ground experiment was conducted under similar conditions. The use of an in-flight centrifuge provided a 1 g gravitational field in space. The cells were metabolically quenched after 5 days via RNAlater injection. The impact on the Arabidopsis transcriptome was investigated by means of whole-genome gene expression analysis. The results show a major impact of nonmicrogravity related spaceflight conditions. Genes that were significantly altered in transcript abundance are mainly involved in protein phosphorylation and MAPK cascade-related signaling processes, as well as in the cellular defense and stress responses. In contrast to short-term effects of microgravity (seconds, minutes), this mission identified only minor changes after 5 days of microgravity. These concerned genes coding for proteins involved in the plastid-associated translation machinery, mitochondrial electron transport, and energy production.}, } @article {pmid25653834, year = {2014}, author = {Strasser, C and Kunze, J and Abrams, S and Cruse, P}, title = {DataUp: A tool to help researchers describe and share tabular data.}, journal = {F1000Research}, volume = {3}, number = {}, pages = {6}, pmid = {25653834}, issn = {2046-1402}, abstract = {Scientific datasets have immeasurable value, but they lose their value over time without proper documentation, long-term storage, and easy discovery and access. Across disciplines as diverse as astronomy, demography, archeology, and ecology, large numbers of small heterogeneous datasets (i.e., the long tail of data) are especially at risk unless they are properly documented, saved, and shared. One unifying factor for many of these at-risk datasets is that they reside in spreadsheets. In response to this need, the California Digital Library (CDL) partnered with Microsoft Research Connections and the Gordon and Betty Moore Foundation to create the DataUp data management tool for Microsoft Excel. Many researchers creating these small, heterogeneous datasets use Excel at some point in their data collection and analysis workflow, so we were interested in developing a data management tool that fits easily into those work flows and minimizes the learning curve for researchers. The DataUp project began in August 2011. We first formally assessed the needs of researchers by conducting surveys and interviews of our target research groups: earth, environmental, and ecological scientists. We found that, on average, researchers had very poor data management practices, were not aware of data centers or metadata standards, and did not understand the benefits of data management or sharing. Based on our survey results, we composed a list of desirable components and requirements and solicited feedback from the community to prioritize potential features of the DataUp tool. These requirements were then relayed to the software developers, and DataUp was successfully launched in October 2012.}, } @article {pmid25651398, year = {2015}, author = {Nowak, MD and Russo, G and Schlapbach, R and Huu, CN and Lenhard, M and Conti, E}, title = {The draft genome of Primula veris yields insights into the molecular basis of heterostyly.}, journal = {Genome biology}, volume = {16}, number = {1}, pages = {12}, pmid = {25651398}, issn = {1474-760X}, mesh = {Amino Acid Sequence ; *Biological Evolution ; Computational Biology ; Flowers/*genetics ; Gene Expression Profiling ; Gene Expression Regulation, Plant ; Genes, Plant ; *Genome, Plant ; Genome-Wide Association Study ; Genomics ; Genotype ; High-Throughput Nucleotide Sequencing ; Molecular Sequence Annotation ; Molecular Sequence Data ; *Phenotype ; Phylogeny ; Polymorphism, Single Nucleotide ; Primula/classification/*genetics ; Quantitative Trait Loci ; Sequence Alignment ; Transcriptome ; }, abstract = {BACKGROUND: The flowering plant Primula veris is a common spring blooming perennial that is widely cultivated throughout Europe. This species is an established model system in the study of the genetics, evolution, and ecology of heterostylous floral polymorphisms. Despite the long history of research focused on this and related species, the continued development of this system has been restricted due the absence of genomic and transcriptomic resources.

RESULTS: We present here a de novo draft genome assembly of P. veris covering 301.8 Mb, or approximately 63% of the estimated 479.22 Mb genome, with an N50 contig size of 9.5 Kb, an N50 scaffold size of 164 Kb, and containing an estimated 19,507 genes. The results of a RADseq bulk segregant analysis allow for the confident identification of four genome scaffolds that are linked to the P. veris S-locus. RNAseq data from both P. veris and the closely related species P. vulgaris allow for the characterization of 113 candidate heterostyly genes that show significant floral morph-specific differential expression. One candidate gene of particular interest is a duplicated GLOBOSA homolog that may be unique to Primula (PveGLO2), and is completely silenced in L-morph flowers.

CONCLUSIONS: The P. veris genome represents the first genome assembled from a heterostylous species, and thus provides an immensely important resource for future studies focused on the evolution and genetic dissection of heterostyly. As the first genome assembled from the Primulaceae, the P. veris genome will also facilitate the expanded application of phylogenomic methods in this diverse family and the eudicots as a whole.}, } @article {pmid25650858, year = {2014}, author = {Carvalho, RM and Nascimento, LF}, title = {Space-time description of dengue outbreaks in Cruzeiro, São Paulo, in 2006 and 2011.}, journal = {Revista da Associacao Medica Brasileira (1992)}, volume = {60}, number = {6}, pages = {565-570}, doi = {10.1590/1806-9282.60.06.016}, pmid = {25650858}, issn = {1806-9282}, mesh = {Brazil/epidemiology ; Cities/epidemiology ; Cluster Analysis ; Dengue/*epidemiology ; Disease Outbreaks/*statistics & numerical data ; Geographic Information Systems ; Geographic Mapping ; Humans ; Incidence ; Seasons ; *Spatio-Temporal Analysis ; }, abstract = {OBJECTIVE: to identify patterns in the spatial and temporal distribution of cases of dengue fever occurring in the city of Cruzeiro, state of São Paulo (SP).

METHODS: an ecological and exploratory study was undertaken using spatial analysis tools and data from dengue cases obtained on the SinanNet. The analysis was carried out by area, using the IBGE census sector as a unit. The months of March to June 2006 and 2011 were assessed, revealing progress of the disease. TerraView 3.3.1 was used to calculate the Global Moran's I, month to month, and the Kernel estimator.

RESULTS: in the year 2006, 691 cases of dengue fever (rate of 864.2 cases/100,000 inhabitants) were georeferenced; and the Moran's I and p-values were significant in the months of April and May (IM = 0.28; p = 0.01; IM = 0.20; p = 0.01) with higher densities in the central, north, northeast and south regions. In the year 2011, 654 cases of dengue fever (rate of 886.8 cases/100,000 inhabitants) were georeferenced; and the Moran's I and p-values were significant in the months of April and May (IM = 0.28; p = 0.01; IM = 0.16; p = 0.05) with densities in the same regions as 2006. The Global Moran's I is a global measure of spatial autocorrelation, which indicates the degree of spatial association in the set of information from the product in relation to the average. The I varies between -1 and +1 and can be attributed to a level of significance (p-value). The positive value points to a positive or direct spatial autocorrelation.

CONCLUSION: we were able to identify patterns in the spatial and temporal distribution of dengue cases occurring in the city of Cruzeiro, SP, and locate the census sectors where the outbreak began and how it evolved.}, } @article {pmid25648928, year = {2016}, author = {Gan, HM and Gan, HY and Tan, MH and Penny, SS and Willan, RC and Austin, CM}, title = {The complete mitogenome of the giant clam Tridacna squamosa (Heterodonta: Bivalvia: Tridacnidae).}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {5}, pages = {3220-3221}, doi = {10.3109/19401736.2015.1007355}, pmid = {25648928}, issn = {2470-1408}, mesh = {Animals ; Base Composition ; Bivalvia/*classification/*genetics ; Codon ; Computational Biology/methods ; Genes, Mitochondrial ; Genome Size ; *Genome, Mitochondrial ; Open Reading Frames ; Regulatory Sequences, Nucleic Acid ; Sequence Analysis, DNA ; Whole Genome Sequencing ; }, abstract = {The complete mitochondrial genome of the commercially and ecologically important and internationally vulnerable giant clam Tridacna squamosa was recovered by genome skimming using the MiSeq platform. The T. squamosa mitogenome has 20,930 base pairs (62.35% A+T content) and is made up of 12 protein-coding genes, 2 ribosomal subunit genes, 24 transfer RNAs, and a 2594 bp non-coding AT-rich region. The mitogenome has a relatively large insertion in the atp6 gene. This is the first mitogenome to be sequenced from the genus Tridacna, and the family Tridacnidae and represents a new gene order.}, } @article {pmid25648772, year = {2015}, author = {Simeonov, KP and Himmelstein, DS}, title = {Lung cancer incidence decreases with elevation: evidence for oxygen as an inhaled carcinogen.}, journal = {PeerJ}, volume = {3}, number = {}, pages = {e705}, pmid = {25648772}, issn = {2167-8359}, support = {T32 EB009383/EB/NIBIB NIH HHS/United States ; }, abstract = {The level of atmospheric oxygen, a driver of free radical damage and tumorigenesis, decreases sharply with rising elevation. To understand whether ambient oxygen plays a role in human carcinogenesis, we characterized age-adjusted cancer incidence (compiled by the National Cancer Institute from 2005 to 2009) across counties of the elevation-varying Western United States and compared trends displayed by respiratory cancer (lung) and non-respiratory cancers (breast, colorectal, and prostate). To adjust for important demographic and cancer-risk factors, 8-12 covariates were considered for each cancer. We produced regression models that captured known risks. Models demonstrated that elevation is strongly, negatively associated with lung cancer incidence (p < 10(-16)), but not with the incidence of non-respiratory cancers. For every 1,000 m rise in elevation, lung cancer incidence decreased by 7.23 99% CI [5.18-9.29] cases per 100,000 individuals, equivalent to 12.7% of the mean incidence, 56.8. As a predictor of lung cancer incidence, elevation was second only to smoking prevalence in terms of significance and effect size. Furthermore, no evidence of ecological fallacy or of confounding arising from evaluated factors was detected: the lung cancer association was robust to varying regression models, county stratification, and population subgrouping; additionally seven environmental correlates of elevation, such as exposure to sunlight and fine particulate matter, could not capture the association. Overall, our findings suggest the presence of an inhaled carcinogen inherently and inversely tied to elevation, offering epidemiological support for oxygen-driven tumorigenesis. Finally, highlighting the need to consider elevation in studies of lung cancer, we demonstrated that previously reported inverse lung cancer associations with radon and UVB became insignificant after accounting for elevation.}, } @article {pmid25647581, year = {2015}, author = {Sinclair, L and Osman, OA and Bertilsson, S and Eiler, A}, title = {Microbial community composition and diversity via 16S rRNA gene amplicons: evaluating the illumina platform.}, journal = {PloS one}, volume = {10}, number = {2}, pages = {e0116955}, pmid = {25647581}, issn = {1932-6203}, mesh = {Bacteria/*classification/*genetics ; *Biodiversity ; Computational Biology ; DNA, Bacterial/*genetics ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, DNA/*methods ; }, abstract = {As new sequencing technologies become cheaper and older ones disappear, laboratories switch vendors and platforms. Validating the new setups is a crucial part of conducting rigorous scientific research. Here we report on the reliability and biases of performing bacterial 16S rRNA gene amplicon paired-end sequencing on the MiSeq Illumina platform. We designed a protocol using 50 barcode pairs to run samples in parallel and coded a pipeline to process the data. Sequencing the same sediment sample in 248 replicates as well as 70 samples from alkaline soda lakes, we evaluated the performance of the method with regards to estimates of alpha and beta diversity. Using different purification and DNA quantification procedures we always found up to 5-fold differences in the yield of sequences between individually barcodes samples. Using either a one-step or a two-step PCR preparation resulted in significantly different estimates in both alpha and beta diversity. Comparing with a previous method based on 454 pyrosequencing, we found that our Illumina protocol performed in a similar manner - with the exception for evenness estimates where correspondence between the methods was low. We further quantified the data loss at every processing step eventually accumulating to 50% of the raw reads. When evaluating different OTU clustering methods, we observed a stark contrast between the results of QIIME with default settings and the more recent UPARSE algorithm when it comes to the number of OTUs generated. Still, overall trends in alpha and beta diversity corresponded highly using both clustering methods. Our procedure performed well considering the precisions of alpha and beta diversity estimates, with insignificant effects of individual barcodes. Comparative analyses suggest that 454 and Illumina sequence data can be combined if the same PCR protocol and bioinformatic workflows are used for describing patterns in richness, beta-diversity and taxonomic composition.}, } @article {pmid25646848, year = {2015}, author = {Mikulic-Petkovsek, M and Samoticha, J and Eler, K and Stampar, F and Veberic, R}, title = {Traditional elderflower beverages: a rich source of phenolic compounds with high antioxidant activity.}, journal = {Journal of agricultural and food chemistry}, volume = {63}, number = {5}, pages = {1477-1487}, doi = {10.1021/jf506005b}, pmid = {25646848}, issn = {1520-5118}, mesh = {Antioxidants/*chemistry ; Beverages/*analysis ; Chromatography, High Pressure Liquid ; Mass Spectrometry ; Plant Extracts/*chemistry ; Sambucus nigra/*chemistry ; }, abstract = {Traditional elderflower beverages are very popular due to their pleasing taste and pro-health properties. Phenolics were quantified in three elderflower extracts (methanolic extraction and two water extracts prepared as fresh drinks according to local recipes) with HPLC-MS. Chromatographic patterns of methanolic and water extracts were quite similar; however, content levels of individual compounds differed between the two extraction solvents. Two feruloylquinic acids and two p-coumaroyl-caffeoylquinic acids and different flavonol glycosides have been identified in elderflowers for the first time. Hydroxycinnamic acids and flavonol glycosides were the major phenolic constituents in elderflowers. Methanolic extract contained higher levels of all phenolic groups compared to water-extracted samples. The yield of elderflower extracts depended on extract solution and time of extraction. Elderflower beverages were characterized by high total phenolic content (91.09 to 746.63 mg GAE/L). The results confirmed that elderflower beverages (sabesa, syrup) should be recommended as a good source of phenolics in human diet.}, } @article {pmid25646484, year = {2015}, author = {Derelle, R and Torruella, G and Klimeš, V and Brinkmann, H and Kim, E and Vlček, Č and Lang, BF and Eliáš, M}, title = {Bacterial proteins pinpoint a single eukaryotic root.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {112}, number = {7}, pages = {E693-9}, pmid = {25646484}, issn = {1091-6490}, support = {55007424//Howard Hughes Medical Institute/United States ; }, mesh = {Bacteria/classification/genetics/*metabolism ; Bacterial Proteins/*physiology ; Datasets as Topic ; *Eukaryota ; Genes, Bacterial ; Phylogeny ; }, abstract = {The large phylogenetic distance separating eukaryotic genes and their archaeal orthologs has prevented identification of the position of the eukaryotic root in phylogenomic studies. Recently, an innovative approach has been proposed to circumvent this issue: the use as phylogenetic markers of proteins that have been transferred from bacterial donor sources to eukaryotes, after their emergence from Archaea. Using this approach, two recent independent studies have built phylogenomic datasets based on bacterial sequences, leading to different predictions of the eukaryotic root. Taking advantage of additional genome sequences from the jakobid Andalucia godoyi and the two known malawimonad species (Malawimonas jakobiformis and Malawimonas californiana), we reanalyzed these two phylogenomic datasets. We show that both datasets pinpoint the same phylogenetic position of the eukaryotic root that is between "Unikonta" and "Bikonta," with malawimonad and collodictyonid lineages on the Unikonta side of the root. Our results firmly indicate that (i) the supergroup Excavata is not monophyletic and (ii) the last common ancestor of eukaryotes was a biflagellate organism. Based on our results, we propose to rename the two major eukaryotic groups Unikonta and Bikonta as Opimoda and Diphoda, respectively.}, } @article {pmid25644986, year = {2015}, author = {Jia, P and Joyner, A}, title = {Human brucellosis occurrences in inner mongolia, China: a spatio-temporal distribution and ecological niche modeling approach.}, journal = {BMC infectious diseases}, volume = {15}, number = {}, pages = {36}, pmid = {25644986}, issn = {1471-2334}, mesh = {Animals ; Animals, Domestic ; Brucellosis/*epidemiology/etiology ; Disease Outbreaks ; *Environment ; Geographic Information Systems ; Humans ; *Models, Biological ; Mongolia/epidemiology ; Topography, Medical ; Zoonoses/epidemiology/etiology ; }, abstract = {BACKGROUND: Brucellosis is a common zoonotic disease and remains a major burden in both human and domesticated animal populations worldwide. Few geographic studies of human Brucellosis have been conducted, especially in China. Inner Mongolia of China is considered an appropriate area for the study of human Brucellosis due to its provision of a suitable environment for animals most responsible for human Brucellosis outbreaks.

METHODS: The aggregated numbers of human Brucellosis cases from 1951 to 2005 at the municipality level, and the yearly numbers and incidence rates of human Brucellosis cases from 2006 to 2010 at the county level were collected. Geographic Information Systems (GIS), remote sensing (RS) and ecological niche modeling (ENM) were integrated to study the distribution of human Brucellosis cases over 1951-2010.

RESULTS: Results indicate that areas of central and eastern Inner Mongolia provide a long-term suitable environment where human Brucellosis outbreaks have occurred and can be expected to persist. Other areas of northeast China and central Mongolia also contain similar environments.

CONCLUSIONS: This study is the first to combine advanced spatial statistical analysis with environmental modeling techniques when examining human Brucellosis outbreaks and will help to inform decision-making in the field of public health.}, } @article {pmid25644761, year = {2015}, author = {Gruber, B and Adamack, AT}, title = {landgenreport: a new r function to simplify landscape genetic analysis using resistance surface layers.}, journal = {Molecular ecology resources}, volume = {15}, number = {5}, pages = {1172-1178}, doi = {10.1111/1755-0998.12381}, pmid = {25644761}, issn = {1755-0998}, mesh = {Biostatistics/methods ; Computational Biology/*methods ; *Genetics, Population ; *Geography ; *Phylogeography ; *Software ; }, abstract = {We describe functions recently added to the r package popgenreport that can be used to perform a landscape genetic analysis (LGA) based on landscape resistance surfaces, which aims to detect the effect of landscape features on gene flow. These functions for the first time implement a LGA in a single framework. Although the approach has been shown to be a valuable tool to study gene flow in landscapes, it has not been widely used to date, despite the type of data being widely available. In part, this is likely due to the necessity to use several software packages to perform landscape genetic analyses. To apply LGA functions, two types of data sets are required: a data set with spatially referenced and genotyped individuals, and a resistance layer representing the effect of the landscape. The function outputs three pairwise distance matrices from these data: a genetic distance matrix, a cost distance matrix and a Euclidean distance matrix. Statistical tests are performed to test whether the cost matrix contributes to the understanding of the observed population structure. A full report on the analysis and outputs in the form of plots and tables of all intermediate steps of the LGA is produced. It is possible to customize the LGA to allow for different cost path approaches and measures of genetic distances. The package is written in the r language and is available through the Comprehensive r Archive. Comprehensive tutorials and information on how to install and use the package are provided at the authors' website (www.popgenreport.org).}, } @article {pmid25641830, year = {2015}, author = {Grieve, AP}, title = {How to test hypotheses if you must.}, journal = {Pharmaceutical statistics}, volume = {14}, number = {2}, pages = {139-150}, doi = {10.1002/pst.1667}, pmid = {25641830}, issn = {1539-1612}, mesh = {Bayes Theorem ; *Data Interpretation, Statistical ; Drug Discovery/*methods/*statistics & numerical data ; Humans ; Sample Size ; }, abstract = {Drug development is not the only industrial-scientific enterprise subject to government regulations. In some fields of ecology and environmental sciences, the application of statistical methods is also regulated by ordinance. Over the past 20years, ecologists and environmental scientists have argued against an unthinking application of null hypothesis significance tests. More recently, Canadian ecologists have suggested a new approach to significance testing, taking account of the costs of both type I and type II errors. In this paper, we investigate the implications of this for testing in drug development and demonstrate that its adoption leads directly to the likelihood principle and Bayesian approaches.}, } @article {pmid25641221, year = {2015}, author = {Sovic, MG and Fries, AC and Gibbs, HL}, title = {AftrRAD: a pipeline for accurate and efficient de novo assembly of RADseq data.}, journal = {Molecular ecology resources}, volume = {15}, number = {5}, pages = {1163-1171}, doi = {10.1111/1755-0998.12378}, pmid = {25641221}, issn = {1755-0998}, mesh = {Computational Biology/*methods ; High-Throughput Nucleotide Sequencing/*methods ; Sequence Analysis, DNA/*methods ; *Software ; }, abstract = {An increase in studies using restriction site-associated DNA sequencing (RADseq) methods has led to a need for both the development and assessment of novel bioinformatic tools that aid in the generation and analysis of these data. Here, we report the availability of AftrRAD, a bioinformatic pipeline that efficiently assembles and genotypes RADseq data, and outputs these data in various formats for downstream analyses. We use simulated and experimental data sets to evaluate AftrRAD's ability to perform accurate de novo assembly of loci, and we compare its performance with two other commonly used programs, stacks and pyrad. We demonstrate that AftrRAD is able to accurately assemble loci, while accounting for indel variation among alleles, in a more computationally efficient manner than currently available programs. AftrRAD run times are not strongly affected by the number of samples in the data set, making this program a useful tool when multicore systems are not available for parallel processing, or when data sets include large numbers of samples.}, } @article {pmid25636385, year = {2015}, author = {Nsoesie, EO and Kluberg, SA and Mekaru, SR and Majumder, MS and Khan, K and Hay, SI and Brownstein, JS}, title = {New digital technologies for the surveillance of infectious diseases at mass gathering events.}, journal = {Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases}, volume = {21}, number = {2}, pages = {134-140}, pmid = {25636385}, issn = {1469-0691}, support = {095066//Wellcome Trust/United Kingdom ; R01 LM010812/LM/NLM NIH HHS/United States ; }, mesh = {Cell Phone ; Communicable Diseases/*epidemiology/*transmission ; *Data Collection ; *Electronic Data Processing ; *Epidemiological Monitoring ; Humans ; Infection Control/*methods ; Internet ; Wireless Technology ; }, abstract = {Outbreaks of infectious diseases at mass gatherings can strain the health system of the host region and pose a threat to local and global health. In addition to strengthening existing surveillance systems, most host nations also use novel technologies to assess disease risk and augment traditional surveillance approaches. We review novel approaches to disease surveillance using the Internet, mobile phone applications, and wireless sensor networks. These novel approaches to disease surveillance can result in prompt detection.}, } @article {pmid25636035, year = {2015}, author = {Zhang, J and Li, Y and Chen, SS and Zhang, L and Wang, J and Yang, Y and Zhang, S and Pan, Y and Wang, Y and Yang, L}, title = {Systems pharmacology dissection of the anti-inflammatory mechanism for the medicinal herb Folium eriobotryae.}, journal = {International journal of molecular sciences}, volume = {16}, number = {2}, pages = {2913-2941}, pmid = {25636035}, issn = {1422-0067}, mesh = {Anti-Inflammatory Agents/*chemistry/pharmacology ; Caco-2 Cells ; Cell Line ; Databases, Factual ; Eriobotrya/*chemistry/metabolism ; Humans ; Metabolic Networks and Pathways/drug effects ; Mitogen-Activated Protein Kinases/metabolism ; NF-kappa B/metabolism ; Permeability/drug effects ; Plants, Medicinal/chemistry/metabolism ; Signal Transduction/drug effects ; }, abstract = {Inflammation is a hallmark of many diseases like diabetes, cancers, atherosclerosis and arthritis. Thus, lots of concerns have been raised toward developing novel anti-inflammatory agents. Many alternative herbal medicines possess excellent anti-inflammatory properties, yet their precise mechanisms of action are yet to be elucidated. Here, a novel systems pharmacology approach based on a large number of chemical, biological and pharmacological data was developed and exemplified by a probe herb Folium Eriobotryae, a widely used clinical anti-inflammatory botanic drug. The results show that 11 ingredients of this herb with favorable pharmacokinetic properties are predicted as active compounds for anti-inflammatory treatment. In addition, via systematic network analyses, their targets are identified to be 43 inflammation-associated proteins including especially COX2, ALOX5, PPARG, TNF and RELA that are mainly involved in the mitogen-activated protein kinase (MAPK) signaling pathway, the rheumatoid arthritis pathway and NF-κB signaling pathway. All these demonstrate that the integrated systems pharmacology method provides not only an effective tool to illustrate the anti-inflammatory mechanisms of herbs, but also a new systems-based approach for drug discovery from, but not limited to, herbs, especially when combined with further experimental validations.}, } @article {pmid25633965, year = {2014}, author = {Vijayakumar, P and Raut, AA and Kumar, P and Sharma, D and Mishra, A}, title = {De novo assembly and analysis of crow lungs transcriptome.}, journal = {Genome}, volume = {57}, number = {9}, pages = {499-506}, doi = {10.1139/gen-2014-0122}, pmid = {25633965}, issn = {1480-3321}, mesh = {Animals ; Avian Proteins/genetics ; Chickens/genetics ; Crows/*genetics/metabolism ; Finches/genetics ; Gene Expression Profiling ; Gene Ontology ; Genetic Markers ; Immune System Phenomena/genetics ; Lung/*metabolism ; *Transcriptome ; }, abstract = {The jungle crow (Corvus macrorhynchos) belongs to the order Passeriformes of bird species and is important for avian ecological and evolutionary genetics studies. However, there is limited information on the transcriptome data of this species. In the present study, we report the characterization of the lung transcriptome of the jungle crow using GS FLX Titanium XLR70. Altogether, 1,510,303 high-quality sequence reads with 581,198,230 bases was de novo assembled into 22,169 isotigs (isotig represents an individual transcript) and 784,009 singletons. Using these isotigs and 581,681 length-filtered (greater than 300 bp) singletons, 20,010 unique protein-coding genes were identified by BLASTx comparison against a nonredundant (nr) protein sequence database. Comparative analysis revealed that 46,604 (70.29%) and 51,642 (72.48%) of the assembled transcripts have significant similarity to zebra finch and chicken RefSeq proteins, respectively. As determined by GO annotation and KEGG pathway mapping, functional annotation of the unigenes recovered diverse biological functions and processes. Transcripts putatively involved in the immune response were identified. Furthermore, 20,599 single nucleotide polymorphisms (SNPs) and 7525 simple sequence repeats (SSRs) were retrieved from the assembled transcript database. This resource should lay an important base for future ecological, evolutionary, and conservation genetic studies on this species and in other related species.}, } @article {pmid25633715, year = {2015}, author = {Budd, A and Dinkel, H and Corpas, M and Fuller, JC and Rubinat, L and Devos, DP and Khoueiry, PH and Förstner, KU and Georgatos, F and Rowland, F and Sharan, M and Binder, JX and Grace, T and Traphagen, K and Gristwood, A and Wood, NT}, title = {Ten simple rules for organizing an unconference.}, journal = {PLoS computational biology}, volume = {11}, number = {1}, pages = {e1003905}, pmid = {25633715}, issn = {1553-7358}, mesh = {Communication ; Computational Biology/*organization & administration ; *Congresses as Topic ; Crowdsourcing ; Humans ; }, } @article {pmid25632000, year = {2015}, author = {Capitán, JA and Bock Axelsen, J and Manrubia, S}, title = {New patterns in human biogeography revealed by networks of contacts between linguistic groups.}, journal = {Proceedings. Biological sciences}, volume = {282}, number = {1802}, pages = {}, pmid = {25632000}, issn = {1471-2954}, mesh = {Cluster Analysis ; Databases, Factual ; Geography ; Humans ; *Language ; Linguistics/*methods ; Models, Theoretical ; }, abstract = {Human languages differ broadly in abundance and are distributed highly unevenly on the Earth. In many qualitative and quantitative aspects, they strongly resemble biodiversity distributions. An intriguing and previously unexplored issue is the architecture of the neighbouring relationships between human linguistic groups. Here we construct and characterize these networks of contacts and show that they represent a new kind of spatial network with uncommon structural properties. Remarkably, language networks share a meaningful property with food webs: both are quasi-interval graphs. In food webs, intervality is linked to the existence of a niche space of low dimensionality; in language networks, we show that the unique relevant variable is the area occupied by the speakers of a language. By means of a range model analogous to niche models in ecology, we show that a geometric restriction of perimeter covering by neighbouring linguistic domains explains the structural patterns observed. Our findings may be of interest in the development of models for language dynamics or regarding the propagation of cultural innovations. In relation to species distribution, they pose the question of whether the spatial features of species ranges share architecture, and eventually generating mechanism, with the distribution of human linguistic groups.}, } @article {pmid25631317, year = {2015}, author = {Lack, JB and Cardeno, CM and Crepeau, MW and Taylor, W and Corbett-Detig, RB and Stevens, KA and Langley, CH and Pool, JE}, title = {The Drosophila genome nexus: a population genomic resource of 623 Drosophila melanogaster genomes, including 197 from a single ancestral range population.}, journal = {Genetics}, volume = {199}, number = {4}, pages = {1229-1241}, pmid = {25631317}, issn = {1943-2631}, support = {R01 HG002942/HG/NHGRI NIH HHS/United States ; HG02942/HG/NHGRI NIH HHS/United States ; T32 HG002760/HG/NHGRI NIH HHS/United States ; F32 GM106594/GM/NIGMS NIH HHS/United States ; R01 GM111797/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Base Sequence ; Contig Mapping ; *Databases, Nucleic Acid ; Drosophila melanogaster/*genetics ; *Genome, Insect ; Molecular Sequence Data ; *Polymorphism, Genetic ; Sequence Alignment ; }, abstract = {Hundreds of wild-derived Drosophila melanogaster genomes have been published, but rigorous comparisons across data sets are precluded by differences in alignment methodology. The most common approach to reference-based genome assembly is a single round of alignment followed by quality filtering and variant detection. We evaluated variations and extensions of this approach and settled on an assembly strategy that utilizes two alignment programs and incorporates both substitutions and short indels to construct an updated reference for a second round of mapping prior to final variant detection. Utilizing this approach, we reassembled published D. melanogaster population genomic data sets and added unpublished genomes from several sub-Saharan populations. Most notably, we present aligned data from phase 3 of the Drosophila Population Genomics Project (DPGP3), which provides 197 genomes from a single ancestral range population of D. melanogaster (from Zambia). The large sample size, high genetic diversity, and potentially simpler demographic history of the DPGP3 sample will make this a highly valuable resource for fundamental population genetic research. The complete set of assemblies described here, termed the Drosophila Genome Nexus, presently comprises 623 consistently aligned genomes and is publicly available in multiple formats with supporting documentation and bioinformatic tools. This resource will greatly facilitate population genomic analysis in this model species by reducing the methodological differences between data sets.}, } @article {pmid25625634, year = {2015}, author = {Hu, X and Hong, W and Qiu, R and Hong, T and Chen, C and Wu, C}, title = {Geographic variations of ecosystem service intensity in Fuzhou City, China.}, journal = {The Science of the total environment}, volume = {512-513}, number = {}, pages = {215-226}, doi = {10.1016/j.scitotenv.2015.01.035}, pmid = {25625634}, issn = {1879-1026}, mesh = {China ; Cities ; Conservation of Natural Resources/*methods ; *Ecosystem ; Environmental Monitoring/*methods ; Geographic Information Systems ; }, abstract = {Ecosystem services are strongly influenced by the landscape configuration of natural and human systems. So they are heterogeneous across landscapes. However lack of the knowledge of spatial variations of ecosystem services constrains the effective management and conservation of ecosystems. We presented a spatially explicit and quantitative assessment of the geographic variations in ecosystem services for the Fuzhou City in 2009 using exploratory spatial data analysis (ESDA) and semivariance analysis. Results confirmed a significant and positive spatial autocorrelation, and revealed several hot-spots and cold-spots for the spatial distribution of ecosystem service intensity (ESI) in the study area. Also the trend surface analysis indicated that the level of ESI tended to be reduced gradually from north to south and from west to east, with a trough in the urban central area, which was quite in accordance with land-use structure. A more precise cluster map was then developed using the range of lag distance, deriving from semivariance analysis, as neighborhood size instead of default value in the software of ESRI ArcGIS 10.0, and geographical clusters where population growth and land-use pressure varied significantly and positively with ESI across the city were also created by geographically weighted regression (GWR). This study has good policy implications applicable to prioritize areas for conservation or construction, and design ecological corridor to improve ecosystem service delivery to benefiting areas.}, } @article {pmid25621766, year = {2015}, author = {Mikheyev, AS and Linksvayer, TA}, title = {Genes associated with ant social behavior show distinct transcriptional and evolutionary patterns.}, journal = {eLife}, volume = {4}, number = {}, pages = {e04775}, pmid = {25621766}, issn = {2050-084X}, mesh = {Aging/genetics ; Animals ; Ants/*genetics ; Behavior, Animal/*physiology ; *Evolution, Molecular ; Gene Expression Regulation ; Gene Ontology ; Gene Regulatory Networks ; *Genes, Insect ; Hierarchy, Social ; *Social Behavior ; *Transcription, Genetic ; Transcriptome/genetics ; }, abstract = {Studies of the genetic basis and evolution of complex social behavior emphasize either conserved or novel genes. To begin to reconcile these perspectives, we studied how the evolutionary conservation of genes associated with social behavior depends on regulatory context, and whether genes associated with social behavior exist in distinct regulatory and evolutionary contexts. We identified modules of co-expressed genes associated with age-based division of labor between nurses and foragers in the ant Monomorium pharaonis, and we studied the relationship between molecular evolution, connectivity, and expression. Highly connected and expressed genes were more evolutionarily conserved, as expected. However, compared to the rest of the genome, forager-upregulated genes were much more highly connected and conserved, while nurse-upregulated genes were less connected and more evolutionarily labile. Our results indicate that the genetic architecture of social behavior includes both highly connected and conserved components as well as loosely connected and evolutionarily labile components.}, } @article {pmid25621460, year = {2015}, author = {Foote, AD and Liu, Y and Thomas, GW and Vinař, T and Alföldi, J and Deng, J and Dugan, S and van Elk, CE and Hunter, ME and Joshi, V and Khan, Z and Kovar, C and Lee, SL and Lindblad-Toh, K and Mancia, A and Nielsen, R and Qin, X and Qu, J and Raney, BJ and Vijay, N and Wolf, JB and Hahn, MW and Muzny, DM and Worley, KC and Gilbert, MT and Gibbs, RA}, title = {Convergent evolution of the genomes of marine mammals.}, journal = {Nature genetics}, volume = {47}, number = {3}, pages = {272-275}, pmid = {25621460}, issn = {1546-1718}, support = {U41 HG002371/HG/NHGRI NIH HHS/United States ; U54 HG003067/HG/NHGRI NIH HHS/United States ; U54 HG003273/HG/NHGRI NIH HHS/United States ; U54 HG003067-08/HG/NHGRI NIH HHS/United States ; }, mesh = {Adaptation, Physiological/*genetics ; Amino Acid Substitution ; Animals ; *Evolution, Molecular ; *Genome ; Humans ; Mammals/*genetics ; Phenotype ; Phylogeny ; Selection, Genetic ; }, abstract = {Marine mammals from different mammalian orders share several phenotypic traits adapted to the aquatic environment and therefore represent a classic example of convergent evolution. To investigate convergent evolution at the genomic level, we sequenced and performed de novo assembly of the genomes of three species of marine mammals (the killer whale, walrus and manatee) from three mammalian orders that share independently evolved phenotypic adaptations to a marine existence. Our comparative genomic analyses found that convergent amino acid substitutions were widespread throughout the genome and that a subset of these substitutions were in genes evolving under positive selection and putatively associated with a marine phenotype. However, we found higher levels of convergent amino acid substitutions in a control set of terrestrial sister taxa to the marine mammals. Our results suggest that, whereas convergent molecular evolution is relatively common, adaptive molecular convergence linked to phenotypic convergence is comparatively rare.}, } @article {pmid25617550, year = {2014}, author = {López Barbancho, D and Terán de Frutos, JM and Candelas González, N and Díaz de Luna, MC and Marrodán Serrano, MD and Lomaglio, DB}, title = {[Weight-for-age percentile curves for the population of Catamarca province (Argentina)].}, journal = {Nutricion hospitalaria}, volume = {31}, number = {2}, pages = {682-688}, doi = {10.3305/nh.2015.31.2.7722}, pmid = {25617550}, issn = {1699-5198}, mesh = {Adult ; Argentina/epidemiology ; Birth Weight ; Body Weight/*physiology ; Data Interpretation, Statistical ; Female ; Fetal Development/*physiology ; Gestational Age ; Humans ; Infant, Newborn ; Pregnancy ; Reference Standards ; Reference Values ; }, abstract = {INTRODUCTION: The assessment of fetal development and birth weight is a priority in the field of nutritional epidemiology and public health. Nowadays, the World Health Organization (WHO) does not have specific birth weight curves for the distinct gestational weeks considering that socio-economic, ecological and ethnic characteristics of the different human groups are found influencing their own growth patterns.

OBJECTIVE: This research develops centile curves for weight by gestational age concerning to resident populations in the province of Catamarca.

METHODS: In order to process data, SPSS statistical program was used, as well as LMS Chart Maker pro program for the subsequent performing of centile curves. The sample ascended to a total of 22,576 childbirths between 1994 and 2003.

DISCUSSION AND CONCLUSION: In the future, these curves make possible a better assessment of intrauterine development and birth weight in this region of Northwest of Argentina.}, } @article {pmid25616198, year = {2015}, author = {Riedmann, RA and Gasic, B and Vernez, D}, title = {Sensitivity analysis, dominant factors, and robustness of the ECETOC TRA v3, Stoffenmanager 4.5, and ART 1.5 occupational exposure models.}, journal = {Risk analysis : an official publication of the Society for Risk Analysis}, volume = {35}, number = {2}, pages = {211-225}, doi = {10.1111/risa.12286}, pmid = {25616198}, issn = {1539-6924}, mesh = {Algorithms ; Decision Support Techniques ; Ecotoxicology/statistics & numerical data ; Hazardous Substances/toxicity ; Humans ; Models, Biological ; Models, Statistical ; Occupational Exposure/*adverse effects/statistics & numerical data ; Risk Assessment/*statistics & numerical data ; }, abstract = {Occupational exposure modeling is widely used in the context of the E.U. regulation on the registration, evaluation, authorization, and restriction of chemicals (REACH). First tier tools, such as European Centre for Ecotoxicology and TOxicology of Chemicals (ECETOC) targeted risk assessment (TRA) or Stoffenmanager, are used to screen a wide range of substances. Those of concern are investigated further using second tier tools, e.g., Advanced REACH Tool (ART). Local sensitivity analysis (SA) methods are used here to determine dominant factors for three models commonly used within the REACH framework: ECETOC TRA v3, Stoffenmanager 4.5, and ART 1.5. Based on the results of the SA, the robustness of the models is assessed. For ECETOC, the process category (PROC) is the most important factor. A failure to identify the correct PROC has severe consequences for the exposure estimate. Stoffenmanager is the most balanced model and decision making uncertainties in one modifying factor are less severe in Stoffenmanager. ART requires a careful evaluation of the decisions in the source compartment since it constitutes ∼75% of the total exposure range, which corresponds to an exposure estimate of 20-22 orders of magnitude. Our results indicate that there is a trade off between accuracy and precision of the models. Previous studies suggested that ART may lead to more accurate results in well-documented exposure situations. However, the choice of the adequate model should ultimately be determined by the quality of the available exposure data: if the practitioner is uncertain concerning two or more decisions in the entry parameters, Stoffenmanager may be more robust than ART.}, } @article {pmid25604335, year = {2015}, author = {Jabłoński, S and Rodowicz, P and Łukaszewicz, M}, title = {Methanogenic archaea database containing physiological and biochemical characteristics.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {65}, number = {Pt 4}, pages = {1360-1368}, doi = {10.1099/ijs.0.000065}, pmid = {25604335}, issn = {1466-5034}, mesh = {Anaerobiosis ; Archaea/*classification/growth & development/metabolism ; Base Composition ; Carbon Cycle ; *Databases, Factual ; Ecosystem ; Methane/biosynthesis ; Methanosarcina/metabolism ; RNA, Ribosomal, 16S/genetics ; Temperature ; }, abstract = {The methanogenic archaea are a group of micro-organisms that have developed a unique metabolic pathway for obtaining energy. There are 150 characterized species in this group; however, novel species continue to be discovered. Since methanogens are considered a crucial part of the carbon cycle in the anaerobic ecosystem, characterization of these micro-organisms is important for understanding anaerobic ecology. A methanogens database (MDB; http://metanogen.biotech.uni.wroc.pl/), including physiological and biochemical characteristics of methanogens, was constructed based on the descriptions of isolated type strains. Analysis of the data revealed that methanogens are able to grow from 0 to 122 °C. Methanogens growing at the same temperature may have very different growth rates. There is no clear correlation between the optimal growth temperature and the DNA G+C content. The following substrate preferences are observed in the database: 74.5% of archaea species utilize H2+CO2, 33% utilize methyl compounds and 8.5% utilize acetate. Utilization of methyl compounds (mainly micro-organisms belonging to the genera Methanosarcina and Methanolobus) is seldom accompanied by an ability to utilize H2+CO2. Very often, data for described species are incomplete, especially substrate preferences. Additional research leading to completion of missing information and development of standards, especially for substrate utilization, would be very helpful.}, } @article {pmid25600733, year = {2016}, author = {Szczecińska, M and Sawicki, J and Chmielewski, J and Bednarek-Ochyra, H and Ochyra, R}, title = {The complete mitochondrial genome of Niphotrichum ericoides (Bryophyta, Grimmiaceae).}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {5}, pages = {3065-3066}, doi = {10.3109/19401736.2014.1003911}, pmid = {25600733}, issn = {2470-1408}, mesh = {Base Composition ; Bryophyta/*classification/*genetics ; Computational Biology/methods ; Genes, Mitochondrial ; Genome Size ; *Genome, Mitochondrial ; Open Reading Frames ; Sequence Analysis, DNA ; Whole Genome Sequencing ; }, abstract = {The mitogenome of Niphotrichum ericoides (GenBank accession number KP 233863) has a total length of 106,727 bp and consists of 40 protein-coding genes, three ribosomal RNAs (rRNAs), and 24 transfer RNAs. The gene order is identical to that known in other moss mitogenomes.}, } @article {pmid25594128, year = {2015}, author = {Lesur, I and Bechade, A and Lalanne, C and Klopp, C and Noirot, C and Leplé, JC and Kremer, A and Plomion, C and Le Provost, G}, title = {A unigene set for European beech (Fagus sylvatica L.) and its use to decipher the molecular mechanisms involved in dormancy regulation.}, journal = {Molecular ecology resources}, volume = {15}, number = {5}, pages = {1192-1204}, doi = {10.1111/1755-0998.12373}, pmid = {25594128}, issn = {1755-0998}, mesh = {Europe ; Expressed Sequence Tags ; Fagus/*genetics/*physiology ; Gene Expression Profiling ; *Gene Expression Regulation, Plant ; Gene Library ; Gene Ontology ; *Genetic Association Studies ; Molecular Sequence Annotation ; Molecular Sequence Data ; *Plant Dormancy ; Polymorphism, Single Nucleotide ; Real-Time Polymerase Chain Reaction ; Sequence Analysis, DNA ; }, abstract = {Systematic sequencing is the method of choice for generating genomic resources for molecular marker development and candidate gene identification in nonmodel species. We generated 47,357 Sanger ESTs and 2.2M Roche-454 reads from five cDNA libraries for European beech (Fagus sylvatica L.). This tree species of high ecological and economic value in Europe is among the most representative trees of deciduous broadleaf forests. The sequences generated were assembled into 21,057 contigs with MIRA software. Functional annotations were obtained for 85% of these contigs, from the proteomes of four plant species, Swissprot accessions and the Gene Ontology database. We were able to identify 28,079 in silico SNPs for future marker development. Moreover, RNAseq and qPCR approaches identified genes and gene networks regulated differentially between two critical phenological stages preceding vegetative bud burst (the quiescent and swelling buds stages). According to climatic model-based projection, some European beech populations may be endangered, particularly at the southern and eastern edges of the European distribution range, which are strongly affected by current climate change. This first genomic resource for the genus Fagus should facilitate the identification of key genes for beech adaptation and management strategies for preserving beech adaptability.}, } @article {pmid25591712, year = {2014}, author = {Winder, IC}, title = {The biogeography of the Papio baboons: a GIS-based analysis of range characteristics and variability.}, journal = {Folia primatologica; international journal of primatology}, volume = {85}, number = {5}, pages = {292-318}, doi = {10.1159/000362545}, pmid = {25591712}, issn = {1421-9980}, mesh = {Africa ; *Animal Distribution ; Animals ; *Ecosystem ; Geographic Information Systems ; Papio/*physiology ; }, abstract = {The Papio baboons are known for their ecological flexibility and wide geographic ranges, as well as their uncertain taxonomy. There have, however, been few systematic comparisons of the environments occupied by the 6 major Papio species, and how differences in range conditions and variability might affect their evolutionary ecology remains unknown. This paper uses geographical information system techniques to explore the environmental associations of all 6 major species. It argues that despite some small differences in the average conditions encountered by each, it is in fact variation within individual ranges that is most apparent. In fact, the differences between the environments occupied by adjacent troops in well-known national parks may be as large or larger than the average differences in the ranges of different species, and this may have important implications for baboon biogeography.}, } @article {pmid25581442, year = {2015}, author = {Spielmann, A and Harris, SA and Boshier, DH and Vinson, CC}, title = {orchard: Paternity program for autotetraploid species.}, journal = {Molecular ecology resources}, volume = {15}, number = {4}, pages = {915-920}, doi = {10.1111/1755-0998.12370}, pmid = {25581442}, issn = {1755-0998}, mesh = {Computational Biology/*methods ; *DNA Fingerprinting ; Dipteryx/*genetics/*physiology ; *Gene Flow ; Microsatellite Repeats ; *Reproduction ; Software ; }, abstract = {Advances in molecular marker technology have provided new opportunities to study the population genetics of polyploid taxa. Paternity analysis using microsatellite markers can be used in detection of gene flow between individuals and populations, in mating system analysis, to identify factors that influence fecundity and fertility, to identify behaviour of parent-offspring relationships and in the analysis of the reproductive success of different ecological groups. As there is no specific program for carrying out paternity analysis in tetraploid species, specialized software was designed for the assignment of paternity for autotetraploid species. orchard is a novel implementation of exclusion and likelihood statistics for carrying out paternity analysis of autotetraploids. First, the program performs an exclusion method, and then, a likelihood statistic is used with nonexcluded candidate fathers. Optional features include estimation of allele dosage of known mother trees and the estimation of pollen flow distances. orchard was tested using a data set of microsatellite data of Dipteryx odorata, a tetraploid Amazonian tree species.}, } @article {pmid25576222, year = {2015}, author = {Niu, J and Hou, X and Fang, C and An, J and Ha, D and Qiu, L and Ju, Y and Zhao, H and Du, W and Qi, J and Zhang, Z and Liu, G and Lin, S}, title = {Transcriptome analysis of distinct Lindera glauca tissues revealed the differences in the unigenes related to terpenoid biosynthesis.}, journal = {Gene}, volume = {559}, number = {1}, pages = {22-30}, doi = {10.1016/j.gene.2015.01.002}, pmid = {25576222}, issn = {1879-0038}, mesh = {Databases, Nucleic Acid ; Gene Expression Regulation, Plant/*physiology ; Genes, Plant/*physiology ; Lindera/genetics/*metabolism ; Plant Components, Aerial/genetics/*metabolism ; Plant Roots/*metabolism ; Terpenes ; Transcriptome/*physiology ; }, abstract = {The Lindera glauca, an economically and ecologically important tree species, has emerged as a novel potential plant for the intensive studies of essential oil owing to its characteristic aroma and medicinal property in distinct tissues. However, the transcriptome information and molecular research on this species is still unknown to date. To reveal the formation and accumulation mechanism of essential oil in distinct L. glauca tissues, it is crucial to analyze transcriptome and to identify the full repertoire of potential unigenes involved in terpenoid biosynthesis. In this paper, the transcriptomes of the roots, sarcocarps, stems, leaves and kernels of L. glauca were analyzed for the first time by using short-read sequencing technology (Illumina). A total of 27.2GB valid reads (the average length=92.7bp) was obtained from distinct L. glauca tissues, and then assembled de novo into 264,831 unigenes by Trinity strategy (mean size=560.2bp). The resulting 98,141 unigenes (38%) of all the assembled unigenes were annotated in multiple public databases, of which 114 potential unigenes were identified to be involved in the terpenoid biosynthetic accumulation in L. glauca. Additionally, the differential expression profiles revealed 675, 697, 432, 1702 and 844 high tissue-specificity expressions of unigenes in the roots, sarcocarps, stems, leaves and kernels of L. glauca, respectively. Overall, these obtained comprehensive unigene resources will contribute to advance the research regarding the specific plant and more specifically discovery of genes participating in the terpenoid pathway and its regulation in specific tissues of the L. glauca, but also could help the understanding of the differential accumulation of secondary metabolites in distinct plant tissues.}, } @article {pmid25575307, year = {2015}, author = {Llorens-Marès, T and Yooseph, S and Goll, J and Hoffman, J and Vila-Costa, M and Borrego, CM and Dupont, CL and Casamayor, EO}, title = {Connecting biodiversity and potential functional role in modern euxinic environments by microbial metagenomics.}, journal = {The ISME journal}, volume = {9}, number = {7}, pages = {1648-1661}, pmid = {25575307}, issn = {1751-7370}, mesh = {Ammonia/metabolism ; Archaea/genetics ; Bacteria/*genetics ; *Biodiversity ; Carbon/metabolism ; Carbon Cycle/genetics ; Denitrification/genetics ; Lakes/chemistry/*microbiology ; Metagenomics/*methods ; Nitrates/metabolism ; Nitrification ; Nitrogen/metabolism ; Nitrogen Fixation/genetics ; Oxidation-Reduction ; Spain ; Sulfur/metabolism ; *Water Microbiology ; }, abstract = {Stratified sulfurous lakes are appropriate environments for studying the links between composition and functionality in microbial communities and are potentially modern analogs of anoxic conditions prevailing in the ancient ocean. We explored these aspects in the Lake Banyoles karstic area (NE Spain) through metagenomics and in silico reconstruction of carbon, nitrogen and sulfur metabolic pathways that were tightly coupled through a few bacterial groups. The potential for nitrogen fixation and denitrification was detected in both autotrophs and heterotrophs, with a major role for nitrogen and carbon fixations in Chlorobiaceae. Campylobacterales accounted for a large percentage of denitrification genes, while Gallionellales were putatively involved in denitrification, iron oxidation and carbon fixation and may have a major role in the biogeochemistry of the iron cycle. Bacteroidales were also abundant and showed potential for dissimilatory nitrate reduction to ammonium. The very low abundance of genes for nitrification, the minor presence of anammox genes, the high potential for nitrogen fixation and mineralization and the potential for chemotrophic CO2 fixation and CO oxidation all provide potential clues on the anoxic zones functioning. We observed higher gene abundance of ammonia-oxidizing bacteria than ammonia-oxidizing archaea that may have a geochemical and evolutionary link related to the dominance of Fe in these environments. Overall, these results offer a more detailed perspective on the microbial ecology of anoxic environments and may help to develop new geochemical proxies to infer biology and chemistry interactions in ancient ecosystems.}, } @article {pmid25571927, year = {2014}, author = {Malde, K}, title = {Estimating the information value of polymorphic sites using pooled sequences.}, journal = {BMC genomics}, volume = {15 Suppl 6}, number = {Suppl 6}, pages = {S20}, pmid = {25571927}, issn = {1471-2164}, mesh = {Algorithms ; Animals ; Computational Biology/*methods ; Datasets as Topic ; Gene Frequency ; Genomics/*methods ; *Polymorphism, Genetic ; Polymorphism, Single Nucleotide ; *Software ; }, abstract = {BACKGROUND: High-throughput sequencing is a cost effective method for identifying genetic variation, and it is currently in use on a large scale across the field of biology, including ecology and population genetics. Correctly identifying variable sites and allele frequencies from sequencing data remains challenging, in large part due to artifacts and biases inherent in the sequencing process. Selecting variants that are diagnostic is commonly done using diversity statistics like FST, but these measures are not ideal for the task.

RESULTS: Here, we develop a method that directly calculates the expected amount of information gained from observing each variant site. We then develop and implement a conservative estimator that takes into account uncertainity introduced by sampling bias and sequencing error. This estimator is applied to simulated and real sequencing data, and we discuss how it performs compared to the commonly used existing methods for identifying diagnostic polymorphisms.

CONCLUSION: The expected information content gives an easy to interpret measure for the usefulness of variant sites. The results show that we achieve a clear separation between true variants and noise, allowing us to select candidate sites with a high degree of confidence.}, } @article {pmid25571578, year = {2014}, author = {Seto, E and Hua, J and Wu, L and Bestick, A and Shia, V and Eom, S and Han, J and Wang, M and Li, Y}, title = {The Kunming CalFit study: modeling dietary behavioral patterns using smartphone data.}, journal = {Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference}, volume = {2014}, number = {}, pages = {6884-6887}, doi = {10.1109/EMBC.2014.6945210}, pmid = {25571578}, issn = {2694-0604}, mesh = {Accelerometry ; Adolescent ; Adult ; *Cell Phone ; *Diet ; Energy Intake ; Energy Metabolism ; Geographic Information Systems ; Humans ; *Models, Biological ; Young Adult ; }, abstract = {Human behavioral interventions aimed at improving health can benefit from objective wearable sensor data and mathematical models. Smartphone-based sensing is particularly practical for monitoring behavioral patterns because smartphones are fairly common, are carried by individuals throughout their daily lives, offer a variety of sensing modalities, and can facilitate various forms of user feedback for intervention studies. We describe our findings from a smartphone-based study, in which an Android-based application we developed called CalFit was used to collect information related to young adults' dietary behaviors. In addition to monitoring dietary patterns, we were interested in understanding contextual factors related to when and where an individual eats, as well as how their dietary intake relates to physical activity (which creates energy demand) and psychosocial stress. 12 participants were asked to use CalFit to record videos of their meals over two 1-week periods, which were translated into nutrient intake by trained dietitians. During this same period, triaxial accelerometry was used to assess each subject's energy expenditure, and GPS was used to record time-location patterns. Ecological momentary assessment was also used to prompt subjects to respond to questions on their phone about their psychological state. The GPS data were processed through a web service we developed called Foodscoremap that is based on the Google Places API to characterize food environments that subjects were exposed to, which may explain and influence dietary patterns. Furthermore, we describe a modeling framework that incorporates all of these information to dynamically infer behavioral patterns that may be used for future intervention studies.}, } @article {pmid25567671, year = {2015}, author = {Kampen, H and Medlock, JM and Vaux, AG and Koenraadt, CJ and van Vliet, AJ and Bartumeus, F and Oltra, A and Sousa, CA and Chouin, S and Werner, D}, title = {Approaches to passive mosquito surveillance in the EU.}, journal = {Parasites & vectors}, volume = {8}, number = {}, pages = {9}, pmid = {25567671}, issn = {1756-3305}, mesh = {*Animal Distribution ; Animals ; Culicidae/*classification/*physiology ; Databases, Factual ; *European Union ; Insect Vectors ; *Introduced Species ; Mosquito Control/methods ; Population Dynamics ; }, abstract = {The recent emergence in Europe of invasive mosquitoes and mosquito-borne disease associated with both invasive and native mosquito species has prompted intensified mosquito vector research in most European countries. Central to the efforts are mosquito monitoring and surveillance activities in order to assess the current species occurrence, distribution and, when possible, abundance, in order to permit the early detection of invasive species and the spread of competent vectors. As active mosquito collection, e.g. by trapping adults, dipping preimaginal developmental stages or ovitrapping, is usually cost-, time- and labour-intensive and can cover only small parts of a country, passive data collection approaches are gradually being integrated into monitoring programmes. Thus, scientists in several EU member states have recently initiated programmes for mosquito data collection and analysis that make use of sources other than targeted mosquito collection. While some of them extract mosquito distribution data from zoological databases established in other contexts, community-based approaches built upon the recognition, reporting, collection and submission of mosquito specimens by citizens are becoming more and more popular and increasingly support scientific research. Based on such reports and submissions, new populations, extended or new distribution areas and temporal activity patterns of invasive and native mosquito species were found. In all cases, extensive media work and communication with the participating individuals or groups was fundamental for success. The presented projects demonstrate that passive approaches are powerful tools to survey the mosquito fauna in order to supplement active mosquito surveillance strategies and render them more focused. Their ability to continuously produce biological data permits the early recognition of changes in the mosquito fauna that may have an impact on biting nuisance and the risk of pathogen transmission associated with mosquitoes. International coordination to explore synergies and increase efficiency of passive surveillance programmes across borders needs to be established.}, } @article {pmid25567233, year = {2015}, author = {Molnár, Z and Gellény, K and Margóczi, K and Biró, M}, title = {Landscape ethnoecological knowledge base and management of ecosystem services in a Székely-Hungarian pre-capitalistic village system (Transylvania, Romania).}, journal = {Journal of ethnobiology and ethnomedicine}, volume = {11}, number = {}, pages = {3}, pmid = {25567233}, issn = {1746-4269}, mesh = {Agriculture/*organization & administration ; *Conservation of Natural Resources ; Crops, Agricultural ; *Ecosystem ; Female ; Forests ; Humans ; Hungary ; *Knowledge Bases ; Male ; Romania/ethnology ; Rural Population ; }, abstract = {BACKGROUND: Previous studies showed an in-depth ecological understanding by traditional people of managing natural resources. We studied the landscape ethnoecological knowledge (LEEK) of Székelys on the basis of 16-19(th) century village laws. We analyzed the habitat types, ecosystem services and sustainable management types on which village laws had focused.

METHODS: Székelys had self-governed communities formed mostly of "noble peasants". Land-use was dominated by commons and regulated by village laws framed by the whole community. Seventy-two archival laws from 52 villages, resulting in 898 regulations, were analyzed using the DPSIR framework. Explicit and implicit information about the contemporary ecological knowledge of Székelys was extracted. We distinguished between responses that limited use and supported regeneration and those that protected produced/available ecosystem services and ensured their fair distribution.

RESULTS: Most regulations referred to forests (674), arable lands (562), meadows (448) and pastures (134). Székelys regulated the proportion of arable land, pasture and forest areas consciously in order to maximize long-term exploitation of ecosystem services. The inner territory was protected against overuse by relocating certain uses to the outer territory. Competition for ecosystem services was demonstrated by conflicts of pressure-related (mostly personal) and response-related (mostly communal) driving forces. Felling of trees (oaks), grazing of forests, meadows and fallows, masting, use of wild apple/pear trees and fishing were strictly regulated. Cutting of leaf-fodder, grazing of green crops, burning of forest litter and the polluting of streams were prohibited. Marketing by villagers and inviting outsiders to use the ecosystem services were strictly regulated, and mostly prohibited. Székelys recognized at least 71 folk habitat types, understood ecological regeneration and degradation processes, the history of their landscape and the management possibilities of ecosystem services. Some aspects of LEEK were so well known within Székely communities that they were not made explicit in village laws, others remained implicit because they were not related to regulations.

CONCLUSIONS: Based on explicit and implicit information, we argue that Székelys possessed detailed knowledge of the local ecological system. Moreover the world's first known explicit mention of ecosystem services ("Benefits that are provided by Nature for free") originated from this region from 1786.}, } @article {pmid25563415, year = {2015}, author = {Unno, T}, title = {Bioinformatic Suggestions on MiSeq-Based Microbial Community Analysis.}, journal = {Journal of microbiology and biotechnology}, volume = {25}, number = {6}, pages = {765-770}, doi = {10.4014/jmb.1409.09057}, pmid = {25563415}, issn = {1738-8872}, mesh = {*Biota ; Computational Biology/*methods ; High-Throughput Nucleotide Sequencing/*methods ; }, abstract = {Recent sequencing technology development has revolutionized fields of microbial ecology. MiSeq-based microbial community analysis allows us to sequence more than a few hundred samples at a time, which is far more cost-effective than pyrosequencing. The approach, however, has not been preferably used owing to computational difficulties of processing huge amounts of data as well as known Illumina-derived artefact problems with amplicon sequencing. The choice of assembly software to take advantage of paired-end sequencing and methods to remove Illumina artefacts sequences are discussed. The protocol we suggest not only removed erroneous reads, but also dramatically reduced computational workload, which allows even a typical desktop computer to process a huge amount of sequence data generated with Illumina sequencers. We also developed a Web interface (http://biotech.jejunu.ac.kr/ ~abl/16s/) that allows users to conduct fastq-merging and mothur batch creation. The study presented here should provide technical advantages and supports in applying MiSeq-based microbial community analysis.}, } @article {pmid25562316, year = {2015}, author = {Deans, AR and Lewis, SE and Huala, E and Anzaldo, SS and Ashburner, M and Balhoff, JP and Blackburn, DC and Blake, JA and Burleigh, JG and Chanet, B and Cooper, LD and Courtot, M and Csösz, S and Cui, H and Dahdul, W and Das, S and Dececchi, TA and Dettai, A and Diogo, R and Druzinsky, RE and Dumontier, M and Franz, NM and Friedrich, F and Gkoutos, GV and Haendel, M and Harmon, LJ and Hayamizu, TF and He, Y and Hines, HM and Ibrahim, N and Jackson, LM and Jaiswal, P and James-Zorn, C and Köhler, S and Lecointre, G and Lapp, H and Lawrence, CJ and Le Novère, N and Lundberg, JG and Macklin, J and Mast, AR and Midford, PE and Mikó, I and Mungall, CJ and Oellrich, A and Osumi-Sutherland, D and Parkinson, H and Ramírez, MJ and Richter, S and Robinson, PN and Ruttenberg, A and Schulz, KS and Segerdell, E and Seltmann, KC and Sharkey, MJ and Smith, AD and Smith, B and Specht, CD and Squires, RB and Thacker, RW and Thessen, A and Fernandez-Triana, J and Vihinen, M and Vize, PD and Vogt, L and Wall, CE and Walls, RL and Westerfeld, M and Wharton, RA and Wirkner, CS and Woolley, JB and Yoder, MJ and Zorn, AM and Mabee, P}, title = {Finding our way through phenotypes.}, journal = {PLoS biology}, volume = {13}, number = {1}, pages = {e1002033}, pmid = {25562316}, issn = {1545-7885}, support = {BBS/E/B/000C0419/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; P30 CA034196/CA/NCI NIH HHS/United States ; P41 HD064556/HD/NICHD NIH HHS/United States ; U41 HG000330/HG/NHGRI NIH HHS/United States ; }, mesh = {Animals ; Computational Biology ; Data Curation ; Databases, Factual/standards ; Gene-Environment Interaction ; *Genetic Association Studies ; Genomics ; Humans ; Phenotype ; Reference Standards ; Reproducibility of Results ; Terminology as Topic ; }, abstract = {Despite a large and multifaceted effort to understand the vast landscape of phenotypic data, their current form inhibits productive data analysis. The lack of a community-wide, consensus-based, human- and machine-interpretable language for describing phenotypes and their genomic and environmental contexts is perhaps the most pressing scientific bottleneck to integration across many key fields in biology, including genomics, systems biology, development, medicine, evolution, ecology, and systematics. Here we survey the current phenomics landscape, including data resources and handling, and the progress that has been made to accurately capture relevant data descriptions for phenotypes. We present an example of the kind of integration across domains that computable phenotypes would enable, and we call upon the broader biology community, publishers, and relevant funding agencies to support efforts to surmount today's data barriers and facilitate analytical reproducibility.}, } @article {pmid25561675, year = {2015}, author = {Buerki, S and Callmander, MW and Bachman, S and Moat, J and Labat, JN and Forest, F}, title = {Incorporating evolutionary history into conservation planning in biodiversity hotspots.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {370}, number = {1662}, pages = {20140014}, pmid = {25561675}, issn = {1471-2970}, mesh = {Base Sequence ; *Biodiversity ; *Biological Evolution ; Cluster Analysis ; Computational Biology ; Conservation of Natural Resources/*methods ; *Ecosystem ; Fabaceae/*genetics/physiology ; Geography ; Madagascar ; *Models, Biological ; Models, Genetic ; Molecular Sequence Data ; *Phylogeny ; Sequence Alignment ; }, abstract = {There is increased evidence that incorporating evolutionary history directly in conservation actions is beneficial, particularly given the likelihood that extinction is not random and that phylogenetic diversity (PD) is lost at higher rates than species diversity. This evidence is even more compelling in biodiversity hotspots, such as Madagascar, where less than 10% of the original vegetation remains. Here, we use the Leguminosae, an ecologically and economically important plant family, and a combination of phylogenetics and species distribution modelling, to assess biodiversity patterns and identify regions, coevolutionary processes and ecological factors that are important in shaping this diversity, especially during the Quaternary. We show evidence that species distribution and community PD are predicted by watershed boundaries, which enable the identification of a network of refugia and dispersal corridors that were perhaps important for maintaining community integrity during past climate change. Phylogenetically clustered communities are found in the southwest of the island at low elevation and share a suite of morphological characters (especially fruit morphology) indicative of coevolution with their main dispersers, the extinct and extant lemurs. Phylogenetically over-dispersed communities are found along the eastern coast at sea level and may have resulted from many independent dispersal events from the drier and more seasonal regions of Madagascar.}, } @article {pmid25559385, year = {2015}, author = {Gryseels, S and Rieger, T and Oestereich, L and Cuypers, B and Borremans, B and Makundi, R and Leirs, H and Günther, S and Goüy de Bellocq, J}, title = {Gairo virus, a novel arenavirus of the widespread Mastomys natalensis: Genetically divergent, but ecologically similar to Lassa and Morogoro viruses.}, journal = {Virology}, volume = {476}, number = {}, pages = {249-256}, doi = {10.1016/j.virol.2014.12.011}, pmid = {25559385}, issn = {1096-0341}, mesh = {Animals ; Antibodies, Viral/immunology ; Arenaviridae Infections/immunology/*veterinary/virology ; Arenavirus/classification/genetics/*isolation & purification ; Disease Reservoirs/virology ; Female ; *Genetic Variation ; Lassa virus/classification/genetics/isolation & purification ; Male ; Molecular Sequence Data ; Murinae/immunology/*virology ; Phylogeny ; Rodent Diseases/immunology/*virology ; Tanzania ; }, abstract = {Despite its near pan-African range, the Natal multimammate mouse, Mastomys natalensis, carries the human pathogen Lassa virus only in West Africa, while the seemingly non-pathogenic arenaviruses Mopeia, Morogoro, and Luna have been detected in this semi-commensal rodent in Mozambique/Zimbabwe, Tanzania and Zambia, respectively. Here, we describe a novel arenavirus in M. natalensis from Gairo district of central Tanzania, for which we propose the name "Gairo virus". Surprisingly, the virus is not closely related with Morogoro virus that infects M. natalensis only 90km south of Gairo, but clusters phylogenetically with Mobala-like viruses that infect non-M. natalensis host species in Central African Republic and Ethiopia. Despite the evolutionary distance, Gairo virus shares basic ecological features with the other M. natalensis-borne viruses Lassa and Morogoro. Our data show that M. natalensis, carrying distantly related viruses even in the same geographical area, is a potent reservoir host for a variety of arenaviruses.}, } @article {pmid25559297, year = {2015}, author = {Li, H and Yao, W and Fu, Y and Li, S and Guo, Q}, title = {De novo assembly and discovery of genes that are involved in drought tolerance in Tibetan Sophora moorcroftiana.}, journal = {PloS one}, volume = {10}, number = {1}, pages = {e111054}, pmid = {25559297}, issn = {1932-6203}, mesh = {Adaptation, Physiological/*genetics ; Altitude ; Cluster Analysis ; *Droughts ; Ecosystem ; Gene Expression Profiling/methods ; *Gene Expression Regulation, Plant ; Gene Ontology ; Molecular Sequence Annotation ; Reverse Transcriptase Polymerase Chain Reaction ; Sequence Analysis, DNA/methods ; Sophora/*genetics ; Tibet ; *Transcriptome ; }, abstract = {Sophora moorcroftiana, a Leguminosae shrub species that is restricted to the arid and semi-arid regions of the Qinghai-Tibet Plateau, is an ecologically important foundation species and exhibits substantial drought tolerance in the Plateau. There are no functional genomics resources in public databases for understanding the molecular mechanism underlying the drought tolerance of S. moorcroftiana. Therefore, we performed a large-scale transcriptome sequencing of this species under drought stress using the Illumina sequencing technology. A total of 62,348,602 clean reads were obtained. The assembly of the clean reads resulted in 146,943 transcripts, including 66,026 unigenes. In the assembled sequences, 1534 transcription factors were identified and classified into 23 different common families, and 9040 SSR loci, from di- to hexa-nucleotides, whose repeat number is greater than five, were presented. In addition, we performed a gene expression profiling analysis upon dehydration treatment. The results indicated significant differences in the gene expression profiles among the control, mild stress and severe stress. In total, 4687, 5648 and 5735 genes were identified from the comparison of mild versus control, severe versus control and severe versus mild stress, respectively. Based on the differentially expressed genes, a Gene Ontology annotation analysis indicated many dehydration-relevant categories, including 'response to water 'stimulus' and 'response to water deprivation'. Meanwhile, the Kyoto Encyclopedia of Genes and Genomes pathway analysis uncovered some important pathways, such as 'metabolic pathways' and 'plant hormone signal transduction'. In addition, the expression patterns of 25 putative genes that are involved in drought tolerance resulting from quantitative real-time PCR were consistent with their transcript abundance changes as identified by RNA-seq. The globally sequenced genes covered a considerable proportion of the S. moorcroftiana transcriptome, and the expression results may be useful to further extend the knowledge on the drought tolerance of this plant species that survives under Plateau conditions.}, } @article {pmid25556688, year = {2015}, author = {Garay, J and Varga, Z and Gámez, M and Cabello, T}, title = {Functional response and population dynamics for fighting predator, based on activity distribution.}, journal = {Journal of theoretical biology}, volume = {368}, number = {}, pages = {74-82}, doi = {10.1016/j.jtbi.2014.12.012}, pmid = {25556688}, issn = {1095-8541}, mesh = {Algorithms ; Animals ; Ecosystem ; *Models, Biological ; *Population Dynamics ; Predatory Behavior/*physiology ; }, abstract = {The classical Holling type II functional response, describing the per capita predation as a function of prey density, was modified by Beddington and de Angelis to include interference of predators that increases with predator density and decreases the number of killed prey. In the present paper we further generalize the Beddington-de Angelis functional response, considering that all predator activities (searching and handling prey, fight and recovery) have time duration, the probabilities of predator activities depend on the encounter probabilities, and hence on the prey and predator abundance, too. Under these conditions, the aim of the study is to introduce a functional response for fighting the predator and to analyse the corresponding dynamics, when predator-predator-prey encounters also occur. From this general approach, the Holling type functional responses can also be obtained as particular cases. In terms of the activity distribution, we give biologically interpretable sufficient conditions for stable coexistence. We consider two-individual (predator-prey) and three-individual (predator-predator-prey) encounters. In the three-individual encounter model there is a relatively higher fighting rate and a lower killing rate. Using numerical simulation, we surprisingly found that when the intrinsic prey growth rate and the conversion rate are small enough, the equilibrium predator abundance is higher in the three-individual encounter case. The above means that, when the equilibrium abundance of the predator is small, coexistence appears first in the three-individual encounter model.}, } @article {pmid25554792, year = {2015}, author = {Neafsey, DE and Waterhouse, RM and Abai, MR and Aganezov, SS and Alekseyev, MA and Allen, JE and Amon, J and Arcà, B and Arensburger, P and Artemov, G and Assour, LA and Basseri, H and Berlin, A and Birren, BW and Blandin, SA and Brockman, AI and Burkot, TR and Burt, A and Chan, CS and Chauve, C and Chiu, JC and Christensen, M and Costantini, C and Davidson, VL and Deligianni, E and Dottorini, T and Dritsou, V and Gabriel, SB and Guelbeogo, WM and Hall, AB and Han, MV and Hlaing, T and Hughes, DS and Jenkins, AM and Jiang, X and Jungreis, I and Kakani, EG and Kamali, M and Kemppainen, P and Kennedy, RC and Kirmitzoglou, IK and Koekemoer, LL and Laban, N and Langridge, N and Lawniczak, MK and Lirakis, M and Lobo, NF and Lowy, E and MacCallum, RM and Mao, C and Maslen, G and Mbogo, C and McCarthy, J and Michel, K and Mitchell, SN and Moore, W and Murphy, KA and Naumenko, AN and Nolan, T and Novoa, EM and O'Loughlin, S and Oringanje, C and Oshaghi, MA and Pakpour, N and Papathanos, PA and Peery, AN and Povelones, M and Prakash, A and Price, DP and Rajaraman, A and Reimer, LJ and Rinker, DC and Rokas, A and Russell, TL and Sagnon, N and Sharakhova, MV and Shea, T and Simão, FA and Simard, F and Slotman, MA and Somboon, P and Stegniy, V and Struchiner, CJ and Thomas, GW and Tojo, M and Topalis, P and Tubio, JM and Unger, MF and Vontas, J and Walton, C and Wilding, CS and Willis, JH and Wu, YC and Yan, G and Zdobnov, EM and Zhou, X and Catteruccia, F and Christophides, GK and Collins, FH and Cornman, RS and Crisanti, A and Donnelly, MJ and Emrich, SJ and Fontaine, MC and Gelbart, W and Hahn, MW and Hansen, IA and Howell, PI and Kafatos, FC and Kellis, M and Lawson, D and Louis, C and Luckhart, S and Muskavitch, MA and Ribeiro, JM and Riehle, MA and Sharakhov, IV and Tu, Z and Zwiebel, LJ and Besansky, NJ}, title = {Mosquito genomics. Highly evolvable malaria vectors: the genomes of 16 Anopheles mosquitoes.}, journal = {Science (New York, N.Y.)}, volume = {347}, number = {6217}, pages = {1258522}, pmid = {25554792}, issn = {1095-9203}, support = {R01 AI080799/AI/NIAID NIH HHS/United States ; R21 AI101459/AI/NIAID NIH HHS/United States ; U41 HG007234/HG/NHGRI NIH HHS/United States ; U19 AI089686/AI/NIAID NIH HHS/United States ; U19 AI110818/AI/NIAID NIH HHS/United States ; R01 AI104956/AI/NIAID NIH HHS/United States ; R01 AI050243/AI/NIAID NIH HHS/United States ; U54 HG003067/HG/NHGRI NIH HHS/United States ; T32 GM080178/GM/NIGMS NIH HHS/United States ; R01 AI095842/AI/NIAID NIH HHS/United States ; R01 AI073745/AI/NIAID NIH HHS/United States ; SC1 AI109055/AI/NIAID NIH HHS/United States ; G1100339/MRC_/Medical Research Council/United Kingdom ; R01 AI063508/AI/NIAID NIH HHS/United States ; R56 AI107263/AI/NIAID NIH HHS/United States ; R01 AI076584/AI/NIAID NIH HHS/United States ; 092654//Wellcome Trust/United Kingdom ; }, mesh = {Animals ; Anopheles/classification/*genetics ; Base Sequence ; Chromosomes, Insect/genetics ; Drosophila/genetics ; *Evolution, Molecular ; *Genome, Insect ; Humans ; Insect Vectors/classification/*genetics ; Malaria/*transmission ; Molecular Sequence Data ; Phylogeny ; Sequence Alignment ; }, abstract = {Variation in vectorial capacity for human malaria among Anopheles mosquito species is determined by many factors, including behavior, immunity, and life history. To investigate the genomic basis of vectorial capacity and explore new avenues for vector control, we sequenced the genomes of 16 anopheline mosquito species from diverse locations spanning ~100 million years of evolution. Comparative analyses show faster rates of gene gain and loss, elevated gene shuffling on the X chromosome, and more intron losses, relative to Drosophila. Some determinants of vectorial capacity, such as chemosensory genes, do not show elevated turnover but instead diversify through protein-sequence changes. This dynamism of anopheline genes and genomes may contribute to their flexible capacity to take advantage of new ecological niches, including adapting to humans as primary hosts.}, } @article {pmid25553568, year = {2015}, author = {Meerburg, FA and Boon, N and Van Winckel, T and Vercamer, JAR and Nopens, I and Vlaeminck, SE}, title = {Toward energy-neutral wastewater treatment: a high-rate contact stabilization process to maximally recover sewage organics.}, journal = {Bioresource technology}, volume = {179}, number = {}, pages = {373-381}, doi = {10.1016/j.biortech.2014.12.018}, pmid = {25553568}, issn = {1873-2976}, mesh = {Biological Oxygen Demand Analysis ; Carbon/analysis ; Chemical Fractionation ; Kinetics ; Methane/biosynthesis ; Organic Chemicals/*isolation & purification ; Sewage/*chemistry ; Thermodynamics ; Wastewater/*chemistry ; Water Purification/*methods ; }, abstract = {The conventional activated sludge process is widely used for wastewater treatment, but to progress toward energy self-sufficiency, the wastewater treatment scheme needs to radically improve energy balances. We developed a high-rate contact stabilization (HiCS) reactor system at high sludge-specific loading rates (>2 kg bCOD kg(-1)TSS d(-1)) and low sludge retention times (<1.2 d) and demonstrate that it is able to recover more chemical energy from wastewater organics than high-rate conventional activated sludge (HiCAS) and the low-rate variants of HiCS and HiCAS. The best HiCS system recovered 36% of the influent chemical energy as methane, due to the combined effects of low production of CO2, high sludge yield, and high methane yield of the produced sludge. The HiCS system imposed a feast-famine cycle and a putative selection pressure on the sludge micro-organisms toward substrate adsorption and storage. Given further optimization, it is a promising process for energy recovery from wastewater.}, } @article {pmid25551223, year = {2014}, author = {Eriksen, RL and Hierro, JL and Eren, Ö and Andonian, K and Török, K and Becerra, PI and Montesinos, D and Khetsuriani, L and Diaconu, A and Kesseli, R}, title = {Dispersal pathways and genetic differentiation among worldwide populations of the invasive weed Centaurea solstitialis L. (Asteraceae).}, journal = {PloS one}, volume = {9}, number = {12}, pages = {e114786}, pmid = {25551223}, issn = {1932-6203}, mesh = {Centaurea/*genetics/*physiology ; Databases, Genetic ; Expressed Sequence Tags/metabolism ; Gene Frequency ; Genetic Loci/genetics ; *Genetic Variation ; *Introduced Species ; Microsatellite Repeats/genetics ; *Plant Dispersal ; Plant Weeds/*genetics/*physiology ; }, abstract = {The natural history of introduced species is often unclear due to a lack of historical records. Even when historical information is readily available, important factors of the invasions such as genetic bottlenecks, hybridization, historical relationships among populations and adaptive changes are left unknown. In this study, we developed a set of nuclear, simple sequence repeat markers and used these to characterize the genetic diversity and population structure among native (Eurasian) and non-native (North and South American) populations of Centaurea solstitialis L., (yellow starthistle). We used these data to test hypotheses about the invasion pathways of the species that were based on historical and geographical records, and we make inferences about historical relationships among populations and demographic processes following invasion. We confirm that the center of diversity and the native range of the species is likely the eastern Mediterranean region in the vicinity of Turkey. From this region, the species likely proceeded to colonize other parts of Europe and Asia via a slow, stepwise range expansion. Spanish populations were the primary source of seed to invade South America via human-mediated events, as was evident from historical records, but populations from the eastern Mediterranean region were also important. North American populations were largely derived from South America, but had secondary contributors. We suggest that the introduction history of non-native populations from disparate parts of the native range have allowed not just one, but multiple opportunities first in South America then again in North America for the creation of novel genotypes via intraspecific hybridization. We propose that multiple intraspecific hybridization events may have created especially potent conditions for the selection of a noxious invader, and may explain differences in genetic patterns among North and South America populations, inferred differences in demographic processes, as well as morphological differences previously reported from common garden experiments.}, } @article {pmid25549621, year = {2015}, author = {Singh, RP and Kumari, P and Reddy, CR}, title = {Antimicrobial compounds from seaweeds-associated bacteria and fungi.}, journal = {Applied microbiology and biotechnology}, volume = {99}, number = {4}, pages = {1571-1586}, doi = {10.1007/s00253-014-6334-y}, pmid = {25549621}, issn = {1432-0614}, mesh = {Anti-Infective Agents/*isolation & purification ; Bacteria/isolation & purification/*metabolism ; Data Mining ; Fungi/isolation & purification/*metabolism ; Metagenomics ; Seaweed/*microbiology ; }, abstract = {In recent decade, seaweeds-associated microbial communities have been significantly evaluated for functional and chemical analyses. Such analyses let to conclude that seaweeds-associated microbial communities are highly diverse and rich sources of bioactive compounds of exceptional molecular structure. Extracting bioactive compounds from seaweed-associated microbial communities have been recently increased due to their broad-spectrum antimicrobial activities including antibacterial, antifungal, antiviral, anti-settlement, antiprotozoan, antiparasitic, and antitumor. These allelochemicals not only provide protection to host from other surrounding pelagic microorganisms, but also ensure their association with the host. Antimicrobial compounds from marine sources are promising and priority targets of biotechnological and pharmaceutical applications. This review describes the bioactive metabolites reported from seaweed-associated bacterial and fungal communities and illustrates their bioactivities. Biotechnological application of metagenomic approach for identifying novel bioactive metabolites is also dealt, in view of their future development as a strong tool to discover novel drug targets from seaweed-associated microbial communities.}, } @article {pmid25548954, year = {2015}, author = {Ji, L and Schüürmann, G}, title = {Computational biotransformation profile of paracetamol catalyzed by cytochrome P450.}, journal = {Chemical research in toxicology}, volume = {28}, number = {4}, pages = {585-596}, doi = {10.1021/tx5003645}, pmid = {25548954}, issn = {1520-5010}, mesh = {Acetaminophen/*pharmacokinetics ; Analgesics/*pharmacokinetics ; Biotransformation ; Catalysis ; *Computational Biology ; Cytochrome P-450 Enzyme System/*metabolism ; }, abstract = {The P450-catalyzed biotransformation of the analgesic drug paracetamol (PAR) is a long-debated topic, involving different mechanistic hypotheses as well as experimental evidence for the metabolites N-acetyl-p-benzoquinone imine (NAPQI), p-benzoquinone, acetamide, and 3-hydroxy-PAR. During the catalytic cycle of P450, a high-valent iron(IV)-oxo species known as Compound I (Cpd I) is formed as the ultimate oxidant, featuring two energetically close-lying ground states in the doublet (low-spin) and quartet (high-spin) spin states, respectively. In order to clarify the catalytic mechanism, a computational chemistry analysis has been undertaken for both the high- and low-spin routes, employing density functional theory (DFT) including PCM (polarized continuum-solvation model) that yields an approximate simulation of the bulk polarization exerted through the protein. The results demonstrate that hydrogen abstraction transfer (HAT) by the P450 oxidant Cpd I (FeO) is kinetically strongly preferred over the alternative pathways of an oxygen addition reaction (OAR) or two consecutive single-electron transfers (SET). Moreover, only the respective high-spin route yields N-acetyl-p-semiquinone imine (NAPSQI) as an intermediate that is converted to the electrophile N-acetyl-p-benzoquinone imine (NAPQI). By contrast, 3-hydroxy-PAR, acetamide, and p-benzoquinone as electrophilic and redox-active agent are formed predominantly in the low-spin state through reactions that do not involve NAPSQI. Thus, all experimentally observed PAR metabolites are in accord with an initial HAT from the phenolic oxygen, and NAPSQI should indeed be the precursor of NAPQI, both of which are generated only via the high-spin pathway.}, } @article {pmid25545995, year = {2015}, author = {Moro, CF and Fukao, Y and Shibato, J and Rakwal, R and Timperio, AM and Zolla, L and Agrawal, GK and Shioda, S and Kouzuma, Y and Yonekura, M}, title = {Unraveling the seed endosperm proteome of the lotus (Nelumbo nucifera Gaertn.) utilizing 1DE and 2DE separation in conjunction with tandem mass spectrometry.}, journal = {Proteomics}, volume = {15}, number = {10}, pages = {1717-1735}, doi = {10.1002/pmic.201400406}, pmid = {25545995}, issn = {1615-9861}, mesh = {Databases, Protein ; Electrophoresis, Gel, Two-Dimensional/*methods ; Endosperm/*metabolism ; Metabolic Networks and Pathways ; Nelumbo/*metabolism ; Plant Proteins/isolation & purification ; Proteome/*metabolism ; Proteomics ; Tandem Mass Spectrometry/*methods ; }, abstract = {Nelumbo nucifera (Gaertn.) or lotus, is an aquatic plant native to India, and presently consumed as food mainly in China and Japan. Lotus is also widely used in Indian and Chinese traditional medicine. Extracts from different parts of the lotus plant have been reported to show diverse biological activities-antioxidant, free radical scavenging, anti-inflammatory, and immunomodulatory. Despite this, little work has been done in isolating and identifying proteins responsible for these activities, or yet importantly to establish a lotus proteome. The aim of our group is to develop a proteome catalog of the lotus plant, starting with its seed, the nutrient rich food source. In this present study, the seed endosperm-most abundant in proteins, and main nutrient storage tissue-was targeted for protein extraction by testing five different extraction protocols, followed by their proteomic analyses using complementary 1DE and 2DE approaches in conjunction with MS/MS. The inventory of 66 nonredundant proteins obtained by 1DE-MS and the 30 obtained by 2DE-MS provides the first catalog of the lotus seed endosperm, where the most abundant protein functions were in categories of metabolic activities related to carbohydrate metabolism and nutrient storage.}, } @article {pmid25545936, year = {2014}, author = {Signorini, M and Cassini, R and Drigo, M and Frangipane di Regalbono, A and Pietrobelli, M and Montarsi, F and Stensgaard, AS}, title = {Ecological niche model of Phlebotomus perniciosus, the main vector of canine leishmaniasis in north-eastern Italy.}, journal = {Geospatial health}, volume = {9}, number = {1}, pages = {193-201}, doi = {10.4081/gh.2014.16}, pmid = {25545936}, issn = {1970-7096}, mesh = {Animals ; Dog Diseases/*parasitology/transmission ; Dogs ; Ecosystem ; Geographic Information Systems ; Insect Vectors/physiology/virology ; Italy/epidemiology ; Leishmaniasis/transmission/*veterinary ; Models, Theoretical ; Phlebotomus/physiology/virology ; Retrospective Studies ; }, abstract = {With respect to the epidemiology of leishmaniasis, it is crucial to take into account the ecoclimatic and environmental characteristics that influence the distribution patterns of the vector sand fly species. It is also important to consider the possible impact of on-going climate changes on the emergence of this disease. In order to map the potential distribution of Phlebotomus perniciosus, the main vector species of canine leishmaniasis in north-eastern Italy, geographical information systems tools, ecological niche models (ENM) and remotely sensed environmental data were applied for a retrospective analysis of an entomological survey conducted in north-eastern Italy over 12 years. Sand fly trapping was conducted from 2001 to 2012 in 175 sites in the provinces of Veneto, Friuli-Venezia Giulia and Trentino-Alto Adige. We developed a predictive model of potential distribution of P. perniciosus using the maximum entropy algorithm software, based on seasonal normalized difference vegetation index, day and night land surface temperature, the Corine land cover 2006, a digital elevation model (GTOPO30) and climate layers obtained from the WorldClim database. The MaxEnt prediction found the more suitable habitat for P. perniciosus to be hilly areas (100-300 m above the mean sea level) characterised by temperate climate during the winter and summer seasons, high winter vegetation cover and moderate rainfall during the activity season of vector sand fly. ENM provided a greater understanding of the geographical distribution and ecological requirements of P. perniciosus in the study area, which can be applied for the development of future surveillance strategies.}, } @article {pmid25545933, year = {2014}, author = {DeGroote, JP and Sugumaran, R and Ecker, M}, title = {Landscape, demographic and climatic associations with human West Nile virus occurrence regionally in 2012 in the United States of America.}, journal = {Geospatial health}, volume = {9}, number = {1}, pages = {153-168}, doi = {10.4081/gh.2014.13}, pmid = {25545933}, issn = {1970-7096}, mesh = {Animals ; *Climate ; Cluster Analysis ; Culex/physiology/virology ; Disease Outbreaks/statistics & numerical data ; *Environment ; Female ; Geographic Information Systems ; Humans ; Insect Vectors/physiology/virology ; Male ; Models, Statistical ; Population Dynamics ; United States/epidemiology ; West Nile Fever/*epidemiology/transmission ; }, abstract = {After several years of low West Nile virus (WNV) occurrence in the United States of America (USA), 2012 witnessed large outbreaks in several parts of the country. In order to understand the outbreak dynamics, spatial clustering and landscape, demographic and climatic associations with WNV occurrence were investigated at a regional level in the USA. Previous research has demonstrated that there are a handful of prominent WNV mosquito vectors with varying ecological requirements responsible for WNV transmission in the USA. Published range maps of these important vectors were georeferenced and used to define eight functional ecological regions in the coterminous USA. The number of human WNV cases and human populations by county were attained in order to calculate a WNV rate for each county in 2012. Additionally, a binary value (high/low) was calculated for each county based on whether the county WNV rate was above or below the rate for the region it fell in. Global Moran's I and Anselin Local Moran's I statistics of spatial association were used per region to examine and visualize clustering of the WNV rate and the high/low rating. Spatial data on landscape, demographic and climatic variables were compiled and derived from a variety of sources and then investigated in relation to human WNV using both Spearman rho correlation coefficients and Poisson regression models. Findings demonstrated significant spatial clustering of WNV and substantial inter-regional differences in relationships between WNV occurrence and landscape, demographic and climatically related variables. The regional associations were consistent with the ecologies of the dominant vectors for those regions. The large outbreak in the Southeast region was preceded by higher than normal winter and spring precipitation followed by dry and hot conditions in the summer.}, } @article {pmid25541974, year = {2014}, author = {Miller, JA and Miller, JH and Pham, DS and Beentjes, KK}, title = {Cyberdiversity: improving the informatic value of diverse tropical arthropod inventories.}, journal = {PloS one}, volume = {9}, number = {12}, pages = {e115750}, pmid = {25541974}, issn = {1932-6203}, mesh = {Animals ; *Biodiversity ; DNA Barcoding, Taxonomic ; Informatics/*methods ; Internet ; Spiders/*classification ; *Tropical Climate ; }, abstract = {In an era of biodiversity crisis, arthropods have great potential to inform conservation assessment and test hypotheses about community assembly. This is because their relatively narrow geographic distributions and high diversity offer high-resolution data on landscape-scale patterns of biodiversity. However, a major impediment to the more widespread application of arthropod data to a range of scientific and policy questions is the poor state of modern arthropod taxonomy, especially in the tropics. Inventories of spiders and other megadiverse arthropods from tropical forests are dominated by undescribed species. Such studies typically organize their data using morphospecies codes, which make it difficult for data from independent inventories to be compared and combined. To combat this shortcoming, we offer cyberdiversity, an online community-based approach for reconciling results of independent inventory studies where current taxonomic knowledge is incomplete. Participating scientists can upload images and DNA barcode sequences to dedicated databases and submit occurrence data and links to a web site (www.digitalSpiders.org). Taxonomic determinations can be shared with a crowdsourcing comments feature, and researchers can discover specimens of interest available for loan and request aliquots of genomic DNA extract. To demonstrate the value of the cyberdiversity framework, we reconcile data from three rapid structured inventories of spiders conducted in Vietnam with an independent inventory (Doi Inthanon, Thailand) using online image libraries. Species richness and inventory completeness were assessed using non-parametric estimators. Community similarity was evaluated using a novel index based on the Jaccard replacing observed with estimated values to correct for unobserved species. We use a distance-decay framework to demonstrate a rudimentary model of landscape-scale changes in community composition that will become increasingly informative as additional inventories participate. With broader adoption of the cyberdiversity approach, networks of information-sharing taxonomists can more efficiently and effectively address taxonomic impediments while elucidating landscape scale patterns of biodiversity.}, } @article {pmid25541569, year = {2014}, author = {T H Wan, T and Masri, MD and Ortiz, J}, title = {Predictors of Rural Health Clinics Managers' Willingness to Join Accountable Care Organizations.}, journal = {Research in the sociology of health care}, volume = {32}, number = {}, pages = {259-273}, pmid = {25541569}, issn = {0275-4959}, support = {U24 MD006954/MD/NIMHD NIH HHS/United States ; }, abstract = {PURPOSE: The implementation of the Patient Protection and Affordable Care Act has facilitated the development of an innovative and integrated delivery care system, Accountable Care Organizations (ACOs). It is timely, to identify how health care managers in rural health clinics are responding to the ACO model. This research examines RHC managers' perceived benefits and barriers for implementing ACOs from an organizational ecology perspective.

METHODOLOGY/APPROACH: A survey was conducted in Spring of 2012 covering the present RHC network working infrastructures - 1) Organizational social network; 2) organizational care delivery structure; 3) ACO knowledge, perceived benefits, and perceived barriers; 4) quality and disease management programs; and 5) health information technology (HIT) infrastructure. One thousand one hundred sixty clinics were surveyed in the United States. They cover eight southeastern states (Alabama, Florida, Georgia, Kentucky, Mississippi, North Carolina, South Carolina, and Tennessee) and California. A total of ninety-one responses were received.

FINDINGS: RHC managers' personal perceptions on ACO's benefits and knowledge level explained the most variance in their willingness to join ACOs. Individual perceptions appear to be more influential than organizational and context factors in the predictive analysis.

The study is primarily focused in the Southeastern region of the U.S. The generalizability is limited to this region. The predictors of rural health clinics' participation in ACOs are germane to guide the development of organizational strategies for enhancing the general knowledge about the innovativeness of delivering coordinated care and containing health care costs inspired by the Affordable Care Act.

ORIGINALITY/VALUE OF PAPER: Rural health clinics are lagged behind the growth curve of ACO adoption. The diffusion of new knowledge about pros and cons of ACO is essential to reinforce the health care reform in the United States.}, } @article {pmid25541156, year = {2015}, author = {Urbisch, D and Mehling, A and Guth, K and Ramirez, T and Honarvar, N and Kolle, S and Landsiedel, R and Jaworska, J and Kern, PS and Gerberick, F and Natsch, A and Emter, R and Ashikaga, T and Miyazawa, M and Sakaguchi, H}, title = {Assessing skin sensitization hazard in mice and men using non-animal test methods.}, journal = {Regulatory toxicology and pharmacology : RTP}, volume = {71}, number = {2}, pages = {337-351}, doi = {10.1016/j.yrtph.2014.12.008}, pmid = {25541156}, issn = {1096-0295}, mesh = {Animal Testing Alternatives/*methods ; Animals ; Cell Line ; *Databases, Factual ; Dermatologic Agents/*toxicity ; Humans ; Mice ; Skin/*drug effects/pathology ; U937 Cells ; }, abstract = {Sensitization, the prerequisite event in the development of allergic contact dermatitis, is a key parameter in both hazard and risk assessments. The pathways involved have recently been formally described in the OECD adverse outcome pathway (AOP) for skin sensitization. One single non-animal test method will not be sufficient to fully address this AOP and in many cases the use of a battery of tests will be necessary. A number of methods are now fully developed and validated. In order to facilitate acceptance of these methods by both the regulatory and scientific communities, results of the single test methods (DPRA, KeratinoSens, LuSens, h-CLAT, (m)MUSST) as well for a the simple '2 out of 3' ITS for 213 substances have been compiled and qualitatively compared to both animal and human data. The dataset was also used to define different mechanistic domains by probable protein-binding mechanisms. In general, the non-animal test methods exhibited good predictivities when compared to local lymph node assay (LLNA) data and even better predictivities when compared to human data. The '2 out of 3' prediction model achieved accuracies of 90% or 79% when compared to human or LLNA data, respectively and thereby even slightly exceeded that of the LLNA.}, } @article {pmid25540958, year = {2014}, author = {Saxena, R and Das, MK and Nagpal, BN and Srivastava, A and Gupta, SK and Kumar, A and Tomar, AS and Sinha, AT and Vidyotma, R and Jeyaseelan, AT and Baraik, VK and Singh, VP}, title = {Identification of risk factors for malaria control by focused interventions in Ranchi district, Jharkhand, India.}, journal = {Journal of vector borne diseases}, volume = {51}, number = {4}, pages = {276-281}, pmid = {25540958}, issn = {0972-9062}, mesh = {Animals ; Communicable Disease Control/methods ; Culicidae/growth & development ; Ecosystem ; *Endemic Diseases ; Entomology ; Geographic Information Systems ; Geography ; Humans ; India/epidemiology ; Malaria/*epidemiology/*prevention & control/transmission ; Phylogeography ; Remote Sensing Technology ; Risk Factors ; Socioeconomic Factors ; }, abstract = {BACKGROUND & OBJECTIVES: Ranchi, the capital of Jharkhand state is endemic for malaria, particularly the Bundu Primary Health Centre (PHC) is the worst affected. Therefore, a study was initiated during 2009 using remote sensing (RS) and geographical information system (GIS) to identify risk factors responsible for high endemicity in this PHC.

METHODS: Bundu and Angara in Ranchi district were identified as high and low malaria endemic PHCs based on epidemiological data of three years (2007-09). The habitation, streams, other water body, landform, PHC and village boundary thematic maps were prepared using IRS-P6/LISS III-IV imageries and macro level breeding sites were identified. Digital elevation model (DEM) of the PHCs was generated using Cartosat Stereo Pair images and from DEM, slope map was derived to calculate flat area. From slope, aspect map was derived to indicate direction of water flow. Length of perennial streams, area under rocky terrain and buffer zones of 250, 500 and 750 m were constructed around streams. High resolution remote sensing imageries were used to identify micro level breeding sites. Based on macro-micro breeding sites, six villages from each PHC were selected randomly having combination of different parameters representing all ecotypes. Entomological data were collected during 2010-11 in pre- and post-monsoon seasons following standard techniques and analyzed statistically. Differential analysis was attempted to comprehend socioeconomic and other determinants associated with malaria transmission.

RESULTS: The study identified eight risk factors responsible for higher malaria endemicity in Bundu in comparison to Angara PHC based on ecological, entomological, socioeconomic and other local parameters.

CONCLUSION: Focused interventions in integrated vector management (IVM) mode are required to be carried out in the district for better management and control of disease.}, } @article {pmid25539005, year = {2014}, author = {Chartier, M and Jabbour, F and Gerber, S and Mitteroecker, P and Sauquet, H and von Balthazar, M and Staedler, Y and Crane, PR and Schönenberger, J}, title = {The floral morphospace--a modern comparative approach to study angiosperm evolution.}, journal = {The New phytologist}, volume = {204}, number = {4}, pages = {841-853}, pmid = {25539005}, issn = {1469-8137}, support = {P 25077/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {*Biological Evolution ; Databases, Factual ; Ecology ; Flowers/*anatomy & histology/*physiology ; Image Processing, Computer-Assisted/methods ; Magnoliopsida/*physiology ; *Models, Theoretical ; Principal Component Analysis ; }, abstract = {Morphospaces are mathematical representations used for studying the evolution of morphological diversity and for the evaluation of evolved shapes among theoretically possible ones. Although widely used in zoology, they--with few exceptions--have been disregarded in plant science and in particular in the study of broad-scale patterns of floral structure and evolution. Here we provide basic information on the morphospace approach; we review earlier morphospace applications in plant science; and as a practical example, we construct and analyze a floral morphospace. Morphospaces are usually visualized with the help of ordination methods such as principal component analysis (PCA) or nonmetric multidimensional scaling (NMDS). The results of these analyses are then coupled with disparity indices that describe the spread of taxa in the space. We discuss these methods and apply modern statistical tools to the first and only angiosperm-wide floral morphospace published by Stebbins in 1951. Despite the incompleteness of Stebbins’ original dataset, our analyses highlight major, angiosperm-wide trends in the diversity of flower morphology and thereby demonstrate the power of this previously neglected approach in plant science.}, } @article {pmid25534614, year = {2015}, author = {Gülay, A and Smets, BF}, title = {An improved method to set significance thresholds for β diversity testing in microbial community comparisons.}, journal = {Environmental microbiology}, volume = {17}, number = {9}, pages = {3154-3167}, doi = {10.1111/1462-2920.12748}, pmid = {25534614}, issn = {1462-2920}, mesh = {Algorithms ; Bacteria/*genetics ; Data Interpretation, Statistical ; Microbial Consortia/*genetics/physiology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Exploring the variation in microbial community diversity between locations (β diversity) is a central topic in microbial ecology. Currently, there is no consensus on how to set the significance threshold for β diversity. Here, we describe and quantify the technical components of β diversity, including those associated with the process of subsampling. These components exist for any proposed β diversity measurement procedure. Further, we introduce a strategy to set significance thresholds for β diversity of any group of microbial samples using rarefaction, invoking the notion of a meta-community. The proposed technique was applied to several in silico generated operational taxonomic unit (OTU) libraries and experimental 16S rRNA pyrosequencing libraries. The latter represented microbial communities from different biological rapid sand filters at a full-scale waterworks. We observe that β diversity, after subsampling, is inflated by intra-sample differences; this inflation is avoided in the proposed method. In addition, microbial community evenness (Gini > 0.08) strongly affects all β diversity estimations due to bias associated with rarefaction. Where published methods to test β significance often fail, the proposed meta-community-based estimator is more successful at rejecting insignificant β diversity values. Applying our approach, we reveal the heterogeneous microbial structure of biological rapid sand filters both within and across filters.}, } @article {pmid25528696, year = {2015}, author = {Soares Sérvulo de Oliveira, F and Oseas de Carvalho Filho, A and Corrêa Silva, A and Cardoso de Paiva, A and Gattass, M}, title = {Classification of breast regions as mass and non-mass based on digital mammograms using taxonomic indexes and SVM.}, journal = {Computers in biology and medicine}, volume = {57}, number = {}, pages = {42-53}, doi = {10.1016/j.compbiomed.2014.11.016}, pmid = {25528696}, issn = {1879-0534}, mesh = {Breast/anatomy & histology/*pathology ; Breast Neoplasms/*diagnostic imaging ; Female ; Humans ; Mammography/*classification/*methods ; Pattern Recognition, Automated ; Radiographic Image Interpretation, Computer-Assisted/*methods ; Support Vector Machine ; Ultrasonography ; }, abstract = {Breast cancer is the second most common type of cancer in the world. Several computer-aided detection and diagnosis systems have been used to assist health experts identify suspicious areas that are difficult to perceive with the human eye, thus aiding in the detection and diagnosis of cancer. This work proposes a methodology for the discrimination and classification of regions extracted from mammograms as mass and non-mass. The Digital Database for Screening Mammography (DDSM) was used in this work for the acquisition of mammograms. The taxonomic diversity index (Δ) and the taxonomic distinctness (Δ(⁎)), which were originally used in ecology, were used to describe the texture of the regions of interest. These indexes were computed based on phylogenetic trees, which were applied to describe the patterns in regions of breast images. Two approaches were used for the analysis of texture: internal and external masks. A support vector machine was used to classify the regions as mass and non-mass. The proposed methodology successfully classified the masses and non-masses, with an average accuracy of 98.88%.}, } @article {pmid25527546, year = {2015}, author = {Mysara, M and Saeys, Y and Leys, N and Raes, J and Monsieurs, P}, title = {CATCh, an ensemble classifier for chimera detection in 16S rRNA sequencing studies.}, journal = {Applied and environmental microbiology}, volume = {81}, number = {5}, pages = {1573-1584}, pmid = {25527546}, issn = {1098-5336}, mesh = {*Cluster Analysis ; Computational Biology/*methods ; DNA, Ribosomal/chemistry/*genetics ; Molecular Sequence Data ; *Phylogeny ; RNA, Ribosomal, 16S/*genetics ; *Recombination, Genetic ; Sequence Analysis, DNA ; }, abstract = {In ecological studies, microbial diversity is nowadays mostly assessed via the detection of phylogenetic marker genes, such as 16S rRNA. However, PCR amplification of these marker genes produces a significant amount of artificial sequences, often referred to as chimeras. Different algorithms have been developed to remove these chimeras, but efforts to combine different methodologies are limited. Therefore, two machine learning classifiers (reference-based and de novo CATCh) were developed by integrating the output of existing chimera detection tools into a new, more powerful method. When comparing our classifiers with existing tools in either the reference-based or de novo mode, a higher performance of our ensemble method was observed on a wide range of sequencing data, including simulated, 454 pyrosequencing, and Illumina MiSeq data sets. Since our algorithm combines the advantages of different individual chimera detection tools, our approach produces more robust results when challenged with chimeric sequences having a low parent divergence, short length of the chimeric range, and various numbers of parents. Additionally, it could be shown that integrating CATCh in the preprocessing pipeline has a beneficial effect on the quality of the clustering in operational taxonomic units.}, } @article {pmid25527032, year = {2014}, author = {Gilchrist, AS and Shearman, DC and Frommer, M and Raphael, KA and Deshpande, NP and Wilkins, MR and Sherwin, WB and Sved, JA}, title = {The draft genome of the pest tephritid fruit fly Bactrocera tryoni: resources for the genomic analysis of hybridising species.}, journal = {BMC genomics}, volume = {15}, number = {1}, pages = {1153}, pmid = {25527032}, issn = {1471-2164}, mesh = {Animals ; Evolution, Molecular ; Female ; Gene Ontology ; *Genomics ; *Hybridization, Genetic ; INDEL Mutation/genetics ; Male ; Molecular Sequence Annotation ; Repetitive Sequences, Nucleic Acid/genetics ; Sequence Analysis ; Species Specificity ; Tephritidae/*genetics ; }, abstract = {BACKGROUND: The tephritid fruit flies include a number of economically important pests of horticulture, with a large accumulated body of research on their biology and control. Amongst the Tephritidae, the genus Bactrocera, containing over 400 species, presents various species groups of potential utility for genetic studies of speciation, behaviour or pest control. In Australia, there exists a triad of closely-related, sympatric Bactrocera species which do not mate in the wild but which, despite distinct morphologies and behaviours, can be force-mated in the laboratory to produce fertile hybrid offspring. To exploit the opportunities offered by genomics, such as the efficient identification of genetic loci central to pest behaviour and to the earliest stages of speciation, investigators require genomic resources for future investigations.

RESULTS: We produced a draft de novo genome assembly of Australia's major tephritid pest species, Bactrocera tryoni. The male genome (650-700 Mbp) includes approximately 150 Mb of interspersed repetitive DNA sequences and 60 Mb of satellite DNA. Assessment using conserved core eukaryotic sequences indicated 98% completeness. Over 16,000 MAKER-derived gene models showed a large degree of overlap with other Dipteran reference genomes. The sequence of the ribosomal RNA transcribed unit was also determined. Unscaffolded assemblies of B. neohumeralis and B. jarvisi were then produced; comparison with B. tryoni showed that the species are more closely related than any Drosophila species pair. The similarity of the genomes was exploited to identify 4924 potentially diagnostic indels between the species, all of which occur in non-coding regions.

CONCLUSIONS: This first draft B. tryoni genome resembles other dipteran genomes in terms of size and putative coding sequences. For all three species included in this study, we have identified a comprehensive set of non-redundant repetitive sequences, including the ribosomal RNA unit, and have quantified the major satellite DNA families. These genetic resources will facilitate the further investigations of genetic mechanisms responsible for the behavioural and morphological differences between these three species and other tephritids. We have also shown how whole genome sequence data can be used to generate simple diagnostic tests between very closely-related species where only one of the species is scaffolded.}, } @article {pmid25522281, year = {2014}, author = {de Froment, AJ and Rubenstein, DI and Levin, SA}, title = {An extra dimension to decision-making in animals: the three-way trade-off between speed, effort per-unit-time and accuracy.}, journal = {PLoS computational biology}, volume = {10}, number = {12}, pages = {e1003937}, pmid = {25522281}, issn = {1553-7358}, support = {/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Animals ; Bees ; Biological Evolution ; Brain/physiology ; Computational Biology/*methods ; Decision Making/*physiology ; Humans ; Mammals ; *Models, Biological ; Time Factors ; }, abstract = {The standard view in biology is that all animals, from bumblebees to human beings, face a trade-off between speed and accuracy as they search for resources and mates, and attempt to avoid predators. For example, the more time a forager spends out of cover gathering information about potential food sources the more likely it is to make accurate decisions about which sources are most rewarding. However, when the cost of time spent out of cover rises (e.g. in the presence of a predator) the optimal strategy is for the forager to spend less time gathering information and to accept a corresponding decline in the accuracy of its decisions. We suggest that this familiar picture is missing a crucial dimension: the amount of effort an animal expends on gathering information in each unit of time. This is important because an animal that can respond to changing time costs by modulating its level of effort per-unit-time does not have to accept the same decrease in accuracy that an animal limited to a simple speed-accuracy trade-off must bear in the same situation. Instead, it can direct additional effort towards (i) reducing the frequency of perceptual errors in the samples it gathers or (ii) increasing the number of samples it gathers per-unit-time. Both of these have the effect of allowing it to gather more accurate information within a given period of time. We use a modified version of a canonical model of decision-making (the sequential probability ratio test) to show that this ability to substitute effort for time confers a fitness advantage in the face of changing time costs. We predict that the ability to modulate effort levels will therefore be widespread in nature, and we lay out testable predictions that could be used to detect adaptive modulation of effort levels in laboratory and field studies. Our understanding of decision-making in all species, including our own, will be improved by this more ecologically-complete picture of the three-way tradeoff between time, effort per-unit-time and accuracy.}, } @article {pmid25515301, year = {2015}, author = {Narum, S and Vines, T and Gow, J}, title = {Technology in the field of molecular ecology continues to advance rapidly. Introduction.}, journal = {Molecular ecology resources}, volume = {15}, number = {1}, pages = {1-7}, doi = {10.1111/1755-0998.12348}, pmid = {25515301}, issn = {1755-0998}, mesh = {Computational Biology/*methods ; Ecology/*methods ; *Editorial Policies ; Molecular Biology/*methods ; *Periodicals as Topic ; }, } @article {pmid25511884, year = {2014}, author = {Xuan, le TT and Van Hau, P and Thu, do T and Toan, do TT}, title = {Estimates of meteorological variability in association with dengue cases in a coastal city in northern Vietnam: an ecological study.}, journal = {Global health action}, volume = {7}, number = {}, pages = {23119}, pmid = {25511884}, issn = {1654-9880}, mesh = {*Climate Change ; Dengue/*epidemiology/etiology ; *Disease Outbreaks ; Humans ; Incidence ; Poisson Distribution ; Risk Factors ; Temperature ; Vietnam/epidemiology ; }, abstract = {BACKGROUND: Dengue fever (DF) is a vector-borne disease that is sensitive to weather and climate variability. To date, however, this relationship in coastal northern Vietnam has not been well documented.

OBJECTIVES: This paper aims to examine the associations between meteorological variables and dengue incidence in Haiphong, Vietnam, over the period 2008-2012.

METHODS: Monthly data on dengue incidence from all commune health stations and hospitals of Haiphong (with a total population of ~1.8 million) were obtained in accordance with the WHO's recommendations over a 5-year period (2008-2012). Temperature, rainfall, and humidity were recorded as monthly averages by local meteorological stations. The association between ecologic weather variables and dengue cases was assessed using a Poisson regression model. The estimation of regression parameters was based on the method of maximum likelihood using the R program package.

RESULTS: From 2008 through 2012, 507 cases of dengue were reported. The risk of dengue was increased by sevenfold during the September-December period compared with other months over the period 2008-2012. DF cases in Haiphong were correlated with rainfall and humidity. In the multivariable Poisson regression model, an increased risk of dengue was independently associated with months with a higher amount of rainfall (RR=1.06; 95% CI 1.00-1.13 per 50 mm increase) and higher humidity (RR=1.05; 95% CI 1.02-1.08 per 1% increase).

CONCLUSION: These data suggest that rainfall and relative humidity could be used as ecological indicators of dengue risk in Haiphong. Intensified surveillance and disease control during periods with high rainfall and humidity are recommended. This study may provide baseline information for identifying potential long-term effects and adaptation needs of global climate change on dengue in the coming decades.}, } @article {pmid25506822, year = {2015}, author = {Guan, J and Fu, J and Wu, M and Chen, L and Ji, G and Quinn Li, Q and Wu, X}, title = {VAAPA: a web platform for visualization and analysis of alternative polyadenylation.}, journal = {Computers in biology and medicine}, volume = {57}, number = {}, pages = {20-25}, doi = {10.1016/j.compbiomed.2014.11.010}, pmid = {25506822}, issn = {1879-0534}, mesh = {Animals ; Arabidopsis ; Computational Biology/*methods ; DNA, Complementary/analysis/chemistry/metabolism ; Humans ; *Internet ; Mice ; Models, Genetic ; Poly A ; *Polyadenylation ; RNA, Messenger/*analysis/chemistry/metabolism ; Sequence Analysis, DNA/*methods ; *Software ; User-Computer Interface ; }, abstract = {Polyadenylation [poly(A)] is an essential process during the maturation of most mRNAs in eukaryotes. Alternative polyadenylation (APA) as an important layer of gene expression regulation has been increasingly recognized in various species. Here, a web platform for visualization and analysis of alternative polyadenylation (VAAPA) was developed. This platform can visualize the distribution of poly(A) sites and poly(A) clusters of a gene or a section of a chromosome. It can also highlight genes with switched APA sites among different conditions. VAAPA is an easy-to-use web-based tool that provides functions of poly(A) site query, data uploading, downloading, and APA sites visualization. It was designed in a multi-tier architecture and developed based on Smart GWT (Google Web Toolkit) using Java as the development language. VAAPA will be a valuable addition to the community for the comprehensive study of APA, not only by making the high quality poly(A) site data more accessible, but also by providing users with numerous valuable functions for poly(A) site analysis and visualization.}, } @article {pmid25505150, year = {2014}, author = {Åkesson, S and Odin, C and Hegedüs, R and Ilieva, M and Sjöholm, C and Farkas, A and Horváth, G}, title = {Testing avian compass calibration: comparative experiments with diurnal and nocturnal passerine migrants in South Sweden.}, journal = {Biology open}, volume = {4}, number = {1}, pages = {35-47}, pmid = {25505150}, issn = {2046-6390}, abstract = {Cue-conflict experiments were performed to study the compass calibration of one predominantly diurnal migrant, the dunnock (Prunella modularis), and two species of nocturnal passerine migrants, the sedge warbler (Acrocephalus schoenobaenus), and the European robin (Erithacus rubecula) during autumn migration in South Sweden. The birds' orientation was recorded in circular cages under natural clear and simulated overcast skies in the local geomagnetic field, and thereafter the birds were exposed to a cue-conflict situation where the horizontal component of the magnetic field (mN) was shifted +90° or -90° at two occasions, one session starting shortly after sunrise and the other ca. 90 min before sunset and lasting for 60 min. The patterns of the degree and angle of skylight polarization were measured by full-sky imaging polarimetry during the cue-conflict exposures and orientation tests. All species showed orientation both under clear and overcast skies that correlated with the expected migratory orientation towards southwest to south. For the European robin the orientation under clear skies was significantly different from that recorded under overcast skies, showing a tendency that the orientation under clear skies was influenced by the position of the Sun at sunset resulting in more westerly orientation. This sun attraction was not observed for the sedge warbler and the dunnock, both orientating south. All species showed similar orientation after the cue-conflict as compared to the preferred orientation recorded before the cue-conflict, with the clearest results in the European robin and thus, the results did not support recalibration of the celestial nor the magnetic compasses as a result of the cue-conflict exposure.}, } @article {pmid25504713, year = {2014}, author = {Jarvis, ED and Mirarab, S and Aberer, AJ and Li, B and Houde, P and Li, C and Ho, SY and Faircloth, BC and Nabholz, B and Howard, JT and Suh, A and Weber, CC and da Fonseca, RR and Li, J and Zhang, F and Li, H and Zhou, L and Narula, N and Liu, L and Ganapathy, G and Boussau, B and Bayzid, MS and Zavidovych, V and Subramanian, S and Gabaldón, T and Capella-Gutiérrez, S and Huerta-Cepas, J and Rekepalli, B and Munch, K and Schierup, M and Lindow, B and Warren, WC and Ray, D and Green, RE and Bruford, MW and Zhan, X and Dixon, A and Li, S and Li, N and Huang, Y and Derryberry, EP and Bertelsen, MF and Sheldon, FH and Brumfield, RT and Mello, CV and Lovell, PV and Wirthlin, M and Schneider, MP and Prosdocimi, F and Samaniego, JA and Vargas Velazquez, AM and Alfaro-Núñez, A and Campos, PF and Petersen, B and Sicheritz-Ponten, T and Pas, A and Bailey, T and Scofield, P and Bunce, M and Lambert, DM and Zhou, Q and Perelman, P and Driskell, AC and Shapiro, B and Xiong, Z and Zeng, Y and Liu, S and Li, Z and Liu, B and Wu, K and Xiao, J and Yinqi, X and Zheng, Q and Zhang, Y and Yang, H and Wang, J and Smeds, L and Rheindt, FE and Braun, M and Fjeldsa, J and Orlando, L and Barker, FK and Jønsson, KA and Johnson, W and Koepfli, KP and O'Brien, S and Haussler, D and Ryder, OA and Rahbek, C and Willerslev, E and Graves, GR and Glenn, TC and McCormack, J and Burt, D and Ellegren, H and Alström, P and Edwards, SV and Stamatakis, A and Mindell, DP and Cracraft, J and Braun, EL and Warnow, T and Jun, W and Gilbert, MT and Zhang, G}, title = {Whole-genome analyses resolve early branches in the tree of life of modern birds.}, journal = {Science (New York, N.Y.)}, volume = {346}, number = {6215}, pages = {1320-1331}, pmid = {25504713}, issn = {1095-9203}, support = {/HHMI/Howard Hughes Medical Institute/United States ; DP1 OD000448/OD/NIH HHS/United States ; R24 GM092842/GM/NIGMS NIH HHS/United States ; DP1OD000448/OD/NIH HHS/United States ; }, mesh = {Animals ; Avian Proteins/genetics ; Base Sequence ; Biological Evolution ; Birds/classification/*genetics ; DNA Transposable Elements ; Genes ; Genetic Speciation ; *Genome ; INDEL Mutation ; Introns ; *Phylogeny ; Sequence Analysis, DNA ; }, abstract = {To better determine the history of modern birds, we performed a genome-scale phylogenetic analysis of 48 species representing all orders of Neoaves using phylogenomic methods created to handle genome-scale data. We recovered a highly resolved tree that confirms previously controversial sister or close relationships. We identified the first divergence in Neoaves, two groups we named Passerea and Columbea, representing independent lineages of diverse and convergently evolved land and water bird species. Among Passerea, we infer the common ancestor of core landbirds to have been an apex predator and confirm independent gains of vocal learning. Among Columbea, we identify pigeons and flamingoes as belonging to sister clades. Even with whole genomes, some of the earliest branches in Neoaves proved challenging to resolve, which was best explained by massive protein-coding sequence convergence and high levels of incomplete lineage sorting that occurred during a rapid radiation after the Cretaceous-Paleogene mass extinction event about 66 million years ago.}, } @article {pmid25500136, year = {2015}, author = {Collins, L and Penman, TD and Price, OF and Bradstock, RA}, title = {Adding fuel to the fire? Revegetation influences wildfire size and intensity.}, journal = {Journal of environmental management}, volume = {150}, number = {}, pages = {196-205}, doi = {10.1016/j.jenvman.2014.11.009}, pmid = {25500136}, issn = {1095-8630}, mesh = {Conservation of Natural Resources ; *Fires ; Geographic Information Systems ; Humans ; Models, Theoretical ; New South Wales ; *Trees ; *Weather ; }, abstract = {The regrowth of woody vegetation in cleared landscapes (i.e. revegetation) has the potential to dramatically alter the spatial characteristics of vegetation and fuels, which will potentially alter fire characteristics. Understanding how revegetation alters fire size and intensity will be critical in determining the social and environmental value of revegetation. We used simulation modelling to examine (i) whether increasing native woody vegetation extent across landscapes cleared for pasture (i.e. revegetation) affects fire size and median fireline intensity and (ii) whether fuel load in the pasture matrix, the initial extent of land clearing and weather conditions during a fire alter the direction and/or magnitude of the relationships between revegetation and fire size or intensity. Simulations revealed that fire size and intensity were altered by increasing woody vegetation extent, though the direction of change was dependent upon landscape context. Increased woody vegetation extent led to (i) increased fire size in landscapes with low pasture fuel load (2 t ha(-1)) regardless of the extent of land clearing, (ii) decreased fire size in highly cleared landscapes with moderate (4.5 t ha(-1)) and high (7 t ha(-1)) pasture fuel load, and (iii) little change to fire size in landscapes subjected to low levels of clearing when pasture fuel load was moderate or high. Similar patterns were observed for fireline intensity. The magnitude of change in fire size and intensity was greatest under extreme fire weather conditions. Revegetation rarely increased median fireline intensity beyond suppressible levels (i.e. 4000 kW m(-1)), with fire weather and pasture fuel load being the main determinants of suppression potential. Our findings show that the response of fire size and intensity to revegetation will depend on landscape scale pasture management.}, } @article {pmid25500135, year = {2015}, author = {Barros, A and Pickering, C and Gudes, O}, title = {Desktop analysis of potential impacts of visitor use: a case study for the highest park in the Southern Hemisphere.}, journal = {Journal of environmental management}, volume = {150}, number = {}, pages = {179-195}, doi = {10.1016/j.jenvman.2014.11.004}, pmid = {25500135}, issn = {1095-8630}, mesh = {Argentina ; *Biodiversity ; Conservation of Natural Resources ; *Environment ; Geographic Information Systems ; Humans ; Ice Cover ; *Mountaineering ; *Recreation ; }, abstract = {Nature-based tourism and recreation activities have a range of environmental impacts, but most protected area agencies have limited capacity to assess them. To prioritise where and what impacts to monitor and manage, we conducted a desktop assessment using Geographical Information Systems (GIS) by combining recreation ecology research with data on visitor usage and key environmental features for a popular protected area used for mountaineering and trekking, Aconcagua Provincial Park (2400-6962 m a.s.l.) in the Andes of Argentina. First, we integrated visitor data from permits with environmental data using GIS. We then identified key impact indicators for different activities based on the recreation ecology literature. Finally, we integrated this data to identify likely ecological impacts based on the types of activities, amount of use and altitudinal zones. Visitors only used 2% of the Park, but use was concentrated in areas of high conservation value including in alpine meadows and glacier lakes. Impacts on water resources were likely to be concentrated in campsites from the intermediate to the nival/glacial zones of the Park while impacts on terrestrial biodiversity were likely to be more severe in the low and intermediate alpine zones (2400-3800 m a.s.l.). These results highlight how visitor data can be used to identify priority areas for on-ground assessment of impacts in key locations. Improvements to the management of visitors in this Park involves more effective ways of dealing with water extraction and human waste in high altitude campsites and the impacts of hikers and pack animals in the low and intermediate alpine zones.}, } @article {pmid25496754, year = {2014}, author = {Barasona, JA and Latham, MC and Acevedo, P and Armenteros, JA and Latham, AD and Gortazar, C and Carro, F and Soriguer, RC and Vicente, J}, title = {Spatiotemporal interactions between wild boar and cattle: implications for cross-species disease transmission.}, journal = {Veterinary research}, volume = {45}, number = {1}, pages = {122}, pmid = {25496754}, issn = {1297-9716}, mesh = {*Animal Distribution ; Animals ; Cattle/physiology ; Cattle Diseases/epidemiology/microbiology/*transmission ; *Feeding Behavior ; Female ; Geographic Information Systems ; Incidence ; Male ; Prevalence ; Spain/epidemiology ; Swine/physiology ; Swine Diseases/epidemiology/microbiology/*transmission ; Tuberculosis, Bovine/epidemiology/microbiology/*transmission ; }, abstract = {Controlling infectious diseases at the wildlife/livestock interface is often difficult because the ecological processes driving transmission between wildlife reservoirs and sympatric livestock populations are poorly understood. Thus, assessing how animals use their environment and how this affects interspecific interactions is an important factor in determining the local risk for disease transmission and maintenance. We used data from concurrently monitored GPS-collared domestic cattle and wild boar (Sus scrofa) to assess spatiotemporal interactions and associated implications for bovine tuberculosis (TB) transmission in a complex ecological and epidemiological system, Doñana National Park (DNP, South Spain). We found that fine-scale spatial overlap of cattle and wild boar was seasonally high in some habitats. In general, spatial interactions between the two species were highest in the marsh-shrub ecotone and at permanent water sources, whereas shrub-woodlands and seasonal grass-marshlands were areas with lower predicted relative interactions. Wild boar and cattle generally used different resources during winter and spring in DNP. Conversely, limited differences in resource selection during summer and autumn, when food and water availability were limiting, resulted in negligible spatial segregation and thus probably high encounter rates. The spatial gradient in potential overlap between the two species across DNP corresponded well with the spatial variation in the observed incidence of TB in cattle and prevalence of TB in wild boar. We suggest that the marsh-shrub ecotone and permanent water sources act as important points of TB transmission in our system, particularly during summer and autumn. Targeted management actions are suggested to reduce potential interactions between cattle and wild boar in order to prevent disease transmission and design effective control strategies.}, } @article {pmid25495900, year = {2014}, author = {Scully, ED and Geib, SM and Carlson, JE and Tien, M and McKenna, D and Hoover, K}, title = {Functional genomics and microbiome profiling of the Asian longhorned beetle (Anoplophora glabripennis) reveal insights into the digestive physiology and nutritional ecology of wood feeding beetles.}, journal = {BMC genomics}, volume = {15}, number = {1}, pages = {1096}, pmid = {25495900}, issn = {1471-2164}, mesh = {*Animal Feed ; *Animal Nutritional Physiological Phenomena ; Animals ; Bacteria/classification/genetics/metabolism ; Biodiversity ; Coleoptera/*microbiology/*physiology ; Computational Biology ; DNA, Intergenic ; *Digestive System Physiological Phenomena ; Fungi/classification/genetics/metabolism ; Gastrointestinal Tract/microbiology/physiology ; Metabolic Networks and Pathways ; *Metagenome ; *Microbiota ; Molecular Sequence Annotation ; Phylogeny ; RNA, Ribosomal, 16S ; }, abstract = {BACKGROUND: Wood-feeding beetles harbor an ecologically rich and taxonomically diverse assemblage of gut microbes that appear to promote survival in woody tissue, which is devoid of nitrogen and essential nutrients. Nevertheless, the contributions of these apparent symbionts to digestive physiology and nutritional ecology remain uncharacterized in most beetle lineages.

RESULTS: Through parallel transcriptome profiling of beetle- and microbial- derived mRNAs, we demonstrate that the midgut microbiome of the Asian longhorned beetle (Anoplophora glabripennis), a member of the beetle family Cerambycidae, is enriched in biosynthetic pathways for the synthesis of essential amino acids, vitamins, and sterols. Consequently, the midgut microbiome of A. glabripennis can provide essential nutrients that the beetle cannot obtain from its woody diet or synthesize itself. The beetle gut microbiota also produce their own suite of transcripts that can enhance lignin degradation, degrade hemicellulose, and ferment xylose and wood sugars. An abundance of cellulases from several glycoside hydrolase families are expressed endogenously by A. glabripennis, as well as transcripts that allow the beetle to convert microbe-synthesized essential amino acids into non-essential amino acids. A. glabripennis and its gut microbes likely collaborate to digest carbohydrates and convert released sugars and amino acid intermediates into essential nutrients otherwise lacking from their woody host plants.

CONCLUSIONS: The nutritional provisioning capabilities of the A. glabripennis gut microbiome may contribute to the beetles' unusually broad host range. The presence of some of the same microbes in the guts of other Cerambycidae and other wood-feeding beetles suggests that partnerships with microbes may be a facilitator of evolutionary radiations in beetles, as in certain other groups of insects, allowing access to novel food sources through enhanced nutritional provisioning.}, } @article {pmid25492498, year = {2015}, author = {Berens, AJ and Hunt, JH and Toth, AL}, title = {Comparative transcriptomics of convergent evolution: different genes but conserved pathways underlie caste phenotypes across lineages of eusocial insects.}, journal = {Molecular biology and evolution}, volume = {32}, number = {3}, pages = {690-703}, doi = {10.1093/molbev/msu330}, pmid = {25492498}, issn = {1537-1719}, mesh = {Animals ; Cluster Analysis ; Computational Biology ; *Evolution, Molecular ; Gene Expression Profiling/*methods ; Genes, Insect/*genetics/physiology ; Hymenoptera/*genetics/physiology ; Phenotype ; Social Behavior ; Transcriptome/*genetics ; }, abstract = {An area of great interest in evolutionary genomics is whether convergently evolved traits are the result of convergent molecular mechanisms. The presence of queen and worker castes in insect societies is a spectacular example of convergent evolution and phenotypic plasticity. Multiple insect lineages have evolved environmentally induced alternative castes. Given multiple origins of eusociality in Hymenoptera (bees, ants, and wasps), it has been proposed that insect castes evolved from common genetic "toolkits" consisting of deeply conserved genes. Here, we combine data from previously published studies on fire ants and honey bees with new data for Polistes metricus paper wasps to assess the toolkit idea by presenting the first comparative transcriptome-wide analysis of caste determination among three major hymenopteran social lineages. Overall, we found few shared caste differentially expressed transcripts across the three social lineages. However, there is substantially more overlap at the levels of pathways and biological functions. Thus, there are shared elements but not on the level of specific genes. Instead, the toolkit appears to be relatively "loose," that is, different lineages show convergent molecular evolution involving similar metabolic pathways and molecular functions but not the exact same genes. Additionally, our paper wasp data do not support a complementary hypothesis that "novel" taxonomically restricted genes are related to caste differences.}, } @article {pmid25485856, year = {2014}, author = {Chen, P and Wang, L and Wang, Y and Li, S and Shen, L and Liu, Q and Ni, J}, title = {Phosphoproteomic profiling of selenate-treated Alzheimer's disease model cells.}, journal = {PloS one}, volume = {9}, number = {12}, pages = {e113307}, pmid = {25485856}, issn = {1932-6203}, mesh = {Alzheimer Disease/*metabolism/pathology ; Amyloid beta-Peptides/metabolism ; Antioxidants/*pharmacology ; Cell Line ; Cell Survival/drug effects ; Computational Biology/methods ; Humans ; Metabolic Networks and Pathways/drug effects ; Molecular Sequence Annotation ; Phosphoproteins/*metabolism ; *Proteome ; *Proteomics/methods ; Selenic Acid/*pharmacology ; }, abstract = {The reversible phosphorylation of proteins regulates most biological processes, while abnormal phosphorylation is a cause or consequence of many diseases including Alzheimer's disease (AD). One of the hallmarks of AD is the formation of neurofibrillary tangles (NFTs), which is composed of hyperphosphorylated tau proteins. Sodium selenate has been recently found to reduce tau hyperphosphorylation and NFTs formation, and to improve spatial learning and motor performance in AD mice. In the current study, the phosphoproteomics of N2aSW cells treated with selenate were investigated. To avoid missing low-abundance phosphoproteins, both the total proteins of cells and the phosphor-enriched proteins were extracted and subjected to the two-dimensional gel electrophoresis with Pro-Q diamond staining and then LC-MS/MS analysis. A total of 65 proteins were altered in phosphorylation level, of which 39 were up-regulated and 26 were down-regulated. All identified phosphoproteins were bioinformatically annotated according to their physiochemical features, subcellular location, and biological function. Most of these significantly changed phosphoproteins are involved in crucial neural processes such as protesome activity, oxidative stress, cysteine and methionine metabolism, and energy metabolism. Furthermore, decreases were found in homocysteine, phosphor-tau and amyloid β upon selenate treatment. Our results suggest that selenate may intervene in the pathological process of AD by altering the phosphorylation of some key proteins involved in oxidative stress, energy metabolism and protein degradation, thus play important roles in maintaining redox homeostasis, generating ATP, and clearing misfolded proteins and aggregates. The present paper provides some new clues to the mechanism of selenate in AD prevention.}, } @article {pmid25480132, year = {2014}, author = {Kristoffersen, AB and Jimenez, D and Viljugrein, H and Grøntvedt, R and Stien, A and Jansen, PA}, title = {Large scale modelling of salmon lice (Lepeophtheirus salmonis) infection pressure based on lice monitoring data from Norwegian salmonid farms.}, journal = {Epidemics}, volume = {9}, number = {}, pages = {31-39}, doi = {10.1016/j.epidem.2014.09.007}, pmid = {25480132}, issn = {1878-0067}, mesh = {Animals ; Copepoda/*physiology ; Female ; Fish Diseases/*parasitology/transmission ; Fisheries ; Models, Biological ; Norway ; Phthiraptera/*physiology ; Salmon/*parasitology ; }, abstract = {Infection by parasitic sea lice is a substantial problem in industrial scale salmon farming. To control the problem, Norwegian salmonid farms are not permitted to exceed a threshold level of infection on their fish, and farms are required to monitor and report lice levels on a weekly basis to ensure compliance with the regulation. In the present study, we combine the monitoring data with a deterministic model for salmon lice population dynamics to estimate farm production of infectious lice stages. Furthermore, we use an empirical estimate of the relative risk of salmon lice transmission between farms, that depend on inter-farm distances, to estimate the external infection pressure at a farm site, i.e. the infection pressure from infective salmon lice of neighbouring farm origin. Finally, we test whether our estimates of infection pressure from neighbouring farms as well as internal within farm infection pressure, predicts subsequent development of infection in cohorts of farmed salmonids in their initial phase of marine production. We find that estimated external infection pressure is a main predictor of salmon lice population dynamics in newly stocked cohorts of salmonids. Our results emphasize the importance of keeping the production of infectious lice stages at low levels within local networks of salmon farms. Our model can easily be implemented for real time estimation of infection pressure at the national scale, utilizing the masses of data generated through the compulsory lice monitoring in salmon farms. The implementation of such a system should give the salmon industry greater predictability with respect to salmon lice infection levels, and aid the decision making process when the development of new farm sites are planned.}, } @article {pmid25479705, year = {2015}, author = {Schilling, KE and Wolter, CF and McLellan, E}, title = {Agro-hydrologic landscapes in the Upper Mississippi and Ohio River basins.}, journal = {Environmental management}, volume = {55}, number = {3}, pages = {646-656}, pmid = {25479705}, issn = {1432-1009}, mesh = {Agriculture/*methods ; Conservation of Natural Resources/*methods ; Environmental Pollutants/*analysis ; Geographic Information Systems ; Hydrology/*methods ; Midwestern United States ; Nitrogen/analysis ; Phosphorus/analysis ; *Rivers ; Soil/*chemistry ; Water Movements ; }, abstract = {A critical part of increasing conservation effectiveness is targeting the "right practice" to the "right place" where it can intercept pollutant flowpaths. Conceptually, these flowpaths can be inferred from soil and slope characteristics, and in this study, we developed an agro-hydrologic classification to identify N and P loss pathways and priority conservation practices in small watersheds in the U.S. Midwest. We developed a GIS framework to classify 11,010 small watersheds in the Upper Mississippi and Ohio River basins based on soil permeability and slope characteristics of agricultural cropland areas in each watershed. The amount of cropland in any given watershed varied from <10 to >60 %. Cropland areas were classified into five main categories, with slope classes of <2, 2-5, and >5 %, and soil drainage classes of poorly and well drained. Watersheds in the Upper Mississippi River basin (UMRB) were dominated by cropland areas in low slopes and poorly drained soils, whereas less-intensively cropped watersheds in Wisconsin and Minnesota (in the UMRB) and throughout the Ohio River basin were overwhelmingly well drained. Hydrologic differences in cropped systems indicate that a one-size-fits-all approach to conservation selection will not work. Consulting the classification scheme proposed herein may be an appropriate first-step in identifying those conservation practices that might be most appropriate for small watersheds in the basin.}, } @article {pmid25477890, year = {2014}, author = {Voitsekhovskaja, OV and Schiermeyer, A and Reumann, S}, title = {Plant peroxisomes are degraded by starvation-induced and constitutive autophagy in tobacco BY-2 suspension-cultured cells.}, journal = {Frontiers in plant science}, volume = {5}, number = {}, pages = {629}, pmid = {25477890}, issn = {1664-462X}, abstract = {Very recently, autophagy has been recognized as an important degradation pathway for quality control of peroxisomes in Arabidopsis plants. To further characterize the role of autophagy in plant peroxisome degradation, we generated stable transgenic suspension-cultured cell lines of heterotrophic Nicotiana tabacum L. cv. Bright Yellow 2 expressing a peroxisome-targeted version of enhanced yellow fluorescent protein. Indeed, this cell line model system proved advantageous for detailed cytological analyses of autophagy stages and for quantification of cellular peroxisome pools under different culturing conditions and upon inhibitor applications. Complementary biochemical, cytological, and pharmacological analyses provided convincing evidence for peroxisome degradation by bulk autophagy during carbohydrate starvation. This degradation was slowed down by the inhibitor of autophagy, 3-methyladenine (3-MA), but the 3-MA effect ceased at advanced stages of starvation, indicating that another degradation mechanism for peroxisomes might have taken over. 3-MA also caused an increase particularly in peroxisomal proteins and cellular peroxisome numbers when applied under nutrient-rich conditions in the logarithmic growth phase, suggesting a high turnover rate for peroxisomes by basal autophagy under non-stress conditions. Together, our data demonstrate that a great fraction of the peroxisome pool is subject to extensive autophagy-mediated turnover under both nutrient starvation and optimal growth conditions. Our analyses of the cellular pool size of peroxisomes provide a new tool for quantitative investigations of the role of plant peroxisomes in reactive oxygen species metabolism.}, } @article {pmid25474573, year = {2014}, author = {Boza, G and Szilágyi, A and Kun, Á and Santos, M and Szathmáry, E}, title = {Evolution of the division of labor between genes and enzymes in the RNA world.}, journal = {PLoS computational biology}, volume = {10}, number = {12}, pages = {e1003936}, pmid = {25474573}, issn = {1553-7358}, mesh = {*Biological Evolution ; Computational Biology ; DNA Replication/genetics ; *Models, Genetic ; RNA/*genetics/*metabolism ; RNA, Catalytic/*genetics/*metabolism ; }, abstract = {The RNA world is a very likely interim stage of the evolution after the first replicators and before the advent of the genetic code and translated proteins. Ribozymes are known to be able to catalyze many reaction types, including cofactor-aided metabolic transformations. In a metabolically complex RNA world, early division of labor between genes and enzymes could have evolved, where the ribozymes would have been transcribed from the genes more often than the other way round, benefiting the encapsulating cells through this dosage effect. Here we show, by computer simulations of protocells harboring unlinked RNA replicators, that the origin of replicational asymmetry producing more ribozymes from a gene template than gene strands from a ribozyme template is feasible and robust. Enzymatic activities of the two modeled ribozymes are in trade-off with their replication rates, and the relative replication rates compared to those of complementary strands are evolvable traits of the ribozymes. The degree of trade-off is shown to have the strongest effect in favor of the division of labor. Although some asymmetry between gene and enzymatic strands could have evolved even in earlier, surface-bound systems, the shown mechanism in protocells seems inevitable and under strong positive selection. This could have preadapted the genetic system for transcription after the subsequent origin of chromosomes and DNA.}, } @article {pmid25474353, year = {2014}, author = {Gavryushkina, A and Welch, D and Stadler, T and Drummond, AJ}, title = {Bayesian inference of sampled ancestor trees for epidemiology and fossil calibration.}, journal = {PLoS computational biology}, volume = {10}, number = {12}, pages = {e1003919}, pmid = {25474353}, issn = {1553-7358}, mesh = {Algorithms ; Bayes Theorem ; Computational Biology/*methods ; Evolution, Molecular ; *Fossils ; HIV Infections/virology ; HIV-1/classification/genetics ; Humans ; *Models, Genetic ; *Phylogeny ; Software ; }, abstract = {Phylogenetic analyses which include fossils or molecular sequences that are sampled through time require models that allow one sample to be a direct ancestor of another sample. As previously available phylogenetic inference tools assume that all samples are tips, they do not allow for this possibility. We have developed and implemented a Bayesian Markov Chain Monte Carlo (MCMC) algorithm to infer what we call sampled ancestor trees, that is, trees in which sampled individuals can be direct ancestors of other sampled individuals. We use a family of birth-death models where individuals may remain in the tree process after sampling, in particular we extend the birth-death skyline model [Stadler et al., 2013] to sampled ancestor trees. This method allows the detection of sampled ancestors as well as estimation of the probability that an individual will be removed from the process when it is sampled. We show that even if sampled ancestors are not of specific interest in an analysis, failing to account for them leads to significant bias in parameter estimates. We also show that sampled ancestor birth-death models where every sample comes from a different time point are non-identifiable and thus require one parameter to be known in order to infer other parameters. We apply our phylogenetic inference accounting for sampled ancestors to epidemiological data, where the possibility of sampled ancestors enables us to identify individuals that infected other individuals after being sampled and to infer fundamental epidemiological parameters. We also apply the method to infer divergence times and diversification rates when fossils are included along with extant species samples, so that fossilisation events are modelled as a part of the tree branching process. Such modelling has many advantages as argued in the literature. The sampler is available as an open-source BEAST2 package (https://github.com/CompEvol/sampled-ancestors).}, } @article {pmid25472614, year = {2015}, author = {Godoy-Ruiz, P and Toner, B and Mason, R and Vidal, C and McKenzie, K}, title = {Intimate Partner Violence and Depression Among Latin American Women in Toronto.}, journal = {Journal of immigrant and minority health}, volume = {17}, number = {6}, pages = {1771-1780}, pmid = {25472614}, issn = {1557-1920}, mesh = {Adult ; Canada/epidemiology ; Central America/ethnology ; Depression/*ethnology/psychology ; Emigrants and Immigrants/*psychology ; Female ; Humans ; Interviews as Topic ; Latin America/ethnology ; Mental Health/*ethnology ; Middle Aged ; Pilot Projects ; Qualitative Research ; Refugees/*psychology ; Spouse Abuse/*ethnology/psychology ; Women's Health/ethnology ; }, abstract = {Research from the United States suggests that Latin American immigrant and refugee women are one of the groups most greatly impacted by intimate partner violence (IPV) and associated mental health consequences including higher rates of depression than women from other ethno-racial groups. In Canada, little is known about the experience of IPV and mental health among this population. Even in the broader North American context, how Latin American women themselves perceive the connection between IPV and depression is unknown. This paper presents the findings of a pilot study that examined the perceived relationship between IPV and depression among Spanish-Speaking Latin American Women in Toronto, Canada. The theoretical framework guiding this qualitative study combined an ecological model for understanding gender based violence and mental health with critical intersectionality theory. Using a convenience and snowball sampling method, semi-structured interviews (n = 12) were conducted and thematic content analysis was completed supported by Nvivo9(®) qualitative data management software. All participants had experienced some form of IPV in their adult lives, with psychological violence being the most common. Women perceived a powerful connection between IPV and depression, a link made stronger by the accumulation of other adverse life experiences including childhood abuse, war traumas and migration. The results suggest that IPV is just one of the challenges experienced by Latin American refugee and immigrant women. IPV is experienced in the context of other traumatic experiences and social hardships that may work to intensify the association of IPV and depression in this population.}, } @article {pmid25471470, year = {2015}, author = {Yang, Y and Li, X and Kong, X and Ma, L and Hu, X and Yang, Y}, title = {Transcriptome analysis reveals diversified adaptation of Stipa purpurea along a drought gradient on the Tibetan Plateau.}, journal = {Functional & integrative genomics}, volume = {15}, number = {3}, pages = {295-307}, pmid = {25471470}, issn = {1438-7948}, mesh = {Acclimatization/*genetics ; Cell Wall/ultrastructure ; *Droughts ; Gene Expression Profiling ; Gene Ontology ; Molecular Sequence Annotation ; Plant Proteins/genetics ; Poaceae/cytology/*genetics/metabolism ; Sequence Analysis, RNA ; Stress, Physiological/genetics ; Tibet ; *Transcriptome ; }, abstract = {Natural selection drives species adaptations to biotic and abiotic stresses. Species distributed along a moisture gradient, such as Stipa purpurea, a dominant grass in alpine arid and semi-arid meadows on the Tibetan Plateau, provide an opportunity to evaluate the effects of long-term adaptation to differing degrees of drought stress on gene expression. However, the genetic basis of this divergence remains largely unknown. Next-generation sequencing technologies have provided important genome-wide insights on the evolution of organisms for which genomic information is lacking. To understand how S. purpurea responds to drought stress, we selected five populations distributed along the degressive rainfall line on the northwestern Tibetan Plateau that currently present evolutionary acclimation to localized drought pressure at the physiological and biochemical levels and compared their transcriptome responses. In addition, we performed de novo assembly of the S. purpurea transcriptome using short read sequencing technology and successfully assembled 84,298 unigenes from approximately 51 million sequencing reads. We quantified gene expression level to compare their transcriptome responses using mRNA-Seq and identified differentially expressed transcripts that are involved in primary and secondary plant metabolism, plant hormone synthesis, defense responses, and cell wall synthesis. Furthermore, physiological and biochemical evidence supports that abscisic acid (ABA) accumulation and cell wall strengthening derived from the differential transcripts contribute to the tolerance of S. purpurea to drought stress. The mechanisms by which S. purpurea adapts to drought stress provide new insight into how plants ecologically adapt and evolve.}, } @article {pmid25470737, year = {2015}, author = {Austin, T and Denoyelle, M and Chaudry, A and Stradling, S and Eadsforth, C}, title = {European Chemicals Agency dossier submissions as an experimental data source: refinement of a fish toxicity model for predicting acute LC50 values.}, journal = {Environmental toxicology and chemistry}, volume = {34}, number = {2}, pages = {369-378}, doi = {10.1002/etc.2817}, pmid = {25470737}, issn = {1552-8618}, mesh = {Animals ; Cyprinidae/*physiology ; *Databases as Topic ; Ecotoxicology ; Europe ; Inhibitory Concentration 50 ; *Models, Biological ; Oncorhynchus mykiss/*physiology ; Quantitative Structure-Activity Relationship ; Reproducibility of Results ; *Toxicity Tests, Acute ; }, abstract = {As a result of the stringent data requirements of the Registration, Evaluation, Authorisation, and Restriction of Chemicals (REACH) regulation, a vast amount of ecotoxicological data has become available through the dissemination portal of the European Chemicals Agency (ECHA). As of April 2014, the database contained 12,439 unique substances from 47,909 dossiers. This vast database could be used to refine existing, or to create new, non-testing methods, such as quantitative structure-activity relationships (QSARs). Acute fish toxicity data were mined from the ECHA database using the eChemPortal; after filtering for single organic substances, 1159 experimental data points remained, representing 564 compounds. To evaluate the quality and accessibility of this data, the authors used the data to refine and improve an existing QSAR. The reliability of the data submitted to the ECHA database, as well as the effectiveness of the Klimisch scoring system, were assessed by comparing the refined QSAR with established QSAR benchmarks. The model developed meets all Organisation for Economic Co-operation and Development principles, has strong internal (leave-one-out internally cross-validated correlation coefficient [Q(2)(LOO)] = 0.91) and external (external coefficient of determination (predicted vs experimental [test set])) validation statistics, and can provide reliable fish median lethal concentration (LC50) predictions for non-polar narcotics. Although some issues with dossier misinformation were discovered, it was found that the ECHA dissemination portal is a valuable and reliable data source. When queried using the eChemPortal, chemical dossiers containing reliable data could be found quickly. The ECHA dissemination portal holds great potential for future QSAR development and improvement, such as updating QSARs within the Ecological Structure-Activity Relationships (ECOSAR) program.}, } @article {pmid25470496, year = {2014}, author = {Hui, M and Liu, Y and Song, C and Li, Y and Shi, G and Cui, Z}, title = {Transcriptome changes in Eriocheir sinensis megalopae after desalination provide insights into osmoregulation and stress adaption in larvae.}, journal = {PloS one}, volume = {9}, number = {12}, pages = {e114187}, pmid = {25470496}, issn = {1932-6203}, mesh = {ATP Synthetase Complexes/chemistry/genetics/metabolism ; Adaptation, Physiological/genetics ; Amino Acid Sequence ; Animals ; Brachyura/*genetics/growth & development/metabolism ; Databases, Factual ; Energy Metabolism/genetics ; Gene Expression Profiling ; Gene Library ; Larva/genetics/metabolism ; Molecular Sequence Annotation ; Molecular Sequence Data ; Osmoregulation/genetics ; Oxidative Phosphorylation ; Oxidative Stress/genetics ; Protein Subunits/chemistry/genetics/metabolism ; Salinity ; Sequence Alignment ; Sequence Analysis, RNA ; *Transcriptome ; }, abstract = {Eriocheir sinensis, an extremely invasive alien crab species, has important economic value in China. It encounters different salinities during its life cycle, and at the megalopal stage it faces a turning point regarding the salinity in its environment. We applied RNA sequencing to E. sinensis megalopae before (MB) and after (MA) desalination, resulting in the discovery of 21,042 unigenes and 908 differentially expressed genes (DEGs, 4.32% of the unigenes). The DEGs primarily belonged to the Gene Ontology groups "Energy metabolism," "Oxidoreductase activity," "Translation," "Transport," "Metabolism," and "Stress response." In total, 33 DEGs related to transport processes were found, including 12 proton pump genes, three ATP-binding cassettes (ABCs), 13 solute carrier (SLC) family members, two sweet sugar transporter (ST) family members and three other substance transporters. Mitochondrial genes as well as genes involved in the tricarboxylic acid cycle, glycolytic pathway, or β-oxidation pathway, which can generate energy in the form of ATP, were typically up-regulated in MA. 11 unigenes related to amino acid metabolism and a large number of genes related to protein synthesis were differentially expressed in MB and MA, indicating that E. sinensis possibly adjusts its concentration of free amino acid osmolytes for hyper-osmoregulation. Additionally, 33 salinity and oxidative stress induced genes were found to be differentially expressed, such as the LEA2, HSPs, GST and coagulation factor genes. Notably, LEA2 is an extremely hydrophilic protein that responds to desiccation and reported for the first time in crabs. Therefore, we suppose that when the environment is hypo-osmotic, the megalopae might compensate for ion loss via hyper-osmoregulation by consuming more energy, accompanied by a series of stress induced adaptions. This study provides the first genome-wide transcriptome analysis of E. sinensis megalopae for studying its osmoregulation and stress adaption mechanisms.}, } @article {pmid25470125, year = {2014}, author = {Guralnick, R and Conlin, T and Deck, J and Stucky, BJ and Cellinese, N}, title = {The trouble with triplets in biodiversity informatics: a data-driven case against current identifier practices.}, journal = {PloS one}, volume = {9}, number = {12}, pages = {e114069}, pmid = {25470125}, issn = {1932-6203}, mesh = {*Biodiversity ; Computational Biology/*methods ; *Database Management Systems ; Databases, Factual ; *Information Storage and Retrieval ; Internet ; }, abstract = {The biodiversity informatics community has discussed aspirations and approaches for assigning globally unique identifiers (GUIDs) to biocollections for nearly a decade. During that time, and despite misgivings, the de facto standard identifier has become the "Darwin Core Triplet", which is a concatenation of values for institution code, collection code, and catalog number associated with biocollections material. Our aim is not to rehash the challenging discussions regarding which GUID system in theory best supports the biodiversity informatics use case of discovering and linking digital data across the Internet, but how well we can link those data together at this moment, utilizing the current identifier schemes that have already been deployed. We gathered Darwin Core Triplets from a subset of VertNet records, along with vertebrate records from GenBank and the Barcode of Life Data System, in order to determine how Darwin Core Triplets are deployed "in the wild". We asked if those triplets follow the recommended structure and whether they provide an easy and unambiguous means to track from specimen records to genetic sequence records. We show that Darwin Core Triplets are often riddled with semantic and syntactic errors when deployed and curated in practice, despite specifications about how to construct them. Our results strongly suggest that Darwin Core Triplets that have not been carefully curated are not currently serving a useful role for relinking data. We briefly consider needed next steps to overcome current limitations.}, } @article {pmid25468931, year = {2014}, author = {Duarte, M and Jauregui, R and Vilchez-Vargas, R and Junca, H and Pieper, DH}, title = {AromaDeg, a novel database for phylogenomics of aerobic bacterial degradation of aromatics.}, journal = {Database : the journal of biological databases and curation}, volume = {2014}, number = {}, pages = {bau118}, pmid = {25468931}, issn = {1758-0463}, mesh = {Aerobiosis ; Bacteria/*metabolism ; Biodegradation, Environmental ; *Databases, Factual ; *Genomics ; Hydrocarbons, Aromatic/*metabolism ; Internet ; *Phylogeny ; Search Engine ; User-Computer Interface ; }, abstract = {Understanding prokaryotic transformation of recalcitrant pollutants and the in-situ metabolic nets require the integration of massive amounts of biological data. Decades of biochemical studies together with novel next-generation sequencing data have exponentially increased information on aerobic aromatic degradation pathways. However, the majority of protein sequences in public databases have not been experimentally characterized and homology-based methods are still the most routinely used approach to assign protein function, allowing the propagation of misannotations. AromaDeg is a web-based resource targeting aerobic degradation of aromatics that comprises recently updated (September 2013) and manually curated databases constructed based on a phylogenomic approach. Grounded in phylogenetic analyses of protein sequences of key catabolic protein families and of proteins of documented function, AromaDeg allows query and data mining of novel genomic, metagenomic or metatranscriptomic data sets. Essentially, each query sequence that match a given protein family of AromaDeg is associated to a specific cluster of a given phylogenetic tree and further function annotation and/or substrate specificity may be inferred from the neighboring cluster members with experimentally validated function. This allows a detailed characterization of individual protein superfamilies as well as high-throughput functional classifications. Thus, AromaDeg addresses the deficiencies of homology-based protein function prediction, combining phylogenetic tree construction and integration of experimental data to obtain more accurate annotations of new biological data related to aerobic aromatic biodegradation pathways. We pursue in future the expansion of AromaDeg to other enzyme families involved in aromatic degradation and its regular update. Database URL: http://aromadeg.siona.helmholtz-hzi.de}, } @article {pmid25466379, year = {2014}, author = {Villeneuve, DL and Crump, D and Garcia-Reyero, N and Hecker, M and Hutchinson, TH and LaLone, CA and Landesmann, B and Lettieri, T and Munn, S and Nepelska, M and Ottinger, MA and Vergauwen, L and Whelan, M}, title = {Adverse outcome pathway development II: best practices.}, journal = {Toxicological sciences : an official journal of the Society of Toxicology}, volume = {142}, number = {2}, pages = {321-330}, pmid = {25466379}, issn = {1096-0929}, mesh = {Animals ; Biomedical Research/*methods/statistics & numerical data ; *Databases, Factual ; Humans ; *Models, Biological ; Toxicology/*methods/statistics & numerical data ; }, abstract = {Organization of existing and emerging toxicological knowledge into adverse outcome pathway (AOP) descriptions can facilitate greater application of mechanistic data, including those derived through high-throughput in vitro, high content omics and imaging, and biomarker approaches, in risk-based decision making. The previously ad hoc process of AOP development is being formalized through development of internationally harmonized guidance and principles. The goal of this article was to outline the information content desired for formal AOP description and some rules of thumb and best practices intended to facilitate reuse and connectivity of elements of an AOP description in a knowledgebase and network context. For example, key events (KEs) are measurements of change in biological state that are indicative of progression of a perturbation toward a specified adverse outcome. Best practices for KE description suggest that each KE should be defined as an independent measurement made at a particular level of biological organization. The concept of "functional equivalence" can help guide both decisions about how many KEs to include in an AOP and the specificity with which they are defined. Likewise, in describing both KEs and evidence that supports a causal linkage or statistical association between them (ie, a key event relationship; KER), best practice is to build from and contribute to existing KE or KER descriptions in the AOP knowledgebase rather than creating redundant descriptions. The best practices proposed address many of the challenges and uncertainties related to AOP development and help promote a consistent and reliable, yet flexible approach.}, } @article {pmid25466378, year = {2014}, author = {Villeneuve, DL and Crump, D and Garcia-Reyero, N and Hecker, M and Hutchinson, TH and LaLone, CA and Landesmann, B and Lettieri, T and Munn, S and Nepelska, M and Ottinger, MA and Vergauwen, L and Whelan, M}, title = {Adverse outcome pathway (AOP) development I: strategies and principles.}, journal = {Toxicological sciences : an official journal of the Society of Toxicology}, volume = {142}, number = {2}, pages = {312-320}, pmid = {25466378}, issn = {1096-0929}, mesh = {Animals ; Biomedical Research/*methods ; *Databases, Factual ; Humans ; *Models, Biological ; Toxicology/*methods ; }, abstract = {An adverse outcome pathway (AOP) is a conceptual framework that organizes existing knowledge concerning biologically plausible, and empirically supported, links between molecular-level perturbation of a biological system and an adverse outcome at a level of biological organization of regulatory relevance. Systematic organization of information into AOP frameworks has potential to improve regulatory decision-making through greater integration and more meaningful use of mechanistic data. However, for the scientific community to collectively develop a useful AOP knowledgebase that encompasses toxicological contexts of concern to human health and ecological risk assessment, it is critical that AOPs be developed in accordance with a consistent set of core principles. Based on the experiences and scientific discourse among a group of AOP practitioners, we propose a set of five fundamental principles that guide AOP development: (1) AOPs are not chemical specific; (2) AOPs are modular and composed of reusable components-notably key events (KEs) and key event relationships (KERs); (3) an individual AOP, composed of a single sequence of KEs and KERs, is a pragmatic unit of AOP development and evaluation; (4) networks composed of multiple AOPs that share common KEs and KERs are likely to be the functional unit of prediction for most real-world scenarios; and (5) AOPs are living documents that will evolve over time as new knowledge is generated. The goal of the present article was to introduce some strategies for AOP development and detail the rationale behind these 5 key principles. Consideration of these principles addresses many of the current uncertainties regarding the AOP framework and its application and is intended to foster greater consistency in AOP development.}, } @article {pmid25466262, year = {2015}, author = {Kataoka, H and Mochimasu, KD and Katayama, A and Kanda, KO and Sakano, N and Tanaka, K and Miyatake, N}, title = {The linkage among ambulance transports, death and climate parameters in Asahikawa City, Japan.}, journal = {Environmental health and preventive medicine}, volume = {20}, number = {1}, pages = {63-67}, pmid = {25466262}, issn = {1347-4715}, mesh = {Ambulances/statistics & numerical data ; Analysis of Variance ; *Climate ; Databases, Factual ; Humans ; Incidence ; Japan/epidemiology ; *Mortality ; Pilot Projects ; Weather ; }, abstract = {OBJECTIVE: The aim of this study was to investigate the linkage among climate parameters, total ambulance transports and the number of deaths in Asahikawa City in northern Japan.

METHODS: Monthly data on total ambulance transports and the number of deaths from January 2004 to December 2011 were obtained from Asahikawa City Fire Department and the Asahikawa City official website. Climate parameters for the required period were also obtained from the Japan Meteorological Agency, Japan. To adjust for the population, we also used monthly population data on Asahikawa City. The linkage among climate parameters, total ambulance transports and the number of deaths was evaluated by ecological analysis.

RESULTS: The mean air temperature in the Asahikawa area was 7.3 ± 10.1 °C. Total ambulance transports (/a hundred thousand people/day) and the number of deaths (/a hundred thousand people/day) were 10.0 ± 0.6 and 2.6 ± 0.3, respectively. Using quadratic curves, total ambulance transports and the number of deaths were weakly correlated with some climate parameters. The number of deaths was weakly and positively correlated with total ambulance transports.

CONCLUSION: A weak linkage among climate parameters, total ambulance transports and the number of deaths was noted in Asahikawa City, Japan. However, these associations were not as high as expected.}, } @article {pmid25463924, year = {2015}, author = {Kauhl, B and Pilot, E and Rao, R and Gruebner, O and Schweikart, J and Krafft, T}, title = {Estimating the spatial distribution of acute undifferentiated fever (AUF) and associated risk factors using emergency call data in India. A symptom-based approach for public health surveillance.}, journal = {Health & place}, volume = {31}, number = {}, pages = {111-119}, doi = {10.1016/j.healthplace.2014.11.002}, pmid = {25463924}, issn = {1873-2054}, mesh = {Adolescent ; Adult ; Child ; Child, Preschool ; *Disease Outbreaks ; Female ; Fever of Unknown Origin/*epidemiology ; Geographic Information Systems ; Humans ; Incidence ; India/epidemiology ; Infant ; Infant, Newborn ; Male ; Pilot Projects ; *Public Health Surveillance ; Risk Factors ; }, abstract = {The System for Early-warning based on Emergency Data (SEED) is a pilot project to evaluate the use of emergency call data with the main complaint acute undifferentiated fever (AUF) for syndromic surveillance in India. While spatio-temporal methods provide signals to detect potential disease outbreaks, additional information about socio-ecological exposure factors and the main population at risk is necessary for evidence-based public health interventions and future preparedness strategies. The goal of this study is to investigate whether a spatial epidemiological analysis at the ecological level provides information on urban-rural inequalities, socio-ecological exposure factors and the main population at risk for AUF. Our results displayed higher risks in rural areas with strong local variation. Household industries and proximity to forests were the main socio-ecological exposure factors and scheduled tribes were the main population at risk for AUF. These results provide additional information for syndromic surveillance and could be used for evidence-based public health interventions and future preparedness strategies.}, } @article {pmid25462609, year = {2014}, author = {Schoen, MW and Moreland-Russell, S and Prewitt, K and Carothers, BJ}, title = {Social network analysis of public health programs to measure partnership.}, journal = {Social science & medicine (1982)}, volume = {123}, number = {}, pages = {90-95}, doi = {10.1016/j.socscimed.2014.10.057}, pmid = {25462609}, issn = {1873-5347}, mesh = {*Community Networks/organization & administration ; *Health Promotion ; Humans ; Missouri ; Obesity/prevention & control ; *Public Health ; Smoking Cessation ; *Social Support ; Surveys and Questionnaires ; }, abstract = {In order to prevent chronic diseases, community-based programs are encouraged to take an ecological approach to public health promotion and involve many diverse partners. Little is known about measuring partnership in implementing public health strategies. We collected data from 23 Missouri communities in early 2012 that received funding from three separate programs to prevent obesity and/or reduce tobacco use. While all of these funding programs encourage partnership, only the Social Innovation for Missouri (SIM) program included a focus on building community capacity and enhancing collaboration. Social network analysis techniques were used to understand contact and collaboration networks in community organizations. Measurements of average degree, density, degree centralization, and betweenness centralization were calculated for each network. Because of the various sizes of the networks, we conducted comparative analyses with and without adjustment for network size. SIM programs had increased measurements of average degree for partner collaboration and larger networks. When controlling for network size, SIM groups had higher measures of network density and lower measures of degree centralization and betweenness centralization. SIM collaboration networks were more dense and less centralized, indicating increased partnership. The methods described in this paper can be used to compare partnership in community networks of various sizes. Further research is necessary to define causal mechanisms of partnership development and their relationship to public health outcomes.}, } @article {pmid25461969, year = {2015}, author = {von Dassow, P and John, U and Ogata, H and Probert, I and Bendif, el M and Kegel, JU and Audic, S and Wincker, P and Da Silva, C and Claverie, JM and Doney, S and Glover, DM and Flores, DM and Herrera, Y and Lescot, M and Garet-Delmas, MJ and de Vargas, C}, title = {Life-cycle modification in open oceans accounts for genome variability in a cosmopolitan phytoplankton.}, journal = {The ISME journal}, volume = {9}, number = {6}, pages = {1365-1377}, pmid = {25461969}, issn = {1751-7370}, mesh = {Animals ; Biomass ; Chlorophyll/chemistry ; Computational Biology ; Diploidy ; Ecology ; Flagella/metabolism ; Gene Expression Profiling ; Genetic Markers/genetics ; Genome ; Genomics ; Genotype ; Haptophyta/*genetics ; Life Cycle Stages ; *Oceans and Seas ; Phytoplankton/*genetics ; }, abstract = {Emiliania huxleyi is the most abundant calcifying plankton in modern oceans with substantial intraspecific genome variability and a biphasic life cycle involving sexual alternation between calcified 2N and flagellated 1N cells. We show that high genome content variability in Emiliania relates to erosion of 1N-specific genes and loss of the ability to form flagellated cells. Analysis of 185 E. huxleyi strains isolated from world oceans suggests that loss of flagella occurred independently in lineages inhabiting oligotrophic open oceans over short evolutionary timescales. This environmentally linked physiogenomic change suggests life cycling is not advantageous in very large/diluted populations experiencing low biotic pressure and low ecological variability. Gene loss did not appear to reflect pressure for genome streamlining in oligotrophic oceans as previously observed in picoplankton. Life-cycle modifications might be common in plankton and cause major functional variability to be hidden from traditional taxonomic or molecular markers.}, } @article {pmid25461814, year = {2015}, author = {Maskow, T and Paufler, S}, title = {What does calorimetry and thermodynamics of living cells tell us?.}, journal = {Methods (San Diego, Calif.)}, volume = {76}, number = {}, pages = {3-10}, doi = {10.1016/j.ymeth.2014.10.035}, pmid = {25461814}, issn = {1095-9130}, mesh = {Calorimetry/*methods ; Data Interpretation, Statistical ; Energy Metabolism ; Thermodynamics ; }, abstract = {This article presents and compares several thermodynamic methods for the quantitative interpretation of data from calorimetric measurements. Heat generation and absorption are universal features of microbial growth and product formation as well as of cell cultures from animals, plants and insects. The heat production rate reflects metabolic changes in real time and is measurable on-line. The detection limit of commercially available calorimetric instruments can be low enough to measure the heat of 100,000 aerobically growing bacteria or of 100 myocardial cells. Heat can be monitored in reaction vessels ranging from a few nanoliters up to many cubic meters. Most important the heat flux measurement does not interfere with the biological process under investigation. The practical advantages of calorimetry include the waiver of labeling and reactants. It is further possible to assemble the thermal transducer in a protected way that reduces aging and thereby signal drifts. Calorimetry works with optically opaque solutions. All of these advantages make calorimetry an interesting method for many applications in medicine, environmental sciences, ecology, biochemistry and biotechnology, just to mention a few. However, in many cases the heat signal is merely used to monitor biological processes but only rarely to quantitatively interpret the data. Therefore, a significant proportion of the information potential of calorimetry remains unutilized. To fill this information gap and to motivate the reader using the full information potential of calorimetry, various methods for quantitative data interpretations are presented, evaluated and compared with each other. Possible errors of interpretation and limitations of quantitative data analysis are also discussed.}, } @article {pmid25461242, year = {2014}, author = {Arboe, B and Laub, RR and Kronborg, G and Knudsen, JD}, title = {Evaluation of the decision support system for antimicrobial treatment, TREAT, in an acute medical ward of a university hospital.}, journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases}, volume = {29}, number = {}, pages = {156-161}, doi = {10.1016/j.ijid.2014.08.019}, pmid = {25461242}, issn = {1878-3511}, mesh = {Adolescent ; Adult ; Aged ; Aged, 80 and over ; Anti-Bacterial Agents/*therapeutic use ; Bacteremia/drug therapy ; Bacterial Infections/*drug therapy ; Cohort Studies ; *Decision Support Systems, Clinical ; Female ; Hospitals, University ; Humans ; Length of Stay ; Male ; Middle Aged ; Prospective Studies ; Retrospective Studies ; Treatment Outcome ; Young Adult ; }, abstract = {OBJECTIVES: TREAT, a decision support system for antimicrobial therapy, was implemented in an acute medical ward.

METHODS: Patients admitted on suspicion of infection were included in the study. The evaluation of TREAT was done both retrospectively and prospectively. Coverage of empirical antimicrobial treatments was compared to recommendations from TREAT and the optimal use of local guidelines.

RESULTS: Five hundred and eleven patients were included, of whom 162 had a microbiologically documented infection. In the retrospective part of the study, TREAT, physician, and guideline antimicrobial coverage rates were 65%, 51%, and 79%, respectively, and in the prospective part, 68%, 62%, and 77%, respectively. TREAT provided lower coverage than local guidelines (p<0.001), but was similar to the performance of physicians in a university hospital (p=0.069). No differences were found in length of hospital stay, or hospital or 30-day mortality. Direct costs were significantly higher for TREAT advice than for local guidelines or the physician prescriptions (p<0.001), but the ecological costs were lower for TREAT advice than for both local guidelines (p<0.001) and physician prescriptions (p=0.247). The coverage of TREAT advice for the bacteraemia patients was non-inferior to the physicians (p=1.00).

CONCLUSIONS: TREAT can potentially improve the ecological costs of empirical antimicrobial therapy for patients in acute medical wards, but provided lower coverage than local guidelines.}, } @article {pmid25460984, year = {2015}, author = {De Francisci, D and Kougias, PG and Treu, L and Campanaro, S and Angelidaki, I}, title = {Microbial diversity and dynamicity of biogas reactors due to radical changes of feedstock composition.}, journal = {Bioresource technology}, volume = {176}, number = {}, pages = {56-64}, doi = {10.1016/j.biortech.2014.10.126}, pmid = {25460984}, issn = {1873-2976}, mesh = {Animals ; Bacteria, Anaerobic/genetics/*physiology ; Base Sequence ; *Biodiversity ; *Biofuels ; Bioreactors/*microbiology ; Carbohydrate Metabolism/physiology ; Cattle ; Computational Biology ; Denmark ; Lipid Metabolism/physiology ; Manure/microbiology ; Metabolic Networks and Pathways/genetics/*physiology ; Molecular Sequence Data ; Principal Component Analysis ; Proteins/metabolism ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {The anaerobic digestion process is often inhibited by alteration of substrates and/or organic overload. This study aimed to elucidate changes of microbial ecology in biogas reactors upon radical changes of substrates and to determine their importance to process imbalance. For this reason, continuously fed reactors were disturbed with pulses of proteins, lipids and carbohydrates and the microbial ecology of the reactors were characterized by 16S rRNA gene sequencing before and after the imposed changes. The microbial composition of the three reactors, initially similar, diverged greatly after substrate change. The greatest increase in diversity was observed in the reactor supplemented with carbohydrates and the microbial community became dominated by lactobacilli, while the lowest corresponded to the reactor overfed with proteins, where only Desulfotomaculum showed significant increase. The overall results suggest that feed composition has a decisive impact on the microbial composition of the reactors, and thereby on their performance.}, } @article {pmid25460761, year = {2015}, author = {Sierra, C and Ordóñez, C and Saavedra, A and Gallego, JR}, title = {Element enrichment factor calculation using grain-size distribution and functional data regression.}, journal = {Chemosphere}, volume = {119}, number = {}, pages = {1192-1199}, doi = {10.1016/j.chemosphere.2014.10.024}, pmid = {25460761}, issn = {1879-1298}, mesh = {Chemistry/*methods ; *Data Interpretation, Statistical ; Ecology/*methods ; Environmental Pollution/*analysis ; *Linear Models ; *Models, Theoretical ; Reproducibility of Results ; Soil Pollutants/*analysis ; Spain ; }, abstract = {In environmental geochemistry studies it is common practice to normalize element concentrations in order to remove the effect of grain size. Linear regression with respect to a particular grain size or conservative element is a widely used method of normalization. In this paper, the utility of functional linear regression, in which the grain-size curve is the independent variable and the concentration of pollutant the dependent variable, is analyzed and applied to detrital sediment. After implementing functional linear regression and classical linear regression models to normalize and calculate enrichment factors, we concluded that the former regression technique has some advantages over the latter. First, functional linear regression directly considers the grain-size distribution of the samples as the explanatory variable. Second, as the regression coefficients are not constant values but functions depending on the grain size, it is easier to comprehend the relationship between grain size and pollutant concentration. Third, regularization can be introduced into the model in order to establish equilibrium between reliability of the data and smoothness of the solutions.}, } @article {pmid25460419, year = {2015}, author = {Marini, C and Fossa, F and Paoli, C and Bellingeri, M and Gnone, G and Vassallo, P}, title = {Predicting bottlenose dolphin distribution along Liguria coast (northwestern Mediterranean Sea) through different modeling techniques and indirect predictors.}, journal = {Journal of environmental management}, volume = {150}, number = {}, pages = {9-20}, doi = {10.1016/j.jenvman.2014.11.008}, pmid = {25460419}, issn = {1095-8630}, mesh = {Animals ; Bottle-Nosed Dolphin/*physiology ; *Ecosystem ; Geographic Information Systems ; Mediterranean Sea ; Population Density ; Probability ; }, abstract = {Habitat modeling is an important tool to investigate the quality of the habitat for a species within a certain area, to predict species distribution and to understand the ecological processes behind it. Many species have been investigated by means of habitat modeling techniques mainly to address effective management and protection policies and cetaceans play an important role in this context. The bottlenose dolphin (Tursiops truncatus) has been investigated with habitat modeling techniques since 1997. The objectives of this work were to predict the distribution of bottlenose dolphin in a coastal area through the use of static morphological features and to compare the prediction performances of three different modeling techniques: Generalized Linear Model (GLM), Generalized Additive Model (GAM) and Random Forest (RF). Four static variables were tested: depth, bottom slope, distance from 100 m bathymetric contour and distance from coast. RF revealed itself both the most accurate and the most precise modeling technique with very high distribution probabilities predicted in presence cells (90.4% of mean predicted probabilities) and with 66.7% of presence cells with a predicted probability comprised between 90% and 100%. The bottlenose distribution obtained with RF allowed the identification of specific areas with particularly high presence probability along the coastal zone; the recognition of these core areas may be the starting point to develop effective management practices to improve T. truncatus protection.}, } @article {pmid25460230, year = {2014}, author = {John, U and Litaker, RW and Montresor, M and Murray, S and Brosnahan, ML and Anderson, DM}, title = {Formal revision of the Alexandrium tamarense species complex (Dinophyceae) taxonomy: the introduction of five species with emphasis on molecular-based (rDNA) classification.}, journal = {Protist}, volume = {165}, number = {6}, pages = {779-804}, pmid = {25460230}, issn = {1618-0941}, support = {P01 ES021923/ES/NIEHS NIH HHS/United States ; 1-P50-ES021923-01/ES/NIEHS NIH HHS/United States ; }, mesh = {DNA, Ribosomal/*genetics ; Databases, Genetic ; Dinoflagellida/*classification/*genetics ; Genetic Markers ; Marine Toxins/chemistry ; Neurotoxins/chemistry ; *Phylogeny ; Saxitoxin/chemistry ; Species Specificity ; }, abstract = {The Alexandrium tamarense species complex is one of the most studied marine dinoflagellate groups due to its ecological, toxicological and economic importance. Several members of this complex produce saxitoxin and its congeners - potent neurotoxins that cause paralytic shellfish poisoning. Isolates from this complex are assigned to A. tamarense, A. fundyense, or A. catenella based on two main morphological characters: the ability to form chains and the presence/absence of a ventral pore between Plates 1' and 4'. However, studies have shown that these characters are not consistent and/or distinctive. Further, phylogenies based on multiple regions in the rDNA operon indicate that the sequences from morphologically indistinguishable isolates partition into five clades. These clades were initially named based on their presumed geographic distribution, but recently were renamed as Groups I-V following the discovery of sympatry among some groups. In this study we present data on morphology, ITS/5.8S genetic distances, ITS2 compensatory base changes, mating incompatibilities, toxicity, the sxtA toxin synthesis gene, and rDNA phylogenies. All results were consistent with each group representing a distinct cryptic species. Accordingly, the groups were assigned species names as follows: Group I, A. fundyense; Group II, A. mediterraneum; Group III, A. tamarense; Group IV, A. pacificum; Group V, A. australiense.}, } @article {pmid25459204, year = {2015}, author = {Carrel, M and Patel, J and Taylor, SM and Janko, M and Mwandagalirwa, MK and Tshefu, AK and Escalante, AA and McCollum, A and Alam, MT and Udhayakumar, V and Meshnick, S and Emch, M}, title = {The geography of malaria genetics in the Democratic Republic of Congo: A complex and fragmented landscape.}, journal = {Social science & medicine (1982)}, volume = {133}, number = {}, pages = {233-241}, pmid = {25459204}, issn = {1873-5347}, support = {1R56AI097609-01/AI/NIAID NIH HHS/United States ; K08 AI100924/AI/NIAID NIH HHS/United States ; R01 AI107949/AI/NIAID NIH HHS/United States ; R56 AI097609/AI/NIAID NIH HHS/United States ; P2C HD050924/HD/NICHD NIH HHS/United States ; K08AI100924/AI/NIAID NIH HHS/United States ; }, mesh = {Blood/parasitology ; Democratic Republic of the Congo ; *Gene Flow ; Genetic Variation ; *Geography, Medical ; Ghana ; Humans ; Kenya ; Malaria, Falciparum/parasitology/*transmission ; Microsatellite Repeats/genetics ; Plasmodium falciparum/*genetics ; Polymerase Chain Reaction/methods ; }, abstract = {Understanding how malaria parasites move between populations is important, particularly given the potential for malaria to be reintroduced into areas where it was previously eliminated. We examine the distribution of malaria genetics across seven sites within the Democratic Republic of Congo (DRC) and two nearby countries, Ghana and Kenya, in order to understand how the relatedness of malaria parasites varies across space, and whether there are barriers to the flow of malaria parasites within the DRC or across borders. Parasite DNA was retrieved from dried blood spots from 7 Demographic and Health Survey sample clusters in the DRC. Malaria genetic characteristics of parasites from Ghana and Kenya were also obtained. For each of 9 geographic sites (7 DRC, 1 Ghana and 1 Kenya), a pair-wise RST statistic was calculated, indicating the genetic distance between malaria parasites found in those locations. Mapping genetics across the spatial extent of the study area indicates a complex genetic landscape, where relatedness between two proximal sites may be relatively high (RST > 0.64) or low (RST < 0.05), and where distal sites also exhibit both high and low genetic similarity. Mantel's tests suggest that malaria genetics differ as geographic distances increase. Principal Coordinate Analysis suggests that genetically related samples are not co-located. Barrier analysis reveals no significant barriers to gene flow between locations. Malaria genetics in the DRC have a complex and fragmented landscape. Limited exchange of genes across space is reflected in greater genetic distance between malaria parasites isolated at greater geographic distances. There is, however, evidence for close genetic ties between distally located sample locations, indicating that movement of malaria parasites and flow of genes is being driven by factors other than distance decay. This research demonstrates the contributions that spatial disease ecology and landscape genetics can make to understanding the evolutionary dynamics of infectious diseases.}, } @article {pmid25458732, year = {2015}, author = {Bogoch, II and Creatore, MI and Cetron, MS and Brownstein, JS and Pesik, N and Miniota, J and Tam, T and Hu, W and Nicolucci, A and Ahmed, S and Yoon, JW and Berry, I and Hay, SI and Anema, A and Tatem, AJ and MacFadden, D and German, M and Khan, K}, title = {Assessment of the potential for international dissemination of Ebola virus via commercial air travel during the 2014 west African outbreak.}, journal = {Lancet (London, England)}, volume = {385}, number = {9962}, pages = {29-35}, pmid = {25458732}, issn = {1474-547X}, support = {095066/WT_/Wellcome Trust/United Kingdom ; R01LM010812/LM/NLM NIH HHS/United States ; R01 LM010812/LM/NLM NIH HHS/United States ; /CAPMC/CIHR/Canada ; /WT_/Wellcome Trust/United Kingdom ; }, mesh = {Air Travel/*statistics & numerical data ; *Disease Outbreaks ; Ebolavirus/*pathogenicity ; Guinea/epidemiology ; Hemorrhagic Fever, Ebola/*epidemiology/transmission ; Humans ; Liberia/epidemiology ; Mass Screening/*standards ; *Models, Statistical ; Public Health ; Risk Factors ; Sierra Leone/epidemiology ; }, abstract = {BACKGROUND: The WHO declared the 2014 west African Ebola epidemic a public health emergency of international concern in view of its potential for further international spread. Decision makers worldwide are in need of empirical data to inform and implement emergency response measures. Our aim was to assess the potential for Ebola virus to spread across international borders via commercial air travel and assess the relative efficiency of exit versus entry screening of travellers at commercial airports.

METHODS: We analysed International Air Transport Association data for worldwide flight schedules between Sept 1, 2014, and Dec 31, 2014, and historic traveller flight itinerary data from 2013 to describe expected global population movements via commercial air travel out of Guinea, Liberia, and Sierra Leone. Coupled with Ebola virus surveillance data, we modelled the expected number of internationally exported Ebola virus infections, the potential effect of air travel restrictions, and the efficiency of airport-based traveller screening at international ports of entry and exit. We deemed individuals initiating travel from any domestic or international airport within these three countries to have possible exposure to Ebola virus. We deemed all other travellers to have no significant risk of exposure to Ebola virus.

FINDINGS: Based on epidemic conditions and international flight restrictions to and from Guinea, Liberia, and Sierra Leone as of Sept 1, 2014 (reductions in passenger seats by 51% for Liberia, 66% for Guinea, and 85% for Sierra Leone), our model projects 2.8 travellers infected with Ebola virus departing the above three countries via commercial flights, on average, every month. 91,547 (64%) of all air travellers departing Guinea, Liberia, and Sierra Leone had expected destinations in low-income and lower-middle-income countries. Screening international travellers departing three airports would enable health assessments of all travellers at highest risk of exposure to Ebola virus infection.

INTERPRETATION: Decision makers must carefully balance the potential harms from travel restrictions imposed on countries that have Ebola virus activity against any potential reductions in risk from Ebola virus importations. Exit screening of travellers at airports in Guinea, Liberia, and Sierra Leone would be the most efficient frontier at which to assess the health status of travellers at risk of Ebola virus exposure, however, this intervention might require international support to implement effectively.

FUNDING: Canadian Institutes of Health Research.}, } @article {pmid25453904, year = {2015}, author = {Huang, K and Ritland, K and Guo, S and Dunn, DW and Chen, D and Ren, Y and Qi, X and Zhang, P and He, G and Li, B}, title = {Estimating pairwise relatedness between individuals with different levels of ploidy.}, journal = {Molecular ecology resources}, volume = {15}, number = {4}, pages = {772-784}, doi = {10.1111/1755-0998.12351}, pmid = {25453904}, issn = {1755-0998}, mesh = {Animals ; Computational Biology/*methods ; Insecta/*classification/*genetics ; *Phylogeny ; Plants/*classification/*genetics ; *Ploidies ; Software ; }, abstract = {Estimates of relatedness coefficients, based on genetic marker data, are often necessary for studies of genetics and ecology. Whilst many estimates based on method-of-moment or maximum-likelihood methods exist for diploid organisms, no such estimators exist for organisms with multiple ploidy levels, which occur in some insect and plant species. Here, we extend five estimators to account for different levels of ploidy: one relatedness coefficient estimator, three coefficients of coancestry estimators and one maximum-likelihood estimator. We use arrhenotoky (when unfertilized eggs develop into haploid males) as an example in evaluations of estimator performance by Monte Carlo simulation. Also, three virtual sex-determination systems are simulated to evaluate their performances for higher levels of ploidy. Additionally, we used two real data sets to test the robustness of these estimators under actual conditions. We make available a software package, PolyRelatedness, for other researchers to apply to organisms that have various levels of ploidy.}, } @article {pmid25453090, year = {2014}, author = {Rittschof, CC and Bukhari, SA and Sloofman, LG and Troy, JM and Caetano-Anollés, D and Cash-Ahmed, A and Kent, M and Lu, X and Sanogo, YO and Weisner, PA and Zhang, H and Bell, AM and Ma, J and Sinha, S and Robinson, GE and Stubbs, L}, title = {Neuromolecular responses to social challenge: common mechanisms across mouse, stickleback fish, and honey bee.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {111}, number = {50}, pages = {17929-17934}, pmid = {25453090}, issn = {1091-6490}, support = {R01 GM082937/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Base Sequence ; Bees/genetics/*physiology ; *Biological Evolution ; Brain/*physiology ; DNA Primers/genetics ; Energy Metabolism/physiology ; Genomics/methods ; Immunohistochemistry ; Mice ; Microscopy, Fluorescence ; Molecular Sequence Annotation ; Molecular Sequence Data ; Polymerase Chain Reaction ; Sequence Analysis, RNA ; Signal Transduction/physiology ; Smegmamorpha/genetics/*physiology ; *Social Behavior ; Species Specificity ; *Territoriality ; Transcription Factors/metabolism ; }, abstract = {Certain complex phenotypes appear repeatedly across diverse species due to processes of evolutionary conservation and convergence. In some contexts like developmental body patterning, there is increased appreciation that common molecular mechanisms underlie common phenotypes; these molecular mechanisms include highly conserved genes and networks that may be modified by lineage-specific mutations. However, the existence of deeply conserved mechanisms for social behaviors has not yet been demonstrated. We used a comparative genomics approach to determine whether shared neuromolecular mechanisms could underlie behavioral response to territory intrusion across species spanning a broad phylogenetic range: house mouse (Mus musculus), stickleback fish (Gasterosteus aculeatus), and honey bee (Apis mellifera). Territory intrusion modulated similar brain functional processes in each species, including those associated with hormone-mediated signal transduction and neurodevelopment. Changes in chromosome organization and energy metabolism appear to be core, conserved processes involved in the response to territory intrusion. We also found that several homologous transcription factors that are typically associated with neural development were modulated across all three species, suggesting that shared neuronal effects may involve transcriptional cascades of evolutionarily conserved genes. Furthermore, immunohistochemical analyses of a subset of these transcription factors in mouse again implicated modulation of energy metabolism in the behavioral response. These results provide support for conserved genetic "toolkits" that are used in independent evolutions of the response to social challenge in diverse taxa.}, } @article {pmid25449705, year = {2015}, author = {Ren, C and Chen, T and Jiang, X and Luo, X and Wang, Y and Hu, C}, title = {The first echinoderm gamma-interferon-inducible lysosomal thiol reductase (GILT) identified from sea cucumber (Stichopus monotuberculatus).}, journal = {Fish & shellfish immunology}, volume = {42}, number = {1}, pages = {41-49}, doi = {10.1016/j.fsi.2014.10.024}, pmid = {25449705}, issn = {1095-9947}, mesh = {Animals ; Base Sequence ; Binding Sites/genetics ; Blotting, Western ; China ; Cloning, Molecular ; Cluster Analysis ; Computational Biology ; DNA Primers/genetics ; Gene Components/genetics ; Gene Expression Profiling ; Immunity, Innate/*genetics ; Molecular Sequence Data ; Oxidoreductases Acting on Sulfur Group Donors/*genetics/isolation & purification/*metabolism ; *Phylogeny ; Recombinant Proteins/metabolism ; Sequence Analysis, DNA ; Stichopus/*enzymology ; }, abstract = {Gamma-interferon-inducible lysosomal thiol reductase (GILT) has been described as a key enzyme that facilitating the processing and presentation of major histocompatibility complex class II-restricted antigen in mammals. In this study, the first echinoderm GILT named StmGILT was identified from sea cucumber (Stichopus monotuberculatus). The StmGILT cDNA is 1529 bp in length, containing a 5'-untranslated region (UTR) of 87 bp, a 3'-UTR of 674 bp and an open reading frame (ORF) of 768 bp that encoding a protein of 255 amino acids with a deduced molecular weight of 27.82 kDa and a predicted isoelectric point of 4.73. The putative StmGILT protein possesses all the main characteristics of known GILT proteins, including a signature sequence, a reductase active site CXXC, twelve conserved cysteines, and two potential N-linked glycosylation sites. For the gene structure, StmGILT contains four exons separated by three introns. In the promoter region of StmGILT gene, an NF-κB binding site and an IFN-γ activation site were found. The thiol reductase activity of recombinant StmGILT protein was also demonstrated in this study. In addition, the highest level of mRNA expression was noticed in coelomocytes of S. monotuberculatus. In in vitro experiments performed in coelomocytes, the expression of StmGILT mRNA was significantly up-regulated by lipopolysaccharides (LPS), inactivated bacteria or polyriboinosinic polyribocytidylic acid [poly (I:C)] challenge, suggested that the sea cucumber GILT might play critical roles in the innate immune defending against bacterial and viral infections.}, } @article {pmid25449372, year = {2015}, author = {Wei, X and Xu, J and Yang, J and Liu, X and Zhang, R and Wang, W and Yang, J}, title = {Involvement of a Serpin serine protease inhibitor (OoSerpin) from mollusc Octopus ocellatus in antibacterial response.}, journal = {Fish & shellfish immunology}, volume = {42}, number = {1}, pages = {79-87}, doi = {10.1016/j.fsi.2014.10.028}, pmid = {25449372}, issn = {1095-9947}, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Computational Biology ; DNA Primers/genetics ; DNA, Complementary/genetics ; Escherichia coli/drug effects/growth & development ; Gene Components ; Gene Expression Profiling ; Gene Expression Regulation/*immunology ; Listonella/*immunology ; Micrococcus luteus/*immunology ; Molecular Sequence Data ; Octopodiformes/*genetics/*immunology/microbiology ; Open Reading Frames/genetics ; Real-Time Polymerase Chain Reaction ; Sequence Analysis, DNA ; Serpins/*genetics/*immunology/pharmacology ; }, abstract = {Serpin is an important member of serine protease inhibitors (SPIs), which is capable of regulating proteolytic events and involving in a variety of physiological processes. In present study, a Serpin homolog was identified from Octopus ocellatus (designated as OoSerpin). Full-length cDNA of OoSerpin was of 1735 bp, containing a 5' untranslated region of 214 bp, a 3' UTR of 282 bp, and an open reading frame of 1239 bp. The open reading frame encoded a polypeptide of 412 amino acids which has a predicted molecular weight of 46.5 kDa and an isoelectric point of 8.52. The OoSerpin protein shares 37% sequence identity with other Serpins from Mus musculus (NP_941373) and Ixodes scapularis (XP_002407493). The existence of a conserved SERPIN domain strongly suggested that OoSerpin was a member of the Serpin subfamily. Expression patterns of OoSerpin, both in tissues and towards bacterial stimulation, were then characterized. The mRNA of OoSerpin was constitutively expressed at different levels in all tested tissues of untreated O. ocellatus, including mantle (lowest), muscle, renal sac, gill, hemocyte, gonad, systemic heart, and hepatopancreas (highest). The transcriptional level of OoSerpin was significantly up-regulated (P<0.01) in O. ocellatus upon bacterial challenges with Vibrio anguillarum and Micrococcus luteus, indicating its involvement in the antibacterial immune response. Furthermore, rOoSerpin, the recombinant protein of OoSerpin, exhibited strong abilities to inhibit proteinase activities of trypsin and chymotrypsin as well as the growth of Escherichia coli. Our results demonstrate that OoSerpin is a potential antibacterial factor involved in the immune response of O. ocellatus against bacterial infection.}, } @article {pmid25448819, year = {2015}, author = {van Gestel, J and Vlamakis, H and Kolter, R}, title = {New tools for comparing microscopy images: quantitative analysis of cell types in Bacillus subtilis.}, journal = {Journal of bacteriology}, volume = {197}, number = {4}, pages = {699-709}, pmid = {25448819}, issn = {1098-5530}, support = {R01 GM058213/GM/NIGMS NIH HHS/United States ; GM58213/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacillus subtilis/*chemistry/genetics/metabolism ; Bacterial Proteins/genetics/metabolism ; Data Mining/*methods ; Gene Expression Regulation, Bacterial ; Image Processing, Computer-Assisted ; Microscopy, Fluorescence ; }, abstract = {Fluorescence microscopy is a method commonly used to examine individual differences between bacterial cells, yet many studies still lack a quantitative analysis of fluorescence microscopy data. Here we introduce some simple tools that microbiologists can use to analyze and compare their microscopy images. We show how image data can be converted to distribution data. These data can be subjected to a cluster analysis that makes it possible to objectively compare microscopy images. The distribution data can further be analyzed using distribution fitting. We illustrate our methods by scrutinizing two independently acquired data sets, each containing microscopy images of a doubly labeled Bacillus subtilis strain. For the first data set, we examined the expression of srfA and tapA, two genes which are expressed in surfactin-producing and matrix-producing cells, respectively. For the second data set, we examined the expression of eps and tapA; these genes are expressed in matrix-producing cells. We show that srfA is expressed by all cells in the population, a finding which contrasts with a previously reported bimodal distribution of srfA expression. In addition, we show that eps and tapA do not always have the same expression profiles, despite being expressed in the same cell type: both operons are expressed in cell chains, while single cells mainly express eps. These findings exemplify that the quantification and comparison of microscopy data can yield insights that otherwise would go unnoticed.}, } @article {pmid25444397, year = {2014}, author = {Anema, A and Kluberg, S and Wilson, K and Hogg, RS and Khan, K and Hay, SI and Tatem, AJ and Brownstein, JS}, title = {Digital surveillance for enhanced detection and response to outbreaks.}, journal = {The Lancet. Infectious diseases}, volume = {14}, number = {11}, pages = {1035-1037}, pmid = {25444397}, issn = {1474-4457}, support = {095066/WT_/Wellcome Trust/United Kingdom ; R01LM010812/LM/NLM NIH HHS/United States ; R01 LM010812/LM/NLM NIH HHS/United States ; /CAPMC/CIHR/Canada ; U19 AI089674/AI/NIAID NIH HHS/United States ; U19AI089674/AI/NIAID NIH HHS/United States ; /WT_/Wellcome Trust/United Kingdom ; }, mesh = {Communicable Disease Control/*methods/*organization & administration ; Data Collection/*methods ; *Disease Outbreaks ; Electronic Data Processing/*methods ; *Epidemiological Monitoring ; Humans ; }, } @article {pmid25437925, year = {2014}, author = {Vallero, DA}, title = {Viewpoint: closing the exposure gap.}, journal = {Environmental science & technology}, volume = {48}, number = {24}, pages = {14075-14076}, doi = {10.1021/es505678p}, pmid = {25437925}, issn = {1520-5851}, mesh = {*Ecology ; *Environmental Exposure ; Humans ; Knowledge Bases ; *Risk Assessment ; }, } @article {pmid25436869, year = {2014}, author = {Zavodna, M and Bagshaw, A and Brauning, R and Gemmell, NJ}, title = {The accuracy, feasibility and challenges of sequencing short tandem repeats using next-generation sequencing platforms.}, journal = {PloS one}, volume = {9}, number = {12}, pages = {e113862}, pmid = {25436869}, issn = {1932-6203}, mesh = {DNA, Fungal/analysis ; Databases, Genetic ; Genetic Variation ; High-Throughput Nucleotide Sequencing/*instrumentation/methods ; *Microsatellite Repeats ; Saccharomyces cerevisiae/genetics ; Sequence Analysis, DNA/*instrumentation/methods ; }, abstract = {To date we have little knowledge of how accurate next-generation sequencing (NGS) technologies are in sequencing repetitive sequences beyond known limitations to accurately sequence homopolymers. Only a handful of previous reports have evaluated the potential of NGS for sequencing short tandem repeats (microsatellites) and no empirical study has compared and evaluated the performance of more than one NGS platform with the same dataset. Here we examined yeast microsatellite variants from both long-read (454-sequencing) and short-read (Illumina) NGS platforms and compared these to data derived through Sanger sequencing. In addition, we investigated any locus-specific biases and differences that might have resulted from variability in microsatellite repeat number, repeat motif or type of mutation. Out of 112 insertion/deletion variants identified among 45 microsatellite amplicons in our study, we found 87.5% agreement between the 454-platform and Sanger sequencing in frequency of variant detection after Benjamini-Hochberg correction for multiple tests. For a subset of 21 microsatellite amplicons derived from Illumina sequencing, the results of short-read platform were highly consistent with the other two platforms, with 100% agreement with 454-sequencing and 93.6% agreement with the Sanger method after Benjamini-Hochberg correction. We found that the microsatellite attributes copy number, repeat motif and type of mutation did not have a significant effect on differences seen between the sequencing platforms. We show that both long-read and short-read NGS platforms can be used to sequence short tandem repeats accurately, which makes it feasible to consider the use of these platforms in high-throughput genotyping. It appears the major requirement for achieving both high accuracy and rare variant detection in microsatellite genotyping is sufficient read depth coverage. This might be a challenge because each platform generates a consistent pattern of non-uniform sequence coverage, which, as our study suggests, may affect some types of tandem repeats more than others.}, } @article {pmid25431989, year = {2015}, author = {Luo, H}, title = {Evolutionary origin of a streamlined marine bacterioplankton lineage.}, journal = {The ISME journal}, volume = {9}, number = {6}, pages = {1423-1433}, pmid = {25431989}, issn = {1751-7370}, mesh = {Alphaproteobacteria/*genetics ; Base Composition ; Bayes Theorem ; Computational Biology ; *Evolution, Molecular ; Genome, Bacterial ; Likelihood Functions ; Phylogeny ; Plankton/*genetics ; Ribosomal Proteins/*chemistry ; Seawater/microbiology ; Water Microbiology ; }, abstract = {Planktonic bacterial lineages with streamlined genomes are prevalent in the ocean. The base composition of their DNA is often highly biased towards low G+C content, a possible source of systematic error in phylogenetic reconstruction. A total of 228 orthologous protein families were sampled that are shared among major lineages of Alphaproteobacteria, including the marine free-living SAR11 clade and the obligate endosymbiotic Rickettsiales. These two ecologically distinct lineages share genome sizes of <1.5 Mbp and genomic G+C content of <30%. Statistical analyses showed that only 28 protein families are composition-homogeneous, whereas the other 200 families significantly violate the composition-homogeneous assumption included in most phylogenetic methods. RAxML analysis based on the concatenation of 24 ribosomal proteins that fall into the heterogeneous protein category clustered the SAR11 and Rickettsiales lineages at the base of the Alphaproteobacteria tree, whereas that based on the concatenation of 28 homogeneous proteins (including 19 ribosomal proteins) disassociated the lineages and placed SAR11 at the base of the non-endosymbiotic lineages. When the two data sets were concatenated, only a model that accounted for compositional bias yielded a tree identical to the tree built with composition-homogeneous proteins. Ancestral genome analysis suggests that the first evolved SAR11 cell had a small genome streamlined from its ancestor by a factor of two and coinciding with an ecological transition, followed by further gradual streamlining towards the extant SAR11 populations.}, } @article {pmid25431190, year = {2014}, author = {Riddell, CE and Lobaton Garces, JD and Adams, S and Barribeau, SM and Twell, D and Mallon, EB}, title = {Differential gene expression and alternative splicing in insect immune specificity.}, journal = {BMC genomics}, volume = {15}, number = {1}, pages = {1031}, pmid = {25431190}, issn = {1471-2164}, support = {//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {*Alternative Splicing ; Animals ; Cluster Analysis ; Computational Biology ; Crithidia ; Gene Expression Profiling ; *Gene Expression Regulation ; Genotype ; Host-Parasite Interactions/genetics/immunology ; Immunity/*genetics ; Insecta/*genetics/*immunology/parasitology ; Serine Proteases/genetics ; Time Factors ; }, abstract = {BACKGROUND: Ecological studies routinely show genotype-genotype interactions between insects and their parasites. The mechanisms behind these interactions are not clearly understood. Using the bumblebee Bombus terrestris/trypanosome Crithidia bombi model system (two bumblebee colonies by two Crithidia strains), we have carried out a transcriptome-wide analysis of gene expression and alternative splicing in bees during C. bombi infection. We have performed four analyses, 1) comparing gene expression in infected and non-infected bees 24 hours after infection by Crithidia bombi, 2) comparing expression at 24 and 48 hours after C. bombi infection, 3) determining the differential gene expression associated with the bumblebee-Crithidia genotype-genotype interaction at 24 hours after infection and 4) determining the alternative splicing associated with the bumblebee-Crithidia genotype-genotype interaction at 24 hours post infection.

RESULTS: We found a large number of genes differentially regulated related to numerous canonical immune pathways. These genes include receptors, signaling pathways and effectors. We discovered a possible interaction between the peritrophic membrane and the insect immune system in defense against Crithidia. Most interestingly, we found differential expression and alternative splicing of immunoglobulin related genes (Dscam and Twitchin) are associated with the genotype-genotype interactions of the given bumblebee colony and Crithidia strain.

CONCLUSIONS: In this paper we have shown that the expression and alternative splicing of immune genes is associated with specific interactions between different host and parasite genotypes in this bumblebee/trypanosome model.}, } @article {pmid25428267, year = {2016}, author = {Kershenbaum, A and Blumstein, DT and Roch, MA and Akçay, Ç and Backus, G and Bee, MA and Bohn, K and Cao, Y and Carter, G and Cäsar, C and Coen, M and DeRuiter, SL and Doyle, L and Edelman, S and Ferrer-i-Cancho, R and Freeberg, TM and Garland, EC and Gustison, M and Harley, HE and Huetz, C and Hughes, M and Hyland Bruno, J and Ilany, A and Jin, DZ and Johnson, M and Ju, C and Karnowski, J and Lohr, B and Manser, MB and McCowan, B and Mercado, E and Narins, PM and Piel, A and Rice, M and Salmi, R and Sasahara, K and Sayigh, L and Shiu, Y and Taylor, C and Vallejo, EE and Waller, S and Zamora-Gutierrez, V}, title = {Acoustic sequences in non-human animals: a tutorial review and prospectus.}, journal = {Biological reviews of the Cambridge Philosophical Society}, volume = {91}, number = {1}, pages = {13-52}, pmid = {25428267}, issn = {1469-185X}, support = {R01 DC009582/DC/NIDCD NIH HHS/United States ; R25 GM064783/GM/NIGMS NIH HHS/United States ; R01DC009582/DC/NIDCD NIH HHS/United States ; }, mesh = {Acoustics ; Animals ; Markov Chains ; Models, Biological ; Perception ; *Vocalization, Animal ; }, abstract = {Animal acoustic communication often takes the form of complex sequences, made up of multiple distinct acoustic units. Apart from the well-known example of birdsong, other animals such as insects, amphibians, and mammals (including bats, rodents, primates, and cetaceans) also generate complex acoustic sequences. Occasionally, such as with birdsong, the adaptive role of these sequences seems clear (e.g. mate attraction and territorial defence). More often however, researchers have only begun to characterise - let alone understand - the significance and meaning of acoustic sequences. Hypotheses abound, but there is little agreement as to how sequences should be defined and analysed. Our review aims to outline suitable methods for testing these hypotheses, and to describe the major limitations to our current and near-future knowledge on questions of acoustic sequences. This review and prospectus is the result of a collaborative effort between 43 scientists from the fields of animal behaviour, ecology and evolution, signal processing, machine learning, quantitative linguistics, and information theory, who gathered for a 2013 workshop entitled, 'Analysing vocal sequences in animals'. Our goal is to present not just a review of the state of the art, but to propose a methodological framework that summarises what we suggest are the best practices for research in this field, across taxa and across disciplines. We also provide a tutorial-style introduction to some of the most promising algorithmic approaches for analysing sequences. We divide our review into three sections: identifying the distinct units of an acoustic sequence, describing the different ways that information can be contained within a sequence, and analysing the structure of that sequence. Each of these sections is further subdivided to address the key questions and approaches in that area. We propose a uniform, systematic, and comprehensive approach to studying sequences, with the goal of clarifying research terms used in different fields, and facilitating collaboration and comparative studies. Allowing greater interdisciplinary collaboration will facilitate the investigation of many important questions in the evolution of communication and sociality.}, } @article {pmid25424532, year = {2014}, author = {Chattopadhyay, B and Garg, KM and Ramakrishnan, U}, title = {Effect of diversity and missing data on genetic assignment with RAD-Seq markers.}, journal = {BMC research notes}, volume = {7}, number = {}, pages = {841}, pmid = {25424532}, issn = {1756-0500}, mesh = {Algorithms ; Animals ; Chiroptera/classification/*genetics ; Data Mining ; *Gene Flow ; *Gene Library ; Genetic Loci ; Genetic Markers ; Genetics, Population ; Phylogeny ; *Polymorphism, Single Nucleotide ; *Software ; }, abstract = {Reduced representation libraries are being used as a preferred source of markers to address population genetic questions. However, libraries of RAD-Seq variants often suffer from significant percentage of missing data. In addition, algorithms used to mine SNPs from the raw data may also underscore biological variation. We investigate the effect of biological diversity in mining SNPs from the program STACKS and the effect of missing data on individual assignment implemented in STRUCTURE. We observed that changing diversity parameters in STACKS significantly alters the number of SNPs discovered and allowing for higher percentage of missing data retrieves more loci and possibly more power for individual assignment.}, } @article {pmid25424327, year = {2014}, author = {Yu, W and Bain, RE and Mansour, S and Wright, JA}, title = {A cross-sectional ecological study of spatial scale and geographic inequality in access to drinking-water and sanitation.}, journal = {International journal for equity in health}, volume = {13}, number = {}, pages = {113}, pmid = {25424327}, issn = {1475-9276}, mesh = {Cross-Sectional Studies ; Developing Countries ; Drinking Water/*standards ; Geographic Information Systems ; Geographic Mapping ; Humans ; Sanitation/*standards ; Socioeconomic Factors ; Water Supply/*standards ; }, abstract = {INTRODUCTION: Measuring inequality in access to safe drinking-water and sanitation is proposed as a component of international monitoring following the expiry of the Millennium Development Goals. This study aims to evaluate the utility of census data in measuring geographic inequality in access to drinking-water and sanitation.

METHODS: Spatially referenced census data were acquired for Colombia, South Africa, Egypt, and Uganda, whilst non-spatially referenced census data were acquired for Kenya. Four variants of the dissimilarity index were used to estimate geographic inequality in access to both services using large and small area units in each country through a cross-sectional, ecological study.

RESULTS: Inequality was greatest for piped water in South Africa in 2001 (based on 53 areas (N) with a median population (MP) of 657,015; D = 0.5599) and lowest for access to an improved water source in Uganda in 2008 (N = 56; MP = 419,399; D = 0.2801). For sanitation, inequality was greatest for those lacking any facility in Kenya in 2009 (N = 158; MP = 216,992; D = 0.6981), and lowest for access to an improved facility in Uganda in 2002 (N = 56; MP = 341,954; D = 0.3403). Although dissimilarity index values were greater for smaller areal units, when study countries were ranked in terms of inequality, these ranks remained unaffected by the choice of large or small areal units. International comparability was limited due to definitional and temporal differences between censuses.

CONCLUSIONS: This five-country study suggests that patterns of inequality for broad regional units do often reflect inequality in service access at a more local scale. This implies household surveys designed to estimate province-level service coverage can provide valuable insights into geographic inequality at lower levels. In comparison with household surveys, censuses facilitate inequality assessment at different spatial scales, but pose challenges in harmonising water and sanitation typologies across countries.}, } @article {pmid25423910, year = {2015}, author = {Rice, A and Glick, L and Abadi, S and Einhorn, M and Kopelman, NM and Salman-Minkov, A and Mayzel, J and Chay, O and Mayrose, I}, title = {The Chromosome Counts Database (CCDB) - a community resource of plant chromosome numbers.}, journal = {The New phytologist}, volume = {206}, number = {1}, pages = {19-26}, doi = {10.1111/nph.13191}, pmid = {25423910}, issn = {1469-8137}, mesh = {Chromosomes, Plant/*genetics ; *Databases, Genetic ; Plants/*genetics ; Polyploidy ; }, } @article {pmid25423027, year = {2015}, author = {Lallias, D and Hiddink, JG and Fonseca, VG and Gaspar, JM and Sung, W and Neill, SP and Barnes, N and Ferrero, T and Hall, N and Lambshead, PJ and Packer, M and Thomas, WK and Creer, S}, title = {Environmental metabarcoding reveals heterogeneous drivers of microbial eukaryote diversity in contrasting estuarine ecosystems.}, journal = {The ISME journal}, volume = {9}, number = {5}, pages = {1208-1221}, pmid = {25423027}, issn = {1751-7370}, mesh = {Animals ; *Biodiversity ; Computational Biology ; DNA Barcoding, Taxonomic ; *Ecosystem ; Environmental Monitoring ; *Estuaries ; *Eukaryota ; Geography ; Phenotype ; RNA, Ribosomal, 18S/genetics ; Salinity ; United Kingdom ; Water Microbiology ; }, abstract = {Assessing how natural environmental drivers affect biodiversity underpins our understanding of the relationships between complex biotic and ecological factors in natural ecosystems. Of all ecosystems, anthropogenically important estuaries represent a 'melting pot' of environmental stressors, typified by extreme salinity variations and associated biological complexity. Although existing models attempt to predict macroorganismal diversity over estuarine salinity gradients, attempts to model microbial biodiversity are limited for eukaryotes. Although diatoms commonly feature as bioindicator species, additional microbial eukaryotes represent a huge resource for assessing ecosystem health. Of these, meiofaunal communities may represent the optimal compromise between functional diversity that can be assessed using morphology and phenotype-environment interactions as compared with smaller life fractions. Here, using 454 Roche sequencing of the 18S nSSU barcode we investigate which of the local natural drivers are most strongly associated with microbial metazoan and sampled protist diversity across the full salinity gradient of the estuarine ecosystem. In order to investigate potential variation at the ecosystem scale, we compare two geographically proximate estuaries (Thames and Mersey, UK) with contrasting histories of anthropogenic stress. The data show that although community turnover is likely to be predictable, taxa are likely to respond to different environmental drivers and, in particular, hydrodynamics, salinity range and granulometry, according to varied life-history characteristics. At the ecosystem level, communities exhibited patterns of estuary-specific similarity within different salinity range habitats, highlighting the environmental sequencing biomonitoring potential of meiofauna, dispersal effects or both.}, } @article {pmid25419221, year = {2014}, author = {Wan, TT}, title = {A TRANSDISCIPLINARY APPROACH TO HEALTH POLICY RESEARCH AND EVALUATION.}, journal = {International journal of public policy}, volume = {10}, number = {4-5}, pages = {161-177}, pmid = {25419221}, issn = {1740-0600}, support = {U24 MD006954/MD/NIMHD NIH HHS/United States ; }, abstract = {An integrated perspective consists of macro- and micro-level approaches to health policy research and evaluation is presented. Analytical strategies are suggested for policy analysis, targeting on health disparities at individual and population levels. This systems approach enables investigators to view how scientific public policy analysis can be implemented to assess policy impacts. In this special issue, five papers are introduced.}, } @article {pmid25416325, year = {2014}, author = {da Costa, BR and Juni, P}, title = {Systematic reviews and meta-analyses of randomized trials: principles and pitfalls.}, journal = {European heart journal}, volume = {35}, number = {47}, pages = {3336-3345}, doi = {10.1093/eurheartj/ehu424}, pmid = {25416325}, issn = {1522-9645}, mesh = {Data Interpretation, Statistical ; *Meta-Analysis as Topic ; Publications/statistics & numerical data ; Random Allocation ; Randomized Controlled Trials as Topic/*methods/standards/statistics & numerical data ; Regression Analysis ; *Review Literature as Topic ; Statistics as Topic/methods ; }, abstract = {Systematic reviews and meta-analyses allow for a more transparent and objective appraisal of the evidence. They may decrease the number of false-negative results and prevent delays in the introduction of effective interventions into clinical practice. However, as for any other tool, their misuse can result in severely misleading results. In this article,we discuss the main steps that should be taken when conducting systematic reviews and meta-analyses, namely the preparation of a review protocol, identification of eligible trials, and data extraction, pooling of treatment effects across trials, investigation of potential reasons for differences in treatment effects across trials, and complete reporting of the review methods and findings.We also discuss common pitfalls that should be avoided, including the use of quality assessment tools to derive summary quality scores, pooling of data across trials as if they belonged to a single large trial, and inappropriate uses of meta-regression that could result in misleading estimates of treatment effects because of regression to the mean or the ecological fallacy. If conducted and reported properly, systematic reviews and meta-analyses will increase our understanding of the strengths and weaknesses of the available evidence, which may eventually facilitate clinical decision making.}, } @article {pmid25414355, year = {2015}, author = {Stoddard, SF and Smith, BJ and Hein, R and Roller, BR and Schmidt, TM}, title = {rrnDB: improved tools for interpreting rRNA gene abundance in bacteria and archaea and a new foundation for future development.}, journal = {Nucleic acids research}, volume = {43}, number = {Database issue}, pages = {D593-8}, pmid = {25414355}, issn = {1362-4962}, support = {R01 GM099549/GM/NIGMS NIH HHS/United States ; M0099549//PHS HHS/United States ; }, mesh = {Archaea/classification ; Bacteria/classification ; *Databases, Nucleic Acid ; Gene Dosage ; *Genes, Archaeal ; *Genes, Bacterial ; *Genes, rRNA ; Genome, Archaeal ; Genome, Bacterial ; Internet ; Operon ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Software ; }, abstract = {Microbiologists utilize ribosomal RNA genes as molecular markers of taxonomy in surveys of microbial communities. rRNA genes are often co-located as part of an rrn operon, and multiple copies of this operon are present in genomes across the microbial tree of life. rrn copy number variability provides valuable insight into microbial life history, but introduces systematic bias when measuring community composition in molecular surveys. Here we present an update to the ribosomal RNA operon copy number database (rrnDB), a publicly available, curated resource for copy number information for bacteria and archaea. The redesigned rrnDB (http://rrndb.umms.med.umich.edu/) brings a substantial increase in the number of genomes described, improved curation, mapping of genomes to both NCBI and RDP taxonomies, and refined tools for querying and analyzing these data. With these changes, the rrnDB is better positioned to remain a comprehensive resource under the torrent of microbial genome sequencing. The enhanced rrnDB will contribute to the analysis of molecular surveys and to research linking genomic characteristics to life history.}, } @article {pmid25412694, year = {2014}, author = {Blake, SB}, title = {Spatial relationships among dairy farms, drinking water quality, and maternal-child health outcomes in the San Joaquin Valley.}, journal = {Public health nursing (Boston, Mass.)}, volume = {31}, number = {6}, pages = {492-499}, doi = {10.1111/phn.12166}, pmid = {25412694}, issn = {1525-1446}, mesh = {Agriculture/*statistics & numerical data ; Animals ; California ; Cattle ; Drinking Water/*chemistry ; Female ; Geographic Information Systems ; Humans ; *Infant, Low Birth Weight ; Infant, Newborn ; Nitrates/*analysis ; Pregnancy ; Socioeconomic Factors ; *Spatial Analysis ; *Water Quality ; }, abstract = {OBJECTIVE: Access to clean and affordable water is a significant public health issue globally, in the United States, and in California where land is heavily used for agriculture and dairy operations. The purpose of this study was to explore the geographic relationships among dairy farms, nitrate levels in drinking water, low birth weight, and socioeconomic data at the ZIP code level in the San Joaquin Valley.

DESIGN AND SAMPLE: This ecological study used a Geographic Information System (GIS) to explore and analyze secondary data.

MEASURES: A total of 211 ZIP codes were analyzed using spatial autocorrelation and regression analysis methods in ArcGIS version 10.1.

RESULTS: ZIP codes with dairies had a higher percentage of Hispanic births (p = .001). Spatial statistics revealed that ZIP codes with more dairy farms and a higher dairy cow density had higher levels of nitrate contamination. No correlation was detected between LBW and unsafe nitrate levels at the ZIP code level.

CONCLUSION: Further research examining communities that use private and small community wells in the San Joaquin Valley should be conducted. Birth data from smaller geographic areas should be used to continue exploring the relationship between birth outcomes and nitrate contamination in drinking water.}, } @article {pmid25411370, year = {2014}, author = {Bik, HM}, title = {Deciphering diversity and ecological function from marine metagenomes.}, journal = {The Biological bulletin}, volume = {227}, number = {2}, pages = {107-116}, doi = {10.1086/BBLv227n2p107}, pmid = {25411370}, issn = {1939-8697}, mesh = {Aquatic Organisms/*genetics ; *Biodiversity ; Computational Biology/trends ; Ecosystem ; Metagenome/*genetics ; Petroleum Pollution ; Research/trends ; Viruses/genetics ; }, abstract = {Metagenomic sequencing now represents a common, powerful approach for investigating diversity and functional relationships in marine ecosystems. High-throughput datasets generated from random fragments of environmental DNA can provide a less biased view of organismal abundance (versus PCR-based amplicon sequencing) and enable novel exploration of microbial genomes by recovering genome assemblies from uncultured species, identifying ecological functions, and reconstructing metabolic pathways. This review highlights the current state of knowledge in marine metagenomics, focusing on biological insights gained from recent environmental studies and detailing commonly employed methods for data collection and analysis.}, } @article {pmid25405872, year = {2014}, author = {Samia, DS and Blumstein, DT}, title = {Phi index: a new metric to test the flush early and avoid the rush hypothesis.}, journal = {PloS one}, volume = {9}, number = {11}, pages = {e113134}, pmid = {25405872}, issn = {1932-6203}, mesh = {Animals ; Birds/*physiology ; Computer Simulation ; *Data Interpretation, Statistical ; Escape Reaction/*physiology ; Flight, Animal/physiology ; *Models, Biological ; Time Factors ; }, abstract = {Optimal escape theory states that animals should counterbalance the costs and benefits of flight when escaping from a potential predator. However, in apparent contradiction with this well-established optimality model, birds and mammals generally initiate escape soon after beginning to monitor an approaching threat, a phenomena codified as the "Flush Early and Avoid the Rush" (FEAR) hypothesis. Typically, the FEAR hypothesis is tested using correlational statistics and is supported when there is a strong relationship between the distance at which an individual first responds behaviorally to an approaching predator (alert distance, AD), and its flight initiation distance (the distance at which it flees the approaching predator, FID). However, such correlational statistics are both inadequate to analyze relationships constrained by an envelope (such as that in the AD-FID relationship) and are sensitive to outliers with high leverage, which can lead one to erroneous conclusions. To overcome these statistical concerns we develop the phi index (Φ), a distribution-free metric to evaluate the goodness of fit of a 1:1 relationship in a constraint envelope (the prediction of the FEAR hypothesis). Using both simulation and empirical data, we conclude that Φ is superior to traditional correlational analyses because it explicitly tests the FEAR prediction, is robust to outliers, and it controls for the disproportionate influence of observations from large predictor values (caused by the constrained envelope in AD-FID relationship). Importantly, by analyzing the empirical data we corroborate the strong effect that alertness has on flight as stated by the FEAR hypothesis.}, } @article {pmid25405758, year = {2014}, author = {Xu, E and Fan, G and Niu, S and Zhao, Z and Deng, M and Dong, Y}, title = {Transcriptome-wide profiling and expression analysis of diploid and autotetraploid Paulownia tomentosa × Paulownia fortunei under drought stress.}, journal = {PloS one}, volume = {9}, number = {11}, pages = {e113313}, pmid = {25405758}, issn = {1932-6203}, mesh = {Adaptation, Physiological/genetics ; Crosses, Genetic ; *Diploidy ; *Droughts ; Gene Expression Profiling/*methods ; *Gene Expression Regulation, Plant ; Gene Ontology ; Gene Regulatory Networks/genetics ; Magnoliopsida/*genetics ; Plant Leaves/genetics ; Reverse Transcriptase Polymerase Chain Reaction ; Seedlings/genetics ; Signal Transduction/genetics ; Stress, Physiological/genetics ; *Tetraploidy ; }, abstract = {Paulownia is a fast-growing deciduous hardwood species native to China, which has high ecological and economic value. In an earlier study, we reported ploidy-dependent differences in Paulownia drought tolerance by the microscopic observations of the leaves. Autotetraploid Paulownia has a higher resistance to drought stress than their diploid relatives. In order to obtain genetic information on molecular mechanisms responses of Paulownia plants to drought, Illumina/Solexa Genome sequencing platform was used to de novo assemble the transcriptomes of leaves from diploid and autotetraploid Paulownia tomentosa × Paulownia fortunei seedlings (PTF2 and PTF4 respectively) grown under control conditions and under drought stress and obtained 98,671 nonredundant unigenes. A comparative transcriptome analysis revealed that hundreds of unigenes were predicted to be involved mainly in ROS-scavenging system, amino acid and carbohydrate metabolism, plant hormone biosynthesis and signal transduction, while these unigenes exhibited differential transcript alteration of the two accessions. This study provides a comprehensive map of how P. tomentosa × P. fortunei responds to drought stress at physiological and molecular levels, which may help in understanding the mechanisms involve in water-deficit response and will be useful for further study of drought tolerance in woody plants.}, } @article {pmid25401184, year = {2014}, author = {Smith, KF and Goldberg, M and Rosenthal, S and Carlson, L and Chen, J and Chen, C and Ramachandran, S}, title = {Global rise in human infectious disease outbreaks.}, journal = {Journal of the Royal Society, Interface}, volume = {11}, number = {101}, pages = {20140950}, pmid = {25401184}, issn = {1742-5662}, mesh = {Communicable Diseases/*epidemiology/*transmission ; *Databases, Factual ; *Disease Outbreaks ; Female ; Humans ; Male ; *Models, Biological ; Retrospective Studies ; }, abstract = {To characterize the change in frequency of infectious disease outbreaks over time worldwide, we encoded and analysed a novel 33-year dataset (1980-2013) of 12,102 outbreaks of 215 human infectious diseases, comprising more than 44 million cases occuring in 219 nations. We merged these records with ecological characteristics of the causal pathogens to examine global temporal trends in the total number of outbreaks, disease richness (number of unique diseases), disease diversity (richness and outbreak evenness) and per capita cases. Bacteria, viruses, zoonotic diseases (originating in animals) and those caused by pathogens transmitted by vector hosts were responsible for the majority of outbreaks in our dataset. After controlling for disease surveillance, communications, geography and host availability, we find the total number and diversity of outbreaks, and richness of causal diseases increased significantly since 1980 (p < 0.0001). When we incorporate Internet usage into the model to control for biased reporting of outbreaks (starting 1990), the overall number of outbreaks and disease richness still increase significantly with time (p < 0.0001), but per capita cases decrease significantly (p = 0.005). Temporal trends in outbreaks differ based on the causal pathogen's taxonomy, host requirements and transmission mode. We discuss our preliminary findings in the context of global disease emergence and surveillance.}, } @article {pmid25398865, year = {2015}, author = {Gibbons, SM and Schwartz, T and Fouquier, J and Mitchell, M and Sangwan, N and Gilbert, JA and Kelley, ST}, title = {Ecological succession and viability of human-associated microbiota on restroom surfaces.}, journal = {Applied and environmental microbiology}, volume = {81}, number = {2}, pages = {765-773}, pmid = {25398865}, issn = {1098-5336}, support = {T32 EB009412/EB/NIBIB NIH HHS/United States ; 5T-32EB-009412/EB/NIBIB NIH HHS/United States ; }, mesh = {Bacteria/*classification/*isolation & purification ; *Biota ; *Environmental Microbiology ; Humans ; Microbial Viability ; Viruses/*classification/*isolation & purification ; }, abstract = {Human-associated bacteria dominate the built environment (BE). Following decontamination of floors, toilet seats, and soap dispensers in four public restrooms, in situ bacterial communities were characterized hourly, daily, and weekly to determine their successional ecology. The viability of cultivable bacteria, following the removal of dispersal agents (humans), was also assessed hourly. A late-successional community developed within 5 to 8 h on restroom floors and showed remarkable stability over weeks to months. Despite late-successional dominance by skin- and outdoor-associated bacteria, the most ubiquitous organisms were predominantly gut-associated taxa, which persisted following exclusion of humans. Staphylococcus represented the majority of the cultivable community, even after several hours of human exclusion. Methicillin-resistant Staphylococcus aureus (MRSA)-associated virulence genes were found on floors but were not present in assembled Staphylococcus pan-genomes. Viral abundances, which were predominantly enterophages, human papilloma virus, and herpesviruses, were significantly correlated with bacterial abundances and showed an unexpectedly low virus-to-bacterium ratio in surface-associated samples, suggesting that bacterial hosts are mostly dormant on BE surfaces.}, } @article {pmid25398000, year = {2015}, author = {Tosa, MI and Schauber, EM and Nielsen, CK}, title = {Familiarity breeds contempt: combining proximity loggers and GPS reveals female white-tailed deer (Odocoileus virginianus) avoiding close contact with neighbors.}, journal = {Journal of wildlife diseases}, volume = {51}, number = {1}, pages = {79-88}, doi = {10.7589/2013-06-139}, pmid = {25398000}, issn = {1943-3700}, mesh = {*Animal Identification Systems ; Animals ; Behavior, Animal/*physiology ; Deer/*physiology ; Female ; *Geographic Information Systems ; *Spatial Behavior ; }, abstract = {Social interactions can influence infectious disease dynamics, particularly for directly transmitted pathogens. Therefore, reliable information on contact frequency within and among groups can better inform disease modeling and management. We compared three methods of assessing contact patterns: (1) space-use overlap (volume of interaction [VI]), (2) direct contact rates measured by simultaneous global positioning system (GPS) locations (<10 m apart), and (3) direct contact rates measured by proximity loggers (PLs; 1-m detection) among female white-tailed deer (Odocoileus virginianus). We calculated the PL∶GPS contact ratios to see whether both devices reveal similar contact patterns and thus predict similar pathogen transmission patterns. Contact rates measured by GPS and PLs were similarly high for two within-group dyads (pairs of deer in the same social groups). Dyads representing separate but neighboring groups (high VI) had PL∶GPS contact ratios near zero, whereas dyads further apart (intermediate VI) had higher PL∶GPS contact ratios. Social networks based on PL contacts showed the fewest connected individuals and lowest mean centrality measures; network metrics were intermediate when based on GPS contacts and greatest when based on VI. Thus, the VI network portrayed animals to be more uniformly and strongly connected than did the PL network. We conclude that simultaneous GPS locations, compared with PLs, substantially underestimate the impact of group membership on direct contact rates of female deer and make networks appear more connected. We also present evidence that deer coming within the general vicinity of each other are less likely to come in close contact if they are in neighboring social groups than deer whose home ranges overlap little if at all. Combined, these results provide evidence that direct transmission of disease agents among female and juvenile white-tailed deer is likely to be constrained both spatially and by social structure, more so than GPS data alone would suggest.}, } @article {pmid25395322, year = {2015}, author = {Hasani Sangani, M and Jabbarian Amiri, B and Alizadeh Shabani, A and Sakieh, Y and Ashrafi, S}, title = {Modeling relationships between catchment attributes and river water quality in southern catchments of the Caspian Sea.}, journal = {Environmental science and pollution research international}, volume = {22}, number = {7}, pages = {4985-5002}, pmid = {25395322}, issn = {1614-7499}, mesh = {Agriculture ; Environmental Monitoring/*methods ; Geographic Information Systems ; Humans ; Hydrology ; *Models, Theoretical ; Oceans and Seas ; *Rivers ; Soil ; *Water Movements ; *Water Quality ; }, abstract = {Increasing land utilization through diverse forms of human activities, such as agriculture, forestry, urban growth, and industrial development, has led to negative impacts on the water quality of rivers. To find out how catchment attributes, such as land use, hydrologic soil groups, and lithology, can affect water quality variables (Ca(2+), Mg(2+), Na(+), Cl(-), HCO 3 (-) , pH, TDS, EC, SAR), a spatio-statistical approach was applied to 23 catchments in southern basins of the Caspian Sea. All input data layers (digital maps of land use, soil, and lithology) were prepared using geographic information system (GIS) and spatial analysis. Relationships between water quality variables and catchment attributes were then examined by Spearman rank correlation tests and multiple linear regression. Stepwise approach-based multiple linear regressions were developed to examine the relationship between catchment attributes and water quality variables. The areas (%) of marl, tuff, or diorite, as well as those of good-quality rangeland and bare land had negative effects on all water quality variables, while those of basalt, forest land cover were found to contribute to improved river water quality. Moreover, lithological variables showed the greatest most potential for predicting the mean concentration values of water quality variables, and noting that measure of EC and TDS have inversely associated with area (%) of urban land use.}, } @article {pmid25393020, year = {2014}, author = {Huang, X and Shi, X and Kotov, AA and Gu, F}, title = {Confirmation through genetic analysis of the existence of many local phyloclades of the genus Simocephalus (Crustacea, Cladocera) in China.}, journal = {PloS one}, volume = {9}, number = {11}, pages = {e112808}, pmid = {25393020}, issn = {1932-6203}, mesh = {Animals ; Arthropod Proteins/*genetics ; China ; Cladocera/*classification/*genetics ; Databases, Nucleic Acid ; Electron Transport Complex IV/*genetics ; Female ; Male ; *Phylogeny ; }, abstract = {Previously, a series of Simocephalus taxa (Cladocera: Daphniidae) from China were described. Most were proposed to be junior synonyms in the last revision of the genus. Using original material from China and data from GenBank, we investigate the biodiversity and phylogeny of Simocephalus using sequences of the cytochrome c oxidase subunit I (COI) and the nuclear 18S genes. In both cases, neighbor-joining, maximum likelihood and Bayesian inference analyses led to highly congruent tree topologies. The grouping of the deeper clades agrees with the inter-generic classification of Orlova-Bienkowskaja (2001). Only the populations of S. serrulatus from Eurasia and North America seem to be closely related, and there are no other shared species between the two continents. Our study unambiguously confirms the existence of many lineages from the subgenera of Simocephalus (Echinocaudus) and Simocephalus s.str. in China, but their morphology needs to be reexamined by taking a wider range of characters (e.g., of female thoracic limbs and adult males) into consideration.}, } @article {pmid25392343, year = {2015}, author = {Xu, G and Zhang, J}, title = {In search of beneficial coding RNA editing.}, journal = {Molecular biology and evolution}, volume = {32}, number = {2}, pages = {536-541}, pmid = {25392343}, issn = {1537-1719}, support = {R01 GM103232/GM/NIGMS NIH HHS/United States ; R01GM103232/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Computational Biology/*methods ; Genome, Human/genetics ; Humans ; RNA/*genetics ; RNA Editing/*genetics ; }, abstract = {RNA editing is a posttranscriptional modification that can lead to a change in the encoded protein sequence of a gene. Although a few cases of mammalian coding RNA editing are known to be functionally important, the vast majority of over 2,000 A-to-I editing sites that have been identified from the coding regions of the human genome are likely nonadaptive, representing tolerable promiscuous targeting of editing enzymes. Finding the potentially tiny fraction of beneficial editing sites from the sea of mostly nearly neutral editing is a difficult but important task. Here, we propose and provide evidence that evolutionarily conserved or "hardwired" residues that experience high-level nonsynonymous RNA editing in a species are enriched with beneficial editing. This simple approach allows the prediction of sites where RNA editing is functionally important. We suggest that priority be given to these candidates in future characterizations of the functional and fitness consequences of RNA editing.}, } @article {pmid25390067, year = {2014}, author = {Odden, M and Athreya, V and Rattan, S and Linnell, JD}, title = {Adaptable neighbours: movement patterns of GPS-collared leopards in human dominated landscapes in India.}, journal = {PloS one}, volume = {9}, number = {11}, pages = {e112044}, pmid = {25390067}, issn = {1932-6203}, mesh = {Animals ; Animals, Wild ; Conservation of Natural Resources ; Female ; *Geographic Information Systems ; Geography ; Homing Behavior ; India ; Male ; Models, Statistical ; *Motor Activity ; Panthera/*physiology ; Population Dynamics ; }, abstract = {Understanding the nature of the interactions between humans and wildlife is of vital importance for conflict mitigation. We equipped five leopards with GPS-collars in Maharashtra (4) and Himachal Pradesh (1), India, to study movement patterns in human-dominated landscapes outside protected areas. An adult male and an adult female were both translocated 52 km, and exhibited extensive, and directional, post release movements (straight line movements: male = 89 km in 37 days, female = 45 km in 5 months), until they settled in home ranges of 42 km2 (male) and 65 km2 (female). The three other leopards, two adult females and a young male were released close to their capture sites and used small home ranges of 8 km2 (male), 11 km2 and 15 km2 (females). Movement patterns were markedly nocturnal, with hourly step lengths averaging 339±9.5 m (SE) during night and 60±4.1 m during day, and night locations were significantly closer to human settlements than day locations. However, more nocturnal movements were observed among those three living in the areas with high human population densities. These visited houses regularly at nighttime (20% of locations <25 m from houses), but rarely during day (<1%). One leopard living in a sparsely populated area avoided human settlements both day and night. The small home ranges of the leopards indicate that anthropogenic food resources may be plentiful although wild prey is absent. The study provides clear insights into the ability of leopards to live and move in landscapes that are extremely modified by human activity.}, } @article {pmid25389644, year = {2015}, author = {Zhang, Y and Sun, J and Mu, H and Li, J and Zhang, Y and Xu, F and Xiang, Z and Qian, PY and Qiu, JW and Yu, Z}, title = {Proteomic basis of stress responses in the gills of the pacific oyster Crassostrea gigas.}, journal = {Journal of proteome research}, volume = {14}, number = {1}, pages = {304-317}, doi = {10.1021/pr500940s}, pmid = {25389644}, issn = {1535-3907}, mesh = {Animals ; Blotting, Western ; China ; Chromatography, Liquid ; Computational Biology ; Crassostrea/genetics/*metabolism ; Gene Expression Regulation/genetics/*physiology ; Gills/*metabolism ; Proteome/*genetics ; Proteomics/methods ; Stress, Physiological/genetics/*physiology ; Tandem Mass Spectrometry ; }, abstract = {The Pacific oyster Crassostrea gigas is one of the dominant sessile inhabitants of the estuarine intertidal zone, which is a physically harsh environment due to the presence of a number of stressors. Oysters have adapted to highly dynamic and stressful environments, but the molecular mechanisms underlying such stress adaptation are largely unknown. In the present study, we examined the proteomic responses in the gills of C. gigas exposed to three stressors (high temperature, low salinity, and aerial exposure) they often encounter in the field. We quantitatively compared the gill proteome profiles using iTRAQ-coupled 2-D LC-MS/MS. There were 3165 identified proteins among which 2379 proteins could be quantified. Heat shock, hyposalinity, and aerial exposure resulted in 50, 15, and 33 differentially expressed gill proteins, respectively. Venn diagram analysis revealed substantial different responses to the three stressors. Only xanthine dehydrogenase/oxidase showed a similar expression pattern across the three stress treatments, suggesting that reduction of ROS accumulation may be a conserved response to these stressors. Heat shock caused significant overexpression of molecular chaperones and production of S-adenosyl-l-methionine, indicating their crucial protective roles against protein denature. In addition, heat shock also activated immune responses, Ca(2+) binding protein expression. By contrast, hyposalinity and aerial exposure resulted in the up-regulation of 3-demethylubiquinone-9 3-methyltransferase, indicating that increase in ubiquinone synthesis may contribute to withstanding both the osmotic and desiccation stress. Strikingly, the majority of desiccation-responsive proteins, including those involved in metabolism, ion transportation, immune responses, DNA duplication, and protein synthesis, were down-regulated, indicating conservation of energy as an important strategy to cope with desiccation stress. There was a high consistency between the expression levels determined by iTRAQ and Western blotting, highlighting the high reproducibility of our proteomic approach and its great value in revealing molecular mechanisms of stress responses.}, } @article {pmid25388775, year = {2015}, author = {Ringler, E and Mangione, R and Ringler, M}, title = {Where have all the tadpoles gone? Individual genetic tracking of amphibian larvae until adulthood.}, journal = {Molecular ecology resources}, volume = {15}, number = {4}, pages = {737-746}, pmid = {25388775}, issn = {1755-0998}, support = {P 24788/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Animals ; Anura/*growth & development ; Computational Biology/*methods ; DNA Fingerprinting/methods ; French Guiana ; Genotyping Techniques/*methods ; *Life Cycle Stages ; *Microsatellite Repeats ; }, abstract = {Reliably marking larvae and reidentifying them after metamorphosis is a challenge that has hampered studies on recruitment, dispersal, migration and survivorship of amphibians for a long time, as conventional tags are not reliably retained through metamorphosis. Molecular methods allow unique genetic fingerprints to be established for individuals. Although microsatellite markers have successfully been applied in mark-recapture studies on several animal species, they have never been previously used in amphibians to follow individuals across different life cycle stages. Here, we evaluate microsatellites for genetic across-stages mark-recapture studies in amphibians and test the suitability of available software packages for genotype matching. We sampled tadpoles of the dendrobatid frog Allobates femoralis, which we introduced on a river island in the Nature Reserve 'Les Nouragues' in French Guiana. In two subsequent recapture sessions, we searched for surviving juveniles and adults, respectively. All individuals were genotyped at 14 highly variable microsatellite loci, which yielded unique genetic fingerprints for all individuals. We found large differences in the identification success of the programs tested. The pairwise-relatedness-based approach, conducted with the programs kingroup or ML-Relate, performed best with our data set. Matching ventral patterns of juveniles and adult individuals acted as a control for the reliability of the genetic identification. Our results demonstrate that microsatellite markers are a highly powerful tool for studying amphibian populations on an individual basis. The ability to individually track amphibian tadpoles throughout metamorphosis until adulthood will be of substantial value for future studies on amphibian population ecology and evolution.}, } @article {pmid25387610, year = {2015}, author = {Law, J and Roulstone, S and Lindsay, G}, title = {Integrating external evidence of intervention effectiveness with both practice and the parent perspective: development of 'What Works' for speech, language, and communication needs.}, journal = {Developmental medicine and child neurology}, volume = {57}, number = {3}, pages = {223-228}, doi = {10.1111/dmcn.12630}, pmid = {25387610}, issn = {1469-8749}, mesh = {Child ; *Databases, Factual/statistics & numerical data ; Evidence-Based Practice/*standards/statistics & numerical data ; Humans ; Language Disorders/*therapy ; Language Therapy/methods/*standards/statistics & numerical data ; *Parents ; *Treatment Outcome ; }, abstract = {AIM: The aim of the study was to develop an ecologically valid synthesis of the evidence underpinning interventions for children with speech, language, and communication needs (SLCN), integrating a range of different data sources.

METHOD: Three sources of information were integrated: the Cochrane Review of interventions for children with primary speech and language delays/disorder; current practice from an online survey of 534 speech and language therapists and other professionals working with children with SLCN; and parent reports of preferred outcomes. Evidence was ranked as strong, moderate, or indicative.

RESULTS: Of the 58 interventions identified, three (5%) were found to have a strong level of evidence, 32 (56%) had moderate evidence, and 23 (39%) had indicative evidence. Five were universal interventions, the remainder targeted and universal. The integrated findings were then turned into an online interactive database, which is moderated and updated at regular intervals.

INTERPRETATION: There are a number of interventions that have a moderate or strong level of evidence underpinning them but they tend not to be those used by practitioners who often favour well-established familiar programmes even if they have only indicative evidence. There is a degree of complementarity between professional and parent views about outcomes, albeit with different emphases.}, } @article {pmid25386926, year = {2014}, author = {Brotons, L}, title = {Species distribution models and impact factor growth in environmental journals: methodological fashion or the attraction of global change science.}, journal = {PloS one}, volume = {9}, number = {11}, pages = {e111996}, pmid = {25386926}, issn = {1932-6203}, mesh = {Bibliometrics ; *Climate Change ; Databases, Bibliographic ; *Ecology ; *Environment ; Journal Impact Factor ; *Periodicals as Topic ; *Research ; }, abstract = {In this work, I evaluate the impact of species distribution models (SDMs) on the current status of environmental and ecological journals by asking the question to which degree development of SDMs in the literature is related to recent changes in the impact factors of ecological journals. The hypothesis evaluated states that research fronts are likely to attract research attention and potentially drive citation patterns, with journals concentrating papers related to the research front receiving more attention and benefiting from faster increases in their impact on the ecological literature. My results indicate a positive relationship between the number of SDM related articles published in a journal and its impact factor (IF) growth during the period 2000-09. However, the percentage of SDM related papers in a journal was strongly and positively associated with the percentage of papers on climate change and statistical issues. The results support the hypothesis that global change science has been critical in the development of SDMs and that interest in climate change research in particular, rather than the usage of SDM per se, appears as an important factor behind journal IF increases in ecology and environmental sciences. Finally, our results on SDM application in global change science support the view that scientific interest rather than methodological fashion appears to be the major driver of research attraction in the scientific literature.}, } @article {pmid25386654, year = {2014}, author = {Sun, Z and Meng, H and Li, J and Wang, J and Li, Q and Wang, Y and Zhang, Y}, title = {Identification of novel knockout targets for improving terpenoids biosynthesis in Saccharomyces cerevisiae.}, journal = {PloS one}, volume = {9}, number = {11}, pages = {e112615}, pmid = {25386654}, issn = {1932-6203}, mesh = {Computational Biology ; Gene Deletion ; Gene Knockout Techniques ; Genetic Engineering ; Organisms, Genetically Modified/*metabolism ; Polycyclic Sesquiterpenes ; Saccharomyces cerevisiae/*genetics/metabolism ; Sesquiterpenes/*metabolism ; Terpenes/*metabolism ; }, abstract = {Many terpenoids have important pharmacological activity and commercial value; however, application of these terpenoids is often limited by problems associated with the production of sufficient amounts of these molecules. The use of Saccharomyces cerevisiae (S. cerevisiae) for the production of heterologous terpenoids has achieved some success. The objective of this study was to identify S. cerevisiae knockout targets for improving the synthesis of heterologous terpeniods. On the basis of computational analysis of the S. cerevisiae metabolic network, we identified the knockout sites with the potential to promote terpenoid production and the corresponding single mutant was constructed by molecular manipulations. The growth rates of these strains were measured and the results indicated that the gene deletion had no adverse effects. Using the expression of amorphadiene biosynthesis as a testing model, the gene deletion was assessed for its effect on the production of exogenous terpenoids. The results showed that the dysfunction of most genes led to increased production of amorphadiene. The yield of amorphadiene produced by most single mutants was 8-10-fold greater compared to the wild type, indicating that the knockout sites can be engineered to promote the synthesis of exogenous terpenoids.}, } @article {pmid25384371, year = {2015}, author = {May, JT and Brown, LR and Rehn, AC and Waite, IR and Ode, PR and Mazor, RD and Schiff, KC}, title = {Correspondence of biological condition models of California streams at statewide and regional scales.}, journal = {Environmental monitoring and assessment}, volume = {187}, number = {1}, pages = {4086}, pmid = {25384371}, issn = {1573-2959}, mesh = {*Biodiversity ; California ; Climate ; Decision Trees ; *Ecosystem ; Environmental Monitoring/*methods ; Geographic Information Systems ; *Models, Biological ; Rivers/*chemistry ; Urbanization ; }, abstract = {We used boosted regression trees (BRT) to model stream biological condition as measured by benthic macroinvertebrate taxonomic completeness, the ratio of observed to expected (O/E) taxa. Models were developed with and without exclusion of rare taxa at a site. BRT models are robust, requiring few assumptions compared with traditional modeling techniques such as multiple linear regression. The BRT models were constructed to provide baseline support to stressor delineation by identifying natural physiographic and human land use gradients affecting stream biological condition statewide and for eight ecological regions within the state, as part of the development of numerical biological objectives for California's wadeable streams. Regions were defined on the basis of ecological, hydrologic, and jurisdictional factors and roughly corresponded with ecoregions. Physiographic and land use variables were derived from geographic information system coverages. The model for the entire state (n = 1,386) identified a composite measure of anthropogenic disturbance (the sum of urban, agricultural, and unmanaged roadside vegetation land cover) within the local watershed as the most important variable, explaining 56% of the variance in O/E values. Models for individual regions explained between 51 and 84% of the variance in O/E values. Measures of human disturbance were important in the three coastal regions. In the South Coast and Coastal Chaparral, local watershed measures of urbanization were the most important variables related to biological condition, while in the North Coast the composite measure of human disturbance at the watershed scale was most important. In the two mountain regions, natural gradients were most important, including slope, precipitation, and temperature. The remaining three regions had relatively small sample sizes (n ≤ 75 sites) and had models that gave mixed results. Understanding the spatial scale at which land use and land cover affect taxonomic completeness is imperative for sound management. Our results suggest that invertebrate taxonomic completeness is affected by human disturbance at the statewide and regional levels, with some differences among regions in the importance of natural gradients and types of human disturbance. The construction and application of models similar to the ones presented here could be useful in the planning and prioritization of actions for protection and conservation of biodiversity in California streams.}, } @article {pmid25383874, year = {2014}, author = {Blonder, B and Sloat, L and Enquist, BJ and McGill, B}, title = {Separating macroecological pattern and process: comparing ecological, economic, and geological systems.}, journal = {PloS one}, volume = {9}, number = {11}, pages = {e112850}, pmid = {25383874}, issn = {1932-6203}, mesh = {*Biodiversity ; Databases, Factual ; Economics ; Ecosystem ; Geology ; Population Dynamics ; }, abstract = {Theories of biodiversity rest on several macroecological patterns describing the relationship between species abundance and diversity. A central problem is that all theories make similar predictions for these patterns despite disparate assumptions. A troubling implication is that these patterns may not reflect anything unique about organizational principles of biology or the functioning of ecological systems. To test this, we analyze five datasets from ecological, economic, and geological systems that describe the distribution of objects across categories in the United States. At the level of functional form ('first-order effects'), these patterns are not unique to ecological systems, indicating they may reveal little about biological process. However, we show that mechanism can be better revealed in the scale-dependency of first-order patterns ('second-order effects'). These results provide a roadmap for biodiversity theory to move beyond traditional patterns, and also suggest ways in which macroecological theory can constrain the dynamics of economic systems.}, } @article {pmid25383632, year = {2014}, author = {Ho, ES and Kuchie, J and Duffy, S}, title = {Bioinformatic analysis reveals genome size reduction and the emergence of tyrosine phosphorylation site in the movement protein of New World bipartite begomoviruses.}, journal = {PloS one}, volume = {9}, number = {11}, pages = {e111957}, pmid = {25383632}, issn = {1932-6203}, support = {K12 GM093854/GM/NIGMS NIH HHS/United States ; K12 GM093854-01/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Begomovirus/*genetics/*metabolism ; Binding Sites ; *Computational Biology ; Evolution, Molecular ; *Genome Size ; Molecular Sequence Data ; *Movement ; Promoter Regions, Genetic ; Protein Transport ; Selection, Genetic ; Species Specificity ; Tyrosine/*metabolism ; Viral Proteins/chemistry/genetics/*metabolism ; }, abstract = {Begomovirus (genus Begomovirus, family Geminiviridae) infection is devastating to a wide variety of agricultural crops including tomato, squash, and cassava. Thus, understanding the replication and adaptation of begomoviruses has important translational value in alleviating substantial economic loss, particularly in developing countries. The bipartite genome of begomoviruses prevalent in the New World and their counterparts in the Old World share a high degree of genome homology except for a partially overlapping reading frame encoding the pre-coat protein (PCP, or AV2). PCP contributes to the essential functions of intercellular movement and suppression of host RNA silencing, but it is only present in the Old World viruses. In this study, we analyzed a set of non-redundant bipartite begomovirus genomes originating from the Old World (N = 28) and the New World (N = 65). Our bioinformatic analysis suggests ∼ 120 nucleotides were deleted from PCP's proximal promoter region that may have contributed to its loss in the New World viruses. Consequently, genomes of the New World viruses are smaller than the Old World counterparts, possibly compensating for the loss of the intercellular movement functions of PCP. Additionally, we detected substantial purifying selection on a portion of the New World DNA-B movement protein (MP, or BC1). Further analysis of the New World MP gene revealed the emergence of a putative tyrosine phosphorylation site, which likely explains the increased purifying selection in that region. These findings provide important information about the strategies adopted by bipartite begomoviruses in adapting to new environment and suggest future in planta experiments.}, } @article {pmid25380807, year = {2014}, author = {Hofberger, JA and Zhou, B and Tang, H and Jones, JD and Schranz, ME}, title = {A novel approach for multi-domain and multi-gene family identification provides insights into evolutionary dynamics of disease resistance genes in core eudicot plants.}, journal = {BMC genomics}, volume = {15}, number = {1}, pages = {966}, pmid = {25380807}, issn = {1471-2164}, mesh = {Cluster Analysis ; Computational Biology ; Conserved Sequence ; *Disease Resistance ; *Evolution, Molecular ; Gene Duplication ; Genetic Loci ; Genome, Plant ; Genomics ; Molecular Sequence Annotation ; *Multigene Family ; Plant Proteins/chemistry/*genetics ; Plants/classification/*genetics ; *Protein Interaction Domains and Motifs/genetics ; Tandem Repeat Sequences ; }, abstract = {BACKGROUND: Recent advances in DNA sequencing techniques resulted in more than forty sequenced plant genomes representing a diverse set of taxa of agricultural, energy, medicinal and ecological importance. However, gene family curation is often only inferred from DNA sequence homology and lacks insights into evolutionary processes contributing to gene family dynamics. In a comparative genomics framework, we integrated multiple lines of evidence provided by gene synteny, sequence homology and protein-based Hidden Markov Modelling to extract homologous super-clusters composed of multi-domain resistance (R)-proteins of the NB-LRR type (for NUCLEOTIDE BINDING/LEUCINE-RICH REPEATS), that are involved in plant innate immunity.

RESULTS: To assess the diversity of R-proteins within and between species, we screened twelve eudicot plant genomes including six major crops and found a total of 2,363 NB-LRR genes. Our curated R-proteins set shows a 50% average for tandem duplicates and a 22% fraction of gene copies retained from ancient polyploidy events (ohnologs). We provide evidence for strong positive selection and show significant differences in molecular evolution rates (Ka/Ks-ratio) among tandem- (mean = 1.59), ohnolog (mean = 1.36) and singleton (mean = 1.22) R-gene duplicates. To foster the process of gene-edited plant breeding, we report species-specific presence/absence of all 140 NB-LRR genes present in the model plant Arabidopsis and describe four distinct clusters of NB-LRR "gatekeeper" loci sharing syntenic orthologs across all analyzed genomes.

CONCLUSION: By curating a near-complete set of multi-domain R-protein clusters in an eudicot-wide scale, our analysis offers significant insight into evolutionary dynamics underlying diversification of the plant innate immune system. Furthermore, our methods provide a blueprint for future efforts to identify and more rapidly clone functional NB-LRR genes from any plant species.}, } @article {pmid25379884, year = {2014}, author = {Smith, DE and Metzger, S and Taylor, JR}, title = {A transparent and transferable framework for tracking quality information in large datasets.}, journal = {PloS one}, volume = {9}, number = {11}, pages = {e112249}, pmid = {25379884}, issn = {1932-6203}, mesh = {Algorithms ; Data Mining/methods ; *Datasets as Topic ; Quality Control ; }, abstract = {The ability to evaluate the validity of data is essential to any investigation, and manual "eyes on" assessments of data quality have dominated in the past. Yet, as the size of collected data continues to increase, so does the effort required to assess their quality. This challenge is of particular concern for networks that automate their data collection, and has resulted in the automation of many quality assurance and quality control analyses. Unfortunately, the interpretation of the resulting data quality flags can become quite challenging with large data sets. We have developed a framework to summarize data quality information and facilitate interpretation by the user. Our framework consists of first compiling data quality information and then presenting it through 2 separate mechanisms; a quality report and a quality summary. The quality report presents the results of specific quality analyses as they relate to individual observations, while the quality summary takes a spatial or temporal aggregate of each quality analysis and provides a summary of the results. Included in the quality summary is a final quality flag, which further condenses data quality information to assess whether a data product is valid or not. This framework has the added flexibility to allow "eyes on" information on data quality to be incorporated for many data types. Furthermore, this framework can aid problem tracking and resolution, should sensor or system malfunctions arise.}, } @article {pmid25379817, year = {2015}, author = {Noordally, ZB and Millar, AJ}, title = {Clocks in algae.}, journal = {Biochemistry}, volume = {54}, number = {2}, pages = {171-183}, doi = {10.1021/bi501089x}, pmid = {25379817}, issn = {1520-4995}, support = {BB/J009423/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Chlorophyta/*physiology ; *Circadian Clocks ; Circadian Rhythm ; Computational Biology ; Dinoflagellida/*physiology ; Euglena gracilis/*physiology ; Rhodophyta/*physiology ; }, abstract = {As major contributors to global oxygen levels and producers of fatty acids, carotenoids, sterols, and phycocolloids, algae have significant ecological and commercial roles. Early algal models have contributed much to our understanding of circadian clocks at physiological and biochemical levels. The genetic and molecular approaches that identified clock components in other taxa have not been as widely applied to algae. We review results from seven species: the chlorophytes Chlamydomonas reinhardtii, Ostreococcus tauri, and Acetabularia spp.; the dinoflagellates Lingulodinium polyedrum and Symbiodinium spp.; the euglenozoa Euglena gracilis; and the red alga Cyanidioschyzon merolae. The relative simplicity, experimental tractability, and ecological and evolutionary diversity of algal systems may now make them particularly useful in integrating quantitative data from "omic" technologies (e.g., genomics, transcriptomics, metabolomics, and proteomics) with computational and mathematical methods.}, } @article {pmid25378740, year = {2014}, author = {Kameda, T and Takahashi, K and Kim, R and Jiang, Y and Movahed, M and Park, EK and Rantanen, J}, title = {Asbestos: use, bans and disease burden in Europe.}, journal = {Bulletin of the World Health Organization}, volume = {92}, number = {11}, pages = {790-797}, pmid = {25378740}, issn = {1564-0604}, support = {001/WHO_/World Health Organization/International ; }, mesh = {Asbestos/*toxicity ; Asbestosis/*mortality ; Databases, Factual ; Europe/epidemiology ; Female ; Humans ; Lung Neoplasms/*mortality ; Male ; Mesothelioma/*mortality ; World Health Organization ; }, abstract = {OBJECTIVE: To analyse national data on asbestos use and related diseases in the European Region of the World Health Organization (WHO).

METHODS: For each of the 53 countries, per capita asbestos use (kg/capita/year) and age-adjusted mortality rates (deaths/million persons/year) due to mesothelioma and asbestosis were calculated using the databases of the United States Geological Survey and WHO, respectively. Countries were further categorized by ban status: early-ban (ban adopted by 2000, n = 17), late-ban (ban adopted 2001-2013, n = 17), and no-ban (n = 19).

FINDINGS: Between 1920-2012, the highest per capita asbestos use was found in the no-ban group. After 2000, early-ban and late-ban groups reduced their asbestos use levels to less than or equal to 0.1 kg/capita/year, respectively, while the no-ban group maintained a very high use at 2.2 kg/capita/year. Between 1994 and 2010, the European Region registered 106,180 deaths from mesothelioma and asbestosis, accounting for 60% of such deaths worldwide. In the early-ban and late-ban groups, 16/17 and 15/17 countries, respectively, reported mesothelioma data to WHO, while only 6/19 countries in the no-ban group reported such data. The age-adjusted mortality rates for mesothelioma for the early-ban, late-ban and no-ban groups were 9.4, 3.7 and 3.2 deaths/million persons/year, respectively. Asbestosis rates for the groups were 0.8, 0.9 and 1.5 deaths/million persons/year, respectively.

CONCLUSION: Within the European Region, the early-ban countries reported most of the current asbestos-related deaths. However, this might shift to the no-ban countries, since the disease burden will likely increase in these countries due the heavy use of asbestos.}, } @article {pmid25378272, year = {2015}, author = {Sackett, DK and Pow, CL and Rubino, MJ and Aday, DD and Cope, WG and Kullman, S and Rice, JA and Kwak, TJ and Law, M}, title = {Sources of endocrine-disrupting compounds in North Carolina waterways: a geographic information systems approach.}, journal = {Environmental toxicology and chemistry}, volume = {34}, number = {2}, pages = {437-445}, doi = {10.1002/etc.2797}, pmid = {25378272}, issn = {1552-8618}, mesh = {Endocrine Disruptors/*analysis ; Estradiol/analysis ; Estrogens/analysis ; *Geographic Information Systems ; Geography ; Least-Squares Analysis ; Models, Theoretical ; North Carolina ; Water Pollutants, Chemical/*analysis ; }, abstract = {The presence of endocrine-disrupting compounds (EDCs), particularly estrogenic compounds, in the environment has drawn public attention across the globe, yet a clear understanding of the extent and distribution of estrogenic EDCs in surface waters and their relationship to potential sources is lacking. The objective of the present study was to identify and examine the potential input of estrogenic EDC sources in North Carolina water bodies using a geographic information system (GIS) mapping and analysis approach. Existing data from state and federal agencies were used to create point and nonpoint source maps depicting the cumulative contribution of potential sources of estrogenic EDCs to North Carolina surface waters. Water was collected from 33 sites (12 associated with potential point sources, 12 associated with potential nonpoint sources, and 9 reference), to validate the predictive results of the GIS analysis. Estrogenicity (measured as 17β-estradiol equivalence) ranged from 0.06 ng/L to 56.9 ng/L. However, the majority of sites (88%) had water 17β-estradiol concentrations below 1 ng/L. Sites associated with point and nonpoint sources had significantly higher 17β-estradiol levels than reference sites. The results suggested that water 17β-estradiol was reflective of GIS predictions, confirming the relevance of landscape-level influences on water quality and validating the GIS approach to characterize such relationships.}, } @article {pmid25375134, year = {2014}, author = {Simental-Rodríguez, SL and Quiñones-Pérez, CZ and Moya, D and Hernández-Tecles, E and López-Sánchez, CA and Wehenkel, C}, title = {The relationship between species diversity and genetic structure in the rare Picea chihuahuana tree species community, Mexico.}, journal = {PloS one}, volume = {9}, number = {11}, pages = {e111623}, pmid = {25375134}, issn = {1932-6203}, mesh = {Amplified Fragment Length Polymorphism Analysis ; *Biodiversity ; Databases, Genetic ; Evolution, Molecular ; Genetic Drift ; Genetic Variation ; Genome, Plant ; Mexico ; Phylogeny ; Phylogeography ; Picea/*classification/*genetics ; }, abstract = {Species diversity and genetic diversity, the most basic elements of biodiversity, have long been treated as separate topics, although populations evolve within a community context. Recent studies on community genetics and ecology have suggested that genetic diversity is not completely independent of species diversity. The Mexican Picea chihuahuana Martínez is an endemic species listed as "Endangered" on the Red List. Forty populations of Chihuahua spruce have been identified. This species is often associated with tree species of eight genera in gallery forests. This rare Picea chihuahuana tree community covers an area no more than 300 ha and has been subject of several studies involving different topics such as ecology, genetic structure and climate change. The overall aim of these studies was to obtain a dataset for developing management tools to help decision makers implement preservation and conservation strategies. However, this unique forest tree community may also represent an excellent subject for helping us to understand the interplay between ecological and evolutionary processes in determining community structure and dynamics. The AFLP technique and species composition data were used together to test the hypothesis that species diversity is related to the adaptive genetic structure of some dominant tree species (Picea chihuahuana, Pinus strobiformis, Pseudotsuga menziesii and Populus tremuloides) of the Picea chihuahuana tree community at fourteen locations. The Hill numbers were used as a diversity measure. The results revealed a significant correlation between tree species diversity and genetic structure in Populus tremuloides. Because the relationship between the two levels of diversity was found to be positive for the putative adaptive AFLP detected, genetic and species structures of the tree community were possibly simultaneously adapted to a combination of ecological or environmental factors. The present findings indicate that interactions between genetic variants and species diversity may be crucial in shaping tree communities.}, } @article {pmid25374310, year = {2014}, author = {Shmool, JL and Kubzansky, LD and Newman, OD and Spengler, J and Shepard, P and Clougherty, JE}, title = {Social stressors and air pollution across New York City communities: a spatial approach for assessing correlations among multiple exposures.}, journal = {Environmental health : a global access science source}, volume = {13}, number = {}, pages = {91}, pmid = {25374310}, issn = {1476-069X}, mesh = {Adolescent ; Adult ; Air Pollutants/*toxicity ; Asthma/chemically induced/*epidemiology ; Child ; Child, Preschool ; *Environmental Exposure ; Geographic Information Systems ; Humans ; Infant ; Infant, Newborn ; New York City/epidemiology ; Nitrogen Dioxide/*toxicity ; Socioeconomic Factors ; Spatial Analysis ; *Stress, Psychological ; }, abstract = {BACKGROUND: Recent toxicological and epidemiological evidence suggests that chronic psychosocial stress may modify pollution effects on health. Thus, there is increasing interest in refined methods for assessing and incorporating non-chemical exposures, including social stressors, into environmental health research, towards identifying whether and how psychosocial stress interacts with chemical exposures to influence health and health disparities. We present a flexible, GIS-based approach for examining spatial patterns within and among a range of social stressors, and their spatial relationships with air pollution, across New York City, towards understanding their combined effects on health.

METHODS: We identified a wide suite of administrative indicators of community-level social stressors (2008-2010), and applied simultaneous autoregressive models and factor analysis to characterize spatial correlations among social stressors, and between social stressors and air pollutants, using New York City Community Air Survey (NYCCAS) data (2008-2009). Finally, we provide an exploratory ecologic analysis evaluating possible modification of the relationship between nitrogen dioxide (NO2) and childhood asthma Emergency Department (ED) visit rates by social stressors, to demonstrate how the methods used to assess stressor exposure (and/or consequent psychosocial stress) may alter model results.

RESULTS: Administrative indicators of a range of social stressors (e.g., high crime rate, residential crowding rate) were not consistently correlated (rho = - 0.44 to 0.89), nor were they consistently correlated with indicators of socioeconomic position (rho = - 0.54 to 0.89). Factor analysis using 26 stressor indicators suggested geographically distinct patterns of social stressors, characterized by three factors: violent crime and physical disorder, crowding and poor access to resources, and noise disruption and property crimes. In an exploratory ecologic analysis, these factors were differentially associated with area-average NO2 and childhood asthma ED visits. For example, only the 'violent crime and disorder' factor was significantly associated with asthma ED visits, and only the 'crowding and resource access' factor modified the association between area-level NO2 and asthma ED visits.

CONCLUSIONS: This spatial approach enabled quantification of complex spatial patterning and confounding between chemical and non-chemical exposures, and can inform study design for epidemiological studies of separate and combined effects of multiple urban exposures.}, } @article {pmid25371429, year = {2015}, author = {Yang, H and He, BZ and Ma, H and Tsaur, SC and Ma, C and Wu, Y and Ting, CT and Zhang, YE}, title = {Expression profile and gene age jointly shaped the genome-wide distribution of premature termination codons in a Drosophila melanogaster population.}, journal = {Molecular biology and evolution}, volume = {32}, number = {1}, pages = {216-228}, pmid = {25371429}, issn = {1537-1719}, support = {//Howard Hughes Medical Institute/United States ; }, mesh = {Animals ; Chromosomes ; *Codon, Nonsense ; Computational Biology/*methods ; Drosophila Proteins/*genetics ; Drosophila melanogaster/*genetics ; Evolution, Molecular ; Gene Expression Profiling ; Sequence Analysis, DNA ; Tissue Distribution ; }, abstract = {Widespread premature termination codon mutations (PTCs) were recently observed in human and fly populations. We took advantage of the population resequencing data in the Drosophila Genetic Reference Panel to investigate how the expression profile and the evolutionary age of genes shaped the allele frequency distribution of PTCs. After generating a high-quality data set of PTCs, we clustered genes harboring PTCs into three categories: genes encoding low-frequency PTCs (≤ 1.5%), moderate-frequency PTCs (1.5-10%), and high-frequency PTCs (>10%). All three groups show narrow transcription compared with PTC-free genes, with the moderate- and high-PTC frequency groups showing a pronounced pattern. Moreover, nearly half (42%) of the PTC-encoding genes are not expressed in any tissue. Interestingly, the moderate-frequency PTC group is strongly enriched for genes expressed in midgut, whereas genes harboring high-frequency PTCs tend to have sex-specific expression. We further find that although young genes born in the last 60 My compose a mere 9% of the genome, they represent 16%, 30%, and 50% of the genes containing low-, moderate-, and high-frequency PTCs, respectively. Among DNA-based and RNA-based duplicated genes, the child copy is approximately twice as likely to contain PTCs as the parent copy, whereas young de novo genes are as likely to encode PTCs as DNA-based duplicated new genes. Based on these results, we conclude that expression profile and gene age jointly shaped the landscape of PTC-mediated gene loss. Therefore, we propose that new genes may need a long time to become stably maintained after the origination.}, } @article {pmid25365070, year = {2014}, author = {Parsons, MB and Gillespie, TR and Lonsdorf, EV and Travis, D and Lipende, I and Gilagiza, B and Kamenya, S and Pintea, L and Vazquez-Prokopec, GM}, title = {Global positioning system data-loggers: a tool to quantify fine-scale movement of domestic animals to evaluate potential for zoonotic transmission to an endangered wildlife population.}, journal = {PloS one}, volume = {9}, number = {11}, pages = {e110984}, pmid = {25365070}, issn = {1932-6203}, support = {R01 AI058715/AI/NIAID NIH HHS/United States ; R01 AI58715/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; *Animals, Domestic ; *Animals, Wild ; *Geographic Information Systems ; Geographic Mapping ; Humans ; Population Dynamics ; Seasons ; Tanzania/epidemiology ; Zoonoses/*epidemiology/*transmission ; }, abstract = {Domesticated animals are an important source of pathogens to endangered wildlife populations, especially when anthropogenic activities increase their overlap with humans and wildlife. Recent work in Tanzania reports the introduction of Cryptosporidium into wild chimpanzee populations and the increased risk of ape mortality associated with SIVcpz-Cryptosporidium co-infection. Here we describe the application of novel GPS technology to track the mobility of domesticated animals (27 goats, 2 sheep and 8 dogs) with the goal of identifying potential routes for Cryptosporidium introduction into Gombe National Park. Only goats (5/27) and sheep (2/2) were positive for Cryptosporidium. Analysis of GPS tracks indicated that a crop field frequented by both chimpanzees and domesticated animals was a potential hotspot for Cryptosporidium transmission. This study demonstrates the applicability of GPS data-loggers in studies of fine-scale mobility of animals and suggests that domesticated animal-wildlife overlap should be considered beyond protected boundaries for long-term conservation strategies.}, } @article {pmid25364821, year = {2014}, author = {Chu, SM and Hsu, JF and Lee, CW and Lien, R and Huang, HR and Chiang, MC and Fu, RH and Tsai, MH}, title = {Neurological complications after neonatal bacteremia: the clinical characteristics, risk factors, and outcomes.}, journal = {PloS one}, volume = {9}, number = {11}, pages = {e105294}, pmid = {25364821}, issn = {1932-6203}, mesh = {*Bacteremia ; Bacterial Infections/*complications/diagnosis/microbiology ; Databases, Factual ; Humans ; Infant ; Infant, Newborn ; Intensive Care Units, Neonatal ; Nervous System Diseases/*diagnosis/*etiology/mortality ; Patient Outcome Assessment ; Retrospective Studies ; Risk Factors ; Survival Analysis ; Time Factors ; }, abstract = {BACKGROUND: Neonates with bacteremia are at risk of neurologic complications. Relevant information warrants further elucidation.

STUDY DESIGN: This was a retrospective cohort study of neonates with bacteremia-related neurologic complications (BNCs) in a tertiary-level neonatal intensive care unit (NICU). A systemic chart review was performed conducted to identify clinical characteristics and outcomes. A cohort of related conditions was constructed as the control group. Logistic regression analysis was used to identify independent risk factors for BNC.

RESULTS: Of 1037 bacteremia episodes, 36 (3.5%) had BNCs. Twenty-four cases of BNCs were related to meningitis, five were presumed meningitis, and seven occurred after septic shock. The most common causative pathogens were Group B streptococcus (41.7%) and E. coli (16.7%). The major BNCs consisted of seizures (28), hydrocephalus (20), encephalomalacia (11), cerebral infarction (7), subdural empyema (6), ventriculitis (8), and abscess (4). Eight (22.8%) neonates died and six (16.7%) were discharged in critical condition when the family withdrew life-sustaining treatment. Among the 22 survivors, eight had neurologic sequelae upon discharge. After multivariate logistic regression analysis, neonates with meningitis caused by Group B streptococcus (adjusted odds ratio [OR]: 8.90, 95% confidence interval [CI]: 2.20-36.08; p = 0.002) and combined meningitis and septic shock (OR, 5.94; 95% CI: 1.53-23.15; p = 0.010) were independently associated with BNCs.

CONCLUSIONS: Neonates with bacteremia-related neurologic complications are associated with adverse outcomes or sequelae. Better strategies aimed at early detection and reducing the emergence of neurologic complications and aggressive treatment of Group B streptococcus sepsis are needed in neonates with meningitis and septic shock.}, } @article {pmid25363121, year = {2014}, author = {Yazdani-Charati, J and Siamian, H and Kazemnejad, A and Mohammad, V}, title = {Spatial clustering of tuberculosis incidence in the North of Iran.}, journal = {Global journal of health science}, volume = {6}, number = {6}, pages = {288-294}, pmid = {25363121}, issn = {1916-9736}, mesh = {Adolescent ; Adult ; Cluster Analysis ; Female ; Geographic Information Systems ; Humans ; Incidence ; Iran/epidemiology ; Male ; Middle Aged ; Tuberculosis/*epidemiology ; }, abstract = {BACKGROUND AND PURPOSE: Tuberculosis (TB) poses a serious threat to public health throughout the world but disproportionately afflicts low-income nations. The aim of this study is to identify the high-risk areas in Mazandaran province (northern Iran) in helping the heath programmer for the best intervention.

MATERIALS & METHODS: This is an ecological study conducted from 1999 through 2008. The sample included 2444 Tuberculosis (TB) patients. The variables were age, gender, type of disease and residential location, analyzed by descriptive statistical methods and spatial analysis to identify cluster of disease incidence. Geographical information system software applied to map of smooth rate of TB.

RESULTS: Of 2444 registered patients, 1283 (52.5%) were male. The data showed 61% urban and 96.4% of them with the Iranian nationality. There was insignificant difference between genders, but the main difference was observed between locations that are the incidence rate in the Tonekabon and Behshahr cities were 30% higher than mean incidence rate of Mazandaran province (P-value<0.05). The comprising chance of acquiring infection between urban and rural was 1.46 with confidence interval of 95% (1.35, 1.59).

CONCLUSION: Geostatistical method showed spatial variability of TB incidence rate in all districts and identifying high-risk area (core areas). The most important core of TB incidence has been noticed in the eastern boundary of Mazandaran in the city of Behshahr which is due to proximity to Golestan Province. The incidence rate of TB in Behshahr city is about two times more than the number observed in Mazandaran province. Lower TB incidence rate has been observed in Golestan province is because there is usually a delay in the diagnosis of the disease especially in the positive smear patients.}, } @article {pmid25357249, year = {2014}, author = {Lindgreen, S and Umu, SU and Lai, AS and Eldai, H and Liu, W and McGimpsey, S and Wheeler, NE and Biggs, PJ and Thomson, NR and Barquist, L and Poole, AM and Gardner, PP}, title = {Robust identification of noncoding RNA from transcriptomes requires phylogenetically-informed sampling.}, journal = {PLoS computational biology}, volume = {10}, number = {10}, pages = {e1003907}, pmid = {25357249}, issn = {1553-7358}, support = {//Wellcome Trust/United Kingdom ; }, mesh = {Archaea/genetics ; Bacteria/genetics ; Cluster Analysis ; Computational Biology ; Databases, Genetic ; Gene Expression Profiling/*methods ; Phylogeny ; RNA, Archaeal/chemistry/classification/genetics ; RNA, Bacterial/chemistry/classification/genetics ; RNA, Untranslated/chemistry/*classification/*genetics ; Transcriptome/*genetics ; }, abstract = {Noncoding RNAs are integral to a wide range of biological processes, including translation, gene regulation, host-pathogen interactions and environmental sensing. While genomics is now a mature field, our capacity to identify noncoding RNA elements in bacterial and archaeal genomes is hampered by the difficulty of de novo identification. The emergence of new technologies for characterizing transcriptome outputs, notably RNA-seq, are improving noncoding RNA identification and expression quantification. However, a major challenge is to robustly distinguish functional outputs from transcriptional noise. To establish whether annotation of existing transcriptome data has effectively captured all functional outputs, we analysed over 400 publicly available RNA-seq datasets spanning 37 different Archaea and Bacteria. Using comparative tools, we identify close to a thousand highly-expressed candidate noncoding RNAs. However, our analyses reveal that capacity to identify noncoding RNA outputs is strongly dependent on phylogenetic sampling. Surprisingly, and in stark contrast to protein-coding genes, the phylogenetic window for effective use of comparative methods is perversely narrow: aggregating public datasets only produced one phylogenetic cluster where these tools could be used to robustly separate unannotated noncoding RNAs from a null hypothesis of transcriptional noise. Our results show that for the full potential of transcriptomics data to be realized, a change in experimental design is paramount: effective transcriptomics requires phylogeny-aware sampling.}, } @article {pmid25350160, year = {2015}, author = {Hartmann, M and Frey, B and Mayer, J and Mäder, P and Widmer, F}, title = {Distinct soil microbial diversity under long-term organic and conventional farming.}, journal = {The ISME journal}, volume = {9}, number = {5}, pages = {1177-1194}, pmid = {25350160}, issn = {1751-7370}, mesh = {Agriculture/*methods ; Bacteria/genetics ; Biodiversity ; Computational Biology ; Ecosystem ; Fertilizers ; Fungi/genetics ; Manure ; Minerals/chemistry ; Organic Agriculture/*methods ; Sequence Analysis, DNA ; *Soil ; *Soil Microbiology ; }, abstract = {Low-input agricultural systems aim at reducing the use of synthetic fertilizers and pesticides in order to improve sustainable production and ecosystem health. Despite the integral role of the soil microbiome in agricultural production, we still have a limited understanding of the complex response of microbial diversity to organic and conventional farming. Here we report on the structural response of the soil microbiome to more than two decades of different agricultural management in a long-term field experiment using a high-throughput pyrosequencing approach of bacterial and fungal ribosomal markers. Organic farming increased richness, decreased evenness, reduced dispersion and shifted the structure of the soil microbiota when compared with conventionally managed soils under exclusively mineral fertilization. This effect was largely attributed to the use and quality of organic fertilizers, as differences became smaller when conventionally managed soils under an integrated fertilization scheme were examined. The impact of the plant protection regime, characterized by moderate and targeted application of pesticides, was of subordinate importance. Systems not receiving manure harboured a dispersed and functionally versatile community characterized by presumably oligotrophic organisms adapted to nutrient-limited environments. Systems receiving organic fertilizer were characterized by specific microbial guilds known to be involved in degradation of complex organic compounds such as manure and compost. The throughput and resolution of the sequencing approach permitted to detect specific structural shifts at the level of individual microbial taxa that harbours a novel potential for managing the soil environment by means of promoting beneficial and suppressing detrimental organisms.}, } @article {pmid25349605, year = {2014}, author = {Sorosjinda-Nunthawarasilp, P and Bhumiratana, A}, title = {Ecotope-based entomological surveillance and molecular xenomonitoring of multidrug resistant malaria parasites in anopheles vectors.}, journal = {Interdisciplinary perspectives on infectious diseases}, volume = {2014}, number = {}, pages = {969531}, pmid = {25349605}, issn = {1687-708X}, abstract = {The emergence and spread of multidrug resistant (MDR) malaria caused by Plasmodium falciparum or Plasmodium vivax have become increasingly important in the Greater Mekong Subregion (GMS). MDR malaria is the heritable and hypermutable property of human malarial parasite populations that can decrease in vitro and in vivo susceptibility to proven antimalarial drugs as they exhibit dose-dependent drug resistance and delayed parasite clearance time in treated patients. MDR malaria risk situations reflect consequences of the national policy and strategy as this influences the ongoing national-level or subnational-level implementation of malaria control strategies in endemic GMS countries. Based on our experience along with current literature review, the design of ecotope-based entomological surveillance (EES) and molecular xenomonitoring of MDR falciparum and vivax malaria parasites in Anopheles vectors is proposed to monitor infection pockets in transmission control areas of forest and forest fringe-related malaria, so as to bridge malaria landscape ecology (ecotope and ecotone) and epidemiology. Malaria ecotope and ecotone are confined to a malaria transmission area geographically associated with the infestation of Anopheles vectors and particular environments to which human activities are related. This enables the EES to encompass mosquito collection and identification, salivary gland DNA extraction, Plasmodium- and species-specific identification, molecular marker-based PCR detection methods for putative drug resistance genes, and data management. The EES establishes strong evidence of Anopheles vectors carrying MDR P. vivax in infection pockets epidemiologically linked with other data obtained during which a course of follow-up treatment of the notified P. vivax patients receiving the first-line treatment was conducted. For regional and global perspectives, the EES would augment the epidemiological surveillance and monitoring of MDR falciparum and vivax malaria parasites in hotspots or suspected areas established in most endemic GMS countries implementing the National Malaria Control Programs, in addition to what is guided by the World Health Organization.}, } @article {pmid25349520, year = {2014}, author = {Gibson, DI and Bray, RA and Hunt, D and Georgiev, BB and Scholz, T and Harris, PD and Bakke, TA and Pojmanska, T and Niewiadomska, K and Kostadinova, A and Tkach, V and Bain, O and Durette-Desset, MC and Gibbons, L and Moravec, F and Petter, A and Dimitrova, ZM and Buchmann, K and Valtonen, ET and de Jong, Y}, title = {Fauna europaea: helminths (animal parasitic).}, journal = {Biodiversity data journal}, volume = {}, number = {2}, pages = {e1060}, pmid = {25349520}, issn = {1314-2828}, abstract = {Fauna Europaea provides a public web-service with an index of scientific names (including important synonyms) of all living European land and freshwater animals, their geographical distribution at country level (up to the Urals, excluding the Caucasus region), and some additional information. The Fauna Europaea project covers about 230,000 taxonomic names, including 130,000 accepted species and 14,000 accepted subspecies, which is much more than the originally projected number of 100,000 species. This represents a huge effort by more than 400 contributing specialists throughout Europe and is a unique (standard) reference suitable for many users in science, government, industry, nature conservation and education. Helminths parasitic in animals represent a large assemblage of worms, representing three phyla, with more than 200 families and almost 4,000 species of parasites from all major vertebrate and many invertebrate groups. A general introduction is given for each of the major groups of parasitic worms, i.e. the Acanthocephala, Monogenea, Trematoda (Aspidogastrea and Digenea), Cestoda and Nematoda. Basic information for each group includes its size, host-range, distribution, morphological features, life-cycle, classification, identification and recent key-works. Tabulations include a complete list of families dealt with, the number of species in each and the name of the specialist responsible for data acquisition, a list of additional specialists who helped with particular groups, and a list of higher taxa dealt with down to the family level. A compilation of useful references is appended.}, } @article {pmid25343723, year = {2014}, author = {Beas-Luna, R and Novak, M and Carr, MH and Tinker, MT and Black, A and Caselle, JE and Hoban, M and Malone, D and Iles, A}, title = {An online database for informing ecological network models: http://kelpforest.ucsc.edu.}, journal = {PloS one}, volume = {9}, number = {10}, pages = {e109356}, pmid = {25343723}, issn = {1932-6203}, mesh = {Databases, Factual ; *Ecosystem ; Humans ; *Internet ; North America ; *Software ; User-Computer Interface ; }, abstract = {Ecological network models and analyses are recognized as valuable tools for understanding the dynamics and resiliency of ecosystems, and for informing ecosystem-based approaches to management. However, few databases exist that can provide the life history, demographic and species interaction information necessary to parameterize ecological network models. Faced with the difficulty of synthesizing the information required to construct models for kelp forest ecosystems along the West Coast of North America, we developed an online database (http://kelpforest.ucsc.edu/) to facilitate the collation and dissemination of such information. Many of the database's attributes are novel yet the structure is applicable and adaptable to other ecosystem modeling efforts. Information for each taxonomic unit includes stage-specific life history, demography, and body-size allometries. Species interactions include trophic, competitive, facilitative, and parasitic forms. Each data entry is temporally and spatially explicit. The online data entry interface allows researchers anywhere to contribute and access information. Quality control is facilitated by attributing each entry to unique contributor identities and source citations. The database has proven useful as an archive of species and ecosystem-specific information in the development of several ecological network models, for informing management actions, and for education purposes (e.g., undergraduate and graduate training). To facilitate adaptation of the database by other researches for other ecosystems, the code and technical details on how to customize this database and apply it to other ecosystems are freely available and located at the following link (https://github.com/kelpforest-cameo/databaseui).}, } @article {pmid25343514, year = {2015}, author = {Müller, AL and Kjeldsen, KU and Rattei, T and Pester, M and Loy, A}, title = {Phylogenetic and environmental diversity of DsrAB-type dissimilatory (bi)sulfite reductases.}, journal = {The ISME journal}, volume = {9}, number = {5}, pages = {1152-1165}, pmid = {25343514}, issn = {1751-7370}, support = {P 23117/FWF_/Austrian Science Fund FWF/Austria ; P 25111/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Archaea/*enzymology/genetics ; Bacteria/*enzymology/genetics ; Biodiversity ; DNA Primers ; Databases, Genetic ; Environment ; Genes, Archaeal ; Genes, Bacterial ; Genetic Variation ; Hydrogensulfite Reductase/*genetics ; Oxidoreductases Acting on Sulfur Group Donors/*genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sulfates/*chemistry ; Sulfite Dehydrogenase/*genetics ; }, abstract = {The energy metabolism of essential microbial guilds in the biogeochemical sulfur cycle is based on a DsrAB-type dissimilatory (bi)sulfite reductase that either catalyzes the reduction of sulfite to sulfide during anaerobic respiration of sulfate, sulfite and organosulfonates, or acts in reverse during sulfur oxidation. Common use of dsrAB as a functional marker showed that dsrAB richness in many environments is dominated by novel sequence variants and collectively represents an extensive, largely uncharted sequence assemblage. Here, we established a comprehensive, manually curated dsrAB/DsrAB database and used it to categorize the known dsrAB diversity, reanalyze the evolutionary history of dsrAB and evaluate the coverage of published dsrAB-targeted primers. Based on a DsrAB consensus phylogeny, we introduce an operational classification system for environmental dsrAB sequences that integrates established taxonomic groups with operational taxonomic units (OTUs) at multiple phylogenetic levels, ranging from DsrAB enzyme families that reflect reductive or oxidative DsrAB types of bacterial or archaeal origin, superclusters, uncultured family-level lineages to species-level OTUs. Environmental dsrAB sequences constituted at least 13 stable family-level lineages without any cultivated representatives, suggesting that major taxa of sulfite/sulfate-reducing microorganisms have not yet been identified. Three of these uncultured lineages occur mainly in marine environments, while specific habitat preferences are not evident for members of the other 10 uncultured lineages. In summary, our publically available dsrAB/DsrAB database, the phylogenetic framework, the multilevel classification system and a set of recommended primers provide a necessary foundation for large-scale dsrAB ecology studies with next-generation sequencing methods.}, } @article {pmid25340824, year = {2014}, author = {Tanaka, R and Hino, A and Tsai, IJ and Palomares-Rius, JE and Yoshida, A and Ogura, Y and Hayashi, T and Maruyama, H and Kikuchi, T}, title = {Assessment of helminth biodiversity in wild rats using 18S rDNA based metagenomics.}, journal = {PloS one}, volume = {9}, number = {10}, pages = {e110769}, pmid = {25340824}, issn = {1932-6203}, mesh = {Animals ; Animals, Wild/*parasitology ; *Biodiversity ; Databases, Genetic ; Helminths/*genetics/isolation & purification ; Intestines/parasitology ; *Metagenomics ; Parasites/genetics/isolation & purification ; Phylogeny ; RNA, Ribosomal, 18S/*genetics ; Rats ; Sequence Analysis, DNA ; Software ; Species Specificity ; }, abstract = {Parasite diversity has important implications in several research fields including ecology, evolutionary biology and epidemiology. Wide-ranging analysis has been restricted because of the difficult, highly specialised and time-consuming processes involved in parasite identification. In this study, we assessed parasite diversity in wild rats using 18S rDNA-based metagenomics. 18S rDNA PCR products were sequenced using an Illumina MiSeq sequencer and the analysis of the sequences using the QIIME software successfully classified them into several parasite groups. The comparison of the results with those obtained using standard methods including microscopic observation of helminth parasites in the rat intestines and PCR amplification/sequencing of 18S rDNA from isolated single worms suggests that this new technique is reliable and useful to investigate parasite diversity.}, } @article {pmid25340520, year = {2014}, author = {Suzuki, T and Miyaki, K and Sasaki, Y and Song, Y and Tsutsumi, A and Kawakami, N and Shimazu, A and Takahashi, M and Inoue, A and Kurioka, S and Shimbo, T}, title = {Optimal cutoff values of WHO-HPQ presenteeism scores by ROC analysis for preventing mental sickness absence in Japanese prospective cohort.}, journal = {PloS one}, volume = {9}, number = {10}, pages = {e111191}, pmid = {25340520}, issn = {1932-6203}, mesh = {Absenteeism ; Adult ; Aged ; Area Under Curve ; Female ; Humans ; Japan ; Longitudinal Studies ; Male ; Mental Disorders/*epidemiology/therapy ; Middle Aged ; Multivariate Analysis ; Odds Ratio ; *Presenteeism ; Prospective Studies ; ROC Curve ; Sensitivity and Specificity ; Social Class ; Surveys and Questionnaires ; Workplace ; World Health Organization ; Young Adult ; }, abstract = {OBJECTIVES: Sickness absence due to mental disease in the workplace has become a global public health problem. Previous studies report that sickness presenteeism is associated with sickness absence. We aimed to determine optimal cutoff scores for presenteeism in the screening of the future absences due to mental disease.

METHODS: A prospective study of 2195 Japanese employees from all areas of Japan was conducted. Presenteeism and depression were measured by the validated Japanese version of the World Health Organization Health and Work Performance Questionnaire (WHO-HPQ) and K6 scale, respectively. Absence due to mental disease across a 2-year follow-up was surveyed using medical certificates obtained for work absence. Socioeconomic status was measured via a self-administered questionnaire. Receiver operating curve (ROC) analysis was used to determine optimal cutoff scores for absolute and relative presenteeism in relation to the area under the curve (AUC), sensitivity, and specificity.

RESULTS: The AUC values for absolute and relative presenteeism were 0.708 (95% CI, 0.618-0.797) and 0.646 (95% CI, 0.546-0.746), respectively. Optimal cutoff scores of absolute and relative presenteeism were 40 and 0.8, respectively. With multivariate adjustment, cohort participants with our proposal cutoff scores for absolute and relative presenteeism were significantly more likely to be absent due to mental disease (OR = 4.85, 95% CI: 2.20-10.73 and OR = 5.37, 95% CI: 2.42-11.93, respectively). The inclusion or exclusion of depressive symptoms (K6≥13) at baseline in the multivariate adjustment did not influence the results.

CONCLUSIONS: Our proposed optimal cutoff scores of absolute and relative presenteeism are 40 and 0.8, respectively. Participants who scored worse than the cutoff scores for presenteeism were significantly more likely to be absent in future because of mental disease. Our findings suggest that the utility of presenteeism in the screening of sickness absence due to mental disease would help prevent such an absence.}, } @article {pmid25340494, year = {2014}, author = {Micarelli, A and Pagani, M and Chiaravalloti, A and Bruno, E and Pavone, I and Candidi, M and Danieli, R and Schillaci, O and Alessandrini, M}, title = {Cortical metabolic arrangement during olfactory processing: proposal for a 18F FDG PET/CT methodological approach.}, journal = {Medicine}, volume = {93}, number = {19}, pages = {e103}, pmid = {25340494}, issn = {1536-5964}, mesh = {Adult ; Brain Mapping/methods ; Cerebral Cortex/diagnostic imaging/metabolism ; Female ; *Fluorodeoxyglucose F18/pharmacokinetics ; Humans ; Image Interpretation, Computer-Assisted/methods ; Male ; Middle Aged ; *Olfactory Pathways/diagnostic imaging/metabolism ; Positron-Emission Tomography/*methods ; Radiopharmaceuticals/pharmacokinetics ; Tomography, X-Ray Computed/*methods ; }, abstract = {The aim of this article is to investigate the cortical metabolic arrangements in olfactory processing by using F fluorodeoxyglucose (FDG) positron emission tomography/computed tomography.Twenty-six normosmic individuals (14 women and 12 men; mean age 46.7 ± 10 years) were exposed to a neutral olfactory condition (NC) and, after 1 month, to a pure olfactory condition (OC) in a relatively ecological environment, that is, outside the scanner. All the subjects were injected with 185-210 megabecquerel of F FDG during both stimulations. Statistical parametric mapping version 2 was used in order to assess differences between NC and OC.As a result, we found a significant higher glucose consumption during OC in the cuneus, lingual, and parahippocampal gyri, mainly in the left hemisphere. During NC, our results show a relative higher glucose metabolism in the left superior, inferior, middle, medial frontal, and orbital gyri as well as in the anterior cingulate cortex.The present investigation, performed with a widely available functional imaging clinical tool, may help to better understand the neural responses associated to olfactory processing in healthy individuals and in patients with olfactory disorders by acquiring data in an ecologic, noise-free, and resting condition in which possible cerebral activations related to unwanted attentional processes might be avoided.}, } @article {pmid25340454, year = {2014}, author = {Liu, R and Li, J and Fok, HS and Shum, CK and Li, Z}, title = {Earth surface deformation in the North China Plain detected by joint analysis of GRACE and GPS data.}, journal = {Sensors (Basel, Switzerland)}, volume = {14}, number = {10}, pages = {19861-19876}, pmid = {25340454}, issn = {1424-8220}, mesh = {Agricultural Irrigation ; China ; *Earth, Planet ; *Environmental Monitoring ; *Geographic Information Systems ; Humans ; Hydrology ; Seasons ; Water Supply ; }, abstract = {Mass redistribution of the Earth causes variable loading that deforms the solid Earth. While most recent studies using geodetic techniques focus on regions (such as the Amazon basin and the Nepal Himalayas) with large seasonal deformation amplitudes on the order of 1-4 cm due to hydrologic loading, few such studies have been conducted on the regions where the seasonal deformation amplitude is half as large. Here, we use joint GPS and GRACE data to investigate the vertical deformation due to hydrologic loading in the North China Plain, where significant groundwater depletion has been reported. We found that the GPS- and GRACE-derived secular trends and seasonal signals are in good agreement, with an uplift magnitude of 1-2 mm/year and a correlation of 85.0%-98.5%, respectively. This uplift rate is consistent with groundwater depletion rate estimated from GRACE data and in-situ groundwater measurements from earlier report studies; whereas the seasonal hydrologic variation reflects human behavior of groundwater pumping for agriculture irrigation in spring, leading to less water storage in summer than that in the winter season. However, less than 20% of weighted root-mean-squared (WRMS) reductions were detected for all the selected GPS stations when GRACE-derived seasonal deformations were removed from detrended GPS height time series. This discrepancy is probably because the GRACE-derived seasonal signals are large-scale, while the GPS-derived signals are local point measurements.}, } @article {pmid25335280, year = {2014}, author = {Kang, CZ and Wang, QQ and Zhou, T and Jiang, WK and Xiao, CH and Xie, Y}, title = {[Study on ecological suitability regionalization of Eucommia ulmoides in Guizhou].}, journal = {Zhong yao cai = Zhongyaocai = Journal of Chinese medicinal materials}, volume = {37}, number = {5}, pages = {760-766}, pmid = {25335280}, issn = {1001-4454}, mesh = {Adaptation, Biological ; China ; Climate ; *Ecology ; Eucommiaceae/chemistry/*growth & development/physiology ; Geographic Information Systems ; *Geography, Medical ; Lignans/analysis ; Models, Theoretical ; Plant Bark/chemistry/growth & development ; Plants, Medicinal/chemistry/*growth & development/physiology ; Soil ; }, abstract = {OBJECTIVE: To study the ecological suitability regionalization of Eucommia ulmoides, for selecting artificial planting base and high-quality industrial raw material purchase area of the herb in Guizhou.

METHODS: Based on the investigation of 14 Eucommia ulmoides producing areas, pinoresinol diglucoside content and ecological factors were obtained. Using spatial analysis method to carry on ecological suitability regionalization. Meanwhile, combining pinoresinol diglucoside content, the correlation of major active components and environmental factors were analyzed by statistical analysis.

RESULTS: The most suitability planting area of Eucommia ulmoides was the northwest of Guizhou. The distribution of Eucommia ulmoides was mainly affected by the type and pH value of soil, and monthly precipitation. The spatial structure of major active components in Eucommia ulmoides were randomly distributed in global space, but had only one aggregation point which had a high positive correlation in local space. The major active components of Eucommia ulmoides had no correlation with altitude, longitude or latitude.

CONCLUSION: Using the spatial analysis method and statistical analysis method, based on environmental factor and pinoresinol diglucoside content, the ecological suitability regionalization of Eucommia ulmoides can provide reference for the selection of suitable planting area, artificial planting base and directing production layout.}, } @article {pmid25335279, year = {2014}, author = {Tan, R and Wang, YJ and Zhou, LS and Tan, E and Ping, A and Zhang, Y}, title = {[Population characteristics and ecological suitability of Saussureae hieracioides].}, journal = {Zhong yao cai = Zhongyaocai = Journal of Chinese medicinal materials}, volume = {37}, number = {5}, pages = {756-759}, pmid = {25335279}, issn = {1001-4454}, mesh = {Acclimatization ; China ; Climate ; *Conservation of Natural Resources ; *Ecosystem ; Geographic Information Systems ; Geography ; Plants, Medicinal/*growth & development/physiology ; Saussurea/*growth & development/physiology ; }, abstract = {OBJECTIVE: To analyze the population characteristics and the appropriate producing area of Saussureae hieracioides in China.

METHODS: Chuanxibei plateau, one of the main producing areas of Saussureae hieracioides, was selected as the analytical basal place. Ecological methods were used to investigate the density and biomass of Saussureae hieracioides. Traditional Chinese Medicine Geographic Information System (TCMGIS-II) was used to analyze the appropriate producing area of Saussureae hieracioides.

RESULTS: Saussureae hieracioides could form the dominant species in its distribution area. The proper region (with similarity of 90% - 100%) of Saussureae hieracioides accounted for 338 776.89 km2, including 5 provinces/municipalities and 226 counties/cities. The largest area among them was Tibet Autonomous Region with area of 148 175.55 km2, followed by Sichuan Province (110 216.46 km2), Qinghai Province (62 947.61 km2), Gansu Province (16 233.09 km2) and Yunnan Province (1 177.18 km2).

CONCLUSION: TCMGIS is much valuable to the recognition of formation of producing area, the division of adaptive area, introduction and acclimatization of medicinal materials, it also provides a scientific reference for the introduction and cultivation of Saussureae hieracioides.}, } @article {pmid25332403, year = {2015}, author = {Poelchau, M and Childers, C and Moore, G and Tsavatapalli, V and Evans, J and Lee, CY and Lin, H and Lin, JW and Hackett, K}, title = {The i5k Workspace@NAL--enabling genomic data access, visualization and curation of arthropod genomes.}, journal = {Nucleic acids research}, volume = {43}, number = {Database issue}, pages = {D714-9}, pmid = {25332403}, issn = {1362-4962}, mesh = {Animals ; Arthropods/*genetics ; Computer Graphics ; *Databases, Genetic ; Genome ; *Genomics ; Internet ; Molecular Sequence Annotation ; }, abstract = {The 5000 arthropod genomes initiative (i5k) has tasked itself with coordinating the sequencing of 5000 insect or related arthropod genomes. The resulting influx of data, mostly from small research groups or communities with little bioinformatics experience, will require visualization, dissemination and curation, preferably from a centralized platform. The National Agricultural Library (NAL) has implemented the i5k Workspace@NAL (http://i5k.nal.usda.gov/) to help meet the i5k initiative's genome hosting needs. Any i5k member is encouraged to contact the i5k Workspace with their genome project details. Once submitted, new content will be accessible via organism pages, genome browsers and BLAST search engines, which are implemented via the open-source Tripal framework, a web interface for the underlying Chado database schema. We also implement the Web Apollo software for groups that choose to curate gene models. New content will add to the existing body of 35 arthropod species, which include species relevant for many aspects of arthropod genomic research, including agriculture, invasion biology, systematics, ecology and evolution, and developmental research.}, } @article {pmid25332377, year = {2015}, author = {Beck, D and Dennis, C and Foster, JA}, title = {Seed: a user-friendly tool for exploring and visualizing microbial community data.}, journal = {Bioinformatics (Oxford, England)}, volume = {31}, number = {4}, pages = {602-603}, pmid = {25332377}, issn = {1367-4811}, support = {F31 GM016448/GM/NIGMS NIH HHS/United States ; P20 GM103408/GM/NIGMS NIH HHS/United States ; P20GM016454/GM/NIGMS NIH HHS/United States ; P20GM16448/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacteria/*classification/*genetics ; Computational Biology/*methods ; *Computer Graphics ; *Ecology ; *Software ; }, abstract = {SUMMARY: In this article we present Simple Exploration of Ecological Data (Seed), a data exploration tool for microbial communities. Seed is written in R using the Shiny library. This provides access to powerful R-based functions and libraries through a simple user interface. Seed allows users to explore ecological datasets using principal coordinate analyses, scatter plots, bar plots, hierarchal clustering and heatmaps.

Seed is open source and available at https://github.com/danlbek/Seed.

CONTACT: danlbek@gmail.com

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, } @article {pmid25330317, year = {2014}, author = {Voges, N and Chaffiol, A and Lucas, P and Martinez, D}, title = {Reactive searching and infotaxis in odor source localization.}, journal = {PLoS computational biology}, volume = {10}, number = {10}, pages = {e1003861}, pmid = {25330317}, issn = {1553-7358}, mesh = {*Algorithms ; Animals ; *Appetitive Behavior ; *Artificial Intelligence ; Computational Biology ; Female ; Flight, Animal ; Male ; *Models, Biological ; Moths ; Odorants/*analysis ; Pheromones ; *Robotics ; }, abstract = {Male moths aiming to locate pheromone-releasing females rely on stimulus-adapted search maneuvers complicated by a discontinuous distribution of pheromone patches. They alternate sequences of upwind surge when perceiving the pheromone and cross- or downwind casting when the odor is lost. We compare four search strategies: three reactive versus one cognitive. The former consist of pre-programmed movement sequences triggered by pheromone detections while the latter uses Bayesian inference to build spatial probability maps. Based on the analysis of triphasic responses of antennal lobe neurons (On, inhibition, Off), we propose three reactive strategies. One combines upwind surge (representing the On response to a pheromone detection) and spiral casting, only. The other two additionally include crosswind (zigzag) casting representing the Off phase. As cognitive strategy we use the infotaxis algorithm which was developed for searching in a turbulent medium. Detection events in the electroantennogram of a moth attached to a robot indirectly control this cyborg, depending on the strategy in use. The recorded trajectories are analyzed with regard to success rates, efficiency, and other features. In addition, we qualitatively compare our robotic trajectories to behavioral search paths. Reactive searching is more efficient (yielding shorter trajectories) for higher pheromone doses whereas cognitive searching works better for lower doses. With respect to our experimental conditions (2 m from starting position to pheromone source), reactive searching with crosswind zigzag yields the shortest trajectories (for comparable success rates). Assuming that the neuronal Off response represents a short-term memory, zigzagging is an efficient movement to relocate a recently lost pheromone plume. Accordingly, such reactive strategies offer an interesting alternative to complex cognitive searching.}, } @article {pmid25329578, year = {2014}, author = {Garcia-Gil, M and Elorza, JM and Banque, M and Comas-Cufí, M and Blanch, J and Ramos, R and Méndez-Boo, L and Hermosilla, E and Bolibar, B and Prieto-Alhambra, D}, title = {Linking of primary care records to census data to study the association between socioeconomic status and cancer incidence in Southern Europe: a nation-wide ecological study.}, journal = {PloS one}, volume = {9}, number = {10}, pages = {e109706}, pmid = {25329578}, issn = {1932-6203}, mesh = {Adolescent ; Adult ; Age Distribution ; *Censuses ; Databases, Factual ; *Electronic Health Records ; Female ; Humans ; Incidence ; Male ; Middle Aged ; Neoplasms/*epidemiology ; *Primary Health Care ; Retrospective Studies ; Sex Distribution ; *Social Class ; Spain/epidemiology ; Young Adult ; }, abstract = {BACKGROUND: Area-based measures of economic deprivation are seldom applied to large medical records databases to establish population-scale associations between deprivation and disease.

OBJECTIVE: To study the association between deprivation and incidence of common cancer types in a Southern European region.

METHODS: Retrospective ecological study using the SIDIAP (Information System for the Development of Research in Primary Care) database of longitudinal electronic medical records for a representative population of Catalonia (Spain) and the MEDEA index based on urban socioeconomic indicators in the Spanish census. Study outcomes were incident cervical, breast, colorectal, prostate, and lung cancer in 2009-2012. The completeness of SIDIAP cancer recording was evaluated through linkage of a geographic data subset to a hospital cancer registry. Associations between MEDEA quintiles and cancer incidence was evaluated using zero-inflated Poisson regression adjusted for sex, age, smoking, alcoholism, obesity, hypertension, and diabetes.

RESULTS: SIDIAP sensitivity was 63% to 92% for the five cancers studied. There was direct association between deprivation and lung, colorectal, and cervical cancer: incidence rate ratios (IRR) 1.82 [1.64-2.01], IRR 1.60 [1.34-1.90], IRR 1.22 [1.07-1.38], respectively, comparing the most deprived to most affluent areas. In wealthy areas, prostate and breast cancers were more common: IRR 0.92 [0.80-1.00], IRR 0.91 [0.78-1.06]. Adjustment for confounders attenuated the association with lung cancer risk (fully adjusted IRR 1.16 [1.08-1.25]), reversed the direction of the association with colorectal cancer (IRR 0.90 [0.84-0.95]), and did not modify the associations with cervical (IRR 1.27 [1.11-1.45]), prostate (0.74 [0.69-0.80]), and breast (0.76 [0.71-0.81]) cancer.

CONCLUSIONS: Deprivation is associated differently with the occurrence of various cancer types. These results provide evidence that MEDEA is a useful, area-based deprivation index for analyses of the SIDIAP database. This information will be useful to improve screening programs, cancer prevention and management strategies, to reach patients more effectively, particularly in deprived urban areas.}, } @article {pmid25326605, year = {2014}, author = {Silva, MF and d'Almeida, OC and Oliveiros, B and Mateus, C and Castelo-Branco, M}, title = {Development and aging of visual hemifield asymmetries in contrast sensitivity.}, journal = {Journal of vision}, volume = {14}, number = {12}, pages = {}, doi = {10.1167/14.12.19}, pmid = {25326605}, issn = {1534-7362}, mesh = {Adolescent ; Adult ; Aged ; Aging/*physiology ; Analysis of Variance ; Anisotropy ; Child ; Contrast Sensitivity/*physiology ; Female ; Flicker Fusion/physiology ; Humans ; Male ; Middle Aged ; Photic Stimulation ; Space Perception/physiology ; Visual Fields/*physiology ; Young Adult ; }, abstract = {The relation of development and aging with models of visual anisotropies and their influence on low-level visual processing remain to be established. Our main goal was to explore visual performance asymmetries in development and normal aging using low-level contrast sensitivity behavioral tasks [probing two distinct spatiotemporal frequency channels, (a) intermediate spatial and null temporal frequency (3.5 cycles per degree (cpd) and 0 Hz); and (b) low spatial and high temporal frequency (0.25 cpd undergoing 25 Hz counterphase flicker)]. Different patterns of functional asymmetries were investigated within four (two neurodevelopmental and two adult) age groups (N = 258 participants; 8-65 years). We found a left visual hemifield/right hemisphere advantage for only the intermediate spatial frequency channel that was present early in life and remained stable throughout adulthood. In contrast, inferior/superior visual hemifield asymmetries, with a direct ecological meaning, were found for both spatiotemporal frequency channels. This inferior visual hemifield advantage emerged early in life and persisted throughout aging. These findings show that both right hemispheric and dorsal retinotopic patterns of dominance in low-level vision emerge early in childhood, maintaining during aging.}, } @article {pmid25324387, year = {2014}, author = {Ford, AT and Goheen, JR and Otieno, TO and Bidner, L and Isbell, LA and Palmer, TM and Ward, D and Woodroffe, R and Pringle, RM}, title = {Large carnivores make savanna tree communities less thorny.}, journal = {Science (New York, N.Y.)}, volume = {346}, number = {6207}, pages = {346-349}, doi = {10.1126/science.1252753}, pmid = {25324387}, issn = {1095-9203}, mesh = {*Acacia ; Animals ; *Antelopes ; *Canidae ; *Food Chain ; Geographic Information Systems ; *Herbivory ; *Panthera ; *Predatory Behavior ; *Trees ; }, abstract = {Understanding how predation risk and plant defenses interactively shape plant distributions is a core challenge in ecology. By combining global positioning system telemetry of an abundant antelope (impala) and its main predators (leopards and wild dogs) with a series of manipulative field experiments, we showed that herbivores' risk-avoidance behavior and plants' antiherbivore defenses interact to determine tree distributions in an African savanna. Well-defended thorny Acacia trees (A. etbaica) were abundant in low-risk areas where impala aggregated but rare in high-risk areas that impala avoided. In contrast, poorly defended trees (A. brevispica) were more abundant in high- than in low-risk areas. Our results suggest that plants can persist in landscapes characterized by intense herbivory, either by defending themselves or by thriving in risky areas where carnivores hunt.}, } @article {pmid25318827, year = {2015}, author = {Tipping, E and Lofts, S}, title = {Testing WHAM-FTOX with laboratory toxicity data for mixtures of metals (Cu, Zn, Cd, Ag, Pb).}, journal = {Environmental toxicology and chemistry}, volume = {34}, number = {4}, pages = {788-798}, doi = {10.1002/etc.2773}, pmid = {25318827}, issn = {1552-8618}, mesh = {Animals ; Binding Sites ; Daphnia ; Data Interpretation, Statistical ; Ecotoxicology/*methods ; *Heavy Metal Poisoning ; *Humic Substances ; Lactuca ; Models, Statistical ; *Poisoning ; Trout ; Water Pollutants, Chemical/*toxicity ; }, abstract = {The Windermere humic aqueous model using the toxicity function (WHAM-FTOX) describes cation toxicity to aquatic organisms in terms of 1) accumulation by the organism of metabolically active protons and metals at reversible binding sites, and 2) differing toxic potencies of the bound cations. Cation accumulation (νi , in mol g(-1)) is estimated through calculations with the WHAM chemical speciation model by assuming that organism binding sites can be represented by those of humic acid. Toxicity coefficients (αi) are combined with νi to obtain the variable FTOX (= Σ αi νi) which, between lower and upper thresholds (FTOX,LT , FTOX,UT), is linearly related to toxic effect. Values of αi , FTOX,LT , and FTOX,LT are obtained by fitting toxicity data. Reasonable fits (72% of variance in toxic effect explained overall) were obtained for 4 large metal mixture acute toxicity experiments involving daphnids (Cu, Zn, Cd), lettuce (Cu, Zn, Ag), and trout (Zn, Cd, Pb). Strong nonadditive effects, most apparent in results for tests involving Cd, could be explained approximately by purely chemical competition for metal accumulation. Tentative interpretation of parameter values obtained from these and other experimental data suggests the following order of bound cation toxicity: H < Al < (Cu Zn Pb UO2) < (Cd Ag). Another trend is a strong increase in Cd toxicity relative to that of Zn as organism complexity increases (from bacteria to fish).}, } @article {pmid25317518, year = {2014}, author = {Pazó, RG and Frauches, Dde O and Molina, Mdel C and Cade, NV}, title = {[Hierarchical modeling of determinants associated with hospitalizations for ambulatory care sensitive conditions in Espírito Santo State, Brazil].}, journal = {Cadernos de saude publica}, volume = {30}, number = {9}, pages = {1891-1902}, doi = {10.1590/0102-311x00099913}, pmid = {25317518}, issn = {1678-4464}, mesh = {Adolescent ; Adult ; Aged ; Ambulatory Care ; Brazil ; Child ; Child, Preschool ; Female ; Hospitalization/*statistics & numerical data ; Humans ; Infant ; Infant, Newborn ; Information Systems ; Male ; Middle Aged ; Poisson Distribution ; Primary Health Care/*statistics & numerical data ; Socioeconomic Factors ; Young Adult ; }, abstract = {The aim of this study was to investigate the relationship between health services organization and hospitalization rates for ambulatory care sensitive conditions after adjusting for socioeconomic and demographic variables in municipalities (counties) in Espírito Santo State, Brazil. In an ecological study, data were collected from the Brazilian Unified National Health System (SUS) on the following variables: hospitalization for ambulatory care sensitive conditions, city size, demographic and socioeconomic characteristics, and health services organization. Rates were analyzed by Poisson regression with robust variance. Models were adjusted for the total population and age group. The explanatory variables were ordered hierarchically. Hospitalization rates for ambulatory care sensitive conditions were associated with illiteracy rate (RR: 1.08-1.17), proportion of beds in the SUS (RR: 1.09-1.12), urbanization (RR: 1.02-1.03), proportion of blacks (RR: 0.97-0.98), and health insurance coverage (RR: 0.97-0.98). Some determinants of hospitalization for ambulatory care sensitive conditions involve patterns of health services use and lie outside the scope of primary care.}, } @article {pmid25315137, year = {2014}, author = {Adams, J and Rosenzweig, F}, title = {Experimental microbial evolution: history and conceptual underpinnings.}, journal = {Genomics}, volume = {104}, number = {6 Pt A}, pages = {393-398}, doi = {10.1016/j.ygeno.2014.10.004}, pmid = {25315137}, issn = {1089-8646}, mesh = {Databases, Genetic/history ; Directed Molecular Evolution/history ; *Evolution, Molecular ; *Genome, Microbial ; High-Throughput Nucleotide Sequencing/history/methods ; History, 20th Century ; History, 21st Century ; }, abstract = {We chronicle and dissect the history of the field of Experimental Microbial Evolution, beginning with work by Monod. Early research was largely carried out by microbiologists and biochemists, who used experimental evolutionary change as a tool to understand structure-function relationships. These studies attracted the interest of evolutionary biologists who recognized the power of the approach to address issues such as the tempo of adaptive change, the costs and benefits of sex, parallelism, and the role which contingency plays in the evolutionary process. In the 1980s and 1990s, an ever-expanding body of microbial, physiological and biochemical data, together with new technologies for manipulating microbial genomes, allowed such questions to be addressed in ever-increasing detail. Since then, technological advances leading to low-cost, high-throughput DNA sequencing have made it possible for these and other fundamental questions in evolutionary biology to be addressed at the molecular level.}, } @article {pmid25314320, year = {2015}, author = {Caro-Quintero, A and Konstantinidis, KT}, title = {Inter-phylum HGT has shaped the metabolism of many mesophilic and anaerobic bacteria.}, journal = {The ISME journal}, volume = {9}, number = {4}, pages = {958-967}, pmid = {25314320}, issn = {1751-7370}, mesh = {Bacteria/classification/*genetics/metabolism ; Bacteria, Anaerobic/*genetics/metabolism ; Computational Biology ; Ecological and Environmental Phenomena ; *Gene Transfer, Horizontal ; Genetic Variation ; Genome, Bacterial ; }, abstract = {Genome sequencing has revealed that horizontal gene transfer (HGT) is a major evolutionary process in bacteria. Although it is generally assumed that closely related organisms engage in genetic exchange more frequently than distantly related ones, the frequency of HGT among distantly related organisms and the effect of ecological relatedness on the frequency has not been rigorously assessed. Here, we devised a novel bioinformatic pipeline, which minimized the effect of over-representation of specific taxa in the available databases and other limitations of homology-based approaches by analyzing genomes in standardized triplets, to quantify gene exchange between bacterial genomes representing different phyla. Our analysis revealed the existence of networks of genetic exchange between organisms with overlapping ecological niches, with mesophilic anaerobic organisms showing the highest frequency of exchange and engaging in HGT twice as frequently as their aerobic counterparts. Examination of individual cases suggested that inter-phylum HGT is more pronounced than previously thought, affecting up to ∼ 16% of the total genes and ∼ 35% of the metabolic genes in some genomes (conservative estimation). In contrast, ribosomal and other universal protein-coding genes were subjected to HGT at least 150 times less frequently than genes encoding the most promiscuous metabolic functions (for example, various dehydrogenases and ABC transport systems), suggesting that the species tree based on the former genes may be reliable. These results indicated that the metabolic diversity of microbial communities within most habitats has been largely assembled from preexisting genetic diversity through HGT and that HGT accounts for the functional redundancy among phyla.}, } @article {pmid25313522, year = {2014}, author = {Nowotny, T and de Bruyne, M and Berna, AZ and Warr, CG and Trowell, SC}, title = {Drosophila olfactory receptors as classifiers for volatiles from disparate real world applications.}, journal = {Bioinspiration & biomimetics}, volume = {9}, number = {4}, pages = {046007}, doi = {10.1088/1748-3182/9/4/046007}, pmid = {25313522}, issn = {1748-3190}, mesh = {Action Potentials/drug effects/*physiology ; Animals ; Biological Assay/*methods ; Biomimetics/*instrumentation ; Biosensing Techniques/instrumentation/methods ; Drosophila melanogaster/*physiology ; Equipment Design ; Equipment Failure Analysis ; Olfactory Receptor Neurons/drug effects/*physiology ; Reproducibility of Results ; Sensitivity and Specificity ; Smell/drug effects/*physiology ; Volatile Organic Compounds/analysis/*pharmacology ; }, abstract = {Olfactory receptors evolved to provide animals with ecologically and behaviourally relevant information. The resulting extreme sensitivity and discrimination has proven useful to humans, who have therefore co-opted some animals' sense of smell. One aim of machine olfaction research is to replace the use of animal noses and one avenue of such research aims to incorporate olfactory receptors into artificial noses. Here, we investigate how well the olfactory receptors of the fruit fly, Drosophila melanogaster, perform in classifying volatile odourants that they would not normally encounter. We collected a large number of in vivo recordings from individual Drosophila olfactory receptor neurons in response to an ecologically relevant set of 36 chemicals related to wine ('wine set') and an ecologically irrelevant set of 35 chemicals related to chemical hazards ('industrial set'), each chemical at a single concentration. Resampled response sets were used to classify the chemicals against all others within each set, using a standard linear support vector machine classifier and a wrapper approach. Drosophila receptors appear highly capable of distinguishing chemicals that they have not evolved to process. In contrast to previous work with metal oxide sensors, Drosophila receptors achieved the best recognition accuracy if the outputs of all 20 receptor types were used.}, } @article {pmid25310057, year = {2015}, author = {Dennis, ML and Scott, CK and Funk, RR and Nicholson, L}, title = {A Pilot Study to Examine the Feasibility and Potential Effectiveness of Using Smartphones to Provide Recovery Support for Adolescents.}, journal = {Substance abuse}, volume = {36}, number = {4}, pages = {486-492}, pmid = {25310057}, issn = {1547-0164}, support = {R01 DA011323/DA/NIDA NIH HHS/United States ; R01 DA021174/DA/NIDA NIH HHS/United States ; R37 DA011323/DA/NIDA NIH HHS/United States ; R37 DA11323/DA/NIDA NIH HHS/United States ; }, mesh = {Adolescent ; *Ecological Momentary Assessment ; Feasibility Studies ; Female ; Humans ; Male ; *Mobile Applications ; Pilot Projects ; *Smartphone ; Substance-Related Disorders/*therapy ; Therapy, Computer-Assisted/*methods ; }, abstract = {BACKGROUND: Smartphone applications can potentially provide recovery monitoring and support in real-time, real-life contexts. Study aims included determining feasibility of (a) adolescents completing ecological momentary assessments (EMAs) and utilizing phone-based ecological momentary interventions (EMIs); and (b) using EMA and EMI data to predict substance use in the subsequent week.

METHODS: Twenty-nine adolescents were recruited at discharge from residential treatment, regardless of their discharge status or length of stay. During the 6-week pilot, youth were prompted to complete an EMA at 6 random times per day and were provided access to a suite of recovery support EMI. Youth completed 87% of the 5580 EMAs. Based on use in the next 7 days, EMA observations were classified into 3 risk groups: "Current Use" in the past 30 minutes (3% of observations), "Unrecognized Risk" (42%), or "Recognized Risk" (55%). All youth had observations in 2 or more risk groups and 38% in all 3. Youth accessed an EMI on average 162 times each week.

RESULTS: Participants were 31% female, 48% African American, 21% Caucasian, 7% Hispanic, and 24% Mixed/Other; average age was 16.6 years. During the 90 days prior to entering treatment, youth reported using alcohol (38%), marijuana (41%), and other drugs (7%). When compared with the "Recognized Risk" group's use in the following week (31%), both the "Unrecognized Risk" (50%, odds ratio [OR]=2.08) and "Current Use" (96%, OR=50.30) groups reported significantly higher rates of use in the next week. When an EMI was accessed 2 or more times within the hour following an EMA, the rate of using during the next week was significantly lower than when EMIs were not accessed (32% vs. 43%, OR=0.62).

CONCLUSIONS: Results demonstrate the feasibility of using smartphones for recovery monitoring and support with adolescents, with potential to reduce use.}, } @article {pmid25306556, year = {2014}, author = {Ryan, DE and Pepper, AE and Campbell, L}, title = {De novo assembly and characterization of the transcriptome of the toxic dinoflagellate Karenia brevis.}, journal = {BMC genomics}, volume = {15}, number = {1}, pages = {888}, pmid = {25306556}, issn = {1471-2164}, mesh = {Algal Proteins/genetics/metabolism ; Calcium Channels/genetics/metabolism ; Computational Biology ; Databases, Genetic ; Dinoflagellida/genetics/*metabolism ; Marine Toxins/*metabolism ; Molecular Sequence Annotation ; Oxocins/*metabolism ; Polymorphism, Single Nucleotide ; Sequence Analysis, RNA ; *Transcriptome ; Voltage-Gated Sodium Channels/genetics/metabolism ; }, abstract = {BACKGROUND: Karenia brevis is a harmful algal species that blooms in the Gulf of Mexico and produces brevetoxins that cause neurotoxic shellfish poisoning. Elevated brevetoxin levels in K. brevis cells have been measured during laboratory hypo-osmotic stress treatments. To investigate mechanisms underlying K. brevis osmoacclimation and osmoregulation and establish a valuable resource for gene discovery, we assembled reference transcriptomes for three clones: Wilson-CCFWC268, SP3, and SP1 (a low-toxin producing variant). K. brevis transcriptomes were annotated with gene ontology terms and searched for putative transmembrane proteins that may elucidate cellular responses to hypo-osmotic stress. An analysis of single nucleotide polymorphisms among clones was used to characterize genetic divergence.

RESULTS: K. brevis reference transcriptomes were assembled with 58.5 (Wilson), 78.0 (SP1), and 51.4 million (SP3) paired reads. Transcriptomes contained 86,580 (Wilson), 93,668 (SP1), and 84,309 (SP3) predicted transcripts. Approximately 40% of the transcripts were homologous to proteins in the BLAST nr database with an E value ≤ 1.00E-6. Greater than 80% of the highly conserved CEGMA core eukaryotic genes were identified in each transcriptome, which supports assembly completeness. Seven putative voltage-gated Na+ or Ca2+ channels, two aquaporin-like proteins, and twelve putative VATPase subunits were discovered in all clones using multiple bioinformatics approaches. Furthermore, 45% (Wilson) and 43% (SP1 and SP3) of the K. brevis putative peptides > 100 amino acids long produced significant hits to a sequence in the NCBI nr protein database. Of these, 77% (Wilson and SP1) and 73% (SP3) were successfully assigned gene ontology functional terms. The predicted single nucleotide polymorphism (SNP) frequencies between clones were 0.0028 (Wilson to SP1), 0.0030 (Wilson to SP3), and 0.0028 (SP1 to SP3).

CONCLUSIONS: The K. brevis transcriptomes assembled here provide a foundational resource for gene discovery and future RNA-seq experiments. The identification of ion channels, VATPases, and aquaporins in all three transcriptomes indicates that K. brevis regulates cellular ion and water concentrations via transmembrane proteins. Additionally, > 40,000 unannotated loci may include potentially novel K. brevis genes. Ultimately, the SNPs identified among the three ecologically diverse clones with different toxin profiles may help to elucidate variations in K. brevis brevetoxin production.}, } @article {pmid25302333, year = {2014}, author = {He, F and Wang, T and Gu, L and Li, T and Jiang, W and Shao, H}, title = {An integrated use of topography with RSI in gully mapping, Shandong Peninsula, China.}, journal = {TheScientificWorldJournal}, volume = {2014}, number = {}, pages = {827124}, pmid = {25302333}, issn = {1537-744X}, mesh = {China ; *Conservation of Natural Resources ; Ecosystem ; *Geographic Information Systems ; *Ponds ; Remote Sensing Technology/instrumentation/*methods ; Satellite Communications/*instrumentation ; Soil ; Water Movements ; }, abstract = {Taking the Quickbird optical satellite imagery of the small watershed of Beiyanzigou valley of Qixia city, Shandong province, as the study data, we proposed a new method by using a fused image of topography with remote sensing imagery (RSI) to achieve a high precision interpretation of gully edge lines. The technique first transformed remote sensing imagery into HSV color space from RGB color space. Then the slope threshold values of gully edge line and gully thalweg were gained through field survey and the slope data were segmented using thresholding, respectively. Based on the fused image in combination with gully thalweg thresholding vectors, the gully thalweg thresholding vectors were amended. Lastly, the gully edge line might be interpreted based on the amended gully thalweg vectors, fused image, gully edge line thresholding vectors, and slope data. A testing region was selected in the study area to assess the accuracy. Then accuracy assessment of the gully information interpreted by both interpreting remote sensing imagery only and the fused image was performed using the deviation, kappa coefficient, and overall accuracy of error matrix. Compared with interpreting remote sensing imagery only, the overall accuracy and kappa coefficient are increased by 24.080% and 264.364%, respectively. The average deviations of gully head and gully edge line are reduced by 60.448% and 67.406%, respectively. The test results show the thematic and the positional accuracy of gully interpreted by new method are significantly higher. Finally, the error sources for interpretation accuracy by the two methods were analyzed.}, } @article {pmid25299459, year = {2014}, author = {Nzeyimana, I and Hartemink, AE and Geissen, V}, title = {GIS-based multi-criteria analysis for Arabica coffee expansion in Rwanda.}, journal = {PloS one}, volume = {9}, number = {10}, pages = {e107449}, doi = {10.1371/journal.pone.0107449}, pmid = {25299459}, issn = {1932-6203}, mesh = {Coffea/*growth & development ; Coffee ; Congo ; Ecology ; Geographic Information Systems ; Rwanda ; Soil ; }, abstract = {The Government of Rwanda is implementing policies to increase the area of Arabica coffee production. Information on the suitable areas for sustainably growing Arabica coffee is still scarce. This study aimed to analyze suitable areas for Arabica coffee production. We analyzed the spatial distribution of actual and potential production zones for Arabica coffee, their productivity levels and predicted potential yields. We used a geographic information system (GIS) for a weighted overlay analysis to assess the major production zones of Arabica coffee and their qualitative productivity indices. Actual coffee yields were measured in the field and were used to assess potential productivity zones and yields using ordinary kriging with ArcGIS software. The production of coffee covers about 32 000 ha, or 2.3% of all cultivated land in the country. The major zones of production are the Kivu Lake Borders, Central Plateau, Eastern Plateau, and Mayaga agro-ecological zones, where coffee is mainly cultivated on moderate slopes. In the highlands, coffee is grown on steep slopes that can exceed 55%. About 21% percent of the country has a moderate yield potential, ranging between 1.0 and 1.6 t coffee ha-1, and 70% has a low yield potential (<1.0 t coffee ha-1). Only 9% of the country has a high yield potential of 1.6-2.4 t coffee ha-1. Those areas are found near Lake Kivu where the dominant soil Orders are Inceptisols and Ultisols. Moderate yield potential is found in the Birunga (volcano), Congo-Nile watershed Divide, Impala and Imbo zones. Low-yield regions (<1 t ha-1) occur in the eastern semi-dry lowlands, Central Plateau, Eastern Plateau, Buberuka Highlands, and Mayaga zones. The weighted overlay analysis and ordinary kriging indicated a large spatial variability of potential productivity indices. Increasing the area and productivity of coffee in Rwanda thus has considerable potential.}, } @article {pmid25297849, year = {2015}, author = {Colicchio, JM and Monnahan, PJ and Kelly, JK and Hileman, LC}, title = {Gene expression plasticity resulting from parental leaf damage in Mimulus guttatus.}, journal = {The New phytologist}, volume = {205}, number = {2}, pages = {894-906}, doi = {10.1111/nph.13081}, pmid = {25297849}, issn = {1469-8137}, mesh = {Epigenesis, Genetic ; *Gene Expression Regulation, Plant ; Gene Ontology ; Metabolic Networks and Pathways/genetics ; Mimulus/*genetics/physiology ; Plant Leaves/genetics/*physiology ; Seedlings/genetics ; }, abstract = {Leaf trichome density in Mimulus guttatus can be altered by the parental environment. In this study, we compared global gene expression patterns in progeny of damaged and control plants. Significant differences in gene expression probably explain the observed trichome response, and identify additional responsive pathways. Using whole transcriptome RNA sequencing, we estimated differential gene expression between isogenic seedlings whose parents had, or had not, been subject to leaf damage. We identified over 900 genes that were differentially expressed in response to parental wounding. These genes clustered into groups involved in cell wall and cell membrane development, stress response pathways, and secondary metabolism. Gene expression is modified as a consequence of the parental environment in a targeted way that probably alters multiple developmental pathways, and may increase progeny fitness if they experience environments similar to that of their parents.}, } @article {pmid25293947, year = {2014}, author = {Trapp, J and Geffard, O and Imbert, G and Gaillard, JC and Davin, AH and Chaumot, A and Armengaud, J}, title = {Proteogenomics of Gammarus fossarum to document the reproductive system of amphipods.}, journal = {Molecular & cellular proteomics : MCP}, volume = {13}, number = {12}, pages = {3612-3625}, pmid = {25293947}, issn = {1535-9484}, mesh = {Amphipoda/*genetics ; Animals ; Copulation/physiology ; Databases, Protein ; Female ; Fresh Water ; Gene Expression Profiling ; Gene Expression Regulation ; *Genome ; Male ; Molecular Sequence Annotation ; Proteome/*genetics ; Reproduction/genetics ; Sex Characteristics ; Spermatogenesis/*genetics ; }, abstract = {Because of their ecological importance, amphipod crustacea are employed worldwide as test species in environmental risk assessment. Although proteomics allows new insights into the molecular mechanisms related to the stress response, such investigations are rare for these organisms because of the lack of comprehensive protein sequence databases. Here, we propose a proteogenomic approach for identifying specific proteins of the freshwater amphipod Gammarus fossarum, a keystone species in European freshwater ecosystems. After deep RNA sequencing, we created a comprehensive ORF database. We identified and annotated the most relevant proteins detected through a shotgun tandem mass spectrometry analysis carried out on the proteomes from three major tissues involved in the organism's reproductive function: the male and female reproductive systems, and the cephalon, where different neuroendocrine glands are present. The 1,873 mass-spectrometry-certified proteins represent the largest crustacean proteomic resource to date, with 218 proteins being lineage specific. Comparative proteomics between the male and female reproductive systems indicated key proteins with strong sexual dimorphism. Protein expression profiles during spermatogenesis at seven different stages highlighted the major gammarid proteins involved in the different facets of reproduction.}, } @article {pmid25292302, year = {2015}, author = {Lu, S and Zhou, M and Guan, X and Tao, L}, title = {An integrated GIS-based interval-probabilistic programming model for land-use planning management under uncertainty--a case study at Suzhou, China.}, journal = {Environmental science and pollution research international}, volume = {22}, number = {6}, pages = {4281-4296}, pmid = {25292302}, issn = {1614-7499}, mesh = {China ; Cities ; Decision Support Techniques ; Environment ; *Geographic Information Systems ; Models, Statistical ; *Models, Theoretical ; Probability ; Reproducibility of Results ; *Uncertainty ; }, abstract = {A large number of mathematical models have been developed for supporting optimization of land-use allocation; however, few of them simultaneously consider land suitability (e.g., physical features and spatial information) and various uncertainties existing in many factors (e.g., land availabilities, land demands, land-use patterns, and ecological requirements). This paper incorporates geographic information system (GIS) technology into interval-probabilistic programming (IPP) for land-use planning management (IPP-LUPM). GIS is utilized to assemble data for the aggregated land-use alternatives, and IPP is developed for tackling uncertainties presented as discrete intervals and probability distribution. Based on GIS, the suitability maps of different land users are provided by the outcomes of land suitability assessment and spatial analysis. The maximum area of every type of land use obtained from the suitability maps, as well as various objectives/constraints (i.e., land supply, land demand of socioeconomic development, future development strategies, and environmental capacity), is used as input data for the optimization of land-use areas with IPP-LUPM model. The proposed model not only considers the outcomes of land suitability evaluation (i.e., topography, ground conditions, hydrology, and spatial location) but also involves economic factors, food security, and eco-environmental constraints, which can effectively reflect various interrelations among different aspects in a land-use planning management system. The case study results at Suzhou, China, demonstrate that the model can help to examine the reliability of satisfying (or risk of violating) system constraints under uncertainty. Moreover, it may identify the quantitative relationship between land suitability and system benefits. Willingness to arrange the land areas based on the condition of highly suitable land will not only reduce the potential conflicts on the environmental system but also lead to a lower economic benefit. However, a strong desire to develop lower suitable land areas will bring not only a higher economic benefit but also higher risks of violating environmental and ecological constraints. The land manager should make decisions through trade-offs between economic objectives and environmental/ecological objectives.}, } @article {pmid25288748, year = {2014}, author = {Estep, MC and McKain, MR and Vela Diaz, D and Zhong, J and Hodge, JG and Hodkinson, TR and Layton, DJ and Malcomber, ST and Pasquet, R and Kellogg, EA}, title = {Allopolyploidy, diversification, and the Miocene grassland expansion.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {111}, number = {42}, pages = {15149-15154}, pmid = {25288748}, issn = {1091-6490}, mesh = {Bayes Theorem ; Biological Evolution ; Computational Biology ; *Diploidy ; Genes, Plant ; *Genetic Speciation ; Genome ; Genomics ; *Grassland ; Likelihood Functions ; Phylogeny ; Poaceae ; *Polyploidy ; Sequence Analysis, DNA ; }, abstract = {The role of polyploidy, particularly allopolyploidy, in plant diversification is a subject of debate. Whole-genome duplications precede the origins of many major clades (e.g., angiosperms, Brassicaceae, Poaceae), suggesting that polyploidy drives diversification. However, theoretical arguments and empirical studies suggest that polyploid lineages may actually have lower speciation rates and higher extinction rates than diploid lineages. We focus here on the grass tribe Andropogoneae, an economically and ecologically important group of C4 species with a high frequency of polyploids. A phylogeny was constructed for ca. 10% of the species of the clade, based on sequences of four concatenated low-copy nuclear loci. Genetic allopolyploidy was documented using the characteristic pattern of double-labeled gene trees. At least 32% of the species sampled are the result of genetic allopolyploidy and result from 28 distinct tetraploidy events plus an additional six hexaploidy events. This number is a minimum, and the actual frequency could be considerably higher. The parental genomes of most Andropogoneae polyploids diverged in the Late Miocene coincident with the expansion of the major C4 grasslands that dominate the earth today. The well-documented whole-genome duplication in Zea mays ssp. mays occurred after the divergence of Zea and Sorghum. We find no evidence that polyploidization is followed by an increase in net diversification rate; nonetheless, allopolyploidy itself is a major mode of speciation.}, } @article {pmid25288507, year = {2015}, author = {Leventer, L and Dicks, M and Duarte, R and Davids, K and Araújo, D}, title = {Emergence of contact injuries in invasion team sports: an ecological dynamics rationale.}, journal = {Sports medicine (Auckland, N.Z.)}, volume = {45}, number = {2}, pages = {153-159}, pmid = {25288507}, issn = {1179-2035}, mesh = {Athletic Injuries/*prevention & control ; Biomedical Research ; Competitive Behavior ; *Environment ; Humans ; Soccer/injuries ; }, abstract = {The incidence of contact injuries in team sports is considerable, and injury mechanisms need to be comprehensively understood to facilitate the adoption of preventive measures. In Association Football, evidence shows that the highest prevalence of contact injuries emerges in one-on-one interactions. However, previous studies have tended to operationally report injury mechanisms in isolation, failing to provide a theoretical rationale to explain how injuries might emerge from interactions between opposing players. In this position paper, we propose an ecological dynamics framework to enhance current understanding of behavioural processes leading to contact injuries in team sports. Based on previous research highlighting the dynamics of performer-environment interactions, contact injuries are proposed to emerge from symmetry-breaking processes during on-field interpersonal interactions among competing players and the ball. Central to this approach is consideration of candidate control parameters that may provide insights on the information sources used by players to reduce risk of contact injuries during performance. Clinically, an ecological dynamics analysis could allow sport practitioners to design training sessions based on selected parameter threshold values as primary and/or secondary preventing measures during training and rehabilitation sessions.}, } @article {pmid25286919, year = {2015}, author = {Schmidt, R and Waschina, S and Boettger-Schmidt, D and Kost, C and Kaleta, C}, title = {Computing autocatalytic sets to unravel inconsistencies in metabolic network reconstructions.}, journal = {Bioinformatics (Oxford, England)}, volume = {31}, number = {3}, pages = {373-381}, doi = {10.1093/bioinformatics/btu658}, pmid = {25286919}, issn = {1367-4811}, mesh = {Bacterial Proteins/*metabolism ; Catalytic Domain ; *Computational Biology ; Genome, Bacterial/*genetics ; Metabolic Networks and Pathways/*genetics ; Models, Biological ; Phenotype ; *Software ; }, abstract = {MOTIVATION: Genome-scale metabolic network reconstructions have been established as a powerful tool for the prediction of cellular phenotypes and metabolic capabilities of organisms. In recent years, the number of network reconstructions has been constantly increasing, mostly because of the availability of novel (semi-)automated procedures, which enabled the reconstruction of metabolic models based on individual genomes and their annotation. The resulting models are widely used in numerous applications. However, the accuracy and predictive power of network reconstructions are commonly limited by inherent inconsistencies and gaps.

RESULTS: Here we present a novel method to validate metabolic network reconstructions based on the concept of autocatalytic sets. Autocatalytic sets correspond to collections of metabolites that, besides enzymes and a growth medium, are required to produce all biomass components in a metabolic model. These autocatalytic sets are well-conserved across all domains of life, and their identification in specific genome-scale reconstructions allows us to draw conclusions about potential inconsistencies in these models. The method is capable of detecting inconsistencies, which are neglected by other gap-finding methods. We tested our method on the Model SEED, which is the largest repository for automatically generated genome-scale network reconstructions. In this way, we were able to identify a significant number of missing pathways in several of these reconstructions. Hence, the method we report represents a powerful tool to identify inconsistencies in large-scale metabolic networks.

The method is available as source code on http://users.minet.uni-jena.de/∼m3kach/ASBIG/ASBIG.zip.

CONTACT: christoph.kaleta@uni-jena.de

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, } @article {pmid25286394, year = {2014}, author = {Das, P and Dileepkumar, R and Anaswara Krishnan, S and Nair, AS and Dhar, PK and Oommen, OV}, title = {Decahydroquinolines from the venom of a formicinae ant, Oecophylla smaragdina.}, journal = {Toxicon : official journal of the International Society on Toxinology}, volume = {92}, number = {}, pages = {50-53}, doi = {10.1016/j.toxicon.2014.09.013}, pmid = {25286394}, issn = {1879-3150}, mesh = {Alkaloids/*chemistry ; Ant Venoms/*analysis ; Gas Chromatography-Mass Spectrometry ; Neurotoxins/*chemistry ; Phenols/*chemistry ; Quinolines/*chemistry ; }, abstract = {Ecologically significant species in controlling pests, Oecophylla smaragdina uses its venom to paralyze their prey and to communicate with their colony mates. But no significant analysis of the ant's venom gland secretions has been carried out hitherto. This study describes the identification of venom constituents of Oecophylla smaragdina using coupled gas chromatography and mass spectroscopy (GC-MS) analysis. The results indicate the anticipated presence of a neurotoxin i.e., 2, 5 dipropyl decahydroquinoline and phenol, 2, 4-bis (1, 1 dimethylethyl). This is the first report on presence of decahydroquinolines in the venom of formicinae ant species of genera Oecophylla.}, } @article {pmid25284310, year = {2015}, author = {Fuerst, PA and Booton, GC and Crary, M}, title = {Phylogenetic analysis and the evolution of the 18S rRNA gene typing system of Acanthamoeba.}, journal = {The Journal of eukaryotic microbiology}, volume = {62}, number = {1}, pages = {69-84}, doi = {10.1111/jeu.12186}, pmid = {25284310}, issn = {1550-7408}, mesh = {Acanthamoeba/classification/*genetics ; DNA, Protozoan/*genetics ; Databases, Genetic ; Evolution, Molecular ; *Genes, rRNA ; Genetic Variation ; *Phylogeny ; RNA, Ribosomal, 18S/*genetics ; Ribotyping/*standards/statistics & numerical data ; Sequence Analysis, DNA ; Terminology as Topic ; }, abstract = {Species of Acanthamoeba were first described using morphological characters including cyst structure and cytology of nuclear division. More than 20 nominal species were proposed using these methods. Morphology, especially cyst shape and size, has proven to be plastic and dependent upon culture conditions. The DNA sequence of the nuclear small-subunit (18S) rRNA, the Rns gene, has become the most widely accepted method for rapid diagnosis and classification of Acanthamoeba. The Byers-Fuerst lab first proposed an Rns typing system in 1996. Subsequent refinements, with an increasing DNA database and analysis of diagnostic fragments within the gene, have become widely accepted by the Acanthamoeba research community. The development of the typing system, including its current state of implementation is illustrated by three cases: (i) the division between sequence types T13 and T16; (ii) the diversity within sequence supertype T2/T6, and (iii) verification of a new sequence type, designated T20. Molecular studies make clear the disconnection between phylogenetic relatedness and species names, as applied for the genus Acanthamoeba. Future reconciliation of genetic types with species names must become a priority, but the possible shortcomings of the use of a single gene when reconstructing the evolutionary history of the acanthamoebidae must also be resolved.}, } @article {pmid25281000, year = {2014}, author = {Maxwell, EK and Schnitzler, CE and Havlak, P and Putnam, NH and Nguyen, AD and Moreland, RT and Baxevanis, AD}, title = {Evolutionary profiling reveals the heterogeneous origins of classes of human disease genes: implications for modeling disease genetics in animals.}, journal = {BMC evolutionary biology}, volume = {14}, number = {}, pages = {212}, pmid = {25281000}, issn = {1471-2148}, mesh = {Animals ; *Biological Evolution ; Disease/*genetics ; *Disease Models, Animal ; Humans ; Models, Genetic ; Species Specificity ; }, abstract = {BACKGROUND: The recent expansion of whole-genome sequence data available from diverse animal lineages provides an opportunity to investigate the evolutionary origins of specific classes of human disease genes. Previous studies have observed that human disease genes are of particularly ancient origin. While this suggests that many animal species have the potential to serve as feasible models for research on genes responsible for human disease, it is unclear whether this pattern has meaningful implications and whether it prevails for every class of human disease.

RESULTS: We used a comparative genomics approach encompassing a broad phylogenetic range of animals with sequenced genomes to determine the evolutionary patterns exhibited by human genes associated with different classes of disease. Our results support previous claims that most human disease genes are of ancient origin but, more importantly, we also demonstrate that several specific disease classes have a significantly large proportion of genes that emerged relatively recently within the metazoans and/or vertebrates. An independent assessment of the synonymous to non-synonymous substitution rates of human disease genes found in mammals reveals that disease classes that arose more recently also display unexpected rates of purifying selection between their mammalian and human counterparts.

CONCLUSIONS: Our results reveal the heterogeneity underlying the evolutionary origins of (and selective pressures on) different classes of human disease genes. For example, some disease gene classes appear to be of uncommonly recent (i.e., vertebrate-specific) origin and, as a whole, have been evolving at a faster rate within mammals than the majority of disease classes having more ancient origins. The novel patterns that we have identified may provide new insight into cases where studies using traditional animal models were unable to produce results that translated to humans. Conversely, we note that the larger set of disease classes do have ancient origins, suggesting that many non-traditional animal models have the potential to be useful for studying many human disease genes. Taken together, these findings emphasize why model organism selection should be done on a disease-by-disease basis, with evolutionary profiles in mind.}, } @article {pmid25280881, year = {2014}, author = {Grose, JH and Jensen, GL and Burnett, SH and Breakwell, DP}, title = {Genomic comparison of 93 Bacillus phages reveals 12 clusters, 14 singletons and remarkable diversity.}, journal = {BMC genomics}, volume = {15}, number = {1}, pages = {855}, pmid = {25280881}, issn = {1471-2164}, mesh = {Bacillus Phages/classification/*genetics ; Chromosome Mapping ; Databases, Genetic ; Endodeoxyribonucleases/genetics ; Genetic Variation ; *Genome, Viral ; Genomics ; Multigene Family ; Open Reading Frames ; Phylogeny ; Proteomics ; Terminal Repeat Sequences/genetics ; Viral Proteins/genetics ; }, abstract = {BACKGROUND: The Bacillus genus of Firmicutes bacteria is ubiquitous in nature and includes one of the best characterized model organisms, B. subtilis, as well as medically significant human pathogens, the most notorious being B. anthracis and B. cereus. As the most abundant living entities on the planet, bacteriophages are known to heavily influence the ecology and evolution of their hosts, including providing virulence factors. Thus, the identification and analysis of Bacillus phages is critical to understanding the evolution of Bacillus species, including pathogenic strains.

RESULTS: Whole genome nucleotide and proteome comparison of the 93 extant Bacillus phages revealed 12 distinct clusters, 28 subclusters and 14 singleton phages. Host analysis of these clusters supports host boundaries at the subcluster level and suggests phages as vectors for genetic transfer within the Bacillus cereus group, with B. anthracis as a distant member of the group. Analysis of the proteins conserved among these phages reveals enormous diversity and the uncharacterized nature of these phages, with a total of 4,922 protein families (phams) of which only 951 (19%) had a predicted function. In addition, 3,058 (62%) of phams were orphams (phams containing a gene product from a single phage). The most populated phams were those encoding proteins involved in DNA metabolism, virion structure and assembly, cell lysis, or host function. These included several genes that may contribute to the pathogenicity of Bacillus strains.

CONCLUSIONS: This analysis provides a basis for understanding and characterizing Bacillus phages and other related phages as well as their contributions to the evolution and pathogenicity of Bacillus cereus group bacteria. The presence of sparsely populated clusters, the high ratio of singletons to clusters, and the large number of uncharacterized, conserved proteins confirms the need for more Bacillus phage isolation in order to understand the full extent of their diversity as well as their impact on host evolution.}, } @article {pmid25279728, year = {2014}, author = {Finseth, FR and Harrison, RG}, title = {A comparison of next generation sequencing technologies for transcriptome assembly and utility for RNA-Seq in a non-model bird.}, journal = {PloS one}, volume = {9}, number = {10}, pages = {e108550}, pmid = {25279728}, issn = {1932-6203}, mesh = {Animals ; Birds/*genetics ; *Computational Biology/methods ; Genomics/methods ; *High-Throughput Nucleotide Sequencing ; Reproducibility of Results ; *Sequence Analysis, RNA ; *Transcriptome ; }, abstract = {De novo assembled transcriptomes, in combination with RNA-Seq, are powerful tools to explore gene sequence and expression level in organisms without reference genomes. Investigators must first choose which high throughput sequencing platforms will provide data most suitable for their experimental goals. In this study, we explore the utility of 454 and Illumina sequences for de novo transcriptome assembly and downstream RNA-Seq applications in a reproductive gland from a non-model bird species, the Japanese quail (Coturnix japonica). Four transcriptomes composed of either pure 454 or Illumina reads or mixtures of read types were assembled and evaluated for the same cost. Illumina assemblies performed best for de novo transcriptome characterization in terms of contig length, transcriptome coverage, and complete assembly of gene transcripts. Improvements over the Hybrid assembly were marginal, with the exception that the addition of 454 data significantly increased the number of genes annotated. The Illumina assembly provided the best reference to align an independent set of RNA-Seq data as ∼84% of reads mapped to single genes in the transcriptome. Contigs constructed solely from 454 data may impose problems for RNA-Seq as our 454 transcriptome revealed a high number of indels and many ambiguously mapped reads. Correcting the 454 transcriptome with Illumina reads was an effective strategy to deal with indel and frameshift errors inherent to the 454 transcriptome, but at the cost of transcriptome coverage. In the absence of a reference genome, we find that Illumina reads alone produced a high quality transcriptome appropriate for RNA-Seq gene expression analyses.}, } @article {pmid25277059, year = {2014}, author = {Stewart, MJ and Favrel, P and Rotgans, BA and Wang, T and Zhao, M and Sohail, M and O'Connor, WA and Elizur, A and Henry, J and Cummins, SF}, title = {Neuropeptides encoded by the genomes of the Akoya pearl oyster Pinctata fucata and Pacific oyster Crassostrea gigas: a bioinformatic and peptidomic survey.}, journal = {BMC genomics}, volume = {15}, number = {1}, pages = {840}, pmid = {25277059}, issn = {1471-2164}, mesh = {Amino Acid Sequence ; Animals ; Crassostrea/*genetics ; Data Mining ; Genome/genetics ; Molecular Sequence Data ; Neuropeptides/chemistry/*genetics ; Pinctada/*genetics/metabolism ; *Proteomics ; }, abstract = {BACKGROUND: Oysters impart significant socio-ecological benefits from primary production of food supply, to estuarine ecosystems via reduction of water column nutrients, plankton and seston biomass. Little though is known at the molecular level of what genes are responsible for how oysters reproduce, filter nutrients, survive stressful physiological events and form reef communities. Neuropeptides represent a diverse class of chemical messengers, instrumental in orchestrating these complex physiological events in other species.

RESULTS: By a combination of in silico data mining and peptide analysis of ganglia, 74 putative neuropeptide genes were identified from genome and transcriptome databases of the Akoya pearl oyster, Pinctata fucata and the Pacific oyster, Crassostrea gigas, encoding precursors for over 300 predicted bioactive peptide products, including three newly identified neuropeptide precursors PFGx8amide, RxIamide and Wx3Yamide. Our findings also include a gene for the gonadotropin-releasing hormone (GnRH) and two egg-laying hormones (ELH) which were identified from both oysters. Multiple sequence alignments and phylogenetic analysis supports similar global organization of these mature peptides. Computer-based peptide modeling of the molecular tertiary structures of ELH highlights the structural homologies within ELH family, which may facilitate ELH activity leading to the release of gametes.

CONCLUSION: Our analysis demonstrates that oysters possess conserved molluscan neuropeptide domains and overall precursor organization whilst highlighting many previously unrecognized bivalve idiosyncrasies. This genomic analysis provides a solid foundation from which further studies aimed at the functional characterization of these molluscan neuropeptides can be conducted to further stimulate advances in understanding the ecology and cultivation of oysters.}, } @article {pmid25276506, year = {2014}, author = {Mahé, F and Rognes, T and Quince, C and de Vargas, C and Dunthorn, M}, title = {Swarm: robust and fast clustering method for amplicon-based studies.}, journal = {PeerJ}, volume = {2}, number = {}, pages = {e593}, pmid = {25276506}, issn = {2167-8359}, abstract = {Popular de novo amplicon clustering methods suffer from two fundamental flaws: arbitrary global clustering thresholds, and input-order dependency induced by centroid selection. Swarm was developed to address these issues by first clustering nearly identical amplicons iteratively using a local threshold, and then by using clusters' internal structure and amplicon abundances to refine its results. This fast, scalable, and input-order independent approach reduces the influence of clustering parameters and produces robust operational taxonomic units.}, } @article {pmid25270225, year = {2015}, author = {Keller, A and Danner, N and Grimmer, G and Ankenbrand, M and von der Ohe, K and von der Ohe, W and Rost, S and Härtel, S and Steffan-Dewenter, I}, title = {Evaluating multiplexed next-generation sequencing as a method in palynology for mixed pollen samples.}, journal = {Plant biology (Stuttgart, Germany)}, volume = {17}, number = {2}, pages = {558-566}, doi = {10.1111/plb.12251}, pmid = {25270225}, issn = {1438-8677}, mesh = {Animals ; Bees ; DNA Barcoding, Taxonomic/*methods ; Databases, Genetic ; Germany ; High-Throughput Nucleotide Sequencing/*methods ; Pollen/*classification/*genetics ; Workflow ; }, abstract = {The identification of pollen plays an important role in ecology, palaeo-climatology, honey quality control and other areas. Currently, expert knowledge and reference collections are essential to identify pollen origin through light microscopy. Pollen identification through molecular sequencing and DNA barcoding has been proposed as an alternative approach, but the assessment of mixed pollen samples originating from multiple plant species is still a tedious and error-prone task. Next-generation sequencing has been proposed to avoid this hindrance. In this study we assessed mixed pollen probes through next-generation sequencing of amplicons from the highly variable, species-specific internal transcribed spacer 2 region of nuclear ribosomal DNA. Further, we developed a bioinformatic workflow to analyse these high-throughput data with a newly created reference database. To evaluate the feasibility, we compared results from classical identification based on light microscopy from the same samples with our sequencing results. We assessed in total 16 mixed pollen samples, 14 originated from honeybee colonies and two from solitary bee nests. The sequencing technique resulted in higher taxon richness (deeper assignments and more identified taxa) compared to light microscopy. Abundance estimations from sequencing data were significantly correlated with counted abundances through light microscopy. Simulation analyses of taxon specificity and sensitivity indicate that 96% of taxa present in the database are correctly identifiable at the genus level and 70% at the species level. Next-generation sequencing thus presents a useful and efficient workflow to identify pollen at the genus and species level without requiring specialised palynological expert knowledge.}, } @article {pmid25268591, year = {2014}, author = {Quintela, M and Skaug, HJ and Øien, N and Haug, T and Seliussen, BB and Solvang, HK and Pampoulie, C and Kanda, N and Pastene, LA and Glover, KA}, title = {Investigating population genetic structure in a highly mobile marine organism: the minke whale Balaenoptera acutorostrata acutorostrata in the North East Atlantic.}, journal = {PloS one}, volume = {9}, number = {9}, pages = {e108640}, pmid = {25268591}, issn = {1932-6203}, mesh = {Animal Distribution ; Animals ; Atlantic Ocean ; Base Sequence ; DNA, Mitochondrial/*genetics ; Europe ; Female ; *Gene Flow ; Genetic Variation ; *Genetics, Population ; Male ; Microsatellite Repeats ; Minke Whale/*genetics ; Molecular Sequence Data ; Spatio-Temporal Analysis ; }, abstract = {Inferring the number of genetically distinct populations and their levels of connectivity is of key importance for the sustainable management and conservation of wildlife. This represents an extra challenge in the marine environment where there are few physical barriers to gene-flow, and populations may overlap in time and space. Several studies have investigated the population genetic structure within the North Atlantic minke whale with contrasting results. In order to address this issue, we analyzed ten microsatellite loci and 331 bp of the mitochondrial D-loop on 2990 whales sampled in the North East Atlantic in the period 2004 and 2007-2011. The primary findings were: (1) No spatial or temporal genetic differentiations were observed for either class of genetic marker. (2) mtDNA identified three distinct mitochondrial lineages without any underlying geographical pattern. (3) Nuclear markers showed evidence of a single panmictic population in the NE Atlantic according STRUCTURE's highest average likelihood found at K = 1. (4) When K = 2 was accepted, based on the Evanno's test, whales were divided into two more or less equally sized groups that showed significant genetic differentiation between them but without any sign of underlying geographic pattern. However, mtDNA for these individuals did not corroborate the differentiation. (5) In order to further evaluate the potential for cryptic structuring, a set of 100 in silico generated panmictic populations was examined using the same procedures as above showing genetic differentiation between two artificially divided groups, similar to the aforementioned observations. This demonstrates that clustering methods may spuriously reveal cryptic genetic structure. Based upon these data, we find no evidence to support the existence of spatial or cryptic population genetic structure of minke whales within the NE Atlantic. However, in order to conclusively evaluate population structure within this highly mobile species, more markers will be required.}, } @article {pmid25267521, year = {2014}, author = {Malik, MI and Bhat, MS}, title = {Integrated approach for prioritizing watersheds for management: a study of lidder catchment of kashmir himalayas.}, journal = {Environmental management}, volume = {54}, number = {6}, pages = {1267-1287}, pmid = {25267521}, issn = {1432-1009}, mesh = {*Conservation of Natural Resources ; Environmental Monitoring/methods ; Geographic Information Systems ; Humans ; India ; Population Density ; Socioeconomic Factors ; Waste Management ; *Water Supply ; }, abstract = {The Himalayan watersheds are susceptible to various forms of degradation due to their sensitive and fragile ecological disposition coupled with increasing anthropogenic disturbances. Owing to the paucity of appropriate technology and financial resources, the prioritization of watersheds has become an inevitable process for effective planning and management of natural resources. Lidder catchment constitutes a segment of the western Himalayas with an area of 1,159.38 km(2). The study is based on integrated analysis of remote sensing, geographic information system, field study, and socioeconomic data. Multicriteria evaluation of geophysical, land-use and land-cover (LULC) change, and socioeconomic indicators is carried out to prioritize watersheds for natural resource conservation and management. Knowledge-based weights and ranks are normalized, and weighted linear combination technique is adopted to determine final priority value. The watersheds are classified into four priority zones (very high priority, high priority, medium priority, and low priority) on the basis of quartiles of the priority value, thus indicating their ecological status in terms of degradation caused by anthropogenic disturbances. The correlation between priority ranks of individual indicators and integrated indicators is drawn. The results reveal that socioeconomic indicators are the most important drivers of LULC change and environmental degradation in the catchment. Moreover, the magnitude and intensity of anthropogenic impact is not uniform in different watersheds of Lidder catchment. Therefore, any conservation and management strategy must be formulated on the basis of watershed prioritization.}, } @article {pmid25265387, year = {2014}, author = {Huang, J and Lu, X and Zhang, W and Huang, R and Chen, S and Zheng, Y}, title = {Transcriptome sequencing and analysis of leaf tissue of Avicennia marina using the Illumina platform.}, journal = {PloS one}, volume = {9}, number = {9}, pages = {e108785}, pmid = {25265387}, issn = {1932-6203}, mesh = {Avicennia/*genetics/microbiology ; Fungi/genetics ; Gene Expression Regulation, Plant ; Gene Ontology ; Molecular Sequence Annotation ; Molecular Sequence Data ; Plant Leaves/*genetics ; Sequence Analysis, DNA/*methods ; Species Specificity ; Transcriptome/*genetics ; }, abstract = {Avicennia marina is a widely distributed mangrove species that thrives in high-salinity habitats. It plays a significant role in supporting coastal ecosystem and holds unique potential for studying molecular mechanisms underlying ecological adaptation. Despite and sometimes because of its numerous merits, this species is facing increasing pressure of exploitation and deforestation. Both study on adaptation mechanisms and conservation efforts necessitate more genomic resources for A. marina. In this study, we used Illumina sequencing of an A. marina foliar cDNA library to generate a transcriptome dataset for gene and marker discovery. We obtained 40 million high-quality reads and assembled them into 91,125 unigenes with a mean length of 463 bp. These unigenes covered most of the publicly available A. marina Sanger ESTs and greatly extended the repertoire of transcripts for this species. A total of 54,497 and 32,637 unigenes were annotated based on homology to sequences in the NCBI non-redundant and the Swiss-prot protein databases, respectively. Both Gene Ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis revealed some transcriptomic signatures of stress adaptation for this halophytic species. We also detected an extraordinary amount of transcripts derived from fungal endophytes and demonstrated the utility of transcriptome sequencing in surveying endophyte diversity without isolating them out of plant tissues. Additionally, we identified 3,423 candidate simple sequence repeats (SSRs) from 3,141 unigenes with a density of one SSR locus every 8.25 kb sequence. Our transcriptomic data will provide valuable resources for ecological, genetic and evolutionary studies in A. marina.}, } @article {pmid25262650, year = {2014}, author = {Foll, M and Gaggiotti, OE and Daub, JT and Vatsiou, A and Excoffier, L}, title = {Widespread signals of convergent adaptation to high altitude in Asia and america.}, journal = {American journal of human genetics}, volume = {95}, number = {4}, pages = {394-407}, pmid = {25262650}, issn = {1537-6605}, mesh = {Acclimatization/*genetics ; Adaptation, Physiological/*genetics ; Algorithms ; *Altitude ; Americas ; Asia ; Bayes Theorem ; *Biological Evolution ; Computer Simulation ; DNA Copy Number Variations/*genetics ; Databases, Genetic ; Gene Expression Profiling ; *Genetics, Population ; Genome, Human ; Humans ; Hypoxia/genetics ; Polymorphism, Single Nucleotide/genetics ; Selection, Genetic/*genetics ; }, abstract = {Living at high altitude is one of the most difficult challenges that humans had to cope with during their evolution. Whereas several genomic studies have revealed some of the genetic bases of adaptations in Tibetan, Andean, and Ethiopian populations, relatively little evidence of convergent evolution to altitude in different continents has accumulated. This lack of evidence can be due to truly different evolutionary responses, but it can also be due to the low power of former studies that have mainly focused on populations from a single geographical region or performed separate analyses on multiple pairs of populations to avoid problems linked to shared histories between some populations. We introduce here a hierarchical Bayesian method to detect local adaptation that can deal with complex demographic histories. Our method can identify selection occurring at different scales, as well as convergent adaptation in different regions. We apply our approach to the analysis of a large SNP data set from low- and high-altitude human populations from America and Asia. The simultaneous analysis of these two geographic areas allows us to identify several candidate genome regions for altitudinal selection, and we show that convergent evolution among continents has been quite common. In addition to identifying several genes and biological processes involved in high-altitude adaptation, we identify two specific biological pathways that could have evolved in both continents to counter toxic effects induced by hypoxia.}, } @article {pmid25262405, year = {2014}, author = {Kiedrzyńska, E and Jóźwik, A and Kiedrzyński, M and Zalewski, M}, title = {Hierarchy of factors exerting an impact on nutrient load of the Baltic Sea and sustainable management of its drainage basin.}, journal = {Marine pollution bulletin}, volume = {88}, number = {1-2}, pages = {162-173}, doi = {10.1016/j.marpolbul.2014.09.010}, pmid = {25262405}, issn = {1879-3363}, mesh = {*Agriculture ; Animals ; Baltic States ; Cattle ; Cluster Analysis ; Conservation of Natural Resources ; *Environment ; Eutrophication ; *Forests ; Humans ; Nitrogen/*analysis ; Oceans and Seas ; Phosphorus/*analysis ; Rivers ; Swine ; Waste Disposal, Fluid ; }, abstract = {The aim of the paper was to evaluate 23 catchment factors that determine total phosphorus and total nitrogen load to the Baltic Sea. Standard correlation analysis and clustering were used. Both phosphorus and nitrogen loads were found to be positively related to the number of pigs and the human population associated with wastewater treatment plants (WWTPs) per km(2), while the number of cattle and agricultural area were found to influence nitrogen rather than phosphorus load, and the area of forests is negatively related to loads of both nutrients. Clustering indicates an overall north-south pattern in the spatial co-occurrence of socio-ecological factors, with some exceptions discussed in the paper. Positive steps in the Baltic Sea region have already been taken, but much remains to be done. The development of coherent response policies to reduce eutrophication in the Baltic Sea should be based on a comprehensive knowledge base, an appropriate information strategy and learning alliance platform in each drainage river catchments.}, } @article {pmid25262151, year = {2014}, author = {Molchanova, I and Mikhailovskaya, L and Antonov, K and Pozolotina, V and Antonova, E}, title = {Current assessment of integrated content of long-lived radionuclides in soils of the head part of the East Ural Radioactive Trace.}, journal = {Journal of environmental radioactivity}, volume = {138}, number = {}, pages = {238-248}, doi = {10.1016/j.jenvrad.2014.09.004}, pmid = {25262151}, issn = {1879-1700}, mesh = {Cesium/*analysis ; Cesium Radioisotopes/analysis ; Data Collection ; Geographic Information Systems ; Models, Statistical ; Monte Carlo Method ; Plutonium/*analysis ; Siberia ; Soil Pollutants, Radioactive/*analysis ; Spatial Analysis ; Strontium/*analysis ; Strontium Radioisotopes/analysis ; }, abstract = {Based on the datasets obtained during investigations from 2003 to 2012, the spatial distributions of (90)Sr, (137)Cs, and (239,240)Pu content in the soils of the head part of the East Ural Radioactive Trace (EURT) were mapped using the geographic information system ArcGIS. Taking into account the presence of spatial autocorrelation and anisotropy in the source data, an ordinary kriging method was applied to interpolate values of radionuclide contamination density at unsampled places. Further geostatistical data analysis was performed to determine the basic parameters of spatial dependencies and to integrally assess the contamination by long-lived radionuclides in soils of the central, east peripheral, and west peripheral parts of the trace. This analysis was based on simplified geometric models (sector- and rectangle-shaped areas). The Monte Carlo method was used to quantitatively assess the uncertainty of the values for the integrated quantities resulting from the statistical errors of the source data approximation.}, } @article {pmid25261696, year = {2014}, author = {Wang, Y and Rannala, B}, title = {Bayesian inference of shared recombination hotspots between humans and chimpanzees.}, journal = {Genetics}, volume = {198}, number = {4}, pages = {1621-1628}, pmid = {25261696}, issn = {1943-2631}, support = {R01 HG001988/HG/NHGRI NIH HHS/United States ; HG01988/HG/NHGRI NIH HHS/United States ; }, mesh = {Algorithms ; Animals ; *Bayes Theorem ; Chromosomes, Human, Pair 21 ; Computational Biology ; Computer Simulation ; Genetics, Population ; Genome ; Genome, Human ; Genomics ; Histocompatibility Antigens/genetics ; Humans ; *Models, Genetic ; Pan troglodytes/*genetics ; Polymorphism, Genetic ; *Recombination, Genetic ; beta-Globins/genetics ; }, abstract = {Recombination generates variation and facilitates evolution. Recombination (or lack thereof) also contributes to human genetic disease. Methods for mapping genes influencing complex genetic diseases via association rely on linkage disequilibrium (LD) in human populations, which is influenced by rates of recombination across the genome. Comparative population genomic analyses of recombination using related primate species can identify factors influencing rates of recombination in humans. Such studies can indicate how variable hotspots for recombination may be both among individuals (or populations) and over evolutionary timescales. Previous studies have suggested that locations of recombination hotspots are not conserved between humans and chimpanzees. We made use of the data sets from recent resequencing projects and applied a Bayesian method for identifying hotspots and estimating recombination rates. We also reanalyzed SNP data sets for regions with known hotspots in humans using samples from the human and chimpanzee. The Bayes factors (BF) of shared recombination hotspots between human and chimpanzee across regions were obtained. Based on the analysis of the aligned regions of human chromosome 21, locations where the two species show evidence of shared recombination hotspots (with high BFs) were identified. Interestingly, previous comparative studies of human and chimpanzee that focused on the known human recombination hotspots within the β-globin and HLA regions did not find overlapping of hotspots. Our results show high BFs of shared hotspots at locations within both regions, and the estimated locations of shared hotspots overlap with the locations of human recombination hotspots obtained from sperm-typing studies.}, } @article {pmid25258734, year = {2014}, author = {Wang, Y and Li, X and Li, J}, title = {Study on the response of ecological capacity to land-use/cover change in Wuhan city: a remote sensing and GIS based approach.}, journal = {TheScientificWorldJournal}, volume = {2014}, number = {}, pages = {794323}, pmid = {25258734}, issn = {1537-744X}, mesh = {Agriculture/trends ; *Algorithms ; China ; Conservation of Natural Resources/*methods/trends ; Ecology/methods/trends ; Ecosystem ; *Geographic Information Systems ; Geography ; Remote Sensing Technology/*methods ; Time Factors ; Urbanization/trends ; }, abstract = {This research examined the spatiotemporal patterns of land-use/cover and the dynamics of ecological capacity in response to land-use/cover change in Wuhan city, central China. The data were derived from five years' remote-sensed images, that is, 1990, 1995, 2000, 2005, and 2010. This paper used an integrated approach of remote sensing and GIS techniques, ecological capacity and the bilateral dynamic degree models. The results are as follows. (1) From 1990 to 2010, remarkable changes in land-use/cover have occurred within the studied area, and the most prominent characteristics of the changes were continuous decline of arable land and rapid increase of built-up land. (2) The total ecological capacity dropped from 450.55 × 10(4) ghm(2) in 1990 to 447.35 × 10(4) ghm(2) in 2010. The eastern, western, and southern parts had higher ecological capacity whereas the northwestern hilly areas and the central district had lower ecological capacity. (3) Due to the conversion from arable land to built-up land, the ecological capacity losses during 1990-1995, 1995-2000, 2000-2005, and 2005-2010 were 155.52 × 10(2) ghm(2), 114.12 × 10(2) ghm(2), 455.48 × 10(2) ghm(2), and 325.26 × 10(2) ghm(2), respectively. The study would contribute to better understanding of the effects of land-use dynamics and the evolution of ecological capacity, which can provide scientific basis for land management and environment protection.}, } @article {pmid25257036, year = {2015}, author = {Quiroz, ZC and Prates, MO and Rue, H}, title = {A Bayesian approach to estimate the biomass of anchovies off the coast of Perú.}, journal = {Biometrics}, volume = {71}, number = {1}, pages = {208-217}, doi = {10.1111/biom.12227}, pmid = {25257036}, issn = {1541-0420}, mesh = {Algorithms ; Animals ; *Bayes Theorem ; *Biomass ; Biometry/*methods ; Computer Simulation ; *Data Interpretation, Statistical ; Environmental Monitoring/methods ; Fishes/*physiology ; *Models, Statistical ; Peru ; Reproducibility of Results ; Sample Size ; Sensitivity and Specificity ; }, abstract = {The Northern Humboldt Current System (NHCS) is the world's most productive ecosystem in terms of fish. In particular, the Peruvian anchovy (Engraulis ringens) is the major prey of the main top predators, like seabirds, fish, humans, and other mammals. In this context, it is important to understand the dynamics of the anchovy distribution to preserve it as well as to exploit its economic capacities. Using the data collected by the "Instituto del Mar del Perú" (IMARPE) during a scientific survey in 2005, we present a statistical analysis that has as main goals: (i) to adapt to the characteristics of the sampled data, such as spatial dependence, high proportions of zeros and big size of samples; (ii) to provide important insights on the dynamics of the anchovy population; and (iii) to propose a model for estimation and prediction of anchovy biomass in the NHCS offshore from Perú. These data were analyzed in a Bayesian framework using the integrated nested Laplace approximation (INLA) method. Further, to select the best model and to study the predictive power of each model, we performed model comparisons and predictive checks, respectively. Finally, we carried out a Bayesian spatial influence diagnostic for the preferred model.}, } @article {pmid25256301, year = {2015}, author = {Ji, Z and Card, KJ and Dazzo, FB}, title = {CMEIAS JFrad: a digital computing tool to discriminate the fractal geometry of landscape architectures and spatial patterns of individual cells in microbial biofilms.}, journal = {Microbial ecology}, volume = {69}, number = {3}, pages = {710-720}, pmid = {25256301}, issn = {1432-184X}, mesh = {*Bacterial Physiological Phenomena ; Bacteriological Techniques/*methods ; *Biofilms ; *Fractals ; Microscopy ; Software ; }, abstract = {Image analysis of fractal geometry can be used to gain deeper insights into complex ecophysiological patterns and processes occurring within natural microbial biofilm landscapes, including the scale-dependent heterogeneities of their spatial architecture, biomass, and cell-cell interactions, all driven by the colonization behavior of optimal spatial positioning of organisms to maximize their efficiency in utilization of allocated nutrient resources. Here, we introduce CMEIAS JFrad, a new computing technology that analyzes the fractal geometry of complex biofilm architectures in digital landscape images. The software uniquely features a data-mining opportunity based on a comprehensive collection of 11 different mathematical methods to compute fractal dimension that are implemented into a wizard design to maximize ease-of-use for semi-automatic analysis of single images or fully automatic analysis of multiple images in a batch process. As examples of application, quantitative analyses of fractal dimension were used to optimize the important variable settings of brightness threshold and minimum object size in order to discriminate the complex architecture of freshwater microbial biofilms at multiple spatial scales, and also to differentiate the spatial patterns of individual bacterial cells that influence their cooperative interactions, resource use, and apportionment in situ. Version 1.0 of JFrad is implemented into a software package containing the program files, user manual, and tutorial images that will be freely available at http://cme.msu.edu/cmeias/. This improvement in computational image informatics will strengthen microscopy-based approaches to analyze the dynamic landscape ecology of microbial biofilm populations and communities in situ at spatial resolutions that range from single cells to microcolonies.}, } @article {pmid25254967, year = {2014}, author = {Haase, D and Rieger, JK and Witten, A and Stoll, M and Bornberg-Bauer, E and Kalbe, M and Reusch, TB}, title = {Specific gene expression responses to parasite genotypes reveal redundancy of innate immunity in vertebrates.}, journal = {PloS one}, volume = {9}, number = {9}, pages = {e108001}, pmid = {25254967}, issn = {1932-6203}, mesh = {Animals ; Gene Expression Regulation/*immunology ; Gene Ontology ; Genomics ; *Genotype ; *Host-Parasite Interactions ; Immunity, Innate/*genetics ; Larva/physiology ; Parasite Load ; RNA, Messenger/genetics/metabolism ; Smegmamorpha/immunology/*parasitology ; Transcriptome/*immunology ; Trematoda/genetics/*physiology ; }, abstract = {Vertebrate innate immunity is the first line of defense against an invading pathogen and has long been assumed to be largely unspecific with respect to parasite/pathogen species. However, recent phenotypic evidence suggests that immunogenetic variation, i.e. allelic variability in genes associated with the immune system, results in host-parasite genotype-by-genotype interactions and thus specific innate immune responses. Immunogenetic variation is common in all vertebrate taxa and this reflects an effective immunological function in complex environments. However, the underlying variability in host gene expression patterns as response of innate immunity to within-species genetic diversity of macroparasites in vertebrates is unknown. We hypothesized that intra-specific variation among parasite genotypes must be reflected in host gene expression patterns. Here we used high-throughput RNA-sequencing to examine the effect of parasite genotypes on gene expression patterns of a vertebrate host, the three-spined stickleback (Gasterosteus aculeatus). By infecting naïve fish with distinct trematode genotypes of the species Diplostomum pseudospathaceum we show that gene activity of innate immunity in three-spined sticklebacks depended on the identity of an infecting macroparasite genotype. In addition to a suite of genes indicative for a general response against the trematode we also find parasite-strain specific gene expression, in particular in the complement system genes, despite similar infection rates of single clone treatments. The observed discrepancy between infection rates and gene expression indicates the presence of alternative pathways which execute similar functions. This suggests that the innate immune system can induce redundant responses specific to parasite genotypes.}, } @article {pmid25252973, year = {2014}, author = {Sergio, F and Tanferna, A and De Stephanis, R and Jiménez, LL and Blas, J and Tavecchia, G and Preatoni, D and Hiraldo, F}, title = {Individual improvements and selective mortality shape lifelong migratory performance.}, journal = {Nature}, volume = {515}, number = {7527}, pages = {410-413}, pmid = {25252973}, issn = {1476-4687}, mesh = {Africa ; Age Factors ; Aging/*physiology ; Animal Migration/*physiology ; Animals ; Conservation of Natural Resources ; Geographic Information Systems ; Global Warming ; Human Activities ; Raptors/*physiology ; Reproduction/physiology ; Spain ; Survival Rate ; Time Factors ; Wind ; }, abstract = {Billions of organisms, from bacteria to humans, migrate each year and research on their migration biology is expanding rapidly through ever more sophisticated remote sensing technologies. However, little is known about how migratory performance develops through life for any organism. To date, age variation has been almost systematically simplified into a dichotomous comparison between recently born juveniles at their first migration versus adults of unknown age. These comparisons have regularly highlighted better migratory performance by adults compared with juveniles, but it is unknown whether such variation is gradual or abrupt and whether it is driven by improvements within the individual, by selective mortality of poor performers, or both. Here we exploit the opportunity offered by long-term monitoring of individuals through Global Positioning System (GPS) satellite tracking to combine within-individual and cross-sectional data on 364 migration episodes from 92 individuals of a raptorial bird, aged 1-27 years old. We show that the development of migratory behaviour follows a consistent trajectory, more gradual and prolonged than previously appreciated, and that this is promoted by both individual improvements and selective mortality, mainly operating in early life and during the pre-breeding migration. Individuals of different age used different travelling tactics and varied in their ability to exploit tailwinds or to cope with wind drift. All individuals seemed aligned along a race with their contemporary peers, whose outcome was largely determined by the ability to depart early, affecting their subsequent recruitment, reproduction and survival. Understanding how climate change and human action can affect the migration of younger animals may be the key to managing and forecasting the declines of many threatened migrants.}, } @article {pmid25251870, year = {2015}, author = {van de Kerk, M and Onorato, DP and Criffield, MA and Bolker, BM and Augustine, BC and McKinley, SA and Oli, MK}, title = {Hidden semi-Markov models reveal multiphasic movement of the endangered Florida panther.}, journal = {The Journal of animal ecology}, volume = {84}, number = {2}, pages = {576-585}, doi = {10.1111/1365-2656.12290}, pmid = {25251870}, issn = {1365-2656}, mesh = {Animals ; Behavior, Animal/*physiology ; Endangered Species ; Female ; Florida ; Gait ; Geographic Information Systems ; *Locomotion ; Male ; Markov Chains ; Models, Statistical ; Puma/*physiology ; Reproduction ; Seasons ; Sex Factors ; }, abstract = {Animals must move to find food and mates, and to avoid predators; movement thus influences survival and reproduction, and ultimately determines fitness. Precise description of movement and understanding of spatial and temporal patterns as well as relationships with intrinsic and extrinsic factors is important both for theoretical and applied reasons. We applied hidden semi-Markov models (HSMM) to hourly geographic positioning system (GPS) location data to understand movement patterns of the endangered Florida panther (Puma concolor coryi) and to discern factors influencing these patterns. Three distinct movement modes were identified: (1) Resting mode, characterized by short step lengths and turning angles around 180(o); (2) Moderately active (or intermediate) mode characterized by intermediate step lengths and variable turning angles, and (3) Traveling mode, characterized by long step lengths and turning angles around 0(o). Males and females, and females with and without kittens, exhibited distinctly different movement patterns. Using the Viterbi algorithm, we show that differences in movement patterns of male and female Florida panthers were a consequence of sex-specific differences in diurnal patterns of state occupancy and sex-specific differences in state-specific movement parameters, whereas the differences between females with and without dependent kittens were caused solely by variation in state occupancy. Our study demonstrates the use of HSMM methodology to precisely describe movement and to dissect differences in movement patterns according to sex, and reproductive status.}, } @article {pmid25251558, year = {2014}, author = {Lei, M and Dong, D and Mu, S and Pan, YH and Zhang, S}, title = {Comparison of brain transcriptome of the greater horseshoe bats (Rhinolophus ferrumequinum) in active and torpid episodes.}, journal = {PloS one}, volume = {9}, number = {9}, pages = {e107746}, pmid = {25251558}, issn = {1932-6203}, mesh = {Adaptation, Physiological/genetics ; Animals ; Brain/*metabolism ; Chiroptera/*genetics ; Gene Expression Profiling/methods ; Gene Ontology ; Hibernation/*genetics ; Seasons ; Sequence Analysis, RNA/methods ; *Transcriptome ; }, abstract = {Hibernation is an energy-saving strategy which is widely adopted by heterothermic mammals to survive in the harsh environment. The greater horseshoe bat (Rhinolophus ferrumequinum) can hibernate for a long period in the hibernation season. However, the global gene expression changes between hibernation and non-hibernation season in the greater horseshoe bat remain largely unknown. We herein reported a comprehensive survey of differential gene expression in the brain between winter hibernating and summer active greater horseshoe bats using next-generation sequencing technology. A total of 90,314,174 reads were generated and we identified 1,573 differentially expressed genes between active and torpid states. Interestingly, we found that differentially expressed genes are over-represented in some GO categories (such as metabolic suppression, cellular stress responses and oxidative stress), which suggests neuroprotective strategies might play an important role in hibernation control mechanisms. Our results determined to what extent the brain tissue of the greater horseshoe bats differ in gene expression between summer active and winter hibernating states and provided comprehensive insights into the adaptive mechanisms of bat hibernation.}, } @article {pmid25251477, year = {2015}, author = {Smoot, E and Haneuse, S}, title = {On the analysis of hybrid designs that combine group- and individual-level data.}, journal = {Biometrics}, volume = {71}, number = {1}, pages = {227-236}, pmid = {25251477}, issn = {1541-0420}, support = {R01 CA125801-01/CA/NCI NIH HHS/United States ; R35 CA197449/CA/NCI NIH HHS/United States ; T32 ES007142/ES/NIEHS NIH HHS/United States ; R01 CA125081/CA/NCI NIH HHS/United States ; T32 A1007358//PHS HHS/United States ; P01 CA134294/CA/NCI NIH HHS/United States ; }, mesh = {Biometry/*methods ; *Birth Rate ; Computer Simulation ; *Data Interpretation, Statistical ; *Epidemiologic Research Design ; Humans ; Infant, Newborn ; *Models, Statistical ; North Carolina ; Reproducibility of Results ; Sensitivity and Specificity ; }, abstract = {Ecological studies that make use of data on groups of individuals, rather than on the individuals themselves, are subject to numerous biases that cannot be resolved without some individual-level data. In the context of a rare outcome, the hybrid design for ecological inference efficiently combines group-level data with individual-level case-control data. Unfortunately, except in relatively simple settings, use of the design in practice is limited since evaluation of the hybrid likelihood is computationally prohibitively expensive. In this article we first propose and develop an alternative representation of the hybrid likelihood. Second, based on this new representation, a series of approximations are proposed that drastically reduce computational burden. A comprehensive simulation shows that, in a broad range of scenarios, estimators based on the approximate hybrid likelihood exhibit the same operating characteristics as the exact hybrid likelihood, without any penalty in terms of increased bias or reduced efficiency. Third, in settings where the approximations may not hold, a pragmatic estimation and inference strategy is developed that uses the approximate form for some likelihood contributions and the exact form for others. The strategy gives researchers the ability to balance computational tractability with accuracy in their own settings. Finally, as a by-product of the development, we provide the first explicit characterization of the hybrid aggregate data design which combines data from an aggregate data study (Prentice and Sheppard, 1995, Biometrika 82, 113-125) with case-control samples. The methods are illustrated using data from North Carolina on births between 2007 and 2009.}, } @article {pmid25250372, year = {2014}, author = {Yan, W and Jiajin, L and Yun, Z}, title = {A multianalyzer machine learning model for marine heterogeneous data schema mapping.}, journal = {TheScientificWorldJournal}, volume = {2014}, number = {}, pages = {248467}, pmid = {25250372}, issn = {1537-744X}, mesh = {*Artificial Intelligence ; *Databases, Factual/statistics & numerical data ; *Marine Biology/statistics & numerical data ; *Models, Theoretical ; }, abstract = {The main challenges that marine heterogeneous data integration faces are the problem of accurate schema mapping between heterogeneous data sources. In order to improve the schema mapping efficiency and get more accurate learning results, this paper proposes a heterogeneous data schema mapping method basing on multianalyzer machine learning model. The multianalyzer analysis the learning results comprehensively, and a fuzzy comprehensive evaluation system is introduced for output results' evaluation and multi factor quantitative judging. Finally, the data mapping comparison experiment on the East China Sea observing data confirms the effectiveness of the model and shows multianalyzer's obvious improvement of mapping error rate.}, } @article {pmid25249477, year = {2014}, author = {Lv, FH and Agha, S and Kantanen, J and Colli, L and Stucki, S and Kijas, JW and Joost, S and Li, MH and Ajmone Marsan, P}, title = {Adaptations to climate-mediated selective pressures in sheep.}, journal = {Molecular biology and evolution}, volume = {31}, number = {12}, pages = {3324-3343}, pmid = {25249477}, issn = {1537-1719}, mesh = {Acclimatization/genetics ; Animals ; Breeding ; Climate ; Evolution, Molecular ; Gene Frequency ; Gene Ontology ; Genes ; Haplotypes ; Linkage Disequilibrium ; Models, Genetic ; *Polymorphism, Single Nucleotide ; Selection, Genetic ; Sheep, Domestic/*genetics ; Species Specificity ; }, abstract = {Following domestication, sheep (Ovis aries) have become essential farmed animals across the world through adaptation to a diverse range of environments and varied production systems. Climate-mediated selective pressure has shaped phenotypic variation and has left genetic "footprints" in the genome of breeds raised in different agroecological zones. Unlike numerous studies that have searched for evidence of selection using only population genetics data, here, we conducted an integrated coanalysis of environmental data with single nucleotide polymorphism (SNP) variation. By examining 49,034 SNPs from 32 old, autochthonous sheep breeds that are adapted to a spectrum of different regional climates, we identified 230 SNPs with evidence for selection that is likely due to climate-mediated pressure. Among them, 189 (82%) showed significant correlation (P ≤ 0.05) between allele frequency and climatic variables in a larger set of native populations from a worldwide range of geographic areas and climates. Gene ontology analysis of genes colocated with significant SNPs identified 17 candidates related to GTPase regulator and peptide receptor activities in the biological processes of energy metabolism and endocrine and autoimmune regulation. We also observed high linkage disequilibrium and significant extended haplotype homozygosity for the core haplotype TBC1D12-CH1 of TBC1D12. The global frequency distribution of the core haplotype and allele OAR22_18929579-A showed an apparent geographic pattern and significant (P ≤ 0.05) correlations with climatic variation. Our results imply that adaptations to local climates have shaped the spatial distribution of some variants that are candidates to underpin adaptive variation in sheep.}, } @article {pmid25247998, year = {2014}, author = {Vieira, WL and Vieira, KS and Nóbrega, RP and Montenegro, PF and Pereira Filho, GA and Santana, GG and Alves, RR and Almeida, WO and Vasconcellos, A}, title = {Species richness and evidence of random patterns in assemblages of South American Titanosauria during the Late Cretaceous (Campanian-Maastrichtian).}, journal = {PloS one}, volume = {9}, number = {9}, pages = {e108307}, pmid = {25247998}, issn = {1932-6203}, mesh = {Animals ; *Biota ; Body Size ; Competitive Behavior ; Databases, Factual ; Dinosaurs/anatomy & histology/*classification ; Ecosystem ; Evolution, Planetary ; Fossils ; Phylogeny ; Selection, Genetic ; South America ; Species Specificity ; Statistics, Nonparametric ; }, abstract = {The Titanosauria were much diversified during the Late Cretaceous, but paleobiological information concerning these sauropods continues to be scarce and no studies have been conducted utilizing modern methods of community analysis to infer possible structural patterns of extinct assemblages. The present study sought to estimate species richness and to investigate the existence of structures in assemblages of the South American Titanosauria during the Late Cretaceous. Estimates of species richness were made utilizing a nonparametric estimator and null models of species co-occurrences and overlapping body sizes were applied to determine the occurrence of structuring in this assemblages. The high estimate of species richness (n = 57) may have been influenced by ecological processes associated with extinction events of sauropod groups and with the structures of the habitats that provided abundant support to the maintenance of large numbers of species. The pseudocommunity analysis did not differ from that expected by chance, indicating the lack of structure in these assemblages. It is possible that these processes originated from phylogenetic inertia, associated with the occurrence of stabilized selection. Additionally, stochastic extinction events and historical factors may also have influenced the formation of the titanosaurian assemblages, in detriment to ecological factors during the Late Cretaceous. However, diagenetic and biostratinomic processes, influenced by the nature of the sedimentary paleoenvironment, could have rendered a random arrangement that would make assemblage structure undetectable.}, } @article {pmid25247299, year = {2014}, author = {Rossi, JP and Nardin, M and Godefroid, M and Ruiz-Diaz, M and Sergent, AS and Martinez-Meier, A and Pâques, L and Rozenberg, P}, title = {Dissecting the space-time structure of tree-ring datasets using the partial triadic analysis.}, journal = {PloS one}, volume = {9}, number = {9}, pages = {e108332}, pmid = {25247299}, issn = {1932-6203}, mesh = {*Chronology as Topic ; *Datasets as Topic ; France ; Time Factors ; Trees/*growth & development/ultrastructure ; }, abstract = {Tree-ring datasets are used in a variety of circumstances, including archeology, climatology, forest ecology, and wood technology. These data are based on microdensity profiles and consist of a set of tree-ring descriptors, such as ring width or early/latewood density, measured for a set of individual trees. Because successive rings correspond to successive years, the resulting dataset is a ring variables × trees × time datacube. Multivariate statistical analyses, such as principal component analysis, have been widely used for extracting worthwhile information from ring datasets, but they typically address two-way matrices, such as ring variables × trees or ring variables × time. Here, we explore the potential of the partial triadic analysis (PTA), a multivariate method dedicated to the analysis of three-way datasets, to apprehend the space-time structure of tree-ring datasets. We analyzed a set of 11 tree-ring descriptors measured in 149 georeferenced individuals of European larch (Larix decidua Miller) during the period of 1967-2007. The processing of densitometry profiles led to a set of ring descriptors for each tree and for each year from 1967-2007. The resulting three-way data table was subjected to two distinct analyses in order to explore i) the temporal evolution of spatial structures and ii) the spatial structure of temporal dynamics. We report the presence of a spatial structure common to the different years, highlighting the inter-individual variability of the ring descriptors at the stand scale. We found a temporal trajectory common to the trees that could be separated into a high and low frequency signal, corresponding to inter-annual variations possibly related to defoliation events and a long-term trend possibly related to climate change. We conclude that PTA is a powerful tool to unravel and hierarchize the different sources of variation within tree-ring datasets.}, } @article {pmid25242526, year = {2015}, author = {Tumburu, L and Andersen, CP and Rygiewicz, PT and Reichman, JR}, title = {Phenotypic and genomic responses to titanium dioxide and cerium oxide nanoparticles in Arabidopsis germinants.}, journal = {Environmental toxicology and chemistry}, volume = {34}, number = {1}, pages = {70-83}, doi = {10.1002/etc.2756}, pmid = {25242526}, issn = {1552-8618}, mesh = {Arabidopsis/*drug effects/genetics/growth & development ; Cerium/*toxicity ; Environmental Pollutants/*toxicity ; Gene Ontology ; *Genome, Plant ; Nanoparticles/*toxicity ; Phenotype ; Seeds/drug effects/genetics/growth & development ; Titanium/*toxicity ; }, abstract = {The effects of exposure to nanoparticles of titanium dioxide (nano-titanium) and cerium oxide (nano-cerium) on gene expression and growth in Arabidopsis thaliana germinants were studied by using microarrays and quantitative real-time polymerase chain reaction (qPCR), and by evaluating germinant phenotypic plasticity. Exposure to 12 d of either nano-titania or nano-ceria altered the regulation of 204 and 142 genes, respectively. Genes induced by the nanoparticles mainly include ontology groups annotated as stimuli responsive, including both abiotic (oxidative stress, salt stress, water transport) and biotic (respiratory burst as a defense against pathogens) stimuli. Further analysis of the differentially expressed genes indicates that both nanoparticles affected a range of metabolic processes (deoxyribonucleic acid [DNA] metabolism, hormone metabolism, tetrapyrrole synthesis, and photosynthesis). Individual exposures to the nanoparticles increased percentages of seeds with emergent radicles, early development of hypocotyls and cotyledons, and those with fully grown leaves. Although there were distinct differences between the nanoparticles in their affect on molecular mechanisms attributable to enhancing germinant growth, both particles altered similar suites of genes related to various pathways and processes related to enhanced growth.}, } @article {pmid25233196, year = {2014}, author = {Libby, E and Ratcliff, W and Travisano, M and Kerr, B}, title = {Geometry shapes evolution of early multicellularity.}, journal = {PLoS computational biology}, volume = {10}, number = {9}, pages = {e1003803}, pmid = {25233196}, issn = {1553-7358}, mesh = {Apoptosis ; *Biological Evolution ; Cell Physiological Phenomena/*physiology ; Computational Biology ; *Models, Biological ; Yeasts/cytology/physiology ; }, abstract = {Organisms have increased in complexity through a series of major evolutionary transitions, in which formerly autonomous entities become parts of a novel higher-level entity. One intriguing feature of the higher-level entity after some major transitions is a division of reproductive labor among its lower-level units in which reproduction is the sole responsibility of a subset of units. Although it can have clear benefits once established, it is unknown how such reproductive division of labor originates. We consider a recent evolution experiment on the yeast Saccharomyces cerevisiae as a unique platform to address the issue of reproductive differentiation during an evolutionary transition in individuality. In the experiment, independent yeast lineages evolved a multicellular "snowflake-like" cluster formed in response to gravity selection. Shortly after the evolution of clusters, the yeast evolved higher rates of cell death. While cell death enables clusters to split apart and form new groups, it also reduces their performance in the face of gravity selection. To understand the selective value of increased cell death, we create a mathematical model of the cellular arrangement within snowflake yeast clusters. The model reveals that the mechanism of cell death and the geometry of the snowflake interact in complex, evolutionarily important ways. We find that the organization of snowflake yeast imposes powerful limitations on the available space for new cell growth. By dying more frequently, cells in clusters avoid encountering space limitations, and, paradoxically, reach higher numbers. In addition, selection for particular group sizes can explain the increased rate of apoptosis both in terms of total cell number and total numbers of collectives. Thus, by considering the geometry of a primitive multicellular organism we can gain insight into the initial emergence of reproductive division of labor during an evolutionary transition in individuality.}, } @article {pmid25231182, year = {2015}, author = {Bouktila, D and Khalfallah, Y and Habachi-Houimli, Y and Mezghani-Khemakhem, M and Makni, M and Makni, H}, title = {Full-genome identification and characterization of NBS-encoding disease resistance genes in wheat.}, journal = {Molecular genetics and genomics : MGG}, volume = {290}, number = {1}, pages = {257-271}, pmid = {25231182}, issn = {1617-4623}, mesh = {Binding Sites ; Chromosomes, Plant ; Conserved Sequence/genetics ; Data Mining ; Disease Resistance/*genetics ; *Genes, Plant ; Models, Genetic ; Nucleotides/*metabolism ; Plant Diseases/*genetics/*immunology ; Sequence Homology, Amino Acid ; Triticum/*genetics/*immunology ; }, abstract = {Host resistance is the most economical, effective and ecologically sustainable method of controlling diseases in crop plants. In bread wheat, despite the high number of resistance loci that have been cataloged to date, only few have been cloned, underlying the need for genomics-guided investigations capable of providing a prompt and acute knowledge on the identity of effective resistance genes that can be used in breeding programs. Proteins with a nucleotide-binding site (NBS) encoded by the major plant disease resistance (R) genes play an important role in the responses of plants to various pathogens. In this study, a comprehensive analysis of NBS-encoding genes within the whole wheat genome was performed, and the genome scale characterization of this gene family was established. From the recently published wheat genome sequence, we used a data mining and automatic prediction pipeline to identify 580 complete ORF candidate NBS-encoding genes and 1,099 partial-ORF ones. Among complete gene models, 464 were longer than 200 aa, among them 436 had less than 70 % of sequence identity to each other. This gene models set was deeply characterized. (1) First, we have analyzed domain architecture and identified, in addition to typical domain combinations, the presence of particular domains like signal peptides, zinc fingers, kinases, heavy-metal-associated and WRKY DNA-binding domains. (2) Functional and expression annotation via homology searches in protein and transcript databases, based on sufficient criteria, enabled identifying similar proteins for 60 % of the studied gene models and expression evidence for 13 % of them. (3) Shared orthologous groups were defined using NBS-domain proteins of rice and Brachypodium distachyon. (4) Finally, alignment of the 436 NBS-containing gene models to the full set of scaffolds from the IWGSC's wheat chromosome survey sequence enabled high-stringence anchoring to chromosome arms. The distribution of the R genes was found balanced on the three wheat sub-genomes. In contrast, at chromosome scale, 50 % of members of this gene family were localized on 6 of the 21 wheat chromosomes and ~22 % of them were localized on homeologous group 7. The results of this study provide a detailed analysis of the largest family of plant disease resistance genes in allohexaploid wheat. Some structural traits reported had not been previously identified and the genome-derived data were confronted with those stored in databases outlining the functional specialization of members of this family. The large reservoir of NBS-type genes presented and discussed will, firstly, form an important framework for marker-assisted improvement of resistance in wheat, and, secondly, open up new perspectives for a better understanding of the evolution dynamics of this gene family in grass species and in polyploid systems.}, } @article {pmid25230133, year = {2014}, author = {Huang, X and Huang, Y and Yang, Y and Wei, S and Qin, Q}, title = {Involvement of fish signal transducer and activator of transcription 3 (STAT3) in SGIV replication and virus induced paraptosis.}, journal = {Fish & shellfish immunology}, volume = {41}, number = {2}, pages = {308-316}, doi = {10.1016/j.fsi.2014.09.011}, pmid = {25230133}, issn = {1095-9947}, mesh = {Amino Acid Sequence ; Aminosalicylic Acids ; Animals ; Base Sequence ; Benzenesulfonates ; Cell Death/*physiology ; Cloning, Molecular ; Cluster Analysis ; Computational Biology ; DNA Primers/genetics ; DNA Virus Infections/metabolism/*veterinary ; Fish Diseases/metabolism/*virology ; Fluorescence ; Gene Components ; Iridoviridae/*physiology ; Molecular Sequence Data ; *Perciformes ; Phosphorylation ; Phylogeny ; Protein Structure, Tertiary ; Real-Time Polymerase Chain Reaction ; STAT3 Transcription Factor/*metabolism ; Sequence Alignment ; Sequence Analysis, DNA/veterinary ; Sequence Homology ; Spleen/metabolism ; Virus Replication/*physiology ; }, abstract = {Signal transducer and activator of transcription 3 (STAT3) is an important transcription factor which plays crucial roles in immune regulation, inflammation, cell proliferation, transformation, and other physiological processes of the organism. In this study, a novel STAT3 gene from orange spotted grouper (Ec-STAT3) was cloned and characterized. Bioinformatic analysis revealed that full-length of Ec-STAT3 was 3105-bp long and contained a 280-bp 5'UTR, a 470-bp 3'UTR, and a 2355-bp open reading frame (ORF) that encoded a 784-amino acid peptide. The deduced protein of Ec-STAT3 showed 98% identity to that of turbot (Scophthalmus maximus). Amino acid alignment showed that Ec-STAT3 contained four conserved domains, including a protein interaction domain, a coiled coil domain, a DNA binding domain, and an SH2 domain. Quantitative real-time PCR analysis showed that the highest expression level was detected in the liver, followed by skin and spleen. After injection with Singapore grouper iridovirus (SGIV), the transcript of Ec-STAT3 in spleen was increased significantly. To further explore the function of Ec-STAT3, we investigated the roles of Ec-STAT3 in SGIV infection in vitro. Immune fluorescence analysis indicated that SGIV infection altered the distribution of phosphorylated Ec-STAT3 in nucleus, and a small part of phosphorylated Ec-STAT3 was associated with virus assembly sites, suggesting that Ec-STAT3 might be important for SGIV infection. Using STAT3 specific inhibitor, S3I-201, we found that inhibition of Ec-STAT3 activation decreased the SGIV replication significantly. Moreover, inhibition of Ec-STAT3 activation obviously altered SGIV infection induced cell cycle arrest and the expression of pro-survival genes, including Bcl-2, Bcl-xL and Bax inhibitor. Together, our results firstly demonstrated the critical roles of fish STAT3 in DNA virus replication and virus induced paraptosis, but also provided new insights into the mechanism of iridovirus pathogenesis.}, } @article {pmid25229745, year = {2014}, author = {D'Alessandro, A and Amelio, I and Berkers, CR and Antonov, A and Vousden, KH and Melino, G and Zolla, L}, title = {Metabolic effect of TAp63α: enhanced glycolysis and pentose phosphate pathway, resulting in increased antioxidant defense.}, journal = {Oncotarget}, volume = {5}, number = {17}, pages = {7722-7733}, pmid = {25229745}, issn = {1949-2553}, support = {18274/CRUK_/Cancer Research UK/United Kingdom ; GGP09133/TI_/Telethon/Italy ; MC_U132670600/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Cell Line, Tumor ; Computational Biology ; Flow Cytometry ; Glycolysis/*physiology ; Humans ; Immunoblotting ; Metabolomics ; Neoplasms/*metabolism ; Oxidative Stress/physiology ; Pentose Phosphate Pathway/*physiology ; Transcription Factors/*metabolism ; Tumor Suppressor Proteins/*metabolism ; }, abstract = {TAp63α is a member of the p53 family, which plays a central role in epithelial cancers. Recently, a role has emerged for p53 family members in cancer metabolic modulation. In order to assess whether TAp63α plays a role in cancer metabolism, we exploited p53-null osteosarcoma Tet-On Saos-2 cells, in which the expression of TAp63α was dependent on doxycycline supplementation to the medium. Metabolomics labeling experiments were performed by incubating the cells in 13C-glucose or 13C15N-glutamine-labeled culture media, as to monitor metabolic fluxes upon induced expression of TAp63α. Induced expression of TAp63α resulted in cell cycle arrest at the G1 phase. From a metabolic standpoint, expression of Tap63α promoted glycolysis and the pentose phosphate pathway, which was uncoupled from nucleotide biosynthesis, albeit prevented oxidative stress in the form of oxidized glutathione. Double 13C-glucose and 13C15N-glutamine metabolic labeling confirmed that induced expression of TAp63α corresponded to a decreased flux of pyruvate to the Krebs cycle and decreased utilization of glutamine for catabolic purposes in the TCA cycle. Results were not conclusive in relation to anabolic utilization of labeled glutamine, since it is unclear to what extent the observed minor TAp63α-dependent increases of glutamine-derived labeling in palmitate could be tied to increased rates of reductive carboxylation and de novo synthesis of fatty acids. Finally, bioinformatics elaborations highlighted a link between patient survival rates and the co-expression of p63 and rate limiting enzymes of the pentose phosphate pathway, G6PD and PGD.}, } @article {pmid25225412, year = {2014}, author = {Reich, PB and Luo, Y and Bradford, JB and Poorter, H and Perry, CH and Oleksyn, J}, title = {Temperature drives global patterns in forest biomass distribution in leaves, stems, and roots.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {111}, number = {38}, pages = {13721-13726}, pmid = {25225412}, issn = {1091-6490}, mesh = {*Biomass ; Carbon/metabolism ; *Climate Change ; Databases, Factual ; *Forests ; Hot Temperature ; Plant Leaves/*growth & development ; Plant Roots/*growth & development ; Plant Stems/*growth & development ; }, abstract = {Whether the fraction of total forest biomass distributed in roots, stems, or leaves varies systematically across geographic gradients remains unknown despite its importance for understanding forest ecology and modeling global carbon cycles. It has been hypothesized that plants should maintain proportionally more biomass in the organ that acquires the most limiting resource. Accordingly, we hypothesize greater biomass distribution in roots and less in stems and foliage in increasingly arid climates and in colder environments at high latitudes. Such a strategy would increase uptake of soil water in dry conditions and of soil nutrients in cold soils, where they are at low supply and are less mobile. We use a large global biomass dataset (>6,200 forests from 61 countries, across a 40 °C gradient in mean annual temperature) to address these questions. Climate metrics involving temperature were better predictors of biomass partitioning than those involving moisture availability, because, surprisingly, fractional distribution of biomass to roots or foliage was unrelated to aridity. In contrast, in increasingly cold climates, the proportion of total forest biomass in roots was greater and in foliage was smaller for both angiosperm and gymnosperm forests. These findings support hypotheses about adaptive strategies of forest trees to temperature and provide biogeographically explicit relationships to improve ecosystem and earth system models. They also will allow, for the first time to our knowledge, representations of root carbon pools that consider biogeographic differences, which are useful for quantifying whole-ecosystem carbon stocks and cycles and for assessing the impact of climate change on forest carbon dynamics.}, } @article {pmid25214513, year = {2014}, author = {Richards, Z and Kostadinov, I and Jones, M and Richard, L and Cargo, M}, title = {Assessing implementation fidelity and adaptation in a community-based childhood obesity prevention intervention.}, journal = {Health education research}, volume = {29}, number = {6}, pages = {918-932}, doi = {10.1093/her/cyu053}, pmid = {25214513}, issn = {1465-3648}, mesh = {Child ; Community Networks/*organization & administration ; Female ; Health Promotion/*organization & administration ; Humans ; Life Style ; Male ; Pediatric Obesity/*prevention & control ; Program Evaluation ; South Australia ; }, abstract = {Little research has assessed the fidelity, adaptation or integrity of activities implemented within community-based obesity prevention initiatives. To address this gap, a mixed-method process evaluation was undertaken in the context of the South Australian Obesity Prevention and Lifestyle (OPAL) initiative. An ecological coding procedure assessed fidelity and adaptation of activity settings, targets and strategies implemented in the second year of four communities. Implementation integrity reflected fidelity and adaptation to local context, whereas efforts resulting in significant deviations from the original plan were deemed to lack fidelity and integrity. Staff implemented 284 strategies in 205 projects. Results show that 68.3 and 2.1% of strategies were implemented with fidelity or adapted, respectively. Overall, 70.4% of all strategies were implemented with integrity. Staff experienced barriers with 29.6% of strategies. Chi-square analyses show statistically significant associations between implementation integrity and strategy type, intervention and behavioural targets. These relationships are weak to modest. The strongest relationship was found between implementation integrity and proximal target. Staff experienced implementation barriers at the coalition, policy, organization, interpersonal and community levels. The greatest range of barriers was encountered working with organizations. To overcome these barriers, staff took greater ownership, invested more time, persisted and allocated more financial resources.}, } @article {pmid25214071, year = {2014}, author = {Hilde, T and Paterson, R}, title = {Integrating ecosystem services analysis into scenario planning practice: accounting for street tree benefits with i-Tree valuation in Central Texas.}, journal = {Journal of environmental management}, volume = {146}, number = {}, pages = {524-534}, doi = {10.1016/j.jenvman.2014.05.039}, pmid = {25214071}, issn = {1095-8630}, mesh = {*City Planning ; Conservation of Natural Resources ; Decision Making ; *Ecosystem ; Environmental Monitoring ; Forecasting/*methods ; Geographic Information Systems ; *Models, Theoretical ; Residence Characteristics ; *Software ; Texas ; *Trees ; United States ; }, abstract = {Scenario planning continues to gain momentum in the United States as an effective process for building consensus on long-range community plans and creating regional visions for the future. However, efforts to integrate more sophisticated information into the analytical framework to help identify important ecosystem services have lagged in practice. This is problematic because understanding the tradeoffs of land consumption patterns on ecological integrity is central to mitigating the environmental degradation caused by land use change and new development. In this paper we describe how an ecosystem services valuation model, i-Tree, was integrated into a mainstream scenario planning software tool, Envision Tomorrow, to assess the benefits of public street trees for alternative future development scenarios. The tool is then applied to development scenarios from the City of Hutto, TX, a Central Texas Sustainable Places Project demonstration community. The integrated tool represents a methodological improvement for scenario planning practice, offers a way to incorporate ecosystem services analysis into mainstream planning processes, and serves as an example of how open source software tools can expand the range of issues available for community and regional planning consideration, even in cases where community resources are limited. The tool also offers room for future improvements; feasible options include canopy analysis of various future land use typologies, as well as a generalized street tree model for broader U.S. application.}, } @article {pmid25211603, year = {2014}, author = {Vincenzi, S and Mangel, M and Crivelli, AJ and Munch, S and Skaug, HJ}, title = {Determining individual variation in growth and its implication for life-history and population processes using the empirical Bayes method.}, journal = {PLoS computational biology}, volume = {10}, number = {9}, pages = {e1003828}, pmid = {25211603}, issn = {1553-7358}, mesh = {Animals ; *Bayes Theorem ; Body Size ; Computational Biology/*methods ; *Growth and Development ; *Models, Biological ; Models, Statistical ; Trout/growth & development ; }, abstract = {The differences in demographic and life-history processes between organisms living in the same population have important consequences for ecological and evolutionary dynamics. Modern statistical and computational methods allow the investigation of individual and shared (among homogeneous groups) determinants of the observed variation in growth. We use an Empirical Bayes approach to estimate individual and shared variation in somatic growth using a von Bertalanffy growth model with random effects. To illustrate the power and generality of the method, we consider two populations of marble trout Salmo marmoratus living in Slovenian streams, where individually tagged fish have been sampled for more than 15 years. We use year-of-birth cohort, population density during the first year of life, and individual random effects as potential predictors of the von Bertalanffy growth function's parameters k (rate of growth) and L∞ (asymptotic size). Our results showed that size ranks were largely maintained throughout marble trout lifetime in both populations. According to the Akaike Information Criterion (AIC), the best models showed different growth patterns for year-of-birth cohorts as well as the existence of substantial individual variation in growth trajectories after accounting for the cohort effect. For both populations, models including density during the first year of life showed that growth tended to decrease with increasing population density early in life. Model validation showed that predictions of individual growth trajectories using the random-effects model were more accurate than predictions based on mean size-at-age of fish.}, } @article {pmid25211117, year = {2014}, author = {Alami, A and Eslami, A and Hashemi, SA}, title = {The query of suitable areas for plantation and development of Taxus baccata L species by using GIS in northern Iran.}, journal = {Anais da Academia Brasileira de Ciencias}, volume = {86}, number = {3}, pages = {1497-1505}, doi = {10.1590/0001-3765201420130107}, pmid = {25211117}, issn = {1678-2690}, mesh = {Agriculture/*methods ; *Geographic Information Systems ; Iran ; Models, Theoretical ; Taxus/classification/*growth & development ; }, abstract = {Taxus baccata is a native species to the Caspian forests and is considered as the identification of these forests by some resources. The aim of this study was to understand the ecological characteristics of T. baccata in order to find suitable areas for its plantation in the Pone Aram preserve of Golestan province. Therefore, Multi-Criteria Evaluation (MCE) methods based on Analytical Hierarchy Process (AHP) were used. In this process at first the needed and effective natural indexes were used as 10 parameters. Then the final map of suitable areas for T. baccata plantation were produced based on Bolian and MCE models. According to the results, in Bolian method about 6218 ha of the total area of the study site (30554 ha) were estimated as suitable and semi suitable and 24336 ha were estimated as unsuitable for MCE model showed that about 2482 ha of the whole 30554 ha area of the study site is adequate for T. baccata plantation and 6181 ha is not adequate for T. baccata plantation. Regarding the results of the MCE and Bolian methods it has been concluded that for dynamic ecological parameters in delineation of suitable areas for T. baccata plantation the MCE weighting is more appropriate than Bolian. Using the results of this investigation it is possible to adequate areas for the presence of T. baccata and to execute a plan in order to facilitate the plantation of T. baccata in northern forests of Iran (watershed 88).}, } @article {pmid25209798, year = {2014}, author = {Carbone, L and Harris, RA and Gnerre, S and Veeramah, KR and Lorente-Galdos, B and Huddleston, J and Meyer, TJ and Herrero, J and Roos, C and Aken, B and Anaclerio, F and Archidiacono, N and Baker, C and Barrell, D and Batzer, MA and Beal, K and Blancher, A and Bohrson, CL and Brameier, M and Campbell, MS and Capozzi, O and Casola, C and Chiatante, G and Cree, A and Damert, A and de Jong, PJ and Dumas, L and Fernandez-Callejo, M and Flicek, P and Fuchs, NV and Gut, I and Gut, M and Hahn, MW and Hernandez-Rodriguez, J and Hillier, LW and Hubley, R and Ianc, B and Izsvák, Z and Jablonski, NG and Johnstone, LM and Karimpour-Fard, A and Konkel, MK and Kostka, D and Lazar, NH and Lee, SL and Lewis, LR and Liu, Y and Locke, DP and Mallick, S and Mendez, FL and Muffato, M and Nazareth, LV and Nevonen, KA and O'Bleness, M and Ochis, C and Odom, DT and Pollard, KS and Quilez, J and Reich, D and Rocchi, M and Schumann, GG and Searle, S and Sikela, JM and Skollar, G and Smit, A and Sonmez, K and ten Hallers, B and Terhune, E and Thomas, GW and Ullmer, B and Ventura, M and Walker, JA and Wall, JD and Walter, L and Ward, MC and Wheelan, SJ and Whelan, CW and White, S and Wilhelm, LJ and Woerner, AE and Yandell, M and Zhu, B and Hammer, MF and Marques-Bonet, T and Eichler, EE and Fulton, L and Fronick, C and Muzny, DM and Warren, WC and Worley, KC and Rogers, J and Wilson, RK and Gibbs, RA}, title = {Gibbon genome and the fast karyotype evolution of small apes.}, journal = {Nature}, volume = {513}, number = {7517}, pages = {195-201}, pmid = {25209798}, issn = {1476-4687}, support = {R01 MH081203/MH/NIMH NIH HHS/United States ; P51 RR000163/RR/NCRR NIH HHS/United States ; U41 HG007497/HG/NHGRI NIH HHS/United States ; 260372/ERC_/European Research Council/International ; /HHMI/Howard Hughes Medical Institute/United States ; U54 HG003273/HG/NHGRI NIH HHS/United States ; U41 HG007234/HG/NHGRI NIH HHS/United States ; R01 HG002939/HG/NHGRI NIH HHS/United States ; R01 GM59290/GM/NIGMS NIH HHS/United States ; U54 HG003079/HG/NHGRI NIH HHS/United States ; T15 LM007088/LM/NLM NIH HHS/United States ; R01 HG002385/HG/NHGRI NIH HHS/United States ; WT098051/WT_/Wellcome Trust/United Kingdom ; U41 HG007497-01/HG/NHGRI NIH HHS/United States ; U54HG003273/HG/NHGRI NIH HHS/United States ; R01 HG005226/HG/NHGRI NIH HHS/United States ; P30CA006973/CA/NCI NIH HHS/United States ; P30 CA006973/CA/NCI NIH HHS/United States ; P30 AA019355/AA/NIAAA NIH HHS/United States ; HG002385/HG/NHGRI NIH HHS/United States ; R01 GM059290/GM/NIGMS NIH HHS/United States ; 095908//Wellcome Trust/United Kingdom ; 15603/CRUK_/Cancer Research UK/United Kingdom ; //Wellcome Trust/United Kingdom ; U41HG007234/HG/NHGRI NIH HHS/United States ; R01_HG005226/HG/NHGRI NIH HHS/United States ; }, mesh = {Animals ; Evolution, Molecular ; Genome/*genetics ; Hominidae/classification/genetics ; Humans ; Hylobates/*classification/*genetics ; *Karyotype ; Molecular Sequence Data ; *Phylogeny ; Retroelements/genetics ; Selection, Genetic ; Transcription Termination, Genetic ; }, abstract = {Gibbons are small arboreal apes that display an accelerated rate of evolutionary chromosomal rearrangement and occupy a key node in the primate phylogeny between Old World monkeys and great apes. Here we present the assembly and analysis of a northern white-cheeked gibbon (Nomascus leucogenys) genome. We describe the propensity for a gibbon-specific retrotransposon (LAVA) to insert into chromosome segregation genes and alter transcription by providing a premature termination site, suggesting a possible molecular mechanism for the genome plasticity of the gibbon lineage. We further show that the gibbon genera (Nomascus, Hylobates, Hoolock and Symphalangus) experienced a near-instantaneous radiation ∼5 million years ago, coincident with major geographical changes in southeast Asia that caused cycles of habitat compression and expansion. Finally, we identify signatures of positive selection in genes important for forelimb development (TBX5) and connective tissues (COL1A1) that may have been involved in the adaptation of gibbons to their arboreal habitat.}, } @article {pmid25209572, year = {2015}, author = {Schmitt, CA and Di Fiore, A}, title = {Predation risk sensitivity and the spatial organization of primate groups: a case study using GIS in lowland Woolly Monkeys (Lagothrix lagotricha poeppigii).}, journal = {American journal of physical anthropology}, volume = {156}, number = {1}, pages = {158-165}, doi = {10.1002/ajpa.22612}, pmid = {25209572}, issn = {1096-8644}, mesh = {Animals ; Atelinae/*physiology ; Female ; Geographic Information Systems ; Male ; Risk ; *Social Behavior ; Spatial Behavior/*physiology ; }, abstract = {Predation risk is thought to be a potent force influencing intragroup cohesion, and the level of risk experienced by an individual is expected to vary with both group size and spatial position within a group. Smaller-bodied and less-experienced individuals are presumed to be more vulnerable to predators, suggesting that within-group spatial organization should show size- and age-dependent patterns in predator sensitive positioning. However, such effects have been difficult to evaluate for arboreal primates living in large groups. We conducted a preliminary study using a novel, spatially explicit method of assessing group spatial organization using GIS data in two groups of wild lowland Woolly monkeys, in which one group had a membership roughly twice as large as the second. In the larger group, group spread was more diffuse and large adult males were more frequently on the outskirts of the group than other age/sex classes, while immatures and females with dependents were more often in the center. Leaf cover around an individual-presumed to index an animal's perception of risk-increased significantly with distance from the group center for all immatures, although they were typically under lower leaf cover than adults; the number of groupmates in proximity also had an effect, but nearest neighbor distance did not. These differences were not detectable in the smaller group. This preliminary study suggests that thorough studies of spatial organization and predation risk sensitivity in arboreal primates are possible and could yield valuable information on how gregarious individuals offset ecological risks through social spacing.}, } @article {pmid25208246, year = {2014}, author = {Ensing, EP and Ciuti, S and de Wijs, FA and Lentferink, DH and Ten Hoedt, A and Boyce, MS and Hut, RA}, title = {GPS based daily activity patterns in European red deer and North American elk (Cervus elaphus): indication for a weak circadian clock in ungulates.}, journal = {PloS one}, volume = {9}, number = {9}, pages = {e106997}, pmid = {25208246}, issn = {1932-6203}, mesh = {*Activities of Daily Living ; Animals ; *Circadian Clocks ; Deer/*physiology ; Female ; *Geographic Information Systems ; Male ; Motor Activity ; }, abstract = {Long-term tracking using global positioning systems (GPS) is widely used to study vertebrate movement ecology, including fine-scale habitat selection as well as large-scale migrations. These data have the potential to provide much more information about the behavior and ecology of wild vertebrates: here we explore the potential of using GPS datasets to assess timing of activity in a chronobiological context. We compared two different populations of deer (Cervus elaphus), one in the Netherlands (red deer), the other in Canada (elk). GPS tracking data were used to calculate the speed of the animals as a measure for activity to deduce unbiased daily activity rhythms over prolonged periods of time. Speed proved a valid measure for activity, this being validated by comparing GPS based activity data with head movements recorded by activity sensors, and the use of GPS locations was effective for generating long term chronobiological data. Deer showed crepuscular activity rhythms with activity peaks at sunrise (the Netherlands) or after sunrise (Canada) and at the end of civil twilight at dusk. The deer in Canada were mostly diurnal while the deer in the Netherlands were mostly nocturnal. On an annual scale, Canadian deer were more active during the summer months while deer in the Netherlands were more active during winter. We suggest that these differences were mainly driven by human disturbance (on a daily scale) and local weather (on an annual scale). In both populations, the crepuscular activity peaks in the morning and evening showed a stable timing relative to dawn and dusk twilight throughout the year, but marked periods of daily a-rhythmicity occurred in the individual records. We suggest that this might indicate that (changes in) light levels around twilight elicit a direct behavioral response while the contribution of an internal circadian timing mechanism might be weak or even absent.}, } @article {pmid25201877, year = {2014}, author = {Pigott, DM and Golding, N and Mylne, A and Huang, Z and Henry, AJ and Weiss, DJ and Brady, OJ and Kraemer, MU and Smith, DL and Moyes, CL and Bhatt, S and Gething, PW and Horby, PW and Bogoch, II and Brownstein, JS and Mekaru, SR and Tatem, AJ and Khan, K and Hay, SI}, title = {Mapping the zoonotic niche of Ebola virus disease in Africa.}, journal = {eLife}, volume = {3}, number = {}, pages = {e04395}, pmid = {25201877}, issn = {2050-084X}, support = {MR/K00669X/1/MRC_/Medical Research Council/United Kingdom ; 095066/WT_/Wellcome Trust/United Kingdom ; R01LM010812/LM/NLM NIH HHS/United States ; /CAPMC/CIHR/Canada ; R01 LM010812/LM/NLM NIH HHS/United States ; U19 AI089674/AI/NIAID NIH HHS/United States ; U19AI089674/AI/NIAID NIH HHS/United States ; /WT_/Wellcome Trust/United Kingdom ; K00669X/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Africa, Central/epidemiology ; Africa, Western/epidemiology ; Aircraft ; Animals ; Chiroptera/*virology ; Disease Outbreaks ; Disease Reservoirs/virology ; Ebolavirus/*physiology ; Geography ; Hemorrhagic Fever, Ebola/epidemiology/transmission/*virology ; Host-Pathogen Interactions ; Humans ; Models, Theoretical ; Primate Diseases/epidemiology/transmission/*virology ; Primates/*virology ; Risk Assessment/statistics & numerical data/trends ; Risk Factors ; Travel ; Zoonoses/epidemiology/*virology ; }, abstract = {Ebola virus disease (EVD) is a complex zoonosis that is highly virulent in humans. The largest recorded outbreak of EVD is ongoing in West Africa, outside of its previously reported and predicted niche. We assembled location data on all recorded zoonotic transmission to humans and Ebola virus infection in bats and primates (1976-2014). Using species distribution models, these occurrence data were paired with environmental covariates to predict a zoonotic transmission niche covering 22 countries across Central and West Africa. Vegetation, elevation, temperature, evapotranspiration, and suspected reservoir bat distributions define this relationship. At-risk areas are inhabited by 22 million people; however, the rarity of human outbreaks emphasises the very low probability of transmission to humans. Increasing population sizes and international connectivity by air since the first detection of EVD in 1976 suggest that the dynamics of human-to-human secondary transmission in contemporary outbreaks will be very different to those of the past.}, } @article {pmid25200494, year = {2014}, author = {Schlegelmilch, K and Keller, A and Zehe, V and Hondke, S and Schilling, T and Jakob, F and Klein-Hitpass, L and Schütze, N}, title = {WISP 1 is an important survival factor in human mesenchymal stromal cells.}, journal = {Gene}, volume = {551}, number = {2}, pages = {243-254}, doi = {10.1016/j.gene.2014.09.002}, pmid = {25200494}, issn = {1879-0038}, mesh = {Aged ; Aged, 80 and over ; Apoptosis/drug effects/genetics ; CCN Intercellular Signaling Proteins/*genetics/metabolism ; Cell Survival/genetics ; Cells, Cultured ; *Gene Expression Profiling ; *Gene Expression Regulation, Neoplastic ; Gene Ontology ; HEK293 Cells ; Humans ; Hydrogen Peroxide/pharmacology ; Mesenchymal Stem Cells/cytology/*metabolism ; Microscopy, Confocal ; Middle Aged ; Oligonucleotide Array Sequence Analysis ; Oxidants/pharmacology ; Proto-Oncogene Proteins/*genetics/metabolism ; RNA Interference ; Reverse Transcriptase Polymerase Chain Reaction ; }, abstract = {WNT-induced secreted protein 1 (WISP1/CCN4), a member of the CCN protein family, acts as a downstream factor of the canonical WNT signaling pathway. Its expression is known to affect proliferation and differentiation of human mesenchymal stromal cells (hMSCs), which are fundamental for the development and maintenance of the musculoskeletal system. Whereas a dysregulated, excessive expression of WISP1 often reflects its oncogenic potential via the inhibition of apoptosis, our study emphasizes the importance of WISP1 signaling for the survival of primary human cells. We have established the efficient and specific down-regulation of endogenous WISP1 transcripts by gene silencing in hMSCs and observed cell death as a consequence of WISP1 deficiency. This was confirmed by Annexin V staining for apoptotic cells. DNA microarray analyses of WISP1 down-regulated versus control samples revealed several clusters of differentially expressed genes important for apoptosis induction such as TNF-related apoptosis-inducing ligand 1 (TRAIL) and the corresponding apoptosis-inducing receptors TRAIL-R1 and -R2. An increased expression of TRAIL and its receptors TRAIL-R1 and -R2 in WISP1-deficient hMSCs was confirmed by immunocytofluorescence. Accordingly, WISP1 deficiency is likely to cause TRAIL-induced apoptosis. This is an important novel finding, which suggests that WISP1 is indispensable for the protection of healthy hMSCs against TRAIL-induced apoptosis.}, } @article {pmid25197495, year = {2014}, author = {Gilbert, JA and Dick, GJ and Jenkins, B and Heidelberg, J and Allen, E and Mackey, KR and DeLong, EF}, title = {Meeting report: Ocean 'omics science, technology and cyberinfrastructure: current challenges and future requirements (August 20-23, 2013).}, journal = {Standards in genomic sciences}, volume = {9}, number = {3}, pages = {1252-1258}, pmid = {25197495}, issn = {1944-3277}, abstract = {The National Science Foundation's EarthCube End User Workshop was held at USC Wrigley Marine Science Center on Catalina Island, California in August 2013. The workshop was designed to explore and characterize the needs and tools available to the community that is focusing on microbial and physical oceanography research with a particular emphasis on 'omic research. The assembled researchers outlined the existing concerns regarding the vast data resources that are being generated, and how we will deal with these resources as their volume and diversity increases. Particular attention was focused on the tools for handling and analyzing the existing data, on the need for the construction and curation of diverse federated databases, as well as development of shared, interoperable, "big-data capable" analytical tools. The key outputs from this workshop include (i) critical scientific challenges and cyber infrastructure constraints, (ii) the current and future ocean 'omics science grand challenges and questions, and (iii) data management, analytical and associated and cyber-infrastructure capabilities required to meet critical current and future scientific challenges. The main thrust of the meeting and the outcome of this report is a definition of the 'omics tools, technologies and infrastructures that facilitate continued advance in ocean science biology, marine biogeochemistry, and biological oceanography.}, } @article {pmid25197480, year = {2014}, author = {Zhou, Y and Li, R and Gao, XY and Lapidus, A and Han, J and Haynes, M and Lobos, E and Huntemann, M and Pati, A and Ivanova, NN and Rohde, M and Mavromatis, K and Tindall, BJ and Markowitz, V and Woyke, T and Klenk, HP and Kyrpides, NC and Li, WJ}, title = {High quality draft genome sequence of the slightly halophilic bacterium Halomonas zhanjiangensis type strain JSM 078169(T) (DSM 21076(T)) from a sea urchin in southern China.}, journal = {Standards in genomic sciences}, volume = {9}, number = {3}, pages = {1020-1030}, pmid = {25197480}, issn = {1944-3277}, abstract = {Halomonas zhanjiangensis Chen et al. 2009 is a member of the genus Halomonas, family Halomonadaceae, class Gammaproteobacteria. Representatives of the genus Halomonas are a group of halophilic bacteria often isolated from salty environments. The type strain H. zhanjiangensis JSM 078169(T) was isolated from a sea urchin (Hemicentrotus pulcherrimus) collected from the South China Sea. The genome of strain JSM 078169(T) is the fourteenth sequenced genome in the genus Halomonas and the fifteenth in the family Halomonadaceae. The other thirteen genomes from the genus Halomonas are H. halocynthiae, H. venusta, H. alkaliphila, H. lutea, H. anticariensis, H. jeotgali, H. titanicae, H. desiderata, H. smyrnensis, H. salifodinae, H. boliviensis, H. elongata and H stevensii. Here, we describe the features of strain JSM 078169(T), together with the complete genome sequence and annotation from a culture of DSM 21076(T). The 4,060,520 bp long draft genome consists of 17 scaffolds with the 3,659 protein-coding and 80 RNA genes and is a part of Genomic Encyclopedia of Type Strains, Phase I: the one thousand microbial genomes (KMG) project.}, } @article {pmid25193439, year = {2014}, author = {Pylro, VS and Roesch, LF and Morais, DK and Clark, IM and Hirsch, PR and Tótola, MR}, title = {Data analysis for 16S microbial profiling from different benchtop sequencing platforms.}, journal = {Journal of microbiological methods}, volume = {107}, number = {}, pages = {30-37}, doi = {10.1016/j.mimet.2014.08.018}, pmid = {25193439}, issn = {1872-8359}, mesh = {Archaea/classification/genetics ; Bacteria/classification/genetics ; Brazil ; *Computational Biology/methods ; *High-Throughput Nucleotide Sequencing ; *Metagenome ; Phylogeny ; *RNA, Ribosomal, 16S ; *Soil Microbiology ; }, abstract = {Progress in microbial ecology is confounded by problems when evaluating results from different sequencing methodologies. Contrary to existing expectations, here we demonstrate that the same biological conclusion is reached using different NGS technologies when stringent sequence quality filtering and accurate clustering algorithms are applied.}, } @article {pmid25193395, year = {2014}, author = {Ren, C and Chen, T and Jiang, X and Wang, Y and Hu, C}, title = {The first characterization of gene structure and biological function for echinoderm translationally controlled tumor protein (TCTP).}, journal = {Fish & shellfish immunology}, volume = {41}, number = {2}, pages = {137-146}, doi = {10.1016/j.fsi.2014.08.030}, pmid = {25193395}, issn = {1095-9947}, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Biological Assay ; Biomarkers, Tumor/*genetics/*metabolism ; Cloning, Molecular ; Cluster Analysis ; Computational Biology ; DNA Primers/genetics ; DNA, Complementary/genetics ; Electrophoresis, Polyacrylamide Gel ; Escherichia coli ; Expressed Sequence Tags/*metabolism ; Gene Components ; Heat-Shock Proteins/metabolism ; Hydrogen Peroxide ; *Models, Molecular ; Molecular Sequence Data ; Oxidative Stress/physiology ; *Phylogeny ; Protein Conformation ; Sea Cucumbers/*genetics/immunology ; Sequence Analysis, DNA ; Tumor Protein, Translationally-Controlled 1 ; }, abstract = {Translationally controlled tumor protein (TCTP) is a multifunctional protein that existed ubiquitously in different eukaryote species and distributed widely in various tissues and cell types. In this study, the gene structure and biological function of TCTP were first characterized in echinoderm. An echinoderm TCTP named StmTCTP was identified from sea cucumber (Stichopus monotuberculatus) by expression sequence tag (EST) analysis and rapid amplification of cDNA ends (RACE) approach. The StmTCTP cDNA is 1219 bp in length, containing a 5'-untranslated region (UTR) of 77 bp, a 3'-UTR of 623 bp and an open reading frame (ORF) of 519 bp that encoding a protein of 172 amino acids with a deduced molecular weight of 19.80 kDa and a predicted isolectric point of 4.66. Two deduced signal signatures termed TCTP1 and TCTP2, a microtubule binding domain, a Ca(2+) binding domain and the conserved residues forming Rab GTPase binding surface were found in the StmTCTP amino acid sequence. For the gene structure, StmTCTP contains four exons separated by three introns. The anti-oxidation and heat shock protein activities of recombinant TCTP protein were also demonstrated in this study. In addition, the expression of StmTCTP was found to be significantly upregulated by polyriboinosinic polyribocytidylic acid [poly (I:C)], lipopolysaccharides (LPS) or inactivated bacteria challenge in in vitro primary culture experiments of coelomocytes, suggested that the sea cucumber TCTP might play critical roles not only in the defense against oxidative and thermal stresses, but also in the innate immune defense against bacterial and viral infections.}, } @article {pmid25191870, year = {2014}, author = {Silva, P and Travassos, B and Vilar, L and Aguiar, P and Davids, K and Araújo, D and Garganta, J}, title = {Numerical relations and skill level constrain co-adaptive behaviors of agents in sports teams.}, journal = {PloS one}, volume = {9}, number = {9}, pages = {e107112}, pmid = {25191870}, issn = {1932-6203}, mesh = {Adaptation, Psychological/*physiology ; Adolescent ; Adult ; *Athletic Performance/psychology/statistics & numerical data ; Competitive Behavior ; Cooperative Behavior ; Faculty ; Geographic Information Systems ; Group Processes ; Humans ; *Interpersonal Relations ; Male ; Soccer ; *Social Skills ; *Sports/psychology/statistics & numerical data ; Young Adult ; }, abstract = {Similar to other complex systems in nature (e.g., a hunting pack, flocks of birds), sports teams have been modeled as social neurobiological systems in which interpersonal coordination tendencies of agents underpin team swarming behaviors. Swarming is seen as the result of agent co-adaptation to ecological constraints of performance environments by collectively perceiving specific possibilities for action (affordances for self and shared affordances). A major principle of invasion team sports assumed to promote effective performance is to outnumber the opposition (creation of numerical overloads) during different performance phases (attack and defense) in spatial regions adjacent to the ball. Such performance principles are assimilated by system agents through manipulation of numerical relations between teams during training in order to create artificially asymmetrical performance contexts to simulate overloaded and underloaded situations. Here we evaluated effects of different numerical relations differentiated by agent skill level, examining emergent inter-individual, intra- and inter-team coordination. Groups of association football players (national--NLP and regional-level--RLP) participated in small-sided and conditioned games in which numerical relations between system agents were manipulated (5v5, 5v4 and 5v3). Typical grouping tendencies in sports teams (major ranges, stretch indices, distances of team centers to goals and distances between the teams' opposing line-forces in specific team sectors) were recorded by plotting positional coordinates of individual agents through continuous GPS tracking. Results showed that creation of numerical asymmetries during training constrained agents' individual dominant regions, the underloaded teams' compactness and each team's relative position on-field, as well as distances between specific team sectors. We also observed how skill level impacted individual and team coordination tendencies. Data revealed emergence of co-adaptive behaviors between interacting neurobiological social system agents in the context of sport performance. Such observations have broader implications for training design involving manipulations of numerical relations between interacting members of social collectives.}, } @article {pmid25188267, year = {2014}, author = {Székely, T and Burrage, K and Mangel, M and Bonsall, MB}, title = {Stochastic dynamics of interacting haematopoietic stem cell niche lineages.}, journal = {PLoS computational biology}, volume = {10}, number = {9}, pages = {e1003794}, pmid = {25188267}, issn = {1553-7358}, mesh = {Computational Biology ; Computer Simulation ; Hematopoietic Stem Cells/*cytology/*physiology ; Humans ; *Models, Biological ; Stem Cell Niche/*physiology ; Stochastic Processes ; }, abstract = {Since we still know very little about stem cells in their natural environment, it is useful to explore their dynamics through modelling and simulation, as well as experimentally. Most models of stem cell systems are based on deterministic differential equations that ignore the natural heterogeneity of stem cell populations. This is not appropriate at the level of individual cells and niches, when randomness is more likely to affect dynamics. In this paper, we introduce a fast stochastic method for simulating a metapopulation of stem cell niche lineages, that is, many sub-populations that together form a heterogeneous metapopulation, over time. By selecting the common limiting timestep, our method ensures that the entire metapopulation is simulated synchronously. This is important, as it allows us to introduce interactions between separate niche lineages, which would otherwise be impossible. We expand our method to enable the coupling of many lineages into niche groups, where differentiated cells are pooled within each niche group. Using this method, we explore the dynamics of the haematopoietic system from a demand control system perspective. We find that coupling together niche lineages allows the organism to regulate blood cell numbers as closely as possible to the homeostatic optimum. Furthermore, coupled lineages respond better than uncoupled ones to random perturbations, here the loss of some myeloid cells. This could imply that it is advantageous for an organism to connect together its niche lineages into groups. Our results suggest that a potential fruitful empirical direction will be to understand how stem cell descendants communicate with the niche and how cancer may arise as a result of a failure of such communication.}, } @article {pmid25182329, year = {2014}, author = {Valentino, MD and Foulston, L and Sadaka, A and Kos, VN and Villet, RA and Santa Maria, J and Lazinski, DW and Camilli, A and Walker, S and Hooper, DC and Gilmore, MS}, title = {Genes contributing to Staphylococcus aureus fitness in abscess- and infection-related ecologies.}, journal = {mBio}, volume = {5}, number = {5}, pages = {e01729-14}, pmid = {25182329}, issn = {2150-7511}, support = {AI083214/AI/NIAID NIH HHS/United States ; R21 AI107248/AI/NIAID NIH HHS/United States ; P01 AI083214/AI/NIAID NIH HHS/United States ; T32 EY007145/EY/NEI NIH HHS/United States ; AI107248/AI/NIAID NIH HHS/United States ; T32-EY007145/EY/NEI NIH HHS/United States ; }, mesh = {Abscess/*microbiology ; Animals ; Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/genetics ; Computational Biology ; DNA Transposable Elements/genetics ; Drug Resistance, Bacterial ; Gene Library ; *Genome, Bacterial ; Male ; Mice ; RNA, Antisense/genetics ; Sequence Analysis, DNA ; Staphylococcal Infections/*microbiology ; Staphylococcus aureus/*genetics ; Virulence Factors/genetics ; }, abstract = {UNLABELLED: Staphylococcus aureus is a leading cause of both community- and hospital-acquired infections that are increasingly antibiotic resistant. The emergence of S. aureus resistance to even last-line antibiotics heightens the need for the development of new drugs with novel targets. We generated a highly saturated transposon insertion mutant library in the genome of S. aureus and used Tn-seq analysis to probe the entire genome, with unprecedented resolution and sensitivity, for genes of importance in infection. We further identified genes contributing to fitness in various infected compartments (blood and ocular fluids) and compared them to genes required for growth in rich medium. This resulted in the identification of 426 genes that were important for S. aureus fitness during growth in infection models, including 71 genes that could be considered essential for survival specifically during infection. These findings highlight novel as well as previously known genes encoding virulence traits and metabolic pathways important for S. aureus proliferation at sites of infection, which may represent new therapeutic targets.

IMPORTANCE: Staphylococcus aureus continues to be a leading cause of antibiotic-resistant community and nosocomial infection. With the bacterium's acquisition of resistance to methicillin and, more recently, vancomycin, the need for the development of new drugs with novel targets is urgent. Applying a highly saturated Tn-seq mutant library to analyze fitness and growth requirements in a murine abscess and in various infection-relevant fluids, we identified S. aureus traits that enable it to survive and proliferate during infection. This identifies potential new targeting opportunities for the development of novel therapeutics.}, } @article {pmid25179523, year = {2014}, author = {Martínez-Cortés, T and Pomar, F and Merino, F and Novo-Uzal, E}, title = {A proteomic approach to Physcomitrella patens rhizoid exudates.}, journal = {Journal of plant physiology}, volume = {171}, number = {17}, pages = {1671-1678}, doi = {10.1016/j.jplph.2014.08.004}, pmid = {25179523}, issn = {1618-1328}, mesh = {Bryopsida/genetics/*metabolism ; Chromatography, Reverse-Phase ; Gene Ontology ; Mass Spectrometry ; Photosynthesis ; Plant Exudates/metabolism ; Plant Proteins/classification/*metabolism ; Plant Roots/metabolism ; *Proteome ; Proteomics/*methods ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ; Stress, Physiological ; }, abstract = {The interaction between plants and the surrounding environment has been widely studied, specially the defence reactions and the plant-plant interactions. One of the most remarkable metabolic features of plant roots is the ability to secrete a vast array of compounds into the rhizosphere, not only of low molecular weight but also polysaccharides and proteins. Here, we took advantage of proteomics to study the rhizoid exudates of Physcomitrella patens at early and late development stages (7 and 28 days of culture in liquid medium). Samples were extracted, separated and detected with nanoLC-MALDI-TOF/TOF MS/MS, identifying 47 proteins at the development stage of 7 days, and 66 proteins at 28 days. Moreover, 21 proteins were common to the two analyzed periods. All the identified proteins were classified into 8 functional categories: response to stress, response to stimulus, oxido-reduction, cell wall modification, photosynthesis and carbohydrate metabolism, transport, DNA metabolic process and regulation/signalling. Our results show important differences in the protein expression profile along the development of P. patens, mainly at the level of regulation- and senescence-related proteins. Defence-related proteins, such as chitinases, thaumatins and peroxidases have a major role in the interaction of P. patens with the environment.}, } @article {pmid25179155, year = {2014}, author = {Bengtsson-Palme, J and Alm Rosenblad, M and Molin, M and Blomberg, A}, title = {Metagenomics reveals that detoxification systems are underrepresented in marine bacterial communities.}, journal = {BMC genomics}, volume = {15}, number = {1}, pages = {749}, pmid = {25179155}, issn = {1471-2164}, mesh = {Bacteria/*genetics/*metabolism ; Bacterial Proteins/genetics/metabolism ; Biotransformation/*genetics ; Cluster Analysis ; Computational Biology/methods ; Datasets as Topic ; *Metagenomics/methods ; Oxidative Stress/genetics ; Seawater/*microbiology ; *Water Microbiology ; }, abstract = {BACKGROUND: Environmental shotgun sequencing (metagenomics) provides a new way to study communities in microbial ecology. We here use sequence data from the Global Ocean Sampling (GOS) expedition to investigate toxicant selection pressures revealed by the presence of detoxification genes in marine bacteria. To capture a broad range of potential toxicants we selected detoxification protein families representing systems protecting microorganisms from a variety of stressors, such as metals, organic compounds, antibiotics and oxygen radicals.

RESULTS: Using a bioinformatics procedure based on comparative analysis to finished bacterial genomes we found that the amount of detoxification genes present in marine microorganisms seems surprisingly small. The underrepresentation is particularly evident for toxicant transporters and proteins involved in detoxifying metals. Exceptions are enzymes involved in oxidative stress defense where peroxidase enzymes are more abundant in marine bacteria compared to bacteria in general. In contrast, catalases are almost completely absent from the open ocean environment, suggesting that peroxidases and peroxiredoxins constitute a core line of defense against reactive oxygen species (ROS) in the marine milieu.

CONCLUSIONS: We found no indication that detoxification systems would be generally more abundant close to the coast compared to the open ocean. On the contrary, for several of the protein families that displayed a significant geographical distribution, like peroxidase, penicillin binding transpeptidase and divalent ion transport protein, the open ocean samples showed the highest abundance. Along the same lines, the abundance of most detoxification proteins did not increase with estimated pollution. The low level of detoxification systems in marine bacteria indicate that the majority of marine bacteria have a low capacity to adapt to increased pollution. Our study exemplifies the use of metagenomics data in ecotoxicology, and in particular how anthropogenic consequences on life in the sea can be examined.}, } @article {pmid25177534, year = {2014}, author = {Lim, YW and Cuevas, DA and Silva, GG and Aguinaldo, K and Dinsdale, EA and Haas, AF and Hatay, M and Sanchez, SE and Wegley-Kelly, L and Dutilh, BE and Harkins, TT and Lee, CC and Tom, W and Sandin, SA and Smith, JE and Zgliczynski, B and Vermeij, MJ and Rohwer, F and Edwards, RA}, title = {Sequencing at sea: challenges and experiences in Ion Torrent PGM sequencing during the 2013 Southern Line Islands Research Expedition.}, journal = {PeerJ}, volume = {2}, number = {}, pages = {e520}, pmid = {25177534}, issn = {2167-8359}, abstract = {Genomics and metagenomics have revolutionized our understanding of marine microbial ecology and the importance of microbes in global geochemical cycles. However, the process of DNA sequencing has always been an abstract extension of the research expedition, completed once the samples were returned to the laboratory. During the 2013 Southern Line Islands Research Expedition, we started the first effort to bring next generation sequencing to some of the most remote locations on our planet. We successfully sequenced twenty six marine microbial genomes, and two marine microbial metagenomes using the Ion Torrent PGM platform on the Merchant Yacht Hanse Explorer. Onboard sequence assembly, annotation, and analysis enabled us to investigate the role of the microbes in the coral reef ecology of these islands and atolls. This analysis identified phosphonate as an important phosphorous source for microbes growing in the Line Islands and reinforced the importance of L-serine in marine microbial ecosystems. Sequencing in the field allowed us to propose hypotheses and conduct experiments and further sampling based on the sequences generated. By eliminating the delay between sampling and sequencing, we enhanced the productivity of the research expedition. By overcoming the hurdles associated with sequencing on a boat in the middle of the Pacific Ocean we proved the flexibility of the sequencing, annotation, and analysis pipelines.}, } @article {pmid25173945, year = {2014}, author = {Kleandrova, VV and Luan, F and González-Díaz, H and Ruso, JM and Melo, A and Speck-Planche, A and Cordeiro, MN}, title = {Computational ecotoxicology: simultaneous prediction of ecotoxic effects of nanoparticles under different experimental conditions.}, journal = {Environment international}, volume = {73}, number = {}, pages = {288-294}, doi = {10.1016/j.envint.2014.08.009}, pmid = {25173945}, issn = {1873-6750}, mesh = {Animals ; Computational Biology ; Daphnia/drug effects ; Ecotoxicology/methods ; Nanoparticles/chemistry/*toxicity ; Nickel/toxicity ; Quantitative Structure-Activity Relationship ; Toxicity Tests/*methods ; }, abstract = {Nanotechnology has brought great advances to many fields of modern science. A manifold of applications of nanoparticles have been found due to their interesting optical, electrical, and biological/chemical properties. However, the potential toxic effects of nanoparticles to different ecosystems are of special concern nowadays. Despite the efforts of the scientific community, the mechanisms of toxicity of nanoparticles are still poorly understood. Quantitative-structure activity/toxicity relationships (QSAR/QSTR) models have just started being useful computational tools for the assessment of toxic effects of nanomaterials. But most QSAR/QSTR models have been applied so far to predict ecotoxicity against only one organism/bio-indicator such as Daphnia magna. This prevents having a deeper knowledge about the real ecotoxic effects of nanoparticles, and consequently, there is no possibility to establish an efficient risk assessment of nanomaterials in the environment. In this work, a perturbation model for nano-QSAR problems is introduced with the aim of simultaneously predicting the ecotoxicity of different nanoparticles against several assay organisms (bio-indicators), by considering also multiple measures of ecotoxicity, as well as the chemical compositions, sizes, conditions under which the sizes were measured, shapes, and the time during which the diverse assay organisms were exposed to nanoparticles. The QSAR-perturbation model was derived from a database containing 5520 cases (nanoparticle-nanoparticle pairs), and it was shown to exhibit accuracies of ca. 99% in both training and prediction sets. In order to demonstrate the practical applicability of our model, three different nickel-based nanoparticles (Ni) with experimental values reported in the literature were predicted. The predictions were found to be in very good agreement with the experimental evidences, confirming that Ni-nanoparticles are not ecotoxic when compared with other nanoparticles. The results of this study thus provide a single valuable tool toward an efficient prediction of the ecotoxicity of nanoparticles under multiple experimental conditions.}, } @article {pmid25171408, year = {2014}, author = {Jarosz, DF and Lancaster, AK and Brown, JCS and Lindquist, S}, title = {An evolutionarily conserved prion-like element converts wild fungi from metabolic specialists to generalists.}, journal = {Cell}, volume = {158}, number = {5}, pages = {1072-1082}, pmid = {25171408}, issn = {1097-4172}, support = {K99 GM098600/GM/NIGMS NIH HHS/United States ; R00 GM098600/GM/NIGMS NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; }, mesh = {Ascomycota/genetics/metabolism ; Bacteria/chemistry/genetics ; Dekkera/genetics/metabolism ; *Epigenesis, Genetic ; Glucose/*metabolism ; Phenotype ; Prions/*metabolism ; Saccharomyces cerevisiae/genetics/*metabolism ; }, abstract = {[GAR(+)] is a protein-based element of inheritance that allows yeast (Saccharomyces cerevisiae) to circumvent a hallmark of their biology: extreme metabolic specialization for glucose fermentation. When glucose is present, yeast will not use other carbon sources. [GAR(+)] allows cells to circumvent this "glucose repression." [GAR(+)] is induced in yeast by a factor secreted by bacteria inhabiting their environment. We report that de novo rates of [GAR(+)] appearance correlate with the yeast's ecological niche. Evolutionarily distant fungi possess similar epigenetic elements that are also induced by bacteria. As expected for a mechanism whose adaptive value originates from the selective pressures of life in biological communities, the ability of bacteria to induce [GAR(+)] and the ability of yeast to respond to bacterial signals have been extinguished repeatedly during the extended monoculture of domestication. Thus, [GAR(+)] is a broadly conserved adaptive strategy that links environmental and social cues to heritable changes in metabolism.}, } @article {pmid25170000, year = {2014}, author = {Holzer, J and Canavan, M and Bradley, E}, title = {County-level correlation between adult obesity rates and prevalence of dentists.}, journal = {Journal of the American Dental Association (1939)}, volume = {145}, number = {9}, pages = {932-939}, doi = {10.14219/jada.2014.48}, pmid = {25170000}, issn = {1943-4723}, support = {T32 HS017589-06/HS/AHRQ HHS/United States ; }, mesh = {Adult ; Cross-Sectional Studies ; Databases, Factual ; Dentists/*supply & distribution ; Female ; Humans ; Male ; Obesity/*epidemiology ; Prevalence ; Residence Characteristics ; Risk Factors ; Socioeconomic Factors ; United States/epidemiology ; }, abstract = {BACKGROUND: Investigators of previous studies regarding the correlation between area-level health care resources and obesity have not examined the association between the prevalence of dentists and rates of adult obesity. The authors conducted a study to address that knowledge gap.

METHODS: Using data compiled in the Robert Wood Johnson County Health Rankings and Roadmaps database, the authors conducted multivariable analyses of the relationship between the prevalence of dentists (from the 2011 Health Resources and Services Administration Area Resource File) and rates of obesity within counties. The authors controlled for prevalence of primary care providers, measures of the built environment (for example, number of recreational facilities per 10,000 population, the percentage of restaurants serving fast food) and county-level sociodemographic and economic factors.

RESULTS: When the authors conducted a multivariable analysis adjusted for state-level fixed effects, they found that having one additional dentist per 10,000 population was associated significantly with a 1-percentage point reduction in the rate of obesity (P < .001). This effect was significantly larger in counties in which 25 percent of children or more (versus less than 25 percent of children) lived in poverty and in counties that had more primary care physicians per 10,000 population (P ≤ .009).

CONCLUSIONS: The association between the prevalence of dentists and obesity, even after adjusting for primary care resources and sociodemographic factors, was evident. Although these data could not be used to assess causality, given the strength of the ecological, cross-sectional association, additional research involving person-level, longitudinal data is warranted.

PRACTICAL IMPLICATIONS: The correlation between the prevalence of dentists and obesity rates highlights the potential for dental professionals, as well as other primary care providers, to provide meaningful health education and support for improved nutritional behaviors, although the increased obesity rates in counties with fewer dentists per capita present challenges.}, } @article {pmid25160510, year = {2014}, author = {Wilson, IM and Graham, K and Taft, A}, title = {Alcohol interventions, alcohol policy and intimate partner violence: a systematic review.}, journal = {BMC public health}, volume = {14}, number = {}, pages = {881}, pmid = {25160510}, issn = {1471-2458}, mesh = {Adult ; Alcohol Drinking/*adverse effects/prevention & control ; Databases, Factual ; Female ; Health Policy ; Humans ; Interpersonal Relations ; Male ; *Spouse Abuse ; Young Adult ; }, abstract = {BACKGROUND: Intimate partner violence (IPV) is a significant global public health issue. The consistent evidence that alcohol use by one or both partners contributes to the risk and severity of IPV suggests that interventions that reduce alcohol consumption may also reduce IPV. This study sought to review the evidence for effects on IPV of alcohol interventions at the population, community, relationship and individual levels using the World Health Organization ecological framework for violence.

METHODS: Eleven databases including Medline, PsycINFO, CINAHL and EMBASE were searched for English-language studies and grey literature published 1 January 1992 - 1 March 2013 investigating whether alcohol interventions/policies were associated with IPV reduction within adult (≥ 18) intimate relationships. Eleven studies meeting design criteria for attributing effects to the intervention and ten studies showing mediation of alcohol consumption were included in the review. The heterogeneity of study designs precluded quantitative meta analysis; therefore, a critical narrative approach was used.

RESULTS: Population-level pricing and taxation studies found weak or no evidence for alcohol price changes influencing IPV. Studies of community-level policies or interventions (e.g., hours of sale, alcohol outlet density) showed weak evidence of an association with IPV. Couples-based and individual alcohol treatment studies found a relationship between reductions in alcohol consumption and reductions in IPV but their designs precluded attributing changes to treatment. Randomized controlled trials of combined alcohol and violence treatment programs found some positive effects of brief alcohol intervention as an adjunct to batterer treatment for hazardous drinking IPV perpetrators, and of brief interventions with non-dependent younger populations, but effects were often not sustained.

CONCLUSIONS: Despite evidence associating problematic alcohol use with IPV, the potential for alcohol interventions to reduce IPV has not been adequately tested, possibly because studies have not focused on those most at risk of alcohol-related IPV. Research using rigorous designs should target young adult populations among whom IPV and drinking is highly prevalent. Combining alcohol and IPV intervention/policy approaches at the population, community, relationship and individual-level may provide the best opportunity for effective intervention.}, } @article {pmid25160316, year = {2014}, author = {Kushniruk, AW and Borycki, EM}, title = {Designing and conducting low-cost in-situ clinical simulations: a methodological approach.}, journal = {Studies in health technology and informatics}, volume = {205}, number = {}, pages = {890-894}, pmid = {25160316}, issn = {1879-8365}, mesh = {British Columbia ; Computer Simulation ; Cost-Benefit Analysis ; Health Information Systems/*classification/*economics ; *Models, Theoretical ; Needs Assessment/*economics ; *User-Computer Interface ; }, abstract = {The need to develop more effective and usable systems in healthcare has led to increasing adoption of usability engineering methods. Primary among these methods has been usability testing, which involves observing representative users while they carry out representative tasks using health information systems. However, such testing may not capture the cognitive and social contexts of use of systems in real settings, necessitating the use of clinical simulations. Such simulations involve testing representative users carrying out representative tasks, systems in realistic and representative environments. In this paper we describe our work in both reducing the cost of simulation testing while at the same time increasing the fidelity of the simulations. We describe an approach which involves conducting simulations within real work environments and contexts as a way to achieve a high level of ecological validity. The stages involved in setting up such low-cost in-situ clinical simulations are detailed in this paper.}, } @article {pmid25160273, year = {2014}, author = {Boyé, M and Grabar, N and Thi Tran, M}, title = {Contrastive conversational analysis of language production by Alzheimer's and control people.}, journal = {Studies in health technology and informatics}, volume = {205}, number = {}, pages = {682-686}, pmid = {25160273}, issn = {1879-8365}, mesh = {Aged, 80 and over ; Alzheimer Disease/complications/*diagnosis ; Diagnosis, Computer-Assisted/*methods ; Female ; Humans ; *Language Tests ; Male ; *Natural Language Processing ; Speech Disorders/*diagnosis/etiology ; Speech Production Measurement/*methods ; }, abstract = {Alzheimer's disease is characterized by memory disorders, although it affects also other cognitive functions (executive functions, attention, gnosia, praxia and language) and the communication ability. Our objective is to study verbal communication of people affected by the Alzheimer's disease at early to moderate stages. One particularity of our approach is that we are working in ecological conversational situations: people are interviewed by persons they know and in non-artificial environment. We propose a contrastive study of verbal productions of five people affected by the Alzheimer's disease and of five control people, both over 80 years old. To obtain quantitative and qualitative results, the oral corpora are transcribed and processed with the NLP methods and tools, and manually. Our results indicate that the Alzheimer's patients present lexical and semantic deficit and that their conversation is reduced comparing to the control people.}, } @article {pmid25144530, year = {2014}, author = {Wang, Y and Wang, H and Xu, K and Ni, P and Zhang, H and Ma, J and Yang, H and Xu, F}, title = {A survey of overlooked viral infections in biological experiment systems.}, journal = {PloS one}, volume = {9}, number = {8}, pages = {e105348}, pmid = {25144530}, issn = {1932-6203}, mesh = {Animals ; Cluster Analysis ; Computational Biology ; Databases, Nucleic Acid ; Gene Expression Profiling ; Genome, Viral ; Host-Pathogen Interactions ; Humans ; Plants ; RNA Interference ; RNA, Small Interfering ; RNA, Viral ; Virus Diseases/epidemiology/*virology ; *Viruses/genetics ; }, abstract = {It is commonly accepted that there are many unknown viruses on the planet. For the known viruses, do we know their prevalence, even in our experimental systems? Here we report a virus survey using recently published small (s)RNA sequencing datasets. The sRNA reads were assembled and contigs were screened for virus homologues against the NCBI nucleotide (nt) database using the BLASTn program. To our surprise, approximately 30% (28 out of 94) of publications had highly scored viral sequences in their datasets. Among them, only two publications reported virus infections. Though viral vectors were used in some of the publications, virus sequences without any identifiable source appeared in more than 20 publications. By determining the distributions of viral reads and the antiviral RNA interference (RNAi) pathways using the sRNA profiles, we showed evidence that many of the viruses identified were indeed infecting and generated host RNAi responses. As virus infections affect many aspects of host molecular biology and metabolism, the presence and impact of viruses needs to be actively investigated in experimental systems.}, } @article {pmid25126611, year = {2014}, author = {Facca, C and Ceoldo, S and Pellegrino, N and Sfriso, A}, title = {Natural recovery and planned intervention in coastal wetlands: Venice Lagoon (northern Adriatic Sea, Italy) as a case study.}, journal = {TheScientificWorldJournal}, volume = {2014}, number = {}, pages = {968618}, pmid = {25126611}, issn = {1537-744X}, mesh = {Aquaculture/methods ; Biomass ; Carbon/analysis ; *Cities ; *Ecosystem ; Environmental Monitoring/*statistics & numerical data ; Environmental Restoration and Remediation/*methods ; *Eutrophication ; Geographic Mapping ; History, 20th Century ; History, 21st Century ; Italy ; Microalgae/physiology ; Nitrogen/analysis ; Phosphorus/analysis ; Water Pollution/*history/statistics & numerical data ; *Wetlands ; }, abstract = {The goals of conservation and sustainable use of environmental ecosystems have increased the need for detailed knowledge of ecological evolution and responses to both anthropogenic pressures and recovery measures. The present study shows the effects of natural processes and planned intervention in terms of reducing nutrient inputs in a highly exploited coastal lagoon, describing its evolution over a 16-year period from the late 1980s (when eutrophication was at its peak) until 2003. Changes in nutrient and carbon concentrations in the top layer of sediments were investigated in parallel with macroalgal and seagrass biomass in the most anthropized basin of Venice Lagoon in four surveys conducted in accordance with the same protocols in 1987, 1993, 1998, and 2003. A pronounced reduction in trophic state (mainly total nitrogen, organic phosphorus, and organic carbon concentrations) and macroalgal biomass was recorded, together with the progressive expansion of seagrass meadows. General considerations are also made on the effects of Manila clam farming and the shift from illegal to managed clam farming.}, } @article {pmid25126580, year = {2014}, author = {Marszalek, J and Morgulec-Adamowicz, N and Rutkowska, I and Kosmol, A}, title = {Using ecological momentary assessment to evaluate current physical activity.}, journal = {BioMed research international}, volume = {2014}, number = {}, pages = {915172}, pmid = {25126580}, issn = {2314-6141}, mesh = {Adolescent ; Adult ; Child ; *Ecology ; Humans ; MEDLINE ; *Motor Activity ; PubMed ; }, abstract = {OBJECTIVE: The purpose of this study was to assess the value of ecological momentary assessment in evaluating physical activity among children, adolescents, and adults. It also determines whether ecological momentary assessment fulfills the criteria of validity, reliability, objectivity, norms, and standardization applied to the tools used for the evaluation of physical activity.

METHODS: The EBSCO-CINHAL, Medline, PsycINFO, PubMed, and SPORTDiscuss databases were reviewed in December 2012 for articles associated with EMA.

RESULTS: Of the 20 articles examined, half (10) used electronic methods for data collection, although various methods were used, ranging from pen and paper to smartphone applications. Ten studies used objective monitoring equipment. Nineteen studies were performed over 4 days. While the validity of the EMA method was discussed in 18 studies, only four found it to be objective. In all cases, the EMA procedures were precisely documented and confirmed to be feasible.

CONCLUSIONS: Ecological momentary assessment is a valid, reliable, and feasible approach to evaluate activity and sedentary behavior. Researchers should be aware that while ecological momentary assessment offers many benefits, it simultaneously imposes many limitations which should be considered when studying physical activity.}, } @article {pmid25124790, year = {2014}, author = {Van Riper, CJ and Kyle, GT}, title = {Capturing multiple values of ecosystem services shaped by environmental worldviews: a spatial analysis.}, journal = {Journal of environmental management}, volume = {145}, number = {}, pages = {374-384}, doi = {10.1016/j.jenvman.2014.06.014}, pmid = {25124790}, issn = {1095-8630}, mesh = {Adult ; Biodiversity ; Community Participation ; *Conservation of Natural Resources/economics/methods/statistics & numerical data ; Data Collection ; Decision Making ; *Ecosystem ; Environmental Policy ; Female ; Geographic Information Systems ; Humans ; Male ; Recreation ; Spatial Analysis ; United States ; }, abstract = {Two related approaches to valuing nature have been advanced in past research including the study of ecosystem services and psychological investigations of the factors that shape behavior. Stronger integration of the insights that emerge from these two lines of enquiry can more effectively sustain ecosystems, economies, and human well-being. Drawing on survey data collected from outdoor recreationists on Santa Cruz Island within Channel Islands National Park, U.S., our study blends these two research approaches to examine a range of tangible and intangible values of ecosystem services provided to stakeholders with differing biocentric and anthropocentric worldviews. We used Public Participation Geographic Information System methods to collect survey data and a Social Values for Ecosystem Services mapping application to spatially analyze a range of values assigned to terrestrial and aquatic ecosystems in the park. Our results showed that preferences for the provision of biological diversity, recreation, and scientific-based values of ecosystem services varied across a spatial gradient. We also observed differences that emerged from a comparison between survey subgroups defined by their worldviews. The implications emanating from this investigation aim to support environmental management decision-making in the context of protected areas.}, } @article {pmid25124098, year = {2014}, author = {Jiang, W and Chen, SY and Wang, H and Li, DZ and Wiens, JJ}, title = {Should genes with missing data be excluded from phylogenetic analyses?.}, journal = {Molecular phylogenetics and evolution}, volume = {80}, number = {}, pages = {308-318}, doi = {10.1016/j.ympev.2014.08.006}, pmid = {25124098}, issn = {1095-9513}, mesh = {Data Interpretation, Statistical ; Likelihood Functions ; *Models, Genetic ; *Phylogeny ; Probability ; Rosales/classification/genetics ; Sequence Analysis, DNA ; Yeasts/cytology/genetics ; }, abstract = {Phylogeneticists often design their studies to maximize the number of genes included but minimize the overall amount of missing data. However, few studies have addressed the costs and benefits of adding characters with missing data, especially for likelihood analyses of multiple loci. In this paper, we address this topic using two empirical data sets (in yeast and plants) with well-resolved phylogenies. We introduce varying amounts of missing data into varying numbers of genes and test whether the benefits of excluding genes with missing data outweigh the costs of excluding the non-missing data that are associated with them. We also test if there is a proportion of missing data in the incomplete genes at which they cease to be beneficial or harmful, and whether missing data consistently bias branch length estimates. Our results indicate that adding incomplete genes generally increases the accuracy of phylogenetic analyses relative to excluding them, especially when there is a high proportion of incomplete genes in the overall dataset (and thus few complete genes). Detailed analyses suggest that adding incomplete genes is especially helpful for resolving poorly supported nodes. Given that we find that excluding genes with missing data often decreases accuracy relative to including these genes (and that decreases are generally of greater magnitude than increases), there is little basis for assuming that excluding these genes is necessarily the safer or more conservative approach. We also find no evidence that missing data consistently bias branch length estimates.}, } @article {pmid25124083, year = {2015}, author = {Hong, Y and Chi, P and Li, X and Zhao, G and Zhao, J and Stanton, B and Li, L}, title = {Community-based family-style group homes for children orphaned by AIDS in rural China: an ethnographic investigation.}, journal = {Health policy and planning}, volume = {30}, number = {7}, pages = {928-937}, pmid = {25124083}, issn = {1460-2237}, support = {P30 MH058107/MH/NIMH NIH HHS/United States ; R01NR13466/NR/NINR NIH HHS/United States ; R01MH76488/MH/NIMH NIH HHS/United States ; }, mesh = {Acquired Immunodeficiency Syndrome ; *Child, Orphaned ; China ; *Community Networks ; *Group Homes ; Humans ; *Rural Population ; }, abstract = {As the number of children orphaned by AIDS (Acquired Immunodeficiency Syndrome) has reached 17.3 million, most living in resource-poor settings, interest has grown in identifying and evaluating appropriate care arrangements for them. In this study, we describe the community-based family-style group homes ('group homes') in rural China. Guided by an ecological framework of children's wellbeing, we conducted a series of ethnographic observations, in-depth interviews and group discussions in the rural areas of Henan Province, which has been severely impacted by the AIDS endemic through commercial blood collection. Based on our observations and discussions, group homes appear to provide stable and safe living environments for children orphaned by AIDS. Adequate financial support from non-government organizations (NGOs) as well as the central and provincial governments has ensured a low child-caregiver ratio and attention to the basic needs of the children at group homes. The foster parents were selected from the local community and appear to have adequate qualifications and dedication. They receive a monthly stipend, periodical evaluation and parenting consultation from supporting NGOs. The foster parents and children in the group homes have formed strong bonds. Both children and foster parents reported positively on health and education. Characteristics of community-based group homes can be replicated in other care arrangements for AIDS orphans in resource-poor settings for the optimal health outcomes of those vulnerable children. We also call for capacity building for caregivers and communities to provide sustainable and supportive living environment for these children.}, } @article {pmid25122209, year = {2014}, author = {Zhang, Y and Sun, Y and Cole, JR}, title = {A scalable and accurate targeted gene assembly tool (SAT-Assembler) for next-generation sequencing data.}, journal = {PLoS computational biology}, volume = {10}, number = {8}, pages = {e1003737}, pmid = {25122209}, issn = {1553-7358}, mesh = {Chromosome Mapping/*methods ; Databases, Genetic ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Metagenomics/*methods ; Microbiota/genetics ; Sequence Analysis, DNA/*methods ; *Software ; }, abstract = {Gene assembly, which recovers gene segments from short reads, is an important step in functional analysis of next-generation sequencing data. Lacking quality reference genomes, de novo assembly is commonly used for RNA-Seq data of non-model organisms and metagenomic data. However, heterogeneous sequence coverage caused by heterogeneous expression or species abundance, similarity between isoforms or homologous genes, and large data size all pose challenges to de novo assembly. As a result, existing assembly tools tend to output fragmented contigs or chimeric contigs, or have high memory footprint. In this work, we introduce a targeted gene assembly program SAT-Assembler, which aims to recover gene families of particular interest to biologists. It addresses the above challenges by conducting family-specific homology search, homology-guided overlap graph construction, and careful graph traversal. It can be applied to both RNA-Seq and metagenomic data. Our experimental results on an Arabidopsis RNA-Seq data set and two metagenomic data sets show that SAT-Assembler has smaller memory usage, comparable or better gene coverage, and lower chimera rate for assembling a set of genes from one or multiple pathways compared with other assembly tools. Moreover, the family-specific design and rapid homology search allow SAT-Assembler to be naturally compatible with parallel computing platforms. The source code of SAT-Assembler is available at https://sourceforge.net/projects/sat-assembler/. The data sets and experimental settings can be found in supplementary material.}, } @article {pmid25119263, year = {2014}, author = {Johnson Pokorná, M and Rovatsos, M and Kratochvíl, L}, title = {Sex chromosomes and karyotype of the (nearly) mythical creature, the Gila monster, Heloderma suspectum (Squamata: Helodermatidae).}, journal = {PloS one}, volume = {9}, number = {8}, pages = {e104716}, pmid = {25119263}, issn = {1932-6203}, mesh = {Animals ; Comparative Genomic Hybridization ; Computational Biology ; DNA Barcoding, Taxonomic ; DNA, Mitochondrial/genetics ; Female ; Image Processing, Computer-Assisted ; In Situ Hybridization ; Karyotyping ; Lizards/*genetics/physiology ; Male ; Sex Chromosomes/*genetics ; Sex Determination Processes/*genetics/physiology ; }, abstract = {A wide variety of sex determination systems exist among squamate reptiles. They can therefore serve as an important model for studies of evolutionary transitions among particular sex determination systems. However, we still have only a limited knowledge of sex determination in certain important lineages of squamates. In this respect, one of the most understudied groups is the family Helodermatidae (Anguimorpha) encompassing the only two venomous species of lizards which are potentially lethal to human beings. We uncovered homomorphic ZZ/ZW sex chromosomes in the Gila monster (Heloderma suspectum) with a highly heterochromatic W chromosome. The sex chromosomes are morphologically similar to the ZZ/ZW sex chromosomes of monitor lizards (Varanidae). If the sex chromosomes of helodermatids and varanids are homologous, female heterogamety may be ancestral for the whole Anguimorpha group. Moreover, we found that the karyotype of the Gila monster consists of 2n = 36 chromosomes (14 larger metacentric chromosomes and 22 acrocentric microchromosomes). 2n = 36 is the widely distributed chromosomal number among squamates. In his pioneering works representing the only previous cytogenetic examination of the family Helodermatidae, Matthey reported the karyotype as 2n = 38 and suggested a different chromosomal morphology for this species. We believe that this was probably erroneously. We also discovered a strong accumulation of telomeric sequences on several pairs of microchromosomes in the Gila monster, which is a trait documented relatively rarely in vertebrates. These new data fill an important gap in our understanding of the sex determination and karyotype evolution of squamates.}, } @article {pmid25118885, year = {2014}, author = {Yarza, P and Yilmaz, P and Pruesse, E and Glöckner, FO and Ludwig, W and Schleifer, KH and Whitman, WB and Euzéby, J and Amann, R and Rosselló-Móra, R}, title = {Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences.}, journal = {Nature reviews. Microbiology}, volume = {12}, number = {9}, pages = {635-645}, pmid = {25118885}, issn = {1740-1534}, mesh = {Archaea/*classification/genetics ; Bacteria/*classification/genetics ; Computational Biology ; DNA, Archaeal/chemistry/genetics ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Databases, Nucleic Acid ; Phylogeny ; RNA, Ribosomal, 16S/chemistry/*genetics ; Ribotyping ; Sequence Analysis, DNA ; }, abstract = {Publicly available sequence databases of the small subunit ribosomal RNA gene, also known as 16S rRNA in bacteria and archaea, are growing rapidly, and the number of entries currently exceeds 4 million. However, a unified classification and nomenclature framework for all bacteria and archaea does not yet exist. In this Analysis article, we propose rational taxonomic boundaries for high taxa of bacteria and archaea on the basis of 16S rRNA gene sequence identities and suggest a rationale for the circumscription of uncultured taxa that is compatible with the taxonomy of cultured bacteria and archaea. Our analyses show that only nearly complete 16S rRNA sequences give accurate measures of taxonomic diversity. In addition, our analyses suggest that most of the 16S rRNA sequences of the high taxa will be discovered in environmental surveys by the end of the current decade.}, } @article {pmid25117551, year = {2014}, author = {Yan, X and Dong, X and Zhang, W and Yin, H and Xiao, H and Chen, P and Ma, XF}, title = {Reference gene selection for quantitative real-time PCR normalization in Reaumuria soongorica.}, journal = {PloS one}, volume = {9}, number = {8}, pages = {e104124}, pmid = {25117551}, issn = {1932-6203}, mesh = {Computational Biology ; Gene Expression Profiling ; Gene Expression Regulation, Plant ; *Genes, Plant ; RNA Stability ; Real-Time Polymerase Chain Reaction ; Reproducibility of Results ; Seeds/genetics ; Tamaricaceae/*genetics ; }, abstract = {Despite its superiority for evaluating gene expression, real-time quantitative polymerase chain reaction (qPCR) results can be significantly biased by the use of inappropriate reference genes under different experimental conditions. Reaumuria soongorica is a dominant species of desert ecosystems in arid central Asia. Given the increasing interest in ecological engineering and potential genetic resources for arid agronomy, it is important to analyze gene function. However, systematic evaluation of stable reference genes should be performed prior to such analyses. In this study, the stabilities of 10 candidate reference genes were analyzed under 4 kinds of abiotic stresses (drought, salt, dark, and heat) within 4 accessions (HG010, HG020, XGG030, and XGG040) from 2 different habitats using 3 algorithms (geNorm, NormFinder, and BestKeeper). After validation of the ribulose-1,5-bisphosphate carboxylase/oxygenase large unite (rbcL) expression pattern, our data suggested that histone H2A (H2A) and eukaryotic initiation factor 4A-2 (EIF4A2) were the most stable reference genes, cyclophilin (CYCL) was moderate, and elongation factor 1α (EF1α) was the worst choice. This first systematic analysis for stably expressed genes will facilitate future functional analyses and deep mining of genetic resources in R. soongorica and other species of the Reaumuria genus.}, } @article {pmid25116381, year = {2014}, author = {Norman, A and Riber, L and Luo, W and Li, LL and Hansen, LH and Sørensen, SJ}, title = {An improved method for including upper size range plasmids in metamobilomes.}, journal = {PloS one}, volume = {9}, number = {8}, pages = {e104405}, pmid = {25116381}, issn = {1932-6203}, mesh = {Computational Biology ; Conjugation, Genetic ; Gene Amplification ; *Genome Size ; High-Throughput Nucleotide Sequencing ; Plasmids/*genetics/*isolation & purification ; }, abstract = {Two recently developed isolation methods have shown promise when recovering pure community plasmid DNA (metamobilomes/plasmidomes), which is useful in conducting culture-independent investigations into plasmid ecology. However, both methods employ multiple displacement amplification (MDA) to ensure suitable quantities of plasmid DNA for high-throughput sequencing. This study demonstrates that MDA greatly favors smaller circular DNA elements (<10 Kbp), which, in turn, leads to stark underrepresentation of upper size range plasmids (>10 Kbp). Throughout the study, we used two model plasmids, a 4.4 Kbp cloning vector (pBR322), and a 56 Kbp conjugative plasmid (pKJK10), to represent lower- and upper plasmid size ranges, respectively. Subjecting a mixture of these plasmids to the overall isolation protocol revealed a 34-fold over-amplification of pBR322 after MDA. To address this bias, we propose the addition of an electroelution step that separates different plasmid size ranges prior to MDA in order to reduce size-dependent competition during incubation. Subsequent analyses of metamobilome data from wastewater spiked with the model plasmids showed in silica recovery of pKJK10 to be very poor with the established method and a 1,300-fold overrepresentation of pBR322. Conversely, complete recovery of pKJK10 was enabled with the new modified protocol although considerable care must be taken during electroelution to minimize cross-contamination between samples. For further validation, non-spiked wastewater metamobilomes were mapped to more than 2,500 known plasmid genomes. This displayed an overall recovery of plasmids well into the upper size range (median size: 30 kilobases) with the modified protocol. Analysis of de novo assembled metamobilome data also suggested distinctly better recovery of larger plasmids, as gene functions associated with these plasmids, such as conjugation, was exclusively encoded in the data output generated through the modified protocol. Thus, with the suggested modification, access to a large uncharacterized pool of accessory elements that reside on medium-to-large plasmids has been improved.}, } @article {pmid25110471, year = {2014}, author = {Krishnappa, YS and Turner, WC}, title = {Software for minimalistic data management in large camera trap studies.}, journal = {Ecological informatics}, volume = {24}, number = {}, pages = {11-16}, pmid = {25110471}, issn = {1574-9541}, support = {R01 GM083863/GM/NIGMS NIH HHS/United States ; }, abstract = {The use of camera traps is now widespread and their importance in wildlife studies well understood. Camera trap studies can produce millions of photographs and there is a need for software to help manage photographs efficiently. In this paper, we describe a software system that was built to successfully manage a large behavioral camera trap study that produced more than a million photographs. We describe the software architecture and the design decisions that shaped the evolution of the program over the study's three year period. The software system has the ability to automatically extract metadata from images, and add customized metadata to the images in a standardized format. The software system can be installed as a standalone application on popular operating systems. It is minimalistic, scalable and extendable so that it can be used by small teams or individual researchers for a broad variety of camera trap studies.}, } @article {pmid25108801, year = {2014}, author = {Manap, N and Voulvoulis, N}, title = {Risk-based decision-making framework for the selection of sediment dredging option.}, journal = {The Science of the total environment}, volume = {496}, number = {}, pages = {607-623}, doi = {10.1016/j.scitotenv.2014.07.009}, pmid = {25108801}, issn = {1879-1026}, mesh = {Decision Making ; *Decision Support Techniques ; Environment ; *Environmental Monitoring ; Geologic Sediments/*analysis/chemistry ; Risk Assessment/methods ; Ships ; Water Pollutants, Chemical/*analysis ; }, abstract = {The aim of this study was to develop a risk-based decision-making framework for the selection of sediment dredging option. Descriptions using case studies of the newly integrated, holistic and staged framework were followed. The first stage utilized the historical dredging monitoring data and the contamination level in media data into Ecological Risk Assessment phases, which have been altered for benefits in cost, time and simplicity. How Multi-Criteria Decision Analysis (MCDA) can be used to analyze and prioritize dredging areas based on environmental, socio-economic and managerial criteria was described for the next stage. The results from MCDA will be integrated into Ecological Risk Assessment to characterize the degree of contamination in the prioritized areas. The last stage was later described using these findings and analyzed using MCDA, in order to identify the best sediment dredging option, accounting for the economic, environmental and technical aspects of dredging, which is beneficial for dredging and sediment management industries.}, } @article {pmid25101771, year = {2014}, author = {Sousa, A and García-Barrón, L and Vetter, M and Morales, J}, title = {The historical distribution of main malaria foci in Spain as related to water bodies.}, journal = {International journal of environmental research and public health}, volume = {11}, number = {8}, pages = {7896-7917}, pmid = {25101771}, issn = {1660-4601}, mesh = {Animal Distribution ; Animals ; Anopheles/physiology ; *Climate Change ; Geographic Information Systems ; Geography ; History, 20th Century ; Malaria/epidemiology/*history/transmission ; Socioeconomic Factors ; Spain/epidemiology ; *Wetlands ; }, abstract = {The possible connectivity between the spatial distribution of water bodies suitable for vectors of malaria and endemic malaria foci in Southern Europe is still not well known. Spain was one of the last countries in Western Europe to be declared free of malaria by the World Health Organization (WHO) in 1964. This study combines, by means of a spatial-temporal analysis, the historical data of patients and deceased with the distribution of water bodies where the disease-transmitting mosquitos proliferate. Therefore, data from historical archives with a Geographic Information System (GIS), using the Inverse Distance Weighted (IDW) interpolation method, was analyzed with the aim of identifying regional differences in the distribution of malaria in Spain. The reasons, why the risk of transmission is concentrated in specific regions, are related to worse socioeconomic conditions (Extremadura), the presence of another vector (Anopheles labranchiae) besides A. atroparvus (Levante) or large areas of water bodies in conditions to reproduce theses vectors (La Mancha and Western Andalusia). In the particular case of Western Andalusia, in 1913, the relatively high percentage of 4.73% of the surface, equal to 202362 ha, corresponds to wetlands and other unhealthy water bodies. These wetlands have been reduced as a result of desiccation policies and climate change such as the Little Ice Age and Global Climate Change. The comprehension of the main factors of these wetland changes in the past can help us interpret accurately the future risk of malaria re-emergence in temperate latitudes, since it reveals the crucial role of unhealthy water bodies on the distribution, endemicity and eradication of malaria in southern Europe.}, } @article {pmid25100971, year = {2014}, author = {Barandiaran, XE and Di Paolo, EA}, title = {A genealogical map of the concept of habit.}, journal = {Frontiers in human neuroscience}, volume = {8}, number = {}, pages = {522}, pmid = {25100971}, issn = {1662-5161}, abstract = {The notion of information processing has dominated the study of the mind for over six decades. However, before the advent of cognitivism, one of the most prominent theoretical ideas was that of Habit. This is a concept with a rich and complex history, which is again starting to awaken interest, following recent embodied, enactive critiques of computationalist frameworks. We offer here a very brief history of the concept of habit in the form of a genealogical network-map. This serves to provide an overview of the richness of this notion and as a guide for further re-appraisal. We identify 77 thinkers and their influences, and group them into seven schools of thought. Two major trends can be distinguished. One is the associationist trend, starting with the work of Locke and Hume, developed by Hartley, Bain, and Mill to be later absorbed into behaviorism through pioneering animal psychologists (Morgan and Thorndike). This tradition conceived of habits atomistically and as automatisms (a conception later debunked by cognitivism). Another historical trend we have called organicism inherits the legacy of Aristotle and develops along German idealism, French spiritualism, pragmatism, and phenomenology. It feeds into the work of continental psychologists in the early 20th century, influencing important figures such as Merleau-Ponty, Piaget, and Gibson. But it has not yet been taken up by mainstream cognitive neuroscience and psychology. Habits, in this tradition, are seen as ecological, self-organizing structures that relate to a web of predispositions and plastic dependencies both in the agent and in the environment. In addition, they are not conceptualized in opposition to rational, volitional processes, but as transversing a continuum from reflective to embodied intentionality. These are properties that make habit a particularly attractive idea for embodied, enactive perspectives, which can now re-evaluate it in light of dynamical systems theory and complexity research.}, } @article {pmid25098421, year = {2014}, author = {Daigle, CL and Banerjee, D and Montgomery, RA and Biswas, S and Siegford, JM}, title = {Moving GIS research indoors: spatiotemporal analysis of agricultural animals.}, journal = {PloS one}, volume = {9}, number = {8}, pages = {e104002}, pmid = {25098421}, issn = {1932-6203}, mesh = {Animal Husbandry/*instrumentation/*methods ; Animals ; Behavior, Animal ; *Chickens ; Female ; *Geographic Information Systems ; Male ; }, abstract = {A proof of concept applying wildlife ecology techniques to animal welfare science in intensive agricultural environments was conducted using non-cage laying hens. Studies of wildlife ecology regularly use Geographic Information Systems (GIS) to assess wild animal movement and behavior within environments with relatively unlimited space and finite resources. However, rather than depicting landscapes, a GIS could be developed in animal production environments to provide insight into animal behavior as an indicator of animal welfare. We developed a GIS-based approach for studying agricultural animal behavior in an environment with finite space and unlimited resources. Concurrent data from wireless body-worn location tracking sensor and video-recording systems, which depicted spatially-explicit behavior of hens (135 hens/room) in two identical indoor enclosures, were collected. The spatial configuration of specific hen behaviors, variation in home range patterns, and variation in home range overlap show that individual hens respond to the same environment differently. Such information could catalyze management practice adjustments (e.g., modifying feeder design and/or location). Genetically-similar hens exhibited diverse behavioral and spatial patterns via a proof of concept approach enabling detailed examinations of individual non-cage laying hen behavior and welfare.}, } @article {pmid25093819, year = {2014}, author = {Kyrpides, NC and Hugenholtz, P and Eisen, JA and Woyke, T and Göker, M and Parker, CT and Amann, R and Beck, BJ and Chain, PS and Chun, J and Colwell, RR and Danchin, A and Dawyndt, P and Dedeurwaerdere, T and DeLong, EF and Detter, JC and De Vos, P and Donohue, TJ and Dong, XZ and Ehrlich, DS and Fraser, C and Gibbs, R and Gilbert, J and Gilna, P and Glöckner, FO and Jansson, JK and Keasling, JD and Knight, R and Labeda, D and Lapidus, A and Lee, JS and Li, WJ and Ma, J and Markowitz, V and Moore, ER and Morrison, M and Meyer, F and Nelson, KE and Ohkuma, M and Ouzounis, CA and Pace, N and Parkhill, J and Qin, N and Rossello-Mora, R and Sikorski, J and Smith, D and Sogin, M and Stevens, R and Stingl, U and Suzuki, K and Taylor, D and Tiedje, JM and Tindall, B and Wagner, M and Weinstock, G and Weissenbach, J and White, O and Wang, J and Zhang, L and Zhou, YG and Field, D and Whitman, WB and Garrity, GM and Klenk, HP}, title = {Genomic encyclopedia of bacteria and archaea: sequencing a myriad of type strains.}, journal = {PLoS biology}, volume = {12}, number = {8}, pages = {e1001920}, pmid = {25093819}, issn = {1545-7885}, mesh = {Archaea/classification/genetics ; Bacteria/classification/genetics ; Databases, Genetic ; Genome, Archaeal/*genetics ; Genome, Bacterial/*genetics ; *Genomics ; Phylogeny ; *Sequence Analysis, DNA ; }, abstract = {Microbes hold the key to life. They hold the secrets to our past (as the descendants of the earliest forms of life) and the prospects for our future (as we mine their genes for solutions to some of the planet's most pressing problems, from global warming to antibiotic resistance). However, the piecemeal approach that has defined efforts to study microbial genetic diversity for over 20 years and in over 30,000 genome projects risks squandering that promise. These efforts have covered less than 20% of the diversity of the cultured archaeal and bacterial species, which represent just 15% of the overall known prokaryotic diversity. Here we call for the funding of a systematic effort to produce a comprehensive genomic catalog of all cultured Bacteria and Archaea by sequencing, where available, the type strain of each species with a validly published name (currently∼11,000). This effort will provide an unprecedented level of coverage of our planet's genetic diversity, allow for the large-scale discovery of novel genes and functions, and lead to an improved understanding of microbial evolution and function in the environment.}, } @article {pmid25093322, year = {2014}, author = {Zhang, J and Li, Y and Chen, X and Pan, Y and Zhang, S and Wang, Y}, title = {Systems pharmacology dissection of multi-scale mechanisms of action for herbal medicines in stroke treatment and prevention.}, journal = {PloS one}, volume = {9}, number = {8}, pages = {e102506}, pmid = {25093322}, issn = {1932-6203}, mesh = {Caco-2 Cells ; Databases, Pharmaceutical ; Drug Evaluation, Preclinical ; Gene Expression Regulation/drug effects ; Herbal Medicine ; Humans ; Molecular Targeted Therapy ; *Pharmacological Phenomena ; Plant Preparations/*pharmacology/*therapeutic use ; Plants, Medicinal ; Salvia miltiorrhiza ; Scutellaria baicalensis ; Stroke/*drug therapy/*prevention & control ; Systems Biology/*methods ; Uncaria ; }, abstract = {Annually, tens of millions of first-ever strokes occur in the world; however, currently there is lack of effective and widely applicable pharmacological treatments for stroke patients. Herbal medicines, characterized as multi-constituent, multi-target and multi-effect, have been acknowledged with conspicuous effects in treating stroke, and attract extensive interest of researchers although the mechanism of action is yet unclear. In this work, we introduce an innovative systems-pharmacology method that combines pharmacokinetic prescreening, target fishing and network analysis to decipher the mechanisms of action of 10 herbal medicines like Salvia miltiorrhizae, Ginkgo biloba and Ephedrae herba which are efficient in stroke treatment and prevention. Our systematic analysis results display that, in these anti-stroke herbal medicines, 168 out of 1285 constituents with the favorable pharmacokinetic profiles might be implicated in stroke therapy, and the systematic use of these compounds probably acts through multiple mechanisms to synergistically benefit patients with stroke, which can roughly be classified as preventing ischemic inflammatory response, scavenging free radicals and inhibiting neuronal apoptosis against ischemic cerebral damage, as well as exhibiting lipid-lowering, anti-diabetic, anti-thrombotic and antiplatelet effects to decrease recurrent strokes. Relying on systems biology-based analysis, we speculate that herbal medicines, being characterized as the classical combination therapies, might be not only engaged in multiple mechanisms of action to synergistically improve the stroke outcomes, but also might be participated in reducing the risk factors for recurrent strokes.}, } @article {pmid25086984, year = {2014}, author = {Gao, B and Zhang, D and Li, X and Yang, H and Wood, AJ}, title = {De novo assembly and characterization of the transcriptome in the desiccation-tolerant moss Syntrichia caninervis.}, journal = {BMC research notes}, volume = {7}, number = {}, pages = {490}, pmid = {25086984}, issn = {1756-0500}, mesh = {Adaptation, Physiological/*genetics ; Bryopsida/*genetics ; Databases, Protein ; *Desiccation ; Gene Ontology ; High-Throughput Nucleotide Sequencing/*methods ; Metabolic Networks and Pathways/genetics ; Models, Biological ; Molecular Sequence Annotation ; RNA, Messenger/genetics/metabolism ; Species Specificity ; Transcription Factors/metabolism ; Transcriptome/*genetics ; }, abstract = {BACKGROUND: Syntrichia caninervis is a desiccation-tolerant moss and the dominant bryophyte of the Biological Soil Crusts (BSCs) found in the Mojave and Gurbantunggut deserts. Next generation high throughput sequencing technologies offer an efficient and economic choice for characterizing non-model organism transcriptomes with little or no prior molecular information available.

RESULTS: In this study, we employed next generation, high-throughput, Illumina RNA-Seq to analyze the poly-(A) + mRNA from hydrated, dehydrating and desiccated S. caninervis gametophores. Approximately 58.0 million paired-end short reads were obtained and 92,240 unigenes were assembled with an average size of 493 bp, N50 value of 662 bp and a total size of 45.48 Mbp. Sequence similarity searches against five public databases (NR, Swiss-Prot, COSMOSS, KEGG and COG) found 54,125 unigenes (58.7%) with significant similarity to an existing sequence (E-value ≤ 1e-5) and could be annotated. Gene Ontology (GO) annotation assigned 24,183 unigenes to the three GO terms: Biological Process, Cellular Component or Molecular Function. GO comparison between P. patens and S. caninervis demonstrated similar sequence enrichment across all three GO categories. 29,370 deduced polypeptide sequences were assigned Pfam domain information and categorized into 4,212 Pfam domains/families. Using the PlantTFDB, 778 unigenes were predicted to be involved in the regulation of transcription and were classified into 49 transcription factor families. Annotated unigenes were mapped to the KEGG pathways and further annotated using MapMan. Comparative genomics revealed that 44% of protein families are shared in common by S. caninervis, P. patens and Arabidopsis thaliana and that 80% are shared by both moss species.

CONCLUSIONS: This study is one of the first comprehensive transcriptome analyses of the moss S. caninervis. Our data extends our knowledge of bryophyte transcriptomes, provides an insight to plants adapted to the arid regions of central Asia, and continues the development of S. caninervis as a model for understanding the molecular aspects of desiccation-tolerance.}, } @article {pmid25086298, year = {2014}, author = {Kim, J and Wozniak, JR and Mueller, BA and Shen, X and Pan, W}, title = {Comparison of statistical tests for group differences in brain functional networks.}, journal = {NeuroImage}, volume = {101}, number = {}, pages = {681-694}, pmid = {25086298}, issn = {1095-9572}, support = {R01 GM081535/GM/NIGMS NIH HHS/United States ; R01 GM113250/GM/NIGMS NIH HHS/United States ; R01GM081535/GM/NIGMS NIH HHS/United States ; R01 HL105397/HL/NHLBI NIH HHS/United States ; R01 HL116720/HL/NHLBI NIH HHS/United States ; R01HL105397/HL/NHLBI NIH HHS/United States ; R01 HL065462/HL/NHLBI NIH HHS/United States ; R01HL65462/HL/NHLBI NIH HHS/United States ; R01HL116720/HL/NHLBI NIH HHS/United States ; }, mesh = {Adolescent ; Brain/*physiology ; Child ; Computer Simulation ; Connectome/*methods ; *Data Interpretation, Statistical ; Fetal Alcohol Spectrum Disorders/physiopathology ; Humans ; Magnetic Resonance Imaging ; Nerve Net/*physiology ; }, abstract = {Brain functional connectivity has been studied by analyzing time series correlations in regional brain activities based on resting-state fMRI data. Brain functional connectivity can be depicted as a network or graph defined as a set of nodes linked by edges. Nodes represent brain regions and an edge measures the strength of functional correlation between two regions. Most of existing work focuses on estimation of such a network. A key but inadequately addressed question is how to test for possible differences of the networks between two subject groups, say between healthy controls and patients. Here we illustrate and compare the performance of several state-of-the-art statistical tests drawn from the neuroimaging, genetics, ecology and high-dimensional data literatures. Both real and simulated data were used to evaluate the methods. We found that Network Based Statistic (NBS) performed well in many but not all situations, and its performance critically depends on the choice of its threshold parameter, which is unknown and difficult to choose in practice. Importantly, two adaptive statistical tests called adaptive sum of powered score (aSPU) and its weighted version (aSPUw) are easy to use and complementary to NBS, being higher powered than NBS in some situations. The aSPU and aSPUw tests can also be applied to adjust for covariates. Between the aSPU and aSPUw tests, they often, but not always, performed similarly with neither one as a uniform winner. On the other hand, Multivariate Matrix Distance Regression (MDMR) has been applied to detect group differences for brain connectivity; with the usual choice of the Euclidean distance, MDMR is a special case of the aSPU test. Consequently NBS, aSPU and aSPUw tests are recommended to test for group differences in functional connectivity.}, } @article {pmid25085641, year = {2014}, author = {Busigny, T and Pagès, B and Barbeau, EJ and Bled, C and Montaut, E and Raposo, N and Albucher, JF and Chollet, F and Pariente, J}, title = {A systematic study of topographical memory and posterior cerebral artery infarctions.}, journal = {Neurology}, volume = {83}, number = {11}, pages = {996-1003}, doi = {10.1212/WNL.0000000000000780}, pmid = {25085641}, issn = {1526-632X}, mesh = {Brain/*pathology ; Diagnosis, Computer-Assisted ; Female ; Functional Laterality ; Humans ; Infarction, Posterior Cerebral Artery/complications/*pathology ; Magnetic Resonance Imaging ; Male ; *Maps as Topic ; Maze Learning ; Memory Disorders/*epidemiology/etiology/*pathology ; Middle Aged ; Neuropsychological Tests ; Pattern Recognition, Visual ; Prevalence ; }, abstract = {OBJECTIVE: To estimate the prevalence of topographical memory impairment following posterior cerebral artery infarctions (PCAI) and define its anatomical correlations.

METHODS: We recruited 15 patients (mean duration of 4 months postinfarct). We administered 2 sets of experimental tests to assess topographical memory: one set included 5 computerized tasks (CompT) and the other set consisted of one ecological topographical orientation test (EcolT) that included 4 tasks (i.e., map drawing, picture recognition and ordering, backward path). Fifteen healthy participants served as controls. Patients and controls underwent a volumetric T1 MRI brain scan. Brain lesions in patients were segmented, normalized, and correlated with performance.

RESULTS: Topographical memory impairments were evidenced in patients with PCAI using both group and individual analyses (50%), with more severe outcomes in patients with PCAI in the right hemisphere. CompT and EcolT were highly correlated, but the ecological test was more sensitive in revealing topographical memory impairments. Voxel-based lesion-symptom mapping demonstrated that 2 regions located in the cuneus and the calcarine sulcus correlated significantly with behavioral performance.

CONCLUSIONS: Topographical memory disorders following PCAI are reported in 50% of the patient population. Our results demonstrate the importance of developing and using dedicated batteries of topographical memory tests, in particular real-life tests, to identify such deficits.}, } @article {pmid25085486, year = {2014}, author = {De Pasquale, I and Di Cagno, R and Buchin, S and De Angelis, M and Gobbetti, M}, title = {Microbial ecology dynamics reveal a succession in the core microbiota involved in the ripening of pasta filata caciocavallo pugliese cheese.}, journal = {Applied and environmental microbiology}, volume = {80}, number = {19}, pages = {6243-6255}, pmid = {25085486}, issn = {1098-5336}, mesh = {Animals ; *Biodiversity ; Cheese/*microbiology ; Computational Biology ; Fatty Acids, Volatile/analysis ; Female ; Food Handling ; *Food Microbiology ; High-Throughput Nucleotide Sequencing ; Microbiota/genetics/*physiology ; Milk/*microbiology ; Proteolysis ; RNA, Bacterial/chemistry/genetics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Pyrosequencing of the 16S rRNA targeting RNA, community-level physiological profiles made with Biolog EcoPlates, proteolysis, and volatile component (VOC) analyses were mainly used to characterize the manufacture and ripening of the pasta filata cheese Caciocavallo Pugliese. Plate counts revealed that cheese manufacture affected the microbial ecology. The results agreed with those from culture-independent approaches. As shown by urea-PAGE, reverse-phase high pressure liquid chromatography (RP-HPLC), and free-amino-acid (FAA) analyses, the extent of secondary proteolysis mainly increased after 30 to 45 days of ripening. VOCs and volatile free fatty acids (VFFA) were identified by a purge-and-trap method (PT) and solid-phase microextraction (SPME) coupled with gas chromatography-mass spectrometry (GC-MS), respectively. Except for aldehydes, the levels of most of VOCs and VFFA mainly increased from 30 to 45 days onwards. As shown through pyrosequencing analysis, raw cows' milk was contaminated by Firmicutes (53%), Proteobacteria (39%), Bacteroidetes (7.8%), Actinobacteria (0.06%), and Fusobacteria (0.03%), with heterogeneity at the genus level. The primary starter Streptococcus thermophilus dominated the curd population. Other genera occurred at low incidence or sporadically. The microbial dynamics reflected on the overall physiological diversity. At 30 days, a microbial succession was clearly highlighted. The relative abundance of Streptococcus sp. and especially St. thermophilus decreased, while that of Lactobacillus casei, Lactobacillus sp., and especially Lactobacillus paracasei increased consistently. Despite the lower relative abundance compared to St. thermophilus, mesophilic lactobacilli were the only organisms positively correlated with the concentration of FAAs, area of hydrophilic peptide peaks, and several VOCs (e.g., alcohols, ketones, esters and all furans). This study showed that a core microbiota was naturally selected during middle ripening, which seemed to be the main factor responsible for cheese ripening.}, } @article {pmid25084228, year = {2014}, author = {Brevé, NWP and Buijse, AD and Kroes, MJ and Wanningen, H and Vriese, FT}, title = {Supporting decision-making for improving longitudinal connectivity for diadromous and potamodromous fishes in complex catchments.}, journal = {The Science of the total environment}, volume = {496}, number = {}, pages = {206-218}, doi = {10.1016/j.scitotenv.2014.07.043}, pmid = {25084228}, issn = {1879-1026}, mesh = {*Animal Migration ; Animals ; Conservation of Natural Resources/*methods ; *Decision Support Techniques ; *Ecosystem ; Europe ; Fishes/*physiology ; Rivers/chemistry ; }, abstract = {Preservation and restoration of Europe's endangered migratory fish species and habitats are high on the international river basin policy agenda. Improvement through restoration of longitudinal connectivity is seen as an important measure, but although prioritization of in-stream barriers has been addressed at local and regional levels the process still lacks adequate priority on the international level. This paper introduces a well-tested method, designed to help decision makers achieve the rehabilitation of targeted ichthyofauna more successfully. This method assesses artificial barriers within waters designated under the Water Framework Directive (WFD), Europe's main legislative driver for ecological improvement of river basins. The method aggregates migratory fish communities (both diadromous and potamodromous) into functional biological units (ecological fish guilds) and defines their most pressing habitat requirements. Using GIS mapping and spatial analysis of the potential ranges (fish zonation) we pin-point the most important barriers, per guild. This method was developed and deployed over a 12 year period as a practical case study, fitting data derived from the 36 regional water management organisations in the Netherlands. We delivered national advice on the prioritization of a total of 2924 barriers located within WFD water bodies, facilitating migration for all 18 indigenous migratory fish species. Scaling up to larger geographical areas can be achieved using datasets from other countries to link water body typologies to distribution ranges of migratory fish species.}, } @article {pmid25084126, year = {2014}, author = {Keller, A and Horn, H and Förster, F and Schultz, J}, title = {Computational integration of genomic traits into 16S rDNA microbiota sequencing studies.}, journal = {Gene}, volume = {549}, number = {1}, pages = {186-191}, doi = {10.1016/j.gene.2014.07.066}, pmid = {25084126}, issn = {1879-0038}, mesh = {Bacteria/classification/*genetics ; Computational Biology/*methods ; DNA Barcoding, Taxonomic ; DNA, Bacterial/*genetics ; DNA, Ribosomal/*genetics ; Genetic Markers ; Genome, Bacterial ; Genomics ; Metagenomics ; Microbiota/*genetics ; Multigene Family ; RNA, Ribosomal, 16S/*genetics ; Reproducibility of Results ; }, abstract = {Molecular sequencing techniques help to understand microbial biodiversity with regard to species richness, assembly structure and function. In this context, available methods are barcoding, metabarcoding, genomics and metagenomics. The first two are restricted to taxonomic assignments, whilst genomics only refers to functional capabilities of a single organism. Metagenomics by contrast yields information about organismal and functional diversity of a community. However currently it is very demanding regarding labour and costs and thus not applicable to most laboratories. Here, we show in a proof-of-concept that computational approaches are able to retain functional information about microbial communities assessed through 16S rDNA (meta)barcoding by referring to reference genomes. We developed an automatic pipeline to show that such integration may infer preliminary or supplementary genomic content of a community. We applied it to two biological datasets and delineated significantly overrepresented protein families between communities. The script alongside supporting data is available at http://bioapps.biozentrum.uni-wuerzburg.de.}, } @article {pmid25081310, year = {2014}, author = {Ocaña-Riola, R and Blanco-Reina, E and Navarro-Moreno, E and Mayoral-Cortés, JM}, title = {Age-period-cohort effects on mortality from cerebrovascular disease in southern Spain.}, journal = {Journal of stroke and cerebrovascular diseases : the official journal of National Stroke Association}, volume = {23}, number = {9}, pages = {2274-2282}, doi = {10.1016/j.jstrokecerebrovasdis.2014.04.015}, pmid = {25081310}, issn = {1532-8511}, mesh = {Adolescent ; Adult ; Age Factors ; Aged ; Aged, 80 and over ; Cerebrovascular Disorders/*mortality ; Cohort Effect ; Data Interpretation, Statistical ; Female ; Geography ; Humans ; Male ; Middle Aged ; Poisson Distribution ; Sex Factors ; Spain/epidemiology ; Young Adult ; }, abstract = {BACKGROUND: The aim of this article is to evaluate the age-period-cohort effects on mortality from cerebrovascular disease in Andalusia (southern Spain) as a whole and in each of its 8 provinces during the period 1981-2008.

METHODS: A population-based ecologic study was conducted. In all, 145,867 deaths were analyzed for individuals between the ages of 15 and 84 years who died in Andalusia in the period of study. A nonlinear regression model was estimated for each gender group and geographic area. The effects of age, year of death, and birth cohort were parameterized using spline smoothing functions.

RESULTS: There is an upward trend in mortality from the age of 25 years. The risk of death was downward for cohorts born after 1896, decreasing after 1970 with steep slope. The analysis of the period effect showed that death rate first declined from 1981 to 1995 and then increased between 1995 and 2000, only to decrease again until 2008.

CONCLUSIONS: There is a similar age-period-cohort effect on male and female mortality from cerebrovascular disease in all the provinces of Andalusia and for Andalusia as a whole. A significant reduction of male and female mortality has been observed during the last decade.}, } @article {pmid25079144, year = {2014}, author = {Fu, KW and Chan, CH and Ip, P}, title = {Exploring the relationship between cyberbullying and unnatural child death: an ecological study of twenty-four European countries.}, journal = {BMC pediatrics}, volume = {14}, number = {}, pages = {195}, pmid = {25079144}, issn = {1471-2431}, mesh = {Accidents/mortality ; Adolescent ; Behavior, Addictive/epidemiology ; *Bullying ; *Cause of Death ; Child ; *Child Mortality ; Databases, Factual ; Europe/epidemiology ; Health Surveys ; Humans ; *Internet ; Models, Statistical ; Poisson Distribution ; Prevalence ; Regression Analysis ; Risk Factors ; Self-Injurious Behavior/epidemiology/etiology ; Violence/statistics & numerical data ; }, abstract = {BACKGROUND: Internet risk has been recognised as a child safety problem, but evidence is insufficient to conclude that a child's online risk exposure can lead to physical harm. This study aims to explore the ecological relationship between Internet risk exposure and unnatural child death.

METHODS: Multiple secondary data sources were used: online exposure to content about self-harm, cyberbullying, and Internet addiction data (EU Kids Online survey, 2010); and mortality data (European Detailed Mortality Database, 2010 or the latest year if not available) of 24 European countries. Correlations were found using quasi-Poisson regression. Countries' prevalence rates of psychiatric problems (European Social Survey Round 3 and 6, 2006 and 2012) were used to test for possible spuriousness.

RESULTS: This study finds that countries with higher rates of cyberbullying were more likely to have a higher incidence of unnatural child death. A 1 percent rise in the prevalence of cyberbullying translated into a 28% increase in risk of unnatural child death (95% CI: 2%-57%). No evidence was found to substantiate confounding effect of the national prevalence of depressive symptoms or traditional bullying.

CONCLUSIONS: Explanations are given for the findings. We conclude that intervention programs designed to serve as precautionary measures for risk minimisation should be considered.}, } @article {pmid25075546, year = {2015}, author = {Ana, GR and Ojelabi, P and Shendell, DG}, title = {Spatial-temporal variations in carbon dioxide levels in Ibadan, Nigeria.}, journal = {International journal of environmental health research}, volume = {25}, number = {3}, pages = {229-240}, doi = {10.1080/09603123.2014.938024}, pmid = {25075546}, issn = {1369-1619}, mesh = {Carbon Dioxide/*analysis ; Cities ; Environmental Monitoring/instrumentation/*methods ; Geographic Information Systems ; Nigeria ; Seasons ; Spatio-Temporal Analysis ; }, abstract = {Growing evidence suggests how global background levels of atmospheric carbon dioxide (CO2) are increasing and this impacts environmental quality and human and ecological health. Data from less developed countries are sparse. We determined spatial and temporal variations in concentrations of CO2 in selected locations in Ibadan, Nigeria with identifiable prominent outdoor sources. Activity driven areas in north and south-west areas were identified and marked with a global positioning system. Waste management practices and activities generating CO2 were documented and described using a technician observation checklist. CO2 levels were measured using a portable TELAIRE 7001 attached to HOBO U12 data loggers across seasons. Mean CO2 levels were compared over seasons, i.e. rainy season months and the dry season months. While CO2 levels recorded outdoors in study areas were comparable to available international data, routine monitoring is recommended to further characterize concurrent pollutants in fossil fuel combustion emissions with known deleterious health effects.}, } @article {pmid25073721, year = {2014}, author = {Stucky, BJ and Deck, J and Conlin, T and Ziemba, L and Cellinese, N and Guralnick, R}, title = {The BiSciCol Triplifier: bringing biodiversity data to the Semantic Web.}, journal = {BMC bioinformatics}, volume = {15}, number = {1}, pages = {257}, pmid = {25073721}, issn = {1471-2105}, mesh = {*Biodiversity ; Computational Biology/*methods ; *Internet ; *Semantics ; *Software ; User-Computer Interface ; }, abstract = {BACKGROUND: Recent years have brought great progress in efforts to digitize the world's biodiversity data, but integrating data from many different providers, and across research domains, remains challenging. Semantic Web technologies have been widely recognized by biodiversity scientists for their potential to help solve this problem, yet these technologies have so far seen little use for biodiversity data. Such slow uptake has been due, in part, to the relative complexity of Semantic Web technologies along with a lack of domain-specific software tools to help non-experts publish their data to the Semantic Web.

RESULTS: The BiSciCol Triplifier is new software that greatly simplifies the process of converting biodiversity data in standard, tabular formats, such as Darwin Core-Archives, into Semantic Web-ready Resource Description Framework (RDF) representations. The Triplifier uses a vocabulary based on the popular Darwin Core standard, includes both Web-based and command-line interfaces, and is fully open-source software.

CONCLUSIONS: Unlike most other RDF conversion tools, the Triplifier does not require detailed familiarity with core Semantic Web technologies, and it is tailored to a widely popular biodiversity data format and vocabulary standard. As a result, the Triplifier can often fully automate the conversion of biodiversity data to RDF, thereby making the Semantic Web much more accessible to biodiversity scientists who might otherwise have relatively little knowledge of Semantic Web technologies. Easy availability of biodiversity data as RDF will allow researchers to combine data from disparate sources and analyze them with powerful linked data querying tools. However, before software like the Triplifier, and Semantic Web technologies in general, can reach their full potential for biodiversity science, the biodiversity informatics community must address several critical challenges, such as the widespread failure to use robust, globally unique identifiers for biodiversity data.}, } @article {pmid25072884, year = {2014}, author = {Lorenz, A and Dhingra, R and Chang, HH and Bisanzio, D and Liu, Y and Remais, JV}, title = {Inter-model comparison of the landscape determinants of vector-borne disease: implications for epidemiological and entomological risk modeling.}, journal = {PloS one}, volume = {9}, number = {7}, pages = {e103163}, pmid = {25072884}, issn = {1932-6203}, support = {K01 AI091864/AI/NIAID NIH HHS/United States ; U01 EH000405/EH/NCEH CDC HHS/United States ; 5 U01 EH000405/EH/NCEH CDC HHS/United States ; K01AI091864/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Communicable Diseases/*epidemiology/*transmission ; Datasets as Topic ; *Disease Vectors ; Humans ; Ixodes ; Lyme Disease/transmission ; *Models, Theoretical ; Odds Ratio ; Reproducibility of Results ; Risk ; United States ; }, abstract = {Extrapolating landscape regression models for use in assessing vector-borne disease risk and other applications requires thoughtful evaluation of fundamental model choice issues. To examine implications of such choices, an analysis was conducted to explore the extent to which disparate landscape models agree in their epidemiological and entomological risk predictions when extrapolated to new regions. Agreement between six literature-drawn landscape models was examined by comparing predicted county-level distributions of either Lyme disease or Ixodes scapularis vector using Spearman ranked correlation. AUC analyses and multinomial logistic regression were used to assess the ability of these extrapolated landscape models to predict observed national data. Three models based on measures of vegetation, habitat patch characteristics, and herbaceous landcover emerged as effective predictors of observed disease and vector distribution. An ensemble model containing these three models improved precision and predictive ability over individual models. A priori assessment of qualitative model characteristics effectively identified models that subsequently emerged as better predictors in quantitative analysis. Both a methodology for quantitative model comparison and a checklist for qualitative assessment of candidate models for extrapolation are provided; both tools aim to improve collaboration between those producing models and those interested in applying them to new areas and research questions.}, } @article {pmid25072414, year = {2015}, author = {Larsen, PE and Scott, N and Post, AF and Field, D and Knight, R and Hamada, Y and Gilbert, JA}, title = {Satellite remote sensing data can be used to model marine microbial metabolite turnover.}, journal = {The ISME journal}, volume = {9}, number = {1}, pages = {166-179}, pmid = {25072414}, issn = {1751-7370}, support = {//Howard Hughes Medical Institute/United States ; }, mesh = {Bacteria/*genetics/metabolism ; England ; Environmental Monitoring/*methods ; Geographic Information Systems ; Humans ; Models, Biological ; *Oceans and Seas ; RNA, Ribosomal, 16S/genetics ; *Satellite Imagery ; Seawater/*microbiology ; *Water Microbiology ; }, abstract = {Sampling ecosystems, even at a local scale, at the temporal and spatial resolution necessary to capture natural variability in microbial communities are prohibitively expensive. We extrapolated marine surface microbial community structure and metabolic potential from 72 16S rRNA amplicon and 8 metagenomic observations using remotely sensed environmental parameters to create a system-scale model of marine microbial metabolism for 5904 grid cells (49 km(2)) in the Western English Chanel, across 3 years of weekly averages. Thirteen environmental variables predicted the relative abundance of 24 bacterial Orders and 1715 unique enzyme-encoding genes that encode turnover of 2893 metabolites. The genes' predicted relative abundance was highly correlated (Pearson Correlation 0.72, P-value <10(-6)) with their observed relative abundance in sequenced metagenomes. Predictions of the relative turnover (synthesis or consumption) of CO2 were significantly correlated with observed surface CO2 fugacity. The spatial and temporal variation in the predicted relative abundances of genes coding for cyanase, carbon monoxide and malate dehydrogenase were investigated along with the predicted inter-annual variation in relative consumption or production of ∼3000 metabolites forming six significant temporal clusters. These spatiotemporal distributions could possibly be explained by the co-occurrence of anaerobic and aerobic metabolisms associated with localized plankton blooms or sediment resuspension, which facilitate the presence of anaerobic micro-niches. This predictive model provides a general framework for focusing future sampling and experimental design to relate biogeochemical turnover to microbial ecology.}, } @article {pmid25065533, year = {2014}, author = {Reddy, BV and Milshteyn, A and Charlop-Powers, Z and Brady, SF}, title = {eSNaPD: a versatile, web-based bioinformatics platform for surveying and mining natural product biosynthetic diversity from metagenomes.}, journal = {Chemistry & biology}, volume = {21}, number = {8}, pages = {1023-1033}, pmid = {25065533}, issn = {1879-1301}, support = {/HHMI/Howard Hughes Medical Institute/United States ; F32 AI110029/AI/NIAID NIH HHS/United States ; R01 GM077516/GM/NIGMS NIH HHS/United States ; GM077516/GM/NIGMS NIH HHS/United States ; }, mesh = {Biological Products/chemistry/*metabolism ; Computational Biology/*methods ; DNA/genetics ; *Metagenome ; }, abstract = {Environmental Surveyor of Natural Product Diversity (eSNaPD) is a web-based bioinformatics and data aggregation platform that aids in the discovery of gene clusters encoding both novel natural products and new congeners of medicinally relevant natural products using (meta)genomic sequence data. Using PCR-generated sequence tags, the eSNaPD data-analysis pipeline profiles biosynthetic diversity hidden within (meta)genomes by comparing sequence tags to a reference data set of characterized gene clusters. Sample mapping, molecule discovery, library mapping, and new clade visualization modules facilitate the interrogation of large (meta)genomic sequence data sets for diverse downstream analyses, including, but not limited to, the identification of environments rich in untapped biosynthetic diversity, targeted molecule discovery efforts, and chemical ecology studies. eSNaPD is designed to generate a global atlas of biosynthetic diversity that can facilitate a systematic, sequence-based interrogation of nature's biosynthetic potential.}, } @article {pmid25063050, year = {2015}, author = {Wohlfahrt, G and Tasser, E}, title = {A mobile system for quantifying the spatial variability of the surface energy balance: design and application.}, journal = {International journal of biometeorology}, volume = {59}, number = {5}, pages = {617-627}, pmid = {25063050}, issn = {1432-1254}, support = {P 23267/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {*Energy Transfer ; Environmental Monitoring/*instrumentation ; Equipment Design ; Equipment Failure Analysis ; Humidity ; Information Storage and Retrieval/methods ; Meteorology/*instrumentation ; Miniaturization ; Radiometry/instrumentation ; Reproducibility of Results ; Sensitivity and Specificity ; Soil/*chemistry ; Surface Properties ; Systems Integration ; Thermography/*instrumentation ; Water/analysis ; *Wind ; }, abstract = {We present a mobile device for the quantification of the small-scale (a few square meters) spatial variability in the surface energy balance components and several auxiliary variables of short-statured (<1 m) canopies. The key element of the mobile device is a handheld four-component net radiometer for the quantification of net radiation, albedo and infrared surface temperature, which is complemented with measurements of air temperature, wind speed, soil temperature and soil water content. Data are acquired by a battery-powered data logger, which is mounted on a backpack together with the auxiliary sensors. The proposed device was developed to bridge between the spatial scales of satellite/airborne remote sensing and fixed, stationary tower-based measurements with an emphasis on micrometeorological, catchment hydrological and landscape-ecological research questions. The potential of the new device is demonstrated through four selected case studies, which cover the issues of net radiation heterogeneity within the footprint of eddy covariance flux measurements due to (1) land use and (2) slope and aspect of the underlying surface, (3) controls on landscape-scale variability in soil temperature and albedo and (4) the estimation of evapotranspiration based exclusively on measurements with the mobile device.}, } @article {pmid25061375, year = {2014}, author = {Lepage, D and Vaidya, G and Guralnick, R}, title = {Avibase - a database system for managing and organizing taxonomic concepts.}, journal = {ZooKeys}, volume = {}, number = {420}, pages = {117-135}, pmid = {25061375}, issn = {1313-2989}, abstract = {Scientific names of biological entities offer an imperfect resolution of the concepts that they are intended to represent. Often they are labels applied to entities ranging from entire populations to individual specimens representing those populations, even though such names only unambiguously identify the type specimen to which they were originally attached. Thus the real-life referents of names are constantly changing as biological circumscriptions are redefined and thereby alter the sets of individuals bearing those names. This problem is compounded by other characteristics of names that make them ambiguous identifiers of biological concepts, including emendations, homonymy and synonymy. Taxonomic concepts have been proposed as a way to address issues related to scientific names, but they have yet to receive broad recognition or implementation. Some efforts have been made towards building systems that address these issues by cataloguing and organizing taxonomic concepts, but most are still in conceptual or proof-of-concept stage. We present the on-line database Avibase as one possible approach to organizing taxonomic concepts. Avibase has been successfully used to describe and organize 844,000 species-level and 705,000 subspecies-level taxonomic concepts across every major bird taxonomic checklist of the last 125 years. The use of taxonomic concepts in place of scientific names, coupled with efficient resolution services, is a major step toward addressing some of the main deficiencies in the current practices of scientific name dissemination and use.}, } @article {pmid25055119, year = {2014}, author = {Jobstvogt, N and Townsend, M and Witte, U and Hanley, N}, title = {How can we identify and communicate the ecological value of deep-sea ecosystem services?.}, journal = {PloS one}, volume = {9}, number = {7}, pages = {e100646}, pmid = {25055119}, issn = {1932-6203}, mesh = {Conservation of Natural Resources/*methods ; Ecology/*methods ; *Ecosystem ; Geographic Information Systems ; Geography ; Humans ; *Oceans and Seas ; Portugal ; Seawater/chemistry ; Water Movements ; }, abstract = {Submarine canyons are considered biodiversity hotspots which have been identified for their important roles in connecting the deep sea with shallower waters. To date, a huge gap exists between the high importance that scientists associate with deep-sea ecosystem services and the communication of this knowledge to decision makers and to the wider public, who remain largely ignorant of the importance of these services. The connectivity and complexity of marine ecosystems makes knowledge transfer very challenging, and new communication tools are necessary to increase understanding of ecological values beyond the science community. We show how the Ecosystem Principles Approach, a method that explains the importance of ocean processes via easily understandable ecological principles, might overcome this challenge for deep-sea ecosystem services. Scientists were asked to help develop a list of clear and concise ecosystem principles for the functioning of submarine canyons through a Delphi process to facilitate future transfers of ecological knowledge. These ecosystem principles describe ecosystem processes, link such processes to ecosystem services, and provide spatial and temporal information on the connectivity between deep and shallow waters. They also elucidate unique characteristics of submarine canyons. Our Ecosystem Principles Approach was successful in integrating ecological information into the ecosystem services assessment process. It therefore has a high potential to be the next step towards a wider implementation of ecological values in marine planning. We believe that successful communication of ecological knowledge is the key to a wider public support for ocean conservation, and that this endeavour has to be driven by scientists in their own interest as major deep-sea stakeholders.}, } @article {pmid25055064, year = {2014}, author = {Almeida, MC and Gomes, Cde M and Nascimento, LF}, title = {Spatial distribution of deaths due to Alzheimer's disease in the state of São Paulo, Brazil.}, journal = {Sao Paulo medical journal = Revista paulista de medicina}, volume = {132}, number = {4}, pages = {199-204}, pmid = {25055064}, issn = {1806-9460}, mesh = {Alzheimer Disease/etiology/*mortality ; Brazil/epidemiology ; Cause of Death/trends ; Cluster Analysis ; Geographic Information Systems ; *Geographic Mapping ; Humans ; Spatial Analysis ; }, abstract = {CONTEXT AND OBJECTIVE: Alzheimer's disease is a common cause of dementia and identifying possible spatial patterns of mortality due to this disease may enable preventive actions. The objective of this study was to identify spatial distribution patterns of mortality due to Alzheimer's disease in the state of São Paulo.

DESIGN AND SETTING: Ecological and exploratory study conducted in all municipalities in the state of São Paulo.

METHODS: Data on Alzheimer's disease mortality in the state of São Paulo between 2004 and 2009 were obtained from DATASUS (the Department of Informatics in the Brazilian Ministry of Health). Death rates per 100,000 inhabitants were then calculated and spatial analysis was performed by constructing a death rate map, global Moran index and local Moran index, which were used to obtain the Moran map. The kernel technique was also applied. The Terra View 4.0.0 software was used.

RESULTS: 13,030 deaths due to Alzheimer were reported in the state of São Paulo (rate of 5.33 deaths/100,000 inhabitants). São José do Rio Preto, Ribeirão Preto, Bauru and Araçatuba had higher rates. The Moran index was I = 0.085 (P < 0.002). The Moran map identified 42 municipalities that merit intervention and the kernel estimator identified a high density of deaths in the northwestern region of the state.

CONCLUSION: Higher densities of deaths due to Alzheimer were concentrated more to the north and northwest of the state of São Paulo. It was possible to identify municipalities that have priority for interventions to reduce the death rates due to this disease.}, } @article {pmid25052703, year = {2014}, author = {Müller, S and Rycak, L and Afonso-Grunz, F and Winter, P and Zawada, AM and Damrath, E and Scheider, J and Schmäh, J and Koch, I and Kahl, G and Rotter, B}, title = {APADB: a database for alternative polyadenylation and microRNA regulation events.}, journal = {Database : the journal of biological databases and curation}, volume = {2014}, number = {}, pages = {}, pmid = {25052703}, issn = {1758-0463}, mesh = {Animals ; Chickens ; Computational Biology/*methods ; Database Management Systems ; *Databases, Genetic ; Humans ; Mice ; *MicroRNAs ; *Polyadenylation ; User-Computer Interface ; }, abstract = {Alternative polyadenylation (APA) is a widespread mechanism that contributes to the sophisticated dynamics of gene regulation. Approximately 50% of all protein-coding human genes harbor multiple polyadenylation (PA) sites; their selective and combinatorial use gives rise to transcript variants with differing length of their 3' untranslated region (3'UTR). Shortened variants escape UTR-mediated regulation by microRNAs (miRNAs), especially in cancer, where global 3'UTR shortening accelerates disease progression, dedifferentiation and proliferation. Here we present APADB, a database of vertebrate PA sites determined by 3' end sequencing, using massive analysis of complementary DNA ends. APADB provides (A)PA sites for coding and non-coding transcripts of human, mouse and chicken genes. For human and mouse, several tissue types, including different cancer specimens, are available. APADB records the loss of predicted miRNA binding sites and visualizes next-generation sequencing reads that support each PA site in a genome browser. The database tables can either be browsed according to organism and tissue or alternatively searched for a gene of interest. APADB is the largest database of APA in human, chicken and mouse. The stored information provides experimental evidence for thousands of PA sites and APA events. APADB combines 3' end sequencing data with prediction algorithms of miRNA binding sites, allowing to further improve prediction algorithms. Current databases lack correct information about 3'UTR lengths, especially for chicken, and APADB provides necessary information to close this gap. Database URL: http://tools.genxpro.net/apadb/.}, } @article {pmid25051756, year = {2014}, author = {Viktorov, AA and Gladkikh, VD and Ksenofontov, AI and Morozova, EE}, title = {[Forecasting of environmental health risk on the basis of the kinetic theory of aging of living systems].}, journal = {Advances in gerontology = Uspekhi gerontologii}, volume = {27}, number = {1}, pages = {37-43}, pmid = {25051756}, issn = {1561-9125}, mesh = {Adaptation, Physiological ; Aging/*physiology ; Data Interpretation, Statistical ; *Environmental Exposure/adverse effects/statistics & numerical data ; Environmental Health/methods ; Humans ; *Life Expectancy ; Models, Theoretical ; Prognosis ; Risk Assessment/*methods ; }, abstract = {The method of iterative congruence of search of parameters of kinetic mathematical model of aging of living systems according to medical statistics is developed. Its opportunities for the description of risk functions of mortality and life expectancy for the person and animals depending on environment factors are illustrated. The concept of forecasting of environmental risks--risks to population health from ecological factors of influence--is formulated.}, } @article {pmid25051698, year = {2014}, author = {Buravtseva, NP and Mezentsev, VM and Riazanova, AG and Pluzhnikova, OV and Eremenko, EI and Maletskaia, OV and Kulichenko, AN}, title = {[Use of GIS technologies in development of a cadaster of stationary unfavorable by anthrax points in Krasnodar region].}, journal = {Zhurnal mikrobiologii, epidemiologii i immunobiologii}, volume = {}, number = {2}, pages = {59-64}, pmid = {25051698}, issn = {0372-9311}, mesh = {Animals ; Anthrax/*epidemiology/microbiology ; Bacillus anthracis/*isolation & purification/pathogenicity ; Cattle ; Epidemiological Monitoring ; Geographic Information Systems/*instrumentation ; Humans ; Russia/epidemiology ; *Soil Microbiology ; Spatio-Temporal Analysis ; }, abstract = {AIM: Development of a cadaster of stationary unfavorable by anthrax points in Krasnodar region by using GIS technologies.

MATERIALS AND METHODS: Ageographical information system (GIS) of ESRI program--Arc GIS 10.1 was used for the composition of an electronic cadaster of stationary unfavorable by anthrax points. Topographic basis--electronic maps of Krasnodar region (M 1:200 000).

RESULTS: An evaluation of safety by anthrax of Krasnodar region areas bythe amount of stationary unfavorable by anthrax points situated in its territories, by their activity during the 76 year observation period was given. Spatial adjoint analysis of ecological timing of stationary unfavorable by anthrax points to soil and landscape zones in Krasnodar region was carried out.

CONCLUSION: Electronic cadaster of stationary unfavorable by anthrax points in Krasnodar region may serve as a basis for purposeful implementation of prophylaxis measures.}, } @article {pmid25050321, year = {2014}, author = {Javelot, H and Spadazzi, A and Weiner, L and Garcia, S and Gentili, C and Kosel, M and Bertschy, G}, title = {Telemonitoring with respect to mood disorders and information and communication technologies: overview and presentation of the PSYCHE project.}, journal = {BioMed research international}, volume = {2014}, number = {}, pages = {104658}, pmid = {25050321}, issn = {2314-6141}, mesh = {*Computer Communication Networks ; Humans ; Medical Informatics/*methods ; Monitoring, Physiologic/*methods ; Mood Disorders/*diagnosis ; *Program Development ; Telemedicine/*methods ; }, abstract = {This paper reviews what we know about prediction in relation to mood disorders from the perspective of clinical, biological, and physiological markers. It then also presents how information and communication technologies have developed in the field of mood disorders, from the first steps, for example, the transition from paper and pencil to more sophisticated methods, to the development of ecological momentary assessment methods and, more recently, wearable systems. These recent developments have paved the way for the use of integrative approaches capable of assessing multiple variables. The PSYCHE project stands for Personalised monitoring SYstems for Care in mental HEalth.}, } @article {pmid25048896, year = {2014}, author = {Olawoyin, R and Heidrich, B and Oyewole, S and Okareh, OT and McGlothlin, CW}, title = {Chemometric analysis of ecological toxicants in petrochemical and industrial environments.}, journal = {Chemosphere}, volume = {112}, number = {}, pages = {114-119}, doi = {10.1016/j.chemosphere.2014.03.107}, pmid = {25048896}, issn = {1879-1298}, mesh = {*Chemical Industry ; Ecotoxicology/*methods ; Environmental Monitoring/*methods ; Humans ; Informatics/*methods ; Metals, Heavy/analysis ; Nigeria ; Petroleum/*analysis ; Polycyclic Aromatic Hydrocarbons/analysis ; Risk Assessment ; Statistics as Topic ; }, abstract = {The application of chemometrics in the assessment of toxicants, such as heavy metals (HMs) and polycyclic aromatic hydrocarbons (PAHs) potentially derived from petrochemical activities in the microenvironment, is vital in providing safeguards for human health of children and adults residing around petrochemical industrial regions. Several multivariate statistical methods are used in geosciences and environmental protection studies to classify, identify and group prevalent pollutants with regard to exhibited trends. Chemometrics can be applied for toxicant source identification, estimation of contaminants contributions to the toxicity of sites of interest, the assessment of the integral risk index of an area and provision of mitigating measures that limit or eliminate the contaminants identified. In this study, the principal component analysis (PCA) was used for dimensionality reduction of both organic and inorganic substances data in the environment, which are potentially hazardous. The high molecular weight (HMW) PAHs correlated positively with stronger impact on the model than the lower molecular weight (LMW) PAHs, the total petroleum hydrocarbons (TPHs), PAHs and BTEX correlate positively in the F1 vs F2 plot indicating similar source contributions of these pollutants in the environmental material. Cu, Cr, Cd, Fe, Zn and Pb all show positive correlation in the same space indicating similar source of contamination. Analytical processes involving environmental assessment data obtained in the Niger Delta area of Nigeria, confirmed the usefulness of chemometrics for comprehensive ecological evaluation.}, } @article {pmid25047861, year = {2014}, author = {Tagu, D and Colbourne, JK and Nègre, N}, title = {Genomic data integration for ecological and evolutionary traits in non-model organisms.}, journal = {BMC genomics}, volume = {15}, number = {1}, pages = {490}, pmid = {25047861}, issn = {1471-2164}, mesh = {*Biological Evolution ; Databases, Genetic ; *Genomics ; }, abstract = {Why is it needed to develop system biology initiatives such as ENCODE on non-model organisms?}, } @article {pmid25047279, year = {2015}, author = {Zhang, Z and Song, X and Chen, Y and Wang, P and Wei, X and Tao, F}, title = {Dynamic variability of the heading-flowering stages of single rice in China based on field observations and NDVI estimations.}, journal = {International journal of biometeorology}, volume = {59}, number = {5}, pages = {643-655}, pmid = {25047279}, issn = {1432-1254}, mesh = {China ; Computer Simulation ; *Data Interpretation, Statistical ; *Ecosystem ; Flowers/*growth & development ; *Models, Statistical ; Oryza/*growth & development ; Remote Sensing Technology/*methods ; Spatio-Temporal Analysis ; }, abstract = {Although many studies have indicated the consistent impact of warming on the natural ecosystem (e.g., an early flowering and prolonged growing period), our knowledge of the impacts on agricultural systems is still poorly understood. In this study, spatiotemporal variability of the heading-flowering stages of single rice was detected and compared at three different scales using field-based methods (FBMs) and satellite-based methods (SBMs). The heading-flowering stages from 2000 to 2009 with a spatial resolution of 1 km were extracted from the SPOT/VGT NDVI time series data using the Savizky-Golay filtering method in the areas in China dominated by single rice of Northeast China (NE), the middle-lower Yangtze River Valley (YZ), the Sichuan Basin (SC), and the Yunnan-Guizhou Plateau (YG). We found that approximately 52.6 and 76.3 % of the estimated heading-flowering stages by a SBM were within ±5 and ±10 days estimation error (a root mean square error (RMSE) of 8.76 days) when compared with those determined by a FBM. Both the FBM data and the SBM data had indicated a similar spatial pattern, with the earliest annual average heading-flowering stages in SC, followed by YG, NE, and YZ, which were inconsistent with the patterns reported in natural ecosystems. Moreover, diverse temporal trends were also detected in the four regions due to different climate conditions and agronomic factors such as cultivar shifts. Nevertheless, there were no significant differences (p > 0.05) between the FBM and the SBM in both the regional average value of the phenological stages and the trends, implying the consistency and rationality of the SBM at three scales.}, } @article {pmid25047274, year = {2014}, author = {Marcelino, JA and Weber, E and Silva, L and Garcia, PV and Soares, AO}, title = {Expedient metrics to describe plant community change across gradients of anthropogenic influence.}, journal = {Environmental management}, volume = {54}, number = {5}, pages = {1121-1130}, pmid = {25047274}, issn = {1432-1009}, mesh = {Azores ; *Biodiversity ; Conservation of Natural Resources/*statistics & numerical data ; Data Interpretation, Statistical ; Ecology/methods ; Human Activities/*statistics & numerical data ; Humans ; Introduced Species/*statistics & numerical data ; *Plant Development ; Population Dynamics ; Species Specificity ; }, abstract = {Human influence associated with land use may cause considerable biodiversity losses, namely in oceanic islands such as the Azores. Our goal was to identify plant indicator species across two gradients of increasing anthropogenic influence and management (arborescent and herbaceous communities) and determine similarity between plant communities of uncategorized vegetation plots to those in reference gradients using metrics derived from R programming. We intend to test and provide an expedient way to determine the conservation value of a given uncategorized vegetation plot based on the number of native, endemic, introduced, and invasive indicator species present. Using the metric IndVal, plant taxa with a significant indicator value for each community type in the two anthropogenic gradients were determined. A new metric, ComVal, was developed to assess the similarity of an uncategorized vegetation plot toward a reference community type, based on (i) the percentage of pre-defined indicator species from reference communities present in the vegetation plots, and (ii) the percentage of indicator species, specific to a given reference community type, present in the vegetation plot. Using a data resampling approach, the communities were randomly used as training or validation sets to classify vegetation plots based on ComVal. The percentage match with reference community types ranged from 77 to 100 % and from 79 to 100 %, for herbaceous and arborescent vegetation plots, respectively. Both IndVal and ComVal are part of a suite of useful tools characterizing plant communities and plant community change along gradients of anthropogenic influence without a priori knowledge of their biology and ecology.}, } @article {pmid25046685, year = {2014}, author = {Osborne, CP and Salomaa, A and Kluyver, TA and Visser, V and Kellogg, EA and Morrone, O and Vorontsova, MS and Clayton, WD and Simpson, DA}, title = {A global database of C4 photosynthesis in grasses.}, journal = {The New phytologist}, volume = {204}, number = {3}, pages = {441-446}, doi = {10.1111/nph.12942}, pmid = {25046685}, issn = {1469-8137}, mesh = {Biological Evolution ; *Databases, Factual ; Ecosystem ; Photosynthesis/*physiology ; Poaceae/classification/genetics/*physiology ; }, } @article {pmid25046634, year = {2014}, author = {Delpla, I and Monteith, DT and Freeman, C and Haftka, J and Hermens, J and Jones, TG and Baurès, E and Jung, AV and Thomas, O}, title = {A decision support system for drinking water production integrating health risks assessment.}, journal = {International journal of environmental research and public health}, volume = {11}, number = {7}, pages = {7354-7375}, pmid = {25046634}, issn = {1660-4601}, mesh = {*Decision Support Techniques ; Disinfection ; *Drinking Water ; Humans ; Reproducibility of Results ; Risk Assessment ; Water Pollutants/analysis ; Water Pollution/prevention & control ; Water Purification ; *Water Quality ; Water Supply ; }, abstract = {The issue of drinking water quality compliance in small and medium scale water services is of paramount importance in relation to the 98/83/CE European Drinking Water Directive (DWD). Additionally, concerns are being expressed over the implementation of the DWD with respect to possible impacts on water quality from forecast changes in European climate with global warming and further anticipated reductions in north European acid emissions. Consequently, we have developed a decision support system (DSS) named ARTEM-WQ (AwaReness Tool for the Evaluation and Mitigation of drinking Water Quality issues resulting from environmental changes) to support decision making by small and medium plant operators and other water stakeholders. ARTEM-WQ is based on a sequential risk analysis approach that includes consideration of catchment characteristics, climatic conditions and treatment operations. It provides a holistic evaluation of the water system, while also assessing human health risks of organic contaminants potentially present in treated waters (steroids, pharmaceuticals, pesticides, bisphenol-a, polychlorobiphenyls, polycyclic aromatic hydrocarbons, petrochemical hydrocarbons and disinfection by-products; n = 109). Moreover, the system provides recommendations for improvement while supporting decision making in its widest context. The tool has been tested on various European catchments and shows a promising potential to inform water managers of risks and appropriate mitigative actions. Further improvements should include toxicological knowledge advancement, environmental background pollutant concentrations and the assessment of the impact of distribution systems on water quality variation.}, } @article {pmid25044053, year = {2014}, author = {Burton, GA and Basu, N and Ellis, BR and Kapo, KE and Entrekin, S and Nadelhoffer, K}, title = {Hydraulic "fracking": are surface water impacts an ecological concern?.}, journal = {Environmental toxicology and chemistry}, volume = {33}, number = {8}, pages = {1679-1689}, doi = {10.1002/etc.2619}, pmid = {25044053}, issn = {1552-8618}, mesh = {Animals ; Databases, Factual ; Ecology ; Ecosystem ; *Environmental Monitoring ; Groundwater/chemistry ; *Mechanical Phenomena ; Mining/*methods ; *Natural Gas ; North America ; Water/*chemistry ; Water Pollutants, Chemical/analysis ; }, abstract = {Use of high-volume hydraulic fracturing (HVHF) in unconventional reservoirs to recover previously inaccessible oil and natural gas is rapidly expanding in North America and elsewhere. Although hydraulic fracturing has been practiced for decades, the advent of more technologically advanced horizontal drilling coupled with improved slickwater chemical formulations has allowed extensive natural gas and oil deposits to be recovered from shale formations. Millions of liters of local groundwaters are utilized to generate extensive fracture networks within these low-permeability reservoirs, allowing extraction of the trapped hydrocarbons. Although the technology is relatively standardized, the geographies and related policies and regulations guiding these operations vary markedly. Some ecosystems are more at risk from these operations than others because of either their sensitivities or the manner in which the HVHF operations are conducted. Generally, the closer geographical proximity of the susceptible ecosystem to a drilling site or a location of related industrial processes, the higher the risk of that ecosystem being impacted by the operation. The associated construction of roads, power grids, pipelines, well pads, and water-extraction systems along with increased truck traffic are common to virtually all HVHF operations. These operations may result in increased erosion and sedimentation, increased risk to aquatic ecosystems from chemical spills or runoff, habitat fragmentation, loss of stream riparian zones, altered biogeochemical cycling, and reduction of available surface and hyporheic water volumes because of withdrawal-induced lowering of local groundwater levels. The potential risks to surface waters from HVHF operations are similar in many ways to those resulting from agriculture, silviculture, mining, and urban development. Indeed, groundwater extraction associated with agriculture is perhaps a larger concern in the long term in some regions. Understanding the ecological impacts of these anthropogenic activities provides useful information for evaluations of potential HVHF hazards. Geographic information system-based modeling combined with strategic site monitoring has provided insights into the relative importance of these and other ecoregion and land-use factors in discerning potential HVHF impacts. Recent findings suggest that proper siting and operational controls along with strategic monitoring can reduce the potential for risks to aquatic ecosystems. Nevertheless, inadequate data exist to predict ecological risk at this time. The authors suggest considering the plausibility of surface water hazards associated with the various HVHF operations in terms of the ecological context and in the context of relevant anthropogenic activities.}, } @article {pmid25042415, year = {2015}, author = {Pascual-Aguilar, J and Andreu, V and Gimeno-García, E and Picó, Y}, title = {Current anthropogenic pressures on agro-ecological protected coastal wetlands.}, journal = {The Science of the total environment}, volume = {503-504}, number = {}, pages = {190-199}, doi = {10.1016/j.scitotenv.2014.07.007}, pmid = {25042415}, issn = {1879-1026}, mesh = {Agriculture/*statistics & numerical data ; Cities/*statistics & numerical data ; Conservation of Natural Resources ; Ecology ; *Environmental Monitoring ; Geographic Information Systems ; Geologic Sediments/chemistry ; Spain ; Water Pollutants, Chemical/*analysis ; *Wetlands ; }, abstract = {Coastal wetlands are areas that suffer from great pressure. Much of it is due to the rapid development of the surrounding artificial landscapes, where socio-economic factors lead to alterations in the nearby environment, affecting the quality of natural and agricultural systems. This work analyses interconnections among landscapes under the hypothesis that urban-artificial impacts could be detected on soils and waters of an agro-ecological protected area, L'Albufera de Valencia Natural Park, located in the vicinity of the City of Valencia, Spain. The methodological framework developed addresses two types of anthropogenic pressure: (1) direct, due to artificialisation of soil covers that cause soil sealing, and (2) indirect, which are related to water flows coming from urban populations through sewage and irrigation systems and which, ultimately, will be identified by the presence of emerging pharmaceutical contaminants in waters of the protected area. For soil sealing, a methodology based on temporal comparison of two digital layers for the years 1991 and 2011, applying Geographical Information Systems and landscapes metrics, was applied. To determine presence of emerging contaminants, 21 water samples within the Natural Park were analysed applying liquid chromatography tandem mass spectrometry for the detection of 17 pharmaceutical compounds. Results showed that both processes are present in the Natural Park, with a clear geographical pattern. Soil sealing and presence of pharmaceuticals are more intensive in the northern part of the study area. This is related to population density (detection of pharmaceuticals) and land cover conversion from agricultural and natural surfaces to artificial ones (soil sealing).}, } @article {pmid25038982, year = {2014}, author = {Zhu, L and Chen, Z and Wang, J and Ding, J and Yu, Y and Li, J and Xiao, N and Jiang, L and Zheng, Y and Rimmington, GM}, title = {Monitoring plant response to phenanthrene using the red edge of canopy hyperspectral reflectance.}, journal = {Marine pollution bulletin}, volume = {86}, number = {1-2}, pages = {332-341}, doi = {10.1016/j.marpolbul.2014.06.046}, pmid = {25038982}, issn = {1879-3363}, mesh = {Biomass ; Chenopodiaceae/drug effects/*growth & development ; China ; Environmental Monitoring/*methods ; Phenanthrenes/*toxicity ; Plant Leaves/drug effects/metabolism ; Poaceae/drug effects/*growth & development ; Remote Sensing Technology/methods ; Rivers ; Soil/chemistry ; Spectrum Analysis ; }, abstract = {To investigate the mechanisms and potential for the remote sensing of phenanthrene-induced vegetation stress, we measured field canopy spectra, and associated plant and soil parameters in the field controlled experiment in the Yellow River Delta of China. Two widely distributed plant communities, separately dominated by reed (Phragmites australis) and glaucous seepweed (Suaeda salsa), were treated with different doses of phenanthrene. The canopy spectral changes of plant community resulted from the decreases of biomass and foliar projective coverage, while leaf photosynthetic pigment concentrations showed no significance difference among treatments. The spectral response to phenanthrene included a flattened red edge, with decreased first derivative of reflectance. The red edge slope and area consistently responded to phenanthrene, showing a strong relationship with aboveground biomass, coverage and canopy pigments density. These results suggest the potential of remote sensing and the importance of field validation to correctly interpret the causes of the spectral changes.}, } @article {pmid25034246, year = {2014}, author = {Moran, M and Van Cauwenberg, J and Hercky-Linnewiel, R and Cerin, E and Deforche, B and Plaut, P}, title = {Understanding the relationships between the physical environment and physical activity in older adults: a systematic review of qualitative studies.}, journal = {The international journal of behavioral nutrition and physical activity}, volume = {11}, number = {}, pages = {79}, pmid = {25034246}, issn = {1479-5868}, mesh = {Aged ; Databases, Factual ; Focus Groups ; Humans ; *Motor Activity ; *Residence Characteristics ; Transportation/methods ; Walking ; }, abstract = {BACKGROUND: While physical activity (PA) provides many physical, social, and mental health benefits for older adults, they are the least physically active age group. Ecological models highlight the importance of the physical environment in promoting PA. However, results of previous quantitative research revealed inconsistencies in environmental correlates of older adults' PA that may be explained by methodological issues. Qualitative studies can inform and complement quantitative research on environment-PA relationships by providing insight into how and why the environment influences participants' PA behaviors. The current study aimed to provide a systematic review of qualitative studies exploring the potential impact of the physical environment on older adults' PA behaviors.

METHODS: A systematic search was conducted in databases of various disciplines, including: health, architecture and urban planning, transportation, and interdisciplinary databases. From 3,047 articles identified in the physical activity, initial search, 31 articles published from 1996 to 2012 met all inclusion criteria. An inductive content analysis was performed on the extracted findings to identify emerging environmental elements related to older adults' PA. The identified environmental elements were then grouped by study methodologies [indoor interviews (individual or focus groups) vs spatial methods (photo-voice, observations, walk-along interviews)].

RESULTS: This review provides detailed information about environmental factors that potentially influence older adults' PA behaviors. These factors were categorized into five themes: pedestrian infrastructure, safety, access to amenities, aesthetics, and environmental conditions. Environmental factors especially relevant to older adults (i.e., access to facilities, green open spaces and rest areas) tended to emerge more frequently in studies that combined interviews with spatial qualitative methods.

CONCLUSIONS: Findings showed that qualitative research can provide in-depth information on environmental elements that influence older adults' PA. Future qualitative studies on the physical environment and older adults' PA would benefit from combining interviews with more spatially-oriented methods. Multidisciplinary mixed-methods studies are recommended to establish quantitative relationships complemented with in-depth qualitative information.}, } @article {pmid25034087, year = {2014}, author = {Leclerc, M and Dussault, C and St-Laurent, MH}, title = {Behavioural strategies towards human disturbances explain individual performance in woodland caribou.}, journal = {Oecologia}, volume = {176}, number = {1}, pages = {297-306}, pmid = {25034087}, issn = {1432-1939}, mesh = {Animals ; Behavior, Animal/*physiology ; Conservation of Natural Resources/*methods ; *Ecosystem ; Female ; Geographic Information Systems ; Homing Behavior/physiology ; Humans ; Population Dynamics ; Predatory Behavior/physiology ; Proportional Hazards Models ; Quebec ; Reindeer/*physiology ; *Trees ; Ursidae/physiology ; }, abstract = {Behavioural strategies may have important fitness, ecological and evolutionary consequences. In woodland caribou, human disturbances are associated with higher predation risk. Between 2004 and 2011, we investigated if habitat selection strategies of female caribou towards disturbances influenced their calf's survival in managed boreal forest with varying intensities of human disturbances. Calf survival was 53% and 43% after 30 and 90 days following birth, respectively, and 52% of calves that died were killed by black bear. The probability that a female lose its calf to predation was not influenced by habitat composition of her annual home range, but decreased with an increase in proportion of open lichen woodland within her calving home range. At the local scale, females that did not lose their calf displayed stronger avoidance of high road density areas than females that lost their calf to predation. Further, females that lost their calf to predation and that had a low proportion of ≤5-year-old cutovers within their calving home range were mostly observed in areas where these young cutovers were locally absent. Also, females that lost their calf to predation and that had a high proportion of ≤5-year-old cutovers within their calving home range were mostly observed in areas with a high local density of ≤5-year-old cutovers. Our study demonstrates that we have to account for human-induced disturbances at both local and regional scales in order to further enhance effective caribou management plans. We demonstrate that disturbances not only impact spatial distribution of individuals, but also their reproductive success.}, } @article {pmid25033033, year = {2014}, author = {Zarecki, R and Oberhardt, MA and Reshef, L and Gophna, U and Ruppin, E}, title = {A novel nutritional predictor links microbial fastidiousness with lowered ubiquity, growth rate, and cooperativeness.}, journal = {PLoS computational biology}, volume = {10}, number = {7}, pages = {e1003726}, pmid = {25033033}, issn = {1553-7358}, mesh = {Bacteria/*genetics/*metabolism ; Databases, Genetic ; Ecosystem ; Genome, Bacterial/*genetics ; Genomics/*methods ; Metabolic Networks and Pathways/*genetics ; Microbiota/*genetics ; }, abstract = {Understanding microbial nutritional requirements is a key challenge in microbiology. Here we leverage the recent availability of thousands of automatically generated genome-scale metabolic models to develop a predictor of microbial minimal medium requirements, which we apply to thousands of species to study the relationship between their nutritional requirements and their ecological and genomic traits. We first show that nutritional requirements are more similar among species that co-habit many ecological niches. We then reveal three fundamental characteristics of microbial fastidiousness (i.e., complex and specific nutritional requirements): (1) more fastidious microorganisms tend to be more ecologically limited; (2) fastidiousness is positively associated with smaller genomes and smaller metabolic networks; and (3) more fastidious species grow more slowly and have less ability to cooperate with other species than more metabolically versatile organisms. These associations reflect the adaptation of fastidious microorganisms to unique niches with few cohabitating species. They also explain how non-fastidious species inhabit many ecological niches with high abundance rates. Taken together, these results advance our understanding microbial nutrition on a large scale, by presenting new nutrition-related associations that govern the distribution of microorganisms in nature.}, } @article {pmid25026440, year = {2014}, author = {Gawryluk, RM and Chisholm, KA and Pinto, DM and Gray, MW}, title = {Compositional complexity of the mitochondrial proteome of a unicellular eukaryote (Acanthamoeba castellanii, supergroup Amoebozoa) rivals that of animals, fungi, and plants.}, journal = {Journal of proteomics}, volume = {109}, number = {}, pages = {400-416}, doi = {10.1016/j.jprot.2014.07.005}, pmid = {25026440}, issn = {1876-7737}, support = {MOP-4124//Canadian Institutes of Health Research/Canada ; }, mesh = {Acanthamoeba castellanii/genetics/*metabolism ; Animals ; Computational Biology ; Fungi ; Mitochondria/genetics/*metabolism ; Mitochondrial Proteins/*metabolism ; Plants ; Proteome/*metabolism ; Proteomics ; Protozoan Proteins/*metabolism ; }, abstract = {UNLABELLED: We present a combined proteomic and bioinformatic investigation of mitochondrial proteins from the amoeboid protist Acanthamoeba castellanii, the first such comprehensive investigation in a free-living member of the supergroup Amoebozoa. This protist was chosen both for its phylogenetic position (as a sister to animals and fungi) and its ecological ubiquity and physiological flexibility. We report 1033 A. castellanii mitochondrial protein sequences, 709 supported by mass spectrometry data (676 nucleus-encoded and 33 mitochondrion-encoded), including two previously unannotated mtDNA-encoded proteins, which we identify as highly divergent mitochondrial ribosomal proteins. Other notable findings include duplicate proteins for all of the enzymes of the tricarboxylic acid (TCA) cycle-which, along with the identification of a mitochondrial malate synthase-isocitrate lyase fusion protein, suggests the interesting possibility that the glyoxylate cycle operates in A. castellanii mitochondria. Additionally, the A. castellanii genome encodes an unusually high number (at least 29) of mitochondrion-targeted pentatricopeptide repeat (PPR) proteins, organellar RNA metabolism factors in other organisms. We discuss several key mitochondrial pathways, including DNA replication, transcription and translation, protein degradation, protein import and Fe-S cluster biosynthesis, highlighting similarities and differences in these pathways in other eukaryotes. In compositional and functional complexity, the mitochondrial proteome of A. castellanii rivals that of multicellular eukaryotes.

BIOLOGICAL SIGNIFICANCE: Comprehensive proteomic surveys of mitochondria have been undertaken in a limited number of predominantly multicellular eukaryotes. This phylogenetically narrow perspective constrains and biases our insights into mitochondrial function and evolution, as it neglects protists, which account for most of the evolutionary and functional diversity within eukaryotes. We report here the first comprehensive investigation of the mitochondrial proteome in a member (A. castellanii) of the eukaryotic supergroup Amoebozoa. Through a combination of tandem mass spectrometry (MS/MS) and in silico data mining, we have retrieved 1033 candidate mitochondrial protein sequences, 709 having MS support. These data were used to reconstruct the metabolic pathways and protein complexes of A. castellanii mitochondria, and were integrated with data from other characterized mitochondrial proteomes to augment our understanding of mitochondrial proteome evolution. Our results demonstrate the power of combining direct proteomic and bioinformatic approaches in the discovery of novel mitochondrial proteins, both nucleus-encoded and mitochondrion-encoded, and highlight the compositional complexity of the A. castellanii mitochondrial proteome, which rivals that of animals, fungi and plants.}, } @article {pmid25025376, year = {2014}, author = {Russell, JR and Hedley, PE and Cardle, L and Dancey, S and Morris, J and Booth, A and Odee, D and Mwaura, L and Omondi, W and Angaine, P and Machua, J and Muchugi, A and Milne, I and Kindt, R and Jamnadass, R and Dawson, IK}, title = {tropiTree: an NGS-based EST-SSR resource for 24 tropical tree species.}, journal = {PloS one}, volume = {9}, number = {7}, pages = {e102502}, pmid = {25025376}, issn = {1932-6203}, mesh = {Base Sequence ; Crops, Agricultural/genetics ; Databases, Genetic ; Expressed Sequence Tags ; *Genes, Plant ; High-Throughput Nucleotide Sequencing ; Microsatellite Repeats ; Sequence Analysis, DNA ; Trees/*genetics ; }, abstract = {The development of genetic tools for non-model organisms has been hampered by cost, but advances in next-generation sequencing (NGS) have created new opportunities. In ecological research, this raises the prospect for developing molecular markers to simultaneously study important genetic processes such as gene flow in multiple non-model plant species within complex natural and anthropogenic landscapes. Here, we report the use of bar-coded multiplexed paired-end Illumina NGS for the de novo development of expressed sequence tag-derived simple sequence repeat (EST-SSR) markers at low cost for a range of 24 tree species. Each chosen tree species is important in complex tropical agroforestry systems where little is currently known about many genetic processes. An average of more than 5,000 EST-SSRs was identified for each of the 24 sequenced species, whereas prior to analysis 20 of the species had fewer than 100 nucleotide sequence citations. To make results available to potential users in a suitable format, we have developed an open-access, interactive online database, tropiTree (http://bioinf.hutton.ac.uk/tropiTree), which has a range of visualisation and search facilities, and which is a model for the efficient presentation and application of NGS data.}, } @article {pmid25016583, year = {2014}, author = {Leblois, R and Pudlo, P and Néron, J and Bertaux, F and Reddy Beeravolu, C and Vitalis, R and Rousset, F}, title = {Maximum-likelihood inference of population size contractions from microsatellite data.}, journal = {Molecular biology and evolution}, volume = {31}, number = {10}, pages = {2805-2823}, doi = {10.1093/molbev/msu212}, pmid = {25016583}, issn = {1537-1719}, mesh = {Animals ; Computational Biology/*methods ; *Likelihood Functions ; *Microsatellite Repeats ; Models, Genetic ; Mutation ; Pongo/*genetics ; Population Density ; Software ; }, abstract = {Understanding the demographic history of populations and species is a central issue in evolutionary biology and molecular ecology. In this work, we develop a maximum-likelihood method for the inference of past changes in population size from microsatellite allelic data. Our method is based on importance sampling of gene genealogies, extended for new mutation models, notably the generalized stepwise mutation model (GSM). Using simulations, we test its performance to detect and characterize past reductions in population size. First, we test the estimation precision and confidence intervals coverage properties under ideal conditions, then we compare the accuracy of the estimation with another available method (MSVAR) and we finally test its robustness to misspecification of the mutational model and population structure. We show that our method is very competitive compared with alternative ones. Moreover, our implementation of a GSM allows more accurate analysis of microsatellite data, as we show that the violations of a single step mutation assumption induce very high bias toward false contraction detection rates. However, our simulation tests also showed some limits, which most importantly are large computation times for strong disequilibrium scenarios and a strong influence of some form of unaccounted population structure. This inference method is available in the latest implementation of the MIGRAINE software package.}, } @article {pmid25014284, year = {2014}, author = {Rodrigues, M and Bonfim, C and Portugal, JL and de Frias, PG and Gurgel, IG and Costa, TR and Medeiros, Z}, title = {[Spatial analysis of infant mortality and the adequacy of vital information: a proposal for defining priority areas].}, journal = {Ciencia & saude coletiva}, volume = {19}, number = {7}, pages = {2047-2054}, doi = {10.1590/1413-81232014197.18012013}, pmid = {25014284}, issn = {1678-4561}, mesh = {Brazil ; *Data Accuracy ; Humans ; Infant ; *Infant Mortality ; Information Systems/*standards ; *Spatial Analysis ; *Vital Statistics ; }, abstract = {This is an ecological study that sought to assess the relationship between the spatial clustering of infant mortality and the adequacy of vital information. The adequacy of information from the Brazilian Live Birth Database (SINASC) and Mortality Database (SIM) were examined using a validated method that uses five indicators calculated by municipality and population size. Municipalities were classified as either having consolidated data, data currently being consolidated, or not having consolidated data. Voronoi polygons were generated for spatial analysis in order to minimize any proximity issues among municipalities. The local Moran index was applied to identify spatial clustering of infant mortality. It was established that 76.2% of all municipalities had consolidated vital data. Infant mortality clustering was seen in 34 municipalities comprising three spatial clusters. An association was also found between the adequacy of vital information and the spatial clustering of infant mortality. Geostatistical techniques proved to have predictive power to identify spatial clustering with consolidated vital information. The approach will contribute to the improvement of data quality and can be used for planning actions seeking to reduce infant mortality.}, } @article {pmid25013139, year = {2014}, author = {Tanizawa, Y and Fujisawa, T and Mochizuki, T and Kaminuma, E and Suzuki, Y and Nakamura, Y and Tohno, M}, title = {Draft Genome Sequence of Weissella oryzae SG25T, Isolated from Fermented Rice Grains.}, journal = {Genome announcements}, volume = {2}, number = {4}, pages = {}, pmid = {25013139}, issn = {2169-8287}, abstract = {Weissella oryzae was originally isolated from fermented rice grains. Here we report the draft genome sequence of the type strain of W. oryzae. This first report on the genomic sequence of this species may help identify the mechanisms underlying bacterial adaptation to the ecological niche of fermented rice grains.}, } @article {pmid25009735, year = {2014}, author = {Haendel, MA and Balhoff, JP and Bastian, FB and Blackburn, DC and Blake, JA and Bradford, Y and Comte, A and Dahdul, WM and Dececchi, TA and Druzinsky, RE and Hayamizu, TF and Ibrahim, N and Lewis, SE and Mabee, PM and Niknejad, A and Robinson-Rechavi, M and Sereno, PC and Mungall, CJ}, title = {Unification of multi-species vertebrate anatomy ontologies for comparative biology in Uberon.}, journal = {Journal of biomedical semantics}, volume = {5}, number = {}, pages = {21}, pmid = {25009735}, issn = {2041-1480}, support = {P41 HG002659/HG/NHGRI NIH HHS/United States ; R24 OD011883/OD/NIH HHS/United States ; U41 HG002273/HG/NHGRI NIH HHS/United States ; U41 HG002659/HG/NHGRI NIH HHS/United States ; }, abstract = {BACKGROUND: Elucidating disease and developmental dysfunction requires understanding variation in phenotype. Single-species model organism anatomy ontologies (ssAOs) have been established to represent this variation. Multi-species anatomy ontologies (msAOs; vertebrate skeletal, vertebrate homologous, teleost, amphibian AOs) have been developed to represent 'natural' phenotypic variation across species. Our aim has been to integrate ssAOs and msAOs for various purposes, including establishing links between phenotypic variation and candidate genes.

RESULTS: Previously, msAOs contained a mixture of unique and overlapping content. This hampered integration and coordination due to the need to maintain cross-references or inter-ontology equivalence axioms to the ssAOs, or to perform large-scale obsolescence and modular import. Here we present the unification of anatomy ontologies into Uberon, a single ontology resource that enables interoperability among disparate data and research groups. As a consequence, independent development of TAO, VSAO, AAO, and vHOG has been discontinued.

CONCLUSIONS: The newly broadened Uberon ontology is a unified cross-taxon resource for metazoans (animals) that has been substantially expanded to include a broad diversity of vertebrate anatomical structures, permitting reasoning across anatomical variation in extinct and extant taxa. Uberon is a core resource that supports single- and cross-species queries for candidate genes using annotations for phenotypes from the systematics, biodiversity, medical, and model organism communities, while also providing entities for logical definitions in the Cell and Gene Ontologies. THE ONTOLOGY RELEASE FILES ASSOCIATED WITH THE ONTOLOGY MERGE DESCRIBED IN THIS MANUSCRIPT ARE AVAILABLE AT: http://purl.obolibrary.org/obo/uberon/releases/2013-02-21/ CURRENT ONTOLOGY RELEASE FILES ARE AVAILABLE ALWAYS AVAILABLE AT: http://purl.obolibrary.org/obo/uberon/releases/}, } @article {pmid25007329, year = {2014}, author = {Quintela, M and Johansson, MP and Kristjánsson, BK and Barreiro, R and Laurila, A}, title = {AFLPs and mitochondrial haplotypes reveal local adaptation to extreme thermal environments in a freshwater gastropod.}, journal = {PloS one}, volume = {9}, number = {7}, pages = {e101821}, pmid = {25007329}, issn = {1932-6203}, mesh = {*Adaptation, Biological ; *Amplified Fragment Length Polymorphism Analysis ; Animals ; Computational Biology/methods ; DNA/*genetics ; Fresh Water ; Gastropoda/*genetics/metabolism ; Haplotypes ; Mitochondria/*genetics ; Molecular Sequence Data ; Selection, Genetic ; Temperature ; }, abstract = {The way environmental variation shapes neutral and adaptive genetic variation in natural populations is a key issue in evolutionary biology. Genome scans allow the identification of the genetic basis of local adaptation without previous knowledge of genetic variation or traits under selection. Candidate loci for divergent adaptation are expected to show higher FST than neutral loci influenced solely by random genetic drift, migration and mutation. The comparison of spatial patterns of neutral markers and loci under selection may help disentangle the effects of gene flow, genetic drift and selection among populations living in contrasting environments. Using the gastropod Radix balthica as a system, we analyzed 376 AFLP markers and 25 mtDNA COI haplotypes for candidate loci and associations with local adaptation among contrasting thermal environments in Lake Mývatn, a volcanic lake in northern Iceland. We found that 2% of the analysed AFLP markers were under directional selection and 12% of the mitochondrial haplotypes correlated with differing thermal habitats. The genetic networks were concordant for AFLP markers and mitochondrial haplotypes, depicting distinct topologies at neutral and candidate loci. Neutral topologies were characterized by intense gene flow revealed by dense nets with edges connecting contrasting thermal habitats, whereas the connections at candidate loci were mostly restricted to populations within each thermal habitat and the number of edges decreased with temperature. Our results suggest microgeographic adaptation within Lake Mývatn and highlight the utility of genome scans in detecting adaptive divergence.}, } @article {pmid25006188, year = {2014}, author = {Moyé, L}, title = {DAMASCENE and Meta-Ecological Research: A Bridge Too Far.}, journal = {Circulation research}, volume = {115}, number = {5}, pages = {484-487}, pmid = {25006188}, issn = {1524-4571}, support = {UM1 HL087318/HL/NHLBI NIH HHS/United States ; UM1 HL087394/HL/NHLBI NIH HHS/United States ; }, mesh = {*Bone Marrow Transplantation ; Cardiovascular Diseases/diagnosis/epidemiology/physiopathology/*surgery ; Cell Phone ; Data Interpretation, Statistical ; *Epidemiologic Research Design ; Evidence-Based Medicine/*methods/statistics & numerical data ; Humans ; *Meta-Analysis as Topic ; Reproducibility of Results ; Risk Assessment ; Risk Factors ; *Stem Cell Transplantation ; Stroke/epidemiology ; Stroke Volume ; Treatment Outcome ; Ventricular Function, Left ; }, abstract = {Population level studies commonly induce the ecological fallacy i.e., the belief that a relationship identified at the population level implies a cause and effect relationship at the level of the individual. A recent research report (DAMASCENE) that related clinical trial effect sizes in cardiovascular cell therapy trials to reporting discrepancies in the trials themselves has compounded meta-analysis difficulties with ecological fallacy issues. This dangerous combination has produced misleading conclusions and speculation that the research community should set aside.}, } @article {pmid25005925, year = {2014}, author = {Mak, WS and Siegel, JB}, title = {Computational enzyme design: transitioning from catalytic proteins to enzymes.}, journal = {Current opinion in structural biology}, volume = {27}, number = {}, pages = {87-94}, doi = {10.1016/j.sbi.2014.05.010}, pmid = {25005925}, issn = {1879-033X}, mesh = {*Biocatalysis ; Computational Biology/*methods ; Enzymes/chemistry/*genetics/*metabolism ; Protein Engineering/*methods ; Proteins/chemistry/*genetics/*metabolism ; }, abstract = {The widespread interest in enzymes stem from their ability to catalyze chemical reactions under mild and ecologically friendly conditions with unparalleled catalytic proficiencies. While thousands of naturally occurring enzymes have been identified and characterized, there are still numerous important applications for which there are no biological catalysts capable of performing the desired chemical transformation. In order to engineer enzymes for which there is no natural starting point, efforts using a combination of quantum chemistry and force-field based protein molecular modeling have led to the design of novel proteins capable of catalyzing chemical reactions not catalyzed by naturally occurring enzymes. Here we discuss the current status and potential avenues to pursue as the field of computational enzyme design moves forward.}, } @article {pmid25000751, year = {2014}, author = {Ordonez, A}, title = {Functional and phylogenetic similarity of alien plants to co-occurring natives.}, journal = {Ecology}, volume = {95}, number = {5}, pages = {1191-1202}, doi = {10.1890/13-1002.1}, pmid = {25000751}, issn = {0012-9658}, mesh = {Databases, Factual ; Demography ; Ecosystem ; Introduced Species ; *Phylogeny ; Plants/*classification/*genetics ; }, abstract = {Over the years, several arguments have been proposed to explain the invasibility of a given community based on the properties of the recipient community. Here, I assessed whether the balance between native species' phylogenetic and functional variability determines vulnerability to invasion. I explored this hypothesis using a consensus phylogenetic tree and a database of leaf, height, and seed traits of alien and native species co-occurring over 83 sites worldwide. An analysis of contrasts between aliens and natives indicates that aliens are as phylogenetically close to the incumbent native community as natives are among themselves (aliens are nested within the native community phylogeny), but functionally distinct to the native community (aliens are more functionally distant to the community of native taxa than natives are among themselves). These contrasting trends are consistent for different comparison criteria (comparisons to all natives or to the nearest native) and comparisons both within and across communities, habitats, and continents. Furthermore, aliens are more functionally divergent than the native community and the closest native relative in both phylogenetically poor and rich communities. The phylogenetic similarity and functional distinctiveness of aliens with respect to the incumbent native community may explain why certain species succeed in some communities and not others. This is a step forward in resolving the long-standing debate on the role diversity--both phylogenetic and functional--plays in determining the success of introduced plants.}, } @article {pmid24999823, year = {2014}, author = {Hinchliff, CE and Smith, SA}, title = {Some limitations of public sequence data for phylogenetic inference (in plants).}, journal = {PloS one}, volume = {9}, number = {7}, pages = {e98986}, pmid = {24999823}, issn = {1932-6203}, mesh = {Biodiversity ; *Computational Biology ; *Databases, Genetic ; National Library of Medicine (U.S.) ; *Phylogeny ; Plants/*classification/*genetics ; United States ; }, abstract = {The GenBank database contains essentially all of the nucleotide sequence data generated for published molecular systematic studies, but for the majority of taxa these data remain sparse. GenBank has value for phylogenetic methods that leverage data-mining and rapidly improving computational methods, but the limits imposed by the sparse structure of the data are not well understood. Here we present a tree representing 13,093 land plant genera--an estimated 80% of extant plant diversity--to illustrate the potential of public sequence data for broad phylogenetic inference in plants, and we explore the limits to inference imposed by the structure of these data using theoretical foundations from phylogenetic data decisiveness. We find that despite very high levels of missing data (over 96%), the present data retain the potential to inform over 86.3% of all possible phylogenetic relationships. Most of these relationships, however, are informed by small amounts of data--approximately half are informed by fewer than four loci, and more than 99% are informed by fewer than fifteen. We also apply an information theoretic measure of branch support to assess the strength of phylogenetic signal in the data, revealing many poorly supported branches concentrated near the tips of the tree, where data are sparse and the limiting effects of this sparseness are stronger. We argue that limits to phylogenetic inference and signal imposed by low data coverage may pose significant challenges for comprehensive phylogenetic inference at the species level. Computational requirements provide additional limits for large reconstructions, but these may be overcome by methodological advances, whereas insufficient data coverage can only be remedied by additional sampling effort. We conclude that public databases have exceptional value for modern systematics and evolutionary biology, and that a continued emphasis on expanding taxonomic and genomic coverage will play a critical role in developing these resources to their full potential.}, } @article {pmid24999094, year = {2014}, author = {Fuerst, PA}, title = {Insights from the DNA databases: approaches to the phylogenetic structure of Acanthamoeba.}, journal = {Experimental parasitology}, volume = {145 Suppl}, number = {}, pages = {S39-45}, doi = {10.1016/j.exppara.2014.06.020}, pmid = {24999094}, issn = {1090-2449}, mesh = {Acanthamoeba/classification/*genetics ; Amebiasis/diagnosis/parasitology ; DNA, Protozoan/*chemistry ; DNA, Ribosomal/chemistry ; Databases, Nucleic Acid/*statistics & numerical data ; Genotype ; *Phylogeny ; RNA, Protozoan/genetics ; RNA, Ribosomal, 18S/*genetics ; *Sequence Analysis, DNA ; }, abstract = {Species of Acanthamoeba have been traditionally described using morphology (primarily cyst structure), or cytology of nuclear division (used by Pussard and Pons, 1977). Twenty-plus putative species were proposed based on such criteria. Morphology, however, is often plastic, dependent upon culture conditions. DNA sequences of the nuclear small subunit (18S) rRNA that can be used for the study of the phylogeny of Acanthamoeba have increased from a single sequence in 1986 to more than 1800 in 2013. Some of the patterns of the sequence data for Acanthamoeba are reviewed, and some of the insights that this data illuminates are illustrated. In particular, the data suggest the existence of 20 or more genotypic types, a number not dissimilar to the number of named species of Acanthamoeba. However, molecular studies make clear that the relationship between phylogenetic relatedness and species names as we know them for Acanthamoeba is tenuous at best.}, } @article {pmid24994012, year = {2014}, author = {Park, MS and Lee, H and Oh, SY and Jung, PE and Seok, SJ and Fong, JJ and Lim, YW}, title = {Species delimitation of three species within the Russula subgenus Compacta in Korea: R. eccentrica, R. nigricans, and R. subnigricans.}, journal = {Journal of microbiology (Seoul, Korea)}, volume = {52}, number = {8}, pages = {631-638}, pmid = {24994012}, issn = {1976-3794}, mesh = {Agaricales/*classification/*genetics ; DNA, Fungal/*genetics ; DNA, Intergenic ; DNA, Ribosomal/genetics ; Databases, Nucleic Acid ; Ecosystem ; Europe ; Genetic Markers ; Genetic Variation ; Japan ; North America ; Phylogeny ; Phylogeography ; Republic of Korea ; Ribosome Subunits, Large ; }, abstract = {Distinguishing individual Russula species can be very difficult due to extensive phenotypic plasticity and obscure morphological and anatomical discontinuities. In this study, we use the internal transcribed spacer (ITS) and 28S nuclear ribosomal large subunit (LSU) markers to identify and study the genetic diversity of species in the Russula subgenus Compacta in Korea. We focus on two morphologically similar species that are often misidentified for each other: R. nigricans and R. subnigricans. Based on molecular phylogenetic analyses, we identify three subgroups of R. nigricans, with two from Asia and one from Europe/North America. Surprisingly, we find Korean R. subnigricans are more closely related to R. eccentrica from North America than the type specimen of R. subnigricans from Japan. These molecular data, along with habitat data, reveal that Korean R. subnigricans had previously been misclassified and should now be recognized as R. eccentrica. Both ITS and LSU exhibit high interspecific and low intraspecific variation for R. eccentrica, R. nigricans, and R. subnigricans. These markers provide enough resolutional power to differentiate these species and uncover phylogeographic structure, and will be powerful tools for future ecological studies of Russula.}, } @article {pmid24992684, year = {2014}, author = {Raghavan, RK and Neises, D and Goodin, DG and Andresen, DA and Ganta, RR}, title = {Bayesian spatio-temporal analysis and geospatial risk factors of human monocytic ehrlichiosis.}, journal = {PloS one}, volume = {9}, number = {7}, pages = {e100850}, pmid = {24992684}, issn = {1932-6203}, support = {R01 AI070908/AI/NIAID NIH HHS/United States ; R56 AI070908/AI/NIAID NIH HHS/United States ; AI070908/AI/NIAID NIH HHS/United States ; }, mesh = {Bayes Theorem ; Climate Change ; Ehrlichiosis/*epidemiology ; Humans ; Kansas/epidemiology ; Risk Factors ; Socioeconomic Factors ; *Spatio-Temporal Analysis ; }, abstract = {Variations in spatio-temporal patterns of Human Monocytic Ehrlichiosis (HME) infection in the state of Kansas, USA were examined and the relationship between HME relative risk and various environmental, climatic and socio-economic variables were evaluated. HME data used in the study was reported to the Kansas Department of Health and Environment between years 2005-2012, and geospatial variables representing the physical environment [National Land cover/Land use, NASA Moderate Resolution Imaging Spectroradiometer (MODIS)], climate [NASA MODIS, Prediction of Worldwide Renewable Energy (POWER)], and socio-economic conditions (US Census Bureau) were derived from publicly available sources. Following univariate screening of candidate variables using logistic regressions, two Bayesian hierarchical models were fit; a partial spatio-temporal model with random effects and a spatio-temporal interaction term, and a second model that included additional covariate terms. The best fitting model revealed that spatio-temporal autocorrelation in Kansas increased steadily from 2005-2012, and identified poverty status, relative humidity, and an interactive factor, 'diurnal temperature range x mixed forest area' as significant county-level risk factors for HME. The identification of significant spatio-temporal pattern and new risk factors are important in the context of HME prevention, for future research in the areas of ecology and evolution of HME, and as well as climate change impacts on tick-borne diseases.}, } @article {pmid24990571, year = {2014}, author = {Oakley, TH and Alexandrou, MA and Ngo, R and Pankey, MS and Churchill, CK and Chen, W and Lopker, KB}, title = {Osiris: accessible and reproducible phylogenetic and phylogenomic analyses within the Galaxy workflow management system.}, journal = {BMC bioinformatics}, volume = {15}, number = {}, pages = {230}, pmid = {24990571}, issn = {1471-2105}, mesh = {Computational Biology/*methods ; *Phylogeny ; Sequence Alignment ; *Software ; User-Computer Interface ; Workflow ; }, abstract = {BACKGROUND: Phylogenetic tools and 'tree-thinking' approaches increasingly permeate all biological research. At the same time, phylogenetic data sets are expanding at breakneck pace, facilitated by increasingly economical sequencing technologies. Therefore, there is an urgent need for accessible, modular, and sharable tools for phylogenetic analysis.

RESULTS: We developed a suite of wrappers for new and existing phylogenetics tools for the Galaxy workflow management system that we call Osiris. Osiris and Galaxy provide a sharable, standardized, modular user interface, and the ability to easily create complex workflows using a graphical interface. Osiris enables all aspects of phylogenetic analysis within Galaxy, including de novo assembly of high throughput sequencing reads, ortholog identification, multiple sequence alignment, concatenation, phylogenetic tree estimation, and post-tree comparative analysis. The open source files are available on in the Bitbucket public repository and many of the tools are demonstrated on a public web server (http://galaxy-dev.cnsi.ucsb.edu/osiris/).

CONCLUSIONS: Osiris can serve as a foundation for other phylogenomic and phylogenetic tool development within the Galaxy platform.}, } @article {pmid24990155, year = {2014}, author = {Naranjo, DP and Qualls, WA and Jurado, H and Perez, JC and Xue, RD and Gomez, E and Beier, JC}, title = {Vector control programs in Saint Johns County, Florida and Guayas, Ecuador: successes and barriers to integrated vector management.}, journal = {BMC public health}, volume = {14}, number = {}, pages = {674}, pmid = {24990155}, issn = {1471-2458}, support = {R01 GM093345/GM/NIGMS NIH HHS/United States ; U19 AI089702/AI/NIAID NIH HHS/United States ; GM093345/GM/NIGMS NIH HHS/United States ; U19AI089702/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; *Community Participation ; Decision Support Techniques ; Disease Vectors ; Ecuador ; *Efficiency, Organizational ; Florida ; Health Policy ; Humans ; Mosquito Control/*methods/organization & administration ; Policy Making ; Public Health ; *Systems Integration ; World Health Organization ; }, abstract = {BACKGROUND: Vector-borne diseases (VBDs) and mosquito control programs (MCPs) diverge in settings and countries, and lead control specialists need to be aware of the most effective control strategies. Integrated Vector Management (IVM) strategies, once implemented in MCPs, aim to reduce cost and optimize protection of the populations against VBDs. This study presents a strengths, weaknesses, opportunities, and threats (SWOT) analysis to compare IVM strategies used by MCPs in Saint Johns County, Florida and Guayas, Ecuador. This research evaluates MCPs strategies to improve vector control activities.

METHODS: Methods included descriptive findings of the MCP operations. Information was obtained from vector control specialists, directors, and residents through field trips, surveys, and questionnaires. Evaluations of the strategies and assets of the control programs where obtained through SWOT analysis and within an IVM approach.

RESULTS: Organizationally, the Floridian MCP is a tax-based District able to make decisions independently from county government officials, with the oversight of an elected board of commissioners. The Guayas program is directed by the country government and assessed by non-governmental organizations like the World health Organization. Operationally, the Floridian MCP conducts entomological surveillance and the Ecuadorian MCP focuses on epidemiological monitoring of human disease cases. Strengths of both MCPs were their community participation and educational programs. Weaknesses for both MCPs included limitations in budgets and technical capabilities. Opportunities, for both MCPs, are additional funding and partnerships with private, non-governmental, and governmental organizations. Threats experienced by both MCPs included political constraints and changes in the social and ecological environment that affect mosquito densities and control efforts. IVM pillars for policy making were used to compare the information among the programs. Differences included how the Ecuadorian MCP relies heavily on the community for vector control while the American MCP relies on technologies and research.

CONCLUSION: IVM based recommendations direct health policy leaders toward improving surveillance systems both entomologically and epidemiologically, improving community risk perceptions by integrating components of community participation, maximizing resources though the use of applied research, and protecting the environment by selecting low-risk pesticides. Outcomes of the research revealed that inter-sectorial and multidisciplinary interventions are critical to improve public health.}, } @article {pmid24989860, year = {2014}, author = {Francisco, JC and Cohan, FM and Krizanc, D}, title = {Accuracy and efficiency of algorithms for the demarcation of bacterial ecotypes from DNA sequence data.}, journal = {International journal of bioinformatics research and applications}, volume = {10}, number = {4-5}, pages = {409-425}, doi = {10.1504/IJBRA.2014.062992}, pmid = {24989860}, issn = {1744-5485}, mesh = {*Algorithms ; Bacillus/*classification/genetics ; Computational Biology/*methods ; *Ecotype ; Genes, Bacterial ; Models, Statistical ; Sequence Analysis, DNA/*methods ; Software ; Species Specificity ; }, abstract = {Identification of closely related, ecologically distinct populations of bacteria would benefit microbiologists working in many fields including systematics, epidemiology and biotechnology. Several laboratories have recently developed algorithms aimed at demarcating such 'ecotypes'. We examine the ability of four of these algorithms to correctly identify ecotypes from sequence data. We tested the algorithms on synthetic sequences, with known history and habitat associations, generated under the stable ecotype model and on data from Bacillus strains isolated from Death Valley where previous work has confirmed the existence of multiple ecotypes. We found that one of the algorithms (ecotype simulation) performs significantly better than the others (AdaptML, GMYC, BAPS) in both instances. Unfortunately, it was also shown to be the least efficient of the four. While ecotype simulation is the most accurate, it is by a large margin the slowest of the algorithms tested. Attempts at improving its efficiency are underway.}, } @article {pmid24989069, year = {2014}, author = {Kampshoff, CS and Jansen, F and van Mechelen, W and May, AM and Brug, J and Chinapaw, MJ and Buffart, LM}, title = {Determinants of exercise adherence and maintenance among cancer survivors: a systematic review.}, journal = {The international journal of behavioral nutrition and physical activity}, volume = {11}, number = {}, pages = {80}, pmid = {24989069}, issn = {1479-5868}, mesh = {Databases, Factual ; Exercise/*physiology ; Health Status ; Humans ; Neoplasms/*rehabilitation ; *Patient Compliance ; Quality of Life ; *Survivors ; }, abstract = {For an exercise intervention to be successful, it is important that cancer survivors adhere to the prescribed program. To be able to improve adherence and to preserve achieved beneficial effects, insights into the relevant and modifiable determinants is important. Therefore, we aimed to systematically review determinants of exercise adherence and maintenance in cancer survivors using a socio-ecological approach.Studies were identified in PubMed, Embase, PsycINFO and SPORTDiscus up to July 2013. We included full-text articles that: 1) were conducted among adult cancer survivors; 2) quantitatively assessed factors associated with intervention adherence and maintenance, and 3) were published in English. The methodological quality of the selected studies was examined. A best evidence synthesis was applied. Eighteen studies were included. Median methodological quality was 53% and ranged from 21-78% of maximum score. Twelve studies focused on determinants of exercise adherence and evaluated 71 potential determinants: 29 demographic and clinical, 27 psychological, ten physical, four social factors, and one environmental factor. Six studies focused on determinants of exercise maintenance after completion of an intervention, and investigated 63 factors: 22 demographic and clinical, 28 psychosocial, nine physical, three social and one environmental factor. We found moderate evidence for a positive association between exercise history and exercise adherence. Inconsistent findings were found for age, gender and education as well as for psychological factors such as stage of change, perceived behavioral control, self-efficacy, extraversion, attitude, intention, fatigue, and quality of life, and physical factors including cardiovascular fitness, body mass index, and baseline physical activity.Exercise history is positively associated with exercise adherence. Future trials should further study the influence of social and environmental determinants on exercise adherence and maintenance in addition to demographic, psychological and physical determinants.}, } @article {pmid24988762, year = {2014}, author = {Wall, J and Wittemyer, G and Klinkenberg, B and Douglas-Hamilton, I}, title = {Novel opportunities for wildlife conservation and research with real-time monitoring.}, journal = {Ecological applications : a publication of the Ecological Society of America}, volume = {24}, number = {4}, pages = {593-601}, doi = {10.1890/13-1971.1}, pmid = {24988762}, issn = {1051-0761}, mesh = {Animals ; Animals, Wild ; Conservation of Natural Resources/*methods ; Ecosystem ; Endangered Species ; Environmental Monitoring/*instrumentation/methods ; Informatics ; Models, Biological ; Population Dynamics ; Research/instrumentation ; Research Design ; }, abstract = {The expansion of global communication networks and advances in animal-tracking technology make possible the real-time telemetry of positional data as recorded by animal-attached tracking units. When combined with continuous, algorithm-based analytical capability, unique opportunities emerge for applied ecological monitoring and wildlife conservation. We present here four broad approaches for algorithmic wildlife monitoring in real time--proximity, geofencing, movement rate, and immobility--designed to examine aspects of wildlife spatial activity and behavior not possible with conventional tracking systems. Application of these four routines to the real-time monitoring of 94 African elephants was made. We also provide details of our cloud-based monitoring system including infrastructure, data collection, and customized software for continuous tracking data analysis. We also highlight future directions of real-time collection and analysis of biological, physiological, and environmental information from wildlife to encourage further development of needed algorithms and monitoring technology. Real-time processing of remotely collected, animal biospatial data promises to open novel directions in ecological research, applied species monitoring, conservation programs, and public outreach and education.}, } @article {pmid24988433, year = {2014}, author = {Clements, HS and Tambling, CJ and Hayward, MW and Kerley, GI}, title = {An objective approach to determining the weight ranges of prey preferred by and accessible to the five large African carnivores.}, journal = {PloS one}, volume = {9}, number = {7}, pages = {e101054}, pmid = {24988433}, issn = {1932-6203}, mesh = {Africa ; Animals ; Body Weight ; Carnivora/*physiology ; Datasets as Topic ; *Food Chain ; Predatory Behavior/*physiology ; }, abstract = {Broad-scale models describing predator prey preferences serve as useful departure points for understanding predator-prey interactions at finer scales. Previous analyses used a subjective approach to identify prey weight preferences of the five large African carnivores, hence their accuracy is questionable. This study uses a segmented model of prey weight versus prey preference to objectively quantify the prey weight preferences of the five large African carnivores. Based on simulations of known predator prey preference, for prey species sample sizes above 32 the segmented model approach detects up to four known changes in prey weight preference (represented by model break-points) with high rates of detection (75% to 100% of simulations, depending on number of break-points) and accuracy (within 1.3±4.0 to 2.7±4.4 of known break-point). When applied to the five large African carnivores, using carnivore diet information from across Africa, the model detected weight ranges of prey that are preferred, killed relative to their abundance, and avoided by each carnivore. Prey in the weight ranges preferred and killed relative to their abundance are together termed "accessible prey". Accessible prey weight ranges were found to be 14-135 kg for cheetah Acinonyx jubatus, 1-45 kg for leopard Panthera pardus, 32-632 kg for lion Panthera leo, 15-1600 kg for spotted hyaena Crocuta crocuta and 10-289 kg for wild dog Lycaon pictus. An assessment of carnivore diets throughout Africa found these accessible prey weight ranges include 88±2% (cheetah), 82±3% (leopard), 81±2% (lion), 97±2% (spotted hyaena) and 96±2% (wild dog) of kills. These descriptions of prey weight preferences therefore contribute to our understanding of the diet spectrum of the five large African carnivores. Where datasets meet the minimum sample size requirements, the segmented model approach provides a means of determining, and comparing, the prey weight range preferences of any carnivore species.}, } @article {pmid24985915, year = {2014}, author = {Chen, ZX and Sturgill, D and Qu, J and Jiang, H and Park, S and Boley, N and Suzuki, AM and Fletcher, AR and Plachetzki, DC and FitzGerald, PC and Artieri, CG and Atallah, J and Barmina, O and Brown, JB and Blankenburg, KP and Clough, E and Dasgupta, A and Gubbala, S and Han, Y and Jayaseelan, JC and Kalra, D and Kim, YA and Kovar, CL and Lee, SL and Li, M and Malley, JD and Malone, JH and Mathew, T and Mattiuzzo, NR and Munidasa, M and Muzny, DM and Ongeri, F and Perales, L and Przytycka, TM and Pu, LL and Robinson, G and Thornton, RL and Saada, N and Scherer, SE and Smith, HE and Vinson, C and Warner, CB and Worley, KC and Wu, YQ and Zou, X and Cherbas, P and Kellis, M and Eisen, MB and Piano, F and Kionte, K and Fitch, DH and Sternberg, PW and Cutter, AD and Duff, MO and Hoskins, RA and Graveley, BR and Gibbs, RA and Bickel, PJ and Kopp, A and Carninci, P and Celniker, SE and Oliver, B and Richards, S}, title = {Comparative validation of the D. melanogaster modENCODE transcriptome annotation.}, journal = {Genome research}, volume = {24}, number = {7}, pages = {1209-1223}, pmid = {24985915}, issn = {1549-5469}, support = {Z01 DK015600//Intramural NIH HHS/United States ; R01 HG004037/HG/NHGRI NIH HHS/United States ; U54 HG003273/HG/NHGRI NIH HHS/United States ; R01 GM100140/GM/NIGMS NIH HHS/United States ; 1R0IGM082843//PHS HHS/United States ; ZIA DK015600-18//Intramural NIH HHS/United States ; U01HB004271/HB/NHLBI NIH HHS/United States ; DK015600-18/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; Cluster Analysis ; Computational Biology/*methods ; Drosophila melanogaster/classification/*genetics ; Evolution, Molecular ; Exons ; Female ; *Gene Expression Profiling ; Genome, Insect ; Humans ; Male ; *Molecular Sequence Annotation ; Nucleotide Motifs ; Phylogeny ; Position-Specific Scoring Matrices ; Promoter Regions, Genetic ; RNA Editing ; RNA Splice Sites ; RNA Splicing ; Reproducibility of Results ; Transcription Initiation Site ; *Transcriptome ; }, abstract = {Accurate gene model annotation of reference genomes is critical for making them useful. The modENCODE project has improved the D. melanogaster genome annotation by using deep and diverse high-throughput data. Since transcriptional activity that has been evolutionarily conserved is likely to have an advantageous function, we have performed large-scale interspecific comparisons to increase confidence in predicted annotations. To support comparative genomics, we filled in divergence gaps in the Drosophila phylogeny by generating draft genomes for eight new species. For comparative transcriptome analysis, we generated mRNA expression profiles on 81 samples from multiple tissues and developmental stages of 15 Drosophila species, and we performed cap analysis of gene expression in D. melanogaster and D. pseudoobscura. We also describe conservation of four distinct core promoter structures composed of combinations of elements at three positions. Overall, each type of genomic feature shows a characteristic divergence rate relative to neutral models, highlighting the value of multispecies alignment in annotating a target genome that should prove useful in the annotation of other high priority genomes, especially human and other mammalian genomes that are rich in noncoding sequences. We report that the vast majority of elements in the annotation are evolutionarily conserved, indicating that the annotation will be an important springboard for functional genetic testing by the Drosophila community.}, } @article {pmid24982883, year = {2014}, author = {Yang, Q and Sun, F and Yang, Z and Li, H}, title = {Comprehensive transcriptome study to develop molecular resources of the copepod Calanus sinicus for their potential ecological applications.}, journal = {BioMed research international}, volume = {2014}, number = {}, pages = {493825}, pmid = {24982883}, issn = {2314-6141}, mesh = {Animals ; Cluster Analysis ; Copepoda/*genetics ; *Ecological and Environmental Phenomena ; Gene Expression Profiling ; Gene Expression Regulation ; Gene Ontology ; Genetic Loci ; Genetic Markers ; Microsatellite Repeats/genetics ; Molecular Sequence Annotation ; Nucleic Acid Denaturation ; Polymorphism, Single Nucleotide/genetics ; RNA, Messenger/genetics/metabolism ; Sequence Analysis, RNA ; Transcriptome/*genetics ; }, abstract = {Calanus sinicus Brodsky (Copepoda, Crustacea) is a dominant zooplanktonic species widely distributed in the margin seas of the Northwest Pacific Ocean. In this study, we utilized an RNA-Seq-based approach to develop molecular resources for C. sinicus. Adult samples were sequenced using the Illumina HiSeq 2000 platform. The sequencing data generated 69,751 contigs from 58.9 million filtered reads. The assembled contigs had an average length of 928.8 bp. Gene annotation allowed the identification of 43,417 unigene hits against the NCBI database. Gene ontology (GO) and KEGG pathway mapping analysis revealed various functional genes related to diverse biological functions and processes. Transcripts potentially involved in stress response and lipid metabolism were identified among these genes. Furthermore, 4,871 microsatellites and 110,137 single nucleotide polymorphisms (SNPs) were identified in the C. sinicus transcriptome sequences. SNP validation by the melting temperature (T m)-shift method suggested that 16 primer pairs amplified target products and showed biallelic polymorphism among 30 individuals. The present work demonstrates the power of Illumina-based RNA-Seq for the rapid development of molecular resources in nonmodel species. The validated SNP set from our study is currently being utilized in an ongoing ecological analysis to support a future study of C. sinicus population genetics.}, } @article {pmid24982879, year = {2014}, author = {Sun, Z and Li, S and Li, F and Xiang, J}, title = {Bioinformatic prediction of WSSV-host protein-protein interaction.}, journal = {BioMed research international}, volume = {2014}, number = {}, pages = {416543}, pmid = {24982879}, issn = {2314-6141}, mesh = {Amino Acid Sequence ; Animals ; Computational Biology/*methods ; Databases, Protein ; *Host-Pathogen Interactions ; Membrane Proteins/metabolism ; Molecular Sequence Data ; Penaeidae/metabolism/*virology ; Protein Binding ; *Protein Interaction Maps ; Proteins/chemistry/*metabolism ; Sequence Analysis, Protein ; Viral Proteins/chemistry/*metabolism ; White spot syndrome virus 1/*metabolism ; }, abstract = {WSSV is one of the most dangerous pathogens in shrimp aquaculture. However, the molecular mechanism of how WSSV interacts with shrimp is still not very clear. In the present study, bioinformatic approaches were used to predict interactions between proteins from WSSV and shrimp. The genome data of WSSV (NC_003225.1) and the constructed transcriptome data of F. chinensis were used to screen potentially interacting proteins by searching in protein interaction databases, including STRING, Reactome, and DIP. Forty-four pairs of proteins were suggested to have interactions between WSSV and the shrimp. Gene ontology analysis revealed that 6 pairs of these interacting proteins were classified into "extracellular region" or "receptor complex" GO-terms. KEGG pathway analysis showed that they were involved in the "ECM-receptor interaction pathway." In the 6 pairs of interacting proteins, an envelope protein called "collagen-like protein" (WSSV-CLP) encoded by an early virus gene "wsv001" in WSSV interacted with 6 deduced proteins from the shrimp, including three integrin alpha (ITGA), two integrin beta (ITGB), and one syndecan (SDC). Sequence analysis on WSSV-CLP, ITGA, ITGB, and SDC revealed that they possessed the sequence features for protein-protein interactions. This study might provide new insights into the interaction mechanisms between WSSV and shrimp.}, } @article {pmid24980130, year = {2014}, author = {Schoch, CL and Robbertse, B and Robert, V and Vu, D and Cardinali, G and Irinyi, L and Meyer, W and Nilsson, RH and Hughes, K and Miller, AN and Kirk, PM and Abarenkov, K and Aime, MC and Ariyawansa, HA and Bidartondo, M and Boekhout, T and Buyck, B and Cai, Q and Chen, J and Crespo, A and Crous, PW and Damm, U and De Beer, ZW and Dentinger, BT and Divakar, PK and Dueñas, M and Feau, N and Fliegerova, K and García, MA and Ge, ZW and Griffith, GW and Groenewald, JZ and Groenewald, M and Grube, M and Gryzenhout, M and Gueidan, C and Guo, L and Hambleton, S and Hamelin, R and Hansen, K and Hofstetter, V and Hong, SB and Houbraken, J and Hyde, KD and Inderbitzin, P and Johnston, PR and Karunarathna, SC and Kõljalg, U and Kovács, GM and Kraichak, E and Krizsan, K and Kurtzman, CP and Larsson, KH and Leavitt, S and Letcher, PM and Liimatainen, K and Liu, JK and Lodge, DJ and Luangsa-ard, JJ and Lumbsch, HT and Maharachchikumbura, SS and Manamgoda, D and Martín, MP and Minnis, AM and Moncalvo, JM and Mulè, G and Nakasone, KK and Niskanen, T and Olariaga, I and Papp, T and Petkovits, T and Pino-Bodas, R and Powell, MJ and Raja, HA and Redecker, D and Sarmiento-Ramirez, JM and Seifert, KA and Shrestha, B and Stenroos, S and Stielow, B and Suh, SO and Tanaka, K and Tedersoo, L and Telleria, MT and Udayanga, D and Untereiner, WA and Diéguez Uribeondo, J and Subbarao, KV and Vágvölgyi, C and Visagie, C and Voigt, K and Walker, DM and Weir, BS and Weiß, M and Wijayawardene, NN and Wingfield, MJ and Xu, JP and Yang, ZL and Zhang, N and Zhuang, WY and Federhen, S}, title = {Finding needles in haystacks: linking scientific names, reference specimens and molecular data for Fungi.}, journal = {Database : the journal of biological databases and curation}, volume = {2014}, number = {}, pages = {}, pmid = {24980130}, issn = {1758-0463}, support = {//Intramural NIH HHS/United States ; }, mesh = {Cluster Analysis ; DNA, Fungal ; DNA, Intergenic ; *Databases, Genetic ; *Fungi/classification/genetics ; Genes, Fungal ; Molecular Sequence Annotation/*methods ; *Sequence Analysis, DNA ; }, abstract = {DNA phylogenetic comparisons have shown that morphology-based species recognition often underestimates fungal diversity. Therefore, the need for accurate DNA sequence data, tied to both correct taxonomic names and clearly annotated specimen data, has never been greater. Furthermore, the growing number of molecular ecology and microbiome projects using high-throughput sequencing require fast and effective methods for en masse species assignments. In this article, we focus on selecting and re-annotating a set of marker reference sequences that represent each currently accepted order of Fungi. The particular focus is on sequences from the internal transcribed spacer region in the nuclear ribosomal cistron, derived from type specimens and/or ex-type cultures. Re-annotated and verified sequences were deposited in a curated public database at the National Center for Biotechnology Information (NCBI), namely the RefSeq Targeted Loci (RTL) database, and will be visible during routine sequence similarity searches with NR_prefixed accession numbers. A set of standards and protocols is proposed to improve the data quality of new sequences, and we suggest how type and other reference sequences can be used to improve identification of Fungi. Database URL: http://www.ncbi.nlm.nih.gov/bioproject/PRJNA177353.}, } @article {pmid24979762, year = {2014}, author = {Malaj, E and von der Ohe, PC and Grote, M and Kühne, R and Mondy, CP and Usseglio-Polatera, P and Brack, W and Schäfer, RB}, title = {Organic chemicals jeopardize the health of freshwater ecosystems on the continental scale.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {111}, number = {26}, pages = {9549-9554}, pmid = {24979762}, issn = {1091-6490}, mesh = {Data Mining/methods ; *Ecosystem ; Environmental Monitoring/*statistics & numerical data ; Europe ; *Fresh Water ; Organic Chemicals/*analysis/toxicity ; Risk Assessment/*statistics & numerical data ; Water Pollutants, Chemical/*analysis/toxicity ; }, abstract = {Organic chemicals can contribute to local and regional losses of freshwater biodiversity and ecosystem services. However, their overall relevance regarding larger spatial scales remains unknown. Here, we present, to our knowledge, the first risk assessment of organic chemicals on the continental scale comprising 4,000 European monitoring sites. Organic chemicals were likely to exert acute lethal and chronic long-term effects on sensitive fish, invertebrate, or algae species in 14% and 42% of the sites, respectively. Of the 223 chemicals monitored, pesticides, tributyltin, polycyclic aromatic hydrocarbons, and brominated flame retardants were the major contributors to the chemical risk. Their presence was related to agricultural and urban areas in the upstream catchment. The risk of potential acute lethal and chronic long-term effects increased with the number of ecotoxicologically relevant chemicals analyzed at each site. As most monitoring programs considered in this study only included a subset of these chemicals, our assessment likely underestimates the actual risk. Increasing chemical risk was associated with deterioration in the quality status of fish and invertebrate communities. Our results clearly indicate that chemical pollution is a large-scale environmental problem and requires far-reaching, holistic mitigation measures to preserve and restore ecosystem health.}, } @article {pmid24972896, year = {2014}, author = {Meitern, R and Andreson, R and Hõrak, P}, title = {Profile of whole blood gene expression following immune stimulation in a wild passerine.}, journal = {BMC genomics}, volume = {15}, number = {1}, pages = {533}, pmid = {24972896}, issn = {1471-2164}, mesh = {Animals ; Blood Cells/*metabolism ; Chickens/genetics ; Computational Biology/methods ; Female ; Gene Expression Profiling/*methods ; *Gene Expression Regulation ; Genomics/methods ; Molecular Sequence Annotation ; Passeriformes/*genetics/immunology ; }, abstract = {BACKGROUND: Immunoecology aims to explain variation among hosts in the strength and efficacy of immunological defences in natural populations. This requires development of biomarkers of the activation of the immune system so that they can be collected non-lethally and sampled from small amounts of easily obtainable tissue. We used transcriptome profiling in wild greenfinches (Carduelis chloris) to detect whole blood transcripts that most profoundly indicate upregulation of antimicrobial defences during acute phase response. The more general aim of this study was to obtain a functional annotation of a substantial portion of the greenfinch transcriptome that would enable to gain access to more specific genomic tools in subsequent studies. The birds received either bacterial lipopolysaccharide or saline injections and RNA-seq transcriptional profiling was performed 12 h after treatment to provide initial functional annotation of the transcriptome and assess whole blood response to immune stimulation.

RESULTS: A total of 66,084 transcripts were obtained from de novo Trinty assembly, out of which 23,153 could be functionally annotated. Only 1,911 of these were significantly upregulated or downregulated. The manipulation caused marked upregulation of several transcripts related to immune activation. These included avian-specific antimicrobial agents avidin and gallinacin, but also some more general host response genes, such as serum amyloid A protein, lymphocyte antigen 75 and copper-transporting ATPase 1. However, links with avian immunity for most differentially regulated transcripts remained rather hypothetical, as a large set of differentially expressed transcripts lacked functional annotation.

CONCLUSIONS: This appears to be the first large scale transcriptional profiling of immune function in passerine birds. The transcriptomic data obtained suggest novel markers for the assessment of the immunological state of wild passerines. Characterizing the function of those possible novel infection markers would assist future vertebrate genome annotation. The extensive sequence information collected enables to identify possible target and housekeeping genes needed to gain access to more specific genomic tools in future studies.}, } @article {pmid24972829, year = {2014}, author = {Pigott, DM and Bhatt, S and Golding, N and Duda, KA and Battle, KE and Brady, OJ and Messina, JP and Balard, Y and Bastien, P and Pratlong, F and Brownstein, JS and Freifeld, CC and Mekaru, SR and Gething, PW and George, DB and Myers, MF and Reithinger, R and Hay, SI}, title = {Global distribution maps of the leishmaniases.}, journal = {eLife}, volume = {3}, number = {}, pages = {}, pmid = {24972829}, issn = {2050-084X}, support = {/WT_/Wellcome Trust/United Kingdom ; 095066/WT_/Wellcome Trust/United Kingdom ; R01 LM010812/LM/NLM NIH HHS/United States ; R01LM010812/LM/NLM NIH HHS/United States ; }, mesh = {Animals ; Disease Reservoirs ; Environment ; Geography ; Global Health ; Humans ; Leishmaniasis, Cutaneous/*epidemiology ; Leishmaniasis, Visceral/*epidemiology ; Models, Theoretical ; Psychodidae ; Public Health ; Regression Analysis ; }, abstract = {The leishmaniases are vector-borne diseases that have a broad global distribution throughout much of the Americas, Africa, and Asia. Despite representing a significant public health burden, our understanding of the global distribution of the leishmaniases remains vague, reliant upon expert opinion and limited to poor spatial resolution. A global assessment of the consensus of evidence for leishmaniasis was performed at a sub-national level by aggregating information from a variety of sources. A database of records of cutaneous and visceral leishmaniasis occurrence was compiled from published literature, online reports, strain archives, and GenBank accessions. These, with a suite of biologically relevant environmental covariates, were used in a boosted regression tree modelling framework to generate global environmental risk maps for the leishmaniases. These high-resolution evidence-based maps can help direct future surveillance activities, identify areas to target for disease control and inform future burden estimation efforts.}, } @article {pmid24972259, year = {2015}, author = {Miao, Q and Chen, D and Buzzelli, M and Aronson, KJ}, title = {Environmental equity research: review with focus on outdoor air pollution research methods and analytic tools.}, journal = {Archives of environmental & occupational health}, volume = {70}, number = {1}, pages = {47-55}, doi = {10.1080/19338244.2014.904266}, pmid = {24972259}, issn = {2154-4700}, mesh = {Air Pollutants/*analysis ; Air Pollution/*analysis ; Biomarkers ; Canada ; Environmental Exposure/*analysis ; Environmental Monitoring/methods ; Geographic Information Systems ; *Health Status Disparities ; Humans ; *Research Design ; Residence Characteristics ; Socioeconomic Factors ; }, abstract = {The objective of this study was to review environmental equity research on outdoor air pollution and, specifically, methods and tools used in research, published in English, with the aim of recommending the best methods and analytic tools. English language publications from 2000 to 2012 were identified in Google Scholar, Ovid MEDLINE, and PubMed. Research methodologies and results were reviewed and potential deficiencies and knowledge gaps identified. The publications show that exposure to outdoor air pollution differs by social factors, but findings are inconsistent in Canada. In terms of study designs, most were small and ecological and therefore prone to the ecological fallacy. Newer tools such as geographic information systems, modeling, and biomarkers offer improved precision in exposure measurement. Higher-quality research using large, individual-based samples and more precise analytic tools are needed to provide better evidence for policy-making to reduce environmental inequities.}, } @article {pmid24972188, year = {2014}, author = {Iversen, M and Fauchald, P and Langeland, K and Ims, RA and Yoccoz, NG and Bråthen, KA}, title = {Phenology and cover of plant growth forms predict herbivore habitat selection in a high latitude ecosystem.}, journal = {PloS one}, volume = {9}, number = {6}, pages = {e100780}, pmid = {24972188}, issn = {1932-6203}, mesh = {Animal Migration ; Animals ; Behavior, Animal/*physiology ; *Ecosystem ; Geographic Information Systems ; Herbivory ; Poaceae/growth & development ; Reindeer ; Seasons ; }, abstract = {The spatial and temporal distribution of forage quality is among the most central factors affecting herbivore habitat selection. Yet, for high latitude areas, forage quantity has been found to be more important than quality. Studies on large ungulate foraging patterns are faced with methodological challenges in both assessing animal movements at the scale of forage distribution, and in assessing forage quality with relevant metrics. Here we use first-passage time analyses to assess how reindeer movements relate to forage quality and quantity measured as the phenology and cover of growth forms along reindeer tracks. The study was conducted in a high latitude ecosystem dominated by low-palatable growth forms. We found that the scale of reindeer movement was season dependent, with more extensive area use as the summer season advanced. Small-scale movement in the early season was related to selection for younger stages of phenology and for higher abundances of generally phenologically advanced palatable growth forms (grasses and deciduous shrubs). Also there was a clear selection for later phenological stages of the most dominant, yet generally phenologically slow and low-palatable growth form (evergreen shrubs). As the summer season advanced only quantity was important, with selection for higher quantities of one palatable growth form and avoidance of a low palatable growth form. We conclude that both forage quality and quantity are significant predictors to habitat selection by a large herbivore at high latitude. The early season selectivity reflected that among dominating low palatability growth forms there were palatable phenological stages and palatable growth forms available, causing herbivores to be selective in their habitat use. The diminishing selectivity and the increasing scale of movement as the season developed suggest a response by reindeer to homogenized forage availability of low quality.}, } @article {pmid24971887, year = {2014}, author = {Bengtsson, D and Avril, A and Gunnarsson, G and Elmberg, J and Söderquist, P and Norevik, G and Tolf, C and Safi, K and Fiedler, W and Wikelski, M and Olsen, B and Waldenström, J}, title = {Movements, home-range size and habitat selection of mallards during autumn migration.}, journal = {PloS one}, volume = {9}, number = {6}, pages = {e100764}, pmid = {24971887}, issn = {1932-6203}, mesh = {Animal Migration/*physiology ; Animals ; Animals, Wild ; Ducks/*physiology ; Ecosystem ; Female ; Geographic Information Systems ; Homing Behavior/*physiology ; Male ; *Seasons ; }, abstract = {The mallard (Anas platyrhynchos) is a focal species in game management, epidemiology and ornithology, but comparably little research has focused on the ecology of the migration seasons. We studied habitat use, time-budgets, home-range sizes, habitat selection, and movements based on spatial data collected with GPS devices attached to wild mallards trapped at an autumn stopover site in the Northwest European flyway. Sixteen individuals (13 males, 3 females) were followed for 15-38 days in October to December 2010. Forty-nine percent (SD = 8.4%) of the ducks' total time, and 85% of the day-time (SD = 28.3%), was spent at sheltered reefs and bays on the coast. Two ducks used ponds, rather than coast, as day-roosts instead. Mallards spent most of the night (76% of total time, SD = 15.8%) on wetlands, mainly on alvar steppe, or in various flooded areas (e.g. coastal meadows). Crop fields with maize were also selectively utilized. Movements between roosting and foraging areas mainly took place at dawn and dusk, and the home-ranges observed in our study are among the largest ever documented for mallards (mean = 6,859 ha; SD = 5,872 ha). This study provides insights into relatively unknown aspects of mallard ecology. The fact that autumn-staging migratory mallards have a well-developed diel activity pattern tightly linked to the use of specific habitats has implications for wetland management, hunting and conservation, as well as for the epidemiology of diseases shared between wildlife and domestic animals.}, } @article {pmid24967601, year = {2014}, author = {Yuan, W and Liu, S and Dong, W and Liang, S and Zhao, S and Chen, J and Xu, W and Li, X and Barr, A and Andrew Black, T and Yan, W and Goulden, ML and Kulmala, L and Lindroth, A and Margolis, HA and Matsuura, Y and Moors, E and van der Molen, M and Ohta, T and Pilegaard, K and Varlagin, A and Vesala, T}, title = {Differentiating moss from higher plants is critical in studying the carbon cycle of the boreal biome.}, journal = {Nature communications}, volume = {5}, number = {}, pages = {4270}, doi = {10.1038/ncomms5270}, pmid = {24967601}, issn = {2041-1723}, mesh = {*Bryophyta ; Carbon ; *Carbon Cycle ; Carbon Dioxide ; *Ecosystem ; Models, Biological ; *Photosynthesis ; Plants ; *Taiga ; }, abstract = {The satellite-derived normalized difference vegetation index (NDVI), which is used for estimating gross primary production (GPP), often includes contributions from both mosses and vascular plants in boreal ecosystems. For the same NDVI, moss can generate only about one-third of the GPP that vascular plants can because of its much lower photosynthetic capacity. Here, based on eddy covariance measurements, we show that the difference in photosynthetic capacity between these two plant functional types has never been explicitly included when estimating regional GPP in the boreal region, resulting in a substantial overestimation. The magnitude of this overestimation could have important implications regarding a change from a current carbon sink to a carbon source in the boreal region. Moss abundance, associated with ecosystem disturbances, needs to be mapped and incorporated into GPP estimates in order to adequately assess the role of the boreal region in the global carbon cycle.}, } @article {pmid24965363, year = {2014}, author = {Eren, AM and Borisy, GG and Huse, SM and Mark Welch, JL}, title = {Oligotyping analysis of the human oral microbiome.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {111}, number = {28}, pages = {E2875-84}, pmid = {24965363}, issn = {1091-6490}, support = {DE022586/DE/NIDCR NIH HHS/United States ; UH3 DK083993/DK/NIDDK NIH HHS/United States ; DK083993/DK/NIDDK NIH HHS/United States ; UH2 DK083993/DK/NIDDK NIH HHS/United States ; R01 DE022586/DE/NIDCR NIH HHS/United States ; }, mesh = {Adolescent ; Adult ; *Bacteria/classification/genetics ; *Databases, Nucleic Acid ; Female ; *Genes, Bacterial ; *Genes, rRNA ; Humans ; Male ; Microbiota ; Mouth Mucosa/*microbiology ; RNA, Bacterial/*genetics ; RNA, Ribosomal, 16S/*genetics ; }, abstract = {The Human Microbiome Project provided a census of bacterial populations in healthy individuals, but an understanding of the biomedical significance of this census has been hindered by limited taxonomic resolution. A high-resolution method termed oligotyping overcomes this limitation by evaluating individual nucleotide positions using Shannon entropy to identify the most information-rich nucleotide positions, which then define oligotypes. We have applied this method to comprehensively analyze the oral microbiome. Using Human Microbiome Project 16S rRNA gene sequence data for the nine sites in the oral cavity, we identified 493 oligotypes from the V1-V3 data and 360 oligotypes from the V3-V5 data. We associated these oligotypes with species-level taxon names by comparison with the Human Oral Microbiome Database. We discovered closely related oligotypes, differing sometimes by as little as a single nucleotide, that showed dramatically different distributions among oral sites and among individuals. We also detected potentially pathogenic taxa in high abundance in individual samples. Numerous oligotypes were preferentially located in plaque, others in keratinized gingiva or buccal mucosa, and some oligotypes were characteristic of habitat groupings such as throat, tonsils, tongue dorsum, hard palate, and saliva. The differing habitat distributions of closely related oligotypes suggest a level of ecological and functional biodiversity not previously recognized. We conclude that the Shannon entropy approach of oligotyping has the capacity to analyze entire microbiomes, discriminate between closely related but distinct taxa and, in combination with habitat analysis, provide deep insight into the microbial communities in health and disease.}, } @article {pmid24959919, year = {2014}, author = {Keeling, PJ and Burki, F and Wilcox, HM and Allam, B and Allen, EE and Amaral-Zettler, LA and Armbrust, EV and Archibald, JM and Bharti, AK and Bell, CJ and Beszteri, B and Bidle, KD and Cameron, CT and Campbell, L and Caron, DA and Cattolico, RA and Collier, JL and Coyne, K and Davy, SK and Deschamps, P and Dyhrman, ST and Edvardsen, B and Gates, RD and Gobler, CJ and Greenwood, SJ and Guida, SM and Jacobi, JL and Jakobsen, KS and James, ER and Jenkins, B and John, U and Johnson, MD and Juhl, AR and Kamp, A and Katz, LA and Kiene, R and Kudryavtsev, A and Leander, BS and Lin, S and Lovejoy, C and Lynn, D and Marchetti, A and McManus, G and Nedelcu, AM and Menden-Deuer, S and Miceli, C and Mock, T and Montresor, M and Moran, MA and Murray, S and Nadathur, G and Nagai, S and Ngam, PB and Palenik, B and Pawlowski, J and Petroni, G and Piganeau, G and Posewitz, MC and Rengefors, K and Romano, G and Rumpho, ME and Rynearson, T and Schilling, KB and Schroeder, DC and Simpson, AG and Slamovits, CH and Smith, DR and Smith, GJ and Smith, SR and Sosik, HM and Stief, P and Theriot, E and Twary, SN and Umale, PE and Vaulot, D and Wawrik, B and Wheeler, GL and Wilson, WH and Xu, Y and Zingone, A and Worden, AZ}, title = {The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): illuminating the functional diversity of eukaryotic life in the oceans through transcriptome sequencing.}, journal = {PLoS biology}, volume = {12}, number = {6}, pages = {e1001889}, pmid = {24959919}, issn = {1545-7885}, mesh = {*Biodiversity ; Databases, Factual ; *Environmental Microbiology ; *Eukaryota ; Molecular Sequence Data ; *Oceans and Seas ; Sequence Analysis ; *Transcriptome ; }, abstract = {Current sampling of genomic sequence data from eukaryotes is relatively poor, biased, and inadequate to address important questions about their biology, evolution, and ecology; this Community Page describes a resource of 700 transcriptomes from marine microbial eukaryotes to help understand their role in the world's oceans.}, } @article {pmid24959900, year = {2014}, author = {Stocks, M and Siol, M and Lascoux, M and De Mita, S}, title = {Amount of information needed for model choice in Approximate Bayesian Computation.}, journal = {PloS one}, volume = {9}, number = {6}, pages = {e99581}, pmid = {24959900}, issn = {1932-6203}, mesh = {Bayes Theorem ; Computational Biology/*methods ; Genetic Variation ; *Models, Statistical ; Population Density ; Principal Component Analysis ; }, abstract = {Approximate Bayesian Computation (ABC) has become a popular technique in evolutionary genetics for elucidating population structure and history due to its flexibility. The statistical inference framework has benefited from significant progress in recent years. In population genetics, however, its outcome depends heavily on the amount of information in the dataset, whether that be the level of genetic variation or the number of samples and loci. Here we look at the power to reject a simple constant population size coalescent model in favor of a bottleneck model in datasets of varying quality. Not only is this power dependent on the number of samples and loci, but it also depends strongly on the level of nucleotide diversity in the observed dataset. Whilst overall model choice in an ABC setting is fairly powerful and quite conservative with regard to false positives, detecting weaker bottlenecks is problematic in smaller or less genetically diverse datasets and limits the inferences possible in non-model organism where the amount of information regarding the two models is often limited. Our results show it is important to consider these limitations when performing an ABC analysis and that studies should perform simulations based on the size and nature of the dataset in order to fully assess the power of the study.}, } @article {pmid24954669, year = {2014}, author = {Lighten, J and van Oosterhout, C and Bentzen, P}, title = {Critical review of NGS analyses for de novo genotyping multigene families.}, journal = {Molecular ecology}, volume = {23}, number = {16}, pages = {3957-3972}, doi = {10.1111/mec.12843}, pmid = {24954669}, issn = {1365-294X}, mesh = {Cluster Analysis ; Computational Biology ; DNA Copy Number Variations ; Genetics, Population ; Genotyping Techniques ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Major Histocompatibility Complex/genetics ; *Multigene Family ; Sequence Analysis, DNA/*methods ; }, abstract = {The genotyping of highly polymorphic multigene families across many individuals used to be a particularly challenging task because of methodological limitations associated with traditional approaches. Next-generation sequencing (NGS) can overcome most of these limitations, and it is increasingly being applied in population genetic studies of multigene families. Here, we critically review NGS bioinformatic approaches that have been used to genotype the major histocompatibility complex (MHC) immune genes, and we discuss how the significant advances made in this field are applicable to population genetic studies of gene families. Increasingly, approaches are introduced that apply thresholds of sequencing depth and sequence similarity to separate alleles from methodological artefacts. We explain why these approaches are particularly sensitive to methodological biases by violating fundamental genotyping assumptions. An alternative strategy that utilizes ultra-deep sequencing (hundreds to thousands of sequences per amplicon) to reconstruct genotypes and applies statistical methods on the sequencing depth to separate alleles from artefacts appears to be more robust. Importantly, the 'degree of change' (DOC) method avoids using arbitrary cut-off thresholds by looking for statistical boundaries between the sequencing depth for alleles and artefacts, and hence, it is entirely repeatable across studies. Although the advances made in generating NGS data are still far ahead of our ability to perform reliable processing, analysis and interpretation, the community is developing statistically rigorous protocols that will allow us to address novel questions in evolution, ecology and genetics of multigene families. Future developments in third-generation single molecule sequencing may potentially help overcome problems that still persist in de novo multigene amplicon genotyping when using current second-generation sequencing approaches.}, } @article {pmid24951834, year = {2014}, author = {Feidas, H and Kouam, MK and Kantzoura, V and Theodoropoulos, G}, title = {Global geographic distribution of Trichinella species and genotypes.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {26}, number = {}, pages = {255-266}, doi = {10.1016/j.meegid.2014.06.009}, pmid = {24951834}, issn = {1567-7257}, mesh = {Animals ; Databases, Factual ; Environment ; *Genotype ; Geography ; *Global Health ; Humans ; Models, Statistical ; Reproducibility of Results ; Spatio-Temporal Analysis ; Trichinella/*genetics ; Trichinellosis/*epidemiology/*parasitology ; }, abstract = {Maximum entropy ecological niche modeling was utilized to describe the global geographic distribution of Trichinella species and genotypes and to assess their invasive risk in new areas other than the ones currently known. Also, space-time scan statistic was utilized to identify global spatiotemporal clusters of infection. A database containing 3209 records for 12 species and genotypes identified at the International Trichinella Reference Center (ITRC) as well as climate, elevation, and land cover data extracted from various databases were used. Ecological niche modeling implemented in the Maxent program indicated new potential ranges for T. spiralis (T1), T. nativa (T2), T. britovi (T3), T. pseudospiralis (T4), T. murrelli (T5), T6, T. papuae (T10), and T. zimbabwensis (T11). The area under the curve values for the test data of the models ranged from 0.901 to 0.998, indicating that the models were very good to excellent. The most important bioclimatic factor in modeling the ranges for T. spiralis (T1), T. nativa (T2), T. britovi (T3), T6, and T. zimbabwensis (T11) was temperature, for T. pseudospiralis (T4) and T. papuae (T10) was precipitation, and for T. murrelli (T5) was land cover. T. spiralis (T1), T. britovi (T3), and T. pseudospiralis (T4) had the same primary land cover which was "Grass Crops". The primary land covers were "Conifer Boreal Forest" for T. nativa (T2), "Cool Fields and Woods" for T. murrelli (T5), "Upland Tundra" for T6, "Tropical Rainforest" for T. papuae (T10), and "Crops and Town" for T. zimbabwensis (T11). The scan statistic analyses revealed the presence of significant spatiotemporal clusters (p<0.05) for T. spiralis (T1), T. nativa (T2), T. britovi (T3), T. pseudospiralis (T4), T. murrelli (T5), T6, and T. nelsoni (T7). No significant clusters were found for T. papuae (T10) and T. zimbabwensis (T11).}, } @article {pmid24948726, year = {2014}, author = {Humle, T and Duffy, R and Roberts, DL and Sandbrook, C and St John, FA and Smith, RJ}, title = {Biology's drones: undermined by fear.}, journal = {Science (New York, N.Y.)}, volume = {344}, number = {6190}, pages = {1351}, doi = {10.1126/science.344.6190.1351-a}, pmid = {24948726}, issn = {1095-9203}, mesh = {*Aircraft ; Animals ; Conservation of Natural Resources/*methods ; *Elephants ; *Geographic Information Systems ; }, } @article {pmid24948464, year = {2014}, author = {Andersson, MN and Videvall, E and Walden, KK and Harris, MO and Robertson, HM and Löfstedt, C}, title = {Sex- and tissue-specific profiles of chemosensory gene expression in a herbivorous gall-inducing fly (Diptera: Cecidomyiidae).}, journal = {BMC genomics}, volume = {15}, number = {}, pages = {501}, pmid = {24948464}, issn = {1471-2164}, mesh = {Animals ; Chromosome Mapping ; Diptera/*genetics/*metabolism ; Female ; *Gene Expression Profiling ; Gene Ontology ; Herbivory/*genetics ; Male ; Membrane Proteins/genetics ; Molecular Sequence Annotation ; Organ Specificity ; RNA, Messenger/genetics/metabolism ; Receptors, Odorant/genetics ; Sensory Receptor Cells/metabolism ; }, abstract = {BACKGROUND: The chemical senses of insects mediate behaviors that are closely linked to survival and reproduction. The order Diptera contains two model organisms, the vinegar fly Drosophila melanogaster and the mosquito Anopheles gambiae, whose chemosensory genes have been extensively studied. Representing a third dipteran lineage with an interesting phylogenetic position, and being ecologically distinct by feeding on plants, the Hessian fly (Mayetiola destructor Say, Diptera: Cecidomyiidae) genome sequence has recently become available. Among plant-feeding insects, the Hessian fly is unusual in 'reprogramming' the plant to create a superior food and in being the target of plant resistance genes, a feature shared by plant pathogens. Chemoreception is essential for reproductive success, including detection of sex pheromone and plant-produced chemicals by males and females, respectively.

RESULTS: We identified genes encoding 122 odorant receptors (OR), 28 gustatory receptors (GR), 39 ionotropic receptors (IR), 32 odorant binding proteins, and 7 sensory neuron membrane proteins in the Hessian fly genome. We then mapped Illumina-sequenced transcriptome reads to the genome to explore gene expression in male and female antennae and terminal abdominal segments. Our results reveal that a large number of chemosensory genes have up-regulated expression in the antennae, and the expression is in many cases sex-specific. Sex-specific expression is particularly evident among the Or genes, consistent with the sex-divergent olfactory-mediated behaviors of the adults. In addition, the large number of Ors in the genome but the reduced set of Grs and divergent Irs suggest that the short-lived adults rely more on long-range olfaction than on short-range gustation. We also report up-regulated expression of some genes from all chemosensory gene families in the terminal segments of the abdomen, which play important roles in reproduction.

CONCLUSIONS: We show that a large number of the chemosensory genes in the Hessian fly genome have sex- and tissue-specific expression profiles. Our findings provide the first insights into the molecular basis of chemoreception in plant-feeding flies, representing an important advance toward a more complete understanding of olfaction in Diptera and its links to ecological specialization.}, } @article {pmid24948393, year = {2014}, author = {Österman, J and Marsh, J and Laine, PK and Zeng, Z and Alatalo, E and Sullivan, JT and Young, JP and Thomas-Oates, J and Paulin, L and Lindström, K}, title = {Genome sequencing of two Neorhizobium galegae strains reveals a noeT gene responsible for the unusual acetylation of the nodulation factors.}, journal = {BMC genomics}, volume = {15}, number = {1}, pages = {500}, pmid = {24948393}, issn = {1471-2164}, mesh = {Acetylation ; Bacterial Proteins/*genetics/*metabolism ; Computational Biology ; Gene Order ; Genetic Variation ; *Genome, Bacterial ; Genomics ; High-Throughput Nucleotide Sequencing ; Lipopolysaccharides/biosynthesis ; Molecular Sequence Data ; Rhizobiaceae/*genetics/*metabolism ; Symbiosis/genetics ; }, abstract = {BACKGROUND: The species Neorhizobium galegae comprises two symbiovars that induce nodules on Galega plants. Strains of both symbiovars, orientalis and officinalis, induce nodules on the same plant species, but fix nitrogen only in their own host species. The mechanism behind this strict host specificity is not yet known. In this study, genome sequences of representatives of the two symbiovars were produced, providing new material for studying properties of N. galegae, with a special interest in genomic differences that may play a role in host specificity.

RESULTS: The genome sequences confirmed that the two representative strains are much alike at a whole-genome level. Analysis of orthologous genes showed that N. galegae has a higher number of orthologs shared with Rhizobium than with Agrobacterium. The symbiosis plasmid of strain HAMBI 1141 was shown to transfer by conjugation under optimal conditions. In addition, both sequenced strains have an acetyltransferase gene which was shown to modify the Nod factor on the residue adjacent to the non-reducing-terminal residue. The working hypothesis that this gene is of major importance in directing host specificity of N. galegae could not, however, be confirmed.

CONCLUSIONS: Strains of N. galegae have many genes differentiating them from strains of Agrobacterium, Rhizobium and Sinorhizobium. However, the mechanism behind their ecological difference is not evident. Although the final determinant for the strict host specificity of N. galegae remains to be identified, the gene responsible for the species-specific acetylation of the Nod factors was identified in this study. We propose the name noeT for this gene to reflect its role in symbiosis.}, } @article {pmid24946746, year = {2014}, author = {Millar, J}, title = {The devil is in the details.}, journal = {Journal of chemical ecology}, volume = {40}, number = {6}, pages = {517-518}, doi = {10.1007/s10886-014-0463-8}, pmid = {24946746}, issn = {1573-1561}, mesh = {Databases, Chemical ; Databases, Factual ; *Ecology/standards ; Ethics, Research ; Gas Chromatography-Mass Spectrometry ; Isomerism ; *Molecular Structure ; Pheromones/analysis/chemistry ; *Research/standards ; }, } @article {pmid24943814, year = {2014}, author = {Trolle, D and Spigel, B and Hamilton, DP and Norton, N and Sutherland, D and Plew, D and Allan, MG}, title = {Application of a three-dimensional water quality model as a decision support tool for the management of land-use changes in the catchment of an oligotrophic lake.}, journal = {Environmental management}, volume = {54}, number = {3}, pages = {479-493}, pmid = {24943814}, issn = {1432-1009}, mesh = {Agriculture ; Chlorophyll/analysis ; Chlorophyll A ; *Decision Support Techniques ; Eutrophication ; Lakes ; *Models, Theoretical ; New Zealand ; Nitrogen/analysis ; Phosphorus/analysis ; Phytoplankton/growth & development ; Water Pollutants, Chemical/analysis ; *Water Quality ; }, abstract = {While expansion of agricultural land area and intensification of agricultural practices through irrigation and fertilizer use can bring many benefits to communities, intensifying land use also causes more contaminants, such as nutrients and pesticides, to enter rivers, lakes, and groundwater. For lakes such as Benmore in the Waitaki catchment, South Island, New Zealand, an area which is currently undergoing agricultural intensification, this could potentially lead to marked degradation of water clarity as well as effects on ecological, recreational, commercial, and tourism values. We undertook a modeling study to demonstrate science-based options for consideration of agricultural intensification in the catchment of Lake Benmore. Based on model simulations of a range of potential future nutrient loadings, it is clear that different areas within Lake Benmore may respond differently to increased nutrient loadings. A western arm (Ahuriri) could be most severely affected by land-use changes and associated increases in nutrient loadings. Lake-wide annual averages of an eutrophication indicator, the trophic level index (TLI) were derived from simulated chlorophyll a, total nitrogen, and total phosphorus concentrations. Results suggest that the lake will shift from oligotrophic (TLI = 2-3) to eutrophic (TLI = 4-5) as external loadings are increased eightfold over current baseline loads, corresponding to the potential land-use intensification in the catchment. This study provides a basis for use of model results in a decision-making process by outlining the environmental consequences of a series of land-use management options, and quantifying nutrient load limits needed to achieve defined trophic state objectives.}, } @article {pmid24942327, year = {2015}, author = {Schuett, W and Dall, SR and Kloesener, MH and Baeumer, J and Beinlich, F and Eggers, T}, title = {Life-history trade-offs mediate 'personality' variation in two colour morphs of the pea aphid, Acyrthosiphon pisum.}, journal = {The Journal of animal ecology}, volume = {84}, number = {1}, pages = {90-101}, doi = {10.1111/1365-2656.12263}, pmid = {24942327}, issn = {1365-2656}, mesh = {Animals ; Aphids/genetics/growth & development/*physiology ; Escape Reaction ; *Food Chain ; Nymph/genetics/physiology ; Personality ; Pigmentation ; Polymorphism, Genetic ; }, abstract = {Life-history trade-offs are considered a major driving force in the emergence of consistent behavioural differences (personality variation); but empirical tests are scarce. We investigated links between a personality trait (escape response), life-history and state variables (growth rate, size and age at first reproduction, age-dependent reproductive rates, lifetime reproductive success, life span) in red and green colour morphs of clonal pea aphids, Acyrthosiphon pisum. Escape response (dropping/non-dropping off a plant upon a predatory attack) was measured repeatedly to classify individuals as consistent droppers, consistent nondroppers or inconsistents. Red morphs experienced stronger trade-offs between early reproduction and life span than green morphs; and red consistent (non)droppers had highest lifetime reproductive success. Red droppers followed a risk-averse life-history strategy (high late reproduction), red nondroppers a risk-prone strategy (high early reproduction), while reproductive rates were equivalent for all green behavioural types and red inconsistents. This suggests that red morphs suffer the highest costs of dropping (they are most conspicuous to predators), which 'equivalates' fitness payoffs to both risk-takers (red non-droppers) and risk-averse red droppers. The strong trade-off also means that committing to a particular lifestyle (being consistent) maximises fitness. Our study suggests that life-history trade-offs likely mediate personality variation but effects might depend on interactions with other organismal characteristics (here: colour morph).}, } @article {pmid24941442, year = {2014}, author = {Cros, A and Ahamad Fatan, N and White, A and Teoh, SJ and Tan, S and Handayani, C and Huang, C and Peterson, N and Venegas Li, R and Siry, HY and Fitriana, R and Gove, J and Acoba, T and Knight, M and Acosta, R and Andrew, N and Beare, D}, title = {The Coral Triangle Atlas: an integrated online spatial database system for improving coral reef management.}, journal = {PloS one}, volume = {9}, number = {6}, pages = {e96332}, pmid = {24941442}, issn = {1932-6203}, mesh = {Animals ; Anthozoa/*physiology ; Asia, Southeastern ; Atlases as Topic ; Conservation of Natural Resources ; *Coral Reefs ; *Databases, Factual ; *Environmental Monitoring ; Geographic Information Systems ; Humans ; Internet ; Pacific Ocean ; }, abstract = {In this paper we describe the construction of an online GIS database system, hosted by WorldFish, which stores bio-physical, ecological and socio-economic data for the 'Coral Triangle Area' in South-east Asia and the Pacific. The database has been built in partnership with all six (Timor-Leste, Malaysia, Indonesia, The Philippines, Solomon Islands and Papua New Guinea) of the Coral Triangle countries, and represents a valuable source of information for natural resource managers at the regional scale. Its utility is demonstrated using biophysical data, data summarising marine habitats, and data describing the extent of marine protected areas in the region.}, } @article {pmid24939717, year = {2014}, author = {Jiang, Q and Li, Q and Yu, H and Kong, L}, title = {Genome-wide analysis of simple sequence repeats in marine animals-a comparative approach.}, journal = {Marine biotechnology (New York, N.Y.)}, volume = {16}, number = {5}, pages = {604-619}, pmid = {24939717}, issn = {1436-2236}, mesh = {Animals ; Chordata, Nonvertebrate/*genetics ; Fishes/*genetics ; Gene Ontology ; Genetic Markers/*genetics ; *Genetic Variation ; Genome Size/genetics ; Genomics/methods ; Invertebrates/*genetics ; Marine Biology/*methods ; Microsatellite Repeats/*genetics ; Species Specificity ; }, abstract = {Tandem simple sequence repeats (SSRs) are one of the most popular molecular markers in genetic analysis owing to their ubiquitous occurrence,high reproducibility, multiallelic nature, and codominant mode. High mutability makes SSRs play a role in genome evolution and correspondingly show different patterns. Comparative analysis of genomic SSRs in different taxonomic groups usually focuses on land species, while marine animals have been neglected. This study examined the abundance of genomic SSRs with repeated unit lengths of 1-6 bp in 30 marine animals including nine taxonomic groups and further compared with the land species. More than thousands of SSRs were discovered in every organism which provided a huge resource for the development of molecular markers. Thirty marine animals showed profound differences in SSR characteristics, but some group-specific trends were also found. Both similarities and differences of repeat patterns were discovered between the land and marine species. Two taxon-specific SSR types were discovered: the pentanucleotides motif AGAGG in Euteleostei and the hexanucleotide repeats of ATGTAC in Porifera and Echinodermata. Gene ontology (GO) enrichment analysis of two representative species (Amphimedon queenslandica for Porifera and Strongylocentrotus purpuratus for Echinodermata) revealed functional preference of the ATGTAC motif associated genes, and this might hint at evolutionary significance.}, } @article {pmid24939468, year = {2014}, author = {Skoglund, P and Sjödin, P and Skoglund, T and Lascoux, M and Jakobsson, M}, title = {Investigating population history using temporal genetic differentiation.}, journal = {Molecular biology and evolution}, volume = {31}, number = {9}, pages = {2516-2527}, pmid = {24939468}, issn = {1537-1719}, mesh = {Algorithms ; Animals ; Computational Biology/methods ; Genetic Drift ; *Genetic Variation ; Humans ; *Phylogeny ; Population Dynamics ; Sampling Studies ; }, abstract = {The rapid advance of sequencing technology, coupled with improvements in molecular methods for obtaining genetic data from ancient sources, holds the promise of producing a wealth of genomic data from time-separated individuals. However, the population-genetic properties of time-structured samples have not been extensively explored. Here, we consider the implications of temporal sampling for analyses of genetic differentiation and use a temporal coalescent framework to show that complex historical events such as size reductions, population replacements, and transient genetic barriers between populations leave a footprint of genetic differentiation that can be traced through history using temporal samples. Our results emphasize explicit consideration of the temporal structure when making inferences and indicate that genomic data from ancient individuals will greatly increase our ability to reconstruct population history.}, } @article {pmid24939150, year = {2014}, author = {Kim, Y and Liesack, W}, title = {DAFGA: diversity analysis of functional gene amplicons.}, journal = {Bioinformatics (Oxford, England)}, volume = {30}, number = {19}, pages = {2820-2821}, doi = {10.1093/bioinformatics/btu394}, pmid = {24939150}, issn = {1367-4811}, mesh = {*Cluster Analysis ; Computational Biology/*methods ; Evolution, Molecular ; *Genes, rRNA ; Phylogeny ; RNA, Ribosomal, 16S/*genetics ; Software ; }, abstract = {SUMMARY: Diversity analysis of functional marker genes provides physiological insights into microbial guilds that perform an ecologically relevant process. However, it is challenging to group functional gene sequences to valid taxonomic units, primarily because of differences in the evolutionary rates of individual genes and possible horizontal gene transfer events. We developed a python script package named DAFGA, which estimates the evolutionary rate of a particular functional gene in a standardized manner by relating its sequence divergence to that of the 16S rRNA gene. As a result, DAFGA provides gene-specific parameter sets for operational taxonomic unit clustering and taxonomic assignment at desired rank, and it can be implemented into the diversity measurements offered by QIIME.

DAFGA is freely available with a manual and test data from https://github.com/outbig/DAFGA.}, } @article {pmid24939130, year = {2014}, author = {Abraham, PE and Giannone, RJ and Xiong, W and Hettich, RL}, title = {Metaproteomics: extracting and mining proteome information to characterize metabolic activities in microbial communities.}, journal = {Current protocols in bioinformatics}, volume = {46}, number = {}, pages = {13.26.1-13.26.14}, doi = {10.1002/0471250953.bi1326s46}, pmid = {24939130}, issn = {1934-340X}, mesh = {Databases, Protein ; Information Storage and Retrieval ; *Microbiota ; Peptides/chemistry ; Proteins/chemistry ; *Proteomics ; }, abstract = {Contemporary microbial ecology studies usually employ one or more "omics" approaches to investigate the structure and function of microbial communities. Among these, metaproteomics aims to characterize the metabolic activities of the microbial membership, providing a direct link between the genetic potential and functional metabolism. The successful deployment of metaproteomics research depends on the integration of high-quality experimental and bioinformatic techniques for uncovering the metabolic activities of a microbial community in a way that is complementary to other "meta-omic" approaches. The essential, quality-defining informatics steps in metaproteomics investigations are: (1) construction of the metagenome, (2) functional annotation of predicted protein-coding genes, (3) protein database searching, (4) protein inference, and (5) extraction of metabolic information. In this article, we provide an overview of current bioinformatic approaches and software implementations in metaproteome studies in order to highlight the key considerations needed for successful implementation of this powerful community-biology tool.}, } @article {pmid24937818, year = {2014}, author = {Amancio, CT and Nascimento, LF}, title = {Cutaneous melanoma in the State of São Paulo: a spatial approach.}, journal = {Anais brasileiros de dermatologia}, volume = {89}, number = {3}, pages = {442-446}, pmid = {24937818}, issn = {1806-4841}, mesh = {Brazil/epidemiology ; Cluster Analysis ; Female ; Geographic Information Systems ; Humans ; Incidence ; Male ; Melanoma/*epidemiology ; Risk Factors ; Sex Distribution ; Skin Neoplasms/*epidemiology ; *Spatial Analysis ; }, abstract = {BACKGROUND: Cutaneous melanoma is a skin cancer with low incidence but high mortality rates. Several factors are associated with increased risk of melanoma, such as excessive sun exposure, fair skin, and family history, among others. Little is known about the spatial distribution of this cancer in Brazil.

OBJECTIVE: To identify, through the use of geostatistical tools, spatial clusters of municipalities in the state of São Paulo based on their incidence of cutaneous melanoma.

METHODS: This was an ecological and exploratory study of data on new cases obtained from Fundação Oncocentro for the period 1 January 2006-31 December 2011. Cases were separated by gender and rates per 100,000 inhabitants were calculated and used to compile thematic maps, Moran maps and kernel maps, using TerraView software.

RESULTS: There were 3,172 new cases of cutaneous melanoma in the study period. High rates were identified in the North, Northwest, Southwest, and Southeast regions of São Paulo state. Global Moran's I values were statistically significant (p<0.05) at 0.12, 0.08, and 0.16, respectively, for males, females, and all cases. Areas such as the Southeast, North, and Northwest of São Paulo were identified as being of high priority for intervention.

CONCLUSION: Spatial clusters of municipalities with high incidence rates of cutaneous melanoma in the state of São Paulo were identified. These data can serve as an important input for public health agencies.}, } @article {pmid24934203, year = {2015}, author = {Sparkes, J and Fleming, PJ and Ballard, G and Scott-Orr, H and Durr, S and Ward, MP}, title = {Canine rabies in Australia: a review of preparedness and research needs.}, journal = {Zoonoses and public health}, volume = {62}, number = {4}, pages = {237-253}, doi = {10.1111/zph.12142}, pmid = {24934203}, issn = {1863-2378}, mesh = {Animals ; Animals, Wild ; Australia/epidemiology ; Behavior, Animal ; Bites and Stings/virology ; Communicable Disease Control/*methods ; Databases, Factual ; Dog Diseases/epidemiology/*prevention & control/*transmission/virology ; Dogs ; Europe/epidemiology ; Humans ; *Rabies/epidemiology/prevention & control/transmission ; Rabies Vaccines ; Research ; Risk Factors ; United States/epidemiology ; }, abstract = {Australia is unique as a populated continent in that canine rabies is exotic, with only one likely incursion in 1867. This is despite the presence of a widespread free-ranging dog population, which includes the naturalized dingo, feral domestic dogs and dingo-dog cross-breeds. To Australia's immediate north, rabies has recently spread within the Indonesian archipelago, with outbreaks occurring in historically free islands to the east including Bali, Flores, Ambon and the Tanimbar Islands. Australia depends on strict quarantine protocols to prevent importation of a rabid animal, but the risk of illegal animal movements by fishing and recreational vessels circumventing quarantine remains. Predicting where rabies will enter Australia is important, but understanding dog population dynamics and interactions, including contact rates in and around human populations, is essential for rabies preparedness. The interactions among and between Australia's large populations of wild, free-roaming and restrained domestic dogs require quantification for rabies incursions to be detected and controlled. The imminent risk of rabies breaching Australian borders makes the development of disease spread models that will assist in the deployment of cost-effective surveillance, improve preventive strategies and guide disease management protocols vitally important. Here, we critically review Australia's preparedness for rabies, discuss prevailing assumptions and models, identify knowledge deficits in free-roaming dog ecology relating to rabies maintenance and speculate on the likely consequences of endemic rabies for Australia.}, } @article {pmid24933820, year = {2014}, author = {Pringle, JM and Byers, JE and Pappalardo, P and Wares, JP and Marshall, D}, title = {Circulation constrains the evolution of larval development modes and life histories in the coastal ocean.}, journal = {Ecology}, volume = {95}, number = {4}, pages = {1022-1032}, doi = {10.1890/13-0970.1}, pmid = {24933820}, issn = {0012-9658}, mesh = {Adaptation, Physiological ; Animals ; Databases, Factual ; Demography ; Genetic Fitness ; Invertebrates/*physiology ; Larva/growth & development ; Models, Biological ; Oceans and Seas ; Temperature ; Zooplankton ; }, abstract = {The evolutionary pressures that drive long larval planktonic durations in some coastal marine organisms, while allowing direct development in others, have been vigorously debated. We introduce into the argument the asymmetric dispersal of larvae by coastal currents and find that the strength of the currents helps determine which dispersal strategies are evolutionarily stable. In a spatially and temporally uniform coastal ocean of finite extent, direct development is always evolutionarily stable. For passively drifting larvae, long planktonic durations are stable when the ratio of mean to fluctuating currents is small and the rate at which larvae increase in size in the plankton is greater than the mortality rate (both in units of per time). However, larval behavior that reduces downstream larval dispersal for a given time in plankton will be selected for, consistent with widespread observations of behaviors that reduce dispersal of marine larvae. Larvae with long planktonic durations are shown to be favored not for the additional dispersal they allow, but for the additional fecundity that larval feeding in the plankton enables. We analyzed the spatial distribution of larval life histories in a large database of coastal marine benthic invertebrates and documented a link between ocean circulation and the frequency of planktotrophy in the coastal ocean. The spatial variation in the frequency of species with planktotrophic larvae is largely consistent with our theory; increases in mean currents lead to a decrease in the fraction of species with planktotrophic larvae over a broad range of temperatures.}, } @article {pmid24932915, year = {2014}, author = {Russo, T and D'Andrea, L and Parisi, A and Cataudella, S}, title = {VMSbase: an R-package for VMS and logbook data management and analysis in fisheries ecology.}, journal = {PloS one}, volume = {9}, number = {6}, pages = {e100195}, pmid = {24932915}, issn = {1932-6203}, mesh = {Animals ; Biodiversity ; Conservation of Natural Resources ; *Databases, Factual ; *Ecology ; *Fisheries ; Fishes/*physiology ; *Software ; }, abstract = {VMSbase is an R package devised to manage, process and visualize information about fishing vessels activity (provided by the vessel monitoring system--VMS) and catches/landings (as reported in the logbooks). VMSbase is primarily conceived to be user-friendly; to this end, a suite of state-of-the-art analyses is accessible via a graphical interface. In addition, the package uses a database platform allowing large datasets to be stored, managed and processed vey efficiently. Methodologies include data cleaning, that is removal of redundant or evidently erroneous records, and data enhancing, that is interpolation and merging with external data sources. In particular, VMSbase is able to estimate sea bottom depth for single VMS pings using an on-line connection to the National Oceanic and Atmospheric Administration (NOAA) database. It also allows VMS pings to be assigned to whatever geographic partitioning has been selected by users. Standard analyses comprise: 1) métier identification (using a modified CLARA clustering approach on Logbook data or Artificial Neural Networks on VMS data); 2) linkage between VMS and Logbook records, with the former organized into fishing trips; 3) discrimination between steaming and fishing points; 4) computation of spatial effort with respect to user-selected grids; 5) calculation of standard fishing effort indicators within Data Collection Framework; 6) a variety of mapping tools, including an interface for Google viewer; 7) estimation of trawled area. Here we report a sample workflow for the accessory sample datasets (available with the package) in order to explore the potentialities of VMSbase. In addition, the results of some performance tests on two large datasets (1×10(5) and 1×10(6) VMS signals, respectively) are reported to inform about the time required for the analyses. The results, although merely illustrative, indicate that VMSbase can represent a step forward in extracting and enhancing information from VMS/logbook data for fisheries studies.}, } @article {pmid24925925, year = {2014}, author = {Chan, YL and Schanzenbach, D and Hickerson, MJ}, title = {Detecting concerted demographic response across community assemblages using hierarchical approximate Bayesian computation.}, journal = {Molecular biology and evolution}, volume = {31}, number = {9}, pages = {2501-2515}, pmid = {24925925}, issn = {1537-1719}, support = {P20 GM103466/GM/NIGMS NIH HHS/United States ; P20 RR016467/RR/NCRR NIH HHS/United States ; 8 P20 GM 103466-11/GM/NIGMS NIH HHS/United States ; 5P20RR016467-11/RR/NCRR NIH HHS/United States ; }, mesh = {Adaptation, Biological ; Animals ; Australia ; Bayes Theorem ; Birds/classification/*genetics ; Computational Biology/*methods ; Computer Simulation ; Models, Statistical ; Phylogeny ; Phylogeography ; Population Density ; }, abstract = {Methods that integrate population-level sampling from multiple taxa into a single community-level analysis are an essential addition to the comparative phylogeographic toolkit. Detecting how species within communities have demographically tracked each other in space and time is important for understanding the effects of future climate and landscape changes and the resulting acceleration of extinctions, biological invasions, and potential surges in adaptive evolution. Here, we present a statistical framework for such an analysis based on hierarchical approximate Bayesian computation (hABC) with the goal of detecting concerted demographic histories across an ecological assemblage. Our method combines population genetic data sets from multiple taxa into a single analysis to estimate: 1) the proportion of a community sample that demographically expanded in a temporally clustered pulse and 2) when the pulse occurred. To validate the accuracy and utility of this new approach, we use simulation cross-validation experiments and subsequently analyze an empirical data set of 32 avian populations from Australia that are hypothesized to have expanded from smaller refugia populations in the late Pleistocene. The method can accommodate data set heterogeneity such as variability in effective population size, mutation rates, and sample sizes across species and exploits the statistical strength from the simultaneous analysis of multiple species. This hABC framework used in a multitaxa demographic context can increase our understanding of the impact of historical climate change by determining what proportion of the community responded in concert or independently and can be used with a wide variety of comparative phylogeographic data sets as biota-wide DNA barcoding data sets accumulate.}, } @article {pmid24924350, year = {2014}, author = {Ma, LG and Zhao, J and Ren, ZP and Wang, YY and Peng, ZQ and Wang, JF and Ma, X}, title = {Spatial patterns of the congenital heart disease prevalence among 0- to 14-year-old children in Sichuan Basin, P. R China, from 2004 to 2009.}, journal = {BMC public health}, volume = {14}, number = {}, pages = {595}, pmid = {24924350}, issn = {1471-2458}, mesh = {Adolescent ; Bayes Theorem ; Child ; Child, Preschool ; China/epidemiology ; Female ; Geographic Information Systems ; Heart Defects, Congenital/*epidemiology/etiology ; Humans ; Infant ; Infant, Newborn ; Male ; Prevalence ; Risk Factors ; }, abstract = {BACKGROUND: Congenital heart disease (CHD) is the most common type of major birth defects in Sichuan, the most populous province in China. The detailed etiology of CHD is unknown but some environmental factors are suspected as the cause of this disease. However, the geographical variations in CHD prevalence would be highly valuable in providing a clue on the role of the environment in CHD etiology. Here, we investigate the spatial patterns and geographic differences in CHD prevalence among 0- to 14-year-old children, discuss the possible environmental risk factors that might be associated with CHD prevalence in Sichuan Basin from 2004 to 2009.

METHODS: The hierarchical Bayesian model was used to estimate CHD prevalence at the township level. Spatial autocorrelation statistics were performed, and a hot-spot analysis with different distance thresholds was used to identify the spatial pattern of CHD prevalence. Distribution and clustering maps were drawn using geographic information system tools.

RESULTS: CHD prevalence was significantly clustered in Sichuan Basin in different spatial scale. Typical hot/cold clusters were identified, and possible CHD causes were discussed. The association between selected hypothetical environmental factors of maternal exposure and CHD prevalence was evaluated.

CONCLUSIONS: The largest hot-spot clustering phenomena and the CHD prevalence clustering trend among 0- to 14-year-old children in the study area showed a plausibly close similarity with those observed in the Tuojiang River Basin. The high ecological risk of heavy metal(Cd, As, and Pb)sediments in the middle and lower streams of the Tuojiang River watershed and ammonia-nitrogen pollution may have contribution to the high prevalence of CHD in this area.}, } @article {pmid24924297, year = {2014}, author = {Lin, Z and Zhang, X and Yang, X and Li, G and Tang, S and Wang, S and Ding, Y and Liu, Z}, title = {Proteomic analysis of proteins related to rice grain chalkiness using iTRAQ and a novel comparison system based on a notched-belly mutant with white-belly.}, journal = {BMC plant biology}, volume = {14}, number = {}, pages = {163}, pmid = {24924297}, issn = {1471-2229}, mesh = {Amylopectin/metabolism ; Down-Regulation/genetics ; Endosperm/metabolism/ultrastructure ; Gene Expression Regulation, Plant ; Gene Ontology ; *Isotope Labeling ; Mutation/*genetics ; Oryza/embryology/genetics/*metabolism/ultrastructure ; Plant Proteins/*metabolism ; Proteomics/*methods ; Seeds/*metabolism/ultrastructure ; Starch/metabolism ; Up-Regulation/genetics ; }, abstract = {BACKGROUND: Grain chalkiness is a complex trait adversely affecting appearance and milling quality, and therefore has been one of principal targets for rice improvement. Eliminating chalkiness from rice has been a daunting task due to the complex interaction between genotype and environment and the lack of molecular markers. In addition, the molecular mechanisms underlying grain chalkiness formation are still imperfectly understood.

RESULTS: We identified a notched-belly mutant (DY1102) with high percentage of white-belly, which only occurs in the bottom part proximal to the embryo. Using this mutant, a novel comparison system that can minimize the effect of genetic background and growing environment was developed. An iTRAQ-based comparative display of the proteins between the bottom chalky part and the upper translucent part of grains of DY1102 was performed. A total of 113 proteins responsible for chalkiness formation was identified. Among them, 70 proteins are up-regulated and 43 down-regulated. Approximately half of these differentially expressed proteins involved in central metabolic or regulatory pathways including carbohydrate metabolism (especially cell wall synthesis) and protein synthesis, folding and degradation, providing proteomic confirmation of the notion that chalkiness formation involves diverse but delicately regulated pathways. Protein metabolism was the most abundant category, accounting for 27.4% of the total differentially expressed proteins. In addition, down regulation of PDIL 2-3 and BiP was detected in the chalky tissue, indicating the important role of protein metabolism in grain chalkiness formation.

CONCLUSIONS: Using this novel comparison system, our comprehensive survey of endosperm proteomics in the notched-belly mutant provides a valuable proteomic resource for the characterization of pathways contributing to chalkiness formation at molecular and biochemical levels.}, } @article {pmid24923325, year = {2014}, author = {Haq, IU and Graupner, K and Nazir, R and van Elsas, JD}, title = {The genome of the fungal-interactive soil bacterium Burkholderia terrae BS001-a plethora of outstanding interactive capabilities unveiled.}, journal = {Genome biology and evolution}, volume = {6}, number = {7}, pages = {1652-1668}, pmid = {24923325}, issn = {1759-6653}, mesh = {Burkholderia/*genetics ; Computational Biology ; *Evolution, Molecular ; Fungi/*genetics ; Genome, Fungal/*genetics ; Phylogeny ; Sequence Alignment ; *Soil Microbiology ; }, abstract = {Burkholderia terrae strain BS001, obtained as an inhabitant of the mycosphere of Laccaria proxima (a close relative of Lyophyllum sp. strain Karsten), actively interacts with Lyophyllum sp. strain Karsten. We here summarize the remarkable ecological behavior of B. terrae BS001 in the mycosphere and add key data to this. Moreover, we extensively analyze the approximately 11.5-Mb five-replicon genome of B. terrae BS001 and highlight its remarkable features. Seventy-nine regions of genomic plasticity (RGP), that is, 16.48% of the total genome size, were found. One 70.42-kb RGP, RGP76, revealed a typical conjugal element structure, including a full type 4 secretion system. Comparative analyses across 24 related Burkholderia genomes revealed that 95.66% of the total BS001 genome belongs to the variable part, whereas the remaining 4.34% constitutes the core genome. Genes for biofilm formation and several secretion systems, under which a type 3 secretion system (T3SS), were found, which is consistent with the hypothesis that T3SSs play a role in the interaction with Lyophyllum sp. strain Karsten. The high number of predicted metabolic pathways and membrane transporters suggested that strain BS001 can take up and utilize a range of sugars, amino acids and organic acids. In particular, a unique glycerol uptake system was found. The BS001 genome further contains genetic systems for the degradation of complex organic compounds. Moreover, gene clusters encoding nonribosomal peptide synthetases (NRPS) and hybrid polyketide synthases/NRPS were found, highlighting the potential role of secondary metabolites in the ecology of strain BS001. The patchwork of genetic features observed in the genome is consistent with the notion that 1) horizontal gene transfer is a main driver of B. terrae BS001 adaptation and 2) the organism is very flexible in its ecological behavior in soil.}, } @article {pmid24922281, year = {2014}, author = {Liu, KJ and Dai, J and Truong, K and Song, Y and Kohn, MH and Nakhleh, L}, title = {An HMM-based comparative genomic framework for detecting introgression in eukaryotes.}, journal = {PLoS computational biology}, volume = {10}, number = {6}, pages = {e1003649}, pmid = {24922281}, issn = {1553-7358}, support = {R01LM009494/LM/NLM NIH HHS/United States ; R01 LM009494/LM/NLM NIH HHS/United States ; T15 LM007093/LM/NLM NIH HHS/United States ; T15LM007093/LM/NLM NIH HHS/United States ; R01 HL091007/HL/NHLBI NIH HHS/United States ; }, mesh = {Algorithms ; Animals ; Chromosome Mapping ; *Comparative Genomic Hybridization ; Computational Biology ; Computer Simulation ; Databases, Genetic ; *Evolution, Molecular ; Genetics, Population ; Genomics ; Markov Chains ; Mice ; *Models, Genetic ; Phylogeny ; }, abstract = {One outcome of interspecific hybridization and subsequent effects of evolutionary forces is introgression, which is the integration of genetic material from one species into the genome of an individual in another species. The evolution of several groups of eukaryotic species has involved hybridization, and cases of adaptation through introgression have been already established. In this work, we report on PhyloNet-HMM-a new comparative genomic framework for detecting introgression in genomes. PhyloNet-HMM combines phylogenetic networks with hidden Markov models (HMMs) to simultaneously capture the (potentially reticulate) evolutionary history of the genomes and dependencies within genomes. A novel aspect of our work is that it also accounts for incomplete lineage sorting and dependence across loci. Application of our model to variation data from chromosome 7 in the mouse (Mus musculus domesticus) genome detected a recently reported adaptive introgression event involving the rodent poison resistance gene Vkorc1, in addition to other newly detected introgressed genomic regions. Based on our analysis, it is estimated that about 9% of all sites within chromosome 7 are of introgressive origin (these cover about 13 Mbp of chromosome 7, and over 300 genes). Further, our model detected no introgression in a negative control data set. We also found that our model accurately detected introgression and other evolutionary processes from synthetic data sets simulated under the coalescent model with recombination, isolation, and migration. Our work provides a powerful framework for systematic analysis of introgression while simultaneously accounting for dependence across sites, point mutations, recombination, and ancestral polymorphism.}, } @article {pmid24921923, year = {2014}, author = {Gog, JR and Ballesteros, S and Viboud, C and Simonsen, L and Bjornstad, ON and Shaman, J and Chao, DL and Khan, F and Grenfell, BT}, title = {Spatial Transmission of 2009 Pandemic Influenza in the US.}, journal = {PLoS computational biology}, volume = {10}, number = {6}, pages = {e1003635}, pmid = {24921923}, issn = {1553-7358}, support = {R01 GM100467/GM/NIGMS NIH HHS/United States ; R24 HD047879/HD/NICHD NIH HHS/United States ; U01 GM070749/GM/NIGMS NIH HHS/United States ; U01-GM070749/GM/NIGMS NIH HHS/United States ; }, mesh = {Adult ; Child ; Cities ; Computational Biology ; History, 21st Century ; Humans ; Humidity ; *Influenza A Virus, H1N1 Subtype ; Influenza, Human/*history/transmission/virology ; Likelihood Functions ; Models, Biological ; Pandemics/*history ; Schools ; Seasons ; United States/epidemiology ; }, abstract = {The 2009 H1N1 influenza pandemic provides a unique opportunity for detailed examination of the spatial dynamics of an emerging pathogen. In the US, the pandemic was characterized by substantial geographical heterogeneity: the 2009 spring wave was limited mainly to northeastern cities while the larger fall wave affected the whole country. Here we use finely resolved spatial and temporal influenza disease data based on electronic medical claims to explore the spread of the fall pandemic wave across 271 US cities and associated suburban areas. We document a clear spatial pattern in the timing of onset of the fall wave, starting in southeastern cities and spreading outwards over a period of three months. We use mechanistic models to tease apart the external factors associated with the timing of the fall wave arrival: differential seeding events linked to demographic factors, school opening dates, absolute humidity, prior immunity from the spring wave, spatial diffusion, and their interactions. Although the onset of the fall wave was correlated with school openings as previously reported, models including spatial spread alone resulted in better fit. The best model had a combination of the two. Absolute humidity or prior exposure during the spring wave did not improve the fit and population size only played a weak role. In conclusion, the protracted spread of pandemic influenza in fall 2009 in the US was dominated by short-distance spatial spread partially catalysed by school openings rather than long-distance transmission events. This is in contrast to the rapid hierarchical transmission patterns previously described for seasonal influenza. The findings underline the critical role that school-age children play in facilitating the geographic spread of pandemic influenza and highlight the need for further information on the movement and mixing patterns of this age group.}, } @article {pmid24921666, year = {2014}, author = {Ames, RM and Money, D and Lovell, SC}, title = {Inferring gene family histories in yeast identifies lineage specific expansions.}, journal = {PloS one}, volume = {9}, number = {6}, pages = {e99480}, pmid = {24921666}, issn = {1932-6203}, support = {BB/I020489/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Databases, Genetic ; *Evolution, Molecular ; Gene Duplication ; Gene Ontology ; *Genes, Fungal ; *Multigene Family ; *Phylogeny ; Reproducibility of Results ; Saccharomyces cerevisiae/*genetics ; }, abstract = {The complement of genes found in the genome is a balance between gene gain and gene loss. Knowledge of the specific genes that are gained and lost over evolutionary time allows an understanding of the evolution of biological functions. Here we use new evolutionary models to infer gene family histories across complete yeast genomes; these models allow us to estimate the relative genome-wide rates of gene birth, death, innovation and extinction (loss of an entire family) for the first time. We show that the rates of gene family evolution vary both between gene families and between species. We are also able to identify those families that have experienced rapid lineage specific expansion/contraction and show that these families are enriched for specific functions. Moreover, we find that families with specific functions are repeatedly expanded in multiple species, suggesting the presence of common adaptations and that these family expansions/contractions are not random. Additionally, we identify potential specialisations, unique to specific species, in the functions of lineage specific expanded families. These results suggest that an important mechanism in the evolution of genome content is the presence of lineage-specific gene family changes.}, } @article {pmid24919962, year = {2014}, author = {Armsworth, PR}, title = {Inclusion of costs in conservation planning depends on limited datasets and hopeful assumptions.}, journal = {Annals of the New York Academy of Sciences}, volume = {1322}, number = {}, pages = {61-76}, doi = {10.1111/nyas.12455}, pmid = {24919962}, issn = {1749-6632}, mesh = {Conservation of Natural Resources/*economics/*methods ; Cost Allocation ; *Databases as Topic ; Ecosystem ; }, abstract = {Many conservation organizations use spatial prioritization to help identify locations in which to work. Increasingly, prioritizations seek to account for spatial heterogeneity in the costs of conservation, motivated in part by claims of large efficiency savings when these costs are included. I critically review the cost estimates on which such claims are based, focusing on acquisition and management costs associated with terrestrial protected areas. If researchers are to evaluate how including costs affects conservation planning outcomes, estimation methods need to preserve the covariation between and relative variation within costs and benefits of conservation activities. However, widely used methods for estimating costs and incorporating them into prioritizations may not meet these standards. For example, among relevant studies, there is surprisingly little attention given to the costs that conservation organizations actually face. Instead, there is a heavy reliance on untested proxies for conservation costs. Analytical shortcuts are also common. Now that debate is moving beyond whether to account for costs in conservation planning, it is time to evaluate just how we can include them to greatest effect.}, } @article {pmid24917590, year = {2015}, author = {Stubbs, B and Hurley, M and Smith, T}, title = {What are the factors that influence physical activity participation in adults with knee and hip osteoarthritis? A systematic review of physical activity correlates.}, journal = {Clinical rehabilitation}, volume = {29}, number = {1}, pages = {80-94}, doi = {10.1177/0269215514538069}, pmid = {24917590}, issn = {1477-0873}, mesh = {Age Distribution ; Aged ; Databases, Bibliographic ; Ethnicity ; Female ; Humans ; Male ; Middle Aged ; Motor Activity/*physiology ; Osteoarthritis, Hip/physiopathology/psychology/*rehabilitation ; Osteoarthritis, Knee/physiopathology/psychology/*rehabilitation ; Patient Acceptance of Health Care/*psychology/statistics & numerical data ; *Quality of Life ; Severity of Illness Index ; Sex Distribution ; *Social Support ; Sociological Factors ; }, abstract = {OBJECTIVE: To determine the factors associated with physical activity participation in adults with hip or knee osteoarthritis.

METHODS: A systematic review was conducted including searches of AMED, PsycINFO, CINAHL, MEDLINE, EMBASE, PubMed and the Cochrane Library from inception until October 2013. Studies presenting quantitative correlates of physical activity in adults with hip and/or knee osteoarthritis were included. Two independent authors conducted the searches, extracted data and completed methodological quality assessment. Correlates were analysed using the summary code approach within the socio-ecological model.

RESULTS: A total of 170 correlates were identified from 29 publications analysing 8076 individual people with hip or knee osteoarthritis. Methodological quality was generally good. For knee osteoarthritis, factors consistently negatively associated with physical activity (reported more than four studies) were increasing age (number of participants in studies supporting association = 4558), non-white ethnicity (n = 3232), increased osteoarthritis symptoms (n = 2374) and female gender (n = 4816). Greater lower limb function (n = 1671) and faster gait speed were (n = 4098) positively associated with physical activity. Social (e.g. support from spouse (n = 141)) and environment (outdoor temperature (n = 38)) factors were identified as possible factors that influence physical activity. For hip osteoarthritis, higher body mass index (n = 99), increased comorbidities (n = 1021), lower mental health (n = 189) and unemployment (n = 65) were negatively associated with physical activity; while better social functioning (n = 1055) and health-related quality of life were positively associated with physical activity (n = 34).

CONCLUSION: Demographic, physical, social, psychological and environmental factors are all important correlates for physical activity for people with knee or hip osteoarthritis. Clinicians should consider these in clinical practice.}, } @article {pmid24916466, year = {2015}, author = {Russo, TA and Fisher, AT and Lockwood, BS}, title = {Assessment of Managed Aquifer Recharge Site Suitability Using a GIS and Modeling.}, journal = {Ground water}, volume = {53}, number = {3}, pages = {389-400}, doi = {10.1111/gwat.12213}, pmid = {24916466}, issn = {1745-6584}, mesh = {California ; *Geographic Information Systems ; Geographic Mapping ; *Groundwater ; Hydrology ; *Models, Theoretical ; *Seawater ; Water Movements ; }, abstract = {We completed a two-step regional analysis of a coastal groundwater basin to (1) assess regional suitability for managed aquifer recharge (MAR), and (2) quantify the relative impact of MAR activities on groundwater levels and sea water intrusion. The first step comprised an analysis of surface and subsurface hydrologic properties and conditions, using a geographic information system (GIS). Surface and subsurface data coverages were compiled, georeferenced, reclassified, and integrated (including novel approaches for combining related datasets) to derive a spatial distribution of MAR suitability values. In the second step, results from the GIS analysis were used with a regional groundwater model to assess the hydrologic impact of potential MAR placement and operating scenarios. For the region evaluated in this study, the Pajaro Valley Groundwater Basin, California, GIS results suggest that about 7% (15 km2) of the basin may be highly suitable for MAR. Modeling suggests that simulated MAR projects placed near the coast help to reduce sea water intrusion more rapidly, but these projects also result in increased groundwater flows to the ocean. In contrast, projects placed farther inland result in more long-term reduction in sea water intrusion and less groundwater flowing to the ocean. This work shows how combined GIS analysis and modeling can assist with regional water supply planning, including evaluation of options for enhancing groundwater resources.}, } @article {pmid24909751, year = {2014}, author = {Giorello, FM and Feijoo, M and D'Elía, G and Valdez, L and Opazo, JC and Varas, V and Naya, DE and Lessa, EP}, title = {Characterization of the kidney transcriptome of the South American olive mouse Abrothrix olivacea.}, journal = {BMC genomics}, volume = {15}, number = {1}, pages = {446}, pmid = {24909751}, issn = {1471-2164}, mesh = {Animals ; Arvicolinae/*genetics ; Computational Biology ; Databases, Genetic ; *Gene Expression Profiling ; Gene Expression Regulation ; High-Throughput Nucleotide Sequencing ; Kidney/*metabolism ; Molecular Sequence Annotation ; Open Reading Frames ; *Transcriptome ; }, abstract = {BACKGROUND: The olive mouse Abrothrix olivacea is a cricetid rodent of the subfamily Sigmodontinae that inhabits a wide range of contrasting environments in southern South America, from aridlands to temperate rainforests. Along its distribution, it presents different geographic forms that make the olive mouse a good focal case for the study of geographical variation in response to environmental variation. We chose to characterize the kidney transcriptome because this organ has been shown to be associated with multiple physiological processes, including water reabsorption.

RESULTS: Transcriptomes of thirteen kidneys from individuals from Argentina and Chile were sequenced using Illumina technology in order to obtain a kidney reference transcriptome. After combining the reads produced for each sample, we explored three assembly strategies to obtain the best reconstruction of transcripts, TrinityNorm and DigiNorm, which include its own normalization algorithms for redundant reads removal, and Multireads, which simply consist on the assembly of the joined reads. We found that Multireads strategy produces a less fragmented assembly than normalization algorithms but recovers fewer number of genes. In general, about 15000 genes were annotated, of which almost half had at least one coding sequence reconstructed at 99% of its length. We also built a list of highly expressed genes, of which several are involved in water conservation under laboratory conditions using mouse models.

CONCLUSION: Based on our assembly results, Trinity's in silico normalization is the best algorithm in terms of cost-benefit returns; however, our results also indicate that normalization should be avoided if complete or nearly complete coding sequences of genes are desired. Given that this work is the first to characterize the transcriptome of any member of Sigmodontinae, a subfamily of cricetid rodents with about 400 living species, it will provide valuable resources for future ecological and evolutionary genomic analyses.}, } @article {pmid24905709, year = {2014}, author = {Nightingale, A and Sharma, JR}, title = {Conflict resilience among community forestry user groups: experiences in Nepal.}, journal = {Disasters}, volume = {38}, number = {3}, pages = {517-539}, doi = {10.1111/disa.12056}, pmid = {24905709}, issn = {1467-7717}, mesh = {*Community Networks ; *Forestry ; Humans ; Nepal ; Program Evaluation ; Violence/*prevention & control ; }, abstract = {This paper explores the impact of violent conflict in Nepal on the functioning of community forestry user groups (CFUGs), particularly those supported by the Livelihoods and Forestry Programme, funded by the United Kingdom's Department for International Development (DFID). The key questions are: (i) what explains the resilience of CFUGs operating at the time of conflict?; (ii) what institutional arrangements and strategies allowed them to continue working under conflict conditions?; and (iii) what lessons can be drawn for donor-supported development around the world? The study contributes to other research on the everyday experiences of residents of Nepal living in a period of conflict. It suggests that CFUG resilience was the result of the institutional set up of community forestry and the employment of various tactics by the CFUGs. While the institutional design of community forestry (structure) was very important for resilience, it was the ability of the CFUGs to support and use it effectively that was the determining factor in this regard.}, } @article {pmid24904932, year = {2014}, author = {Chi, J and Parrow, MW and Dunthorn, M}, title = {Cryptic sex in Symbiodinium (Alveolata, Dinoflagellata) is supported by an inventory of meiotic genes.}, journal = {The Journal of eukaryotic microbiology}, volume = {61}, number = {3}, pages = {322-327}, doi = {10.1111/jeu.12110}, pmid = {24904932}, issn = {1550-7408}, mesh = {Alveolata/cytology/*genetics/*physiology ; Computational Biology/methods ; *Genes, Protozoan ; *Meiosis ; Recombination, Genetic ; }, abstract = {Symbiodinium encompasses a diverse clade of dinoflagellates that are ecologically important as symbionts of corals and other marine organisms. Despite decades of study, cytological evidence of sex (karyogamy and meiosis) has not been demonstrated in Symbiodinium, although molecular population genetic patterns support the occurrence of sexual recombination. Here, we provide additional support for sex in Symbiodinium by uncovering six meiosis-specific and 25 meiosis-related genes in three published genomes. Cryptic sex may be occurring in Symbiodinium's seldom-seen free-living state while being inactive in the symbiotic state.}, } @article {pmid24902875, year = {2015}, author = {Kivelä, M and Arnaud-Haond, S and Saramäki, J}, title = {EDENetworks: a user-friendly software to build and analyse networks in biogeography, ecology and population genetics.}, journal = {Molecular ecology resources}, volume = {15}, number = {1}, pages = {117-122}, doi = {10.1111/1755-0998.12290}, pmid = {24902875}, issn = {1755-0998}, mesh = {Computational Biology/*methods ; Ecology/*methods ; Genetics, Population/*methods ; Phylogeography/*methods ; *Software ; }, abstract = {The recent application of graph-based network theory analysis to biogeography, community ecology and population genetics has created a need for user-friendly software, which would allow a wider accessibility to and adaptation of these methods. EDENetworks aims to fill this void by providing an easy-to-use interface for the whole analysis pipeline of ecological and evolutionary networks starting from matrices of species distributions, genotypes, bacterial OTUs or populations characterized genetically. The user can choose between several different ecological distance metrics, such as Bray-Curtis or Sorensen distance, or population genetic metrics such as FST or Goldstein distances, to turn the raw data into a distance/dissimilarity matrix. This matrix is then transformed into a network by manual or automatic thresholding based on percolation theory or by building the minimum spanning tree. The networks can be visualized along with auxiliary data and analysed with various metrics such as degree, clustering coefficient, assortativity and betweenness centrality. The statistical significance of the results can be estimated either by resampling the original biological data or by null models based on permutations of the data.}, } @article {pmid24901618, year = {2014}, author = {Jung, JH and Park, JY and Lim, HM and Yoon, YH and Kim, WJ}, title = {Decision support for ecological river rehabilitation using fish habitat database.}, journal = {Water science and technology : a journal of the International Association on Water Pollution Research}, volume = {69}, number = {11}, pages = {2243-2251}, doi = {10.2166/wst.2014.118}, pmid = {24901618}, issn = {0273-1223}, mesh = {Animals ; China ; *Conservation of Natural Resources ; *Databases, Factual ; Decision Making ; *Ecosystem ; Fishes/*physiology ; *Rivers ; Water Pollution ; Water Quality ; }, abstract = {After the recent success of several river rehabilitation projects including the Cheong-gye river case, a large number of local governments have been promoting their own projects in Korea. Most of the projects are aimed at securing the soundness of aquatic ecosystems according to the guidelines presented by the Korea Ministry of Environment. However, there is no clear guidance for the management goals of water quality and quantity. In this study, we have made an attempt to construct a habitat database (DB) for each domestic freshwater fish species. The fish population, and physical and physicochemical properties of the habitat of 70 domestic freshwater fish species were investigated using field monitoring data. After the statistical processing, the inhabitable range and optimal range of each species were suggested. Furthermore, based on the DB, a decision support system for ecological river restoration and rehabilitation has been developed, and applied for field tests. It became clear that the decision support procedure based on the fish habitat DB is useful in the planning stage of river rehabilitation projects to select the flagship fish, to decide the restoration goals considering their appropriate habitat and to suggest the optimum quantitative combination of each available water resource.}, } @article {pmid24896260, year = {2014}, author = {Grimm, A and Gruber, B and Henle, K}, title = {Reliability of different mark-recapture methods for population size estimation tested against reference population sizes constructed from field data.}, journal = {PloS one}, volume = {9}, number = {6}, pages = {e98840}, pmid = {24896260}, issn = {1932-6203}, mesh = {Datasets as Topic ; Ecology/*methods ; *Models, Theoretical ; *Population Density ; Reproducibility of Results ; }, abstract = {Reliable estimates of population size are fundamental in many ecological studies and biodiversity conservation. Selecting appropriate methods to estimate abundance is often very difficult, especially if data are scarce. Most studies concerning the reliability of different estimators used simulation data based on assumptions about capture variability that do not necessarily reflect conditions in natural populations. Here, we used data from an intensively studied closed population of the arboreal gecko Gehyra variegata to construct reference population sizes for assessing twelve different population size estimators in terms of bias, precision, accuracy, and their 95%-confidence intervals. Two of the reference populations reflect natural biological entities, whereas the other reference populations reflect artificial subsets of the population. Since individual heterogeneity was assumed, we tested modifications of the Lincoln-Petersen estimator, a set of models in programs MARK and CARE-2, and a truncated geometric distribution. Ranking of methods was similar across criteria. Models accounting for individual heterogeneity performed best in all assessment criteria. For populations from heterogeneous habitats without obvious covariates explaining individual heterogeneity, we recommend using the moment estimator or the interpolated jackknife estimator (both implemented in CAPTURE/MARK). If data for capture frequencies are substantial, we recommend the sample coverage or the estimating equation (both models implemented in CARE-2). Depending on the distribution of catchabilities, our proposed multiple Lincoln-Petersen and a truncated geometric distribution obtained comparably good results. The former usually resulted in a minimum population size and the latter can be recommended when there is a long tail of low capture probabilities. Models with covariates and mixture models performed poorly. Our approach identified suitable methods and extended options to evaluate the performance of mark-recapture population size estimators under field conditions, which is essential for selecting an appropriate method and obtaining reliable results in ecology and conservation biology, and thus for sound management.}, } @article {pmid24895604, year = {2014}, author = {Polonikov, AV and Ivanov, VP and Bogomazov, AD and Freidin, MB and Illig, T and Solodilova, MA}, title = {Antioxidant defense enzyme genes and asthma susceptibility: gender-specific effects and heterogeneity in gene-gene interactions between pathogenetic variants of the disease.}, journal = {BioMed research international}, volume = {2014}, number = {}, pages = {708903}, pmid = {24895604}, issn = {2314-6141}, mesh = {Adolescent ; Adult ; Aged ; Antioxidants/*metabolism ; Asthma/*enzymology/*genetics ; Case-Control Studies ; *Epistasis, Genetic ; Female ; Gene Frequency/genetics ; Genetic Association Studies ; *Genetic Heterogeneity ; Genetic Loci ; *Genetic Predisposition to Disease ; Humans ; Male ; Middle Aged ; Models, Genetic ; Multifactor Dimensionality Reduction ; Oxidation-Reduction ; Polymorphism, Single Nucleotide/genetics ; Risk Factors ; *Sex Characteristics ; Statistics as Topic ; Young Adult ; }, abstract = {Oxidative stress resulting from an increased amount of reactive oxygen species and an imbalance between oxidants and antioxidants plays an important role in the pathogenesis of asthma. The present study tested the hypothesis that genetic susceptibility to allergic and nonallergic variants of asthma is determined by complex interactions between genes encoding antioxidant defense enzymes (ADE). We carried out a comprehensive analysis of the associations between adult asthma and 46 single nucleotide polymorphisms of 34 ADE genes and 12 other candidate genes of asthma in Russian population using set association analysis and multifactor dimensionality reduction approaches. We found for the first time epistatic interactions between ADE genes underlying asthma susceptibility and the genetic heterogeneity between allergic and nonallergic variants of the disease. We identified GSR (glutathione reductase) and PON2 (paraoxonase 2) as novel candidate genes for asthma susceptibility. We observed gender-specific effects of ADE genes on the risk of asthma. The results of the study demonstrate complexity and diversity of interactions between genes involved in oxidative stress underlying susceptibility to allergic and nonallergic asthma.}, } @article {pmid24893879, year = {2015}, author = {Vukosavljev, M and Esselink, GD and van 't Westende, WP and Cox, P and Visser, RG and Arens, P and Smulders, MJ}, title = {Efficient development of highly polymorphic microsatellite markers based on polymorphic repeats in transcriptome sequences of multiple individuals.}, journal = {Molecular ecology resources}, volume = {15}, number = {1}, pages = {17-27}, doi = {10.1111/1755-0998.12289}, pmid = {24893879}, issn = {1755-0998}, mesh = {Computational Biology/*methods ; *Genetic Variation ; Genotyping Techniques/*methods ; *Microsatellite Repeats ; Molecular Sequence Data ; *Repetitive Sequences, Nucleic Acid ; Rosa/classification/genetics ; Sequence Analysis, DNA ; *Transcriptome ; }, abstract = {The first hurdle in developing microsatellite markers, cloning, has been overcome by next-generation sequencing. The second hurdle is testing to differentiate polymorphic from nonpolymorphic loci. The third hurdle, somewhat hidden, is that only polymorphic markers with a large effective number of alleles are sufficiently informative to be deployed in multiple studies. Both steps are laborious and still performed manually. We have developed a strategy in which we first screen reads from multiple genotypes for repeats that show the most length variants, and only these are subsequently developed into markers. We validated our strategy in tetraploid garden rose using Illumina paired-end transcriptome sequences of 11 roses. Of 48 tested two markers failed to amplify, but all others were polymorphic. Ten loci amplified more than one locus, indicating duplicated genes or gene families. Completely avoiding duplicated loci will be difficult because the range of numbers of predicted alleles of highly polymorphic single- and multilocus markers largely overlapped. Of the remainder, half were replicate markers (i.e. multiple primer pairs for one locus), indicating the difficulty of correctly filtering short reads containing repeat sequences. We subsequently refined the approach to eliminate multiple primer sets to the same loci. The remaining 18 markers were all highly polymorphic, amplifying on average 11.7 alleles per marker (range = 6-20) in 11 tetraploid roses, exceeding the 8.2 alleles per marker of the 24 most polymorphic markers genotyped previously. This strategy therefore represents a major step forward in the development of highly polymorphic microsatellite markers.}, } @article {pmid24893019, year = {2014}, author = {Zhang, JC and Liu, WD and Liang, Q and Hu, JL and Norris, J and Wu, Y and Bao, CJ and Tang, FY and Huang, P and Zhao, Y and Yu, RB and Zhou, MH and Shen, HB and Chen, F and Peng, ZH}, title = {Spatial distribution and risk factors of influenza in Jiangsu province, China, based on geographical information system.}, journal = {Geospatial health}, volume = {8}, number = {2}, pages = {429-435}, doi = {10.4081/gh.2014.31}, pmid = {24893019}, issn = {1970-7096}, mesh = {China/epidemiology ; Epidemics/statistics & numerical data ; *Geographic Information Systems ; Geography, Medical ; Humans ; Influenza, Human/*epidemiology/etiology/transmission ; Risk Factors ; Spatio-Temporal Analysis ; }, abstract = {Influenza poses a constant, heavy burden on society. Recent research has focused on ecological factors associated with influenza incidence and has also studied influenza with respect to its geographic spread at different scales. This research explores the temporal and spatial parameters of influenza and identifies factors influencing its transmission. A spatial autocorrelation analysis, a spatial-temporal cluster analysis and a spatial regression analysis of influenza rates, carried out in Jiangsu province from 2004 to 2011, found that influenza rates to be spatially dependent in 2004, 2005, 2006 and 2008. South-western districts consistently revealed hotspots of high-incidence influenza. The regression analysis indicates that railways, rivers and lakes are important predictive environmental variables for influenza risk. A better understanding of the epidemic pattern and ecological factors associated with pandemic influenza should benefit public health officials with respect to prevention and controlling measures during future epidemics.}, } @article {pmid24893014, year = {2014}, author = {Ngui, R and Shafie, A and Chua, KH and Mistam, MS and Al-Mekhlafi, HM and Sulaiman, WW and Mahmud, R and Lim, YA}, title = {Mapping and modelling the geographical distribution of soil-transmitted helminthiases in Peninsular Malaysia: implications for control approaches.}, journal = {Geospatial health}, volume = {8}, number = {2}, pages = {365-376}, doi = {10.4081/gh.2014.26}, pmid = {24893014}, issn = {1970-7096}, mesh = {Animals ; Geographic Information Systems ; Helminthiasis/*epidemiology/prevention & control/transmission ; Helminths ; Humans ; Malaysia/epidemiology ; Models, Statistical ; Prevalence ; Soil/*parasitology ; Spatial Analysis ; }, abstract = {Soil-transmitted helminth (STH) infections in Malaysia are still highly prevalent, especially in rural and remote communities. Complete estimations of the total disease burden in the country has not been performed, since available data are not easily accessible in the public domain. The current study utilised geographical information system (GIS) to collate and map the distribution of STH infections from available empirical survey data in Peninsular Malaysia, highlighting areas where information is lacking. The assembled database, comprising surveys conducted between 1970 and 2012 in 99 different locations, represents one of the most comprehensive compilations of STH infections in the country. It was found that the geographical distribution of STH varies considerably with no clear pattern across the surveyed locations. Our attempt to generate predictive risk maps of STH infections on the basis of ecological limits such as climate and other environmental factors shows that the prevalence of Ascaris lumbricoides is low along the western coast and the southern part of the country, whilst the prevalence is high in the central plains and in the North. In the present study, we demonstrate that GIS can play an important role in providing data for the implementation of sustainable and effective STH control programmes to policy-makers and authorities in charge.}, } @article {pmid24892286, year = {2014}, author = {Baker, LL and Jonsen, ID and Mills Flemming, JE and Lidgard, DC and Bowen, WD and Iverson, SJ and Webber, DM}, title = {Probability of detecting marine predator-prey and species interactions using novel hybrid acoustic transmitter-receiver tags.}, journal = {PloS one}, volume = {9}, number = {6}, pages = {e98117}, pmid = {24892286}, issn = {1932-6203}, mesh = {*Acoustics ; Animals ; Aquatic Organisms/*physiology ; Canada ; *Ecosystem ; *Geographic Information Systems ; Geography ; Predatory Behavior/*physiology ; *Probability ; Seals, Earless/*physiology ; Species Specificity ; }, abstract = {Understanding the nature of inter-specific and conspecific interactions in the ocean is challenging because direct observation is usually impossible. The development of dual transmitter/receivers, Vemco Mobile Transceivers (VMT), and satellite-linked (e.g. GPS) tags provides a unique opportunity to better understand between and within species interactions in space and time. Quantifying the uncertainty associated with detecting a tagged animal, particularly under varying field conditions, is vital for making accurate biological inferences when using VMTs. We evaluated the detection efficiency of VMTs deployed on grey seals, Halichoerus grypus, off Sable Island (NS, Canada) in relation to environmental characteristics and seal behaviour using generalized linear models (GLM) to explore both post-processed detection data and summarized raw VMT data. When considering only post-processed detection data, only about half of expected detections were recorded at best even when two VMT-tagged seals were estimated to be within 50-200 m of one another. At a separation of 400 m, only about 15% of expected detections were recorded. In contrast, when incomplete transmissions from the summarized raw data were also considered, the ratio of complete transmission to complete and incomplete transmissions was about 70% for distances ranging from 50-1000 m, with a minimum of around 40% at 600 m and a maximum of about 85% at 50 m. Distance between seals, wind stress, and depth were the most important predictors of detection efficiency. Access to the raw VMT data allowed us to focus on the physical and environmental factors that limit a transceiver's ability to resolve a transmitter's identity.}, } @article {pmid24887330, year = {2014}, author = {Tytgat, B and Verleyen, E and Obbels, D and Peeters, K and De Wever, A and D'hondt, S and De Meyer, T and Van Criekinge, W and Vyverman, W and Willems, A}, title = {Bacterial diversity assessment in Antarctic terrestrial and aquatic microbial mats: a comparison between bidirectional pyrosequencing and cultivation.}, journal = {PloS one}, volume = {9}, number = {6}, pages = {e97564}, pmid = {24887330}, issn = {1932-6203}, mesh = {Antarctic Regions ; Bacteria/*genetics/*growth & development ; Base Composition/genetics ; Databases, Nucleic Acid ; *Genetic Variation ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Seawater/*microbiology ; Sequence Analysis, DNA/*methods ; *Temperature ; }, abstract = {The application of high-throughput sequencing of the 16S rRNA gene has increased the size of microbial diversity datasets by several orders of magnitude, providing improved access to the rare biosphere compared with cultivation-based approaches and more established cultivation-independent techniques. By contrast, cultivation-based approaches allow the retrieval of both common and uncommon bacteria that can grow in the conditions used and provide access to strains for biotechnological applications. We performed bidirectional pyrosequencing of the bacterial 16S rRNA gene diversity in two terrestrial and seven aquatic Antarctic microbial mat samples previously studied by heterotrophic cultivation. While, not unexpectedly, 77.5% of genera recovered by pyrosequencing were not among the isolates, 25.6% of the genera picked up by cultivation were not detected by pyrosequencing. To allow comparison between both techniques, we focused on the five phyla (Proteobacteria, Actinobacteria, Bacteroidetes, Firmicutes and Deinococcus-Thermus) recovered by heterotrophic cultivation. Four of these phyla were among the most abundantly recovered by pyrosequencing. Strikingly, there was relatively little overlap between cultivation and the forward and reverse pyrosequencing-based datasets at the genus (17.1-22.2%) and OTU (3.5-3.6%) level (defined on a 97% similarity cut-off level). Comparison of the V1-V2 and V3-V2 datasets of the 16S rRNA gene revealed remarkable differences in number of OTUs and genera recovered. The forward dataset missed 33% of the genera from the reverse dataset despite comprising 50% more OTUs, while the reverse dataset did not contain 40% of the genera of the forward dataset. Similar observations were evident when comparing the forward and reverse cultivation datasets. Our results indicate that the region under consideration can have a large impact on perceived diversity, and should be considered when comparing different datasets. Finally, a high number of OTUs could not be classified using the RDP reference database, suggesting the presence of a large amount of novel diversity.}, } @article {pmid24885832, year = {2014}, author = {Riesgo, A and Peterson, K and Richardson, C and Heist, T and Strehlow, B and McCauley, M and Cotman, C and Hill, M and Hill, A}, title = {Transcriptomic analysis of differential host gene expression upon uptake of symbionts: a case study with Symbiodinium and the major bioeroding sponge Cliona varians.}, journal = {BMC genomics}, volume = {15}, number = {1}, pages = {376}, pmid = {24885832}, issn = {1471-2164}, mesh = {Animals ; Computational Biology ; Dinoflagellida/*genetics ; *Gene Expression Profiling ; Gene Expression Regulation ; Molecular Sequence Annotation ; Porifera/*genetics ; Reproducibility of Results ; Symbiosis/*genetics ; *Transcriptome ; }, abstract = {BACKGROUND: We have a limited understanding of genomic interactions that occur among partners for many symbioses. One of the most important symbioses in tropical reef habitats involves Symbiodinium. Most work examining Symbiodinium-host interactions involves cnidarian partners. To fully and broadly understand the conditions that permit Symbiodinium to procure intracellular residency, we must explore hosts from different taxa to help uncover universal cellular and genetic strategies for invading and persisting in host cells. Here, we present data from gene expression analyses involving the bioeroding sponge Cliona varians that harbors Clade G Symbiodinium.

RESULTS: Patterns of differential gene expression from distinct symbiont states ("normal", "reinfected", and "aposymbiotic") of the sponge host are presented based on two comparative approaches (transcriptome sequencing and suppressive subtractive hybridization (SSH)). Transcriptomic profiles were different when reinfected tissue was compared to normal and aposymbiotic tissue. We characterized a set of 40 genes drawn from a pool of differentially expressed genes in "reinfected" tissue compared to "aposymbiotic" tissue via SSH. As proof of concept, we determined whether some of the differentially expressed genes identified above could be monitored in sponges grown under ecologically realistic field conditions. We allowed aposymbiotic sponge tissue to become re-populated by natural pools of Symbiodinium in shallow water flats in the Florida Keys, and we analyzed gene expression profiles for two genes found to be increased in expression in "reinfected" tissue in both the transcriptome and via SSH. These experiments highlighted the experimental tractability of C. varians to explore with precision the genetic events that occur upon establishment of the symbiosis. We briefly discuss lab- and field-based experimental approaches that promise to offer insights into the co-opted genetic networks that may modulate uptake and regulation of Symbiondinium populations in hospite.

CONCLUSIONS: This work provides a sponge transcriptome, and a database of putative genes and genetic pathways that may be involved in Symbiodinium interactions. The relative patterns of gene expression observed in these experiments will need to be evaluated on a gene-by-gene basis in controlled and natural re-infection experiments. We argue that sponges offer particularly useful characteristics for discerning essential dimensions of the Symbiodinium niche.}, } @article {pmid24883050, year = {2014}, author = {Mitchell, JT and Schick, RS and Hallyburton, M and Dennis, MF and Kollins, SH and Beckham, JC and McClernon, FJ}, title = {Combined ecological momentary assessment and global positioning system tracking to assess smoking behavior: a proof of concept study.}, journal = {Journal of dual diagnosis}, volume = {10}, number = {1}, pages = {19-29}, pmid = {24883050}, issn = {1550-4271}, support = {R21 DA034471/DA/NIDA NIH HHS/United States ; K23 DA032577/DA/NIDA NIH HHS/United States ; K24 DA023464/DA/NIDA NIH HHS/United States ; K24 DA016388/DA/NIDA NIH HHS/United States ; R03 DA029694/DA/NIDA NIH HHS/United States ; }, mesh = {Adult ; Attention Deficit Disorder with Hyperactivity/*epidemiology/psychology ; Female ; Geographic Information Systems ; Humans ; Male ; Smoking/*epidemiology/psychology ; }, abstract = {OBJECTIVE: Ecological momentary assessment (EMA) methods have provided a rich assessment of the contextual factors associated with a wide range of behaviors including alcohol use, eating, physical activity, and smoking. Despite this rich database, this information has not been linked to specific locations in space. Such location information, which can now be easily acquired from global positioning system (GPS) tracking devices, could provide unique information regarding the space-time distribution of behaviors and new insights into their determinants. In a proof of concept study, we assessed the acceptability and feasibility of acquiring and combining EMA and GPS data from adult smokers with attention deficit hyperactivity disorder (ADHD).

METHODS: Participants were adults with ADHD who were enrolled in a larger EMA study on smoking and psychiatric symptoms. Among those enrolled in the latter study who were approached to participate (N = 11), 10 consented, provided daily EMA entries, and carried a GPS device with them during a 7-day assessment period to assess aspects of their smoking behavior.

RESULTS: The majority of those eligible to participate were willing to carry a GPS device and signed the consent (10 out of 11, 91%). Of the 10 who consented, 7 participants provided EMA entries and carried the GPS device with them daily for at least 70% of the sampling period. Data are presented on the spatial distribution of smoking episodes and ADHD symptoms on a subset of the sample to demonstrate applications of GPS data.

CONCLUSIONS: We conclude by discussing how EMA and GPS might be used to study the ecology of smoking and make recommendations for future research and analysis.}, } @article {pmid24881052, year = {2014}, author = {Cheng, F and Jia, P and Wang, Q and Lin, CC and Li, WH and Zhao, Z}, title = {Studying tumorigenesis through network evolution and somatic mutational perturbations in the cancer interactome.}, journal = {Molecular biology and evolution}, volume = {31}, number = {8}, pages = {2156-2169}, pmid = {24881052}, issn = {1537-1719}, support = {P50 CA095103/CA/NCI NIH HHS/United States ; R03CA167695/CA/NCI NIH HHS/United States ; P50CA098131/CA/NCI NIH HHS/United States ; R21HG006037/HG/NHGRI NIH HHS/United States ; R01 LM011177/LM/NLM NIH HHS/United States ; P30CA068485/CA/NCI NIH HHS/United States ; R03 CA167695/CA/NCI NIH HHS/United States ; P50CA095103/CA/NCI NIH HHS/United States ; R01LM011177/LM/NLM NIH HHS/United States ; P50 CA098131/CA/NCI NIH HHS/United States ; R21 HG006037/HG/NHGRI NIH HHS/United States ; P30 CA068485/CA/NCI NIH HHS/United States ; }, mesh = {Carcinogenesis/*genetics ; Computational Biology/*methods ; Databases, Genetic ; *Gene Regulatory Networks ; Genes, Essential ; Humans ; Models, Genetic ; Mutation ; Protein Interaction Mapping/methods ; Selection, Genetic ; }, abstract = {Cells govern biological functions through complex biological networks. Perturbations to networks may drive cells to new phenotypic states, for example, tumorigenesis. Identifying how genetic lesions perturb molecular networks is a fundamental challenge. This study used large-scale human interactome data to systematically explore the relationship among network topology, somatic mutation, evolutionary rate, and evolutionary origin of cancer genes. We found the unique network centrality of cancer proteins, which is largely independent of gene essentiality. Cancer genes likely have experienced a lower evolutionary rate and stronger purifying selection than those of noncancer, Mendelian disease, and orphan disease genes. Cancer proteins tend to have ancient histories, likely originated in early metazoan, although they are younger than proteins encoded by Mendelian disease genes, orphan disease genes, and essential genes. We found that the protein evolutionary origin (age) positively correlates with protein connectivity in the human interactome. Furthermore, we investigated the network-attacking perturbations due to somatic mutations identified from 3,268 tumors across 12 cancer types in The Cancer Genome Atlas. We observed a positive correlation between protein connectivity and the number of nonsynonymous somatic mutations, whereas a weaker or insignificant correlation between protein connectivity and the number of synonymous somatic mutations. These observations suggest that somatic mutational network-attacking perturbations to hub genes play an important role in tumor emergence and evolution. Collectively, this work has broad biomedical implications for both basic cancer biology and the development of personalized cancer therapy.}, } @article {pmid24881050, year = {2014}, author = {Mitchell, KJ and Pratt, RC and Watson, LN and Gibb, GC and Llamas, B and Kasper, M and Edson, J and Hopwood, B and Male, D and Armstrong, KN and Meyer, M and Hofreiter, M and Austin, J and Donnellan, SC and Lee, MS and Phillips, MJ and Cooper, A}, title = {Molecular phylogeny, biogeography, and habitat preference evolution of marsupials.}, journal = {Molecular biology and evolution}, volume = {31}, number = {9}, pages = {2322-2330}, doi = {10.1093/molbev/msu176}, pmid = {24881050}, issn = {1537-1719}, mesh = {Adaptation, Biological ; Animals ; *Biological Evolution ; Computational Biology/*methods ; DNA, Mitochondrial/analysis ; *Ecosystem ; Evolution, Molecular ; Marsupialia/classification/*genetics ; Phylogeny ; Phylogeography ; Sequence Analysis, DNA ; }, abstract = {Marsupials exhibit great diversity in ecology and morphology. However, compared with their sister group, the placental mammals, our understanding of many aspects of marsupial evolution remains limited. We use 101 mitochondrial genomes and data from 26 nuclear loci to reconstruct a dated phylogeny including 97% of extant genera and 58% of modern marsupial species. This tree allows us to analyze the evolution of habitat preference and geographic distributions of marsupial species through time. We found a pattern of mesic-adapted lineages evolving to use more arid and open habitats, which is broadly consistent with regional climate and environmental change. However, contrary to the general trend, several lineages subsequently appear to have reverted from drier to more mesic habitats. Biogeographic reconstructions suggest that current views on the connectivity between Australia and New Guinea/Wallacea during the Miocene and Pliocene need to be revised. The antiquity of several endemic New Guinean clades strongly suggests a substantially older period of connection stretching back to the Middle Miocene and implies that New Guinea was colonized by multiple clades almost immediately after its principal formation.}, } @article {pmid24880242, year = {2014}, author = {Venkatesh, G and Sægrov, S and Brattebø, H}, title = {Dynamic metabolism modelling of urban water services--demonstrating effectiveness as a decision-support tool for Oslo, Norway.}, journal = {Water research}, volume = {61}, number = {}, pages = {19-33}, doi = {10.1016/j.watres.2014.05.004}, pmid = {24880242}, issn = {1879-2448}, mesh = {Cities ; Conservation of Natural Resources/*methods ; *Decision Support Techniques ; Environment ; Models, Theoretical ; Norway ; Wastewater/*analysis ; Water Supply/*analysis ; }, abstract = {Urban water services are challenged from many perspectives and different stakeholders demand performance improvements along economic, social and environmental dimensions of sustainability. In response, urban water utilities systematically give more attention to criteria such as water safety, climate change adaptation and mitigation, environmental life cycle assessment (LCA), total cost efficiency, and on how to improve their operations within the water-energy-carbon nexus. The authors of this paper collaborated in the development of a 'Dynamic Metabolism Model' (DMM). The model is developed for generic use in the sustainability assessment of urban water services, and it has been initially tested for the city of Oslo, Norway. The purpose has been to adopt a holistic systemic perspective to the analysis of metabolism and environmental impacts of resource flows in urban water and wastewater systems, in order to offer a tool for the examination of future strategies and intervention options in such systems. This paper describes the model and its application to the city of Oslo for the analysis time period 2013-2040. The external factors impacting decision-making and interventions are introduced along with realistic scenarios developed for the testing, after consultation with officials at the Oslo Water and Wastewater Works (Norway). Possible interventions that the utility intends to set in motion are defined and numerically interpreted for incorporation into the model, and changes in the indicator values over the time period are determined. This paper aims to demonstrate the effectiveness and usefulness of the DMM, as a decision-support tool for water-wastewater utilities. The scenarios considered and interventions identified do not include all possible scenarios and interventions that can be relevant for water-wastewater utilities.}, } @article {pmid24865419, year = {2014}, author = {Shi, M and Huang, R and Du, F and Pei, Y and Liao, L and Zhu, Z and Wang, Y}, title = {RNA-seq profiles from grass carp tissues after reovirus (GCRV) infection based on singular and modular enrichment analyses.}, journal = {Molecular immunology}, volume = {61}, number = {1}, pages = {44-53}, doi = {10.1016/j.molimm.2014.05.004}, pmid = {24865419}, issn = {1872-9142}, mesh = {Animals ; Carps/genetics/*immunology/virology ; Cluster Analysis ; Fish Diseases/genetics/*immunology/virology ; Gene Expression Profiling/*methods ; Gene Ontology ; Gills/immunology/metabolism/virology ; Host-Pathogen Interactions/immunology ; Intestinal Mucosa/metabolism ; Intestines/immunology/virology ; Liver/immunology/metabolism/virology ; Oligonucleotide Array Sequence Analysis ; RNA, Messenger/genetics/metabolism ; Reoviridae/*immunology/physiology ; Reverse Transcriptase Polymerase Chain Reaction ; Spleen/immunology/metabolism/virology ; Time Factors ; Transcriptome/*immunology ; }, abstract = {Hemorrhagic disease of the grass carp, Ctenopharyngodon idella, is a fatal disease in fingerlings and yearlings caused by a reovirus, GCRV. RNA-seq data from four diseased grass carp tissues (gill, intestine, liver and spleen) were obtained at 2h before and six times after (2h, 24h, 48h, 72h, 96h and 120h) GCRV challenge. A total of 7.25±0.18 million (M) clean reads and 3.53±0.37M unique reads were obtained per RNA-seq analysis. Compared with controls, there were 9060 unique differentially expressed genes (DEGs) in the four tissues at the six time points post-GCRV challenge. Hierarchical clustering analysis of the DEGs showed that the data from the six time points fell into three branches: 2h, 24h/48h, and 72h/96h/120h. Singular (SEA) and modular enrichment analyses of DEGs per RNA-seq dataset were performed based on gene ontology. The results showed that immune responses occurred in all four tissues, indicating that GCRV probably does not target any tissue specifically. Moreover, during the course of disease, disturbances were observed in lipid and carbohydrate metabolism in each of the organs. SEA of DEGs based on the Kyoto Encyclopedia of Genes and Genomes database was also performed, and this indicated that the complement system and cellular immunity played an important role during the course of hemorrhagic disease. The qPCR of pooled samples of duplicate challenge experiment were used to confirm our RNA-seq approach.}, } @article {pmid24865398, year = {2014}, author = {Kolena, B and Petrovicova, I and Pilka, T and Pucherova, Z and Munk, M and Matula, B and Vankova, V and Petlus, P and Jenisova, Z and Rozova, Z and Wimmerova, S and Trnovec, T}, title = {Phthalate exposure and health-related outcomes in specific types of work environment.}, journal = {International journal of environmental research and public health}, volume = {11}, number = {6}, pages = {5628-5639}, pmid = {24865398}, issn = {1660-4601}, mesh = {Adult ; Anthropometry ; Biomarkers ; Female ; *Health Status ; Humans ; Linear Models ; Lung/*drug effects/physiology ; Male ; Middle Aged ; Occupational Exposure/adverse effects/*analysis ; Phthalic Acids/*adverse effects/*urine ; Respiratory Function Tests ; Slovakia ; Spirometry ; *Waste Management ; }, abstract = {Many toxic substances in the workplace can modify human health and quality of life and there is still insufficient data on respiratory outcomes in adults exposed to phthalates. The aim of this work was to assess in waste management workers from the Nitra region of Slovakia (n = 30) the extent of exposure to phthalates and health-related outcomes. Four urinary phthalate metabolites mono(2-ethylhexyl) phthalate (MEHP), monobutyl phthalate (MnBP), monoethyl phthalate (MEP) and monoisononyl phthalate (MiNP) were determined by high-performance liquid chromatography with mass spectrometry (HPLC-MS/MS). Urinary concentration of MEHP was positively associated with ratio of forced expiratory volume in 1 s to forced vital capacity % (FEV1/FVC) (r = 0.431; p = 0.018) and MiNP with fat free mass index (FFMI) (r = 0.439; p = 0.015). The strongest predictor of pulmonary function was the pack/year index as smoking history that predicted a decrease of pulmonary parameters, the FEV1/FVC, % of predicted values of peak expiratory flow (PEF % of PV) and FEV1 % of PV. Unexpectedly, urinary MEHP and MINP were positively associated with pulmonary function expressed as PEF % of PV and FEV1/FVC. We hypothesize that occupational exposure to phthalates estimated from urinary metabolites (MEHP, MiNP) can modify pulmonary function on top of lifestyle factors.}, } @article {pmid24865297, year = {2014}, author = {Hori, K and Maruyama, F and Fujisawa, T and Togashi, T and Yamamoto, N and Seo, M and Sato, S and Yamada, T and Mori, H and Tajima, N and Moriyama, T and Ikeuchi, M and Watanabe, M and Wada, H and Kobayashi, K and Saito, M and Masuda, T and Sasaki-Sekimoto, Y and Mashiguchi, K and Awai, K and Shimojima, M and Masuda, S and Iwai, M and Nobusawa, T and Narise, T and Kondo, S and Saito, H and Sato, R and Murakawa, M and Ihara, Y and Oshima-Yamada, Y and Ohtaka, K and Satoh, M and Sonobe, K and Ishii, M and Ohtani, R and Kanamori-Sato, M and Honoki, R and Miyazaki, D and Mochizuki, H and Umetsu, J and Higashi, K and Shibata, D and Kamiya, Y and Sato, N and Nakamura, Y and Tabata, S and Ida, S and Kurokawa, K and Ohta, H}, title = {Klebsormidium flaccidum genome reveals primary factors for plant terrestrial adaptation.}, journal = {Nature communications}, volume = {5}, number = {}, pages = {3978}, pmid = {24865297}, issn = {2041-1723}, mesh = {Adaptation, Physiological/*genetics ; Chlorophyll/metabolism ; Electron Transport ; Fluorescence ; Genes, Plant ; *Genome, Plant ; Mass Spectrometry ; Microscopy, Interference ; Molecular Sequence Data ; Multigene Family ; Phylogeny ; Plant Growth Regulators/metabolism ; Protein Structure, Tertiary ; Sequence Analysis, DNA ; Signal Transduction ; Streptophyta/*genetics ; }, abstract = {The colonization of land by plants was a key event in the evolution of life. Here we report the draft genome sequence of the filamentous terrestrial alga Klebsormidium flaccidum (Division Charophyta, Order Klebsormidiales) to elucidate the early transition step from aquatic algae to land plants. Comparison of the genome sequence with that of other algae and land plants demonstrate that K. flaccidum acquired many genes specific to land plants. We demonstrate that K. flaccidum indeed produces several plant hormones and homologues of some of the signalling intermediates required for hormone actions in higher plants. The K. flaccidum genome also encodes a primitive system to protect against the harmful effects of high-intensity light. The presence of these plant-related systems in K. flaccidum suggests that, during evolution, this alga acquired the fundamental machinery required for adaptation to terrestrial environments.}, } @article {pmid24860790, year = {2014}, author = {Minard, G and Tran, FH and Dubost, A and Tran-Van, V and Mavingui, P and Moro, CV}, title = {Pyrosequencing 16S rRNA genes of bacteria associated with wild tiger mosquito Aedes albopictus: a pilot study.}, journal = {Frontiers in cellular and infection microbiology}, volume = {4}, number = {}, pages = {59}, pmid = {24860790}, issn = {2235-2988}, mesh = {Aedes/*microbiology ; Animals ; Bacteria/classification/*genetics ; Biodiversity ; Computational Biology ; Female ; Microbiota ; Pilot Projects ; RNA, Bacterial ; *RNA, Ribosomal, 16S ; Sequence Analysis, DNA ; }, abstract = {The Asian tiger mosquito Aedes (Stegomya) albopictus is an invasive species that has spread across the world in the last two decades, showing a great capacity to adapt to contrasting climates and environments. While demonstrated in many insects, the contribution of bacterial symbionts in Aedes ecology is a challenging aspect that needs to be investigated. Also some bacterial species have already been identified in Ae. albopictus using classical methods, but a more accurate survey of mosquito-associated bacterial diversity is needed to decipher the potential biological functions of bacterial symbionts in mediating or constraining insect adaptation. We surveyed the bacteria associated with field populations of Ae. albopictus from Madagascar by pyrosequencing 16S rRNA gene amplicons. Different aspects of amplicon preparation and sequencing depth were tested to optimize the breadth of bacterial diversity identified. The results revealed that all mosquitoes collected from different sites have a bacterial microbiota dominated by a single taxon, Wolbachia pipientis, which accounted for about 99% of all 92,615 sequences obtained. As Ae. albopictus is known to harbor two Wolbachia strains (wAlbA and wAlbB), a quantitative PCR was used to estimate the relative densities, (i.e., the bacteria-to-host gene ratios) of each strains in individual mosquitoes. Relative densities were between 6.25 × 10(0.01) and 5.47 × 10(0.1) for wAlbA and between 2.03 × 10(0.1) and 1.4 × 10(1) for wAlbB. Apart from Wolbachia, a total of 31 bacterial taxa were identified at the genus level using different method variations. Diversity index values were low and probably underestimated the true diversity due to the high abundance of Wolbachia sequences vastly outnumbering sequences from other taxa. Further studies should implement alternative strategies to specifically discard from analysis any sequences from Wolbachia, the dominant endosymbiotic bacterium in Ae. albopictus from this area.}, } @article {pmid24858224, year = {2014}, author = {Mallinis, G and Koutsias, N and Arianoutsou, M}, title = {Monitoring land use/land cover transformations from 1945 to 2007 in two peri-urban mountainous areas of Athens metropolitan area, Greece.}, journal = {The Science of the total environment}, volume = {490}, number = {}, pages = {262-278}, doi = {10.1016/j.scitotenv.2014.04.129}, pmid = {24858224}, issn = {1879-1026}, mesh = {Agriculture/statistics & numerical data ; Cities/statistics & numerical data ; Conservation of Natural Resources ; Crops, Agricultural ; Ecosystem ; *Environmental Monitoring ; *Forests ; Geographic Information Systems ; Greece ; Remote Sensing Technology ; Urbanization/*trends ; }, abstract = {The aims of this study were to map and analyze land use/land cover transitions and landscape changes in the Parnitha and Penteli mountains, which surround the Athens metropolitan area of Attica, Greece over a period of 62 years. In order to quantify the changes between land categories through time, we computed the transition matrices for three distinct periods (1945-1960, 1960-1996, and 1996-2007), on the basis of available aerial photographs used to create multi-temporal maps. We identified systematic and stationary transitions with multi-level intensity analysis. Forest areas in Parnitha remained the dominant class of land cover throughout the 62 years studied, while transitional woodlands and shrublands were the main classes involved in LULC transitions. Conversely, in Penteli, transitional woodlands, along with shrublands, dominated the study site. The annual rate of change was faster in the first and third time intervals, compared to the second (1960-1996) time interval, in both study areas. The category level analysis results indicated that in both sites annual crops avoided to gain while discontinuous urban fabric avoided to lose areas. At the transition level of analysis, similarities as well as distinct differences existed between the two areas. In both sites the gaining pattern of permanent crops with respect to annual crops and the gain of forest with respect to transitional woodland/shrublands were stationary across the three time intervals. Overall, we identified more systematic transitions and stationary processes in Penteli. We discussed these LULC changes and associated them with human interference (activity) and other major socio-economic developments that were simultaneously occurring in the area. The different patterns of change of the areas, despite their geographical proximity, throughout the period of analysis imply that site-specific studies are needed in order to comprehensively assess the driving forces and develop models of landscape transformation in Mediterranean areas.}, } @article {pmid24854184, year = {2014}, author = {Suzuki, E and Mitsuhashi, T and Tsuda, T and Yamamoto, E}, title = {A simple example as a pedagogical device?.}, journal = {Annals of epidemiology}, volume = {24}, number = {7}, pages = {560-561}, doi = {10.1016/j.annepidem.2014.04.003}, pmid = {24854184}, issn = {1873-2585}, mesh = {*Causality ; *Epidemiologic Methods ; Humans ; }, } @article {pmid24852444, year = {2014}, author = {Bhattacharyya, T and Falconar, AK and Luquetti, AO and Costales, JA and Grijalva, MJ and Lewis, MD and Messenger, LA and Tran, TT and Ramirez, JD and Guhl, F and Carrasco, HJ and Diosque, P and Garcia, L and Litvinov, SV and Miles, MA}, title = {Development of peptide-based lineage-specific serology for chronic Chagas disease: geographical and clinical distribution of epitope recognition.}, journal = {PLoS neglected tropical diseases}, volume = {8}, number = {5}, pages = {e2892}, pmid = {24852444}, issn = {1935-2735}, mesh = {Algorithms ; Amino Acid Sequence ; Animals ; Antibodies, Protozoan/blood ; Antigens, Protozoan/chemistry/*immunology ; Chagas Disease/*immunology/*parasitology ; Computational Biology ; Epitopes/chemistry/*immunology ; Humans ; Mice ; Molecular Sequence Data ; Peptides/chemistry/*immunology ; Serotyping/methods ; South America ; Triatoma/parasitology ; Trypanosoma cruzi/*classification/immunology ; Variant Surface Glycoproteins, Trypanosoma/chemistry/immunology ; }, abstract = {BACKGROUND: Chagas disease, caused by infection with the protozoan Trypanosoma cruzi, remains a serious public health issue in Latin America. Genetically diverse, the species is sub-divided into six lineages, known as TcI-TcVI, which have disparate geographical and ecological distributions. TcII, TcV, and TcVI are associated with severe human disease in the Southern Cone countries, whereas TcI is associated with cardiomyopathy north of the Amazon. T. cruzi persists as a chronic infection, with cardiac and/or gastrointestinal symptoms developing years or decades after initial infection. Identifying an individual's history of T. cruzi lineage infection directly by genotyping of the parasite is complicated by the low parasitaemia and sequestration in the host tissues.

We have applied here serology against lineage-specific epitopes of the T. cruzi surface antigen TSSA, as an indirect approach to allow identification of infecting lineage. Chagasic sera from chronic patients from a range of endemic countries were tested by ELISA against synthetic peptides representing lineage-specific TSSA epitopes bound to avidin-coated ELISA plates via a biotin labelled polyethylene glycol-glycine spacer to increase rotation and ensure each amino acid side chain could freely interact with their antibodies. 79/113 (70%) of samples from Brazil, Bolivia, and Argentina recognised the TSSA epitope common to lineages TcII/TcV/TcVI. Comparison with clinical information showed that a higher proportion of Brazilian TSSApep-II/V/VI responders had ECG abnormalities than non-responders (38% vs 17%; p<0.0001). Among northern chagasic sera 4/20 (20%) from Ecuador reacted with this peptide; 1/12 Venezuelan and 1/34 Colombian samples reacted with TSSApep-IV. In addition, a proposed TcI-specific epitope, described elsewhere, was demonstrated here to be highly conserved across lineages and therefore not applicable to lineage-specific serology.

CONCLUSIONS/SIGNIFICANCE: These results demonstrate the considerable potential for synthetic peptide serology to investigate the infection history of individuals, geographical and clinical associations of T. cruzi lineages.}, } @article {pmid24848051, year = {2014}, author = {Lawley, R and Emmett, BA and Robinson, DA}, title = {Databases: Soil observatory lets researchers dig deep.}, journal = {Nature}, volume = {509}, number = {7501}, pages = {427}, pmid = {24848051}, issn = {1476-4687}, mesh = {Agriculture/methods ; Biodiversity ; *Databases, Factual ; Information Dissemination ; Internet ; London ; Research Personnel ; Soil/*chemistry ; }, } @article {pmid24845052, year = {2014}, author = {Caira, JN and Jensen, K}, title = {A digest of elasmobranch tapeworms.}, journal = {The Journal of parasitology}, volume = {100}, number = {4}, pages = {373-391}, doi = {10.1645/14-516.1}, pmid = {24845052}, issn = {1937-2345}, mesh = {Animals ; Cestoda/anatomy & histology/*classification/physiology ; Cestode Infections/parasitology/*veterinary ; Databases, Factual ; Elasmobranchii/*parasitology ; Fish Diseases/*parasitology ; Host-Parasite Interactions ; Life Cycle Stages ; }, abstract = {This review brings together decades of work on elasmobranch tapeworms. The field has advanced significantly over the past 20 yr, with an emphasis on the discovery and description of novel taxa, and the establishment of phylogenetic frameworks for individual orders and their interrelationships. Tapeworms parasitizing elasmobranchs represent 9 orders and include 977 species and 201 genera-over 250 species and 50 genera are new within the last 2 decades. The 9 orders are treated individually, highlighting recent assessments of phylogenetic relationships informed by molecular sequence data. All but the "Tetraphyllidea" are monophyletic. Although much remains to be learned about their interrelationships, existing phylogenetic hypotheses suggest that elasmobranch tapeworms have played a key role in the evolution of the cestodes of essentially all other vertebrate groups. The apical organ is a defining feature (i.e., a synapomorphy) of a clade consisting of acetabulate taxa and Litobothriidea. Novel hook amino acid composition data support the independent origin of hooks in the various groups of hooked tapeworms. Cestode records exist for representatives of most of the major groups of elasmobranchs, however skates (Rajiformes) and catsharks ("Scyliorhinidae") are particularly neglected in terms of species sampled. The majority of tapeworm species are extremely host-specific exhibiting species-specific (i.e., oioxenous) associations with their hosts. Rapid advancements in elasmobranch taxonomy, with over 300 of the 1,200 species appearing new in the past 20 yr, signal the need for careful attention to be paid to host identifications; such identifications are best documented using a combination of specimen, photographic, and molecular data. Above the species level, many cestode taxa are restricted to host orders, families, or even genera. Documentation of these affiliations allows robust predictions to be made regarding the cestode faunas of unexplored elasmobranchs. Trypanorhynchs are the notable exceptions. Life cycles remain poorly known. Recent applications of molecular methods to larval identifications have reinvigorated this area of research. Tapeworms are more diverse in elasmobranchs of tropical and subtropical waters, but they occur globally not only at the poles and in deep waters, but also in freshwaters of South America and Southeast Asia. The cestode faunas of batoids are much more speciose and complex than those of sharks. The faunas of deeper water sharks are particularly depauperate. The tapeworms of elasmobranchs and their hosts are now among the most well documented host-parasite systems in existence. This system has not yet reached its potential as a resource for investigations of basic ecological and evolutionary principles.}, } @article {pmid24843128, year = {2014}, author = {Domingue, BW and Fletcher, J and Conley, D and Boardman, JD}, title = {Genetic and educational assortative mating among US adults.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {111}, number = {22}, pages = {7996-8000}, pmid = {24843128}, issn = {1091-6490}, support = {R24HD066613/HD/NICHD NIH HHS/United States ; R21 HD078031/HD/NICHD NIH HHS/United States ; U01 AG009740/AG/NIA NIH HHS/United States ; R21 HD071884/HD/NICHD NIH HHS/United States ; P30 AG017266/AG/NIA NIH HHS/United States ; R21HD078031/HD/NICHD NIH HHS/United States ; R24 HD066613/HD/NICHD NIH HHS/United States ; 1R21HD071884/HD/NICHD NIH HHS/United States ; RC2 AG036495/AG/NIA NIH HHS/United States ; P2C HD066613/HD/NICHD NIH HHS/United States ; RC2AG036495/AG/NIA NIH HHS/United States ; RC4 AG039029/AG/NIA NIH HHS/United States ; RC4AG039029/AG/NIA NIH HHS/United States ; U01AG009740/AG/NIA NIH HHS/United States ; P2C HD047873/HD/NICHD NIH HHS/United States ; }, mesh = {Databases, Genetic ; Educational Status ; Ethnicity/genetics ; Female ; Genome-Wide Association Study ; Genotype ; Humans ; Male ; *Marriage ; Metagenomics/*methods ; Phenotype ; Racial Groups/genetics ; *Sexual Behavior ; *Spouses ; United States ; }, abstract = {Understanding the social and biological mechanisms that lead to homogamy (similar individuals marrying one another) has been a long-standing issue across many fields of scientific inquiry. Using a nationally representative sample of non-Hispanic white US adults from the Health and Retirement Study and information from 1.7 million single-nucleotide polymorphisms, we compare genetic similarity among married couples to noncoupled pairs in the population. We provide evidence for genetic assortative mating in this population but the strength of this association is substantially smaller than the strength of educational assortative mating in the same sample. Furthermore, genetic similarity explains at most 10% of the assortative mating by education levels. Results are replicated using comparable data from the Framingham Heart Study.}, } @article {pmid24838766, year = {2014}, author = {Steinert, G and Whitfield, S and Taylor, MW and Thoms, C and Schupp, PJ}, title = {Application of diffusion growth chambers for the cultivation of marine sponge-associated bacteria.}, journal = {Marine biotechnology (New York, N.Y.)}, volume = {16}, number = {5}, pages = {594-603}, pmid = {24838766}, issn = {1436-2236}, mesh = {Animals ; Bacteria/*genetics/*growth & development ; Base Sequence ; Cell Culture Techniques/*methods ; Computational Biology ; Diffusion Chambers, Culture ; Likelihood Functions ; Marine Biology ; Models, Genetic ; Molecular Sequence Data ; *Phylogeny ; Porifera/*microbiology ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Marine sponges contain dense and diverse microbial communities, which are renowned as a source of bioactive metabolites. The biological activities of sponge-microbe natural products span a broad spectrum, from antibacterial and antifungal to antitumor and antiviral applications. However, the potential of sponge-derived compounds has not been fully realized, due largely to the acknowledged "supply issue." Most bacteria from environmental samples have resisted cultivation on artificial growth media, and cultivation of sponge-associated bacteria has been a major focus in the search for novel marine natural products. One approach to isolate so-called "uncultivable" microorganisms from different environments is the diffusion growth chamber method. Here, we describe the first application of diffusion growth chambers for the isolation of cultivable and previously uncultivated bacteria from sponges. The study was conducted by implanting diffusion growth chambers in the tissue of Rhabdastrella globostellata reef sponges. In total, 255 16S rRNA gene sequences were obtained, with phylogenetic analyses revealing their affiliations with the Alpha- and Gammaproteobacteria, Bacteroidetes, Actinobacteria, and Firmicutes. Fifteen sequences represented previously uncultivated bacteria belonging to the Bacteroidetes and Proteobacteria (Alpha and Gamma classes). Our results indicate that the diffusion growth chamber approach can be successfully applied in a natural, living marine environment such as sponges.}, } @article {pmid24835514, year = {2014}, author = {Desvignes, T and Beam, MJ and Batzel, P and Sydes, J and Postlethwait, JH}, title = {Expanding the annotation of zebrafish microRNAs based on small RNA sequencing.}, journal = {Gene}, volume = {546}, number = {2}, pages = {386-389}, pmid = {24835514}, issn = {1879-0038}, support = {R01 OD011116/OD/NIH HHS/United States ; R24 OD011199/OD/NIH HHS/United States ; U01 DE020076/DE/NIDCR NIH HHS/United States ; 5R240D011199//PHS HHS/United States ; }, mesh = {Animals ; *Databases, Nucleic Acid ; Humans ; MicroRNAs/*genetics ; *Molecular Sequence Annotation ; *Sequence Analysis, RNA ; Zebrafish/*genetics ; }, abstract = {MicroRNAs (miRs) are short non-coding RNAs that fine-tune the regulation of gene expression to coordinate a wide range of biological processes. Because of their role in the regulation of gene expression, miRs are essential players in development by acting on cell fate determination and progression towards cell differentiation and are increasingly relevant to human health and disease. Although the zebrafish Danio rerio is a major model for studies of development, genetics, physiology, evolution, and human biology, the annotation of zebrafish miR-producing genes remains limited. In the present work, we report deep sequencing data of zebrafish small RNAs from brain, heart, testis, and ovary. Results provide evidence for the expression of 56 un-annotated mir genes and 248 un-annotated mature strands, increasing the number of zebrafish mir genes over those already deposited in miRBase by 16% and the number of mature sequences by 63%. We also describe the existence of three pairs of mirror-mir genes and two mirtron genes, genetic features previously undescribed in non-mammalian vertebrates. This report provides information that substantially increases our knowledge of the zebrafish miRNome and will benefit the entire miR community.}, } @article {pmid24830675, year = {2014}, author = {Veeramah, KR and Gutenkunst, RN and Woerner, AE and Watkins, JC and Hammer, MF}, title = {Evidence for increased levels of positive and negative selection on the X chromosome versus autosomes in humans.}, journal = {Molecular biology and evolution}, volume = {31}, number = {9}, pages = {2267-2282}, pmid = {24830675}, issn = {1537-1719}, support = {R01_HG005226/HG/NHGRI NIH HHS/United States ; }, mesh = {Africa, Western ; Amino Acid Substitution ; Black People/*genetics ; Chromosomes, Human/*genetics ; Chromosomes, Human, X/*genetics ; Computational Biology/*methods ; CpG Islands ; Evolution, Molecular ; Exome ; Female ; Gene Frequency ; Genetic Fitness ; Humans ; Male ; Models, Genetic ; Selection, Genetic ; Sequence Analysis, DNA ; }, abstract = {Partially recessive variants under positive selection are expected to go to fixation more quickly on the X chromosome as a result of hemizygosity, an effect known as faster-X. Conversely, purifying selection is expected to reduce substitution rates more effectively on the X chromosome. Previous work in humans contrasted divergence on the autosomes and X chromosome, with results tending to support the faster-X effect. However, no study has yet incorporated both divergence and polymorphism to quantify the effects of both purifying and positive selection, which are opposing forces with respect to divergence. In this study, we develop a framework that integrates previously developed theory addressing differential rates of X and autosomal evolution with methods that jointly estimate the level of purifying and positive selection via modeling of the distribution of fitness effects (DFE). We then utilize this framework to estimate the proportion of nonsynonymous substitutions fixed by positive selection (α) using exome sequence data from a West African population. We find that varying the female to male breeding ratio (β) has minimal impact on the DFE for the X chromosome, especially when compared with the effect of varying the dominance coefficient of deleterious alleles (h). Estimates of α range from 46% to 51% and from 4% to 24% for the X chromosome and autosomes, respectively. While dependent on h, the magnitude of the difference between α values estimated for these two systems is highly statistically significant over a range of biologically realistic parameter values, suggesting faster-X has been operating in humans.}, } @article {pmid24830392, year = {2014}, author = {O'Farrill, G and Gauthier Schampaert, K and Rayfield, B and Bodin, Ö and Calmé, S and Sengupta, R and Gonzalez, A}, title = {The potential connectivity of waterhole networks and the effectiveness of a protected area under various drought scenarios.}, journal = {PloS one}, volume = {9}, number = {5}, pages = {e95049}, pmid = {24830392}, issn = {1932-6203}, support = {R56 AG056046/AG/NIA NIH HHS/United States ; }, mesh = {Animals ; Climate ; *Climate Change ; Conservation of Natural Resources/*methods ; *Droughts ; Ecosystem ; Geographic Information Systems ; Geography ; Mexico ; Models, Theoretical ; Rain ; }, abstract = {Landscape connectivity is considered a priority for ecosystem conservation because it may mitigate the synergistic effects of climate change and habitat loss. Climate change predictions suggest changes in precipitation regimes, which will affect the availability of water resources, with potential consequences for landscape connectivity. The Greater Calakmul Region of the Yucatan Peninsula (Mexico) has experienced a 16% decrease in precipitation over the last 50 years, which we hypothesise has affected water resource connectivity. We used a network model of connectivity, for three large endangered species (Baird's tapir, white-lipped peccary and jaguar), to assess the effect of drought on waterhole availability and connectivity in a forested landscape inside and adjacent to the Calakmul Biosphere Reserve. We used reported travel distances and home ranges for our species to establish movement distances in our model. Specifically, we compared the effects of 10 drought scenarios on the number of waterholes (nodes) and the subsequent changes in network structure and node importance. Our analysis revealed that drought dramatically influenced spatial structure and potential connectivity of the network. Our results show that waterhole connectivity and suitable habitat (area surrounding waterholes) is lost faster inside than outside the reserve for all three study species, an outcome that may drive them outside the reserve boundaries. These results emphasize the need to assess how the variability in the availability of seasonal water resource may affect the viability of animal populations under current climate change inside and outside protected areas.}, } @article {pmid24824011, year = {2014}, author = {Kang, M and Kim, DW and Baek, YJ and Moon, SH and Jung, HJ and Song, YJ and Paik, HY}, title = {Dietary supplement use and its effect on nutrient intake in Korean adult population in the Korea National Health and Nutrition Examination Survey IV (2007-2009) data.}, journal = {European journal of clinical nutrition}, volume = {68}, number = {7}, pages = {804-810}, pmid = {24824011}, issn = {1476-5640}, mesh = {Adult ; Age Factors ; Aged ; Databases, Factual ; *Diet ; Dietary Supplements/*statistics & numerical data ; Educational Status ; Energy Intake ; Female ; Humans ; Male ; Middle Aged ; Minerals/*administration & dosage ; Nutrition Policy ; Nutrition Surveys ; Nutritional Requirements ; *Nutritive Value ; Republic of Korea ; Sex Factors ; Trace Elements/*administration & dosage ; Vitamins/*administration & dosage ; Young Adult ; }, abstract = {BACKGROUND/OBJECTIVES: Although there is an increasing trend of dietary supplement (DS) use, few researches have evaluated nutrient intake from DS. This study aimed to establish a nutrient database (NDB) for DS and estimate the effect of DS on total nutrient intake by Korean adults.

SUBJECTS/METHODS: The NDB for DS was established using the label information of products reported in the Korea National Health and Nutrition Examination Survey (KNHANES) IV. Of the 16,031 participants who were ≥20 years old, 2053 products were reported as being taken by 5606 subjects. But nutrient composition could be identified by searching product name only in 1158 products consumed by 3844 subjects (DS users). Total nutrient intake of DS users was obtained by combining intakes from diet and DS.

RESULTS: Dietary supplement use was higher in women, in middle-aged people and in those with higher education and low smoking and drinking preferences. Nutrients obtained from food were higher in DS users than in nonusers for most nutrients, particularly in women. When total nutrient intake was evaluated in DS users, the percentage of subjects whose intake was below the estimated average requirement for Koreans decreased for several vitamins and minerals, but the percentage of subjects whose intake was above the tolerable upper intake levels increased for vitamin A, vitamin C and iron.

CONCLUSIONS: The newly developed NDB for DS will be an important resource for more accurate assessment of nutrient intake as well as evaluation of the relationship between nutrition and health. Further research is needed to update a more comprehensive NDB applicable to diverse populations.}, } @article {pmid24823770, year = {2014}, author = {Balakirev, ES and Chechetkin, VR and Lobzin, VV and Ayala, FJ}, title = {Computational methods of identification of pseudogenes based on functionality: entropy and GC content.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1167}, number = {}, pages = {41-62}, doi = {10.1007/978-1-4939-0835-6_4}, pmid = {24823770}, issn = {1940-6029}, mesh = {Animals ; Base Composition ; Codon ; Computational Biology/*methods ; Drosophila melanogaster/genetics ; Entropy ; Genomics/*methods ; Multigene Family ; Pseudogenes/*genetics ; }, abstract = {Spectral entropy and GC content analyses reveal comprehensive structural features of DNA sequences. To illustrate the significance of these features, we analyze the β-esterase gene cluster, including the Est-6 gene and the ψEst-6 putative pseudogene, in seven species of the Drosophila melanogaster subgroup. The spectral entropies show distinctly lower structural ordering for ψEst-6 than for Est-6 in all species studied. However, entropy accumulation is not a completely random process for either gene and it shows to be nucleotide dependent. Furthermore, GC content in synonymous positions is uniformly higher in Est-6 than in ψEst-6, in agreement with the reduced GC content generally observed in pseudogenes and nonfunctional sequences. The observed differences in entropy and GC content reflect an evolutionary shift associated with the process of pseudogenization and subsequent functional divergence of ψEst-6 and Est-6 after the duplication event. The data obtained show the relevance and significance of entropy and GC content analyses for pseudogene identification and for the comparative study of gene-pseudogene evolution.}, } @article {pmid24823303, year = {2014}, author = {Huang, X and Wu, S and Guan, Y and Li, Y and He, M}, title = {Identification of sixteen single-nucleotide polymorphism markers in the pearl oyster, Pinctada fucata, for population genetic structure analysis.}, journal = {Journal of genetics}, volume = {93}, number = {1}, pages = {e1-4}, doi = {10.1007/s12041-014-0357-0}, pmid = {24823303}, issn = {0973-7731}, mesh = {Animals ; Computational Biology ; Genetic Loci ; *Genetic Markers ; *Genetics, Population ; Pinctada/*genetics ; *Polymorphism, Single Nucleotide ; }, } @article {pmid24821516, year = {2014}, author = {Cunningham, JA and Rahman, IA and Lautenschlager, S and Rayfield, EJ and Donoghue, PC}, title = {A virtual world of paleontology.}, journal = {Trends in ecology & evolution}, volume = {29}, number = {6}, pages = {347-357}, doi = {10.1016/j.tree.2014.04.004}, pmid = {24821516}, issn = {1872-8383}, mesh = {Animals ; Computer Simulation ; Fossils/*anatomy & histology ; Image Interpretation, Computer-Assisted ; Paleontology/*methods ; Tomography, X-Ray Computed ; }, abstract = {Computer-aided visualization and analysis of fossils has revolutionized the study of extinct organisms. Novel techniques allow fossils to be characterized in three dimensions and in unprecedented detail. This has enabled paleontologists to gain important insights into their anatomy, development, and preservation. New protocols allow more objective reconstructions of fossil organisms, including soft tissues, from incomplete remains. The resulting digital reconstructions can be used in functional analyses, rigorously testing long-standing hypotheses regarding the paleobiology of extinct organisms. These approaches are transforming our understanding of long-studied fossil groups, and of the narratives of organismal and ecological evolution that have been built upon them.}, } @article {pmid24817095, year = {2014}, author = {Sirová, D and Santrůček, J and Adamec, L and Bárta, J and Borovec, J and Pech, J and Owens, SM and Santrůčková, H and Schäufele, R and Storchová, H and Vrba, J}, title = {Dinitrogen fixation associated with shoots of aquatic carnivorous plants: is it ecologically important?.}, journal = {Annals of botany}, volume = {114}, number = {1}, pages = {125-133}, pmid = {24817095}, issn = {1095-8290}, mesh = {Ammonium Compounds/analysis ; Bacteria/genetics/*isolation & purification/metabolism ; Base Sequence ; Droseraceae/*metabolism/microbiology ; Ecology ; Ecosystem ; Magnoliopsida/*metabolism/microbiology ; Molecular Sequence Data ; Nitrogen/*metabolism ; *Nitrogen Fixation ; Nitrogen Isotopes ; Plant Shoots/metabolism ; RNA, Bacterial/chemistry/genetics ; RNA, Ribosomal, 16S/chemistry/genetics ; Sequence Analysis, RNA ; Water/metabolism ; }, abstract = {BACKGROUND AND AIMS: Rootless carnivorous plants of the genus Utricularia are important components of many standing waters worldwide, as well as suitable model organisms for studying plant-microbe interactions. In this study, an investigation was made of the importance of microbial dinitrogen (N2) fixation in the N acquisition of four aquatic Utricularia species and another aquatic carnivorous plant, Aldrovanda vesiculosa.

METHODS: 16S rRNA amplicon sequencing was used to assess the presence of micro-organisms with known ability to fix N2. Next-generation sequencing provided information on the expression of N2 fixation-associated genes. N2 fixation rates were measured following (15)N2-labelling and were used to calculate the plant assimilation rate of microbially fixed N2.

KEY RESULTS: Utricularia traps were confirmed as primary sites of N2 fixation, with up to 16 % of the plant-associated microbial community consisting of bacteria capable of fixing N2. Of these, rhizobia were the most abundant group. Nitrogen fixation rates increased with increasing shoot age, but never exceeded 1·3 μmol N g(-1) d. mass d(-1). Plant assimilation rates of fixed N2 were detectable and significant, but this fraction formed less than 1 % of daily plant N gain. Although trap fluid provides conditions favourable for microbial N2 fixation, levels of nif gene transcription comprised <0·01 % of the total prokaryotic transcripts.

CONCLUSIONS: It is hypothesized that the reason for limited N2 fixation in aquatic Utricularia, despite the large potential capacity, is the high concentration of NH4-N (2·0-4·3 mg L(-1)) in the trap fluid. Resulting from fast turnover of organic detritus, it probably inhibits N2 fixation in most of the microorganisms present. Nitrogen fixation is not expected to contribute significantly to N nutrition of aquatic carnivorous plants under their typical growth conditions; however, on an annual basis the plant-microbe system can supply nitrogen in the order of hundreds of mg m(-2) into the nutrient-limited littoral zone, where it may thus represent an important N source.}, } @article {pmid24816593, year = {2014}, author = {Young, J and Iwanowicz, L and Sperry, A and Blazer, V}, title = {A landscape-based reconnaissance survey of estrogenic activity in streams of the upper Potomac, upper James, and Shenandoah Rivers, USA.}, journal = {Environmental monitoring and assessment}, volume = {186}, number = {9}, pages = {5531-5545}, pmid = {24816593}, issn = {1573-2959}, mesh = {Agriculture ; Endocrine Disruptors/*analysis ; Environmental Monitoring/*methods ; Estrogens/*analysis ; Geographic Information Systems ; Humans ; Rivers/*chemistry ; Water Pollutants, Chemical/*analysis ; }, abstract = {Endocrine-disrupting compounds (EDCs) are becoming of increasing concern in waterways of the USA and worldwide. What remains poorly understood, however, is how prevalent these emerging contaminants are in the environment and what methods are best able to determine landscape sources of EDCs. We describe the development of a spatially structured sampling design and a reconnaissance survey of estrogenic activity along gradients of land use within sub-watersheds. We present this example as a useful approach for state and federal agencies with an interest in identifying locations potentially impacted by EDCs that warrant more intensive, focused research. Our study confirms the importance of agricultural activities on levels of a measured estrogenic equivalent (E2Eq) and also highlights the importance of other potential sources of E2Eq in areas where intensive agriculture is not the dominant land use. Through application of readily available geographic information system (GIS) data, coupled with spatial statistical analysis, we demonstrate the correlation of specific land use types to levels of estrogenic activity across a large area in a consistent and unbiased manner.}, } @article {pmid24813772, year = {2014}, author = {Uca Avci, ZD and Karaman, M and Ozelkan, E and Kumral, M and Budakoglu, M}, title = {OBIA based hierarchical image classification for industrial lake water.}, journal = {The Science of the total environment}, volume = {487}, number = {}, pages = {565-573}, doi = {10.1016/j.scitotenv.2014.04.048}, pmid = {24813772}, issn = {1879-1026}, mesh = {Ecosystem ; Environmental Monitoring/*methods ; Lakes/*chemistry ; Satellite Imagery/*classification ; Water Pollution/analysis/statistics & numerical data ; Wetlands ; }, abstract = {Water management is very important in water mining regions for the sustainability of the natural environment and for industrial activities. This study focused on Acigol Lake, which is an important wetland for sodium sulphate (Na2SO4) production, a significant natural protection area and habitat for local bird species and endemic species of this saline environment, and a stopover for migrating flamingos. By a hierarchical classification method, ponds representing the industrial part were classified according to in-situ measured Baumé values, and lake water representing the natural part was classified according to in-situ measurements of water depth. The latter is directly related to the water level, which should not exceed a critical level determined by the regulatory authorities. The resulting data, produced at an accuracy of around 80%, illustrates the status in two main regions for a single date. The output of the analysis may be meaningful for firms and environmental researchers, and authorizations can provide a good perspective for decision making for sustainable resource management in the region which has uncommon and specific ecological characteristics.}, } @article {pmid24806844, year = {2014}, author = {Lepais, O and Weir, JT}, title = {SimRAD: an R package for simulation-based prediction of the number of loci expected in RADseq and similar genotyping by sequencing approaches.}, journal = {Molecular ecology resources}, volume = {14}, number = {6}, pages = {1314-1321}, doi = {10.1111/1755-0998.12273}, pmid = {24806844}, issn = {1755-0998}, mesh = {Computational Biology/*methods ; *Computer Simulation ; Genotyping Techniques/methods ; High-Throughput Nucleotide Sequencing/methods ; Polymorphism, Single Nucleotide ; *Restriction Mapping ; }, abstract = {Application of high-throughput sequencing platforms in the field of ecology and evolutionary biology is developing quickly with the introduction of efficient methods to reduce genome complexity. Numerous approaches for genome complexity reduction have been developed using different combinations of restriction enzymes, library construction strategies and fragment size selection. As a result, the choice of which techniques to use may become cumbersome, because it is difficult to anticipate the number of loci resulting from each method. We developed SimRAD, an R package that performs in silico restriction enzyme digests and fragment size selection as implemented in most restriction site associated DNA polymorphism and genotyping by sequencing methods. In silico digestion is performed on a reference genome or on a randomly generated DNA sequence when no reference genome sequence is available. SimRAD accurately predicts the number of loci under alternative protocols when a reference genome sequence is available for the targeted species (or a close relative) but may be unreliable when no reference genome is available. SimRAD is also useful for fine-tuning a given protocol to adjust the number of targeted loci. Here, we outline the functionality of SimRAD and provide an illustrative example of the use of the package (available on the CRAN at http://cran.r-project.org/web/packages/SimRAD).}, } @article {pmid24804449, year = {2014}, author = {Murtaugh, PA}, title = {Rejoinder.}, journal = {Ecology}, volume = {95}, number = {3}, pages = {651-653}, doi = {10.1890/13-1858.1}, pmid = {24804449}, issn = {0012-9658}, mesh = {*Data Interpretation, Statistical ; *Models, Statistical ; *Research Design ; }, } @article {pmid24804448, year = {2014}, author = {Spanos, A}, title = {Recurring controversies about P values and confidence intervals revisited.}, journal = {Ecology}, volume = {95}, number = {3}, pages = {645-651}, doi = {10.1890/13-1291.1}, pmid = {24804448}, issn = {0012-9658}, mesh = {*Data Interpretation, Statistical ; *Models, Statistical ; *Research Design ; }, abstract = {The paper focused primarily on certain charges, claims, and interpretations of the P value as they relate to CIs and the AIC. It as argued that some of these comparisons and claims are misleading because they ignore key differences in the procedures being compared, such as (1) their primary aims and objectives, (2) the nature of the question posed to the data, as well as (3) the nature of their underlying reasoning and the ensuing inferences. In the case of the P value, the crucial issue is whether Fisher's evidential interpretation of the P value as "indicating the strength of evidence against H0" is appropriate. It is argued that, despite Fisher's maligning of the Type II error, a principled way to provide an adequate evidential account, in the form of post-data severity evaluation, calls for taking into account the power of the test. The error-statistical perspective brings out a key weakness of the P value and addresses several foundational issues raised in frequentist testing, including the fallacies of acceptance and rejection as well as misinterpretations of observed CIs: see Mayo-Spanos (2011). The paper also uncovers the connection between model selection procedures and hypothesis testing, revealing the inherent unreliability of the former. Hence, the choice between different procedures should not be "stylistic" (Murtaugh 2013), but should depend on the questions of interest, the answers sought, and the reliability of the procedures.}, } @article {pmid24804447, year = {2014}, author = {Lavine, M}, title = {Comment on Murtaugh.}, journal = {Ecology}, volume = {95}, number = {3}, pages = {642-645}, doi = {10.1890/13-1112.1}, pmid = {24804447}, issn = {0012-9658}, mesh = {*Data Interpretation, Statistical ; *Models, Statistical ; *Research Design ; }, abstract = {Murtaugh and I agree on an important point: abandon accept/reject declarations. That alone will go a long way to improving statistical practice. (2) Don't confuse P values or deltaAIC with binary declarations. An argument against one is not necessarily an argument against the other. (3) Be careful interpreting a P value or deltaAIC as strength of evidence. That interpretation cannot be made formal and the connection between P, deltaAIC, and evidence must be recalibrated for each new problem. (4) Plot. Check models. Plot. Check assumptions. Plot.}, } @article {pmid24804446, year = {2014}, author = {Stanton-Geddes, J and de Freitas, CG and Dambros, Cde S}, title = {In defense of P values: comment on the statistical methods actually used by ecologists.}, journal = {Ecology}, volume = {95}, number = {3}, pages = {637-642}, doi = {10.1890/13-1156.1}, pmid = {24804446}, issn = {0012-9658}, mesh = {*Data Interpretation, Statistical ; *Models, Statistical ; *Research Design ; }, } @article {pmid24804445, year = {2014}, author = {Aho, K and Derryberry, D and Peterson, T}, title = {Model selection for ecologists: the worldviews of AIC and BIC.}, journal = {Ecology}, volume = {95}, number = {3}, pages = {631-636}, doi = {10.1890/13-1452.1}, pmid = {24804445}, issn = {0012-9658}, mesh = {*Data Interpretation, Statistical ; *Models, Statistical ; *Research Design ; }, } @article {pmid24804444, year = {2014}, author = {Burnham, KP and Anderson, DR}, title = {P values are only an index to evidence: 20th- vs. 21st-century statistical science.}, journal = {Ecology}, volume = {95}, number = {3}, pages = {627-630}, doi = {10.1890/13-1066.1}, pmid = {24804444}, issn = {0012-9658}, mesh = {*Data Interpretation, Statistical ; *Models, Statistical ; *Research Design ; }, abstract = {Early statistical methods focused on pre-data probability statements (i.e., data as random variables) such as P values; these are not really inferences nor are P values evidential. Statistical science clung to these principles throughout much of the 20th century as a wide variety of methods were developed for special cases. Looking back, it is clear that the underlying paradigm (i.e., testing and P values) was weak. As Kuhn (1970) suggests, new paradigms have taken the place of earlier ones: this is a goal of good science. New methods have been developed and older methods extended and these allow proper measures of strength of evidence and multimodel inference. It is time to move forward with sound theory and practice for the difficult practical problems that lie ahead. Given data the useful foundation shifts to post-data probability statements such as model probabilities (Akaike weights) or related quantities such as odds ratios and likelihood intervals. These new methods allow formal inference from multiple models in the a prior set. These quantities are properly evidential. The past century was aimed at finding the "best" model and making inferences from it. The goal in the 21st century is to base inference on all the models weighted by their model probabilities (model averaging). Estimates of precision can include model selection uncertainty leading to variances conditional on the model set. The 21st century will be about the quantification of information, proper measures of evidence, and multi-model inference. Nelder (1999:261) concludes, "The most important task before us in developing statistical science is to demolish the P-value culture, which has taken root to a frightening extent in many areas of both pure and applied science and technology".}, } @article {pmid24804443, year = {2014}, author = {Barber, JJ and Ogle, K}, title = {To P or not to P?.}, journal = {Ecology}, volume = {95}, number = {3}, pages = {621-626}, doi = {10.1890/13-1402.1}, pmid = {24804443}, issn = {0012-9658}, mesh = {*Data Interpretation, Statistical ; *Models, Statistical ; *Research Design ; }, } @article {pmid24804442, year = {2014}, author = {de Valpine, P}, title = {The common sense of P values.}, journal = {Ecology}, volume = {95}, number = {3}, pages = {617-621}, doi = {10.1890/13-1271.1}, pmid = {24804442}, issn = {0012-9658}, mesh = {*Data Interpretation, Statistical ; *Models, Statistical ; *Research Design ; }, } @article {pmid24804441, year = {2014}, author = {Murtaugh, PA}, title = {In defense of P values.}, journal = {Ecology}, volume = {95}, number = {3}, pages = {611-617}, doi = {10.1890/13-0590.1}, pmid = {24804441}, issn = {0012-9658}, mesh = {*Data Interpretation, Statistical ; *Models, Statistical ; *Research Design ; }, abstract = {Statistical hypothesis testing has been widely criticized by ecologists in recent years. I review some of the more persistent criticisms of P values and argue that most stem from misunderstandings or incorrect interpretations, rather than from intrinsic shortcomings of the P value. I show that P values are intimately linked to confidence intervals and to differences in Akaike's information criterion (deltaAIC), two metrics that have been advocated as replacements for the P value. The choice of a threshold value of deltaAIC that breaks ties among competing models is as arbitrary as the choice of the probability of a Type I error in hypothesis testing, and several other criticisms of the P value apply equally to deltaAIC. Since P values, confidence intervals, and deltaAIC are based on the same statistical information, all have their places in modern statistical practice. The choice of which to use should be stylistic, dictated by details of the application rather than by dogmatic, a priori considerations.}, } @article {pmid24804440, year = {2014}, author = {Ellison, AM and Gotelli, NJ and Inouye, BD and Strong, DR}, title = {P values, hypothesis testing, and model selection: it's déjà vu all over again.}, journal = {Ecology}, volume = {95}, number = {3}, pages = {609-610}, doi = {10.1890/13-1911.1}, pmid = {24804440}, issn = {0012-9658}, mesh = {*Data Interpretation, Statistical ; Models, Biological ; Models, Statistical ; *Research Design ; }, } @article {pmid24801602, year = {2014}, author = {Johnson, GE and Soeteman-Hernández, LG and Gollapudi, BB and Bodger, OG and Dearfield, KL and Heflich, RH and Hixon, JG and Lovell, DP and MacGregor, JT and Pottenger, LH and Thompson, CM and Abraham, L and Thybaud, V and Tanir, JY and Zeiger, E and van Benthem, J and White, PA}, title = {Derivation of point of departure (PoD) estimates in genetic toxicology studies and their potential applications in risk assessment.}, journal = {Environmental and molecular mutagenesis}, volume = {55}, number = {8}, pages = {609-623}, pmid = {24801602}, issn = {1098-2280}, support = {NC/K500033/1/NC3RS_/National Centre for the Replacement, Refinement and Reduction of Animals in Research/United Kingdom ; }, mesh = {Animals ; Benchmarking ; Databases, Factual ; Dose-Response Relationship, Drug ; Ecotoxicology/*methods ; Ethyl Methanesulfonate/toxicity ; Ethylnitrosourea/*toxicity ; Humans ; Methyl Methanesulfonate/toxicity ; Methylnitrosourea/*toxicity ; Mutagens/toxicity ; No-Observed-Adverse-Effect Level ; Risk Assessment/*methods ; }, abstract = {Genetic toxicology data have traditionally been employed for qualitative, rather than quantitative evaluations of hazard. As a continuation of our earlier report that analyzed ethyl methanesulfonate (EMS) and methyl methanesulfonate (MMS) dose-response data (Gollapudi et al., 2013), here we present analyses of 1-ethyl-1-nitrosourea (ENU) and 1-methyl-1-nitrosourea (MNU) dose-response data and additional approaches for the determination of genetic toxicity point-of-departure (PoD) metrics. We previously described methods to determine the no-observed-genotoxic-effect-level (NOGEL), the breakpoint-dose (BPD; previously named Td), and the benchmark dose (BMD10) for genetic toxicity endpoints. In this study we employed those methods, along with a new approach, to determine the non-linear slope-transition-dose (STD), and alternative methods to determine the BPD and BMD, for the analyses of nine ENU and 22 MNU datasets across a range of in vitro and in vivo endpoints. The NOGEL, BMDL10 and BMDL1SD PoD metrics could be readily calculated for most gene mutation and chromosomal damage studies; however, BPDs and STDs could not always be derived due to data limitations and constraints of the underlying statistical methods. The BMDL10 values were often lower than the other PoDs, and the distribution of BMDL10 values produced the lowest median PoD. Our observations indicate that, among the methods investigated in this study, the BMD approach is the preferred PoD for quantitatively describing genetic toxicology data. Once genetic toxicology PoDs are calculated via this approach, they can be used to derive reference doses and margin of exposure values that may be useful for evaluating human risk and regulatory decision making.}, } @article {pmid24789642, year = {2014}, author = {Barcellos, C and Zaluar, A}, title = {[Homicides and territorial struggles in Rio de Janeiro favelas].}, journal = {Revista de saude publica}, volume = {48}, number = {1}, pages = {94-102}, pmid = {24789642}, issn = {1518-8787}, mesh = {Brazil/epidemiology ; Cause of Death ; Female ; Health Information Systems ; Homicide/ethnology/*statistics & numerical data ; Humans ; Male ; *Poverty Areas ; Residence Characteristics ; Socioeconomic Factors ; *Violence/ethnology/trends ; }, abstract = {OBJECTIVE: To evaluate the risk of homicide in Rio de Janeiro’s favelas, taking into account the territorial disputes taking place in the city.

METHODS: The study is based on data on mortality from homicide in the city of Rio de Janeiro between 2006 and 2009. Risks in favelas and in surrounding areas were evaluated, as was the domination of armed groups and drug dealing. Geographic and ethnographic concepts and methods were employed, using participant observation, interviews and analysis of secondary data on health.

RESULTS: Within the favelas, mortality rates from homicide were equivalent to, or lower than, the rest of the city, although they were considerably higher in areas surrounding the favelas, especially in areas where there was conflict between armed rival gangs.

CONCLUSIONS: The presence of trafficking crews and turf war in strategic areas of the city increases homicide rates and promotes the “ecology of danger” in these areas.}, } @article {pmid24789073, year = {2014}, author = {Adams, DC}, title = {A generalized K statistic for estimating phylogenetic signal from shape and other high-dimensional multivariate data.}, journal = {Systematic biology}, volume = {63}, number = {5}, pages = {685-697}, doi = {10.1093/sysbio/syu030}, pmid = {24789073}, issn = {1076-836X}, mesh = {Animals ; Classification/*methods ; Data Interpretation, Statistical ; Head/*anatomy & histology ; *Models, Statistical ; Multivariate Analysis ; Phylogeny ; Urodela/*anatomy & histology/*classification ; }, abstract = {Phylogenetic signal is the tendency for closely related species to display similar trait values due to their common ancestry. Several methods have been developed for quantifying phylogenetic signal in univariate traits and for sets of traits treated simultaneously, and the statistical properties of these approaches have been extensively studied. However, methods for assessing phylogenetic signal in high-dimensional multivariate traits like shape are less well developed, and their statistical performance is not well characterized. In this article, I describe a generalization of the K statistic of Blomberg et al. that is useful for quantifying and evaluating phylogenetic signal in highly dimensional multivariate data. The method (K(mult)) is found from the equivalency between statistical methods based on covariance matrices and those based on distance matrices. Using computer simulations based on Brownian motion, I demonstrate that the expected value of K(mult) remains at 1.0 as trait variation among species is increased or decreased, and as the number of trait dimensions is increased. By contrast, estimates of phylogenetic signal found with a squared-change parsimony procedure for multivariate data change with increasing trait variation among species and with increasing numbers of trait dimensions, confounding biological interpretations. I also evaluate the statistical performance of hypothesis testing procedures based on K(mult) and find that the method displays appropriate Type I error and high statistical power for detecting phylogenetic signal in high-dimensional data. Statistical properties of K(mult) were consistent for simulations using bifurcating and random phylogenies, for simulations using different numbers of species, for simulations that varied the number of trait dimensions, and for different underlying models of trait covariance structure. Overall these findings demonstrate that K(mult) provides a useful means of evaluating phylogenetic signal in high-dimensional multivariate traits. Finally, I illustrate the utility of the new approach by evaluating the strength of phylogenetic signal for head shape in a lineage of Plethodon salamanders.}, } @article {pmid24782441, year = {2014}, author = {Roux, J and Privman, E and Moretti, S and Daub, JT and Robinson-Rechavi, M and Keller, L}, title = {Patterns of positive selection in seven ant genomes.}, journal = {Molecular biology and evolution}, volume = {31}, number = {7}, pages = {1661-1685}, pmid = {24782441}, issn = {1537-1719}, mesh = {Animals ; Ants/classification/*genetics ; Databases, Genetic ; Evolution, Molecular ; *Genes, Mitochondrial ; Genome, Insect ; Insect Proteins/*genetics ; Multigene Family ; Phylogeny ; Selection, Genetic ; }, abstract = {The evolution of ants is marked by remarkable adaptations that allowed the development of very complex social systems. To identify how ant-specific adaptations are associated with patterns of molecular evolution, we searched for signs of positive selection on amino-acid changes in proteins. We identified 24 functional categories of genes which were enriched for positively selected genes in the ant lineage. We also reanalyzed genome-wide data sets in bees and flies with the same methodology to check whether positive selection was specific to ants or also present in other insects. Notably, genes implicated in immunity were enriched for positively selected genes in the three lineages, ruling out the hypothesis that the evolution of hygienic behaviors in social insects caused a major relaxation of selective pressure on immune genes. Our scan also indicated that genes implicated in neurogenesis and olfaction started to undergo increased positive selection before the evolution of sociality in Hymenoptera. Finally, the comparison between these three lineages allowed us to pinpoint molecular evolution patterns that were specific to the ant lineage. In particular, there was ant-specific recurrent positive selection on genes with mitochondrial functions, suggesting that mitochondrial activity was improved during the evolution of this lineage. This might have been an important step toward the evolution of extreme lifespan that is a hallmark of ants.}, } @article {pmid24780230, year = {2014}, author = {Bruggemann, R and Scherb, H and Schramm, KW and Cok, I and Voigt, K}, title = {CombiSimilarity, an innovative method to compare environmental and health data sets with different attribute sizes example: eighteen Organochlorine Pesticides in soil and human breast milk samples.}, journal = {Ecotoxicology and environmental safety}, volume = {105}, number = {}, pages = {29-35}, doi = {10.1016/j.ecoenv.2014.03.031}, pmid = {24780230}, issn = {1090-2414}, mesh = {*Data Interpretation, Statistical ; Environmental Monitoring/*methods ; Humans ; Hydrocarbons, Chlorinated/*analysis ; Milk, Human/*chemistry ; Models, Statistical ; Soil/*chemistry ; Soil Pollutants/*analysis ; }, abstract = {Human health and the health of the environment have entwined. In this paper we underpin this position by presenting a modeling approach named CombiSimilarity, which has been developed by the first author in the software tool PyHasse comprising a wide variety of partial ordering tools. A case study of 18 Organochlorine Pesticides (OCPs) detected in soil as well as in human breast milk samples in the Taurus Mountains in Turkey is carried out. Seven soil samples and 44 breast milk samples were measured. We seek to answer the question whether the contamination pattern in breast milk is associated with the contamination pattern in soil by studying the mutual quantitative relationships of the chemicals involved. We could demonstrate that there is a similarity with respect to the concentration profiles between the soil and breast milk pollution. Therefore the hypothesis may be formulated that the concentrations of chemicals in the milk samples are strongly related to the soil contamination. This supports the concept that soil could be a surrogate for human exposure at background locations.}, } @article {pmid24779578, year = {2014}, author = {Le Cornu, E and Kittinger, JN and Koehn, JZ and Finkbeiner, EM and Crowder, LB}, title = {Current practice and future prospects for social data in coastal and ocean planning.}, journal = {Conservation biology : the journal of the Society for Conservation Biology}, volume = {28}, number = {4}, pages = {902-911}, doi = {10.1111/cobi.12310}, pmid = {24779578}, issn = {1523-1739}, mesh = {Biodiversity ; Conservation of Natural Resources/*methods/trends ; Data Collection ; Decision Support Techniques ; Humans ; *Oceans and Seas ; }, abstract = {Coastal and ocean planning comprises a broad field of practice. The goals, political processes, and approaches applied to planning initiatives may vary widely. However, all planning processes ultimately require adequate information on both the biophysical and social attributes of a planning region. In coastal and ocean planning practice, there are well-established methods to assess biophysical attributes; however, less is understood about the role and assessment of social data. We conducted the first global assessment of the incorporation of social data in coastal and ocean planning. We drew on a comprehensive review of planning initiatives and a survey of coastal and ocean practitioners. There was significantly more incorporation of social data in multiuse versus conservation-oriented planning. Practitioners engaged a wide range of social data, including governance, economic, and cultural attributes of planning regions and human impacts data. Less attention was given to ecosystem services and social-ecological linkages, both of which could improve coastal and ocean planning practice. Although practitioners recognize the value of social data, little funding is devoted to its collection and incorporation in plans. Increased capacity and sophistication in acquiring critical social and ecological data for planning is necessary to develop plans for more resilient coastal and ocean ecosystems and communities. We suggest that improving social data monitoring, and in particular spatial social data, to complement biophysical data, is necessary for providing holistic information for decision-support tools and other methods. Moving beyond people as impacts to people as beneficiaries, through ecosystem services assessments, holds much potential to better incorporate the tenets of ecosystem-based management into coastal and ocean planning by providing targets for linked biodiversity conservation and human welfare outcomes.}, } @article {pmid24773483, year = {2014}, author = {Tetko, IV and Schramm, KW and Knepper, T and Peijnenburg, WJ and Hendriks, AJ and Navas, JM and Nicholls, IA and Oberg, T and Todeschini, R and Schlosser, E and Brandmaier, S}, title = {Experimental and theoretical studies in the EU FP7 Marie Curie Initial Training Network Project, Environmental ChemOinformatics (ECO).}, journal = {Alternatives to laboratory animals : ATLA}, volume = {42}, number = {1}, pages = {7-11}, doi = {10.1177/026119291404200103}, pmid = {24773483}, issn = {0261-1929}, mesh = {Animal Use Alternatives ; Animals ; Computational Biology/*education ; Ecology/*education ; European Union ; Humans ; Informatics/*education ; Models, Theoretical ; Quantitative Structure-Activity Relationship ; Toxicity Tests ; }, } @article {pmid24771343, year = {2014}, author = {Jonker, MJ and de Leeuw, WC and Marinković, M and Wittink, FR and Rauwerda, H and Bruning, O and Ensink, WA and Fluit, AC and Boel, CH and Jong, Md and Breit, TM}, title = {Absence/presence calling in microarray-based CGH experiments with non-model organisms.}, journal = {Nucleic acids research}, volume = {42}, number = {11}, pages = {e94}, pmid = {24771343}, issn = {1362-4962}, mesh = {Animals ; Comparative Genomic Hybridization/*methods ; Data Interpretation, Statistical ; *Genomic Structural Variation ; Genomics ; High-Throughput Nucleotide Sequencing ; Models, Genetic ; Oligonucleotide Array Sequence Analysis/*methods ; Oligonucleotide Probes ; Staphylococcus aureus/genetics ; }, abstract = {Structural variations in genomes are commonly studied by (micro)array-based comparative genomic hybridization. The data analysis methods to infer copy number variation in model organisms (human, mouse) are established. In principle, the procedures are based on signal ratios between test and reference samples and the order of the probe targets in the genome. These procedures are less applicable to experiments with non-model organisms, which frequently comprise non-sequenced genomes with an unknown order of probe targets. We therefore present an additional analysis approach, which does not depend on the structural information of a reference genome, and quantifies the presence or absence of a probe target in an unknown genome. The principle is that intensity values of target probes are compared with the intensities of negative-control probes and positive-control probes from a control hybridization, to determine if a probe target is absent or present. In a test, analyzing the genome content of a known bacterial strain: Staphylococcus aureus MRSA252, this approach proved to be successful, demonstrated by receiver operating characteristic area under the curve values larger than 0.9995. We show its usability in various applications, such as comparing genome content and validating next-generation sequencing reads from eukaryotic non-model organisms.}, } @article {pmid24768450, year = {2015}, author = {Ramachandra, TV and Bharath, AH and Sowmyashree, MV}, title = {Monitoring urbanization and its implications in a mega city from space: spatiotemporal patterns and its indicators.}, journal = {Journal of environmental management}, volume = {148}, number = {}, pages = {67-81}, doi = {10.1016/j.jenvman.2014.02.015}, pmid = {24768450}, issn = {1095-8630}, mesh = {*Cities ; *Conservation of Natural Resources ; Environment ; Environmental Monitoring/*methods ; Geographic Information Systems ; Humans ; India ; Spatio-Temporal Analysis ; Urbanization/*trends ; }, abstract = {Rapid and invasive urbanization has been associated with depletion of natural resources (vegetation and water resources), which in turn deteriorates the landscape structure and conditions in the local environment. Rapid increase in population due to the migration from rural areas is one of the critical issues of the urban growth. Urbanisation in India is drastically changing the land cover and often resulting in the sprawl. The sprawl regions often lack basic amenities such as treated water supply, sanitation, etc. This necessitates regular monitoring and understanding of the rate of urban development in order to ensure the sustenance of natural resources .Urban sprawl is the extent of urbanization which leads to the development of urban forms with the destruction of ecology and natural landforms. The rate of change of land use and extent of urban sprawl can be efficiently visualized and modelled with the help of geoinformatics. The knowledge of urban area, especially the growth magnitude, shape geometry, and spatial pattern is essential to understand the growth and characteristics of urbanization process. Urban pattern, shape and growth can be quantified using spatial metrics. This communication quantifies the urbanisation and associated growth pattern in Delhi. Spatial data of four decades were analysed to understand land over and land use dynamics. Further the region was divided into 4 zones and into circles of 1 km incrementing radius to understand and quantify the local spatial changes. Results of the landscape metrics indicate that the urban center was highly aggregated and the outskirts and the buffer regions were in the verge of aggregating urban patches. Shannon's Entropy index clearly depicted the outgrowth of sprawl areas in different zones of Delhi.}, } @article {pmid24763610, year = {2014}, author = {Heymans, JJ and Coll, M and Libralato, S and Morissette, L and Christensen, V}, title = {Global patterns in ecological indicators of marine food webs: a modelling approach.}, journal = {PloS one}, volume = {9}, number = {4}, pages = {e95845}, pmid = {24763610}, issn = {1932-6203}, mesh = {Algorithms ; Animal Distribution ; Animals ; Aquatic Organisms/physiology ; *Computer Simulation ; Data Interpretation, Statistical ; Fisheries ; *Food Chain ; Humans ; }, abstract = {BACKGROUND: Ecological attributes estimated from food web models have the potential to be indicators of good environmental status given their capabilities to describe redundancy, food web changes, and sensitivity to fishing. They can be used as a baseline to show how they might be modified in the future with human impacts such as climate change, acidification, eutrophication, or overfishing.

METHODOLOGY: In this study ecological network analysis indicators of 105 marine food web models were tested for variation with traits such as ecosystem type, latitude, ocean basin, depth, size, time period, and exploitation state, whilst also considering structural properties of the models such as number of linkages, number of living functional groups or total number of functional groups as covariate factors.

PRINCIPAL FINDINGS: Eight indicators were robust to model construction: relative ascendency; relative overhead; redundancy; total systems throughput (TST); primary production/TST; consumption/TST; export/TST; and total biomass of the community. Large-scale differences were seen in the ecosystems of the Atlantic and Pacific Oceans, with the Western Atlantic being more complex with an increased ability to mitigate impacts, while the Eastern Atlantic showed lower internal complexity. In addition, the Eastern Pacific was less organised than the Eastern Atlantic although both of these systems had increased primary production as eastern boundary current systems. Differences by ecosystem type highlighted coral reefs as having the largest energy flow and total biomass per unit of surface, while lagoons, estuaries, and bays had lower transfer efficiencies and higher recycling. These differences prevailed over time, although some traits changed with fishing intensity. Keystone groups were mainly higher trophic level species with mostly top-down effects, while structural/dominant groups were mainly lower trophic level groups (benthic primary producers such as seagrass and macroalgae, and invertebrates). Keystone groups were prevalent in estuarine or small/shallow systems, and in systems with reduced fishing pressure. Changes to the abundance of key functional groups might have significant implications for the functioning of ecosystems and should be avoided through management.

CONCLUSION/SIGNIFICANCE: Our results provide additional understanding of patterns of structural and functional indicators in different ecosystems. Ecosystem traits such as type, size, depth, and location need to be accounted for when setting reference levels as these affect absolute values of ecological indicators. Therefore, establishing absolute reference values for ecosystem indicators may not be suitable to the ecosystem-based, precautionary approach. Reference levels for ecosystem indicators should be developed for individual ecosystems or ecosystems with the same typologies (similar location, ecosystem type, etc.) and not benchmarked against all other ecosystems.}, } @article {pmid24762576, year = {2014}, author = {Helfrich, EJ and Reiter, S and Piel, J}, title = {Recent advances in genome-based polyketide discovery.}, journal = {Current opinion in biotechnology}, volume = {29}, number = {}, pages = {107-115}, doi = {10.1016/j.copbio.2014.03.004}, pmid = {24762576}, issn = {1879-0429}, mesh = {Animals ; Biosynthetic Pathways/genetics ; Computational Biology ; Data Mining ; Genomics/*methods ; High-Throughput Nucleotide Sequencing ; Humans ; Polyketides/*metabolism ; }, abstract = {Polyketides are extraordinarily diverse secondary metabolites of great pharmacological value and with interesting ecological functions. The post-genomics era has led to fundamental changes in natural product research by inverting the workflow of secondary metabolite discovery. As opposed to traditional bioactivity-guided screenings, genome mining is an in silico method to screen and analyze sequenced genomes for natural product biosynthetic gene clusters. Since genes for known compounds can be recognized at the early computational stage, genome mining presents an opportunity for dereplication. This review highlights recent progress in bioinformatics, pathway engineering and chemical analytics to extract the biosynthetic secrets hidden in the genome of both well-known natural product sources as well as previously neglected bacteria.}, } @article {pmid24761614, year = {2014}, author = {Liu, B and Tan, Y and Gan, ML and Zhou, HX and Wang, YG and Ping, YH and Li, B and Yang, ZY and Xiao, CL}, title = {[Identification of tetracenomycin X from a marine-derived Saccharothrix sp. guided by genes sequence analysis].}, journal = {Yao xue xue bao = Acta pharmaceutica Sinica}, volume = {49}, number = {2}, pages = {230-236}, pmid = {24761614}, issn = {0513-4870}, mesh = {Actinomycetales/*chemistry/genetics ; Anti-Bacterial Agents/chemistry/*isolation & purification/pharmacology ; Antineoplastic Agents/chemistry/*isolation & purification/pharmacology ; Benzodiazepinones/chemistry/isolation & purification/pharmacology ; Cell Line, Tumor ; Data Mining/methods ; Drug Resistance, Bacterial ; Enterococcus faecalis/drug effects ; Fermentation ; Genomics ; Humans ; Inhibitory Concentration 50 ; Marine Biology ; Methicillin-Resistant Staphylococcus aureus/drug effects ; Microbial Sensitivity Tests ; Molecular Structure ; Naphthacenes/chemistry/isolation & purification/pharmacology ; Phylogeny ; Staphylococcus epidermidis/drug effects ; }, abstract = {The crude extracts of the fermentation broth from a marine sediment-derived actinomycete strain, Saccharothrix sp. 10-10, showed significant antibacterial activities against drug-resistant pathogens. A genome-mining PCR-based experiment targeting the genes encoding key enzymes involved in the biosynthesis of secondary metabolites indicated that the strain 10-10 showed the potential to produce tetracenomycin-like compounds. Further chemical investigation of the cultures of this strain led to the identification of two antibiotics, including a tetracenomycin (Tcm) analogs, Tcm X (1), and a tomaymycin derivative, oxotomaymycin (2). Their structures were identified by spectroscopic data analysis, including UV, 1D-NMR, 2D-NMR and MS spectra. Tcm X (1) showed moderate antibacterial activities against a number of drug-resistant pathogens, including methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant Enterococci (VRE) pathogens, with the MIC values in the range of 32-64 microg x mL(-1). In addition, 1 also displayed significant cytotoxic activities against human cancer cell lines, including HL60 (leukemia), HepG2 (liver), and MCF-7 (breast) with the IC 50 values of 5.1, 9.7 and 18.0 micromol x L(-1), respectively. Guided by the PCR-based gene sequence analysis, Tcm X (1) and oxotomaymycin (2) were identified from the genus of Saccharothrix and their 13C NMR data were correctly assigned on the basis of 2D NMR spectroscopic data analysis for the first time.}, } @article {pmid24759834, year = {2014}, author = {Venteris, ER and May, CJ}, title = {Cost-effective mapping of benthic habitats in inland reservoirs through split-beam sonar, indicator kriging, and historical geologic data.}, journal = {PloS one}, volume = {9}, number = {4}, pages = {e95940}, pmid = {24759834}, issn = {1932-6203}, mesh = {Animals ; Conservation of Natural Resources ; *Ecosystem ; Fishes ; Geographic Information Systems ; *Geologic Sediments/chemistry ; *Lakes ; Ohio ; }, abstract = {Because bottom substrate composition is an important control on the temporal and spatial location of the aquatic community, accurate maps of benthic habitats of inland lakes and reservoirs provide valuable information to managers, recreational users, and scientists. Therefore, we collected vertical, split-beam sonar data (roughness [E1], hardness [E2], and bathymetry) and sediment samples to make such maps. Statistical calibration between sonar parameters and sediment classes was problematic because the E1:E2 ratios for soft (muck and clay) sediments overlapped a lower and narrower range for hard (gravel) substrates. Thus, we used indicator kriging (IK) to map the probability that unsampled locations did not contain coarse sediments. To overcome the calibration issue we tested proxies for the natural processes and anthropogenic history of the reservoir as potential predictive variables. Of these, a geologic map proved to be the most useful. The central alluvial valley and mudflats contained mainly muck and organic-rich clays. The surrounding glacial till and shale bedrock uplands contained mainly poorly sorted gravels. Anomalies in the sonar data suggested that the organic-rich sediments also contained trapped gases, presenting additional interpretive issues for the mapping. We extended the capability of inexpensive split-beam sonar units through the incorporation of historic geologic maps and other records as well as validation with dredge samples. Through the integration of information from multiple data sets, were able to objectively identify bottom substrate and provide reservoir users with an accurate map of available benthic habitat.}, } @article {pmid24759094, year = {2014}, author = {Roy, RS and Price, DC and Schliep, A and Cai, G and Korobeynikov, A and Yoon, HS and Yang, EC and Bhattacharya, D}, title = {Single cell genome analysis of an uncultured heterotrophic stramenopile.}, journal = {Scientific reports}, volume = {4}, number = {}, pages = {4780}, pmid = {24759094}, issn = {2045-2322}, mesh = {Biodiversity ; Computational Biology ; *Genomics ; Phylogeny ; Proteome ; Proteomics ; RNA, Ribosomal, 18S/genetics ; Seawater ; *Single-Cell Analysis ; Stramenopiles/classification/*genetics/metabolism ; }, abstract = {A broad swath of eukaryotic microbial biodiversity cannot be cultivated in the lab and is therefore inaccessible to conventional genome-wide comparative methods. One promising approach to study these lineages is single cell genomics (SCG), whereby an individual cell is captured from nature and genome data are produced from the amplified total DNA. Here we tested the efficacy of SCG to generate a draft genome assembly from a single sample, in this case a cell belonging to the broadly distributed MAST-4 uncultured marine stramenopiles. Using de novo gene prediction, we identified 6,996 protein-encoding genes in the MAST-4 genome. This genetic inventory was sufficient to place the cell within the ToL using multigene phylogenetics and provided preliminary insights into the complex evolutionary history of horizontal gene transfer (HGT) in the MAST-4 lineage.}, } @article {pmid24755991, year = {2014}, author = {Boenigk, J and Beisser, D and Zimmermann, S and Bock, C and Jakobi, J and Grabner, D and Groβmann, L and Rahmann, S and Barcikowski, S and Sures, B}, title = {Effects of silver nitrate and silver nanoparticles on a planktonic community: general trends after short-term exposure.}, journal = {PloS one}, volume = {9}, number = {4}, pages = {e95340}, pmid = {24755991}, issn = {1932-6203}, mesh = {Cell Count ; *Environmental Exposure ; Metal Nanoparticles/toxicity/ultrastructure ; Molecular Sequence Annotation ; Particle Size ; Plankton/*drug effects/genetics/*growth & development ; Sequence Analysis, DNA ; Silver/*toxicity ; Silver Nitrate/*toxicity ; Spectrum Analysis ; Time Factors ; Transcriptome/genetics ; Water/chemistry ; }, abstract = {Among metal pollutants silver ions are one of the most toxic forms, and have thus been assigned to the highest toxicity class. Its toxicity to a wide range of microorganisms combined with its low toxicity to humans lead to the development of a wealth of silver-based products in many bactericidal applications accounting to more than 1000 nano-technology-based consumer products. Accordingly, silver is a widely distributed metal in the environment originating from its different forms of application as metal, salt and nanoparticle. A realistic assessment of silver nanoparticle toxicity in natural waters is, however, problematic and needs to be linked to experimental approaches. Here we apply metatranscriptome sequencing allowing for elucidating reactions of whole communities present in a water sample to stressors. We compared the toxicity of ionic silver and ligand-free silver nanoparticles by short term exposure on a natural community of aquatic microorganisms. We analyzed the effects of the treatments on metabolic pathways and species composition on the eukaryote metatranscriptome level in order to describe immediate molecular responses of organisms using a community approach. We found significant differences between the samples treated with 5 µg/L AgNO3 compared to the controls, but no significant differences in the samples treated with AgNP compared to the control samples. Statistical analysis yielded 126 genes (KO-IDs) with significant differential expression with a false discovery rate (FDR) <0.05 between the control (KO) and AgNO3 (NO3) groups. A KEGG pathway enrichment analysis showed significant results with a FDR below 0.05 for pathways related to photosynthesis. Our study therefore supports the view that ionic silver rather than silver nanoparticles are responsible for silver toxicity. Nevertheless, our results highlight the strength of metatranscriptome approaches for assessing metal toxicity on aquatic communities.}, } @article {pmid24752974, year = {2014}, author = {Kim, JY and Lee, JL}, title = {Multipurpose assessment for the quantification of Vibrio spp. and total bacteria in fish and seawater using multiplex real-time polymerase chain reaction.}, journal = {Journal of the science of food and agriculture}, volume = {94}, number = {13}, pages = {2807-2817}, pmid = {24752974}, issn = {1097-0010}, mesh = {Animals ; Aquaculture ; Atlantic Ocean ; Colony Count, Microbial ; Conserved Sequence ; DNA, Bacterial/metabolism ; DNA, Ribosomal/metabolism ; Databases, Nucleic Acid ; Delaware ; Fishes/*microbiology ; Food Inspection/*methods ; Gram-Negative Bacteria/classification/growth & development/*isolation & purification/metabolism ; Gram-Positive Bacteria/classification/growth & development/*isolation & purification/metabolism ; Molecular Typing ; Multiplex Polymerase Chain Reaction ; RNA, Ribosomal, 16S/metabolism ; Real-Time Polymerase Chain Reaction ; Seafood/economics/*microbiology ; Seawater/*microbiology ; Vibrio/classification/growth & development/*isolation & purification/metabolism ; Vibrio parahaemolyticus/classification/growth & development/isolation & purification/metabolism ; Vibrio vulnificus/classification/growth & development/isolation & purification/metabolism ; }, abstract = {BACKGROUND: This study describes the first multiplex real-time polymerase chain reaction assay developed, as a multipurpose assessment, for the simultaneous quantification of total bacteria and three Vibrio spp. (V. parahaemolyticus, V. vulnificus and V. anguillarum) in fish and seawater. The consumption of raw finfish as sushi or sashimi has been increasing the chance of Vibrio outbreaks in consumers. Freshness and quality of fishery products also depend on the total bacterial populations present.

RESULTS: The detection sensitivity of the specific targets for the multiplex assay was 1 CFU mL⁻¹ in pure culture and seawater, and 10 CFU g⁻¹ in fish. While total bacterial counts by the multiplex assay were similar to those obtained by cultural methods, the levels of Vibrio detected by the multiplex assay were generally higher than by cultural methods of the same populations. Among the natural samples without Vibrio spp. inoculation, eight out of 10 seawater and three out of 20 fish samples were determined to contain Vibrio spp.

CONCLUSION: Our data demonstrate that this multiplex assay could be useful for the rapid detection and quantification of Vibrio spp. and total bacteria as a multipurpose tool for surveillance of fish and water quality as well as diagnostic method.}, } @article {pmid24748384, year = {2014}, author = {Schilling, MP and Wolf, PG and Duffy, AM and Rai, HS and Rowe, CA and Richardson, BA and Mock, KE}, title = {Genotyping-by-sequencing for Populus population genomics: an assessment of genome sampling patterns and filtering approaches.}, journal = {PloS one}, volume = {9}, number = {4}, pages = {e95292}, pmid = {24748384}, issn = {1932-6203}, mesh = {Genome, Plant ; *Genotype ; Populus/*genetics ; }, abstract = {Continuing advances in nucleotide sequencing technology are inspiring a suite of genomic approaches in studies of natural populations. Researchers are faced with data management and analytical scales that are increasing by orders of magnitude. With such dramatic advances comes a need to understand biases and error rates, which can be propagated and magnified in large-scale data acquisition and processing. Here we assess genomic sampling biases and the effects of various population-level data filtering strategies in a genotyping-by-sequencing (GBS) protocol. We focus on data from two species of Populus, because this genus has a relatively small genome and is emerging as a target for population genomic studies. We estimate the proportions and patterns of genomic sampling by examining the Populus trichocarpa genome (Nisqually-1), and demonstrate a pronounced bias towards coding regions when using the methylation-sensitive ApeKI restriction enzyme in this species. Using population-level data from a closely related species (P. tremuloides), we also investigate various approaches for filtering GBS data to retain high-depth, informative SNPs that can be used for population genetic analyses. We find a data filter that includes the designation of ambiguous alleles resulted in metrics of population structure and Hardy-Weinberg equilibrium that were most consistent with previous studies of the same populations based on other genetic markers. Analyses of the filtered data (27,910 SNPs) also resulted in patterns of heterozygosity and population structure similar to a previous study using microsatellites. Our application demonstrates that technically and analytically simple approaches can readily be developed for population genomics of natural populations.}, } @article {pmid24748132, year = {2014}, author = {Shen, YY and Dai, K and Cao, X and Murphy, RW and Shen, XJ and Zhang, YP}, title = {The updated phylogenies of the phasianidae based on combined data of nuclear and mitochondrial DNA.}, journal = {PloS one}, volume = {9}, number = {4}, pages = {e95786}, pmid = {24748132}, issn = {1932-6203}, mesh = {Animals ; Coturnix ; *DNA, Mitochondrial ; Datasets as Topic ; Galliformes/*classification/*genetics ; Molecular Sequence Data ; *Phylogeny ; *Retroelements ; }, abstract = {The phylogenetic relationships of species in the Phasianidae, Order Galliformes, are the object of intensive study. However, convergent morphological evolution and rapid species radiation result in much ambiguity in the group. Further, matrilineal (mtDNA) genealogies conflict with trees based on nuclear DNA retrotransposable elements. Herein, we analyze 39 nearly complete mitochondrial genomes (three new) and up to seven nuclear DNA segments. We combine these multiple unlinked, more informative genetic markers to infer historical relationships of the major groups of phasianids. The nuclear DNA tree is largely congruent with the tree derived from mt genomes. However, branching orders of mt/nuclear trees largely conflict with those based on retrotransposons. For example, Gallus/Bambusicola/Francolinus forms the sister-group of Coturnix/Alectoris in the nuclear/mtDNA trees, yet the tree based on retrotransposable elements roots the former at the base of the tree and not with the latter. Further, while peafowls cluster with Gallus/Coturnix in the mt tree, they root at the base of the phasianids following Gallus in the tree based on retrotransposable elements. The conflicting branch orders in nuclear/mtDNA and retrotransposons-based trees in our study reveal the complex topology of the Phasianidae.}, } @article {pmid24742908, year = {2014}, author = {Fresia, P and Silver, M and Mastrangelo, T and De Azeredo-Espin, AM and Lyra, ML}, title = {Applying spatial analysis of genetic and environmental data to predict connection corridors to the New World screwworm populations in South America.}, journal = {Acta tropica}, volume = {138 Suppl}, number = {}, pages = {S34-41}, doi = {10.1016/j.actatropica.2014.04.003}, pmid = {24742908}, issn = {1873-6254}, mesh = {Animal Migration ; Animals ; Biota ; Diptera/*classification/*genetics/growth & development ; Geographic Information Systems ; Models, Statistical ; *Phylogeography ; South America ; Spatial Analysis ; }, abstract = {The myiasis causing New World screwworm (NWS) fly is responsible for substantial losses to livestock breeders in the Americas. Due to the negative impact of the NWS fly in animal health, expansion of successful NWS fly eradication programmes is under discussion. However, the effects of geography and environmental diversity on NWS population structure and migration patterns need to be assessed before any political decision is made to implement such a programme. We present a GIS tool to construct potential connection corridors among sampling localities based on genetic and environmental data. We integrate, through a home-made python script, a friction raster based on a Maxent niche model and the pairwise ΦST statistic. Among 38 NWS fly sampling localities from South America, we find a high population connectivity among the sampling localities from the south of the Amazon region. The region along the Atlantic Ocean was identified as the most probable migration corridor between the north (NAG) and the south (SAG) of the Amazon region. The approach highlighted previously undetected population structure within NAG showing low to medium connectivity through the Andes, correlating with current understanding of NWS fly migration in South America. Also, the approach is flexible, allowing future research to incorporate other niche simulations and genetic differentiation metrics. With this flexibility, the tool could become part of any AW-IPM by helping to target regions for control.}, } @article {pmid24736744, year = {2014}, author = {Wald, DM and Jacobson, SK}, title = {A multivariate model of stakeholder preference for lethal cat management.}, journal = {PloS one}, volume = {9}, number = {4}, pages = {e93118}, pmid = {24736744}, issn = {1932-6203}, mesh = {Animals ; *Attitude ; Cats ; *Culture ; Environment ; Humans ; *Models, Theoretical ; }, abstract = {Identifying stakeholder beliefs and attitudes is critical for resolving management conflicts. Debate over outdoor cat management is often described as a conflict between two groups, environmental advocates and animal welfare advocates, but little is known about the variables predicting differences among these critical stakeholder groups. We administered a mail survey to randomly selected stakeholders representing both of these groups (n=1,596) in Florida, where contention over the management of outdoor cats has been widespread. We used a structural equation model to evaluate stakeholder intention to support non-lethal management. The cognitive hierarchy model predicted that values influenced beliefs, which predicted general and specific attitudes, which in turn, influenced behavioral intentions. We posited that specific attitudes would mediate the effect of general attitudes, beliefs, and values on management support. Model fit statistics suggested that the final model fit the data well (CFI=0.94, RMSEA=0.062). The final model explained 74% of the variance in management support, and positive attitudes toward lethal management (humaneness) had the largest direct effect on management support. Specific attitudes toward lethal management and general attitudes toward outdoor cats mediated the relationship between positive (p<0.05) and negative cat-related impact beliefs (p<0.05) and support for management. These results supported the specificity hypothesis and the use of the cognitive hierarchy to assess stakeholder intention to support non-lethal cat management. Our findings suggest that stakeholders can simultaneously perceive both positive and negative beliefs about outdoor cats, which influence attitudes toward and support for non-lethal management.}, } @article {pmid24735398, year = {2014}, author = {Pédron, J and Mondy, S and des Essarts, YR and Van Gijsegem, F and Faure, D}, title = {Genomic and metabolic comparison with Dickeya dadantii 3937 reveals the emerging Dickeya solani potato pathogen to display distinctive metabolic activities and T5SS/T6SS-related toxin repertoire.}, journal = {BMC genomics}, volume = {15}, number = {}, pages = {283}, pmid = {24735398}, issn = {1471-2164}, mesh = {Bacterial Toxins/*genetics/metabolism ; Clustered Regularly Interspaced Short Palindromic Repeats ; Computational Biology ; DNA Transposable Elements ; Enterobacteriaceae/*genetics/*metabolism ; Gene Expression Regulation, Bacterial ; Gene Order ; Gene Regulatory Networks ; Genes, Bacterial ; Genetic Variation ; Genome, Bacterial ; Genomic Islands ; *Genomics ; Host-Pathogen Interactions ; *Metabolomics ; Plant Diseases/microbiology ; Solanum tuberosum/*microbiology ; Virulence/genetics ; Virulence Factors/genetics ; }, abstract = {BACKGROUND: The pectinolytic enterobacteria of the Pectobacterium and Dickeya genera are causative agents of maceration-associated diseases affecting a wide variety of crops and ornamentals. For the past decade, the emergence of a novel species D. solani was observed in potato fields in Europe and the Mediterranean basin. The purpose of this study is to search by comparative genomics the genetic traits that could be distinctive to other Dickeya species and be involved in D. solani adaptation to the potato plant host.

RESULTS: D. solani 3337 exhibits a 4.9 Mb circular genome that is characterized by a low content in mobile elements with the identification of only two full length insertion sequences. A genomic comparison with the deeply-annotated model D. dadantii 3937 strain was performed. While a large majority of Dickeya virulence genes are shared by both strains, a few hundreds genes of D. solani 3337, mostly regrouped in 25 genomic regions, are distinctive to D. dadantii 3937. These genomic regions are present in the other available draft genomes of D. solani strains and interestingly some of them were not found in the sequenced genomes of the other Dickeya species. These genomic regions regroup metabolic genes and are often accompanied by genes involved in transport systems. A metabolic analysis correlated some metabolic genes with distinctive functional traits of both D. solani 3337 and D. dadantii 3937. Three identified D. solani genomic regions also regroup NRPS/PKS encoding genes. In addition, D. solani encodes a distinctive arsenal of T5SS and T6SS-related toxin-antitoxin systems. These genes may contribute to bacteria-bacteria interactions and to the fitness of D. solani to the plant environment.

CONCLUSIONS: This study highlights the genomic specific traits of the emerging pathogen D. solani and will provide the basis for studying those that are involved in the successful adaptation of this emerging pathogen to the potato plant host.}, } @article {pmid24728855, year = {2014}, author = {Pennell, MW and Eastman, JM and Slater, GJ and Brown, JW and Uyeda, JC and FitzJohn, RG and Alfaro, ME and Harmon, LJ}, title = {geiger v2.0: an expanded suite of methods for fitting macroevolutionary models to phylogenetic trees.}, journal = {Bioinformatics (Oxford, England)}, volume = {30}, number = {15}, pages = {2216-2218}, doi = {10.1093/bioinformatics/btu181}, pmid = {24728855}, issn = {1367-4811}, mesh = {Algorithms ; Bayes Theorem ; *Biological Evolution ; Computational Biology/*methods ; Likelihood Functions ; *Models, Biological ; *Phylogeny ; *Programming Languages ; }, abstract = {SUMMARY: Phylogenetic comparative methods are essential for addressing evolutionary hypotheses with interspecific data. The scale and scope of such data have increased dramatically in the past few years. Many existing approaches are either computationally infeasible or inappropriate for data of this size. To address both of these problems, we present geiger v2.0, a complete overhaul of the popular R package geiger. We have reimplemented existing methods with more efficient algorithms and have developed several new approaches for accomodating heterogeneous models and data types.

 This R package is available on the CRAN repository http://cran.r-project.org/web/packages/geiger/. All source code is also available on github http://github.com/mwpennell/geiger-v2. geiger v2.0 depends on the ape package.

CONTACT: mwpennell@gmail.com

SUPPLEMENTARY INFORMATION:  Supplementary data are available at Bioinformatics online.}, } @article {pmid24727806, year = {2014}, author = {Jones, HE and Hickman, M and Welton, NJ and De Angelis, D and Harris, RJ and Ades, AE}, title = {Recapture or precapture? Fallibility of standard capture-recapture methods in the presence of referrals between sources.}, journal = {American journal of epidemiology}, volume = {179}, number = {11}, pages = {1383-1393}, pmid = {24727806}, issn = {1476-6256}, support = {RP-DG-0610-10055/DH_/Department of Health/United Kingdom ; G0802413/MRC_/Medical Research Council/United Kingdom ; U105260566/MRC_/Medical Research Council/United Kingdom ; MC_U105260556/MRC_/Medical Research Council/United Kingdom ; MR/K023233/1/MRC_/Medical Research Council/United Kingdom ; G1000021/MRC_/Medical Research Council/United Kingdom ; MC_U145079307/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Bias ; Data Collection ; *Data Interpretation, Statistical ; England/epidemiology ; *Epidemiologic Research Design ; Humans ; Linear Models ; *Models, Statistical ; *Population Density ; *Referral and Consultation ; Substance-Related Disorders/epidemiology ; }, abstract = {Capture-recapture methods, largely developed in ecology, are now commonly used in epidemiology to adjust for incomplete registries and to estimate the size of difficult-to-reach populations such as problem drug users. Overlapping lists of individuals in the target population, taken from administrative data sources, are considered analogous to overlapping "captures" of animals. Log-linear models, incorporating interaction terms to account for dependencies between sources, are used to predict the number of unobserved individuals and, hence, the total population size. A standard assumption to ensure parameter identifiability is that the highest-order interaction term is 0. We demonstrate that, when individuals are referred directly between sources, this assumption will often be violated, and the standard modeling approach may lead to seriously biased estimates. We refer to such individuals as having been "precaptured," rather than truly recaptured. Although sometimes an alternative identifiable log-linear model could accommodate the referral structure, this will not always be the case. Further, multiple plausible models may fit the data equally well but provide widely varying estimates of the population size. We demonstrate an alternative modeling approach, based on an interpretable parameterization and driven by careful consideration of the relationships between the sources, and we make recommendations for capture-recapture in practice.}, } @article {pmid24727042, year = {2014}, author = {Lenzen, M and Geschke, A and Wiedmann, T and Lane, J and Anderson, N and Baynes, T and Boland, J and Daniels, P and Dey, C and Fry, J and Hadjikakou, M and Kenway, S and Malik, A and Moran, D and Murray, J and Nettleton, S and Poruschi, L and Reynolds, C and Rowley, H and Ugon, J and Webb, D and West, J}, title = {Compiling and using input-output frameworks through collaborative virtual laboratories.}, journal = {The Science of the total environment}, volume = {485-486}, number = {}, pages = {241-251}, doi = {10.1016/j.scitotenv.2014.03.062}, pmid = {24727042}, issn = {1879-1026}, mesh = {Australia ; *Cooperative Behavior ; Databases, Factual ; Environment ; *Laboratories ; *Software ; *User-Computer Interface ; *Workflow ; }, abstract = {Compiling, deploying and utilising large-scale databases that integrate environmental and economic data have traditionally been labour- and cost-intensive processes, hindered by the large amount of disparate and misaligned data that must be collected and harmonised. The Australian Industrial Ecology Virtual Laboratory (IELab) is a novel, collaborative approach to compiling large-scale environmentally extended multi-region input-output (MRIO) models. The utility of the IELab product is greatly enhanced by avoiding the need to lock in an MRIO structure at the time the MRIO system is developed. The IELab advances the idea of the "mother-daughter" construction principle, whereby a regionally and sectorally very detailed "mother" table is set up, from which "daughter" tables are derived to suit specific research questions. By introducing a third tier - the "root classification" - IELab users are able to define their own mother-MRIO configuration, at no additional cost in terms of data handling. Customised mother-MRIOs can then be built, which maximise disaggregation in aspects that are useful to a family of research questions. The second innovation in the IELab system is to provide a highly automated collaborative research platform in a cloud-computing environment, greatly expediting workflows and making these computational benefits accessible to all users. Combining these two aspects realises many benefits. The collaborative nature of the IELab development project allows significant savings in resources. Timely deployment is possible by coupling automation procedures with the comprehensive input from multiple teams. User-defined MRIO tables, coupled with high performance computing, mean that MRIO analysis will be useful and accessible for a great many more research applications than would otherwise be possible. By ensuring that a common set of analytical tools such as for hybrid life-cycle assessment is adopted, the IELab will facilitate the harmonisation of fragmented, dispersed and misaligned raw data for the benefit of all interested parties.}, } @article {pmid24725914, year = {2014}, author = {Kaier, K and Lambert, ML and Frank, UK and Vach, W and Wolkewitz, M and Tacconelli, E and Rello, J and Theuretzbacher, U and Martin, M}, title = {Impact of availability of guidelines and active surveillance in reducing the incidence of ventilator-associated pneumonia in Europe and worldwide.}, journal = {BMC infectious diseases}, volume = {14}, number = {}, pages = {199}, pmid = {24725914}, issn = {1471-2334}, mesh = {Europe/epidemiology ; Female ; Global Health ; Guideline Adherence/*statistics & numerical data ; Health Care Surveys ; Humans ; Incidence ; Male ; Pneumonia, Ventilator-Associated/epidemiology/*prevention & control ; *Population Surveillance ; *Practice Guidelines as Topic ; Practice Patterns, Physicians'/*statistics & numerical data ; Surveys and Questionnaires ; }, abstract = {BACKGROUND: To analyse whether the availability of written standards for management of mechanically ventilated patients and/or the existence of a surveillance system for cases of ventilation-associated pneumonia (VAP) are positively associated with compliance with 6 well-established VAP prevention measures.

METHODS: Ecological study based on responses to an online-questionnaire completed by 1730 critical care physicians. Replies were received from 77 different countries, of which the majority, i.e. 1351, came from 36 European countries.

RESULTS: On a cross-country level, compliance with VAP prevention measures is higher in countries with a large number of prevention standards and/or VAP surveillance systems in place at ICU level., Likewise, implementation of standards and VAP surveillance systems has a significant impact on self-reported total compliance with VAP prevention measures (both p < 0.001). Moreover, predictions of overall prevention measure compliance show the effect size of the availability of written standards and existence of surveillance system. For instance, a female physician with 10 years of experience in critical care working in a 15-bed ICU in France has a predicted baseline level of VAP prevention measure compliance of 63 per cent. This baseline level increases by 9.5 percentage points (p < 0.001) if a written clinical VAP prevention standard is available in the ICU, and by another 4 percentage points (p < 0.001) if complemented by a VAP surveillance system.

CONCLUSIONS: The existence of written standards for management of mechanically ventilated patients in an ICU and the availability of VAP surveillance systems have shown to be positively associated with compliance with VAP prevention measures and should be fostered on a policy level.}, } @article {pmid24725361, year = {2014}, author = {Lessio, F and Tota, F and Alma, A}, title = {Tracking the dispersion of Scaphoideus titanus Ball (Hemiptera: Cicadellidae) from wild to cultivated grapevine: use of a novel mark-capture technique.}, journal = {Bulletin of entomological research}, volume = {104}, number = {4}, pages = {432-443}, doi = {10.1017/S0007485314000030}, pmid = {24725361}, issn = {1475-2670}, mesh = {Albumins ; Animal Distribution/*physiology ; Animals ; Biomarkers/*metabolism ; Caseins ; *Ecosystem ; Enzyme-Linked Immunosorbent Assay ; Female ; Geographic Information Systems ; Hemiptera/*physiology ; Male ; Regression Analysis ; Specimen Handling/*methods ; Vitis/*parasitology ; }, abstract = {The dispersion of Scaphoideus titanus Ball adults from wild to cultivated grapevines was studied using a novel mark-capture technique. The crowns of wild grapevines located at a distance from vineyards ranging from 5 to 330 m were sprayed with a water solution of either cow milk (marker: casein) or chicken egg whites (marker: albumin) and insects captured in yellow sticky traps placed on the canopy of grapes were analyzed via an indirect ELISA for markers' identification. Data were subject to exponential regression as a function of distance from wild grapevine, and to spatial interpolation (Inverse Distance Weighted and Kernel interpolation with barriers) using ArcGIS Desktop 10.1 software. The influence of rainfall and time elapsed after marking on markers' effectiveness, and the different dispersion of males and females were studied with regression analyses. Of a total of 5417 insects analyzed, 43% were positive to egg; whereas 18% of 536 tested resulted marked with milk. No influence of rainfall or time elapsed was observed for egg, whereas milk was affected by time. Males and females showed no difference in dispersal. Marked adults decreased exponentially along with distance from wild grapevine and up to 80% of them were captured within 30 m. However, there was evidence of long-range dispersal up to 330 m. The interpolation maps showed a clear clustering of marked S. titanus close to the treated wild grapevine, and the pathways to the vineyards did not always seem to go along straight lines but mainly along ecological corridors. S. titanus adults are therefore capable of dispersing from wild to cultivated grapevine, and this may affect pest management strategies.}, } @article {pmid24389655, year = {2014}, author = {Gregori, J and Salicrú, M and Domingo, E and Sanchez, A and Esteban, JI and Rodríguez-Frías, F and Quer, J}, title = {Inference with viral quasispecies diversity indices: clonal and NGS approaches.}, journal = {Bioinformatics (Oxford, England)}, volume = {30}, number = {8}, pages = {1104-1111}, doi = {10.1093/bioinformatics/btt768}, pmid = {24389655}, issn = {1367-4811}, mesh = {Computational Biology ; *Genetic Variation ; Hepacivirus/*genetics ; *High-Throughput Nucleotide Sequencing ; RNA, Viral/genetics ; Sequence Analysis, RNA ; }, abstract = {UNLABELLED: Given the inherent dynamics of a viral quasispecies, we are often interested in the comparison of diversity indices of sequential samples of a patient, or in the comparison of diversity indices of virus in groups of patients in a treated versus control design. It is then important to make sure that the diversity measures from each sample may be compared with no bias and within a consistent statistical framework. In the present report, we review some indices often used as measures for viral quasispecies complexity and provide means for statistical inference, applying procedures taken from the ecology field. In particular, we examine the Shannon entropy and the mutation frequency, and we discuss the appropriateness of different normalization methods of the Shannon entropy found in the literature. By taking amplicons ultra-deep pyrosequencing (UDPS) raw data as a surrogate of a real hepatitis C virus viral population, we study through in-silico sampling the statistical properties of these indices under two methods of viral quasispecies sampling, classical cloning followed by Sanger sequencing (CCSS) and next-generation sequencing (NGS) such as UDPS. We propose solutions specific to each of the two sampling methods-CCSS and NGS-to guarantee statistically conforming conclusions as free of bias as possible.

CONTACT: josep.gregori@gmail.com Supplementary information: Supplementary data are available at Bioinformatics online.}, } @article {pmid24389654, year = {2014}, author = {Valle, M and Schabauer, H and Pacher, C and Stockinger, H and Stamatakis, A and Robinson-Rechavi, M and Salamin, N}, title = {Optimization strategies for fast detection of positive selection on phylogenetic trees.}, journal = {Bioinformatics (Oxford, England)}, volume = {30}, number = {8}, pages = {1129-1137}, pmid = {24389654}, issn = {1367-4811}, mesh = {Algorithms ; Codon ; Computational Biology ; *Evolution, Molecular ; Likelihood Functions ; *Phylogeny ; *Selection, Genetic ; *Software ; }, abstract = {MOTIVATION: The detection of positive selection is widely used to study gene and genome evolution, but its application remains limited by the high computational cost of existing implementations. We present a series of computational optimizations for more efficient estimation of the likelihood function on large-scale phylogenetic problems. We illustrate our approach using the branch-site model of codon evolution.

RESULTS: We introduce novel optimization techniques that substantially outperform both CodeML from the PAML package and our previously optimized sequential version SlimCodeML. These techniques can also be applied to other likelihood-based phylogeny software. Our implementation scales well for large numbers of codons and/or species. It can therefore analyse substantially larger datasets than CodeML. We evaluated FastCodeML on different platforms and measured average sequential speedups of FastCodeML (single-threaded) versus CodeML of up to 5.8, average speedups of FastCodeML (multi-threaded) versus CodeML on a single node (shared memory) of up to 36.9 for 12 CPU cores, and average speedups of the distributed FastCodeML versus CodeML of up to 170.9 on eight nodes (96 CPU cores in total).

ftp://ftp.vital-it.ch/tools/FastCodeML/ CONTACT: selectome@unil.ch or nicolas.salamin@unil.ch.}, } @article {pmid24722744, year = {2013}, author = {Finck Barboza, C and Monteiro, SM and Barradas, SC and Sarmiento, OL and Rios, P and Ramirez, A and Mahecha, MP and Pratt, M}, title = {Physical activity, nutrition and behavior change in Latin America: a systematic review.}, journal = {Global health promotion}, volume = {20}, number = {4 Suppl}, pages = {65-81}, doi = {10.1177/1757975913502240}, pmid = {24722744}, issn = {1757-9767}, mesh = {Adolescent ; Adult ; Chronic Disease/*prevention & control ; Databases, Bibliographic ; *Diet ; Female ; *Health Behavior ; Humans ; Latin America ; Male ; *Motor Activity ; Young Adult ; }, abstract = {Physical activity (PA) and nutrition are key health behaviors underlying the design and implementation of prevention strategies for non-communicable diseases (NCDs) in Latin America. Nevertheless, research still reports low prevalence of PA and fruit and vegetable consumption throughout the region. This paper aims at reviewing the ways in which models of behavior change theory have been applied in study development and implementation regarding nutrition and PA in Latin America. In August 2011 we conducted a systematic literature review of the behavior change studies that targeted such NCDs risk factors published until then. Out of 4279 surveyed abstracts, only 29 corresponded to articles that met our inclusion criteria. Twenty-six articles reported the application of behavior change theory, with the trans-theoretical model (n = 12) being the most frequently used. Other theories and models included the socio-ecological model (n = 4), cognitive theory (n = 3), social cognitive theory (n = 2) and theories related to health education and counseling (n = 5). Based on this review, we recommend that the application of behavior change theory be explicitly reported in Latin American peer-reviewed articles, and that outcome evaluations include behavior change constructs so as to better assess their contribution to the effectiveness of nutrition and PA interventions in the region. Furthermore, we state the need for a better understanding of the behavior change mechanisms that may be specific to the Latin American context.}, } @article {pmid24722365, year = {2014}, author = {Qi, H and Olson, CA and Wu, NC and Ke, R and Loverdo, C and Chu, V and Truong, S and Remenyi, R and Chen, Z and Du, Y and Su, SY and Al-Mawsawi, LQ and Wu, TT and Chen, SH and Lin, CY and Zhong, W and Lloyd-Smith, JO and Sun, R}, title = {A quantitative high-resolution genetic profile rapidly identifies sequence determinants of hepatitis C viral fitness and drug sensitivity.}, journal = {PLoS pathogens}, volume = {10}, number = {4}, pages = {e1004064}, pmid = {24722365}, issn = {1553-7374}, support = {R25 CA098010/CA/NCI NIH HHS/United States ; P30CA016042/CA/NCI NIH HHS/United States ; AI078133/AI/NIAID NIH HHS/United States ; P30AI028697/AI/NIAID NIH HHS/United States ; R25 CA 098010/CA/NCI NIH HHS/United States ; P30 CA016042/CA/NCI NIH HHS/United States ; R21 AI078133/AI/NIAID NIH HHS/United States ; P30 AI028697/AI/NIAID NIH HHS/United States ; }, mesh = {Carbamates ; Cell Line ; *Drug Resistance, Viral/drug effects/genetics ; *Gene Expression Profiling ; *Genetic Fitness ; Hepacivirus/*physiology ; *Hepatitis C/drug therapy/genetics/metabolism/pathology ; Humans ; Imidazoles/*pharmacology ; Pyrrolidines ; Valine/analogs & derivatives ; Viral Nonstructural Proteins/genetics/metabolism ; *Virus Replication/drug effects/genetics ; }, abstract = {Widely used chemical genetic screens have greatly facilitated the identification of many antiviral agents. However, the regions of interaction and inhibitory mechanisms of many therapeutic candidates have yet to be elucidated. Previous chemical screens identified Daclatasvir (BMS-790052) as a potent nonstructural protein 5A (NS5A) inhibitor for Hepatitis C virus (HCV) infection with an unclear inhibitory mechanism. Here we have developed a quantitative high-resolution genetic (qHRG) approach to systematically map the drug-protein interactions between Daclatasvir and NS5A and profile genetic barriers to Daclatasvir resistance. We implemented saturation mutagenesis in combination with next-generation sequencing technology to systematically quantify the effect of every possible amino acid substitution in the drug-targeted region (domain IA of NS5A) on replication fitness and sensitivity to Daclatasvir. This enabled determination of the residues governing drug-protein interactions. The relative fitness and drug sensitivity profiles also provide a comprehensive reference of the genetic barriers for all possible single amino acid changes during viral evolution, which we utilized to predict clinical outcomes using mathematical models. We envision that this high-resolution profiling methodology will be useful for next-generation drug development to select drugs with higher fitness costs to resistance, and also for informing the rational use of drugs based on viral variant spectra from patients.}, } @article {pmid24719854, year = {2014}, author = {D'Argenio, V and Casaburi, G and Precone, V and Salvatore, F}, title = {Comparative metagenomic analysis of human gut microbiome composition using two different bioinformatic pipelines.}, journal = {BioMed research international}, volume = {2014}, number = {}, pages = {325340}, pmid = {24719854}, issn = {2314-6141}, mesh = {Bacteria/classification/*genetics ; Computational Biology/*methods ; Gastrointestinal Tract/microbiology ; High-Throughput Nucleotide Sequencing ; Humans ; Metagenome ; *Metagenomics ; Microbiota/*genetics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Technological advances in next-generation sequencing-based approaches have greatly impacted the analysis of microbial community composition. In particular, 16S rRNA-based methods have been widely used to analyze the whole set of bacteria present in a target environment. As a consequence, several specific bioinformatic pipelines have been developed to manage these data. MetaGenome Rapid Annotation using Subsystem Technology (MG-RAST) and Quantitative Insights Into Microbial Ecology (QIIME) are two freely available tools for metagenomic analyses that have been used in a wide range of studies. Here, we report the comparative analysis of the same dataset with both QIIME and MG-RAST in order to evaluate their accuracy in taxonomic assignment and in diversity analysis. We found that taxonomic assignment was more accurate with QIIME which, at family level, assigned a significantly higher number of reads. Thus, QIIME generated a more accurate BIOM file, which in turn improved the diversity analysis output. Finally, although informatics skills are needed to install QIIME, it offers a wide range of metrics that are useful for downstream applications and, not less important, it is not dependent on server times.}, } @article {pmid24719265, year = {2015}, author = {Keutmann, MK and Moore, SL and Savitt, A and Gur, RC}, title = {Generating an item pool for translational social cognition research: methodology and initial validation.}, journal = {Behavior research methods}, volume = {47}, number = {1}, pages = {228-234}, doi = {10.3758/s13428-014-0464-0}, pmid = {24719265}, issn = {1554-3528}, support = {R01-MH060722/MH/NIMH NIH HHS/United States ; R01-MH084856/MH/NIMH NIH HHS/United States ; }, mesh = {Adult ; Aged ; Audiovisual Aids/standards ; Behavioral Research/methods ; Child ; *Cognition ; Databases, Factual ; *Expressed Emotion ; Humans ; Neuropsychological Tests/standards ; Psychometrics/instrumentation/methods ; Reproducibility of Results ; *Social Behavior ; }, abstract = {Existing sets of social and emotional stimuli suitable for social cognition research are limited in many ways, including size, unimodal stimulus delivery, and restriction to major universal emotions. Existing measures of social cognition could be improved by taking advantage of item response theory and adaptive testing technology to develop instruments that obtain more efficient measures of multimodal social cognition. However, for this to be possible, large pools of emotional stimuli must be obtained and validated. We present the development of a large, high-quality multimedia stimulus set produced by professional adult and child actors (ages 5 to 74) containing both visual and vocal emotional expressions. We obtained over 74,000 audiovisual recordings of a wide array of emotional and social behaviors, including the main universal emotions (happiness, sadness, anger, fear, disgust, and surprise), as well as more complex social expressions (pride, affection, sarcasm, jealousy, and shame). The actors generated a high quantity of technically superior, ecologically valid stimuli that were digitized, archived, and rated for accuracy and intensity of expressions. A subset of these facial and vocal expressions of emotion and social behavior were submitted for quantitative ratings to generate parameters for validity and discriminability. These stimuli are suitable for affective neuroscience-based psychometric tests, functional neuroimaging, and social cognitive rehabilitation programs. The purposes of this report are to describe the method of obtaining and validating this database and to make it accessible to the scientific community. We invite all those interested in participating in the use and validation of these stimuli to access them at www.med.upenn.edu/bbl/actors/index.shtml .}, } @article {pmid24717283, year = {2014}, author = {Ozdogan, M}, title = {A practical and automated approach to large area forest disturbance mapping with remote sensing.}, journal = {PloS one}, volume = {9}, number = {4}, pages = {e78438}, pmid = {24717283}, issn = {1932-6203}, mesh = {Automation ; *Forests ; *Geographic Information Systems ; Geography ; ROC Curve ; Remote Sensing Technology/*methods ; Time Factors ; Wisconsin ; }, abstract = {In this paper, I describe a set of procedures that automate forest disturbance mapping using a pair of Landsat images. The approach is built on the traditional pair-wise change detection method, but is designed to extract training data without user interaction and uses a robust classification algorithm capable of handling incorrectly labeled training data. The steps in this procedure include: i) creating masks for water, non-forested areas, clouds, and cloud shadows; ii) identifying training pixels whose value is above or below a threshold defined by the number of standard deviations from the mean value of the histograms generated from local windows in the short-wave infrared (SWIR) difference image; iii) filtering the original training data through a number of classification algorithms using an n-fold cross validation to eliminate mislabeled training samples; and finally, iv) mapping forest disturbance using a supervised classification algorithm. When applied to 17 Landsat footprints across the U.S. at five-year intervals between 1985 and 2010, the proposed approach produced forest disturbance maps with 80 to 95% overall accuracy, comparable to those obtained from traditional approaches to forest change detection. The primary sources of mis-classification errors included inaccurate identification of forests (errors of commission), issues related to the land/water mask, and clouds and cloud shadows missed during image screening. The approach requires images from the peak growing season, at least for the deciduous forest sites, and cannot readily distinguish forest harvest from natural disturbances or other types of land cover change. The accuracy of detecting forest disturbance diminishes with the number of years between the images that make up the image pair. Nevertheless, the relatively high accuracies, little or no user input needed for processing, speed of map production, and simplicity of the approach make the new method especially practical for forest cover change analysis over very large regions.}, } @article {pmid24714108, year = {2014}, author = {Zhukovsky, M and Varaksin, A and Pakholkina, O}, title = {Statistical analysis of observational study of the influence of radon and other risk factors on lung cancer incidence.}, journal = {Radiation protection dosimetry}, volume = {160}, number = {1-3}, pages = {108-111}, doi = {10.1093/rpd/ncu069}, pmid = {24714108}, issn = {1742-3406}, mesh = {Adult ; Aged ; Aged, 80 and over ; Air Pollutants, Radioactive/*adverse effects ; Case-Control Studies ; Cohort Studies ; Data Interpretation, Statistical ; Dose-Response Relationship, Radiation ; Female ; Follow-Up Studies ; Humans ; Incidence ; Lung Neoplasms/*epidemiology/etiology ; Male ; Middle Aged ; Mining ; Neoplasms, Radiation-Induced/*epidemiology/etiology ; Occupational Exposure/*adverse effects ; Prognosis ; Radon/*adverse effects ; Risk Factors ; Russia/epidemiology ; Uranium/adverse effects ; }, abstract = {An observational study is a type of epidemiological study when the researcher observes the situation but is not able to change the conditions of the experiment. The statistical analysis of the observational study of the population of Lermontov city (North Caucasus) was conducted. In the initial group, there were 121 people with lung cancer diagnosis and 196 people of the control group. Statistical analysis was performed only for men (95 cases and 76 controls). The use of logistic regression with correction on age gives the value of odds ratio 1.95 (0.87÷4.37; 90% CI) per 100 working levels per month of combined (occupational and domestic) radon exposure. It was demonstrated that chronic lung diseases are an additional risk factor for uranium miners but it is not a significant risk factor for general population. Thus, the possibility of obtaining statistically reliable results in the observational studies when using the correct methods of analysis is demonstrated.}, } @article {pmid24709341, year = {2014}, author = {Sevini, F and Giuliani, C and Vianello, D and Giampieri, E and Santoro, A and Biondi, F and Garagnani, P and Passarino, G and Luiselli, D and Capri, M and Franceschi, C and Salvioli, S}, title = {mtDNA mutations in human aging and longevity: controversies and new perspectives opened by high-throughput technologies.}, journal = {Experimental gerontology}, volume = {56}, number = {}, pages = {234-244}, doi = {10.1016/j.exger.2014.03.022}, pmid = {24709341}, issn = {1873-6815}, mesh = {Age Factors ; Aging/*genetics/metabolism ; Computational Biology ; DNA Damage ; DNA Mutational Analysis ; DNA, Mitochondrial/*genetics/metabolism ; Epigenesis, Genetic ; Gene Expression Regulation ; Genotype ; *High-Throughput Nucleotide Sequencing/methods ; Humans ; Longevity/*genetics ; *Mutation ; Phenotype ; }, abstract = {The last 30 years of research greatly contributed to shed light on the role of mitochondrial DNA (mtDNA) variability in aging, although contrasting results have been reported, mainly due to bias regarding the population size and stratification, and to the use of analysis methods (haplogroup classification) that resulted to be not sufficiently adequate to grasp the complexity of the phenomenon. A 5-years European study (the GEHA EU project) collected and analyzed data on mtDNA variability on an unprecedented number of long-living subjects (enriched for longevity genes) and a comparable number of controls (matched for gender and ethnicity) in Europe. This very large study allowed a reappraisal of the role of both the inherited and the somatic mtDNA variability in aging, as an association with longevity emerged only when mtDNA variants in OXPHOS complexes co-occurred. Moreover, the availability of data from both nuclear and mitochondrial genomes on a large number of subjects paves the way for an evaluation at a very large scale of the epistatic interactions at a higher level of complexity. This scenario is expected to be even more clarified in the next future with the use of next generation sequencing (NGS) techniques, which are becoming applicable to evaluate mtDNA variability and, then, new mathematical/bioinformatic analysis methods are urgently needed. Recent advances of association studies on age-related diseases and mtDNA variability will also be discussed in this review, taking into account the bias hidden by population stratification. Finally, very recent findings in terms of mtDNA heteroplasmy (i.e. the coexistence of wild type and mutated copies of mtDNA) and aging as well as mitochondrial epigenetic mechanisms will also be discussed.}, } @article {pmid24703617, year = {2014}, author = {Moon-van der Staay, SY and van der Staay, GW and Michalowski, T and Jouany, JP and Pristas, P and Javorský, P and Kišidayová, S and Varadyova, Z and McEwan, NR and Newbold, CJ and van Alen, T and de Graaf, R and Schmid, M and Huynen, MA and Hackstein, JH}, title = {The symbiotic intestinal ciliates and the evolution of their hosts.}, journal = {European journal of protistology}, volume = {50}, number = {2}, pages = {166-173}, doi = {10.1016/j.ejop.2014.01.004}, pmid = {24703617}, issn = {1618-0429}, mesh = {Animals ; Biodiversity ; Ciliophora/*classification/genetics/*physiology ; Feces/parasitology ; Intestines/*parasitology ; *Phylogeny ; RNA, Ribosomal, 18S/genetics ; Rumen/parasitology ; Ruminants/*classification/genetics/*parasitology ; }, abstract = {The evolution of sophisticated differentiations of the gastro-intestinal tract enabled herbivorous mammals to digest dietary cellulose and hemicellulose with the aid of a complex anaerobic microbiota. Distinctive symbiotic ciliates, which are unique to this habitat, are the largest representatives of this microbial community. Analyses of a total of 484 different 18S rRNA genes show that extremely complex, but related ciliate communities can occur in the rumen of cattle, sheep, goats and red deer (301 sequences). The communities in the hindgut of equids (Equus caballus, Equus quagga), and elephants (Elephas maximus, Loxodonta africanus; 162 sequences), which are clearly distinct from the ruminant ciliate biota, exhibit a much higher diversity than anticipated on the basis of their morphology. All these ciliates from the gastro-intestinal tract constitute a monophyletic group, which consists of two major taxa, i.e. Vestibuliferida and Entodiniomorphida. The ciliates from the evolutionarily older hindgut fermenters exhibit a clustering that is specific for higher taxa of their hosts, as extant species of horse and zebra on the one hand, and Africa and Indian elephant on the other hand, share related ciliates. The evolutionary younger ruminants altogether share the various entodiniomorphs and the vestibuliferids from ruminants.}, } @article {pmid24698953, year = {2014}, author = {Winegard, T and Herr, J and Mena, C and Lee, B and Dinov, I and Bird, D and Bernards, M and Hobel, S and Van Valkenburgh, B and Toga, A and Fudge, D}, title = {Coiling and maturation of a high-performance fibre in hagfish slime gland thread cells.}, journal = {Nature communications}, volume = {5}, number = {}, pages = {3534}, pmid = {24698953}, issn = {2041-1723}, support = {P41 EB015922/EB/NIBIB NIH HHS/United States ; 5P41EB015922-16/EB/NIBIB NIH HHS/United States ; }, mesh = {Animal Structures/*cytology/metabolism/ultrastructure ; Animals ; Fish Proteins/metabolism/*ultrastructure ; Hagfishes/cytology/*metabolism/ultrastructure ; Intermediate Filament Proteins/*chemistry/metabolism/ultrastructure ; }, abstract = {The defensive slime of hagfishes contains thousands of intermediate filament protein threads that are manufactured within specialized gland thread cells. The material properties of these threads rival those of spider dragline silks, which makes them an ideal model for biomimetic efforts to produce sustainable protein materials, yet how the thread is produced and organized within the cell is not well understood. Here we show how changes in nuclear morphology, size and position can explain the three-dimensional pattern of thread coiling in gland thread cells, and how the ultrastructure of the thread changes as very young thread cells develop into large cells with fully mature coiled threads. Our model provides an explanation for the complex process of thread assembly and organization that has fascinated and perplexed biologists for over a century, and provides valuable insights for the quest to manufacture high-performance biomimetic protein materials.}, } @article {pmid24698885, year = {2014}, author = {Gillespie, AI and Gooding, W and Rosen, C and Gartner-Schmidt, J}, title = {Correlation of VHI-10 to voice laboratory measurements across five common voice disorders.}, journal = {Journal of voice : official journal of the Voice Foundation}, volume = {28}, number = {4}, pages = {440-448}, doi = {10.1016/j.jvoice.2013.10.023}, pmid = {24698885}, issn = {1873-4588}, mesh = {Adult ; Databases, Factual ; *Disability Evaluation ; Disabled Persons ; Female ; Humans ; Laryngeal Muscles/physiopathology ; Male ; Phonation/physiology ; Retrospective Studies ; *Severity of Illness Index ; Speech Acoustics ; Vocal Cord Paralysis/diagnosis/physiopathology ; Vocal Cords/physiopathology ; Voice/*physiology ; Voice Disorders/*diagnosis/*physiopathology ; }, abstract = {OBJECTIVE: To correlate change in Voice Handicap Index (VHI)-10 scores with corresponding voice laboratory measures across five voice disorders.

STUDY DESIGN: Retrospective study.

METHODS: One hundred fifty patients aged >18 years with primary diagnosis of vocal fold lesions, primary muscle tension dysphonia-1, atrophy, unilateral vocal fold paralysis (UVFP), and scar. For each group, participants with the largest change in VHI-10 between two periods (TA and TB) were selected. The dates of the VHI-10 values were linked to corresponding acoustic/aerodynamic and audio-perceptual measures. Change in voice laboratory values were analyzed for correlation with each other and with VHI-10.

RESULTS: VHI-10 scores were greater for patients with UVFP than other disorders. The only disorder-specific correlation between voice laboratory measure and VHI-10 was average phonatory airflow in speech for patients with UVFP. Average airflow in repeated phonemes was strongly correlated with average airflow in speech (r=0.75). Acoustic measures did not significantly change between time points.

CONCLUSIONS: The lack of correlations between the VHI-10 change scores and voice laboratory measures may be due to differing constructs of each measure; namely, handicap versus physiological function. Presuming corroboration between these measures may be faulty. Average airflow in speech may be the most ecologically valid measure for patients with UVFP. Although aerodynamic measures changed between the time points, acoustic measures did not. Correlations to VHI-10 and change between time points may be found with other acoustic measures.}, } @article {pmid24694827, year = {2014}, author = {Müller, B and Groscurth, S and Menzel, M and Rüping, BA and Twyman, RM and Prüfer, D and Noll, GA}, title = {Molecular and ultrastructural analysis of forisome subunits reveals the principles of forisome assembly.}, journal = {Annals of botany}, volume = {113}, number = {7}, pages = {1121-1137}, pmid = {24694827}, issn = {1095-8290}, mesh = {Amino Acid Sequence ; Computational Biology ; Fabaceae/chemistry/*genetics/metabolism ; Microscopy, Confocal ; Microscopy, Electron, Scanning ; Microscopy, Electron, Transmission ; Molecular Sequence Data ; Phylogeny ; Plant Proteins/*genetics/metabolism/*ultrastructure ; Sequence Alignment ; }, abstract = {BACKGROUND AND AIMS: Forisomes are specialized structural phloem proteins that mediate sieve element occlusion after wounding exclusively in papilionoid legumes, but most studies of forisome structure and function have focused on the Old World clade rather than the early lineages. A comprehensive phylogenetic, molecular, structural and functional analysis of forisomes from species covering a broad spectrum of the papilionoid legumes was therefore carried out, including the first analysis of Dipteryx panamensis forisomes, representing the earliest branch of the Papilionoideae lineage. The aim was to study the molecular, structural and functional conservation among forisomes from different tribes and to establish the roles of individual forisome subunits.

METHODS: Sequence analysis and bioinformatics were combined with structural and functional analysis of native forisomes and artificial forisome-like protein bodies, the latter produced by expressing forisome genes from different legumes in a heterologous background. The structure of these bodies was analysed using a combination of confocal laser scanning microscopy (CLSM), scanning electron microscopy (SEM) and transmission electron microscopy (TEM), and the function of individual subunits was examined by combinatorial expression, micromanipulation and light microscopy.

KEY RESULTS: Dipteryx panamensis native forisomes and homomeric protein bodies assembled from the single sieve element occlusion by forisome (SEO-F) subunit identified in this species were structurally and functionally similar to forisomes from the Old World clade. In contrast, homomeric protein bodies assembled from individual SEO-F subunits from Old World species yielded artificial forisomes differing in proportion to their native counterparts, suggesting that multiple SEO-F proteins are required for forisome assembly in these plants. Structural differences between Medicago truncatula native forisomes, homomeric protein bodies and heteromeric bodies containing all possible subunit combinations suggested that combinations of SEO-F proteins may fine-tune the geometric proportions and reactivity of forisomes.

CONCLUSIONS: It is concluded that forisome structure and function have been strongly conserved during evolution and that species-dependent subsets of SEO-F proteins may have evolved to fine-tune the structure of native forisomes.}, } @article {pmid24691166, year = {2014}, author = {Xu, Z and Hansen, MA and Hansen, LH and Jacquiod, S and Sørensen, SJ}, title = {Bioinformatic approaches reveal metagenomic characterization of soil microbial community.}, journal = {PloS one}, volume = {9}, number = {4}, pages = {e93445}, pmid = {24691166}, issn = {1932-6203}, mesh = {*Biodiversity ; Biomarkers ; Computational Biology/*methods ; Ecosystem ; Metabolomics/methods ; Metagenome ; Metagenomics/*methods ; Microbial Interactions ; Phylogeny ; *Soil Microbiology ; }, abstract = {As is well known, soil is a complex ecosystem harboring the most prokaryotic biodiversity on the Earth. In recent years, the advent of high-throughput sequencing techniques has greatly facilitated the progress of soil ecological studies. However, how to effectively understand the underlying biological features of large-scale sequencing data is a new challenge. In the present study, we used 33 publicly available metagenomes from diverse soil sites (i.e. grassland, forest soil, desert, Arctic soil, and mangrove sediment) and integrated some state-of-the-art computational tools to explore the phylogenetic and functional characterizations of the microbial communities in soil. Microbial composition and metabolic potential in soils were comprehensively illustrated at the metagenomic level. A spectrum of metagenomic biomarkers containing 46 taxa and 33 metabolic modules were detected to be significantly differential that could be used as indicators to distinguish at least one of five soil communities. The co-occurrence associations between complex microbial compositions and functions were inferred by network-based approaches. Our results together with the established bioinformatic pipelines should provide a foundation for future research into the relation between soil biodiversity and ecosystem function.}, } @article {pmid24690219, year = {2014}, author = {Kenall, A and Harold, S and Foote, C}, title = {An open future for ecological and evolutionary data?.}, journal = {BMC ecology}, volume = {14}, number = {}, pages = {10}, pmid = {24690219}, issn = {1472-6785}, mesh = {Biological Evolution ; *Databases, Factual ; Ecology ; Editorial Policies ; *Information Dissemination ; *Periodicals as Topic ; Research ; }, abstract = {As part of BioMed Central's open science mission, we are pleased to announce that two of our journals have integrated with the open data repository Dryad. Authors submitting their research to either BMC Ecology or BMC Evolutionary Biology will now have the opportunity to deposit their data directly into the Dryad archive and will receive a permanent, citable link to their dataset. Although this does not affect any of our current data deposition policies at these journals, we hope to encourage a more widespread adoption of open data sharing in the fields of ecology and evolutionary biology by facilitating this process for our authors. We also take this opportunity to discuss some of the wider issues that may concern researchers when making their data openly available. Although we offer a number of positive examples from different fields of biology, we also recognise that reticence to data sharing still exists, and that change must be driven from within research communities in order to create future science that is fit for purpose in the digital age. This editorial was published jointly in both BMC Ecology and BMC Evolutionary Biology.}, } @article {pmid24688116, year = {2014}, author = {Deelen, J and Beekman, M and Uh, HW and Broer, L and Ayers, KL and Tan, Q and Kamatani, Y and Bennet, AM and Tamm, R and Trompet, S and Guðbjartsson, DF and Flachsbart, F and Rose, G and Viktorin, A and Fischer, K and Nygaard, M and Cordell, HJ and Crocco, P and van den Akker, EB and Böhringer, S and Helmer, Q and Nelson, CP and Saunders, GI and Alver, M and Andersen-Ranberg, K and Breen, ME and van der Breggen, R and Caliebe, A and Capri, M and Cevenini, E and Collerton, JC and Dato, S and Davies, K and Ford, I and Gampe, J and Garagnani, P and de Geus, EJ and Harrow, J and van Heemst, D and Heijmans, BT and Heinsen, FA and Hottenga, JJ and Hofman, A and Jeune, B and Jonsson, PV and Lathrop, M and Lechner, D and Martin-Ruiz, C and Mcnerlan, SE and Mihailov, E and Montesanto, A and Mooijaart, SP and Murphy, A and Nohr, EA and Paternoster, L and Postmus, I and Rivadeneira, F and Ross, OA and Salvioli, S and Sattar, N and Schreiber, S and Stefánsson, H and Stott, DJ and Tiemeier, H and Uitterlinden, AG and Westendorp, RG and Willemsen, G and Samani, NJ and Galan, P and Sørensen, TI and Boomsma, DI and Jukema, JW and Rea, IM and Passarino, G and de Craen, AJ and Christensen, K and Nebel, A and Stefánsson, K and Metspalu, A and Magnusson, P and Blanché, H and Christiansen, L and Kirkwood, TB and van Duijn, CM and Franceschi, C and Houwing-Duistermaat, JJ and Slagboom, PE}, title = {Genome-wide association meta-analysis of human longevity identifies a novel locus conferring survival beyond 90 years of age.}, journal = {Human molecular genetics}, volume = {23}, number = {16}, pages = {4420-4432}, pmid = {24688116}, issn = {1460-2083}, support = {U01DK066134/DK/NIDDK NIH HHS/United States ; 084762/WT_/Wellcome Trust/United Kingdom ; NIMH U24 MH068457-06//PHS HHS/United States ; MR/J012165/1/MRC_/Medical Research Council/United Kingdom ; T32 HG002536/HG/NHGRI NIH HHS/United States ; R01D0042157-01A//PHS HHS/United States ; BB/F010966/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; MH081802/MH/NIMH NIH HHS/United States ; G0500997/MRC_/Medical Research Council/United Kingdom ; BB/I020748/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; P01AG08761/AG/NIA NIH HHS/United States ; 087436/WT_/Wellcome Trust/United Kingdom ; U41 HG007234/HG/NHGRI NIH HHS/United States ; G0601333/MRC_/Medical Research Council/United Kingdom ; 230374/ERC_/European Research Council/International ; MR/K006312/1/MRC_/Medical Research Council/United Kingdom ; MR/J50001X/1/MRC_/Medical Research Council/United Kingdom ; R124/0509/DMT_/The Dunhill Medical Trust/United Kingdom ; 085475/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Age Factors ; Aged ; Aged, 80 and over ; Cardiovascular Diseases/genetics ; Chromosome Mapping ; Chromosomes, Human, Pair 19 ; Chromosomes, Human, Pair 5 ; Female ; Genetic Loci/*physiology ; Genome-Wide Association Study ; Humans ; Hypertension/genetics ; Longevity/*genetics ; Male ; Phenotype ; Prospective Studies ; White People ; }, abstract = {The genetic contribution to the variation in human lifespan is ∼ 25%. Despite the large number of identified disease-susceptibility loci, it is not known which loci influence population mortality. We performed a genome-wide association meta-analysis of 7729 long-lived individuals of European descent (≥ 85 years) and 16 121 younger controls (<65 years) followed by replication in an additional set of 13 060 long-lived individuals and 61 156 controls. In addition, we performed a subset analysis in cases aged ≥ 90 years. We observed genome-wide significant association with longevity, as reflected by survival to ages beyond 90 years, at a novel locus, rs2149954, on chromosome 5q33.3 (OR = 1.10, P = 1.74 × 10(-8)). We also confirmed association of rs4420638 on chromosome 19q13.32 (OR = 0.72, P = 3.40 × 10(-36)), representing the TOMM40/APOE/APOC1 locus. In a prospective meta-analysis (n = 34 103), the minor allele of rs2149954 (T) on chromosome 5q33.3 associates with increased survival (HR = 0.95, P = 0.003). This allele has previously been reported to associate with low blood pressure in middle age. Interestingly, the minor allele (T) associates with decreased cardiovascular mortality risk, independent of blood pressure. We report on the first GWAS-identified longevity locus on chromosome 5q33.3 influencing survival in the general European population. The minor allele of this locus associates with low blood pressure in middle age, although the contribution of this allele to survival may be less dependent on blood pressure. Hence, the pleiotropic mechanisms by which this intragenic variation contributes to lifespan regulation have to be elucidated.}, } @article {pmid24684691, year = {2014}, author = {Judson, R and Houck, K and Martin, M and Knudsen, T and Thomas, RS and Sipes, N and Shah, I and Wambaugh, J and Crofton, K}, title = {In vitro and modelling approaches to risk assessment from the U.S. Environmental Protection Agency ToxCast programme.}, journal = {Basic & clinical pharmacology & toxicology}, volume = {115}, number = {1}, pages = {69-76}, doi = {10.1111/bcpt.12239}, pmid = {24684691}, issn = {1742-7843}, mesh = {Databases, Factual ; Humans ; Models, Biological ; No-Observed-Adverse-Effect Level ; Pharmacokinetics ; Risk Assessment ; Toxicity Tests/methods ; United States ; United States Environmental Protection Agency/*legislation & jurisprudence/*standards ; Xenobiotics/toxicity ; }, abstract = {A significant challenge in toxicology is the 'too many chemicals' problem. Human beings and environmental species are exposed to tens of thousands of chemicals, only a small percentage of which have been tested thoroughly using standard in vivo test methods. This study reviews several approaches that are being developed to deal with this problem by the U.S. Environmental Protection Agency, under the umbrella of the ToxCast programme (http://epa.gov/ncct/toxcast/). The overall approach is broken into seven tasks: (i) identifying biological pathways that, when perturbed, can lead to toxicity; (ii) developing high-throughput in vitro assays to test chemical perturbations of these pathways; (iii) identifying the universe of chemicals with likely human or ecological exposure; (iv) testing as many of these chemicals as possible in the relevant in vitro assays; (v) developing hazard models that take the results of these tests and identify chemicals as being potential toxicants; (vi) generating toxicokinetics data on these chemicals to predict the doses at which these hazard pathways would be activated; and (vii) developing exposure models to identify chemicals for which these hazardous dose levels could be achieved. This overall strategy is described and briefly illustrated with recent examples from the ToxCast programme.}, } @article {pmid24682889, year = {2014}, author = {Cardazone, G and U Sy, A and Chik, I and Corlew, LK}, title = {Mapping one strong 'Ohana: using network analysis and GIS to enhance the effectiveness of a statewide coalition to prevent child abuse and neglect.}, journal = {American journal of community psychology}, volume = {53}, number = {3-4}, pages = {346-356}, doi = {10.1007/s10464-014-9641-7}, pmid = {24682889}, issn = {1573-2770}, support = {U54 CA153499/CA/NCI NIH HHS/United States ; }, mesh = {Child ; Child Abuse/*prevention & control ; *Community Networks ; Cooperative Behavior ; *Geographic Information Systems ; Hawaii ; Health Promotion/*organization & administration ; Humans ; *Quality Improvement ; }, abstract = {Network analysis and GIS enable the presentation of meaningful data about organizational relationships and community characteristics, respectively. Together, these tools can provide a concrete representation of the ecological context in which coalitions operate, and may help coalitions identify opportunities for growth and enhanced effectiveness. This study uses network analysis and GIS mapping as part of an evaluation of the One Strong 'Ohana (OSO) campaign. The OSO campaign was launched in 2012 via a partnership between the Hawai'i Children's Trust Fund (HCTF) and the Joyful Heart Foundation. The OSO campaign uses a collaborative approach aimed at increasing public awareness of child maltreatment and protective factors that can prevent maltreatment, as well as enhancing the effectiveness of the HCTF Coalition. This study focuses on three elements of the OSO campaign evaluation: (1) Network analysis exploring the relationships between 24 active Coalition member organizations, (2) GIS mapping of responses to a randomized statewide phone survey (n = 1,450) assessing awareness of factors contributing to child maltreatment, and (3) Combined GIS maps and network data, illustrating opportunities for geographically-targeted coalition building and public awareness activities.}, } @article {pmid24680756, year = {2014}, author = {Peck, SL}, title = {Perspectives on why digital ecologies matter: combining population genetics and ecologically informed agent-based models with GIS for managing dipteran livestock pests.}, journal = {Acta tropica}, volume = {138 Suppl}, number = {}, pages = {S22-5}, doi = {10.1016/j.actatropica.2014.03.006}, pmid = {24680756}, issn = {1873-6254}, mesh = {Animals ; *Biota ; Computer Simulation ; Diptera/*classification/*growth & development ; Genetics, Population ; Geographic Information Systems ; Insect Control/*methods ; Livestock/*parasitology ; *Phylogeography ; }, abstract = {It is becoming clear that handling the inherent complexity found in ecological systems is an essential task for finding ways to control insect pests of tropical livestock such as tsetse flies, and old and new world screwworms. In particular, challenging multivalent management programs, such as Area Wide Integrated Pest Management (AW-IPM), face daunting problems of complexity at multiple spatial scales, ranging from landscape level processes to those of smaller scales such as the parasite loads of individual animals. Daunting temporal challenges also await resolution, such as matching management time frames to those found on ecological and even evolutionary temporal scales. How does one deal with representing processes with models that involve multiple spatial and temporal scales? Agent-based models (ABM), combined with geographic information systems (GIS), may allow for understanding, predicting and managing pest control efforts in livestock pests. This paper argues that by incorporating digital ecologies in our management efforts clearer and more informed decisions can be made. I also point out the power of these models in making better predictions in order to anticipate the range of outcomes possible or likely.}, } @article {pmid24680726, year = {2014}, author = {Savage, AE and Kiemnec-Tyburczy, KM and Ellison, AR and Fleischer, RC and Zamudio, KR}, title = {Conservation and divergence in the frog immunome: pyrosequencing and de novo assembly of immune tissue transcriptomes.}, journal = {Gene}, volume = {542}, number = {2}, pages = {98-108}, doi = {10.1016/j.gene.2014.03.051}, pmid = {24680726}, issn = {1879-0038}, mesh = {Animals ; Anura/genetics/metabolism/microbiology ; Costa Rica ; Evolution, Molecular ; Female ; Gene Ontology ; Genome/immunology ; High-Throughput Nucleotide Sequencing ; Immune System/*physiology ; Inflammation/genetics/immunology ; Intestines/immunology ; Male ; Muramidase/genetics/immunology ; Mycoses/microbiology/veterinary ; Panama ; Polymorphism, Single Nucleotide ; Proteins/*genetics/immunology ; Ranidae/*genetics/*immunology/microbiology ; Skin/immunology ; Spleen/immunology/physiology ; *Transcriptome ; }, abstract = {BACKGROUND: Frogs are a diverse group of vertebrates for which limited genomic resources are available. Natural frog populations face a multitude of threats, including habitat degradation, infectious disease, and environmental change. Characterizing the functional genomics of anuran tissues in general - and the immune system in particular - will enhance our knowledge of genetic and epigenetic responses to environmental threats and inform conservation and recovery efforts.

RESULTS: To increase the number of species with genomic datasets and characterize gene expression in immune-related tissues, we sequenced the transcriptomes of three tissues from two frogs (Espadarana prosoblepon and Lithobates yavapaiensis) on the Roche 454 GS FLX platform. Our sequencing produced 8881 E. prosoblepon and 5428 L. yavapaiensis annotated gene products after de novo assembly and Gene Ontology classification. Transcripts of the innate and acquired immune system were expressed in all three tissues. Inflammatory response and acquired immunity transcripts were significantly more diverged between E. prosoblepon and L. yavapaiensis compared to innate immunity and immune system development transcripts. Immune-related transcripts did not show an overall elevated rate of functional evolution, with the exception of glycosyl proteases, which include lysozymes, central bacterial and fungal-killing enzymes of the innate immune system.

CONCLUSIONS: The three frog transcriptomes provide more than 600 Mbp of new genomic data, and will serve as a valuable framework for future comparative studies of non-model anurans. Additionally, we show that immune gene divergence varies by functional group and that transcriptome studies can be useful in comparing rates of evolutionary change across gene families.}, } @article {pmid24678894, year = {2014}, author = {Wei, X and Ai, J and Deng, Y and Guan, X and Johnson, DR and Ang, CY and Zhang, C and Perkins, EJ}, title = {Identification of biomarkers that distinguish chemical contaminants based on gene expression profiles.}, journal = {BMC genomics}, volume = {15}, number = {}, pages = {248}, pmid = {24678894}, issn = {1471-2164}, mesh = {Algorithms ; Animals ; Biomarkers ; Cluster Analysis ; Computational Biology ; *Ecotoxicology/methods/standards ; *Gene Expression Profiling ; Gene Expression Regulation/drug effects ; Gene Regulatory Networks ; Hazardous Substances/classification/*toxicity ; Male ; Metabolic Networks and Pathways ; Models, Statistical ; Rats ; Reproducibility of Results ; Signal Transduction ; Support Vector Machine ; *Transcriptome ; }, abstract = {BACKGROUND: High throughput transcriptomics profiles such as those generated using microarrays have been useful in identifying biomarkers for different classification and toxicity prediction purposes. Here, we investigated the use of microarrays to predict chemical toxicants and their possible mechanisms of action.

RESULTS: In this study, in vitro cultures of primary rat hepatocytes were exposed to 105 chemicals and vehicle controls, representing 14 compound classes. We comprehensively compared various normalization of gene expression profiles, feature selection and classification algorithms for the classification of these 105 chemicals into14 compound classes. We found that normalization had little effect on the averaged classification accuracy. Two support vector machine (SVM) methods, LibSVM and sequential minimal optimization, had better classification performance than other methods. SVM recursive feature selection (SVM-RFE) had the highest overfitting rate when an independent dataset was used for a prediction. Therefore, we developed a new feature selection algorithm called gradient method that had a relatively high training classification as well as prediction accuracy with the lowest overfitting rate of the methods tested. Analysis of biomarkers that distinguished the 14 classes of compounds identified a group of genes principally involved in cell cycle function that were significantly downregulated by metal and inflammatory compounds, but were induced by anti-microbial, cancer related drugs, pesticides, and PXR mediators.

CONCLUSIONS: Our results indicate that using microarrays and a supervised machine learning approach to predict chemical toxicants, their potential toxicity and mechanisms of action is practical and efficient. Choosing the right feature and classification algorithms for this multiple category classification and prediction is critical.}, } @article {pmid24678534, year = {2014}, author = {Mascarelli, A}, title = {Research tools: Jump off the page.}, journal = {Nature}, volume = {507}, number = {7493}, pages = {523-525}, doi = {10.1038/nj7493-523a}, pmid = {24678534}, issn = {1476-4687}, mesh = {Access to Information ; Animals ; Archives ; Computational Biology/methods ; Ecology/methods ; Information Dissemination/*methods ; Information Management/*methods ; *Internet/statistics & numerical data ; *Records ; *Research ; Research Personnel/psychology ; }, } @article {pmid24677699, year = {2015}, author = {Shimoda, H and Inoue, A and Tsuno, K and Kawakami, N}, title = {One-year test-retest reliability of a Japanese web-based version of the WHO Composite International Diagnostic Interview (CIDI) for major depression in a working population.}, journal = {International journal of methods in psychiatric research}, volume = {24}, number = {3}, pages = {204-212}, pmid = {24677699}, issn = {1557-0657}, mesh = {Adult ; Age Distribution ; Depressive Disorder, Major/*diagnosis/*epidemiology ; Diagnostic and Statistical Manual of Mental Disorders ; Female ; Humans ; Interview, Psychological/*methods ; Japan/epidemiology ; Male ; Middle Aged ; Occupational Diseases/diagnosis/epidemiology ; *Online Systems ; Reproducibility of Results ; Retrospective Studies ; Sexism ; *Translating ; World Health Organization ; Young Adult ; }, abstract = {The purpose of this study was to investigate the one-year test-retest reliability and the demographic correlates of a self-administered web-based depression section of the World Health Organization-Composite International Diagnostic Interview (WHO-CIDI) in a working population. Overall, 1060 out of all employees (N = 1279) from a manufacturing company in Japan responded to two web-based surveys of depression of the WHO-CIDI within a one-year interval in 2009 and 2010. The concordance between lifetime diagnoses of major depressive disorder on two occasions was calculated as percent agreement (%), Gwet's AC1 , and Yule's Q indicators were compared by gender, age, education, and marital status. For the total sample, percent agreement was 94%, AC1 was 0.93, and Yule's Q was 0.82. The concordance rate was low (0.15) among those who were diagnosed at either time or both times. The concordance differed significantly across education and marital status. While the agreement indicators were relatively high, consistent with previous reports based on face-to-face interviews conducted within a shorter interval, the low stability of positive cases may challenge the accuracy of lifetime diagnosis of major depressive disorder using a web version of the WHO-CIDI. Education and marital status might affect the test-retest reliability. Copyright © 2014 John Wiley & Sons, Ltd.}, } @article {pmid24675669, year = {2014}, author = {Coverdale, TC and Brisson, CP and Young, EW and Yin, SF and Donnelly, JP and Bertness, MD}, title = {Indirect human impacts reverse centuries of carbon sequestration and salt marsh accretion.}, journal = {PloS one}, volume = {9}, number = {3}, pages = {e93296}, pmid = {24675669}, issn = {1932-6203}, mesh = {Animals ; Brachyura/physiology ; Carbon/*chemistry ; Carbon Sequestration/*physiology ; *Conservation of Natural Resources ; Geographic Information Systems ; Humans ; Salinity ; Salts ; Soil ; United States ; Water Movements ; *Wetlands ; }, abstract = {Direct and indirect human impacts on coastal ecosystems have increased over the last several centuries, leading to unprecedented degradation of coastal habitats and loss of ecological services. Here we document a two-century temporal disparity between salt marsh accretion and subsequent loss to indirect human impacts. Field surveys, manipulative experiments and GIS analyses reveal that crab burrowing weakens the marsh peat base and facilitates further burrowing, leading to bank calving, disruption of marsh accretion, and a loss of over two centuries of sequestered carbon from the marsh edge in only three decades. Analogous temporal disparities exist in other systems and are a largely unrecognized obstacle in attaining sustainable ecosystem services in an increasingly human impacted world. In light of the growing threat of indirect impacts worldwide and despite uncertainties in the fate of lost carbon, we suggest that estimates of carbon emissions based only on direct human impacts may significantly underestimate total anthropogenic carbon emissions.}, } @article {pmid24671007, year = {2014}, author = {Vandenabeele, SP and Grundy, E and Friswell, MI and Grogan, A and Votier, SC and Wilson, RP}, title = {Excess baggage for birds: inappropriate placement of tags on gannets changes flight patterns.}, journal = {PloS one}, volume = {9}, number = {3}, pages = {e92657}, pmid = {24671007}, issn = {1932-6203}, mesh = {Acceleration ; Animals ; Biomechanical Phenomena ; Birds/*physiology ; Energy Metabolism ; Feeding Behavior/physiology ; Flight, Animal/*physiology ; *Geographic Information Systems ; }, abstract = {Devices attached to flying birds can hugely enhance our understanding of their behavioural ecology for periods when they cannot be observed directly. For this, scientists routinely attach units to either birds' backs or their tails. However, inappropriate payload distribution is critical in aircraft and, since birds and planes are subject to the same laws of physics during flight, we considered aircraft aerodynamic constraints to explain flight patterns displayed by northern gannets Sula bassana equipped with (small ca. 14 g) tail- and back-mounted accelerometers and (larger ca. 30 g) tail-mounted GPS units. Tail-mounted GPS-fitted birds showed significantly higher cumulative numbers of flap-glide cycles and a higher pitch angle of the tail than accelerometer-equipped birds, indicating problems with balancing inappropriately placed weights with knock-on consequences relating to energy expenditure. These problems can be addressed by carefully choosing where to place tags on birds according to the mass of the tags and the lifestyle of the subject species.}, } @article {pmid24665665, year = {2014}, author = {Kiefer, B}, title = {[Personalized medicine and narcissistic future].}, journal = {Revue medicale suisse}, volume = {10}, number = {419}, pages = {512}, pmid = {24665665}, issn = {1660-9379}, mesh = {Altruism ; Biomedical Technology/trends ; Ecology ; Forecasting ; Humans ; Medical Informatics/trends ; *Narcissism ; Precision Medicine/methods/*trends ; User-Computer Interface ; }, } @article {pmid24663058, year = {2014}, author = {Zhang, X and Deng, M and Fan, G}, title = {Differential transcriptome analysis between Paulownia fortunei and its synthesized autopolyploid.}, journal = {International journal of molecular sciences}, volume = {15}, number = {3}, pages = {5079-5093}, pmid = {24663058}, issn = {1422-0067}, mesh = {*Diploidy ; Gene Expression Profiling/methods ; Gene Library ; Gene Ontology ; Magnoliopsida/*genetics ; Molecular Sequence Annotation ; Reverse Transcriptase Polymerase Chain Reaction ; *Tetraploidy ; Transcriptome/*genetics ; Trees/genetics ; }, abstract = {Paulownia fortunei is an ecologically and economically important tree species that is widely used as timber and chemical pulp. Its autotetraploid, which carries a number of valuable traits, was successfully induced with colchicine. To identify differences in gene expression between P. fortunei and its synthesized autotetraploid, we performed transcriptome sequencing using an Illumina Genome Analyzer IIx (GAIIx). About 94.8 million reads were generated and assembled into 383,056 transcripts, including 18,984 transcripts with a complete open reading frame. A conducted Basic Local Alignment Search Tool (BLAST) search indicated that 16,004 complete transcripts had significant hits in the National Center for Biotechnology Information (NCBI) non-redundant database. The complete transcripts were given functional assignments using three public protein databases. One thousand one hundred fifty eight differentially expressed complete transcripts were screened through a digital abundance analysis, including transcripts involved in energy metabolism and epigenetic regulation. Finally, the expression levels of several transcripts were confirmed by quantitative real-time PCR. Our results suggested that polyploidization caused epigenetic-related changes, which subsequently resulted in gene expression variation between diploid and autotetraploid P. fortunei. This might be the main mechanism affected by the polyploidization. Our results represent an extensive survey of the P. fortunei transcriptome and will facilitate subsequent functional genomics research in P. fortunei. Moreover, the gene expression profiles of P. fortunei and its autopolyploid will provide a valuable resource for the study of polyploidization.}, } @article {pmid24662602, year = {2014}, author = {Sümbül, U and Song, S and McCulloch, K and Becker, M and Lin, B and Sanes, JR and Masland, RH and Seung, HS}, title = {A genetic and computational approach to structurally classify neuronal types.}, journal = {Nature communications}, volume = {5}, number = {}, pages = {3512}, pmid = {24662602}, issn = {2041-1723}, support = {R01 NS029169/NS/NINDS NIH HHS/United States ; R37 NS029169/NS/NINDS NIH HHS/United States ; }, mesh = {*Algorithms ; Animals ; Computational Biology/*methods ; Dendrites/ultrastructure ; Image Processing, Computer-Assisted ; Mice ; Neurons/*classification/*cytology ; Retina/*cytology ; }, abstract = {The importance of cell types in understanding brain function is widely appreciated but only a tiny fraction of neuronal diversity has been catalogued. Here we exploit recent progress in genetic definition of cell types in an objective structural approach to neuronal classification. The approach is based on highly accurate quantification of dendritic arbor position relative to neurites of other cells. We test the method on a population of 363 mouse retinal ganglion cells. For each cell, we determine the spatial distribution of the dendritic arbors, or arbor density, with reference to arbors of an abundant, well-defined interneuronal type. The arbor densities are sorted into a number of clusters that is set by comparison with several molecularly defined cell types. The algorithm reproduces the genetic classes that are pure types, and detects six newly clustered cell types that await genetic definition.}, } @article {pmid24658631, year = {2014}, author = {Petchey, OL and Fox, JW and Haddon, L}, title = {Imbalance in individual researcher's peer review activities quantified for four British Ecological Society journals, 2003-2010.}, journal = {PloS one}, volume = {9}, number = {3}, pages = {e92896}, pmid = {24658631}, issn = {1932-6203}, mesh = {Databases, Factual ; Humans ; *Peer Review, Research ; *Periodicals as Topic ; Publishing ; *Research Personnel ; United Kingdom ; }, abstract = {Researchers contribute to the scientific peer review system by providing reviews, and "withdraw" from it by submitting manuscripts that are subsequently reviewed. So far as we are aware, there has been no quantification of the balance of individual's contributions and withdrawals. We compared the number of reviews provided by individual researchers (i.e., their contribution) to the number required by their submissions (i.e. their withdrawals) in a large and anonymised database provided by the British Ecological Society. The database covered the Journal of Ecology, Journal of Animal Ecology, Journal of Applied Ecology, and Functional Ecology from 2003-2010. The majority of researchers (64%) did not have balanced contributions and withdrawals. Depending on assumptions, 12% to 44% contributed more than twice as much as required; 20% to 52% contributed less than half as much as required. Balance, or lack thereof, varied little in relation to the number of years a researcher had been active (reviewing or submitting). Researchers who contributed less than required did not lack the opportunity to review. Researchers who submitted more were more likely to accept invitations to review. These finding suggest overall that peer review of the four analysed journals is not in crisis, but only due to the favourable balance of over- and under-contributing researchers. These findings are limited to the four journals analysed, and therefore cannot include researcher's other peer review activities, which if included might change the proportions reported. Relatively low effort was required to assemble, check, and analyse the data. Broader analyses of individual researcher's peer review activities would contribute to greater quality, efficiency, and fairness in the peer review system.}, } @article {pmid24651646, year = {2014}, author = {Lei, BR and Olival, KJ}, title = {Contrasting patterns in mammal-bacteria coevolution: bartonella and leptospira in bats and rodents.}, journal = {PLoS neglected tropical diseases}, volume = {8}, number = {3}, pages = {e2738}, pmid = {24651646}, issn = {1935-2735}, support = {R01 AI079231/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Bartonella/classification/genetics/*isolation & purification/physiology ; Chiroptera/*microbiology ; Computational Biology ; *Evolution, Molecular ; Host Specificity ; Leptospira/classification/genetics/*isolation & purification/physiology ; Phylogeny ; Rodentia/*microbiology ; }, abstract = {BACKGROUND: Emerging bacterial zoonoses in bats and rodents remain relatively understudied. We conduct the first comparative host-pathogen coevolutionary analyses of bacterial pathogens in these hosts, using Bartonella spp. and Leptospira spp. as a model.

We used published genetic data for 51 Bartonella genotypes from 24 bat species, 129 Bartonella from 38 rodents, and 26 Leptospira from 20 bats. We generated maximum likelihood and Bayesian phylogenies for hosts and bacteria, and tested for coevoutionary congruence using programs ParaFit, PACO, and Jane. Bartonella spp. and their bat hosts had a significant coevolutionary fit (ParaFitGlobal = 1.9703, P≤0.001; m2 global value = 7.3320, P≤0.0001). Bartonella spp. and rodent hosts also indicated strong overall patterns of cospeciation (ParaFitGlobal = 102.4409, P≤0.001; m2 global value = 86.532, P≤0.0001). In contrast, we were unable to reject independence of speciation events in Leptospira and bats (ParaFitGlobal = 0.0042, P = 0.84; m2 global value = 4.6310, P = 0.5629). Separate analyses of New World and Old World data subsets yielded results congruent with analysis from entire datasets. We also conducted event-based cophylogeny analyses to reconstruct likely evolutionary histories for each group of pathogens and hosts. Leptospira and bats had the greatest number of host switches per parasite (0.731), while Bartonella and rodents had the fewest (0.264).

CONCLUSIONS/SIGNIFICANCE: In both bat and rodent hosts, Bartonella exhibits significant coevolution with minimal host switching, while Leptospira in bats lacks evolutionary congruence with its host and has high number of host switches. Reasons underlying these variable coevolutionary patterns in host range are likely due to differences in disease-specific transmission and host ecology. Understanding the coevolutionary patterns and frequency of host-switching events between bacterial pathogens and their hosts will allow better prediction of spillover between mammal reservoirs, and ultimately to humans.}, } @article {pmid24651253, year = {2014}, author = {Choi, Y and Lee, MJ and Kang, HC and Lee, MS and Yoon, S}, title = {Development and application of a web-based nutritional management program to improve dietary behaviors for the prevention of metabolic syndrome.}, journal = {Computers, informatics, nursing : CIN}, volume = {32}, number = {5}, pages = {232-241}, doi = {10.1097/CIN.0000000000000054}, pmid = {24651253}, issn = {1538-9774}, mesh = {Adult ; Body Mass Index ; Feeding Behavior/*physiology ; Female ; Humans ; Internet ; Male ; Medical Informatics Applications ; Metabolic Syndrome/diet therapy/*prevention & control ; Middle Aged ; Nutrition Therapy/*methods ; Surveys and Questionnaires ; }, abstract = {The purpose of this study was to develop a Web-based nutritional management program for the prevention of metabolic syndrome and to evaluate how the program affects health-related behaviors and the health status of office workers with metabolic syndrome risk factors. For the pilot test of the Web-based nutritional management program, 29 employees (19 males, 10 females) with more than one metabolic syndrome risk factor participated in the Web-based nutritional management program for 16 weeks. Participants visited the Web site more than two times per week and completed customized assessments of health status, smoking habits, alcohol consumption, dietary habits, food intake, ideal body weight, energy requirements, and exercise. Subjects had a significant decrease in body weight, waist circumference, body mass index (P < .01 in males, P < .05 in females), and body fat (P < .01 in males). The frequency of dietary habits such as eating snacks, eating out, and dining with others decreased, whereas the frequency of intake of foods such as whole grains, seaweed, fruit, and low-fat milk increased after intervention. After 16 weeks, program satisfaction was evaluated using a Web evaluation questionnaire, and most of the participants were highly satisfied with Web site components such as the loading speed, configuration, privacy, design, functionality, and contents.}, } @article {pmid24651252, year = {2014}, author = {Silva, MA and Jonsen, I and Russell, DJ and Prieto, R and Thompson, D and Baumgartner, MF}, title = {Assessing performance of Bayesian state-space models fit to Argos satellite telemetry locations processed with Kalman filtering.}, journal = {PloS one}, volume = {9}, number = {3}, pages = {e92277}, pmid = {24651252}, issn = {1932-6203}, mesh = {*Algorithms ; Animal Migration/*physiology ; Animals ; Bayes Theorem ; Behavior, Animal ; Geographic Information Systems ; Least-Squares Analysis ; *Models, Theoretical ; Phoca/physiology ; Research Design ; *Satellite Communications ; *Telemetry ; Whales/physiology ; }, abstract = {Argos recently implemented a new algorithm to calculate locations of satellite-tracked animals that uses a Kalman filter (KF). The KF algorithm is reported to increase the number and accuracy of estimated positions over the traditional Least Squares (LS) algorithm, with potential advantages to the application of state-space methods to model animal movement data. We tested the performance of two Bayesian state-space models (SSMs) fitted to satellite tracking data processed with KF algorithm. Tracks from 7 harbour seals (Phoca vitulina) tagged with ARGOS satellite transmitters equipped with Fastloc GPS loggers were used to calculate the error of locations estimated from SSMs fitted to KF and LS data, by comparing those to "true" GPS locations. Data on 6 fin whales (Balaenoptera physalus) were used to investigate consistency in movement parameters, location and behavioural states estimated by switching state-space models (SSSM) fitted to data derived from KF and LS methods. The model fit to KF locations improved the accuracy of seal trips by 27% over the LS model. 82% of locations predicted from the KF model and 73% of locations from the LS model were <5 km from the corresponding interpolated GPS position. Uncertainty in KF model estimates (5.6 ± 5.6 km) was nearly half that of LS estimates (11.6 ± 8.4 km). Accuracy of KF and LS modelled locations was sensitive to precision but not to observation frequency or temporal resolution of raw Argos data. On average, 88% of whale locations estimated by KF models fell within the 95% probability ellipse of paired locations from LS models. Precision of KF locations for whales was generally higher. Whales' behavioural mode inferred by KF models matched the classification from LS models in 94% of the cases. State-space models fit to KF data can improve spatial accuracy of location estimates over LS models and produce equally reliable behavioural estimates.}, } @article {pmid24647562, year = {2014}, author = {Corley, CD and Pullum, LL and Hartley, DM and Benedum, C and Noonan, C and Rabinowitz, PM and Lancaster, MJ}, title = {Disease prediction models and operational readiness.}, journal = {PloS one}, volume = {9}, number = {3}, pages = {e91989}, pmid = {24647562}, issn = {1932-6203}, mesh = {*Biosurveillance ; *Decision Support Techniques ; Disaster Planning ; *Disease ; *Forecasting ; Humans ; *Models, Biological ; Reproducibility of Results ; Statistics as Topic ; }, abstract = {The objective of this manuscript is to present a systematic review of biosurveillance models that operate on select agents and can forecast the occurrence of a disease event. We define a disease event to be a biological event with focus on the One Health paradigm. These events are characterized by evidence of infection and or disease condition. We reviewed models that attempted to predict a disease event, not merely its transmission dynamics and we considered models involving pathogens of concern as determined by the US National Select Agent Registry (as of June 2011). We searched commercial and government databases and harvested Google search results for eligible models, using terms and phrases provided by public health analysts relating to biosurveillance, remote sensing, risk assessments, spatial epidemiology, and ecological niche modeling. After removal of duplications and extraneous material, a core collection of 6,524 items was established, and these publications along with their abstracts are presented in a semantic wiki at http://BioCat.pnnl.gov. As a result, we systematically reviewed 44 papers, and the results are presented in this analysis. We identified 44 models, classified as one or more of the following: event prediction (4), spatial (26), ecological niche (28), diagnostic or clinical (6), spread or response (9), and reviews (3). The model parameters (e.g., etiology, climatic, spatial, cultural) and data sources (e.g., remote sensing, non-governmental organizations, expert opinion, epidemiological) were recorded and reviewed. A component of this review is the identification of verification and validation (V&V) methods applied to each model, if any V&V method was reported. All models were classified as either having undergone Some Verification or Validation method, or No Verification or Validation. We close by outlining an initial set of operational readiness level guidelines for disease prediction models based upon established Technology Readiness Level definitions.}, } @article {pmid24640964, year = {2014}, author = {Jayanthi, KP and Kempraj, V and Aurade, RM and Roy, TK and Shivashankara, KS and Verghese, A}, title = {Computational reverse chemical ecology: virtual screening and predicting behaviorally active semiochemicals for Bactrocera dorsalis.}, journal = {BMC genomics}, volume = {15}, number = {}, pages = {209}, pmid = {24640964}, issn = {1471-2164}, mesh = {Animals ; Behavior, Animal/*drug effects ; Binding Sites ; *Computational Biology ; Molecular Docking Simulation ; Pheromones/chemistry/metabolism/*pharmacology ; Protein Structure, Tertiary ; Receptors, Odorant/chemistry/metabolism ; Tephritidae/*chemistry/metabolism ; }, abstract = {BACKGROUND: Semiochemical is a generic term used for a chemical substance that influences the behaviour of an organism. It is a common term used in the field of chemical ecology to encompass pheromones, allomones, kairomones, attractants and repellents. Insects have mastered the art of using semiochemicals as communication signals and rely on them to find mates, host or habitat. This dependency of insects on semiochemicals has allowed chemical ecologists to develop environment friendly pest management strategies. However, discovering semiochemicals is a laborious process that involves a plethora of behavioural and analytical techniques, making it expansively time consuming. Recently, reverse chemical ecology approach using odorant binding proteins (OBPs) as target for elucidating behaviourally active compounds is gaining eminence. In this scenario, we describe a "computational reverse chemical ecology" approach for rapid screening of potential semiochemicals.

RESULTS: We illustrate the high prediction accuracy of our computational method. We screened 25 semiochemicals for their binding potential to a GOBP of B. dorsalis using molecular docking (in silico) and molecular dynamics. Parallely, compounds were subjected to fluorescent quenching assays (Experimental). The correlation between in silico and experimental data were significant (r2 = 0.9408; P < 0.0001). Further, predicted compounds were subjected to behavioral bioassays and were found to be highly attractive to insects.

CONCLUSIONS: The present study provides a unique methodology for rapid screening and predicting behaviorally active semiochemicals. This methodology may be developed as a viable approach for prospecting active semiochemicals for pest control, which otherwise is a laborious process.}, } @article {pmid24640546, year = {2014}, author = {Thorson, JT and Cope, JM and Patrick, WS}, title = {Assessing the quality of life history information in publicly available databases.}, journal = {Ecological applications : a publication of the Ecological Society of America}, volume = {24}, number = {1}, pages = {217-226}, doi = {10.1890/12-1855.1}, pmid = {24640546}, issn = {1051-0761}, mesh = {Animals ; Bayes Theorem ; Databases, Factual/*standards ; Fishes/*physiology ; Reproduction ; }, abstract = {Single-species life history parameters are central to ecological research and management, including the fields of macro-ecology, fisheries science, and ecosystem modeling. However, there has been little independent evaluation of the precision and accuracy of the life history values in global and publicly available databases. We therefore develop a novel method based on a Bayesian errors-in-variables model that compares database entries with estimates from local experts, and we illustrate this process by assessing the accuracy and precision of entries in FishBase, one of the largest and oldest life history databases. This model distinguishes biases among seven life history parameters, two types of information available in FishBase (i.e., published values and those estimated from other parameters), and two taxa (i.e., bony and cartilaginous fishes) relative to values from regional experts in the United States, while accounting for additional variance caused by sex- and region-specific life history traits. For published values in FishBase, the model identifies a small positive bias in natural mortality and negative bias in maximum age, perhaps caused by unacknowledged mortality caused by fishing. For life history values calculated by FishBase, the model identified large and inconsistent biases. The model also demonstrates greatest precision for body size parameters, decreased precision for values derived from geographically distant populations, and greatest between-sex differences in age at maturity. We recommend that our bias and precision estimates be used in future errors-in-variables models as a prior on measurement errors. This approach is broadly applicable to global databases of life history traits and, if used, will encourage further development and improvements in these databases.}, } @article {pmid24637619, year = {2014}, author = {Farag, IF and Davis, JP and Youssef, NH and Elshahed, MS}, title = {Global patterns of abundance, diversity and community structure of the Aminicenantes (candidate phylum OP8).}, journal = {PloS one}, volume = {9}, number = {3}, pages = {e92139}, pmid = {24637619}, issn = {1932-6203}, mesh = {Bacteria/classification/drug effects/genetics/*growth & development ; *Biodiversity ; Databases, Genetic ; *Internationality ; Oxygen/pharmacology ; RNA, Ribosomal, 16S/genetics ; Salinity ; Sequence Analysis, DNA ; Temperature ; }, abstract = {We investigated the global patterns of abundance, diversity, and community structure of members of the Aminicenantes (candidate phylum OP8). Our aim was to identify the putative ecological role(s) played by members of this poorly characterized bacterial lineages in various ecosystems. Analysis of near full-length 16S rRNA genes identified four classes and eight orders within the Aminicenantes. Within 3,134 datasets comprising ∼1.8 billion high throughput-generated partial 16S rRNA genes, 47,351 Aminicenantes-affiliated sequences were identified in 913 datasets. The Aminicenantes exhibited the highest relative abundance in hydrocarbon-impacted environments, followed by marine habitats (especially hydrothermal vents and coral-associated microbiome samples), and aquatic, non-marine habitats (especially in terrestrial springs and groundwater samples). While the overall abundance of the Aminicenantes was higher in low oxygen tension as well as non-saline and low salinity habitats, it was encountered in a wide range of oxygen tension, salinities, and temperatures. Analysis of the community structure of the Aminicenantes showed distinct patterns across various datasets that appear to be, mostly, driven by habitat variations rather than prevalent environmental parameters. We argue that the detection of the Aminicenantes across environmental extremes and the observed distinct community structure patterns reflect a high level of intraphylum metabolic diversity and adaptive capabilities that enable its survival and growth in a wide range of habitats and environmental conditions.}, } @article {pmid24636830, year = {2014}, author = {Takechi, U and Matsunaga, K and Nakanishi, R and Yamanaga, H and Murayama, N and Mafune, K and Tsuji, S}, title = {Longitudinal changes of motor cortical excitability and transcallosal inhibition after subcortical stroke.}, journal = {Clinical neurophysiology : official journal of the International Federation of Clinical Neurophysiology}, volume = {125}, number = {10}, pages = {2055-2069}, doi = {10.1016/j.clinph.2014.01.034}, pmid = {24636830}, issn = {1872-8952}, mesh = {Adult ; Aged ; Aged, 80 and over ; Electromyography ; Evoked Potentials, Motor/*physiology ; Female ; Functional Laterality/physiology ; Humans ; Longitudinal Studies ; Male ; Middle Aged ; Motor Cortex/*physiopathology ; Neural Inhibition/*physiology ; Prognosis ; Pyramidal Tracts/physiopathology ; Recovery of Function/*physiology ; Stroke/*physiopathology ; Transcranial Magnetic Stimulation ; }, abstract = {OBJECTIVE: A general lack of longitudinal studies on interhemispheric interactions following stroke led us to use transcranial magnetic stimulation (TMS) to examine changes in corticospinal/intracortical excitability and transcallosal inhibition over a 1-year period following subcortical stroke.

METHODS: We measured TMS parameters such as motor threshold (MT), short-interval intracortical inhibition (SICI), and ipsilateral silent period (iSP) and evaluated clinical scores at three time-points (T1, T2, and T3) in 24 patients and 25 age-matched healthy subjects.

RESULTS: At T1, we observed reduced MTs and SICIs with prolonged iSPs in the unaffected hemisphere (UH). In contrast, increased MTs and reduced SICIs were observed in the affected hemisphere (AH). These abnormalities gradually reduced and no MEP response to TMS at T1 predicted a worse prognosis. The prolonged iSP at T1 was associated with more severe impairments, but it did not necessarily predict a worse prognosis after 1year.

CONCLUSIONS: UH excitability was increased at the post-acute time-period, which may have resulted in enhanced transcallosal inhibition to the AH. However, it is unclear whether there was a causal relationship between the enhanced transcallosal inhibition and the extent of clinical recovery.

SIGNIFICANCE: This is the first study to demonstrate changes in transcallosal inhibition over a longitudinal period following stroke.}, } @article {pmid24633599, year = {2014}, author = {Romeis, J and Meissle, M and Alvarez-Alfageme, F and Bigler, F and Bohan, DA and Devos, Y and Malone, LA and Pons, X and Rauschen, S}, title = {Potential use of an arthropod database to support the non-target risk assessment and monitoring of transgenic plants.}, journal = {Transgenic research}, volume = {23}, number = {6}, pages = {995-1013}, pmid = {24633599}, issn = {1573-9368}, mesh = {Animals ; Arthropods/*physiology ; *Databases, Factual ; Environmental Exposure/prevention & control ; Environmental Monitoring/*methods ; Pest Control, Biological/*methods ; Plants, Genetically Modified/parasitology/*toxicity ; Risk Assessment/*methods ; Zea mays/*parasitology ; }, abstract = {Worldwide, plants obtained through genetic modification are subject to a risk analysis and regulatory approval before they can enter the market. An area of concern addressed in environmental risk assessments is the potential of genetically modified (GM) plants to adversely affect non-target arthropods and the valued ecosystem services they provide. Environmental risk assessments are conducted case-by-case for each GM plant taking into account the plant species, its trait(s), the receiving environments into which the GM plant is to be released and its intended uses, and the combination of these characteristics. To facilitate the non-target risk assessment of GM plants, information on arthropods found in relevant agro-ecosystems in Europe has been compiled in a publicly available database of bio-ecological information during a project commissioned by the European Food Safety Authority (EFSA). Using different hypothetical GM maize case studies, we demonstrate how the information contained in the database can assist in identifying valued species that may be at risk and in selecting suitable species for laboratory testing, higher-tier studies, as well as post-market environmental monitoring.}, } @article {pmid24629545, year = {2014}, author = {Reitzel, LR and Kendzor, DE and Nguyen, N and Regan, SD and Okuyemi, KS and Castro, Y and Wetter, DW and Businelle, MS}, title = {Shelter proximity and affect among homeless smokers making a quit attempt.}, journal = {American journal of health behavior}, volume = {38}, number = {2}, pages = {161-169}, pmid = {24629545}, issn = {1945-7359}, support = {K01 CA157689/CA/NCI NIH HHS/United States ; P30 CA016672/CA/NCI NIH HHS/United States ; UL1 TR001105/TR/NCATS NIH HHS/United States ; CA016672/CA/NCI NIH HHS/United States ; }, mesh = {Affective Symptoms/epidemiology/*psychology ; Case-Control Studies ; Cell Phone/statistics & numerical data ; Female ; Follow-Up Studies ; Geographic Information Systems ; Health Status Disparities ; Ill-Housed Persons/*psychology/statistics & numerical data ; *Housing ; Humans ; Linear Models ; Male ; Middle Aged ; Patient Compliance/statistics & numerical data ; Program Evaluation ; Smoking/adverse effects/epidemiology ; Smoking Cessation/methods/*psychology ; Social Class ; *Social Environment ; Surveys and Questionnaires ; Texas/epidemiology ; Tobacco Use Disorder/epidemiology/therapy ; }, abstract = {OBJECTIVES: To explore the associations between shelter proximity and real-time affect during a specific smoking quit attempt among 22 homeless adults.

METHODS: Affect was measured via 485 smartphone-based Ecological Momentary Assessments randomly administered during the weeks immediately before and after the quit day, and proximity to the shelter was measured via GPS. Adjusted linear mixed model regressions examined associations between shelter proximity and affect.

RESULTS: Closer proximity to the shelter was associated with greater negative affect only during the post-quit attempt week (p = .008). All participants relapsed to smoking by one week post-quit attempt.

CONCLUSIONS: Among homeless smokers trying to quit, the shelter may be associated with unexpected negative affect/stress. Potential intervention applications are suggested.}, } @article {pmid24626288, year = {2014}, author = {Zhao, Z and Wu, X and Kumar, PK and Dong, M and Ji, G and Li, QQ and Liang, C}, title = {Bioinformatics analysis of alternative polyadenylation in green alga Chlamydomonas reinhardtii using transcriptome sequences from three different sequencing platforms.}, journal = {G3 (Bethesda, Md.)}, volume = {4}, number = {5}, pages = {871-883}, pmid = {24626288}, issn = {2160-1836}, support = {R15 GM094732/GM/NIGMS NIH HHS/United States ; 1R15GM94732-1 A1/GM/NIGMS NIH HHS/United States ; }, mesh = {Alternative Splicing ; Chlamydomonas reinhardtii/*genetics ; Computational Biology ; Datasets as Topic ; *Gene Expression Regulation, Plant ; Genome, Plant ; High-Throughput Nucleotide Sequencing/methods ; Introns ; Open Reading Frames ; Poly A ; Polyadenylation/*genetics ; Polymorphism, Single Nucleotide ; Transcription, Genetic ; *Transcriptome ; }, abstract = {Messenger RNA 3'-end formation is an essential posttranscriptional processing step for most eukaryotic genes. Different from plants and animals where AAUAAA and its variants routinely are found as the main poly(A) signal, Chlamydomonas reinhardtii uses UGUAA as the major poly(A) signal. The advance of sequencing technology provides an enormous amount of sequencing data for us to explore the variations of poly(A) signals, alternative polyadenylation (APA), and its relationship with splicing in this algal species. Through genome-wide analysis of poly(A) sites in C. reinhardtii, we identified a large number of poly(A) sites: 21,041 from Sanger expressed sequence tags, 88,184 from 454, and 195,266 from Illumina sequence reads. In comparison with previous collections, more new poly(A) sites are found in coding sequences and intron and intergenic regions by deep-sequencing. Interestingly, G-rich signals are particularly abundant in intron and intergenic regions. The prevalence of different poly(A) signals between coding sequences and a 3'-untranslated region implies potentially different polyadenylation mechanisms. Our data suggest that the APA occurs in about 68% of C. reinhardtii genes. Using Gene Ontolgy analysis, we found most of the APA genes are involved in RNA regulation and metabolic process, protein synthesis, hydrolase, and ligase activities. Moreover, intronic poly(A) sites are more abundant in constitutively spliced introns than retained introns, suggesting an interplay between polyadenylation and splicing. Our results support that APA, as in higher eukaryotes, may play significant roles in increasing transcriptome diversity and gene expression regulation in this algal species. Our datasets also provide useful information for accurate annotation of transcript ends in C. reinhardtii.}, } @article {pmid24626233, year = {2014}, author = {Varela, S and González-Hernández, J and Casabella, E and Barrientos, R}, title = {rAvis: an R-package for downloading information stored in Proyecto AVIS, a citizen science bird project.}, journal = {PloS one}, volume = {9}, number = {3}, pages = {e91650}, pmid = {24626233}, issn = {1932-6203}, mesh = {Animals ; Biodiversity ; *Birds ; Computational Biology/*methods ; *Databases, Factual ; Ecology/methods ; Geography ; Internet ; Population Dynamics ; Programming Languages ; Research Design ; *Software ; Spain ; Time Factors ; Volunteers ; }, abstract = {Citizen science projects store an enormous amount of information about species distribution, diversity and characteristics. Researchers are now beginning to make use of this rich collection of data. However, access to these databases is not always straightforward. Apart from the largest and international projects, citizen science repositories often lack specific Application Programming Interfaces (APIs) to connect them to the scientific environments. Thus, it is necessary to develop simple routines to allow researchers to take advantage of the information collected by smaller citizen science projects, for instance, programming specific packages to connect them to popular scientific environments (like R). Here, we present rAvis, an R-package to connect R-users with Proyecto AVIS (http://proyectoavis.com), a Spanish citizen science project with more than 82,000 bird observation records. We develop several functions to explore the database, to plot the geographic distribution of the species occurrences, and to generate personal queries to the database about species occurrences (number of individuals, distribution, etc.) and birdwatcher observations (number of species recorded by each collaborator, UTMs visited, etc.). This new R-package will allow scientists to access this database and to exploit the information generated by Spanish birdwatchers over the last 40 years.}, } @article {pmid24622821, year = {2014}, author = {Williams, R and Kelly, N and Boebel, O and Friedlaender, AS and Herr, H and Kock, KH and Lehnert, LS and Maksym, T and Roberts, J and Scheidat, M and Siebert, U and Brierley, AS}, title = {Counting whales in a challenging, changing environment.}, journal = {Scientific reports}, volume = {4}, number = {}, pages = {4170}, pmid = {24622821}, issn = {2045-2322}, mesh = {Animals ; Antarctic Regions ; *Climate Change ; *Conservation of Natural Resources ; *Data Collection ; Ecosystem ; Ice Cover ; *Minke Whale ; Oceans and Seas ; Population Density ; Population Dynamics ; }, abstract = {Estimating abundance of Antarctic minke whales is central to the International Whaling Commission's conservation and management work and understanding impacts of climate change on polar marine ecosystems. Detecting abundance trends is problematic, in part because minke whales are frequently sighted within Antarctic sea ice where navigational safety concerns prevent ships from surveying. Using icebreaker-supported helicopters, we conducted aerial surveys across a gradient of ice conditions to estimate minke whale density in the Weddell Sea. The surveys revealed substantial numbers of whales inside the sea ice. The Antarctic summer sea ice is undergoing rapid regional change in annual extent, distribution, and length of ice-covered season. These trends, along with substantial interannual variability in ice conditions, affect the proportion of whales available to be counted by traditional shipboard surveys. The strong association between whales and the dynamic, changing sea ice requires reexamination of the power to detect trends in whale abundance or predict ecosystem responses to climate change.}, } @article {pmid24621592, year = {2014}, author = {Leisnham, PT and LaDeau, SL and Juliano, SA}, title = {Spatial and temporal habitat segregation of mosquitoes in urban Florida.}, journal = {PloS one}, volume = {9}, number = {3}, pages = {e91655}, pmid = {24621592}, issn = {1932-6203}, support = {R01 AI044793/AI/NIAID NIH HHS/United States ; R01- AI-44793/AI/NIAID NIH HHS/United States ; }, mesh = {*Aedes ; Agriculture ; Animals ; *Culex ; Databases, Factual ; *Ecosystem ; Florida ; Seasons ; *Spatio-Temporal Analysis ; }, abstract = {Understanding mechanisms fostering coexistence between invasive and resident species is important in predicting ecological, economic, or health impacts of invasive species. The non-native mosquitoes Aedes aegypti and Culex quinquefasciatus have been resident in the southeastern United States for over a century. They coexist at some urban sites with the more recent invasive Aedes albopictus, which is usually superior in interspecific competition. We tested predictions of temporal and spatial habitat segregation that foster coexistence of these resident species with the superior invasive competitor. We measured spatial and temporal patterns of site occupancy and abundance for all three species among standard oviposition traps in metropolitan Tampa, Florida. Consistent with the condition-specific competition hypothesis, A. albopictus and A. aegypti abundances were greater and C. quinquefasciatus abundance was lower late (September) versus early (June) in the rainy season, and the proportional increase of A. albopictus abundance was greater than that of A. aegypti. These results are postulated to result from greater dry-season egg mortality and associated greater rainy-season competitive superiority of larvae of A. albopictus, followed by A. aegypti, and C. quinquefasciatus. Spatial partitioning among landscape variables was also evident among species, with A. albopictus more likely to oviposit across a range of open grass landscapes whereas A. aegypti were mostly restricted to cemeteries. Culex quinquefasciatus showed a shift in abundance from cemeteries early in the rainy season to developed areas characterized by built environments with large proportions of impervious surfaces late in the rainy season, where A. albopictus was not in its highest abundance. These results suggest that both temporal and spatial variation, and their interaction, may contribute to local coexistence between Aedes and Culex mosquito species in urban areas.}, } @article {pmid24621524, year = {2014}, author = {Larsson, J and Celepli, N and Ininbergs, K and Dupont, CL and Yooseph, S and Bergman, B and Ekman, M}, title = {Picocyanobacteria containing a novel pigment gene cluster dominate the brackish water Baltic Sea.}, journal = {The ISME journal}, volume = {8}, number = {9}, pages = {1892-1903}, pmid = {24621524}, issn = {1751-7370}, mesh = {Cyanobacteria/classification/*genetics/isolation & purification ; Genes, Bacterial ; *Multigene Family ; Oceans and Seas ; Phycocyanin/classification/*genetics ; Phycoerythrin/classification/*genetics ; Phylogeny ; Seawater/*microbiology ; }, abstract = {Photoautotrophic picocyanobacteria harvest light via phycobilisomes (PBS) consisting of the pigments phycocyanin (PC) and phycoerythrin (PE), encoded by genes in conserved gene clusters. The presence and arrangement of these gene clusters give picocyanobacteria characteristic light absorption properties and allow the colonization of specific ecological niches. To date, a full understanding of the evolution and distribution of the PBS gene cluster in picocyanobacteria has been hampered by the scarcity of genome sequences from fresh- and brackish water-adapted strains. To remediate this, we analysed genomes assembled from metagenomic samples collected along a natural salinity gradient, and over the course of a growth season, in the Baltic Sea. We found that while PBS gene clusters in picocyanobacteria sampled in marine habitats were highly similar to known references, brackish-adapted genotypes harboured a novel type not seen in previously sequenced genomes. Phylogenetic analyses showed that the novel gene cluster belonged to a clade of uncultivated picocyanobacteria that dominate the brackish Baltic Sea throughout the summer season, but are uncommon in other examined aquatic ecosystems. Further, our data suggest that the PE genes were lost in the ancestor of PC-containing coastal picocyanobacteria and that multiple horizontal gene transfer events have re-introduced PE genes into brackish-adapted strains, including the novel clade discovered here.}, } @article {pmid24619947, year = {2014}, author = {Hashizume, N and Tanabe, A and Inoue, Y and Sawada, T and Murakami, H and Suzuki, Y and Sumi, S and Tsubokura, Y and Yoshida, T and Ajimi, S and Tsuji, T and Furukawa, K}, title = {Prediction of the bioconcentration factor in common carp (Cyprinus carpio L.) using data from the dietary exposure bioaccumulation fish test.}, journal = {Environmental toxicology and chemistry}, volume = {33}, number = {6}, pages = {1406-1414}, doi = {10.1002/etc.2572}, pmid = {24619947}, issn = {1552-8618}, mesh = {Animals ; Carps/*metabolism ; Databases, Chemical ; Diet/*adverse effects ; Ecotoxicology/*methods ; Endpoint Determination ; Environmental Pollutants/*metabolism ; Guidelines as Topic ; Japan ; Kinetics ; Models, Biological ; Social Control, Formal ; }, abstract = {An approach to predicting the bioconcentration factor (BCFpre) from the predicted uptake rate constant (k1 pre) and the depuration rate constant measured in the dietary exposure bioaccumulation fish test (k2 dietary) [BCFpre = k1 pre /k2 dietary ] is proposed in test guideline 305 of the Organization for Economic Cooperation and Development Guidelines for Testing of Chemicals. Data were collected on the BCFs of 197 test chemicals from Japan's Chemical Substances Control Law database. To demonstrate how the BCFpre compares with experimentally derived BCF under optimum conditions, 48 of 197 test chemicals, including a number of studies that could be considered problematic, were excluded from the analysis. The k1 pre was calculated by using 22 published prediction methods: the correlations between experimental uptake rate constants (k1 aqueous) and k1 pre for all prediction methods were very low and were statistically nonsignificant (p > 0.05). Three prediction methods were also selected that gave relatively good values for the geometric mean of k1 pre /k1 aqueous and calculated values of BCFpre for 12 test chemicals. Linear relationships (p < 0.05) are presented between logarithm of experimental and predicted BCF. The correlation coefficients of growth-corrected experimental and predicted BCF tended to be higher than values that were not growth corrected. For some test chemicals, use of predicted BCF led to a bioaccumulation classification different from that of existing regulatory criteria.}, } @article {pmid24619117, year = {2014}, author = {Zhang, Z and Xiao, R and Shortridge, A and Wu, J}, title = {Spatial point pattern analysis of human settlements and geographical associations in eastern coastal China - a case study.}, journal = {International journal of environmental research and public health}, volume = {11}, number = {3}, pages = {2818-2833}, pmid = {24619117}, issn = {1660-4601}, mesh = {China ; *Geographic Information Systems ; Geography/*methods ; Humans ; Monte Carlo Method ; Urbanization ; }, abstract = {Understanding the spatial point pattern of human settlements and their geographical associations are important for understanding the drivers of land use and land cover change and the relationship between environmental and ecological processes on one hand and cultures and lifestyles on the other. In this study, a Geographic Information System (GIS) approach, Ripley's K function and Monte Carlo simulation were used to investigate human settlement point patterns. Remotely sensed tools and regression models were employed to identify the effects of geographical determinants on settlement locations in the Wen-Tai region of eastern coastal China. Results indicated that human settlements displayed regular-random-cluster patterns from small to big scale. Most settlements located on the coastal plain presented either regular or random patterns, while those in hilly areas exhibited a clustered pattern. Moreover, clustered settlements were preferentially located at higher elevations with steeper slopes and south facing aspects than random or regular settlements. Regression showed that influences of topographic factors (elevation, slope and aspect) on settlement locations were stronger across hilly regions. This study demonstrated a new approach to analyzing the spatial patterns of human settlements from a wide geographical prospective. We argue that the spatial point patterns of settlements, in addition to the characteristics of human settlements, such as area, density and shape, should be taken into consideration in the future, and land planners and decision makers should pay more attention to city planning and management. Conceptual and methodological bridges linking settlement patterns to regional and site-specific geographical characteristics will be a key to human settlement studies and planning.}, } @article {pmid24618891, year = {2014}, author = {Mühleisen, TW and Leber, M and Schulze, TG and Strohmaier, J and Degenhardt, F and Treutlein, J and Mattheisen, M and Forstner, AJ and Schumacher, J and Breuer, R and Meier, S and Herms, S and Hoffmann, P and Lacour, A and Witt, SH and Reif, A and Müller-Myhsok, B and Lucae, S and Maier, W and Schwarz, M and Vedder, H and Kammerer-Ciernioch, J and Pfennig, A and Bauer, M and Hautzinger, M and Moebus, S and Priebe, L and Czerski, PM and Hauser, J and Lissowska, J and Szeszenia-Dabrowska, N and Brennan, P and McKay, JD and Wright, A and Mitchell, PB and Fullerton, JM and Schofield, PR and Montgomery, GW and Medland, SE and Gordon, SD and Martin, NG and Krasnow, V and Chuchalin, A and Babadjanova, G and Pantelejeva, G and Abramova, LI and Tiganov, AS and Polonikov, A and Khusnutdinova, E and Alda, M and Grof, P and Rouleau, GA and Turecki, G and Laprise, C and Rivas, F and Mayoral, F and Kogevinas, M and Grigoroiu-Serbanescu, M and Propping, P and Becker, T and Rietschel, M and Nöthen, MM and Cichon, S}, title = {Genome-wide association study reveals two new risk loci for bipolar disorder.}, journal = {Nature communications}, volume = {5}, number = {}, pages = {3339}, doi = {10.1038/ncomms4339}, pmid = {24618891}, issn = {2041-1723}, support = {001/WHO_/World Health Organization/International ; MOP-13506/CAPMC/CIHR/Canada ; 084703/WT_/Wellcome Trust/United Kingdom ; 64410/CAPMC/CIHR/Canada ; }, mesh = {Adenylyl Cyclases/genetics ; Bipolar Disorder/*genetics ; Female ; Genetic Predisposition to Disease/genetics ; Genome-Wide Association Study/*methods ; Humans ; Male ; Polymorphism, Single Nucleotide/genetics ; }, abstract = {Bipolar disorder (BD) is a common and highly heritable mental illness and genome-wide association studies (GWAS) have robustly identified the first common genetic variants involved in disease aetiology. The data also provide strong evidence for the presence of multiple additional risk loci, each contributing a relatively small effect to BD susceptibility. Large samples are necessary to detect these risk loci. Here we present results from the largest BD GWAS to date by investigating 2.3 million single-nucleotide polymorphisms (SNPs) in a sample of 24,025 patients and controls. We detect 56 genome-wide significant SNPs in five chromosomal regions including previously reported risk loci ANK3, ODZ4 and TRANK1, as well as the risk locus ADCY2 (5p15.31) and a region between MIR2113 and POU3F2 (6q16.1). ADCY2 is a key enzyme in cAMP signalling and our finding provides new insights into the biological mechanisms involved in the development of BD.}, } @article {pmid24618462, year = {2014}, author = {Angly, FE and Fields, CJ and Tyson, GW}, title = {The Bio-Community Perl toolkit for microbial ecology.}, journal = {Bioinformatics (Oxford, England)}, volume = {30}, number = {13}, pages = {1926-1927}, pmid = {24618462}, issn = {1367-4811}, mesh = {Computational Biology/methods ; *Ecosystem ; Humans ; Microbiological Techniques ; Microbiology ; Software Design ; }, abstract = {The development of bioinformatic solutions for microbial ecology in Perl is limited by the lack of modules to represent and manipulate microbial community profiles from amplicon and meta-omics studies. Here we introduce Bio-Community, an open-source, collaborative toolkit that extends BioPerl. Bio-Community interfaces with commonly used programs using various file formats, including BIOM, and provides operations such as rarefaction and taxonomic summaries. Bio-Community will help bioinformaticians to quickly piece together custom analysis pipelines and develop novel software. Availability an implementation: Bio-Community is cross-platform Perl code available from http://search.cpan.org/dist/Bio-Community under the Perl license. A readme file describes software installation and how to contribute.}, } @article {pmid24617898, year = {2014}, author = {Whitehead, AL and Kujala, H and Ives, CD and Gordon, A and Lentini, PE and Wintle, BA and Nicholson, E and Raymond, CM}, title = {Integrating biological and social values when prioritizing places for biodiversity conservation.}, journal = {Conservation biology : the journal of the Society for Conservation Biology}, volume = {28}, number = {4}, pages = {992-1003}, doi = {10.1111/cobi.12257}, pmid = {24617898}, issn = {1523-1739}, mesh = {*Biodiversity ; Conflict, Psychological ; Conservation of Natural Resources/*methods ; Geographic Information Systems ; New South Wales ; *Social Values ; Software ; }, abstract = {The consideration of information on social values in conjunction with biological data is critical for achieving both socially acceptable and scientifically defensible conservation planning outcomes. However, the influence of social values on spatial conservation priorities has received limited attention and is poorly understood. We present an approach that incorporates quantitative data on social values for conservation and social preferences for development into spatial conservation planning. We undertook a public participation GIS survey to spatially represent social values and development preferences and used species distribution models for 7 threatened fauna species to represent biological values. These spatially explicit data were simultaneously included in the conservation planning software Zonation to examine how conservation priorities changed with the inclusion of social data. Integrating spatially explicit information about social values and development preferences with biological data produced prioritizations that differed spatially from the solution based on only biological data. However, the integrated solutions protected a similar proportion of the species' distributions, indicating that Zonation effectively combined the biological and social data to produce socially feasible conservation solutions of approximately equivalent biological value. We were able to identify areas of the landscape where synergies and conflicts between different value sets are likely to occur. Identification of these synergies and conflicts will allow decision makers to target communication strategies to specific areas and ensure effective community engagement and positive conservation outcomes.}, } @article {pmid24615368, year = {2014}, author = {Blackburn, DF and Tran, D and Crawley, A and Lynds, S and Champagne, A and Bresee, L and Remillard, AJ}, title = {Do prior authorization policies discourage first-line antipsychotic use in patients newly discharged from a hospitalization for schizophrenia in Saskatchewan?.}, journal = {Journal of population therapeutics and clinical pharmacology = Journal de la therapeutique des populations et de la pharmacologie clinique}, volume = {21}, number = {1}, pages = {e31-7}, pmid = {24615368}, issn = {2561-8741}, mesh = {Adult ; Antipsychotic Agents/*therapeutic use ; Benzodiazepines/therapeutic use ; Cohort Studies ; Databases, Factual ; Dibenzothiazepines/therapeutic use ; Female ; Humans ; *Insurance, Health, Reimbursement ; Male ; Olanzapine ; Patient Discharge ; Practice Patterns, Physicians'/*statistics & numerical data ; Quetiapine Fumarate ; Retrospective Studies ; Risperidone/therapeutic use ; Saskatchewan ; Schizophrenia/*drug therapy ; }, abstract = {BACKGROUND: Drug benefit providers can decrease prescribing of specific medications through prior authorization policies. In Saskatchewan, certain second generation antipsychotics (SGAs) are recognized as first-line agents to manage schizophrenia; but, require prior authorization because their coverage is restricted in other conditions. We aimed to determine if the need for prior-authorization substantially diminishes prescribing of first-line SGAs in comparison to unrestricted agents.

OBJECTIVES: To conduct an ecological comparison of SGA prescribing with changes in prior- authorization policies between 1997 and 2005 using health-administrative databases in Saskatchewan, Canada.

METHOD: Eligible subjects were discharged from hospital with a first-time primary diagnosis of schizophrenia between 1997 and 2005. SGAs dispensed within 7 days of discharge were used to estimate prescribing preferences for olanzapine and quetiapine relative to risperidone. Percentages of SGA use were age and sex standardized to the 2000 cohort.

RESULTS: Out of 1,277 eligible patients, 521 (41%) received 564 SGA dispensations within 7-days of hospital discharge. Between 1997 and 1998, risperidone was the only SGA covered for first-line use and made up 72.6% (82/113) of SGA use while olanzapine made up 27.4% (31/113) for a crude preference ratio of 0.38 (27.4/72.6). Risperidone use decreased to 65.8% in 1999-2002 and to 47.4% in 2003-2005 as a percentage of SGA dispensations. Correspondingly, the preference ratios for olanzapine and quetiapine increased from 0.40 to 0.57 and from 0.12 to 0.54 in these respective periods.

CONCLUSIONS: The requirement for prior-authorization does not appear to substantially diminish prescribing of first-line SGAs for the treatment of schizophrenia in Saskatchewan, Canada.}, } @article {pmid24614682, year = {2014}, author = {Inoue, A and Kawakami, N and Tsutsumi, A and Shimazu, A and Miyaki, K and Takahashi, M and Kurioka, S and Eguchi, H and Tsuchiya, M and Enta, K and Kosugi, Y and Sakata, T and Totsuzaki, T}, title = {Association of job demands with work engagement of Japanese employees: comparison of challenges with hindrances (J-HOPE).}, journal = {PloS one}, volume = {9}, number = {3}, pages = {e91583}, pmid = {24614682}, issn = {1932-6203}, mesh = {*Asian People ; Demography ; Employment ; Female ; Humans ; Japan ; Male ; *Work ; *Workload ; }, abstract = {OBJECTIVES: Recent epidemiological research in Europe has reported that two groups of job demands, i.e., challenges and hindrances, are differently associated with work engagement. The purpose of the present study was to replicate the cross-sectional association of workload and time pressure (as a challenge) and role ambiguity (as a hindrance) with work engagement among Japanese employees.

METHODS: Between October 2010 and December 2011, a total of 9,134 employees (7,101 men and 1,673 women) from 12 companies in Japan were surveyed using a self-administered questionnaire comprising the Job Content Questionnaire, National Institute for Occupational Safety and Health Generic Job Stress Questionnaire, short 10-item version of the Effort-Reward Imbalance Questionnaire, short nine-item version of the Utrecht Work Engagement Scale, and demographic characteristics. Multilevel regression analyses with a random intercept model were conducted.

RESULTS: After adjusting for demographic characteristics, workload and time pressure showed a positive association with work engagement with a small effect size (standardized coefficient [β] = 0.102, Cohen's d [d] = 0.240) while role ambiguity showed a negative association with a large effect size (β = -0.429, d = 1.011). After additionally adjusting for job resources (i.e., decision latitude, supervisor support, co-worker support, and extrinsic reward), the effect size of workload and time pressure was not attenuated (β = 0.093, d = 0.234) while that of role ambiguity was attenuated but still medium (β = -0.242, d = 0.609).

CONCLUSIONS: Among Japanese employees, challenges such as having higher levels of workload and time pressure may enhance work engagement but hindrances, such as role ambiguity, may reduce it.}, } @article {pmid24614330, year = {2014}, author = {Tang, B and Chen, J and Hou, Y and Meng, E}, title = {Transcriptome immune analysis of the invasive beetle Octodonta nipae (Maulik) (Coleoptera: Chrysomelidae) parasitized by Tetrastichus brontispae Ferrière (Hymenoptera: Eulophidae).}, journal = {PloS one}, volume = {9}, number = {3}, pages = {e91482}, pmid = {24614330}, issn = {1932-6203}, mesh = {Animals ; Cluster Analysis ; Coleoptera/*genetics/*immunology/parasitology ; *Gene Expression Profiling ; Gene Ontology ; Genes, Insect ; Host-Parasite Interactions/genetics ; Hymenoptera/*physiology ; *Introduced Species ; Molecular Sequence Annotation ; Pupa/genetics/parasitology ; Reproducibility of Results ; Reverse Transcriptase Polymerase Chain Reaction ; Sequence Analysis, DNA ; Species Specificity ; Transcription, Genetic ; }, abstract = {The beetle Octodonta nipae (Maulik) (Coleoptera: Chrysomelidae) is a serious invasive insect pest of palm plants in southern China, and the endoparasitoid Tetrastichus brontispae Ferrière (Hymenoptera: Eulophidae) is a natural enemy of this pest that exhibits great ability in the biocontrol of O. nipae. For successful parasitism, endoparasitoids often introduce or secrete various virulence factors to suppress host immunity. To investigate the effects of parasitization by T. brontispae on the O. nipae immune system, the transcriptome of O. nipae pupae was analyzed with a focus on immune-related genes through Illumina sequencing. De novo assembly generated 49,919 unigenes with a mean length of 598 bp. Of these genes, 27,490 unigenes (55.1% of all unigenes) exhibited clear homology to known genes in the NCBI nr database. Parasitization had significant effects on the transcriptome profile of O. nipae pupae, and most of these differentially expressed genes were down-regulated. Importantly, the expression profiles of immune-related genes were significantly regulated after parasitization. Taken together, these transcriptome sequencing efforts shed valuable light on the host (O. nipae) manipulation mechanisms induced by T. brontispae, which will pave the way for the development of novel immune defense-based management strategies of O. nipae, and provide a springboard for further molecular analyses, particularly of O. nipae invasion.}, } @article {pmid24613632, year = {2014}, author = {Voogt, CV and Kuntsche, E and Kleinjan, M and Engels, RC}, title = {The effect of the 'What Do You Drink' web-based brief alcohol intervention on self-efficacy to better understand changes in alcohol use over time: randomized controlled trial using ecological momentary assessment.}, journal = {Drug and alcohol dependence}, volume = {138}, number = {}, pages = {89-97}, doi = {10.1016/j.drugalcdep.2014.02.009}, pmid = {24613632}, issn = {1879-0046}, mesh = {Alcohol Drinking/*prevention & control/*psychology/therapy ; Female ; Humans ; *Internet ; Male ; Models, Psychological ; *Self Efficacy ; *Symptom Assessment ; *Therapy, Computer-Assisted ; Young Adult ; }, abstract = {BACKGROUND: To examine whether (1) the 'What Do You Drink' (WDYD) intervention resulted in drinking refusal self-efficacy (DRSE) changes directly after the intervention, and if so, whether these changes sustained at six-months follow-up and (2) DRSE was related to alcohol use over time, and if so, whether the strength of these relationships differed across conditions. Insight herein can help explain the sustained preventive effects of the WDYD intervention on alcohol use, as reported previously.

METHODS: Alcohol use and DRSE data were collected from 907 participants (60.3% male; M=20.8 (SD=1.7) in a two-arm parallel group randomized controlled trial applying ecological momentary assessment with 30 time-points. Participants were randomized to the experimental (n=456: WDYD intervention) or control condition (n=451: no intervention).

RESULTS: Latent Growth Curve (LGC) analyses that modeled individual change in DRSE over time by condition revealed that participants in the experimental condition experienced a higher social pressure DRSE compared to participants in the control condition at six-months follow-up. Moreover, LGC analyses with time-varying covariates revealed that DRSE was negatively related to weekly alcohol consumption and social pressure DRSE to frequency of binge drinking. The WDYD intervention did not affect the strength of these relationships.

CONCLUSIONS: The WDYD intervention increased the level of social pressure DRSE directly after the intervention that sustained at six-months follow-up. This change is likely to be responsible for the sustained preventive effects of the WDYD intervention on alcohol use, as reported previously.}, } @article {pmid24613138, year = {2014}, author = {Christie, AE}, title = {Prediction of the peptidomes of Tigriopus californicus and Lepeophtheirus salmonis (Copepoda, Crustacea).}, journal = {General and comparative endocrinology}, volume = {201}, number = {}, pages = {87-106}, doi = {10.1016/j.ygcen.2014.02.015}, pmid = {24613138}, issn = {1095-6840}, mesh = {Amino Acid Sequence ; Animals ; *Computational Biology ; Copepoda/genetics/*metabolism ; Crustacea/genetics/*metabolism ; Expressed Sequence Tags ; Molecular Sequence Data ; Peptide Fragments/analysis/genetics/*metabolism ; Peptide Hormones/analysis/genetics/*metabolism ; Proteome/*analysis ; Sequence Homology, Amino Acid ; }, abstract = {Transcriptome mining is a powerful method for crustacean peptide discovery, especially when large sequence datasets are available and an appropriate reference is extant. Recently, a 206,041-sequence transcriptome for the copepod Calanus finmarchicus was mined for peptide-encoding transcripts, with ones for 17 families/subfamilies identified. Here, the deduced Calanus pre/preprohormones were used as templates for peptide discovery in the copepods Tigriopus californicus and Lepeophtheirus salmonis; large transcriptome shotgun assembly datasets are publicly accessible for both species. Sixty-five Tigriopus and 17 Lepeophtheirus transcripts, encompassing 22 and 13 distinct peptide families/subfamilies, respectively, were identified, with the structures of 161 and 70 unique mature peptides predicted from the deduced precursors. The identified peptides included members of the allatostatin A, allatostatin C, bursicon α, bursicon β, CAPA/periviscerokinin/pyrokinin, crustacean cardioactive peptide, crustacean hyperglycemic hormone/ion transport peptide, diuretic hormone 31, FLRFamide, leucokinin, myosuppressin, neuroparsin, neuropeptide F, orcokinin, and tachykinin-related peptide families, most of which possess novel structures, though isoforms from other copepods are known. Of particular note was the discovery of novel isoforms of adipokinetic hormone-corazonin-like peptide, allatotropin, corazonin, eclosion hormone and intocin, peptide families previously unidentified in copepods. In addition, Tigriopus precursors for two previously unknown peptide groups were discovered, one encoding GSEFLamides and the other DXXRLamides; precursors for the novel FXGGXamide family were identified from both Tigriopus and Lepeophtheirus. These data not only greatly expand the catalog of known copepod peptides, but also provide strong foundations for future functional studies of peptidergic signaling in members of this ecologically important crustacean subclass.}, } @article {pmid24608033, year = {2014}, author = {Claes, F and Kuznetsov, D and Liechti, R and Von Dobschuetz, S and Truong, BD and Gleizes, A and Conversa, D and Colonna, A and Demaio, E and Ramazzotto, S and Larfaoui, F and Pinto, J and Le Mercier, P and Xenarios, I and Dauphin, G}, title = {The EMPRES-i genetic module: a novel tool linking epidemiological outbreak information and genetic characteristics of influenza viruses.}, journal = {Database : the journal of biological databases and curation}, volume = {2014}, number = {}, pages = {bau008}, pmid = {24608033}, issn = {1758-0463}, mesh = {*Algorithms ; Computational Biology/*methods ; *Databases, Genetic ; *Disease Outbreaks ; Humans ; Influenza, Human/*epidemiology/genetics/*virology ; Orthomyxoviridae/*genetics/isolation & purification ; Reproducibility of Results ; }, abstract = {Combining epidemiological information, genetic characterization and geomapping in the analysis of influenza can contribute to a better understanding and description of influenza epidemiology and ecology, including possible virus reassortment events. Furthermore, integration of information such as agroecological farming system characteristics can provide new knowledge on risk factors of influenza emergence and spread. Integrating viral characteristics into an animal disease information system is therefore expected to provide a unique tool to trace-and-track particular virus strains; generate clade distributions and spatiotemporal clusters; screen for distribution of viruses with specific molecular markers; identify potential risk factors; and analyze or map viral characteristics related to vaccines used for control and/or prevention. For this purpose, a genetic module was developed within EMPRES-i (FAO's global animal disease information system) linking epidemiological information from influenza events with virus characteristics and enabling combined analysis. An algorithm was developed to act as the interface between EMPRES-i disease event data and publicly available influenza virus sequences in OpenfluDB. This algorithm automatically computes potential links between outbreak event and sequences, which are subsequently manually validated by experts. Subsequently, other virus characteristics such as antiviral resistance can then be associated to outbreak data. To visualize such characteristics on a geographic map, shape files with virus characteristics to overlay on other EMPRES-i map layers (e.g. animal densities) can be generated. The genetic module allows export of associated epidemiological and sequence data for further analysis. FAO has made this tool available for scientists and policy makers. Contributions are expected from users to improve and validate the number of linked influenza events and isolate information as well as the quality of information. Possibilities to interconnect with other influenza sequence databases or to expand the genetic module to other viral diseases (e.g. foot and mouth disease) are being explored. Database OpenfluDB URL: http://openflu.vital-it.ch Database EMPRES-i URL: http://EMPRES-i.fao.org/.}, } @article {pmid24607969, year = {2014}, author = {Cole, JR and Tiedje, JM}, title = {History and impact of RDP: a legacy from Carl Woese to microbiology.}, journal = {RNA biology}, volume = {11}, number = {3}, pages = {239-243}, pmid = {24607969}, issn = {1555-8584}, support = {P42 ES004911/ES/NIEHS NIH HHS/United States ; UH2 DK083993/DK/NIDDK NIH HHS/United States ; UH3 DK083993/DK/NIDDK NIH HHS/United States ; P42-ES004911/ES/NIEHS NIH HHS/United States ; }, mesh = {*Databases, Genetic ; Microbiological Phenomena ; Phylogeny ; RNA, Ribosomal/*genetics ; Sequence Analysis, RNA ; }, abstract = {The Ribosomal Database Project (RDP) grew out of Carl Woese's vision of how rRNA comparative methods could transform biology. First at the University of Illinois Urbana-Champaign, and later at Michigan State University's Center for Microbial Ecology, the project has grown from a few hundred to several million rRNA gene sequences. In the years since Woese started the RDP, publications describing the database and related tools have been cited over 11,000 times in journals spanning a wide range of disciplines, while the RDP website is accessed by 10,000 researchers in over 20,000 analysis sessions each month. This article describes the history of RDP's development over the last two decades.}, } @article {pmid24606915, year = {2014}, author = {Perina, A and von Reumont, BM and Martínez-Lage, A and González-Tizón, AM}, title = {Accessing transcriptomic data for ecologically important genes in the goose barnacle (Pollicipes pollicipes), with particular focus on cement proteins.}, journal = {Marine genomics}, volume = {15}, number = {}, pages = {9-11}, doi = {10.1016/j.margen.2014.02.003}, pmid = {24606915}, issn = {1876-7478}, mesh = {Animals ; Base Sequence ; Cluster Analysis ; Computational Biology ; *Expressed Sequence Tags ; *Gene Library ; Molecular Sequence Annotation ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction ; Proteins/*genetics ; Sequence Analysis, DNA ; Spain ; Thoracica/*genetics/*metabolism ; Transcriptome/*genetics ; }, abstract = {In this study 4310 expressed sequence tags (ESTs) were used to identify potentially useful transcripts for future studies in the gooseneck barnacle Pollicipes pollicipes (Gmelin, 1789). 119 ESTs were obtained in this work and 4191 were taken from Meusemann et al. (2010). The gooseneck barnacle is a sessile pedunculate cirripede of great economic importance that occurs in dense aggregations, and is harvested for human consumption. The assembly of these ESTs yielded 1805 unigenes (461 contigs and 1344 singlets). The identification of cement proteins in our data is particularly interesting for cirripedes. Only a small part of the assembled unigenes could be functionally annotated. However, our results greatly improve our understanding of the biological features of P. pollicipes. In addition to this, a large number of potentially interesting genes were identified in order to serve as the base for future evolutionary studies in P. pollicipes.}, } @article {pmid24606580, year = {2014}, author = {Ma, L and Ma, Q and Li, X and Cheng, L and Li, K and Li, S}, title = {Transcriptomic analysis of differentially expressed genes in the Ras1(CA)-overexpressed and wildtype posterior silk glands.}, journal = {BMC genomics}, volume = {15}, number = {1}, pages = {182}, pmid = {24606580}, issn = {1471-2164}, mesh = {Animals ; Animals, Genetically Modified ; Bombyx/*genetics/metabolism ; Cell Cycle ; Computational Biology/methods ; *Gene Expression Profiling ; *Gene Expression Regulation ; High-Throughput Nucleotide Sequencing ; Insulin/metabolism ; MAP Kinase Signaling System ; Mechanistic Target of Rapamycin Complex 1 ; Molecular Sequence Annotation ; Multiprotein Complexes/metabolism ; Neoplasms/genetics/metabolism ; Phosphatidylinositol 3-Kinases/metabolism ; Purines/metabolism ; Pyrimidines/metabolism ; Reproducibility of Results ; Sequence Analysis, RNA ; Signal Transduction ; TOR Serine-Threonine Kinases/metabolism ; *Transcriptome ; raf Kinases/metabolism ; ras Proteins/*genetics/metabolism ; }, abstract = {BACKGROUND: Using the piggyBac-mediated GAL4/UAS transgenic system established in the silkworm, Bombyx mori, we have previously reported that overexpression of the Ras1(CA) oncogene specifically in the posterior silk gland (PSG) improved cell growth, fibroin synthesis, and thus silk yield. However, the detailed molecular mechanism remains to be fully elucidated. To achieve this goal, Illumina sequencing was used in the present study to compare the transcriptomes of the Ras1(CA)-overexpressed and wildtype PSGs.

RESULTS: The transcriptomic sequencing results in 56 million reads following filtering steps. Most of the reads (~70%) are successfully mapped to the Bombyx genome. The mapped reads are situated within at least 9,133 predicted genes, covering 62.46% genes of the Bombyx genome. GO annotation shows that 2512 of the 2,636 differentially expressed genes (DEGs) are mostly distributed in metabolic process, cell and cell part, and binding, and KEGG annotation shows that 1,941 DEGs are mapped into 277 pathways. Importantly, Ras1(CA) overexpression in the PSG upregulated many DEGs distributed in "pathways in cancer", "insulin signaling pathway", and "MAPK signaling pathway" as well as "purine metabolism" and "pyrimidine metabolism". Transcriptional regulation of these DEGs was verified by quantitative real-time PCR. Moreover, injection of small-molecule chemical inhibitors of the Ras1 downstream effectors into the Ras1(CA)-overexpressed silkworms revealed that both Raf-MAPK and PI3K-TORC1 pathways are required for the Ras1-induced DEG expression.

CONCLUSION: The transcriptomic analysis illustrates that, apart from phosphorylational regulation, Ras1 activates its downstream Raf-MAPK and PI3K-TORC1 pathways at the transcriptional level. Meanwhile, Ras1 increases DNA content and induces endoreplication, at least in part, by upregulating genes in "nucleotide metabolism" and "cell cycle". This study provides further insights into the molecular mechanism of how Ras1(CA) overexpression in the PSG improves silk yield.}, } @article {pmid24606032, year = {2014}, author = {Malé, PJ and Bardon, L and Besnard, G and Coissac, E and Delsuc, F and Engel, J and Lhuillier, E and Scotti-Saintagne, C and Tinaut, A and Chave, J}, title = {Genome skimming by shotgun sequencing helps resolve the phylogeny of a pantropical tree family.}, journal = {Molecular ecology resources}, volume = {14}, number = {5}, pages = {966-975}, doi = {10.1111/1755-0998.12246}, pmid = {24606032}, issn = {1755-0998}, mesh = {Chrysobalanaceae/*classification/*genetics ; Computational Biology/*methods ; DNA, Chloroplast/chemistry/genetics ; DNA, Mitochondrial/chemistry/genetics ; DNA, Plant/chemistry/genetics ; *Genome, Plant ; Molecular Sequence Data ; *Phylogeny ; Sequence Analysis, DNA ; }, abstract = {Whole genome sequencing is helping generate robust phylogenetic hypotheses for a range of taxonomic groups that were previously recalcitrant to classical molecular phylogenetic approaches. As a case study, we performed a shallow shotgun sequencing of eight species in the tropical tree family Chrysobalanaceae to retrieve large fragments of high-copy number DNA regions and test the potential of these regions for phylogeny reconstruction. We were able to assemble the nuclear ribosomal cluster (nrDNA), the complete plastid genome (ptDNA) and a large fraction of the mitochondrial genome (mtDNA) with approximately 1000×, 450× and 120× sequencing depth respectively. The phylogenetic tree obtained with ptDNA resolved five of the seven internal nodes. In contrast, the tree obtained with mtDNA and nrDNA data were largely unresolved. This study demonstrates that genome skimming is a cost-effective approach and shows potential in plant molecular systematics within Chrysobalanaceae and other under-studied groups.}, } @article {pmid24603653, year = {2014}, author = {Wang, C and Wachholtz, M and Wang, J and Liao, X and Lu, G}, title = {Analysis of the skin transcriptome in two oujiang color varieties of common carp.}, journal = {PloS one}, volume = {9}, number = {3}, pages = {e90074}, pmid = {24603653}, issn = {1932-6203}, mesh = {Animals ; Carps/*genetics/metabolism ; *Color ; Gene Ontology ; Metabolic Networks and Pathways/genetics ; Polymorphism, Single Nucleotide ; Sequence Analysis, DNA ; Skin/metabolism ; Skin Pigmentation/*genetics ; *Transcriptome ; }, abstract = {BACKGROUND: Body color and coloration patterns are important phenotypic traits to maintain survival and reproduction activities. The Oujiang color varieties of common carp (Cyprinus carpio var. color), with a narrow distribution in Zhejiang Province of China and a history of aquaculture for over 1,200 years, consistently exhibit a variety of body color patterns. The molecular mechanism underlying diverse color patterns in these variants is unknown. To the practical end, it is essential to develop molecular markers that can distinguish different phenotypes and assist selective breeding.

In this exploratory study, we conducted Roche 454 transcriptome sequencing of two pooled skin tissue samples of Oujiang common carp, which correspond to distinct color patterns, red with big black spots (RB) and whole white (WW), and a total of 737,525 sequence reads were generated. The reads obtained in this study were co-assembled jointly with common carp Roche 454 sequencing reads downloaded from NCBI SRA database, resulting in 43,923 isotigs and 546,676 singletons. Over 31 thousand (31,445; 71.6%) isotigs were found with significant BLAST matches (E<1e-10) to the nr protein database, which corresponds to 12,597 annotated zebrafish genes. A total of 70,947 isotigs and singletons (transcripts) were annotated with Gene Ontology, and 60,221 transcripts were found with corresponding EC numbers. Out of 145 zebrafish pigmentation genes, orthologs for 117 were recovered in Oujiang color carp transcriptome, including 18 found only among singletons. Our transcriptome analysis revealed over 52,902 SNPs in Oujiang common carp, and identified 63 SNP markers that are putatively unique either for RB or WW.

CONCLUSIONS: The transcriptome of Oujiang color varieties of common carp obtained through this study, along with the pigmentation genes recovered and the color pattern-specific molecular markers developed, will facilitate future research on the molecular mechanism of color patterns and promote aquaculture of Oujiang color varieties of common carp through molecular marker assisted-selective breeding.}, } @article {pmid24603433, year = {2014}, author = {Aylagas, E and Borja, A and Rodríguez-Ezpeleta, N}, title = {Environmental status assessment using DNA metabarcoding: towards a genetics based Marine Biotic Index (gAMBI).}, journal = {PloS one}, volume = {9}, number = {3}, pages = {e90529}, pmid = {24603433}, issn = {1932-6203}, mesh = {Animals ; Aquatic Organisms/*classification/*genetics ; *Biodiversity ; DNA Barcoding, Taxonomic/*methods ; DNA Primers/genetics ; Databases, Genetic ; }, abstract = {Marine ecosystem protection and conservation initiatives rely on the assessment of ecological integrity and health status of marine environments. The AZTI's Marine Biotic Index (AMBI), which consists on using macroinvertebrate diversity as indicator of ecosystem health, is used worldwide for this purpose. Yet, this index requires taxonomic assignment of specimens, which typically involves a time and resource consuming visual identification of each sample. DNA barcoding or metabarcoding are potential harmonized, faster and cheaper alternatives for species identification, although the suitability of these methods for easing the implementation of the AMBI is yet to be evaluated. Here, we analyze the requirements for the implementation of a genetics based AMBI (gAMBI), and show, using available sequence data, that information about presence/absence of the most frequently occurring species provides accurate AMBI values. Our results set the basics for the implementation of the gAMBI, which has direct implications for a faster and cheaper marine monitoring and health status assessment.}, } @article {pmid24603359, year = {2014}, author = {Yan, X and Fan, Y and Wei, W and Wang, P and Liu, Q and Wei, Y and Zhang, L and Zhao, G and Yue, J and Zhou, Z}, title = {Production of bioactive ginsenoside compound K in metabolically engineered yeast.}, journal = {Cell research}, volume = {24}, number = {6}, pages = {770-773}, pmid = {24603359}, issn = {1748-7838}, mesh = {Arthritis/prevention & control ; Databases, Genetic ; Expressed Sequence Tags ; Ginsenosides/*biosynthesis/chemistry/therapeutic use ; Humans ; *Metabolic Engineering ; Monosaccharides/chemistry/metabolism ; Open Reading Frames/genetics ; Panax/genetics/metabolism ; Plant Proteins/genetics/metabolism ; Saccharomyces cerevisiae/*metabolism ; }, } @article {pmid24602988, year = {2014}, author = {Zhi, XY and Yao, JC and Li, HW and Huang, Y and Li, WJ}, title = {Genome-wide identification, domain architectures and phylogenetic analysis provide new insights into the early evolution of shikimate pathway in prokaryotes.}, journal = {Molecular phylogenetics and evolution}, volume = {75}, number = {}, pages = {154-164}, doi = {10.1016/j.ympev.2014.02.015}, pmid = {24602988}, issn = {1095-9513}, mesh = {3-Phosphoshikimate 1-Carboxyvinyltransferase/genetics ; Aldehyde-Ketone Transferases/genetics ; Archaea/enzymology/*genetics ; Bacteria/enzymology/*genetics ; *Biological Evolution ; Computational Biology ; Gene Transfer, Horizontal ; Markov Chains ; Metabolic Networks and Pathways/genetics ; Multigene Family ; Phosphorus-Oxygen Lyases/genetics ; Phosphotransferases (Alcohol Group Acceptor)/genetics ; *Phylogeny ; Proteome/analysis ; Sequence Analysis, DNA ; Shikimic Acid/*metabolism ; }, abstract = {Despite intense scrutiny from researchers in the fields of biochemistry and metabolism, our understanding of the evolutionary history of the key anabolic shikimate pathway remains limited. To shed light on the early evolutionary events leading to the assembly of the pathway, we investigated the distributions, domain architectures and phylogenies of component enzymes using a bioinformatic procedure based on Hidden Markov Model profiles. The aro genes for the canonical shikimate pathway had most wider distribution in prokaryotes; and the variant pathway coordinated by 2-amino-3,7-dideoxy-D-threo-hept-6-ulosonic acid (ADH) synthase and type II 3-dehydroquinate (DHQ) synthase could be identified in most of archaeal species. In addition, the ancient bidirectional horizontal gene transfer events had happened between two prokaryotic domains: Bacteria and Archaea. Besides 3-deoxy-D-arabino-heptulosonate 7-phosphate (DAHP) synthase, the phylogenetically distinct subfamilies of 5-enolpyruvylshikimate 3-phosphate (EPSP) synthase and chorismate synthase had ever emerged in the evolutionary history of shikimate pathway. These findings provide new insight into the early evolution of the shikimate pathway and advance our understanding of the evolution of metabolic pathways.}, } @article {pmid24602261, year = {2014}, author = {Wang, B and Ekblom, R and Bunikis, I and Siitari, H and Höglund, J}, title = {Whole genome sequencing of the black grouse (Tetrao tetrix): reference guided assembly suggests faster-Z and MHC evolution.}, journal = {BMC genomics}, volume = {15}, number = {1}, pages = {180}, pmid = {24602261}, issn = {1471-2164}, mesh = {Animals ; Birds/*genetics ; Chromosomes ; Computational Biology/methods ; Evolution, Molecular ; *Genome ; *Genomics ; *High-Throughput Nucleotide Sequencing ; Major Histocompatibility Complex/genetics ; Male ; Molecular Sequence Annotation ; Polymorphism, Single Nucleotide ; Repetitive Sequences, Nucleic Acid ; }, abstract = {BACKGROUND: The different regions of a genome do not evolve at the same rate. For example, comparative genomic studies have suggested that the sex chromosomes and the regions harbouring the immune defence genes in the Major Histocompatability Complex (MHC) may evolve faster than other genomic regions. The advent of the next generation sequencing technologies has made it possible to study which genomic regions are evolutionary liable to change and which are static, as well as enabling an increasing number of genome studies of non-model species. However, de novo sequencing of the whole genome of an organism remains non-trivial. In this study, we present the draft genome of the black grouse, which was developed using a reference-guided assembly strategy.

RESULTS: We generated 133 Gbp of sequence data from one black grouse individual by the SOLiD platform and used a combination of de novo assembly and chicken reference genome mapping to assemble the reads into 4572 scaffolds with a total length of 1022 Mb. The draft genome well covers the main chicken chromosomes 1 ~ 28 and Z which have a total length of 1001 Mb. The draft genome is fragmented, but has a good coverage of the homologous chicken genes. Especially, 33.0% of the coding regions of the homologous genes have more than 90% proportion of their sequences covered. In addition, we identified ~1 M SNPs from the genome and identified 106 genomic regions which had a high nucleotide divergence between black grouse and chicken or between black grouse and turkey.

CONCLUSIONS: Our results support the hypothesis that the chromosome X (Z) evolves faster than the autosomes and our data are consistent with the MHC regions being more liable to change than the genome average. Our study demonstrates how a moderate sequencing effort can be combined with existing genome references to generate a draft genome for a non-model species.}, } @article {pmid24598422, year = {2014}, author = {Stewart, TA and Smith, WL and Coates, MI}, title = {The origins of adipose fins: an analysis of homoplasy and the serial homology of vertebrate appendages.}, journal = {Proceedings. Biological sciences}, volume = {281}, number = {1781}, pages = {20133120}, pmid = {24598422}, issn = {1471-2954}, mesh = {Adaptation, Biological/physiology ; Adipose Tissue/*anatomy & histology ; Animal Fins/*anatomy & histology ; Animals ; *Biological Evolution ; Computational Biology ; *Fishes ; Likelihood Functions ; Models, Genetic ; *Phylogeny ; Species Specificity ; }, abstract = {Adipose fins are appendages found on the dorsal midline between the dorsal and caudal fins in more than 6000 living species of teleost fishes. It has been consistently argued that adipose fins evolved once and have been lost repeatedly across teleosts owing to limited function. Here, we demonstrate that adipose fins originated repeatedly by using phylogenetic and anatomical evidence. This suggests that adipose fins are adaptive, although their function remains undetermined. To test for generalities in the evolution of form in de novo vertebrate fins, we studied the skeletal anatomy of adipose fins across 620 species belonging to 186 genera and 55 families. Adipose fins have repeatedly evolved endoskeletal plates, anterior dermal spines and fin rays. The repeated evolution of fin rays in adipose fins suggests that these fins can evolve new tissue types and increased structural complexity by expressing fin-associated developmental modules in these new territories. Patterns of skeletal elaboration differ between the various occurrences of adipose fins and challenge prevailing hypotheses for vertebrate fin origin. Adipose fins represent a powerful and, thus far, barely studied model for exploring the evolution of vertebrate limbs and the roles of adaptation and generative biases in morphological evolution.}, } @article {pmid24595283, year = {2014}, author = {Peng, Y and Gao, X and Li, R and Cao, G}, title = {Transcriptome sequencing and De Novo analysis of Youngia japonica using the illumina platform.}, journal = {PloS one}, volume = {9}, number = {3}, pages = {e90636}, pmid = {24595283}, issn = {1932-6203}, mesh = {Asteraceae/*genetics ; Databases, Protein ; Gene Expression Profiling ; Gene Ontology ; Genes, Plant ; Genetic Variation ; Molecular Sequence Annotation ; RNA, Plant/genetics/isolation & purification ; Sequence Analysis, RNA ; *Transcriptome ; }, abstract = {Youngia japonica, a weed species distributed worldwide, has been widely used in traditional Chinese medicine. It is an ideal plant for studying the evolution of Asteraceae plants because of its short life history and abundant source. However, little is known about its evolution and genetic diversity. In this study, de novo transcriptome sequencing was conducted for the first time for the comprehensive analysis of the genetic diversity of Y. japonica. The Y. japonica transcriptome was sequenced using Illumina paired-end sequencing technology. We produced 21,847,909 high-quality reads for Y. japonica and assembled them into contigs. A total of 51,850 unigenes were identified, among which 46,087 were annotated in the NCBI non-redundant protein database and 41,752 were annotated in the Swiss-Prot database. We mapped 9,125 unigenes onto 163 pathways using the Kyoto Encyclopedia of Genes and Genomes Pathway database. In addition, 3,648 simple sequence repeats (SSRs) were detected. Our data provide the most comprehensive transcriptome resource currently available for Y. japonica. C4 photosynthesis unigenes were found in the biological process of Y. japonica. There were 5596 unigenes related to defense response and 1344 ungienes related to signal transduction mechanisms (10.95%). These data provide insights into the genetic diversity of Y. japonica. Numerous SSRs contributed to the development of novel markers. These data may serve as a new valuable resource for genomic studies on Youngia and, more generally, Cichoraceae.}, } @article {pmid24595056, year = {2014}, author = {Walls, RL and Deck, J and Guralnick, R and Baskauf, S and Beaman, R and Blum, S and Bowers, S and Buttigieg, PL and Davies, N and Endresen, D and Gandolfo, MA and Hanner, R and Janning, A and Krishtalka, L and Matsunaga, A and Midford, P and Morrison, N and Ó Tuama, É and Schildhauer, M and Smith, B and Stucky, BJ and Thomer, A and Wieczorek, J and Whitacre, J and Wooley, J}, title = {Semantics in support of biodiversity knowledge discovery: an introduction to the biological collections ontology and related ontologies.}, journal = {PloS one}, volume = {9}, number = {3}, pages = {e89606}, pmid = {24595056}, issn = {1932-6203}, support = {U54 HG004028/HG/NHGRI NIH HHS/United States ; }, mesh = {*Biodiversity ; *Knowledge ; *Semantics ; }, abstract = {The study of biodiversity spans many disciplines and includes data pertaining to species distributions and abundances, genetic sequences, trait measurements, and ecological niches, complemented by information on collection and measurement protocols. A review of the current landscape of metadata standards and ontologies in biodiversity science suggests that existing standards such as the Darwin Core terminology are inadequate for describing biodiversity data in a semantically meaningful and computationally useful way. Existing ontologies, such as the Gene Ontology and others in the Open Biological and Biomedical Ontologies (OBO) Foundry library, provide a semantic structure but lack many of the necessary terms to describe biodiversity data in all its dimensions. In this paper, we describe the motivation for and ongoing development of a new Biological Collections Ontology, the Environment Ontology, and the Population and Community Ontology. These ontologies share the aim of improving data aggregation and integration across the biodiversity domain and can be used to describe physical samples and sampling processes (for example, collection, extraction, and preservation techniques), as well as biodiversity observations that involve no physical sampling. Together they encompass studies of: 1) individual organisms, including voucher specimens from ecological studies and museum specimens, 2) bulk or environmental samples (e.g., gut contents, soil, water) that include DNA, other molecules, and potentially many organisms, especially microbes, and 3) survey-based ecological observations. We discuss how these ontologies can be applied to biodiversity use cases that span genetic, organismal, and ecosystem levels of organization. We argue that if adopted as a standard and rigorously applied and enriched by the biodiversity community, these ontologies would significantly reduce barriers to data discovery, integration, and exchange among biodiversity resources and researchers.}, } @article {pmid24590051, year = {2014}, author = {Xie, H and Yao, G and Wang, P}, title = {Identifying regional key eco-space to maintain ecological security using GIS.}, journal = {International journal of environmental research and public health}, volume = {11}, number = {3}, pages = {2550-2568}, pmid = {24590051}, issn = {1660-4601}, mesh = {China ; Conservation of Natural Resources/*methods ; Ecology/*methods ; *Ecosystem ; *Geographic Information Systems ; }, abstract = {Ecological security and environmental sustainability are the foundations of sustainable development. With the acceleration of urbanization, increasing human activities have promoted greater impacts on the eco-spaces that maintain ecological security. Regional key eco-space has become the primary need to maintain environmental sustainability and can offer society with continued ecosystem services. In this paper, considering the security of water resources, biodiversity conservation, disaster avoidance and protection and natural recreation, an integrated index of eco-space importance was established and a method for identifying key eco-space was created using GIS, with Lanzhou City, China as a case study. The results show that the area of core eco-space in the Lanzhou City is approximately 50,908.7 hm(2), accounting for 40% of the region's total area. These areas mainly consist of geological hazard protection zones and the core zones of regional river systems, wetlands, nature reserves, forest parks and scenic spots. The results of this study provide some guidance for the management of ecological security, ecological restoration and environmental sustainability.}, } @article {pmid24588726, year = {2014}, author = {Forkman, J and Piepho, HP}, title = {Parametric bootstrap methods for testing multiplicative terms in GGE and AMMI models.}, journal = {Biometrics}, volume = {70}, number = {3}, pages = {639-647}, doi = {10.1111/biom.12162}, pmid = {24588726}, issn = {1541-0420}, mesh = {Algorithms ; Biometry/*methods ; Computer Simulation ; Data Interpretation, Statistical ; *Gene-Environment Interaction ; Genetic Association Studies/*methods ; Genotype ; *Models, Genetic ; *Models, Statistical ; Plants/*genetics ; }, abstract = {The genotype main effects and genotype-by-environment interaction effects (GGE) model and the additive main effects and multiplicative interaction (AMMI) model are two common models for analysis of genotype-by-environment data. These models are frequently used by agronomists, plant breeders, geneticists and statisticians for analysis of multi-environment trials. In such trials, a set of genotypes, for example, crop cultivars, are compared across a range of environments, for example, locations. The GGE and AMMI models use singular value decomposition to partition genotype-by-environment interaction into an ordered sum of multiplicative terms. This article deals with the problem of testing the significance of these multiplicative terms in order to decide how many terms to retain in the final model. We propose parametric bootstrap methods for this problem. Models with fixed main effects, fixed multiplicative terms and random normally distributed errors are considered. Two methods are derived: a full and a simple parametric bootstrap method. These are compared with the alternatives of using approximate F-tests and cross-validation. In a simulation study based on four multi-environment trials, both bootstrap methods performed well with regard to Type I error rate and power. The simple parametric bootstrap method is particularly easy to use, since it only involves repeated sampling of standard normally distributed values. This method is recommended for selecting the number of multiplicative terms in GGE and AMMI models. The proposed methods can also be used for testing components in principal component analysis.}, } @article {pmid24587745, year = {2014}, author = {D'Oliveira Albanus, R and Siqueira Dalmolin, RJ and Rybarczyk-Filho, JL and Alves Castro, MA and Fonseca Moreira, JC}, title = {Differential evolutionary constraints in the evolution of chemoreceptors: a murine and human case study.}, journal = {TheScientificWorldJournal}, volume = {2014}, number = {}, pages = {696485}, pmid = {24587745}, issn = {1537-744X}, mesh = {Analysis of Variance ; Animals ; Chemoreceptor Cells/*metabolism ; Cluster Analysis ; Computational Biology ; *Evolution, Molecular ; Gene Ontology ; Humans ; Mice ; Models, Genetic ; Phylogeny ; Rats ; Receptors, G-Protein-Coupled/*genetics/metabolism ; Signal Transduction/*genetics ; Species Specificity ; }, abstract = {Chemoreception is among the most important sensory modalities in animals. Organisms use the ability to perceive chemical compounds in all major ecological activities. Recent studies have allowed the characterization of chemoreceptor gene families. These genes present strikingly high variability in copy numbers and pseudogenization degrees among different species, but the mechanisms underlying their evolution are not fully understood. We have analyzed the functional networks of these genes, their orthologs distribution, and performed phylogenetic analyses in order to investigate their evolutionary dynamics. We have modeled the chemosensory networks and compared the evolutionary constraints of their genes in Mus musculus, Homo sapiens, and Rattus norvegicus. We have observed significant differences regarding the constraints on the orthologous groups and network topologies of chemoreceptors and signal transduction machinery. Our findings suggest that chemosensory receptor genes are less constrained than their signal transducing machinery, resulting in greater receptor diversity and conservation of information processing pathways. More importantly, we have observed significant differences among the receptors themselves, suggesting that olfactory and bitter taste receptors are more conserved than vomeronasal receptors.}, } @article {pmid24587335, year = {2014}, author = {Glaubitz, JC and Casstevens, TM and Lu, F and Harriman, J and Elshire, RJ and Sun, Q and Buckler, ES}, title = {TASSEL-GBS: a high capacity genotyping by sequencing analysis pipeline.}, journal = {PloS one}, volume = {9}, number = {2}, pages = {e90346}, pmid = {24587335}, issn = {1932-6203}, mesh = {Animals ; Breeding ; Data Mining ; Genetics, Population ; Genotyping Techniques/economics/*methods ; High-Throughput Nucleotide Sequencing ; Humans ; Polymorphism, Single Nucleotide ; *Software ; Zea mays/*genetics ; }, abstract = {Genotyping by sequencing (GBS) is a next generation sequencing based method that takes advantage of reduced representation to enable high throughput genotyping of large numbers of individuals at a large number of SNP markers. The relatively straightforward, robust, and cost-effective GBS protocol is currently being applied in numerous species by a large number of researchers. Herein we describe a bioinformatics pipeline, TASSEL-GBS, designed for the efficient processing of raw GBS sequence data into SNP genotypes. The TASSEL-GBS pipeline successfully fulfills the following key design criteria: (1) Ability to run on the modest computing resources that are typically available to small breeding or ecological research programs, including desktop or laptop machines with only 8-16 GB of RAM, (2) Scalability from small to extremely large studies, where hundreds of thousands or even millions of SNPs can be scored in up to 100,000 individuals (e.g., for large breeding programs or genetic surveys), and (3) Applicability in an accelerated breeding context, requiring rapid turnover from tissue collection to genotypes. Although a reference genome is required, the pipeline can also be run with an unfinished "pseudo-reference" consisting of numerous contigs. We describe the TASSEL-GBS pipeline in detail and benchmark it based upon a large scale, species wide analysis in maize (Zea mays), where the average error rate was reduced to 0.0042 through application of population genetic-based SNP filters. Overall, the GBS assay and the TASSEL-GBS pipeline provide robust tools for studying genomic diversity.}, } @article {pmid24587272, year = {2014}, author = {Ultsch, A and Lötsch, J}, title = {Functional abstraction as a method to discover knowledge in gene ontologies.}, journal = {PloS one}, volume = {9}, number = {2}, pages = {e90191}, pmid = {24587272}, issn = {1932-6203}, mesh = {Computational Biology/*methods ; Data Mining/*methods ; *Gene Ontology ; Humans ; Vocabulary, Controlled ; }, abstract = {Computational analyses of functions of gene sets obtained in microarray analyses or by topical database searches are increasingly important in biology. To understand their functions, the sets are usually mapped to Gene Ontology knowledge bases by means of over-representation analysis (ORA). Its result represents the specific knowledge of the functionality of the gene set. However, the specific ontology typically consists of many terms and relationships, hindering the understanding of the 'main story'. We developed a methodology to identify a comprehensibly small number of GO terms as "headlines" of the specific ontology allowing to understand all central aspects of the roles of the involved genes. The Functional Abstraction method finds a set of headlines that is specific enough to cover all details of a specific ontology and is abstract enough for human comprehension. This method exceeds the classical approaches at ORA abstraction and by focusing on information rather than decorrelation of GO terms, it directly targets human comprehension. Functional abstraction provides, with a maximum of certainty, information value, coverage and conciseness, a representation of the biological functions in a gene set plays a role. This is the necessary means to interpret complex Gene Ontology results thus strengthening the role of functional genomics in biomarker and drug discovery.}, } @article {pmid24587222, year = {2014}, author = {Paynter, S and Yakob, L and Simões, EA and Lucero, MG and Tallo, V and Nohynek, H and Ware, RS and Weinstein, P and Williams, G and Sly, PD}, title = {Using mathematical transmission modelling to investigate drivers of respiratory syncytial virus seasonality in children in the Philippines.}, journal = {PloS one}, volume = {9}, number = {2}, pages = {e90094}, pmid = {24587222}, issn = {1932-6203}, mesh = {Algorithms ; Child ; Child, Preschool ; Humans ; Incidence ; Infant ; Infant, Newborn ; *Models, Theoretical ; Philippines/epidemiology ; Respiratory Syncytial Virus Infections/*epidemiology/*transmission ; *Respiratory Syncytial Virus, Human ; *Seasons ; Seroepidemiologic Studies ; }, abstract = {We used a mathematical transmission model to estimate when ecological drivers of respiratory syncytial virus (RSV) transmissibility would need to act in order to produce the observed seasonality of RSV in the Philippines. We estimated that a seasonal peak in transmissibility would need to occur approximately 51 days prior to the observed peak in RSV cases (range 49 to 67 days). We then compared this estimated seasonal pattern of transmissibility to the seasonal patterns of possible ecological drivers of transmissibility: rainfall, humidity and temperature patterns, nutritional status, and school holidays. The timing of the seasonal patterns of nutritional status and rainfall were both consistent with the estimated seasonal pattern of transmissibility and these are both plausible drivers of the seasonality of RSV in this setting.}, } @article {pmid24587149, year = {2014}, author = {Ducatez, S and Lefebvre, L}, title = {Patterns of research effort in birds.}, journal = {PloS one}, volume = {9}, number = {2}, pages = {e89955}, pmid = {24587149}, issn = {1932-6203}, mesh = {*Animal Distribution ; Animals ; Birds/*genetics/*physiology ; Databases, Factual ; Geography ; History, 20th Century ; History, 21st Century ; *Phylogeny ; Physiology, Comparative/*methods ; Research/*history ; Research Design/*trends ; Species Specificity ; }, abstract = {Between species differences in research effort can lead to biases in our global view of evolution, ecology and conservation. The increase in meta-taxonomic comparative analyses on birds underlines the need to better address how research effort is distributed in this class. Methods have been developed to choose which species should be studied to obtain unbiased comparative data sets, but a precise and global knowledge of research effort is required to be able to properly apply them. We address this issue by providing a data set of research effort (number of papers from 1978 to 2008 in the Zoological Record database) estimates for the 10,064 species of birds. We then test whether research effort is associated with phylogeny, geography and eleven different life history and ecological traits. We show that phylogeny accounts for a large proportion of the variance, while geographic range and all the tested traits are also significant contributors to research effort variance. We identify avian taxa that are under- and overstudied and address the importance of research effort biases in evaluating vulnerability to extinction, with non-threatened species studied twice as much as threatened ones. Our research effort data set covering the entire class Aves provides a tool for researchers to incorporate this potential confounding variable in comparative analyses.}, } @article {pmid24586863, year = {2014}, author = {Dupont, CL and Larsson, J and Yooseph, S and Ininbergs, K and Goll, J and Asplund-Samuelsson, J and McCrow, JP and Celepli, N and Allen, LZ and Ekman, M and Lucas, AJ and Hagström, Å and Thiagarajan, M and Brindefalk, B and Richter, AR and Andersson, AF and Tenney, A and Lundin, D and Tovchigrechko, A and Nylander, JA and Brami, D and Badger, JH and Allen, AE and Rusch, DB and Hoffman, J and Norrby, E and Friedman, R and Pinhassi, J and Venter, JC and Bergman, B}, title = {Functional tradeoffs underpin salinity-driven divergence in microbial community composition.}, journal = {PloS one}, volume = {9}, number = {2}, pages = {e89549}, pmid = {24586863}, issn = {1932-6203}, mesh = {Bacteria/*classification/genetics ; Baltic States ; Ecosystem ; *Metagenome ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S ; *Salinity ; Seawater/*microbiology ; *Water Microbiology ; }, abstract = {Bacterial community composition and functional potential change subtly across gradients in the surface ocean. In contrast, while there are significant phylogenetic divergences between communities from freshwater and marine habitats, the underlying mechanisms to this phylogenetic structuring yet remain unknown. We hypothesized that the functional potential of natural bacterial communities is linked to this striking divide between microbiomes. To test this hypothesis, metagenomic sequencing of microbial communities along a 1,800 km transect in the Baltic Sea area, encompassing a continuous natural salinity gradient from limnic to fully marine conditions, was explored. Multivariate statistical analyses showed that salinity is the main determinant of dramatic changes in microbial community composition, but also of large scale changes in core metabolic functions of bacteria. Strikingly, genetically and metabolically different pathways for key metabolic processes, such as respiration, biosynthesis of quinones and isoprenoids, glycolysis and osmolyte transport, were differentially abundant at high and low salinities. These shifts in functional capacities were observed at multiple taxonomic levels and within dominant bacterial phyla, while bacteria, such as SAR11, were able to adapt to the entire salinity gradient. We propose that the large differences in central metabolism required at high and low salinities dictate the striking divide between freshwater and marine microbiomes, and that the ability to inhabit different salinity regimes evolved early during bacterial phylogenetic differentiation. These findings significantly advance our understanding of microbial distributions and stress the need to incorporate salinity in future climate change models that predict increased levels of precipitation and a reduction in salinity.}, } @article {pmid24586306, year = {2014}, author = {Schweingruber, FH and Ríha, P and Doležal, J}, title = {Variation in stem anatomical characteristics of Campanuloideae species in relation to evolutionary history and ecological preferences.}, journal = {PloS one}, volume = {9}, number = {2}, pages = {e88199}, pmid = {24586306}, issn = {1932-6203}, mesh = {Adaptation, Biological/genetics/*physiology ; Bayes Theorem ; *Biological Evolution ; Campanulaceae/*anatomy & histology ; Computational Biology ; *Ecosystem ; Models, Genetic ; *Phylogeny ; Plant Stems/*anatomy & histology ; Species Specificity ; }, abstract = {BACKGROUND: The detailed knowledge of plant anatomical characters and their variation among closely related taxa is key to understanding their evolution and function. We examined anatomical variation in 46 herbaceous taxa from the subfamily Campanuloideae (Campanulaceae) to link this information with their phylogeny, ecology and comparative material of 56 woody tropical taxa from the subfamily Lobelioideae. The species studied covered major environmental gradients from Mediterranean to Arctic zones, allowing us to test hypotheses on the evolution of anatomical structure in relation to plant competitive ability and ecological preferences.

To understand the evolution of anatomical diversity, we reconstructed the phylogeny of studied species from nucleotide sequences and examined the distribution of anatomical characters on the resulting phylogenetic tree. Redundancy analysis, with phylogenetic corrections, was used to separate the evolutionary inertia from the adaptation to the environment. A large anatomical diversity exists within the Campanuloideae. Traits connected with the quality of fibres were the most congruent with phylogeny, and the Rapunculus 2 ("phyteumoid") clade was especially distinguished by a number of characters (absence of fibres, pervasive parenchyma, type of rays) from two other clades (Campanula s. str. and Rapunculus 1) characterized by the dominance of fibres and the absence of parenchyma. Septate fibres are an exclusive trait in the Lobelioideae, separating it clearly from the Campanuloideae where annual rings, pervasive parenchyma and crystals in the phellem are characteristic features.

CONCLUSIONS/SIGNIFICANCE: Despite clear phylogenetic inertia in the anatomical features studied, the ecological attributes and plant height had a significant effect on anatomical divergence. From all three evolutionary clades, the taller species converged towards similar anatomical structure, characterized by a smaller number of early wood vessels of large diameter, thinner cell-walls and alternate intervessel pits, while the opposite trend was found in small Arctic and alpine taxa. This supports the existing generalization that narrower vessels allow plants to grow in colder places where they can avoid freezing-induced embolism, while taller plants have wider vessels to minimize hydraulic resistance with their greater path lengths.}, } @article {pmid24586133, year = {2014}, author = {Garcia, T and Brunnet, LG and De Monte, S}, title = {Differential adhesion between moving particles as a mechanism for the evolution of social groups.}, journal = {PLoS computational biology}, volume = {10}, number = {2}, pages = {e1003482}, pmid = {24586133}, issn = {1553-7358}, mesh = {Algorithms ; Bacterial Adhesion/*physiology ; *Biological Evolution ; Cell Adhesion/*physiology ; Computational Biology ; Dictyosteliida/physiology ; Game Theory ; Humans ; *Models, Biological ; Motion ; Myxococcales/physiology ; Selection, Genetic ; Social Behavior ; }, abstract = {The evolutionary stability of cooperative traits, that are beneficial to other individuals but costly to their carrier, is considered possible only through the establishment of a sufficient degree of assortment between cooperators. Chimeric microbial populations, characterized by simple interactions between unrelated individuals, restrain the applicability of standard mechanisms generating such assortment, in particular when cells disperse between successive reproductive events such as happens in Dicyostelids and Myxobacteria. In this paper, we address the evolutionary dynamics of a costly trait that enhances attachment to others as well as group cohesion. By modeling cells as self-propelled particles moving on a plane according to local interaction forces and undergoing cycles of aggregation, reproduction and dispersal, we show that blind differential adhesion provides a basis for assortment in the process of group formation. When reproductive performance depends on the social context of players, evolution by natural selection can lead to the success of the social trait, and to the concomitant emergence of sizeable groups. We point out the conditions on the microscopic properties of motion and interaction that make such evolutionary outcome possible, stressing that the advent of sociality by differential adhesion is restricted to specific ecological contexts. Moreover, we show that the aggregation process naturally implies the existence of non-aggregated particles, and highlight their crucial evolutionary role despite being largely neglected in theoretical models for the evolution of sociality.}, } @article {pmid24586132, year = {2014}, author = {Lao, O and Liu, F and Wollstein, A and Kayser, M}, title = {GAGA: a new algorithm for genomic inference of geographic ancestry reveals fine level population substructure in Europeans.}, journal = {PLoS computational biology}, volume = {10}, number = {2}, pages = {e1003480}, pmid = {24586132}, issn = {1553-7358}, mesh = {*Algorithms ; Analysis of Variance ; Computational Biology ; Computer Simulation ; Databases, Genetic/statistics & numerical data ; Europe ; Genetic Variation ; Genetics, Population/*statistics & numerical data ; Genome, Human ; Humans ; Models, Genetic ; Multigene Family ; Polymorphism, Single Nucleotide ; White People/genetics ; }, abstract = {Attempts to detect genetic population substructure in humans are troubled by the fact that the vast majority of the total amount of observed genetic variation is present within populations rather than between populations. Here we introduce a new algorithm for transforming a genetic distance matrix that reduces the within-population variation considerably. Extensive computer simulations revealed that the transformed matrix captured the genetic population differentiation better than the original one which was based on the T1 statistic. In an empirical genomic data set comprising 2,457 individuals from 23 different European subpopulations, the proportion of individuals that were determined as a genetic neighbour to another individual from the same sampling location increased from 25% with the original matrix to 52% with the transformed matrix. Similarly, the percentage of genetic variation explained between populations by means of Analysis of Molecular Variance (AMOVA) increased from 1.62% to 7.98%. Furthermore, the first two dimensions of a classical multidimensional scaling (MDS) using the transformed matrix explained 15% of the variance, compared to 0.7% obtained with the original matrix. Application of MDS with Mclust, SPA with Mclust, and GemTools algorithms to the same dataset also showed that the transformed matrix gave a better association of the genetic clusters with the sampling locations, and particularly so when it was used in the AMOVA framework with a genetic algorithm. Overall, the new matrix transformation introduced here substantially reduces the within population genetic differentiation, and can be broadly applied to methods such as AMOVA to enhance their sensitivity to reveal population substructure. We herewith provide a publically available (http://www.erasmusmc.nl/fmb/resources/GAGA) model-free method for improved genetic population substructure detection that can be applied to human as well as any other species data in future studies relevant to evolutionary biology, behavioural ecology, medicine, and forensics.}, } @article {pmid24582916, year = {2014}, author = {Forbush, KT and Hunt, TK}, title = {Characterization of eating patterns among individuals with eating disorders: what is the state of the plate?.}, journal = {Physiology & behavior}, volume = {134}, number = {}, pages = {92-109}, doi = {10.1016/j.physbeh.2014.02.045}, pmid = {24582916}, issn = {1873-507X}, mesh = {Databases, Bibliographic/statistics & numerical data ; Diet/*psychology ; Energy Intake ; Energy Metabolism ; Feeding Behavior/physiology/*psychology ; Feeding and Eating Disorders/diagnosis/*physiopathology/*psychology ; Humans ; }, abstract = {Eating disorders will affect approximately 18 million individuals in the United States at some point in their lives, and are associated with significant psychological distress, psychosocial and quality-of-life impairment, medical morbidity, and mortality. Although aberrant eating behaviors play a central role in diagnostic definitions for eating disorders, much remains to be learned about eating patterns, diet quality, and energy balance among individuals with eating pathology. The goal of the current paper was to systematically review and integrate findings from published research studies characterizing the eating behaviors of individuals with eating disorders, including findings from both descriptive and laboratory-based research. We also describe results from studies using ecological momentary assessment - a methodology that assesses individuals' behaviors in their natural environment as they occur, which may reduce retrospective recall bias, and provide improved ability to prospectively assess the temporal occur of changes in multiple eating behaviors over time. We conclude with suggestions for future research, including the need for additional studies to test for differences in eating patterns among different demographic groups of individuals with eating disorders, and the need for new, more objective, assessment tools.}, } @article {pmid24576006, year = {2014}, author = {Latimer, CA and McGuigan, K and Wilson, RS and Blows, MW and Chenoweth, SF}, title = {The contribution of spontaneous mutations to thermal sensitivity curve variation in Drosophila serrata.}, journal = {Evolution; international journal of organic evolution}, volume = {68}, number = {6}, pages = {1824-1837}, doi = {10.1111/evo.12392}, pmid = {24576006}, issn = {1558-5646}, mesh = {Animals ; *Cold-Shock Response ; Data Interpretation, Statistical ; Drosophila/*genetics ; Female ; *Genetic Variation ; *Heat-Shock Response ; *Locomotion ; Male ; *Mutation ; Sex Factors ; }, abstract = {Many traits studied in ecology and evolutionary biology change their expression in response to a continuously varying environmental factor. One well-studied example are thermal performance curves (TPCs); continuous reaction norms that describe the relationship between organismal performance and temperature and are useful for understanding the trade-offs involved in thermal adaptation. We characterized curves describing the thermal sensitivity of voluntary locomotor activity in a set of 66 spontaneous mutation accumulation lines in the fly Drosophila serrata. Factor-analytic modeling of the mutational variance-covariance matrix, M, revealed support for three axes of mutational variation in males and two in females. These independent axes of mutational variance corresponded well to the major axes of TPC variation required for different types of thermal adaptation; "faster-slower" representing changes in performance largely independent of temperature, and the "hotter-colder" and "generalist-specialist" axes, representing trade-offs. In contrast to its near-absence from standing variance in this species, a "faster-slower" axis, accounted for most mutational variance (75% in males and 66% in females) suggesting selection may easily fix or remove these types of mutations in outbred populations. Axes resembling the "hotter-colder" and "generalist-specialist" modes of variation contributed less mutational variance but nonetheless point to an appreciable input of new mutations that may contribute to thermal adaptation.}, } @article {pmid24575518, year = {2013}, author = {Severinghaus, MR}, title = {Caring about community, ecology and the lives of women.}, journal = {Beginnings (American Holistic Nurses' Association)}, volume = {33}, number = {5}, pages = {14-16}, pmid = {24575518}, issn = {1071-2984}, mesh = {Community Networks/*organization & administration ; Cooperative Behavior ; Dominican Republic ; Environmental Health/*methods ; Female ; Health Promotion/*methods ; Holistic Nursing/*methods ; Humans ; *Nurse's Role ; Socioeconomic Factors ; *Women's Health ; }, abstract = {The front lines of caring extend far beyond U.S. borders. Some holistic nurses are using their skill and knowledge to create sustainable change in other countries. With the help of her local Vermont community, AHNA member Margarita (Rita) Severinghaus is applying the principles and values of holistic nursing to improve women's lives in her mother's childhood village in the Dominican Republic.}, } @article {pmid24573307, year = {2014}, author = {Oeberst, A and von der Beck, I and Nestler, S}, title = {Reading about explanations enhances perceptions of inevitability and foreseeability: a cross-cultural study with Wikipedia articles.}, journal = {Cognitive processing}, volume = {15}, number = {3}, pages = {343-349}, pmid = {24573307}, issn = {1612-4790}, mesh = {Adolescent ; Adult ; Analysis of Variance ; Bias ; *Causality ; *Cross-Cultural Comparison ; Female ; Humans ; Judgment ; *Life Change Events ; Male ; *Online Systems ; Perception/*physiology ; Probability ; *Reading ; Young Adult ; }, abstract = {In hindsight, people often perceive events to be more inevitable and foreseeable than in foresight. According to Causal Model Theory (Nestler et al. in J Exp Psychol Learn Mem Cogn 34: 1043-1054, 2008), causal explanations are crucial for such hindsight distortions to occur. The present study provides further empirical support for this notion but extends previous findings in several ways. First, ecologically valid materials were used. Second, the effect of causal information on hindsight distortions was investigated in the realm of previously known events. Third, cross-cultural differences in reasoning (analytic vs. holistic) were taken into account. Specifically, German and Vietnamese participants in our study were presented with Wikipedia articles about the nuclear power plant in Fukushima Daiichi, Japan. They read either the version that existed before the nuclear disaster unfolded (Version 1) or the article that existed 8 weeks after the catastrophe commenced (Version 2). Only the latter contained elaborations on causal antecedents and therefore provided an explanation for the disaster. Reading that version led participants to perceive the nuclear disaster to be more likely inevitable and foreseeable when compared to reading Version 1. Cultural background did not exert a significant effect on these perceptions. Hence, hindsight distortions were obtained for ecologically valid materials even if the event was already known. Implications and directions for future research are discussed.}, } @article {pmid24571583, year = {2015}, author = {Gou, S and Gonzales, S and Miller, GR}, title = {Mapping potential groundwater-dependent ecosystems for sustainable management.}, journal = {Ground water}, volume = {53}, number = {1}, pages = {99-110}, doi = {10.1111/gwat.12169}, pmid = {24571583}, issn = {1745-6584}, mesh = {Algorithms ; Climate ; *Conservation of Natural Resources ; *Ecosystem ; Geographic Information Systems ; *Groundwater ; Hydrology ; *Plant Dispersal ; Remote Sensing Technology ; Satellite Imagery ; Soil ; Texas ; }, abstract = {Ecosystems which rely on either the surface expression or subsurface presence of groundwater are known as groundwater-dependent ecosystems (GDEs). A comprehensive inventory of GDE locations at an appropriate management scale is a necessary first-step for sustainable management of supporting aquifers; however, this information is unavailable for most areas of concern. To address this gap, this study created a two-step algorithm which analyzed existing geospatial and remote sensing data to identify potential GDEs at both state/province and aquifer/basin scales. At the state/province scale, a geospatial information system (GIS) database was constructed for Texas, including climate, topography, hydrology, and ecology data. From these data, a GDE index was calculated, which combined vegetative and hydrological indicators. The results indicated that central Texas, particularly the Edwards Aquifer region, had highest potential to host GDEs. Next, an aquifer/basin scale remote sensing-based algorithm was created to provide more detailed maps of GDEs in the Edwards Aquifer region. This algorithm used Landsat ETM+ and MODIS images to track the changes of NDVI for each vegetation pixel. The NDVI dynamics were used to identify the vegetation with high potential to use groundwater--such plants remain high NDVI during extended dry periods and also exhibit low seasonal and inter-annual NDVI changes between dry and wet seasons/years. The results indicated that 8% of natural vegetation was very likely using groundwater. Of the potential GDEs identified, 75% were located on shallow soil averaging 45 cm in depth. The dominant GDE species were live oak, ashe juniper, and mesquite.}, } @article {pmid24568948, year = {2014}, author = {Oliveri, P and Fortunato, AE and Petrone, L and Ishikawa-Fujiwara, T and Kobayashi, Y and Todo, T and Antonova, O and Arboleda, E and Zantke, J and Tessmar-Raible, K and Falciatore, A}, title = {The Cryptochrome/Photolyase Family in aquatic organisms.}, journal = {Marine genomics}, volume = {14}, number = {}, pages = {23-37}, doi = {10.1016/j.margen.2014.02.001}, pmid = {24568948}, issn = {1876-7478}, mesh = {Animals ; Annelida/*genetics ; Base Sequence ; Cluster Analysis ; Cryptochromes/*genetics ; Data Mining ; Deoxyribodipyrimidine Photo-Lyase/*genetics ; Diatoms/*genetics ; *Evolution, Molecular ; Fishes/*genetics ; Gene Duplication/genetics ; Likelihood Functions ; Marine Biology ; Models, Genetic ; Multigene Family/*genetics ; Phylogeny ; Proteins/genetics ; Sea Urchins/*genetics ; Sequence Alignment ; Transcriptome ; }, abstract = {The Cryptochrome/Photolyase Family (CPF) represents an ancient group of widely distributed UV-A/blue-light sensitive proteins sharing common structures and chromophores. During the course of evolution, different CPFs acquired distinct functions in DNA repair, light perception and circadian clock regulation. Previous phylogenetic analyses of the CPF have allowed reconstruction of the evolution and distribution of the different CPF super-classes in the tree of life. However, so far only limited information is available from the CPF orthologs in aquatic organisms that evolved in environments harboring great diversity of life forms and showing peculiar light distribution and rhythms. To gain new insights into the evolutionary and functional relationships within the CPF family, we performed a detailed study of CPF members from marine (diatoms, sea urchin and annelid) and freshwater organisms (teleost) that populate diverse habitats and exhibit different life strategies. In particular, we first extended the CPF family phylogeny by including genes from aquatic organisms representative of several branches of the tree of life. Our analysis identifies four major super-classes of CPF proteins and importantly singles out the presence of a plant-like CRY in diatoms and in metazoans. Moreover, we show a dynamic evolution of Cpf genes in eukaryotes with various events of gene duplication coupled to functional diversification and gene loss, which have shaped the complex array of Cpf genes in extant aquatic organisms. Second, we uncover clear rhythmic diurnal expression patterns and light-dependent regulation for the majority of the analyzed Cpf genes in our reference species. Our analyses reconstruct the molecular evolution of the CPF family in eukaryotes and provide a solid foundation for a systematic characterization of novel light activated proteins in aquatic environments.}, } @article {pmid24565058, year = {2013}, author = {Shang, L and Gardner, DP and Xu, W and Cannone, JJ and Miranker, DP and Ozer, S and Gutell, RR}, title = {Two accurate sequence, structure, and phylogenetic template-based RNA alignment systems.}, journal = {BMC systems biology}, volume = {7 Suppl 4}, number = {Suppl 4}, pages = {S13}, pmid = {24565058}, issn = {1752-0509}, support = {R01 GM067317/GM/NIGMS NIH HHS/United States ; R01 GM085337/GM/NIGMS NIH HHS/United States ; GM085337/GM/NIGMS NIH HHS/United States ; GM067317/GM/NIGMS NIH HHS/United States ; }, mesh = {Base Sequence ; Computational Biology/*methods ; Databases, Genetic ; *Phylogeny ; RNA/*genetics ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Alignment/*methods ; *Templates, Genetic ; }, abstract = {BACKGROUND: The analysis of RNA sequences, once a small niche field for a small collection of scientists whose primary emphasis was the structure and function of a few RNA molecules, has grown most significantly with the realizations that 1) RNA is implicated in many more functions within the cell, and 2) the analysis of ribosomal RNA sequences is revealing more about the microbial ecology within all biological and environmental systems. The accurate and rapid alignment of these RNA sequences is essential to decipher the maximum amount of information from this data.

METHODS: Two computer systems that utilize the Gutell lab's RNA Comparative Analysis Database (rCAD) were developed to align sequences to an existing template alignment available at the Gutell lab's Comparative RNA Web (CRW) Site. Multiple dimensions of cross-indexed information are contained within the relational database--rCAD, including sequence alignments, the NCBI phylogenetic tree, and comparative secondary structure information for each aligned sequence. The first program, CRWAlign-1 creates a phylogenetic-based sequence profile for each column in the alignment. The second program, CRWAlign-2 creates a profile based on phylogenetic, secondary structure, and sequence information. Both programs utilize their profiles to align new sequences into the template alignment.

RESULTS: The accuracies of the two CRWAlign programs were compared with the best template-based rRNA alignment programs and the best de-novo alignment programs. We have compared our programs with a total of eight alternative alignment methods on different sets of 16S rRNA alignments with sequence percent identities ranging from 50% to 100%. Both CRWAlign programs were superior to these other programs in accuracy and speed.

CONCLUSIONS: Both CRWAlign programs can be used to align the very extensive amount of RNA sequencing that is generated due to the rapid next-generation sequencing technology. This latter technology is augmenting the new paradigm that RNA is intimately implicated in a significant number of functions within the cell. In addition, the use of bacterial 16S rRNA sequencing in the identification of the microbiome in many different environmental systems creates a need for rapid and highly accurate alignment of bacterial 16S rRNA sequences.}, } @article {pmid24563514, year = {2014}, author = {Zhang, JY and Deng, XM and Li, FP and Wang, L and Huang, QY and Zhang, CC and Chen, WL}, title = {RNase E forms a complex with polynucleotide phosphorylase in cyanobacteria via a cyanobacterial-specific nonapeptide in the noncatalytic region.}, journal = {RNA (New York, N.Y.)}, volume = {20}, number = {4}, pages = {568-579}, pmid = {24563514}, issn = {1469-9001}, mesh = {Amino Acid Sequence ; Catalytic Domain ; Computational Biology ; Cyanobacteria/genetics/growth & development/*metabolism ; Endoribonucleases/genetics/*metabolism ; Immunoblotting ; Molecular Sequence Data ; Oligopeptides/*metabolism ; Polyribonucleotide Nucleotidyltransferase/genetics/*metabolism ; RNA, Bacterial/*genetics/metabolism ; Recombinant Proteins/genetics/metabolism ; Sequence Homology, Amino Acid ; Two-Hybrid System Techniques ; }, abstract = {RNase E, a central component involved in bacterial RNA metabolism, usually has a highly conserved N-terminal catalytic domain but an extremely divergent C-terminal domain. While the C-terminal domain of RNase E in Escherichia coli recruits other components to form an RNA degradation complex, it is unknown if a similar function can be found for RNase E in other organisms due to the divergent feature of this domain. Here, we provide evidence showing that RNase E forms a complex with another essential ribonuclease-the polynucleotide phosphorylase (PNPase)-in cyanobacteria, a group of ecologically important and phylogenetically ancient organisms. Sequence alignment for all cyanobacterial RNase E proteins revealed several conserved and variable subregions in their noncatalytic domains. One such subregion, an extremely conserved nonapeptide (RRRRRRSSA) located near the very end of RNase E, serves as the PNPase recognition site in both the filamentous cyanobacterium Anabaena PCC7120 and the unicellular cyanobacterium Synechocystis PCC6803. These results indicate that RNase E and PNPase form a ribonuclease complex via a common mechanism in cyanobacteria. The PNPase-recognition motif in cyanobacterial RNase E is distinct from those previously identified in Proteobacteria, implying a mechanism of coevolution for PNPase and RNase E in different organisms.}, } @article {pmid24559402, year = {2014}, author = {Feldmesser, E and Rosenwasser, S and Vardi, A and Ben-Dor, S}, title = {Improving transcriptome construction in non-model organisms: integrating manual and automated gene definition in Emiliania huxleyi.}, journal = {BMC genomics}, volume = {15}, number = {}, pages = {148}, pmid = {24559402}, issn = {1471-2164}, mesh = {Computational Biology/*methods/standards ; Expressed Sequence Tags ; Gene Expression Profiling/*methods/standards ; Haptophyta/*genetics ; Molecular Sequence Annotation ; Molecular Sequence Data ; Quality Control ; RNA Splice Sites ; RNA Splicing/genetics ; Transcription, Genetic ; *Transcriptome ; }, abstract = {BACKGROUND: The advent of Next Generation Sequencing technologies and corresponding bioinformatics tools allows the definition of transcriptomes in non-model organisms. Non-model organisms are of great ecological and biotechnological significance, and consequently the understanding of their unique metabolic pathways is essential. Several methods that integrate de novo assembly with genome-based assembly have been proposed. Yet, there are many open challenges in defining genes, particularly where genomes are not available or incomplete. Despite the large numbers of transcriptome assemblies that have been performed, quality control of the transcript building process, particularly on the protein level, is rarely performed if ever. To test and improve the quality of the automated transcriptome reconstruction, we used manually defined and curated genes, several of them experimentally validated.

RESULTS: Several approaches to transcript construction were utilized, based on the available data: a draft genome, high quality RNAseq reads, and ESTs. In order to maximize the contribution of the various data, we integrated methods including de novo and genome based assembly, as well as EST clustering. After each step a set of manually curated genes was used for quality assessment of the transcripts. The interplay between the automated pipeline and the quality control indicated which additional processes were required to improve the transcriptome reconstruction. We discovered that E. huxleyi has a very high percentage of non-canonical splice junctions, and relatively high rates of intron retention, which caused unique issues with the currently available tools. While individual tools missed genes and artificially joined overlapping transcripts, combining the results of several tools improved the completeness and quality considerably. The final collection, created from the integration of several quality control and improvement rounds, was compared to the manually defined set both on the DNA and protein levels, and resulted in an improvement of 20% versus any of the read-based approaches alone.

CONCLUSIONS: To the best of our knowledge, this is the first time that an automated transcript definition is subjected to quality control using manually defined and curated genes and thereafter the process is improved. We recommend using a set of manually curated genes to troubleshoot transcriptome reconstruction.}, } @article {pmid24554146, year = {2014}, author = {Racicot, A and Babin-Roussel, V and Dauphinais, JF and Joly, JS and Noël, P and Lavoie, C}, title = {A framework to predict the impacts of shale gas infrastructures on the forest fragmentation of an agroforest region.}, journal = {Environmental management}, volume = {53}, number = {5}, pages = {1023-1033}, pmid = {24554146}, issn = {1432-1009}, mesh = {Conservation of Natural Resources/*methods ; Extraction and Processing Industry/*methods ; Geographic Information Systems ; Models, Theoretical ; *Natural Gas ; *Oil and Gas Fields ; Quebec ; Transportation/*methods ; *Trees ; }, abstract = {We propose a framework to facilitate the evaluation of the impacts of shale gas infrastructures (well pads, roads, and pipelines) on land cover features, especially with regards to forest fragmentation. We used a geographic information system and realistic development scenarios largely inspired by the PA (United States) experience, but adapted to a region of QC (Canada) with an already fragmented forest cover and a high gas potential. The scenario with the greatest impact results from development limited by regulatory constraints only, with no access to private roads for connecting well pads to the public road network. The scenario with the lowest impact additionally integrates ecological constraints (deer yards, maple woodlots, and wetlands). Overall the differences between these two scenarios are relatively minor, with <1 % of the forest cover lost in each case. However, large areas of core forests would be lost in both scenarios and the number of forest patches would increase by 13-21 % due to fragmentation. The pipeline network would have a much greater footprint on the land cover than access roads. Using data acquired since the beginning of the shale gas industry, we show that it is possible, within a reasonable time frame, to produce a robust assessment of the impacts of shale gas extraction. The framework we propose could easily be applied to other contexts or jurisdictions.}, } @article {pmid24550506, year = {2014}, author = {Barribeau, SM and Sadd, BM and du Plessis, L and Schmid-Hempel, P}, title = {Gene expression differences underlying genotype-by-genotype specificity in a host-parasite system.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {111}, number = {9}, pages = {3496-3501}, pmid = {24550506}, issn = {1091-6490}, support = {268853/ERC_/European Research Council/International ; }, mesh = {Analysis of Variance ; Animals ; Base Sequence ; Bees/immunology/*parasitology ; *Biological Evolution ; Computational Biology ; Crithidia/*physiology ; DNA Primers/genetics ; Gene Expression Profiling ; Gene Expression Regulation/genetics/*immunology ; Gene Ontology ; Genotype ; Host-Parasite Interactions/genetics/*immunology ; Molecular Sequence Data ; Sequence Analysis, RNA ; Species Specificity ; Switzerland ; }, abstract = {In many systems, host-parasite evolutionary dynamics have led to the emergence and maintenance of diverse parasite and host genotypes within the same population. Genotypes vary in key attributes: Parasite genotypes vary in ability to infect, host genotypes vary in susceptibility, and infection outcome is frequently the result of both parties' genotypic identities. These host-parasite genotype-by-genotype (GH × GP) interactions influence evolutionary and ecological dynamics in important ways. Interactions can be produced through genetic variation; however, here, we assess the role of variable gene expression as an additional source of GH × GP interactions. The bumblebee Bombus terrestris and its trypanosome gut parasite Crithidia bombi are a model system for host-parasite matching. Full-transcriptome sequencing of the bumblebee host revealed that different parasite genotypes indeed induce fundamentally different host expression responses and host genotypes vary in their responses to the infecting parasite genotype. It appears that broadly and successfully infecting parasite genotypes lead to reduced host immune gene expression relative to unexposed bees but induce the expression of genes responsible for controlling gene expression. Contrastingly, a poorly infecting parasite genotype induced the expression of immunologically important genes, including antimicrobial peptides. A targeted expression assay confirmed the transcriptome results and also revealed strong host genotype effects. In all, the expression of a number of genes depends on the host genotype and the parasite genotype and the interaction between both host and parasite genotypes. These results suggest that alongside sequence variation in coding immunological genes, variation that controls immune gene expression can also produce patterns of host-parasite specificity.}, } @article {pmid24550454, year = {2014}, author = {Root, ED and Lucero, M and Nohynek, H and Anthamatten, P and Thomas, DS and Tallo, V and Tanskanen, A and Quiambao, BP and Puumalainen, T and Lupisan, SP and Ruutu, P and Ladesma, E and Williams, GM and Riley, I and Simões, EA}, title = {Distance to health services affects local-level vaccine efficacy for pneumococcal conjugate vaccine (PCV) among rural Filipino children.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {111}, number = {9}, pages = {3520-3525}, pmid = {24550454}, issn = {1091-6490}, mesh = {Geographic Information Systems ; Geography ; Health Services Accessibility/*statistics & numerical data ; Humans ; Infant ; Mass Vaccination/*methods ; Philippines/epidemiology ; Pneumococcal Vaccines/*administration & dosage ; Pneumonia, Pneumococcal/*epidemiology/*prevention & control ; Regression Analysis ; Rural Population/*statistics & numerical data ; Spatial Analysis ; }, abstract = {Pneumococcal conjugate vaccines (PCVs) have demonstrated efficacy against childhood pneumococcal disease in several regions globally. We demonstrate how spatial epidemiological analysis of a PCV trial can assist in developing vaccination strategies that target specific geographic subpopulations at greater risk for pneumococcal pneumonia. We conducted a secondary analysis of a randomized, placebo-controlled, double-blind vaccine trial that examined the efficacy of an 11-valent PCV among children less than 2 y of age in Bohol, Philippines. Trial data were linked to the residential location of each participant using a geographic information system. We use spatial interpolation methods to create smoothed surface maps of vaccination rates and local-level vaccine efficacy across the study area. We then measure the relationship between distance to the main study hospital and local-level vaccine efficacy, controlling for ecological factors, using spatial autoregressive models with spatial autoregressive disturbances. We find a significant amount of spatial variation in vaccination rates across the study area. For the primary study endpoint vaccine efficacy increased with distance from the main study hospital from -14% for children living less than 1.5 km from Bohol Regional Hospital (BRH) to 55% for children living greater than 8.5 km from BRH. Spatial regression models indicated that after adjustment for ecological factors, distance to the main study hospital was positively related to vaccine efficacy, increasing at a rate of 4.5% per kilometer distance. Because areas with poor access to care have significantly higher VE, targeted vaccination of children in these areas might allow for a more effective implementation of global programs.}, } @article {pmid24549691, year = {2014}, author = {Fromberger, P and Jordan, K and Müller, JL}, title = {[Use of virtual reality in forensic psychiatry. A new paradigm?].}, journal = {Der Nervenarzt}, volume = {85}, number = {3}, pages = {298-303}, pmid = {24549691}, issn = {1433-0407}, mesh = {Diagnosis, Computer-Assisted/*methods ; Forensic Psychiatry/*methods ; Humans ; Mental Disorders/*diagnosis/psychology/*therapy ; Psychological Tests ; Psychometrics/methods ; Therapy, Computer-Assisted/*methods ; *User-Computer Interface ; Virtual Reality Exposure Therapy/*methods ; }, abstract = {BACKGROUND: For more than 20 years virtual realities (VR) have been successfully used in the assessment and treatment of psychiatric disorders. The most important advantages of VR are the high ecological validity of virtual environments, the entire controllability of virtual stimuli in the virtual environment and the capability to induce the sensation of being in the virtual environment instead of the physical environment. VRs provide the opportunity to face the user with stimuli and situations which are not available or too risky in reality. Despite these advantages VR-based applications have not yet been applied in forensic psychiatry.

OBJECTIVES AND METHODS: On the basis of an overview of the recent state-of-the-art in VR-based applications in general psychiatry, the article demonstrates the advantages and possibilities of VR-based applications in forensic psychiatry.

RESULTS AND CONCLUSIONS: Up to now only preliminary studies regarding the VR-based assessment of pedophilic interests exist. These studies demonstrate the potential of ecologically valid VR-based applications for the assessment of forensically relevant disorders. One of the most important advantages is the possibility of VR to assess the behavior of forensic inpatients in crime-related situations without endangering others. This provides completely new possibilities not only regarding the assessment but also for the treatment of forensic inpatients. Before utilizing these possibilities in the clinical practice exhaustive research and development will be necessary. Given the high potential of VR-based applications, this effort would be worth it.}, } @article {pmid24549675, year = {2014}, author = {Voelker, RB and Cresko, WA and Berglund, JA}, title = {Computational approaches to mine publicly available databases.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1126}, number = {}, pages = {325-340}, doi = {10.1007/978-1-62703-980-2_24}, pmid = {24549675}, issn = {1940-6029}, support = {R01 AR059833/AR/NIAMS NIH HHS/United States ; }, mesh = {Computational Biology/*methods ; Data Mining/*methods ; *Databases, Nucleic Acid ; Molecular Sequence Annotation/methods ; }, abstract = {Publicly available sequence annotation data is a vital resource for researchers. Many types of information are available, including structural annotations (i.e., the locations and identities of genomic features) and functional annotations (e.g., gene expression and protein interactions). Annotation data is especially useful for interrogating Next-Gen sequencing data (e.g., identifying genomic features that are associated with mapped reads). Additionally, the vast amount of data that is available offers researchers the opportunity to mine existing data sets and make new discoveries. The ability to efficiently obtain, manipulate, and interrogate this data is a valuable and empowering skill. In this chapter, we introduce several primary data repositories and describe the most commonly encountered file formats. In order to highlight some of the key concepts, operations, and utilities that are involved in working with annotation data we provide a fully worked example of using annotations to answer some basic questions about a particular CHIP-seq data set.}, } @article {pmid24535731, year = {2014}, author = {Klong-Klaew, T and Sukontason, K and Ngoen-klan, R and Moophayak, K and Irvine, KN and Kurahashi, H and Prangkio, C and Sanit, S and Sukontason, KL}, title = {Impact of abiotic factor changes in blowfly, Achoetandrus rufifacies (Diptera: Calliphoridae), in northern Thailand.}, journal = {Parasitology research}, volume = {113}, number = {4}, pages = {1353-1360}, pmid = {24535731}, issn = {1432-1955}, mesh = {Animals ; *Climate ; Diptera/*physiology ; Female ; Geographic Information Systems ; Humidity ; Male ; Population Density ; Population Dynamics ; *Seasons ; Sunlight ; Temperature ; Thailand ; Trees ; }, abstract = {Understanding how medically important flies respond to abiotic factor changes is necessary for predicting their population dynamics. In this study, we investigated the geographical distribution of the medically important blowfly, Achoetandrus rufifacies (Macquart) (Diptera: Calliphoridae), and ascertained the response to climatic and physio-environmental factors in Chiang Mai, northern Thailand. Adult fly surveys were carried out every 2 weeks from May 2009 to May 2010 at 18 systematically randomized study sites in three districts of Chiang Mai province (Mueang Chiang Mai, Mae Rim, and Hang Dong), using reconstructable funnel traps with 1-day tainted beef offal as bait. During the study period, 8,861 adult A. rufifacies were captured, with peak densities being observed at the end of winter (i.e., late February) and throughout most of the summer (May to March). Population density had a weak but significant (α = 0.05) positive correlation with temperature (r = 0.329) and light intensity (r = 0.231), and a weak but significant (α = 0.05) negative correlation with relative humidity (r = -0.236). From the six ecological land use types (disturbed mixed deciduous forest, mixed deciduous forest, mixed orchard, lowland village, city town, and paddy field), greater fly densities were observed generally in the disturbed mixed deciduous forest and lowland village, but not in the paddy fields. In conclusion, A. rufifacies are abundant from the end of winter and throughout most of the summer in northern Thailand, with population density being weakly positively correlated with temperature and light intensity, but weakly negatively correlated with relative humidity. The greatest densities of this fly species were collected in disturbed mixed deciduous forest and lowland village land uses. The prediction of annual and season specific distributions of A. rufifacies were provided in each season and all-year patterns using a co-kriging approach (ArcGIS9.2).}, } @article {pmid24532282, year = {2014}, author = {Kura, NU and Ramli, MF and Ibrahim, S and Sulaiman, WN and Aris, AZ}, title = {An integrated assessment of seawater intrusion in a small tropical island using geophysical, geochemical, and geostatistical techniques.}, journal = {Environmental science and pollution research international}, volume = {21}, number = {11}, pages = {7047-7064}, pmid = {24532282}, issn = {1614-7499}, mesh = {Ecology/*methods ; Electric Impedance ; Environmental Monitoring/*methods/statistics & numerical data ; Geographic Information Systems ; Geological Phenomena ; Groundwater/*chemistry ; Ions/analysis ; *Islands ; Malaysia ; Salinity ; Seawater/*analysis ; Tropical Climate ; *Water Movements ; }, abstract = {In this study, geophysics, geochemistry, and geostatistical techniques were integrated to assess seawater intrusion in Kapas Island due to its geological complexity and multiple contamination sources. Five resistivity profiles were measured using an electric resistivity technique. The results reveal very low resistivity <1 Ωm, suggesting either marine clay deposit or seawater intrusion or both along the majority of the resistivity images. As a result, geochemistry was further employed to verify the resistivity evidence. The Chadha and Stiff diagrams classify the island groundwater into Ca-HCO3, Ca-Na-HCO3, Na-HCO3, and Na-Cl water types, with Ca-HCO3 as the dominant. The Mg(2+)/Mg(2+)+Ca(2+), HCO3 (-)/anion, Cl(-)/HCO3 (-), Na(+)/Cl(-), and SO4 (2-)/Cl(-) ratios show that some sampling sites are affected by seawater intrusion; these sampling sites fall within the same areas that show low-resistivity values. The resulting ratios and resistivity values were then used in the geographical information system (GIS) environment to create the geostatistical map of individual indicators. These maps were then overlaid to create the final map showing seawater-affected areas. The final map successfully delineates the area that is actually undergoing seawater intrusion. The proposed technique is not area specific, and hence, it can work in any place with similar completed characteristics or under the influence of multiple contaminants so as to distinguish the area that is truly affected by any targeted pollutants from the rest. This information would provide managers and policy makers with the knowledge of the current situation and will serve as a guide and standard in water research for sustainable management plan.}, } @article {pmid24529453, year = {2014}, author = {Volchko, Y and Norrman, J and Rosén, L and Bergknut, M and Josefsson, S and Söderqvist, T and Norberg, T and Wiberg, K and Tysklind, M}, title = {Using soil function evaluation in multi-criteria decision analysis for sustainability appraisal of remediation alternatives.}, journal = {The Science of the total environment}, volume = {485-486}, number = {}, pages = {785-791}, doi = {10.1016/j.scitotenv.2014.01.087}, pmid = {24529453}, issn = {1879-1026}, mesh = {Conservation of Natural Resources/methods ; *Decision Support Techniques ; Environmental Monitoring/*methods ; Environmental Pollution/*statistics & numerical data ; Environmental Restoration and Remediation/*methods ; Soil/*chemistry ; }, abstract = {Soil contamination is one of the major threats constraining proper functioning of the soil and thus provision of ecosystem services. Remedial actions typically only address the chemical soil quality by reducing total contaminant concentrations to acceptable levels guided by land use. However, emerging regulatory requirements on soil protection demand a holistic view on soil assessment in remediation projects thus accounting for a variety of soil functions. Such a view would require not only that the contamination concentrations are assessed and attended to, but also that other aspects are taking into account, thus addressing also physical and biological as well as other chemical soil quality indicators (SQIs). This study outlines how soil function assessment can be a part of a holistic sustainability appraisal of remediation alternatives using multi-criteria decision analysis (MCDA). The paper presents a method for practitioners for evaluating the effects of remediation alternatives on selected ecological soil functions using a suggested minimum data set (MDS) containing physical, biological and chemical SQIs. The measured SQIs are transformed into sub-scores by the use of scoring curves, which allows interpretation and the integration of soil quality data into the MCDA framework. The method is demonstrated at a study site (Marieberg, Sweden) and the results give an example of how soil analyses using the suggested MDS can be used for soil function assessment and subsequent input to the MCDA framework.}, } @article {pmid24529003, year = {2014}, author = {Paunović, K and Stojanov, V and Jakovljević, B and Belojević, G}, title = {Thoracic bioelectrical impedance assessment of the hemodynamic reactions to recorded road-traffic noise in young adults.}, journal = {Environmental research}, volume = {129}, number = {}, pages = {52-58}, doi = {10.1016/j.envres.2014.01.001}, pmid = {24529003}, issn = {1096-0953}, mesh = {Adolescent ; Adult ; Auditory Perception/physiology ; Blood Pressure/physiology ; Cardiac Output/physiology ; Cardiography, Impedance ; Data Interpretation, Statistical ; Female ; Heart Rate/physiology ; Hemodynamics/*physiology ; Humans ; Male ; Noise, Transportation/*adverse effects ; Sex Factors ; Vascular Resistance/physiology ; Young Adult ; }, abstract = {Noise exposure increases blood pressure in both experimental and field studies. The underlying mechanisms may be evaluated by thoracic bioelectrical impedance. The aim of this experimental study was to assess changes in blood pressure, cardiac and hemodynamic parameters provoked by recorded traffic noise in young adults. The study included 130 participants (42 men and 88 women), aged 24.88±2.67 years. Thoracic electrical bioimpedance device was applied to monitor cardiac parameters, hemodynamic parameters, heart rate variability, blood pressure and heart rate. The testing procedure consisted of three phases. Participants were exposed to recorded road-traffic noise (Leq=89dBA) for 10min and relaxed in quiet conditions (Leq=40dBA) before and after noise exposure. Listening to recorded noise resulted in significant decrease of stroke volume and cardiac output, and an increase of vascular resistance. Heart rate variability and the overall sympathovagal balance remained similar through all experimental conditions. During noise exposure, systolic pressure increased by 2mmHg among women (95% confidence interval=0.97-2.73mmHg), and by 4mmHg among men (95% confidence interval=2.16-5.00mmHg). Similarly, diastolic pressure increased by 2mmHg among women (95% confidence interval=0.95-2.47mmHg), and by 4mmHg among men (95% confidence interval=2.46-5.28mmHg). Once noise ceased, both pressures returned to pre-exposure levels. Experimental exposure to recorded road-traffic noise of 89dBA for 10min provoked significant hemodynamic changes in young adults, including vasoconstriction (increase of vascular resistance), and hypodynamics (decrease of global heart flow). The interaction of these effects resulted in the elevation of blood pressure during noise exposure.}, } @article {pmid24527958, year = {2014}, author = {Gonzalez-Quevedo, C and Davies, RG and Richardson, DS}, title = {Predictors of malaria infection in a wild bird population: landscape-level analyses reveal climatic and anthropogenic factors.}, journal = {The Journal of animal ecology}, volume = {83}, number = {5}, pages = {1091-1102}, doi = {10.1111/1365-2656.12214}, pmid = {24527958}, issn = {1365-2656}, mesh = {Animal Husbandry ; Animals ; Bird Diseases/*parasitology ; *Climate ; Ecosystem ; Female ; Geographic Information Systems ; Haemosporida/genetics/*isolation & purification ; Human Activities ; Malaria, Avian/*epidemiology/genetics ; Male ; Passeriformes/genetics/*parasitology ; Plasmodium/genetics/*isolation & purification ; Ponds ; Poultry ; Spain ; Temperature ; }, abstract = {How the environment influences the transmission and prevalence of disease in a population of hosts is a key aspect of disease ecology. The role that environmental factors play in host-pathogen systems has been well studied at large scales, that is, differences in pathogen pressures among separate populations of hosts or across land masses. However, despite considerable understanding of how environmental conditions vary at fine spatial scales, the effect of these parameters on host-pathogen dynamics at such scales has been largely overlooked. Here, we used a combination of molecular screening and GIS-based analysis to investigate how environmental factors determine the distribution of malaria across the landscape in a population of Berthelot's pipit (Anthus berthelotii, Bolle 1862) on the island of Tenerife (Canary Islands, Spain) using spatially explicit models that account for spatial autocorrelation. Minimum temperature of the coldest month was found to be the most important predictor of malaria infection at the landscape scale across this population. Additionally, anthropogenic factors such as distance to artificial water reservoirs and distance to poultry farms were important predictors of malaria. A model including these factors, and the interaction between distance to artificial water reservoirs and minimum temperature, best explained the distribution of malaria infection in this system. These results suggest that levels of malaria infection in this endemic species may be artificially elevated by the impact of humans. Studies such as the one described here improve our understanding of how environmental factors, and their heterogeneity, affect the distribution of pathogens within wild populations. The results demonstrate the importance of measuring fine-scale variation - and not just regional effects - to understand how environmental variation can influence wildlife diseases. Such understanding is important for predicting the future spread and impact of disease and may help inform disease management programmes as well as the conservation of specific host species.}, } @article {pmid24525844, year = {2014}, author = {Lu, S and Guan, X and Zhou, M and Wang, Y}, title = {Land resources allocation strategies in an urban area involving uncertainty: a case study of Suzhou, in the Yangtze River Delta of China.}, journal = {Environmental management}, volume = {53}, number = {5}, pages = {894-912}, pmid = {24525844}, issn = {1432-1009}, mesh = {China ; *Cities ; Decision Support Techniques ; *Models, Theoretical ; Resource Allocation/*methods ; Rivers ; Socioeconomic Factors ; Stochastic Processes ; *Uncertainty ; }, abstract = {A large number of mathematical models have been developed to support land resource allocation decisions and land management needs; however, few of them can address various uncertainties that exist in relation to many factors presented in such decisions (e.g., land resource availabilities, land demands, land-use patterns, and social demands, as well as ecological requirements). In this study, a multi-objective interval-stochastic land resource allocation model (MOISLAM) was developed for tackling uncertainty that presents as discrete intervals and/or probability distributions. The developed model improves upon the existing multi-objective programming and inexact optimization approaches. The MOISLAM not only considers economic factors, but also involves food security and eco-environmental constraints; it can, therefore, effectively reflect various interrelations among different aspects in a land resource management system. Moreover, the model can also help examine the reliability of satisfying (or the risk of violating) system constraints under uncertainty. In this study, the MOISLAM was applied to a real case of long-term urban land resource allocation planning in Suzhou, in the Yangtze River Delta of China. Interval solutions associated with different risk levels of constraint violation were obtained. The results are considered useful for generating a range of decision alternatives under various system conditions, and thus helping decision makers to identify a desirable land resource allocation strategy under uncertainty.}, } @article {pmid24523893, year = {2014}, author = {Rivers, JW and Johnson, JM and Haig, SM and Schwarz, CJ and Glendening, JW and Burnett, LJ and George, D and Grantham, J}, title = {Resource selection by the California condor (Gymnogyps californianus) relative to terrestrial-based habitats and meteorological conditions.}, journal = {PloS one}, volume = {9}, number = {2}, pages = {e88430}, pmid = {24523893}, issn = {1932-6203}, mesh = {Animals ; *Behavior, Animal ; California ; *Ecosystem ; Endangered Species ; Female ; Geographic Information Systems ; Geography ; Male ; Raptors/*physiology ; Weather ; }, abstract = {Condors and vultures are distinct from most other terrestrial birds because they use extensive soaring flight for their daily movements. Therefore, assessing resource selection by these avian scavengers requires quantifying the availability of terrestrial-based habitats, as well as meteorological variables that influence atmospheric conditions necessary for soaring. In this study, we undertook the first quantitative assessment of habitat- and meteorological-based resource selection in the endangered California condor (Gymnogyps californianus) within its California range and across the annual cycle. We found that condor use of terrestrial areas did not change markedly within the annual cycle, and that condor use was greatest for habitats where food resources and potential predators could be detected and where terrain was amenable for taking off from the ground in flight (e.g., sparse habitats, coastal areas). Condors originating from different release sites differed in their use of habitat, but this was likely due in part to variation in habitats surrounding release sites. Meteorological conditions were linked to condor use of ecological subregions, with thermal height, thermal velocity, and wind speed having both positive (selection) and negative (avoidance) effects on condor use in different areas. We found little evidence of systematic effects between individual characteristics (i.e., sex, age, breeding status) or components of the species management program (i.e., release site, rearing method) relative to meteorological conditions. Our findings indicate that habitat type and meteorological conditions can interact in complex ways to influence condor resource selection across landscapes, which is noteworthy given the extent of anthropogenic stressors that may impact condor populations (e.g., lead poisoning, wind energy development). Additional studies will be valuable to assess small-scale condor movements in light of these stressors to help minimize their risk to this critically endangered species.}, } @article {pmid24516555, year = {2014}, author = {Hadziavdic, K and Lekang, K and Lanzen, A and Jonassen, I and Thompson, EM and Troedsson, C}, title = {Characterization of the 18S rRNA gene for designing universal eukaryote specific primers.}, journal = {PloS one}, volume = {9}, number = {2}, pages = {e87624}, pmid = {24516555}, issn = {1932-6203}, mesh = {Biodiversity ; DNA Primers/*genetics ; Eukaryota/*genetics ; *Eukaryotic Cells ; High-Throughput Nucleotide Sequencing ; Phylogeny ; RNA, Ribosomal, 18S/*genetics ; }, abstract = {High throughput sequencing technology has great promise for biodiversity studies. However, an underlying assumption is that the primers used in these studies are universal for the prokaryotic or eukaryotic groups of interest. Full primer universality is difficult or impossible to achieve and studies using different primer sets make biodiversity comparisons problematic. The aim of this study was to design and optimize universal eukaryotic primers that could be used as a standard in future biodiversity studies. Using the alignment of all eukaryotic sequences from the publicly available SILVA database, we generated a full characterization of variable versus conserved regions in the 18S rRNA gene. All variable regions within this gene were analyzed and our results suggested that the V2, V4 and V9 regions were best suited for biodiversity assessments. Previously published universal eukaryotic primers as well as a number of self-designed primers were mapped to the alignment. Primer selection will depend on sequencing technology used, and this study focused on the 454 pyrosequencing GS FLX Titanium platform. The results generated a primer pair yielding theoretical matches to 80% of the eukaryotic and 0% of the prokaryotic sequences in the SILVA database. An empirical test of marine sediments using the AmpliconNoise pipeline for analysis of the high throughput sequencing data yielded amplification of sequences for 71% of all eukaryotic phyla with no isolation of prokaryotic sequences. To our knowledge this is the first characterization of the complete 18S rRNA gene using all eukaryotes present in the SILVA database, providing a robust test for universal eukaryotic primers. Since both in silico and empirical tests using high throughput sequencing retained high inclusion of eukaryotic phyla and exclusion of prokaryotes, we conclude that these primers are well suited for assessing eukaryote diversity, and can be used as a standard in biodiversity studies.}, } @article {pmid24515888, year = {2014}, author = {Liu, S and Molenaar, PC}, title = {iVAR: a program for imputing missing data in multivariate time series using vector autoregressive models.}, journal = {Behavior research methods}, volume = {46}, number = {4}, pages = {1138-1148}, doi = {10.3758/s13428-014-0444-4}, pmid = {24515888}, issn = {1554-3528}, mesh = {Analysis of Variance ; Computer Simulation ; Data Interpretation, Statistical ; Humans ; *Mathematical Computing ; *Models, Statistical ; *Multivariate Analysis ; Regression Analysis ; *Software ; Support Vector Machine ; }, abstract = {This article introduces iVAR, an R program for imputing missing data in multivariate time series on the basis of vector autoregressive (VAR) models. We conducted a simulation study to compare iVAR with three methods for handling missing data: listwise deletion, imputation with sample means and variances, and multiple imputation ignoring time dependency. The results showed that iVAR produces better estimates for the cross-lagged coefficients than do the other three methods. We demonstrate the use of iVAR with an empirical example of time series electrodermal activity data and discuss the advantages and limitations of the program.}, } @article {pmid24515372, year = {2014}, author = {Gifford, S and Satinsky, B and Moran, MA}, title = {Quantitative microbial metatranscriptomics.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1096}, number = {}, pages = {213-229}, doi = {10.1007/978-1-62703-712-9_17}, pmid = {24515372}, issn = {1940-6029}, mesh = {Computational Biology/methods ; *Environmental Microbiology ; Gene Expression Profiling/methods ; *Metagenomics/methods ; *Transcriptome ; }, abstract = {The direct retrieval and sequencing of environmental RNA is emerging as a powerful technique to elucidate the in situ activities of microbial communities. Here we provide a metatranscriptomic protocol describing environmental sample collection, rRNA depletion, mRNA amplification, cDNA synthesis, and bioinformatic analysis. In addition, the preparation of internal RNA standards and their addition to the sample are discussed, providing a method by which transcript numbers can be expressed as absolute abundances in the environment and more readily compared to other biogeochemical and ecological measurements.}, } @article {pmid24509165, year = {2014}, author = {Minetto, D and Libralato, G and Volpi Ghirardini, A}, title = {Ecotoxicity of engineered TiO2 nanoparticles to saltwater organisms: an overview.}, journal = {Environment international}, volume = {66}, number = {}, pages = {18-27}, doi = {10.1016/j.envint.2014.01.012}, pmid = {24509165}, issn = {1873-6750}, mesh = {Animals ; Aquatic Organisms/*drug effects ; Bacteria/drug effects ; Cetacea ; Chlorophyta/drug effects ; Ecotoxicology/*standards ; Fishes ; Invertebrates/drug effects ; Metal Nanoparticles/*toxicity ; Titanium/*toxicity ; Water Pollutants, Chemical/*toxicity ; }, abstract = {The innovative properties of nanomaterials make them suitable for various applications in many fields. In particular, TiO2 nanoparticles (nTiO2) are widely used in paints, in cosmetics and in sunscreens that are products accessible to the mass market. Despite the great increase in the use of such nanomaterials, there is a paucity of general information about their potential effects to the aquatic species, especially to saltwater ones. Moreover, the difficulties of determining the effective exposure scenario make the acquired information low comparable. In this work, questions about the complexity of the real exposure scenario determination are discussed. The state of the art, concerning the experimental activities with nTiO2 toward the saltwater organisms is firstly illustrated, providing statistical information about the different matrices, organisms and nanoparticles employed. A comparison of the nTiO2 ecotoxicity effects, grouped by taxonomic classes, is provided illustrating their relative experimental conditions. Findings show the need to develop specific protocols for toxicity tests with ENPs to control the variability of experimental conditions. Some advices are finally proposed for the future experimental activities.}, } @article {pmid24506558, year = {2014}, author = {Benova, L and Cumming, O and Campbell, OM}, title = {Systematic review and meta-analysis: association between water and sanitation environment and maternal mortality.}, journal = {Tropical medicine & international health : TM & IH}, volume = {19}, number = {4}, pages = {368-387}, doi = {10.1111/tmi.12275}, pmid = {24506558}, issn = {1365-3156}, mesh = {Africa/epidemiology ; Databases, Bibliographic ; Female ; Humans ; *Maternal Mortality ; Obstetric Labor Complications/microbiology/mortality ; Pregnancy ; Pregnancy Complications, Infectious/etiology/microbiology/*mortality ; Sanitation/*statistics & numerical data ; Sepsis/complications/etiology/*mortality ; Sewage/adverse effects/microbiology ; Water Microbiology ; Water Pollutants/adverse effects ; Water Supply/*statistics & numerical data ; }, abstract = {OBJECTIVE: To assess whether the lack of water or the lack of sanitation facilities in either the home or in health facilities is associated with an increased risk of maternal mortality and to quantify the effect sizes.

METHODS: Systematic review of published literature in Medline, Embase, Popline and Africa Wide EBSCO 1980.

RESULTS: Fourteen articles were found. Four of five ecological studies that considered sanitation found that poor sanitation was associated with higher maternal mortality. Meta-analysis of adjusted estimates in individual-level studies indicated that women in households with poor sanitation had 3.07 (95% CI 1.72-5.49) higher odds of maternal mortality. Four of six ecological studies assessing water environment found that poor water environment was associated with higher maternal mortality. The only individual-level study looking at the adjusted effect of water showed a significant association with maternal mortality (OR = 1.50, 95% CI 1.10-2.10). Two ecological and one facility-based study found an association between a combined measure of water and sanitation environment and maternal mortality.

CONCLUSIONS: There is evidence of association between sanitation and maternal mortality and between water and maternal mortality. Both associations are of substantial magnitude and are maintained after adjusting for confounders. However, these conclusions are based on a very small number of studies, few of which set out to examine sanitation or water as risk factors, and only some of which adjusted for potential confounders. Nevertheless, there are plausible pathways through which such associations may operate.}, } @article {pmid24506554, year = {2014}, author = {Sundling, K and Craciun, G and Schultz, I and Hook, S and Nagler, J and Cavileer, T and Verducci, J and Liu, Y and Kim, J and Hayton, W}, title = {Modeling the endocrine control of vitellogenin production in female rainbow trout.}, journal = {Mathematical biosciences and engineering : MBE}, volume = {11}, number = {3}, pages = {621-639}, pmid = {24506554}, issn = {1551-0018}, support = {T32 GM008349/GM/NIGMS NIH HHS/United States ; T32 GM008692/GM/NIGMS NIH HHS/United States ; T32GM08349/GM/NIGMS NIH HHS/United States ; T32GM008692/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Computational Biology ; Estradiol/metabolism ; Female ; Fish Proteins/*biosynthesis/genetics ; Liver/metabolism ; Mathematical Concepts ; *Models, Biological ; Oncorhynchus mykiss/genetics/*physiology ; Ovary/metabolism ; Photoperiod ; RNA, Messenger/genetics/metabolism ; Receptors, Estrogen/genetics/metabolism ; Reproduction/genetics/physiology ; Seasons ; Vitellogenesis/genetics/physiology ; Vitellogenins/*biosynthesis/genetics ; }, abstract = {The rainbow trout endocrine system is sensitive to changes in annual day length, which is likely the principal environmental cue controlling its reproductive cycle. This study focuses on the endocrine regulation of vitellogenin (Vg) protein synthesis, which is the major egg yolk precursor in this fish species. We present a model of Vg production in female rainbow trout which incorporates a biological pathway beginning with sex steroid estradiol-17β levels in the plasma and concluding with Vg secretion by the liver and sequestration in the oocytes. Numerical simulation results based on this model are compared with experimental data for estrogen receptor mRNA, Vg mRNA, and Vg in the plasma from female rainbow trout over a normal annual reproductive cycle. We also analyze the response of the model to parameter changes. The model is subsequently tested against experimental data from female trout under a compressed photoperiod regime. Comparison of numerical and experimental results suggests the possibility of a time-dependent change in oocyte Vg uptake rate. This model is part of a larger effort that is developing a mathematical description of the endocrine control of reproduction in female rainbow trout. We anticipate that these mathematical and computational models will play an important role in future regulatory toxicity assessments and in the prediction of ecological risk.}, } @article {pmid24506552, year = {2014}, author = {Martín-Fernández, L and Gilioli, G and Lanzarone, E and Miguez, J and Pasquali, S and Ruggeri, F and Ruiz, DP}, title = {A Rao-Blackwellized particle filter for joint parameter estimation and biomass tracking in a stochastic predator-prey system.}, journal = {Mathematical biosciences and engineering : MBE}, volume = {11}, number = {3}, pages = {573-597}, doi = {10.3934/mbe.2014.11.573}, pmid = {24506552}, issn = {1551-0018}, mesh = {Algorithms ; Animals ; *Biomass ; Computational Biology ; Computer Simulation ; Ecosystem ; *Food Chain ; Host-Pathogen Interactions/physiology ; Markov Chains ; Mathematical Concepts ; Mites/pathogenicity/physiology ; *Models, Biological ; Monte Carlo Method ; Nonlinear Dynamics ; Pest Control, Biological/statistics & numerical data ; Predatory Behavior/physiology ; Stochastic Processes ; Tetranychidae/pathogenicity/physiology ; }, abstract = {Functional response estimation and population tracking in predator-prey systems are critical problems in ecology. In this paper we consider a stochastic predator-prey system with a Lotka-Volterra functional response and propose a particle filtering method for: (a) estimating the behavioral parameter representing the rate of effective search per predator in the functional response and (b) forecasting the population biomass using field data. In particular, the proposed technique combines a sequential Monte Carlo sampling scheme for tracking the time-varying biomass with the analytical integration of the unknown behavioral parameter. In order to assess the performance of the method, we show results for both synthetic and observed data collected in an acarine predator-prey system, namely the pest mite Tetranychus urticae and the predatory mite Phytoseiulus persimilis.}, } @article {pmid24505511, year = {2014}, author = {Hassan, OA and Ahlm, C and Evander, M}, title = {A need for One Health approach - lessons learned from outbreaks of Rift Valley fever in Saudi Arabia and Sudan.}, journal = {Infection ecology & epidemiology}, volume = {4}, number = {}, pages = {}, pmid = {24505511}, issn = {2000-8686}, abstract = {INTRODUCTION: Rift Valley fever (RVF) is an emerging viral zoonosis that impacts human and animal health. It is transmitted from animals to humans directly through exposure to blood, body fluids, or tissues of infected animals or via mosquito bites. The disease is endemic to Africa but has recently spread to Saudi Arabia and Yemen. Our aim was to compare two major outbreaks of RVF in Saudi Arabia (2000) and Sudan (2007) from a One Health perspective.

METHODS: Using the terms 'Saudi Arabia', 'Sudan', and 'RVF', articles were identified by searching PubMed, Google Scholar, and web pages of international organizations as well as local sources in Saudi Arabia and Sudan.

RESULTS: The outbreak in Saudi Arabia caused 883 human cases, with a case fatality rate of 14% and more than 40,000 dead sheep and goats. In Sudan, 698 human cases of RVF were recognized (case fatality, 31.5%), but no records of affected animals were available. The ecology and environment of the affected areas were similar with irrigation canals and excessive rains providing an attractive habitat for mosquito vectors to multiply. The outbreaks resulted in livestock trade bans leading to a vast economic impact on the animal market in the two countries. The surveillance system in Sudan showed a lack of data management and communication between the regional and federal health authorities, while in Saudi Arabia which is the stronger economy, better capacity and contingency plans resulted in efficient countermeasures. Studies of the epidemiology and vectors were also performed in Saudi Arabia, while in Sudan these issues were only partly studied.

CONCLUSION: We conclude that a One Health approach is the best option to mitigate outbreaks of RVF. Collaboration between veterinary, health, and environmental authorities both on national and regional levels is needed.}, } @article {pmid24502093, year = {2013}, author = {Maksimović, M and Vlajinac, H and Radak, D and Marinković, J and Maksimović, J and Jorga, J}, title = {Sex differences of cardiovascular risk factors in patients with symptomatic carotid disease.}, journal = {Srpski arhiv za celokupno lekarstvo}, volume = {141}, number = {11-12}, pages = {758-763}, doi = {10.2298/sarh1312758m}, pmid = {24502093}, issn = {0370-8179}, mesh = {Adult ; Aged ; Body Mass Index ; Cardiovascular Diseases/*epidemiology ; Carotid Artery Diseases/epidemiology ; Carotid Stenosis/*epidemiology ; Cross-Sectional Studies ; Depression/epidemiology ; Dyslipidemias/epidemiology ; Female ; Humans ; Hypertension/*epidemiology ; Hyperuricemia/epidemiology ; Logistic Models ; Male ; Metabolic Syndrome/*epidemiology ; Middle Aged ; Obesity, Abdominal/epidemiology ; Risk Factors ; Sedentary Behavior ; Serbia/epidemiology ; Sex Factors ; Smoking/*epidemiology ; Stroke/epidemiology ; }, abstract = {INTRODUCTION: Cardiovascular diseases, especially heart disease and stroke are the cause of more than a half of the total number of deaths in Serbia.

OBJECTIVES: The aim of the present study was to determine sex differences of atherosclerotic risk factors in patients with symptomatic carotid disease.

METHODS: The cross-sectional study, involving 657 consecutive patients with verified carotid atherosclerotic disease, was performed in Belgrade, Serbia. Sex differences of anthropometric parameters and atherosclerotic risk factors were analyzed by means of the univariate logistic regression.

RESULTS: In comparison with men, lower education and physical inactivity were significantly more frequent in women, and the frequency of metabolic syndrome (MetS), lower high-density cholesterol, abdominal obesity, body mass index > or = 30.0 kg/m2, hypercholesterolemia and depression were also significantly higher in women. Smoking and high serum uric acid level were significantly more frequent in men than in women. Women had significantly higher number of MetS components per person, but there were no significant sex differences in the number of other risk factors. Out of all observed risk factors, including MetS components, physical inactivity and hypertension were most frequent in both sexes followed by ever smoking and low education in men and low education and dyslipidemia in women.

CONCLUSION: There were significant sex differences in the distribution of some atherosclerotic risk factors, but not in their number per person. Only the number of MetS components was significantly higher in women.}, } @article {pmid24501396, year = {2014}, author = {Gaby, JC and Buckley, DH}, title = {A comprehensive aligned nifH gene database: a multipurpose tool for studies of nitrogen-fixing bacteria.}, journal = {Database : the journal of biological databases and curation}, volume = {2014}, number = {}, pages = {bau001}, pmid = {24501396}, issn = {1758-0463}, mesh = {Base Composition/genetics ; Base Sequence ; Computational Biology/*methods ; *Databases, Genetic ; Genes, Bacterial/*genetics ; Multigene Family ; Nitrogen Fixation/*genetics ; Oxidoreductases/*genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Alignment/*methods ; }, abstract = {We describe a nitrogenase gene sequence database that facilitates analysis of the evolution and ecology of nitrogen-fixing organisms. The database contains 32 954 aligned nitrogenase nifH sequences linked to phylogenetic trees and associated sequence metadata. The database includes 185 linked multigene entries including full-length nifH, nifD, nifK and 16S ribosomal RNA (rRNA) gene sequences. Evolutionary analyses enabled by the multigene entries support an ancient horizontal transfer of nitrogenase genes between Archaea and Bacteria and provide evidence that nifH has a different history of horizontal gene transfer from the nifDK enzyme core. Further analyses show that lineages in nitrogenase cluster I and cluster III have different rates of substitution within nifD, suggesting that nifD is under different selection pressure in these two lineages. Finally, we find that that the genetic divergence of nifH and 16S rRNA genes does not correlate well at sequence dissimilarity values used commonly to define microbial species, as stains having <3% sequence dissimilarity in their 16S rRNA genes can have up to 23% dissimilarity in nifH. The nifH database has a number of uses including phylogenetic and evolutionary analyses, the design and assessment of primers/probes and the evaluation of nitrogenase sequence diversity. Database URL: http://www.css.cornell.edu/faculty/buckley/nifh.htm.}, } @article {pmid24499518, year = {2013}, author = {Mereta, ST and Yewhalaw, D and Boets, P and Ahmed, A and Duchateau, L and Speybroeck, N and Vanwambeke, SO and Legesse, W and De Meester, L and Goethals, PL}, title = {Physico-chemical and biological characterization of anopheline mosquito larval habitats (Diptera: Culicidae): implications for malaria control.}, journal = {Parasites & vectors}, volume = {6}, number = {1}, pages = {320}, pmid = {24499518}, issn = {1756-3305}, mesh = {Animals ; Biological Phenomena ; Chemical Phenomena ; Culicidae/*physiology ; Decision Support Techniques ; *Ecosystem ; Ethiopia ; Humans ; *Insect Vectors ; Larva/physiology ; Malaria/*prevention & control ; Mosquito Control/*methods ; }, abstract = {BACKGROUND: A fundamental understanding of the spatial distribution and ecology of mosquito larvae is essential for effective vector control intervention strategies. In this study, data-driven decision tree models, generalized linear models and ordination analysis were used to identify the most important biotic and abiotic factors that affect the occurrence and abundance of mosquito larvae in Southwest Ethiopia.

METHODS: In total, 220 samples were taken at 180 sampling locations during the years 2010 and 2012. Sampling sites were characterized based on physical, chemical and biological attributes. The predictive performance of decision tree models was evaluated based on correctly classified instances (CCI), Cohen's kappa statistic (κ) and the determination coefficient (R2). A conditional analysis was performed on the regression tree models to test the relation between key environmental and biological parameters and the abundance of mosquito larvae.

RESULTS: The decision tree model developed for anopheline larvae showed a good model performance (CCI = 84 ± 2%, and κ = 0.66 ± 0.04), indicating that the genus has clear habitat requirements. Anopheline mosquito larvae showed a widespread distribution and especially occurred in small human-made aquatic habitats. Water temperature, canopy cover, emergent vegetation cover, and presence of predators and competitors were found to be the main variables determining the abundance and distribution of anopheline larvae. In contrast, anopheline mosquito larvae were found to be less prominently present in permanent larval habitats. This could be attributed to the high abundance and diversity of natural predators and competitors suppressing the mosquito population densities.

CONCLUSIONS: The findings of this study suggest that targeting smaller human-made aquatic habitats could result in effective larval control of anopheline mosquitoes in the study area. Controlling the occurrence of mosquito larvae via drainage of permanent wetlands may not be a good management strategy as it negatively affects the occurrence and abundance of mosquito predators and competitors and promotes an increase in anopheline population densities.}, } @article {pmid24499424, year = {2014}, author = {Cizauskas, CA and Bellan, SE and Turner, WC and Vance, RE and Getz, WM}, title = {Frequent and seasonally variable sublethal anthrax infections are accompanied by short-lived immunity in an endemic system.}, journal = {The Journal of animal ecology}, volume = {83}, number = {5}, pages = {1078-1090}, pmid = {24499424}, issn = {1365-2656}, support = {R01 GM083863/GM/NIGMS NIH HHS/United States ; GM083863/GM/NIGMS NIH HHS/United States ; }, mesh = {Adaptive Immunity ; Animals ; Antelopes/*immunology/*microbiology ; Anthrax/*immunology/*veterinary ; Antibodies, Bacterial/blood ; Elephants/*immunology/*microbiology ; Equidae/*immunology/*microbiology ; *Host-Pathogen Interactions ; Namibia/epidemiology ; *Seasons ; }, abstract = {Few studies have examined host-pathogen interactions in wildlife from an immunological perspective, particularly in the context of seasonal and longitudinal dynamics. In addition, though most ecological immunology studies employ serological antibody assays, endpoint titre determination is usually based on subjective criteria and needs to be made more objective. Despite the fact that anthrax is an ancient and emerging zoonotic infectious disease found world-wide, its natural ecology is not well understood. In particular, little is known about the adaptive immune responses of wild herbivore hosts against Bacillus anthracis. Working in the natural anthrax system of Etosha National Park, Namibia, we collected 154 serum samples from plains zebra (Equus quagga), 21 from springbok (Antidorcas marsupialis) and 45 from African elephants (Loxodonta africana) over 2-3 years, resampling individuals when possible for seasonal and longitudinal comparisons. We used enzyme-linked immunosorbent assays to measure anti-anthrax antibody titres and developed three increasingly conservative models to determine endpoint titres with more rigourous, objective mensuration. Between 52 and 87% of zebra, 0-15% of springbok and 3-52% of elephants had measurable anti-anthrax antibody titres, depending on the model used. While the ability of elephants and springbok to mount anti-anthrax adaptive immune responses is still equivocal, our results indicate that zebra in ENP often survive sublethal anthrax infections, encounter most B. anthracis in the wet season and can partially booster their immunity to B. anthracis. Thus, rather than being solely a lethal disease, anthrax often occurs as a sublethal infection in some susceptible hosts. Though we found that adaptive immunity to anthrax wanes rapidly, subsequent and frequent sublethal B. anthracis infections cause maturation of anti-anthrax immunity. By triggering host immune responses, these common sublethal infections may act as immunomodulators and affect population dynamics through indirect immunological and co-infection effects. In addition, with our three endpoint titre models, we introduce more mensuration rigour into serological antibody assays, even under the often-restrictive conditions that come with adapting laboratory immunology methods to wild systems. With these methods, we identified significantly more zebras responding immunologically to anthrax than have previous studies using less comprehensive titre analyses.}, } @article {pmid24499292, year = {2014}, author = {Huse, SM and Mark Welch, DB and Voorhis, A and Shipunova, A and Morrison, HG and Eren, AM and Sogin, ML}, title = {VAMPS: a website for visualization and analysis of microbial population structures.}, journal = {BMC bioinformatics}, volume = {15}, number = {}, pages = {41}, pmid = {24499292}, issn = {1471-2105}, mesh = {*Bacteria/classification/genetics/metabolism ; Computational Biology/*methods ; Computer Graphics ; High-Throughput Nucleotide Sequencing ; Internet ; Microbiota ; *Software ; User-Computer Interface ; }, abstract = {BACKGROUND: The advent of next-generation DNA sequencing platforms has revolutionized molecular microbial ecology by making the detailed analysis of complex communities over time and space a tractable research pursuit for small research groups. However, the ability to generate 10[5]-10[8] reads with relative ease brings with it many downstream complications. Beyond the computational resources and skills needed to process and analyze data, it is difficult to compare datasets in an intuitive and interactive manner that leads to hypothesis generation and testing.

RESULTS: We developed the free web service VAMPS (Visualization and Analysis of Microbial Population Structures, http://vamps.mbl.edu) to address these challenges and to facilitate research by individuals or collaborating groups working on projects with large-scale sequencing data. Users can upload marker gene sequences and associated metadata; reads are quality filtered and assigned to both taxonomic structures and to taxonomy-independent clusters. A simple point-and-click interface allows users to select for analysis any combination of their own or their collaborators' private data and data from public projects, filter these by their choice of taxonomic and/or abundance criteria, and then explore these data using a wide range of analytic methods and visualizations. Each result is extensively hyperlinked to other analysis and visualization options, promoting data exploration and leading to a greater understanding of data relationships.

CONCLUSIONS: VAMPS allows researchers using marker gene sequence data to analyze the diversity of microbial communities and the relationships between communities, to explore these analyses in an intuitive visual context, and to download data, results, and images for publication. VAMPS obviates the need for individual research groups to make the considerable investment in computational infrastructure and bioinformatic support otherwise necessary to process, analyze, and interpret massive amounts of next-generation sequence data. Any web-capable device can be used to upload, process, explore, and extract data and results from VAMPS. VAMPS encourages researchers to share sequence and metadata, and fosters collaboration between researchers of disparate biomes who recognize common patterns in shared data.}, } @article {pmid24496027, year = {2014}, author = {Csépe, Z and Makra, L and Voukantsis, D and Matyasovszky, I and Tusnády, G and Karatzas, K and Thibaudon, M}, title = {Predicting daily ragweed pollen concentrations using Computational Intelligence techniques over two heavily polluted areas in Europe.}, journal = {The Science of the total environment}, volume = {476-477}, number = {}, pages = {542-552}, doi = {10.1016/j.scitotenv.2014.01.056}, pmid = {24496027}, issn = {1879-1026}, mesh = {Air Pollutants/*analysis ; Air Pollution/*statistics & numerical data ; Allergens/*analysis ; Antigens, Plant/*analysis ; Artificial Intelligence ; Environmental Monitoring/*methods ; Forecasting ; France ; Hungary ; Models, Chemical ; Plant Extracts/*analysis ; Pollen ; Seasons ; }, abstract = {Forecasting ragweed pollen concentration is a useful tool for sensitive people in order to prepare in time for high pollen episodes. The aim of the study is to use methods of Computational Intelligence (CI) (Multi-Layer Perceptron, M5P, REPTree, DecisionStump and MLPRegressor) for predicting daily values of Ambrosia pollen concentrations and alarm levels for 1-7 days ahead for Szeged (Hungary) and Lyon (France), respectively. Ten-year daily mean ragweed pollen data (within 1997-2006) are considered for both cities. 10 input variables are used in the models including pollen level or alarm level on the given day, furthermore the serial number of the given day of the year within the pollen season and altogether 8 meteorological variables. The study has novelties as (1) daily alarm thresholds are firstly predicted in the aerobiological literature; (2) data-driven modelling methods including neural networks have never been used in forecasting daily Ambrosia pollen concentration; (3) algorithm J48 has never been used in palynological forecasts; (4) we apply a rarely used technique, namely factor analysis with special transformation, to detect the importance of the influencing variables in defining the pollen levels for 1-7 days ahead. When predicting pollen concentrations, for Szeged Multi-Layer Perceptron models deliver similar results with tree-based models 1 and 2 days ahead; while for Lyon only Multi-Layer Perceptron provides acceptable result. When predicting alarm levels, the performance of Multi-Layer Perceptron is the best for both cities. It is presented that the selection of the optimal method depends on climate, as a function of geographical location and relief. The results show that the more complex CI methods perform well, and their performance is case-specific for ≥2 days forecasting horizon. A determination coefficient of 0.98 (Ambrosia, Szeged, one day and two days ahead) using Multi-Layer Perceptron ranks this model the best one in the literature.}, } @article {pmid24495199, year = {2014}, author = {Andrews, KR and Luikart, G}, title = {Recent novel approaches for population genomics data analysis.}, journal = {Molecular ecology}, volume = {23}, number = {7}, pages = {1661-1667}, doi = {10.1111/mec.12686}, pmid = {24495199}, issn = {1365-294X}, mesh = {Data Interpretation, Statistical ; Genetics, Population/*methods ; Genomics/*methods ; High-Throughput Nucleotide Sequencing/*methods ; Sequence Analysis, DNA/*methods ; }, abstract = {Next-generation sequencing (NGS) technology is revolutionizing the fields of population genetics, molecular ecology and conservation biology. But it can be challenging for researchers to learn the new and rapidly evolving techniques required to use NGS data. A recent workshop entitled 'Population Genomic Data Analysis' was held to provide training in conceptual and practical aspects of data production and analysis for population genomics, with an emphasis on NGS data analysis. This workshop brought together 16 instructors who were experts in the field of population genomics and 31 student participants. Instructors provided helpful and often entertaining advice regarding how to choose and use a NGS method for a given research question, and regarding critical aspects of NGS data production and analysis such as library preparation, filtering to remove sequencing errors and outlier loci, and genotype calling. In addition, instructors provided general advice about how to approach population genomics data analysis and how to build a career in science. The overarching messages of the workshop were that NGS data analysis should be approached with a keen understanding of the theoretical models underlying the analyses, and with analyses tailored to each research question and project. When analysed carefully, NGS data provide extremely powerful tools for answering crucial questions in disciplines ranging from evolution and ecology to conservation and agriculture, including questions that could not be answered prior to the development of NGS technology.}, } @article {pmid24494694, year = {2014}, author = {Kuester, A and Conner, JK and Culley, T and Baucom, RS}, title = {How weeds emerge: a taxonomic and trait-based examination using United States data.}, journal = {The New phytologist}, volume = {202}, number = {3}, pages = {1055-1068}, pmid = {24494694}, issn = {1469-8137}, mesh = {Adaptation, Physiological ; *Databases as Topic ; Genome Size ; Genome, Plant/genetics ; Herbicide Resistance ; Introduced Species ; Logistic Models ; Phenotype ; Plant Weeds/*classification/genetics/*growth & development ; *Quantitative Trait, Heritable ; Reproduction ; Species Specificity ; United States ; }, abstract = {Weeds can cause great economic and ecological harm to ecosystems. Despite their importance, comparisons of the taxonomy and traits of successful weeds often focus on a few specific comparisons - for example, introduced versus native weeds. We used publicly available inventories of US plant species to make comprehensive comparisons of the factors that underlie weediness. We quantitatively examined taxonomy to determine if certain genera are overrepresented by introduced, weedy or herbicide-resistant species, and we compared phenotypic traits of weeds to those of nonweeds, whether introduced or native. We uncovered genera that have more weeds and introduced species than expected by chance and plant families that have more herbicide-resistant species than expected by chance. Certain traits, generally related to fast reproduction, were more likely to be associated with weedy plants regardless of species' origins. We also found stress tolerance traits associated with either native or introduced weeds compared with native or introduced nonweeds. Weeds and introduced species have significantly smaller genomes than nonweeds and native species. These results support trends for weedy plants reported from other floras, suggest that native and introduced weeds have different stress adaptations, and provide a comprehensive survey of trends across weeds within the USA.}, } @article {pmid24492920, year = {2014}, author = {Roche, DG and Lanfear, R and Binning, SA and Haff, TM and Schwanz, LE and Cain, KE and Kokko, H and Jennions, MD and Kruuk, LE}, title = {Troubleshooting public data archiving: suggestions to increase participation.}, journal = {PLoS biology}, volume = {12}, number = {1}, pages = {e1001779}, pmid = {24492920}, issn = {1545-7885}, mesh = {*Communication ; Communication Barriers ; Cost-Benefit Analysis ; Databases, Factual ; Humans ; Information Dissemination/*ethics ; }, abstract = {An increasing number of publishers and funding agencies require public data archiving (PDA) in open-access databases. PDA has obvious group benefits for the scientific community, but many researchers are reluctant to share their data publicly because of real or perceived individual costs. Improving participation in PDA will require lowering costs and/or increasing benefits for primary data collectors. Small, simple changes can enhance existing measures to ensure that more scientific data are properly archived and made publicly available: (1) facilitate more flexible embargoes on archived data, (2) encourage communication between data generators and re-users, (3) disclose data re-use ethics, and (4) encourage increased recognition of publicly archived data.}, } @article {pmid24487216, year = {2014}, author = {Suzuki, E and Mitsuhashi, T and Tsuda, T and Yamamoto, E}, title = {Alternative definitions of "proportion eliminated".}, journal = {Epidemiology (Cambridge, Mass.)}, volume = {25}, number = {2}, pages = {308-309}, doi = {10.1097/EDE.0000000000000050}, pmid = {24487216}, issn = {1531-5487}, mesh = {*Causality ; *Effect Modifier, Epidemiologic ; *Health Policy ; }, } @article {pmid24486469, year = {2014}, author = {Hanewinkel, M and Cullmann, DA and Michiels, HG and Kändler, G}, title = {Converting probabilistic tree species range shift projections into meaningful classes for management.}, journal = {Journal of environmental management}, volume = {134}, number = {}, pages = {153-165}, doi = {10.1016/j.jenvman.2014.01.010}, pmid = {24486469}, issn = {1095-8630}, mesh = {*Algorithms ; *Climate Change ; Decision Making ; Europe ; Fagus ; Humans ; Linear Models ; Models, Theoretical ; Picea ; Trees/*classification ; Uncertainty ; }, abstract = {The paper deals with the management problem how to decide on tree species suitability under changing environmental conditions. It presents an algorithm that classifies the output of a range shift model for major tree species in Europe into multiple classes that can be linked to qualities characterizing the ecological niche of the species. The classes: i) Core distribution area, ii) Extended distribution area, iii) Occasional occurrence area, and iv) No occurrence area are first theoretically developed and then statistically described. The classes are interpreted from an ecological point of view using criteria like population structure, competitive strength, site spectrum and vulnerability to biotic hazards. The functioning of the algorithm is demonstrated using the example of a generalized linear model that was fitted to a pan-European dataset of presence/absence of major tree species with downscaled climate data from a General Circulation Model (GCM). Applications of the algorithm to tree species suitability classification on a European and regional level are shown. The thresholds that are used by the algorithm are precision-based and include Cohen's Kappa. A validation of the algorithm using an independent dataset of the German National Forest Inventory shows good accordance of the statistically derived classes with ecological traits for Norway spruce, while the differentiation especially between core and extended distribution for European beech that is in the centre of its natural range in this area is less accurate. We hypothesize that for species in the core of their range regional factors like forest history superimpose climatic factors. Problems of uncertainty issued from potentially applying a multitude of modelling approaches and/or climate realizations within the range shift model are discussed and a way to deal with the uncertainty by revealing the underlying attitude towards risk of the decision maker is proposed.}, } @article {pmid24486190, year = {2015}, author = {Garg, JK}, title = {Wetland assessment, monitoring and management in India using geospatial techniques.}, journal = {Journal of environmental management}, volume = {148}, number = {}, pages = {112-123}, doi = {10.1016/j.jenvman.2013.12.018}, pmid = {24486190}, issn = {1095-8630}, mesh = {*Conservation of Natural Resources ; Ecosystem ; Environmental Monitoring/*methods ; Geographic Information Systems ; Humans ; India ; Remote Sensing Technology ; *Wetlands ; }, abstract = {Satellite remote sensing and GIS have emerged as the most powerful tools for inventorying, monitoring and management of natural resources and environment. In the special context of wetland ecosystems, remotely sensed data from orbital platforms have been extensively used in India for the inventory, monitoring and preparation of action plans for conservation and management. First scientific inventory of wetlands in India was carried out in 1998 by Space Applications Centre (ISRO), Ahmedabad using indigenous IRS (Indian Remote Sensing Satellite) data of 1992-93 timeframe, which stimulated extensive use of geospatial techniques for wetland conservation and management. Subsequently, with advances in GIS, studies were carried out for development of Wetland Information System for a state (West Bengal) and for Loktak lake wetland (a Ramsar site) as a prelude to National Wetland Information System. Research has also been carried out for preparation of action plans especially for Ramsar sites in the country. In a novel research, use of the geospatial technology has also been demonstrated for biodiversity conservation using landscape ecological metrics. A country-wide estimate of emission of methane, a Green House Gas, from wetlands has also been made using MODIS data. Present article critically reviews the work carried out in India for wetland conservation and management using geospatial techniques.}, } @article {pmid24483071, year = {2013}, author = {Li, WT and Huang, LF and Du, J and Chen, SL}, title = {[Relationships between Dendrobium quality and ecological factors based on partial least square regression].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {24}, number = {10}, pages = {2787-2792}, pmid = {24483071}, issn = {1001-9332}, mesh = {China ; Dendrobium/chemistry/*classification/*growth & development ; *Ecosystem ; Geographic Information Systems ; Least-Squares Analysis ; Models, Theoretical ; *Quality Control ; Regression Analysis ; Temperature ; }, abstract = {A total of eleven ecological factors values were obtained from the ecological suitability database of the geographic information system for traditional Chinese medicines production areas (TCM-GIS), and the relationships between the chemical components of Dendrobium and the ecological factors were analyzed by partial least square (PLS) regression. There existed significant differences in the chemical components contents of the same species of Dendrobium in different areas. The polysaccharides content of D. officinale had significant positive correlation with soil type, the accumulated dendrobine in D. nobile was significantly positively correlated with annual precipitation, and the erianin content of D. chrysotoxum was mainly affected by air temperature. The principal component analysis (PCA) showed that Zhejiang Province was the optimal production area for D. officinale, Guizhou Province was the most appropriate planting area for D. nobile, and Yunnan Province was the best production area of D. chrysotoxum.}, } @article {pmid24479665, year = {2014}, author = {Malde, K}, title = {Simulating a population genomics data set using FlowSim.}, journal = {BMC research notes}, volume = {7}, number = {}, pages = {68}, pmid = {24479665}, issn = {1756-0500}, mesh = {Computational Biology/*methods ; *Computer Simulation ; Genetics, Population/methods ; Genomics/*methods ; High-Throughput Nucleotide Sequencing/methods/statistics & numerical data ; Reproducibility of Results ; Sequence Analysis, DNA/*methods/statistics & numerical data ; }, abstract = {BACKGROUND: The field of population genetics use the genetic composition of populations to study the effects of ecological and evolutionary factors, including selection, genetic drift, mating structure, and migration. Until recently, these studies were usually based upon the analysis of relatively few (typically 10-20) DNA markers on samples from multiple populations. In contrast, high-throughput sequencing provides large amounts of data and consequently very high resolution genetic information. Recent technological developments are rapidly making this a cost-effective alternative. In addition, sequencing allows both the direct study of genomic differences between population, and the discovery of single nucleotide polymorphism marker that can be subsequently used in high-throughput genotyping. Much of the analysis in population genetics was developed before large scale sequencing became feasible. Methods often do not take into account the characteristics of the different sequencing technologies, and consequently, may not always be well suited to this kind of data.

RESULTS: Although the FlowSim suite of tools originally targeted simulation of de novo 454 genomics data, recent developments and enhancements makes it suitable also for simulating other kinds of data. We examine its application to population genomics, and provide examples and supplementary scripts and utilities to aid in this task.

CONCLUSIONS: Simulation is an important tool to study and develop methods in many fields, and here we demonstrate how to simulate a high-throughput sequencing dataset for population genomics.}, } @article {pmid24479613, year = {2014}, author = {Elsik, CG and Worley, KC and Bennett, AK and Beye, M and Camara, F and Childers, CP and de Graaf, DC and Debyser, G and Deng, J and Devreese, B and Elhaik, E and Evans, JD and Foster, LJ and Graur, D and Guigo, R and , and Hoff, KJ and Holder, ME and Hudson, ME and Hunt, GJ and Jiang, H and Joshi, V and Khetani, RS and Kosarev, P and Kovar, CL and Ma, J and Maleszka, R and Moritz, RF and Munoz-Torres, MC and Murphy, TD and Muzny, DM and Newsham, IF and Reese, JT and Robertson, HM and Robinson, GE and Rueppell, O and Solovyev, V and Stanke, M and Stolle, E and Tsuruda, JM and Vaerenbergh, MV and Waterhouse, RM and Weaver, DB and Whitfield, CW and Wu, Y and Zdobnov, EM and Zhang, L and Zhu, D and Gibbs, RA and , }, title = {Finding the missing honey bee genes: lessons learned from a genome upgrade.}, journal = {BMC genomics}, volume = {15}, number = {}, pages = {86}, pmid = {24479613}, issn = {1471-2164}, support = {U54 HG003273/HG/NHGRI NIH HHS/United States ; }, mesh = {Animals ; Base Composition ; Bees/*genetics ; Databases, Genetic ; *Genes, Insect ; Interspersed Repetitive Sequences/genetics ; Molecular Sequence Annotation ; Open Reading Frames/genetics ; Peptides/analysis ; Sequence Analysis, RNA ; Sequence Homology, Amino Acid ; }, abstract = {BACKGROUND: The first generation of genome sequence assemblies and annotations have had a significant impact upon our understanding of the biology of the sequenced species, the phylogenetic relationships among species, the study of populations within and across species, and have informed the biology of humans. As only a few Metazoan genomes are approaching finished quality (human, mouse, fly and worm), there is room for improvement of most genome assemblies. The honey bee (Apis mellifera) genome, published in 2006, was noted for its bimodal GC content distribution that affected the quality of the assembly in some regions and for fewer genes in the initial gene set (OGSv1.0) compared to what would be expected based on other sequenced insect genomes.

RESULTS: Here, we report an improved honey bee genome assembly (Amel_4.5) with a new gene annotation set (OGSv3.2), and show that the honey bee genome contains a number of genes similar to that of other insect genomes, contrary to what was suggested in OGSv1.0. The new genome assembly is more contiguous and complete and the new gene set includes ~5000 more protein-coding genes, 50% more than previously reported. About 1/6 of the additional genes were due to improvements to the assembly, and the remaining were inferred based on new RNAseq and protein data.

CONCLUSIONS: Lessons learned from this genome upgrade have important implications for future genome sequencing projects. Furthermore, the improvements significantly enhance genomic resources for the honey bee, a key model for social behavior and essential to global ecology through pollination.}, } @article {pmid24478338, year = {2014}, author = {Izquierdo-Carrasco, F and Cazes, J and Smith, SA and Stamatakis, A}, title = {PUmPER: phylogenies updated perpetually.}, journal = {Bioinformatics (Oxford, England)}, volume = {30}, number = {10}, pages = {1476-1477}, pmid = {24478338}, issn = {1367-4811}, mesh = {Databases, Genetic ; Embryophyta/genetics ; *Phylogeny ; Sequence Alignment/*methods ; Software ; }, abstract = {SUMMARY: New sequence data useful for phylogenetic and evolutionary analyses continues to be added to public databases. The construction of multiple sequence alignments and inference of huge phylogenies comprising large taxonomic groups are expensive tasks, both in terms of man hours and computational resources. Therefore, maintaining comprehensive phylogenies, based on representative and up-to-date molecular sequences, is challenging. PUmPER is a framework that can perpetually construct multi-gene alignments (with PHLAWD) and phylogenetic trees (with ExaML or RAxML-Light) for a given NCBI taxonomic group. When sufficient numbers of new gene sequences for the selected taxonomic group have accumulated in GenBank, PUmPER automatically extends the alignment and infers extended phylogenetic trees by using previously inferred smaller trees as starting topologies. Using our framework, large phylogenetic trees can be perpetually updated without human intervention. Importantly, resulting phylogenies are not statistically significantly worse than trees inferred from scratch.

PUmPER can run in stand-alone mode on a single server, or offload the computationally expensive phylogenetic searches to a parallel computing cluster. Source code, documentation, and tutorials are available at https://github.com/fizquierdo/perpetually-updated-trees.

CONTACT: Fernando.Izquierdo@h-its.org

SUPPLEMENTARY INFORMATION: Supplementary Material is available at Bioinformatics online.}, } @article {pmid24476672, year = {2014}, author = {Caprarelli, G and Fletcher, S}, title = {A brief review of spatial analysis concepts and tools used for mapping, containment and risk modelling of infectious diseases and other illnesses.}, journal = {Parasitology}, volume = {141}, number = {5}, pages = {581-601}, doi = {10.1017/S0031182013001972}, pmid = {24476672}, issn = {1469-8161}, mesh = {Communicable Diseases/*epidemiology/parasitology ; Containment of Biohazards ; Geographic Information Systems ; Geography ; Humans ; Models, Statistical ; Population Surveillance ; Public Health ; Software ; Spatial Analysis ; }, abstract = {Fast response and decision making about containment, management, eradication and prevention of diseases, are increasingly important aspects of the work of public health officers and medical providers. Diseases and the agents causing them are spatially and temporally distributed, and effective countermeasures rely on methods that can timely locate the foci of infection, predict the distribution of illnesses and their causes, and evaluate the likelihood of epidemics. These methods require the use of large datasets from ecology, microbiology, health and environmental geography. Geodatabases integrating data from multiple sets of information are managed within the frame of geographic information systems (GIS). Many GIS software packages can be used with minimal training to query, map, analyse and interpret the data. In combination with other statistical or modelling software, predictive and spatio-temporal modelling can be carried out. This paper reviews some of the concepts and tools used in epidemiology and parasitology. The purpose of this review is to provide public health officers with the critical tools to decide about spatial analysis resources and the architecture for the prevention and surveillance systems best suited to their situations.}, } @article {pmid24475265, year = {2014}, author = {Amorim, F and Carvalho, SB and Honrado, J and Rebelo, H}, title = {Designing optimized multi-species monitoring networks to detect range shifts driven by climate change: a case study with bats in the North of Portugal.}, journal = {PloS one}, volume = {9}, number = {1}, pages = {e87291}, pmid = {24475265}, issn = {1932-6203}, mesh = {Animal Distribution/*physiology ; Animals ; Chiroptera/*physiology ; *Climate Change ; Computer Simulation ; Conservation of Natural Resources/*methods ; Decision Support Techniques ; Ecological Parameter Monitoring/*methods ; Models, Biological ; Population Dynamics ; Portugal ; Species Specificity ; }, abstract = {Here we develop a framework to design multi-species monitoring networks using species distribution models and conservation planning tools to optimize the location of monitoring stations to detect potential range shifts driven by climate change. For this study, we focused on seven bat species in Northern Portugal (Western Europe). Maximum entropy modelling was used to predict the likely occurrence of those species under present and future climatic conditions. By comparing present and future predicted distributions, we identified areas where each species is likely to gain, lose or maintain suitable climatic space. We then used a decision support tool (the Marxan software) to design three optimized monitoring networks considering: a) changes in species likely occurrence, b) species conservation status, and c) level of volunteer commitment. For present climatic conditions, species distribution models revealed that areas suitable for most species occur in the north-eastern part of the region. However, areas predicted to become climatically suitable in the future shifted towards west. The three simulated monitoring networks, adaptable for an unpredictable volunteer commitment, included 28, 54 and 110 sampling locations respectively, distributed across the study area and covering the potential full range of conditions where species range shifts may occur. Our results show that our framework outperforms the traditional approach that only considers current species ranges, in allocating monitoring stations distributed across different categories of predicted shifts in species distributions. This study presents a straightforward framework to design monitoring schemes aimed specifically at testing hypotheses about where and when species ranges may shift with climatic changes, while also ensuring surveillance of general population trends.}, } @article {pmid24475074, year = {2014}, author = {Williams, R and Ma, X and Schott, RK and Mohammad, N and Ho, CY and Li, CF and Chang, BS and Demetriou, M and Dennis, JW}, title = {Encoding asymmetry of the N-glycosylation motif facilitates glycoprotein evolution.}, journal = {PloS one}, volume = {9}, number = {1}, pages = {e86088}, pmid = {24475074}, issn = {1932-6203}, support = {MOP-62975/CAPMC/CIHR/Canada ; T32AI060573/AI/NIAID NIH HHS/United States ; R01AI082266/AI/NIAID NIH HHS/United States ; T32 AI060573/AI/NIAID NIH HHS/United States ; R01 AI082266/AI/NIAID NIH HHS/United States ; }, mesh = {Amino Acids/chemistry/metabolism ; Animals ; Base Composition ; *Biological Evolution ; Codon ; Databases, Protein ; Glycoproteins/*chemistry/genetics/*metabolism ; Glycosylation ; Humans ; Mutation ; Polysaccharides/metabolism ; Protein Binding ; Selection, Genetic ; }, abstract = {Protein N-glycosylation is found in all domains of life and has a conserved role in glycoprotein folding and stability. In animals, glycoproteins transit through the Golgi where the N-glycans are trimmed and rebuilt with sequences that bind lectins, an innovation that greatly increases structural diversity and redundancy of glycoprotein-lectin interaction at the cell surface. Here we ask whether the natural tension between increasing diversity (glycan-protein interactions) and site multiplicity (backup and status quo) might be revealed by a phylogenic examination of glycoproteins and NXS/T(X ≠ P) N-glycosylation sites. Site loss is more likely by mutation at Asn encoded by two adenosine (A)-rich codons, while site gain is more probable by generating Ser or Thr downstream of an existing Asn. Thus mutations produce sites at novel positions more frequently than the reversal of recently lost sites, and therefore more paths though sequence space are made available to natural selection. An intra-species comparison of secretory and cytosolic proteins revealed a departure from equilibrium in sequences one-mutation-away from NXS/T and in (A) content, indicating strong selective pressures and exploration of N-glycosylation positions during vertebrate evolution. Furthermore, secretory proteins have evolved at rates proportional to N-glycosylation site number, indicating adaptive interactions between the N-glycans and underlying protein. Given the topology of the genetic code, mutation of (A) is more often nonsynonomous, and Lys, another target of many PTMs, is also encoded by two (A)-rich codons. An examination of acetyl-Lys sites in proteins indicated similar evolutionary dynamics, consistent with asymmetry of the target and recognition portions of modified sites. Our results suggest that encoding asymmetry is an ancient mechanism of evolvability that increases diversity and experimentation with PTM site positions. Strong selective pressures on PTMs may have contributed to the A+T → G+C shift in genome-wide nucleotide composition during metazoan radiation.}, } @article {pmid24475070, year = {2014}, author = {Moskalev, A and Shaposhnikov, M and Snezhkina, A and Kogan, V and Plyusnina, E and Peregudova, D and Melnikova, N and Uroshlev, L and Mylnikov, S and Dmitriev, A and Plusnin, S and Fedichev, P and Kudryavtseva, A}, title = {Mining gene expression data for pollutants (dioxin, toluene, formaldehyde) and low dose of gamma-irradiation.}, journal = {PloS one}, volume = {9}, number = {1}, pages = {e86051}, pmid = {24475070}, issn = {1932-6203}, support = {R24 MD001090/MD/NIMHD NIH HHS/United States ; }, mesh = {Animals ; Cluster Analysis ; Computational Biology/methods ; *Data Mining ; Drosophila ; Environmental Pollutants/*adverse effects ; Female ; Gamma Rays/*adverse effects ; *Gene Expression Profiling ; Gene Expression Regulation/*drug effects/*radiation effects ; Gene Regulatory Networks ; *Gene-Environment Interaction ; Male ; }, abstract = {General and specific effects of molecular genetic responses to adverse environmental factors are not well understood. This study examines genome-wide gene expression profiles of Drosophila melanogaster in response to ionizing radiation, formaldehyde, toluene, and 2,3,7,8-tetrachlorodibenzo-p-dioxin. We performed RNA-seq analysis on 25,415 transcripts to measure the change in gene expression in males and females separately. An analysis of the genes unique to each treatment yielded a list of genes as a gene expression signature. In the case of radiation exposure, both sexes exhibited a reproducible increase in their expression of the transcription factors sugarbabe and tramtrack. The influence of dioxin up-regulated metabolic genes, such as anachronism, CG16727, and several genes with unknown function. Toluene activated a gene involved in the response to the toxins, Cyp12d1-p; the transcription factor Fer3's gene; the metabolic genes CG2065, CG30427, and CG34447; and the genes Spn28Da and Spn3, which are responsible for reproduction and immunity. All significantly differentially expressed genes, including those shared among the stressors, can be divided into gene groups using Gene Ontology Biological Process identifiers. These gene groups are related to defense response, biological regulation, the cell cycle, metabolic process, and circadian rhythms. KEGG molecular pathway analysis revealed alteration of the Notch signaling pathway, TGF-beta signaling pathway, proteasome, basal transcription factors, nucleotide excision repair, Jak-STAT signaling pathway, circadian rhythm, Hippo signaling pathway, mTOR signaling pathway, ribosome, mismatch repair, RNA polymerase, mRNA surveillance pathway, Hedgehog signaling pathway, and DNA replication genes. Females and, to a lesser extent, males actively metabolize xenobiotics by the action of cytochrome P450 when under the influence of dioxin and toluene. Finally, in this work we obtained gene expression signatures pollutants (dioxin, toluene), low dose of gamma-irradiation and common molecular pathways for different kind of stressors.}, } @article {pmid24473682, year = {2014}, author = {Nestlerode, JA and Hansen, VD and Teague, A and Harwell, MC}, title = {Application of a three-tier framework to assess ecological condition of Gulf of Mexico coastal wetlands.}, journal = {Environmental monitoring and assessment}, volume = {186}, number = {6}, pages = {3477-3493}, pmid = {24473682}, issn = {1573-2959}, mesh = {Conservation of Natural Resources/legislation & jurisprudence ; Ecology ; Environmental Monitoring/legislation & jurisprudence/*methods ; Geographic Information Systems ; Gulf of Mexico ; Hydrology ; Seawater/chemistry ; Soil/chemistry ; United States ; United States Environmental Protection Agency ; *Wetlands ; }, abstract = {A multi-level coastal wetland assessment strategy was applied to wetlands in the northern Gulf of Mexico (GOM) to evaluate the feasibility of this approach for a broad national scale wetland condition assessment (US Environmental Protection Agency's National Wetlands Condition Assessment). Landscape-scale assessment indicators (tier 1) were developed and applied at the sub-watershed (12-digit hydrologic unit code (HUC)) level within the GOM coastal wetland sample frame with scores calculated using land-use maps and geographic information system. Rapid assessment protocols (tier 2), using a combination of data analysis and field work, evaluated metrics associated with landscape context, hydrology, physical structure, and biological structure. Intensive site monitoring (tier 3) included measures of soil chemistry and composition, water column and pore-water chemistry, and dominant macrophyte community composition and tissue chemistry. Relationships within and among assessment levels were evaluated using multivariate analyses with few significant correlations found. More detailed measures of hydrology, soils, and macrophyte species composition from sites across a known condition gradient, in conjunction with validation of standardized rapid assessment method, may be necessary to fully characterize coastal wetlands across the region.}, } @article {pmid24473680, year = {2014}, author = {Saranya, KR and Reddy, CS and Rao, PV and Jha, CS}, title = {Decadal time-scale monitoring of forest fires in Similipal Biosphere Reserve, India using remote sensing and GIS.}, journal = {Environmental monitoring and assessment}, volume = {186}, number = {5}, pages = {3283-3296}, pmid = {24473680}, issn = {1573-2959}, mesh = {Biodiversity ; Conservation of Natural Resources ; Databases, Factual ; Environmental Monitoring/*methods ; *Fires ; *Geographic Information Systems ; India ; *Remote Sensing Technology ; *Trees ; }, abstract = {Analyzing the spatial extent and distribution of forest fires is essential for sustainable forest resource management. There is no comprehensive data existing on forest fires on a regular basis in Biosphere Reserves of India. The present work have been carried out to locate and estimate the spatial extent of forest burnt areas using Resourcesat-1 data and fire frequency covering decadal fire events (2004-2013) in Similipal Biosphere Reserve. The anomalous quantity of forest burnt area was recorded during 2009 as 1,014.7 km(2). There was inconsistency in the fire susceptibility across the different vegetation types. The spatial analysis of burnt area shows that an area of 34.2 % of dry deciduous forests, followed by tree savannah, shrub savannah, and grasslands affected by fires in 2013. The analysis based on decadal time scale satellite data reveals that an area of 2,175.9 km(2) (59.6 % of total vegetation cover) has been affected by varied rate of frequency of forest fires. Fire density pattern indicates low count of burnt area patches in 2013 estimated at 1,017 and high count at 1,916 in 2004. An estimate of fire risk area over a decade identifies 12.2 km(2) is experiencing an annual fire damage. Summing the fire frequency data across the grids (each 1 km(2)) indicates 1,211 (26 %) grids are having very high disturbance regimes due to repeated fires in all the 10 years, followed by 711 grids in 9 years and 418 in 8 years and 382 in 7 years. The spatial database offers excellent opportunities to understand the ecological impact of fires on biodiversity and is helpful in formulating conservation action plans.}, } @article {pmid24467996, year = {2014}, author = {Pineda-Mendoza, RM and Zúñiga, G and Martínez-Jerónimo, F}, title = {Infochemicals released by Daphnia magna fed on Microcystis aeruginosa affect mcyA gene expression.}, journal = {Toxicon : official journal of the International Society on Toxinology}, volume = {80}, number = {}, pages = {78-86}, doi = {10.1016/j.toxicon.2014.01.008}, pmid = {24467996}, issn = {1879-3150}, mesh = {Animals ; Bacterial Proteins/*genetics/metabolism ; Chlorophyll/metabolism ; Chlorophyll A ; Computational Biology ; DNA, Bacterial/genetics ; Daphnia/*chemistry ; *Gene Expression ; Microcystins/toxicity ; Microcystis/*genetics/metabolism ; }, abstract = {Microcystins (MCs) are toxic heptapeptides produced by cyanobacteria during blooms that are noxious to diverse organisms, from bacteria to vertebrates. Specifically in daphnids, they cause reduced growth, a low reproductive rate, and, in extreme cases, death; however, different infochemicals released by cladocerans stimulate MCs synthesis. Ecological cyanobacteria-daphnids interactions are complex and not clear yet. In this study, we evaluated the effects of infochemicals released by Daphnia magna neonates and adults fed with different concentrations of Microcystis aeruginosa on population growth of strains Ch10 and UTEX LB2385 of M. aeruginosa, mcyA gene expression in real time qPCR, and the intracellular concentration of MCs. In addition, we assessed the relation between the cellular diameter and the intracellular concentration of MCs in both strains. Chlorophyll content per cell was affected by the presence of infochemicals from D. magna neonates and adults. mcyA gene was significantly overexpressed in the early stages of population growth (5 days) in all treatments with strain UTEX LB2385, whereas overexpression was observed in strain Ch10 at the end stage of the exponential and stationary phases (10 and 15 days). Intracellular concentration of MCs varied with the tested factor. Results suggest that the increase in mcyA gene expression and in MCs production could be defense mechanisms against the consumption by D. magna. Results also demonstrate the physiological plasticity among Microcystis strains, which could explain the permanence and dominance of this genus in toxic blooms.}, } @article {pmid24466198, year = {2014}, author = {Syed, K and Shale, K and Pagadala, NS and Tuszynski, J}, title = {Systematic identification and evolutionary analysis of catalytically versatile cytochrome p450 monooxygenase families enriched in model basidiomycete fungi.}, journal = {PloS one}, volume = {9}, number = {1}, pages = {e86683}, pmid = {24466198}, issn = {1932-6203}, mesh = {Basidiomycota/classification/*genetics/*metabolism ; Catalysis ; Cytochrome P-450 Enzyme System/*genetics/*metabolism ; Databases, Genetic ; *Evolution, Molecular ; Gene Duplication ; Genome, Fungal ; Genome-Wide Association Study ; *Multigene Family ; Oxidation-Reduction ; Phylogeny ; Substrate Specificity ; }, abstract = {Genome sequencing of basidiomycetes, a group of fungi capable of degrading/mineralizing plant material, revealed the presence of numerous cytochrome P450 monooxygenases (P450s) in their genomes, with some exceptions. Considering the large repertoire of P450s found in fungi, it is difficult to identify P450s that play an important role in fungal metabolism and the adaptation of fungi to diverse ecological niches. In this study, we followed Sir Charles Darwin's theory of natural selection to identify such P450s in model basidiomycete fungi showing a preference for different types of plant components degradation. Any P450 family comprising a large number of member P450s compared to other P450 families indicates its natural selection over other P450 families by its important role in fungal physiology. Genome-wide comparative P450 analysis in the basidiomycete species, Phanerochaete chrysosporium, Phanerochaete carnosa, Agaricus bisporus, Postia placenta, Ganoderma sp. and Serpula lacrymans, revealed enrichment of 11 P450 families (out of 68 P450 families), CYP63, CYP512, CYP5035, CYP5037, CYP5136, CYP5141, CYP5144, CYP5146, CYP5150, CYP5348 and CYP5359. Phylogenetic analysis of the P450 family showed species-specific alignment of P450s across the P450 families with the exception of P450s of Phanerochaete chrysosporium and Phanerochaete carnosa, suggesting paralogous evolution of P450s in model basidiomycetes. P450 gene-structure analysis revealed high conservation in the size of exons and the location of introns. P450s with the same gene structure were found tandemly arranged in the genomes of selected fungi. This clearly suggests that extensive gene duplications, particularly tandem gene duplications, led to the enrichment of selective P450 families in basidiomycetes. Functional analysis and gene expression profiling data suggest that members of the P450 families are catalytically versatile and possibly involved in fungal colonization of plant material. To our knowledge, this is the first report on the identification and comparative-evolutionary analysis of P450 families enriched in model basidiomycetes.}, } @article {pmid24465810, year = {2014}, author = {Shamblin, BM and Bolten, AB and Abreu-Grobois, FA and Bjorndal, KA and Cardona, L and Carreras, C and Clusa, M and Monzón-Argüello, C and Nairn, CJ and Nielsen, JT and Nel, R and Soares, LS and Stewart, KR and Vilaça, ST and Türkozan, O and Yilmaz, C and Dutton, PH}, title = {Geographic patterns of genetic variation in a broadly distributed marine vertebrate: new insights into loggerhead turtle stock structure from expanded mitochondrial DNA sequences.}, journal = {PloS one}, volume = {9}, number = {1}, pages = {e85956}, pmid = {24465810}, issn = {1932-6203}, mesh = {Animals ; Atlantic Ocean ; Conservation of Natural Resources ; DNA, Mitochondrial/*genetics ; Female ; *Genetic Variation ; Genetics, Population ; Haplotypes ; Indian Ocean ; Mediterranean Sea ; Mitochondria/genetics ; Molecular Sequence Data ; Phylogeny ; Phylogeography ; Sequence Analysis, DNA ; Turtles/*genetics ; }, abstract = {Previous genetic studies have demonstrated that natal homing shapes the stock structure of marine turtle nesting populations. However, widespread sharing of common haplotypes based on short segments of the mitochondrial control region often limits resolution of the demographic connectivity of populations. Recent studies employing longer control region sequences to resolve haplotype sharing have focused on regional assessments of genetic structure and phylogeography. Here we synthesize available control region sequences for loggerhead turtles from the Mediterranean Sea, Atlantic, and western Indian Ocean basins. These data represent six of the nine globally significant regional management units (RMUs) for the species and include novel sequence data from Brazil, Cape Verde, South Africa and Oman. Genetic tests of differentiation among 42 rookeries represented by short sequences (380 bp haplotypes from 3,486 samples) and 40 rookeries represented by long sequences (∼800 bp haplotypes from 3,434 samples) supported the distinction of the six RMUs analyzed as well as recognition of at least 18 demographically independent management units (MUs) with respect to female natal homing. A total of 59 haplotypes were resolved. These haplotypes belonged to two highly divergent global lineages, with haplogroup I represented primarily by CC-A1, CC-A4, and CC-A11 variants and haplogroup II represented by CC-A2 and derived variants. Geographic distribution patterns of haplogroup II haplotypes and the nested position of CC-A11.6 from Oman among the Atlantic haplotypes invoke recent colonization of the Indian Ocean from the Atlantic for both global lineages. The haplotypes we confirmed for western Indian Ocean RMUs allow reinterpretation of previous mixed stock analysis and further suggest that contemporary migratory connectivity between the Indian and Atlantic Oceans occurs on a broader scale than previously hypothesized. This study represents a valuable model for conducting comprehensive international cooperative data management and research in marine ecology.}, } @article {pmid24464649, year = {2014}, author = {Green, JW and Springer, TA and Saulnier, AN and Swintek, J}, title = {Statistical analysis of histopathological endpoints.}, journal = {Environmental toxicology and chemistry}, volume = {33}, number = {5}, pages = {1108-1116}, doi = {10.1002/etc.2530}, pmid = {24464649}, issn = {1552-8618}, mesh = {Animals ; Data Interpretation, Statistical ; Ecotoxicology/*methods ; Female ; *Fishes ; Liver/pathology ; Male ; Oryzias ; Research Design ; Toxicity Tests/*methods ; }, abstract = {Histopathological assessments of fish from aquatic ecotoxicology studies are being performed with increasing frequency. Aquatic ecotoxicology studies performed for submission to regulatory agencies are usually conducted with multiple subjects (e.g., fish) in each of multiple vessels (replicates) within a water control and within each of several concentrations of a test substance. A number of histopathological endpoints are evaluated in each fish, and a severity score is generally recorded for each endpoint. The severity scores are often recorded using a nonquantitative scale of 0 to 4, with 0 indicating no effect, 1 indicating minimal effect, through 4 for severe effect. Statistical methods often used to analyze these scores suffer from several shortcomings: computing average scores as though scores were quantitative values, considering only the frequency of abnormality while ignoring severity, ignoring any concentration-response trend, and ignoring the possible correlation between responses of individuals within test vessels. A new test, the Rao-Scott Cochran-Armitage by Slices (RSCABS), is proposed that incorporates the replicate vessel experimental design and the biological expectation that the severity of the effect tends to increase with increasing doses or concentrations, while retaining the individual subject scores and taking into account the severity as well as frequency of scores. A power simulation and examples demonstrate the performance of the test. R-based software has been developed to carry out this test and is available free of charge at www.epa.gov/med/Prods_Pubs/rscabs.htm. The SAS-based RSCABS software is available from the first and third authors.}, } @article {pmid24463412, year = {2014}, author = {Shen, P and Han, F and Su, S and Zhang, J and Chen, Z and Li, J and Gan, J and Feng, B and Wu, B}, title = {Using pig manure to promote fermentation of sugarcane molasses alcohol wastewater and its effects on microbial community structure.}, journal = {Bioresource technology}, volume = {155}, number = {}, pages = {323-329}, doi = {10.1016/j.biortech.2013.12.073}, pmid = {24463412}, issn = {1873-2976}, mesh = {Alcohols/*analysis ; Anaerobiosis ; Animals ; Base Sequence ; *Biofuels ; Biological Oxygen Demand Analysis ; Computational Biology ; DNA Primers/genetics ; Fermentation ; Manure/*analysis/microbiology ; Microbiota/*genetics ; Molasses/*analysis ; Molecular Sequence Data ; Polymerase Chain Reaction ; Principal Component Analysis ; RNA, Ribosomal, 18S/genetics ; Saccharum/*chemistry ; Sequence Analysis, DNA ; Swine ; Wastewater/*chemistry ; }, abstract = {Molasses alcohol wastewater (MAW) is difficult to be bio-treated and converted into biogas. In this study, MAW mixed with pig manure (PM) in different ratios was co-digested. Biogas production, chemical oxygen demand (COD) removal and the structure of microbial communities were monitored in the process. Our results showed that under the optimal COD ratio of PM:MAW (1.0:1.5), CODremoval and biogas yield were the highest. And in fermentation tanks with different PM to MAW ratios, the structure and composition of bacterial communities varied in the early and late stage. Furthermore, the type of main bacterial operational taxonomic units (OTUs) have no differences, yet the relative abundance of OTUs varied. The current research showed that there was a good potential to the use of PM as a co-digested material to anaerobic treatment of MAW and provided references for further improving bio-treatment of MAW.}, } @article {pmid24462940, year = {2014}, author = {Karimi, A and Hanafi-Bojd, AA and Yaghoobi-Ershadi, MR and Akhavan, AA and Ghezelbash, Z}, title = {Spatial and temporal distributions of phlebotomine sand flies (Diptera: Psychodidae), vectors of leishmaniasis, in Iran.}, journal = {Acta tropica}, volume = {132}, number = {}, pages = {131-139}, doi = {10.1016/j.actatropica.2014.01.004}, pmid = {24462940}, issn = {1873-6254}, mesh = {Animals ; Databases, Factual ; Female ; *Insect Vectors ; Iran/epidemiology ; Leishmaniasis/epidemiology/transmission ; *Phylogeography ; Psychodidae/*growth & development ; }, abstract = {Leishmaniasis is a major vector-borne disease and health problem in Iran. Studies on sand flies, as the vectors of the disease, began in the Northern and Western parts of the country in 1930 and have been continued up to now. Concerning many published information in the field of sand flies, providing a digital database for the country will help the public health authorities to make more correct and prompt decisions for planning leishmaniasis control programs as well as modeling and forecasting of transmission potential across the country. All published data on phlebotomine sand flies of Iran were collected. A database was then designed in Excel format, including all available information regarding sand flies. The valid data were transferred to ArcGIS9.3 to prepare the first spatial database of sand flies of Iran. The IrSandflybase includes 131 papers, 2 abstracts and 71 PhD/MSc theses, reporting studies conducted during 1930-2012. This database contains different available data covering all aspects of ecology and biology of 50 sand fly species in two genera of Phlebotomus and Sergentomyia in the country. The temporal activity of sand flies is reported 9 months in warm regions of the southern part, while it may reduce to 7-8 months in central plateau or 4-5 months in cold areas of the northwest. Occasional studies reported rare species from the borderlines of Iran. It seems that changing the climate due to global warming may affect the spatial distribution of different species and expand it into the country, the issue that can be followed by an updated database.}, } @article {pmid24462499, year = {2014}, author = {Dato, S and Soerensen, M and Lagani, V and Montesanto, A and Passarino, G and Christensen, K and Tan, Q and Christiansen, L}, title = {Contribution of genetic polymorphisms on functional status at very old age: a gene-based analysis of 38 genes (311 SNPs) in the oxidative stress pathway.}, journal = {Experimental gerontology}, volume = {52}, number = {}, pages = {23-29}, pmid = {24462499}, issn = {1873-6815}, support = {P01 AG008761/AG/NIA NIH HHS/United States ; P01 AG08761/AG/NIA NIH HHS/United States ; }, mesh = {*Activities of Daily Living ; Aged ; Aged, 80 and over ; Cognition ; Female ; Humans ; Male ; *Oxidative Stress ; *Polymorphism, Single Nucleotide ; }, abstract = {Preservation of functional ability is a well-recognized marker of longevity. At a molecular level, a major determinant of the physiological decline occurring with aging is the imbalance between production and accumulation of oxidative damage to macromolecules, together with a decreased efficiency of stress response to avoid or repair such damage. In this paper we investigated the association of 38 genes (311 SNPs) belonging to the pro-antioxidant pathways with physical and cognitive performances, by analyzing single SNP and gene-based associations with Hand Grip strength (HG), Activities of Daily Living (ADL), Walking Speed (WS), Mini Mental State Examination (MMSE) and Composite Cognitive Score (CCS) in a Cohort of 1089 Danish nonagenarians. Moreover, for each gene analyzed in the pro-antioxidant pathway, we tested the influence on longitudinal survival. In the whole sample, nominal associations were found for TXNRD1 variability with ADL and WS, NDUFS1 and UCP3 with HG and WS, GCLC and UCP2 with WS (p<0.05). Stronger associations although not holding the multiple comparison correction, were observed between MMSE and NDUFV1, MT1A and GSTP1 variability (p<0.009). Moreover, we found that association between genetic variability in the pro-antioxidant pathway and functional status at old age is influenced by sex. In particular, most significant associations were observed in nonagenarian females, between HG scores and GLRX and UCP3 variability, between ADL levels and TXNRD1, MMSE and MT1A genetic variability. In males, a borderline statistically significant association with ADL level was found for UQCRFS1 gene. Nominally significant associations in relation to survival were found in the female sample only with SOD2, NDUFS1, UCP3 and TXNRD1 variability, the latter two confirming previous observations reported in the same cohort. Overall, our work supports the evidence that genes belonging to the pro-anti-oxidant pathway are able to modulate physical and cognitive performance after the ninth decade of life, finally influencing extreme survival.}, } @article {pmid24460904, year = {2014}, author = {Huang, K and Ritland, K and Guo, S and Shattuck, M and Li, B}, title = {A pairwise relatedness estimator for polyploids.}, journal = {Molecular ecology resources}, volume = {14}, number = {4}, pages = {734-744}, doi = {10.1111/1755-0998.12217}, pmid = {24460904}, issn = {1755-0998}, mesh = {Computational Biology/*methods ; Genetic Markers ; *Genetic Variation ; *Polyploidy ; Software ; }, abstract = {Studies in genetics and ecology often require estimates of relatedness coefficients based on genetic marker data. Many diploid estimators have been developed using either method-of-moments or maximum-likelihood estimates. However, there are no relatedness estimators for polyploids. The development of a moment estimator for polyploids with polysomic inheritance, which simultaneously incorporates the two-gene relatedness coefficient and various 'higher-order' coefficients, is described here. The performance of the estimator is compared to other estimators under a variety of conditions. When using a small number of loci, the estimator is biased because of an increase in ill-conditioned matrices. However, the estimator becomes asymptotically unbiased with large numbers of loci. The ambiguity of polyploid heterozygotes (when balanced heterozygotes cannot be distinguished from unbalanced heterozygotes) is also considered; as with low numbers of loci, genotype ambiguity leads to bias. A software, PolyRelatedness, implementing this method and supporting a maximum ploidy of 8 is provided.}, } @article {pmid24454840, year = {2014}, author = {Kalwij, JM and Robertson, MP and Ronk, A and Zobel, M and Pärtel, M}, title = {Spatially-explicit estimation of geographical representation in large-scale species distribution datasets.}, journal = {PloS one}, volume = {9}, number = {1}, pages = {e85306}, pmid = {24454840}, issn = {1932-6203}, mesh = {*Biodiversity ; Datasets as Topic ; Europe ; *Geography ; Plants/*classification ; }, abstract = {Much ecological research relies on existing multispecies distribution datasets. Such datasets, however, can vary considerably in quality, extent, resolution or taxonomic coverage. We provide a framework for a spatially-explicit evaluation of geographical representation within large-scale species distribution datasets, using the comparison of an occurrence atlas with a range atlas dataset as a working example. Specifically, we compared occurrence maps for 3773 taxa from the widely-used Atlas Florae Europaeae (AFE) with digitised range maps for 2049 taxa of the lesser-known Atlas of North European Vascular Plants. We calculated the level of agreement at a 50-km spatial resolution using average latitudinal and longitudinal species range, and area of occupancy. Agreement in species distribution was calculated and mapped using Jaccard similarity index and a reduced major axis (RMA) regression analysis of species richness between the entire atlases (5221 taxa in total) and between co-occurring species (601 taxa). We found no difference in distribution ranges or in the area of occupancy frequency distribution, indicating that atlases were sufficiently overlapping for a valid comparison. The similarity index map showed high levels of agreement for central, western, and northern Europe. The RMA regression confirmed that geographical representation of AFE was low in areas with a sparse data recording history (e.g., Russia, Belarus and the Ukraine). For co-occurring species in south-eastern Europe, however, the Atlas of North European Vascular Plants showed remarkably higher richness estimations. Geographical representation of atlas data can be much more heterogeneous than often assumed. Level of agreement between datasets can be used to evaluate geographical representation within datasets. Merging atlases into a single dataset is worthwhile in spite of methodological differences, and helps to fill gaps in our knowledge of species distribution ranges. Species distribution dataset mergers, such as the one exemplified here, can serve as a baseline towards comprehensive species distribution datasets.}, } @article {pmid24454810, year = {2014}, author = {Meier, K and Hansen, MM and Normandeau, E and Mensberg, KL and Frydenberg, J and Larsen, PF and Bekkevold, D and Bernatchez, L}, title = {Local adaptation at the transcriptome level in brown trout: evidence from early life history temperature genomic reaction norms.}, journal = {PloS one}, volume = {9}, number = {1}, pages = {e85171}, pmid = {24454810}, issn = {1932-6203}, mesh = {Adaptation, Physiological/*genetics ; Animals ; Female ; Gene Ontology ; *Genomics ; Molecular Sequence Data ; Oligonucleotide Array Sequence Analysis ; *Temperature ; *Transcriptome ; Trout/*genetics/*physiology ; }, abstract = {Local adaptation and its underlying molecular basis has long been a key focus in evolutionary biology. There has recently been increased interest in the evolutionary role of plasticity and the molecular mechanisms underlying local adaptation. Using transcriptome analysis, we assessed differences in gene expression profiles for three brown trout (Salmo trutta) populations, one resident and two anadromous, experiencing different temperature regimes in the wild. The study was based on an F2 generation raised in a common garden setting. A previous study of the F1 generation revealed different reaction norms and significantly higher QST than FST among populations for two early life-history traits. In the present study we investigated if genomic reaction norm patterns were also present at the transcriptome level. Eggs from the three populations were incubated at two temperatures (5 and 8 degrees C) representing conditions encountered in the local environments. Global gene expression for fry at the stage of first feeding was analysed using a 32k cDNA microarray. The results revealed differences in gene expression between populations and temperatures and population × temperature interactions, the latter indicating locally adapted reaction norms. Moreover, the reaction norms paralleled those observed previously at early life-history traits. We identified 90 cDNA clones among the genes with an interaction effect that were differently expressed between the ecologically divergent populations. These included genes involved in immune- and stress response. We observed less plasticity in the resident as compared to the anadromous populations, possibly reflecting that the degree of environmental heterogeneity encountered by individuals throughout their life cycle will select for variable level of phenotypic plasticity at the transcriptome level. Our study demonstrates the usefulness of transcriptome approaches to identify genes with different temperature reaction norms. The responses observed suggest that populations may vary in their susceptibility to climate change.}, } @article {pmid24453902, year = {2013}, author = {Chuang, HM and Lin, CK and Chen, DR and Chen, YS}, title = {Evolving MCDM applications using hybrid expert-based ISM and DEMATEL models: an example of sustainable ecotourism.}, journal = {TheScientificWorldJournal}, volume = {2013}, number = {}, pages = {751728}, pmid = {24453902}, issn = {1537-744X}, mesh = {Conservation of Natural Resources/*methods ; *Decision Support Techniques ; *Ecosystem ; *Models, Organizational ; Taiwan ; Travel ; }, abstract = {Ecological degradation is an escalating global threat. Increasingly, people are expressing awareness and priority for concerns about environmental problems surrounding them. Environmental protection issues are highlighted. An appropriate information technology tool, the growing popular social network system (virtual community, VC), facilitates public education and engagement with applications for existent problems effectively. Particularly, the exploration of related involvement behavior of VC member engagement is an interesting topic. Nevertheless, member engagement processes comprise interrelated sub-processes that reflect an interactive experience within VCs as well as the value co-creation model. To address the top-focused ecotourism VCs, this study presents an application of a hybrid expert-based ISM model and DEMATEL model based on multi-criteria decision making tools to investigate the complex multidimensional and dynamic nature of member engagement. Our research findings provide insightful managerial implications and suggest that the viral marketing of ecotourism protection is concerned with practitioners and academicians alike.}, } @article {pmid24452712, year = {2014}, author = {Yang, Q and Yin, J and Li, G and Qi, L and Yang, F and Wang, R and Li, G}, title = {Reference gene selection for qRT-PCR in Caragana korshinskii Kom. under different stress conditions.}, journal = {Molecular biology reports}, volume = {41}, number = {4}, pages = {2325-2334}, pmid = {24452712}, issn = {1573-4978}, mesh = {Caragana/*genetics/metabolism ; Computational Biology ; Gene Expression Profiling ; *Gene Expression Regulation, Plant ; *Genes, Plant ; RNA Stability ; Real-Time Polymerase Chain Reaction ; Stress, Physiological/*genetics ; }, abstract = {Caragana korshinskii Kom., which is widely distributed in the northwest China and Mongolia, is an important forage bush belonging to the legume family with high economic and ecological value. Strong tolerance ability to various stresses makes C. korshinskii Kom. a valuable species for plant stress research. In this study, suitable reference genes for quantitative real-time reverse transcription PCR (qRT-PCR) were screened from 11 candidate reference genes, including ACT, GAPDH, EF1α, UBQ, TUA, CAP, TUB, TUB3, SKIP1, SKIP5-1 and SKIP5-2. A total of 129 samples under drought, heat, cold, salt, ABA and high pH treatment were profiled, and software such as geNORM, NormFinder and BestKeeper were used for reference gene evaluation and selection. Different suitable reference genes were selected under different stresses. Across all 129 samples, GAPDH, EF1α and SKIP5-1 were found to be the most stable reference genes, and EF1α+SKIP5-1 is the most stable reference gene combination. Conversely, TUA, TUB and SKIP1 were not suitable for using as reference genes owing to their great expression variation under some stress conditions. The relative expression levels of CkWRKY1 were detected using the stable and unstable reference genes and their applicability was confirmed. These results provide some stable reference genes and reference gene combinations for qRT-PCR under different stresses in C. korshinskii Kom. for future research work, and indicate that CkWRKY1 plays essential roles in response to stresses in C. korshinskii.}, } @article {pmid24448554, year = {2014}, author = {Mejía-León, ME and Petrosino, JF and Ajami, NJ and Domínguez-Bello, MG and de la Barca, AM}, title = {Fecal microbiota imbalance in Mexican children with type 1 diabetes.}, journal = {Scientific reports}, volume = {4}, number = {}, pages = {3814}, pmid = {24448554}, issn = {2045-2322}, mesh = {Adolescent ; Bacteria/*classification/*genetics ; Case-Control Studies ; Child ; Computational Biology ; Cross-Sectional Studies ; DNA, Bacterial/genetics ; Diabetes Mellitus, Type 1/*microbiology ; Feces/*microbiology ; Female ; Follow-Up Studies ; Gastrointestinal Tract/microbiology ; Humans ; Male ; Mexico ; *Microbiota ; Prognosis ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Dysbiosis of the intestinal microbiota affecting the gut barrier could be triggering Type 1 Diabetes (T1D), the second most frequent autoimmune disease in childhood. This study compared the structure of the fecal microbiota in 29 mestizo children aged 7-18 years, including 8 T1D at onset, 13 T1D after 2 years treatment, and 8 healthy controls. Clinical information was collected, predisposing haplotypes were determined; the fecal DNA was extracted, the V4 region of the 16S rRNA gene amplified and 454-pyrosequenced. The newly diagnosed T1D cases had high levels of the genus Bacteroides (p < 0.004), whereas the control group had a gut microbiota dominated by Prevotella. Children with T1D treated for ≥2 years had levels of Bacteroides and Prevotella compared to those of the control group. The gut microbiota of newly diagnosed T1D cases is altered, but whether it is involved in disease causation or is a consequence of host selection remains unclear.}, } @article {pmid24447661, year = {2014}, author = {Zhang, Z and Sheppard, JK and Swaisgood, RR and Wang, G and Nie, Y and Wei, W and Zhao, N and Wei, F}, title = {Ecological scale and seasonal heterogeneity in the spatial behaviors of giant pandas.}, journal = {Integrative zoology}, volume = {9}, number = {1}, pages = {46-60}, doi = {10.1111/1749-4877.12030}, pmid = {24447661}, issn = {1749-4877}, mesh = {*Altitude ; Animals ; China ; Female ; Geographic Information Systems ; Homing Behavior/*physiology ; Male ; *Seasons ; Spatial Behavior/*physiology ; Telemetry ; Ursidae/*physiology ; }, abstract = {We report on the first study to track the spatial behaviors of wild giant pandas (Ailuropoda melanoleuca) using high-resolution global positioning system (GPS) telemetry. Between 2008 and 2009, 4 pandas (2 male and 2 female) were tracked in Foping Reserve, China for an average of 305 days (± 54.8 SE). Panda home ranges were larger than those of previous very high frequency tracking studies, with a bimodal distribution of space-use and distinct winter and summer centers of activity. Home range sizes were larger in winter than in summer, although there was considerable individual variability. All tracked pandas exhibited individualistic, unoriented and multiphasic movement paths, with a high level of tortuosity within seasonal core habitats and directed, linear, large-scale movements between habitats. Pandas moved from low elevation winter habitats to high elevation (>2000 m) summer habitats in May, when temperatures averaged 17.5 °C (± 0.3 SE), and these large-scale movements took <1 month to complete. The peak in panda mean elevation occurred in Jul, after which they began slow, large-scale movements back to winter habitats that were completed in Nov. An adult female panda made 2 longdistance movements during the mating season. Pandas remain close to rivers and streams during winter, possibly reflecting the elevated water requirements to digest their high-fiber food. Panda movement path tortuosity and first-passage-time as a function of spatial scale indicated a mean peak in habitat search effort and patch use of approximately 700 m. Despite a high degree of spatial overlap between panda home ranges, particularly in winter, we detected neither avoidance nor attraction behavior between conspecifics.}, } @article {pmid24445578, year = {2014}, author = {Mattei, G and Ferrari, S and Pingani, L and Rigatelli, M}, title = {Short-term effects of the 2008 Great Recession on the health of the Italian population: an ecological study.}, journal = {Social psychiatry and psychiatric epidemiology}, volume = {49}, number = {6}, pages = {851-858}, pmid = {24445578}, issn = {1433-9285}, mesh = {Accidents, Traffic/economics/mortality ; Adult ; Alcohol Drinking/mortality/psychology ; Cardiovascular Diseases/mortality/psychology ; *Economic Recession ; Humans ; Italy ; MEDLINE ; Male ; Mental Health/economics/*statistics & numerical data ; Reproducibility of Results ; Suicide, Attempted/economics/statistics & numerical data ; Time Factors ; Unemployment/statistics & numerical data ; }, abstract = {PURPOSE: To report on the effects on health that the 2008 Great Recession is producing in Italy, by comparing the consistency of Italian data with general observations reported in the scientific literature, and by pointing out consequences on the rates of all-cause mortality, cardiovascular mortality, male suicidal behaviours, daytime alcohol drinking and traffic fatalities.

METHODS: This is an ecological study in which MEDLINE, PsycINFO and PubMed were searched for the literature with combinations of the following keywords: economic recession, financial crisis, unemployment, health, suicide and mental health. Data from two Italian government agencies (Italian Institute of Statistics, ISTAT, and Italian Agency of Drugs, AIFA) in the years from 2000 to 2010 were obtained and analysed, by producing models of multiple linear regressions.

RESULTS: After the recession onset, all-cause mortality remained stable, and was not associated with the economic fluctuations. Differently, cardiovascular mortality was associated with the rate of unemployment, and showed a significant increase in 2010. Alcohol consumption increased in 2009, the year with the worst real GDP decrease (-5.1 %). Though the total rate of suicide was not associated with the economic situation, male completed and attempted suicides due to financial crisis were significantly associated with the rate of unemployment and the real GDP. The increasing diffusion of antidepressants was not associated with a lowering of the rate of suicide.

CONCLUSIONS: The data on the Italian situation here discussed are sufficiently reliable to conclude that a link exists between the ongoing economic recession and health and mental health of Italians. Further research is needed to understand more in detail and with stronger reliability such link, to support primary and secondary preventive interventions and orient the development of effective sociopolitical interventions.}, } @article {pmid24444191, year = {2014}, author = {Santoferrara, LF and Grattepanche, JD and Katz, LA and McManus, GB}, title = {Pyrosequencing for assessing diversity of eukaryotic microbes: analysis of data on marine planktonic ciliates and comparison with traditional methods.}, journal = {Environmental microbiology}, volume = {16}, number = {9}, pages = {2752-2763}, doi = {10.1111/1462-2920.12380}, pmid = {24444191}, issn = {1462-2920}, mesh = {*Biodiversity ; Ciliophora/*classification/genetics ; Computational Biology ; Connecticut ; Estuaries ; Gene Library ; New York ; Phylogeny ; Seawater/microbiology ; Sequence Analysis, DNA/*methods ; }, abstract = {Assessing microbial diversity requires analysis of all three domains of life, including eukaryotic microbes. We examined the diversity of two ecologically important clades of microbial eukaryotes, ciliates in the subclasses Oligotrichia and Choreotrichia (class Spirotrichea), by comparing pyrosequencing to Sanger-sequenced clone libraries and microscopy. Using samples from a large temperate estuary (Long Island Sound, USA), we gained three major insights. First, richness estimates varied by up to one order of magnitude either using different criteria for pyrosequence processing or among pyrosequencing, cloning and microscopy, while taxon identification was almost always coherent. Error-correcting algorithms for pyrosequences ('denoising') reduced discrepancies in richness but also removed known morphospecies from the data. Second, although most of the pyrosequenced operational taxonomic units (OTUs) were distributed within known orders and families, we found evidence of a previously uncharacterized or unknown clade even in these ciliate lineages that have a rich history of morphological description. Third, pyrosequencing allowed the detection of OTUs that were either dominant or extremely rare in different samples. Our findings confirm the potential of pyrosequencing for quantifying microbial diversity, but also highlight the importance of careful evaluation of pyrosequence processing for using this method to address ecological questions.}, } @article {pmid24443642, year = {2013}, author = {Holden, RJ and Rivera-Rodriguez, AJ and Faye, H and Scanlon, MC and Karsh, BT}, title = {Automation and adaptation: Nurses' problem-solving behavior following the implementation of bar coded medication administration technology.}, journal = {Cognition, technology & work (Online)}, volume = {15}, number = {3}, pages = {283-296}, pmid = {24443642}, issn = {1435-5558}, support = {R01 LM008923/LM/NLM NIH HHS/United States ; UL1 TR000427/TR/NCATS NIH HHS/United States ; R01 HS013610/HS/AHRQ HHS/United States ; TL1 RR025013/RR/NCRR NIH HHS/United States ; T32 HS000083/HS/AHRQ HHS/United States ; }, abstract = {The most common change facing nurses today is new technology, particularly bar coded medication administration technology (BCMA). However, there is a dearth of knowledge on how BCMA alters nursing work. This study investigated how BCMA technology affected nursing work, particularly nurses' operational problem-solving behavior. Cognitive systems engineering observations and interviews were conducted after the implementation of BCMA in three nursing units of a freestanding pediatric hospital. Problem-solving behavior, associated problems, and goals, were specifically defined and extracted from observed episodes of care. Three broad themes regarding BCMA's impact on problem solving were identified. First, BCMA allowed nurses to invent new problem-solving behavior to deal with pre-existing problems. Second, BCMA made it difficult or impossible to apply some problem-solving behaviors that were commonly used pre-BCMA, often requiring nurses to use potentially risky workarounds to achieve their goals. Third, BCMA created new problems that nurses were either able to solve using familiar or novel problem-solving behaviors, or unable to solve effectively. Results from this study shed light on hidden hazards and suggest three critical design needs: (1) ecologically valid design; (2) anticipatory control; and (3) basic usability. Principled studies of the actual nature of clinicians' work, including problem solving, are necessary to uncover hidden hazards and to inform health information technology design and redesign.}, } @article {pmid24441685, year = {2014}, author = {Togashi, T and Sasaki, H and Yoshimura, J}, title = {A geometrical approach explains Lake Ball (Marimo) formations in the green alga, Aegagropila linnaei.}, journal = {Scientific reports}, volume = {4}, number = {}, pages = {3761}, pmid = {24441685}, issn = {2045-2322}, mesh = {Biomass ; Chlorophyta/genetics/*growth & development ; *Environment ; *Marine Biology ; }, abstract = {An extremely rare alga, Aegagropila linnaei, is known for its beautiful spherical filamentous aggregations called Lake Ball (Marimo). It has long been a mystery in biology as to why this species forms 3D ball-like aggregations. This alga also forms two-dimensional mat-like aggregations. Here we show that forming ball-like aggregations is an adaptive strategy to increase biomass in the extremely limited environments suitable for growth of this alga. We estimate the maximum biomass attained by ball colonies and compare it to that attained by mat colonies. As a result, a ball colony can become larger in areal biomass than the mat colony. In the two large ball colonies studied so far, they actually have larger biomasses than the mat colonies. The uniqueness of Lake Balls in nature seems to be due to the rarity of such environmental conditions. This implies that the conservation of this alga is difficult, but important.}, } @article {pmid24438509, year = {2014}, author = {Kawakami, T and Darby, BJ and Ungerer, MC}, title = {Transcriptome resources for the perennial sunflower Helianthus maximiliani obtained from ecologically divergent populations.}, journal = {Molecular ecology resources}, volume = {14}, number = {4}, pages = {812-819}, doi = {10.1111/1755-0998.12227}, pmid = {24438509}, issn = {1755-0998}, mesh = {Computational Biology/*methods ; Ecosystem ; Genomics/*methods ; Helianthus/*genetics ; Phylogeography ; *Transcriptome ; }, abstract = {Next-generation sequencing (NGS) technologies provide a rapid means to generate genomic resources for species exhibiting interesting ecological and evolutionary variation but for which such resources are scant or nonexistent. In the current report, we utilize 454 pyrosequencing to obtain transcriptome information for multiple individuals and tissue types from geographically disparate and ecologically differentiated populations of the perennial sunflower species Helianthus maximiliani. A total of 850 275 raw reads were obtained averaging 355 bp in length. Reads were assembled, postprocessing, into 16 681 unique contigs with an N50 of 898 bp and a total length of 13.6 Mb. A majority (67%) of these contigs were annotated based on comparison with the Arabidopsis thaliana genome (TAIR10). Contigs were identified that exhibit high similarity to genes associated with natural variation in flowering time and freezing tolerance in other plant species and will facilitate future studies aimed at elucidating the molecular basis of clinal life history variation and adaptive differentiation in H. maximiliani. Large numbers of gene-associated simple sequence repeats (SSRs) and single-nucleotide polymorphisms (SNPs) also were identified that can be deployed in mapping and population genomic analyses.}, } @article {pmid24434032, year = {2014}, author = {Tang, W and Yu, L and He, W and Yang, G and Ke, F and Baxter, SW and You, S and Douglas, CJ and You, M}, title = {DBM-DB: the diamondback moth genome database.}, journal = {Database : the journal of biological databases and curation}, volume = {2014}, number = {}, pages = {bat087}, pmid = {24434032}, issn = {1758-0463}, mesh = {Animals ; *Databases, Genetic ; Expressed Sequence Tags ; Genes, Insect ; Genome, Insect/*genetics ; Molecular Sequence Annotation ; Moths/*genetics ; *Software ; Transcriptome/genetics ; }, abstract = {The diamondback moth Genome Database (DBM-DB) is a central online repository for storing and integrating genomic data of diamondback moth (DBM), Plutella xylostella (L.). It provides comprehensive search tools and downloadable datasets for scientists to study comparative genomics, biological interpretation and gene annotation of this insect pest. DBM-DB contains assembled transcriptome datasets from multiple DBM strains and developmental stages, and the annotated genome of P. xylostella (version 2). We have also integrated publically available ESTs from NCBI and a putative gene set from a second DBM genome (KONAGbase) to enable users to compare different gene models. DBM-DB was developed with the capacity to incorporate future data resources, and will serve as a long-term and open-access database that can be conveniently used for research on the biology, distribution and evolution of DBM. This resource aims to help reduce the impact DBM has on agriculture using genomic and molecular tools. Database URL: http://iae.fafu.edu.cn/DBM/}, } @article {pmid24416429, year = {2014}, author = {Hedd, A and Montevecchi, WA and Phillips, RA and Fifield, DA}, title = {Seasonal sexual segregation by monomorphic Sooty Shearwaters Puffinus griseus reflects different reproductive roles during the pre-laying period.}, journal = {PloS one}, volume = {9}, number = {1}, pages = {e85572}, pmid = {24416429}, issn = {1932-6203}, mesh = {Animal Migration/physiology ; Animals ; Breeding ; Falkland Islands ; Feeding Behavior/physiology ; Female ; Geographic Information Systems ; Geography ; Male ; Oceanography ; Oceans and Seas ; Oviposition/*physiology ; *Seasons ; Sexual Behavior, Animal/*physiology ; Soot ; }, abstract = {Tracking technology has revolutionized knowledge of seabird movements; yet, few studies have examined sex differences in distribution and behavior of small to medium-sized, sexually-monomorphic seabirds. Application of bird-borne geolocation-immersion loggers revealed seasonal segregation in the sexually-monomorphic Sooty Shearwater Puffinus griseus, mainly in the pre-laying period, when there were clear differences in reproductive roles. Shearwaters first returned to the Falkland Islands on 27 Sept±8 d; males, on average, 8 d earlier than females. Prior to egg-laying, distribution at sea, colony attendance and behaviour depended on sex. Males foraged locally over the southern Patagonian Shelf and Burdwood Bank, spending mainly single days at sea and intervening nights in the burrow. Females, who flew for more of the day during this time, foraged in more distant areas of the northern Patagonian Shelf and Argentine Basin that were deeper, warmer and relatively more productive. Attendance of females at the colony was also more variable than that of males and, overall, males were present for significantly more of the pre-laying period (38 vs. 19% of time). Sex differences were reduced following egg-laying, with males and females using similar foraging areas and making trips of similar mean duration in incubation (7.6±2.7 d) and chick-rearing (1.4±1.3 d). Congruence continued into the non-breeding period, with both sexes showing similar patterns of activity and areas of occupancy in the NW Atlantic. Thus, seasonal changes in reproductive roles influenced patterns of sexual segregation; this occurred only early in the season, when male Sooty Shearwaters foraged locally, returning regularly to the colony to defend (or maintain) the burrow or the mate, while females concentrated on building resources for egg development in distant and relatively more productive waters.}, } @article {pmid24416350, year = {2014}, author = {Baruch-Mordo, S and Wilson, KR and Lewis, DL and Broderick, J and Mao, JS and Breck, SW}, title = {Stochasticity in natural forage production affects use of urban areas by black bears: implications to management of human-bear conflicts.}, journal = {PloS one}, volume = {9}, number = {1}, pages = {e85122}, pmid = {24416350}, issn = {1932-6203}, mesh = {Animals ; Colorado ; *Conservation of Natural Resources ; Ecosystem ; Female ; Food ; Geographic Information Systems ; Humans ; Male ; *Models, Statistical ; Population Dynamics ; Reproduction/*physiology ; Stochastic Processes ; Urban Renewal/*statistics & numerical data ; Ursidae/*physiology ; }, abstract = {The rapid expansion of global urban development is increasing opportunities for wildlife to forage and become dependent on anthropogenic resources. Wildlife using urban areas are often perceived dichotomously as urban or not, with some individuals removed in the belief that dependency on anthropogenic resources is irreversible and can lead to increased human-wildlife conflict. For American black bears (Ursus americanus), little is known about the degree of bear urbanization and its ecological mechanisms to guide the management of human-bear conflicts. Using 6 years of GPS location and activity data from bears in Aspen, Colorado, USA, we evaluated the degree of bear urbanization and the factors that best explained its variations. We estimated space use, activity patterns, survival, and reproduction and modeled their relationship with ecological covariates related to bear characteristics and natural food availability. Space use and activity patterns were dependent on natural food availability (good or poor food years), where bears used higher human density areas and became more nocturnal in poor food years. Patterns were reversible, i.e., individuals using urban areas in poor food years used wildland areas in subsequent good food years. While reproductive output was similar across years, survival was lower in poor food years when bears used urban areas to a greater extent. Our findings suggest that bear use of urban areas is reversible and fluctuates with the availability of natural food resources, and that removal of urban individuals in times of food failures has the potential to negatively affect bear populations. Given that under current predictions urbanization is expected to increase by 11% across American black bear range, and that natural food failure years are expected to increase in frequency with global climate change, alternative methods of reducing urban human-bear conflict are required if the goal is to prevent urban areas from becoming population sinks.}, } @article {pmid24416180, year = {2014}, author = {Poor, EE and Jakes, A and Loucks, C and Suitor, M}, title = {Modeling fence location and density at a regional scale for use in wildlife management.}, journal = {PloS one}, volume = {9}, number = {1}, pages = {e83912}, pmid = {24416180}, issn = {1932-6203}, mesh = {Agriculture ; Animals ; Animals, Wild/*physiology ; Antelopes ; *Conservation of Natural Resources ; Geographic Information Systems ; Geography ; *Models, Theoretical ; Montana ; Ownership ; Seasons ; }, abstract = {Barbed and woven wire fences, common structures across western North America, act as impediments to wildlife movements. In particular, fencing influences pronghorn (Antilocapra americana) daily and seasonal movements, as well as modifying habitat selection. Because of fencing's impacts to pronghorn and other wildlife, it is a potentially important factor in both wildlife movement and habitat selection models. At this time, no geospatial fencing data is available at regional scales. Consequently, we constructed a regional fence model using a series of land tenure assumptions for the Hi-Line region of northern Montana--an area consisting of 13 counties over 103,400 km(2). Randomized 3.2 km long transects (n = 738) on both paved and unpaved roads were driven to collect information on habitat, fence densities and fence type. Using GIS, we constructed a fence location and a density model incorporating ownership, size, neighboring parcels, township boundaries and roads. Local knowledge of land ownership and land use assisted in improving the final models. We predict there is greater than 263,300 km of fencing in the Hi-Line region, with a maximum density of 6.8 km of fencing per km(2) and mean density of 2.4 km of fencing per km(2). Using field data to assess model accuracy, Cohen's Kappa was measured at 0.40. On-the-ground fence modification or removal could be prioritized by identifying high fence densities in critical wildlife areas such as pronghorn migratory pathways or sage grouse lekking habitat. Such novel fence data can assist wildlife and land managers to assess effects of anthropogenic features to wildlife at various scales; which in turn may help conserve declining grassland species and overall ecological functionality.}, } @article {pmid24413622, year = {2014}, author = {Savage, SA and Piguet, O and Hodges, JR}, title = {Giving words new life: generalization of word retraining outcomes in semantic dementia.}, journal = {Journal of Alzheimer's disease : JAD}, volume = {40}, number = {2}, pages = {309-317}, doi = {10.3233/JAD-131826}, pmid = {24413622}, issn = {1875-8908}, mesh = {Aged ; Cognitive Behavioral Therapy/*methods ; Comprehension ; Frontotemporal Dementia/*rehabilitation ; *Generalization, Psychological ; Humans ; Magnetic Resonance Imaging ; Middle Aged ; Neuropsychological Tests ; Online Systems ; Photic Stimulation ; *Verbal Learning ; *Vocabulary ; }, abstract = {BACKGROUND: Anomia is a common and debilitating symptom for many dementia sufferers, but is particularly marked in patients with the semantic variant of primary progressive aphasia, semantic dementia (SD). Recent studies have demonstrated that through cognitive training these patients can re-learn the names of objects, but it remains unclear whether this translates to improved use of these relearned words in contexts other than picture naming.

METHODS: Five SD patients completed a 2-month, online word training program and were assessed pre- and post-intervention on picture naming and spoken word-picture-matching plus two novel ecological tasks: video description and responses to verbal requests.

RESULTS: All participants showed clear gains in naming the trained pictures (p < 0.001). Importantly, improvements were also observed for four out of the five patients on the video description task. Milder patients also demonstrated improved comprehension of verbal instructions. Severe SD patients showed improvements on matching trained words to pictures. As expected, improvements were not found for untrained items.

CONCLUSION: There was clear evidence of generalization especially in patients with milder semantic impairments. Future studies should investigate the utility of this training in other forms of dementia.}, } @article {pmid24402271, year = {2014}, author = {Harfoot, M and Roberts, D}, title = {Taxonomy: Call for ecosystem modelling data.}, journal = {Nature}, volume = {505}, number = {7482}, pages = {160}, pmid = {24402271}, issn = {1476-4687}, mesh = {Animals ; Classification ; Computational Biology ; Databases, Factual ; Ecology ; *Ecosystem ; *Models, Biological ; }, } @article {pmid24402124, year = {2014}, author = {Zan, J and Liu, Y and Fuqua, C and Hill, RT}, title = {Acyl-homoserine lactone quorum sensing in the Roseobacter clade.}, journal = {International journal of molecular sciences}, volume = {15}, number = {1}, pages = {654-669}, pmid = {24402124}, issn = {1422-0067}, mesh = {Acyl-Butyrolactones/chemistry/*metabolism ; Animals ; Bacterial Proteins/metabolism ; Computational Biology ; Dinoflagellida/physiology ; Porifera/physiology ; *Quorum Sensing ; Repressor Proteins/metabolism ; Roseobacter/*physiology ; Trans-Activators/metabolism ; Transcription Factors/metabolism ; Virulence Factors/metabolism ; }, abstract = {Members of the Roseobacter clade are ecologically important and numerically abundant in coastal environments and can associate with marine invertebrates and nutrient-rich marine snow or organic particles, on which quorum sensing (QS) may play an important role. In this review, we summarize current research progress on roseobacterial acyl-homoserine lactone-based QS, particularly focusing on three relatively well-studied representatives, Phaeobacter inhibens DSM17395, the marine sponge symbiont Ruegeria sp. KLH11 and the dinoflagellate symbiont Dinoroseobacter shibae. Bioinformatic survey of luxI homologues revealed that over 80% of available roseobacterial genomes encode at least one luxI homologue, reflecting the significance of QS controlled regulatory pathways in adapting to the relevant marine environments. We also discuss several areas that warrant further investigation, including studies on the ecological role of these diverse QS pathways in natural environments.}, } @article {pmid24398621, year = {2014}, author = {Christens, BD and Inzeo, PT and Faust, V}, title = {Channeling power across ecological systems: social regularities in community organizing.}, journal = {American journal of community psychology}, volume = {53}, number = {3-4}, pages = {419-431}, doi = {10.1007/s10464-013-9620-4}, pmid = {24398621}, issn = {1573-2770}, mesh = {Community Networks/*organization & administration ; Humans ; *Interpersonal Relations ; Organizational Case Studies ; *Power, Psychological ; Wisconsin ; }, abstract = {Relational and social network perspectives provide opportunities for more holistic conceptualizations of phenomena of interest in community psychology, including power and empowerment. In this article, we apply these tools to build on multilevel frameworks of empowerment by proposing that networks of relationships between individuals constitute the connective spaces between ecological systems. Drawing on an example of a model for grassroots community organizing practiced by WISDOM—a statewide federation supporting local community organizing initiatives in Wisconsin—we identify social regularities (i.e., relational and temporal patterns) that promote empowerment and the development and exercise of social power through building and altering relational ties. Through an emphasis on listening-focused one-to-one meetings, reflection, and social analysis, WISDOM organizing initiatives construct and reinforce social regularities that develop social power in the organizing initiatives and advance psychological empowerment among participant leaders in organizing. These patterns are established by organizationally driven brokerage and mobilization of interpersonal ties, some of which span ecological systems.Hence, elements of these power-focused social regularities can be conceptualized as cross-system channels through which micro-level empowerment processes feed into macro-level exercise of social power, and vice versa. We describe examples of these channels in action, and offer recommendations for theory and design of future action research [corrected] .}, } @article {pmid24394959, year = {2014}, author = {Hata, S and Nakao, H and Mikhailov, AS}, title = {Dispersal-induced destabilization of metapopulations and oscillatory Turing patterns in ecological networks.}, journal = {Scientific reports}, volume = {4}, number = {}, pages = {3585}, pmid = {24394959}, issn = {2045-2322}, abstract = {As shown by Alan Turing in 1952, differential diffusion may destabilize uniform distributions of reacting species and lead to emergence of patterns. While stationary Turing patterns are broadly known, the oscillatory instability, leading to traveling waves in continuous media and sometimes called the wave bifurcation, remains less investigated. Here, we extend the original analysis by Turing to networks and apply it to ecological metapopulations with dispersal connections between habitats. Remarkably, the oscillatory Turing instability does not lead to wave patterns in networks, but to spontaneous development of heterogeneous oscillations and possible extinction of species. We find such oscillatory instabilities for all possible food webs with three predator or prey species, under various assumptions about the mobility of individual species and nonlinear interactions between them. Hence, the oscillatory Turing instability should be generic and must play a fundamental role in metapopulation dynamics, providing a common mechanism for dispersal-induced destabilization of ecosystems.}, } @article {pmid24393604, year = {2014}, author = {Hook, SE and Osborn, HL and Gissi, F and Moncuquet, P and Twine, NA and Wilkins, MR and Adams, MS}, title = {RNA-Seq analysis of the toxicant-induced transcriptome of the marine diatom, Ceratoneis closterium.}, journal = {Marine genomics}, volume = {16}, number = {}, pages = {45-53}, doi = {10.1016/j.margen.2013.12.004}, pmid = {24393604}, issn = {1876-7478}, mesh = {Aquatic Organisms/drug effects/genetics ; Diatoms/*drug effects/*genetics ; Sequence Analysis, RNA ; Stress, Physiological/drug effects/genetics ; Transcriptome/*drug effects ; Water Pollutants, Chemical/*toxicity ; }, abstract = {Diatoms are of enormous ecological importance as they account for as much as 20% of global primary production, yet they are still understudied from a genomic perspective. The benthic diatom Ceratoneis closterium is well-characterized from an ecotoxicological perspective including its use in ecotoxicological risk assessments and investigating the mode-of-action of metal toxicity. However, this organism has little sequence information available. In this study, 454 pyrosequencing of the stressor-responsive transcriptome was undertaken. These transcripts could be used to characterize general physiological processes such as photosynthesis and respiration, as well as to enable a description of the ecotoxicogenomic responses of this organism. After a 96 h exposure to the concentration of toxicant that inhibited growth rate by 10% (IC10) for the following common coastal contaminants: ammonia, copper, crude oil and simazine (a photosystem II inhibiting herbicide), diatom cells were harvested for RNA extraction and their transcriptomes characterized via 454 pyrosequencing. This resulted in 1.25 million reads, which were assembled into 4768 contigs, when contigs encoding rRNA were removed. More than 80% of the remaining contigs had an ortholog in the BLASTx protein databases. These contigs represented 1660 unique transcripts. The role of these transcripts in stress response, as well as photosynthesis and respiration is discussed. Overall, this study greatly enhances the genomic information available for this important taxonomic group.}, } @article {pmid24392153, year = {2014}, author = {Hughes, GM and Teeling, EC and Higgins, DG}, title = {Loss of olfactory receptor function in hominin evolution.}, journal = {PloS one}, volume = {9}, number = {1}, pages = {e84714}, pmid = {24392153}, issn = {1932-6203}, mesh = {Amino Acid Sequence ; Animals ; *Biological Evolution ; Databases, Nucleic Acid ; Evolution, Molecular ; Genome ; Genomics ; Hominidae/*genetics ; Humans ; Molecular Sequence Data ; Multigene Family ; Olfactory Receptor Neurons/*metabolism ; Phylogeny ; Receptors, Odorant/chemistry/classification/*genetics ; Sequence Alignment ; }, abstract = {The mammalian sense of smell is governed by the largest gene family, which encodes the olfactory receptors (ORs). The gain and loss of OR genes is typically correlated with adaptations to various ecological niches. Modern humans have 853 OR genes but 55% of these have lost their function. Here we show evidence of additional OR loss of function in the Neanderthal and Denisovan hominin genomes using comparative genomic methodologies. Ten Neanderthal and 8 Denisovan ORs show evidence of loss of function that differ from the reference modern human OR genome. Some of these losses are also present in a subset of modern humans, while some are unique to each lineage. Morphological changes in the cranium of Neanderthals suggest different sensory arrangements to that of modern humans. We identify differences in functional olfactory receptor genes among modern humans, Neanderthals and Denisovans, suggesting varied loss of function across all three taxa and we highlight the utility of using genomic information to elucidate the sensory niches of extinct species.}, } @article {pmid24392128, year = {2014}, author = {Wang, Y and Liu, L and Chen, L and Chen, T and Sun, F}, title = {Comparison of metatranscriptomic samples based on k-tuple frequencies.}, journal = {PloS one}, volume = {9}, number = {1}, pages = {e84348}, pmid = {24392128}, issn = {1932-6203}, support = {R21 HG006199/HG/NHGRI NIH HHS/United States ; R21HG006199/HG/NHGRI NIH HHS/United States ; }, mesh = {Algorithms ; Cluster Analysis ; Computational Biology/methods ; Databases, Nucleic Acid ; Internet ; *Metagenomics/methods ; Microbiota ; Seawater/microbiology ; Software ; *Transcriptome ; Water Microbiology ; }, abstract = {BACKGROUND: The comparison of samples, or beta diversity, is one of the essential problems in ecological studies. Next generation sequencing (NGS) technologies make it possible to obtain large amounts of metagenomic and metatranscriptomic short read sequences across many microbial communities. De novo assembly of the short reads can be especially challenging because the number of genomes and their sequences are generally unknown and the coverage of each genome can be very low, where the traditional alignment-based sequence comparison methods cannot be used. Alignment-free approaches based on k-tuple frequencies, on the other hand, have yielded promising results for the comparison of metagenomic samples. However, it is not known if these approaches can be used for the comparison of metatranscriptome datasets and which dissimilarity measures perform the best.

RESULTS: We applied several beta diversity measures based on k-tuple frequencies to real metatranscriptomic datasets from pyrosequencing 454 and Illumina sequencing platforms to evaluate their effectiveness for the clustering of metatranscriptomic samples, including three d2-type dissimilarity measures, one dissimilarity measure in CVTree, one relative entropy based measure S2 and three classical 1p-norm distances. Results showed that the measure d2(S) can achieve superior performance on clustering metatranscriptomic samples into different groups under different sequencing depths for both 454 and Illumina datasets, recovering environmental gradients affecting microbial samples, classifying coexisting metagenomic and metatranscriptomic datasets, and being robust to sequencing errors. We also investigated the effects of tuple size and order of the background Markov model. A software pipeline to implement all the steps of analysis is built and is available at http://code.google.com/p/d2-tools/.

CONCLUSIONS: The k-tuple based sequence signature measures can effectively reveal major groups and gradient variation among metatranscriptomic samples from NGS reads. The d2(S) dissimilarity measure performs well in all application scenarios and its performance is robust with respect to tuple size and order of the Markov model.}, } @article {pmid24391791, year = {2013}, author = {Peng, G and Bing, W and Guangpo, G and Guangcan, Z}, title = {Spatial distribution of soil organic carbon and total nitrogen based on GIS and geostatistics in a small watershed in a hilly area of northern China.}, journal = {PloS one}, volume = {8}, number = {12}, pages = {e83592}, pmid = {24391791}, issn = {1932-6203}, mesh = {Carbon/*analysis ; Carbon Cycle ; China ; Climate Change ; Environmental Monitoring ; Geographic Information Systems ; Groundwater ; Nitrogen/*analysis ; Regression Analysis ; Soil/*chemistry ; Spatial Analysis ; }, abstract = {The spatial variability of soil organic carbon (SOC) and total nitrogen (STN) levels is important in both global carbon-nitrogen cycle and climate change research. There has been little research on the spatial distribution of SOC and STN at the watershed scale based on geographic information systems (GIS) and geostatistics. Ninety-seven soil samples taken at depths of 0-20 cm were collected during October 2010 and 2011 from the Matiyu small watershed (4.2 km(2)) of a hilly area in Shandong Province, northern China. The impacts of different land use types, elevation, vegetation coverage and other factors on SOC and STN spatial distributions were examined using GIS and a geostatistical method, regression-kriging. The results show that the concentration variations of SOC and STN in the Matiyu small watershed were moderate variation based on the mean, median, minimum and maximum, and the coefficients of variation (CV). Residual values of SOC and STN had moderate spatial autocorrelations, and the Nugget/Sill were 0.2% and 0.1%, respectively. Distribution maps of regression-kriging revealed that both SOC and STN concentrations in the Matiyu watershed decreased from southeast to northwest. This result was similar to the watershed DEM trend and significantly correlated with land use type, elevation and aspect. SOC and STN predictions with the regression-kriging method were more accurate than those obtained using ordinary kriging. This research indicates that geostatistical characteristics of SOC and STN concentrations in the watershed were closely related to both land-use type and spatial topographic structure and that regression-kriging is suitable for investigating the spatial distributions of SOC and STN in the complex topography of the watershed.}, } @article {pmid24389116, year = {2014}, author = {Sauer, UG and Wächter, T and Hareng, L and Wareing, B and Langsch, A and Zschunke, M and Alvers, MR and Landsiedel, R}, title = {Automatic sorting of toxicological information into the IUCLID (International Uniform Chemical Information Database) endpoint-categories making use of the semantic search engine Go3R.}, journal = {Toxicology in vitro : an international journal published in association with BIBRA}, volume = {28}, number = {4}, pages = {571-587}, doi = {10.1016/j.tiv.2013.12.011}, pmid = {24389116}, issn = {1879-3177}, mesh = {Animal Testing Alternatives/*methods ; Animal Welfare ; Animals ; Biomedical Research/methods ; *Databases, Factual ; Documentation ; Hazardous Substances/*toxicity ; Research Design ; *Search Engine ; *Terminology as Topic ; }, abstract = {The knowledge-based search engine Go3R, www.Go3R.org, has been developed to assist scientists from industry and regulatory authorities in collecting comprehensive toxicological information with a special focus on identifying available alternatives to animal testing. The semantic search paradigm of Go3R makes use of expert knowledge on 3Rs methods and regulatory toxicology, laid down in the ontology, a network of concepts, terms, and synonyms, to recognize the contents of documents. Search results are automatically sorted into a dynamic table of contents presented alongside the list of documents retrieved. This table of contents allows the user to quickly filter the set of documents by topics of interest. Documents containing hazard information are automatically assigned to a user interface following the endpoint-specific IUCLID5 categorization scheme required, e.g. for REACH registration dossiers. For this purpose, complex endpoint-specific search queries were compiled and integrated into the search engine (based upon a gold standard of 310 references that had been assigned manually to the different endpoint categories). Go3R sorts 87% of the references concordantly into the respective IUCLID5 categories. Currently, Go3R searches in the 22 million documents available in the PubMed and TOXNET databases. However, it can be customized to search in other databases including in-house databanks.}, } @article {pmid24387194, year = {2014}, author = {Benedict, MN and Henriksen, JR and Metcalf, WW and Whitaker, RJ and Price, ND}, title = {ITEP: an integrated toolkit for exploration of microbial pan-genomes.}, journal = {BMC genomics}, volume = {15}, number = {}, pages = {8}, pmid = {24387194}, issn = {1471-2164}, mesh = {Algorithms ; Bacterial Proteins/genetics/metabolism ; Clostridium/classification/genetics ; Cluster Analysis ; Databases, Genetic ; Genome, Bacterial/*genetics ; Genomics/*methods ; Genotype ; Internet ; Metabolic Networks and Pathways/genetics ; Phenotype ; Phylogeny ; Ribosomal Proteins/genetics/metabolism ; *Software ; User-Computer Interface ; }, abstract = {BACKGROUND: Comparative genomics is a powerful approach for studying variation in physiological traits as well as the evolution and ecology of microorganisms. Recent technological advances have enabled sequencing large numbers of related genomes in a single project, requiring computational tools for their integrated analysis. In particular, accurate annotations and identification of gene presence and absence are critical for understanding and modeling the cellular physiology of newly sequenced genomes. Although many tools are available to compare the gene contents of related genomes, new tools are necessary to enable close examination and curation of protein families from large numbers of closely related organisms, to integrate curation with the analysis of gain and loss, and to generate metabolic networks linking the annotations to observed phenotypes.

RESULTS: We have developed ITEP, an Integrated Toolkit for Exploration of microbial Pan-genomes, to curate protein families, compute similarities to externally-defined domains, analyze gene gain and loss, and generate draft metabolic networks from one or more curated reference network reconstructions in groups of related microbial species among which the combination of core and variable genes constitute the their "pan-genomes". The ITEP toolkit consists of: (1) a series of modular command-line scripts for identification, comparison, curation, and analysis of protein families and their distribution across many genomes; (2) a set of Python libraries for programmatic access to the same data; and (3) pre-packaged scripts to perform common analysis workflows on a collection of genomes. ITEP's capabilities include de novo protein family prediction, ortholog detection, analysis of functional domains, identification of core and variable genes and gene regions, sequence alignments and tree generation, annotation curation, and the integration of cross-genome analysis and metabolic networks for study of metabolic network evolution.

CONCLUSIONS: ITEP is a powerful, flexible toolkit for generation and curation of protein families. ITEP's modular design allows for straightforward extension as analysis methods and tools evolve. By integrating comparative genomics with the development of draft metabolic networks, ITEP harnesses the power of comparative genomics to build confidence in links between genotype and phenotype and helps disambiguate gene annotations when they are evaluated in both evolutionary and metabolic network contexts.}, } @article {pmid24386481, year = {2013}, author = {van Gurp, TP and McIntyre, LM and Verhoeven, KJ}, title = {Consistent errors in first strand cDNA due to random hexamer mispriming.}, journal = {PloS one}, volume = {8}, number = {12}, pages = {e85583}, pmid = {24386481}, issn = {1932-6203}, mesh = {DNA Primers/*chemistry ; DNA, Complementary/*biosynthesis/chemistry ; Datasets as Topic ; RNA, Plant/*chemistry/genetics ; *Reverse Transcription ; Taraxacum/*chemistry/genetics ; }, abstract = {Priming of random hexamers in cDNA synthesis is known to show sequence bias, but in addition it has been suggested recently that mismatches in random hexamer priming could be a cause of mismatches between the original RNA fragment and observed sequence reads. To explore random hexamer mispriming as a potential source of these errors, we analyzed two independently generated RNA-seq datasets of synthetic ERCC spikes for which the reference is known. First strand cDNA synthesized by random hexamer priming on RNA showed consistent position and nucleotide-specific mismatch errors in the first seven nucleotides. The mismatch errors found in both datasets are consistent in distribution and thermodynamically stable mismatches are more common. This strongly indicates that RNA-DNA mispriming of specific random hexamers causes these errors. Due to their consistency and specificity, mispriming errors can have profound implications for downstream applications if not dealt with properly.}, } @article {pmid26259292, year = {2014}, author = {Cabanis, EA and de Kervasdoué, J}, title = {[Informatics and health, from digitization to information and communication technologies (TIC)].}, journal = {Bulletin de l'Academie nationale de medecine}, volume = {198}, number = {1}, pages = {131-144}, pmid = {26259292}, issn = {0001-4079}, mesh = {Humans ; *Medical Informatics ; }, abstract = {Integrating the progress that has been made on a daily basis since it was jointly commissioned in 2013 by the French National Academy of Medicine (Biotechnology Committee XX, Prof Emmanuel-Alain Cabanis) and the Technologies Academy (Pr Jean de Kervasdoué), this report, covering such a vast subject, can only represent one step in a long process. Summarized here in a volume compatible with the Bulletin, it makes reference to the full report (52 pages ; 22 pages of text, 4 pages of references, a 20-page glossary for physicians, plus 522 figures spanning 6 pages), which is available on the Academy's website. The six chapters first define "health" (WHO) and "informatics" and provide a brief history. The first chapter, on technologies, is divided into "bad" news (cybercrime, ecological risks) and advances relevant to health. The next four chapters describe the contribution of digitization to patient management, ranging from "fragile" individuals (from the gamete to old age and dependency) to healthy subjects trained to work in hostile situations (scuba diving to space exploration), and finally research. The last chapter proposes 7 areas for progress: expansion of the national imaging and communications platforms, stimulation of the medical robotics industry, extension of telemedicine to all medical and surgical specialties, support for drug dispensing and therapeutic education, and foundation of a European portal for m-health certification, research prioritization according to multiyear health plans, and reinforcement of mathematic education, starting in primary school (see: "La main à la pâte" ("Going hands-on").}, } @article {pmid26215298, year = {2014}, author = {Backonja, U and Hall, AK and Thielke, S}, title = {Older Adults' Current and Potential Uses of Information Technologies in a Changing World: A Theoretical Perspective.}, journal = {International journal of aging & human development}, volume = {80}, number = {1}, pages = {41-63}, pmid = {26215298}, issn = {0091-4150}, support = {K23 MH093591/MH/NIMH NIH HHS/United States ; T15 LM007442/LM/NLM NIH HHS/United States ; T15LM007442/LM/NLM NIH HHS/United States ; }, mesh = {Aged ; Aging/*psychology ; *Health Promotion ; Humans ; *Medical Informatics ; *Models, Theoretical ; Motivation/*physiology ; }, abstract = {Technologies have become a major force in people's lives. They change how people interact with the environment, even as the environment changes. We propose that technology use in the setting of changing environments is motivated by essential needs and tensions experienced by the individual. We apply three developmental and behavioral theories (Erikson's stages of psychosocial development, Maslow's hierarchy of needs, and Bronfenbrenner's ecological model) to explain technology-related behaviors among older adults. We consider how technology use has addressed and can address major ecological changes, in three areas: health promotion, natural disasters, and disparities. We propose that considering these theories can help researchers and developers ensure that technologies will help promote a healthier world for older adults.}, } @article {pmid25984346, year = {2014}, author = {Mylne, A and Brady, OJ and Huang, Z and Pigott, DM and Golding, N and Kraemer, MU and Hay, SI}, title = {A comprehensive database of the geographic spread of past human Ebola outbreaks.}, journal = {Scientific data}, volume = {1}, number = {}, pages = {140042}, pmid = {25984346}, issn = {2052-4463}, support = {/WT_/Wellcome Trust/United Kingdom ; 095066/WT_/Wellcome Trust/United Kingdom ; }, mesh = {*Databases, Factual ; *Disease Outbreaks ; *Ebolavirus ; Hemorrhagic Fever, Ebola/*epidemiology/transmission ; Humans ; }, abstract = {Ebola is a zoonotic filovirus that has the potential to cause outbreaks of variable magnitude in human populations. This database collates our existing knowledge of all known human outbreaks of Ebola for the first time by extracting details of their suspected zoonotic origin and subsequent human-to-human spread from a range of published and non-published sources. In total, 22 unique Ebola outbreaks were identified, composed of 117 unique geographic transmission clusters. Details of the index case and geographic spread of secondary and imported cases were recorded as well as summaries of patient numbers and case fatality rates. A brief text summary describing suspected routes and means of spread for each outbreak was also included. While we cannot yet include the ongoing Guinea and DRC outbreaks until they are over, these data and compiled maps can be used to gain an improved understanding of the initial spread of past Ebola outbreaks and help evaluate surveillance and control guidelines for limiting the spread of future epidemics.}, } @article {pmid25984344, year = {2014}, author = {Pigott, DM and Golding, N and Messina, JP and Battle, KE and Duda, KA and Balard, Y and Bastien, P and Pratlong, F and Brownstein, JS and Freifeld, CC and Mekaru, SR and Madoff, LC and George, DB and Myers, MF and Hay, SI}, title = {Global database of leishmaniasis occurrence locations, 1960-2012.}, journal = {Scientific data}, volume = {1}, number = {}, pages = {140036}, pmid = {25984344}, issn = {2052-4463}, support = {095066//Wellcome Trust/United Kingdom ; R01 LM010812/LM/NLM NIH HHS/United States ; R01LM010812/LM/NLM NIH HHS/United States ; }, mesh = {Data Collection/methods ; *Databases, Factual ; Humans ; Leishmaniasis/*epidemiology ; Leishmaniasis, Cutaneous/epidemiology ; Leishmaniasis, Visceral/epidemiology ; Neglected Diseases/*epidemiology ; Public Health ; }, abstract = {The leishmaniases are neglected tropical diseases of significant public health importance. However, information on their global occurrence is disparate and sparse. This database represents an attempt to collate reported leishmaniasis occurrences from 1960 to 2012. Methodology for the collection of data from the literature, abstraction of case locations and data processing procedures are described here. In addition, strain archives and online data resources were accessed. A total of 12,563 spatially and temporally unique occurrences of both cutaneous and visceral leishmaniasis comprise the database, ranging in geographic scale from villages to states. These data can be used for a variety of mapping and spatial analyses covering multiple resolutions.}, } @article {pmid25977762, year = {2014}, author = {Messina, JP and Brady, OJ and Pigott, DM and Brownstein, JS and Hoen, AG and Hay, SI}, title = {A global compendium of human dengue virus occurrence.}, journal = {Scientific data}, volume = {1}, number = {}, pages = {140004}, pmid = {25977762}, issn = {2052-4463}, support = {/WT_/Wellcome Trust/United Kingdom ; 095066/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Animals ; *Databases, Factual ; Dengue/*epidemiology ; *Dengue Virus ; Disease Outbreaks ; Humans ; Risk ; }, abstract = {A global geographic database of human dengue virus occurrence was produced to generate a global risk map and associated burden estimates(1). Herein we present the database, which comprises occurrence data linked to point or polygon locations, derived from peer-reviewed literature and case reports as well as informal online sources. Entries date from 1960 to 2012. We describe all data collection processes in full, as well as geo-positioning, database management and quality-control procedures. This is the most comprehensive database of confirmed human dengue infection to-date, consisting of 8,309 geo-positioned occurrences in total.}, } @article {pmid25977753, year = {2014}, author = {Ahmed, Z and Zeeshan, S and Fleischmann, P and Rössler, W and Dandekar, T}, title = {Ant-App-DB: a smart solution for monitoring arthropods activities, experimental data management and solar calculations without GPS in behavioral field studies.}, journal = {F1000Research}, volume = {3}, number = {}, pages = {311}, pmid = {25977753}, issn = {2046-1402}, abstract = {Field studies on arthropod ecology and behaviour require simple and robust monitoring tools, preferably with direct access to an integrated database. We have developed and here present a database tool allowing smart-phone based monitoring of arthropods. This smart phone application provides an easy solution to collect, manage and process the data in the field which has been a very difficult task for field biologists using traditional methods. To monitor our example species, the desert ant Cataglyphis fortis, we considered behavior, nest search runs, feeding habits and path segmentations including detailed information on solar position and azimuth calculation, ant orientation and time of day. For this we established a user friendly database system integrating the Ant-App-DB with a smart phone and tablet application, combining experimental data manipulation with data management and providing solar position and timing estimations without any GPS or GIS system. Moreover, the new desktop application Dataplus allows efficient data extraction and conversion from smart phone application to personal computers, for further ecological data analysis and sharing. All features, software code and database as well as Dataplus application are made available completely free of charge and sufficiently generic to be easily adapted to other field monitoring studies on arthropods or other migratory organisms. The software applications Ant-App-DB and Dataplus described here are developed using the Android SDK, Java, XML, C# and SQLite Database.}, } @article {pmid25848615, year = {2014}, author = {Revere, D and Dixon, BE and Hills, R and Williams, JL and Grannis, SJ}, title = {Leveraging health information exchange to improve population health reporting processes: lessons in using a collaborative-participatory design process.}, journal = {EGEMS (Washington, DC)}, volume = {2}, number = {3}, pages = {1082}, pmid = {25848615}, issn = {2327-9214}, support = {R01 HS020909/HS/AHRQ HHS/United States ; }, abstract = {INTRODUCTION: Surveillance, or the systematic monitoring of disease within a population, is a cornerstone function of public health. Despite significant investment in information technologies (IT) to improve the public's health, health care providers continue to rely on manual, spontaneous reporting processes that can result in incomplete and delayed surveillance activities.

BACKGROUND: Participatory design principles advocate including real users and stakeholders when designing an information system to ensure high ecological validity of the product, incorporate relevance and context into the design, reduce misconceptions designers can make due to insufficient domain expertise, and ultimately reduce barriers to adoption of the system. This paper focuses on the collaborative and informal participatory design process used to develop enhanced, IT-enabled reporting processes that leverage available electronic health records in a health information exchange to prepopulate notifiable-conditions report forms used by public health authorities.

METHODS: Over nine months, public health stakeholders, technical staff, and informatics researchers were engaged in a multiphase participatory design process that included public health stakeholder focus groups, investigator-engineering team meetings, public health survey and census regarding high-priority data elements, and codesign of exploratory prototypes and final form mock-ups.

FINDINGS: A number of state-mandated report fields that are not highly used or desirable for disease investigation were eliminated, which allowed engineers to repurpose form space for desired and high-priority data elements and improve the usability of the forms. Our participatory design process ensured that IT development was driven by end user expertise and needs, resulting in significant improvements to the layout and functionality of the reporting forms.

DISCUSSION: In addition to informing report form development, engaging with public health end users and stakeholders through the participatory design process provided new insights into public health workflow and allowed the team to quickly triage user requests while managing user expectations within the realm of engineering possibilities.

CONCLUSION: Engaging public health, engineering staff, and investigators in a shared codesigning process ensured that the new forms will not only meet real-life needs but will also support development of a product that will be adopted and, ultimately, improve communicable and infectious disease reporting by clinicians to public health.}, } @article {pmid24379395, year = {2014}, author = {Adler, PB and Salguero-Gómez, R and Compagnoni, A and Hsu, JS and Ray-Mukherjee, J and Mbeau-Ache, C and Franco, M}, title = {Functional traits explain variation in plant life history strategies.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {111}, number = {2}, pages = {740-745}, pmid = {24379395}, issn = {1091-6490}, mesh = {Adaptation, Biological/*physiology ; Databases, Factual ; Fertility/physiology ; Genetic Fitness/*physiology ; Phylogeny ; Plant Leaves/physiology ; Plant Physiological Phenomena/*physiology ; Population Dynamics ; Regression Analysis ; Seeds/cytology ; Species Specificity ; Wood/physiology ; }, abstract = {Ecologists seek general explanations for the dramatic variation in species abundances in space and time. An increasingly popular solution is to predict species distributions, dynamics, and responses to environmental change based on easily measured anatomical and morphological traits. Trait-based approaches assume that simple functional traits influence fitness and life history evolution, but rigorous tests of this assumption are lacking, because they require quantitative information about the full lifecycles of many species representing different life histories. Here, we link a global traits database with empirical matrix population models for 222 species and report strong relationships between functional traits and plant life histories. Species with large seeds, long-lived leaves, or dense wood have slow life histories, with mean fitness (i.e., population growth rates) more strongly influenced by survival than by growth or fecundity, compared with fast life history species with small seeds, short-lived leaves, or soft wood. In contrast to measures of demographic contributions to fitness based on whole lifecycles, analyses focused on raw demographic rates may underestimate the strength of association between traits and mean fitness. Our results help establish the physiological basis for plant life history evolution and show the potential for trait-based approaches in population dynamics.}, } @article {pmid24378926, year = {2014}, author = {van Dijk, A and Mount, R and Gibbons, P and Vardon, M and Canadell, P}, title = {Environmental reporting and accounting in Australia: progress, prospects and research priorities.}, journal = {The Science of the total environment}, volume = {473-474}, number = {}, pages = {338-349}, doi = {10.1016/j.scitotenv.2013.12.053}, pmid = {24378926}, issn = {1879-1026}, mesh = {Australia ; *Conservation of Natural Resources ; Data Collection ; Environmental Monitoring/*methods/standards ; }, abstract = {Despite strong demand for information to support the sustainable use of Australia's natural resources and conserve environmental values and despite considerable effort and investment, nation-wide environmental data collection and analysis remains a substantially unmet challenge. We review progress in producing national environmental reports and accounts, identify challenges and opportunities, and analyse the potential role of research in addressing these. Australia's low and concentrated population density and the short history since European settlement contribute to the lack of environmental data. There are additional factors: highly diverse data requirements and standards, disagreement on information priorities, poorly measurable management objectives, lack of coordination, over-reliance on researchers and businesses for data collection, lack of business engagement, and short-term, project-based activities. New opportunities have arisen to overcome some of these challenges: enhanced monitoring networks, standardisation, data management and modelling, greater commitment to share and integrate data, community monitoring, increasing acceptance of environmental and sustainability indicators, and progress in environmental accounting practices. Successes in generating climate, water and greenhouse gas information appear to be attributable to an unambiguous data requirement, considerable investment, and legislative instruments that enhance data sharing and create a clearly defined role for operational agencies. Based on the analysis presented, we suggest six priorities for research: (1) common definitions and standards for information that address management objectives, (2) ecological measures that are scalable from local to national level, (3) promotion of long-term data collection and reporting by researchers, (4) efficient satellite and sensor network technologies and data analysis methods, (5) environmental modelling approaches that can reconcile multiple data sources, and (6) experimental accounting to pursue consistent, credible and relevant information structures and to identify new data requirements. Opportunities exist to make progress in each of these areas and help secure a more sustainable future.}, } @article {pmid24375420, year = {2014}, author = {Gregory, T and Mullett, A and Norconk, MA}, title = {Strategies for navigating large areas: a GIS spatial ecology analysis of the bearded saki monkey, Chiropotes sagulatus, in Suriname.}, journal = {American journal of primatology}, volume = {76}, number = {6}, pages = {586-595}, doi = {10.1002/ajp.22251}, pmid = {24375420}, issn = {1098-2345}, mesh = {Animals ; *Behavior, Animal ; *Ecosystem ; Female ; Geographic Information Systems ; Male ; *Pitheciidae ; Suriname ; }, abstract = {Animals with long day paths and large home ranges expend a considerable amount of energy on travel. Studies have shown that in the interest of reducing energy expenditure, animals selectively navigate the landscape using a variety of strategies. However, these studies have generally focused on terrestrial animals. Here we present data on an exceedingly mobile arboreal animal, bearded saki monkeys, in a topographically variable landscape in Suriname. Using ArcMap and Google Earth, we explore two potential navigation strategies: the nonrandom use of travel areas and the use of ridges in slope navigation. Over a year of data collection, bearded sakis were found to use relatively long travel paths daily, use some areas more intensely than others for travel, and when travel paths were converted to strings of points, 40.3% and 63.9% of the points were located on (50 m from the main ridgeline) or near (100 m from the main ridgeline) ridge tops, respectively. Thus in a habitat of high relief we found support for intensive use of ridge tops or slopes close to ridge tops by bearded sakis. Selective habitat use may be related to surveying tree crowns for fruit by large, fast moving groups of bearded sakis or monitoring the presence of potential predators.}, } @article {pmid24368631, year = {2014}, author = {Lyons, BP}, title = {Nutrition education intervention with community-dwelling older adults: research challenges and opportunities.}, journal = {Journal of community health}, volume = {39}, number = {4}, pages = {810-818}, pmid = {24368631}, issn = {1573-3610}, mesh = {Aged ; Aged, 80 and over ; Databases, Bibliographic ; Female ; Health Education/*methods ; Humans ; Male ; Middle Aged ; Nutritional Sciences/*education ; *Outcome and Process Assessment, Health Care ; Research Design ; }, abstract = {This study critically reviewed empirical literature examining nutrition education intervention studies with community-dwelling older adults over the period 2003-2012 to: (1) determine the number, (2) evaluate the research designs, and (3) report the study outcomes. A search of online databases yielded 74 studies six of which met our criteria. The studies reported favorable intervention outcomes. Because of the number, variability in the types, designs, measures, scope, educational and behavioral strategies, results can only inform future studies and encourage scholars to use strong evaluation design. We recommend the utilization of an ecological conceptual model when conducting nutrition interventions studies and discussed implications in terms of research and practice.}, } @article {pmid24367656, year = {2013}, author = {Mattern, T and Ellenberg, U and Houston, DM and Lamare, M and Davis, LS and van Heezik, Y and Seddon, PJ}, title = {Straight line foraging in yellow-eyed penguins: new insights into cascading fisheries effects and orientation capabilities of marine predators.}, journal = {PloS one}, volume = {8}, number = {12}, pages = {e84381}, pmid = {24367656}, issn = {1932-6203}, mesh = {Animals ; *Aquatic Organisms ; *Fisheries ; Geographic Information Systems ; Oceans and Seas ; *Predatory Behavior ; *Spatial Behavior ; *Spheniscidae ; }, abstract = {Free-ranging marine predators rarely search for prey along straight lines because dynamic ocean processes usually require complex search strategies. If linear movement patterns occur they are usually associated with travelling events or migratory behaviour. However, recent fine scale tracking of flying seabirds has revealed straight-line movements while birds followed fishing vessels. Unlike flying seabirds, penguins are not known to target and follow fishing vessels. Yet yellow-eyed penguins from New Zealand often exhibit directed movement patterns while searching for prey at the seafloor, a behaviour that seems to contradict common movement ecology theories. While deploying GPS dive loggers on yellow-eyed penguins from the Otago Peninsula we found that the birds frequently followed straight lines for several kilometres with little horizontal deviation. In several cases individuals swam up and down the same line, while some of the lines were followed by more than one individual. Using a remote operated vehicle (ROV) we found a highly visible furrow on the seafloor most likely caused by an otter board of a demersal fish trawl, which ran in a straight line exactly matching the trajectory of a recent line identified from penguin tracks. We noted high abundances of benthic scavengers associated with fisheries-related bottom disturbance. While our data demonstrate the acute way-finding capabilities of benthic foraging yellow-eyed penguins, they also highlight how hidden cascading effects of coastal fisheries may alter behaviour and potentially even population dynamics of marine predators, an often overlooked fact in the examination of fisheries' impacts.}, } @article {pmid24367098, year = {2014}, author = {Raichlen, DA and Wood, BM and Gordon, AD and Mabulla, AZ and Marlowe, FW and Pontzer, H}, title = {Evidence of Levy walk foraging patterns in human hunter-gatherers.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {111}, number = {2}, pages = {728-733}, pmid = {24367098}, issn = {1091-6490}, mesh = {Appetitive Behavior/*physiology ; Ethnicity/*history ; Geographic Information Systems ; History, Ancient ; Humans ; Likelihood Functions ; Locomotion/*physiology ; Models, Statistical ; Statistics, Nonparametric ; Tanzania ; }, abstract = {When searching for food, many organisms adopt a superdiffusive, scale-free movement pattern called a Lévy walk, which is considered optimal when foraging for heterogeneously located resources with little prior knowledge of distribution patterns [Viswanathan GM, da Luz MGE, Raposo EP, Stanley HE (2011) The Physics of Foraging: An Introduction to Random Searches and Biological Encounters]. Although memory of food locations and higher cognition may limit the benefits of random walk strategies, no studies to date have fully explored search patterns in human foraging. Here, we show that human hunter-gatherers, the Hadza of northern Tanzania, perform Lévy walks in nearly one-half of all foraging bouts. Lévy walks occur when searching for a wide variety of foods from animal prey to underground tubers, suggesting that, even in the most cognitively complex forager on Earth, such patterns are essential to understanding elementary foraging mechanisms. This movement pattern may be fundamental to how humans experience and interact with the world across a wide range of ecological contexts, and it may be adaptive to food distribution patterns on the landscape, which previous studies suggested for organisms with more limited cognition. Additionally, Lévy walks may have become common early in our genus when hunting and gathering arose as a major foraging strategy, playing an important role in the evolution of human mobility.}, } @article {pmid24367073, year = {2014}, author = {Marino, S and Baxter, NT and Huffnagle, GB and Petrosino, JF and Schloss, PD}, title = {Mathematical modeling of primary succession of murine intestinal microbiota.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {111}, number = {1}, pages = {439-444}, pmid = {24367073}, issn = {1091-6490}, support = {U19AI090871/AI/NIAID NIH HHS/United States ; U19 AI090871/AI/NIAID NIH HHS/United States ; R01 HG005975/HG/NHGRI NIH HHS/United States ; R01GM095356/GM/NIGMS NIH HHS/United States ; P30 DK034933/DK/NIDDK NIH HHS/United States ; R01HG005975/HG/NHGRI NIH HHS/United States ; P30DK034933/DK/NIDDK NIH HHS/United States ; R01 GM099514/GM/NIGMS NIH HHS/United States ; }, mesh = {Algorithms ; Animals ; Bacteroidetes ; Computational Biology/methods ; DNA, Bacterial/genetics ; Female ; Genes, rRNA ; Intestines/*microbiology ; Lactobacillus ; Mice ; Mice, Inbred C57BL ; *Microbiota ; *Models, Theoretical ; RNA, Ribosomal, 16S/metabolism ; Sequence Analysis, DNA ; Time Factors ; }, abstract = {Understanding the nature of interpopulation interactions in host-associated microbial communities is critical to understanding gut colonization, responses to perturbations, and transitions between health and disease. Characterizing these interactions is complicated by the complexity of these communities and the observation that even if populations can be cultured, their in vitro and in vivo phenotypes differ significantly. Dynamic models are the cornerstone of computational systems biology and a key objective of computational systems biologists is the reconstruction of biological networks (i.e., network inference) from high-throughput data. When such computational models reflect biology, they provide an opportunity to generate testable hypotheses as well as to perform experiments that are impractical or not feasible in vivo or in vitro. We modeled time-series data for murine microbial communities using statistical approaches and systems of ordinary differential equations. To obtain the dense time-series data, we sequenced the 16S ribosomal RNA (rRNA) gene from DNA isolated from the fecal material of germfree mice colonized with cecal contents of conventionally raised animals. The modeling results suggested a lack of mutualistic interactions within the community. Among the members of the Bacteroidetes, there was evidence for closely related pairs of populations to exhibit parasitic interactions. Among the Firmicutes, the interactions were all competitive. These results suggest future animal and in silico experiments. Our modeling approach can be applied to other systems to provide a greater understanding of the dynamics of communities associated with health and disease.}, } @article {pmid24365133, year = {2013}, author = {Mayne, DJ and Morgan, GG and Willmore, A and Rose, N and Jalaludin, B and Bambrick, H and Bauman, A}, title = {An objective index of walkability for research and planning in the Sydney metropolitan region of New South Wales, Australia: an ecological study.}, journal = {International journal of health geographics}, volume = {12}, number = {}, pages = {61}, pmid = {24365133}, issn = {1476-072X}, mesh = {*Ecological and Environmental Phenomena ; *Environment Design ; *Geographic Information Systems ; Humans ; New South Wales/epidemiology ; Principal Component Analysis/methods ; *Urban Population ; *Walking/physiology ; }, abstract = {BACKGROUND: Walkability describes the capacity of the built environment to support walking for various purposes. This paper describes the construction and validation of two objective walkability indexes for Sydney, Australia.

METHODS: Walkability indexes using residential density, intersection density, land use mix, with and without retail floor area ratio were calculated for 5,858 Sydney Census Collection Districts in a geographical information system. Associations between variables were evaluated using Spearman's rho (ρ). Internal consistency and factor structure of indexes were estimated with Cronbach's alpha and principal components analysis; convergent and predictive validity were measured using weighted kappa (κw) and by comparison with reported walking to work at the 2006 Australian Census using logistic regression. Spatial variation in walkability was assessed using choropleth maps and Moran's I.

RESULTS: A three-attribute abridged Sydney Walkability Index comprising residential density, intersection density and land use mix was constructed for all Sydney as retail floor area was only available for 5.3% of Census Collection Districts. A four-attribute full index including retail floor area ratio was calculated for 263 Census Collection Districts in the Sydney Central Business District. Abridged and full walkability index scores for these 263 areas were strongly correlated (ρ=0.93) and there was good agreement between walkability quartiles (κw=0.73). Internal consistency ranged from 0.60 to 0.71, and all index variables loaded highly on a single factor. The percentage of employed persons who walked to work increased with increasing walkability: 3.0% in low income-low walkability areas versus 7.9% in low income-high walkability areas; and 2.1% in high income-low walkability areas versus 11% in high income-high walkability areas. The adjusted odds of walking to work were 1.05 (0.96-1.15), 1.58 (1.45-1.71) and 3.02 (2.76-3.30) times higher in medium, high and very high compared to low walkability areas. Associations were similar for full and abridged indexes.

CONCLUSIONS: The abridged Sydney Walkability Index has predictive validity for utilitarian walking, will inform urban planning in Sydney, and will be used as an objective measure of neighbourhood walkability in a large population cohort. Abridged walkability indexes may be useful in settings where retail floor area data are unavailable.}, } @article {pmid24361994, year = {2014}, author = {Lee, YC and Langley, CH and Begun, DJ}, title = {Differential strengths of positive selection revealed by hitchhiking effects at small physical scales in Drosophila melanogaster.}, journal = {Molecular biology and evolution}, volume = {31}, number = {4}, pages = {804-816}, pmid = {24361994}, issn = {1537-1719}, support = {R01 GM084056/GM/NIGMS NIH HHS/United States ; R01 HG002942/HG/NHGRI NIH HHS/United States ; HG02942/HG/NHGRI NIH HHS/United States ; }, mesh = {Amino Acid Substitution ; Animals ; Drosophila Proteins/genetics ; Drosophila melanogaster/*genetics ; *Evolution, Molecular ; Gene Ontology ; Models, Genetic ; Polymorphism, Genetic ; Regression Analysis ; *Selection, Genetic ; }, abstract = {The long time scale of adaptive evolution makes it difficult to directly observe the spread of most beneficial mutations through natural populations. Therefore, inferring attributes of beneficial mutations by studying the genomic signals left by directional selection is an important component of population genetics research. One kind of signal is a trough in nearby neutral genetic variation due to selective fixation of initially rare alleles, a phenomenon known as "genetic hitchhiking." Accumulated evidence suggests that a considerable fraction of substitutions in the Drosophila genome results from positive selection, most of which are expected to have small selection coefficients and influence the population genetics of sites in the immediate vicinity. Using Drosophila melanogaster population genomic data, we found that the heterogeneity in synonymous polymorphism surrounding different categories of coding fixations is readily observable even within 25 bp of focal substitutions, which we interpret as the result of small-scale hitchhiking effects. The strength of natural selection on different sites appears to be quite heterogeneous. Particularly, neighboring fixations that changed amino acid polarities in a way that maintained the overall polarities of a protein were under stronger selection than other categories of fixations. Interestingly, we found that substitutions in slow-evolving genes are associated with stronger hitchhiking effects. This is consistent with the idea that adaptive evolution may involve few substitutions with large effects or many substitutions with small effects. Because our approach only weakly depends on the numbers of recent nonsynonymous substitutions, it can provide a complimentary view to the adaptive evolution inferred by other divergence-based evolutionary genetic methods.}, } @article {pmid24361065, year = {2014}, author = {Vines, TH and Albert, AYK and Andrew, RL and Débarre, F and Bock, DG and Franklin, MT and Gilbert, KJ and Moore, JS and Renaut, S and Rennison, DJ}, title = {The availability of research data declines rapidly with article age.}, journal = {Current biology : CB}, volume = {24}, number = {1}, pages = {94-97}, doi = {10.1016/j.cub.2013.11.014}, pmid = {24361065}, issn = {1879-0445}, mesh = {Biomedical Research ; *Databases, Factual ; Internet ; Publishing/*statistics & numerical data ; Time Factors ; }, abstract = {Policies ensuring that research data are available on public archives are increasingly being implemented at the government [1], funding agency [2-4], and journal [5, 6] level. These policies are predicated on the idea that authors are poor stewards of their data, particularly over the long term [7], and indeed many studies have found that authors are often unable or unwilling to share their data [8-11]. However, there are no systematic estimates of how the availability of research data changes with time since publication. We therefore requested data sets from a relatively homogenous set of 516 articles published between 2 and 22 years ago, and found that availability of the data was strongly affected by article age. For papers where the authors gave the status of their data, the odds of a data set being extant fell by 17% per year. In addition, the odds that we could find a working e-mail address for the first, last, or corresponding author fell by 7% per year. Our results reinforce the notion that, in the long term, research data cannot be reliably preserved by individual researchers, and further demonstrate the urgent need for policies mandating data sharing via public archives.}, } @article {pmid24358313, year = {2013}, author = {Gao, T and Yang, X and Jin, Y and Ma, H and Li, J and Yu, H and Yu, Q and Zheng, X and Xu, B}, title = {Spatio-temporal variation in vegetation biomass and its relationships with climate factors in the Xilingol grasslands, Northern China.}, journal = {PloS one}, volume = {8}, number = {12}, pages = {e83824}, pmid = {24358313}, issn = {1932-6203}, mesh = {*Biomass ; China ; Climate ; *Ecosystem ; Geography ; *Spatio-Temporal Analysis ; }, abstract = {Knowledge about grassland biomass and its dynamics is critical for studying regional carbon cycles and for the sustainable use of grassland resources. In this study, we investigated the spatio-temporal variation of biomass in the Xilingol grasslands of northern China. Field-based biomass samples and MODIS time series data sets were used to establish two empirical models based on the relationship of the normalized difference vegetation index (NDVI) with above-ground biomass (AGB) as well as that of AGB with below-ground biomass (BGB). We further explored the climatic controls of these variations. Our results showed that the biomass averaged 99.01 Tg (1 Tg=10(12) g) over a total area of 19.6 × 10(4) km(2) and fluctuated with no significant trend from 2001 to 2012. The mean biomass density was 505.4 g/m(2), with 62.6 g/m(2) in AGB and 442.8 g/m(2) in BGB, which generally decreased from northeast to southwest and exhibited a large spatial heterogeneity. The year-to-year AGB pattern was generally consistent with the inter-annual variation in the growing season precipitation (GSP), showing a robust positive correlation (R(2)=0.82, P<0.001), but an opposite coupled pattern was observed with the growing season temperature (GST) (R(2)=0.61, P=0.003). Climatic factors also affected the spatial distribution of AGB, which increased progressively with the GSP gradient (R(2)=0.76, P<0.0001) but decreased with an increasing GST (R(2)=0.70, P<0.0001). An improved moisture index that combined the effects of GST and GSP explained more variation in AGB than did precipitation alone (R(2)=0.81, P<0.0001). The relationship between AGB and GSP could be fit by a power function. This increasing slope of the GSP-AGB relationships along the GSP gradient may be partly explained by the GST-GSP spatial pattern in Xilingol. Our findings suggest that the relationships between climatic factors and AGB may be scale-dependent and that multi-scale studies and sufficient long-term field data are needed to examine the relationships between AGB and climatic factors.}, } @article {pmid24352706, year = {2015}, author = {Moreta, DE and Mathur, PN and van Zonneveld, M and Amaya, K and Arango, J and Selvaraj, MG and Dedicova, B}, title = {Current issues in cereal crop biodiversity.}, journal = {Advances in biochemical engineering/biotechnology}, volume = {147}, number = {}, pages = {1-35}, doi = {10.1007/10_2013_263}, pmid = {24352706}, issn = {0724-6145}, mesh = {Agriculture/*methods ; *Biodiversity ; Breeding/*methods ; Conservation of Natural Resources/*methods ; Crops, Agricultural/classification/genetics/*growth & development ; Edible Grain/classification/genetics/*growth & development ; Genetic Enhancement/*methods ; Geographic Information Systems ; }, abstract = {The exploration, conservation, and use of agricultural biodiversity are essential components of efficient transdisciplinary research for a sustainable agriculture and food sector. Most recent advances on plant biotechnology and crop genomics must be complemented with a holistic management of plant genetic resources. Plant breeding programs aimed at improving agricultural productivity and food security can benefit from the systematic exploitation and conservation of genetic diversity to meet the demands of a growing population facing climate change. The genetic diversity of staple small grains, including rice, maize, wheat, millets, and more recently quinoa, have been surveyed to encourage utilization and prioritization of areas for germplasm conservation. Geographic information system technologies and spatial analysis are now being used as powerful tools to elucidate genetic and ecological patterns in the distribution of cultivated and wild species to establish coherent programs for the management of plant genetic resources for food and agriculture.}, } @article {pmid24350717, year = {2014}, author = {Stoklosa, J and Gibb, H and Warton, DI}, title = {Fast forward selection for generalized estimating equations with a large number of predictor variables.}, journal = {Biometrics}, volume = {70}, number = {1}, pages = {110-120}, doi = {10.1111/biom.12118}, pmid = {24350717}, issn = {1541-0420}, mesh = {*Algorithms ; Animals ; Arthropods/growth & development ; Australia ; Computer Simulation ; *Data Interpretation, Statistical ; Ecosystem ; *Likelihood Functions ; Longitudinal Studies/*methods ; *Models, Statistical ; }, abstract = {We propose a new variable selection criterion designed for use with forward selection algorithms; the score information criterion (SIC). The proposed criterion is based on score statistics which incorporate correlated response data. The main advantage of the SIC is that it is much faster to compute than existing model selection criteria when the number of predictor variables added to a model is large, this is because SIC can be computed for all candidate models without actually fitting them. A second advantage is that it incorporates the correlation between variables into its quasi-likelihood, leading to more desirable properties than competing selection criteria. Consistency and prediction properties are shown for the SIC. We conduct simulation studies to evaluate the selection and prediction performances, and compare these, as well as computational times, with some well-known variable selection criteria. We apply the SIC on a real data set collected on arthropods by considering variable selection on a large number of interactions terms consisting of species traits and environmental covariates.}, } @article {pmid24346860, year = {2014}, author = {Meyer, AL and Pie, MR and Passos, FC}, title = {Assessing the exposure of lion tamarins (Leontopithecus spp.) to future climate change.}, journal = {American journal of primatology}, volume = {76}, number = {6}, pages = {551-562}, doi = {10.1002/ajp.22247}, pmid = {24346860}, issn = {1098-2345}, mesh = {Animals ; Brazil ; *Climate Change ; *Ecosystem ; Geographic Information Systems ; *Leontopithecus ; *Models, Theoretical ; }, abstract = {Understanding how biodiversity will respond to climate change is a major challenge in conservation science. Climatic changes are likely to impose serious threats to many organisms, especially those with narrow distribution ranges, small populations and low dispersal capacity. Lion tamarins (Leontopithecus spp.) are endangered primates endemic to Brazilian Atlantic Forest (BAF), and all four living species are typical examples of these aggravating conditions. Here, we integrate ecological niche modeling and GIS-based information about BAF remnants and protected areas to estimate the exposure (i.e., the extent of climate change predicted to be experienced by a species) of current suitable habitats to climate change for 2050 and 2080, and to evaluate the efficacy of existing reserves to protect climatically suitable areas. Niche models were built using Maxent and then projected onto seven global circulation models derived from the A1B climatic scenario. According to our projections, the occurrence area of L. caissara will be little exposed to climate change. Western populations of L. chrysomelas could be potentially exposed, while climatically suitable habitats will be maintained only in part of the eastern region. Protected areas that presently harbor large populations of L. chrysopygus and L. rosalia will not retain climatic suitability by 2080. Monitoring trends of exposed populations and protecting areas predicted to hold suitable conditions should be prioritized. Given the potential exposure of key lion tamarin populations, we stress the importance of conducting additional studies to assess other aspects of their vulnerability (i.e., sensitivity to climate and adaptive capacity) and, therefore, to provide a more solid framework for future management decisions in the context of climate change.}, } @article {pmid24342708, year = {2014}, author = {Satoh, M and Tokaji, Y and Nagano, AJ and Hara-Nishimura, I and Hayashi, M and Nishimura, M and Ohta, H and Masuda, S}, title = {Arabidopsis mutants affecting oxylipin signaling in photo-oxidative stress responses.}, journal = {Plant physiology and biochemistry : PPB}, volume = {81}, number = {}, pages = {90-95}, doi = {10.1016/j.plaphy.2013.11.023}, pmid = {24342708}, issn = {1873-2690}, mesh = {Adaptation, Physiological ; Arabidopsis/genetics/*physiology/radiation effects ; Arabidopsis Proteins/*genetics ; Cyclopentanes/metabolism ; DNA-Binding Proteins/genetics ; Fatty Acids, Unsaturated/metabolism ; *Gene Expression Regulation, Plant ; Genetic Complementation Test ; Heat Shock Transcription Factors ; Heat-Shock Proteins/genetics ; Heat-Shock Response ; Light ; Oxidation-Reduction ; Oxidative Stress ; Oxylipins/*metabolism ; Plant Growth Regulators/metabolism ; Plant Proteins/genetics ; Plants, Genetically Modified ; Promoter Regions, Genetic/genetics ; Reactive Oxygen Species/metabolism ; Sequence Deletion ; *Signal Transduction ; Thylakoids/metabolism ; Transcription Factors/genetics ; }, abstract = {Plant oxylipins derive from oxygenation of polyunsaturated fatty acids in thylakoid membranes and oxylipins such as jasmonic acid (JA) and 12-oxo-phytodienoic acid (OPDA) play important roles in adaptation to photo-oxidative stress. OPDA functions both as a JA precursor and as a biologically active signaling molecule that induces expression of a specific set of genes. These genes can be induced by OPDA in the JA-insensitive coronatine insensitive1 (coi1) mutant, suggesting that there is an alternative pathway for OPDA signaling, independent of COI1-dependent JA signaling. However, little is known about OPDA signaling in photo-oxidative stress responses. In this study, we isolated Arabidopsis mutants with constitutively enhanced expression from the OPDA-responsive HsfA2 promoter. We used deletion mapping and complementation analysis to identify one responsible gene as CATALASE2. Our results thus indicate that ROS-producing cellular metabolism links to OPDA signaling.}, } @article {pmid24342585, year = {2014}, author = {Omer, S and Kirkbride, JB and Pringle, DG and Russell, V and O'Callaghan, E and Waddington, JL}, title = {Neighbourhood-level socio-environmental factors and incidence of first episode psychosis by place at onset in rural Ireland: the Cavan-Monaghan First Episode Psychosis Study [CAMFEPS].}, journal = {Schizophrenia research}, volume = {152}, number = {1}, pages = {152-157}, pmid = {24342585}, issn = {1573-2509}, support = {085540//Wellcome Trust/United Kingdom ; }, mesh = {Adolescent ; Adult ; Cohort Studies ; Databases, Factual/statistics & numerical data ; Female ; Humans ; Incidence ; Ireland/epidemiology ; Male ; Psychotic Disorders/*epidemiology/psychology ; *Residence Characteristics ; Risk Factors ; Rural Population ; *Social Environment ; Urban Population ; Young Adult ; }, abstract = {BACKGROUND: Little is known about associations between the social environment and risk for psychosis within rural settings. This study sought to investigate whether such associations exist within a rural context using a prospective dataset of unusual epidemiological completeness.

METHOD: Using the Cavan-Monaghan First Episode Psychosis Study database of people aged 16 years and older, both ecological analyses and multilevel modelling were applied to investigate associations between incidence of psychosis by place at onset and socio-environmental risk factors of material deprivation, social fragmentation and urban-rural classification across electoral divisions.

RESULTS: The primary finding was an association between more deprived social contexts and higher rates of psychotic disorder, after adjustment for age and sex [all psychoses: incidence rate ratio (IRR)=1.12, 95% CI (1.03-1.23)].

CONCLUSIONS: These findings support an association between adverse socio-environmental factors and increase in risk for psychosis by place at onset within a predominantly rural environment. This study suggests that social environmental characteristics may have an impact on risk across the urban-rural gradient.}, } @article {pmid24338098, year = {2014}, author = {Deb, S and Ahmed, A and Datta, D}, title = {An alternative approach for delineating eco-sensitive zones around a wildlife sanctuary applying geospatial techniques.}, journal = {Environmental monitoring and assessment}, volume = {186}, number = {4}, pages = {2641-2651}, pmid = {24338098}, issn = {1573-2959}, mesh = {Biodiversity ; Conservation of Natural Resources/*methods ; *Ecosystem ; Environmental Monitoring/*methods ; Geographic Information Systems ; India ; }, abstract = {The dynamics, degradation, and conservation of forest ecosystems are matters of prime concerns worldwide at the present. Proper planning and management of a forest area are essentially needed to protect it from the grasp of burgeoning pressure of urban-industrial sprawl. Establishment of eco-sensitive zones (ESZs), which act as buffer areas around the core forests, is one of the key approaches towards achieving this goal. This paper deals with the applicability of geospatial techniques to identify the ESZ around an Indian wildlife sanctuary following the different rules and acts prescribed by the Government of India. Gumti Wildlife Sanctuary, located in the northeastern state of Tripura in India, has been selected here as a case study. Collected pieces of information on the distribution of biodiversity and human population in the area were also used to make the approach more holistic. As inferred from this study, remote sensing and geographical information systems were found to be easily implementable and time as well as cost-effective tools for this purpose with a distinct advantage of spatial as well as temporal accuracy in identifying the existing land use and land cover patterns in pilot assessments. However, the results indicated that only appropriate hybridization of field-based information on the biodiversity and ecological aspects of the forest as well as patterns of human interferences with the remote sensing and GIS-based data could make this approach more relevant in actual implementations.}, } @article {pmid24332365, year = {2014}, author = {Epstein, DH and Tyburski, M and Craig, IM and Phillips, KA and Jobes, ML and Vahabzadeh, M and Mezghanni, M and Lin, JL and Furr-Holden, CDM and Preston, KL}, title = {Real-time tracking of neighborhood surroundings and mood in urban drug misusers: application of a new method to study behavior in its geographical context.}, journal = {Drug and alcohol dependence}, volume = {134}, number = {}, pages = {22-29}, pmid = {24332365}, issn = {1879-0046}, support = {ZIA DA000499-06//Intramural NIH HHS/United States ; ZIA DA000536-06//Intramural NIH HHS/United States ; }, mesh = {Adult ; *Affect ; Behavior, Addictive/diagnosis/*epidemiology/psychology ; Cohort Studies ; Computer Systems/trends ; Drug Users/psychology ; Female ; *Geographic Information Systems/trends ; Humans ; Longitudinal Studies ; Male ; Middle Aged ; *Residence Characteristics ; Stress, Psychological/diagnosis/epidemiology/psychology ; Substance-Related Disorders/diagnosis/*epidemiology/psychology ; *Urban Population/trends ; Young Adult ; }, abstract = {BACKGROUND: Maladaptive behaviors may be more fully understood and efficiently prevented by ambulatory tools that assess people's ongoing experience in the context of their environment.

METHODS: To demonstrate new field-deployable methods for assessing mood and behavior as a function of neighborhood surroundings (geographical momentary assessment; GMA), we collected time-stamped GPS data and ecological momentary assessment (EMA) ratings of mood, stress, and drug craving over 16 weeks at randomly prompted times during the waking hours of opioid-dependent polydrug users receiving methadone maintenance. Locations of EMA entries and participants' travel tracks calculated for the 12 before each EMA entry were mapped. Associations between subjective ratings and objective environmental ratings were evaluated at the whole neighborhood and 12-h track levels.

RESULTS: Participants (N=27) were compliant with GMA data collection; 3711 randomly prompted EMA entries were matched to specific locations. At the neighborhood level, physical disorder was negatively correlated with negative mood, stress, and heroin and cocaine craving (ps<.0001-.0335); drug activity was negatively correlated with stress, heroin and cocaine craving (ps .0009-.0134). Similar relationships were found for the environments around respondents' tracks in the 12h preceding EMA entries.

CONCLUSIONS: The results support the feasibility of GMA. The relationships between neighborhood characteristics and participants' reports were counterintuitive and counter-hypothesized, and challenge some assumptions about how ostensibly stressful environments are associated with lived experience and how such environments ultimately impair health. GMA methodology may have applications for development of individual- or neighborhood-level interventions.}, } @article {pmid24324770, year = {2013}, author = {Arlt, D and Low, M and Pärt, T}, title = {Effect of geolocators on migration and subsequent breeding performance of a long-distance passerine migrant.}, journal = {PloS one}, volume = {8}, number = {12}, pages = {e82316}, pmid = {24324770}, issn = {1932-6203}, mesh = {Animal Migration/*physiology ; Animals ; *Breeding ; Female ; *Geographic Information Systems ; Male ; Oviposition/physiology ; Passeriformes/*physiology ; Reproduction/physiology ; Survival Analysis ; Sweden ; Time Factors ; }, abstract = {Geolocators are small light-weight data loggers used to track individual migratory routes, and their use has increased exponentially in birds. However, the effects of geolocators on individual performance are still poorly known. We studied geolocator effects on a long-distance migrating passerine bird, the northern wheatear (Oenanthe oenanthe L.). We asked the general question of whether geolocators affect migratory behaviour and subsequent reproductive performance of small passerines by comparing arrival time, breeding time, breeding success and survival of geolocator versus control birds of known identity and breeding history. During two years geolocator birds (n=37) displayed a lower apparent survival (30%) as compared to controls (45%, n=164). Furthermore, returning geolocator birds (n=12) arrived on average 3.5 days later, started laying eggs 6.3 days later, and had lower nest success (25%) than control birds (78%). Our results suggest that geolocators affect migratory performance with carry-over effects to the timing of breeding and reproductive success in the subsequent breeding season. We discuss the implications of such geolocator effects for the study of migratory strategies of small passerines in general and suggest how to identify and investigate such effects in the future.}, } @article {pmid24324760, year = {2013}, author = {Cui, Z and Li, X and Liu, Y and Song, C and Hui, M and Shi, G and Luo, D and Li, Y}, title = {Transcriptome profiling analysis on whole bodies of microbial challenged Eriocheir sinensis larvae for immune gene identification and SNP development.}, journal = {PloS one}, volume = {8}, number = {12}, pages = {e82156}, pmid = {24324760}, issn = {1932-6203}, mesh = {Animals ; Brachyura/genetics/*immunology/*microbiology ; Female ; *Gene Expression Profiling ; Gene Ontology ; Genetic Markers ; Larva/genetics/immunology/microbiology ; MAP Kinase Signaling System/genetics ; Micrococcus luteus/*physiology ; Molecular Sequence Annotation ; Pichia/*physiology ; Polymorphism, Single Nucleotide/*genetics ; Proteins/genetics/metabolism ; Sequence Analysis, RNA ; Signal Transduction/genetics ; Vibrio/*physiology ; }, abstract = {To study crab immunogenetics of individuals, newly hatched Eriocheir sinensis larvae were stimulated with a mixture of three pathogen strains (Gram-positive bacteria Micrococcus luteus, Gram-negative bacteria Vibrio alginolyticus and fungi Pichia pastoris; 10(8) cfu·mL(-1)). A total of 44,767,566 Illumina clean reads corresponding to 4.52 Gb nucleotides were generated and assembled into 100,252 unigenes (average length: 1,042 bp; range: 201-19,357 bp). 17,097 (26.09%) of 65,535 non-redundant unigenes were annotated in NCBI non-redundant protein (Nr) database. Moreover, 23,188 (35.38%) unigenes were assigned to three Gene Ontology (GO) categories, 15,071 (23.00%) to twenty-six Clusters of orthologous Groups (COG) and 8,574 (13.08%) to six Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, respectively. Numerous genes were further identified to be associated with multiple immune pathways, including Toll, immune deficiency (IMD), janus kinase (JAK)-signal transducers and activators of transcription (STAT) and mitogen-activated protein kinase (MAPK) pathways. Some of them, such as tumor necrosis factor receptor associated factor 6 (TRAF6), fibroblast growth factor (FGF), protein-tyrosine phosphatase (PTP), JNK-interacting protein 1 (JIP1), were first identified in E. sinensis. TRAF6 was even first discovered in crabs. Additionally, 49,555 single nucleotide polymorphisms (SNPs) were developed from over 13,309 unigenes. This is the first transcriptome report of whole bodies of E. sinensis larvae after immune challenge. Data generated here not only provide detail information to identify novel genes in genome reference-free E. sinensis, but also facilitate our understanding on host immunity and defense mechanism of the crab at whole transcriptome level.}, } @article {pmid24324143, year = {2014}, author = {Kamilar, JM and Atkinson, QD}, title = {Cultural assemblages show nested structure in humans and chimpanzees but not orangutans.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {111}, number = {1}, pages = {111-115}, pmid = {24324143}, issn = {1091-6490}, mesh = {Animals ; Behavior, Animal ; Biological Evolution ; *Cultural Evolution ; Databases, Factual ; Ecology ; Ecosystem ; Environment ; Geography ; Humans ; North America ; *Pan troglodytes ; *Pongo ; Species Specificity ; Time Factors ; }, abstract = {The evolution of hominin culture is well-documented in the archeological and fossil record, but such a record is largely absent for nonhuman primates. An alternative approach to studying cultural evolution is to examine patterns of modern cultural variation. In this article we measure nestedness across human and great ape "cultural repertoires" to gain insight into the accumulation and maintenance of putative cultural diversity in these species. Cultural assemblages are nested if cultures with a small repertoire of traits tend to comprise a proper subset of those traits present in more complex cultures. This nesting will occur if some traits are sequentially gained or lost, which may be because of the differential dispersal or extinction of traits. Here we apply statistical tools from ecology to examine the degree of nestedness in four datasets documenting the presence or absence of specific cultural traits across indigenous human populations in North America and New Guinea. We then compare the human data to patterns observed for putative cultural traits in chimpanzee and orangutan populations. In both humans and chimpanzees, cultural diversity is highly nonrandom, showing significant nested structure for all of the datasets examined. We find no evidence for nestedness in the orangutan cultural data. These findings are consistent with a sequential "layering" of cultural diversity in humans and chimpanzees, but not orangutans. Such an interpretation implies that the traits required for sequential cultural evolution first appeared in the last common ancestor of chimpanzees and humans.}, } @article {pmid24323571, year = {2014}, author = {Shiffman, S}, title = {Conceptualizing analyses of ecological momentary assessment data.}, journal = {Nicotine & tobacco research : official journal of the Society for Research on Nicotine and Tobacco}, volume = {16 Suppl 2}, number = {Suppl 2}, pages = {S76-87}, pmid = {24323571}, issn = {1469-994X}, support = {R01-DA006084/DA/NIDA NIH HHS/United States ; R01-DA020742/DA/NIDA NIH HHS/United States ; DA020742/DA/NIDA NIH HHS/United States ; U01-HL097839/HL/NHLBI NIH HHS/United States ; R01-HL107370/HL/NHLBI NIH HHS/United States ; R01-DA033303/DA/NIDA NIH HHS/United States ; }, mesh = {Data Collection/methods ; Data Interpretation, Statistical ; Humans ; Models, Statistical ; Psychopharmacology/*methods ; Recurrence ; *Research Design ; Smoking/*psychology ; Smoking Cessation/psychology ; Social Environment ; Time Factors ; Tobacco Use/*psychology ; }, abstract = {Ecological momentary assessment (EMA) methods, which involve collection of real-time data in subjects' real-world environments, are particularly well suited to studying tobacco use. Analyzing EMA datasets can be challenging, as the datasets include a large and varied number of observations per subject and are relatively unstructured. This paper suggests that time is typically a key organizing principle in EMA data and that conceptualizing the data as a timeline of events, behaviors, and experiences can help define analytic approaches. EMA datasets lend themselves to answering a diverse array of research questions, and the research question must drive how data are arranged for analysis, and the kinds of statistical models that are applied. This is illustrated this with brief examples of diverse analyses applied to answer different questions from an EMA study of tobacco use and relapse.}, } @article {pmid24320872, year = {2014}, author = {Duardo-Sánchez, A and Munteanu, CR and Riera-Fernández, P and López-Díaz, A and Pazos, A and González-Díaz, H}, title = {Modeling complex metabolic reactions, ecological systems, and financial and legal networks with MIANN models based on Markov-Wiener node descriptors.}, journal = {Journal of chemical information and modeling}, volume = {54}, number = {1}, pages = {16-29}, doi = {10.1021/ci400280n}, pmid = {24320872}, issn = {1549-960X}, mesh = {Algorithms ; Computational Biology ; Databases, Factual ; Ecosystem ; Jurisprudence ; Markov Chains ; Metabolic Networks and Pathways ; *Models, Biological ; Models, Econometric ; Models, Theoretical ; *Neural Networks, Computer ; Social Support ; Software ; }, abstract = {The use of numerical parameters in Complex Network analysis is expanding to new fields of application. At a molecular level, we can use them to describe the molecular structure of chemical entities, protein interactions, or metabolic networks. However, the applications are not restricted to the world of molecules and can be extended to the study of macroscopic nonliving systems, organisms, or even legal or social networks. On the other hand, the development of the field of Artificial Intelligence has led to the formulation of computational algorithms whose design is based on the structure and functioning of networks of biological neurons. These algorithms, called Artificial Neural Networks (ANNs), can be useful for the study of complex networks, since the numerical parameters that encode information of the network (for example centralities/node descriptors) can be used as inputs for the ANNs. The Wiener index (W) is a graph invariant widely used in chemoinformatics to quantify the molecular structure of drugs and to study complex networks. In this work, we explore for the first time the possibility of using Markov chains to calculate analogues of node distance numbers/W to describe complex networks from the point of view of their nodes. These parameters are called Markov-Wiener node descriptors of order k(th) (W(k)). Please, note that these descriptors are not related to Markov-Wiener stochastic processes. Here, we calculated the W(k)(i) values for a very high number of nodes (>100,000) in more than 100 different complex networks using the software MI-NODES. These networks were grouped according to the field of application. Molecular networks include the Metabolic Reaction Networks (MRNs) of 40 different organisms. In addition, we analyzed other biological and legal and social networks. These include the Interaction Web Database Biological Networks (IWDBNs), with 75 food webs or ecological systems and the Spanish Financial Law Network (SFLN). The calculated W(k)(i) values were used as inputs for different ANNs in order to discriminate correct node connectivity patterns from incorrect random patterns. The MIANN models obtained present good values of Sensitivity/Specificity (%): MRNs (78/78), IWDBNs (90/88), and SFLN (86/84). These preliminary results are very promising from the point of view of a first exploratory study and suggest that the use of these models could be extended to the high-throughput re-evaluation of connectivity in known complex networks (collation).}, } @article {pmid24320199, year = {2013}, author = {Beati, L and Nava, S and Burkman, EJ and Barros-Battesti, DM and Labruna, MB and Guglielmone, AA and Cáceres, AG and Guzmán-Cornejo, CM and León, R and Durden, LA and Faccini, JL}, title = {Amblyomma cajennense (Fabricius, 1787) (Acari: Ixodidae), the Cayenne tick: phylogeography and evidence for allopatric speciation.}, journal = {BMC evolutionary biology}, volume = {13}, number = {}, pages = {267}, pmid = {24320199}, issn = {1471-2148}, mesh = {Animals ; Arthropod Proteins/genetics ; DNA, Mitochondrial/genetics ; DNA, Ribosomal/genetics ; Databases, Genetic ; *Genetic Speciation ; Genetic Variation ; Ixodidae/*classification/*genetics ; Molecular Sequence Data ; Phylogeography ; }, abstract = {BACKGROUND: Amblyomma cajennense F. is one of the best known and studied ticks in the New World because of its very wide distribution, its economical importance as pest of domestic ungulates, and its association with a variety of animal and human pathogens. Recent observations, however, have challenged the taxonomic status of this tick and indicated that intraspecific cryptic speciation might be occurring. In the present study, we investigate the evolutionary and demographic history of this tick and examine its genetic structure based on the analyses of three mitochondrial (12SrDNA, d-loop, and COII) and one nuclear (ITS2) genes. Because A. cajennense is characterized by a typical trans-Amazonian distribution, lineage divergence dating is also performed to establish whether genetic diversity can be linked to dated vicariant events which shaped the topology of the Neotropics.

RESULTS: Total evidence analyses of the concatenated mtDNA and nuclear + mtDNA datasets resulted in well-resolved and fully congruent reconstructions of the relationships within A. cajennense. The phylogenetic analyses consistently found A. cajennense to be monophyletic and to be separated into six genetic units defined by mutually exclusive haplotype compositions and habitat associations. Also, genetic divergence values showed that these lineages are as distinct from each other as recognized separate species of the same genus. The six clades are deeply split and node dating indicates that they started diverging in the middle-late Miocene.

CONCLUSIONS: Behavioral differences and the results of laboratory cross-breeding experiments had already indicated that A. cajennense might be a complex of distinct taxonomic units. The combined and congruent mitochondrial and nuclear genetic evidence from this study reveals that A. cajennense is an assembly of six distinct species which have evolved separately from each other since at least 13.2 million years ago (Mya) in the earliest and 3.3 Mya in the latest lineages. The temporal and spatial diversification modes of the six lineages overlap the phylogeographical history of other organisms with similar extant trans-Amazonian distributions and are consistent with the present prevailing hypothesis that Neotropical diversity often finds its origins in the Miocene, after the Andean uplift changed the topology and consequently the climate and ecology of the Neotropics.}, } @article {pmid24318999, year = {2014}, author = {Lartillot, N}, title = {A phylogenetic Kalman filter for ancestral trait reconstruction using molecular data.}, journal = {Bioinformatics (Oxford, England)}, volume = {30}, number = {4}, pages = {488-496}, doi = {10.1093/bioinformatics/btt707}, pmid = {24318999}, issn = {1367-4811}, mesh = {*Algorithms ; Archaea/*genetics/growth & development ; Base Composition ; *Bayes Theorem ; *Biological Evolution ; Data Interpretation, Statistical ; Linear Models ; Markov Chains ; Models, Biological ; Monte Carlo Method ; Phenotype ; *Phylogeny ; RNA, Ribosomal/genetics ; Temperature ; }, abstract = {MOTIVATION: Correlation between life history or ecological traits and genomic features such as nucleotide or amino acid composition can be used for reconstructing the evolutionary history of the traits of interest along phylogenies. Thus far, however, such ancestral reconstructions have been done using simple linear regression approaches that do not account for phylogenetic inertia. These reconstructions could instead be seen as a genuine comparative regression problem, such as formalized by classical generalized least-square comparative methods, in which the trait of interest and the molecular predictor are represented as correlated Brownian characters coevolving along the phylogeny.

RESULTS: Here, a Bayesian sampler is introduced, representing an alternative and more efficient algorithmic solution to this comparative regression problem, compared with currently existing generalized least-square approaches. Technically, ancestral trait reconstruction based on a molecular predictor is shown to be formally equivalent to a phylogenetic Kalman filter problem, for which backward and forward recursions are developed and implemented in the context of a Markov chain Monte Carlo sampler. The comparative regression method results in more accurate reconstructions and a more faithful representation of uncertainty, compared with simple linear regression. Application to the reconstruction of the evolution of optimal growth temperature in Archaea, using GC composition in ribosomal RNA stems and amino acid composition of a sample of protein-coding genes, confirms previous findings, in particular, pointing to a hyperthermophilic ancestor for the kingdom.

The program is freely available at www.phylobayes.org.}, } @article {pmid24314153, year = {2013}, author = {Kahramanoğulları, O and Lynch, JF}, title = {Stochastic flux analysis of chemical reaction networks.}, journal = {BMC systems biology}, volume = {7}, number = {}, pages = {133}, pmid = {24314153}, issn = {1752-0509}, mesh = {*Algorithms ; Computational Biology/*methods ; Models, Biological ; Programming Languages ; Stochastic Processes ; Time Factors ; }, abstract = {BACKGROUND: Chemical reaction networks provide an abstraction scheme for a broad range of models in biology and ecology. The two common means for simulating these networks are the deterministic and the stochastic approaches. The traditional deterministic approach, based on differential equations, enjoys a rich set of analysis techniques, including a treatment of reaction fluxes. However, the discrete stochastic simulations, which provide advantages in some cases, lack a quantitative treatment of network fluxes.

RESULTS: We describe a method for flux analysis of chemical reaction networks, where flux is given by the flow of species between reactions in stochastic simulations of the network. Extending discrete event simulation algorithms, our method constructs several data structures, and thereby reveals a variety of statistics about resource creation and consumption during the simulation. We use these structures to quantify the causal interdependence and relative importance of the reactions at arbitrary time intervals with respect to the network fluxes. This allows us to construct reduced networks that have the same flux-behavior, and compare these networks, also with respect to their time series. We demonstrate our approach on an extended example based on a published ODE model of the same network, that is, Rho GTP-binding proteins, and on other models from biology and ecology.

CONCLUSIONS: We provide a fully stochastic treatment of flux analysis. As in deterministic analysis, our method delivers the network behavior in terms of species transformations. Moreover, our stochastic analysis can be applied, not only at steady state, but at arbitrary time intervals, and used to identify the flow of specific species between specific reactions. Our cases study of Rho GTP-binding proteins reveals the role played by the cyclic reverse fluxes in tuning the behavior of this network.}, } @article {pmid24313439, year = {2013}, author = {Lubinski, L and Urbaszek, P and Gajewicz, A and Cronin, MT and Enoch, SJ and Madden, JC and Leszczynska, D and Leszczynski, J and Puzyn, T}, title = {Evaluation criteria for the quality of published experimental data on nanomaterials and their usefulness for QSAR modelling.}, journal = {SAR and QSAR in environmental research}, volume = {24}, number = {12}, pages = {995-1008}, doi = {10.1080/1062936X.2013.840679}, pmid = {24313439}, issn = {1029-046X}, mesh = {*Algorithms ; Animals ; Databases, Factual ; Ecotoxicology ; Nanoparticles/chemistry/toxicity ; Nanostructures/*chemistry/*toxicity ; Nanotechnology ; *Quantitative Structure-Activity Relationship ; }, abstract = {Nowadays nanotechnology is one of the most promising areas of science. The number and quantity of synthesized nanomaterials increase exponentially, therefore it is reasonable to expect that comprehensive risk assessment based only on empirical testing of all novel engineered nanoparticles (NPs) will very soon become impossible. Hence, the development of computational methods complementary to experimentation is very important. Quantitative structure-property relationship (QSPR) and quantitative structure-activity relationship (QSAR) models widely used in pharmaceutical chemistry and environmental science can also be modified and adopted for nanotechnology to predict physico-chemical properties and toxicity of empirically untested nanomaterials. All QSPR/QSAR modelling activities are based on experimentally derived data. It is important that, within a given data set, all values should be consistent, of high quality and measured according to a standardized protocol. Unfortunately, the amount of such data available for engineered nanoparticles in various data sources (i.e. databases and the literature) is very limited and seldom measured with a standardized protocol. Therefore, we have proposed a framework for collecting and evaluating the existing data, with the focus on possible applications for computational evaluation of properties and biological activities of nanomaterials.}, } @article {pmid24311565, year = {2014}, author = {Lemfack, MC and Nickel, J and Dunkel, M and Preissner, R and Piechulla, B}, title = {mVOC: a database of microbial volatiles.}, journal = {Nucleic acids research}, volume = {42}, number = {Database issue}, pages = {D744-8}, pmid = {24311565}, issn = {1362-4962}, mesh = {Bacteria/*chemistry ; *Databases, Chemical ; Fungi/*chemistry ; Internet ; Volatile Organic Compounds/*chemistry ; }, abstract = {Scents are well known to be emitted from flowers and animals. In nature, these volatiles are responsible for inter- and intra-organismic communication, e.g. attraction and defence. Consequently, they influence and improve the establishment of organisms and populations in ecological niches by acting as single compounds or in mixtures. Despite the known wealth of volatile organic compounds (VOCs) from species of the plant and animal kingdom, in the past, less attention has been focused on volatiles of microorganisms. Although fast and affordable sequencing methods facilitate the detection of microbial diseases, however, the analysis of signature or fingerprint volatiles will be faster and easier. Microbial VOCs (mVOCs) are presently used as marker to detect human diseases, food spoilage or moulds in houses. Furthermore, mVOCs exhibited antagonistic potential against pathogens in vitro, but their biological roles in the ecosystems remain to be investigated. Information on volatile emission from bacteria and fungi is presently scattered in the literature, and no public and up-to-date collection on mVOCs is available. To address this need, we have developed mVOC, a database available online at http://bioinformatics.charite.de/mvoc.}, } @article {pmid24308365, year = {2013}, author = {Ghosh, S and Baloni, P and Mukherjee, S and Anand, P and Chandra, N}, title = {A multi-level multi-scale approach to study essential genes in Mycobacterium tuberculosis.}, journal = {BMC systems biology}, volume = {7}, number = {}, pages = {132}, pmid = {24308365}, issn = {1752-0509}, mesh = {Amino Acid Sequence ; Bacterial Proteins/chemistry/genetics/metabolism ; Computational Biology/*methods ; Conserved Sequence ; *Genes, Bacterial ; Genomics ; Metabolic Networks and Pathways ; Models, Molecular ; Molecular Sequence Data ; Mycobacterium tuberculosis/*genetics/metabolism ; Oligonucleotide Array Sequence Analysis ; Phylogeny ; Protein Conformation ; Protein Interaction Mapping ; }, abstract = {BACKGROUND: The set of indispensable genes that are required by an organism to grow and sustain life are termed as essential genes. There is a strong interest in identification of the set of essential genes, particularly in pathogens, not only for a better understanding of the pathogen biology, but also for identifying drug targets and the minimal gene set for the organism. Essentiality is inherently a systems property and requires consideration of the system as a whole for their identification. The available experimental approaches capture some aspects but each method comes with its own limitations. Moreover, they do not explain the basis for essentiality in most cases. A powerful prediction method to recognize this gene pool including rationalization of the known essential genes in a given organism would be very useful. Here we describe a multi-level multi-scale approach to identify the essential gene pool in a deadly pathogen, Mycobacterium tuberculosis.

RESULTS: The multi-level workflow analyses the bacterial cell by studying (a) genome-wide gene expression profiles to identify the set of genes which show consistent and significant levels of expression in multiple samples of the same condition, (b) indispensability for growth by using gene expression integrated flux balance analysis of a genome-scale metabolic model, (c) importance for maintaining the integrity and flow in a protein-protein interaction network and (d) evolutionary conservation in a set of genomes of the same ecological niche. In the gene pool identified, the functional basis for essentiality has been addressed by studying residue level conservation and the sub-structure at the ligand binding pockets, from which essential amino acid residues in that pocket have also been identified. 283 genes were identified as essential genes with high-confidence. An agreement of about 73.5% is observed with that obtained from the experimental transposon mutagenesis technique. A large proportion of the identified genes belong to the class of intermediary metabolism and respiration.

CONCLUSIONS: The multi-scale, multi-level approach described can be generally applied to other pathogens as well. The essential gene pool identified form a basis for designing experiments to probe their finer functional roles and also serve as a ready shortlist for identifying drug targets.}, } @article {pmid24307248, year = {2014}, author = {Sirota, M and Kostovičová, L and Juanchich, M}, title = {The effect of iconicity of visual displays on statistical reasoning: evidence in favor of the null hypothesis.}, journal = {Psychonomic bulletin & review}, volume = {21}, number = {4}, pages = {961-968}, pmid = {24307248}, issn = {1531-5320}, mesh = {Adolescent ; Adult ; Aged ; *Bayes Theorem ; Female ; Humans ; Male ; Middle Aged ; Pattern Recognition, Visual/*physiology ; Thinking/*physiology ; Young Adult ; }, abstract = {Knowing which properties of visual displays facilitate statistical reasoning bears practical and theoretical implications. Therefore, we studied the effect of one property of visual diplays - iconicity (i.e., the resemblance of a visual sign to its referent) - on Bayesian reasoning. Two main accounts of statistical reasoning predict different effect of iconicity on Bayesian reasoning. The ecological-rationality account predicts a positive iconicity effect, because more highly iconic signs resemble more individuated objects, which tap better into an evolutionary-designed frequency-coding mechanism that, in turn, facilitates Bayesian reasoning. The nested-sets account predicts a null iconicity effect, because iconicity does not affect the salience of a nested-sets structure-the factor facilitating Bayesian reasoning processed by a general reasoning mechanism. In two well-powered experiments (N = 577), we found no support for a positive iconicity effect across different iconicity levels that were manipulated in different visual displays (meta-analytical overall effect: log OR = -0.13, 95% CI [-0.53, 0.28]). A Bayes factor analysis provided strong evidence in favor of the null hypothesis-the null iconicity effect. Thus, these findings corroborate the nested-sets rather than the ecological-rationality account of statistical reasoning.}, } @article {pmid24299081, year = {2013}, author = {Snover, AK and Mantua, NJ and Littell, JS and Alexander, MA and McClure, MM and Nye, J}, title = {Choosing and using climate-change scenarios for ecological-impact assessments and conservation decisions.}, journal = {Conservation biology : the journal of the Society for Conservation Biology}, volume = {27}, number = {6}, pages = {1147-1157}, doi = {10.1111/cobi.12163}, pmid = {24299081}, issn = {1523-1739}, mesh = {*Climate Change ; *Computer Simulation ; *Conservation of Natural Resources ; Decision Making, Computer-Assisted ; Endangered Species ; Risk Assessment ; }, abstract = {Increased concern over climate change is demonstrated by the many efforts to assess climate effects and develop adaptation strategies. Scientists, resource managers, and decision makers are increasingly expected to use climate information, but they struggle with its uncertainty. With the current proliferation of climate simulations and downscaling methods, scientifically credible strategies for selecting a subset for analysis and decision making are needed. Drawing on a rich literature in climate science and impact assessment and on experience working with natural resource scientists and decision makers, we devised guidelines for choosing climate-change scenarios for ecological impact assessment that recognize irreducible uncertainty in climate projections and address common misconceptions about this uncertainty. This approach involves identifying primary local climate drivers by climate sensitivity of the biological system of interest; determining appropriate sources of information for future changes in those drivers; considering how well processes controlling local climate are spatially resolved; and selecting scenarios based on considering observed emission trends, relative importance of natural climate variability, and risk tolerance and time horizon of the associated decision. The most appropriate scenarios for a particular analysis will not necessarily be the most appropriate for another due to differences in local climate drivers, biophysical linkages to climate, decision characteristics, and how well a model simulates the climate parameters and processes of interest. Given these complexities, we recommend interaction among climate scientists, natural and physical scientists, and decision makers throughout the process of choosing and using climate-change scenarios for ecological impact assessment. Selección y Uso de Escenarios de Cambio Climático para Estudios de Impacto Ecológico y Decisiones de Conservación.}, } @article {pmid24296905, year = {2013}, author = {Rico, C and Normandeau, E and Dion-Côté, AM and Rico, MI and Côté, G and Bernatchez, L}, title = {Combining next-generation sequencing and online databases for microsatellite development in non-model organisms.}, journal = {Scientific reports}, volume = {3}, number = {}, pages = {3376}, pmid = {24296905}, issn = {2045-2322}, mesh = {Animals ; Databases, Genetic ; Expressed Sequence Tags/metabolism ; Fishes/*genetics/metabolism ; Genetic Markers/genetics ; Genetics, Population/methods ; High-Throughput Nucleotide Sequencing/methods ; Microsatellite Repeats/*genetics ; Transcriptome/*genetics ; }, abstract = {Next-generation sequencing (NGS) is revolutionising marker development and the rapidly increasing amount of transcriptomes published across a wide variety of taxa is providing valuable sequence databases for the identification of genetic markers without the need to generate new sequences. Microsatellites are still the most important source of polymorphic markers in ecology and evolution. Motivated by our long-term interest in the adaptive radiation of a non-model species complex of whitefishes (Coregonus spp.), in this study, we focus on microsatellite characterisation and multiplex optimisation using transcriptome sequences generated by Illumina® and Roche-454, as well as online databases of Expressed Sequence Tags (EST) for the study of whitefish evolution and demographic history. We identified and optimised 40 polymorphic loci in multiplex PCR reactions and validated the robustness of our analyses by testing several population genetics and phylogeographic predictions using 494 fish from five lakes and 2 distinct ecotypes.}, } @article {pmid24296455, year = {2014}, author = {Li, Y and Chen, L and Wen, H and Zhou, T and Zhang, T and Gao, X}, title = {454 pyrosequencing analysis of bacterial diversity revealed by a comparative study of soils from mining subsidence and reclamation areas.}, journal = {Journal of microbiology and biotechnology}, volume = {24}, number = {3}, pages = {313-323}, doi = {10.4014/jmb.1309.09001}, pmid = {24296455}, issn = {1738-8872}, mesh = {Bacteria/*classification/genetics ; *Biota ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; *Environmental Restoration and Remediation ; *Mining ; Molecular Sequence Data ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Soil Microbiology ; }, abstract = {Significant alteration in the microbial community can occur across reclamation areas suffering subsidence from mining. A reclamation site undergoing fertilization practices and an adjacent coal-excavated subsidence site (sites A and B, respectively) were examined to characterize the bacterial diversity using 454 high-throughput 16S rDNA sequencing. The dominant taxonomic groups in both the sites were Proteobacteria, Acidobacteria, Bacteroidetes, Betaproteobacteria, Actinobacteria, Gammaproteobacteria, Alphaproteobacteria, Deltaproteobacteria, Chloroflexi, and Firmicutes. However, the bacterial communities' abundance, diversity, and composition differed significantly between the sites. Site A presented higher bacterial diversity and more complex community structures than site B. The majority of sequences related to Proteobacteria, Gemmatimonadetes, Chloroflexi, Nitrospirae, Firmicutes, Betaproteobacteria, Deltaproteobacteria, and Anaerolineae were from site A; whereas those related to Actinobacteria, Planctomycetes, Bacteroidetes, Verrucomicrobia, Gammaproteobacteria, Nitriliruptoria, Alphaproteobacteria, and Phycisphaerae originated from site B. The distribution of some bacterial groups and subgroups in the two sites correlated with soil properties and vegetation due to reclamation practice. Site A exhibited enriched bacterial community, soil organic matter (SOM), and total nitrogen (TN), suggesting the presence of relatively diverse microorganisms. SOM and TN were important factors shaping the underlying microbial communities. Furthermore, the specific plant functional group (legumes) was also an important factor influencing soil microbial community composition. Thus, the effectiveness of 454 pyrosequencing in analyzing soil bacterial diversity was validated and an association between land ecological system restoration, mostly mediated by microbial communities, and an improvement in soil properties in coalmining reclamation areas was suggested.}, } @article {pmid24289184, year = {2013}, author = {Roux, E and Gaborit, P and Romaña, CA and Girod, R and Dessay, N and Dusfour, I}, title = {Objective sampling design in a highly heterogeneous landscape - characterizing environmental determinants of malaria vector distribution in French Guiana, in the Amazonian region.}, journal = {BMC ecology}, volume = {13}, number = {}, pages = {45}, pmid = {24289184}, issn = {1472-6785}, mesh = {Animals ; *Anopheles/parasitology ; Cluster Analysis ; Ecology/methods ; *Ecosystem ; Environmental Monitoring/*methods ; French Guiana/epidemiology ; Geographic Information Systems ; *Insect Vectors/parasitology ; Malaria/epidemiology ; Remote Sensing Technology ; }, abstract = {BACKGROUND: Sampling design is a key issue when establishing species inventories and characterizing habitats within highly heterogeneous landscapes. Sampling efforts in such environments may be constrained and many field studies only rely on subjective and/or qualitative approaches to design collection strategy. The region of Cacao, in French Guiana, provides an excellent study site to understand the presence and abundance of Anopheles mosquitoes, their species dynamics and the transmission risk of malaria across various environments. We propose an objective methodology to define a stratified sampling design. Following thorough environmental characterization, a factorial analysis of mixed groups allows the data to be reduced and non-collinear principal components to be identified while balancing the influences of the different environmental factors. Such components defined new variables which could then be used in a robust k-means clustering procedure. Then, we identified five clusters that corresponded to our sampling strata and selected sampling sites in each stratum.

RESULTS: We validated our method by comparing the species overlap of entomological collections from selected sites and the environmental similarities of the same sites. The Morisita index was significantly correlated (Pearson linear correlation) with environmental similarity based on i) the balanced environmental variable groups considered jointly (p = 0.001) and ii) land cover/use (p-value << 0.001). The Jaccard index was significantly correlated with land cover/use-based environmental similarity (p-value = 0.001).

CONCLUSIONS: The results validate our sampling approach. Land cover/use maps (based on high spatial resolution satellite images) were shown to be particularly useful when studying the presence, density and diversity of Anopheles mosquitoes at local scales and in very heterogeneous landscapes.}, } @article {pmid24288368, year = {2014}, author = {Cole, JR and Wang, Q and Fish, JA and Chai, B and McGarrell, DM and Sun, Y and Brown, CT and Porras-Alfaro, A and Kuske, CR and Tiedje, JM}, title = {Ribosomal Database Project: data and tools for high throughput rRNA analysis.}, journal = {Nucleic acids research}, volume = {42}, number = {Database issue}, pages = {D633-42}, pmid = {24288368}, issn = {1362-4962}, support = {P42 ES004911/ES/NIEHS NIH HHS/United States ; UH3 DK083993/DK/NIDDK NIH HHS/United States ; U01 HL098961/HL/NHLBI NIH HHS/United States ; }, mesh = {Archaea/classification ; Bacteria/classification ; *Databases, Nucleic Acid ; Fungi/classification ; Genes, Archaeal ; Genes, Bacterial ; Genes, Fungal ; *Genes, Microbial ; *Genes, rRNA ; *High-Throughput Nucleotide Sequencing ; Internet ; Oligonucleotide Probes ; Sequence Alignment ; Software ; }, abstract = {Ribosomal Database Project (RDP; http://rdp.cme.msu.edu/) provides the research community with aligned and annotated rRNA gene sequence data, along with tools to allow researchers to analyze their own rRNA gene sequences in the RDP framework. RDP data and tools are utilized in fields as diverse as human health, microbial ecology, environmental microbiology, nucleic acid chemistry, taxonomy and phylogenetics. In addition to aligned and annotated collections of bacterial and archaeal small subunit rRNA genes, RDP now includes a collection of fungal large subunit rRNA genes. RDP tools, including Classifier and Aligner, have been updated to work with this new fungal collection. The use of high-throughput sequencing to characterize environmental microbial populations has exploded in the past several years, and as sequence technologies have improved, the sizes of environmental datasets have increased. With release 11, RDP is providing an expanded set of tools to facilitate analysis of high-throughput data, including both single-stranded and paired-end reads. In addition, most tools are now available as open source packages for download and local use by researchers with high-volume needs or who would like to develop custom analysis pipelines.}, } @article {pmid24285751, year = {2014}, author = {Nakamura, Y and Afendi, FM and Parvin, AK and Ono, N and Tanaka, K and Hirai Morita, A and Sato, T and Sugiura, T and Altaf-Ul-Amin, M and Kanaya, S}, title = {KNApSAcK Metabolite Activity Database for retrieving the relationships between metabolites and biological activities.}, journal = {Plant & cell physiology}, volume = {55}, number = {1}, pages = {e7}, doi = {10.1093/pcp/pct176}, pmid = {24285751}, issn = {1471-9053}, mesh = {*Biological Phenomena ; Cluster Analysis ; *Databases as Topic ; Humans ; *Metabolome ; Statistics as Topic ; }, abstract = {Databases (DBs) are required by various omics fields because the volume of molecular biology data is increasing rapidly. In this study, we provide instructions for users and describe the current status of our metabolite activity DB. To facilitate a comprehensive understanding of the interactions between the metabolites of organisms and the chemical-level contribution of metabolites to human health, we constructed a metabolite activity DB known as the KNApSAcK Metabolite Activity DB. It comprises 9,584 triplet relationships (metabolite-biological activity-target species), including 2,356 metabolites, 140 activity categories, 2,963 specific descriptions of biological activities and 778 target species. Approximately 46% of the activities described in the DB are related to chemical ecology, most of which are attributed to antimicrobial agents and plant growth regulators. The majority of the metabolites with antimicrobial activities are flavonoids and phenylpropanoids. The metabolites with plant growth regulatory effects include plant hormones. Over half of the DB contents are related to human health care and medicine. The five largest groups are toxins, anticancer agents, nervous system agents, cardiovascular agents and non-therapeutic agents, such as flavors and fragrances. The KNApSAcK Metabolite Activity DB is integrated within the KNApSAcK Family DBs to facilitate further systematized research in various omics fields, especially metabolomics, nutrigenomics and foodomics. The KNApSAcK Metabolite Activity DB could also be utilized for developing novel drugs and materials, as well as for identifying viable drug resources and other useful compounds.}, } @article {pmid24284892, year = {2014}, author = {Cazelles, B and Cazelles, K and Chavez, M}, title = {Wavelet analysis in ecology and epidemiology: impact of statistical tests.}, journal = {Journal of the Royal Society, Interface}, volume = {11}, number = {91}, pages = {20130585}, pmid = {24284892}, issn = {1742-5662}, mesh = {Algorithms ; Data Interpretation, Statistical ; Dengue/epidemiology ; *Ecology ; *Epidemiology ; Fourier Analysis ; Humans ; Markov Chains ; Models, Statistical ; Normal Distribution ; Thailand/epidemiology ; Time Factors ; *Wavelet Analysis ; }, abstract = {Wavelet analysis is now frequently used to extract information from ecological and epidemiological time series. Statistical hypothesis tests are conducted on associated wavelet quantities to assess the likelihood that they are due to a random process. Such random processes represent null models and are generally based on synthetic data that share some statistical characteristics with the original time series. This allows the comparison of null statistics with those obtained from original time series. When creating synthetic datasets, different techniques of resampling result in different characteristics shared by the synthetic time series. Therefore, it becomes crucial to consider the impact of the resampling method on the results. We have addressed this point by comparing seven different statistical testing methods applied with different real and simulated data. Our results show that statistical assessment of periodic patterns is strongly affected by the choice of the resampling method, so two different resampling techniques could lead to two different conclusions about the same time series. Moreover, our results clearly show the inadequacy of resampling series generated by white noise and red noise that are nevertheless the methods currently used in the wide majority of wavelets applications. Our results highlight that the characteristics of a time series, namely its Fourier spectrum and autocorrelation, are important to consider when choosing the resampling technique. Results suggest that data-driven resampling methods should be used such as the hidden Markov model algorithm and the 'beta-surrogate' method.}, } @article {pmid24284397, year = {2013}, author = {McLean, RJ and Kakirde, KS}, title = {Enhancing metagenomics investigations of microbial interactions with biofilm technology.}, journal = {International journal of molecular sciences}, volume = {14}, number = {11}, pages = {22246-22257}, pmid = {24284397}, issn = {1422-0067}, mesh = {Biofilms/*growth & development ; Computational Biology ; Ecology ; Environment ; *Metagenomics ; *Microbial Interactions ; }, abstract = {Investigations of microbial ecology and diversity have been greatly enhanced by the application of culture-independent techniques. One such approach, metagenomics, involves sample collections from soil, water, and other environments. Extracted nucleic acids from bulk environmental samples are sequenced and analyzed, which allows microbial interactions to be inferred on the basis of bioinformatics calculations. In most environments, microbial interactions occur predominately in surface-adherent, biofilm communities. In this review, we address metagenomics sampling and biofilm biology, and propose an experimental strategy whereby the resolving power of metagenomics can be enhanced by incorporating a biofilm-enrichment step during sample acquisition.}, } @article {pmid24283800, year = {2015}, author = {van der Linde, BW and van Netten, JJ and Otten, E and Postema, K and Geuze, RH and Schoemaker, MM}, title = {A systematic review of instruments for assessment of capacity in activities of daily living in children with developmental co-ordination disorder.}, journal = {Child: care, health and development}, volume = {41}, number = {1}, pages = {23-34}, doi = {10.1111/cch.12124}, pmid = {24283800}, issn = {1365-2214}, mesh = {*Activities of Daily Living ; Adolescent ; Child ; Child, Preschool ; Databases, Bibliographic ; *Disability Evaluation ; Humans ; Infant ; Motor Skills Disorders/diagnosis/*physiopathology ; Psychometrics/*instrumentation ; *Severity of Illness Index ; Young Adult ; }, abstract = {Children with developmental co-ordination disorder (DCD) face evident motor difficulties in activities of daily living (ADL). Assessment of their capacity in ADL is essential for diagnosis and intervention, in order to limit the daily consequences of the disorder. The aim of this study is to systematically review potential instruments for standardized and objective assessment of children's capacity in ADL, suited for children with DCD. As a first step, databases of MEDLINE, EMBASE, CINAHL and PsycINFO were searched to identify studies that described instruments with potential for assessment of capacity in ADL. Second, instruments were included for review when two independent reviewers agreed that the instruments (1) are standardized and objective; (2) assess at activity level and comprise items that reflect ADL; and (3) are applicable to school-aged children that can move independently. Out of 1507 publications, 66 publications were selected, describing 39 instruments. Seven of these instruments were found to fulfil the criteria and were included for review: the Bruininks-Oseretsky Test of Motor Performance-2 (BOT2); the Do-Eat (Do-Eat); the Movement Assessment Battery for Children-2 (MABC2); the school-Assessment of Motor and Process Skills (schoolAMPS); the Tuffts Assessment of Motor Performance (TAMP); the Test of Gross Motor Development (TGMD); and the Functional Independence Measure for Children (WeeFIM). As a third step, for the included instruments, suitability for children with DCD was discussed based on the ADL comprised, ecological validity and other psychometric properties. We concluded that current instruments do not provide comprehensive and ecologically valid assessment of capacity in ADL as required for children with DCD.}, } @article {pmid24281676, year = {2014}, author = {Cakmak, D and Perovic, V and Saljnikov, E and Jaramaz, D and Sikiric, B}, title = {Spatial modeling of ecological areas by fitting the limiting factors for As in the vicinity of mine, Serbia.}, journal = {Environmental science and pollution research international}, volume = {21}, number = {5}, pages = {3764-3773}, pmid = {24281676}, issn = {1614-7499}, mesh = {Agriculture ; Antimony ; Arsenic/*analysis ; Ecosystem ; Environmental Monitoring/statistics & numerical data ; Geographic Information Systems ; Mining ; *Models, Theoretical ; Serbia ; Soil Pollutants/*analysis ; Spatial Analysis ; }, abstract = {Elevated arsenic (As) concentrations in soil are often found in the vicinity of certain mineral deposits that have been, or are currently, under exploitation, regardless of the target resource. Detailed study of such areas for safe agriculture requires considerable financial costs and long periods of time. Application of an appropriate spatial model that describes the behavior of arsenic in soil and plants can significantly ease the whole investigation process. This paper presents a model of ecological security of an area that, in the past, was an antimony mine and has a naturally high content of arsenic. For simulation and modeling the geographic information science (GIS) technology with the inserted predictors influencing the accessibility of As and its content in plants was used. The results obtained were the following: (1) a categorization of contaminated soils according to soil properties was developed; (2) the proposed methodology allows focusing on particular suspect area saving an energy and human resource input; and (3) new safe areas for growing crops in contaminated area were modeled. The application of the proposed model of As solubility to various crops grown around a former antimony mine near the village of Lisa, southwest Serbia showed that significant expansion of the areas suitable for growing potato, raspberry, and pasture was possible.}, } @article {pmid24278356, year = {2013}, author = {Clavel, J and Poulet, N and Porcher, E and Blanchet, S and Grenouillet, G and Pavoine, S and Biton, A and Seon-Massin, N and Argillier, C and Daufresne, M and Teillac-Deschamps, P and Julliard, R}, title = {A new freshwater biodiversity indicator based on fish community assemblages.}, journal = {PloS one}, volume = {8}, number = {11}, pages = {e80968}, pmid = {24278356}, issn = {1932-6203}, mesh = {Animals ; *Biodiversity ; Databases, Factual ; Datasets as Topic ; Ecosystem ; *Fishes ; France ; *Fresh Water ; Humans ; Spatio-Temporal Analysis ; }, abstract = {Biodiversity has reached a critical state. In this context, stakeholders need indicators that both provide a synthetic view of the state of biodiversity and can be used as communication tools. Using river fishes as model, we developed community indicators that aim at integrating various components of biodiversity including interactions between species and ultimately the processes influencing ecosystem functions. We developed indices at the species level based on (i) the concept of specialization directly linked to the niche theory and (ii) the concept of originality measuring the overall degree of differences between a species and all other species in the same clade. Five major types of originality indices, based on phylogeny, habitat-linked and diet-linked morphology, life history traits, and ecological niche were analyzed. In a second step, we tested the relationship between all biodiversity indices and land use as a proxy of human pressures. Fish communities showed no significant temporal trend for most of these indices, but both originality indices based on diet- and habitat- linked morphology showed a significant increase through time. From a spatial point of view, all indices clearly singled out Corsica Island as having higher average originality and specialization. Finally, we observed that the originality index based on niche traits might be used as an informative biodiversity indicator because we showed it is sensitive to different land use classes along a landscape artificialization gradient. Moreover, its response remained unchanged over two other land use classifications at the global scale and also at the regional scale.}, } @article {pmid24275610, year = {2014}, author = {Jones, RA}, title = {Trends in plant virus epidemiology: opportunities from new or improved technologies.}, journal = {Virus research}, volume = {186}, number = {}, pages = {3-19}, doi = {10.1016/j.virusres.2013.11.003}, pmid = {24275610}, issn = {1872-7492}, mesh = {Agriculture ; Aviation ; Crops, Agricultural/*virology ; Information Systems/statistics & numerical data ; Molecular Epidemiology/instrumentation/methods/*trends ; Molecular Typing ; Plant Diseases/*prevention & control/virology ; Plant Viruses/*genetics/growth & development/isolation & purification ; Plants/*virology ; Remote Sensing Technology/statistics & numerical data ; Spatio-Temporal Analysis ; }, abstract = {This review focuses on new or improved technologies currently being applied, or likely to be applied in the future, to worldwide research on plant virus epidemiology. Recent technological advances and innovations provide many opportunities to improve understanding of the way diverse types of plant virus epidemics develop and how to manage them. The review starts at the macro level by considering how recent innovations in remote sensing and precision agriculture can provide valuable information about (i) virus epidemics occurring at continental, regional or district scales (via satellites) and within individual crops (mostly via lightweight unmanned aerial vehicles), and (ii) exactly where to target control measures. It then considers recent improvements in information systems and innovations in modelling that improve (i) understanding of virus epidemics and ability to predict them, and (ii) delivery to end-users of critical advice on control measures, such as Internet-based Decision Support Systems. The review goes on to discuss how advances in analysis of spatiotemporal virus spread patterns within crops can help to enhance understanding of how virus epidemics develop and validate potentially useful virus control measures. At the micro level, the review then considers the many insights that advances in molecular epidemiology can provide about genetic variation within plant virus populations involved in epidemics, and how this variation drives what occurs at the macro level. Next, it describes how recent innovations in virus detection technologies are providing many opportunities to collect and analyse new types, and ever increasing amounts, of data about virus epidemics, and the genetic variability of the virus populations involved. Finally, the implications for plant virus epidemiology of technologies likely to be important in the future are considered. To address looming world food insecurity and threats to plant biodiversity resulting from climate change and rapid population growth, it is important that new and improved technologies that help understand and control epidemics of damaging plant viruses are adopted as smoothly and speedily as possible.}, } @article {pmid24269880, year = {2013}, author = {Cevenini, E and Cotichini, R and Stazi, MA and Toccaceli, V and Scurti, M and Mari, V and Berardelli, M and Passarino, G and Jeune, B and Franceschi, C and , }, title = {How to classify the oldest old according to their health status: a study on 1160 subjects belonging to 552 90+ Italian sib-ships characterized by familial longevity recruited within the GEHA EU Project.}, journal = {Mechanisms of ageing and development}, volume = {134}, number = {11-12}, pages = {560-569}, doi = {10.1016/j.mad.2013.11.001}, pmid = {24269880}, issn = {1872-6216}, support = {BB/C008200/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {*Aged, 80 and over ; Databases, Factual ; *Family Health ; Female ; Geography ; *Health Status ; Humans ; Italy ; Longevity ; Male ; Phenotype ; Risk ; Sex Factors ; *Siblings ; }, abstract = {The health status of the oldest old, the fastest increasing population segment worldwide, progressively becomes more heterogeneous, and this peculiarity represents a major obstacle to their classification. We compared the effectiveness of four previously proposed criteria (Franceschi et al., 2000; Evert et al., 2003; Gondo et al., 2006; Andersen-Ranberg et al., 2001) in 1160 phenotypically fully characterized Italian siblings of 90 years of age and older (90+, mean age: 93 years; age range: 90-106 years) belonging to 552 sib-ships, recruited in Northern, Central and Southern Italy within the EU-funded project GEHA, followed for a six-year-survival. Main findings were: (i) "healthy" subjects varied within a large range, i.e. 5.2% (Gondo), 8.7% (Evert), 17.7% (Franceschi), and 28.5% (Andersen-Ranberg); (ii) Central Italy subjects showed better health than those from Northern and Southern Italy; (iii) mortality risk was correlated with health status independently of geographical areas; and (iv) 90+ males, although fewer in number, were healthier than females, but with no survival advantage. In conclusion, we identified a modified version of Andersen-Ranberg criteria, based on the concomitant assessment of two basic domains (cognitive, SMMSE; physical, ADL), called "Simple Model of Functional Status" (SMFS), as the most effective proxy to distinguish healthy from not-healthy subjects. This model showed that health status was correlated within sib-ships, suggesting a familial/genetic component.}, } @article {pmid24260395, year = {2013}, author = {Yang, L and Ding, G and Lin, H and Cheng, H and Kong, Y and Wei, Y and Fang, X and Liu, R and Wang, L and Chen, X and Yang, C}, title = {Transcriptome analysis of medicinal plant Salvia miltiorrhiza and identification of genes related to tanshinone biosynthesis.}, journal = {PloS one}, volume = {8}, number = {11}, pages = {e80464}, pmid = {24260395}, issn = {1932-6203}, mesh = {Abietanes/*biosynthesis ; Alkyl and Aryl Transferases/metabolism ; Biosynthetic Pathways ; Computational Biology/methods ; Cytochrome P-450 Enzyme System/genetics ; Gene Expression Profiling ; Gene Expression Regulation, Plant ; High-Throughput Nucleotide Sequencing ; Molecular Sequence Data ; Phylogeny ; Plant Leaves/genetics/metabolism ; Plant Roots/genetics/metabolism ; Plants, Medicinal/*genetics/*metabolism ; Salvia miltiorrhiza/classification/*genetics/*metabolism ; Terpenes/metabolism ; Transcription Factors/metabolism ; *Transcriptome ; }, abstract = {Salvia miltiorrhiza Bunge, a perennial plant of Lamiaceae, accumulates abietane-type diterpenoids of tanshinones in root, which have been used as traditional Chinese medicine to treat neuroasthenic insomnia and cardiovascular diseases. However, to date the biosynthetic pathway of tanshinones is only partially elucidated and the mechanism for their root-specific accumulation remains unknown. To identify enzymes and transcriptional regulators involved in the biosynthesis of tanshinones, we conducted transcriptome profiling of S. miltiorrhiza root and leaf tissues using the 454 GS-FLX pyrosequencing platform, which generated 550,546 and 525,292 reads, respectively. RNA sequencing reads were assembled and clustered into 64,139 unigenes (29,883 isotigs and 34,256 singletons). NCBI non-redundant protein databases (NR) and Swiss-Prot database searches anchored 32,096 unigenes (50%) with functional annotations based on sequence similarities. Further assignments with Gene Ontology (GO) terms and KEGG biochemical pathways identified 168 unigenes referring to the terpenoid backbone biosynthesis (including 144 MEP and MVA pathway genes and 24 terpene synthases). Comparative analysis of the transcriptomes identified 2,863 unigenes that were highly expressed in roots, including those encoding enzymes of early steps of tanshinone biosynthetic pathway, such as copalyl diphosphate synthase (SmCPS), kaurene synthase-like (SmKSL) and CYP76AH1. Other differentially expressed unigenes predicted to be related to tanshinone biosynthesis fall into cytochrome P450 monooxygenases, dehydrogenases and reductases, as well as regulatory factors. In addition, 21 P450 genes were selectively confirmed by real-time PCR. Thus we have generated a large unigene dataset which provides a valuable resource for further investigation of the radix development and biosynthesis of tanshinones.}, } @article {pmid24259686, year = {2014}, author = {Price, CA and Munro, PR and Weitz, JS}, title = {Estimates of leaf vein density are scale dependent.}, journal = {Plant physiology}, volume = {164}, number = {1}, pages = {173-180}, pmid = {24259686}, issn = {1532-2548}, mesh = {Apocynaceae/anatomy & histology ; Image Interpretation, Computer-Assisted/*methods ; Plant Leaves/*anatomy & histology ; Rosales/anatomy & histology ; Wisteria/anatomy & histology ; }, abstract = {Leaf vein density (LVD) has garnered considerable attention of late, with numerous studies linking it to the physiology, ecology, and evolution of land plants. Despite this increased attention, little consideration has been given to the effects of measurement methods on estimation of LVD. Here, we focus on the relationship between measurement methods and estimates of LVD. We examine the dependence of LVD on magnification, field of view (FOV), and image resolution. We first show that estimates of LVD increase with increasing image magnification and resolution. We then demonstrate that estimates of LVD are higher with higher variance at small FOV, approaching asymptotic values as the FOV increases. We demonstrate that these effects arise due to three primary factors: (1) the tradeoff between FOV and magnification; (2) geometric effects of lattices at small scales; and; (3) the hierarchical nature of leaf vein networks. Our results help to explain differences in previously published studies and highlight the importance of using consistent magnification and scale, when possible, when comparing LVD and other quantitative measures of venation structure across leaves.}, } @article {pmid24259313, year = {2013}, author = {Wisecaver, JH and Brosnahan, ML and Hackett, JD}, title = {Horizontal gene transfer is a significant driver of gene innovation in dinoflagellates.}, journal = {Genome biology and evolution}, volume = {5}, number = {12}, pages = {2368-2381}, pmid = {24259313}, issn = {1759-6653}, mesh = {Cells, Cultured ; Databases, Nucleic Acid ; Dinoflagellida/*genetics/metabolism ; Evolution, Molecular ; Gene Deletion ; *Gene Transfer, Horizontal ; Genetic Variation ; Genome, Protozoan/genetics ; Isocitrate Dehydrogenase/genetics ; Ketone Oxidoreductases/genetics ; Mitochondria/*genetics/metabolism ; Molecular Sequence Data ; NADH Dehydrogenase/genetics ; Oxidative Phosphorylation ; Pentose Phosphate Pathway/genetics ; Phylogeny ; Sequence Analysis, DNA ; Transcriptome/genetics ; }, abstract = {The dinoflagellates are an evolutionarily and ecologically important group of microbial eukaryotes. Previous work suggests that horizontal gene transfer (HGT) is an important source of gene innovation in these organisms. However, dinoflagellate genomes are notoriously large and complex, making genomic investigation of this phenomenon impractical with currently available sequencing technology. Fortunately, de novo transcriptome sequencing and assembly provides an alternative approach for investigating HGT. We sequenced the transcriptome of the dinoflagellate Alexandrium tamarense Group IV to investigate how HGT has contributed to gene innovation in this group. Our comprehensive A. tamarense Group IV gene set was compared with those of 16 other eukaryotic genomes. Ancestral gene content reconstruction of ortholog groups shows that A. tamarense Group IV has the largest number of gene families gained (314-1,563 depending on inference method) relative to all other organisms in the analysis (0-782). Phylogenomic analysis indicates that genes horizontally acquired from bacteria are a significant proportion of this gene influx, as are genes transferred from other eukaryotes either through HGT or endosymbiosis. The dinoflagellates also display curious cases of gene loss associated with mitochondrial metabolism including the entire Complex I of oxidative phosphorylation. Some of these missing genes have been functionally replaced by bacterial and eukaryotic xenologs. The transcriptome of A. tamarense Group IV lends strong support to a growing body of evidence that dinoflagellate genomes are extraordinarily impacted by HGT.}, } @article {pmid24259310, year = {2013}, author = {Hernández-López, A and Chabrol, O and Royer-Carenzi, M and Merhej, V and Pontarotti, P and Raoult, D}, title = {To tree or not to tree? Genome-wide quantification of recombination and reticulate evolution during the diversification of strict intracellular bacteria.}, journal = {Genome biology and evolution}, volume = {5}, number = {12}, pages = {2305-2317}, pmid = {24259310}, issn = {1759-6653}, mesh = {Base Sequence ; Computational Biology/methods ; Databases, Nucleic Acid ; *Evolution, Molecular ; Gene Regulatory Networks/*genetics ; Gene Transfer, Horizontal/*genetics ; Genetic Speciation ; Genetic Variation ; Genome, Bacterial/genetics ; Phylogeny ; Proteome/genetics ; Recombination, Genetic ; Rickettsia/*classification/*genetics ; Sequence Alignment ; }, abstract = {It is well known that horizontal gene transfer (HGT) is a major force in the evolution of prokaryotes. During the adaptation of a bacterial population to a new ecological niche, and particularly for intracellular bacteria, selective pressures are shifted and ecological niches reduced, resulting in a lower rate of genetic connectivity. HGT and positive selection are therefore two important evolutionary forces in microbial pathogens that drive adaptation to new hosts. In this study, we use genomic distance analyses, phylogenomic networks, tree topology comparisons, and Bayesian inference methods to investigate to what extent HGT has occurred during the evolution of the genus Rickettsia, the effect of the use of different genomic regions in estimating reticulate evolution and HGT events, and the link of these to host range. We show that ecological specialization restricts recombination occurrence in Rickettsia, but other evolutionary processes and genome architecture are also important for the occurrence of HGT. We found that recombination, genomic rearrangements, and genome conservation all show evidence of network-like evolution at whole-genome scale. We show that reticulation occurred mainly, but not only, during the early Rickettsia radiation, and that core proteome genes of every major functional category have experienced reticulated evolution and possibly HGT. Overall, the evolution of Rickettsia bacteria has been tree-like, with evidence of HGT and reticulated evolution for around 10-25% of the core Rickettsia genome. We present evidence of extensive recombination/incomplete lineage sorting (ILS) during the radiation of the genus, probably linked with the emergence of intracellularity in a wide range of hosts.}, } @article {pmid24256552, year = {2014}, author = {Laurent, J and Venn, A and Tambutté, É and Ganot, P and Allemand, D and Tambutté, S}, title = {Regulation of intracellular pH in cnidarians: response to acidosis in Anemonia viridis.}, journal = {The FEBS journal}, volume = {281}, number = {3}, pages = {683-695}, doi = {10.1111/febs.12614}, pmid = {24256552}, issn = {1742-4658}, mesh = {Acid-Base Equilibrium ; *Allostasis ; Alveolata/*physiology ; Amino Acid Sequence ; Animals ; Cation Transport Proteins/chemistry/*metabolism ; Databases, Protein ; Hydrogen-Ion Concentration ; Intracellular Fluid/metabolism ; Ion Transport ; Mediterranean Sea ; *Models, Biological ; Phylogeny ; Protein Isoforms/chemistry/metabolism ; Salinity ; Sea Anemones/parasitology/*physiology ; Sequence Alignment ; Sodium-Hydrogen Exchangers/chemistry/*metabolism ; *Symbiosis ; }, abstract = {The regulation of intracellular pH (pHi) is a fundamental aspect of cell physiology that has received little attention in studies of the phylum Cnidaria, which includes ecologically important sea anemones and reef-building corals. Like all organisms, cnidarians must maintain pH homeostasis to counterbalance reductions in pHi, which can arise because of changes in either intrinsic or extrinsic parameters. Corals and sea anemones face natural daily changes in internal fluids, where the extracellular pH can range from 8.9 during the day to 7.4 at night. Furthermore, cnidarians are likely to experience future CO2-driven declines in seawater pH, a process known as ocean acidification. Here, we carried out the first mechanistic investigation to determine how cnidarian pHi regulation responds to decreases in extracellular and intracellular pH. Using the anemone Anemonia viridis, we employed confocal live cell imaging and a pH-sensitive dye to track the dynamics of pHi after intracellular acidosis induced by acute exposure to decreases in seawater pH and NH4Cl prepulses. The investigation was conducted on cells that contained intracellular symbiotic algae (Symbiodinium sp.) and on symbiont-free endoderm cells. Experiments using inhibitors and Na[+]-free seawater indicate a potential role of Na[+]/H[+] plasma membrane exchangers (NHEs) in mediating pHi recovery following intracellular acidosis in both cell types. We also measured the buffering capacity of cells, and obtained values between 20.8 and 43.8 mM per pH unit, which are comparable to those in other invertebrates. Our findings provide the first steps towards a better understanding of acid-base regulation in these basal metazoans, for which information on cell physiology is extremely limited.}, } @article {pmid24256179, year = {2014}, author = {Canales, J and Bautista, R and Label, P and Gómez-Maldonado, J and Lesur, I and Fernández-Pozo, N and Rueda-López, M and Guerrero-Fernández, D and Castro-Rodríguez, V and Benzekri, H and Cañas, RA and Guevara, MA and Rodrigues, A and Seoane, P and Teyssier, C and Morel, A and Ehrenmann, F and Le Provost, G and Lalanne, C and Noirot, C and Klopp, C and Reymond, I and García-Gutiérrez, A and Trontin, JF and Lelu-Walter, MA and Miguel, C and Cervera, MT and Cantón, FR and Plomion, C and Harvengt, L and Avila, C and Gonzalo Claros, M and Cánovas, FM}, title = {De novo assembly of maritime pine transcriptome: implications for forest breeding and biotechnology.}, journal = {Plant biotechnology journal}, volume = {12}, number = {3}, pages = {286-299}, doi = {10.1111/pbi.12136}, pmid = {24256179}, issn = {1467-7652}, mesh = {*Biotechnology ; Breeding ; DNA, Complementary/genetics ; Databases, Genetic ; Genome Size ; Genome, Plant/*genetics ; Genotype ; High-Throughput Nucleotide Sequencing/*methods ; Microsatellite Repeats/genetics ; Molecular Sequence Annotation ; Multigene Family ; Pinus/*genetics ; *Polymorphism, Single Nucleotide ; RNA, Plant/genetics ; Sequence Analysis, DNA ; Transcription Factors/genetics ; *Transcriptome ; Trees ; }, abstract = {Maritime pine (Pinus pinasterAit.) is a widely distributed conifer species in Southwestern Europe and one of the most advanced models for conifer research. In the current work, comprehensive characterization of the maritime pine transcriptome was performed using a combination of two different next-generation sequencing platforms, 454 and Illumina. De novo assembly of the transcriptome provided a catalogue of 26 020 unique transcripts in maritime pine trees and a collection of 9641 full-length cDNAs. Quality of the transcriptome assembly was validated by RT-PCR amplification of selected transcripts for structural and regulatory genes. Transcription factors and enzyme-encoding transcripts were annotated. Furthermore, the available sequencing data permitted the identification of polymorphisms and the establishment of robust single nucleotide polymorphism (SNP) and simple-sequence repeat (SSR) databases for genotyping applications and integration of translational genomics in maritime pine breeding programmes. All our data are freely available at SustainpineDB, the P. pinaster expressional database. Results reported here on the maritime pine transcriptome represent a valuable resource for future basic and applied studies on this ecological and economically important pine species.}, } @article {pmid24253663, year = {2014}, author = {Bibby, K}, title = {Improved bacteriophage genome data is necessary for integrating viral and bacterial ecology.}, journal = {Microbial ecology}, volume = {67}, number = {2}, pages = {242-244}, pmid = {24253663}, issn = {1432-184X}, mesh = {Bacteriophages/*genetics ; Databases, Factual ; Ecology ; *Genome, Bacterial ; *Genome, Viral ; Sequence Analysis, DNA ; }, abstract = {The recent rise in "omics"-enabled approaches has lead to improved understanding in many areas of microbial ecology. However, despite the importance that viruses play in a broad microbial ecology context, viral ecology remains largely not integrated into high-throughput microbial ecology studies. A fundamental hindrance to the integration of viral ecology into omics-enabled microbial ecology studies is the lack of suitable reference bacteriophage genomes in reference databases-currently, only 0.001% of bacteriophage diversity is represented in genome sequence databases. This commentary serves to highlight this issue and to promote bacteriophage genome sequencing as a valuable scientific undertaking to both better understand bacteriophage diversity and move towards a more holistic view of microbial ecology.}, } @article {pmid24250829, year = {2013}, author = {Li, C and Jiang, Z and Fang, H and Li, C}, title = {A spatially explicit model of functional connectivity for the endangered Przewalski's gazelle (Procapra przewalskii) in a patchy landscape.}, journal = {PloS one}, volume = {8}, number = {11}, pages = {e80065}, pmid = {24250829}, issn = {1932-6203}, mesh = {Animals ; *Antelopes ; Biodiversity ; *Conservation of Natural Resources ; Ecosystem ; *Endangered Species ; *Geographic Information Systems ; Humans ; Inbreeding ; }, abstract = {BACKGROUND: Habitat fragmentation, associated with human population expansion, impedes dispersal, reduces gene flow and aggravates inbreeding in species on the brink of extinction. Both scientific and conservation communities increasingly realize that maintaining and restoring landscape connectivity is of vital importance in biodiversity conservation. Prior to any conservation initiatives, it is helpful to present conservation practitioners with a spatially explicit model of functional connectivity for the target species or landscape.

Using Przewalski's gazelle (Procapra przewalskii) as a model of endangered ungulate species in highly fragmented landscape, we present a model providing spatially explicit information to inform the long-term preservation of well-connected metapopulations. We employed a Geographic Information System (GIS) and expert-literature method to create a habitat suitability map, to identify potential habitats and to delineate a functional connectivity network (least-cost movement corridors and paths) for the gazelle. Results indicated that there were limited suitable habitats for the gazelle, mainly found to the north and northwest of the Qinghai Lake where four of five potential habitat patches were identified. Fifteen pairs of least-cost corridors and paths were mapped connecting eleven extant populations and two neighboring potential patches. The least-cost paths ranged from 0.2 km to 26.8 km in length (averaging 12.4 km) and were all longer than corresponding Euclidean distances.

CONCLUSIONS/SIGNIFICANCE: The model outputs were validated and supported by the latest findings in landscape genetics of the species, and may provide impetus for connectivity conservation programs. Dispersal barriers were examined and appropriate mitigation strategies were suggested. This study provides conservation practitioners with thorough and visualized information to reserve the landscape connectivity for Przewalski's gazelle. In a general sense, we proposed a heuristic framework for species with similar biological and ecological characteristics.}, } @article {pmid24248343, year = {2013}, author = {Tedstone, AJ and Nienow, PW and Sole, AJ and Mair, DW and Cowton, TR and Bartholomew, ID and King, MA}, title = {Greenland ice sheet motion insensitive to exceptional meltwater forcing.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {110}, number = {49}, pages = {19719-19724}, pmid = {24248343}, issn = {1091-6490}, mesh = {*Climate ; *Fresh Water ; Geographic Information Systems ; Greenland ; Hydrology ; Ice Cover/*chemistry ; *Water Movements ; }, abstract = {Changes to the dynamics of the Greenland ice sheet can be forced by various mechanisms including surface-melt-induced ice acceleration and oceanic forcing of marine-terminating glaciers. We use observations of ice motion to examine the surface melt-induced dynamic response of a land-terminating outlet glacier in southwest Greenland to the exceptional melting observed in 2012. During summer, meltwater generated on the Greenland ice sheet surface accesses the ice sheet bed, lubricating basal motion and resulting in periods of faster ice flow. However, the net impact of varying meltwater volumes upon seasonal and annual ice flow, and thus sea level rise, remains unclear. We show that two extreme melt events (98.6% of the Greenland ice sheet surface experienced melting on July 12, the most significant melt event since 1889, and 79.2% on July 29) and summer ice sheet runoff ~3.9 σ above the 1958-2011 mean resulted in enhanced summer ice motion relative to the average melt year of 2009. However, despite record summer melting, subsequent reduced winter ice motion resulted in 6% less net annual ice motion in 2012 than in 2009. Our findings suggest that surface melt-induced acceleration of land-terminating regions of the ice sheet will remain insignificant even under extreme melting scenarios.}, } @article {pmid24246945, year = {2014}, author = {Sobanska, MA and Cesnaitis, R and Sobanski, T and Versonnen, B and Bonnomet, V and Tarazona, JV and De Coen, W}, title = {Analysis of the ecotoxicity data submitted within the framework of the REACH Regulation. Part 1. General overview and data availability for the first registration deadline.}, journal = {The Science of the total environment}, volume = {470-471}, number = {}, pages = {1225-1232}, doi = {10.1016/j.scitotenv.2013.10.074}, pmid = {24246945}, issn = {1879-1026}, mesh = {*Databases, Chemical ; Ecotoxicology ; *Environmental Policy ; Environmental Pollution/*legislation & jurisprudence ; Hazardous Substances/*toxicity ; Toxicity Tests ; }, abstract = {REACH(1) entered into force in June 2007 and has hence been operational for six years. With the first registration deadline in November 2010, the European Chemicals Agency (ECHA(2)) has received a large amount of scientific and administrative information related to chemical substances. In order to understand what type of data on ecotoxicity endpoints was submitted under the REACH framework a detailed analysis of the availability and content of relevant information was performed. To avoid unnecessary testing, the REACH Regulation provides registrants with the possibility to build testing strategies and to adopt the standard information requirements based on the specific conditions listed in the regulation. The types of information submitted by registrants to fulfil data requirements for aquatic, sediment and terrestrial toxicity endpoints were analysed. The REACH database analysis confirms large differences in the availability of experimental aquatic versus sediment and soil ecotoxicity data. Information requirements on aquatic organisms are mainly covered by experimental data, while those for sediment and soil are mostly waived.}, } @article {pmid24246193, year = {2014}, author = {Pramanik, S and Roy, K}, title = {Exploring QSTR modeling and toxicophore mapping for identification of important molecular features contributing to the chemical toxicity in Escherichia coli.}, journal = {Toxicology in vitro : an international journal published in association with BIBRA}, volume = {28}, number = {2}, pages = {265-272}, doi = {10.1016/j.tiv.2013.11.002}, pmid = {24246193}, issn = {1879-3177}, mesh = {Algorithms ; Bacterial Toxins/*chemistry/toxicity ; Biodiversity ; Databases, Factual ; Escherichia coli/*chemistry ; Hydrophobic and Hydrophilic Interactions ; Imaging, Three-Dimensional ; Models, Biological ; Models, Chemical ; Models, Molecular ; Models, Statistical ; Models, Theoretical ; Quantitative Structure-Activity Relationship ; Reproducibility of Results ; Software ; }, abstract = {Biodiversity deprivation can affect functions and services of the ecosystem. Changes in biodiversity alter ecosystem processes and change the resilience of ecosystems to ecological changes. Bacterial communities are the main form of biomass in the ecosystem and one of largest populations on the planet. Bacterial communities provide important services to biodiversity. They break down pollutants, municipal waste and ingested food, and they are the primary route for recycling of organic matter to plants and other autotrophs, conversion of inorganic matter into new biological tissue using sunlight, management of energy crisis through use of biofuel. In the present study, computational chemistry and statistical modeling have been used to develop mathematical equations which can be applied to calculate toxicity of new/unknown chemicals/biofuels/metabolites in Escherichia coli. 2D and 3D descriptors were generated from molecular structure of compounds and mathematical models have been developed using genetic function approximation followed by multiple linear regression (GFA-MLR) method. Model validity was checked through defined internal (R(2)=0.751 and Q(2)=0.711), and external (Rpred(2)=0.773) statistical parameters. Molecular features responsible for toxicity were also assessed through 3D toxicophore study. The toxicophore-based model was validated (R=0.785) using qualitative statistical metrics and randomization test (Fischer validation).}, } @article {pmid24238386, year = {2013}, author = {Doll, HM and Armitage, DW and Daly, RA and Emerson, JB and Goltsman, DS and Yelton, AP and Kerekes, J and Firestone, MK and Potts, MD}, title = {Utilizing novel diversity estimators to quantify multiple dimensions of microbial biodiversity across domains.}, journal = {BMC microbiology}, volume = {13}, number = {}, pages = {259}, pmid = {24238386}, issn = {1471-2180}, mesh = {*Biota ; Computational Biology/methods ; Ecology/*methods ; }, abstract = {BACKGROUND: Microbial ecologists often employ methods from classical community ecology to analyze microbial community diversity. However, these methods have limitations because microbial communities differ from macro-organismal communities in key ways. This study sought to quantify microbial diversity using methods that are better suited for data spanning multiple domains of life and dimensions of diversity. Diversity profiles are one novel, promising way to analyze microbial datasets. Diversity profiles encompass many other indices, provide effective numbers of diversity (mathematical generalizations of previous indices that better convey the magnitude of differences in diversity), and can incorporate taxa similarity information. To explore whether these profiles change interpretations of microbial datasets, diversity profiles were calculated for four microbial datasets from different environments spanning all domains of life as well as viruses. Both similarity-based profiles that incorporated phylogenetic relatedness and naïve (not similarity-based) profiles were calculated. Simulated datasets were used to examine the robustness of diversity profiles to varying phylogenetic topology and community composition.

RESULTS: Diversity profiles provided insights into microbial datasets that were not detectable with classical univariate diversity metrics. For all datasets analyzed, there were key distinctions between calculations that incorporated phylogenetic diversity as a measure of taxa similarity and naïve calculations. The profiles also provided information about the effects of rare species on diversity calculations. Additionally, diversity profiles were used to examine thousands of simulated microbial communities, showing that similarity-based and naïve diversity profiles only agreed approximately 50% of the time in their classification of which sample was most diverse. This is a strong argument for incorporating similarity information and calculating diversity with a range of emphases on rare and abundant species when quantifying microbial community diversity.

CONCLUSIONS: For many datasets, diversity profiles provided a different view of microbial community diversity compared to analyses that did not take into account taxa similarity information, effective diversity, or multiple diversity metrics. These findings are a valuable contribution to data analysis methodology in microbial ecology.}, } @article {pmid25600166, year = {2013}, author = {Unertl, KM and Johnson, KB and Gadd, CS and Lorenzi, NM}, title = {Bridging organizational divides in health care: an ecological view of health information exchange.}, journal = {JMIR medical informatics}, volume = {1}, number = {1}, pages = {e3}, pmid = {25600166}, issn = {2291-9694}, support = {T15 LM007450/LM/NLM NIH HHS/United States ; }, abstract = {BACKGROUND: The fragmented nature of health care delivery in the United States leads to fragmented health information and impedes patient care continuity and safety. Technologies to support interorganizational health information exchange (HIE) are becoming more available. Understanding how HIE technology changes health care delivery and affects people and organizations is crucial to long-term successful implementation.

OBJECTIVE: Our study investigated the impacts of HIE technology on organizations, health care providers, and patients through a new, context-aware perspective, the Regional Health Information Ecology.

METHODS: We conducted more than 180 hours of direct observation, informal interviews during observation, and 9 formal semi-structured interviews. Data collection focused on workflow and information flow among health care team members and patients and on health care provider use of HIE technology.

RESULTS: We structured the data analysis around five primary information ecology components: system, locality, diversity, keystone species, and coevolution. Our study identified three main roles, or keystone species, involved in HIE: information consumers, information exchange facilitators, and information repositories. The HIE technology impacted patient care by allowing providers direct access to health information, reducing time to obtain health information, and increasing provider awareness of patient interactions with the health care system. Developing the infrastructure needed to support HIE technology also improved connections among information technology support groups at different health care organizations. Despite the potential of this type of technology to improve continuity of patient care, HIE technology adoption by health care providers was limited.

CONCLUSIONS: To successfully build a HIE network, organizations had to shift perspectives from an ownership view of health data to a continuity of care perspective. To successfully integrate external health information into clinical work practices, health care providers had to move toward understanding potential contributions of external health information. Our study provides a foundation for future context-aware development and implementation of HIE technology. Integrating concepts from the Regional Health Information Ecology into design and implementation may lead to wider diffusion and adoption of HIE technology into clinical work.}, } @article {pmid25145244, year = {2013}, author = {Hummel, HE and Langner, SS and Eisinger, MT}, title = {Pheromone dispensers, including organic polymer fibers, described in the crop protection literature: comparison of their innovation potential.}, journal = {Communications in agricultural and applied biological sciences}, volume = {78}, number = {2}, pages = {233-252}, pmid = {25145244}, issn = {1379-1176}, mesh = {Animals ; Crops, Agricultural/parasitology ; Databases, Factual ; Female ; Insect Control/instrumentation/*methods ; Insecta/*drug effects/physiology ; Male ; Pest Control, Biological/instrumentation/*methods ; Pheromones/*pharmacology ; Plant Diseases/parasitology/*prevention & control ; Sexual Behavior, Animal ; }, abstract = {Pheromone dispensers, although known in a variety of different designs, are one of the few remaining technical bottlenecks along the way to a sustainable pheromone based strategy in integrated pest management (IPM). Mating disruption with synthetic pheromones is a viable pest management approach. Suitable pheromone dispensers for these mating disruption schemes, however, are lagging behind the general availability of pheromones. Specifically, there is a need for matching the properties of the synthetic pheromones, the release rates suitable for certain insect species, and the environmental requirements of specific crop management. The "ideal" dispenser should release pheromones at a constant but pre-adjustable rate, should be mechanically applicable, completely biodegradable and thus save the costs for recovering spent dispensers. These should be made from renewable, cheap organic material, be economically inexpensive, and be toxicologically and eco-toxicologically inert to provide satisfactory solutions for the needs of practicing growers. In favourable cases, they will be economically competitive with conventional pesticide treatments and by far superior in terms of environmental and eco-toxicological suitability. In the course of the last 40 years, mating disruption, a non-toxicological approach, provided proof for its potential in dozens of pest insects of various orders and families. Applications for IPM in many countries of the industrialized and developing world have been reported. While some dispensers have reached wide circulation, only few of the key performing parameters fit the above requirements ideally and must be approximated with some sacrifice in performance. A fair comparison of the innovation potential of currently available pheromone dispensers is attempted. The authors advance here the use of innovative electrospun organic fibers with dimensions in the "meso" (high nano- to low micrometer) region. Due to their unique multitude of adjustable parameters, they hold considerable promise for future pest control against a variety of pest insects. In combination with well known synthetic sex pheromones, they can be used for communication disruption studies. One example, the pheromone of the European grape vine moth Lobesia botrana (Lepidoptera: Tortricidae), in combination with Ecoflex fibers, has been thoroughly tested in vineyards of Freiburg, Southwest Germany, with promising results. Seven weeks of communication disruption have been achieved, long enough to cover any one of several flights of this multivoltine grape pest. Disruption effects of around 95% have been achieved which are statistically indistinguishable from positive controls tested simultaneously with Isonet LE fibers, while an untreated negative control is significantly different. Ecoflex is a cheap organic co-polyester and completely biodegradable within half a year. Thus, an extra recovery step as with some other dispensers is unnecessary. This co-polyester is also of proven non-toxicity. The extension of the seven week disruption period towards half a year (the entire duration of all 3 Lobesia flights combined) is desirable and is under additional investigation in the near future. The discovery of suitable mesofibers is protected by European and US patents. The pheromone literature appearing between 1959 and today contains more than 25,000 references. This wealth of information is immediately applicable to pest management. It has major impacts on chemical ecology and IPM. In this paper, an attempt is made to compare the systems described in the literature and to derive some predictions about their prospective innovation potential. Special emphasis is given to the new development of organic biodegradable microfibers. To this end, a new electronic searching algorithm is introduced for reviewing the entries to be found in 4 specific databases. Its prominent features will be described. Surprisingly we found no previous entries in the literature linking pheromones with biodegradable organic polymer fibers whose diameters are in the dimension range of low micrometers and in the upper nanometer scale. In conclusion, the microfiber-pheromone combination must be considered as a novel approach whose virtues should be further explored for IPM in the near future.}, } @article {pmid26168460, year = {2012}, author = {Miller, G}, title = {The Smartphone Psychology Manifesto.}, journal = {Perspectives on psychological science : a journal of the Association for Psychological Science}, volume = {7}, number = {3}, pages = {221-237}, doi = {10.1177/1745691612441215}, pmid = {26168460}, issn = {1745-6916}, abstract = {By 2025, when most of today's psychology undergraduates will be in their mid-30s, more than 5 billion people on our planet will be using ultra-broadband, sensor-rich smartphones far beyond the abilities of today's iPhones, Androids, and Blackberries. Although smartphones were not designed for psychological research, they can collect vast amounts of ecologically valid data, easily and quickly, from large global samples. If participants download the right "psych apps," smartphones can record where they are, what they are doing, and what they can see and hear and can run interactive surveys, tests, and experiments through touch screens and wireless connections to nearby screens, headsets, biosensors, and other peripherals. This article reviews previous behavioral research using mobile electronic devices, outlines what smartphones can do now and will be able to do in the near future, explains how a smartphone study could work practically given current technology (e.g., in studying ovulatory cycle effects on women's sexuality), discusses some limitations and challenges of smartphone research, and compares smartphones to other research methods. Smartphone research will require new skills in app development and data analysis and will raise tough new ethical issues, but smartphones could transform psychology even more profoundly than PCs and brain imaging did.}, } @article {pmid24493986, year = {2010}, author = {Masic, I and Toromanovic, S}, title = {International public health.}, journal = {Materia socio-medica}, volume = {22}, number = {4}, pages = {229-231}, doi = {10.5455/msm.2010.22.229-231}, pmid = {24493986}, issn = {1512-7680}, abstract = {Public health is a broad field that touches several different medical disciplines such as epidemiology, public health informatics, health statistics, environmental protection (ecology), sociology, health promotion, disease prevention and organization of health care for nosological groups of the population. In Europe and the world today is developed a fairly extensive network of scientific and professional institutions engaged in research projects, studies, organization of scientific conferences and publishing scientific and professional articles from the field of public health. Their goal is to promote scientific advances in the field of public health through the exchange of experiences of public-health professionals, training, demonstration of appropriate research models, simulation and application in medical practice.}, } @article {pmid24237761, year = {2014}, author = {Liu, J and Yang, J and Bi, H and Zhang, P}, title = {Why mosaic? Gene expression profiling of African cassava mosaic virus-infected cassava reveals the effect of chlorophyll degradation on symptom development.}, journal = {Journal of integrative plant biology}, volume = {56}, number = {2}, pages = {122-132}, doi = {10.1111/jipb.12133}, pmid = {24237761}, issn = {1744-7909}, mesh = {Begomovirus/*physiology ; Chlorophyll/*metabolism ; Chloroplasts/ultrastructure ; Fluorescence ; *Gene Expression Profiling ; Gene Expression Regulation, Plant ; Gene Library ; Gene Ontology ; Manihot/ultrastructure/*virology ; Molecular Sequence Annotation ; Phenotype ; Plant Diseases/*genetics/*virology ; Real-Time Polymerase Chain Reaction ; Reproducibility of Results ; }, abstract = {Cassava mosaic disease, caused by cassava begomoviruses, is the most serious disease for cassava in Africa. However, the pathogenesis of this disease is poorly understood. We employed high throughput digital gene expression profiling based on the Illumina Solexa sequencing technology to investigate the global transcriptional response of cassava to African cassava mosaic virus infection. We found that 3,210 genes were differentially expressed in virus-infected cassava leaves. Gene ontology term and Kyoto Encyclopedia of Genes and Genomes pathway analysis indicated that genes implicated in photosynthesis were most affected, consistent with the chlorotic symptoms observed in infected leaves. The upregulation of chlorophyll degradation genes, including the genes encoding chlorophyllase, pheophytinase, and pheophorbide a oxygenase, and downregulation of genes encoding the major apoproteins in light-harvesting complex II were confirmed by qRT-PCR. These findings, together with the reduction of chlorophyll b content and fewer grana stacks in the infected leaf cells, reveal that the degradation of chlorophyll plays an important role in African cassava mosaic virus symptom development. This study will provide a road map for future investigations into viral pathogenesis.}, } @article {pmid24237665, year = {2014}, author = {McCoy, RC and Garud, NR and Kelley, JL and Boggs, CL and Petrov, DA}, title = {Genomic inference accurately predicts the timing and severity of a recent bottleneck in a nonmodel insect population.}, journal = {Molecular ecology}, volume = {23}, number = {1}, pages = {136-150}, pmid = {24237665}, issn = {1365-294X}, support = {R01GM100366/GM/NIGMS NIH HHS/United States ; T32 HG000044/HG/NHGRI NIH HHS/United States ; R01GM097415/GM/NIGMS NIH HHS/United States ; R01 GM097415/GM/NIGMS NIH HHS/United States ; R01 GM100366/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Colorado ; Computational Biology ; Gene Frequency ; Gene Library ; *Genetics, Population ; *Genome, Insect ; Lepidoptera/*genetics ; *Models, Genetic ; Molecular Sequence Annotation ; Polymorphism, Single Nucleotide ; Sequence Analysis, RNA ; Transcriptome ; Wyoming ; }, abstract = {The analysis of molecular data from natural populations has allowed researchers to answer diverse ecological questions that were previously intractable. In particular, ecologists are often interested in the demographic history of populations, information that is rarely available from historical records. Methods have been developed to infer demographic parameters from genomic data, but it is not well understood how inferred parameters compare to true population history or depend on aspects of experimental design. Here, we present and evaluate a method of SNP discovery using RNA sequencing and demographic inference using the program δaδi, which uses a diffusion approximation to the allele frequency spectrum to fit demographic models. We test these methods in a population of the checkerspot butterfly Euphydryas gillettii. This population was intentionally introduced to Gothic, Colorado in 1977 and has as experienced extreme fluctuations including bottlenecks of fewer than 25 adults, as documented by nearly annual field surveys. Using RNA sequencing of eight individuals from Colorado and eight individuals from a native population in Wyoming, we generate the first genomic resources for this system. While demographic inference is commonly used to examine ancient demography, our study demonstrates that our inexpensive, all-in-one approach to marker discovery and genotyping provides sufficient data to accurately infer the timing of a recent bottleneck. This demographic scenario is relevant for many species of conservation concern, few of which have sequenced genomes. Our results are remarkably insensitive to sample size or number of genomic markers, which has important implications for applying this method to other nonmodel systems.}, } @article {pmid24229408, year = {2013}, author = {Martins, WS and Carmo, WC and Longo, HJ and Rosa, TC and Rangel, TF}, title = {SUNPLIN: simulation with uncertainty for phylogenetic investigations.}, journal = {BMC bioinformatics}, volume = {14}, number = {}, pages = {324}, pmid = {24229408}, issn = {1471-2105}, mesh = {*Algorithms ; Amphibian Proteins/genetics ; Animals ; Avian Proteins/genetics ; Biological Evolution ; Carnivora/genetics ; Chiroptera/genetics ; Computational Biology/methods/statistics & numerical data ; Computer Simulation ; Consensus Sequence ; Evolution, Molecular ; *Phylogeny ; *Software ; Uncertainty ; }, abstract = {BACKGROUND: Phylogenetic comparative analyses usually rely on a single consensus phylogenetic tree in order to study evolutionary processes. However, most phylogenetic trees are incomplete with regard to species sampling, which may critically compromise analyses. Some approaches have been proposed to integrate non-molecular phylogenetic information into incomplete molecular phylogenies. An expanded tree approach consists of adding missing species to random locations within their clade. The information contained in the topology of the resulting expanded trees can be captured by the pairwise phylogenetic distance between species and stored in a matrix for further statistical analysis. Thus, the random expansion and processing of multiple phylogenetic trees can be used to estimate the phylogenetic uncertainty through a simulation procedure. Because of the computational burden required, unless this procedure is efficiently implemented, the analyses are of limited applicability.

RESULTS: In this paper, we present efficient algorithms and implementations for randomly expanding and processing phylogenetic trees so that simulations involved in comparative phylogenetic analysis with uncertainty can be conducted in a reasonable time. We propose algorithms for both randomly expanding trees and calculating distance matrices. We made available the source code, which was written in the C++ language. The code may be used as a standalone program or as a shared object in the R system. The software can also be used as a web service through the link: http://purl.oclc.org/NET/sunplin/.

CONCLUSION: We compare our implementations to similar solutions and show that significant performance gains can be obtained. Our results open up the possibility of accounting for phylogenetic uncertainty in evolutionary and ecological analyses of large datasets.}, } @article {pmid24227048, year = {2013}, author = {Maklakov, AA and Immler, S and Gonzalez-Voyer, A and Rönn, J and Kolm, N}, title = {Brains and the city in passerine birds: re-analysis and confirmation of the original result.}, journal = {Biology letters}, volume = {9}, number = {6}, pages = {20130859}, pmid = {24227048}, issn = {1744-957X}, mesh = {Animals ; Behavior, Animal ; Brain/*physiology ; *Cities ; *Data Interpretation, Statistical ; Logistic Models ; Passeriformes/*physiology ; Phylogeny ; Reproducibility of Results ; Sexual Behavior, Animal ; }, } @article {pmid24225318, year = {2014}, author = {Moretti, S and Laurenczy, B and Gharib, WH and Castella, B and Kuzniar, A and Schabauer, H and Studer, RA and Valle, M and Salamin, N and Stockinger, H and Robinson-Rechavi, M}, title = {Selectome update: quality control and computational improvements to a database of positive selection.}, journal = {Nucleic acids research}, volume = {42}, number = {Database issue}, pages = {D917-21}, pmid = {24225318}, issn = {1362-4962}, mesh = {*Databases, Nucleic Acid ; Genetic Variation ; Genomics/standards ; Humans ; Internet ; Quality Control ; *Selection, Genetic ; Sequence Alignment ; }, abstract = {Selectome (http://selectome.unil.ch/) is a database of positive selection, based on a branch-site likelihood test. This model estimates the number of nonsynonymous substitutions (dN) and synonymous substitutions (dS) to evaluate the variation in selective pressure (dN/dS ratio) over branches and over sites. Since the original release of Selectome, we have benchmarked and implemented a thorough quality control procedure on multiple sequence alignments, aiming to provide minimum false-positive results. We have also improved the computational efficiency of the branch-site test implementation, allowing larger data sets and more frequent updates. Release 6 of Selectome includes all gene trees from Ensembl for Primates and Glires, as well as a large set of vertebrate gene trees. A total of 6810 gene trees have some evidence of positive selection. Finally, the web interface has been improved to be more responsive and to facilitate searches and browsing.}, } @article {pmid24222037, year = {2013}, author = {McQuaid, CF and Britton, NF}, title = {Network dynamics contribute to structure: nestedness in mutualistic networks.}, journal = {Bulletin of mathematical biology}, volume = {75}, number = {12}, pages = {2372-2388}, doi = {10.1007/s11538-013-9896-4}, pmid = {24222037}, issn = {1522-9602}, mesh = {Animals ; Biological Evolution ; Computational Biology ; Ecosystem ; Mathematical Concepts ; *Models, Biological ; Plant Physiological Phenomena ; Population Dynamics ; *Symbiosis ; }, abstract = {Both ecological and evolutionary timescales are of importance when considering an ecological system; population dynamics affect the evolution of species traits, and vice versa. Recently, these two timescales have been used to explain structural patterns in host-parasite networks, where the evolution of the manner in which species balance the use of their resources in interactions with each other was examined.One of these patterns was nestedness, in which the set of parasite species within a particular host forms a subset of those within a more species-rich host. Patterns of both nestedness and anti-nestedness have been observed significantly more often than expected due to chance in host-parasite networks. In contrast, mutualistic networks tend to display a significant degree of nestedness, but are rarely anti-nested. Within networks with different interaction types, therefore, there appears to be a feature promoting non-random structural patterns, such as nestedness and anti-nestedness, depending on the interaction types involved.Here, we invoke the co-evolution of species trait-values when allocating resources to interactions to explain the structural pattern of nestedness in a mutualistic community. We look at a bipartite, multi-species system, in which the strength of an interaction between two species is determined by the resources that each species invests in that relationship. We then analyze the evolution of these interactions using adaptive dynamics.We found that the evolution of these interactions, reflecting the trade-off of resources, could be used to accurately predict that nestedness occurs significantly more often than expect due to chance alone in a mutualistic network. This complements previous results applying the same concept to an antagonistic network. We conclude that population dynamics and resource trade-offs could be important promoters of structural patterns in ecological networks of different types.}, } @article {pmid24220518, year = {2013}, author = {Zheng, Q and Jiao, N and Zhang, R and Chen, F and Suttle, CA}, title = {Prevalence of psbA-containing cyanobacterial podoviruses in the ocean.}, journal = {Scientific reports}, volume = {3}, number = {}, pages = {3207}, pmid = {24220518}, issn = {2045-2322}, mesh = {Bacteriophages/genetics ; Cyanobacteria/*genetics ; Databases, Genetic ; Genome, Viral/genetics ; Metagenomics/methods ; Oceans and Seas ; Photosystem II Protein Complex/*genetics ; Phylogeny ; Podoviridae/*genetics ; Prevalence ; Seawater/*microbiology/*virology ; }, abstract = {Podoviruses that infect marine picocyanobacteria are abundant and could play a significant role on regulating host populations due to their specific phage-host relationship. Genome sequencing of cyanophages has unveiled that many marine cyanophages encode certain photosynthetic genes like psbA. It appears that psbA is only present in certain groups of cyanopodovirus isolates. In order to better understand the prevalence of psbA in cyanobacterial podoviruses, we searched the marine metagenomic database (GOS, BATS, HOT and MarineVirome). Our study suggests that 89% of recruited cyanopodovirus scaffolds from the GOS database contained the psbA gene, supporting the ecological relevance of the photosynthesis gene for surface oceanic cyanophages. Diversification between Clade A and B are consistent with recent finding of two major groups of cyanopodoviruses. All the data also shows that Clade B cyanopodoviruses dominate the surface ocean water, while Clade A cyanopodoviruses become more important in the coastal and estuarine environments.}, } @article {pmid24215429, year = {2014}, author = {Dellicour, S and Mardulyn, P}, title = {spads 1.0: a toolbox to perform spatial analyses on DNA sequence data sets.}, journal = {Molecular ecology resources}, volume = {14}, number = {3}, pages = {647-651}, doi = {10.1111/1755-0998.12200}, pmid = {24215429}, issn = {1755-0998}, mesh = {*Databases, Nucleic Acid/statistics & numerical data ; Genetic Variation ; Genetics, Population/*instrumentation/statistics & numerical data ; Sequence Analysis, DNA/*instrumentation ; *Software ; }, abstract = {SPADS 1.0 (for 'Spatial and Population Analysis of DNA Sequences') is a population genetic toolbox for characterizing genetic variability within and among populations from DNA sequences. In view of the drastic increase in genetic information available through sequencing methods, spads was specifically designed to deal with multilocus data sets of DNA sequences. It computes several summary statistics from populations or groups of populations, performs input file conversions for other population genetic programs and implements locus-by-locus and multilocus versions of two clustering algorithms to study the genetic structure of populations. The toolbox also includes two MATLAB and r functions, GDISPAL and GDIVPAL, to display differentiation and diversity patterns across landscapes. These functions aim to generate interpolating surfaces based on multilocus distance and diversity indices. In the case of multiple loci, such surfaces can represent a useful alternative to multiple pie charts maps traditionally used in phylogeography to represent the spatial distribution of genetic diversity. These coloured surfaces can also be used to compare different data sets or different diversity and/or distance measures estimated on the same data set.}, } @article {pmid24214839, year = {2014}, author = {Awkerman, JA and Raimondo, S and Jackson, CR and Barron, MG}, title = {Augmenting aquatic species sensitivity distributions with interspecies toxicity estimation models.}, journal = {Environmental toxicology and chemistry}, volume = {33}, number = {3}, pages = {688-695}, doi = {10.1002/etc.2456}, pmid = {24214839}, issn = {1552-8618}, mesh = {Aquatic Organisms/*drug effects ; Databases, Factual ; *Models, Biological ; Models, Statistical ; Risk Assessment ; Species Specificity ; Uncertainty ; Water Pollutants, Chemical/*toxicity ; }, abstract = {Species sensitivity distributions (SSDs) are cumulative distribution functions of species toxicity values. The SSD approach is being used increasingly in ecological risk assessment but is often limited by available toxicity data needed for diverse species representation. In the present study, the authors evaluate augmenting aquatic species databases limited to standard test species using toxicity values extrapolated from interspecies correlation estimation (ICE) models for SSD development. The authors compared hazard concentrations at the 5th centile (HC5) of SSDs developed using limited measured data augmented with ICE toxicity values (augmented SSDs) with those estimated using larger measured toxicity datasets of diverse species (reference SSDs). When SSDs had similar species composition to the reference SSDs, 0.76 of the HC5 estimates were closer to the reference HC5; however, the proportion of augmented HC5s that were within 5-fold of the reference HC5s was 0.94, compared with 0.96 when predicted SSDs had random species assemblages. The range of toxicity values among represented species in all SSDs also depended on a chemical's mode of action. Predicted HC5 estimations for acetylcholinesterase inhibitors showed the greatest discrepancies from the reference HC5 when SSDs were limited to commonly tested species. The results of the present study indicate that ICE models used to augment datasets for SSDs do not greatly affect HC5 uncertainty. Uncertainty analysis of risk assessments using SSD hazard concentrations should address species composition, especially for chemicals with known taxa-specific differences in toxicological effects. This article is a US Government work and is in the public domain in the USA.}, } @article {pmid24211348, year = {2014}, author = {Guo, Z and Hu, D and Zhang, F and Huang, G and Xiao, Q}, title = {An integrated material metabolism model for stocks of urban road system in Beijing, China.}, journal = {The Science of the total environment}, volume = {470-471}, number = {}, pages = {883-894}, doi = {10.1016/j.scitotenv.2013.10.041}, pmid = {24211348}, issn = {1879-1026}, mesh = {China ; Construction Materials/economics/*statistics & numerical data ; Environmental Monitoring ; Geographic Information Systems ; *Models, Theoretical ; Transportation/economics/*statistics & numerical data ; Urbanization ; }, abstract = {Rapid urbanization has greatly altered the urban metabolism of material and energy. As a significant part of the infrastructure, urban roads are being rapidly developed worldwide. Quantitative analysis of metabolic processes on urban road systems, especially the scale, composition and spatial distribution of their stocks, could help to assess the resource appropriation and potential environmental impacts, as well as improve urban metabolism models. In this paper, an integrated model, which covered all types of roads, intersection structures and ancillary facilities, was built for calculating the material stocks of urban road systems. Based on a bottom-up method, the total stocks were disassembled into a number of stock parts rather than obtained by input-output data, which provided an approach promoting data availability and inner structure understanding. The combination with GIS enabled the model to tackle the complex structures of road networks and avoid double counting. In the case study of Beijing, the following results are shown: 1) The total stocks for the entire road system reached 159 million tons, of which nearly 80% was stored in roads, and 20% in ancillary facilities. 2) Macadam was the largest stock (111 million tons), while stone mastic asphalt, polyurethane plastics, and atactic polypropylene accounted for smaller components of the overall system. 3) The stock per unit area of pedestrian overcrossing was higher than that of the other stock units in the entire system, and its steel stocks reached 0.49 t/m(2), which was 10 times as high as that in interchanges. 4) The high stock areas were mainly distributed in ring-shaped and radial expressways, as well as in major interchanges. 5) Expressways and arterials were excessively emphasized, while minor roads were relatively ignored. However, the variation of cross-sectional thickness in branches and neighborhood roads will have a significant impact on the scale of material stocks in the entire road system.}, } @article {pmid24205374, year = {2013}, author = {Lemke, HW and Tarka, M and Klaassen, RH and Åkesson, M and Bensch, S and Hasselquist, D and Hansson, B}, title = {Annual cycle and migration strategies of a trans-Saharan migratory songbird: a geolocator study in the great reed warbler.}, journal = {PloS one}, volume = {8}, number = {10}, pages = {e79209}, pmid = {24205374}, issn = {1932-6203}, mesh = {Adaptation, Physiological ; Africa, Northern ; *Animal Migration ; Animals ; Geographic Information Systems ; Male ; Periodicity ; Seasons ; Songbirds/*physiology ; }, abstract = {Recent technological advancements now allow us to obtain geographical position data for a wide range of animal movements. Here we used light-level geolocators to study the annual migration cycle in great reed warblers (Acrocephalus arundinaceus), a passerine bird breeding in Eurasia and wintering in sub-Saharan Africa. We were specifically interested in seasonal strategies in routes and schedules of migration. We found that the great reed warblers (all males, no females were included) migrated from the Swedish breeding site in early August. After spending up to three weeks at scattered stopover sites in central to south-eastern Europe, they resumed migration and crossed the Mediterranean Sea and Sahara Desert without lengthy stopovers. They then spread out over a large overwintering area and each bird utilised two (or even three) main wintering sites that were spatially separated by a distinct mid-winter movement. Spring migration initiation date differed widely between individuals (1-27 April). Several males took a more westerly route over the Sahara in spring than in autumn, and in general there were fewer long-distance travels and more frequent shorter stopovers, including one in northern Africa, in spring. The shorter stopovers made spring migration on average faster than autumn migration. There was a strong correlation between the spring departure dates from wintering sites and the arrival dates at the breeding ground. All males had a high migration speed in spring despite large variation in departure dates, indicating a time-minimization strategy to achieve an early arrival at the breeding site; the latter being decisive for high reproductive success in great reed warblers. Our results have important implications for the understanding of long-distance migrants' ability to predict conditions at distant breeding sites and adapt to rapid environmental change.}, } @article {pmid24205306, year = {2013}, author = {Zhao, H and Chen, D and Peng, Z and Wang, L and Gao, Z}, title = {Identification and characterization of microRNAs in the leaf of ma bamboo (Dendrocalamus latiflorus) by deep sequencing.}, journal = {PloS one}, volume = {8}, number = {10}, pages = {e78755}, pmid = {24205306}, issn = {1932-6203}, mesh = {*Computational Biology ; *High-Throughput Nucleotide Sequencing ; Light ; MicroRNAs/*genetics ; Plant Leaves/*genetics ; RNA, Plant/*genetics ; Sasa/*genetics/radiation effects ; Sequence Analysis, RNA ; Transcriptome/radiation effects ; }, abstract = {MicroRNAs (miRNAs), a class of non-coding small endogenous RNAs of approximately 22 nucleotides, regulate gene expression at the post-transcriptional levels by targeting mRNAs for degradation or by inhibiting protein translation. Thousands of miRNAs have been identified in many species. However, there is no information available concerning miRNAs in ma bamboo (Dendrocalamus latiflorus), one of the most important non-timber forest products, which has essential ecological roles in forests. To identify miRNAs in D. latiflorus, a small RNA library was constructed from leaf tissues. Using next generation high-throughput sequencing technology and bioinformatics analysis, we obtained 11,513,607 raw sequence reads and identified 84 conserved miRNAs (54 mature miRNAs and 30 star miRNAs) belonging to 17 families, and 81 novel miRNAs (76 mature miRNAs and five star miRNAs) in D. latiflorus. One hundred and sixty-two potential targets were identified for the 81 novel bamboo miRNAs. Several targets for the novel miRNAs are transcription factors that play important roles in plant development. Among the novel miRNAs, 30 were selected and their expression profiles in response to different light conditions were validated by qRT-PCR. This study provides the first large-scale cloning and characterization of miRNAs in D. latiflorus. Eighty-four conserved and 81 novel miRNAs were identified in D. latiflorus. Our results present a broad survey of bamboo miRNAs based on experimental and bioinformatics analysis. Although it will be necessary to validate the functions of miRNAs by further experimental research, these results represent a starting point for future research on D. latiflorus and related species.}, } @article {pmid24204767, year = {2013}, author = {Fahlgren, N and Bollmann, SR and Kasschau, KD and Cuperus, JT and Press, CM and Sullivan, CM and Chapman, EJ and Hoyer, JS and Gilbert, KB and Grünwald, NJ and Carrington, JC}, title = {Phytophthora have distinct endogenous small RNA populations that include short interfering and microRNAs.}, journal = {PloS one}, volume = {8}, number = {10}, pages = {e77181}, pmid = {24204767}, issn = {1932-6203}, support = {R01 AI043288/AI/NIAID NIH HHS/United States ; R21 AI043288/AI/NIAID NIH HHS/United States ; R37 AI043288/AI/NIAID NIH HHS/United States ; AI043288/AI/NIAID NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; *Computational Biology ; DNA Transposable Elements ; Eosinophil Cationic Protein/classification/*genetics/metabolism ; Fibronectins/genetics/metabolism ; Gene Expression Regulation ; Genetic Loci ; *Genome ; High-Throughput Nucleotide Sequencing ; MicroRNAs/classification/*genetics/metabolism ; Molecular Sequence Annotation ; Molecular Sequence Data ; *Phylogeny ; Phytophthora/classification/*genetics/metabolism ; Plant Diseases ; RNA Interference ; RNA, Small Interfering/classification/*genetics/metabolism ; Sequence Alignment ; Sequence Homology, Amino Acid ; }, abstract = {In eukaryotes, RNA silencing pathways utilize 20-30-nucleotide small RNAs to regulate gene expression, specify and maintain chromatin structure, and repress viruses and mobile genetic elements. RNA silencing was likely present in the common ancestor of modern eukaryotes, but most research has focused on plant and animal RNA silencing systems. Phytophthora species belong to a phylogenetically distinct group of economically important plant pathogens that cause billions of dollars in yield losses annually as well as ecologically devastating outbreaks. We analyzed the small RNA-generating components of the genomes of P. infestans, P. sojae and P. ramorum using bioinformatics, genetic, phylogenetic and high-throughput sequencing-based methods. Each species produces two distinct populations of small RNAs that are predominantly 21- or 25-nucleotides long. The 25-nucleotide small RNAs were primarily derived from loci encoding transposable elements and we propose that these small RNAs define a pathway of short-interfering RNAs that silence repetitive genetic elements. The 21-nucleotide small RNAs were primarily derived from inverted repeats, including a novel microRNA family that is conserved among the three species, and several gene families, including Crinkler effectors and type III fibronectins. The Phytophthora microRNA is predicted to target a family of amino acid/auxin permeases, and we propose that 21-nucleotide small RNAs function at the post-transcriptional level. The functional significance of microRNA-guided regulation of amino acid/auxin permeases and the association of 21-nucleotide small RNAs with Crinkler effectors remains unclear, but this work provides a framework for testing the role of small RNAs in Phytophthora biology and pathogenesis in future work.}, } @article {pmid24204682, year = {2013}, author = {Jin, S and Fu, H and Zhou, Q and Sun, S and Jiang, S and Xiong, Y and Gong, Y and Qiao, H and Zhang, W}, title = {Transcriptome analysis of androgenic gland for discovery of novel genes from the oriental river prawn, Macrobrachium nipponense, using Illumina Hiseq 2000.}, journal = {PloS one}, volume = {8}, number = {10}, pages = {e76840}, pmid = {24204682}, issn = {1932-6203}, mesh = {Animals ; Arthropod Proteins/*genetics ; Expressed Sequence Tags ; Gene Expression Profiling/*methods ; Gene Ontology ; Genitalia, Male/*metabolism ; Male ; Microsatellite Repeats ; Palaemonidae/*genetics ; Polymorphism, Single Nucleotide ; Rivers ; Sequence Analysis, DNA/*methods ; }, abstract = {BACKGROUND: The oriental river prawn, Macrobrachium nipponense, is an important aquaculture species in China, even in whole of Asia. The androgenic gland produces hormones that play crucial roles in sexual differentiation to maleness. This study is the first de novo M. nipponense transcriptome analysis using cDNA prepared from mRNA isolated from the androgenic gland. Illumina/Solexa was used for sequencing.

The total volume of RNA sample was more than 5 ug. We generated 70,853,361 high quality reads after eliminating adapter sequences and filtering out low-quality reads. A total of 78,408 isosequences were obtained by clustering and assembly of the clean reads, producing 57,619 non-redundant transcripts with an average length of 1244.19 bp. In total 70,702 isosequences were matched to the Nr database, additional analyses were performed by GO (33,203), KEGG (17,868), and COG analyses (13,817), identifying the potential genes and their functions. A total of 47 sex-determination related gene families were identified from the M. nipponense androgenic gland transcriptome based on the functional annotation of non-redundant transcripts and comparisons with the published literature. Furthermore, a total of 40 candidate novel genes were found, that may contribute to sex-determination based on their extremely high expression levels in the androgenic compared to other sex glands,. Further, 437 SSRs and 65,535 high-confidence SNPs were identified in this EST dataset from which 14 EST-SSR markers have been isolated.

CONCLUSION: Our study provides new sequence information for M. nipponense, which will be the basis for further genetic studies on decapods crustaceans. More importantly, this study dramatically improves understanding of sex-determination mechanisms, and advances sex-determination research in all crustacean species. The huge number of potential SSR and SNP markers isolated from the transcriptome may shed the lights on research in many fields, including the evolution and molecular ecology of Macrobrachium species.}, } @article {pmid24202283, year = {2014}, author = {Midha, N and Mathur, PK}, title = {Channel characteristics and planform dynamics in the Indian Terai, Sharda River.}, journal = {Environmental management}, volume = {53}, number = {1}, pages = {120-134}, pmid = {24202283}, issn = {1432-1009}, mesh = {Conservation of Natural Resources ; Ecosystem ; Geographic Information Systems ; India ; *Rivers ; Satellite Communications ; *Water Movements ; }, abstract = {The Sharda River creates and maintains the ecologically diverse remnant patches of rare Terai ecosystem in northern India. This study used repeat satellite imagery and geographic information system analysis to assess the planform dynamics along a 60 km length of the Sharda River between 1977 and 2001 to understand the altered dynamics and its plausible causes in this data-poor region. Analyses revealed that the Sharda River has undergone significant change corresponding to enhanced instability in terms of increased number of neck cut-offs and consistent occurrence of avulsions in subsequent shorter assessment periods. An increased channel area (8%), decreased sinuosity (15%), increased braiding intensity, and abrupt migrations were also documented. The river has migrated toward the east with its west bankline being more unstable. The maximum shifts were 2.85 km in 13 years (1977-1990), 2.33 km in next 9 years (1990-1999), and a substantial shift of 2.39 km in just 2 years (1999-2001). The altered dynamics is making the future of critical wildlife habitats in Kishanpur Wildlife Sanctuary and North Kheri Forest Division precarious and causing significant economic damage. Extensive deforestation and expansion of agriculture since the 1950s in the catchment area are presumed to have severely impacted the equilibrium of the river, which urgently needs a management plan including wildlife habitat conservation, control, and risk reduction. The present study provides a strong foundation for understanding channel changes in the Sharda River and the finding can serve as a valuable information base for effective management planning and ecological restoration.}, } @article {pmid24198935, year = {2013}, author = {Ojanen, SP and Nieminen, M and Meyke, E and Pöyry, J and Hanski, I}, title = {Long-term metapopulation study of the Glanville fritillary butterfly (Melitaea cinxia): survey methods, data management, and long-term population trends.}, journal = {Ecology and evolution}, volume = {3}, number = {11}, pages = {3713-3737}, pmid = {24198935}, issn = {2045-7758}, support = {232826/ERC_/European Research Council/International ; }, abstract = {Long-term observational studies conducted at large (regional) spatial scales contribute to better understanding of landscape effects on population and evolutionary dynamics, including the conditions that affect long-term viability of species, but large-scale studies are expensive and logistically challenging to keep running for a long time. Here, we describe the long-term metapopulation study of the Glanville fritillary butterfly (Melitaea cinxia) that has been conducted since 1991 in a large network of 4000 habitat patches (dry meadows) within a study area of 50 by 70 km in the Åland Islands in Finland. We explain how the landscape structure has been described, including definition, delimitation, and mapping of the habitat patches; methods of field survey, including the logistics, cost, and reliability of the survey; and data management using the EarthCape biodiversity platform. We describe the long-term metapopulation dynamics of the Glanville fritillary based on the survey. There has been no long-term change in the overall size of the metapopulation, but the level of spatial synchrony and hence the amplitude of fluctuations in year-to-year metapopulation dynamics have increased over the years, possibly due to increasing frequency of exceptional weather conditions. We discuss the added value of large-scale and long-term population studies, but also emphasize the need to integrate more targeted experimental studies in the context of long-term observational studies. For instance, in the case of the Glanville fritillary project, the long-term study has produced an opportunity to sample individuals for experiments from local populations with a known demographic history. These studies have demonstrated striking differences in dispersal rate and other life-history traits of individuals from newly established local populations (the offspring of colonizers) versus individuals from old, established local populations. The long-term observational study has stimulated the development of metapopulation models and provided an opportunity to test model predictions. This combination of empirical studies and modeling has facilitated the study of key phenomena in spatial dynamics, such as extinction threshold and extinction debt.}, } @article {pmid24195573, year = {2013}, author = {Burwell-Naney, K and Zhang, H and Samantapudi, A and Jiang, C and Dalemarre, L and Rice, L and Williams, E and Wilson, S}, title = {Spatial disparity in the distribution of superfund sites in South Carolina: an ecological study.}, journal = {Environmental health : a global access science source}, volume = {12}, number = {}, pages = {96}, pmid = {24195573}, issn = {1476-069X}, support = {P20 MD001770/MD/NIMHD NIH HHS/United States ; 3P20MD001770-07S1/MD/NIMHD NIH HHS/United States ; 1R21ES017950-01/ES/NIEHS NIH HHS/United States ; }, mesh = {Demography ; *Environmental Exposure ; *Environmental Pollution ; Geographic Information Systems ; *Geographic Mapping ; Hazardous Waste/*analysis ; Humans ; *Refuse Disposal ; Regression Analysis ; Socioeconomic Factors ; South Carolina ; }, abstract = {BACKGROUND: According to the US Environmental Protection Agency (EPA), Superfund is a federal government program implemented to clean up uncontrolled hazardous waste sites. Twenty-six sites in South Carolina (SC) have been included on the National Priorities List (NPL), which has serious human health and environmental implications. The purpose of this study was to assess spatial disparities in the distribution of Superfund sites in SC.

METHODS: The 2000 US census tract and block level data were used to generate population characteristics, which included race/ethnicity, socioeconomic status (SES), education, home ownership, and home built before 1950. Geographic Information Systems (GIS) were used to map Superfund facilities and develop choropleth maps based on the aforementioned sociodemographic variables. Spatial methods, including mean and median distance analysis, buffer analysis, and spatial approximation were employed to characterize burden disparities. Regression analysis was performed to assess the relationship between the number of Superfund facilities and population characteristics.

RESULTS: Spatial coincidence results showed that of the 29.5% of Blacks living in SC, 55.9% live in Superfund host census tracts. Among all populations in SC living below poverty (14.2%), 57.2% were located in Superfund host census tracts. Buffer analyses results (0.5mi, 1.0mi, 5.0mi, 0.5km, 1.0km, and 5.0km) showed a higher percentage of Whites compared to Blacks hosting a Superfund facility. Conversely, a slightly higher percentage of Blacks hosted (30.2%) a Superfund facility than those not hosting (28.8%) while their White counterparts had more equivalent values (66.7% and 67.8%, respectively). Regression analyses in the reduced model (Adj. R2 = 0.038) only explained a small percentage of the variance. In addition, the mean distance for percent of Blacks in the 90th percentile for Superfund facilities was 0.48mi.

CONCLUSION: Burden disparities exist in the distribution of Superfund facilities in SC at the block and census tract levels across varying levels of demographic composition for race/ethnicity and SES.}, } @article {pmid24185102, year = {2013}, author = {Green, J and Wheeler, JR}, title = {The use of carrier solvents in regulatory aquatic toxicology testing: practical, statistical and regulatory considerations.}, journal = {Aquatic toxicology (Amsterdam, Netherlands)}, volume = {144-145}, number = {}, pages = {242-249}, doi = {10.1016/j.aquatox.2013.10.004}, pmid = {24185102}, issn = {1879-1514}, mesh = {Animals ; Aquatic Organisms/*drug effects ; Data Interpretation, Statistical ; Drug Interactions ; Ecotoxicology/*methods/*standards ; Solvents/chemistry/*toxicity ; Toxicity Tests/standards ; Water/chemistry ; }, abstract = {Solvents are often used to aid test item preparation in aquatic ecotoxicity experiments. This paper discusses the practical, statistical and regulatory considerations. The selection of the appropriate control (if a solvent is used) for statistical analysis is investigated using a database of 141 responses (endpoints) from 71 experiments. The advantages and disadvantages of basing the statistical analysis of treatment effects to the water control alone, solvent control alone, combined controls, or a conditional strategy of combining controls, when not statistically significantly different, are tested. The latter two approaches are shown to have distinct advantages. It is recommended that this approach continue to be the standard used for regulatory and research aquatic ecotoxicology studies. However, wherever technically feasible a solvent should not be employed or at least the concentration minimized.}, } @article {pmid24184058, year = {2014}, author = {Parsons, TD and Courtney, CG}, title = {An initial validation of the Virtual Reality Paced Auditory Serial Addition Test in a college sample.}, journal = {Journal of neuroscience methods}, volume = {222}, number = {}, pages = {15-23}, doi = {10.1016/j.jneumeth.2013.10.006}, pmid = {24184058}, issn = {1872-678X}, mesh = {Adolescent ; Adult ; Aged ; *Attention ; *Auditory Perception ; Databases, Factual ; Female ; Humans ; Learning ; Male ; *Mathematical Concepts ; Memory ; Middle Aged ; *Neuropsychological Tests ; Space Perception ; Students ; Universities ; *User-Computer Interface ; Visual Perception ; Young Adult ; }, abstract = {BACKGROUND: Numerous studies have demonstrated that the Paced Auditory Serial Addition Test (PASAT) has utility for the detection of cognitive processing deficits. While the PASAT has demonstrated high levels of internal consistency and test-retest reliability, administration of the PASAT has been known to create undue anxiety and frustration in participants. As a result, degradation of performance may be found on the PASAT. The difficult nature of the PASAT may subsequently decrease the probability of their return for follow up testing.

NEW METHOD: This study is a preliminary attempt at assessing the potential of a PASAT embedded in a virtual reality environment. The Virtual Reality PASAT (VR-PASAT) was compared with a paper-and-pencil version of the PASAT as well as other standardized neuropsychological measures. The two modalities of the PASAT were conducted with a sample of 50 healthy university students, between the ages of 19 and 34 years. Equivalent distributions were found for age, gender, education, and computer familiarity.

RESULTS: Moderate relationships were found between VR-PASAT and other putative attentional processing measures. The VR-PASAT was unrelated to indices of learning, memory, or visuospatial processing.

Comparison of the VR-PASAT with the traditional paper-and-pencil PASAT indicated that both versions require the examinee to sustain attention at an increasingly demanding, externally determined rate.

CONCLUSIONS: Results offer preliminary support for the construct validity (in a college sample) of the VR-PASAT as an attentional processing measure and suggest that this task may provide some unique information not tapped by traditional attentional processing tasks.}, } @article {pmid24180093, year = {2013}, author = {Darnell, A and Wise, R and Quaranta, J}, title = {Comparison of ArcToolbox and Terrain Tiles processing procedures for inundation mapping in mountainous terrain.}, journal = {Journal of emergency management (Weston, Mass.)}, volume = {11}, number = {2}, pages = {133-141}, doi = {10.5055/jem.2013.0132}, pmid = {24180093}, issn = {1543-5865}, mesh = {*Disaster Planning ; *Floods ; *Geographic Information Systems ; *Geographic Mapping ; Hydrology ; Insurance ; Models, Theoretical ; Rivers ; }, abstract = {Floodplain management consists of efforts to reduce flood damage to critical infrastructure and to protect the life and health of individuals from flooding. A major component of this effort is the monitoring of flood control structures such as dams because the potential failure of these structures may have catastrophic consequences. To prepare for these threats, engineers use inundation maps that illustrate the flood resulting from high river stages. To create the maps, the structure and river systems are modeled using engineering software programs, and hydrologic events are used to simulate the conditions leading to the failure of the structure. The output data are then exported to other software programs for the creation of inundation maps. Although the computer programs for this process have been established, the processing procedures vary and yield inconsistent results. Thus, these processing methods need to be examined to determine the functionality of each in floodplain management practices. The main goal of this article is to present the development of a more integrated, accurate, and precise graphical interface tool for interpretation by emergency managers and floodplain engineers. To accomplish this purpose, a potential dam failure was simulated and analyzed for a candidate river system using two processing methods: ArcToolbox and Terrain Tiles. The research involved performing a comparison of the outputs, which revealed that both procedures yielded similar inundations for single river reaches. However, the results indicated key differences when examining outputs for large river systems. On the basis of criteria involving the hydrologic accuracy and effects on infrastructure, the Terrain Tiles inundation surpassed the ArcToolbox inundation in terms of following topography and depicting flow rates and flood extents at confluences, bends, and tributary streams. Thus, the Terrain Tiles procedure is a more accurate representation of flood extents for use by floodplain engineers, hydrologists, geographers, and emergency managers.}, } @article {pmid24175541, year = {2013}, author = {Zhang, H and Luo, YM}, title = {[Assessment system for watershed ecological health in the United States: development and application].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {24}, number = {7}, pages = {2063-2072}, pmid = {24175541}, issn = {1001-9332}, mesh = {Conservation of Natural Resources ; *Ecosystem ; Environmental Health/*organization & administration ; Environmental Monitoring/methods/standards ; Fresh Water/analysis ; Risk Assessment ; United States ; United States Environmental Protection Agency ; Waste Management/legislation & jurisprudence/*standards ; Water Pollution/*prevention & control ; Water Supply/legislation & jurisprudence/*standards ; }, abstract = {To meet the water quality goals of the Clean Water Act, the environmental agencies in the United States (U.S.) have developed a comprehensive ecological assessment system of watershed health in the last two decades. The system employs a watershed approach, and includes a large set of hydrological, chemical, and biological indices, having become an essential part of the watershed water quality management system in the U.S. and provided strong support for the protection of water environment and the restoration of aquatic system. In this paper, the development and application of the ecological assessment system of watershed health by the U.S. environmental regulators, especially the U.S. Environmental Protection Agency (US EPA), were overviewed from the aspects of related laws and regulations, ecosystem function analysis, ecological health indicators, comprehensive assessment system, and monitoring and data management systems, and the health assessment systems for the rivers, lakes, estuaries, coasts, and wetlands adopted by the National$t1-1-1 Aquatic Resource Surveys (NARS) were introduced. Some suggestions for the future development of the scientific ecological assessment system of watershed health in China were put forward based on the understanding of the protection and remediation practices of our water environment.}, } @article {pmid24175529, year = {2013}, author = {Wang, ML and Bing, LF and Xi, FM and Wu, R and Geng, Y}, title = {[Spatiotemporal patterns and driving forces of land use change in industrial relocation area: a case study of old industrial area in Tiexi of Shenyang, Northeast China].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {24}, number = {7}, pages = {1969-1976}, pmid = {24175529}, issn = {1001-9332}, mesh = {China ; *City Planning ; Conservation of Natural Resources/*methods ; *Ecosystem ; *Environment Design ; Geographic Information Systems ; Industry ; Mining ; Remote Sensing Technology ; Spatio-Temporal Analysis ; }, abstract = {Based on the QuickBird remote sensing images and with the support of GIS, this paper analyzed the spatiotemporal characteristics of land use change and its driving forces in old industrial area of Tiexi, Shenyang City of Liaoning Province in 2000-2010. During the study period, the industrial and mining warehouse land pattern had the greatest change, evolving from the historical pattern of residential land in the south and of industrial land in the north into residential land as the dominant land use pattern. In the last decade, the residential land area increased by 9%, mainly transferred from the industrial and mining warehouse land located in the north of Jianshe Road, while the industrial and mining warehouse land area decreased by 20%. The land areas for the commercial service and for the administrative and public services were increased by 1.3% and 3.1%, respectively. The land area for construction had a greater change, with an overall change rate being 76.9%. The land use change rate in 2000-2005 was greater than that in 2005-2010. National development strategies and policies, regional development planning, administrative reform, and industrial upgrading were the main driving forces of the land use change in old industrial area of Tiexi.}, } @article {pmid24173913, year = {2014}, author = {Chao, YT and Su, CL and Jean, WH and Chen, WC and Chang, YC and Shih, MC}, title = {Identification and characterization of the microRNA transcriptome of a moth orchid Phalaenopsis aphrodite.}, journal = {Plant molecular biology}, volume = {84}, number = {4-5}, pages = {529-548}, pmid = {24173913}, issn = {1573-5028}, mesh = {Base Sequence ; Cluster Analysis ; Gene Expression Regulation, Plant ; Gene Library ; Gene Ontology ; High-Throughput Nucleotide Sequencing ; MicroRNAs/chemistry/*genetics ; Molecular Sequence Data ; Nucleic Acid Conformation ; Oligonucleotide Array Sequence Analysis ; Orchidaceae/*genetics ; Plant Proteins/genetics ; RNA Precursors/genetics ; RNA, Plant/chemistry/*genetics ; Reverse Transcriptase Polymerase Chain Reaction ; Sequence Homology, Nucleic Acid ; *Transcriptome ; }, abstract = {Orchids display unique phenotypes, functional characteristics and ecological adaptations that are not found in model plants. In this study, we aimed to characterize the microRNA (miRNA) transcriptome and identify species- and tissue-specific miRNAs in Phalaenopsis aphrodite. After data filtering and cleanup, a total of 59,387,374 reads, representing 1,649,996 unique reads, were obtained from four P. aphrodite small RNA libraries. A systematic bioinformatics analysis pipeline was developed that can be used for miRNA and precursor mining, and target gene prediction in non-model plants. A total of 3,251 unique reads for 181 known plant miRNAs (belonging to 88 miRNA families), 23 new miRNAs and 91 precursors were identified. All the miRNA star sequences (miRNA*), the complementary strands of miRNA that from miRNA/miRNA* duplexes, of the predicted new miRNAs were detected in our small RNA libraries, providing additional evidence for their existence as new miRNAs in P. aphrodite. Furthermore, 240 potential miRNA-targets that appear to be involved in many different biological activities and molecular functions, especially transcription factors, were identified, suggesting that miRNAs can impact multiple processes in P. aphrodite. We also verified the cleavage sites for six targets using RNA ligase-mediated rapid amplification of 5' ends assay. The results provide valuable information about the composition, expression and function of miRNA in P. aphrodite, and will aid functional genomics studies of orchids.}, } @article {pmid24169408, year = {2013}, author = {Yang, B and Li, MH and Li, S}, title = {Design-with-nature for multifunctional landscapes: environmental benefits and social barriers in community development.}, journal = {International journal of environmental research and public health}, volume = {10}, number = {11}, pages = {5433-5458}, pmid = {24169408}, issn = {1660-4601}, mesh = {Conservation of Natural Resources/*methods ; *Ecosystem ; *Environment Design ; Geographic Information Systems ; Housing ; Social Change ; Texas ; }, abstract = {Since the early 1970s, Ian McHarg's design-with-nature concept has been inspiring landscape architects, community and regional planners, and liked-minded professionals to create designs that take advantage of ecosystem services and promote environmental and public health. This study bridges the gap in the literature that has resulted from a lack of empirical examinations on the multiple performance benefits derived through design-with-nature and the under-investigated social aspect emanated from McHarg's Ecological Determinism design approach. The Woodlands, TX, USA, an ecologically designed community development under McHarg's approach, is compared with two adjacent communities that follow the conventional design approach. Using national environmental databases and multiple-year residents' survey information, this study assesses three landscape performance metrics of McHarg's approach: stormwater runoff, urban heat island effect, and social acceptance. Geographic Information Systems (GIS) was used to assess the development extent and land surface temperature distribution. Results show that McHarg's approach demonstrates benefits in reducing runoff and urban heat island effect, whereas it confronts challenges with the general acceptance of manicured landscapes and thus results in a low safety perception level when residents interact with naturally designed landscapes. The authors argue that design-with-nature warrants multifunctionality because of its intrinsic interdisciplinary approach. Moreover, education and dissemination of successful examples can achieve a greater level of awareness among the public and further promote multifunctional design for landscape sustainability.}, } @article {pmid24167551, year = {2013}, author = {Giugno, R and Bonnici, V and Bombieri, N and Pulvirenti, A and Ferro, A and Shasha, D}, title = {GRAPES: a software for parallel searching on biological graphs targeting multi-core architectures.}, journal = {PloS one}, volume = {8}, number = {10}, pages = {e76911}, pmid = {24167551}, issn = {1932-6203}, support = {R01 GM032877/GM/NIGMS NIH HHS/United States ; GM32877-21/22/GM/NIGMS NIH HHS/United States ; 2R01GM032877-25A1/GM/NIGMS NIH HHS/United States ; }, mesh = {*Antiviral Agents ; *Databases, Factual ; *Models, Biological ; *Software ; }, abstract = {Biological applications, from genomics to ecology, deal with graphs that represents the structure of interactions. Analyzing such data requires searching for subgraphs in collections of graphs. This task is computationally expensive. Even though multicore architectures, from commodity computers to more advanced symmetric multiprocessing (SMP), offer scalable computing power, currently published software implementations for indexing and graph matching are fundamentally sequential. As a consequence, such software implementations (i) do not fully exploit available parallel computing power and (ii) they do not scale with respect to the size of graphs in the database. We present GRAPES, software for parallel searching on databases of large biological graphs. GRAPES implements a parallel version of well-established graph searching algorithms, and introduces new strategies which naturally lead to a faster parallel searching system especially for large graphs. GRAPES decomposes graphs into subcomponents that can be efficiently searched in parallel. We show the performance of GRAPES on representative biological datasets containing antiviral chemical compounds, DNA, RNA, proteins, protein contact maps and protein interactions networks.}, } @article {pmid24167248, year = {2013}, author = {Boscaro, V and Felletti, M and Vannini, C and Ackerman, MS and Chain, PS and Malfatti, S and Vergez, LM and Shin, M and Doak, TG and Lynch, M and Petroni, G}, title = {Polynucleobacter necessarius, a model for genome reduction in both free-living and symbiotic bacteria.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {110}, number = {46}, pages = {18590-18595}, pmid = {24167248}, issn = {1091-6490}, mesh = {Amino Acid Sequence ; Base Sequence ; Burkholderiaceae/*genetics ; Computational Biology ; Euplotes/*microbiology ; *Evolution, Molecular ; Genome Size/*genetics ; Genome, Bacterial/*genetics ; Molecular Sequence Annotation ; Molecular Sequence Data ; Sequence Alignment ; Sequence Analysis, DNA ; Symbiosis/*genetics ; }, abstract = {We present the complete genomic sequence of the essential symbiont Polynucleobacter necessarius (Betaproteobacteria), which is a valuable case study for several reasons. First, it is hosted by a ciliated protist, Euplotes; bacterial symbionts of ciliates are still poorly known because of a lack of extensive molecular data. Second, the single species P. necessarius contains both symbiotic and free-living strains, allowing for a comparison between closely related organisms with different ecologies. Third, free-living P. necessarius strains are exceptional by themselves because of their small genome size, reduced metabolic flexibility, and high worldwide abundance in freshwater systems. We provide a comparative analysis of P. necessarius metabolism and explore the peculiar features of a genome reduction that occurred on an already streamlined genome. We compare this unusual system with current hypotheses for genome erosion in symbionts and free-living bacteria, propose modifications to the presently accepted model, and discuss the potential consequences of translesion DNA polymerase loss.}, } @article {pmid24165880, year = {2014}, author = {Hunter, S and Corbett, M and Denise, H and Fraser, M and Gonzalez-Beltran, A and Hunter, C and Jones, P and Leinonen, R and McAnulla, C and Maguire, E and Maslen, J and Mitchell, A and Nuka, G and Oisel, A and Pesseat, S and Radhakrishnan, R and Rocca-Serra, P and Scheremetjew, M and Sterk, P and Vaughan, D and Cochrane, G and Field, D and Sansone, SA}, title = {EBI metagenomics--a new resource for the analysis and archiving of metagenomic data.}, journal = {Nucleic acids research}, volume = {42}, number = {Database issue}, pages = {D600-6}, pmid = {24165880}, issn = {1362-4962}, support = {BB/I02612X/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/I000771/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/E025080/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/H024921/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/I025840/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {*Databases, Genetic ; Gene Expression Profiling ; Internet ; Metabolomics ; *Metagenomics ; Proteomics ; Software ; }, abstract = {Metagenomics is a relatively recently established but rapidly expanding field that uses high-throughput next-generation sequencing technologies to characterize the microbial communities inhabiting different ecosystems (including oceans, lakes, soil, tundra, plants and body sites). Metagenomics brings with it a number of challenges, including the management, analysis, storage and sharing of data. In response to these challenges, we have developed a new metagenomics resource (http://www.ebi.ac.uk/metagenomics/) that allows users to easily submit raw nucleotide reads for functional and taxonomic analysis by a state-of-the-art pipeline, and have them automatically stored (together with descriptive, standards-compliant metadata) in the European Nucleotide Archive.}, } @article {pmid24165825, year = {2014}, author = {Jin, Z and Xu, W and Liu, A}, title = {Genomic surveys and expression analysis of bZIP gene family in castor bean (Ricinus communis L.).}, journal = {Planta}, volume = {239}, number = {2}, pages = {299-312}, pmid = {24165825}, issn = {1432-2048}, mesh = {Basic-Leucine Zipper Transcription Factors/classification/*genetics ; Binding Sites ; Ricinus communis/*genetics/growth & development ; Databases, Genetic ; Dimerization ; Endosperm/genetics/growth & development ; Euphorbiaceae/genetics/growth & development ; Evolution, Molecular ; Gene Expression Profiling ; *Gene Expression Regulation, Plant ; *Genomics ; High-Throughput Nucleotide Sequencing ; Multigene Family ; Organ Specificity ; Phylogeny ; Plant Leaves/genetics/growth & development ; Plant Proteins/classification/genetics ; Plant Roots/genetics/growth & development ; Seeds/genetics/growth & development ; Sequence Analysis, DNA ; }, abstract = {The basic leucine zipper (bZIP) transcription factors comprise a family of transcriptional regulators present extensively in plants, involved in regulating diverse biological processes such as flower and vascular development, seed maturation, stress signaling and pathogen defense. Castor bean (Ricinus communis L. Euphorbiaceae) is one of the most important non-edible oilseed crops and its seed oil is broadly used for industrial applications. We performed a comprehensive genome-wide identification and analysis of the bZIP transcription factors that exist in the castor bean genome in this study. In total, 49 RcbZIP transcription factors were identified, characterized and categorized into 11 groups (I-XI) based on their gene structure, DNA-binding sites, conserved motifs, and phylogenetic relationships. The dimerization properties of 49 RcbZIP proteins were predicted on the basis of the characteristic features in the leucine zipper. Global expression profiles of 49 RcbZIP genes among different tissues were examined using high-throughput sequencing of digital gene expression profiles, and resulted in diverse expression patterns that may provide basic information to further reveal the function of the 49 RcbZIP genes in castor bean. The results obtained from this study would provide valuable information in understanding the molecular basis of the RcbZIP transcription factor family and their potential function in regulating the growth and development, particularly in seed filling of castor bean.}, } @article {pmid24165114, year = {2014}, author = {Vlajinac, H and Marinkovic, J and Maksimovic, M and Radak, D}, title = {Factors related to venous ulceration: a cross-sectional study.}, journal = {Angiology}, volume = {65}, number = {9}, pages = {824-830}, doi = {10.1177/0003319713508218}, pmid = {24165114}, issn = {1940-1574}, mesh = {Adult ; Aged ; Chronic Disease ; Cross-Sectional Studies ; Female ; Humans ; Logistic Models ; Male ; Middle Aged ; Multivariate Analysis ; Odds Ratio ; Risk Factors ; Varicose Ulcer/diagnosis/*etiology ; }, abstract = {The aim of the study was to determine the factors related to venous ulceration. Patients with venous ulceration (278 patients) were compared with 1401 patients in other categories of clinical classification of venous disease (clinical, etiologic, anatomic, and pathophysiological [CEAP]). Demographic, anthropometric, and clinical data were collected. Univariate and multivariate logistic regression analyses were used. According to multivariate analyses, risk factors for venous ulceration were age, male sex, personal history of superficial and deep venous thrombosis, diabetes, high blood pressure, skeletal or joint disease in the legs and emphysema or chronic obstructive pulmonary disease, higher body mass index and physical inactivity, parental history of ankle ulcer as well as reflux in deep and perforator veins, deep obstruction, and combination of reflux and obstruction. It seems reasonable to pay special attention to patients in whom the postulated risk factors for venous ulceration are present.}, } @article {pmid24152717, year = {2014}, author = {Glass, EM and Dribinsky, Y and Yilmaz, P and Levin, H and Van Pelt, R and Wendel, D and Wilke, A and Eisen, JA and Huse, S and Shipanova, A and Sogin, M and Stajich, J and Knight, R and Meyer, F and Schriml, LM}, title = {MIxS-BE: a MIxS extension defining a minimum information standard for sequence data from the built environment.}, journal = {The ISME journal}, volume = {8}, number = {1}, pages = {1-3}, pmid = {24152717}, issn = {1751-7370}, mesh = {Databases, Factual/*standards ; Databases, Nucleic Acid/*standards ; Environmental Microbiology/*standards ; Meta-Analysis as Topic ; }, } @article {pmid24145862, year = {2013}, author = {Lin, YG and Weadick, CJ and Santini, F and Chang, BS}, title = {Molecular evolutionary analysis of vertebrate transducins: a role for amino acid variation in photoreceptor deactivation.}, journal = {Journal of molecular evolution}, volume = {77}, number = {5-6}, pages = {231-245}, pmid = {24145862}, issn = {1432-1432}, mesh = {Amino Acid Sequence/genetics ; Animals ; Codon/genetics ; Computational Biology ; DNA Primers/genetics ; *Evolution, Molecular ; *Genetic Variation ; Models, Genetic ; Photoreceptor Cells/metabolism/*physiology ; *Phylogeny ; Sequence Alignment ; Species Specificity ; Transducin/*genetics/metabolism ; Vertebrates/*genetics ; }, abstract = {Transducin is a heterotrimeric G protein that plays a critical role in phototransduction in the rod and cone photoreceptor cells of the vertebrate retina. Rods, highly sensitive cells that recover from photoactivation slowly, underlie dim-light vision, whereas cones are less sensitive, recover more quickly, and underlie bright-light vision. Transducin deactivation is a critical step in photoreceptor recovery and may underlie the functional distinction between rods and cones. Rods and cones possess distinct transducin α subunits, yet they share a common deactivation mechanism, the GTPase activating protein (GAP) complex. Here, we used codon models to examine patterns of sequence evolution in rod (GNAT1) and cone (GNAT2) α subunits. Our results indicate that purifying selection is the dominant force shaping GNAT1 and GNAT2 evolution, but that GNAT2 has additionally been subject to positive selection operating at multiple phylogenetic scales; phylogeny-wide analysis identified several sites in the GNAT2 helical domain as having substantially elevated dN/dS estimates, and branch-site analysis identified several nearby sites as targets of strong positive selection during early vertebrate history. Examination of aligned GNAT and GAP complex crystal structures revealed steric clashes between several positively selected sites and the deactivating GAP complex. This suggests that GNAT2 sequence variation could play an important role in adaptive evolution of the vertebrate visual system via effects on photoreceptor deactivation kinetics and provides an alternative perspective to previous work that focused instead on the effect of GAP complex concentration. Our findings thus further the understanding of the molecular biology, physiology, and evolution of vertebrate visual systems.}, } @article {pmid24140818, year = {2013}, author = {Besson, H and Paccaud, F and Marques-Vidal, P}, title = {Ecologic correlations of selected food groups with disease incidence and mortality in Switzerland.}, journal = {Journal of epidemiology}, volume = {23}, number = {6}, pages = {466-473}, pmid = {24140818}, issn = {1349-9092}, mesh = {Cardiovascular Diseases/*epidemiology ; Databases, Factual ; Diet/*adverse effects/statistics & numerical data ; Female ; Food Supply/*statistics & numerical data ; Humans ; Incidence ; Male ; Mortality/*trends ; Neoplasms/*epidemiology ; Registries ; Switzerland/epidemiology ; }, abstract = {BACKGROUND: There is little information regarding the impact of diet on disease incidence and mortality in Switzerland. We assessed ecologic correlations between food availability and disease.

METHODS: In this ecologic study for the period 1970-2009, food availability was measured using the food balance sheets of the Food and Agriculture Organization of the United Nations. Standardized mortality rates (SMRs) were obtained from the Swiss Federal Office of Statistics. Cancer incidence data were obtained from the World Health Organization Health For All database and the Vaud Cancer Registry. Associations between food availability and mortality/incidence were assessed at lags 0, 5, 10, and 15 years by multivariate regression adjusted for total caloric intake.

RESULTS: Alcoholic beverages and fruit availability were positively associated, and fish availability was inversely associated, with SMRs for cardiovascular diseases. Animal products, meat, and animal fats were positively associated with the SMR for ischemic heart disease only. For cancer, the results of analysis using SMRs and incidence rates were contradictory. Alcoholic beverages and fruits were positively associated with SMRs for all cancer but inversely associated with all-cancer incidence rates. Similar findings were obtained for all other foods except vegetables, which were weakly inversely associated with SMRs and incidence rates. Use of a 15-year lag reversed the associations with animal and vegetal products, weakened the association with alcohol and fruits, and strengthened the association with fish.

CONCLUSIONS: Ecologic associations between food availability and disease vary considerably on the basis of whether mortality or incidence rates are used in the analysis. Great care is thus necessary when interpreting our results.}, } @article {pmid24138771, year = {2013}, author = {Laverdure, F and Gaudin, A and Bourgain, JL}, title = {[Impact of the decrease of nitrous oxide use on the consumption of halogenated agents].}, journal = {Annales francaises d'anesthesie et de reanimation}, volume = {32}, number = {11}, pages = {766-771}, doi = {10.1016/j.annfar.2013.09.001}, pmid = {24138771}, issn = {1769-6623}, mesh = {Adult ; Aged ; Aged, 80 and over ; Air Pollution/prevention & control ; Anesthesia, Inhalation/economics/*statistics & numerical data ; Anesthetics, Inhalation/economics/*supply & distribution ; Conscious Sedation/economics/statistics & numerical data ; Databases, Factual ; Desflurane ; Drug Costs ; Drug Utilization ; Female ; France ; Global Warming ; Hospital Costs ; Humans ; Isoflurane/analogs & derivatives/economics/supply & distribution ; Male ; Methyl Ethers/economics/supply & distribution ; Middle Aged ; Nitrous Oxide/economics/*supply & distribution ; Retrospective Studies ; Sevoflurane ; }, abstract = {OBJECTIVE: Nitrous oxide (N2O) toxicity and its impact on pollution lead to restrict its use. A decrease of N2O consumption should increase the hypnotic inhaled consumption. This monocentric study estimated consumptions and costs of halogenated agents (HA) and N2O over 5 years when the N2O consumption was reduced.

STUDY DESIGN: Retrospective from a computerized database.

PATIENTS: Between 2006 and 2010, 34,097 procedures were studied after two meetings exposing the risks of the N2O.

METHODS: At the end of anesthesia, consumptions of hypnotic agents (millilitres transmitted by the injectors and the blender) were archived in the database. The annual consumption of agents was obtained by adding the individual consumptions, then divided by the annual number of cases. The costs were given by the hospital pharmacy from invoices.

RESULTS: N2O consumption per anesthesia constantly decreased during the study, from 75.1L by act to 22.7L. The sum of the annual consumptions of N2O and air did not change suggesting that total fresh gas flow remained stable. Between 2006 and 2010, the sevoflurane consumption by act increased by 25%, from 16.5 to 20.6mL, and desflurane consumption by 37%, from 46.1 to 63.1mL by patient. The costs of the administration of hypnotic agents remained stable.

CONCLUSION: N2O consumption decrease had an impact on the consumption of HA. The cost reduction of the N2O was counterbalanced by the increase of halogenated vapor cost. The profit of the ecological impact of the reduction in N2O use could be quantified.}, } @article {pmid24134514, year = {2013}, author = {Saraceni, V and Talhari, CC and Pereira, GF and Golub, JE and Talhari, S and Miranda, AE}, title = {AIDS-related Kaposi's sarcoma in Brazil: trends and geopolitical distribution.}, journal = {International journal of dermatology}, volume = {52}, number = {12}, pages = {1525-1529}, doi = {10.1111/ijd.12116}, pmid = {24134514}, issn = {1365-4632}, support = {#U2RTW006885//PHS HHS/United States ; ICOHRTA-NIH AI066994/AI/NIAID NIH HHS/United States ; }, mesh = {Acquired Immunodeficiency Syndrome/drug therapy/*epidemiology/mortality ; Adolescent ; Adult ; Antiretroviral Therapy, Highly Active ; Brazil/epidemiology ; Databases, Factual ; Female ; Humans ; Male ; Politics ; Prevalence ; Sarcoma, Kaposi/*epidemiology/mortality ; Skin Neoplasms/*epidemiology/mortality ; Substance-Related Disorders/*epidemiology/mortality ; Young Adult ; }, abstract = {BACKGROUND: AIDS-related Kaposi's sarcoma (KS) is a unique model of the relationship between viral infection, immunity, environmental, and genetic factors in viral cancers. The goal was to determine the distribution of KS cases among Brazilian geopolitical regions, looking at the ecological relationship with median CD4 cell count.

METHODS: Ecological study using Brazilian National Diseases Reporting Databases: 1982-2009. Subjects ≥ 13 years of age who have KS cited in their AIDS reporting form were selected, and demographic and HIV exposure data were collected.

RESULTS: We found 11,731 KS cases in the period, with a prevalence of 2.4% among AIDS cases; 88% were male, and 68% lived in the Southeast region, which accounted for 59% of AIDS cases. The regional and national prevalence trends were similar, although the highest proportion among women was found in the North region, which has the lowest number of both AIDS and KS cases. Heterosexual transmission accounted for 87% of HIV among women compared to 18% among men. Fifty-seven percent of all KS cases were diagnosed before antiretroviral therapy (ART). Injection drug use accounted for 11% of KS cases. Median survival was 472 days before the ART era and 1482 after it (P < 0.001). Median CD4 counts increased in all regions in the period as ART coverage expanded, and a resulting correlating decline in KS cases was observed.

CONCLUSIONS: Prevalence of KS declined after the introduction of ART in all regions of Brazil, suggesting individual protection conveyed by ART.}, } @article {pmid24134332, year = {2013}, author = {Guisan, A and Tingley, R and Baumgartner, JB and Naujokaitis-Lewis, I and Sutcliffe, PR and Tulloch, AI and Regan, TJ and Brotons, L and McDonald-Madden, E and Mantyka-Pringle, C and Martin, TG and Rhodes, JR and Maggini, R and Setterfield, SA and Elith, J and Schwartz, MW and Wintle, BA and Broennimann, O and Austin, M and Ferrier, S and Kearney, MR and Possingham, HP and Buckley, YM}, title = {Predicting species distributions for conservation decisions.}, journal = {Ecology letters}, volume = {16}, number = {12}, pages = {1424-1435}, pmid = {24134332}, issn = {1461-0248}, mesh = {*Conservation of Natural Resources ; Decision Making ; *Decision Support Techniques ; Ecology/*methods ; Endangered Species ; *Models, Theoretical ; Research Design ; }, abstract = {Species distribution models (SDMs) are increasingly proposed to support conservation decision making. However, evidence of SDMs supporting solutions for on-ground conservation problems is still scarce in the scientific literature. Here, we show that successful examples exist but are still largely hidden in the grey literature, and thus less accessible for analysis and learning. Furthermore, the decision framework within which SDMs are used is rarely made explicit. Using case studies from biological invasions, identification of critical habitats, reserve selection and translocation of endangered species, we propose that SDMs may be tailored to suit a range of decision-making contexts when used within a structured and transparent decision-making process. To construct appropriate SDMs to more effectively guide conservation actions, modellers need to better understand the decision process, and decision makers need to provide feedback to modellers regarding the actual use of SDMs to support conservation decisions. This could be facilitated by individuals or institutions playing the role of 'translators' between modellers and decision makers. We encourage species distribution modellers to get involved in real decision-making processes that will benefit from their technical input; this strategy has the potential to better bridge theory and practice, and contribute to improve both scientific knowledge and conservation outcomes.}, } @article {pmid24132490, year = {2013}, author = {Schürch, R and Couvillon, MJ and Burns, DD and Tasman, K and Waxman, D and Ratnieks, FL}, title = {Incorporating variability in honey bee waggle dance decoding improves the mapping of communicated resource locations.}, journal = {Journal of comparative physiology. A, Neuroethology, sensory, neural, and behavioral physiology}, volume = {199}, number = {12}, pages = {1143-1152}, pmid = {24132490}, issn = {1432-1351}, mesh = {*Animal Communication ; Animals ; Bees/*physiology ; Calibration ; Computer Simulation ; Entomology/methods ; Ethology/methods ; Feeding Behavior/*physiology ; Female ; Geographic Information Systems ; Markov Chains ; Models, Biological ; Monte Carlo Method ; Spatial Behavior/*physiology ; }, abstract = {Honey bees communicate to nestmates locations of resources, including food, water, tree resin and nest sites, by making waggle dances. Dances are composed of repeated waggle runs, which encode the distance and direction vector from the hive or swarm to the resource. Distance is encoded in the duration of the waggle run, and direction is encoded in the angle of the dancer's body relative to vertical. Glass-walled observation hives enable researchers to observe or video, and decode waggle runs. However, variation in these signals makes it impossible to determine exact locations advertised. We present a Bayesian duration to distance calibration curve using Markov Chain Monte Carlo simulations that allows us to quantify how accurately distance to a food resource can be predicted from waggle run durations within a single dance. An angular calibration shows that angular precision does not change over distance, resulting in spatial scatter proportional to distance. We demonstrate how to combine distance and direction to produce a spatial probability distribution of the resource location advertised by the dance. Finally, we show how to map honey bee foraging and discuss how our approach can be integrated with Geographic Information Systems to better understand honey bee foraging ecology.}, } @article {pmid24130470, year = {2013}, author = {Aguas, R and Ferguson, NM}, title = {Feature selection methods for identifying genetic determinants of host species in RNA viruses.}, journal = {PLoS computational biology}, volume = {9}, number = {10}, pages = {e1003254}, pmid = {24130470}, issn = {1553-7358}, support = {MR/K010174/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Algorithms ; Animals ; Artificial Intelligence ; Binding Sites ; Chiroptera/virology ; Computational Biology/*methods ; *Evolution, Molecular ; Genes, Viral/genetics ; Host-Pathogen Interactions/*genetics ; Humans ; Phenotype ; Principal Component Analysis ; RNA Viruses/*genetics ; Receptors, Cell Surface/chemistry/genetics/metabolism ; Viral Proteins/chemistry/*genetics/metabolism ; Virus Diseases/*virology ; Zoonoses ; }, abstract = {Despite environmental, social and ecological dependencies, emergence of zoonotic viruses in human populations is clearly also affected by genetic factors which determine cross-species transmission potential. RNA viruses pose an interesting case study given their mutation rates are orders of magnitude higher than any other pathogen--as reflected by the recent emergence of SARS and Influenza for example. Here, we show how feature selection techniques can be used to reliably classify viral sequences by host species, and to identify the crucial minority of host-specific sites in pathogen genomic data. The variability in alleles at those sites can be translated into prediction probabilities that a particular pathogen isolate is adapted to a given host. We illustrate the power of these methods by: 1) identifying the sites explaining SARS coronavirus differences between human, bat and palm civet samples; 2) showing how cross species jumps of rabies virus among bat populations can be readily identified; and 3) de novo identification of likely functional influenza host discriminant markers.}, } @article {pmid24129912, year = {2014}, author = {Wass, SV and Porayska-Pomsta, K}, title = {The uses of cognitive training technologies in the treatment of autism spectrum disorders.}, journal = {Autism : the international journal of research and practice}, volume = {18}, number = {8}, pages = {851-871}, doi = {10.1177/1362361313499827}, pmid = {24129912}, issn = {1461-7005}, support = {MC_UP_A060_1104/MRC_/Medical Research Council/United Kingdom ; G0701484/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Child ; Child Development Disorders, Pervasive/psychology/*therapy ; Cognitive Behavioral Therapy/*methods ; Emotions ; Face ; Fixation, Ocular ; Humans ; Language Development ; Patient Education as Topic/*methods ; Recognition, Psychology ; Robotics ; Social Behavior ; Software ; Technology/*methods ; Therapy, Computer-Assisted/methods ; Virtual Reality Exposure Therapy/methods ; }, abstract = {In this review, we focus on research that has used technology to provide cognitive training - i.e. to improve performance on some measurable aspect of behaviour - in individuals with autism spectrum disorders. We review technology-enhanced interventions that target three different cognitive domains: (a) emotion and face recognition, (b) language and literacy, and (c) social skills. The interventions reviewed allow for interaction through different modes, including point-and-click and eye-gaze contingent software, and are delivered through diverse implementations, including virtual reality and robotics. In each case, we examine the evidence of the degree of post-training improvement observed following the intervention, including evidence of transfer to altered behaviour in ecologically valid contexts. We conclude that a number of technological interventions have found that observed improvements within the computerised training paradigm fail to generalise to altered behaviour in more naturalistic settings, which may result from problems that people with autism spectrum disorders experience in generalising and extrapolating knowledge. However, we also point to several promising findings in this area. We discuss possible directions for future work.}, } @article {pmid24129700, year = {2013}, author = {Potts, MB and Kim, HS and Fisher, KW and Hu, Y and Carrasco, YP and Bulut, GB and Ou, YH and Herrera-Herrera, ML and Cubillos, F and Mendiratta, S and Xiao, G and Hofree, M and Ideker, T and Xie, Y and Huang, LJ and Lewis, RE and MacMillan, JB and White, MA}, title = {Using functional signature ontology (FUSION) to identify mechanisms of action for natural products.}, journal = {Science signaling}, volume = {6}, number = {297}, pages = {ra90}, pmid = {24129700}, issn = {1937-9145}, support = {CA90400/CA/NCI NIH HHS/United States ; R01 CA149833/CA/NCI NIH HHS/United States ; R01 CA157774/CA/NCI NIH HHS/United States ; CA071443/CA/NCI NIH HHS/United States ; R01 CA152301/CA/NCI NIH HHS/United States ; R01 CA129451/CA/NCI NIH HHS/United States ; P30 CA142543/CA/NCI NIH HHS/United States ; P30 CA036727/CA/NCI NIH HHS/United States ; CA149833/CA/NCI NIH HHS/United States ; R01 CA071443/CA/NCI NIH HHS/United States ; T32 CA124334/CA/NCI NIH HHS/United States ; CA152301/CA/NCI NIH HHS/United States ; R01 CA090400/CA/NCI NIH HHS/United States ; CA129451/CA/NCI NIH HHS/United States ; CA157774/CA/NCI NIH HHS/United States ; P41 GM103504/GM/NIGMS NIH HHS/United States ; U01 CA176284/CA/NCI NIH HHS/United States ; }, mesh = {Animals ; Autophagy/drug effects/genetics ; Bacteria/chemistry/classification ; Biological Products/chemistry/isolation & purification/*pharmacology ; Cell Line, Tumor ; Cells, Cultured ; Cluster Analysis ; Computational Biology/methods ; Drug Evaluation, Preclinical/methods ; Gene Expression Regulation, Neoplastic/*drug effects ; *Gene Ontology ; Gene Regulatory Networks/drug effects/genetics ; HCT116 Cells ; Humans ; Invertebrates/chemistry ; MCF-7 Cells ; Marine Biology ; Mice ; Mice, Inbred BALB C ; MicroRNAs/genetics ; Molecular Structure ; Oligonucleotide Array Sequence Analysis ; RNA Interference ; Transcriptome/*drug effects ; }, abstract = {A challenge for biomedical research is the development of pharmaceuticals that appropriately target disease mechanisms. Natural products can be a rich source of bioactive chemicals for medicinal applications but can act through unknown mechanisms and can be difficult to produce or obtain. To address these challenges, we developed a new marine-derived, renewable natural products resource and a method for linking bioactive derivatives of this library to the proteins and biological processes that they target in cells. We used cell-based screening and computational analysis to match gene expression signatures produced by natural products to those produced by small interfering RNA (siRNA) and synthetic microRNA (miRNA) libraries. With this strategy, we matched proteins and miRNAs with diverse biological processes and also identified putative protein targets and mechanisms of action for several previously undescribed marine-derived natural products. We confirmed mechanistic relationships for selected siRNAs, miRNAs, and compounds with functional roles in autophagy, chemotaxis mediated by discoidin domain receptor 2, or activation of the kinase AKT. Thus, this approach may be an effective method for screening new drugs while simultaneously identifying their targets.}, } @article {pmid24129116, year = {2013}, author = {Congdon, P}, title = {Spatially interpolated disease prevalence estimation using collateral indicators of morbidity and ecological risk.}, journal = {International journal of environmental research and public health}, volume = {10}, number = {10}, pages = {5011-5025}, pmid = {24129116}, issn = {1660-4601}, mesh = {Asthma/*epidemiology ; Cluster Analysis ; Data Interpretation, Statistical ; Humans ; London/epidemiology ; *Models, Biological ; Risk Factors ; Socioeconomic Factors ; Urban Health/*statistics & numerical data ; }, abstract = {This paper considers estimation of disease prevalence for small areas (neighbourhoods) when the available observations on prevalence are for an alternative partition of a region, such as service areas. Interpolation to neighbourhoods uses a kernel method extended to take account of two types of collateral information. The first is morbidity and service use data, such as hospital admissions, observed for neighbourhoods. Variations in morbidity and service use are expected to reflect prevalence. The second type of collateral information is ecological risk factors (e.g., pollution indices) that are expected to explain variability in prevalence in service areas, but are typically observed only for neighbourhoods. An application involves estimating neighbourhood asthma prevalence in a London health region involving 562 neighbourhoods and 189 service (primary care) areas.}, } @article {pmid24129021, year = {2013}, author = {Hu, H and Krasoulis, A and Lutman, M and Bleeck, S}, title = {Development of a real time sparse non-negative matrix factorization module for cochlear implants by using xPC target.}, journal = {Sensors (Basel, Switzerland)}, volume = {13}, number = {10}, pages = {13861-13878}, pmid = {24129021}, issn = {1424-8220}, mesh = {*Algorithms ; *Cochlear Implants ; Computer Systems ; Humans ; Pattern Recognition, Automated/*methods ; Reproducibility of Results ; Sensitivity and Specificity ; *Signal Processing, Computer-Assisted ; Signal-To-Noise Ratio ; Sound Spectrography/instrumentation/*methods ; Speech Production Measurement/instrumentation/*methods ; *Speech Recognition Software ; Therapy, Computer-Assisted/methods ; }, abstract = {Cochlear implants (CIs) require efficient speech processing to maximize information transmission to the brain, especially in noise. A novel CI processing strategy was proposed in our previous studies, in which sparsity-constrained non-negative matrix factorization (NMF) was applied to the envelope matrix in order to improve the CI performance in noisy environments. It showed that the algorithm needs to be adaptive, rather than fixed, in order to adjust to acoustical conditions and individual characteristics. Here, we explore the benefit of a system that allows the user to adjust the signal processing in real time according to their individual listening needs and their individual hearing capabilities. In this system, which is based on MATLAB®, SIMULINK® and the xPC Target™ environment, the input/outupt (I/O) boards are interfaced between the SIMULINK blocks and the CI stimulation system, such that the output can be controlled successfully in the manner of a hardware-in-the-loop (HIL) simulation, hence offering a convenient way to implement a real time signal processing module that does not require any low level language. The sparsity constrained parameter of the algorithm was adapted online subjectively during an experiment with normal-hearing subjects and noise vocoded speech simulation. Results show that subjects chose different parameter values according to their own intelligibility preferences, indicating that adaptive real time algorithms are beneficial to fully explore subjective preferences. We conclude that the adaptive real time systems are beneficial for the experimental design, and such systems allow one to conduct psychophysical experiments with high ecological validity.}, } @article {pmid24128146, year = {2014}, author = {Bacci, G and Bazzicalupo, M and Benedetti, A and Mengoni, A}, title = {StreamingTrim 1.0: a Java software for dynamic trimming of 16S rRNA sequence data from metagenetic studies.}, journal = {Molecular ecology resources}, volume = {14}, number = {2}, pages = {426-434}, doi = {10.1111/1755-0998.12187}, pmid = {24128146}, issn = {1755-0998}, mesh = {Computational Biology/*methods ; Metagenomics/*methods ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, DNA/*methods ; Software ; }, abstract = {Next-generation sequencing technologies are extensively used in the field of molecular microbial ecology to describe taxonomic composition and to infer functionality of microbial communities. In particular, the so-called barcode or metagenetic applications that are based on PCR amplicon library sequencing are very popular at present. One of the problems, related to the utilization of the data of these libraries, is the analysis of reads quality and removal (trimming) of low-quality segments, while retaining sufficient information for subsequent analyses (e.g. taxonomic assignment). Here, we present StreamingTrim, a DNA reads trimming software, written in Java, with which researchers are able to analyse the quality of DNA sequences in fastq files and to search for low-quality zones in a very conservative way. This software has been developed with the aim to provide a tool capable of trimming amplicon library data, retaining as much as taxonomic information as possible. This software is equipped with a graphical user interface for a user-friendly usage. Moreover, from a computational point of view, StreamingTrim reads and analyses sequences one by one from an input fastq file, without keeping anything in memory, permitting to run the computation on a normal desktop PC or even a laptop. Trimmed sequences are saved in an output file, and a statistics summary is displayed that contains the mean and standard deviation of the length and quality of the whole sequence file. Compiled software, a manual and example data sets are available under the BSD-2-Clause License at the GitHub repository at https://github.com/GiBacci/StreamingTrim/.}, } @article {pmid24127252, year = {2014}, author = {Senn, S and Nanda, V and Falkowski, P and Bromberg, Y}, title = {Function-based assessment of structural similarity measurements using metal co-factor orientation.}, journal = {Proteins}, volume = {82}, number = {4}, pages = {648-656}, doi = {10.1002/prot.24442}, pmid = {24127252}, issn = {1097-0134}, mesh = {Algorithms ; Amino Acid Sequence ; Amino Acid Substitution ; Cellular Microenvironment ; Computational Biology ; Metalloproteins/*chemistry/*ultrastructure ; Metals/*chemistry ; Models, Molecular ; Protein Folding ; Protein Structure, Secondary ; Sequence Alignment ; }, abstract = {Structure comparison is widely used to quantify protein relationships. Although there are several approaches to calculate structural similarity, specifying significance thresholds for similarity metrics is difficult due to the inherent likeness of common secondary structure elements. In this study, metal co-factor location is used to assess the biological relevance of structural alignments. The distance between the centroids of bound co-factors adds a chemical and function-relevant constraint to the structural superimposition of two proteins. This additional dimension can be used to define cut-off values for discriminating valid and spurious alignments in large alignment sets. The hypothesis underlying our approach is that metal coordination sites constrain structural evolution, thus revealing functional relationships between distantly related proteins. A comparison of three related nitrogenases shows the sequence and fold constraints imposed on the protein structures up to 18 Å away from the centers of their bound metal clusters.}, } @article {pmid24121566, year = {2014}, author = {Garrido, L and Sánchez, O and Ferrera, I and Tomàs, N and Mas, J}, title = {Dynamics of microbial diversity profiles in waters of different qualities. Approximation to an ecological quality indicator.}, journal = {The Science of the total environment}, volume = {468-469}, number = {}, pages = {1154-1161}, doi = {10.1016/j.scitotenv.2013.08.065}, pmid = {24121566}, issn = {1879-1026}, mesh = {Analysis of Variance ; Bacteroidetes/genetics/growth & development ; Base Sequence ; Betaproteobacteria/genetics/growth & development ; Computational Biology ; DNA Fingerprinting ; Denaturing Gradient Gel Electrophoresis ; Gammaproteobacteria/genetics/growth & development ; *Microbiota ; Molecular Sequence Data ; Polymerase Chain Reaction ; RNA, Ribosomal/genetics ; Sequence Analysis, RNA ; Time Factors ; Wastewater/*microbiology ; Water Microbiology/*standards ; Water Quality/*standards ; }, abstract = {Over the past two decades, the amount of reclaimed water has increased throughout the world to face the current water shortage, and as a consequence there is an increasing interest to develop good indicators of water quality, beyond the traditional fecal indicators. In order to meet this need, in this work the microbial profiles of different wastewater treatment plant effluents, both secondary and tertiary, were studied and compared with water samples from an uncontaminated natural aquifer. Taking into account the most abundant phylogenetic groups found in these water samples, we calculated the Bacteroidetes, Gammaproteobacteria and Nitrospira/Betaproteobacteria (BGN:β) ratio and found significant differences between the mean ratios of the four water qualities. The secondary effluent ratios were never below 1.3 and the tertiary effluent and groundwater ratios were never over 0.85. Furthermore, calculation of this index with previous published data supports our results and indicates that the BGN:β ratio is a possible alternative indicator of water quality.}, } @article {pmid24119028, year = {2013}, author = {Mann, IK and Wegrzyn, JL and Rajora, OP}, title = {Generation, functional annotation and comparative analysis of black spruce (Picea mariana) ESTs: an important conifer genomic resource.}, journal = {BMC genomics}, volume = {14}, number = {}, pages = {702}, pmid = {24119028}, issn = {1471-2164}, mesh = {Base Sequence ; Conserved Sequence/genetics ; Contig Mapping ; DNA, Complementary/genetics ; Databases, Protein ; Evolution, Molecular ; Expressed Sequence Tags/*metabolism ; Gene Expression Regulation, Plant ; Gene Ontology ; Genes, Plant/genetics ; Genetic Association Studies ; *Genomics ; Molecular Sequence Annotation/*methods ; Molecular Sequence Data ; Multigene Family/genetics ; Peptides/genetics ; Picea/*genetics ; Pinus/genetics ; RNA, Messenger/genetics/metabolism ; Sequence Homology, Nucleic Acid ; }, abstract = {BACKGROUND: EST (expressed sequence tag) sequences and their annotation provide a highly valuable resource for gene discovery, genome sequence annotation, and other genomics studies that can be applied in genetics, breeding and conservation programs for non-model organisms. Conifers are long-lived plants that are ecologically and economically important globally, and have a large genome size. Black spruce (Picea mariana), is a transcontinental species of the North American boreal and temperate forests. However, there are limited transcriptomic and genomic resources for this species. The primary objective of our study was to develop a black spruce transcriptomic resource to facilitate on-going functional genomics projects related to growth and adaptation to climate change.

RESULTS: We conducted bidirectional sequencing of cDNA clones from a standard cDNA library constructed from black spruce needle tissues. We obtained 4,594 high quality (2,455 5' end and 2,139 3' end) sequence reads, with an average read-length of 532 bp. Clustering and assembly of ESTs resulted in 2,731 unique sequences, consisting of 2,234 singletons and 497 contigs. Approximately two-thirds (63%) of unique sequences were functionally annotated. Genes involved in 36 molecular functions and 90 biological processes were discovered, including 24 putative transcription factors and 232 genes involved in photosynthesis. Most abundantly expressed transcripts were associated with photosynthesis, growth factors, stress and disease response, and transcription factors. A total of 216 full-length genes were identified. About 18% (493) of the transcripts were novel, representing an important addition to the Genbank EST database (dbEST). Fifty-seven di-, tri-, tetra- and penta-nucleotide simple sequence repeats were identified.

CONCLUSIONS: We have developed the first high quality EST resource for black spruce and identified 493 novel transcripts, which may be species-specific related to life history and ecological traits. We have also identified full-length genes and microsatellite-containing ESTs. Based on EST sequence similarities, black spruce showed close evolutionary relationships with congeneric Picea glauca and Picea sitchensis compared to other Pinaceae members and angiosperms. The EST sequences reported here provide an important resource for genome annotation, functional and comparative genomics, molecular breeding, conservation and management studies and applications in black spruce and related conifer species.}, } @article {pmid24119022, year = {2014}, author = {van der Merwe, M and McPherson, H and Siow, J and Rossetto, M}, title = {Next-Gen phylogeography of rainforest trees: exploring landscape-level cpDNA variation from whole-genome sequencing.}, journal = {Molecular ecology resources}, volume = {14}, number = {1}, pages = {199-208}, doi = {10.1111/1755-0998.12176}, pmid = {24119022}, issn = {1755-0998}, mesh = {Computational Biology ; DNA, Chloroplast/*genetics ; *Genetic Variation ; *Genome, Plant ; High-Throughput Nucleotide Sequencing ; *Phylogeography ; Sequence Analysis, DNA ; Trees/*genetics ; }, abstract = {Standardized phylogeographic studies across codistributed taxa can identify important refugia and biogeographic barriers, and potentially uncover how changes in adaptive constraints through space and time impact on the distribution of genetic diversity. The combination of next-generation sequencing and methodologies that enable uncomplicated analysis of the full chloroplast genome may provide an invaluable resource for such studies. Here, we assess the potential of a shotgun-based method across twelve nonmodel rainforest trees sampled from two evolutionary distinct regions. Whole genomic shotgun sequencing libraries consisting of pooled individuals were used to assemble species-specific chloroplast references (in silicio). For each species, the pooled libraries allowed for the detection of variation within and between data sets (each representing a geographic region). The potential use of nuclear rDNA as an additional marker from the NGS libraries was investigated by mapping reads against available references. We successfully obtained phylogeographically informative sequence data from a range of previously unstudied rainforest trees. Greater levels of diversity were found in northern refugial rainforests than in southern expansion areas. The genetic signatures of varying evolutionary histories were detected, and interesting associative patterns between functional characteristics and genetic diversity were identified. This approach can suit a wide range of landscape-level studies. As the key laboratory-based steps do not require prior species-specific knowledge and can be easily outsourced, the techniques described here are even suitable for researchers without access to wet-laboratory facilities, making evolutionary ecology questions increasingly accessible to the research community.}, } @article {pmid24118837, year = {2014}, author = {Eiler, A and Zaremba-Niedzwiedzka, K and Martínez-García, M and McMahon, KD and Stepanauskas, R and Andersson, SG and Bertilsson, S}, title = {Productivity and salinity structuring of the microplankton revealed by comparative freshwater metagenomics.}, journal = {Environmental microbiology}, volume = {16}, number = {9}, pages = {2682-2698}, pmid = {24118837}, issn = {1462-2920}, mesh = {Archaea/classification/genetics ; Bacteria/*classification/genetics ; Data Mining ; Fresh Water/*microbiology ; Lakes/microbiology ; Metabolic Networks and Pathways ; Metagenome ; *Metagenomics ; Molecular Sequence Annotation ; *Phylogeny ; RNA, Ribosomal/genetics ; *Salinity ; Seawater/microbiology ; Sequence Analysis, DNA ; }, abstract = {Little is known about the diversity and structuring of freshwater microbial communities beyond the patterns revealed by tracing their distribution in the landscape with common taxonomic markers such as the ribosomal RNA. To address this gap in knowledge, metagenomes from temperate lakes were compared to selected marine metagenomes. Taxonomic analyses of rRNA genes in these freshwater metagenomes confirm the previously reported dominance of a limited subset of uncultured lineages of freshwater bacteria, whereas Archaea were rare. Diversification into marine and freshwater microbial lineages was also reflected in phylogenies of functional genes, and there were also significant differences in functional beta-diversity. The pathways and functions that accounted for these differences are involved in osmoregulation, active transport, carbohydrate and amino acid metabolism. Moreover, predicted genes orthologous to active transporters and recalcitrant organic matter degradation were more common in microbial genomes from oligotrophic versus eutrophic lakes. This comparative metagenomic analysis allowed us to formulate a general hypothesis that oceanic- compared with freshwater-dwelling microorganisms, invest more in metabolism of amino acids and that strategies of carbohydrate metabolism differ significantly between marine and freshwater microbial communities.}, } @article {pmid24117189, year = {2015}, author = {Keith Barker, F and Oyler-McCance, S and Tomback, DF}, title = {Blood from a turnip: tissue origin of low-coverage shotgun sequencing libraries affects recovery of mitogenome sequences.}, journal = {Mitochondrial DNA}, volume = {26}, number = {3}, pages = {384-388}, doi = {10.3109/19401736.2013.840588}, pmid = {24117189}, issn = {1940-1744}, mesh = {Animals ; Brassica napus/*genetics ; DNA/*blood/isolation & purification ; Databases, Genetic ; Gene Library ; *Genome, Mitochondrial ; High-Throughput Nucleotide Sequencing ; Microsatellite Repeats/genetics ; Muscle, Skeletal/metabolism ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; }, abstract = {Next generation sequencing methods allow rapid, economical accumulation of data that have many applications, even at relatively low levels of genome coverage. However, the utility of shotgun sequencing data sets for specific goals may vary depending on the biological nature of the samples sequenced. We show that the ability to assemble mitogenomes from three avian samples of two different tissue types varies widely. In particular, data with coverage typical of microsatellite development efforts (∼1×) from DNA extracted from avian blood failed to cover even 50% of the mitogenome, relative to at least 500-fold coverage from muscle-derived data. Researchers should consider possible applications of their data and select the tissue source for their work accordingly. Practitioners analyzing low-coverage shotgun sequencing data (including for microsatellite locus development) should consider the potential benefits of mitogenome assembly, including internal barcode verification of species identity, mitochondrial primer development, and phylogenetics.}, } @article {pmid24115604, year = {2013}, author = {Liberles, DA and Teufel, AI and Liu, L and Stadler, T}, title = {On the need for mechanistic models in computational genomics and metagenomics.}, journal = {Genome biology and evolution}, volume = {5}, number = {10}, pages = {2008-2018}, pmid = {24115604}, issn = {1759-6653}, mesh = {Bacteria/genetics ; *Computational Biology ; DNA-Binding Proteins/*genetics ; Ecology ; *Evolution, Molecular ; Gene Duplication ; Gene Expression Regulation ; Gene Regulatory Networks/genetics ; *Metagenomics ; Models, Theoretical ; }, abstract = {Computational genomics is now generating very large volumes of data that have the potential to be used to address important questions in both basic biology and biomedicine. Addressing these important biological questions becomes possible when mechanistic models rooted in biochemistry and evolutionary/population genetic processes are developed, instead of fitting data to off-the-shelf statistical distributions that do not enable mechanistic inference. Three examples are presented, the first involving ecological processes inferred from metagenomic data, the second involving mechanisms of gene regulation rooted in protein-DNA interactions with consideration of DNA structure, and the third involving existing models for the retention of duplicate genes that enables prediction of evolutionary mechanisms. This description of mechanistic models is generalized toward future developments in computational genomics and the need for biological mechanisms and processes in biological models.}, } @article {pmid24114867, year = {2013}, author = {Mramba, LK and Barber, S and Hommola, K and Dyer, LA and Wilson, JS and Forister, ML and Gilks, WR}, title = {Permutation tests for analyzing cospeciation in multiple phylogenies: applications in tri-trophic ecology.}, journal = {Statistical applications in genetics and molecular biology}, volume = {12}, number = {6}, pages = {679-701}, doi = {10.1515/sagmb-2012-0073}, pmid = {24114867}, issn = {1544-6115}, mesh = {Algorithms ; Animals ; Bacteria/genetics ; Biological Evolution ; Computer Simulation ; Data Interpretation, Statistical ; Genetic Speciation ; Host-Parasite Interactions/genetics ; Isoptera/genetics/microbiology ; *Models, Genetic ; Phylogeny ; Symbiosis ; }, abstract = {There is a need for a reliable statistical test which is appropriate for assessing cospeciation of more than two phylogenies. We have developed an algorithm using a permutation method that can be used to test for and infer tri-trophic evolutionary relationships of organisms given both their phylogenies and pairwise interactions. An overall statistic has been developed based on the dominant eigenvalue of a covariance matrix, and compared to values of the statistic computed when tree labels are permuted. The resulting overall p-value is used to test for the presence or absence of cospeciation in a tri-trophic system. If cospeciation is detected, we propose new test statistics based on partial correlations to uncover more details about the relationships between multiple phylogenies. One of the strengths of our method is that it allows more parasites than hosts or more hosts than parasites, with multiple associations and more than one parasite attached to a host (or one parasite attached to multiple hosts). The new method does not require any parametric assumptions of the distribution of the data, and unlike the old methods, which utilize several pairwise steps, the overall statistic used is obtained in one step. We have applied our method to two published datasets where we obtained detailed information about the strength of associations among species with calculated partial p-values and one overall p-value from the dominant eigenvalue test statistic. Our permutation method produces reliable results with a clear procedure and statistics applied in an intuitive manner. Our algorithm is useful in testing evidence for three-way cospeciation in multiple phylogenies with tri-trophic associations and determining which phylogenies are involved in cospeciation.}, } @article {pmid24112409, year = {2013}, author = {Kõljalg, U and Nilsson, RH and Abarenkov, K and Tedersoo, L and Taylor, AF and Bahram, M and Bates, ST and Bruns, TD and Bengtsson-Palme, J and Callaghan, TM and Douglas, B and Drenkhan, T and Eberhardt, U and Dueñas, M and Grebenc, T and Griffith, GW and Hartmann, M and Kirk, PM and Kohout, P and Larsson, E and Lindahl, BD and Lücking, R and Martín, MP and Matheny, PB and Nguyen, NH and Niskanen, T and Oja, J and Peay, KG and Peintner, U and Peterson, M and Põldmaa, K and Saag, L and Saar, I and Schüßler, A and Scott, JA and Senés, C and Smith, ME and Suija, A and Taylor, DL and Telleria, MT and Weiss, M and Larsson, KH}, title = {Towards a unified paradigm for sequence-based identification of fungi.}, journal = {Molecular ecology}, volume = {22}, number = {21}, pages = {5271-5277}, doi = {10.1111/mec.12481}, pmid = {24112409}, issn = {1365-294X}, mesh = {DNA Barcoding, Taxonomic ; DNA, Fungal/genetics ; DNA, Ribosomal Spacer/genetics ; *Databases, Nucleic Acid ; Fungi/*classification/genetics ; Internet ; *Phylogeny ; }, abstract = {The nuclear ribosomal internal transcribed spacer (ITS) region is the formal fungal barcode and in most cases the marker of choice for the exploration of fungal diversity in environmental samples. Two problems are particularly acute in the pursuit of satisfactory taxonomic assignment of newly generated ITS sequences: (i) the lack of an inclusive, reliable public reference data set and (ii) the lack of means to refer to fungal species, for which no Latin name is available in a standardized stable way. Here, we report on progress in these regards through further development of the UNITE database (http://unite.ut.ee) for molecular identification of fungi. All fungal species represented by at least two ITS sequences in the international nucleotide sequence databases are now given a unique, stable name of the accession number type (e.g. Hymenoscyphus pseudoalbidus|GU586904|SH133781.05FU), and their taxonomic and ecological annotations were corrected as far as possible through a distributed, third-party annotation effort. We introduce the term 'species hypothesis' (SH) for the taxa discovered in clustering on different similarity thresholds (97-99%). An automatically or manually designated sequence is chosen to represent each such SH. These reference sequences are released (http://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and in the QIIME pipeline. The system and the data will be updated automatically as the number of public fungal ITS sequences grows. We invite everybody in the position to improve the annotation or metadata associated with their particular fungal lineages of expertise to do so through the new Web-based sequence management system in UNITE.}, } @article {pmid24105951, year = {2014}, author = {Judd, N and Tear, L and Toll, J}, title = {From sediment to tissue and tissue to sediment: an evaluation of statistical bioaccumulation models.}, journal = {Integrated environmental assessment and management}, volume = {10}, number = {1}, pages = {102-113}, doi = {10.1002/ieam.1484}, pmid = {24105951}, issn = {1551-3793}, mesh = {Animals ; Biota ; Confidence Intervals ; *Databases, Factual ; Geologic Sediments/*analysis ; Invertebrates ; *Models, Statistical ; Polychlorinated Biphenyls/analysis/pharmacokinetics ; Regression Analysis ; United States ; Water Pollutants, Chemical/*analysis/*pharmacokinetics ; }, abstract = {Biota-sediment accumulation factors (BSAFs) and biota-sediment accumulation regressions (BSARs) are statistical models that may be used to estimate tissue chemical concentrations from sediment chemical concentrations or vice versa. Biota-sediment accumulation factors and BSARs are used to fill tissue concentration data gaps, set sediment preliminary remediation goals (PRGs), and make projections about the effectiveness of potential sediment cleanup projects in reducing tissue chemical concentrations. We explored field-based, benthic invertebrate biota-sediment chemical concentration relationships using data from the US Environmental Protection Agency (USEPA) Mid-Continent Ecology Division (MED) BSAF database. Approximately two thirds of the 262 relationships investigated were very poor (r(2) < 0.3 or p-value ≥ 0.05); for some of the biota-sediment relationships that did have a significant nonzero slope (p-value < 0.05), lipid-normalized tissue concentrations tended to decrease as the colocated organic carbon (OC)-normalized sediment concentration increased. Biota-sediment relationships were further evaluated for 3 of the 262 datasets. Biota-sediment accumulation factors, linear regressions, model II regressions, illustrative sediment PRGs, and confidence intervals (CIs) were calculated for each of the three examples. These examples illustrate some basic but important statistical practices that should be followed before selecting a BSAR or BSAF or relying on these simple models of biota-sediment relationships to support consequential management decisions. These practices include the following: one should not assume that the relationship between chemical concentrations in tissue and sediment is necessarily linear, one should not assume the model intercept to be zero, and one should not place too much stock on models that are heavily influenced by one or a few high chemical concentration data points. People will continue to use statistical models of field-based biota-sediment chemical concentration relationships to support sediment investigations and remedial action decisions. However, it should not be assumed that the models will be reliable. In developing and applying BSAFs and BSARs, it is essential that best practices are followed and model limitations and uncertainties are understood, acknowledged, and quantified as much as possible.}, } @article {pmid24102517, year = {2014}, author = {Loozen, G and Ozcelik, O and Boon, N and De Mol, A and Schoen, C and Quirynen, M and Teughels, W}, title = {Inter-bacterial correlations in subgingival biofilms: a large-scale survey.}, journal = {Journal of clinical periodontology}, volume = {41}, number = {1}, pages = {1-10}, doi = {10.1111/jcpe.12167}, pmid = {24102517}, issn = {1600-051X}, mesh = {Antibiosis/physiology ; Bacteria/*classification/isolation & purification ; Bacterial Load ; Bacteroides/isolation & purification ; *Biofilms ; Cross-Sectional Studies ; Databases as Topic ; Dental Plaque/*microbiology ; Eubacterium/isolation & purification ; Gingiva/*microbiology ; Humans ; Microbial Interactions ; Periodontal Pocket/classification/*microbiology ; Periodontitis/classification/*microbiology ; Porphyromonas/isolation & purification ; Porphyromonas gingivalis/isolation & purification ; Prevotella intermedia/isolation & purification ; Retrospective Studies ; Streptococcus/isolation & purification ; Treponema denticola/isolation & purification ; }, abstract = {AIM: Although the complexity of the oral ecology and the ecological differences between health and disease are well accepted, a clear view on the dynamics in relation to disease is lacking. In this study, the prevalence and abundance of 20 key oral bacteria was assessed in health and disease and more importantly a closer look was given to the inter-bacterial relationships.

MATERIALS AND METHODS: A blinded microbiological database was analysed in this cross-sectional, retrospective study. The database was constructed based on microbiological analyses of samples from 6308 patients, with gradations of periodontitis (healthy to periodontitis). Data concerning the abundance of 20 oral bacteria and probing pocket depth were provided.

RESULTS: Porphyromonas gingivalis, Tannerella forsythia, Treponema denticola, Eubacterium nodatum, Porphyromonas micra and Porphyromonas intermedia showed a clear increase in abundance and prevalence with increasing pocket depth. Correlation matrices illustrated that almost all microorganisms were in one way correlated to other species and most of these correlations were significant. Several beneficial bacteria showed strong correlations with other beneficial bacteria.

CONCLUSION: Knowledge on bacterial correlations can pave the way for new treatment options focusing on restoring the shifted balance.}, } @article {pmid24101210, year = {2013}, author = {Shi, JJ and Huang, JF and Zhang, F}, title = {Multi-year monitoring of paddy rice planting area in Northeast China using MODIS time series data.}, journal = {Journal of Zhejiang University. Science. B}, volume = {14}, number = {10}, pages = {934-946}, pmid = {24101210}, issn = {1862-1783}, mesh = {Agriculture/*methods ; Algorithms ; China ; Environmental Monitoring/methods ; Geographic Information Systems/*instrumentation ; Geography ; Image Processing, Computer-Assisted ; Models, Statistical ; Oryza/*genetics/*physiology ; Reproducibility of Results ; Satellite Imagery/instrumentation/statistics & numerical data ; Software ; Spatio-Temporal Analysis ; Time Factors ; Water Purification/methods ; }, abstract = {The objective of this study was to investigate the tempo-spatial distribution of paddy rice in Northeast China using moderate resolution imaging spectroradiometer (MODIS) data. We developed an algorithm for detection and estimation of the transplanting and flooding periods of paddy rice with a combination of enhanced vegetation index (EVI) and land surface water index with a central wavelength at 2130 nm (LSWI2130). In two intensive sites in Northeast China, fine resolution satellite imagery was used to validate the performance of the algorithm at pixel and 3×3 pixel window levels, respectively. The commission and omission errors in both of the intensive sites were approximately less than 20%. Based on the algorithm, annual distribution of paddy rice in Northeast China from 2001 to 2009 was mapped and analyzed. The results demonstrated that the MODIS-derived area was highly correlated with published agricultural statistical data with a coefficient of determination (R(2)) value of 0.847. It also revealed a sharp decline in 2003, especially in the Sanjiang Plain located in the northeast of Heilongjiang Province, due to the oversupply and price decline of rice in 2002. These results suggest that the approaches are available for accurate and reliable monitoring of rice cultivated areas and variation on a large scale.}, } @article {pmid24098800, year = {2013}, author = {Hayashi, Y and Shigenobu, S and Watanabe, D and Toga, K and Saiki, R and Shimada, K and Bourguignon, T and Lo, N and Hojo, M and Maekawa, K and Miura, T}, title = {Construction and characterization of normalized cDNA libraries by 454 pyrosequencing and estimation of DNA methylation levels in three distantly related termite species.}, journal = {PloS one}, volume = {8}, number = {9}, pages = {e76678}, pmid = {24098800}, issn = {1932-6203}, mesh = {Animals ; Computational Biology ; DNA Methylation/*genetics ; DNA Primers/genetics ; Expressed Sequence Tags ; *Gene Library ; *Genetic Variation ; Genetics, Population ; Hierarchy, Social ; Isoptera/*genetics ; Sequence Analysis, DNA/methods ; Species Specificity ; }, abstract = {In termites, division of labor among castes, categories of individuals that perform specialized tasks, increases colony-level productivity and is the key to their ecological success. Although molecular studies on caste polymorphism have been performed in termites, we are far from a comprehensive understanding of the molecular basis of this phenomenon. To facilitate future molecular studies, we aimed to construct expressed sequence tag (EST) libraries covering wide ranges of gene repertoires in three representative termite species, Hodotermopsis sjostedti, Reticulitermes speratus and Nasutitermes takasagoensis. We generated normalized cDNA libraries from whole bodies, except for guts containing microbes, of almost all castes, sexes and developmental stages and sequenced them with the 454 GS FLX titanium system. We obtained >1.2 million quality-filtered reads yielding >400 million bases for each of the three species. Isotigs, which are analogous to individual transcripts, and singletons were produced by assembling the reads and annotated using public databases. Genes related to juvenile hormone, which plays crucial roles in caste differentiation of termites, were identified from the EST libraries by BLAST search. To explore the potential for DNA methylation, which plays an important role in caste differentiation of honeybees, tBLASTn searches for DNA methyltransferases (dnmt1, dnmt2 and dnmt3) and methyl-CpG binding domain (mbd) were performed against the EST libraries. All four of these genes were found in the H. sjostedti library, while all except dnmt3 were found in R. speratus and N. takasagoensis. The ratio of the observed to the expected CpG content (CpG O/E), which is a proxy for DNA methylation level, was calculated for the coding sequences predicted from the isotigs and singletons. In all of the three species, the majority of coding sequences showed depletion of CpG O/E (less than 1), and the distributions of CpG O/E were bimodal, suggesting the presence of DNA methylation.}, } @article {pmid24098759, year = {2013}, author = {Ghosh, S and Singh, UK and Meli, VS and Kumar, V and Kumar, A and Irfan, M and Chakraborty, N and Chakraborty, S and Datta, A}, title = {Induction of senescence and identification of differentially expressed genes in tomato in response to monoterpene.}, journal = {PloS one}, volume = {8}, number = {9}, pages = {e76029}, pmid = {24098759}, issn = {1932-6203}, mesh = {Acyclic Monoterpenes ; Cell Wall/metabolism ; Cloning, Molecular ; Ethylenes/metabolism ; Gene Expression Profiling ; Gene Expression Regulation, Plant/*drug effects ; Gene Ontology ; Solanum lycopersicum/*drug effects/*growth & development/*metabolism ; Molecular Structure ; NADPH Oxidases/metabolism ; Reactive Oxygen Species/metabolism ; Terpenes/administration & dosage/chemistry/*pharmacology ; Transcriptome/*drug effects ; }, abstract = {Monoterpenes, which are among the major components of plant essential oils, are known for their ecological roles as well for pharmaceutical properties. Geraniol, an acyclic monoterpene induces cell cycle arrest and apoptosis/senescence in various cancer cells and plants; however, the genes involved in the process and the underlying molecular mechanisms are not well understood. In this study, we demonstrate that treatment of tomato plants with geraniol results in induction of senescence due to a substantial alteration in transcriptome. We have identified several geraniol-responsive protein encoding genes in tomato using suppression subtractive hybridization (SSH) approach. These genes comprise of various components of signal transduction, cellular metabolism, reactive oxygen species (ROS), ethylene signalling, apoptosis and DNA damage response. Upregulation of NADPH oxidase and antioxidant genes, and increase in ROS level after geraniol treatment point towards the involvement of ROS in geraniol-mediated senescence. The delayed onset of seedling death and induced expression of geraniol-responsive genes in geraniol-treated ethylene receptor mutant (Nr) suggest that geraniol-mediated senescence involves both ethylene dependent and independent pathways. Moreover, expression analysis during tomato ripening revealed that geraniol-responsive genes are also associated with the natural organ senescence process.}, } @article {pmid24096010, year = {2013}, author = {Martins, A and Guimarães, L and Guilhermino, L}, title = {Chronic toxicity of the veterinary antibiotic florfenicol to Daphnia magna assessed at two temperatures.}, journal = {Environmental toxicology and pharmacology}, volume = {36}, number = {3}, pages = {1022-1032}, doi = {10.1016/j.etap.2013.09.001}, pmid = {24096010}, issn = {1872-7077}, mesh = {Algorithms ; Animals ; Anti-Bacterial Agents/*toxicity ; Daphnia/*physiology ; Data Interpretation, Statistical ; Reproducibility of Results ; Spectrophotometry, Ultraviolet ; Temperature ; Thiamphenicol/*analogs & derivatives/toxicity ; Veterinary Drugs/*toxicity ; }, abstract = {The hypothesis that temperature variation is able to modify the chronic toxicity of the antibiotic florfenicol (FLO) to Daphnia magna was tested in the present study. Twenty-one day laboratory bioassays were carried out at 20 and 25 °C. FLO concentrations and its potential decay during the assays were checked by spectrophotometry. At 20 °C, FLO significantly reduced the D. magna somatic growth (≥1.6 mg/L) and impaired its reproduction (EC20=6.9 mg/L; EC50=7.6 mg/L), with the population growth rate becoming negative at 12.6 mg/L. At 25 °C, the EC values were lower (1.7 and 1.9 mg/L, respectively) than at 20 °C, as well as the lowest exposure concentration causing a negative population growth rate (3.1 mg/L). These results clearly indicate that temperature raise from 20 to 25 °C was able to modify the FLO toxicity. Therefore, more studies on the combined effects of temperature changes and environmental contaminants are needed to improve the basis for ecological risk assessment, environmental and human safety.}, } @article {pmid24094331, year = {2013}, author = {Nakhleh, L}, title = {Computational approaches to species phylogeny inference and gene tree reconciliation.}, journal = {Trends in ecology & evolution}, volume = {28}, number = {12}, pages = {719-728}, pmid = {24094331}, issn = {1872-8383}, support = {R01 LM009494/LM/NLM NIH HHS/United States ; R01LM009494/LM/NLM NIH HHS/United States ; }, mesh = {Animals ; Computational Biology/*trends ; *Phylogeny ; }, abstract = {An intricate relation exists between gene trees and species phylogenies, due to evolutionary processes that act on the genes within and across the branches of the species phylogeny. From an analytical perspective, gene trees serve as character states for inferring accurate species phylogenies, and species phylogenies serve as a backdrop against which gene trees are contrasted for elucidating evolutionary processes and parameters. In a 1997 paper, Maddison discussed this relation, reviewed the signatures left by three major evolutionary processes on the gene trees, and surveyed parsimony and likelihood criteria for utilizing these signatures to elucidate computationally this relation. Here, I review progress that has been made in developing computational methods for analyses under these two criteria, and survey remaining challenges.}, } @article {pmid24089937, year = {2013}, author = {Kramer, S and Bollt, EM}, title = {Spatially dependent parameter estimation and nonlinear data assimilation by autosynchronization of a system of partial differential equations.}, journal = {Chaos (Woodbury, N.Y.)}, volume = {23}, number = {3}, pages = {033101}, doi = {10.1063/1.4812722}, pmid = {24089937}, issn = {1089-7682}, mesh = {Algorithms ; Animals ; Data Interpretation, Statistical ; Ecology/methods ; Ecosystem ; Models, Statistical ; *Nonlinear Dynamics ; Oceans and Seas ; Phytoplankton/physiology ; Plankton ; Population Dynamics ; Predatory Behavior ; Remote Sensing Technology/methods ; Satellite Imagery ; Signal Processing, Computer-Assisted ; Species Specificity ; Zooplankton/physiology ; }, abstract = {Given multiple images that describe chaotic reaction-diffusion dynamics, parameters of a partial differential equation (PDE) model are estimated using autosynchronization, where parameters are controlled by synchronization of the model to the observed data. A two-component system of predator-prey reaction-diffusion PDEs is used with spatially dependent parameters to benchmark the methods described. Applications to modeling the ecological habitat of marine plankton blooms by nonlinear data assimilation through remote sensing are discussed.}, } @article {pmid24088796, year = {2013}, author = {Sugimoto, C and Ikeda, Y}, title = {Comparison of the ontogeny of hunting behavior in pharaoh cuttlefish (Sepia pharaonis) and oval squid (Sepioteuthis lessoniana).}, journal = {The Biological bulletin}, volume = {225}, number = {1}, pages = {50-59}, doi = {10.1086/BBLv225n1p50}, pmid = {24088796}, issn = {1939-8697}, mesh = {Animals ; Biological Ontologies ; Decapodiformes/anatomy & histology/*physiology ; *Predatory Behavior ; Species Specificity ; }, abstract = {Animals adopt various forms of hunting according to their ecological, morphological, and cognitive features, and their specific hunting skills are acquired ontogenetically in relation to these features. It is noted that cuttlefish and squid hunt prey through the elongation of tentacles used specifically to capture prey. However, these two cephalopods have different lifestyles, leading to questions such as whether hunting skill is acquired similarly after birth and whether tentacle elongation is behaviorally identical. To address these questions, we observed and compared how captive pharaoh cuttlefish (Sepia pharaonis) and oval squid (Sepioteuthis lessoniana) attack prey during their early life stages. Like the adults, S. pharaonis hatchlings used the tentacular lunge attack, whereas S. lessoniana hatchlings used the arm-opening attack. S. lessoniana began to exhibit the tentacular strike attack after 30 days of age. In addition to timing of the emergence of a specific hunting mode, some differences were observed in the physical aspect of hunting behavior. For cuttlefish, maximum tentacle length and maximum speed of tentacle elongation increased from hatching to 30 days of age and then decreased. In contrast, for squid, maximum tentacle length increased from hatching to 30 days of age and then became constant. The distance to prey was positively correlated with maximum length and speed of tentacle elongation in S. pharaonis and with maximum swimming speed in S. lessoniana. These results show that cuttlefish mainly use an ambush strategy and that squid use a pursuit strategy. Possible causes for the ontogenetic differences in hunting behavior are discussed.}, } @article {pmid24086671, year = {2013}, author = {Boyer, S and Wratten, SD and Holyoake, A and Abdelkrim, J and Cruickshank, RH}, title = {Using next-generation sequencing to analyse the diet of a highly endangered land snail (Powelliphanta augusta) feeding on endemic earthworms.}, journal = {PloS one}, volume = {8}, number = {9}, pages = {e75962}, pmid = {24086671}, issn = {1932-6203}, mesh = {Animals ; Computational Biology ; DNA/*genetics ; DNA Primers/genetics ; *Diet ; *Endangered Species ; Feces/chemistry ; Gene Library ; High-Throughput Nucleotide Sequencing/methods ; New Zealand ; Oligochaeta/*genetics ; RNA, Ribosomal, 16S/genetics ; Snails/*physiology ; }, abstract = {Predation is often difficult to observe or quantify for species that are rare, very small, aquatic or nocturnal. The assessment of such species' diet can be conducted using molecular methods that target prey DNA remaining in predators' guts and faeces. These techniques do not require high taxonomic expertise, are applicable to soft-bodied prey and allow for identification at the species level. However, for generalist predators, the presence of mixed prey DNA in guts and faeces can be a major impediment as it requires development of specific primers for each potential prey species for standard (Sanger) sequencing. Therefore, next generation sequencing methods have recently been applied to such situations. In this study, we used 454-pyrosequencing to analyse the diet of Powelliphantaaugusta, a carnivorous landsnail endemic to New Zealand and critically endangered after most of its natural habitat has been lost to opencast mining. This species was suspected to feed mainly on earthworms. Although earthworm tissue was not detectable in snail faeces, earthworm DNA was still present in sufficient quantity to conduct molecular analyses. Based on faecal samples collected from 46 landsnails, our analysis provided a complete map of the earthworm-based diet of P. augusta. Predated species appear to be earthworms that live in the leaf litter or earthworms that come to the soil surface at night to feed on the leaf litter. This indicates that P. augusta may not be selective and probably predates any earthworm encountered in the leaf litter. These findings are crucial for selecting future translocation areas for this highly endangered species. The molecular diet analysis protocol used here is particularly appropriate to study the diet of generalist predators that feed on liquid or soft-bodied prey. Because it is non-harmful and non-disturbing for the studied animals, it is also applicable to any species of conservation interest.}, } @article {pmid24086359, year = {2013}, author = {Sabri, A and Vandermoten, S and Leroy, PD and Haubruge, E and Hance, T and Thonart, P and De Pauw, E and Francis, F}, title = {Proteomic investigation of aphid honeydew reveals an unexpected diversity of proteins.}, journal = {PloS one}, volume = {8}, number = {9}, pages = {e74656}, pmid = {24086359}, issn = {1932-6203}, mesh = {Animals ; Aphids/*metabolism ; Bacterial Proteins/metabolism ; Databases, Protein ; Insect Proteins/*metabolism ; Proteomics/*methods ; Two-Dimensional Difference Gel Electrophoresis ; }, abstract = {Aphids feed on the phloem sap of plants, and are the most common honeydew-producing insects. While aphid honeydew is primarily considered to comprise sugars and amino acids, its protein diversity has yet to be documented. Here, we report on the investigation of the honeydew proteome from the pea aphid Acyrthosiphon pisum. Using a two-Dimensional Differential in-Gel Electrophoresis (2D-Dige) approach, more than 140 spots were isolated, demonstrating that aphid honeydew also represents a diverse source of proteins. About 66% of the isolated spots were identified through mass spectrometry analysis, revealing that the protein diversity of aphid honeydew originates from several organisms (i.e. the host aphid and its microbiota, including endosymbiotic bacteria and gut flora). Interestingly, our experiments also allowed to identify some proteins like chaperonin, GroEL and Dnak chaperones, elongation factor Tu (EF-Tu), and flagellin that might act as mediators in the plant-aphid interaction. In addition to providing the first aphid honeydew proteome analysis, we propose to reconsider the importance of this substance, mainly acknowledged to be a waste product, from the aphid ecology perspective.}, } @article {pmid24076510, year = {2013}, author = {Li, X and Lao, C and Liu, Y and Liu, X and Chen, Y and Li, S and Ai, B and He, Z}, title = {Early warning of illegal development for protected areas by integrating cellular automata with neural networks.}, journal = {Journal of environmental management}, volume = {130}, number = {}, pages = {106-116}, doi = {10.1016/j.jenvman.2013.08.055}, pmid = {24076510}, issn = {1095-8630}, mesh = {China ; *Conservation of Natural Resources ; Economic Development ; Geographic Information Systems ; Models, Theoretical ; *Neural Networks, Computer ; }, abstract = {Ecological security has become a major issue under fast urbanization in China. As the first two cities in this country, Shenzhen and Dongguan issued the ordinance of Eco-designated Line of Control (ELC) to "wire" ecologically important areas for strict protection in 2005 and 2009 respectively. Early warning systems (EWS) are a useful tool for assisting the implementation ELC. In this study, a multi-model approach is proposed for the early warning of illegal development by integrating cellular automata (CA) and artificial neural networks (ANN). The objective is to prevent the ecological risks or catastrophe caused by such development at an early stage. The integrated model is calibrated by using the empirical information from both remote sensing and handheld GPS (global positioning systems). The MAR indicator which is the ratio of missing alarms to all the warnings is proposed for better assessment of the model performance. It is found that the fast urban development has caused significant threats to natural-area protection in the study area. The integration of CA, ANN and GPS provides a powerful tool for describing and predicting illegal development which is in highly non-linear and fragmented forms. The comparison shows that this multi-model approach has much better performances than the single-model approach for the early warning. Compared with the single models of CA and ANN, this integrated multi-model can improve the value of MAR by 65.48% and 5.17% respectively.}, } @article {pmid24069279, year = {2013}, author = {Garcia-Vedrenne, AE and Groner, M and Page-Karjian, A and Siegmund, GF and Singhal, S and Sziklay, J and Roberts, S}, title = {Development of genomic resources for a thraustochytrid pathogen and investigation of temperature influences on gene expression.}, journal = {PloS one}, volume = {8}, number = {9}, pages = {e74196}, pmid = {24069279}, issn = {1932-6203}, mesh = {Animals ; Base Composition ; Computational Biology/methods ; *Gene Expression Regulation ; Genome Size ; Genome, Protozoan ; Genomics ; Mercenaria/*genetics ; Polymorphism, Single Nucleotide ; *Temperature ; Transcriptome ; }, abstract = {Understanding how environmental changes influence the pathogenicity and virulence of infectious agents is critical for predicting epidemiological patterns of disease. Thraustochytrids, part of the larger taxonomic class Labyrinthulomycetes, contain several highly pathogenic species, including the hard clam pathogen quahog parasite unknown (QPX). QPX has been associated with large-scale mortality events along the northeastern coast of North America. Growth and physiology of QPX is temperature-dependent, and changes in local temperature profiles influence pathogenicity. In this study we characterize the partial genome of QPX and examine the influence of temperature on gene expression. Genes involved in several biological processes are differentially expressed upon temperature change, including those associated with altered growth and metabolism and virulence. The genomic and transcriptomic resources developed in this study provide a foundation for better understanding virulence, pathogenicity and life history of thraustochytrid pathogens.}, } @article {pmid24066564, year = {2013}, author = {Quan, ZJ and Li, Y and Li, JS and Han, Y and Xiao, NW and Fu, MD}, title = {[Ecological vulnerability of coal mining area: a case study of Shengli Coalfield in Xilinguole of Inner Mongolia, China].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {24}, number = {6}, pages = {1729-1738}, pmid = {24066564}, issn = {1001-9332}, mesh = {China ; *Coal Mining ; *Ecosystem ; Geographic Information Systems ; *Models, Theoretical ; Remote Sensing Technology ; }, abstract = {In this paper, an ecological vulnerability evaluation index system for the Shengli Coalfield in Xilinguole of Inner Mongolia was established, which included 16 factors in ecological sensitivity, natural and social pressure, and ecological recovery capacity, respectively. Based on the expert scoring method and analytic hierarchy process (AHP), an ecological vulnerability model was built for the calculation of the regional ecological vulnerability by means of RS and GIS spatial analysis. An analysis of the relationships between land use and ecological vulnerability was also made, and the results were tested by spatial auto-correlation analysis. Overall, the ecological vulnerability of the study area was at medium-high level. The exploitation of four opencast areas in the Coalfield caused a significant increase of ecological vulnerability. Moreover, due to the effects of mine drained water and human activities, the 300 -2000 m around the opencast areas was turning into higher ecologically fragile area. With further exploitation, the whole Coalfield was evolved into moderate and heavy ecological vulnerability area, and the coal resources mining was a key factor in this process. The cluster analysis showed that the spatial distribution of the ecological vulnerability in the study area had reasonable clustering characteristics. To decrease the population density, control the grazing capacity of grassland, and regulate the ratios of construction land and cultivated land could be the optimal ways for resolving the natural and social pressure, and to increase the investment and improve the vegetation recovery coefficient could be the fundamental measures for decreasing the ecological vulnerability of the study area.}, } @article {pmid24063811, year = {2013}, author = {Lane-deGraaf, KE and Kennedy, RC and Arifin, SM and Madey, GR and Fuentes, A and Hollocher, H}, title = {A test of agent-based models as a tool for predicting patterns of pathogen transmission in complex landscapes.}, journal = {BMC ecology}, volume = {13}, number = {}, pages = {35}, pmid = {24063811}, issn = {1472-6785}, mesh = {Animal Distribution ; Animals ; Computer Simulation ; Ecology/methods ; Entamoeba/*pathogenicity ; Entamoebiasis/*transmission ; *Environment ; Gene Flow ; Geographic Information Systems ; Macaca/genetics/*parasitology ; *Models, Biological ; }, abstract = {BACKGROUND: Landscape complexity can mitigate or facilitate host dispersal, influencing patterns of pathogen transmission. Spatial transmission of pathogens through landscapes, therefore, presents an important but not fully elucidated aspect of transmission dynamics. Using an agent-based model (LiNK) that incorporates GIS data, we examined the effects of landscape information on the spatial patterns of host movement and pathogen transmission in a system of long-tailed macaques and their gut parasites. We first examined the role of the landscape to identify any individual or additive effects on host movement. We then compared modeled dispersal distance to patterns of actual macaque gene flow to both confirm our model's predictions and to understand the role of individual land uses on dispersal. Finally, we compared the rate and the spread of two gastrointestinal parasites, Entamoeba histolytica and E. dispar, to understand how landscape complexity influences spatial patterns of pathogen transmission.

RESULTS: LiNK captured emergent properties of the landscape, finding that interaction effects between landscape layers could mitigate the rate of infection in a non-additive way. We also found that the inclusion of landscape information facilitated an accurate prediction of macaque dispersal patterns across a complex landscape, as confirmed by Mantel tests comparing genetic and simulated dispersed distances. Finally, we demonstrated that landscape heterogeneity proved a significant barrier for a highly virulent pathogen, limiting the dispersal ability of hosts and thus its own transmission into distant populations.

CONCLUSIONS: Landscape complexity plays a significant role in determining the path of host dispersal and patterns of pathogen transmission. Incorporating landscape heterogeneity and host behavior into disease management decisions can be important in targeting response efforts, identifying cryptic transmission opportunities, and reducing or understanding potential for unintended ecological and evolutionary consequences. The inclusion of these data into models of pathogen transmission patterns improves our understanding of these dynamics, ultimately proving beneficial for sound public health policy.}, } @article {pmid24063355, year = {2013}, author = {Fletcher, RS and Mullen, JL and Yoder, S and Bauerle, WL and Reuning, G and Sen, S and Meyer, E and Juenger, TE and McKay, JK}, title = {Development of a next-generation NIL library in Arabidopsis thaliana for dissecting complex traits.}, journal = {BMC genomics}, volume = {14}, number = {}, pages = {655}, pmid = {24063355}, issn = {1471-2164}, mesh = {Arabidopsis/*genetics ; Chromosomes, Plant/genetics ; Crosses, Genetic ; *Gene Library ; Gene Ontology ; Genetic Markers ; Genome, Plant/genetics ; Genotype ; Genotyping Techniques ; Heterozygote ; Homozygote ; *Inbreeding ; Lod Score ; Physical Chromosome Mapping ; Polymorphism, Genetic ; Quantitative Trait Loci/genetics ; *Quantitative Trait, Heritable ; Reproducibility of Results ; }, abstract = {BACKGROUND: The identification of the loci and specific alleles underlying variation in quantitative traits is an important goal for evolutionary biologists and breeders. Despite major advancements in genomics technology, moving from QTL to causal alleles remains a major challenge in genetics research. Near-isogenic lines are the ideal raw material for QTL validation, refinement of QTL location and, ultimately, gene discovery.

RESULTS: In this study, a population of 75 Arabidopsis thaliana near-isogenic lines was developed from an existing recombinant inbred line (RIL) population derived from a cross between physiologically divergent accessions Kas-1 and Tsu-1. First, a novel algorithm was developed to utilize genome-wide marker data in selecting RILs fully isogenic to Kas-1 for a single chromosome. Seven such RILs were used in 2 generations of crossing to Tsu-1 to create BC1 seed. BC1 plants were genotyped with SSR markers so that lines could be selected that carried Kas-1 introgressions, resulting in a population carrying chromosomal introgressions spanning the genome. BC1 lines were genotyped with 48 genome-wide SSRs to identify lines with a targeted Kas-1 introgression and the fewest genomic introgressions elsewhere. 75 such lines were selected and genotyped at an additional 41 SNP loci and another 930 tags using 2b-RAD genotyping by sequencing. The final population carried an average of 1.35 homozygous and 2.49 heterozygous introgressions per line with average introgression sizes of 5.32 and 5.16 Mb, respectively. In a simple case study, we demonstrate the advantage of maintaining heterozygotes in our library whereby fine-mapping efforts are conducted simply by self-pollination. Crossovers in the heterozygous interval during this single selfing generation break the introgression into smaller, homozygous fragments (sub-NILs). Additionally, we utilize a homozygous NIL for validation of a QTL underlying stomatal conductance, a low heritability trait.

CONCLUSIONS: The present results introduce a new and valuable resource to the Brassicaceae research community that enables rapid fine-mapping of candidate loci in parallel with QTL validation. These attributes along with dense marker coverage and genome-wide chromosomal introgressions make this population an ideal starting point for discovery of genes underlying important complex traits of agricultural and ecological significance.}, } @article {pmid24063231, year = {2013}, author = {Zhao, Q and Yu, S and Shi, J}, title = {[Applications of elementary mode analysis in biological network and pathway analysis].}, journal = {Sheng wu gong cheng xue bao = Chinese journal of biotechnology}, volume = {29}, number = {6}, pages = {701-715}, pmid = {24063231}, issn = {1000-3061}, mesh = {Algorithms ; Bacteria/genetics/*metabolism ; *Computational Biology ; Computer Simulation ; Humans ; Metabolic Engineering/*methods ; *Metabolic Networks and Pathways ; Signal Transduction ; Software ; }, abstract = {Elementary mode analysis is the widely applied tool in metabolic pathway analysis. Studies based on elementary mode analysis (EMA) were performed for both metabolic network and signal transduction network. Its analytical objective is from cell to bioreactor, and even ecological system. EMA is available to describe biological behaviors by steady state and dynamic models. Not only microorganism metabolism but also human health could be evaluated by EMA. The algorithms and software for calculating elementary mode (EM) were analyzed. The applications of EMA are reviewed such as special metabolic pathway and robustness of metabolic network, metabolic flux decomposition, metabolic flux analysis at steady state, dynamic model and bioprocess simulation, network structure and regulation, strain design and signal transduction network. Solving combinatorial explosion, exploring the relations between EM and metabolic regulation, and improving the algorithm efficiency of strain design are important issues of EMA in future.}, } @article {pmid24060384, year = {2013}, author = {Libralato, G and Minetto, D and Totaro, S and Mičetić, I and Pigozzo, A and Sabbioni, E and Marcomini, A and Volpi Ghirardini, A}, title = {Embryotoxicity of TiO2 nanoparticles to Mytilus galloprovincialis (Lmk).}, journal = {Marine environmental research}, volume = {92}, number = {}, pages = {71-78}, doi = {10.1016/j.marenvres.2013.08.015}, pmid = {24060384}, issn = {1879-0291}, mesh = {Animals ; Ecotoxicology/*methods ; Embryo, Nonmammalian/drug effects ; Female ; Larva/drug effects ; Microscopy, Electron, Transmission ; Mytilus/*drug effects/*embryology ; Nanoparticles/analysis/*toxicity ; Regression Analysis ; Titanium/*toxicity ; Water Pollutants, Chemical/toxicity ; }, abstract = {Few data exist on the ecotoxicological effects of nanosized titanium dioxide (nTiO2) towards marine species with specific reference to bivalve molluscs and their relative life stages. Mytilus galloprovincialis Lamarck was selected to assess the potential adverse effects of nTiO2 (0-64 mg/L) on its early larval development stages (pre-D shell stage, malformed D-shell stage and normal D-shell stage larvae) considering two exposure scenarios characterised by total darkness (ASTM protocol) and natural photoperiod (light/dark). This approach was considered to check the presence of potential effects associated to the photocatalytic properties of nTiO2. Parallel experiments were carried on with the bulk reference TiCl4. The toxicity of nTiO2 showed to be mainly related to its "nano" condition and to be influenced by the exposure to light that supported the increase in the number of pre-D shell stage (retarded) larvae compared to the malformed ones especially at the maximum effect concentrations (4 and 8 mg nTiO2/L). The non-linear regression toxicity data analysis showed the presence of two EC50 values per exposure scenario: a) EC(50)1 = 1.23 mg/L (0.00-4.15 mg/L) and EC(50)2 = 38.56 mg/L (35.64-41.47 mg/L) for the dark exposure conditions; b) EC(50)1 = 1.65 mg/L (0.00-4.74 mg/L) and EC(50)2 = 16.39 mg/L (13.31-19.48 mg/L) for the light/dark exposure conditions. The potential implication of agglomeration and sedimentation phenomena on ecotoxicological data was discussed.}, } @article {pmid24060132, year = {2013}, author = {Sloan, DB and Bennett, GM and Engel, P and Williams, D and Ochman, H}, title = {Disentangling associated genomes.}, journal = {Methods in enzymology}, volume = {531}, number = {}, pages = {445-464}, doi = {10.1016/B978-0-12-407863-5.00020-4}, pmid = {24060132}, issn = {1557-7988}, support = {F32 GM099334/GM/NIGMS NIH HHS/United States ; R01 GM074738/GM/NIGMS NIH HHS/United States ; GM101209/GM/NIGMS NIH HHS/United States ; 1F32GM099334/GM/NIGMS NIH HHS/United States ; R01 GM056120/GM/NIGMS NIH HHS/United States ; }, mesh = {Algorithms ; Bacteria/*genetics ; *Computational Biology ; *Genome, Bacterial ; Metagenomics/*methods ; }, abstract = {The recovery and assembly of genome sequences from samples containing communities of organisms pose several challenges. Because it is rarely possible to disassociate the resident organisms prior to sequencing, a major obstacle is the assignment of sequences to a single genome that can be fully assembled. This chapter delineates many of the decisions, methodologies, and approaches that can lead to the generation of complete or nearly complete microbial genome sequences from heterogeneous samples-that is, the procedures that allow us to turn metagenomes into genomes.}, } @article {pmid24060131, year = {2013}, author = {Navas-Molina, JA and Peralta-Sánchez, JM and González, A and McMurdie, PJ and Vázquez-Baeza, Y and Xu, Z and Ursell, LK and Lauber, C and Zhou, H and Song, SJ and Huntley, J and Ackermann, GL and Berg-Lyons, D and Holmes, S and Caporaso, JG and Knight, R}, title = {Advancing our understanding of the human microbiome using QIIME.}, journal = {Methods in enzymology}, volume = {531}, number = {}, pages = {371-444}, pmid = {24060131}, issn = {1557-7988}, support = {R01 GM086884/GM/NIGMS NIH HHS/United States ; T32 GM008759/GM/NIGMS NIH HHS/United States ; T32 GM142607/GM/NIGMS NIH HHS/United States ; R01GM086884/GM/NIGMS NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; }, mesh = {Animals ; Bacteria/*genetics/pathogenicity ; Computational Biology ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Mice ; Microbiota/*genetics ; Phylogeny ; Software ; }, abstract = {High-throughput DNA sequencing technologies, coupled with advanced bioinformatics tools, have enabled rapid advances in microbial ecology and our understanding of the human microbiome. QIIME (Quantitative Insights Into Microbial Ecology) is an open-source bioinformatics software package designed for microbial community analysis based on DNA sequence data, which provides a single analysis framework for analysis of raw sequence data through publication-quality statistical analyses and interactive visualizations. In this chapter, we demonstrate the use of the QIIME pipeline to analyze microbial communities obtained from several sites on the bodies of transgenic and wild-type mice, as assessed using 16S rRNA gene sequences generated on the Illumina MiSeq platform. We present our recommended pipeline for performing microbial community analysis and provide guidelines for making critical choices in the process. We present examples of some of the types of analyses that are enabled by QIIME and discuss how other tools, such as phyloseq and R, can be applied to expand upon these analyses.}, } @article {pmid24060130, year = {2013}, author = {Preheim, SP and Perrotta, AR and Friedman, J and Smilie, C and Brito, I and Smith, MB and Alm, E}, title = {Computational methods for high-throughput comparative analyses of natural microbial communities.}, journal = {Methods in enzymology}, volume = {531}, number = {}, pages = {353-370}, doi = {10.1016/B978-0-12-407863-5.00018-6}, pmid = {24060130}, issn = {1557-7988}, mesh = {Classification ; Computational Biology/*methods ; Genetic Variation ; High-Throughput Nucleotide Sequencing ; Humans ; *Metagenomics ; Microbial Consortia/*genetics ; Phylogeny ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, DNA ; }, abstract = {One of the most widely employed methods in metagenomics is the amplification and sequencing of the highly conserved ribosomal RNA (rRNA) genes from organisms in complex microbial communities. rRNA surveys, typically using the 16S rRNA gene for prokaryotic identification, provide information about the total diversity and taxonomic affiliation of organisms present in a sample. Greatly enhanced by high-throughput sequencing, these surveys have uncovered the remarkable diversity of uncultured organisms and revealed unappreciated ecological roles ranging from nutrient cycling to human health. This chapter outlines the best practices for comparative analyses of microbial community surveys. We explain how to transform raw data into meaningful units for further analysis and discuss how to calculate sample diversity and community distance metrics. Finally, we outline how to find associations of species with specific metadata and true correlations between species from compositional data. We focus on data generated by next-generation sequencing platforms, using the Illumina platform as a test case, because of its widespread use especially among researchers just entering the field.}, } @article {pmid24059730, year = {2014}, author = {Newman, MG and Przeworski, A and Consoli, AJ and Taylor, CB}, title = {A randomized controlled trial of ecological momentary intervention plus brief group therapy for generalized anxiety disorder.}, journal = {Psychotherapy (Chicago, Ill.)}, volume = {51}, number = {2}, pages = {198-206}, pmid = {24059730}, issn = {1939-1536}, support = {R01 MH039172-13/MH/NIMH NIH HHS/United States ; }, mesh = {Adult ; Anxiety Disorders/psychology/*therapy ; Cognitive Behavioral Therapy/*methods ; Female ; Follow-Up Studies ; Humans ; Male ; Middle Aged ; Pilot Projects ; Psychiatric Status Rating Scales/statistics & numerical data ; Psychotherapy, Group/*methods ; Therapy, Computer-Assisted/*methods ; Treatment Outcome ; }, abstract = {Momentary intervention has been proposed as a cost-effective, generalizable, and ecologically valid method to increase the efficiency of face-to-face cognitive-behavioral therapy (CBT). The purpose of the current pilot study was to evaluate the efficacy of a six-session palmtop computer-assisted Group CBT for generalized anxiety disorder (GAD) (CAGT6) in comparison with a six-session Group CBT for GAD without the computer (CBGT6) and typical (12 session) Group CBT for GAD (CBGT12) in a randomized controlled trial. Thirty-four individuals with a primary diagnosis of GAD were randomized to one of the three conditions and completed measures of GAD and anxiety before therapy, after therapy, and at 6-, and 12-month follow-ups. Results indicated that CAGT6 was superior to CBGT6 at posttreatment, but not significantly different from CBGT12. At 6- and 12-month follow-ups, CAGT6 was neither significantly different from CBGT6, nor from CBGT12. Percentages of individuals achieving reliable change on two of the three GAD measures favored CAGT6 over CBGT6 at posttreatment, suggesting promise for the added value of the mobile technology.}, } @article {pmid24058638, year = {2013}, author = {Groen, Y and Gaastra, GF and Lewis-Evans, B and Tucha, O}, title = {Risky behavior in gambling tasks in individuals with ADHD--a systematic literature review.}, journal = {PloS one}, volume = {8}, number = {9}, pages = {e74909}, pmid = {24058638}, issn = {1932-6203}, mesh = {Attention Deficit Disorder with Hyperactivity/physiopathology/*psychology ; Female ; Gambling/physiopathology/*psychology ; Humans ; Male ; PubMed ; *Risk-Taking ; }, abstract = {OBJECTIVE: The aim of this review was to gain insight into the relationship between Attention deficit hyperactivity disorder (ADHD) and risky performance in gambling tasks and to identify any potential alternate explanatory factors.

METHODS: PsycINFO, PubMed, and Web of Knowledge were searched for relevant literature comparing individuals with ADHD to normal controls (NCs) in relation to their risky performance on a gambling task. In total, fourteen studies in children/adolescents and eleven studies in adults were included in the review.

RESULTS: Half of the studies looking at children/adolescents with ADHD found evidence that they run more risks on gambling tasks when compared to NCs. Only a minority of the studies on adults with ADHD reported aberrant risky behavior. The effect sizes ranged from small to large for both age groups and the outcome pattern did not differ between studies that applied an implicit or explicit gambling task. Two studies demonstrated that comorbid oppositional defiant disorder (ODD) and conduct disorder (CD) increased risky behavior in ADHD. Limited and/or inconsistent evidence was found that comorbid internalizing disorders (IDs), ADHD subtype, methylphenidate use, and different forms of reward influenced the outcomes.

CONCLUSION: The evidence for increased risky performance of individuals with ADHD on gambling tasks is mixed, but is stronger for children/adolescents with ADHD than for adults with ADHD, which may point to developmental changes in reward and/or penalty sensitivity or a publication bias for positive findings in children/adolescents. The literature suggests that comorbid ODD/CD is a risk factor in ADHD for increased risky behavior. Comorbid IDs, ADHD subtype, methylphenidate use, and the form of reward received may affect risky performance in gambling tasks; however, these factors need further examination. Finally, the implications of the findings for ADHD models and the ecological validity of gambling tasks are discussed.}, } @article {pmid24056322, year = {2013}, author = {Dagnino, A and Bo, T and Copetta, A and Fenoglio, S and Oliveri, C and Bencivenga, M and Felli, A and Viarengo, A}, title = {Development and application of an innovative expert decision support system to manage sediments and to assess environmental risk in freshwater ecosystems.}, journal = {Environment international}, volume = {60}, number = {}, pages = {171-182}, doi = {10.1016/j.envint.2013.08.011}, pmid = {24056322}, issn = {1873-6750}, mesh = {Biodiversity ; *Decision Making, Computer-Assisted ; Decision Support Techniques ; *Ecosystem ; Environmental Monitoring/*methods ; *Expert Systems ; Fresh Water/*analysis ; Geologic Sediments/*analysis/microbiology/parasitology ; Humans ; Italy ; Mutagenicity Tests ; Rivers/chemistry/microbiology/parasitology ; Water Pollutants, Chemical/*analysis ; }, abstract = {With the aim of supporting decision makers to manage contamination in freshwater environments, an innovative expert decision support system (EDSS) was developed. The EDSS was applied in a sediment quality assessment along the Bormida river (NW, Italy) which has been heavily contaminated by an upstream industrial site for more than a century. Sampling sites were classified by means of comparing chemical concentrations with effect-based target values (threshold and probable effect concentrations). The level of each contaminant and the combined toxic pressure were used to rank sites into three categories: (i) uncontaminated (8 sites), (ii) mildly contaminated (4) and (iii) heavily contaminated (19). In heavily contaminated sediments, an environmental risk index (EnvRI) was determined by means of integrating chemical data with ecotoxicological and ecological parameters (triad approach). In addition a sediment risk index (SedRI) was computed from combining chemical and ecotoxicological data. Eight sites exhibited EnvRI values ≥0.25, the safety threshold level (range of EnvRI values: 0.14-0.31) whereas SedRI exceeded the safety threshold level at 6 sites (range of SedRI values: 0.16-0.36). At sites classified as mildly contaminated, sublethal biomarkers were integrated with chemical data into a biological vulnerability index (BVI), which exceeded the safety threshold level at one site (BVI value: 0.28). Finally, potential human risk was assessed in selected stations (11 sites) by integrating genotoxicity biomarkers (GTI index falling in the range 0.00-0.53). General conclusions drawn from the EDSS data include: (i) in sites classified as heavily contaminated, only a few exhibited some significant, yet limited, effects on biodiversity; (ii) restrictions in re-using sediments from heavily contaminated sites found little support in ecotoxicological data; (iii) in the majority of the sites classified as mildly contaminated, tested organisms exhibited low response levels; (iv) preliminary results on genotoxicity biomarkers indicate possible negative consequences for humans if exposed to river sediments from target areas.}, } @article {pmid24056283, year = {2013}, author = {Rodríguez-Morales, B and Díaz-Varela, ER and Marey-Pérez, MF}, title = {Spatiotemporal analysis of vehicle collisions involving wild boar and roe deer in NW Spain.}, journal = {Accident; analysis and prevention}, volume = {60}, number = {}, pages = {121-133}, doi = {10.1016/j.aap.2013.07.032}, pmid = {24056283}, issn = {1879-2057}, mesh = {Accidents, Traffic/prevention & control/*statistics & numerical data ; Animals ; Cluster Analysis ; Databases, Factual ; *Deer ; Environment Design ; Geographic Information Systems ; Humans ; Models, Statistical ; Risk Factors ; Safety ; Seasons ; Spain ; *Spatio-Temporal Analysis ; *Sus scrofa ; }, abstract = {Ungulate-vehicle collisions pose a serious traffic safety hazard in the North of Spain. The understanding of underlying temporal and spatial structure of these non-random events is imperative to develop appropriate mitigation measures. This study analyses the temporal, spatial and spatiotemporal patterns of car crashes involving wild boar and roe deer in the province of Lugo (NW Spain) in the period 2006-2010 using geographic information systems (GIS) and spatial statistics. The temporal analysis--conducted at three scales: daily, weekly and seasonal--revealed that accidents are related to specific animal's life cycles and to interactions with human activities. The localization of collision points with GIS discovered the sections of the autonomic road network where accidents with the two studied species concentrate. Besides, the spatial arrangement of significant hotspots was mapped through kernel density estimation over two time scales (daily and seasonal), distinguishing among 41 sets, sequentially arranged to facilitate clustering comparison and determination of spatiotemporal risky areas. This work is of valuable help for road managers to design the appropriate mitigation measures that will improve traffic safety and animal welfare.}, } @article {pmid24055723, year = {2013}, author = {Fu, D and Wei, L and Xiao, M and Hayward, A}, title = {New insights into helitron transposable elements in the mesopolyploid species Brassica rapa.}, journal = {Gene}, volume = {532}, number = {2}, pages = {236-245}, doi = {10.1016/j.gene.2013.09.033}, pmid = {24055723}, issn = {1879-0038}, mesh = {Base Composition ; Base Sequence ; Brassica rapa/*genetics ; Chromosome Mapping ; *DNA Transposable Elements ; Gene Ontology ; *Genes, Plant ; MicroRNAs/genetics ; Microsatellite Repeats ; Molecular Sequence Annotation ; }, abstract = {Helitrons are DNA transposable elements that are widely present in the genomes of diverse eukaryotic taxa. Helitrons are distinct from other transposons in their ability to capture gene fragments and their rolling-replication mechanism. Brassica rapa is a mesopolyploid species and one of the most important vegetable and oil crops globally. A total of 787 helitrons were identified in the B. rapa genome and were assigned to 662 families and 700 subfamilies. More than 21,806 repetitive sequences were found within the helitrons, whose G+C content correlated negatively to that of the host helitron. Each helitron contained an average of 2.9 gene fragments and 1.9 intact genes, of which the majority were annotated with binding functions in metabolic processes. In addition, a set of 114 nonredundant microRNAs were detected within 174 helitrons and predicted to regulate a set of 787 nonredundant target genes. These results suggest that helitrons contribute to genomic structural and transcriptional variation by capturing gene fragments and generating microRNAs.}, } @article {pmid24051802, year = {2013}, author = {Roth, RE}, title = {An empirically-derived taxonomy of interaction primitives for interactive cartography and geovisualization.}, journal = {IEEE transactions on visualization and computer graphics}, volume = {19}, number = {12}, pages = {2356-2365}, doi = {10.1109/TVCG.2013.130}, pmid = {24051802}, issn = {1941-0506}, mesh = {*Algorithms ; Artificial Intelligence ; *Computer Graphics ; *Expert Systems ; Geography/*methods ; Humans ; Image Enhancement/methods ; Image Interpretation, Computer-Assisted/methods ; *Maps as Topic ; Multimodal Imaging/*methods ; Pattern Recognition, Visual/*physiology ; Reproducibility of Results ; Sensitivity and Specificity ; *User-Computer Interface ; }, abstract = {Proposals to establish a 'science of interaction' have been forwarded from Information Visualization and Visual Analytics, as well as Cartography, Geovisualization, and GIScience. This paper reports on two studies to contribute to this call for an interaction science, with the goal of developing a functional taxonomy of interaction primitives for map-based visualization. A semi-structured interview study first was conducted with 21 expert interactive map users to understand the way in which map-based visualizations currently are employed. The interviews were transcribed and coded to identify statements representative of either the task the user wished to accomplish (i.e., objective primitives) or the interactive functionality included in the visualization to achieve this task (i.e., operator primitives). A card sorting study then was conducted with 15 expert interactive map designers to organize these example statements into logical structures based on their experience translating client requests into interaction designs. Example statements were supplemented with primitive definitions in the literature and were separated into two sorting exercises: objectives and operators. The objective sort suggested five objectives that increase in cognitive sophistication (identify, compare, rank, associate, & delineate), but exhibited a large amount of variation across participants due to consideration of broader user goals (procure, predict, & prescribe) and interaction operands (space-alone, attributes-in-space, & space-in-time; elementary & general). The operator sort suggested five enabling operators (import, export, save, edit, & annotate) and twelve work operators (reexpress, arrange, sequence, resymbolize, overlay, pan, zoom, reproject, search, filter, retrieve, & calculate). This taxonomy offers an empirically-derived and ecologically-valid structure to inform future research and design on interaction.}, } @article {pmid24050412, year = {2013}, author = {Kirchner, TR and Cantrell, J and Anesetti-Rothermel, A and Ganz, O and Vallone, DM and Abrams, DB}, title = {Geospatial exposure to point-of-sale tobacco: real-time craving and smoking-cessation outcomes.}, journal = {American journal of preventive medicine}, volume = {45}, number = {4}, pages = {379-385}, pmid = {24050412}, issn = {1873-2607}, support = {RC1 DA028710/DA/NIDA NIH HHS/United States ; RC1-DA028710/DA/NIDA NIH HHS/United States ; }, mesh = {Adult ; District of Columbia/epidemiology ; Female ; *Geographic Information Systems ; Humans ; Male ; Marketing/*statistics & numerical data ; Middle Aged ; Recurrence ; Smoking Cessation/*psychology ; Socioeconomic Factors ; Tobacco Use Disorder/*psychology ; Tobacco Products ; }, abstract = {BACKGROUND: Little is known about the factors that drive the association between point-of-sale marketing and behavior, because methods that directly link individual-level use outcomes to real-world point-of-sale exposure are only now beginning to be developed.

PURPOSE: Daily outcomes during smoking cessation were examined as a function of both real-time geospatial exposure to point-of-sale tobacco (POST) and subjective craving to smoke.

METHODS: Continuous individual geospatial location data collected over the first month of a smoking-cessation attempt in 2010-2012 (N=475) were overlaid on a POST outlet geodatabase (N=1060). Participants' mobility data were used to quantify the number of times they came into contact with a POST outlet. Participants recorded real-time craving levels and smoking status via ecological momentary assessment (EMA) on cellular telephones.

RESULTS: The final data set spanned a total of 12,871 days of EMA and geospatial tracking. Lapsing was significantly more likely on days with any POST contact (OR=1.19, 95% CI=1.18, 1.20), and increasingly likely as the number of daily POST contacts increased (OR=1.07, 95% CI=1.06, 1.08). Overall, daily POST exposure was significantly associated with lapsing when craving was low (OR=1.22, 95% CI=1.20, 1.23); high levels of craving were more directly associated with lapse outcomes.

CONCLUSIONS: These data shed light on the way mobility patterns drive a dynamic interaction between individuals and the POST environment, demonstrating that quantification of individuals' exposure to POST marketing can be used to identify previously unrecognized patterns of association among individual mobility, the built environment, and behavioral outcomes.}, } @article {pmid24046238, year = {2014}, author = {Mamat, Z and Yimit, H and Eziz, A and Ablimit, A}, title = {Oasis land-use change and its effects on the eco-environment in Yanqi Basin, Xinjiang, China.}, journal = {Environmental monitoring and assessment}, volume = {186}, number = {1}, pages = {335-348}, pmid = {24046238}, issn = {1573-2959}, mesh = {Agriculture ; Biodiversity ; China ; Climate ; *Conservation of Natural Resources ; Economic Development ; *Ecosystem ; *Environmental Monitoring ; Geographic Information Systems ; Water Supply ; Wetlands ; }, abstract = {Satellite data and the published coefficients about the world's and China's ecosystem were used to analyze the effects of land-use changes on the ecosystem service in the Yanqi Basin. Both economic developments and arid, fragile ecosystems have strongly affected the land use. A sensitivity analysis determined the effect of manipulating the coefficients on the estimated values. Results indicated that (1) the total value of ecosystem services in the Yanqi Basin were 9,374.66, 10,450.52, 9,964.20, and 9,8707.77 million Yuan in 1990, 2000, 2005, and 2011, respectively. The net increase in ecosystem service values were about 496.11 million Yuan within 1990-2011; (2) The aggregated ecosystem service values of water body, wetlands, grasslands, and croplands were about 99.25 % of the total value; (3) Waste treatment and soil formation were the top two ecological functions with high service values and contributing about 61.70 % of the total service values; and (4) Ecosystem service values estimated in this study were inelastic with respect to the value coefficients; therefore, the estimation was robust in spite of uncertainties on the value coefficients. A reasonable land-use plan should be based on rigorous environmental impact analyses for maintaining stability and sustainable development of the Yanqi Basin.}, } @article {pmid24045641, year = {2013}, author = {Wang, Q and Quensen, JF and Fish, JA and Lee, TK and Sun, Y and Tiedje, JM and Cole, JR}, title = {Ecological patterns of nifH genes in four terrestrial climatic zones explored with targeted metagenomics using FrameBot, a new informatics tool.}, journal = {mBio}, volume = {4}, number = {5}, pages = {e00592-13}, pmid = {24045641}, issn = {2150-7511}, support = {UH3 DK083993/DK/NIDDK NIH HHS/United States ; UH3DK083993/DK/NIDDK NIH HHS/United States ; }, mesh = {Alaska ; Algorithms ; Amino Acid Sequence ; Bacteria/classification/*enzymology/genetics/isolation & purification ; Bacterial Proteins/*genetics ; Ecosystem ; Florida ; Frameshift Mutation ; Hawaii ; Metagenomics/*instrumentation/methods ; Molecular Sequence Data ; Oxidoreductases/*genetics ; Phylogeny ; Soil Microbiology ; Utah ; }, abstract = {UNLABELLED: Biological nitrogen fixation is an important component of sustainable soil fertility and a key component of the nitrogen cycle. We used targeted metagenomics to study the nitrogen fixation-capable terrestrial bacterial community by targeting the gene for nitrogenase reductase (nifH). We obtained 1.1 million nifH 454 amplicon sequences from 222 soil samples collected from 4 National Ecological Observatory Network (NEON) sites in Alaska, Hawaii, Utah, and Florida. To accurately detect and correct frameshifts caused by indel sequencing errors, we developed FrameBot, a tool for frameshift correction and nearest-neighbor classification, and compared its accuracy to that of two other rapid frameshift correction tools. We found FrameBot was, in general, more accurate as long as a reference protein sequence with 80% or greater identity to a query was available, as was the case for virtually all nifH reads for the 4 NEON sites. Frameshifts were present in 12.7% of the reads. Those nifH sequences related to the Proteobacteria phylum were most abundant, followed by those for Cyanobacteria in the Alaska and Utah sites. Predominant genera with nifH sequences similar to reads included Azospirillum, Bradyrhizobium, and Rhizobium, the latter two without obvious plant hosts at the sites. Surprisingly, 80% of the sequences had greater than 95% amino acid identity to known nifH gene sequences. These samples were grouped by site and correlated with soil environmental factors, especially drainage, light intensity, mean annual temperature, and mean annual precipitation. FrameBot was tested successfully on three ecofunctional genes but should be applicable to any.

IMPORTANCE: High-throughput phylogenetic analysis of microbial communities using rRNA-targeted sequencing is now commonplace; however, such data often allow little inference with respect to either the presence or the diversity of genes involved in most important ecological processes. To study the gene pool for these processes, it is more straightforward to assess the genes directly responsible for the ecological function (ecofunctional genes). However, analyzing these genes involves technical challenges beyond those seen for rRNA. In particular, frameshift errors cause garbled downstream protein translations. Our FrameBot tool described here both corrects frameshift errors in query reads and determines their closest matching protein sequences in a set of reference sequences. We validated this new tool with sequences from defined communities and demonstrated the tool's utility on nifH gene fragments sequenced from soils in well-characterized and major terrestrial ecosystem types.}, } @article {pmid24041833, year = {2013}, author = {Seligmann, H and Labra, A}, title = {Tetracoding increases with body temperature in Lepidosauria.}, journal = {Bio Systems}, volume = {114}, number = {3}, pages = {155-163}, doi = {10.1016/j.biosystems.2013.09.002}, pmid = {24041833}, issn = {1872-8324}, mesh = {Adaptation, Biological/*genetics ; Animals ; Base Pairing ; Body Temperature/*physiology ; Codon/*genetics/physiology ; Computational Biology ; Lizards/*genetics/physiology ; Models, Genetic ; Mutagenesis, Insertional/genetics ; Phylogeny ; RNA, Transfer/genetics ; Statistics, Nonparametric ; }, abstract = {Codons expanded by a silent position (quadruplet or tetracodons) may solve the conundrum that at life's origins, the weak tricodon-anticodon interactions could not promote translation in the absence of complex ribosomes. Modern genomes have isolated tetracodons resulting from insertion mutations. Some bioinformatic analyses suggest that tetracoding stretches overlap with regular mitochondrial protein coding genes. These tetragenes are probably decoded by (antisense) tRNAs with expanded anticodons. They are GC-rich, which produce stronger basepairs than A:T interactions, suggesting expression at high temperatures. The hypothesis that tetracoding is an adaptation to high temperatures is tested here by comparing predicted mitochondrial tetracoding in Lepidosauria (lizards, amphisbaenia, and Sphenodon), in relation to body temperature, expecting more tetracoding in species with high body temperature. The association between tRNAs with expanded anticodons and tetracoding previously described for mammals and Drosophila is confirmed for Lepidosauria. Independent evidence indicates that tetracoding increases with body temperature, supporting the hypothesis that tetracoding is an adaptation for efficient translation when conditions (temperature) make triplet codon-anticodons too unstable to allow efficient protein elongation.}, } @article {pmid24040344, year = {2013}, author = {Nakazawa, Y and Lash, RR and Carroll, DS and Damon, IK and Karem, KL and Reynolds, MG and Osorio, JE and Rocke, TE and Malekani, JM and Muyembe, JJ and Formenty, P and Peterson, AT}, title = {Mapping monkeypox transmission risk through time and space in the Congo Basin.}, journal = {PloS one}, volume = {8}, number = {9}, pages = {e74816}, pmid = {24040344}, issn = {1932-6203}, support = {R01 TW008859/TW/FIC NIH HHS/United States ; 1R01TW008859-01/TW/FIC NIH HHS/United States ; }, mesh = {Algorithms ; Animals ; Area Under Curve ; Cameroon/epidemiology ; Central African Republic/epidemiology ; Congo/epidemiology ; Democratic Republic of the Congo/epidemiology ; Environment ; Epidemiological Monitoring ; Gabon/epidemiology ; Geographic Information Systems ; *Geographic Mapping ; Geography ; Humans ; Macaca fascicularis ; *Models, Biological ; Mpox (monkeypox)/*transmission ; ROC Curve ; Risk ; Spatio-Temporal Analysis ; }, abstract = {Monkeypox is a major public health concern in the Congo Basin area, with changing patterns of human case occurrences reported in recent years. Whether this trend results from better surveillance and detection methods, reduced proportions of vaccinated vs. non-vaccinated human populations, or changing environmental conditions remains unclear. Our objective is to examine potential correlations between environment and transmission of monkeypox events in the Congo Basin. We created ecological niche models based on human cases reported in the Congo Basin by the World Health Organization at the end of the smallpox eradication campaign, in relation to remotely-sensed Normalized Difference Vegetation Index datasets from the same time period. These models predicted independent spatial subsets of monkeypox occurrences with high confidence; models were then projected onto parallel environmental datasets for the 2000s to create present-day monkeypox suitability maps. Recent trends in human monkeypox infection are associated with broad environmental changes across the Congo Basin. Our results demonstrate that ecological niche models provide useful tools for identification of areas suitable for transmission, even for poorly-known diseases like monkeypox.}, } @article {pmid24039277, year = {2013}, author = {Narayanan, S and Georgiou, PG}, title = {Behavioral Signal Processing: Deriving Human Behavioral Informatics From Speech and Language: Computational techniques are presented to analyze and model expressed and perceived human behavior-variedly characterized as typical, atypical, distressed, and disordered-from speech and language cues and their applications in health, commerce, education, and beyond.}, journal = {Proceedings of the IEEE. Institute of Electrical and Electronics Engineers}, volume = {101}, number = {5}, pages = {1203-1233}, pmid = {24039277}, issn = {0018-9219}, support = {R01 AA018673/AA/NIAAA NIH HHS/United States ; }, abstract = {The expression and experience of human behavior are complex and multimodal and characterized by individual and contextual heterogeneity and variability. Speech and spoken language communication cues offer an important means for measuring and modeling human behavior. Observational research and practice across a variety of domains from commerce to healthcare rely on speech- and language-based informatics for crucial assessment and diagnostic information and for planning and tracking response to an intervention. In this paper, we describe some of the opportunities as well as emerging methodologies and applications of human behavioral signal processing (BSP) technology and algorithms for quantitatively understanding and modeling typical, atypical, and distressed human behavior with a specific focus on speech- and language-based communicative, affective, and social behavior. We describe the three important BSP components of acquiring behavioral data in an ecologically valid manner across laboratory to real-world settings, extracting and analyzing behavioral cues from measured data, and developing models offering predictive and decision-making support. We highlight both the foundational speech and language processing building blocks as well as the novel processing and modeling opportunities. Using examples drawn from specific real-world applications ranging from literacy assessment and autism diagnostics to psychotherapy for addiction and marital well being, we illustrate behavioral informatics applications of these signal processing techniques that contribute to quantifying higher level, often subjectively described, human behavior in a domain-sensitive fashion.}, } @article {pmid24039008, year = {2013}, author = {Holland, T and Blessing, D and Hellwig, S and Sack, M}, title = {The in-line measurement of plant cell biomass using radio frequency impedance spectroscopy as a component of process analytical technology.}, journal = {Biotechnology journal}, volume = {8}, number = {10}, pages = {1231-1240}, doi = {10.1002/biot.201300125}, pmid = {24039008}, issn = {1860-7314}, mesh = {*Biomass ; Bioreactors ; Biotechnology/methods ; Cell Line ; *Dielectric Spectroscopy/instrumentation/methods ; Fermentation ; Online Systems ; Plant Cells/*physiology ; Plants, Genetically Modified/physiology ; Software ; Nicotiana/*physiology ; }, abstract = {Radio frequency impedance spectroscopy (RFIS) is a robust method for the determination of cell biomass during fermentation. RFIS allows non-invasive in-line monitoring of the passive electrical properties of cells in suspension and can distinguish between living and dead cells based on their distinct behavior in an applied radio frequency field. We used continuous in situ RFIS to monitor batch-cultivated plant suspension cell cultures in stirred-tank bioreactors and compared the in-line data to conventional off-line measurements. RFIS-based analysis was more rapid and more accurate than conventional biomass determination, and was sensitive to changes in cell viability. The higher resolution of the in-line measurement revealed subtle changes in cell growth which were not accessible using conventional methods. Thus, RFIS is well suited for correlating such changes with intracellular states and product accumulation, providing unique opportunities for employing systems biotechnology and process analytical technology approaches to increase product yield and quality.}, } @article {pmid24037350, year = {2013}, author = {Andrade Filho, VS and Artaxo, P and Hacon, S and Carmo, CN and Cirino, G}, title = {Aerosols from biomass burning and respiratory diseases in children, Manaus, Northern Brazil.}, journal = {Revista de saude publica}, volume = {47}, number = {2}, pages = {239-247}, doi = {10.1590/S0034-8910.2013047004011}, pmid = {24037350}, issn = {1518-8787}, mesh = {Aerosols/*adverse effects/analysis/*toxicity ; Biomass ; Brazil/epidemiology ; Child ; Child, Preschool ; Environmental Monitoring ; Female ; *Fires ; Health Information Systems ; Hospitalization/*statistics & numerical data ; Humans ; Infant ; Linear Models ; Male ; Meteorological Concepts ; National Health Programs ; Particulate Matter/*adverse effects/analysis/*toxicity ; Respiratory Tract Diseases/epidemiology/*etiology ; }, abstract = {OBJECTIVE: To investigate the effects of fine particulate matter emitted through biomass burning on hospitalizations for respiratory diseases in children living in Manaus, Northern Brazil.

METHODS: Descriptive study with ecologic time series design carried out in Manaus from 2002 to 2009. Hospital admission data were obtained from the Unified Health System database. PM2.5 levels were estimated using aerosol remote sensing through the measurement of aerosol optical depth at a wavelength of 550 nm. Statistical methods were used in the data analysis, with Pearson correlation and multiple linear regression between variables, with a 95% confidence interval.

RESULTS: The region of Manaus showed low PM2.5 concentrations when compared to the Southern Amazonian region. Between August and November (dry period in the region), was when the highest mean levels of PM2.5, estimated between 18 to 23 µg/m3, and the largest number of fires were observed. For the rainy season, an average of 12 µg/m3, 66% lower than the dry season measurements (20.6 µg/m3) was observed. The highest rates of hospitalization were observed during the rainy season and April was the month with the highest levels at 2.51/1,000 children. A positive association between hospital admissions and relative humidity (R = 0.126; p-value = 0.005) was observed, while the association between admissions and PM2.5 was negative and statistically significant (R = -0.168; p-value = 0.003). The R 2 of the final model (Hospitalizations = 2.19*Humidity - 1.60*PM2.5 - 0.23*Precipitation) explained 84% of hospitalizations due to respiratory disease in children living in Manaus, considering the independent variables statistically significant (humidity, PM2.5, and precipitation).

CONCLUSIONS: Hospital admissions for respiratory diseases in children in Manaus, were more related to weather conditions and in particular relative humidity, than to exposure to aerosols emitted by biomass burning in the Amazonian region.}, } @article {pmid24033703, year = {2014}, author = {Baba, S and Goto, A and Reich, MR}, title = {Recent pregnancy trends among early adolescent girls in Japan.}, journal = {The journal of obstetrics and gynaecology research}, volume = {40}, number = {1}, pages = {125-132}, doi = {10.1111/jog.12138}, pmid = {24033703}, issn = {1447-0756}, mesh = {Abortion, Induced/trends ; Adolescent ; Birth Rate/ethnology/trends ; Child ; Child Abuse, Sexual/ethnology/trends ; Databases, Factual ; Female ; Humans ; Japan/epidemiology ; Juvenile Delinquency/ethnology/trends ; Live Birth/ethnology ; Pregnancy ; Pregnancy Rate/ethnology/trends ; *Pregnancy in Adolescence/ethnology ; Public Health Surveillance ; }, abstract = {AIM: The paper examines recent time trends, explores potentially influential background factors and discusses prevention strategies of pregnancy among girls under 15 years of age in Japan.

METHODS: Using Japanese government data, we first analyzed time trends of early adolescence (<15 years of age) abortion, live birth and child sexual abuse from 2003 to 2010. Second, we analyzed ecological correlations of early adolescent pregnancy (abortion, live birth and stillbirth) with pregnancy in other age groups, child sexual abuse, and indicators of juvenile victimization and juvenile delinquency, using prefectural data.

RESULTS: We found that rates of both abortion and live birth in early adolescents have increased since 2005 (annual percent change 5.3% and 2.3%, respectively), despite declining rates in older age groups. The abortion ratio in early adolescence remained the highest among all age groups in Japan. The early adolescent pregnancy rate showed significant correlation with the rates of juvenile victimization of welfare crimes (obscenity, alcohol drinking, smoking and drug use) (Spearman's rank correlation coefficient [rs] = 0.42, P = 0.00) and juvenile delinquency among junior high school students (12-14 years of age) (rs = 0.69, P = 0.00).

CONCLUSION: The observed rise in rates of abortion, live birth and child sexual abuse among early adolescents along with strong ecological correlations of their pregnancy rate with juvenile victimization and delinquency indicators suggests that epidemiological investigation and public health programs at the individual and community levels are needed to address the complex social roots of these trends and to produce effective improvements in early adolescent reproductive health.}, } @article {pmid24030594, year = {2014}, author = {Hartmann, M and Niklaus, PA and Zimmermann, S and Schmutz, S and Kremer, J and Abarenkov, K and Lüscher, P and Widmer, F and Frey, B}, title = {Resistance and resilience of the forest soil microbiome to logging-associated compaction.}, journal = {The ISME journal}, volume = {8}, number = {1}, pages = {226-244}, pmid = {24030594}, issn = {1751-7370}, mesh = {Bacteria/classification/genetics ; *Bacterial Physiological Phenomena ; Biodiversity ; DNA, Ribosomal Spacer/genetics ; Fungi/classification/genetics/*physiology ; Microbiota/*physiology ; Porosity ; RNA, Ribosomal, 16S/genetics ; Soil/chemistry ; *Soil Microbiology ; Time Factors ; }, abstract = {Soil compaction is a major disturbance associated with logging, but we lack a fundamental understanding of how this affects the soil microbiome. We assessed the structural resistance and resilience of the microbiome using a high-throughput pyrosequencing approach in differently compacted soils at two forest sites and correlated these findings with changes in soil physical properties and functions. Alterations in soil porosity after compaction strongly limited the air and water conductivity. Compaction significantly reduced abundance, increased diversity, and persistently altered the structure of the microbiota. Fungi were less resistant and resilient than bacteria; clayey soils were less resistant and resilient than sandy soils. The strongest effects were observed in soils with unfavorable moisture conditions, where air and water conductivities dropped well below 10% of their initial value. Maximum impact was observed around 6-12 months after compaction, and microbial communities showed resilience in lightly but not in severely compacted soils 4 years post disturbance. Bacteria capable of anaerobic respiration, including sulfate, sulfur, and metal reducers of the Proteobacteria and Firmicutes, were significantly associated with compacted soils. Compaction detrimentally affected ectomycorrhizal species, whereas saprobic and parasitic fungi proportionally increased in compacted soils. Structural shifts in the microbiota were accompanied by significant changes in soil processes, resulting in reduced carbon dioxide, and increased methane and nitrous oxide emissions from compacted soils. This study demonstrates that physical soil disturbance during logging induces profound and long-lasting changes in the soil microbiome and associated soil functions, raising awareness regarding sustainable management of economically driven logging operations.}, } @article {pmid24023883, year = {2013}, author = {Miya, M and Friedman, M and Satoh, TP and Takeshima, H and Sado, T and Iwasaki, W and Yamanoue, Y and Nakatani, M and Mabuchi, K and Inoue, JG and Poulsen, JY and Fukunaga, T and Sato, Y and Nishida, M}, title = {Evolutionary origin of the Scombridae (tunas and mackerels): members of a paleogene adaptive radiation with 14 other pelagic fish families.}, journal = {PloS one}, volume = {8}, number = {9}, pages = {e73535}, pmid = {24023883}, issn = {1932-6203}, mesh = {Animals ; Biodiversity ; Computational Biology ; Ecosystem ; *Evolution, Molecular ; *Geological Phenomena ; Perciformes/genetics/*physiology ; Tuna/genetics/*physiology ; }, abstract = {Uncertainties surrounding the evolutionary origin of the epipelagic fish family Scombridae (tunas and mackerels) are symptomatic of the difficulties in resolving suprafamilial relationships within Percomorpha, a hyperdiverse teleost radiation that contains approximately 17,000 species placed in 13 ill-defined orders and 269 families. Here we find that scombrids share a common ancestry with 14 families based on (i) bioinformatic analyses using partial mitochondrial and nuclear gene sequences from all percomorphs deposited in GenBank (10,733 sequences) and (ii) subsequent mitogenomic analysis based on 57 species from those targeted 15 families and 67 outgroup taxa. Morphological heterogeneity among these 15 families is so extraordinary that they have been placed in six different perciform suborders. However, members of the 15 families are either coastal or oceanic pelagic in their ecology with diverse modes of life, suggesting that they represent a previously undetected adaptive radiation in the pelagic realm. Time-calibrated phylogenies imply that scombrids originated from a deep-ocean ancestor and began to radiate after the end-Cretaceous when large predatory epipelagic fishes were selective victims of the Cretaceous-Paleogene mass extinction. We name this clade of open-ocean fishes containing Scombridae "Pelagia" in reference to the common habitat preference that links the 15 families.}, } @article {pmid24021386, year = {2013}, author = {Robertson, CE and Harris, JK and Wagner, BD and Granger, D and Browne, K and Tatem, B and Feazel, LM and Park, K and Pace, NR and Frank, DN}, title = {Explicet: graphical user interface software for metadata-driven management, analysis and visualization of microbiome data.}, journal = {Bioinformatics (Oxford, England)}, volume = {29}, number = {23}, pages = {3100-3101}, pmid = {24021386}, issn = {1367-4811}, support = {R21 HG005964/HG/NHGRI NIH HHS/United States ; HG005964/HG/NHGRI NIH HHS/United States ; }, mesh = {Computational Biology ; *Computer Graphics ; *Database Management Systems ; High-Throughput Nucleotide Sequencing ; Humans ; Metagenome ; Microbiota/*genetics ; Sequence Analysis, DNA ; *Software ; *User-Computer Interface ; }, abstract = {Studies of the human microbiome, and microbial community ecology in general, have blossomed of late and are now a burgeoning source of exciting research findings. Along with the advent of next-generation sequencing platforms, which have dramatically increased the scope of microbiome-related projects, several high-performance sequence analysis pipelines (e.g. QIIME, MOTHUR, VAMPS) are now available to investigators for microbiome analysis. The subject of our manuscript, the graphical user interface-based Explicet software package, fills a previously unmet need for a robust, yet intuitive means of integrating the outputs of the software pipelines with user-specified metadata and then visualizing the combined data.}, } @article {pmid24021385, year = {2013}, author = {Howison, M and Zapata, F and Dunn, CW}, title = {Toward a statistically explicit understanding of de novo sequence assembly.}, journal = {Bioinformatics (Oxford, England)}, volume = {29}, number = {23}, pages = {2959-2963}, doi = {10.1093/bioinformatics/btt525}, pmid = {24021385}, issn = {1367-4811}, mesh = {*Computational Biology ; High-Throughput Nucleotide Sequencing/*methods ; Sequence Analysis, DNA/*methods ; }, abstract = {MOTIVATION: Draft de novo genome assemblies are now available for many organisms. These assemblies are point estimates of the true genome sequences. Each is a specific hypothesis, drawn from among many alternative hypotheses, of the sequence of a genome. Assembly uncertainty, the inability to distinguish between multiple alternative assembly hypotheses, can be due to real variation between copies of the genome in the sample, errors and ambiguities in the sequenced data and assumptions and heuristics of the assemblers. Most assemblers select a single assembly according to ad hoc criteria, and do not yet report and quantify the uncertainty of their outputs. Those assemblers that do report uncertainty take different approaches to describing multiple assembly hypotheses and the support for each.

RESULTS: Here we review and examine the problem of representing and measuring uncertainty in assemblies. A promising recent development is the implementation of assemblers that are built according to explicit statistical models. Some new assembly methods, for example, estimate and maximize assembly likelihood. These advances, combined with technical advances in the representation of alternative assembly hypotheses, will lead to a more complete and biologically relevant understanding of assembly uncertainty. This will in turn facilitate the interpretation of downstream analyses and tests of specific biological hypotheses.}, } @article {pmid24010368, year = {2013}, author = {Korucu, MK and Arslan, O and Karademir, A}, title = {Siting a municipal solid waste disposal facility, Part One: An evaluation of different scenarios for a site selection procedure.}, journal = {Journal of the Air & Waste Management Association (1995)}, volume = {63}, number = {8}, pages = {879-885}, doi = {10.1080/10962247.2013.788459}, pmid = {24010368}, issn = {1096-2247}, mesh = {Decision Support Techniques ; Geography ; *Waste Management ; }, abstract = {UNLABELLED: This study includes an application of the first two phases of a new three-phased decision-making structure that was developed to overcome the problems related to ecological safety and social justice in site selection applications. It was conducted on a current site selection problem related to the municipal solid waste disposal facilities in Kocaeli, the most industrialized region of Turkey. In order to assess the deficiencies of the legal site selection procedures related to ecological safety, two different decision tree modes were applied separately. The first mode ("Legislation") concerns the current buffer zone applications given in the regulations, while the second one ("Proposed") includes the applications of the new decision-making structure proposed in this study. Since it was assumed that the subjective tendencies of the decision makers on the weightings would have a significant effect on the final decision, these two modes were assessed by employing two different weighting models. The results were obtained from all of the scenarios related to selection of suitable sites with three different area requirements (15, 250, and 500 acres) for the solid wastes generated in the Kocaeli region. The results showed that the possible changes in the decision structure could cause significant differences in the final decision related to selection of the most suitable sites. The most highest and lowest differences were at the "Legislation" mode for 15 acres and 500 acres, respectively. Furthermore, the results obtained in the study showed that the possible differentiations in the criteria weightings could also cause significant differences in the suitability ranking. Therefore, to get a reliable final decision, a statistical assessment of these differentiations should be made.

IMPLICATIONS: The results showed that the possible changes in the decision structure could cause significant differences in the final decision related to selection of the most suitable sites. Furthermore, the results obtained in the study showed that the possible differentiations in the criteria weightings could also cause significant differences in the suitability ranking. Therefore, to get a reliable final decision, a statistical assessment of these differentiations should be made.}, } @article {pmid24010278, year = {2013}, author = {Zhou, LY and Liu, JS and Yang, QS and Zhou, JL and Zhu, SD and Ma, WF and Guo, LP}, title = {[Resources investigation of medicinal plants of Huangfu mountain in city of Chuzhou based on grid sampling method].}, journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica}, volume = {38}, number = {11}, pages = {1688-1691}, pmid = {24010278}, issn = {1001-5302}, mesh = {China ; Conservation of Natural Resources/*methods ; Drugs, Chinese Herbal/analysis/pharmacology ; Ecology ; *Geographic Information Systems/instrumentation ; Plants, Medicinal/chemistry/classification/*growth & development ; }, abstract = {OBJECTIVE: To conduct preliminary investigation to the species and reserves of medicinal plants in Huangfu Mountain, and to provide references to the general survey of those plants for medicine.

METHOD: Combined with global positioning system (GPS), the program of investigation with grid sampling was used in this resource survey of medicinal plants.

RESULT: After the preliminary investigation of the plants for medical use of Huangfu Mountain, it is found that there are 103 families with 313 kinds of plants. There are many medicinal plants and large distribution, such as Pseudostellaria heterophylla, Semiaguilegia adoxoides and Pinellia ternate.

CONCLUSION: Huangfu Mount, with so many different kinds of medicinal plants and comfortable environment for part of the medicinal plants to grow, could be developed as a base for planting Chinese herbal medicines.}, } @article {pmid24007337, year = {2013}, author = {Gilbert, JD and Acquisti, C and Martinson, HM and Elser, JJ and Kumar, S and Fagan, WF}, title = {GRASP [Genomic Resource Access for Stoichioproteomics]: comparative explorations of the atomic content of 12 Drosophila proteomes.}, journal = {BMC genomics}, volume = {14}, number = {}, pages = {599}, pmid = {24007337}, issn = {1471-2164}, support = {R01 HG002096/HG/NHGRI NIH HHS/United States ; HG002096-12/HG/NHGRI NIH HHS/United States ; }, mesh = {Amino Acids/genetics ; Animals ; Computational Biology ; Diet ; Drosophila/*genetics ; Drosophila Proteins/genetics ; Ecology ; Evolution, Molecular ; Internet ; *Knowledge Bases ; Phylogeny ; Proteome/*genetics ; Proteomics/*methods ; }, abstract = {BACKGROUND: "Stoichioproteomics" relates the elemental composition of proteins and proteomes to variation in the physiological and ecological environment. To help harness and explore the wealth of hypotheses made possible under this framework, we introduce GRASP (http://www.graspdb.net), a public bioinformatic knowledgebase containing information on the frequencies of 20 amino acids and atomic composition of their side chains. GRASP integrates comparative protein composition data with annotation data from multiple public databases. Currently, GRASP includes information on proteins of 12 sequenced Drosophila (fruit fly) proteomes, which will be expanded to include increasingly diverse organisms over time. In this paper we illustrate the potential of GRASP for testing stoichioproteomic hypotheses by conducting an exploratory investigation into the composition of 12 Drosophila proteomes, testing the prediction that protein atomic content is associated with species ecology and with protein expression levels.

RESULTS: Elements varied predictably along multivariate axes. Species were broadly similar, with the D. willistoni proteome a clear outlier. As expected, individual protein atomic content within proteomes was influenced by protein function and amino acid biochemistry. Evolution in elemental composition across the phylogeny followed less predictable patterns, but was associated with broad ecological variation in diet. Using expression data available for D. melanogaster, we found evidence consistent with selection for efficient usage of elements within the proteome: as expected, nitrogen content was reduced in highly expressed proteins in most tissues, most strongly in the gut, where nutrients are assimilated, and least strongly in the germline.

CONCLUSIONS: The patterns identified here using GRASP provide a foundation on which to base future research into the evolution of atomic composition in Drosophila and other taxa.}, } @article {pmid24003144, year = {2013}, author = {Rabosky, DL and Matute, DR}, title = {Macroevolutionary speciation rates are decoupled from the evolution of intrinsic reproductive isolation in Drosophila and birds.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {110}, number = {38}, pages = {15354-15359}, pmid = {24003144}, issn = {1091-6490}, mesh = {Age Factors ; Animals ; *Biological Evolution ; Birds/*genetics/physiology ; Computational Biology ; Computer Simulation ; Drosophila/*genetics/physiology ; *Genetic Speciation ; Models, Genetic ; Phylogeny ; *Reproductive Isolation ; Species Specificity ; }, abstract = {The rate at which speciation occurs varies greatly among different kinds of organisms and is frequently assumed to result from species- or clade-specific factors that influence the rate at which populations acquire reproductive isolation. This premise leads to a fundamental prediction that has never been tested: Organisms that quickly evolve prezygotic or postzygotic reproductive isolation should have faster rates of speciation than organisms that slowly acquire reproductive isolation. We combined phylogenetic estimates of speciation rates from Drosophila and birds with a method for analyzing interspecific hybridization data to test whether the rate at which individual lineages evolve reproductive isolation predicts their macroevolutionary rate of species formation. We find that some lineages evolve reproductive isolation much more quickly than others, but this variation is decoupled from rates of speciation as measured on phylogenetic trees. For the clades examined here, reproductive isolation--especially intrinsic, postzygotic isolation--does not seem to be the rate-limiting control on macroevolutionary diversification dynamics. These results suggest that factors associated with intrinsic reproductive isolation may have less to do with the tremendous variation in species diversity across the evolutionary tree of life than is generally assumed.}, } @article {pmid23994579, year = {2013}, author = {Volchko, Y and Norrman, J and Bergknut, M and Rosén, L and Söderqvist, T}, title = {Incorporating the soil function concept into sustainability appraisal of remediation alternatives.}, journal = {Journal of environmental management}, volume = {129}, number = {}, pages = {367-376}, doi = {10.1016/j.jenvman.2013.07.025}, pmid = {23994579}, issn = {1095-8630}, mesh = {Conservation of Natural Resources/*methods ; Decision Support Techniques ; Ecology/*methods ; *Ecosystem ; Environmental Restoration and Remediation/*methods ; Models, Theoretical ; *Soil ; Terminology as Topic ; }, abstract = {Soil functions are critical for ecosystem survival and thus for an ecosystem's provision of services to humans. This is recognized in the proposed EU Soil Framework Directive from 2006, which lists seven important soil functions and services to be considered in a soil management practice. Emerging regulatory requirements demand a holistic view on soil evaluation in remediation projects. This paper presents a multi-scale, structured and transparent approach for incorporating the soil function concept into sustainability appraisal of remediation alternatives using a set of ecological, socio-cultural and economic criteria. The basis for the presented approach is a conceptualization of the linkages between soil functions and ecosystem services connected to with the sustainability paradigm. The approach suggests using (1) soil quality indicators (i.e. physical, chemical and biological soil properties) for exploring the performance of soil functions at the site level, and (2) soil service indicators (i.e. value-related measurements) for evaluating the performance of services resulting from soil functions across all levels of the spatial scale. The suggested approach is demonstrated by application in a Multi-Criteria Decision Analysis (MCDA) framework for sustainability appraisals of remediation alternatives. Further, the possibilities of using soil quality indicators for soil function evaluation are explored by reviewing existing literature on potential negative and positive effects of remediation technologies on the functionality of the treated soil. The suggested approach for including the soil function concept in remediation projects is believed to provide a basis for better informed decisions that will facilitate efficient management of contaminated land and to meet emerging regulatory requirements on soil protection.}, } @article {pmid23977144, year = {2013}, author = {Di Minin, E and Hunter, LT and Balme, GA and Smith, RJ and Goodman, PS and Slotow, R}, title = {Creating larger and better connected protected areas enhances the persistence of big game species in the maputaland-pondoland-albany biodiversity hotspot.}, journal = {PloS one}, volume = {8}, number = {8}, pages = {e71788}, pmid = {23977144}, issn = {1932-6203}, mesh = {Acinonyx ; Animal Distribution ; Animals ; *Animals, Wild ; Conservation of Natural Resources ; Decision Support Techniques ; *Dogs ; Elephants ; *Endangered Species ; Lions ; Models, Statistical ; Population Dynamics ; South Africa ; Urbanization ; }, abstract = {The ideal conservation planning approach would enable decision-makers to use population viability analysis to assess the effects of management strategies and threats on all species at the landscape level. However, the lack of high-quality data derived from long-term studies, and uncertainty in model parameters and/or structure, often limit the use of population models to only a few species of conservation concern. We used spatially explicit metapopulation models in conjunction with multi-criteria decision analysis to assess how species-specific threats and management interventions would affect the persistence of African wild dog, black rhino, cheetah, elephant, leopard and lion, under six reserve scenarios, thereby providing the basis for deciding on a best course of conservation action in the South African province of KwaZulu-Natal, which forms the central component of the Maputaland-Pondoland-Albany biodiversity hotspot. Overall, the results suggest that current strategies of managing populations within individual, small, fenced reserves are unlikely to enhance metapopulation persistence should catastrophic events affect populations in the future. Creating larger and better-connected protected areas would ensure that threats can be better mitigated in the future for both African wild dog and leopard, which can disperse naturally, and black rhino, cheetah, elephant, and lion, which are constrained by electric fences but can be managed using translocation. The importance of both size and connectivity should inform endangered megafauna conservation and management, especially in the context of restoration efforts in increasingly human-dominated landscapes.}, } @article {pmid23977014, year = {2013}, author = {Jenkins, WD and Christian, WJ and Mueller, G and Robbins, KT}, title = {Population cancer risks associated with coal mining: a systematic review.}, journal = {PloS one}, volume = {8}, number = {8}, pages = {e71312}, pmid = {23977014}, issn = {1932-6203}, mesh = {*Coal Mining ; Databases, Bibliographic ; Environmental Exposure/adverse effects ; Female ; Humans ; Incidence ; Lung Neoplasms/*epidemiology/etiology ; Male ; Occupational Exposure/adverse effects ; Risk ; Stomach Neoplasms/*epidemiology/etiology ; United States/epidemiology ; }, abstract = {BACKGROUND: Coal is produced across 25 states and provides 42% of US energy. With production expected to increase 7.6% by 2035, proximate populations remain at risk of exposure to carcinogenic coal products such as silica dust and organic compounds. It is unclear if population exposure is associated with increased risk, or even which cancers have been studied in this regard.

METHODS: We performed a systematic review of English-language manuscripts published since 1980 to determine if coal mining exposure was associated with increased cancer risk (incidence and mortality).

RESULTS: Of 34 studies identified, 27 studied coal mining as an occupational exposure (coal miner cohort or as a retrospective risk factor) but only seven explored health effects in surrounding populations. Overall, risk assessments were reported for 20 cancer site categories, but their results and frequency varied considerably. Incidence and mortality risk assessments were: negative (no increase) for 12 sites; positive for 1 site; and discordant for 7 sites (e.g. lung, gastric). However, 10 sites had only a single study reporting incidence risk (4 sites had none), and 11 sites had only a single study reporting mortality risk (2 sites had none). The ecological study data were particularly meager, reporting assessments for only 9 sites. While mortality assessments were reported for each, 6 had only a single report and only 2 sites had reported incidence assessments.

CONCLUSIONS: The reported assessments are too meager, and at times contradictory, to make definitive conclusions about population cancer risk due to coal mining. However, the preponderance of this and other data support many of Hill's criteria for causation. The paucity of data regarding population exposure and risk, the widespread geographical extent of coal mining activity, and the continuing importance of coal for US energy, warrant further studies of population exposure and risk.}, } @article {pmid23974552, year = {2013}, author = {Kushniruk, A and Nohr, C and Jensen, S and Borycki, EM}, title = {From Usability Testing to Clinical Simulations: Bringing Context into the Design and Evaluation of Usable and Safe Health Information Technologies. Contribution of the IMIA Human Factors Engineering for Healthcare Informatics Working Group.}, journal = {Yearbook of medical informatics}, volume = {8}, number = {}, pages = {78-85}, pmid = {23974552}, issn = {2364-0502}, mesh = {Ergonomics ; Humans ; *Medical Informatics ; *User-Computer Interface ; }, abstract = {OBJECTIVES: The objective of this paper is to explore human factors approaches to understanding the use of health information technology (HIT) by extending usability engineering approaches to include analysis of the impact of clinical context through use of clinical simulations.

METHODS: Methods discussed are considered on a continuum from traditional laboratory-based usability testing to clinical simulations. Clinical simulations can be conducted in a simulation laboratory and they can also be conducted in real-world settings. The clinical simulation approach attempts to bring the dimension of clinical context into stronger focus. This involves testing of systems with representative users doing representative tasks, in representative settings/environments.

RESULTS: Application of methods where realistic clinical scenarios are used to drive the study of users interacting with systems under realistic conditions and settings can lead to identification of problems and issues with systems that may not be detected using traditional usability engineering methods. In conducting such studies, careful consideration is needed in creating ecologically valid test scenarios. The evidence obtained from such evaluation can be used to improve both the usability and safety of HIT. In addition, recent work has shown that clinical simulations, in particular those conducted in-situ, can lead to considerable benefits when compared to the costs of running such studies.

CONCLUSION: In order to bring context of use into the testing of HIT, clinical simulation, involving observing representative users carrying out tasks in representative settings, holds considerable promise.}, } @article {pmid23974136, year = {2013}, author = {Preheim, SP and Perrotta, AR and Martin-Platero, AM and Gupta, A and Alm, EJ}, title = {Distribution-based clustering: using ecology to refine the operational taxonomic unit.}, journal = {Applied and environmental microbiology}, volume = {79}, number = {21}, pages = {6593-6603}, pmid = {23974136}, issn = {1098-5336}, mesh = {*Algorithms ; Base Sequence ; Classification/*methods ; Cluster Analysis ; Computational Biology ; DNA Primers/genetics ; Microbiota/*genetics ; Molecular Sequence Data ; RNA, Ribosomal, 16S/*genetics ; Real-Time Polymerase Chain Reaction ; Sensitivity and Specificity ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {16S rRNA sequencing, commonly used to survey microbial communities, begins by grouping individual reads into operational taxonomic units (OTUs). There are two major challenges in calling OTUs: identifying bacterial population boundaries and differentiating true diversity from sequencing errors. Current approaches to identifying taxonomic groups or eliminating sequencing errors rely on sequence data alone, but both of these activities could be informed by the distribution of sequences across samples. Here, we show that using the distribution of sequences across samples can help identify population boundaries even in noisy sequence data. The logic underlying our approach is that bacteria in different populations will often be highly correlated in their abundance across different samples. Conversely, 16S rRNA sequences derived from the same population, whether slightly different copies in the same organism, variation of the 16S rRNA gene within a population, or sequences generated randomly in error, will have the same underlying distribution across sampled environments. We present a simple OTU-calling algorithm (distribution-based clustering) that uses both genetic distance and the distribution of sequences across samples and demonstrate that it is more accurate than other methods at grouping reads into OTUs in a mock community. Distribution-based clustering also performs well on environmental samples: it is sensitive enough to differentiate between OTUs that differ by a single base pair yet predicts fewer overall OTUs than most other methods. The program can decrease the total number of OTUs with redundant information and improve the power of many downstream analyses to describe biologically relevant trends.}, } @article {pmid23973872, year = {2013}, author = {Brown, W and Yen, PY and Rojas, M and Schnall, R}, title = {Assessment of the Health IT Usability Evaluation Model (Health-ITUEM) for evaluating mobile health (mHealth) technology.}, journal = {Journal of biomedical informatics}, volume = {46}, number = {6}, pages = {1080-1087}, pmid = {23973872}, issn = {1532-0480}, support = {T15 LM007079/LM/NLM NIH HHS/United States ; KL2 TR000081/TR/NCATS NIH HHS/United States ; P30NR010677/NR/NINR NIH HHS/United States ; 5T15LM007079-22/LM/NLM NIH HHS/United States ; KL2TR000081/TR/NCATS NIH HHS/United States ; KL2RR024157/RR/NCRR NIH HHS/United States ; P30 NR010677/NR/NINR NIH HHS/United States ; }, mesh = {Evaluation Studies as Topic ; Focus Groups ; Humans ; *Information Services ; *Telemedicine ; }, abstract = {BACKGROUND: Over two decades of research has been conducted using mobile devices for health related behaviors yet many of these studies lack rigor. There are few evaluation frameworks for assessing the usability of mHealth, which is critical as the use of this technology proliferates. As the development of interventions using mobile technology increase, future work in this domain necessitates the use of a rigorous usability evaluation framework.

METHODS: We used two exemplars to assess the appropriateness of the Health IT Usability Evaluation Model (Health-ITUEM) for evaluating the usability of mHealth technology. In the first exemplar, we conducted 6 focus group sessions to explore adolescents' use of mobile technology for meeting their health Information needs. In the second exemplar, we conducted 4 focus group sessions following an Ecological Momentary Assessment study in which 60 adolescents were given a smartphone with pre-installed health-related applications (apps).

DATA ANALYSIS: We coded the focus group data using the 9 concepts of the Health-ITUEM: Error prevention, Completeness, Memorability, Information needs, Flexibility/Customizability, Learnability, Performance speed, Competency, Other outcomes. To develop a finer granularity of analysis, the nine concepts were broken into positive, negative, and neutral codes. A total of 27 codes were created. Two raters (R1 and R2) initially coded all text and a third rater (R3) reconciled coding discordance between raters R1 and R2.

RESULTS: A total of 133 codes were applied to Exemplar 1. In Exemplar 2 there were a total of 286 codes applied to 195 excerpts. Performance speed, Other outcomes, and Information needs were among the most frequently occurring codes.

CONCLUSION: Our two exemplars demonstrated the appropriateness and usefulness of the Health-ITUEM in evaluating mobile health technology. Further assessment of this framework with other study populations should consider whether Memorability and Error prevention are necessary to include when evaluating mHealth technology.}, } @article {pmid23969110, year = {2014}, author = {Paparoditis, P and Västermark, A and Le, AJ and Fuerst, JA and Saier, MH}, title = {Bioinformatic analyses of integral membrane transport proteins encoded within the genome of the planctomycetes species, Rhodopirellula baltica.}, journal = {Biochimica et biophysica acta}, volume = {1838}, number = {1 Pt B}, pages = {193-215}, pmid = {23969110}, issn = {0006-3002}, support = {R01 GM077402/GM/NIGMS NIH HHS/United States ; GM077402/GM/NIGMS NIH HHS/United States ; }, mesh = {Aquatic Organisms ; Bacterial Proteins/genetics/*metabolism ; Biological Evolution ; *Computational Biology ; Databases, Genetic ; Electron Transport ; *Genome, Bacterial ; Membrane Proteins/genetics/*metabolism ; Membrane Transport Proteins/genetics/*metabolism ; Phylogeny ; Planctomycetales/classification/genetics/*metabolism ; }, abstract = {Rhodopirellula baltica (R. baltica) is a Planctomycete, known to have intracellular membranes. Because of its unusual cell structure and ecological significance, we have conducted comprehensive analyses of its transmembrane transport proteins. The complete proteome of R. baltica was screened against the Transporter Classification Database (TCDB) to identify recognizable integral membrane transport proteins. 342 proteins were identified with a high degree of confidence, and these fell into several different classes. R. baltica encodes in its genome channels (12%), secondary carriers (33%), and primary active transport proteins (41%) in addition to classes represented in smaller numbers. Relative to most non-marine bacteria, R. baltica possesses a larger number of sodium-dependent symporters but fewer proton-dependent symporters, and it has dimethylsulfoxide (DMSO) and trimethyl-amine-oxide (TMAO) reductases, consistent with its Na(+)-rich marine environment. R. baltica also possesses a Na(+)-translocating NADH:quinone dehydrogenase (Na(+)-NDH), a Na(+) efflux decarboxylase, two Na(+)-exporting ABC pumps, two Na(+)-translocating F-type ATPases, two Na(+):H(+) antiporters and two K(+):H(+) antiporters. Flagellar motility probably depends on the sodium electrochemical gradient. Surprisingly, R. baltica also has a complete set of H(+)-translocating electron transport complexes similar to those present in α-proteobacteria and eukaryotic mitochondria. The transport proteins identified proved to be typical of the bacterial domain with little or no indication of the presence of eukaryotic-type transporters. However, novel functionally uncharacterized multispanning membrane proteins were identified, some of which are found only in Rhodopirellula species, but others of which are widely distributed in bacteria. The analyses lead to predictions regarding the physiology, ecology and evolution of R. baltica.}, } @article {pmid23966100, year = {2014}, author = {Hartikainen, H and Ashford, OS and Berney, C and Okamura, B and Feist, SW and Baker-Austin, C and Stentiford, GD and Bass, D}, title = {Lineage-specific molecular probing reveals novel diversity and ecological partitioning of haplosporidians.}, journal = {The ISME journal}, volume = {8}, number = {1}, pages = {177-186}, pmid = {23966100}, issn = {1751-7370}, mesh = {*Biodiversity ; Data Mining ; Ecology ; Ecosystem ; *Environmental Microbiology ; Europe ; Haplosporida/*classification/genetics/*physiology ; Molecular Probes ; *Phylogeny ; }, abstract = {Haplosporidians are rhizarian parasites of mostly marine invertebrates. They include the causative agents of diseases of commercially important molluscs, including MSX disease in oysters. Despite their importance for food security, their diversity and distributions are poorly known. We used a combination of group-specific PCR primers to probe environmental DNA samples from planktonic and benthic environments in Europe, South Africa and Panama. This revealed several highly distinct novel clades, novel lineages within known clades and seasonal (spring vs autumn) and habitat-related (brackish vs littoral) variation in assemblage composition. High frequencies of haplosporidian lineages in the water column provide the first evidence for life cycles involving planktonic hosts, host-free stages or both. The general absence of haplosporidian lineages from all large online sequence data sets emphasises the importance of lineage-specific approaches for studying these highly divergent and diverse lineages. Combined with host-based field surveys, environmental sampling for pathogens will enhance future detection of known and novel pathogens and the assessment of disease risk.}, } @article {pmid23965821, year = {2013}, author = {Barón, SD and Morillas-Márquez, F and Morales-Yuste, M and Díaz-Sáez, V and Gállego, M and Molina, R and Martín-Sánchez, J}, title = {Predicting the risk of an endemic focus of Leishmania tropica becoming established in South-Western Europe through the presence of its main vector, Phlebotomus sergenti Parrot, 1917.}, journal = {Parasitology}, volume = {140}, number = {11}, pages = {1413-1421}, doi = {10.1017/S0031182013000942}, pmid = {23965821}, issn = {1469-8161}, mesh = {Animals ; Europe/epidemiology ; Geographic Information Systems ; Humans ; Insect Vectors/*parasitology ; Leishmania tropica/*isolation & purification/physiology ; Leishmaniasis, Cutaneous/*epidemiology/parasitology ; *Models, Statistical ; Phlebotomus/*parasitology ; Risk ; Spatial Analysis ; }, abstract = {The aim of the study was the construction of risk maps for exposure to Phlebotomus sergenti, the main vector of Leishmania tropica, with a view to identifying hot spots for the potential establishment of this parasite in the southwest of Europe. Data were collected on the presence/absence of this vector and the ecological and climatic characteristics of 662 sampling sites located in the southeast, centre and northeast of the Iberian Peninsula (south-western Europe). The environmental factors associated with the distribution of P. sergenti were determined. The best predictors for the presence of this dipteran were ‘altitude’, ‘land use’, ‘land surface temperature’, ‘aspect’, ‘adjacent land cover’, ‘absence of vegetation in wall’ and the ‘absence of PVC pipes in the drainage holes of retaining walls’. Risk maps for exposure to the vector were drawn up based on these variables. The validation of the predictive risk model confirmed its usefulness in the detection of areas with a high risk of P. sergenti being present. These locations represent potential hot spots for an autochthonous focus of L. tropica becoming established. The risk maps produced for P. sergenti presence revealed several areas in the centre and south of the Iberian Peninsula to be the most prone to this process, which would make it possible for the disease to enter south-western Europe.}, } @article {pmid23962299, year = {2013}, author = {Martin, TM and Grulke, CM and Young, DM and Russom, CL and Wang, NY and Jackson, CR and Barron, MG}, title = {Prediction of aquatic toxicity mode of action using linear discriminant and random forest models.}, journal = {Journal of chemical information and modeling}, volume = {53}, number = {9}, pages = {2229-2239}, doi = {10.1021/ci400267h}, pmid = {23962299}, issn = {1549-960X}, mesh = {Aquatic Organisms/*drug effects ; Computational Biology/*methods ; Discriminant Analysis ; Quantitative Structure-Activity Relationship ; Reproducibility of Results ; *Toxicity Tests ; }, abstract = {The ability to determine the mode of action (MOA) for a diverse group of chemicals is a critical part of ecological risk assessment and chemical regulation. However, existing MOA assignment approaches in ecotoxicology have been limited to a relatively few MOAs, have high uncertainty, or rely on professional judgment. In this study, machine based learning algorithms (linear discriminant analysis and random forest) were used to develop models for assigning aquatic toxicity MOA. These methods were selected since they have been shown to be able to correlate diverse data sets and provide an indication of the most important descriptors. A data set of MOA assignments for 924 chemicals was developed using a combination of high confidence assignments, international consensus classifications, ASTER (ASessment Tools for the Evaluation of Risk) predictions, and weight of evidence professional judgment based an assessment of structure and literature information. The overall data set was randomly divided into a training set (75%) and a validation set (25%) and then used to develop linear discriminant analysis (LDA) and random forest (RF) MOA assignment models. The LDA and RF models had high internal concordance and specificity and were able to produce overall prediction accuracies ranging from 84.5 to 87.7% for the validation set. These results demonstrate that computational chemistry approaches can be used to determine the acute toxicity MOAs across a large range of structures and mechanisms.}, } @article {pmid23956693, year = {2013}, author = {Xu, K and Jiang, Y and Tang, M and Yuan, C and Tang, C}, title = {PRESEE: an MDL/MML algorithm to time-series stream segmenting.}, journal = {TheScientificWorldJournal}, volume = {2013}, number = {}, pages = {386180}, doi = {10.1155/2013/386180}, pmid = {23956693}, issn = {1537-744X}, mesh = {*Algorithms ; Data Mining ; *Time ; }, abstract = {Time-series stream is one of the most common data types in data mining field. It is prevalent in fields such as stock market, ecology, and medical care. Segmentation is a key step to accelerate the processing speed of time-series stream mining. Previous algorithms for segmenting mainly focused on the issue of ameliorating precision instead of paying much attention to the efficiency. Moreover, the performance of these algorithms depends heavily on parameters, which are hard for the users to set. In this paper, we propose PRESEE (parameter-free, real-time, and scalable time-series stream segmenting algorithm), which greatly improves the efficiency of time-series stream segmenting. PRESEE is based on both MDL (minimum description length) and MML (minimum message length) methods, which could segment the data automatically. To evaluate the performance of PRESEE, we conduct several experiments on time-series streams of different types and compare it with the state-of-art algorithm. The empirical results show that PRESEE is very efficient for real-time stream datasets by improving segmenting speed nearly ten times. The novelty of this algorithm is further demonstrated by the application of PRESEE in segmenting real-time stream datasets from ChinaFLUX sensor networks data stream.}, } @article {pmid23955518, year = {2013}, author = {Iwasaki, W and Fukunaga, T and Isagozawa, R and Yamada, K and Maeda, Y and Satoh, TP and Sado, T and Mabuchi, K and Takeshima, H and Miya, M and Nishida, M}, title = {MitoFish and MitoAnnotator: a mitochondrial genome database of fish with an accurate and automatic annotation pipeline.}, journal = {Molecular biology and evolution}, volume = {30}, number = {11}, pages = {2531-2540}, pmid = {23955518}, issn = {1537-1719}, mesh = {Animals ; *Databases, Genetic ; Evolution, Molecular ; Fishes/*genetics ; *Genome, Mitochondrial ; Genomics ; High-Throughput Nucleotide Sequencing ; Molecular Sequence Annotation/*methods ; Phylogeny ; RNA, Transfer/genetics ; Software ; }, abstract = {Mitofish is a database of fish mitochondrial genomes (mitogenomes) that includes powerful and precise de novo annotations for mitogenome sequences. Fish occupy an important position in the evolution of vertebrates and the ecology of the hydrosphere, and mitogenomic sequence data have served as a rich source of information for resolving fish phylogenies and identifying new fish species. The importance of a mitogenomic database continues to grow at a rapid pace as massive amounts of mitogenomic data are generated with the advent of new sequencing technologies. A severe bottleneck seems likely to occur with regard to mitogenome annotation because of the overwhelming pace of data accumulation and the intrinsic difficulties in annotating sequences with degenerating transfer RNA structures, divergent start/stop codons of the coding elements, and the overlapping of adjacent elements. To ease this data backlog, we developed an annotation pipeline named MitoAnnotator. MitoAnnotator automatically annotates a fish mitogenome with a high degree of accuracy in approximately 5 min; thus, it is readily applicable to data sets of dozens of sequences. MitoFish also contains re-annotations of previously sequenced fish mitogenomes, enabling researchers to refer to them when they find annotations that are likely to be erroneous or while conducting comparative mitogenomic analyses. For users who need more information on the taxonomy, habitats, phenotypes, or life cycles of fish, MitoFish provides links to related databases. MitoFish and MitoAnnotator are freely available at http://mitofish.aori.u-tokyo.ac.jp/ (last accessed August 28, 2013); all of the data can be batch downloaded, and the annotation pipeline can be used via a web interface.}, } @article {pmid23955517, year = {2013}, author = {Chu, JH and Wegmann, D and Yeh, CF and Lin, RC and Yang, XJ and Lei, FM and Yao, CT and Zou, FS and Li, SH}, title = {Inferring the geographic mode of speciation by contrasting autosomal and sex-linked genetic diversity.}, journal = {Molecular biology and evolution}, volume = {30}, number = {11}, pages = {2519-2530}, doi = {10.1093/molbev/mst140}, pmid = {23955517}, issn = {1537-1719}, mesh = {Animals ; Bayes Theorem ; Computational Biology ; Female ; Finches/*classification/*genetics ; Gene Flow ; Genetic Loci ; *Genetic Speciation ; *Genetic Variation ; Geographic Mapping ; Male ; Models, Genetic ; Polymorphism, Genetic ; Population Density ; Selection, Genetic ; Sex Chromosomes/*genetics ; }, abstract = {When geographic isolation drives speciation, concurrent termination of gene flow among genomic regions will occur immediately after the formation of the barrier between diverging populations. Alternatively, if speciation is driven by ecologically divergent selection, gene flow of selectively neutral genomic regions may go on between diverging populations until the completion of reproductive isolation. It may also lead to an unsynchronized termination of gene flow between genomic regions with different roles in the speciation process. Here, we developed a novel Approximate Bayesian Computation pipeline to infer the geographic mode of speciation by testing for a lack of postdivergence gene flow and a concurrent termination of gene flow in autosomal and sex-linked markers jointly. We applied this approach to infer the geographic mode of speciation for two allopatric highland rosefinches, the vinaceous rosefinch Carpodacus vinaceus and the Taiwan rosefinch C. formosanus from DNA polymorphisms of both autosomal and Z-linked loci. Our results suggest that the two rosefinch species diverged allopatrically approximately 0.5 Ma. Our approach allowed us further to infer that female effective population sizes are about five times larger than those of males, an estimate potentially useful when comparing the intensity of sexual selection across species.}, } @article {pmid23954257, year = {2013}, author = {Tian, J and Zheng, M and Yang, G and Zheng, L and Chen, J and Yang, B}, title = {Cloning and stress-responding expression analysis of malonyl CoA-acyl carrier protein transacylase gene of Nannochloropsis gaditana.}, journal = {Gene}, volume = {530}, number = {1}, pages = {33-38}, doi = {10.1016/j.gene.2013.08.002}, pmid = {23954257}, issn = {1879-0038}, mesh = {Acyl-Carrier Protein S-Malonyltransferase/*genetics/isolation & purification ; Amino Acid Sequence ; *Cloning, Molecular ; Computational Biology ; Databases, Protein ; Fatty Acids/biosynthesis/*genetics ; Mutagenesis, Site-Directed ; Sequence Alignment ; Stramenopiles/*genetics ; }, abstract = {Malonyl CoA-acyl carrier protein transacylase (MCAT, E2.3.1.39) is closely associated with the FASII pathway of fatty acid biosynthesis. However, the information about microalgal MCAT is scarce. In this study, a MCAT gene was isolated from Nannochloropsis gaditana with its deduced protein (NgMCAT) characterized with bioinformatic tools. The abundance of the NgMCAT transcript under different environmental conditions was determined with real-time quantitative PCR. Results showed that the open reading frame (ORF) of NgMCAT was 1059 bp in length, which encoded 352 amino acid residues. The abundance of NgMCAT transcript reached the maximum (5.17-fold) at 6h when sodium nitrate was limited, and reached the maximum (4.25-fold) at 12h at low temperature (15°C). The abundance of NgMCAT transcript fluctuated at high temperature (35°C) when the concentration of nitrate and sodium chloride exceeded 150 mg/L and 62 g/L, respectively. In addition, some components of fatty acid that changed with the expression of NgMCAT were also observed.}, } @article {pmid23954071, year = {2013}, author = {Liu, X and Li, R and Lanza, ST and Vasilenko, SA and Piper, M}, title = {Understanding the role of cessation fatigue in the smoking cessation process.}, journal = {Drug and alcohol dependence}, volume = {133}, number = {2}, pages = {548-555}, pmid = {23954071}, issn = {1879-0046}, support = {M01-RR03186/RR/NCRR NIH HHS/United States ; R01 HL109031/HL/NHLBI NIH HHS/United States ; P50 CA084724/CA/NCI NIH HHS/United States ; R01 CA168676/CA/NCI NIH HHS/United States ; P50-DA010075-15/DA/NIDA NIH HHS/United States ; T32 DA017629/DA/NIDA NIH HHS/United States ; P50 DA010075/DA/NIDA NIH HHS/United States ; M01 RR003186/RR/NCRR NIH HHS/United States ; P50 DA019706/DA/NIDA NIH HHS/United States ; P50-CA84724/CA/NCI NIH HHS/United States ; P50-DA0197/DA/NIDA NIH HHS/United States ; T32-DA017629/DA/NIDA NIH HHS/United States ; }, mesh = {Adult ; Algorithms ; Combined Modality Therapy ; Data Interpretation, Statistical ; Fatigue/*psychology ; Female ; Humans ; Longitudinal Studies ; Male ; Middle Aged ; Models, Psychological ; Recurrence ; Sex Characteristics ; Smoking Cessation/*psychology ; Software ; Treatment Outcome ; }, abstract = {BACKGROUND: To understand the dynamic process of cessation fatigue (i.e., the tiredness of trying to quit smoking) with respect to its average trend, effect on relapse, time-varying relations with craving and negative affect, and differences among genders and treatment groups.

METHOD: Randomized placebo-controlled clinical trial. Participants received either placebo, monotherapy (bupropion SR, nicotine patch, nicotine lozenge), or combined pharmacotherapy (bupropion SR+nicotine lozenge, nicotine patch+nicotine lozenge). Data were collected from 1504 daily smokers who were motivated to quit smoking. The participants completed baseline assessments and ecological momentary assessments for 2 weeks post-quit.

RESULTS: Cessation fatigue reduced the likelihood of 6-month post-quit abstinence (OR=0.97, 95% CI (0.95, 0.99)), and was positively associated with craving and negative affect. After controlling for these two factors, average cessation fatigue increased over time. Compared to men, women experienced greater fatigue (t=-10.69, p<0.0001) and a stronger relation between fatigue and craving (t=-8.80, p<0.0001). The relationship between fatigue and negative affect was significantly stronger in men (t=5.73, p<0.0001). Cessation fatigue was significantly reduced by combined pharmacotherapy (t=-13.4, p<0.0001), as well as monotherapy (t=-6.2, p<0.0001).

CONCLUSIONS: Cessation fatigue was closely related to craving, negative affect, and cessation outcomes. Women reported greater cessation fatigue than men. Current treatments appeared to reduce fatigue and weaken its relations with craving and negative affect.}, } @article {pmid23951705, year = {2013}, author = {Northrup, JM and Hooten, MB and Anderson, CR and Wittemyer, G}, title = {Practical guidance on characterizing availability in resource selection functions under a use-availability design.}, journal = {Ecology}, volume = {94}, number = {7}, pages = {1456-1463}, doi = {10.1890/12-1688.1}, pmid = {23951705}, issn = {0012-9658}, mesh = {Animals ; Bias ; Computer Simulation ; Deer/physiology ; Demography ; *Ecosystem ; Geographic Information Systems ; *Models, Biological ; Telemetry/veterinary ; }, abstract = {Habitat selection is a fundamental aspect of animal ecology, the understanding of which is critical to management and conservation. Global positioning system data from animals allow fine-scale assessments of habitat selection and typically are analyzed in a use availability framework, whereby animal locations are contrasted with random locations (the availability sample). Although most use-availability methods are in fact spatial point process models, they often are fit using logistic regression. This framework offers numerous methodological challenges, for which the literature provides little guidance. Specifically, the size and spatial extent of the availability sample influences coefficient estimates potentially causing interpretational bias. We examined the influence of availability on statistical inference through simulations and analysis of serially correlated mule deer GPS data. Bias in estimates arose from incorrectly assessing and sampling the spatial extent of availability. Spatial autocorrelation in covariates, which is common for landscape characteristics, exacerbated the error in availability sampling leading to increased bias. These results have strong implications for habitat selection analyses using GPS data, which are increasingly prevalent in the literature. We recommend that researchers assess the sensitivity of their results to their availability sample and, where bias is likely, take care with interpretations and use cross validation to assess robustness.}, } @article {pmid23950996, year = {2013}, author = {Humbert, JF and Barbe, V and Latifi, A and Gugger, M and Calteau, A and Coursin, T and Lajus, A and Castelli, V and Oztas, S and Samson, G and Longin, C and Medigue, C and de Marsac, NT}, title = {A tribute to disorder in the genome of the bloom-forming freshwater cyanobacterium Microcystis aeruginosa.}, journal = {PloS one}, volume = {8}, number = {8}, pages = {e70747}, pmid = {23950996}, issn = {1932-6203}, mesh = {Base Composition ; Computational Biology/methods ; Ecosystem ; Fresh Water/*microbiology ; Gene Order ; Gene Transfer, Horizontal ; Genome Size ; *Genome, Bacterial ; Microcystis/classification/*genetics/metabolism ; Multigene Family ; Phylogeny ; Repetitive Sequences, Nucleic Acid ; *Water Microbiology ; }, abstract = {Microcystis aeruginosa is one of the most common bloom-forming cyanobacteria in freshwater ecosystems worldwide. This species produces numerous secondary metabolites, including microcystins, which are harmful to human health. We sequenced the genomes of ten strains of M. aeruginosa in order to explore the genomic basis of their ability to occupy varied environments and proliferate. Our findings show that M. aeruginosa genomes are characterized by having a large open pangenome, and that each genome contains similar proportions of core and flexible genes. By comparing the GC content of each gene to the mean value of the whole genome, we estimated that in each genome, around 11% of the genes seem to result from recent horizontal gene transfer events. Moreover, several large gene clusters resulting from HGT (up to 19 kb) have been found, illustrating the ability of this species to integrate such large DNA molecules. It appeared also that all M. aeruginosa displays a large genomic plasticity, which is characterized by a high proportion of repeat sequences and by low synteny values between the strains. Finally, we identified 13 secondary metabolite gene clusters, including three new putative clusters. When comparing the genomes of Microcystis and Prochlorococcus, one of the dominant picocyanobacteria living in marine ecosystems, our findings show that they are characterized by having almost opposite evolutionary strategies, both of which have led to ecological success in their respective environments.}, } @article {pmid23949660, year = {2014}, author = {Lagkouvardos, I and Weinmaier, T and Lauro, FM and Cavicchioli, R and Rattei, T and Horn, M}, title = {Integrating metagenomic and amplicon databases to resolve the phylogenetic and ecological diversity of the Chlamydiae.}, journal = {The ISME journal}, volume = {8}, number = {1}, pages = {115-125}, pmid = {23949660}, issn = {1751-7370}, support = {281633/ERC_/European Research Council/International ; }, mesh = {Bacterial Proteins/genetics ; *Biodiversity ; Chlamydiaceae/*classification/*genetics ; Databases, Genetic ; Ecology ; Environmental Microbiology ; Metagenomics ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {In the era of metagenomics and amplicon sequencing, comprehensive analyses of available sequence data remain a challenge. Here we describe an approach exploiting metagenomic and amplicon data sets from public databases to elucidate phylogenetic diversity of defined microbial taxa. We investigated the phylum Chlamydiae whose known members are obligate intracellular bacteria that represent important pathogens of humans and animals, as well as symbionts of protists. Despite their medical relevance, our knowledge about chlamydial diversity is still scarce. Most of the nine known families are represented by only a few isolates, while previous clone library-based surveys suggested the existence of yet uncharacterized members of this phylum. Here we identified more than 22,000 high quality, non-redundant chlamydial 16S rRNA gene sequences in diverse databases, as well as 1900 putative chlamydial protein-encoding genes. Even when applying the most conservative approach, clustering of chlamydial 16S rRNA gene sequences into operational taxonomic units revealed an unexpectedly high species, genus and family-level diversity within the Chlamydiae, including 181 putative families. These in silico findings were verified experimentally in one Antarctic sample, which contained a high diversity of novel Chlamydiae. In our analysis, the Rhabdochlamydiaceae, whose known members infect arthropods, represents the most diverse and species-rich chlamydial family, followed by the protist-associated Parachlamydiaceae, and a putative new family (PCF8) with unknown host specificity. Available information on the origin of metagenomic samples indicated that marine environments contain the majority of the newly discovered chlamydial lineages, highlighting this environment as an important chlamydial reservoir.}, } @article {pmid23949381, year = {2013}, author = {Cattaneo, L and Maule, F and Barchiesi, G and Rizzolatti, G}, title = {The motor system resonates to the distal goal of observed actions: testing the inverse pliers paradigm in an ecological setting.}, journal = {Experimental brain research}, volume = {231}, number = {1}, pages = {37-49}, pmid = {23949381}, issn = {1432-1106}, mesh = {Biomechanical Phenomena ; Data Interpretation, Statistical ; Evoked Potentials, Motor/physiology ; Female ; Fingers/innervation/physiology ; Goals ; Hand/innervation/physiology ; Hand Strength/*physiology ; Humans ; Male ; Motor Skills/*physiology ; Muscle, Skeletal/innervation/physiology ; *Observation ; Psychomotor Performance/*physiology ; Regression Analysis ; Transcranial Magnetic Stimulation ; Young Adult ; }, abstract = {Does motor mirroring in humans reflect the observed movements or the goal of the observed motor acts? Tools that dissociate the agent/object dynamics from the movements of the body parts used to operate them provide a model for testing resonance to both movements and goals. Here, we describe the temporal relationship of the observer's motor excitability, assessed with transcranial magnetic stimulation (TMS), with the observed goal-directed tool actions, in an ecological setting. Motor-evoked potentials (MEPs) to TMS were recorded from the opponens pollicis (OP, thumb flexor) and the extensor indicis proprius (EIP, index extensor) muscles of participants while they observed a person moving several small objects with a pair of normal pliers (closed by finger flexion) or reverse pliers (opened by finger flexion). The MEPs were a significant predictor of the pliers' kinematics that occurred in a variable time interval between -400 and +300 ms from TMS. Whatever pliers' type was being observed, OP MEPs correlated positively and EIP MEPs correlated negatively with the velocity of pliers' tips closure. This datum was confirmed both at individual and at a group level. Motor simulation can be demonstrated in single observers in a "real-life" ecological setting. The relation of motor resonance to the tool type shows that the observer's motor system codes the distal goal of the observed acts (i.e., grasping and releasing objects) in terms of its own motor vocabulary, irrespective of the actual finger movements that were performed by the observed actor.}, } @article {pmid23947284, year = {2013}, author = {Massawe, E}, title = {Nanomaterials for environmental remediation: investigating the role of nanoinformatics in support of environmental, health, and safety oversight of nanotechnologies at the local level.}, journal = {Journal of environmental health}, volume = {76}, number = {1}, pages = {8-17}, pmid = {23947284}, issn = {0022-0892}, support = {000-8457B//PHS HHS/United States ; }, mesh = {Environmental Exposure ; Environmental Health/*organization & administration ; Environmental Monitoring ; Environmental Pollutants ; Environmental Restoration and Remediation/*methods ; Focus Groups ; Humans ; Nanostructures/*adverse effects ; *Nanotechnology ; Public Health Informatics/*methods ; Safety Management/*methods ; State Government ; Surveys and Questionnaires ; United States ; }, abstract = {Nanotechnology is the science and practice of manipulating matter at or near atomic scale to create new materials of unique and novel properties for specific applications. Nanomaterials, including engineered nanoparticles (ENPs), have been used successfully for remediation since they are superior in technical performance and cost-effectiveness than traditional remedial technologies. Evidence indicates, however, that exposure to nanomaterials may lead to significant safety and health impacts. To protect human health against undesired risks from nanomaterials requires that safe and sustainable development of nanotechnology is in tandem with the availability of relevant information. State agencies responsible for the environment, safety, and public health were surveyed to understand their current and future information needs and capabilities to regulate nanomaterials. Because significant data gaps still exist on the toxicity and ecological impacts of nanomaterials, precautionary measures should be taken. Research to develop techniques for exposure assessments, surveillance and monitoring, databases, and characteristics of workplaces where ENPs are used is encouraged.}, } @article {pmid23944375, year = {2013}, author = {Rojas, D and Mancina, CA and Flores-Martínez, JJ and Navarro, L}, title = {Phylogenetic signal, feeding behaviour and brain volume in Neotropical bats.}, journal = {Journal of evolutionary biology}, volume = {26}, number = {9}, pages = {1925-1933}, doi = {10.1111/jeb.12190}, pmid = {23944375}, issn = {1420-9101}, mesh = {Animals ; Bayes Theorem ; Body Size ; Brain/*anatomy & histology/physiology ; Chiroptera/*genetics/physiology ; Computational Biology ; DNA, Mitochondrial/genetics ; DNA-Binding Proteins/genetics ; Feeding Behavior/*physiology ; Models, Biological ; Models, Genetic ; Organ Size/physiology ; *Phylogeny ; *Selection, Genetic ; South America ; von Willebrand Factor/genetics ; }, abstract = {Comparative correlational studies of brain size and ecological traits (e.g. feeding habits and habitat complexity) have increased our knowledge about the selective pressures on brain evolution. Studies conducted in bats as a model system assume that shared evolutionary history has a maximum effect on the traits. However, this effect has not been quantified. In addition, the effect of levels of diet specialization on brain size remains unclear. We examined the role of diet on the evolution of brain size in Mormoopidae and Phyllostomidae using two comparative methods. Body mass explained 89% of the variance in brain volume. The effect of feeding behaviour (either characterized as feeding habits, as levels of specialization on a type of item or as handling behaviour) on brain volume was also significant albeit not consistent after controlling for body mass and the strength of the phylogenetic signal (λ). Although the strength of the phylogenetic signal of brain volume and body mass was high when tested individually, λ values in phylogenetic generalized least squares models were significantly different from 1. This suggests that phylogenetic independent contrasts models are not always the best approach for the study of ecological correlates of brain size in New World bats.}, } @article {pmid23944235, year = {2013}, author = {Vermeulen, CJ and Sørensen, P and Kirilova Gagalova, K and Loeschcke, V}, title = {Transcriptomic analysis of inbreeding depression in cold-sensitive Drosophila melanogaster shows upregulation of the immune response.}, journal = {Journal of evolutionary biology}, volume = {26}, number = {9}, pages = {1890-1902}, doi = {10.1111/jeb.12183}, pmid = {23944235}, issn = {1420-9101}, mesh = {Animals ; Cluster Analysis ; *Cold Temperature ; Computational Biology ; Drosophila melanogaster/genetics/*immunology ; Gene Expression Regulation/*immunology ; Immunity, Innate/*immunology ; *Inbreeding ; Male ; Oligonucleotide Array Sequence Analysis ; Reverse Transcriptase Polymerase Chain Reaction ; Stress, Physiological/*genetics ; }, abstract = {In sexually reproducing species, increased homozygosity often causes a decline in fitness, called inbreeding depression. Recently, researchers started describing the functional genomic changes that occur during inbreeding, both in benign conditions and under environmental stress. To further this aim, we have performed a genome-wide gene expression study of inbreeding depression, manifesting as cold sensitivity and conditional lethality. Our focus was to describe general patterns of gene expression during inbreeding depression and to identify specific processes affected in our line. There was a clear difference in gene expression between the stressful restrictive environment and the benign permissive environment in both the affected inbred line and the inbred control line. We noted a strong inbreeding-by-environment interaction, whereby virtually all transcriptional differences between lines were found in the restrictive environment. Functional annotation showed enrichment of transcripts coding for serine proteases and their inhibitors (serpins and BPTI/Kunitz family), which indicates activation of the innate immune response. These genes have previously been shown to respond transcriptionally to cold stress, suggesting the conditional lethal effect is associated with an exaggerated cold stress response. The set of differentially expressed genes significantly overlapped with those found in three other studies of inbreeding depression, demonstrating that it is possible to detect a common signature across different genetic backgrounds.}, } @article {pmid23944141, year = {2013}, author = {Srinivasan, K and Natesan, U}, title = {Spatio-temporal variations in water quality of Muttukadu Backwaters, Tamilnadu, India.}, journal = {Water environment research : a research publication of the Water Environment Federation}, volume = {85}, number = {7}, pages = {587-595}, doi = {10.2175/106143012x13560205144812}, pmid = {23944141}, issn = {1061-4303}, mesh = {Environmental Monitoring ; Geographic Information Systems ; India ; Nitrates/analysis ; Nitrites/analysis ; Nitrogen/analysis ; Phosphates/analysis ; Principal Component Analysis ; Seasons ; Water Pollutants/analysis ; *Water Quality ; }, abstract = {Muttukadu Backwater, located on the east coast of Tamilnadu, is one of healthiest estuarine environments in the region. A study pertaining to seasonal variations in physico-chemical properties in water was conducted at nine sites of Muttukadu Backwater for a period of one year (January to December 2009). Multivariate statistical techniques, such as cluster analysis and principal component analysis (PCA), were applied to evaluate the variation in water quality of Muttukadu Backwater and to identify pollution sources. In order to analyze water quality, a geographic information systems (GIS) software package, Arc GIS version 9.3, was used (Esri, Redlands, California). An interpolation technique, inverse distance weighting, was used to produce the spatial distribution of water quality parameters over the backwater. The purpose of the technique was to aid in protection of the environment and ecology of the estuary and aid in effective management. In the present study, observed values of salinity, nitrite, nitrate, ammonia, total nitrogen, phosphate, and silicate were significantly high in the estuarine zone. PCA resulted in three factors explaining 75.9% of the total variance. Principal component 1 exhibited a high correlation with significant physico-chemical variables representing the influence of tidal action and sandbar formation. Principal component 2 represented natural pollution as a result of surface runoff. Principal component 3 represented natural pollution as a result of nutrient pollution.}, } @article {pmid23940768, year = {2013}, author = {Gong, ZJ and Wu, YQ and Miao, J and Duan, Y and Jiang, YL and Li, T}, title = {Global transcriptome analysis of orange wheat blossom midge, Sitodiplosis mosellana (Gehin) (Diptera: Cecidomyiidae) to identify candidate transcripts regulating diapause.}, journal = {PloS one}, volume = {8}, number = {8}, pages = {e71564}, pmid = {23940768}, issn = {1932-6203}, mesh = {Animals ; Diapause, Insect/*genetics ; Diptera/*genetics/growth & development ; Female ; *Gene Expression Profiling ; Gene Ontology ; *Genetic Association Studies/methods ; Life Cycle Stages/genetics ; Male ; Molecular Sequence Annotation ; Sequence Analysis, DNA ; Transcriptome ; }, abstract = {BACKGROUND: Many insects enter a developmental arrest (diapause) that allows them to survive harsh seasonal conditions. Despite the well-established ecological significance of diapause, the molecular basis of this crucial adaptation remains largely unresolved. Sitodiplosis mosellana (Gehin), the orange wheat blossom midge (OWBM), causes serious damage to wheat throughout the northern hemisphere, and sporadic outbreaks occur in the world. Traits related to diapause appear to be important factors contributing to their rapid spread and outbreak. To better understand the diapause mechanisms of OWBM, we sequenced the transcriptome and determined the gene expression profile of this species.

In this study, we performed de novo transcriptome analysis using short-read sequencing technology (Illumina) and gene expression analysis with a tag-based digital gene expression (DGE) system. The sequencing results generated 89,117 contigs, and 45,713 unigenes. These unigenes were annotated by Blastx alignment against the NCBI non-redundant (nr), Clusters of orthologous groups (COG), gene orthology (GO), and the Kyoto Encyclopedia of Genes and Genomes (KEGG) databases. 20,802 unigenes (45.5% of the total) matched with protein in the NCBI nr database. Two digital gene expression (DGE) libraries were constructed to determine differences in gene expression profiles during diapause and non-diapause developmental stages. Genes related to diapause were analyzed in detail and in addition, nine diapause-related genes were analyzed by real time PCR.

CONCLUSIONS/SIGNIFICANCE: The OWBM transcriptome greatly improves our genetic understanding and provides a platform for functional genomics research of this species. The DGE profiling data provides comprehensive information at the transcriptional level that facilitates our understanding of the molecular mechanisms of various physiological aspects including development and diapause stages in OWBM. From this study it is evident that various genes coding metabolic enzymes are crucial for diapause and metamorphosis.}, } @article {pmid23939388, year = {2013}, author = {Johnston, L and Doyle, J and Morgan, B and Atkinson-Briggs, S and Firebrace, B and Marika, M and Reilly, R and Cargo, M and Riley, T and Rowley, K}, title = {A review of programs that targeted environmental determinants of Aboriginal and Torres Strait Islander health.}, journal = {International journal of environmental research and public health}, volume = {10}, number = {8}, pages = {3518-3542}, pmid = {23939388}, issn = {1660-4601}, mesh = {Chronic Disease/therapy ; Databases, Bibliographic ; *Environment ; *Health Promotion ; Humans ; Motor Activity ; Nutrition Policy ; *Program Evaluation ; Social Environment ; Substance-Related Disorders/prevention & control ; }, abstract = {OBJECTIVE: Effective interventions to improve population and individual health require environmental change as well as strategies that target individual behaviours and clinical factors. This is the basis of implementing an ecological approach to health programs and health promotion. For Aboriginal People and Torres Strait Islanders, colonisation has made the physical and social environment particularly detrimental for health.

METHODS AND RESULTS: We conducted a literature review to identify Aboriginal health interventions that targeted environmental determinants of health, identifying 21 different health programs. Program activities that targeted environmental determinants of health included: Caring for Country; changes to food supply and/or policy; infrastructure for physical activity; housing construction and maintenance; anti-smoking policies; increased workforce capacity; continuous quality improvement of clinical systems; petrol substitution; and income management. Targets were categorised according to Miller's Living Systems Theory. Researchers using an Indigenous community based perspective more often identified interpersonal and community-level targets than were identified using a Western academic perspective.

CONCLUSIONS: Although there are relatively few papers describing interventions that target environmental determinants of health, many of these addressed such determinants at multiple levels, consistent to some degree with an ecological approach. Interpretation of program targets sometimes differed between academic and community-based perspectives, and was limited by the type of data reported in the journal articles, highlighting the need for local Indigenous knowledge for accurate program evaluation.

IMPLICATIONS: While an ecological approach to Indigenous health is increasingly evident in the health research literature, the design and evaluation of such programs requires a wide breadth of expertise, including local Indigenous knowledge.}, } @article {pmid23937578, year = {2013}, author = {, and Agostini, C and Albaladejo, RG and Aparicio, A and Arthofer, W and Berrebi, P and Boag, PT and Carbone, I and Conroy, GC and Cortesero, AM and Costa Gonçalves, E and Costa, D and Couto, A and De Girolamo, M and Du, H and Fu, SJ and Garrido-Garduño, T and Gettová, L and Gilles, A and Guerreiro Hamoy, I and Herrera, CM and Heussler, C and Isidro, E and Josso, C and Krapf, P and Lamont, RW and Le Ralec, A and Lopes, S and Luís, C and Luo, H and Mahéo, F and Marino, IA and Mieuzet, L and Murray, BW and Ogbourne, SM and Pallavicini, A and Parejo-Farnés, C and Patarnello, T and Paty, C and Pereira, C and Pinho, C and Pinto, P and Poinsot, D and Powell, A and Putman, AI and Santoro, A and Santos, S and Schlick-Steiner, BC and Scott, C and Silvanira Barbosa, M and Šimková, A and Simon, JC and Solé-Cava, A and Steiner, FM and Sun, Z and Torboli, V and Tredway, LP and Van Coeverden de Groot, PJ and Vasconcellos, A and Vázquez-Domínguez, E and Wang, DQ and Wang, YX and Wei, QW and Zane, L and Zhang, SH}, title = {Permanent genetic resources added to molecular ecology resources database 1 April 2013-31 May 2013.}, journal = {Molecular ecology resources}, volume = {13}, number = {5}, pages = {966-968}, doi = {10.1111/1755-0998.12140}, pmid = {23937578}, issn = {1755-0998}, mesh = {Animals ; Computational Biology/methods ; Databases, Genetic ; *Microsatellite Repeats ; }, abstract = {This article documents the addition of 234 microsatellite marker loci to the Molecular Ecology Resources Database. Loci were developed for the following species: Acipenser sinensis, Aleochara bilineata, Aleochara bipustulata, Barbus meridionalis, Colossoma macropomum, Delia radicum, Drosophila nigrosparsa, Fontainea picrosperma, Helianthemum cinereum, Liomys pictus, Megabalanus azoricus, Pelteobagrus vachelli, Pleuragramma antarcticum, Podarcis hispanica type 1A, Sardinella brasiliensis and Sclerotinia homoeocarpa. These loci were cross-tested on the following species: Acipenser dabryanus, Barbus balcanicus, Barbus barbus, Barbus cyclolepis, Drosophila hydei, Drosophila melanogaster, Drosophila obscura, Drosophila subobscura, Fontainea australis, Fontainea fugax, Fontainea oraria, Fontainea rostrata, Fontainea venosa, Podarcis bocagei, Podarcis carbonelli, Podarcis liolepis, Podarcis muralis and Podarcis vaucheri.}, } @article {pmid23929986, year = {2012}, author = {Aparna, S and Ved, DK and Lalitha, S and Venkatasubramanian, P}, title = {Botanical identity of plant sources of Daśamūla drugs through an analysis of published literature.}, journal = {Ancient science of life}, volume = {32}, number = {1}, pages = {3-10}, pmid = {23929986}, issn = {0257-7941}, abstract = {BACKGROUND: Daśamūla (DM) is a top-traded group of medicinal plants used by the Ayurvedic industry. Through literature survey and analysis, this article has enlisted the botanical sources of DM, as correlated by several scholars. Such a list is not available from any single, earlier publication. It brings to light the confusion that exists in terms of botanical sources correlated to Ayurvedic entities. There is quite a bit of difference in the botanical correlation, parts, and substitutes reported in the different scholarly works, particularly for Pṛṣṇiparṇī, and Agnimantha. For e.g., is Uraria picta the original intended Pṛṣṇiparṇī, as the Ayurvedic Formulary of India (AFI) stipulates or is it U. lagopoidiodes or Desmodium gangeticum as other scholars report? While AFI provides two botanical correlations to Agnimantha in its two editions, namely Premna integrifolia and Clerodendrum phlomidis, other scholars correlate it to other Premna and Clerodendrum species. Why has AFI provided stem bark and whole plant as substitutes for roots of DM? Are substitutes recommended by AFI only for ecological or practical convenience or is there an Ayurvedic or pharmacological explanation for the same?

AIM: There are many species used in the name of Daśamūla,, in this article all the species are listed out to find the differences in the usage of the drugs.

MATERIALS AND METHODS: Ayurveda texts and lexicons along with the texts which have done correlation work were considered to arrive at a list of various species used as Dasmula.

RESULTS AND CONCLUSION: Since neither the methodology nor the logic behind the correlation have been discussed in these scholarly works, including the AFI, the same is not available for analysis or scrutiny. Such a list as provided in this article can form an essential base for a much needed systematic approach at etymological analysis, botanical correlation, and further scientific work to establish legitimacy of substitutes prescribed.}, } @article {pmid23922936, year = {2013}, author = {Bekaert, M and Lowe, NR and Bishop, SC and Bron, JE and Taggart, JB and Houston, RD}, title = {Sequencing and characterisation of an extensive Atlantic salmon (Salmo salar L.) microRNA repertoire.}, journal = {PloS one}, volume = {8}, number = {7}, pages = {e70136}, pmid = {23922936}, issn = {1932-6203}, support = {BB/F001959/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/D/20211552/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/F002750/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; MR/K001744/1/MRC_/Medical Research Council/United Kingdom ; BB/H022007/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; Base Sequence ; Computational Biology ; Conserved Sequence ; Gene Dosage ; Gene Expression Regulation ; Genetic Markers ; High-Throughput Nucleotide Sequencing ; MicroRNAs/*genetics ; Repetitive Sequences, Nucleic Acid ; Salmo salar/*genetics ; *Transcriptome ; }, abstract = {Atlantic salmon (Salmo salar L.), a member of the family Salmonidae, is a totemic species of ecological and cultural significance that is also economically important in terms of both sports fisheries and aquaculture. These factors have promoted the continuous development of genomic resources for this species, furthering both fundamental and applied research. MicroRNAs (miRNA) are small endogenous non-coding RNA molecules that control spatial and temporal expression of targeted genes through post-transcriptional regulation. While miRNA have been characterised in detail for many other species, this is not yet the case for Atlantic salmon. To identify miRNAs from Atlantic salmon, we constructed whole fish miRNA libraries for 18 individual juveniles (fry, four months post hatch) and characterised them by Illumina high-throughput sequencing (total of 354,505,167 paired-ended reads). We report an extensive and partly novel repertoire of miRNA sequences, comprising 888 miRNA genes (547 unique mature miRNA sequences), quantify their expression levels in basal conditions, examine their homology to miRNAs from other species and identify their predicted target genes. We also identify the location and putative copy number of the miRNA genes in the draft Atlantic salmon reference genome sequence. The Atlantic salmon miRNAs experimentally identified in this study provide a robust large-scale resource for functional genome research in salmonids. There is an opportunity to explore the evolution of salmonid miRNAs following the relatively recent whole genome duplication event in salmonid species and to investigate the role of miRNAs in the regulation of gene expression in particular their contribution to variation in economically and ecologically important traits.}, } @article {pmid23921637, year = {2013}, author = {Roller, M and Lucić, V and Nagy, I and Perica, T and Vlahovicek, K}, title = {Environmental shaping of codon usage and functional adaptation across microbial communities.}, journal = {Nucleic acids research}, volume = {41}, number = {19}, pages = {8842-8852}, pmid = {23921637}, issn = {1362-4962}, support = {MC_U105161047/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Adaptation, Biological/*genetics ; Animals ; *Codon ; Ecosystem ; Genome, Bacterial ; Humans ; *Metagenome ; Metagenomics ; Mice ; Phylogeny ; Proteomics ; }, abstract = {Microbial communities represent the largest portion of the Earth's biomass. Metagenomics projects use high-throughput sequencing to survey these communities and shed light on genetic capabilities that enable microbes to inhabit every corner of the biosphere. Metagenome studies are generally based on (i) classifying and ranking functions of identified genes; and (ii) estimating the phyletic distribution of constituent microbial species. To understand microbial communities at the systems level, it is necessary to extend these studies beyond the species' boundaries and capture higher levels of metabolic complexity. We evaluated 11 metagenome samples and demonstrated that microbes inhabiting the same ecological niche share common preferences for synonymous codons, regardless of their phylogeny. By exploring concepts of translational optimization through codon usage adaptation, we demonstrated that community-wide bias in codon usage can be used as a prediction tool for lifestyle-specific genes across the entire microbial community, effectively considering microbial communities as meta-genomes. These findings set up a 'functional metagenomics' platform for the identification of genes relevant for adaptations of entire microbial communities to environments. Our results provide valuable arguments in defining the concept of microbial species through the context of their interactions within the community.}, } @article {pmid23919449, year = {2013}, author = {Yang, Y and Li, B and Ju, F and Zhang, T}, title = {Exploring variation of antibiotic resistance genes in activated sludge over a four-year period through a metagenomic approach.}, journal = {Environmental science & technology}, volume = {47}, number = {18}, pages = {10197-10205}, doi = {10.1021/es4017365}, pmid = {23919449}, issn = {1520-5851}, mesh = {Computational Biology ; Drug Resistance, Microbial/*genetics ; Environmental Monitoring ; Hong Kong ; Metagenomics ; Sewage/*analysis ; }, abstract = {In this study, the profiles of ARGs in activated sludge from the Shatin WWTP of Hong Kong were investigated using metagenomic analysis over a four-year period. Forty giga base pairs of metagenomic data were generated from eight activated sludge samples collected biannually at two seasons (winter and summer) from July 2007 to January 2011. A structured database of ARGs was proposed and constructed to facilitate the classification of ARGs in the collected samples from metagenomic data using a customized script. Analysis of the data showed the existence of a broad-spectrum of different ARGs, some of which have never been reported in activated sludge before. The most abundant ARGs were aminoglycoside and tetracycline resistance genes, followed by resistance genes of sulfonamide, multidrug, and chloramphenicol. Seasonal fluctuations were observed for 3 types of ARGs, that is, resistance genes of tetracycline, sulfonamide, and vancomycin. The abundances of these resistance genes were generally higher in the samples collected in the winters than the samples collected in the contiguous summer. Further analyses were carried out for the presence of subtypes of ARGs for aminoglycoside, tetracycline, and beta-lactam. The abundances of some ARGs subtypes were inconsistent with those reported in previous studies of activated sludge using the PCR approach. Statistical analyses showed that the activated sludge data sets from this study can be distinguished from other types of samples based on their ARGs profiles. Furthermore, the results of this study demonstrate that a high throughput-based metagenomic approach combined with a structured database of ARGs provides a powerful tool for a comprehensive survey of the various ARGs not only in the activated sludge of a WWTP but in other environmental samples as well. Thus, the profiling of ARGs in other ecologically important environmental matrixes may help elucidate those environmental factors contributing to the spread of ARGs.}, } @article {pmid23915718, year = {2013}, author = {Capra, JA and Stolzer, M and Durand, D and Pollard, KS}, title = {How old is my gene?.}, journal = {Trends in genetics : TIG}, volume = {29}, number = {11}, pages = {659-668}, pmid = {23915718}, issn = {0168-9525}, support = {U01 HL098179/HL/NHLBI NIH HHS/United States ; UM1 HL098179/HL/NHLBI NIH HHS/United States ; HL098179/HL/NHLBI NIH HHS/United States ; }, mesh = {Computational Biology ; Databases, Genetic ; *Evolution, Molecular ; Genes/*physiology ; *Models, Genetic ; Paleontology/*methods ; Phylogeny ; }, abstract = {Gene functions, interactions, disease associations, and ecological distributions are all correlated with gene age. However, it is challenging to estimate the intricate series of evolutionary events leading to a modern-day gene and then to reduce this history to a single age estimate. Focusing on eukaryotic gene families, we introduce a framework that can be used to compare current strategies for quantifying gene age, discuss key differences between these methods, and highlight several common problems. We argue that genes with complex evolutionary histories do not have a single well-defined age. As a result, care must be taken to articulate the goals and assumptions of any analysis that uses gene age estimates. Recent algorithmic advances offer the promise of gene age estimates that are fast, accurate, and consistent across gene families. This will enable a shift to integrated genome-wide analyses of all events in gene evolutionary histories in the near future.}, } @article {pmid23913584, year = {2014}, author = {Pichancourt, JB and Firn, J and Chadès, I and Martin, TG}, title = {Growing biodiverse carbon-rich forests.}, journal = {Global change biology}, volume = {20}, number = {2}, pages = {382-393}, doi = {10.1111/gcb.12345}, pmid = {23913584}, issn = {1365-2486}, mesh = {*Biodiversity ; *Carbon Sequestration ; *Decision Support Techniques ; Ecosystem ; Forestry/*methods ; Models, Biological ; Queensland ; Soil/chemistry ; Trees/*chemistry/*growth & development ; }, abstract = {Regrowing forests on cleared land is a key strategy to achieve both biodiversity conservation and climate change mitigation globally. Maximizing these co-benefits, however, remains theoretically and technically challenging because of the complex relationship between carbon sequestration and biodiversity in forests, the strong influence of climate variability and landscape position on forest development, the large number of restoration strategies possible, and long time-frames needed to declare success. Through the synthesis of three decades of knowledge on forest dynamics and plant functional traits combined with decision science, we demonstrate that we cannot always maximize carbon sequestration by simply increasing the functional trait diversity of trees planted. The relationships between plant functional diversity, carbon sequestration rates above ground and in the soil are dependent on climate and landscape positions. We show how to manage 'identities' and 'complementarities' between plant functional traits to achieve systematically maximal cobenefits in various climate and landscape contexts. We provide examples of optimal planting and thinning rules that satisfy this ecological strategy and guide the restoration of forests that are rich in both carbon and plant functional diversity. Our framework provides the first mechanistic approach for generating decision-makingrules that can be used to manage forests for multiple objectives, and supports joined carbon credit and biodiversity conservation initiatives, such as Reducing Emissions from Deforestation and forest Degradation REDD+. The decision framework can also be linked to species distribution models and socio-economic models to find restoration solutions that maximize simultaneously biodiversity, carbon stocks, and other ecosystem services across landscapes. Our study provides the foundation for developing and testing cost-effective and adaptable forest management rules to achieve biodiversity, carbon sequestration, and other socio-economic co-benefits under global change.}, } @article {pmid23913468, year = {2014}, author = {Hill, RA and Pyper, BJ and Lawrence, GS and Mann, GS and Allard, P and Mackintosh, CE and Healey, N and Dwyer, J and Trowell, J}, title = {Using sparse dose-response data for wildlife risk assessment.}, journal = {Integrated environmental assessment and management}, volume = {10}, number = {1}, pages = {3-11}, doi = {10.1002/ieam.1477}, pmid = {23913468}, issn = {1551-3793}, mesh = {Animals ; *Animals, Wild ; Databases, Factual ; *Dose-Response Relationship, Drug ; Ecotoxicology/methods ; *Models, Theoretical ; Risk Assessment/*methods ; }, abstract = {Hazard quotients based on a point-estimate comparison of exposure to a toxicity reference value (TRV) are commonly used to characterize risks for wildlife. Quotients may be appropriate for screening-level assessments but should be avoided in detailed assessments, because they provide little insight regarding the likely magnitude of effects and associated uncertainty. To better characterize risks to wildlife and support more informed decision making, practitioners should make full use of available dose-response data. First, relevant studies should be compiled and data extracted. Data extractions are not trivial--practitioners must evaluate the potential use of each study or its components, extract numerous variables, and in some cases, calculate variables of interest. Second, plots should be used to thoroughly explore the data, especially in the range of doses relevant to a given risk assessment. Plots should be used to understand variation in dose-response among studies, species, and other factors. Finally, quantitative dose-response models should be considered if they are likely to provide an improved basis for decision making. The most common dose-response models are simple models for data from a particular study for a particular species, using generalized linear models or other models appropriate for a given endpoint. Although simple models work well in some instances, they generally do not reflect the full breadth of information in a dose-response data set, because they apply only for particular studies, species, and endpoints. More advanced models are available that explicitly account for variation among studies and species, or that standardize multiple endpoints to a common response variable. Application of these models may be useful in some cases when data are abundant, but there are challenges to implementing and interpreting such models when data are sparse.}, } @article {pmid23910579, year = {2013}, author = {Ji, Y and Ashton, L and Pedley, SM and Edwards, DP and Tang, Y and Nakamura, A and Kitching, R and Dolman, PM and Woodcock, P and Edwards, FA and Larsen, TH and Hsu, WW and Benedick, S and Hamer, KC and Wilcove, DS and Bruce, C and Wang, X and Levi, T and Lott, M and Emerson, BC and Yu, DW}, title = {Reliable, verifiable and efficient monitoring of biodiversity via metabarcoding.}, journal = {Ecology letters}, volume = {16}, number = {10}, pages = {1245-1257}, doi = {10.1111/ele.12162}, pmid = {23910579}, issn = {1461-0248}, mesh = {Animals ; Arthropods/physiology ; *Biodiversity ; Computational Biology ; Ecology/*methods ; *Electronic Data Processing ; Environmental Monitoring/*methods ; }, abstract = {To manage and conserve biodiversity, one must know what is being lost, where, and why, as well as which remedies are likely to be most effective. Metabarcoding technology can characterise the species compositions of mass samples of eukaryotes or of environmental DNA. Here, we validate metabarcoding by testing it against three high-quality standard data sets that were collected in Malaysia (tropical), China (subtropical) and the United Kingdom (temperate) and that comprised 55,813 arthropod and bird specimens identified to species level with the expenditure of 2,505 person-hours of taxonomic expertise. The metabarcode and standard data sets exhibit statistically correlated alpha- and beta-diversities, and the two data sets produce similar policy conclusions for two conservation applications: restoration ecology and systematic conservation planning. Compared with standard biodiversity data sets, metabarcoded samples are taxonomically more comprehensive, many times quicker to produce, less reliant on taxonomic expertise and auditable by third parties, which is essential for dispute resolution.}, } @article {pmid23907860, year = {2013}, author = {Diandini, R and Takahashi, K and Park, EK and Jiang, Y and Movahed, M and Le, GV and Lee, LJ and Delgermaa, V and Kim, R}, title = {Potential years of life lost (PYLL) caused by asbestos-related diseases in the world.}, journal = {American journal of industrial medicine}, volume = {56}, number = {9}, pages = {993-1000}, doi = {10.1002/ajim.22206}, pmid = {23907860}, issn = {1097-0274}, mesh = {Adult ; Aged ; Aged, 80 and over ; Asbestosis/*mortality ; *Cost of Illness ; Databases, Factual ; Female ; Global Health/*statistics & numerical data ; Humans ; *Life Tables ; Male ; Mesothelioma/*mortality ; Middle Aged ; }, abstract = {BACKGROUND: We applied the well-established, but rather under-utilized, indicator of Potential Years of Life Lost (PYLL) to estimate the global burden of mesothelioma and asbestosis.

METHODS: We analyzed all deaths caused by mesothelioma and asbestosis that were reported by 82 and 55 countries, respectively, to the World Health Organization (WHO) from 1994 to 2010.

RESULTS: The 128,015 and 13,885 persons who died of mesothelioma and asbestosis, potentially lost a total of 2.18 million and 180,000 years of life (PYLL), or, an annual average PYLL of 201,000 years and 17,000 years, respectively. The average PYLL per decedent were 17.0 and 13.0 years for mesothelioma and asbestosis, respectively.

CONCLUSIONS: The current burden of asbestos-related diseases (ARDs) in terms of PYLL is substantial. The future burden of ARDs can be eliminated by stopping the use of asbestos.}, } @article {pmid23900082, year = {2013}, author = {Liu, S and Crossman, ND and Nolan, M and Ghirmay, H}, title = {Bringing ecosystem services into integrated water resources management.}, journal = {Journal of environmental management}, volume = {129}, number = {}, pages = {92-102}, doi = {10.1016/j.jenvman.2013.06.047}, pmid = {23900082}, issn = {1095-8630}, mesh = {Australia ; Conservation of Natural Resources/*methods ; Decision Support Techniques ; Ecology/*methods ; *Ecosystem ; Models, Theoretical ; Policy Making ; Rivers ; *Water Resources ; }, abstract = {In this paper we propose an ecosystem service framework to support integrated water resource management and apply it to the Murray-Darling Basin in Australia. Water resources in the Murray-Darling Basin have been over-allocated for irrigation use with the consequent degradation of freshwater ecosystems. In line with integrated water resource management principles, Australian Government reforms are reducing the amount of water diverted for irrigation to improve ecosystem health. However, limited understanding of the broader benefits and trade-offs associated with reducing irrigation diversions has hampered the planning process supporting this reform. Ecosystem services offer an integrative framework to identify the broader benefits associated with integrated water resource management in the Murray-Darling Basin, thereby providing support for the Government to reform decision-making. We conducted a multi-criteria decision analysis for ranking regional potentials to provide ecosystem services at river basin scale. We surveyed the wider public about their understanding of, and priorities for, managing ecosystem services and then integrated the results with spatially explicit indicators of ecosystem service provision. The preliminary results of this work identified the sub-catchments with the greatest potential synergies and trade-offs of ecosystem service provision under the integrated water resources management reform process. With future development, our framework could be used as a decision support tool by those grappling with the challenge of the sustainable allocation of water between irrigation and the environment.}, } @article {pmid23898669, year = {2013}, author = {Wang, JL and Ran, YY and Zhang, YJ and Cao, XM and Yang, F}, title = {[Land cover and landscape pattern changes in Poyang Lake region of China in 1980-2010].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {24}, number = {4}, pages = {1085-1093}, pmid = {23898669}, issn = {1001-9332}, mesh = {China ; Crops, Agricultural/*growth & development ; *Ecosystem ; Environmental Monitoring ; Geographic Information Systems ; *Lakes ; Remote Sensing Technology ; Trees/*growth & development ; Urbanization ; }, abstract = {Based on the land cover datasets of Poyang Lake region in 1980, 2005, and 2010, and by using GIS, RS, and landscape ecology approaches, this paper studied the land cover and landscape pattern changes in this region from 1980 to 2010, and quantitatively analyzed the land cover types change degree, patch area index, patch shape index, margin density index, and landscape diversity index. In 1980-2010, the main land cover types in this region were paddy field, inland water, evergreen broadleaf forest, and urban built-up area, and their areas and spatial patterns varied dramatically. Overall, the areas of inland water and urban built-up area had a significant increase, while those of paddy field and dry farmland decreased somewhat. Due to the effects of population growth and economic development, the landscape fragmentation degree and landscape diversity index presented a decreasing trend, but the decrement was small, which implied that the previous environmental management of this region had exerted important roles, but a long term challenge was still faced with between the regional environmental protection and sustainable development.}, } @article {pmid23898667, year = {2013}, author = {Bu, CQ and Hu, ZB and Yu, LZ and Yan, QL and Zheng, X}, title = {[Forest resources in Qungyuan County of Liaoning, Northeast China: the structure and optimal spatial allocation].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {24}, number = {4}, pages = {1070-1076}, pmid = {23898667}, issn = {1001-9332}, mesh = {*Biomass ; China ; Conservation of Natural Resources/*methods ; *Ecosystem ; Forestry/*economics ; Geographic Information Systems ; Remote Sensing Technology ; Spatial Analysis ; Trees/*growth & development ; }, abstract = {By using RS/GIS techniques and the method of multiple objective grey situation decision, and in considering the forest economic benefits (biomass and stand productivity) and ecological benefits (water and soil conservation) , an optimal spatial allocation of the present forest types in Qingyuan County of Liaoning, Northeast China was approached in this study. After the optimization of spatial allocation, the structural proportions of different forest types in Qingyuan County changed obviously, with the area of coniferous forests reduced from 43% to 23% , the area of broadleaved forests reduced from 51% to 31% , the area of mixed coniferous-broadleaf forests increased from 3% to 43% , and the area of shrubs remained unchanged. As compared with the results before optimization, the biomass, stand productivity, and water conservation function of the forest ecosystem in Qingyuan County after optimization increased by 0.6%, 2.1% , and 31.7%, respectively, and the soil conservation function remained unchanged. It could be concluded that after the optimization of spatial allocation, the forest ecosystem of Qingyuan County could maintain its soil conservation function, and, at the time of keeping higher timber production, fully exert waler conservation function, realizing the maximization of the economic and ecological benefits of the forest ecosystem.}, } @article {pmid23898649, year = {2013}, author = {Kong, FT and Xi, M and Li, Y and Kong, FL and Chen, W}, title = {[Wetland landscape pattern change based on GIS and RS: a review].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {24}, number = {4}, pages = {941-946}, pmid = {23898649}, issn = {1001-9332}, mesh = {Biodiversity ; China ; *Conservation of Natural Resources ; *Ecosystem ; Environment Design ; Geographic Information Systems ; Remote Sensing Technology ; *Wetlands ; }, abstract = {Wetland is an ecological landscape with most biodiversity in nature, which has unique ecological structure and function, and contains abundant natural resources to provide material guarantee for human's living and development. Wetland landscape pattern is the comprehensive result of various ecological processes, and has become a hot issue in wetland ecological study. At present, the combination of geographic information system (GIS) and remote sensing (RS) technologies is an important way to study the wetland landscape pattern change. This paper reviewed the research progress in the wetland landscape change based on GIS and RS from the aspects of the research methods of wetland landscape pattern, index of wetland landscape pattern, and driving forces of wetland landscape pattern evolution, and discussed the applications of the combination of GIS and RS in monitoring the wetland landscape pattern change, the index selection of wetland landscape pattern, and the driving mechanisms of the combined action of human and nature. Some deficiencies in the current studies were put forward, and the directions of the future-studies were prospected.}, } @article {pmid23898213, year = {2013}, author = {Kampa, A and Gagunashvili, AN and Gulder, TA and Morinaka, BI and Daolio, C and Godejohann, M and Miao, VP and Piel, J and Andrésson, Ó}, title = {Metagenomic natural product discovery in lichen provides evidence for a family of biosynthetic pathways in diverse symbioses.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {110}, number = {33}, pages = {E3129-37}, pmid = {23898213}, issn = {1091-6490}, mesh = {Base Sequence ; Biological Products/chemistry/isolation & purification ; Biosynthetic Pathways/*genetics ; Chromatography, High Pressure Liquid ; Cluster Analysis ; Computational Biology ; Data Mining ; Gene Components ; Iceland ; Lichens/*genetics ; Magnetic Resonance Spectroscopy ; Mass Spectrometry ; Metagenome/*genetics ; Metagenomics/methods ; Molecular Sequence Data ; Molecular Structure ; Multigene Family/genetics ; Polyketide Synthases/*genetics ; Sequence Analysis, DNA ; Species Specificity ; Symbiosis/*genetics ; }, abstract = {Bacteria are a major source of natural products that provide rich opportunities for both chemical and biological investigation. Although the vast majority of known bacterial metabolites derive from free-living organisms, increasing evidence supports the widespread existence of chemically prolific bacteria living in symbioses. A strategy based on bioinformatic prediction, symbiont cultivation, isotopic enrichment, and advanced analytics was used to characterize a unique polyketide, nosperin, from a lichen-associated Nostoc sp. cyanobacterium. The biosynthetic gene cluster and the structure of nosperin, determined from 30 μg of compound, are related to those of the pederin group previously known only from nonphotosynthetic bacteria associated with beetles and marine sponges. The presence of this natural product family in such highly dissimilar associations suggests that some bacterial metabolites may be specific to symbioses with eukaryotes and encourages exploration of other symbioses for drug discovery and better understanding of ecological interactions mediated by complex bacterial metabolites.}, } @article {pmid23894077, year = {2013}, author = {Wöhlbrand, L and Trautwein, K and Rabus, R}, title = {Proteomic tools for environmental microbiology--a roadmap from sample preparation to protein identification and quantification.}, journal = {Proteomics}, volume = {13}, number = {18-19}, pages = {2700-2730}, doi = {10.1002/pmic.201300175}, pmid = {23894077}, issn = {1615-9861}, mesh = {*Analytic Sample Preparation Methods ; Bacterial Proteins/*metabolism ; Databases, Protein ; *Environmental Microbiology ; Mass Spectrometry ; Proteomics/*methods ; }, abstract = {The steadily increasing amount of (meta-)genomic sequence information of diverse organisms and habitats has a strong impact on research in microbial physiology and ecology. In-depth functional understanding of metabolic processes and overall physiological adaptation to environmental changes, however, requires application of proteomics, as the context specific proteome constitutes the true functional output of a cell. Considering the enormous structural and functional diversity of proteins, only rational combinations of various analytical approaches allow a holistic view on the overall state of the cell. Within the past decade, proteomic methods became increasingly accessible to microbiologists mainly due to the robustness of analytical methods (e.g. 2DE), and affordability of mass spectrometers and their relative ease of use. This review provides an overview on the complex portfolio of state-of-the-art proteomics and highlights the basic principles of key methods, ranging from sample preparation of laboratory or environmental samples, via protein/peptide separation (gel-based or gel-free) and different types of mass spectrometric protein/peptide analyses, to protein identification and abundance determination.}, } @article {pmid23894053, year = {2013}, author = {Dellicour, S and Lecocq, T}, title = {GCALIGNER 1.0: an alignment program to compute a multiple sample comparison data matrix from large eco-chemical datasets obtained by GC.}, journal = {Journal of separation science}, volume = {36}, number = {19}, pages = {3206-3209}, doi = {10.1002/jssc.201300388}, pmid = {23894053}, issn = {1615-9314}, mesh = {*Algorithms ; Chromatography, Gas ; *Databases, Chemical ; *Software ; }, abstract = {GCALIGNER 1.0 is a computer program designed to perform a preliminary data comparison matrix of chemical data obtained by GC without MS information. The alignment algorithm is based on the comparison between the retention times of each detected compound in a sample. In this paper, we test the GCALIGNER efficiency on three datasets of the chemical secretions of bumble bees. The algorithm performs the alignment with a low error rate (<3%). GCALIGNER 1.0 is a useful, simple and free program based on an algorithm that enables the alignment of table-type data from GC.}, } @article {pmid23892676, year = {2013}, author = {Vicente Sánchez, MP and Macías Saint-Gerons, D and de la Fuente Honrubia, C and González Bermejo, D and Montero Corominas, D and Catalá-López, F}, title = {[Trends of use of anxiolytics and hypnotics in Spain from 2000 to 2011].}, journal = {Revista espanola de salud publica}, volume = {87}, number = {3}, pages = {247-255}, doi = {10.4321/S1135-57272013000300004}, pmid = {23892676}, issn = {2173-9110}, mesh = {Alprazolam/therapeutic use ; Anti-Anxiety Agents/*therapeutic use ; Databases, Factual ; Drug Prescriptions/statistics & numerical data ; Europe ; Humans ; Hydroxyzine/therapeutic use ; Hypnotics and Sedatives/*therapeutic use ; Lorazepam/analogs & derivatives/therapeutic use ; Pyridines/therapeutic use ; Spain ; Zolpidem ; }, abstract = {BACKGROUND: For years, anxiolytics and hypnotics have been one of the most prescribed drug classes in most developed countries. The main aim of this study is to explore the pattern of use of anxiolytic and hypnotic drugs during the period 2000-2011, comparing their growth with that of five european countries.

METHOD: We performed an ecological and descriptive study of anxiolytics and hypnotics consumption in Spain. Consumption data were obtained from the databases of medications dispensed in community pharmacies and charged through official prescriptions to the totality of the Spanish National Health System. Annual and total-period consumptions were expressed in defined daily doses (DDD) per 1000 inhabitants per day (DDD/1000 person/day) by each treatment subgroup, active substance and attending the plasma half-life of the medication. Approximate comparisons were also made with some European countries.

RESULTS: The use of anxiolytics and hypnotics drugs was 56.7 DDD/1000 person/day in 2000 and 82.9 DDD/1000 person/day in 2011 (a +46.1% increase across the period). Lorazepam and alprazolam were the most used anxiolytics (20.5 and 15.6 DDD/1000 person/day in 2011, respectively), whereas lormetazepam was among the hypnotics (18.3 DDD/1000 person/day in 2011). In relative terms, hypnotics´ lormetazepam and zolpidem increased their use by 103.3% and 85.1%, respectively; while anxiolytics´ lorazepam and hydroxyzine increased 75.1% and 72.8%, respectively. In Spain (period 2003-2010), the total increase in the consumption of anxiolytics and hypnotics was +34.3%, with 24.0% for Portugal, 4.0% for Italy, but a reduction of -6.1% for France.

CONCLUSIONS: A considerable increase in anxiolytics and hypnotics´ consumption has occurred in Spain during the last decade, being the growth higher than that reported in other European countries.}, } @article {pmid23892384, year = {2013}, author = {Murata, A and Matsuda, S}, title = {Association between ambulance distance to hospitals and mortality from acute diseases in Japan: national database analysis.}, journal = {Journal of public health management and practice : JPHMP}, volume = {19}, number = {5}, pages = {E23-8}, doi = {10.1097/PHH.0b013e31828b7150}, pmid = {23892384}, issn = {1550-5022}, mesh = {Acute Disease ; *Ambulances ; Brain Infarction/*mortality ; *Critical Care ; Databases, Factual ; Health Policy ; *Health Services Accessibility ; Humans ; Japan/epidemiology ; Linear Models ; Myocardial Infarction/*mortality ; Outcome Assessment, Health Care ; Pneumonia/*mortality ; Subarachnoid Hemorrhage/*mortality ; Time Factors ; }, abstract = {OBJECTIVE: The aim of this study was to evaluate the relationship between ambulance distance to hospitals and mortality from acute diseases using the national database in Japan.

DESIGN: Geospatial ecological study.

SETTING: We collected the data of transport distance to hospitals from the Diagnosis Procedure Combination database and that of mortality per 100 000 from some acute diseases from the database of life tables by the Ministry of Health, Labour and Welfare in Japan.

PARTICIPANTS: A total of 108 314 patients (40 882 patients with acute myocardial infarction, 31 632 patients with brain infarction, 4992 patients with subarachnoid hemorrhage, and 30 808 patients with pneumonia) were referred in Japan in 2008.

MAIN OUTCOME MEASURES: We evaluated the association between the mean transport distance to hospitals and the mortality from acute diseases using simple linear regression analysis. This correlation was evaluated separately for each acute disease.

RESULTS: The mean transport distances to hospitals were 8.1 km for acute myocardial infarction, 8.3 km for brain infarction, 9.5 km for subarachnoid hemorrhage, and 7.6 km for pneumonia, whereas the mortalities per 100,000 were 34.6 for acute myocardial infarction, 60.4 for brain infarction, 11.2 for subarachnoid hemorrhage, and 91.6 for pneumonia. Simple linear regression analysis revealed significant positive correlations between transport distance and mortality per 100,000 for acute myocardial infarction and brain infarction (R2 = 0.315 and 0.398, P < .001, respectively). Otherwise, moderate positive correlations between transport distance and mortality per 100,000 were shown for subarachnoid hemorrhage and pneumonia (R2 = 0.112, P < .012 and .233, P < .001, respectively).

CONCLUSIONS: This study suggests that the ambulance distance to hospitals significantly influences the risk of mortality for some acute diseases in Japan. Further studies are needed to confirm this association.}, } @article {pmid23891591, year = {2013}, author = {Zhang, L and Sun, W and Cai, W and Zhang, Z and Gu, Y and Chen, H and Ma, S and Jia, X}, title = {Differential response of two ferritin subunit genes (VpFer1 and VpFer2) from Venerupis philippinarum following pathogen and heavy metals challenge.}, journal = {Fish & shellfish immunology}, volume = {35}, number = {5}, pages = {1658-1662}, doi = {10.1016/j.fsi.2013.07.030}, pmid = {23891591}, issn = {1095-9947}, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Bivalvia/*genetics/immunology/microbiology ; Cloning, Molecular ; Computational Biology ; DNA Primers/genetics ; DNA, Complementary/genetics ; Ferritins/*genetics/metabolism ; Gene Expression Regulation/*drug effects ; Hepatopancreas/metabolism ; Metals, Heavy/*toxicity ; Molecular Sequence Data ; Protein Subunits/*genetics/metabolism ; RNA, Messenger/metabolism ; Real-Time Polymerase Chain Reaction ; Reverse Transcriptase Polymerase Chain Reaction ; Sequence Analysis, DNA ; Vibrio/*immunology ; }, abstract = {As a principal extracellular iron storage molecule, ferritin plays an important role in the iron-withholding strategy of innate immunity and detoxification system. In this study, we cloned and characterized another ferritin from Venerupis philippinarum (designated as VpFer2), in addition to one previously reported (VpFer1). VpFer2 possessed all the conserved features critical for the fundamental structure and function of ferritin H subunit. VpFer1 and VpFer2 mRNA were both found to be most abundantly expressed in hepatopancreas. Vibrio challenge could significantly up-regulate the mRNA expression of VpFers, and VpFer2 showed more sensitive to Vibrio anguillarum infection. For heavy metals exposure, the expression level of VpFer1 was significantly induced by Cd at 48 h, but kept relatively constant after exposure to Cu. With regards to VpFer2, the expression level dropped significantly at 24 h, then began to increase to the peak value at 48 h under Cd exposure, while Cu exposure constantly depressed the expression level of VpFer2 throughout the time course. Similarly, VpFer2 seemed to be more sensitive to heavy metals exposure than VpFer1 as its mRNA level changed by higher magnitudes. All these results suggested that VpFers may be important proteins involved in host immune defense and heavy metals detoxification. The diverse expression patterns of VpFers demonstrated that VpFer2 was an early and sensitive responder to environmental stress in V. philippinarum.}, } @article {pmid23889972, year = {2014}, author = {Avarre, JC and Dugué, R and Alonso, P and Diombokho, A and Joffrois, C and Faivre, N and Cochet, C and Durand, JD}, title = {Analysis of the black-chinned tilapia Sarotherodon melanotheron heudelotii reproducing under a wide range of salinities: from RNA-seq to candidate genes.}, journal = {Molecular ecology resources}, volume = {14}, number = {1}, pages = {139-149}, doi = {10.1111/1755-0998.12148}, pmid = {23889972}, issn = {1755-0998}, mesh = {Animals ; Cichlids/*genetics/*physiology ; Computational Biology ; High-Throughput Nucleotide Sequencing ; Molecular Sequence Data ; *Osmotic Pressure ; *Salinity ; Sequence Analysis ; *Transcriptome ; }, abstract = {The black-chinned tilapia Sarotherodon melanotheron heudelotii is an ecologically appealing model as it shows exceptional adaptive capacities, especially with regard to salinity. In spite of this, this species is devoid of genomic resources, which impedes the understanding of such remarkable features. De novo assembly of transcript sequences produced by next-generation sequencing technologies offers a rapid approach to obtain expressed gene sequences for non-model organisms. It also facilitates the development of quantitative real-time PCR (qPCR) assays for analysing gene expression under different environmental conditions. Nevertheless, obtaining accurate and reliable qPCR results from such data requires a number of validations prior to interpretation. The transcriptome of S. melanotheron was sequenced to discover transcripts potentially involved in the plasticity of male reproduction in response to salinity variations. A set of 54 candidate and reference genes was selected through a digital gene expression (DGE) approach, and a de novo qPCR assay using these genes was validated for further detailed expression analyses. A user-friendly web interface was created for easy handling of the sequence data. This sequence collection represents a major transcriptomic resource for S. melanotheron and will provide a useful tool for functional genomics and genetics studies.}, } @article {pmid23885568, year = {2013}, author = {Monge-Nájera, J and Nielsen-Muñoz, V and Azofeifa-Mora, AB}, title = {Subject and authorship of records related to the Organization for Tropical Studies (OTS) in BINABITROP, a comprehensive database about Costa Rican biology.}, journal = {Revista de biologia tropical}, volume = {61}, number = {2}, pages = {493-500}, doi = {10.15517/rbt.v61i2.11142}, pmid = {23885568}, issn = {0034-7744}, mesh = {Animals ; *Authorship ; *Bibliometrics ; Biology/*statistics & numerical data ; Costa Rica ; *Databases, Bibliographic ; Periodicals as Topic/*statistics & numerical data ; Tropical Climate ; }, abstract = {BINABITROP is a bibliographical database of more than 38000 records about the ecosystems and organisms of Costa Rica. In contrast with commercial databases, such as Web of Knowledge and Scopus, which exclude most of the scientific journals published in tropical countries, BINABITROP is a comprehensive record of knowledge on the tropical ecosystems and organisms of Costa Rica. We analyzed its contents in three sites (La Selva, Palo Verde and Las Cruces) and recorded scientific field, taxonomic group and authorship. We found that most records dealt with ecology and systematics, and that most authors published only one article in the study period (1963-2011). Most research was published in four journals: Biotropica, Revista de Biología Tropical/ International Journal of Tropical Biology and Conservation, Zootaxa and Brenesia. This may be the first study of a such a comprehensive database for any case of tropical biology literature.}, } @article {pmid23883524, year = {2013}, author = {Cridland, JM and Macdonald, SJ and Long, AD and Thornton, KR}, title = {Abundance and distribution of transposable elements in two Drosophila QTL mapping resources.}, journal = {Molecular biology and evolution}, volume = {30}, number = {10}, pages = {2311-2327}, pmid = {23883524}, issn = {1537-1719}, support = {R01 OD010974/OD/NIH HHS/United States ; R01-OD010974/OD/NIH HHS/United States ; R01 GM085183/GM/NIGMS NIH HHS/United States ; LM007443/LM/NLM NIH HHS/United States ; T15 LM007443/LM/NLM NIH HHS/United States ; R01-GM085183/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Computational Biology ; *DNA Transposable Elements ; Drosophila melanogaster/*genetics ; Evolution, Molecular ; Female ; Genetic Fitness ; Genome ; Male ; Models, Genetic ; Multigene Family ; Polymorphism, Single Nucleotide ; *Quantitative Trait Loci ; Selection, Genetic ; X Chromosome/genetics ; }, abstract = {Here we present computational machinery to efficiently and accurately identify transposable element (TE) insertions in 146 next-generation sequenced inbred strains of Drosophila melanogaster. The panel of lines we use in our study is composed of strains from a pair of genetic mapping resources: the Drosophila Genetic Reference Panel (DGRP) and the Drosophila Synthetic Population Resource (DSPR). We identified 23,087 TE insertions in these lines, of which 83.3% are found in only one line. There are marked differences in the distribution of elements over the genome, with TEs found at higher densities on the X chromosome, and in regions of low recombination. We also identified many more TEs per base pair of intronic sequence and fewer TEs per base pair of exonic sequence than expected if TEs are located at random locations in the euchromatic genome. There was substantial variation in TE load across genes. For example, the paralogs derailed and derailed-2 show a significant difference in the number of TE insertions, potentially reflecting differences in the selection acting on these loci. When considering TE families, we find a very weak effect of gene family size on TE insertions per gene, indicating that as gene family size increases the number of TE insertions in a given gene within that family also increases. TEs are known to be associated with certain phenotypes, and our data will allow investigators using the DGRP and DSPR to assess the functional role of TE insertions in complex trait variation more generally. Notably, because most TEs are very rare and often private to a single line, causative TEs resulting in phenotypic differences among individuals may typically fail to replicate across mapping panels since individual elements are unlikely to segregate in both panels. Our data suggest that "burden tests" that test for the effect of TEs as a class may be more fruitful.}, } @article {pmid23878813, year = {2013}, author = {López-Giráldez, F and Moeller, AH and Townsend, JP}, title = {Evaluating phylogenetic informativeness as a predictor of phylogenetic signal for metazoan, fungal, and mammalian phylogenomic data sets.}, journal = {BioMed research international}, volume = {2013}, number = {}, pages = {621604}, pmid = {23878813}, issn = {2314-6141}, mesh = {Animals ; Chromosome Mapping/*methods ; Computer Simulation ; Conserved Sequence ; *Databases, Genetic ; *Evolution, Molecular ; Fungi/genetics ; Genetic Markers/*genetics ; Genome/*genetics ; Mammals ; *Models, Genetic ; *Phylogeny ; Sequence Analysis, DNA/methods ; }, abstract = {Phylogenetic research is often stymied by selection of a marker that leads to poor phylogenetic resolution despite considerable cost and effort. Profiles of phylogenetic informativeness provide a quantitative measure for prioritizing gene sampling to resolve branching order in a particular epoch. To evaluate the utility of these profiles, we analyzed phylogenomic data sets from metazoans, fungi, and mammals, thus encompassing diverse time scales and taxonomic groups. We also evaluated the utility of profiles created based on simulated data sets. We found that genes selected via their informativeness dramatically outperformed haphazard sampling of markers. Furthermore, our analyses demonstrate that the original phylogenetic informativeness method can be extended to trees with more than four taxa. Thus, although the method currently predicts phylogenetic signal without specifically accounting for the misleading effects of stochastic noise, it is robust to the effects of homoplasy. The phylogenetic informativeness rankings obtained will allow other researchers to select advantageous genes for future studies within these clades, maximizing return on effort and investment. Genes identified might also yield efficient experimental designs for phylogenetic inference for many sister clades and outgroup taxa that are closely related to the diverse groups of organisms analyzed.}, } @article {pmid23878337, year = {2013}, author = {Maniatis, D and Gaugris, J and Mollicone, D and Scriven, J and Corblin, A and Ndikumagenge, C and Aquino, A and Crete, P and Sanz-Sanchez, MJ}, title = {Financing and current capacity for REDD+ readiness and monitoring, measurement, reporting and verification in the Congo Basin.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {368}, number = {1625}, pages = {20120310}, pmid = {23878337}, issn = {1471-2970}, mesh = {Africa, Central ; Climate Change/statistics & numerical data ; Congo ; Conservation of Natural Resources/*economics/methods/statistics & numerical data ; Databases, Factual ; Ecological Parameter Monitoring/*economics/*methods/statistics & numerical data ; Ecosystem ; Financing, Government ; *Trees ; }, abstract = {This paper provides the first critical analysis of the financing and current capacity for REDD+ readiness in the Congo Basin, with a particular focus on the REDD+ component of national forest monitoring and measurement, reporting and verification (M&MRV). We focus on three areas of analysis: (i) general financing for REDD+ readiness especially M&MRV; (ii) capacity and information for REDD+ implementation and M&MRV; (iii) prospects and challenges for REDD+ and M&MRV readiness in terms of financing and capacity. For the first area of analysis, a REDD+ and M&MRV readiness financing database was created based on the information from the REDD+ voluntary database and Internet searches. For the second area of analysis, a qualitative approach to data collection was adopted (semi-structured interviews with key stakeholders, surveys and observations). All 10 countries were visited between 2010 and 2012. We find that: (i) a significant amount of REDD+ financing flows into the Congo Basin (±US$550 million or almost half of the REDD+ financing for the African continent); (ii) across countries, there is an important disequilibrium in terms of REDD+ and M&MRV readiness financing, political engagement, comprehension and capacity, which also appears to be a key barrier to countries receiving equal resources; (iii) most financing appears to go to smaller scale (subnational) REDD+ projects; (iv) four distinct country groups in terms of REDD+ readiness and M&MRV status are identified; and (v) the Congo Basin has a distinct opportunity to have a specific REDD+ financing window for large-scale and more targeted national REDD+ programmes through a specific fund for the region.}, } @article {pmid23878336, year = {2013}, author = {Gond, V and Fayolle, A and Pennec, A and Cornu, G and Mayaux, P and Camberlin, P and Doumenge, C and Fauvet, N and Gourlet-Fleury, S}, title = {Vegetation structure and greenness in Central Africa from Modis multi-temporal data.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {368}, number = {1625}, pages = {20120309}, pmid = {23878336}, issn = {1471-2970}, mesh = {Africa, Central ; Carbon Cycle ; Climate Change ; Congo ; Databases, Factual ; Ecological Parameter Monitoring/statistics & numerical data ; Ecosystem ; Humans ; Rain ; Seasons ; Time Factors ; *Trees/physiology ; }, abstract = {African forests within the Congo Basin are generally mapped at a regional scale as broad-leaved evergreen forests, with the main distinction being between terra-firme and swamp forest types. At the same time, commercial forest inventories, as well as national maps, have highlighted a strong spatial heterogeneity of forest types. A detailed vegetation map generated using consistent methods is needed to inform decision makers about spatial forest organization and their relationships with environmental drivers in the context of global change. We propose a multi-temporal remotely sensed data approach to characterize vegetation types using vegetation index annual profiles. The classifications identified 22 vegetation types (six savannas, two swamp forests, 14 forest types) improving existing vegetation maps. Among forest types, we showed strong variations in stand structure and deciduousness, identifying (i) two blocks of dense evergreen forests located in the western part of the study area and in the central part on sandy soils; (ii) semi-deciduous forests are located in the Sangha River interval which has experienced past fragmentation and human activities. For all vegetation types enhanced vegetation index profiles were highly seasonal and strongly correlated to rainfall and to a lesser extent, to light regimes. These results are of importance to predict spatial variations of carbon stocks and fluxes, because evergreen/deciduous forests (i) have contrasted annual dynamics of photosynthetic activity and foliar water content and (ii) differ in community dynamics and ecosystem processes.}, } @article {pmid23875910, year = {2013}, author = {, and Coltman, DW and Hogg, JT and Miller, JM}, title = {Genomic resources notes accepted 1 April 2013-31 May 2013.}, journal = {Molecular ecology resources}, volume = {13}, number = {5}, pages = {965}, doi = {10.1111/1755-0998.12142}, pmid = {23875910}, issn = {1755-0998}, mesh = {Animals ; Computational Biology/methods ; Databases, Genetic ; *Polymorphism, Single Nucleotide ; Sheep, Bighorn/*genetics ; }, abstract = {This article documents the public availability of approximately 15 000 polymorphic SNP loci for the bighorn sheep Ovis canadensis.}, } @article {pmid23874623, year = {2013}, author = {Yates, KL and Schoeman, DS}, title = {Spatial access priority mapping (SAPM) with fishers: a quantitative GIS method for participatory planning.}, journal = {PloS one}, volume = {8}, number = {7}, pages = {e68424}, pmid = {23874623}, issn = {1932-6203}, mesh = {Conservation of Natural Resources ; Fisheries/*methods ; *Geographic Information Systems ; Humans ; }, abstract = {Spatial management tools, such as marine spatial planning and marine protected areas, are playing an increasingly important role in attempts to improve marine management and accommodate conflicting needs. Robust data are needed to inform decisions among different planning options, and early inclusion of stakeholder involvement is widely regarded as vital for success. One of the biggest stakeholder groups, and the most likely to be adversely impacted by spatial restrictions, is the fishing community. In order to take their priorities into account, planners need to understand spatial variation in their perceived value of the sea. Here a readily accessible, novel method for quantitatively mapping fishers' spatial access priorities is presented. Spatial access priority mapping, or SAPM, uses only basic functions of standard spreadsheet and GIS software. Unlike the use of remote-sensing data, SAPM actively engages fishers in participatory mapping, documenting rather than inferring their priorities. By so doing, SAPM also facilitates the gathering of other useful data, such as local ecological knowledge. The method was tested and validated in Northern Ireland, where over 100 fishers participated in a semi-structured questionnaire and mapping exercise. The response rate was excellent, 97%, demonstrating fishers' willingness to be involved. The resultant maps are easily accessible and instantly informative, providing a very clear visual indication of which areas are most important for the fishers. The maps also provide quantitative data, which can be used to analyse the relative impact of different management options on the fishing industry and can be incorporated into planning software, such as MARXAN, to ensure that conservation goals can be met at minimum negative impact to the industry. This research shows how spatial access priority mapping can facilitate the early engagement of fishers and the ready incorporation of their priorities into the decision-making process in a transparent, quantitative way.}, } @article {pmid23870280, year = {2013}, author = {Rajkumar, AP and Brinda, EM and Duba, AS and Thangadurai, P and Jacob, KS}, title = {National suicide rates and mental health system indicators: an ecological study of 191 countries.}, journal = {International journal of law and psychiatry}, volume = {36}, number = {5-6}, pages = {339-342}, doi = {10.1016/j.ijlp.2013.06.004}, pmid = {23870280}, issn = {1873-6386}, mesh = {Databases, Factual ; Health Services Accessibility ; Humans ; *Internationality ; Mental Health Services/*standards ; *Quality Indicators, Health Care ; Suicide/*statistics & numerical data/trends ; }, abstract = {PURPOSE: The relative contributions of psychiatric morbidity and psychosocial stress to suicide, and the efficacy of mental health systems in reducing population suicide rates, are currently unclear. This study, therefore, aimed to investigate whether national suicide rates are associated with their corresponding mental health system indicators.

METHODS: Relevant data were retrieved from the following sources: the World Health Organization, the United Nations Statistics Division and the Central Intelligence Agency World Fact book. Suicide rates of 191 countries were compared with their mental health system indicators using an ecological study design and multivariate non-parametric robust regression models.

RESULTS: Significant positive correlations between suicide rates and mental health system indicators (p<0.001) were documented. After adjusting for the effects of major macroeconomic indices using multivariate analyses, numbers of psychiatrists (p=0.006) and mental health beds (p<0.001) were significantly positively associated with population suicide rates.

CONCLUSIONS: Countries with better psychiatric services experience higher suicide rates. Although these associations should be interpreted with caution, as the issues are complex, we suggest that population-based public health strategies may have greater impact on national suicide rates than curative mental health services for individuals.}, } @article {pmid23866038, year = {2013}, author = {Guerbois, C and Dufour, AB and Mtare, G and Fritz, H}, title = {Insights for integrated conservation from attitudes of people toward protected areas near Hwange National Park, Zimbabwe.}, journal = {Conservation biology : the journal of the Society for Conservation Biology}, volume = {27}, number = {4}, pages = {844-855}, doi = {10.1111/cobi.12108}, pmid = {23866038}, issn = {1523-1739}, mesh = {*Attitude ; *Biodiversity ; Conservation of Natural Resources/*methods/statistics & numerical data ; Geographic Information Systems ; Humans ; Interviews as Topic ; Linear Models ; *Population Dynamics ; Public Opinion ; Social Values ; Zimbabwe ; }, abstract = {Increase in human settlements at the edge of protected areas (PAs) is perceived as a major threat to conservation of biodiversity. Although it is crucial to integrate the interests of surrounding communities into PA management, key drivers of changes in local populations and the effects of conservation on local livelihoods and perceptions remain poorly understood. We assessed population changes from 1990 to 2010 in 9 villages located between 2 PAs with different management policies (access to natural resources or not). We conducted semi-directive interviews at the household level (n =217) to document reasons for settlement in the area and villager's attitudes toward the PAs. We examined drivers of these attitudes relative to household typology, feelings about conservation, and concerns for the future with mixed linear models. Population increased by 61% from 2000 to 2010, a period of political and economic crisis in Zimbabwe. Forty-seven percent of immigrants were attracted by the area; others had been resettled from other villages or were returning to family lands. Attitudes toward PAs were generally positive, but immigrants attracted by the area and who used resources within the PA with fewer restrictions expressed more negative attitudes toward PAs. Household location, losses due to wild animals, and restrictions on access to natural resources were the main drivers of this negative attitude. Profit-seeking migrants did not expect these constraints and were particularly concerned with local overpopulation and access to natural resources. To avoid socio-ecological traps near PAs (i.e., unforeseen reduced adaptive capacity) integrated conservation should address mismatches between management policy and local expectations. This requires accounting for endogenous processes, for example, local socio-ecological dynamics and values that shape the coexistence between humans and wildlife.}, } @article {pmid23864529, year = {2013}, author = {Pett, W and Lavrov, DV}, title = {The twin-arginine subunit C in Oscarella: origin, evolution, and potential functional significance.}, journal = {Integrative and comparative biology}, volume = {53}, number = {3}, pages = {495-502}, doi = {10.1093/icb/ict079}, pmid = {23864529}, issn = {1557-7023}, mesh = {Amino Acid Sequence ; Animals ; Bayes Theorem ; Computational Biology/methods ; DNA, Mitochondrial/*genetics ; Electron Transport Complex III/genetics/metabolism ; *Evolution, Molecular ; Membrane Transport Proteins/*genetics/metabolism ; Models, Genetic ; Molecular Sequence Data ; *Phylogeny ; Porifera/*genetics ; Sequence Alignment ; Sequence Homology ; }, abstract = {The twin-arginine translocation (Tat) pathway is a protein transport system that moves completely folded proteins across lipid membranes. Genes encoding components of the pathway have been found in the genomes of many Bacteria, Archaea, and eukaryotic organelles including chloroplasts, plant mitochondria, and the mitochondria of many protists. However, with a single exception, Tat genes are absent from the mitochondrial genomes of all animals. The only exception comes from the homoscleromorph sponges in the family Oscarellidae, whose mitochondrial genomes encode a gene for tatC, the largest subunit of the complex. Here, we explore the origin and evolution of the mitochondrial tatC gene in Oscarellidae, and use bioinformatic approaches to evaluate its functional significance. We conclude that tatC in Homoscleromorpha sponges was likely inherited from the ancestral proto-mitochondrial genome, implying multiple independent losses of the mitochondrial Tat pathway during the evolution of opisthokonts. In addition, bioinformatic evidence suggests that tatC comprises the entire Tat pathway in Oscarellidae, and that the Rieske Fe/S protein of mitochondrial complex III is its likely substrate.}, } @article {pmid23864253, year = {2013}, author = {Benson, JF and Patterson, BR}, title = {Inter-specific territoriality in a Canis hybrid zone: spatial segregation between wolves, coyotes, and hybrids.}, journal = {Oecologia}, volume = {173}, number = {4}, pages = {1539-1550}, pmid = {23864253}, issn = {1432-1939}, mesh = {Animals ; Coyotes/*genetics ; Ecosystem ; Genetics, Population ; Geographic Information Systems ; *Hybridization, Genetic ; Ontario ; *Territoriality ; Wolves/*genetics ; }, abstract = {Gray wolves (Canis lupus) and coyotes (Canis latrans) generally exhibit intraspecific territoriality manifesting in spatial segregation between adjacent packs. However, previous studies have found a high degree of interspecific spatial overlap between sympatric wolves and coyotes. Eastern wolves (Canis lycaon) are the most common wolf in and around Algonquin Provincial Park (APP), Ontario, Canada and hybridize with sympatric gray wolves and coyotes. We hypothesized that all Canis types (wolves, coyotes, and hybrids) exhibit a high degree of spatial segregation due to greater genetic, morphologic, and ecological similarities between wolves and coyotes in this hybrid system compared with western North American ecosystems. We used global positioning system telemetry and probabilistic measures of spatial overlap to investigate spatial segregation between adjacent Canis packs. Our hypothesis was supported as: (1) the probability of locating wolves, coyotes, and hybrids within home ranges ([Formula: see text] = 0.05) or core areas ([Formula: see text] < 0.01) of adjacent packs was low; and (2) the amount of shared space use was negligible. Spatial segregation did not vary substantially in relation to genotypes of adjacent packs or local environmental conditions (i.e., harvest regulations or road densities). We provide the first telemetry-based demonstration of spatial segregation between wolves and coyotes, highlighting the novel relationships between Canis types in the Ontario hybrid zone relative to areas where wolves and coyotes are reproductively isolated. Territoriality among Canis may increase the likelihood of eastern wolves joining coyote and hybrid packs, facilitate hybridization, and could play a role in limiting expansion of the genetically distinct APP eastern wolf population.}, } @article {pmid23861841, year = {2013}, author = {Chen, S and Huang, X and Yan, X and Liang, Y and Wang, Y and Li, X and Peng, X and Ma, X and Zhang, L and Cai, Y and Ma, T and Cheng, L and Qi, D and Zheng, H and Yang, X and Li, X and Liu, G}, title = {Transcriptome analysis in sheepgrass (Leymus chinensis): a dominant perennial grass of the Eurasian Steppe.}, journal = {PloS one}, volume = {8}, number = {7}, pages = {e67974}, pmid = {23861841}, issn = {1932-6203}, mesh = {Asia ; Databases, Genetic ; Europe ; Expressed Sequence Tags ; Gene Expression Profiling ; *Gene Expression Regulation, Plant ; *Genome, Plant ; Hordeum/classification/genetics ; Microsatellite Repeats ; Molecular Sequence Annotation ; Molecular Typing ; Phylogeny ; Poaceae/classification/*genetics ; Sequence Analysis, DNA ; *Transcriptome ; Triticum/classification/genetics ; }, abstract = {BACKGROUND: Sheepgrass [Leymus chinensis (Trin.) Tzvel.] is an important perennial forage grass across the Eurasian Steppe and is known for its adaptability to various environmental conditions. However, insufficient data resources in public databases for sheepgrass limited our understanding of the mechanism of environmental adaptations, gene discovery and molecular marker development.

RESULTS: The transcriptome of sheepgrass was sequenced using Roche 454 pyrosequencing technology. We assembled 952,328 high-quality reads into 87,214 unigenes, including 32,416 contigs and 54,798 singletons. There were 15,450 contigs over 500 bp in length. BLAST searches of our database against Swiss-Prot and NCBI non-redundant protein sequences (nr) databases resulted in the annotation of 54,584 (62.6%) of the unigenes. Gene Ontology (GO) analysis assigned 89,129 GO term annotations for 17,463 unigenes. We identified 11,675 core Poaceae-specific and 12,811 putative sheepgrass-specific unigenes by BLAST searches against all plant genome and transcriptome databases. A total of 2,979 specific freezing-responsive unigenes were found from this RNAseq dataset. We identified 3,818 EST-SSRs in 3,597 unigenes, and some SSRs contained unigenes that were also candidates for freezing-response genes. Characterizations of nucleotide repeats and dominant motifs of SSRs in sheepgrass were also performed. Similarity and phylogenetic analysis indicated that sheepgrass is closely related to barley and wheat.

CONCLUSIONS: This research has greatly enriched sheepgrass transcriptome resources. The identified stress-related genes will help us to decipher the genetic basis of the environmental and ecological adaptations of this species and will be used to improve wheat and barley crops through hybridization or genetic transformation. The EST-SSRs reported here will be a valuable resource for future gene-phenotype studies and for the molecular breeding of sheepgrass and other Poaceae species.}, } @article {pmid23858025, year = {2014}, author = {Matić, PA and Vlajinac, HD and Marinković, JM and Maksimović, MŽ and Radak, DJ}, title = {Chronic venous disease: Correlation between ultrasound findings and the clinical, etiologic, anatomic and pathophysiologic classification.}, journal = {Phlebology}, volume = {29}, number = {8}, pages = {522-527}, doi = {10.1177/0268355513497360}, pmid = {23858025}, issn = {1758-1125}, mesh = {Adolescent ; Adult ; Aged ; *Angiography ; Chronic Disease ; *Echocardiography, Doppler, Color ; Female ; Humans ; Male ; Middle Aged ; *Vascular Diseases/classification/diagnostic imaging/etiology/physiopathology ; }, abstract = {OBJECTIVE: The aim of the study was to investigate association between clinical manifestation of chronic venous disease and the presence and severity of functional venous disease.

METHOD: A cross-sectional study was conducted in 14 towns in Serbia. All men and women aged >18 years, consecutively coming to venous specialists (47 specialists) were included in the study. Patients who were previously treated for chronic venous disease were excluded. Patients were classified according to the clinical category of clinical, etiologic, anatomic and pathophysiologic classification for chronic venous disease. Reflux and/or obstruction were determined by using a color duplex ultrasound.

RESULTS: The study included 1679 chronic venous disease patients. Color duplex ultrasound was performed in 1029 (61.3%) of them who formed the final study group. Reflux was found in 76.8% of patients - 53.1% had reflux in superficial, 7.2% in deep and 16.1% in perforator veins. Obstruction was found in 31.9% of patients - superficial in 14.8% of patients and deep in 16.9%. Deep obstruction was even found in clinical, etiologic, anatomic and pathophysiologic C0s-C1 categories. Reflux and obstruction combined were revealed in 19.1% of patients. Reflux in deep and perforator veins and reflux and obstruction combined were significantly associated with clinical, etiologic, anatomic and pathophysiologic clinical categories being the most frequent in patients with venous ulcers.

CONCLUSION: Clinical, etiologic, anatomic and pathophysiologic clinical categories of chronic venous disease are strongly correlated with functional disease especially with reflux in deep and perforator veins, and reflux and obstruction combined. The presence of deep obstruction in patients with chronic venous disease belonging to clinical, etiologic, anatomic and pathophysiologic C0s-C1 category could justify recommendation for color duplex ultrasonography in all patients with symptoms of chronic venous disease but without clear clinical signs.}, } @article {pmid23856617, year = {2013}, author = {Krause, J and Krause, S and Arlinghaus, R and Psorakis, I and Roberts, S and Rutz, C}, title = {Reality mining of animal social systems.}, journal = {Trends in ecology & evolution}, volume = {28}, number = {9}, pages = {541-551}, doi = {10.1016/j.tree.2013.06.002}, pmid = {23856617}, issn = {1872-8383}, support = {BB/G023913/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; Birds/*physiology ; Data Mining/*methods ; Electronic Data Processing ; Humans ; Models, Biological ; *Movement ; Remote Sensing Technology/instrumentation/*methods ; *Social Behavior ; }, abstract = {The increasing miniaturisation of animal-tracking technology has made it possible to gather exceptionally detailed machine-sensed data on the social dynamics of almost entire populations of individuals, in both terrestrial and aquatic study systems. Here, we review important issues concerning the collection of such data, and their processing and analysis, to identify the most promising approaches in the emerging field of 'reality mining'. Automated technologies can provide data sensing at time intervals small enough to close the gap between social patterns and their underlying processes, providing insights into how social structures arise and change dynamically over different timescales. Especially in conjunction with experimental manipulations, reality mining promises significant advances in basic and applied research on animal social systems.}, } @article {pmid23855883, year = {2013}, author = {Morellet, N and Bonenfant, C and Börger, L and Ossi, F and Cagnacci, F and Heurich, M and Kjellander, P and Linnell, JD and Nicoloso, S and Sustr, P and Urbano, F and Mysterud, A}, title = {Seasonality, weather and climate affect home range size in roe deer across a wide latitudinal gradient within Europe.}, journal = {The Journal of animal ecology}, volume = {82}, number = {6}, pages = {1326-1339}, doi = {10.1111/1365-2656.12105}, pmid = {23855883}, issn = {1365-2656}, mesh = {Animals ; *Climate ; Deer/*physiology ; Europe ; Female ; Geographic Information Systems ; *Homing Behavior ; *Seasons ; *Weather ; }, abstract = {1. Because many large mammal species have wide geographical ranges, spatially distant populations may be confronted with different sets of environmental conditions. Investigating how home range (HR) size varies across environmental gradients should yield a better understanding of the factors affecting large mammal ecology. 2. We evaluated how HR size of a large herbivore, the roe deer (Capreolus capreolus), varies in relation to seasonality, latitude (climate), weather, plant productivity and landscape features across its geographical range in Western Europe. As roe deer are income breeders, expected to adjust HR size continuously to temporal variation in food resources and energetic requirements, our baseline prediction was for HR size to decrease with proxies of resource availability. 3. We used GPS locations of roe deer collected from seven study sites (EURODEER collaborative project) to estimate fixed-kernel HR size at weekly and monthly temporal scales. We performed an unusually comprehensive analysis of variation in HR size among and within populations over time across the geographical range of a single species using generalized additive mixed models and linear mixed models, respectively. 4. Among populations, HR size decreased with increasing values for proxies of forage abundance, but increased with increases in seasonality, stochastic variation of temperature, latitude and snow cover. Within populations, roe deer HR size varied over time in relation to seasonality and proxies of forage abundance in a consistent way across the seven populations. Thus, our findings were broadly consistent across the distributional range of this species, demonstrating a strong and ubiquitous link between the amplitude and timing of environmental seasonality and HR size at the continental scale. 5. Overall, the variability in average HR size of roe deer across Europe reflects the interaction among local weather, climate and seasonality, providing valuable insight into the limiting factors affecting this large herbivore under contrasting conditions. The complexity of the relationships suggests that predicting ranging behaviour of large herbivores in relation to current and future climate change will require detailed knowledge not only about predicted increases in temperature, but also how this interacts with factors such as day length and climate predictability.}, } @article {pmid23855518, year = {2014}, author = {Zhou, ZC and Dong, Y and Sun, HJ and Yang, AF and Chen, Z and Gao, S and Jiang, JW and Guan, XY and Jiang, B and Wang, B}, title = {Transcriptome sequencing of sea cucumber (Apostichopus japonicus) and the identification of gene-associated markers.}, journal = {Molecular ecology resources}, volume = {14}, number = {1}, pages = {127-138}, doi = {10.1111/1755-0998.12147}, pmid = {23855518}, issn = {1755-0998}, mesh = {Animals ; Asia, Southeastern ; Computational Biology ; *Genetic Markers ; *High-Throughput Nucleotide Sequencing ; Lipopolysaccharides/*toxicity ; Microsatellite Repeats ; Molecular Sequence Data ; Polymorphism, Single Nucleotide ; Sea Cucumbers/*drug effects/*genetics ; *Stress, Physiological ; *Transcriptome ; }, abstract = {Sea cucumber (Apostichopus japonicus) is an ecologically and economically important species in East and South-East Asia. This project aimed to identify large numbers of gene-associated markers and differentially expressed genes (DEGs) after lipopolysaccharides (LPS) challenge in A. japonicus using high-throughput transcriptome sequencing. A total of 162 million high-quality reads of 174 million raw reads were obtained by deep sequencing using Illumina HiSeq™ 2000 platform. Assembly of these reads generated 94 704 unigenes, with read length ranging from 200 to 16 153 bp (average length of 810 bp). A total of 36 005 were identified as coding sequences (CDSs), 32 479 of which were successfully annotated. Based on the assembly transcriptome, we identified 142 511 high-quality single nucleotide polymorphisms (SNPs). Among them, 33 775, 63 120 and 45 616 were located in sequences without predicted CDS (non-CDSs), CDSs and untranslated regions (UTRs), respectively. These putative SNPs included 82 664 transitions and 59 847 transversions. Totally, 89 375 (59.1%) were distributed in 15 473 known genes. A total of 6417 microsatellites were detected in 5970 unigenes, 3216 of which were annotated and 2481 were successfully subjected for primer design. The numbers of simple sequence repeats (SSRs) identified in non-CDSs, CDSs and UTRs were 2367, 2316 and 1734. These potential SNPs and SSRs are expected to provide abundant resources for genetic, evolutionary and ecological studies in sea cucumber. Transcriptome comparison revealed 1330, 1347 and 1291 DEGs in the coelomocytes of A. japonicus at 4 h, 24 h and 72 h after LPS challenge, respectively. Approximately 58.4% (1802) of total DEGs have been successfully annotated.}, } @article {pmid23849157, year = {2013}, author = {Brooks, JM and Tang, Y and Chapman, CG and Cook, EA and Chrischilles, EA}, title = {What is the effect of area size when using local area practice style as an instrument?.}, journal = {Journal of clinical epidemiology}, volume = {66}, number = {8 Suppl}, pages = {S69-83}, pmid = {23849157}, issn = {1878-5921}, support = {RC4 AG038635/AG/NIA NIH HHS/United States ; }, mesh = {Aged ; Aged, 80 and over ; Angiotensin Receptor Antagonists/*therapeutic use ; Angiotensin-Converting Enzyme Inhibitors/*therapeutic use ; Automobile Driving ; Bias ; Confounding Factors, Epidemiologic ; Data Interpretation, Statistical ; Family Practice/statistics & numerical data ; Female ; Humans ; Least-Squares Analysis ; Male ; Medicare ; Myocardial Infarction/drug therapy/*mortality ; Outcome Assessment, Health Care/*statistics & numerical data ; Practice Patterns, Physicians'/*statistics & numerical data ; Residence Characteristics/*statistics & numerical data ; Time Factors ; United States/epidemiology ; }, abstract = {OBJECTIVES: Discuss the tradeoffs inherent in choosing a local area size when using a measure of local area practice style as an instrument in instrumental variable estimation when assessing treatment effectiveness.

STUDY DESIGN: Assess the effectiveness of angiotensin converting-enzyme inhibitors and angiotensin receptor blockers on survival after acute myocardial infarction for Medicare beneficiaries using practice style instruments based on different-sized local areas around patients. We contrasted treatment effect estimates using different local area sizes in terms of the strength of the relationship between local area practice styles and individual patient treatment choices; and indirect assessments of the assumption violations.

RESULTS: Using smaller local areas to measure practice styles exploits more treatment variation and results in smaller standard errors. However, if treatment effects are heterogeneous, the use of smaller local areas may increase the risk that local practice style measures are dominated by differences in average treatment effectiveness across areas and bias results toward greater effectiveness.

CONCLUSION: Local area practice style measures can be useful instruments in instrumental variable analysis, but the use of smaller local area sizes to generate greater treatment variation may result in treatment effect estimates that are biased toward higher effectiveness. Assessment of whether ecological bias can be mitigated by changing local area size requires the use of outside data sources.}, } @article {pmid23850847, year = {2013}, author = {Macías-Díaz, JE and Macías, S and Medina-Ramírez, IE}, title = {An efficient nonlinear finite-difference approach in the computational modeling of the dynamics of a nonlinear diffusion-reaction equation in microbial ecology.}, journal = {Computational biology and chemistry}, volume = {47}, number = {}, pages = {24-30}, doi = {10.1016/j.compbiolchem.2013.05.003}, pmid = {23850847}, issn = {1476-928X}, mesh = {Bacteria/classification/growth & development/*metabolism ; Biofilms ; Computational Biology ; *Computer Simulation ; Diffusion ; *Ecosystem ; *Models, Biological ; *Nonlinear Dynamics ; }, abstract = {In this manuscript, we present a computational model to approximate the solutions of a partial differential equation which describes the growth dynamics of microbial films. The numerical technique reported in this work is an explicit, nonlinear finite-difference methodology which is computationally implemented using Newton's method. Our scheme is compared numerically against an implicit, linear finite-difference discretization of the same partial differential equation, whose computer coding requires an implementation of the stabilized bi-conjugate gradient method. Our numerical results evince that the nonlinear approach results in a more efficient approximation to the solutions of the biofilm model considered, and demands less computer memory. Moreover, the positivity of initial profiles is preserved in the practice by the nonlinear scheme proposed.}, } @article {pmid23845962, year = {2013}, author = {Haas, BJ and Papanicolaou, A and Yassour, M and Grabherr, M and Blood, PD and Bowden, J and Couger, MB and Eccles, D and Li, B and Lieber, M and MacManes, MD and Ott, M and Orvis, J and Pochet, N and Strozzi, F and Weeks, N and Westerman, R and William, T and Dewey, CN and Henschel, R and LeDuc, RD and Friedman, N and Regev, A}, title = {De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis.}, journal = {Nature protocols}, volume = {8}, number = {8}, pages = {1494-1512}, pmid = {23845962}, issn = {1750-2799}, support = {HHSN272200900018C/AI/NIAID NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; 1R01HG005232-01A1/HG/NHGRI NIH HHS/United States ; P50 HG006193/HG/NHGRI NIH HHS/United States ; 5P50HG006193-02/HG/NHGRI NIH HHS/United States ; R01 HG005232/HG/NHGRI NIH HHS/United States ; }, mesh = {Base Sequence ; Gene Expression Profiling/*methods ; RNA/*chemistry ; Schizosaccharomyces/genetics ; Schizosaccharomyces pombe Proteins/chemistry/genetics ; Sequence Analysis, RNA/methods ; *Software ; *Transcriptome ; }, abstract = {De novo assembly of RNA-seq data enables researchers to study transcriptomes without the need for a genome sequence; this approach can be usefully applied, for instance, in research on 'non-model organisms' of ecological and evolutionary importance, cancer samples or the microbiome. In this protocol we describe the use of the Trinity platform for de novo transcriptome assembly from RNA-seq data in non-model organisms. We also present Trinity-supported companion utilities for downstream applications, including RSEM for transcript abundance estimation, R/Bioconductor packages for identifying differentially expressed transcripts across samples and approaches to identify protein-coding genes. In the procedure, we provide a workflow for genome-independent transcriptome analysis leveraging the Trinity platform. The software, documentation and demonstrations are freely available from http://trinityrnaseq.sourceforge.net. The run time of this protocol is highly dependent on the size and complexity of data to be analyzed. The example data set analyzed in the procedure detailed herein can be processed in less than 5 h.}, } @article {pmid23843385, year = {2013}, author = {Drake, JM}, title = {Early warning signals of stochastic switching.}, journal = {Proceedings. Biological sciences}, volume = {280}, number = {1766}, pages = {20130686}, pmid = {23843385}, issn = {1471-2954}, mesh = {Data Interpretation, Statistical ; Decision Theory ; *Models, Theoretical ; *Stochastic Processes ; }, } @article {pmid23843191, year = {2013}, author = {Patil, KR and McHardy, AC}, title = {Alignment-free genome tree inference by learning group-specific distance metrics.}, journal = {Genome biology and evolution}, volume = {5}, number = {8}, pages = {1470-1484}, pmid = {23843191}, issn = {1759-6653}, mesh = {Algorithms ; Computational Biology/*methods ; Evolution, Molecular ; *Genome, Microbial ; *Phylogeny ; *Sequence Alignment ; }, abstract = {Understanding the evolutionary relationships between organisms is vital for their in-depth study. Gene-based methods are often used to infer such relationships, which are not without drawbacks. One can now attempt to use genome-scale information, because of the ever increasing number of genomes available. This opportunity also presents a challenge in terms of computational efficiency. Two fundamentally different methods are often employed for sequence comparisons, namely alignment-based and alignment-free methods. Alignment-free methods rely on the genome signature concept and provide a computationally efficient way that is also applicable to nonhomologous sequences. The genome signature contains evolutionary signal as it is more similar for closely related organisms than for distantly related ones. We used genome-scale sequence information to infer taxonomic distances between organisms without additional information such as gene annotations. We propose a method to improve genome tree inference by learning specific distance metrics over the genome signature for groups of organisms with similar phylogenetic, genomic, or ecological properties. Specifically, our method learns a Mahalanobis metric for a set of genomes and a reference taxonomy to guide the learning process. By applying this method to more than a thousand prokaryotic genomes, we showed that, indeed, better distance metrics could be learned for most of the 18 groups of organisms tested here. Once a group-specific metric is available, it can be used to estimate the taxonomic distances for other sequenced organisms from the group. This study also presents a large scale comparison between 10 methods--9 alignment-free and 1 alignment-based.}, } @article {pmid23831580, year = {2013}, author = {Sablok, G and Milev, I and Minkov, G and Minkov, I and Varotto, C and Yahubyan, G and Baev, V}, title = {isomiRex: web-based identification of microRNAs, isomiR variations and differential expression using next-generation sequencing datasets.}, journal = {FEBS letters}, volume = {587}, number = {16}, pages = {2629-2634}, doi = {10.1016/j.febslet.2013.06.047}, pmid = {23831580}, issn = {1873-3468}, mesh = {Algorithms ; Animals ; Base Sequence ; Databases, Genetic ; *Gene Expression Profiling ; Humans ; Internet ; MicroRNAs/*genetics/metabolism ; Molecular Sequence Data ; Reproducibility of Results ; Sequence Analysis, RNA/*methods ; Sequence Homology, Nucleic Acid ; Software ; }, abstract = {We present an open-access web platform isomiRex, to identify isomiRs and on the fly graphical visualization of the differentially expressed miRNAs in control as well as treated library. The open-access web-platform is not restricted only to NGS sequence dataset from animals and potentially analyzes a wider dataset for plants, animals and viral NGS dataset supporting miRBase (version 19 supporting 193 species). The platform can handle the bloated amount of the read counts and reports the annotated microRNAs from plant, animal and viral NGS datasets. isomiRex also provides an estimation of the the isomiRs, of miRNAs with higher copy number relative to their mature reference sequences indexed in miRBase (version 19 supporting 193 species). Visually enhanced graphs potentially display differentially expressed isomiRs, which will help the user to demonstrate and correlate the abundance of the isomiR as a signature event to the specific condition. An additional module for estimating the differential expression has been implemented allowing the users to postulate the differential expression across the user input samples. The developed web-platform can be accessed at http://bioinfo1.uni-plovdiv.bg/isomiRex/.}, } @article {pmid23826978, year = {2013}, author = {Vandepoele, K and Van Bel, M and Richard, G and Van Landeghem, S and Verhelst, B and Moreau, H and Van de Peer, Y and Grimsley, N and Piganeau, G}, title = {pico-PLAZA, a genome database of microbial photosynthetic eukaryotes.}, journal = {Environmental microbiology}, volume = {15}, number = {8}, pages = {2147-2153}, doi = {10.1111/1462-2920.12174}, pmid = {23826978}, issn = {1462-2920}, mesh = {Chlorophyta/genetics ; DNA Barcoding, Taxonomic ; Databases, Genetic/*standards/*trends ; Diatoms/genetics ; Eukaryota/*genetics ; Genetic Variation ; Genome, Plant/genetics ; *Genomics ; }, abstract = {With the advent of next generation genome sequencing, the number of sequenced algal genomes and transcriptomes is rapidly growing. Although a few genome portals exist to browse individual genome sequences, exploring complete genome information from multiple species for the analysis of user-defined sequences or gene lists remains a major challenge. pico-PLAZA is a web-based resource (http://bioinformatics.psb.ugent.be/pico-plaza/) for algal genomics that combines different data types with intuitive tools to explore genomic diversity, perform integrative evolutionary sequence analysis and study gene functions. Apart from homologous gene families, multiple sequence alignments, phylogenetic trees, Gene Ontology, InterPro and text-mining functional annotations, different interactive viewers are available to study genome organization using gene collinearity and synteny information. Different search functions, documentation pages, export functions and an extensive glossary are available to guide non-expert scientists. To illustrate the versatility of the platform, different case studies are presented demonstrating how pico-PLAZA can be used to functionally characterize large-scale EST/RNA-Seq data sets and to perform environmental genomics. Functional enrichments analysis of 16 Phaeodactylum tricornutum transcriptome libraries offers a molecular view on diatom adaptation to different environments of ecological relevance. Furthermore, we show how complementary genomic data sources can easily be combined to identify marker genes to study the diversity and distribution of algal species, for example in metagenomes, or to quantify intraspecific diversity from environmental strains.}, } @article {pmid23826151, year = {2013}, author = {Wu, YT and Wubet, T and Trogisch, S and Both, S and Scholten, T and Bruelheide, H and Buscot, F}, title = {Forest Age and Plant Species Composition Determine the Soil Fungal Community Composition in a Chinese Subtropical Forest.}, journal = {PloS one}, volume = {8}, number = {6}, pages = {e66829}, pmid = {23826151}, issn = {1932-6203}, mesh = {Altitude ; *Biodiversity ; China ; Classification ; Computational Biology ; Conservation of Natural Resources ; DNA Barcoding, Taxonomic ; DNA, Fungal ; *Forests ; *Fungi/genetics ; *Plants ; *Soil Microbiology ; Time Factors ; }, abstract = {Fungal diversity and community composition are mainly related to soil and vegetation factors. However, the relative contribution of the different drivers remains largely unexplored, especially in subtropical forest ecosystems. We studied the fungal diversity and community composition of soils sampled from 12 comparative study plots representing three forest age classes (Young: 10-40 yrs; Medium: 40-80 yrs; Old: ≥80 yrs) in Gutianshan National Nature Reserve in South-eastern China. Soil fungal communities were assessed employing ITS rDNA pyrotag sequencing. Members of Basidiomycota and Ascomycota dominated the fungal community, with 22 putative ectomycorrhizal fungal families, where Russulaceae and Thelephoraceae were the most abundant taxa. Analysis of similarity showed that the fungal community composition significantly differed among the three forest age classes. Forest age class, elevation of the study plots, and soil organic carbon (SOC) were the most important factors shaping the fungal community composition. We found a significant correlation between plant and fungal communities at different taxonomic and functional group levels, including a strong relationship between ectomycorrhizal fungal and non-ectomycorrhizal plant communities. Our results suggest that in subtropical forests, plant species community composition is the main driver of the soil fungal diversity and community composition.}, } @article {pmid23822767, year = {2013}, author = {Yvert, G and Ohnuki, S and Nogami, S and Imanaga, Y and Fehrmann, S and Schacherer, J and Ohya, Y}, title = {Single-cell phenomics reveals intra-species variation of phenotypic noise in yeast.}, journal = {BMC systems biology}, volume = {7}, number = {}, pages = {54}, pmid = {23822767}, issn = {1752-0509}, support = {281359/ERC_/European Research Council/International ; }, mesh = {Computational Biology/*methods ; Evolution, Molecular ; *Phenotype ; Phylogeny ; Saccharomyces cerevisiae/*cytology/genetics ; *Single-Cell Analysis ; Species Specificity ; }, abstract = {BACKGROUND: Most quantitative measures of phenotypic traits represent macroscopic contributions of large numbers of cells. Yet, cells of a tissue do not behave similarly, and molecular studies on several organisms have shown that regulations can be highly stochastic, sometimes generating diversified cellular phenotypes within tissues. Phenotypic noise, defined here as trait variability among isogenic cells of the same type and sharing a common environment, has therefore received a lot of attention. Given the potential fitness advantage provided by phenotypic noise in fluctuating environments, the possibility that it is directly subjected to evolutionary selection is being considered. For selection to act, phenotypic noise must differ between contemporary genotypes. Whether this is the case or not remains, however, unclear because phenotypic noise has very rarely been quantified in natural populations.

RESULTS: Using automated image analysis, we describe here the phenotypic diversity of S. cerevisiae morphology at single-cell resolution. We profiled hundreds of quantitative traits in more than 1,000 cells of 37 natural strains, which represent various geographical and ecological origins of the species. We observed abundant trait variation between strains, with no correlation with their ecological origin or population history. Phenotypic noise strongly depended on the strain background. Noise variation was largely trait-specific (specific strains showing elevated noise for subset of traits) but also global (a few strains displaying elevated noise for many unrelated traits).

CONCLUSIONS: Our results demonstrate that phenotypic noise does differ quantitatively between natural populations. This supports the possibility that, if noise is adaptive, microevolution may tune it in the wild. This tuning may happen on specific traits or by varying the degree of global phenotypic buffering.}, } @article {pmid23818615, year = {2013}, author = {Sheppard, SK and Didelot, X and Meric, G and Torralbo, A and Jolley, KA and Kelly, DJ and Bentley, SD and Maiden, MC and Parkhill, J and Falush, D}, title = {Genome-wide association study identifies vitamin B5 biosynthesis as a host specificity factor in Campylobacter.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {110}, number = {29}, pages = {11923-11927}, pmid = {23818615}, issn = {1091-6490}, support = {/WT_/Wellcome Trust/United Kingdom ; 087622/WT_/Wellcome Trust/United Kingdom ; MR/K010174/1/MRC_/Medical Research Council/United Kingdom ; /BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; Base Sequence ; *Biological Evolution ; Biosynthetic Pathways/*genetics ; Campylobacter/*genetics ; Cattle/*microbiology ; Chickens/microbiology ; Cluster Analysis ; Computational Biology ; Genetics, Population ; Genome, Bacterial/genetics ; Genome-Wide Association Study/*methods ; Host Specificity/*genetics ; Models, Genetic ; Molecular Sequence Data ; Pantothenic Acid/*biosynthesis ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {Genome-wide association studies have the potential to identify causal genetic factors underlying important phenotypes but have rarely been performed in bacteria. We present an association mapping method that takes into account the clonal population structure of bacteria and is applicable to both core and accessory genome variation. Campylobacter is a common cause of human gastroenteritis as a consequence of its proliferation in multiple farm animal species and its transmission via contaminated meat and poultry. We applied our association mapping method to identify the factors responsible for adaptation to cattle and chickens among 192 Campylobacter isolates from these and other host sources. Phylogenetic analysis implied frequent host switching but also showed that some lineages were strongly associated with particular hosts. A seven-gene region with a host association signal was found. Genes in this region were almost universally present in cattle but were frequently absent in isolates from chickens and wild birds. Three of the seven genes encoded vitamin B5 biosynthesis. We found that isolates from cattle were better able to grow in vitamin B5-depleted media and propose that this difference may be an adaptation to host diet.}, } @article {pmid23817568, year = {2013}, author = {Haudry, A and Platts, AE and Vello, E and Hoen, DR and Leclercq, M and Williamson, RJ and Forczek, E and Joly-Lopez, Z and Steffen, JG and Hazzouri, KM and Dewar, K and Stinchcombe, JR and Schoen, DJ and Wang, X and Schmutz, J and Town, CD and Edger, PP and Pires, JC and Schumaker, KS and Jarvis, DE and Mandáková, T and Lysak, MA and van den Bergh, E and Schranz, ME and Harrison, PM and Moses, AM and Bureau, TE and Wright, SI and Blanchette, M}, title = {An atlas of over 90,000 conserved noncoding sequences provides insight into crucifer regulatory regions.}, journal = {Nature genetics}, volume = {45}, number = {8}, pages = {891-898}, pmid = {23817568}, issn = {1546-1718}, mesh = {Arabidopsis/genetics ; Brassicaceae/classification/*genetics ; Cluster Analysis ; Computational Biology ; *Conserved Sequence ; Evolution, Molecular ; Gene Deletion ; Gene Duplication ; Gene Expression Regulation, Plant ; Genome, Plant ; Genomics ; High-Throughput Nucleotide Sequencing ; Molecular Sequence Annotation ; Nucleotide Motifs ; Phylogeny ; *Regulatory Sequences, Nucleic Acid ; Selection, Genetic ; }, abstract = {Despite the central importance of noncoding DNA to gene regulation and evolution, understanding of the extent of selection on plant noncoding DNA remains limited compared to that of other organisms. Here we report sequencing of genomes from three Brassicaceae species (Leavenworthia alabamica, Sisymbrium irio and Aethionema arabicum) and their joint analysis with six previously sequenced crucifer genomes. Conservation across orthologous bases suggests that at least 17% of the Arabidopsis thaliana genome is under selection, with nearly one-quarter of the sequence under selection lying outside of coding regions. Much of this sequence can be localized to approximately 90,000 conserved noncoding sequences (CNSs) that show evidence of transcriptional and post-transcriptional regulation. Population genomics analyses of two crucifer species, A. thaliana and Capsella grandiflora, confirm that most of the identified CNSs are evolving under medium to strong purifying selection. Overall, these CNSs highlight both similarities and several key differences between the regulatory DNA of plants and other species.}, } @article {pmid23800682, year = {2013}, author = {Shi, Z and Hou, J and Guo, X and Zhang, H and Yang, F and Dai, J}, title = {Testicular phosphoproteome in perfluorododecanoic acid-exposed rats.}, journal = {Toxicology letters}, volume = {221}, number = {2}, pages = {91-101}, doi = {10.1016/j.toxlet.2013.06.219}, pmid = {23800682}, issn = {1879-3169}, mesh = {Animals ; CDC2 Protein Kinase ; Chromatography, Liquid ; Computational Biology ; Cyclin-Dependent Kinases/genetics/metabolism ; Fluorocarbons ; Lauric Acids/*toxicity ; Leydig Cells/*drug effects/metabolism ; Male ; Mitogen-Activated Protein Kinases/metabolism ; Phosphopeptides/*metabolism ; Phosphorylation ; Proteome/*metabolism ; Rats ; Rats, Sprague-Dawley ; Spermatogenesis/drug effects ; Tandem Mass Spectrometry ; }, abstract = {Perfluorododecanoic acid (PFDoA) is a common environmental pollutant, which has been detected in human sera and has adverse effects on testicular function in animal models. Exploring phosphorylation events in testes helps elucidate the specific phosphorylation signals involved in testicular toxicity of PFDoA. Combining efficient prefractionation of tryptic peptide mixtures using self-packed reversed phase C18 columns with TiO2 and IMAC phosphopeptide enrichment techniques followed by 2D-LC-MS/MS, we identified 4077 unique phosphopeptides from 1777 proteins with a false discovery rate below 1.0% in the testes of rats exposed to PFDoA for 110 days. In addition, 937 novel phosphorylation sites were discovered in testicular proteins. Hundreds of phosphorylated proteins identified might be involved in spermatogenesis and sperm function. With increasing PFDoA dosage, the number of casein kinase 2 kinase-modified peptides significantly increased. Pathway analysis suggested that the mitogen-activated protein kinase pathway and cell division cycle protein 2 (CDC2) may have contributed to sperm activity and testicular function. By in vitro experiments, CDC2 phosphorylation activity was found to be likely involved in PFDoA-induced toxicity in Leydig cells. This study provides the first examination of the whole proteins' phosphorylation profile in rat testis and suggests that the MAPK pathway and CDC2 protein phosphorylation are critical for PFDoA testicular toxicity.}, } @article {pmid23800136, year = {2013}, author = {Konwar, KM and Hanson, NW and Pagé, AP and Hallam, SJ}, title = {MetaPathways: a modular pipeline for constructing pathway/genome databases from environmental sequence information.}, journal = {BMC bioinformatics}, volume = {14}, number = {}, pages = {202}, pmid = {23800136}, issn = {1471-2105}, mesh = {Algorithms ; Animals ; *Databases, Genetic ; Databases, Nucleic Acid ; Ecosystem ; *Environment ; Forecasting ; Genomics ; Humans ; Phylogeny ; *Software ; }, abstract = {BACKGROUND: A central challenge to understanding the ecological and biogeochemical roles of microorganisms in natural and human engineered ecosystems is the reconstruction of metabolic interaction networks from environmental sequence information. The dominant paradigm in metabolic reconstruction is to assign functional annotations using BLAST. Functional annotations are then projected onto symbolic representations of metabolism in the form of KEGG pathways or SEED subsystems.

RESULTS: Here we present MetaPathways, an open source pipeline for pathway inference that uses the PathoLogic algorithm to map functional annotations onto the MetaCyc collection of reactions and pathways, and construct environmental Pathway/Genome Databases (ePGDBs) compatible with the editing and navigation features of Pathway Tools. The pipeline accepts assembled or unassembled nucleotide sequences, performs quality assessment and control, predicts and annotates noncoding genes and open reading frames, and produces inputs to PathoLogic. In addition to constructing ePGDBs, MetaPathways uses MLTreeMap to build phylogenetic trees for selected taxonomic anchor and functional gene markers, converts General Feature Format (GFF) files into concatenated GenBank files for ePGDB construction based on third-party annotations, and generates useful file formats including Sequin files for direct GenBank submission and gene feature tables summarizing annotations, MLTreeMap trees, and ePGDB pathway coverage summaries for statistical comparisons.

CONCLUSIONS: MetaPathways provides users with a modular annotation and analysis pipeline for predicting metabolic interaction networks from environmental sequence information using an alternative to KEGG pathways and SEED subsystems mapping. It is extensible to genomic and transcriptomic datasets from a wide range of sequencing platforms, and generates useful data products for microbial community structure and function analysis. The MetaPathways software package, installation instructions, and example data can be obtained from http://hallam.microbiology.ubc.ca/MetaPathways.}, } @article {pmid23790998, year = {2013}, author = {Yoon, S and Elhadad, N and Bakken, S}, title = {A practical approach for content mining of Tweets.}, journal = {American journal of preventive medicine}, volume = {45}, number = {1}, pages = {122-129}, pmid = {23790998}, issn = {1873-2607}, support = {P30 NR010677/NR/NINR NIH HHS/United States ; R01 HS019853/HS/AHRQ HHS/United States ; T32 NR007969/NR/NINR NIH HHS/United States ; T32NR007969/NR/NINR NIH HHS/United States ; }, mesh = {Data Collection/methods ; Data Mining/*methods ; *Health Behavior ; Humans ; Internet/*statistics & numerical data ; Research/organization & administration ; Research Design ; Social Media/*statistics & numerical data ; }, abstract = {Use of data generated through social media for health studies is gradually increasing. Twitter is a short-text message system developed 6 years ago, now with more than 100 million users generating over 300 million Tweets every day. Twitter may be used to gain real-world insights to promote healthy behaviors. The purposes of this paper are to describe a practical approach to analyzing Tweet contents and to illustrate an application of the approach to the topic of physical activity. The approach includes five steps: (1) selecting keywords to gather an initial set of Tweets to analyze; (2) importing data; (3) preparing data; (4) analyzing data (topic, sentiment, and ecologic context); and (5) interpreting data. The steps are implemented using tools that are publically available and free of charge and designed for use by researchers with limited programming skills. Content mining of Tweets can contribute to addressing challenges in health behavior research.}, } @article {pmid23794254, year = {2014}, author = {Sirota, M and Juanchich, M and Hagmayer, Y}, title = {Ecological rationality or nested sets? Individual differences in cognitive processing predict Bayesian reasoning.}, journal = {Psychonomic bulletin & review}, volume = {21}, number = {1}, pages = {198-204}, pmid = {23794254}, issn = {1531-5320}, mesh = {Adolescent ; Adult ; Bayes Theorem ; Cognition/*physiology ; Female ; Humans ; *Individuality ; Male ; Predictive Value of Tests ; Thinking/*physiology ; Young Adult ; }, abstract = {The presentation of a Bayesian inference problem in terms of natural frequencies rather than probabilities has been shown to enhance performance. The effect of individual differences in cognitive processing on Bayesian reasoning has rarely been studied, despite enabling us to test process-oriented variants of the two main accounts of the facilitative effect of natural frequencies: The ecological rationality account (ERA), which postulates an evolutionarily shaped ease of natural frequency automatic processing, and the nested sets account (NSA), which posits analytical processing of nested sets. In two experiments, we found that cognitive reflection abilities predicted normative performance equally well in tasks featuring whole and arbitrarily parsed objects (Experiment 1) and that cognitive abilities and thinking dispositions (analytical vs. intuitive) predicted performance with single-event probabilities, as well as natural frequencies (Experiment 2). Since these individual differences indicate that analytical processing improves Bayesian reasoning, our findings provide stronger support for the NSA than for the ERA.}, } @article {pmid23793647, year = {2013}, author = {Che, Y and Yang, K and Jin, Y and Zhang, W and Shang, Z and Tai, J}, title = {Residents' concerns and attitudes toward a municipal solid waste landfill: integrating a questionnaire survey and GIS techniques.}, journal = {Environmental monitoring and assessment}, volume = {185}, number = {12}, pages = {10001-10013}, pmid = {23793647}, issn = {1573-2959}, mesh = {Attitude ; China ; Decision Making ; Environmental Monitoring/*methods ; *Geographic Information Systems ; Humans ; Odorants ; Perception ; Refuse Disposal/*methods ; *Solid Waste ; *Surveys and Questionnaires ; *Waste Disposal Facilities ; }, abstract = {The ever-growing industry of municipal solid waste (MSW) disposal appeals to the growing need for disposal facilities, and MSW treatment facilities are increasingly an environmental and public health concern. Residents living near MSW management facilities are confronted with various risk perceptions, especially odour. In this study, in an effort to assist responsible decision-makers in better planning and managing such a project, a structured questionnaire was designed and distributed to assess the nearby residents' concerns and attitudes surrounding the Laogang Landfill in Shanghai. Geographic information system techniques and relevance analysis were employed to conduct the spatial analysis of physical perceptions, especially odour annoyance. The findings of the research indicate that a significant percentage of the responding sample was aware of the negative impacts of landfills on the environment and public health, and residents in close proximity preferred to live farther from the landfill. The results from the spatial analysis demonstrated a definite degree of correlation between odour annoyance and distance to the facility and proved that the benefits of the socially disadvantaged have been neglected. The research findings also direct attention to the important role of public participation, information disclosure, transparency in management, and mutual communication to avoid conflicts and build social trust.}, } @article {pmid23793624, year = {2013}, author = {Kozich, JJ and Westcott, SL and Baxter, NT and Highlander, SK and Schloss, PD}, title = {Development of a dual-index sequencing strategy and curation pipeline for analyzing amplicon sequence data on the MiSeq Illumina sequencing platform.}, journal = {Applied and environmental microbiology}, volume = {79}, number = {17}, pages = {5112-5120}, pmid = {23793624}, issn = {1098-5336}, support = {R01 HG005975/HG/NHGRI NIH HHS/United States ; U54HG004973/HG/NHGRI NIH HHS/United States ; P30 DK034933/DK/NIDDK NIH HHS/United States ; R01HG005975/HG/NHGRI NIH HHS/United States ; U54 HG004973/HG/NHGRI NIH HHS/United States ; 5R01GM099514/GM/NIGMS NIH HHS/United States ; P30DK034933/DK/NIDDK NIH HHS/United States ; R01 GM099514/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; *Biota ; Computational Biology/*methods ; Feces/microbiology ; High-Throughput Nucleotide Sequencing/*methods/*standards ; Humans ; *Metagenome ; Mice ; Soil Microbiology ; }, abstract = {Rapid advances in sequencing technology have changed the experimental landscape of microbial ecology. In the last 10 years, the field has moved from sequencing hundreds of 16S rRNA gene fragments per study using clone libraries to the sequencing of millions of fragments per study using next-generation sequencing technologies from 454 and Illumina. As these technologies advance, it is critical to assess the strengths, weaknesses, and overall suitability of these platforms for the interrogation of microbial communities. Here, we present an improved method for sequencing variable regions within the 16S rRNA gene using Illumina's MiSeq platform, which is currently capable of producing paired 250-nucleotide reads. We evaluated three overlapping regions of the 16S rRNA gene that vary in length (i.e., V34, V4, and V45) by resequencing a mock community and natural samples from human feces, mouse feces, and soil. By titrating the concentration of 16S rRNA gene amplicons applied to the flow cell and using a quality score-based approach to correct discrepancies between reads used to construct contigs, we were able to reduce error rates by as much as two orders of magnitude. Finally, we reprocessed samples from a previous study to demonstrate that large numbers of samples could be multiplexed and sequenced in parallel with shotgun metagenomes. These analyses demonstrate that our approach can provide data that are at least as good as that generated by the 454 platform while providing considerably higher sequencing coverage for a fraction of the cost.}, } @article {pmid23790154, year = {2013}, author = {Yang, I and Nell, S and Suerbaum, S}, title = {Survival in hostile territory: the microbiota of the stomach.}, journal = {FEMS microbiology reviews}, volume = {37}, number = {5}, pages = {736-761}, doi = {10.1111/1574-6976.12027}, pmid = {23790154}, issn = {1574-6976}, mesh = {Animals ; Computational Biology ; Helicobacter pylori/isolation & purification ; Humans ; *Microbiota ; Stomach/anatomy & histology/*microbiology/physiology ; }, abstract = {The human stomach is a formidable barrier to orally ingested microorganisms and was long thought to be sterile. The discovery of Helicobacter pylori, a carcinogenic bacterial pathogen that infects the stomach mucosa of more than one half of all humans globally, has started a major paradigm shift in our understanding of the stomach as an ecological niche for bacteria. The special adaptations that enable H. pylori to colonize this well-protected habitat have been intensively studied over the last three decades. In contrast, our knowledge concerning bacteria other than H. pylori in the human stomach is still quite limited. However, a substantial body of evidence documents convincingly that bacteria can regularly be sampled from the stomachs of healthy adults. Commonly detected phyla include Firmicutes, Actinobacteria, Bacteroidetes, and Proteobacteria, and characteristic genera are Lactobacillus, Streptococcus, and Propionibacterium. In this review, we summarize the available literature about the gastric microbiota in humans and selected model animals, discuss the methods used in its characterization, and identify gaps in our knowledge that need to be addressed to advance our understanding of the bacterial colonization of the different layers of the gastric mucosa and its potential role in health and disease.}, } @article {pmid23785456, year = {2013}, author = {Morris, BD and White, EP}, title = {The EcoData retriever: improving access to existing ecological data.}, journal = {PloS one}, volume = {8}, number = {6}, pages = {e65848}, pmid = {23785456}, issn = {1932-6203}, mesh = {Database Management Systems ; *Databases, Factual ; *Ecology ; Humans ; Internet ; *Software ; Software Design ; User-Computer Interface ; }, abstract = {Ecological research relies increasingly on the use of previously collected data. Use of existing datasets allows questions to be addressed more quickly, more generally, and at larger scales than would otherwise be possible. As a result of large-scale data collection efforts, and an increasing emphasis on data publication by journals and funding agencies, a large and ever-increasing amount of ecological data is now publicly available via the internet. Most ecological datasets do not adhere to any agreed-upon standards in format, data structure or method of access. Some may be broken up across multiple files, stored in compressed archives, and violate basic principles of data structure. As a result acquiring and utilizing available datasets can be a time consuming and error prone process. The EcoData Retriever is an extensible software framework which automates the tasks of discovering, downloading, and reformatting ecological data files for storage in a local data file or relational database. The automation of these tasks saves significant time for researchers and substantially reduces the likelihood of errors resulting from manual data manipulation and unfamiliarity with the complexities of individual datasets.}, } @article {pmid23785443, year = {2013}, author = {Chiu, GS and Wu, MA and Lu, L}, title = {Model-based assessment of estuary ecosystem health using the latent health factor index, with application to the richibucto estuary.}, journal = {PloS one}, volume = {8}, number = {6}, pages = {e65697}, pmid = {23785443}, issn = {1932-6203}, mesh = {Algorithms ; *Ecosystem ; Environment ; *Environmental Health ; *Estuaries ; *Models, Statistical ; New Brunswick ; Salinity ; }, abstract = {The ability to quantitatively assess ecological health is of great interest to those tasked with monitoring and conserving ecosystems. For decades, biomonitoring research and policies have relied on multimetric health indices of various forms. Although indices are numbers, many are constructed based on qualitative procedures, thus limiting the quantitative rigor of the practical interpretations of such indices. The statistical modeling approach to construct the latent health factor index (LHFI) was recently developed. With ecological data that otherwise are used to construct conventional multimetric indices, the LHFI framework expresses such data in a rigorous quantitative model, integrating qualitative features of ecosystem health and preconceived ecological relationships among such features. This hierarchical modeling approach allows unified statistical inference of health for observed sites (along with prediction of health for partially observed sites, if desired) and of the relevance of ecological drivers, all accompanied by formal uncertainty statements from a single, integrated analysis. Thus far, the LHFI approach has been demonstrated and validated in a freshwater context. We adapt this approach to modeling estuarine health, and illustrate it on the previously unassessed system in Richibucto in New Brunswick, Canada, where active oyster farming is a potential stressor through its effects on sediment properties. Field data correspond to health metrics that constitute the popular AZTI marine biotic index and the infaunal trophic index, as well as abiotic predictors preconceived to influence biota. Our paper is the first to construct a scientifically sensible model that rigorously identifies the collective explanatory capacity of salinity, distance downstream, channel depth, and silt-clay content-all regarded a priori as qualitatively important abiotic drivers-towards site health in the Richibucto ecosystem. This suggests the potential effectiveness of the LHFI approach for assessing not only freshwater systems but aquatic ecosystems in general.}, } @article {pmid23776535, year = {2013}, author = {Balderas-Martínez, YI and Savageau, M and Salgado, H and Pérez-Rueda, E and Morett, E and Collado-Vides, J}, title = {Transcription factors in Escherichia coli prefer the holo conformation.}, journal = {PloS one}, volume = {8}, number = {6}, pages = {e65723}, pmid = {23776535}, issn = {1932-6203}, support = {R01 GM030054/GM/NIGMS NIH HHS/United States ; R01 GM071962/GM/NIGMS NIH HHS/United States ; 5R01GM071962-08/GM/NIGMS NIH HHS/United States ; R01GM030054-23/GM/NIGMS NIH HHS/United States ; }, mesh = {Databases, Genetic ; Escherichia coli K12/*genetics ; Gene Regulatory Networks/*genetics ; *Protein Conformation ; Regulon/genetics ; Transcription Factors/*chemistry/classification ; }, abstract = {The transcriptional regulatory network of Escherichia coli K-12 is among the best studied gene networks of any living cell. Transcription factors bind to DNA either with their effector bound (holo conformation), or as a free protein (apo conformation) regulating transcription initiation. By using RegulonDB, the functional conformations (holo or apo) of transcription factors, and their mode of regulation (activator, repressor, or dual) were exhaustively analyzed. We report a striking discovery in the architecture of the regulatory network, finding a strong under-representation of the apo conformation (without allosteric metabolite) of transcription factors when binding to their DNA sites to activate transcription. This observation is supported at the level of individual regulatory interactions on promoters, even if we exclude the promoters regulated by global transcription factors, where three-quarters of the known promoters are regulated by a transcription factor in holo conformation. This genome-scale analysis enables us to ask what are the implications of these observations for the physiology and for our understanding of the ecology of E. coli. We discuss these ideas within the framework of the demand theory of gene regulation.}, } @article {pmid23775559, year = {2013}, author = {Claeys, L and Iaccino, F and Janssen, CR and Van Sprang, P and Verdonck, F}, title = {Development and validation of a quantitative structure-activity relationship for chronic narcosis to fish.}, journal = {Environmental toxicology and chemistry}, volume = {32}, number = {10}, pages = {2217-2225}, doi = {10.1002/etc.2301}, pmid = {23775559}, issn = {1552-8618}, mesh = {Animals ; Databases, Factual ; European Union ; Fishes/*physiology ; Multivariate Analysis ; Organic Chemicals/chemistry/*toxicity ; *Quantitative Structure-Activity Relationship ; Regression Analysis ; Stupor/*chemically induced ; Water Pollutants, Chemical/chemistry/*toxicity ; }, abstract = {Vertebrate testing under the European Union's regulation on Registration, Evaluation, Authorisation and Restriction of Chemical substances (REACH) is discouraged, and the use of alternative nontesting approaches such as quantitative structure-activity relationships (QSARs) is encouraged. However, robust QSARs predicting chronic ecotoxicity of organic compounds to fish are not available. The Ecological Structure Activity Relationships (ECOSAR) Class Program is a computerized predictive system that estimates the acute and chronic toxicity of organic compounds for several chemical classes based on their log octanol-water partition coefficient (K(OW)). For those chemical classes for which chronic training data sets are lacking, acute to chronic ratios are used to predict chronic toxicity to aquatic organisms. Although ECOSAR reaches a high score against the Organisation for Economic Co-operation and Development (OECD) principles for QSAR validation, the chronic QSARs in ECOSAR are not fully compliant with OECD criteria in the framework of REACH or CLP (classification, labeling, and packaging) regulation. The objective of the present study was to develop a chronic ecotoxicity QSAR for fish for compounds acting via nonpolar and polar narcosis. These QSARs were built using a database of quality screened toxicity values, considering only chronic exposure durations and relevant end points. After statistical multivariate diagnostic analysis, literature-based, mechanistically relevant descriptors were selected to develop a multivariate regression model. Finally, these QSARs were tested for their acceptance for regulatory purposes and were found to be compliant with the OECD principles for the validation of a QSAR.}, } @article {pmid23773974, year = {2013}, author = {Liang, B and Scammon, DL}, title = {Incidence of online health information search: a useful proxy for public health risk perception.}, journal = {Journal of medical Internet research}, volume = {15}, number = {6}, pages = {e114}, pmid = {23773974}, issn = {1438-8871}, mesh = {Health Education/*methods ; Humans ; *Information Storage and Retrieval ; *Internet ; Mass Media ; Models, Theoretical ; *Public Health ; *Risk Assessment ; }, abstract = {BACKGROUND: Internet users use search engines to look for information online, including health information. Researchers in medical informatics have found a high correlation of the occurrence of certain search queries and the incidence of certain diseases. Consumers' search for information about diseases is related to current health status with regard to a disease and to the social environments that shape the public's attitudes and behaviors.

OBJECTIVE: This study aimed to investigate the extent to which public health risk perception as demonstrated by online information searches related to a health risk can be explained by the incidence of the health risk and social components of a specific population's environment. Using an ecological perspective, we suggest that a population's general concern for a health risk is formed by the incidence of the risk and social (eg, media attention) factors related with the risk.

METHODS: We constructed a dataset that included state-level data from 32 states on the incidence of the flu; a number of social factors, such as media attention to the flu; private resources, such as education and health insurance coverage; public resources, such as hospital beds and primary physicians; and utilization of these resources, including inpatient days and outpatient visits. We then explored whether online information searches about the flu (seasonal and pandemic flu) can be predicted using these variables. We used factor analysis to construct indexes for sets of social factors (private resources, public resources). We then applied panel data multiple regression analysis to exploit both time-series and cross-sectional variation in the data over a 7-year period.

RESULTS: Overall, the results provide evidence that the main effects of independent variables-the incidence of the flu (P<.001); social factors, including media attention (P<.001); private resources, including life quality (P<.001) and health lifestyles (P=.009); and public resources, such as hospital care utilization (P=.008) and public health funds (P=.02)-have significant effects on Web searches for queries related to the flu. After controlling for the number of reported disease cases and Internet access rate by state, we estimate the contribution of social factors to the public health risk perception levels by state (R(2)=23.37%). The interaction effects between flu incidence and social factors for our search terms did not add to the explanatory power of our regression models (R(2)<1%).

CONCLUSIONS: Our study suggests a practical way to measure the public's health risk perception for certain diseases using online information search volume by state. The social environment influences public risk perception regardless of disease incidence. Thus, monitoring the social variables can be very helpful in being ready to respond to the public's behavior in dealing with public health threats.}, } @article {pmid23773094, year = {2013}, author = {Pennell, MW and Harmon, LJ}, title = {An integrative view of phylogenetic comparative methods: connections to population genetics, community ecology, and paleobiology.}, journal = {Annals of the New York Academy of Sciences}, volume = {1289}, number = {}, pages = {90-105}, doi = {10.1111/nyas.12157}, pmid = {23773094}, issn = {1749-6632}, mesh = {Algorithms ; Animals ; Biodiversity ; *Biological Evolution ; Computational Biology/methods ; *Ecology ; Fossils ; Genetics ; Genetics, Population ; Models, Biological ; Models, Statistical ; Paleontology/methods ; *Phylogeny ; Software ; Time Factors ; }, abstract = {Recent innovations in phylogenetic comparative methods (PCMs) have spurred a renaissance of research into the causes and consequences of large-scale patterns of biodiversity. In this paper, we review these advances. We also highlight the potential of comparative methods to integrate across fields and focus on three examples where such integration might be particularly valuable: quantitative genetics, community ecology, and paleobiology. We argue that PCMs will continue to be a key set of tools in evolutionary biology, shedding new light on how evolutionary processes have shaped patterns of biodiversity through deep time.}, } @article {pmid23773093, year = {2013}, author = {Faith, DP}, title = {Biodiversity and evolutionary history: useful extensions of the PD phylogenetic diversity assessment framework.}, journal = {Annals of the New York Academy of Sciences}, volume = {1289}, number = {}, pages = {69-89}, doi = {10.1111/nyas.12186}, pmid = {23773093}, issn = {1749-6632}, mesh = {Algorithms ; Animals ; *Biodiversity ; *Biological Evolution ; Cluster Analysis ; Databases, Factual ; Decision Making ; Ecology ; Ecosystem ; Models, Biological ; Models, Statistical ; *Phylogeny ; Risk ; }, abstract = {Evolutionary biology is a core discipline in biodiversity science. Evolutionary history or phylogeny provides one natural measure of biodiversity through the popular phylogenetic diversity (PD) measure. The evolutionary model underlying PD means that it can be interpreted as quantifying the relative feature diversity of sets of species. Quantifying feature diversity measures possible future uses and benefits or option values. Interpretation of PD as counting-up features is the basis for an emerging broad family of PD calculations, of use to both biodiversity researchers and decision makers. Many of these calculations extend conventional species-level indices to the features level. Useful PD calculations include PD complementarity and endemism, Hill and Valley numbers incorporating abundance, and PD dissimilarities. A flexible analysis framework is provided by expected PD calculations, applied to either probabilities of extinction or presence-absence. Practical extensions include phylogenetic risk analysis and measures of distinctiveness and endemism. These support the integration of phylogenetic diversity into biodiversity conservation and monitoring programs.}, } @article {pmid23770768, year = {2013}, author = {Bhattacharya, D and Price, DC and Chan, CX and Qiu, H and Rose, N and Ball, S and Weber, AP and Arias, MC and Henrissat, B and Coutinho, PM and Krishnan, A and Zäuner, S and Morath, S and Hilliou, F and Egizi, A and Perrineau, MM and Yoon, HS}, title = {Genome of the red alga Porphyridium purpureum.}, journal = {Nature communications}, volume = {4}, number = {}, pages = {1941}, pmid = {23770768}, issn = {2041-1723}, mesh = {Algal Proteins/genetics ; Carbohydrate Metabolism/genetics ; Cytochrome P-450 Enzyme System/metabolism ; Gene Ontology ; Gene Transfer, Horizontal ; Genome/*genetics ; Glycolipids/biosynthesis ; Light-Harvesting Protein Complexes/metabolism ; Meiosis/genetics ; Membrane Transport Proteins/metabolism ; Molecular Weight ; Phylogeny ; Porphyridium/cytology/enzymology/*genetics ; Reproduction/genetics ; Sphingolipids/metabolism ; Starch/biosynthesis ; }, abstract = {The limited knowledge we have about red algal genomes comes from the highly specialized extremophiles, Cyanidiophyceae. Here, we describe the first genome sequence from a mesophilic, unicellular red alga, Porphyridium purpureum. The 8,355 predicted genes in P. purpureum, hundreds of which are likely to be implicated in a history of horizontal gene transfer, reside in a genome of 19.7 Mbp with 235 spliceosomal introns. Analysis of light-harvesting complex proteins reveals a nuclear-encoded phycobiliprotein in the alga. We uncover a complex set of carbohydrate-active enzymes, identify the genes required for the methylerythritol phosphate pathway of isoprenoid biosynthesis, and find evidence of sexual reproduction. Analysis of the compact, function-rich genome of P. purpureum suggests that ancestral lineages of red algae acted as mediators of horizontal gene transfer between prokaryotes and photosynthetic eukaryotes, thereby significantly enriching genomes across the tree of photosynthetic life.}, } @article {pmid23763602, year = {2013}, author = {Primmer, CR and Papakostas, S and Leder, EH and Davis, MJ and Ragan, MA}, title = {Annotated genes and nonannotated genomes: cross-species use of Gene Ontology in ecology and evolution research.}, journal = {Molecular ecology}, volume = {22}, number = {12}, pages = {3216-3241}, doi = {10.1111/mec.12309}, pmid = {23763602}, issn = {1365-294X}, mesh = {Biological Evolution ; Computational Biology ; *Databases, Genetic ; Ecology/methods ; *Gene Ontology ; *Molecular Sequence Annotation ; }, abstract = {Recent advances in molecular technologies have opened up unprecedented opportunities for molecular ecologists to better understand the molecular basis of traits of ecological and evolutionary importance in almost any organism. Nevertheless, reliable and systematic inference of functionally relevant information from these masses of data remains challenging. The aim of this review is to highlight how the Gene Ontology (GO) database can be of use in resolving this challenge. The GO provides a largely species-neutral source of information on the molecular function, biological role and cellular location of tens of thousands of gene products. As it is designed to be species-neutral, the GO is well suited for cross-species use, meaning that, functional annotation derived from model organisms can be transferred to inferred orthologues in newly sequenced species. In other words, the GO can provide gene annotation information for species with nonannotated genomes. In this review, we describe the GO database, how functional information is linked with genes/gene products in model organisms, and how molecular ecologists can utilize this information to annotate their own data. Then, we outline various applications of GO for enhancing the understanding of molecular basis of traits in ecologically relevant species. We also highlight potential pitfalls, provide step-by-step recommendations for conducting a sound study in nonmodel organisms, suggest avenues for future research and outline a strategy for maximizing the benefits of a more ecological and evolutionary genomics-oriented ontology by ensuring its compatibility with the GO.}, } @article {pmid23759696, year = {2013}, author = {Stelfox, HT and Foster, G and Niven, D and Kirkpatrick, AW and Goldsmith, CH}, title = {Capture-mark-recapture to estimate the number of missed articles for systematic reviews in surgery.}, journal = {American journal of surgery}, volume = {206}, number = {3}, pages = {439-440}, doi = {10.1016/j.amjsurg.2012.11.017}, pmid = {23759696}, issn = {1879-1883}, support = {KRS-91770//Canadian Institutes of Health Research/Canada ; }, mesh = {Databases, Bibliographic ; Decision Support Techniques ; *General Surgery ; Humans ; Models, Statistical ; Quality Indicators, Health Care ; Research Design ; *Review Literature as Topic ; *Traumatology ; }, abstract = {BACKGROUND: Systematic reviews are an important knowledge synthesis tool, but with new literature available each day, reviewers must balance identifying all relevant literature against timely synthesis.

METHODS: This study tested capture-mark-recapture (CMR), an ecology-based technique, to estimate the total number of articles in the literature identified in a systematic review of adult trauma care quality indicators.

RESULTS: The systematic review included 40 articles identified from online searches and citation references. The CMR model suggested that 3 (95% confidence interval [CI]: 0 to 6) articles were missed and the database search provided 93% (one-sided 95% CI: ≥83%) of known articles for inclusion in the systematic review. The search order used for identifying the articles was optimal among the 24 that could have been used.

CONCLUSIONS: The CMR technique can be used in systematic reviews in surgery to estimate the closeness to capturing the total body of literature for a specific topic.}, } @article {pmid23757140, year = {2013}, author = {Barret, M and Egan, F and O'Gara, F}, title = {Distribution and diversity of bacterial secretion systems across metagenomic datasets.}, journal = {Environmental microbiology reports}, volume = {5}, number = {1}, pages = {117-126}, doi = {10.1111/j.1758-2229.2012.00394.x}, pmid = {23757140}, issn = {1758-2229}, mesh = {Bacteria/*genetics/metabolism ; Bacterial Proteins/*genetics/metabolism ; *Bacterial Secretion Systems ; *Databases, Genetic ; Metagenomics/*methods ; Microbiota ; Phylogeny ; }, abstract = {Bacteria can manipulate their surrounding environment through the secretion of proteins into other living organisms and into the extracellular milieu. In Gram stain negative bacteria this process is mediated by different types of secretion systems from type I through type VI secretion system (T1SS-T6SS). In this study the prevalence of these secretion systems in 312 publicly available microbiomes derived from a wide range of ecosystems was investigated by a gene-centric approach. Our analysis demonstrates that some secretion systems are over-represented in some specific samples. In addition, some T3SS and T6SS phylogenetic clusters were specifically enriched in particular ecological niches, which could indicate specific bacterial adaptation to these environments.}, } @article {pmid23757040, year = {2013}, author = {Delmont, TO and Simonet, P and Vogel, TM}, title = {Mastering methodological pitfalls for surviving the metagenomic jungle.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {35}, number = {8}, pages = {744-754}, doi = {10.1002/bies.201200155}, pmid = {23757040}, issn = {1521-1878}, mesh = {Biodiversity ; Biotechnology ; Computational Biology ; DNA/analysis ; Ecology ; Ecosystem ; Genes, Bacterial ; Genetic Variation ; Humans ; *Metagenome ; Microbiota/*genetics ; Polymerase Chain Reaction/methods ; Sequence Analysis, DNA ; Soil Microbiology ; }, abstract = {Metagenomics is a culture- and PCR-independent approach that is now widely exploited for directly studying microbial evolution, microbial ecology, and developing biotechnologies. Observations and discoveries are critically dependent on DNA extraction methods, sequencing technologies, and bioinformatics tools. The potential pitfalls need to be understood and, to some degree, mastered if the resulting data are to survive scrutiny. In particular, methodological variations appear to affect results from different ecosystems differently, thus increasing the risk of biological and ecological misinterpretation. Part of the difficulty is derived from the lack of knowledge concerning the true microbial diversity and because no approach can guarantee accessing microorganisms in the same proportion in which they exist in the environment. However, the variation between different approaches (e.g. DNA extraction techniques, sequence annotation systems) can be used to evaluate whether observations are meaningful. These methodological variations can be integrated into the error analysis before comparing microbial communities.}, } @article {pmid23756871, year = {2013}, author = {Ma, B and Gong, J}, title = {A meta-analysis of the publicly available bacterial and archaeal sequence diversity in saline soils.}, journal = {World journal of microbiology & biotechnology}, volume = {29}, number = {12}, pages = {2325-2334}, pmid = {23756871}, issn = {1573-0972}, mesh = {Archaea/*classification/*genetics ; Bacteria/*classification/*genetics ; Biodiversity ; DNA, Archaeal/genetics ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; *Databases, Genetic ; Genetic Variation ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Salinity ; *Soil Microbiology ; }, abstract = {An integrated view of bacterial and archaeal diversity in saline soil habitats is essential for understanding the biological and ecological processes and exploiting potential of microbial resources from such environments. This study examined the collective bacterial and archaeal diversity in saline soils using a meta-analysis approach. All available 16S rDNA sequences recovered from saline soils were retrieved from publicly available databases and subjected to phylogenetic and statistical analyses. A total of 9,043 bacterial and 1,039 archaeal sequences, each longer than 250 bp, were examined. The bacterial sequences were assigned into 5,784 operational taxonomic units (OTUs, based on ≥97 % sequence identity), representing 24 known bacterial phyla, with Proteobacteria (44.9 %), Actinobacteria (12.3 %), Firmicutes (10.4 %), Acidobacteria (9.0 %), Bacteroidetes (6.8 %), and Chloroflexi (5.9 %) being predominant. Lysobacter (12.8 %) was the dominant bacterial genus in saline soils, followed by Sphingomonas (4.5 %), Halomonas (2.5 %), and Gemmatimonas (2.5 %). Archaeal sequences were assigned to 602 OTUs, primarily from the phyla Euryarchaeota (88.7 %) and Crenarchaeota (11.3 %). Halorubrum and Thermofilum were the dominant archaeal genera in saline soils. Rarefaction analysis indicated that less than 25 % of bacterial diversity, and approximately 50 % of archaeal diversity, in saline soil habitats has been sampled. This analysis of the global bacterial and archaeal diversity in saline soil habitats can guide future studies to further examine the microbial diversity of saline soils.}, } @article {pmid23755133, year = {2014}, author = {Gao, J and Sun, L and Yang, X and Liu, JX}, title = {Transcriptomic analysis of cadmium stress response in the heavy metal hyperaccumulator Sedum alfredii Hance.}, journal = {PloS one}, volume = {8}, number = {6}, pages = {e64643}, pmid = {23755133}, issn = {1932-6203}, mesh = {Cadmium/*toxicity ; Ecotype ; *Gene Expression Profiling ; Gene Expression Regulation, Plant/drug effects ; Gene Ontology ; Molecular Sequence Annotation ; Molecular Sequence Data ; Plant Proteins/genetics/metabolism ; Plant Shoots/drug effects/genetics ; Sedum/drug effects/*genetics/*physiology ; Stress, Physiological/drug effects/*genetics ; Transcriptome/drug effects/genetics ; }, abstract = {The Sedum alfredii Hance hyperaccumulating ecotype (HE) has the ability to hyperaccumulate cadmium (Cd), as well as zinc (Zn) and lead (Pb) in above-ground tissues. Although many physiological studies have been conducted with these plants, the molecular mechanisms underlying their hyper-tolerance to heavy metals are largely unknown. Here we report on the generation of 9.4 gigabases of adaptor-trimmed raw sequences and the assembly of 57,162 transcript contigs in S. alfredii Hance (HE) shoots by the combination of Roche 454 and Illumina/Solexa deep sequencing technologies. We also have functionally annotated the transcriptome and analyzed the transcriptome changes upon Cd hyperaccumulation in S. alfredii Hance (HE) shoots. There are 110 contigs and 123 contigs that were up-regulated (Fold Change ≥ 2.0) and down-regulated (Fold Change
A total of 53,193,660 clean paired-end reads was generated from the Illumina HiSeq™ 2000 platform. By assembly with Trinity, we got 173,700 contigs and 77,647 unigenes with mean length of 677 bp and N50 of 1109 bp. Over 55% (43,054) unigenes were successfully annotated based on sequence similarity against public databases as well as Rfam and Pfam database. Local BLAST and Kyoto Encyclopedia of Genes and Genomes (KEGG) maps were used to further exhausting seek for candidate genes related to drought adaptation and a set of 123 putative candidate genes were identified. Moreover, all the C4 photosynthesis genes existed and were active in R. soongorica, which has been regarded as a typical C3 plant.

CONCLUSION/SIGNIFICANCE: The assembled unigenes in present work provide abundant genomic information for the functional assignments in an extreme xerophyte R. soongorica, and will help us exploit the genetic basis of how desert plants adapt to drought environment in the near future.}, } @article {pmid23707726, year = {2013}, author = {Mitchell, J and Arnot, JA and Jolliet, O and Georgopoulos, PG and Isukapalli, S and Dasgupta, S and Pandian, M and Wambaugh, J and Egeghy, P and Cohen Hubal, EA and Vallero, DA}, title = {Comparison of modeling approaches to prioritize chemicals based on estimates of exposure and exposure potential.}, journal = {The Science of the total environment}, volume = {458-460}, number = {}, pages = {555-567}, pmid = {23707726}, issn = {1879-1026}, support = {P30 ES005022/ES/NIEHS NIH HHS/United States ; }, mesh = {*Databases, Chemical ; Environmental Exposure/*statistics & numerical data ; Hazardous Substances/*classification/*toxicity ; *Models, Theoretical ; United States ; United States Environmental Protection Agency ; }, abstract = {While only limited data are available to characterize the potential toxicity of over 8 million commercially available chemical substances, there is even less information available on the exposure and use-scenarios that are required to link potential toxicity to human and ecological health outcomes. Recent improvements and advances such as high throughput data gathering, high performance computational capabilities, and predictive chemical inherency methodology make this an opportune time to develop an exposure-based prioritization approach that can systematically utilize and link the asymmetrical bodies of knowledge for hazard and exposure. In response to the US EPA's need to develop novel approaches and tools for rapidly prioritizing chemicals, a "Challenge" was issued to several exposure model developers to aid the understanding of current systems in a broader sense and to assist the US EPA's effort to develop an approach comparable to other international efforts. A common set of chemicals were prioritized under each current approach. The results are presented herein along with a comparative analysis of the rankings of the chemicals based on metrics of exposure potential or actual exposure estimates. The analysis illustrates the similarities and differences across the domains of information incorporated in each modeling approach. The overall findings indicate a need to reconcile exposures from diffuse, indirect sources (far-field) with exposures from directly, applied chemicals in consumer products or resulting from the presence of a chemical in a microenvironment like a home or vehicle. Additionally, the exposure scenario, including the mode of entry into the environment (i.e. through air, water or sediment) appears to be an important determinant of the level of agreement between modeling approaches.}, } @article {pmid23706558, year = {2013}, author = {Karl, JW and Gillan, JK and Herrick, JE}, title = {Geographic searching for ecological studies: a new frontier.}, journal = {Trends in ecology & evolution}, volume = {28}, number = {7}, pages = {383-384}, doi = {10.1016/j.tree.2013.05.001}, pmid = {23706558}, issn = {1872-8383}, mesh = {Ecology/*methods/trends ; Ecosystem ; Geographic Information Systems ; *Geographic Mapping ; Periodicals as Topic ; Research Design/trends ; }, } @article {pmid23706481, year = {2014}, author = {Gooday, RD and Anthony, SG and Chadwick, DR and Newell-Price, P and Harris, D and Duethmann, D and Fish, R and Collins, AL and Winter, M}, title = {Modelling the cost-effectiveness of mitigation methods for multiple pollutants at farm scale.}, journal = {The Science of the total environment}, volume = {468-469}, number = {}, pages = {1198-1209}, doi = {10.1016/j.scitotenv.2013.04.078}, pmid = {23706481}, issn = {1879-1026}, mesh = {Agriculture/*methods/standards ; *Algorithms ; Cost-Benefit Analysis ; *Decision Support Techniques ; Ecological Parameter Monitoring/*methods ; England ; Environmental Pollution/*prevention & control ; Manure/analysis ; Uncertainty ; Wales ; }, abstract = {Reductions in agricultural pollution are essential for meeting nationally and internationally agreed policy targets for losses to both air and water. Numerous studies quantify the impact of relevant mitigation methods by field experimentation or computer modelling. The majority of these studies have addressed individual methods and frequently also individual pollutants. This paper presents a conceptual model for the synthesis of the evidence base to calculate the impact of multiple methods addressing multiple pollutants in order to identify least cost solutions for multiple policy objectives. The model is implemented as a farm scale decision support tool that quantifies baseline pollutant losses for identifiable sources, areas and pathways and incorporates a genetic algorithm based multi-objective procedure for determining optimal suites of mitigation methods. The tool is generic as baseline losses can be replaced with measured data and the default library of mitigation methods can be edited and expanded. The tool is demonstrated through application to two contrasting farm systems, using survey data on agricultural practices typical of England and Wales. These examples show how the tool could be used to help target the adoption of mitigation options for the control of diffuse pollution from agriculture. The feedback from workshops where Farmscoper was demonstrated is included to highlight the potential role of Farmscoper as part of the farm advisory process.}, } @article {pmid23703936, year = {2013}, author = {Malloy, TF and Sinsheimer, PJ and Blake, A and Linkov, I}, title = {Use of multi-criteria decision analysis in regulatory alternatives analysis: a case study of lead free solder.}, journal = {Integrated environmental assessment and management}, volume = {9}, number = {4}, pages = {652-664}, doi = {10.1002/ieam.1449}, pmid = {23703936}, issn = {1551-3793}, mesh = {*Decision Support Techniques ; Ecotoxicology ; Environmental Pollutants/*analysis ; Humans ; Lead/*analysis ; Risk Assessment ; *Social Control, Formal ; }, abstract = {Regulators are implementing new programs that require manufacturers of products containing certain chemicals of concern to identify, evaluate, and adopt viable, safer alternatives. Such programs raise the difficult question for policymakers and regulated businesses of which alternatives are "viable" and "safer." To address that question, these programs use "alternatives analysis," an emerging methodology that integrates issues of human health and environmental effects with technical feasibility and economic impact. Despite the central role that alternatives analysis plays in these programs, the methodology itself is neither well-developed nor tailored to application in regulatory settings. This study uses the case of Pb-based bar solder and its non-Pb-based alternatives to examine the application of 2 multi-criteria decision analysis (MCDA) methods to alternatives analysis: multi-attribute utility analysis and outranking. The article develops and evaluates an alternatives analysis methodology and supporting decision-analysis software for use in a regulatory context, using weighting of the relevant decision criteria generated from a stakeholder elicitation process. The analysis produced complete rankings of the alternatives, including identification of the relative contribution to the ranking of each of the highest level decision criteria such as human health impacts, technical feasibility, and economic feasibility. It also examined the effect of variation in data conventions, weighting, and decision frameworks on the outcome. The results indicate that MCDA can play a critical role in emerging prevention-based regulatory programs. Multi-criteria decision analysis methods offer a means for transparent, objective, and rigorous analysis of products and processes, providing regulators and stakeholders with a common baseline understanding of the relative performance of alternatives and the trade-offs they present.}, } @article {pmid23701397, year = {2013}, author = {Catchen, J and Hohenlohe, PA and Bassham, S and Amores, A and Cresko, WA}, title = {Stacks: an analysis tool set for population genomics.}, journal = {Molecular ecology}, volume = {22}, number = {11}, pages = {3124-3140}, pmid = {23701397}, issn = {1365-294X}, support = {P30 GM103324/GM/NIGMS NIH HHS/United States ; R24 OD011199/OD/NIH HHS/United States ; R24 GM079486/GM/NIGMS NIH HHS/United States ; P20RR16448/RR/NCRR NIH HHS/United States ; R24 RR032670/RR/NCRR NIH HHS/United States ; 1R24GM079486-01A1/GM/NIGMS NIH HHS/United States ; F32GM095213-01/GM/NIGMS NIH HHS/United States ; P20 RR016448/RR/NCRR NIH HHS/United States ; F32 GM095213/GM/NIGMS NIH HHS/United States ; }, mesh = {Databases, Nucleic Acid ; Electronic Data Processing/*methods ; Genetic Markers ; Genotype ; High-Throughput Nucleotide Sequencing/*methods ; Metagenomics/*methods ; Polymorphism, Single Nucleotide ; Sequence Analysis, DNA ; Software ; }, abstract = {Massively parallel short-read sequencing technologies, coupled with powerful software platforms, are enabling investigators to analyse tens of thousands of genetic markers. This wealth of data is rapidly expanding and allowing biological questions to be addressed with unprecedented scope and precision. The sizes of the data sets are now posing significant data processing and analysis challenges. Here we describe an extension of the Stacks software package to efficiently use genotype-by-sequencing data for studies of populations of organisms. Stacks now produces core population genomic summary statistics and SNP-by-SNP statistical tests. These statistics can be analysed across a reference genome using a smoothed sliding window. Stacks also now provides several output formats for several commonly used downstream analysis packages. The expanded population genomics functions in Stacks will make it a useful tool to harness the newest generation of massively parallel genotyping data for ecological and evolutionary genetics.}, } @article {pmid23701213, year = {2013}, author = {Hudson, LN and Isaac, NJ and Reuman, DC}, title = {The relationship between body mass and field metabolic rate among individual birds and mammals.}, journal = {The Journal of animal ecology}, volume = {82}, number = {5}, pages = {1009-1020}, pmid = {23701213}, issn = {1365-2656}, mesh = {Animals ; Biological Evolution ; Birds/*metabolism ; Body Temperature Regulation ; Body Weight/*physiology ; Classification ; Databases, Factual ; Energy Metabolism/*physiology ; Mammals/*metabolism ; Models, Biological ; }, abstract = {1. The power-law dependence of metabolic rate on body mass has major implications at every level of ecological organization. However, the overwhelming majority of studies examining this relationship have used basal or resting metabolic rates, and/or have used data consisting of species-averaged masses and metabolic rates. Field metabolic rates are more ecologically relevant and are probably more directly subject to natural selection than basal rates. Individual rates might be more important than species-average rates in determining the outcome of ecological interactions, and hence selection. 2. We here provide the first comprehensive database of published field metabolic rates and body masses of individual birds and mammals, containing measurements of 1498 animals of 133 species in 28 orders. We used linear mixed-effects models to answer questions about the body mass scaling of metabolic rate and its taxonomic universality/heterogeneity that have become classic areas of controversy. Our statistical approach allows mean scaling exponents and taxonomic heterogeneity in scaling to be analysed in a unified way while simultaneously accounting for nonindependence in the data due to shared evolutionary history of related species. 3. The mean power-law scaling exponents of metabolic rate vs. body mass relationships were 0.71 [95% confidence intervals (CI) 0.625-0.795] for birds and 0.64 (95% CI 0.564-0.716) for mammals. However, these central tendencies obscured meaningful taxonomic heterogeneity in scaling exponents. The primary taxonomic level at which heterogeneity occurred was the order level. Substantial heterogeneity also occurred at the species level, a fact that cannot be revealed by species-averaged data sets used in prior work. Variability in scaling exponents at both order and species levels was comparable to or exceeded the differences 3/4-2/3 = 1/12 and 0.71-0.64. 4. Results are interpreted in the light of a variety of existing theories. In particular, results are consistent with the heat dissipation theory of Speakman & Król (2010) and provided some support for the metabolic levels boundary hypothesis of Glazier (2010). 5. Our analysis provides the first comprehensive empirical analysis of the scaling relationship between field metabolic rate and body mass in individual birds and mammals. Our data set is a valuable contribution to those interested in theories of the allometry of metabolic rates.}, } @article {pmid23696105, year = {2013}, author = {Connally, NP and Yousey-Hindes, K and Meek, J}, title = {Selection of neighborhood controls for a population-based Lyme disease case-control study by using a commercial marketing database.}, journal = {American journal of epidemiology}, volume = {178}, number = {2}, pages = {276-279}, doi = {10.1093/aje/kws464}, pmid = {23696105}, issn = {1476-6256}, support = {1U01CI000167/CI/NCPDCID CDC HHS/United States ; }, mesh = {*Case-Control Studies ; Connecticut ; Data Collection/*methods ; *Databases, Factual ; Geographic Information Systems ; Humans ; Lyme Disease/*etiology ; *Matched-Pair Analysis ; *Patient Selection ; Risk Factors ; }, abstract = {The selection of controls is an important methodological consideration for case-control studies. Neighborhood-matched control selection is particularly crucial for studies of vector-borne disease, such as Lyme disease, for which risk is intrinsically linked to geographical location. The matching of case-control pairs on neighborhood can help control for variation in ecological risk factors that are tied to geographical location, like vector and host habitat in the peridomestic environment. Random-digit dialing has been used to find neighborhood controls by using the area code and exchange of the case to generate lists of potential control households. An alternative to random-digit dialing is the purchase of residential telephone numbers from a commercial marketing database. This report describes the utility of the InfoUSA.com (InfoGroup, Papillion, Nebraska) commercial marketing database for neighborhood control recruitment in a Lyme disease case-control study in Connecticut during 2005-2007.}, } @article {pmid23695673, year = {2013}, author = {Lanfear, R and Ho, SY and Jonathan Davies, T and Moles, AT and Aarssen, L and Swenson, NG and Warman, L and Zanne, AE and Allen, AP}, title = {Taller plants have lower rates of molecular evolution.}, journal = {Nature communications}, volume = {4}, number = {}, pages = {1879}, pmid = {23695673}, issn = {2041-1723}, mesh = {Amino Acid Substitution/genetics ; Cell Nucleus/genetics ; Chloroplasts/genetics ; Databases, Genetic ; *Evolution, Molecular ; Least-Squares Analysis ; Magnoliopsida/anatomy & histology/genetics ; Phylogeny ; Plants/*anatomy & histology/*genetics ; RNA, Ribosomal/genetics ; Regression Analysis ; Wood/anatomy & histology ; }, abstract = {Rates of molecular evolution have a central role in our understanding of many aspects of species' biology. However, the causes of variation in rates of molecular evolution remain poorly understood, particularly in plants. Here we show that height accounts for about one-fifth of the among-lineage rate variation in the chloroplast and nuclear genomes of plants. This relationship holds across 138 families of flowering plants, and when accounting for variation in species richness, temperature, ultraviolet radiation, latitude and growth form. Our observations can be explained by a link between height and rates of genome copying in plants, and we propose a mechanistic hypothesis to account for this-the 'rate of mitosis' hypothesis. This hypothesis has the potential to explain many disparate observations about rates of molecular evolution across the tree of life. Our results have implications for understanding the evolutionary history and future of plant lineages in a changing world.}, } @article {pmid23693143, year = {2013}, author = {, and Arias, MC and Atteke, C and Augusto, SC and Bailey, J and Bazaga, P and Beheregaray, LB and Benoit, L and Blatrix, R and Born, C and Brito, RM and Chen, HK and Covarrubias, S and de Vega, C and Djiéto-Lordon, C and Dubois, MP and Francisco, FO and García, C and Gonçalves, PH and González, C and Gutiérrez-Rodríguez, C and Hammer, MP and Herrera, CM and Itoh, H and Kamimura, S and Karaoglu, H and Kojima, S and Li, SL and Ling, HJ and Matos-Maraví, PF and McKey, D and Mezui-M'Eko, J and Ornelas, JF and Park, RF and Pozo, MI and Ramula, S and Rigueiro, C and Sandoval-Castillo, J and Santiago, LR and Seino, MM and Song, CB and Takeshima, H and Vasemägi, A and Wellings, CR and Yan, J and Yu-Zhou, D and Zhang, CR and Zhang, TY}, title = {Permanent genetic resources added to Molecular Ecology Resources Database 1 February 2013-31 March 2013.}, journal = {Molecular ecology resources}, volume = {13}, number = {4}, pages = {760-762}, doi = {10.1111/1755-0998.12121}, pmid = {23693143}, issn = {1755-0998}, mesh = {Animals ; Bees/genetics ; Birds/genetics ; Computational Biology/*methods ; Fishes/genetics ; Fungi/genetics ; Genomics/*methods ; *Microsatellite Repeats ; Plants/genetics ; }, abstract = {This article documents the addition of 142 microsatellite marker loci to the Molecular Ecology Resources database. Loci were developed for the following species: Agriophyllum squarrosum, Amazilia cyanocephala, Batillaria attramentaria, Fungal strain CTeY1 (Ascomycota), Gadopsis marmoratus, Juniperus phoenicea subsp. turbinata, Liriomyza sativae, Lupinus polyphyllus, Metschnikowia reukaufii, Puccinia striiformis and Xylocopa grisescens. These loci were cross-tested on the following species: Amazilia beryllina, Amazilia candida, Amazilia rutila, Amazilia tzacatl, Amazilia violiceps, Amazilia yucatanensis, Campylopterus curvipennis, Cynanthus sordidus, Hylocharis leucotis, Juniperus brevifolia, Juniperus cedrus, Juniperus osteosperma, Juniperus oxycedrus, Juniperus thurifera, Liriomyza bryoniae, Liriomyza chinensis, Liriomyza huidobrensis and Liriomyza trifolii.}, } @article {pmid23692675, year = {2013}, author = {Cariveau, DP and Williams, NM and Benjamin, FE and Winfree, R}, title = {Response diversity to land use occurs but does not consistently stabilise ecosystem services provided by native pollinators.}, journal = {Ecology letters}, volume = {16}, number = {7}, pages = {903-911}, doi = {10.1111/ele.12126}, pmid = {23692675}, issn = {1461-0248}, mesh = {Animals ; Bees/*physiology ; *Ecosystem ; Geographic Information Systems ; *Pollination ; }, abstract = {More diverse biological communities may provide ecosystem services that are less variable over space or time. However, the mechanisms underlying this relationship are rarely investigated empirically in real-world ecosystems. Here, we investigate how a potentially important stabilising mechanism, response diversity, the differential response to environmental change among species, stabilises pollination services against land-use change. We measured crop pollination services provided by native bees across land-use gradients in three crop systems. We found that bee species responded differentially to increasing agricultural land cover in all three systems, demonstrating that response diversity occurs. Similarly, we found response diversity in pollination services in two of the systems. However, there was no evidence that response diversity, in general, stabilised ecosystem services. Our results suggest that either response diversity is not the primary stabilising mechanism in our system, or that new measures of response diversity are needed that better capture the stabilising effects it provides.}, } @article {pmid23692056, year = {2013}, author = {Pe'er, G and Matsinos, YG and Johst, K and Franz, KW and Turlure, C and Radchuk, V and Malinowska, AH and Curtis, JM and Naujokaitis-Lewis, I and Wintle, BA and Henle, K}, title = {A protocol for better design, application, and communication of population viability analyses.}, journal = {Conservation biology : the journal of the Society for Conservation Biology}, volume = {27}, number = {4}, pages = {644-656}, doi = {10.1111/cobi.12076}, pmid = {23692056}, issn = {1523-1739}, mesh = {Communication ; Conservation of Natural Resources/*methods/statistics & numerical data ; Databases, Factual ; Ecology/*methods ; Guidelines as Topic ; *Models, Biological ; Population Dynamics ; Population Growth ; Statistics as Topic/*methods ; Uncertainty ; }, abstract = {Population viability analyses (PVAs) contribute to conservation theory, policy, and management. Most PVAs focus on single species within a given landscape and address a specific problem. This specificity often is reflected in the organization of published PVA descriptions. Many lack structure, making them difficult to understand, assess, repeat, or use for drawing generalizations across PVA studies. In an assessment comparing published PVAs and existing guidelines, we found that model selection was rarely justified; important parameters remained neglected or their implementation was described vaguely; limited details were given on parameter ranges, sensitivity analysis, and scenarios; and results were often reported too inconsistently to enable repeatability and comparability. Although many guidelines exist on how to design and implement reliable PVAs and standards exist for documenting and communicating ecological models in general, there is a lack of organized guidelines for designing, applying, and communicating PVAs that account for their diversity of structures and contents. To fill this gap, we integrated published guidelines and recommendations for PVA design and application, protocols for documenting ecological models in general and individual-based models in particular, and our collective experience in developing, applying, and reviewing PVAs. We devised a comprehensive protocol for the design, application, and communication of PVAs (DAC-PVA), which has 3 primary elements. The first defines what a useful PVA is; the second element provides a workflow for the design and application of a useful PVA and highlights important aspects that need to be considered during these processes; and the third element focuses on communication of PVAs to ensure clarity, comprehensiveness, repeatability, and comparability. Thereby, DAC-PVA should strengthen the credibility and relevance of PVAs for policy and management, and improve the capacity to generalize PVA findings across studies.}, } @article {pmid23691993, year = {2013}, author = {Dong, J and Gao, Z and Liu, S and Li, G and Yang, Z and Huang, H and Xu, L}, title = {SLIDE, the protein interacting domain of Imitation Switch remodelers, binds DDT-domain proteins of different subfamilies in chromatin remodeling complexes.}, journal = {Journal of integrative plant biology}, volume = {55}, number = {10}, pages = {928-937}, doi = {10.1111/jipb.12069}, pmid = {23691993}, issn = {1744-7909}, mesh = {Adenosine Triphosphatases/*chemistry/*metabolism ; Amino Acid Sequence ; Arabidopsis/growth & development/metabolism ; Arabidopsis Proteins/*chemistry/*metabolism ; *Chromatin Assembly and Disassembly ; Computational Biology ; Conserved Sequence ; Evolution, Molecular ; Humans ; Molecular Sequence Data ; Phenotype ; Protein Binding ; *Protein Interaction Domains and Motifs ; Sequence Alignment ; Sequence Deletion ; Transcription Factors/*chemistry/*metabolism ; }, abstract = {The Imitation Switch (ISWI) type adenosine triphosphate (ATP)-dependent chromatin remodeling factors are conserved proteins in eukaryotes, and some of them are known to form stable remodeling complexes with members from a family of proteins, termed DDT-domain proteins. Although it is well documented that ISWIs play important roles in different biological processes in many eukaryotic species, the molecular basis for protein interactions in ISWI complexes has not been fully addressed. Here, we report the identification of interaction domains for both ISWI and DDT-domain proteins. By analyzing CHROMATIN REMODELING11 (CHR11) and RINGLET1 (RLT1), an Arabidopsis thaliana ISWI (AtISWI) and AtDDT-domain protein, respectively, we show that the SLIDE domain of CHR11 and the DDT domain together with an adjacent sequence of RLT1 are responsible for their binding. The Arabidopsis genome contains at least 12 genes that encode DDT-domain proteins, which could be grouped into five subfamilies based on the sequence similarity. The SLIDE domain of AtISWI is able to bind members from different AtDDT subfamilies. Moreover, a human ISWI protein SNF2H is capable of binding AtDDT-domain proteins through its SLIDE domain, suggesting that binding to DDT-domain proteins is a conserved biochemical function for the SLIDE domain of ISWIs in eukaryotes.}, } @article {pmid23690980, year = {2013}, author = {Boyd, JD and Brightsmith, DJ}, title = {Error properties of Argos satellite telemetry locations using least squares and Kalman filtering.}, journal = {PloS one}, volume = {8}, number = {5}, pages = {e63051}, pmid = {23690980}, issn = {1932-6203}, mesh = {*Animal Migration ; Animals ; Data Interpretation, Statistical ; Ethology/*methods ; Peru ; *Psittaciformes ; *Research Design ; *Satellite Communications ; Telemetry/*methods ; }, abstract = {Study of animal movements is key for understanding their ecology and facilitating their conservation. The Argos satellite system is a valuable tool for tracking species which move long distances, inhabit remote areas, and are otherwise difficult to track with traditional VHF telemetry and are not suitable for GPS systems. Previous research has raised doubts about the magnitude of position errors quoted by the satellite service provider CLS. In addition, no peer-reviewed publications have evaluated the usefulness of the CLS supplied error ellipses nor the accuracy of the new Kalman filtering (KF) processing method. Using transmitters hung from towers and trees in southeastern Peru, we show the Argos error ellipses generally contain <25% of the true locations and therefore do not adequately describe the true location errors. We also find that KF processing does not significantly increase location accuracy. The errors for both LS and KF processing methods were found to be lognormally distributed, which has important repercussions for error calculation, statistical analysis, and data interpretation. In brief, "good" positions (location codes 3, 2, 1, A) are accurate to about 2 km, while 0 and B locations are accurate to about 5-10 km. However, due to the lognormal distribution of the errors, larger outliers are to be expected in all location codes and need to be accounted for in the user's data processing. We evaluate five different empirical error estimates and find that 68% lognormal error ellipses provided the most useful error estimates. Longitude errors are larger than latitude errors by a factor of 2 to 3, supporting the use of elliptical error ellipses. Numerous studies over the past 15 years have also found fault with the CLS-claimed error estimates yet CLS has failed to correct their misleading information. We hope this will be reversed in the near future.}, } @article {pmid23688576, year = {2014}, author = {Kaye, J and Mattek, N and Dodge, HH and Campbell, I and Hayes, T and Austin, D and Hatt, W and Wild, K and Jimison, H and Pavel, M}, title = {Unobtrusive measurement of daily computer use to detect mild cognitive impairment.}, journal = {Alzheimer's & dementia : the journal of the Alzheimer's Association}, volume = {10}, number = {1}, pages = {10-17}, pmid = {23688576}, issn = {1552-5279}, support = {R01AG024059/AG/NIA NIH HHS/United States ; P30 AG024978/AG/NIA NIH HHS/United States ; R01 AG024059/AG/NIA NIH HHS/United States ; P30 AG008017/AG/NIA NIH HHS/United States ; P30AG024978/AG/NIA NIH HHS/United States ; R01 AG033581/AG/NIA NIH HHS/United States ; }, mesh = {Activities of Daily Living/psychology ; Aged, 80 and over ; Algorithms ; Chi-Square Distribution ; Cognitive Dysfunction/*diagnosis/*physiopathology ; Cohort Studies ; *Computers ; Female ; Humans ; Male ; Mental Status Schedule ; Neuropsychological Tests ; Psychomotor Performance/*physiology ; Surveys and Questionnaires ; }, abstract = {BACKGROUND: Mild disturbances of higher order activities of daily living are present in people diagnosed with mild cognitive impairment (MCI). These deficits may be difficult to detect among those still living independently. Unobtrusive continuous assessment of a complex activity such as home computer use may detect mild functional changes and identify MCI. We sought to determine whether long-term changes in remotely monitored computer use differ in persons with MCI in comparison with cognitively intact volunteers.

METHODS: Participants enrolled in a longitudinal cohort study of unobtrusive in-home technologies to detect cognitive and motor decline in independently living seniors were assessed for computer use (number of days with use, mean daily use, and coefficient of variation of use) measured by remotely monitoring computer session start and end times.

RESULTS: More than 230,000 computer sessions from 113 computer users (mean age, 85 years; 38 with MCI) were acquired during a mean of 36 months. In mixed-effects models, there was no difference in computer use at baseline between MCI and intact participants controlling for age, sex, education, race, and computer experience. However, over time, between MCI and intact participants, there was a significant decrease in number of days with use (P = .01), mean daily use (∼1% greater decrease/month; P = .009), and an increase in day-to-day use variability (P = .002).

CONCLUSIONS: Computer use change can be monitored unobtrusively and indicates individuals with MCI. With 79% of those 55 to 64 years old now online, this may be an ecologically valid and efficient approach to track subtle, clinically meaningful change with aging.}, } @article {pmid23686583, year = {2013}, author = {Sidle, RC and Benson, WH and Carriger, JF and Kamai, T}, title = {Broader perspective on ecosystem sustainability: consequences for decision making.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {110}, number = {23}, pages = {9201-9208}, pmid = {23686583}, issn = {1091-6490}, mesh = {China ; Conservation of Natural Resources/*methods ; *Decision Support Techniques ; *Ecosystem ; Environment ; Landslides ; Louisiana ; *Models, Biological ; Papua New Guinea ; Wetlands ; }, abstract = {Although the concept of ecosystem sustainability has a long-term focus, it is often viewed from a static system perspective. Because most ecosystems are dynamic, we explore sustainability assessments from three additional perspectives: resilient systems; systems where tipping points occur; and systems subject to episodic resetting. Whereas foundations of ecosystem resilience originated in ecology, recent discussions have focused on geophysical attributes, and it is recognized that dynamic system components may not return to their former state following perturbations. Tipping points emerge when chronic changes (typically anthropogenic, but sometimes natural) push ecosystems to thresholds that cause collapse of process and function and may become permanent. Ecosystem resetting occurs when episodic natural disasters breach thresholds with little or no warning, resulting in long-term changes to environmental attributes or ecosystem function. An example of sustainability assessment of ecosystem goods and services along the Gulf Coast (USA) demonstrates the need to include both the resilient and dynamic nature of biogeomorphic components. Mountain road development in northwest Yunnan, China, makes rivers and related habitat vulnerable to tipping points. Ecosystems reset by natural disasters are also presented, emphasizing the need to understand the magnitude frequency and interrelationships among major disturbances, as shown by (i) the 2011 Great East Japan Earthquake and resulting tsunami, including how unsustainable urban development exacerbates geodisaster propagation, and (ii) repeated major earthquakes and associated geomorphic and vegetation disturbances in Papua New Guinea. Although all of these ecosystem perturbations and shifts are individually recognized, they are not embraced in contemporary sustainable decision making.}, } @article {pmid23680301, year = {2013}, author = {Mendes, PS and Ribeiro, Hda C and Mendes, CM}, title = {Temporal trends of overall mortality and hospital morbidity due to diarrheal disease in Brazilian children younger than 5 years from 2000 to 2010.}, journal = {Jornal de pediatria}, volume = {89}, number = {3}, pages = {315-325}, doi = {10.1016/j.jped.2012.10.002}, pmid = {23680301}, issn = {1678-4782}, mesh = {Brazil/epidemiology ; Child, Preschool ; Diarrhea/*mortality ; Hospital Mortality/*trends ; Humans ; Infant ; Length of Stay/economics/*statistics & numerical data ; Residence Characteristics/statistics & numerical data ; Time Factors ; }, abstract = {OBJECTIVE: To verify the temporal trends of the indicators of overall mortality and hospital morbidity due to diarrheal disease in children younger than 1 year and between 1 and 4 years, according to the region of Brazil, between 2000 and 2010.

METHOD: This was an ecological study of temporal series. Data on hospital admission authorization, mean length of stay, and mean value of the authorization were obtained from the Hospital Information System. The number of infant deaths was obtained from the Mortality Information System; information on live births and the general population were obtained from the Information System on Live Births and Demographic Censuses, respectively. These data were available at the website of the informatics department of the Brazilian Unified Health System/Ministry of Health

RESULTS: Mortality due to diarrheal disease in Brazil showed a downwards trend in both age groups. Regarding hospitalization, there was a slight downwards trend in children younger than 1 year and a non-significant upwards trend between 1-4 years, with a shorter hospital stay and lower mean value of hospital stay, regardless of age and region. The North and Northeast had the highest mortality rates and the highest percentage of hospitalizations in children younger than 1 year. The Midwest had the highest mean annual reduction in hospital stay.

CONCLUSION: Currently, the indicators of overall mortality and hospital morbidity due to diarrhea in Brazilian children are generally lower, but decreasing slowly.}, } @article {pmid23677899, year = {2013}, author = {Wang, J and McLenachan, PA and Biggs, PJ and Winder, LH and Schoenfeld, BI and Narayan, VV and Phiri, BJ and Lockhart, PJ}, title = {Environmental bio-monitoring with high-throughput sequencing.}, journal = {Briefings in bioinformatics}, volume = {14}, number = {5}, pages = {575-588}, doi = {10.1093/bib/bbt032}, pmid = {23677899}, issn = {1477-4054}, mesh = {Algorithms ; Animals ; Computational Biology/education ; Databases, Genetic/statistics & numerical data ; Ecosystem ; Environmental Monitoring/*statistics & numerical data ; High-Throughput Nucleotide Sequencing/*statistics & numerical data ; Metagenomics/statistics & numerical data ; Software ; }, abstract = {There is much interest in using high-throughput DNA sequencing methodology to monitor microorganisms, complex plant and animal communities. However, there are experimental and analytical issues to consider before applying a sequencing technology, which was originally developed for genome projects, to ecological projects. Many of these issues have been highlighted by recent microbial studies. Understanding how high-throughput sequencing is best implemented is important for the interpretation of recent results and the success of future applications. Addressing complex biological questions with metagenomics requires the interaction of researchers who bring different skill sets to problem solving. Educators can help by nurturing a collaborative interdisciplinary approach to genome science, which is essential for effective problem solving. Educators are in a position to help students, teachers, the public and policy makers interpret the new knowledge that metagenomics brings. To do this, they need to understand, not only the excitement of the science but also the pitfalls and shortcomings of methodology and research designs. We review these issues and some of the research directions that are helping to move the field forward.}, } @article {pmid23671698, year = {2013}, author = {Ning, J and Wang, M and Li, C and Sun, S}, title = {Transcriptome sequencing and de novo analysis of the copepod Calanus sinicus using 454 GS FLX.}, journal = {PloS one}, volume = {8}, number = {5}, pages = {e63741}, pmid = {23671698}, issn = {1932-6203}, mesh = {Animals ; Base Sequence ; Copepoda/*genetics/metabolism ; Gene Expression Profiling ; Gene Expression Regulation ; Gene Ontology ; High-Throughput Nucleotide Sequencing ; Larva/genetics/metabolism ; Molecular Sequence Annotation ; Polymorphism, Single Nucleotide ; Real-Time Polymerase Chain Reaction ; *Sequence Analysis, DNA ; *Transcriptome ; }, abstract = {BACKGROUND: Despite their species abundance and primary economic importance, genomic information about copepods is still limited. In particular, genomic resources are lacking for the copepod Calanus sinicus, which is a dominant species in the coastal waters of East Asia. In this study, we performed de novo transcriptome sequencing to produce a large number of expressed sequence tags for the copepod C. sinicus.

RESULTS: Copepodid larvae and adults were used as the basic material for transcriptome sequencing. Using 454 pyrosequencing, a total of 1,470,799 reads were obtained, which were assembled into 56,809 high quality expressed sequence tags. Based on their sequence similarity to known proteins, about 14,000 different genes were identified, including members of all major conserved signaling pathways. Transcripts that were putatively involved with growth, lipid metabolism, molting, and diapause were also identified among these genes. Differentially expressed genes related to several processes were found in C. sinicus copepodid larvae and adults. We detected 284,154 single nucleotide polymorphisms (SNPs) that provide a resource for gene function studies.

CONCLUSION: Our data provide the most comprehensive transcriptome resource available for C. sinicus. This resource allowed us to identify genes associated with primary physiological processes and SNPs in coding regions, which facilitated the quantitative analysis of differential gene expression. These data should provide foundation for future genetic and genomic studies of this and related species.}, } @article {pmid23662775, year = {2013}, author = {Stecher, B and Berry, D and Loy, A}, title = {Colonization resistance and microbial ecophysiology: using gnotobiotic mouse models and single-cell technology to explore the intestinal jungle.}, journal = {FEMS microbiology reviews}, volume = {37}, number = {5}, pages = {793-829}, doi = {10.1111/1574-6976.12024}, pmid = {23662775}, issn = {1574-6976}, mesh = {Animals ; Computational Biology ; *Germ-Free Life ; Intestines/*microbiology ; Isotope Labeling ; Mice ; *Microbiota ; *Models, Animal ; Single-Cell Analysis/*methods ; Symbiosis ; }, abstract = {The highly diverse intestinal microbiota forms a structured community engaged in constant communication with itself and its host and is characterized by extensive ecological interactions. A key benefit that the microbiota affords its host is its ability to protect against infections in a process termed colonization resistance (CR), which remains insufficiently understood. In this review, we connect basic concepts of CR with new insights from recent years and highlight key technological advances in the field of microbial ecology. We present a selection of statistical and bioinformatics tools used to generate hypotheses about synergistic and antagonistic interactions in microbial ecosystems from metagenomic datasets. We emphasize the importance of experimentally testing these hypotheses and discuss the value of gnotobiotic mouse models for investigating specific aspects related to microbiota-host-pathogen interactions in a well-defined experimental system. We further introduce new developments in the area of single-cell analysis using fluorescence in situ hybridization in combination with metabolic stable isotope labeling technologies for studying the in vivo activities of complex community members. These approaches promise to yield novel insights into the mechanisms of CR and intestinal ecophysiology in general, and give researchers the means to experimentally test hypotheses in vivo at varying levels of biological and ecological complexity.}, } @article {pmid23658762, year = {2013}, author = {Vermeulen, CJ and Pedersen, KS and Beck, HC and Petersen, J and Gagalova, KK and Loeschcke, V}, title = {Proteomic characterization of inbreeding-related cold sensitivity in Drosophila melanogaster.}, journal = {PloS one}, volume = {8}, number = {5}, pages = {e62680}, pmid = {23658762}, issn = {1932-6203}, mesh = {Animals ; *Cold Temperature ; Cold-Shock Response/genetics ; Drosophila melanogaster/*genetics/*metabolism/physiology ; Female ; Gene Ontology ; Gluconeogenesis/genetics ; Hexoses/metabolism ; *Inbreeding ; Insect Proteins/metabolism ; Male ; Principal Component Analysis ; *Proteomics ; Transcriptome ; }, abstract = {Inbreeding depression is a widespread phenomenon of central importance to agriculture, medicine, conservation biology and evolutionary biology. Although the population genetic principles of inbreeding depression are well understood, we know little about its functional genomic causes. To provide insight into the molecular interplay between intrinsic stress responses, inbreeding depression and temperature tolerance, we performed a proteomic characterization of a well-defined conditional inbreeding effect in a single line of Drosophila melanogaster, which suffers from extreme cold sensitivity and lethality. We identified 48 differentially expressed proteins in a conditional lethal line as compared to two control lines. These proteins were enriched for proteins involved in hexose metabolism, in particular pyruvate metabolism, and many were found to be associated with lipid particles. These processes can be linked to known cold tolerance mechanisms, such as the production of cryoprotectants, membrane remodeling and the build-up of energy reserves. We checked mRNA-expression of seven genes with large differential protein expression. Although protein expression poorly correlated with gene expression, we found a single gene (CG18067) that, after cold shock, was upregulated in the conditional lethal line both at the mRNA and protein level. Expression of CG18067 also increased in control flies after cold shock, and has previously been linked to cold exposure and chill coma recovery time. Many differentially expressed proteins in our study appear to be involved in cold tolerance in non-inbred individuals. This suggest the conditional inbreeding effect to be caused by misregulation of physiological cold tolerance mechanisms.}, } @article {pmid23657177, year = {2014}, author = {Maksimovic, M and Vlajinac, H and Marinkovic, J and Kocev, N and Voskresenski, T and Radak, D}, title = {Health-related quality of life among patients with peripheral arterial disease.}, journal = {Angiology}, volume = {65}, number = {6}, pages = {501-506}, doi = {10.1177/0003319713488640}, pmid = {23657177}, issn = {1940-1574}, mesh = {Aged ; Comorbidity ; Cross-Sectional Studies ; Educational Status ; Female ; Humans ; Male ; Middle Aged ; Peripheral Arterial Disease/*psychology ; *Quality of Life ; Sedentary Behavior ; Severity of Illness Index ; Surveys and Questionnaires ; }, abstract = {We evaluated health-related quality of life (HRQoL) among patients with peripheral arterial disease (PAD) and compared the results with those of the general population. We also evaluated the possible association between some demographic and clinical characteristics of patients with PAD and HRQoL. A cross-sectional study involved 102 consecutive patients with verified PAD referred to the Dedinje Vascular Surgery Clinic in Belgrade. The HRQoL was measured using Medical Outcome Survey Short Form 36 (SF-36). Patients with PAD had significantly lower mean SF-36 scores for physical functioning, role-physical, bodily pain, social functioning, role-emotional, and mental health in comparison with the general population. The HRQoL was significantly more impaired in patients with severe PAD. Patients with PAD had a reduced HRQoL compared with the general population. The impact of PAD on HRQoL was independent of other factors related to both the disease and the HRQoL.}, } @article {pmid23650175, year = {2013}, author = {McArthur, AG and Waglechner, N and Nizam, F and Yan, A and Azad, MA and Baylay, AJ and Bhullar, K and Canova, MJ and De Pascale, G and Ejim, L and Kalan, L and King, AM and Koteva, K and Morar, M and Mulvey, MR and O'Brien, JS and Pawlowski, AC and Piddock, LJ and Spanogiannopoulos, P and Sutherland, AD and Tang, I and Taylor, PL and Thaker, M and Wang, W and Yan, M and Yu, T and Wright, GD}, title = {The comprehensive antibiotic resistance database.}, journal = {Antimicrobial agents and chemotherapy}, volume = {57}, number = {7}, pages = {3348-3357}, pmid = {23650175}, issn = {1098-6596}, support = {//Canadian Institutes of Health Research/Canada ; //Medical Research Council/United Kingdom ; }, mesh = {*Anti-Infective Agents ; Base Sequence ; Computational Biology ; *Databases, Genetic ; Drug Resistance, Microbial/*genetics ; *Genes, Bacterial ; Genome, Bacterial ; Internet ; User-Computer Interface ; }, abstract = {The field of antibiotic drug discovery and the monitoring of new antibiotic resistance elements have yet to fully exploit the power of the genome revolution. Despite the fact that the first genomes sequenced of free living organisms were those of bacteria, there have been few specialized bioinformatic tools developed to mine the growing amount of genomic data associated with pathogens. In particular, there are few tools to study the genetics and genomics of antibiotic resistance and how it impacts bacterial populations, ecology, and the clinic. We have initiated development of such tools in the form of the Comprehensive Antibiotic Research Database (CARD; http://arpcard.mcmaster.ca). The CARD integrates disparate molecular and sequence data, provides a unique organizing principle in the form of the Antibiotic Resistance Ontology (ARO), and can quickly identify putative antibiotic resistance genes in new unannotated genome sequences. This unique platform provides an informatic tool that bridges antibiotic resistance concerns in health care, agriculture, and the environment.}, } @article {pmid23649877, year = {2013}, author = {Zhu, J and Li, W and Yang, W and Qi, L and Han, S}, title = {Identification of microRNAs in Caragana intermedia by high-throughput sequencing and expression analysis of 12 microRNAs and their targets under salt stress.}, journal = {Plant cell reports}, volume = {32}, number = {9}, pages = {1339-1349}, pmid = {23649877}, issn = {1432-203X}, mesh = {Caragana/*genetics/physiology ; Computational Biology ; Conserved Sequence ; Gene Expression Regulation, Plant ; High-Throughput Nucleotide Sequencing ; MicroRNAs/*genetics ; Multigene Family ; Plant Leaves/genetics ; RNA, Plant/genetics ; Reverse Transcriptase Polymerase Chain Reaction ; Sodium Chloride/*pharmacology ; *Stress, Physiological ; Transcriptome ; }, abstract = {142 miRNAs were identified and 38 miRNA targets were predicted, 4 of which were validated, in C. intermedia . The expression of 12 miRNAs in salt-stressed leaves was assessed by qRT-PCR. MicroRNAs (miRNAs) are endogenous small RNAs that play important roles in various biological and metabolic processes in plants. Caragana intermedia is an important ecological and economic tree species prominent in the desert environment of west and northwest China. To date, no investigation into C. intermedia miRNAs has been reported. In this study, high-throughput sequencing of small RNAs and analysis of transcriptome data were performed to identify both conserved and novel miRNAs, and also their target mRNA genes in C. intermedia. Based on sequence similarity and hairpin structure prediction, 132 putative conserved miRNAs (12 of which were confirmed to form hairpin precursors) belonging to 31 known miRNA families were identified. Ten novel miRNAs (including the miRNA* sequences of three novel miRNAs) were also discovered. Furthermore, 36 potential target genes of 17 known miRNA families and 2 potential target genes of 1 novel miRNA were predicted; 4 of these were validated by 5' RACE. The expression of 12 miRNAs was validated in different tissues, and these and five target mRNAs were assessed by qRT-PCR after salt treatment. The expression levels of seven miRNAs (cin-miR157a, cin-miR159a, cin-miR165a, cin-miR167b, cin-miR172b, cin-miR390a and cin-miR396a) were upregulated, while cin-miR398a expression was downregulated after salt treatment. The targets of cin-miR157a, cin-miR165a, cin-miR172b and cin-miR396a were downregulated and showed an approximately negative correlation with their corresponding miRNAs under salt treatment. These results would help further understanding of miRNA regulation in response to abiotic stress in C. intermedia.}, } @article {pmid23649610, year = {2013}, author = {Anastasopoulos, D and Ziavra, N and Pearce, R and Bronstein, AM}, title = {Trunk bradykinesia and foveation delays during whole-body turns in spasmodic torticollis.}, journal = {Journal of neurology}, volume = {260}, number = {8}, pages = {2057-2065}, pmid = {23649610}, issn = {1432-1459}, support = {G0600183/MRC_/Medical Research Council/United Kingdom ; MR/J004685/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Adult ; Aged ; Data Interpretation, Statistical ; Female ; Fixation, Ocular/physiology ; Head Movements/physiology ; Humans ; Hypokinesia/*etiology/physiopathology ; Male ; Middle Aged ; Neurologic Examination ; Orientation/physiology ; Posture ; Psychomotor Performance/physiology ; Thorax/physiology ; Torticollis/*complications/physiopathology ; }, abstract = {We have investigated how the abnormal head posture and motility in spasmodic torticollis interferes with ecological movements such as combined eye-to-foot whole-body reorientations to visual targets. Eight mildly affected patients and 10 controls voluntarily rotated eyes and body in response to illuminated targets of eccentricities up to ± 180°. The experimental protocol allowed separate evaluation of the effects of target location, visibility and predictability on movement parameters. Patients' latencies of eye, head, trunk and foot motion were prolonged but showed a normal modification pattern when target location was predictable. Peak head-on-trunk displacement and velocity were reduced both ipsi- and contralaterally with respect to the direction of torticollis. Surprisingly, peak trunk velocity was also reduced, even more than in previously studied patients with Parkinson's disease. As a consequence, patients made short, hypometric gaze saccades and only exceptionally foveated initially nonvisible targets with a single large gaze shift (4 % of predictable trials as opposed to 30 % in controls). Foveation of distant targets was massively delayed by more than half a second on average. Spontaneous dystonic head movements did not interfere with the execution of voluntary gaze shifts. The results show that neck dystonia does not arise from gaze (head-eye) motor centres but the eye-to-foot turning synergy is seriously compromised. For the first time we identify significant 'secondary' complications of torticollis such as trunk bradykinesia and foveation delays, likely to cause additional disability in patients. Eye movements per se are intact and compensate for the reduced head/trunk performance in an adaptive manner.}, } @article {pmid23645554, year = {2013}, author = {Bhattacharya, D and Pelletreau, KN and Price, DC and Sarver, KE and Rumpho, ME}, title = {Genome analysis of Elysia chlorotica Egg DNA provides no evidence for horizontal gene transfer into the germ line of this Kleptoplastic Mollusc.}, journal = {Molecular biology and evolution}, volume = {30}, number = {8}, pages = {1843-1852}, pmid = {23645554}, issn = {1537-1719}, mesh = {Animals ; Computational Biology/methods ; *DNA ; Databases, Nucleic Acid ; Gastropoda/*genetics/metabolism ; *Gene Transfer, Horizontal ; *Genomics ; Germ Cells/*metabolism ; Transcription, Genetic ; }, abstract = {The sea slug Elysia chlorotica offers a unique opportunity to study the evolution of a novel function (photosynthesis) in a complex multicellular host. Elysia chlorotica harvests plastids (absent of nuclei) from its heterokont algal prey, Vaucheria litorea. The "stolen" plastids are maintained for several months in cells of the digestive tract and are essential for animal development. The basis of long-term maintenance of photosynthesis in this sea slug was thought to be explained by extensive horizontal gene transfer (HGT) from the nucleus of the alga to the animal nucleus, followed by expression of algal genes in the gut to provide essential plastid-destined proteins. Early studies of target genes and proteins supported the HGT hypothesis, but more recent genome-wide data provide conflicting results. Here, we generated significant genome data from the E. chlorotica germ line (egg DNA) and from V. litorea to test the HGT hypothesis. Our comprehensive analyses fail to provide evidence for alga-derived HGT into the germ line of the sea slug. Polymerase chain reaction analyses of genomic DNA and cDNA from different individual E. chlorotica suggest, however, that algal nuclear genes (or gene fragments) are present in the adult slug. We suggest that these nucleic acids may derive from and/or reside in extrachromosomal DNAs that are made available to the animal through contact with the alga. These data resolve a long-standing issue and suggest that HGT is not the primary reason underlying long-term maintenance of photosynthesis in E. chlorotica. Therefore, sea slug photosynthesis is sustained in as yet unexplained ways that do not appear to endanger the animal germ line through the introduction of dozens of foreign genes.}, } @article {pmid23644393, year = {2013}, author = {Factor, R and Awerbuch, T and Levins, R}, title = {Social and land use composition determinants of health: variability in health indicators.}, journal = {Health & place}, volume = {22}, number = {}, pages = {90-97}, doi = {10.1016/j.healthplace.2013.04.001}, pmid = {23644393}, issn = {1873-2054}, mesh = {Adolescent ; Adult ; Databases, Factual ; Female ; *Health Status Indicators ; Humans ; Israel/epidemiology ; Male ; Middle Aged ; *Ownership ; Poverty Areas ; *Social Class ; Young Adult ; }, abstract = {Previous studies have shown that a community's socioeconomic status has a significant impact on its residents' health, and that vulnerability in deprived populations expresses itself as variability in health outcomes. The current study adds to this ecological research approach the notion that underlying community vulnerabilities are also related to the physical environment and population growth of a locality. The paper explores the variability in various health indicators in 252 localities in Israel as a function of the localities' socioeconomic status, population growth, and land use composition measures. The results indicate that a locality's socioeconomic status and its land use composition are both strongly associated with various health outcomes and their variability. These findings are of particular interest in light of the fact that the results were obtained from a country with a universal healthcare system.}, } @article {pmid23637123, year = {2013}, author = {Kober, KM and Pogson, GH}, title = {Genome-wide patterns of codon bias are shaped by natural selection in the purple sea urchin, Strongylocentrotus purpuratus.}, journal = {G3 (Bethesda, Md.)}, volume = {3}, number = {7}, pages = {1069-1083}, pmid = {23637123}, issn = {2160-1836}, mesh = {Animals ; Base Composition/genetics ; Bias ; Codon/*genetics ; Computational Biology ; *Evolution, Molecular ; Genome ; Introns ; Mutation ; *Selection, Genetic ; Strongylocentrotus purpuratus/*genetics ; }, abstract = {Codon usage bias has been documented in a wide diversity of species, but the relative contributions of mutational bias and various forms of natural selection remain unclear. Here, we describe for the first time genome-wide patterns of codon bias at 4623 genes in the purple sea urchin, Strongylocentrotus purpuratus. Preferred codons were identified at 18 amino acids that exclusively used G or C at third positions, which contrasted with the strong AT bias of the genome (overall GC content is 36.9%). The GC content of third positions and coding regions exhibited significant correlations with the magnitude of codon bias. In contrast, the GC content of introns and flanking regions was indistinguishable from the genome-wide background, which suggested a limited contribution of mutational bias to synonymous codon usage. Five distinct clusters of genes were identified that had significantly different synonymous codon usage patterns. A significant correlation was observed between codon bias and mRNA expression supporting translational selection, but this relationship was driven by only one highly biased cluster that represented only 8.6% of all genes. In all five clusters preferred codons were evolutionarily conserved to a similar degree despite differences in their synonymous codon usage distributions and magnitude of codon bias. The third positions of preferred codons in two codon usage groups also paired significantly more often in stems than in loops of mRNA secondary structure predictions, which suggested that codon bias might also affect mRNA stability. Our results suggest that mutational bias has played a minor role in determining codon bias in S. purpuratus and that preferred codon usage may be heterogeneous across different genes and subject to different forms of natural selection.}, } @article {pmid23630581, year = {2013}, author = {McMurdie, PJ and Holmes, S}, title = {phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data.}, journal = {PloS one}, volume = {8}, number = {4}, pages = {e61217}, pmid = {23630581}, issn = {1932-6203}, support = {R01 GM086884/GM/NIGMS NIH HHS/United States ; R01GM086884/GM/NIGMS NIH HHS/United States ; }, mesh = {Data Interpretation, Statistical ; Humans ; *Metagenome ; Multivariate Analysis ; Phylogeny ; Principal Component Analysis ; Sequence Analysis, DNA ; *Software ; }, abstract = {BACKGROUND: the analysis of microbial communities through dna sequencing brings many challenges: the integration of different types of data with methods from ecology, genetics, phylogenetics, multivariate statistics, visualization and testing. With the increased breadth of experimental designs now being pursued, project-specific statistical analyses are often needed, and these analyses are often difficult (or impossible) for peer researchers to independently reproduce. The vast majority of the requisite tools for performing these analyses reproducibly are already implemented in R and its extensions (packages), but with limited support for high throughput microbiome census data.

RESULTS: Here we describe a software project, phyloseq, dedicated to the object-oriented representation and analysis of microbiome census data in R. It supports importing data from a variety of common formats, as well as many analysis techniques. These include calibration, filtering, subsetting, agglomeration, multi-table comparisons, diversity analysis, parallelized Fast UniFrac, ordination methods, and production of publication-quality graphics; all in a manner that is easy to document, share, and modify. We show how to apply functions from other R packages to phyloseq-represented data, illustrating the availability of a large number of open source analysis techniques. We discuss the use of phyloseq with tools for reproducible research, a practice common in other fields but still rare in the analysis of highly parallel microbiome census data. We have made available all of the materials necessary to completely reproduce the analysis and figures included in this article, an example of best practices for reproducible research.

CONCLUSIONS: The phyloseq project for R is a new open-source software package, freely available on the web from both GitHub and Bioconductor.}, } @article {pmid23628960, year = {2013}, author = {Bergsten, J and Nilsson, AN and Ronquist, F}, title = {Bayesian tests of topology hypotheses with an example from diving beetles.}, journal = {Systematic biology}, volume = {62}, number = {5}, pages = {660-673}, pmid = {23628960}, issn = {1076-836X}, mesh = {Animals ; Bayes Theorem ; Classification/*methods ; Coleoptera/*classification ; *Phylogeny ; }, abstract = {We review Bayesian approaches to model testing in general and to the assessment of topological hypotheses in particular. We show that the standard way of setting up Bayes factor tests of the monophyly of a group, or the placement of a sample sequence in a known reference tree, can be misleading. The reason for this is related to the well-known dependency of Bayes factors on model-specific priors. Specifically, when testing tree hypotheses it is important that each hypothesis is associated with an appropriate tree space in the prior. This can be achieved by using appropriately constrained searches or by filtering trees in the posterior sample, but in a more elaborate way than typically implemented. If it is difficult to find the appropriate tree sets to be contrasted, then the posterior model odds may be more informative than the Bayes factor. We illustrate the recommended techniques using an empirical test case addressing the issue of whether two genera of diving beetles (Coleoptera: Dytiscidae), Suphrodytes and Hydroporus, should be synonymized. Our refined Bayes factor tests, in contrast to standard analyses, show that there is strong support for Suphrodytes nesting inside Hydroporus, and the genera are therefore synonymized.}, } @article {pmid23626913, year = {2013}, author = {de Lusignan, S}, title = {Informatics as tool for quality improvement: rapid implementation of guidance for the management of chronic kidney disease in England as an exemplar.}, journal = {Healthcare informatics research}, volume = {19}, number = {1}, pages = {9-15}, pmid = {23626913}, issn = {2093-3681}, abstract = {OBJECTIVES: Chronic kidney disease (CKD) is an important cause of excess cardiovascular mortality and morbidity; as well as being associated with progression to end stage renal disease. This condition was largely unheard of in English primary care prior to the introduction of pay-for-performance targets for management in 2006. A realist review of how informatics has been a mechanism for national implementation of guidance for the improved management of CKD.

METHODS: Realist review of context, the English National Health Service with a drive to implement explicit national quality standards; mechanism, the informatics infrastructure and its alignment with policy objectives; and outcomes are describe at the micro-data and messaging, meso-patient care and quality improvement initiatives, and marco-national policy levels.

RESULTS: At the micro-level computerised medical records can be used to reliably identify people with CKD; though differences in creatinine assays, fluctuation in renal function, and errors in diabetes coding were less well understood. At the meso-level more aggressive management of blood pressure (BP) in individual patients appears to slow or reverse decline in renal function; technology can support case finding and quality improvement at the general practice level. At the macro-level informaticians can help ensure that leverage from informatics is incorporated in policy, and ecological investigations inform if there is any association with improved health outcomes.

CONCLUSIONS: In the right policy context informatics appears to be an enabler of rapid quality improvement. However, a causal relationship or generalisability of these findings has not been demonstrated.}, } @article {pmid23624424, year = {2013}, author = {D'Antonio, A and Monz, C and Newman, P and Lawson, S and Taff, D}, title = {Enhancing the utility of visitor impact assessment in parks and protected areas: a combined social-ecological approach.}, journal = {Journal of environmental management}, volume = {124}, number = {}, pages = {72-81}, doi = {10.1016/j.jenvman.2013.03.036}, pmid = {23624424}, issn = {1095-8630}, mesh = {Colorado ; Conservation of Natural Resources ; *Ecology ; Geographic Information Systems ; Humans ; *Recreation ; }, abstract = {Understanding the ecological consequences of visitor use in parks and how visitors interact with resource conditions is essential for avoiding the impairment of park and protected area resources and visitor experiences. This study combined ecological measures of off-trail resource impacts with social science techniques to understand visitor judgments of ecological impacts and visitors' degree of exposure to impacts. Specifically, this paper reports on a novel integration of techniques that was tested in the Bear Lake Road Corridor of Rocky Mountain National Park, CO, USA in which resource change, as a result of visitor use off designated trails and sites, was assessed and combined with social science and visitor use data. Visual survey techniques were used to understand visitor judgments of ecologically important resource impacts and GPS-tracking of visitor use and behavior allowed for the determination of the degree of visitor's exposure to impaired resources. Results suggest that resource impacts are prevalent and intense throughout the area, but tended to be spatially limited in proximity to attraction sites. Visitors are interacting with resource conditions reported to be unacceptable for significant portions of their hikes. Overall, the work represents an advancement of predictive capabilities when managing park and protected area resources.}, } @article {pmid23622087, year = {2013}, author = {Bennett, CV and Goswami, A}, title = {Statistical support for the hypothesis of developmental constraint in marsupial skull evolution.}, journal = {BMC biology}, volume = {11}, number = {}, pages = {52}, pmid = {23622087}, issn = {1741-7007}, mesh = {Animals ; *Biological Evolution ; Databases as Topic ; Ecosystem ; Extinction, Biological ; Fossils ; Marsupialia/*anatomy & histology/*growth & development ; *Models, Biological ; Principal Component Analysis ; Skull/*anatomy & histology/*growth & development ; *Statistics as Topic ; }, abstract = {BACKGROUND: In contrast to placental neonates, in which all cranial bones are ossified, marsupial young have only the bones of the oral region and the exoccipital ossified at birth, in order to facilitate suckling at an early stage of development. In this study, we investigated whether this heterochronic shift in the timing of cranial ossification constrains cranial disparity in marsupials relative to placentals.

METHODS: We collected three-dimensional (3D) landmark data about the crania of a wide range of extant placentals and marsupials, and from six fossil metatherians (the clade including extant marsupials and their stem relatives), using a laser scanner and a 3D digitizer. Principal components analysis and delta variance tests were used to investigate the distribution and disparity of cranial morphology between different landmark sets (optimizing either number of landmarks or number of taxa) of the whole skull and of individual developmental or functional regions (neurocranium, viscerocranium, oral region) for extant placentals and marsupials. Marsupial and placental data was also compared based on shared ecological aspects including diet, habitat, and time of peak activity.

RESULTS: We found that the extant marsupial taxa investigated here occupy a much smaller area of morphospace than the placental taxa, with a significantly (P<0.01) smaller overall variance. Inclusion of fossil taxa did not significantly increase the variance of metatherian cranial shape. Fossil forms generally plotted close to or within the realm of their extant marsupial relatives. When the disparities of cranial regions were investigated separately, significant differences between placentals and marsupials were seen for the viscerocranial and oral regions, but not for the neurocranial region.

CONCLUSION: These results support the hypothesis of developmental constraint limiting the evolution of the marsupial skull, and further suggest that the marsupial viscerocranium as a whole, rather than just the early-ossifying oral region, is developmentally constrained.}, } @article {pmid23621713, year = {2013}, author = {Wolf, JB}, title = {Principles of transcriptome analysis and gene expression quantification: an RNA-seq tutorial.}, journal = {Molecular ecology resources}, volume = {13}, number = {4}, pages = {559-572}, doi = {10.1111/1755-0998.12109}, pmid = {23621713}, issn = {1755-0998}, mesh = {Computational Biology/*methods ; Gene Expression Profiling/*methods ; High-Throughput Nucleotide Sequencing/*methods ; }, abstract = {Genome-wide analyses and high-throughput screening was long reserved for biomedical applications and genetic model organisms. With the rapid development of massively parallel sequencing nanotechnology (or next-generation sequencing) and simultaneous maturation of bioinformatic tools, this situation has dramatically changed. Genome-wide thinking is forging its way into disciplines like evolutionary biology or molecular ecology that were historically confined to small-scale genetic approaches. Accessibility to genome-scale information is transforming these fields, as it allows us to answer long-standing questions like the genetic basis of local adaptation and speciation or the evolution of gene expression profiles that until recently were out of reach. Many in the eco-evolutionary sciences will be working with large-scale genomic data sets, and a basic understanding of the concepts and underlying methods is necessary to judge the work of others. Here, I briefly introduce next-generation sequencing and then focus on transcriptome shotgun sequencing (RNA-seq). This article gives a broad overview and provides practical guidance for the many steps involved in a typical RNA-seq work flow from sampling, to RNA extraction, library preparation and data analysis. I focus on principles, present useful tools where appropriate and point out where caution is needed or progress to be expected. This tutorial is mostly targeted at beginners, but also contains potentially useful reflections for the more experienced.}, } @article {pmid23620068, year = {2013}, author = {Lunde, KB and Cover, MR and Mazor, RD and Sommers, CA and Resh, VH}, title = {Identifying reference conditions and quantifying biological variability within benthic macroinvertebrate communities in perennial and non-perennial northern California streams.}, journal = {Environmental management}, volume = {51}, number = {6}, pages = {1262-1273}, pmid = {23620068}, issn = {1432-1009}, mesh = {Animals ; *Biodiversity ; California ; Geographic Information Systems ; Invertebrates/*classification ; *Rivers ; }, abstract = {Identification of minimally disturbed reference sites is a critical step in developing precise and informative ecological indicators. We tested procedures to select reference sites, and quantified natural variation (inter-site and -annual variability) among reference conditions using a macroinvertebrate data set collected from 429 mediterranean-climate stream reaches in the San Francisco Bay Area, California (USA). We determined that a landscape GIS-based stressor screen followed by a local field-based stressor screen effectively identified least-disturbed reference sites that, based on NMS ordination results, supported different biological communities than sites identified with only landscape (GIS) or local (field) stressors. An examination of least-disturbed reference sites indicated that inter-site variability was strongly associated with stream hydrology (i.e., perennial vs. non-perennial flow) and annual precipitation, which highlights the need to control for such variation when developing biological indicators through natural gradient modeling or using unique biological indicators for both non-perennial and perennial streams. Metrics were more variable among non-perennial streams, indicating that additional modeling may be needed to develop precise biological indicators for non-perennial streams. Among 192 sites sampled two to six times over the 8-year study period, the biological community showed moderate inter-annual variability, with the 100 point index of biotic integrity scores varying from 0 to 51 points (mean = 11.5). Variance components analysis indicated that inter-annual variability explained only a fraction (5-18 %) of the total variation when compared against site-level variation; thus efforts to understand causes of natural variation between sites will produce more precise and accurate biological indicators.}, } @article {pmid23617921, year = {2013}, author = {Naya, DE and Spangenberg, L and Naya, H and Bozinovic, F}, title = {How does evolutionary variation in Basal metabolic rates arise? A statistical assessment and a mechanistic model.}, journal = {Evolution; international journal of organic evolution}, volume = {67}, number = {5}, pages = {1463-1476}, doi = {10.1111/evo.12042}, pmid = {23617921}, issn = {1558-5646}, mesh = {Animals ; Basal Metabolism/*genetics ; Climate ; Data Interpretation, Statistical ; Environment ; *Evolution, Molecular ; *Genetic Variation ; Models, Genetic ; Rodentia/genetics/metabolism ; }, abstract = {Metabolic rates are related to the pace of life. Hence, research into their variability at global scales is of vital importance for several contemporary theories in physiology, ecology, and evolution. Here we evaluated the effect of latitude, climate, primary productivity, habitat aridity, and species trophic habits, on mass-independent basal metabolic rates (BMRs) for 195 rodent species. The aims of this article were twofold. First, we evaluated the predictive power of different statistical models (via a model selection approach), using a dimensional reduction technique on the exogenous factor matrix to achieve a clear interpretation of the selected models. Second, we evaluated three specific predictions derived from a recently proposed hypothesis, herein called the "obligatory heat" model (OHM), for the evolution of BMR. Obtained results indicate that mean/minimum environmental temperature, rainfall/primary productivity and, finally, species trophic habits are, in this order, the major determinants of mass-independent BMR. Concerning the mechanistic causes behind this variation, obtained data agree with the predictions of the OHM: (1) mean annual environmental temperature was the best single predictor of residual variation in BMR, (2) herbivorous species have greater mass-independent metabolic rates, and tend to be present at high-latitude cold environments, than species in other trophic categories.}, } @article {pmid23617918, year = {2013}, author = {Schlicht, E and Kempenaers, B}, title = {Effects of social and extra-pair mating on sexual selection in blue tits (cyanistes caeruleus).}, journal = {Evolution; international journal of organic evolution}, volume = {67}, number = {5}, pages = {1420-1434}, doi = {10.1111/evo.12073}, pmid = {23617918}, issn = {1558-5646}, mesh = {Animals ; Data Interpretation, Statistical ; *Mating Preference, Animal ; Passeriformes/*genetics ; Population/genetics ; }, abstract = {The contribution of extra-pair paternity (EPP) to sexual selection has received considerable attention, particularly in socially monogamous species. However, the importance of EPP remains difficult to assess quantitatively, especially when many extra-pair young have unknown sires. Here, we combine measurements of the opportunity for selection (I), the opportunity for sexual selection (IS), and the strength of selection on mating success (Bateman gradient, βSS) with a novel simulation of random mating tailored to the specific mating system of the blue tit (Cyanistes caeruleus). In a population where social polygyny and EPP are common, the opportunity for sexual selection was significantly stronger and Bateman gradients significantly steeper for resident males than for females. In general, success with the social mate(s) contributed most to variation in male reproductive success. Effects of EPP were small, but significantly higher than expected under random mating. We used sibship analysis to estimate the number of unknown sires in our population. Under the assumption that the unknown sires are nonbreeding males, EPP reduced the variance in and the strength of selection on mating success, a possibility that hitherto has not been considered.}, } @article {pmid23617735, year = {2013}, author = {Schulz, B and Eckstein, RL and Durka, W}, title = {Scoring and analysis of methylation-sensitive amplification polymorphisms for epigenetic population studies.}, journal = {Molecular ecology resources}, volume = {13}, number = {4}, pages = {642-653}, doi = {10.1111/1755-0998.12100}, pmid = {23617735}, issn = {1755-0998}, mesh = {*DNA Methylation ; *Data Interpretation, Statistical ; *Epigenesis, Genetic ; Nucleic Acid Amplification Techniques/*methods ; Viola/*genetics/metabolism ; }, abstract = {DNA methylation is an important, heritable epigenetic modification in most eukaryotic organisms that is connected with numerous biological processes. To study the impact of natural epigenetic variation in an ecological or evolutionary context, epigenetic studies are increasingly using methylation-sensitive amplification polymorphism (MSAP) for surveys at the population or species level. However, no consensus exists on how to interpret and score the multistate information obtained from the MSAP banding patterns. Here, we review the previously used scoring approaches for population epigenetic studies and develop new alternatives. To assess effects of the different approaches on parameters of epigenetic diversity and differentiation, we applied eight scoring schemes to a case study of three populations of the plant species Viola elatior. For a total number of 168 detected polymorphic MSAP fragments, the number of ultimately scored polymorphic epiloci ranged between 78 and 286 depending on the particular scoring scheme. Both, estimates of epigenetic diversity and differentiation varied strongly between scoring approaches. However, linear regression and PCoA revealed qualitatively similar patterns, suggesting that the scoring approaches are largely consistent. For single-locus analyses of MSAP data, for example the search for loci under selection, we advocate a new scoring approach that separately takes into account different methylation types and thus seems appropriate for drawing more detailed conclusions in ecological or evolutionary contexts. An R script (MSAP_score.r) for scoring and basic data analysis is provided.}, } @article {pmid23615313, year = {2013}, author = {DeWoody, JA and Abts, KC and Fahey, AL and Ji, Y and Kimble, SJ and Marra, NJ and Wijayawardena, BK and Willoughby, JR}, title = {Of contigs and quagmires: next-generation sequencing pitfalls associated with transcriptomic studies.}, journal = {Molecular ecology resources}, volume = {13}, number = {4}, pages = {551-558}, doi = {10.1111/1755-0998.12107}, pmid = {23615313}, issn = {1755-0998}, mesh = {Computational Biology/*methods ; *DNA Contamination ; High-Throughput Nucleotide Sequencing/*methods/standards ; *Transcriptome ; }, abstract = {Molecular ecologists have good reasons to be excited about the newest DNA/RNA sequencing technologies. However, this exuberance should be tempered with a hefty dose of reality: new sequencing technologies come with significant new challenges. Herein, we offer a brief overview of some practical problems encountered during transcriptomics studies conducted in our laboratory, and of nontrivial issues that prospective practitioners should consider. These include template contamination (e.g. from xenobiotics) and the cutting-room floor problem, whereby most of the data are often unassembled, unannotated and unused. We also highlight computational requirements, including hardware, personnel time and associated skill sets. We are very optimistic about the future of molecular ecology, but we hope this cautionary overview will help neophytes better recognize some key challenges associated with new technologies.}, } @article {pmid23613273, year = {2013}, author = {Zerbe, P and Hamberger, B and Yuen, MM and Chiang, A and Sandhu, HK and Madilao, LL and Nguyen, A and Hamberger, B and Bach, SS and Bohlmann, J}, title = {Gene discovery of modular diterpene metabolism in nonmodel systems.}, journal = {Plant physiology}, volume = {162}, number = {2}, pages = {1073-1091}, pmid = {23613273}, issn = {1532-2548}, mesh = {Cloning, Molecular ; Cytochrome P-450 Enzyme System/*genetics ; Data Mining ; Databases, Genetic ; Diterpenes/*metabolism ; Evolution, Molecular ; Molecular Biology/*methods ; Molecular Sequence Data ; Phylogeny ; Plant Proteins/genetics/metabolism ; Plants/*genetics/*metabolism ; Transcriptome ; }, abstract = {Plants produce over 10,000 different diterpenes of specialized (secondary) metabolism, and fewer diterpenes of general (primary) metabolism. Specialized diterpenes may have functions in ecological interactions of plants with other organisms and also benefit humanity as pharmaceuticals, fragrances, resins, and other industrial bioproducts. Examples of high-value diterpenes are taxol and forskolin pharmaceuticals or ambroxide fragrances. Yields and purity of diterpenes obtained from natural sources or by chemical synthesis are often insufficient for large-volume or high-end applications. Improvement of agricultural or biotechnological diterpene production requires knowledge of biosynthetic genes and enzymes. However, specialized diterpene pathways are extremely diverse across the plant kingdom, and most specialized diterpenes are taxonomically restricted to a few plant species, genera, or families. Consequently, there is no single reference system to guide gene discovery and rapid annotation of specialized diterpene pathways. Functional diversification of genes and plasticity of enzyme functions of these pathways further complicate correct annotation. To address this challenge, we used a set of 10 different plant species to develop a general strategy for diterpene gene discovery in nonmodel systems. The approach combines metabolite-guided transcriptome resources, custom diterpene synthase (diTPS) and cytochrome P450 reference gene databases, phylogenies, and, as shown for select diTPSs, single and coupled enzyme assays using microbial and plant expression systems. In the 10 species, we identified 46 new diTPS candidates and over 400 putatively terpenoid-related P450s in a resource of nearly 1 million predicted transcripts of diterpene-accumulating tissues. Phylogenetic patterns of lineage-specific blooms of genes guided functional characterization.}, } @article {pmid23610389, year = {2013}, author = {Gómez, JM and Nunn, CL and Verdú, M}, title = {Centrality in primate-parasite networks reveals the potential for the transmission of emerging infectious diseases to humans.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {110}, number = {19}, pages = {7738-7741}, pmid = {23610389}, issn = {1091-6490}, mesh = {Algorithms ; Animals ; Biodiversity ; Communicable Disease Control ; Communicable Diseases, Emerging/*epidemiology/genetics ; Databases, Factual ; Geography ; Humans ; Models, Biological ; Multivariate Analysis ; Parasites ; Parasitic Diseases, Animal/*transmission ; Population Density ; Primates/genetics/*parasitology ; }, abstract = {Most emerging infectious diseases (EIDs) in humans have arisen from animals. Identifying high-risk hosts is therefore vital for the control and surveillance of these diseases. Viewing hosts as connected through the parasites they share, we use network tools to investigate predictors of parasitism and sources of future EIDs. We generated host-parasite networks that link hosts when they share a parasite, using nonhuman primates as a model system because--owing to their phylogenetic proximity and ecological overlap with humans--they are an important source of EIDs to humans. We then tested whether centrality in the network of host species--a measurement of the importance of a given node (i.e., host species) in the network--is associated with that host serving as a potential EID source. We found that centrality covaries with key predictors of parasitism, such as population density and geographic range size. Importantly, we also found that primate species having higher values of centrality in the primate-parasite network harbored more parasites identified as EIDs in humans and had parasite communities more similar to those found in humans. These relationships were robust to the use of different centrality metrics and to multiple ways of controlling for variation in how well each species has been studied (i.e., sampling effort). Centrality may therefore estimate the role of a host as a source of EIDs to humans in other multispecific host-parasite networks.}, } @article {pmid23608176, year = {2013}, author = {Garbolino, E and De Ruffray, P and Brisse, H and Grandjouan, G}, title = {[Probable flora: an expression mean of ecological gradients in France].}, journal = {Comptes rendus biologies}, volume = {336}, number = {2}, pages = {73-81}, doi = {10.1016/j.crvi.2013.02.003}, pmid = {23608176}, issn = {1768-3238}, mesh = {Algorithms ; Atlantic Ocean ; Classification ; Data Collection ; Databases, Factual ; *Environment ; France ; Mediterranean Region ; *Plants/classification/genetics ; Soil/chemistry ; }, abstract = {The application of the criterion of fidelity of plants to plants over four millions botanical observations in France is considered to characterize the ecology of 215,000 phytosociological surveys. Among those discriminant plants, some are missing of the surveys, but they can have a certain probability of occurrence: these plants are called "probable plants" and they represent the "probable flora" of a territory. The study of their geographical distribution shows ecological gradients of flora across France in a better way than only considering the botanical observations. In fact, this method mitigates the discontinuities of taxa observations whose absence may be due to historical and/or anthropogenic factors.}, } @article {pmid23608174, year = {2013}, author = {Budrienė, A and Budrys, E and Nevronytė, Ž}, title = {Sexual size dimorphism in the ontogeny of the solitary predatory wasp Symmorphus allobrogus (Hymenoptera: Vespidae).}, journal = {Comptes rendus biologies}, volume = {336}, number = {2}, pages = {57-64}, doi = {10.1016/j.crvi.2013.03.001}, pmid = {23608174}, issn = {1768-3238}, mesh = {Analysis of Variance ; Animals ; Biological Evolution ; Body Size/*physiology ; Body Weight/physiology ; Data Interpretation, Statistical ; Eating ; Female ; Growth/physiology ; Larva/growth & development/physiology ; Male ; Ovum/ultrastructure ; Sex Characteristics ; Wasps/*physiology ; }, abstract = {Sex-specific patterns of individual growth, resulting in sexual size dimorphism (SSD), are a little studied aspect of the ontogeny related to the evolutionary history and affected by the ecology of a species. We used empirical data on the development of the predatory wasp Symmorphus allobrogus (Hymenoptera, Vespidae) to test the hypotheses that sexual differences of growth resulting in the female-biased SSD embrace the difference in (1) the egg size and the starting size of larva, (2) the larval development duration, and (3) the larval growth rate. We found that eggs developing into males and females have significant differences in size. There was no significant difference between the sexes in the duration of larval development. The relative growth rate and the food assimilation efficiency of female larvae were significantly higher than compared to those of male larvae. Thus, the SSD of S. allobrogus is mediated mainly by sexual differences in egg size and larval growth rate.}, } @article {pmid23605638, year = {2013}, author = {Lankapalli, AR and Kannabiran, K}, title = {Interaction of marine Streptomyces compounds with selected cancer drug target proteins by in silico molecular docking studies.}, journal = {Interdisciplinary sciences, computational life sciences}, volume = {5}, number = {1}, pages = {37-44}, doi = {10.1007/s12539-013-0146-0}, pmid = {23605638}, issn = {1867-1462}, mesh = {Alkaloids/chemistry/metabolism ; Anthraquinones/chemistry/metabolism ; Antineoplastic Agents/analysis/*metabolism ; Benzopyrenes/metabolism ; Computational Biology ; Cyclin-Dependent Kinase 4/*metabolism ; Humans ; Indoles/metabolism ; Lactones/metabolism ; Marine Biology ; Models, Molecular ; Molecular Docking Simulation/*methods ; Netropsin/analogs & derivatives/metabolism ; Oxazoles/metabolism ; Pyridines/chemistry/metabolism ; Pyridones/metabolism ; Receptor, ErbB-2/*metabolism ; Streptomyces/*chemistry ; Sulfur Compounds/chemistry/metabolism ; }, abstract = {The criteria currently followed for selecting antitumor compounds include agents that can target apoptosis inhibitor proteins and cancer cell markers. In silico studies are often used to identify suitable antitumor compounds for the cancer targets. The aim of the present study is to evaluate the interactions of some antitumor compounds reported from marine Streptomyces with cancer target proteins. Nine compounds were selected from marine Streptomyces based on previous reports and evaluated for their interactions with cancer target proteins by in silico molecular docking approach. Interactions of the selected ligand with target proteins were studied by PatchDock bioinformatics docking tool. Among the compounds tested marmycin A was interacted very effectively with human epidermal growth factor receptor 2 (HER2) and showed a least binding energy of -472.92 kcal/mol. The compound altemicidin showed a least binding energy of -415.66 kcal/mol with cyclin dependent kinase 4 (CDK4). The ligands resistoflavine and resistomycin also interacted with HER2 and showed the binding energy of -402.10 kcal/mol and -377.78 kcal/mol respectively. Other ligands proximycin A, chandrananimycin C, echinosporin, streptochlorin and streptokordin also showed the binding energy of -341.11 kcal/mol, -313.31 kcal/mol, -305.64 kcal/mol, -291.91 kcal/mol and 222.34 kcal/mol respectively with CDK4 protein. These results of our study suggest that HER2 and CDK4 are better cancer drug targets for therapy.}, } @article {pmid23603020, year = {2013}, author = {Zheng, M and Tian, J and Yang, G and Zheng, L and Chen, G and Chen, J and Wang, B}, title = {Transcriptome sequencing, annotation and expression analysis of Nannochloropsis sp. at different growth phases.}, journal = {Gene}, volume = {523}, number = {2}, pages = {117-121}, doi = {10.1016/j.gene.2013.04.005}, pmid = {23603020}, issn = {1879-0038}, mesh = {Computational Biology/methods ; *Gene Expression Profiling ; *Gene Expression Regulation ; Metabolic Networks and Pathways ; Microalgae/*genetics/growth & development/metabolism ; *Molecular Sequence Annotation ; Oligonucleotide Array Sequence Analysis ; Stramenopiles/*genetics/growth & development/metabolism ; Transcription Factors/genetics/metabolism ; *Transcriptome ; }, abstract = {Nannochloropsis sp. is an oil-rich microalga. The lipid content of cells at stationary growth phase was much higher than that of cells at logarithm growth phase, but very little information focusing on the abundances of gene transcripts concerning lipid accumulation is available. In present study, the second generation Illumina sequencing was used to investigate the genes and pathways of Nannochloropsis sp. in order to identify those involved in lipid metabolism. In total, 29,203 unigenes were obtained from logarithm and stationary growth phases. The transcripts of some unigenes were differentially abundant at two growth phases. Among the unigenes obtained, about 195 unigenes were involved in lipid metabolism and 315 unigenes were putatively transcription factors. These genes are a very useful resource for the future studies of Nannochloropsis sp.}, } @article {pmid23600258, year = {2013}, author = {Greenacre, M}, title = {The contributions of rare objects in correspondence analysis.}, journal = {Ecology}, volume = {94}, number = {1}, pages = {241-249}, doi = {10.1890/11-1730.1}, pmid = {23600258}, issn = {0012-9658}, mesh = {Animals ; *Data Interpretation, Statistical ; Ecology/methods ; *Ecosystem ; Models, Biological ; }, abstract = {Correspondence analysis, when used to understand relationships in a table of counts (for example, abundance data in ecology), has been criticized as being too sensitive to objects (for example, species) that occur with very low frequency or in very few samples. Here I show that this criticism is generally unfounded. This is demonstrated in several data sets by calculating the actual contributions of rare objects to the results of correspondence analysis and canonical correspondence analysis, both to the determination of the ordination axes and to the chi-square distance. It is a fact that rare objects are often positioned as outliers in correspondence analysis ordinations, which gives the impression that they are highly influential, but their low weight offsets their distant positions and reduces their effect on the results. An alternative scaling of the correspondence analysis solution, the contribution biplot, is proposed as a way of displaying the results in order to avoid the problem of outlying and low contributing rare objects. In this new scaling of the biplot (or triplot in canonical correspondence analysis), species points have coordinates that are directly related to their contributions to the solution.}, } @article {pmid23595644, year = {2013}, author = {Gordon, AD and Johnson, SE and Louis, EE}, title = {Females are the ecological sex: sex-specific body mass ecogeography in wild sifaka populations (Propithecus spp.).}, journal = {American journal of physical anthropology}, volume = {151}, number = {1}, pages = {77-87}, doi = {10.1002/ajpa.22259}, pmid = {23595644}, issn = {1096-8644}, mesh = {Animals ; Anthropology, Physical ; Body Size/*physiology ; Cluster Analysis ; *Environment ; Female ; Geographic Information Systems ; Madagascar ; Male ; Models, Biological ; Phylogeny ; Sex Factors ; Strepsirhini/*anatomy & histology/*physiology ; }, abstract = {Previous work in primates has shown that body size often covaries with ecological parameters related to resource or energy availability in the environment. This relationship may differ for males and females as access to resources has greater importance for reproductive success in females. We test the hypotheses that (1) female body mass may be more tightly constrained than male body mass by ecological variables, and (2) female body mass may respond more strongly than male body mass to changes in ecological variables (i.e., population-specific female mass may vary more across an ecological gradient than male mass). Specifically, we investigate the relationship between climatic variables and sex-specific body mass in Propithecus, a genus in which species-specific body mass has already been demonstrated to covary significantly with climatic variables. Data from 733 wild sifakas are used to identify sex-specific body mass for 27 populations representing all nine described sifaka species, and climatic data for each population are derived from the WorldClim database. We use phylogenetic generalized least squares models to demonstrate that body mass in both sexes is significantly correlated with annual rainfall and number of dry months. Furthermore, coefficients of determination are always higher for female models, and coefficients for each climatic variable are higher for females in all significant models. These results support the two hypotheses tested, indicating that ecological forces can have a greater impact on female mass than on male mass in primates.}, } @article {pmid23594555, year = {2013}, author = {Spiegel, O and Getz, WM and Nathan, R}, title = {Factors influencing foraging search efficiency: why do scarce lappet-faced vultures outperform ubiquitous white-backed vultures?.}, journal = {The American naturalist}, volume = {181}, number = {5}, pages = {E102-15}, doi = {10.1086/670009}, pmid = {23594555}, issn = {1537-5323}, support = {GM083863/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Falconiformes/*physiology ; *Feeding Behavior ; Geographic Information Systems ; Models, Biological ; Species Specificity ; }, abstract = {The search phase is a critical component of foraging behavior, affecting interspecific competition and community dynamics. Nevertheless, factors determining interspecific variation in search efficiency are still poorly understood. We studied differences in search efficiency between the lappet-faced vulture (Torgos tracheliotus; LFV) and the white-backed vulture (Gyps africanus; WBV) foraging on spatiotemporally unpredictable carcasses in Etosha National Park, Namibia. We used experimental food supply and high-resolution GPS tracking of free-ranging vultures to quantify search efficiency and elucidate the factors underlying the observed interspecific differences using a biased correlated random walk simulation model bootstrapped with the GPS tracking data. We found that LFV's search efficiency was higher than WBV's in both first-to-find, first-to-land, and per-individual-finding rate measures. Modifying species-specific traits in the simulation model allows us to assess the relative role of each factor in LFV's higher efficiency. Interspecific differences in morphology (through the effect on perceptual range and motion ability) and searchers' spatial dispersion (due to different roost arrangements) are in correspondence with the empirically observed advantage of LFV over WBV searchers, whereas differences in other aspects of the movement patterns appear to play a minor role. Our results provide mechanistic explanations for interspecific variation in search efficiency for species using similar resources and foraging modes.}, } @article {pmid23592960, year = {2013}, author = {Lonardi, S and Duma, D and Alpert, M and Cordero, F and Beccuti, M and Bhat, PR and Wu, Y and Ciardo, G and Alsaihati, B and Ma, Y and Wanamaker, S and Resnik, J and Bozdag, S and Luo, MC and Close, TJ}, title = {Combinatorial pooling enables selective sequencing of the barley gene space.}, journal = {PLoS computational biology}, volume = {9}, number = {4}, pages = {e1003010}, pmid = {23592960}, issn = {1553-7358}, support = {//Wellcome Trust/United Kingdom ; }, mesh = {Chromosomes, Artificial, Bacterial ; Cloning, Molecular ; Computational Biology/methods ; Computer Simulation ; Contig Mapping/*methods ; Genes, Plant ; Genetic Markers/genetics ; Genomic Library ; Genomics ; Hordeum/*genetics ; Models, Genetic ; Oryza/genetics ; Physical Chromosome Mapping ; *Sequence Analysis, DNA ; Species Specificity ; }, abstract = {For the vast majority of species - including many economically or ecologically important organisms, progress in biological research is hampered due to the lack of a reference genome sequence. Despite recent advances in sequencing technologies, several factors still limit the availability of such a critical resource. At the same time, many research groups and international consortia have already produced BAC libraries and physical maps and now are in a position to proceed with the development of whole-genome sequences organized around a physical map anchored to a genetic map. We propose a BAC-by-BAC sequencing protocol that combines combinatorial pooling design and second-generation sequencing technology to efficiently approach denovo selective genome sequencing. We show that combinatorial pooling is a cost-effective and practical alternative to exhaustive DNA barcoding when preparing sequencing libraries for hundreds or thousands of DNA samples, such as in this case gene-bearing minimum-tiling-path BAC clones. The novelty of the protocol hinges on the computational ability to efficiently compare hundred millions of short reads and assign them to the correct BAC clones (deconvolution) so that the assembly can be carried out clone-by-clone. Experimental results on simulated data for the rice genome show that the deconvolution is very accurate, and the resulting BAC assemblies have high quality. Results on real data for a gene-rich subset of the barley genome confirm that the deconvolution is accurate and the BAC assemblies have good quality. While our method cannot provide the level of completeness that one would achieve with a comprehensive whole-genome sequencing project, we show that it is quite successful in reconstructing the gene sequences within BACs. In the case of plants such as barley, this level of sequence knowledge is sufficient to support critical end-point objectives such as map-based cloning and marker-assisted breeding.}, } @article {pmid23592793, year = {2013}, author = {Kostic, AD and Howitt, MR and Garrett, WS}, title = {Exploring host-microbiota interactions in animal models and humans.}, journal = {Genes & development}, volume = {27}, number = {7}, pages = {701-718}, pmid = {23592793}, issn = {1549-5477}, support = {R01CA154426/CA/NCI NIH HHS/United States ; AI078942/AI/NIAID NIH HHS/United States ; R01 DK092405/DK/NIDDK NIH HHS/United States ; K08 AI078942/AI/NIAID NIH HHS/United States ; R01 CA154426/CA/NCI NIH HHS/United States ; F32DK098826/DK/NIDDK NIH HHS/United States ; R01 GM099537/GM/NIGMS NIH HHS/United States ; F32 DK098826/DK/NIDDK NIH HHS/United States ; GM099531/GM/NIGMS NIH HHS/United States ; R01DK092405/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; Bacterial Physiological Phenomena ; Biological Evolution ; Computational Biology ; Gastrointestinal Tract/microbiology ; Humans ; Metagenome/genetics/*physiology ; *Symbiosis ; }, abstract = {The animal and bacterial kingdoms have coevolved and coadapted in response to environmental selective pressures over hundreds of millions of years. The meta'omics revolution in both sequencing and its analytic pipelines is fostering an explosion of interest in how the gut microbiome impacts physiology and propensity to disease. Gut microbiome studies are inherently interdisciplinary, drawing on approaches and technical skill sets from the biomedical sciences, ecology, and computational biology. Central to unraveling the complex biology of environment, genetics, and microbiome interaction in human health and disease is a deeper understanding of the symbiosis between animals and bacteria. Experimental model systems, including mice, fish, insects, and the Hawaiian bobtail squid, continue to provide critical insight into how host-microbiota homeostasis is constructed and maintained. Here we consider how model systems are influencing current understanding of host-microbiota interactions and explore recent human microbiome studies.}, } @article {pmid23590585, year = {2013}, author = {Shyu, HJ and Lung, CC and Ho, CC and Sun, YH and Ko, PC and Huang, JY and Pan, CC and Chiang, YC and Chen, SC and Liaw, YP}, title = {Geographic patterns of hepatocellular carcinoma mortality with exposure to iron in groundwater in Taiwanese population: an ecological study.}, journal = {BMC public health}, volume = {13}, number = {}, pages = {352}, pmid = {23590585}, issn = {1471-2458}, mesh = {Adolescent ; Aged, 80 and over ; Carcinoma, Hepatocellular/*mortality ; Child ; Child, Preschool ; Cluster Analysis ; Environmental Exposure/*adverse effects ; Female ; Geographic Information Systems ; Geography, Medical ; Groundwater/*chemistry ; Humans ; Infant ; Iron/*poisoning ; Liver Neoplasms/*mortality ; Male ; Registries ; Risk Factors ; Taiwan/epidemiology ; }, abstract = {BACKGROUND: Many studies have examined the risk factors for HCC (including hepatitis B virus, hepatitis C virus, aflatoxin, retinol, cigarette smoking, and alcohol consumption). However, data from previous studies on the association between iron exposure, land subsidence, and HCC mortality/incidence were limited, especially in Taiwanese population. We aimed to explore the geographical distribution of HCC mortality rates by township-specific data and to evaluate the association between HCC mortality, land subsidence, and iron levels in groundwater in Taiwan.

METHODS: We conducted an ecological study and calculated the HCC age-standardized mortality/incidence rates according to death certificates issued in Taiwan from 1992 to 2001 and incidence data from 1995-1998. The land subsidence dataset before 2005 and iron concentrations in groundwater in 1989 are also involved in this study. Both geographical information systems and Pearson correlation coefficients were used to analyze the relationship between HCC mortality rates, land subsidence, and iron concentrations in groundwater.

RESULTS: Township-specific HCC mortality rates are higher in southwestern coastal townships where serious land subsidence and higher township-specific concentrations of iron in groundwater are present. The Pearson correlation coefficients of iron concentrations in groundwater and ASRs of HCC were 0.286 (P = 0.004) in males and 0.192 (P = 0.058) in females for mortality data; the coefficients were 0.375 (P < 0.001) in males and 0.210 (P = 0.038) in females for incidence data.

CONCLUSIONS: This study showed that HCC mortality is clustered in southwestern Taiwan and the association with the iron levels in groundwater in Taiwanese population warrant further investigation.}, } @article {pmid23586558, year = {2013}, author = {Mendoza, E and Fuller, TL and Thomassen, HA and Buermann, W and Ramírez-Mejía, D and Smith, TB}, title = {A preliminary assessment of the effectiveness of the Mesoamerican Biological Corridor for protecting potential Baird's tapir (Tapirus bairdii) habitat in Southern Mexico.}, journal = {Integrative zoology}, volume = {8}, number = {1}, pages = {35-47}, doi = {10.1111/1749-4877.12005}, pmid = {23586558}, issn = {1749-4877}, mesh = {*Animal Distribution ; Animals ; Conservation of Natural Resources/*methods ; *Ecosystem ; Geographic Information Systems ; Mexico ; *Models, Theoretical ; Perissodactyla/*physiology ; }, abstract = {Baird's tapir (Tapirus bairdii) is one of the most emblematic mammals of Mesoamerica, but like other large-bodied animals, it is facing an increasing risk of extinction due primarily to habitat loss. Mexico's 'ortion of the Mesoamerican Biological Corridor (MBC-M) is located in one of the main strongholds for Bairds tapir. To assess the MBC-M's effectiveness for tapir conservation, we estimated the distribution of the species' potential habitat by applying 2 modelling approaches (random forest and Maxent) to a set of uncorrelated environmental variables and a 157-point presence dataset. We calculated the extent of tapir habitat in within the MBC-M and modelled new corridors and conservation areas, which we compared to the MBC-M. Moreover, we assessed deforestation patterns in the region. Twenty-seven percent of highly suitable tapir habitat occurred in protected areas, 15% in corridors and 58.3% was outside the MBC-M and associated reserves. The spatial configuration of the MBC-M was partially concordant with the modelled set of conservation areas and corridors. The main dissimilarity was that the modelled corridors traversed forests in Belize and Guatemala to connect conservation areas. Analyses of deforestation since 1993 and human population density in the vicinity of the MBC-M indicated that future conservation efforts should give particular attention to the Montes Azules-El Triunfo Corridor due to greater habitat threat. The MBC-M has a great potential to play a prominent role in the conservation of tapir habitat but there is an urgent need to implement management plans that reinforce and complement this conservation initiative.}, } @article {pmid23584854, year = {2013}, author = {Jean, FA and Swendsen, JD and Sibon, I and Fehér, K and Husky, M}, title = {Daily life behaviors and depression risk following stroke: a preliminary study using ecological momentary assessment.}, journal = {Journal of geriatric psychiatry and neurology}, volume = {26}, number = {3}, pages = {138-143}, doi = {10.1177/0891988713484193}, pmid = {23584854}, issn = {0891-9887}, mesh = {Activities of Daily Living/*psychology ; Aged ; Data Interpretation, Statistical ; Depression/epidemiology/*etiology/*psychology ; Employment ; Female ; Follow-Up Studies ; Humans ; Leisure Activities ; Male ; Marital Status ; Middle Aged ; Neuropsychological Tests ; Psychiatric Status Rating Scales ; Risk Assessment ; Social Behavior ; Social Environment ; Stroke/*complications/epidemiology/*psychology ; }, abstract = {Approximately one-third of stroke survivors have symptoms of depression. A better understanding of the early risk factors implicated in this form of comorbidity may contribute to the development of early prevention strategies and to improving outcomes for this population. The current study uses ecological momentary assessment techniques to identify behavioral risk factors for depression 3 months after stroke. Thirty-six participants completed ambulatory monitoring of daily life circumstances (location, social environment, and activity) 5 times per day during a 1-week period after hospital discharge. Clinician-administered measures of depression were also provided before discharge and 3 months later. Ambulatory monitoring revealed that depression scores at 3 months were lower among individuals with more social interactions but higher among those who reported having sports activities and working in the week following hospital discharge. Daily life behaviors may have important implications for understanding the risk of poststroke depression, and mobile technologies may provide important contributions to their investigation.}, } @article {pmid23582740, year = {2013}, author = {Wenkel, KO and Berg, M and Mirschel, W and Wieland, R and Nendel, C and Köstner, B}, title = {LandCaRe DSS--an interactive decision support system for climate change impact assessment and the analysis of potential agricultural land use adaptation strategies.}, journal = {Journal of environmental management}, volume = {127 Suppl}, number = {}, pages = {S168-83}, doi = {10.1016/j.jenvman.2013.02.051}, pmid = {23582740}, issn = {1095-8630}, mesh = {*Agriculture ; Climate Change ; Conservation of Natural Resources/*methods ; Decision Support Techniques ; Geographic Information Systems ; *Models, Theoretical ; }, abstract = {Decision support to develop viable climate change adaptation strategies for agriculture and regional land use management encompasses a wide range of options and issues. Up to now, only a few suitable tools and methods have existed for farmers and regional stakeholders that support the process of decision-making in this field. The interactive model-based spatial information and decision support system LandCaRe DSS attempts to close the existing methodical gap. This system supports interactive spatial scenario simulations, multi-ensemble and multi-model simulations at the regional scale, as well as the complex impact assessment of potential land use adaptation strategies at the local scale. The system is connected to a local geo-database and via the internet to a climate data server. LandCaRe DSS uses a multitude of scale-specific ecological impact models, which are linked in various ways. At the local scale (farm scale), biophysical models are directly coupled with a farm economy calculator. New or alternative simulation models can easily be added, thanks to the innovative architecture and design of the DSS. Scenario simulations can be conducted with a reasonable amount of effort. The interactive LandCaRe DSS prototype also offers a variety of data analysis and visualisation tools, a help system for users and a farmer information system for climate adaptation in agriculture. This paper presents the theoretical background, the conceptual framework, and the structure and methodology behind LandCaRe DSS. Scenario studies at the regional and local scale for the two Eastern German regions of Uckermark (dry lowlands, 2600 km(2)) and Weißeritz (humid mountain area, 400 km(2)) were conducted in close cooperation with stakeholders to test the functionality of the DSS prototype. The system is gradually being transformed into a web version (http://www.landcare-dss.de) to ensure the broadest possible distribution of LandCaRe DSS to the public. The system will be continuously developed, updated and used in different research projects and as a learning and knowledge-sharing tool for students. The main objective of LandCaRe DSS is to provide information on the complex long-term impacts of climate change and on potential management options for adaptation by answering "what-if" type questions.}, } @article {pmid23579690, year = {2013}, author = {Lederer, FL and Weinert, U and Günther, TJ and Raff, J and Weiß, S and Pollmann, K}, title = {Identification of multiple putative S-layer genes partly expressed by Lysinibacillus sphaericus JG-B53.}, journal = {Microbiology (Reading, England)}, volume = {159}, number = {Pt 6}, pages = {1097-1108}, doi = {10.1099/mic.0.065763-0}, pmid = {23579690}, issn = {1465-2080}, mesh = {Bacillaceae/classification/*genetics/isolation & purification ; Computational Biology ; DNA, Bacterial/chemistry/genetics ; Environmental Microbiology ; *Gene Expression ; Gene Expression Profiling ; Germany ; High-Throughput Nucleotide Sequencing ; Membrane Glycoproteins/biosynthesis/chemistry/*genetics ; Molecular Sequence Data ; Molecular Weight ; Sequence Homology, Amino Acid ; }, abstract = {Lysinibacillus sphaericus JG-B53 was isolated from the uranium mining waste pile Haberland near Johanngeorgenstadt, Germany. Previous studies have shown that many bacteria that have been isolated from these heavy metal contaminated environments possess surface layer (S-layer) proteins that enable the bacteria to survive by binding metals with high affinity. Conversely, essential trace elements are able to cross the filter layer and reach the interior of the cell. This is especially true of the S-layer of L. sphaericus JG-B53, which possesses outstanding recrystallization and metal-binding properties. In this study, S-layer protein gene sequences encoded in the genome of L. sphaericus JG-B53 were identified using next-generation sequencing technology followed by bioinformatic analyses. The genome of L. sphaericus JG-B53 encodes at least eight putative S-layer protein genes with distinct differences. Using mRNA analysis the expression of the putative S-layer protein genes was studied. The functional S-layer protein B53 Slp1 was identified as the dominantly expressed S-layer protein in L. sphaericus JG-B53 by mRNA studies, SDS-PAGE and N-terminal sequencing. B53 Slp1 is characterized by square lattice symmetry and a molecular mass of 116 kDa. The S-layer protein B53 Slp1 shows a high similarity to the functional S-layer protein of L. sphaericus JG-A12, which was isolated from the same uranium mining waste pile Haberland and has been described by previous research. These similarities indicate horizontal gene transfer and DNA rearrangements between these bacteria. The presence of multiple S-layer gene copies may enable the bacterial strains to quickly adapt to changing environments.}, } @article {pmid23575356, year = {2013}, author = {Huang, HH and Huang, JY and Lung, CC and Wu, CL and Ho, CC and Sun, YH and Ko, PC and Su, SY and Chen, SC and Liaw, YP}, title = {Cell-type specificity of lung cancer associated with low-dose soil heavy metal contamination in Taiwan: an ecological study.}, journal = {BMC public health}, volume = {13}, number = {}, pages = {330}, pmid = {23575356}, issn = {1471-2458}, mesh = {Adenocarcinoma/chemically induced/epidemiology ; Adenocarcinoma of Lung ; Adult ; Carcinoma, Squamous Cell/chemically induced/epidemiology ; Dose-Response Relationship, Drug ; Environmental Exposure/*adverse effects/analysis ; *Environmental Monitoring ; Female ; Geographic Information Systems ; Humans ; Lung Neoplasms/chemically induced/*epidemiology/pathology ; Male ; Metals, Heavy/*adverse effects/analysis ; Poisson Distribution ; Registries ; Soil Pollutants/adverse effects/*analysis ; Taiwan/epidemiology ; }, abstract = {BACKGROUND: Numerous studies have examined the association between heavy metal contamination (including arsenic [As], cadmium [Cd], chromium [Cr], copper [Cu], mercury [Hg], nickel [Ni], lead [Pb], and zinc [Zn]) and lung cancer. However, data from previous studies on pathological cell types are limited, particularly regarding exposure to low-dose soil heavy metal contamination. The purpose of this study was to explore the association between soil heavy metal contamination and lung cancer incidence by specific cell type in Taiwan.

METHODS: We conducted an ecological study and calculated the annual averages of eight soil heavy metals (i.e., As, Cd, Cr, Cu, Hg, Ni, Pb, and Zn) by using data from the Taiwan Environmental Protection Administration from1982 to 1986. The age-standardized incidence rates of lung cancer according to two major pathological types (adenocarcinoma [AC] and squamous cell carcinoma [SCC]) were obtained from the National Cancer Registry Program conducted in Taiwan from 2001 to 2005. A geographical information system was used to plot the maps of soil heavy metal concentration and lung cancer incidence rates. Poisson regression models were used to obtain the adjusted relative ratios (RR) and 95% confidence intervals (CI) for the lung cancer incidence associated with soil heavy metals.

RESULTS: For males, the trend test for lung SCC incidence caused by exposure to Cr, Cu, Hg, Ni, and Zn showed a statistically significant dose-response relationship. However, for lung AC, only Cu and Ni had a significant dose-response relationship. As for females, those achieving a statistically significant dose-response relationship for the trend test were Cr (P = 0.02), Ni (P = 0.02), and Zn (P= 0.02) for lung SCC, and Cu (P < 0.01) and Zn (P = 0.02) for lung AC.

CONCLUSION: The current study suggests that a dose-response relationship exists between low-dose soil heavy metal concentration and lung cancer occurrence by specific cell-type; however, the relevant mechanism should be explored further.}, } @article {pmid23568771, year = {2013}, author = {Piel, FB and Howes, RE and Nyangiri, OA and Moyes, CL and Williams, TN and Weatherall, DJ and Hay, SI}, title = {Online biomedical resources for malaria-related red cell disorders.}, journal = {Human mutation}, volume = {34}, number = {7}, pages = {937-944}, pmid = {23568771}, issn = {1098-1004}, support = {095066/WT_/Wellcome Trust/United Kingdom ; MC_UU_12009/13/MRC_/Medical Research Council/United Kingdom ; 092654/WT_/Wellcome Trust/United Kingdom ; 091835/WT_/Wellcome Trust/United Kingdom ; 085406/WT_/Wellcome Trust/United Kingdom ; 091758/WT_/Wellcome Trust/United Kingdom ; }, mesh = {*Databases, Factual ; *Databases, Genetic ; *Hemoglobinopathies/epidemiology/genetics/physiopathology ; Humans ; *Internet ; *Malaria/epidemiology/genetics/physiopathology ; }, abstract = {Warnings about the expected increase of the global public health burden of malaria-related red cell disorders are accruing. Past and present epidemiological data are necessary to track spatial and temporal changes in the frequencies of these genetic disorders. A number of open access biomedical databases including data on malaria-related red cell disorders have been launched over the last two decades. Here, we review the content of these databases, most of which focus on genetic diversity, and we describe a new epidemiological resource developed by the Malaria Atlas Project. To tackle upcoming public health challenges, the integration of epidemiological and genetic data is important. As many countries are considering implementing national screening programs, strategies to make such data more accessible are also needed.}, } @article {pmid23568535, year = {2013}, author = {Chen, W and Armstrong, BK and Rahman, B and Zheng, R and Zhang, S and Clements, M}, title = {Relationship between cancer survival and ambient ultraviolet B irradiance in China.}, journal = {Cancer causes & control : CCC}, volume = {24}, number = {7}, pages = {1323-1330}, doi = {10.1007/s10552-013-0210-4}, pmid = {23568535}, issn = {1573-7225}, mesh = {China/epidemiology ; Databases, Factual ; Female ; Humans ; Incidence ; Male ; Neoplasms/*epidemiology/mortality ; Ultraviolet Rays/*adverse effects ; }, abstract = {BACKGROUND: Ecological studies in predominantly European populations have reported higher cancer survival in areas of higher solar ultraviolet (UV) B irradiation, perhaps due to a cancer protective effect of vitamin D synthesized photochemically in the skin. Such studies have not been done in developing countries, perhaps because of lack of cancer registries that can do outcome follow-up. One minus the mortality-to-incidence ratio (1-MIR), however, can be used as a measure of survival, and MIR as a measure of fatality, in developing country cancer registries. We analyzed the association between ambient solar UVB and MIR in China.

METHODS: National cancer registration data in 32 counties of China in 2004-2005 were used to estimate MIR by age, sex, and area. The accuracy of 1-MIR as a measure of survival was assessed in the Cixian County cancer registry. Contemporary satellite measurements of cloud-adjusted ambient UVB intensity at 305 nm were taken from an NASA database and spatial Kriging methods used to estimate the average daily irradiance in each county. We estimated mortality hazard ratios (HRs) per 10 mW/m(2) of UVB for all cancers together, and the ten commonest cancer types by fitting a generalized linear model assuming mortality had a binomial distribution conditional on the sum of mortality and incidence, adjusted for sex, age, and location.

RESULTS: The 5-year survival proportions for the main cancer types were in good agreement with 1-MIR in Cixian County. MIR ratios for all cancers combined were inversely associated with ambient UVB in men (HR = 0.96, 95% CI 0.93-0.99) and women (HR = 0.91, 95% CI 0.88-0.94) and in urban (HR = 0.95, 95% CI 0.94-0.96) and rural areas (HR = 0.90, 95% CI 0.87-0.93). Similar inverse associations were present for cancers of esophagus, stomach, and bladder in both sexes together and breast cancer in women. They were present in urban residents for all major cancers except liver cancer, bladder cancer, and breast cancer in women. For rural residents, most HRs were <1.0 but, with the exception of breast cancer, their upper 95% confidence bounds were >1.0.

CONCLUSION: Ambient UVB was significantly inversely associated with MIR for all cancers together and four of ten cancer types. Solar UVB may increase survival from some cancers in China.}, } @article {pmid23565134, year = {2013}, author = {Parmentier, I and Duminil, J and Kuzmina, M and Philippe, M and Thomas, DW and Kenfack, D and Chuyong, GB and Cruaud, C and Hardy, OJ}, title = {How effective are DNA barcodes in the identification of African rainforest trees?.}, journal = {PloS one}, volume = {8}, number = {4}, pages = {e54921}, pmid = {23565134}, issn = {1932-6203}, mesh = {Cameroon ; *DNA Barcoding, Taxonomic ; Databases, Genetic ; Genes, Plant ; Plastids/genetics ; Polymorphism, Genetic ; Species Specificity ; Trees/*classification/*genetics ; Tropical Climate ; }, abstract = {BACKGROUND: DNA barcoding of rain forest trees could potentially help biologists identify species and discover new ones. However, DNA barcodes cannot always distinguish between closely related species, and the size and completeness of barcode databases are key parameters for their successful application. We test the ability of rbcL, matK and trnH-psbA plastid DNA markers to identify rain forest trees at two sites in Atlantic central Africa under the assumption that a database is exhaustive in terms of species content, but not necessarily in terms of haplotype diversity within species.

We assess the accuracy of identification to species or genus using a genetic distance matrix between samples either based on a global multiple sequence alignment (GD) or on a basic local alignment search tool (BLAST). Where a local database is available (within a 50 ha plot), barcoding was generally reliable for genus identification (95-100% success), but less for species identification (71-88%). Using a single marker, best results for species identification were obtained with trnH-psbA. There was a significant decrease of barcoding success in species-rich clades. When the local database was used to identify the genus of trees from another region and did include all genera from the query individuals but not all species, genus identification success decreased to 84-90%. The GD method performed best but a global multiple sequence alignment is not applicable on trnH-psbA.

CONCLUSIONS/SIGNIFICANCE: Barcoding is a useful tool to assign unidentified African rain forest trees to a genus, but identification to a species is less reliable, especially in species-rich clades, even using an exhaustive local database. Combining two markers improves the accuracy of species identification but it would only marginally improve genus identification. Finally, we highlight some limitations of the BLAST algorithm as currently implemented and suggest possible improvements for barcoding applications.}, } @article {pmid23565065, year = {2013}, author = {Hay, SI and George, DB and Moyes, CL and Brownstein, JS}, title = {Big data opportunities for global infectious disease surveillance.}, journal = {PLoS medicine}, volume = {10}, number = {4}, pages = {e1001413}, pmid = {23565065}, issn = {1549-1676}, support = {095066/WT_/Wellcome Trust/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; 091835/WT_/Wellcome Trust/United Kingdom ; R01 LM010812/LM/NLM NIH HHS/United States ; G08 LM009776/LM/NLM NIH HHS/United States ; }, mesh = {Communicable Diseases/*epidemiology ; *Data Mining ; Disease Outbreaks/statistics & numerical data ; *Global Health ; Humans ; International Cooperation ; Population Surveillance/*methods ; Risk ; Social Media ; }, abstract = {Simon Hay and colleagues discuss the potential and challenges of producing continually updated infectious disease risk maps using diverse and large volume data sources such as social media.}, } @article {pmid23564007, year = {2013}, author = {Yang, S and Sun, W and Zhang, F and Li, Z}, title = {Phylogenetically diverse denitrifying and ammonia-oxidizing bacteria in corals Alcyonium gracillimum and Tubastraea coccinea.}, journal = {Marine biotechnology (New York, N.Y.)}, volume = {15}, number = {5}, pages = {540-551}, pmid = {23564007}, issn = {1436-2236}, mesh = {Ammonia/metabolism ; Animals ; Anthozoa/*microbiology ; Bacteria/*genetics/*metabolism ; Base Sequence ; China ; Cluster Analysis ; Computational Biology ; DNA Primers/genetics ; Denitrification/genetics/physiology ; Gene Library ; Genetic Markers/genetics ; Microbiota/*genetics ; Molecular Sequence Data ; Nitrite Reductases/genetics ; Oceans and Seas ; Oxidation-Reduction ; Oxidoreductases/genetics ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Species Specificity ; *Symbiosis ; }, abstract = {To date, the association of coral-bacteria and the ecological roles of bacterial symbionts in corals remain largely unknown. In particular, little is known about the community components of bacterial symbionts of corals involved in the process of denitrification and ammonia oxidation. In this study, the nitrite reductase (nirS and nirK) and ammonia monooxygenase subunit A (amoA) genes were used as functional markers. Diverse bacteria with the potential to be active as denitrifiers and ammonia-oxidizing bacteria (AOB) were found in two East China Sea corals: stony coral Alcyonium gracillimum and soft coral Tubastraea coccinea. The 16S rRNA gene library analysis demonstrated different communities of bacterial symbionts in these two corals of the same location. Nitrite reductase nirK gene was found only in T. coccinea, while both nirK and nirS genes were detected in A. gracillimum, which might be the result of the presence of different bacterial symbionts in these two corals. AOB rather than ammonia-oxidizing archaea were detected in both corals, suggesting that AOB might play an important role in the ammonia oxidation process of the corals. This study indicates that the coral bacterial symbionts with the potential for nitrite reduction and ammonia oxidation might have multiple ecological roles in the coral holobiont, which promotes our understanding of bacteria-mediated nitrogen cycling in corals. To our knowledge, this study is the first assessment of the community structure and phylogenetic diversity of denitrifying bacteria and AOB in corals based on nirK, nirS, and amoA gene library analysis.}, } @article {pmid23563266, year = {2013}, author = {Bhatt, S and Gething, PW and Brady, OJ and Messina, JP and Farlow, AW and Moyes, CL and Drake, JM and Brownstein, JS and Hoen, AG and Sankoh, O and Myers, MF and George, DB and Jaenisch, T and Wint, GR and Simmons, CP and Scott, TW and Farrar, JJ and Hay, SI}, title = {The global distribution and burden of dengue.}, journal = {Nature}, volume = {496}, number = {7446}, pages = {504-507}, pmid = {23563266}, issn = {1476-4687}, support = {R01 AI069341/AI/NIAID NIH HHS/United States ; 084368/WT_/Wellcome Trust/United Kingdom ; /BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; 097318/WT_/Wellcome Trust/United Kingdom ; R01 GM083224/GM/NIGMS NIH HHS/United States ; R01 AI091980/AI/NIAID NIH HHS/United States ; /WT_/Wellcome Trust/United Kingdom ; 089276/WT_/Wellcome Trust/United Kingdom ; 095066/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Cohort Studies ; Databases, Factual/standards ; Dengue/*epidemiology/transmission/virology ; Dengue Virus/physiology ; Global Health/*statistics & numerical data ; Humans ; Incidence ; Public Health/statistics & numerical data ; Quality Control ; Rain ; Risk Factors ; Temperature ; Tropical Climate ; Urbanization ; World Health Organization ; }, abstract = {Dengue is a systemic viral infection transmitted between humans by Aedes mosquitoes. For some patients, dengue is a life-threatening illness. There are currently no licensed vaccines or specific therapeutics, and substantial vector control efforts have not stopped its rapid emergence and global spread. The contemporary worldwide distribution of the risk of dengue virus infection and its public health burden are poorly known. Here we undertake an exhaustive assembly of known records of dengue occurrence worldwide, and use a formal modelling framework to map the global distribution of dengue risk. We then pair the resulting risk map with detailed longitudinal information from dengue cohort studies and population surfaces to infer the public health burden of dengue in 2010. We predict dengue to be ubiquitous throughout the tropics, with local spatial variations in risk influenced strongly by rainfall, temperature and the degree of urbanization. Using cartographic approaches, we estimate there to be 390 million (95% credible interval 284-528) dengue infections per year, of which 96 million (67-136) manifest apparently (any level of disease severity). This infection total is more than three times the dengue burden estimate of the World Health Organization. Stratification of our estimates by country allows comparison with national dengue reporting, after taking into account the probability of an apparent infection being formally reported. The most notable differences are discussed. These new risk maps and infection estimates provide novel insights into the global, regional and national public health burden imposed by dengue. We anticipate that they will provide a starting point for a wider discussion about the global impact of this disease and will help to guide improvements in disease control strategies using vaccine, drug and vector control methods, and in their economic evaluation.}, } @article {pmid23557596, year = {2013}, author = {Nazi, KM}, title = {The personal health record paradox: health care professionals' perspectives and the information ecology of personal health record systems in organizational and clinical settings.}, journal = {Journal of medical Internet research}, volume = {15}, number = {4}, pages = {e70}, pmid = {23557596}, issn = {1438-8871}, mesh = {Attitude of Health Personnel ; Delivery of Health Care ; *Health Personnel ; *Health Records, Personal ; Humans ; Patient Participation ; Telemedicine/*statistics & numerical data ; United States ; United States Department of Veterans Affairs ; }, abstract = {BACKGROUND: Despite significant consumer interest and anticipated benefits, overall adoption of personal health records (PHRs) remains relatively low. Understanding the consumer perspective is necessary, but insufficient by itself. Consumer PHR use also has broad implications for health care professionals and organizational delivery systems; however, these have received less attention. An exclusive focus on the PHR as a tool for consumer empowerment does not adequately take into account the social and organizational context of health care delivery, and the reciprocal nature of patient engagement.

OBJECTIVE: The purpose of this study was to examine the experiences of physicians, nurses, and pharmacists at the Department of Veterans Affairs (VA) using an organizationally sponsored PHR to develop insights into the interaction of technology and processes of health care delivery. The conceptual framework for the study draws on an information ecology perspective, which recognizes that a vibrant dynamic exists among technologies, people, practices, and values, accounting for both the values and norms of the participants and the practices of the local setting. The study explores the experiences and perspectives of VA health care professionals related to patient use of the My HealtheVet PHR portal and secure messaging systems.

METHODS: In-depth interviews were conducted with 30 VA health care professionals engaged in providing direct patient care who self-reported that they had experiences with at least 1 of 4 PHR features. Interviews were transcribed, coded, and analyzed to identify inductive themes. Organizational documents and artifacts were reviewed and analyzed to trace the trajectory of secure messaging implementation as part of the VA Patient Aligned Care Team (PACT) model.

RESULTS: Study findings revealed a variety of factors that have facilitated or inhibited PHR adoption, use, and endorsement of patient use by health care professionals. Health care professionals' accounts and analysis of organizational documents revealed a multidimensional dynamic between the trajectory of secure messaging implementation and its impact on organizational actors and their use of technology, influencing workflow, practices, and the flow of information. In effect, secure messaging was the missing element of complex information ecology and its implementation acted as a catalyst for change. Secure messaging was found to have important consequences for access, communication, patient self-report, and patient/provider relationships.

CONCLUSIONS: Study findings have direct implications for the development and implementation of PHR systems to ensure adequate training and support for health care professionals, alignment with clinical workflow, and features that enable information sharing and communication. Study findings highlight the importance of clinician endorsement and engagement, and the need to further examine both intended and unintended consequences of use. This research provides an integral step toward better understanding the social and organizational context and impact of PHR and secure messaging use in clinical practice settings.}, } @article {pmid23555227, year = {2013}, author = {Korolev, KS}, title = {The fate of cooperation during range expansions.}, journal = {PLoS computational biology}, volume = {9}, number = {3}, pages = {e1002994}, pmid = {23555227}, issn = {1553-7358}, mesh = {*Animal Migration ; Animals ; Biological Evolution ; Computational Biology ; *Cooperative Behavior ; Diffusion ; Ecology ; Feedback ; *Models, Biological ; Population Dynamics ; *Selection, Genetic ; Spatial Behavior ; }, abstract = {Species expand their geographical ranges following an environmental change, long range dispersal, or a new adaptation. Range expansions not only bring an ecological change, but also affect the evolution of the expanding species. Although the dynamics of deleterious, neutral, and beneficial mutations have been extensively studied in expanding populations, the fate of alleles under frequency-dependent selection remains largely unexplored. The dynamics of cooperative alleles are particularly interesting because selection can be both frequency and density dependent, resulting in a coupling between population and evolutionary dynamics. This coupling leads to an increase in the frequency of cooperators at the expansion front, and, under certain conditions, the entire front can be taken over by cooperators. Thus, a mixed population wave can split into an expansion wave of only cooperators followed by an invasion wave of defectors. After the splitting, cooperators increase in abundance by expanding into new territories faster than they are invaded by defectors. Our results not only provide an explanation for the maintenance of cooperation but also elucidate the effect of eco-evolutionary feedback on the maintenance of genetic diversity during range expansions. When cooperators do not split away, we find that defectors can spread much faster with cooperators than they would be able to on their own or by invading cooperators. This enhanced rate of expansion in mixed waves could counterbalance the loss of genetic diversity due to the founder effect for mutations under frequency-dependent selection. Although we focus on cooperator-defector interactions, our analysis could also be relevant for other systems described by reaction-diffusion equations.}, } @article {pmid23555219, year = {2013}, author = {Garnier, S and Murphy, T and Lutz, M and Hurme, E and Leblanc, S and Couzin, ID}, title = {Stability and responsiveness in a self-organized living architecture.}, journal = {PLoS computational biology}, volume = {9}, number = {3}, pages = {e1002984}, pmid = {23555219}, issn = {1553-7358}, mesh = {Animal Communication ; Animals ; Ants/*physiology ; Appetitive Behavior/*physiology ; Biomechanical Phenomena/physiology ; Computational Biology ; Computer Simulation ; Motor Activity/physiology ; Statistics, Nonparametric ; }, abstract = {Robustness and adaptability are central to the functioning of biological systems, from gene networks to animal societies. Yet the mechanisms by which living organisms achieve both stability to perturbations and sensitivity to input are poorly understood. Here, we present an integrated study of a living architecture in which army ants interconnect their bodies to span gaps. We demonstrate that these self-assembled bridges are a highly effective means of maintaining traffic flow over unpredictable terrain. The individual-level rules responsible depend only on locally-estimated traffic intensity and the number of neighbours to which ants are attached within the structure. We employ a parameterized computational model to reveal that bridges are tuned to be maximally stable in the face of regular, periodic fluctuations in traffic. However analysis of the model also suggests that interactions among ants give rise to feedback processes that result in bridges being highly responsive to sudden interruptions in traffic. Subsequent field experiments confirm this prediction and thus the dual nature of stability and flexibility in living bridges. Our study demonstrates the importance of robust and adaptive modular architecture to efficient traffic organisation and reveals general principles regarding the regulation of form in biological self-assemblies.}, } @article {pmid23553986, year = {2013}, author = {DeForest, DK and Schlekat, CE}, title = {Species sensitivity distribution evaluation for chronic nickel toxicity to marine organisms.}, journal = {Integrated environmental assessment and management}, volume = {9}, number = {4}, pages = {580-589}, doi = {10.1002/ieam.1419}, pmid = {23553986}, issn = {1551-3793}, mesh = {Animals ; Aquatic Organisms/*drug effects ; Databases, Factual ; Ecotoxicology/*methods ; Environmental Pollutants/*toxicity ; Nickel/*toxicity ; Seawater/chemistry ; Species Specificity ; Time Factors ; }, abstract = {In Europe, the European Union's Existing Substances Regulation (EEC 793/93), the REACH Regulation, and Water Framework Directive all share common guidance for conducting environmental effects assessments, which can be further used to derive predicted no effect concentrations (PNECs) and environmental quality standards (EQS) for chemical substances. To meet the criteria for using a species sensitivity distribution (SSD) in the effects assessment of Ni for marine organisms, chronic toxicity data from the published scientific literature were augmented with toxicity testing of several additional marine species including: a unicellular alga (Dunalliela tertiolecta), a diatom (Skeletonema costatum), 2 macroalgae (Champia parvula, Macrocystis pyrifera), 2 mollusks (Crassostrea gigas, Mytilus galloprovincialis), 2 echinoderms (Dendraster excentricus, Strongylocentrotus purpuratus), a polychaete (Neanthes arenaceodentata), and a fish (Cyprinodon variegatus). Based on this updated database, which includes chronic Ni toxicity data for a total of 17 marine species, HC5 values (hazardous concentrations to 5% of the species) were derived using an SSD. The most sensitive species is a tropical sea urchin from the Caribbean region, Diadema antillarum, which has an EC10 that is approximately 6-fold less than the EC10 for the second most sensitive species tested. There is some uncertainty in the representativeness of D. antillarum to temperate European marine waters because 1) a European sea urchin species (Paracentrotus lividus) is approximately 48-fold less sensitive to Ni, and (2) ambient marine Ni concentrations in at least some European waters closely approach the D. antillarum EC10. The HC5 values with and without D. antillarum included in the SSD are 3.9 and 20.9 μg/L, respectively. Site-specific toxicity testing with local species may be warranted for locations where Ni concentrations fall between the range in HC5s of 3.9 to 20.9 μg/L.}, } @article {pmid23552231, year = {2013}, author = {Kaufmann Alves, I}, title = {A mathematical approach to find long-term strategies for the implementation of resource-orientated sanitation.}, journal = {Water science and technology : a journal of the International Association on Water Pollution Research}, volume = {67}, number = {7}, pages = {1442-1454}, doi = {10.2166/wst.2013.691}, pmid = {23552231}, issn = {0273-1223}, mesh = {Decision Support Techniques ; *Models, Theoretical ; Sanitation/*statistics & numerical data ; Waste Management/*statistics & numerical data ; Water Supply/*statistics & numerical data ; }, abstract = {In the present discussion of sustainability centralised water infrastructures are exposed to new challenges, which may cause a conceptual alteration in urban water management. If technologies for closing urban water and nutrient cycles are to at least partially replace existing systems, then intensive reconstruction work becomes essential. The paper presents the development and implementation of a mathematical approach to minimise environmental impact and economic costs on the way to more source-controlled future states in urban water management. To find an optimal transformation strategy, a simultaneous project scheduling and network flow problem was defined as a bi-criteria mixed-integer program. An optimal solution is found by minimising two objective functions concurrently - the economic costs and 'ecologic costs' for the period of consideration. This paper discusses the influence of the weighting of these two costs on optimal transformation strategies for a real catchment in Germany. The results show that the approach can very well support decision makers when showing all impacts of transformation processes in detail. All in all, the developed model can be seen as a first step in strategy-finding for transformations in existing urban water systems.}, } @article {pmid23550586, year = {2013}, author = {Díez, CM and Gaut, BS and Meca, E and Scheinvar, E and Montes-Hernandez, S and Eguiarte, LE and Tenaillon, MI}, title = {Genome size variation in wild and cultivated maize along altitudinal gradients.}, journal = {The New phytologist}, volume = {199}, number = {1}, pages = {264-276}, pmid = {23550586}, issn = {1469-8137}, support = {P50 GM076516/GM/NIGMS NIH HHS/United States ; P50GM76516/GM/NIGMS NIH HHS/United States ; }, mesh = {Altitude ; Climate ; Crops, Agricultural ; Data Interpretation, Statistical ; Genetic Variation ; Genetics, Population ; *Genome Size ; *Genome, Plant ; Mexico ; Selection, Genetic ; Zea mays/*genetics ; }, abstract = {It is still an open question as to whether genome size (GS) variation is shaped by natural selection. One approach to address this question is a population-level survey that assesses both the variation in GS and the relationship of GS to ecological variants. We assessed GS in Zea mays, a species that includes the cultivated crop, maize, and its closest wild relatives, the teosintes. We measured GS in five plants of each of 22 maize landraces and 21 teosinte populations from Mexico sampled from parallel altitudinal gradients. GS was significantly smaller in landraces than in teosintes, but the largest component of GS variation was among landraces and among populations. In maize, GS correlated negatively with altitude; more generally, the best GS predictors were linked to geography. By contrast, GS variation in teosintes was best explained by temperature and precipitation. Overall, our results further document the size flexibility of the Zea genome, but also point to a drastic shift in patterns of GS variation since domestication. We argue that such patterns may reflect the indirect action of selection on GS, through a multiplicity of phenotypes and life-history traits.}, } @article {pmid23550145, year = {2012}, author = {Nasir, A and Kim, KM and Caetano-Anollés, G}, title = {Viral evolution: Primordial cellular origins and late adaptation to parasitism.}, journal = {Mobile genetic elements}, volume = {2}, number = {5}, pages = {247-252}, pmid = {23550145}, issn = {2159-2543}, abstract = {Explaining the origin of viruses remains an important challenge for evolutionary biology. Previous explanatory frameworks described viruses as founders of cellular life, as parasitic reductive products of ancient cellular organisms or as escapees of modern genomes. Each of these frameworks endow viruses with distinct molecular, cellular, dynamic and emergent properties that carry broad and important implications for many disciplines, including biology, ecology and epidemiology. In a recent genome-wide structural phylogenomic analysis, we have shown that large-to-medium-sized viruses coevolved with cellular ancestors and have chosen the evolutionary reductive route. Here we interpret these results and provide a parsimonious hypothesis for the origin of viruses that is supported by molecular data and objective evolutionary bioinformatic approaches. Results suggest two important phases in the evolution of viruses: (1) origin from primordial cells and coexistence with cellular ancestors, and (2) prolonged pressure of genome reduction and relatively late adaptation to the parasitic lifestyle once virions and diversified cellular life took over the planet. Under this evolutionary model, new viral lineages can evolve from existing cellular parasites and enhance the diversity of the world's virosphere.}, } @article {pmid23546798, year = {2013}, author = {Kim, KS and Sappington, TW}, title = {Microsatellite data analysis for population genetics.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1006}, number = {}, pages = {271-295}, doi = {10.1007/978-1-62703-389-3_19}, pmid = {23546798}, issn = {1940-6029}, mesh = {Computational Biology/instrumentation/*methods ; Ecology ; Gene Flow ; Genetic Variation ; Genetics ; *Genetics, Population ; Genotype ; Microsatellite Repeats/*genetics ; *Software ; }, abstract = {Theories and analytical tools of population genetics have been widely applied for addressing various questions in the fields of ecological genetics, conservation biology, and any context where the role of dispersal or gene flow is important. Underlying much of population genetics is the analysis of variation at selectively neutral marker loci, and microsatellites continue to be a popular choice of marker. In recent decades, software programs to estimate population genetics parameters have been developed at an increasing pace as computational science and theoretical knowledge advance. Numerous population genetics software programs are presently available to analyze microsatellite genotype data, but only a handful are commonly employed for calculating parameters such as genetic variation, genetic structure, patterns of spatial and temporal gene flow, population demography, individual population assignment, and genetic relationships within and between populations. In this chapter, we introduce statistical analyses and relevant population genetic software programs that are commonly employed in the field of population genetics and molecular ecology.}, } @article {pmid23537801, year = {2013}, author = {Miller, WC and Powers, KA and Smith, MK and Cohen, MS}, title = {Community viral load as a measure for assessment of HIV treatment as prevention.}, journal = {The Lancet. Infectious diseases}, volume = {13}, number = {5}, pages = {459-464}, pmid = {23537801}, issn = {1474-4457}, support = {T32 AI007001/AI/NIAID NIH HHS/United States ; R01 DK049381/DK/NIDDK NIH HHS/United States ; R37DK049381/DK/NIDDK NIH HHS/United States ; P30 AI050410/AI/NIAID NIH HHS/United States ; T32AI007001/AI/NIAID NIH HHS/United States ; R37 DK049381/DK/NIDDK NIH HHS/United States ; R01AI083059/AI/NIAID NIH HHS/United States ; R01 AI083059/AI/NIAID NIH HHS/United States ; }, mesh = {Anti-Retroviral Agents/administration & dosage ; Databases, Factual ; Disease Transmission, Infectious/prevention & control ; HIV/*pathogenicity ; HIV Infections/diagnosis/drug therapy/epidemiology/*prevention & control ; Humans ; Population Surveillance ; Prevalence ; Sexual Behavior ; Time Factors ; *Viral Load ; }, abstract = {Community viral load, defined as an aggregation of individual viral loads of people infected with HIV in a specific community, has been proposed as a useful measure to monitor HIV treatment uptake and quantify its effect on transmission. The first reports of community viral load were published in 2009, and the measure was subsequently incorporated into the US National HIV/AIDS Strategy. Although intuitively an appealing strategy, measurement of community viral load has several theoretical limitations and biases that need further assessment, which can be grouped into four categories: issues of selection and measurement, the importance of HIV prevalence in determining the potential for ongoing HIV transmission, interpretation of community viral load and its effect on ongoing HIV transmission in a community, and the ecological fallacy (ie, ecological bias). These issues need careful assessment as community viral load is being considered as a public health measurement to assess the effect of HIV care on prevention.}, } @article {pmid23536290, year = {2013}, author = {Hugoni, M and Taib, N and Debroas, D and Domaizon, I and Jouan Dufournel, I and Bronner, G and Salter, I and Agogué, H and Mary, I and Galand, PE}, title = {Structure of the rare archaeal biosphere and seasonal dynamics of active ecotypes in surface coastal waters.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {110}, number = {15}, pages = {6004-6009}, pmid = {23536290}, issn = {1091-6490}, mesh = {Archaea/genetics/*physiology ; Computational Biology ; DNA, Ribosomal/genetics ; Ecology ; *Ecotype ; Mediterranean Sea ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Seasons ; *Seawater ; Sequence Analysis, RNA ; Water Microbiology ; }, abstract = {Marine Archaea are important players among microbial plankton and significantly contribute to biogeochemical cycles, but details regarding their community structure and long-term seasonal activity and dynamics remain largely unexplored. In this study, we monitored the interannual archaeal community composition of abundant and rare biospheres in northwestern Mediterranean Sea surface waters by pyrosequencing 16S rDNA and rRNA. A detailed analysis of the rare biosphere structure showed that the rare archaeal community was composed of three distinct fractions. One contained the rare Archaea that became abundant at different times within the same ecosystem; these cells were typically not dormant, and we hypothesize that they represent a local seed bank that is specific and essential for ecosystem functioning through cycling seasonal environmental conditions. The second fraction contained cells that were uncommon in public databases and not active, consisting of aliens to the studied ecosystem and representing a nonlocal seed bank of potential colonizers. The third fraction contained Archaea that were always rare but actively growing; their affiliation and seasonal dynamics were similar to the abundant microbes and could not be considered a seed bank. We also showed that the major archaeal groups, Thaumarchaeota marine group I and Euryarchaeota group II.B in winter and Euryarchaeota group II.A in summer, contained different ecotypes with varying activities. Our findings suggest that archaeal diversity could be associated with distinct metabolisms or life strategies, and that the rare archaeal biosphere is composed of a complex assortment of organisms with distinct histories that affect their potential for growth.}, } @article {pmid23535014, year = {2013}, author = {Gimpel, A and Stelzenmüller, V and Cormier, R and Floeter, J and Temming, A}, title = {A spatially explicit risk approach to support marine spatial planning in the German EEZ.}, journal = {Marine environmental research}, volume = {86}, number = {}, pages = {56-69}, doi = {10.1016/j.marenvres.2013.02.013}, pmid = {23535014}, issn = {1879-0291}, mesh = {Animals ; Conservation of Natural Resources/*legislation & jurisprudence/*methods ; *Ecosystem ; Fisheries/*methods ; Flounder/*growth & development ; Geographic Information Systems ; Germany ; North Sea ; Risk Assessment ; }, abstract = {An ecosystem approach to marine spatial planning (MSP) promotes sustainable development by organizing human activities in a geo-spatial and temporal context. (1) This study develops and tests a spatially explicit risk assessment to support MSP. Using the German exclusive economic zone (EEZ) of the North Sea as a case study area, current and future spatial management scenarios are assessed. (2) Different tools are linked in order to carry out a comprehensive spatial risk assessment of current and future spatial management scenarios for ecologic and economic ecosystem components, i.e. Pleuronectes platessa nursery grounds. With the identification of key inputs and outputs the suitability of each tool is tested. (3) Here, the procedure as well as the main findings of the spatially explicit risk approach are summarised to demonstrate the applicability of the framework and the need for an ecosystem approach to risk management techniques using geo-spatial tools.}, } @article {pmid23534863, year = {2013}, author = {Lindahl, BD and Nilsson, RH and Tedersoo, L and Abarenkov, K and Carlsen, T and Kjøller, R and Kõljalg, U and Pennanen, T and Rosendahl, S and Stenlid, J and Kauserud, H}, title = {Fungal community analysis by high-throughput sequencing of amplified markers--a user's guide.}, journal = {The New phytologist}, volume = {199}, number = {1}, pages = {288-299}, pmid = {23534863}, issn = {1469-8137}, mesh = {Biota ; Computational Biology/*methods ; DNA Primers ; DNA, Fungal/analysis ; DNA, Intergenic ; Fungi/classification/*genetics ; *Genetic Markers ; High-Throughput Nucleotide Sequencing/*methods ; Mycorrhizae/genetics ; Polymerase Chain Reaction/methods ; Soil Microbiology ; }, abstract = {Novel high-throughput sequencing methods outperform earlier approaches in terms of resolution and magnitude. They enable identification and relative quantification of community members and offer new insights into fungal community ecology. These methods are currently taking over as the primary tool to assess fungal communities of plant-associated endophytes, pathogens, and mycorrhizal symbionts, as well as free-living saprotrophs. Taking advantage of the collective experience of six research groups, we here review the different stages involved in fungal community analysis, from field sampling via laboratory procedures to bioinformatics and data interpretation. We discuss potential pitfalls, alternatives, and solutions. Highlighted topics are challenges involved in: obtaining representative DNA/RNA samples and replicates that encompass the targeted variation in community composition, selection of marker regions and primers, options for amplification and multiplexing, handling of sequencing errors, and taxonomic identification. Without awareness of methodological biases, limitations of markers, and bioinformatics challenges, large-scale sequencing projects risk yielding artificial results and misleading conclusions.}, } @article {pmid23534706, year = {2013}, author = {Asmarian, NS and Ruzitalab, A and Amir, K and Masoud, S and Mahaki, B}, title = {Area-to-Area Poisson Kriging analysis of mapping of county- level esophageal cancer incidence rates in Iran.}, journal = {Asian Pacific journal of cancer prevention : APJCP}, volume = {14}, number = {1}, pages = {11-13}, doi = {10.7314/apjcp.2013.14.1.11}, pmid = {23534706}, issn = {2476-762X}, mesh = {Esophageal Neoplasms/*epidemiology ; Geographic Information Systems ; Humans ; Incidence ; Iran/epidemiology ; Poisson Distribution ; *Spatial Analysis ; }, abstract = {BACKGROUND: Esophagus cancer, the third most common gastrointestinal cancer overall, demonstrates high incidence in parts of Iran. The counties of Iran vary in size, shape and population size. The aim of this study was to account for spatial support with Area-to-Area (ATA) Poisson Kriging to increase precision of parameter estimates and yield correct variance and create maps of disease rates.

MATERIALS AND METHODS: This study involved application/ecology methodology, illustrated using esophagus cancer data recorded by the Ministry of Health and Medical Education (in the Non-infectious Diseases Management Center) of Iran. The analysis focused on the 336 counties over the years 2003-2007. ATA was used for estimating the parameters of the map with SpaceStat and ArcGIS9.3 software for analysing the data and drawing maps.

RESULTS: Northern counties of Iran have high risk estimation. The ATA Poisson Kriging approach yielded variance increase in large sparsely populated counties. So, central counties had the most prediction variance.

CONCLUSIONS: The ATAPoisson kriging approach is recommended for estimating parameters of disease mapping since this method accounts for spatial support and patterns in irregular spatial areas. The results demonstrate that the counties in provinces Ardebil, Mazandaran and Kordestan have higher risk than other counties.}, } @article {pmid23533370, year = {2013}, author = {Fortuna, MA and Zaman, L and Wagner, AP and Ofria, C}, title = {Evolving digital ecological networks.}, journal = {PLoS computational biology}, volume = {9}, number = {3}, pages = {e1002928}, pmid = {23533370}, issn = {1553-7358}, mesh = {Animals ; *Biological Evolution ; *Computational Biology ; Computer Simulation ; *Ecology ; Genome ; Host-Parasite Interactions ; *Models, Biological ; Plants ; Symbiosis ; }, abstract = {"It is hard to realize that the living world as we know it is just one among many possibilities" [1]. Evolving digital ecological networks are webs of interacting, self-replicating, and evolving computer programs (i.e., digital organisms) that experience the same major ecological interactions as biological organisms (e.g., competition, predation, parasitism, and mutualism). Despite being computational, these programs evolve quickly in an open-ended way, and starting from only one or two ancestral organisms, the formation of ecological networks can be observed in real-time by tracking interactions between the constantly evolving organism phenotypes. These phenotypes may be defined by combinations of logical computations (hereafter tasks) that digital organisms perform and by expressed behaviors that have evolved. The types and outcomes of interactions between phenotypes are determined by task overlap for logic-defined phenotypes and by responses to encounters in the case of behavioral phenotypes. Biologists use these evolving networks to study active and fundamental topics within evolutionary ecology (e.g., the extent to which the architecture of multispecies networks shape coevolutionary outcomes, and the processes involved).}, } @article {pmid23532510, year = {2013}, author = {Wycisk, P and Stollberg, R and Neumann, C and Gossel, W and Weiss, H and Weber, R}, title = {Integrated methodology for assessing the HCH groundwater pollution at the multi-source contaminated mega-site Bitterfeld/Wolfen.}, journal = {Environmental science and pollution research international}, volume = {20}, number = {4}, pages = {1907-1917}, pmid = {23532510}, issn = {1614-7499}, mesh = {Chemical Industry ; Computer Simulation ; Environmental Monitoring/*methods ; Geographic Information Systems ; Germany ; Groundwater/*chemistry ; Hexachlorocyclohexane/*analysis ; Hydrology ; Industrial Waste/*analysis ; Models, Theoretical ; Water Pollutants, Chemical/*analysis ; Water Pollution, Chemical/*analysis ; }, abstract = {A large-scale groundwater contamination characterises the Pleistocene groundwater system of the former industrial and abandoned mining region Bitterfeld/Wolfen, Eastern Germany. For more than a century, local chemical production and extensive lignite mining caused a complex contaminant release from local production areas and related dump sites. Today, organic pollutants (mainly organochlorines) are present in all compartments of the environment at high concentration levels. An integrated methodology for characterising the current situation of pollution as well as the future fate development of hazardous substances is highly required to decide on further management and remediation strategies. Data analyses have been performed on regional groundwater monitoring data from about 10 years, containing approximately 3,500 samples, and up to 180 individual organic parameters from almost 250 observation wells. Run-off measurements as well as water samples were taken biweekly from local creeks during a period of 18 months. A kriging interpolation procedure was applied on groundwater analytics to generate continuous distribution patterns of the nodal contaminant samples. High-resolution geological 3-D modelling serves as a database for a regional 3-D groundwater flow model. Simulation results support the future fate assessment of contaminants. A first conceptual model of the contamination has been developed to characterise the contamination in regional surface waters and groundwater. A reliable explanation of the variant hexachlorocyclohexane (HCH) occurrence within the two local aquifer systems has been derived from the regionalised distribution patterns. Simulation results from groundwater flow modelling provide a better understanding of the future pollutant migration paths and support the overall site characterisation. The presented case study indicates that an integrated assessment of large-scale groundwater contaminations often needs more data than only from local groundwater monitoring. The developed methodology is appropriate to assess POP-contaminated mega-sites including, e.g. HCH deposits. Although HCH isomers are relevant groundwater pollutants at this site, further organochlorine pollutants are present at considerably higher levels. The study demonstrates that an effective evaluation of the current situation of contamination as well as of the related future fate development requires detailed information of the entire observed system.}, } @article {pmid23532294, year = {2013}, author = {Gonzaga, CM and Freitas-Junior, R and Barbaresco, AA and Martins, E and Bernardes, BT and Resende, AP}, title = {Cervical cancer mortality trends in Brazil: 1980-2009.}, journal = {Cadernos de saude publica}, volume = {29}, number = {3}, pages = {599-608}, doi = {10.1590/s0102-311x2013000300017}, pmid = {23532294}, issn = {1678-4464}, mesh = {Adult ; Aged ; Brazil/epidemiology ; Epidemiologic Methods ; Female ; Humans ; Information Systems ; Middle Aged ; Mortality/trends ; Uterine Cervical Neoplasms/*mortality ; Young Adult ; }, abstract = {The objective was to describe time trends in cervical cancer mortality rates in Brazil as a whole and in the country's major geographic regions and States from 1980 to 2009. This was an ecological time series study using data recorded in the Mortality Information System (SIM) and census data collected by the Brazilian Institute of Geography and Statistics (IBGE). Analysis of mortality trends was performed using Poisson regression. Cervical cancer mortality rates in Brazil tended to stabilize. In the geographic regions, a downward trend was observed in the South (-4.1%), Southeast (-3.3%), and Central-West (-1%) and an upward trend in the Northeast (3.5%) and North (2.7%). The largest decreases were observed in the States of São Paulo (-5.1%), Rio Grande do Sul, Espírito Santo, and Paraná (-4.0%). The largest increases in mortality trends occurred in Paraíba (12.4%), Maranhão (9.8%), and Tocantins (8.9%). Cervical cancer mortality rates stabilized in the country as a whole, but there was a downward trend in three geographic regions and 10 States, while two geographic regions and another 10 States showed increasing rates.}, } @article {pmid23530197, year = {2013}, author = {Duncan, RP and Boyer, AG and Blackburn, TM}, title = {Magnitude and variation of prehistoric bird extinctions in the Pacific.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {110}, number = {16}, pages = {6436-6441}, pmid = {23530197}, issn = {1091-6490}, mesh = {Animals ; Bayes Theorem ; *Biodiversity ; Birds/*physiology ; Databases, Factual ; *Extinction, Biological ; *Fossils ; Human Activities ; *Models, Biological ; Pacific Islands ; Phylogeography ; }, abstract = {The largest extinction event in the Holocene occurred on Pacific islands, where Late Quaternary fossils reveal the loss of thousands of bird populations following human colonization of the region. However, gaps in the fossil record mean that considerable uncertainty surrounds the magnitude and pattern of these extinctions. We use a Bayesian mark-recapture approach to model gaps in the fossil record and to quantify losses of nonpasserine landbirds on 41 Pacific islands. Two-thirds of the populations on these islands went extinct in the period between first human arrival and European contact, with extinction rates linked to island and species characteristics that increased susceptibility to hunting and habitat destruction. We calculate that human colonization of remote Pacific islands caused the global extinction of close to 1,000 species of nonpasserine landbird alone; nonpasserine seabird and passerine extinctions will add to this total.}, } @article {pmid23521844, year = {2013}, author = {, and Arranz, SE and Avarre, JC and Balasundaram, C and Bouza, C and Calcaterra, NB and Cezilly, F and Chen, SL and Cipriani, G and Cruz, VP and D'Esposito, D and Daniel, C and Dejean, A and Dharaneedharan, S and Díaz, J and Du, M and Durand, JD and Dziadek, J and Foresti, F and Peng-cheng, F and Gao, QB and García, G and Gauffre-Autelin, P and Giovino, A and Goswami, M and Guarino, C and Guerra-Varela, J and Gutiérrez, V and Harris, DJ and Heo, MS and Khan, G and Kim, M and Lakra, WS and Lauth, J and Leclercq, P and Lee, J and Lee, SH and Lee, S and Lee, T and Li, YH and Liu, H and Liu, S and Malé, PJ and Mandhan, RP and Martinez, P and Mayer, VE and Mendel, J and Mendes, NJ and Mendonça, FF and Minias, A and Minias, P and Oh, KS and Oliveira, C and Orivel, J and Orsini, L and Pardo, BG and Perera, A and Procaccini, G and Rato, C and Ríos, N and Scibetta, S and Sharma, BS and Sierens, T and Singh, A and Terer, T and Triest, L and Urbánková, S and Vera, M and Villanova, GV and Voglmayr, H and Vyskočilová, M and Wang, H and Wang, JL and Wattier, RA and Xing, R and Yadav, K and Yin, G and Yuan, Y and Yun, JC and Zhang, FQ and Zhang, JH and Zhuang, Z}, title = {Permanent genetic resources added to molecular ecology resources database 1 December 2012-31 January 2013.}, journal = {Molecular ecology resources}, volume = {13}, number = {3}, pages = {546-549}, doi = {10.1111/1755-0998.12095}, pmid = {23521844}, issn = {1755-0998}, mesh = {DNA Primers/genetics ; Databases, Genetic/*statistics & numerical data ; Microsatellite Repeats/*genetics ; Species Specificity ; }, abstract = {This article documents the addition of 268 microsatellite marker loci to the Molecular Ecology Resources Database. Loci were developed for the following species: Alburnoides bipunctatus, Chamaerops humilis, Chlidonias hybrida, Cyperus papyrus, Fusarium graminearum, Loxigilla barbadensis, Macrobrachium rosenbergii, Odontesthes bonariensis, Pelteobagrus vachelli, Posidonia oceanica, Potamotrygon motoro, Rhamdia quelen, Sarotherodon melanotheron heudelotii, Sibiraea angustata, Takifugu rubripes, Tarentola mauritanica, Trimmatostroma sp. and Wallago attu. These loci were cross-tested on the following species: Alburnoides fasciatus, Alburnoides kubanicus, Alburnoides maculatus, Alburnoides ohridanus, Alburnoides prespensis, Alburnoides rossicus, Alburnoides strymonicus, Alburnoides thessalicus, Alburnoides tzanevi, Carassius carassius, Fusarium asiaticum, Leucaspius delineatus, Loxigilla noctis dominica, Pelecus cultratus, Phoenix canariensis, Potamotrygon falkneri, Trachycarpus fortune and Vimba vimba.}, } @article {pmid23519314, year = {2013}, author = {Innocenti, P and Chenoweth, SF}, title = {Interspecific divergence of transcription networks along lines of genetic variance in Drosophila: dimensionality, evolvability, and constraint.}, journal = {Molecular biology and evolution}, volume = {30}, number = {6}, pages = {1358-1367}, doi = {10.1093/molbev/mst047}, pmid = {23519314}, issn = {1537-1719}, mesh = {Animals ; Databases, Genetic ; Drosophila/classification/*genetics ; *Evolution, Molecular ; Female ; *Gene Regulatory Networks ; *Genes, Insect ; Genetic Variation ; Male ; Models, Genetic ; Multivariate Analysis ; Species Specificity ; }, abstract = {Change in gene expression is a major facilitator of phenotypic evolution. Understanding the evolutionary potential of gene expression requires taking into account complex systems of regulatory networks, the structure of which could potentially bias evolutionary trajectories. We analyzed the evolutionary potential and divergence of multigene expression in three well-characterized signaling pathways in Drosophila, the mitogen-activated protein kinase (MapK), the Toll, and the insulin receptor/Foxo (InR/Foxo or InR/TOR) pathways in a multivariate quantitative genetic framework. Gene expression data from a natural population of D. melanogaster were used to estimate the genetic variance-covariance matrices (G) for each network. Although most genes within each pathway exhibited significant genetic variance, the number of independent dimensions of multivariate genetic variance was fewer than the number of genes analyzed. However, for expression, the reduction in dimensionality was not as large as seen for other trait types such as morphology. We then tested whether gene expression divergence between D. melanogaster and an additional six species of the Drosophila genus was biased along the major axes of standing variation observed in D. melanogaster. In many cases, divergence was restricted to directions of phenotypic space harboring above average levels of genetic variance in D. melanogaster, indicating that genetic covariances between genes within pathways have biased interspecific divergence. We tested whether co-expression of genes in both sexes has also biased the pattern of divergence. Including cross-sex genetic covariances increased the degree to which divergence was biased along major axes of genetic variance, suggesting that the co-expression of genes in males and females can generate further constraints on divergence across the Drosophila phylogeny. In contrast to patterns seen for morphological traits in vertebrates, transcriptional constraints do not appear to break down as divergence time between species increases, instead they persist over tens of millions of years of divergence.}, } @article {pmid23519313, year = {2013}, author = {Wang, Z and Wu, M}, title = {A phylum-level bacterial phylogenetic marker database.}, journal = {Molecular biology and evolution}, volume = {30}, number = {6}, pages = {1258-1262}, doi = {10.1093/molbev/mst059}, pmid = {23519313}, issn = {1537-1719}, mesh = {Bacteria/*classification/*genetics ; Computational Biology/*methods ; *Databases, Genetic ; *Genes, Bacterial ; Genetic Markers/*genetics ; Phenotype ; Phylogeny ; }, abstract = {Large-scale, genome-level molecular phylogenetic analyses present both opportunities and challenges for bacterial evolutionary and ecological studies. We constructed a phylum-level bacterial phylogenetic marker database by surveying all complete bacterial genomes and identifying single-copy genes that were widely distributed in each of the 20 bacterial phyla. We showed that phylum trees made using these markers were highly resolved and were more robust than the bacterial genome tree based on 31 universal bacterial marker genes. In addition, using the Global Ocean Sampling data set as an example, we demonstrated that the expanded marker database greatly increased the power of metagenomic phylotyping. We incorporated the database into an automated phylogenomic inference application (Phyla-AMPHORA) and made it publicly available. We believe that this centralized resource should have broad applicability in bacterial systematics, phylogenetics, and metagenomic studies.}, } @article {pmid23516388, year = {2013}, author = {Buttigieg, PL and Hankeln, W and Kostadinov, I and Kottmann, R and Yilmaz, P and Duhaime, MB and Glöckner, FO}, title = {Ecogenomic perspectives on domains of unknown function: correlation-based exploration of marine metagenomes.}, journal = {PloS one}, volume = {8}, number = {3}, pages = {e50869}, pmid = {23516388}, issn = {1932-6203}, mesh = {Cluster Analysis ; Computational Biology/methods ; Cyanobacteria/classification/genetics/metabolism ; *Ecosystem ; Iron/metabolism ; *Metagenome ; *Metagenomics ; Photosynthesis/physiology ; Protein Interaction Domains and Motifs/*physiology ; Seawater/*microbiology ; }, abstract = {BACKGROUND: The proportion of conserved DNA sequences with no clear function is steadily growing in bioinformatics databases. Studies of sequence and structural homology have indicated that many uncharacterized protein domain sequences are variants of functionally described domains. If these variants promote an organism's ecological fitness, they are likely to be conserved in the genome of its progeny and the population at large. The genetic composition of microbial communities in their native ecosystems is accessible through metagenomics. We hypothesize the co-variation of protein domain sequences across metagenomes from similar ecosystems will provide insights into their potential roles and aid further investigation.

We calculated the correlation of Pfam protein domain sequences across the Global Ocean Sampling metagenome collection, employing conservative detection and correlation thresholds to limit results to well-supported hits and associations. We then examined intercorrelations between domains of unknown function (DUFs) and domains involved in known metabolic pathways using network visualization and cluster-detection tools. We used a cautious "guilty-by-association" approach, referencing knowledge-level resources to identify and discuss associations that offer insight into DUF function. We observed numerous DUFs associated to photobiologically active domains and prevalent in the Cyanobacteria. Other clusters included DUFs associated with DNA maintenance and repair, inorganic nutrient metabolism, and sodium-translocating transport domains. We also observed a number of clusters reflecting known metabolic associations and cases that predicted functional reclassification of DUFs.

CONCLUSION/SIGNIFICANCE: Critically examining domain covariation across metagenomic datasets can grant new perspectives on the roles and associations of DUFs in an ecological setting. Targeted attempts at DUF characterization in the laboratory or in silico may draw from these insights and opportunities to discover new associations and corroborate existing ones will arise as more large-scale metagenomic datasets emerge.}, } @article {pmid23505972, year = {2013}, author = {Rajpurohit, S and Oliveira, CC and Etges, WJ and Gibbs, AG}, title = {Functional genomic and phenotypic responses to desiccation in natural populations of a desert drosophilid.}, journal = {Molecular ecology}, volume = {22}, number = {10}, pages = {2698-2715}, pmid = {23505972}, issn = {1365-294X}, support = {P20 GM103440/GM/NIGMS NIH HHS/United States ; P20 RR016464/RR/NCRR NIH HHS/United States ; 5P20RR016464-11/RR/NCRR NIH HHS/United States ; 8P20GM103440-11/GM/NIGMS NIH HHS/United States ; }, mesh = {Analysis of Variance ; Animals ; Body Weight ; Computational Biology ; Dehydration ; Desert Climate ; Drosophila/*genetics/metabolism/physiology ; Female ; Fertility/genetics ; Gene Expression Profiling ; Gene Expression Regulation/*physiology ; Hydrocarbons/*metabolism ; Male ; Mexico ; Microarray Analysis ; Molecular Sequence Annotation ; Mortality ; *Phenotype ; Species Specificity ; Time Factors ; }, abstract = {We used whole-transcriptome microarrays to assess changes in gene expression and monitored mortality rates and epicuticular hydrocarbons (CHCs) in response to desiccation stress in four natural populations of Drosophila mojavensis from Baja California and mainland Mexico. Desiccation had the greatest effect on gene expression, followed by biogeographical variation at regional and population levels. Genes involved in environmental sensing and cuticular structure were up-regulated in dry conditions, while genes involved in transcription itself were down-regulated. Flies from Baja California had higher expression of reproductive and mitochondrial genes, suggesting that these populations have greater fecundity and higher metabolic rates. Host plant differences had a surprisingly minor effect on the transcriptome. In most cases, desiccation-caused mortality was greater in flies reared on fermenting cactus tissues than that on laboratory media. Water content of adult females and males was significantly different and was lower in Baja California males. Different groups of CHCs simultaneously increased and decreased in amounts due to desiccation exposure of 9 and 18 h and were population-specific and dependent on larval rearing substrates. Overall, we observed that changes in gene expression involved a coordinated response of behavioural, cuticular and metabolic genes. Together with differential expression of cuticular hydrocarbons, this study revealed some of the mechanisms that have allowed D. mojavensis to exploit its harsh desert conditions. Certainly, for D. mojavensis that uses different host plants, population-level understanding of responses to stressors associated with future climate change in desert regions must be evaluated across geographical and local ecological scales.}, } @article {pmid23505408, year = {2013}, author = {Costello, MJ and Bouchet, P and Boxshall, G and Fauchald, K and Gordon, D and Hoeksema, BW and Poore, GC and van Soest, RW and Stöhr, S and Walter, TC and Vanhoorne, B and Decock, W and Appeltans, W}, title = {Global coordination and standardisation in marine biodiversity through the World Register of Marine Species (WoRMS) and related databases.}, journal = {PloS one}, volume = {8}, number = {1}, pages = {e51629}, pmid = {23505408}, issn = {1932-6203}, mesh = {Animals ; Aquatic Organisms/*classification ; *Biodiversity ; *Databases, Factual ; *Internet ; *Marine Biology ; }, abstract = {The World Register of Marine Species is an over 90% complete open-access inventory of all marine species names. Here we illustrate the scale of the problems with species names, synonyms, and their classification, and describe how WoRMS publishes online quality assured information on marine species. Within WoRMS, over 100 global, 12 regional and 4 thematic species databases are integrated with a common taxonomy. Over 240 editors from 133 institutions and 31 countries manage the content. To avoid duplication of effort, content is exchanged with 10 external databases. At present WoRMS contains 460,000 taxonomic names (from Kingdom to subspecies), 368,000 species level combinations of which 215,000 are currently accepted marine species names, and 26,000 related but non-marine species. Associated information includes 150,000 literature sources, 20,000 images, and locations of 44,000 specimens. Usage has grown linearly since its launch in 2007, with about 600,000 unique visitors to the website in 2011, and at least 90 organisations from 12 countries using WoRMS for their data management. By providing easy access to expert-validated content, WoRMS improves quality control in the use of species names, with consequent benefits to taxonomy, ecology, conservation and marine biodiversity research and management. The service manages information on species names that would otherwise be overly costly for individuals, and thus minimises errors in the application of nomenclature standards. WoRMS' content is expanding to include host-parasite relationships, additional literature sources, locations of specimens, images, distribution range, ecological, and biological data. Species are being categorised as introduced (alien, invasive), of conservation importance, and on other attributes. These developments have a multiplier effect on its potential as a resource for biodiversity research and management. As a consequence of WoRMS, we are witnessing improved communication within the scientific community, and anticipate increased taxonomic efficiency and quality control in marine biodiversity research and management.}, } @article {pmid23497587, year = {2013}, author = {Thomas, LF and de Glanville, WA and Cook, EA and Fèvre, EM}, title = {The spatial ecology of free-ranging domestic pigs (Sus scrofa) in western Kenya.}, journal = {BMC veterinary research}, volume = {9}, number = {}, pages = {46}, pmid = {23497587}, issn = {1746-6148}, support = {085308//Wellcome Trust/United Kingdom ; 095831//Wellcome Trust/United Kingdom ; //Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animal Husbandry ; Animals ; Ascariasis/epidemiology/veterinary ; Coccidiosis/epidemiology/veterinary ; Cysticercosis/epidemiology/veterinary ; Ecology ; Female ; Geographic Information Systems ; Kenya/epidemiology ; Male ; *Spatial Behavior ; Strongylida Infections/epidemiology/veterinary ; *Sus scrofa/parasitology/psychology ; Swine ; Swine Diseases/epidemiology/parasitology ; }, abstract = {BACKGROUND: In many parts of the developing world, pigs are kept under low-input systems where they roam freely to scavenge food. These systems allow poor farmers the opportunity to enter into livestock keeping without large capital investments. This, combined with a growing demand for pork, especially in urban areas, has led to an increase in the number of small-holder farmers keeping free range pigs as a commercial enterprise. Despite the benefits which pig production can bring to a household, keeping pigs under a free range system increases the risk of the pig acquiring diseases, either production-limiting or zoonotic in nature. This study used Global Positioning System (GPS) technology to track free range domestic pigs in rural western Kenya, in order to understand their movement patterns and interactions with elements of the peri-domestic environment.

RESULTS: We found that these pigs travel an average of 4,340 m in a 12 hr period and had a mean home range of 10,343 m(2) (range 2,937-32,759 m(2)) within which the core utilisation distribution was found to be 964 m(2) (range 246-3,289 m(2)) with pigs spending on average 47% of their time outside their homestead of origin.

CONCLUSION: These are the first data available on the home range of domestic pigs kept under a free range system: the data show that pigs in these systems spend much of their time scavenging outside their homesteads, suggesting that these pigs may be exposed to infectious agents over a wide area. Control policies for diseases such as Taenia solium, Trypanosomiasis, Trichinellosis, Toxoplasmosis or African Swine Fever therefore require a community-wide focus and pig farmers require education on the inherent risks of keeping pigs under a free range system. The work presented here will enable future research to incorporate movement data into studies of disease transmission, for example for the understanding of transmission of African Swine Fever between individuals, or in relation to the life-cycle of parasites including Taenia solium.}, } @article {pmid23497206, year = {2013}, author = {McPherson, H and van der Merwe, M and Delaney, SK and Edwards, MA and Henry, RJ and McIntosh, E and Rymer, PD and Milner, ML and Siow, J and Rossetto, M}, title = {Capturing chloroplast variation for molecular ecology studies: a simple next generation sequencing approach applied to a rainforest tree.}, journal = {BMC ecology}, volume = {13}, number = {}, pages = {8}, pmid = {23497206}, issn = {1472-6785}, mesh = {Australia ; Computational Biology ; DNA, Chloroplast/genetics ; DNA, Plant/genetics ; *Genome, Chloroplast ; Meliaceae/*genetics ; Molecular Sequence Data ; Phylogeography ; *Polymorphism, Single Nucleotide ; Sequence Analysis, DNA/*methods ; Trees/genetics ; }, abstract = {BACKGROUND: With high quantity and quality data production and low cost, next generation sequencing has the potential to provide new opportunities for plant phylogeographic studies on single and multiple species. Here we present an approach for in silicio chloroplast DNA assembly and single nucleotide polymorphism detection from short-read shotgun sequencing. The approach is simple and effective and can be implemented using standard bioinformatic tools.

RESULTS: The chloroplast genome of Toona ciliata (Meliaceae), 159,514 base pairs long, was assembled from shotgun sequencing on the Illumina platform using de novo assembly of contigs. To evaluate its practicality, value and quality, we compared the short read assembly with an assembly completed using 454 data obtained after chloroplast DNA isolation. Sanger sequence verifications indicated that the Illumina dataset outperformed the longer read 454 data. Pooling of several individuals during preparation of the shotgun library enabled detection of informative chloroplast SNP markers. Following validation, we used the identified SNPs for a preliminary phylogeographic study of T. ciliata in Australia and to confirm low diversity across the distribution.

CONCLUSIONS: Our approach provides a simple method for construction of whole chloroplast genomes from shotgun sequencing of whole genomic DNA using short-read data and no available closely related reference genome (e.g. from the same species or genus). The high coverage of Illumina sequence data also renders this method appropriate for multiplexing and SNP discovery and therefore a useful approach for landscape level studies of evolutionary ecology.}, } @article {pmid23496796, year = {2013}, author = {Mardulyn, P and Goffredo, M and Conte, A and Hendrickx, G and Meiswinkel, R and Balenghien, T and Sghaier, S and Lohr, Y and Gilbert, M}, title = {Climate change and the spread of vector-borne diseases: using approximate Bayesian computation to compare invasion scenarios for the bluetongue virus vector Culicoides imicola in Italy.}, journal = {Molecular ecology}, volume = {22}, number = {9}, pages = {2456-2466}, doi = {10.1111/mec.12264}, pmid = {23496796}, issn = {1365-294X}, mesh = {Animals ; *Bayes Theorem ; Bluetongue virus ; Ceratopogonidae/*genetics/virology ; *Climate Change ; Computational Biology ; France/epidemiology ; Genetic Loci ; Genetic Markers ; Genetic Variation ; Genotype ; Insect Vectors/*genetics/virology ; Italy/epidemiology ; Microsatellite Repeats ; Sheep ; }, abstract = {Bluetongue (BT) is a commonly cited example of a disease with a distribution believed to have recently expanded in response to global warming. The BT virus is transmitted to ruminants by biting midges of the genus Culicoides, and it has been hypothesized that the emergence of BT in Mediterranean Europe during the last two decades is a consequence of the recent colonization of the region by Culicoides imicola and linked to climate change. To better understand the mechanism responsible for the northward spread of BT, we tested the hypothesis of a recent colonization of Italy by C. imicola, by obtaining samples from more than 60 localities across Italy, Corsica, Southern France, and Northern Africa (the hypothesized source point for the recent invasion of C. imicola), and by genotyping them with 10 newly identified microsatellite loci. The patterns of genetic variation within and among the sampled populations were characterized and used in a rigorous approximate Bayesian computation framework to compare three competing historical hypotheses related to the arrival and establishment of C. imicola in Italy. The hypothesis of an ancient presence of the insect vector was strongly favoured by this analysis, with an associated P ≥ 99%, suggesting that causes other than the northward range expansion of C. imicola may have supported the emergence of BT in southern Europe. Overall, this study illustrates the potential of molecular genetic markers for exploring the assumed link between climate change and the spread of diseases.}, } @article {pmid23493255, year = {2013}, author = {Naggan Perl, T and Schmid, BG and Schwirz, J and Chipman, AD}, title = {The evolution of the knirps family of transcription factors in arthropods.}, journal = {Molecular biology and evolution}, volume = {30}, number = {6}, pages = {1348-1357}, doi = {10.1093/molbev/mst046}, pmid = {23493255}, issn = {1537-1719}, mesh = {Amino Acid Sequence ; Animals ; Arthropod Proteins/*genetics ; Arthropods/*genetics ; Conserved Sequence ; DNA-Binding Proteins/*genetics ; Databases, Genetic ; Evolution, Molecular ; Genes ; Molecular Sequence Data ; Phylogeny ; Sequence Alignment ; Transcription Factors/*genetics ; }, abstract = {The orphan nuclear receptor gene knirps and its relatives encode a small family of highly conserved proteins. We take advantage of the conservation of the family, using the recent prevalence of genomic data, to reconstruct its evolutionary history, identifying duplication events and tracing the intron-exon structure of the genes over evolution. Many arthropod species have two or three members of this family, but the orthology between members is unclear. We have analyzed the protein coding sequences of members of this family from 15 arthropod species covering all four main arthropod classes, including a total of 28 genes. All members of the family encode a highly conserved 94 amino acid core sequence, part of which is encoded by a single invariant exon. We find that many of the automated predictions of these genes contain errors, while some copies of the gene were not uncovered by automated pipelines, requiring manual corrections and curation. We use the coding sequences to present a phylogenetic analysis of the knirps family. Our analysis indicates that there was a duplication of a single ancestral gene in the lineage leading to insects, which gave rise to two paralogs, eagle and knirps-related. Descendants of this duplication can be identified by the presence or absence of a short protein-coding motif. Independent, lineage-specific duplications occurred in the two crustaceans we sampled. Within the insects, the knirps-related gene underwent further lineage-specific duplications, giving rise to--among others--the Drosophila gap gene knirps.}, } @article {pmid23487930, year = {2013}, author = {Wang, HB and Chen, WH and Li, XS and Li, SH and Yan, BL}, title = {[Isolation and identification of Marinobacter adhaerens HY-3 and its allelopathy on Skeletonema costatum].}, journal = {Huan jing ke xue= Huanjing kexue}, volume = {34}, number = {1}, pages = {145-149}, pmid = {23487930}, issn = {0250-3301}, mesh = {*Allelopathy ; Diatoms/*growth & development/*physiology ; Eutrophication ; Marine Biology ; Marinobacter/*isolation & purification/*physiology ; }, abstract = {UNLABELLED: The allelopathy between bacteria and algae is a very complicated physical and ecological phenomenon. A marine bacterium was isolated from the water of a shrimp and crab mix-culturing pond. By 16S rRNA analysis, it was identified as Marinobacter adhaerens HY-3. Skeletonema costatum, a common dominant species of red-tide microorganism in China, was chosen as the other research object. The allelopathic effect of Marinobacter adhaerens HY- 3 on S. costatum was studied. Using the growth mass of Skeletonema costatum and the content of chlorophyll a as the parameters, the effects of HY-3 on the growth and photosynthesis of Skeletonema costatum were studied after co-cultivation and addition of extracellular metabolites of HY-3. The results showed that the growth of S. costatum was inhibited when the concentration of the strain HY-3 was above 10(4), and the growth mass of the 10(4), 10(6) and 10(8) HY-3 group was 70%, 23% and 22% of the control group respectively on the 10th day, with the content of chlorophyll being 88%, 62% and 60% of the control group, respectively. Therefore, the suppression increased with increasing concentration of HY-3. However, addition of extracellular metabolites of HY-3 had no effect on the growth of S. costatum.

CONCLUSIONS: M. adhaerens HY-3 had certain allelopathy on S. costatum and affected its growth and photosynthesis. Moreover, interaction between M. adhaerens HY-3 and S. costatum was achieved by their direct contact and the extracellular metabolites did not contain allelopathy factors.}, } @article {pmid23487185, year = {2013}, author = {Rosikiewicz, M and Comte, A and Niknejad, A and Robinson-Rechavi, M and Bastian, FB}, title = {Uncovering hidden duplicated content in public transcriptomics data.}, journal = {Database : the journal of biological databases and curation}, volume = {2013}, number = {}, pages = {bat010}, pmid = {23487185}, issn = {1758-0463}, mesh = {*Databases, Genetic ; *Gene Expression Profiling ; Gene Expression Regulation ; Humans ; Oligonucleotide Array Sequence Analysis ; *Statistics as Topic ; }, abstract = {As part of the development of the database Bgee (a dataBase for Gene Expression Evolution), we annotate and analyse expression data from different types and different sources, notably Affymetrix data from GEO and ArrayExpress, and RNA-Seq data from SRA. During our quality control procedure, we have identified duplicated content in GEO and ArrayExpress, affecting ∼14% of our data: fully or partially duplicated experiments from independent data submissions, Affymetrix chips reused in several experiments, or reused within an experiment. We present here the procedure that we have established to filter such duplicates from Affymetrix data, and our procedure to identify future potential duplicates in RNA-Seq data.}, } @article {pmid23486178, year = {2012}, author = {Bustamante, P and Covarrubias, PC and Levicán, G and Katz, A and Tapia, P and Holmes, D and Quatrini, R and Orellana, O}, title = {ICE Afe 1, an actively excising genetic element from the biomining bacterium Acidithiobacillus ferrooxidans.}, journal = {Journal of molecular microbiology and biotechnology}, volume = {22}, number = {6}, pages = {399-407}, doi = {10.1159/000346669}, pmid = {23486178}, issn = {1660-2412}, mesh = {Acidithiobacillus/drug effects/*genetics ; Computational Biology ; Gene Expression ; *Gene Transfer, Horizontal ; *Interspersed Repetitive Sequences ; Mitomycin/metabolism ; Recombination, Genetic ; Transcriptional Activation/drug effects ; }, abstract = {Integrative conjugative elements (ICEs) are self-transferred mobile genetic elements that contribute to horizontal gene transfer. An ICE (ICEAfe1) was identified in the genome of Acidithiobacillus ferrooxidans ATCC 23270. Excision of the element and expression of relevant genes under normal and DNA-damaging growth conditions was analyzed. Bioinformatic tools and DNA amplification methods were used to identify and to assess the excision and expression of genes related to the mobility of the element. Both basal and mitomycin C-inducible excision as well as expression and induction of the genes for integration/excision are demonstrated, suggesting that ICEAfe1 is an actively excising SOS-regulated mobile genetic element. The presence of a complete set of genes encoding self-transfer functions that are induced in response to DNA damage caused by mitomycin C additionally suggests that this element is capable of conjugative transfer to suitable recipient strains. Transfer of ICEAfe1 may provide selective advantages to other acidophiles in this ecological niche through dissemination of gene clusters expressing transfer RNAs, CRISPRs, and exopolysaccharide biosynthesis enzymes, probably by modification of translation efficiency, resistance to bacteriophage infection and biofilm formation, respectively. These data open novel avenues of research on conjugative transformation of biotechnologically relevant microorganisms recalcitrant to genetic manipulation.}, } @article {pmid23485434, year = {2013}, author = {Gasser, RB}, title = {A perfect time to harness advanced molecular technologies to explore the fundamental biology of Toxocara species.}, journal = {Veterinary parasitology}, volume = {193}, number = {4}, pages = {353-364}, doi = {10.1016/j.vetpar.2012.12.031}, pmid = {23485434}, issn = {1873-2550}, mesh = {Animals ; *Computational Biology ; Dogs ; Genes, Mitochondrial/genetics ; Genetic Markers/genetics ; *Genetic Variation ; Genetics, Population ; Host-Parasite Interactions ; Humans ; Molecular Biology ; Public Health ; Systems Biology ; Toxocara/genetics/immunology/*physiology ; Toxocara canis/genetics/immunology/physiology ; Toxocariasis/epidemiology/immunology/*parasitology ; Zoonoses ; }, abstract = {Toxocarosis is of major canine health and socioeconomic importance worldwide. Although many studies have given insights into toxocarosis, to date, there has been limited exploration of the molecular biology, biochemistry, genetics, epidemiology and ecology of Toxocara species as well as parasite-host interactions using '-omic' technologies. The present article gives a background on Toxocara species and toxocarosis, describes molecular tools for specific identification and genetic analysis, and provides a prospective view of the benefits that advanced molecular technologies will have towards better understanding the parasites and disease. Tackling key biological questions employing a 'systems biology' approach should lead to new and improved strategies for the treatment, diagnosis and control of toxocarosis.}, } @article {pmid23481711, year = {2013}, author = {Zhu, W and Xu, C and Qian, X and Wei, H}, title = {Statistical analysis of the spatial-temporal distribution of aerosol extinction retrieved by micro-pulse lidar in Kashgar, China.}, journal = {Optics express}, volume = {21}, number = {3}, pages = {2531-2537}, doi = {10.1364/OE.21.002531}, pmid = {23481711}, issn = {1094-4087}, mesh = {Aerosols/*analysis ; Air Pollution/*analysis/*statistics & numerical data ; China ; *Data Interpretation, Statistical ; Environmental Monitoring/instrumentation/*methods/*statistics & numerical data ; *Lasers ; Spatio-Temporal Analysis ; }, abstract = {The spatial-temporal distribution of dust aerosol is important in climate model and ecological environment. An observation experiment of the aerosol vertical distribution in the low troposphere was made using the micro-pulse lidar system from Sept. 2008 to Aug. 2009 at the oasis city Kashgar, China, which is near the major dust source area of the Taklimakan desert. The monthly averaged temporal variation of aerosol extinction profiles are given in the paper. The profile of aerosol extinction coefficient suggested that the dust aerosol could be vertically transported from the ground level to the higher altitude of above 5 km around the source region, and the temporal distribution showed that the dust aerosol layer of a few hundred meters thick appeared in the seasons of early spring and summer near the ground surface.}, } @article {pmid23478154, year = {2013}, author = {Guilamo-Ramos, V and Jaccard, J and McCarthy, K and Quiñones, Z and Lushin, V and Skinner-Day, M and Padilla, M and Meisterlin, L}, title = {Taxonomy of Caribbean tourism alcohol venues: implications for HIV transmission.}, journal = {Drug and alcohol dependence}, volume = {132}, number = {1-2}, pages = {238-243}, pmid = {23478154}, issn = {1879-0046}, support = {R21 AA018078/AA/NIAAA NIH HHS/United States ; 1R21AA018078/AA/NIAAA NIH HHS/United States ; }, mesh = {Adult ; Alcohol Drinking/*epidemiology ; Alcoholic Beverages/statistics & numerical data ; Caribbean Region/epidemiology ; Cluster Analysis ; Condoms ; Data Interpretation, Statistical ; Dominican Republic/epidemiology ; Female ; HIV Infections/epidemiology/*transmission ; Homosexuality, Male/statistics & numerical data ; Humans ; Male ; Risk-Taking ; Sex Work/statistics & numerical data ; Sex Workers/statistics & numerical data ; Transsexualism ; Travel/*classification/statistics & numerical data ; }, abstract = {BACKGROUND: Tourism areas represent ecologies of heightened HIV vulnerability characterized by a disproportionate concentration of alcohol venues. Limited research has explored how alcohol venues facilitate HIV transmission.

METHODS: We spatially mapped locations of alcohol venues in a Dominican tourism town and conducted a venue-based survey of key informants (n=135) focused on three facets of alcohol venues: structural features, type of patrons, and HIV risk behaviors. Using latent class analysis, we identified evidence-based typologies of alcohol venues for each of the three facets. Focused contrasts identified the co-occurrence of classes of structural features, classes of types of patrons, and classes of HIV risk behavior, thus elaborating the nature of high risk venues.

RESULTS: We identified three categories of venue structural features, three for venue patrons, and five for HIV risk behaviors. Analysis revealed that alcohol venues with the greatest structural risks (e.g. sex work on-site with lack of HIV prevention services) were most likely frequented by the venue patron category characterized by high population-mixing between locals and foreign tourists, who were in turn most likely to engage in the riskiest behaviors.

CONCLUSION: Our results highlight the stratification of venue patrons into groups who engage in behaviors of varying risk in structural settings that vary in risk. The convergence of high-risk patron groups in alcohol venues with the greatest structural risk suggests these locations have potential for HIV transmission. Policymakers and prevention scientists can use these methods and data to target HIV prevention resources to identified priority areas.}, } @article {pmid23474377, year = {2013}, author = {Arslan, O and Çepni, MS and Etiler, N}, title = {Spatial analysis of perinatal mortality rates with geographic information systems in Kocaeli, Turkey.}, journal = {Public health}, volume = {127}, number = {4}, pages = {369-379}, doi = {10.1016/j.puhe.2012.12.009}, pmid = {23474377}, issn = {1476-5616}, mesh = {*Geographic Information Systems ; Humans ; *Perinatal Mortality ; Registries ; Risk Factors ; *Spatial Analysis ; Topography, Medical ; Turkey/epidemiology ; }, abstract = {OBJECTIVES: To determine the spatial patterns of perinatal mortality in Kocaeli, Turkey using geographic information systems (GIS); to examine whether regional differences exist for the period selected; and whether these differences are linked to regional risk factors.

STUDY DESIGN: Ecological research.

METHODS: Data were obtained from the linked birth-death records data registry maintained by Kocaeli Provincial Health Directorate. Mortality data are added to the geodatabase on a monthly basis. Spatial patterns of mortality rates were determined with GIS by mapping the case differences in the districts, and spatial autocorrelation was used to examine the spatial pattern of mortality rates in the region.

RESULTS: Various risk factors contributing to spatial variation of perinatal mortality were revealed in the region. Districts with high mortality rates were shown to be sensitive to these risk factors. The results of this study confirm the direct link between perinatal mortality and poor environmental conditions in the study region. The analyses applied in the study showed that some complex demographic and socio-economic factors should be associated with perinatal mortality rates to identify the geographic patterns of mortality.

CONCLUSIONS: Implementation of spatial tools within GIS for mortality data showed the efficiency of GIS in perinatal mortality surveillance. This study also demonstrated the capability and utility of GIS to clarify the geographical distribution of perinatal mortality rates in the study area.}, } @article {pmid23463502, year = {2013}, author = {Olson, DH and Aanensen, DM and Ronnenberg, KL and Powell, CI and Walker, SF and Bielby, J and Garner, TW and Weaver, G and , and Fisher, MC}, title = {Mapping the global emergence of Batrachochytrium dendrobatidis, the amphibian chytrid fungus.}, journal = {PloS one}, volume = {8}, number = {2}, pages = {e56802}, pmid = {23463502}, issn = {1932-6203}, support = {//Wellcome Trust/United Kingdom ; WT08972/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Amphibians/*microbiology ; Animals ; *Biodiversity ; *Chytridiomycota ; Communicable Diseases, Emerging/epidemiology/prevention & control/*veterinary ; Databases, Factual ; *Demography ; Dermatomycoses/epidemiology/prevention & control/*veterinary ; Geographic Mapping ; Internet ; Logistic Models ; *Models, Biological ; Species Specificity ; Temperature ; }, abstract = {The rapid worldwide emergence of the amphibian pathogen Batrachochytrium dendrobatidis (Bd) is having a profound negative impact on biodiversity. However, global research efforts are fragmented and an overarching synthesis of global infection data is lacking. Here, we provide results from a community tool for the compilation of worldwide Bd presence and report on the analyses of data collated over a four-year period. Using this online database, we analysed: 1) spatial and taxonomic patterns of infection, including amphibian families that appear over- and under-infected; 2) relationships between Bd occurrence and declining amphibian species, including associations among Bd occurrence, species richness, and enigmatic population declines; and 3) patterns of environmental correlates with Bd, including climate metrics for all species combined and three families (Hylidae, Bufonidae, Ranidae) separately, at both a global scale and regional (U.S.A.) scale. These associations provide new insights for downscaled hypothesis testing. The pathogen has been detected in 52 of 82 countries in which sampling was reported, and it has been detected in 516 of 1240 (42%) amphibian species. We show that detected Bd infections are related to amphibian biodiversity and locations experiencing rapid enigmatic declines, supporting the hypothesis that greater complexity of amphibian communities increases the likelihood of emergence of infection and transmission of Bd. Using a global model including all sampled species, the odds of Bd detection decreased with increasing temperature range at a site. Further consideration of temperature range, rather than maximum or minimum temperatures, may provide new insights into Bd-host ecology. Whereas caution is necessary when interpreting such a broad global dataset, the use of our pathogen database is helping to inform studies of the epidemiology of Bd, as well as enabling regional, national, and international prioritization of conservation efforts. We provide recommendations for adaptive management to enhance the database utility and relevance.}, } @article {pmid23463233, year = {2013}, author = {Barsoum, MJ and Sellers, PJ and Campbell, AM and Heyer, LJ and Paradise, CJ}, title = {Implementing recommendations for introductory biology by writing a new textbook.}, journal = {CBE life sciences education}, volume = {12}, number = {1}, pages = {106-116}, pmid = {23463233}, issn = {1931-7913}, support = {52006292//Howard Hughes Medical Institute/United States ; }, mesh = {Attitude ; Biology/*education/statistics & numerical data ; *Curriculum/statistics & numerical data ; Data Collection ; Data Interpretation, Statistical ; Educational Measurement ; Humans ; Knowledge ; Program Evaluation/statistics & numerical data ; *Textbooks as Topic ; *Writing ; }, abstract = {We redesigned the undergraduate introductory biology course by writing a new textbook (Integrating Concepts in Biology [ICB]) that follows first principles of learning. Our approach emphasizes primary data interpretation and the utility of mathematics in biology, while de-emphasizing memorization. This redesign divides biology into five big ideas (information, evolution, cells, emergent properties, homeostasis), addressing each at five levels of organization (molecules, cells, organisms, populations, ecological systems). We compared our course outcomes with two sections that used a traditional textbook and were taught by different instructors. On data interpretation assessments administered periodically during the semester, our students performed better than students in the traditional sections (p = 0.046) and exhibited greater improvement over the course of the semester (p = 0.015). On factual content assessments, our students performed similarly to students in the other sections (p = 0.737). Pre- and postsemester assessment of disciplinary perceptions and self-appraisal indicate that our students acquired a more accurate perception of biology as a discipline and may have developed a more realistic evaluation of their scientific abilities than did the control students (p < 0.05). We conclude that ICB improves critical thinking, metacognition, and disciplinary perceptions without compromising content knowledge in introductory biology.}, } @article {pmid23460886, year = {2013}, author = {Ascunce, MS and Toups, MA and Kassu, G and Fane, J and Scholl, K and Reed, DL}, title = {Nuclear genetic diversity in human lice (Pediculus humanus) reveals continental differences and high inbreeding among worldwide populations.}, journal = {PloS one}, volume = {8}, number = {2}, pages = {e57619}, pmid = {23460886}, issn = {1932-6203}, mesh = {Animals ; Cell Nucleus/*genetics ; Databases, Nucleic Acid ; Gene Flow/genetics ; Genetic Loci/genetics ; *Genetic Variation ; Genetics, Population ; *Geography ; Humans ; *Inbreeding ; Microsatellite Repeats/genetics ; Multigene Family/genetics ; Pediculus/*genetics ; Phylogeny ; Polymorphism, Genetic ; Selection, Genetic ; }, abstract = {Understanding the evolution of parasites is important to both basic and applied evolutionary biology. Knowledge of the genetic structure of parasite populations is critical for our ability to predict how an infection can spread through a host population and for the design of effective control methods. However, very little is known about the genetic structure of most human parasites, including the human louse (Pediculus humanus). This species is composed of two ecotypes: the head louse (Pediculus humanus capitis De Geer), and the clothing (body) louse (Pediculus humanus humanus Linnaeus). Hundreds of millions of head louse infestations affect children every year, and this number is on the rise, in part because of increased resistance to insecticides. Clothing lice affect mostly homeless and refugee-camp populations and although they are less prevalent than head lice, the medical consequences are more severe because they vector deadly bacterial pathogens. In this study we present the first assessment of the genetic structure of human louse populations by analyzing the nuclear genetic variation at 15 newly developed microsatellite loci in 93 human lice from 11 sites in four world regions. Both ecotypes showed heterozygote deficits relative to Hardy-Weinberg equilibrium and high inbreeding values, an expected pattern given their parasitic life history. Bayesian clustering analyses assigned lice to four distinct genetic clusters that were geographically structured. The low levels of gene flow among louse populations suggested that the evolution of insecticide resistance in lice would most likely be affected by local selection pressures, underscoring the importance of tailoring control strategies to population-specific genetic makeup and evolutionary history. Our panel of microsatellite markers provides powerful data to investigate not only ecological and evolutionary processes in lice, but also those in their human hosts because of the long-term coevolutionary association between lice and humans.}, } @article {pmid23458856, year = {2013}, author = {de Juan, D and Pazos, F and Valencia, A}, title = {Emerging methods in protein co-evolution.}, journal = {Nature reviews. Genetics}, volume = {14}, number = {4}, pages = {249-261}, pmid = {23458856}, issn = {1471-0064}, mesh = {Animals ; Computational Biology/*methods ; *Evolution, Molecular ; Humans ; Models, Genetic ; Models, Molecular ; Mutation ; Phylogeny ; *Protein Structure, Tertiary ; Proteins/*chemistry/classification/*genetics ; }, abstract = {Co-evolution is a fundamental component of the theory of evolution and is essential for understanding the relationships between species in complex ecological networks. A wide range of co-evolution-inspired computational methods has been designed to predict molecular interactions, but it is only recently that important advances have been made. Breakthroughs in the handling of phylogenetic information and in disentangling indirect relationships have resulted in an improved capacity to predict interactions between proteins and contacts between different protein residues. Here, we review the main co-evolution-based computational approaches, their theoretical basis, potential applications and foreseeable developments.}, } @article {pmid23458322, year = {2013}, author = {Peterson, EE and Ver Hoef, JM and Isaak, DJ and Falke, JA and Fortin, MJ and Jordan, CE and McNyset, K and Monestiez, P and Ruesch, AS and Sengupta, A and Som, N and Steel, EA and Theobald, DM and Torgersen, CE and Wenger, SJ}, title = {Modelling dendritic ecological networks in space: an integrated network perspective.}, journal = {Ecology letters}, volume = {16}, number = {5}, pages = {707-719}, doi = {10.1111/ele.12084}, pmid = {23458322}, issn = {1461-0248}, mesh = {*Ecology/methods ; Ecosystem ; Linear Models ; *Models, Biological ; *Models, Statistical ; *Rivers ; }, abstract = {Dendritic ecological networks (DENs) are a unique form of ecological networks that exhibit a dendritic network topology (e.g. stream and cave networks or plant architecture). DENs have a dual spatial representation; as points within the network and as points in geographical space. Consequently, some analytical methods used to quantify relationships in other types of ecological networks, or in 2-D space, may be inadequate for studying the influence of structure and connectivity on ecological processes within DENs. We propose a conceptual taxonomy of network analysis methods that account for DEN characteristics to varying degrees and provide a synthesis of the different approaches within the context of stream ecology. Within this context, we summarise the key innovations of a new family of spatial statistical models that describe spatial relationships in DENs. Finally, we discuss how different network analyses may be combined to address more complex and novel research questions. While our main focus is streams, the taxonomy of network analyses is also relevant anywhere spatial patterns in both network and 2-D space can be used to explore the influence of multi-scale processes on biota and their habitat (e.g. plant morphology and pest infestation, or preferential migration along stream or road corridors).}, } @article {pmid23456223, year = {2013}, author = {Jordan, G and Abdaal, A}, title = {Decision support methods for the environmental assessment of contamination at mining sites.}, journal = {Environmental monitoring and assessment}, volume = {185}, number = {9}, pages = {7809-7832}, pmid = {23456223}, issn = {1573-2959}, mesh = {Chemical Hazard Release/*statistics & numerical data ; *Decision Support Techniques ; Environment ; Environmental Monitoring/*methods ; Industrial Waste/statistics & numerical data ; *Mining ; }, abstract = {Polluting mine accidents and widespread environmental contamination associated with historic mining in Europe and elsewhere has triggered the improvement of related environmental legislation and of the environmental assessment and management methods for the mining industry. Mining has some unique features such as natural background pollution associated with natural mineral deposits, industrial activities and contamination located in the three-dimensional sub-surface space, the problem of long-term remediation after mine closure, problem of secondary contaminated areas around mine sites and abandoned mines in historic regions like Europe. These mining-specific problems require special tools to address the complexity of the environmental problems of mining-related contamination. The objective of this paper is to review and evaluate some of the decision support methods that have been developed and applied to mining contamination. In this paper, only those methods that are both efficient decision support tools and provide a 'holistic' approach to the complex problem as well are considered. These tools are (1) landscape ecology, (2) industrial ecology, (3) landscape geochemistry, (4) geo-environmental models, (5) environmental impact assessment, (6) environmental risk assessment, (7) material flow analysis and (8) life cycle assessment. This unique inter-disciplinary study should enable both the researcher and the practitioner to obtain broad view on the state-of-the-art of decision support methods for the environmental assessment of contamination at mine sites. Documented examples and abundant references are also provided.}, } @article {pmid23450659, year = {2013}, author = {Willner, D and Hugenholtz, P}, title = {From deep sequencing to viral tagging: recent advances in viral metagenomics.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {35}, number = {5}, pages = {436-442}, doi = {10.1002/bies.201200174}, pmid = {23450659}, issn = {1521-1878}, mesh = {Bacteria/virology ; Computational Biology ; DNA, Viral/chemistry/*genetics ; *Genome, Viral ; High-Throughput Nucleotide Sequencing/instrumentation/*methods ; Host-Pathogen Interactions ; *Metagenomics ; Staining and Labeling/instrumentation/methods ; Viruses/*genetics ; }, abstract = {Culture-independent high-throughput sequencing has provided unprecedented insights into microbial ecology, particularly for Earth's most ubiquitous and diverse inhabitants - the viruses. A plethora of methods now exist for amplifying the vanishingly small amounts of nucleic acids in natural viral communities in order to sequence them, and sequencing depth is now so great that viral genomes can be detected and assembled even amid large concentrations of non-viral DNA. Complementing these advances in amplification and sequencing is the ability to physically link fluorescently labeled viruses to their host cells via high-throughput flow sorting. Sequencing of such isolated virus-host pairs facilitates cultivation-independent exploration of the natural host range of viruses. Within the next decade, as these technologies become widespread, we can expect to see a systematic expansion of our knowledge of viruses and their hosts.}, } @article {pmid23450193, year = {2013}, author = {Raymann, K and Bobay, LM and Doak, TG and Lynch, M and Gribaldo, S}, title = {A genomic survey of Reb homologs suggests widespread occurrence of R-bodies in proteobacteria.}, journal = {G3 (Bethesda, Md.)}, volume = {3}, number = {3}, pages = {505-516}, pmid = {23450193}, issn = {2160-1836}, mesh = {Bacterial Physiological Phenomena ; Bacterial Proteins/*genetics ; Databases, Genetic ; Evolution, Molecular ; *Genome, Bacterial ; Molecular Sequence Data ; Phylogeny ; Protein Structure, Secondary ; Proteobacteria/classification/*genetics/physiology ; Sequence Analysis, Protein ; Sequence Homology, Amino Acid ; Species Specificity ; Symbiosis ; Synteny ; }, abstract = {Bacteria and eukaryotes are involved in many types of interaction in nature, with important ecological consequences. However, the diversity, occurrence, and mechanisms of these interactions often are not fully known. The obligate bacterial endosymbionts of Paramecium provide their hosts with the ability to kill sensitive Paramecium strains through the production of R-bodies, highly insoluble coiled protein ribbons. R-bodies have been observed in a number of free-living bacteria, where their function is unknown. We have performed an exhaustive survey of genes coding for homologs of Reb proteins (R-body components) in complete bacterial genomes. We found that reb genes are much more widespread than previously thought, being present in representatives of major Proteobacterial subdivisions, including many free-living taxa, as well as taxa known to be involved in various kinds of interactions with eukaryotes, from mutualistic associations to pathogenicity. Reb proteins display very good conservation at the sequence level, suggesting that they may produce functional R-bodies. Phylogenomic analysis indicates that reb genes underwent a complex evolutionary history and allowed the identification of candidates potentially involved in R-body assembly, functioning, regulation, or toxicity. Our results strongly suggest that the ability to produce R-bodies is likely widespread in Proteobacteria. The potential involvement of R-bodies in as yet unexplored interactions with eukaryotes and the consequent ecological implications are discussed.}, } @article {pmid23445951, year = {2013}, author = {Haase, D and Roth, O and Kalbe, M and Schmiedeskamp, G and Scharsack, JP and Rosenstiel, P and Reusch, TB}, title = {Absence of major histocompatibility complex class II mediated immunity in pipefish, Syngnathus typhle: evidence from deep transcriptome sequencing.}, journal = {Biology letters}, volume = {9}, number = {2}, pages = {20130044}, pmid = {23445951}, issn = {1744-957X}, mesh = {Animals ; Behavior, Animal ; Biological Evolution ; Cloning, Molecular ; Computational Biology ; Expressed Sequence Tags ; Fishes/genetics/*immunology/microbiology ; *Gene Expression Profiling ; Gene Library ; *Genes, MHC Class II ; Gills/immunology/microbiology/pathology ; High-Throughput Nucleotide Sequencing ; Species Specificity ; Transcriptome ; Vibrio/immunology/pathogenicity ; Vibrio Infections/immunology/microbiology/*veterinary ; }, abstract = {The major histocompatibility complex (MHC)-mediated adaptive immune system is the hallmark of gnathostome immune defence. Recent work suggests that cod-like fishes (Gadidae) lack important components of the MHC class II mediated immunity. Here, we report a putative independent loss of functionality of this pathway in another species, the pipefish Syngnathus typhle, that belongs to a distantly related fish family (Syngnathidae). In a deep transcriptome sequencing approach comprising several independent normalized and non-normalized expressed sequence tag (EST) libraries with approximately 7.5 × 10(8) reads, sequenced with two next generation platforms (454 and Illumina), we were unable to identify MHC class IIα/β genes as well as genes encoding associated receptors. Along with the recent findings in cod, our results suggest that immune systems of the Euteleosts may be more variable than previously assumed.}, } @article {pmid23437888, year = {2013}, author = {Pérez-Porro, AR and Navarro-Gómez, D and Uriz, MJ and Giribet, G}, title = {A NGS approach to the encrusting Mediterranean sponge Crella elegans (Porifera, Demospongiae, Poecilosclerida): transcriptome sequencing, characterization and overview of the gene expression along three life cycle stages.}, journal = {Molecular ecology resources}, volume = {13}, number = {3}, pages = {494-509}, doi = {10.1111/1755-0998.12085}, pmid = {23437888}, issn = {1755-0998}, mesh = {Animals ; Base Sequence ; Computational Biology ; Gene Expression Profiling ; Gene Expression Regulation, Developmental/*genetics ; High-Throughput Nucleotide Sequencing ; Life Cycle Stages/*genetics ; Molecular Sequence Annotation ; Molecular Sequence Data ; Porifera/*genetics/growth & development ; Spectrophotometry, Ultraviolet ; }, abstract = {Sponges can be dominant organisms in many marine and freshwater habitats where they play essential ecological roles. They also represent a key group to address important questions in early metazoan evolution. Recent approaches for improving knowledge on sponge biological and ecological functions as well as on animal evolution have focused on the genetic toolkits involved in ecological responses to environmental changes (biotic and abiotic), development and reproduction. These approaches are possible thanks to newly available, massive sequencing technologies-such as the Illumina platform, which facilitate genome and transcriptome sequencing in a cost-effective manner. Here we present the first NGS (next-generation sequencing) approach to understanding the life cycle of an encrusting marine sponge. For this we sequenced libraries of three different life cycle stages of the Mediterranean sponge Crella elegans and generated de novo transcriptome assemblies. Three assemblies were based on sponge tissue of a particular life cycle stage, including non-reproductive tissue, tissue with sperm cysts and tissue with larvae. The fourth assembly pooled the data from all three stages. By aggregating data from all the different life cycle stages we obtained a higher total number of contigs, contigs with blast hit and annotated contigs than from one stage-based assemblies. In that multi-stage assembly we obtained a larger number of the developmental regulatory genes known for metazoans than in any other assembly. We also advance the differential expression of selected genes in the three life cycle stages to explore the potential of RNA-seq for improving knowledge on functional processes along the sponge life cycle.}, } @article {pmid23437004, year = {2013}, author = {Thornton, KR and Foran, AJ and Long, AD}, title = {Properties and modeling of GWAS when complex disease risk is due to non-complementing, deleterious mutations in genes of large effect.}, journal = {PLoS genetics}, volume = {9}, number = {2}, pages = {e1003258}, pmid = {23437004}, issn = {1553-7404}, support = {R01 GM085183/GM/NIGMS NIH HHS/United States ; R01 GM085251/GM/NIGMS NIH HHS/United States ; R01 RR024862/RR/NCRR NIH HHS/United States ; }, mesh = {Alleles ; Databases, Genetic ; Genetic Linkage ; *Genetic Predisposition to Disease ; *Genome-Wide Association Study ; Haplotypes ; Humans ; Linkage Disequilibrium/genetics ; *Models, Genetic ; Polymorphism, Single Nucleotide/genetics ; }, abstract = {Current genome-wide association studies (GWAS) have high power to detect intermediate frequency SNPs making modest contributions to complex disease, but they are underpowered to detect rare alleles of large effect (RALE). This has led to speculation that the bulk of variation for most complex diseases is due to RALE. One concern with existing models of RALE is that they do not make explicit assumptions about the evolution of a phenotype and its molecular basis. Rather, much of the existing literature relies on arbitrary mapping of phenotypes onto genotypes obtained either from standard population-genetic simulation tools or from non-genetic models. We introduce a novel simulation of a 100-kilobase gene region, based on the standard definition of a gene, in which mutations are unconditionally deleterious, are continuously arising, have partially recessive and non-complementing effects on phenotype (analogous to what is widely observed for most Mendelian disorders), and are interspersed with neutral markers that can be genotyped. Genes evolving according to this model exhibit a characteristic GWAS signature consisting of an excess of marginally significant markers. Existing tests for an excess burden of rare alleles in cases have low power while a simple new statistic has high power to identify disease genes evolving under our model. The structure of linkage disequilibrium between causative mutations and significantly associated markers under our model differs fundamentally from that seen when rare causative markers are assumed to be neutral. Rather than tagging single haplotypes bearing a large number of rare causative alleles, we find that significant SNPs in a GWAS tend to tag single causative mutations of small effect relative to other mutations in the same gene. Our results emphasize the importance of evaluating the power to detect associations under models that are genetically and evolutionarily motivated.}, } @article {pmid23433634, year = {2013}, author = {Gastin, PB and McLean, O and Spittle, M and Breed, RV}, title = {Quantification of tackling demands in professional Australian football using integrated wearable athlete tracking technology.}, journal = {Journal of science and medicine in sport}, volume = {16}, number = {6}, pages = {589-593}, doi = {10.1016/j.jsams.2013.01.007}, pmid = {23433634}, issn = {1878-1861}, mesh = {Accelerometry ; Adult ; Australia ; Biomechanical Phenomena ; Football/*physiology ; Geographic Information Systems ; Humans ; Male ; Young Adult ; }, abstract = {OBJECTIVES: To describe and quantify the frequency, velocity and acceleration at impact during tackling in Australian football using a combination of video and athlete tracking technology.

DESIGN: Quasi-experimental.

METHODS: Data was collected from twenty professional Australian Football League players during four in-season matches. All tackles made by the player and those against the player were video-coded and time stamped at the point of contact and then subjectively categorised into low, medium and high intensity impact groups. Peak GPS and acceleration data were identified at the point of contact. Two-way analysis of variance was used to assess differences (p<0.05) between tackle type (made and against) and tackle intensity.

RESULTS: A total of 173 tackles made and 179 tackles against were recorded. Significant differences were found between all tackle intensity groups. Peak velocity was significantly greater in high (19.5±6.1 k mh(-1)) compared to medium (13.4±5.8 k mh(-1)) and low intensity (11.3±5.0 k mh(-1)) tackles. Peak Player Load, a modified vector magnitude of tri-axial acceleration, was significantly greater in high (7.5±1.7 a.u.) compared to medium (4.9±1.5 a.u.) and low intensity (4.0±1.3 a.u.) tackles.

CONCLUSIONS: High intensity tackles, although less frequent, are significantly greater in speed of movement immediately prior to contact and in the resultant impact acceleration compared to tackles of lower intensity. Differences in accelerometer data between tackles observed to be progressively greater in intensity suggest a level of ecological validity and provide preliminary support for the use of accelerometers to assess impact forces in contact invasion sports.}, } @article {pmid23433376, year = {2013}, author = {Vangay, P and Fugett, EB and Sun, Q and Wiedmann, M}, title = {Food microbe tracker: a web-based tool for storage and comparison of food-associated microbes.}, journal = {Journal of food protection}, volume = {76}, number = {2}, pages = {283-294}, doi = {10.4315/0362-028X.JFP-12-276}, pmid = {23433376}, issn = {1944-9097}, support = {N01-A1-30054//PHS HHS/United States ; }, mesh = {Bacterial Typing Techniques ; DNA, Bacterial/analysis/isolation & purification ; Databases, Factual ; *Databases, Genetic ; Food Contamination/analysis ; *Food Microbiology ; Internet ; *Public Health ; }, abstract = {Large amounts of molecular subtyping information are generated by the private sector, academia, and government agencies. However, use of subtype data is limited by a lack of effective data storage and sharing mechanisms that allow comparison of subtype data from multiple sources. Currently available subtype databases are generally limited in scope to a few data types (e.g., MLST. net) or are not publicly available (e.g., PulseNet). We describe the development and initial implementation of Food Microbe Tracker, a public Web-based database that allows archiving and exchange of a variety of molecular subtype data that can be cross-referenced with isolate source data, genetic data, and phenotypic characteristics. Data can be queried with a variety of search criteria, including DNA sequences and banding pattern data (e.g., ribotype or pulsed-field gel electrophoresis type). Food Microbe Tracker allows the deposition of data on any bacterial genus and species, bacteriophages, and other viruses. The bacterial genera and species that currently have the most entries in this database are Listeria monocytogenes, Salmonella, Streptococcus spp., Pseudomonas spp., Bacillus spp., and Paenibacillus spp., with over 40,000 isolates. The combination of pathogen and spoilage microorganism data in the database will facilitate source tracking and outbreak detection, improve discovery of emerging subtypes, and increase our understanding of transmission and ecology of these microbes. Continued addition of subtyping, genetic or phenotypic data for a variety of microbial species will broaden the database and facilitate large-scale studies on the diversity of food-associated microbes.}, } @article {pmid23431807, year = {2012}, author = {Sun, YG and Zhao, DZ and Zhang, FS and Wei, BQ and Chu, JL and Su, X}, title = {[Spatiotemporal dynamic fuzzy evaluation of wetland environmental pollution risk in Dayang estuary of Liaoning Province, Northeast China based on remote sensing].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {23}, number = {11}, pages = {3180-3186}, pmid = {23431807}, issn = {1001-9332}, mesh = {China ; Environmental Monitoring/*methods ; Environmental Pollution/*analysis ; Estuaries ; Fuzzy Logic ; Geographic Information Systems ; Human Activities ; *Remote Sensing Technology ; Risk Assessment ; Rivers ; Spatio-Temporal Analysis ; *Wetlands ; }, abstract = {Based on the aerial image data of Dayang estuary in 2008, and by virtue of Analytic Hierarchy Process (AHP) , remote sensing technology, and GIS spatial analysis, a spatiotemporal evaluation was made on the comprehensive level of wetland environmental pollution risk in Dayang estuary, with the impacts of typical human activities on the dynamic variation of this comprehensive level discussed. From 1958 to 2008, the comprehensive level of the environmental pollution risk in study area presented an increasing trend. Spatially, this comprehensive level declined from land to ocean, and showed a zonal distribution. Tourism development activities unlikely led to the increase of the comprehensive level, while human inhabitation, transportation, and aquaculture would exacerbate the risk of environmental pollution. This study could provide reference for the sea area use planning, ecological function planning, and pollutants control of estuary region.}, } @article {pmid23431801, year = {2012}, author = {Sun, XP and Wang, TM and Wu, JG and Ge, JP}, title = {[Change trend of vegetation cover in Beijing metropolitan region before and after the 2008 Olympics].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {23}, number = {11}, pages = {3133-3140}, pmid = {23431801}, issn = {1001-9332}, mesh = {China ; Cities ; *Conservation of Natural Resources ; Crops, Agricultural/growth & development ; *Ecosystem ; Environmental Monitoring/methods ; Geographic Information Systems ; Poaceae/growth & development ; *Remote Sensing Technology ; Satellite Communications ; Sports ; Trees/*growth & development ; }, abstract = {The MODIS-NDVI data from 2000 to 2009 were used to analyze the temporal dynamics and spatial distribution of the vegetation cover in the Beijing metropolitan region before and after the 2008 Olympics. During the study period, the proportion of the significantly increased pixels of NDVI occupied 20.7% while that of the significantly decreased pixels only occupied 4.1% of the total, and the decreasing rate of the NDVI was slightly faster than the increasing rate. The significant changes of the NDVI were mainly concentrated in the low altitude and small slope areas with intensive human activities, and two bands were formed in the plain area, i. e., the vegetation increasing band within the 5th Ring Road and the vegetation decreasing band from the 5th Ring Road to the outside areas of the 6th Ring Road. In the areas with significant vegetation change, there was an obvious transition between the high and low NDVI sections but less change in the medium NDVI section, mainly due to the conversion of land cover type. In the Capital function core area and ecological conservation zones, vegetation change represented a positive trend; while in the urban function expansion area and urban development area, vegetation change had the dual characteristics of both positive and negative trends. A series of ecological engineering projects during the preparatory period of the 2008 Olympics was the main cause of the vegetation increase in the study area.}, } @article {pmid23430580, year = {2014}, author = {Sugimoto-Matsuda, JJ and Braun, KL}, title = {The role of collaboration in facilitating policy change in youth violence prevention: a review of the literature.}, journal = {Prevention science : the official journal of the Society for Prevention Research}, volume = {15}, number = {2}, pages = {194-204}, pmid = {23430580}, issn = {1573-6695}, support = {U54 MD007584/MD/NIMHD NIH HHS/United States ; }, mesh = {Adolescent ; Community Health Services/organization & administration ; Community Networks/*organization & administration ; *Cooperative Behavior ; Female ; Humans ; Juvenile Delinquency/*prevention & control ; Male ; Primary Prevention/*organization & administration ; Social Change ; Social Work/organization & administration ; Violence/*prevention & control ; }, abstract = {Youth violence remains a serious public health issue nationally and internationally. The social ecological model has been recommended as a framework to design youth violence prevention initiatives, requiring interventions at the micro-, meso-, exo-, and macro-levels. However, documentation of interventions at the macro-level, particularly those that address policy issues, is limited. This study examines a recommendation in the literature that formalized collaborations play a vital role in stimulating macro-level policy change. The purpose of this systematic literature review is to examine existing youth violence prevention collaborations and evaluate their policy-related outcomes. The search found 23 unique collaborations focused on youth violence prevention. These were organized into three groups based on the "catalyst" for action for the collaboration-internal (momentum began within the community), external (sparked by an external agency), or policy (mandated by law). Findings suggest that internally catalyzed collaborations were most successful at changing laws to address youth violence, while both internally and externally catalyzed collaborations successfully attained policy change at the organizational level. A conceptual model is proposed, describing a potential pathway for achieving macro-level change via collaboration. Recommendations for future research and practice are suggested, including expansion of this study to capture additional collaborations, investigation of macro-level changes with a primary prevention focus, and improvement of evaluation, dissemination, and translation of macro-level initiatives.}, } @article {pmid23428518, year = {2012}, author = {Palaniyandi, M}, title = {The role of remote sensing and GIS for spatial prediction of vector-borne diseases transmission: a systematic review.}, journal = {Journal of vector borne diseases}, volume = {49}, number = {4}, pages = {197-204}, pmid = {23428518}, issn = {0972-9062}, mesh = {Animals ; Communicable Diseases/parasitology/*transmission/virology ; Geographic Information Systems/*statistics & numerical data ; Geographic Mapping ; Humans ; Insect Vectors/parasitology/*physiology ; Remote Sensing Technology/*methods ; Risk Assessment ; Seasons ; }, abstract = {There have been several attempts made to the appreciation of remote sensing and GIS for the study of vectors, biodiversity, vector presence, vector abundance and the vector-borne diseases with respect to space and time. This study was made for reviewing and appraising the potential use of remote sensing and GIS applications for spatial prediction of vector-borne diseases transmission. The nature of the presence and the abundance of vectors and vector-borne diseases, disease infection and the disease transmission are not ubiquitous and are confined with geographical, environmental and climatic factors, and are localized. The presence of vectors and vector-borne diseases is most complex in nature, however, it is confined and fueled by the geographical, climatic and environmental factors including man-made factors. The usefulness of the present day availability of the information derived from the satellite data including vegetation indices of canopy cover and its density, soil types, soil moisture, soil texture, soil depth, etc. is integrating the information in the expert GIS engine for the spatial analysis of other geoclimatic and geoenvironmental variables. The present study gives the detailed information on the classical studies of the past and present, and the future role of remote sensing and GIS for the vector-borne diseases control. The ecological modeling directly gives us the relevant information to understand the spatial variation of the vector biodiversity, vector presence, vector abundance and the vector-borne diseases in association with geoclimatic and the environmental variables. The probability map of the geographical distribution and seasonal variations of horizontal and vertical distribution of vector abundance and its association with vector -borne diseases can be obtained with low cost remote sensing and GIS tool with reliable data and speed.}, } @article {pmid23425437, year = {2013}, author = {Sartorius, K and Sartorius, BK}, title = {A spatial model to quantify the mortality impact of service delivery in Sub-Saharan Africa: an ecological design utilizing data from South Africa.}, journal = {International journal of health geographics}, volume = {12}, number = {}, pages = {8}, pmid = {23425437}, issn = {1476-072X}, mesh = {Africa South of the Sahara/epidemiology ; Bayes Theorem ; *Databases, Factual/statistics & numerical data ; Delivery of Health Care/*economics/statistics & numerical data ; Environmental Monitoring/*methods ; Humans ; Mortality/*trends ; South Africa/epidemiology ; }, abstract = {BACKGROUND: Sub Saharan Africa is confronted with a wide range of interlinked health and economic problems that include high levels of mortality and poor service delivery. The objective of the paper is to develop a spatial model for Sub-Saharan Africa that can quantify the mortality impact of (poor) service delivery at sub-district level in order to integrate related health and local level policy interventions. In this regard, an expanded composite service delivery index was developed, and the data were analysed using a Bayesian Poisson spatial model.

RESULTS: The results indicate significant differences in the risk of mortality and poor service delivery at sub-district level. In particular, the results indicate clusters of high mortality and poor service delivery in two of the bigger, poorer provinces with large rural communities. Conversely, two of the wealthier provinces have lower levels of mortality and higher levels of service delivery, but income inequality is more widespread. The bivariate and multivariate models, moreover, reflect significant positive linkages (p < 0.01) between increased mortality and poor service delivery after adjusting for HIV/AIDS, income inequality, population density and the protective influence of metropolitan areas. Finally, the hypothesized provision of a basket of services reduced the mortality rate in South Africa's 248 sub-districts by an average of 5.3 (0.3-15.4) deaths per 1000.

CONCLUSION: The results indicate that the model can accurately plot mortality and service delivery "hotspots' at sub-district level, as well as explain their associations and causality. A mortality reduction index shows that mortality in the highest risk sub-districts can be reduced by as much as 15.4 deaths per 1000 by providing a range of basic services. The ability to use the model in a wider SSA context and elsewhere is also feasible given the innovative use of available databases. Finally, the paper illustrates the importance of developing policy in SSA that can simultaneously solve both economic and health problems.}, } @article {pmid23424850, year = {2012}, author = {Tîrlã, L}, title = {Elaboration of climatic maps using GIS. Case study: Olãnesti drainage basin, Romania.}, journal = {Journal of environmental biology}, volume = {33}, number = {2 Suppl}, pages = {449-454}, pmid = {23424850}, issn = {0254-8704}, mesh = {*Climate ; *Geographic Information Systems ; Geological Phenomena ; *Rivers ; Romania ; Water Movements ; }, abstract = {Creating precise climatic maps (temperature and precipitation map especially) on small areas such as drainage basins or landform units is always very useful for ecology of plants, distribution of vegetation and also different types of agricultural land. The geographic information system (GIS) analysis of several key-factors (aspect and slope of terrain, insolation degree, thermal gradient, geology and structure of landforms) offers the necessary tools to operate with in order to create an accurate climatic map. This method was applied in order to create a map showing the distribution of temperatures in the Olanesti drainages basin, a 235 km2 area located at middle latitude, in Romania. After creating the DEM, aspect and slope of the terrain, reclassifying categories and calculating the thermal gradient, a map showing the distribution of the annual mean temperature is obtained. Other climatic parameters could be calculated for small areas too, with precise results. These demonstrate that not only elevation and mathematical location of an area are important factors in the distribution of temperature, but also the aspect, the gradient, the insolation, the type of rock and the structure.}, } @article {pmid23424642, year = {2013}, author = {Fernandez-Silva, I and Whitney, J and Wainwright, B and Andrews, KR and Ylitalo-Ward, H and Bowen, BW and Toonen, RJ and Goetze, E and Karl, SA}, title = {Microsatellites for next-generation ecologists: a post-sequencing bioinformatics pipeline.}, journal = {PloS one}, volume = {8}, number = {2}, pages = {e55990}, pmid = {23424642}, issn = {1932-6203}, mesh = {Animals ; Computational Biology/*methods ; Data Mining ; Databases, Genetic ; *Ecology ; Fishes/genetics ; Genetic Loci/genetics ; Microsatellite Repeats/*genetics ; *Sequence Analysis ; Starfish/genetics ; }, abstract = {Microsatellites are the markers of choice for a variety of population genetic studies. The recent advent of next-generation pyrosequencing has drastically accelerated microsatellite locus discovery by providing a greater amount of DNA sequencing reads at lower costs compared to other techniques. However, laboratory testing of PCR primers targeting potential microsatellite markers remains time consuming and costly. Here we show how to reduce this workload by screening microsatellite loci via bioinformatic analyses prior to primer design. Our method emphasizes the importance of sequence quality, and we avoid loci associated with repetitive elements by screening with repetitive sequence databases available for a growing number of taxa. Testing with the Yellowstripe Goatfish Mulloidichthys flavolineatus and the marine planktonic copepod Pleuromamma xiphias we show higher success rate of primers selected by our pipeline in comparison to previous in silico microsatellite detection methodologies. Following the same pipeline, we discover and select microsatellite loci in nine additional species including fishes, sea stars, copepods and octopuses.}, } @article {pmid23413125, year = {2013}, author = {Kördel, W and Garelick, H and Gawlik, BM and Kandile, NG and Peijnenburg, WJ and Rüdel, H}, title = {Substance-related environmental monitoring strategies regarding soil, groundwater and surface water - an overview.}, journal = {Environmental science and pollution research international}, volume = {20}, number = {5}, pages = {2810-2827}, pmid = {23413125}, issn = {1614-7499}, mesh = {Environmental Monitoring/legislation & jurisprudence/*methods ; Environmental Pollution/analysis/*legislation & jurisprudence ; Fresh Water/analysis ; Groundwater/analysis ; Seawater/analysis ; Soil/analysis ; Soil Pollutants/*analysis ; Water Pollutants/*analysis ; }, abstract = {Substance-related monitoring is an essential tool within environmental risk assessment processes. The soundness of policy decisions including risk management measures is often directly related to the reliability of the environmental monitoring programs. In addition, monitoring programs are required for identifying new and less-investigated pollutants of concern in different environmental media. Scientifically sound and feasible monitoring concepts strongly depend on the aim of the study. The proper definition of questions to be answered is thus of pivotal importance. Decisions on sample handling, storage and the analysis of the samples are important steps for the elaboration of problem-oriented monitoring strategies. The same applies to the selection of the sampling sites as being representative for scenarios to be investigated. These steps may become critical to handle for larger international monitoring programs and thus trigger the quality of their results. This study based on the work of an IUPAC (International Union of Pure and Applied Chemistry) task group addresses different kinds and approaches of substance-related monitoring of different compartments of soil, groundwater and surface water, and discusses their advantages and limitations. Further important aspects are the monitoring across policies and the monitoring data management using information systems.}, } @article {pmid23409735, year = {2013}, author = {Rushworth, AM and Bowman, AW and Brewer, MJ and Langan, SJ}, title = {Distributed lag models for hydrological data.}, journal = {Biometrics}, volume = {69}, number = {2}, pages = {537-544}, doi = {10.1111/biom.12008}, pmid = {23409735}, issn = {1541-0420}, mesh = {Biometry/*methods ; Data Interpretation, Statistical ; Hydrology/*statistics & numerical data ; *Models, Statistical ; Rain ; Rivers ; Scotland ; Time Factors ; }, abstract = {The distributed lag model (DLM), used most prominently in air pollution studies, finds application wherever the effect of a covariate is delayed and distributed through time. We specify modified formulations of DLMs to provide computationally attractive, flexible varying-coefficient models that are applicable in any setting in which lagged covariates are regressed on a time-dependent response. We investigate the application of such models to rainfall and river flow and in particular their role in understanding the impact of hidden variables at work in river systems. We apply two models to data from a Scottish mountain river, and we fit to some simulated data to check the efficacy of our model approach. During heavy rainfall conditions, changes in the influence of rainfall on flow arise through a complex interaction between antecedent ground wetness and a time-delay in rainfall. The models identify subtle changes in responsiveness to rainfall, particularly in the location of peak influence in the lag structure.}, } @article {pmid23408602, year = {2013}, author = {Oliveira, H and Melo, LD and Santos, SB and Nóbrega, FL and Ferreira, EC and Cerca, N and Azeredo, J and Kluskens, LD}, title = {Molecular aspects and comparative genomics of bacteriophage endolysins.}, journal = {Journal of virology}, volume = {87}, number = {8}, pages = {4558-4570}, pmid = {23408602}, issn = {1098-5514}, mesh = {Bacteriophages/*enzymology ; Computational Biology ; Endopeptidases/*genetics/*metabolism ; Hydrolysis ; Peptidoglycan/metabolism ; Phylogeny ; Sequence Homology, Amino Acid ; Viral Proteins/genetics/metabolism ; }, abstract = {Phages are recognized as the most abundant and diverse entities on the planet. Their diversity is determined predominantly by their dynamic adaptation capacities when confronted with different selective pressures in an endless cycle of coevolution with a widespread group of bacterial hosts. At the end of the infection cycle, progeny virions are confronted with a rigid cell wall that hinders their release into the environment and the opportunity to start a new infection cycle. Consequently, phages encode hydrolytic enzymes, called endolysins, to digest the peptidoglycan. In this work, we bring to light all phage endolysins found in completely sequenced double-stranded nucleic acid phage genomes and uncover clues that explain the phage-endolysin-host ecology that led phages to recruit unique and specialized endolysins.}, } @article {pmid23407591, year = {2012}, author = {Wommack, KE and Bhavsar, J and Polson, SW and Chen, J and Dumas, M and Srinivasiah, S and Furman, M and Jamindar, S and Nasko, DJ}, title = {VIROME: a standard operating procedure for analysis of viral metagenome sequences.}, journal = {Standards in genomic sciences}, volume = {6}, number = {3}, pages = {427-439}, pmid = {23407591}, issn = {1944-3277}, abstract = {One consistent finding among studies using shotgun metagenomics to analyze whole viral communities is that most viral sequences show no significant homology to known sequences. Thus, bioinformatic analyses based on sequence collections such as GenBank nr, which are largely comprised of sequences from known organisms, tend to ignore a majority of sequences within most shotgun viral metagenome libraries. Here we describe a bioinformatic pipeline, the Viral Informatics Resource for Metagenome Exploration (VIROME), that emphasizes the classification of viral metagenome sequences (predicted open-reading frames) based on homology search results against both known and environmental sequences. Functional and taxonomic information is derived from five annotated sequence databases which are linked to the UniRef 100 database. Environmental classifications are obtained from hits against a custom database, MetaGenomes On-Line, which contains 49 million predicted environmental peptides. Each predicted viral metagenomic ORF run through the VIROME pipeline is placed into one of seven ORF classes, thus, every sequence receives a meaningful annotation. Additionally, the pipeline includes quality control measures to remove contaminating and poor quality sequence and assesses the potential amount of cellular DNA contamination in a viral metagenome library by screening for rRNA genes. Access to the VIROME pipeline and analysis results are provided through a web-application interface that is dynamically linked to a relational back-end database. The VIROME web-application interface is designed to allow users flexibility in retrieving sequences (reads, ORFs, predicted peptides) and search results for focused secondary analyses.}, } @article {pmid23402594, year = {2013}, author = {Cozzi, G and Broekhuis, F and McNutt, JW and Schmid, B}, title = {Comparison of the effects of artificial and natural barriers on large African carnivores: implications for interspecific relationships and connectivity.}, journal = {The Journal of animal ecology}, volume = {82}, number = {3}, pages = {707-715}, doi = {10.1111/1365-2656.12039}, pmid = {23402594}, issn = {1365-2656}, mesh = {*Animal Distribution ; Animals ; Botswana ; Carnivora/*physiology ; *Conservation of Natural Resources ; Ecosystem ; Geographic Information Systems ; *Predatory Behavior ; Spatial Analysis ; Species Specificity ; }, abstract = {1. Physical barriers contribute to habitat fragmentation, influence species distribution and ranging behaviour, and impact long-term population viability. Barrier permeability varies among species and can potentially impact the competitive balance within animal communities by differentially affecting co-occurring species. The influence of barriers on the spatial distribution of species within whole communities has nonetheless received little attention. 2. During a 4-year period, we studied the influence of a fence and rivers, two landscape features that potentially act as barriers on space use and ranging behaviour of lions Panthera leo, spotted hyenas Crocuta crocuta, African wild dogs Lycaon pictus and cheetahs Acinonyx jubatus in Northern Botswana. We compared the tendencies of these species to cross the barriers using data generated from GPS-radio collars fitted to a total of 35 individuals. Barrier permeability was inferred by calculating the number of times animals crossed a barrier vs. the number of times they did not cross. Finally, based on our results, we produced a map of connectivity for the broader landscape system. 3. Permeability varied significantly between fence and rivers and among species. The fence represented an obstacle for lions (permeability = 7.2%), while it was considerably more permeable for hyenas (35.6%) and wild dogs and cheetahs (≥ 50%). In contrast, the rivers and associated floodplains were relatively permeable to lions (14.4%) while they represented a nearly impassable obstacle for the other species (<2%). 4. The aversion of lions to cross the fence resulted in a relatively lion-free habitat patch on one side of the fence, which might provide a potential refuge for other species. For instance, the competitively inferior wild dogs used this refuge significantly more intensively than the side of the fence with a high presence of lions. 5. We showed that the influence of a barrier on the distribution of animals could potentially result in a broad-scale modification of community structure and ecology within a guild of co-occurring species. As habitat fragmentation increases, understanding the impact of barriers on species distributions is thus essential for the implementation of landscape-scale management strategies, the development and maintenance of corridors and the enhancement of connectivity.}, } @article {pmid23399467, year = {2013}, author = {Modarai, F and Mack, K and Hicks, P and Benoit, S and Park, S and Jones, C and Proescholdbell, S and Ising, A and Paulozzi, L}, title = {Relationship of opioid prescription sales and overdoses, North Carolina.}, journal = {Drug and alcohol dependence}, volume = {132}, number = {1-2}, pages = {81-86}, doi = {10.1016/j.drugalcdep.2013.01.006}, pmid = {23399467}, issn = {1879-0046}, mesh = {Analgesics, Opioid/economics/*supply & distribution ; Cluster Analysis ; Commerce ; Data Interpretation, Statistical ; Drug Overdose/*epidemiology ; Humans ; Linear Models ; North Carolina/epidemiology ; Population Density ; Prescription Drugs/economics/*supply & distribution ; Rural Population ; Urban Population ; }, abstract = {BACKGROUND: In the United States, fatal drug overdoses have tripled since 1991. This escalation in deaths is believed to be driven primarily by prescription opioid medications. This investigation compared trends and patterns in sales of opioids, opioid drug overdoses treated in emergency departments (EDs), and unintentional overdose deaths in North Carolina (NC).

METHODS: Our ecological study compared rates of opioid sales, opioid related ED overdoses, and unintentional drug overdose deaths in NC. Annual sales data, provided by the Drug Enforcement Administration, for select opioids were converted into morphine equivalents and aggregated by zip code. These opioid drug sales rates were trended from 1997 to 2010. In addition, opioid sales were correlated and compared to opioid related ED visits, which came from a Centers for Disease Control and Prevention syndromic surveillance system, and unintentional overdose deaths, which came from NC Vital Statistics, from 2008 to 2010. Finally, spatial cluster analysis was performed and rates were mapped by zip code in 2010.

RESULTS: Opioid sales increased substantially from 1997 to 2010. From 2008 to 2010, the quarterly rates of opioid drug overdoses treated in EDs and opioid sales correlated (r=0.68, p=0.02). Specific regions of the state, particularly in the southern and western corners, had both high rates of prescription opioid sales and overdoses.

CONCLUSIONS: Temporal trends in sales of prescription opioids correlate with trends in opioid related ED visits. The spatial correlation of opioid sales with ED visit rates shows that opioid sales data may be a timely way to identify high-risk communities in the absence of timely ED data.}, } @article {pmid23368516, year = {2013}, author = {Durno, WE and Hanson, NW and Konwar, KM and Hallam, SJ}, title = {Expanding the boundaries of local similarity analysis.}, journal = {BMC genomics}, volume = {14 Suppl 1}, number = {Suppl 1}, pages = {S3}, pmid = {23368516}, issn = {1471-2164}, mesh = {Algorithms ; Computational Biology ; Female ; Humans ; Internet ; Intestines/microbiology ; Male ; Metagenome ; Mouth/microbiology ; Saccharomyces cerevisiae/genetics ; Skin/microbiology ; *Software ; User-Computer Interface ; }, abstract = {BACKGROUND: Pairwise comparison of time series data for both local and time-lagged relationships is a computationally challenging problem relevant to many fields of inquiry. The Local Similarity Analysis (LSA) statistic identifies the existence of local and lagged relationships, but determining significance through a p-value has been algorithmically cumbersome due to an intensive permutation test, shuffling rows and columns and repeatedly calculating the statistic. Furthermore, this p-value is calculated with the assumption of normality -- a statistical luxury dissociated from most real world datasets.

RESULTS: To improve the performance of LSA on big datasets, an asymptotic upper bound on the p-value calculation was derived without the assumption of normality. This change in the bound calculation markedly improved computational speed from O(pm²n) to O(m²n), where p is the number of permutations in a permutation test, m is the number of time series, and n is the length of each time series. The bounding process is implemented as a computationally efficient software package, FASTLSA, written in C and optimized for threading on multi-core computers, improving its practical computation time. We computationally compare our approach to previous implementations of LSA, demonstrate broad applicability by analyzing time series data from public health, microbial ecology, and social media, and visualize resulting networks using the Cytoscape software.

CONCLUSIONS: The FASTLSA software package expands the boundaries of LSA allowing analysis on datasets with millions of co-varying time series. Mapping metadata onto force-directed graphs derived from FASTLSA allows investigators to view correlated cliques and explore previously unrecognized network relationships. The software is freely available for download at: http://www.cmde.science.ubc.ca/hallam/fastLSA/.}, } @article {pmid23391811, year = {2013}, author = {Sagris, V and Wojda, P and Milenov, P and Devos, W}, title = {The harmonised data model for assessing Land Parcel Identification Systems compliance with requirements of direct aid and agri-environmental schemes of the CAP.}, journal = {Journal of environmental management}, volume = {118}, number = {}, pages = {40-48}, doi = {10.1016/j.jenvman.2012.12.019}, pmid = {23391811}, issn = {1095-8630}, mesh = {Agriculture/*legislation & jurisprudence ; Conservation of Natural Resources/*methods ; Environmental Policy/*legislation & jurisprudence ; European Union ; *Geographic Information Systems ; *Government Regulation ; Models, Theoretical ; }, abstract = {The EU Common Agricultural Policy (CAP) subsidies to farmers are administered through dedicated information systems, a part of which is the GIS-based Land Parcel Identification System (LPIS). The requirement to map and record land eligible for payments has led to a situation where the agricultural administrations have acquired a large amount of geographic data. As the geospatial community of data producers, custodians and users has grown during the last decades, so has the need to assess the quality and consistency of the LPIS towards the EU regulations on the CAP as well as for cross compliance with environmental legislation. In view of this, a LPIS Conceptual Model (LCM) is presented in this paper in order to address harmonisation and data quality needs. The ISO 19100 series standards on geoinformatics were used for LCM development, including an UML modelling approach and the handling of the quality of geographical information. This paper describes the core elements of the LCM and their integration with data supporting management of agri-environment schemes. Later, the paper shows how the LCM is used for conformity and quality checks of the member states' LPIS system; an Abstract Test Suite (ATS) for mapping the LCM model against existing system implementations was developed and tested in collaboration with several member states.}, } @article {pmid23389537, year = {2013}, author = {Jansson, JK and Prosser, JI}, title = {Microbiology: The life beneath our feet.}, journal = {Nature}, volume = {494}, number = {7435}, pages = {40-41}, pmid = {23389537}, issn = {1476-4687}, mesh = {*Data Mining ; Ecology/methods ; Geologic Sediments/*microbiology ; Metagenome/*genetics ; *Models, Biological ; Sequence Analysis, DNA ; *Soil Microbiology ; }, } @article {pmid23387123, year = {2012}, author = {Gonzalez-Mirelis, G and Lindegarth, M}, title = {Predicting the distribution of out-of-reach biotopes with decision trees in a Swedish marine protected area.}, journal = {Ecological applications : a publication of the Ecological Society of America}, volume = {22}, number = {8}, pages = {2248-2264}, doi = {10.1890/11-1608.1}, pmid = {23387123}, issn = {1051-0761}, mesh = {Animals ; Conservation of Natural Resources/*methods ; Demography ; *Ecosystem ; Fishes/*physiology ; Geographic Information Systems ; *Models, Biological ; Oceans and Seas ; Sweden ; }, abstract = {Through spatially explicit predictive models, knowledge of spatial patterns of biota can be generated for out-of-reach environments, where there is a paucity of survey data. This knowledge is invaluable for conservation decisions. We used distribution modeling to predict the occurrence of benthic biotopes, or megafaunal communities of the seabed, to support the spatial planning of a marine national park. Nine biotope classes were obtained prior to modeling from multivariate species data derived from point source, underwater imagery. Five map layers relating to depth and terrain were used as predictor variables. Biotope type was predicted on a pixel-by-pixel basis, where pixel size was 15 x 15 m and total modeled area was 455 km2. To choose a suitable modeling technique we compared the performance of five common models based on recursive partitioning: two types of classification and regression trees ([1] pruned by 10-fold cross-validation and [2] pruned by minimizing complexity), random forests, conditional inference (CI) trees, and CI forests. The selected model was a CI forest (an ensemble of CI trees), a machine-learning technique whose discriminatory power (class-by-class area under the curve [AUC] ranged from 0.75 to 0.86) and classification accuracy (72%) surpassed those of the other methods tested. Conditional inference trees are virtually new to the field of ecology. The final model's overall prediction error was 28%. Model predictions were also checked against a custom-built measure of dubiousness, calculated at the polygon level. Key factors other than the choice of modeling technique include: the use of a multinomial response, accounting for the heterogeneity of observations, and spatial autocorrelation. To illustrate how the model results can be implemented in spatial planning, representation of biodiversity in the national park was described and quantified. Given a goal of maximizing classification accuracy, we conclude that conditional inference trees are a promising tool to map biota. Species distribution modeling is presented as an ecological tool that can handle a wide variety of systems (e.g., the benthic system).}, } @article {pmid23387119, year = {2012}, author = {Sheldon, F and Peterson, EE and Boone, EL and Sippel, S and Bunn, SE and Harch, BD}, title = {Identifying the spatial scale of land use that most strongly influences overall river ecosystem health score.}, journal = {Ecological applications : a publication of the Ecological Society of America}, volume = {22}, number = {8}, pages = {2188-2203}, doi = {10.1890/11-1792.1}, pmid = {23387119}, issn = {1051-0761}, mesh = {Animals ; Climate ; Conservation of Natural Resources ; *Ecosystem ; Fishes/physiology ; Geographic Information Systems ; Human Activities ; Queensland ; Rain ; *Rivers ; Seasons ; Trees ; }, abstract = {Catchment and riparian degradation has resulted in declining ecosystem health of streams worldwide. With restoration a priority in many regions, there is an increasing interest in the scale at which land use influences stream ecosystem health. Our goal was to use a substantial data set collected as part of a monitoring program (the Southeast Queensland, Australia, Ecological Health Monitoring Program data set, collected at 116 sites over six years) to identify the spatial scale of land use, or the combination of spatial scales, that most strongly influences overall ecosystem health. In addition, we aimed to determine whether the most influential scale differed for different aspects of ecosystem health. We used linear-mixed models and a Bayesian model-averaging approach to generate models for the overall aggregated ecosystem health score and for each of the five component indicators (fish, macroinvertebrates, water quality, nutrients, and ecosystem processes) that make up the score. Dense forest close to the survey site, mid-dense forest in the hydrologically active near-stream areas of the catchment, urbanization in the riparian buffer, and tree cover at the reach scale were all significant in explaining ecosystem health, suggesting an overriding influence of forest cover, particularly close to the stream. Season and antecedent rainfall were also important explanatory variables, with some land-use variables showing significant seasonal interactions. There were also differential influences of land use for each of the component indicators. Our approach is useful given that restoring general ecosystem health is the focus of many stream restoration projects; it allowed us to predict the scale and catchment position of restoration that would result in the greatest improvement of ecosystem health in the regions streams and rivers. The models we generated suggested that good ecosystem health can be maintained in catchments where 80% of hydrologically active areas in close proximity to the stream have mid-dense forest cover and moderate health can be obtained with 60% cover.}, } @article {pmid23386120, year = {2013}, author = {Munn, AJ and Dawson, TJ and McLeod, SR and Dennis, T and Maloney, SK}, title = {Energy, water and space use by free-living red kangaroos Macropus rufus and domestic sheep Ovis aries in an Australian rangeland.}, journal = {Journal of comparative physiology. B, Biochemical, systemic, and environmental physiology}, volume = {183}, number = {6}, pages = {843-858}, pmid = {23386120}, issn = {1432-136X}, mesh = {Animals ; Australia ; Deuterium ; Ecology ; Energy Metabolism/*physiology ; Environment ; Female ; Geographic Information Systems ; Macropodidae/blood/*physiology/urine ; Osmolar Concentration ; Oxygen Isotopes ; Sheep, Domestic/blood/*physiology/urine ; Water/*metabolism ; }, abstract = {We used doubly labelled water to measure field metabolic rates (FMR) and water turnover rates (WTR) in one of Australia's largest native herbivores, the red kangaroo (Macropus rufus) and one of Australia's dominant livestock species, the wool-breed Merino sheep, under free-living conditions in a typical Australian rangeland. Also, we used GPS technology to examine animal space use, along with the comparisons of urine concentration, diet, diet digestibility, and subsequent grazing pressures. We found smaller space-use patterns than previously reported for kangaroos, which were between 14 and 25 % those of sheep. The FMR of a 25-kg kangaroo was 30 % that of a 45-kg sheep, while WTR was 15 % and both were associated with smaller travel distances, lower salt intakes, and higher urine concentration in kangaroos than sheep. After accounting for differences in dry matter digestibility of food eaten by kangaroos (51 %) and sheep (58 %), the relative grazing pressure of a standard (mature, non-reproductive) 25-kg kangaroo was 35 % that of a 45-kg sheep. Even for animals of the same body mass (35 kg), the relative grazing pressure of the kangaroo was estimated to be only 44 % that of the sheep. After accounting for the energetic costs of wool growth by sheep, the FMRs of our sheep and kangaroos were 2-3 times their expected BMRs, which is typical for mammalian FMR:BMRs generally. Notably, data collected from our free-living animals were practically identical to those from animals confined to a semi-natural enclosure (collected in an earlier study under comparable environmental conditions), supporting the idea that FMRs are relatively constrained within species.}, } @article {pmid23385958, year = {2013}, author = {Golka, K and Ickstadt, K and Selinski, S and Hengstler, JG and Wilhelm, M}, title = {Second symposium on Environmental Toxicology in North Rhine-Westphalia, Germany-interdisciplinary research activities in toxicology, statistics, hygiene and medicine: meeting report on a symposium held in Dortmund May 19-20, 2011.}, journal = {Archives of toxicology}, volume = {87}, number = {3}, pages = {555-561}, doi = {10.1007/s00204-013-1014-8}, pmid = {23385958}, issn = {1432-0738}, mesh = {Animals ; Biomedical Research/*statistics & numerical data ; *Cooperative Behavior ; Data Interpretation, Statistical ; Ecotoxicology/*statistics & numerical data ; Environmental Exposure ; Environmental Pollutants/*adverse effects ; Gene Expression Regulation/drug effects ; Genome-Wide Association Study/statistics & numerical data ; Germany/epidemiology ; Humans ; *Hygiene ; *Interdisciplinary Communication ; Mutagenicity Tests/statistics & numerical data ; Occupational Diseases/*chemically induced/epidemiology/genetics ; Occupational Exposure ; Risk Assessment ; }, } @article {pmid23382431, year = {2013}, author = {Hay, SI and Battle, KE and Pigott, DM and Smith, DL and Moyes, CL and Bhatt, S and Brownstein, JS and Collier, N and Myers, MF and George, DB and Gething, PW}, title = {Global mapping of infectious disease.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {368}, number = {1614}, pages = {20120250}, pmid = {23382431}, issn = {1471-2970}, support = {/WT_/Wellcome Trust/United Kingdom ; 095066/WT_/Wellcome Trust/United Kingdom ; MR/K00669X/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Biosurveillance/methods ; Communicable Diseases/*epidemiology ; Computational Biology/methods/*trends ; Crowdsourcing/methods ; *Geographic Mapping ; Global Health/*statistics & numerical data ; Humans ; }, abstract = {The primary aim of this review was to evaluate the state of knowledge of the geographical distribution of all infectious diseases of clinical significance to humans. A systematic review was conducted to enumerate cartographic progress, with respect to the data available for mapping and the methods currently applied. The results helped define the minimum information requirements for mapping infectious disease occurrence, and a quantitative framework for assessing the mapping opportunities for all infectious diseases. This revealed that of 355 infectious diseases identified, 174 (49%) have a strong rationale for mapping and of these only 7 (4%) had been comprehensively mapped. A variety of ambitions, such as the quantification of the global burden of infectious disease, international biosurveillance, assessing the likelihood of infectious disease outbreaks and exploring the propensity for infectious disease evolution and emergence, are limited by these omissions. An overview of the factors hindering progress in disease cartography is provided. It is argued that rapid improvement in the landscape of infectious diseases mapping can be made by embracing non-conventional data sources, automation of geo-positioning and mapping procedures enabled by machine learning and information technology, respectively, in addition to harnessing labour of the volunteer 'cognitive surplus' through crowdsourcing.}, } @article {pmid23381971, year = {2013}, author = {Kaazke, J and Meneses, M and Wilke, BM and Rotter, VS}, title = {Environmental evaluation of waste treatment scenarios for the towns Khanty-Mansiysk and Surgut, Russia.}, journal = {Waste management & research : the journal of the International Solid Wastes and Public Cleansing Association, ISWA}, volume = {31}, number = {3}, pages = {315-326}, doi = {10.1177/0734242X12473792}, pmid = {23381971}, issn = {1096-3669}, mesh = {Decision Support Techniques ; *Environment ; Incineration ; Siberia ; Solid Waste/analysis ; Waste Management/*methods ; Water Pollutants, Chemical ; }, abstract = {Khanty-Mansiysk Autonomous Okrug - Ugra in Siberia has recently started to play a major role in the Russian economy because key oil and gas extraction sites are located in this region. As a result, the extensions of infrastructure and higher incomes have been leading to an accelerated population growth and consequent increase in the generation of solid household waste. The current methods of waste disposal have now reached their limits, especially in the towns Khanty-Mansiysk and Surgut. The key objectives of this study were to identify the influence of waste composition and transport routes on the life cycle assessment (LCA) results and to assess the current waste treatment option for solid household waste and to compare it with proposed scenarios. Furthermore, recommendations for an optimal use of LCA within a decision-making process for a waste management plan are presented. LCA methodology was used to evaluate different waste management scenarios such as landfilling and incineration. One result was that the options 'incineration with recycling' and 'anaerobic mechanical-biological treatment with recycling' demonstrated lower environmental impact in both Khanty-Mansiysk and Surgut. Another finding was that there were hardly any differences in the ranking of the scenarios for Surgut and Khanty-Mansiysk. However, the special socio-cultural circumstances and location of each town have to be considered seriously in the development of a sustainable waste management plan.}, } @article {pmid23373871, year = {2013}, author = {Fienen, MN}, title = {We speak for the data.}, journal = {Ground water}, volume = {51}, number = {2}, pages = {157}, doi = {10.1111/gwat.12018}, pmid = {23373871}, issn = {1745-6584}, mesh = {Hydrology/*trends ; Informatics ; Models, Theoretical ; }, } @article {pmid23373607, year = {2012}, author = {Jovanovski, D and Zakzanis, K and Ruttan, L and Campbell, Z and Erb, S and Nussbaum, D}, title = {Ecologically valid assessment of executive dysfunction using a novel virtual reality task in patients with acquired brain injury.}, journal = {Applied neuropsychology. Adult}, volume = {19}, number = {3}, pages = {207-220}, doi = {10.1080/09084282.2011.643956}, pmid = {23373607}, issn = {2327-9109}, mesh = {Adult ; Aged ; Brain Injuries/*psychology ; Cognition/physiology ; Computers ; Data Interpretation, Statistical ; Educational Status ; Executive Function/*physiology ; Female ; Frontal Lobe/physiology ; Glasgow Coma Scale ; Humans ; Intelligence Tests ; Male ; Mental Recall/physiology ; Middle Aged ; Neuropsychological Tests ; Observer Variation ; Psychomotor Performance/*physiology ; Reproducibility of Results ; Stroke/psychology ; Surveys and Questionnaires ; *User-Computer Interface ; Wechsler Scales ; }, abstract = {The current investigation sought to further establish the psychometric properties and ecological validity of the Multitasking in the City Test (MCT) in a clinical population. Ecological validity was addressed via correlational analyses between performance on this test and a subjective measure of everyday executive functioning (Frontal Systems Behavior Scale; FrSBe). The sample was composed of 13 individuals (11 males) who suffered a stroke or traumatic brain injury. A neuropsychological test battery consisting of the MCT and common executive and nonexecutive measures was administered. The only executive function tests that were significantly related to the FrSBe were the MCT and a semantic fluency test. Compared with a sample of normal participants, the patient group produced better plans but completed fewer tasks on the MCT. Patients made similar types of errors as normals, although some of these errors occurred more frequently in the patient sample. This study demonstrated the ecological validity of the MCT and suggested that patients can be differentiated from healthy individuals by quantitative (i.e., number of errors) rather than qualitative (i.e., type of errors) aspects of performance. Further interpretation of MCT performance and comparison with existing executive function tests is discussed.}, } @article {pmid23373603, year = {2012}, author = {Jovanovski, D and Zakzanis, K and Campbell, Z and Erb, S and Nussbaum, D}, title = {Development of a novel, ecologically oriented virtual reality measure of executive function: the Multitasking in the City Test.}, journal = {Applied neuropsychology. Adult}, volume = {19}, number = {3}, pages = {171-182}, doi = {10.1080/09084282.2011.643955}, pmid = {23373603}, issn = {2327-9109}, mesh = {Adolescent ; Adult ; Cognition/physiology ; Computer Graphics ; Data Interpretation, Statistical ; Environment ; Executive Function/*physiology ; Female ; Humans ; Male ; Memory/physiology ; *Neuropsychological Tests ; Observer Variation ; Orientation/physiology ; Sex Characteristics ; Trail Making Test ; *User-Computer Interface ; Wechsler Scales ; Young Adult ; }, abstract = {A novel virtual reality executive function task (Multitasking in the City Test [MCT]) was developed with the aim of investigating planning and multitasking with ecological validity in mind in a normal population. Thirty healthy participants (21 females) completed a neuropsychological test battery that included the MCT along with standardized tests of executive and other cognitive functions. The sample performed within normal limits on the standardized tests. The MCT was performed successfully, although specific types of errors occurred frequently. Spearman correlation coefficients were computed between the various test measures. Only the plan score from the MCT was significantly associated with one of the executive function tests administered (Modified Six Elements Test), suggesting that both variables may be measuring a similar construct. Statistically significant correlations were also found between the MCT and the Trail-Making Test Part A and Judgment of Line Orientation, suggesting that "basic" cognitive functions such as information-processing speed and visuospatial skills are being tapped on the MCT. Preliminary evidence from this study suggested that the MCT may be an ecologically valid method of evaluating executive functioning. The clinical implications of these findings are discussed.}, } @article {pmid23372828, year = {2013}, author = {Otegui, J and Ariño, AH and Encinas, MA and Pando, F}, title = {Assessing the primary data hosted by the Spanish node of the Global Biodiversity Information Facility (GBIF).}, journal = {PloS one}, volume = {8}, number = {1}, pages = {e55144}, pmid = {23372828}, issn = {1932-6203}, mesh = {*Biodiversity ; *Databases, Factual ; Forms and Records Control ; Government Programs ; Humans ; Internet ; Publishing ; Spain ; }, abstract = {In order to effectively understand and cope with the current 'biodiversity crisis', having large-enough sets of qualified data is necessary. Information facilitators such as the Global Biodiversity Information Facility (GBIF) are ensuring increasing availability of primary biodiversity records by linking data collections spread over several institutions that have agreed to publish their data in a common access schema. We have assessed the primary records that one such publisher, the Spanish node of GBIF (GBIF.ES), hosts on behalf of a number of institutions, considered to be a highly representative sample of the total mass of available data for a country in order to know the quantity and quality of the information made available. Our results may provide an indication of the overall fitness-for-use in these data. We have found a number of patterns in the availability and accrual of data that seem to arise naturally from the digitization processes. Knowing these patterns and features may help deciding when and how these data can be used. Broadly, the error level seems low. The available data may be of capital importance for the development of biodiversity research, both locally and globally. However, wide swaths of records lack data elements such as georeferencing or taxonomical levels. Although the remaining information is ample and fit for many uses, improving the completeness of the records would likely increase the usability span for these data.}, } @article {pmid23367888, year = {2012}, author = {Ribeiro-Neto, PJ and Raposo, EP and Araújo, HA and Faustino, CL and da Luz, MG and Viswanathan, GM}, title = {Dissipative Lévy random searches: universal behavior at low target density.}, journal = {Physical review. E, Statistical, nonlinear, and soft matter physics}, volume = {86}, number = {6 Pt 1}, pages = {061102}, doi = {10.1103/PhysRevE.86.061102}, pmid = {23367888}, issn = {1550-2376}, mesh = {Algorithms ; Binding Sites ; Biophysics/*methods ; Computational Biology/methods ; DNA/*chemistry ; Ecology/methods ; Models, Statistical ; Models, Theoretical ; Probability ; Protein Binding ; }, abstract = {We investigate the problem of survival at the very low target-density limit and report on a second-order phase transition for one-dimensional random searches in which the energy cost of locomotion is a function of the distance traveled by the searcher. Surprisingly, from analytical calculations (also tested numerically) we find identical critical exponents for arbitrary energy cost functions. We conclude that there is a single universality class that describes this process.}, } @article {pmid23363430, year = {2013}, author = {He, Q and Bertness, MD and Altieri, AH}, title = {Global shifts towards positive species interactions with increasing environmental stress.}, journal = {Ecology letters}, volume = {16}, number = {5}, pages = {695-706}, doi = {10.1111/ele.12080}, pmid = {23363430}, issn = {1461-0248}, mesh = {Climate ; Databases, Factual ; Ecosystem ; Environment ; Mortality ; Multifactorial Inheritance ; *Plant Physiological Phenomena ; *Stress, Physiological ; }, abstract = {The study of positive species interactions is a rapidly evolving field in ecology. Despite decades of research, controversy has emerged as to whether positive and negative interactions predictably shift with increasing environmental stress as hypothesised by the stress-gradient hypothesis (SGH). Here, we provide a synthesis of 727 tests of the SGH in plant communities across the globe to examine its generality across a variety of ecological factors. Our results show that plant interactions change with stress through an outright shift to facilitation (survival) or a reduction in competition (growth and reproduction). In a limited number of cases, plant interactions do not respond to stress, but they never shift towards competition with stress. These findings are consistent across stress types, plant growth forms, life histories, origins (invasive vs. native), climates, ecosystems and methodologies, though the magnitude of the shifts towards facilitation with stress is dependent on these factors. We suggest that future studies should employ standardised definitions and protocols to test the SGH, take a multi-factorial approach that considers variables such as plant traits in addition to stress, and apply the SGH to better understand how species and communities will respond to environmental change.}, } @article {pmid23359700, year = {2013}, author = {Hadid, Y and Tzur, S and Pavlícek, T and Šumbera, R and Šklíba, J and Lövy, M and Fragman-Sapir, O and Beiles, A and Arieli, R and Raz, S and Nevo, E}, title = {Possible incipient sympatric ecological speciation in blind mole rats (Spalax).}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {110}, number = {7}, pages = {2587-2592}, pmid = {23359700}, issn = {1091-6490}, mesh = {Adaptation, Biological/genetics/*physiology ; Analysis of Variance ; Animals ; Base Sequence ; Computational Biology ; DNA, Mitochondrial/genetics ; *Ecosystem ; *Genetic Speciation ; *Genetic Variation ; Genetics, Population ; Haplotypes/genetics ; Israel ; Molecular Sequence Data ; Oxygen Consumption/physiology ; Selection, Genetic ; Sequence Analysis, DNA ; Soil/*analysis ; Spalax/*genetics/physiology ; Species Specificity ; }, abstract = {Sympatric speciation has been controversial since it was first proposed as a mode of speciation. Subterranean blind mole rats (Spalacidae) are considered to speciate allopatrically or peripatrically. Here, we report a possible incipient sympatric adaptive ecological speciation in Spalax galili (2n = 52). The study microsite (0.04 km(2)) is sharply subdivided geologically, edaphically, and ecologically into abutting barrier-free ecologies divergent in rock, soil, and vegetation types. The Pleistocene Alma basalt abuts the Cretaceous Senonian Kerem Ben Zimra chalk. Only 28% of 112 plant species were shared between the soils. We examined mitochondrial DNA in the control region and ATP6 in 28 mole rats from basalt and in 14 from chalk habitats. We also sequenced the complete mtDNA (16,423 bp) of four animals, two from each soil type. Remarkably, the frequency of all major haplotype clusters (HC) was highly soil-biased. HCI and HCII are chalk biased. HC-III was abundant in basalt (36%) but absent in chalk; HC-IV was prevalent in basalt (46.5%) but was low (20%) in chalk. Up to 40% of the mtDNA diversity was edaphically dependent, suggesting constrained gene flow. We identified a homologous recombinant mtDNA in the basalt/chalk studied area. Phenotypically significant divergences differentiate the two populations, inhabiting different soils, in adaptive oxygen consumption and in the amount of outside-nest activity. This identification of a possible incipient sympatric adaptive ecological speciation caused by natural selection indirectly refutes the allopatric alternative. Sympatric ecological speciation may be more prevalent in nature because of abundant and sharply abutting divergent ecologies.}, } @article {pmid23356940, year = {2013}, author = {, and Aksoy, S and Almeida-Val, VM and Azevedo, VC and Baucom, R and Bazaga, P and Beheregaray, LB and Bennetzen, JL and Brassaloti, RA and Burgess, TI and Caccone, A and Chang, SM and Ciampi, AY and Ciancaleoni, S and Clímaco, GT and Clouet, C and Coimbra, MR and Coutinho, LL and Dantas, HL and De Vega, C and Echodu, R and Enyaru, J and Figueira, A and Filho, MA and Foltz, B and Fressigné, L and Gadomski, M and Gauthier, N and Herrera, CM and Hyseni, C and Jorge, EC and Kaczmarczyk, D and Knott, E and Kuester, A and Lima, AP and Lima, MA and Lima, MP and Longo, AL and Lor, G and Maggioni, R and Marques, TS and Martins, AR and Matoso, DA and Medrano, M and Mendonça, MA and Mettler, R and Nascimento, PR and Negri, V and Oliveira, KK and Oliveira, LO and Ovcarenko, I and Paula-Silva, MN and Raggi, L and Sandoval-Castillo, J and Santos, CH and Martin Schaefer, H and Segelbacher, G and Seino, MM and Sistrom, M and Taole, MM and Teske, PR and Tsagkarakou, A and Verdade, LM and Villela, PM and Vinson, CC and Wingfield, BD and Wingfield, MJ}, title = {Permanent genetic resources added to molecular ecology resources database 1 October 2012-30 November 2012.}, journal = {Molecular ecology resources}, volume = {13}, number = {2}, pages = {341-343}, doi = {10.1111/1755-0998.12061}, pmid = {23356940}, issn = {1755-0998}, support = {R03 TW008413/TW/FIC NIH HHS/United States ; }, mesh = {Animals ; Ascomycota/*genetics ; *Databases, Genetic ; Diptera/*genetics ; Ecology ; Microsatellite Repeats ; Molecular Sequence Data ; Plants/*genetics ; Trypanosoma brucei brucei/*genetics ; }, abstract = {This article documents the addition of 153 microsatellite marker loci to the Molecular Ecology Resources Database. Loci were developed for the following species: Brassica oleracea, Brycon amazonicus, Dimorphandra wilsonii, Eupallasella percnurus, Helleborus foetidus, Ipomoea purpurea, Phrynops geoffroanus, Prochilodus argenteus, Pyura sp., Sylvia atricapilla, Teratosphaeria suttonii, Trialeurodes vaporariorum and Trypanosoma brucei. These loci were cross-tested on the following species: Dimorphandra coccicinea, Dimorphandra cuprea, Dimorphandra gardneriana, Dimorphandra jorgei, Dimorphandra macrostachya, Dimorphandra mollis, Dimorphandra parviflora and Dimorphandra pennigera.}, } @article {pmid23356610, year = {2013}, author = {Shah, P and Fitzpatrick, BM and Fordyce, JA}, title = {A parametric method for assessing diversification-rate variation in phylogenetic trees.}, journal = {Evolution; international journal of organic evolution}, volume = {67}, number = {2}, pages = {368-377}, doi = {10.1111/j.1558-5646.2012.01791.x}, pmid = {23356610}, issn = {1558-5646}, mesh = {Adaptation, Biological/genetics ; Algorithms ; Animals ; Data Interpretation, Statistical ; Evolution, Molecular ; *Genetic Variation ; *Models, Genetic ; *Models, Statistical ; *Phylogeny ; Urodela/genetics ; }, abstract = {Phylogenetic hypotheses are frequently used to examine variation in rates of diversification across the history of a group. Patterns of diversification-rate variation can be used to infer underlying ecological and evolutionary processes responsible for patterns of cladogenesis. Most existing methods examine rate variation through time. Methods for examining differences in diversification among groups are more limited. Here, we present a new method, parametric rate comparison (PRC), that explicitly compares diversification rates among lineages in a tree using a variety of standard statistical distributions. PRC can identify subclades of the tree where diversification rates are at variance with the remainder of the tree. A randomization test can be used to evaluate how often such variance would appear by chance alone. The method also allows for comparison of diversification rate among a priori defined groups. Further, the application of the PRC method is not restricted to monophyletic groups. We examined the performance of PRC using simulated data, which showed that PRC has acceptable false-positive rates and statistical power to detect rate variation. We apply the PRC method to the well-studied radiation of North American Plethodon salamanders, and support the inference that the large-bodied Plethodon glutinosus clade has a higher historical rate of diversification compared to other Plethodon salamanders.}, } @article {pmid23354617, year = {2013}, author = {Vu, VH and Le, XQ and Pham, NH and Hens, L}, title = {Application of GIS and modelling in health risk assessment for urban road mobility.}, journal = {Environmental science and pollution research international}, volume = {20}, number = {8}, pages = {5138-5149}, pmid = {23354617}, issn = {1614-7499}, mesh = {Adult ; Air Pollutants/analysis/*toxicity ; Geographic Information Systems ; Hospitalization ; Humans ; *Models, Theoretical ; Motor Vehicles ; Particulate Matter/analysis/*toxicity ; Pulmonary Disease, Chronic Obstructive ; Risk Assessment/methods ; Uncertainty ; Vehicle Emissions/analysis/*toxicity ; Vietnam ; }, abstract = {Transport is an essential sector in modern societies. It connects economic sectors and industries. Next to its contribution to economic development and social interconnection, it also causes adverse impacts on the environment and results in health hazards. Transport is a major source of ground air pollution, especially in urban areas, and therefore contributes to the health problems, such as cardiovascular and respiratory diseases, cancer and physical injuries. This paper presents the results of a health risk assessment that quantifies the mortality and the diseases associated with particulate matter pollution resulting from urban road transport in Haiphong City, Vietnam. The focus is on the integration of modelling and geographic information system approaches in the exposure analysis to increase the accuracy of the assessment and to produce timely and consistent assessment results. The modelling was done to estimate traffic conditions and concentrations of particulate matters based on geo-referenced data. The study shows that health burdens due to particulate matter in Haiphong include 1,200 extra deaths for the situation in 2007. This figure can double by 2020 as the result of the fast economic development the city pursues. In addition, 51,000 extra hospital admissions and more than 850,000 restricted activity days are expected by 2020.}, } @article {pmid23351042, year = {2013}, author = {Gautestad, AO and Loe, LE and Mysterud, A}, title = {Inferring spatial memory and spatiotemporal scaling from GPS data: comparing red deer Cervus elaphus movements with simulation models.}, journal = {The Journal of animal ecology}, volume = {82}, number = {3}, pages = {572-586}, doi = {10.1111/1365-2656.12027}, pmid = {23351042}, issn = {1365-2656}, mesh = {Animals ; *Computer Simulation ; Deer/*physiology ; Female ; Geographic Information Systems ; Homing Behavior ; *Memory, Long-Term ; *Models, Biological ; *Movement ; Norway ; }, abstract = {1. Increased inference regarding underlying behavioural mechanisms of animal movement can be achieved by comparing GPS data with statistical mechanical movement models such as random walk and Lévy walk with known underlying behaviour and statistical properties. 2. GPS data are typically collected with ≥ 1 h intervals not exactly tracking every mechanistic step along the movement path, so a statistical mechanical model approach rather than a mechanistic approach is appropriate. However, comparisons require a coherent framework involving both scaling and memory aspects of the underlying process. Thus, simulation models have recently been extended to include memory-guided returns to previously visited patches, that is, site fidelity. 3. We define four main classes of movement, differing in incorporation of memory and scaling (based on respective intervals of the statistical fractal dimension D and presence/absence of site fidelity). Using three statistical protocols to estimate D and site fidelity, we compare these main movement classes with patterns observed in GPS data from 52 females of red deer (Cervus elaphus). 4. The results show best compliance with a scale-free and memory-enhanced kind of space use; that is, a power law distribution of step lengths, a fractal distribution of the spatial scatter of fixes and site fidelity. 5. Our study thus demonstrates how inference regarding memory effects and a hierarchical pattern of space use can be derived from analysis of GPS data.}, } @article {pmid23344628, year = {2013}, author = {Dobbie, MJ and Negus, P}, title = {Addressing statistical and operational challenges in designing large-scale stream condition surveys.}, journal = {Environmental monitoring and assessment}, volume = {185}, number = {9}, pages = {7231-7243}, pmid = {23344628}, issn = {1573-2959}, mesh = {*Ecosystem ; Environmental Monitoring/*methods ; Geographic Information Systems ; *Rivers ; Statistics as Topic ; }, abstract = {Implementing a statistically valid and practical monitoring design for large-scale stream condition monitoring and assessment programs can be difficult due to factors including the likely existence of a diversity of ecosystem types such as ephemeral streams over the sampling domain; limited resources to undertake detailed monitoring surveys and address knowledge gaps; and operational constraints on effective sampling at monitoring sites. In statistical speak, these issues translate to defining appropriate target populations and sampling units; designing appropriate spatial and temporal sample site selection methods; selection and use of appropriate indicators; and setting effect sizes with limited ecological and statistical information about the indicators of interest. We identify the statistical and operational challenges in designing large-scale stream condition surveys and discuss general approaches for addressing them. The ultimate aim in drawing attention to these challenges is to ensure operational practicality in carrying out future monitoring programs and that the resulting inferences about stream condition are statistically valid and relevant.}, } @article {pmid23343858, year = {2013}, author = {de Vocht, F and Hannam, K and Buchan, I}, title = {Environmental risk factors for cancers of the brain and nervous system: the use of ecological data to generate hypotheses.}, journal = {Occupational and environmental medicine}, volume = {70}, number = {5}, pages = {349-356}, doi = {10.1136/oemed-2012-100954}, pmid = {23343858}, issn = {1470-7926}, support = {MC_PC_13042/MRC_/Medical Research Council/United Kingdom ; MR/K006665/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Brain/*pathology ; Brain Neoplasms/epidemiology/*etiology ; Cell Phone ; Central Nervous System Neoplasms ; Confounding Factors, Epidemiologic ; *Databases, Factual ; Ecology ; Electromagnetic Radiation ; Environmental Exposure/*adverse effects ; Epidemiologic Methods ; Global Health ; Humans ; Incidence ; Income ; Multivariate Analysis ; Risk Factors ; }, abstract = {BACKGROUND: There is a public health need to balance timely generation of hypotheses with cautious causal inference. For rare cancers this is particularly challenging because standard epidemiological study designs may not be able to elucidate causal factors in an early period of newly emerging risks. Alternative methodologies need to be considered for generating and shaping hypotheses prior to definitive investigation.

OBJECTIVES: To evaluate whether open-access databases can be used to explore links between potential risk factors and cancers at an ecological level, using the case study of brain and nervous system cancers as an example.

METHODS: National age-adjusted cancer incidence rates were obtained from the GLOBOCAN 2008 resource and combined with data from the United Nations Development Report and the World Bank list of development indicators. Data were analysed using multivariate regression models.

RESULTS: Cancer rates, potential confounders and environmental risk factors were available for 165 of 208 countries. 2008 national incidences of brain and nervous system cancers were associated with continent, gross national income in 2008 and Human Development Index Score. The only exogenous risk factor consistently associated with higher incidence was the penetration rate of mobile/cellular telecommunications subscriptions, although other factors were highlighted. According to these ecological results the latency period is at least 11-12 years, but probably more than 20 years. Missing data on cancer incidence and for other potential risk factors prohibit more detailed investigation of exposure-response associations and/or explore other hypotheses.

CONCLUSIONS: Readily available ecological data may be underused, particularly for the study of risk factors for rare diseases and those with long latencies. The results of ecological analyses in general should not be overinterpreted in causal inference, but equally they should not be ignored where alternative signals of aetiology are lacking.}, } @article {pmid23326357, year = {2013}, author = {Pardo, I and Pata, MP and Gómez, D and García, MB}, title = {A novel method to handle the effect of uneven sampling effort in biodiversity databases.}, journal = {PloS one}, volume = {8}, number = {1}, pages = {e52786}, pmid = {23326357}, issn = {1932-6203}, mesh = {*Algorithms ; *Biodiversity ; Computer Simulation ; Conservation of Natural Resources/*methods ; Databases, Factual/standards/*statistics & numerical data ; Geography ; Logistic Models ; Reproducibility of Results ; Spain ; }, abstract = {How reliable are results on spatial distribution of biodiversity based on databases? Many studies have evidenced the uncertainty related to this kind of analysis due to sampling effort bias and the need for its quantification. Despite that a number of methods are available for that, little is known about their statistical limitations and discrimination capability, which could seriously constrain their use. We assess for the first time the discrimination capacity of two widely used methods and a proposed new one (FIDEGAM), all based on species accumulation curves, under different scenarios of sampling exhaustiveness using Receiver Operating Characteristic (ROC) analyses. Additionally, we examine to what extent the output of each method represents the sampling completeness in a simulated scenario where the true species richness is known. Finally, we apply FIDEGAM to a real situation and explore the spatial patterns of plant diversity in a National Park. FIDEGAM showed an excellent discrimination capability to distinguish between well and poorly sampled areas regardless of sampling exhaustiveness, whereas the other methods failed. Accordingly, FIDEGAM values were strongly correlated with the true percentage of species detected in a simulated scenario, whereas sampling completeness estimated with other methods showed no relationship due to null discrimination capability. Quantifying sampling effort is necessary to account for the uncertainty in biodiversity analyses, however, not all proposed methods are equally reliable. Our comparative analysis demonstrated that FIDEGAM was the most accurate discriminator method in all scenarios of sampling exhaustiveness, and therefore, it can be efficiently applied to most databases in order to enhance the reliability of biodiversity analyses.}, } @article {pmid23324389, year = {2013}, author = {Nmor, JC and Sunahara, T and Goto, K and Futami, K and Sonye, G and Akweywa, P and Dida, G and Minakawa, N}, title = {Topographic models for predicting malaria vector breeding habitats: potential tools for vector control managers.}, journal = {Parasites & vectors}, volume = {6}, number = {}, pages = {14}, pmid = {23324389}, issn = {1756-3305}, mesh = {Africa/epidemiology ; Animals ; Anopheles/*physiology ; Data Collection ; Ecosystem ; *Geographic Information Systems ; Geography ; Humans ; Insect Vectors/*physiology ; Kenya/epidemiology ; Larva ; Logistic Models ; Malaria/*epidemiology/prevention & control/transmission ; Models, Theoretical ; *Mosquito Control ; *Remote Sensing Technology ; Reproducibility of Results ; Seasons ; }, abstract = {BACKGROUND: Identification of malaria vector breeding sites can enhance control activities. Although associations between malaria vector breeding sites and topography are well recognized, practical models that predict breeding sites from topographic information are lacking. We used topographic variables derived from remotely sensed Digital Elevation Models (DEMs) to model the breeding sites of malaria vectors. We further compared the predictive strength of two different DEMs and evaluated the predictability of various habitat types inhabited by Anopheles larvae.

METHODS: Using GIS techniques, topographic variables were extracted from two DEMs: 1) Shuttle Radar Topography Mission 3 (SRTM3, 90-m resolution) and 2) the Advanced Spaceborne Thermal Emission Reflection Radiometer Global DEM (ASTER, 30-m resolution). We used data on breeding sites from an extensive field survey conducted on an island in western Kenya in 2006. Topographic variables were extracted for 826 breeding sites and for 4520 negative points that were randomly assigned. Logistic regression modelling was applied to characterize topographic features of the malaria vector breeding sites and predict their locations. Model accuracy was evaluated using the area under the receiver operating characteristics curve (AUC).

RESULTS: All topographic variables derived from both DEMs were significantly correlated with breeding habitats except for the aspect of SRTM. The magnitude and direction of correlation for each variable were similar in the two DEMs. Multivariate models for SRTM and ASTER showed similar levels of fit indicated by Akaike information criterion (3959.3 and 3972.7, respectively), though the former was slightly better than the latter. The accuracy of prediction indicated by AUC was also similar in SRTM (0.758) and ASTER (0.755) in the training site. In the testing site, both SRTM and ASTER models showed higher AUC in the testing sites than in the training site (0.829 and 0.799, respectively). The predictability of habitat types varied. Drains, foot-prints, puddles and swamp habitat types were most predictable.

CONCLUSIONS: Both SRTM and ASTER models had similar predictive potentials, which were sufficiently accurate to predict vector habitats. The free availability of these DEMs suggests that topographic predictive models could be widely used by vector control managers in Africa to complement malaria control strategies.}, } @article {pmid23324024, year = {2013}, author = {Boyle, B and Hopkins, N and Lu, Z and Raygoza Garay, JA and Mozzherin, D and Rees, T and Matasci, N and Narro, ML and Piel, WH and McKay, SJ and Lowry, S and Freeland, C and Peet, RK and Enquist, BJ}, title = {The taxonomic name resolution service: an online tool for automated standardization of plant names.}, journal = {BMC bioinformatics}, volume = {14}, number = {}, pages = {16}, pmid = {23324024}, issn = {1471-2105}, mesh = {Algorithms ; Classification/methods ; Databases, Factual ; Internet ; Names ; Plants/*classification ; *Software ; User-Computer Interface ; }, abstract = {BACKGROUND: The digitization of biodiversity data is leading to the widespread application of taxon names that are superfluous, ambiguous or incorrect, resulting in mismatched records and inflated species numbers. The ultimate consequences of misspelled names and bad taxonomy are erroneous scientific conclusions and faulty policy decisions. The lack of tools for correcting this 'names problem' has become a fundamental obstacle to integrating disparate data sources and advancing the progress of biodiversity science.

RESULTS: The TNRS, or Taxonomic Name Resolution Service, is an online application for automated and user-supervised standardization of plant scientific names. The TNRS builds upon and extends existing open-source applications for name parsing and fuzzy matching. Names are standardized against multiple reference taxonomies, including the Missouri Botanical Garden's Tropicos database. Capable of processing thousands of names in a single operation, the TNRS parses and corrects misspelled names and authorities, standardizes variant spellings, and converts nomenclatural synonyms to accepted names. Family names can be included to increase match accuracy and resolve many types of homonyms. Partial matching of higher taxa combined with extraction of annotations, accession numbers and morphospecies allows the TNRS to standardize taxonomy across a broad range of active and legacy datasets.

CONCLUSIONS: We show how the TNRS can resolve many forms of taxonomic semantic heterogeneity, correct spelling errors and eliminate spurious names. As a result, the TNRS can aid the integration of disparate biological datasets. Although the TNRS was developed to aid in standardizing plant names, its underlying algorithms and design can be extended to all organisms and nomenclatural codes. The TNRS is accessible via a web interface at http://tnrs.iplantcollaborative.org/ and as a RESTful web service and application programming interface. Source code is available at https://github.com/iPlantCollaborativeOpenSource/TNRS/.}, } @article {pmid23320463, year = {2013}, author = {Orsini, L and Andrew, R and Eizaguirre, C}, title = {Evolutionary ecological genomics.}, journal = {Molecular ecology}, volume = {22}, number = {3}, pages = {527-531}, doi = {10.1111/mec.12177}, pmid = {23320463}, issn = {1365-294X}, mesh = {*Biological Evolution ; Computational Biology ; *Ecology ; Genetic Fitness ; Genetic Speciation ; *Genomics ; Hybridization, Genetic ; }, } @article {pmid23313953, year = {2013}, author = {You, M and Yue, Z and He, W and Yang, X and Yang, G and Xie, M and Zhan, D and Baxter, SW and Vasseur, L and Gurr, GM and Douglas, CJ and Bai, J and Wang, P and Cui, K and Huang, S and Li, X and Zhou, Q and Wu, Z and Chen, Q and Liu, C and Wang, B and Li, X and Xu, X and Lu, C and Hu, M and Davey, JW and Smith, SM and Chen, M and Xia, X and Tang, W and Ke, F and Zheng, D and Hu, Y and Song, F and You, Y and Ma, X and Peng, L and Zheng, Y and Liang, Y and Chen, Y and Yu, L and Zhang, Y and Liu, Y and Li, G and Fang, L and Li, J and Zhou, X and Luo, Y and Gou, C and Wang, J and Wang, J and Yang, H and Wang, J}, title = {A heterozygous moth genome provides insights into herbivory and detoxification.}, journal = {Nature genetics}, volume = {45}, number = {2}, pages = {220-225}, pmid = {23313953}, issn = {1546-1718}, mesh = {Adaptation, Biological/*genetics ; Animals ; Base Sequence ; China ; Chromosomes, Artificial, Bacterial ; Computational Biology ; Evolution, Molecular ; Expressed Sequence Tags ; Female ; Gene Expression Profiling ; *Genetic Variation ; Genome/*genetics ; Glucosinolates/*metabolism ; Herbivory/*genetics ; *Heterozygote ; Male ; Molecular Sequence Annotation ; Molecular Sequence Data ; Moths/*genetics/metabolism ; Mutation/genetics ; Pest Control/methods ; *Phylogeny ; Polymorphism, Single Nucleotide ; Real-Time Polymerase Chain Reaction ; Sequence Analysis, DNA ; Sulfatases/genetics ; }, abstract = {How an insect evolves to become a successful herbivore is of profound biological and practical importance. Herbivores are often adapted to feed on a specific group of evolutionarily and biochemically related host plants, but the genetic and molecular bases for adaptation to plant defense compounds remain poorly understood. We report the first whole-genome sequence of a basal lepidopteran species, Plutella xylostella, which contains 18,071 protein-coding and 1,412 unique genes with an expansion of gene families associated with perception and the detoxification of plant defense compounds. A recent expansion of retrotransposons near detoxification-related genes and a wider system used in the metabolism of plant defense compounds are shown to also be involved in the development of insecticide resistance. This work shows the genetic and molecular bases for the evolutionary success of this worldwide herbivore and offers wider insights into insect adaptation to plant feeding, as well as opening avenues for more sustainable pest management.}, } @article {pmid23307317, year = {2013}, author = {von Stackelberg, KE}, title = {Decision analytic strategies for integrating ecosystem services and risk assessment.}, journal = {Integrated environmental assessment and management}, volume = {9}, number = {2}, pages = {260-268}, doi = {10.1002/ieam.1393}, pmid = {23307317}, issn = {1551-3793}, mesh = {Animals ; Conservation of Natural Resources ; Decision Making ; *Decision Support Techniques ; *Ecosystem ; Humans ; Risk Assessment ; }, abstract = {Ecosystem services as a concept and guiding principle are enjoying wide popularity and endorsement from high-level policy thinkers to industry as support for sustainability goals continue to grow. However, explicit incorporation of ecosystem services into decision making still lacks practical implementation at more local scales and faces significant regulatory and technical constraints. Risk assessment represents an example of a regulatory process for which guidance exists that makes it challenging to incorporate ecosystem service endpoints. Technical constraints exist in the quantification of the relationships between ecological functions and services and endpoints valued by humans, and the complexity of those interactions with respect to bundling and stacking. In addition, ecosystem services, by their very definition, represent an anthropogenic construct with no inherent ecological value, which, in practical terms, requires a far more inclusionary decision making process explicitly incorporating a greater diversity of stakeholder values. Despite these constraints, it is possible, given a commitment to sustainable decision making, to simplify the process based on strategic outcomes (e.g., identifying desired end-states in general terms). Decision analytic techniques provide a mechanism for evaluating tradeoffs across key ecosystem services valued by stakeholders and to develop criteria drawn from the entire spectrum of stakeholders in evaluating potential alternatives. This article highlights several examples of ways in which ecosystem service endpoints can be incorporated into the decision-making process.}, } @article {pmid23305074, year = {2013}, author = {Aimone, AM and Perumal, N and Cole, DC}, title = {A systematic review of the application and utility of geographical information systems for exploring disease-disease relationships in paediatric global health research: the case of anaemia and malaria.}, journal = {International journal of health geographics}, volume = {12}, number = {}, pages = {1}, pmid = {23305074}, issn = {1476-072X}, mesh = {Anemia/diagnosis/*epidemiology ; *Biomedical Research/methods ; Geographic Information Systems/*statistics & numerical data ; *Global Health ; Humans ; Malaria/diagnosis/*epidemiology ; }, abstract = {Malaria and anaemia are important health problems among children globally. Iron deficiency anaemia may offer protection against malaria infection and iron supplementation may increase the risk of malaria-related hospitalization and mortality. The nature and mechanism of these relationships, however, remain largely unresolved, resulting in concern and uncertainty around policies for non-selective iron supplementation in malaria endemic areas. Use of geographical information systems (GIS) to investigate this disease-disease interaction could contribute important new information for developing safe and effective anaemia and malaria interventions. To assess the current state of knowledge we conducted a systematic review of peer-reviewed and grey literature. Our primary objective was to qualitatively assess the application and utility of geographical concepts or spatial analyses in paediatric global health research. The secondary objective was to identify geographical factors that may be associated with anaemia and malaria prevalence or incidence among children 0-5 years of age living in low- and middle-income countries. Evaluation tools for assessing the quality of geographical data could not be found in the peer-reviewed or grey literature, and thus adapted versions of the STROBE (Strengthening The Reporting of Observational Studies in Epidemiology) and GRADE (Grades of Recommendation, Assessment, Development and Evaluation) methods were used to create reporting, and overall evidence quality scoring systems. Among the 20 included studies, we found that both malaria and anaemia were more prevalent in rural communities compared to urban areas. Geographical factors associated with malaria prevalence included regional transmission stability, and proximity to a mosquito breeding area. The prevalence of anaemia tended to vary inversely with greater or poorer access to community services such as piped water. Techniques for investigating geographic relationships ranged from simple descriptive mapping of spatial distribution patterns, to more complex statistical models that incorporated environmental factors such as seasonal temperature and rain fall. Including GIS in paediatric global health research may be an effective approach to explore relationships between childhood diseases and contribute key evidence for safe implementation of anaemia control programs in malaria endemic areas. Further, GIS presentation of ecological health data could provide an efficient means of translating this knowledge to lay audiences.}, } @article {pmid23282177, year = {2012}, author = {Fettweis, JM and Serrano, MG and Sheth, NU and Mayer, CM and Glascock, AL and Brooks, JP and Jefferson, KK and , and Buck, GA}, title = {Species-level classification of the vaginal microbiome.}, journal = {BMC genomics}, volume = {13 Suppl 8}, number = {Suppl 8}, pages = {S17}, pmid = {23282177}, issn = {1471-2164}, support = {UH2/UH3AI083263/AI/NIAID NIH HHS/United States ; }, mesh = {Algorithms ; Bacteria/*classification/genetics ; Databases, Genetic ; Female ; Humans ; *Metagenome ; RNA, Ribosomal, 16S/genetics ; Vagina/*microbiology ; }, abstract = {BACKGROUND: The application of next-generation sequencing to the study of the vaginal microbiome is revealing the spectrum of microbial communities that inhabit the human vagina. High-resolution identification of bacterial taxa, minimally to the species level, is necessary to fully understand the association of the vaginal microbiome with bacterial vaginosis, sexually transmitted infections, pregnancy complications, menopause, and other physiological and infectious conditions. However, most current taxonomic assignment strategies based on metagenomic 16S rDNA sequence analysis provide at best a genus-level resolution. While surveys of 16S rRNA gene sequences are common in microbiome studies, few well-curated, body-site-specific reference databases of 16S rRNA gene sequences are available, and no such resource is available for vaginal microbiome studies.

RESULTS: We constructed the Vaginal 16S rDNA Reference Database, a comprehensive and non-redundant database of 16S rDNA reference sequences for bacterial taxa likely to be associated with vaginal health, and we developed STIRRUPS, a new method that employs the USEARCH algorithm with a curated reference database for rapid species-level classification of 16S rDNA partial sequences. The method was applied to two datasets of V1-V3 16S rDNA reads: one generated from a mock community containing DNA from six bacterial strains associated with vaginal health, and a second generated from over 1,000 mid-vaginal samples collected as part of the Vaginal Human Microbiome Project at Virginia Commonwealth University. In both datasets, STIRRUPS, used in conjunction with the Vaginal 16S rDNA Reference Database, classified more than 95% of processed reads to a species-level taxon using a 97% global identity threshold for assignment.

CONCLUSIONS: This database and method provide accurate species-level classifications of metagenomic 16S rDNA sequence reads that will be useful for analysis and comparison of microbiome profiles from vaginal samples. STIRRUPS can be used to classify 16S rDNA sequence reads from other ecological niches if an appropriate reference database of 16S rDNA sequences is available.}, } @article {pmid23301093, year = {2013}, author = {Elbroch, LM and Wittmer, HU}, title = {Nuisance ecology: do scavenging condors exact foraging costs on pumas in Patagonia?.}, journal = {PloS one}, volume = {8}, number = {1}, pages = {e53595}, pmid = {23301093}, issn = {1932-6203}, mesh = {Animals ; *Birds ; Chile ; Cluster Analysis ; *Competitive Behavior ; Ecology ; Feeding Behavior ; Geographic Information Systems ; Meat ; Models, Theoretical ; *Predatory Behavior ; *Puma ; }, abstract = {Predation risk describes the energetic cost an animal suffers when making a trade off between maximizing energy intake and minimizing threats to its survival. We tested whether Andean condors (Vultur gryphus) influenced the foraging behaviors of a top predator in Patagonia, the puma (Puma concolor), in ways comparable to direct risks of predation for prey to address three questions: 1) Do condors exact a foraging cost on pumas?; 2) If so, do pumas exhibit behaviors indicative of these risks?; and 3) Do pumas display predictable behaviors associated with prey species foraging in risky environments? Using GPS location data, we located 433 kill sites of 9 pumas and quantified their kill rates. Based upon time pumas spent at a carcass, we quantified handling time. Pumas abandoned >10% of edible meat at 133 of 266 large carcasses after a single night, and did so most often in open grasslands where their carcasses were easily detected by condors. Our data suggested that condors exacted foraging costs on pumas by significantly decreasing puma handling times at carcasses, and that pumas increased their kill rates by 50% relative to those reported for North America to compensate for these losses. Finally, we determined that the relative risks of detection and associated harassment by condors, rather than prey densities, explained puma "giving up times" (GUTs) across structurally variable risk classes in the study area, and that, like many prey species, pumas disproportionately hunted in high-risk, high-resource reward areas.}, } @article {pmid23301083, year = {2013}, author = {Ono, M and Tanaka, RJ and Kano, M and Sugiman, T}, title = {Visualising the cross-level relationships between pathological and physiological processes and gene expression: analyses of haematological diseases.}, journal = {PloS one}, volume = {8}, number = {1}, pages = {e53544}, pmid = {23301083}, issn = {1932-6203}, mesh = {Algorithms ; Antigens, CD34/metabolism ; Cell Differentiation ; Cluster Analysis ; Computational Biology/methods ; Gene Expression Profiling/*methods ; *Gene Expression Regulation ; Hematologic Diseases/*genetics/physiopathology ; Humans ; Immunophenotyping ; Leukemia/metabolism ; Myelodysplastic Syndromes/metabolism ; Oligonucleotide Array Sequence Analysis/methods ; Proportional Hazards Models ; Stem Cells ; Transcriptome ; }, abstract = {The understanding of pathological processes is based on the comparison between physiological and pathological conditions, and transcriptomic analysis has been extensively applied to various diseases for this purpose. However, the way in which the transcriptomic data of pathological cells relate to the transcriptomes of normal cellular counterparts has not been fully explored, and may provide new and unbiased insights into the mechanisms of these diseases. To achieve this, it is necessary to develop a method to simultaneously analyse components across different levels, namely genes, normal cells, and diseases. Here we propose a multidimensional method that visualises the cross-level relationships between these components at three different levels based on transcriptomic data of physiological and pathological processes, by adapting Canonical Correspondence Analysis, which was developed in ecology and sociology, to microarray data (CCA on Microarray data, CCAM). Using CCAM, we have analysed transcriptomes of haematological disorders and those of normal haematopoietic cell differentiation. First, by analysing leukaemia data, CCAM successfully visualised known relationships between leukaemia subtypes and cellular differentiation, and their characteristic genes, which confirmed the relevance of CCAM. Next, by analysing transcriptomes of myelodysplastic syndromes (MDS), we have shown that CCAM was effective in both generating and testing hypotheses. CCAM showed that among MDS patients, high-risk patients had transcriptomes that were more similar to those of both haematopoietic stem cells (HSC) and megakaryocyte-erythroid progenitors (MEP) than low-risk patients, and provided a prognostic model. Collectively, CCAM reveals hidden relationships between pathological and physiological processes and gene expression, providing meaningful clinical insights into haematological diseases, and these could not be revealed by other univariate and multivariate methods. Furthermore, CCAM was effective in identifying candidate genes that are correlated with cellular phenotypes of interest. We expect that CCAM will benefit a wide range of medical fields.}, } @article {pmid23300719, year = {2012}, author = {McRae, BH and Hall, SA and Beier, P and Theobald, DM}, title = {Where to restore ecological connectivity? Detecting barriers and quantifying restoration benefits.}, journal = {PloS one}, volume = {7}, number = {12}, pages = {e52604}, pmid = {23300719}, issn = {1932-6203}, mesh = {Animal Distribution ; Animals ; Climate Change ; Conservation of Natural Resources/*methods ; Ecosystem ; Gene Flow ; Genetics, Population ; Geographic Information Systems ; Geographic Mapping ; Humans ; Models, Theoretical ; Washington ; }, abstract = {Landscape connectivity is crucial for many ecological processes, including dispersal, gene flow, demographic rescue, and movement in response to climate change. As a result, governmental and non-governmental organizations are focusing efforts to map and conserve areas that facilitate movement to maintain population connectivity and promote climate adaptation. In contrast, little focus has been placed on identifying barriers-landscape features which impede movement between ecologically important areas-where restoration could most improve connectivity. Yet knowing where barriers most strongly reduce connectivity can complement traditional analyses aimed at mapping best movement routes. We introduce a novel method to detect important barriers and provide example applications. Our method uses GIS neighborhood analyses in conjunction with effective distance analyses to detect barriers that, if removed, would significantly improve connectivity. Applicable in least-cost, circuit-theoretic, and simulation modeling frameworks, the method detects both complete (impermeable) barriers and those that impede but do not completely block movement. Barrier mapping complements corridor mapping by broadening the range of connectivity conservation alternatives available to practitioners. The method can help practitioners move beyond maintaining currently important areas to restoring and enhancing connectivity through active barrier removal. It can inform decisions on trade-offs between restoration and protection; for example, purchasing an intact corridor may be substantially more costly than restoring a barrier that blocks an alternative corridor. And it extends the concept of centrality to barriers, highlighting areas that most diminish connectivity across broad networks. Identifying which modeled barriers have the greatest impact can also help prioritize error checking of land cover data and collection of field data to improve connectivity maps. Barrier detection provides a different way to view the landscape, broadening thinking about connectivity and fragmentation while increasing conservation options.}, } @article {pmid23292820, year = {2013}, author = {Jacoby, M and Averbuch, S and Sacher, Y and Katz, N and Weiss, PL and Kizony, R}, title = {Effectiveness of executive functions training within a virtual supermarket for adults with traumatic brain injury: a pilot study.}, journal = {IEEE transactions on neural systems and rehabilitation engineering : a publication of the IEEE Engineering in Medicine and Biology Society}, volume = {21}, number = {2}, pages = {182-190}, doi = {10.1109/TNSRE.2012.2235184}, pmid = {23292820}, issn = {1558-0210}, mesh = {Activities of Daily Living ; Adult ; Brain Injuries/complications/*physiopathology/*rehabilitation ; Cognition Disorders/etiology/*physiopathology/*rehabilitation ; *Executive Function ; Female ; Humans ; Male ; Middle Aged ; Pilot Projects ; Therapy, Computer-Assisted/*methods ; Treatment Outcome ; *User-Computer Interface ; Young Adult ; }, abstract = {Impairments of executive functions (EF) significantly affect the ability to lead an independent lifestyle. Virtual environments offer a way to rehabilitate EF due to their ecological validity. The purpose of this pilot study was to examine the effectiveness of a virtual reality (VR) supermarket (VMall) for treatment of EF in patients with Traumatic Brain Injury (TBI), compared to conventional occupational therapy (OT), in order to provide initial data regarding the effect sizes for calculation of sample size as well as to establish an intervention protocol for future Randomized Control Trials (RCTs). Twelve men and women, aged 19-55 years, who had TBI resulting in EF impairments participated in this study. Outcome measures were the Multiple Errands Test-Simplified Version (MET-SV) and the Executive Function Performance Test (EFPT). Cognitive treatment provided to both groups was based on the same principles; the participants in the experimental group received 10 45-min VR-based treatment sessions and the control group participants received 10 sessions of occupational therapy cognitive retraining without VR. Baseline performance prior to intervention showed no statistically significant differences between groups. Most participants improved their performance after therapy. Following a Bonferroni correction for multiple comparisons, no significant between or within group differences were found, Nevertheless, large effect sizes (0.51) for the percent (%) relative change of the MET-SV total score and EFPT total score after intervention were high in favor of the experimental group indicating a larger improvement in EF. Based on this pilot study, results show a trend towards an advantage to VR therapy compared to cognitive retraining OT without VR, as it leads to greater improvement in complex everyday activities.}, } @article {pmid23277544, year = {2013}, author = {Condon, RH and Duarte, CM and Pitt, KA and Robinson, KL and Lucas, CH and Sutherland, KR and Mianzan, HW and Bogeberg, M and Purcell, JE and Decker, MB and Uye, S and Madin, LP and Brodeur, RD and Haddock, SH and Malej, A and Parry, GD and Eriksen, E and Quiñones, J and Acha, M and Harvey, M and Arthur, JM and Graham, WM}, title = {Recurrent jellyfish blooms are a consequence of global oscillations.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {110}, number = {3}, pages = {1000-1005}, pmid = {23277544}, issn = {1091-6490}, mesh = {Animals ; Climate Change ; Cnidaria/growth & development ; Ctenophora/growth & development ; Databases, Factual ; Ecological and Environmental Phenomena ; Ecosystem ; Humans ; *Periodicity ; Population Dynamics ; Scyphozoa/*growth & development ; Time Factors ; Urochordata/growth & development ; Zooplankton/growth & development ; }, abstract = {A perceived recent increase in global jellyfish abundance has been portrayed as a symptom of degraded oceans. This perception is based primarily on a few case studies and anecdotal evidence, but a formal analysis of global temporal trends in jellyfish populations has been missing. Here, we analyze all available long-term datasets on changes in jellyfish abundance across multiple coastal stations, using linear and logistic mixed models and effect-size analysis to show that there is no robust evidence for a global increase in jellyfish. Although there has been a small linear increase in jellyfish since the 1970s, this trend was unsubstantiated by effect-size analysis that showed no difference in the proportion of increasing vs. decreasing jellyfish populations over all time periods examined. Rather, the strongest nonrandom trend indicated jellyfish populations undergo larger, worldwide oscillations with an approximate 20-y periodicity, including a rising phase during the 1990s that contributed to the perception of a global increase in jellyfish abundance. Sustained monitoring is required over the next decade to elucidate with statistical confidence whether the weak increasing linear trend in jellyfish after 1970 is an actual shift in the baseline or part of an oscillation. Irrespective of the nature of increase, given the potential damage posed by jellyfish blooms to fisheries, tourism, and other human industries, our findings foretell recurrent phases of rise and fall in jellyfish populations that society should be prepared to face.}, } @article {pmid23274217, year = {2013}, author = {Reen, FJ and Barret, M and Fargier, E and O'Muinneacháin, M and O'Gara, F}, title = {Molecular evolution of LysR-type transcriptional regulation in Pseudomonas aeruginosa.}, journal = {Molecular phylogenetics and evolution}, volume = {66}, number = {3}, pages = {1041-1049}, doi = {10.1016/j.ympev.2012.12.014}, pmid = {23274217}, issn = {1095-9513}, mesh = {Bacterial Proteins/*genetics ; Base Composition/genetics ; Cluster Analysis ; Computational Biology ; *Evolution, Molecular ; Likelihood Functions ; Models, Genetic ; Multigene Family/*genetics ; *Phylogeny ; Pseudomonas aeruginosa/*genetics ; Regulatory Elements, Transcriptional/*genetics ; Transcription Factors/*genetics ; }, abstract = {Signal perception and transduction through tightly coordinated circuits is integral to the survival and persistence of microbes in diverse ecological niches. The capacity to adapt to changes in the environment is central to their ability to thrive under adverse circumstances. Signal dependent transcriptional regulators are a key mechanism through which microbes assimilate environmental cues and mediate the appropriate adaptive response. By far the largest class of transcriptional regulator is the LysR-class, which is universally distributed among bacteria, archaea, and even eukaryotic organisms. The number of LysR-Type Transcriptional Regulators (LTTRs) varies among species with one of the largest repertoires encoded in the genome of the nosocomial pathogen Pseudomonas aeruginosa. To understand the evolutionary basis for this, we undertook to analyse the relationship between the LTTRs, both at the species and genus level. Phylogenetic analysis of the complete Pseudomonas LTTR dataset revealed significant cluster patterns based on full length and domain analysis. Interestingly, evidence of acquisition through horizontal gene transfer was rare, with divergent evolution apparently favoured. Furthermore, genes that appear to have been acquired, as well as those with a non-classical topological arrangement were clustered in distinct groups in the phylogenetic trees, indicating some ancestral association. The conservation within clusters identified in this study will provide a useful platform for future molecular analyses.}, } @article {pmid23271811, year = {2013}, author = {Payne, RJ and Dise, NB and Stevens, CJ and Gowing, DJ and , }, title = {Impact of nitrogen deposition at the species level.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {110}, number = {3}, pages = {984-987}, pmid = {23271811}, issn = {1091-6490}, mesh = {Air Pollutants/toxicity ; Air Pollution/*prevention & control ; Databases, Factual ; *Ecosystem ; Europe ; No-Observed-Adverse-Effect Level ; Poaceae/drug effects/metabolism ; Reactive Nitrogen Species/*toxicity ; Species Specificity ; }, abstract = {In Europe and, increasingly, the rest of the world, the key policy tool for the control of air pollution is the critical load, a level of pollution below which there are no known significant harmful effects on the environment. Critical loads are used to map sensitive regions and habitats, permit individual polluting activities, and frame international negotiations on transboundary air pollution. Despite their fundamental importance in environmental science and policy, there has been no systematic attempt to verify a critical load with field survey data. Here, we use a large dataset of European grasslands along a gradient of nitrogen (N) deposition to show statistically significant declines in the abundance of species from the lowest level of N deposition at which it is possible to identify a change. Approximately 60% of species change points occur at or below the range of the currently established critical load. If this result is found more widely, the underlying principle of no harm in pollution policy may need to be modified to one of informed decisions on how much harm is acceptable. Our results highlight the importance of protecting currently unpolluted areas from new pollution sources, because we cannot rule out ecological impacts from even relatively small increases in reactive N deposition.}, } @article {pmid23270314, year = {2012}, author = {Weissbrodt, DG and Shani, N and Sinclair, L and Lefebvre, G and Rossi, P and Maillard, J and Rougemont, J and Holliger, C}, title = {PyroTRF-ID: a novel bioinformatics methodology for the affiliation of terminal-restriction fragments using 16S rRNA gene pyrosequencing data.}, journal = {BMC microbiology}, volume = {12}, number = {}, pages = {306}, pmid = {23270314}, issn = {1471-2180}, mesh = {*Biota ; Computational Biology/*methods ; DNA, Ribosomal/chemistry/*genetics ; Groundwater/microbiology ; *Phylogeny ; *Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, DNA ; Wastewater/microbiology ; }, abstract = {BACKGROUND: In molecular microbial ecology, massive sequencing is gradually replacing classical fingerprinting techniques such as terminal-restriction fragment length polymorphism (T-RFLP) combined with cloning-sequencing for the characterization of microbiomes. Here, a bioinformatics methodology for pyrosequencing-based T-RF identification (PyroTRF-ID) was developed to combine pyrosequencing and T-RFLP approaches for the description of microbial communities. The strength of this methodology relies on the identification of T-RFs by comparison of experimental and digital T-RFLP profiles obtained from the same samples. DNA extracts were subjected to amplification of the 16S rRNA gene pool, T-RFLP with the HaeIII restriction enzyme, 454 tag encoded FLX amplicon pyrosequencing, and PyroTRF-ID analysis. Digital T-RFLP profiles were generated from the denoised full pyrosequencing datasets, and the sequences contributing to each digital T-RF were classified to taxonomic bins using the Greengenes reference database. The method was tested both on bacterial communities found in chloroethene-contaminated groundwater samples and in aerobic granular sludge biofilms originating from wastewater treatment systems.

RESULTS: PyroTRF-ID was efficient for high-throughput mapping and digital T-RFLP profiling of pyrosequencing datasets. After denoising, a dataset comprising ca. 10'000 reads of 300 to 500 bp was typically processed within ca. 20 minutes on a high-performance computing cluster, running on a Linux-related CentOS 5.5 operating system, enabling parallel processing of multiple samples. Both digital and experimental T-RFLP profiles were aligned with maximum cross-correlation coefficients of 0.71 and 0.92 for high- and low-complexity environments, respectively. On average, 63±18% of all experimental T-RFs (30 to 93 peaks per sample) were affiliated to phylotypes.

CONCLUSIONS: PyroTRF-ID profits from complementary advantages of pyrosequencing and T-RFLP and is particularly adapted for optimizing laboratory and computational efforts to describe microbial communities and their dynamics in any biological system. The high resolution of the microbial community composition is provided by pyrosequencing, which can be performed on a restricted set of selected samples, whereas T-RFLP enables simultaneous fingerprinting of numerous samples at relatively low cost and is especially adapted for routine analysis and follow-up of microbial communities on the long run.}, } @article {pmid23269552, year = {2013}, author = {Yang, C and Ji, Y and Wang, X and Yang, C and Yu, DW}, title = {Testing three pipelines for 18S rDNA-based metabarcoding of soil faunal diversity.}, journal = {Science China. Life sciences}, volume = {56}, number = {1}, pages = {73-81}, doi = {10.1007/s11427-012-4423-7}, pmid = {23269552}, issn = {1869-1889}, mesh = {Animals ; Annelida/classification/genetics/growth & development ; Arthropods/classification/genetics/growth & development ; *Biodiversity ; Computational Biology/*methods ; DNA Barcoding, Taxonomic ; DNA, Ribosomal/chemistry/genetics ; Eukaryota/classification/genetics/growth & development ; *Genetic Variation ; Nematoda/classification/genetics/growth & development ; Phylogeny ; RNA, Ribosomal, 18S/*genetics ; Sequence Analysis, DNA ; Soil/*parasitology ; }, abstract = {A number of basic and applied questions in ecology and environmental management require the characterization of soil and leaf litter faunal diversity. Recent advances in high-throughput sequencing of barcode-gene amplicons ('metabarcoding') have made it possible to survey biodiversity in a robust and efficient way. However, one obstacle to the widespread adoption of this technique is the need to choose amongst many candidates for bioinformatic processing of the raw sequencing data. We compare three candidate pipelines for the processing of 18S small subunit rDNA metabarcode data from solid substrates: (i) USEARCH/CROP, (ii) Denoiser/UCLUST, and (iii) OCTUPUS. The three pipelines produced reassuringly similar and highly correlated assessments of community composition that are dominated by taxa known to characterize the sampled environments. However, OCTUPUS appears to inflate phylogenetic diversity, because of higher sequence noise. We therefore recommend either the USEARCH/CROP or Denoiser/UCLUST pipelines, both of which can be run within the QIIME (Quantitative Insights Into Microbial Ecology) environment.}, } @article {pmid23262143, year = {2013}, author = {Tabadkani, SM and Ahsaei, SM and Hosseininaveh, V and Nozari, J}, title = {Food stress prompts dispersal behavior in apterous pea aphids: do activated aphids incur energy loss?.}, journal = {Physiology & behavior}, volume = {110-111}, number = {}, pages = {221-225}, doi = {10.1016/j.physbeh.2012.12.004}, pmid = {23262143}, issn = {1873-507X}, mesh = {Animals ; Aphids/*physiology ; Behavior, Animal/*physiology ; Body Weight/physiology ; Carbohydrate Metabolism/physiology ; Data Interpretation, Statistical ; Dietary Carbohydrates/pharmacology ; Dietary Fats/pharmacology ; Dietary Proteins/pharmacology ; Energy Metabolism/*physiology ; Environment ; *Food ; Glycogen/metabolism ; Pisum sativum/*physiology ; Pigmentation ; Stress, Psychological/metabolism/*psychology ; }, abstract = {The pea aphid, Acyrthosiphon pisum (Hem: Aphididae), has been repeatedly used as a model species in a wide range of biological studies including genetics, ecology, physiology, and behavior. When red pea aphids feed on low quality plants in crowded conditions, some individuals lose their color shade and become pale yellowish, while other individuals on the same host plants remain changeless. The pale aphids have been shown to walk significantly faster and migrate more frequently to neighboring plants compared to the original red ones. We hypothesized that the color change and higher activity of pale aphids are directly associated with their suboptimal nutritional status. We showed that the pale aphids have significantly lower wet and dry weights than red ones. Analyses of energy reserves in individual aphids revealed that the pale aphids suffer a significant loss in their lipid and soluble carbohydrate contents. Our results provide a strong link between host quality, body color, dispersal rate, and energy reserves of pea aphids. Apparently, utilization of energy reserves resulted from an imbalance in food sources received by the aphids stimulates them to walk more actively to find new hosts and restore their lost energy. This reversible shift enables aphids to quickly respond to deprived host plants much earlier than the appearance of winged morph and restore their original status when they find appropriate host.}, } @article {pmid23257059, year = {2012}, author = {Smith, B and Harms, WD and Burres, S and Korda, H and Rosen, H and Davis, J}, title = {Enhancing behavioral health treatment and crisis management through mobile ecological momentary assessment and SMS messaging.}, journal = {Health informatics journal}, volume = {18}, number = {4}, pages = {294-308}, doi = {10.1177/1460458212445349}, pmid = {23257059}, issn = {1741-2811}, mesh = {Afghan Campaign 2001- ; *Cell Phone ; Computers, Handheld ; Crisis Intervention ; Disaster Planning/*standards ; Feasibility Studies ; Feedback, Psychological ; *Health Behavior ; Humans ; Iraq War, 2003-2011 ; Mental Health Services ; Organizational Innovation ; Patient Discharge ; Pilot Projects ; Remote Consultation/*methods ; Text Messaging/*statistics & numerical data ; Veterans/psychology/statistics & numerical data ; }, abstract = {Many veterans returning from service in Afghanistan or Iraq suffer from post-traumatic stress disorder or mild traumatic brain injury. Treating these conditions can be challenging because of high rates of relapse and associated memory impairments. We report on a pilot study that assessed the utility of mobile health (mHealth) technologies, including personal digital assistant-based ecological momentary assessment and two-way interactive text (SMS) messaging, for providing treatment feedback to clinicians, encouraging and motivating veterans throughout treatment, and monitoring participants for relapse after treatment discharge. The results of the pilot suggest that mHealth technologies are feasible adjuncts to traditional mental treatment in the veteran population. Additional work is needed to establish the degree of clinical and economic value.}, } @article {pmid23250724, year = {2013}, author = {Armanini, DG and Monk, WA and Carter, L and Cote, D and Baird, DJ}, title = {Towards generalised reference condition models for environmental assessment: a case study on rivers in Atlantic Canada.}, journal = {Environmental monitoring and assessment}, volume = {185}, number = {8}, pages = {6247-6259}, pmid = {23250724}, issn = {1573-2959}, mesh = {Animals ; Ecosystem ; Environment ; Environmental Monitoring/*methods ; Geographic Information Systems ; Invertebrates/classification ; *Models, Biological ; *Rivers ; }, abstract = {Evaluation of the ecological status of river sites in Canada is supported by building models using the reference condition approach. However, geography, data scarcity and inter-operability constraints have frustrated attempts to monitor national-scale status and trends. This issue is particularly true in Atlantic Canada, where no ecological assessment system is currently available. Here, we present a reference condition model based on the River Invertebrate Prediction and Classification System approach with regional-scale applicability. To achieve this, we used biological monitoring data collected from wadeable streams across Atlantic Canada together with freely available, nationally consistent geographic information system (GIS) environmental data layers. For the first time, we demonstrated that it is possible to use data generated from different studies, even when collected using different sampling methods, to generate a robust predictive model. This model was successfully generated and tested using GIS-based rather than local habitat variables and showed improved performance when compared to a null model. In addition, ecological quality ratio data derived from the model responded to observed stressors in a test dataset. Implications for future large-scale implementation of river biomonitoring using a standardised approach with global application are presented.}, } @article {pmid23250300, year = {2013}, author = {Mikolajczyk, RT and Kraut, AA and Horn, J and Schulze-Rath, R and Garbe, E}, title = {Changes in incidence of anogenital warts diagnoses after the introduction of human papillomavirus vaccination in Germany-an ecologic study.}, journal = {Sexually transmitted diseases}, volume = {40}, number = {1}, pages = {28-31}, doi = {10.1097/OLQ.0b013e3182756efd}, pmid = {23250300}, issn = {1537-4521}, mesh = {Adolescent ; Adult ; Age Distribution ; Aged ; Alphapapillomavirus/*immunology ; Child ; Cohort Studies ; Condylomata Acuminata/epidemiology/*prevention & control/virology ; Databases, Factual ; Female ; Germany/epidemiology ; Humans ; Incidence ; Male ; Middle Aged ; *Papillomavirus Vaccines ; Poisson Distribution ; Sex Distribution ; Time Factors ; *Vaccination ; Young Adult ; }, abstract = {In a large health insurance database in Germany, incidence of anogenital warts among 15- to 19-year-old females decreased from 316/100,000 person-years in 2007 to 242 in 2008 (23% reduction, P = 0.0001). The decrease started between the first and second quarter of 2007 (human papillomavirus vaccination was introduced in March 2007).}, } @article {pmid23239979, year = {2012}, author = {Rodríguez, A and Negro, JJ and Mulero, M and Rodríguez, C and Hernández-Pliego, J and Bustamante, J}, title = {The eye in the sky: combined use of unmanned aerial systems and GPS data loggers for ecological research and conservation of small birds.}, journal = {PloS one}, volume = {7}, number = {12}, pages = {e50336}, pmid = {23239979}, issn = {1932-6203}, mesh = {Animals ; *Behavior, Animal ; Conservation of Natural Resources ; Ecosystem ; Environment ; Environmental Monitoring ; Falconiformes/*physiology ; *Flight, Animal ; Geographic Information Systems/*instrumentation ; }, abstract = {Technological advances for wildlife monitoring have expanded our ability to study behavior and space use of many species. But biotelemetry is limited by size, weight, data memory and battery power of the attached devices, especially in animals with light body masses, such as the majority of bird species. In this study, we describe the combined use of GPS data logger information obtained from free-ranging birds, and environmental information recorded by unmanned aerial systems (UASs). As a case study, we studied habitat selection of a small raptorial bird, the lesser kestrel Falco naumanni, foraging in a highly dynamic landscape. After downloading spatio-temporal information from data loggers attached to the birds, we programmed the UASs to fly and take imagery by means of an onboard digital camera documenting the flight paths of those same birds shortly after their recorded flights. This methodology permitted us to extract environmental information at quasi-real time. We demonstrate that UASs are a useful tool for a wide variety of wildlife studies.}, } @article {pmid23228011, year = {2013}, author = {Alex Smith, M and Fernández-Triana, JL and Eveleigh, E and Gómez, J and Guclu, C and Hallwachs, W and Hebert, PD and Hrcek, J and Huber, JT and Janzen, D and Mason, PG and Miller, S and Quicke, DL and Rodriguez, JJ and Rougerie, R and Shaw, MR and Várkonyi, G and Ward, DF and Whitfield, JB and Zaldívar-Riverón, A}, title = {DNA barcoding and the taxonomy of Microgastrinae wasps (Hymenoptera, Braconidae): impacts after 8 years and nearly 20 000 sequences.}, journal = {Molecular ecology resources}, volume = {13}, number = {2}, pages = {168-176}, doi = {10.1111/1755-0998.12038}, pmid = {23228011}, issn = {1755-0998}, mesh = {Animals ; Base Sequence ; *DNA Barcoding, Taxonomic ; Molecular Sequence Data ; *Phylogeny ; Sequence Analysis, DNA ; Wasps/*classification/*genetics ; }, abstract = {Microgastrine wasps are among the most species-rich and numerous parasitoids of caterpillars (Lepidoptera). They are often host-specific and thus are extensively used in biological control efforts and figure prominently in trophic webs. However, their extraordinary diversity coupled with the occurrence of many cryptic species produces a significant taxonomic impediment. We present and release the results of 8 years (2004-2011) of DNA barcoding microgastrine wasps. Currently they are the best represented group of parasitoid Hymenoptera in the Barcode of Life Data System (BOLD), a massive barcode storage and analysis data management site for the International Barcoding of Life (iBOL) program. There are records from more than 20 000 specimens from 75 countries, including 50 genera (90% of the known total) and more than 1700 species (as indicated by Barcode Index Numbers and 2% MOTU). We briefly discuss the importance of this DNA data set and its collateral information for future research in: (1) discovery of cryptic species and description of new taxa; (2) estimating species numbers in biodiversity inventories; (3) clarification of generic boundaries; (4) biological control programmes; (5) molecular studies of host-parasitoid biology and ecology; (6) evaluation of shifts in species distribution and phenology; and (7) fostering collaboration at national, regional and world levels. The integration of DNA barcoding with traditional morphology-based taxonomy, host records, and other data has substantially improved the accuracy of microgastrine wasp identifications and will significantly accelerate further studies on this group of parasitoids.}, } @article {pmid23226495, year = {2012}, author = {Bass, D and Yabuki, A and Santini, S and Romac, S and Berney, C}, title = {Reticulamoeba is a long-branched Granofilosean (Cercozoa) that is missing from sequence databases.}, journal = {PloS one}, volume = {7}, number = {12}, pages = {e49090}, pmid = {23226495}, issn = {1932-6203}, mesh = {Animals ; Base Sequence ; Cercozoa/classification/*genetics ; DNA Primers ; *Databases, Genetic ; Information Storage and Retrieval ; Likelihood Functions ; Phylogeny ; }, abstract = {We sequenced the 18S ribosomal RNA gene of seven isolates of the enigmatic marine amoeboflagellate Reticulamoeba Grell, which resolved into four genetically distinct Reticulamoeba lineages, two of which correspond to R. gemmipara Grell and R. minor Grell, another with a relatively large cell body forming lacunae, and another that has similarities to both R. minor and R. gemmipara but with a greater propensity to form cell clusters. These lineages together form a long-branched clade that branches within the cercozoan class Granofilosea (phylum Cercozoa), showing phylogenetic affinities with the genus Mesofila. The basic morphology of Reticulamoeba is a roundish or ovoid cell with a more or less irregular outline. Long and branched reticulopodia radiate from the cell. The reticulopodia bear granules that are bidirectionally motile. There is also a biflagellate dispersal stage. Reticulamoeba is frequently observed in coastal marine environmental samples. PCR primers specific to the Reticulamoeba clade confirm that it is a frequent member of benthic marine microbial communities, and is also found in brackish water sediments and freshwater biofilm. However, so far it has not been found in large molecular datasets such as the nucleotide database in NCBI GenBank, metagenomic datasets in Camera, and the marine microbial eukaryote sampling and sequencing consortium BioMarKs, although closely related lineages can be found in some of these datasets using a highly targeted approach. Therefore, although such datasets are very powerful tools in microbial ecology, they may, for several methodological reasons, fail to detect ecologically and evolutionary key lineages.}, } @article {pmid23226313, year = {2012}, author = {Bidder, OR and Qasem, LA and Wilson, RP}, title = {On higher ground: how well can dynamic body acceleration determine speed in variable terrain?.}, journal = {PloS one}, volume = {7}, number = {11}, pages = {e50556}, pmid = {23226313}, issn = {1932-6203}, mesh = {*Acceleration ; Geographic Information Systems ; Humans ; Kinetics ; Linear Models ; *Movement ; Telemetry ; }, abstract = {INTRODUCTION: Animal travel speed is an ecologically significant parameter, with implications for the study of energetics and animal behaviour. It is also necessary for the calculation of animal paths by dead-reckoning. Dead-reckoning uses heading and speed to calculate an animal's path through its environment on a fine scale. It is often used in aquatic environments, where transmission telemetry is difficult. However, its adoption for tracking terrestrial animals is limited by our ability to measure speed accurately on a fine scale. Recently, tri-axial accelerometers have shown promise for estimating speed, but their accuracy appears affected by changes in substrate and surface gradients. The purpose of the present study was to evaluate four metrics of acceleration; Overall dynamic body acceleration (ODBA), vectorial dynamic body acceleration (VDBA), acceleration peak frequency and acceleration peak amplitude, as proxies for speed over hard, soft and inclined surfaces, using humans as a model species.

RESULTS: A general linear model (GLM) showed a significant difference in the relationships between the metrics and speed depending on substrate or surface gradient. When the data from all surface types were considered together, VeDBA had the highest coefficient of determination.

CONCLUSIONS: All of the metrics showed some variation in their relationship with speed according to the surface type. This indicates that changes in the substrate or surface gradient during locomotion by animals would produce errors in speed estimates, and also in dead-reckoned tracks if they were calculated from speeds based entirely on a priori calibrations. However, we describe a method by which the relationship between acceleration metrics and speed can be corrected ad hoc, until tracks accord with periodic ground truthed positions, obtained via a secondary means (e.g. VHF or GPS telemetry). In this way, dead-reckoning provides a means to obtain fine scale movement data for terrestrial animals, without the need for additional data on substrate or gradient.}, } @article {pmid23224610, year = {2013}, author = {Martinez, C and Marzec, T and Smith, CD and Tell, LA and Sehgal, RN}, title = {Identification and expression of maebl, an erythrocyte-binding gene, in Plasmodium gallinaceum.}, journal = {Parasitology research}, volume = {112}, number = {3}, pages = {945-954}, pmid = {23224610}, issn = {1432-1955}, support = {R25 GM048972/GM/NIGMS NIH HHS/United States ; SC2 AI089120/AI/NIAID NIH HHS/United States ; 2R25-GM048972-11/GM/NIGMS NIH HHS/United States ; SC2AI089120-01A1/AI/NIAID NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Animals ; Antigens, Protozoan/*biosynthesis/genetics ; Chickens ; Cluster Analysis ; Computational Biology ; Conserved Sequence ; *Gene Expression Profiling ; Molecular Sequence Data ; Phylogeny ; Plasmodium gallinaceum/genetics/isolation & purification/*pathogenicity ; Polymerase Chain Reaction ; Poultry Diseases/parasitology ; Protozoan Proteins/*biosynthesis/genetics ; Receptors, Cell Surface/*biosynthesis/genetics ; Sequence Alignment ; Sequence Analysis, DNA ; Virulence Factors/*biosynthesis/genetics ; }, abstract = {Avian malaria is of significant ecological importance and serves as a model system to study broad patterns of host switching and host specificity. The erythrocyte invasion mechanism of the malaria parasite Plasmodium is mediated, in large part, by proteins of the erythrocyte-binding-like (ebl) family of genes. However, little is known about how these genes are conserved across different species of Plasmodium, especially those that infect birds. Using bioinformatical methods in conjunction with polymerase chain reaction (PCR) and genetic sequencing, we identified and annotated one member of the ebl family, merozoite apical erythrocyte-binding ligand (maebl), from the chicken parasite Plasmodium gallinaceum. We then detected the expression of maebl in P. gallinaceum by PCR analysis of cDNA isolated from the blood of infected chickens. We found that maebl is a conserved orthologous gene in avian, mammalian, and rodent Plasmodium species. The duplicate extracellular binding domains of MAEBL, responsible for erythrocyte binding, are the most conserved regions. Our combined data corroborate the conservation of maebl throughout the Plasmodium genus and may help elucidate the mechanisms of erythrocyte invasion in P. gallinaceum and the host specificity of Plasmodium parasites.}, } @article {pmid23224572, year = {2013}, author = {Rigobello-Masini, M and Penteado, JC and Masini, JC}, title = {Monolithic columns in plant proteomics and metabolomics.}, journal = {Analytical and bioanalytical chemistry}, volume = {405}, number = {7}, pages = {2107-2122}, doi = {10.1007/s00216-012-6574-6}, pmid = {23224572}, issn = {1618-2650}, mesh = {Chromatography, Liquid/*instrumentation/methods ; Metabolomics/*instrumentation/methods ; Plant Proteins/chemistry/*isolation & purification ; Plants/*chemistry ; Proteomics/*instrumentation/methods ; }, abstract = {Since "omics" techniques emerged, plant studies, from biochemistry to ecology, have become more comprehensive. Plant proteomics and metabolomics enable the construction of databases that, with the help of genomics and informatics, show the data obtained as a system. Thus, all the constituents of the system can be seen with their interactions in both space and time. For instance, perturbations in a plant ecosystem as a consequence of application of herbicides or exposure to pollutants can be predicted by using information gathered from these databases. Analytical chemistry has been involved in this scientific evolution. Proteomics and metabolomics are emerging fields that require separation, identification, and quantification of proteins, peptides, and small molecules of metabolites in complex biological samples. The success of this work relies on efficient chromatographic and electrophoretic techniques, and on mass spectrometric detection. This paper reviews recent developments in the use of monolithic columns, focusing on their applications in "top-down" and "bottom-up" approaches, including their use as supports for immobilization of proteolytic enzymes and their use in two-dimensional and multidimensional chromatography. Whereas polymeric columns have been predominantly used for separation of proteins and polypeptides, silica-based monoliths have been more extensively used for separation of small molecules of metabolites. Representative applications in proteomics and in analysis of plant metabolites are given and summarized in tables.}, } @article {pmid23223880, year = {2013}, author = {Balsera, M and Uberegui, E and Susanti, D and Schmitz, RA and Mukhopadhyay, B and Schürmann, P and Buchanan, BB}, title = {Ferredoxin:thioredoxin reductase (FTR) links the regulation of oxygenic photosynthesis to deeply rooted bacteria.}, journal = {Planta}, volume = {237}, number = {2}, pages = {619-635}, pmid = {23223880}, issn = {1432-2048}, mesh = {Amino Acid Sequence ; Bacteria/classification/*enzymology/genetics/radiation effects ; Bacterial Proteins/genetics/metabolism ; Carbon Dioxide/metabolism ; Chloroplast Proteins/genetics/metabolism ; Chloroplasts/*enzymology/genetics ; Databases, Genetic ; Evolution, Molecular ; Ferredoxins/metabolism ; Iron-Sulfur Proteins/genetics/*metabolism ; Light ; Molecular Sequence Data ; Oxidation-Reduction ; Oxidoreductases/genetics/*metabolism ; Oxygen/metabolism ; Phosphotransferases (Alcohol Group Acceptor)/genetics/metabolism ; *Photosynthesis ; Phylogeny ; Plants/classification/enzymology/genetics/radiation effects ; Sequence Alignment ; }, abstract = {Uncovered in studies on photosynthesis 35 years ago, redox regulation has been extended to all types of living cells. We understand a great deal about the occurrence, function, and mechanism of action of this mode of regulation, but we know little about its origin and its evolution. To help fill this gap, we have taken advantage of available genome sequences that make it possible to trace the phylogenetic roots of members of the system that was originally described for chloroplasts-ferredoxin, ferredoxin:thioredoxin reductase (FTR), and thioredoxin as well as target enzymes. The results suggest that: (1) the catalytic subunit, FTRc, originated in deeply rooted microaerophilic, chemoautotrophic bacteria where it appears to function in regulating CO(2) fixation by the reverse citric acid cycle; (2) FTRc was incorporated into oxygenic photosynthetic organisms without significant structural change except for addition of a variable subunit (FTRv) seemingly to protect the Fe-S cluster against oxygen; (3) new Trxs and target enzymes were systematically added as evolution proceeded from bacteria through the different types of oxygenic photosynthetic organisms; (4) an oxygenic type of regulation preceded classical light-dark regulation in the regulation of enzymes of CO(2) fixation by the Calvin-Benson cycle; (5) FTR is not universally present in oxygenic photosynthetic organisms, and in certain early representatives is seemingly functionally replaced by NADP-thioredoxin reductase; and (6) FTRc underwent structural diversification to meet the ecological needs of a variety of bacteria and archaea.}, } @article {pmid23209397, year = {2012}, author = {Kubicek, A and Muhando, C and Reuter, H}, title = {Simulations of long-term community dynamics in coral reefs--how perturbations shape trajectories.}, journal = {PLoS computational biology}, volume = {8}, number = {11}, pages = {e1002791}, pmid = {23209397}, issn = {1553-7358}, mesh = {Animals ; Anthozoa/physiology ; Chlorophyta/physiology ; Computational Biology ; *Coral Reefs ; *Ecosystem ; Microalgae/physiology ; *Models, Biological ; Population Dynamics ; Tanzania ; Temperature ; }, abstract = {Tropical coral reefs feature extraordinary biodiversity and high productivity rates in oligotrophic waters. Due to increasing frequencies of perturbations--anthropogenic and natural--many reefs are under threat. Such perturbations often have devastating effects on these unique ecosystems and especially if they occur simultaneously and amplify each other's impact, they might trigger a phase shift and create irreversible conditions.We developed a generic, spatially explicit, individual-based model in which competition drives the dynamics of a virtual benthic reef community--comprised of scleractinian corals and algae--under different environmental settings. Higher system properties, like population dynamics or community composition arise through self-organization as emergent properties. The model was parameterized for a typical coral reef site at Zanzibar, Tanzania and features coral bleaching and physical disturbance regimes as major sources of perturbations. Our results show that various types and modes (intensities and frequencies) of perturbations create diverse outcomes and that the switch from high diversity to single species dominance can be evoked by small changes in a key parameter. Here we extend the understanding of coral reef resilience and the identification of key processes, drivers and respective thresholds, responsible for changes in local situations. One future goal is to provide a tool which may aid decision making processes in management of coral reefs.}, } @article {pmid23203890, year = {2013}, author = {Pan, B and Sheng, J and Sun, W and Zhao, Y and Hao, P and Li, X}, title = {OrysPSSP: a comparative platform for small secreted proteins from rice and other plants.}, journal = {Nucleic acids research}, volume = {41}, number = {Database issue}, pages = {D1192-8}, pmid = {23203890}, issn = {1362-4962}, mesh = {*Databases, Protein ; Genomics ; Internet ; Oryza/genetics/*metabolism ; Plant Proteins/genetics/*metabolism ; Secretory Pathway ; Software ; User-Computer Interface ; }, abstract = {Plants have large diverse families of small secreted proteins (SSPs) that play critical roles in the processes of development, differentiation, defense, flowering, stress response, symbiosis, etc. Oryza sativa is one of the major crops worldwide and an excellent model for monocotyledonous plants. However, there had not been any effort to systematically analyze rice SSPs. Here, we constructed a comparative platform, OrysPSSP (http://www.genoportal.org/PSSP/index.do), involving >100 000 SSPs from rice and 25 plant species. OrysPSSP is composed of a core SSP database and a dynamic web interface that integrates a variety of user tools and resources. The current release (v0530) of core SSP database contains a total of 101 048 predicted SSPs, which were generated through a rigid computation/curation pipeline. The web interface consists of eight different modules, providing users with rich resources/functions, e.g. browsing SSP by chromosome, searching and filtering SSP, validating SSP with omics data, comparing SSP among multiple species and querying core SSP database with BLAST. Some cases of application are discussed to demonstrate the utility of OrysPSSP. OrysPSSP serves as a comprehensive resource to explore SSP on the genome scale and across the phylogeny of plant species.}, } @article {pmid23202833, year = {2012}, author = {Lin, YP and Hong, NM and Chiang, LC and Liu, YL and Chu, HJ}, title = {Adaptation of land-use demands to the impact of climate change on the hydrological processes of an urbanized watershed.}, journal = {International journal of environmental research and public health}, volume = {9}, number = {11}, pages = {4083-4102}, pmid = {23202833}, issn = {1660-4601}, mesh = {*Climate Change ; *Geographic Information Systems ; *Hydrology ; *Urban Population ; Water Movements ; }, abstract = {The adaptation of land-use patterns is an essential aspect of minimizing the inevitable impact of climate change at regional and local scales; for example, adapting watershed land-use patterns to mitigate the impact of climate change on a region's hydrology. The objective of this study is to simulate and assess a region's ability to adapt to hydrological changes by modifying land-use patterns in the Wu-Du watershed in northern Taiwan. A hydrological GWLF (Generalized Watershed Loading Functions) model is used to simulate three hydrological components, namely, runoff, groundwater and streamflow, based on various land-use scenarios under six global climate models. The land-use allocations are simulated by the CLUE-s model for the various development scenarios. The simulation results show that runoff and streamflow are strongly related to the precipitation levels predicted by different global climate models for the wet and dry seasons, but groundwater cycles are more related to land-use. The effects of climate change on groundwater and runoff can be mitigated by modifying current land-use patterns; and slowing the rate of urbanization would also reduce the impact of climate change on hydrological components. Thus, land-use adaptation on a local/regional scale provides an alternative way to reduce the impacts of global climate change on local hydrology.}, } @article {pmid23202431, year = {2013}, author = {Bordier, C and Puja, F and Macaluso, E}, title = {Sensory processing during viewing of cinematographic material: computational modeling and functional neuroimaging.}, journal = {NeuroImage}, volume = {67}, number = {}, pages = {213-226}, pmid = {23202431}, issn = {1095-9572}, support = {242809/ERC_/European Research Council/International ; }, mesh = {Auditory Cortex/*physiology ; Auditory Perception/*physiology ; Brain Mapping/*methods ; Computer Simulation ; Female ; Humans ; Image Interpretation, Computer-Assisted/*methods ; Magnetic Resonance Imaging/methods ; Male ; *Models, Neurological ; Reproducibility of Results ; Sensitivity and Specificity ; Television ; Visual Cortex/*physiology ; Visual Perception/*physiology ; Young Adult ; }, abstract = {The investigation of brain activity using naturalistic, ecologically-valid stimuli is becoming an important challenge for neuroscience research. Several approaches have been proposed, primarily relying on data-driven methods (e.g. independent component analysis, ICA). However, data-driven methods often require some post-hoc interpretation of the imaging results to draw inferences about the underlying sensory, motor or cognitive functions. Here, we propose using a biologically-plausible computational model to extract (multi-)sensory stimulus statistics that can be used for standard hypothesis-driven analyses (general linear model, GLM). We ran two separate fMRI experiments, which both involved subjects watching an episode of a TV-series. In Exp 1, we manipulated the presentation by switching on-and-off color, motion and/or sound at variable intervals, whereas in Exp 2, the video was played in the original version, with all the consequent continuous changes of the different sensory features intact. Both for vision and audition, we extracted stimulus statistics corresponding to spatial and temporal discontinuities of low-level features, as well as a combined measure related to the overall stimulus saliency. Results showed that activity in occipital visual cortex and the superior temporal auditory cortex co-varied with changes of low-level features. Visual saliency was found to further boost activity in extra-striate visual cortex plus posterior parietal cortex, while auditory saliency was found to enhance activity in the superior temporal cortex. Data-driven ICA analyses of the same datasets also identified "sensory" networks comprising visual and auditory areas, but without providing specific information about the possible underlying processes, e.g., these processes could relate to modality, stimulus features and/or saliency. We conclude that the combination of computational modeling and GLM enables the tracking of the impact of bottom-up signals on brain activity during viewing of complex and dynamic multisensory stimuli, beyond the capability of purely data-driven approaches.}, } @article {pmid23202299, year = {2013}, author = {Gomiero, A and Dagnino, A and Nasci, C and Viarengo, A}, title = {The use of protozoa in ecotoxicology: application of multiple endpoint tests of the ciliate E. crassus for the evaluation of sediment quality in coastal marine ecosystems.}, journal = {The Science of the total environment}, volume = {442}, number = {}, pages = {534-544}, doi = {10.1016/j.scitotenv.2012.10.023}, pmid = {23202299}, issn = {1879-1026}, mesh = {Biological Assay ; Data Interpretation, Statistical ; *Ecosystem ; Ecotoxicology/*methods ; Endpoint Determination ; Environmental Monitoring/*methods ; Euplotes/*drug effects/growth & development ; Geologic Sediments/*chemistry ; Italy ; Oceans and Seas ; Water Pollutants, Chemical/*toxicity ; }, abstract = {Despite an increasing number of surveys describing adverse effects of contaminated sediments on marine organisms, few studies have addressed protists. In this study, the free-crawling marine ciliate Euplotes crassus was evaluated as the test organism for the screening of sediment toxicity using sediments from both coastal and estuarine sites of the Venice Lagoon (Marghera harbour [MH], Valle Millecampi [MV], Murano island [MI] and Lido inlet [LI]). Two endpoints of high ecological value, mortality (Mry) and replication rate (RpR), were assessed in combination with the two sublethal biomarkers of stress, endocytotic rate (Ecy) and lysosomal membrane stability (NRRT). The results showed a significant inhibition of RpR, Ecy and NRRT paralleled by a small and insignificantly increased Mry of the exposed specimens. Our results thus demonstrate that only a combination of mortality and sublethal biomarkers was able to characterise an exposure-related stress syndrome. The suite of biomarkers described here was also able to detect and resolve a pollution-induced stress syndrome at an early stage of pollution. The contamination level of the sediments was assessed using chemical analysis, by estimating bioavailability and by computing a toxic pressure coefficient (TPC) to account for potential additive effects of different pollutants. The observed biological responses were consistent with the contamination levels in sediments, suggesting a high potential for using Protozoa in bioassays to assess environmental risk in coastal marine systems.}, } @article {pmid23201236, year = {2013}, author = {Saive, AL and Ravel, N and Thévenet, M and Royet, JP and Plailly, J}, title = {A novel experimental approach to episodic memory in humans based on the privileged access of odors to memories.}, journal = {Journal of neuroscience methods}, volume = {213}, number = {1}, pages = {22-31}, doi = {10.1016/j.jneumeth.2012.11.010}, pmid = {23201236}, issn = {1872-678X}, mesh = {Adult ; Data Interpretation, Statistical ; Female ; Humans ; Image Processing, Computer-Assisted ; Magnetic Resonance Imaging ; Male ; *Memory, Episodic ; Mental Recall/physiology ; *Odorants ; Photic Stimulation ; Psychomotor Performance/physiology ; Reaction Time/physiology ; Recognition, Psychology/physiology ; Smell/physiology ; Stimulation, Chemical ; Young Adult ; }, abstract = {Episodic memory is defined as the conscious recollection of a personal event (What) in its spatial (Where) and contextual (Which context) environment. In existing approaches, human episodic memory is either explored separately from real-life situations or is not fully controlled. In this study, we propose an intermediate approach, inspired by animal studies, that permits the control of the encoding and recall phases, while still being ecologically valid. As odors are known to be especially evocative reminders, we explored the memory of olfactory episodes. During trial-unique encoding, participants freely explored three episodes, one episode per day, each composed of three unnamable odors (What) that were positioned at specific locations on a board (Where) within a visual context (Which context). On the fourth day, both old and new odors were presented, and when an odor was recognized, the participants had to remember both its spatial location and the visual context in which it occurred. In Experiment 1, the participants were highly proficient at recognizing odors, and they recall the spatio-contextual environment associated with these odors in approximately half of the trials. To adapt the recall procedure to the constraints of fMRI, we conducted Experiment 2 demonstrating that trial repetition did not disturb the memory process. Thus, we first validated our protocol, which investigates the memory of olfactory episodes in a fully controlled way that is as close as possible to real-life situations. Then, we demonstrated the adaptability of our protocol for the future exploration of the neural networks implicated in episodic recall.}, } @article {pmid23200504, year = {2012}, author = {Morse, SS and Mazet, JA and Woolhouse, M and Parrish, CR and Carroll, D and Karesh, WB and Zambrana-Torrelio, C and Lipkin, WI and Daszak, P}, title = {Prediction and prevention of the next pandemic zoonosis.}, journal = {Lancet (London, England)}, volume = {380}, number = {9857}, pages = {1956-1965}, pmid = {23200504}, issn = {1474-547X}, support = {R01 AI092571/AI/NIAID NIH HHS/United States ; U54 AI057158/AI/NIAID NIH HHS/United States ; 2R01-TW005869/TW/FIC NIH HHS/United States ; //Wellcome Trust/United Kingdom ; R01 TW005869/TW/FIC NIH HHS/United States ; AI079231/AI/NIAID NIH HHS/United States ; R01 AI079231/AI/NIAID NIH HHS/United States ; R01 GM100471/GM/NIGMS NIH HHS/United States ; AI57158/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Blood-Borne Pathogens ; Communicable Diseases, Emerging/epidemiology/prevention & control ; Environmental Monitoring ; Global Health ; Health Policy ; Humans ; International Cooperation ; Pandemics/*prevention & control ; Travel ; Virus Diseases/epidemiology/prevention & control ; Zoonoses/*epidemiology ; }, abstract = {Most pandemics--eg, HIV/AIDS, severe acute respiratory syndrome, pandemic influenza--originate in animals, are caused by viruses, and are driven to emerge by ecological, behavioural, or socioeconomic changes. Despite their substantial effects on global public health and growing understanding of the process by which they emerge, no pandemic has been predicted before infecting human beings. We review what is known about the pathogens that emerge, the hosts that they originate in, and the factors that drive their emergence. We discuss challenges to their control and new efforts to predict pandemics, target surveillance to the most crucial interfaces, and identify prevention strategies. New mathematical modelling, diagnostic, communications, and informatics technologies can identify and report hitherto unknown microbes in other species, and thus new risk assessment approaches are needed to identify microbes most likely to cause human disease. We lay out a series of research and surveillance opportunities and goals that could help to overcome these challenges and move the global pandemic strategy from response to pre-emption.}, } @article {pmid23199639, year = {2012}, author = {Fattorini, S and Santoro, R and Maurizi, E and Acosta, AT and Di Giulio, A}, title = {Environmental tuning of an insect ensemble: the tenebrionid beetles inhabiting a Mediterranean coastal dune zonation.}, journal = {Comptes rendus biologies}, volume = {335}, number = {10-11}, pages = {708-711}, doi = {10.1016/j.crvi.2012.09.009}, pmid = {23199639}, issn = {1768-3238}, mesh = {Algorithms ; Analysis of Variance ; Animals ; *Biodiversity ; Coleoptera/*physiology ; Data Collection ; Data Interpretation, Statistical ; Ecosystem ; *Environment ; Mediterranean Region ; Phylogeny ; Plants ; Population ; Seasons ; }, abstract = {Few studies have investigated insect ensembles, i.e. phylogenetically bounded groups of species that use a similar set of resources within a community. The zonation of dune vegetation makes these ecosystems ideal for the study of insect ensembles in a short space. In this study, we investigated if the tenebrionid beetles forming an ensemble on a dune zonation showed variations in community organization (relative abundances and species diversity) in different but spatially associated biotopes defined by different plant communities. Three biotopes (corresponding to European Commission habitat 2110, 2120 and 2230) of a well-preserved Mediterranean dune were sampled using square plots of 2×2 m at three places. To investigate if there was some association between species and habitat we applied a χ(2) test. Variations in community structure parameters were investigated using Shannon index. The three biotopes host tenebrionid communities with similar species composition and overall abundances, confirming that they form a single ensemble. However, tenebrionid species are differently associated with different biotopes along the zonation, with some species occurring with different proportions among the biotopes. A local selection process can be postulated as a mechanism responsible for these differences.}, } @article {pmid23193954, year = {2012}, author = {Kozman, D and Graziul, C and Gibbons, R and Alexander, GC}, title = {Association between unemployment rates and prescription drug utilization in the United States, 2007-2010.}, journal = {BMC health services research}, volume = {12}, number = {}, pages = {435}, pmid = {23193954}, issn = {1472-6963}, mesh = {Adult ; Databases, Factual ; Economic Recession ; Female ; Humans ; Male ; Middle Aged ; Prescription Drugs/*therapeutic use ; Retrospective Studies ; Unemployment/statistics & numerical data/*trends ; United States ; Young Adult ; }, abstract = {BACKGROUND: While extensive evidence suggests that the economic recession has had far reaching effects on many economic sectors, little is known regarding its impact on prescription drug utilization. The purpose of this study is to describe the association between state-level unemployment rates and retail sales of seven therapeutic classes (statins, antidepressants, antipsychotics, angiotensin-converting enzyme [ACE] inhibitors, opiates, phosphodiesterase [PDE] inhibitors and oral contraceptives) in the United States.

METHODS: Using a retrospective mixed ecological design, we examined retail prescription sales using IMS Health Xponent™ from September 2007 through July 2010, and we used the Bureau of Labor Statistics to derive population-based rates and mixed-effects modeling with state-level controls to examine the association between unemployment and utilization. Our main outcome measure was state-level utilization per 100,000 people for each class.

RESULTS: Monthly unemployment levels and rates of use of each class varied substantially across the states. There were no statistically significant associations between use of ACE inhibitors or SSRIs/SNRIs and average unemployment in analyses across states, while for opioids and PDE inhibitors there were small statistically significant direct associations, and for the remaining classes inverse associations. Analyses using each state as its own control collectively exhibited statistically significant positive associations between increases in unemployment and prescription drug utilization for five of seven areas examined. This relationship was greatest for statins (on average, a 4% increase in utilization per 1% increased unemployment) and PDE inhibitors (3% increase in utilization per 1% increased unemployment), and lower for oral contraceptives and atypical antipsychotics.

CONCLUSION: We found no evidence of an association between increasing unemployment and decreasing prescription utilization, suggesting that any effects of the recent economic recession have been mitigated by other market forces.}, } @article {pmid23193296, year = {2013}, author = {Goldman, AD and Bernhard, TM and Dolzhenko, E and Landweber, LF}, title = {LUCApedia: a database for the study of ancient life.}, journal = {Nucleic acids research}, volume = {41}, number = {Database issue}, pages = {D1079-82}, pmid = {23193296}, issn = {1362-4962}, mesh = {*Databases, Genetic ; *Evolution, Molecular ; Internet ; Metabolic Networks and Pathways ; Multigene Family ; Origin of Life ; Phylogeny ; Proteins/chemistry/classification ; Software ; }, abstract = {Organisms represented by the root of the universal evolutionary tree were most likely complex cells with a sophisticated protein translation system and a DNA genome encoding hundreds of genes. The growth of bioinformatics data from taxonomically diverse organisms has made it possible to infer the likely properties of early life in greater detail. Here we present LUCApedia, (http://eeb.princeton.edu/lucapedia), a unified framework for simultaneously evaluating multiple data sets related to the Last Universal Common Ancestor (LUCA) and its predecessors. This unification is achieved by mapping eleven such data sets onto UniProt, KEGG and BioCyc IDs. LUCApedia may be used to rapidly acquire evidence that a certain gene or set of genes is ancient, to examine the early evolution of metabolic pathways, or to test specific hypotheses related to ancient life by corroborating them against the rest of the database.}, } @article {pmid23193246, year = {2013}, author = {Hu, XB and Wang, M and Di Paolo, E}, title = {Calculating complete and exact Pareto front for multiobjective optimization: a new deterministic approach for discrete problems.}, journal = {IEEE transactions on cybernetics}, volume = {43}, number = {3}, pages = {1088-1101}, doi = {10.1109/TSMCB.2012.2223756}, pmid = {23193246}, issn = {2168-2275}, mesh = {*Algorithms ; *Artificial Intelligence ; *Decision Support Techniques ; *Game Theory ; Pattern Recognition, Automated/*methods ; *Signal Processing, Computer-Assisted ; }, abstract = {Searching the Pareto front for multiobjective optimization problems usually involves the use of a population-based search algorithm or of a deterministic method with a set of different single aggregate objective functions. The results are, in fact, only approximations of the real Pareto front. In this paper, we propose a new deterministic approach capable of fully determining the real Pareto front for those discrete problems for which it is possible to construct optimization algorithms to find the k best solutions to each of the single-objective problems. To this end, two theoretical conditions are given to guarantee the finding of the actual Pareto front rather than its approximation. Then, a general methodology for designing a deterministic search procedure is proposed. A case study is conducted, where by following the general methodology, a ripple-spreading algorithm is designed to calculate the complete exact Pareto front for multiobjective route optimization. When compared with traditional Pareto front search methods, the obvious advantage of the proposed approach is its unique capability of finding the complete Pareto front. This is illustrated by the simulation results in terms of both solution quality and computational efficiency.}, } @article {pmid23190494, year = {2012}, author = {Müller, T and Ensminger, I and Schmid, KJ}, title = {A catalogue of putative unique transcripts from Douglas-fir (Pseudotsuga menziesii) based on 454 transcriptome sequencing of genetically diverse, drought stressed seedlings.}, journal = {BMC genomics}, volume = {13}, number = {}, pages = {673}, pmid = {23190494}, issn = {1471-2164}, mesh = {Acclimatization/genetics ; Adaptation, Physiological/*genetics ; Base Sequence ; Climate ; *Databases, Nucleic Acid ; Droughts ; Gene Library ; Genetic Variation ; *Genome, Plant ; Genotype ; Geography ; Polymorphism, Single Nucleotide ; Pseudotsuga/*genetics/physiology ; Seedlings/*genetics/physiology ; Sequence Analysis, DNA ; Stress, Physiological/*genetics ; *Transcriptome ; }, abstract = {BACKGROUND: Douglas-fir (Pseudotsuga menziesii) extends over a wide range of contrasting environmental conditions, reflecting substantial local adaptation. For this reason, it is an interesting model species to study plant adaptation and the effects of global climate change such as increased temperatures and significant periods of drought on individual trees and the forest landscape in general. However, genomic data and tools for studying genetic variation in natural populations to understand the genetic and physiological mechanisms of adaptation are currently missing for Douglas-fir. This study represents a first step towards characterizing the Douglas-fir transcriptome based on 454 sequencing of twelve cDNA libraries. The libraries were constructed from needle and wood tissue of coastal and interior provenances subjected to drought stress experiments.

RESULTS: The 454 sequencing of twelve normalized cDNA libraries resulted in 3.6 million reads from which a set of 170,859 putative unique transcripts (PUTs) was assembled. Functional annotation by BLAST searches and Gene Ontology mapping showed that the composition of functional classes is very similar to other plant transcriptomes and demonstrated that a large fraction of the Douglas-fir transcriptome is tagged by the PUTs. Based on evolutionary conservation, we identified about 1,000 candidate genes related to drought stress. A total number of 187,653 single nucleotide polymorphisms (SNPs) were detected by three SNP detection tools. However, only 27,688 SNPs were identified by all three methods, indicating that SNP detection depends on the particular method used. The two alleles of about 60% of the 27,688 SNPs are segregating simultaneously in both coastal and interior provenances, which indicates a high proportion of ancestral shared polymorphisms or a high level of gene flow between these two ecologically and phenotypically different varieties.

CONCLUSIONS: We established a catalogue of PUTs and large SNP database for Douglas-fir. Both will serve as a useful resource for the further characterization of the genome and transcriptome of Douglas-fir and for the analysis of genetic variation using genotyping or resequencing methods.}, } @article {pmid23189687, year = {2012}, author = {Zhu, YJ and Bourgeois, C and Lin, GX and Wu, XD and Guo, JL and Guo, ZH}, title = {[Spatial characteristics of grain size of surface sediments in mangrove wetlands in Gaoqiao of Zhanjiang, Guangdong province of South China].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {23}, number = {8}, pages = {2114-2120}, pmid = {23189687}, issn = {1001-9332}, mesh = {China ; Geographic Information Systems ; Geologic Sediments/*chemistry ; Oceans and Seas ; Particle Size ; Rhizophoraceae/*growth & development ; Spatial Analysis ; *Wetlands ; }, abstract = {Mangrove wetland is an important type of coastal wetlands, and also, an important sediment trap. Sediment is an essential medium for mangrove recruitment and development, which records the environmental history of mangrove wetlands and can be used for the analysis of material sources and the inference of the materials depositing process, being essential to the ecological restoration and conservation of mangrove. In this paper, surface sediment samples were collected along a hydrodynamic gradient in Gaoqiao, Zhanjiang Mangrove National Nature Reserve in 2011. The characteristics of the surface sediments were analyzed based on grain size analysis, and the prediction surfaces were generated by the geo-statistical methods with ArcGIS 9.2 software. A correlation analysis was also conducted on the sediment organic matter content and the mangrove community structure. In the study area, clay and silt dominated the sediment texture, and the mean content of sand, silt, and clay was (27.8 +/- 15.4)%, (40.3 +/- 15.4)%, and (32.1 +/- 11.4)%, respectively. The spatial gradient of the sediment characteristics was expressed in apparent interpolation raster. With increasing distance from the seawall, the sediment sand content increased, clay content decreased, and silt content was relatively stable at a certain level. There was a positive correlation between the contents of sediment organic matter and silt, and a negative correlation between the contents of sediment organic matter and sand. Much more sediment organic matter was located at the high tide area with weak tide energy. There existed apparent discrepancies in the characteristics of the surface sediments in different biotopes. The sediment characteristics had definite correlations with the community structure of mangroves, reflecting the complicated correlations between the hydrodynamic conditions and the mangroves.}, } @article {pmid23185439, year = {2012}, author = {Nagy, LG and Kocsubé, S and Csanádi, Z and Kovács, GM and Petkovits, T and Vágvölgyi, C and Papp, T}, title = {Re-mind the gap! Insertion - deletion data reveal neglected phylogenetic potential of the nuclear ribosomal internal transcribed spacer (ITS) of fungi.}, journal = {PloS one}, volume = {7}, number = {11}, pages = {e49794}, pmid = {23185439}, issn = {1932-6203}, mesh = {Algorithms ; DNA, Ribosomal Spacer/*genetics ; Evolution, Molecular ; Fungi/*genetics ; INDEL Mutation/*genetics ; Phylogeny ; Ribosomes/genetics ; *Sequence Alignment ; }, abstract = {Rapidly evolving, indel-rich phylogenetic markers play a pivotal role in our understanding of the relationships at multiple levels of the tree of life. There is extensive evidence that indels provide conserved phylogenetic signal, however, the range of phylogenetic depths for which gaps retain tree signal has not been investigated in detail. Here we address this question using the fungal internal transcribed spacer (ITS), which is central in many phylogenetic studies, molecular ecology, detection and identification of pathogenic and non-pathogenic species. ITS is repeatedly criticized for indel-induced alignment problems and the lack of phylogenetic resolution above species level, although these have not been critically investigated. In this study, we examined whether the inclusion of gap characters in the analyses shifts the phylogenetic utility of ITS alignments towards earlier divergences. By re-analyzing 115 published fungal ITS alignments, we found that indels are slightly more conserved than nucleotide substitutions, and when included in phylogenetic analyses, improved the resolution and branch support of phylogenies across an array of taxonomic ranges and extended the resolving power of ITS towards earlier nodes of phylogenetic trees. Our results reconcile previous contradicting evidence for the effects of data exclusion: in the case of more sophisticated indel placement, the exclusion of indel-rich regions from the analyses results in a loss of tree resolution, whereas in the case of simpler alignment methods, the exclusion of gapped sites improves it. Although the empirical datasets do not provide to measure alignment accuracy objectively, our results for the ITS region are consistent with previous simulations studies alignment algorithms. We suggest that sophisticated alignment algorithms and the inclusion of indels make the ITS region and potentially other rapidly evolving indel-rich loci valuable sources of phylogenetic information, which can be exploited at multiple taxonomic levels.}, } @article {pmid23185309, year = {2012}, author = {Leese, F and Brand, P and Rozenberg, A and Mayer, C and Agrawal, S and Dambach, J and Dietz, L and Doemel, JS and Goodall-Copstake, WP and Held, C and Jackson, JA and Lampert, KP and Linse, K and Macher, JN and Nolzen, J and Raupach, MJ and Rivera, NT and Schubart, CD and Striewski, S and Tollrian, R and Sands, CJ}, title = {Exploring Pandora's box: potential and pitfalls of low coverage genome surveys for evolutionary biology.}, journal = {PloS one}, volume = {7}, number = {11}, pages = {e49202}, pmid = {23185309}, issn = {1932-6203}, mesh = {Animals ; Bacteria/genetics ; Cell Nucleus/genetics ; Contig Mapping ; DNA/genetics ; DNA, Mitochondrial/genetics ; *Data Collection ; Databases, Genetic ; *Evolution, Molecular ; Gene Library ; Genes, Mitochondrial/genetics ; Genetic Markers ; Genome/*genetics ; Genome Size/genetics ; Genome, Mitochondrial/genetics ; Microsatellite Repeats/genetics ; RNA, Ribosomal/genetics ; Sequence Analysis, DNA ; Viral Proteins/genetics ; }, abstract = {High throughput sequencing technologies are revolutionizing genetic research. With this "rise of the machines", genomic sequences can be obtained even for unknown genomes within a short time and for reasonable costs. This has enabled evolutionary biologists studying genetically unexplored species to identify molecular markers or genomic regions of interest (e.g. micro- and minisatellites, mitochondrial and nuclear genes) by sequencing only a fraction of the genome. However, when using such datasets from non-model species, it is possible that DNA from non-target contaminant species such as bacteria, viruses, fungi, or other eukaryotic organisms may complicate the interpretation of the results. In this study we analysed 14 genomic pyrosequencing libraries of aquatic non-model taxa from four major evolutionary lineages. We quantified the amount of suitable micro- and minisatellites, mitochondrial genomes, known nuclear genes and transposable elements and searched for contamination from various sources using bioinformatic approaches. Our results show that in all sequence libraries with estimated coverage of about 0.02-25%, many appropriate micro- and minisatellites, mitochondrial gene sequences and nuclear genes from different KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways could be identified and characterized. These can serve as markers for phylogenetic and population genetic analyses. A central finding of our study is that several genomic libraries suffered from different biases owing to non-target DNA or mobile elements. In particular, viruses, bacteria or eukaryote endosymbionts contributed significantly (up to 10%) to some of the libraries analysed. If not identified as such, genetic markers developed from high-throughput sequencing data for non-model organisms may bias evolutionary studies or fail completely in experimental tests. In conclusion, our study demonstrates the enormous potential of low-coverage genome survey sequences and suggests bioinformatic analysis workflows. The results also advise a more sophisticated filtering for problematic sequences and non-target genome sequences prior to developing markers.}, } @article {pmid23185044, year = {2013}, author = {Danks, G and Campsteijn, C and Parida, M and Butcher, S and Doddapaneni, H and Fu, B and Petrin, R and Metpally, R and Lenhard, B and Wincker, P and Chourrout, D and Thompson, EM and Manak, JR}, title = {OikoBase: a genomics and developmental transcriptomics resource for the urochordate Oikopleura dioica.}, journal = {Nucleic acids research}, volume = {41}, number = {Database issue}, pages = {D845-53}, pmid = {23185044}, issn = {1362-4962}, mesh = {Animals ; Data Mining ; *Databases, Genetic ; Gene Expression Profiling ; *Genomics ; Internet ; Molecular Sequence Annotation ; Oligonucleotide Array Sequence Analysis ; *Transcriptome ; Urochordata/embryology/*genetics/growth & development ; }, abstract = {We report the development of OikoBase (http://oikoarrays.biology.uiowa.edu/Oiko/), a tiling array-based genome browser resource for Oikopleura dioica, a metazoan belonging to the urochordates, the closest extant group to vertebrates. OikoBase facilitates retrieval and mining of a variety of useful genomics information. First, it includes a genome browser which interrogates 1260 genomic sequence scaffolds and features gene, transcript and CDS annotation tracks. Second, we annotated gene models with gene ontology (GO) terms and InterPro domains which are directly accessible in the browser with links to their entries in the GO (http://www.geneontology.org/) and InterPro (http://www.ebi.ac.uk/interpro/) databases, and we provide transcript and peptide links for sequence downloads. Third, we introduce the transcriptomics of a comprehensive set of developmental stages of O. dioica at high resolution and provide downloadable gene expression data for all developmental stages. Fourth, we incorporate a BLAST tool to identify homologs of genes and proteins. Finally, we include a tutorial that describes how to use OikoBase as well as a link to detailed methods, explaining the data generation and analysis pipeline. OikoBase will provide a valuable resource for research in chordate development, genome evolution and plasticity and the molecular ecology of this important marine planktonic organism.}, } @article {pmid23184592, year = {2012}, author = {Kuczynski, J and Stombaugh, J and Walters, WA and González, A and Caporaso, JG and Knight, R}, title = {Using QIIME to analyze 16S rRNA gene sequences from microbial communities.}, journal = {Current protocols in microbiology}, volume = {Chapter 1}, number = {}, pages = {Unit 1E.5.}, pmid = {23184592}, issn = {1934-8533}, support = {HG4872/HG/NHGRI NIH HHS/United States ; T32 GM008759/GM/NIGMS NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; U01 HG004866/HG/NHGRI NIH HHS/United States ; GM65103/GM/NIGMS NIH HHS/United States ; R01 HG004872/HG/NHGRI NIH HHS/United States ; GM8759/GM/NIGMS NIH HHS/United States ; HG4866/HG/NHGRI NIH HHS/United States ; LM9451/LM/NLM NIH HHS/United States ; DK83981/DK/NIDDK NIH HHS/United States ; UH2 DK083981/DK/NIDDK NIH HHS/United States ; P01 DK078669/DK/NIDDK NIH HHS/United States ; UH3 DK083981/DK/NIDDK NIH HHS/United States ; T15 LM009451/LM/NLM NIH HHS/United States ; DK78669/DK/NIDDK NIH HHS/United States ; T32 GM065103/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacteria/classification/*genetics/isolation & purification ; Biodiversity ; Computational Biology/instrumentation/*methods ; DNA, Bacterial/genetics ; Phylogeny ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, DNA/instrumentation/*methods ; *Software ; }, abstract = {QIIME (canonically pronounced "chime") is a software application that performs microbial community analysis. It is an acronym for Quantitative Insights Into Microbial Ecology, and has been used to analyze and interpret nucleic acid sequence data from fungal, viral, bacterial, and archaeal communities. The following protocols describe how to install QIIME on a single computer and use it to analyze microbial 16S sequence data from nine distinct microbial communities.}, } @article {pmid23180770, year = {2012}, author = {Zeng, V and Extavour, CG}, title = {ASGARD: an open-access database of annotated transcriptomes for emerging model arthropod species.}, journal = {Database : the journal of biological databases and curation}, volume = {2012}, number = {}, pages = {bas048}, pmid = {23180770}, issn = {1758-0463}, mesh = {*Access to Information ; Animals ; Arthropods/*genetics ; Base Sequence ; *Databases, Genetic ; Genes ; Models, Animal ; Molecular Sequence Annotation/*methods ; Species Specificity ; Transcriptome/*genetics ; User-Computer Interface ; }, abstract = {The increased throughput and decreased cost of next-generation sequencing (NGS) have shifted the bottleneck genomic research from sequencing to annotation, analysis and accessibility. This is particularly challenging for research communities working on organisms that lack the basic infrastructure of a sequenced genome, or an efficient way to utilize whatever sequence data may be available. Here we present a new database, the Assembled Searchable Giant Arthropod Read Database (ASGARD). This database is a repository and search engine for transcriptomic data from arthropods that are of high interest to multiple research communities but currently lack sequenced genomes. We demonstrate the functionality and utility of ASGARD using de novo assembled transcriptomes from the milkweed bug Oncopeltus fasciatus, the cricket Gryllus bimaculatus and the amphipod crustacean Parhyale hawaiensis. We have annotated these transcriptomes to assign putative orthology, coding region determination, protein domain identification and Gene Ontology (GO) term annotation to all possible assembly products. ASGARD allows users to search all assemblies by orthology annotation, GO term annotation or Basic Local Alignment Search Tool. User-friendly features of ASGARD include search term auto-completion suggestions based on database content, the ability to download assembly product sequences in FASTA format, direct links to NCBI data for predicted orthologs and graphical representation of the location of protein domains and matches to similar sequences from the NCBI non-redundant database. ASGARD will be a useful repository for transcriptome data from future NGS studies on these and other emerging model arthropods, regardless of sequencing platform, assembly or annotation status. This database thus provides easy, one-stop access to multi-species annotated transcriptome information. We anticipate that this database will be useful for members of multiple research communities, including developmental biology, physiology, evolutionary biology, ecology, comparative genomics and phylogenomics. Database URL: asgard.rc.fas.harvard.edu.}, } @article {pmid23176377, year = {2013}, author = {, and Ahanchédé, A and Alfaya, JE and Andersen, LW and Azam, D and Bautista, MA and Besnard, AL and Bigatti, G and Bouétard, A and Coutellec, MA and Ewédjè, EE and Fuseya, R and García-Jiménez, R and Haratian, M and Hardy, OJ and Holm, LE and Hoy, CW and Koshimizu, E and Loeschcke, V and López-Márquez, V and Machado, CA and Machordom, A and Marchi, C and Michel, AP and Micheneau, C and Mittapalli, O and Nagai, T and Okamoto, N and Pan, Y and Panitz, F and Safaie, N and Sakamoto, T and Sharifnabi, B and Tian, EW and Yu, H}, title = {Permanent genetic resources added to Molecular Ecology Resources Database 1 August 2012 - 30 September 2012.}, journal = {Molecular ecology resources}, volume = {13}, number = {1}, pages = {158-159}, doi = {10.1111/1755-0998.12035}, pmid = {23176377}, issn = {1755-0998}, mesh = {Animals ; Base Sequence ; DNA Primers/*genetics ; *Databases, Genetic ; Ecology/methods ; Microsatellite Repeats/*genetics ; Molecular Biology/methods ; Molecular Sequence Data ; Polymorphism, Single Nucleotide/*genetics ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {This article documents the addition of 83 microsatellite marker loci and 96 pairs of single-nucleotide polymorphism (SNP) sequencing primers to the Molecular Ecology Resources Database. Loci were developed for the following species: Bembidion lampros, Inimicus japonicus, Lymnaea stagnalis, Panopea abbreviata, Pentadesma butyracea, Sycoscapter hirticola and Thanatephorus cucumeris (anamorph: Rhizoctonia solani). These loci were cross-tested on the following species: Pentadesma grandifolia and Pentadesma reyndersii. This article also documents the addition of 96 sequencing primer pairs and 88 allele-specific primers or probes for Plutella xylostella.}, } @article {pmid23171877, year = {2012}, author = {Blackburn, H and Labarthe, D}, title = {Stories from the evolution of guidelines for causal inference in epidemiologic associations: 1953-1965.}, journal = {American journal of epidemiology}, volume = {176}, number = {12}, pages = {1071-1077}, pmid = {23171877}, issn = {1476-6256}, support = {G13 LM008214/LM/NLM NIH HHS/United States ; 5G13-LM008214-02/LM/NLM NIH HHS/United States ; }, mesh = {*Causality ; Data Interpretation, Statistical ; *Epidemiologic Methods ; Epidemiology/*history ; *Guidelines as Topic ; History, 20th Century ; Humans ; Lung Neoplasms/epidemiology/history ; Smoking/epidemiology/history ; United Kingdom ; United States ; }, abstract = {Guidelines for causal inference in epidemiologic associations were a major contribution to modern epidemiologic analysis in the 1960s. This story recounts dramatic elements in a series of exchanges leading to their formulation and effective use in the 1964 Report of the Advisory Committee to the US Surgeon General on Smoking and Health, the landmark report which concluded that cigarette smoking caused lung cancer. The opening salvo was precipitated by Ancel Keys' presentation of an ecologic correlation between diet and cardiac death, which was vigorously criticized in an article by Jacob Yerushalmy calling for "proper handling" of bias and confounding in observational evidence. The dispute demonstrated a need for guidelines for causal inference and set off their serial refinement among US thinkers. Less well documented parallel efforts went on in the United Kingdom, leading to the criteria that Bradford Hill presented in his 1965 President's Address to the Royal Society of Medicine. Here the authors recount experiences with some of the principals involved in development of these criteria and note the omission from both classic reports of proper attribution to those who helped create the guidelines. They also present direct, if unsatisfying, evidence about those particular lapses.}, } @article {pmid23169633, year = {2012}, author = {Cordero, OX and Ventouras, LA and DeLong, EF and Polz, MF}, title = {Public good dynamics drive evolution of iron acquisition strategies in natural bacterioplankton populations.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {109}, number = {49}, pages = {20059-20064}, pmid = {23169633}, issn = {1091-6490}, mesh = {Atlantic Ocean ; *Biological Evolution ; Computational Biology ; Iron/*metabolism ; Massachusetts ; Microbial Interactions/*physiology ; Models, Biological ; Plankton/*metabolism/microbiology ; Seawater/*microbiology ; Siderophores/biosynthesis/metabolism ; Vibrionaceae/*metabolism ; }, abstract = {A common strategy among microbes living in iron-limited environments is the secretion of siderophores, which can bind poorly soluble iron and make it available to cells via active transport mechanisms. Such siderophore-iron complexes can be thought of as public goods that can be exploited by local communities and drive diversification, for example by the evolution of "cheating." However, it is unclear whether bacterial populations in the environment form stable enough communities such that social interactions significantly impact evolutionary dynamics. Here we show that public good games drive the evolution of iron acquisition strategies in wild populations of marine bacteria. We found that within nonclonal but ecologically cohesive genotypic clusters of closely related Vibrionaceae, only an intermediate percentage of genotypes are able to produce siderophores. Nonproducers within these clusters exhibited selective loss of siderophore biosynthetic pathways, whereas siderophore transport mechanisms were retained, suggesting that these nonproducers can act as cheaters that benefit from siderophore producers in their local environment. In support of this hypothesis, these nonproducers in iron-limited media suffer a significant decrease in growth, which can be alleviated by siderophores, presumably owing to the retention of transport mechanisms. Moreover, using ecological data of resource partitioning, we found that cheating coevolves with the ecological specialization toward association with larger particles in the water column, suggesting that these can harbor stable enough communities for dependencies among organisms to evolve.}, } @article {pmid23166775, year = {2012}, author = {Guzman, F and Almerão, MP and Körbes, AP and Loss-Morais, G and Margis, R}, title = {Identification of microRNAs from Eugenia uniflora by high-throughput sequencing and bioinformatics analysis.}, journal = {PloS one}, volume = {7}, number = {11}, pages = {e49811}, pmid = {23166775}, issn = {1932-6203}, mesh = {*Computational Biology ; Conserved Sequence ; Gene Expression Regulation, Plant ; Gene Library ; *High-Throughput Nucleotide Sequencing ; MicroRNAs/chemistry/*genetics/metabolism ; Molecular Sequence Annotation ; Nucleic Acid Conformation ; RNA Precursors/chemistry/genetics/metabolism ; RNA, Plant/chemistry/genetics/metabolism ; Syzygium/*genetics/metabolism ; }, abstract = {BACKGROUND: microRNAs or miRNAs are small non-coding regulatory RNAs that play important functions in the regulation of gene expression at the post-transcriptional level by targeting mRNAs for degradation or inhibiting protein translation. Eugenia uniflora is a plant native to tropical America with pharmacological and ecological importance, and there have been no previous studies concerning its gene expression and regulation. To date, no miRNAs have been reported in Myrtaceae species.

RESULTS: Small RNA and RNA-seq libraries were constructed to identify miRNAs and pre-miRNAs in Eugenia uniflora. Solexa technology was used to perform high throughput sequencing of the library, and the data obtained were analyzed using bioinformatics tools. From 14,489,131 small RNA clean reads, we obtained 1,852,722 mature miRNA sequences representing 45 conserved families that have been identified in other plant species. Further analysis using contigs assembled from RNA-seq allowed the prediction of secondary structures of 25 known and 17 novel pre-miRNAs. The expression of twenty-seven identified miRNAs was also validated using RT-PCR assays. Potential targets were predicted for the most abundant mature miRNAs in the identified pre-miRNAs based on sequence homology.

CONCLUSIONS: This study is the first large scale identification of miRNAs and their potential targets from a species of the Myrtaceae family without genomic sequence resources. Our study provides more information about the evolutionary conservation of the regulatory network of miRNAs in plants and highlights species-specific miRNAs.}, } @article {pmid23166774, year = {2012}, author = {Krieger, J and Grandy, R and Drew, MM and Erland, S and Stensmyr, MC and Harzsch, S and Hansson, BS}, title = {Giant robber crabs monitored from space: GPS-based telemetric studies on Christmas Island (Indian Ocean).}, journal = {PloS one}, volume = {7}, number = {11}, pages = {e49809}, pmid = {23166774}, issn = {1932-6203}, mesh = {Animals ; Behavior, Animal ; Circadian Rhythm ; Crustacea/*physiology ; Ecosystem ; Female ; *Geographic Information Systems ; Indian Ocean ; Islands ; Male ; Population Dynamics ; *Telemetry ; }, abstract = {We investigated the navigational capabilities of the world's largest land-living arthropod, the giant robber crab Birgus latro (Anomura, Coenobitidae); this crab reaches 4 kg in weight and can reach an age of up to 60 years. Populations are distributed over small Indo-Pacific islands of the tropics, including Christmas Island (Indian Ocean). Although this species has served as a crustacean model to explore anatomical, physiological, and ecological aspects of terrestrial adaptations, few behavioral analyses of it exist. We used a GPS-based telemetric system to analyze movements of freely roaming robber crabs, the first large-scale study of any arthropod using GPS technology to monitor behavior. Although female robber crabs are known to migrate to the coast for breeding, no such observations have been recorded for male animals. In total, we equipped 55 male robber crabs with GPS tags, successfully recording more than 1,500 crab days of activity, and followed some individual animals for as long as three months. Besides site fidelity with short-distance excursions, our data reveal long-distance movements (several kilometers) between the coast and the inland rainforest. These movements are likely related to mating, saltwater drinking and foraging. The tracking patterns indicate that crabs form route memories. Furthermore, translocation experiments show that robber crabs are capable of homing over large distances. We discuss if the search behavior induced in these experiments suggests path integration as another important navigation strategy.}, } @article {pmid23166754, year = {2012}, author = {Giroux, MA and Dussault, C and Lecomte, N and Tremblay, JP and Côté, SD}, title = {A new way of assessing foraging behaviour at the individual level using faeces marking and satellite telemetry.}, journal = {PloS one}, volume = {7}, number = {11}, pages = {e49719}, pmid = {23166754}, issn = {1932-6203}, mesh = {Animals ; *Appetitive Behavior ; *Deer ; Ecosystem ; Feces/*chemistry ; Feeding Behavior ; Female ; *Geographic Information Systems ; Male ; Population Dynamics ; *Satellite Communications ; Seasons ; *Telemetry ; }, abstract = {Heterogeneity in foraging behaviour can profoundly influence ecological processes shaping populations. To scale-up from individual foraging behaviour to processes occurring at the population scale, one needs to sample foraging behaviour at the individual level, and over large temporal scales or during critical seasons known to influence life-history traits. We developed an innovative technique to monitor foraging behaviour at the individual level in secretive species, a technique that can be ultimately used to investigate the links between foraging behaviour and life-history traits. First, the technique used a novel approach, namely the combination of telemetry tracking and biomarking of faeces with food dyes to locate fresh signs of presence left by individuals equipped with GPS collars. Second, the technique is based on the simultaneous or successive sampling of life-history traits and individual foraging behaviour, using tracks with high probabilities of recovery of dyed faeces. We first describe our methodological approach, using a case study of a large herbivore, and then provide recommendations and guidelines for its use. Sampling single snow tracks of individuals equipped with a GPS collar was a reliable way to assess individual winter foraging behaviour in a white-tailed deer (Odocoileus virginianus Zimmermann) population. During that period, the probability of recovery of dyed faeces within the range of the collar precision was very high for single snow tracks of equipped deer (97%). Our approach is well suited to study individual foraging behaviour, and could ultimately be used to investigate the interplay between intra-population heterogeneity in foraging behaviour, life-history traits, and demographic processes.}, } @article {pmid23166742, year = {2012}, author = {Tanferna, A and López-Jiménez, L and Blas, J and Hiraldo, F and Sergio, F}, title = {Different location sampling frequencies by satellite tags yield different estimates of migration performance: pooling data requires a common protocol.}, journal = {PloS one}, volume = {7}, number = {11}, pages = {e49659}, pmid = {23166742}, issn = {1932-6203}, mesh = {*Animal Migration ; Animals ; *Birds ; *Geographic Information Systems/instrumentation ; Linear Models ; *Satellite Communications/instrumentation ; }, abstract = {BACKGROUND: Migration research is in rapid expansion and increasingly based on sophisticated satellite-tracking devices subject to constant technological refinement, but is still ripe with descriptive studies and in need of meta-analyses looking for emergent generalisations. In particular, coexistence of studies and devices with different frequency of location sampling and spatial accuracy generates doubts of data compatibility, potentially preventing meta-analyses. We used satellite-tracking data on a migratory raptor to: (1) test whether data based on different location sampling frequencies and on different position subsampling approaches are compatible, and (2) seek potential solutions that enhance compatibility and enable eventual meta-analyses.

We used linear mixed models to analyse the differences in the speed and route length of the migration tracks of 36 Black kites (Milvus migrans) satellite-tagged with two different types of devices (Argos vs GPS tags), entailing different regimes of position sampling frequency. We show that different location sampling frequencies and data subsampling approaches generate large (up to 33%) differences in the estimates of route length and migration speed of this migratory bird.

CONCLUSIONS/SIGNIFICANCE: Our results show that the abundance of locations available for analysis affects the tortuosity and realism of the estimated migration path. To avoid flaws in future meta-analyses or unnecessary loss of data, we urge researchers to reach an agreement on a common protocol of data presentation, and to recognize that all transmitter-based studies are likely to underestimate the actual distance traveled by the marked animal. As ecological research becomes increasingly technological, new technologies should be matched with improvements in analytical capacity that guarantee data compatibility.}, } @article {pmid23166587, year = {2012}, author = {Shaw, TI and Srivastava, A and Chou, WC and Liu, L and Hawkinson, A and Glenn, TC and Adams, R and Schountz, T}, title = {Transcriptome sequencing and annotation for the Jamaican fruit bat (Artibeus jamaicensis).}, journal = {PloS one}, volume = {7}, number = {11}, pages = {e48472}, pmid = {23166587}, issn = {1932-6203}, support = {N01AI25489/AI/NIAID NIH HHS/United States ; R15 AI089419/AI/NIAID NIH HHS/United States ; AI089419/AI/NIAID NIH HHS/United States ; AI25489/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Arenaviridae Infections/*genetics/immunology ; *Arenaviruses, New World ; Base Sequence ; Chiroptera/*genetics/metabolism ; Computational Biology ; Contig Mapping ; *Disease Models, Animal ; Jamaica ; Kidney/metabolism ; Likelihood Functions ; Lung/metabolism ; Models, Genetic ; Molecular Sequence Annotation ; Molecular Sequence Data ; *Phylogeny ; Polymorphism, Single Nucleotide/genetics ; *Selection, Genetic ; Sequence Alignment ; Sequence Analysis, DNA ; Species Specificity ; Spleen/metabolism ; Transcriptome/*genetics ; }, abstract = {The Jamaican fruit bat (Artibeus jamaicensis) is one of the most common bats in the tropical Americas. It is thought to be a potential reservoir host of Tacaribe virus, an arenavirus closely related to the South American hemorrhagic fever viruses. We performed transcriptome sequencing and annotation from lung, kidney and spleen tissues using 454 and Illumina platforms to develop this species as an animal model. More than 100,000 contigs were assembled, with 25,000 genes that were functionally annotated. Of the remaining unannotated contigs, 80% were found within bat genomes or transcriptomes. Annotated genes are involved in a broad range of activities ranging from cellular metabolism to genome regulation through ncRNAs. Reciprocal BLAST best hits yielded 8,785 sequences that are orthologous to mouse, rat, cattle, horse and human. Species tree analysis of sequences from 2,378 loci was used to achieve 95% bootstrap support for the placement of bat as sister to the clade containing horse, dog, and cattle. Through substitution rate estimation between bat and human, 32 genes were identified with evidence for positive selection. We also identified 466 immune-related genes, which may be useful for studying Tacaribe virus infection of this species. The Jamaican fruit bat transcriptome dataset is a resource that should provide additional candidate markers for studying bat evolution and ecology, and tools for analysis of the host response and pathology of disease.}, } @article {pmid23164541, year = {2013}, author = {Taylor, S and Kumar, L}, title = {Potential distribution of an invasive species under climate change scenarios using CLIMEX and soil drainage: a case study of Lantana camara L. in Queensland, Australia.}, journal = {Journal of environmental management}, volume = {114}, number = {}, pages = {414-422}, doi = {10.1016/j.jenvman.2012.10.039}, pmid = {23164541}, issn = {1095-8630}, mesh = {*Climate Change ; Geographic Information Systems ; *Introduced Species ; *Lantana ; *Models, Biological ; Queensland ; *Soil ; }, abstract = {Invasive species pose a major threat to biodiversity which may be intensified by the effects of climate change, particularly if favourable climate conditions allow invasives to spread to new areas. This research explores the combined effects of climate change and soil drainage on the potential future distribution of Lantana camara L. (lantana) in Queensland, Australia. Lantana is an invasive woody shrub species that has a profound economic and environmental impact worldwide. CLIMEX was used to develop a process-based niche model of lantana to estimate its potential distribution under current and future climate. Two Global Climate Models (GCMs), CSIRO-Mk3.0 and MIROC-H, were used to explore the impacts of climate change. These models were run with the A1B and A2 scenarios for 2030, 2070 and 2100. Further refinements of the potential distributions were carried out through the integration of fine scale soil drainage data in a Geographic Information System (GIS). The results from both GCMs show a progressive reduction in climatic suitability for lantana in Queensland. The MIROC-H projects a larger area as remaining at risk of lantana invasion in 2100 compared to CSIRO-Mk3.0. Inclusion of soil drainage data results in a more refined distribution. Overall results show a dramatic reduction in potential distribution of lantana in Queensland in the long term (2100). However, in the short term (2030), areas such as South East Queensland and the Wet Tropics, both regions of significant ecological importance, remain at risk of invasion consistently under both GCMs and with both the climate only and climate and soil drainage models. Management of lantana in these regions will need to be prioritized to protect environmental assets of ecological significance.}, } @article {pmid23164199, year = {2013}, author = {Yovcheva, Z and van Elzakker, CP and Köbben, B}, title = {User requirements for geo-collaborative work with spatio-temporal data in a web-based virtual globe environment.}, journal = {Applied ergonomics}, volume = {44}, number = {6}, pages = {929-939}, doi = {10.1016/j.apergo.2012.10.015}, pmid = {23164199}, issn = {1872-9126}, mesh = {Cooperative Behavior ; Data Display ; Ecology ; Focus Groups ; *Geographic Information Systems ; Geographic Mapping ; Geography ; Geology ; Humans ; Hydrology ; Internet ; *Needs Assessment ; *Software Design ; Spatio-Temporal Analysis ; Surveys and Questionnaires ; *User-Computer Interface ; }, abstract = {Web-based tools developed in the last couple of years offer unique opportunities to effectively support scientists in their effort to collaborate. Communication among environmental researchers often involves not only work with geographical (spatial), but also with temporal data and information. Literature still provides limited documentation when it comes to user requirements for effective geo-collaborative work with spatio-temporal data. To start filling this gap, our study adopted a User-Centered Design approach and first explored the user requirements of environmental researchers working on distributed research projects for collaborative dissemination, exchange and work with spatio-temporal data. Our results show that system design will be mainly influenced by the nature and type of data users work with. From the end-users' perspective, optimal conversion of huge files of spatio-temporal data for further dissemination, accuracy of conversion, organization of content and security have a key role for effective geo-collaboration.}, } @article {pmid23139155, year = {2012}, author = {Minichilli, F and Nuvolone, D and Bustaffa, E and Cipriani, F and Vigotti, MA and Bianchi, F}, title = {[State of health of populations residing in geothermal areas of Tuscany].}, journal = {Epidemiologia e prevenzione}, volume = {36}, number = {5 Suppl 1}, pages = {1-104}, pmid = {23139155}, issn = {1120-9763}, mesh = {Adult ; Aged ; Air Pollution/adverse effects ; Cause of Death ; Environmental Exposure/analysis ; Environmental Pollution/*adverse effects ; Female ; Geothermal Energy/*adverse effects/statistics & numerical data ; *Health Status ; Humans ; Infant, Newborn ; Italy/epidemiology ; Male ; Medical Records Systems, Computerized/statistics & numerical data ; Middle Aged ; Mortality/*trends ; Neoplasms/mortality ; Pneumonia/mortality ; Power Plants/statistics & numerical data ; Pregnancy ; Pregnancy Complications/epidemiology ; Risk Factors ; Sex Distribution ; Time Factors ; }, abstract = {OBJECTIVE: The limited scientific knowledge on relationship between exposure and health effects in relation to geothermal activity motivated an epidemiologic investigation in Tuscan geothermal area. The study aims to describe the health status of populations living in Tuscany municipalities where concessions for exploitation of geothermal resources were granted.

DESIGN: This is an ecological study, so it is not useful to produce evidence to sustain a judgment on the cause-effect link. The major limits of this type of study are the use of the residence at municipal level as a proxy of exposure to both environmental and socioeconomic factors and the use of aggregated data of health outcomes that can lead to the well-known ecological fallacy.

SETTING AND PARTICIPANTS: Sixteen municipalities were included in the study area: eight are part of the so-called "traditional" geothermal area, defined as Northern Geothermal Area (NGA) and eight located in the Amiata Mountain defined as Southern Geothermal Area (SGA). In 2000-2006, the average resident population in the overall area was approximately 43,000 inhabitants. Thirty-one geothermal power plants were active, with a production capacity of 811 MW, 5 of them with 88 MW located in the SGA. Statistical analyses on the entire geothermal area, NGA and SGA subareas, and the sixteen municipalities were performed.

MAIN OUTCOME MEASURES: Mortality data were obtained from Tuscany Regional Mortality Registry for the 1971-2006 period, analysing 60 causes of death, of interest for population health status or consistent with "Project SENTIERI" criteria. Hospital discharge records of residents in Tuscany Region in 2004-2006, anywhere admitted to hospital, were analyzed considering only the main diagnosis, excluding repeated admissions for the same cause. The causes taken into account are the same analysed for mortality were considered. Age-standardized mortality rates (TSDM) and the temporal trends of TSDM for four periods (1971-1979, 1980-1989, 1990-1999, 2000-2006) were computed. Age-standardized mortality/hospitalization ratios (SMR/SHR), with and without adjustment for the deprivation index based on 2001 census data, were calculated: mortality in the years 2000-2006 and hospitalization in 2004-2006. The expected number of events were computed using rates of residents in neighbouring municipalities (municipalities included in 50 km radius circle centred on the study area). Bayesian estimates of mortality/hospitalization ratios (BMR/BHR) at municipal level only and relating maps of the Bayesian risk estimators were elaborated. Congenital malformations (MC) were analysed using data from Tuscan Registry of Birth Defect in 1992-2006 period, relative to outcomes of pregnancies in women resident in the municipalities of study area, wherever the birth or termination of pregnancy occurred. The ratio between observed and expected cases (O/A), with expected defined according to regional rate, were calculated and O/A Bayesian estimates (BMR) are showed only at municipal level. The low weight and the males/females ratio at birth were analysed using data from Tuscany Birth Certificates, covering period 2001-2007, excluding births occurred in facilities outside Tuscany Region. For Low birth weight (< 2,500 grams), very low birth weight (< 1,500 grams), low birth weight in women with normal gestational age or greater than 36 weeks, gestational age less than 36 weeks, and the frequency of males, the observed/expected ratio was calculated, with the expected number defined according to regional rate.

RESULTS: ENVIRONMENTAL BACKGROUND: High levels of arsenic in drinking water distribution emerges as a critical element, so that several municipalities resorted to granting exemptions for the parameters laid down by the Legislative Decree in force (D.Lgs 31/01). However, during the final phase of the study, new blast systems activated in the SGA decreased the arsenic levels in the water supply, reaching values not requiring derogations, which, instead, are still effective in some NGA municipalities. Air quality data, from Tuscany Regional Agency for Environmental Protection-ARPAT, show that geothermal activities are able to affect air quality, especially with hydrogen sulphide in NGA, and hydrogen sulphide and mercury in SGA. A significant contribution to the presence of mercury in air is due to previous metallurgical sites. Although mercury levels are below WHO guideline values, in SGA nearby Siena, values were significantly higher than in other geothermal areas, because of power plant PC2 (turned off in July 2011) in Piancastagnaio municipality. The hydrogen sulphide concentration levels were generally lower than WHO reference values, with occasional excesses over guideline value for health protection (150 µg/m3 as average of the 24 hours). Olfactory pollution was more critic with values exceeding 7-10 µg/m3 range even in areas without geothermal plants.

RESULTS: POPULATION'S HEALTH STATUS: This study evaluated health status of resident population in geothermal areas analysing geographic and temporal distribution of mortality, hospitalization and reproductive health outcomes (congenital malformations, low birth weight, sex ratio among newborns). In both geothermal areas mortality rates steadily declined from 1971 to 2006, in males and females, in line with the regional trends. In 2000-2006 period, in the overall geothermal area a significant mortality excess was observed for all causes among males (2,312 deaths, 2,146 expected), but not among females, using as reference residents in neighbouring municipalities. The mortality excess among males was more evident for infectious diseases (25 deaths, 10 expected), especially tuberculosis (8 deaths, 2 expected), for respiratory diseases (218 deaths, 170 expected), in particular pneumoconiosis, including deaths from silicosis (51 deaths, 14 expected), and for nervous system diseases (72 deaths, 56 expected). Among females significant mortality excess for liver cirrhosis (35 deaths, 25 expected) emerged, while mortality from cardiovascular diseases and ischemic heart diseases were significantly lower than expected. In the NGA, mortality among men was lower than expected for all cancers (-15%), in particular for lung cancer (- 25%), while values significantly in excesses were observed for infectious diseases (11 observed, 4 expected) and respiratory diseases (90 observed, 73 expected), expecially pneumoconiosis (20 observed, 6 expected). Among females, significant mortality excesses for ovarian cancer (17 observed, 10 expected) and for circulatory disorders of brain (170 observed, 140 expected) resulted. In the SGA, mortality was more critical, accounting for majority of the excesses detected in overall Geothermal Area. In fact, only infectious diseases and pneumoconiosis were detected in excess in both the geothermal areas. In the SGA, excess of general mortality among males (1,431 deaths; 1,245 expected) but not among females emerged. Even for all cancers, an excess among males (505 deaths, 419 expected) was observed, in particular for cancer of stomach (53 deaths, 44 expected, not statistically significant after adjusting for DI), liver (39 deaths, 23 expected) and lung (124 deaths, 102 expected) cancer. Mortality in SGA was also in excess for respiratory diseases only among men (128 deaths, 97 expected), mostly due to silicosis (31 deaths, 8 expected), although steadily decreasing since 1971 as observed at regional level. Also tuberculosis resulted in excess in SGA (7 deaths, 1 expected). Among females acute respiratory disease mortality was significantly in excess (41 observed, 29 expected). Temporal trend showed a decline from the 70s to the 90s, with a rising trend in recent years in line with Tuscany region. It should be considered that pneumonia was the commonest cause of death of acute respiratory diseases, which allow for lower reliability of death certificate, especially among the elderly (> 64 years). Among females resident in SGA a mortality excess from digestive system diseases was observed (72 observed, 55 expected). The hospitalization in the overall Geothermal Area did not show any excess for all causes and all tumours in both genders. Statistically significant excesses for hospital admission from stomach cancer among males (49 observed, 38 expected) and females (42 observed, 28 expected), and from lymphohematopoietic tumours among females, particularly from lymphatic leukaemia (15 observed, 5 expected), were observed. As mortality analysis highlighted, also hospital admissions by geothermal areas and gender showed a worst picture in SGA than in NGA. In the latter, a significant excess of hospital admissions from all causes among females (1,357 observed, 1,284 expected) but not among males (1,193 observed, 1,141 expected) and an excess - close to statistical significance - from all tumours only among females (297 observed; 272 expected) were observed. Furthermore, statistically significant excesses of hospital admissions from digestive system diseases in both genders (M: 392 observed, 350 expected; F: 300 observed, 268 expected), from dementias (16 observed, 8 expected) and from lympho hematopoietic cancers among females, particularly from lymphatic leukaemia (9 observed, 2 expected), were observed. In the SGA, statistically significant excesses of hospital admissions for stomach cancer (M: 32 observed, 21 expected, not significant after adjusting by DI; F: 29 observed, 18 expected), for respiratory diseases (M: 408 observed, 351 expected; F: 339 observed, 277 expected) and for renal failure (M: 61 observed, 41 expected; F: 52 observed, 34 expected) were observed in both genders. (ABSTRACT TRUNCATED)}, } @article {pmid23160122, year = {2013}, author = {Choi, EJ and Jin, HM and Lee, SH and Math, RK and Madsen, EL and Jeon, CO}, title = {Comparative genomic analysis and benzene, toluene, ethylbenzene, and o-, m-, and p-xylene (BTEX) degradation pathways of Pseudoxanthomonas spadix BD-a59.}, journal = {Applied and environmental microbiology}, volume = {79}, number = {2}, pages = {663-671}, pmid = {23160122}, issn = {1098-5336}, mesh = {Computational Biology ; Gasoline ; *Genome, Bacterial ; Hydrocarbons/*metabolism ; Metabolic Networks and Pathways/*genetics ; Soil Microbiology ; Soil Pollutants/*metabolism ; Xanthomonadaceae/*genetics/isolation & purification/*metabolism ; }, abstract = {Pseudoxanthomonas spadix BD-a59, isolated from gasoline-contaminated soil, has the ability to degrade all six BTEX (benzene, toluene, ethylbenzene, and o-, m-, and p-xylene) compounds. The genomic features of strain BD-a59 were analyzed bioinformatically and compared with those of another fully sequenced Pseudoxanthomonas strain, P. suwonensis 11-1, which was isolated from cotton waste compost. The genome of strain BD-a59 differed from that of strain 11-1 in many characteristics, including the number of rRNA operons, dioxygenases, monooxygenases, genomic islands (GIs), and heavy metal resistance genes. A high abundance of phage integrases and GIs and the patterns in several other genetic measures (e.g., GC content, GC skew, Karlin signature, and clustered regularly interspaced short palindromic repeat [CRISPR] gene homology) indicated that strain BD-a59's genomic architecture may have been altered through horizontal gene transfers (HGT), phage attack, and genetic reshuffling during its evolutionary history. The genes for benzene/toluene, ethylbenzene, and xylene degradations were encoded on GI-9, -13, and -21, respectively, which suggests that they may have been acquired by HGT. We used bioinformatics to predict the biodegradation pathways of the six BTEX compounds, and these pathways were proved experimentally through the analysis of the intermediates of each BTEX compound using a gas chromatograph and mass spectrometry (GC-MS). The elevated abundances of dioxygenases, monooxygenases, and rRNA operons in strain BD-a59 (relative to strain 11-1), as well as other genomic characteristics, likely confer traits that enhance ecological fitness by enabling strain BD-a59 to degrade hydrocarbons in the soil environment.}, } @article {pmid23158554, year = {2012}, author = {Gething, PW and Johnson, FA and Frempong-Ainguah, F and Nyarko, P and Baschieri, A and Aboagye, P and Falkingham, J and Matthews, Z and Atkinson, PM}, title = {Geographical access to care at birth in Ghana: a barrier to safe motherhood.}, journal = {BMC public health}, volume = {12}, number = {}, pages = {991}, pmid = {23158554}, issn = {1471-2458}, mesh = {Adolescent ; Adult ; Female ; Geographic Information Systems ; Ghana ; Health Facilities/*statistics & numerical data ; Health Services Accessibility/*standards/statistics & numerical data ; *Health Status Disparities ; Humans ; Maternal Health Services/*standards/statistics & numerical data ; Middle Aged ; Mothers ; Pregnancy ; *Pregnant Women ; Time Factors ; Travel/*statistics & numerical data ; Women's Health ; Young Adult ; }, abstract = {BACKGROUND: Appropriate facility-based care at birth is a key determinant of safe motherhood but geographical access remains poor in many high burden regions. Despite its importance, geographical access is rarely audited systematically, preventing integration in national-level maternal health system assessment and planning. In this study, we develop a uniquely detailed set of spatially-linked data and a calibrated geospatial model to undertake a national-scale audit of geographical access to maternity care at birth in Ghana, a high-burden country typical of many in sub-Saharan Africa.

METHODS: We assembled detailed spatial data on the population, health facilities, and landscape features influencing journeys. These were used in a geospatial model to estimate journey-time for all women of childbearing age (WoCBA) to their nearest health facility offering differing levels of care at birth, taking into account different transport types and availability. We calibrated the model using data on actual journeys made by women seeking care.

RESULTS: We found that a third of women (34%) in Ghana live beyond the clinically significant two-hour threshold from facilities likely to offer emergency obstetric and neonatal care (EmONC) classed at the 'partial' standard or better. Nearly half (45%) live that distance or further from 'comprehensive' EmONC facilities, offering life-saving blood transfusion and surgery. In the most remote regions these figures rose to 63% and 81%, respectively. Poor levels of access were found in many regions that meet international targets based on facilities-per-capita ratios.

CONCLUSIONS: Detailed data assembly combined with geospatial modelling can provide nation-wide audits of geographical access to care at birth to support systemic maternal health planning, human resource deployment, and strategic targeting. Current international benchmarks of maternal health care provision are inadequate for these purposes because they fail to take account of the location and accessibility of services relative to the women they serve.}, } @article {pmid23157494, year = {2013}, author = {Li, T and Hu, YJ and Hao, ZP and Li, H and Wang, YS and Chen, BD}, title = {First cloning and characterization of two functional aquaporin genes from an arbuscular mycorrhizal fungus Glomus intraradices.}, journal = {The New phytologist}, volume = {197}, number = {2}, pages = {617-630}, doi = {10.1111/nph.12011}, pmid = {23157494}, issn = {1469-8137}, mesh = {Aquaporins/*genetics ; Calcium/metabolism ; Cloning, Molecular ; Colony Count, Microbial ; Computational Biology ; Droughts ; Fungal Proteins/chemistry/genetics/metabolism ; Gene Expression Regulation, Plant ; Genes, Fungal/*genetics ; Glomeromycota/*genetics/growth & development ; Molecular Sequence Data ; Mycelium/genetics ; Mycorrhizae/*genetics/growth & development ; Osmotic Pressure ; Phylogeny ; Pichia/growth & development/metabolism ; Plant Roots/genetics/microbiology ; Protein Transport/genetics ; Protons ; Protoplasts/metabolism ; Stress, Physiological/genetics ; Transformation, Genetic ; Water/metabolism ; Zea mays/genetics/microbiology ; }, abstract = {Arbuscular mycorrhizal (AM) symbiosis is known to stimulate plant drought tolerance. However, the molecular basis for the direct involvement of AM fungi (AMF) in plant water relations has not been established. Two full-length aquaporin genes, namely GintAQPF1 and GintAQPF2, were cloned by rapid amplification of cDNA 5'- and 3'-ends from an AMF, Glomus intraradices. Aquaporin localization, activities and water permeability were examined by heterologous expression in yeast. Gene expression during symbiosis was also analyzed by quantitative real-time polymerase chain reaction. GintAQPF1 was localized to the plasma membrane of yeast, whereas GintAQPF2 was localized to both plasma and intracellular membranes. Transformed yeast cells exhibited a significant decrease in cell volume on hyperosmotic shock and faster protoplast bursting on hypo-osmotic shock. Polyethylene glycol (PEG) stimulated, but glycerol inhibited, the aquaporin activities. Furthermore, the expression of the two genes in arbuscule-enriched cortical cells and extraradical mycelia of maize roots was also enhanced significantly under drought stress. GintAQPF1 and GintAQPF2 are the first two functional aquaporin genes from AMF reported to date. Our data strongly support potential water transport via AMF to host plants, which leads to a better understanding of the important role of AMF in plant drought tolerance.}, } @article {pmid23152426, year = {2012}, author = {Anderson, EC}, title = {Large-scale parentage inference with SNPs: an efficient algorithm for statistical confidence of parent pair allocations.}, journal = {Statistical applications in genetics and molecular biology}, volume = {11}, number = {5}, pages = {}, doi = {10.1515/1544-6115.1833}, pmid = {23152426}, issn = {1544-6115}, mesh = {*Algorithms ; Animals ; *Computer Simulation ; Data Interpretation, Statistical ; Female ; Gene Frequency ; Likelihood Functions ; Lod Score ; Male ; Markov Chains ; *Models, Genetic ; Monte Carlo Method ; Pedigree ; *Polymorphism, Single Nucleotide ; Salmon/genetics ; *Software ; }, abstract = {Advances in genotyping that allow tens of thousands of individuals to be genotyped at a moderate number of single nucleotide polymorphisms (SNPs) permit parentage inference to be pursued on a very large scale. The intergenerational tagging this capacity allows is revolutionizing the management of cultured organisms (cows, salmon, etc.) and is poised to do the same for scientific studies of natural populations. Currently, however, there are no likelihood-based methods of parentage inference which are implemented in a manner that allows them to quickly handle a very large number of potential parents or parent pairs. Here we introduce an efficient likelihood-based method applicable to the specialized case of cultured organisms in which both parents can be reliably sampled. We develop a Markov chain representation for the cumulative number of Mendelian incompatibilities between an offspring and its putative parents and we exploit it to develop a fast algorithm for simulation-based estimates of statistical confidence in SNP-based assignments of offspring to pairs of parents. The method is implemented in the freely available software SNPPIT. We describe the method in detail, then assess its performance in a large simulation study using known allele frequencies at 96 SNPs from ten hatchery salmon populations. The simulations verify that the method is fast and accurate and that 96 well-chosen SNPs can provide sufficient power to identify the correct pair of parents from amongst millions of candidate pairs.}, } @article {pmid23152345, year = {2012}, author = {Roza, DL and Caccia-Bava, Mdo C and Martinez, EZ}, title = {Spatio-temporal patterns of tuberculosis incidence in Ribeirão Preto, State of São Paulo, southeast Brazil, and their relationship with social vulnerability: a Bayesian analysis.}, journal = {Revista da Sociedade Brasileira de Medicina Tropical}, volume = {45}, number = {5}, pages = {607-615}, doi = {10.1590/s0037-86822012000500013}, pmid = {23152345}, issn = {1678-9849}, mesh = {Bayes Theorem ; Brazil/epidemiology ; Disease Notification ; Educational Status ; Effect Modifier, Epidemiologic ; Female ; Health Information Systems ; Humans ; Incidence ; Income ; Male ; Risk Factors ; *Socioeconomic Factors ; Spatio-Temporal Analysis ; Tuberculosis/*epidemiology ; Urban Population ; }, abstract = {INTRODUCTION: The purpose of this ecological study was to evaluate the urban spatial and temporal distribution of tuberculosis (TB) in Ribeirão Preto, State of São Paulo, southeast Brazil, between 2006 and 2009 and to evaluate its relationship with factors of social vulnerability such as income and education level.

METHODS: We evaluated data from TBWeb, an electronic notification system for TB cases. Measures of social vulnerability were obtained from the SEADE Foundation, and information about the number of inhabitants, education and income of the households were obtained from Brazilian Institute of Geography and Statistics. Statistical analyses were conducted by a Bayesian regression model assuming a Poisson distribution for the observed new cases of TB in each area. A conditional autoregressive structure was used for the spatial covariance structure.

RESULTS: The Bayesian model confirmed the spatial heterogeneity of TB distribution in Ribeirão Preto, identifying areas with elevated risk and the effects of social vulnerability on the disease. We demonstrated that the rate of TB was correlated with the measures of income, education and social vulnerability. However, we observed areas with low vulnerability and high education and income, but with high estimated TB rates.

CONCLUSIONS: The study identified areas with different risks for TB, given that the public health system deals with the characteristics of each region individually and prioritizes those that present a higher propensity to risk of TB. Complex relationships may exist between TB incidence and a wide range of environmental and intrinsic factors, which need to be studied in future research.}, } @article {pmid23147825, year = {2012}, author = {Pavarini, DP and da Silva, DB and Carollo, CA and Portella, AP and Latansio-Aidar, SR and Cavalin, PO and Oliveira, VC and Rosado, BH and Aidar, MP and Bolzani, VS and Lopes, NP and Joly, CA}, title = {Application of MALDI-MS analysis of Rainforest chemodiversity: a keystone for biodiversity conservation and sustainable use.}, journal = {Journal of mass spectrometry : JMS}, volume = {47}, number = {11}, pages = {1482-1485}, doi = {10.1002/jms.3100}, pmid = {23147825}, issn = {1096-9888}, mesh = {Alkaloids/analysis ; *Biodiversity ; Brazil ; *Conservation of Natural Resources ; Databases, Factual ; Ecology ; High-Throughput Screening Assays/methods ; Plant Extracts/chemistry ; Plant Leaves/chemistry ; Rubiaceae/chemistry ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/*methods ; Trees/*chemistry ; }, } @article {pmid23144824, year = {2012}, author = {Kim, CK and Toft, JE and Papenfus, M and Verutes, G and Guerry, AD and Ruckelshaus, MH and Arkema, KK and Guannel, G and Wood, SA and Bernhardt, JR and Tallis, H and Plummer, ML and Halpern, BS and Pinsky, ML and Beck, MW and Chan, F and Chan, KM and Levin, PS and Polasky, S}, title = {Catching the right wave: evaluating wave energy resources and potential compatibility with existing marine and coastal uses.}, journal = {PloS one}, volume = {7}, number = {11}, pages = {e47598}, pmid = {23144824}, issn = {1932-6203}, mesh = {Algorithms ; British Columbia ; Conservation of Natural Resources ; Decision Support Techniques ; Electricity ; Environment ; Fisheries/statistics & numerical data ; Humans ; Oceans and Seas ; Renewable Energy/*economics ; Software ; *Water Movements ; }, abstract = {Many hope that ocean waves will be a source for clean, safe, reliable and affordable energy, yet wave energy conversion facilities may affect marine ecosystems through a variety of mechanisms, including competition with other human uses. We developed a decision-support tool to assist siting wave energy facilities, which allows the user to balance the need for profitability of the facilities with the need to minimize conflicts with other ocean uses. Our wave energy model quantifies harvestable wave energy and evaluates the net present value (NPV) of a wave energy facility based on a capital investment analysis. The model has a flexible framework and can be easily applied to wave energy projects at local, regional, and global scales. We applied the model and compatibility analysis on the west coast of Vancouver Island, British Columbia, Canada to provide information for ongoing marine spatial planning, including potential wave energy projects. In particular, we conducted a spatial overlap analysis with a variety of existing uses and ecological characteristics, and a quantitative compatibility analysis with commercial fisheries data. We found that wave power and harvestable wave energy gradually increase offshore as wave conditions intensify. However, areas with high economic potential for wave energy facilities were closer to cable landing points because of the cost of bringing energy ashore and thus in nearshore areas that support a number of different human uses. We show that the maximum combined economic benefit from wave energy and other uses is likely to be realized if wave energy facilities are sited in areas that maximize wave energy NPV and minimize conflict with existing ocean uses. Our tools will help decision-makers explore alternative locations for wave energy facilities by mapping expected wave energy NPV and helping to identify sites that provide maximal returns yet avoid spatial competition with existing ocean uses.}, } @article {pmid23139734, year = {2012}, author = {Hampton, J and Lladser, ME}, title = {Estimation of distribution overlap of urn models.}, journal = {PloS one}, volume = {7}, number = {11}, pages = {e42368}, pmid = {23139734}, issn = {1932-6203}, support = {R01 HG004872/HG/NHGRI NIH HHS/United States ; HG4872/HG/NHGRI NIH HHS/United States ; }, mesh = {Databases as Topic ; Humans ; Metagenome/genetics ; Models, Biological ; *Models, Statistical ; *Probability ; }, abstract = {A classical problem in statistics is estimating the expected coverage of a sample, which has had applications in gene expression, microbial ecology, optimization, and even numismatics. Here we consider a related extension of this problem to random samples of two discrete distributions. Specifically, we estimate what we call the dissimilarity probability of a sample, i.e., the probability of a draw from one distribution not being observed in [Formula: see text] draws from another distribution. We show our estimator of dissimilarity to be a [Formula: see text]-statistic and a uniformly minimum variance unbiased estimator of dissimilarity over the largest appropriate range of [Formula: see text]. Furthermore, despite the non-Markovian nature of our estimator when applied sequentially over [Formula: see text], we show it converges uniformly in probability to the dissimilarity parameter, and we present criteria when it is approximately normally distributed and admits a consistent jackknife estimator of its variance. As proof of concept, we analyze V35 16S rRNA data to discern between various microbial environments. Other potential applications concern any situation where dissimilarity of two discrete distributions may be of interest. For instance, in SELEX experiments, each urn could represent a random RNA pool and each draw a possible solution to a particular binding site problem over that pool. The dissimilarity of these pools is then related to the probability of finding binding site solutions in one pool that are absent in the other.}, } @article {pmid23138971, year = {2013}, author = {Cohen, Y and Rallo, R and Liu, R and Liu, HH}, title = {In silico analysis of nanomaterials hazard and risk.}, journal = {Accounts of chemical research}, volume = {46}, number = {3}, pages = {802-812}, doi = {10.1021/ar300049e}, pmid = {23138971}, issn = {1520-4898}, mesh = {Cell Survival/drug effects ; Computer Simulation ; Humans ; Nanoparticles/chemistry ; Nanostructures/*chemistry/toxicity ; Risk Factors ; Structure-Activity Relationship ; Toxicity Tests/*methods/standards ; }, abstract = {Because a variety of human-related activities, engineer-ed nanoparticles (ENMs) may be released to various environmental media and may cross environmental boundaries, and thus will be found in most media. Therefore, the potential environmental impacts of ENMs must be assessed from a multimedia perspective and with an integrated risk management approach that considers rapid developments and increasing use of new nanomaterials. Accordingly, this Account presents a rational process for the integration of in silico ENM toxicity and fate and transport analyses for environmental impact assessment. This approach requires knowledge of ENM toxicity and environmental exposure concentrations. Considering the large number of current different types of ENMs and that those numbers are likely to increase, there is an urgent need to accelerate the evaluation of their toxicity and the assessment of their potential distribution in the environment. Developments in high throughput screening (HTS) are now enabling the rapid generation of large data sets for ENM toxicity assessment. However, these analyses require the establishment of reliable toxicity metrics, especially when HTS includes data from multiple assays, cell lines, or organisms. Establishing toxicity metrics with HTS data requires advanced data processing techniques in order to clearly identify significant biological effects associated with exposure to ENMs. HTS data can form the basis for developing and validating in silico toxicity models (e.g., quantitative structure-activity relationships) and for generating data-driven hypotheses to aid in establishing and/or validating possible toxicity mechanisms. To correlate the toxicity of ENMs with their physicochemical properties, researchers will need to develop quantitative structure-activity relationships for nanomaterials (i.e., nano-SARs). However, as nano-SARs are applied in regulatory applications, researchers must consider their applicability and the acceptance level of false positive relative to false negative predictions and the reliability of toxicity data. To establish the environmental impact of ENMs identified as toxic, researchers will need to estimate the potential level of environmental exposure concentration of ENMs in the various media such as air, water, soil, and vegetation. When environmental monitoring data are not available, models of ENMs fate and transport (at various levels of complexity) serve as alternative approaches for estimating exposure concentrations. Risk management decisions regarding the manufacturing, use, and environmental regulations of ENMs would clearly benefit from both the assessment of potential ENMs exposure concentrations and suitable toxicity metrics. The decision process should consider the totality of available information: quantitative and qualitative data and the analysis of nanomaterials toxicity, and fate and transport behavior in the environment. Effective decision-making to address the potential impacts of nanomaterials will require considerations of the relevant environmental, ecological, technological, economic, and sociopolitical factors affecting the complete lifecycle of nanomaterials, while accounting for data and modeling uncertainties. Accordingly, researchers will need to establish standardized data management and analysis tools through nanoinformatics as a basis for the development of rational decision tools.}, } @article {pmid23137142, year = {2013}, author = {Wang, IJ and Glor, RE and Losos, JB}, title = {Quantifying the roles of ecology and geography in spatial genetic divergence.}, journal = {Ecology letters}, volume = {16}, number = {2}, pages = {175-182}, doi = {10.1111/ele.12025}, pmid = {23137142}, issn = {1461-0248}, mesh = {Animals ; DNA, Mitochondrial ; *Ecology ; Gene Flow ; Genetic Speciation ; Genetic Variation ; *Genetics, Population ; Geographic Information Systems ; Lizards/*genetics ; *Models, Theoretical ; }, abstract = {Investigating the properties of ecological landscapes that influence gene flow among populations can provide key insights into the earliest stages of biological divergence. Both ecological and geographical factors can reduce gene flow, which can lead to population divergence, but we know little of the relative strengths of these phenomena in nature. Here, we use a novel application of structural equation modelling to quantify the contributions of ecological and geographical isolation to spatial genetic divergence in 17 species of Anolis lizards. Our comparative analysis shows that although both processes contributed significantly, geographical isolation explained substantially more genetic divergence than ecological isolation (36.3 vs. 17.9% of variance respectively), suggesting that despite the proposed ubiquity of ecological divergence, non-ecological factors play the dominant role in the evolution of spatial genetic divergence.}, } @article {pmid23134687, year = {2012}, author = {Hu, Q and Ma, T and Wang, K and Xu, T and Liu, J and Qiu, Q}, title = {The Yak genome database: an integrative database for studying yak biology and high-altitude adaption.}, journal = {BMC genomics}, volume = {13}, number = {}, pages = {600}, pmid = {23134687}, issn = {1471-2164}, mesh = {Altitude ; Animals ; Cattle ; *Databases, Genetic ; *Genome ; Internet ; User-Computer Interface ; }, abstract = {BACKGROUND: The yak (Bos grunniens) is a long-haired bovine that lives at high altitudes and is an important source of milk, meat, fiber and fuel. The recent sequencing, assembly and annotation of its genome are expected to further our understanding of the means by which it has adapted to life at high altitudes and its ecologically important traits.

DESCRIPTION: The Yak Genome Database (YGD) is an internet-based resource that provides access to genomic sequence data and predicted functional information concerning the genes and proteins of Bos grunniens. The curated data stored in the YGD includes genome sequences, predicted genes and associated annotations, non-coding RNA sequences, transposable elements, single nucleotide variants, and three-way whole-genome alignments between human, cattle and yak. YGD offers useful searching and data mining tools, including the ability to search for genes by name or using function keywords as well as GBrowse genome browsers and/or BLAST servers, which can be used to visualize genome regions and identify similar sequences. Sequence data from the YGD can also be downloaded to perform local searches.

CONCLUSIONS: A new yak genome database (YGD) has been developed to facilitate studies on high-altitude adaption and bovine genomics. The database will be continuously updated to incorporate new information such as transcriptome data and population resequencing data. The YGD can be accessed at http://me.lzu.edu.cn/yak.}, } @article {pmid23133553, year = {2012}, author = {Marinković, M and de Leeuw, WC and de Jong, M and Kraak, MH and Admiraal, W and Breit, TM and Jonker, MJ}, title = {Combining next-generation sequencing and microarray technology into a transcriptomics approach for the non-model organism Chironomus riparius.}, journal = {PloS one}, volume = {7}, number = {10}, pages = {e48096}, pmid = {23133553}, issn = {1932-6203}, mesh = {Animals ; Base Sequence ; Chironomidae/*genetics ; Comparative Genomic Hybridization ; Databases, Genetic ; Expressed Sequence Tags ; Gene Expression Profiling ; Gene Library ; Genome ; Microarray Analysis/*methods ; Models, Genetic ; Molecular Sequence Data ; Oligonucleotide Array Sequence Analysis ; RNA, Messenger/metabolism ; Sequence Analysis, DNA/*methods ; *Transcriptome ; }, abstract = {Whole-transcriptome gene-expression analyses are commonly performed in species that have a sequenced genome and for which microarrays are commercially available. To do such analyses in species with no or limited genome data, i.e. non-model organisms, necessary transcriptomics resources, i.e. an annotated transcriptome and a validated gene-expression microarray, must first be developed. The aim of the present study was to establish an advanced approach for developing transcriptomics resources for non-model organisms by combining next-generation sequencing (NGS) and microarray technology. We applied our approach to the non-biting midge Chironomus riparius, an ecologically relevant species that is widely used in sediment ecotoxicity testing. We sampled extensively covering all C. riparius developmental stages as well as toxicant exposed larvae and obtained from a normalized cDNA library 1.5 M NGS reads totalling 501 Mbp. Using the NGS data we developed transcriptomics resources in several steps. First, we designed 844 k probes directly on the NGS reads, as well as 76 k probes targeting expressed sequence tags of related species. These probes were tested for their affinity to C. riparius DNA and mRNA, by performing two biological experiments with a 1 M probe-selection microarray that contained the entire probe-library. Subsequently, the 1.5 M NGS reads were assembled into 23,709 isotigs and 135,082 singletons, which were associated to ~55 k, respectively, ~61 k gene ontology terms and which corresponded together to 22,593 unique protein accessions. An algorithm was developed that took the assembly and the probe affinities to DNA and mRNA into account, what resulted in 59 k highly-reliable probes that targeted uniquely 95% of the isotigs and 18% of the singletons. Concluding, our approach allowed the development of high-quality transcriptomics resources for C. riparius, and is applicable to any non-model organism. It is expected, that these resources will advance ecotoxicity testing with C. riparius as whole-transcriptome gene-expression analysis are now possible with this species.}, } @article {pmid23133363, year = {2012}, author = {Patil, K and Pressnitzer, D and Shamma, S and Elhilali, M}, title = {Music in our ears: the biological bases of musical timbre perception.}, journal = {PLoS computational biology}, volume = {8}, number = {11}, pages = {e1002759}, pmid = {23133363}, issn = {1553-7358}, support = {R01 AG036424/AG/NIA NIH HHS/United States ; 1R01AG036424-01/AG/NIA NIH HHS/United States ; }, mesh = {Acoustic Stimulation ; Adult ; Algorithms ; Auditory Cortex/*physiology ; Auditory Perception/*physiology ; Computational Biology ; Female ; Humans ; Judgment/physiology ; Male ; *Models, Neurological ; *Music ; Psychophysics ; Recognition, Psychology/physiology ; Sound ; }, abstract = {Timbre is the attribute of sound that allows humans and other animals to distinguish among different sound sources. Studies based on psychophysical judgments of musical timbre, ecological analyses of sound's physical characteristics as well as machine learning approaches have all suggested that timbre is a multifaceted attribute that invokes both spectral and temporal sound features. Here, we explored the neural underpinnings of musical timbre. We used a neuro-computational framework based on spectro-temporal receptive fields, recorded from over a thousand neurons in the mammalian primary auditory cortex as well as from simulated cortical neurons, augmented with a nonlinear classifier. The model was able to perform robust instrument classification irrespective of pitch and playing style, with an accuracy of 98.7%. Using the same front end, the model was also able to reproduce perceptual distance judgments between timbres as perceived by human listeners. The study demonstrates that joint spectro-temporal features, such as those observed in the mammalian primary auditory cortex, are critical to provide the rich-enough representation necessary to account for perceptual judgments of timbre by human listeners, as well as recognition of musical instruments.}, } @article {pmid23133348, year = {2012}, author = {Kembel, SW and Wu, M and Eisen, JA and Green, JL}, title = {Incorporating 16S gene copy number information improves estimates of microbial diversity and abundance.}, journal = {PLoS computational biology}, volume = {8}, number = {10}, pages = {e1002743}, pmid = {23133348}, issn = {1553-7358}, mesh = {Bacteria/*genetics ; *Biodiversity ; Cluster Analysis ; Computer Simulation ; Databases, Genetic ; *Gene Dosage ; Humans ; Microbial Consortia ; Models, Biological ; Oceans and Seas ; Phylogeny ; RNA, Ribosomal, 16S/*genetics ; Skin/microbiology ; Water Microbiology ; }, abstract = {The abundance of different SSU rRNA ("16S") gene sequences in environmental samples is widely used in studies of microbial ecology as a measure of microbial community structure and diversity. However, the genomic copy number of the 16S gene varies greatly - from one in many species to up to 15 in some bacteria and to hundreds in some microbial eukaryotes. As a result of this variation the relative abundance of 16S genes in environmental samples can be attributed both to variation in the relative abundance of different organisms, and to variation in genomic 16S copy number among those organisms. Despite this fact, many studies assume that the abundance of 16S gene sequences is a surrogate measure of the relative abundance of the organisms containing those sequences. Here we present a method that uses data on sequences and genomic copy number of 16S genes along with phylogenetic placement and ancestral state estimation to estimate organismal abundances from environmental DNA sequence data. We use theory and simulations to demonstrate that 16S genomic copy number can be accurately estimated from the short reads typically obtained from high-throughput environmental sequencing of the 16S gene, and that organismal abundances in microbial communities are more strongly correlated with estimated abundances obtained from our method than with gene abundances. We re-analyze several published empirical data sets and demonstrate that the use of gene abundance versus estimated organismal abundance can lead to different inferences about community diversity and structure and the identity of the dominant taxa in microbial communities. Our approach will allow microbial ecologists to make more accurate inferences about microbial diversity and abundance based on 16S sequence data.}, } @article {pmid23125408, year = {2013}, author = {Blair, C and Davy, CM and Ngo, A and Orlov, NL and Shi, HT and Lu, SQ and Gao, L and Rao, DQ and Murphy, RW}, title = {Genealogy and Demographic History of a Widespread Amphibian throughout Indochina.}, journal = {The Journal of heredity}, volume = {104}, number = {1}, pages = {72-85}, doi = {10.1093/jhered/ess079}, pmid = {23125408}, issn = {1465-7333}, mesh = {Animals ; Anura/*genetics ; Asia, Southeastern ; Base Sequence ; Bayes Theorem ; *Biological Evolution ; Climate ; Computational Biology ; DNA Primers/genetics ; DNA, Mitochondrial/genetics ; *Demography ; *Genetic Variation ; *Genetics, Population ; Geography ; Models, Genetic ; Molecular Sequence Data ; *Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA ; }, abstract = {Relatively little is known about spatial patterns of cryptic diversity in tropical species and the processes that generate them. Few studies examine the geographic distribution of genetic lineages in Southeast Asia, an area hypothesized to harbor substantial cryptic diversity. We investigated the evolutionary history of Asian tree frogs of the Polypedates leucomystax complex (n = 172) based on 1800 bp of the mtDNA genes ND1 and cytochrome b and tested hypotheses pertaining to climate, geology, and dispersal patterns. Analyses revealed substantial genetic diversity and lineage divergence throughout the region with evidence for widespread sympatric lineages and a general north versus south clustering. Relaxed molecular clock analysis and tests for demographic expansion identified an initial cladogenesis during the Miocene with subsequent Plio-Pleistocene diversification, with the former corresponding to periods of increased aridity and the onset of monsoonal weather systems. Rates of diversification were relatively constant until the Early Pleistocene when rates increased exponentially. We found equivocal evidence for isolation-by-distance and a potential role of some landscape features as partial barriers to dispersal. Finally, our analyses showed that divergence between insular and mainland populations occurred before Homo sapiens colonized Southeast Asia, suggesting that historical human-mediated dispersal did not drive insular diversification. Our results suggested that demographic expansion in the Late Pleistocene resulted in widespread sympatric lineages in the P. leucomystax complex throughout southern China and Indochina and further clarified the evolutionary history of lineages within P. leucomystax.}, } @article {pmid23124743, year = {2012}, author = {Oh, J and Kim, BK and Cho, WS and Hong, SG and Kim, KM}, title = {PyroTrimmer: a software with GUI for pre-processing 454 amplicon sequences.}, journal = {Journal of microbiology (Seoul, Korea)}, volume = {50}, number = {5}, pages = {766-769}, pmid = {23124743}, issn = {1976-3794}, mesh = {Bacteria/genetics ; DNA Primers/analysis ; Databases, Nucleic Acid ; High-Throughput Nucleotide Sequencing ; Sequence Analysis, DNA/*instrumentation ; *Software ; }, abstract = {The ultimate goal of metagenome research projects is to understand the ecological roles and physiological functions of the microbial communities in a given natural environment. The 454 pyrosequencing platform produces the longest reads among the most widely used next generation sequencing platforms. Since the relatively longer reads of the 454 platform provide more information for identification of microbial sequences, this platform is dedicated to microbial community and population studies. In order to accurately perform the downstream analysis of the 454 multiplex datasets, it is necessary to remove artificially designed sequences located at either ends of individual reads and to correct low-quality sequences. We have developed a program called PyroTrimmer that removes the barcodes, linkers, and primers, trims sequence regions with low quality scores, and filters out low-quality sequence reads. Although these functions have previously been implemented in other programs as well, PyroTrimmer has novelty in terms of the following features: i) more sensitive primer detection using Levenstein distance and global pairwise alignment, ii) the first stand-alone software with a graphic user interface, and iii) various options for trimming and filtering out the low-quality sequence reads. PyroTrimmer, written in JAVA, is compatible with multiple operating systems and can be downloaded free at http://pyrotrimmer.kobic.re.kr.}, } @article {pmid23121389, year = {2012}, author = {Schnoor, JL}, title = {The future of higher education.}, journal = {Environmental science & technology}, volume = {46}, number = {23}, pages = {12753}, doi = {10.1021/es304366k}, pmid = {23121389}, issn = {1520-5851}, mesh = {Ecology/*economics/*education/trends ; *Online Systems/economics/trends ; Universities/*economics/trends ; }, } @article {pmid23117719, year = {2013}, author = {Zaugg, I and Magni, C and Panzeri, D and Daminati, MG and Bollini, R and Benrey, B and Bacher, S and Sparvoli, F}, title = {QUES, a new Phaseolus vulgaris genotype resistant to common bean weevils, contains the Arcelin-8 allele coding for new lectin-related variants.}, journal = {TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik}, volume = {126}, number = {3}, pages = {647-661}, pmid = {23117719}, issn = {1432-2242}, mesh = {*Alleles ; Animals ; Breeding ; Computational Biology ; DNA, Complementary/genetics/isolation & purification ; Electrophoresis, Polyacrylamide Gel ; Genetic Loci ; *Genotype ; Phaseolus/*genetics ; Phytohemagglutinins/genetics/metabolism ; Plant Lectins/*genetics/metabolism ; Proteomics ; Sequence Analysis, DNA ; *Weevils ; }, abstract = {In common bean (Phaseolus vulgaris L.), the most abundant seed proteins are the storage protein phaseolin and the family of closely related APA proteins (arcelin, phytohemagglutinin and α-amylase inhibitor). High variation in APA protein composition has been described and the presence of arcelin (Arc) has been associated with bean resistance against two bruchid beetles, the bean weevil (Acanthoscelides obtectus Say) and the Mexican bean weevil (Zabrotes subfasciatus Bohemian). So far, seven Arc variants have been identified, all in wild accessions, however, only those containing Arc-4 were reported to be resistant to both species. Although many efforts have been made, a successful breeding of this genetic trait into cultivated genotypes has not yet been achieved. Here, we describe a newly collected wild accession (named QUES) and demonstrate its resistance to both A. obtectus and Z. subfasciatus. Immunological and proteomic analyses of QUES seed protein composition indicated the presence of new Arc and arcelin-like (ARL) polypeptides of about 30 and 27 kDa, respectively. Sequencing of cDNAs coding for QUES APA proteins confirmed that this accession contains new APA variants, here referred to as Arc-8 and ARL-8. Moreover, bioinformatic analysis showed the two proteins are closely related to APA components present in the G12949 wild bean accession, which contains the Arc-4 variant. The presence of these new APA components, combined with the observations that they are poorly digested and remain very abundant in A. obtectus feces, so-called frass, suggest that the QUES APA locus is involved in the bruchid resistance. Moreover, molecular analysis indicated a lower complexity of the locus compared to that of G12949, suggesting that QUES should be considered a valuable source of resistance for further breeding purposes.}, } @article {pmid23114029, year = {2012}, author = {Szilágyi, A and Kun, A and Szathmáry, E}, title = {Early evolution of efficient enzymes and genome organization.}, journal = {Biology direct}, volume = {7}, number = {}, pages = {38; discussion 38}, pmid = {23114029}, issn = {1745-6150}, support = {294332/ERC_/European Research Council/International ; }, mesh = {Catalysis ; *Chromosomes ; Computational Biology ; Enzymes/*genetics/*metabolism ; *Evolution, Molecular ; Genome ; Metabolic Networks and Pathways ; Models, Genetic ; RNA, Catalytic/*genetics ; Selection, Genetic ; Substrate Specificity ; }, abstract = {BACKGROUND: Cellular life with complex metabolism probably evolved during the reign of RNA, when it served as both information carrier and enzyme. Jensen proposed that enzymes of primordial cells possessed broad specificities: they were generalist. When and under what conditions could primordial metabolism run by generalist enzymes evolve to contemporary-type metabolism run by specific enzymes?

RESULTS: Here we show by numerical simulation of an enzyme-catalyzed reaction chain that specialist enzymes spread after the invention of the chromosome because protocells harbouring unlinked genes maintain largely non-specific enzymes to reduce their assortment load. When genes are linked on chromosomes, high enzyme specificity evolves because it increases biomass production, also by reducing taxation by side reactions.

CONCLUSION: The constitution of the genetic system has a profound influence on the limits of metabolic efficiency. The major evolutionary transition to chromosomes is thus proven to be a prerequisite for a complex metabolism. Furthermore, the appearance of specific enzymes opens the door for the evolution of their regulation.

REVIEWERS: This article was reviewed by Sándor Pongor, Gáspár Jékely, and Rob Knight.}, } @article {pmid23110540, year = {2013}, author = {Som, C and Nowack, B and Krug, HF and Wick, P}, title = {Toward the development of decision supporting tools that can be used for safe production and use of nanomaterials.}, journal = {Accounts of chemical research}, volume = {46}, number = {3}, pages = {863-872}, doi = {10.1021/ar3000458}, pmid = {23110540}, issn = {1520-4898}, mesh = {*Decision Support Techniques ; Humans ; Nanostructures/*chemistry ; *Risk Assessment ; Safety ; }, abstract = {Although researchers have intentionally produced and used nanomaterials for more than a century, nanotechnology has made its mark in most areas of daily life in the past 20 years. Now thousands of products contain nanoparticles, nanofibers, or nanostructured parts. Because some chemical products have caused severe problems to human health and to the environment, we should consider the overall biological and toxicological effects of nanomaterials as we decide whether to use them in various products. We should also reflect on the mechanisms for making these decisions, which may greatly influence the development, production, and use of such products. The preselection of appropriate materials during the early product design state should allow industry and applied researchers to mitigate the risks of these new materials. However, currently the human and ecological risks of the applied nanomaterials during their life cycle are unknown. A large set of physicochemical characteristics can determine the potential human and environmental exposure to and hazards from nanomaterials. Thus, researchers will need many years to gather and analyze all the data to perform a comprehensive risk assessment for engineered nanomaterials and to develop a sound decision making process. The ideal risk assessment approach would include cost-effective screening processes to target resources toward the risks of greatest concern. The outcome of the risk assessment is only as good as the quality of the data used. Unfortunately, the actual review process of most journals that publish on nanotoxicology focuses on "mechanistic studies and results" rather than a toxicologically relevant outcome. For example, journals often do not include studies that show no effect as worthy of publication ("no-effect-studies" dilemma), which can lead to misleading interpretations of toxicological data for hazard identification. However, even with insufficient data sets, researchers can produce a preliminary comparable risk assessment ("approximate" risk assessment). Researchers have already performed risk-based evaluations of nanomaterials grounded on the comparison of exposure concentrations with no-effect levels (as required for chemical risk assessment), examining generic nanomaterials such as "nano-TiO2" but not specific forms or modifications. Even though these data sets on hazard and exposure are incomplete, they already provide the basis to illustrate the current state of knowledge and uncertainties. Therefore industry and applied researchers can calculate the probability that an adverse effect might occur and begin to balance the benefits and potential risks of an innovation. Based on the increasing numbers of nanotoxicology publications and funding programs, this Account reviews the decision support approaches that already exist to safely implement engineered nanomaterials during an early phase of innovation.}, } @article {pmid23110105, year = {2012}, author = {Ma, K and You, L and Liu, J and Zhang, M}, title = {A hybrid wetland map for China: a synergistic approach using census and spatially explicit datasets.}, journal = {PloS one}, volume = {7}, number = {10}, pages = {e47814}, pmid = {23110105}, issn = {1932-6203}, mesh = {Censuses ; China ; Databases, Factual ; Fuzzy Logic ; *Geographic Mapping ; Geography ; *Wetlands ; }, abstract = {Wetlands play important ecological, economic, and cultural roles in societies around the world. However, wetland degradation has become a serious ecological issue, raising the global sustainability concern. An accurate wetland map is essential for wetland management. Here we used a fuzzy method to create a hybrid wetland map for China through the combination of five existing wetlands datasets, including four spatially explicit wetland distribution data and one wetland census. Our results show the total wetland area is 384,864 km(2), 4.08% of China's national surface area. The hybrid wetland map also shows spatial distribution of wetlands with a spatial resolution of 1 km. The reliability of the map is demonstrated by comparing it with spatially explicit datasets on lakes and reservoirs. The hybrid wetland map is by far the first wetland mapping that is consistent with the statistical data at the national and provincial levels in China. It provides a benchmark map for research on wetland protection and management. The method presented here is applicable for not only wetland mapping but also for other thematic mapping in China and beyond.}, } @article {pmid23106138, year = {2012}, author = {MacDonell, K and Gibson-Scipio, W and Lam, P and Naar-King, S and Chen, X}, title = {Text messaging to measure asthma medication use and symptoms in urban African American emerging adults: a feasibility study.}, journal = {The Journal of asthma : official journal of the Association for the Care of Asthma}, volume = {49}, number = {10}, pages = {1092-1096}, doi = {10.3109/02770903.2012.733993}, pmid = {23106138}, issn = {1532-4303}, support = {P30 HL101301/HL/NHLBI NIH HHS/United States ; 1P30HL10301-01/HL/NHLBI NIH HHS/United States ; }, mesh = {Adolescent ; Adult ; *Black or African American ; Anti-Asthmatic Agents/*administration & dosage/therapeutic use ; Asthma/*drug therapy ; Female ; Humans ; Male ; *Medication Adherence ; Patient Satisfaction ; Reminder Systems/instrumentation ; *Text Messaging ; Time Factors ; *Urban Population ; Young Adult ; }, abstract = {OBJECTIVE: Urban African American adolescents and young adults face disproportionate risk of asthma morbidity and mortality. This study was the first to assess the feasibility of Ecological Momentary Assessment via text messaging to measure asthma medication use and symptoms in African Americans aged 18-25 years.

METHODS: This study used automated text messaging with N = 6 participants for 14 consecutive days. Participants sent event-based messages whenever they experienced asthma symptoms or took asthma rescue or controller medications. They also received time-based messages daily that prompted for a response about asthma medications or symptoms.

RESULTS: Feasibility was assessed using response rates and participant feedback. Rates of event-based messages were relatively low (M = 0.85 messages sent per participant/day), but participants were very responsive to time-based messages (78.5%). All participants expressed positive feedback about the program, though 40.0% reported confusion with event-based messages and most preferred time-based messages. The assessment found low medication adherence rates and reasons for missing medication consistent with previous research with youth with asthma.

CONCLUSION: Text messaging may be a useful method to measure medication use and symptoms in "real time," particularly using time-based prompts. Results could be used to provide personalized feedback on adherence as part of a tailored intervention.}, } @article {pmid23099930, year = {2012}, author = {Wang, X and Cao, Y and Zhong, X and Gao, P}, title = {A new method of regional eco-environmental quality assessment and its application.}, journal = {Journal of environmental quality}, volume = {41}, number = {5}, pages = {1393-1401}, doi = {10.2134/jeq2011.0390}, pmid = {23099930}, issn = {0047-2425}, mesh = {Algorithms ; Delphi Technique ; Ecology/methods ; *Environment ; Fuzzy Logic ; Geographic Information Systems ; Tibet ; }, abstract = {Eco-environmental quality assessment (EQA) is an intricate and challenging task that must take into account numerous natural, economic, political, and social factors, which are subject to multiple conflicting criteria. In this paper, a methodological reference framework is developed for EQA that combines the fuzzy Delphi method (FDM) and fuzzy analytical hierarchy process (FAHP) with a geographic information system (GIS). The proposed method significantly improves the accuracy and reliability of evaluation results through the incorporation of fuzzy set theory. A GIS not only has the ability to store and analyze large amounts of spatial data from different sources but also provides a consistent visualization environment for displaying the input data and the results of EQA. Furthermore, unlike prior EQAs, the proposed method can support the dynamic estimation of regional eco-environmental quality by updating historical spatiotemporal data at little additional cost. A case study is presented for the western Tibetan Plateau. The study results show that worse, bad, and moderate eco-environmental quality classes comprised 16.58, 20.15, and 24.84% of the total area, respectively. Good and better eco-environmental quality classes accounted for 38.43%. This result indicates that nearly 62% of the total area is eco-environmentally vulnerable. The results verified the usefulness and feasibility of the proposed method. The EQA can also help local managers make scientifically based and effective decisions about Tibetan eco-environmental protection and land use.}, } @article {pmid23095173, year = {2012}, author = {Grundt, JH and Nakling, J and Eide, GE and Markestad, T}, title = {Possible relation between maternal consumption of added sugar and sugar-sweetened beverages and birth weight--time trends in a population.}, journal = {BMC public health}, volume = {12}, number = {}, pages = {901}, pmid = {23095173}, issn = {1471-2458}, mesh = {Adult ; Beverages/*analysis ; *Birth Weight ; Databases, Factual ; Diet/trends ; Dietary Sucrose/*adverse effects ; Female ; Humans ; Infant, Newborn ; Norway ; Pregnancy ; *Prenatal Nutritional Physiological Phenomena ; Prospective Studies ; Sweetening Agents/*adverse effects ; Young Adult ; }, abstract = {BACKGROUND: High birth weight (BW) is a risk factor for later obesity. In Norway, mean BW and proportion of large newborns increased from 1989 to 2000 and subsequently decreased to the 1989 level by 2010. The purpose of the study was to explore causes of this temporary increase.

METHODS: From a regional prospective database pregnancy and newborn data were extracted for all 33088 singleton pregnancies resulting in live infants born at term without malformations during 1989-2010. Trends in BW, ponderal index and proportion of large newborns were related to individual prenatal exposures, including pre-pregnancy body mass index (PP-BMI) and gestational weight gain (GWG) for the years 2001-2010, and thereafter related ecologically to national population data on consumption of nutrients and physical activity.

RESULTS: For the regional cohort mean (standard deviation) BW increased from 3580 (453) grams in 1989/90 to 3633 (493) grams in 2001/02 (p<0.001), and decreased to 3583 (481) grams in 2009/10 (p<0.001). The proportion with BW>4500 grams increased from 2.6% to 4.8% (p<0.001) and subsequently decreased to 3.3% (p=0.002). The trends remained after adjustment for relevant exposures. For the years 2001/02 to 2009/10 (n= 15240) mean (SD) PP-BMI increased from 24.36 (4.44) to 24.85 (5.02) kg/m2 (p<0.001) while GWG decreased from 14.79 (5.85) to 13.86 (5.79) kg (p<0.001). The estimated net effect of changes in PP-BMI, GWG and other known exposures was a 6 grams reduction in BW from 2001/02 to 2009/10, leaving 44 grams reduction unexplained. National consumption of major nutrients did not change, but consumption of sucrose, in large part as sugar-sweetened beverages (SSB) changed in parallel to the BW trends.

CONCLUSION: The temporary increase in BW and large babies in the regional cohort was identical to that reported for Norway. Individual level data on known pregnancy related predictors for BW could not explain these changes, but the parallel time trend in national consumption of sucrose, in particular as SSB, may lend support to a hypothesis that intake of sugar may have a direct effect on BW and infant body proportions independent of effects through PP-BMI and GWG.}, } @article {pmid23092397, year = {2012}, author = {Cheng, F and Li, W and Zhou, Y and Shen, J and Wu, Z and Liu, G and Lee, PW and Tang, Y}, title = {admetSAR: a comprehensive source and free tool for assessment of chemical ADMET properties.}, journal = {Journal of chemical information and modeling}, volume = {52}, number = {11}, pages = {3099-3105}, doi = {10.1021/ci300367a}, pmid = {23092397}, issn = {1549-960X}, mesh = {*Algorithms ; Animals ; Consumer Product Safety ; Databases, Chemical ; Food Additives/*chemistry/pharmacokinetics/toxicity ; Humans ; Internet ; Logistic Models ; Pesticides/*chemistry/pharmacokinetics/toxicity ; Prescription Drugs/*chemistry/pharmacokinetics/toxicity ; *Software ; Structure-Activity Relationship ; }, abstract = {Absorption, distribution, metabolism, excretion, and toxicity (ADMET) properties play key roles in the discovery/development of drugs, pesticides, food additives, consumer products, and industrial chemicals. This information is especially useful when to conduct environmental and human hazard assessment. The most critical rate limiting step in the chemical safety assessment workflow is the availability of high quality data. This paper describes an ADMET structure-activity relationship database, abbreviated as admetSAR. It is an open source, text and structure searchable, and continually updated database that collects, curates, and manages available ADMET-associated properties data from the published literature. In admetSAR, over 210,000 ADMET annotated data points for more than 96,000 unique compounds with 45 kinds of ADMET-associated properties, proteins, species, or organisms have been carefully curated from a large number of diverse literatures. The database provides a user-friendly interface to query a specific chemical profile, using either CAS registry number, common name, or structure similarity. In addition, the database includes 22 qualitative classification and 5 quantitative regression models with highly predictive accuracy, allowing to estimate ecological/mammalian ADMET properties for novel chemicals. AdmetSAR is accessible free of charge at http://www.admetexp.org.}, } @article {pmid23084936, year = {2012}, author = {Osbourn, A and Papadopoulou, KK and Qi, X and Field, B and Wegel, E}, title = {Finding and analyzing plant metabolic gene clusters.}, journal = {Methods in enzymology}, volume = {517}, number = {}, pages = {113-138}, doi = {10.1016/B978-0-12-404634-4.00006-1}, pmid = {23084936}, issn = {1557-7988}, support = {BBS/E/J/00000614/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/C504435/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Avena/genetics ; Cloning, Molecular/methods ; Computational Biology ; Gene Knockout Techniques ; *Genes, Plant ; Genetic Linkage ; Genetic Loci ; Genetic Vectors/genetics/metabolism ; Intramolecular Transferases/genetics/metabolism ; Metabolome/*genetics ; Metabolomics/methods ; *Multigene Family ; Mutation ; Phenotype ; Plant Proteins/genetics/metabolism ; Reverse Genetics/methods ; Saponins/*analysis/genetics/metabolism ; Terpenes/analysis/*metabolism ; Yeasts/genetics/metabolism ; }, abstract = {Plants produce an array of diverse secondary metabolites with important ecological functions, providing protection against pests, diseases, and abiotic stresses. Secondary metabolites are also a rich source of bioactive compounds for drug and agrochemical development. Despite the importance of these compounds, the metabolic diversity of plants remains largely unexploited, primarily due to the problems associated with mining large and complex genomes. It has recently emerged that genes for the synthesis of multiple major classes of plant-derived secondary metabolites (benzoxinones, diterpenes, triterpenes, and cyanogenic glycosides) are organized in clusters reminiscent of the metabolic gene clusters found in microbes. Many more secondary metabolic clusters are likely to emerge as the body of sequence information available for plants continues to grow, accelerated by high-throughput sequencing. Here, we describe approaches for the identification of secondary metabolic gene clusters in plants through forward and reverse genetics, map-based cloning, and genome mining and give examples of methods used for the analysis and functional confirmation of new clusters.}, } @article {pmid23083429, year = {2012}, author = {Nagata, T and Takamori, A and Berg, HY and Hasselberg, M}, title = {Comparing the impact of socio-demographic factors associated with traffic injury among older road users and the general population in Japan.}, journal = {BMC public health}, volume = {12}, number = {}, pages = {887}, pmid = {23083429}, issn = {1471-2458}, mesh = {Accidents, Traffic/mortality/*statistics & numerical data ; Aged ; Alcohol Drinking/*epidemiology ; Databases, Factual ; Environment Design/*statistics & numerical data ; Humans ; Japan/epidemiology ; Risk Factors ; Socioeconomic Factors ; Wounds and Injuries/*epidemiology ; }, abstract = {BACKGROUND: The increasing number of older road users represents a public health issue because older individuals are more susceptible to traffic injury and mortality than the general population. This study investigated the association between socio-demographic factors and traffic injury and traffic mortality for the general population and among older road users in Japan.

METHODS: An ecological study was conducted using national data in Japan. Multivariate regression methods were applied to investigate the association of traffic injury and traffic mortality for the general population and among older road users with significant demographic, economic, road traffic, and medical/cultural factors.

RESULTS: Income per capita, total road length, and alcohol consumption per person were significantly associated with traffic injury and traffic mortality both for the general population and among older road users in Japan. Income per capita and alcohol consumption per person were negatively associated with traffic mortality for both groups. Meanwhile, for both groups, income per capita was positively associated with traffic injury, while total road length and alcohol consumption per person were negatively associated with traffic injury.

CONCLUSIONS: The effects of socio-demographic factors on traffic injury and traffic mortality in Japan were similar for both the general population and older road users. The study results suggest that injury preventive measures designed for the general population will be beneficial also for older road users in Japan.}, } @article {pmid23080249, year = {2012}, author = {Carlson, RP and Oshota, OJ and Taffs, RL}, title = {Systems analysis of microbial adaptations to simultaneous stresses.}, journal = {Sub-cellular biochemistry}, volume = {64}, number = {}, pages = {139-157}, doi = {10.1007/978-94-007-5055-5_7}, pmid = {23080249}, issn = {0306-0225}, mesh = {*Adaptation, Physiological/genetics ; Computational Biology/methods ; Ecosystem ; *Metabolic Networks and Pathways/genetics ; *Microbiological Phenomena/genetics ; Phenotype ; *Stress, Physiological/genetics ; Systems Analysis ; Systems Biology/methods ; }, abstract = {Microbes live in multi-factorial environments and have evolved under a variety of concurrent stresses including resource scarcity. Their metabolic organization is a reflection of their evolutionary histories and, in spite of decades of research, there is still a need for improved theoretical tools to explain fundamental aspects of microbial physiology. Using ecological and economic concepts, this chapter explores a resource-ratio based theory to elucidate microbial strategies for extracting and channeling mass and energy. The theory assumes cellular fitness is maximized by allocating scarce resources in appropriate proportions to multiple stress responses. Presented case studies deconstruct metabolic networks into a complete set of minimal biochemical pathways known as elementary flux modes. An economic analysis of the elementary flux modes tabulates enzyme atomic synthesis requirements from amino acid sequences and pathway operating costs from catabolic efficiencies, permitting characterization of inherent tradeoffs between resource investment and phenotype. A set of elementary flux modes with competitive tradeoffs properties can be mathematically projected onto experimental fluxomics datasets to decompose measured phenotypes into metabolic adaptations, interpreted as cellular responses proportional to the experienced culturing stresses. The resource-ratio based method describes the experimental phenotypes with greater accuracy than other contemporary approaches and further analysis suggests the results are both statistically and biologically significant. The insight into metabolic network design principles including tradeoffs associated with concurrent stress adaptation provides a foundation for interpreting physiology as well as for rational control and engineering of medically, environmentally, and industrially relevant microbes.}, } @article {pmid23078351, year = {2013}, author = {Ager, AA and Buonopane, M and Reger, A and Finney, MA}, title = {Wildfire exposure analysis on the national forests in the Pacific Northwest, USA.}, journal = {Risk analysis : an official publication of the Society for Risk Analysis}, volume = {33}, number = {6}, pages = {1000-1020}, doi = {10.1111/j.1539-6924.2012.01911.x}, pmid = {23078351}, issn = {1539-6924}, mesh = {Animals ; *Animals, Wild ; *Fires ; Geographic Information Systems ; Northwestern United States ; Risk Assessment ; *Trees ; }, abstract = {We analyzed wildfire exposure for key social and ecological features on the national forests in Oregon and Washington. The forests contain numerous urban interfaces, old growth forests, recreational sites, and habitat for rare and endangered species. Many of these resources are threatened by wildfire, especially in the east Cascade Mountains fire-prone forests. The study illustrates the application of wildfire simulation for risk assessment where the major threat is from large and rare naturally ignited fires, versus many previous studies that have focused on risk driven by frequent and small fires from anthropogenic ignitions. Wildfire simulation modeling was used to characterize potential wildfire behavior in terms of annual burn probability and flame length. Spatial data on selected social and ecological features were obtained from Forest Service GIS databases and elsewhere. The potential wildfire behavior was then summarized for each spatial location of each resource. The analysis suggested strong spatial variation in both burn probability and conditional flame length for many of the features examined, including biodiversity, urban interfaces, and infrastructure. We propose that the spatial patterns in modeled wildfire behavior could be used to improve existing prioritization of fuel management and wildfire preparedness activities within the Pacific Northwest region.}, } @article {pmid23077284, year = {2012}, author = {Brien, S and Kwong, JC and Charland, KM and Verma, AD and Brownstein, JS and Buckeridge, DL}, title = {Neighborhood determinants of 2009 pandemic A/H1N1 influenza vaccination in Montreal, Quebec, Canada.}, journal = {American journal of epidemiology}, volume = {176}, number = {10}, pages = {897-908}, pmid = {23077284}, issn = {1476-6256}, support = {R01 LM010812/LM/NLM NIH HHS/United States ; }, mesh = {Adolescent ; Adult ; Age Factors ; Aged ; Bayes Theorem ; Child ; Child, Preschool ; Female ; Humans ; Infant ; Infant, Newborn ; *Influenza A Virus, H1N1 Subtype ; Influenza Vaccines/*therapeutic use ; Influenza, Human/epidemiology/*prevention & control ; Logistic Models ; Male ; Middle Aged ; Pandemics/*prevention & control/statistics & numerical data ; Pregnancy ; Quebec/epidemiology ; Registries ; Residence Characteristics/*statistics & numerical data ; Risk Factors ; Sex Factors ; Socioeconomic Factors ; Vaccination/statistics & numerical data ; Young Adult ; }, abstract = {Neighborhood-level analyses of influenza vaccination can identify the characteristics of vulnerable neighborhoods, which can inform public health strategy for future pandemics. In this study, the authors analyzed rates of 2009 pandemic A/H1N1 influenza vaccination in Montreal, Quebec, Canada, using individual-level vaccination records from a vaccination registry with census, survey, and administrative data to estimate the population at risk. The neighborhood socioeconomic and demographic determinants of vaccination were identified using Bayesian ecologic logistic regression, with random effects to account for spatial autocorrelation. A total of 918,773 (49.9%) Montreal residents were vaccinated against pandemic A/H1N1 influenza from October 22, 2009, through April 8, 2010. Coverage was greatest among females, children under age 5 years, and health-care workers. Neighborhood vaccine coverage ranged from 33.6% to 71.0%. Neighborhoods with high percentages of immigrants (per 5% increase, odds ratio = 0.90, 95% credible interval: 0.86, 0.95) and material deprivation (per 1-unit increase in deprivation score, odds ratio = 0.93, 95% credible interval: 0.88, 0.98) had lower vaccine coverage. Half of the Montreal population was vaccinated; however, considerable heterogeneity in coverage was observed between neighborhoods and subgroups. In future vaccination campaigns, neighborhoods that are materially deprived or have high percentages of immigrants may benefit from focused interventions.}, } @article {pmid23071656, year = {2012}, author = {Chuang, TW and Wimberly, MC}, title = {Remote sensing of climatic anomalies and West Nile virus incidence in the northern Great Plains of the United States.}, journal = {PloS one}, volume = {7}, number = {10}, pages = {e46882}, pmid = {23071656}, issn = {1932-6203}, support = {R01 AI079411/AI/NIAID NIH HHS/United States ; R01-AI079411/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; *Climate ; Culicidae/virology ; Environmental Monitoring/methods ; Forecasting ; Geographic Information Systems/statistics & numerical data/trends ; Geography ; Humans ; Incidence ; Insect Vectors/virology ; Models, Biological ; Rain ; Remote Sensing Technology/*methods ; Reproducibility of Results ; Rural Population/statistics & numerical data ; Seasons ; Temperature ; United States/epidemiology ; West Nile Fever/*epidemiology ; West Nile virus/*isolation & purification ; }, abstract = {The northern Great Plains (NGP) of the United States has been a hotspot of West Nile virus (WNV) incidence since 2002. Mosquito ecology and the transmission of vector-borne disease are influenced by multiple environmental factors, and climatic variability is an important driver of inter-annual variation in WNV transmission risk. This study applied multiple environmental predictors including land surface temperature (LST), the normalized difference vegetation index (NDVI) and actual evapotranspiration (ETa) derived from Moderate-Resolution Imaging Spectroradiometer (MODIS) products to establish prediction models for WNV risk in the NGP. These environmental metrics are sensitive to seasonal and inter-annual fluctuations in temperature and precipitation, and are hypothesized to influence mosquito population dynamics and WNV transmission. Non-linear generalized additive models (GAMs) were used to evaluate the influences of deviations of cumulative LST, NDVI, and ETa on inter-annual variations of WNV incidence from 2004-2010. The models were sensitive to the timing of spring green up (measured with NDVI), temperature variability in early spring and summer (measured with LST), and moisture availability from late spring through early summer (measured with ETa), highlighting seasonal changes in the influences of climatic fluctuations on WNV transmission. Predictions based on these variables indicated a low WNV risk across the NGP in 2011, which is concordant with the low case reports in this year. Environmental monitoring using remote-sensed data can contribute to surveillance of WNV risk and prediction of future WNV outbreaks in space and time.}, } @article {pmid23057437, year = {2013}, author = {Santini, A and Ghelardini, L and De Pace, C and Desprez-Loustau, ML and Capretti, P and Chandelier, A and Cech, T and Chira, D and Diamandis, S and Gaitniekis, T and Hantula, J and Holdenrieder, O and Jankovsky, L and Jung, T and Jurc, D and Kirisits, T and Kunca, A and Lygis, V and Malecka, M and Marcais, B and Schmitz, S and Schumacher, J and Solheim, H and Solla, A and Szabò, I and Tsopelas, P and Vannini, A and Vettraino, AM and Webber, J and Woodward, S and Stenlid, J}, title = {Biogeographical patterns and determinants of invasion by forest pathogens in Europe.}, journal = {The New phytologist}, volume = {197}, number = {1}, pages = {238-250}, doi = {10.1111/j.1469-8137.2012.04364.x}, pmid = {23057437}, issn = {1469-8137}, mesh = {Climate ; *Databases, Factual ; Ecosystem ; Europe ; Fungi/classification/*pathogenicity/physiology ; Geography ; *Introduced Species ; Linear Models ; Plant Diseases/microbiology ; Population Density ; Principal Component Analysis ; Rain ; Socioeconomic Factors ; Temperature ; Time Factors ; Trees/*microbiology/physiology ; }, abstract = {A large database of invasive forest pathogens (IFPs) was developed to investigate the patterns and determinants of invasion in Europe. Detailed taxonomic and biological information on the invasive species was combined with country-specific data on land use, climate, and the time since invasion to identify the determinants of invasiveness, and to differentiate the class of environments which share territorial and climate features associated with a susceptibility to invasion. IFPs increased exponentially in the last four decades. Until 1919, IFPs already present moved across Europe. Then, new IFPs were introduced mainly from North America, and recently from Asia. Hybrid pathogens also appeared. Countries with a wider range of environments, higher human impact or international trade hosted more IFPs. Rainfall influenced the diffusion rates. Environmental conditions of the new and original ranges and systematic and ecological attributes affected invasiveness. Further spread of established IFPs is expected in countries that have experienced commercial isolation in the recent past. Densely populated countries with high environmental diversity may be the weakest links in attempts to prevent new arrivals. Tight coordination of actions against new arrivals is needed. Eradication seems impossible, and prevention seems the only reliable measure, although this will be difficult in the face of global mobility.}, } @article {pmid23055916, year = {2012}, author = {Rigoux, L and Guigon, E}, title = {A model of reward- and effort-based optimal decision making and motor control.}, journal = {PLoS computational biology}, volume = {8}, number = {10}, pages = {e1002716}, pmid = {23055916}, issn = {1553-7358}, mesh = {Algorithms ; Animals ; Computational Biology/*methods ; Computer Simulation ; Decision Making/*physiology ; Humans ; *Models, Neurological ; Motor Activity/*physiology ; Motor Cortex/physiology ; Rats ; *Reward ; }, abstract = {Costs (e.g. energetic expenditure) and benefits (e.g. food) are central determinants of behavior. In ecology and economics, they are combined to form a utility function which is maximized to guide choices. This principle is widely used in neuroscience as a normative model of decision and action, but current versions of this model fail to consider how decisions are actually converted into actions (i.e. the formation of trajectories). Here, we describe an approach where decision making and motor control are optimal, iterative processes derived from the maximization of the discounted, weighted difference between expected rewards and foreseeable motor efforts. The model accounts for decision making in cost/benefit situations, and detailed characteristics of control and goal tracking in realistic motor tasks. As a normative construction, the model is relevant to address the neural bases and pathological aspects of decision making and motor control.}, } @article {pmid23055062, year = {2012}, author = {Baiser, B and Olden, JD and Record, S and Lockwood, JL and McKinney, ML}, title = {Pattern and process of biotic homogenization in the New Pangaea.}, journal = {Proceedings. Biological sciences}, volume = {279}, number = {1748}, pages = {4772-4777}, pmid = {23055062}, issn = {1471-2954}, mesh = {Analysis of Variance ; Animals ; Biodiversity ; *Biota ; Databases, Factual ; Extinction, Biological ; *Introduced Species ; *Models, Theoretical ; Phylogeography ; Plants ; }, abstract = {Human activities have reorganized the earth's biota resulting in spatially disparate locales becoming more or less similar in species composition over time through the processes of biotic homogenization and biotic differentiation, respectively. Despite mounting evidence suggesting that this process may be widespread in both aquatic and terrestrial systems, past studies have predominantly focused on single taxonomic groups at a single spatial scale. Furthermore, change in pairwise similarity is itself dependent on two distinct processes, spatial turnover in species composition and changes in gradients of species richness. Most past research has failed to disentangle the effect of these two mechanisms on homogenization patterns. Here, we use recent statistical advances and collate a global database of homogenization studies (20 studies, 50 datasets) to provide the first global investigation of the homogenization process across major faunal and floral groups and elucidate the relative role of changes in species richness and turnover. We found evidence of homogenization (change in similarity ranging from -0.02 to 0.09) across nearly all taxonomic groups, spatial extent and grain sizes. Partitioning of change in pairwise similarity shows that overall change in community similarity is driven by changes in species richness. Our results show that biotic homogenization is truly a global phenomenon and put into question many of the ecological mechanisms invoked in previous studies to explain patterns of homogenization.}, } @article {pmid23054170, year = {2013}, author = {Zeldin, S and Christens, BD and Powers, JL}, title = {The psychology and practice of youth-adult partnership: bridging generations for youth development and community change.}, journal = {American journal of community psychology}, volume = {51}, number = {3-4}, pages = {385-397}, doi = {10.1007/s10464-012-9558-y}, pmid = {23054170}, issn = {1573-2770}, mesh = {Adolescent ; Adult ; *Community Networks ; Community-Based Participatory Research ; Decision Making ; Humans ; *Intergenerational Relations ; *Mentors ; *Social Justice ; United States ; }, abstract = {Youth-adult partnership (Y-AP) has become a phenomenon of interest to scholars and practitioners. Despite the potential of Y-AP to promote positive youth development, increase civic engagement, and support community change, the practice remains unfamiliar to many. Although research has increased over the past decade, the construct remains vague with an insufficient grounding in developmental theory and community practice. This article seeks to address these gaps by synthesizing data and insights from the historical foundations of Y-AP, community based research, and case study. We propose Y-AP as a unifying concept, distinct from other forms of youth-adult relationships, with four core elements: authentic decision making, natural mentors, reciprocity, and community connectedness. We conclude that Y-AP functions as an active ingredient and fundamental practice for positive youth development and civic engagement. Directions for future research are offered.}, } @article {pmid23052472, year = {2012}, author = {Duguy, B and Alloza, JA and Baeza, MJ and De la Riva, J and Echeverría, M and Ibarra, P and Llovet, J and Cabello, FP and Rovira, P and Vallejo, RV}, title = {Modelling the ecological vulnerability to forest fires in mediterranean ecosystems using geographic information technologies.}, journal = {Environmental management}, volume = {50}, number = {6}, pages = {1012-1026}, pmid = {23052472}, issn = {1432-1009}, mesh = {Ecology ; Environmental Monitoring/*methods ; *Fires ; Geographic Information Systems ; Mediterranean Region ; *Trees ; }, abstract = {Forest fires represent a major driver of change at the ecosystem and landscape levels in the Mediterranean region. Environmental features and vegetation are key factors to estimate the ecological vulnerability to fire; defined as the degree to which an ecosystem is susceptible to, and unable to cope with, adverse effects of fire (provided a fire occurs). Given the predicted climatic changes for the region, it is urgent to validate spatially explicit tools for assessing this vulnerability in order to support the design of new fire prevention and restoration strategies. This work presents an innovative GIS-based modelling approach to evaluate the ecological vulnerability to fire of an ecosystem, considering its main components (soil and vegetation) and different time scales. The evaluation was structured in three stages: short-term (focussed on soil degradation risk), medium-term (focussed on changes in vegetation), and coupling of the short- and medium-term vulnerabilities. The model was implemented in two regions: Aragón (inland North-eastern Spain) and Valencia (eastern Spain). Maps of the ecological vulnerability to fire were produced at a regional scale. We partially validated the model in a study site combining two complementary approaches that focused on testing the adequacy of model's predictions in three ecosystems, all very common in fire-prone landscapes of eastern Spain: two shrublands and a pine forest. Both approaches were based on the comparison of model's predictions with values of NDVI (Normalized Difference Vegetation Index), which is considered a good proxy for green biomass. Both methods showed that the model's performance is satisfactory when applied to the three selected vegetation types.}, } @article {pmid23051560, year = {2012}, author = {St-Hilaire, S and Ezike, VO and Stryhn, H and Thomas, MA}, title = {An ecological study on childhood autism.}, journal = {International journal of health geographics}, volume = {11}, number = {}, pages = {44}, pmid = {23051560}, issn = {1476-072X}, support = {P20 GM103408/GM/NIGMS NIH HHS/United States ; P20 RR0116454/RR/NCRR NIH HHS/United States ; }, mesh = {Adolescent ; Autistic Disorder/epidemiology/*etiology ; California/epidemiology ; Child ; Databases, Factual ; Environmental Exposure/*adverse effects ; Female ; Humans ; Male ; *Meteorological Concepts ; Oregon/epidemiology ; Washington/epidemiology ; }, abstract = {BACKGROUND AND METHODS: Idiopathic autism, suspected to be caused by exposure of genetically susceptible individuals to unknown environmental triggers, has increased dramatically in the past 25 years. The objectives of our study were to determine, using a linear regression model, whether the county prevalence of autism in the Pacific Northwest of the United States was associated with the source of drinking water for that county and whether this relationship was dependent on the level of environmental pollutants and meteorological factors in the county.

RESULTS: We found the previously reported relationship between precipitation and autism in a county was dependent on the amount of drinking water derived from surface sources in the county. We also found a positive association between the EPA's risk of neurological disease and autism, but this relationship was only present in warm areas.

CONCLUSIONS: Our study provides evidence for the hypothesis that environmental factors are associated with autism and that meteorological factors play a role in this relationship.}, } @article {pmid23049882, year = {2012}, author = {Topping, CJ and Dalkvist, T and Grimm, V}, title = {Post-hoc pattern-oriented testing and tuning of an existing large model: lessons from the field vole.}, journal = {PloS one}, volume = {7}, number = {9}, pages = {e45872}, pmid = {23049882}, issn = {1932-6203}, mesh = {Animals ; Arvicolinae/*physiology ; Computer Simulation ; Ecology ; *Ecosystem ; Environment ; Female ; Geographic Information Systems ; Geography ; Male ; Models, Biological ; Pattern Recognition, Automated ; Population Dynamics ; }, abstract = {Pattern-oriented modeling (POM) is a general strategy for modeling complex systems. In POM, multiple patterns observed at different scales and hierarchical levels are used to optimize model structure, to test and select sub-models of key processes, and for calibration. So far, POM has been used for developing new models and for models of low to moderate complexity. It remains unclear, though, whether the basic idea of POM to utilize multiple patterns, could also be used to test and possibly develop existing and established models of high complexity. Here, we use POM to test, calibrate, and further develop an existing agent-based model of the field vole (Microtus agrestis), which was developed and tested within the ALMaSS framework. This framework is complex because it includes a high-resolution representation of the landscape and its dynamics, of the individual's behavior, and of the interaction between landscape and individual behavior. Results of fitting to the range of patterns chosen were generally very good, but the procedure required to achieve this was long and complicated. To obtain good correspondence between model and the real world it was often necessary to model the real world environment closely. We therefore conclude that post-hoc POM is a useful and viable way to test a highly complex simulation model, but also warn against the dangers of over-fitting to real world patterns that lack details in their explanatory driving factors. To overcome some of these obstacles we suggest the adoption of open-science and open-source approaches to ecological simulation modeling.}, } @article {pmid23047052, year = {2013}, author = {Müller, DW and Codron, D and Meloro, C and Munn, A and Schwarm, A and Hummel, J and Clauss, M}, title = {Assessing the Jarman-Bell Principle: Scaling of intake, digestibility, retention time and gut fill with body mass in mammalian herbivores.}, journal = {Comparative biochemistry and physiology. Part A, Molecular & integrative physiology}, volume = {164}, number = {1}, pages = {129-140}, doi = {10.1016/j.cbpa.2012.09.018}, pmid = {23047052}, issn = {1531-4332}, mesh = {Adaptation, Physiological ; Animals ; *Body Weight ; Confidence Intervals ; Databases, Factual ; *Digestion ; Eating/*physiology ; Fermentation ; Gastrointestinal Tract/*physiology ; Herbivory/*physiology ; Least-Squares Analysis ; Mammals/*physiology ; Organ Size ; Phylogeny ; Species Specificity ; Time Factors ; }, abstract = {Differences in allometric scaling of physiological characters have the appeal to explain species diversification and niche differentiation along a body mass (BM) gradient - because they lead to different combinations of physiological properties, and thus may facilitate different adaptive strategies. An important argument in physiological ecology is built on the allometries of gut fill (assumed to scale to BM(1.0)) and energy requirements/intake (assumed to scale to BM(0.75)) in mammalian herbivores. From the difference in exponents, it has been postulated that the mean retention time (MRT) of digesta should scale to BM(1.0-0.75)=BM(0.25). This has been used to argue that larger animals have an advantage in digestive efficiency and hence can tolerate lower-quality diets. However, empirical data does not support the BM(0.25) scaling of MRT, and the deduction of MRT scaling implies, according to physical principles, no scaling of digestibility; basing assumptions on digestive efficiency on the thus-derived MRT scaling amounts to circular reasoning. An alternative explanation considers a higher scaling exponent for food intake than for metabolism, allowing larger animals to eat more of a lower quality food without having to increase digestive efficiency; to date, this concept has only been explored in ruminants. Here, using data for 77 species in which intake, digestibility and MRT were measured (allowing the calculation of the dry matter gut contents (DMC)), we show that the unexpected shallow scaling of MRT is common in herbivores and may result from deviations of other scaling exponents from expectations. Notably, DMC have a lower scaling exponent than 1.0, and the 95% confidence intervals of the scaling exponents for intake and DMC generally overlap. Differences in the scaling of wet gut contents and dry matter gut contents confirm a previous finding that the dry matter concentration of gut contents decreases with body mass, possibly compensating for the less favorable volume-surface ratio in the guts of larger organisms. These findings suggest that traditional explanations for herbivore niche differentiation along a BM gradient should not be based on allometries of digestive physiology. In contrast, they support the recent interpretation that larger species can tolerate lower-quality diets because their intake has a higher allometric scaling than their basal metabolism, allowing them to eat relatively more of a lower quality food without having to increase digestive efficiency.}, } @article {pmid23044401, year = {2013}, author = {Tao, W and Mayden, RL and He, S}, title = {Remarkable phylogenetic resolution of the most complex clade of Cyprinidae (Teleostei: Cypriniformes): a proof of concept of homology assessment and partitioning sequence data integrated with mixed model Bayesian analyses.}, journal = {Molecular phylogenetics and evolution}, volume = {66}, number = {3}, pages = {603-616}, doi = {10.1016/j.ympev.2012.09.024}, pmid = {23044401}, issn = {1095-9513}, mesh = {Animals ; Base Sequence ; Bayes Theorem ; Classification/methods ; Cyprinidae/*classification/*genetics ; Data Interpretation, Statistical ; Likelihood Functions ; *Models, Genetic ; Molecular Sequence Data ; *Phylogeny ; Sequence Analysis, DNA ; }, abstract = {Despite many efforts to resolve evolutionary relationships among major clades of Cyprinidae, some nodes have been especially problematic and remain unresolved. In this study, we employ four nuclear gene fragments (3.3kb) to infer interrelationships of the Cyprinidae. A reconstruction of the phylogenetic relationships within the family using maximum parsimony, maximum likelihood, and Bayesian analyses is presented. Among the taxa within the monophyletic Cyprinidae, Rasborinae is the basal-most lineage; Cyprinine is sister to Leuciscine. The monophyly for the subfamilies Gobioninae, Leuciscinae and Acheilognathinae were resolved with high nodal support. Although our results do not completely resolve relationships within Cyprinidae, this study presents novel and significant findings having major implications for a highly diverse and enigmatic clade of East-Asian cyprinids. Within this monophyletic group five closely-related subgroups are identified. Tinca tinca, one of the most phylogenetically enigmatic genera in the family, is strongly supported as having evolutionary affinities with this East-Asian clade; an established yet remarkable association because of the natural variation in phenotypes and generalized ecological niches occupied by these taxa. Our results clearly argue that the choice of partitioning strategies has significant impacts on the phylogenetic reconstructions, especially when multiple genes are being considered. The most highly partitioned model (partitioned by codon positions within genes) extracts the strongest phylogenetic signals and performs better than any other partitioning schemes supported by the strongest 2Δln Bayes factor. Future studies should include higher levels of taxon sampling and partitioned, model-based analyses.}, } @article {pmid23039950, year = {2013}, author = {Kane, NC and Burke, JM and Marek, L and Seiler, G and Vear, F and Baute, G and Knapp, SJ and Vincourt, P and Rieseberg, LH}, title = {Sunflower genetic, genomic and ecological resources.}, journal = {Molecular ecology resources}, volume = {13}, number = {1}, pages = {10-20}, doi = {10.1111/1755-0998.12023}, pmid = {23039950}, issn = {1755-0998}, mesh = {*Biological Evolution ; *Databases, Genetic ; Ecology/*methods ; Genetic Markers/genetics ; Genome, Plant/*genetics ; Helianthus/*genetics ; Physical Chromosome Mapping ; *Seeds ; *Specimen Handling ; }, abstract = {Long a major focus of genetic research and breeding, sunflowers (Helianthus) are emerging as an increasingly important experimental system for ecological and evolutionary studies. Here, we review the various attributes of wild and domesticated sunflowers that make them valuable for ecological experimentation and describe the numerous publicly available resources that have enabled rapid advances in ecological and evolutionary genetics. Resources include seed collections available from germplasm centres at the USDA and INRA, genomic and EST sequences, mapping populations, genetic markers, genetic and physical maps and other forward- and reverse-genetic tools. We also discuss some of the key evolutionary, genetic and ecological questions being addressed in sunflowers, as well as gaps in our knowledge and promising areas for future research.}, } @article {pmid23038160, year = {2012}, author = {Chatterjee, HJ and Tse, JS and Turvey, ST}, title = {Using ecological niche modelling to predict spatial and temporal distribution patterns in Chinese gibbons: lessons from the present and the past.}, journal = {Folia primatologica; international journal of primatology}, volume = {83}, number = {2}, pages = {85-99}, doi = {10.1159/000342696}, pmid = {23038160}, issn = {1421-9980}, mesh = {Animals ; China ; Climate ; *Climate Change ; Computer Simulation ; Databases, Factual ; Demography/*history ; *Ecosystem ; *Fossils ; Geographic Information Systems ; Geography ; History, Ancient ; Hylobates/*physiology ; *Models, Theoretical ; Time Factors ; }, abstract = {Ecological niche modelling (ENM) is used to predict species' tolerance to changing environmental conditions. Understanding changes in the spatial distribution of species across time is essential in order to develop effective conservation strategies. Here we map the past and present distribution of gibbons across China, a country experiencing extensive anthropogenic habitat destruction and ongoing biodiversity loss. The distribution of gibbons across three time intervals is described based on fossil, historical and modern-day data, and ENM, implemented using DIVA-GIS, is used to predict how modern-day gibbon distributions might respond to future climate change. Predictions based on modern-day data alone fail to reveal patterns of environmental tolerance and geographical distribution shown by gibbons in the relatively recent historical period, emphasizing the need to incorporate past as well as present data in conservation analyses.}, } @article {pmid23033934, year = {2012}, author = {Moktali, V and Park, J and Fedorova-Abrams, ND and Park, B and Choi, J and Lee, YH and Kang, S}, title = {Systematic and searchable classification of cytochrome P450 proteins encoded by fungal and oomycete genomes.}, journal = {BMC genomics}, volume = {13}, number = {}, pages = {525}, pmid = {23033934}, issn = {1471-2164}, mesh = {Cluster Analysis ; Cytochrome P-450 Enzyme System/classification/*genetics ; Databases, Protein ; Evolution, Molecular ; Fungi/*genetics/metabolism ; *Genome ; Genome, Fungal ; Models, Genetic ; Oomycetes/*genetics/metabolism ; Phylogeny ; }, abstract = {BACKGROUND: Cytochrome P450 proteins (CYPs) play diverse and pivotal roles in fungal metabolism and adaptation to specific ecological niches. Fungal genomes encode extremely variable "CYPomes" ranging from one to more than 300 CYPs. Despite the rapid growth of sequenced fungal and oomycete genomes and the resulting influx of predicted CYPs, the vast majority of CYPs remain functionally uncharacterized. To facilitate the curation and functional and evolutionary studies of CYPs, we previously developed Fungal Cytochrome P450 Database (FCPD), which included CYPs from 70 fungal and oomycete species. Here we present a new version of FCPD (1.2) with more data and an improved classification scheme.

RESULTS: The new database contains 22,940 CYPs from 213 species divided into 2,579 clusters and 115 clans. By optimizing the clustering pipeline, we were able to uncover 36 novel clans and to assign 153 orphan CYP families to specific clans. To augment their functional annotation, CYP clusters were mapped to David Nelson's P450 databases, which archive a total of 12,500 manually curated CYPs. Additionally, over 150 clusters were functionally classified based on sequence similarity to experimentally characterized CYPs. Comparative analysis of fungal and oomycete CYPomes revealed cases of both extreme expansion and contraction. The most dramatic expansions in fungi were observed in clans CYP58 and CYP68 (Pezizomycotina), clans CYP5150 and CYP63 (Agaricomycotina), and family CYP509 (Mucoromycotina). Although much of the extraordinary diversity of the pan-fungal CYPome can be attributed to gene duplication and adaptive divergence, our analysis also suggests a few potential horizontal gene transfer events. Updated families and clans can be accessed through the new version of the FCPD database.

CONCLUSIONS: FCPD version 1.2 provides a systematic and searchable catalogue of 9,550 fungal CYP sequences (292 families) encoded by 108 fungal species and 147 CYP sequences (9 families) encoded by five oomycete species. In comparison to the first version, it offers a more comprehensive clan classification, is fully compatible with Nelson's P450 databases, and has expanded functional categorization. These features will facilitate functional annotation and classification of CYPs encoded by newly sequenced fungal and oomycete genomes. Additionally, the classification system will aid in studying the roles of CYPs in the evolution of fungal adaptation to specific ecological niches.}, } @article {pmid23032286, year = {2012}, author = {Valencia-López, N and Malone, JB and Carmona, CG and Velásquez, LE}, title = {Climate-based risk models for Fasciola hepatica in Colombia.}, journal = {Geospatial health}, volume = {6}, number = {3}, pages = {S67-85}, doi = {10.4081/gh.2012.125}, pmid = {23032286}, issn = {1970-7096}, mesh = {Animals ; Cattle ; *Climate ; Colombia/epidemiology ; Disease Vectors ; Entropy ; *Fasciola hepatica ; Fascioliasis/*epidemiology ; *Geographic Information Systems ; *Geographic Mapping ; Humans ; Models, Theoretical ; Public Health ; Risk Assessment ; Time Factors ; }, abstract = {A predictive Fasciola hepatica model, based on the growing degree day-water budget (GDD-WB) concept and the known biological requirements of the parasite, was developed within a geographical information system (GIS) in Colombia. Climate-based forecast index (CFI) values were calculated and represented in a national-scale, climate grid (18 x 18 km) using ArcGIS 9.3. A mask overlay was used to exclude unsuitable areas where mean annual temperature exceeded 25 °C, the upper threshold for development and propagation of the F. hepatica life cycle. The model was then validated and further developed by studies limited to one department in northwest Colombia. F. hepatica prevalence data was obtained from a 2008-2010 survey in 10 municipalities of 6,016 dairy cattle at 673 herd study sites, for which global positioning system coordinates were recorded. The CFI map results were compared to F. hepatica environmental risk models for the survey data points that had over 5% prevalence (231 of the 673 sites) at the 1 km2 scale using two independent approaches: (i) a GIS map query based on satellite data parameters including elevation, enhanced vegetation index and land surface temperature day-night difference; and (ii) an ecological niche model (MaxEnt), for which geographic point coordinates of F. hepatica survey farms were used with BioClim data as environmental variables to develop a probability map. The predicted risk pattern of both approaches was similar to that seen in the forecast index grid. The temporal risk, evaluated by the monthly CFIs and a daily GDD-WB forecast software for 2007 and 2008, revealed a major July-August to January transmission period with considerable inter-annual differences.}, } @article {pmid23032284, year = {2012}, author = {Mischler, P and Kearney, M and McCarroll, JC and Scholte, RG and Vounatsou, P and Malone, JB}, title = {Environmental and socio-economic risk modelling for Chagas disease in Bolivia.}, journal = {Geospatial health}, volume = {6}, number = {3}, pages = {S59-66}, doi = {10.4081/gh.2012.123}, pmid = {23032284}, issn = {1970-7096}, mesh = {Bolivia/epidemiology ; Chagas Disease/*epidemiology ; Ecosystem ; Entropy ; *Environment ; *Geographic Information Systems ; Geography ; Health Surveys ; Humans ; Neglected Diseases/*epidemiology ; Public Health ; ROC Curve ; Remote Sensing Technology ; Risk Assessment ; Socioeconomic Factors ; Software ; }, abstract = {Accurately defining disease distributions and calculating disease risk is an important step in the control and prevention of diseases. Geographical information systems (GIS) and remote sensing technologies, with maximum entropy (Maxent) ecological niche modelling computer software, were used to create predictive risk maps for Chagas disease in Bolivia. Prevalence rates were calculated from 2007 to 2009 household infection survey data for Bolivia, while environmental data were compiled from the Worldclim database and MODIS satellite imagery. Socio-economic data were obtained from the Bolivian National Institute of Statistics. Disease models identified altitudes at 500-3,500 m above the mean sea level (MSL), low annual precipitation (45-250 mm), and higher diurnal range of temperature (10-19 °C; peak 16 °C) as compatible with the biological requirements of the insect vectors. Socio-economic analyses demonstrated the importance of improved housing materials and water source. Home adobe wall materials and having to fetch drinking water from rivers or wells without pump were found to be highly related to distribution of the disease by the receiver operator characteristic (ROC) area under the curve (AUC) (0.69 AUC, 0.67 AUC and 0.62 AUC, respectively), while areas with hardwood floors demonstrated a direct negative relationship (-0.71 AUC). This study demonstrates that Maxent modelling can be used in disease prevalence and incidence studies to provide governmental agencies with an easily learned, understandable method to define areas as either high, moderate or low risk for the disease. This information may be used in resource planning, targeting and implementation. However, access to high-resolution, sub-municipality socio-economic data (e.g. census tracts) would facilitate elucidation of the relative influence of poverty-related factors on regional disease dynamics.}, } @article {pmid23032283, year = {2012}, author = {Delgado-Petrocelli, L and Córdova, K and Camardiel, A and Aguilar, VH and Hernández, D and Ramos, S}, title = {Analysis of the El Niño/La Niña-Southern Oscillation variability and malaria in the Estado Sucre, Venezuela.}, journal = {Geospatial health}, volume = {6}, number = {3}, pages = {S51-7}, doi = {10.4081/gh.2012.122}, pmid = {23032283}, issn = {1970-7096}, mesh = {Analysis of Variance ; *El Nino-Southern Oscillation ; Epidemiologic Methods ; *Geographic Information Systems ; *Geographic Mapping ; Humans ; Malaria, Falciparum/*epidemiology ; Population Surveillance ; Prevalence ; Public Health/*methods ; Risk Assessment/methods ; Venezuela/epidemiology ; }, abstract = {The last decade has seen an unprecedented, worldwide acceleration of environmental and climate changes. These processes impact the dynamics of natural systems, which include components associated with human communities such as vector-borne diseases. The dynamics of environmental and climate variables, altered by global change as reported by the Intergovernmental Panel on Climate Change, affect the distribution of many tropical diseases. Complex systems, e.g. the El Niño/La Niña-Southern Oscillation (ENSO), in which environmental variables operate synergistically, can provoke the reemergence and emergence of vector-borne diseases at new sites. This research investigated the influence of ENSO events on malaria incidence by determining the relationship between climate variations, expressed as warm, cold and neutral phases, and their relation to the number of malaria cases in some north-eastern municipalities of Venezuela (Estado Sucre) during the period 1990-2000. Significant differences in malaria incidence were found, particularly in the La Niña ENSO phases (cold) of moderate intensity. These findings should be taken into account for surveillance and control in the future as they shed light on important indicators that can lead to reduced vulnerability to malaria.}, } @article {pmid23032277, year = {2012}, author = {Mudenda, NB and Malone, JB and Kearney, MT and Mischler, PD and Nieto, Pdel M and McCarroll, JC and Vounatsou, P}, title = {Modelling the ecological niche of hookworm in Brazil based on climate.}, journal = {Geospatial health}, volume = {6}, number = {3}, pages = {S111-23}, doi = {10.4081/gh.2012.129}, pmid = {23032277}, issn = {1970-7096}, mesh = {*Ancylostomatoidea ; Animals ; Brazil/epidemiology ; *Climate ; Disease Models, Animal ; *Geographic Information Systems ; Geographic Mapping ; Humans ; Models, Theoretical ; *Necator americanus ; Necatoriasis/*epidemiology/transmission ; Population Surveillance ; Prevalence ; Risk Assessment/methods ; }, abstract = {The distribution of hookworm in schistosomiasis-endemic areas in Brazil was mapped based on climate suitability. Known biological requirements of hookworm were fitted to data in a monthly long-term normal climate grid (18 x 18 km) using geographical information systems. Hookworm risk models were produced using the growing degree day (GDD) water budget (WB) concept. A moisture-adjusted model (MA-GDD) was developed based on accumulation of monthly temperatures above a base temperature of 15 °C (below which there is no lifecycle progression of Necator americanus) conditional on concurrent monthly values (rain/potential, evapotranspiration) of over 0.4. A second model, designated the gradient index, was calculated based on the monthly accumulation of the product of GDD and monthly WB values (GDD x WB). Both parameters had a significant positive correlation to hookworm prevalence. In the northeastern part of Brazil (the Caatinga), low hookworm prevalence was due to low soil moisture content, while the low prevalence in southern Brazil was related to low mean monthly temperatures. Both environmental temperature and soil moisture content were found to be important parameters for predicting the prevalence of N. americanus.}, } @article {pmid23030974, year = {2012}, author = {Chen, X and Szolnoki, A and Perc, M}, title = {Risk-driven migration and the collective-risk social dilemma.}, journal = {Physical review. E, Statistical, nonlinear, and soft matter physics}, volume = {86}, number = {3 Pt 2}, pages = {036101}, doi = {10.1103/PhysRevE.86.036101}, pmid = {23030974}, issn = {1550-2376}, mesh = {Computer Simulation ; *Decision Making ; *Decision Support Techniques ; *Game Theory ; Humans ; *Models, Theoretical ; *Risk Management ; *Social Behavior ; }, abstract = {A collective-risk social dilemma implies that personal endowments will be lost if contributions to the common pool within a group are too small. Failure to reach the collective target thus has dire consequences for all group members, independently of their strategies. Wanting to move away from unfavorable locations is therefore anything but surprising. Inspired by these observations, we here propose and study a collective-risk social dilemma where players are allowed to move if the collective failure becomes too probable. More precisely, this so-called risk-driven migration is launched depending on the difference between the actual contributions and the declared target. Mobility therefore becomes an inherent property that is utilized in an entirely self-organizing manner. We show that under these assumptions cooperation is promoted much more effectively than under the action of manually determined migration rates. For the latter, we in fact identify parameter regions where the evolution of cooperation is greatly inhibited. Moreover, we find unexpected spatial patterns where cooperators that do not form compact clusters outperform those that do, and where defectors are able to utilize strikingly different ways of invasion. The presented results support the recently revealed importance of percolation for the successful evolution of public cooperation, while at the same time revealing surprisingly simple methods of self-organization towards socially desirable states.}, } @article {pmid23030125, year = {2012}, author = {Barnett, L and Bossomaier, T}, title = {Transfer entropy as a log-likelihood ratio.}, journal = {Physical review letters}, volume = {109}, number = {13}, pages = {138105}, doi = {10.1103/PhysRevLett.109.138105}, pmid = {23030125}, issn = {1079-7114}, abstract = {Transfer entropy, an information-theoretic measure of time-directed information transfer between joint processes, has steadily gained popularity in the analysis of complex stochastic dynamics in diverse fields, including the neurosciences, ecology, climatology, and econometrics. We show that for a broad class of predictive models, the log-likelihood ratio test statistic for the null hypothesis of zero transfer entropy is a consistent estimator for the transfer entropy itself. For finite Markov chains, furthermore, no explicit model is required. In the general case, an asymptotic χ2 distribution is established for the transfer entropy estimator. The result generalizes the equivalence in the Gaussian case of transfer entropy and Granger causality, a statistical notion of causal influence based on prediction via vector autoregression, and establishes a fundamental connection between directed information transfer and causality in the Wiener-Granger sense.}, } @article {pmid23029053, year = {2012}, author = {Chan, WP and Yuan, HW and Huang, CY and Wang, CH and Lin, SD and Lo, YC and Huang, BW and Hatch, KA and Shiu, HJ and You, CF and Chang, YM and Shen, SF}, title = {Regional scale high resolution δ18O prediction in precipitation using MODIS EVI.}, journal = {PloS one}, volume = {7}, number = {9}, pages = {e45496}, pmid = {23029053}, issn = {1932-6203}, mesh = {*Climate ; Geographic Information Systems ; Hydrology ; Models, Theoretical ; Oxygen Isotopes/*chemistry ; Taiwan ; Water/*chemistry ; }, abstract = {The natural variation in stable water isotope ratio data, also known as water isoscape, is a spatiotemporal fingerprint and a powerful natural tracer that has been widely applied in disciplines as diverse as hydrology, paleoclimatology, ecology and forensic investigation. Although much effort has been devoted to developing a predictive water isoscape model, it remains a central challenge for scientists to generate high accuracy, fine scale spatiotemporal water isoscape prediction. Here we develop a novel approach of using the MODIS-EVI (the Moderate Resolution Imagining Spectroradiometer-Enhanced Vegetation Index), to predict δ(18)O in precipitation at the regional scale. Using a structural equation model, we show that the EVI and precipitated δ(18)O are highly correlated and thus the EVI is a good predictor of precipitated δ(18)O. We then test the predictability of our EVI-δ(18)O model and demonstrate that our approach can provide high accuracy with fine spatial (250×250 m) and temporal (16 days) scale δ(18)O predictions (annual and monthly predictabilities [r] are 0.96 and 0.80, respectively). We conclude the merging of the EVI and δ(18)O in precipitation can greatly extend the spatial and temporal data availability and thus enhance the applicability for both the EVI and water isoscape.}, } @article {pmid23028711, year = {2012}, author = {Fabina, NS and Putnam, HM and Franklin, EC and Stat, M and Gates, RD}, title = {Transmission mode predicts specificity and interaction patterns in coral-Symbiodinium networks.}, journal = {PloS one}, volume = {7}, number = {9}, pages = {e44970}, pmid = {23028711}, issn = {1932-6203}, mesh = {Animals ; Anthozoa/*physiology ; Databases, Factual ; Dinoflagellida/*physiology ; Species Specificity ; }, abstract = {Most reef-building corals in the order Scleractinia depend on endosymbiotic algae in the genus Symbiodinium for energy and survival. Significant levels of taxonomic diversity in both partners result in numerous possible combinations of coral-Symbiodinium associations with unique functional characteristics. We created and analyzed the first coral-Symbiodinium networks utilizing a global dataset of interaction records from coral reefs in the tropical Indo-Pacific and Atlantic Oceans for 1991 to 2010. Our meta-analysis reveals that the majority of coral species and Symbiodinium types are specialists, but failed to detect any one-to-one obligate relationships. Symbiont specificity is correlated with a host's transmission mode, with horizontally transmitting corals being more likely to interact with generalist symbionts. Globally, Symbiodinium types tend to interact with only vertically or horizontally transmitting corals, and only a few generalist types are found with both. Our results demonstrate a strong correlation between symbiont specificity, symbiont transmission mode, and community partitioning. The structure and dynamics of these network interactions underlie the fundamental biological partnership that determines the condition and resilience of coral reef ecosystems.}, } @article {pmid23025286, year = {2012}, author = {Favaro, S and Lijoi, A and Prünster, I}, title = {A new estimator of the discovery probability.}, journal = {Biometrics}, volume = {68}, number = {4}, pages = {1188-1196}, doi = {10.1111/j.1541-0420.2012.01793.x}, pmid = {23025286}, issn = {1541-0420}, mesh = {*Algorithms ; Chromosome Mapping/*methods ; Computer Simulation ; *Data Interpretation, Statistical ; *Expressed Sequence Tags ; *Models, Statistical ; Sequence Analysis, DNA/*methods ; }, abstract = {Species sampling problems have a long history in ecological and biological studies and a number of issues, including the evaluation of species richness, the design of sampling experiments, and the estimation of rare species variety, are to be addressed. Such inferential problems have recently emerged also in genomic applications, however, exhibiting some peculiar features that make them more challenging: specifically, one has to deal with very large populations (genomic libraries) containing a huge number of distinct species (genes) and only a small portion of the library has been sampled (sequenced). These aspects motivate the Bayesian nonparametric approach we undertake, since it allows to achieve the degree of flexibility typically needed in this framework. Based on an observed sample of size n, focus will be on prediction of a key aspect of the outcome from an additional sample of size m, namely, the so-called discovery probability. In particular, conditionally on an observed basic sample of size n, we derive a novel estimator of the probability of detecting, at the (n+m+1)th observation, species that have been observed with any given frequency in the enlarged sample of size n+m. Such an estimator admits a closed-form expression that can be exactly evaluated. The result we obtain allows us to quantify both the rate at which rare species are detected and the achieved sample coverage of abundant species, as m increases. Natural applications are represented by the estimation of the probability of discovering rare genes within genomic libraries and the results are illustrated by means of two expressed sequence tags datasets.}, } @article {pmid23023987, year = {2012}, author = {Boettger, D and Bergmann, H and Kuehn, B and Shelest, E and Hertweck, C}, title = {Evolutionary imprint of catalytic domains in fungal PKS-NRPS hybrids.}, journal = {Chembiochem : a European journal of chemical biology}, volume = {13}, number = {16}, pages = {2363-2373}, doi = {10.1002/cbic.201200449}, pmid = {23023987}, issn = {1439-7633}, mesh = {Amino Acids/chemistry ; Aspergillus/*enzymology/genetics/metabolism ; Biocatalysis ; *Biological Evolution ; Computational Biology ; Indole Alkaloids/chemistry ; Lovastatin/chemistry ; Models, Molecular ; Molecular Conformation ; Peptide Synthases/analysis/genetics/*metabolism ; Phylogeny ; Polyketide Synthases/analysis/genetics/*metabolism ; Polyketides/chemistry ; Sequence Alignment ; }, abstract = {Fungal hybrid enzymes consisting of a polyketide synthase (PKS) and a nonribosomal peptide synthetase (NRPS) module are involved in the biosynthesis of a vast array of ecologically and medicinally relevant natural products. Whereas a dozen gene clusters could be assigned to the requisite PKS-NRPS pathways, the programming of the multifunctional enzymes is still enigmatic. Through engineering and heterologously expressing a chimera of PKS (lovastatin synthase, LovB) and NRPS (cytochalasin synthase, CheA) in Aspergillus terreus, we noted the potential incompatibility of a fungal highly reducing PKS (hrPKS) with the NRPS component of fungal PKS-NRPS hybrids. To rationalize the unexpected outcome of the gene fusion experiments, we conducted extensive bioinformatic analyses of fungal PKS-NRPS hybrids and LovB-type PKS. From motif studies and the function of the engineered chimeras, a noncanonical function of C-terminal condensation (C) domains in truncated PKS-NRPS homologues was inferred. More importantly, sequence alignments and phylogenetic trees revealed an evolutionary imprint of the PKS-NRPS domains, which reflect the evolutionary history of the entire megasynthase. Furthermore, a detailed investigation of C and adenylation (A) domains provides support for a scenario in which not only the A domain but also the C domain participates in amino acid selection. These findings shed new light on the complex code of this emerging class of multifunctional enzymes and will greatly facilitate future combinatorial biosynthesis and pathway engineering approaches towards natural product analogues.}, } @article {pmid23017295, year = {2013}, author = {Kluge, A and Grauel, B and Burkolter, D}, title = {Combining principles of Cognitive Load Theory and diagnostic error analysis for designing job aids: Effects on motivation and diagnostic performance in a process control task.}, journal = {Applied ergonomics}, volume = {44}, number = {2}, pages = {285-296}, doi = {10.1016/j.apergo.2012.08.001}, pmid = {23017295}, issn = {1872-9126}, mesh = {Adult ; Attention ; Attitude ; Awareness ; *Decision Support Techniques ; Decision Trees ; *Ecological Systems, Closed ; Equipment Failure ; Female ; Humans ; Knowledge ; Learning ; Male ; *Motivation ; Psychological Theory ; *Task Performance and Analysis ; Workload/*psychology ; Young Adult ; }, abstract = {Two studies are presented in which the design of a procedural aid and the impact of an additional decision aid for process control were assessed. In Study 1, a procedural aid was developed that avoids imposing unnecessary extraneous cognitive load on novices when controlling a complex technical system. This newly designed procedural aid positively affected germane load, attention, satisfaction, motivation, knowledge acquisition and diagnostic speed for novel faults. In Study 2, the effect of a decision aid for use before the procedural aid was investigated, which was developed based on an analysis of diagnostic errors committed in Study 1. Results showed that novices were able to diagnose both novel faults and practised faults, and were even faster at diagnosing novel faults. This research contributes to the question of how to optimally support novices in dealing with technical faults in process control.}, } @article {pmid23015629, year = {2012}, author = {Delmore, KE and Fox, JW and Irwin, DE}, title = {Dramatic intraspecific differences in migratory routes, stopover sites and wintering areas, revealed using light-level geolocators.}, journal = {Proceedings. Biological sciences}, volume = {279}, number = {1747}, pages = {4582-4589}, pmid = {23015629}, issn = {1471-2954}, mesh = {*Animal Migration ; Animals ; Canada ; Central America ; Geographic Information Systems ; Geography ; Haplotypes ; Mexico ; *Reproductive Isolation ; Seasons ; Songbirds/*physiology ; United States ; }, abstract = {Migratory divides are contact zones between breeding populations that use divergent migratory routes and have been described in a variety of species. These divides are of major importance to evolution, ecology and conservation but have been identified using limited band recovery data and/or indirect methods. Data from band recoveries and mitochondrial haplotypes suggested that inland and coastal Swainson's thrushes (Catharus ustulatus) form a migratory divide in western North America. We attached light-level geolocators to birds at the edges of this contact zone to provide, to our knowledge, the first direct test of a putative divide using data from individual birds over the entire annual cycle. Coastal thrushes migrated along the west coast to Mexico, Guatemala and Honduras. Some of these birds used multiple wintering sites. Inland thrushes migrated across the Rocky Mountains, through central North America to Columbia and Venezuela. These birds migrated longer distances than coastal birds and performed a loop migration, navigating over the Gulf of Mexico in autumn and around this barrier in spring. These findings support the suggestion that divergent migratory behaviour could contribute to reproductive isolation between migrants, advance our understanding of their non-breeding ecology, and are integral to development of detailed conservation strategies for this group.}, } @article {pmid23013614, year = {2012}, author = {Lehmann, K and Werner, D and Hoffmann, B and Kampen, H}, title = {PCR identification of culicoid biting midges (Diptera, Ceratopogonidae) of the Obsoletus complex including putative vectors of bluetongue and Schmallenberg viruses.}, journal = {Parasites & vectors}, volume = {5}, number = {}, pages = {213}, pmid = {23013614}, issn = {1756-3305}, mesh = {Animals ; Bluetongue virus/isolation & purification ; Ceratopogonidae/*classification/*genetics/virology ; Computational Biology ; *Disease Vectors ; Electron Transport Complex IV/genetics ; Entomology/*methods ; Germany ; Male ; Mitochondrial Proteins/genetics ; Orthobunyavirus/isolation & purification ; Polymerase Chain Reaction/*methods ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: Biting midges of the Obsoletus species complex of the ceratopogonid genus Culicoides were assumed to be the major vectors of bluetongue virus (BTV) in northern and central Europe during the 2006 outbreak of bluetongue disease (BT). Most recently, field specimens of the same group of species have also been shown to be infected with the newly emerged Schmallenberg virus (SBV) in Europe. A reliable identification of the cryptic species of this group is fundamental for both understanding the epidemiology of the diseases and for targeted vector control. In the absence of classical morphological characters unambiguously identifying the species, DNA sequence-based tests have been established for the distinction of selected species in some parts of Europe. Since specificity and sensitivity of these tests have been shown to be in need of improvement, an alternative PCR assay targeting the mitochondrial cytochrome oxidase subunit I (COI) gene was developed for the identification of the three Obsoletus complex species endemic to Germany (C. obsoletus, C. scoticus, C. chiopterus) plus the isomorphic species C. dewulfi.

METHODS: Biting midges of the genus Culicoides caught by UV light traps all over Germany were morphologically pre-identified to species or complex level. The COI region was amplified from their extracted DNA and sequenced. Final species assignment was done by sequence comparison to GenBank entries and to morphologically identified males. Species-specific consensus sequences were aligned and polymorphisms were utilized to design species-specific primers to PCR-identify specimens when combined with a universal primer.

RESULTS: The newly developed multiplex PCR assay was successfully tested on genetically defined Obsoletus complex material as well as on morphologically pre-identified field material. The intended major advantage of the assay as compared to other PCR approaches, namely the production of only one single characteristic band for each species, could be realized with high specificity and sensitivity.

CONCLUSION: To elucidate the biological characteristics of potential vectors of disease agents, such as ecology, behaviour and vector competence, and the role of these haematophagous arthropods in the epidemiology of the diseases, simple, cost-effective and, most importantly, reliable identification techniques are necessary. The PCR assay presented will help to identify culicoid vector species and therefore add to bluetongue and Schmallenberg disease research including vector control and monitoring.}, } @article {pmid23011849, year = {2013}, author = {Azócar, DL and Vanhooydonck, B and Bonino, MF and Perotti, MG and Abdala, CS and Schulte, JA and Cruz, FB}, title = {Chasing the Patagonian sun: comparative thermal biology of Liolaemus lizards.}, journal = {Oecologia}, volume = {171}, number = {4}, pages = {773-788}, pmid = {23011849}, issn = {1432-1939}, mesh = {Acclimatization/*physiology ; Animals ; Argentina ; *Biological Evolution ; Body Temperature ; Body Temperature Regulation/*physiology ; Computational Biology ; Likelihood Functions ; Lizards/*physiology ; *Models, Biological ; Models, Genetic ; Phylogeny ; Species Specificity ; Temperature ; }, abstract = {The importance of the thermal environment for ectotherms and its relationship with thermal physiology and ecology is widely recognized. Several models have been proposed to explain the evolution of the thermal biology of ectotherms, but experimental studies have provided mixed support. Lizards from the Liolaemus goetschi group can be found along a wide latitudinal range across Argentina. The group is monophyletic and widely distributed, and therefore provides excellent opportunities to study the evolution of thermal biology. We studied thermal variables of 13 species of the L. goetschi group, in order to answer three questions. First, are aspects of the thermal biology of the L. goetschi group modelled by the environment or are they evolutionarily conservative? Second, have thermal characteristics of these animals co-evolved? And third, how do the patterns of co-evolution observed within the L. goetschi group compare to those in a taxonomically wider selection of species of Liolaemus? We collected data on 13 focal species and used species information of Liolaemus lizards available in the literature and additional data obtained by the authors. We tackled these questions using both conventional and phylogenetically based analyses. Our results show that lizards from the L. goetschi group and the genus Liolaemus in general vary in critical thermal minimum in relation to mean air temperature, and particularly the L. goetschi group shows that air temperature is associated with critical thermal range, as well as with body temperature. Although the effect of phylogeny cannot be ignored, our results indicate that these thermal biology aspects are modelled by cold environments of Patagonia, while other aspects (preferred body temperature and critical thermal maximum) are more conservative. We found evidence of co-evolutionary patterns between critical thermal minimum and preferred body temperature at both phylogenetic scales (the L. goetschi group and the extended sample of 68 Liolaemus species).}, } @article {pmid23007599, year = {2013}, author = {Rempala, GA and Seweryn, M}, title = {Methods for diversity and overlap analysis in T-cell receptor populations.}, journal = {Journal of mathematical biology}, volume = {67}, number = {6-7}, pages = {1339-1368}, pmid = {23007599}, issn = {1432-1416}, support = {R01 CA152158/CA/NCI NIH HHS/United States ; R01CA-152158/CA/NCI NIH HHS/United States ; }, mesh = {Animals ; Data Interpretation, Statistical ; Genetic Variation/*immunology ; Mice ; Receptors, Antigen, T-Cell/genetics/*immunology ; T-Lymphocyte Subsets/*immunology ; T-Lymphocytes/*immunology ; }, abstract = {The paper presents some novel approaches to the empirical analysis of diversity and similarity (overlap) in biological or ecological systems. The analysis is motivated by the molecular studies of highly diverse mammalian T-cell receptor (TCR) populations, and is related to the classical statistical problem of analyzing two-way contingency tables with missing cells and low cell counts. The new measures of diversity and overlap are proposed, based on the information-theoretic as well as geometric considerations, with the capacity to naturally up-weight or down-weight the rare and abundant population species. The consistent estimates are derived by applying the Good-Turing sample-coverage correction. In particular, novel consistent estimates of the Shannon entropy function and the Morisita-Horn index are provided. Data from TCR populations in mice are used to illustrate the empirical performance of the proposed methods vis a vis the existing alternatives.}, } @article {pmid23006415, year = {2012}, author = {, and Barat, A and Bravo, SP and Chandra, S and Corrêa, AS and Giombini, MI and Guedes, RN and Huailei, M and Lal, KK and Liang, L and Matura, R and Mohindra, V and Oliveira, LO and Patangia, R and Qiyong, L and Sah, RS and Singh, A and Singh, BK and Singh, RK and Tosto, DS and Tripathi, RK and Vinson, CC}, title = {Permanent genetic resources added to Molecular Ecology Resources Database 1 June 2012-31 July 2012.}, journal = {Molecular ecology resources}, volume = {12}, number = {6}, pages = {1196-1197}, doi = {10.1111/1755-0998.12016}, pmid = {23006415}, issn = {1755-0998}, mesh = {Animals ; Arecaceae/classification/genetics ; Chordata/classification/genetics ; Computational Biology/*methods ; Ecology/*methods ; *Microsatellite Repeats ; Molecular Biology/*methods ; Weevils/classification/genetics ; }, abstract = {This article documents the addition of 96 microsatellite marker loci to the Molecular Ecology Resources Database. Loci were developed for the following species: Clarias batrachus, Marmota himalayana, Schizothorax richardsonii, Sitophilus zeamais and Syagrus romanzoffiana. These loci were cross-tested on the following species: Clarias dussumeri, Clarias gariepinus, Heteropneustus fossilis, Sitophilus granarius and Sitophilus oryzae.}, } @article {pmid23005188, year = {2012}, author = {Chen, X and Szolnoki, A and Perc, M and Wang, L}, title = {Impact of generalized benefit functions on the evolution of cooperation in spatial public goods games with continuous strategies.}, journal = {Physical review. E, Statistical, nonlinear, and soft matter physics}, volume = {85}, number = {6 Pt 2}, pages = {066133}, doi = {10.1103/PhysRevE.85.066133}, pmid = {23005188}, issn = {1550-2376}, mesh = {*Competitive Behavior ; Computer Simulation ; Cooperative Behavior ; *Decision Making ; *Decision Support Techniques ; *Game Theory ; *Models, Theoretical ; }, abstract = {Cooperation and defection may be considered to be two extreme responses to a social dilemma. Yet the reality is much less clear-cut. Between the two extremes lies an interval of ambivalent choices, which may be captured theoretically by means of continuous strategies defining the extent of the contributions of each individual player to the common pool. If strategies are chosen from the unit interval, where 0 corresponds to pure defection and 1 corresponds to the maximal contribution, the question is what is the characteristic level of individual investments to the common pool that emerges if the evolution is guided by different benefit functions. Here we consider the steepness and the threshold as two parameters defining an array of generalized benefit functions, and we show that in a structured population there exist intermediate values of both at which the collective contributions are maximal. However, as the cost-to-benefit ratio of cooperation increases, the characteristic threshold decreases while the corresponding steepness increases. Our observations remain valid if more complex sigmoid functions are used, thus reenforcing the importance of carefully adjusted benefits for high levels of public cooperation.}, } @article {pmid23002793, year = {2013}, author = {Gijbels, I and Omelka, M}, title = {Testing for homogeneity of multivariate dispersions using dissimilarity measures.}, journal = {Biometrics}, volume = {69}, number = {1}, pages = {137-145}, doi = {10.1111/j.1541-0420.2012.01797.x}, pmid = {23002793}, issn = {1541-0420}, mesh = {*Analysis of Variance ; Animals ; Anthozoa/growth & development ; Computer Simulation ; *Data Interpretation, Statistical ; *Ecosystem ; *Multivariate Analysis ; Sparrows/growth & development ; }, abstract = {Testing homogeneity of dispersions may be of its own scientific interest as well as an important auxiliary step verifying assumptions of a main analysis. The problem is that many biological and ecological data are highly skewed and zero-inflated. Also the number of variables often exceeds the sample size. Thus data analysts often do not rely on parametric assumptions, but use a particular dissimilarity measure to calculate a matrix of pairwise differences. This matrix is then the basis for further statistical inference. Anderson (2006) proposed a distance-based test of homogeneity of multivariate dispersions for a one-way ANOVA design, for which a matrix of pairwise dissimilarities can be taken as an input. The key idea, like in Levene's test, is to replace each observation with its distance to an estimated group center. In this paper we suggest an alternative approach that is based on the means of within-group distances and does not require group centre calculations to obtain the test statistic. We show that this approach can have theoretical as well as practical advantages. A permutation procedure that gives type I error close to the prescribed value even in small samples is described.}, } @article {pmid23002615, year = {2012}, author = {Li, YJ and Yang, SL and Hou, LJ and Zhou, JZ and Liu, YW}, title = {[Spatial distribution and contamination evaluation of heavy metals in the intertidal surface sediments of Eastern Chongming].}, journal = {Huan jing ke xue= Huanjing kexue}, volume = {33}, number = {7}, pages = {2368-2375}, pmid = {23002615}, issn = {0250-3301}, mesh = {Cadmium/analysis ; China ; Copper/analysis ; Ecosystem ; Environmental Monitoring/*methods ; Geographic Information Systems ; Geologic Sediments/*chemistry ; Lead/analysis ; Metals, Heavy/*analysis ; Rivers ; Spatial Analysis ; Water Pollutants, Chemical/*analysis ; }, abstract = {Using the ArcGIS geostatistical analysis module, this work investigated the spatial distribution pattern of heavy metals (Cu, Pb, Zn, Cr, Cd) and their deposition fluxes in the intertidal surface sediments of Eastern Chongming based on the analysis of grain size, heavy metal concentrations and organic carbon content. The spatial interpolation (Kriging) was performed to estimate the deposition fluxes, and the contamination status of heavy metals was evaluated using geoaccumulation index and potential ecological risk index. The results showed that the average contents of Cu, Pb, Zn, Cr and Cd were 42, 27, 69, 71 and 0.23 microg x g(-1), respectively, all of which exceeded the background value in the Shanghai tidal flat. The contents of heavy metals showed a landward as well as northward increasing trend due to the influences of sediment grain size and organic carbon content. The annual deposition of Cu, Pb, Zn, Cr and Cd in Eastern Chongming were 187, 121, 395, 312 and 1.04 t, respectively; the total deposition flux of these heavy metals was 11 g x (m2 x a)-1. Although the overall contamination level of heavy metals in Eastern Chongming was relatively low, Cd, Pb and Cu had a potential pollution threat to the sediment environment.}, } @article {pmid23002599, year = {2012}, author = {Hao, JF and Liu, HY and Hu, HB and An, J and Zhang, XH}, title = {[Responses of wetland water quality to influence the strengthness of urbanization in Nanjing, China].}, journal = {Huan jing ke xue= Huanjing kexue}, volume = {33}, number = {7}, pages = {2259-2264}, pmid = {23002599}, issn = {0250-3301}, mesh = {China ; Cities ; Environmental Monitoring/*methods ; Geographic Information Systems ; Seasons ; *Urbanization ; Water Quality/*standards ; *Wetlands ; }, abstract = {28 typical wetlands were selected to monitor the contaminants in water monthly, that influenced by urbanization in different scales. On the other hand, the land use types such as impervious area and forest area in the catchments of urban wetlands were analyzed by GIS and landscape ecology. And then the effects of urbanization index (UEI) was employed to reveal the relationship between urbanization level and water quality in Xianlin New City of Nanjing. Results indicated that: (1) the seasonal variations of water quality showed that water quality in summer was worse than those in other seasons, and the water quality in winter was good. However there were no significant differences between the spring and the autumn. (2) the relationship was significant between urbanization level and water quality, and the water quality tended to be getting worse when the urbanization level was getting higher. The concentrations of TP, TN, NH(4+)-N, and Chla were 0.27, 1.07, 0.15 and 17.94 mg x L(-1) respectively in the high urbanization (HU) level wetland while the concentrations were 0.12, 0.56, 0.12 and 4.85 mg x L(-1) in the low urbanization (LW) level wetland. (3) there was a threshold between UEI and the water quality. On the whole, the water quality would get worse quickly when the value of UEI exceeded 2.2.}, } @article {pmid23001959, year = {2012}, author = {Lindsay, SM}, title = {Dispersal of marine organisms and the grand challenges in biology: an introduction to the symposium.}, journal = {Integrative and comparative biology}, volume = {52}, number = {4}, pages = {443-446}, doi = {10.1093/icb/ics106}, pmid = {23001959}, issn = {1557-7023}, mesh = {Animals ; Databases, Factual ; Demography ; Fishes/*physiology ; *Food Chain ; Invertebrates/*physiology ; Larva ; Oceans and Seas ; Plankton/*physiology ; }, abstract = {Understanding dispersal and its complex variables is critical to understanding the ecology and evolution of life histories of species, but research on dispersal tends to reflect or emphasize particular disciplines, such as population genetics, functional morphology, evolutionary and developmental biology, physiology, and biophysics, or to emphasize a particular clade or functional group (e.g., fish, planktotrophs or lecithotrophs, pelagic or benthic organisms) in marine ecosystems. The symposium on "Dispersal of Marine Organisms" assembled an interdisciplinary group of outstanding young and established speakers to address dispersal in marine organisms in order to foster integration and cross-talk among different disciplines and to identify gaps in our knowledge and suggest areas for future research.}, } @article {pmid22999180, year = {2012}, author = {Weng, JK and Noel, JP}, title = {Structure-function analyses of plant type III polyketide synthases.}, journal = {Methods in enzymology}, volume = {515}, number = {}, pages = {317-335}, doi = {10.1016/B978-0-12-394290-6.00014-8}, pmid = {22999180}, issn = {1557-7988}, support = {//Howard Hughes Medical Institute/United States ; }, mesh = {Acyltransferases/*chemistry/classification/genetics ; Arabidopsis/*enzymology/genetics ; Arabidopsis Proteins/chemistry/genetics ; Catalytic Domain ; Coenzyme A Ligases/chemistry/genetics ; Computational Biology/methods ; Decarboxylation ; Enzyme Activation ; *Gene Expression Regulation, Enzymologic ; *Gene Expression Regulation, Plant ; Genes, Plant ; Metabolic Engineering/methods ; Mutagenesis, Site-Directed ; Phylogeny ; Protein Folding ; Recombinant Fusion Proteins/genetics/metabolism ; Structure-Activity Relationship ; }, abstract = {Plant type III polyketide synthases (PKSs) form a superfamily of biosynthetic enzymes involved in the production of a plethora of polyketide-derived natural products important for ecological adaptations and the fitness of land plants. Moreover, tremendous interest in bioengineering of type III PKSs to produce high-value compounds is increasing. Compared to type I and type II PKSs, which form either large modular protein complexes or dissociable molecular assemblies, type III PKSs exist as smaller homodimeric proteins, technically more amenable for detailed quantitative biochemical and phylogenetic analyses. In this chapter, we summarize a collection of approaches, including bioinformatics, genetics, protein crystallography, in vitro biochemistry, and mutagenesis, together affording a comprehensive interrogation of the structure-function-evolutionary relationships in the plant type III PKS family.}, } @article {pmid22985547, year = {2013}, author = {Schueller, SM and Leykin, Y and Pérez-Stable, EJ and Muñoz, RF}, title = {Selection of intervention components in an internet stop smoking participant preference trial: beyond randomized controlled trials.}, journal = {Psychiatry research}, volume = {205}, number = {1-2}, pages = {159-164}, pmid = {22985547}, issn = {1872-7123}, support = {U01CA86117/CA/NCI NIH HHS/United States ; K08 MH091501/MH/NIMH NIH HHS/United States ; 5K08MH091501/MH/NIMH NIH HHS/United States ; F32 MH095345/MH/NIMH NIH HHS/United States ; U01 CA086117/CA/NCI NIH HHS/United States ; F32MH095345/MH/NIMH NIH HHS/United States ; }, mesh = {Adolescent ; Adult ; Aged ; Choice Behavior ; Cognitive Behavioral Therapy/statistics & numerical data ; Computer-Assisted Instruction ; *Consumer Behavior ; Depression/therapy ; Female ; Health Services Needs and Demand ; Humans ; *Internet ; Male ; Middle Aged ; Randomized Controlled Trials as Topic/psychology ; Self-Help Groups/statistics & numerical data ; Smoking/*therapy ; Smoking Cessation/*methods ; Therapy, Computer-Assisted/*methods ; Tobacco Use Cessation Devices/statistics & numerical data ; Treatment Outcome ; Young Adult ; }, abstract = {To address health problems that have a major impact on global health requires research designs that go beyond randomized controlled trials. One such design, the participant preference trial, provides additional information in an ecologically valid manner, once intervention efficacy has been demonstrated. The current study presents illustrative data from a participant preference trial of an internet-based smoking cessation intervention. Participants (N=7763) from 124 countries accessed the intervention and were allowed to choose from nine different site components to aid their quit attempt. Of consenting participants, 36.7% completed at least one follow-up assessment. Individuals with depression were more likely to choose a mood management module and participants who smoked a higher number of cigarettes were more likely to choose a cigarette counter and a nicotine replacement therapy guide. Furthermore, depressed participants selecting the mood management component were more likely to report at least one successful 7 day quit (37.2% vs. 22.2%) in the 12 months following the intervention. Thus, participants with depressive symptoms appear to make choices on the basis of their needs and to benefit from these decisions. This suggests that providing the ability to customize previously validated resources may be a successful way to widely disseminate interventions.}, } @article {pmid22985105, year = {2013}, author = {Tannenbaum, LV and Gulsby, WD and Zobel, SS and Miller, KV}, title = {Where deer roam: chronic yet acute site exposures preclude ecological risk assessment.}, journal = {Risk analysis : an official publication of the Society for Risk Analysis}, volume = {33}, number = {5}, pages = {789-799}, doi = {10.1111/j.1539-6924.2012.01890.x}, pmid = {22985105}, issn = {1539-6924}, mesh = {Animals ; *Deer ; *Ecology ; *Environmental Exposure ; Environmental Pollutants ; Geographic Information Systems ; Georgia ; *Risk Assessment ; }, abstract = {Global positioning system (GPS) technology has made possible the detailed tracking of the spatial movements of wildlife. Using GPS tracking collars placed on female white-tailed deer (Odocoileus virginianus) over a protracted period, we illustrate that this species is spatially irrelevant for consideration in ecological risk assessments (ERAs) for commonly assessed contaminated sites. Specifically, deer movements do not allow for a sufficiency of chemical exposures to occur such that toxicological endpoints would be triggered. Deer are spatially irrelevant not only because their home ranges and overall utilized areas dwarf prototypical hazardous waste sites. They are also inappropriate for assessment because they only minimally contact reasonably sized preferred locations, this while demonstrating a confounding high degree of site affinity for them. Our spatial movements analysis suggests that deer introduce the ERA novelty of a species displaying elements of both chronic and acute site exposure. We further suggest that other large commonly assessed high-profile mammals could also be found to be spatially irrelevant for ERAs were they to submit to the GPS tracking and subsequent data analysis we performed for the deer. Recognizing that certain receptors need not be considered in ERAs can help to simplify the ERA process.}, } @article {pmid22984782, year = {2012}, author = {Gordo, SM and Pinheiro, DG and Moreira, EC and Rodrigues, SM and Poltronieri, MC and de Lemos, OF and da Silva, IT and Ramos, RT and Silva, A and Schneider, H and Silva, WA and Sampaio, I and Darnet, S}, title = {High-throughput sequencing of black pepper root transcriptome.}, journal = {BMC plant biology}, volume = {12}, number = {}, pages = {168}, pmid = {22984782}, issn = {1471-2229}, mesh = {Arabidopsis/genetics/metabolism ; Databases, Genetic ; Gene Expression Profiling ; Gene Library ; Genome, Plant ; *High-Throughput Nucleotide Sequencing ; Microsatellite Repeats ; Molecular Sequence Annotation ; Phylogeny ; Piper nigrum/*genetics/metabolism ; Plant Proteins/genetics/metabolism ; Plant Roots/*genetics/metabolism ; Proteome/genetics/metabolism ; RNA, Plant/genetics/metabolism ; Sequence Analysis, RNA ; Sequence Homology, Amino Acid ; *Transcriptome ; }, abstract = {BACKGROUND: Black pepper (Piper nigrum L.) is one of the most popular spices in the world. It is used in cooking and the preservation of food and even has medicinal properties. Losses in production from disease are a major limitation in the culture of this crop. The major diseases are root rot and foot rot, which are results of root infection by Fusarium solani and Phytophtora capsici, respectively. Understanding the molecular interaction between the pathogens and the host's root region is important for obtaining resistant cultivars by biotechnological breeding. Genetic and molecular data for this species, though, are limited. In this paper, RNA-Seq technology has been employed, for the first time, to describe the root transcriptome of black pepper.

RESULTS: The root transcriptome of black pepper was sequenced by the NGS SOLiD platform and assembled using the multiple-k method. Blast2Go and orthoMCL methods were used to annotate 10338 unigenes. The 4472 predicted proteins showed about 52% homology with the Arabidopsis proteome. Two root proteomes identified 615 proteins, which seem to define the plant's root pattern. Simple-sequence repeats were identified that may be useful in studies of genetic diversity and may have applications in biotechnology and ecology.

CONCLUSIONS: This dataset of 10338 unigenes is crucially important for the biotechnological breeding of black pepper and the ecogenomics of the Magnoliids, a major group of basal angiosperms.}, } @article {pmid22984421, year = {2012}, author = {Hector, A and von Felten, S and Hautier, Y and Weilenmann, M and Bruelheide, H}, title = {Effects of dominance and diversity on productivity along Ellenberg's experimental water table gradients.}, journal = {PloS one}, volume = {7}, number = {9}, pages = {e43358}, pmid = {22984421}, issn = {1932-6203}, mesh = {*Biodiversity ; Biomass ; Databases as Topic ; *Groundwater ; *Models, Biological ; Poaceae/*growth & development ; Soil ; }, abstract = {Heinz Ellenberg's historically important work on changes in the abundances of a community of grass species growing along experimental gradients of water table depth has played an important role in helping to identify the hydrological niches of plant species in wet meadows. We present a previously unpublished complete version of Ellenberg's dataset from the 1950s together with the results of a series of modern statistical analyses testing for hypothesized overyielding of aboveground net primary production as a consequence of resource-based niche differentiation. Interactions of species with water table depth and soil type in the results of our analyses are qualitatively consistent with earlier interpretations of evidence for differences in the fundamental and realized niches of species. Arrhenatherum elatius tended to dominate communities and this effect was generally positively related to increasing water table depth. There was little overyielding of aboveground net primary production during the two repeats of the experiment conducted in successive single growing seasons. Examination of how the effects of biodiversity on ecosystem processes vary across environmental gradients is an underutilized approach--particularly where the gradient is thought to be an axis of niche differentiation as is the case with water availability. Furthermore, advances in ecology and statistics during the 60 years since Ellenberg's classic experiment was performed suggest that it may be worth repeating over a longer duration and with modern experimental design and methodologies.}, } @article {pmid22984399, year = {2012}, author = {Taylor, PJ and Stoffberg, S and Monadjem, A and Schoeman, MC and Bayliss, J and Cotterill, FP}, title = {Four new bat species (Rhinolophus hildebrandtii complex) reflect Plio-Pleistocene divergence of dwarfs and giants across an Afromontane archipelago.}, journal = {PloS one}, volume = {7}, number = {9}, pages = {e41744}, pmid = {22984399}, issn = {1932-6203}, mesh = {Acoustics ; Africa ; Animals ; *Biological Evolution ; *Body Size/genetics ; Chiroptera/*anatomy & histology/classification/*genetics ; Cytochromes b/genetics ; Databases, Genetic ; Dwarfism/genetics/veterinary ; Echolocation ; Female ; *Genetic Variation ; Genotype ; Geography ; Gigantism/genetics/veterinary ; *Islands ; Male ; Molecular Sequence Data ; Phylogeny ; Principal Component Analysis ; Time Factors ; }, abstract = {Gigantism and dwarfism evolve in vertebrates restricted to islands. We describe four new species in the Rhinolophus hildebrandtii species-complex of horseshoe bats, whose evolution has entailed adaptive shifts in body size. We postulate that vicissitudes of palaeoenvironments resulted in gigantism and dwarfism in habitat islands fragmented across eastern and southern Africa. Mitochondrial and nuclear DNA sequences recovered two clades of R. hildebrandtii senso lato which are paraphyletic with respect to a third lineage (R. eloquens). Lineages differ by 7.7 to 9.0% in cytochrome b sequences. Clade 1 includes R. hildebrandtii sensu stricto from the east African highlands and three additional vicariants that speciated across an Afromontane archipelago through the Plio-Pleistocene, extending from the Kenyan Highlands through the Eastern Arc, northern Mozambique and the Zambezi Escarpment to the eastern Great Escarpment of South Africa. Clade 2 comprises one species confined to lowland savanna habitats (Mozambique and Zimbabwe). A third clade comprises R. eloquens from East Africa. Speciation within Clade 1 is associated with fixed differences in echolocation call frequency, and cranial shape and size in populations isolated since the late Pliocene (ca 3.74 Mya). Relative to the intermediate-sized savanna population (Clade 2), these island-populations within Clade 1 are characterised by either gigantism (South African eastern Great Escarpment and Mts Mabu and Inago in Mozambique) or dwarfism (Lutope-Ngolangola Gorge, Zimbabwe and Soutpansberg Mountains, South Africa). Sympatry between divergent clades (Clade 1 and Clade 2) at Lutope-Ngolangola Gorge (NW Zimbabwe) is attributed to recent range expansions. We propose an "Allometric Speciation Hypothesis", which attributes the evolution of this species complex of bats to divergence in constant frequency (CF) sonar calls. The origin of species-specific peak frequencies (overall range = 32 to 46 kHz) represents the allometric effect of adaptive divergence in skull size, represented in the evolution of gigantism and dwarfism in habitat islands.}, } @article {pmid22983289, year = {2012}, author = {Carvalho, RM and Nascimento, LF}, title = {Spatial distribution of dengue in the city of Cruzeiro, São Paulo State, Brazil: use of geoprocessing tools.}, journal = {Revista do Instituto de Medicina Tropical de Sao Paulo}, volume = {54}, number = {5}, pages = {261-266}, doi = {10.1590/s0036-46652012000500005}, pmid = {22983289}, issn = {1678-9946}, mesh = {Brazil/epidemiology ; Dengue/*epidemiology ; *Geographic Information Systems ; Geographic Mapping ; Humans ; Seasons ; }, abstract = {The aim of this article is to identify patterns in spatial distribution of cases of dengue fever that occurred in the municipality of Cruzeiro, State of São Paulo, in 2006. This is an ecological and exploratory study using the tools of spatial analysis in the preparation of thematic maps with data from Sinan-Net. An analysis was made by area, taking as unit the IBGE census, the analysis included four months in 2006 which show the occurrence of the disease in the city. The thematic maps were constructed by TerraView 3.3.1 software, the same software provided the values of the indicators of Global Moran (I M) every month and the Kernel estimation. In the year 2006, 691 cases of dengue were georeferenced (with a rate of 864.2 cases/100,000 inhabitants); the indicators of Moran and p-values obtained were I M = 0.080 (March) p = 0.11; I M = 0.285 (April) p = 0.01; I M = 0.201 (May) p = 0.01 and I M = 0.002 (June) p = 0.57. The first cases were identified in the Northeast and Central areas of Cruzeiro and the recent cases, in the North, Northeast and Central. It was possible to identify census tracts where the epidemic began and how it occurred temporally and spatially in the city.}, } @article {pmid22978681, year = {2012}, author = {Carneiro, J and Pereira, F and Amorim, A}, title = {SPInDel: a multifunctional workbench for species identification using insertion/deletion variants.}, journal = {Molecular ecology resources}, volume = {12}, number = {6}, pages = {1190-1195}, doi = {10.1111/1755-0998.12011}, pmid = {22978681}, issn = {1755-0998}, mesh = {Animals ; Anura/classification/genetics ; Asia, Southeastern ; Classification/*methods ; Computational Biology/*methods ; Genomics/*methods ; *INDEL Mutation ; Perciformes/classification/genetics ; Software ; }, abstract = {The majority of the available methods for the molecular identification of species use pairwise sequence divergences between the query and reference sequences (DNA barcoding). The presence of multiple insertions and deletions (indels) in the target genomic regions is generally regarded as a problem, as it introduces ambiguities in sequence alignments. However, we have recently shown that a high level of species discrimination is attainable in all taxa of life simply by considering the length of hypervariable regions defined by indel variants. Each species is tagged with a numeric profile of fragment lengths-a true numeric barcode. In this study, we describe a multifunctional computational workbench (named SPInDel for SPecies Identification by Insertions/Deletions) to assist researchers using variable-length DNA sequences, and we demonstrate its applicability in molecular ecology. The SPInDel workbench provides a step-by-step environment for the alignment of target sequences, selection of informative hypervariable regions, design of PCR primers and the statistical validation of the species-identification process. In our test data sets, we were able to discriminate all species from two genera of frogs (Ansonia and Leptobrachium) inhabiting lowland rainforests and mountain regions of South-East Asia and species from the most common genus of coral reef fishes (Apogon). Our method can complement conventional DNA barcoding systems when indels are common (e.g. in rRNA genes) without the required step of DNA sequencing. The executable files, source code, documentation and test data sets are freely available at http://www.portugene.com/SPInDel/SPInDel_webworkbench.html.}, } @article {pmid22977117, year = {2013}, author = {Oakley, TH and Wolfe, JM and Lindgren, AR and Zaharoff, AK}, title = {Phylotranscriptomics to bring the understudied into the fold: monophyletic ostracoda, fossil placement, and pancrustacean phylogeny.}, journal = {Molecular biology and evolution}, volume = {30}, number = {1}, pages = {215-233}, doi = {10.1093/molbev/mss216}, pmid = {22977117}, issn = {1537-1719}, mesh = {Animals ; Cell Nucleus/genetics ; Crustacea/*classification/*genetics ; DNA, Ribosomal/genetics ; Databases, Genetic ; Evolution, Molecular ; Expressed Sequence Tags ; *Fossils ; Genome, Mitochondrial ; Insecta/classification/genetics ; *Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA ; *Transcriptome ; }, abstract = {An ambitious, yet fundamental goal for comparative biology is to understand the evolutionary relationships for all of life. However, many important taxonomic groups have remained recalcitrant to inclusion into broader scale studies. Here, we focus on collection of 9 new 454 transcriptome data sets from Ostracoda, an ancient and diverse group with a dense fossil record, which is often undersampled in broader studies. We combine the new transcriptomes with a new morphological matrix (including fossils) and existing expressed sequence tag, mitochondrial genome, nuclear genome, and ribosomal DNA data. Our analyses lead to new insights into ostracod and pancrustacean phylogeny. We obtained support for three epic pancrustacean clades that likely originated in the Cambrian: Oligostraca (Ostracoda, Mystacocarida, Branchiura, and Pentastomida); Multicrustacea (Copepoda, Malacostraca, and Thecostraca); and a clade we refer to as Allotriocarida (Hexapoda, Remipedia, Cephalocarida, and Branchiopoda). Within the Oligostraca clade, our results support the unresolved question of ostracod monophyly. Within Multicrustacea, we find support for Thecostraca plus Copepoda, for which we suggest the name Hexanauplia. Within Allotriocarida, some analyses support the hypothesis that Remipedia is the sister taxon to Hexapoda, but others support Branchiopoda + Cephalocarida as the sister group of hexapods. In multiple different analyses, we see better support for equivocal nodes using slow-evolving genes or when excluding distant outgroups, highlighting the increased importance of conditional data combination in this age of abundant, often anonymous data. However, when we analyze the same set of species and ignore rate of gene evolution, we find higher support when including all data, more in line with a "total evidence" philosophy. By concatenating molecular and morphological data, we place pancrustacean fossils in the phylogeny, which can be used for studies of divergence times in Pancrustacea, Arthropoda, or Metazoa. Our results and new data will allow for attributes of Ostracoda, such as its amazing fossil record and diverse biology, to be leveraged in broader scale comparative studies. Further, we illustrate how adding extensive next-generation sequence data from understudied groups can yield important new phylogenetic insights into long-standing questions, especially when carefully analyzed in combination with other data.}, } @article {pmid22971047, year = {2012}, author = {Pickles, BJ and Genney, DR and Anderson, IC and Alexander, IJ}, title = {Spatial analysis of ectomycorrhizal fungi reveals that root tip communities are structured by competitive interactions.}, journal = {Molecular ecology}, volume = {21}, number = {20}, pages = {5110-5123}, doi = {10.1111/j.1365-294X.2012.05739.x}, pmid = {22971047}, issn = {1365-294X}, mesh = {*Biodiversity ; DNA, Fungal/genetics ; DNA, Ribosomal Spacer/genetics ; Databases, Nucleic Acid ; Meristem/*microbiology ; Mycorrhizae/*genetics/physiology ; Pinus/microbiology ; Polymorphism, Restriction Fragment Length ; Soil Microbiology ; Spatial Analysis ; Stochastic Processes ; }, abstract = {Microbial ecology has made large advances over the last decade, mostly because of improvements in molecular analysis techniques that have enabled the detection and identification of progressively larger numbers of microbial species. However, determining the ecological patterns and processes taking place in communities of microbes remains a significant challenge. Are communities randomly assembled through dispersal and priority effects, or do species interact with each other leading to positive and negative associations? For mycorrhizal fungi, evidence is accumulating that stochastic and competitive interactions between species may both have a role in shaping community structure. Could the methodological approach, which is often incidence based, impact the outcomes detected? Here, we applied an incidence-based Terminal Restriction Fragment Length Polymorphism (T-RFLP) database approach to examine species diversity and ecological interactions within a community of ectomycorrhizal (ECM) fungi. Co-occurrence analysis revealed that the ECM community colonizing root tips was strongly structured by competitive interactions, or ecological processes generating a similar spatial pattern, rather than neutral processes. Analysis of β-diversity indicated that community structure was significantly more similar (spatially autocorrelated) at distances equal to or <3.41 m. The eight most frequently encountered species in the root tip community of ECM fungi displayed significant competitive interactions with at least one other species, showing that the incidence-based approach was capable of detecting this sort of ecological information.}, } @article {pmid22970178, year = {2012}, author = {Kidd, TJ and Ritchie, SR and Ramsay, KA and Grimwood, K and Bell, SC and Rainey, PB}, title = {Pseudomonas aeruginosa exhibits frequent recombination, but only a limited association between genotype and ecological setting.}, journal = {PloS one}, volume = {7}, number = {9}, pages = {e44199}, pmid = {22970178}, issn = {1932-6203}, support = {//Wellcome Trust/United Kingdom ; }, mesh = {Base Sequence ; Cystic Fibrosis/microbiology ; Databases, Genetic ; *Ecosystem ; Environmental Microbiology ; Genetic Variation ; Genotype ; Geography ; Humans ; Multilocus Sequence Typing ; Mutation/genetics ; Phylogeny ; Pseudomonas aeruginosa/classification/*genetics/isolation & purification ; Queensland ; *Recombination, Genetic ; }, abstract = {Pseudomonas aeruginosa is an opportunistic pathogen and an important cause of infection, particularly amongst cystic fibrosis (CF) patients. While specific strains capable of patient-to-patient transmission are known, many infections appear to be caused by unique and unrelated strains. There is a need to understand the relationship between strains capable of colonising the CF lung and the broader set of P. aeruginosa isolates found in natural environments. Here we report the results of a multilocus sequence typing (MLST)-based study designed to understand the genetic diversity and population structure of an extensive regional sample of P. aeruginosa isolates from South East Queensland, Australia. The analysis is based on 501 P. aeruginosa isolates obtained from environmental, animal and human (CF and non-CF) sources with particular emphasis on isolates from the Lower Brisbane River and isolates from CF patients obtained from the same geographical region. Overall, MLST identified 274 different sequence types, of which 53 were shared between one or more ecological settings. Our analysis revealed a limited association between genotype and environment and evidence of frequent recombination. We also found that genetic diversity of P. aeruginosa in Queensland, Australia was indistinguishable from that of the global P. aeruginosa population. Several CF strains were encountered frequently in multiple ecological settings; however, the most frequently encountered CF strains were confined to CF patients. Overall, our data confirm a non-clonal epidemic structure and indicate that most CF strains are a random sample of the broader P. aeruginosa population. The increased abundance of some CF strains in different geographical regions is a likely product of chance colonisation events followed by adaptation to the CF lung and horizontal transmission among patients.}, } @article {pmid22970111, year = {2012}, author = {Goldman, AD and Baross, JA and Samudrala, R}, title = {The enzymatic and metabolic capabilities of early life.}, journal = {PloS one}, volume = {7}, number = {9}, pages = {e39912}, pmid = {22970111}, issn = {1932-6203}, support = {DP1 LM011509/LM/NLM NIH HHS/United States ; DP1 OD006779/OD/NIH HHS/United States ; }, mesh = {Computational Biology ; Enzymes/chemistry/*metabolism ; Metabolic Networks and Pathways ; Metals/metabolism ; Nucleotides/metabolism ; Protein Structure, Secondary ; }, abstract = {We introduce the concept of metaconsensus and employ it to make high confidence predictions of early enzyme functions and the metabolic properties that they may have produced. Several independent studies have used comparative bioinformatics methods to identify taxonomically broad features of genomic sequence data, protein structure data, and metabolic pathway data in order to predict physiological features that were present in early, ancestral life forms. But all such methods carry with them some level of technical bias. Here, we cross-reference the results of these previous studies to determine enzyme functions predicted to be ancient by multiple methods. We survey modern metabolic pathways to identify those that maintain the highest frequency of metaconsensus enzymes. Using the full set of modern reactions catalyzed by these metaconsensus enzyme functions, we reconstruct a representative metabolic network that may reflect the core metabolism of early life forms. Our results show that ten enzyme functions, four hydrolases, three transferases, one oxidoreductase, one lyase, and one ligase, are determined by metaconsensus to be present at least as late as the last universal common ancestor. Subnetworks within central metabolic processes related to sugar and starch metabolism, amino acid biosynthesis, phospholipid metabolism, and CoA biosynthesis, have high frequencies of these enzyme functions. We demonstrate that a large metabolic network can be generated from this small number of enzyme functions.}, } @article {pmid22965695, year = {2013}, author = {Nelson, G and Macnaughton, E and Goering, P and Dudley, M and O'Campo, P and Patterson, M and Piat, M and Prévost, N and Strehlau, V and Vallée, C}, title = {Planning a multi-site, complex intervention for homeless people with mental illness: the relationships between the national team and local sites in Canada's At Home/Chez Soi project.}, journal = {American journal of community psychology}, volume = {51}, number = {3-4}, pages = {347-358}, doi = {10.1007/s10464-012-9554-2}, pmid = {22965695}, issn = {1573-2770}, mesh = {Canada ; *Community Networks ; Focus Groups ; Health Plan Implementation/organization & administration ; Ill-Housed Persons/*psychology ; Housing ; Humans ; Mental Disorders/*therapy ; *Mental Health Services ; *Program Development/methods ; Qualitative Research ; Social Support ; }, abstract = {This research focused on the relationships between a national team and five project sites across Canada in planning a complex, community intervention for homeless people with mental illness called At Home/Chez Soi, which is based on the Housing First model. The research addressed two questions: (a) what are the challenges in planning? and (b) what factors that helped or hindered moving project planning forward? Using qualitative methods, 149 national, provincial, and local stakeholders participated in key informant or focus group interviews. We found that planning entails not only intervention and research tasks, but also relational processes that occur within an ecology of time, local context, and values. More specifically, the relationships between the national team and the project sites can be conceptualized as a collaborative process in which national and local partners bring different agendas to the planning process and must therefore listen to, negotiate, discuss, and compromise with one another. A collaborative process that involves power-sharing and having project coordinators at each site helped to bridge the differences between these two stakeholder groups, to find common ground, and to accomplish planning tasks within a compressed time frame. While local context and culture pushed towards unique adaptations of Housing First, the principles of the Housing First model provided a foundation for a common approach across sites and interventions. The implications of the findings for future planning and research of multi-site, complex, community interventions are noted.}, } @article {pmid22960144, year = {2013}, author = {Chang, YM and Chang, CL and Li, WH and Shih, AC}, title = {Historical profiling of maize duplicate genes sheds light on the evolution of C4 photosynthesis in grasses.}, journal = {Molecular phylogenetics and evolution}, volume = {66}, number = {2}, pages = {453-462}, doi = {10.1016/j.ympev.2012.08.009}, pmid = {22960144}, issn = {1095-9513}, mesh = {*Biological Evolution ; Cluster Analysis ; Databases, Genetic ; *Genes, Duplicate ; Genes, Plant ; Genomics/methods ; Photosynthesis/*genetics ; Phylogeny ; Zea mays/enzymology/*genetics ; }, abstract = {C4 plants evolved from C3 plants through a series of complex evolutionary steps. On the basis of the evolution of key C4 enzyme genes, the evolution of C4 photosynthesis has been considered a story of gene/genome duplications and subsequent modifications of gene function. If whole-genome duplication has contributed to the evolution of C4 photosynthesis, other genes should have been duplicated together with these C4 genes. However, which genes were co-duplicated with C4 genes and whether they have also played a role in C4 evolution are largely unknown. In this study, we developed a simple method to characterize the historical profile of the paralogs of a gene by tracing back to the most recent common ancestor (MRCA) of the gene and its paralog(s) and then counting the number of paralogs at each MRCA. We clustered the genes into clusters with similar duplication profiles and inferred their functional enrichments. Applying our method to maize, a familiar C4 plant, we identified many genes that show similar duplication profiles with those of the key C4 enzyme genes and found that the functional preferences of the C4 gene clusters are not only similar to those identified by an experimental approach in a recent study but also highly consistent with the functions required for the C4 photosynthesis evolutionary model proposed by S.F. Sage. Some of these genes might have co-evolved with the key C4 enzyme genes to increase the strength of C4 photosynthesis. Moreover, our results suggested that most key C4 enzyme genes had different origins and have undergone a long evolutionary process before the emergence of C4 grasses (Andropogoneae), consistent with the conclusion proposed by previous authors.}, } @article {pmid22952856, year = {2012}, author = {Thessen, AE and Patterson, DJ and Murray, SA}, title = {The taxonomic significance of species that have only been observed once: the genus Gymnodinium (Dinoflagellata) as an example.}, journal = {PloS one}, volume = {7}, number = {8}, pages = {e44015}, pmid = {22952856}, issn = {1932-6203}, mesh = {Classification/*methods ; Dinoflagellida/*classification ; Ecological and Environmental Phenomena ; Language ; Observer Variation ; Uncertainty ; }, abstract = {Taxonomists have been tasked with cataloguing and quantifying the Earth's biodiversity. Their progress is measured in code-compliant species descriptions that include text, images, type material and molecular sequences. It is from this material that other researchers are to identify individuals of the same species in future observations. It has been estimated that 13% to 22% (depending on taxonomic group) of described species have only ever been observed once. Species that have only been observed at the time and place of their original description are referred to as oncers. Oncers are important to our current understanding of biodiversity. They may be validly described species that are members of a rare biosphere, or they may indicate endemism, or that these species are limited to very constrained niches. Alternatively, they may reflect that taxonomic practices are too poor to allow the organism to be re-identified or that the descriptions are unknown to other researchers. If the latter are true, our current tally of species will not be an accurate indication of what we know. In order to investigate this phenomenon and its potential causes, we examined the microbial eukaryote genus Gymnodinium. This genus contains 268 extant species, 103 (38%) of which have not been observed since their original description. We report traits of the original descriptions and interpret them in respect to the status of the species. We conclude that the majority of oncers were poorly described and their identity is ambiguous. As a result, we argue that the genus Gymnodinium contains only 234 identifiable species. Species that have been observed multiple times tend to have longer descriptions, written in English. The styles of individual authors have a major effect, with a few authors describing a disproportionate number of oncers. The information about the taxonomy of Gymnodinium that is available via the internet is incomplete, and reliance on it will not give access to all necessary knowledge. Six new names are presented - Gymnodinium campbelli for the homonymous name Gymnodinium translucens Campbell 1973, Gymnodinium antarcticum for the homonymous name Gymnodinium frigidum Balech 1965, Gymnodinium manchuriensis for the homonymous name Gymnodinium autumnale Skvortzov 1968, Gymnodinium christenum for the homonymous name Gymnodinium irregulare Christen 1959, Gymnodinium conkufferi for the homonymous name Gymnodinium irregulare Conrad & Kufferath 1954 and Gymnodinium chinensis for the homonymous name Gymnodinium frigidum Skvortzov 1968.}, } @article {pmid22951575, year = {2012}, author = {Bouquet, J and Cherel, P and Pavio, N}, title = {Genetic characterization and codon usage bias of full-length Hepatitis E virus sequences shed new lights on genotypic distribution, host restriction and genome evolution.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {12}, number = {8}, pages = {1842-1853}, doi = {10.1016/j.meegid.2012.07.021}, pmid = {22951575}, issn = {1567-7257}, mesh = {Animals ; *Codon ; Computational Biology ; Evolution, Molecular ; Feces/virology ; Genes, Viral ; *Genome, Viral ; Genotype ; Hepatitis E/veterinary/*virology ; Hepatitis E virus/classification/*genetics ; Host-Pathogen Interactions ; Humans ; Open Reading Frames ; Phylogeny ; Statistics, Nonparametric ; Swine ; Viral Proteins/chemistry/genetics ; Zoonoses/virology ; }, abstract = {Hepatitis E virus (HEV) is present in different species and ecological niches. It has been divided into 4 major mammalian genotypes. In this study, 3 new full-length genomes of swine HEV were sequenced and the results did not reveal any particular host determinant in comparison with human isolates belonging to the same genotype. Nucleotide composition and codon usage bias were determined to characterize HEV host restriction and genome evolution. Peculiar nucleotide bias was observed for A and C nucleotides in all HEV genotypes. Apart from the ORF1 hypervariable region and the ORF2/3 overlapping region, no nucleotide bias was observed between the 3 codon positions. CpG dinucleotides were also shown to be under-represented in HEV as in most RNA viruses. The effective number of codon used in HEV genome was high, indicating a lack of codon bias. Correspondence analysis of the relative synonymous codon usage was performed and demonstrated that evolution of HEV is not driven by geographical or host factors, but is representative of HEV phylogeny. These results confirm that HEV genome evolution is mainly based on mutational pressure. Natural selection, for instance involving fine-tuning translation kinetics and escape from the host immune system, may also play a role in shaping the HEV genome, particularly in the ORF1 hypervariable region and the ORF2/3 overlapping region. These regions might be involved in host restriction. Finally this study revealed the need to re-evaluate the possible subtyping classification.}, } @article {pmid22941988, year = {2012}, author = {Moretti, S and Murri, R and Maffioletti, S and Kuzniar, A and Castella, B and Salamin, N and Robinson-Rechavi, M and Stockinger, H}, title = {gcodeml: a Grid-enabled tool for detecting positive selection in biological evolution.}, journal = {Studies in health technology and informatics}, volume = {175}, number = {}, pages = {59-68}, pmid = {22941988}, issn = {0926-9630}, mesh = {*Algorithms ; DNA/*genetics ; Data Mining/*methods ; *Databases, Genetic ; *Evolution, Molecular ; Proteins/*genetics ; Sequence Analysis/*methods ; *Software ; *User-Computer Interface ; }, abstract = {One of the important questions in biological evolution is to know if certain changes along protein coding genes have contributed to the adaptation of species. This problem is known to be biologically complex and computationally very expensive. It, therefore, requires efficient Grid or cluster solutions to overcome the computational challenge. We have developed a Grid-enabled tool (gcodeml) that relies on the PAML (codeml) package to help analyse large phylogenetic datasets on both Grids and computational clusters. Although we report on results for gcodeml, our approach is applicable and customisable to related problems in biology or other scientific domains.}, } @article {pmid22937805, year = {2012}, author = {Dorazio, RM}, title = {Predicting the geographic distribution of a species from presence-only data subject to detection errors.}, journal = {Biometrics}, volume = {68}, number = {4}, pages = {1303-1312}, doi = {10.1111/j.1541-0420.2012.01779.x}, pmid = {22937805}, issn = {1541-0420}, mesh = {*Algorithms ; *Artifacts ; *Censuses ; *Data Interpretation, Statistical ; Demography/*statistics & numerical data ; Sample Size ; }, abstract = {Several models have been developed to predict the geographic distribution of a species by combining measurements of covariates of occurrence at locations where the species is known to be present with measurements of the same covariates at other locations where species occurrence status (presence or absence) is unknown. In the absence of species detection errors, spatial point-process models and binary-regression models for case-augmented surveys provide consistent estimators of a species' geographic distribution without prior knowledge of species prevalence. In addition, these regression models can be modified to produce estimators of species abundance that are asymptotically equivalent to those of the spatial point-process models. However, if species presence locations are subject to detection errors, neither class of models provides a consistent estimator of covariate effects unless the covariates of species abundance are distinct and independently distributed from the covariates of species detection probability. These analytical results are illustrated using simulation studies of data sets that contain a wide range of presence-only sample sizes. Analyses of presence-only data of three avian species observed in a survey of landbirds in western Montana and northern Idaho are compared with site-occupancy analyses of detections and nondetections of these species.}, } @article {pmid22937656, year = {2012}, author = {Li, JY and Hu, YM and Chen, W and Liu, M and Hu, JB and Zhong, QL and Lu, N}, title = {[Spatial distribution characteristics of urban potential population in Shenyang City based on QuickBird image and GIS].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {23}, number = {6}, pages = {1649-1654}, pmid = {22937656}, issn = {1001-9332}, mesh = {China ; *City Planning ; Conservation of Natural Resources/*methods ; *Ecosystem ; *Environment Design ; Geographic Information Systems ; Population Density ; Remote Sensing Technology ; Urban Population ; }, abstract = {Population is the most active factor affecting city development. To understand the distribution characteristics of urban population is of significance for making city policy decisions and for optimizing the layout of various urban infrastructures. In this paper, the information of the residential buildings in Shenyang urban area was extracted from the QuickBird remote sensing images, and the spatial distribution characteristics of the population within the Third-Ring Road of the City were analyzed, according to the social and economic statistics data. In 2010, the population density in different types of residential buildings within the Third-Ring Road of the City decreased in the order of high-storey block, mixed block, mixed garden, old multi-storey building, high-storey garden, multi-storey block, multi-storey garden, villa block, shanty, and villa garden. The vacancy rate of the buildings within the Third-Ring Road was more than 30%, meaning that the real estate market was seriously overstocked. Among the five Districts of Shenyang City, Shenhe District had the highest potential population density, while Tiexi District and Dadong District had a lower one. The gravity center of the City and its five Districts was also analyzed, which could provide basic information for locating commercial facilities and planning city infrastructure.}, } @article {pmid22934781, year = {2012}, author = {Pallmann, P and Schaarschmidt, F and Hothorn, LA and Fischer, C and Nacke, H and Priesnitz, KU and Schork, NJ}, title = {Assessing group differences in biodiversity by simultaneously testing a user-defined selection of diversity indices.}, journal = {Molecular ecology resources}, volume = {12}, number = {6}, pages = {1068-1078}, pmid = {22934781}, issn = {1755-0998}, support = {5 UL1 RR025774/RR/NCRR NIH HHS/United States ; 5 R01 AG035020/AG/NIA NIH HHS/United States ; R01 DA030976/DA/NIDA NIH HHS/United States ; U19 AG023122/AG/NIA NIH HHS/United States ; 5 P01 AG027734/AG/NIA NIH HHS/United States ; 5 R01 HL089655/HL/NHLBI NIH HHS/United States ; 2 U19 AI063603/AI/NIAID NIH HHS/United States ; U01 DA024417/DA/NIDA NIH HHS/United States ; 5 R01 DA030976/DA/NIDA NIH HHS/United States ; R01 MH093500/MH/NIMH NIH HHS/United States ; U19 AI063603/AI/NIAID NIH HHS/United States ; 2 U19 AG023122/AG/NIA NIH HHS/United States ; P01 AG027734/AG/NIA NIH HHS/United States ; 1 R01 MH093500/MH/NIMH NIH HHS/United States ; UL1 RR025774/RR/NCRR NIH HHS/United States ; R01 HL089655/HL/NHLBI NIH HHS/United States ; R01 AG035020/AG/NIA NIH HHS/United States ; 5 U01 DA024417/DA/NIDA NIH HHS/United States ; }, mesh = {*Biodiversity ; Biostatistics/*methods ; *Data Interpretation, Statistical ; Software ; }, abstract = {Comparing diversities between groups is a task biologists are frequently faced with, for example in ecological field trials or when dealing with metagenomics data. However, researchers often waver about which measure of diversity to choose as there is a multitude of approaches available. As Jost (2008, Molecular Ecology, 17, 4015) has pointed out, widely used measures such as the Shannon or Simpson index have undesirable properties which make them hard to compare and interpret. Many of the problems associated with the use of these 'raw' indices can be corrected by transforming them into 'true' diversity measures. We introduce a technique that allows the comparison of two or more groups of observations and simultaneously tests a user-defined selection of a number of 'true' diversity measures. This procedure yields multiplicity-adjusted P-values according to the method of Westfall and Young (1993, Resampling-Based Multiple Testing: Examples and Methods for p-Value Adjustment, 49, 941), which ensures that the rate of false positives (type I error) does not rise when the number of groups and/or diversity indices is extended. Software is available in the R package 'simboot'.}, } @article {pmid22934641, year = {2012}, author = {Roossinck, MJ}, title = {Plant virus metagenomics: biodiversity and ecology.}, journal = {Annual review of genetics}, volume = {46}, number = {}, pages = {359-369}, doi = {10.1146/annurev-genet-110711-155600}, pmid = {22934641}, issn = {1545-2948}, mesh = {Base Sequence ; Computational Biology ; *Ecosystem ; *Environmental Microbiology ; Evolution, Molecular ; *Genetic Variation ; *Genome, Viral ; Information Storage and Retrieval ; Metagenomics/methods ; Plant Diseases/virology ; Plant Viruses/*genetics ; Plants/virology ; RNA, Small Interfering/genetics ; }, abstract = {Viral metagenomics is the study of viruses in environmental samples, using next generation sequencing that produces very large data sets. For plant viruses, these studies are still relatively new, but are already indicating that our current knowledge grossly underestimates the diversity of these viruses. Some plant virus studies are using thousands of individual plants so that each sequence can be traced back to its precise host. These studies should allow for deeper ecological and evolutionary analyses. The finding of so many new plant viruses that do not cause any obvious symptoms in wild plant hosts certainly changes our perception of viruses and how they interact with their hosts. The major difficulty in these (as in all) metagenomic studies continues to be the need for better bioinformatics tools to decipher the large data sets. The implications of this new information on plant viruses for international agriculture remain to be addressed.}, } @article {pmid22925629, year = {2012}, author = {Weiser, EL and Grueber, CE and Jamieson, IG}, title = {AlleleRetain: a program to assess management options for conserving allelic diversity in small, isolated populations.}, journal = {Molecular ecology resources}, volume = {12}, number = {6}, pages = {1161-1167}, doi = {10.1111/j.1755-0998.2012.03176.x}, pmid = {22925629}, issn = {1755-0998}, mesh = {*Alleles ; Animals ; Computational Biology/*methods ; *Genetic Variation ; Genetics, Population/*methods ; *Software ; Statistics as Topic ; }, abstract = {Preserving genetic health is an important aspect of species conservation. Allelic diversity is particularly important to conserve, as it provides capacity for adaptation and thus enables long-term population viability. Allele retention is difficult to predict beyond one generation for real populations with complex demography and life-history traits, so we developed a computer model to simulate allele retention in small populations. AlleleRetain is an individual-based model implemented in r and can be applied to assess management options for conserving allelic diversity in small populations of animals with overlapping generations. AlleleRetain remedies the limitations of similar existing software, and its source code is freely available for further modification. AlleleRetain and its supporting materials can be downloaded from https://sites.google.com/site/alleleretain/ or CRAN (http://cran.r-project.org).}, } @article {pmid22925603, year = {2012}, author = {Robledo-Arnuncio, JJ and Grivet, D and Smouse, PE and Sork, VL}, title = {PSA: software for parental structure analysis of seed or seedling patches.}, journal = {Molecular ecology resources}, volume = {12}, number = {6}, pages = {1180-1189}, doi = {10.1111/1755-0998.12005}, pmid = {22925603}, issn = {1755-0998}, mesh = {Computational Biology/methods ; Genotype ; Inheritance Patterns ; Molecular Biology/methods ; Plants/*genetics ; Seedlings/*genetics ; Seeds/*genetics ; *Software ; }, abstract = {Parental structure analysis (PSA) is a computer program to analyse separate contributions of paternal and maternal parents to postdispersal plant offspring. The program provides joint estimates of maternal, paternal and cross-parental correlations within and among a set of predefined groups of seeds or seedlings, as well as derivative estimates of effective parental numbers. PSA utilizes data sets that distinguish between maternal and paternal contributions to the genotype of each offspring in the sample, but does not require parental samples per se. The approach requires assay of codominant diploid markers from both seed coat (maternally inherited) and seedling/embryo (biparentally inherited) tissues for each offspring. A simulation analysis of PSA's performance shows that it provides fairly accurate parental correlation estimates from affordable sampling effort. PSA should be of interest to plant biologists studying the interplay between dispersal, demography and genetics, as well as plant-animal interactions.}, } @article {pmid22924343, year = {2013}, author = {Whitmee, S and Orme, CD}, title = {Predicting dispersal distance in mammals: a trait-based approach.}, journal = {The Journal of animal ecology}, volume = {82}, number = {1}, pages = {211-221}, doi = {10.1111/j.1365-2656.2012.02030.x}, pmid = {22924343}, issn = {1365-2656}, mesh = {Animals ; Databases, Factual ; Demography ; Mammals/*classification/genetics/*physiology ; *Models, Biological ; Phylogeny ; Species Specificity ; }, abstract = {Dispersal is one of the principal mechanisms influencing ecological and evolutionary processes but quantitative empirical data are unfortunately scarce. As dispersal is likely to influence population responses to climate change, whether by adaptation or by migration, there is an urgent need to obtain estimates of dispersal distance. Cross-species correlative approaches identifying predictors of dispersal distance can provide much-needed insights into this data-scarce area. Here, we describe the compilation of a new data set of natal dispersal distances and use it to test life-history predictors of dispersal distance in mammals and examine the strength of the phylogenetic signal in dispersal distance. We find that both maximum and median dispersal distances have strong phylogenetic signals. No single model performs best in describing either maximum or median dispersal distances when phylogeny is taken into account but many models show high explanatory power, suggesting that dispersal distance per generation can be estimated for mammals with comparatively little data availability. Home range area, geographic range size and body mass are identified as the most important terms across models. Cross-validation of models supports the ability of these variables to predict dispersal distances, suggesting that models may be extended to species where dispersal distance is unknown.}, } @article {pmid22923770, year = {2013}, author = {Shifotoka, A and Fogarty, AW}, title = {Is the human sex ratio at birth a sentinel health indicator that is associated with HIV/AIDS and tuberculosis prevalences in the 21st century?.}, journal = {Journal of epidemiology and community health}, volume = {67}, number = {4}, pages = {327-331}, doi = {10.1136/jech-2011-200744}, pmid = {22923770}, issn = {1470-2738}, mesh = {Adult ; Birth Rate/*trends ; Confounding Factors, Epidemiologic ; Databases, Factual ; Environmental Exposure ; Female ; Global Health/statistics & numerical data ; HIV Infections/*epidemiology ; *Health Status Indicators ; Humans ; Male ; Middle Aged ; Prevalence ; Sentinel Surveillance ; *Sex Ratio ; Tuberculosis, Pulmonary/*epidemiology ; World Health Organization ; Young Adult ; }, abstract = {BACKGROUND: A reduction in sex ratio at live birth has been proposed as a sentinel health indicator that can be used to monitor the health of populations.

OBJECTIVE: To test the hypothesis that a lower sex ratio is associated with adverse national population health using the prevalences of HIV and tuberculosis as measures of societal well-being.

METHODS: An ecological study design using routinely collected data and adjusting for potential confounding factors.

RESULTS: The mean global sex ratio was 1.05. There was marked heterogeneity in the sex ratio between different global regions (p<0.0001). Those regions with the highest prevalences of HIV infection had lower sex ratios, with the value for the highest quartile being 0.022 (95% CIs CI 0.013 to 0.031) lower than the lowest quartile. Similarly, those areas with the highest quartile of tuberculosis infection had a sex ratio of 0.016 (95% CI 0.004 to 0.028) lower than those in the lowest quartile. Similar results were observed in a subgroup analysis limited to countries from the African continent.

CONCLUSIONS: The data are consistent with the hypothesis that a reduced sex ratio at live birth is a potential sentinel health indicator of lower population health. However, these data do not demonstrate either a casual relationship or reveal any biological mechanisms that may account for these observations.}, } @article {pmid22912854, year = {2012}, author = {Qiao, H and Lin, C and Ji, L and Jiang, Z}, title = {mMWeb--an online platform for employing multiple ecological niche modeling algorithms.}, journal = {PloS one}, volume = {7}, number = {8}, pages = {e43327}, pmid = {22912854}, issn = {1932-6203}, mesh = {*Algorithms ; Computational Biology/*methods ; Ecology/*methods ; *Ecosystem ; *Internet ; *Models, Biological ; *Software ; }, abstract = {BACKGROUND: Predicting the ecological niche and potential habitat distribution of a given organism is one of the central domains of ecological and biogeographical research. A wide variety of modeling techniques have been developed for this purpose. In order to implement these models, the users must prepare a specific runtime environment for each model, learn how to use multiple model platforms, and prepare data in a different format each time. Additionally, often model results are difficult to interpret, and a standardized method for comparing model results across platforms does not exist. We developed a free and open source online platform, the multi-models web-based (mMWeb) platform, to address each of these problems, providing a novel environment in which the user can implement and compare multiple ecological niche model (ENM) algorithms.

METHODOLOGY: mMWeb combines 18 existing ENMs and their corresponding algorithms and provides a uniform procedure for modeling the potential habitat niche of a species via a common web browser. mMWeb uses Java Native Interface (JNI), Java R Interface to combine the different ENMs and executes multiple tasks in parallel on a super computer. The cross-platform, user-friendly interface of mMWeb simplifies the process of building ENMs, providing an accessible and efficient environment from which to explore and compare different model algorithms.}, } @article {pmid22912736, year = {2012}, author = {Leprieur, F and Albouy, C and De Bortoli, J and Cowman, PF and Bellwood, DR and Mouillot, D}, title = {Quantifying phylogenetic beta diversity: distinguishing between 'true' turnover of lineages and phylogenetic diversity gradients.}, journal = {PloS one}, volume = {7}, number = {8}, pages = {e42760}, pmid = {22912736}, issn = {1932-6203}, mesh = {Animals ; Computational Biology/*methods ; Coral Reefs ; *Evolution, Molecular ; Fishes/genetics ; *Genetic Linkage ; *Genetic Variation ; *Phylogeny ; }, abstract = {The evolutionary dissimilarity between communities (phylogenetic beta diversity PBD) has been increasingly explored by ecologists and biogeographers to assess the relative roles of ecological and evolutionary processes in structuring natural communities. Among PBD measures, the PhyloSor and UniFrac indices have been widely used to assess the level of turnover of lineages over geographical and environmental gradients. However, these indices can be considered as 'broad-sense' measures of phylogenetic turnover as they incorporate different aspects of differences in evolutionary history between communities that may be attributable to phylogenetic diversity gradients. In the present study, we extend an additive partitioning framework proposed for compositional beta diversity to PBD. Specifically, we decomposed the PhyloSor and UniFrac indices into two separate components accounting for 'true' phylogenetic turnover and phylogenetic diversity gradients, respectively. We illustrated the relevance of this framework using simple theoretical and archetypal examples, as well as an empirical study based on coral reef fish communities. Overall, our results suggest that using PhyloSor and UniFrac may greatly over-estimate the level of spatial turnover of lineages if the two compared communities show contrasting levels of phylogenetic diversity. We therefore recommend that future studies use the 'true' phylogenetic turnover component of these indices when the studied communities encompass a large phylogenetic diversity gradient.}, } @article {pmid22912699, year = {2012}, author = {Pitzer, VE and Atkins, KE and de Blasio, BF and Van Effelterre, T and Atchison, CJ and Harris, JP and Shim, E and Galvani, AP and Edmunds, WJ and Viboud, C and Patel, MM and Grenfell, BT and Parashar, UD and Lopman, BA}, title = {Direct and indirect effects of rotavirus vaccination: comparing predictions from transmission dynamic models.}, journal = {PloS one}, volume = {7}, number = {8}, pages = {e42320}, pmid = {22912699}, issn = {1932-6203}, support = {R01 GM083983/GM/NIGMS NIH HHS/United States ; R24 HD047879/HD/NICHD NIH HHS/United States ; R01 GM083983-01/GM/NIGMS NIH HHS/United States ; }, mesh = {Computational Biology/*methods ; *Models, Statistical ; Rotavirus/*physiology ; Rotavirus Infections/epidemiology/*prevention & control/*transmission ; Time Factors ; *Vaccination ; }, abstract = {Early observations from countries that have introduced rotavirus vaccination suggest that there may be indirect protection for unvaccinated individuals, but it is unclear whether these benefits will extend to the long term. Transmission dynamic models have attempted to quantify the indirect protection that might be expected from rotavirus vaccination in developed countries, but results have varied. To better understand the magnitude and sources of variability in model projections, we undertook a comparative analysis of transmission dynamic models for rotavirus. We fit five models to reported rotavirus gastroenteritis (RVGE) data from England and Wales, and evaluated outcomes for short- and long-term vaccination effects. All of our models reproduced the important features of rotavirus epidemics in England and Wales. Models predicted that during the initial year after vaccine introduction, incidence of severe RVGE would be reduced 1.8-2.9 times more than expected from the direct effects of the vaccine alone (28-50% at 90% coverage), but over a 5-year period following vaccine introduction severe RVGE would be reduced only by 1.1-1.7 times more than expected from the direct effects (54-90% at 90% coverage). Projections for the long-term reduction of severe RVGE ranged from a 55% reduction at full coverage to elimination with at least 80% coverage. Our models predicted short-term reductions in the incidence of RVGE that exceeded estimates of the direct effects, consistent with observations from the United States and other countries. Some of the models predicted that the short-term indirect benefits may be offset by a partial shifting of the burden of RVGE to older unvaccinated individuals. Nonetheless, even when such a shift occurs, the overall reduction in severe RVGE is considerable. Discrepancies among model predictions reflect uncertainties about age variation in the risk and reporting of RVGE, and the duration of natural and vaccine-induced immunity, highlighting important questions for future research.}, } @article {pmid22910727, year = {2012}, author = {Pilgrim, NA and Blum, RW}, title = {Adolescent mental and physical health in the English-speaking Caribbean.}, journal = {Revista panamericana de salud publica = Pan American journal of public health}, volume = {32}, number = {1}, pages = {62-69}, doi = {10.1590/s1020-49892012000700010}, pmid = {22910727}, issn = {1680-5348}, mesh = {Adolescent ; *Adolescent Behavior ; Caribbean Region/epidemiology ; Child ; Databases, Bibliographic ; Depression/epidemiology ; Diabetes Mellitus, Type 2/*epidemiology ; Family ; Feeding and Eating Disorders/epidemiology ; Female ; Humans ; Hypertension/*epidemiology ; Male ; Mental Disorders/*epidemiology ; *Psychology, Adolescent ; Research Design ; Risk-Taking ; Socioeconomic Factors ; Substance-Related Disorders/epidemiology ; Suicide, Attempted/statistics & numerical data ; Violence ; Young Adult ; }, abstract = {OBJECTIVE: Bronfenbrenner's ecological systems theory, a multisystem framework, was used to identify risk and protective factors associated with adolescent mental and physical health (AMPH) in the English-speaking Caribbean.

METHODS: A structured literature review, using the online databases of Medline, PsychInfo, and Scopus, was conducted to identify peer-reviewed studies published between January 1998 and July 2011 focused on adolescents ages 10-19 years.

RESULTS: Sixty-eight articles were examined: 40 on adolescent mental health (AMH), 27 on adolescent physical health (APH), and 1 on both topics. Key individual factors included gender and age. Religiosity and engagement in other risk behaviors were associated with AMH, while the presence of other chronic illnesses affected APH. Significant determinants of AMH in the microsystem included family and school connectedness, family structure, and socioeconomic status. Maternal obesity, parental education, and school environment influenced APH. Studies that investigated macrosystem factors reported few consistent findings related to AMPH. A history of family mental health problems and physical and sexual abuse was significantly associated with AMH in the chronosystem, while a family history of diabetes and low birth weight were associated with APH. Studies did not examine the exosystem or the mesosystem.

CONCLUSIONS: AMPH in the English-speaking Caribbean is affected by a variety factors in developing adolescents and their surroundings. Gender, family, and early exposure to negative environments are salient factors influencing AMPH and present potential avenues for prevention and intervention. A fuller understanding of AMPH in this region, however, requires scientifically rigorous studies that incorporate a multisystem approach.}, } @article {pmid22905118, year = {2012}, author = {Malcevschi, S and Marchini, A and Savini, D and Facchinetti, T}, title = {Opportunities for web-based indicators in environmental sciences.}, journal = {PloS one}, volume = {7}, number = {8}, pages = {e42128}, pmid = {22905118}, issn = {1932-6203}, mesh = {Air ; Conservation of Natural Resources/methods ; Databases, Factual ; Ecology/*methods ; Ecosystem ; Environment ; Environmental Monitoring/methods ; Internet ; Search Engine ; Time Factors ; Water ; }, abstract = {This paper proposes a set of web-based indicators for quantifying and ranking the relevance of terms related to key-issues in Ecology and Sustainability Science. Search engines that operate in different contexts (e.g. global, social, scientific) are considered as web information carriers (WICs) and are able to analyse; (i) relevance on different levels: global web, individual/personal sphere, on-line news, and culture/science; (ii) time trends of relevance; (iii) relevance of keywords for environmental governance. For the purposes of this study, several indicators and specific indices (relational indices and dynamic indices) were applied to a test-set of 24 keywords. Outputs consistently show that traditional study topics in environmental sciences such as water and air have remained the most quantitatively relevant keywords, while interest in systemic issues (i.e. ecosystem and landscape) has grown over the last 20 years. Nowadays, the relevance of new concepts such as resilience and ecosystem services is increasing, but the actual ability of these concepts to influence environmental governance needs to be further studied and understood. The proposed approach, which is based on intuitive and easily replicable procedures, can support the decision-making processes related to environmental governance.}, } @article {pmid22902357, year = {2013}, author = {Kwon, JW and Lee, HJ and Hyun, MK and Choi, JE and Kim, JH and Lee, NR and Hwang, JS and Lee, EJ}, title = {Trends in the incidence of subarachnoid hemorrhage in South Korea from 2006-2009: an ecological study.}, journal = {World neurosurgery}, volume = {79}, number = {3-4}, pages = {499-503}, doi = {10.1016/j.wneu.2012.07.032}, pmid = {22902357}, issn = {1878-8769}, mesh = {Adolescent ; Adult ; Age Factors ; Aged ; Aged, 80 and over ; Data Interpretation, Statistical ; Databases, Factual ; Environment ; Female ; Humans ; International Classification of Diseases ; Male ; Middle Aged ; National Health Programs/statistics & numerical data ; Prevalence ; Republic of Korea/epidemiology ; Sex Factors ; Subarachnoid Hemorrhage/*epidemiology ; Young Adult ; }, abstract = {OBJECTIVE: The purpose of this study is to investigate trends in the incidence of subarachnoid hemorrhage (SAH) in South Korea from 2006-2009.

METHODS: We used the national health claim database managed by Health Insurance Review and Assessment Service, which contains all hospital records of every Korean citizen. Patients with SAH were defined as International Classification of Diseases-10 codes with a hospitalization period of ≥ 14 days or death within 14 days of hospitalization. We evaluated trends in the incidence of SAH during a 4-year period using the Cochran-Armitage trend test.

RESULTS: We identified 35,263 patients with SAH among adult patients (≥ 18 years old) from 2005-2009. Age-adjusted SAH incidence rates decreased from 13.4 in 2006 to 12.4 in 2009/100,000 men (P = 0.0025) and women also showed a decrease from 19.4-17.3/100,000 (P < 0.0001). However, this decreasing pattern was not shown in patients less than 50 years of age. SAH incidence showed gender differences dependent on age; men who were 40 years old or less had a higher incidence than women.

CONCLUSIONS: The age-adjusted incidence rates of SAH were slightly decreased in South Korea. Further research should be conducted to identify the clinical risk factors to reduce SAH incidence rates even more, especially in younger people.}, } @article {pmid22902072, year = {2012}, author = {Pavey, SA and Bernatchez, L and Aubin-Horth, N and Landry, CR}, title = {What is needed for next-generation ecological and evolutionary genomics?.}, journal = {Trends in ecology & evolution}, volume = {27}, number = {12}, pages = {673-678}, doi = {10.1016/j.tree.2012.07.014}, pmid = {22902072}, issn = {1872-8383}, mesh = {*Biological Evolution ; Data Interpretation, Statistical ; Databases, Factual ; *Ecosystem ; Genetic Variation ; Genomics/*methods ; Models, Genetic ; }, abstract = {Ecological and evolutionary genomics (EEG) aims to link gene functions and genomic features to phenotypes and ecological factors. Although the rapid development of technologies allows central questions to be addressed at an unprecedented level of molecular detail, they do not alleviate one of the major challenges of EEG, which is that a large fraction of genes remains without any annotation. Here, we propose two solutions to this challenge. The first solution is in the form of a database that regroups associations between genes, organismal attributes and abiotic and biotic conditions. This database would result in an ecological annotation of genes by allowing cross-referencing across studies and taxa. Our second solution is to use new functional techniques to characterize genes implicated in the response to ecological challenges.}, } @article {pmid22900027, year = {2012}, author = {Faircloth, BC and Glenn, TC}, title = {Not all sequence tags are created equal: designing and validating sequence identification tags robust to indels.}, journal = {PloS one}, volume = {7}, number = {8}, pages = {e42543}, pmid = {22900027}, issn = {1932-6203}, mesh = {Computational Biology/methods ; DNA Mutational Analysis/methods ; *Expressed Sequence Tags ; *High-Throughput Nucleotide Sequencing ; *INDEL Mutation ; Internet ; Reproducibility of Results ; Software ; }, abstract = {Ligating adapters with unique synthetic oligonucleotide sequences (sequence tags) onto individual DNA samples before massively parallel sequencing is a popular and efficient way to obtain sequence data from many individual samples. Tag sequences should be numerous and sufficiently different to ensure sequencing, replication, and oligonucleotide synthesis errors do not cause tags to be unrecoverable or confused. However, many design approaches only protect against substitution errors during sequencing and extant tag sets contain too few tag sequences. We developed an open-source software package to validate sequence tags for conformance to two distance metrics and design sequence tags robust to indel and substitution errors. We use this software package to evaluate several commercial and non-commercial sequence tag sets, design several large sets (max(count) = 7,198) of edit metric sequence tags having different lengths and degrees of error correction, and integrate a subset of these edit metric tags to polymerase chain reaction (PCR) primers and sequencing adapters. We validate a subset of these edit metric tagged PCR primers and sequencing adapters by sequencing on several platforms and subsequent comparison to commercially available alternatives. We find that several commonly used sets of sequence tags or design methodologies used to produce sequence tags do not meet the minimum expectations of their underlying distance metric, and we find that PCR primers and sequencing adapters incorporating edit metric sequence tags designed by our software package perform as well as their commercial counterparts. We suggest that researchers evaluate sequence tags prior to use or evaluate tags that they have been using. The sequence tag sets we design improve on extant sets because they are large, valid across the set, and robust to the suite of substitution, insertion, and deletion errors affecting massively parallel sequencing workflows on all currently used platforms.}, } @article {pmid22898652, year = {2012}, author = {Nekrutenko, A and Taylor, J}, title = {Next-generation sequencing data interpretation: enhancing reproducibility and accessibility.}, journal = {Nature reviews. Genetics}, volume = {13}, number = {9}, pages = {667-672}, pmid = {22898652}, issn = {1471-0064}, support = {U41 HG006620/HG/NHGRI NIH HHS/United States ; HG005133/HG/NHGRI NIH HHS/United States ; HG006620/HG/NHGRI NIH HHS/United States ; HG004909/HG/NHGRI NIH HHS/United States ; }, mesh = {Access to Information ; Base Sequence ; Data Interpretation, Statistical ; Genetic Privacy ; High-Throughput Nucleotide Sequencing/*methods/*trends ; Humans ; Molecular Sequence Data ; Reproducibility of Results ; Sequence Analysis, DNA/*methods/*trends ; }, abstract = {Areas of life sciences research that were previously distant from each other in ideology, analysis practices and toolkits, such as microbial ecology and personalized medicine, have all embraced techniques that rely on next-generation sequencing instruments. Yet the capacity to generate the data greatly outpaces our ability to analyse it. Existing sequencing technologies are more mature and accessible than the methodologies that are available for individual researchers to move, store, analyse and present data in a fashion that is transparent and reproducible. Here we discuss currently pressing issues with analysis, interpretation, reproducibility and accessibility of these data, and we present promising solutions and venture into potential future developments.}, } @article {pmid22898144, year = {2012}, author = {, and Abelló, P and Ai, W and Altmann, C and Bernardi, G and Bonato, O and Burchhardt, KM and Chen, X and Chen, Z and Cížková, D and Clouet, C and Cubeta, MA and Garcia-Merchan, VH and Gauthier, N and Gibson, S and Halačka, K and Hamdi, F and Hankeln, T and Hochkirch, A and Hrbek, T and Jackson, AM and Lin, C and Lin, SM and Macpherson, E and Macrander, J and Marešová, E and Mendel, J and Nowak, M and Orti, G and Palero, F and Papoušek, I and Pascual, M and Schmitt, T and Semmens, BX and Streito, JC and Tian, EW and Tseng, SP and Veith, M and Vetešník, L and Wang, HY and Weyer, J and Willis, S and Yu, H and Zhou, Z}, title = {Permanent genetic resources added to molecular ecology resources database 1 April 2012 - 31 May 2012.}, journal = {Molecular ecology resources}, volume = {12}, number = {5}, pages = {972-974}, doi = {10.1111/j.1755-0998.2012.03173.x}, pmid = {22898144}, issn = {1755-0998}, mesh = {Animals ; Computational Biology/*methods ; *Databases, Genetic ; Ecology/*methods ; Fungi ; *Microsatellite Repeats ; }, abstract = {This article documents the addition of 123 microsatellite marker loci to the Molecular Ecology Resources Database. Loci were developed for the following species: Brenthis ino, Cichla orinocensis, Cichla temensis, Epinephelus striatus, Gobio gobio, Liocarcinus depurator, Macrolophus pygmaeus, Monilinia vaccinii-corymbosi, Pelochelys cantorii, Philotrypesis josephi, Romanogobio vladykovi, Takydromus luyeanus and Takydromus viridipunctatus. These loci were cross-tested on the following species: Cichla intermedia, Cichla ocellaris, Cichla pinima, Epinephelus acanthistius, Gobio carpathicus, Gobio obtusirostris, Gobio sp. 1, Gobio volgensis, Macrolophus costalis, Macrolophus melanotoma, Macrolophus pygmaeus, Romanogobio albipinnatus, Romanogobio banaticus, Romanogobio belingi, Romanogobio kesslerii, Romanogobio parvus, Romanogobio pentatrichus, Romanogobio uranoscopus, Takydromus formosanus, Takydromus hsuehshanesis and Takydromus stejnegeri.}, } @article {pmid22896561, year = {2012}, author = {Meirmans, PG}, title = {AMOVA-based clustering of population genetic data.}, journal = {The Journal of heredity}, volume = {103}, number = {5}, pages = {744-750}, doi = {10.1093/jhered/ess047}, pmid = {22896561}, issn = {1465-7333}, mesh = {Algorithms ; Bayes Theorem ; *Cluster Analysis ; Computer Simulation ; *Databases, Genetic ; *Genetics, Population ; Models, Biological ; Software ; }, abstract = {Determining the genetic structure of populations is becoming an increasingly important aspect of genetic studies. One of the most frequently used methods is the calculation of F-statistics using an Analysis of Molecular Variance (AMOVA). However, this has the drawback that the population hierarchy has to be known a priori. Therefore, the population structure is often based on the results of a clustering analysis. Here I show how these two steps, clustering and calculation of F-statistics, can be combined in a single analysis. I do this by showing how the AMOVA framework is theoretically related to the widely used method of K-means clustering and can be used for the clustering of populations into groups. Simulations were used to show that the method performed very well both under random mating and under nonrandom mating. However, when the migration rates were high, the results were better under random mating than under predominant selfing or clonal reproduction. Two summary statistics were tested for estimating the number of clusters. Overall, pseudo-F showed the better performance, but BIC is better for detecting whether any significant structure is present. The results show that the AMOVA-based K-means clustering is useful for clustering population genetic data. Programs to perform the clustering can be downloaded from www.patrickmeirmans.com/software.}, } @article {pmid22893308, year = {2013}, author = {Stahl, C and Cimorelli, A}, title = {A demonstration of the necessity and feasibility of using a clumsy decision analytic approach on wicked environmental problems.}, journal = {Integrated environmental assessment and management}, volume = {9}, number = {1}, pages = {17-30}, doi = {10.1002/ieam.1356}, pmid = {22893308}, issn = {1551-3793}, mesh = {Air/analysis ; Air Pollution/statistics & numerical data ; Data Interpretation, Statistical ; *Decision Making ; Ecology ; *Environment ; Environmental Policy ; Feasibility Studies ; United States ; *United States Environmental Protection Agency ; }, abstract = {Because controversy, conflict, and lawsuits frequently characterize US Environmental Protection Agency (USEPA) decisions, it is important that USEPA decision makers understand how to evaluate and then make decisions that have simultaneously science-based, social, and political implications. Air quality management is one category of multidimensional decision making at USEPA. The Philadelphia, Pennsylvania metropolitan area experiences unhealthy levels of ozone, fine particulate matter, and air toxics. Many ozone precursors are precursors for particulate matter and certain air toxics. Additionally, some precursors for particulate matter are air toxics. However, air quality management practices have typically evaluated these problems separately. This approach has led to the development of independent (and potentially counterproductive) implementation strategies. This is a methods article about the necessity and feasibility of using a clumsy approach on wicked problems, using an example case study. Air quality management in Philadelphia is a wicked problem. Wicked problems are those where stakeholders define or view the problem differently, there are many different ways to describe the problem (i.e., different dimensions or levels of abstraction), no efficient or optimal solutions exist, and they are often complicated by moral, political, or professional dimensions. The USEPA has developed the multicriteria integrated resource assessment (MIRA) decision analytic approach that engages stakeholder participation through transparency, transdisciplinary learning, and the explicit use of value sets; in other words, a clumsy approach. MIRA's approach to handling technical indicators, expert judgment, and stakeholder values makes it a potentially effective method for tackling wicked environmental problems.}, } @article {pmid22893288, year = {2012}, author = {Vankudavath, RN and Bodanapu, R and Sreelakshmi, Y and Sharma, R}, title = {High-throughput phenotyping of plant populations using a personal digital assistant.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {918}, number = {}, pages = {97-116}, doi = {10.1007/978-1-61779-995-2_8}, pmid = {22893288}, issn = {1940-6029}, mesh = {*Computers ; Solanum lycopersicum/*anatomy & histology ; *Phenotype ; Photography/*instrumentation ; Programming Languages ; Statistics as Topic ; }, abstract = {During many biological experiments voluminous data is acquired, which can be best collected with -portable data acquisition devices and later analyzed with a personal computer (PC). Public domain software catering to data acquisition and analysis is currently limited. The necessity of phenotyping large plant populations led to the development of the application "PHENOME" to manage the data. PHENOME allows acquisition of phenotypic data using a personal digital assistant (PDA) with a built-in barcode scanner. The acquired data can be exported to a customized database on a PC for further analysis and cataloging. PHENOME can be used for a variety of applications, for example high-throughput phenotyping of a mutagenized or mapping population, or phenotyping of several individuals in one or more ecological niches.}, } @article {pmid22892145, year = {2012}, author = {Sanon, S and Hein, T and Douven, W and Winkler, P}, title = {Quantifying ecosystem service trade-offs: the case of an urban floodplain in Vienna, Austria.}, journal = {Journal of environmental management}, volume = {111}, number = {}, pages = {159-172}, doi = {10.1016/j.jenvman.2012.06.008}, pmid = {22892145}, issn = {1095-8630}, mesh = {Agriculture ; Algorithms ; Austria ; Cities ; Conservation of Natural Resources/*methods ; *Decision Support Techniques ; Drinking Water ; Ecosystem ; *Environmental Policy ; Fisheries ; Recreation ; *Rivers ; *Wetlands ; }, abstract = {Wetland ecosystems provide multiple functions and services for the well-being of humans. In urban environments, planning and decision making about wetland restoration inevitably involves conflicting objectives, trade-offs, uncertainties and conflicting value judgments. This study applied trade-off and multi criteria decision analysis to analyze and quantify the explicit trade-offs between the stakeholder's objectives related to management options for the restoration of an urban floodplain, the Lobau, in Vienna, Austria. The Lobau has been disconnected from the main channel of the Danube River through flood protection schemes 130 years ago that have reduced the hydraulic exchange processes. Urban expansion has also changed the adjacent areas and led to increased numbers of visitors, which hampers the maximum potential for ecosystem development and exerts additional pressure on the sensitive habitats in the national park area. The study showed that increased hydraulic connectivity would benefit several stakeholders that preferred the ecological development of the floodplain habitats. However, multiple uses including fishery, agriculture and recreation, exploring the maximum potential in line with national park regulations, were also possible under the increased hydraulic connectivity options. The largest trade-offs were quantified to be at 0.50 score between the ecological condition of the aquatic habitats and the drinking water production and 0.49 score between the ecological condition of the terrestrial habitats and the drinking water production. At this point, the drinking water production was traded-off with 0.40 score, while the ecological condition of the aquatic habitats and the ecological condition of the terrestrial habitats were traded off with 0.30 and 0.23 score, respectively. The majority of the stakeholders involved preferred the management options that increased the hydraulic connectivity compared with the current situation which was not preferred by any stakeholders. These findings highlight the need for targeted restoration measures. By that, it is recommended that additional measures to ensure reliable drinking water production should be developed, if the higher connectivity options would be implemented. In the next step it is recommended to include cost and flood risk criteria in the decision matrix for more specific developed measures. The research showed that pair-wise trade-off figures provided a useful means to elaborate and quantify the real trade-offs. Finally, the research also showed that the use of multi criteria decision analyses should be based on a participatory approach, in which the process of arriving at the final ranking should be equal or more important than the outcome of the ranking itself.}, } @article {pmid22891967, year = {2012}, author = {van der Fels-Klerx, HJ and Olesen, JE and Naustvoll, LJ and Friocourt, Y and Mengelers, MJ and Christensen, JH}, title = {Climate change impacts on natural toxins in food production systems, exemplified by deoxynivalenol in wheat and diarrhetic shellfish toxins.}, journal = {Food additives & contaminants. Part A, Chemistry, analysis, control, exposure & risk assessment}, volume = {29}, number = {10}, pages = {1647-1659}, doi = {10.1080/19440049.2012.714080}, pmid = {22891967}, issn = {1944-0057}, mesh = {Animals ; *Climate Change ; Crops, Agricultural/*chemistry/growth & development/microbiology ; Databases, Factual ; Dinoflagellida/growth & development/metabolism ; Europe ; *Food Contamination ; Food Industry/trends ; Forecasting ; Fungi/growth & development/metabolism ; Harmful Algal Bloom ; Humans ; Marine Toxins/analysis/*biosynthesis ; Models, Biological ; Mollusca/chemistry/growth & development/parasitology ; North Sea ; Phytoplankton/growth & development/metabolism ; Seeds/chemistry/growth & development/microbiology ; Shellfish/*analysis/microbiology ; Spatio-Temporal Analysis ; Trichothecenes/analysis/*biosynthesis ; Triticum/*chemistry/growth & development/microbiology ; }, abstract = {Climate change is expected to affect food and feed safety, including the occurrence of natural toxins in primary crop and seafood production; however, to date, quantitative estimates are scarce. This study aimed to estimate the impact of climate change effects on mycotoxin contamination of cereal grains cultivated in the terrestrial area of north west Europe, and on the frequency of harmful algal blooms and contamination of shellfish with marine biotoxins in the North Sea coastal zone. The study focused on contamination of wheat with deoxynivalenol, and on abundance of Dinophysis spp. and the possible relationship with diarrhetic shellfish toxins. The study used currently available data and models. Global and regional climate models were combined with models of crop phenology, mycotoxin prediction models, hydrodynamic models and ecological models, with the output of one model being used as input for the other. In addition, statistical data analyses using existing national datasets from the study area were performed to obtain information on the relationships between Dinophysis spp. cell counts and contamination of shellfish with diarrhetic shellfish toxins as well as on frequency of cereal cropping. In this paper, a summary of the study is presented, and overall conclusions and recommendations are given. Climate change projections for the years 2031-2050 were used as the starting point of the analyses relative to a preceding 20-year baseline period from which the climate change signal was calculated. Results showed that, in general, climate change effects lead to advanced flowering and harvest of wheat, and increased risk of contamination of wheat with deoxynivalenol. Blooms of dinoflagellates were estimated to occur more often. If the group of Dinophysis spp. behaves similarly to other flagellates in the future then frequency of harmful algal blooms of Dinophysis spp. may also increase, but consequences for contamination of shellfish with diarrhetic shellfish toxins are uncertain. Climate change will also have indirect effects on toxin contamination, which may be equally important. For example, the frequency of cropping of wheat and maize in north Europe was projected to increase under climate change, which will also increase the risk of contamination of the grains with deoxynivalenol. Risk managers are encouraged to consider the entire range of the predictions of climate change effects on food safety hazards, rather than median or average values only. Furthermore, it is recommended to closely monitor levels of mycotoxins and marine biotoxins in the future, in particular related to risky situations associated with favourable climatic conditions for toxin producing organisms. In particular, it is important to pay attention to the continuity of collecting the right data, and the availability and accessibility of databases. On a European level, it is important to stress the need for harmonisation of terminology and data collection.}, } @article {pmid22883857, year = {2012}, author = {Winter, DJ}, title = {MMOD: an R library for the calculation of population differentiation statistics.}, journal = {Molecular ecology resources}, volume = {12}, number = {6}, pages = {1158-1160}, doi = {10.1111/j.1755-0998.2012.03174.x}, pmid = {22883857}, issn = {1755-0998}, mesh = {Computational Biology/*methods ; Genetics, Population/*methods ; *Software ; *Statistics as Topic ; }, abstract = {MMOD is a library for the R programming language that allows the calculation of the population differentiation measures D(est), G″(ST) and φ'(ST). R provides a powerful environment in which to conduct and record population genetic analyses but, at present, no R libraries provide functions for the calculation of these statistics from standard population genetic files. In addition to the calculation of differentiation measures, mmod can produce parametric bootstrap and jackknife samples of data sets for further analysis. By integrating with and complimenting the existing libraries adegenet and pegas, mmod extends the power of R as a population genetic platform.}, } @article {pmid22883685, year = {2012}, author = {Kemal Korucu, M and Erdagi, B}, title = {A criticism of applications with multi-criteria decision analysis that are used for the site selection for the disposal of municipal solid wastes.}, journal = {Waste management (New York, N.Y.)}, volume = {32}, number = {12}, pages = {2315-2323}, doi = {10.1016/j.wasman.2012.07.003}, pmid = {22883685}, issn = {1879-2456}, mesh = {Conservation of Natural Resources ; Decision Support Techniques ; Ecosystem ; Environmental Pollution/*prevention & control ; Human Activities ; Refuse Disposal/*methods ; }, abstract = {The main aim of this study is to criticize the process of selecting the most appropriate site for the disposal of municipal solid wastes which is one of the problematic issues of waste management operations. These kinds of problems are pathological symptoms of existing problematical human-nature relationship which is related to the syndrome called ecological crisis. In this regard, solving the site selection problem, which is just a small part of a larger entity, for the good of ecological rationality and social justice is only possible by founding a new and extensive type of human-nature relationship. In this study, as a problematic point regarding the discussions on ecological problems, the existing structure of the applications using multi-criteria decision analysis in the process of site selection with three main criteria is criticized. Based on this critique, fundamental problematic points (to which applications are insufficient to find solutions) will be defined. Later, some modifications will be suggested in order to provide solutions to these problematical points. Finally, the criticism addressed to the structure of the method with three main criteria and the feasibility of the new method with four main criteria is subjected to an evaluation process. As a result, it is emphasized that the new structure with four main criteria may be effective in solution of the fundamental problematic points.}, } @article {pmid22882383, year = {2012}, author = {Kubartová, A and Ottosson, E and Dahlberg, A and Stenlid, J}, title = {Patterns of fungal communities among and within decaying logs, revealed by 454 sequencing.}, journal = {Molecular ecology}, volume = {21}, number = {18}, pages = {4514-4532}, doi = {10.1111/j.1365-294X.2012.05723.x}, pmid = {22882383}, issn = {1365-294X}, mesh = {Ascomycota/*classification/genetics ; Basidiomycota/*classification/genetics ; *Biota ; Computational Biology ; DNA, Fungal/genetics ; DNA, Ribosomal Spacer/genetics ; Sequence Analysis, DNA ; Sweden ; Wood/*microbiology ; }, abstract = {Owing to previous methodological limitations, knowledge about the fine-scale distribution of fungal mycelia in decaying logs is limited. We investigated fungal communities in decaying Norway spruce logs at various spatial scales at two environmentally different locations in Sweden. On the basis of 454 pyrosequencing of the ITS2 region of rDNA, 1914 operational taxonomic units (OTUs) were detected in 353 samples. The communities differed significantly among logs, but the physical distance between logs was not found to have a significant effect on whether fungal communities had any resemblance to each other. Within a log, samples that were closer together generally had communities that showed more resemblance to each other than those that were further apart. OTUs characteristic for particular positions on the logs could be identified. In general, these OTUs did not overlap with the most abundant OTUs, and their ecological role was often unknown. Only a few OTUs were detected in the majority of logs, whereas numerous OTUs were rare and present in only one or a few logs. Wood-decaying Basidiomycetes were often represented by higher sequence reads in individual logs than Ascomycete OTUs, suggesting that Basidiomycete mycelia spread out more rapidly when established. OTU richness tended to increase with the decay stage of the sample; however, the known wood decayers were most abundant in less-decomposed samples. The fungi identified in the logs represented different ecological strategies. Our findings differ from previously published sporocarp studies, indicating that the highly abundant fruiting species may respond to environment in different ways than the rest of the fungal community.}, } @article {pmid22880076, year = {2012}, author = {Vasileiadis, S and Puglisi, E and Arena, M and Cappa, F and Cocconcelli, PS and Trevisan, M}, title = {Soil bacterial diversity screening using single 16S rRNA gene V regions coupled with multi-million read generating sequencing technologies.}, journal = {PloS one}, volume = {7}, number = {8}, pages = {e42671}, pmid = {22880076}, issn = {1932-6203}, mesh = {Bacteria/classification/*genetics ; Base Sequence ; Computer Simulation ; Databases, Genetic ; Entropy ; *Genetic Variation ; Phylogeny ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, DNA/*methods ; *Soil Microbiology ; }, abstract = {The novel multi-million read generating sequencing technologies are very promising for resolving the immense soil 16S rRNA gene bacterial diversity. Yet they have a limited maximum sequence length screening ability, restricting studies in screening DNA stretches of single 16S rRNA gene hypervariable (V) regions. The aim of the present study was to assess the effects of properties of four consecutive V regions (V3-6) on commonly applied analytical methodologies in bacterial ecology studies. Using an in silico approach, the performance of each V region was compared with the complete 16S rRNA gene stretch. We assessed related properties of the soil derived bacterial sequence collection of the Ribosomal Database Project (RDP) database and concomitantly performed simulations based on published datasets. Results indicate that overall the most prominent V region for soil bacterial diversity studies was V3, even though it was outperformed in some of the tests. Despite its high performance during most tests, V4 was less conserved along flanking sites, thus reducing its ability for bacterial diversity coverage. V5 performed well in the non-redundant RDP database based analysis. However V5 did not resemble the full-length 16S rRNA gene sequence results as well as V3 and V4 did when the natural sequence frequency and occurrence approximation was considered in the virtual experiment. Although, the highly conserved flanking sequence regions of V6 provide the ability to amplify partial 16S rRNA gene sequences from very diverse owners, it was demonstrated that V6 was the least informative compared to the rest examined V regions. Our results indicate that environment specific database exploration and theoretical assessment of the experimental approach are strongly suggested in 16S rRNA gene based bacterial diversity studies.}, } @article {pmid22873717, year = {2012}, author = {Seedat, M and McClure, R and Suffla, S and van Niekerk, A}, title = {Developing the evidence-base for Safe Communities: a multi-level, partly randomised, controlled trial.}, journal = {International journal of injury control and safety promotion}, volume = {19}, number = {3}, pages = {231-241}, doi = {10.1080/17457300.2012.705303}, pmid = {22873717}, issn = {1745-7319}, mesh = {Accident Prevention ; Africa ; *Community Networks ; *Evidence-Based Practice ; Humans ; *Program Development ; *Safety ; Violence/prevention & control ; }, abstract = {Safe Communities, representing a global activation of the public health logic, may be strengthened through theoretical, methodological and empirical support. In the spirit of this Special Issue that aims to analyse the achievements and challenges inherent to Safe Communities, we offer our contribution in the form of a methodology of a multi-country child safety, peace and health promotion study. The study, situated within an African-centred initiative called Ukuphepha - an isiZulu word meaning demonstrating African safety - is underpinned by four theoretical claims that frame injury and violence prevention as a multi-disciplinary issue to be addressed through a suite of interventions to family and extended social systems. The interventions, sensitive to the priorities of each participating country, have been informed by the literature on effective interventions and the authors' joint experiences of community development. The study is designed as a population-based, multi-level, multi-intervention partly randomised controlled trial, and there are potentially 24 participant communities representing South Africa, Mozambique, Egypt, Zambia, Uganda, Bangladesh, Malaysia and Australia - over three commencement phases. Whereas process evaluation will focus on community engagement, impact evaluation will consider risk and protective factors, and outcome evaluation will examine the overall effectiveness of the interventions. Notwithstanding the many challenges, the study will provide insights into the methodology and mechanisms of ecologically-oriented interventions that locate injury and violence prevention as an activity arising from safety, peace and health promotion.}, } @article {pmid22870338, year = {2012}, author = {Van Belleghem, SM and Roelofs, D and Van Houdt, J and Hendrickx, F}, title = {De novo transcriptome assembly and SNP discovery in the wing polymorphic salt marsh beetle Pogonus chalceus (Coleoptera, Carabidae).}, journal = {PloS one}, volume = {7}, number = {8}, pages = {e42605}, pmid = {22870338}, issn = {1932-6203}, mesh = {Animals ; Coleoptera/*genetics/metabolism ; *Databases, Nucleic Acid ; *Databases, Protein ; Insect Proteins/genetics/metabolism ; *Polymorphism, Single Nucleotide ; *Sequence Analysis, DNA ; Transcriptome/*physiology ; }, abstract = {BACKGROUND: The salt marsh beetle Pogonus chalceus represents a unique opportunity to understand and study the origin and evolution of dispersal polymorphisms as remarkable inter-population divergence in dispersal related traits (e.g. wing development, body size and metabolism) has been shown to persist in face of strong homogenizing gene flow. Sequencing and assembling the transcriptome of P. chalceus is a first step in developing large scale genetic information that will allow us to further study the recurrent phenotypic evolution in dispersal traits in these natural populations.

METHODOLOGY/RESULTS: We used the Illumina HiSeq2000 to sequence 37 Gbases of the transcriptome and performed de novo transcriptome assembly with the Trinity short read assembler. This resulted in 65,766 contigs, clustering into 39,393 unique transcripts (unigenes). A subset of 12,987 show similarity (BLAST) to known proteins in the NCBI database and 7,589 are assigned Gene Ontology (GO). Using homology searches we identified all reported genes involved in wing development, juvenile- and ecdysteroid hormone pathways in Tribolium castaneum. About half (56.7%) of the unique assembled genes are shared among three life stages (third-instar larva, pupa, and imago). We identified 38,141 single nucleotide polymorphisms (SNPs) in these unigenes. Of these SNPs, 26,823 (70.3%) were found in a predicted open reading frame (ORF) and 6,998 (18.3%) were nonsynonymous.

CONCLUSIONS: The assembled transcriptome and SNP data are essential genomic resources for further study of the developmental pathways, genetic mechanisms and metabolic consequences of adaptive divergence in dispersal power in natural populations.}, } @article {pmid22865356, year = {2012}, author = {Yoshihama, M and Ramakrishnan, A and Hammock, AC and Khaliq, M}, title = {Intimate partner violence prevention program in an Asian immigrant community: integrating theories, data, and community.}, journal = {Violence against women}, volume = {18}, number = {7}, pages = {763-783}, doi = {10.1177/1077801212455163}, pmid = {22865356}, issn = {1552-8448}, support = {CE000507-04/CE/NCIPC CDC HHS/United States ; }, mesh = {Asian/education/*psychology ; Capacity Building ; Community Networks/*organization & administration ; Community Participation ; Emigrants and Immigrants/education/*psychology ; Female ; Humans ; Interpersonal Relations ; Male ; Midwestern United States ; Program Development ; Residence Characteristics ; Sexual Partners/*psychology ; Social Marketing ; Violence/ethnology/*prevention & control ; }, abstract = {To fill an existing gap in research and practice on intimate partner violence (IPV) in immigrant communities, the authors developed an IPV prevention program, called the Shanti Project, in an Asian Indian community in the Midwest. Building on the notion of shanti (harmony/peace), a cherished value and strength of the community, we created a communications campaign that combined social marketing and community-based participatory approaches. Recognizing the interactive influences of multiple levels of social ecology, campaign activities were designed to bring about changes at the individual, relationship/family, organization, and community levels. This article presents the development of this theoretically, empirically, and community-based IPV prevention program.}, } @article {pmid22864551, year = {2012}, author = {Guillard, C and Zezere, J}, title = {Landslide susceptibility assessment and validation in the framework of municipal planning in Portugal: the case of Loures Municipality.}, journal = {Environmental management}, volume = {50}, number = {4}, pages = {721-735}, doi = {10.1007/s00267-012-9921-7}, pmid = {22864551}, issn = {1432-1009}, mesh = {*Disasters ; Environmental Monitoring ; Forecasting ; Geographic Information Systems ; *Geological Phenomena ; Geology ; Portugal ; Reproducibility of Results ; Risk Assessment ; *Soil ; }, abstract = {The legislation that demands the evaluation of landslide susceptibility in Portugal at the municipal level is the National Ecological Reserve (NER). A methodology for the evaluation of landslide susceptibility to be used in municipal planning is applied in Loures Municipality (169.3 km[2]) located north of Lisbon (Portugal). A landslide inventory was made for the whole area interpreting orthophoto maps and aerial photographs and using standard geomorphologic techniques in field work. It consists of 686 polygons, each polygon representing a rotational, a deep translational or a shallow translational slide, and is integrated into a GIS database. Landslide susceptibility is evaluated using algorithms based on statistical/probabilistic analysis (Information Value Method) over unique-condition terrain units in a raster basis. Three susceptibility models are elaborated independently according to the type of slide (rotational, deep translational, shallow translational). The landslide susceptibility maps are prepared by sorting all pixels according to the pixel susceptibility value in descending order. The robustness and accuracy of the landslide susceptibility models are evaluated by prediction-rate curves, which are used for the quantitative interpretation of the landslide susceptibility maps. Unstable slopes that have to be included into the National Ecological Reserve are extracted from the three susceptibility maps following the general rules to draw the NER that state that the area to be included in the NER should guarantee the inclusion of at least 70 % of the landslides identified in the landslide inventory. The obtained results allow us to conclude that 70 % of the future landslides should occur in these areas, classified as most susceptible to landslides corresponding to 20.3 % of the total area of Municipality. Thus, the consideration of these 20.3 % as regards prevention and protection of landslide risk could potentially reduce damage resulting from 70 % of future landslides in the Loures Municipality.}, } @article {pmid22864169, year = {2012}, author = {Deng, X and Wang, P}, title = {Isolation of marine bacteria highly resistant to mercury and their bioaccumulation process.}, journal = {Bioresource technology}, volume = {121}, number = {}, pages = {342-347}, doi = {10.1016/j.biortech.2012.07.017}, pmid = {22864169}, issn = {1873-2976}, mesh = {Bacteria/growth & development/*isolation & purification/*metabolism ; Biodegradation, Environmental ; Carbon Dioxide/metabolism ; Computational Biology ; DNA Primers/genetics ; Hydrogen-Ion Concentration ; Mercury/*pharmacokinetics/toxicity ; Phylogeny ; Seawater/*microbiology ; Species Specificity ; Spectrum Analysis ; Water Pollutants, Chemical/*pharmacokinetics/toxicity ; Water Pollution/*prevention & control ; }, abstract = {The marine bacteria strains S1, S2 and S3, were isolated on seawater culturing medium containing Hg(2+), Cd(2+), Cr(6+) or Ni(2+) at concentrations of 20 mg L(-1) and more. The isolates showed tolerance to these heavy metals. S1 grew in the presence of 120 mg L(-1) of Hg(2+) and accumulated Hg(2+) at pH 4-10. For the effect of co-existing cations on bioaccumulation of target metal, it was found that the effect depended on not only the variety and initial concentration of co-existing ions, but also the initial concentration of target metal and biomass dosage. A new parameter, the ratio of remaining bioaccumulation capacity (RRBC) of biomass, was therefore defined to evaluate such effect. Furthermore, the mechanism evaluation revealed that S1 bound about 70% Hg(2+) on the cell surface, and carboxyl group played an important role in Hg(2+) binding.}, } @article {pmid22862796, year = {2012}, author = {Moore, JL and Runge, MC}, title = {Combining structured decision making and value-of-information analyses to identify robust management strategies.}, journal = {Conservation biology : the journal of the Society for Conservation Biology}, volume = {26}, number = {5}, pages = {810-820}, doi = {10.1111/j.1523-1739.2012.01907.x}, pmid = {22862796}, issn = {1523-1739}, mesh = {Conservation of Natural Resources/economics/*methods ; Decision Making ; *Decision Support Techniques ; Ecosystem ; Fires ; *Introduced Species ; Models, Biological ; Population Dynamics ; Salix/*physiology ; Uncertainty ; Victoria ; }, abstract = {Structured decision making and value-of-information analyses can be used to identify robust management strategies even when uncertainty about the response of the system to management is high. We used these methods in a case study of management of the non-native invasive species gray sallow willow (Salix cinerea) in alpine Australia. Establishment of this species is facilitated by wildfire. Managers are charged with developing a management strategy despite extensive uncertainty regarding the frequency of fires, the willow's demography, and the effectiveness of management actions. We worked with managers in Victoria to conduct a formal decision analysis. We used a dynamic model to identify the best management strategy for a range of budgets. We evaluated the robustness of the strategies to uncertainty with value-of-information analyses. Results of the value-of-information analysis indicated that reducing uncertainty would not change which management strategy was identified as the best unless budgets increased substantially. This outcome suggests there would be little value in implementing adaptive management for the problem we analyzed. The value-of-information analyses also highlighted that the main driver of gray sallow willow invasion (i.e., fire frequency) is not necessarily the same factor that is most important for decision making (i.e., willow seed dispersal distance). Value of-information analyses enables managers to better target monitoring and research efforts toward factors critical to making the decision and to assess the need for adaptive management.}, } @article {pmid22856455, year = {2012}, author = {Yongye, AB and Medina-Franco, JL}, title = {Data mining of protein-binding profiling data identifies structural modifications that distinguish selective and promiscuous compounds.}, journal = {Journal of chemical information and modeling}, volume = {52}, number = {9}, pages = {2454-2461}, doi = {10.1021/ci3002606}, pmid = {22856455}, issn = {1549-960X}, mesh = {Data Mining ; *Database Management Systems ; Marine Biology ; Protein Binding ; }, abstract = {Activity profiling of compound collections across multiple targets is increasingly being used in probe and drug discovery. Herein, we discuss an approach to systematically analyzing the structure-activity relationships of a large screening profile data with emphasis on identifying structural changes that have a significant impact on the number of proteins to which a compound binds. As a case study, we analyzed a recently released public data set of more than 15 000 compounds screened across 100 sequence-unrelated proteins. The screened compounds have different origins and include natural products, synthetic molecules from academic groups, and commercial compounds. Similar synthetic structures from academic groups showed, overall, greater promiscuity differences than do natural products and commercial compounds. The method implemented in this work readily identified structural changes that differentiated highly specific from promiscuous compounds. This approach is general and can be applied to analyze any other large-scale protein-binding profile data.}, } @article {pmid22851645, year = {2012}, author = {Wang, C and Schroeder, KB and Rosenberg, NA}, title = {A maximum-likelihood method to correct for allelic dropout in microsatellite data with no replicate genotypes.}, journal = {Genetics}, volume = {192}, number = {2}, pages = {651-669}, pmid = {22851645}, issn = {1943-2631}, support = {R01 GM081441/GM/NIGMS NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; R01-HG005855/HG/NHGRI NIH HHS/United States ; R01 HG005855/HG/NHGRI NIH HHS/United States ; R01-GM081441/GM/NIGMS NIH HHS/United States ; }, mesh = {Algorithms ; Alleles ; Computer Simulation ; Data Interpretation, Statistical ; *Genetics, Population ; Genotype ; Heterozygote ; Humans ; Inbreeding ; Indians, North American ; *Likelihood Functions ; Microsatellite Repeats/*genetics ; *Models, Theoretical ; }, abstract = {Allelic dropout is a commonly observed source of missing data in microsatellite genotypes, in which one or both allelic copies at a locus fail to be amplified by the polymerase chain reaction. Especially for samples with poor DNA quality, this problem causes a downward bias in estimates of observed heterozygosity and an upward bias in estimates of inbreeding, owing to mistaken classifications of heterozygotes as homozygotes when one of the two copies drops out. One general approach for avoiding allelic dropout involves repeated genotyping of homozygous loci to minimize the effects of experimental error. Existing computational alternatives often require replicate genotyping as well. These approaches, however, are costly and are suitable only when enough DNA is available for repeated genotyping. In this study, we propose a maximum-likelihood approach together with an expectation-maximization algorithm to jointly estimate allelic dropout rates and allele frequencies when only one set of nonreplicated genotypes is available. Our method considers estimates of allelic dropout caused by both sample-specific factors and locus-specific factors, and it allows for deviation from Hardy-Weinberg equilibrium owing to inbreeding. Using the estimated parameters, we correct the bias in the estimation of observed heterozygosity through the use of multiple imputations of alleles in cases where dropout might have occurred. With simulated data, we show that our method can (1) effectively reproduce patterns of missing data and heterozygosity observed in real data; (2) correctly estimate model parameters, including sample-specific dropout rates, locus-specific dropout rates, and the inbreeding coefficient; and (3) successfully correct the downward bias in estimating the observed heterozygosity. We find that our method is fairly robust to violations of model assumptions caused by population structure and by genotyping errors from sources other than allelic dropout. Because the data sets imputed under our model can be investigated in additional subsequent analyses, our method will be useful for preparing data for applications in diverse contexts in population genetics and molecular ecology.}, } @article {pmid22849829, year = {2012}, author = {Logares, R and Haverkamp, TH and Kumar, S and Lanzén, A and Nederbragt, AJ and Quince, C and Kauserud, H}, title = {Environmental microbiology through the lens of high-throughput DNA sequencing: synopsis of current platforms and bioinformatics approaches.}, journal = {Journal of microbiological methods}, volume = {91}, number = {1}, pages = {106-113}, doi = {10.1016/j.mimet.2012.07.017}, pmid = {22849829}, issn = {1872-8359}, mesh = {Computational Biology/*methods/trends ; *Environmental Microbiology ; High-Throughput Nucleotide Sequencing/*methods/trends ; Metagenomics/*methods/trends ; }, abstract = {The incursion of High-Throughput Sequencing (HTS) in environmental microbiology brings unique opportunities and challenges. HTS now allows a high-resolution exploration of the vast taxonomic and metabolic diversity present in the microbial world, which can provide an exceptional insight on global ecosystem functioning, ecological processes and evolution. This exploration has also economic potential, as we will have access to the evolutionary innovation present in microbial metabolisms, which could be used for biotechnological development. HTS is also challenging the research community, and the current bottleneck is present in the data analysis side. At the moment, researchers are in a sequence data deluge, with sequencing throughput advancing faster than the computer power needed for data analysis. However, new tools and approaches are being developed constantly and the whole process could be depicted as a fast co-evolution between sequencing technology, informatics and microbiologists. In this work, we examine the most popular and recently commercialized HTS platforms as well as bioinformatics methods for data handling and analysis used in microbial metagenomics. This non-exhaustive review is intended to serve as a broad state-of-the-art guide to researchers expanding into this rapidly evolving field.}, } @article {pmid22847648, year = {2012}, author = {Scholey, AB and Benson, S and Neale, C and Owen, L and Tiplady, B}, title = {Neurocognitive and mood effects of alcohol in a naturalistic setting.}, journal = {Human psychopharmacology}, volume = {27}, number = {5}, pages = {514-516}, doi = {10.1002/hup.2245}, pmid = {22847648}, issn = {1099-1077}, mesh = {Adolescent ; Affect/*drug effects ; Alcohol Drinking/*adverse effects ; Cognition/drug effects ; Diagnosis, Computer-Assisted ; Ethanol/administration & dosage/*adverse effects/blood ; Humans ; Neuropsychological Tests ; Pilot Projects ; Psychomotor Performance/*drug effects ; Young Adult ; }, abstract = {OBJECTIVE: The current pilot study aimed to assess the effects of drinking alcohol in a naturalistic setting on aspects of performance.

METHODS: Thirty individuals were approached and tested individually in a university campus bar. They provided details regarding alcoholic drinks consumption. Each was breathalysed before and after completion of a computerised test battery administered on a handheld device. The battery consisted of visual analogue mood scales, a series of alcohol-sensitive psychomotor and cognitive tests.

RESULTS: There were highly significant correlations between measured blood alcohol concentrations, estimated units of alcohol consumed and scores on a 'sober-drunk' VAS (p < 0.001 in all cases). For performance, there was a characteristic alcohol-associated shift in the speed/accuracy trade-off (SATO), which was reflected as significantly more errors with less effect on speed across several measures (including maze performance and Serial Sevens). Individuals who were more intoxicated were also significantly less alert.

CONCLUSIONS: The data suggest that controlled laboratory tests into the effects of alcohol intoxication may have ecological validity, with SATO shifts amongst the characteristic impairments seen in both controlled and naturalistic settings.}, } @article {pmid22847014, year = {2012}, author = {Gismondi, A and Rolfo, MF and Leonardi, D and Rickards, O and Canini, A}, title = {Identification of ancient Olea europaea L. and Cornus mas L. seeds by DNA barcoding.}, journal = {Comptes rendus biologies}, volume = {335}, number = {7}, pages = {472-479}, doi = {10.1016/j.crvi.2012.05.004}, pmid = {22847014}, issn = {1768-3238}, mesh = {Agriculture/*history ; Archaeology/*methods ; Caves ; Cornus/classification/*genetics ; DNA Barcoding, Taxonomic ; DNA, Plant/*analysis/isolation & purification ; Databases, Genetic ; *Fossils ; *Genes, Plant ; History, Ancient ; Italy ; Microscopy, Electron, Scanning ; Olea/classification/*genetics ; Polymerase Chain Reaction/methods ; Seeds/*chemistry/ultrastructure ; Sequence Alignment ; Sequence Homology, Nucleic Acid ; Species Specificity ; }, abstract = {The analysis of ancient DNA (aDNA) provides archaeologists and anthropologists with innovative, scientific and accurate data to study and understand the past. In this work, ancient seeds, found in the "Mora Cavorso" archaeological site (Latium, Central Italy), were analyzed to increase information about Italian Neolithic populations (plant use, agriculture, diet, trades, customs and ecology). We performed morphological and genetic techniques to identify fossil botanical species. In particular, this study also suggests and emphasizes the use of DNA barcode method for ancient plant sample analysis. Scanning electron microscope (SEM) observations showed seed compact structure and irregular surface but they did not permit a precise nor empirical classification: so, a molecular approach was necessary. DNA was extracted from ancient seeds and then it was used, as template, for PCR amplifications of standardized barcode genes. Although aDNA could be highly degraded by the time, successful PCR products were obtained, sequenced and compared to nucleotide sequence databases. Positive outcomes (supported by morphological comparison with modern seeds, geographical distribution and historical data) indicated that seeds could be identified as belonging to two plant species: Olea europaea L. and Cornus mas L.}, } @article {pmid22844235, year = {2012}, author = {De Boer, RJ}, title = {Which of our modeling predictions are robust?.}, journal = {PLoS computational biology}, volume = {8}, number = {7}, pages = {e1002593}, pmid = {22844235}, issn = {1553-7358}, mesh = {Chronic Disease ; Computational Biology/*methods ; Humans ; *Models, Biological ; Virus Diseases/immunology/virology ; }, abstract = {In theoretical ecology it is well known that the steady state expressions of the variables in a food chain crucially depend on the parity of the length of the chain. This poses a major problem for modeling real food webs because it is difficult to establish their true number of trophic levels, with sometimes rare predators and often rampant pathogens. Similar problems arise in the modeling of chronic viral infections. We review examples where seemingly general interpretations strongly depend on the number of levels in a model, and on its specific equations. This Perspective aims to open the discussion on this problem.}, } @article {pmid22843397, year = {2012}, author = {Gilbert, J and Li, LL and Taghavi, S and McCorkle, SM and Tringe, S and van der Lelie, D}, title = {Bioprospecting metagenomics for new glycoside hydrolases.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {908}, number = {}, pages = {141-151}, doi = {10.1007/978-1-61779-956-3_14}, pmid = {22843397}, issn = {1940-6029}, mesh = {Bacterial Proteins/*genetics ; Biomass ; Cloning, Molecular ; Data Mining/*methods ; *Databases, Genetic ; *Genetic Variation ; Glycoside Hydrolases/*genetics ; Metagenomics/*methods ; Open Reading Frames/genetics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {To efficiently deconstruct recalcitrant plant biomass to fermentable sugars in industrial processes, biocatalysts of higher performance and lower cost are required. The genetic diversity found in the metagenomes of natural microbial biomass decay communities may harbor such enzymes. The aim of this chapter is to describe strategies, based on metagenomic approaches, for the discovery of glycoside hydrolases (GHases) from microbial biomass decay communities, especially those from unknown or never-been-cultivated microorganisms.}, } @article {pmid22839777, year = {2012}, author = {Fernández-Gómez, B and Fernàndez-Guerra, A and Casamayor, EO and González, JM and Pedrós-Alió, C and Acinas, SG}, title = {Patterns and architecture of genomic islands in marine bacteria.}, journal = {BMC genomics}, volume = {13}, number = {}, pages = {347}, pmid = {22839777}, issn = {1471-2164}, mesh = {Aquatic Organisms/genetics ; Bacteria/*genetics ; Databases, Genetic ; *Gene Transfer, Horizontal ; *Genome, Bacterial ; *Genomic Islands ; Molecular Sequence Annotation ; Phylogeny ; Water Microbiology ; }, abstract = {BACKGROUND: Genomic Islands (GIs) have key roles since they modulate the structure and size of bacterial genomes displaying a diverse set of laterally transferred genes. Despite their importance, GIs in marine bacterial genomes have not been explored systematically to uncover possible trends and to analyze their putative ecological significance.

RESULTS: We carried out a comprehensive analysis of GIs in 70 selected marine bacterial genomes detected with IslandViewer to explore the distribution, patterns and functional gene content in these genomic regions. We detected 438 GIs containing a total of 8152 genes. GI number per genome was strongly and positively correlated with the total GI size. In 50% of the genomes analyzed the GIs accounted for approximately 3% of the genome length, with a maximum of 12%. Interestingly, we found transposases particularly enriched within Alphaproteobacteria GIs, and site-specific recombinases in Gammaproteobacteria GIs. We described specific Homologous Recombination GIs (HR-GIs) in several genera of marine Bacteroidetes and in Shewanella strains among others. In these HR-GIs, we recurrently found conserved genes such as the β-subunit of DNA-directed RNA polymerase, regulatory sigma factors, the elongation factor Tu and ribosomal protein genes typically associated with the core genome.

CONCLUSIONS: Our results indicate that horizontal gene transfer mediated by phages, plasmids and other mobile genetic elements, and HR by site-specific recombinases play important roles in the mobility of clusters of genes between taxa and within closely related genomes, modulating the flexible pool of the genome. Our findings suggest that GIs may increase bacterial fitness under environmental changing conditions by acquiring novel foreign genes and/or modifying gene transcription and/or transduction.}, } @article {pmid22838958, year = {2012}, author = {Nair, A and Gopalan, SV and George, S and Kumar, KS and Merilä, J}, title = {Cross-species testing and utility of microsatellite loci in Indirana frogs.}, journal = {BMC research notes}, volume = {5}, number = {}, pages = {389}, pmid = {22838958}, issn = {1756-0500}, mesh = {Animals ; DNA, Mitochondrial/*analysis ; Databases, Genetic ; *Endangered Species ; Evolution, Molecular ; *Genetic Loci ; Genetic Markers ; *Genomics/methods ; India ; *Microsatellite Repeats ; Polymerase Chain Reaction ; Polymorphism, Genetic ; RNA, Ribosomal, 16S/*analysis ; Ranidae/classification/*genetics ; Species Specificity ; }, abstract = {BACKGROUND: Microsatellite loci are widely used in population and conservation genetic studies of amphibians, but the availability of such markers for tropical and subtropical taxa is currently very limited. In order to develop resources for conservation genetic studies in the genus Indirana, we tested amplification success and polymorphism in 62 previously developed microsatellite loci, in eight Indirana species - including new candidate species. Developing genomic resources for this amphibian taxon is particularly important as it is endemic to the Western Ghats biodiversity hotspot, and harbours several endangered species.

FINDINGS: The cross-species amplification success rate varied from 11.3 % to 29.0 % depending on the species, with 29 - 80 % of the amplifying loci being polymorphic. A strong negative correlation between cross-species amplification success (and polymorphism) and genetic distance separating target from source species was observed.

CONCLUSIONS: Our results provide additional genetic support for the existence of genetically divergent cryptic species within the genus Indirana. The tested markers should be useful for population and conservation genetic studies in this genus, and in particular, for species closely related to the source species, I. beddomii.}, } @article {pmid22837673, year = {2012}, author = {Li, XS and Yang, HL and Zhang, DY and Zhang, YM and Wood, AJ}, title = {Reference gene selection in the desert plant Eremosparton songoricum.}, journal = {International journal of molecular sciences}, volume = {13}, number = {6}, pages = {6944-6963}, pmid = {22837673}, issn = {1422-0067}, mesh = {Cloning, Molecular ; Computational Biology ; DNA Primers ; DNA, Plant/genetics ; Desert Climate ; Fabaceae/*genetics ; Gene Expression Profiling ; *Gene Expression Regulation, Plant ; *Genes, Plant ; Germination ; Oxygen/chemistry ; RNA, Plant/genetics ; Real-Time Polymerase Chain Reaction ; Software ; Transcription Factors/metabolism ; }, abstract = {Eremosparton songoricum (Litv.) Vass. (E. songoricum) is a rare and extremely drought-tolerant desert plant that holds promise as a model organism for the identification of genes associated with water deficit stress. Here, we cloned and evaluated the expression of eight candidate reference genes using quantitative real-time reverse transcriptase polymerase chain reactions. The expression of these candidate reference genes was analyzed in a diverse set of 20 samples including various E. songoricum plant tissues exposed to multiple environmental stresses. GeNorm analysis indicated that expression stability varied between the reference genes in the different experimental conditions, but the two most stable reference genes were sufficient for normalization in most conditions. EsEF and Esα-TUB were sufficient for various stress conditions, EsEF and EsACT were suitable for samples of differing germination stages, and EsGAPDHand EsUBQ were most stable across multiple adult tissue samples. The Es18S gene was unsuitable as a reference gene in our analysis. In addition, the expression level of the drought-stress related transcription factor EsDREB2 verified the utility of E. songoricum reference genes and indicated that no single gene was adequate for normalization on its own. This is the first systematic report on the selection of reference genes in E. songoricum, and these data will facilitate future work on gene expression in this species.}, } @article {pmid22836536, year = {2012}, author = {Yin, Z and Moore, JB and Johnson, MH and Vernon, MM and Grimstvedt, M and Gutin, B}, title = {Micro- and macro-level correlates of adiposity in children.}, journal = {Journal of public health management and practice : JPHMP}, volume = {18}, number = {5}, pages = {445-452}, doi = {10.1097/PHH.0b013e31821dce0d}, pmid = {22836536}, issn = {1550-5022}, support = {R01 DK063391/DK/NIDDK NIH HHS/United States ; DK063391/DK/NIDDK NIH HHS/United States ; }, mesh = {Absorptiometry, Photon/methods ; Adipose Tissue/diagnostic imaging/*physiology ; Adiposity/ethnology/*physiology ; Body Composition/*physiology ; Body Mass Index ; *Cardiovascular System ; Child ; Cholesterol/blood ; Cross-Sectional Studies ; Female ; Geographic Information Systems ; Georgia ; *Health Knowledge, Attitudes, Practice/ethnology ; Heart Rate/physiology ; Humans ; Male ; Obesity/ethnology/prevention & control ; *Physical Fitness/psychology ; Residence Characteristics/statistics & numerical data ; Sex Distribution ; Sex Factors ; Socioeconomic Factors ; Surveys and Questionnaires ; }, abstract = {CONTEXT: Recently, studies using a social ecological perspective have identified important micro- and macro-level risk factors for excessive adiposity in youth. Although considerable research exists examining these relationships, few studies have applied a socioecological approach to simultaneously examine both micro- and macro-level factors in young children while objectively assessing adiposity via dual-energy x-ray absorptiometry (DXA).

OBJECTIVE: To examine race and sex differences in adiposity measured by DXA in a large sample of young children and to identify both micro- and macro-level correlates of adiposity.

DESIGN: Cross-sectional.

SETTING AND PARTICIPANTS: Elementary school children (N = 495) from the southeastern United States participated. Anthropometrics, percentage body fat via DXA, and psychosocial variables via questionnaire were assessed in the Fall of 2003. Community-level sociodemographic data and built-environment variables via geographic information system were collected in Spring 2009. Data analyses were completed in the Spring of 2010.

RESULTS: Percentage body fat in white children was higher than in nonwhite children. Higher percentage body fat and poorer cardiovascular fitness were found in females compared with males. Percentage body fat was higher in children who had lower athletic competence and lived in neighborhoods with higher percentages of minority residents.

CONCLUSION: This study provides preliminary support for the social-ecological model to explain variance in adiposity in children. Developers of health promotion programs for children living in minority neighborhoods should consider factors at multiple levels of the ecological model when designing and implementing programs.}, } @article {pmid22834757, year = {2012}, author = {Hardy, OJ and Pavoine, S}, title = {Assessing phylogenetic signal with measurement error: a comparison of Mantel tests, Blomberg et al.'s K, and phylogenetic distograms.}, journal = {Evolution; international journal of organic evolution}, volume = {66}, number = {8}, pages = {2614-2621}, doi = {10.1111/j.1558-5646.2012.01623.x}, pmid = {22834757}, issn = {1558-5646}, mesh = {*Biological Evolution ; *Data Interpretation, Statistical ; Models, Genetic ; *Phylogeny ; Research Design ; }, abstract = {In macroevolutionary studies, different approaches are commonly used to measure phylogenetic signal--the tendency of related taxa to resemble one another--including the K statistic and the Mantel test. The latter was recently criticized for lacking statistical power. Using new simulations, we show that the power of the Mantel test depends on the metrics used to define trait distances and phylogenetic distances between species. Increasing power is obtained by lowering variance and increasing negative skewness in interspecific distances, as obtained using Euclidean trait distances and the complement of Abouheif proximity as a phylogenetic distance. We show realistic situations involving "measurement error" due to intraspecific variability where the Mantel test is more powerful to detect a phylogenetic signal than a permutation test based on the K statistic. We highlight limitations of the K-statistic (univariate measure) and show that its application should take into account measurement errors using repeated measures per species to avoid estimation bias. Finally, we argue that phylogenetic distograms representing Euclidean trait distance as a function of the square root of patristic distance provide an insightful representation of the phylogenetic signal that can be used to assess both the impact of measurement error and the departure from a Brownian evolution model.}, } @article {pmid22832834, year = {2012}, author = {Vargas, MH and Campos-Bedolla, P and Segura, P}, title = {[Inverse association between asthma and neural tube defects: a binational ecological study].}, journal = {Salud publica de Mexico}, volume = {54}, number = {4}, pages = {418-424}, doi = {10.1590/s0036-36342012000400012}, pmid = {22832834}, issn = {1606-7916}, mesh = {Adolescent ; Adult ; Age Distribution ; Aged ; Anencephaly/epidemiology/prevention & control ; Asthma/*epidemiology ; Child ; Child, Preschool ; Databases, Factual ; Diet ; Dietary Supplements ; Female ; Folic Acid/administration & dosage ; Geography, Medical ; Humans ; Incidence ; Infant ; Infant, Newborn ; Male ; Mexico/epidemiology ; Middle Aged ; Morbidity/trends ; Neural Tube Defects/*epidemiology/prevention & control ; Pregnancy ; Spinal Dysraphism/epidemiology/prevention & control ; United States/epidemiology ; Young Adult ; }, abstract = {OBJECTIVE: Dietary intake of methyl donors such as folic acid prevents neural tube defects (NTD), but recent studies showed that it might also favor the development of asthma. In this work a possible ecological association between NTD and asthma was explored.

MATERIAL AND METHODS: Data bases from Mexico and the United States (US) were reviewed to obtain information about geographical distribution (by state) and temporal trends (by year) of NTD and asthma.

RESULTS: Those states with the lowest frequency of NTD had the highest frequency of asthma, both in Mexico (rS=-0.48, p=0.005) and US (rS=-0.39, p=0.005). Temporal trends also showed an inverse correlation in Mexico (1997-2007, rS=-0.73, p=0.01) and US (1979-1998, rS=-0.91, p<0.001).

CONCLUSIONS: In both countries the frequency of asthma inversely correlated with the frequency of NTD, both in geographical distribution and annual trends, giving support to the possibility that methyl donors intake in diet or supplements is influencing the asthma frequency.}, } @article {pmid22824070, year = {2012}, author = {Bengtsson, J and Hartmann, M and Unterseher, M and Vaishampayan, P and Abarenkov, K and Durso, L and Bik, EM and Garey, JR and Eriksson, KM and Nilsson, RH}, title = {Megraft: a software package to graft ribosomal small subunit (16S/18S) fragments onto full-length sequences for accurate species richness and sequencing depth analysis in pyrosequencing-length metagenomes and similar environmental datasets.}, journal = {Research in microbiology}, volume = {163}, number = {6-7}, pages = {407-412}, doi = {10.1016/j.resmic.2012.07.001}, pmid = {22824070}, issn = {1769-7123}, mesh = {Computational Biology/*methods ; DNA, Ribosomal/chemistry/*genetics ; *Environmental Microbiology ; *Metagenome ; Metagenomics/*methods ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 18S/genetics ; *Software ; }, abstract = {Metagenomic libraries represent subsamples of the total DNA found at a study site and offer unprecedented opportunities to study ecological and functional aspects of microbial communities. To examine the depth of a community sequencing effort, rarefaction analysis of the ribosomal small subunit (SSU/16S/18S) gene in the metagenome is usually performed. The fragmentary, non-overlapping nature of SSU sequences in metagenomic libraries poses a problem for this analysis, however. We introduce a software package - Megraft - that grafts SSU fragments onto full-length SSU sequences, accounting for observed and unobserved variability, for accurate assessment of species richness and sequencing depth in metagenomics endeavors.}, } @article {pmid22820204, year = {2012}, author = {Peakall, R and Smouse, PE}, title = {GenAlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and research--an update.}, journal = {Bioinformatics (Oxford, England)}, volume = {28}, number = {19}, pages = {2537-2539}, pmid = {22820204}, issn = {1367-4811}, mesh = {Computational Biology/methods ; Gene Frequency ; Genetic Markers ; Genetics, Population/*education/*methods ; Haplotypes ; Linkage Disequilibrium ; *Software ; User-Computer Interface ; }, abstract = {SUMMARY: GenAlEx: Genetic Analysis in Excel is a cross-platform package for population genetic analyses that runs within Microsoft Excel. GenAlEx offers analysis of diploid codominant, haploid and binary genetic loci and DNA sequences. Both frequency-based (F-statistics, heterozygosity, HWE, population assignment, relatedness) and distance-based (AMOVA, PCoA, Mantel tests, multivariate spatial autocorrelation) analyses are provided. New features include calculation of new estimators of population structure: G'(ST), G''(ST), Jost's D(est) and F'(ST) through AMOVA, Shannon Information analysis, linkage disequilibrium analysis for biallelic data and novel heterogeneity tests for spatial autocorrelation analysis. Export to more than 30 other data formats is provided. Teaching tutorials and expanded step-by-step output options are included. The comprehensive guide has been fully revised.

GenAlEx is written in VBA and provided as a Microsoft Excel Add-in (compatible with Excel 2003, 2007, 2010 on PC; Excel 2004, 2011 on Macintosh). GenAlEx, and supporting documentation and tutorials are freely available at: http://biology.anu.edu.au/GenAlEx.

CONTACT: rod.peakall@anu.edu.au.}, } @article {pmid22814884, year = {2012}, author = {Bouétard, A and Noirot, C and Besnard, AL and Bouchez, O and Choisne, D and Robe, E and Klopp, C and Lagadic, L and Coutellec, MA}, title = {Pyrosequencing-based transcriptomic resources in the pond snail Lymnaea stagnalis, with a focus on genes involved in molecular response to diquat-induced stress.}, journal = {Ecotoxicology (London, England)}, volume = {21}, number = {8}, pages = {2222-2234}, pmid = {22814884}, issn = {1573-3017}, mesh = {Animals ; Databases, Genetic ; Diquat/*pharmacology ; Expressed Sequence Tags ; Gene Expression Profiling ; Herbicides/*pharmacology ; Lymnaea/*drug effects/*genetics ; Sequence Analysis, DNA ; *Transcriptome ; }, abstract = {Due to their ability to explore whole genome response to drugs and stressors, omics-based approaches are widely used in toxicology and ecotoxicology, and identified as powerful tools for future ecological risk assessment and environmental monitoring programs. Understanding the long-term effects of contaminants may indeed benefit from the coupling of genomics and eco-evolutionary hypotheses. Next-generation sequencing provides a new way to investigate pollutants impact, by targeting early responses, screening chemicals, and directly quantifying gene expression, even in organisms without reference genome. Lymnaea stagnalis is a freshwater mollusk in which access to genomic resources is critical for many scientific issues, especially in ecotoxicology. We used 454-pyrosequencing to obtain new transcriptomic resources in L. stagnalis and to preliminarily explore gene expression response to a redox-cycling pesticide, diquat. We obtained 151,967 and 128,945 high-quality reads from control and diquat-exposed individuals, respectively. Sequence assembly provided 141,999 contigs, of which 124,387 were singletons. BlastX search revealed significant match for 34.6 % of the contigs (21.2 % protein hits). KEGG annotation showed a predominance of hits with genes involved in energy metabolism and circulatory system, and revealed more than 400 putative genes involved in oxidative stress, cellular/molecular stress and signaling pathways, apoptosis, and metabolism of xenobiotics. Results also suggest that diquat may have a great diversity of molecular effects. Moreover, new genetic markers (putative SNPs) were discovered. We also created a Ensembl-like web-tool for data-mining (http://genotoul-contigbrowser.toulouse.inra.fr:9095/Lymnaea_stagnalis/index.html). This resource is expected to be relevant for any genomic approach aimed at understanding the molecular basis of physiological and evolutionary responses to environmental stress in L. stagnalis.}, } @article {pmid22814493, year = {2012}, author = {Rhee, JS and Choi, BS and Han, J and Hwang, SJ and Choi, IY and Lee, JS}, title = {Draft genome database construction from four strains (NIES-298, FCY- 26, -27, and -28) of the cyanobacterium Microcystis aeruginosa.}, journal = {Journal of microbiology and biotechnology}, volume = {22}, number = {9}, pages = {1208-1213}, doi = {10.4014/jmb.1112.12034}, pmid = {22814493}, issn = {1738-8872}, mesh = {Bacterial Proteins/genetics ; *Databases, Genetic ; Genes, Bacterial ; *Genome, Bacterial ; Harmful Algal Bloom ; Microcystis/*classification/*genetics ; Sequence Analysis, DNA ; }, abstract = {Microcystis aeruginosa is a cyanobacterium that can form harmful algal blooms (HABs) producing toxic secondary metabolites. We provide here draft genome information of four strains of this freshwater cyanobacterium that was obtained by the Next Generation Sequencing approach to provide a better understanding of molecular mechanisms at the physiological and ecological levels. After gene assembly, genes of each strain were identified and annotated, and a genome database and G-browser of M. aeruginosa were subsequently constructed. Such genome information resources will enable us to obtain useful information for molecular ecological studies with a better understanding of modulating mechanisms of environmental factors associated with blooming.}, } @article {pmid22809620, year = {2012}, author = {Woltedji, D and Song, F and Zhang, L and Gala, A and Han, B and Feng, M and Fang, Y and Li, J}, title = {Western honeybee drones and workers (Apis mellifera ligustica) have different olfactory mechanisms than eastern honeybees (Apis cerana cerana).}, journal = {Journal of proteome research}, volume = {11}, number = {9}, pages = {4526-4540}, doi = {10.1021/pr300298w}, pmid = {22809620}, issn = {1535-3907}, mesh = {Animals ; Arthropod Antennae/anatomy & histology/*chemistry ; Bees/anatomy & histology/*chemistry/*physiology ; Behavior, Animal ; Computational Biology ; Electrophoresis, Gel, Two-Dimensional ; Insect Proteins/*analysis/chemistry/classification ; Polymerase Chain Reaction ; Protein Interaction Maps/physiology ; Proteome/*analysis/chemistry ; Reproducibility of Results ; Smell/physiology ; }, abstract = {The honeybees Apis mellifera ligustica (Aml) and Apis cerana cerana (Acc) are two different western and eastern bee species that evolved in distinct ecologies and developed specific antennal olfactory systems for their survival. Knowledge of how their antennal olfactory systems function in regards to the success of each respective bee species is scarce. We compared the antennal morphology and proteome between respective sexually mature drones and foraging workers of both species using a scanning electron microscope, two-dimensional electrophoresis, mass spectrometry, bioinformatics, and quantitative real-time polymerase chain reaction. Despite the general similarities in antennal morphology of the drone and worker bees between the two species, a total of 106 and 100 proteins altered their expression in the drones' and the workers' antennae, respectively. This suggests that the differences in the olfactory function of each respective bee are supported by the change of their proteome. Of the 106 proteins that altered their expression in the drones, 72 (68%) and 34 (32%) were overexpressed in the drones of Aml and Acc, respectively. The antennae of the Aml drones were built up by the highly expressed proteins that were involved in carbohydrate metabolism and energy production, molecular transporters, antioxidation, and fatty acid metabolism in contrast to the Acc drones. This is believed to enhance the antennal olfactory functions of the Aml drones as compared to the Acc drones during their mating flight. Likewise, of the 100 proteins with expression changes between the worker bees of the two species, 67% were expressed in higher levels in the antennae of Aml worker contrasting to 33% in the Acc worker. The overall higher expressions of proteins related to carbohydrate metabolism and energy production, molecular transporters, and antioxidation in the Aml workers compared with the Acc workers indicate the Aml workers require more antennal proteins for their olfactory mechanisms to perform efficient foraging activities than do the Acc worker bees. These data decipher the mechanisms of the western and eastern drone and worker bees acting in response to their different olfactory system in their distinct ecosystem.}, } @article {pmid22809407, year = {2012}, author = {Banu, S and Hu, W and Hurst, C and Guo, Y and Islam, MZ and Tong, S}, title = {Space-time clusters of dengue fever in Bangladesh.}, journal = {Tropical medicine & international health : TM & IH}, volume = {17}, number = {9}, pages = {1086-1091}, doi = {10.1111/j.1365-3156.2012.03038.x}, pmid = {22809407}, issn = {1365-3156}, mesh = {Bangladesh/epidemiology ; Dengue/*epidemiology/transmission ; Disease Outbreaks ; Geographic Information Systems/*statistics & numerical data ; Humans ; Risk Factors ; Space-Time Clustering ; }, abstract = {OBJECTIVE: To examine the space-time clustering of dengue fever (DF) transmission in Bangladesh using geographical information system and spatial scan statistics (SaTScan).

METHODS: We obtained data on monthly suspected DF cases and deaths by district in Bangladesh for the period of 2000-2009 from Directorate General of Health Services. Population and district boundary data of each district were collected from national census managed by Bangladesh Bureau of Statistics. To identify the space-time clusters of DF transmission a discrete Poisson model was performed using SaTScan software.

RESULTS: Space-time distribution of DF transmission was clustered during three periods 2000-2002, 2003-2005 and 2006-2009. Dhaka was the most likely cluster for DF in all three periods. Several other districts were significant secondary clusters. However, the geographical range of DF transmission appears to have declined in Bangladesh over the last decade.

CONCLUSION: There were significant space-time clusters of DF in Bangladesh over the last decade. Our results would prompt future studies to explore how social and ecological factors may affect DF transmission and would also be useful for improving DF control and prevention programs in Bangladesh.}, } @article {pmid22808280, year = {2012}, author = {Toju, H and Tanabe, AS and Yamamoto, S and Sato, H}, title = {High-coverage ITS primers for the DNA-based identification of ascomycetes and basidiomycetes in environmental samples.}, journal = {PloS one}, volume = {7}, number = {7}, pages = {e40863}, pmid = {22808280}, issn = {1932-6203}, mesh = {Ascomycota/*classification/*genetics ; Base Pair Mismatch ; Base Sequence ; Basidiomycota/*classification/*genetics ; Cell Nucleus/genetics ; Computational Biology ; DNA Primers/*metabolism ; DNA, Fungal/*genetics ; DNA, Intergenic/*genetics ; Environmental Microbiology ; Mycological Typing Techniques ; Nucleic Acid Renaturation/genetics ; Plants/genetics ; Polymerase Chain Reaction ; RNA, Ribosomal/genetics ; Temperature ; }, abstract = {The kingdom Fungi is estimated to include 1.5 million or more species, playing key roles as decomposers, mutualists, and parasites in every biome on the earth. To comprehensively understand the diversity and ecology of this huge kingdom, DNA barcoding targeting the internal transcribed spacer (ITS) region of the nuclear ribosomal repeat has been regarded as a prerequisite procedure. By extensively surveying ITS sequences in public databases, we designed new ITS primers with improved coverage across diverse taxonomic groups of fungi compared to existing primers. An in silico analysis based on public sequence databases indicated that the newly designed primers matched 99% of ascomycete and basidiomycete ITS taxa (species, subspecies or varieties), causing little taxonomic bias toward either fungal group. Two of the newly designed primers could inhibit the amplification of plant sequences and would enable the selective investigation of fungal communities in mycorrhizal associations, soil, and other types of environmental samples. Optimal PCR conditions for the primers were explored in an in vitro investigation. The new primers developed in this study will provide a basis for ecological studies on the diversity and community structures of fungi in the era of massive DNA sequencing.}, } @article {pmid22808241, year = {2012}, author = {Hoenner, X and Whiting, SD and Hindell, MA and McMahon, CR}, title = {Enhancing the use of Argos satellite data for home range and long distance migration studies of marine animals.}, journal = {PloS one}, volume = {7}, number = {7}, pages = {e40713}, pmid = {22808241}, issn = {1932-6203}, mesh = {Animal Migration/*physiology ; Animals ; Australia ; *Ecosystem ; Female ; Geographic Information Systems ; Geography ; Homing Behavior/*physiology ; Likelihood Functions ; *Satellite Communications ; Turtles/*physiology ; }, abstract = {Accurately quantifying animals' spatial utilisation is critical for conservation, but has long remained an elusive goal due to technological impediments. The Argos telemetry system has been extensively used to remotely track marine animals, however location estimates are characterised by substantial spatial error. State-space models (SSM) constitute a robust statistical approach to refine Argos tracking data by accounting for observation errors and stochasticity in animal movement. Despite their wide use in ecology, few studies have thoroughly quantified the error associated with SSM predicted locations and no research has assessed their validity for describing animal movement behaviour. We compared home ranges and migratory pathways of seven hawksbill sea turtles (Eretmochelys imbricata) estimated from (a) highly accurate Fastloc GPS data and (b) locations computed using common Argos data analytical approaches. Argos 68(th) percentile error was <1 km for LC 1, 2, and 3 while markedly less accurate (>4 km) for LC ≤ 0. Argos error structure was highly longitudinally skewed and was, for all LC, adequately modelled by a Student's t distribution. Both habitat use and migration routes were best recreated using SSM locations post-processed by re-adding good Argos positions (LC 1, 2 and 3) and filtering terrestrial points (mean distance to migratory tracks ± SD = 2.2 ± 2.4 km; mean home range overlap and error ratio = 92.2% and 285.6 respectively). This parsimonious and objective statistical procedure however still markedly overestimated true home range sizes, especially for animals exhibiting restricted movements. Post-processing SSM locations nonetheless constitutes the best analytical technique for remotely sensed Argos tracking data and we therefore recommend using this approach to rework historical Argos datasets for better estimation of animal spatial utilisation for research and evidence-based conservation purposes.}, } @article {pmid22808216, year = {2012}, author = {Yi, Z and Katz, LA and Song, W}, title = {Assessing whether alpha-tubulin sequences are suitable for phylogenetic reconstruction of Ciliophora with insights into its evolution in euplotids.}, journal = {PloS one}, volume = {7}, number = {7}, pages = {e40635}, pmid = {22808216}, issn = {1932-6203}, mesh = {Amino Acid Sequence ; Base Sequence ; Ciliophora/*genetics ; DNA, Ribosomal/genetics ; Databases, Genetic ; Genes/genetics ; Genetic Variation ; Likelihood Functions ; *Phylogeny ; Ribosome Subunits, Small, Eukaryotic/genetics ; Species Specificity ; Tubulin/chemistry/*genetics ; }, abstract = {The current understanding of ciliate phylogeny is mainly based on analyses of a single gene, the small subunit ribosomal RNA (SSU-rDNA). However, phylogenetic trees based on single gene sequence are not reliable estimators of species trees, and SSU-rDNA genealogies are not useful for resolution of some branches within Ciliophora. Since congruence between multiple loci is the best tool to determine evolutionary history, we assessed the usefulness of alpha-tubulin gene, a protein-coding gene that is frequently sequenced, for ciliate phylogeny. Here, we generate alpha-tubulin gene sequences of 12 genera and 30 species within the order Euplotida, one of the most frequently encountered ciliate clades with numerous apparently cosmopolitan species, as well as four genera within its putative sister order Discocephalida. Analyses of the resulting data reveal that: 1) the alpha-tubulin gene is suitable phylogenetic marker for euplotids at the family level, since both nucleotide and amino acid phylogenies recover all monophyletic euplotid families as defined by both morphological criteria and SSU-rDNA trees; however, alpha-tubulin gene is not a good marker for defining species, order and subclass; 2) for seven out of nine euplotid species for which paralogs are detected, gene duplication appears recent as paralogs are monophyletic; 3) the order Euplotida is non-monophyletic, and the family Uronychiidae with sequences from four genera, is non-monophyletic; and 4) there is more genetic diversity within the family Euplotidae than is evident from dargyrome (geometrical pattern of dorsal "silverline system" in ciliates) patterns, habit and SSU-rDNA phylogeny, which indicates the urgent need for taxonomic revision in this area.}, } @article {pmid22807668, year = {2012}, author = {Faust, K and Sathirapongsasuti, JF and Izard, J and Segata, N and Gevers, D and Raes, J and Huttenhower, C}, title = {Microbial co-occurrence relationships in the human microbiome.}, journal = {PLoS computational biology}, volume = {8}, number = {7}, pages = {e1002606}, pmid = {22807668}, issn = {1553-7358}, support = {U54HG004969/HG/NHGRI NIH HHS/United States ; P30 DK043351/DK/NIDDK NIH HHS/United States ; R01 HG005969/HG/NHGRI NIH HHS/United States ; U54 HG004969/HG/NHGRI NIH HHS/United States ; CA139193/CA/NCI NIH HHS/United States ; R21 CA139193/CA/NCI NIH HHS/United States ; 1R01HG005969/HG/NHGRI NIH HHS/United States ; }, mesh = {Bacteria/*classification ; *Bacterial Physiological Phenomena ; Computational Biology ; DNA, Bacterial/chemistry ; Ecosystem ; Female ; Gastrointestinal Tract/microbiology ; Genes, rRNA/genetics ; Humans ; Linear Models ; Male ; Metagenome/*physiology ; Microbial Interactions/physiology ; Nasal Cavity/microbiology ; Phylogeny ; Skin/microbiology ; Vagina/microbiology ; }, abstract = {The healthy microbiota show remarkable variability within and among individuals. In addition to external exposures, ecological relationships (both oppositional and symbiotic) between microbial inhabitants are important contributors to this variation. It is thus of interest to assess what relationships might exist among microbes and determine their underlying reasons. The initial Human Microbiome Project (HMP) cohort, comprising 239 individuals and 18 different microbial habitats, provides an unprecedented resource to detect, catalog, and analyze such relationships. Here, we applied an ensemble method based on multiple similarity measures in combination with generalized boosted linear models (GBLMs) to taxonomic marker (16S rRNA gene) profiles of this cohort, resulting in a global network of 3,005 significant co-occurrence and co-exclusion relationships between 197 clades occurring throughout the human microbiome. This network revealed strong niche specialization, with most microbial associations occurring within body sites and a number of accompanying inter-body site relationships. Microbial communities within the oropharynx grouped into three distinct habitats, which themselves showed no direct influence on the composition of the gut microbiota. Conversely, niches such as the vagina demonstrated little to no decomposition into region-specific interactions. Diverse mechanisms underlay individual interactions, with some such as the co-exclusion of Porphyromonaceae family members and Streptococcus in the subgingival plaque supported by known biochemical dependencies. These differences varied among broad phylogenetic groups as well, with the Bacilli and Fusobacteria, for example, both enriched for exclusion of taxa from other clades. Comparing phylogenetic versus functional similarities among bacteria, we show that dominant commensal taxa (such as Prevotellaceae and Bacteroides in the gut) often compete, while potential pathogens (e.g. Treponema and Prevotella in the dental plaque) are more likely to co-occur in complementary niches. This approach thus serves to open new opportunities for future targeted mechanistic studies of the microbial ecology of the human microbiome.}, } @article {pmid22807061, year = {2012}, author = {Hood, LE and Omenn, GS and Moritz, RL and Aebersold, R and Yamamoto, KR and Amos, M and Hunter-Cevera, J and Locascio, L and , }, title = {New and improved proteomics technologies for understanding complex biological systems: addressing a grand challenge in the life sciences.}, journal = {Proteomics}, volume = {12}, number = {18}, pages = {2773-2783}, pmid = {22807061}, issn = {1615-9861}, support = {RC2 HG005805/HG/NHGRI NIH HHS/United States ; U24 CA160034/CA/NCI NIH HHS/United States ; }, mesh = {Agriculture/economics/education/methods ; Animals ; Biological Science Disciplines/economics/education/*methods ; Computational Biology/economics/education/*methods ; Ecology/economics/education/methods ; Genome ; Human Genome Project ; Humans ; Mass Spectrometry/economics/methods ; Protein Folding ; Proteins/*analysis/genetics/metabolism ; Proteomics/economics/education/*methods ; Research/economics/education ; Systems Biology/economics/education/methods ; United States ; }, abstract = {This White Paper sets out a Life Sciences Grand Challenge for Proteomics Technologies to enhance our understanding of complex biological systems, link genomes with phenotypes, and bring broad benefits to the biosciences and the US economy. The paper is based on a workshop hosted by the National Institute of Standards and Technology (NIST) in Gaithersburg, MD, 14-15 February 2011, with participants from many federal R&D agencies and research communities, under the aegis of the US National Science and Technology Council (NSTC). Opportunities are identified for a coordinated R&D effort to achieve major technology-based goals and address societal challenges in health, agriculture, nutrition, energy, environment, national security, and economic development.}, } @article {pmid22805179, year = {2012}, author = {Li, C and Riethoven, JJ and Naylor, GJ}, title = {EvolMarkers: a database for mining exon and intron markers for evolution, ecology and conservation studies.}, journal = {Molecular ecology resources}, volume = {12}, number = {5}, pages = {967-971}, doi = {10.1111/j.1755-0998.2012.03167.x}, pmid = {22805179}, issn = {1755-0998}, mesh = {Animals ; Computational Biology/*methods ; *Databases, Genetic ; Ecology/*methods ; Evolution, Molecular ; Exons ; *Genetic Markers ; Introns ; Plants ; }, abstract = {Recent innovations in next-generation sequencing have lowered the cost of genome projects. Nevertheless, sequencing entire genomes for all representatives in a study remains expensive and unnecessary for most studies in ecology, evolution and conservation. It is still more cost-effective and efficient to target and sequence single-copy nuclear gene markers for such studies. Many tools have been developed for identifying nuclear markers, but most of these have focused on particular taxonomic groups. We have built a searchable database, EvolMarkers, for developing single-copy coding sequence (CDS) and exon-primed-intron-crossing (EPIC) markers that is designed to work across a broad range of phylogenetic divergences. The database is made up of single-copy CDS derived from BLAST searches of a variety of metazoan genomes. Users can search the database for different types of markers (CDS or EPIC) that are common to different sets of input species with different divergence characteristics. EvolMarkers can be applied to any taxonomic group for which genome data are available for two or more species. We included 82 genomes in the first version of EvolMarkers and have found the methods to be effective across Placozoa, Cnidaria, Arthropod, Nematoda, Annelida, Mollusca, Echinodermata, Hemichordata, Chordata and plants. We demonstrate the effectiveness of searching for CDS markers within annelids and show how to find potentially useful intronic markers within the lizard Anolis.}, } @article {pmid22803479, year = {2012}, author = {Pan, JH and Su, YC and Huang, YS and Liu, X}, title = {[Dynamic changes of land use and landscape patterns in middle reaches of Shule River, Northwest China].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {23}, number = {4}, pages = {1090-1096}, pmid = {22803479}, issn = {1001-9332}, mesh = {China ; Climate Change ; *Conservation of Natural Resources ; Construction Industry ; Crops, Agricultural/*growth & development ; *Ecosystem ; Geographic Information Systems ; Rivers ; }, abstract = {By using the MSS images in 1976, TM images in 1989 and 2010, and ETM+ images in 2000, in combining with GIS and landscape ecological methods, this paper analyzed the changes of land use/cover and landscape patterns in Yumen County at the middle reaches of Shule River from 1976 to 2010. In the study period, the major patterns of land use change in the County were the conversions from grassland and Gobi to farmland, from farmland to construction land, and from grassland to Gobi. Such a land use change underwent a process of 'slow - tremendous - obvious', during which, the landscape density increased, the largest path index decreased after an initial increase, the weighted area index increased, and the landscape shape became irregular. In the meantime, the nearest distances between patches and the separation among different patches decreased, the patches became more complex, and the landscape diversity and evenness increased after an initial decrease. The increased landscape diversity and fragmentation also showed that the land uses became more complex. The growth of agricultural population and the development of economy were the most direct driving forces of the land use/cover change in Yumen City, whereas the climatic and policy factors also had important effects on the land use change in the study area.}, } @article {pmid22802667, year = {2012}, author = {Zammit-Mangion, A and Dewar, M and Kadirkamanathan, V and Sanguinetti, G}, title = {Point process modelling of the Afghan War Diary.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {109}, number = {31}, pages = {12414-12419}, pmid = {22802667}, issn = {1091-6490}, mesh = {*Afghan Campaign 2001- ; Ecology/history ; History, 21st Century ; Humans ; *Models, Theoretical ; }, abstract = {Modern conflicts are characterized by an ever increasing use of information and sensing technology, resulting in vast amounts of high resolution data. Modelling and prediction of conflict, however, remain challenging tasks due to the heterogeneous and dynamic nature of the data typically available. Here we propose the use of dynamic spatiotemporal modelling tools for the identification of complex underlying processes in conflict, such as diffusion, relocation, heterogeneous escalation, and volatility. Using ideas from statistics, signal processing, and ecology, we provide a predictive framework able to assimilate data and give confidence estimates on the predictions. We demonstrate our methods on the WikiLeaks Afghan War Diary. Our results show that the approach allows deeper insights into conflict dynamics and allows a strikingly statistically accurate forward prediction of armed opposition group activity in 2010, based solely on data from previous years.}, } @article {pmid22799480, year = {2012}, author = {Fenton, M}, title = {Community design and policies for free-range children: creating environments that support routine physical activity.}, journal = {Childhood obesity (Print)}, volume = {8}, number = {1}, pages = {44-51}, doi = {10.1089/chi.2011.0122}, pmid = {22799480}, issn = {2153-2176}, mesh = {Behavior Control/methods ; Child ; Community Networks/organization & administration ; *Environment Design/economics/standards ; *Environmental Policy ; Fitness Centers/organization & administration ; Health Behavior ; Health Promotion/*organization & administration ; Humans ; *Motor Activity ; *Obesity/prevention & control/psychology ; Policy Making ; Public Facilities/standards ; Resource Allocation/methods ; }, abstract = {Growing concern over childhood obesity has prompted a focus on underlying epidemics of physical inactivity and poor nutrition. Regarding the former, there is increasing understanding that behavior change promotion alone has not increased population physical activity levels and that an ecological approach is necessary. Therefore, the public health profession has moved beyond traditional behavior change campaigns toward a growing focus on altering policies and the built environment to create settings that support increases in routine, not just exercise or leisure time, physical activity among children. A survey of the literature suggests four broad factors that define settings where routine physical activity, especially active transportation, is more likely to occur: • a compact variety of land uses, with a mix of destinations in close proximity; • a comprehensive network of bicycle, pedestrian, and transit facilities; • inviting and functional site designs for pedestrians, cyclists, and transit users; • safety and access for users of all ages, incomes, abilities and disabilities. Although these principles are increasingly accepted as beneficial, not just to health but to a community's economic, environmental, and social well-being, many contemporary ordinances and development practices undermine these outcomes. Therefore, five specific policy and intervention approaches are recommended to guide communities to these outcomes: 1. zoning and development policies to protect open space, contain sprawl, and focus investment toward thriving, mixed downtowns and village centers; 2. Complete Streets policies, which require roadways that are safe and functional for pedestrians, bicyclists, and transit users, as well as motor vehicles; 3. a transportation- (not just recreation-) oriented trail network; 4. creation of bicycle- and transit-friendly infrastructure and incentive policies; 5. development of policy-based Safe Routes to School interventions. This proposed intervention framework requires evaluation both of effectiveness in increasing childhood physical activity and of the most promising means of getting policies implemented.}, } @article {pmid22795359, year = {2012}, author = {Merlo, J and Viciana-Fernández, FJ and Ramiro-Fariñas, D and , }, title = {Bringing the individual back to small-area variation studies: a multilevel analysis of all-cause mortality in Andalusia, Spain.}, journal = {Social science & medicine (1982)}, volume = {75}, number = {8}, pages = {1477-1487}, doi = {10.1016/j.socscimed.2012.06.004}, pmid = {22795359}, issn = {1873-5347}, mesh = {Aged ; *Cause of Death ; Databases, Factual ; Female ; Humans ; Longitudinal Studies ; Male ; Middle Aged ; Multilevel Analysis/*methods ; Risk Factors ; *Small-Area Analysis ; Spain/epidemiology ; }, abstract = {We performed a multilevel analysis (including individuals, households, census tracts, municipalities and provinces) on a 10% sample (N=230,978) from the Longitudinal Database of the Andalusian Population (LDAP). We aimed to investigate place effects on 8-year individual mortality risk. Moreover, besides calculating association (yielding odds ratios, ORs) between area socio-economic circumstances and individual risk, we wanted to estimate variance and clustering using the variance partition coefficient (VPC). We explicitly proclaim the relevance of considering general contextual effects (i.e. the degree to which the context, as a whole, affects individual variance in mortality risk) under at least two circumstances. The first of these concerns the interpretation of specific contextual effects (i.e. the association between a particular area characteristic and individual risk) obtained from multilevel regression analyses. The second involves the interpretation of geographical variance obtained from classic ecological spatial analyses. The so-called "ecological fallacy" apart, the lack of individual-level information renders geographical variance unrelated to the total individual variation and, therefore, difficult to interpret. Finally, we stress the importance of considering the familial household in multilevel analyses. We observed an association between percentage of people with a low educational level in the census tract and individual mortality risk (OR, highest v. lowest quintile=1.14; 95% confidence interval, CI 1.08-1.20). However, only a minor proportion of the total individual variance in the probability of dying was at the municipality (M) and census tract (CT) levels (VPC(M)=0.2% and VPC(CT)=0.3%). Conversely, the household (H) level appeared much more relevant (VPC(H)=18.6%) than the administrative geographical areas. Without considering general contextual effects, both multilevel analyses of specific contextual effects and ecological studies of small-area variation may provide a misleading picture that overstates the role of administrative areas as contextual determinants of individual differences in mortality.}, } @article {pmid22794089, year = {2012}, author = {Lenzen, M and Kanemoto, K and Moran, D and Geschke, A}, title = {Mapping the structure of the world economy.}, journal = {Environmental science & technology}, volume = {46}, number = {15}, pages = {8374-8381}, doi = {10.1021/es300171x}, pmid = {22794089}, issn = {1520-5851}, mesh = {*Economics ; Information Systems ; *Internationality ; }, abstract = {We have developed a new series of environmentally extended multi-region input-output (MRIO) tables with applications in carbon, water, and ecological footprinting, and Life-Cycle Assessment, as well as trend and key driver analyses. Such applications have recently been at the forefront of global policy debates, such as about assigning responsibility for emissions embodied in internationally traded products. The new time series was constructed using advanced parallelized supercomputing resources, and significantly advances the previous state of art because of four innovations. First, it is available as a continuous 20-year time series of MRIO tables. Second, it distinguishes 187 individual countries comprising more than 15,000 industry sectors, and hence offers unsurpassed detail. Third, it provides information just 1-3 years delayed therefore significantly improving timeliness. Fourth, it presents MRIO elements with accompanying standard deviations in order to allow users to understand the reliability of data. These advances will lead to material improvements in the capability of applications that rely on input-output tables. The timeliness of information means that analyses are more relevant to current policy questions. The continuity of the time series enables the robust identification of key trends and drivers of global environmental change. The high country and sector detail drastically improves the resolution of Life-Cycle Assessments. Finally, the availability of information on uncertainty allows policy-makers to quantitatively judge the level of confidence that can be placed in the results of analyses.}, } @article {pmid22791706, year = {2012}, author = {Richardson, AJ and Brown, CJ and Brander, K and Bruno, JF and Buckley, L and Burrows, MT and Duarte, CM and Halpern, BS and Hoegh-Guldberg, O and Holding, J and Kappel, CV and Kiessling, W and Moore, PJ and O'Connor, MI and Pandolfi, JM and Parmesan, C and Schoeman, DS and Schwing, F and Sydeman, WJ and Poloczanska, ES}, title = {Climate change and marine life.}, journal = {Biology letters}, volume = {8}, number = {6}, pages = {907-909}, pmid = {22791706}, issn = {1744-957X}, mesh = {*Climate Change ; Data Collection ; Data Interpretation, Statistical ; *Ecosystem ; Geography ; Marine Biology/*methods/*trends ; Oceanography/methods ; Oceans and Seas ; Time Factors ; }, abstract = {A Marine Climate Impacts Workshop was held from 29 April to 3 May 2012 at the US National Center of Ecological Analysis and Synthesis in Santa Barbara. This workshop was the culmination of a series of six meetings over the past three years, which had brought together 25 experts in climate change ecology, analysis of large datasets, palaeontology, marine ecology and physical oceanography. Aims of these workshops were to produce a global synthesis of climate impacts on marine biota, to identify sensitive habitats and taxa, to inform the current Intergovernmental Panel on Climate Change (IPCC) process, and to strengthen research into ecological impacts of climate change.}, } @article {pmid22789655, year = {2012}, author = {Chang, NB and Qi, C and Yang, YJ}, title = {Optimal expansion of a drinking water infrastructure system with respect to carbon footprint, cost-effectiveness and water demand.}, journal = {Journal of environmental management}, volume = {110}, number = {}, pages = {194-206}, doi = {10.1016/j.jenvman.2012.06.004}, pmid = {22789655}, issn = {1095-8630}, mesh = {*Carbon Footprint ; Conservation of Natural Resources/economics/*methods ; Cost-Benefit Analysis ; Decision Making ; *Decision Support Techniques ; Florida ; Groundwater ; Models, Theoretical ; Systems Analysis ; Water Resources ; *Water Supply ; }, abstract = {Urban water infrastructure expansion requires careful long-term planning to reduce the risk from climate change during periods of both economic boom and recession. As part of the adaptation management strategies, capacity expansion in concert with other management alternatives responding to the population dynamics, ecological conservation, and water management policies should be systematically examined to balance the water supply and demand temporally and spatially with different scales. To mitigate the climate change impact, this practical implementation often requires a multiobjective decision analysis that introduces economic efficiencies and carbon-footprint matrices simultaneously. The optimal expansion strategies for a typical water infrastructure system in South Florida demonstrate the essence of the new philosophy. Within our case study, the multiobjective modeling framework uniquely features an integrated evaluation of transboundary surface and groundwater resources and quantitatively assesses the interdependencies among drinking water supply, wastewater reuse, and irrigation water permit transfer as the management options expand throughout varying dimensions. With the aid of a multistage planning methodology over the partitioned time horizon, such a systems analysis has resulted in a full-scale screening and sequencing of multiple competing objectives across a suite of management strategies. These strategies that prioritize 20 options provide a possible expansion schedule over the next 20 years that improve water infrastructure resilience and at low life-cycle costs. The proposed method is transformative to other applications of similar water infrastructure systems elsewhere in the world.}, } @article {pmid22789640, year = {2012}, author = {Busza, J and Walker, D and Hairston, A and Gable, A and Pitter, C and Lee, S and Katirayi, L and Simiyu, R and Mpofu, D}, title = {Community-based approaches for prevention of mother to child transmission in resource-poor settings: a social ecological review.}, journal = {Journal of the International AIDS Society}, volume = {15 Suppl 2}, number = {Suppl 2}, pages = {17373}, pmid = {22789640}, issn = {1758-2652}, mesh = {Communicable Disease Control/*methods ; Community Networks ; Female ; HIV Infections/economics/*prevention & control/*transmission ; Humans ; Infectious Disease Transmission, Vertical/economics/*prevention & control ; Male ; *Social Support ; }, abstract = {INTRODUCTION: Numerous barriers to optimal uptake of prevention of mother to child transmission (PMTCT) services occur at community level (i.e., outside the healthcare setting). To achieve elimination of paediatric HIV, therefore, interventions must also work within communities to address these barriers and increase service use and need to be informed by evidence. This paper reviews community-based approaches that have been used in resource-limited settings to increase rates of PMTCT enrolment, retention in care and successful treatment outcomes. It aims to identify which interventions work, why they may do so and what knowledge gaps remain.

METHODS: First, we identified barriers to PMTCT that originate outside the health system. These were used to construct a social ecological framework categorizing barriers to PMTCT into the following levels of influence: individual, peer and family, community and sociocultural. We then used this conceptual framework to guide a review of the literature on community-based approaches, defined as interventions delivered outside of formal health settings, with the goal of increasing uptake, retention, adherence and positive psychosocial outcomes in PMTCT programmes in resource-poor countries.

RESULTS: Our review found evidence of effectiveness of strategies targeting individuals and peer/family levels (e.g., providing household HIV testing and training peer counsellors to support exclusive breastfeeding) and at community level (e.g., participatory women's groups and home-based care to support adherence and retention). Evidence is more limited for complex interventions combining multiple strategies across different ecological levels. There is often little information describing implementation; and approaches such as "community mobilization" remain poorly defined.

CONCLUSIONS: Evidence from existing community approaches can be adapted for use in planning PMTCT. However, for successful replication of evidence-based interventions to occur, comprehensive process evaluations are needed to elucidate the pathways through which specific interventions achieve desired PMTCT outcomes. A social ecological framework can help analyze the complex interplay of facilitators and barriers to PMTCT service uptake in each context, thus helping to inform selection of locally relevant community-based interventions.}, } @article {pmid22785566, year = {2012}, author = {Hirata, M and Tateno, M and Sakuma, M and Nakanishi, N and Izawa, M and Asari, Y and Okamura, M and Shimokawa Miyama, T and Setoguchi, A and Endo, Y}, title = {An epidemiological survey of hemoplasma infection in Iriomote cats (Prionailurus bengalensis iriomotensis).}, journal = {The Journal of veterinary medical science}, volume = {74}, number = {12}, pages = {1531-1537}, doi = {10.1292/jvms.12-0094}, pmid = {22785566}, issn = {1347-7439}, mesh = {Animals ; Base Sequence ; Cluster Analysis ; Computational Biology ; DNA Primers/genetics ; *Endangered Species ; Felidae/*microbiology ; Female ; Japan/epidemiology ; Male ; Molecular Sequence Data ; Mycoplasma/*genetics ; Mycoplasma Infections/blood/*epidemiology/*veterinary ; *Phylogeny ; Polymerase Chain Reaction/veterinary ; Prevalence ; Sequence Analysis, DNA/veterinary ; Species Specificity ; }, abstract = {An epidemiological survey of Iriomote cats (Prionailurus bengalensis iriomotensis) was conducted to understand the prevalence and molecular characteristics of hemotropic mycoplasma (hemoplasma). A series of ecological surveys of Iriomote cats were performed between November 2003 and September 2010. During this period, 31 Iriomote cats were captured or found, and 39 blood samples were collected. Polymerase chain reaction screening for hemoplasmas and BLAST searches revealed that 4 of the 31 cats were positive for hemoplasma infection (n=3, Mycoplasma haemofelis [Mhf]; n=1, 'Candidatus M. turicensis' [CMt]). The 4 infected cats were captured or found in the northern area of the island of Iriomote. Phylogenetic analyses revealed close relationships between Mhf and CMt isolated from Iriomote cats compared with those from domestic cats and other wild felids. In our study, we identified two species of hemoplasma in Iriomote cats. The number and location of the hemoplasma-positive cats appeared to be limited; however, continuous surveillance of hemoplasma infection in Iriomote cats is necessary.}, } @article {pmid22784095, year = {2012}, author = {Balakirev, ES and Krupnova, TN and Ayala, FJ}, title = {DNA variation in the phenotypically-diverse brown alga Saccharina japonica.}, journal = {BMC plant biology}, volume = {12}, number = {}, pages = {108}, pmid = {22784095}, issn = {1471-2229}, mesh = {Base Sequence ; Cell Nucleus/genetics ; DNA, Algal/*genetics ; DNA, Chloroplast/*genetics ; DNA, Mitochondrial/*genetics ; Databases, Genetic ; Electron Transport Complex IV/genetics ; Genetic Markers ; Mitochondria/genetics ; Molecular Sequence Data ; Phaeophyceae/*genetics ; *Phenotype ; Phylogeny ; Plastids/genetics ; *Polymorphism, Genetic ; Recombination, Genetic ; Ribulose-Bisphosphate Carboxylase/genetics ; }, abstract = {BACKGROUND: Saccharina japonica (Areschoug) Lane, Mayes, Druehl et Saunders is an economically important and highly morphologically variable brown alga inhabiting the northwest Pacific marine waters. On the basis of nuclear (ITS), plastid (rbcLS) and mitochondrial (COI) DNA sequence data, we have analyzed the genetic composition of typical Saccharina japonica (TYP) and its two common morphological varieties, known as the "longipes" (LON) and "shallow-water" (SHA) forms seeking to clarify their taxonomical status and to evaluate the possibility of cryptic species within S. japonica.

RESULTS: The data show that the TYP and LON forms are very similar genetically in spite of drastic differences in morphology, life history traits, and ecological preferences. Both, however, are genetically quite different from the SHA form. The two Saccharina lineages are distinguished by 109 fixed single nucleotide differences as well as by seven fixed length polymorphisms (based on a 4,286 bp concatenated dataset that includes three gene regions). The GenBank database reveals a close affinity of the TYP and LON forms to S. japonica and the SHA form to S. cichorioides. The three gene markers used in the present work have different sensitivity for the algal species identification. COI gene was the most discriminant gene marker. However, we have detected instances of interspecific COI recombination reflecting putative historical hybridization events between distantly related algal lineages. The recombinant sequences show highly contrasted level of divergence in the 5'- and 3'- regions of the gene, leading to significantly different tree topologies depending on the gene segment (5'- or 3'-) used for tree reconstruction. Consequently, the 5'-COI "barcoding" region (~ 650 bp) can be misleading for identification purposes, at least in the case of algal species that might have experienced historical hybridization events.

CONCLUSION: Taking into account the potential roles of phenotypic plasticity in evolution, we conclude that the TYP and LON forms represent examples of algae phenotypic diversification that enables successful adaptation to contrasting shallow- and deep-water marine environments, while the SHA form is very similar to S. cichorioides and should be considered a different species. Practical applications for algal management and conservation are briefly considered.}, } @article {pmid22782093, year = {2012}, author = {Rodrigues, M and Bonfim, C and de Frias, PG and Braga, C and Gurgel, IG and Medeiros, Z}, title = {Differentials in vital information in the state of Pernambuco, Brazil, 2006-2008.}, journal = {Revista brasileira de epidemiologia = Brazilian journal of epidemiology}, volume = {15}, number = {2}, pages = {275-284}, doi = {10.1590/s1415-790x2012000200005}, pmid = {22782093}, issn = {1980-5497}, mesh = {Birth Rate/*trends ; Brazil ; Humans ; Infant ; Infant Mortality/*trends ; Infant, Newborn ; Information Systems/*standards ; Vital Statistics ; }, abstract = {OBJECTIVE: To assess differentials in official birth and death data for estimating infant mortality.

METHODS: An ecological study was conducted based on data obtained from birth and death information systems in the state of Pernambuco, northeastern Brazil, between 2006 and 2008. The following indicators were used: age-standardized mortality rate, relative mean deviation of mortality rate, ratio of reported to estimated live births, relative mean deviation of birth rate and proportion of deaths of unknown cause. These indicators were grouped into three dimensions: mortality, fertility and ill-defined causes. Based on predetermined criteria, municipalities were classified as follows: consolidated vital data; vital data in the consolidation phase; and non-consolidated data. The data were analyzed using EpiInfo and Terraview for map preparation.

RESULTS: Of the 185 municipalities in the state of Pernambuco, 141 (76.2%) were classified as having consolidated vital data, accounting for about 85% of the state population, and 17 (9.2%) were classified as having non-consolidated data, accounting for only 4.9% of the population. Larger municipalities (50,000 inhabitants or more) showed better data quality.

CONCLUSION: The approach studied proved itself valuable to assess the quality of vital information and identify inequalities in Pernambuco. Reduction of inequalities is a challenge in this state in the sense of enabling vital information to be analyzed directly from data systems at the local level. It will also allow assessing the effectiveness of initiatives to reduce infant mortality in Pernambuco.}, } @article {pmid22781559, year = {2013}, author = {Schneider, S and Gruber, J}, title = {Neighbourhood deprivation and outlet density for tobacco, alcohol and fast food: first hints of obesogenic and addictive environments in Germany.}, journal = {Public health nutrition}, volume = {16}, number = {7}, pages = {1168-1177}, pmid = {22781559}, issn = {1475-2727}, mesh = {*Alcohol Drinking ; *Environment ; Fast Foods/*statistics & numerical data ; Food Supply/statistics & numerical data ; Geographic Information Systems/statistics & numerical data ; Germany ; Humans ; Life Style ; Residence Characteristics/*statistics & numerical data ; Restaurants/statistics & numerical data ; Risk Factors ; Schools/statistics & numerical data ; *Smoking ; Social Environment ; Socioeconomic Factors ; }, abstract = {OBJECTIVE: The current discussion regarding ‘place effects on health’ is increasingly focusing on the characteristics of a specific physical environment. Our study investigated whether socially deprived residential areas are more likely than affluent neighbourhoods to provide access to addictive substances and fast food.

DESIGN: In this ecological study the total number of tobacco, alcohol and fastfood outlets was recorded and visualized using a geographic information system. Area affluence was measured through the percentage of parents with children of kindergarten or school age with joint annual taxable income ,h12 272.

SETTING: Eighteen social areas in Cologne, Germany.

SUBJECTS: All social areas in four districts in Cologne, Germany, with a total of 92 000 inhabitants, were analysed.

RESULTS: In the investigation area, 339 tobacco, 353 alcohol and sixty-seven fastfood outlets were identified. As area affluence declined the availability of the following potentially health damaging sources increased: cigarettes (Kendall’s tau50?433; P50?012), alcohol (Kendall’s tau50?341, P50?049) and fast food (Kendall’s tau50?473; P50?009).

CONCLUSIONS: The availability of addictive substances and fast food can be seen to have a contextual influence on an individual’s lifestyle and can, in the form of physical exposure to obesogenic and addictive environments, contribute to a culmination of health risks.}, } @article {pmid22781075, year = {2012}, author = {Geary, J and Satti, M and Moreno, Y and Madrill, N and Whitten, D and Headley, SA and Agnew, D and Geary, T and Mackenzie, C}, title = {First analysis of the secretome of the canine heartworm, Dirofilaria immitis.}, journal = {Parasites & vectors}, volume = {5}, number = {}, pages = {140}, pmid = {22781075}, issn = {1756-3305}, mesh = {Amino Acid Motifs ; Animals ; Databases, Protein ; Dirofilaria immitis/*metabolism ; Dirofilariasis/*parasitology ; Dog Diseases/*parasitology ; Dogs ; Electrophoresis, Polyacrylamide Gel ; Female ; Helminth Proteins/analysis/*isolation & purification/metabolism ; Male ; Mass Spectrometry ; Molecular Sequence Annotation ; *Proteome ; Species Specificity ; }, abstract = {BACKGROUND: The characterization of proteins released from filariae is an important step in addressing many of the needs in the diagnosis and treatment of these clinically important parasites, as well as contributing to a clearer understanding of their biology. This report describes findings on the proteins released during in vitro cultivation of adult Dirofilaria immitis , the causative agent of canine and feline heartworm disease. Differences in protein secretion among nematodes in vivo may relate to the ecological niche of each parasite and the pathological changes that they induce.

METHODS: The proteins in the secretions of cultured adult worms were run on Tris-Glycine gels, bands separated and peptides from each band analysed by ultra mass spectrometry and compared with a FastA dataset of predicted tryptic peptides derived from a genome sequence of D. immitis.

RESULTS: This study identified 110 proteins. Of these proteins, 52 were unique to D. immitis. A total of 23 (44%) were recognized as proteins likely to be secreted. Although these proteins were unique, the motifs were conserved compared with proteins secreted by other nematodes.

CONCLUSION: The present data indicate that D. immitis secretes proteins that are unique to this species, when compared with Brugia malayi. The two major functional groups of molecules represented were those representing cellular and of metabolic processes. Unique proteins might be important for maintaining an infection in the host environment, intimately involved in the pathogenesis of disease and may also provide new tools for the diagnosis of heartworm infection.}, } @article {pmid22776566, year = {2012}, author = {Mathieu, B and Cêtre-Sossah, C and Garros, C and Chavernac, D and Balenghien, T and Carpenter, S and Setier-Rio, ML and Vignes-Lebbe, R and Ung, V and Candolfi, E and Delécolle, JC}, title = {Development and validation of IIKC: an interactive identification key for Culicoides (Diptera: Ceratopogonidae) females from the Western Palaearctic region.}, journal = {Parasites & vectors}, volume = {5}, number = {}, pages = {137}, pmid = {22776566}, issn = {1756-3305}, support = {BBS/E/I/00001701/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; Ceratopogonidae/*anatomy & histology/*classification ; *Databases, Factual ; Europe ; Female ; Reproducibility of Results ; }, abstract = {BACKGROUND AND METHODS: The appearance of bluetongue virus (BTV) in 2006 within northern Europe exposed a lack of expertise and resources available across this region to enable the accurate morphological identification of species of Culicoides Latreille biting midges, some of which are the major vectors of this pathogen. This work aims to organise extant Culicoides taxonomic knowledge into a database and to produce an interactive identification key for females of Culicoides in the Western Palaearctic (IIKC: Interactive identification key for Culicoides). We then validated IIKC using a trial carried out by six entomologists based in this region with variable degrees of experience in identifying Culicoides.

RESULTS: The current version of the key includes 98 Culicoides species with 10 morphological variants, 61 descriptors and 837 pictures and schemes. Validation was carried out by six entomologists as a blind trial with two users allocated to three classes of expertise (beginner, intermediate and advanced). Slides were identified using a median of seven steps and seven minutes and user confidence in the identification varied from 60% for failed identifications to a maximum of 80% for successful ones. By user class, the beginner group successfully identified 44.6% of slides, the intermediate 56.8% and the advanced 74.3%.

CONCLUSIONS: Structured as a multi-entry key, IIKC is a powerful database for the morphological identification of female Culicoides from the Western Palaearctic region. First developed for use as an interactive identification key, it was revealed to be a powerful back-up tool for training new taxonomists and to maintain expertise level. The development of tools for arthropod involvement in pathogen transmission will allow clearer insights into the ecology and dynamics of Culicoides and in turn assist in understanding arbovirus epidemiology.}, } @article {pmid22775323, year = {2012}, author = {McCarthy, HR and Luo, Y and Wullschleger, SD}, title = {Integrating empirical-modeling approaches to improve understanding of terrestrial ecology processes.}, journal = {The New phytologist}, volume = {195}, number = {3}, pages = {523-525}, doi = {10.1111/j.1469-8137.2012.04222.x}, pmid = {22775323}, issn = {1469-8137}, mesh = {Carbon Cycle ; Climate Change ; Congresses as Topic ; Databases, Factual ; Ecology/*methods ; *Ecosystem ; Empirical Research ; Environmental Monitoring/methods ; Forecasting ; Models, Biological ; Plants/*chemistry ; }, } @article {pmid22766352, year = {2012}, author = {Watanabe, NM and Stahlman, WD and Blaisdell, AP and Garlick, D and Fast, CD and Blumstein, DT}, title = {Quantifying personality in the terrestrial hermit crab: different measures, different inferences.}, journal = {Behavioural processes}, volume = {91}, number = {2}, pages = {133-140}, doi = {10.1016/j.beproc.2012.06.007}, pmid = {22766352}, issn = {1872-8308}, mesh = {Animals ; Anomura/*physiology ; Behavior, Animal/*physiology ; Data Interpretation, Statistical ; Electroshock ; Environment ; Exploratory Behavior/physiology ; Individuality ; Personality/*physiology ; Photic Stimulation ; Predatory Behavior ; Temperament ; }, abstract = {There is much interest in studying animal personalities but considerable debate as to how to define and evaluate them. We assessed the utility of one proposed framework while studying personality in terrestrial hermit crabs (Coenobita clypeatus). We recorded the latency of individuals to emerge from their shells over multiple trials in four unique manipulations. We used the specific testing situations within these manipulations to define two temperament categories (shyness-boldness and exploration-avoidance). Our results identified individual behavioral consistency (i.e., personality) across repeated trials of the same situations, within both categories. Additionally, we found correlations between behaviors across contexts (traits) that suggested that the crabs had behavioral syndromes. While we found some correlations between behaviors that are supposed to measure the same temperament trait, these correlations were not inevitable. Furthermore, a principal component analysis (PCA) of our data revealed new relationships between behaviors and provided the foundation for an alternate interpretation: measured behaviors may be situation-specific, and may not reflect general personality traits at all. These results suggest that more attention must be placed on how we infer personalities from standardized methods, and that we must be careful to not force our data to fit our frameworks.}, } @article {pmid22764507, year = {2012}, author = {Yaari, G and Ben-Zion, Y and Shnerb, NM and Vasseur, DA}, title = {Consistent scaling of persistence time in metapopulations.}, journal = {Ecology}, volume = {93}, number = {5}, pages = {1214-1227}, doi = {10.1890/11-1077.1}, pmid = {22764507}, issn = {0012-9658}, mesh = {*Ecosystem ; Logistic Models ; *Models, Biological ; Population Dynamics ; Stochastic Processes ; }, abstract = {Recent theory and experimental work in metapopulations and metacommunities demonstrates that long-term persistence is maximized when the rate at which individuals disperse among patches within the system is intermediate; if too low, local extinctions are more frequent than recolonizations, increasing the chance of regional-scale extinctions, and if too high, dynamics exhibit region-wide synchrony, and local extinctions occur in near unison across the region. Although common, little is known about how the size and topology of the metapopulation (metacommunity) affect this bell-shaped relationship between dispersal rate and regional persistence time. Using a suite of mathematical models, we examined the effects of dispersal, patch number, and topology on the regional persistence time when local populations are subject to demographic stochasticity. We found that the form of the relationship between regional persistence time and the number of patches is consistent across all models studied; however, the form of the relationship is distinctly different among low, intermediate, and high dispersal rates. Under low and intermediate dispersal rates, regional persistence times increase logarithmically and exponentially (respectively) with increasing numbers of patches, whereas under high dispersal, the form of the relationship depends on local dynamics. Furthermore, we demonstrate that the forms of these relationships, which give rise to the bell-shaped relationship between dispersal rate and persistence time, are a product of recolonization and the region-wide synchronization (or lack thereof) of population dynamics. Identifying such metapopulation attributes that impact extinction risk is of utmost importance for managing and conserving the earth's evermore fragmented populations.}, } @article {pmid22760973, year = {2012}, author = {Perry, CK and Garside, H and Morones, S and Hayman, LL}, title = {Physical activity interventions for adolescents: an ecological perspective.}, journal = {The journal of primary prevention}, volume = {33}, number = {2-3}, pages = {111-135}, pmid = {22760973}, issn = {1573-6547}, mesh = {Adolescent ; Adolescent Behavior/*psychology ; Child ; Databases, Bibliographic ; Ecology ; Female ; Humans ; Male ; Models, Psychological ; *Motor Activity ; Self Efficacy ; }, abstract = {Many factors contribute to the decline in physical activity (PA) observed during adolescence. We used an ecological framework to review 30 publications of PA interventions published between 1977 and 2009 targeting youth aged 12-18 years (19 PA interventions). We included studies that measured a primary outcome of PA and also examined intervening variables. Most studies targeted the intrapersonal and environmental domains. The body of literature on PA interventions in youth suggests the importance of targeting ecological domains beyond the individual level. Future investigations should be theory-based and include analysis of mediators across ecological domains in order to identify the most effective combination of factors to promote PA in youth.}, } @article {pmid22754369, year = {2012}, author = {Tseng, CW and Huang, HC and Shih, AC and Chang, YY and Hsu, CC and Chang, JY and Li, WH and Juan, HF}, title = {Revealing the anti-tumor effect of artificial miRNA p-27-5p on human breast carcinoma cell line T-47D.}, journal = {International journal of molecular sciences}, volume = {13}, number = {5}, pages = {6352-6369}, pmid = {22754369}, issn = {1422-0067}, mesh = {3' Untranslated Regions ; Breast Neoplasms/*drug therapy/*genetics/metabolism ; Cell Line, Tumor ; Cell Proliferation ; Cyclin-Dependent Kinase 4/*genetics/metabolism ; Down-Regulation/*drug effects ; Female ; G1 Phase Cell Cycle Checkpoints ; Gene Expression Regulation, Neoplastic ; Humans ; MCF-7 Cells ; MicroRNAs/*pharmacology ; Phosphorylation ; Retinoblastoma Protein/*metabolism ; }, abstract = {microRNAs (miRNAs) cause mRNA degradation or translation suppression of their target genes. Previous studies have found direct involvement of miRNAs in cancer initiation and progression. Artificial miRNAs, designed to target single or multiple genes of interest, provide a new therapeutic strategy for cancer. This study investigates the anti-tumor effect of a novel artificial miRNA, miR P-27-5p, on breast cancer. In this study, we reveal that miR P-27-5p downregulates the differential gene expressions associated with the protein modification process and regulation of cell cycle in T-47D cells. Introduction of this novel artificial miRNA, miR P-27-5p, into breast cell lines inhibits cell proliferation and induces the first "gap" phase (G1) cell cycle arrest in cancer cell lines but does not affect normal breast cells. We further show that miR P-27-5p targets the 3'-untranslated mRNA region (3'-UTR) of cyclin-dependent kinase 4 (CDK4) and reduces both the mRNA and protein level of CDK4, which in turn, interferes with phosphorylation of the retinoblastoma protein (RB1). Overall, our data suggest that the effects of miR p-27-5p on cell proliferation and G1 cell cycle arrest are through the downregulation of CDK4 and the suppression of RB1 phosphorylation. This study opens avenues for future therapies targeting breast cancer.}, } @article {pmid22752512, year = {2012}, author = {Sun, L and Klein, EY and Laxminarayan, R}, title = {Seasonality and temporal correlation between community antibiotic use and resistance in the United States.}, journal = {Clinical infectious diseases : an official publication of the Infectious Diseases Society of America}, volume = {55}, number = {5}, pages = {687-694}, doi = {10.1093/cid/cis509}, pmid = {22752512}, issn = {1537-6591}, mesh = {Anti-Bacterial Agents/*therapeutic use ; Bacterial Infections/*drug therapy/*epidemiology ; Databases, Factual ; *Drug Resistance, Bacterial ; Escherichia coli/drug effects ; Humans ; Prevalence ; Retrospective Studies ; Seasons ; Staphylococcus aureus/drug effects ; United States ; }, abstract = {BACKGROUND: Therapeutic antibiotic use in humans is a significant driver of antibiotic resistance. The seasonal effect of antibiotic use on antibiotic resistance has been poorly quantified because of lack of large-scale, spatially disaggregated time-series data on antibiotic use and resistance.

METHODS: We used time-series analysis (Box-Jenkins) on US antibiotic usage from IMS Health and on antibiotic resistance from The Surveillance Network from 1999-2007 to estimate the effect of aminopenicillin, fluoroquinolone, trimethoprim/sulfamethoxazole, and tetracycline usage on resistance of Escherichia coli to drugs within these classes. We also quantified the effect of fluoroquinolone and macrolide/lincosamide usage on resistance of methicillin-resistant Staphylococcus aureus (MRSA) to ciprofloxacin and clindamycin (which has a similar mode of action to macrolides), respectively.

RESULTS: Prevalence of resistant Escherichia coli was significantly correlated with lagged (by 1 month) antibiotic prescriptions for aminopenicillins (0.22, P = .03) and fluoroquinolones (0.24, P = .02), which are highly prescribed, but was uncorrelated to antibiotic classes with lower prescription levels. Fluoroquinolone prescriptions were also significantly correlated with a 1-month lag with the prevalence of ciprofloxacin-resistant MRSA (0.23, P = .03).

CONCLUSIONS: Large-scale usage of antibiotics can generate seasonal patterns of resistance that fluctuate on a short time scale with changes in antibiotic retail sales, suggesting that use of antibiotics in the winter could have a significant effect on resistance. In addition, the strong correlation between community use of antibiotics and resistance isolated in the hospital indicates that restrictions imposed at the hospital level are unlikely to be effective unless coordinated with campaigns to reduce unnecessary antibiotic use at the community level.}, } @article {pmid22748172, year = {2011}, author = {Stevens, KB and Pfeiffer, DU}, title = {Spatial modelling of disease using data- and knowledge-driven approaches.}, journal = {Spatial and spatio-temporal epidemiology}, volume = {2}, number = {3}, pages = {125-133}, doi = {10.1016/j.sste.2011.07.007}, pmid = {22748172}, issn = {1877-5853}, mesh = {Animals ; Bayes Theorem ; *Data Interpretation, Statistical ; Disease Outbreaks/*statistics & numerical data ; Factor Analysis, Statistical ; Geographic Information Systems ; Geography, Medical/methods/statistics & numerical data ; Humans ; *Models, Statistical ; Risk ; *Spatial Analysis ; }, abstract = {The purpose of spatial modelling in animal and public health is three-fold: describing existing spatial patterns of risk, attempting to understand the biological mechanisms that lead to disease occurrence and predicting what will happen in the medium to long-term future (temporal prediction) or in different geographical areas (spatial prediction). Traditional methods for temporal and spatial predictions include general and generalized linear models (GLM), generalized additive models (GAM) and Bayesian estimation methods. However, such models require both disease presence and absence data which are not always easy to obtain. Novel spatial modelling methods such as maximum entropy (MAXENT) and the genetic algorithm for rule set production (GARP) require only disease presence data and have been used extensively in the fields of ecology and conservation, to model species distribution and habitat suitability. Other methods, such as multicriteria decision analysis (MCDA), use knowledge of the causal factors of disease occurrence to identify areas potentially suitable for disease. In addition to their less restrictive data requirements, some of these novel methods have been shown to outperform traditional statistical methods in predictive ability (Elith et al., 2006). This review paper provides details of some of these novel methods for mapping disease distribution, highlights their advantages and limitations, and identifies studies which have used the methods to model various aspects of disease distribution.}, } @article {pmid22744689, year = {2012}, author = {Tevi, G and Tevi, A}, title = {Remote sensing and GIS techniques for assessment of the soil water content in order to improve agricultural practice and reduce the negative impact on groundwater: case study, agricultural area Ştefan cel Mare, Călăraşi County.}, journal = {Water science and technology : a journal of the International Association on Water Pollution Research}, volume = {66}, number = {3}, pages = {580-587}, doi = {10.2166/wst.2012.209}, pmid = {22744689}, issn = {0273-1223}, mesh = {Agriculture/*methods ; *Geographic Information Systems ; Geography ; Groundwater/*analysis ; Remote Sensing Technology/*methods ; Romania ; Soil/*analysis ; Spectrum Analysis ; }, abstract = {Traditional agricultural practices based on non-customized irrigation and soil fertilization are harmful for the environment, and may pose a risk for human health. By continuing the use of these practices, it is not possible to ensure effective land management, which might be acquired by using advanced satellite technology configured for modern agricultural development. The paper presents a methodology based on the correlation between remote sensing data and field observations, aiming to identify the key features and to establish an interpretation pattern for the inhomogeneity highlighted by the remote sensing data. Instead of using classical methods for the evaluation of land features (field analysis, measurements and mapping), the approach is to use high resolution multispectral and hyperspectral methods, in correlation with data processing and geographic information systems (GIS), in order to improve the agricultural practices and mitigate their environmental impact (soil and shallow aquifer).}, } @article {pmid22738820, year = {2012}, author = {Lash, RR and Carroll, DS and Hughes, CM and Nakazawa, Y and Karem, K and Damon, IK and Peterson, AT}, title = {Effects of georeferencing effort on mapping monkeypox case distributions and transmission risk.}, journal = {International journal of health geographics}, volume = {11}, number = {}, pages = {23}, pmid = {22738820}, issn = {1476-072X}, mesh = {*Geographic Information Systems ; *Geographic Mapping ; Humans ; Internationality ; Mpox (monkeypox)/*epidemiology/*transmission ; Population Surveillance/*methods ; Risk Assessment ; }, abstract = {BACKGROUND: Maps of disease occurrences and GIS-based models of disease transmission risk are increasingly common, and both rely on georeferenced diseases data. Automated methods for georeferencing disease data have been widely studied for developed countries with rich sources of geographic referenced data. However, the transferability of these methods to countries without comparable geographic reference data, particularly when working with historical disease data, has not been as widely studied. Historically, precise geographic information about where individual cases occur has been collected and stored verbally, identifying specific locations using place names. Georeferencing historic data is challenging however, because it is difficult to find appropriate geographic reference data to match the place names to. Here, we assess the degree of care and research invested in converting textual descriptions of disease occurrence locations to numerical grid coordinates (latitude and longitude). Specifically, we develop three datasets from the same, original monkeypox disease occurrence data, with varying levels of care and effort: the first based on an automated web-service, the second improving on the first by reference to additional maps and digital gazetteers, and the third improving still more based on extensive consultation of legacy surveillance records that provided considerable additional information about each case. To illustrate the implications of these seemingly subtle improvements in data quality, we develop ecological niche models and predictive maps of monkeypox transmission risk based on each of the three occurrence data sets.

RESULTS: We found macrogeographic variations in ecological niche models depending on the type of georeferencing method used. Less-careful georeferencing identified much smaller areas as having potential for monkeypox transmission in the Sahel region, as well as around the rim of the Congo Basin. These results have implications for mapping efforts, as each higher level of georeferencing precision required considerably greater time investment.

CONCLUSIONS: The importance of careful georeferencing cannot be overlooked, despite it being a time- and labor-intensive process. Investment in archival storage of primary disease-occurrence data is merited, and improved digital gazetteers are needed to support public health mapping activities, particularly in developing countries, where maps and geographic information may be sparse.}, } @article {pmid22730433, year = {2012}, author = {Otegui, J and Ariño, AH}, title = {BIDDSAT: visualizing the content of biodiversity data publishers in the Global Biodiversity Information Facility network.}, journal = {Bioinformatics (Oxford, England)}, volume = {28}, number = {16}, pages = {2207-2208}, doi = {10.1093/bioinformatics/bts359}, pmid = {22730433}, issn = {1367-4811}, mesh = {*Biodiversity ; Data Mining/*methods ; Databases, Factual ; *Information Services ; *Internet ; *Software ; Workflow ; }, abstract = {UNLABELLED: In any data quality workflow, data publishers must become aware of issues in their data so these can be corrected. User feedback mechanisms provide one avenue, while global assessments of datasets provide another. To date, there is no publicly available tool to allow both biodiversity data institutions sharing their data through the Global Biodiversity Information Facility network and its potential users to assess datasets as a whole. Contributing to bridge this gap both for publishers and users, we introduce BIoDiversity DataSets Assessment Tool, an online tool that enables selected diagnostic visualizations on the content of data publishers and/or their individual collections.

The online application is accessible at http://www.unav.es/unzyec/mzna/biddsat/ and is supported by all major browsers. The source code is licensed under the GNU GPLv3 license (http://www.gnu.org/licenses/gpl-3.0.txt) and is available at https://github.com/jotegui/BIDDSAT.}, } @article {pmid22721448, year = {2012}, author = {Zhou, Y and Gao, F and Liu, R and Feng, J and Li, H}, title = {De novo sequencing and analysis of root transcriptome using 454 pyrosequencing to discover putative genes associated with drought tolerance in Ammopiptanthus mongolicus.}, journal = {BMC genomics}, volume = {13}, number = {}, pages = {266}, pmid = {22721448}, issn = {1471-2164}, mesh = {Databases, Genetic ; Droughts ; Expressed Sequence Tags ; Fabaceae/*genetics ; *Genes, Plant ; Genetic Markers ; Microsatellite Repeats ; Plant Proteins/genetics/metabolism ; Plant Roots/genetics ; Sequence Analysis, DNA ; *Transcriptome ; }, abstract = {BACKGROUND: De novo assembly of transcript sequences produced by next-generation sequencing technologies offers a rapid approach to obtain expressed gene sequences for non-model organisms. Ammopiptanthus mongolicus, a super-xerophytic broadleaf evergreen wood, is an ecologically important foundation species in desert ecosystems and exhibits substantial drought tolerance in Mid-Asia desert. Root plays an important role in water absorption of plant. There are insufficient transcriptomic and genomic data in public databases for understanding of the molecular mechanism underlying the drought tolerance of A. mongolicus. Thus, high throughput transcriptome sequencing from A. mongolicus root is helpful to generate a large amount of transcript sequences for gene discovery and molecular marker development.

RESULTS: A total of 672,002 sequencing reads were obtained from a 454 GS XLR70 Titanium pyrosequencer with a mean length of 279 bp. These reads were assembled into 29,056 unique sequences including 15,173 contigs and 13,883 singlets. In our assembled sequences, 1,827 potential simple sequence repeats (SSR) molecular markers were discovered. Based on sequence similarity with known plant proteins, the assembled sequences represent approximately 9,771 proteins in PlantGDB. Based on the Gene ontology (GO) analysis, hundreds of drought stress-related genes were found. We further analyzed the gene expression profiles of 27 putative genes involved in drought tolerance using quantitative real-time PCR (qRT-PCR) assay.

CONCLUSIONS: Our sequence collection represents a major transcriptomic resource for A. mongolicus, and the large number of genetic markers predicted should contribute to future research in Ammopiptanthus genus. The potential drought stress related transcripts identified in this study provide a good start for further investigation into the drought adaptation in Ammopiptanthus.}, } @article {pmid22719260, year = {2012}, author = {Rho, M and Wu, YW and Tang, H and Doak, TG and Ye, Y}, title = {Diverse CRISPRs evolving in human microbiomes.}, journal = {PLoS genetics}, volume = {8}, number = {6}, pages = {e1002441}, pmid = {22719260}, issn = {1553-7404}, support = {R01 HG004908/HG/NHGRI NIH HHS/United States ; 1R01HG004908/HG/NHGRI NIH HHS/United States ; }, mesh = {Archaea/genetics ; Bacteria/genetics/virology ; Bacteriophages/genetics ; Base Sequence ; DNA, Intergenic/*genetics ; *Evolution, Molecular ; Genome, Bacterial ; Humans ; Inverted Repeat Sequences/*genetics ; Metagenome/*genetics ; Metagenomics ; Molecular Sequence Data ; Plasmids/genetics ; Sequence Analysis, DNA ; Streptococcus/genetics/virology ; }, abstract = {CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) loci, together with cas (CRISPR-associated) genes, form the CRISPR/Cas adaptive immune system, a primary defense strategy that eubacteria and archaea mobilize against foreign nucleic acids, including phages and conjugative plasmids. Short spacer sequences separated by the repeats are derived from foreign DNA and direct interference to future infections. The availability of hundreds of shotgun metagenomic datasets from the Human Microbiome Project (HMP) enables us to explore the distribution and diversity of known CRISPRs in human-associated microbial communities and to discover new CRISPRs. We propose a targeted assembly strategy to reconstruct CRISPR arrays, which whole-metagenome assemblies fail to identify. For each known CRISPR type (identified from reference genomes), we use its direct repeat consensus sequence to recruit reads from each HMP dataset and then assemble the recruited reads into CRISPR loci; the unique spacer sequences can then be extracted for analysis. We also identified novel CRISPRs or new CRISPR variants in contigs from whole-metagenome assemblies and used targeted assembly to more comprehensively identify these CRISPRs across samples. We observed that the distributions of CRISPRs (including 64 known and 86 novel ones) are largely body-site specific. We provide detailed analysis of several CRISPR loci, including novel CRISPRs. For example, known streptococcal CRISPRs were identified in most oral microbiomes, totaling ∼8,000 unique spacers: samples resampled from the same individual and oral site shared the most spacers; different oral sites from the same individual shared significantly fewer, while different individuals had almost no common spacers, indicating the impact of subtle niche differences on the evolution of CRISPR defenses. We further demonstrate potential applications of CRISPRs to the tracing of rare species and the virus exposure of individuals. This work indicates the importance of effective identification and characterization of CRISPR loci to the study of the dynamic ecology of microbiomes.}, } @article {pmid22719239, year = {2012}, author = {Wodarz, D and Hofacre, A and Lau, JW and Sun, Z and Fan, H and Komarova, NL}, title = {Complex spatial dynamics of oncolytic viruses in vitro: mathematical and experimental approaches.}, journal = {PLoS computational biology}, volume = {8}, number = {6}, pages = {e1002547}, pmid = {22719239}, issn = {1553-7358}, support = {R01 CA129286/CA/NCI NIH HHS/United States ; 1R01CA129286/CA/NCI NIH HHS/United States ; R01 AI093998/AI/NIAID NIH HHS/United States ; P30 CA062203/CA/NCI NIH HHS/United States ; R01 AI058153/AI/NIAID NIH HHS/United States ; R01AI058153/AI/NIAID NIH HHS/United States ; T32 EB009418/EB/NIBIB NIH HHS/United States ; }, mesh = {Adenoviruses, Human/genetics/physiology ; Computational Biology ; Computer Simulation ; Genetic Engineering ; Green Fluorescent Proteins/genetics ; HEK293 Cells ; Humans ; *Models, Biological ; Neoplasms/therapy/virology ; Oncolytic Virotherapy/*methods ; Oncolytic Viruses/genetics/*physiology ; Virus Replication ; }, abstract = {Oncolytic viruses replicate selectively in tumor cells and can serve as targeted treatment agents. While promising results have been observed in clinical trials, consistent success of therapy remains elusive. The dynamics of virus spread through tumor cell populations has been studied both experimentally and computationally. However, a basic understanding of the principles underlying virus spread in spatially structured target cell populations has yet to be obtained. This paper studies such dynamics, using a newly constructed recombinant adenovirus type-5 (Ad5) that expresses enhanced jellyfish green fluorescent protein (EGFP), AdEGFPuci, and grows on human 293 embryonic kidney epithelial cells, allowing us to track cell numbers and spatial patterns over time. The cells are arranged in a two-dimensional setting and allow virus spread to occur only to target cells within the local neighborhood. Despite the simplicity of the setup, complex dynamics are observed. Experiments gave rise to three spatial patterns that we call "hollow ring structure", "filled ring structure", and "disperse pattern". An agent-based, stochastic computational model is used to simulate and interpret the experiments. The model can reproduce the experimentally observed patterns, and identifies key parameters that determine which pattern of virus growth arises. The model is further used to study the long-term outcome of the dynamics for the different growth patterns, and to investigate conditions under which the virus population eliminates the target cells. We find that both the filled ring structure and disperse pattern of initial expansion are indicative of treatment failure, where target cells persist in the long run. The hollow ring structure is associated with either target cell extinction or low-level persistence, both of which can be viewed as treatment success. Interestingly, it is found that equilibrium properties of ordinary differential equations describing the dynamics in local neighborhoods in the agent-based model can predict the outcome of the spatial virus-cell dynamics, which has important practical implications. This analysis provides a first step towards understanding spatial oncolytic virus dynamics, upon which more detailed investigations and further complexity can be built.}, } @article {pmid22719234, year = {2012}, author = {Abubucker, S and Segata, N and Goll, J and Schubert, AM and Izard, J and Cantarel, BL and Rodriguez-Mueller, B and Zucker, J and Thiagarajan, M and Henrissat, B and White, O and Kelley, ST and Methé, B and Schloss, PD and Gevers, D and Mitreva, M and Huttenhower, C}, title = {Metabolic reconstruction for metagenomic data and its application to the human microbiome.}, journal = {PLoS computational biology}, volume = {8}, number = {6}, pages = {e1002358}, pmid = {22719234}, issn = {1553-7358}, support = {R01 HG005969/HG/NHGRI NIH HHS/United States ; R21 DE017106/DE/NIDCR NIH HHS/United States ; CA139193/CA/NCI NIH HHS/United States ; U54HG004968/HG/NHGRI NIH HHS/United States ; 5R01HG005975/HG/NHGRI NIH HHS/United States ; U54HG004969/HG/NHGRI NIH HHS/United States ; T32 AI007528/AI/NIAID NIH HHS/United States ; R01 HG005975/HG/NHGRI NIH HHS/United States ; U54 HG004968/HG/NHGRI NIH HHS/United States ; R21 CA139193/CA/NCI NIH HHS/United States ; 1R01HG005969/HG/NHGRI NIH HHS/United States ; DE017106/DE/NIDCR NIH HHS/United States ; U54 HG004969/HG/NHGRI NIH HHS/United States ; }, mesh = {Computational Biology ; Digestive System/metabolism/microbiology ; Female ; Genetics, Microbial ; Glycosaminoglycans/metabolism ; Humans ; Hydrogen-Ion Concentration ; Metabolic Networks and Pathways/genetics ; Metabolome/genetics ; *Metagenome ; Multigene Family ; Vagina/metabolism/microbiology ; }, abstract = {Microbial communities carry out the majority of the biochemical activity on the planet, and they play integral roles in processes including metabolism and immune homeostasis in the human microbiome. Shotgun sequencing of such communities' metagenomes provides information complementary to organismal abundances from taxonomic markers, but the resulting data typically comprise short reads from hundreds of different organisms and are at best challenging to assemble comparably to single-organism genomes. Here, we describe an alternative approach to infer the functional and metabolic potential of a microbial community metagenome. We determined the gene families and pathways present or absent within a community, as well as their relative abundances, directly from short sequence reads. We validated this methodology using a collection of synthetic metagenomes, recovering the presence and abundance both of large pathways and of small functional modules with high accuracy. We subsequently applied this method, HUMAnN, to the microbial communities of 649 metagenomes drawn from seven primary body sites on 102 individuals as part of the Human Microbiome Project (HMP). This provided a means to compare functional diversity and organismal ecology in the human microbiome, and we determined a core of 24 ubiquitously present modules. Core pathways were often implemented by different enzyme families within different body sites, and 168 functional modules and 196 metabolic pathways varied in metagenomic abundance specifically to one or more niches within the microbiome. These included glycosaminoglycan degradation in the gut, as well as phosphate and amino acid transport linked to host phenotype (vaginal pH) in the posterior fornix. An implementation of our methodology is available at http://huttenhower.sph.harvard.edu/humann. This provides a means to accurately and efficiently characterize microbial metabolic pathways and functional modules directly from high-throughput sequencing reads, enabling the determination of community roles in the HMP cohort and in future metagenomic studies.}, } @article {pmid22712577, year = {2012}, author = {Didelot, X and Méric, G and Falush, D and Darling, AE}, title = {Impact of homologous and non-homologous recombination in the genomic evolution of Escherichia coli.}, journal = {BMC genomics}, volume = {13}, number = {}, pages = {256}, pmid = {22712577}, issn = {1471-2164}, support = {087646/Z/08/Z//Wellcome Trust/United Kingdom ; G0800778//Department of Health/United Kingdom ; //Biotechnology and Biological Sciences Research Council/United Kingdom ; //Medical Research Council/United Kingdom ; }, mesh = {Biological Evolution ; Databases, Genetic ; Escherichia coli/classification/*genetics ; Genome, Bacterial/*genetics ; Homologous Recombination/*genetics ; Phylogeny ; }, abstract = {BACKGROUND: Escherichia coli is an important species of bacteria that can live as a harmless inhabitant of the guts of many animals, as a pathogen causing life-threatening conditions or freely in the non-host environment. This diversity of lifestyles has made it a particular focus of interest for studies of genetic variation, mainly with the aim to understand how a commensal can become a deadly pathogen. Many whole genomes of E. coli have been fully sequenced in the past few years, which offer helpful data to help understand how this important species evolved.

RESULTS: We compared 27 whole genomes encompassing four phylogroups of Escherichia coli (A, B1, B2 and E). From the core-genome we established the clonal relationships between the isolates as well as the role played by homologous recombination during their evolution from a common ancestor. We found strong evidence for sexual isolation between three lineages (A+B1, B2, E), which could be explained by the ecological structuring of E. coli and may represent on-going speciation. We identified three hotspots of homologous recombination, one of which had not been previously described and contains the aroC gene, involved in the essential shikimate metabolic pathway. We also described the role played by non-homologous recombination in the pan-genome, and showed that this process was highly heterogeneous. Our analyses revealed in particular that the genomes of three enterohaemorrhagic (EHEC) strains within phylogroup B1 have converged from originally separate backgrounds as a result of both homologous and non-homologous recombination.

CONCLUSIONS: Recombination is an important force shaping the genomic evolution and diversification of E. coli, both by replacing fragments of genes with an homologous sequence and also by introducing new genes. In this study, several non-random patterns of these events were identified which correlated with important changes in the lifestyle of the bacteria, and therefore provide additional evidence to explain the relationship between genomic variation and ecological adaptation.}, } @article {pmid22710931, year = {2012}, author = {Brischoux, F and Rolland, V and Bonnet, X and Caillaud, M and Shine, R}, title = {Effects of oceanic salinity on body condition in sea snakes.}, journal = {Integrative and comparative biology}, volume = {52}, number = {2}, pages = {235-244}, doi = {10.1093/icb/ics081}, pmid = {22710931}, issn = {1557-7023}, mesh = {Adaptation, Physiological ; Animals ; Aquatic Organisms/physiology ; Body Size ; Computational Biology ; Ecosystem ; Elapidae/*physiology ; Linear Models ; Models, Biological ; Oceans and Seas ; *Salinity ; Species Specificity ; Time Factors ; *Water-Electrolyte Balance ; }, abstract = {Since the transition from terrestrial to marine environments poses strong osmoregulatory and energetic challenges, temporal and spatial fluctuations in oceanic salinity might influence salt and water balance (and hence, body condition) in marine tetrapods. We assessed the effects of salinity on three species of sea snakes studied by mark-recapture in coral-reef habitats in the Neo-Caledonian Lagoon. These three species include one fully aquatic hydrophiine (Emydocephalus annulatus), one primarily aquatic laticaudine (Laticauda laticaudata), and one frequently terrestrial laticaudine (Laticauda saintgironsi). We explored how oceanic salinity affected the snakes' body condition across various temporal and spatial scales relevant to each species' ecology, using linear mixed models and multimodel inference. Mean annual salinity exerted a consistent and negative effect on the body condition of all three snake species. The most terrestrial taxon (L. saintgironsi) was sensitive to salinity over a short temporal scale, corresponding to the duration of a typical marine foraging trip for this species. In contrast, links between oceanic salinity and body condition in the fully aquatic E. annulatus and the highly aquatic L. laticaudata were strongest at a long-term (annual) scale. The sophisticated salt-excreting systems of sea snakes allow them to exploit marine environments, but do not completely overcome the osmoregulatory challenges posed by oceanic conditions. Future studies could usefully explore such effects in other secondarily marine taxa such as seabirds, turtles, and marine mammals.}, } @article {pmid22709906, year = {2012}, author = {Gawryluk, RM and Chisholm, KA and Pinto, DM and Gray, MW}, title = {Composition of the mitochondrial electron transport chain in acanthamoeba castellanii: structural and evolutionary insights.}, journal = {Biochimica et biophysica acta}, volume = {1817}, number = {11}, pages = {2027-2037}, doi = {10.1016/j.bbabio.2012.06.005}, pmid = {22709906}, issn = {0006-3002}, mesh = {Acanthamoeba castellanii/genetics/*metabolism ; Amino Acid Sequence ; Computational Biology ; Electron Transport ; Electron Transport Chain Complex Proteins/*analysis/*chemistry/physiology ; Electron Transport Complex I/analysis/chemistry/physiology ; Electron Transport Complex II/analysis/physiology ; Electron Transport Complex III/analysis/physiology ; Electron Transport Complex IV/analysis/physiology ; Evolution, Molecular ; Mitochondria/*metabolism ; Molecular Sequence Data ; Proteome ; }, abstract = {The mitochondrion, derived in evolution from an α-proteobacterial progenitor, plays a key metabolic role in eukaryotes. Mitochondria house the electron transport chain (ETC) that couples oxidation of organic substrates and electron transfer to proton pumping and synthesis of ATP. The ETC comprises several multiprotein enzyme complexes, all of which have counterparts in bacteria. However, mitochondrial ETC assemblies from animals, plants and fungi are generally more complex than their bacterial counterparts, with a number of 'supernumerary' subunits appearing early in eukaryotic evolution. Little is known, however, about the ETC of unicellular eukaryotes (protists), which are key to understanding the evolution of mitochondria and the ETC. We present an analysis of the ETC proteome from Acanthamoeba castellanii, an ecologically, medically and evolutionarily important member of Amoebozoa (sister to Opisthokonta). Data obtained from tandem mass spectrometric (MS/MS) analyses of purified mitochondria as well as ETC complexes isolated via blue native polyacrylamide gel electrophoresis are combined with the results of bioinformatic queries of sequence databases. Our bioinformatic analyses have identified most of the ETC subunits found in other eukaryotes, confirming and extending previous observations. The assignment of proteins as ETC subunits by MS/MS provides important insights into the primary structures of ETC proteins and makes possible, through the use of sensitive profile-based similarity searches, the identification of novel constituents of the ETC along with the annotation of highly divergent but phylogenetically conserved ETC subunits.}, } @article {pmid22708576, year = {2012}, author = {Luque Fernandez, MA and Schomaker, M and Mason, PR and Fesselet, JF and Baudot, Y and Boulle, A and Maes, P}, title = {Elevation and cholera: an epidemiological spatial analysis of the cholera epidemic in Harare, Zimbabwe, 2008-2009.}, journal = {BMC public health}, volume = {12}, number = {}, pages = {442}, pmid = {22708576}, issn = {1471-2458}, mesh = {Cholera/*epidemiology ; Demography/statistics & numerical data/trends ; Disease Outbreaks/prevention & control/*statistics & numerical data ; Geographic Information Systems ; Humans ; Population Surveillance ; Space-Time Clustering ; *Spatial Analysis ; Suburban Population/*statistics & numerical data/trends ; Water Supply/standards ; Zimbabwe/epidemiology ; }, abstract = {BACKGROUND: In highly populated African urban areas where access to clean water is a challenge, water source contamination is one of the most cited risk factors in a cholera epidemic. During the rainy season, where there is either no sewage disposal or working sewer system, runoff of rains follows the slopes and gets into the lower parts of towns where shallow wells could easily become contaminated by excretes. In cholera endemic areas, spatial information about topographical elevation could help to guide preventive interventions. This study aims to analyze the association between topographic elevation and the distribution of cholera cases in Harare during the cholera epidemic in 2008 and 2009.

METHODS: We developed an ecological study using secondary data. First, we described attack rates by suburb and then calculated rate ratios using whole Harare as reference. We illustrated the average elevation and cholera cases by suburbs using geographical information. Finally, we estimated a generalized linear mixed model (under the assumption of a Poisson distribution) with an Empirical Bayesian approach to model the relation between the risk of cholera and the elevation in meters in Harare. We used a random intercept to allow for spatial correlation of neighboring suburbs.

RESULTS: This study identifies a spatial pattern of the distribution of cholera cases in the Harare epidemic, characterized by a lower cholera risk in the highest elevation suburbs of Harare. The generalized linear mixed model showed that for each 100 meters of increase in the topographical elevation, the cholera risk was 30% lower with a rate ratio of 0.70 (95% confidence interval=0.66-0.76). Sensitivity analysis confirmed the risk reduction with an overall estimate of the rate ratio between 20% and 40%.

CONCLUSION: This study highlights the importance of considering topographical elevation as a geographical and environmental risk factor in order to plan cholera preventive activities linked with water and sanitation in endemic areas. Furthermore, elevation information, among other risk factors, could help to spatially orientate cholera control interventions during an epidemic.}, } @article {pmid22705880, year = {2012}, author = {Sikhakolli, UR and López-Giráldez, F and Li, N and Common, R and Townsend, JP and Trail, F}, title = {Transcriptome analyses during fruiting body formation in Fusarium graminearum and Fusarium verticillioides reflect species life history and ecology.}, journal = {Fungal genetics and biology : FG & B}, volume = {49}, number = {8}, pages = {663-673}, doi = {10.1016/j.fgb.2012.05.009}, pmid = {22705880}, issn = {1096-0937}, mesh = {Apoptosis/genetics ; Cluster Analysis ; Computational Biology/methods ; *Ecosystem ; Fruiting Bodies, Fungal/*genetics/*growth & development/ultrastructure ; Fusarium/*genetics/*growth & development/ultrastructure ; Gene Expression Profiling ; Gene Expression Regulation, Fungal ; Lipid Metabolism/genetics ; Mating Factor ; Peptides/genetics ; Phenotype ; *Transcriptome ; }, abstract = {Fusarium graminearum and F. verticillioides are devastating cereal pathogens with very different life history and ecological characteristics. F. graminearum is homothallic, and sexual spores are an important component of its life cycle, responsible for disease initiation. F. verticilloides is heterothallic, and produces only modest numbers of fruiting bodies, which are not a significant source of inoculum. To identify corresponding differences in the transcriptional program underlying fruiting body development in the two species, comparative expression was performed, analyzing six developmental stages. To accompany the transcriptional analysis, detailed morphological characterization of F. verticillioides development was performed and compared to a previous morphological analysis of F. graminearum. Morphological development was similar between the two species, except for the observation of possible trichogynes in F. verticillioides ascogonia, which have not been previously reported for any Fusarium species. Expression of over 9000 orthologous genes were measured for the two species. Functional assignments of highly expressed orthologous genes at each time-point revealed the majority of highly expressed genes fell into the "unclassified proteins" category, reflecting the lack of characterization of genes for sexual development in both species. Simultaneous examination of morphological development and stage-specific gene expression suggests that degeneration of the paraphyses during sexual development is an apoptotic process. Expression of mating type genes in the two species differed, possibly reflecting the divergent roles they play in sexual development. Overall, the differences in gene expression reflect the greater role of fruiting bodies in the life cycle and ecology of F. graminearum versus F. verticillioides.}, } @article {pmid22704231, year = {2012}, author = {Scheuring, I}, title = {How robust are the models of the origin of life?: Commentary on "Evolutionary dynamics of RNA-like replicator systems: A bioinformatic approach to the origin of life".}, journal = {Physics of life reviews}, volume = {9}, number = {3}, pages = {264-5; discussion 279-84}, doi = {10.1016/j.plrev.2012.06.004}, pmid = {22704231}, issn = {1873-1457}, mesh = {Computational Biology/*methods ; *Evolution, Molecular ; *Origin of Life ; *RNA ; }, } @article {pmid22702658, year = {2012}, author = {Büchel, K and McDowell, E and Nelson, W and Descour, A and Gershenzon, J and Hilker, M and Soderlund, C and Gang, DR and Fenning, T and Meiners, T}, title = {An elm EST database for identifying leaf beetle egg-induced defense genes.}, journal = {BMC genomics}, volume = {13}, number = {}, pages = {242}, pmid = {22702658}, issn = {1471-2164}, mesh = {Animals ; Coleoptera/*growth & development ; Computational Biology ; Cyclopentanes/metabolism ; *Databases, Genetic ; Expressed Sequence Tags ; Gene Expression Profiling ; Gene Library ; Metabolic Networks and Pathways ; Ovum/chemistry/metabolism ; Oxylipins/metabolism ; Photosynthesis/genetics ; Plant Leaves/genetics ; Ulmus/*genetics ; }, abstract = {BACKGROUND: Plants can defend themselves against herbivorous insects prior to the onset of larval feeding by responding to the eggs laid on their leaves. In the European field elm (Ulmus minor), egg laying by the elm leaf beetle (Xanthogaleruca luteola) activates the emission of volatiles that attract specialised egg parasitoids, which in turn kill the eggs. Little is known about the transcriptional changes that insect eggs trigger in plants and how such indirect defense mechanisms are orchestrated in the context of other biological processes.

RESULTS: Here we present the first large scale study of egg-induced changes in the transcriptional profile of a tree. Five cDNA libraries were generated from leaves of (i) untreated control elms, and elms treated with (ii) egg laying and feeding by elm leaf beetles, (iii) feeding, (iv) artificial transfer of egg clutches, and (v) methyl jasmonate. A total of 361,196 ESTs expressed sequence tags (ESTs) were identified which clustered into 52,823 unique transcripts (Unitrans) and were stored in a database with a public web interface. Among the analyzed Unitrans, 73% could be annotated by homology to known genes in the UniProt (Plant) database, particularly to those from Vitis, Ricinus, Populus and Arabidopsis. Comparative in silico analysis among the different treatments revealed differences in Gene Ontology term abundances. Defense- and stress-related gene transcripts were present in high abundance in leaves after herbivore egg laying, but transcripts involved in photosynthesis showed decreased abundance. Many pathogen-related genes and genes involved in phytohormone signaling were expressed, indicative of jasmonic acid biosynthesis and activation of jasmonic acid responsive genes. Cross-comparisons between different libraries based on expression profiles allowed the identification of genes with a potential relevance in egg-induced defenses, as well as other biological processes, including signal transduction, transport and primary metabolism.

CONCLUSION: Here we present a dataset for a large-scale study of the mechanisms of plant defense against insect eggs in a co-evolved, natural ecological plant-insect system. The EST database analysis provided here is a first step in elucidating the transcriptional responses of elm to elm leaf beetle infestation, and adds further to our knowledge on insect egg-induced transcriptomic changes in plants. The sequences identified in our comparative analysis give many hints about novel defense mechanisms directed towards eggs.}, } @article {pmid22701662, year = {2012}, author = {Bik, HM and Halanych, KM and Sharma, J and Thomas, WK}, title = {Dramatic shifts in benthic microbial eukaryote communities following the Deepwater Horizon oil spill.}, journal = {PloS one}, volume = {7}, number = {6}, pages = {e38550}, pmid = {22701662}, issn = {1932-6203}, mesh = {Base Sequence ; *Biodiversity ; Computational Biology ; *Ecosystem ; Eukaryota/cytology/*drug effects/*genetics ; Genetic Markers/genetics ; Gulf of Mexico ; Marine Biology ; Molecular Sequence Data ; Petroleum Pollution/*adverse effects ; *Phylogeny ; Population Dynamics ; RNA, Ribosomal, 18S/genetics ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {Benthic habitats harbour a significant (yet unexplored) diversity of microscopic eukaryote taxa, including metazoan phyla, protists, algae and fungi. These groups are thought to underpin ecosystem functioning across diverse marine environments. Coastal marine habitats in the Gulf of Mexico experienced visible, heavy impacts following the Deepwater Horizon oil spill in 2010, yet our scant knowledge of prior eukaryotic biodiversity has precluded a thorough assessment of this disturbance. Using a marker gene and morphological approach, we present an intensive evaluation of microbial eukaryote communities prior to and following oiling around heavily impacted shorelines. Our results show significant changes in community structure, with pre-spill assemblages of diverse Metazoa giving way to dominant fungal communities in post-spill sediments. Post-spill fungal taxa exhibit low richness and are characterized by an abundance of known hydrocarbon-degrading genera, compared to prior communities that contained smaller and more diverse fungal assemblages. Comparative taxonomic data from nematodes further suggests drastic impacts; while pre-spill samples exhibit high richness and evenness of genera, post-spill communities contain mainly predatory and scavenger taxa alongside an abundance of juveniles. Based on this community analysis, our data suggest considerable (hidden) initial impacts across Gulf beaches may be ongoing, despite the disappearance of visible surface oil in the region.}, } @article {pmid22701613, year = {2012}, author = {White, JR and Patel, J and Ottesen, A and Arce, G and Blackwelder, P and Lopez, JV}, title = {Pyrosequencing of bacterial symbionts within Axinella corrugata sponges: diversity and seasonal variability.}, journal = {PloS one}, volume = {7}, number = {6}, pages = {e38204}, pmid = {22701613}, issn = {1932-6203}, mesh = {Animals ; Bacteria/*genetics ; Base Sequence ; *Biodiversity ; Cluster Analysis ; Computational Biology ; Florida ; Microscopy, Electron, Transmission ; Molecular Sequence Data ; Phylogeny ; Porifera/*microbiology/ultrastructure ; Principal Component Analysis ; RNA, Ribosomal, 16S/genetics ; *Seasons ; Sequence Analysis, DNA ; Species Specificity ; *Symbiosis ; }, abstract = {BACKGROUND: Marine sponge species are of significant interest to many scientific fields including marine ecology, conservation biology, genetics, host-microbe symbiosis and pharmacology. One of the most intriguing aspects of the sponge "holobiont" system is the unique physiology, interaction with microbes from the marine environment and the development of a complex commensal microbial community. However, intraspecific variability and temporal stability of sponge-associated bacterial symbionts remain relatively unknown.

We have characterized the bacterial symbiont community biodiversity of seven different individuals of the Caribbean reef sponge Axinella corrugata, from two different Florida reef locations during variable seasons using multiplex 454 pyrosequencing of 16 S rRNA amplicons. Over 265,512 high-quality 16 S rRNA sequences were generated and analyzed. Utilizing versatile bioinformatics methods and analytical software such as the QIIME and CloVR packages, we have identified 9,444 distinct bacterial operational taxonomic units (OTUs). Approximately 65,550 rRNA sequences (24%) could not be matched to bacteria at the class level, and may therefore represent novel taxa. Differentially abundant classes between seasonal Axinella communities included Gammaproteobacteria, Flavobacteria, Alphaproteobacteria, Cyanobacteria, Acidobacter and Nitrospira. Comparisons with a proximal outgroup sponge species (Amphimedon compressa), and the growing sponge symbiont literature, indicate that this study has identified approximately 330 A. corrugata-specific symbiotic OTUs, many of which are related to the sulfur-oxidizing Ectothiorhodospiraceae. This family appeared exclusively within A. corrugata, comprising >34.5% of all sequenced amplicons. Other A. corrugata symbionts such as Deltaproteobacteria, Bdellovibrio, and Thiocystis among many others are described.

CONCLUSIONS/SIGNIFICANCE: Slight shifts in several bacterial taxa were observed between communities sampled during spring and fall seasons. New 16 S rDNA sequences and concomitant identifications greatly expand the microbial community profile for this model reef sponge, and will likely be useful as a baseline for any future comparisons regarding sponge microbial community dynamics.}, } @article {pmid22697244, year = {2012}, author = {Manolopoulou, I and Emerson, BC}, title = {Phylogeographic ancestral inference using the coalescent model on haplotype trees.}, journal = {Journal of computational biology : a journal of computational molecular cell biology}, volume = {19}, number = {6}, pages = {745-755}, doi = {10.1089/cmb.2012.0038}, pmid = {22697244}, issn = {1557-8666}, mesh = {Animals ; DNA, Mitochondrial/classification/*genetics ; Databases, Nucleic Acid ; Evolution, Molecular ; *Genetic Speciation ; *Haplotypes ; *Models, Genetic ; Phylogeny ; Phylogeography ; Portugal ; Spain ; Weevils/classification/*genetics ; }, abstract = {Phylogeographic ancestral inference is issue frequently arising in population ecology that aims to understand the geographical roots and structure of species. Here, we specifically address relatively small scale mtDNA datasets (typically less than 500 sequences with fewer than 1000 nucleotides), focusing on ancestral location inference. Our approach uses a coalescent modelling framework projected onto haplotype trees in order to reduce computational complexity, at the same time adhering to complex evolutionary processes. Statistical innovations of the last few years have allowed for computationally feasible yet accurate inferences in phylogenetic frameworks. We implement our methods on a set of synthetic datasets and show how, despite high uncertainty in terms of identifying the root haplotype, estimation of the ancestral location naturally encompasses lower uncertainty, allowing us to pinpoint the Maximum A Posteriori estimates for ancestral locations. We exemplify our methods on a set of synthetic datasets and then combine our inference methods with the phylogeographic clustering approach presented in Manolopoulou et al. (2011) on a real dataset from weevils in the Iberian peninsula in order to infer ancestral locations as well as population substructure.}, } @article {pmid22696284, year = {2012}, author = {Elbroch, LM and Wittmer, HU}, title = {Table scraps: inter-trophic food provisioning by pumas.}, journal = {Biology letters}, volume = {8}, number = {5}, pages = {776-779}, pmid = {22696284}, issn = {1744-957X}, mesh = {Animals ; Behavior, Animal ; Biodiversity ; Birds ; Chile ; Conservation of Natural Resources ; Ecology ; Environmental Monitoring/methods ; Feeding Behavior ; Female ; Geographic Information Systems ; Geography ; Male ; *Predatory Behavior ; Puma ; Species Specificity ; Time Factors ; Wolves/physiology ; }, abstract = {Large carnivores perform keystone ecological functions through direct predation, or indirectly, through food subsidies to scavengers or trophic cascades driven by their influence on the distributions of their prey. Pumas (Puma concolor) are an elusive, cryptic species difficult to study and little is known about their inter-trophic-level interactions in natural communities. Using new GPS technology, we discovered that pumas in Patagonia provided 232 ± 31 kg of edible meat/month/100 km(2) to near-threatened Andean condors (Vultur gryphus) and other members of a diverse scavenger community. This is up to 3.1 times the contributions by wolves (Canis lupus) to communities in Yellowstone National Park, USA, and highlights the keystone role large, solitary felids play in natural systems. These findings are more pertinent than ever, for managers increasingly advocate controlling pumas and other large felids to bolster prey populations and mitigate concerns over human and livestock safety, without a full understanding of the potential ecological consequences of their actions.}, } @article {pmid22693586, year = {2012}, author = {Shamoun-Baranes, J and Bom, R and van Loon, EE and Ens, BJ and Oosterbeek, K and Bouten, W}, title = {From sensor data to animal behaviour: an oystercatcher example.}, journal = {PloS one}, volume = {7}, number = {5}, pages = {e37997}, pmid = {22693586}, issn = {1932-6203}, mesh = {Acceleration ; Animals ; *Behavior, Animal ; *Charadriiformes/physiology ; Female ; Geographic Information Systems ; Locomotion ; Male ; *Models, Statistical ; Time Factors ; }, abstract = {Animal-borne sensors enable researchers to remotely track animals, their physiological state and body movements. Accelerometers, for example, have been used in several studies to measure body movement, posture, and energy expenditure, although predominantly in marine animals. In many studies, behaviour is often inferred from expert interpretation of sensor data and not validated with direct observations of the animal. The aim of this study was to derive models that could be used to classify oystercatcher (Haematopus ostralegus) behaviour based on sensor data. We measured the location, speed, and tri-axial acceleration of three oystercatchers using a flexible GPS tracking system and conducted simultaneous visual observations of the behaviour of these birds in their natural environment. We then used these data to develop three supervised classification trees of behaviour and finally applied one of the models to calculate time-activity budgets. The model based on accelerometer data developed to classify three behaviours (fly, terrestrial locomotion, and no movement) was much more accurate (cross-validation error = 0.14) than the model based on GPS-speed alone (cross-validation error = 0.35). The most parsimonious acceleration model designed to classify eight behaviours could distinguish five: fly, forage, body care, stand, and sit (cross-validation error = 0.28); other behaviours that were observed, such as aggression or handling of prey, could not be distinguished. Model limitations and potential improvements are discussed. The workflow design presented in this study can facilitate model development, be adapted to a wide range of species, and together with the appropriate measurements, can foster the study of behaviour and habitat use of free living animals throughout their annual routine.}, } @article {pmid22693434, year = {2012}, author = {Arenas, M}, title = {Simulation of molecular data under diverse evolutionary scenarios.}, journal = {PLoS computational biology}, volume = {8}, number = {5}, pages = {e1002495}, pmid = {22693434}, issn = {1553-7358}, mesh = {Computational Biology/*methods ; Computer Simulation ; Europe ; *Evolution, Molecular ; Humans ; *Models, Genetic ; Recombination, Genetic ; Selection, Genetic ; }, } @article {pmid22690147, year = {2012}, author = {Goulitquer, S and Potin, P and Tonon, T}, title = {Mass spectrometry-based metabolomics to elucidate functions in marine organisms and ecosystems.}, journal = {Marine drugs}, volume = {10}, number = {4}, pages = {849-880}, pmid = {22690147}, issn = {1660-3397}, mesh = {Animals ; Aquatic Organisms/*metabolism ; *Ecosystem ; Environment ; Humans ; Mass Spectrometry/*methods ; Metabolomics/*methods ; }, abstract = {Marine systems are very diverse and recognized as being sources of a wide range of biomolecules. This review provides an overview of metabolite profiling based on mass spectrometry (MS) approaches in marine organisms and their environments, focusing on recent advances in the field. We also point out some of the technical challenges that need to be overcome in order to increase applications of metabolomics in marine systems, including extraction of chemical compounds from different matrices and data management. Metabolites being important links between genotype and phenotype, we describe added value provided by integration of data from metabolite profiling with other layers of omics, as well as their importance for the development of systems biology approaches in marine systems to study several biological processes, and to analyze interactions between organisms within communities. The growing importance of MS-based metabolomics in chemical ecology studies in marine ecosystems is also illustrated.}, } @article {pmid22685537, year = {2012}, author = {Hadrys, H and Simon, S and Kaune, B and Schmitt, O and Schöner, A and Jakob, W and Schierwater, B}, title = {Isolation of Hox cluster genes from insects reveals an accelerated sequence evolution rate.}, journal = {PloS one}, volume = {7}, number = {6}, pages = {e34682}, pmid = {22685537}, issn = {1932-6203}, mesh = {Amino Acid Sequence ; Animals ; Cloning, Molecular ; Databases, Genetic ; *Evolution, Molecular ; Genes, Homeobox/*genetics ; Homeodomain Proteins/classification/genetics/isolation & purification ; Insecta/classification/*genetics ; Molecular Sequence Data ; *Multigene Family ; Phylogeny ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; }, abstract = {Among gene families it is the Hox genes and among metazoan animals it is the insects (Hexapoda) that have attracted particular attention for studying the evolution of development. Surprisingly though, no Hox genes have been isolated from 26 out of 35 insect orders yet, and the existing sequences derive mainly from only two orders (61% from Hymenoptera and 22% from Diptera). We have designed insect specific primers and isolated 37 new partial homeobox sequences of Hox cluster genes (lab, pb, Hox3, ftz, Antp, Scr, abd-a, Abd-B, Dfd, and Ubx) from six insect orders, which are crucial to insect phylogenetics. These new gene sequences provide a first step towards comparative Hox gene studies in insects. Furthermore, comparative distance analyses of homeobox sequences reveal a correlation between gene divergence rate and species radiation success with insects showing the highest rate of homeobox sequence evolution.}, } @article {pmid22683238, year = {2012}, author = {Dave, M and Higgins, PD and Middha, S and Rioux, KP}, title = {The human gut microbiome: current knowledge, challenges, and future directions.}, journal = {Translational research : the journal of laboratory and clinical medicine}, volume = {160}, number = {4}, pages = {246-257}, doi = {10.1016/j.trsl.2012.05.003}, pmid = {22683238}, issn = {1878-1810}, mesh = {Adaptive Immunity/physiology ; Bacteria/*classification ; Computational Biology ; Gastrointestinal Tract/*microbiology ; Humans ; Immunity, Innate/physiology ; }, abstract = {The Human Genome Project was completed a decade ago, leaving a legacy of process, tools, and infrastructure now being turned to the study of the microbes that reside in and on the human body as determinants of health and disease, and has been branded "The Human Microbiome Project." Of the various niches under investigation, the human gut houses the most complex and abundant microbial community and is an arena for important host-microbial interactions that have both local and systemic impact. Initial studies of the human microbiome have been largely descriptive, a testing ground for innovative molecular techniques and new hypotheses. Methods for studying the microbiome have quickly evolved from low-resolution surveys of microbial community structure to high-definition description of composition, function, and ecology. Next-generation sequencing technologies combined with advanced bioinformatics place us at the doorstep of revolutionary insight into the composition, capability, and activity of the human intestinal microbiome. Renewed efforts to cultivate previously "uncultivable" microbes will be important to the overall understanding of gut ecology. There remain numerous methodological challenges to the effective study and understanding of the gut microbiome, largely relating to study design, sample collection, and the number of predictor variables. Strategic collaboration of clinicians, microbiologists, molecular biologists, computational scientists, and bioinformaticians is the ideal paradigm for success in this field. Meaningful interpretation of the gut microbiome requires that host genetic and environmental influences be controlled or accounted for. Understanding the gut microbiome in healthy humans is a foundation for discovering its influence in various important gastrointestinal and nutritional diseases (eg, inflammatory bowel disease, diabetes, and obesity), and for rational translation to human health gains.}, } @article {pmid22682658, year = {2012}, author = {Van Zundert, RM and Kuntsche, E and Engels, RC}, title = {In the heat of the moment: alcohol consumption and smoking lapse and relapse among adolescents who have quit smoking.}, journal = {Drug and alcohol dependence}, volume = {126}, number = {1-2}, pages = {200-205}, doi = {10.1016/j.drugalcdep.2012.05.016}, pmid = {22682658}, issn = {1879-0046}, mesh = {Adolescent ; Alcohol Drinking/*psychology ; Data Interpretation, Statistical ; Female ; Humans ; Individuality ; Male ; Recurrence ; Smoking/*psychology ; Smoking Cessation/*psychology ; Surveys and Questionnaires ; Young Adult ; }, abstract = {BACKGROUND: The present study tested the co-occurrence of alcohol use and the first lapse and relapse into smoking among daily smoking adolescents who quit smoking.

METHODS: In this ecological momentary assessment study, participants completed web-based questionnaires three times a day during one week prior to and three weeks after a quit attempt in their own natural environments. Participants were 134 daily smoking adolescents in the aged 15-19. Hierarchical linear modeling was applied to test whether alcohol use was related to the first lapse and relapse. Lapse was defined as the first incidence of smoking after achieving 24-h abstinence, relapse was defined as smoking at least five cigarettes on three consecutive days.

RESULTS: The first lapse was strongly associated with alcohol use. Individual characteristics (age, sex, and baseline smoking status) did not predict the first lapse nor did they moderate the association between alcohol use and the first lapse. Progression from lapse to relapse did not seem to be associated with alcohol consumption, although this association appeared to be moderated by baseline smoking status. More specifically, alcohol use only posed a significant risk factor for relapse among those who smoked less frequently before the start of the study than others who relapsed. Intermittent smoking between the first lapse and relapse (or end of data) was strongly associated with alcohol use.

CONCLUSIONS: Adolescent drinking during smoking cessation seems to be associated with the first lapse into smoking after quitting and subsequent intermittent smoking and should be targeted in adolescent smoking cessation interventions.}, } @article {pmid22668789, year = {2012}, author = {Debastiani, VJ and Pillar, VD}, title = {SYNCSA--R tool for analysis of metacommunities based on functional traits and phylogeny of the community components.}, journal = {Bioinformatics (Oxford, England)}, volume = {28}, number = {15}, pages = {2067-2068}, doi = {10.1093/bioinformatics/bts325}, pmid = {22668789}, issn = {1367-4811}, mesh = {*Biota ; Computational Biology/methods ; Ecology/*methods ; *Phylogeny ; *Software ; }, abstract = {SUMMARY: SYNCSA is an R package for the analysis of metacommunities based on functional traits and phylogeny of the community components. It offers tools to calculate several matrix correlations that express trait-convergence assembly patterns, trait-divergence assembly patterns and phylogenetic signal in functional traits at the species pool level and at the metacommunity level.

SYNCSA is a package for the R environment, under a GPL-2 open-source license and freely available on CRAN official web server for R (http://cran.r-project.org).

CONTACT: vanderleidebastiani@yahoo.com.br.}, } @article {pmid22666489, year = {2012}, author = {Boyer, S and Brown, SD and Collins, RA and Cruickshank, RH and Lefort, MC and Malumbres-Olarte, J and Wratten, SD}, title = {Sliding window analyses for optimal selection of mini-barcodes, and application to 454-pyrosequencing for specimen identification from degraded DNA.}, journal = {PloS one}, volume = {7}, number = {5}, pages = {e38215}, pmid = {22666489}, issn = {1932-6203}, mesh = {Animals ; Computational Biology ; DNA/*chemistry/*genetics ; DNA Barcoding, Taxonomic/*methods ; DNA, Ribosomal/chemistry/genetics ; Digestion ; Genetic Markers/genetics ; Mollusca/physiology ; Oligochaeta/classification/genetics ; }, abstract = {DNA barcoding remains a challenge when applied to diet analyses, ancient DNA studies, environmental DNA samples and, more generally, in any cases where DNA samples have not been adequately preserved. Because the size of the commonly used barcoding marker (COI) is over 600 base pairs (bp), amplification fails when the DNA molecule is degraded into smaller fragments. However, relevant information for specimen identification may not be evenly distributed along the barcoding region, and a shorter target can be sufficient for identification purposes. This study proposes a new, widely applicable, method to compare the performance of all potential 'mini-barcodes' for a given molecular marker and to objectively select the shortest and most informative one. Our method is based on a sliding window analysis implemented in the new R package SPIDER (Species IDentity and Evolution in R). This method is applicable to any taxon and any molecular marker. Here, it was tested on earthworm DNA that had been degraded through digestion by carnivorous landsnails. A 100 bp region of 16 S rDNA was selected as the shortest informative fragment (mini-barcode) required for accurate specimen identification. Corresponding primers were designed and used to amplify degraded earthworm (prey) DNA from 46 landsnail (predator) faeces using 454-pyrosequencing. This led to the detection of 18 earthworm species in the diet of the snail. We encourage molecular ecologists to use this method to objectively select the most informative region of the gene they aim to amplify from degraded DNA. The method and tools provided here, can be particularly useful (1) when dealing with degraded DNA for which only small fragments can be amplified, (2) for cases where no consensus has yet been reached on the appropriate barcode gene, or (3) to allow direct analysis of short reads derived from massively parallel sequencing without the need for bioinformatic consolidation.}, } @article {pmid22665285, year = {2012}, author = {Hohenlohe, PA and Catchen, J and Cresko, WA}, title = {Population genomic analysis of model and nonmodel organisms using sequenced RAD tags.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {888}, number = {}, pages = {235-260}, doi = {10.1007/978-1-61779-870-2_14}, pmid = {22665285}, issn = {1940-6029}, support = {1R24GM079486-01A1/GM/NIGMS NIH HHS/United States ; F32GM076995/GM/NIGMS NIH HHS/United States ; F32GM095213/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; *Computational Biology ; DNA/analysis ; Evolution, Molecular ; Genetic Markers ; *Genome ; Genome-Wide Association Study ; High-Throughput Nucleotide Sequencing ; Humans ; Metagenomics/*methods ; Polymorphism, Single Nucleotide/*genetics ; Restriction Mapping/*methods ; Sequence Tagged Sites ; *Software ; }, abstract = {The evolutionary processes of mutation, migration, genetic drift, and natural selection shape patterns of genetic variation among individuals, populations, and species, and they can do so differentially across genomes. The field of population genomics provides a comprehensive genome-scale view of these processes, even beyond traditional model organisms. Until recently, genome-wide studies of genetic variation have been prohibitively expensive. However, next-generation sequencing (NGS) technologies are revolutionizing the field of population genomics, allowing for genetic analysis at scales not previously possible even in organisms for which few genomic resources presently exist. To speed this revolution in evolutionary genetics, we and colleagues developed Restriction site Associated DNA (RAD) sequencing, a method that uses Illumina NGS to simultaneously type and score tens to hundreds of thousands of single nucleotide polymorphism (SNP) markers in hundreds of individuals for minimal investment of resources. The core molecular protocol is described elsewhere in this volume, which can be modified to suit a diversity of evolutionary genetic questions. In this chapter, we outline the conceptual framework of population genomics, relate genomic patterns of variation to evolutionary processes, and discuss how RAD sequencing can be used to study population genomics. In addition, we discuss bioinformatic considerations that arise from unique aspects of NGS data as compared to traditional marker based approaches, and we outline some general analytical approaches for RAD-seq and similar data, including a computational pipeline that we developed called Stacks. This software can be used for the analysis of RAD-seq data in organisms with and without a reference genome. Nonetheless, the development of analytical tools remains in its infancy, and further work is needed to fully quantify sampling variance and biases in these data types. As data-gathering technology continues to advance, our ability to understand genomic evolution in natural populations will be limited more by conceptual and analytical weaknesses than by the amount of molecular data.}, } @article {pmid22665283, year = {2012}, author = {Dlugosch, KM and Bonin, A}, title = {Allele identification in assembled genomic sequence datasets.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {888}, number = {}, pages = {197-211}, doi = {10.1007/978-1-61779-870-2_12}, pmid = {22665283}, issn = {1940-6029}, mesh = {*Alleles ; Animals ; Arabidopsis ; Databases, Genetic ; Drosophila melanogaster ; Gene Duplication ; Gene Frequency ; *Genetic Loci ; Genetic Variation ; *Genome ; Genomics/*methods ; *Haplotypes ; High-Throughput Nucleotide Sequencing ; Humans ; Polymorphism, Single Nucleotide ; Transcriptome ; }, abstract = {Allelic variation within species provides fundamental insights into the evolution and ecology of organisms, and information about this variation is becoming increasingly available in sequence datasets of multiple and/or outbred individuals. Unfortunately, identifying true allelic variants poses a number of challenges, given the presence of both sequencing errors and alleles from other closely related loci. We outline the key considerations involved in this process, including assessing the accuracy of allele resolution in sequence assembly, clustering of alleles within and among individuals, and identifying clusters that are most likely to correspond to true allelic variants of a single locus. Our focus is particularly on the case where alleles must be identified without a fully resolved reference genome, and where sequence depth information cannot be used to infer the putative number of loci sharing a sequence, such as in transcriptome or post-assembly datasets. Throughout, we provide information about publicly available tools to aid allele identification in such cases.}, } @article {pmid22664261, year = {2012}, author = {Jiang, J and Wang, P and Lung, WS and Guo, L and Li, M}, title = {A GIS-based generic real-time risk assessment framework and decision tools for chemical spills in the river basin.}, journal = {Journal of hazardous materials}, volume = {227-228}, number = {}, pages = {280-291}, doi = {10.1016/j.jhazmat.2012.05.051}, pmid = {22664261}, issn = {1873-3336}, mesh = {*Chemical Hazard Release ; China ; *Decision Support Techniques ; *Geographic Information Systems ; Hazardous Substances/toxicity ; Nitrobenzenes ; Risk Assessment/*methods ; *Rivers ; }, abstract = {This paper presents a generic framework and decision tools of real-time risk assessment on Emergency Environmental Decision Support System for response to chemical spills in river basin. The generic "4-step-3-model" framework is able to delineate the warning area and the impact on vulnerable receptors considering four types of hazards referring to functional area, societal impact, and human health and ecology system. Decision tools including the stand-alone system and software components were implemented on GIS platform. A detailed case study on the Songhua River nitrobenzene spill illustrated the goodness of the framework and tool Spill first responders and decision makers of catchment management will benefit from the rich, visual and dynamic hazard information output from the software.}, } @article {pmid22649536, year = {2012}, author = {Lamb, T and Beamer, DA}, title = {Digits lost or gained? Evidence for pedal evolution in the dwarf salamander complex (Eurycea, Plethodontidae).}, journal = {PloS one}, volume = {7}, number = {5}, pages = {e37544}, pmid = {22649536}, issn = {1932-6203}, mesh = {Animals ; Base Sequence ; Bayes Theorem ; *Biological Evolution ; Body Size ; Computational Biology ; DNA, Mitochondrial/genetics ; Demography ; Extremities/*anatomy & histology ; Likelihood Functions ; Models, Genetic ; Molecular Sequence Data ; *Phylogeny ; Sequence Analysis, DNA ; Species Specificity ; Texas ; Urodela/*anatomy & histology/classification ; }, abstract = {Change in digit number, particularly digit loss, has occurred repeatedly over the evolutionary history of tetrapods. Although digit loss has been documented among distantly related species of salamanders, it is relatively uncommon in this amphibian order. For example, reduction from five to four toes appears to have evolved just three times in the morphologically and ecologically diverse family Plethodontidae. Here we report a molecular phylogenetic analysis for one of these four-toed lineages--the Eurycea quadridigitata complex (dwarf salamanders)--emphasizing relationships to other species in the genus. A multilocus phylogeny reveals that dwarf salamanders are paraphyletic with respect to a complex of five-toed, paedomorphic Eurycea from the Edwards Plateau in Texas. We use this phylogeny to examine evolution of digit number within the dwarf-Edwards Plateau clade, testing contrasting hypotheses of digit loss (parallelism among dwarf salamanders) versus digit gain (re-evolution in the Edwards Plateau complex). Bayes factors analysis provides statistical support for a five-toed common ancestor at the dwarf-Edwards node, favoring, slightly, the parallelism hypothesis for digit loss. More importantly, our phylogenetic results pinpoint a rare event in the pedal evolution of plethodontid salamanders.}, } @article {pmid22646978, year = {2012}, author = {Deng, Y and Jiang, YH and Yang, Y and He, Z and Luo, F and Zhou, J}, title = {Molecular ecological network analyses.}, journal = {BMC bioinformatics}, volume = {13}, number = {}, pages = {113}, pmid = {22646978}, issn = {1471-2105}, mesh = {Computational Biology/*methods ; Ecology/*methods ; Ecosystem ; Genes, rRNA ; Metagenomics/*methods ; RNA, Ribosomal, 16S/genetics ; Software ; Soil/analysis ; Soil Microbiology ; Temperature ; }, abstract = {BACKGROUND: Understanding the interaction among different species within a community and their responses to environmental changes is a central goal in ecology. However, defining the network structure in a microbial community is very challenging due to their extremely high diversity and as-yet uncultivated status. Although recent advance of metagenomic technologies, such as high throughout sequencing and functional gene arrays, provide revolutionary tools for analyzing microbial community structure, it is still difficult to examine network interactions in a microbial community based on high-throughput metagenomics data.

RESULTS: Here, we describe a novel mathematical and bioinformatics framework to construct ecological association networks named molecular ecological networks (MENs) through Random Matrix Theory (RMT)-based methods. Compared to other network construction methods, this approach is remarkable in that the network is automatically defined and robust to noise, thus providing excellent solutions to several common issues associated with high-throughput metagenomics data. We applied it to determine the network structure of microbial communities subjected to long-term experimental warming based on pyrosequencing data of 16 S rRNA genes. We showed that the constructed MENs under both warming and unwarming conditions exhibited topological features of scale free, small world and modularity, which were consistent with previously described molecular ecological networks. Eigengene analysis indicated that the eigengenes represented the module profiles relatively well. In consistency with many other studies, several major environmental traits including temperature and soil pH were found to be important in determining network interactions in the microbial communities examined. To facilitate its application by the scientific community, all these methods and statistical tools have been integrated into a comprehensive Molecular Ecological Network Analysis Pipeline (MENAP), which is open-accessible now (http://ieg2.ou.edu/MENA).

CONCLUSIONS: The RMT-based molecular ecological network analysis provides powerful tools to elucidate network interactions in microbial communities and their responses to environmental changes, which are fundamentally important for research in microbial ecology and environmental microbiology.}, } @article {pmid22645818, year = {2012}, author = {Buhle, ER and Feist, BE and Hilborn, R}, title = {Population dynamics and control of invasive Spartina alterniflora: inference and forecasting under uncertainty.}, journal = {Ecological applications : a publication of the Ecological Society of America}, volume = {22}, number = {3}, pages = {880-893}, doi = {10.1890/11-0593.1}, pmid = {22645818}, issn = {1051-0761}, mesh = {Decision Support Techniques ; *Ecosystem ; *Introduced Species ; Models, Biological ; Poaceae/*physiology ; Population Dynamics ; Washington ; }, abstract = {Managing invaded ecosystems entails making decisions about control strategies in the face of scientific uncertainty and ecological stochasticity. Statistical tools such as model selection and Bayesian decision analysis can guide decision-making by estimating probabilities of outcomes under alternative management scenarios, but these tools have seldom been applied in invasion ecology. We illustrate the use of model selection and Bayesian methods in a case study of smooth cordgrass (Spartina alterniflora) invading Willapa Bay, Washington. To address uncertainty in model structure, we quantified the weight of evidence for two previously proposed hypotheses, that S. alterniflora recruitment varies with climatic conditions (represented by sea surface temperature) and that recruitment is subject to an Allee effect due to pollen limitation. By fitting models to time series data, we found strong support for climate effects, with higher per capita seedling production in warmer years, but no evidence for an Allee effect based on either the total area invaded or the mean distance between neighboring clones. We used the best-supported model to compare alternative control strategies, incorporating uncertainty in parameter estimates and population dynamics. For a fixed annual removal effort, the probability of eradication in 10 years was highest, and final invaded area lowest, if removals targeted the smallest clones rather than the largest or randomly selected clones. The relationship between removal effort and probability of eradication was highly nonlinear, with a sharp threshold separating -0% and -100% probability of success, and this threshold was 95% lower in simulations beginning early rather than late in the invasion. This advantage of a rapid response strategy is due to density-dependent population growth, which produces alternative stable equilibria depending on the initial invasion size when control begins. Our approach could be applied to a wide range of invasive species management problems where appropriate data are available.}, } @article {pmid22643823, year = {2012}, author = {Biedenweg, K and Akyuz, K and Skeele, R}, title = {Balancing riparian management and river recreation: methods and applications for exploring floater behavior and their interaction with large wood.}, journal = {Environmental management}, volume = {50}, number = {2}, pages = {283-295}, pmid = {22643823}, issn = {1432-1009}, mesh = {Adolescent ; Adult ; Child ; *Conservation of Natural Resources ; Environmental Monitoring ; Female ; Geographic Information Systems ; Humans ; Male ; Public Opinion ; *Recreation ; Risk-Taking ; *Rivers ; Suburban Population ; *Trees ; Washington ; Young Adult ; }, abstract = {River managers are tasked with meeting both ecological and human needs. In the Puget Sound lowland, riparian management often includes placing or allowing the presence of large wood to stabilize riverbanks and enhance salmon habitat. Although this practice benefits humans by protecting infrastructure and natural resources, it is unclear how such practices interact with an additional human interest, recreation. Furthermore, we were unable to find studies that describe how an agency can go about researching the interaction between recreation and large wood management practices. This study tested methods for describing and estimating the number of river floaters, where they float in relationship to river projects, the risks they take while floating, and their perceptions of large wood in the river. Selecting a high-use suburban river in Washington State, we used riverside observations, interviews, and an infrared counter to gather data in the summer of 2010. Statistical analyses provided general characteristics of users, trends in engaging in risky behaviors, and estimates of use for the entire season and on the busiest day. Data mapping with GIS presented the density of use along the river and frequency of use of specific float routes. Finally, qualitative analysis of interviews clarified floaters' perspectives of large wood. To address the multiple mandates of river managers, it is important to understand recreation users, the factors that could be putting them at risk, and how the actual users perceive large wood in the river. This study demonstrates methods for scientifically gathering such information and applying it when making riparian management decisions.}, } @article {pmid22642264, year = {2012}, author = {, and Andris, M and Arias, MC and Barthel, BL and Bluhm, BH and Bried, J and Canal, D and Chen, XM and Cheng, P and Chiappero, MB and Coelho, MM and Collins, AB and Dash, M and Davis, MC and Duarte, M and Dubois, MP and Françoso, E and Galmes, MA and Gopal, K and Jarne, P and Kalbe, M and Karczmarski, L and Kim, H and Martella, MB and McBride, RS and Negri, V and Negro, JJ and Newell, AD and Piedade, AF and Puchulutegui, C and Raggi, L and Samonte, IE and Sarasola, JH and See, DR and Seyoum, S and Silva, MC and Solaro, C and Tolley, KA and Tringali, MD and Vasemägi, A and Xu, LS and Zanón-Martínez, JI}, title = {Permanent genetic resources added to Molecular Ecology Resources Database 1 February 2012 - 31 March 2012.}, journal = {Molecular ecology resources}, volume = {12}, number = {4}, pages = {779-781}, doi = {10.1111/j.1755-0998.2012.03155.x}, pmid = {22642264}, issn = {1755-0998}, mesh = {*Databases, Genetic ; Ecology ; Genetic Markers ; *Microsatellite Repeats ; *Polymorphism, Single Nucleotide ; }, abstract = {This article documents the addition of 171 microsatellite marker loci and 27 pairs of single nucleotide polymorphism (SNP) sequencing primers to the Molecular Ecology Resources Database. Loci were developed for the following species: Bombus pauloensis, Cephalorhynchus heavisidii, Cercospora sojina, Harpyhaliaetus coronatus, Hordeum vulgare, Lachnolaimus maximus, Oceanodroma monteiroi, Puccinia striiformis f. sp. tritici, Rhea americana, Salmo salar, Salmo trutta, Schistocephalus solidus, Sousa plumbea and Tursiops aduncus. These loci were cross-tested on the following species: Aquila heliaca, Bulweria bulwerii, Buteo buteo, Buteo swainsoni, Falco rusticolus, Haliaeetus albicilla, Halobaena caerulea, Hieraaetus fasciatus, Oceanodroma castro, Puccinia graminis f. sp. Tritici, Puccinia triticina, Rhea pennata and Schistocephalus pungitii. This article also documents the addition of 27 sequencing primer pairs for Puffinus baroli and Bulweria bulwerii and cross-testing of these loci in Oceanodroma castro, Pelagodroma marina, Pelecanoides georgicus, Pelecanoides urinatrix, Thalassarche chrysostoma and Thalassarche melanophrys.}, } @article {pmid22640012, year = {2012}, author = {Folta, SC and Seguin, RA and Ackerman, J and Nelson, ME}, title = {A qualitative study of leadership characteristics among women who catalyze positive community change.}, journal = {BMC public health}, volume = {12}, number = {}, pages = {383}, pmid = {22640012}, issn = {1471-2458}, support = {K01 HL108807/HL/NHLBI NIH HHS/United States ; }, mesh = {Adult ; Aged ; Community Networks/*organization & administration ; Female ; Humans ; *Leadership ; Middle Aged ; Obesity/prevention & control ; Public Health ; Qualitative Research ; United States ; }, abstract = {BACKGROUND: Leadership is critical to making changes at multiple levels of the social ecological model, including the environmental and policy levels, and will therefore likely contribute to solutions to the obesity epidemic and other public health issues. The literature describing the relative leadership styles and strengths of women versus men is mixed and virtually all research comes from sectors outside of public health. The purpose of this qualitative study is to identify specific leadership skills and characteristics in women who have successfully created change predominantly within the food and physical activity environments in their communities and beyond. The second purpose of this study is to understand best practices for training and nurturing women leaders, to maximize their effectiveness in creating social change.

METHODS: Key informant interviews were conducted with 16 women leaders in the public health sector from November 2008 through February 2010. The sample represented a broad spectrum of leaders from across the United States, identified through web searches and through networks of academic and professional colleagues. Most were working on improving the food and physical activity environments within their communities. Questions were designed to determine leaders' career path, motivation, characteristics, definition of success, and challenges. The initial coding framework was based on the questioning structure. Using a grounded theory approach, additional themes were added to the framework as they emerged. The NVivo program was used to help code the data.

RESULTS: Respondents possessed a vision, a strong drive to carry it out, and an ability to mobilize others around the vision. Their definitions of success most often included changing the lives of others in a sustainable way. Persistence and communications skills were important to their success. The mentoring they received was critical. Challenges included fundraising and drifting from their original mission.

CONCLUSIONS: These findings may be used to help develop or inform a model of women's leadership in public health and to improve the training and nurturance of leaders who promote health in their communities and beyond.}, } @article {pmid22639950, year = {2013}, author = {Mishina, H and Hilton, JF and Takayama, JI}, title = {Trends and variations in infant mortality among 47 prefectures in Japan.}, journal = {Journal of evaluation in clinical practice}, volume = {19}, number = {5}, pages = {849-854}, doi = {10.1111/j.1365-2753.2012.01862.x}, pmid = {22639950}, issn = {1365-2753}, mesh = {Data Interpretation, Statistical ; *Delivery of Health Care/methods/statistics & numerical data ; *Educational Status ; Female ; Humans ; Infant ; Infant Mortality/*trends ; Japan/epidemiology ; Male ; Outcome Assessment, Health Care/methods ; Public Health/statistics & numerical data ; Regional Health Planning ; Socioeconomic Factors ; *Water Supply ; }, abstract = {OBJECTIVES: To determine IMR trends and regional variations among 47 prefectures in Japan and to identify associated population-based factors.

METHODS: We conducted an ecological study of infant mortality rate (IMR) by analyzing publicly available data from the Ministry of Health, Labour and Welfare of Japan. Outcome measure for trend is the IMR for each of 47 prefectures from 1999 to 2007; for variation, IMRs for 2006 and 2007 in each prefecture were averaged. We considered as covariates prefecture-level variables related to public health, socio-economic status, clinical services and health care facilities. We conducted multivariate statistical analyses to determine covariates most strongly associated with both 1999-2007 IMR trends and 2006-2007 IMR.

RESULTS: The mean IMR decreased from 3.42 deaths per 1000 live births (range 2.1 to 5.1) in 1999 to 2.54 (range 1.5 to 4.4) in 2007; reductions were greater in prefectures with higher concentrations of public health nurses (PHNs) and nurses. In 2006-2007, nine prefectures had IMRs ≤ 2.25; eight had IMRs ≥ 3.0. When low-, moderate- and high-IMR prefectures were compared, per capita PHNs, maternal education, centralized water supply and household income were identified as significant covariates.

CONCLUSIONS: Both national and prefecture-level IMR in Japan decreased from 1999 to 2007; however, the degree of reduction varied by prefecture. Given that more nurses and PHNs per capita were associated with greater IMR reductions from 1999 to 2007 and more PHNs with lower 2006-2007 IMRs, distribution of preventive health services may play a major role in reducing regional disparities in IMR.}, } @article {pmid22635036, year = {2012}, author = {Araújo, CL and Shimizu, HE and Sousa, AI and Hamann, EM}, title = {Incidence of congenital syphilis in Brazil and its relationship with the Family Health Strategy.}, journal = {Revista de saude publica}, volume = {46}, number = {3}, pages = {479-486}, doi = {10.1590/s0034-89102012000300010}, pmid = {22635036}, issn = {1518-8787}, mesh = {Brazil/epidemiology ; *Family Health ; Female ; Humans ; Incidence ; Pregnancy ; *Prenatal Care ; Risk Factors ; Socioeconomic Factors ; Syphilis, Congenital/*epidemiology/prevention & control ; }, abstract = {OBJECTIVE: To estimate the incidence of congenital syphilis and identify its relationship with Family Health Strategy coverage.

METHODS: An observational ecological study was carried out with both descriptive and analytical components, by two different approaches: one that explores a temporal series (2003 to 2008) and one that focuses on the 2008 data. The secondary data (epidemiological, demographic, and socioeconomic) were obtained from the Department of Informatics of the Unified Health System and the Brazilian Institute of Geography and Statistics. Analysis of the possible effects of the implementation of the Family Health Strategy on the prevention of congenital syphilis was performed on selected subgroups of counties according to two approaches: a) the variation of the average annual rate of incidence of congenital syphilis in different strata of Family Health Program coverage between 2003 and 2008 and the calculation of the simple linear regression coefficient; and b) a negative binomial regression analysis of data from 2008 to control for confounding factors.

RESULTS: Increasingly trends of congenital syphilis notification in Brazil reflect social inequalities in the distribution of cases. The incidence of congenital syphilis was lower in the counties with high Family Health Strategy coverage; however, after controlling for the co-variables, such an effect might be attributed to the coverage of prenatal care and the demographic characteristics of the counties where the implementation of the Strategy was a priority.

CONCLUSIONS: Despite the increase in prenatal care coverage, the actions implemented still exhibit low effectiveness in the prevention of congenital syphilis. Prenatal care performed by Family Health Strategy teams did not control syphilis better than the prenatal care performed within the context of other models of assistance.}, } @article {pmid22629169, year = {2012}, author = {León Ruiz, EJ and García Mozo, H and Domínguez Vilches, E and Galán, C}, title = {The use of geostatistics in the study of floral phenology of Vulpia geniculata (L.) link.}, journal = {TheScientificWorldJournal}, volume = {2012}, number = {}, pages = {624247}, pmid = {22629169}, issn = {1537-744X}, mesh = {*Data Interpretation, Statistical ; Environmental Monitoring/*methods ; *Geographic Information Systems ; Poaceae/*growth & development ; }, abstract = {Traditionally phenology studies have been focused on changes through time, but there exist many instances in ecological research where it is necessary to interpolate among spatially stratified samples. The combined use of Geographical Information Systems (GIS) and Geostatistics can be an essential tool for spatial analysis in phenological studies. Geostatistics are a family of statistics that describe correlations through space/time and they can be used for both quantifying spatial correlation and interpolating unsampled points. In the present work, estimations based upon Geostatistics and GIS mapping have enabled the construction of spatial models that reflect phenological evolution of Vulpia geniculata (L.) Link throughout the study area during sampling season. Ten sampling points, scattered throughout the city and low mountains in the "Sierra de Córdoba" were chosen to carry out the weekly phenological monitoring during flowering season. The phenological data were interpolated by applying the traditional geostatitical method of Kriging, which was used to elaborate weekly estimations of V. geniculata phenology in unsampled areas. Finally, the application of Geostatistics and GIS to create phenological maps could be an essential complement in pollen aerobiological studies, given the increased interest in obtaining automatic aerobiological forecasting maps.}, } @article {pmid22628532, year = {2012}, author = {Stergiopoulos, I and Kourmpetis, YA and Slot, JC and Bakker, FT and De Wit, PJ and Rokas, A}, title = {In silico characterization and molecular evolutionary analysis of a novel superfamily of fungal effector proteins.}, journal = {Molecular biology and evolution}, volume = {29}, number = {11}, pages = {3371-3384}, doi = {10.1093/molbev/mss143}, pmid = {22628532}, issn = {1537-1719}, mesh = {Amino Acid Sequence ; Computational Biology/*methods ; *Evolution, Molecular ; Fungal Proteins/chemistry/*genetics ; Fungi/classification/genetics ; Gene Duplication/genetics ; Genetic Speciation ; Genome, Fungal/genetics ; Models, Genetic ; Molecular Sequence Annotation ; Molecular Sequence Data ; *Multigene Family ; Phylogeny ; Protein Structure, Tertiary ; Species Specificity ; }, abstract = {Most fungal plant pathogens secrete effector proteins during pathogenesis to manipulate their host's defense and promote disease. These are so highly diverse in sequence and distribution, they are essentially considered as species-specific. However, we have recently shown the presence of homologous effectors in fungal species of the Dothideomycetes class. One such example is Ecp2, an effector originally described in the tomato pathogen Cladosporium fulvum but later detected in the plant pathogenic fungi Mycosphaerella fijiensis and Mycosphaerella graminicola as well. Here, using in silico sequence-similarity searches against a database of 135 fungal genomes and GenBank, we extend our queries for homologs of Ecp2 to the fungal kingdom and beyond, and further study their history of diversification. Our analyses show that Ecp2 homologs are members of an ancient and widely distributed superfamily of putative fungal effectors, which we term Hce2 for Homologs of C. fulvum Ecp2. Molecular evolutionary analyses show that the superfamily originated and diversified within the fungal kingdom, experiencing multiple lineage-specific expansions and losses that are consistent with the birth-and-death model of gene family evolution. Newly formed paralogs appear to be subject to diversification early after gene duplication events, whereas at later stages purifying selection acts to preserve diversity and the newly evolved putative functions. Some members of the Hce2 superfamily are fused to fungal Glycoside Hydrolase family 18 chitinases that show high similarity to the Zymocin killer toxin from the dairy yeast Kluyveromyces lactis, suggesting an analogous role in antagonistic interactions. The observed high rates of gene duplication and loss in the Hce2 superfamily, combined with diversification in both sequence and possibly functions within and between species, suggest that Hce2s are involved in adaptation to stresses and new ecological niches. Such findings address the need to rationalize effector biology and evolution beyond the perspective of solely host-microbe interactions.}, } @article {pmid22628380, year = {2012}, author = {Herben, T and Suda, J and Klimesová, J and Mihulka, S and Ríha, P and Símová, I}, title = {Ecological effects of cell-level processes: genome size, functional traits and regional abundance of herbaceous plant species.}, journal = {Annals of botany}, volume = {110}, number = {7}, pages = {1357-1367}, pmid = {22628380}, issn = {1095-8290}, mesh = {Cell Division ; Cell Size ; Chromosomes, Plant/genetics ; Czech Republic ; DNA, Plant/analysis/genetics ; Databases, Nucleic Acid ; Ecology ; Genome Size/*physiology ; Genome, Plant/*genetics ; Magnoliopsida/genetics/growth & development/*physiology ; Phenotype ; Phylogeny ; Plant Leaves/genetics ; Ploidies ; Seeds/genetics ; }, abstract = {BACKGROUND AND AIMS: Genome size is known to be correlated with a number of phenotypic traits associated with cell sizes and cell-division rates. Genome size was therefore used as a proxy for them in order to assess how common plant traits such as height, specific leaf area and seed size/number predict species regional abundance. In this study it is hypothesized that if there is residual correlation between genome size and abundance after these traits are partialled out, there must be additional ecological effects of cell size and/or cell-division rate.

METHODS: Variation in genome size, plant traits and regional abundance were examined in 436 herbaceous species of central European flora, and relationships were sought for among these variables by correlation and path analysis.

KEY RESULTS: Species regional abundance was weakly but significantly correlated with genome size; the relationship was stronger for annuals (R(2) = 0·145) than for perennials (R(2) = 0·027). In annuals, genome size was linked to abundance via its effect on seed size, which constrains seed number and hence population growth rate. In perennials, it weakly affected (via height and specific leaf area) competitive ability. These relationships did not change qualitatively after phylogenetic correction. In both annuals and perennials there was an unresolved effect of genome size on abundance.

CONCLUSIONS: The findings indicate that additional predictors of regional abundance should be sought among variables that are linked to cell size and cell-division rate. Signals of these cell-level processes remain identifiable even at the landscape scale, and show deep differences between perennials and annuals. Plant population biology could thus possibly benefit from more systematic use of indicators of cell-level processes.}, } @article {pmid22622308, year = {2012}, author = {Zhang, Y and Zhang, S and Han, S and Li, X and Qi, L}, title = {Transcriptome profiling and in silico analysis of somatic embryos in Japanese larch (Larix leptolepis).}, journal = {Plant cell reports}, volume = {31}, number = {9}, pages = {1637-1657}, pmid = {22622308}, issn = {1432-203X}, mesh = {Base Sequence ; Biosynthetic Pathways/genetics ; Computational Biology/*methods ; Databases, Protein ; Expressed Sequence Tags ; Gene Expression Profiling/*methods ; Gene Expression Regulation, Developmental ; Gene Expression Regulation, Plant ; Gene Regulatory Networks/genetics ; Japan ; Larix/*embryology/*genetics ; Molecular Sequence Annotation ; Plant Proteins/genetics/metabolism ; Seeds/*genetics ; Sequence Analysis, DNA ; Signal Transduction/genetics ; }, abstract = {UNLABELLED: Japanese larch (Larix leptolepis) is an ecologically and economically important species mainly grown in northeastern China, Japan and Europe. However, erratic flowering and poor germplasm resources caused by high embryo abortion rates have hampered breeding of Larix species. Somatic embryogenesis (SE) is an effective tool for the production of L. leptolepis with desirable characteristics, such as expression of totipotency, preparation of synthetic seeds, and genetic transformation. However, public genomic resources for this species are limited. We sequenced 591,759 raw expressed sequence tags (ESTs) from a 454 sequencing cDNA library of L. leptolepis somatic embryos, resulting in 572,403 high-quality reads. These reads were assembled into 70,927 unique sequences (UniGenes), including 32,321 contigs and 38,606 singletons. After removal of low-quality sequences, 65,115 UniGenes were annotated using the UniProtKB program. Based on their sequence similarity with known proteins, the matched 30,372 sequences from 664 species were estimated to represent approximately 19,000 unique genes. Gene ontology analysis revealed 21,324 UniGenes assigned to 51 categories. By Kyoto Encyclopedia of Genes and Genomes mapping, 25,773 transcripts were associated with 160 biochemical pathways. Further analysis screened four signal transduction pathways represented by 337 enzymes and 17 secondary metabolites. In silico analysis reveals that 207 UniESTs in Larix are homologous to MAPKs genes identified from other model plants, which may be involved in regulating SE development. This study provides an initial insight into the Larix transcriptomes of the pro-embryogenic mass and is a sound basis for future studies.

KEY MESSAGE: We constructed a large, full-length 454 sequencing cDNA library of Larix leptolepis during somatic embryogenesis. More than 590,000 sequences were obtained and a deep-coverage EST database was constructed.}, } @article {pmid22620266, year = {2012}, author = {Charreire, H and Weber, C and Chaix, B and Salze, P and Casey, R and Banos, A and Badariotti, D and Kesse-Guyot, E and Hercberg, S and Simon, C and Oppert, JM}, title = {Identifying built environmental patterns using cluster analysis and GIS: relationships with walking, cycling and body mass index in French adults.}, journal = {The international journal of behavioral nutrition and physical activity}, volume = {9}, number = {}, pages = {59}, pmid = {22620266}, issn = {1479-5868}, mesh = {Adult ; Aged ; *Bicycling ; *Body Mass Index ; Body Weight ; Cluster Analysis ; Cross-Sectional Studies ; *Environment Design ; Female ; Follow-Up Studies ; Geographic Information Systems/*instrumentation ; Health Behavior ; *Health Knowledge, Attitudes, Practice ; Humans ; Logistic Models ; Male ; Middle Aged ; Paris ; Randomized Controlled Trials as Topic ; Recreation ; Residence Characteristics ; Socioeconomic Factors ; Surveys and Questionnaires ; *Walking ; White People ; }, abstract = {BACKGROUND: Socio-ecological models suggest that both individual and neighborhood characteristics contribute to facilitating health-enhancing behaviors such as physical activity. Few European studies have explored relationships between local built environmental characteristics, recreational walking and cycling and weight status in adults. The aim of this study was to identify built environmental patterns in a French urban context and to assess associations with recreational walking and cycling behaviors as performed by middle-aged adult residents.

METHODS: We used a two-step procedure based on cluster analysis to identify built environmental patterns in the region surrounding Paris, France, using measures derived from Geographic Information Systems databases on green spaces, proximity facilities (destinations) and cycle paths. Individual data were obtained from participants in the SU.VI.MAX cohort; 1,309 participants residing in the Ile-de-France in 2007 were included in this analysis. Associations between built environment patterns, leisure walking/cycling data (h/week) and measured weight status were assessed using multinomial logistic regression with adjustment for individual and neighborhood characteristics.

RESULTS: Based on accessibility to green spaces, proximity facilities and availability of cycle paths, seven built environmental patterns were identified. The geographic distribution of built environmental patterns in the Ile-de-France showed that a pattern characterized by poor spatial accessibility to green spaces and proximity facilities and an absence of cycle paths was found only in neighborhoods in the outer suburbs, whereas patterns characterized by better spatial accessibility to green spaces, proximity facilities and cycle paths were more evenly distributed across the region. Compared to the reference pattern (poor accessibility to green areas and facilities, absence of cycle paths), subjects residing in neighborhoods characterized by high accessibility to green areas and local facilities and by a high density of cycle paths were more likely to walk/cycle, after adjustment for individual and neighborhood sociodemographic characteristics (OR = 2.5 95%CI 1.4-4.6). Body mass index did not differ across patterns.

CONCLUSIONS: Built environmental patterns were associated with walking and cycling among French adults. These analyses may be useful in determining urban and public health policies aimed at promoting a healthy lifestyle.}, } @article {pmid22619109, year = {2012}, author = {Hickey, GL and Craig, PS and Luttik, R and de Zwart, D}, title = {On the quantification of intertest variability in ecotoxicity data with application to species sensitivity distributions.}, journal = {Environmental toxicology and chemistry}, volume = {31}, number = {8}, pages = {1903-1910}, doi = {10.1002/etc.1891}, pmid = {22619109}, issn = {1552-8618}, mesh = {Bayes Theorem ; Ecotoxicology/instrumentation/*methods/*standards/statistics & numerical data ; Environmental Monitoring/*methods/*standards ; European Union ; Lethal Dose 50 ; Models, Biological ; *Models, Statistical ; Reproducibility of Results ; Risk Assessment/methods ; Species Specificity ; Toxicity Tests, Chronic/statistics & numerical data ; }, abstract = {Ecotoxicological hazard assessment relies on species effect data to estimate quantities such as the predicted no-effect concentration. While there is a concerted effort to quantify uncertainty in risk assessments, the uncertainty due to intertest variability in species effect measurements is an overlooked component. The European Union Registration, Evaluation, Authorisation, and Restriction of Chemicals (REACH) guidance document suggests that multiple toxicity records for a given chemical-species combination should be aggregated by the geometric mean. Ignoring this issue or applying unjustified so-called harmonization methods weakens the defensibility of uncertainty quantification and interpretation about properties of ecological models, for example, the predicted no-effect concentration. In the present study, the authors propose a simple and broadly theoretically justifiable model to quantify intertest variability and analyze it using Bayesian methods. The value of data in ecotoxicity databases is maximized by using (interval-)censored data. An exploratory analysis is provided to support the model. The authors conclude, based on a large ecotoxicity database of acute effects to aquatic species, that the standard deviation of intertest variability is approximately a factor (or fold-difference) of 3. The consequences for decision makers of (not) adjusting for intertest variability are demonstrated.}, } @article {pmid22615391, year = {2012}, author = {Sibly, RM and Witt, CC and Wright, NA and Venditti, C and Jetz, W and Brown, JH}, title = {Energetics, lifestyle, and reproduction in birds.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {109}, number = {27}, pages = {10937-10941}, pmid = {22615391}, issn = {1091-6490}, mesh = {Adaptation, Physiological/physiology ; Animals ; Behavior, Animal/*physiology ; Birds/*physiology ; Body Size/physiology ; Clutch Size/physiology ; Databases, Factual ; Ecology/methods ; Energy Metabolism/*physiology ; Environment ; Female ; Male ; Nesting Behavior/*physiology ; Phylogeny ; Reproduction/*physiology ; }, abstract = {Theoretical and empirical studies of life history aim to account for resource allocation to the different components of fitness: survival, growth, and reproduction. The pioneering evolutionary ecologist David Lack [(1968) Ecological Adaptations for Breeding in Birds (Methuen and Co., London)] suggested that reproductive output in birds reflects adaptation to environmental factors such as availability of food and risk of predation, but subsequent studies have not always supported Lack's interpretation. Here using a dataset for 980 bird species (Dataset S1), a phylogeny, and an explicit measure of reproductive productivity, we test predictions for how mass-specific productivity varies with body size, phylogeny, and lifestyle traits. We find that productivity varies negatively with body size and energetic demands of parental care and positively with extrinsic mortality. Specifically: (i) altricial species are 50% less productive than precocial species; (ii) species with female-only care of offspring are about 20% less productive than species with other methods of parental care; (iii) nonmigrants are 14% less productive than migrants; (iv) frugivores and nectarivores are about 20% less productive than those eating other foods; and (v) pelagic foragers are 40% less productive than those feeding in other habitats. A strong signal of phylogeny suggests that syndromes of similar life-history traits tend to be conservative within clades but also to have evolved independently in different clades. Our results generally support both Lack's pioneering studies and subsequent research on avian life history.}, } @article {pmid22608875, year = {2012}, author = {Plumb, J and Weinstein, LC and Brawer, R and Scott, K}, title = {Community-based partnerships for improving chronic disease management.}, journal = {Primary care}, volume = {39}, number = {2}, pages = {433-447}, doi = {10.1016/j.pop.2012.03.011}, pmid = {22608875}, issn = {1558-299X}, mesh = {Chronic Disease ; Community Networks/*organization & administration ; *Cooperative Behavior ; Diabetes Mellitus/*drug therapy/prevention & control ; *Disease Management ; Humans ; *Models, Organizational ; Nutritional Status ; }, abstract = {With the growing burden of chronic disease, the medical and public health communities are re-examining their roles and opportunities for more effective prevention and clinical interventions. The potential to significantly improve chronic disease prevention and have an impact on morbidity and mortality from chronic conditions is enhanced by adopting strategies that incorporate a social ecology perspective, realigning the patient-physician relationship, integrating population health perspectives into the Chronic Care Model, and effectively engaging communities using established principles of community engagement.}, } @article {pmid22590806, year = {2012}, author = {Peters, PA and Oliver, LN and Carrière, GM}, title = {Geozones: an area-based method for analysis of health outcomes.}, journal = {Health reports}, volume = {23}, number = {1}, pages = {55-64}, pmid = {22590806}, issn = {0840-6529}, mesh = {Canada ; Censuses ; Data Interpretation, Statistical ; Health Services/statistics & numerical data ; *Health Status ; Humans ; Income/*statistics & numerical data ; Indians, North American/*statistics & numerical data ; Inuit/*statistics & numerical data ; Outcome Assessment, Health Care/*methods ; *Small-Area Analysis ; Socioeconomic Factors ; }, abstract = {BACKGROUND: Administrative datasets often lack information about individual characteristics such as Aboriginal identity and income. However, these datasets frequently contain individual-level geographic information (such as postal codes). This paper explains the methodology for creating Geozones, which are area-based thresholds of population characteristics derived from census data, which can be used in the analysis of social or economic differences in health and health service utilization.

DATA AND METHODS: With aggregate 2006 Census information at the Dissemination Area level, population concentration and exposure for characteristics of interest are analysed using threshold tables and concentration curves. Examples are presented for the Aboriginal population and for income gradients.

RESULTS: The patterns of concentration of First Nations people, Métis, and Inuit differ from those of non-Aboriginal people and between urban and rural areas. The spatial patterns of concentration and exposure by income gradients also differ.

INTERPRETATION: The Geozones method is a relatively easy way of identifying areas with lower and higher concentrations of subgroups. Because it is ecological-based, Geozones has the inherent strengths and weaknesses of this approach.}, } @article {pmid22587709, year = {2012}, author = {Ware, AL and Crocker, N and O'Brien, JW and Deweese, BN and Roesch, SC and Coles, CD and Kable, JA and May, PA and Kalberg, WO and Sowell, ER and Jones, KL and Riley, EP and Mattson, SN and , }, title = {Executive function predicts adaptive behavior in children with histories of heavy prenatal alcohol exposure and attention-deficit/hyperactivity disorder.}, journal = {Alcoholism, clinical and experimental research}, volume = {36}, number = {8}, pages = {1431-1441}, pmid = {22587709}, issn = {1530-0277}, support = {U01 AA014834-08/AA/NIAAA NIH HHS/United States ; U01 AA014834/AA/NIAAA NIH HHS/United States ; U24 AA014818-08/AA/NIAAA NIH HHS/United States ; U24 AA014815-08/AA/NIAAA NIH HHS/United States ; U24 AA014811/AA/NIAAA NIH HHS/United States ; U24 AA014815/AA/NIAAA NIH HHS/United States ; U24 AA014818/AA/NIAAA NIH HHS/United States ; U24 AA014811-08/AA/NIAAA NIH HHS/United States ; U01 AA017122/AA/NIAAA NIH HHS/United States ; }, mesh = {Adaptation, Psychological/*physiology ; Adolescent ; Adult ; Aging/psychology ; Analysis of Variance ; Attention Deficit Disorder with Hyperactivity/*psychology ; Child ; Data Interpretation, Statistical ; Ethnicity ; *Executive Function ; Female ; Fetal Alcohol Spectrum Disorders/psychology ; Functional Laterality ; Humans ; Intelligence Tests ; Male ; Neuropsychological Tests ; Predictive Value of Tests ; Pregnancy ; Prenatal Exposure Delayed Effects/*psychology ; Regression Analysis ; Sex Characteristics ; Stroop Test ; United States ; }, abstract = {BACKGROUND: Prenatal exposure to alcohol often results in disruption to discrete cognitive and behavioral domains, including executive function (EF) and adaptive functioning. In the current study, the relation between these 2 domains was examined in children with histories of heavy prenatal alcohol exposure, nonexposed children with a diagnosis of attention-deficit/hyperactivity disorder (ADHD), and typically developing controls.

METHODS: As part of a multisite study, 3 groups of children (8 to 18 years, M = 12.10) were tested: children with histories of heavy prenatal alcohol exposure (ALC, n = 142), nonexposed children with ADHD (ADHD, n = 82), and typically developing controls (CON, n = 133) who did not have ADHD or a history of prenatal alcohol exposure. Children completed subtests of the Delis-Kaplan Executive Function System (D-KEFS), and their primary caregivers completed the Vineland Adaptive Behavior Scales-II. Data were analyzed using regression analyses.

RESULTS: Analyses showed that EF measures were predictive of adaptive abilities, and significant interactions between D-KEFS measures and group were present. For the ADHD group, the relation between adaptive abilities and EF was more general, with 3 of the 4 EF measures showing a significant relation with adaptive score. In contrast, for the ALC group, this relation was specific to the nonverbal EF measures. In the CON group, performance on EF tasks did not predict adaptive scores over the influence of age.

CONCLUSIONS: These results support prior research in ADHD, suggesting that EF deficits are predictive of poorer adaptive behavior and extend this finding to include children with heavy prenatal exposure to alcohol. However, the relation between EF and adaptive ability differed by group, suggesting unique patterns of abilities in these children. These results provide enhanced understanding of adaptive deficits in these populations, as well as demonstrate the ecological validity of laboratory measures of EF.}, } @article {pmid22586973, year = {2012}, author = {Fu, SF and Zhang, P and Jiang, JL}, title = {[Evaluation of land resources carrying capacity of development zone based on planning environment impact assessment].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {23}, number = {2}, pages = {459-467}, pmid = {22586973}, issn = {1001-9332}, mesh = {China ; *Conservation of Natural Resources ; *Ecosystem ; Environment Design ; Environmental Monitoring/methods ; Evaluation Studies as Topic ; Geographic Information Systems ; Population Growth ; *Soil ; }, abstract = {Assessment of land resources carrying capacity is the key point of planning environment impact assessment and the main foundation to determine whether the planning could be implemented or not. With the help of the space analysis function of Geographic Information System, and selecting altitude, slope, land use type, distance from resident land, distance from main traffic roads, and distance from environmentally sensitive area as the sensitive factors, a comprehensive assessment on the ecological sensitivity and its spatial distribution in Zhangzhou Merchants Economic and Technological Development Zone, Fujian Province of East China was conducted, and the assessment results were combined with the planning land layout diagram for the ecological suitability analysis. In the Development Zone, 84.0% of resident land, 93.1% of industrial land, 86.0% of traffic land, and 76. 0% of other constructive lands in planning were located in insensitive and gently sensitive areas, and thus, the implement of the land use planning generally had little impact on the ecological environment, and the land resources in the planning area was able to meet the land use demand. The assessment of the population carrying capacity with ecological land as the limiting factor indicated that in considering the highly sensitive area and 60% of the moderately sensitive area as ecological land, the population within the Zone in the planning could reach 240000, and the available land area per capita could be 134.0 m2. Such a planned population scale is appropriate, according to the related standards of constructive land.}, } @article {pmid22583666, year = {2012}, author = {Zainal, K and Al-Madany, I and Al-Sayed, H and Khamis, A and Al Shuhaby, S and Al Hisaby, A and Elhoussiny, W and Khalaf, E}, title = {The cumulative impacts of reclamation and dredging on the marine ecology and land-use in the Kingdom of Bahrain.}, journal = {Marine pollution bulletin}, volume = {64}, number = {7}, pages = {1452-1458}, doi = {10.1016/j.marpolbul.2012.04.004}, pmid = {22583666}, issn = {1879-3363}, mesh = {Bahrain ; *Conservation of Natural Resources ; *Ecosystem ; Environment ; *Environmental Monitoring ; Geographic Information Systems ; Marine Biology ; Oceans and Seas ; Ships/methods ; }, abstract = {This article assesses the ecological and economic impacts of land reclamation and dredging through consulting recent environmental impact assessment reports. Geographic features of Bahrain during 1963-2008 are produced using Geographical Information System. Extensive but inexpensive shallow coastal areas and tidal flats have been reclaimed particularly from 1997 to 2007 at a high rate of 21 km(2)/year. Formal records show the increase in the original land mass by the year 2008 to be 91 km(2). An estimated total cumulative loss of major habitats resulting from 10 reclamation projects was around 153.58 km(2). Also much larger scale impacts should be considered resulting from the borrow areas used for the extraction of sand or infill materials. A number of key habitats and species are affected in the vicinity of these projects. The study attempts to assign a monetary value to the marine ecosystem functions. There is a need for efficient coastal zone management to regulate a sustainable use of the marine resources.}, } @article {pmid22582339, year = {2012}, author = {Kudielka, BM and Gierens, A and Hellhammer, DH and Wüst, S and Schlotz, W}, title = {Salivary cortisol in ambulatory assessment--some dos, some don'ts, and some open questions.}, journal = {Psychosomatic medicine}, volume = {74}, number = {4}, pages = {418-431}, doi = {10.1097/PSY.0b013e31825434c7}, pmid = {22582339}, issn = {1534-7796}, mesh = {Adolescent ; Adult ; Area Under Curve ; Child ; Circadian Rhythm/*physiology ; Data Interpretation, Statistical ; Female ; Health Status ; Humans ; Hydrocortisone/*metabolism ; Hypothalamo-Hypophyseal System/*physiology ; Male ; Monitoring, Ambulatory/*methods ; Patient Compliance ; Pituitary-Adrenal System/*physiology ; Risk Factors ; Saliva/chemistry ; Specimen Handling/instrumentation/methods ; Stress, Psychological/*metabolism ; Time Factors ; }, abstract = {The impact of stress on health and disease is an important research topic in psychosomatic medicine. Because research on hypothalamic-pituitary-adrenal (HPA) axis regulation under controlled laboratory studies lacks ecological validity, it needs to be complemented by a research program that includes momentary ambulatory assessment. The measurement of salivary cortisol offers the possibility to trace the free steroid hormone concentrations in ambulant settings. Therefore, in this article, we first discuss the role of salivary cortisol in ambulatory monitoring. We start with a brief description of HPA axis regulation, and we then consider cortisol assessments in other organic materials, followed by a presentation of common salivary markers of HPA axis regulation suitable for ambulatory assessment. We further provide an overview on assessment designs and sources of variability within and between subjects (intervening variables), acknowledge the issue of (non)compliance, and address statistical aspects. We further give an overview of associations with psychosocial and health-related variables relevant for ambulatory assessment. Finally, we deal with preanalytical aspects of laboratory salivary cortisol analysis. The relative simplicity of salivary cortisol assessment protocols may lead to an overoptimistic view of the robustness of this method. We thus discuss several important issues related to the collection and storage of saliva samples and present empirical data on the stability of salivary cortisol measurements over time.}, } @article {pmid22578577, year = {2012}, author = {Samraoui, F and Nedjah, R and Boucheker, A and Alfarhan, AH and Samraoui, B}, title = {Patterns of resource partitioning by nesting herons and ibis: how are odonata exploited?.}, journal = {Comptes rendus biologies}, volume = {335}, number = {4}, pages = {310-317}, doi = {10.1016/j.crvi.2012.03.009}, pmid = {22578577}, issn = {1768-3238}, mesh = {Algeria ; Algorithms ; Animals ; Birds/*physiology ; Data Interpretation, Statistical ; Diet ; Ecosystem ; Feeding Behavior/physiology ; *Insecta ; Larva ; Multivariate Analysis ; Nesting Behavior/physiology ; Predatory Behavior/*physiology ; Sexual Behavior, Animal/physiology ; Species Specificity ; Sympatry ; Wetlands ; }, abstract = {Herons and ibis are colonially nesting waders which, owing to their number, mobility and trophic role as top predators, play a key role in aquatic ecosystems. They are also good biological models to investigate interspecific competition between sympatric species and predation; two processes which structure ecological communities. Odonata are also numerous, diverse, mobile and can play an important role in aquatic ecosystems by serving as prey for herons and ibis. A relationship between prey size and bird predator has been observed in Numidia wetlands (NE Algeria) after analyzing food boluses regurgitated by six species of birds (Purple Heron, Black-crowned Night Heron, Glossy Ibis, Little Egret, Squacco Heron and Cattle Egret) during the breeding period, which also shows a temporal gradient for the six species. Both the Levins index and preliminary multivariate analysis of the Odonata as prey fed to nestling herons and ibis, indicated a high degree of resource overlap. However, a distinction of prey based on taxonomy (suborder and family) and developmental stage (larvae or adults) reveals a clear size dichotomy with large-sized predators (Purple Heron, Black-crowned Night Heron and Glossy Ibis) preying on large preys like Aeshnids and Libellulids and small-sized predators feeding mainly on small prey like Zygoptera. Overall, the resource utilization suggests a pattern of resource segregation by coexisting nesting herons and ibis based on the timing of reproduction, prey types, prey size and foraging microhabitats.}, } @article {pmid22577307, year = {2012}, author = {Marewski, JN and Gigerenzer, G}, title = {Heuristic decision making in medicine.}, journal = {Dialogues in clinical neuroscience}, volume = {14}, number = {1}, pages = {77-89}, pmid = {22577307}, issn = {1958-5969}, mesh = {Decision Making/*physiology ; *Decision Support Techniques ; *Decision Trees ; Humans ; Mental Disorders/psychology/therapy ; *Models, Psychological ; Psychiatry/education/*methods/*trends ; }, abstract = {Can less information be more helpful when it comes to making medical decisions? Contrary to the common intuition that more information is always better, the use of heuristics can help both physicians and patients to make sound decisions. Heuristics are simple decision strategies that ignore part of the available information, basing decisions on only a few relevant predictors. We discuss: (i) how doctors and patients use heuristics; and (ii) when heuristics outperform information-greedy methods, such as regressions in medical diagnosis. Furthermore, we outline those features of heuristics that make them useful in health care settings. These features include their surprising accuracy, transparency, and wide accessibility, as well as the low costs and little time required to employ them. We close by explaining one of the statistical reasons why heuristics are accurate, and by pointing to psychiatry as one area for future research on heuristics in health care.}, } @article {pmid22576789, year = {2012}, author = {Masel, J}, title = {Rethinking Hardy-Weinberg and genetic drift in undergraduate biology.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {34}, number = {8}, pages = {701-710}, doi = {10.1002/bies.201100178}, pmid = {22576789}, issn = {1521-1878}, mesh = {Computational Biology/education ; Education, Medical, Undergraduate/*methods ; Gene Frequency ; *Genetic Drift ; Genetics, Population/*education ; Mutation ; Population Density ; Selection, Genetic ; Stochastic Processes ; Teaching/methods ; }, abstract = {Population genetics is often taught in introductory biology classes, starting with the Hardy-Weinberg principle (HWP) and genetic drift. Here I argue that teaching these two topics first aligns neither with current expert knowledge, nor with good pedagogy. Student difficulties with mathematics in general, and probability in particular, make population genetics difficult to teach and learn. I recommend an alternative, historically inspired ordering of population genetics topics, based on progressively increasing mathematical difficulty. This progression can facilitate just-in-time math instruction. This alternative ordering includes, but does not privilege, the HWP and genetic drift. Stochastic events whose consequences are felt within a single generation, and the deterministic accumulation of the effects of selection across multiple generations, are both taught before tackling the stochastic accumulation of the effects of accidents of sampling.}, } @article {pmid22576178, year = {2012}, author = {Piasecka, B and Robinson-Rechavi, M and Bergmann, S}, title = {Correcting for the bias due to expression specificity improves the estimation of constrained evolution of expression between mouse and human.}, journal = {Bioinformatics (Oxford, England)}, volume = {28}, number = {14}, pages = {1865-1872}, pmid = {22576178}, issn = {1367-4811}, mesh = {Animals ; Computational Biology/*methods ; *Evolution, Molecular ; *Gene Expression ; Gene Expression Profiling/*methods ; Humans ; Mice ; Transcriptome ; }, abstract = {MOTIVATION: Comparative analyses of gene expression data from different species have become an important component of the study of molecular evolution. Thus methods are needed to estimate evolutionary distances between expression profiles, as well as a neutral reference to estimate selective pressure. Divergence between expression profiles of homologous genes is often calculated with Pearson's or Euclidean distance. Neutral divergence is usually inferred from randomized data. Despite being widely used, neither of these two steps has been well studied. Here, we analyze these methods formally and on real data, highlight their limitations and propose improvements.

RESULTS: It has been demonstrated that Pearson's distance, in contrast to Euclidean distance, leads to underestimation of the expression similarity between homologous genes with a conserved uniform pattern of expression. Here, we first extend this study to genes with conserved, but specific pattern of expression. Surprisingly, we find that both Pearson's and Euclidean distances used as a measure of expression similarity between genes depend on the expression specificity of those genes. We also show that the Euclidean distance depends strongly on data normalization. Next, we show that the randomization procedure that is widely used to estimate the rate of neutral evolution is biased when broadly expressed genes are abundant in the data. To overcome this problem, we propose a novel randomization procedure that is unbiased with respect to expression profiles present in the datasets. Applying our method to the mouse and human gene expression data suggests significant gene expression conservation between these species.}, } @article {pmid22574714, year = {2012}, author = {Karl, SA and Toonen, RJ and Grant, WS and Bowen, BW}, title = {Common misconceptions in molecular ecology: echoes of the modern synthesis.}, journal = {Molecular ecology}, volume = {21}, number = {17}, pages = {4171-4189}, doi = {10.1111/j.1365-294X.2012.05576.x}, pmid = {22574714}, issn = {1365-294X}, mesh = {Animals ; Bayes Theorem ; Cell Nucleus/genetics ; Computational Biology ; DNA, Mitochondrial/genetics ; Ecology/*methods ; Evolution, Molecular ; Genetic Markers ; Genetics, Population/*methods ; Microsatellite Repeats ; Models, Genetic ; Molecular Biology/*methods ; }, abstract = {The field of molecular ecology has burgeoned into a large discipline spurred on by technical innovations that facilitate the rapid acquisition of large amounts of genotypic data, by the continuing development of theory to interpret results, and by the availability of computer programs to analyse data sets. As the discipline grows, however, misconceptions have become enshrined in the literature and are perpetuated by routine citations to other articles in molecular ecology. These misconceptions hamper a better understanding of the processes that influence genetic variation in natural populations and sometimes lead to erroneous conclusions. Here, we consider eight misconceptions commonly appearing in the literature: (i) some molecular markers are inherently better than other markers; (ii) mtDNA produces higher F(ST) values than nDNA; (iii) estimated population coalescences are real; (iv) more data are always better; (v) one needs to do a Bayesian analysis; (vi) selective sweeps influence mtDNA data; (vii) equilibrium conditions are critical for estimating population parameters; and (viii) having better technology makes us smarter than our predecessors. This is clearly not an exhaustive list and many others can be added. It is, however, sufficient to illustrate why we all need to be more critical of our own understanding of molecular ecology and to be suspicious of self-evident truths.}, } @article {pmid22574681, year = {2012}, author = {Kahlke, T and Goesmann, A and Hjerde, E and Willassen, NP and Haugen, P}, title = {Unique core genomes of the bacterial family vibrionaceae: insights into niche adaptation and speciation.}, journal = {BMC genomics}, volume = {13}, number = {}, pages = {179}, pmid = {22574681}, issn = {1471-2164}, mesh = {Adaptation, Biological/*genetics ; Cluster Analysis ; Databases, Genetic ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Multigene Family ; Phylogeny ; Software ; Species Specificity ; Vibrionaceae/classification/*genetics ; }, abstract = {BACKGROUND: The criteria for defining bacterial species and even the concept of bacterial species itself are under debate, and the discussion is apparently intensifying as more genome sequence data is becoming available. However, it is still unclear how the new advances in genomics should be used most efficiently to address this question. In this study we identify genes that are common to any group of genomes in our dataset, to determine whether genes specific to a particular taxon exist and to investigate their potential role in adaptation of bacteria to their specific niche. These genes were named unique core genes. Additionally, we investigate the existence and importance of unique core genes that are found in isolates of phylogenetically non-coherent groups. These groups of isolates, that share a genetic feature without sharing a closest common ancestor, are termed genophyletic groups.

RESULTS: The bacterial family Vibrionaceae was used as the model, and we compiled and compared genome sequences of 64 different isolates. Using the software orthoMCL we determined clusters of homologous genes among the investigated genome sequences. We used multilocus sequence analysis to build a host phylogeny and mapped the numbers of unique core genes of all distinct groups of isolates onto the tree. The results show that unique core genes are more likely to be found in monophyletic groups of isolates. Genophyletic groups of isolates, in contrast, are less common especially for large groups of isolate. The subsequent annotation of unique core genes that are present in genophyletic groups indicate a high degree of horizontally transferred genes. Finally, the annotation of the unique core genes of Vibrio cholerae revealed genes involved in aerotaxis and biosynthesis of the iron-chelator vibriobactin.

CONCLUSION: The presented work indicates that genes specific for any taxon inside the bacterial family Vibrionaceae exist. These unique core genes encode conserved metabolic functions that can shed light on the adaptation of a species to its ecological niche. Additionally, our study suggests that unique core genes can be used to aid classification of bacteria and contribute to a bacterial species definition on a genomic level. Furthermore, these genes may be of importance in clinical diagnostics and drug development.}, } @article {pmid22566671, year = {2012}, author = {Chown, SL}, title = {Trait-based approaches to conservation physiology: forecasting environmental change risks from the bottom up.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {367}, number = {1596}, pages = {1615-1627}, pmid = {22566671}, issn = {1471-2970}, mesh = {Animals ; *Biodiversity ; Biological Evolution ; Body Size ; *Climate Change ; Clutch Size/physiology ; Conservation of Natural Resources/*methods ; Ecosystem ; Environmental Pollution ; Extinction, Biological ; Forecasting/methods ; Introduced Species ; Physiological Phenomena/*physiology ; Risk Assessment ; Time Factors ; }, abstract = {Trait-based approaches have long been a feature of physiology and of ecology. While the latter fields drifted apart in the twentieth century, they are converging owing at least partly to growing similarities in their trait-based approaches, which have much to offer conservation biology. The convergence of spatially explicit approaches to understanding trait variation and its ecological implications, such as encapsulated in community assembly and macrophysiology, provides a significant illustration of the similarity of these areas. Both adopt trait-based informatics approaches which are not only providing fundamental biological insights, but are also delivering new information on how environmental change is affecting diversity and how such change may perhaps be mitigated. Such trait-based conservation physiology is illustrated here for each of the major environmental change drivers, specifically: the consequences of overexploitation for body size and physiological variation; the impacts of vegetation change on thermal safety margins; the consequences of changing net primary productivity and human use thereof for physiological variation and ecosystem functioning; the impacts of rising temperatures on water loss in ectotherms; how hemisphere-related variation in traits may affect responses to changing rainfall regimes and pollution; and how trait-based approaches may enable interactions between climate change and biological invasions to be elucidated.}, } @article {pmid22563400, year = {2012}, author = {Math, RK and Jin, HM and Kim, JM and Hahn, Y and Park, W and Madsen, EL and Jeon, CO}, title = {Comparative genomics reveals adaptation by Alteromonas sp. SN2 to marine tidal-flat conditions: cold tolerance and aromatic hydrocarbon metabolism.}, journal = {PloS one}, volume = {7}, number = {4}, pages = {e35784}, pmid = {22563400}, issn = {1932-6203}, mesh = {Alteromonas/*genetics/isolation & purification ; Cold Temperature ; Databases, Genetic ; Genome, Bacterial ; *Genomics ; Geologic Sediments/microbiology ; Hydrocarbons, Aromatic/*metabolism ; Molecular Chaperones/genetics/metabolism ; Molecular Sequence Data ; Multigene Family ; RNA, Transfer/genetics/metabolism ; RNA, Untranslated/genetics/metabolism ; Signal Transduction/genetics ; }, abstract = {Alteromonas species are globally distributed copiotrophic bacteria in marine habitats. Among these, sea-tidal flats are distinctive: undergoing seasonal temperature and oxygen-tension changes, plus periodic exposure to petroleum hydrocarbons. Strain SN2 of the genus Alteromonas was isolated from hydrocarbon-contaminated sea-tidal flat sediment and has been shown to metabolize aromatic hydrocarbons there. Strain SN2's genomic features were analyzed bioinformatically and compared to those of Alteromonas macleodii ecotypes: AltDE and ATCC 27126. Strain SN2's genome differs from that of the other two strains in: size, average nucleotide identity value, tRNA genes, noncoding RNAs, dioxygenase gene content, signal transduction genes, and the degree to which genes collected during the Global Ocean Sampling project are represented. Patterns in genetic characteristics (e.g., GC content, GC skew, Karlin signature, CRISPR gene homology) indicate that strain SN2's genome architecture has been altered via horizontal gene transfer (HGT). Experiments proved that strain SN2 was far more cold tolerant, especially at 5°C, than the other two strains. Consistent with the HGT hypothesis, a total of 15 genomic islands in strain SN2 likely confer ecological fitness traits (especially membrane transport, aromatic hydrocarbon metabolism, and fatty acid biosynthesis) specific to the adaptation of strain SN2 to its seasonally cold sea-tidal flat habitat.}, } @article {pmid22563389, year = {2012}, author = {Mah, CL and Blake, DB}, title = {Global diversity and phylogeny of the Asteroidea (Echinodermata).}, journal = {PloS one}, volume = {7}, number = {4}, pages = {e35644}, pmid = {22563389}, issn = {1932-6203}, mesh = {Animals ; *Biodiversity ; Databases, Factual ; Echinodermata/*classification ; Minor Planets ; *Phylogeny ; }, abstract = {Members of the Asteroidea (phylum Echinodermata), popularly known as starfish or sea stars, are ecologically important and diverse members of marine ecosystems in all of the world's oceans. We present a comprehensive overview of diversity and phylogeny as they have figured into the evolution of the Asteroidea from Paleozoic to the living fauna. Living post-Paleozoic asteroids, the Neoasteroidea, are morphologically separate from those in the Paleozoic. Early Paleozoic asteroid faunas were diverse and displayed morphology that foreshadowed later living taxa. Preservation presents significant difficulties, but fossil occurrence and current accounts suggests a diverse Paleozoic fauna, which underwent extinction around the Permian-Triassic interval was followed by re-diversification of at least one surviving lineage. Ongoing phylogenetic classification debates include the status of the Paxillosida and the Concentricycloidea. Fossil and molecular evidence has been and continues to be part of the ongoing evolution of asteroid phylogenetic research. The modern lineages of asteroids include the Valvatacea, the Forcipulatacea, the Spinlosida, and the Velatida. We present an overview of diversity in these taxa, as well as brief notes on broader significance, ecology, and functional morphology of each. Although much asteroid taxonomy is stable, many new taxa remain to be discovered with many new species currently awaiting description. The Goniasteridae is currently one of the most diverse families within the Asteroidea. New data from molecular phylogenetics and the advent of global biodiversity databases, such as the World Asteroidea Database (http://www.marinespecies.org/Asteroidea/) present important new springboards for understanding the global biodiversity and evolution of asteroids.}, } @article {pmid22558157, year = {2012}, author = {González-Caro, S and Parra, JL and Graham, CH and McGuire, JA and Cadena, CD}, title = {Sensitivity of metrics of phylogenetic structure to scale, source of data and species pool of hummingbird assemblages along elevational gradients.}, journal = {PloS one}, volume = {7}, number = {4}, pages = {e35472}, pmid = {22558157}, issn = {1932-6203}, mesh = {*Altitude ; Analysis of Variance ; Animals ; Bayes Theorem ; Birds/*genetics ; Colombia ; Computational Biology ; *Demography ; *Ecosystem ; Models, Genetic ; Museums ; *Phylogeny ; Phylogeography ; Species Specificity ; }, abstract = {Patterns of phylogenetic structure of assemblages are increasingly used to gain insight into the ecological and evolutionary processes involved in the assembly of co-occurring species. Metrics of phylogenetic structure can be sensitive to scaling issues and data availability. Here we empirically assess the sensitivity of four metrics of phylogenetic structure of assemblages to changes in (i) the source of data, (ii) the spatial grain at which assemblages are defined, and (iii) the definition of species pools using hummingbird (Trochilidae) assemblages along an elevational gradient in Colombia. We also discuss some of the implications in terms of the potential mechanisms driving these patterns. To explore how source of data influence phylogenetic structure we defined assemblages using three sources of data: field inventories, museum specimens, and range maps. Assemblages were defined at two spatial grains: coarse-grained (elevational bands of 800-m width) and fine-grained (1-km(2) plots). We used three different species pools: all species contained in assemblages, all species within half-degree quadrats, and all species either above or below 2000 m elevation. Metrics considering phylogenetic relationships among all species within assemblages showed phylogenetic clustering at high elevations and phylogenetic evenness in the lowlands, whereas those metrics considering only the closest co-occurring relatives showed the opposite trend. This result suggests that using multiple metrics of phylogenetic structure should provide greater insight into the mechanisms shaping assemblage structure. The source and spatial grain of data had important influences on estimates of both richness and phylogenetic structure. Metrics considering the co-occurrence of close relatives were particularly sensitive to changes in the spatial grain. Assemblages based on range maps included more species and showed less phylogenetic structure than assemblages based on museum or field inventories. Coarse-grained assemblages included more distantly related species and thus showed a more even phylogenetic structure than fine-grained assemblages. Our results emphasize the importance of carefully selecting the scale, source of data and metric used in analysis of the phylogenetic structure of assemblages.}, } @article {pmid22558115, year = {2012}, author = {Ogilvie, LA and Caplin, J and Dedi, C and Diston, D and Cheek, E and Bowler, L and Taylor, H and Ebdon, J and Jones, BV}, title = {Comparative (meta)genomic analysis and ecological profiling of human gut-specific bacteriophage φB124-14.}, journal = {PloS one}, volume = {7}, number = {4}, pages = {e35053}, pmid = {22558115}, issn = {1932-6203}, support = {G0901553/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Amino Acid Sequence ; Bacteroides fragilis/*virology ; Base Sequence ; Cluster Analysis ; Computational Biology ; Demography ; Europe ; Gastrointestinal Tract/*microbiology/virology ; Genome Components ; Genome, Viral/*genetics ; Humans ; Japan ; Metagenome/*genetics ; Microscopy, Electron, Transmission ; Molecular Sequence Data ; Phylogeny ; Proteomics ; Sequence Analysis, DNA ; Sequence Homology ; Siphoviridae/*genetics/pathogenicity/ultrastructure ; United States ; }, abstract = {Bacteriophage associated with the human gut microbiome are likely to have an important impact on community structure and function, and provide a wealth of biotechnological opportunities. Despite this, knowledge of the ecology and composition of bacteriophage in the gut bacterial community remains poor, with few well characterized gut-associated phage genomes currently available. Here we describe the identification and in-depth (meta)genomic, proteomic, and ecological analysis of a human gut-specific bacteriophage (designated φB124-14). In doing so we illuminate a fraction of the biological dark matter extant in this ecosystem and its surrounding eco-genomic landscape, identifying a novel and uncharted bacteriophage gene-space in this community. φB124-14 infects only a subset of closely related gut-associated Bacteroides fragilis strains, and the circular genome encodes functions previously found to be rare in viral genomes and human gut viral metagenome sequences, including those which potentially confer advantages upon phage and/or host bacteria. Comparative genomic analyses revealed φB124-14 is most closely related to φB40-8, the only other publically available Bacteroides sp. phage genome, whilst comparative metagenomic analysis of both phage failed to identify any homologous sequences in 136 non-human gut metagenomic datasets searched, supporting the human gut-specific nature of this phage. Moreover, a potential geographic variation in the carriage of these and related phage was revealed by analysis of their distribution and prevalence within 151 human gut microbiomes and viromes from Europe, America and Japan. Finally, ecological profiling of φB124-14 and φB40-8, using both gene-centric alignment-driven phylogenetic analyses, as well as alignment-free gene-independent approaches was undertaken. This not only verified the human gut-specific nature of both phage, but also indicated that these phage populate a distinct and unexplored ecological landscape within the human gut microbiome.}, } @article {pmid22558086, year = {2012}, author = {Novais, SC and Arrais, J and Lopes, P and Vandenbrouck, T and De Coen, W and Roelofs, D and Soares, AM and Amorim, MJ}, title = {Enchytraeus albidus microarray: enrichment, design, annotation and database (EnchyBASE).}, journal = {PloS one}, volume = {7}, number = {4}, pages = {e34266}, pmid = {22558086}, issn = {1932-6203}, mesh = {Animals ; Base Sequence ; Cluster Analysis ; Computational Biology ; DNA, Complementary/genetics ; *Databases, Genetic ; *Expressed Sequence Tags ; Internet ; Metals, Heavy/*toxicity ; Microarray Analysis ; Molecular Sequence Data ; Oligochaeta/*genetics ; Oligonucleotide Array Sequence Analysis ; Pesticides/*toxicity ; Sequence Analysis, DNA ; }, abstract = {Enchytraeus albidus (Oligochaeta) is an ecologically relevant species used as standard test organisms for risk assessment. Effects of stressors in this species are commonly determined at the population level using reproduction and survival as endpoints. The assessment of transcriptomic responses can be very useful e.g. to understand underlying mechanisms of toxicity with gene expression fingerprinting. In the present paper the following is being addressed: 1) development of suppressive subtractive hybridization (SSH) libraries enriched for differentially expressed genes after metal and pesticide exposures; 2) sequencing and characterization of all generated cDNA inserts; 3) development of a publicly available genomic database on E. albidus. A total of 2100 Expressed Sequence Tags (ESTs) were isolated, sequenced and assembled into 1124 clusters (947 singletons and 177 contigs). From these sequences, 41% matched known proteins in GenBank (BLASTX, e-value ≤ 10(-5)) and 37% had at least one Gene Ontology (GO) term assigned. In total, 5.5% of the sequences were assigned to a metabolic pathway, based on KEGG. With this new sequencing information, an Agilent custom oligonucleotide microarray was designed, representing a potential tool for transcriptomic studies. EnchyBASE (http://bioinformatics.ua.pt/enchybase/) was developed as a web freely available database containing genomic information on E. albidus and will be further extended in the near future for other enchytraeid species. The database so far includes all ESTs generated for E. albidus from three cDNA libraries. This information can be downloaded and applied in functional genomics and transcription studies.}, } @article {pmid22554016, year = {2012}, author = {Stankov, I and Olds, T and Cargo, M}, title = {Overweight and obese adolescents: what turns them off physical activity?.}, journal = {The international journal of behavioral nutrition and physical activity}, volume = {9}, number = {}, pages = {53}, pmid = {22554016}, issn = {1479-5868}, mesh = {Adolescent ; Body Image ; Bullying ; Child ; Databases, Factual ; Environment ; Ethnicity ; Female ; Humans ; Male ; *Motor Activity ; Obesity/*psychology ; Overweight/*psychology ; Schools ; Self Concept ; Socioeconomic Factors ; }, abstract = {A systematic review of qualitative studies was undertaken to understand the barriers to physical activity experienced by adolescents who were overweight or obese. From a search of electronic databases and 'grey' literature, published between 1950 and 2009, 15 studies met the inclusion criteria. Bronfenbrenner's model of human development provided an ecological lens for identifying and synthesising barriers to physical activity. Two reviewers appraised study quality. Miles and Huberman's cross-case analysis was integrated with thematic networking to synthesize the individual, interpersonal and environmental level barriers for boys and girls of different ethnicities and socioeconomic status, across school settings and generalised context. Thirty-five barriers were identified, 13 of which occurred in physical activity situations in the school setting, 18 were not linked to a specific setting, and the remainder were common across both contexts. The fact that these barriers emerged from studies that focused on topics such as victimisation and mental health is particularly poignant and reflects the potentially pervasive influence of adolescent's excessive weight not only in relation to physical activity situations but other aspects of their lives. Furthermore, socioeconomic status and ethnicity was poorly considered, with only one study linking these participant characteristics to quotations and discussing the potential implications. At present, there are few qualitative studies with sufficiently thick description or interpretive validity that provide insight into this vulnerable group of adolescents, and give them a voice to influence policy and practice.}, } @article {pmid22545695, year = {2012}, author = {Mossman, D and Wygant, DB and Gervais, RO}, title = {Estimating the accuracy of neurocognitive effort measures in the absence of a "gold standard".}, journal = {Psychological assessment}, volume = {24}, number = {4}, pages = {815-822}, doi = {10.1037/a0028195}, pmid = {22545695}, issn = {1939-134X}, mesh = {Adult ; *Bayes Theorem ; *Data Interpretation, Statistical ; Female ; Forensic Psychiatry/methods ; Humans ; Male ; Middle Aged ; Neuropsychology/*methods ; }, abstract = {Psychologists frequently use symptom validity tests (SVTs) to help determine whether evaluees' test performance or reported symptoms accurately represent their true functioning and capability. Most studies evaluating the accuracy of SVTs have used either known-group comparisons or simulation designs, but these approaches have well-known limitations (potential misclassifications or lack of ecological validity). This study uses latent class modeling (LCM) implemented in a Bayesian framework to estimate SVT classification accuracy based on data obtained from real-life forensic evaluations. We obtained archival data from 1,301 outpatient evaluees who underwent testing with the Computerized Assessment of Response Bias (CARB), the Test of Memory Malingering (TOMM), and the Word Memory Test (WMT) in a forensic evaluation context. Under various data models, Markov chain Monte Carlo methods implemented via WinBUGS converged to target distributions that permitted Bayesian estimates of SVT accuracy. Under the most plausible model (conditional dependence in test results), classification accuracies (expressed as area under the "trapezoidal" receiver operating characteristic curve ± standard deviation) were as follows: CARB = 0.765 ± 0.030, WMT = 0.929 ± 0.020, and TOMM = 0.771 ± 0.034. At decision thresholds that hold false positive rates at 0.02, the SVTs would detect invalid responses (true positives) at rates of approximately 35%, 65%, and 49%, respectively, for the 3 tests. Though LCM methods have limitations, this study suggests that they offer an approach to SVT evaluation that avoids methodological pitfalls of known-group research designs while retaining ecological validity that is absent in simulation studies.}, } @article {pmid22542930, year = {2012}, author = {Graz, FP and Westbrooke, ME and Florentine, SK}, title = {Modelling the effects of water-point closure and fencing removal: a GIS approach.}, journal = {Journal of environmental management}, volume = {104}, number = {}, pages = {186-194}, doi = {10.1016/j.jenvman.2012.03.014}, pmid = {22542930}, issn = {1095-8630}, mesh = {Australia ; Conservation of Natural Resources ; Ecosystem ; Environmental Monitoring/*methods ; *Geographic Information Systems ; New South Wales ; *Water ; }, abstract = {Artificial water-points in the form of troughs or ground tanks are used to augment natural water supplies within rangelands in many parts of the world. Access to such water-points leads to the development of a distinct ecological sub-system, the piosphere, where trampling and grazing impact modify the vegetation. This study aims to consolidate existing information in a GIS based model to investigate grazing patterns within the landscape. The model focuses on the closure of water-points and removal of fences on Nanya Station, New South Wales, Australia. We found that the manipulation of water-points and fences in one management intervention may change grazing activity in a way different to that which would be experienced if each had been modified separately. Such effects are further modified by the spatial distribution of the water-points and the underlying vegetation.}, } @article {pmid22538320, year = {2012}, author = {Rodgers, KS and Kido, MH and Jokiel, PL and Edmonds, T and Brown, EK}, title = {Use of integrated landscape indicators to evaluate the health of linked watersheds and coral reef environments in the Hawaiian islands.}, journal = {Environmental management}, volume = {50}, number = {1}, pages = {21-30}, pmid = {22538320}, issn = {1432-1009}, mesh = {Agriculture ; Conservation of Natural Resources/*methods ; *Coral Reefs ; Databases, Factual ; *Ecosystem ; Embryophyta/growth & development ; Environmental Monitoring/*methods ; Environmental Policy ; Geographic Information Systems ; Hawaii ; Models, Theoretical ; Pacific Ocean ; *Seawater ; }, abstract = {A linkage between the condition of watersheds and adjacent nearshore coral reef communities is an assumed paradigm in the concept of integrated coastal management. However, quantitative evidence for this "catchment to sea" or "ridge to reef" relationship on oceanic islands is lacking and would benefit from the use of appropriate marine and terrestrial landscape indicators to quantify and evaluate ecological status on a large spatial scale. To address this need, our study compared the Hawai'i Watershed Health Index (HI-WHI) and Reef Health Index (HI-RHI) derived independently of each other over the past decade. Comparisons were made across 170 coral reef stations at 52 reef sites adjacent to 42 watersheds throughout the main Hawaiian Islands. A significant positive relationship was shown between the health of watersheds and that of adjacent reef environments when all sites and depths were considered. This relationship was strongest for sites facing in a southerly direction, but diminished for north facing coasts exposed to persistent high surf. High surf conditions along the north shore increase local wave driven currents and flush watershed-derived materials away from nearshore waters. Consequently, reefs in these locales are less vulnerable to the deposition of land derived sediments, nutrients and pollutants transported from watersheds to ocean. Use of integrated landscape health indices can be applied to improve regional-scale conservation and resource management.}, } @article {pmid22526936, year = {2012}, author = {Ricotta, C and Bacaro, G and Marignani, M and Godefroid, S and Mazzoleni, S}, title = {Computing diversity from dated phylogenies and taxonomic hierarchies: does it make a difference to the conclusions?.}, journal = {Oecologia}, volume = {170}, number = {2}, pages = {501-506}, pmid = {22526936}, issn = {1432-1939}, mesh = {*Biodiversity ; Calibration ; Conservation of Natural Resources ; Data Interpretation, Statistical ; *Phylogeny ; Plants/classification ; Software ; }, abstract = {Recently, dated phylogenies have been increasingly used for ecological studies on community structure and conservation planning. There is, however, a major impediment to a systematic application of phylogenetic methods in ecology: reliable phylogenies with time-calibrated branch lengths are lacking for a large number of taxonomic groups and this condition is likely to continue for a long time. A solution for this problem consists in using undated phylogenies or taxonomic hierarchies as proxies for dated phylogenies. Nonetheless, little is known on the potential loss of information of these approaches compared to studies using dated phylogenies with time-calibrated branch lengths. The aim of this study is to ask how the use of undated phylogenies and taxonomic hierarchies biases a very simple measure of diversity, the mean pairwise phylogenetic distance between community species, compared to the diversity of dated phylogenies derived from the freely available software Phylomatic. This is illustrated with three sets of data on plant species sampled at different scales. Our results show that: (1) surprisingly, the diversity computed from dated phylogenies derived from Phylomatic is more strongly related to the diversity computed from taxonomic hierarchies than to the diversity computed from undated phylogenies, while (2) less surprisingly, the strength of this relationship increases if we consider only angiosperm species.}, } @article {pmid22521137, year = {2012}, author = {Rocchini, D and Neteler, M}, title = {Let the four freedoms paradigm apply to ecology.}, journal = {Trends in ecology & evolution}, volume = {27}, number = {6}, pages = {310-311}, doi = {10.1016/j.tree.2012.03.009}, pmid = {22521137}, issn = {1872-8383}, mesh = {*Access to Information ; Data Interpretation, Statistical ; Databases, Factual ; Ecology/statistics & numerical data/*trends ; Software ; }, } @article {pmid22513215, year = {2013}, author = {Howard, BJ and Beresford, NA and Copplestone, D and Telleria, D and Proehl, G and Fesenko, S and Jeffree, RA and Yankovich, TL and Brown, JE and Higley, K and Johansen, MP and Mulye, H and Vandenhove, H and Gashchak, S and Wood, MD and Takata, H and Andersson, P and Dale, P and Ryan, J and Bollhöfer, A and Doering, C and Barnett, CL and Wells, C}, title = {The IAEA handbook on radionuclide transfer to wildlife.}, journal = {Journal of environmental radioactivity}, volume = {121}, number = {}, pages = {55-74}, doi = {10.1016/j.jenvrad.2012.01.027}, pmid = {22513215}, issn = {1879-1700}, mesh = {Animals ; *Databases, Factual ; Ecosystem ; *Environmental Exposure ; Food Chain ; Fresh Water ; Gastrointestinal Tract/radiation effects ; International Agencies ; Models, Theoretical ; Mollusca ; Plant Roots ; Plants/radiation effects ; Polonium/analysis ; Radiation Monitoring/*methods ; *Radioactive Pollutants ; *Radioisotopes/analysis ; Soil ; }, abstract = {An IAEA handbook presenting transfer parameter values for wildlife has recently been produced. Concentration ratios (CRwo-media) between the whole organism (fresh weight) and either soil (dry weight) or water were collated for a range of wildlife groups (classified taxonomically and by feeding strategy) in terrestrial, freshwater, marine and brackish generic ecosystems. The data have been compiled in an on line database, which will continue to be updated in the future providing the basis for subsequent revision of the Wildlife TRS values. An overview of the compilation and analysis, and discussion of the extent and limitations of the data is presented. Example comparisons of the CRwo-media values are given for polonium across all wildlife groups and ecosystems and for molluscs for all radionuclides. The CRwo-media values have also been compared with those currently used in the ERICA Tool which represented the most complete published database for wildlife transfer values prior to this work. The use of CRwo-media values is a pragmatic approach to predicting radionuclide activity concentrations in wildlife and is similar to that used for screening assessments for the human food chain. The CRwo-media values are most suitable for a screening application where there are several conservative assumptions built into the models which will, to varying extents, compensate for the variable data quality and quantity, and associated uncertainty.}, } @article {pmid22511121, year = {2012}, author = {Brown, CM and Arbour, JH and Jackson, DA}, title = {Testing of the effect of missing data estimation and distribution in morphometric multivariate data analyses.}, journal = {Systematic biology}, volume = {61}, number = {6}, pages = {941-954}, doi = {10.1093/sysbio/sys047}, pmid = {22511121}, issn = {1076-836X}, mesh = {Alligators and Crocodiles/anatomy & histology/classification ; Animals ; *Data Interpretation, Statistical ; Principal Component Analysis ; }, abstract = {Missing data are an unavoidable problem in biological data sets and the performance of missing data deletion and estimation techniques in morphometric data sets is poorly understood. Here, a novel method is used to measure the introduced error of multiple techniques on a representative sample. A large sample of extant crocodilian skulls was measured and analyzed with principal component analysis (PCA). Twenty-three different proportions of missing data were introduced into the data set, estimated, analyzed, and compared with the original result using Procrustes superimposition. Previous work investigating the effects of missing data input missing values randomly, a non-biological phenomenon. Here, missing data were introduced into the data set using three methodologies: purely at random, as a function of the Euclidean distance between respective measurements (simulating anatomical regions), and as a function of the portion of the sample occupied by each taxon (simulating unequal missing data in rare taxa). Gower's distance was found to be the best performing non-estimation method, and Bayesian PCA the best performing estimation method. Specimens of the taxa with small sample sizes and those most morphologically disparate had the highest estimation error. Distribution of missing data had a significant effect on the estimation error for almost all methods and proportions. Taxonomically biased missing data tended to show similar trends to random, but with higher error rates. Anatomically biased missing data showed a much greater deviation from random than the taxonomic bias, and with magnitudes dependent on the estimation method.}, } @article {pmid22509129, year = {2012}, author = {Bellan, SE and Pulliam, JR and Scott, JC and Dushoff, J and , }, title = {How to make epidemiological training infectious.}, journal = {PLoS biology}, volume = {10}, number = {4}, pages = {e1001295}, pmid = {22509129}, issn = {1545-7885}, support = {R01 GM083863/GM/NIGMS NIH HHS/United States ; R24 TW008822/TW/FIC NIH HHS/United States ; GM83863/GM/NIGMS NIH HHS/United States ; R24TW008822/TW/FIC NIH HHS/United States ; }, mesh = {Data Interpretation, Statistical ; Epidemics/statistics & numerical data ; Epidemiologic Factors ; Epidemiology/*education ; Humans ; Models, Biological ; Models, Statistical ; *Problem-Based Learning ; }, abstract = {Modern infectious disease epidemiology builds on two independently developed fields: classical epidemiology and dynamical epidemiology. Over the past decade, integration of the two fields has increased in research practice, but training options within the fields remain distinct with few opportunities for integration in the classroom. The annual Clinic on the Meaningful Modeling of Epidemiological Data (MMED) at the African Institute for Mathematical Sciences has begun to address this gap. MMED offers participants exposure to a broad range of concepts and techniques from both epidemiological traditions. During MMED 2010 we developed a pedagogical approach that bridges the traditional distinction between classical and dynamical epidemiology and can be used at multiple educational levels, from high school to graduate level courses. The approach is hands-on, consisting of a real-time simulation of a stochastic outbreak in course participants, including realistic data reporting, followed by a variety of mathematical and statistical analyses, stemming from both epidemiological traditions. During the exercise, dynamical epidemiologists developed empirical skills such as study design and learned concepts of bias while classical epidemiologists were trained in systems thinking and began to understand epidemics as dynamic nonlinear processes. We believe this type of integrated educational tool will prove extremely valuable in the training of future infectious disease epidemiologists. We also believe that such interdisciplinary training will be critical for local capacity building in analytical epidemiology as Africa continues to produce new cohorts of well-trained mathematicians, statisticians, and scientists. And because the lessons draw on skills and concepts from many fields in biology--from pathogen biology, evolutionary dynamics of host--pathogen interactions, and the ecology of infectious disease to bioinformatics, computational biology, and statistics--this exercise can be incorporated into a broad array of life sciences courses.}, } @article {pmid22509033, year = {2012}, author = {Price, SA and Hopkins, SS and Smith, KK and Roth, VL}, title = {Tempo of trophic evolution and its impact on mammalian diversification.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {109}, number = {18}, pages = {7008-7012}, pmid = {22509033}, issn = {1091-6490}, mesh = {Adaptation, Physiological ; Animals ; Biodiversity ; *Biological Evolution ; Carnivory ; Databases, Factual ; *Diet ; Ecosystem ; Extinction, Biological ; Herbivory ; Humans ; Mammals/*classification/*physiology ; Phylogeny ; }, abstract = {Mammals are characterized by the complex adaptations of their dentition, which are an indication that diet has played a critical role in their evolutionary history. Although much attention has focused on diet and the adaptations of specific taxa, the role of diet in large-scale diversification patterns remains unresolved. Contradictory hypotheses have been proposed, making prediction of the expected relationship difficult. We show that net diversification rate (the cumulative effect of speciation and extinction), differs significantly among living mammals, depending upon trophic strategy. Herbivores diversify fastest, carnivores are intermediate, and omnivores are slowest. The tempo of transitions between the trophic strategies is also highly biased: the fastest rates occur into omnivory from herbivory and carnivory and the lowest transition rates are between herbivory and carnivory. Extant herbivore and carnivore diversity arose primarily through diversification within lineages, whereas omnivore diversity evolved by transitions into the strategy. The ability to specialize and subdivide the trophic niche allowed herbivores and carnivores to evolve greater diversity than omnivores.}, } @article {pmid22505626, year = {2012}, author = {King, EG and Macdonald, SJ and Long, AD}, title = {Properties and power of the Drosophila Synthetic Population Resource for the routine dissection of complex traits.}, journal = {Genetics}, volume = {191}, number = {3}, pages = {935-949}, pmid = {22505626}, issn = {1943-2631}, support = {R01 GM085251/GM/NIGMS NIH HHS/United States ; R01 RR024862/RR/NCRR NIH HHS/United States ; }, mesh = {Animals ; Chromosome Mapping ; Computational Biology/*methods ; Drosophila melanogaster/*genetics ; Female ; Genetic Markers/genetics ; Genome, Insect/genetics ; Genotype ; *Inbreeding ; Markov Chains ; *Phenotype ; Quantitative Trait Loci/genetics ; }, abstract = {The Drosophila Synthetic Population Resource (DSPR) is a newly developed multifounder advanced intercross panel consisting of >1600 recombinant inbred lines (RILs) designed for the genetic dissection of complex traits. Here, we describe the inference of the underlying mosaic founder structure for the full set of RILs from a dense set of semicodominant restriction-site-associated DNA (RAD) markers and use simulations to explore how variation in marker density and sequencing coverage affects inference. For a given sequencing effort, marker density is more important than sequence coverage per marker in terms of the amount of genetic information we can infer. We also assessed the power of the DSPR by assigning genotypes at a hidden QTL to each RIL on the basis of the inferred founder state and simulating phenotypes for different experimental designs, different genetic architectures, different sample sizes, and QTL of varying effect sizes. We found the DSPR has both high power (e.g., 84% power to detect a 5% QTL) and high mapping resolution (e.g., ∼1.5 cM for a 5% QTL).}, } @article {pmid22498355, year = {2012}, author = {Yang, H and Zang, Y and Yuan, Y and Tang, J and Chen, X}, title = {Selectivity by host plants affects the distribution of arbuscular mycorrhizal fungi: evidence from ITS rDNA sequence metadata.}, journal = {BMC evolutionary biology}, volume = {12}, number = {}, pages = {50}, pmid = {22498355}, issn = {1471-2148}, mesh = {Computational Biology ; DNA, Ribosomal Spacer/genetics ; *Demography ; *Genetic Variation ; Likelihood Functions ; Models, Genetic ; Mycorrhizae/classification/*genetics ; *Phylogeny ; Plants/*microbiology ; *Symbiosis ; }, abstract = {BACKGROUND: Arbuscular mycorrhizal fungi (AMF) can form obligate symbioses with the vast majority of land plants, and AMF distribution patterns have received increasing attention from researchers. At the local scale, the distribution of AMF is well documented. Studies at large scales, however, are limited because intensive sampling is difficult. Here, we used ITS rDNA sequence metadata obtained from public databases to study the distribution of AMF at continental and global scales. We also used these sequence metadata to investigate whether host plant is the main factor that affects the distribution of AMF at large scales.

RESULTS: We defined 305 ITS virtual taxa (ITS-VTs) among all sequences of the Glomeromycota by using a comprehensive maximum likelihood phylogenetic analysis. Each host taxonomic order averaged about 53% specific ITS-VTs, and approximately 60% of the ITS-VTs were host specific. Those ITS-VTs with wide host range showed wide geographic distribution. Most ITS-VTs occurred in only one type of host functional group. The distributions of most ITS-VTs were limited across ecosystem, across continent, across biogeographical realm, and across climatic zone. Non-metric multidimensional scaling analysis (NMDS) showed that AMF community composition differed among functional groups of hosts, and among ecosystem, continent, biogeographical realm, and climatic zone. The Mantel test showed that AMF community composition was significantly correlated with plant community composition among ecosystem, among continent, among biogeographical realm, and among climatic zone. The structural equation modeling (SEM) showed that the effects of ecosystem, continent, biogeographical realm, and climatic zone were mainly indirect on AMF distribution, but plant had strongly direct effects on AMF.

CONCLUSION: The distribution of AMF as indicated by ITS rDNA sequences showed a pattern of high endemism at large scales. This pattern indicates high specificity of AMF for host at different scales (plant taxonomic order and functional group) and high selectivity from host plants for AMF. The effects of ecosystemic, biogeographical, continental and climatic factors on AMF distribution might be mediated by host plants.}, } @article {pmid22494610, year = {2012}, author = {Le Comber, SC and Stevenson, MD}, title = {From Jack the Ripper to epidemiology and ecology.}, journal = {Trends in ecology & evolution}, volume = {27}, number = {6}, pages = {307-308}, doi = {10.1016/j.tree.2012.03.004}, pmid = {22494610}, issn = {1872-8383}, mesh = {Conservation of Natural Resources ; Crime/statistics & numerical data ; Disease Outbreaks ; Ecology/*methods ; *Epidemiologic Methods ; *Geographic Information Systems ; Humans ; Models, Theoretical ; }, } @article {pmid22489500, year = {2012}, author = {Liang, YQ and Zeng, H and Li, J}, title = {[Influence of land use change on vegetation cover dynamics in Dapeng Peninsula of Shenzhen, Guangdong Province of South China].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {23}, number = {1}, pages = {199-205}, pmid = {22489500}, issn = {1001-9332}, mesh = {China ; *Conservation of Natural Resources ; Crops, Agricultural/growth & development ; *Ecosystem ; Geographic Information Systems ; Humans ; Population Growth ; Remote Sensing Technology ; Soil/*analysis ; Trees/*growth & development ; Urbanization ; }, abstract = {To study the vegetation cover dynamics under urbanization is of significance to direct regional ecological conservation. Based on the 1995-2007 remote sensing data and the investigation data of 1996 and 2007 land use change in Shenzhen, and by using NDVI index tracking and algebraic overlay calculation, this paper analyzed the vegetation types and their spatial differentiation, land use change pattern, and the relationships between land use change and vegetation cover dynamics in Dapeng Peninsula of Shenzhen. In 1995-2007, the vegetation cover in 65% of the study area changed significantly, with an overall increasing trend. Land use change was mainly caused by the development of urbanization and commercial agriculture, with 31% of the land surface changed in land use function. The land use change was one of the main causes of vegetation cover dynamics, and about 35% of the region where vegetation cover significantly degraded was related to land use change. 55% of the region where land use function changed due to mechanical disturbance caused the degradation of vegetation cover, but by the end of the study period, the vegetation cover in most of the degraded region had being improved significantly.}, } @article {pmid22486823, year = {2012}, author = {Yoccoz, NG}, title = {The future of environmental DNA in ecology.}, journal = {Molecular ecology}, volume = {21}, number = {8}, pages = {2031-2038}, doi = {10.1111/j.1365-294X.2012.05505.x}, pmid = {22486823}, issn = {1365-294X}, mesh = {Animals ; Biodiversity ; Computational Biology/*methods ; DNA/*analysis ; DNA Barcoding, Taxonomic/*methods ; Diet ; Ecology/*methods ; *Environment ; Food Chain ; Humans ; Sequence Analysis, DNA ; }, abstract = {The contributions of environmental DNA to ecology are reviewed, focusing on diet, trophic interactions, species distributions and biodiversity assessment. Environmental DNA has the potential to dramatically improve quantitative studies in these fields. Achieving this, however, will require large investments of time and money into developing the relevant databases, models, and software.}, } @article {pmid22486822, year = {2012}, author = {Coissac, E and Riaz, T and Puillandre, N}, title = {Bioinformatic challenges for DNA metabarcoding of plants and animals.}, journal = {Molecular ecology}, volume = {21}, number = {8}, pages = {1834-1847}, doi = {10.1111/j.1365-294X.2012.05550.x}, pmid = {22486822}, issn = {1365-294X}, mesh = {Animals ; Base Sequence ; Biodiversity ; Computational Biology/*methods ; DNA/analysis/genetics ; DNA Barcoding, Taxonomic/*methods ; DNA Primers ; DNA, Plant/analysis/genetics ; Plants/genetics ; Species Specificity ; }, abstract = {Almost all empirical studies in ecology have to identify the species involved in the ecological process under examination. DNA metabarcoding, which couples the principles of DNA barcoding with next generation sequencing technology, provides an opportunity to easily produce large amounts of data on biodiversity. Microbiologists have long used metabarcoding approaches, but use of this technique in the assessment of biodiversity in plant and animal communities is under-explored. Despite its relationship with DNA barcoding, several unique features of DNA metabarcoding justify the development of specific data analysis methodologies. In this review, we describe the bioinformatics tools available for DNA metabarcoding of plants and animals, and we revisit others developed for DNA barcoding or microbial metabarcoding. We also discuss the principles and associated tools for evaluating and comparing DNA barcodes in the context of DNA metabarcoding, for designing new custom-made barcodes adapted to specific ecological question, for dealing with PCR and sequencing errors, and for inferring taxonomical data from sequences.}, } @article {pmid22481248, year = {2012}, author = {Harel, A and Falkowski, P and Bromberg, Y}, title = {TrAnsFuSE refines the search for protein function: oxidoreductases.}, journal = {Integrative biology : quantitative biosciences from nano to macro}, volume = {4}, number = {7}, pages = {765-777}, doi = {10.1039/c2ib00131d}, pmid = {22481248}, issn = {1757-9708}, mesh = {Algorithms ; Catalytic Domain ; Computational Biology/*methods ; Copper/chemistry ; Databases, Protein ; Genomics ; Iron/chemistry ; Molybdenum/chemistry ; Oxidation-Reduction ; Oxidoreductases/*genetics/*physiology ; Protein Binding ; Reproducibility of Results ; Sequence Alignment ; Software ; }, abstract = {Non-equilibrium catalysis of electron transfer reactions (i.e. redox) regulates the flux of key elements found in biological macromolecules. The enzymes responsible, oxidoreductases, contain specific transition metals in poorly sequence-conserved domains. These domains evolved ∼2.4 billion years ago in microbes and spread across the tree of life. We lack understanding of how oxidoreductases evolved; divergence of sequences makes identification difficult. We developed a method to recognise the various versions of these enzyme-domains in unannotated sequence-space. Often, homology is used to transfer function annotations from experimentally resolved domains to unannotated sequences. Unreliability of inferring homology below 30% sequence identity limits single-sequence based searches. Misaligned functional sites may compromise annotation transfer from even very similar sequences. Combining profile-based searches with knowledge of functional sites could improve domain detection accuracy. Here we present an approach that enhances the search for redox domains using catalytic site annotations. From the scientific literature, we validated annotations of 104 InterPro domains indicated as using "transition metals in redox reactions." These domains mediate electron transfer in 20% of oxidoreductases, primarily employing iron, copper and molybdenum. We used the experimentally identified catalytic residues in these domains to validate sequence alignment-based protein function annotations. Our method, TrAnsFuSE, is 11% and 14% more accurate than PSI-BLAST and InterPro, respectively. Moreover, it is robust for use with other functional residues-we attain higher accuracy at comparable coverage using metal binding, in addition to catalytic, sites. TrAnsFuSE can be used to focus the study of the vast amounts of unannotated sequencing data from meta-/genome projects.}, } @article {pmid22479605, year = {2012}, author = {Goodenough, AE and Hart, AG and Stafford, R}, title = {Regression with empirical variable selection: description of a new method and application to ecological datasets.}, journal = {PloS one}, volume = {7}, number = {3}, pages = {e34338}, pmid = {22479605}, issn = {1932-6203}, mesh = {Animals ; Birds ; Databases, Factual ; Ecology/*methods ; *Models, Biological ; Models, Statistical ; *Regression Analysis ; }, abstract = {Despite recent papers on problems associated with full-model and stepwise regression, their use is still common throughout ecological and environmental disciplines. Alternative approaches, including generating multiple models and comparing them post-hoc using techniques such as Akaike's Information Criterion (AIC), are becoming more popular. However, these are problematic when there are numerous independent variables and interpretation is often difficult when competing models contain many different variables and combinations of variables. Here, we detail a new approach, REVS (Regression with Empirical Variable Selection), which uses all-subsets regression to quantify empirical support for every independent variable. A series of models is created; the first containing the variable with most empirical support, the second containing the first variable and the next most-supported, and so on. The comparatively small number of resultant models (n = the number of predictor variables) means that post-hoc comparison is comparatively quick and easy. When tested on a real dataset--habitat and offspring quality in the great tit (Parus major)--the optimal REVS model explained more variance (higher R(2)), was more parsimonious (lower AIC), and had greater significance (lower P values), than full, stepwise or all-subsets models; it also had higher predictive accuracy based on split-sample validation. Testing REVS on ten further datasets suggested that this is typical, with R(2) values being higher than full or stepwise models (mean improvement = 31% and 7%, respectively). Results are ecologically intuitive as even when there are several competing models, they share a set of "core" variables and differ only in presence/absence of one or two additional variables. We conclude that REVS is useful for analysing complex datasets, including those in ecology and environmental disciplines.}, } @article {pmid22476515, year = {2012}, author = {Pebsworth, PA and Morgan, HR and Huffman, MA}, title = {Evaluating home range techniques: use of Global Positioning System (GPS) collar data from chacma baboons.}, journal = {Primates; journal of primatology}, volume = {53}, number = {4}, pages = {345-355}, pmid = {22476515}, issn = {1610-7365}, mesh = {Animals ; Ecology/*methods ; Environment ; Ethology/*methods ; Geographic Information Systems ; *Homing Behavior ; Male ; Papio ursinus/*physiology ; South Africa ; }, abstract = {Global Positioning System (GPS) collars have revolutionized the field of spatial ecology, but to date, few primate studies have used them. We fitted a free-ranging, semi-habituated, juvenile male chacma baboon (Papio hamadryas ursinus) with an automatic self-releasing GPS collar and tracked his movements for 359 days. The collar captured 4254 fixes out of 5719 programmed opportunities, a 74.4 % acquisition rate, suggesting that the collar effectively tracked this baboon in a variety of habitat types. Of the data points captured, 73.7 % were three-dimensional fixes, and of these fixes, 66.9 % were highly accurate, having a dilution of precision of less than four. We calculated home range using three protocols with three estimation methods: minimum convex polygon, fixed kernel-density estimation (KDE), and fixed r local convex hull. Using all data points and the 95 % contour, these methods created home range estimations ranging from 10.8 to 23.1 km(2) for this baboon troop. Our results indicate that the KDE output using all data locations most accurately represented our data set, as it created a continuous home range boundary that excluded unused areas and outlying, potentially exploratory data points while including all seven sleeping sites and a movement corridor. However, home range estimations generated from KDE varied from 15.4 to 18.8 km(2) depending on the smoothing parameter used. Our results demonstrated that the ad hoc smoothing parameter selection technique was a better method for our data set than either the least squares cross-validation or biased cross-validation techniques. Our results demonstrate the need for primatologists to develop a standardized reporting method which documents the tool, screening protocol, and smoothing parameter used in the creation of home range estimations in order to make comparisons that are meaningful.}, } @article {pmid22475219, year = {2012}, author = {Bruggemann, R and Carlsen, L}, title = {Multi-criteria decision analyses. Viewing MCDA in terms of both process and aggregation methods: some thoughts, motivated by the paper of Huang, Keisler and Linkov.}, journal = {The Science of the total environment}, volume = {425}, number = {}, pages = {293-295}, doi = {10.1016/j.scitotenv.2012.02.062}, pmid = {22475219}, issn = {1879-1026}, mesh = {*Decision Support Techniques ; Ecology/*trends ; }, abstract = {The paper of Huang, Keisler and Linkov (HKL) (Huang et al., 2011) has motivated us to this note about the relation between ranking procedures and Multi-Criteria Decision Analysis (MCDA) tools. The key concept in the HKL-paper is in our eyes the 'trade-off'. A 'trade-off' seems necessary, when conflicting indicator values are present. HKL stress that the general application of MCDA is hampered by different terminology. We do not claim to have a solution for that problem. Nevertheless, we think that the discussion is worthwhile and this note presents some of our ideas, which basically imply the need of a broadening of the definition of MCDA.}, } @article {pmid22464158, year = {2012}, author = {Puett, RC and Lamichhane, AP and D Nichols, M and Lawson, AB and A Standiford, D and Liu, L and Dabelea, D and Liese, AD}, title = {Neighborhood context and incidence of type 1 diabetes: the SEARCH for Diabetes in Youth study.}, journal = {Health & place}, volume = {18}, number = {4}, pages = {911-916}, pmid = {22464158}, issn = {1873-2054}, support = {R01 DK077131/DK/NIDDK NIH HHS/United States ; R01 DK077131-01/DK/NIDDK NIH HHS/United States ; R01DK077131/DK/NIDDK NIH HHS/United States ; }, mesh = {Adolescent ; Child ; Child, Preschool ; Diabetes Mellitus, Type 1/*epidemiology ; Female ; Geographic Information Systems ; Health Surveys ; Humans ; Incidence ; Infant ; Male ; Residence Characteristics ; Risk Factors ; *Social Class ; United States/epidemiology ; Young Adult ; }, abstract = {Findings regarding type 1 diabetes mellitus (T1DM) and neighborhood-level characteristics are mixed, with few US studies examining the influence of race/ethnicity. We conducted an ecologic study using SEARCH for Diabetes in Youth Study data to explore the association of neighborhood characteristics and T1DM incidence. 2002-2003 incident cases among youth at four SEARCH centers were included. Residential addresses were geocoded to US Census Tract. Standardized incidence ratios tended to increase with increasing education and median household income. Results from Poisson regression mixed models were similar and stable across race/ethnic groups and population density. Our study suggests a relationship of T1DM incidence with neighborhood-level socioeconomic status, independent of individual-level race/ethnic differences.}, } @article {pmid22459246, year = {2012}, author = {Gotelli, NJ and Ellison, AM and Ballif, BA}, title = {Environmental proteomics, biodiversity statistics and food-web structure.}, journal = {Trends in ecology & evolution}, volume = {27}, number = {8}, pages = {436-442}, pmid = {22459246}, issn = {1872-8383}, support = {P20 RR016462/RR/NCRR NIH HHS/United States ; P20 RR016462-09/RR/NCRR NIH HHS/United States ; P20 RR16462/RR/NCRR NIH HHS/United States ; }, mesh = {*Biodiversity ; Biota ; Computational Biology ; *Environment ; *Food Chain ; Models, Biological ; Models, Statistical ; *Proteomics ; }, abstract = {Pioneering studies in environmental proteomics have revealed links between protein diversity and ecological function in simple ecological communities, such as microbial biofilms. In the near future, high-throughput proteomic methods will be applied to more complex ecological systems in which microbes and macrobes interact. Data structures in biodiversity and protein surveys have many similarities, so the statistical methods that ecologists use for analyzing biodiversity data should be adapted for use with quantitative surveys of protein diversity. However, increasing quantities of protein and bioinformatics data will not, by themselves, reveal the functional significance of proteins. Instead, ecologists should be measuring changes in the abundance of protein cohorts in response to replicated field manipulations, including nutrient enrichment and removal of top predators.}, } @article {pmid22458817, year = {2012}, author = {Piasecka, B and Kutalik, Z and Roux, J and Bergmann, S and Robinson-Rechavi, M}, title = {Comparative modular analysis of gene expression in vertebrate organs.}, journal = {BMC genomics}, volume = {13}, number = {}, pages = {124}, pmid = {22458817}, issn = {1471-2164}, mesh = {*Algorithms ; Animals ; Computational Biology/*methods ; Gene Expression Profiling/*methods ; Humans ; Mice ; Organ Specificity ; Sequence Homology, Nucleic Acid ; Species Specificity ; Vertebrates/*genetics ; }, abstract = {BACKGROUND: The degree of conservation of gene expression between homologous organs largely remains an open question. Several recent studies reported some evidence in favor of such conservation. Most studies compute organs' similarity across all orthologous genes, whereas the expression level of many genes are not informative about organ specificity.

RESULTS: Here, we use a modularization algorithm to overcome this limitation through the identification of inter-species co-modules of organs and genes. We identify such co-modules using mouse and human microarray expression data. They are functionally coherent both in terms of genes and of organs from both organisms. We show that a large proportion of genes belonging to the same co-module are orthologous between mouse and human. Moreover, their zebrafish orthologs also tend to be expressed in the corresponding homologous organs. Notable exceptions to the general pattern of conservation are the testis and the olfactory bulb. Interestingly, some co-modules consist of single organs, while others combine several functionally related organs. For instance, amygdala, cerebral cortex, hypothalamus and spinal cord form a clearly discernible unit of expression, both in mouse and human.

CONCLUSIONS: Our study provides a new framework for comparative analysis which will be applicable also to other sets of large-scale phenotypic data collected across different species.}, } @article {pmid22449217, year = {2012}, author = {Cortese, S and Castelnau, P and Morcillo, C and Roux, S and Bonnet-Brilhault, F}, title = {Psychostimulants for ADHD-like symptoms in individuals with autism spectrum disorders.}, journal = {Expert review of neurotherapeutics}, volume = {12}, number = {4}, pages = {461-473}, doi = {10.1586/ern.12.23}, pmid = {22449217}, issn = {1744-8360}, mesh = {Attention Deficit Disorder with Hyperactivity/*etiology/*therapy ; Central Nervous System Stimulants/*therapeutic use ; Child ; Child Development Disorders, Pervasive/*complications ; Databases, Bibliographic/statistics & numerical data ; Humans ; }, abstract = {We conducted a comprehensive review of studies assessing the efficacy and tolerability of psychostimulants for ADHD-like symptoms in individuals with autism spectrum disorder (encompassing autism disorder, Asperger's syndrome and pervasive developmental disorders not otherwise specified). PubMed, Ovid, EMBASE, Web of Science, ERIC and CINHAL were searched through 3 January 2012. From a pool of 348 potentially relevant references, 12 citations (11 studies) were retained as pertinent. Four of the included studies had a randomized controlled design. Most of the studies assessed methylphenidate immediate release. Despite inter-study heterogeneity, taken together, the results of the selected reports suggest that psychostimulants may be effective for ADHD-like symptoms in autism spectrum disorder individuals. The most common adverse events reported in the included trials were appetite reduction, sleep-onset difficulties, irritability and emotional outbursts. We discuss future directions in the field, including the need for trials assessing more ecological outcomes and combined treatment strategies tailored to the specific individual features.}, } @article {pmid22448966, year = {2012}, author = {, and Arias, MC and Arnoux, E and Bell, JJ and Bernadou, A and Bino, G and Blatrix, R and Bourguet, D and Carrea, C and Clamens, AL and Cunha, HA and d'Alençon, E and Ding, Y and Djieto-Lordon, C and Dubois, MP and Dumas, P and Eraud, C and Faivre, B and Francisco, FO and Françoso, E and Garcia, M and Gardner, JP and Garnier, S and Gimenez, S and Gold, JR and Harris, DJ and He, G and Hellemans, B and Hollenbeck, CM and Jing, S and Kergoat, GJ and Liu, B and McDowell, JR and McKey, D and Miller, TL and Newton, E and Pagenkopp Lohan, KM and Papetti, C and Paterson, I and Peccoud, J and Peng, X and Piatscheck, F and Ponsard, S and Reece, KS and Reisser, CM and Renshaw, MA and Ruzzante, DE and Sauve, M and Shields, JD and Solé-Cava, A and Souche, EL and Van Houdt, JK and Vasconcellos, A and Volckaert, FA and Wang, S and Xiao, J and Yu, H and Zane, L and Zannato, B and Zemlak, TS and Zhang, C and Zhao, Y and Zhou, X and Zhu, L}, title = {Permanent genetic resources added to Molecular Ecology Resources Database 1 December 2011-31 January 2012.}, journal = {Molecular ecology resources}, volume = {12}, number = {3}, pages = {570-572}, doi = {10.1111/j.1755-0998.2012.03133.x}, pmid = {22448966}, issn = {1755-0998}, mesh = {*Biota ; DNA Primers/*genetics ; *Databases, Genetic ; Ecology/*methods ; *Microsatellite Repeats ; *Polymorphism, Single Nucleotide ; }, abstract = {This article documents the addition of 473 microsatellite marker loci and 71 pairs of single-nucleotide polymorphism (SNP) sequencing primers to the Molecular Ecology Resources Database. Loci were developed for the following species: Barteria fistulosa, Bombus morio, Galaxias platei, Hematodinium perezi, Macrocentrus cingulum Brischke (a.k.a. M. abdominalis Fab., M. grandii Goidanich or M. gifuensis Ashmead), Micropogonias furnieri, Nerita melanotragus, Nilaparvata lugens Stål, Sciaenops ocellatus, Scomber scombrus, Spodoptera frugiperda and Turdus lherminieri. These loci were cross-tested on the following species: Barteria dewevrei, Barteria nigritana, Barteria solida, Cynoscion acoupa, Cynoscion jamaicensis, Cynoscion leiarchus, Cynoscion nebulosus, Cynoscion striatus, Cynoscion virescens, Macrodon ancylodon, Menticirrhus americanus, Nilaparvata muiri and Umbrina canosai. This article also documents the addition of 116 sequencing primer pairs for Dicentrarchus labrax.}, } @article {pmid22447411, year = {2012}, author = {Ho, KT and Pelletier, MC and Campbell, DE and Burgess, RM and Johnson, RL and Rocha, KJ}, title = {Diagnosis of potential stressors adversely affecting benthic communities in New Bedford Harbor, MA (USA).}, journal = {Integrated environmental assessment and management}, volume = {8}, number = {4}, pages = {685-702}, doi = {10.1002/ieam.1303}, pmid = {22447411}, issn = {1551-3793}, mesh = {Animals ; Aquatic Organisms/drug effects/metabolism ; Decision Support Techniques ; Environmental Monitoring/*methods ; Estuaries ; Geologic Sediments ; Invertebrates/*drug effects/metabolism ; Massachusetts ; Retrospective Studies ; Water Pollutants, Chemical/*analysis/*toxicity ; }, abstract = {Diagnosing the causes of impaired ecosystems in the marine environment is critical for effective management action. When ecological impairment is based on toxicological or biological criteria (i.e., degraded benthic community composition or toxicity test results), managers are faced with the additional problem of diagnosing the cause of impairment before plans can be initiated to reduce the pollutant loading. We evaluated a number of diagnostic tools to determine their ability to identify pollutants in New Bedford Harbor (NBH), Massachusetts (USA), using a modified version of the US Environmental Protection Agency's (USEPA) stressor identification (SI) guidance. In this study, we linked chemical sources and toxic chemicals in the sediment with spatial concentration studies; we also linked toxic chemicals in the sediment with toxicity test results using toxicity identification and evaluation (TIE) studies. We used geographical information systems (GIS) maps to determine sources and to aid in determining spatially integrated inorganic nitrogen (SIIN). The SIIN values of reference and test estuaries were quantified and compared. Using this approach, we determined that toxic chemicals continue to be active stressors in NBH and that a moderate nutrient stress exists, but we were unable to link the nutrient stressor with a source. Also excess sedimentation was evaluated, but it does not appear to be an active stressor in this harbor. The research included an evaluation of the effectiveness of tools under development that may be used to evaluate stressors in water bodies. We found that the following tools were useful in diagnosing active stressors: toxicity tests, toxicity identification and evaluation (TIE) methods, comparison of grain size-normalized total organic carbon (TOC) ratios with reference sites, and comparison of SIIN with reference sites. This approach allowed us to successfully evaluate stressors in NBH retrospectively; however, a limitation in using retrospective data sets is that the approach may underestimate current or newly emerging stressors.}, } @article {pmid22447338, year = {2012}, author = {Gordon, AK and Mantel, SK and Muller, NW}, title = {Review of toxicological effects caused by episodic stressor exposure.}, journal = {Environmental toxicology and chemistry}, volume = {31}, number = {5}, pages = {1169-1174}, doi = {10.1002/etc.1781}, pmid = {22447338}, issn = {1552-8618}, mesh = {Animals ; Aquatic Organisms/drug effects ; Biota ; Databases, Factual ; Ecotoxicology/*methods ; Toxicity Tests/methods ; Water Pollutants/*toxicity ; *Water Quality ; }, abstract = {Water quality monitoring tools that rely on data from stress-response tests with continuous exposure at constant concentrations are not always appropriately protective when stressor exposure in the field is episodic in nature. The present study identifies various approaches that have attempted to account for episodic stressor exposure, describes the development of a toxicological effects database of episodic stressor exposure collated from published scientific literature, and discusses whether any discernible trends are evident when these data are reviewed. The episodic stressor exposure literature indicated that few generalizations can be made regarding associated biological responses. Instead, when attempting to characterize the hazard of a certain episodic pollution event, the following situation-specific information is required: the specific species affected and its age, the specific stressor and its concentration, the number of exposures to the stressor, the duration of exposure to the stressor, and the recovery time after each exposure. The present study identifies four main challenges to the inclusion of episodic toxicity data in environmental water quality management: varying stressor concentration profiles, defining episodic stressor concentration levels, variation resulting from routes of exposure and modes of action, and species-specific responses to episodic stressor exposure. The database, available at http://iwr.ru.ac.za/iwr/download, could be particularly useful for site-specific risk assessments related to episodic exposures.}, } @article {pmid22444143, year = {2012}, author = {Coyne, RS and Stover, NA and Miao, W}, title = {Whole genome studies of Tetrahymena.}, journal = {Methods in cell biology}, volume = {109}, number = {}, pages = {53-81}, doi = {10.1016/B978-0-12-385967-9.00004-9}, pmid = {22444143}, issn = {0091-679X}, support = {1R24GM089662/GM/NIGMS NIH HHS/United States ; 5P40RR019688-06/RR/NCRR NIH HHS/United States ; }, mesh = {ATP-Binding Cassette Transporters/genetics/metabolism ; Chromosome Structures/genetics/metabolism ; Chromosomes/genetics/metabolism ; Cytochrome P-450 Enzyme System/genetics/metabolism ; DNA, Protozoan/genetics/metabolism ; Databases, Genetic ; Evolution, Molecular ; Gene Expression Profiling ; Genetic Variation ; *Genome, Protozoan ; Intracellular Membranes/metabolism ; Macronucleus/*genetics/metabolism ; Micronucleus, Germline/*genetics/metabolism ; Molecular Sequence Annotation ; Phylogeny ; Proteomics/methods ; RNA, Protozoan/genetics/metabolism ; Tetrahymena thermophila/classification/*genetics/metabolism ; Transcriptome ; }, abstract = {Within the past decade, genomic studies have emerged as essential and highly productive tools to explore the biology of Tetrahymena thermophila. The current major resources, which have been extensively mined by the research community, are the annotated macronuclear genome assembly, transcriptomic data and the databases that house this information. Efforts in progress will soon improve these data sources and expand their scope, including providing annotated micronuclear and comparative genomic sequences. Future studies of Tetrahymena cell and molecular biology, development, physiology, evolution and ecology will benefit greatly from these resources and the advanced genomic technologies they enable.}, } @article {pmid22440092, year = {2012}, author = {Willocks, LJ and Bhaskar, A and Ramsay, CN and Lee, D and Brewster, DH and Fischbacher, CM and Chalmers, J and Morris, G and Scott, EM}, title = {Cardiovascular disease and air pollution in Scotland: no association or insufficient data and study design?.}, journal = {BMC public health}, volume = {12}, number = {}, pages = {227}, pmid = {22440092}, issn = {1471-2458}, mesh = {Air Pollution/*adverse effects ; Cities ; Coronary Disease/*epidemiology/therapy ; Data Interpretation, Statistical ; Environmental Exposure/*adverse effects ; Hospitalization/*statistics & numerical data ; Humans ; Linear Models ; Particulate Matter/*analysis ; Research Design ; Risk Factors ; Scotland/epidemiology ; Stroke/*epidemiology/therapy ; Urban Health/*trends ; }, abstract = {BACKGROUND: Coronary heart disease and stroke are leading causes of mortality and ill health in Scotland, and clear associations have been found in previous studies between air pollution and cardiovascular disease. This study aimed to use routinely available data to examine whether there is any evidence of an association between short-term exposure to particulate matter (measured as PM10, particles less than 10 micrograms per cubic metre) and hospital admissions due to cardiovascular disease, in the two largest cities in Scotland during the years 2000 to 2006.

METHODS: The study utilised an ecological time series design, and the analysis was based on overdispersed Poisson log-linear models.

RESULTS: No consistent associations were found between PM₁₀ concentrations and cardiovascular hospital admissions in either of the cities studied, as all of the estimated relative risks were close to one, and all but one of the associated 95% confidence intervals contained the null risk of one.

CONCLUSIONS: This study suggests that in small cities, where air quality is relatively good, then either PM₁₀ concentrations have no effect on cardiovascular ill health, or that the routinely available data and the corresponding study design are not sufficient to detect an association.}, } @article {pmid22438741, year = {2012}, author = {Deng, Y and Fan, F and Chen, R}, title = {Extraction and analysis of impervious surfaces based on a spectral un-mixing method using Pearl River Delta of China Landsat TM/ETM+ imagery from 1998 to 2008.}, journal = {Sensors (Basel, Switzerland)}, volume = {12}, number = {2}, pages = {1846-1862}, pmid = {22438741}, issn = {1424-8220}, mesh = {*Algorithms ; China ; *Geographic Information Systems ; Image Interpretation, Computer-Assisted/*methods ; Remote Sensing Technology/*methods ; Rivers/*chemistry ; *Spacecraft ; }, abstract = {Impervious surface area (ISA) is considered as an indicator of environment change and is regarded as an important input parameter for hydrological cycle simulation, water management and area pollution assessment. The Pearl River Delta (PRD), the 3rd most important economic district of China, is chosen in this paper to extract the ISA information based on Landsat images of 1998, 2003 and 2008 by using a linear spectral un-mixing method and to monitor impervious surface change by analyzing the multi-temporal Landsat-derived fractional impervious surface. Results of this study were as follows: (1) the area of ISA in the PRD increased 79.09% from 1998 to 2003 and 26.88% from 2003 to 2008 separately; (2) the spatial distribution of ISA was described according to the 1998/2003 percentage respectively. Most of middle and high percentage ISA was located in northwestern and southeastern of the whole delta, and middle percentage ISA was mainly located in the city interior, high percentage ISA was mainly located in the suburban around the city accordingly; (3) the expanding direction and trend of high percentage ISA was discussed in order to understand the change of urban in this delta; High percentage ISA moved from inner city to edge of urban area during 1998-2003 and moved to the suburban area that far from the urban area mixed with jumpily and gradually during 2003-2008. According to the discussion of high percentage ISA spatial expanded direction, it could be found out that high percentage ISA moved outward from the centre line of Pearl River of the whole delta while a high ISA percentage in both shores of the Pearl River Estuary moved toward the Pearl River; (4) combining the change of ISA with social conditions, the driving relationship was analyzed in detail. It was evident that ISA percentage change had a deep relationship with the economic development of this region in the past ten years. Contemporaneous major sport events (16th Asia Games of Guangzhou, 26th Summer Universidad of Shenzhen) and the government policies also promoted the development of the ISA. Meanwhile, topographical features like the National Nature Reserve of China restricted and affected the expansion of the ISA. Above all, this paper attempted to extract ISA in a major region of the PRD; the temporal and spatial analyses to PRD ISA demonstrated the drastic changes in developed areas of China. These results were important and valuable for land use management, ecological protection and policy establishment.}, } @article {pmid22438428, year = {2012}, author = {Howe, LD and Galobardes, B and Matijasevich, A and Gordon, D and Johnston, D and Onwujekwe, O and Patel, R and Webb, EA and Lawlor, DA and Hargreaves, JR}, title = {Measuring socio-economic position for epidemiological studies in low- and middle-income countries: a methods of measurement in epidemiology paper.}, journal = {International journal of epidemiology}, volume = {41}, number = {3}, pages = {871-886}, pmid = {22438428}, issn = {1464-3685}, support = {G0600705//Medical Research Council/United Kingdom ; }, mesh = {Data Collection/methods ; Data Interpretation, Statistical ; *Developing Countries ; *Epidemiologic Methods ; Humans ; Socioeconomic Factors ; }, abstract = {Much has been written about the measurement of socio-economic position (SEP) in high-income countries (HIC). Less has been written for an epidemiology, health systems and public health audience about the measurement of SEP in low- and middle-income countries (LMIC). The social stratification processes in many LMIC-and therefore the appropriate measurement tools-differ considerably from those in HIC. Many measures of SEP have been utilized in epidemiological studies; the aspects of SEP captured by these measures and the pathways through which they may affect health are likely to be slightly different but overlapping. No single measure of SEP will be ideal for all studies and contexts; the strengths and limitations of a given indicator are likely to vary according to the specific research question. Understanding the general properties of different indicators, however, is essential for all those involved in the design or interpretation of epidemiological studies. In this article, we describe the measures of SEP used in LMIC. We concentrate on measures of individual or household-level SEP rather than area-based or ecological measures such as gross domestic product. We describe each indicator in terms of its theoretical basis, interpretation, measurement, strengths and limitations. We also provide brief comparisons between LMIC and HIC for each measure.}, } @article {pmid22433126, year = {2012}, author = {Linard, C and Tatem, AJ}, title = {Large-scale spatial population databases in infectious disease research.}, journal = {International journal of health geographics}, volume = {11}, number = {}, pages = {7}, pmid = {22433126}, issn = {1476-072X}, support = {//Wellcome Trust/United Kingdom ; }, mesh = {Communicable Diseases/diagnosis/*epidemiology ; Databases, Factual/*trends ; Demography/*trends ; Humans ; *Population Surveillance ; }, abstract = {Modelling studies on the spatial distribution and spread of infectious diseases are becoming increasingly detailed and sophisticated, with global risk mapping and epidemic modelling studies now popular. Yet, in deriving populations at risk of disease estimates, these spatial models must rely on existing global and regional datasets on population distribution, which are often based on outdated and coarse resolution data. Moreover, a variety of different methods have been used to model population distribution at large spatial scales. In this review we describe the main global gridded population datasets that are freely available for health researchers and compare their construction methods, and highlight the uncertainties inherent in these population datasets. We review their application in past studies on disease risk and dynamics, and discuss how the choice of dataset can affect results. Moreover, we highlight how the lack of contemporary, detailed and reliable data on human population distribution in low income countries is proving a barrier to obtaining accurate large-scale estimates of population at risk and constructing reliable models of disease spread, and suggest research directions required to further reduce these barriers.}, } @article {pmid22422763, year = {2012}, author = {Bryant, D and Bouckaert, R and Felsenstein, J and Rosenberg, NA and RoyChoudhury, A}, title = {Inferring species trees directly from biallelic genetic markers: bypassing gene trees in a full coalescent analysis.}, journal = {Molecular biology and evolution}, volume = {29}, number = {8}, pages = {1917-1932}, pmid = {22422763}, issn = {1537-1719}, support = {(R01 GM 081441/GM/NIGMS NIH HHS/United States ; R01 HG004839/HG/NHGRI NIH HHS/United States ; R01 GM081441/GM/NIGMS NIH HHS/United States ; R01 GM071639-01A1/GM/NIGMS NIH HHS/United States ; R01 GM071639/GM/NIGMS NIH HHS/United States ; P01 GM045344/GM/NIGMS NIH HHS/United States ; GM-45344/GM/NIGMS NIH HHS/United States ; }, mesh = {Algorithms ; *Alleles ; Amplified Fragment Length Polymorphism Analysis ; Computer Simulation ; Databases, Genetic ; Digitalis/*genetics ; Genes, Plant/*genetics ; Genetic Markers ; Likelihood Functions ; New Zealand ; *Phylogeny ; Species Specificity ; }, abstract = {The multispecies coalescent provides an elegant theoretical framework for estimating species trees and species demographics from genetic markers. However, practical applications of the multispecies coalescent model are limited by the need to integrate or sample over all gene trees possible for each genetic marker. Here we describe a polynomial-time algorithm that computes the likelihood of a species tree directly from the markers under a finite-sites model of mutation effectively integrating over all possible gene trees. The method applies to independent (unlinked) biallelic markers such as well-spaced single nucleotide polymorphisms, and we have implemented it in SNAPP, a Markov chain Monte Carlo sampler for inferring species trees, divergence dates, and population sizes. We report results from simulation experiments and from an analysis of 1997 amplified fragment length polymorphism loci in 69 individuals sampled from six species of Ourisia (New Zealand native foxglove).}, } @article {pmid22420488, year = {2012}, author = {Chenuil, A}, title = {How to infer reliable diploid genotypes from NGS or traditional sequence data: from basic probability to experimental optimization.}, journal = {Journal of evolutionary biology}, volume = {25}, number = {5}, pages = {949-960}, doi = {10.1111/j.1420-9101.2012.02488.x}, pmid = {22420488}, issn = {1420-9101}, mesh = {Alleles ; Bayes Theorem ; Biomarkers ; Cloning, Molecular ; Databases, Genetic ; *Diploidy ; Genetic Loci ; Genetics, Population ; Genotyping Techniques/methods/standards ; Heterozygote ; Homozygote ; *Models, Genetic ; Mutation ; *Reproducibility of Results ; Sequence Analysis, DNA/methods/*standards ; }, abstract = {The use of diploid sequence markers is still challenging despite the good quality of the information they provide. There is a common problem to all sequencing approaches [traditional cloning and sequencing of PCR amplicons as well as next-generation sequencing (NGS)]: when no variation is found within the sequences from a given individual, homozygozity can never be asserted with certainty. As a consequence, sequence data from diploid markers are mostly analysed at the population (not the individual level) particularly in animal studies. This study aims at contributing to solve this. Using the Bayes theorem and the binomial law, useful results are derived, among which: (i) the number of sequence reads per individual (or sequencing depth) which is required to ensure, at a given probability threshold, that some heterozygotes are not considered erroneously as homozygotes, as a function of the observed heterozygozity (H(o)) of the locus in the population; (ii) a way of estimating H(o) from low coverage NGS data; (iii) a way of testing the null hypothesis that a genetic marker corresponds to a single and diploid locus, in the absence of data from controlled crosses; (iv) strategies for characterizing sequence genotypes in populations minimizing the average number of sequence reads per individual; (v) a rationale to decide which are the variations that one needs to consider along the sequence, as a function of the sequencing depth affordable, the level of polymorphism desired and the risk of sequencing error. For traditional sequencing technology, optimal strategies appear surprisingly different from the usual empirical ones. The average number of sequence reads required to obtain 99% of fully determined genotypes never exceeds six, this value corresponding to the worst situation when H(o) equals 0.6. This threshold value of H(o) is strikingly stable when the tolerated proportion of nonfully resolved genotypes varies in a reasonable range. These results do not rely on the Hardy-Weinberg equilibrium assumption or on diallelism of nucleotidic sites.}, } @article {pmid22420049, year = {2012}, author = {Gross, M}, title = {Barcoding biodiversity.}, journal = {Current biology : CB}, volume = {22}, number = {3}, pages = {R73-6}, doi = {10.1016/j.cub.2012.01.036}, pmid = {22420049}, issn = {1879-0445}, mesh = {Animals ; *Biodiversity ; *DNA Barcoding, Taxonomic ; DNA, Mitochondrial/chemistry ; Databases, Genetic ; Fishes/genetics ; }, abstract = {Analysis of short, species-specific sequences known as DNA barcodes has become a widespread practice in biodiversity and ecological research, and also finds practical applications from trade control to biomedicine. One of the challenges is to ensure that the molecular information is reliably linked to physical specimens in collections.}, } @article {pmid22419398, year = {2012}, author = {Bajocco, S and De Angelis, A and Perini, L and Ferrara, A and Salvati, L}, title = {The impact of land use/land cover changes on land degradation dynamics: a Mediterranean case study.}, journal = {Environmental management}, volume = {49}, number = {5}, pages = {980-989}, pmid = {22419398}, issn = {1432-1009}, mesh = {Agriculture/economics/*trends ; *Climate Change ; Conservation of Natural Resources/economics/methods/*trends ; *Ecosystem ; *Environmental Pollution ; Geographic Information Systems ; Italy ; Mediterranean Sea ; Models, Theoretical ; Socioeconomic Factors ; }, abstract = {In the last decades, due to climate changes, soil deterioration, and Land Use/Land Cover Changes (LULCCs), land degradation risk has become one of the most important ecological issues at the global level. Land degradation involves two interlocking systems: the natural ecosystem and the socio-economic system. The complexity of land degradation processes should be addressed using a multidisciplinary approach. Therefore, the aim of this work is to assess diachronically land degradation dynamics under changing land covers. This paper analyzes LULCCs and the parallel increase in the level of land sensitivity to degradation along the coastal belt of Sardinia (Italy), a typical Mediterranean region where human pressure affects the landscape characteristics through fires, intensive agricultural practices, land abandonment, urban sprawl, and tourism concentration. Results reveal that two factors mainly affect the level of land sensitivity to degradation in the study area: (i) land abandonment and (ii) unsustainable use of rural and peri-urban areas. Taken together, these factors represent the primary cause of the LULCCs observed in coastal Sardinia. By linking the structural features of the Mediterranean landscape with its functional land degradation dynamics over time, these results contribute to orienting policies for sustainable land management in Mediterranean coastal areas.}, } @article {pmid22419396, year = {2012}, author = {Tercek, MT and Gray, ST and Nicholson, CM}, title = {Climate zone delineation: evaluating approaches for use in natural resource management.}, journal = {Environmental management}, volume = {49}, number = {5}, pages = {1076-1091}, pmid = {22419396}, issn = {1432-1009}, mesh = {*Climate ; *Climate Change ; Cluster Analysis ; Conservation of Natural Resources/*methods/statistics & numerical data ; Environmental Monitoring/*methods/statistics & numerical data ; Geographic Information Systems ; Geological Phenomena ; Northwestern United States ; Principal Component Analysis ; *Seasons ; }, abstract = {Recent efforts by the United States Department of the Interior (DOI) have the potential to make climate zones the basic geographic units guiding monitoring and resource management programs in the western U.S. We evaluated a new National Park Service approach for delineating climate zones that will likely be a model for other DOI agencies. Using the test case of the Greater Yellowstone Area in Wyoming, Montana and Idaho, we conducted three separate analyses, each based on a different dataset. Cluster analysis of 1971-2000 temperature and precipitation normals grouped weather stations according to similarities in seasonal patterns. Principal Components Analysis (PCAs) of 1895-2008 monthly data grouped stations by similarities in long-term variability. Finally, an analysis of snow data further subdivided the zones defined by the other two analyses. The climate zones produced by the cluster analysis and the PCAs were roughly similar to each other, but the differences were significant. The two sets of zones may be useful for different applications. For example, studies that analyze links between climate patterns and the demography of threatened species should focus on the results of the PCAs. The broad similarity among results produced by the different approaches supported the application of these zones in climate-related monitoring and analysis. However, since choices in data and methodology can affect the details of maps depicting zone boundaries, there are practical limitations to their use.}, } @article {pmid22417507, year = {2011}, author = {Rodríguez-Lerma, GK and Gutiérrez-Moreno, K and Cárdenas-Manríquez, M and Botello-Álvarez, E and Jiménez-Islas, H and Rico-Martínez, R and Navarrete-Bolaños, JL}, title = {Microbial ecology studies of spontaneous fermentation: starter culture selection for prickly pear wine production.}, journal = {Journal of food science}, volume = {76}, number = {6}, pages = {M346-52}, doi = {10.1111/j.1750-3841.2011.02208.x}, pmid = {22417507}, issn = {1750-3841}, mesh = {Beverages/analysis/*microbiology ; Databases, Factual ; Diet/ethnology ; Ethanol/analysis ; Fermentation ; Flame Ionization ; Fruit/chemistry/*microbiology ; Gas Chromatography-Mass Spectrometry ; Kinetics ; Mexico ; Molecular Typing ; Mycological Typing Techniques ; Opuntia/chemistry/*microbiology ; Pichia/classification/isolation & purification/*metabolism ; Quality Control ; Rural Population ; Saccharomyces cerevisiae/classification/isolation & purification/*metabolism ; Species Specificity ; Volatile Organic Compounds/analysis/chemistry ; Wine/*analysis/*microbiology ; }, abstract = {A procedure for designing starter cultures for fermentation is illustrated for prickly pear wine production. The illustration includes kinetic studies on inoculated and spontaneous fermentation, microorganism identification studies based on molecular biology tools, and microbial ecology studies, which led to the selection of strains that are capable of synthesizing alcohol and desirable volatile compounds. Results show that a mixed starter inoculum containing Pichia fermentans and Saccharomyces cerevisiae leads to a fermented product that contains 8.37% alcohol (v/v). The gas chromatography and mass spectrometry (GC-MS) analysis shows the presence of 9 major volatile compounds (Isobutanol, Isopentanol, Ethyl acetate, Isoamyl acetate, Ethyl octanoate, Ethyl decanoate, Ethyl 9-decanoate, β-Phenylethyl acetate, and Phenylethyl alcohol) that have ethereal, fruity, aromatic notes that are considered to be essential for a fine wine flavor. These compounds harmonically synergize with the alcohol to produce a fermented product with a unique flavor and taste. Several assays using the mixed culture show that the process is stable, predictable, controllable, and reproducible. Moreover, the results show that a mixed culture leads to a broader range of aromatic products than that produced by a single, pure culture. Therefore, we conclude that combinations of Saccharomyces strains and non-Saccharomyces strains can be used to obtain high-quality fermented beverages from prickly pear juice.}, } @article {pmid22415845, year = {2013}, author = {Hoang, TH and Mouton, A and Lock, K and De Pauw, N and Goethals, PL}, title = {Integrating data-driven ecological models in an expert-based decision support system for water management in the Du river basin (Vietnam).}, journal = {Environmental monitoring and assessment}, volume = {185}, number = {1}, pages = {631-642}, pmid = {22415845}, issn = {1573-2959}, mesh = {Conservation of Natural Resources/*methods ; *Decision Support Techniques ; Environmental Monitoring/*methods ; Expert Systems ; Models, Theoretical ; Rivers/chemistry ; Vietnam ; Water Pollutants/analysis ; Water Pollution/*statistics & numerical data ; Water Supply/statistics & numerical data ; }, abstract = {In this study, classification trees were combined with the Water Framework Directive (WFD)-Explorer, a modular toolbox that supports integrated water management in a river basin to evaluate the impact of different restoration measures on river ecology. First, the WFD-Explorer toolbox analysed the effect of different restoration options on the abiotic river characteristics based on the water and substance balance embedded in the simulation environment. Based on these abiotic characteristics, the biological index Biological Monitoring Working Party for Vietnam was then predicted by classification trees that were trained on biological and abiotic data collected in the Du river basin in northern Vietnam. The ecological status of streams in the basin ranged from nearly pristine headwaters to severely impacted river stretches. Elimination of point sources from ore extraction and decentralised domestic wastewater treatment proved to be the most effective measures to improve the ecological condition of the Du river basin. The combination of the WFD-Explorer results with data-driven models enabled model application in a situation where expert knowledge was lacking. Consequently, this approach appeared promising for decision support in the context of river restoration and conservation management.}, } @article {pmid22414578, year = {2012}, author = {Kolanczyk, RC and Schmieder, P and Jones, WJ and Mekenyan, OG and Chapkanov, A and Temelkov, S and Kotov, S and Velikova, M and Kamenska, V and Vasilev, K and Veith, GD}, title = {MetaPath: an electronic knowledge base for collating, exchanging and analyzing case studies of xenobiotic metabolism.}, journal = {Regulatory toxicology and pharmacology : RTP}, volume = {63}, number = {1}, pages = {84-96}, doi = {10.1016/j.yrtph.2012.02.013}, pmid = {22414578}, issn = {1096-0295}, mesh = {Animals ; *Databases, Factual ; Environmental Pollutants/pharmacokinetics ; Humans ; Inactivation, Metabolic ; *Knowledge Bases ; Risk Assessment ; Software ; Xenobiotics/*pharmacokinetics ; }, abstract = {The MetaPath knowledge base was developed for the purpose of archiving, sharing and analyzing experimental data on metabolism, metabolic pathways and crucial supporting metadata. The MetaPath system grew out of the need to compile and organize the results of metabolism studies into a systematic database to facilitate data comparisons and evaluations. Specialized MetaPath data evaluation tools facilitate the review of pesticide metabolism data submitted for regulatory risk assessments as well as exchange of results of complex analyses used in regulation and research. Customized screen editors called Composers were developed to automate data entry into MetaPath while also streamlining the production of agency specific study summaries such as the Data Evaluation Records (DER) used by the US EPA Office of Pesticide Programs. Efforts are underway through an Organization for Economic Co-operation and Development (OECD) work group to extend the use of DER Composers as harmonized templates for rat metabolism, livestock residue, plant residue and environmental degradation studies.}, } @article {pmid22408426, year = {2012}, author = {Judson, RS and Martin, MT and Egeghy, P and Gangwal, S and Reif, DM and Kothiya, P and Wolf, M and Cathey, T and Transue, T and Smith, D and Vail, J and Frame, A and Mosher, S and Hubal, EAC and Richard, AM}, title = {Aggregating data for computational toxicology applications: The U.S. Environmental Protection Agency (EPA) Aggregated Computational Toxicology Resource (ACToR) System.}, journal = {International journal of molecular sciences}, volume = {13}, number = {2}, pages = {1805-1831}, pmid = {22408426}, issn = {1422-0067}, mesh = {Algorithms ; Computational Biology/*methods ; *Databases, Factual/standards/supply & distribution ; Ecotoxicology/*methods/organization & administration ; Environmental Pollutants/toxicity ; Humans ; Software ; United States ; *United States Environmental Protection Agency/organization & administration ; }, abstract = {Computational toxicology combines data from high-throughput test methods, chemical structure analyses and other biological domains (e.g., genes, proteins, cells, tissues) with the goals of predicting and understanding the underlying mechanistic causes of chemical toxicity and for predicting toxicity of new chemicals and products. A key feature of such approaches is their reliance on knowledge extracted from large collections of data and data sets in computable formats. The U.S. Environmental Protection Agency (EPA) has developed a large data resource called ACToR (Aggregated Computational Toxicology Resource) to support these data-intensive efforts. ACToR comprises four main repositories: core ACToR (chemical identifiers and structures, and summary data on hazard, exposure, use, and other domains), ToxRefDB (Toxicity Reference Database, a compilation of detailed in vivo toxicity data from guideline studies), ExpoCastDB (detailed human exposure data from observational studies of selected chemicals), and ToxCastDB (data from high-throughput screening programs, including links to underlying biological information related to genes and pathways). The EPA DSSTox (Distributed Structure-Searchable Toxicity) program provides expert-reviewed chemical structures and associated information for these and other high-interest public inventories. Overall, the ACToR system contains information on about 400,000 chemicals from 1100 different sources. The entire system is built using open source tools and is freely available to download. This review describes the organization of the data repository and provides selected examples of use cases.}, } @article {pmid22406614, year = {2012}, author = {Han, TA and Traulsen, A and Gokhale, CS}, title = {On equilibrium properties of evolutionary multi-player games with random payoff matrices.}, journal = {Theoretical population biology}, volume = {81}, number = {4}, pages = {264-272}, doi = {10.1016/j.tpb.2012.02.004}, pmid = {22406614}, issn = {1096-0325}, mesh = {*Game Theory ; *Models, Theoretical ; Probability ; }, abstract = {The analysis of equilibrium points in biological dynamical systems has been of great interest in a variety of mathematical approaches to biology, such as population genetics, theoretical ecology or evolutionary game theory. The maximal number of equilibria and their classification based on stability have been the primary subjects of these studies, for example in the context of two-player games with multiple strategies. Herein, we address a different question using evolutionary game theory as a tool. If the payoff matrices are drawn randomly from an arbitrary distribution, what are the probabilities of observing a certain number of (stable) equilibria? We extend the domain of previous results for the two-player framework, which corresponds to a single diploid locus in population genetics, by addressing the full complexity of multi-player games with multiple strategies. In closing, we discuss an application and illustrate how previous results on the number of equilibria, such as the famous Feldman-Karlin conjecture on the maximal number of isolated fixed points in a viability selection model, can be obtained as special cases of our results based on multi-player evolutionary games. We also show how the probability of realizing a certain number of equilibria changes as we increase the number of players and number of strategies.}, } @article {pmid22399458, year = {2012}, author = {Zhen, Y and Andolfatto, P}, title = {Methods to detect selection on noncoding DNA.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {856}, number = {}, pages = {141-159}, pmid = {22399458}, issn = {1940-6029}, support = {R01 GM083228/GM/NIGMS NIH HHS/United States ; R01-GM083228/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Computational Biology/*methods ; DNA/*genetics ; Evolution, Molecular ; Humans ; Phylogeny ; Polymorphism, Genetic/genetics ; *Selection, Genetic ; }, abstract = {Vast tracts of noncoding DNA contain elements that regulate gene expression in higher eukaryotes. Describing these regulatory elements and understanding how they evolve represent major challenges for biologists. Advances in the ability to survey genome-scale DNA sequence data are providing unprecedented opportunities to use evolutionary models and computational tools to identify functionally important elements and the mode of selection acting on them in multiple species. This chapter reviews some of the current methods that have been developed and applied on noncoding DNA, what they have shown us, and how they are limited. Results of several recent studies reveal that a significantly larger fraction of noncoding DNA in eukaryotic organisms is likely to be functional than previously believed, implying that the functional annotation of most noncoding DNA in these organisms is largely incomplete. In Drosophila, recent studies have further suggested that a large fraction of noncoding DNA divergence observed between species may be the product of recurrent adaptive substitution. Similar studies in humans have revealed a more complex pattern, with signatures of recurrent positive selection being largely concentrated in conserved noncoding DNA elements. Understanding these patterns and the extent to which they generalize to other organisms awaits the analysis of forthcoming genome-scale polymorphism and divergence data from more species.}, } @article {pmid22395617, year = {2012}, author = {McKenzie, D and Kennedy, MC}, title = {Power laws reveal phase transitions in landscape controls of fire regimes.}, journal = {Nature communications}, volume = {3}, number = {}, pages = {726}, pmid = {22395617}, issn = {2041-1723}, mesh = {Databases, Factual ; *Ecosystem ; *Environment ; *Fires ; Models, Theoretical ; Plants ; *Trees ; *Weather ; }, abstract = {Understanding the environmental controls on historical wildfires, and how they changed across spatial scales, is difficult because there are no surviving explicit records of either weather or vegetation (fuels). Here we show how power laws associated with fire-event time series arise in limited domains of parameters that represent critical transitions in the controls on landscape fire. Comparison to a self-organized criticality model shows that the latter mimics historical fire only in a limited domain of criticality, and is not an adequate mechanism to explain landscape fire dynamics, which are shaped by both endogenous and exogenous controls. Our results identify a continuous phase transition in landscape controls, marked by power laws, and provide an ecological analogue to critical behaviour in physical and chemical systems. This explicitly cross-scale analysis provides a paradigm for identifying critical thresholds in landscape dynamics that may be crossed in a rapidly changing climate.}, } @article {pmid22393396, year = {2012}, author = {Tezuka, A and Matsushima, N and Nemoto, Y and Akashi, HD and Kawata, M and Makino, T}, title = {Comprehensive primer design for analysis of population genetics in non-sequenced organisms.}, journal = {PloS one}, volume = {7}, number = {2}, pages = {e32314}, pmid = {22393396}, issn = {1932-6203}, mesh = {Animals ; Computational Biology/methods ; DNA Primers/*genetics ; Databases, Genetic ; Drosophila melanogaster ; Genetic Markers ; Genetics, Population ; Genome ; Genomics ; Introns ; Lizards ; Molecular Sequence Data ; Poecilia ; Polymorphism, Genetic ; Ranidae ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {Nuclear sequence markers are useful tool for the study of the history of populations and adaptation. However, it is not easy to obtain multiple nuclear primers for organisms with poor or no genomic sequence information. Here we used the genomes of organisms that have been fully sequenced to design comprehensive sets of primers to amplify polymorphic genomic fragments of multiple nuclear genes in non-sequenced organisms. First, we identified a large number of candidate polymorphic regions that were flanked on each side by conserved regions in the reference genomes. We then designed primers based on these conserved sequences and examined whether the primers could be used to amplify sequences in target species, montane brown frog (Rana ornativentris), anole lizard (Anolis sagrei), guppy (Poecilia reticulata), and fruit fly (Drosophila melanogaster), for population genetic analysis. We successfully obtained polymorphic markers for all target species studied. In addition, we found that sequence identities of the regions between the primer sites in the reference genomes affected the experimental success of DNA amplification and identification of polymorphic loci in the target genomes, and that exonic primers had a higher success rate than intronic primers in amplifying readable sequences. We conclude that this comparative genomic approach is a time- and cost-effective way to obtain polymorphic markers for non-sequenced organisms, and that it will contribute to the further development of evolutionary ecology and population genetics for non-sequenced organisms, aiding in the understanding of the genetic basis of adaptation.}, } @article {pmid22393364, year = {2012}, author = {Dong, D and Jin, K and Wu, X and Zhong, Y}, title = {CRDB: database of chemosensory receptor gene families in vertebrate.}, journal = {PloS one}, volume = {7}, number = {2}, pages = {e31540}, pmid = {22393364}, issn = {1932-6203}, mesh = {Animals ; Chemotaxis ; Data Mining/methods ; *Databases, Factual ; Genome ; Humans ; Internet ; Mammals/physiology ; Multigene Family ; Polymerase Chain Reaction ; Proteins/*chemistry/*metabolism ; Receptors, Odorant/chemistry ; Sequence Alignment ; Species Specificity ; Vertebrates/*physiology ; }, abstract = {Chemosensory receptors (CR) are crucial for animals to sense the environmental changes and survive on earth. The emergence of whole-genome sequences provides us an opportunity to identify the entire CR gene repertoires. To completely gain more insight into the evolution of CR genes in vertebrates, we identified the nearly all CR genes in 25 vertebrates using homology-based approaches. Among these CR gene repertoires, nearly half of them were identified for the first time in those previously uncharacterized species, such as the guinea pig, giant panda and elephant, etc. Consistent with previous findings, we found that the numbers of CR genes vary extensively among different species, suggesting an extreme form of 'birth-and-death' evolution. For the purpose of facilitating CR gene analysis, we constructed a database with the goals to provide a resource for CR genes annotation and a web tool for exploring their evolutionary patterns. Besides a search engine for the gene extraction from a specific chromosome region, an easy-to-use phylogenetic analysis tool was also provided to facilitate online phylogeny study of CR genes. Our work can provide a rigorous platform for further study on the evolution of CR genes in vertebrates.}, } @article {pmid22393319, year = {2012}, author = {Farkaš, I and Malík, T and Rebrová, K}, title = {Grounding the Meanings in Sensorimotor Behavior using Reinforcement Learning.}, journal = {Frontiers in neurorobotics}, volume = {6}, number = {}, pages = {1}, pmid = {22393319}, issn = {1662-5218}, abstract = {The recent outburst of interest in cognitive developmental robotics is fueled by the ambition to propose ecologically plausible mechanisms of how, among other things, a learning agent/robot could ground linguistic meanings in its sensorimotor behavior. Along this stream, we propose a model that allows the simulated iCub robot to learn the meanings of actions (point, touch, and push) oriented toward objects in robot's peripersonal space. In our experiments, the iCub learns to execute motor actions and comment on them. Architecturally, the model is composed of three neural-network-based modules that are trained in different ways. The first module, a two-layer perceptron, is trained by back-propagation to attend to the target position in the visual scene, given the low-level visual information and the feature-based target information. The second module, having the form of an actor-critic architecture, is the most distinguishing part of our model, and is trained by a continuous version of reinforcement learning to execute actions as sequences, based on a linguistic command. The third module, an echo-state network, is trained to provide the linguistic description of the executed actions. The trained model generalizes well in case of novel action-target combinations with randomized initial arm positions. It can also promptly adapt its behavior if the action/target suddenly changes during motor execution.}, } @article {pmid22393001, year = {2012}, author = {Ziv, G and Baran, E and Nam, S and Rodríguez-Iturbe, I and Levin, SA}, title = {Trading-off fish biodiversity, food security, and hydropower in the Mekong River Basin.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {109}, number = {15}, pages = {5609-5614}, pmid = {22393001}, issn = {1091-6490}, mesh = {Animal Migration ; Animals ; *Biodiversity ; Biomass ; China ; Decision Support Techniques ; Fishes/*growth & development ; *Food Supply ; *Power Plants ; *Rivers ; }, abstract = {The Mekong River Basin, site of the biggest inland fishery in the world, is undergoing massive hydropower development. Planned dams will block critical fish migration routes between the river's downstream floodplains and upstream tributaries. Here we estimate fish biomass and biodiversity losses in numerous damming scenarios using a simple ecological model of fish migration. Our framework allows detailing trade-offs between dam locations, power production, and impacts on fish resources. We find that the completion of 78 dams on tributaries, which have not previously been subject to strategic analysis, would have catastrophic impacts on fish productivity and biodiversity. Our results argue for reassessment of several dams planned, and call for a new regional agreement on tributary development of the Mekong River Basin.}, } @article {pmid22392861, year = {2013}, author = {Bourguignon, M and De Tiège, X and de Beeck, MO and Ligot, N and Paquier, P and Van Bogaert, P and Goldman, S and Hari, R and Jousmäki, V}, title = {The pace of prosodic phrasing couples the listener's cortex to the reader's voice.}, journal = {Human brain mapping}, volume = {34}, number = {2}, pages = {314-326}, pmid = {22392861}, issn = {1097-0193}, mesh = {Adult ; Algorithms ; Auditory Cortex/*physiology ; Auditory Perception ; Biomechanical Phenomena ; Data Interpretation, Statistical ; Female ; Functional Laterality/physiology ; Humans ; Image Processing, Computer-Assisted ; Language ; Magnetic Resonance Imaging ; Magnetoencephalography ; Male ; Music ; Nerve Net/physiology ; Reading ; Sex Characteristics ; Speech Perception/*physiology ; Temporal Lobe/physiology ; *Voice ; Young Adult ; }, abstract = {We studied online coupling between a reader's voice and a listener's cortical activity using a novel, ecologically valid continuous listening paradigm. Whole-scalp magnetoencephalographic (MEG) signals were recorded from 10 right-handed, native French-speaking listeners in four conditions: a female (Exp1f) and a male (Exp1m) reading the same text in French; a male reading a text in Finnish (Exp 2), a language incomprehensible for the subjects, and a male humming Exp1 text (Exp 3). The fundamental frequency (f0) of the reader's voice was recorded with an accelerometer attached to the throat, and coherence was computed between f0 time-course and listener's MEG. Similar levels of right-hemisphere-predominant coherence were found at ˜0.5 Hz in Exps 1-3. Dynamic imaging of coherent sources revealed that the most coherent brain regions were located in the right posterior superior temporal sulcus (pSTS) and posterior superior temporal gyrus (pSTG) in Exps 1-2 and in the right supratemporal auditory cortex in Exp 3. Comparison between speech rhythm and phrasing suggested a connection of the observed coherence to pauses at the sentence level both in the spoken and hummed text. These results demonstrate significant coupling at ∼0.5 Hz between reader's voice and listener's cortical signals during listening to natural continuous voice. The observed coupling suggests that voice envelope fluctuations, due to prosodic rhythmicity at the phrasal and sentence levels, are reflected in the listener's cortex as rhythmicity of about 2-s cycles. The predominance of the coherence in the right pSTS and pSTG suggests hemispherical asymmetry in processing of speech sounds at subsentence time scales.}, } @article {pmid22385976, year = {2012}, author = {Dwivedi, B and Schmieder, R and Goldsmith, DB and Edwards, RA and Breitbart, M}, title = {PhiSiGns: an online tool to identify signature genes in phages and design PCR primers for examining phage diversity.}, journal = {BMC bioinformatics}, volume = {13}, number = {}, pages = {37}, pmid = {22385976}, issn = {1471-2105}, mesh = {Bacteriophages/*classification/*genetics/isolation & purification ; Biological Evolution ; Computational Biology ; Genome, Viral ; Phylogeny ; Polymerase Chain Reaction/*methods ; Sewage/*virology ; *Software ; Virology/*methods ; }, abstract = {BACKGROUND: Phages (viruses that infect bacteria) have gained significant attention because of their abundance, diversity and important ecological roles. However, the lack of a universal gene shared by all phages presents a challenge for phage identification and characterization, especially in environmental samples where it is difficult to culture phage-host systems. Homologous conserved genes (or "signature genes") present in groups of closely-related phages can be used to explore phage diversity and define evolutionary relationships amongst these phages. Bioinformatic approaches are needed to identify candidate signature genes and design PCR primers to amplify those genes from environmental samples; however, there is currently no existing computational tool that biologists can use for this purpose.

RESULTS: Here we present PhiSiGns, a web-based and standalone application that performs a pairwise comparison of each gene present in user-selected phage genomes, identifies signature genes, generates alignments of these genes, and designs potential PCR primer pairs. PhiSiGns is available at (http://www.phantome.org/phisigns/; http://phisigns.sourceforge.net/) with a link to the source code. Here we describe the specifications of PhiSiGns and demonstrate its application with a case study.

CONCLUSIONS: PhiSiGns provides phage biologists with a user-friendly tool to identify signature genes and design PCR primers to amplify related genes from uncultured phages in environmental samples. This bioinformatics tool will facilitate the development of novel signature genes for use as molecular markers in studies of phage diversity, phylogeny, and evolution.}, } @article {pmid22384609, year = {2011}, author = {Li, WJ and Zhang, SH and Wang, HM}, title = {[Ecosystem services evaluation based on geographic information system and remote sensing technology: a review].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {22}, number = {12}, pages = {3358-3364}, pmid = {22384609}, issn = {1001-9332}, mesh = {*Conservation of Natural Resources ; Ecology/economics ; *Ecosystem ; Evaluation Studies as Topic ; *Geographic Information Systems ; Models, Theoretical ; *Remote Sensing Technology ; Systems Integration ; }, abstract = {Ecosystem services evaluation is a hot topic in current ecosystem management, and has a close link with human beings welfare. This paper summarized the research progress on the evaluation of ecosystem services based on geographic information system (GIS) and remote sensing (RS) technology, which could be reduced to the following three characters, i. e., ecological economics theory is widely applied as a key method in quantifying ecosystem services, GIS and RS technology play a key role in multi-source data acquisition, spatiotemporal analysis, and integrated platform, and ecosystem mechanism model becomes a powerful tool for understanding the relationships between natural phenomena and human activities. Aiming at the present research status and its inadequacies, this paper put forward an "Assembly Line" framework, which was a distributed one with scalable characteristics, and discussed the future development trend of the integration research on ecosystem services evaluation based on GIS and RS technologies.}, } @article {pmid22384602, year = {2011}, author = {Zhou, Y and Shi, TM and Hu, YM and Gao, C and Liu, M and Song, LQ}, title = {[Location selection for Shenyang urban parks based on GIS and multi-objective location allocation model].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {22}, number = {12}, pages = {3307-3314}, pmid = {22384602}, issn = {1001-9332}, mesh = {Air Pollution/analysis ; China ; Cities ; *City Planning ; Conservation of Natural Resources/*methods ; *Ecosystem ; *Geographic Information Systems ; *Models, Theoretical ; }, abstract = {Based on geographic information system (GIS) technology and multi-objective location-allocation (LA) model, and in considering of four relatively independent objective factors (population density level, air pollution level, urban heat island effect level, and urban land use pattern), an optimized location selection for the urban parks within the Third Ring of Shenyang was conducted, and the selection results were compared with the spatial distribution of existing parks, aimed to evaluate the rationality of the spatial distribution of urban green spaces. In the location selection of urban green spaces in the study area, the factor air pollution was most important, and, compared with single objective factor, the weighted analysis results of multi-objective factors could provide optimized spatial location selection of new urban green spaces. The combination of GIS technology with LA model would be a new approach for the spatial optimizing of urban green spaces.}, } @article {pmid22369237, year = {2011}, author = {Mohammed, MH and Ghosh, TS and Reddy, RM and Reddy, CV and Singh, NK and Mande, SS}, title = {INDUS - a composition-based approach for rapid and accurate taxonomic classification of metagenomic sequences.}, journal = {BMC genomics}, volume = {12 Suppl 3}, number = {Suppl 3}, pages = {S4}, pmid = {22369237}, issn = {1471-2164}, mesh = {Algorithms ; Classification/*methods ; *Databases, Factual ; Genome ; Internet ; *Metagenomics ; User-Computer Interface ; }, abstract = {BACKGROUND: Taxonomic classification of metagenomic sequences is the first step in metagenomic analysis. Existing taxonomic classification approaches are of two types, similarity-based and composition-based. Similarity-based approaches, though accurate and specific, are extremely slow. Since, metagenomic projects generate millions of sequences, adopting similarity-based approaches becomes virtually infeasible for research groups having modest computational resources. In this study, we present INDUS - a composition-based approach that incorporates the following novel features. First, INDUS discards the 'one genome-one composition' model adopted by existing compositional approaches. Second, INDUS uses 'compositional distance' information for identifying appropriate assignment levels. Third, INDUS incorporates steps that attempt to reduce biases due to database representation.

RESULTS: INDUS is able to rapidly classify sequences in both simulated and real metagenomic sequence data sets with classification efficiency significantly higher than existing composition-based approaches. Although the classification efficiency of INDUS is observed to be comparable to those by similarity-based approaches, the binning time (as compared to alignment based approaches) is 23-33 times lower.

CONCLUSION: Given it's rapid execution time, and high levels of classification efficiency, INDUS is expected to be of immense interest to researchers working in metagenomics and microbial ecology.

AVAILABILITY: A web-server for the INDUS algorithm is available at http://metagenomics.atc.tcs.com/INDUS/}, } @article {pmid22384206, year = {2012}, author = {Zhu, JY and Zhao, N and Yang, B}, title = {Global transcriptome profiling of the pine shoot beetle, Tomicus yunnanensis (Coleoptera: Scolytinae).}, journal = {PloS one}, volume = {7}, number = {2}, pages = {e32291}, pmid = {22384206}, issn = {1932-6203}, mesh = {Amino Acid Motifs ; Amino Acid Sequence ; Animals ; Cluster Analysis ; Coleoptera ; Computational Biology/methods ; Databases, Genetic ; Ecology ; *Gene Expression Profiling ; Gene Expression Regulation ; Gene Library ; Glutathione Transferase/metabolism ; Heat-Shock Proteins/metabolism ; Insecticide Resistance ; Models, Biological ; Models, Genetic ; Molecular Sequence Data ; Sequence Homology, Amino Acid ; }, abstract = {BACKGROUND: The pine shoot beetle Tomicus yunnanensis (Coleoptera: Scolytinae) is an economically important pest of Pinus yunnanensis in southwestern China. Developed resistance to insecticides due to chemical pesticides being used for a long time is a factor involved in its serious damage, which poses a challenge for management. In addition, highly efficient adaptation to divergent environmental ecologies results in this pest posing great potential threat to pine forests. However, the molecular mechanisms remain unknown as only limited nucleotide sequence data for this species is available.

In this study, we applied next generation sequencing (Illumina sequencing) to sequence the adult transcriptome of T. yunnanensis. A total of 51,822,230 reads were obtained. They were assembled into 140,702 scaffolds, and 60,031 unigenes. The unigenes were further functionally annotated with gene descriptions, Gene Ontology (GO), Clusters of Orthologous Groups (COG), and Kyoto Encyclopedia of Genes and Genome (KEGG). In total, 80,932 unigenes were classified into GO, 13,599 unigenes were assigned to COG, and 33,875 unigenes were found in KO categories. A biochemical pathway database containing 219 predicted pathways was also created based on the annotations. In depth analysis of the data revealed a large number of genes related to insecticides resistance and heat shock protein genes associated with environmental stress.

CONCLUSIONS/SIGNIFICANCE: The results facilitate the investigations of molecular resistance mechanisms to insecticides and environmental stress. This study lays the foundation for future functional genomics studies of important biological questions of this pest.}, } @article {pmid22384202, year = {2012}, author = {Rest, JS and Bullaughey, K and Morris, GP and Li, WH}, title = {Contribution of transcription factor binding site motif variants to condition-specific gene expression patterns in budding yeast.}, journal = {PloS one}, volume = {7}, number = {2}, pages = {e32274}, pmid = {22384202}, issn = {1932-6203}, support = {GM30998/GM/NIGMS NIH HHS/United States ; R01 GM081724/GM/NIGMS NIH HHS/United States ; GM081724/GM/NIGMS NIH HHS/United States ; R37 GM030998/GM/NIGMS NIH HHS/United States ; R01 GM030998/GM/NIGMS NIH HHS/United States ; }, mesh = {Allosteric Site ; Amino Acid Motifs ; Binding Sites ; Computational Biology/methods ; *Gene Expression Profiling ; *Gene Expression Regulation, Fungal ; Genome, Fungal ; Genomics ; Models, Statistical ; Nucleotides/genetics ; Phylogeny ; Reproducibility of Results ; Saccharomyces/*genetics/physiology ; Saccharomycetales/*genetics/physiology ; Species Specificity ; Transcription Factors/*chemistry/*genetics ; }, abstract = {It is now experimentally well known that variant sequences of a cis transcription factor binding site motif can contribute to differential regulation of genes. We characterize the relationship between motif variants and gene expression by analyzing expression microarray data and binding site predictions. To accomplish this, we statistically detect motif variants with effects that differ among environments. Such environmental specificity may be due to either affinity differences between variants or, more likely, differential interactions of TFs bound to these variants with cofactors, and with differential presence of cofactors across environments. We examine conservation of functional variants across four Saccharomyces species, and find that about a third of transcription factors have target genes that are differentially expressed in a condition-specific manner that is correlated with the nucleotide at variant motif positions. We find good correspondence between our results and some cases in the experimental literature (Reb1, Sum1, Mcm1, and Rap1). These results and growing consensus in the literature indicates that motif variants may often be functionally distinct, that this may be observed in genomic data, and that variants play an important role in condition-specific gene regulation.}, } @article {pmid22374109, year = {2012}, author = {Guyon, I and Dror, G and Lemaire, V and Silver, DL and Taylor, G and Aha, DW}, title = {Analysis of the IJCNN 2011 UTL challenge.}, journal = {Neural networks : the official journal of the International Neural Network Society}, volume = {32}, number = {}, pages = {174-178}, doi = {10.1016/j.neunet.2012.02.010}, pmid = {22374109}, issn = {1879-2782}, mesh = {Algorithms ; *Artificial Intelligence ; Databases, Factual ; Ecology ; Handwriting ; Image Processing, Computer-Assisted ; Neural Networks, Computer ; Pattern Recognition, Automated ; Principal Component Analysis ; Reproducibility of Results ; Word Processing ; }, abstract = {We organized a challenge in "Unsupervised and Transfer Learning": the UTL challenge (http://clopinet.com/ul). We made available large datasets from various application domains: handwriting recognition, image recognition, video processing, text processing, and ecology. The goal was to learn data representations that capture regularities of an input space for re-use across tasks. The representations were evaluated on supervised learning "target tasks" unknown to the participants. The first phase of the challenge was dedicated to "unsupervised transfer learning" (the competitors were given only unlabeled data). The second phase was dedicated to "cross-task transfer learning" (the competitors were provided with a limited amount of labeled data from "source tasks", distinct from the "target tasks"). The analysis indicates that learned data representations yield significantly better results than those obtained with original data or data preprocessed with standard normalizations and functional transforms.}, } @article {pmid22373233, year = {2011}, author = {Ariño, AH and Chavan, V and King, N}, title = {The Biodiversity Informatics Potential Index.}, journal = {BMC bioinformatics}, volume = {12 Suppl 15}, number = {Suppl 15}, pages = {S4}, pmid = {22373233}, issn = {1471-2105}, mesh = {*Biodiversity ; Ecology ; *Informatics ; Information Services ; Models, Theoretical ; Publishing ; }, abstract = {BACKGROUND: Biodiversity informatics is a relatively new discipline extending computer science in the context of biodiversity data, and its development to date has not been uniform throughout the world. Digitizing effort and capacity building are costly, and ways should be found to prioritize them rationally. The proposed 'Biodiversity Informatics Potential (BIP) Index' seeks to fulfill such a prioritization role. We propose that the potential for biodiversity informatics be assessed through three concepts: (a) the intrinsic biodiversity potential (the biological richness or ecological diversity) of a country; (b) the capacity of the country to generate biodiversity data records; and (c) the availability of technical infrastructure in a country for managing and publishing such records.

METHODS: Broadly, the techniques used to construct the BIP Index were rank correlation, multiple regression analysis, principal components analysis and optimization by linear programming. We built the BIP Index by finding a parsimonious set of country-level human, economic and environmental variables that best predicted the availability of primary biodiversity data accessible through the Global Biodiversity Information Facility (GBIF) network, and constructing an optimized model with these variables. The model was then applied to all countries for which sufficient data existed, to obtain a score for each country. Countries were ranked according to that score.

RESULTS: Many of the current GBIF participants ranked highly in the BIP Index, although some of them seemed not to have realized their biodiversity informatics potential. The BIP Index attributed low ranking to most nonparticipant countries; however, a few of them scored highly, suggesting that these would be high-return new participants if encouraged to contribute towards the GBIF mission of free and open access to biodiversity data.

CONCLUSIONS: The BIP Index could potentially help in (a) identifying countries most likely to contribute to filling gaps in digitized biodiversity data; (b) assisting countries potentially in need (for example mega-diverse) to mobilize resources and collect data that could be used in decision-making; and (c) allowing identification of which biodiversity informatics-resourced countries could afford to assist countries lacking in biodiversity informatics capacity, and which data-rich countries should benefit most from such help.}, } @article {pmid22369274, year = {2012}, author = {Lü, Y and Liu, S and Fu, B}, title = {Ecosystem service: from virtual reality to ground truth.}, journal = {Environmental science & technology}, volume = {46}, number = {5}, pages = {2492-2493}, doi = {10.1021/es300475w}, pmid = {22369274}, issn = {1520-5851}, mesh = {Biophysical Phenomena ; Decision Support Techniques ; *Ecosystem ; Models, Theoretical ; Publications ; *User-Computer Interface ; }, } @article {pmid22363808, year = {2012}, author = {Krüger, D and Kapturska, D and Fischer, C and Daniel, R and Wubet, T}, title = {Diversity measures in environmental sequences are highly dependent on alignment quality--data from ITS and new LSU primers targeting basidiomycetes.}, journal = {PloS one}, volume = {7}, number = {2}, pages = {e32139}, pmid = {22363808}, issn = {1932-6203}, mesh = {Base Sequence ; Basidiomycota/classification/*genetics ; DNA Primers/*metabolism ; DNA, Fungal/genetics ; DNA, Ribosomal/genetics ; DNA, Ribosomal Spacer/*genetics ; Databases, Genetic ; Entropy ; *Environmental Microbiology ; *Genetic Variation ; Molecular Sequence Data ; Ribosome Subunits, Large, Eukaryotic/*genetics ; Sequence Alignment/*standards ; Soil Microbiology ; }, abstract = {The ribosomal DNA comprised of the ITS1-5.8S-ITS2 regions is widely used as a fungal marker in molecular ecology and systematics but cannot be aligned with confidence across genetically distant taxa. In order to study the diversity of Agaricomycotina in forest soils, we designed primers targeting the more alignable 28S (LSU) gene, which should be more useful for phylogenetic analyses of the detected taxa. This paper compares the performance of the established ITS1F/4B primer pair, which targets basidiomycetes, to that of two new pairs. Key factors in the comparison were the diversity covered, off-target amplification, rarefaction at different Operational Taxonomic Unit (OTU) cutoff levels, sensitivity of the method used to process the alignment to missing data and insecure positional homology, and the congruence of monophyletic clades with OTU assignments and BLAST-derived OTU names. The ITS primer pair yielded no off-target amplification but also exhibited the least fidelity to the expected phylogenetic groups. The LSU primers give complementary pictures of diversity, but were more sensitive to modifications of the alignment such as the removal of difficult-to align stretches. The LSU primers also yielded greater numbers of singletons but also had a greater tendency to produce OTUs containing sequences from a wider variety of species as judged by BLAST similarity. We introduced some new parameters to describe alignment heterogeneity based on Shannon entropy and the extent and contents of the OTUs in a phylogenetic tree space. Our results suggest that ITS should not be used when calculating phylogenetic trees from genetically distant sequences obtained from environmental DNA extractions and that it is inadvisable to define OTUs on the basis of very heterogeneous alignments.}, } @article {pmid22363748, year = {2012}, author = {Nyári, ÁS and Joseph, L}, title = {Evolution in Australasian mangrove forests: multilocus phylogenetic analysis of the Gerygone warblers (Aves: Acanthizidae).}, journal = {PloS one}, volume = {7}, number = {2}, pages = {e31840}, pmid = {22363748}, issn = {1932-6203}, mesh = {Animals ; Australasia ; Avicennia/*genetics ; Bayes Theorem ; *Biological Evolution ; Databases, Genetic ; Genetic Loci/genetics ; Genetic Speciation ; Likelihood Functions ; Molecular Sequence Data ; Multilocus Sequence Typing/*methods ; *Phylogeny ; Songbirds/*classification/*genetics ; Species Specificity ; Time Factors ; Trees/*genetics ; }, abstract = {The mangrove forests of Australasia have many endemic bird species but their evolution and radiation in those habitats has been little studied. One genus with several mangrove specialist species is Gerygone (Passeriformes: Acanthizidae). The phylogeny of the Acanthizidae is reasonably well understood but limited taxon sampling for Gerygone has constrained understanding of its evolution and historical biogeography in mangroves. Here we report on a phylogenetic analysis of Gerygone based on comprehensive taxon sampling and a multilocus dataset of thirteen loci spread across the avian genome (eleven nuclear and two mitochondrial loci). Since Gerygone includes three species restricted to Australia's coastal mangrove forests, we particularly sought to understand the biogeography of their evolution in that ecosystem. Analyses of individual loci, as well as of a concatenated dataset drawn from previous molecular studies indicates that the genus as currently defined is not monophyletic, and that the Grey Gerygone (G. cinerea) from New Guinea should be transferred to the genus Acanthiza. The multilocus approach has permitted the nuanced view of the group's evolution into mangrove ecosystems having occurred on multiple occasions, in three non-overlapping time frames, most likely first by the G. magnirostris lineage, and subsequently followed by those of G. tenebrosa and G. levigaster.}, } @article {pmid22363520, year = {2012}, author = {Toulza, E and Tagliabue, A and Blain, S and Piganeau, G}, title = {Analysis of the global ocean sampling (GOS) project for trends in iron uptake by surface ocean microbes.}, journal = {PloS one}, volume = {7}, number = {2}, pages = {e30931}, pmid = {22363520}, issn = {1932-6203}, mesh = {Adaptation, Physiological/drug effects/genetics ; Bacteria/classification/drug effects/genetics ; Biomarkers/metabolism ; Databases as Topic ; Ecosystem ; Genes, Bacterial/genetics ; Geography ; *Internationality ; Iron/*metabolism/pharmacology ; Metabolic Networks and Pathways/drug effects ; Oceanography/*methods ; Oceans and Seas ; Seawater/*microbiology ; Surface Properties/drug effects ; }, abstract = {Microbial metagenomes are DNA samples of the most abundant, and therefore most successful organisms at the sampling time and location for a given cell size range. The study of microbial communities via their DNA content has revolutionized our understanding of microbial ecology and evolution. Iron availability is a critical resource that limits microbial communities' growth in many oceanic areas. Here, we built a database of 2319 sequences, corresponding to 140 gene families of iron metabolism with a large phylogenetic spread, to explore the microbial strategies of iron acquisition in the ocean's bacterial community. We estimate iron metabolism strategies from metagenome gene content and investigate whether their prevalence varies with dissolved iron concentrations obtained from a biogeochemical model. We show significant quantitative and qualitative variations in iron metabolism pathways, with a higher proportion of iron metabolism genes in low iron environments. We found a striking difference between coastal and open ocean sites regarding Fe(2+) versus Fe(3+) uptake gene prevalence. We also show that non-specific siderophore uptake increases in low iron open ocean environments, suggesting bacteria may acquire iron from natural siderophore-like organic complexes. Despite the lack of knowledge of iron uptake mechanisms in most marine microorganisms, our approach provides insights into how the iron metabolic pathways of microbial communities may vary with seawater iron concentrations.}, } @article {pmid22361586, year = {2012}, author = {Roos, V and Gunnarsson, L and Fick, J and Larsson, DG and Rudén, C}, title = {Prioritising pharmaceuticals for environmental risk assessment: Towards adequate and feasible first-tier selection.}, journal = {The Science of the total environment}, volume = {421-422}, number = {}, pages = {102-110}, doi = {10.1016/j.scitotenv.2012.01.039}, pmid = {22361586}, issn = {1879-1026}, mesh = {Animals ; Databases, Factual ; Drug-Related Side Effects and Adverse Reactions ; Ecotoxicology ; Environmental Exposure/adverse effects ; *Environmental Monitoring/methods/standards/statistics & numerical data ; Feasibility Studies ; Fishes/blood ; Models, Biological ; Pharmaceutical Preparations/*analysis/blood/chemistry ; Quantitative Structure-Activity Relationship ; Risk Assessment ; Water Pollutants, Chemical/*analysis/blood/chemistry/toxicity ; }, abstract = {The presence of pharmaceuticals in the aquatic environment, and the concerns for negative effects on aquatic organisms, has gained increasing attention over the last years. As ecotoxicity data are lacking for most active pharmaceutical ingredients (APIs), it is important to identify strategies to prioritise APIs for ecotoxicity testing and environmental monitoring. We have used nine previously proposed prioritisation schemes, both risk- and hazard-based, to rank 582 APIs. The similarities and differences in overall ranking results and input data were compared. Moreover, we analysed how well the methods ranked seven relatively well-studied APIs. It is concluded that the hazard-based methods were more successful in correctly ranking the well-studied APIs, but the fish plasma model, which includes human pharmacological data, also showed a high success rate. The results of the analyses show that the input data availability vary significantly; some data, such as logP, are available for most API while information about environmental concentrations and bioconcentration are still scarce. The results also suggest that the exposure estimates in risk-based methods need to be improved and that the inclusion of effect measures at first-tier prioritisation might underestimate risks. It is proposed that in order to develop an adequate prioritisation scheme, improved data on exposure such as degradation and sewage treatment removal and bioconcentration ability should be further considered. The use of ATC codes may also be useful for the development of a prioritisation scheme that includes the mode of action of pharmaceuticals and, to some extent, mixture effects.}, } @article {pmid22357592, year = {2012}, author = {Nathan, R and Spiegel, O and Fortmann-Roe, S and Harel, R and Wikelski, M and Getz, WM}, title = {Using tri-axial acceleration data to identify behavioral modes of free-ranging animals: general concepts and tools illustrated for griffon vultures.}, journal = {The Journal of experimental biology}, volume = {215}, number = {Pt 6}, pages = {986-996}, pmid = {22357592}, issn = {1477-9145}, support = {R01 GM083863/GM/NIGMS NIH HHS/United States ; GM083863/GM/NIGMS NIH HHS/United States ; }, mesh = {*Acceleration ; Animals ; Behavior, Animal/*physiology ; Biomechanical Phenomena/physiology ; Falconiformes/*physiology ; Geographic Information Systems ; Movement/*physiology ; }, abstract = {Integrating biomechanics, behavior and ecology requires a mechanistic understanding of the processes producing the movement of animals. This calls for contemporaneous biomechanical, behavioral and environmental data along movement pathways. A recently formulated unifying movement ecology paradigm facilitates the integration of existing biomechanics, optimality, cognitive and random paradigms for studying movement. We focus on the use of tri-axial acceleration (ACC) data to identify behavioral modes of GPS-tracked free-ranging wild animals and demonstrate its application to study the movements of griffon vultures (Gyps fulvus, Hablizl 1783). In particular, we explore a selection of nonlinear and decision tree methods that include support vector machines, classification and regression trees, random forest methods and artificial neural networks and compare them with linear discriminant analysis (LDA) as a baseline for classifying behavioral modes. Using a dataset of 1035 ground-truthed ACC segments, we found that all methods can accurately classify behavior (80-90%) and, as expected, all nonlinear methods outperformed LDA. We also illustrate how ACC-identified behavioral modes provide the means to examine how vulture flight is affected by environmental factors, hence facilitating the integration of behavioral, biomechanical and ecological data. Our analysis of just over three-quarters of a million GPS and ACC measurements obtained from 43 free-ranging vultures across 9783 vulture-days suggests that their annual breeding schedule might be selected primarily in response to seasonal conditions favoring rising-air columns (thermals) and that rare long-range forays of up to 1750 km from the home range are performed despite potentially heavy energetic costs and a low rate of food intake, presumably to explore new breeding, social and long-term resource location opportunities.}, } @article {pmid22356676, year = {2012}, author = {Foth, C and Brusatte, SL and Butler, RJ}, title = {Do different disparity proxies converge on a common signal? Insights from the cranial morphometrics and evolutionary history of Pterosauria (Diapsida: Archosauria).}, journal = {Journal of evolutionary biology}, volume = {25}, number = {5}, pages = {904-915}, doi = {10.1111/j.1420-9101.2012.02479.x}, pmid = {22356676}, issn = {1420-9101}, mesh = {Animals ; *Biological Evolution ; Body Size ; Databases, Factual ; Fossils ; *Morphogenesis ; Phylogeny ; Reptiles/anatomy & histology/classification/growth & development/*physiology ; Skull/anatomy & histology/growth & development/*physiology ; Species Specificity ; Time Factors ; }, abstract = {Disparity, or morphological diversity, is often quantified by evolutionary biologists investigating the macroevolutionary history of clades over geological timescales. Disparity is typically quantified using proxies for morphology, such as measurements, discrete anatomical characters, or geometric morphometrics. If different proxies produce differing results, then the accurate quantification of disparity in deep time may be problematic. However, despite this, few studies have attempted to examine disparity of a single clade using multiple morphological proxies. Here, as a case study for this question, we examine the disparity of the volant Mesozoic fossil reptile clade Pterosauria, an intensively studied group that achieved substantial morphological, ecological and taxonomic diversity during their 145+ million-year evolutionary history. We characterize broadscale patterns of cranial morphological disparity for pterosaurs for the first time using landmark-based geometric morphometrics and make comparisons to calculations of pterosaur disparity based on alternative metrics. Landmark-based disparity calculations suggest that monofenestratan pterosaurs were more diverse cranially than basal non-monofenestratan pterosaurs (at least when the aberrant anurognathids are excluded), and that peak cranial disparity may have occurred in the Early Cretaceous, relatively late in pterosaur evolution. Significantly, our cranial disparity results are broadly congruent with those based on whole skeleton discrete character and limb proportion data sets, indicating that these divergent approaches document a consistent pattern of pterosaur morphological evolution. Therefore, pterosaurs provide an exemplar case demonstrating that different proxies for morphological form can converge on the same disparity signal, which is encouraging because often only one such proxy is available for extinct clades represented by fossils. Furthermore, mapping phylogeny into cranial morphospace demonstrates that pterosaur cranial morphology is significantly correlated with, and potentially constrained by, phylogenetic relationships.}, } @article {pmid22355719, year = {2011}, author = {Ishak, HD and Miller, JL and Sen, R and Dowd, SE and Meyer, E and Mueller, UG}, title = {Microbiomes of ant castes implicate new microbial roles in the fungus-growing ant Trachymyrmex septentrionalis.}, journal = {Scientific reports}, volume = {1}, number = {}, pages = {204}, pmid = {22355719}, issn = {2045-2322}, mesh = {Animals ; Ants/*microbiology/*physiology ; Biodiversity ; Computational Biology ; Female ; Male ; *Metagenome ; RNA, Ribosomal, 16S/genetics ; Seasons ; Sequence Analysis, DNA ; Symbiosis/genetics ; }, abstract = {Fungus-growing ants employ several defenses against diseases, including disease-suppressing microbial biofilms on their integument and in fungal gardens. Here, we compare the phenology of microbiomes in natural nests of the temperate fungus-growing ant Trachymyrmex septentrionalis using culture-dependent isolations and culture-independent 16S-amplicon 454-sequencing. 454-sequencing revealed diverse actinobacteria associated with ants, including most prominently Solirubrobacter (12.2-30.9% of sequence reads), Pseudonocardia (3.5-42.0%), and Microlunatus (0.4-10.8%). Bacterial abundances remained relatively constant in monthly surveys throughout the annual active period (late winter to late summer), except Pseudonocardia abundance declined in females during the reproductive phase. Pseudonocardia species found on ants are phylogenetically different from those in gardens and soil, indicating ecological separation of these Pseudonocardia types. Because the pathogen Escovopsis is not known to infect gardens of T. septentrionalis, the ant-associated microbes do not seem to function in Escovopsis suppression, but could protect against ant diseases, help in nest sanitation, or serve unknown functions.}, } @article {pmid22355533, year = {2011}, author = {Madin, EM and Madin, JS and Booth, DJ}, title = {Landscape of fear visible from space.}, journal = {Scientific reports}, volume = {1}, number = {}, pages = {14}, pmid = {22355533}, issn = {2045-2322}, mesh = {Animals ; Conservation of Natural Resources/*methods ; Environmental Monitoring/*methods ; Image Interpretation, Computer-Assisted/*methods ; Predatory Behavior/*physiology ; *Spacecraft ; }, abstract = {By linking ecological theory with freely-available Google Earth satellite imagery, landscape-scale footprints of behavioural interactions between predators and prey can be observed remotely. A Google Earth image survey of the lagoon habitat at Heron Island within Australia's Great Barrier Reef revealed distinct halo patterns within algal beds surrounding patch reefs. Ground truth surveys confirmed that, as predicted, algal canopy height increases with distance from reef edges. A grazing assay subsequently demonstrated that herbivore grazing was responsible for this pattern. In conjunction with recent behavioural ecology studies, these findings demonstrate that herbivores' collective antipredator behavioural patterns can shape vegetation distributions on a scale clearly visible from space. By using sequential Google Earth images of specific locations over time, this technique could potentially allow rapid, inexpensive remote monitoring of cascading, indirect effects of predator removals (e.g., fishing; hunting) and/or recovery and reintroductions (e.g., marine or terrestrial reserves) nearly anywhere on earth.}, } @article {pmid22353237, year = {2012}, author = {Reading, BJ and Chapman, RW and Schaff, JE and Scholl, EH and Opperman, CH and Sullivan, CV}, title = {An ovary transcriptome for all maturational stages of the striped bass (Morone saxatilis), a highly advanced perciform fish.}, journal = {BMC research notes}, volume = {5}, number = {}, pages = {111}, pmid = {22353237}, issn = {1756-0500}, mesh = {Animals ; Bass/*genetics ; DNA, Complementary/chemistry/genetics ; Databases, Genetic ; Estuaries ; Expressed Sequence Tags ; Female ; Fisheries ; Gene Expression Profiling ; *Gene Expression Regulation, Developmental ; Gene Library ; High-Throughput Nucleotide Sequencing ; Oocytes/cytology/*metabolism ; Oogenesis/*genetics ; Ovary/cytology/*metabolism ; Sequence Analysis, DNA ; *Transcriptome ; Zebrafish/genetics ; }, abstract = {BACKGROUND: The striped bass and its relatives (genus Morone) are important fisheries and aquaculture species native to estuaries and rivers of the Atlantic coast and Gulf of Mexico in North America. To open avenues of gene expression research on reproduction and breeding of striped bass, we generated a collection of expressed sequence tags (ESTs) from a complementary DNA (cDNA) library representative of their ovarian transcriptome.

RESULTS: Sequences of a total of 230,151 ESTs (51,259,448 bp) were acquired by Roche 454 pyrosequencing of cDNA pooled from ovarian tissues obtained at all stages of oocyte growth, at ovulation (eggs), and during preovulatory atresia. Quality filtering of ESTs allowed assembly of 11,208 high-quality contigs ≥ 100 bp, including 2,984 contigs 500 bp or longer (average length 895 bp). Blastx comparisons revealed 5,482 gene orthologues (E-value < 10-3), of which 4,120 (36.7% of total contigs) were annotated with Gene Ontology terms (E-value < 10-6). There were 5,726 remaining unknown unique sequences (51.1% of total contigs). All of the high-quality EST sequences are available in the National Center for Biotechnology Information (NCBI) Short Read Archive (GenBank: SRX007394). Informative contigs were considered to be abundant if they were assembled from groups of ESTs comprising ≥ 0.15% of the total short read sequences (≥ 345 reads/contig). Approximately 52.5% of these abundant contigs were predicted to have predominant ovary expression through digital differential display in silico comparisons to zebrafish (Danio rerio) UniGene orthologues. Over 1,300 Gene Ontology terms from Biological Process classes of Reproduction, Reproductive process, and Developmental process were assigned to this collection of annotated contigs.

CONCLUSIONS: This first large reference sequence database available for the ecologically and economically important temperate basses (genus Morone) provides a foundation for gene expression studies in these species. The predicted predominance of ovary gene expression and assignment of directly relevant Gene Ontology classes suggests a powerful utility of this dataset for analysis of ovarian gene expression related to fundamental questions of oogenesis. Additionally, a high definition Agilent 60-mer oligo ovary 'UniClone' microarray with 8 × 15,000 probe format has been designed based on this striped bass transcriptome (eArray Group: Striper Group, Design ID: 029004).}, } @article {pmid22350421, year = {2012}, author = {Park, IW}, title = {Digital herbarium archives as a spatially extensive, taxonomically discriminate phenological record; a comparison to MODIS satellite imagery.}, journal = {International journal of biometeorology}, volume = {56}, number = {6}, pages = {1179-1182}, pmid = {22350421}, issn = {1432-1254}, mesh = {*Databases, Factual ; Flowers/physiology ; Periodicity ; *Plant Physiological Phenomena ; Plants/classification ; *Satellite Communications ; South Carolina ; }, abstract = {This study demonstrates that phenological information included in digital herbarium archives can produce annual phenological estimates correlated to satellite-derived green wave phenology at a regional scale (R = 0.183, P = 0.03). Thus, such records may be utilized in a fashion similar to other annual phenological records and, due to their longer duration and ability to discriminate among the various components of the plant community, hold significant potential for use in future research to supplement the deficiencies of other data sources as well as address a wide array of important issues in ecology and bioclimatology that cannot be addressed easily using more traditional methods.}, } @article {pmid22348881, year = {2012}, author = {Joutsa, J and Johansson, J and Niemelä, S and Ollikainen, A and Hirvonen, MM and Piepponen, P and Arponen, E and Alho, H and Voon, V and Rinne, JO and Hietala, J and Kaasinen, V}, title = {Mesolimbic dopamine release is linked to symptom severity in pathological gambling.}, journal = {NeuroImage}, volume = {60}, number = {4}, pages = {1992-1999}, doi = {10.1016/j.neuroimage.2012.02.006}, pmid = {22348881}, issn = {1095-9572}, mesh = {Corpus Striatum/diagnostic imaging/*metabolism ; Dopamine/*metabolism ; Dopamine Antagonists ; Gambling/*diagnostic imaging/*metabolism ; Humans ; Image Interpretation, Computer-Assisted ; Male ; Positron-Emission Tomography ; Raclopride ; Radiopharmaceuticals ; *Reward ; }, abstract = {BACKGROUND: Brain dopamine neurons code rewarding environmental stimuli by releasing endogenous dopamine, a transmission signal that is important for reinforcement learning. Human reward-seeking gambling behavior, and especially pathological gambling, has been presumed to be modulated by brain dopamine.

METHODS: Striatal dopamine release was studied with [(11)C]raclopride positron emission tomography (PET) during gambling with an ecologically valid slot machine gambling task. Twenty-four males with and without pathological gambling (DSM-IV) were scanned three times, and the effects of different gambling outcomes (high-reward and low-reward vs. control task) on dopamine release were evaluated.

RESULTS: Striatal dopamine was released in both groups during high-reward but also low-reward tasks. The dopamine release during the low-reward task was located in the associative part of the caudate nucleus. During the high-reward task, the effect was also seen in the ventral striatum and the magnitude of dopamine release was associated with parallel gambling "high". Furthermore, there was a positive correlation between dopamine release during the low-reward and the high-reward task. There was no general difference in the magnitude of dopamine release between pathological gamblers and controls. However, in pathological gamblers, dopamine release correlated positively with gambling symptom severity.

CONCLUSIONS: Striatal dopamine is released during gambling irrespective of gambling outcome suggesting that the mere expectation/prediction of reward is sufficient to induce dopaminergic changes. Although dopamine release during slot machine gambling is comparable between healthy controls and pathological gamblers, greater gambling symptom severity is associated with greater dopaminergic responses. Thus, as the dopamine reward deficiency theory predicts blunted mesolimbic dopamine responses to gambling in addicted individuals, our results question the validity of the reward deficiency hypothesis in pathological gambling.}, } @article {pmid22342514, year = {2012}, author = {Sibley, CD and Peirano, G and Church, DL}, title = {Molecular methods for pathogen and microbial community detection and characterization: current and potential application in diagnostic microbiology.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {12}, number = {3}, pages = {505-521}, pmid = {22342514}, issn = {1567-7257}, mesh = {Bacteria/genetics/isolation & purification/pathogenicity ; Communicable Diseases/*diagnosis/epidemiology/microbiology ; Computational Biology ; Fungi/genetics/isolation & purification/pathogenicity ; *Genome, Bacterial ; *Genome, Fungal ; Genotyping Techniques ; Humans ; Microarray Analysis/methods ; Microbiological Techniques/*methods/standards ; Molecular Typing/*methods ; Polymerase Chain Reaction/methods ; Polymorphism, Restriction Fragment Length ; Reagent Kits, Diagnostic ; }, abstract = {Clinical microbiology laboratories worldwide have historically relied on phenotypic methods (i.e., culture and biochemical tests) for detection, identification and characterization of virulence traits (e.g., antibiotic resistance genes, toxins) of human pathogens. However, limitations to implementation of molecular methods for human infectious diseases testing are being rapidly overcome allowing for the clinical evaluation and implementation of diverse technologies with expanding diagnostic capabilities. The advantages and limitation of molecular techniques including real-time polymerase chain reaction, partial or whole genome sequencing, molecular typing, microarrays, broad-range PCR and multiplexing will be discussed. Finally, terminal restriction fragment length polymorphism (T-RFLP) and deep sequencing are introduced as technologies at the clinical interface with the potential to dramatically enhance our ability to diagnose infectious diseases and better define the epidemiology and microbial ecology of a wide range of complex infections.}, } @article {pmid22339816, year = {2012}, author = {Renison, B and Ponsford, J and Testa, R and Richardson, B and Brownfield, K}, title = {The ecological and construct validity of a newly developed measure of executive function: the Virtual Library Task.}, journal = {Journal of the International Neuropsychological Society : JINS}, volume = {18}, number = {3}, pages = {440-450}, doi = {10.1017/S1355617711001883}, pmid = {22339816}, issn = {1469-7661}, mesh = {Activities of Daily Living ; Brain Injuries/complications ; Cognition Disorders/*diagnosis/etiology ; *Ecology ; Executive Function/*physiology ; Glasgow Coma Scale ; Humans ; Libraries, Digital/*standards ; Memory ; *Neuropsychological Tests ; Reproducibility of Results ; Statistics as Topic ; Surveys and Questionnaires ; Verbal Learning ; }, abstract = {Virtual reality (VR) assessment paradigms have the potential to address the limited ecological validity of pen and paper measures of executive function (EF) and the pragmatic and reliability issues associated with functional measures. To investigate the ecological validity and construct validity of a newly developed VR measure of EF, the Virtual Library Task (VLT); a real life analogous task--the Real Library Task (RLT); and five neuropsychological measures of EF were administered to 30 patients with traumatic brain injury (TBI) and 30 healthy Controls. Significant others for each participant also completed the Dysexecutive Questionnaire (DEX), which is a behavioral rating scale of everyday EF. Performances on the VLT and the RLT were significantly positively correlated indicating that VR performance is similar to real world performance. The TBI group performed significantly worse than the Control group on the VLT and the Modified Six Elements Test (MSET) but the other four neuropsychological measures of EF failed to differentiate the groups. Both the MSET and the VLT significantly predicted everyday EF suggesting that they are both ecologically valid tools for the assessment of EF. The VLT has the advantage over the MSET of providing objective measurement of individual components of EF.}, } @article {pmid22331453, year = {2013}, author = {Coskun Hepcan, C}, title = {Quantifying landscape pattern and connectivity in a Mediterranean coastal settlement: the case of the Urla district, Turkey.}, journal = {Environmental monitoring and assessment}, volume = {185}, number = {1}, pages = {143-155}, pmid = {22331453}, issn = {1573-2959}, mesh = {Biodiversity ; City Planning ; Conservation of Natural Resources/*methods ; Environmental Monitoring/*methods ; Geographic Information Systems ; Humans ; Plants/classification ; Turkey ; Urbanization/*trends ; }, abstract = {This study was aimed at analyzing and interpreting changes in landscape pattern and connectivity in the Urla district, Turkey using core landscape metrics based on a 42-year data derived from 1963 CORONA and 2005 ASTER satellite images and ten 1/25,000 topographical maps (1963-2005). The district represents a distinctive example of re-emerged suburbanization in the Izmir metropolitan area. In order to explore landscape characteristics of the study area, nine landscape composition and configuration metrics were chosen as follows: class area, percentage of landscape, number of patches, patch density, largest patch index, landscape shape index, mean patch size, perimeter area fractal dimension, and connectance index. The landscape configurations in the Urla district changed significantly by 2005 in that the process of (sub-)urbanization in the study area evolved from a rural, monocentric urban typology to a more suburban, polycentric morphology. Agricultural, maquis-phrygana, and forest areas decreased, while the built-up, olive plantation and phrygana areas increased. There was nearly a fivefold increase in the built-up areas during the study period, and the connectivity of the natural landscape declined. To prevent further fragmentation, it is important to keep the existing natural land cover types and agricultural areas intact. More importantly, a sustainable development scenario is required that contains a green infrastructure, or an ecological network planning for conservation and rehabilitation of the vital natural resources in the study area.}, } @article {pmid22331182, year = {2012}, author = {Boing, AF and Vicenzi, RB and Magajewski, F and Boing, AC and Moretti-Pires, RO and Peres, KG and Lindner, SR and Peres, MA}, title = {Reduction of ambulatory care sensitive conditions in Brazil between 1998 and 2009.}, journal = {Revista de saude publica}, volume = {46}, number = {2}, pages = {359-366}, doi = {10.1590/s0034-89102012005000011}, pmid = {22331182}, issn = {1518-8787}, mesh = {Age Distribution ; Ambulatory Care/*statistics & numerical data ; Brazil/epidemiology ; Female ; Health Services Accessibility ; Hospitalization/statistics & numerical data/*trends ; Humans ; Information Systems ; Male ; Primary Health Care/*statistics & numerical data ; Quality of Health Care ; Sex Distribution ; Socioeconomic Factors ; Time Factors ; }, abstract = {OBJECTIVE: To describe the trends in hospitalizations for ambulatory care sensitive conditions between 1998 and 2009 in Brazil.

METHODS: The ecological time series study used secondary data on hospitalizations for ACSC in the Sistema Único de Saúde (SUS, National Unified Health System). Data were obtained from the Hospital Information System. Hospital admission rates per 10,000 inhabitants were standardized by age range and gender, using the 2000 census male Brazilian population as standard. Trend analysis of the historic series was performed through generalized linear regression using the Prais-Winsten method.

RESULTS: Between 1998 and 2009, there was an average annual reduction in admissions for ambulatory care sensitive conditions of 3.7% in men (95%CI -2.3;-5.1) and women (95%CI -2.5; -5.6). The trend varied in each state, although no increase in admissions was observed in any state. In both men and women, the highest reductions were observed in hospitalizations for gastrointestinal ulcers (-11.7% a year and -12.1%, respectively), avoidable conditions (-8.8% and -8.9%) and lower respiratory diseases (-8.0% and -8.1%). Hospitalization increased only for angina (men), kidney infections and urinary tract infections (men and women) and conditions related to prenatal care and delivery (women). The three groups of illness which led to the most admissions were infectious gastroenteritis and its complications, cardiac insufficiency and asthma.

CONCLUSIONS: Between 1998 and 2009, there was a substantial reduction in admissions for ambulatory care sensitive conditions in Brazil, although some illnesses presented stability or even an increase, which calls for attention from the health sector.}, } @article {pmid22325066, year = {2012}, author = {Liu, Y and Li, X and Wang, W and Li, Z and Hou, M and He, Y and Wu, W and Wang, H and Liang, H and Guo, X}, title = {Investigation of space-time clusters and geospatial hot spots for the occurrence of tuberculosis in Beijing.}, journal = {The international journal of tuberculosis and lung disease : the official journal of the International Union against Tuberculosis and Lung Disease}, volume = {16}, number = {4}, pages = {486-491}, doi = {10.5588/ijtld.11.0255}, pmid = {22325066}, issn = {1815-7920}, mesh = {Adult ; China/epidemiology ; Disease Notification ; Female ; Geographic Information Systems ; Humans ; Incidence ; Male ; Middle Aged ; Socioeconomic Factors ; Space-Time Clustering ; Tuberculosis/*epidemiology ; Young Adult ; }, abstract = {OBJECTIVE: To characterise the geographic and spatiotemporal distribution of confirmed tuberculosis (TB) cases in Beijing between 2005 and 2009.

DESIGN: The yearly notification rate maps were used to describe the distribution of confirmed adult TB patients. Spatial autocorrelation (Moran's I) and hot-spot analysis were adopted to detect the clusters and hot spots of TB.

RESULTS: The TB incidence rate (cases per 100,000 population) in Beijing increased from 29.8 in 2005 to 35.0 in 2009. The incidence rate was significantly higher in the Urban Development New District and the Ecologic Reservation Development District (>30/100,000) than in the other districts. There was a significant spatial autocorrelation throughout the city (u = 2.58, P = 0.01). Evident clusters were observed in the Capital Functional Core District and the Urban Function Extension District (G(i)* > 1).

CONCLUSION: Spatial autocorrelation and hot-spot analysis may serve as efficient tools to detect space-time clusters and geospatial hot spots of TB incidence. Between 2005 and 2009, TB incidence in Beijing showed population density and mobility-dependent and eco-social status-dependent space-time clusters and geospatial hot spots.}, } @article {pmid22319160, year = {2012}, author = {Weadick, CJ and Chang, BS}, title = {An improved likelihood ratio test for detecting site-specific functional divergence among clades of protein-coding genes.}, journal = {Molecular biology and evolution}, volume = {29}, number = {5}, pages = {1297-1300}, doi = {10.1093/molbev/msr311}, pmid = {22319160}, issn = {1537-1719}, mesh = {Animals ; Chiroptera/genetics ; *Codon ; Computer Simulation ; Databases, Genetic ; *Evolution, Molecular ; *Genes ; *Models, Genetic ; Mole Rats/genetics ; Primates/genetics ; Proteins/*genetics ; Rhodopsin/genetics ; Ribonucleases/genetics ; }, abstract = {Maximum likelihood codon substitution models have proven useful for studying when and how protein function evolves, but they have recently been criticized on a number of fronts. The strengths and weaknesses of such methods must therefore be identified and improved upon. Here, using simulations, we show that the Clade model C versus M1a test for functional divergence among clades is prone to false positives under simple evolutionary conditions. We then propose a new null model (M2a_rel) that better accounts for among-site variation in selective constraint. We show that the revised test has an improved false-positive rate and good power. Applying this test to previously analyzed data sets of primate ribonucleases and mammalian rhodopsins reveals that some conclusions may have been misled by the original method. The improved test should prove useful for identifying patterns of divergence in selective constraint among paralogous gene families and among orthologs from ecologically divergent species.}, } @article {pmid22319123, year = {2012}, author = {Bock, DG and MacIsaac, HJ and Cristescu, ME}, title = {Multilocus genetic analyses differentiate between widespread and spatially restricted cryptic species in a model ascidian.}, journal = {Proceedings. Biological sciences}, volume = {279}, number = {1737}, pages = {2377-2385}, pmid = {22319123}, issn = {1471-2954}, mesh = {Animals ; Base Sequence ; Bayes Theorem ; *Biological Evolution ; Cluster Analysis ; Computational Biology ; DNA Primers/genetics ; DNA, Mitochondrial/genetics ; *Demography ; Europe ; Genetics, Population ; Geography ; *Introduced Species ; Microsatellite Repeats/genetics ; Models, Genetic ; Molecular Sequence Data ; North America ; *Phylogeny ; Phylogeography ; *Polymorphism, Genetic ; Sequence Analysis, DNA ; Species Specificity ; Urochordata/*classification/*genetics ; }, abstract = {Elucidating the factors that shape species distributions has long been a fundamental goal in ecology and evolutionary biology. In spite of significant theoretical advancements, empirical studies of range limits have lagged behind. Specifically, little is known about how the attributes that allow species to expand their ranges and become widespread vary across phylogenies. Here, we studied the ascidian Botryllus schlosseri, a worldwide invasive species that is also characterized by marked genetic subdivision. Our study includes phylogenetic and population genetic data based on mitochondrial and nuclear genes, as well as polymorphic microsatellites for B. schlosseri colonies sampled from the southern and northern coasts of Europe and the eastern and western coasts of North America. We demonstrate that this well-known model organism comprises three highly divergent and probably reproductively isolated cryptic species (A, D and E), with two more (B and C) being suggested by data retrieved from GenBank. Among these, species A, recovered in all of the surveyed regions, is by far the most common and widespread. By contrast, species B-E, occurring mostly in sites from northern Europe, are considerably more geographically restricted. These findings, along with inferences made on transport opportunity, suggest that divergent evolutionary histories promoted differences in invasive potential between B. schlosseri sibling species, indicating that attributes that facilitate dramatic shifts in range limits can evolve more easily and frequently than previously thought. We propose environmental disturbance as a selective force that could have shaped the evolution of invasiveness in the B. schlosseri complex.}, } @article {pmid22317411, year = {2012}, author = {Montague, E and Asan, O}, title = {Considering social ergonomics: the effects of HIT on interpersonal relationships between patients and clinicians.}, journal = {Work (Reading, Mass.)}, volume = {41 Suppl 1}, number = {Suppl 1}, pages = {4479-4483}, pmid = {22317411}, issn = {1875-9270}, support = {KL2 RR025012/RR/NCRR NIH HHS/United States ; UL1 RR025011/RR/NCRR NIH HHS/United States ; }, mesh = {Adolescent ; Adult ; Aged ; *Electronic Health Records ; Ergonomics ; Family Practice ; Female ; Humans ; Male ; Medical Informatics ; Middle Aged ; *Patient Satisfaction ; *Physician-Patient Relations ; Time Factors ; Young Adult ; }, abstract = {This study explored physicians' interactions with EHRs to understand the qualities that contribute to patient satisfaction with their use of the technologies and patient satisfaction with physician. Video-taped observations of 100 medical consultations were used to distinguish interaction patterns between physicians and EHRs. Quantified observational methods were used to contribute to ecological validity. Ten primary care physicians and 100 patients from five clinics participated in the study. Visits were videotaped and coded using an objective coding methodology to understand how physicians interacted with electronic health records. Results indicate, a variety of EHR interaction styles may be effective in providing patient-centered care.}, } @article {pmid22312865, year = {2011}, author = {Shipov, AA and Myznikov, IL}, title = {[Journal "Aerospace and Ecological Medicine" in the content of international science data bases. Aerospace medicine].}, journal = {Aviakosmicheskaia i ekologicheskaia meditsina = Aerospace and environmental medicine}, volume = {45}, number = {5}, pages = {59-60}, pmid = {22312865}, issn = {0233-528X}, mesh = {Aerospace Medicine/*trends ; Bibliographies as Topic ; Databases, Bibliographic/*statistics & numerical data ; Humans ; }, } @article {pmid22312116, year = {2012}, author = {Egan, AN and Schlueter, J and Spooner, DM}, title = {Applications of next-generation sequencing in plant biology.}, journal = {American journal of botany}, volume = {99}, number = {2}, pages = {175-185}, doi = {10.3732/ajb.1200020}, pmid = {22312116}, issn = {1537-2197}, mesh = {Chromosomes, Plant/genetics ; Computational Biology ; DNA, Plant/genetics ; Databases, Genetic ; Ecosystem ; *Genome, Plant ; Hybridization, Genetic ; Magnoliopsida/classification/*genetics ; Microsatellite Repeats ; Phylogeny ; Polymorphism, Single Nucleotide ; Polyploidy ; Sensitivity and Specificity ; Sequence Analysis, DNA/*methods ; Sequence Analysis, RNA/*methods ; }, abstract = {The last several years have seen revolutionary advances in DNA sequencing technologies with the advent of next-generation sequencing (NGS) techniques. NGS methods now allow millions of bases to be sequenced in one round, at a fraction of the cost relative to traditional Sanger sequencing. As costs and capabilities of these technologies continue to improve, we are only beginning to see the possibilities of NGS platforms, which are developing in parallel with online availability of a wide range of biological data sets and scientific publications and allowing us to address a variety of questions not possible before. As techniques and data sets continue to improve and grow, we are rapidly moving to the point where every organism, not just select "model organisms", is open to the power of NGS. This volume presents a brief synopsis of NGS technologies and the development of exemplary applications of such methods in the fields of molecular marker development, hybridization and introgression, transcriptome investigations, phylogenetic and ecological studies, polyploid genetics, and applications for large genebank collections.}, } @article {pmid22303677, year = {2011}, author = {Chen, ZZ and Cai, WG and Xu, SN and Huang, ZR and Qiu, YS}, title = {[Risk assessment of coastal ecosystem in Beibu Gulf, Guangxi of South China].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {22}, number = {11}, pages = {2977-2986}, pmid = {22303677}, issn = {1001-9332}, mesh = {Biodiversity ; China ; *Ecosystem ; *Environmental Monitoring ; Geographic Information Systems ; Oceans and Seas ; Risk Assessment ; Seawater/*analysis ; Water Pollution/*analysis ; }, abstract = {Based on the marine ecological investigation in the coastal area of Beibu Gulf, Guangxi in September 2009, a GIS-based evaluation was conducted on the present status of ecological environment quality, including seawater quality, nutrient level, biomass, primary productivity, biodiversity, and ecological buffer capacity, in the area in autumn, and the integrated ecological risk index (ERI) was adopted to assess the risk of the coastal ecosystem in the Gulf. In September 2009, the study area had a better ecological environment quality. Most of the risk indicators were at medium or lower level, and the total area was overall at low ecological risk level. The ERI showed that there was an obvious spatial heterogeneity in the distribution of the ecological risk. The nearer to the harbors, the higher the risk was.}, } @article {pmid22297926, year = {2012}, author = {Zhang, W and Wang, K and Chen, H and He, X and Zhang, J}, title = {Ancillary information improves kriging on soil organic carbon data for a typical karst peak cluster depression landscape.}, journal = {Journal of the science of food and agriculture}, volume = {92}, number = {5}, pages = {1094-1102}, doi = {10.1002/jsfa.5593}, pmid = {22297926}, issn = {1097-0010}, mesh = {Agriculture ; Carbon/*analysis ; China ; *Data Interpretation, Statistical ; Ecosystem ; *Geological Phenomena ; *Plants ; Regression Analysis ; Soil/*chemistry ; }, abstract = {BACKGROUND: Soil carbon management at landscape scale requires reliable information on the spatial distribution of soil organic carbon (SOC). However, how to improve the accuracy of spatial prediction is not well addressed in the karst region of southwestern China. This study evaluates the performance of univariate kriging (ordinary kriging (OK)) and hybrid kriging (co-kriging (CK), regression kriging (RK) and residual maximum likelihood (REML)) in mapping the spatial distribution of SOC at a depth of 0-15 cm. Terrain attributes and the normalised difference vegetation index (NDVI) were used as ancillary variables.

RESULTS: The distribution of SOC was significantly related to NDVI and terrain attributes. Furthermore, geostatistical analyses reflected a moderately structured spatial correlation of SOC. Regression analyses identified the NDVI and slope as the best predictors for describing the spatial pattern of SOC. Combined with NDVI and slope gradient, REML and RK performed better in increasing map prediction accuracy and decreasing the soothing effect of kriging.

CONCLUSION: The spatial pattern of SOC was controlled by topography and cultivation activity. The predictive abilities of OK and CK were limited. Combined with the auxiliary variables, REML and RK can improve the prediction accuracy. This study is beneficial for the further research of precise SOC management in the typical karst landscape.}, } @article {pmid22296658, year = {2012}, author = {, and Abreu, AG and Albaina, A and Alpermann, TJ and Apkenas, VE and Bankhead-Dronnet, S and Bergek, S and Berumen, ML and Cho, CH and Clobert, J and Coulon, A and DE Feraudy, D and Estonba, A and Hankeln, T and Hochkirch, A and Hsu, TW and Huang, TJ and Irigoien, X and Iriondo, M and Kay, KM and Kinitz, T and Kothera, L and LE Hénanff, M and Lieutier, F and Lourdais, O and Macrini, CM and Manzano, C and Martin, C and Morris, VR and Nanninga, G and Pardo, MA and Plieske, J and Pointeau, S and Prestegaard, T and Quack, M and Richard, M and Savage, HM and Schwarcz, KD and Shade, J and Simms, EL and Solferini, VN and Stevens, VM and Veith, M and Wen, MJ and Wicker, F and Yost, JM and Zarraonaindia, I}, title = {Permanent genetic resources added to Molecular Ecology Resources Database 1 October 2011-30 November 2011.}, journal = {Molecular ecology resources}, volume = {12}, number = {2}, pages = {374-376}, doi = {10.1111/j.1755-0998.2011.03109.x}, pmid = {22296658}, issn = {1755-0998}, support = {CC999999//Intramural CDC HHS/United States ; }, mesh = {Animals ; Arthropods/genetics ; *Databases, Genetic ; Microsatellite Repeats ; Molecular Sequence Data ; Plants/genetics ; Vertebrates/genetics ; }, abstract = {This article documents the addition of 139 microsatellite marker loci and 90 pairs of single-nucleotide polymorphism sequencing primers to the Molecular Ecology Resources Database. Loci were developed for the following species: Aglaoctenus lagotis, Costus pulverulentus, Costus scaber, Culex pipiens, Dascyllus marginatus, Lupinus nanus Benth, Phloeomyzus passerini, Podarcis muralis, Rhododendron rubropilosum Hayata var. taiwanalpinum and Zoarces viviparus. These loci were cross-tested on the following species: Culex quinquefasciatus, Rhododendron pseudochrysanthum Hay. ssp. morii (Hay.) Yamazaki and R. pseudochrysanthum Hayata. This article also documents the addition of 48 sequencing primer pairs and 90 allele-specific primers for Engraulis encrasicolus.}, } @article {pmid22291572, year = {2012}, author = {Moreno-Mateos, D and Power, ME and Comín, FA and Yockteng, R}, title = {Structural and functional loss in restored wetland ecosystems.}, journal = {PLoS biology}, volume = {10}, number = {1}, pages = {e1001247}, pmid = {22291572}, issn = {1545-7885}, mesh = {Animals ; Australia ; Biodiversity ; Carbon/chemistry ; China ; Climate ; Conservation of Natural Resources/*trends ; Databases, Bibliographic ; Environmental Restoration and Remediation/methods/*trends ; Europe ; North America ; Plants ; Soil/chemistry ; Tidal Waves ; Vertebrates ; Water Cycle ; *Wetlands ; }, abstract = {Wetlands are among the most productive and economically valuable ecosystems in the world. However, because of human activities, over half of the wetland ecosystems existing in North America, Europe, Australia, and China in the early 20th century have been lost. Ecological restoration to recover critical ecosystem services has been widely attempted, but the degree of actual recovery of ecosystem functioning and structure from these efforts remains uncertain. Our results from a meta-analysis of 621 wetland sites from throughout the world show that even a century after restoration efforts, biological structure (driven mostly by plant assemblages), and biogeochemical functioning (driven primarily by the storage of carbon in wetland soils), remained on average 26% and 23% lower, respectively, than in reference sites. Either recovery has been very slow, or postdisturbance systems have moved towards alternative states that differ from reference conditions. We also found significant effects of environmental settings on the rate and degree of recovery. Large wetland areas (>100 ha) and wetlands restored in warm (temperate and tropical) climates recovered more rapidly than smaller wetlands and wetlands restored in cold climates. Also, wetlands experiencing more (riverine and tidal) hydrologic exchange recovered more rapidly than depressional wetlands. Restoration performance is limited: current restoration practice fails to recover original levels of wetland ecosystem functions, even after many decades. If restoration as currently practiced is used to justify further degradation, global loss of wetland ecosystem function and structure will spread.}, } @article {pmid22285560, year = {2012}, author = {Niknejad, A and Comte, A and Parmentier, G and Roux, J and Bastian, FB and Robinson-Rechavi, M}, title = {vHOG, a multispecies vertebrate ontology of homologous organs groups.}, journal = {Bioinformatics (Oxford, England)}, volume = {28}, number = {7}, pages = {1017-1020}, pmid = {22285560}, issn = {1367-4811}, mesh = {Animals ; Biological Evolution ; Computational Biology/methods ; *Databases, Factual ; Gene Expression ; *Terminology as Topic ; Vertebrates/*anatomy & histology/classification ; Vocabulary, Controlled ; }, abstract = {MOTIVATION: Most anatomical ontologies are species-specific, whereas a framework for comparative studies is needed. We describe the vertebrate Homologous Organs Groups ontology, vHOG, used to compare expression patterns between species.

RESULTS: vHOG is a multispecies anatomical ontology for the vertebrate lineage. It is based on the HOGs used in the Bgee database of gene expression evolution. vHOG version 1.4 includes 1184 terms, follows OBO principles and is based on the Common Anatomy Reference Ontology (CARO). vHOG only describes structures with historical homology relations between model vertebrate species. The mapping to species-specific anatomical ontologies is provided as a separate file, so that no homology hypothesis is stated within the ontology itself. Each mapping has been manually reviewed, and we provide support codes and references when available.

vHOG is available from the Bgee download site (http://bgee.unil.ch/), as well as from the OBO Foundry and the NCBO Bioportal websites.

CONTACT: bgee@isb-sib.ch; frederic.bastian@unil.ch.}, } @article {pmid22279593, year = {2012}, author = {Sorani, MD}, title = {Informatics technology mimics ecology: dense, mutualistic collaboration networks are associated with higher publication rates.}, journal = {PloS one}, volume = {7}, number = {1}, pages = {e30463}, pmid = {22279593}, issn = {1932-6203}, mesh = {Animals ; Biodiversity ; Computational Biology/methods/statistics & numerical data/trends ; Ecology/*methods/statistics & numerical data/trends ; Humans ; Medical Informatics/*methods/statistics & numerical data/trends ; *Models, Theoretical ; *Programming Languages ; PubMed/statistics & numerical data ; Publications/statistics & numerical data/trends ; Technology Transfer ; }, abstract = {Information technology (IT) adoption enables biomedical research. Publications are an accepted measure of research output, and network models can describe the collaborative nature of publication. In particular, ecological networks can serve as analogies for publication and technology adoption. We constructed network models of adoption of bioinformatics programming languages and health IT (HIT) from the literature.We selected seven programming languages and four types of HIT. We performed PubMed searches to identify publications since 2001. We calculated summary statistics and analyzed spatiotemporal relationships. Then, we assessed ecological models of specialization, cooperativity, competition, evolution, biodiversity, and stability associated with publications.Adoption of HIT has been variable, while scripting languages have experienced rapid adoption. Hospital systems had the largest HIT research corpus, while Perl had the largest language corpus. Scripting languages represented the largest connected network components. The relationship between edges and nodes was linear, though Bioconductor had more edges than expected and Perl had fewer. Spatiotemporal relationships were weak. Most languages shared a bioinformatics specialization and appeared mutualistic or competitive. HIT specializations varied. Specialization was highest for Bioconductor and radiology systems. Specialization and cooperativity were positively correlated among languages but negatively correlated among HIT. Rates of language evolution were similar. Biodiversity among languages grew in the first half of the decade and stabilized, while diversity among HIT was variable but flat. Compared with publications in 2001, correlation with publications one year later was positive while correlation after ten years was weak and negative.Adoption of new technologies can be unpredictable. Spatiotemporal relationships facilitate adoption but are not sufficient. As with ecosystems, dense, mutualistic, specialized co-habitation is associated with faster growth. There are rapidly changing trends in external technological and macroeconomic influences. We propose that a better understanding of how technologies are adopted can facilitate their development.}, } @article {pmid22278502, year = {2012}, author = {Dunlop, RA and Noad, MJ and Cato, DH}, title = {Behavioral-response studies: problems with statistical power.}, journal = {Advances in experimental medicine and biology}, volume = {730}, number = {}, pages = {293-297}, doi = {10.1007/978-1-4419-7311-5_65}, pmid = {22278502}, issn = {0065-2598}, mesh = {Animal Communication ; Animals ; *Behavior, Animal ; Biomedical Research/methods ; *Data Interpretation, Statistical ; Humpback Whale/physiology ; Models, Biological ; Research Design/*statistics & numerical data ; }, } @article {pmid22277925, year = {2012}, author = {Lenz, PH and Unal, E and Hassett, RP and Smith, CM and Bucklin, A and Christie, AE and Towle, DW}, title = {Functional genomics resources for the North Atlantic copepod, Calanus finmarchicus: EST database and physiological microarray.}, journal = {Comparative biochemistry and physiology. Part D, Genomics & proteomics}, volume = {7}, number = {2}, pages = {110-123}, pmid = {22277925}, issn = {1878-0407}, support = {P20 RR016463-10/RR/NCRR NIH HHS/United States ; P20 RR016463/RR/NCRR NIH HHS/United States ; P20 RR016463-09/RR/NCRR NIH HHS/United States ; P20 RR016463-08/RR/NCRR NIH HHS/United States ; P20 RR016463-05/RR/NCRR NIH HHS/United States ; }, mesh = {Animals ; Atlantic Ocean ; Copepoda/genetics/metabolism/*physiology ; *Databases, Genetic ; *Expressed Sequence Tags ; Female ; Gene Expression Profiling ; Gene Library ; Genes/genetics ; Genomics/*methods ; Metabolic Networks and Pathways ; Oligonucleotide Array Sequence Analysis ; Transcriptome ; }, abstract = {The copepod, Calanus finmarchicus is a keystone species for the North Atlantic. Because of recent changes in the geographic distribution of this species, there are questions as to how this organism responds physiologically to environmental cues. Molecular techniques allow for examination and new understanding of these physiological changes. Here, we describe the development of a microarray for high-throughput studies of the physiological ecology of C. finmarchicus. An EST database was generated for this species using a normalized cDNA library derived from adult and sub-adult individuals. Sequence data were clustered into contigs and annotated using Blastx. Target transcripts were selected, and unique, 50 base-pair, oligomer probes were generated for 995 genes. Blast2GO processing provided detailed information on gene function. The selected targets included broad representation of biological processes, cellular components, and molecular functions. The microarray was tested in two sets of comparisons: adult females maintained at different food concentrations and field-caught sub-adults showing differences in lipid storage. Up-regulated and down-regulated transcripts were identified for both comparisons. Only a small subset of the genes up-regulated in low food individuals were also up-regulated in lipid-poor animals; no overlap was seen between the genes down-regulated in the two comparisons.}, } @article {pmid22276693, year = {2012}, author = {Hosoya, T and Hirokawa, T and Takagi, M and Shin-ya, K}, title = {Trichostatin analogues JBIR-109, JBIR-110, and JBIR-111 from the marine sponge-derived Streptomyces sp. RM72.}, journal = {Journal of natural products}, volume = {75}, number = {2}, pages = {285-289}, doi = {10.1021/np200843k}, pmid = {22276693}, issn = {1520-6025}, mesh = {Animals ; Histone Deacetylase Inhibitors/chemistry/*isolation & purification/pharmacology ; Humans ; Hydroxamic Acids ; Japan ; Marine Biology ; Molecular Structure ; Nuclear Magnetic Resonance, Biomolecular ; Porifera/*microbiology ; Quantitative Structure-Activity Relationship ; Streptomyces/*chemistry ; }, abstract = {Three new trichostatin analogues, JBIR-109 (1), JBIR-110 (2), and JBIR-111 (3), were isolated from the culture of the marine sponge-derived Streptomyces sp. strain RM72, together with trichostatin A (4) and trichostatic acid (5). The planar structures of 1-3 were determined on the basis of extensive NMR and MS analyses. In addition, the absolute configurations of the amino acid residues were determined by Marfey's method. The histone deacetylase inhibitory activities of 1-5 were examined, and their structure-activity relationships are discussed.}, } @article {pmid22275765, year = {2012}, author = {Liu, Y and Moskwa, NL and Goffinet, B}, title = {Development of eight mitochondrial markers for Funariaceae (Musci) and their amplification success in other mosses.}, journal = {American journal of botany}, volume = {99}, number = {2}, pages = {e62-5}, doi = {10.3732/ajb.1100402}, pmid = {22275765}, issn = {1537-2197}, mesh = {Base Sequence ; Bryophyta/classification/*genetics ; DNA Primers/genetics ; DNA, Mitochondrial/*genetics ; DNA, Plant/genetics ; Databases, Genetic ; Genetic Loci ; Genetic Markers ; INDEL Mutation ; Mitochondria/*genetics ; Phylogeny ; Polymerase Chain Reaction ; Sequence Alignment ; Sequence Analysis, DNA ; }, abstract = {PREMISE OF THE STUDY: In comparison to the wide use of chloroplast markers, few mitochondrial markers are available for phylogenetic studies in bryophytes. We investigated the phylogenetic suitability of several mtDNA markers within the Funariaceae and across mosses.

METHODS AND RESULTS: By comparing mitochondrial genomes of two mosses, eight regions with higher substitution rates were identified and sequenced for three species in the Funariaceae and one outgroup taxon. Variations in the substitution rate of these new loci were compared to previously used markers. Thirty-four samples representing all major moss lineages were targeted to assess the universality of the newly designed primers.

CONCLUSIONS: The new markers provided similar or more sequence variations in Funariaceae compared to previously developed mtDNA markers. Five out of eight loci were amplified in 70% of other taxa, indicating that these markers may be suitable for phylogenetic studies in other moss lineages.}, } @article {pmid22272326, year = {2012}, author = {Claisse, JT and Pondella, DJ and Williams, JP and Sadd, J}, title = {Using GIS mapping of the extent of nearshore rocky reefs to estimate the abundance and reproductive output of important fishery species.}, journal = {PloS one}, volume = {7}, number = {1}, pages = {e30290}, pmid = {22272326}, issn = {1932-6203}, mesh = {Animals ; Bass/growth & development ; Bays ; Biomass ; California ; Conservation of Natural Resources/methods/statistics & numerical data ; Ecosystem ; Fisheries/*statistics & numerical data ; Fishes/classification/*growth & development ; *Geographic Information Systems ; Geology ; Perciformes/growth & development ; Population Density ; Population Dynamics ; Reproduction ; *Software ; }, abstract = {Kelp Bass (Paralabrax clathratus) and California Sheephead (Semicossyphus pulcher) are economically and ecologically valuable rocky reef fishes in southern California, making them likely indicator species for evaluating resource management actions. Multiple spatial datasets, aerial and satellite photography, underwater observations and expert judgment were used to produce a comprehensive map of nearshore natural rocky reef habitat for the Santa Monica Bay region (California, USA). It was then used to examine the relative contribution of individual reefs to a regional estimate of abundance and reproductive potential of the focal species. For the reefs surveyed for fishes (i.e. 18 out of the 22 in the region, comprising 82% the natural rocky reef habitat <30 m depth, with a total area of 1850 ha), total abundance and annual egg production of California Sheephead were 451 thousand fish (95% CI: 369 to 533 thousand) and 203 billion eggs (95% CI: 135 to 272 billion). For Kelp Bass, estimates were 805 thousand fish (95% CI: 669 to 941 thousand) and 512 billion eggs (95% CI: 414 to 610 billion). Size structure and reef area were key factors in reef-specific contributions to the regional egg production. The size structures of both species illustrated impacts from fishing, and results demonstrate the potential that relatively small increases in the proportion of large females on larger reefs could have on regional egg production. For California Sheephead, a substantial proportion of the regional egg production estimate (>30%) was produced from a relatively small proportion of the regional reef area (c. 10%). Natural nearshore rocky reefs make up only 11% of the area in the newly designated MPAs in this region, but results provide some optimism that regional fisheries could benefit through an increase in overall reproductive output, if adequate increases in size structure of targeted species are realized.}, } @article {pmid22271559, year = {2012}, author = {Kamilar, JM and Muldoon, KM and Lehman, SM and Herrera, JP}, title = {Testing Bergmann's rule and the resource seasonality hypothesis in Malagasy primates using GIS-based climate data.}, journal = {American journal of physical anthropology}, volume = {147}, number = {3}, pages = {401-408}, doi = {10.1002/ajpa.22002}, pmid = {22271559}, issn = {1096-8644}, mesh = {Animals ; Anthropology, Physical ; Body Size/*physiology ; Climate ; Ecosystem ; Female ; Geographic Information Systems ; Lemur/anatomy & histology/*physiology ; Madagascar ; Male ; *Models, Biological ; Phylogeny ; Principal Component Analysis ; Regression Analysis ; }, abstract = {We tested four major hypotheses on the ecological aspects of body mass variation in extant Malagasy strepsirrhines: thermoregulation, resource seasonality/scarcity, resource quality, and primary productivity. These biogeographic hypotheses focus on the ecological aspects of body mass variation, largely ignoring the role of phylogeny for explaining body mass variation within lineages. We tested the independent effects of climate and resource-related variables on variation in body mass among Malagasy primates using recently developed comparative methods that account for phylogenetic history and spatial autocorrelation. We extracted data on lemur body mass and climate variables for a total of 43 species from 39 sites. Climatic data were obtained from the WorldClim database, which is based on climate data from weather stations compiled around the world. Using generalized linear models that incorporate parameters to account for phylogenetic and spatial autocorrelation, we found that diet and climate variables were weak predictors of lemur body mass. Moreover, there was a strong phylogenetic effect relative to the effects of space on lemur body mass in all models. Thus, we failed to find support for any of the four hypotheses on patterns of geography and body mass in extant strepsirrhines. Our results indicate that body mass has been conserved since early in the evolutionary history of each genus, while species diversified into different environmental niches. Our findings are in contrast to some previous studies that have suggested resource and climate related effects on body mass, though these studies have examined this question at different taxonomic and/or geographic scales.}, } @article {pmid22268720, year = {2012}, author = {Jennions, MD and Kokko, H and Klug, H}, title = {The opportunity to be misled in studies of sexual selection.}, journal = {Journal of evolutionary biology}, volume = {25}, number = {3}, pages = {591-598}, doi = {10.1111/j.1420-9101.2011.02451.x}, pmid = {22268720}, issn = {1420-9101}, mesh = {Animals ; Data Interpretation, Statistical ; Female ; Male ; Mating Preference, Animal/*physiology ; *Models, Biological ; Sample Size ; *Sex Ratio ; *Stochastic Processes ; }, abstract = {It is a challenge to measure sexual selection because both stochastic events (chance) and deterministic factors (selection) generate variation in individuals' reproductive success. Most researchers realize that random events ('noise') make it difficult to detect a relationship between a trait and mating success (i.e. the presence of sexual selection). There is, however, less appreciation of the dangers that arise if stochastic events vary systematically. Systematic variation makes variance-based approaches to measuring the role of selection problematic. This is why measuring the opportunity for sexual selection (I(s) and I(mates)) is so vulnerable to misinterpretation. Although I(s) does not measure actual sexual selection (because it includes stochastic variation in mating/fertilization success) it is often implicitly assumed that it will be correlated with the actual strength of sexual selection. The hidden assumption is that random noise is randomly distributed across populations, species or the sexes. Here we present a simple numerical example showing why this practice is worrisome. Specifically, we show that chance variation in mating success is higher when there are fewer potential mates per individual of the focal sex [i.e. when the operational sex ratio (OSR), is more biased]. This will lead to the OSR covarying with I(s) even when the strength of sexual selection is unaffected by the OSR. This can generate false confidence in identifying factors that determine variation in the strength of sexual selection. We emphasize that in nature, even when sexual selection is strong, chance variation in mating success is still inevitable because the number of mates per individual is a discrete number. We hope that our worked example will clarify a recent debate about how best to measure sexual selection.}, } @article {pmid22268676, year = {2012}, author = {Wilson, JS and Forister, ML and Dyer, LA and O'Connor, JM and Burls, K and Feldman, CR and Jaramillo, MA and Miller, JS and Rodríguez-Castañeda, G and Tepe, EJ and Whitfield, JB and Young, B}, title = {Host conservatism, host shifts and diversification across three trophic levels in two Neotropical forests.}, journal = {Journal of evolutionary biology}, volume = {25}, number = {3}, pages = {532-546}, doi = {10.1111/j.1420-9101.2011.02446.x}, pmid = {22268676}, issn = {1420-9101}, mesh = {Animals ; Base Sequence ; Bayes Theorem ; Computational Biology ; Costa Rica ; DNA, Mitochondrial/genetics ; Ecuador ; Evolution, Molecular ; *Food Chain ; Genetic Speciation ; Host-Pathogen Interactions/*genetics/physiology ; Larva/parasitology/physiology ; Models, Genetic ; Molecular Sequence Data ; Moths/classification/*genetics/*parasitology/physiology ; Phylogeny ; Piper/*genetics ; Sequence Analysis, DNA ; *Trees ; Wasps/*genetics/physiology ; }, abstract = {Host-parasite systems have been models for understanding the connection between shifts in resource use and diversification. Despite theoretical expectations, ambiguity remains regarding the frequency and importance of host switches as drivers of speciation in herbivorous insects and their parasitoids. We examine phylogenetic patterns with multiple genetic markers across three trophic levels using a diverse lineage of geometrid moths (Eois), specialist braconid parasitoids (Parapanteles) and plants in the genus Piper. Host-parasite associations are mapped onto phylogenies, and levels of cospeciation are assessed. We find nonrandom patterns of host use within both the moth and wasp phylogenies. The moth-plant associations in particular are characterized by small radiations of moths associated with unique host plants in the same geographic area (i.e. closely related moths using the same host plant species). We suggest a model of diversification that emphasizes an interplay of factors including host shifts, vicariance and adaptation to intraspecific variation within hosts.}, } @article {pmid22268225, year = {2012}, author = {Grover, CE and Salmon, A and Wendel, JF}, title = {Targeted sequence capture as a powerful tool for evolutionary analysis.}, journal = {American journal of botany}, volume = {99}, number = {2}, pages = {312-319}, doi = {10.3732/ajb.1100323}, pmid = {22268225}, issn = {1537-2197}, mesh = {*Base Sequence ; Computational Biology/methods ; Ecosystem ; Epigenesis, Genetic ; Epigenomics/*methods ; *Evolution, Molecular ; Expressed Sequence Tags ; *Gene Expression Regulation, Plant ; Gene Flow ; *Genes, Plant ; Genetic Loci ; Genetic Variation ; Phylogeny ; Phylogeography ; }, abstract = {Next-generation sequencing technologies (NGS) have revolutionized biological research by significantly increasing data generation while simultaneously decreasing the time to data output. For many ecologists and evolutionary biologists, the research opportunities afforded by NGS are substantial; even for taxa lacking genomic resources, large-scale genome-level questions can now be addressed, opening up many new avenues of research. While rapid and massive sequencing afforded by NGS increases the scope and scale of many research objectives, whole genome sequencing is often unwarranted and unnecessarily complex for specific research questions. Recently developed targeted sequence enrichment, coupled with NGS, represents a beneficial strategy for enhancing data generation to answer questions in ecology and evolutionary biology. This marriage of technologies offers researchers a simple method to isolate and analyze a few to hundreds, or even thousands, of genes or genomic regions from few to many samples in a relatively efficient and effective manner. These strategies can be applied to questions at both the infra- and interspecific levels, including those involving parentage, gene flow, divergence, phylogenetics, reticulate evolution, and many more. Here we provide a brief overview of targeted sequence enrichment, and emphasize the power of this technology to increase our ability to address a wide range of questions of interest to ecologists and evolutionary biologists, particularly for those working with taxa for which few genomic resources are available.}, } @article {pmid22257507, year = {2012}, author = {Zhao, H and Xia, B and Fan, C and Zhao, P and Shen, S}, title = {Human health risk from soil heavy metal contamination under different land uses near Dabaoshan Mine, Southern China.}, journal = {The Science of the total environment}, volume = {417-418}, number = {}, pages = {45-54}, doi = {10.1016/j.scitotenv.2011.12.047}, pmid = {22257507}, issn = {1879-1026}, mesh = {China ; Computer Simulation ; Environmental Exposure/analysis ; Geographic Information Systems ; Humans ; Metals, Heavy/*analysis/metabolism ; Mining ; Oryza/*chemistry/metabolism ; Soil Pollutants/*analysis/metabolism ; Stochastic Processes ; Tropical Climate ; Vegetables/*chemistry/metabolism ; }, abstract = {Soil heavy metal contamination is a major environmental concern, and the ecological risk associated with heavy metals is increasing. In this paper, we investigated heavy metal contamination near Dabaoshan Mine by: using sequential indicator simulation to delineate the spatial patterns of soil data; fitting multiple linear regression models for heavy metal uptake by crops; interpreting land uses from remote sensing images and integrating the spatial patterns, uptake models and land uses into a dose-response model for human health risks from heavy metals. The areas with elevated soil heavy metal concentrations are mainly located at the Dabaoshan Mine site and in the watershed basins of the Hengshi, Tielong and Chuandu rivers. The average concentrations of Cu, Zn, Cd and Pb in soil in the study area are all above the natural soil background levels, but Cd is the major contributor to human health risk in the area. Areas of low soil pH are also found throughout the watershed basins of the Hengshi, Tielong and Chuandu rivers. Of the different land use types in the study area, agricultural and residential land uses have the highest human health risk because ingestion is the dominant exposure pathway for heavy metals. The spatial patterns of the heavy metal concentrations and soil pH indicate that the areas with the highest human health risk regions do not directly coincide with the areas of highest heavy metal concentrations, but do coincide with the areas of lower soil pH. The contamination with high concentrations of heavy metals provides the risk source, but the combination of high heavy metal concentrations, low pH and agricultural or residential land use is required for human health risks to be present. The spatial pattern of the hazard quotients indicates that Cd is the most important pollutant contributing to the human health risk.}, } @article {pmid22255662, year = {2011}, author = {Boissy, P and Brière, S and Hamel, M and Jog, M and Speechley, M and Karelis, A and Frank, J and Vincent, C and Edwards, R and Duval, C and , }, title = {Wireless inertial measurement unit with GPS (WIMU-GPS)--wearable monitoring platform for ecological assessment of lifespace and mobility in aging and disease.}, journal = {Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference}, volume = {2011}, number = {}, pages = {5815-5819}, doi = {10.1109/IEMBS.2011.6091439}, pmid = {22255662}, issn = {2694-0604}, support = {//Canadian Institutes of Health Research/Canada ; }, mesh = {*Acceleration ; Actigraphy/*instrumentation ; Aged ; Aged, 80 and over ; *Cell Phone ; *Ecosystem ; Geographic Information Systems/*instrumentation ; Humans ; Male ; Monitoring, Ambulatory/*instrumentation ; Remote Sensing Technology/*instrumentation ; }, abstract = {This paper proposes an innovative ambulatory mobility and activity monitoring approach based on a wearable datalogging platform that combines inertial sensing with GPS tracking to assess the lifespace and mobility profile of individuals in their home and community environments. The components, I/O architecture, sensors and functions of the WIMU-GPS are presented. Outcome variables that can be measured with it are described and illustrated. Data on the power usage, operating autonomy of the WIMU-GPS and the GPS tracking performances and time to first fix of the unit are presented. The study of lifespace and mobility with the WIMU-GPS can potentially provide unique insights into intrapersonal and environmental factors contributing to mobility restriction. On-going studies are underway to establish the validity and reliability of the WIMU-GPS in characterizing the lifespace and mobility profile of older adults.}, } @article {pmid22254107, year = {2011}, author = {Barclay, AW and Brand-Miller, J}, title = {The Australian paradox: a substantial decline in sugars intake over the same timeframe that overweight and obesity have increased.}, journal = {Nutrients}, volume = {3}, number = {4}, pages = {491-504}, pmid = {22254107}, issn = {2072-6643}, mesh = {Adolescent ; Adult ; Australia/epidemiology ; Beverages ; Carbonated Beverages ; Child ; Child, Preschool ; Dietary Sucrose/*administration & dosage ; Female ; Fruit ; Humans ; MEDLINE ; Male ; Obesity/*epidemiology ; Overweight/*epidemiology ; United Kingdom/epidemiology ; United States/epidemiology ; }, abstract = {Ecological research from the USA has demonstrated a positive relationship between sugars consumption and prevalence of obesity; however, the relationship in other nations is not well described. The aim of this study was to analyze the trends in obesity and sugar consumption in Australia over the past 30 years and to compare and contrast obesity trends and sugar consumption patterns in Australia with the UK and USA. Data on consumption of sugar in Australia, the UK and USA were obtained from the Food and Agriculture Organization for the years 1980-2003. The prevalence of obesity has increased 3 fold in Australians since 1980. In Australia, the UK and USA, per capita consumption of refined sucrose decreased by 23%, 10% and 20% respectively from 1980 to 2003. When all sources of nutritive sweeteners, including high fructose corn syrups, were considered, per capita consumption decreased in Australia (-16%) and the UK (-5%), but increased in the USA (+23%). In Australia, there was a reduction in sales of nutritively sweetened beverages by 64 million liters from 2002 to 2006 and a reduction in percentage of children consuming sugar-sweetened beverages between 1995 and 2007. The findings confirm an "Australian Paradox"--a substantial decline in refined sugars intake over the same timeframe that obesity has increased. The implication is that efforts to reduce sugar intake may reduce consumption but may not reduce the prevalence of obesity.}, } @article {pmid22253877, year = {2012}, author = {Yergeau, E and Sanschagrin, S and Beaumier, D and Greer, CW}, title = {Metagenomic analysis of the bioremediation of diesel-contaminated Canadian high arctic soils.}, journal = {PloS one}, volume = {7}, number = {1}, pages = {e30058}, pmid = {22253877}, issn = {1932-6203}, mesh = {Arctic Regions ; Bacteria/classification/genetics ; Base Sequence ; Biodegradation, Environmental ; Canada ; Databases, Genetic ; Dioxygenases/genetics ; Environmental Pollution/*analysis ; Gasoline/*microbiology ; Gene Expression Regulation, Bacterial ; Genes, Bacterial/genetics ; Humans ; Hydrocarbons/metabolism ; Metagenomics/*methods ; Mixed Function Oxygenases/genetics ; Real-Time Polymerase Chain Reaction ; Sequence Analysis, DNA ; *Soil Microbiology ; Soil Pollutants/*analysis ; }, abstract = {As human activity in the Arctic increases, so does the risk of hydrocarbon pollution events. On site bioremediation of contaminated soil is the only feasible clean up solution in these remote areas, but degradation rates vary widely between bioremediation treatments. Most previous studies have focused on the feasibility of on site clean-up and very little attention has been given to the microbial and functional communities involved and their ecology. Here, we ask the question: which microorganisms and functional genes are abundant and active during hydrocarbon degradation at cold temperature? To answer this question, we sequenced the soil metagenome of an ongoing bioremediation project in Alert, Canada through a time course. We also used reverse-transcriptase real-time PCR (RT-qPCR) to quantify the expression of several hydrocarbon-degrading genes. Pseudomonas species appeared as the most abundant organisms in Alert soils right after contamination with diesel and excavation (t = 0) and one month after the start of the bioremediation treatment (t = 1m), when degradation rates were at their highest, but decreased after one year (t = 1y), when residual soil hydrocarbons were almost depleted. This trend was also reflected in hydrocarbon degrading genes, which were mainly affiliated with Gammaproteobacteria at t = 0 and t = 1m and with Alphaproteobacteria and Actinobacteria at t = 1y. RT-qPCR assays confirmed that Pseudomonas and Rhodococcus species actively expressed hydrocarbon degradation genes in Arctic biopile soils. Taken together, these results indicated that biopile treatment leads to major shifts in soil microbial communities, favoring aerobic bacteria that can degrade hydrocarbons.}, } @article {pmid22253699, year = {2012}, author = {Tänzler, R and Sagata, K and Surbakti, S and Balke, M and Riedel, A}, title = {DNA barcoding for community ecology--how to tackle a hyperdiverse, mostly undescribed Melanesian fauna.}, journal = {PloS one}, volume = {7}, number = {1}, pages = {e28832}, pmid = {22253699}, issn = {1932-6203}, mesh = {Animals ; *Biota ; Cluster Analysis ; DNA Barcoding, Taxonomic/*methods ; Databases as Topic ; Electron Transport Complex IV/genetics ; Genetic Markers ; Geography ; Likelihood Functions ; Melanesia ; Models, Biological ; Molecular Sequence Data ; New Guinea ; Sequence Analysis, DNA ; Species Specificity ; Weevils/*genetics ; }, abstract = {BACKGROUND: Trigonopterus weevils are widely distributed throughout Melanesia and hyperdiverse in New Guinea. They are a dominant feature in natural forests, with narrow altitudinal zonation. Their use in community ecology has been precluded by the "taxonomic impediment".

We sampled >6,500 specimens from seven areas across New Guinea; 1,002 specimens assigned to 270 morphospecies were DNA sequenced. Objective clustering of a refined dataset (excluding nine cryptic species) at 3% threshold revealed 324 genetic clusters (DNA group count relative to number of morphospecies = 20.0% overestimation of species diversity, or 120.0% agreement) and 85.6% taxonomic accuracy (the proportion of DNA groups that "perfectly" agree with morphology-based species hypotheses). Agreement and accuracy were best at an 8% threshold. GMYC analysis revealed 328 entities (21.5% overestimation) with 227 perfect GMYC entities (84.1% taxonomic accuracy). Both methods outperform the parataxonomist (19% underestimation; 31.6% taxonomic accuracy). The number of species found in more than one sampling area was highest in the Eastern Highlands and Huon (Sørensen similarity index 0.07, 4 shared species); ⅓ of all areas had no species overlap. Success rates of DNA barcoding methods were lowest when species showed a pronounced geographical structure. In general, Trigonopterus show high α and β-diversity across New Guinea.

CONCLUSIONS/SIGNIFICANCE: DNA barcoding is an excellent tool for biodiversity surveys but success rates might drop when closer localities are included. Hyperdiverse Trigonopterus are a useful taxon for evaluating forest remnants in Melanesia, allowing finer-grained analyses than would be possible with vertebrate taxa commonly used to date. Our protocol should help establish other groups of hyperdiverse fauna as target taxa for community ecology. Sequencing delivers objective data on taxa of incredible diversity but mostly without a solid taxonomic foundation and should help pave the road for the eventual formal naming of new species.}, } @article {pmid22251028, year = {2012}, author = {Kelly, J and Gooding, P and Pratt, D and Ainsworth, J and Welford, M and Tarrier, N}, title = {Intelligent real-time therapy: harnessing the power of machine learning to optimise the delivery of momentary cognitive-behavioural interventions.}, journal = {Journal of mental health (Abingdon, England)}, volume = {21}, number = {4}, pages = {404-414}, doi = {10.3109/09638237.2011.638001}, pmid = {22251028}, issn = {1360-0567}, mesh = {*Artificial Intelligence ; Cell Phone ; Cognitive Behavioral Therapy/*methods ; Computers, Handheld ; Humans ; Therapy, Computer-Assisted/*methods ; User-Computer Interface ; *Suicide Prevention ; }, abstract = {BACKGROUND: Experience sampling methodology (ESM) [Csikszentmihalyi, M. & Larson, R. (1987). Validity and reliability of the experience-sampling method. Journal of Nervous and Mental Disease, 175(9), 526-536] has been used to elucidate the cognitive-behavioural mechanisms underlying the development and maintenance of complex mental disorders as well as mechanisms involved in resilience from such states. We present an argument for the development of intelligent real-time therapy (iRTT). Machine learning and reinforcement learning specifically may be used to optimise the delivery of interventions by observing and altering the timing of real-time therapies based on ongoing ESM measures.

AIMS: The aims of the present article are to outline the principles of iRTT and to consider how it would be applied to complex problems such as suicide prevention.

METHODS: Relevant literature was identified through use of PychInfo.

RESULTS: iRTT may provide an important and ecologically valid adjunct to traditional CBT, providing a means of balancing population-based data with individual data, thus addressing the "knowledge-practice gap" [Tarrier, N. (2010b). The cognitive and behavioral treatment of PTSD, what is known and what is known to be unknown: How not to fall into the practice gap. Clinical Psychology: Science and Practice, 17(2), 134-143] and facilitating the delivery of interventions in situ, thereby addressing the "therapy-real-world gap".

CONCLUSIONS: iRTT may provide a platform for the development of individualised and multifaceted momentary intervention strategies that are ecologically valid and aimed at attenuating pathological pathways to complex mental health problems and amplifying pathways associated with resilience.}, } @article {pmid22244672, year = {2012}, author = {Bik, HM and Porazinska, DL and Creer, S and Caporaso, JG and Knight, R and Thomas, WK}, title = {Sequencing our way towards understanding global eukaryotic biodiversity.}, journal = {Trends in ecology & evolution}, volume = {27}, number = {4}, pages = {233-243}, pmid = {22244672}, issn = {1872-8383}, support = {P20 RR030360/RR/NCRR NIH HHS/United States ; P20 RR030360-01/RR/NCRR NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; 1P20RR030360-01/RR/NCRR NIH HHS/United States ; }, mesh = {*Biodiversity ; Computational Biology ; Eukaryota/*classification/genetics ; Genetic Markers ; Sequence Analysis, DNA ; }, abstract = {Microscopic eukaryotes are abundant, diverse and fill critical ecological roles across every ecosystem on Earth, yet there is a well-recognized gap in understanding of their global biodiversity. Fundamental advances in DNA sequencing and bioinformatics now allow accurate en masse biodiversity assessments of microscopic eukaryotes from environmental samples. Despite a promising outlook, the field of eukaryotic marker gene surveys faces significant challenges: how to generate data that are most useful to the community, especially in the face of evolving sequencing technologies and bioinformatics pipelines, and how to incorporate an expanding number of target genes.}, } @article {pmid22244455, year = {2012}, author = {Bidder, OR and Soresina, M and Shepard, EL and Halsey, LG and Quintana, F and Gómez-Laich, A and Wilson, RP}, title = {The need for speed: testing acceleration for estimating animal travel rates in terrestrial dead-reckoning systems.}, journal = {Zoology (Jena, Germany)}, volume = {115}, number = {1}, pages = {58-64}, doi = {10.1016/j.zool.2011.09.003}, pmid = {22244455}, issn = {1873-2720}, mesh = {*Acceleration ; Animals ; Calibration ; Ecology/instrumentation/*methods/trends ; Geographic Information Systems ; Humans ; Motor Activity/*physiology ; Regression Analysis ; Telemetry/instrumentation/*methods/trends ; }, abstract = {Numerous methods are currently available to track animal movements. However, only one of these, dead-reckoning, has the capacity to provide continuous data for animal movements over fine scales. Dead-reckoning has been applied almost exclusively in the study of marine species, in part due to the difficulty of accurately measuring the speed of terrestrial species. In the present study we evaluate the use of accelerometers and a metric known as overall dynamic body acceleration (ODBA) as a proxy for the measurement of speed for use in dead-reckoning. Data were collated from previous studies, for 10 species locomoting on a treadmill and their ODBA measured by an attached data logger. All species except one showed a highly significant linear relationship between speed and ODBA; however, there was appreciable inter- and intra-specific variance in this relationship. ODBA was then used to estimate speed in a simple trial run of a dead-reckoning track. Estimating distance travelled using speed derived from prior calibration for ODBA resulted in appreciable errors. We describe a method by which these errors can be minimised, by periodic ground-truthing (e.g., by GPS or VHF telemetry) of the dead-reckoned track and adjusting the relationship between speed and ODBA until actual known positions and dead-reckoned positions accord.}, } @article {pmid22242120, year = {2011}, author = {Muszewska, A and Hoffman-Sommer, M and Grynberg, M}, title = {LTR retrotransposons in fungi.}, journal = {PloS one}, volume = {6}, number = {12}, pages = {e29425}, pmid = {22242120}, issn = {1932-6203}, mesh = {Base Sequence ; Cluster Analysis ; Databases, Genetic ; Evolution, Molecular ; Fungi/enzymology/*genetics ; Genome, Fungal/genetics ; Integrases/chemistry/genetics ; Likelihood Functions ; Peptide Hydrolases/chemistry/genetics ; Protein Structure, Tertiary ; RNA-Directed DNA Polymerase/chemistry/genetics ; Retroelements/*genetics ; Ribonuclease H/chemistry/genetics ; Terminal Repeat Sequences/*genetics ; }, abstract = {Transposable elements with long terminal direct repeats (LTR TEs) are one of the best studied groups of mobile elements. They are ubiquitous elements present in almost all eukaryotic genomes. Their number and state of conservation can be a highlight of genome dynamics. We searched all published fungal genomes for LTR-containing retrotransposons, including both complete, functional elements and remnant copies. We identified a total of over 66,000 elements, all of which belong to the Ty1/Copia or Ty3/Gypsy superfamilies. Most of the detected Gypsy elements represent Chromoviridae, i.e. they carry a chromodomain in the pol ORF. We analyzed our data from a genome-ecology perspective, looking at the abundance of various types of LTR TEs in individual genomes and at the highest-copy element from each genome. The TE content is very variable among the analyzed genomes. Some genomes are very scarce in LTR TEs (<50 elements), others demonstrate huge expansions (>8000 elements). The data shows that transposon expansions in fungi usually involve an increase both in the copy number of individual elements and in the number of element types. The majority of the highest-copy TEs from all genomes are Ty3/Gypsy transposons. Phylogenetic analysis of these elements suggests that TE expansions have appeared independently of each other, in distant genomes and at different taxonomical levels. We also analyzed the evolutionary relationships between protein domains encoded by the transposon pol ORF and we found that the protease is the fastest evolving domain whereas reverse transcriptase and RNase H evolve much slower and in correlation with each other.}, } @article {pmid22240206, year = {2012}, author = {Davies, BS and Rafique, J and Vincent, TR and Fairclough, J and Packer, MH and Vincent, R and Haq, I}, title = {Mobile Medical Education (MoMEd) - how mobile information resources contribute to learning for undergraduate clinical students - a mixed methods study.}, journal = {BMC medical education}, volume = {12}, number = {}, pages = {1}, pmid = {22240206}, issn = {1472-6920}, mesh = {Adult ; Clinical Competence ; Computers, Handheld/economics/*statistics & numerical data ; Cost-Benefit Analysis ; Education, Medical, Undergraduate/*methods ; *Educational Measurement ; Female ; Focus Groups ; Humans ; Male ; Medical Informatics Computing/standards ; Pilot Projects ; Students, Medical/statistics & numerical data ; Surveys and Questionnaires ; United Kingdom ; }, abstract = {BACKGROUND: Mobile technology is increasingly being used by clinicians to access up-to-date information for patient care. These offer learning opportunities in the clinical setting for medical students but the underlying pedagogic theories are not clear. A conceptual framework is needed to understand these further. Our initial questions were how the medical students used the technology, how it enabled them to learn and what theoretical underpinning supported the learning.

METHODS: 387 medical students were provided with a personal digital assistant (PDA) loaded with medical resources for the duration of their clinical studies. Outcomes were assessed by a mixed-methods triangulation approach using qualitative and quantitative analysis of surveys, focus groups and usage tracking data.

RESULTS: Learning occurred in context with timely access to key facts and through consolidation of knowledge via repetition. The PDA was an important addition to the learning ecology rather than a replacement. Contextual factors impacted on use both positively and negatively. Barriers included concerns of interrupting the clinical interaction and of negative responses from teachers and patients. Students preferred a future involving smartphone platforms.

CONCLUSIONS: This is the first study to describe the learning ecology and pedagogic basis behind the use of mobile learning technologies in a large cohort of undergraduate medical students in the clinical environment. We have developed a model for mobile learning in the clinical setting that shows how different theories contribute to its use taking into account positive and negative contextual factors.The lessons from this study are transferable internationally, to other health care professions and to the development of similar initiatives with newer technology such as smartphones or tablet computers.}, } @article {pmid22240191, year = {2012}, author = {Michener, WK and Jones, MB}, title = {Ecoinformatics: supporting ecology as a data-intensive science.}, journal = {Trends in ecology & evolution}, volume = {27}, number = {2}, pages = {85-93}, doi = {10.1016/j.tree.2011.11.016}, pmid = {22240191}, issn = {1872-8383}, mesh = {Computational Biology ; Databases as Topic ; Ecology/*methods/trends ; Software ; }, abstract = {Ecology is evolving rapidly and increasingly changing into a more open, accountable, interdisciplinary, collaborative and data-intensive science. Discovering, integrating and analyzing massive amounts of heterogeneous data are central to ecology as researchers address complex questions at scales from the gene to the biosphere. Ecoinformatics offers tools and approaches for managing ecological data and transforming the data into information and knowledge. Here, we review the state-of-the-art and recent advances in ecoinformatics that can benefit ecologists and environmental scientists as they tackle increasingly challenging questions that require voluminous amounts of data across disciplines and scales of space and time. We also highlight the challenges and opportunities that remain.}, } @article {pmid22240003, year = {2012}, author = {He, W and You, M and Vasseur, L and Yang, G and Xie, M and Cui, K and Bai, J and Liu, C and Li, X and Xu, X and Huang, S}, title = {Developmental and insecticide-resistant insights from the de novo assembled transcriptome of the diamondback moth, Plutella xylostella.}, journal = {Genomics}, volume = {99}, number = {3}, pages = {169-177}, doi = {10.1016/j.ygeno.2011.12.009}, pmid = {22240003}, issn = {1089-8646}, mesh = {Animals ; Databases, Nucleic Acid ; *Expressed Sequence Tags ; Gene Expression Profiling/methods ; Gene Expression Regulation ; Genotyping Techniques ; High-Throughput Nucleotide Sequencing/methods ; Insecticide Resistance/*genetics ; Moths/*genetics ; Polymorphism, Single Nucleotide ; RNA, Messenger/*genetics ; }, abstract = {We present here the de novo assembly and annotation of the transcriptome of Plutella xylostella (diamondback moth (DBM)), a widespread destructive pest of cruciferous plants, using short reads generated by Illumina sequencing from different developmental stages and insecticide-resistant strains. A total of 171,262 non-redundant sequences, denoted as unigenes, were obtained. They represented approximately 100-fold of all DBM mRNA and EST sequences in GenBank thus far. We identified 38,255 unigenes highly similar to the known functional protein-coding genes, most of which were annotated using gene ontology (GO) and orthologous groups of proteins (COG). Global profiling of differentially expressed unigenes revealed enriched GOs and biological pathways that were related to specific developmental stages and insecticide resistance. We also evaluated the resistance-related single nucleotide polymorphism (SNP) using this high-throughput genotyping method. The newly developed transcriptome will facilitate researches on the DBM developmental biology and insecticide resistance evolution, and ultimately provide better pest management systems.}, } @article {pmid22238692, year = {2012}, author = {Năpăruş, M and Kuntner, M}, title = {A GIS model predicting potential distributions of a lineage: a test case on hermit spiders (Nephilidae: Nephilengys).}, journal = {PloS one}, volume = {7}, number = {1}, pages = {e30047}, pmid = {22238692}, issn = {1932-6203}, mesh = {Africa ; Animals ; Asia ; Australia ; Biodiversity ; Brazil ; Demography/*methods ; Ecology ; Ecosystem ; Environmental Monitoring/methods ; Geographic Information Systems/*statistics & numerical data ; Geography ; Madagascar ; *Models, Theoretical ; *Spiders/growth & development ; }, abstract = {BACKGROUND: Although numerous studies model species distributions, these models are almost exclusively on single species, while studies of evolutionary lineages are preferred as they by definition study closely related species with shared history and ecology. Hermit spiders, genus Nephilengys, represent an ecologically important but relatively species-poor lineage with a globally allopatric distribution. Here, we model Nephilengys global habitat suitability based on known localities and four ecological parameters.

We geo-referenced 751 localities for the four most studied Nephilengys species: N. cruentata (Africa, New World), N. livida (Madagascar), N. malabarensis (S-SE Asia), and N. papuana (Australasia). For each locality we overlaid four ecological parameters: elevation, annual mean temperature, annual mean precipitation, and land cover. We used linear backward regression within ArcGIS to select two best fit parameters per species model, and ModelBuilder to map areas of high, moderate and low habitat suitability for each species within its directional distribution. For Nephilengys cruentata suitable habitats are mid elevation tropics within Africa (natural range), a large part of Brazil and the Guianas (area of synanthropic spread), and even North Africa, Mediterranean, and Arabia. Nephilengys livida is confined to its known range with suitable habitats being mid-elevation natural and cultivated lands. Nephilengys malabarensis, however, ranges across the Equator throughout Asia where the model predicts many areas of high ecological suitability in the wet tropics. Its directional distribution suggests the species may potentially spread eastwards to New Guinea where the suitable areas of N. malabarensis largely surpass those of the native N. papuana, a species that prefers dry forests of Australian (sub)tropics.

CONCLUSIONS: Our model is a customizable GIS tool intended to predict current and future potential distributions of globally distributed terrestrial lineages. Its predictive potential may be tested in foreseeing species distribution shifts due to habitat destruction and global climate change.}, } @article {pmid22238424, year = {2012}, author = {Tseng, YY and Li, WH}, title = {Classification of protein functional surfaces using structural characteristics.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {109}, number = {4}, pages = {1170-1175}, pmid = {22238424}, issn = {1091-6490}, support = {R01 GM030998/GM/NIGMS NIH HHS/United States ; R37 GM030998/GM/NIGMS NIH HHS/United States ; GM30998/GM/NIGMS NIH HHS/United States ; }, mesh = {Binding Sites/genetics ; Databases, Genetic ; Flavin Mononucleotide/metabolism ; *Models, Molecular ; Oxidoreductases/chemistry/classification ; *Protein Conformation ; Protein Folding ; Proteins/*chemistry/*classification/metabolism ; *Surface Properties ; }, abstract = {Protein structure and function are closely related, especially in functional surfaces, which are local spatial regions that perform the biological functions. Also, protein structures tend to evolve more slowly than amino acid sequences. We have therefore developed a method to classify proteins using the structures of functional surfaces; we call it protein surface classification (PSC). PSC may reflect functional relationships among proteins and may detect evolutionary relationships among highly divergent sequences. We focused on the surfaces of ligand-bound regions because they represent well-defined structures. Specifically, we used structural attributes to measure similarities between binding surfaces and constructed a PSC library of ~2,000 binding surface types from the bound forms. Using flavin mononucleotide-binding proteins and glycosidases as examples, we show how the evolutionary position of an uncharacterized protein can be defined and its function inferred from the characterized members of the same surface subtype. We found that proteins with the same enzyme nomenclature may be divided into subtypes and that two proteins in the same CATH (Class, Architecture, Topology, Homologous superfamily) fold may belong to two different surface types. In conclusion, our approach complements the sequence-based and fold-domain classifications and has the advantage of associating the shape of a protein with its biological function. As an expandable library, PSC provides a resource of spatial patterns for studying the evolution of protein structure and function.}, } @article {pmid22236999, year = {2012}, author = {Racine, M and Tousignant-Laflamme, Y and Kloda, LA and Dion, D and Dupuis, G and Choinière, M}, title = {A systematic literature review of 10 years of research on sex/gender and pain perception - part 2: do biopsychosocial factors alter pain sensitivity differently in women and men?.}, journal = {Pain}, volume = {153}, number = {3}, pages = {619-635}, doi = {10.1016/j.pain.2011.11.026}, pmid = {22236999}, issn = {1872-6623}, support = {//Canadian Institutes of Health Research/Canada ; }, mesh = {Biological Factors ; Biomedical Research/*statistics & numerical data ; Databases, Bibliographic/statistics & numerical data ; Female ; Humans ; Longitudinal Studies ; Male ; Nervous System/physiopathology ; *Pain/complications/metabolism/psychology ; Pain Perception/*physiology ; Pain Threshold/*physiology ; *Psychology ; *Sex Characteristics ; Stress, Psychological/physiopathology ; }, abstract = {This systematic review summarizes the results of 10 years of laboratory research on pain and sex/gender. An electronic search strategy was designed by a medical librarian to access multiple databases. A total of 172 articles published between 1998 and 2008 were retrieved, analyzed, and synthesized. The second set of results presented in this review (129 articles) examined various biopsychosocial factors that may contribute to differences in pain sensitivity between healthy women and men. The results revealed that the involvement of hormonal and physiological factors is either inconsistent or absent. Some studies suggest that temporal summation, allodynia, and secondary hyperalgesia may be more pronounced in women than in men. The evidence to support less efficient endogenous pain inhibitory systems in women is mixed and does not necessarily apply to all pain modalities. With regard to psychological factors, depression may not mediate sex differences in pain perception, while the role of anxiety is ambiguous. Cognitive and social factors appear to partly explain some sex-related differences. Finally, past individual history may be influential in female pain responses. However, these conclusions must be treated with much circumspection for various methodological reasons. Furthermore, some factors/mechanisms remain understudied in the field. There is also a need to assess and improve the ecological validity of findings from laboratory studies on healthy subjects, and perhaps a change of paradigm needs to be considered at this point in time to better understand the factors that influence the experience of women and men who suffer from acute or chronic pain.}, } @article {pmid22230091, year = {2012}, author = {Wang, M and Bai, Y and Chen, W and Markert, B and Peng, C and Ouyang, Z}, title = {A GIS technology based potential eco-risk assessment of metals in urban soils in Beijing, China.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {161}, number = {}, pages = {235-242}, doi = {10.1016/j.envpol.2011.09.030}, pmid = {22230091}, issn = {1873-6424}, mesh = {China ; Cities ; Environmental Monitoring/instrumentation/*methods ; Environmental Pollution/statistics & numerical data ; *Geographic Information Systems ; Metals, Heavy/*analysis ; Risk Assessment/methods ; Soil Pollutants/*analysis ; }, abstract = {Ecological risks of heavy metals in urban soils were evaluated using Beijing, China as an example. Cadmium, Cu, Zn, Pb, Cr and Ni contents of 233 surface soils sampled by 1 min latitude × 1 min longitude grid were used to identify their spatial distribution patterns and potential emission sources. Throughout the city, longer the duration of urbanization greater was the accumulations of heavy metals especially, Cd, Cu, Pb, and Zn. The soil Zn mainly came from the wears of vehicular tires. Point source emissions of heavy metals were few and far in the downwind south-east quadrant of Beijing. The calculated risk indices showed potential median eco-risks in the ancient central city. No potential high eco-risk due to soil-borne heavy metals was found. The potential medium eco-risk areas in Beijing would expand from the initial 24 to 110 km(2) if soil pH were to reduce by 0.5 units in anticipation.}, } @article {pmid22225882, year = {2013}, author = {Nemmi, F and Piras, F and Péran, P and Incoccia, C and Sabatini, U and Guariglia, C}, title = {Landmark sequencing and route knowledge: an fMRI study.}, journal = {Cortex; a journal devoted to the study of the nervous system and behavior}, volume = {49}, number = {2}, pages = {507-519}, doi = {10.1016/j.cortex.2011.11.016}, pmid = {22225882}, issn = {1973-8102}, mesh = {Adult ; Brain/*physiology ; Caudate Nucleus/*physiology ; Cerebral Cortex/physiology ; Cognition/physiology ; Data Interpretation, Statistical ; Female ; Hippocampus/*physiology ; Humans ; Image Processing, Computer-Assisted ; Magnetic Resonance Imaging ; Male ; Nerve Net/physiology ; Orientation/*physiology ; Photic Stimulation ; Psychomotor Performance/physiology ; Rome ; Space Perception ; Young Adult ; }, abstract = {INTRODUCTION: The ability to navigate in a familiar environment mainly relies on route knowledge, that is, a mental representation of relevant locations along a way, sequenced according to a navigational goal. Despite the clear ecological validity of this issue, route navigation and route knowledge have been scarcely investigated and little is known about the neural and cognitive bases of this navigational strategy. Using functional magnetic resonance imaging (fMRI) we tested the validity of the predictions based on the main cognitive models of spatial knowledge acquisition about route-based navigation.

METHODS: An order judgment task was used with two conditions (route and activity). Subjects were required to detect potential mismatches between a current sensory input and expectations deriving from route and activity knowledge.

RESULTS: A medial occipto-temporal (e.g., lingual gyrus, calcarine cortex, fusiform gyrus, parahippocampal cortex) network was found activated during the route task, whereas a temporo-parietal (temporo-parietal junction) and frontal (e.g., Broca's area) network was related to the activity task.

CONCLUSIONS: Functional data are congruent with cognitive models of route-based navigation. The route task activated areas related to both landmark identity and landmark order. Data are discussed in view of route-based navigation models.}, } @article {pmid22223439, year = {2012}, author = {Cruz, F and Brennan, AC and Gonzalez-Voyer, A and Muñoz-Fuentes, V and Eaaswarkhanth, M and Roques, S and Picó, FX}, title = {Genetics and genomics in wildlife studies: implications for ecology, evolution, and conservation biology.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {34}, number = {3}, pages = {245-246}, doi = {10.1002/bies.201100171}, pmid = {22223439}, issn = {1521-1878}, mesh = {*Adaptation, Biological ; Animals ; *Biological Evolution ; Conservation of Natural Resources/*methods ; *Ecology ; Environment ; Genotype ; Information Storage and Retrieval/methods ; Mammals ; Metagenomics/*methods ; Selection, Genetic ; }, } @article {pmid22223350, year = {2012}, author = {Scocco, P and Brusaferro, A and Catorci, A}, title = {Comparison between two different methods for evaluating rumen papillae measures related to different diets.}, journal = {Microscopy research and technique}, volume = {75}, number = {7}, pages = {884-889}, doi = {10.1002/jemt.22008}, pmid = {22223350}, issn = {1097-0029}, mesh = {Animals ; Biometry/*methods ; Diet/*methods ; Geographic Information Systems ; Image Processing, Computer-Assisted/*methods ; *Intestinal Absorption ; Intestinal Mucosa/*anatomy & histology/physiology ; Rumen/*anatomy & histology/physiology ; Sheep ; }, abstract = {Although the Geographical Information System (GIS), which integrates computerized drawing computer assisted design (CAD) and relational databases (data base management system (DBMS)), is best known for applications in geographical and planning cartography, it can also use many kinds of information concerning the territory. A multidisciplinary project was initiated since 5 years a multidisciplinary study was initiated to use GIS to integrate environmental and ecological data with findings on animal health, ethology, and anatomy. This study is chiefly aimed at comparing two different methods for measuring the absorptive surface of rumen papillae. To this scope, 21 female sheep (Ovis aries) on different alimentary regimes (e.g., milk and forage mixed diet, early herbaceous diet, dry hay diet, and fresh hay diet at the maximum of pasture flowering and at the maximum of pasture dryness) were used; after slaughtering, 20 papillae were randomly removed from each sample collected from four indicator regions of rumen wall, placed near a metric reference and digitally photographed. The images were developed with the ArcGIS™ software to calculate the area of rumen papillae by means of GIS and to measure their mid-level width and length to calculate the papillae area as previously performed with a different method. Spatial measurements were analyzed using univariate and multivariate methods. This work demonstrates that the GIS methodology can be efficiently used for measuring the absorptive surface of rumen papillae. In addition, GIS demonstrated to be a rapid, precise, and objective tool when compared with previously used method.}, } @article {pmid22208064, year = {2011}, author = {Hurtado, J and Clark, DB}, title = {Local technicians in long-term research projects: evaluation of 25 years experience in an active tropical research station.}, journal = {Revista de biologia tropical}, volume = {59}, number = {4}, pages = {1455-1462}, doi = {10.15517/rbt.v59i4.3410}, pmid = {22208064}, issn = {0034-7744}, mesh = {Costa Rica ; Ecology/*education ; Education, Nonprofessional/*methods/standards ; Humans ; Personnel Turnover ; *Research ; Research Personnel/education/*standards ; *Rural Population ; Staff Development/*methods/standards ; Time Factors ; Workforce ; }, abstract = {Most field ecology is conceived and financed by scientists from urban areas but is actually carried out in rural areas. Field staff can either be imported from urban areas or recruited from local residents. We evaluated the advantages and disadvantages of involving rural residents as local technicians over a 25- year period at active field research site in Costa Rica. We defined "local technicians" as local residents with no university education who acquired significant experience in field data collection, data management and/or laboratory work. We analyzed the experiences of incorporating these technicians into field research in developing countries from the points of view of scientist and of the local technicians themselves. Primary data were written responses from to a standardized survey of 19 senior scientists and Ph.D. students,and results from standardized personal interviews with 22 local technicians. Researchers highlighted the advantages of highly-skilled technicians with minimal staff turnover, as well as the technicians' knowledge of local ecological conditions. Local technicians considered the primary advantages of their jobs to be opportunities for continuing education training in science as well as cultural enrichment through interactions with people of different cultures. The main challenges identified by researchers were the lack of long-term funding for projects and extended training required for local technicians. Local technicians can be of great benefit to research projects by providing high-quality data collection at reasonable costs with low staff turnover. Over the last 25 years the research model at the field station we studied has evolved to the point that most long-term projects now depend heavily on local technicians. This model of involving local technicians in long-term research has multiple benefits for the researchers, the technicians and the local community, and could be adapted to a variety of settings in rural areas of developing countries.}, } @article {pmid22201170, year = {2012}, author = {Nachman, MW and Payseur, BA}, title = {Recombination rate variation and speciation: theoretical predictions and empirical results from rabbits and mice.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {367}, number = {1587}, pages = {409-421}, pmid = {22201170}, issn = {1471-2970}, support = {R01 GM074245/GM/NIGMS NIH HHS/United States ; }, mesh = {Animal Migration/physiology ; Animals ; Centromere/genetics ; Chromosomes, Mammalian/genetics ; Computational Biology ; Gene Flow ; Gene Frequency ; *Genetic Speciation ; Genetic Variation ; Genetics, Population ; Mice/*genetics/physiology ; Models, Genetic ; Rabbits/*genetics/physiology ; *Recombination, Genetic ; Selection, Genetic ; Sequence Analysis, DNA ; }, abstract = {Recently diverged taxa may continue to exchange genes. A number of models of speciation with gene flow propose that the frequency of gene exchange will be lower in genomic regions of low recombination and that these regions will therefore be more differentiated. However, several population-genetic models that focus on selection at linked sites also predict greater differentiation in regions of low recombination simply as a result of faster sorting of ancestral alleles even in the absence of gene flow. Moreover, identifying the actual amount of gene flow from patterns of genetic variation is tricky, because both ancestral polymorphism and migration lead to shared variation between recently diverged taxa. New analytic methods have been developed to help distinguish ancestral polymorphism from migration. Along with a growing number of datasets of multi-locus DNA sequence variation, these methods have spawned a renewed interest in speciation models with gene flow. Here, we review both speciation and population-genetic models that make explicit predictions about how the rate of recombination influences patterns of genetic variation within and between species. We then compare those predictions with empirical data of DNA sequence variation in rabbits and mice. We find strong support for the prediction that genomic regions experiencing low levels of recombination are more differentiated. In most cases, reduced gene flow appears to contribute to the pattern, although disentangling the relative contribution of reduced gene flow and selection at linked sites remains a challenge. We suggest fruitful areas of research that might help distinguish between different models.}, } @article {pmid22201163, year = {2012}, author = {Nosil, P and Feder, JL}, title = {Genomic divergence during speciation: causes and consequences.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {367}, number = {1587}, pages = {332-342}, pmid = {22201163}, issn = {1471-2970}, mesh = {Animals ; Computational Biology ; Gene Flow ; *Genetic Speciation ; *Genetic Variation ; *Genome ; Recombination, Genetic ; Reproductive Isolation ; }, abstract = {Speciation is a fundamental process responsible for the diversity of life. Progress has been made in detecting individual 'speciation genes' that cause reproductive isolation. In contrast, until recently, less attention has been given to genome-wide patterns of divergence during speciation. Thus, major questions remain concerning how individual speciation genes are arrayed within the genome, and how this affects speciation. This theme issue is dedicated to exploring this genomic perspective of speciation. Given recent sequencing and computational advances that now allow genomic analyses in most organisms, the goal is to help move the field towards a more integrative approach. This issue draws upon empirical studies in plants and animals, and theoretical work, to review and further document patterns of genomic divergence. In turn, these studies begin to disentangle the role that different processes, such as natural selection, gene flow and recombination rate, play in generating observed patterns. These factors are considered in the context of how genomes diverge as speciation unfolds, from beginning to end. The collective results point to how experimental work is now required, in conjunction with theory and sequencing studies, to move the field from descriptive studies of patterns of divergence towards a predictive framework that tackles the causes and consequences of genome-wide patterns.}, } @article {pmid22198678, year = {2012}, author = {Yalachkov, Y and Kaiser, J and Naumer, MJ}, title = {Functional neuroimaging studies in addiction: multisensory drug stimuli and neural cue reactivity.}, journal = {Neuroscience and biobehavioral reviews}, volume = {36}, number = {2}, pages = {825-835}, doi = {10.1016/j.neubiorev.2011.12.004}, pmid = {22198678}, issn = {1873-7528}, mesh = {Animals ; *Brain/blood supply/diagnostic imaging/physiopathology ; *Brain Mapping ; *Cues ; Databases, Bibliographic/statistics & numerical data ; Humans ; Neuroimaging ; Radionuclide Imaging ; Substance-Related Disorders/*pathology/physiopathology/psychology ; }, abstract = {Neuroimaging studies on cue reactivity have substantially contributed to the understanding of addiction. In the majority of studies drug cues were presented in the visual modality. However, exposure to conditioned cues in real life occurs often simultaneously in more than one sensory modality. Therefore, multisensory cues should elicit cue reactivity more consistently than unisensory stimuli and increase the ecological validity and the reliability of brain activation measurements. This review includes the data from 44 whole-brain functional neuroimaging studies with a total of 1168 subjects (812 patients and 356 controls). Correlations between neural cue reactivity and clinical covariates such as craving have been reported significantly more often for multisensory than unisensory cues in the motor cortex, insula and posterior cingulate cortex. Thus, multisensory drug cues are particularly effective in revealing brain-behavior relationships in neurocircuits of addiction responsible for motivation, craving awareness and self-related processing.}, } @article {pmid22194950, year = {2011}, author = {Soldatini, C and Albores-Barajas, YV and Lovato, T and Andreon, A and Torricelli, P and Montemaggiori, A and Corsa, C and Georgalas, V}, title = {Wildlife strike risk assessment in several Italian airports: lessons from BRI and a new methodology implementation.}, journal = {PloS one}, volume = {6}, number = {12}, pages = {e28920}, pmid = {22194950}, issn = {1932-6203}, mesh = {Accidents, Aviation/*prevention & control/*statistics & numerical data ; Aircraft/*statistics & numerical data ; *Airports ; Animals ; *Animals, Wild/physiology ; *Birds/physiology ; Italy ; Linear Models ; Risk Assessment/*methods ; Survival Rate ; Time Factors ; }, abstract = {The presence of wildlife in airport areas poses substantial hazards to aviation. Wildlife aircraft collisions (hereafter wildlife strikes) cause losses in terms of human lives and direct monetary losses for the aviation industry. In recent years, wildlife strikes have increased in parallel with air traffic increase and species habituation to anthropic areas. In this paper, we used an ecological approach to wildlife strike risk assessment to eight Italian international airports. The main achievement is a site-specific analysis that avoids flattening wildlife strike events on a large scale while maintaining comparable airport risk assessments. This second version of the Birdstrike Risk Index (BRI2) is a sensitive tool that provides different time scale results allowing appropriate management planning. The methodology applied has been developed in accordance with the Italian Civil Aviation Authority, which recognizes it as a national standard implemented in the advisory circular ENAC APT-01B.}, } @article {pmid22189864, year = {2012}, author = {Ekkers, DM and Cretoiu, MS and Kielak, AM and Elsas, JD}, title = {The great screen anomaly--a new frontier in product discovery through functional metagenomics.}, journal = {Applied microbiology and biotechnology}, volume = {93}, number = {3}, pages = {1005-1020}, pmid = {22189864}, issn = {1432-0614}, mesh = {Biological Factors/genetics/*metabolism ; Biotechnology/*methods ; Computational Biology/methods ; Ecosystem ; *Environmental Microbiology ; Gene Library ; *Genes ; Metagenomics/*methods ; }, abstract = {Functional metagenomics, the study of the collective genome of a microbial community by expressing it in a foreign host, is an emerging field in biotechnology. Over the past years, the possibility of novel product discovery through metagenomics has developed rapidly. Thus, metagenomics has been heralded as a promising mining strategy of resources for the biotechnological and pharmaceutical industry. However, in spite of innovative work in the field of functional genomics in recent years, yields from function-based metagenomics studies still fall short of producing significant amounts of new products that are valuable for biotechnological processes. Thus, a new set of strategies is required with respect to fostering gene expression in comparison to the traditional work. These new strategies should address a major issue, that is, how to successfully express a set of unknown genes of unknown origin in a foreign host in high throughput. This article is an opinionating review of functional metagenomic screening of natural microbial communities, with a focus on the optimization of new product discovery. It first summarizes current major bottlenecks in functional metagenomics and then provides an overview of the general metagenomic assessment strategies, with a focus on the challenges that are met in the screening for, and selection of, target genes in metagenomic libraries. To identify possible screening limitations, strategies to achieve optimal gene expression are reviewed, examining the molecular events all the way from the transcription level through to the secretion of the target gene product.}, } @article {pmid22189545, year = {2012}, author = {Zeng, X and Yuan, Z and Tong, X and Li, Q and Gao, W and Qin, M and Liu, Z}, title = {Phylogenetic study of Oryzoideae species and related taxa of the Poaceae based on atpB-rbcL and ndhF DNA sequences.}, journal = {Molecular biology reports}, volume = {39}, number = {5}, pages = {5737-5744}, pmid = {22189545}, issn = {1573-4978}, mesh = {Base Sequence ; DNA, Intergenic/genetics ; Databases, Nucleic Acid ; Evolution, Molecular ; Genes, Chloroplast/genetics ; Genes, Plant/genetics ; Genetic Variation ; Geography ; NADH Dehydrogenase/*genetics ; Nucleotides/genetics ; *Phylogeny ; Plant Proteins/*genetics ; Poaceae/*classification/enzymology/*genetics ; Ribulose-Bisphosphate Carboxylase/*genetics ; Sequence Homology, Nucleic Acid ; Species Specificity ; Time Factors ; }, abstract = {Oryzoideae (Poaceae) plants have economic and ecological value. However, the phylogenetic position of some plants is not clear, such as Hygroryza aristata (Retz.) Nees. and Porteresia coarctata (Roxb.) Tateoka (syn. Oryza coarctata). Comprehensive molecular phylogenetic studies have been carried out on many genera in the Poaceae. The different DNA sequences, including nuclear and chloroplast sequences, had been extensively employed to determine relationships at both higher and lower taxonomic levels in the Poaceae. Chloroplast DNA ndhF gene and atpB-rbcL spacer were used to construct phylogenetic trees and estimate the divergence time of Oryzoideae, Bambusoideae, Panicoideae, Pooideae and so on. Complete sequences of atpB-rbcL and ndhF were generated for 17 species representing six species of the Oryzoideae and related subfamilies. Nicotiana tabacum L. was the outgroup species. The two DNA datasets were analyzed, using Maximum Parsimony and Bayesian analysis methods. The molecular phylogeny revealed that H. aristata (Retz.) Nees was the sister to Chikusichloa aquatica Koidz. Moreover, P. coarctata (Roxb.) Tateoka was in the genus Oryza. Furthermore, the result of evolution analysis, which based on the ndhF marker, indicated that the time of origin of Oryzoideae might be 31 million years ago.}, } @article {pmid22185615, year = {2011}, author = {Gething, PW and Patil, AP and Smith, DL and Guerra, CA and Elyazar, IR and Johnston, GL and Tatem, AJ and Hay, SI}, title = {A new world malaria map: Plasmodium falciparum endemicity in 2010.}, journal = {Malaria journal}, volume = {10}, number = {}, pages = {378}, pmid = {22185615}, issn = {1475-2875}, support = {095066/WT_/Wellcome Trust/United Kingdom ; #079091/WT_/Wellcome Trust/United Kingdom ; #091835/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Algorithms ; Bayes Theorem ; Computational Biology ; Databases, Factual ; Endemic Diseases/prevention & control/*statistics & numerical data ; Global Health ; Humans ; Malaria, Falciparum/*epidemiology/parasitology/prevention & control ; *Maps as Topic ; Models, Statistical ; Plasmodium falciparum/*pathogenicity ; Risk Factors ; }, abstract = {BACKGROUND: Transmission intensity affects almost all aspects of malaria epidemiology and the impact of malaria on human populations. Maps of transmission intensity are necessary to identify populations at different levels of risk and to evaluate objectively options for disease control. To remain relevant operationally, such maps must be updated frequently. Following the first global effort to map Plasmodium falciparum malaria endemicity in 2007, this paper describes the generation of a new world map for the year 2010. This analysis is extended to provide the first global estimates of two other metrics of transmission intensity for P. falciparum that underpin contemporary questions in malaria control: the entomological inoculation rate (PfEIR) and the basic reproductive number (PfR).

METHODS: Annual parasite incidence data for 13,449 administrative units in 43 endemic countries were sourced to define the spatial limits of P. falciparum transmission in 2010 and 22,212 P. falciparum parasite rate (PfPR) surveys were used in a model-based geostatistical (MBG) prediction to create a continuous contemporary surface of malaria endemicity within these limits. A suite of transmission models were developed that link PfPR to PfEIR and PfR and these were fitted to field data. These models were combined with the PfPR map to create new global predictions of PfEIR and PfR. All output maps included measured uncertainty.

RESULTS: An estimated 1.13 and 1.44 billion people worldwide were at risk of unstable and stable P. falciparum malaria, respectively. The majority of the endemic world was predicted with a median PfEIR of less than one and a median PfRc of less than two. Values of either metric exceeding 10 were almost exclusive to Africa. The uncertainty described in both PfEIR and PfR was substantial in regions of intense transmission.

CONCLUSIONS: The year 2010 has a particular significance as an evaluation milestone for malaria global health policy. The maps presented here contribute to a rational basis for control and elimination decisions and can serve as a baseline assessment as the global health community looks ahead to the next series of milestones targeted at 2015.}, } @article {pmid22185587, year = {2012}, author = {DeGue, S and Holt, MK and Massetti, GM and Matjasko, JL and Tharp, AT and Valle, LA}, title = {Looking ahead toward community-level strategies to prevent sexual violence.}, journal = {Journal of women's health (2002)}, volume = {21}, number = {1}, pages = {1-3}, pmid = {22185587}, issn = {1931-843X}, support = {CC999999/ImCDC/Intramural CDC HHS/United States ; }, mesh = {Centers for Disease Control and Prevention, U.S. ; Community Health Services/*organization & administration ; *Community Networks ; Domestic Violence/prevention & control ; Female ; Health Promotion/organization & administration ; Humans ; Interpersonal Relations ; Male ; Primary Prevention/*organization & administration ; Rape/*prevention & control ; Residence Characteristics ; Risk Factors ; Social Environment ; *Social Support ; Social Values ; Socioeconomic Factors ; Spouse Abuse/*prevention & control ; United States ; }, abstract = {The Division of Violence Prevention within CDC's National Center for Injury Prevention and Control recently undertook a systematic review of primary prevention strategies for sexual violence (SV) perpetration. This review identified the lack of community-level strategies to prevent SV as a critical gap in the literature. Community-level strategies function by modifying the characteristics of settings (e.g., schools, workplaces, neighborhoods) that increase the risk for violence victimization and perpetration. Identification of evidence-based strategies at the community level would allow implementation of ecologic approaches to SV prevention with a greater potential for reducing the prevalence of SV perpetration. The field will face several challenges in identifying and evaluating the effectiveness of promising community-level strategies to prevent SV. These challenges include limited knowledge of community-level and societal-level risk factors for SV, a lack of theoretical or empirical guidance in the SV literature for identification of promising community-level approaches, and challenges in evaluating SV outcomes at the community level. Recognition of these challenges should guide future research and foster dialogue within the SV prevention field. The development and evaluation of community-level approaches to SV prevention represent a vital and logical next step toward the implementation of effective, multilevel prevention efforts and a population-level reduction in the prevalence of SV.}, } @article {pmid22180036, year = {2011}, author = {Zhou, MB and Liu, XM and Tang, DQ}, title = {Transposable elements in Phyllostachys pubescens (Poaceae) genome survey sequences and the full-length cDNA sequences, and their association with simple-sequence repeats.}, journal = {Genetics and molecular research : GMR}, volume = {10}, number = {4}, pages = {3026-3037}, doi = {10.4238/2011.December.6.3}, pmid = {22180036}, issn = {1676-5680}, mesh = {Bambusa/*genetics ; DNA Transposable Elements ; DNA, Complementary/*genetics ; Databases, Genetic ; Evolution, Molecular ; *Genome, Plant ; Genomics/*methods ; *Microsatellite Repeats ; Phylogeny ; Sequence Analysis, DNA ; Systems Biology/*methods ; Transcription Factors/genetics ; }, abstract = {Phyllostachys pubescens is a woody bamboo with the highest ecological, economic, and cultural values of all bamboos in Asia. There is more genomic data available for P. pubescens than for any other bamboo species, including 2.12-Mb genome survey sequences (GSS) and 11.4-Mb full-length cDNA sequences (FL-cDNAs) currently deposited in GenBank. Analysis of these sequences revealed that transposable elements (TEs) are abundant, diverse and polyphyletic in the P. pubescens genome, of which Ty3-gypsy and Ty1-copia are the two most abundant families. Phylogenic analysis showed that both elements probably arose before the Bambusoideae separated from the other Poaceae subfamilies. We found evidence that the distribution of some intragenic TEs correlated with transcript profiles, of which Mutator elements preferred to insert in the transcripts of transcription factors. Additionally, we found that the abundance of SSRs in TEs (4.56%) was significantly higher than in GSS (0.098%) and in FL-cDNAs (2.60%) in P. pubescens genome, and TA/AT and CT/AG repeats were found to be intimately associated with En/Spm and Mutator elements, respectively. Our data provide a glimpse of the structure and evolution of P. pubescens genome, although large-scale sequencing of the genome would be required to fully understand the architecture of the P. pubescens genome.}, } @article {pmid22174780, year = {2011}, author = {Matzen da Silva, J and Dos Santos, A and Cunha, MR and Costa, FO and Creer, S and Carvalho, GR}, title = {Multigene molecular systematics confirm species status of morphologically convergent Pagurus hermit crabs.}, journal = {PloS one}, volume = {6}, number = {12}, pages = {e28233}, pmid = {22174780}, issn = {1932-6203}, mesh = {Animals ; Anomura/*anatomy & histology/*genetics ; Atlantic Ocean ; Base Sequence ; Bayes Theorem ; Databases, Genetic ; Electron Transport Complex IV/genetics ; Genetic Variation ; Mediterranean Sea ; Models, Genetic ; Multigene Family/*genetics ; Nucleotides/genetics ; Phylogeny ; Species Specificity ; }, abstract = {INTRODUCTION: In spite of contemporary morphological taxonomy appraisals, apparent high morphological similarity raises uncertainty about the species status of certain Pagurus hermit crabs. This is exemplified between two European species, Pagurus excavatus (Herbst, 1791) and Pagurus alatus (Fabricius 1775), whose species status is still difficult to resolve using morphological criteria alone.

To address such ambiguities, we used combinations of Maximum Likelihood (ML) and Bayesian Inference (BI) methods to delineate species boundaries of P. alatus and P. excavatus and formulate an intermediate Pagurus phylogenetic hypothesis, based upon single and concatenated mitochondrial (cytochrome oxidase I [COI]) and nuclear (16S and 28s ribosomal RNA) gene partitions. The molecular data supported the species status of P. excavatus and P. alatus and also clearly resolved two divergent clades within hermit crabs from the Northeast Atlantic Ocean and the Mediterranean Sea.

CONCLUSIONS/SIGNIFICANCE: Despite the abundance and prominent ecological role of hermit crabs, Pagurus, in North East Atlantic Ocean and Mediterranean Sea ecosystems, many important aspects of their taxonomy, biology, systematics and evolution remain poorly explored. The topologies presented here should be regarded as hypotheses that can be incorporated into the robust and integrated understanding of the systematic relationships within and between species of the genus Pagurus inhabiting the Northeast Atlantic Ocean and the Mediterranean Sea.}, } @article {pmid22169329, year = {2012}, author = {Kamilar, JM and Marshack, JL}, title = {Does geography or ecology best explain 'cultural' variation among chimpanzee communities?.}, journal = {Journal of human evolution}, volume = {62}, number = {2}, pages = {256-260}, doi = {10.1016/j.jhevol.2011.11.008}, pmid = {22169329}, issn = {1095-8606}, mesh = {Analysis of Variance ; Animals ; Anthropology, Cultural ; Anthropology, Physical ; *Biological Evolution ; *Cultural Evolution ; Databases, Factual ; Ecosystem ; Feeding Behavior ; Pan troglodytes/*physiology ; Tool Use Behavior ; }, abstract = {Much attention has been paid to geographic variation in chimpanzee behavior, but few studies have applied quantitative techniques to explain this variation. Here, we apply methods typically utilized in macroecology to explain variation in the putative cultural traits of chimpanzees. We analyzed published data containing 39 behavioral traits from nine chimpanzee communities. We used a canonical correspondence analysis to examine the relative importance of environmental characteristics and geography, which may be a proxy for inter-community gene flow and/or social transmission, for explaining geographic variation in chimpanzee behavior. We found that geography, and longitude in particular, was the best predictor of behavioral variation. Chimpanzee communities in close longitudinal proximity to each other exhibit similar behavioral repertoires, independent of local ecological factors. No ecological variables were significantly related to behavioral variation. These results support the idea that inter-community dispersal patterns have played a major role in structuring behavioral variation. We cannot be certain whether behavioral variation has a genetic basis, is the result of innovation and diffusion, or a combination of the two.}, } @article {pmid22164829, year = {2011}, author = {Lajeunessei, MJ}, title = {On the meta-analysis of response ratios for studies with correlated and multi-group designs.}, journal = {Ecology}, volume = {92}, number = {11}, pages = {2049-2055}, doi = {10.1890/11-0423.1}, pmid = {22164829}, issn = {0012-9658}, mesh = {Data Interpretation, Statistical ; Ecology/*methods ; *Ecosystem ; *Meta-Analysis as Topic ; *Research Design ; }, abstract = {A common effect size metric used to quantify the outcome of experiments for ecological meta-analysis is the response ratio (RR): the log proportional change in the means of a treatment and control group. Estimates of the variance of RR are also important for meta-analysis because they serve as weights when effect sizes are averaged and compared. The variance of an effect size is typically a function of sampling error; however, it can also be influenced by study design. Here, I derive new variances and covariances for RR for several often-encountered experimental designs: when the treatment and control means are correlated; when multiple treatments have a common control; when means are based on repeated measures; and when the study has a correlated factorial design, or is multivariate. These developments are useful for improving the quality of data extracted from studies for meta-analysis and help address some of the common challenges meta-analysts face when quantifying a diversity of experimental designs with the response ratio.}, } @article {pmid22163286, year = {2011}, author = {Recio, MR and Mathieu, R and Denys, P and Sirguey, P and Seddon, PJ}, title = {Lightweight GPS-tags, one giant leap for wildlife tracking? An assessment approach.}, journal = {PloS one}, volume = {6}, number = {12}, pages = {e28225}, pmid = {22163286}, issn = {1932-6203}, mesh = {Animal Migration ; Animals ; Behavior, Animal ; Cats ; Ecology/*methods ; Ecosystem ; Environment ; Environmental Monitoring/methods ; Female ; *Geographic Information Systems ; Male ; Models, Statistical ; Monitoring, Ambulatory ; Motion ; Movement ; New Zealand ; Reproducibility of Results ; Seasons ; Trees ; }, abstract = {Recent technological improvements have made possible the development of lightweight GPS-tagging devices suitable to track medium-to-small sized animals. However, current inferences concerning GPS performance are based on heavier designs, suitable only for large mammals. Lightweight GPS-units are deployed close to the ground, on species selecting micro-topographical features and with different behavioural patterns in comparison to larger mammal species. We assessed the effects of vegetation, topography, motion, and behaviour on the fix success rate for lightweight GPS-collar across a range of natural environments, and at the scale of perception of feral cats (Felis catus). Units deployed at 20 cm above the ground in sites of varied vegetation and topography showed that trees (native forest) and shrub cover had the largest influence on fix success rate (89% on average); whereas tree cover, sky availability, number of satellites and horizontal dilution of position (HDOP) were the main variables affecting location error (±39.5 m and ±27.6 m before and after filtering outlier fixes). Tests on HDOP or number of satellites-based screening methods to remove inaccurate locations achieved only a small reduction of error and discarded many accurate locations. Mobility tests were used to simulate cats' motion, revealing a slightly lower performance as compared to the fixed sites. GPS-collars deployed on 43 cats showed no difference in fix success rate by sex or season. Overall, fix success rate and location error values were within the range of previous tests carried out with collars designed for larger species. Lightweight GPS-tags are a suitable method to track medium to small size species, hence increasing the range of opportunities for spatial ecology research. However, the effects of vegetation, topography and behaviour on location error and fix success rate need to be evaluated prior to deployment, for the particular study species and their habitats.}, } @article {pmid22163212, year = {2011}, author = {Gao, Y and Gao, J and Chen, J and Xu, Y and Zhao, J}, title = {Regionalizing aquatic ecosystems based on the river subbasin taxonomy concept and spatial clustering techniques.}, journal = {International journal of environmental research and public health}, volume = {8}, number = {11}, pages = {4367-4385}, pmid = {22163212}, issn = {1660-4601}, mesh = {Animals ; Aquatic Organisms ; Biodiversity ; China ; Cluster Analysis ; Conservation of Natural Resources/*methods ; *Ecosystem ; Environmental Monitoring/*methods ; Geographic Information Systems ; Geography ; *Lakes ; Maps as Topic ; *Rivers ; }, abstract = {Aquatic ecoregions were increasingly used as spatial units for aquatic ecosystem management at the watershed scale. In this paper, the principle of including land area, comprehensiveness and dominance, conjugation and hierarchy were selected as regionalizing principles. Elevation and drainage density were selected as the regionalizing indicators for the delineation of level I aquatic ecoregions, and percent of construction land area, percent of cultivated land area, soil type and slope for the level II. Under the support of GIS technology, the spatial distribution maps of the two indicators for level I and the four indicators for level II aquatic ecoregion delineation were generated from the raster data based on the 1,107 subwatersheds. River subbasin taxonomy concept, two-step spatial clustering analysis approach and manual-assisted method were used to regionalize aquatic ecosystems in the Taihu Lake watershed. Then the Taihu Lake watershed was divided into two level I aquatic ecoregions, including Ecoregion I1 and Ecoregion I2, and five level II aquatic subecoregions, including Subecoregion II11, Subecoregion II12, Subecoregion II21, Subecoregion II22 and Subecoregion II23. Moreover, the characteristics of the two level I aquatic ecoregions and five level II aquatic subecoregions in the Taihu Lake watershed were summarized, showing that there were significant differences in topography, socio-economic development, water quality and aquatic ecology, etc. The results of quantitative comparison of aquatic life also indicated that the dominant species of fish, benthic density, biomass, dominant species, Shannon-Wiener diversity index, Margalef species richness index, Pielou evenness index and ecological dominance showed great spatial variability between the two level I aquatic ecoregions and five level II aquatic subecoregions. It reflected the spatial heterogeneities and the uneven natures of aquatic ecosystems in the Taihu Lake watershed.}, } @article {pmid22154516, year = {2012}, author = {Parr, CS and Guralnick, R and Cellinese, N and Page, RD}, title = {Evolutionary informatics: unifying knowledge about the diversity of life.}, journal = {Trends in ecology & evolution}, volume = {27}, number = {2}, pages = {94-103}, doi = {10.1016/j.tree.2011.11.001}, pmid = {22154516}, issn = {1872-8383}, mesh = {*Biodiversity ; Biological Evolution ; Computational Biology/*methods ; Ecology/methods/trends ; Phylogeny ; }, abstract = {The accelerating growth of data and knowledge in evolutionary biology is indisputable. Despite this rapid progress, information remains scattered, poorly documented and in formats that impede discovery and integration. A grand challenge is the creation of a linked system of all evolutionary data, information and knowledge organized around Darwin's ever-growing Tree of Life. Such a system, accommodating topological disagreement where necessary, would consolidate taxon names, phenotypic and geographical distributional data across clades, and serve as an integrated community resource. The field of evolutionary informatics, reviewed here for the first time, has matured into a robust discipline that is developing the conceptual, infrastructure and community frameworks for meeting this grand challenge.}, } @article {pmid22146370, year = {2011}, author = {Jia, XD and Wang, T and Zhai, M and Li, YR and Guo, ZR}, title = {Genetic diversity and identification of Chinese-grown pecan using ISSR and SSR markers.}, journal = {Molecules (Basel, Switzerland)}, volume = {16}, number = {12}, pages = {10078-10092}, pmid = {22146370}, issn = {1420-3049}, mesh = {Base Sequence ; Carya/*genetics/*growth & development ; China ; Cluster Analysis ; Databases, Genetic ; Ecotype ; Genetic Markers ; *Genetic Variation ; Microsatellite Repeats/*genetics ; Molecular Sequence Data ; Phylogeny ; }, abstract = {Pecan is an important horticultural nut crop originally from North America and now widely cultivated in China for its high ecological, ornamental and economic value. Currently, there are over one hundred cultivars grown in China, including introduced American cultivars and Chinese seedling breeding cultivars. Molecular markers were used to assess the genetic diversity of these cultivars and to identify the pedigrees of fine pecan plants with good characteristics and no cultivar-related data. A total of 77 samples grown in China were studied, including 14 introduced cultivars, 12 domestic seedling breeding cultivars, and 49 fine pecan plants with no cultivar data, together with Carya cathayensis and Juglans nigra. A total of 77 ISSR and 19 SSR primers were prescreened; 10 ISSR and eight SSR primers were selected, yielding a total of 94 amplified bands (100% polymorphic) in the range of 140-1,950 bp for the ISSR and 70 amplified bands (100% polymorphic) in the range of 50-350 bp for SSR markers. Genetic diversity analyses indicated Chinese-grown pecan cultivars and fine plants had significant diversity at the DNA level. The dengrograms constructed with ISSR, SSR or combined data were very similar, but showed very weak grouping association with morphological characters. However, the progeny were always grouped with the parents. The great diversity found among the Chinese cultivars and the interesting germplasm of the fine pecan plants analyzed in this study are very useful for increasing the diversity of the pecan gene pool. All 77 accessions in this study could be separated based on the ISSR and SSR fingerprints produced by one or more primers. The results of our study also showed that ISSR and SSR techniques were both suitable for genetic diversity analyses and the identification of pecan resources.}, } @article {pmid22144390, year = {2012}, author = {Tucker, A and Duplisea, D}, title = {Bioinformatics tools in predictive ecology: applications to fisheries.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {367}, number = {1586}, pages = {279-290}, pmid = {22144390}, issn = {1471-2970}, mesh = {Algorithms ; Animals ; Bayes Theorem ; Computational Biology/*methods ; Ecology/*methods ; Fisheries/methods ; Forecasting/*methods ; Gadus morhua/growth & development ; }, abstract = {There has been a huge effort in the advancement of analytical techniques for molecular biological data over the past decade. This has led to many novel algorithms that are specialized to deal with data associated with biological phenomena, such as gene expression and protein interactions. In contrast, ecological data analysis has remained focused to some degree on off-the-shelf statistical techniques though this is starting to change with the adoption of state-of-the-art methods, where few assumptions can be made about the data and a more explorative approach is required, for example, through the use of Bayesian networks. In this paper, some novel bioinformatics tools for microarray data are discussed along with their 'crossover potential' with an application to fisheries data. In particular, a focus is made on the development of models that identify functionally equivalent species in different fish communities with the aim of predicting functional collapse.}, } @article {pmid22144147, year = {2012}, author = {Williamson, SJ and Yooseph, S}, title = {From bacterial to microbial ecosystems (metagenomics).}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {804}, number = {}, pages = {35-55}, doi = {10.1007/978-1-61779-361-5_3}, pmid = {22144147}, issn = {1940-6029}, mesh = {Computational Biology/*methods ; DNA, Bacterial/*isolation & purification ; *Ecosystem ; Gene Library ; Metagenome/*genetics ; Metagenomics/*methods ; Sequence Analysis, DNA/*methods ; Specimen Handling/*methods ; }, abstract = {Metagenomics is revolutionizing the field of microbial ecology through techniques that eliminate the prerequisite of culturing. Metagenomic studies of microbial populations in different environments reveal the incredible diversity and adaptive capabilities of these organisms. With the advent of cheaper, high-throughput sequencing technologies, these studies are also producing vast amounts of sequence data. Here, we discuss the different components of a metagenomic study including sample collection, DNA extraction, sequencing, and informatics. We highlight their issues and challenges, and review the solutions that are currently in use. We conclude with examples of metagenomic studies conducted on environments of varying complexities.}, } @article {pmid22143240, year = {2011}, author = {Wittkopp, PJ and Kalay, G}, title = {Cis-regulatory elements: molecular mechanisms and evolutionary processes underlying divergence.}, journal = {Nature reviews. Genetics}, volume = {13}, number = {1}, pages = {59-69}, pmid = {22143240}, issn = {1471-0064}, mesh = {Animals ; Base Sequence ; Computational Biology ; Conserved Sequence/genetics ; Enhancer Elements, Genetic/genetics ; *Evolution, Molecular ; Gene Expression Regulation/*genetics ; Genome ; Genomics ; Humans ; Mice ; *Regulatory Sequences, Nucleic Acid/genetics ; }, abstract = {Cis-regulatory sequences, such as enhancers and promoters, control development and physiology by regulating gene expression. Mutations that affect the function of these sequences contribute to phenotypic diversity within and between species. With many case studies implicating divergent cis-regulatory activity in phenotypic evolution, researchers have recently begun to elucidate the genetic and molecular mechanisms that are responsible for cis-regulatory divergence. Approaches include detailed functional analysis of individual cis-regulatory elements and comparing mechanisms of gene regulation among species using the latest genomic tools. Despite the limited number of mechanistic studies published to date, this work shows how cis-regulatory activity can diverge and how studies of cis-regulatory divergence can address long-standing questions about the genetic mechanisms of phenotypic evolution.}, } @article {pmid22143174, year = {2011}, author = {Choi, MH and Cheong, KS and Cho, BM and Hwang, IK and Kim, CH and Kim, MH and Hwang, SS and Lim, JH and Yoon, TH}, title = {Deprivation and mortality at the town level in Busan, Korea: an ecological study.}, journal = {Journal of preventive medicine and public health = Yebang Uihakhoe chi}, volume = {44}, number = {6}, pages = {242-248}, pmid = {22143174}, issn = {2233-4521}, mesh = {Cause of Death ; Confidence Intervals ; Geographic Information Systems ; Health Services Accessibility ; *Health Status Disparities ; Humans ; Korea/epidemiology ; Life Expectancy ; Mortality/*trends ; Normal Distribution ; Poverty/*statistics & numerical data ; Regression Analysis ; Risk ; Socioeconomic Factors ; }, abstract = {OBJECTIVES: Busan is reported to have the highest mortality rate among 16 provinces in Korea, as well as considerable health inequality across its districts. This study sought to examine overall and cause-specific mortality and deprivation at the town level in Busan, thereby identifying towns and causes of deaths to be targeted for improving overall health and alleviating health inequality.

METHODS: Standardized mortality ratios (SMRs) for all-cause and four specific leading causes of death were calculated at the town level in Busan for the years 2005 through 2008. To construct a deprivation index, principal components and factor analysis were adopted, using 10% sample data from the 2005 census. Geographic information system (GIS) mapping techniques were applied to compare spatial distributions between the deprivation index and SMRs. We fitted the Gaussian conditional autoregressive model (CAR) to estimate the relative risks of mortality by deprivation level, controlling for both the heterogeneity effect and spatial autocorrelation.

RESULTS: The SMRs of towns in Busan averaged 100.3, ranging from 70.7 to 139.8. In old inner cities and towns reclaimed for replaced households, the deprivation index and SMRs were relatively high. CAR modeling showed that gaps in SMRs for heart disease, cerebrovascular disease, and physical injury were particularly high.

CONCLUSIONS: Our findings indicate that more deprived towns are likely to have higher mortality, in particular from cardiovascular disease and physical injury. To improve overall health status and address health inequality, such deprived towns should be targeted.}, } @article {pmid22142623, year = {2012}, author = {Hordijk, W and Steel, M}, title = {Predicting template-based catalysis rates in a simple catalytic reaction model.}, journal = {Journal of theoretical biology}, volume = {295}, number = {}, pages = {132-138}, doi = {10.1016/j.jtbi.2011.11.024}, pmid = {22142623}, issn = {1095-8541}, mesh = {*Biocatalysis ; Computational Biology/methods ; Computer Simulation ; *Models, Chemical ; Origin of Life ; }, abstract = {We show that in a particular model of catalytic reaction systems, known as the binary polymer model, there is a mathematical concordance between two versions of the model: (1) random catalysis and (2) template-based catalysis. In particular, we derive an analytical calculation that allows us to accurately predict the (observed) required level of catalysis in one version of the model from that in the other version, for a given probability of having self-sustaining autocatalytic sets exist in instances of both model versions. This provides a tractable connection between two models that have been investigated in theoretical origin-of-life studies.}, } @article {pmid22138161, year = {2012}, author = {Castro-Nallar, E and Pérez-Losada, M and Burton, GF and Crandall, KA}, title = {The evolution of HIV: inferences using phylogenetics.}, journal = {Molecular phylogenetics and evolution}, volume = {62}, number = {2}, pages = {777-792}, pmid = {22138161}, issn = {1095-9513}, support = {R01GM66276/GM/NIGMS NIH HHS/United States ; R56AI39963/AI/NIAID NIH HHS/United States ; R56 AI039963-08/AI/NIAID NIH HHS/United States ; R56 AI039963/AI/NIAID NIH HHS/United States ; R01 GM066276/GM/NIGMS NIH HHS/United States ; R01 GM066276-04/GM/NIGMS NIH HHS/United States ; }, mesh = {Adaptation, Physiological ; Africa ; Anti-HIV Agents/administration & dosage ; Asia ; *Computational Biology ; Drug Resistance, Viral ; Europe ; *Evolution, Molecular ; Genetics, Population ; *Genome, Viral ; HIV/*genetics ; HIV Infections/drug therapy/transmission/*virology ; Humans ; *Mutation ; North America ; *Phylogeny ; }, abstract = {Molecular phylogenetics has revolutionized the study of not only evolution but also disparate fields such as genomics, bioinformatics, epidemiology, ecology, microbiology, molecular biology and biochemistry. Particularly significant are its achievements in population genetics as a result of the development of coalescent theory, which have contributed to more accurate model-based parameter estimation and explicit hypothesis testing. The study of the evolution of many microorganisms, and HIV in particular, have benefited from these new methodologies. HIV is well suited for such sophisticated population analyses because of its large population sizes, short generation times, high substitution rates and relatively small genomes. All these factors make HIV an ideal and fascinating model to study molecular evolution in real time. Here we review the significant advances made in HIV evolution through the application of phylogenetic approaches. We first examine the relative roles of mutation and recombination on the molecular evolution of HIV and its adaptive response to drug therapy and tissue allocation. We then review some of the fundamental questions in HIV evolution in relation to its origin and diversification and describe some of the insights gained using phylogenies. Finally, we show how phylogenetic analysis has advanced our knowledge of HIV dynamics (i.e., phylodynamics).}, } @article {pmid22136175, year = {2012}, author = {, and A'Hara, SW and Amouroux, P and Argo, EE and Avand-Faghih, A and Barat, A and Barbieri, L and Bert, TM and Blatrix, R and Blin, A and Bouktila, D and Broome, A and Burban, C and Capdevielle-Dulac, C and Casse, N and Chandra, S and Cho, KJ and Cottrell, JE and Crawford, CR and Davis, MC and Delatte, H and Desneux, N and Djieto-Lordon, C and Dubois, MP and El-Mergawy, RA and Gallardo-Escárate, C and Garcia, M and Gardiner, MM and Guillemaud, T and Haye, PA and Hellemans, B and Hinrichsen, P and Jeon, JH and Kerdelhué, C and Kharrat, I and Kim, KH and Kim, YY and Kwan, YS and Labbe, EM and LaHood, E and Lee, KM and Lee, WO and Lee, YH and Legoff, I and Li, H and Lin, CP and Liu, SS and Liu, YG and Long, D and Maes, GE and Magnoux, E and Mahanta, PC and Makni, H and Makni, M and Malausa, T and Matura, R and McKey, D and McMillen-Jackson, AL and Méndez, MA and Mezghani-Khemakhem, M and Michel, AP and Paul, M and Muriel-Cunha, J and Nibouche, S and Normand, F and Palkovacs, EP and Pande, V and Parmentier, K and Peccoud, J and Piatscheck, F and Puchulutegui, C and Ramos, R and Ravest, G and Richner, H and Robbens, J and Rochat, D and Rousselet, J and Saladin, V and Sauve, M and Schlei, O and Schultz, TF and Scobie, AR and Segovia, NI and Seyoum, S and Silvain, JF and Tabone, E and Van Houdt, JK and Vandamme, SG and Volckaert, FA and Wenburg, J and Willis, TV and Won, YJ and Ye, NH and Zhang, W and Zhang, YX}, title = {Permanent genetic resources added to Molecular Ecology Resources Database 1 August 2011-30 September 2011.}, journal = {Molecular ecology resources}, volume = {12}, number = {1}, pages = {185-189}, doi = {10.1111/j.1755-0998.2011.03088.x}, pmid = {22136175}, issn = {1755-0998}, mesh = {Animals ; *Databases, Genetic ; Fishes/*genetics ; Insecta/*genetics ; Invertebrates/*genetics ; Microsatellite Repeats ; Molecular Sequence Data ; Pinus/*genetics ; }, abstract = {This article documents the addition of 299 microsatellite marker loci and nine pairs of single-nucleotide polymorphism (SNP) EPIC primers to the Molecular Ecology Resources (MER) Database. Loci were developed for the following species: Alosa pseudoharengus, Alosa aestivalis, Aphis spiraecola, Argopecten purpuratus, Coreoleuciscus splendidus, Garra gotyla, Hippodamia convergens, Linnaea borealis, Menippe mercenaria, Menippe adina, Parus major, Pinus densiflora, Portunus trituberculatus, Procontarinia mangiferae, Rhynchophorus ferrugineus, Schizothorax richardsonii, Scophthalmus rhombus, Tetraponera aethiops, Thaumetopoea pityocampa, Tuta absoluta and Ugni molinae. These loci were cross-tested on the following species: Barilius bendelisis, Chiromantes haematocheir, Eriocheir sinensis, Eucalyptus camaldulensis, Eucalyptus cladocalix, Eucalyptus globulus, Garra litaninsis vishwanath, Garra para lissorhynchus, Guindilla trinervis, Hemigrapsus sanguineus, Luma chequen. Guayaba, Myrceugenia colchagüensis, Myrceugenia correifolia, Myrceugenia exsucca, Parasesarma plicatum, Parus major, Portunus pelagicus, Psidium guayaba, Schizothorax richardsonii, Scophthalmus maximus, Tetraponera latifrons, Thaumetopoea bonjeani, Thaumetopoea ispartensis, Thaumetopoea libanotica, Thaumetopoea pinivora, Thaumetopoea pityocampa ena clade, Thaumetopoea solitaria, Thaumetopoea wilkinsoni and Tor putitora. This article also documents the addition of nine EPIC primer pairs for Euphaea decorata, Euphaea formosa, Euphaea ornata and Euphaea yayeyamana.}, } @article {pmid22134646, year = {2012}, author = {McDonald, D and Price, MN and Goodrich, J and Nawrocki, EP and DeSantis, TZ and Probst, A and Andersen, GL and Knight, R and Hugenholtz, P}, title = {An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea.}, journal = {The ISME journal}, volume = {6}, number = {3}, pages = {610-618}, pmid = {22134646}, issn = {1751-7370}, support = {UH2/UH3CA140233/CA/NCI NIH HHS/United States ; U01 HG004866/HG/NHGRI NIH HHS/United States ; R01 HG004872/HG/NHGRI NIH HHS/United States ; U01-HG004866/HG/NHGRI NIH HHS/United States ; /HHMI_/Howard Hughes Medical Institute/United States ; }, mesh = {Archaea/*classification/genetics ; Bacteria/*classification/genetics ; Classification/*methods ; *Databases, Genetic ; Metagenomics ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Software ; }, abstract = {Reference phylogenies are crucial for providing a taxonomic framework for interpretation of marker gene and metagenomic surveys, which continue to reveal novel species at a remarkable rate. Greengenes is a dedicated full-length 16S rRNA gene database that provides users with a curated taxonomy based on de novo tree inference. We developed a 'taxonomy to tree' approach for transferring group names from an existing taxonomy to a tree topology, and used it to apply the Greengenes, National Center for Biotechnology Information (NCBI) and cyanoDB (Cyanobacteria only) taxonomies to a de novo tree comprising 408,315 sequences. We also incorporated explicit rank information provided by the NCBI taxonomy to group names (by prefixing rank designations) for better user orientation and classification consistency. The resulting merged taxonomy improved the classification of 75% of the sequences by one or more ranks relative to the original NCBI taxonomy with the most pronounced improvements occurring in under-classified environmental sequences. We also assessed candidate phyla (divisions) currently defined by NCBI and present recommendations for consolidation of 34 redundantly named groups. All intermediate results from the pipeline, which includes tree inference, jackknifing and transfer of a donor taxonomy to a recipient tree (tax2tree) are available for download. The improved Greengenes taxonomy should provide important infrastructure for a wide range of megasequencing projects studying ecosystems on scales ranging from our own bodies (the Human Microbiome Project) to the entire planet (the Earth Microbiome Project). The implementation of the software can be obtained from http://sourceforge.net/projects/tax2tree/.}, } @article {pmid22132191, year = {2011}, author = {Milano, I and Babbucci, M and Panitz, F and Ogden, R and Nielsen, RO and Taylor, MI and Helyar, SJ and Carvalho, GR and Espiñeira, M and Atanassova, M and Tinti, F and Maes, GE and Patarnello, T and , and Bargelloni, L}, title = {Novel tools for conservation genomics: comparing two high-throughput approaches for SNP discovery in the transcriptome of the European hake.}, journal = {PloS one}, volume = {6}, number = {11}, pages = {e28008}, pmid = {22132191}, issn = {1932-6203}, mesh = {Animals ; Conservation of Natural Resources/*methods ; Databases, Genetic ; Europe ; Gadiformes/*genetics ; Gene Frequency/genetics ; Genomics/*methods ; Geography ; Heterozygote ; High-Throughput Nucleotide Sequencing/*methods ; Molecular Sequence Annotation ; Polymorphism, Single Nucleotide/*genetics ; ROC Curve ; Reproducibility of Results ; Sequence Analysis, DNA ; Transcriptome/*genetics ; }, abstract = {The growing accessibility to genomic resources using next-generation sequencing (NGS) technologies has revolutionized the application of molecular genetic tools to ecology and evolutionary studies in non-model organisms. Here we present the case study of the European hake (Merluccius merluccius), one of the most important demersal resources of European fisheries. Two sequencing platforms, the Roche 454 FLX (454) and the Illumina Genome Analyzer (GAII), were used for Single Nucleotide Polymorphisms (SNPs) discovery in the hake muscle transcriptome. De novo transcriptome assembly into unique contigs, annotation, and in silico SNP detection were carried out in parallel for 454 and GAII sequence data. High-throughput genotyping using the Illumina GoldenGate assay was performed for validating 1,536 putative SNPs. Validation results were analysed to compare the performances of 454 and GAII methods and to evaluate the role of several variables (e.g. sequencing depth, intron-exon structure, sequence quality and annotation). Despite well-known differences in sequence length and throughput, the two approaches showed similar assay conversion rates (approximately 43%) and percentages of polymorphic loci (67.5% and 63.3% for GAII and 454, respectively). Both NGS platforms therefore demonstrated to be suitable for large scale identification of SNPs in transcribed regions of non-model species, although the lack of a reference genome profoundly affects the genotyping success rate. The overall efficiency, however, can be improved using strict quality and filtering criteria for SNP selection (sequence quality, intron-exon structure, target region score).}, } @article {pmid22126052, year = {2011}, author = {Sun, YG and Li, XZ and Guo, WY and He, YL and Jia, Y}, title = {[Ecological benefits of greening and related controlling factors in urban residential areas of Hangzhou: a quantitative analysis].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {22}, number = {9}, pages = {2383-2390}, pmid = {22126052}, issn = {1001-9332}, mesh = {China ; Cities ; *City Planning ; *Ecosystem ; *Environment Design ; Geographic Information Systems ; *Plant Development ; Remote Sensing Technology ; }, abstract = {Based on the 1 m x 1 m high resolution aerial images in 2007 and the 30 m x 30 m Landsat 5 TM images in summer 2007, and with the help of GIS and remote sensing image interpretation, this paper calculated the normalized difference vegetation indices (NDVI) representing the overall ecological benefits of greening as well as the six controlling factors, i.e., multilayer structure height, area ratio of softness to hardness, greening rate, floor area ratio, greening area, and building density, in 30 typical urban residential quarters of west Hangzhou. The contributions of the controlling factors to the ecological benefits of greening as well as the quantitative relationships between the overall ecological benefits and the six controlling factors were analyzed by multiple linear regression and correspondence analysis, and some advises were given for the improvement of the ecological benefits. The contribution rate of the six factors was in the order of multilayer structure height > area ratio of softness to hardness > greening rate > floor area ratio > greening area > building density, and the contribution of multilayer structure height was far greater than that of the others whereas building density had the weakest effect on the ecological benefits. Correspondence analysis was effective in simplifying a complex data table into an intuitive two-dimensional chart, and thus, a potential powerful tool in decision-making for the improvement of ecological benefits of greening in urban residential quarters.}, } @article {pmid22126051, year = {2011}, author = {Bai, Y and Zheng, H and Ouyang, ZY and Xu, WH and Jiang, B and Fang, Y}, title = {[Ecological function regionalization of Haihe River basin].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {22}, number = {9}, pages = {2377-2382}, pmid = {22126051}, issn = {1001-9332}, mesh = {China ; *Conservation of Natural Resources ; Ecology ; *Ecosystem ; Environmental Monitoring/*methods ; Geographic Information Systems ; Remote Sensing Technology ; Rivers ; *Water Supply ; }, abstract = {Aiming at the features of Haihe River basin, and by using RS and GIS technologies in combining with qualitative and quantitative analyses, a regionalization was conducted on the ecological function of the basin. The Haihe River basin could be divided into 5 ecoregions, 24 sub-ecoregions, and 114 eco-functional zones. Furthermore, 11 critical eco-functional zones were identified, according to the dominant functions (water conservation, soil conservation, wind prevention and sand fixation, and biodiversity protection) at basin scale. This regionalization made clear the regions important for the ecological security of Haihe River basin, which could guide the orderly exploitation and utilization of natural resources and the rational distribution of industries, offer scientific basis for the ecological environment protection, and maintain the ecological security of the basin.}, } @article {pmid22124620, year = {2012}, author = {Campbell, R and Greeson, MR and Bybee, D and Fehler-Cabral, G}, title = {Adolescent sexual assault victims and the legal system: building community relationships to improve prosecution rates.}, journal = {American journal of community psychology}, volume = {50}, number = {1-2}, pages = {141-154}, doi = {10.1007/s10464-011-9485-3}, pmid = {22124620}, issn = {1573-2770}, mesh = {Adolescent ; *Community Networks ; *Cooperative Behavior ; DNA/analysis ; Female ; Humans ; Male ; Program Evaluation ; Resource Allocation ; Sex Offenses/*legislation & jurisprudence ; United States/epidemiology ; }, abstract = {Adolescents are at high risk for sexual assault, but few of these crimes are reported to the police and prosecuted by the criminal justice system. To address this problem, communities throughout the United States have implemented multidisciplinary interventions to improve post-assault care for victims and increase prosecution rates. The two most commonly implemented interventions are Sexual Assault Nurse Examiner (SANE) Programs and Sexual Assault Response Teams (SARTs). The purpose of this study was to determine whether community-level context (i.e., stakeholder engagement and collaboration) was predictive of adolescent legal case outcomes, after accounting for "standard" factors that affect prosecution success (i.e., victim, assault, and evidence characteristics). Overall, 40% of the adolescent cases from these two SANE-SART programs (over a 10-year period) were successfully prosecuted. Cases were more likely to be prosecuted for younger victims, those with disabilities, those who knew their offenders, and instances in which the rape evidence collection kit was submitted by police for analysis. After accounting for these influences, multi-level modeling results revealed that in one site decreased allocation of community resources to adolescent sexual assault cases had a significant negative effect on prosecution case outcomes. Results are explained in terms of Wolff's (Am J Community Psychol 29:173-191, 2001) concept of "over-coalitioned" communities and Kelly's (1968) ecological principles.}, } @article {pmid22122883, year = {2012}, author = {Christie-Oleza, JA and Piña-Villalonga, JM and Bosch, R and Nogales, B and Armengaud, J}, title = {Comparative proteogenomics of twelve Roseobacter exoproteomes reveals different adaptive strategies among these marine bacteria.}, journal = {Molecular & cellular proteomics : MCP}, volume = {11}, number = {2}, pages = {M111.013110}, pmid = {22122883}, issn = {1535-9484}, mesh = {*Adaptation, Physiological ; Bacterial Proteins/*genetics/*metabolism ; Chromatography, Liquid ; Computational Biology ; *Genomics ; Proteome/*analysis ; *Proteomics ; Roseobacter/genetics/*metabolism ; Seawater/*microbiology ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ; }, abstract = {Roseobacters are generalist bacteria abundantly found in the oceans. Because little is known on how marine microorganisms interact in association or competition, we focused our attention on the microbial exoproteome, a key component in their interaction with extracellular milieu. Here we present a comparative analysis of the theoretically encoded exoproteome of twelve members of the Roseobacter group validated by extensive comparative proteogenomics. In silico analysis revealed that 30% of the encoded proteome of these microorganisms could be exported. The ratio of the different protein categories varied in accordance to the ecological distinctness of each strain, a trait reinforced by quantitative proteomics data. Despite the interspecies variations found, the most abundantly detected proteins by shotgun proteomics were from transporter, adhesion, motility, and toxin-like protein categories, defining four different plausible adaptive strategies within the Roseobacter group. In some strains the toxin-secretion strategy was over-represented with repeats-in-toxin-like proteins. Our results show that exoproteomes strongly depend on bacterial trophic strategy and can slightly change because of culture conditions. Simulated natural conditions and the effect of the indigenous microbial community on the exoproteome of Ruegeria pomeroyi DSS-3 were also assayed. Interestingly, we observed a significant depletion of the toxin-like proteins usually secreted by R. pomeroyi DSS-3 when grown in presence of a natural community sampled from a Mediterranean Sea port. The significance of this specific fraction of the exoproteome is discussed.}, } @article {pmid22118495, year = {2012}, author = {Higgs, MD and Ver Hoef, JM}, title = {Discretized and aggregated: modeling dive depth of harbor seals from ordered categorical data with temporal autocorrelation.}, journal = {Biometrics}, volume = {68}, number = {3}, pages = {965-974}, doi = {10.1111/j.1541-0420.2011.01710.x}, pmid = {22118495}, issn = {1541-0420}, mesh = {Alaska ; Animals ; Bayes Theorem ; Behavior, Animal ; Biometry ; Data Interpretation, Statistical ; Diving/*physiology ; Female ; Male ; *Models, Biological ; *Models, Statistical ; Normal Distribution ; Phoca/*physiology ; Probability ; Regression Analysis ; Time Factors ; }, abstract = {Ordered categorical data are pervasive in environmental and ecological data, and often arise from constraints that require discretizing a continuous variable into ordered categories. A great deal of data have been collected toward the study of marine mammal dive behavior using satellite depth recorders (SDRs), which often discretize a continuous variable such as depth. Additionally, data storage or transmission constraints may also necessitate the aggregation of data over time intervals of a specified length. The categorization and aggregation create a time series of ordered multicategory counts for each animal, which present challenges in terms of statistical modeling and practical interpretation. We describe an intuitive strategy for modeling such aggregated, ordered categorical data allowing for inference regarding the category probabilities and a measure of central tendency on the original scale of the data (e.g., meters), along with incorporation of temporal correlation and overdispersion. The strategy extends covariate-specific cutpoint models for ordinal data. We demonstrate the method in an analysis of SDR dive-depth data collected on harbor seals in Alaska. The primary goal of the analysis is to assess the relationship of covariates, such as time of day, with number of dives and maximum depth of dives. We also predict missing values and introduce novel graphical summaries of the data and results.}, } @article {pmid22116848, year = {2011}, author = {Pennisi, E}, title = {Animal ecology. Global tracking of small animals gains momentum.}, journal = {Science (New York, N.Y.)}, volume = {334}, number = {6059}, pages = {1042}, doi = {10.1126/science.334.6059.1042}, pmid = {22116848}, issn = {1095-9203}, mesh = {*Animal Migration ; Animals ; Ecosystem ; *Geographic Information Systems ; *Remote Sensing Technology ; *Spacecraft ; }, } @article {pmid22110245, year = {2012}, author = {Lischer, HE and Excoffier, L}, title = {PGDSpider: an automated data conversion tool for connecting population genetics and genomics programs.}, journal = {Bioinformatics (Oxford, England)}, volume = {28}, number = {2}, pages = {298-299}, doi = {10.1093/bioinformatics/btr642}, pmid = {22110245}, issn = {1367-4811}, mesh = {*Genetics, Population ; *Genomics ; *Information Storage and Retrieval ; *Software ; User-Computer Interface ; }, abstract = {UNLABELLED: The analysis of genetic data often requires a combination of several approaches using different and sometimes incompatible programs. In order to facilitate data exchange and file conversions between population genetics programs, we introduce PGDSpider, a Java program that can read 27 different file formats and export data into 29, partially overlapping, other file formats. The PGDSpider package includes both an intuitive graphical user interface and a command-line version allowing its integration in complex data analysis pipelines.

AVAILABILITY: PGDSpider is freely available under the BSD 3-Clause license on http://cmpg.unibe.ch/software/PGDSpider/.}, } @article {pmid22110026, year = {2012}, author = {Goodstein, DM and Shu, S and Howson, R and Neupane, R and Hayes, RD and Fazo, J and Mitros, T and Dirks, W and Hellsten, U and Putnam, N and Rokhsar, DS}, title = {Phytozome: a comparative platform for green plant genomics.}, journal = {Nucleic acids research}, volume = {40}, number = {Database issue}, pages = {D1178-86}, pmid = {22110026}, issn = {1362-4962}, mesh = {*Databases, Nucleic Acid ; *Genes, Plant ; *Genome, Plant ; Genomics ; Multigene Family ; Software ; }, abstract = {The number of sequenced plant genomes and associated genomic resources is growing rapidly with the advent of both an increased focus on plant genomics from funding agencies, and the application of inexpensive next generation sequencing. To interact with this increasing body of data, we have developed Phytozome (http://www.phytozome.net), a comparative hub for plant genome and gene family data and analysis. Phytozome provides a view of the evolutionary history of every plant gene at the level of sequence, gene structure, gene family and genome organization, while at the same time providing access to the sequences and functional annotations of a growing number (currently 25) of complete plant genomes, including all the land plants and selected algae sequenced at the Joint Genome Institute, as well as selected species sequenced elsewhere. Through a comprehensive plant genome database and web portal, these data and analyses are available to the broader plant science research community, providing powerful comparative genomics tools that help to link model systems with other plants of economic and ecological importance.}, } @article {pmid22109861, year = {2011}, author = {Machado da Silva, AV and Magalhães, Mde A and Peçanha Brazil, R and Carreira, JC}, title = {Ecological study and risk mapping of leishmaniasis in an endemic area of Brazil based on a geographical information systems approach.}, journal = {Geospatial health}, volume = {6}, number = {1}, pages = {33-40}, doi = {10.4081/gh.2011.155}, pmid = {22109861}, issn = {1970-7096}, mesh = {Animals ; Brazil/epidemiology ; Dog Diseases/epidemiology/prevention & control/transmission ; Dogs ; Endemic Diseases/*prevention & control ; *Geographic Information Systems ; Humans ; Insect Vectors ; Insecticides/*administration & dosage ; Leishmaniasis, Visceral/*epidemiology/*prevention & control/transmission ; Risk Assessment ; }, abstract = {Visceral leishmaniasis is a vector-borne disease highly influenced by eco-epidemiological factors. Geographical information systems (GIS) have proved to be a suitable approach for the analysis of environmental components that affect the spatial distribution of diseases. Exploiting this methodology, a model was developed for the mapping of the distribution and incidence of canine leishmaniasis in an endemic area of Brazil. Local variations were observed with respect to infection incidence and distribution of serological titers, i.e. high titers were noted close to areas with preserved vegetation, while low titers were more frequent in areas where people kept chickens. Based on these results, we conclude that the environment plays an important role in generating relatively protected areas within larger endemic regions, but that it can also contribute to the creation of hotspots with clusters of comparatively high serological titers indicating a high level of transmission compared with neighbouring areas.}, } @article {pmid22109729, year = {2012}, author = {Cardille, JA and White, JC and Wulder, MA and Holland, T}, title = {Representative landscapes in the forested area of Canada.}, journal = {Environmental management}, volume = {49}, number = {1}, pages = {163-173}, pmid = {22109729}, issn = {1432-1009}, mesh = {Canada ; Conservation of Natural Resources ; Ecology ; Ecosystem ; Geographic Information Systems ; Geography ; *Trees ; }, abstract = {Canada is a large nation with forested ecosystems that occupy over 60% of the national land base, and knowledge of the patterns of Canada's land cover is important to proper environmental management of this vast resource. To this end, a circa 2000 Landsat-derived land cover map of the forested ecosystems of Canada has created a new window into understanding the composition and configuration of land cover patterns in forested Canada. Strategies for summarizing such large expanses of land cover are increasingly important, as land managers work to study and preserve distinctive areas, as well as to identify representative examples of current land-cover and land-use assemblages. Meanwhile, the development of extremely efficient clustering algorithms has become increasingly important in the world of computer science, in which billions of pieces of information on the internet are continually sifted for meaning for a vast variety of applications. One recently developed clustering algorithm quickly groups large numbers of items of any type in a given data set while simultaneously selecting a representative-or "exemplar"-from each cluster. In this context, the availability of both advanced data processing methods and a nationally available set of landscape metrics presents an opportunity to identify sets of representative landscapes to better understand landscape pattern, variation, and distribution across the forested area of Canada. In this research, we first identify and provide context for a small, interpretable set of exemplar landscapes that objectively represent land cover in each of Canada's ten forested ecozones. Then, we demonstrate how this approach can be used to identify flagship and satellite long-term study areas inside and outside protected areas in the province of Ontario. These applications aid our understanding of Canada's forest while augmenting its management toolbox, and may signal a broad range of applications for this versatile approach.}, } @article {pmid22098693, year = {2011}, author = {Damiani, G and Farelli, V and Anselmi, A and Sicuro, L and Solipaca, A and Burgio, A and Iezzi, DF and Ricciardi, W}, title = {Patterns of Long Term Care in 29 European countries: evidence from an exploratory study.}, journal = {BMC health services research}, volume = {11}, number = {}, pages = {316}, pmid = {22098693}, issn = {1472-6963}, mesh = {Aged ; Databases, Factual ; Europe ; Factor Analysis, Statistical ; Health Expenditures ; Health Services Needs and Demand ; Health Services for the Aged/economics/*organization & administration/trends ; Humans ; Long-Term Care/economics/*organization & administration/trends ; }, abstract = {BACKGROUND: The challenges posed by the rapidly ageing population, and the increased preponderance of disabled people in this group, coupled with the rising level of public expenditure required to service the complex organization of long term care (LTC) delivery are causing increased pressure on LTC systems in Europe. A pan-European survey was carried out to evaluate whether patterns of LTC can be identified across Europe and what are the trends of the countries along them.

METHODS: An ecological study was conducted on the 27 EU Member States plus Norway and Iceland, referring to the period 2003-2007. Several variables related to organizational features, elderly needs and expenditure were drawn from OECD Health Data and the Eurostat Statistics database and combined using Multiple Factor Analysis (MFA).

RESULTS: Two global Principal Components were taken into consideration given that their expressed total variance was greater than 60%. They were interpreted according to the higher (more than 0.5) positive or negative correlation coefficients between them and the original variables; thus patterns of LTC were identified. High alignment between old age related expenditure and elderly needs characterizes Nordic and Western European countries, the former also having a higher level of formal care than the latter. Mediterranean as well as Central and South Eastern European countries show lower alignment between old age related expenditure and elderly needs, coupled with a level of provision of formal care that is around or slightly above the average European level. In the dynamic comparison, linear, stable or unclear trends were shown for the studied countries.

CONCLUSIONS: The analysis carried out is an explorative and descriptive study, which is an attempt to reveal patterns and trends of LTC in Europe, allowing comparisons between countries. It also stimulates further researches with lower aggregated data useful to gain meaningful policy-making evidence.Please see related article: http://www.biomedcentral.com/1741-7015/9/124.}, } @article {pmid22097371, year = {2011}, author = {Liu, ZJ and Yu, XX and Li, L and Huang, M}, title = {[Vulnerability assessment of eco-environment in Yimeng mountainous area of Shandong Province based on SRP conceptual model].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {22}, number = {8}, pages = {2084-2090}, pmid = {22097371}, issn = {1001-9332}, mesh = {China ; *Conservation of Natural Resources ; Ecology ; *Environment ; Environmental Monitoring/*methods ; Geographic Information Systems ; *Models, Theoretical ; Principal Component Analysis ; Risk Assessment ; }, abstract = {Based on the ecological sensitivity-resilience-pressure (SRP) conceptual model, and selecting 13 indices including landscape diversity index, soil erosion, and elevation, etc. , the vulnerability of the eco-environment in Yimeng mountainous area of Shandong Province was assessed under the support of GIS and by using principal component analysis and hierarchy analytical method. According to the eco-environmental vulnerability index (EVI) values, the eco-environment vulnerability of study area was classified into 5 levels, i.e., slight (<1.8), light (1.8-2.8), moderate (2.8-3.5), heavy (3.5-4.0), and extreme vulnerability (>4.0). In the study area, moderately vulnerable area occupied 43.3% of the total, while the slightly, lightly, heavily, and extremely vulnerable areas occupied 6.1%, 33.8%, 15.9%, and 0.9%, respectively. The heavily and extremely vulnerable areas mainly located in the topographically complicated hilly area or the hill-plain ecotone with frequent human activities.}, } @article {pmid22091556, year = {2012}, author = {Geeta, R and Dávalos, LM and Levy, A and Bohs, L and Lavin, M and Mummenhoff, K and Sinha, N and Wojciechowski, MF}, title = {Keeping it simple: flowering plants tend to retain, and revert to, simple leaves.}, journal = {The New phytologist}, volume = {193}, number = {2}, pages = {481-493}, doi = {10.1111/j.1469-8137.2011.03951.x}, pmid = {22091556}, issn = {1469-8137}, mesh = {Biological Evolution ; Computer Simulation ; Databases as Topic ; Likelihood Functions ; Magnoliopsida/*anatomy & histology/genetics ; Models, Biological ; Phylogeny ; Plant Leaves/*anatomy & histology/genetics ; }, abstract = {• A wide range of factors (developmental, physiological, ecological) with unpredictable interactions control variation in leaf form. Here, we examined the distribution of leaf morphologies (simple and complex forms) across angiosperms in a phylogenetic context to detect patterns in the directions of changes in leaf shape. • Seven datasets (diverse angiosperms and six nested clades, Sapindales, Apiales, Papaveraceae, Fabaceae, Lepidium, Solanum) were analysed using maximum likelihood and parsimony methods to estimate asymmetries in rates of change among character states. • Simple leaves are most frequent among angiosperm lineages today, were inferred to be ancestral in angiosperms and tended to be retained in evolution (stasis). Complex leaves slowly originated ('gains') and quickly reverted to simple leaves ('losses') multiple times, with a significantly greater rate of losses than gains. Lobed leaves may be a labile intermediate step between different forms. The nested clades showed mixed trends; Solanum, like the angiosperms in general, had higher rates of losses than gains, but the other clades had higher rates of gains than losses. • The angiosperm-wide pattern could be taken as a null model to test leaf evolution patterns in particular clades, in which patterns of variation suggest clade-specific processes that have yet to be investigated fully.}, } @article {pmid22087321, year = {2011}, author = {Valle, D and Clark, JS and Zhao, K}, title = {Enhanced understanding of infectious diseases by fusing multiple datasets: a case study on malaria in the Western Brazilian Amazon region.}, journal = {PloS one}, volume = {6}, number = {11}, pages = {e27462}, pmid = {22087321}, issn = {1932-6203}, mesh = {Brazil/epidemiology ; Cohort Studies ; Communicable Diseases/*epidemiology ; Databases, Factual ; Health Surveys/*methods ; Humans ; Malaria/*epidemiology/etiology ; Microscopy ; Public Health ; Risk Factors ; }, abstract = {BACKGROUND: A common challenge to the study of several infectious diseases consists in combining limited cross-sectional survey data, collected with a more sensitive detection method, with a more extensive (but biased) syndromic sentinel surveillance data, collected with a less sensitive method. Our article describes a novel modeling framework that overcomes this challenge, resulting in enhanced understanding of malaria in the Western Brazilian Amazon.

A cohort of 486 individuals was monitored using four cross-sectional surveys, where all participants were sampled regardless of symptoms (aggressive-active case detection), resulting in 1,383 microscopy and 1,400 polymerase chain reaction tests. Data on the same individuals were also obtained from the local surveillance facility (i.e., passive and active case detection), totaling 1,694 microscopy tests. Our model accommodates these multiple pathogen and case detection methods. This model is shown to outperform logistic regression in terms of interpretability of its parameters, ability to recover the true parameter values, and predictive performance. We reveal that the main infection determinant was the extent of forest, particularly during the rainy season and in close proximity to water bodies, and participation on forest activities. We find that time residing in Acrelandia (as a proxy for past malaria exposure) decreases infection risk but surprisingly increases the likelihood of reporting symptoms once infected, possibly because non-naïve settlers are only susceptible to more virulent Plasmodium strains. We suggest that the search for asymptomatic carriers should focus on those at greater risk of being infected but lower risk of reporting symptoms once infected.

CONCLUSIONS/SIGNIFICANCE: The modeling framework presented here combines cross-sectional survey data and syndromic sentinel surveillance data to shed light on several aspects of malaria that are critical for public health policy. This framework can be adapted to enhance inference on infectious diseases whenever asymptomatic carriers are important and multiple datasets are available.}, } @article {pmid22086462, year = {2012}, author = {Liu, X and Bolla, K and Ashforth, EJ and Zhuo, Y and Gao, H and Huang, P and Stanley, SA and Hung, DT and Zhang, L}, title = {Systematics-guided bioprospecting for bioactive microbial natural products.}, journal = {Antonie van Leeuwenhoek}, volume = {101}, number = {1}, pages = {55-66}, doi = {10.1007/s10482-011-9671-1}, pmid = {22086462}, issn = {1572-9699}, mesh = {Biological Products/*isolation & purification/*metabolism ; Computational Biology/*methods ; Drug Evaluation, Preclinical/methods ; *Ecosystem ; Genomics/*methods ; High-Throughput Screening Assays ; Metabolic Engineering/methods ; Metabolic Networks and Pathways/*genetics ; }, abstract = {Advances in the taxonomic characterization of microorganisms have accelerated the rate at which new producers of natural products can be understood in relation to known organisms. Yet for many reasons, chemical efforts to characterize new compounds from new microbes have not kept pace with taxonomic advances. That there exists an ever-widening gap between the biological versus chemical characterization of new microorganisms creates tremendous opportunity for the discovery of novel natural products through the calculated selection and study of organisms from unique, untapped, ecological niches. A systematics-guided bioprospecting, including the construction of high quality libraries of marine microbes and their crude extracts, investigation of bioactive compounds, and increasing the active compounds by precision engineering, has become an efficient approach to drive drug leads discovery. This review outlines the recent advances in these issues and shares our experiences on anti-infectious drug discovery and improvement of avermectins production as well.}, } @article {pmid22086215, year = {2012}, author = {Franco-Pereira, AM and Lillo, RE and Romo, J}, title = {Comparing quantile residual life functions by confidence bands.}, journal = {Lifetime data analysis}, volume = {18}, number = {2}, pages = {195-214}, pmid = {22086215}, issn = {1572-9249}, mesh = {Animals ; Biostatistics ; Caloric Restriction ; *Confidence Intervals ; Data Interpretation, Statistical ; Humans ; *Life Tables ; Longevity ; Models, Statistical ; Neoplasms/therapy ; Plant Physiological Phenomena ; Rats ; Statistics, Nonparametric ; Stochastic Processes ; Survival Analysis ; }, abstract = {In this article we present a nonparametric method for constructing confidence bands for the difference of two quantile residual life (qrl) functions. These bands provide evidence for two random variables ordering with respect to the qrl order. The comparison of qrl functions is of importance, specially in the treatment of cancer when there exists a possibility of benefiting from a new secondary therapy. A qrl function is the quantile of the remaining life of a surviving subject, as it varies with time. We show the applicability of this approach in Medicine and Ecology. A simulation study has been carried out to evaluate and illustrate the performance and the consistency of this new methodology.}, } @article {pmid22084509, year = {2011}, author = {Delgermaa, V and Takahashi, K and Park, EK and Le, GV and Hara, T and Sorahan, T}, title = {Global mesothelioma deaths reported to the World Health Organization between 1994 and 2008.}, journal = {Bulletin of the World Health Organization}, volume = {89}, number = {10}, pages = {716-24, 724A-724C}, pmid = {22084509}, issn = {1564-0604}, mesh = {Adult ; Aged ; Aged, 80 and over ; Databases, Factual ; Developing Countries ; Female ; *Global Health ; Humans ; Incidence ; Internationality ; Male ; Mesothelioma/epidemiology/*mortality ; Middle Aged ; Mortality/*trends ; Regression Analysis ; Risk Factors ; Time Factors ; *World Health Organization ; }, abstract = {OBJECTIVE: To carry out a descriptive analysis of mesothelioma deaths reported worldwide between 1994 and 2008.

METHODS: We extracted data on mesothelioma deaths reported to the World Health Organization mortality database since 1994, when the disease was first recorded. We also sought information from other English-language sources. Crude and age-adjusted mortality rates were calculated and mortality trends were assessed from the annual percentage change in the age-adjusted mortality rate.

FINDINGS: In total, 92,253 mesothelioma deaths were reported by 83 countries. Crude and age-adjusted mortality rates were 6.2 and 4.9 per million population, respectively. The age-adjusted mortality rate increased by 5.37% per year and consequently more than doubled during the study period. The mean age at death was 70 years and the male-to-female ratio was 3.6:1. The disease distribution by anatomical site was: pleura, 41.3%; peritoneum, 4.5%; pericardium, 0.3%; and unspecified sites, 43.1%. The geographical distribution of deaths was skewed towards high-income countries: the United States of America reported the highest number, while over 50% of all deaths occurred in Europe. In contrast, less than 12% occurred in middle- and low-income countries. The overall trend in the age-adjusted mortality rate was increasing in Europe and Japan but decreasing in the United States.

CONCLUSION: The number of mesothelioma deaths reported and the number of countries reporting deaths increased during the study period, probably due to better disease recognition and an increase in incidence. The different time trends observed between countries may be an early indication that the disease burden is slowly shifting towards those that have used asbestos more recently.}, } @article {pmid22079552, year = {2012}, author = {Murray, SW and Campbell, P and Kingston, T and Zubaid, A and Francis, CM and Kunz, TH}, title = {Molecular phylogeny of hipposiderid bats from Southeast Asia and evidence of cryptic diversity.}, journal = {Molecular phylogenetics and evolution}, volume = {62}, number = {2}, pages = {597-611}, doi = {10.1016/j.ympev.2011.10.021}, pmid = {22079552}, issn = {1095-9513}, mesh = {Animals ; Asia, Southeastern ; Bayes Theorem ; *Biological Evolution ; Cell Nucleus/*genetics ; Chiroptera/anatomy & histology/classification/*genetics ; *Computational Biology ; DNA, Mitochondrial/classification/*genetics/isolation & purification ; Echolocation/physiology ; Female ; Genetic Speciation ; Genetic Variation ; Male ; Mitochondria/genetics ; Models, Genetic ; *Phylogeny ; Sequence Analysis, DNA ; }, abstract = {Old World leaf-nosed bats (Hipposideridae) are among the most widespread and ecologically diverse groups of insectivorous bats in the Old World tropics. However, phylogenetic relationships in Hipposideridae are poorly resolved at both the generic and species levels, and deep genetic divergence within several Southeast Asian species suggests that current taxonomy underestimates hipposiderid diversity in this region. We used mitochondrial and nuclear sequence data to conduct the first extensive molecular phylogenetic analysis of Southeast Asian hipposiderid bats. Inclusion of multiple samples per taxon allowed testing for evidence of evolutionarily distinct lineages within taxa currently defined as single species. In contrast to earlier phylogenies based on morphometrics, molecular data support monophyly of Hipposideros, but are ambiguous regarding the monophyly of Hipposideridae. With a few exceptions, molecular data also support currently recognized species groups classified by qualitative morphological characters. Widespread paraphyly and polyphyly within many currently recognized species of Hipposideros indicates that evolutionary diversity in the genus is underrepresented by current nomenclature. Comparison of available morphological and echolocation data suggest that both geographic isolation and ecological selection have contributed to the diversification of Southeast Asian hipposiderid bats.}, } @article {pmid22073646, year = {2011}, author = {Olden, JD and Vander Zanden, MJ and Johnson, PT}, title = {Assessing ecosystem vulnerability to invasive rusty crayfish (Orconectes rusticus).}, journal = {Ecological applications : a publication of the Ecological Society of America}, volume = {21}, number = {7}, pages = {2587-2599}, doi = {10.1890/10-2051.1}, pmid = {22073646}, issn = {1051-0761}, mesh = {Animals ; Astacoidea/*physiology ; Competitive Behavior ; Databases, Factual ; *Ecosystem ; Environment ; Introduced Species ; Lakes ; Models, Biological ; Wisconsin ; }, abstract = {Despite the widespread introduction of nonnative species and the heterogeneity of ecosystems in their sensitivity to ecological impacts, few studies have assessed ecosystem vulnerability to the entire invasion process, from arrival to establishment and impacts. Our study addresses this challenge by presenting a probabilistic, spatially explicit approach to predicting ecosystem vulnerability to species invasions. Using the freshwater-rich landscapes of Wisconsin, USA, we model invasive rusty crayfish (Orconectes rusticus) as a function of exposure risk (i.e., likelihood of introduction and establishment of O. rusticus based on a species distribution model) and the sensitivity of the recipient community (i.e., likelihood of impacts on native O. virilis and O. propinquus based on a retrospective analysis of population changes). Artificial neural networks predicted that approximately 10% of 4200 surveyed lakes (n = 388) and approximately 25% of mapped streams (23 523 km total length) are suitable for O. rusticus introduction and establishment. A comparison of repeated surveys before vs. post-1985 revealed that O. virilis was six times as likely and O. propinquus was twice as likely to be extirpated in streams invaded by O. rusticus, compared to streams that were not invaded. Similarly, O. virilis was extirpated in over three-quarters of lakes invaded by O. rusticus compared to half of the uninvaded lakes, whereas no difference was observed for O. propinquus. We identified 115 lakes (approximately 3% of lakes) and approximately 5000 km of streams (approximately 6% of streams) with a 25% chance of introduction, establishment, and extirpation by O. rusticus of either native congener. By identifying highly vulnerable ecosystems, our study offers an effective strategy for prioritizing on-the-ground management action and informing decisions about the most efficient allocation of resources. Moreover, our results provide the flexibility for stakeholders to identify priority sites for prevention efforts given a maximum level of acceptable risk or based on budgetary or time restrictions. To this end, we incorporate the model predictions into a new online mapping tool with the intention of closing the communication gap between academic research and stakeholders that requires information on the prospects of future invasions.}, } @article {pmid22056882, year = {2012}, author = {Santos, AM and Branco, M}, title = {The quality of name-based species records in databases.}, journal = {Trends in ecology & evolution}, volume = {27}, number = {1}, pages = {6-7; author reply 7-8}, doi = {10.1016/j.tree.2011.10.004}, pmid = {22056882}, issn = {1872-8383}, mesh = {*Biodiversity ; *Databases, Factual ; Ecology/*standards ; Information Management/*methods ; Research/*standards ; }, } @article {pmid22053738, year = {2012}, author = {Rosenthal, T}, title = {Geographic variation in health care.}, journal = {Annual review of medicine}, volume = {63}, number = {}, pages = {493-509}, doi = {10.1146/annurev-med-050710-134438}, pmid = {22053738}, issn = {1545-326X}, mesh = {Delivery of Health Care/*statistics & numerical data ; Geographic Information Systems/*statistics & numerical data ; *Health Policy ; Health Services Accessibility/*statistics & numerical data ; Humans ; Socioeconomic Factors ; United States/epidemiology ; }, abstract = {Measurements of health care spending and outcomes in a geographic area and comparisons of one area to another have been used to make observations about health delivery systems and guide health care policy. Medicare claims files are a ready source of data about health care utilization and have served as the basis for a large number of studies in the United States. If ecologic studies are to accurately reflect local practices, potential variables must be accounted for. In the United States, differences in disease burden and socioeconomic factors are important variables affecting health care spending and outcomes. The assertion that regional variation in Medicare spending in the last two years of life is indicative of widespread waste in the U.S. health care system became a controversial part of the health care reform debate in 2009-2010.}, } @article {pmid22047020, year = {2011}, author = {Siddiqui, H and Nederbragt, AJ and Lagesen, K and Jeansson, SL and Jakobsen, KS}, title = {Assessing diversity of the female urine microbiota by high throughput sequencing of 16S rDNA amplicons.}, journal = {BMC microbiology}, volume = {11}, number = {}, pages = {244}, pmid = {22047020}, issn = {1471-2180}, mesh = {Adult ; Bacteria/*classification/genetics ; DNA, Bacterial/genetics ; Databases, Nucleic Acid ; Female ; *Genetic Variation ; High-Throughput Nucleotide Sequencing ; Humans ; *Metagenome ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Urine/*microbiology ; }, abstract = {BACKGROUND: Urine within the urinary tract is commonly regarded as "sterile" in cultivation terms. Here, we present a comprehensive in-depth study of bacterial 16S rDNA sequences associated with urine from healthy females by means of culture-independent high-throughput sequencing techniques.

RESULTS: Sequencing of the V1V2 and V6 regions of the 16S ribosomal RNA gene using the 454 GS FLX system was performed to characterize the possible bacterial composition in 8 culture-negative (<100,000 CFU/ml) healthy female urine specimens. Sequences were compared to 16S rRNA databases and showed significant diversity, with the predominant genera detected being Lactobacillus, Prevotella and Gardnerella. The bacterial profiles in the female urine samples studied were complex; considerable variation between individuals was observed and a common microbial signature was not evident. Notably, a significant amount of sequences belonging to bacteria with a known pathogenic potential was observed. The number of operational taxonomic units (OTUs) for individual samples varied substantially and was in the range of 20-500.

CONCLUSIONS: Normal female urine displays a noticeable and variable bacterial 16S rDNA sequence richness, which includes fastidious and anaerobic bacteria previously shown to be associated with female urogenital pathology.}, } @article {pmid22046002, year = {2012}, author = {Vandebergh, W and Bossuyt, F}, title = {Radiation and functional diversification of alpha keratins during early vertebrate evolution.}, journal = {Molecular biology and evolution}, volume = {29}, number = {3}, pages = {995-1004}, doi = {10.1093/molbev/msr269}, pmid = {22046002}, issn = {1537-1719}, mesh = {Adaptation, Biological/*genetics ; Animals ; Bayes Theorem ; Computational Biology ; *Evolution, Molecular ; Expressed Sequence Tags ; Gene Duplication/genetics ; Keratins/*genetics/*metabolism ; Models, Genetic ; *Phylogeny ; Species Specificity ; Vertebrates/*genetics ; }, abstract = {The conquest of land was arguably one of the most fundamental ecological transitions in vertebrates and entailed significant changes in skin structure and appendages to cope with the new environment. In extant tetrapods, the rigidity of the integument is largely created by type I and type II keratins, which are structural proteins essential in forming a strong cytoplasmic network. It is expected that such proteins have undergone fundamental changes in both stem and crown tetrapods. Here, we integrate genomic, phylogenetic, and expression data in a comprehensive study on the early evolution and functional diversification of tetrapod keratins. Our analyses reveal that all type I and type II tetrapod keratins evolved from only two genes that were present in the ancestor of extant vertebrates. Subsequently, the water-to-land transition in the stem lineage of tetrapods was associated with a major radiation and functional diversification of keratin genes. These duplications acquired functions that serve rigidity in integumental hard structures and were the prime for subsequent independent keratin diversification in tetrapod lineages.}, } @article {pmid22042526, year = {2011}, author = {Dufresne, F and Jeffery, N}, title = {A guided tour of large genome size in animals: what we know and where we are heading.}, journal = {Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology}, volume = {19}, number = {7}, pages = {925-938}, pmid = {22042526}, issn = {1573-6849}, mesh = {Adaptation, Biological ; Animals ; DNA Transposable Elements ; Databases, Genetic ; *Evolution, Molecular ; *Genome ; *Genome Size ; Genomics/*methods ; High-Throughput Nucleotide Sequencing ; Humans ; Phylogeny ; Repetitive Sequences, Nucleic Acid/*genetics ; }, abstract = {The study of genome size diversity is an ever-expanding field that is highly relevant in today's world of rapid and efficient DNA sequencing. Animal genome sizes range from 0.02 to 132.83 pg but the majority of animal genomes are small, with the most of these genome sizes being less than 5 pg. Animals with large genomes (> 10 pg) are scattered within some invertebrates, including the Platyhelminthes, crustaceans, and orthopterans, and also the vertebrates including the Actinopterygii, Chondrichthyes, and some amphibians. In this paper, we explore the connections between organismal phenotype, physiology, and ecology to genome size. We also discuss some of the molecular mechanisms of genome shrinkage and expansion obtained through comparative studies of species with full genome sequences and how this may apply to species with large genomes. As most animal species sequenced to date have been in the small range for genome size (especially invertebrates) due to sequencing costs and to difficulties associated with large genome assemblies, an understanding of the structural composition of large genomes is still lacking. Studies using next-generation sequencing are being attempted for the first time in animals with larger genomes. Such analyses using low genome coverage are providing a glimpse of the composition of repetitive elements in animals with more complex genomes. These future studies will allow a better understanding of factors leading to genomic obesity in animals.}, } @article {pmid22040283, year = {2012}, author = {Ferrer, M and Werner, J and Chernikova, TN and Bargiela, R and Fernández, L and La Cono, V and Waldmann, J and Teeling, H and Golyshina, OV and Glöckner, FO and Yakimov, MM and Golyshin, PN and , }, title = {Unveiling microbial life in the new deep-sea hypersaline Lake Thetis. Part II: a metagenomic study.}, journal = {Environmental microbiology}, volume = {14}, number = {1}, pages = {268-281}, doi = {10.1111/j.1462-2920.2011.02634.x}, pmid = {22040283}, issn = {1462-2920}, mesh = {Archaea/*genetics ; Autotrophic Processes ; Bacteria/*genetics ; Carbon Dioxide/metabolism ; Computational Biology ; Mediterranean Sea ; *Metagenome ; Metagenomics ; Oxidation-Reduction ; Phylogeny ; Ribulose-Bisphosphate Carboxylase/genetics ; Seawater/*chemistry/*microbiology ; Sequence Analysis, DNA ; Sulfur Compounds/metabolism ; Water Microbiology ; }, abstract = {So far only little is known about the microbial ecology of Mediterranean deep-sea hypersaline anoxic lakes (DHALs). These brine lakes were formed by evaporite dissolution/brine seeps and are important model environments to provide insights into possible metabolisms and distributions of microorganisms on the early Earth. Our study on the Lake Thetis, a new thalassohaline DHAL located South-East of the Medriff Corridor, has revealed microbial communities of contrasting compositions with a high number of novel prokaryotic candidate divisions. The major finding of our present work is co-occurrence of at least three autotrophic carbon dioxide fixation pathways in the brine-seawater interface that are likely fuelled by an active ramified sulphur cycle. Genes for the reductive acetyl-CoA and reductive TCA pathways were also found in the brine suggesting that these pathways are operational even at extremely elevated salinities and that autotrophy is more important in hypersaline environments than previously assumed. Surprisingly, genes coding for RuBisCo were found in the highly reduced brine. Three types of sulphide oxidation pathways were found in the interface. The first involves a multienzyme Sox complex catalysing the complete oxidation of reduced sulphur compounds to sulphate, the second type recruits SQR sulphide:quinone reductase for oxidation of sulphide to elemental sulphur, which, in the presence of sulphide, could further be reduced by polysulphide reductases in the third pathway. The presence of the latter two allows a maximal energy yield from the oxidation of sulphide and at the same time prevents the acidification and the accumulation of S(0) deposits. Amino acid composition analysis of deduced proteins revealed a significant overrepresentation of acidic residues in the brine compared with the interface. This trait is typical for halophilic organisms as an adaptation to the brine's extreme hypersalinity. This work presents the first metagenomic survey of the microbial communities of the recently discovered Lake Thetis whose brine constitutes one of saltiest water bodies ever reported.}, } @article {pmid22036178, year = {2011}, author = {Wernberg, T and Russell, BD and Thomsen, MS and Gurgel, CF and Bradshaw, CJ and Poloczanska, ES and Connell, SD}, title = {Seaweed communities in retreat from ocean warming.}, journal = {Current biology : CB}, volume = {21}, number = {21}, pages = {1828-1832}, doi = {10.1016/j.cub.2011.09.028}, pmid = {22036178}, issn = {1879-0445}, mesh = {Aquatic Organisms ; Australia ; *Climate Change ; Databases, Factual ; *Ecosystem ; Indian Ocean ; Pacific Ocean ; Seaweed/*physiology ; }, abstract = {In recent decades, global climate change [1] has caused profound biological changes across the planet [2-6]. However, there is a great disparity in the strength of evidence among different ecosystems and between hemispheres: changes on land have been well documented through long-term studies, but similar direct evidence for impacts of warming is virtually absent from the oceans [3, 7], where only a few studies on individual species of intertidal invertebrates, plankton, and commercially important fish in the North Atlantic and North Pacific exist. This disparity of evidence is precarious for biological conservation because of the critical role of the marine realm in regulating the Earth's environmental and ecological functions, and the associated socioeconomic well-being of humans [8]. We interrogated a database of >20,000 herbarium records of macroalgae collected in Australia since the 1940s and documented changes in communities and geographical distribution limits in both the Indian and Pacific Oceans, consistent with rapid warming over the past five decades [9, 10]. We show that continued warming might drive potentially hundreds of species toward and beyond the edge of the Australian continent where sustained retreat is impossible. The potential for global extinctions is profound considering the many endemic seaweeds and seaweed-dependent marine organisms in temperate Australia.}, } @article {pmid22034358, year = {2011}, author = {Ferreira, N and Lins, L and Fink, D and Kelling, S and Wood, C and Freire, J and Silva, C}, title = {BirdVis: visualizing and understanding bird populations.}, journal = {IEEE transactions on visualization and computer graphics}, volume = {17}, number = {12}, pages = {2374-2383}, doi = {10.1109/TVCG.2011.176}, pmid = {22034358}, issn = {1941-0506}, mesh = {Animals ; Artificial Intelligence ; *Birds/physiology ; *Computer Graphics ; Computer Simulation ; Databases, Factual ; Ecosystem ; Flight, Animal ; Models, Biological ; Population Dynamics ; Software ; Songbirds/physiology ; Species Specificity ; User-Computer Interface ; }, abstract = {Birds are unrivaled windows into biotic processes at all levels and are proven indicators of ecological well-being. Understanding the determinants of species distributions and their dynamics is an important aspect of ecology and is critical for conservation and management. Through crowdsourcing, since 2002, the eBird project has been collecting bird observation records. These observations, together with local-scale environmental covariates such as climate, habitat, and vegetation phenology have been a valuable resource for a global community of educators, land managers, ornithologists, and conservation biologists. By associating environmental inputs with observed patterns of bird occurrence, predictive models have been developed that provide a statistical framework to harness available data for predicting species distributions and making inferences about species-habitat associations. Understanding these models, however, is challenging because they require scientists to quantify and compare multiscale spatialtemporal patterns. A large series of coordinated or sequential plots must be generated, individually programmed, and manually composed for analysis. This hampers the exploration and is a barrier to making the cross-species comparisons that are essential for coordinating conservation and extracting important ecological information. To address these limitations, as part of a collaboration among computer scientists, statisticians, biologists and ornithologists, we have developed BirdVis, an interactive visualization system that supports the analysis of spatio-temporal bird distribution models. BirdVis leverages visualization techniques and uses them in a novel way to better assist users in the exploration of interdependencies among model parameters. Furthermore, the system allows for comparative visualization through coordinated views, providing an intuitive interface to identify relevant correlations and patterns. We justify our design decisions and present case studies that show how BirdVis has helped scientists obtain new evidence for existing hypotheses, as well as formulate new hypotheses in their domain.}, } @article {pmid22025609, year = {2011}, author = {Tian, S and Lu, L and Labavitch, J and Yang, X and He, Z and Hu, H and Sarangi, R and Newville, M and Commisso, J and Brown, P}, title = {Cellular sequestration of cadmium in the hyperaccumulator plant species Sedum alfredii.}, journal = {Plant physiology}, volume = {157}, number = {4}, pages = {1914-1925}, pmid = {22025609}, issn = {1532-2548}, support = {P41 RR001209/RR/NCRR NIH HHS/United States ; }, mesh = {Cadmium/analysis/*metabolism/pharmacology ; Calcium/metabolism ; Carboxylic Acids/*metabolism ; Fluorescence ; Image Interpretation, Computer-Assisted ; Lasers ; Malates/metabolism ; Mass Spectrometry/methods ; Plant Epidermis/cytology/drug effects/metabolism ; Plant Leaves/cytology/drug effects/metabolism ; Plant Roots/cytology/drug effects/metabolism ; Plant Stems/cytology/drug effects/metabolism ; Sedum/*cytology/drug effects/*metabolism ; Seedlings/cytology/drug effects/metabolism ; Spectrometry, X-Ray Emission ; Synchrotrons ; X-Ray Absorption Spectroscopy ; }, abstract = {Spatial imaging of cadmium (Cd) in the hyperaccumulator Sedum alfredii was investigated in vivo by laser ablation inductively coupled plasma mass spectrometry and x-ray microfluorescence imaging. Preferential Cd accumulation in the pith and cortex was observed in stems of the Cd hyperaccumulating ecotype (HE), whereas Cd was restricted to the vascular bundles in its contrasting nonhyperaccumulating ecotype. Cd concentrations of up to 15,000 μg g(-1) were measured in the pith cells, which was many fold higher than the concentrations in the stem epidermis and vascular bundles in the HE plants. In the leaves of the HE, Cd was mainly localized to the mesophyll and vascular cells rather than the epidermis. The distribution pattern of Cd in both stems and leaves of the HE was very similar to calcium but not zinc, irrespective of Cd exposure levels. Extended x-ray absorption fine structure spectroscopy analysis showed that Cd in the stems and leaves of the HE was mainly associated with oxygen ligands, and a larger proportion (about 70% in leaves and 47% in stems) of Cd was bound with malic acid, which was the major organic acid in the shoots of the plants. These results indicate that a majority of Cd in HE accumulates in the parenchyma cells, especially in stems, and is likely associated with calcium pathways and bound with organic acid (malate), which is indicative of a critical role of vacuolar sequestration of Cd in the HE S. alfredii.}, } @article {pmid22022440, year = {2011}, author = {Ausec, L and Zakrzewski, M and Goesmann, A and Schlüter, A and Mandic-Mulec, I}, title = {Bioinformatic analysis reveals high diversity of bacterial genes for laccase-like enzymes.}, journal = {PloS one}, volume = {6}, number = {10}, pages = {e25724}, pmid = {22022440}, issn = {1932-6203}, mesh = {Bacteria/*enzymology/*genetics ; Base Sequence ; Computational Biology/*methods ; Data Collection ; Databases, Genetic ; Gene Transfer, Horizontal/genetics ; Genes, Bacterial/*genetics ; *Genetic Variation ; Laccase/chemistry/classification/*genetics ; Markov Chains ; Metagenomics ; Oceans and Seas ; Protein Structure, Tertiary ; }, abstract = {Fungal laccases have been used in various fields ranging from processes in wood and paper industries to environmental applications. Although a few bacterial laccases have been characterized in recent years, prokaryotes have largely been neglected as a source of novel enzymes, in part due to the lack of knowledge about the diversity and distribution of laccases within Bacteria. In this work genes for laccase-like enzymes were searched for in over 2,200 complete and draft bacterial genomes and four metagenomic datasets, using the custom profile Hidden Markov Models for two- and three-domain laccases. More than 1,200 putative genes for laccase-like enzymes were retrieved from chromosomes and plasmids of diverse bacteria. In 76% of the genes, signal peptides were predicted, indicating that these bacterial laccases may be exported from the cytoplasm, which contrasts with the current belief. Moreover, several examples of putatively horizontally transferred bacterial laccase genes were described. Many metagenomic sequences encoding fragments of laccase-like enzymes could not be phylogenetically assigned, indicating considerable novelty. Laccase-like genes were also found in anaerobic bacteria, autotrophs and alkaliphiles, thus opening new hypotheses regarding their ecological functions. Bacteria identified as carrying laccase genes represent potential sources for future biotechnological applications.}, } @article {pmid22021835, year = {2011}, author = {Stokstad, E}, title = {Network science. Open-source ecology takes root across the world.}, journal = {Science (New York, N.Y.)}, volume = {334}, number = {6054}, pages = {308-309}, doi = {10.1126/science.334.6054.308}, pmid = {22021835}, issn = {1095-9203}, mesh = {Animals ; Databases, Factual ; *Ecology ; *Ecosystem ; Publishing ; *Research/economics ; *Research Design ; Research Support as Topic ; }, } @article {pmid22019413, year = {2012}, author = {Jetz, W and McPherson, JM and Guralnick, RP}, title = {Integrating biodiversity distribution knowledge: toward a global map of life.}, journal = {Trends in ecology & evolution}, volume = {27}, number = {3}, pages = {151-159}, doi = {10.1016/j.tree.2011.09.007}, pmid = {22019413}, issn = {1872-8383}, mesh = {*Biodiversity ; *Conservation of Natural Resources ; Data Collection/*methods ; Environment ; Informatics ; Internet ; Maps as Topic ; Species Specificity ; }, abstract = {Global knowledge about the spatial distribution of species is orders of magnitude coarser in resolution than other geographically-structured environmental datasets such as topography or land cover. Yet such knowledge is crucial in deciphering ecological and evolutionary processes and in managing global change. In this review, we propose a conceptual and cyber-infrastructure framework for refining species distributional knowledge that is novel in its ability to mobilize and integrate diverse types of data such that their collective strengths overcome individual weaknesses. The ultimate aim is a public, online, quality-vetted 'Map of Life' that for every species integrates and visualizes available distributional knowledge, while also facilitating user feedback and dynamic biodiversity analyses. First milestones toward such an infrastructure have now been implemented.}, } @article {pmid22018924, year = {2012}, author = {Rhee, JS and Won, EJ and Kim, RO and Choi, BS and Choi, IY and Park, GS and Shin, KH and Lee, YM and Lee, JS}, title = {The polychaete, Perinereis nuntia ESTs and its use to uncover potential biomarker genes for molecular ecotoxicological studies.}, journal = {Environmental research}, volume = {112}, number = {}, pages = {48-57}, doi = {10.1016/j.envres.2011.09.012}, pmid = {22018924}, issn = {1096-0953}, mesh = {Animals ; DNA, Complementary/genetics ; Databases, Genetic ; *Ecotoxicology ; *Environmental Monitoring ; *Expressed Sequence Tags ; Gene Library ; Genetic Markers ; Geologic Sediments/chemistry ; High-Throughput Screening Assays ; Polychaeta/*drug effects/*genetics ; RNA/genetics ; Water Pollutants, Chemical/*toxicity ; }, abstract = {The polychaete, Perinereis nuntia, has been used as an indicator species to assess the environmental condition of benthic communities in coastal marine environments. Recently, high-throughput sequencing technology has been proven to be a useful method for analyzing expressed sequence tags (ESTs) in non-model species. Thus, we have obtained extensive cDNA information by the pyrosequencing method, to utilize the polychaete species as a test organism for sediment quality monitoring studies. From the total RNA of P. nuntia, cDNA was reversely synthesized and randomly sequenced using a GS-FLX sequencer. In the assembly stage 1, 40,379 transcripts (13,666 contigs and 26,713 singletons) were acquired and showed 47% hitting rate compared with the GenBank non-redundant (NR) amino acid sequence database using BLASTX. After the stage-2 assembly, 21,657 transcripts were identified and showed 28% hitting rate. Finally, we obtained 6 064 unigenes that corresponded to the GenBank NR amino acid sequence database using BLASTX. Of the transcripts obtained in this species, we found a number of stress- and cell defense-related genes (e.g. heat shock protein family, antioxidant-related genes, cytochrome P450 genes) that are potentially useful for sediment monitoring at the molecular level, indicating that the pyrosequencing method is an effective approach to uncover gene families of potential biomarker genes simultaneously, and thus make transcriptomic studies possible. To confirm the usefulness of those potential biomarker genes, we analyzed the comparative profiling of P. nuntia mRNA transcripts between the samples collected from the polychaete aquaculture farm and the southern coast field of South Korea. In this paper, we summarize the expressed cDNA information of P. nuntia and discussed its potential use in environmental genomics and ecotoxicological studies for uncovering the potential molecular mechanisms of environmental stresses and chemical toxicity to the indicator species, P. nuntia in marine sediments.}, } @article {pmid22018222, year = {2012}, author = {Franklin, EC and Stat, M and Pochon, X and Putnam, HM and Gates, RD}, title = {GeoSymbio: a hybrid, cloud-based web application of global geospatial bioinformatics and ecoinformatics for Symbiodinium-host symbioses.}, journal = {Molecular ecology resources}, volume = {12}, number = {2}, pages = {369-373}, doi = {10.1111/j.1755-0998.2011.03081.x}, pmid = {22018222}, issn = {1755-0998}, mesh = {Animals ; Computational Biology/*instrumentation/methods ; Dinoflagellida/genetics/*physiology ; Invertebrates/genetics/*physiology ; *Software ; *Symbiosis ; User-Computer Interface ; }, abstract = {The genus Symbiodinium encompasses a group of unicellular, photosynthetic dinoflagellates that are found free living or in hospite with a wide range of marine invertebrate hosts including scleractinian corals. We present GeoSymbio, a hybrid web application that provides an online, easy to use and freely accessible interface for users to discover, explore and utilize global geospatial bioinformatic and ecoinformatic data on Symbiodinium-host symbioses. The novelty of this application lies in the combination of a variety of query and visualization tools, including dynamic searchable maps, data tables with filter and grouping functions, and interactive charts that summarize the data. Importantly, this application is hosted remotely or 'in the cloud' using Google Apps, and therefore does not require any specialty GIS, web programming or data programming expertise from the user. The current version of the application utilizes Symbiodinium data based on the ITS2 genetic marker from PCR-based techniques, including denaturing gradient gel electrophoresis, sequencing and cloning of specimens collected during 1982-2010. All data elements of the application are also downloadable as spatial files, tables and nucleic acid sequence files in common formats for desktop analysis. The application provides a unique tool set to facilitate research on the basic biology of Symbiodinium and expedite new insights into their ecology, biogeography and evolution in the face of a changing global climate. GeoSymbio can be accessed at https://sites.google.com/site/geosymbio/.}, } @article {pmid22017755, year = {2012}, author = {Zhang, H and Han, B and Wang, T and Chen, S and Li, H and Zhang, Y and Dai, S}, title = {Mechanisms of plant salt response: insights from proteomics.}, journal = {Journal of proteome research}, volume = {11}, number = {1}, pages = {49-67}, doi = {10.1021/pr200861w}, pmid = {22017755}, issn = {1535-3907}, mesh = {Crops, Agricultural/cytology/genetics/metabolism/physiology ; Databases, Protein ; Gene Expression Regulation, Plant ; Plant Proteins/genetics/*metabolism ; Proteome/genetics/*metabolism ; Proteomics ; Salt-Tolerant Plants/cytology/genetics/metabolism/*physiology ; *Stress, Physiological ; }, abstract = {Soil salinity is a major abiotic stress that limits plant growth and agriculture productivity. To cope with salt stress, plants have evolved complex salt-responsive signaling and metabolic processes at the cellular, organ, and whole-plant levels. Investigation of the physiological and molecular mechanisms underlying plant salinity tolerance will provide valuable information for effective engineering strategies. Current proteomics provides a high-throughput approach to study sophisticated molecular networks in plants. In this review, we describe a salt-responsive protein database by an integrated analysis of proteomics-based studies. The database contains 2171 salt-responsive protein identities representing 561 unique proteins. These proteins have been identified from leaves, roots, shoots, seedlings, unicells, grains, hypocotyls, radicles, and panicles from 34 plant species. The identified proteins provide invaluable information toward understanding the complex and fine-tuned plant salt-tolerance mechanisms in photosynthesis, reactive oxygen species (ROS) scavenging, ion homeostasis, osmotic modulation, signaling transduction, transcription, protein synthesis/turnover, cytoskeleton dynamics, and cross-tolerance to different stress conditions.}, } @article {pmid22017744, year = {2012}, author = {Knape, J and de Valpine, P}, title = {Are patterns of density dependence in the Global Population Dynamics Database driven by uncertainty about population abundance?.}, journal = {Ecology letters}, volume = {15}, number = {1}, pages = {17-23}, doi = {10.1111/j.1461-0248.2011.01702.x}, pmid = {22017744}, issn = {1461-0248}, mesh = {*Databases, Factual ; Ecosystem ; *Models, Biological ; Population Density ; Population Dynamics ; *Uncertainty ; }, abstract = {Density dependence in population growth rates is of immense importance to ecological theory and application, but is difficult to estimate. The Global Population Dynamics Database (GPDD), one of the largest collections of population time series available, has been extensively used to study cross-taxa patterns in density dependence. A major difficulty with assessing density dependence from time series is that uncertainty in population abundance estimates can cause strong bias in both tests and estimates of strength. We analyse 627 data sets in the GPDD using Gompertz population models and account for uncertainty via the Kalman filter. Results suggest that at least 45% of the time series display density dependence, but that it is weak and difficult to detect for a large fraction. When uncertainty is ignored, magnitude of and evidence for density dependence is strong, illustrating that uncertainty in abundance estimates qualitatively changes conclusions about density dependence drawn from the GPDD.}, } @article {pmid22014198, year = {2011}, author = {Ojha, RP and Offutt-Powell, TN and Evans, EL and Singh, KP}, title = {Correlation coefficients in ecologic studies of environment and cancer.}, journal = {Archives of environmental & occupational health}, volume = {66}, number = {4}, pages = {241-244}, doi = {10.1080/19338244.2010.539641}, pmid = {22014198}, issn = {2154-4700}, mesh = {Data Interpretation, Statistical ; Environment ; Environmental Exposure/*statistics & numerical data ; Humans ; Neoplasms/*chemically induced/epidemiology ; *Statistics as Topic ; }, abstract = {The objective of this study was to determine the proportion of ecologic studies published during a 20-year period regarding environmental exposures and cancer in which correlation coefficients or coefficients of determination were used as a measure of association. The authors performed a descriptive analysis of published literature by conducting a systematic review of PubMed to identify eligible ecologic studies published between 1991 and 2010. The reported measure of association was extracted for all eligible studies. During the 20-year study period, 35/105 (33%, 95% confidence limits [CL]: 25%, 43%) ecologic studies used correlation coefficients or coefficients of determination as a measure of association. These results indicate that the use of correlation coefficients and coefficients of determination as measures of association in ecologic studies of environmental exposures and cancer is relatively common, despite extensive literature discouraging their interpretation as valid measures of association.}, } @article {pmid22010858, year = {2012}, author = {McCarthy, KP and Fletcher, RJ and Rota, CT and Hutto, RL}, title = {Predicting species distributions from samples collected along roadsides.}, journal = {Conservation biology : the journal of the Society for Conservation Biology}, volume = {26}, number = {1}, pages = {68-77}, doi = {10.1111/j.1523-1739.2011.01754.x}, pmid = {22010858}, issn = {1523-1739}, mesh = {Animals ; *Birds ; Conservation of Natural Resources/*methods ; Geographic Information Systems ; Idaho ; Models, Statistical ; Montana ; Population Density ; }, abstract = {Predictive models of species distributions are typically developed with data collected along roads. Roadside sampling may provide a biased (nonrandom) sample; however, it is currently unknown whether roadside sampling limits the accuracy of predictions generated by species distribution models. We tested whether roadside sampling affects the accuracy of predictions generated by species distribution models by using a prospective sampling strategy designed specifically to address this issue. We built models from roadside data and validated model predictions at paired locations on unpaved roads and 200 m away from roads (off road), spatially and temporally independent from the data used for model building. We predicted species distributions of 15 bird species on the basis of point-count data from a landbird monitoring program in Montana and Idaho (U.S.A.). We used hierarchical occupancy models to account for imperfect detection. We expected predictions of species distributions derived from roadside-sampling data would be less accurate when validated with data from off-road sampling than when it was validated with data from roadside sampling and that model accuracy would be differentially affected by whether species were generalists, associated with edges, or associated with interior forest. Model performance measures (kappa, area under the curve of a receiver operating characteristic plot, and true skill statistic) did not differ between model predictions of roadside and off-road distributions of species. Furthermore, performance measures did not differ among edge, generalist, and interior species, despite a difference in vegetation structure along roadsides and off road and that 2 of the 15 species were more likely to occur along roadsides. If the range of environmental gradients is surveyed in roadside-sampling efforts, our results suggest that surveys along unpaved roads can be a valuable, unbiased source of information for species distribution models.}, } @article {pmid22010832, year = {2012}, author = {Carroll, C and McRae, BH and Brookes, A}, title = {Use of linkage mapping and centrality analysis across habitat gradients to conserve connectivity of gray wolf populations in western North America.}, journal = {Conservation biology : the journal of the Society for Conservation Biology}, volume = {26}, number = {1}, pages = {78-87}, doi = {10.1111/j.1523-1739.2011.01753.x}, pmid = {22010832}, issn = {1523-1739}, mesh = {Animals ; Canada ; Conservation of Natural Resources/*methods ; Ecosystem ; Geographic Information Systems ; Idaho ; Population Density ; Population Dynamics ; Wolves/*physiology ; Wyoming ; }, abstract = {Centrality metrics evaluate paths between all possible pairwise combinations of sites on a landscape to rank the contribution of each site to facilitating ecological flows across the network of sites. Computational advances now allow application of centrality metrics to landscapes represented as continuous gradients of habitat quality. This avoids the binary classification of landscapes into patch and matrix required by patch-based graph analyses of connectivity. It also avoids the focus on delineating paths between individual pairs of core areas characteristic of most corridor- or linkage-mapping methods of connectivity analysis. Conservation of regional habitat connectivity has the potential to facilitate recovery of the gray wolf (Canis lupus), a species currently recolonizing portions of its historic range in the western United States. We applied 3 contrasting linkage-mapping methods (shortest path, current flow, and minimum-cost-maximum-flow) to spatial data representing wolf habitat to analyze connectivity between wolf populations in central Idaho and Yellowstone National Park (Wyoming). We then applied 3 analogous betweenness centrality metrics to analyze connectivity of wolf habitat throughout the northwestern United States and southwestern Canada to determine where it might be possible to facilitate range expansion and interpopulation dispersal. We developed software to facilitate application of centrality metrics. Shortest-path betweenness centrality identified a minimal network of linkages analogous to those identified by least-cost-path corridor mapping. Current flow and minimum-cost-maximum-flow betweenness centrality identified diffuse networks that included alternative linkages, which will allow greater flexibility in planning. Minimum-cost-maximum-flow betweenness centrality, by integrating both land cost and habitat capacity, allows connectivity to be considered within planning processes that seek to maximize species protection at minimum cost. Centrality analysis is relevant to conservation and landscape genetics at a range of spatial extents, but it may be most broadly applicable within single- and multispecies planning efforts to conserve regional habitat connectivity.}, } @article {pmid22007442, year = {2011}, author = {Peng, SZ and Zhao, CY and Zheng, XL and Xu, ZL and He, L}, title = {[Spatial distribution characteristics of the biomass and carbon storage of Qinghai spruce (Picea crassifolia) forests in Qilian Mountains].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {22}, number = {7}, pages = {1689-1694}, pmid = {22007442}, issn = {1001-9332}, mesh = {*Biomass ; Carbon/*metabolism ; China ; *Ecosystem ; Geographic Information Systems ; Picea/*growth & development/*metabolism ; Temperature ; }, abstract = {This paper estimated the biomass and carbon storage and their spatial distributions of Qinghai spruce (Picea crassifolia) forests in Qilian Mountains, based on the field investigation, forest map, and meteorological data, and with the help of GIS technology. In 2008, the biomass of the forests was averagely 209.24 t x hm(-2), with a total biomass of 3.4 x 10(7) t. Due to the difference of water and thermal condition, there existed great differences in the biomass of Qinghai spruce within the Mountains. The biomass increased by 3.12 t x hm(-2) with increasing 1 degrees longitude and decreased by 3.8 t x hm(-2) with increasing 1 degrees latitude, and decreased by 0.05 t x hm(-2) with the elevation increasing 100 m. The carbon density of the forests ranged from 70.4 to 131.1 t x hm(-2), averagely 109.8 t x hm(-2), and the average carbon density was 83.8 t x hm(-2) for the young forest, 109.6 t x hm(-2) for the middle age forest, 122 t x hm(-2) for the near-mature forest, 124.2 t x hm(-2) for the mature forest, and 117.1 t x hm(-2) for the over-mature forest. The total carbon storage of Qinghai spruce forests in the study area was 1.8 x 10(7) t.}, } @article {pmid22005515, year = {2011}, author = {Qi, ZH and Liu, YF and Wang, WN and Wu, X and Xin, Y and Lu, YF and Wang, AL}, title = {Molecular characterization and functional analysis of a complement C3 molecule in the orange-spotted grouper (Epinephelus coioides).}, journal = {Fish & shellfish immunology}, volume = {31}, number = {6}, pages = {1284-1290}, doi = {10.1016/j.fsi.2011.09.018}, pmid = {22005515}, issn = {1095-9947}, mesh = {Amino Acid Sequence ; Analysis of Variance ; Animals ; Base Sequence ; Complement C3/*genetics ; Computational Biology ; DNA Primers/genetics ; DNA, Complementary/genetics ; Gene Expression Profiling ; Gene Expression Regulation/*physiology ; Gene Library ; Hydrogen-Ion Concentration ; Molecular Sequence Data ; Nucleic Acid Amplification Techniques ; Open Reading Frames/genetics ; Perciformes/*genetics ; Real-Time Polymerase Chain Reaction ; Reverse Transcriptase Polymerase Chain Reaction ; Sequence Analysis, DNA ; Stress, Physiological/*physiology ; Temperature ; }, abstract = {Complement component C3 is a key molecule in the complement system whose activation is essential for all the important functions performed by this system. In this study, we examined a temperature-subtracted library from the orange-spotted grouper (Epinephelus coioides), and identified a sequence with high similarity to other complement C3 proteins. Rapid amplification of the cDNA ends (RACE) yielded the full open reading frame of this protein, and subsequent analysis indicated that the Ec-C3 (E. coioides-C3) gene encodes a protein of 1657 amino acid residues with a molecular mass of 184.56 kDa. The deduced amino acid sequence showed that Ec-C3 has conserved residues and domains known to be critical for C3 function. RT-PCR assays showed that under normal physiological conditions Ec-C3 mRNA is most strongly expressed in the liver, but relatively high levels were also found in many other tissues, including intestine, muscles, gills, hemocytes, heart, spleen, head, kidney and brain. Further analysis of Ec-C3 gene expression in liver tissue by quantitative real-time PCR demonstrated that Ec-C3 transcript levels increased when the fish were exposed to both pH and temperature stress, but the time when its expression level peaked differed under these stresses. The results show that Ec-C3 mRNA expression in the orange-spotted grouper is influenced by pH and temperature stress and that Ec-C3 may play an important role in antioxidation mechanisms.}, } @article {pmid22002713, year = {2011}, author = {Diamond, JM and Latimer, HA and Munkittrick, KR and Thornton, KW and Bartell, SM and Kidd, KA}, title = {Prioritizing contaminants of emerging concern for ecological screening assessments.}, journal = {Environmental toxicology and chemistry}, volume = {30}, number = {11}, pages = {2385-2394}, doi = {10.1002/etc.667}, pmid = {22002713}, issn = {1552-8618}, mesh = {Animals ; Aquatic Organisms/drug effects ; Databases, Factual ; Ecology ; *Environmental Monitoring ; Hazardous Substances/*analysis ; Risk Assessment ; Water Pollutants/*analysis ; }, } @article {pmid22002248, year = {2012}, author = {Bess, KD and Speer, PW and Perkins, DD}, title = {Ecological contexts in the development of coalitions for youth violence prevention: an organizational network analysis.}, journal = {Health education & behavior : the official publication of the Society for Public Health Education}, volume = {39}, number = {5}, pages = {526-537}, doi = {10.1177/1090198111419656}, pmid = {22002248}, issn = {1552-6127}, support = {5U49CE001022/CE/NCIPC CDC HHS/United States ; }, mesh = {Adolescent ; Community Networks/*organization & administration ; Humans ; *Program Development ; Qualitative Research ; Tennessee ; Violence/*prevention & control ; }, abstract = {Community coalitions are a recognized strategy for addressing pressing public health problems. Despite the promise of coalitions as an effective prevention strategy, results linking coalition efforts to positive community outcomes are mixed. To date, research has primarily focused on determining organizational attributes related to successful internal coalition functioning. The authors' research complements and adds to this literature by offering a network conceptualization of coalition formation in which coalition participation is studied within the broader context of local organizational networks both within and beyond a coalition. The authors examine participation in the first year of a youth violence prevention coalition exploring both differences between participating and nonparticipating organizations and levels of participation. Each network variable, reflecting prior collaboration and being viewed by other organizations as a local leader, approximately doubled the explained variance in coalition participation beyond the predictive power of all available organizational attributes combined. Results suggest that initial coalition participation emerged out of a preexisting network of interorganizational relations and provide an alternative perspective on coalition formation that goes beyond conceptual orientations that treat coalitions as bounded organizational entities that exist apart from the communities in which they are embedded.}, } @article {pmid22001528, year = {2012}, author = {Brewer, S and Jackson, ST and Williams, JW}, title = {Paleoecoinformatics: applying geohistorical data to ecological questions.}, journal = {Trends in ecology & evolution}, volume = {27}, number = {2}, pages = {104-112}, doi = {10.1016/j.tree.2011.09.009}, pmid = {22001528}, issn = {1872-8383}, mesh = {Animals ; Biological Evolution ; Body Size ; *Databases, Factual ; Ecology/*methods ; Geological Phenomena ; Geology/methods ; }, abstract = {Paleoecoinformatics, the development and use of paleoecological databases and tools, has a strong tradition of community support, and is rapidly growing as new tools bring new opportunities to advance understanding of ecological and evolutionary dynamics, from regional to global scales, and across the entire history of life on earth. Paleoecoinformatics occupies the intersection of ecoinformatics and geoinformatics. All face shared challenges, including developing frameworks to store heterogeneous and dynamic datasets, facilitating data contributions, linking heterogeneous data, and tracking improvements in data quality and scientific understanding. The three communities will benefit from increased engagement and exchange.}, } @article {pmid21999815, year = {2012}, author = {Earnest, A and Hock Ong, ME and Shahidah, N and Min Ng, W and Foo, C and Nott, DJ}, title = {Spatial analysis of ambulance response times related to prehospital cardiac arrests in the city-state of Singapore.}, journal = {Prehospital emergency care}, volume = {16}, number = {2}, pages = {256-265}, doi = {10.3109/10903127.2011.615974}, pmid = {21999815}, issn = {1545-0066}, mesh = {Adult ; Age Factors ; Aged ; Ambulances/*organization & administration/*statistics & numerical data ; Bayes Theorem ; Databases, Factual ; Emergencies ; Emergency Medical Services/*standards/trends ; Female ; Health Services Accessibility ; Humans ; Male ; Middle Aged ; Out-of-Hospital Cardiac Arrest/mortality/*therapy ; Retrospective Studies ; Risk Assessment ; Singapore ; Socioeconomic Factors ; Survival Analysis ; Time Factors ; Urban Population ; }, abstract = {OBJECTIVES: The main objective of this study was to establish the spatial variation in ambulance response times for out-of-hospital cardiac arrests (OHCAs) in the city-state of Singapore. The secondary objective involved studying the relationships between various covariates, such as traffic condition and time and day of collapse, and ambulance response times.

METHODS: The study design was observational and ecological in nature. Data on OHCAs were collected from a nationally representative database for the period October 2001 to October 2004. We used the conditional autoregressive (CAR) model to analyze the data. Within the Bayesian framework of analysis, we used a Weibull regression model that took into account spatial random effects. The regression model was used to study the independent effects of each covariate.

RESULTS: Our results showed that there was spatial heterogeneity in the ambulance response times in Singapore. Generally, areas in the far outskirts (suburbs), such as Boon Lay (in the west) and Sembawang (in the north), fared badly in terms of ambulance response times. This improved when adjusted for key covariates, including distance from the nearest fire station. Ambulance response time was also associated with better traffic conditions, weekend OHCAs, distance from the nearest fire station, and OHCAs occurring during nonpeak driving hours. For instance, the hazard ratio for good ambulance response time was 2.35 (95% credible interval [CI] 1.97-2.81) when traffic conditions were light and 1.72 (95% CI 1.51-1.97) when traffic conditions were moderate, as compared with heavy traffic.

CONCLUSIONS: We found a clear spatial gradient for ambulance response times, with far-outlying areas' exhibiting poorer response times. Our study highlights the utility of this novel approach, which may be helpful for planning emergency medical services and public emergency responses.}, } @article {pmid21995558, year = {2011}, author = {Fisher-Reid, MC and Wiens, JJ}, title = {What are the consequences of combining nuclear and mitochondrial data for phylogenetic analysis? Lessons from Plethodon salamanders and 13 other vertebrate clades.}, journal = {BMC evolutionary biology}, volume = {11}, number = {}, pages = {300}, pmid = {21995558}, issn = {1471-2148}, mesh = {Animals ; Base Sequence ; Bayes Theorem ; Cell Nucleus/*genetics ; Computational Biology ; DNA Primers/genetics ; DNA, Mitochondrial/*genetics ; Data Collection/*methods ; Models, Genetic ; Molecular Sequence Data ; *Phylogeny ; Sequence Analysis, DNA ; Urodela/*genetics ; Vertebrates/*genetics ; }, abstract = {BACKGROUND: The use of mitochondrial DNA data in phylogenetics is controversial, yet studies that combine mitochondrial and nuclear DNA data (mtDNA and nucDNA) to estimate phylogeny are common, especially in vertebrates. Surprisingly, the consequences of combining these data types are largely unexplored, and many fundamental questions remain unaddressed in the literature. For example, how much do trees from mtDNA and nucDNA differ? How are topological conflicts between these data types typically resolved in the combined-data tree? What determines whether a node will be resolved in favor of mtDNA or nucDNA, and are there any generalities that can be made regarding resolution of mtDNA-nucDNA conflicts in combined-data trees? Here, we address these and related questions using new and published nucDNA and mtDNA data for Plethodon salamanders and published data from 13 other vertebrate clades (including fish, frogs, lizards, birds, turtles, and mammals).

RESULTS: We find widespread discordance between trees from mtDNA and nucDNA (30-70% of nodes disagree per clade), but this discordance is typically not strongly supported. Despite often having larger numbers of variable characters, mtDNA data do not typically dominate combined-data analyses, and combined-data trees often share more nodes with trees from nucDNA alone. There is no relationship between the proportion of nodes shared between combined-data and mtDNA trees and relative numbers of variable characters or levels of homoplasy in the mtDNA and nucDNA data sets. Congruence between trees from mtDNA and nucDNA is higher on branches that are longer and deeper in the combined-data tree, but whether a conflicting node will be resolved in favor mtDNA or nucDNA is unrelated to branch length. Conflicts that are resolved in favor of nucDNA tend to occur at deeper nodes in the combined-data tree. In contrast to these overall trends, we find that Plethodon have an unusually large number of strongly supported conflicts between data types, which are generally resolved in favor of mtDNA in the combined-data tree (despite the large number of nuclear loci sampled).

CONCLUSIONS: Overall, our results from 14 vertebrate clades show that combined-data analyses are not necessarily dominated by the more variable mtDNA data sets. However, given cases like Plethodon, there is also the need for routine checking of incongruence between mtDNA and nucDNA data and its impacts on combined-data analyses.}, } @article {pmid21994784, year = {2011}, author = {Han, GZ and Worobey, M}, title = {Homologous recombination in negative sense RNA viruses.}, journal = {Viruses}, volume = {3}, number = {8}, pages = {1358-1373}, pmid = {21994784}, issn = {1999-4915}, mesh = {Coinfection ; Computational Biology/standards ; Evolution, Molecular ; Genes, Viral ; *Homologous Recombination ; Phylogeny ; RNA Viruses/*genetics ; RNA, Viral/*genetics ; Virus Cultivation/standards ; }, abstract = {Recombination is an important process that influences biological evolution at many different levels. More and more homologous recombination events have been reported among negative sense RNA viruses recently. While sporadic authentic examples indicate that homologous recombination does occur, recombination seems to be generally rare or even absent in most negative sense RNA viruses, and most of the homologous recombination events reported in the literature were likely generated artificially due to lab contamination or inappropriate bioinformatics methods. Homologous recombination in negative sense RNA viruses should be reported with caution in the future, and only after stringent quality control efforts. Moreover, co-infection experiments should be performed to confirm whether recombination can occur.}, } @article {pmid21994619, year = {2010}, author = {Brister, JR and Bao, Y and Kuiken, C and Lefkowitz, EJ and Mercier, PL and Leplae, R and Madupu, R and Scheuermann, RH and Schobel, S and Seto, D and Shrivastava, S and Sterk, P and Zeng, Q and Klimke, W and Tatusova, T}, title = {Towards Viral Genome Annotation Standards, Report from the 2010 NCBI Annotation Workshop.}, journal = {Viruses}, volume = {2}, number = {10}, pages = {2258-2268}, pmid = {21994619}, issn = {1999-4915}, abstract = {Improvements in DNA sequencing technologies portend a new era in virology and could possibly lead to a giant leap in our understanding of viral evolution and ecology. Yet, as viral genome sequences begin to fill the world's biological databases, it is critically important to recognize that the scientific promise of this era is dependent on consistent and comprehensive genome annotation. With this in mind, the NCBI Genome Annotation Workshop recently hosted a study group tasked with developing sequence, function, and metadata annotation standards for viral genomes. This report describes the issues involved in viral genome annotation and reviews policy recommendations presented at the NCBI Annotation Workshop.}, } @article {pmid21994228, year = {2011}, author = {Riba-Grognuz, O and Keller, L and Falquet, L and Xenarios, I and Wurm, Y}, title = {Visualization and quality assessment of de novo genome assemblies.}, journal = {Bioinformatics (Oxford, England)}, volume = {27}, number = {24}, pages = {3425-3426}, doi = {10.1093/bioinformatics/btr569}, pmid = {21994228}, issn = {1367-4811}, mesh = {*Chromosome Mapping ; Computational Biology ; Genome ; Sequence Analysis, DNA/*methods ; Software ; Synteny ; }, abstract = {SUMMARY: Recent technological progress has greatly facilitated de novo genome sequencing. However, de novo assemblies consist in many pieces of contiguous sequence (contigs) arranged in thousands of scaffolds instead of small numbers of chromosomes. Confirming and improving the quality of such assemblies is critical for subsequent analysis. We present a method to evaluate genome scaffolding by aligning independently obtained transcriptome sequences to the genome and visually summarizing the alignments using the Cytoscape software. Applying this method to the genome of the red fire ant Solenopsis invicta allowed us to identify inconsistencies in 7%, confirm contig order in 20% and extend 16% of scaffolds.

CONTACT: oksana.ribagrognuz@unil.ch; yannick.wurm@unil.ch

AVAILABILITY: Scripts that generate tables for visualization in Cytoscape from FASTA sequence and scaffolding information files are publicly available at https://github.com/ksanao/TGNet.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, } @article {pmid21993642, year = {2012}, author = {Baart, GJ and Martens, DE}, title = {Genome-scale metabolic models: reconstruction and analysis.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {799}, number = {}, pages = {107-126}, doi = {10.1007/978-1-61779-346-2_7}, pmid = {21993642}, issn = {1940-6029}, mesh = {Computational Biology ; Energy Metabolism/*physiology ; Enzymes/*metabolism ; Genomics/*methods ; Internet ; Metabolic Networks and Pathways/*physiology ; Metabolomics/*methods ; *Models, Biological ; Molecular Sequence Annotation/*methods ; }, abstract = {Metabolism can be defined as the complete set of chemical reactions that occur in living organisms in order to maintain life. Enzymes are the main players in this process as they are responsible for catalyzing the chemical reactions. The enzyme-reaction relationships can be used for the reconstruction of a network of reactions, which leads to a metabolic model of metabolism. A genome-scale metabolic network of chemical reactions that take place inside a living organism is primarily reconstructed from the information that is present in its genome and the literature and involves steps such as functional annotation of the genome, identification of the associated reactions and determination of their stoichiometry, assignment of localization, determination of the biomass composition, estimation of energy requirements, and definition of model constraints. This information can be integrated into a stoichiometric model of metabolism that can be used for detailed analysis of the metabolic potential of the organism using constraint-based modeling approaches and hence is valuable in understanding its metabolic capabilities.}, } @article {pmid21985473, year = {2012}, author = {Rinta-Kanto, JM and Sun, S and Sharma, S and Kiene, RP and Moran, MA}, title = {Bacterial community transcription patterns during a marine phytoplankton bloom.}, journal = {Environmental microbiology}, volume = {14}, number = {1}, pages = {228-239}, doi = {10.1111/j.1462-2920.2011.02602.x}, pmid = {21985473}, issn = {1462-2920}, mesh = {Bacteria/*genetics/growth & development/metabolism ; Computational Biology ; *Eutrophication ; Genes, Bacterial ; Genomic Library ; Phytoplankton/genetics/*growth & development/metabolism ; RNA, Bacterial/genetics ; RNA, Messenger/genetics ; Seawater/microbiology ; Transcription, Genetic ; *Transcriptome ; }, abstract = {Bacterioplankton consume a large proportion of photosynthetically fixed carbon in the ocean and control its biogeochemical fate. We used an experimental metatranscriptomics approach to compare bacterial activities that route energy and nutrients during a phytoplankton bloom compared with non-bloom conditions. mRNAs were sequenced from duplicate bloom and control microcosms 1 day after a phytoplankton biomass peak, and transcript copies per litre of seawater were calculated using an internal mRNA standard. Transcriptome analysis revealed a potential novel mechanism for enhanced efficiency during carbon-limited growth, mediated through membrane-bound pyrophosphatases [V-type H(+)-translocating; hppA]; bloom bacterioplankton participated less in this metabolic energy scavenging than non-bloom bacterioplankton, with possible implications for differences in growth yields on organic substrates. Bloom bacterioplankton transcribed more copies of genes predicted to increase cell surface adhesiveness, mediated by changes in bacterial signalling molecules related to biofilm formation and motility; these may be important in microbial aggregate formation. Bloom bacterioplankton also transcribed more copies of genes for organic acid utilization, suggesting an increased importance of this compound class in the bioreactive organic matter released during phytoplankton blooms. Transcription patterns were surprisingly faithful within a taxon regardless of treatment, suggesting that phylogeny broadly predicts the ecological roles of bacterial groups across 'boom' and 'bust' environmental backgrounds.}, } @article {pmid21983753, year = {2012}, author = {Ippolito, A and Todeschini, R and Vighi, M}, title = {Sensitivity assessment of freshwater macroinvertebrates to pesticides using biological traits.}, journal = {Ecotoxicology (London, England)}, volume = {21}, number = {2}, pages = {336-352}, pmid = {21983753}, issn = {1573-3017}, mesh = {Amphipoda/*drug effects ; Animals ; Behavior, Animal/drug effects ; Carbamates/toxicity ; Databases, Factual ; Environmental Monitoring ; Fresh Water ; Insecta/*drug effects ; Organophosphates/toxicity ; Pesticides/*toxicity ; Predictive Value of Tests ; Pyrethrins/toxicity ; Species Specificity ; Toxicity Tests ; United States ; United States Environmental Protection Agency ; Water Pollutants, Chemical/*toxicity ; }, abstract = {Assessing the sensitivity of different species to chemicals is one of the key points in predicting the effects of toxic compounds in the environment. Trait-based predicting methods have proved to be extremely efficient for assessing the sensitivity of macroinvertebrates toward compounds with non specific toxicity (narcotics). Nevertheless, predicting the sensitivity of organisms toward compounds with specific toxicity is much more complex, since it depends on the mode of action of the chemical. The aim of this work was to predict the sensitivity of several freshwater macroinvertebrates toward three classes of plant protection products: organophosphates, carbamates and pyrethroids. Two databases were built: one with sensitivity data (retrieved, evaluated and selected from the U.S. Environmental Protection Agency ECOTOX database) and the other with biological traits. Aside from the "traditional" traits usually considered in ecological analysis (i.e. body size, respiration technique, feeding habits, etc.), multivariate analysis was used to relate the sensitivity of organisms to some other characteristics which may be involved in the process of intoxication. Results confirmed that, besides traditional biological traits, related to uptake capability (e.g. body size and body shape) some traits more related to particular metabolic characteristics or patterns have a good predictive capacity on the sensitivity to these kinds of toxic substances. For example, behavioral complexity, assumed as an indicator of nervous system complexity, proved to be an important predictor of sensitivity towards these compounds. These results confirm the need for more complex traits to predict effects of highly specific substances. One key point for achieving a complete mechanistic understanding of the process is the choice of traits, whose role in the discrimination of sensitivity should be clearly interpretable, and not only statistically significant.}, } @article {pmid21980457, year = {2011}, author = {Kent, R and Bar-Massada, A and Carmel, Y}, title = {Multiscale analyses of mammal species composition--environment relationship in the contiguous USA.}, journal = {PloS one}, volume = {6}, number = {9}, pages = {e25440}, pmid = {21980457}, issn = {1932-6203}, mesh = {Animals ; Data Interpretation, Statistical ; *Ecological and Environmental Phenomena ; *Environment ; Geography ; Mammals/*classification ; United States ; }, abstract = {Relationships between species composition and its environmental determinants are a basic objective of ecology. Such relationships are scale dependent, and predictors of species composition typically include variables such as climate, topographic, historical legacies, land uses, human population levels, and random processes. Our objective was to quantify the effect of environmental determinants on U.S. mammal composition at various spatial scales. We found that climate was the predominant factor affecting species composition, and its relative impact increased in correlation with the increase of the spatial scale. Another factor affecting species composition is land-use-land-cover. Our findings showed that its impact decreased as the spatial scale increased. We provide quantitative indication of highly significant effect of climate and land-use-land-cover variables on mammal composition at multiple scales.}, } @article {pmid21980436, year = {2011}, author = {Folcher, L and Bourguet, D and Thiéry, D and Pélozuelo, L and Phalip, M and Weissenberger, A and Eychenne, N and Regnault-Roger, C and Delos, M}, title = {Changes in parasitoid communities over time and space: a historical case study of the maize pest Ostrinia nubilalis.}, journal = {PloS one}, volume = {6}, number = {9}, pages = {e25374}, pmid = {21980436}, issn = {1932-6203}, mesh = {Animals ; Biodiversity ; Databases, Factual ; Environment ; History, 20th Century ; History, 21st Century ; Human Activities ; Larva/physiology ; Moths/classification/*physiology ; Zea mays/*parasitology ; }, abstract = {Understanding the ways in which human environmental modifications affect biodiversity is a key challenge in conservation planning, pest control and evolutionary ecology. Parasitoid communities, particularly those associated with agricultural pests, may be susceptible to such modifications. We document here changes in the larval parasitoid communities of Ostrinia nubilalis--the main pest of maize--and its sibling species O. scapulalis, based on two historical datasets, one collected from 1921-1928 and the other from 2001-2005. Each of these datasets encompasses several years and large geographical areas and was based on several thousands/millions of host larvae. The 80-year interval between the two datasets was marked by a decrease in O. nubilalis parasitism to about two thirds its initial level, mostly due to a decrease in the rate of parasitism by hymenopterans. However, a well balanced loss and gain of species ensured that species richness remained stable. Conversely, O. scapulalis displayed stable rates of parasitism over this period, with a decline in the species richness of its parasitoid community. Rates of parasitism and species richness in regions colonized by O. nubilalis during the 1950s were one half to one third those in regions displaying long-term colonisation by this pest. During the recent human activity-driven expansion of its range, O. nubilalis has neither captured native parasitoids nor triggered parasite spill back or spill over.}, } @article {pmid21978194, year = {2011}, author = {Clark, JS and Bell, DM and Hersh, MH and Kwit, MC and Moran, E and Salk, C and Stine, A and Valle, D and Zhu, K}, title = {Individual-scale variation, species-scale differences: inference needed to understand diversity.}, journal = {Ecology letters}, volume = {14}, number = {12}, pages = {1273-1287}, doi = {10.1111/j.1461-0248.2011.01685.x}, pmid = {21978194}, issn = {1461-0248}, mesh = {Animals ; *Biodiversity ; Computational Biology/*methods ; Ecology/*methods ; *Models, Biological ; }, abstract = {As ecological data are usually analysed at a scale different from the one at which the process of interest operates, interpretations can be confusing and controversial. For example, hypothesised differences between species do not operate at the species level, but concern individuals responding to environmental variation, including competition with neighbours. Aggregated data from many individuals subject to spatio-temporal variation are used to produce species-level averages, which marginalise away the relevant (process-level) scale. Paradoxically, the higher the dimensionality, the more ways there are to differ, yet the more species appear the same. The aggregate becomes increasingly irrelevant and misleading. Standard analyses can make species look the same, reverse species rankings along niche axes, make the surprising prediction that a species decreases in abundance when a competitor is removed from a model, or simply preclude parameter estimation. Aggregation explains why niche differences hidden at the species level become apparent upon disaggregation to the individual level, why models suggest that individual-level variation has a minor impact on diversity when disaggregation shows it to be important, and why literature-based synthesis can be unfruitful. We show how to identify when aggregation is the problem, where it has caused controversy, and propose three ways to address it.}, } @article {pmid21973161, year = {2012}, author = {Vanderhaeghe, F and Smolders, AJ and Roelofs, JG and Hoffmann, M}, title = {Selecting predictors for discriminant analysis of species performance: an example from an amphibious softwater plant.}, journal = {Plant biology (Stuttgart, Germany)}, volume = {14}, number = {2}, pages = {271-277}, doi = {10.1111/j.1438-8677.2011.00497.x}, pmid = {21973161}, issn = {1438-8677}, mesh = {Chi-Square Distribution ; Data Mining/*methods ; Discriminant Analysis ; Ecology/*methods ; Eleocharis/*physiology ; Models, Statistical ; Principal Component Analysis ; Species Specificity ; }, abstract = {Selecting an appropriate variable subset in linear multivariate methods is an important methodological issue for ecologists. Interest often exists in obtaining general predictive capacity or in finding causal inferences from predictor variables. Because of a lack of solid knowledge on a studied phenomenon, scientists explore predictor variables in order to find the most meaningful (i.e. discriminating) ones. As an example, we modelled the response of the amphibious softwater plant Eleocharis multicaulis using canonical discriminant function analysis. We asked how variables can be selected through comparison of several methods: univariate Pearson chi-square screening, principal components analysis (PCA) and step-wise analysis, as well as combinations of some methods. We expected PCA to perform best. The selected methods were evaluated through fit and stability of the resulting discriminant functions and through correlations between these functions and the predictor variables. The chi-square subset, at P < 0.05, followed by a step-wise sub-selection, gave the best results. In contrast to expectations, PCA performed poorly, as so did step-wise analysis. The different chi-square subset methods all yielded ecologically meaningful variables, while probable noise variables were also selected by PCA and step-wise analysis. We advise against the simple use of PCA or step-wise discriminant analysis to obtain an ecologically meaningful variable subset; the former because it does not take into account the response variable, the latter because noise variables are likely to be selected. We suggest that univariate screening techniques are a worthwhile alternative for variable selection in ecology.}, } @article {pmid21967662, year = {2012}, author = {Mulvaney, SA and Rothman, RL and Dietrich, MS and Wallston, KA and Grove, E and Elasy, TA and Johnson, KB}, title = {Using mobile phones to measure adolescent diabetes adherence.}, journal = {Health psychology : official journal of the Division of Health Psychology, American Psychological Association}, volume = {31}, number = {1}, pages = {43-50}, pmid = {21967662}, issn = {1930-7810}, support = {K24 DK077875/DK/NIDDK NIH HHS/United States ; P60 DK020593/DK/NIDDK NIH HHS/United States ; P30 DK092986/DK/NIDDK NIH HHS/United States ; DK020593/DK/NIDDK NIH HHS/United States ; RR024975/RR/NCRR NIH HHS/United States ; UL1 RR024975/RR/NCRR NIH HHS/United States ; }, mesh = {Adolescent ; Blood Glucose/analysis ; Blood Glucose Self-Monitoring ; *Cell Phone ; Child ; Data Collection/methods ; Diabetes Mellitus ; Diabetes Mellitus, Type 1/*blood/*drug therapy/psychology ; Humans ; Hypoglycemic Agents/*administration & dosage ; Insulin/*administration & dosage ; Male ; Medication Adherence/*statistics & numerical data ; Self Care ; Weights and Measures ; }, abstract = {OBJECTIVES: 1) describe and determine the feasibility of using cell-phone-based ecological momentary assessment (EMA) to measure blood glucose monitoring and insulin administration in adolescent Type 1 diabetes, 2) relate EMA to traditional self-report and glycemic control, and 3) identify patterns of adherence by time of day and over time using EMA.

METHOD: Adolescents with Type 1 diabetes (n = 96) completed baseline measures of cell phone use and adherence. Glycemic control (measured by levels of HbA1c) was obtained from medical records. A subgroup of adolescents (n = 50) completed 10 days of EMA to assess blood glucose monitoring frequency, timing of glucose monitoring, insulin administration, and insulin dosing. One third of adolescents were not allowed to use their cell phones for diabetes at school. Parental restrictions on cell phone use at home were not prevalent.

RESULTS: The EMA response rate (59%) remained stable over the 10-day calling period. Morning time was associated with worse monitoring and insulin administration, accounting for 59-74% of missed self-care tasks. EMA-reported missed glucose checks and missed insulin doses were correlated to traditional self-report data, but not to HbA1c levels. Trajectory analyses identified two subgroups: one with consistently adequate adherence, and one with more variable, and worse, adherence. The latter adherence style showed worse glycemic control.

CONCLUSION: Mobile phones provide a feasible method to measure glucose monitoring and insulin administration in adolescents, given a limited assessment duration. The method provided novel insights regarding patterns of adherence and should be explored in clinical settings for targeting or tailoring interventions.}, } @article {pmid21967377, year = {2011}, author = {Luo, J and Hendryx, M}, title = {Environmental carcinogen releases and lung cancer mortality in rural-urban areas of the United States.}, journal = {The Journal of rural health : official journal of the American Rural Health Association and the National Rural Health Care Association}, volume = {27}, number = {4}, pages = {342-349}, doi = {10.1111/j.1748-0361.2010.00357.x}, pmid = {21967377}, issn = {1748-0361}, support = {1 U1CRH10664-01-00//PHS HHS/United States ; }, mesh = {Carcinogens, Environmental/*toxicity ; Chemical Hazard Release ; Databases, Factual ; Environmental Exposure/*adverse effects ; Female ; Health Status Disparities ; Humans ; Linear Models ; Lung Neoplasms/*mortality ; Male ; *Rural Health ; United States/epidemiology ; *Urban Health ; }, abstract = {PURPOSE: Environmental hazards are unevenly distributed across communities and populations; however, little is known about the distribution of environmental carcinogenic pollutants and lung cancer risk across populations defined by race, sex, and rural-urban setting.

METHODS: We used the Toxics Release Inventory (TRI) database to conduct an ecological study at the county level (a total of 3,141 counties). Multiple linear regressions were used to assess the associations of carcinogenic discharges from TRI sites and lung cancer mortality rates at the county level in the United States during the years 1990 through 2007.

FINDINGS: We observed an excess risk of population lung cancer mortality associated with higher amounts of environmental carcinogen releases from TRI facilities in both males and females, and in both whites and African Americans. The strength of these associations tended to be stronger in African Americans. A significant dose-response relationship was observed for the total volume of carcinogen releases or carcinogen releases to the air, but not releases to water. These associations appeared to be present within nonmetropolitan counties but not metropolitan counties, and to be concentrated in certain urban-rural county typologies.

CONCLUSIONS: Our results suggest that exposure to higher carcinogen releases from industrial or chemical facilities in rural areas may increase the risk of lung cancer mortality. Our findings add to the evidence for undertaking prudent efforts to limit the release of carcinogenic chemicals into the environment.}, } @article {pmid21967038, year = {2011}, author = {Goldie, X and Lanfear, R and Bromham, L}, title = {Diversification and the rate of molecular evolution: no evidence of a link in mammals.}, journal = {BMC evolutionary biology}, volume = {11}, number = {}, pages = {286}, pmid = {21967038}, issn = {1471-2148}, mesh = {Animals ; *Biodiversity ; Body Size ; Computational Biology ; *Evolution, Molecular ; Mammals/*genetics ; *Phylogeny ; Regression Analysis ; }, abstract = {BACKGROUND: Recent research has indicated a positive association between rates of molecular evolution and diversification in a number of taxa. However debate continues concerning the universality and cause of this relationship. Here, we present the first systematic investigation of this relationship within the mammals. We use phylogenetically independent sister-pair comparisons to test for a relationship between substitution rates and clade size at a number of taxonomic levels. Total, non-synonymous and synonymous substitution rates were estimated from mitochondrial and nuclear DNA sequences.

RESULTS: We found no evidence for an association between clade size and substitution rates in mammals, for either the nuclear or the mitochondrial sequences. We found significant associations between body size and substitution rates, as previously reported.

CONCLUSIONS: Our results present a contrast to previous research, which has reported significant positive associations between substitution rates and diversification for birds, angiosperms and reptiles. There are three possible reasons for the differences between the observed results in mammals versus other clades. First, there may be no link between substitution rates and diversification in mammals. Second, this link may exist, but may be much weaker in mammals than in other clades. Third, the link between substitution rates and diversification may exist in mammals, but may be confounded by other variables.}, } @article {pmid21958017, year = {2012}, author = {Rosselló-Móra, R}, title = {Towards a taxonomy of Bacteria and Archaea based on interactive and cumulative data repositories.}, journal = {Environmental microbiology}, volume = {14}, number = {2}, pages = {318-334}, doi = {10.1111/j.1462-2920.2011.02599.x}, pmid = {21958017}, issn = {1462-2920}, mesh = {Archaea/*classification/genetics ; Bacteria/*classification/genetics ; Genomics/methods ; *Information Storage and Retrieval ; Phylogeny ; }, abstract = {Taxonomy in the second decade of the 21st century is benefiting from technological advances in molecular microbiology, especially those related to genomics. Gene and genome databases are significantly increasing due to intense research activities in the field of molecular ecology and genomics. Taxa, and especially species, are tailored by means of the recognition of a phylogenetic, genomic and phenotypic coherence that reveal their uniqueness in the classification schema. Phylogenetic coherence is mainly revealed by means of 16S rRNA gene analyses for which curated databases such as EzTaxon and LTP provide a valuable tool for tree reconstruction to taxonomy users. On the other hand, in silico full or partial genomic sequence comparisons are called on to substitute cumbersome techniques such as DNA-DNA hybridization (DDH) to genomically circumscribe species. DDH similarity values around 70% would be equivalent to ANI values of 96%. Finally, finding an exclusive phenotypic property for the taxa to be classified is of paramount relevance to producing an operative and predictive classification system. The current methods used for taxonomic classification require significant laboratory experimentation, and generally will not produce interactive databases. The new high-throughput metabolomic technologies, such as ICR-FT and MALDI-TOF mass spectrometry methods, open the door to the construction of metabolic databases for taxonomic purposes. It is to be foreseen that, in the future, taxonomists will benefit significantly from public databases speeding up the classification process. However, serious effort will be needed to harmonize them and to prevent inaccurate material.}, } @article {pmid21956023, year = {2011}, author = {Seekell, DA and Carpenter, SR and Pace, ML}, title = {Conditional heteroscedasticity as a leading indicator of ecological regime shifts.}, journal = {The American naturalist}, volume = {178}, number = {4}, pages = {442-451}, doi = {10.1086/661898}, pmid = {21956023}, issn = {1537-5323}, mesh = {Adaptation, Physiological/*physiology ; Analysis of Variance ; Computer Simulation ; *Data Interpretation, Statistical ; Ecology ; *Ecosystem ; *Models, Biological ; }, abstract = {Regime shifts are massive, often irreversible, rearrangements of nonlinear ecological processes that occur when systems pass critical transition points. Ecological regime shifts sometimes have severe consequences for human well-being, including eutrophication in lakes, desertification, and species extinctions. Theoretical and laboratory evidence suggests that statistical anomalies may be detectable leading indicators of regime shifts in ecological time series, making it possible to foresee and potentially avert incipient regime shifts. Conditional heteroscedasticity is persistent variance characteristic of time series with clustered volatility. Here, we analyze conditional heteroscedasticity as a potential leading indicator of regime shifts in ecological time series. We evaluate conditional heteroscedasticity by using ecological models with and without four types of critical transition. On approaching transition points, all time series contain significant conditional heteroscedasticity. This signal is detected hundreds of time steps in advance of the regime shift. Time series without regime shifts do not have significant conditional heteroscedasticity. Because probability values are easily associated with tests for conditional heteroscedasticity, detection of false positives in time series without regime shifts is minimized. This property reduces the need for a reference system to compare with the perturbed system.}, } @article {pmid21951598, year = {2011}, author = {, and Barker, FK and Bell, JJ and Bogdanowicz, SM and Bonatto, SL and Cezilly, F and Collins, SM and Dubreuil, C and Dufort, MJ and Eraud, C and Fuseya, R and Heap, EA and Jacobsen, N and Madders, M and McEwing, R and Michel, AP and Mougeot, F and Ogden, RS and Orantes, LC and Othman, AS and Parent, E and Pulido-Santacruz, P and Rioux-Paré, R and Roberts, MF and Rosazlina, R and Sakamoto, T and De-León, PS and Sévigny, JM and St-Onge, P and Terraube, J and Tingay, RE and Tremblay, R and Watanabe, S and Wattier, RA}, title = {Permanent Genetic Resources added to Molecular Ecology Resources Database 1 June 2011-31 July 2011.}, journal = {Molecular ecology resources}, volume = {11}, number = {6}, pages = {1124-1126}, doi = {10.1111/j.1755-0998.2011.03068.x}, pmid = {21951598}, issn = {1755-0998}, mesh = {DNA Primers/genetics ; *Databases, Genetic ; Ecology/*methods ; Microsatellite Repeats/*genetics ; Polymorphism, Single Nucleotide/*genetics ; Species Specificity ; }, abstract = {This article documents the addition of 112 microsatellite marker loci and 24 pairs of single nucleotide polymorphism (SNP) sequencing primers to the Molecular Ecology Resources Database. Loci were developed for the following species: Agelaius phoeniceus, Austrolittorina cincta, Circus cyaneus, Circus macrourus, Circus pygargus, Cryptocoryne × purpurea Ridl. nothovar. purpurea, Mya arenaria, Patagioenas squamosa, Prochilodus mariae, Scylla serrata and Scytalopus speluncae. These loci were cross-tested on the following species: Cryptocoryne × purpurea nothovar. purpurea, Cryptocoryne affinis, Cryptocoryne ciliata, Cryptocoryne cordata var. cordata, Cryptocoryne elliptica, Cryptocoryne griffithii, Cryptocoryne minima, Cryptocoryne nurii and Cryptocoryne schulzei. This article also documents the addition of 24 sequencing primer pairs and 24 allele-specific primers or probes for Aphis glycines.}, } @article {pmid21949797, year = {2011}, author = {Tedersoo, L and Abarenkov, K and Nilsson, RH and Schüssler, A and Grelet, GA and Kohout, P and Oja, J and Bonito, GM and Veldre, V and Jairus, T and Ryberg, M and Larsson, KH and Kõljalg, U}, title = {Tidying up international nucleotide sequence databases: ecological, geographical and sequence quality annotation of its sequences of mycorrhizal fungi.}, journal = {PloS one}, volume = {6}, number = {9}, pages = {e24940}, pmid = {21949797}, issn = {1932-6203}, mesh = {DNA, Ribosomal Spacer/*genetics ; *Databases, Nucleic Acid ; Ecology ; *Geography ; International Cooperation ; *Internet ; Mycorrhizae/*genetics ; Plant Roots/genetics ; rRNA Operon/*genetics ; }, abstract = {Sequence analysis of the ribosomal RNA operon, particularly the internal transcribed spacer (ITS) region, provides a powerful tool for identification of mycorrhizal fungi. The sequence data deposited in the International Nucleotide Sequence Databases (INSD) are, however, unfiltered for quality and are often poorly annotated with metadata. To detect chimeric and low-quality sequences and assign the ectomycorrhizal fungi to phylogenetic lineages, fungal ITS sequences were downloaded from INSD, aligned within family-level groups, and examined through phylogenetic analyses and BLAST searches. By combining the fungal sequence database UNITE and the annotation and search tool PlutoF, we also added metadata from the literature to these accessions. Altogether 35,632 sequences belonged to mycorrhizal fungi or originated from ericoid and orchid mycorrhizal roots. Of these sequences, 677 were considered chimeric and 2,174 of low read quality. Information detailing country of collection, geographical coordinates, interacting taxon and isolation source were supplemented to cover 78.0%, 33.0%, 41.7% and 96.4% of the sequences, respectively. These annotated sequences are publicly available via UNITE (http://unite.ut.ee/) for downstream biogeographic, ecological and taxonomic analyses. In European Nucleotide Archive (ENA; http://www.ebi.ac.uk/ena/), the annotated sequences have a special link-out to UNITE. We intend to expand the data annotation to additional genes and all taxonomic groups and functional guilds of fungi.}, } @article {pmid21946148, year = {2011}, author = {Pischedda, L and Militon, C and Gilbert, F and Cuny, P}, title = {Characterization of specificity of bacterial community structure within the burrow environment of the marine polychaete Hediste (Nereis) diversicolor.}, journal = {Research in microbiology}, volume = {162}, number = {10}, pages = {1033-1042}, doi = {10.1016/j.resmic.2011.07.008}, pmid = {21946148}, issn = {1769-7123}, mesh = {Animals ; Bacteria/*classification/genetics/isolation & purification ; Bacterial Physiological Phenomena ; Biodiversity ; Computational Biology ; *Ecosystem ; Gene Library ; Geologic Sediments/*microbiology ; Mediterranean Sea ; Molecular Sequence Data ; Polychaeta/*physiology ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Bioturbation is known to stimulate microbial communities, especially in macrofaunal burrows where the abundance and activities of bacteria are increased. Until now, these microbial communities have been poorly characterized and an important ecological question remains: do burrow walls harbor similar or specific communities compared with anoxic and surface sediments? The bacterial community structure of coastal sediments inhabited by the polychaete worm Hediste diversicolor was investigated. Surface, burrow wall and anoxic sediments were collected at the Carteau beach (Gulf of Fos, Mediterranean Sea). Bacterial diversity was determined by analyzing small subunit ribosomal RNA (16S rRNA) sequences from three clone libraries (168, 179 and 129 sequences for the surface, burrow wall and anoxic sediments, respectively). Libraries revealed 306 different operational taxonomic units (OTUs) belonging to at least 15 bacterial phyla. Bioinformatic analyses and comparisons between the three clone libraries showed that the burrow walls harbored a specific bacterial community structure which differed from the surface and anoxic environments. More similarities were nevertheless found with the surface assemblage. Inside the burrow walls, the bacterial community was characterized by high biodiversity, which probably results from the biogeochemical heterogeneity of the burrow system.}, } @article {pmid21943882, year = {2011}, author = {Stedmon, CA and Seredyńska-Sobecka, B and Boe-Hansen, R and Le Tallec, N and Waul, CK and Arvin, E}, title = {A potential approach for monitoring drinking water quality from groundwater systems using organic matter fluorescence as an early warning for contamination events.}, journal = {Water research}, volume = {45}, number = {18}, pages = {6030-6038}, doi = {10.1016/j.watres.2011.08.066}, pmid = {21943882}, issn = {1879-2448}, mesh = {Denmark ; Drinking Water/*standards ; Environmental Monitoring/*methods ; Factor Analysis, Statistical ; Filtration ; Fluorescence ; Groundwater/*standards ; Online Systems ; Organic Chemicals/*chemistry ; Ultraviolet Rays ; Waste Disposal, Fluid ; Water Pollution/*analysis ; Water Quality/*standards ; }, abstract = {The fluorescence characteristics of natural organic matter in a groundwater based drinking water supply plant were studied with the aim of applying it as a technique to identify contamination of the water supply. Excitation-emission matrices were measured and modeled using parallel factor analysis (PARAFAC) and used to identify which wavelengths provide the optimal signal for monitoring contamination events. The fluorescence was characterized by four components: three humic-like and one amino acid-like. The results revealed that the relative amounts of two of the humic-like components were very stable within the supply plant and distribution net and changed in a predictable fashion depending on which wells were supplying the water. A third humic-like component and an amino acid-like component did not differ between wells. Laboratory contamination experiments with wastewater revealed that combined they could be used as an indicator of microbial contamination. Their fluorescence spectra did not overlap with the other components and therefore the raw broadband fluorescence at the wavelengths specific to their fluorescence could be used to detect contamination. Contamination could be detected at levels equivalent to the addition of 60 μg C/L in drinking water with a TOC concentration of 3.3 mg C/L. The results of this study suggest that these types of drinking water systems, which are vulnerable to microbial contamination due to the lack of disinfectant treatment, can be easily monitored using online organic matter fluorescence as an early warning system to prompt further intensive sampling and appropriate corrective measures.}, } @article {pmid21943518, year = {2011}, author = {Tirelli, T and Favaro, L and Gamba, M and Pessani, D}, title = {Performance comparison among multivariate and data mining approaches to model presence/absence of Austropotamobius pallipes complex in Piedmont (North Western Italy).}, journal = {Comptes rendus biologies}, volume = {334}, number = {10}, pages = {695-704}, doi = {10.1016/j.crvi.2011.07.002}, pmid = {21943518}, issn = {1768-3238}, mesh = {Analysis of Variance ; Animals ; Artificial Intelligence ; Astacoidea/genetics/*physiology ; Climate ; Conservation of Natural Resources ; Data Collection ; Data Mining/*methods ; Decision Trees ; Environment ; Fresh Water/chemistry ; Geography ; Italy ; Logistic Models ; Models, Statistical ; Neural Networks, Computer ; Principal Component Analysis ; Rivers ; Software ; }, abstract = {Freshwater inhabitants in Piedmont (Italy) have been deeply disadvantaged by environmental changes caused by human disturbance. Hence there are engendered species that need human intervention of an entirely different kind - better management through the development of innovative practical tools. The most ecologically important of the river-dwelling invertebrates is a threatened species, the native white-clawed crayfish Austropotamobius pallipes. This is the species that we focused on in our effort to contribute to species conservation. Specifically we contrasted three different techniques of managing data relating to the presence/absence of this species: logistic regression, decision-tree models and artificial neural networks (ANN). Logistic regression and decision tree models (unpruned and pruned) performed worse than ANN. In this case, tree-pruning techniques did not make these models significantly more reliable, but did make the trees less complex and therefore did make the models clearer. ANN performed the best. Therefore we have judged them to be the most effective techniques.}, } @article {pmid21943048, year = {2011}, author = {Tomita, M and Okutani, A and Beiles, A and Nevo, E}, title = {Genomic, RNA, and ecological divergences of the Revolver transposon-like multi-gene family in Triticeae.}, journal = {BMC evolutionary biology}, volume = {11}, number = {}, pages = {269}, pmid = {21943048}, issn = {1471-2148}, mesh = {Chromatography, Gel ; Computational Biology ; DNA Primers/genetics ; DNA Transposable Elements/*genetics ; Demography ; *Expressed Sequence Tags ; Gene Components ; Gene Dosage/genetics ; *Genetic Variation ; Israel ; Multigene Family/*genetics ; Open Reading Frames/genetics ; Poaceae/*genetics ; Polymerase Chain Reaction ; Protein Conformation ; Reverse Transcriptase Polymerase Chain Reaction ; }, abstract = {BACKGROUND: Revolver is a newly discovered multi-gene family of transposable elements in the Triticeae genome. Revolver encompasses 2929 to 3041 bp, has 20 bp of terminal inverted repeated sequences at both ends, and contains a transcriptionally active gene encoding a DNA-binding-like protein. A putative TATA box is located at base 221, with a cap site at base 261 and a possible polyadenylation signal AATAAA at base 2918. Revolver shows considerable quantitative variation in wheat and its relatives.

RESULTS: Revolver cDNAs varied between 395 and 2,182 bp in length. The first exon exhibited length variation, but the second and third exons were almost identical. These variants in the Revolver family shared the downstream region of the second intron, but varied structurally at the 5' first exon. There were 58 clones, which showed partial homology to Revolver, among 440,000 expressed sequence tagged (EST) clones sourced from Triticeae. In these Revolver homologues with lengths of 360-744 bp, the portion after the 2nd exon was conserved (65-79% homology), but the 1st exon sequences had mutually low homology, with mutations classified into 12 types, and did not have EST sequences with open reading frames (ORFs). By PCR with the 3'-flanking region of a typical genomic clone of Revolver-2 used as a single primer, rye chromosomes 1R and 5R could be simultaneously identified. Extensive eco-geographic diversity and divergence was observed among 161 genotypes of the single species Triticum dicoccoides collected from 18 populations in Israel with varying exposures to abiotic and biotic stresses (soil, temperature, altitude, water availability, and pathogens).

CONCLUSIONS: On the base of existing differences between Revolver variants, the molecular markers that can distinguish different rye chromosomes were developed. Eco-geographic diversification of wild emmer T. dicoccoides in Israel and high Revolver copy numbers are associated with higher rainfall and biotic stresses. The remarkable quantitative differences among copy numbers of Revolver in the same species from different ecosystems suggest strong amplification activity within the last 10,000 years. It is the interesting finding because the majority of Triticeae high-copy transposable elements seem to be inactive at the recent time except for BARE-1 element in Hordeum and the fact might be interesting to perceive the processes of plant adaptive evolution.}, } @article {pmid21943000, year = {2011}, author = {Andam, CP and Gogarten, JP}, title = {Biased gene transfer and its implications for the concept of lineage.}, journal = {Biology direct}, volume = {6}, number = {}, pages = {47}, pmid = {21943000}, issn = {1745-6150}, mesh = {Alleles ; Archaea/classification/*genetics/metabolism ; Bacteria/classification/*genetics/metabolism ; Biological Evolution ; Databases, Protein ; *Gene Transfer, Horizontal ; Genes, Archaeal ; Genes, Bacterial ; Genes, rRNA ; Phenylalanine-tRNA Ligase/genetics/metabolism ; Phylogeny ; RNA, Transfer/genetics/metabolism ; Sequence Alignment ; Serine-tRNA Ligase/*genetics/metabolism ; Threonine-tRNA Ligase/*genetics/metabolism ; }, abstract = {BACKGROUND: In the presence of horizontal gene transfer (HGT), the concepts of lineage and genealogy in the microbial world become more ambiguous because chimeric genomes trace their ancestry from a myriad of sources, both living and extinct.

RESULTS: We present the evolutionary histories of three aminoacyl-tRNA synthetases (aaRS) to illustrate that the concept of organismal lineage in the prokaryotic world is defined by both vertical inheritance and reticulations due to HGT. The acquisition of a novel gene from a distantly related taxon can be considered as a shared derived character that demarcates a group of organisms, as in the case of the spirochaete Phenylalanyl-tRNA synthetase (PheRS). On the other hand, when organisms transfer genetic material with their close kin, the similarity and therefore relatedness observed among them is essentially shaped by gene transfer. Studying the distribution patterns of divergent genes with identical functions, referred to as homeoalleles, can reveal preferences for transfer partners. We describe the very ancient origin and the distribution of the archaeal homeoalleles for Threonyl-tRNA synthetases (ThrRS) and Seryl-tRNA synthetases (SerRS).

CONCLUSIONS: Patterns created through biased HGT can be undistinguishable from those created through shared organismal ancestry. A re-evaluation of the definition of lineage is necessary to reflect genetic relatedness due to both HGT and vertical inheritance. In most instances, HGT bias will maintain and strengthen similarity within groups. Only in cases where HGT bias is due to other factors, such as shared ecological niche, do patterns emerge from gene phylogenies that are in conflict with those reflecting shared organismal ancestry.}, } @article {pmid21941758, year = {2011}, author = {Yang, YZ and Chang, Y and Hu, YM and Liu, M and Li, YH}, title = {[Application of small remote sensing satellite constellations for environmental hazards in wetland landscape mapping: taking Liaohe Delta, Liaoning Province of Northeast China as a case].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {22}, number = {6}, pages = {1552-1558}, pmid = {21941758}, issn = {1001-9332}, mesh = {China ; Conservation of Natural Resources ; Ecosystem ; Environmental Exposure/adverse effects/*analysis ; *Environmental Health ; Environmental Monitoring/*methods ; Geographic Information Systems ; Models, Theoretical ; Remote Sensing Technology ; Rivers ; *Satellite Communications ; *Wetlands ; }, abstract = {To timely and accurately acquire the spatial distribution pattern of wetlands is of significance for the dynamic monitoring, conservation, and sustainable utilization of wetlands. The small remote sensing satellite constellations A/B stars (HJ-1A/1B stars) for environmental hazards were launched by China for monitoring terrestrial resources, which could provide a new data source of remote sensing image acquisition for retrieving wetland types. Taking Liaohe Delta as a case, this paper compared the accuracy of wetland classification map and the area of each wetland type retrieved from CCD data (HJ CCD data) and TM5 data, and validated and explored the applicability and the applied potential of HJ CCD data in wetland resources dynamic monitoring. The results showed that HJ CCD data could completely replace Landsat TM5 data in feature extraction and remote sensing classification. In real-time monitoring, due to its 2 days of data acquisition cycle, HJ CCD data had the priority to Landsat TM5 data (16 days of data acquisition cycle).}, } @article {pmid21940800, year = {2011}, author = {Dufault, B and Klar, N}, title = {The quality of modern cross-sectional ecologic studies: a bibliometric review.}, journal = {American journal of epidemiology}, volume = {174}, number = {10}, pages = {1101-1107}, doi = {10.1093/aje/kwr241}, pmid = {21940800}, issn = {1476-6256}, mesh = {Cross-Sectional Studies ; *Data Interpretation, Statistical ; *Epidemiologic Studies ; Humans ; }, abstract = {The ecologic study design is routinely used by epidemiologists in spite of its limitations. It is presently unknown how well the challenges of the design are dealt with in epidemiologic research. The purpose of this bibliometric review was to critically evaluate the characteristics, statistical methods, and reporting of results of modern cross-sectional ecologic papers. A search through 6 major epidemiology journals identified all cross-sectional ecologic studies published since January 1, 2000. A total of 125 articles met the inclusion requirements and were assessed via common evaluative criteria. It was found that a considerable number of cross-sectional ecologic studies use unreliable methods or contain statistical oversights; most investigators who adjusted their outcomes for age or sex did so improperly (64%), statistical validity was a potential issue for 20% of regression models, and simple linear regression was the most common analytic approach (31%). Many authors omitted important information when discussing the ecologic nature of their study (31%), the choice of study design (58%), and the susceptibility of their research to the ecological fallacy (49%). These results suggest that there is a need for an international set of guidelines that standardizes reporting on ecologic studies. Additionally, greater attention should be given to the relevant biostatistical literature.}, } @article {pmid21939067, year = {2011}, author = {Millar, RB and Anderson, MJ and Tolimieri, N}, title = {Much ado about nothings: using zero similarity points in distance-decay curves.}, journal = {Ecology}, volume = {92}, number = {9}, pages = {1717-1722}, doi = {10.1890/11-0029.1}, pmid = {21939067}, issn = {0012-9658}, mesh = {Data Interpretation, Statistical ; Demography ; *Ecosystem ; Linear Models ; *Models, Biological ; }, abstract = {Distance decay is used to describe the (usually exponential) decay in ecological similarity of assemblages between two sites as a function of their distance apart along an environmental gradient. Exponential distance-decay curves are routinely fitted by calculating the ecological similarity between each pair of sites, and fitting a linear regression to the points on a scatter plot of log-similarity vs. distance (x-axis). However, pairs of sites where the assemblages have no species in common pose a problem, because the similarity is zero, and the log transformation cannot be applied. Common fixes to this problem (i.e., either removing or transforming the zero values) are shown to have undesirable consequences and to give widely disparate estimates. A new method is presented as a special case of a generalized dissimilarity model. It is fitted very quickly and easily using existing software, and it does not require removal or transformation of the zero similarity points. Its simplicity makes it convenient for use in conjunction with the resampling methods that are routinely employed to test hypotheses, to obtain standard errors of estimated parameters, or to compare distance-decay curves. A word of caution about standard application of the bootstrap is noted, and modified bootstrap and jackknife alternatives are demonstrated.}, } @article {pmid21939059, year = {2011}, author = {Mandel, JT and Bohrer, G and Winkler, DW and Barber, DR and Houston, CS and Bildstein, KL}, title = {Migration path annotation: cross-continental study of migration-flight response to environmental conditions.}, journal = {Ecological applications : a publication of the Ecological Society of America}, volume = {21}, number = {6}, pages = {2258-2268}, doi = {10.1890/10-1651.1}, pmid = {21939059}, issn = {1051-0761}, mesh = {Animal Migration/*physiology ; Animals ; Databases, Factual ; *Environment ; Falconiformes/*physiology ; Flight, Animal/*physiology ; Models, Biological ; North America ; }, abstract = {Understanding the movements of animals is pivotal for understanding their ecology and predicting their survival in the face of rapid global changes to climate, land use, and habitats, thus facilitating more effective habitat management. Migration by flying animals is an extreme form of movement that may be especially influenced by weather. With satellite telemetry studies, and the growing availability of information about the Earth's weather and land surface conditions, many data are collected that can advance our understanding about the mechanisms that shape migrations. We present the track annotation approach for movement data analysis using information about weather from the North American Reanalysis data set, a publicly available, regional, high-resolution model-observation hybrid product, and about topography, from a publicly available high-resolution digital elevation model (DEM). As a case study, we present the analysis of the response to environmental conditions in three contrasting populations of Turkey Vultures (Cathartes aura) across North America, tracked with a three-dimensional GPS-based sensor. Two populations in the east and west coasts of the United States responded similarly to weather, indicating use of both slope and thermal soaring. Continental-interior, "Plains populations," exhibited a different migratory pattern primarily indicative of thermal soaring. These differences help us understand the constraints and behaviors of soaring migrants. The track annotation approach allowed large-scale comparative study of movement in an important migratory species, and will enable similar studies at local to global scales.}, } @article {pmid21930222, year = {2011}, author = {Souffreau, C and Verbruggen, H and Wolfe, AP and Vanormelingen, P and Siver, PA and Cox, EJ and Mann, DG and Van de Vijver, B and Sabbe, K and Vyverman, W}, title = {A time-calibrated multi-gene phylogeny of the diatom genus Pinnularia.}, journal = {Molecular phylogenetics and evolution}, volume = {61}, number = {3}, pages = {866-879}, doi = {10.1016/j.ympev.2011.08.031}, pmid = {21930222}, issn = {1095-9513}, mesh = {Bayes Theorem ; Calibration ; Databases, Nucleic Acid ; Diatoms/classification/*genetics/ultrastructure ; Fossils ; Genes/*genetics ; *Phylogeny ; Time Factors ; }, abstract = {Pinnularia is an ecologically important and species-rich genus of freshwater diatoms (Bacillariophyceae) showing considerable variation in frustule morphology. Interspecific evolutionary relationships were inferred for 36 Pinnularia taxa using a five-locus dataset. A range of fossil taxa, including newly discovered Middle Eocene forms of Pinnularia, was used to calibrate a relaxed molecular clock analysis and investigate temporal aspects of the genus' diversification. The multi-gene approach resulted in a well-resolved phylogeny of three major clades and several subclades that were frequently, but not universally, delimited by valve morphology. The genus Caloneis was not recovered as monophyletic, confirming that, as currently delimited, this genus is not evolutionarily meaningful and should be merged with Pinnularia. The Pinnularia-Caloneis complex is estimated to have diverged between the Upper Cretaceous and the early Eocene, implying a ghost range of at least 10 million year (Ma) in the fossil record.}, } @article {pmid21924269, year = {2011}, author = {Vas, Z and Lefebvre, L and Johnson, KP and Reiczigel, J and Rózsa, L}, title = {Clever birds are lousy: co-variation between avian innovation and the taxonomic richness of their amblyceran lice.}, journal = {International journal for parasitology}, volume = {41}, number = {12}, pages = {1295-1300}, doi = {10.1016/j.ijpara.2011.07.011}, pmid = {21924269}, issn = {1879-0135}, mesh = {Amblycera/*classification/genetics ; Animals ; Behavior ; *Biodiversity ; Bird Diseases/*parasitology ; Birds/*parasitology ; Brain/anatomy & histology ; Ectoparasitic Infestations/*parasitology ; Female ; Male ; Phylogeny ; Statistics as Topic ; }, abstract = {Lice (Insecta: Phthiraptera) are ectoparasites that reduce host life expectancy and sexual attractiveness. Their taxonomic richness varies considerably among their hosts. Previous studies have already explored some important factors shaping louse diversity. An unexplored potential correlate of louse taxonomic richness is host behavioural flexibility. In this comparative study, we examine the relationship between louse generic richness, innovative capabilities (as a proxy for behavioural flexibility), and brain size while controlling for host species diversity, phylogeny, body size and research effort. Using data for 108 avian families, we found a highly significant positive relationship between host innovative capabilities and the taxonomic richness of amblyceran lice, but a lack of a similar relationship in ischnoceran lice. Host brain size had only a marginal impact on amblyceran diversity and no correlation with ischnoceran diversity. This suggests that the effect in Amblycera is not mediated by metabolic limitations due to the energetic costs of brain size and maintenance, rather directly caused by the ecological differences between hosts with differing cognitive capabilities. We propose four alternative and mutually non-exclusive hypotheses that may explain this phenomenon.}, } @article {pmid21924168, year = {2011}, author = {Catchen, JM and Braasch, I and Postlethwait, JH}, title = {Conserved synteny and the zebrafish genome.}, journal = {Methods in cell biology}, volume = {104}, number = {}, pages = {259-285}, doi = {10.1016/B978-0-12-374814-0.00015-X}, pmid = {21924168}, issn = {0091-679X}, support = {R01 RR020833/RR/NCRR NIH HHS/United States ; 1F32GM095213-01/GM/NIGMS NIH HHS/United States ; R01RR020833/RR/NCRR NIH HHS/United States ; }, mesh = {Animals ; Data Mining/methods ; Databases, Genetic ; Evolution, Molecular ; Fish Proteins/genetics ; Gene Deletion ; Gene Duplication ; *Genome ; Humans ; Models, Genetic ; Phylogeny ; Receptors, Nerve Growth Factor/genetics ; Sequence Homology, Nucleic Acid ; Smegmamorpha/genetics ; *Synteny ; Zebrafish/*genetics ; }, abstract = {Zebrafish offers significant opportunities for the investigation of vertebrate development, evolution, physiology, and behavior and provides numerous models of human disease. Connecting zebrafish phenogenetic biology to that of humans and other vertebrates, however, requires the proper assignment of gene orthologies. Orthology assignments by phylogenetic analysis or by reciprocal best sequence similarity searches can lead to errors, especially in cases of gene duplication followed by gene loss or rapid lineage-specific gene evolution. Conserved synteny analysis provides a method that helps overcome such problems. Here we describe conserved synteny analysis for zebrafish genes and discuss the Synteny Database, a website specifically designed to identify conserved syntenies for zebrafish that takes into account the teleost genome duplication (TGD). We utilize the Synteny Database to demonstrate its power to resolve our understanding of the evolution of nerve growth factor receptor related genes, including Ngfr and the enigmatic Nradd. Finally, we compare conserved syntenies between zebrafish, stickleback, spotted gar, and human to understand the timing of chromosome rearrangements in teleost genome evolution. An improved understanding of gene histories that comes from the application of tools provided by the Synteny Database can facilitate the connectivity of zebrafish and human genomes.}, } @article {pmid21919188, year = {2012}, author = {Diamond, J and Denton, D and Anderson, B and Phillips, B}, title = {It is time for changes in the analysis of whole effluent toxicity data.}, journal = {Integrated environmental assessment and management}, volume = {8}, number = {2}, pages = {351-358}, doi = {10.1002/ieam.278}, pmid = {21919188}, issn = {1551-3793}, mesh = {Data Interpretation, Statistical ; Environmental Monitoring/economics/*methods ; Toxicity Tests/economics/*methods/statistics & numerical data ; United States ; United States Environmental Protection Agency ; Water Pollutants, Chemical/*analysis/toxicity ; Water Pollution, Chemical/*statistics & numerical data ; }, abstract = {The whole effluent toxicity (WET) program in the United States, Canada, and other countries typically requires multi concentration testing of effluents. While multiconcentration testing of chemicals is desirable for regulatory and scientific reasons, we believe this requirement is not as efficient for evaluating effluent compliance in a WET program. The key regulatory question of concern is whether an effluent is toxic or not, which is best answered statistically using a hypothesis approach, not a point estimate approach. However, the traditional hypothesis approach currently recommended does not reward high within-test precision. This report describes the need for 3 specific changes in the analysis of WET compliance data that we believe would yield a more robust WET regulatory program: (1) restate the null hypothesis so that test power is associated with demonstrating that the effluent is not toxic, (2) use USEPA's Test of Significant Toxicity (based on the noninferiority approach) to identify unacceptable toxicity as well as acceptable effects with a high probability, and (3) evaluate only the test control and the critical concentration of concern (e.g., instream waste concentration). We demonstrate that instituting these 3 changes would provide: Positive incentives for permittees to produce high-quality WET data, a transparent analysis approach in which the permittee could have greater control over regulatory decisions based on test results, and potentially a less expensive testing program because fewer effluent concentrations need to be examined within a test. As a result, WET test frequency could be increased for the same cost as current testing programs while providing greater representativeness of effluent quality.}, } @article {pmid21917173, year = {2011}, author = {Castillo, DM and Mell, JC and Box, KS and Blumenstiel, JP}, title = {Molecular evolution under increasing transposable element burden in Drosophila: a speed limit on the evolutionary arms race.}, journal = {BMC evolutionary biology}, volume = {11}, number = {}, pages = {258}, pmid = {21917173}, issn = {1471-2148}, mesh = {Animals ; Bayes Theorem ; Codon/genetics ; Computational Biology ; DNA Transposable Elements/*genetics ; Drosophila/*genetics ; *Evolution, Molecular ; Genetic Drift ; *Genetic Variation ; Likelihood Functions ; *Models, Genetic ; Mutation/genetics ; Phylogeny ; RNA, Small Interfering/metabolism ; Regression Analysis ; *Selection, Genetic ; Species Specificity ; }, abstract = {BACKGROUND: Genome architecture is profoundly influenced by transposable elements (TEs), and natural selection against their harmful effects is a critical factor limiting their spread. Genome defense by the piRNA silencing pathway also plays a crucial role in limiting TE proliferation. How these two forces jointly determine TE abundance is not well understood. To shed light on the nature of factors that predict TE success, we test three distinct hypotheses in the Drosophila genus. First, we determine whether TE abundance and relaxed genome-wide purifying selection on protein sequences are positively correlated. This serves to test the hypothesis that variation in TE abundance in the Drosophila genus can be explained by the strength of natural selection, relative to drift, acting in parallel against mildly deleterious non-synonymous mutations. Second, we test whether increasing TE abundance is correlated with an increased rate of amino-acid evolution in genes encoding the piRNA machinery, as might be predicted by an evolutionary arms race model. Third, we test whether increasing TE abundance is correlated with greater codon bias in genes of the piRNA machinery. This is predicted if increasing TE abundance selects for increased efficiency in the machinery of genome defense.

RESULTS: Surprisingly, we find neither of the first two hypotheses to be true. Specifically, we found that genome-wide levels of purifying selection, measured by the ratio of non-synonymous to synonymous substitution rates (ω), were greater in species with greater TE abundance. In addition, species with greater TE abundance have greater levels of purifying selection in the piRNA machinery. In contrast, it appears that increasing TE abundance has primarily driven adaptation in the piRNA machinery by increasing codon bias.

CONCLUSIONS: These results indicate that within the Drosophila genus, a historically reduced strength of selection relative to drift is unlikely to explain patterns of increased TE success across species. Other factors, such as ecological exposure, are likely to contribute to variation in TE abundances within species. Furthermore, constraints on the piRNA machinery may temper the evolutionary arms race that would drive increasing rates of evolution at the amino acid level. In the face of these constraints, selection may act primarily by improving the translational efficiency of the machinery of genome defense through efficient codon usage.}, } @article {pmid21915329, year = {2011}, author = {Quan, RC and Ren, G and Behm, JE and Wang, L and Huang, Y and Long, Y and Zhu, J}, title = {Why does Rhinopithecus bieti prefer the highest elevation range in winter? A test of the sunshine hypothesis.}, journal = {PloS one}, volume = {6}, number = {9}, pages = {e24449}, pmid = {21915329}, issn = {1932-6203}, mesh = {*Altitude ; Animals ; Colobinae/*physiology ; *Ecosystem ; Geographic Information Systems ; *Seasons ; *Sunlight ; }, abstract = {Environmental factors that affect spatiotemporal distribution patterns of animals usually include resource availability, temperature, and the risk of predation. However, they do not explain the counterintuitive preference of high elevation range in winter by the black-and-white snub-nosed monkey (Rhinopithecus bieti). We asked whether variation of sunshine along with elevations is the key driving force. To test this hypothesis, we conducted field surveys to demonstrate that there was a statistically significant pattern of high elevation use during winter. We then asked whether this pattern can be explained by certain environmental factors, namely temperature, sunshine duration and solar radiation. Finally, we concluded with a possible ecological mechanism for this pattern. In this study, we employed GIS technology to quantify solar radiation and sunshine duration across the monkey's range. Our results showed that: 1) R. bieti used the high altitude range between 4100-4400 m in winter although the yearly home range spanned from 3500-4500 m; 2) both solar radiation and sunshine duration increased with elevation while temperature decreased with elevation; 3) within the winter range, the use of range was significantly correlated with solar radiation and sunshine duration; 4) monkeys moved to the areas with high solar radiation and duration following a snowfall, where the snow melts faster and food is exposed earlier. We concluded that sunshine was the main factor that influences selection of high elevation habitat for R. bieti in winter. Since some other endotherms in the area exhibit similar winter distributional patterns, we developed a sunshine hypothesis to explain this phenomenon. In addition, our work also represented a new method of integrating GIS models into traditional field ecology research to study spatiotemporal distribution pattern of wildlife. We suggest that further theoretical and empirical studies are necessary for better understanding of sunshine influence on wildlife range use.}, } @article {pmid21914682, year = {2011}, author = {Busch-Armendariz, NB and Johnson, RJ and Buel, S and Lungwitz, J}, title = {Building community partnerships to end interpersonal violence: a collaboration of the schools of social work, law, and nursing.}, journal = {Violence against women}, volume = {17}, number = {9}, pages = {1194-1206}, doi = {10.1177/1077801211419330}, pmid = {21914682}, issn = {1552-8448}, mesh = {Battered Women/*education/legislation & jurisprudence ; Community Medicine ; Community Networks/*organization & administration ; Community-Institutional Relations ; Domestic Violence/legislation & jurisprudence/*prevention & control ; Female ; Humans ; Schools, Nursing/organization & administration ; Sex Offenses/prevention & control ; Social Work/organization & administration ; Texas ; Universities/*organization & administration ; }, abstract = {The article discusses the University of Texas at Austin's (UT Austin) Institute on Domestic Violence and Sexual Assault (IDVSA), an institution that was established in 2001. IDVSA is a collaboration of the Schools of Social Work, Law, and Nursing, and 150 community affiliates. Recognizing that interpersonal violence does not occur in a vacuum, the IDVSA operates within an ecological framework in which explanations for interpersonal violence acknowledge that individuals and families are nested in larger mezzo and macro systems, and factors such as gender, poverty, ethnicity, religion, disability, sexual orientation, and immigration status play influential roles in our understanding of these issues. The overarching goal is to advance knowledge and meaningful practice in the field through partnerships with survivors and community practitioners. Specifically, the mission is to advance the knowledge related to domestic violence and sexual assault in order to end interpersonal violence. IDVSA seeks to achieve its mission by focusing on three key areas: (1) rigorous research and scholarship on domestic violence and sexual assault; (2) comprehensive training, technical assistance, and information dissemination to the practitioner community and the community at large; and (3) substantial collaboration with our community partners. This article summarizes the authors' pursuit.}, } @article {pmid21912871, year = {2012}, author = {Peng, J and Liu, Y and Shen, H and Han, Y and Pan, Y}, title = {Vegetation coverage change and associated driving forces in mountain areas of Northwestern Yunnan, China using RS and GIS.}, journal = {Environmental monitoring and assessment}, volume = {184}, number = {8}, pages = {4787-4798}, pmid = {21912871}, issn = {1573-2959}, mesh = {China ; Conservation of Natural Resources ; Environment ; Environmental Monitoring/instrumentation/*methods ; *Geographic Information Systems ; *Plant Development ; Remote Sensing Technology ; *Spacecraft ; Urbanization ; }, abstract = {The dynamics of vegetation coverage and associated driving forces are one of the key issues in global environmental change. In the study, taking Lijiang County as a case, the Normalized Difference Vegetation Index was used to quantify vegetation coverage change in mountain areas of Northwestern Yunnan, China, with the application of remote sensing data and GIS technologies. And associated driving forces of vegetation coverage change were also analyzed, with a focus on land use change and elevation. The results showed that there was high vegetation coverage with a significant increase in the whole county during 1986-2002. However, due to economic development and the implementation of environmental protection polices, vegetation coverage change in the county showed distinct spatial diversity, which mainly behaved as the increasing in the northwest of the county with low human activities, and the decreasing in the south with high economic development. The results also showed that as a restrictive factor, elevation was of great signification on the spatial distribution of vegetation coverage in a broad scale; while in the county level, it was land use that determined the vegetation coverage, since the change of vegetation coverage grades in the study area was mainly associated with the change of land use types.}, } @article {pmid21909377, year = {2011}, author = {Hu, W and O'Leary, RA and Mengersen, K and Low Choy, S}, title = {Bayesian classification and regression trees for predicting incidence of cryptosporidiosis.}, journal = {PloS one}, volume = {6}, number = {8}, pages = {e23903}, pmid = {21909377}, issn = {1932-6203}, mesh = {Bayes Theorem ; Cryptosporidiosis/*epidemiology ; Databases as Topic ; Geography ; Humans ; Incidence ; Models, Biological ; Queensland/epidemiology ; Rain ; Regression Analysis ; Reproducibility of Results ; Temperature ; }, abstract = {BACKGROUND: Classification and regression tree (CART) models are tree-based exploratory data analysis methods which have been shown to be very useful in identifying and estimating complex hierarchical relationships in ecological and medical contexts. In this paper, a Bayesian CART model is described and applied to the problem of modelling the cryptosporidiosis infection in Queensland, Australia.

We compared the results of a Bayesian CART model with those obtained using a Bayesian spatial conditional autoregressive (CAR) model. Overall, the analyses indicated that the nature and magnitude of the effect estimates were similar for the two methods in this study, but the CART model more easily accommodated higher order interaction effects.

CONCLUSIONS/SIGNIFICANCE: A Bayesian CART model for identification and estimation of the spatial distribution of disease risk is useful in monitoring and assessment of infectious diseases prevention and control.}, } @article {pmid21906783, year = {2011}, author = {Gottardo, S and Semenzin, E and Giove, S and Zabeo, A and Critto, A and de Zwart, D and Ginebreda, A and Marcomini, A}, title = {Integrated risk assessment for WFD ecological status classification applied to Llobregat river basin (Spain). Part I-Fuzzy approach to aggregate biological indicators.}, journal = {The Science of the total environment}, volume = {409}, number = {22}, pages = {4701-4712}, doi = {10.1016/j.scitotenv.2011.07.052}, pmid = {21906783}, issn = {1879-1026}, mesh = {*Biota ; *Decision Support Techniques ; *Ecosystem ; Fuzzy Logic ; Geographic Information Systems ; Risk Assessment/*methods ; *Rivers ; *Software ; Spain ; Uncertainty ; Water Quality/*standards ; }, abstract = {Water Framework Directive (WFD) requirements and recommendations for Ecological Status (ES) classification of surface water bodies do not address all issues that Member States have to face in the implementation process, such as selection of appropriate stressor-specific environmental indicators, definition of class boundaries, aggregation of heterogeneous data and information and uncertainty evaluation. In this context the "One-Out, All-Out" (OOAO) principle is the suggested approach to lead the entire classification procedure and ensure conservative results. In order to support water managers in achieving a more comprehensive and realistic evaluation of ES, an Integrated Risk Assessment (IRA) methodology was developed. It is based on the Weight of Evidence approach and implements a Fuzzy Inference System in order to hierarchically aggregate a set of environmental indicators, which are grouped into five Lines of Evidence (i.e. Biology, Chemistry, Ecotoxicology, Physico-chemistry and Hydromorphology). The whole IRA methodology has been implemented as an individual module into a freeware GIS (Geographic Information System)-based Decision Support System (DSS), named MODELKEY DSS. The paper focuses on the conceptual and mathematical procedure underlying the evaluation of the most complex Line of Evidence, i.e. Biology, which identifies the biological communities that are potentially at risk and the stressors that are most likely responsible for the observed alterations. The results obtained from testing the procedure through application of the MODELKEY DSS to the Llobregat case study are reported and discussed.}, } @article {pmid21906780, year = {2011}, author = {Gottardo, S and Semenzin, E and Giove, S and Zabeo, A and Critto, A and de Zwart, D and Ginebreda, A and von der Ohe, PC and Marcomini, A}, title = {Integrated Risk Assessment for WFD Ecological Status classification applied to Llobregat river basin (Spain). Part II - Evaluation process applied to five environmental Lines of Evidence.}, journal = {The Science of the total environment}, volume = {409}, number = {22}, pages = {4681-4692}, doi = {10.1016/j.scitotenv.2011.07.050}, pmid = {21906780}, issn = {1879-1026}, mesh = {*Decision Support Techniques ; *Ecosystem ; Geographic Information Systems ; Risk Assessment/*methods/*statistics & numerical data ; *Rivers ; *Software ; Spain ; Water Quality/*standards ; }, abstract = {Many indicators and indices related to a variety of biological, physico-chemical, chemical, and hydromorphological water conditions have been recently developed or adapted by scientists in order to support water managers in the Water Framework Directive (WFD) implementation. In this context, the achievement of a comprehensive and reliable Ecological Status classification of water bodies across Europe is hampered by the lack of harmonised procedures for selecting an appropriate set of indicators and integrating heterogeneous information in a flexible way. To this purpose, an Integrated Risk Assessment (IRA)(2) methodology was developed based on the Weight of Evidence approach. This method analyses and combines a set of environmental indicators grouped into five Lines of Evidence (LoE), i.e. Biology, Chemistry, Ecotoxicology, Physico-chemistry and Hydromorphology. The whole IRA methodology has been implemented as a specific module into a freeware GIS (Geographic Information System)-based Decision Support System, named MODELKEY DSS. This paper focuses on the evaluation of the four supporting LoE (i.e. Chemistry, Ecotoxicology, Physico-chemistry and Hydromorphology), and includes a procedure for a comparison of each indicator with proper thresholds and a subsequent integration process to combine the obtained output with the LoE Biology results in order to provide a single score expressing the Ecological Status classification. The approach supports the identification of the most prominent stressors, which are responsible for the observed alterations in the river basin under investigation. The results provided by the preliminary testing of the IRA methodology through application of the MODELKEY DSS to the Llobregat case study are finally reported and discussed.}, } @article {pmid21905436, year = {2011}, author = {Auger-Méthé, M and St Clair, CC and Lewis, MA and Derocher, AE}, title = {Sampling rate and misidentification of Lévy and non-Lévy movement paths: comment.}, journal = {Ecology}, volume = {92}, number = {8}, pages = {1699-701; discussion 1701-2}, doi = {10.1890/10-1704.1}, pmid = {21905436}, issn = {0012-9658}, mesh = {Animals ; Behavior, Animal/*physiology ; Data Interpretation, Statistical ; Ecosystem ; *Models, Biological ; *Movement ; *Research Design ; Spatial Behavior/*physiology ; }, } @article {pmid21901361, year = {2011}, author = {Keenan, TF and Carbone, MS and Reichstein, M and Richardson, AD}, title = {The model-data fusion pitfall: assuming certainty in an uncertain world.}, journal = {Oecologia}, volume = {167}, number = {3}, pages = {587-597}, pmid = {21901361}, issn = {1432-1939}, mesh = {Bayes Theorem ; Carbon/*analysis/metabolism ; Carbon Cycle ; Data Interpretation, Statistical ; Ecology/*methods/trends ; Models, Biological ; *Models, Statistical ; Uncertainty ; }, abstract = {Model-data fusion is a powerful framework by which to combine models with various data streams (including observations at different spatial or temporal scales), and account for associated uncertainties. The approach can be used to constrain estimates of model states, rate constants, and driver sensitivities. The number of applications of model-data fusion in environmental biology and ecology has been rising steadily, offering insights into both model and data strengths and limitations. For reliable model-data fusion-based results, however, the approach taken must fully account for both model and data uncertainties in a statistically rigorous and transparent manner. Here we review and outline the cornerstones of a rigorous model-data fusion approach, highlighting the importance of properly accounting for uncertainty. We conclude by suggesting a code of best practices, which should serve to guide future efforts.}, } @article {pmid21901082, year = {2011}, author = {Rasmussen, DA and Ratmann, O and Koelle, K}, title = {Inference for nonlinear epidemiological models using genealogies and time series.}, journal = {PLoS computational biology}, volume = {7}, number = {8}, pages = {e1002136}, pmid = {21901082}, issn = {1553-7358}, mesh = {*Algorithms ; Bayes Theorem ; Computational Biology/methods ; *Disease Transmission, Infectious ; Epidemics ; *Epidemiologic Methods ; *Models, Biological ; Monte Carlo Method ; *Nonlinear Dynamics ; Phylogeny ; Population Dynamics ; Prevalence ; Stochastic Processes ; }, abstract = {Phylodynamics - the field aiming to quantitatively integrate the ecological and evolutionary dynamics of rapidly evolving populations like those of RNA viruses - increasingly relies upon coalescent approaches to infer past population dynamics from reconstructed genealogies. As sequence data have become more abundant, these approaches are beginning to be used on populations undergoing rapid and rather complex dynamics. In such cases, the simple demographic models that current phylodynamic methods employ can be limiting. First, these models are not ideal for yielding biological insight into the processes that drive the dynamics of the populations of interest. Second, these models differ in form from mechanistic and often stochastic population dynamic models that are currently widely used when fitting models to time series data. As such, their use does not allow for both genealogical data and time series data to be considered in tandem when conducting inference. Here, we present a flexible statistical framework for phylodynamic inference that goes beyond these current limitations. The framework we present employs a recently developed method known as particle MCMC to fit stochastic, nonlinear mechanistic models for complex population dynamics to gene genealogies and time series data in a Bayesian framework. We demonstrate our approach using a nonlinear Susceptible-Infected-Recovered (SIR) model for the transmission dynamics of an infectious disease and show through simulations that it provides accurate estimates of past disease dynamics and key epidemiological parameters from genealogies with or without accompanying time series data.}, } @article {pmid21900262, year = {2011}, author = {Arthur, RK and Ruvinsky, I}, title = {Evidence that purifying selection acts on promoter sequences.}, journal = {Genetics}, volume = {189}, number = {3}, pages = {1121-1126}, pmid = {21900262}, issn = {1943-2631}, support = {P50 GM081892/GM/NIGMS NIH HHS/United States ; T32 GM007197/GM/NIGMS NIH HHS/United States ; P50GM081892/GM/NIGMS NIH HHS/United States ; T32GM007197/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Bacteria/genetics ; *Computational Biology ; Conserved Sequence ; *Evolution, Molecular ; Mutation ; Nucleotides/genetics ; Promoter Regions, Genetic/*genetics ; *Selection, Genetic ; Yeasts/genetics ; }, abstract = {We tested whether functionally important sites in bacterial, yeast, and animal promoters are more conserved than their neighbors. We found that substitutions are predominantly seen in less important sites and that those that occurred tended to have less impact on gene expression than possible alternatives. These results suggest that purifying selection operates on promoter sequences.}, } @article {pmid21899426, year = {2011}, author = {Matroud, AA and Tuffley, CP and Hendy, MD}, title = {An algorithm to solve the motif alignment problem for approximate nested tandem repeats in biological sequences.}, journal = {Journal of computational biology : a journal of computational molecular cell biology}, volume = {18}, number = {9}, pages = {1211-1218}, doi = {10.1089/cmb.2011.0101}, pmid = {21899426}, issn = {1557-8666}, mesh = {*Algorithms ; Data Mining/methods ; Sequence Alignment/*methods ; Sequence Analysis, DNA/*methods ; *Tandem Repeat Sequences ; }, abstract = {An approximate nested tandem repeat (NTR) in a string T is a complex repetitive structure consisting of many approximate copies of two substrings x and X ("motifs") interspersed with one another. NTRs fall into a class of repetitive structures broadly known as subrepeats. NTRs have been found in real DNA sequences and are expected to be important in evolutionary biology, both in understanding evolution of the ribosomal DNA (where NTRs can occur), and as a potential marker in population genetic and phylogenetic studies. This article describes an alignment algorithm for the verification phase of the software tool NTRFinder developed for database searches for NTRs. When the search algorithm has located a subsequence containing a possible NTR, with motifs X and x, a verification step aligns this subsequence against an exact NTR built from the templates X and x, to determine whether the subsequence contains an approximate NTR and its extent. This article describes an algorithm to solve this alignment problem in O(|T|(|X| + |x|)) space and time. The algorithm is based on Fischetti et al.'s wrap-around dynamic programming.}, } @article {pmid21896335, year = {2011}, author = {Hausberger, B and Kimpel, D and van Neer, A and Korb, J}, title = {Uncovering cryptic species diversity of a termite community in a West African savanna.}, journal = {Molecular phylogenetics and evolution}, volume = {61}, number = {3}, pages = {964-969}, doi = {10.1016/j.ympev.2011.08.015}, pmid = {21896335}, issn = {1095-9513}, mesh = {Africa, Western ; Animals ; Base Sequence ; Bayes Theorem ; Cluster Analysis ; DNA, Ribosomal/genetics ; Databases, Nucleic Acid ; *Ecosystem ; Electron Transport Complex IV/genetics ; *Genetic Variation ; Isoptera/*genetics ; Likelihood Functions ; Phylogeny ; Species Specificity ; }, abstract = {To uncover the termite species diversity of a natural African savanna ecosystem, we combined morphological analyses and sequencing of three gene fragments (cytochrome oxidase I, cytochrome oxidase II and 28SrDNA, total length about 2450 bp) to infer putative species from phylogenetic trees. We identified 18 putative species clusters with high support values and which we retrieved consistently. Samples from two genera (Ancistrotermes and Microcerotermes) were excluded from the mitochondrial phylogenetic analyses as they might represent nuclear mitochondrial sequences (NUMTs). In total, our data suggest a species richness of at least 20 species, all but one belonging to the Termitidae (higher termites), and among them the fungus-growing Macrotermitinae were most prevalent with at least nine putative species. Within the fungus-growers the most species-rich genus was Microtermes and its four putative species were all cryptic species. Their abundance in the samples suggests that they play an important ecological role which is completely unstudied also due to the lack of reliable identification means. Our study shows that morphological traits are unreliable means of species identification for several termite taxa. Yet reliable and consistent identification is necessary for studying the functional role of termites in ecosystem and global processes.}, } @article {pmid21887854, year = {2011}, author = {Sheng, L and Huang, JF and Tang, XL}, title = {A tasseled cap transformation for CBERS-02B CCD data.}, journal = {Journal of Zhejiang University. Science. B}, volume = {12}, number = {9}, pages = {780-786}, pmid = {21887854}, issn = {1862-1783}, mesh = {Agriculture/methods ; Algorithms ; Computer Communication Networks ; Ecology/*methods ; Environmental Monitoring/*methods ; Geographic Information Systems ; Models, Statistical ; *Satellite Communications ; Trees ; }, abstract = {The tasseled cap transformation of remote sensing data has been widely used in agriculture, forest, ecology, and landscape. In this paper, tasseled cap transformation coefficients appropriate for data from a new sensor (China & Brazil Earth Resource Satellite (CBERS-02B)) are presented. The first three components after transformation captured 98% of the four-band variance, and represent the physical characteristics of brightness (coefficients: 0.509, 0.431, 0.330, and 0.668), greenness (coefficients: -0.494, -0.318, -0.324, and 0.741), and blueness (coefficients: 0.581, -0.070, -0.811, and 0.003), respectively. We hope these results will enhance the application of CBERS-02B charge-coupled device (CCD) data in the areas of agriculture, forest, ecology, and landscape.}, } @article {pmid21887231, year = {2011}, author = {Kou, X and Li, Q and Liu, S}, title = {Quantifying species' range shifts in relation to climate change: a case study of Abies spp. in China.}, journal = {PloS one}, volume = {6}, number = {8}, pages = {e23115}, pmid = {21887231}, issn = {1932-6203}, mesh = {Abies/*physiology ; *Biodiversity ; China ; *Climate Change ; Databases as Topic ; Models, Biological ; Models, Statistical ; Species Specificity ; }, abstract = {Predicting species range shifts in response to climatic change is a central aspect of global change studies. An ever growing number of species have been modeled using a variety of species distribution models (SDMs). However, quantitative studies of the characteristics of range shifts are rare, predictions of range changes are hard to interpret, analyze and summarize, and comparisons between the various models are difficult to make when the number of species modeled is large. Maxent was used to model the distribution of 12 Abies spp. in China under current and possible future climate conditions. Two fuzzy set defined indices, range increment index (I) and range overlapping index (O), were used to quantify range shifts of the chosen species. Correlation analyses were used to test the relationships between these indices and species distribution characteristics. Our results show that Abies spp. range increments (I) were highly correlated with longitude, latitude, and mean roughness of their current distributions. Species overlapping (O) was moderately, or not, correlated with these parameters. Neither range increments nor overlapping showed any correlation with species prevalence. These fuzzy sets defined indices provide ideal measures of species range shifts because they are stable and threshold-free. They are reliable indices that allow large numbers of species to be described, modeled, and compared on a variety of taxonomic levels.}, } @article {pmid21877229, year = {2012}, author = {Beaudouin, R and Ginot, V and Monod, G}, title = {Improving mesocosm data analysis through individual-based modelling of control population dynamics: a case study with mosquitofish (Gambusia holbrooki).}, journal = {Ecotoxicology (London, England)}, volume = {21}, number = {1}, pages = {155-164}, pmid = {21877229}, issn = {1573-3017}, mesh = {Animals ; *Cyprinodontiformes ; Databases, Factual ; Ecosystem ; Ecotoxicology/*methods ; Endpoint Determination ; Environmental Monitoring/*methods ; Female ; Male ; Models, Biological ; Population Dynamics ; Reproducibility of Results ; Water Pollutants, Chemical/analysis/*toxicity ; }, abstract = {Experimental ecosystems such as mesocosms have been developed to improve the ecological relevance of ecotoxicity test. However, in mesocosm studies, the number of replicates is limited by practical and financial constraints. In addition, high levels of biological organization are characterized by a high variability of descriptive variables. This variability and the poor number of replicates have been recognized as a major drawback for detecting significant effects of chemicals in mesocosm studies. In this context, a tool able to predict precisely control mesocosms outputs, to which endpoints in mesocosms exposed to chemicals could be compared should constitute a substantial improvement. We evaluated here a solution which consists in stochastic modelling of the control fish populations to assess the probabilistic distributions of population endpoints. An individual-based approach was selected, because it generates realistic fish length distributions and accounts for both individual and environmental sources of variability. This strategy was applied to mosquitofish (Gambusia holbrooki) populations monitored in lentic mesocosms. We chose the number of founders as a so-called "stressor" because subsequent consequences at the population level could be expected. Using this strategy, we were able to detect more significant and biologically relevant perturbations than using classical methods. We conclude that designing an individual-based model is very promising for improving mesocosm data analysis. This methodology is currently being applied to ecotoxicological issues.}, } @article {pmid21877006, year = {2011}, author = {Gonçalves, AC and Costa, Mda C and Braga, JU}, title = {[Spatial analysis of neonatal mortality and associated factors in Salvador, Bahia State, Brazil, 2000-2006].}, journal = {Cadernos de saude publica}, volume = {27}, number = {8}, pages = {1581-1592}, doi = {10.1590/s0102-311x2011000800013}, pmid = {21877006}, issn = {1678-4464}, mesh = {Brazil/epidemiology ; Cause of Death ; Cluster Analysis ; Geographic Information Systems ; Humans ; *Infant Mortality ; Infant, Newborn ; Linear Models ; Residence Characteristics ; Risk Assessment ; Risk Factors ; Socioeconomic Factors ; }, abstract = {An ecological study was performed to identify patterns in the spatial distribution of neonatal mortality and risk areas as well as associated factors in Salvador, Bahia State, Brazil, 2000-2006. A thematic map was constructed, and techniques were used for formal assessment of spatial dependence. No spatial and spatial regression models were used to assess possible relationships between selected factors and spatial distribution of neonatal mortality. Spatial autocorrelation was observed in neonatal mortality (I = 0.17; p = 0.0100), so its distribution was non-random. The analysis showed a spatial pattern in which the highest risk (> 9.0/1,000 live births) was concentrated in the downtown areas and peripheral neighborhoods with the highest concentration of low-income families, and this was associated with the target risk factors. The proportion of low birth weight newborns was the only variable that was significantly associated with neonatal mortality. Living conditions may have contributed to the uneven spatial distribution of neonatal mortality in this city.}, } @article {pmid21876665, year = {2011}, author = {Shrestha, S and King, AA and Rohani, P}, title = {Statistical inference for multi-pathogen systems.}, journal = {PLoS computational biology}, volume = {7}, number = {8}, pages = {e1002135}, pmid = {21876665}, issn = {1553-7358}, mesh = {Coinfection/microbiology/virology ; Communicable Diseases/*microbiology/virology ; Computational Biology ; Computer Simulation ; *Microbial Interactions ; *Models, Biological ; Stochastic Processes ; }, abstract = {There is growing interest in understanding the nature and consequences of interactions among infectious agents. Pathogen interactions can be operational at different scales, either within a co-infected host or in host populations where they co-circulate, and can be either cooperative or competitive. The detection of interactions among pathogens has typically involved the study of synchrony in the oscillations of the protagonists, but as we show here, phase association provides an unreliable dynamical fingerprint for this task. We assess the capacity of a likelihood-based inference framework to accurately detect and quantify the presence and nature of pathogen interactions on the basis of realistic amounts and kinds of simulated data. We show that when epidemiological and demographic processes are well understood, noisy time series data can contain sufficient information to allow correct inference of interactions in multi-pathogen systems. The inference power is dependent on the strength and time-course of the underlying mechanism: stronger and longer-lasting interactions are more easily and more precisely quantified. We examine the limitations of our approach to stochastic temporal variation, under-reporting, and over-aggregation of data. We propose that likelihood shows promise as a basis for detection and quantification of the effects of pathogen interactions and the determination of their (competitive or cooperative) nature on the basis of population-level time-series data.}, } @article {pmid21875054, year = {2011}, author = {Carriger, JF and Barron, MG}, title = {Minimizing risks from spilled oil to ecosystem services using influence diagrams: the Deepwater Horizon spill response.}, journal = {Environmental science & technology}, volume = {45}, number = {18}, pages = {7631-7639}, doi = {10.1021/es201037u}, pmid = {21875054}, issn = {1520-5851}, mesh = {Cost-Benefit Analysis ; Decision Making ; *Decision Support Techniques ; Disasters/economics ; *Ecosystem ; Environmental Restoration and Remediation/economics ; Gulf of Mexico ; *Petroleum Pollution/economics ; Risk ; Risk Assessment ; }, abstract = {Decision science tools can be used in evaluating response options and making inferences on risks to ecosystem services (ES) from ecological disasters. Influence diagrams (IDs) are probabilistic networks that explicitly represent the decisions related to a problem and their influence on desired or undesired outcomes. To examine how IDs might be useful in probabilistic risk management for spill response efforts, an ID was constructed to display the potential interactions between exposure events and the trade-offs between costs and ES impacts from spilled oil and response decisions in the DWH spill event. Quantitative knowledge was not formally incorporated but an ID platform for doing this was examined. Probabilities were assigned for conditional relationships in the ID and scenarios examining the impact of different response actions on components of spilled oil were investigated in hypothetical scenarios. Given the structure of the ID, potential knowledge gaps included understanding of the movement of oil, the ecological risk of different spill-related stressors to key receptors (e.g., endangered species, fisheries), and the need for stakeholder valuation of the ES benefits that could be impacted by a spill. Framing the Deepwater Horizon problem domain in an ID conceptualized important variables and relationships that could be optimally accounted for in preparing and managing responses in future spills. These features of the developed IDs may assist in better investigating the uncertainty, costs, and the trade-offs if large-scale, deep ocean spills were to occur again.}, } @article {pmid21874332, year = {2011}, author = {Zobitz, JM and Desai, AR and Moore, DJ and Chadwick, MA}, title = {A primer for data assimilation with ecological models using Markov Chain Monte Carlo (MCMC).}, journal = {Oecologia}, volume = {167}, number = {3}, pages = {599-611}, pmid = {21874332}, issn = {1432-1939}, mesh = {Animals ; Aquatic Organisms/growth & development/*physiology ; Data Interpretation, Statistical ; Ecology/*methods/trends ; Insecta/growth & development/*physiology ; Markov Chains ; Models, Biological ; Models, Statistical ; Monte Carlo Method ; Population Dynamics ; Trees/growth & development/*physiology ; }, abstract = {Data assimilation, or the fusion of a mathematical model with ecological data, is rapidly expanding knowledge of ecological systems across multiple spatial and temporal scales. As the amount of ecological data available to a broader audience increases, quantitative proficiency with data assimilation tools and techniques will be an essential skill for ecological analysis in this data-rich era. We provide a data assimilation primer for the novice user by (1) reviewing data assimilation terminology and methodology, (2) showcasing a variety of data assimilation studies across the ecological, environmental, and atmospheric sciences with the aim of gaining an understanding of potential applications of data assimilation, and (3) applying data assimilation in specific ecological examples to determine the components of net ecosystem carbon uptake in a forest and also the population dynamics of the mayfly (Hexagenia limbata, Serville). The review and examples are then used to provide guiding principles to newly proficient data assimilation practitioners.}, } @article {pmid21873643, year = {2011}, author = {Hardy, SM and Lindgren, M and Konakanchi, H and Huettmann, F}, title = {Predicting the distribution and ecological niche of unexploited snow crab (Chionoecetes opilio) populations in Alaskan waters: a first open-access ensemble model.}, journal = {Integrative and comparative biology}, volume = {51}, number = {4}, pages = {608-622}, doi = {10.1093/icb/icr102}, pmid = {21873643}, issn = {1557-7023}, mesh = {Alaska ; Animals ; Arctic Regions ; Biomass ; Brachyura/*physiology ; Environment ; Geographic Information Systems ; *Models, Biological ; Population Density ; Population Dynamics ; }, abstract = {Populations of the snow crab (Chionoecetes opilio) are widely distributed on high-latitude continental shelves of the North Pacific and North Atlantic, and represent a valuable resource in both the United States and Canada. In US waters, snow crabs are found throughout the Arctic and sub-Arctic seas surrounding Alaska, north of the Aleutian Islands, yet commercial harvest currently focuses on the more southerly population in the Bering Sea. Population dynamics are well-monitored in exploited areas, but few data exist for populations further north where climate trends in the Arctic appear to be affecting species' distributions and community structure on multiple trophic levels. Moreover, increased shipping traffic, as well as fisheries and petroleum resource development, may add additional pressures in northern portions of the range as seasonal ice cover continues to decline. In the face of these pressures, we examined the ecological niche and population distribution of snow crabs in Alaskan waters using a GIS-based spatial modeling approach. We present the first quantitative open-access model predictions of snow-crab distribution, abundance, and biomass in the Chukchi and Beaufort Seas. Multi-variate analysis of environmental drivers of species' distribution and community structure commonly rely on multiple linear regression methods. The spatial modeling approach employed here improves upon linear regression methods in allowing for exploration of nonlinear relationships and interactions between variables. Three machine-learning algorithms were used to evaluate relationships between snow-crab distribution and environmental parameters, including TreeNet, Random Forests, and MARS. An ensemble model was then generated by combining output from these three models to generate consensus predictions for presence-absence, abundance, and biomass of snow crabs. Each algorithm identified a suite of variables most important in predicting snow-crab distribution, including nutrient and chlorophyll-a concentrations in overlying waters, temperature, salinity, and annual sea-ice cover; this information may be used to develop and test hypotheses regarding the ecology of this species. This is the first such quantitative model for snow crabs, and all GIS-data layers compiled for this project are freely available from the authors, upon request, for public use and improvement.}, } @article {pmid21871967, year = {2011}, author = {Feldman, CR and Flores-Villela, O and Papenfuss, TJ}, title = {Phylogeny, biogeography, and display evolution in the tree and brush lizard genus Urosaurus (Squamata: Phrynosomatidae).}, journal = {Molecular phylogenetics and evolution}, volume = {61}, number = {3}, pages = {714-725}, doi = {10.1016/j.ympev.2011.08.008}, pmid = {21871967}, issn = {1095-9513}, mesh = {Animals ; Bayes Theorem ; DNA, Mitochondrial/genetics ; Databases, Genetic ; *Evolution, Molecular ; Lizards/*genetics ; Male ; Mexico ; Models, Genetic ; Molecular Sequence Data ; *Phylogeny ; *Phylogeography ; *Trees ; United States ; }, abstract = {The brush and tree lizards (Urosaurus) are a small clade of phrynosomatid lizards native to western North America. Though not as well known as their diverse sister clade, the spiny lizards (Sceloporus), some Urosaurus have nonetheless become model organisms in integrative biology. In particular, dramatic phenotypic and behavioral differences associated with specific mating strategies have been exploited to address a range of ecological and evolutionary questions. However, only two phylogenies have been proposed for the group, one of which is pre-cladistic and both based principally on morphological characters that might not provide robust support for relationships within the group. To help provide investigators working on Urosaurus with a robust phylogeny in which to frame ecological and evolutionary questions, we establish a molecular phylogeny for the group. We sampled three mitochondrial and three nuclear loci, and estimated phylogenetic relationships within Urosaurus using both maximum parsimony (MP) and Bayesian inference (BI), as well as a coalescent-based species tree approach. Finally, we used two methods of ancestral state reconstruction (ASR) to gain insight into the evolution of microhabitat preference and male display signals, traits that have been the focus of studies on Urosaurus. All reconstruction methods yield nearly the same ingroup topology that is concordant in most respects with the previous cladistic analysis of the group but with some significant differences; our data suggest the primary divergence in Urosaurus occurs between a clade endemic to the Pacific versant of Mexico and the lineages of Baja California and the southwestern US, rather than placing Urosaurus graciosus as the basal taxon and linking the Baja and Mexican endemics. We find support for a single transition to a saxicolous lifestyle within the group, and either the independent gain or loss of arboreality. The evolution of throat color patterns (i.e. dewlaps) appears complex, with multiple color morphs likely involving orange reconstructed as ancestral to the group and to most lineages, followed by a single transition to a fixed blue-throated morph in one clade. These results should provide a useful framework for additional comparative work with Urosaurus, and establish the phylogenetic context in which Urosaurus diversity arose.}, } @article {pmid21871665, year = {2011}, author = {Vaj, C and Barmaz, S and Sørensen, PB and Spurgeon, D and Vighi, M}, title = {Assessing, mapping and validating site-specific ecotoxicological risk for pesticide mixtures: a case study for small scale hot spots in aquatic and terrestrial environments.}, journal = {Ecotoxicology and environmental safety}, volume = {74}, number = {8}, pages = {2156-2166}, doi = {10.1016/j.ecoenv.2011.07.011}, pmid = {21871665}, issn = {1090-2414}, mesh = {Agriculture ; Ecology ; Ecosystem ; Ecotoxicology ; Environment ; *Environmental Monitoring ; Environmental Pollutants/*analysis/toxicity ; Geographic Information Systems ; Italy ; Pesticides/*analysis/toxicity ; Risk Assessment ; Rivers/chemistry ; Water Pollutants, Chemical/analysis/toxicity ; }, abstract = {Mixture toxicity is a real world problem and as such requires risk assessment solutions that can be applied within different geographic regions, across different spatial scales and in situations where the quantity of data available for the assessment varies. Moreover, the need for site specific procedures for assessing ecotoxicological risk for non-target species in non-target ecosystems also has to be recognised. The work presented in the paper addresses the real world effects of pesticide mixtures on natural communities. Initially, the location of risk hotspots is theoretically estimated through exposure modelling and the use of available toxicity data to predict potential community effects. The concept of Concentration Addition (CA) is applied to describe responses resulting from exposure of multiple pesticides The developed and refined exposure models are georeferenced (GIS-based) and include environmental and physico-chemical parameters, and site specific information on pesticide usage and land use. As a test of the risk assessment framework, the procedures have been applied on a suitable study areas, notably the River Meolo basin (Northern Italy), a catchment characterised by intensive agriculture, as well as comparative area for some assessments. Within the studied areas, the risks for individual chemicals and complex mixtures have been assessed on aquatic and terrestrial aboveground and belowground communities. Results from ecological surveys have been used to validate these risk assessment model predictions. Value and limitation of the approaches are described and the possibilities for larger scale applications in risk assessment are also discussed.}, } @article {pmid21868607, year = {2011}, author = {Bataillon, T and Zhang, T and Kassen, R}, title = {Cost of adaptation and fitness effects of beneficial mutations in Pseudomonas fluorescens.}, journal = {Genetics}, volume = {189}, number = {3}, pages = {939-949}, pmid = {21868607}, issn = {1943-2631}, mesh = {Adaptation, Physiological/*genetics ; Carbon/metabolism ; Computational Biology ; DNA, Bacterial/genetics ; Databases, Factual ; Gene-Environment Interaction ; Genetic Fitness/*genetics ; *Mutation ; Pseudomonas fluorescens/*genetics/growth & development/metabolism/*physiology ; }, abstract = {Adaptations are constructed through the sequential substitution of beneficial mutations by natural selection. However, the rarity of beneficial mutations has precluded efforts to describe even their most basic properties. Do beneficial mutations typically confer small or large fitness gains? Are their fitness effects environment specific, or are they broadly beneficial across a range of environments? To answer these questions, we used two subsets (n = 18 and n = 63) of a large library of mutants carrying antibiotic resistance mutations in the bacterium Pseudomonas fluorescens whose fitness, along with the antibiotic sensitive ancestor, was assayed across 95 novel environments differing in the carbon source available for growth. We explore patterns of genotype-by-environment (G × E) interactions and ecological specialization among the 18 mutants initially found superior to the sensitive ancestor in one environment. We find that G × E is remarkably similar between the two sets of mutants and that beneficial mutants are not typically associated with large costs of adaptation. Fitness effects among beneficial mutants depart from a strict exponential distribution: they assume a variety of shapes that are often roughly L shaped but always right truncated. Distributions of (beneficial) fitness effects predicted by a landscape model assuming multiple traits underlying fitness and a single optimum often provide a good description of the empirical distributions in our data. Simulations of data sets containing a mixture of single and double mutants under this landscape show that inferences about the distribution of fitness effects of beneficial mutants is quite robust to contamination by second-site mutations.}, } @article {pmid21865243, year = {2012}, author = {Shamoun-Baranes, J and van Loon, EE and Purves, RS and Speckmann, B and Weiskopf, D and Camphuysen, CJ}, title = {Analysis and visualization of animal movement.}, journal = {Biology letters}, volume = {8}, number = {1}, pages = {6-9}, pmid = {21865243}, issn = {1744-957X}, mesh = {Animals ; Charadriiformes/physiology ; Computer Graphics ; *Congresses as Topic ; Ecology/*methods/trends ; Geographic Information Systems ; *Interdisciplinary Communication ; Movement/*physiology ; Netherlands ; }, abstract = {The interdisciplinary workshop 'Analysis and Visualization of Moving Objects' was held at the Lorentz Centre in Leiden, The Netherlands, from 27 June to 1 July 2011. It brought together international specialists from ecology, computer science and geographical information science actively involved in the exploration, visualization and analysis of moving objects, such as marine reptiles, mammals, birds, storms, ships, cars and pedestrians. The aim was to share expertise, methodologies, data and common questions between different fields, and to work towards making significant advances in movement research. A data challenge based on GPS tracking of lesser black-backed gulls (Larus fuscus) was used to stimulate initial discussions, cross-fertilization between research groups and to serve as an initial focus for activities during the workshop.}, } @article {pmid21864693, year = {2011}, author = {Garcia, JA and Fernández-Guerra, A and Casamayor, EO}, title = {A close relationship between primary nucleotides sequence structure and the composition of functional genes in the genome of prokaryotes.}, journal = {Molecular phylogenetics and evolution}, volume = {61}, number = {3}, pages = {650-658}, doi = {10.1016/j.ympev.2011.08.011}, pmid = {21864693}, issn = {1095-9513}, mesh = {Base Sequence ; Computational Biology ; DNA, Archaeal/genetics ; DNA, Bacterial/genetics ; Genome, Archaeal/*genetics ; Genome, Bacterial/*genetics ; Multigene Family/genetics ; Nucleotides/*genetics ; *Phylogeny ; Prokaryotic Cells/*metabolism ; }, abstract = {Comparative genomics is an essential tool to unravel how genomes change over evolutionary time and to gain clues on the links between functional genomics and evolution. In prokaryotes, the large, good quality, genome sequences available in public databases and the recently developed large-scale computational methods, offer an unprecedent view on the ecology and evolution of microorganisms through comparative genomics. In this work, we examined the links among genome structure (i.e., the sequential distribution of nucleotides itself by detrended fluctuation analysis, DFA) and genomic diversity (i.e., gene functionality by Clusters of Orthologous Genes, COGs) in 828 full sequenced prokaryotic genomes from 548 different bacteria and archaea species. DFA scaling exponent α indicated persistent long-range correlations (fractality) in each genome analyzed. Higher resolution power was found when considering the sequential succession of purine (AG) vs. pyrimidine (CT) bases than either keto (GT) to amino (AC) forms or strongly (GC) vs. weakly (AT) bonded nucleotides. Interestingly, the phyla Aquificae, Fusobacteria, Dictyoglomi, Nitrospirae, and Thermotogae were closer to archaea than to their bacterial counterparts. A strong significant correlation was found between scaling exponent α and COGs distribution, and we consistently observed that the larger α the more heterogeneous was the gene distribution within each functional category, suggesting a close relationship between primary nucleotides sequence structure and functional genes composition.}, } @article {pmid21864032, year = {2011}, author = {Al-Meeri, A and Non, AL and Lajoie, TW and Mulligan, CJ}, title = {Effect of different sampling strategies for a single geographic region in Yemen on standard genetic analyses of mitochondrial DNA sequence data.}, journal = {Mitochondrial DNA}, volume = {22}, number = {3}, pages = {66-70}, doi = {10.3109/19401736.2011.606462}, pmid = {21864032}, issn = {1940-1744}, mesh = {Base Sequence ; DNA, Mitochondrial/analysis/*genetics ; Data Interpretation, Statistical ; Family ; Genetics, Population/*methods/standards/statistics & numerical data ; Geography ; Haplotypes ; Humans ; Phylogeny ; Rural Population/statistics & numerical data ; Sample Size ; Sampling Studies ; Sequence Analysis, DNA/standards/*statistics & numerical data ; Urban Population/statistics & numerical data ; Yemen/epidemiology ; }, abstract = {Collection of biological samples is the foundation of genetic studies ranging from estimation of genetic diversity to reconstruction of population history. Sample collections are intended to accurately represent the genetic, biological, ecological, cultural, geographic, and/or linguistic diversity of a particular region or population by providing a small, but representative, set of samples. In this study, we analyze human mitochondrial DNA variation in samples collected using four different sampling strategies to represent the same geographic region. Specifically, samples were collected from a village, a rural area, a regional clinic, and a national university in the governorate of Dhamar in Yemen. All samples were assayed for mitochondrial hypervariable region I DNA sequence variation and data were subjected to standard molecular genetic analyses. Our results suggest that analyses in which individual DNA sequences are explicitly compared or evaluated, e.g. phylogenetic and network analyses, may be more sensitive to sample collection design than analyses in which data are averaged across individuals or are analyzed more indirectly, e.g. summary statistics.}, } @article {pmid21863372, year = {2011}, author = {Zhang, M and Zhang, C and Wang, K and Yue, Y and Qi, X and Fan, F}, title = {Spatiotemporal variation of karst ecosystem service values and its correlation with environmental factors in northwest Guangxi, China.}, journal = {Environmental management}, volume = {48}, number = {5}, pages = {933-944}, pmid = {21863372}, issn = {1432-1009}, mesh = {China ; Conservation of Natural Resources/*methods ; *Ecosystem ; *Environment Design ; Environmental Monitoring/*methods ; Geographic Information Systems ; Plants, Edible/growth & development/physiology ; Rain ; Soil/chemistry ; Trees/growth & development/physiology ; Water Supply ; }, abstract = {In this investigation we analyzed the spatiotemporal variation of ecosystem service values (ESVs) and its correlation with numerous environmental factors (EFs) for the karst region of Northwest Guangxi, China, from 1985 to 2005 using remote sensing, geographic information systems (GIS) and statistical techniques. The results indicate that historically ESVs for this karst region decreased from 1985 (109.652 billion yuan) to 1990 (88.789 billion yuan) and then increased at the turn of the twenty-first century. However, the ESVs in both 2000 (103.384 billion yuan) and 2005 (106.257 billion yuan) never achieved the level recorded in 1985. The total of nutrient cycling, organic production and gas regulation combined were 72.69, 64.57, 70.18 and 72.10% of ESVs in 1985, 1990, 2000 and 2005, respectively. In contrast, the ESVs of water conservation, soil reservation, recreation and culture were determined to be relatively low contributing only 17.44, 23.82, 19.26 and 24.76% of total ESVs, respectively, during these four years. With regards to the spatial distribution of ESVs, larger values were recorded in the west and smaller ones recorded in the east. The most significant factors that were deemed to influence ESVs are annual rainfall, per capita cropland, slope and vegetation coverage. Annual rainfall and slope exert a negative force, whereas per capita cropland and vegetation coverage exert a positive force on ESVs. The results of the study would suggest that ecosystem conditions of this important karst region have been improved as the result of the implementation of rocky desertification control policies.}, } @article {pmid21854517, year = {2012}, author = {Luo, H and Löytynoja, A and Moran, MA}, title = {Genome content of uncultivated marine Roseobacters in the surface ocean.}, journal = {Environmental microbiology}, volume = {14}, number = {1}, pages = {41-51}, doi = {10.1111/j.1462-2920.2011.02528.x}, pmid = {21854517}, issn = {1462-2920}, support = {GR078968//Wellcome Trust/United Kingdom ; }, mesh = {Computational Biology ; DNA, Bacterial/genetics ; *Genome, Bacterial ; *Metagenome ; Metagenomics ; Multigene Family ; Oceans and Seas ; Phylogeny ; Roseobacter/classification/*genetics/metabolism ; Seawater/*microbiology ; Sequence Analysis, DNA ; }, abstract = {Understanding of the ecological roles and evolutionary histories of marine bacterial taxa can be complicated by mismatches in genome content between wild populations and their better-studied cultured relatives. We used computed patterns of non-synonymous (amino acid-altering) nucleotide diversity in marine metagenomic data to provide high-confidence identification of DNA fragments from uncultivated members of the Roseobacter clade, an abundant taxon of heterotrophic marine bacterioplankton in the world's oceans. Differences in gene stoichiometry in the Global Ocean Survey metagenomic data set compared with 39 sequenced isolates indicated that natural Roseobacter populations differ systematically in several genomic attributes from their cultured representatives, including fewer genes for signal transduction and cell surface modifications but more genes for Sec-like protein secretion systems, anaplerotic CO(2) incorporation, and phosphorus and sulfate uptake. Several of these trends match well with characteristics previously identified as distinguishing r- versus K-selected ecological strategies in bacteria, suggesting that the r-strategist model assigned to cultured roseobacters may be less applicable to their free-living oceanic counterparts. The metagenomic Roseobacter DNA fragments revealed several traits with evolutionary histories suggestive of horizontal gene transfer from other marine bacterioplankton taxa or viruses, including pyrophosphatases and glycosylation proteins.}, } @article {pmid21849714, year = {2011}, author = {Pajić, V}, title = {Putting encyclopaedia knowledge into structural form: finite state transducers approach.}, journal = {Journal of integrative bioinformatics}, volume = {8}, number = {2}, pages = {164}, doi = {10.2390/biecoll-jib-2011-164}, pmid = {21849714}, issn = {1613-4516}, mesh = {Bacteria/classification ; Computational Biology/*methods ; Databases, Factual ; *Encyclopedias as Topic ; Information Storage and Retrieval ; *Knowledge ; Software ; }, abstract = {In biology and functional genomics in particular, understanding the dependence and interplay between different genome and ecological characteristics of organisms is a very challenging problem. There are some public databases which combine this kind of information, but there is still much more information about microbes and other organisms that reside in unstructured and semi-structured documents, such as encyclopaedias. In this paper we present a method for extracting information from semi-structured resources, such as encyclopaedias, based on finite state transducers, consisting of two clearly distinguished phases. The first phase strongly relies on the analysis of the document structure and it is used for locating records of data in the text. The second phase is based on the finite state transducers created for extracting the data, which can be modified so as to achieve the preferred efficiency and it is used for extracting the particular characteristic from the text. We show how the two phase method is applied to the text of the encyclopaedia "Systematic Bacteriology". A fully structured database with genotype and phenotype characteristics of organisms has been created from the encyclopaedia unstructured descriptions.}, } @article {pmid21848985, year = {2011}, author = {Gonzalez-Voyer, A and Kolm, N}, title = {Rates of phenotypic evolution of ecological characters and sexual traits during the Tanganyikan cichlid adaptive radiation.}, journal = {Journal of evolutionary biology}, volume = {24}, number = {11}, pages = {2378-2388}, doi = {10.1111/j.1420-9101.2011.02365.x}, pmid = {21848985}, issn = {1420-9101}, mesh = {Adaptation, Biological/*physiology ; Animals ; *Biological Evolution ; Cichlids/*anatomy & histology/genetics ; Cluster Analysis ; Computational Biology ; *Genetic Speciation ; Models, Genetic ; *Phenotype ; Phylogeny ; Selection, Genetic ; *Sex Characteristics ; Tanzania ; Time Factors ; }, abstract = {Theory suggests that sexual traits evolve faster than ecological characters. However, characteristics of a species niche may also influence evolution of sexual traits. Hence, a pending question is whether ecological characters and sexual traits present similar tempo and mode of evolution during periods of rapid ecological divergence, such as adaptive radiation. Here, we use recently developed phylogenetic comparative methods to analyse the temporal dynamics of evolution for ecological and sexual traits in Tanganyikan cichlids. Our results indicate that whereas disparity in ecological characters was concentrated early in the radiation, disparity in sexual traits remained high throughout the radiation. Thus, closely related Tanganyikan cichlids presented higher disparity in sexual traits than ecological characters. Sexual traits were also under stronger selection than ecological characters. In sum, our results suggest that ecological characters and sexual traits present distinct evolutionary patterns, and that sexual traits can evolve faster than ecological characters, even during adaptive radiation.}, } @article {pmid21844350, year = {2011}, author = {Tsoar, A and Nathan, R and Bartan, Y and Vyssotski, A and Dell'Omo, G and Ulanovsky, N}, title = {Large-scale navigational map in a mammal.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {108}, number = {37}, pages = {E718-24}, pmid = {21844350}, issn = {1091-6490}, mesh = {Animals ; Chiroptera/*physiology ; Egypt ; Female ; Geographic Information Systems ; Homing Behavior/*physiology ; Male ; Vision, Ocular/physiology ; }, abstract = {Navigation, the ability to reach desired goal locations, is critical for animals and humans. Animal navigation has been studied extensively in birds, insects, and some marine vertebrates and invertebrates, yet we are still far from elucidating the underlying mechanisms in other taxonomic groups, especially mammals. Here we report a systematic study of the mechanisms of long-range mammalian navigation. High-resolution global positioning system tracking of bats was conducted here, which revealed high, fast, and very straight commuting flights of Egyptian fruit bats (Rousettus aegyptiacus) from their cave to remote fruit trees. Bats returned to the same individual trees night after night. When displaced 44 km south, bats homed directly to one of two goal locations--familiar fruit tree or cave--ruling out beaconing, route-following, or path-integration mechanisms. Bats released 84 km south, within a deep natural crater, were initially disoriented (but eventually left the crater toward the home direction and homed successfully), whereas bats released at the crater-edge top homed directly, suggesting navigation guided primarily by distal visual landmarks. Taken together, these results provide evidence for a large-scale "cognitive map" that enables navigation of a mammal within its visually familiar area, and they also demonstrate the ability to home back when translocated outside the visually familiar area.}, } @article {pmid21842709, year = {2011}, author = {Tarocco, S and Amoruso, I and Caravello, G}, title = {Holistic model-based monitoring of the human health status in an urban environment system: pilot study in Verona city, Italy.}, journal = {Journal of preventive medicine and hygiene}, volume = {52}, number = {2}, pages = {73-82}, pmid = {21842709}, issn = {1121-2233}, mesh = {Attitude to Health ; Data Interpretation, Statistical ; Environment Design ; *Health Status ; *Holistic Health ; Humans ; Italy/epidemiology ; Models, Statistical ; Pilot Projects ; *Population Dynamics ; Residence Characteristics ; *Urban Health ; Urban Population/*statistics & numerical data ; }, abstract = {INTRODUCTION: In recent decades the global health paradigm gained an increasing systemic characterization. The ecosystem health theory states that a healthy ecosystem, whether natural or artificial, significantly contributes to the good health status of the human population.

METHODS: The present study describes an interdisciplinary monitoring model that retrospectively analyzes the intersection between the urban environment and citizens. The model analyzes both the biophysical and the anthropic subsystems through the application of landscape ecology and environmental quality indexes along with human health indicators. Particularly, ecological quality of landscape pattern, atmospheric pollution, outdoor noise levels and local health indicators were assessed. Verona municipality was chosen as study area to test the preliminary efficiency of the model. Territory was split into two superimposed layers of land units, which were further geo-referentiated with Geographical Information System (GIS) technology. Interdependence of any of the analyzed traits was further investigated with Fisher exact test.

RESULTS: Landscape composition was assessed and an Average Ecological Quality (AEQ) score assigned to each land unit. A direct proportionality emerged for concentrations of considered air pollutants and traffic levels: a spatial model for the atmospheric pollution was drawn. A map depicting the distribution of traffic-related noise levels was also drawn. From chosen indicators, a quality class score was assigned to every minor and major land unit. Age-standardised rates about hospitalizations for the municipal population and specific rates for the over-65s/1000 inhabitants were calculated. Quality class assignement for each health indicator was graphically rendered. After direct standardisation of rates for the population sample, data were compared with two reference populations, the Regional population and the Local Socio-sanitary Unit (ULSS20) population. Standardised hospitalization rates for the whole municipal population always resulted lower than the ULSS20 rates, except for auditory pathologies. It was notable that rates of hospitalizations for cancerous diseases for Verona municipal population were four times and two times lower than the ULSS20 and the Regional population ones, respectively. Contingency table were made for the health main indicator (specific rates for the over-65s/1000 inhabitants) and the environmental quality key factors of landscape ecological quality, outdoor noise level and air pollution. H0 of independence was rejected for respiratory pathologies and air pollution and for the triad cardiocirculatory pathologies, air pollution and landscape ecological quality at (a = 0.05). Fisher exact test confirmed the non-independence of cardiocirculatory diseases and biophysical environment and the analogous association for respiratory pathologies when comparison was made with global environmental quality index.

DISCUSSION: The first testing of the model suggests some possible elements of implementation and integration which could further enhance it. Among them, the subjective investigation of the health status assumes a primary role. On the whole the monitoring model seems to effectively represent the real complexity of the urban environment systems and should be regarded as an important contribution to the new way of health research.}, } @article {pmid21831429, year = {2011}, author = {Vindevogel, S and Coppens, K and Derluyn, I and De Schryver, M and Loots, G and Broekaert, E}, title = {Forced conscription of children during armed conflict: experiences of former child soldiers in northern Uganda.}, journal = {Child abuse & neglect}, volume = {35}, number = {7}, pages = {551-562}, doi = {10.1016/j.chiabu.2011.03.011}, pmid = {21831429}, issn = {1873-7757}, mesh = {Adolescent ; Child Abuse ; *Coercion ; Databases, Factual ; Female ; Humans ; Male ; Military Personnel/*psychology ; Uganda ; *Warfare ; }, abstract = {OBJECTIVE: Child soldiering can be considered as one of the worst practices of institutionalized child abuse. However, little is known about the scope and nature of this abuse and the consequent experiences of children enrolled in an armed faction. This research aims at enriching the knowledge on the experiences of child soldiers in the Lord's Resistance Army (LRA) in northern Uganda.

METHODS: The databases of 4 former Interim Care Centres for returned child soldiers in northern Uganda, comprising socio-demographic information of 8,790 returnees, and additional data from the Rachele Rehabilitation Centre on war-related experiences of 1,995 former child soldiers, are analyzed using descriptive statistics, analysis of covariance and regression analysis.

RESULTS: During on average 1.5 years in captivity, nearly all participants had various war-related experiences, whereby 88% witnessed and 76% forcibly participated in atrocities. Variations in exposure to warfare appear to be mainly associated with age of abduction, duration of captivity, location of captivity, being military trained, and being a rebel's wife.

CONCLUSIONS: These findings testify to the vastness of abuse lived through by the child soldiers in this study. They fulfilled a multifaceted position in the LRA, which delivers a range of potential direct and indirect consequences. The variables decisive in differential experiences unveil trends in the strategic abduction by the LRA and in differential exposure to warfare among child soldiers.

IMPLICATIONS: The variation in exposure to warfare urges for an individualized approach and monitoring of returning child soldiers. In order to address the potential indirect impact of child soldiering, support also needs to be oriented towards the child's network, based on a socio-ecological approach.}, } @article {pmid21830701, year = {2011}, author = {Wolf, A and Field, CB and Berry, JA}, title = {Allometric growth and allocation in forests: a perspective from FLUXNET.}, journal = {Ecological applications : a publication of the Ecological Society of America}, volume = {21}, number = {5}, pages = {1546-1556}, doi = {10.1890/10-1201.1}, pmid = {21830701}, issn = {1051-0761}, mesh = {Databases, Factual ; *Ecosystem ; *Models, Biological ; Photosynthesis/physiology ; Plant Roots/growth & development ; Trees/*growth & development/*physiology ; }, abstract = {To develop a scheme for partitioning the products of photosynthesis toward different biomass components in land-surface models, a database on component mass and net primary productivity (NPP), collected from FLUXNET sites, was examined to determine allometric patterns of allocation. We found that NPP per individual of foliage (Gfol), stem and branches (Gstem), coarse roots (Gcroot) and fine roots (Gfroot) in individual trees is largely explained (r2 = 67-91%) by the magnitude of total NPP per individual (G). Gfol scales with G isometrically, meaning it is a fixed fraction of G (25%). Root-shoot trade-offs were manifest as a slow decline in Gfroot, as a fraction of G, from 50% to 25% as stands increased in biomass, with Gstem and Gcroot increasing as a consequence. These results indicate that a functional trade-off between aboveground and belowground allocation is essentially captured by variations in G, which itself is largely governed by stand biomass and only secondarily by site-specific resource availability. We argue that forests are characterized by strong competition for light, observed as a race for individual trees to ascend by increasing partitioning toward wood, rather than by growing more leaves, and that this competition stronglyconstrains the allocational plasticity that trees may be capable of. The residual variation in partitioning was not related to climatic or edaphic factors, nor did plots with nutrient or water additions show a pattern of partitioning distinct from that predicted by G alone. These findings leverage short-term process studies of the terrestrial carbon cycle to improve decade-scale predictions of biomass accumulation in forests. An algorithm for calculating partitioning in land-surface models is presented.}, } @article {pmid21830700, year = {2011}, author = {Hobbs, NT and Ogle, K}, title = {Introducing data-model assimilation to students of ecology.}, journal = {Ecological applications : a publication of the Ecological Society of America}, volume = {21}, number = {5}, pages = {1537-1545}, doi = {10.1890/09-1576.1}, pmid = {21830700}, issn = {1051-0761}, mesh = {Computer Simulation ; Curriculum ; *Data Interpretation, Statistical ; Ecology/*education/*methods/trends ; Forecasting/*methods ; Models, Statistical ; Models, Theoretical ; Students ; }, abstract = {Quantitative training for students of ecology has traditionally emphasized two sets of topics: mathematical modeling and statistical analysis. Until recently, these topics were taught separately, modeling courses emphasizing mathematical techniques for symbolic analysis and statistics courses emphasizing procedures for analyzing data. We advocate the merger of these traditions in ecological education by outlining a curriculum for an introductory course in data-model assimilation. This course replaces the procedural emphasis of traditional introductory material in statistics with an emphasis on principles needed to develop hierarchical models of ecological systems, fusing models of data with models of ecological processes. We sketch nine elements of such a course: (1) models as routes to insight, (2) uncertainty, (3) basic probability theory, (4) hierarchical models, (5) data simulation, (6) likelihood and Bayes, (7) computational methods, (8) research design, and (9) problem solving. The outcome of teaching these combined elements can be the fundamental understanding and quantitative confidence needed by students to create revealing analyses for a broad array of research problems.}, } @article {pmid21830699, year = {2011}, author = {Clark, JS and Agarwal, P and Bell, DM and Flikkema, PG and Gelfand, A and Nguyen, X and Ward, E and Yang, J}, title = {Inferential ecosystem models, from network data to prediction.}, journal = {Ecological applications : a publication of the Ecological Society of America}, volume = {21}, number = {5}, pages = {1523-1536}, doi = {10.1890/09-1212.1}, pmid = {21830699}, issn = {1051-0761}, mesh = {Bayes Theorem ; Data Interpretation, Statistical ; Ecology/*methods ; *Ecosystem ; Forecasting/*methods ; *Models, Biological ; Models, Statistical ; Plant Transpiration ; Plants/metabolism ; Time Factors ; }, abstract = {Recent developments suggest that predictive modeling could begin to play a larger role not only for data analysis, but also for data collection. We address the example of efficient wireless sensor networks, where inferential ecosystem models can be used to weigh the value of an observation against the cost of data collection. Transmission costs make observations "expensive"; networks will typically be deployed in remote locations without access to infrastructure (e.g., power). The capacity to sample intensively makes sensor networks valuable, but high-frequency data are informative only at specific times and locations. Sampling intervals will range from meters and seconds to landscapes and years, depending on the process, the current states of the system, the uncertainty about those states, and the perceived potential for rapid change. Given that intensive sampling is sometimes critical, but more often wasteful, how do we develop tools to control the measurement and transmission processes? We address the potential of data collection controlled and/or supplemented by inferential ecosystem models. In a given model, the value of an observation can be evaluated in terms of its contribution to estimates of state variables and important parameters. There will be more than one model applied to network data that will include as state variables water, carbon, energy balance, biogeochemistry, tree ecophysiology, and forest demographic processes. The value of an observation will depend on the application. Inference is needed to weigh the contributions against transmission cost. Network control must be dynamic and driven by models capable of learning about both the environment and the network. We discuss application of Bayesian inference to model data from a developing sensor network as a basis for controlling the measurement and transmission processes. Our examples involve soil moisture and sap flux, but we discuss broader application of the approach, including its implications for network design.}, } @article {pmid21830698, year = {2011}, author = {Spadavecchia, L and Williams, M and Law, BE}, title = {Uncertainty in predictions of forest carbon dynamics: separating driver error from model error.}, journal = {Ecological applications : a publication of the Ecological Society of America}, volume = {21}, number = {5}, pages = {1506-1522}, doi = {10.1890/09-1183.1}, pmid = {21830698}, issn = {1051-0761}, mesh = {Carbon/*metabolism ; Computer Simulation ; Data Interpretation, Statistical ; *Ecosystem ; *Models, Biological ; Pinus/metabolism ; Rain ; Soil ; Trees/*metabolism ; *Uncertainty ; Water ; }, abstract = {We present an analysis of the relative magnitude and contribution of parameter and driver uncertainty to the confidence intervals on estimates of net carbon fluxes. Model parameters may be difficult or impractical to measure, while driver fields are rarely complete, with data gaps due to sensor failure and sparse observational networks. Parameters are generally derived through some optimization method, while driver fields may be interpolated from available data sources. For this study, we used data from a young ponderosa pine stand at Metolius, Central Oregon, and a simple daily model of coupled carbon and water fluxes (DALEC). An ensemble of acceptable parameterizations was generated using an ensemble Kalman filter and eddy covariance measurements of net C exchange. Geostatistical simulations generated an ensemble of meteorological driving variables for the site, consistent with the spatiotemporal autocorrelations inherent in the observational data from 13 local weather stations. Simulated meteorological data were propagated through the model to derive the uncertainty on the CO2 flux resultant from driver uncertainty typical of spatially extensive modeling studies. Furthermore, the model uncertainty was partitioned between temperature and precipitation. With at least one meteorological station within 25 km of the study site, driver uncertainty was relatively small (10% of the total net flux), while parameterization uncertainty was larger, 50% of the total net flux. The largest source of driver uncertainty was due to temperature (8% of the total flux). The combined effect of parameter and driver uncertainty was 57% of the total net flux. However, when the nearest meteorological station was > 100 km from the study site, uncertainty in net ecosystem exchange (NEE) predictions introduced by meteorological drivers increased by 88%. Precipitation estimates were a larger source of bias in NEE estimates than were temperature estimates, although the biases partly compensated for each other. The time scales on which precipitation errors occurred in the simulations were shorter than the temporal scales over which drought developed in the model, so drought events were reasonably simulated. The approach outlined here provides a means to assess the uncertainty and bias introduced by meteorological drivers in regional-scale ecological forecasting.}, } @article {pmid21830697, year = {2011}, author = {Weng, E and Luo, Y}, title = {Relative information contributions of model vs. data to short- and long-term forecasts of forest carbon dynamics.}, journal = {Ecological applications : a publication of the Ecological Society of America}, volume = {21}, number = {5}, pages = {1490-1505}, doi = {10.1890/09-1394.1}, pmid = {21830697}, issn = {1051-0761}, mesh = {Carbon/*metabolism ; Data Interpretation, Statistical ; *Ecosystem ; Forecasting/*methods ; *Models, Biological ; Time Factors ; Trees/*metabolism ; }, abstract = {Biogeochemical models have been used to evaluate long-term ecosystem responses to global change on decadal and century time scales. Recently, data assimilation has been applied to improve these models for ecological forecasting. It is not clear what the relative information contributions of model (structure and parameters) vs. data are to constraints of short- and long-term forecasting. In this study, we assimilated eight sets of 10-year data (foliage, woody, and fine root biomass, litter fall, forest floor carbon [C], microbial C, soil C, and soil respiration) collected from Duke Forest into a Terrestrial Ecosystem model (TECO). The relative information contribution was measured by Shannon information index calculated from probability density functions (PDFs) of carbon pool sizes. The null knowledge without a model or data was defined by the uniform PDF within a prior range. The relative model contribution was information content in the PDF of modeled carbon pools minus that in the uniform PDF, while the relative data contribution was the information content in the PDF of modeled carbon pools after data was assimilated minus that before data assimilation. Our results showed that the information contribution of the model to constrain carbon dynamics increased with time whereas the data contribution declined. The eight data sets contributed more than the model to constrain C dynamics in foliage and fine root pools over the 100-year forecasts. The model, however, contributed more than the data sets to constrain the litter, fast soil organic matter (SOM), and passive SOM pools. For the two major C pools, woody biomass and slow SOM, the model contributed less information in the first few decades and then more in the following decades than the data. Knowledge of relative information contributions of model vs. data is useful for model development, uncertainty analysis, future data collection, and evaluation of ecological forecasting.}, } @article {pmid21830695, year = {2011}, author = {Gao, C and Wang, H and Weng, E and Lakshmivarahan, S and Zhang, Y and Luo, Y}, title = {Assimilation of multiple data sets with the ensemble Kalman filter to improve forecasts of forest carbon dynamics.}, journal = {Ecological applications : a publication of the Ecological Society of America}, volume = {21}, number = {5}, pages = {1461-1473}, doi = {10.1890/09-1234.1}, pmid = {21830695}, issn = {1051-0761}, mesh = {Carbon/*metabolism ; *Computer Simulation ; Data Interpretation, Statistical ; Ecology/methods ; Forecasting/*methods ; *Models, Biological ; Time Factors ; Trees/*physiology ; }, abstract = {The ensemble Kalman filter (EnKF) has been used in weather forecasting to assimilate observations into weather models. In this study, we examine how effectively forecasts of a forest carbon cycle can be improved by assimilating observations with the EnKF. We used the EnKF to assimilate into the terrestrial ecosystem (TECO) model eight data sets collected at the Duke Forest between 1996 and 2004 (foliage biomass, fine root biomass, woody biomass, litterfall, microbial biomass, forest floor carbon, soil carbon, and soil respiration). We then used the trained model to forecast changes in carbon pools from 2004 to 2012. Our daily analysis of parameters indicated that all the exit rates were well constrained by the EnKF, with the exception of the exit rates controlling the loss of metabolic litter and passive soil organic matter. The poor constraint of these two parameters resulted from the low sensitivity of TECO predictions to their values and the poor correlation between these parameters and the observed variables. Using the estimated parameters, the model predictions and observations were in agreement. Model forecasts indicate 15 380-15 660 g C/ m2 stored in Duke Forest by 2012 (a 27% increase since 2004). Parameter uncertainties decreased as data were sequentially assimilated into the model using the EnKF. Uncertainties in forecast carbon sinks increased over time for the long-term carbon pools (woody biomass, structure litter, slow and passive SOM) but remained constant over time for the short-term carbon pools (foliage, fine root, metabolic litter, and microbial carbon). Overall, EnKF can effectively assimilate multiple data sets into an ecosystem model to constrain parameters, forecast dynamics of state variables, and evaluate uncertainty.}, } @article {pmid21829563, year = {2011}, author = {Siebert, S and Robinson, MD and Tintori, SC and Goetz, F and Helm, RR and Smith, SA and Shaner, N and Haddock, SH and Dunn, CW}, title = {Differential gene expression in the siphonophore Nanomia bijuga (Cnidaria) assessed with multiple next-generation sequencing workflows.}, journal = {PloS one}, volume = {6}, number = {7}, pages = {e22953}, pmid = {21829563}, issn = {1932-6203}, mesh = {Animals ; Cnidaria/*genetics/metabolism ; Databases, Genetic ; *Gene Expression Profiling ; *High-Throughput Nucleotide Sequencing ; In Situ Hybridization ; Oligonucleotide Array Sequence Analysis ; RNA, Messenger/genetics ; Reverse Transcriptase Polymerase Chain Reaction ; Sequence Analysis, DNA ; Software ; }, abstract = {We investigated differential gene expression between functionally specialized feeding polyps and swimming medusae in the siphonophore Nanomia bijuga (Cnidaria) with a hybrid long-read/short-read sequencing strategy. We assembled a set of partial gene reference sequences from long-read data (Roche 454), and generated short-read sequences from replicated tissue samples that were mapped to the references to quantify expression. We collected and compared expression data with three short-read expression workflows that differ in sample preparation, sequencing technology, and mapping tools. These workflows were Illumina mRNA-Seq, which generates sequence reads from random locations along each transcript, and two tag-based approaches, SOLiD SAGE and Helicos DGE, which generate reads from particular tag sites. Differences in expression results across workflows were mostly due to the differential impact of missing data in the partial reference sequences. When all 454-derived gene reference sequences were considered, Illumina mRNA-Seq detected more than twice as many differentially expressed (DE) reference sequences as the tag-based workflows. This discrepancy was largely due to missing tag sites in the partial reference that led to false negatives in the tag-based workflows. When only the subset of reference sequences that unambiguously have tag sites was considered, we found broad congruence across workflows, and they all identified a similar set of DE sequences. Our results are promising in several regards for gene expression studies in non-model organisms. First, we demonstrate that a hybrid long-read/short-read sequencing strategy is an effective way to collect gene expression data when an annotated genome sequence is not available. Second, our replicated sampling indicates that expression profiles are highly consistent across field-collected animals in this case. Third, the impacts of partial reference sequences on the ability to detect DE can be mitigated through workflow choice and deeper reference sequencing.}, } @article {pmid21829332, year = {2011}, author = {Magori, K and Bajwa, WI and Bowden, S and Drake, JM}, title = {Decelerating spread of West Nile virus by percolation in a heterogeneous urban landscape.}, journal = {PLoS computational biology}, volume = {7}, number = {7}, pages = {e1002104}, pmid = {21829332}, issn = {1553-7358}, mesh = {Animals ; Birds/virology ; Communicable Diseases, Emerging/epidemiology/prevention & control/transmission/*virology ; Computational Biology ; Databases, Factual ; *Disease Outbreaks ; Humans ; Models, Biological ; New York City/epidemiology ; *Urban Health ; West Nile Fever/epidemiology/prevention & control/*transmission ; *West Nile virus ; }, abstract = {Vector-borne diseases are emerging and re-emerging in urban environments throughout the world, presenting an increasing challenge to human health and a major obstacle to development. Currently, more than half of the global population is concentrated in urban environments, which are highly heterogeneous in the extent, degree, and distribution of environmental modifications. Because the prevalence of vector-borne pathogens is so closely coupled to the ecologies of vector and host species, this heterogeneity has the potential to significantly alter the dynamical systems through which pathogens propagate, and also thereby affect the epidemiological patterns of disease at multiple spatial scales. One such pattern is the speed of spread. Whereas standard models hold that pathogens spread as waves with constant or increasing speed, we hypothesized that heterogeneity in urban environments would cause decelerating travelling waves in incipient epidemics. To test this hypothesis, we analysed data on the spread of West Nile virus (WNV) in New York City (NYC), the 1999 epicentre of the North American pandemic, during annual epizootics from 2000-2008. These data show evidence of deceleration in all years studied, consistent with our hypothesis. To further explain these patterns, we developed a spatial model for vector-borne disease transmission in a heterogeneous environment. An emergent property of this model is that deceleration occurs only in the vicinity of a critical point. Geostatistical analysis suggests that NYC may be on the edge of this criticality. Together, these analyses provide the first evidence for the endogenous generation of decelerating travelling waves in an emerging infectious disease. Since the reported deceleration results from the heterogeneity of the environment through which the pathogen percolates, our findings suggest that targeting control at key sites could efficiently prevent pathogen spread to remote susceptible areas or even halt epidemics.}, } @article {pmid21816034, year = {2011}, author = {Skogerson, K and Wohlgemuth, G and Barupal, DK and Fiehn, O}, title = {The volatile compound BinBase mass spectral database.}, journal = {BMC bioinformatics}, volume = {12}, number = {}, pages = {321}, pmid = {21816034}, issn = {1471-2105}, support = {R01 ES13932/ES/NIEHS NIH HHS/United States ; }, mesh = {Algorithms ; *Databases, Factual ; Gas Chromatography-Mass Spectrometry ; *Mass Spectrometry ; Oils, Volatile/chemistry ; Plant Oils/chemistry ; Plants/chemistry ; Software ; User-Computer Interface ; Volatile Organic Compounds/*chemistry ; }, abstract = {BACKGROUND: Volatile compounds comprise diverse chemical groups with wide-ranging sources and functions. These compounds originate from major pathways of secondary metabolism in many organisms and play essential roles in chemical ecology in both plant and animal kingdoms. In past decades, sampling methods and instrumentation for the analysis of complex volatile mixtures have improved; however, design and implementation of database tools to process and store the complex datasets have lagged behind.

DESCRIPTION: The volatile compound BinBase (vocBinBase) is an automated peak annotation and database system developed for the analysis of GC-TOF-MS data derived from complex volatile mixtures. The vocBinBase DB is an extension of the previously reported metabolite BinBase software developed to track and identify derivatized metabolites. The BinBase algorithm uses deconvoluted spectra and peak metadata (retention index, unique ion, spectral similarity, peak signal-to-noise ratio, and peak purity) from the Leco ChromaTOF software, and annotates peaks using a multi-tiered filtering system with stringent thresholds. The vocBinBase algorithm assigns the identity of compounds existing in the database. Volatile compound assignments are supported by the Adams mass spectral-retention index library, which contains over 2,000 plant-derived volatile compounds. Novel molecules that are not found within vocBinBase are automatically added using strict mass spectral and experimental criteria. Users obtain fully annotated data sheets with quantitative information for all volatile compounds for studies that may consist of thousands of chromatograms. The vocBinBase database may also be queried across different studies, comprising currently 1,537 unique mass spectra generated from 1.7 million deconvoluted mass spectra of 3,435 samples (18 species). Mass spectra with retention indices and volatile profiles are available as free download under the CC-BY agreement (http://vocbinbase.fiehnlab.ucdavis.edu).

CONCLUSIONS: The BinBase database algorithms have been successfully modified to allow for tracking and identification of volatile compounds in complex mixtures. The database is capable of annotating large datasets (hundreds to thousands of samples) and is well-suited for between-study comparisons such as chemotaxonomy investigations. This novel volatile compound database tool is applicable to research fields spanning chemical ecology to human health. The BinBase source code is freely available at http://binbase.sourceforge.net/ under the LGPL 2.0 license agreement.}, } @article {pmid21813467, year = {2012}, author = {Emera, D and Casola, C and Lynch, VJ and Wildman, DE and Agnew, D and Wagner, GP}, title = {Convergent evolution of endometrial prolactin expression in primates, mice, and elephants through the independent recruitment of transposable elements.}, journal = {Molecular biology and evolution}, volume = {29}, number = {1}, pages = {239-247}, doi = {10.1093/molbev/msr189}, pmid = {21813467}, issn = {1537-1719}, mesh = {Animals ; Atelinae ; *DNA Transposable Elements ; Databases, Genetic ; Elephants ; Endometrium/*metabolism ; *Evolution, Molecular ; Female ; Humans ; Mice ; Phylogeny ; Pregnancy ; Prolactin/*biosynthesis/*genetics ; Promoter Regions, Genetic ; Sequence Alignment ; Species Specificity ; Transcription, Genetic ; }, abstract = {Prolactin (PRL) is a multifunctional signaling molecule best known for its role in regulating lactation in mammals. Systemic PRL is produced by the anterior pituitary, but extrapituitary PRL has also been detected in many tissues including the human endometrium. Prolactin is essential for pregnancy in rodents and one of the most dramatically induced genes in the endometrium during human pregnancy. The promoter for human endometrial Prl is located about 5.8 kb upstream of the pituitary promoter and is derived from a transposable element called MER39. Although it has been shown that prolactin is expressed in the pregnant endometrium of a few mammals other than humans, MER39 has been described as primate specific. Thus, in an effort to understand mechanisms of prolactin regulatory evolution, we sought to determine how uterine prolactin is transcribed in species that lack MER39. Using a variety of complementary strategies, including reverse transcriptase-polymerase chain reaction, 5' rapid amplification of cDNA ends, and whole-transcriptome sequencing, we show that endometrial Prl expression is not a shared character of all placental mammals, as it is not expressed in rabbits, pigs, dogs, or armadillos. We show that in primates, mice, and elephants, prolactin mRNA is transcribed in the pregnant endometrium from alternative promoters, different from the pituitary promoter and different from each other. Moreover, we demonstrate that the spider monkey promoter derives from the long terminal repeat (LTR) element MER39 as in humans, the mouse promoter derives from the LTR element MER77, and the elephant promoter derives from the lineage-specific LINE retrotransposon L1-2_LA. We also find surprising variation of transcriptional start sites within these transposable elements and of Prl splice variants, suggesting a high degree of flexibility in the promoter architecture even among closely related species. Finally, the three groups shown here to express endometrial prolactin-the higher primates, the rodents, and the elephant-represent three of the four lineages that showed adaptive evolution of the Prl gene in an earlier study (Wallis M. 2000. Episodic evolution of protein hormones: molecular evolution of pituitary prolactin. J Mol Evol. 50:465-473), which supports our findings and suggests that the selective forces responsible for accelerated Prl evolution were in the endometrium. This is the first reported case of convergent evolution of gene expression through the independent recruitment of different transposable elements, highlighting the importance of transposable elements in gene regulatory, and potentially adaptive, evolution.}, } @article {pmid21813466, year = {2012}, author = {Takuno, S and Gaut, BS}, title = {Body-methylated genes in Arabidopsis thaliana are functionally important and evolve slowly.}, journal = {Molecular biology and evolution}, volume = {29}, number = {1}, pages = {219-227}, doi = {10.1093/molbev/msr188}, pmid = {21813466}, issn = {1537-1719}, mesh = {Arabidopsis/*genetics ; CpG Islands ; *DNA Methylation ; Databases, Genetic ; *Evolution, Molecular ; Exons ; Gene Knockout Techniques ; *Genes, Essential ; *Genes, Plant ; Nucleosomes/genetics ; Sequence Alignment ; }, abstract = {DNA methylation of coding regions, known as gene body methylation, is conserved across eukaryotic lineages. The function of body methylation is not known, but it may either prevent aberrant expression from intragenic promoters or enhance the accuracy of splicing. Given these putative functions, we hypothesized that body-methylated genes would be both longer and more functionally important than unmethylated genes. To test these hypotheses, we reanalyzed single-base resolution bisulfite sequence data from Arabidopsis thaliana to differentiate body-methylated genes from unmethylated genes using a probabilistic approach. Contrasting genic characteristics between the two groups, we found that body-methylated genes tend to be longer and to be more functionally important, as measured by phenotypic effects of insertional mutants and by gene expression, than unmethylated genes. We also found that methylated genes evolve more slowly than unmethylated genes, despite the potential for increased mutation rates in methylated CpG dinucleotides. We propose that slower rates in body-methylated genes are a function of higher selective constraint, lower nucleosome occupancy, and a lower proportion of CpG dinucleotides.}, } @article {pmid21802710, year = {2011}, author = {Liu, H and Weng, Q and Gaines, D}, title = {Geographic incidence of human West Nile virus in northern Virginia, USA, in relation to incidence in birds and variations in urban environment.}, journal = {The Science of the total environment}, volume = {409}, number = {20}, pages = {4235-4241}, doi = {10.1016/j.scitotenv.2011.07.012}, pmid = {21802710}, issn = {1879-1026}, mesh = {Animal Migration ; Animals ; Bird Diseases/*epidemiology/transmission/virology ; Birds ; Discriminant Analysis ; *Disease Outbreaks ; Disease Reservoirs/virology ; *Geographic Information Systems ; Humans ; Incidence ; Urbanization ; Virginia/epidemiology ; West Nile Fever/*epidemiology/transmission/veterinary/virology ; *West Nile virus/isolation & purification ; }, abstract = {Previous studies have analyzed the number and location of bird infections with human incidence of West Nile virus (WNV) as well as the effects of environmental and socioeconomic factors on WNV propagation. However, such associations require more quantitative analyses. This study is intended to quantitatively analyze the relationship in eight counties/independent cities in the northern Virginia, based on an integrated analysis of spatially explicit information on precipitation, land cover, infrastructure, and demographic data using Geographical Information Systems, remote sensing, and statistics. Results show that bird infections in years 2002-2003 were closely associated with low to medium level of impervious surface with certain percentage of canopy and precipitation. Environmental and socioeconomic factors such as percentages of impervious surface, canopy, senior population (65 and older), old houses, bird risk areas, and low-income population were important indicators of human WNV risk in 2002. Limited impervious surface with some canopy provides suitable habitats for WNV transmission, where bird-feeding mosquitoes can forage for blood meals from nesting/roosting birds. Certain socioeconomic conditions such as old houses were linked with human infections by providing favorable environmental conditions, i.e., mature trees with abundant canopy and settled storm sewer systems. It should be noted that the current results may be biased toward urban environments, where dead birds were more likely found, and because the sampling efforts for the bird mortality were rather based on local residents' reports than a designed random sampling method. This geospatial study contributes toward better targeting of WNV prevention within the study area. It also provides an example of how geospatial methods and variables may be used in understanding the ecology of human WNV risk for other areas.}, } @article {pmid21800605, year = {2011}, author = {Li, L and Zhang, JS and Zhu, WQ and Hu, TG and Hou, D}, title = {[Winter wheat area estimation with MODIS-NDVI time series based on parcel].}, journal = {Guang pu xue yu guang pu fen xi = Guang pu}, volume = {31}, number = {5}, pages = {1379-1383}, pmid = {21800605}, issn = {1000-0593}, mesh = {Geographic Information Systems ; Regression Analysis ; Remote Sensing Technology ; *Satellite Communications ; Triticum/*growth & development ; }, abstract = {Several attributes of MODIS (moderate resolution imaging spectrometer) data, especially the short temporal intervals and the global coverage, provide an extremely efficient way to map cropland and monitor its seasonal change. However, the reliability of their measurement results is challenged because of the limited spatial resolution. The parcel data has clear geo-location and obvious boundary information of cropland. Also, the spectral differences and the complexity of mixed pixels are weak in parcels. All of these make that area estimation based on parcels presents more advantage than on pixels. In the present study, winter wheat area estimation based on MODIS-NDVI time series has been performed with the support of cultivated land parcel in Tongzhou, Beijing. In order to extract the regional winter wheat acreage, multiple regression methods were used to simulate the stable regression relationship between MODIS-NDVI time series data and TM samples in parcels. Through this way, the consistency of the extraction results from MODIS and TM can stably reach up to 96% when the amount of samples accounts for 15% of the whole area. The results shows that the use of parcel data can effectively improve the error in recognition results in MODIS-NDVI based multi-series data caused by the low spatial resolution. Therefore, with combination of moderate and low resolution data, the winter wheat area estimation became available in large-scale region which lacks completed medium resolution images or has images covered with clouds. Meanwhile, it carried out the preliminary experiments for other crop area estimation.}, } @article {pmid21794894, year = {2011}, author = {Carafa, R and Faggiano, L and Real, M and Munné, A and Ginebreda, A and Guasch, H and Flo, M and Tirapu, L and von der Ohe, PC}, title = {Water toxicity assessment and spatial pollution patterns identification in a Mediterranean River Basin District. Tools for water management and risk analysis.}, journal = {The Science of the total environment}, volume = {409}, number = {20}, pages = {4269-4279}, doi = {10.1016/j.scitotenv.2011.06.053}, pmid = {21794894}, issn = {1879-1026}, mesh = {Aquatic Organisms/drug effects ; Databases, Factual ; Environmental Monitoring/legislation & jurisprudence/*methods/statistics & numerical data ; Government Regulation ; Models, Theoretical ; Neural Networks, Computer ; Principal Component Analysis ; Risk Assessment ; Risk Management ; Rivers/*chemistry ; Spain ; Water Pollutants, Chemical/*analysis/*toxicity ; Water Supply/legislation & jurisprudence/*standards ; }, abstract = {In compliance with the requirements of the EU Water Framework Directive, monitoring of the ecological and chemical status of Catalan river basins (NE Spain) is carried out by the Catalan Water Agency. The large amount of data collected and the complex relationships among the environmental variables monitored often mislead data interpretation in terms of toxic impact, especially considering that even pollutants at very low concentrations might contribute to the total toxicity. The total dataset of chemical monitoring carried out between 2007 and 2008 (232 sampling stations and 60 pollutants) has been analyzed using sequential advanced modeling techniques. Data on concentrations of contaminants in water were pre-treated in order to calculate the bioavailable fraction, depending on substance properties and local environmental conditions. The resulting values were used to predict the potential impact of toxic substances in complex mixtures on aquatic biota and to identify hot spots. Exposure assessment with Species Sensitivity Distribution (SSD) and mixture toxicity rules were used to compute the multi-substances Potentially Affected Fraction (msPAF). The combined toxicity of the pollutants analyzed in the Catalan surface waters might potentially impact more than 50% of the species in 10% of the sites. In order to understand and visualize the spatial distribution of the toxic risk, Self Organising Map (SOM), based on the Kohonen's Artificial Neural Network (ANN) algorithm, was applied on the output data of these models. Principal Component Analysis (PCA) was performed on top of Neural Network results in order to identify main influential variables which account for the pollution trends. Finally, predicted toxic impacts on biota have been linked and correlated to field data on biological quality indexes using macroinvertebrate and diatom communities (IBMWP and IPS). The methodology presented could represent a suitable tool for water managers in environmental risk assessment and management.}, } @article {pmid21791545, year = {2011}, author = {Hsiao, YY and Pan, ZJ and Hsu, CC and Yang, YP and Hsu, YC and Chuang, YC and Shih, HH and Chen, WH and Tsai, WC and Chen, HH}, title = {Research on orchid biology and biotechnology.}, journal = {Plant & cell physiology}, volume = {52}, number = {9}, pages = {1467-1486}, doi = {10.1093/pcp/pcr100}, pmid = {21791545}, issn = {1471-9053}, mesh = {*Biotechnology ; Breeding ; DNA, Plant/genetics ; Databases, Nucleic Acid ; Flowers/genetics/growth & development/*physiology ; Genes, Plant ; Genome, Chloroplast ; Genome, Plant ; Genomics ; Karyotype ; Odorants ; Orchidaceae/*genetics/growth & development/physiology ; Pigments, Biological/genetics ; Taiwan ; Transformation, Genetic ; }, abstract = {Orchidaceae constitute one of the largest families of angiosperms. They are one of the most ecological and evolutionary significant plants and have successfully colonized almost every habitat on earth. Because of the significance of plant biology, market needs and the current level of breeding technologies, basic research into orchid biology and the application of biotechnology in the orchid industry are continually endearing scientists to orchids in Taiwan. In this introductory review, we give an overview of the research activities in orchid biology and biotechnology, including the status of genomics, transformation technology, flowering regulation, molecular regulatory mechanisms of floral development, scent production and color presentation. This information will provide a broad scope for study of orchid biology and serve as a starting point for uncovering the mysteries of orchid evolution.}, } @article {pmid21791039, year = {2011}, author = {Blavet, N and Charif, D and Oger-Desfeux, C and Marais, GA and Widmer, A}, title = {Comparative high-throughput transcriptome sequencing and development of SiESTa, the Silene EST annotation database.}, journal = {BMC genomics}, volume = {12}, number = {}, pages = {376}, pmid = {21791039}, issn = {1471-2164}, mesh = {*Databases, Genetic ; Dianthus/genetics ; Ecological and Environmental Phenomena ; Evolution, Molecular ; Expressed Sequence Tags/*metabolism ; Genome Size ; Heterozygote ; High-Throughput Nucleotide Sequencing/*methods ; Molecular Sequence Annotation/*methods ; Polymorphism, Single Nucleotide/genetics ; Reproducibility of Results ; Sequence Homology, Nucleic Acid ; Silene/*genetics ; Transcriptome/*genetics ; }, abstract = {BACKGROUND: The genus Silene is widely used as a model system for addressing ecological and evolutionary questions in plants, but advances in using the genus as a model system are impeded by the lack of available resources for studying its genome. Massively parallel sequencing cDNA has recently developed into an efficient method for characterizing the transcriptomes of non-model organisms, generating massive amounts of data that enable the study of multiple species in a comparative framework. The sequences generated provide an excellent resource for identifying expressed genes, characterizing functional variation and developing molecular markers, thereby laying the foundations for future studies on gene sequence and gene expression divergence. Here, we report the results of a comparative transcriptome sequencing study of eight individuals representing four Silene and one Dianthus species as outgroup. All sequences and annotations have been deposited in a newly developed and publicly available database called SiESTa, the Silene EST annotation database.

RESULTS: A total of 1,041,122 EST reads were generated in two runs on a Roche GS-FLX 454 pyrosequencing platform. EST reads were analyzed separately for all eight individuals sequenced and were assembled into contigs using TGICL. These were annotated with results from BLASTX searches and Gene Ontology (GO) terms, and thousands of single-nucleotide polymorphisms (SNPs) were characterized. Unassembled reads were kept as singletons and together with the contigs contributed to the unigenes characterized in each individual. The high quality of unigenes is evidenced by the proportion (49%) that have significant hits in similarity searches with the A. thaliana proteome. The SiESTa database is accessible at http://www.siesta.ethz.ch.

CONCLUSION: The sequence collections established in the present study provide an important genomic resource for four Silene and one Dianthus species and will help to further develop Silene as a plant model system. The genes characterized will be useful for future research not only in the species included in the present study, but also in related species for which no genomic resources are yet available. Our results demonstrate the efficiency of massively parallel transcriptome sequencing in a comparative framework as an approach for developing genomic resources in diverse groups of non-model organisms.}, } @article {pmid21790583, year = {2011}, author = {Lenz, TL}, title = {Computational prediction of MHC II-antigen binding supports divergent allele advantage and explains trans-species polymorphism.}, journal = {Evolution; international journal of organic evolution}, volume = {65}, number = {8}, pages = {2380-2390}, doi = {10.1111/j.1558-5646.2011.01288.x}, pmid = {21790583}, issn = {1558-5646}, mesh = {*Alleles ; Animals ; Bacteria/genetics/growth & development/metabolism ; Bacterial Infections/immunology/metabolism/pathology ; Binding Sites ; Computational Biology/*methods ; *Evolution, Molecular ; Exons ; Genes, MHC Class II ; Histocompatibility Antigens Class II/*genetics/immunology/metabolism ; Humans ; *Polymorphism, Genetic ; }, abstract = {The major histocompatibility complex (MHC), coding for antigen presenting molecules of the adaptive immune system, represents one of the most polymorphic regions in the vertebrate genome. The exceptional polymorphism, which is potentially maintained by balancing selection under host-parasite coevolution, comprises excessive sequence divergence among alleles as well as ancient allelic lineages that predate species divergence (trans-species polymorphism). Here, the mechanisms that are proposed to maintain such sequence divergence and ancient lineages are investigated. Established computational antigen-binding prediction algorithms, which are based on empirical databases, are employed to determine the overlap in bound antigens among individual MHC class IIB alleles. The results show that genetically more divergent allele pairs experience less overlap and thus present a broader range of potential antigens. These findings support the divergent allele advantage hypothesis and furthermore suggest an evolutionary advantage explaining the maintenance of divergent allelic lineages, that is, trans-species polymorphism. In addressing a quantitative rather than qualitative aspect of MHC alleles, these insights highlight a new direction for future research on MHC evolution.}, } @article {pmid21778493, year = {2011}, author = {Finney, JW and Humphreys, K and Kivlahan, DR and Harris, AH}, title = {Why health care process performance measures can have different relationships to outcomes for patients and hospitals: understanding the ecological fallacy.}, journal = {American journal of public health}, volume = {101}, number = {9}, pages = {1635-1642}, pmid = {21778493}, issn = {1541-0048}, mesh = {Bias ; Confounding Factors, Epidemiologic ; Data Interpretation, Statistical ; Environment ; Health Services Administration/*statistics & numerical data ; Health Services Research/methods/*statistics & numerical data ; Humans ; Outcome and Process Assessment, Health Care/*statistics & numerical data ; Quality Indicators, Health Care/*statistics & numerical data ; Substance-Related Disorders/rehabilitation ; }, abstract = {Relationships between health care process performance measures (PPMs) and outcomes can differ in magnitude and even direction for patients versus higher level units (e.g., health care facilities). Such discrepancies can arise because facility-level relationships ignore PPM-outcome relationships for patients within facilities, may have different confounders than patient-level PPM-outcome relationships, and may reflect facility effect modification of patient PPM-outcome relationships. If a patient-level PPM is related to better patient outcomes, that care process should be encouraged. However, the finding in a multilevel analysis that the proportion of patients receiving PPM care across facilities nevertheless is linked to poor hospital outcomes would suggest that interventions targeting the health care facility also are needed.}, } @article {pmid21777938, year = {2011}, author = {Sforzini, S and Dagnino, A and Oliveri, L and Canesi, L and Viarengo, A}, title = {Effects of dioxin exposure in Eisenia andrei: integration of biomarker data by an Expert System to rank the development of pollutant-induced stress syndrome in earthworms.}, journal = {Chemosphere}, volume = {85}, number = {6}, pages = {934-942}, doi = {10.1016/j.chemosphere.2011.06.059}, pmid = {21777938}, issn = {1879-1298}, mesh = {Animals ; Biomarkers/metabolism ; Calcium-Transporting ATPases/metabolism ; DNA Damage ; Data Interpretation, Statistical ; Dioxins/*toxicity ; Dose-Response Relationship, Drug ; Ecotoxicology/*methods ; Environmental Exposure/*adverse effects ; Environmental Pollutants/*toxicity ; *Expert Systems ; Intestinal Mucosa/drug effects/enzymology ; Intracellular Membranes/drug effects/metabolism ; Kinetics ; Lipofuscin/metabolism ; Lysosomes/drug effects/metabolism ; Neutral Red/metabolism ; Oligochaeta/cytology/*drug effects/enzymology/physiology ; Stress, Physiological/*drug effects ; Time Factors ; }, abstract = {A battery of biomarkers has recently been developed in the earthworm Eisenia andrei. In this study, different biomarkers (i.e. Ca[2+]-ATPase activity, lysosomal membrane stability-LMS, lysosomal lipofuscin and neutral lipid content) were utilized to evaluate the alterations in the physiological status of animals, induced by exposure for 3d to different sublethal concentrations of TCDD (2,3,7,8-tetrachlorodibenzo-p-dioxin) (1.5 × 10[-3], 1.5 × 10[-2], 1.5×10[-1] ng mL[-1]) utilizing the paper contact toxicity test. Lysosome/cytoplasm volume ratio and DNA damage were also evaluated as a biomarker at the tissue level and as a biomarker of genotoxicity, respectively. Moreover, the NR retention time assay conditions were optimized for the determination of in vivo LMS in earthworm coelomocytes. The results demonstrate that LMS and Ca[2+]-ATPase activity were early warning biomarkers able to detect the effects of minimal amounts of TCDD and that biomarkers evaluated at the tissue level are important for following the evolution of the stress syndrome in earthworms. To evaluate the health status of the animals, an Earthworm Expert System (EES) for biomarker data integration and interpretation was developed. The EES proved to be a suitable tool able to rank, objectively, the different levels of the stress syndrome in E. andrei induced by the different concentrations of TCDD.}, } @article {pmid21777398, year = {2011}, author = {, and Bonizzoni, M and Bourjea, J and Chen, B and Crain, BJ and Cui, L and Fiorentino, V and Hartmann, S and Hendricks, S and Ketmaier, V and Ma, X and Muths, D and Pavesi, L and Pfautsch, S and Rieger, MA and Santonastaso, T and Sattabongkot, J and Taron, CH and Taron, DJ and Tiedemann, R and Yan, G and Zheng, B and Zhong, D}, title = {Permanent Genetic Resources added to Molecular Ecology Resources Database 1 April 2011-31 May 2011.}, journal = {Molecular ecology resources}, volume = {11}, number = {5}, pages = {935-936}, doi = {10.1111/j.1755-0998.2011.03046.x}, pmid = {21777398}, issn = {1755-0998}, support = {U19 AI089672/AI/NIAID NIH HHS/United States ; }, mesh = {Amphipoda/*genetics ; Animals ; Anopheles/*genetics ; *Databases, Genetic ; Gastropoda/*genetics ; Genetic Markers/genetics ; Microsatellite Repeats/*genetics ; Moths/*genetics ; Perciformes/*genetics ; }, abstract = {This article documents the addition of 92 microsatellite marker loci to the Molecular Ecology Resources Database. Loci were developed for the following species: Anopheles minimus, An. sinensis, An. dirus, Calephelis mutica, Lutjanus kasmira, Murella muralis and Orchestia montagui. These loci were cross-tested on the following species: Calephelis arizonensi, Calephelis borealis, Calephelis nemesis, Calephelis virginiensis and Lutjanus bengalensis.}, } @article {pmid21777367, year = {2011}, author = {Berelson, WM and Corsetti, FA and Pepe-Ranney, C and Hammond, DE and Beaumont, W and Spear, JR}, title = {Hot spring siliceous stromatolites from Yellowstone National Park: assessing growth rate and laminae formation.}, journal = {Geobiology}, volume = {9}, number = {5}, pages = {411-424}, doi = {10.1111/j.1472-4669.2011.00288.x}, pmid = {21777367}, issn = {1472-4669}, mesh = {Bacteria/classification/genetics/*growth & development ; Carbon Radioisotopes/analysis ; Cesium/analysis ; Cyanobacteria/classification/genetics/growth & development ; DNA, Bacterial/*analysis/genetics ; Freshwater Biology/*methods ; Geologic Sediments/chemistry/*microbiology ; Hot Springs/chemistry/*microbiology ; Image Interpretation, Computer-Assisted ; Microscopy, Electron, Scanning ; Phylogeny ; Radiometric Dating ; Radium/analysis ; Sequence Analysis, DNA ; Thorium/analysis ; Wyoming ; }, abstract = {Stromatolites are commonly interpreted as evidence of ancient microbial life, yet stromatolite morphogenesis is poorly understood. We apply radiometric tracer and dating techniques, molecular analyses and growth experiments to investigate siliceous stromatolite morphogenesis in Obsidian Pool Prime (OPP), a hot spring in Yellowstone National Park. We examine rates of stromatolite growth and the environmental and/or biologic conditions that affect lamination formation and preservation, both difficult features to constrain in ancient examples. The "main body" of the stromatolite is composed of finely laminated, porous, light-dark couplets of erect (surface normal) and reclining (surface parallel) silicified filamentous bacteria, interrupted by a less-distinct, well-cemented "drape" lamination. Results from dating studies indicate a growth rate of 1-5 cm year(-1) ; however, growth is punctuated. (14)C as a tracer demonstrates that stromatolite cyanobacterial communities fix CO(2) derived from two sources, vent water (radiocarbon dead) and the atmosphere (modern (14)C). The drape facies contained a greater proportion of atmospheric CO(2) and more robust silica cementation (vs. the main body facies), which we interpret as formation when spring level was lower. Systematic changes in lamination style are likely related to environmental forcing and larger scale features (tectonic, climatic). Although the OPP stromatolites are composed of silica and most ancient forms are carbonate, their fine lamination texture requires early lithification. Without early lithification, whether silica or carbonate, it is unlikely that a finely laminated structure representing an ancient microbial mat would be preserved. In OPP, lithification on the nearly diurnal time scale is likely related to temperature control on silica solubility.}, } @article {pmid21776223, year = {2011}, author = {Yu, HL and Wang, CH and Liu, MC and Kuo, YM}, title = {Estimation of fine particulate matter in Taipei using landuse regression and bayesian maximum entropy methods.}, journal = {International journal of environmental research and public health}, volume = {8}, number = {6}, pages = {2153-2169}, pmid = {21776223}, issn = {1660-4601}, mesh = {Air Pollutants/*analysis ; Bayes Theorem ; *Entropy ; Environmental Monitoring/*methods ; Geographic Information Systems ; Humans ; Particle Size ; Particulate Matter/*analysis ; Taiwan ; *Urbanization ; }, abstract = {Fine airborne particulate matter (PM2.5) has adverse effects on human health. Assessing the long-term effects of PM2.5 exposure on human health and ecology is often limited by a lack of reliable PM2.5 measurements. In Taipei, PM2.5 levels were not systematically measured until August, 2005. Due to the popularity of geographic information systems (GIS), the landuse regression method has been widely used in the spatial estimation of PM concentrations. This method accounts for the potential contributing factors of the local environment, such as traffic volume. Geostatistical methods, on other hand, account for the spatiotemporal dependence among the observations of ambient pollutants. This study assesses the performance of the landuse regression model for the spatiotemporal estimation of PM2.5 in the Taipei area. Specifically, this study integrates the landuse regression model with the geostatistical approach within the framework of the Bayesian maximum entropy (BME) method. The resulting epistemic framework can assimilate knowledge bases including: (a) empirical-based spatial trends of PM concentration based on landuse regression, (b) the spatio-temporal dependence among PM observation information, and (c) site-specific PM observations. The proposed approach performs the spatiotemporal estimation of PM2.5 levels in the Taipei area (Taiwan) from 2005-2007.}, } @article {pmid21774422, year = {2011}, author = {Hanks, EM and Hooten, MB and Baker, FA}, title = {Reconciling multiple data sources to improve accuracy of large-scale prediction of forest disease incidence.}, journal = {Ecological applications : a publication of the Ecological Society of America}, volume = {21}, number = {4}, pages = {1173-1188}, doi = {10.1890/09-1549.1}, pmid = {21774422}, issn = {1051-0761}, mesh = {Bayes Theorem ; Databases, Factual ; Host-Parasite Interactions ; Minnesota ; Models, Biological ; Picea/*parasitology ; Trees ; Viscaceae/*physiology ; }, abstract = {Ecological spatial data often come from multiple sources, varying in extent and accuracy. We describe a general approach to reconciling such data sets through the use of the Bayesian hierarchical framework. This approach provides a way for the data sets to borrow strength from one another while allowing for inference on the underlying ecological process. We apply this approach to study the incidence of eastern spruce dwarf mistletoe (Arceuthobium pusillum) in Minnesota black spruce (Picea mariana). A Minnesota Department of Natural Resources operational inventory of black spruce stands in northern Minnesota found mistletoe in 11% of surveyed stands, while a small, specific-pest survey found mistletoe in 56% of the surveyed stands. We reconcile these two surveys within a Bayesian hierarchical framework and predict that 35-59% of black spruce stands in northern Minnesota are infested with dwarf mistletoe.}, } @article {pmid21773863, year = {2012}, author = {Harwood, JJ and Stroud, RA}, title = {A survey on the utility of the USEPA CADDIS stressor identification procedure.}, journal = {Environmental monitoring and assessment}, volume = {184}, number = {6}, pages = {3805-3812}, pmid = {21773863}, issn = {1573-2959}, mesh = {Environmental Monitoring/*methods/standards ; Guidelines as Topic ; Humans ; Information Dissemination ; Information Management ; Internet ; *Online Systems ; Surveys and Questionnaires ; United States ; United States Environmental Protection Agency ; }, abstract = {The Environmental Protection Agency (EPA) has made available on the worldwide web a systematic stream stressor identification procedure, the "Causal Analysis/Diagnosis Decision Information System" or CADDIS. We report here the results of a survey of regulators and scientists in 11 states who use CADDIS or another stressor identification procedure in their work. The 13 survey questions address guidelines as to what impairment scenarios to approach with stressor identification, what information is needed to perform stressor identification, and what the stakeholder role is in performing stressor identification. At the time of this survey (the summer of 2009), the EPA CADDIS website was less commonly used among the state regulators surveyed than the published EPA stressor identification document on which it is based. The respondents generally find the EPA stressor identification procedure useful and capable of being adapted to their individual needs. Survey respondents all use stressor identification in their Total Maximum Daily Load work, but also in a wide variety of other applications. All the "types of evidence" included in the CADDIS stressor identification procedure are used by the practitioners surveyed with the exception of the results of ecological simulation models. While the CADDIS documentation encourages the involvement of stakeholders in stressor identification, most respondents do not assemble stakeholder teams of local officials and citizens to participate in stressor analyses.}, } @article {pmid21767398, year = {2011}, author = {Bajgain, P and Richardson, BA and Price, JC and Cronn, RC and Udall, JA}, title = {Transcriptome characterization and polymorphism detection between subspecies of big sagebrush (Artemisia tridentata).}, journal = {BMC genomics}, volume = {12}, number = {}, pages = {370}, pmid = {21767398}, issn = {1471-2164}, mesh = {Alleles ; Artemisia/*genetics ; Contig Mapping ; Databases, Protein ; *Gene Expression Profiling ; *Polymorphism, Single Nucleotide ; Protein Structure, Tertiary ; Sequence Alignment ; Sequence Analysis, DNA ; Species Specificity ; Tandem Repeat Sequences ; }, abstract = {BACKGROUND: Big sagebrush (Artemisia tridentata) is one of the most widely distributed and ecologically important shrub species in western North America. This species serves as a critical habitat and food resource for many animals and invertebrates. Habitat loss due to a combination of disturbances followed by establishment of invasive plant species is a serious threat to big sagebrush ecosystem sustainability. Lack of genomic data has limited our understanding of the evolutionary history and ecological adaptation in this species. Here, we report on the sequencing of expressed sequence tags (ESTs) and detection of single nucleotide polymorphism (SNP) and simple sequence repeat (SSR) markers in subspecies of big sagebrush.

RESULTS: cDNA of A. tridentata sspp. tridentata and vaseyana were normalized and sequenced using the 454 GS FLX Titanium pyrosequencing technology. Assembly of the reads resulted in 20,357 contig consensus sequences in ssp. tridentata and 20,250 contigs in ssp. vaseyana. A BLASTx search against the non-redundant (NR) protein database using 29,541 consensus sequences obtained from a combined assembly resulted in 21,436 sequences with significant blast alignments (≤ 1e⁻¹⁵). A total of 20,952 SNPs and 119 polymorphic SSRs were detected between the two subspecies. SNPs were validated through various methods including sequence capture. Validation of SNPs in different individuals uncovered a high level of nucleotide variation in EST sequences. EST sequences of a third, tetraploid subspecies (ssp. wyomingensis) obtained by Illumina sequencing were mapped to the consensus sequences of the combined 454 EST assembly. Approximately one-third of the SNPs between sspp. tridentata and vaseyana identified in the combined assembly were also polymorphic within the two geographically distant ssp. wyomingensis samples.

CONCLUSION: We have produced a large EST dataset for Artemisia tridentata, which contains a large sample of the big sagebrush leaf transcriptome. SNP mapping among the three subspecies suggest the origin of ssp. wyomingensis via mixed ancestry. A large number of SNP and SSR markers provide the foundation for future research to address questions in big sagebrush evolution, ecological genetics, and conservation using genomic approaches.}, } @article {pmid21764422, year = {2011}, author = {Huang, IB and Keisler, J and Linkov, I}, title = {Multi-criteria decision analysis in environmental sciences: ten years of applications and trends.}, journal = {The Science of the total environment}, volume = {409}, number = {19}, pages = {3578-3594}, doi = {10.1016/j.scitotenv.2011.06.022}, pmid = {21764422}, issn = {1879-1026}, mesh = {Conservation of Natural Resources ; *Decision Support Techniques ; Ecology/methods/*trends ; Environmental Restoration and Remediation ; Geographic Information Systems ; Waste Management ; Water Quality ; }, abstract = {Decision-making in environmental projects requires consideration of trade-offs between socio-political, environmental, and economic impacts and is often complicated by various stakeholder views. Multi-criteria decision analysis (MCDA) emerged as a formal methodology to face available technical information and stakeholder values to support decisions in many fields and can be especially valuable in environmental decision making. This study reviews environmental applications of MCDA. Over 300 papers published between 2000 and 2009 reporting MCDA applications in the environmental field were identified through a series of queries in the Web of Science database. The papers were classified by their environmental application area, decision or intervention type. In addition, the papers were also classified by the MCDA methods used in the analysis (analytic hierarchy process, multi-attribute utility theory, and outranking). The results suggest that there is a significant growth in environmental applications of MCDA over the last decade across all environmental application areas. Multiple MCDA tools have been successfully used for environmental applications. Even though the use of the specific methods and tools varies in different application areas and geographic regions, our review of a few papers where several methods were used in parallel with the same problem indicates that recommended course of action does not vary significantly with the method applied.}, } @article {pmid21763781, year = {2012}, author = {Cheng, KC and Hinton, DE and Mattingly, CJ and Planchart, A}, title = {Aquatic models, genomics and chemical risk management.}, journal = {Comparative biochemistry and physiology. Toxicology & pharmacology : CBP}, volume = {155}, number = {1}, pages = {169-173}, pmid = {21763781}, issn = {1532-0456}, support = {R01 AR052535/AR/NIAMS NIH HHS/United States ; R01AR052535/AR/NIAMS NIH HHS/United States ; R21 ES017828/ES/NIEHS NIH HHS/United States ; R24 RR017441/RR/NCRR NIH HHS/United States ; P42 ES010356/ES/NIEHS NIH HHS/United States ; R01ES014065/ES/NIEHS NIH HHS/United States ; R01ES019604/ES/NIEHS NIH HHS/United States ; R24RR017441/RR/NCRR NIH HHS/United States ; R01 ES019604/ES/NIEHS NIH HHS/United States ; R24 OD011152/OD/NIH HHS/United States ; R01 ES014065/ES/NIEHS NIH HHS/United States ; R21ES016892/ES/NIEHS NIH HHS/United States ; P42 ES10356/ES/NIEHS NIH HHS/United States ; R01CA242956/CA/NCI NIH HHS/United States ; }, mesh = {Animals ; Computational Biology/*methods ; *Databases, Factual ; Ecotoxicology ; Environmental Exposure/analysis ; Environmental Monitoring/methods ; Fishes/anatomy & histology/genetics/physiology ; Gene-Environment Interaction ; Genomics/methods ; Internet ; Models, Animal ; Risk Factors ; *User-Computer Interface ; }, abstract = {The 5th Aquatic Animal Models for Human Disease meeting follows four previous meetings (Nairn et al., 2001; Schmale, 2004; Schmale et al., 2007; Hinton et al., 2009) in which advances in aquatic animal models for human disease research were reported, and community discussion of future direction was pursued. At this meeting, discussion at a workshop entitled Bioinformatics and Computational Biology with Web-based Resources (20 September 2010) led to an important conclusion: Aquatic model research using feral and experimental fish, in combination with web-based access to annotated anatomical atlases and toxicological databases, yields data that advance our understanding of human gene function, and can be used to facilitate environmental management and drug development. We propose here that the effects of genes and environment are best appreciated within an anatomical context - the specifically affected cells and organs in the whole animal. We envision the use of automated, whole-animal imaging at cellular resolution and computational morphometry facilitated by high-performance computing and automated entry into toxicological databases, as anchors for genetic and toxicological data, and as connectors between human and model system data. These principles should be applied to both laboratory and feral fish populations, which have been virtually irreplaceable sentinals for environmental contamination that results in human morbidity and mortality. We conclude that automation, database generation, and web-based accessibility, facilitated by genomic/transcriptomic data and high-performance and cloud computing, will potentiate the unique and potentially key roles that aquatic models play in advancing systems biology, drug development, and environmental risk management.}, } @article {pmid21762488, year = {2011}, author = {Fernández-Pozo, N and Canales, J and Guerrero-Fernández, D and Villalobos, DP and Díaz-Moreno, SM and Bautista, R and Flores-Monterroso, A and Guevara, MÁ and Perdiguero, P and Collada, C and Cervera, MT and Soto, A and Ordás, R and Cantón, FR and Avila, C and Cánovas, FM and Claros, MG}, title = {EuroPineDB: a high-coverage web database for maritime pine transcriptome.}, journal = {BMC genomics}, volume = {12}, number = {}, pages = {366}, pmid = {21762488}, issn = {1471-2164}, mesh = {*Databases, Genetic ; *Gene Expression Profiling ; Gene Library ; Internet ; Pinus/*genetics ; }, abstract = {BACKGROUND: Pinus pinaster is an economically and ecologically important species that is becoming a woody gymnosperm model. Its enormous genome size makes whole-genome sequencing approaches are hard to apply. Therefore, the expressed portion of the genome has to be characterised and the results and annotations have to be stored in dedicated databases.

DESCRIPTION: EuroPineDB is the largest sequence collection available for a single pine species, Pinus pinaster (maritime pine), since it comprises 951 641 raw sequence reads obtained from non-normalised cDNA libraries and high-throughput sequencing from adult (xylem, phloem, roots, stem, needles, cones, strobili) and embryonic (germinated embryos, buds, callus) maritime pine tissues. Using open-source tools, sequences were optimally pre-processed, assembled, and extensively annotated (GO, EC and KEGG terms, descriptions, SNPs, SSRs, ORFs and InterPro codes). As a result, a 10.5× P. pinaster genome was covered and assembled in 55 322 UniGenes. A total of 32 919 (59.5%) of P. pinaster UniGenes were annotated with at least one description, revealing at least 18 466 different genes. The complete database, which is designed to be scalable, maintainable, and expandable, is freely available at: http://www.scbi.uma.es/pindb/. It can be retrieved by gene libraries, pine species, annotations, UniGenes and microarrays (i.e., the sequences are distributed in two-colour microarrays; this is the only conifer database that provides this information) and will be periodically updated. Small assemblies can be viewed using a dedicated visualisation tool that connects them with SNPs. Any sequence or annotation set shown on-screen can be downloaded. Retrieval mechanisms for sequences and gene annotations are provided.

CONCLUSIONS: The EuroPineDB with its integrated information can be used to reveal new knowledge, offers an easy-to-use collection of information to directly support experimental work (including microarray hybridisation), and provides deeper knowledge on the maritime pine transcriptome.}, } @article {pmid21761247, year = {2011}, author = {Xie, X and Wang, Q and Dai, L and Su, D and Wang, X and Qi, G and Ye, Y}, title = {Application of China's National Forest Continuous Inventory database.}, journal = {Environmental management}, volume = {48}, number = {6}, pages = {1095-1106}, pmid = {21761247}, issn = {1432-1009}, mesh = {China ; Conservation of Natural Resources ; *Databases, Factual ; Ecosystem ; Forestry/methods ; Geographic Information Systems ; Geography ; *Trees ; }, abstract = {The maintenance of a timely, reliable and accurate spatial database on current forest ecosystem conditions and changes is essential to characterize and assess forest resources and support sustainable forest management. Information for such a database can be obtained only through a continuous forest inventory. The National Forest Continuous Inventory (NFCI) is the first level of China's three-tiered inventory system. The NFCI is administered by the State Forestry Administration; data are acquired by five inventory institutions around the country. Several important components of the database include land type, forest classification and ageclass/ age-group. The NFCI database in China is constructed based on 5-year inventory periods, resulting in some of the data not being timely when reports are issued. To address this problem, a forest growth simulation model has been developed to update the database for years between the periodic inventories. In order to aid in forest plan design and management, a three-dimensional virtual reality system of forest landscapes for selected units in the database (compartment or sub-compartment) has also been developed based on Virtual Reality Modeling Language. In addition, a transparent internet publishing system for a spatial database based on open source WebGIS (UMN Map Server) has been designed and utilized to enhance public understanding and encourage free participation of interested parties in the development, implementation, and planning of sustainable forest management.}, } @article {pmid21760944, year = {2011}, author = {Yeakel, JD and Novak, M and Guimarães, PR and Dominy, NJ and Koch, PL and Ward, EJ and Moore, JW and Semmens, BX}, title = {Merging resource availability with isotope mixing models: the role of neutral interaction assumptions.}, journal = {PloS one}, volume = {6}, number = {7}, pages = {e22015}, pmid = {21760944}, issn = {1932-6203}, mesh = {Animals ; Bayes Theorem ; Biota ; Databases as Topic ; *Food Chain ; Gastropoda/physiology ; *Isotope Labeling ; *Models, Biological ; New Zealand ; Predatory Behavior ; Reproducibility of Results ; Species Specificity ; }, abstract = {BACKGROUND: Bayesian mixing models have allowed for the inclusion of uncertainty and prior information in the analysis of trophic interactions using stable isotopes. Formulating prior distributions is relatively straightforward when incorporating dietary data. However, the use of data that are related, but not directly proportional, to diet (such as prey availability data) is often problematic because such information is not necessarily predictive of diet, and the information required to build a reliable prior distribution for all prey species is often unavailable. Omitting prey availability data impacts the estimation of a predator's diet and introduces the strong assumption of consumer ultrageneralism (where all prey are consumed in equal proportions), particularly when multiple prey have similar isotope values.

METHODOLOGY: We develop a procedure to incorporate prey availability data into bayesian mixing models conditional on the similarity of isotope values between two prey. If a pair of prey have similar isotope values (resulting in highly uncertain mixing model results), our model increases the weight of availability data in estimating the contribution of prey to a predator's diet. We test the utility of this method in an intertidal community against independently measured feeding rates.

CONCLUSIONS: Our results indicate that our weighting procedure increases the accuracy by which consumer diets can be inferred in situations where multiple prey have similar isotope values. This suggests that the exchange of formalism for predictive power is merited, particularly when the relationship between prey availability and a predator's diet cannot be assumed for all species in a system.}, } @article {pmid21755426, year = {2012}, author = {Wu, L and Long, TY and Liu, X and Mmereki, D}, title = {Simulation of soil loss processes based on rainfall runoff and the time factor of governance in the Jialing River Watershed, China.}, journal = {Environmental monitoring and assessment}, volume = {184}, number = {6}, pages = {3731-3748}, pmid = {21755426}, issn = {1573-2959}, mesh = {China ; Computer Simulation ; Environmental Monitoring ; Geographic Information Systems ; Geologic Sediments/*chemistry ; *Geological Phenomena ; Kinetics ; Rain/*chemistry ; Soil/*chemistry ; Time ; Water Movements ; }, abstract = {Jialing River is the largest tributary in the catchment area of Three Gorges Reservoir, and it is also one of the important areas of sediment yield in the upper reaches of the Yangtze River. In recent years, significant changes of water and sediment characteristics have taken place. The "Long Control" Project implemented since 1989 had greatly changed the surface appearance of the Jialing River Watershed (JRW), and it had made the environments of the watershed sediment yield and sediment transport change significantly. In this research, the Revised Universal Soil Loss Equation was selected and used to predict the annual average amount of soil erosion for the special water and sediment environments in the JRW after the implementation of the "Long Control" Project, and then the rainfall-runoff modulus and the time factor of governance were both considered as dynamic factors, the dynamic sediment transport model was built for soil erosion monitoring and forecasting based on the average sediment yield model. According to the dynamic model, the spatial and temporal distribution of soil erosion amount and sediment transport amount of the JRW from 1990 to 2007 was simulated using geographic information system (GIS) technology and space-grid algorithm. Simulation results showed that the average relative error of sediment transport was less than 10% except for the extreme hydrological year. The relationship between water and sediment from 1990 to 2007 showed that sediment interception effects of the soil and water conservation projects were obvious: the annual average sediment discharge reduced from 145.3 to 35 million tons, the decrement of sediment amount was about 111 million tons, and decreasing amplitude was 76%; the sediment concentration was also decreased from 2.01 to 0.578 kg/m(3). These data are of great significance for the prediction and estimation of the future changing trends of sediment storage in the Three Gorges Reservoir and the particulate non-point source pollution load carried by sediment transport from watershed surface.}, } @article {pmid21754987, year = {2011}, author = {Margam, VM and Coates, BS and Bayles, DO and Hellmich, RL and Agunbiade, T and Seufferheld, MJ and Sun, W and Kroemer, JA and Ba, MN and Binso-Dabire, CL and Baoua, I and Ishiyaku, MF and Covas, FG and Srinivasan, R and Armstrong, J and Murdock, LL and Pittendrigh, BR}, title = {Transcriptome sequencing, and rapid development and application of SNP markers for the legume pod borer Maruca vitrata (Lepidoptera: Crambidae).}, journal = {PloS one}, volume = {6}, number = {7}, pages = {e21388}, pmid = {21754987}, issn = {1932-6203}, mesh = {Africa ; Animals ; DNA, Complementary/genetics ; Databases, Genetic ; Digestive System/metabolism ; Expressed Sequence Tags ; Fruit/*parasitology ; Gene Expression Profiling/*methods ; Genes, Insect/genetics ; Genetic Markers ; Genetics, Population ; Genotype ; Geography ; Larva/genetics ; Lepidoptera/*genetics ; Molecular Sequence Annotation ; Molecular Sequence Data ; Phylogeny ; Polymorphism, Single Nucleotide/*genetics ; Regression Analysis ; Salivary Glands/metabolism ; Sequence Analysis, DNA/*methods ; Sequence Homology, Nucleic Acid ; Software ; }, abstract = {The legume pod borer, Maruca vitrata (Lepidoptera: Crambidae), is an insect pest species of crops grown by subsistence farmers in tropical regions of Africa. We present the de novo assembly of 3729 contigs from 454- and Sanger-derived sequencing reads for midgut, salivary, and whole adult tissues of this non-model species. Functional annotation predicted that 1320 M. vitrata protein coding genes are present, of which 631 have orthologs within the Bombyx mori gene model. A homology-based analysis assigned M. vitrata genes into a group of paralogs, but these were subsequently partitioned into putative orthologs following phylogenetic analyses. Following sequence quality filtering, a total of 1542 putative single nucleotide polymorphisms (SNPs) were predicted within M. vitrata contig assemblies. Seventy one of 1078 designed molecular genetic markers were used to screen M. vitrata samples from five collection sites in West Africa. Population substructure may be present with significant implications in the insect resistance management recommendations pertaining to the release of biological control agents or transgenic cowpea that express Bacillus thuringiensis crystal toxins. Mutation data derived from transcriptome sequencing is an expeditious and economical source for genetic markers that allow evaluation of ecological differentiation.}, } @article {pmid21750734, year = {2011}, author = {Lam, CH and Tsontos, VM}, title = {Integrated management and visualization of electronic tag data with Tagbase.}, journal = {PloS one}, volume = {6}, number = {7}, pages = {e21810}, pmid = {21750734}, issn = {1932-6203}, mesh = {Animals ; Computational Biology/*methods ; *Database Management Systems ; *Databases, Factual ; Geographic Information Systems ; Information Storage and Retrieval/*methods ; Marine Biology/methods ; Reproducibility of Results ; }, abstract = {Electronic tags have been used widely for more than a decade in studies of diverse marine species. However, despite significant investment in tagging programs and hardware, data management aspects have received insufficient attention, leaving researchers without a comprehensive toolset to manage their data easily. The growing volume of these data holdings, the large diversity of tag types and data formats, and the general lack of data management resources are not only complicating integration and synthesis of electronic tagging data in support of resource management applications but potentially threatening the integrity and longer-term access to these valuable datasets. To address this critical gap, Tagbase has been developed as a well-rounded, yet accessible data management solution for electronic tagging applications. It is based on a unified relational model that accommodates a suite of manufacturer tag data formats in addition to deployment metadata and reprocessed geopositions. Tagbase includes an integrated set of tools for importing tag datasets into the system effortlessly, and provides reporting utilities to interactively view standard outputs in graphical and tabular form. Data from the system can also be easily exported or dynamically coupled to GIS and other analysis packages. Tagbase is scalable and has been ported to a range of database management systems to support the needs of the tagging community, from individual investigators to large scale tagging programs. Tagbase represents a mature initiative with users at several institutions involved in marine electronic tagging research.}, } @article {pmid21749924, year = {2011}, author = {Wallentin, M and Nielsen, AH and Vuust, P and Dohn, A and Roepstorff, A and Lund, TE}, title = {Amygdala and heart rate variability responses from listening to emotionally intense parts of a story.}, journal = {NeuroImage}, volume = {58}, number = {3}, pages = {963-973}, doi = {10.1016/j.neuroimage.2011.06.077}, pmid = {21749924}, issn = {1095-9572}, mesh = {Adult ; Amygdala/*physiology ; Auditory Perception/*physiology ; *Brain Mapping ; Emotions/*physiology ; Female ; Heart Rate/*physiology ; Humans ; Image Interpretation, Computer-Assisted ; Magnetic Resonance Imaging ; Male ; Middle Aged ; Young Adult ; }, abstract = {Emotions are often understood in relation to conditioned responses. Narrative emotions, however, cannot be reduced to a simple associative relationship between emotion words and their experienced counterparts. Intensity in stories may arise without any overt emotion depicting words and vice versa. In this fMRI study we investigated BOLD responses to naturally fluctuating emotions evoked by listening to a story. The emotional intensity profile of the text was found through a rating study. The validity of this profile was supported by heart rate variability (HRV) data showing a significant correspondence across participants between intensity ratings and HRV measurements obtained during fMRI. With this ecologically valid stimulus we found that narrative intensity was accompanied by activation in temporal cortices, medial geniculate nuclei in the thalamus and amygdala, brain regions that are all part of the system for processing conditioned emotional responses to auditory stimuli. These findings suggest that this system also underpins narrative emotions in spite of their complex nature. Traditional language regions and premotor cortices were also activated during intense parts of the story whereas orbitofrontal cortex was found linked to emotion with positive valence, regardless of level of intensity.}, } @article {pmid21749684, year = {2011}, author = {Hsiao, YY and Chen, YW and Huang, SC and Pan, ZJ and Fu, CH and Chen, WH and Tsai, WC and Chen, HH}, title = {Gene discovery using next-generation pyrosequencing to develop ESTs for Phalaenopsis orchids.}, journal = {BMC genomics}, volume = {12}, number = {}, pages = {360}, pmid = {21749684}, issn = {1471-2164}, mesh = {Contig Mapping ; Databases, Protein ; *Expressed Sequence Tags ; Gene Expression Profiling ; *Genetic Association Studies ; Orchidaceae/*genetics ; Plant Proteins/genetics ; Sequence Analysis, DNA ; Transcription Factors/genetics ; }, abstract = {BACKGROUND: Orchids are one of the most diversified angiosperms, but few genomic resources are available for these non-model plants. In addition to the ecological significance, Phalaenopsis has been considered as an economically important floriculture industry worldwide. We aimed to use massively parallel 454 pyrosequencing for a global characterization of the Phalaenopsis transcriptome.

RESULTS: To maximize sequence diversity, we pooled RNA from 10 samples of different tissues, various developmental stages, and biotic- or abiotic-stressed plants. We obtained 206,960 expressed sequence tags (ESTs) with an average read length of 228 bp. These reads were assembled into 8,233 contigs and 34,630 singletons. The unigenes were searched against the NCBI non-redundant (NR) protein database. Based on sequence similarity with known proteins, these analyses identified 22,234 different genes (E-value cutoff, e-7). Assembled sequences were annotated with Gene Ontology, Gene Family and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. Among these annotations, over 780 unigenes encoding putative transcription factors were identified.

CONCLUSION: Pyrosequencing was effective in identifying a large set of unigenes from Phalaenopsis. The informative EST dataset we developed constitutes a much-needed resource for discovery of genes involved in various biological processes in Phalaenopsis and other orchid species. These transcribed sequences will narrow the gap between study of model organisms with many genomic resources and species that are important for ecological and evolutionary studies.}, } @article {pmid21744152, year = {2011}, author = {Dikou, A and Papapanagiotou, E and Troumbis, A}, title = {Integrating landscape ecology and geoinformatics to decipher landscape dynamics for regional planning.}, journal = {Environmental management}, volume = {48}, number = {3}, pages = {523-538}, pmid = {21744152}, issn = {1432-1009}, mesh = {Agriculture/*methods ; Conservation of Natural Resources/*methods ; *Ecosystem ; Environmental Monitoring/*methods/statistics & numerical data ; *Geographic Information Systems ; Greece ; Humans ; Multivariate Analysis ; Population Density ; Seawater/analysis ; Urbanization ; Water Supply/analysis ; }, abstract = {We used remote sensing and GIS in conjunction with multivariate statistical methods to: (i) quantify landscape composition (land cover types) and configuration (patch density, diversity, fractal dimension, contagion) for five coastal watersheds of Kalloni gulf, Lesvos Island, Greece, in 1945, 1960, 1971, 1990 and 2002/2003, (ii) evaluate the relative importance of physical (slope, geologic substrate, stream order) and human (road network, population density) variables on landscape composition and configuration, and (iii) characterize processes that led to land cover changes through land cover transitions between these five successive periods in time. Distributions of land cover types did not differ among the five time periods at the five watersheds studied because the largest cumulative changes between 1945 and 2002/2003 did not take place at dominant land cover types. Landscape composition related primarily to the physical attributes of the landscape. Nevertheless, increase in population density and the road network were found to increase heterogeneity of the landscape mosaic (patchiness), complexity of patch shape (fractal dimension), and patch disaggregation (contagion). Increase in road network was also found to increase landscape diversity due to the creation of new patches. The main processes involved in land cover changes were plough-land abandonment and ecological succession. Landscape dynamics during the last 50 years corroborate the ecotouristic-agrotouristic model for regional development to reverse trends in agricultural land abandonment and human population decline and when combined with hypothetical regulatory approaches could predict how this landscape could develop in the future, thus, providing a valuable tool to regional planning.}, } @article {pmid21742924, year = {2011}, author = {Constant, P and Chowdhury, SP and Hesse, L and Pratscher, J and Conrad, R}, title = {Genome data mining and soil survey for the novel group 5 [NiFe]-hydrogenase to explore the diversity and ecological importance of presumptive high-affinity H(2)-oxidizing bacteria.}, journal = {Applied and environmental microbiology}, volume = {77}, number = {17}, pages = {6027-6035}, pmid = {21742924}, issn = {1098-5336}, mesh = {Bacteria/*classification/*enzymology/genetics/metabolism ; *Biodiversity ; Computational Biology ; *Genetic Variation ; Hydrogen/*metabolism ; Hydrogenase/*genetics ; Metagenome ; Oxidation-Reduction ; *Soil Microbiology ; }, abstract = {Streptomyces soil isolates exhibiting the unique ability to oxidize atmospheric H(2) possess genes specifying a putative high-affinity [NiFe]-hydrogenase. This study was undertaken to explore the taxonomic diversity and the ecological importance of this novel functional group. We propose to designate the genes encoding the small and large subunits of the putative high-affinity hydrogenase hhyS and hhyL, respectively. Genome data mining revealed that the hhyL gene is unevenly distributed in the phyla Actinobacteria, Proteobacteria, Chloroflexi, and Acidobacteria. The hhyL gene sequences comprised a phylogenetically distinct group, namely, the group 5 [NiFe]-hydrogenase genes. The presumptive high-affinity H(2)-oxidizing bacteria constituting group 5 were shown to possess a hydrogenase gene cluster, including the genes encoding auxiliary and structural components of the enzyme and four additional open reading frames (ORFs) of unknown function. A soil survey confirmed that both high-affinity H(2) oxidation activity and the hhyL gene are ubiquitous. A quantitative PCR assay revealed that soil contained 10(6) to 10(8) hhyL gene copies g (dry weight)(-1). Assuming one hhyL gene copy per genome, the abundance of presumptive high-affinity H(2)-oxidizing bacteria was higher than the maximal population size for which maintenance energy requirements would be fully supplied through the H(2) oxidation activity measured in soil. Our data indicate that the abundance of the hhyL gene should not be taken as a reliable proxy for the uptake of atmospheric H(2) by soil, because high-affinity H(2) oxidation is a facultatively mixotrophic metabolism, and microorganisms harboring a nonfunctional group 5 [NiFe]-hydrogenase may occur.}, } @article {pmid21740769, year = {2011}, author = {Sun, L and Shao, Q and Wang, ZQ and Kang, DM and Li, SW and Li, XG and Xue, FZ and Wang, JZ}, title = {Spatial structure of rodent populations and infection patterns of hantavirus in seven villages of Shandong Province from February 2006 to January 2007.}, journal = {Chinese medical journal}, volume = {124}, number = {11}, pages = {1639-1646}, pmid = {21740769}, issn = {2542-5641}, mesh = {Animals ; Geographic Information Systems ; Orthohantavirus ; Hemorrhagic Fever with Renal Syndrome/*epidemiology/*virology ; Humans ; Rats ; Rodentia/*virology ; }, abstract = {BACKGROUND: Hemorrhagic fever with renal syndrome (HFRS) is endemic in Junan county, Shandong Province, China. We conducted geographic information system (GIS)-based spatial analysis with the objective of estimating the spatial distribution of rodent populations and their hantavirus infection patterns, to describe the spatial relationships of hantavirus strains in small ecological areas and to identify key areas in endemic areas of HFRS for future public health planning and resource allocation.

METHODS: Rodent sampling was conducted in seven villages in Junan county from February 2006 to January 2007 using field epidemiological surveillance. Dynamics of hantavirus infection and population densities in rodents were investigated. Spatial statistical techniques including Ripley' L index and nearest neighbour hierarchical (NNH) clustering analysis were conducted to reveal the spatial structure of rodent populations in seven villages. Phylogenetic analysis and two-dimensional minimal spanning tree (2-D MST) models were employed to describe the spatial relationship of hantavirus strains.

RESULTS: Data showed that Mus musculus was the most common species in our study area, followed by Rattus norvegicus. Ripley's L index and NNH analysis showed that the spatial distribution of all captured rodents, Mus musculus and Rattus norvegicus in seven villages were clustered and there were hotspot areas of rodent distribution. The branches of 2-D MSTs had similar topologies to those of corresponding phylogenetic trees, and hantavirus strains exhibited obvious connective traces in seven villages.

CONCLUSIONS: These results contribute to the understanding of the spatial distribution of rodent populations and hantavirus infection patterns in small areas, and identify priority areas within the epidemic areas for the development of a better prevention strategy against hemorrhagic fever with renal syndrome in a small ecological area.}, } @article {pmid21737436, year = {2011}, author = {Eastman, JM and Paine, CE and Hardy, OJ}, title = {spacodiR: structuring of phylogenetic diversity in ecological communities.}, journal = {Bioinformatics (Oxford, England)}, volume = {27}, number = {17}, pages = {2437-2438}, doi = {10.1093/bioinformatics/btr403}, pmid = {21737436}, issn = {1367-4811}, mesh = {*Biota ; Data Interpretation, Statistical ; *Phylogeny ; *Software ; }, abstract = {MOTIVATION: spacodiR is a cross-platform package, written for the R environment, for studying partitioning of diversity among natural communities in space and time. Complementing and extending existing software, spacodiR allows for hypothesis testing and parameter estimation in studying spatial structuring of species-, phylogenetic- and trait diversities.

AVAILABILITY: Integrated with other software in the R environment and with well documented and demonstrated functions, spacodiR is an open-source package and available at http://cran.r-project.org.

CONTACT: jonathan.eastman@gmail.com; ohardy@ulb.ac.be.}, } @article {pmid21736740, year = {2011}, author = {McAlexander, KM and Mama, SK and Medina, A and O'Connor, DP and Lee, RE}, title = {The concordance of directly and indirectly measured built environment attributes and physical activity adoption.}, journal = {The international journal of behavioral nutrition and physical activity}, volume = {8}, number = {}, pages = {72}, pmid = {21736740}, issn = {1479-5868}, support = {R01 CA109403/CA/NCI NIH HHS/United States ; }, mesh = {Black or African American ; Cross-Sectional Studies ; *Environment Design ; Female ; Geographic Information Systems ; Health Behavior ; Hispanic or Latino ; Humans ; Interviews as Topic ; Longitudinal Studies ; Obesity/epidemiology ; *Residence Characteristics ; Self Report ; Socioeconomic Factors ; Surveys and Questionnaires ; *Walking ; }, abstract = {BACKGROUND: Physical activity (PA) adoption is essential for obesity prevention and control, yet ethnic minority women report lower levels of PA and are at higher risk for obesity and its comorbidities compared to Caucasians. Epidemiological studies and ecologic models of health behavior suggest that built environmental factors are associated with health behaviors like PA, but few studies have examined the association between built environment attribute concordance and PA, and no known studies have examined attribute concordance and PA adoption.

PURPOSE: The purpose of this study was to associate the degree of concordance between directly and indirectly measured built environment attributes with changes in PA over time among African American and Hispanic Latina women participating in a PA intervention.

METHOD: Women (N = 410) completed measures of PA at Time 1 (T1) and Time 2 (T2); environmental data collected at T1 were used to compute concordance between directly and indirectly measured built environment attributes. The association between changes in PA and the degree of concordance between each directly and indirectly measured environmental attribute was assessed using repeated measures analyses.

RESULTS: There were no significant associations between built environment attribute concordance values and change in self-reported or objectively measured PA. Self-reported PA significantly increased over time (F(1,184) = 7.82, p = .006), but this increase did not vary by ethnicity or any built environment attribute concordance variable.

CONCLUSIONS: Built environment attribute concordance may not be associated with PA changes over time among minority women. In an effort to promote PA, investigators should clarify specific built environment attributes that are important for PA adoption and whether accurate perceptions of these attributes are necessary, particularly among the vulnerable population of minority women.}, } @article {pmid21736485, year = {2011}, author = {Cherry, NA and Maggi, RG and Rossmeisl, JH and Hegarty, BC and Breitschwerdt, EB}, title = {Ecological diversity of Bartonella species infection among dogs and their owner in Virginia.}, journal = {Vector borne and zoonotic diseases (Larchmont, N.Y.)}, volume = {11}, number = {11}, pages = {1425-1432}, doi = {10.1089/vbz.2010.0201}, pmid = {21736485}, issn = {1557-7759}, mesh = {Animal Husbandry ; Animals ; Bartonella/*genetics/isolation & purification ; Bartonella Infections/diagnosis/*microbiology/transmission ; Breeding ; Databases, Nucleic Acid ; Dog Diseases/diagnosis/*microbiology/transmission ; Dogs ; Ecology ; Female ; Genotype ; Humans ; Polymerase Chain Reaction ; Virginia ; }, abstract = {Bartonella species comprise a genus of gram-negative, fastidious, intracellular bacteria that have been implicated in association with an increasing spectrum of disease manifestations in dogs and human patients. In this study, chronic canine and human disease, for which causation was not diagnostically defined, were reported by the breeder of a kennel of Doberman pinschers. In addition to other diagnostic tests, serology, polymerase chain reaction, and enrichment blood culture were used to assess the prevalence of Bartonella sp. infection in the dogs and their owner. From five dogs, Bartonella vinsonii subsp. berkhoffii genotype I, multiple Bartonella henselae strains, and a species most similar to Candidatus B. volans, a rodent-associated Bartonella sp., were amplified and sequenced from biopsy tissues, cerebrospinal fluid, or blood enrichment cultures. The owner was bacteremic with B. vinsonii subsp. berkhoffii genotype I, the same subsp. and genotype detected in one of her dogs. These results further emphasize the ecological complexity of Bartonella sp. transmission in nature.}, } @article {pmid21731546, year = {2011}, author = {Hu, GP and Yuan, J and Sun, L and She, ZG and Wu, JH and Lan, XJ and Zhu, X and Lin, YC and Chen, SP}, title = {Statistical research on marine natural products based on data obtained between 1985 and 2008.}, journal = {Marine drugs}, volume = {9}, number = {4}, pages = {514-525}, pmid = {21731546}, issn = {1660-3397}, mesh = {Animals ; Aquatic Organisms/metabolism ; Biological Products/chemistry/*isolation & purification/pharmacology ; Databases, Factual ; *Drug Discovery ; Invertebrates/metabolism ; *Marine Biology ; Phytoplankton/metabolism ; }, abstract = {Since the 1960s, more than 20,000 compounds were discovered from marine organisms. In this paper we performed a quantitative analysis for the novel marine natural products reported between 1985 and 2008. The data was extracted mainly from the reviews of Faulkner and Blunt [1-26]. The organisms producing these marine natural products are divided into three major biological classes: marine microorganisms (including phytoplankton), marine algae and marine invertebrate. The marine natural products are divided into seven classes based on their chemical structure: terpenoids, steroids (including steroidal saponins), alkaloids, ethers (including ketals), phenols (including quinones), strigolactones, and peptides. The distribution and the temporal trend of these classes (biological classes and chemical structure classes) were investigated. We hope this article provides a comprehensive perspective on the research of marine natural products.}, } @article {pmid21730340, year = {2011}, author = {Simon, MF and Grether, R and de Queiroz, LP and Särkinen, TE and Dutra, VF and Hughes, CE}, title = {The evolutionary history of Mimosa (Leguminosae): toward a phylogeny of the sensitive plants.}, journal = {American journal of botany}, volume = {98}, number = {7}, pages = {1201-1221}, doi = {10.3732/ajb.1000520}, pmid = {21730340}, issn = {1537-2197}, mesh = {Adaptation, Physiological/*genetics ; Base Sequence ; DNA, Plant/genetics ; Databases, Genetic ; Geography ; Mimosa/anatomy & histology/classification/*genetics/*physiology ; *Phylogeny ; Quantitative Trait, Heritable ; Radiometric Dating ; }, abstract = {PREMISE OF THE STUDY: Large genera provide remarkable opportunities to investigate patterns of morphological evolution and historical biogeography in plants. A molecular phylogeny of the species-rich and morphologically and ecologically diverse genus Mimosa was generated to evaluate its infrageneric classification, reconstruct the evolution of a set of morphological characters, and establish the relationships of Old World species to the rest of the genus.

METHODS: We used trnD-trnT plastid sequences for 259 species of Mimosa (ca. 50% of the total) to reconstruct the phylogeny of the genus. Six morphological characters (petiolar nectary, inflorescence type, number of stamens, number of petals, pollen type, and seismonasty) were optimized onto the molecular tree.

KEY RESULTS: Mimosa was recovered as a monophyletic clade nested within the Piptadenia group and includes the former members of Schrankia, corroborating transfer of that genus to Mimosa. Although we found good support for several infrageneric groups, only one section (Mimadenia) was recovered as monophyletic. All but one of the morphological characters analyzed showed high levels of homoplasy. High levels of geographic structure were found, with species from the same area tending to group together in the phylogeny. Old World species of Mimosa form a monophyletic clade deeply nested within New World groups, indicating recent (6-10 Ma) long-distance dispersal.

CONCLUSIONS: Although based on a single plastid region, our results establish a preliminary phylogenetic framework for Mimosa that can be used to infer patterns of morphological evolution and relationships and which provides pointers toward a revised infrageneric classification.}, } @article {pmid21728289, year = {2011}, author = {Motohashi, K and Inaba, K and Fuse, S and Doi, T and Izumikawa, M and Khan, ST and Takagi, M and Takahashi, T and Shin-ya, K}, title = {JBIR-56 and JBIR-57, 2(1H)-pyrazinones from a marine sponge-derived Streptomyces sp. SpD081030SC-03.}, journal = {Journal of natural products}, volume = {74}, number = {7}, pages = {1630-1635}, doi = {10.1021/np200386c}, pmid = {21728289}, issn = {1520-6025}, mesh = {Animals ; Marine Biology ; Molecular Structure ; Nuclear Magnetic Resonance, Biomolecular ; Oligopeptides/chemistry/*isolation & purification ; Porifera/*microbiology ; Pyrazines/chemistry/*isolation & purification ; Streptomyces/*chemistry ; }, abstract = {Strain SpD081030SC-03, representing a novel species of Streptomyces, was isolated from a marine sponge. Two 3,5,6-trisubstituted 2(1H)-pyrazinones, JBIR-56 (1) and JBIR-57 (2), were isolated from a culture of SpD081030SC-03. The planar structures of 1 and 2 were assigned on the basis of extensive NMR and MS analyses. In addition, analyses of the methylated derivative of 1 confirmed a 3,5,6-trisubstituted 2(1H)-pyrazinone moiety. The absolute configurations of the amino acid residues were determined by application of Marfey's method. Because 1 did not appear to comprise the normal connection of amino acid units, we confirmed its structure by the total synthesis of 1. Biosynthetically, 1 consists of a unique skeleton connected to the peptide chain at C-5 of the pyrazinone ring.}, } @article {pmid21728180, year = {2011}, author = {Xia, B and Tai, ZF and Gu, YC and Li, BJ and Ding, LS and Zhou, Y}, title = {MyMolDB: a micromolecular database solution with open source and free components.}, journal = {Journal of computational chemistry}, volume = {32}, number = {13}, pages = {2942-2948}, doi = {10.1002/jcc.21874}, pmid = {21728180}, issn = {1096-987X}, mesh = {*Database Management Systems/economics/trends ; Databases, Factual/economics/trends ; Molecular Structure ; Search Engine/economics/trends ; Time Factors ; User-Computer Interface ; }, abstract = {BACKGROUND: To manage chemical structures in small laboratories is one of the important daily tasks. Few solutions are available on the internet, and most of them are closed source applications. The open-source applications typically have limited capability and basic cheminformatics functionalities. In this article, we describe an open-source solution to manage chemicals in research groups based on open source and free components. It has a user-friendly interface with the functions of chemical handling and intensive searching.

RESULTS: MyMolDB is a micromolecular database solution that supports exact, substructure, similarity, and combined searching. This solution is mainly implemented using scripting language Python with a web-based interface for compound management and searching. Almost all the searches are in essence done with pure SQL on the database by using the high performance of the database engine. Thus, impressive searching speed has been archived in large data sets for no external Central Processing Unit (CPU) consuming languages were involved in the key procedure of the searching.

AVAILABILITY: MyMolDB is an open-source software and can be modified and/or redistributed under GNU General Public License version 3 published by the Free Software Foundation (Free Software Foundation Inc. The GNU General Public License, Version 3, 2007. Available at: http://www.gnu.org/licenses/gpl.html). The software itself can be found at http://code.google.com/p/mymoldb/.}, } @article {pmid21723570, year = {2011}, author = {Bennett, S and Roca, G and Romero, J and Alcoverro, T}, title = {Ecological status of seagrass ecosystems: An uncertainty analysis of the meadow classification based on the Posidonia oceanica multivariate index (POMI).}, journal = {Marine pollution bulletin}, volume = {62}, number = {8}, pages = {1616-1621}, doi = {10.1016/j.marpolbul.2011.06.016}, pmid = {21723570}, issn = {1879-3363}, mesh = {Alismatales/classification/*growth & development/metabolism ; *Ecosystem ; Environmental Monitoring/legislation & jurisprudence/*methods/statistics & numerical data ; European Union ; Information Systems ; Multivariate Analysis ; Time Factors ; Uncertainty ; Water Pollutants/*analysis/metabolism/toxicity ; Zosteraceae/classification/*growth & development/metabolism ; }, abstract = {Quantifying the uncertainty associated with monitoring protocols is essential to prevent the misclassification of ecological status and to improve sampling design. We assessed the Posidonia oceanica multivariate index (POMI) bio-monitoring program for its robustness in classifying the ecological status of coastal waters within the Water Framework Directive. We used a 7-year data set covering 30 sites along 500 km of the Catalonian coastline to examine which version of POMI (14 or 9 metrics) maximises precision in classifying the ecological status of meadows. Five factors (zones within a site, sites within a water body, depth, years and surveyors) that potentially generate classification uncertainty were examined in detail. Of these, depth was a major source of uncertainty, while all the remaining spatial and temporal factors displayed low variability. POMI 9 matched POMI 14 in all factors, and could effectively replace it in future monitoring programs.}, } @article {pmid21723426, year = {2011}, author = {D'Alessandro, A and D'Amici, GM and Timperio, AM and Merendino, N and Zolla, L}, title = {Docosohaexanoic acid-supplemented PACA44 cell lines and over-activation of Krebs cycle: an integrated proteomic, metabolomic and interactomic overview.}, journal = {Journal of proteomics}, volume = {74}, number = {10}, pages = {2138-2158}, doi = {10.1016/j.jprot.2011.06.006}, pmid = {21723426}, issn = {1876-7737}, mesh = {Adenocarcinoma/*metabolism ; Apoptosis/*drug effects ; Cell Line, Tumor ; Citric Acid Cycle/*drug effects ; Computational Biology ; Docosahexaenoic Acids/*pharmacology ; Glutathione/*metabolism ; Glutathione Disulfide/*metabolism ; Humans ; Metabolomics ; Pancreatic Neoplasms/*metabolism ; Proteomics ; }, abstract = {Recent investigations have pointed out the ability of fatty acids, in particular of docosohaexanoic acid (DHA), to induce growth inhibition and apoptosis in the human PaCa-44 pancreatic cancer cell line through a series of mechanisms which has been hypothesized to mimic apoptosis. While preliminary evidences indicated the involvement of lipid-targeting oxidative stress in DHA-induced apoptotic processes, mainly through the alteration of the glutathione (GSH) homeostasis and oxidized-glutathione (GSSG) turn-over through their extra-cellular extrusion, no further molecular data have been hitherto accumulated. To this end, we hereby propose simultaneous protein-targeting and metabolite-oriented analyses, which have been integrated through the auxilium of in silico elaboration of those protein-protein interaction pathways and enrichment of biological/molecular functions. To determine the most suitable time window for the early onset of the DHA-triggered apoptosis phenomena we performed flow cytometry-based apoptotic assessment at 24, 48 and 72 h. Results indicated that the focus of apoptosis onset ranged from 48 to 72 h. From these analyses it emerges that the metabolism of control human PaCa-44 pancreatic cancer cell line mainly leans on glycolytic pathways, while it is promptly switched to Kreb's cycle activation (overexpression of Kreb's cycle enzymes in DHA-treated cells against controls) and modulation of the GSH homeostasis through an increased production of GSSG-reducing NADPH coenzyme via the shift of the glycolytic energy flux towards the pentose phosphate pathway. Interestingly, it also emerges a role for structural protein alteration in DHA-treated cells, which might be linked to cytoskeletal alterations occurring during apoptosis.}, } @article {pmid21715042, year = {2011}, author = {Croft, DP and Madden, JR and Franks, DW and James, R}, title = {Hypothesis testing in animal social networks.}, journal = {Trends in ecology & evolution}, volume = {26}, number = {10}, pages = {502-507}, doi = {10.1016/j.tree.2011.05.012}, pmid = {21715042}, issn = {1872-8383}, mesh = {Animals ; *Behavior, Animal ; Data Interpretation, Statistical ; Ecology ; *Research Design ; *Social Behavior ; Sociobiology ; }, abstract = {Behavioural ecologists are increasingly using social network analysis to describe the social organisation of animal populations and to test hypotheses. However, the statistical analysis of network data presents a number of challenges. In particular the non-independent nature of the data violates the assumptions of many common statistical approaches. In our opinion there is currently confusion and uncertainty amongst behavioural ecologists concerning the potential pitfalls when hypotheses testing using social network data. Here we review what we consider to be key considerations associated with the analysis of animal social networks and provide a practical guide to the use of null models based on randomisation to control for structure and non-independence in the data.}, } @article {pmid21714939, year = {2011}, author = {Beiko, RG}, title = {Telling the whole story in a 10,000-genome world.}, journal = {Biology direct}, volume = {6}, number = {}, pages = {34}, pmid = {21714939}, issn = {1745-6150}, mesh = {Algorithms ; Archaea/classification/genetics ; Bacteria/classification/*genetics ; Bacterial Proteins/chemistry/genetics ; *Biological Evolution ; Computer Graphics ; Databases, Protein ; Gene Transfer, Horizontal ; Genomics/methods ; Metagenome ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Alignment ; Sequence Homology, Amino Acid ; }, abstract = {BACKGROUND: Genome sequencing has revolutionized our view of the relationships among genomes, particularly in revealing the confounding effects of lateral genetic transfer (LGT). Phylogenomic techniques have been used to construct purported trees of microbial life. Although such trees are easily interpreted and allow the use of a subset of genomes as "proxies" for the full set, LGT and other phenomena impact the positioning of different groups in genome trees, confounding and potentially invalidating attempts to construct a phylogeny-based taxonomy of microorganisms. Network and graph approaches can reveal complex sets of relationships, but applying these techniques to large data sets is a significant challenge. Notwithstanding the question of what exactly it might represent, generating and interpreting a Tree or Network of All Genomes will only be feasible if current algorithms can be improved upon.

RESULTS: Complex relationships among even the most-similar genomes demonstrate that proxy-based approaches to simplifying large sets of genomes are not alone sufficient to solve the analysis problem. A phylogenomic analysis of 1173 sequenced bacterial and archaeal genomes generated phylogenetic trees for 159,905 distinct homologous gene sets. The relationships inferred from this set can be heavily dependent on the inclusion of other taxa: for example, phyla such as Spirochaetes, Proteobacteria and Firmicutes are recovered as cohesive groups or split depending on the presence of other specific lineages. Furthermore, named groups such as Acidithiobacillus, Coprothermobacter and Brachyspira show a multitude of affiliations that are more consistent with their ecology than with small subunit ribosomal DNA-based taxonomy. Network and graph representations can illustrate the multitude of conflicting affinities, but all methods impose constraints on the input data and create challenges of construction and interpretation.

CONCLUSIONS: These complex relationships highlight the need for an inclusive approach to genomic data, and current methods with minor alterations will likely scale to allow the analysis of data sets with 10,000 or more genomes. The main challenges lie in the visualization and interpretation of genomic relationships, and the redefinition of microbial taxonomy when subsets of genomic data are so evidently in conflict with one another, and with the "canonical" molecular taxonomy.}, } @article {pmid21714315, year = {2011}, author = {Moore, S and Kestens, Y}, title = {Neighbourhood environmental correlates of perceived park proximity in Montreal.}, journal = {Canadian journal of public health = Revue canadienne de sante publique}, volume = {102}, number = {3}, pages = {176-179}, pmid = {21714315}, issn = {0008-4263}, mesh = {Adult ; *City Planning ; Cross-Sectional Studies ; *Environment Design ; *Exercise ; Female ; Geographic Information Systems ; *Health Promotion ; Humans ; Logistic Models ; Male ; Middle Aged ; Multivariate Analysis ; Quebec ; Residence Characteristics ; Socioeconomic Factors ; *Spatial Behavior ; Urban Health ; }, abstract = {OBJECTIVES: Perceived proximity to recreational settings has been shown to be associated with increased physical activity levels. We examined individual socio-demographic and environmental correlates of perceived park proximity in Montreal to assess targets for ecological interventions to improve physical activity.

METHODS: A stratified clustered sampling design was used to collect data on perceived park proximity from 864 adults residing in 300 Montreal census tracts. Perceived park proximity was measured by asking participants if they perceived a park as within walking distance of their home. Objective measures of park proximity and park density were constructed using geographic information systems (GIS). Canada Census data provided information on census tract population density and median income levels. Multilevel logistic regression was used to examine the likelihood of not perceiving a park as proximate.

RESULTS: Older adults were more likely to perceive a park as not proximate to their home (OR: 1.04; 95% CI: 1.02-1.07). Perceived park proximity varied across Montreal neighbourhoods with an interclass correlation coefficient of 16.10%. Objective distance to the closest park (OR: 1.45; 95% CI: 1.10-1.92) was associated with adults' subjective perceptions of park proximity. Residents of neighbourhoods with higher population density (OR: 0.92; 95% CI: 0.87-0.97) and higher average income (OR: 0.45; 95% CI: 0.24-0.87) were less likely to view a park as outside walking distance to their residence.

CONCLUSION: Regardless of the actual distance to the park, neighbourhood environmental factors are associated with people's perceptions of having a park within walking distance of their homes.}, } @article {pmid21713030, year = {2011}, author = {Field, D and Amaral-Zettler, L and Cochrane, G and Cole, JR and Dawyndt, P and Garrity, GM and Gilbert, J and Glöckner, FO and Hirschman, L and Karsch-Mizrachi, I and Klenk, HP and Knight, R and Kottmann, R and Kyrpides, N and Meyer, F and San Gil, I and Sansone, SA and Schriml, LM and Sterk, P and Tatusova, T and Ussery, DW and White, O and Wooley, J}, title = {The Genomic Standards Consortium.}, journal = {PLoS biology}, volume = {9}, number = {6}, pages = {e1001088}, pmid = {21713030}, issn = {1545-7885}, mesh = {*Databases, Genetic ; Genomics/*standards ; *International Cooperation ; Metagenome ; }, abstract = {A vast and rich body of information has grown up as a result of the world's enthusiasm for 'omics technologies. Finding ways to describe and make available this information that maximise its usefulness has become a major effort across the 'omics world. At the heart of this effort is the Genomic Standards Consortium (GSC), an open-membership organization that drives community-based standardization activities, Here we provide a short history of the GSC, provide an overview of its range of current activities, and make a call for the scientific community to join forces to improve the quality and quantity of contextual information about our public collections of genomes, metagenomes, and marker gene sequences.}, } @article {pmid21712480, year = {2011}, author = {Garamszegi, LZ and Møller, AP}, title = {Nonrandom variation in within-species sample size and missing data in phylogenetic comparative studies.}, journal = {Systematic biology}, volume = {60}, number = {6}, pages = {876-880}, doi = {10.1093/sysbio/syr060}, pmid = {21712480}, issn = {1076-836X}, mesh = {Classification/*methods ; *Data Interpretation, Statistical ; Genetic Variation ; Phylogeny ; }, } @article {pmid21709388, year = {2011}, author = {Fazzo, L and De Santis, M and Mitis, F and Benedetti, M and Martuzzi, M and Comba, P and Fusco, M}, title = {Ecological studies of cancer incidence in an area interested by dumping waste sites in Campania (Italy).}, journal = {Annali dell'Istituto superiore di sanita}, volume = {47}, number = {2}, pages = {181-191}, doi = {10.4415/ANN_11_02_10}, pmid = {21709388}, issn = {2384-8553}, mesh = {Bayes Theorem ; Cluster Analysis ; Databases, Factual ; Environmental Exposure ; Female ; Hazardous Waste/*statistics & numerical data ; Humans ; Incidence ; Italy/epidemiology ; Liver Neoplasms/epidemiology ; Male ; Neoplasms/*epidemiology ; Refuse Disposal ; Registries ; Regression Analysis ; Urban Population ; }, abstract = {Cancer incidence was investigated in an area which has been affected by the illegal practices of dumping hazardous waste and setting fire to mismanaged waste. For the 35 municipalities of this area that are served by a Cancer Registry, municipal standardized incidence ratios (SIR) and hierarchical Bayesian estimators (BIR) were computed. Moreover, municipal spatial clustering and a Poisson regression by municipality index of waste-related exposure were performed for 10 cancer types. Increased municipality SIRs were found for some cancer types. The BIRs confirmed the increases for liver cancer in two municipalities. Statistically significant clusters were detected for liver, lung, leukaemia and soft tissue sarcomas. In the regression analysis, testis cancer showed significant trend with the index of waste-related exposure (RR = 1.18).}, } @article {pmid21707958, year = {2012}, author = {Canbäck, B and André, C and Galindo, J and Johannesson, K and Johansson, T and Panova, M and Tunlid, A and Butlin, R}, title = {The Littorina sequence database (LSD)--an online resource for genomic data.}, journal = {Molecular ecology resources}, volume = {12}, number = {1}, pages = {142-148}, doi = {10.1111/j.1755-0998.2011.03042.x}, pmid = {21707958}, issn = {1755-0998}, mesh = {Animals ; *Databases, Genetic ; Gastropoda/*genetics ; Genetic Markers ; Genomics/*instrumentation ; Internet ; Online Systems ; User-Computer Interface ; }, abstract = {We present an interactive, searchable expressed sequence tag database for the periwinkle snail Littorina saxatilis, an upcoming model species in evolutionary biology. The database is the result of a hybrid assembly between Sanger and 454 sequences, 1290 and 147,491 sequences respectively. Normalized and non-normalized cDNA was obtained from different ecotypes of L. saxatilis collected in the UK and Sweden. The Littorina sequence database (LSD) contains 26,537 different contigs, of which 2453 showed similarity with annotated proteins in UniProt. Querying the LSD permits the selection of the taxonomic origin of blast hits for each contig, and the search can be restricted to particular taxonomic groups. The database allows access to UniProt annotations, blast output, protein family domains (PFAM) and Gene Ontology. The database will allow users to search for genetic markers and identifying candidate genes or genes for expression analyses. It is open for additional deposition of sequence information for L. saxatilis and other species of the genus Littorina. The LSD is available at http://mbio-serv2.mbioekol.lu.se/Littorina/.}, } @article {pmid21707472, year = {2012}, author = {Royer, A and Grosselin, A and Bellot, C and Pellet, J and Billard, S and Lang, F and Brouillet, D and Massoubre, C}, title = {Is there any impact of cognitive remediation on an ecological test in schizophrenia?.}, journal = {Cognitive neuropsychiatry}, volume = {17}, number = {1}, pages = {19-35}, doi = {10.1080/13546805.2011.564512}, pmid = {21707472}, issn = {1464-0619}, mesh = {Adult ; Antipsychotic Agents/therapeutic use ; Attention/physiology ; Cognition/*physiology ; Cognition Disorders/etiology/psychology ; Cognitive Behavioral Therapy/*methods ; Diagnostic and Statistical Manual of Mental Disorders ; Educational Status ; Executive Function ; Female ; Humans ; Intelligence Tests ; Learning/physiology ; Male ; Neuropsychological Tests ; Schizophrenia/*diagnosis/rehabilitation/*therapy ; *Schizophrenic Psychology ; Social Behavior ; Therapy, Computer-Assisted ; }, abstract = {INTRODUCTION: Cognitive deficits are commonly reported in schizophrenia and have a significant impact on the daily life of patients and on their social and work inclusion. Cognitive remediation therapies (CRT) may enhance the capabilities of schizophrenia patients. Although social and work integration is the ultimate goal of CRT, previous studies have failed to carry out a detailed assessment of the effects on everyday life.

METHODS: Fifty-nine schizophrenia patients were randomised into two groups (remediation or usual treatment) to test the effects of a new remediation programme, which included both rehearsal and strategy learning, on cognitive functions. An ecological test was used to evaluate its transfer to daily living skills.

RESULTS: Cognitive improvements are revealed in CRT patients, mainly in memory and executive functions. Patients showing some deficiencies to perform the ecological test had better scores after the CRT. Moreover, they significantly improve their social activity scores.

CONCLUSIONS: CRT would facilitate mental load monitoring by enhancing or reallocating cognitive resources, facilitating the patient's organisation and autonomy. The rehearsal learning approach improves the ability to carry out automatic operations that are less demanding in terms of cognitive resources, thereby increasing the resources available for acquisition and efficient use of strategies provided during the strategy learning approach.}, } @article {pmid21695036, year = {2011}, author = {Zhang, J and Wang, K and Chen, X and Zhu, W}, title = {Combining a fuzzy matter-element model with a geographic information system in eco-environmental sensitivity and distribution of land use planning.}, journal = {International journal of environmental research and public health}, volume = {8}, number = {4}, pages = {1206-1221}, doi = {10.3390/ijerph8041206}, pmid = {21695036}, issn = {1660-4601}, mesh = {Atmosphere ; Biodiversity ; China ; *Conservation of Natural Resources ; *Environment ; Fuzzy Logic ; Geographic Information Systems ; *Geography ; Soil ; Water ; }, abstract = {Sustainable ecological and environmental development is the basis of regional development. The sensitivity classification of the ecological environment is the premise of its spatial distribution for land use planning. In this paper, a fuzzy matter-element model and factor-overlay method were employed to analyze the ecological sensitivity in Yicheng City. Four ecological indicators, including soil condition,, water condition,, atmospheric conditions and biodiversity were used to classify the ecological sensitivity. The results were categorized into five ranks: insensitive, slightly sensitive, moderately sensitive, highly sensitive and extremely sensitive zones. The spatial distribution map of environmental sensitivity for land use planning was obtained using GIS (Geographical Information System) techniques. The results illustrated that the extremely sensitive and highly sensitive areas accounted for 14.40% and 30.12% of the total area, respectively, while the moderately sensitive and slightly sensitive areas are 25.99% and 29.49%, respectively. The results provide the theoretical foundation for land use planning by categorizing all kinds of land types in Yicheng City.}, } @article {pmid21695028, year = {2011}, author = {Sun, S and Yan, X and Cui, P and Feng, J}, title = {A four-step method for optimising the normal water level of reservoirs based on a mathematical programming model--a case study for the Songyuan backwater dam in Jilin Province, China.}, journal = {International journal of environmental research and public health}, volume = {8}, number = {4}, pages = {1049-1060}, pmid = {21695028}, issn = {1660-4601}, mesh = {China ; Conservation of Natural Resources ; *Decision Support Techniques ; Engineering ; Principal Component Analysis ; *Water Supply ; }, abstract = {Determination of the optimal normal water level of reservoirs (RNWL) was investigated, incorporating environmental ecology as a primary consideration. RNWL constitutes a relatively significant eigenvalue of any water conservancy project. In the present study, a four-step method based on a mathematical programming model and suitable for RNWL decision making was developed and applied to the water conservancy project of the Songyuan backwater dam in China. System analysis, correlation analysis, significance testing, principal component analysis, sensitivity analysis, and system optimisation theory are used in the solution process. In this study, various factors that impact the economic viability, engineering characteristics, environmental and urban ecology are considered for holistic optimisation. The study shows that the proposed four-step method may provide a feasible quantitative form of support for RNWL decision making.}, } @article {pmid21689383, year = {2011}, author = {Cawthorn, DM and Steinman, HA and Witthuhn, RC}, title = {Establishment of a mitochondrial DNA sequence database for the identification of fish species commercially available in South Africa.}, journal = {Molecular ecology resources}, volume = {11}, number = {6}, pages = {979-991}, doi = {10.1111/j.1755-0998.2011.03039.x}, pmid = {21689383}, issn = {1755-0998}, mesh = {Animals ; Base Sequence ; Cluster Analysis ; *Commerce ; Conservation of Natural Resources/*methods ; DNA Primers/genetics ; DNA, Mitochondrial/*genetics ; *Databases, Genetic ; Fishes/classification/*genetics ; Models, Genetic ; Molecular Sequence Data ; *Phylogeny ; Sequence Analysis, DNA ; South Africa ; }, abstract = {The limitations intrinsic to morphology-based identification systems have created an urgent need for reliable genetic methods that enable the unequivocal recognition of fish species, particularly those that are prone to overexploitation and/or market substitution. The aim of this study was to develop a comprehensive reference library of DNA sequence data to allow the explicit identification of 53 commercially available fish species in South Africa, most of which were locally caught marine species. Sequences of approximately 655 base pairs were generated for all species from the cytochrome c oxidase I (COI) gene, the region widely adopted for DNA barcoding. Specimens of the genus Thunnus were examined in further detail, employing additional mitochondrial DNA control region sequencing. Cumulative analysis of the sequences from the COI region revealed mean conspecific, congeneric and confamilial Kimura 2-parameter distances of 0.10%, 4.58% and 15.43%, respectively. The results showed that the vast majority (98%) of fish species examined could be readily differentiated by their COI barcodes, but that supplementary control region sequencing was more useful for the discrimination of three Thunnus species. Additionally, the analysis of COI data raised the prospect that Thyrsites atun (snoek) could constitute a species pair. The present study has established the necessary genetic information to permit the unambiguous identification of 53 commonly marketed fish species in South Africa, the applications of which hold a plethora of benefits relating to ecology research, fisheries management and control of commercial practices.}, } @article {pmid21687975, year = {2012}, author = {Yang, H and Zhang, D and Wang, J and Wood, AJ and Zhang, Y}, title = {Molecular cloning of a stress-responsive aldehyde dehydrogenase gene ScALDH21 from the desiccation-tolerant moss Syntrichia caninervis and its responses to different stresses.}, journal = {Molecular biology reports}, volume = {39}, number = {3}, pages = {2645-2652}, pmid = {21687975}, issn = {1573-4978}, mesh = {Adaptation, Physiological/*genetics ; Aldehyde Dehydrogenase/*genetics/*metabolism ; Base Sequence ; Bryopsida/*enzymology ; Cloning, Molecular ; Computational Biology ; DNA Primers/genetics ; Dehydration/*genetics ; Desert Climate ; Electrophoresis, Polyacrylamide Gel ; Genetic Vectors/genetics ; Molecular Sequence Data ; Real-Time Polymerase Chain Reaction ; Sequence Analysis, DNA ; Stress, Physiological/*genetics ; }, abstract = {Aldehyde dehydrogenases (ALDHs) are key enzymes of abiotic stress-tolerance in a variety of organisms. The ALDH gene superfamily in eukaryotes has identified 22 protein families based upon sequence identity. ALDH21 is unique to mosses and represented by a single transcript gene in the desiccation-tolerant moss Tortula ruralis. We describe the cloning and characterization of an ALDH21 homologue from Syntrichia caninervis (ScALDH21), an extremely desiccation-tolerant moss found in deserts of Central Asia. The ScALDH21 cDNA is 1,452 bp and encodes a deduced polypeptide of 483 amino acids (53 kDa), approximately 97% identical to T. ruralis ALDH21 (TrALDH21A). The ScALDH21 gene was subcloned into pET26b(+) and expressed in Escherichia coli (Rosetta) to determine the peptides function in response to desiccation and salinity. Quantitative RT-PCR was used to analyze steady-state mRNA amounts in response to Abscisic acid (ABA) and desiccation. ScALDH21 transcript levels increased significantly in response to both desiccation and ABA. In the transgenic E. coli, ScALDH21 protein could be induced under the salinity and desiccation stress and was more abundant within salt-treated gametophores relative to control tissue. The data suggest that ScALDH21 participates in the stress-resistant pathways and plays an important role in response to desiccation and salinity stresses.}, } @article {pmid21686072, year = {2011}, author = {Langley, SA and Messina, JP}, title = {Embracing the Open-Source Movement for the Management of Spatial Data: A Case Study of African Trypanosomiasis in Kenya.}, journal = {Journal of map & geography libraries}, volume = {7}, number = {1}, pages = {87-113}, pmid = {21686072}, issn = {1542-0353}, support = {R21 GM084704/GM/NIGMS NIH HHS/United States ; R21 GM084704-04/GM/NIGMS NIH HHS/United States ; }, abstract = {The past decade has seen an explosion in the availability of spatial data not only for researchers, but the public alike. As the quantity of data increases, the ability to effectively navigate and understand the data becomes more challenging. Here we detail a conceptual model for a spatially explicit database management system that addresses the issues raised with the growing data management problem. We demonstrate utility with a case study in disease ecology: to develop a multi-scale predictive model of African Trypanosomiasis in Kenya. International collaborations and varying technical expertise necessitate a modular open-source software solution. Finally, we address three recurring problems with data management: scalability, reliability, and security.}, } @article {pmid21683421, year = {2011}, author = {Navas, JM and Telfer, TC and Ross, LG}, title = {Spatial modeling of environmental vulnerability of marine finfish aquaculture using GIS-based neuro-fuzzy techniques.}, journal = {Marine pollution bulletin}, volume = {62}, number = {8}, pages = {1786-1799}, doi = {10.1016/j.marpolbul.2011.05.019}, pmid = {21683421}, issn = {1879-3363}, mesh = {Environmental Monitoring/*methods/statistics & numerical data ; *Fisheries ; Fuzzy Logic ; *Geographic Information Systems ; Ireland ; Marine Biology/*methods ; *Models, Biological ; Nitrogen/analysis ; }, abstract = {Combining GIS with neuro-fuzzy modeling has the advantage that expert scientific knowledge in coastal aquaculture activities can be incorporated into a geospatial model to classify areas particularly vulnerable to pollutants. Data on the physical environment and its suitability for aquaculture in an Irish fjard, which is host to a number of different aquaculture activities, were derived from a three-dimensional hydrodynamic and GIS models. Subsequent incorporation into environmental vulnerability models, based on neuro-fuzzy techniques, highlighted localities particularly vulnerable to aquaculture development. The models produced an overall classification accuracy of 85.71%, with a Kappa coefficient of agreement of 81%, and were sensitive to different input parameters. A statistical comparison between vulnerability scores and nitrogen concentrations in sediment associated with salmon cages showed good correlation. Neuro-fuzzy techniques within GIS modeling classify vulnerability of coastal regions appropriately and have a role in policy decisions for aquaculture site selection.}, } @article {pmid21680810, year = {2011}, author = {Sanderson, MJ and McMahon, MM and Steel, M}, title = {Terraces in phylogenetic tree space.}, journal = {Science (New York, N.Y.)}, volume = {333}, number = {6041}, pages = {448-450}, doi = {10.1126/science.1206357}, pmid = {21680810}, issn = {1095-9203}, mesh = {Algorithms ; Animals ; Arthropods/*classification/genetics ; Bayes Theorem ; Biological Evolution ; Colubridae/*classification/genetics ; Data Interpretation, Statistical ; Genomics/methods ; Likelihood Functions ; Magnoliopsida/*classification/genetics ; *Models, Statistical ; *Phylogeny ; Poaceae/classification/genetics ; Sequence Alignment ; }, abstract = {A key step in assembling the tree of life is the construction of species-rich phylogenies from multilocus--but often incomplete--sequence data sets. We describe previously unknown structure in the landscape of solutions to the tree reconstruction problem, comprising sometimes vast "terraces" of trees with identical quality, arranged on islands of phylogenetically similar trees. Phylogenetic ambiguity within a terrace can be characterized efficiently and then ameliorated by new algorithms for obtaining a terrace's maximum-agreement subtree or by identifying the smallest set of new targets for additional sequencing. Algorithms to find optimal trees or estimate Bayesian posterior tree distributions may need to navigate strategically in the neighborhood of large terraces in tree space.}, } @article {pmid21677297, year = {2012}, author = {Dhoul, N and de Lusignan, S and Dmitrieva, O and Stevens, P and O'Donoghue, D}, title = {Quality achievement and disease prevalence in primary care predicts regional variation in renal replacement therapy (RRT) incidence: an ecological study.}, journal = {Nephrology, dialysis, transplantation : official publication of the European Dialysis and Transplant Association - European Renal Association}, volume = {27}, number = {2}, pages = {739-746}, doi = {10.1093/ndt/gfr347}, pmid = {21677297}, issn = {1460-2385}, mesh = {Age Distribution ; Databases, Factual ; Diabetes Mellitus/diagnosis/*epidemiology/therapy ; Female ; Follow-Up Studies ; Humans ; Hypertension/diagnosis/epidemiology/therapy ; Incidence ; Kidney Failure, Chronic/diagnosis/*epidemiology/*therapy ; Male ; Primary Health Care/*standards/trends ; *Quality Assurance, Health Care ; Registries ; Renal Replacement Therapy/methods/*statistics & numerical data ; Severity of Illness Index ; Sex Distribution ; Survival Rate ; Treatment Outcome ; United Kingdom ; }, abstract = {BACKGROUND: Diabetes Meillitus (DM) and hypertension (HT) are important causes of end-stage renal disease (ESRD) and renal replacement therapy (RRT) is the standard active treatment. Financially, incentivized quality initiatives for primary care include pay-for-performance (P4P) in DM and HT. Our aim was to examine any effect of disease prevalence and P4P on RRT incidence and regional variation.

METHODS: The incidence of RRT, sex and ethnicity data and P4P disease register and achievement data were obtained for each NHS locality. We calculated correlation coefficients for P4P indicators since 2004/05 and socio-demographic data for these 152 localities. We then developed a regression model and regression coefficient (R(2)) to assess to what extent these variables might predict RRT incidence.

RESULTS: Many of the P4P indicators were weakly but highly significantly correlated with RRT incidence. The strongest correlation was 2004/05 for DM prevalence and 2006/07 for HT quality. DM prevalence and the percentage with blood pressure control in HT target (HT quality) were the most predictive in our regression model R(2) = 0.096 and R(2) = 0.085, respectively (P < 0.001). Combined they predicted a fifth of RRT incidence (R(2) = 0.2, P < 0.001) while ethnicity and deprivation a quarter (R(2) = 0.25, P < 0.001). Our final model contained proportion of population >75 years, DM prevalence, HT quality, ethnicity and deprivation index and predicted 40% of variation (R(2) = 0.4, P < 0.001).

CONCLUSION: Our findings add prevalence of DM and quality of HT management to the known predictors of variation in RRT, ethnicity and deprivation. They raise the possibility that interventions in primary care might influence later events in specialist care.}, } @article {pmid21677033, year = {2011}, author = {Gharib, WH and Robinson-Rechavi, M}, title = {When orthologs diverge between human and mouse.}, journal = {Briefings in bioinformatics}, volume = {12}, number = {5}, pages = {436-441}, pmid = {21677033}, issn = {1477-4054}, mesh = {Animals ; Databases, Genetic ; *Evolution, Molecular ; Gene Expression Profiling ; Genome ; Genomics/*methods ; Humans ; Mice ; Species Specificity ; }, abstract = {Despite the common assumption that orthologs usually share the same function, there have been various reports of divergence between orthologs, even among species as close as mammals. The comparison of mouse and human is of special interest, because mouse is often used as a model organism to understand human biology. We review the literature on evidence for divergence between human and mouse orthologous genes, and discuss it in the context of biomedical research.}, } @article {pmid21676972, year = {2011}, author = {Srivastava, A and Rogers, WL and Breton, CM and Cai, L and Malmberg, RL}, title = {Transcriptome analysis of sarracenia, an insectivorous plant.}, journal = {DNA research : an international journal for rapid publication of reports on genes and genomes}, volume = {18}, number = {4}, pages = {253-261}, pmid = {21676972}, issn = {1756-1663}, mesh = {Computational Biology ; Ecosystem ; Gene Duplication ; *Gene Expression Profiling ; Genome, Plant ; Molecular Sequence Annotation ; Sarraceniaceae/*genetics ; }, abstract = {Sarracenia species (pitcher plants) are carnivorous plants which obtain a portion of their nutrients from insects captured in the pitchers. To investigate these plants, we sequenced the transcriptome of two species, Sarracenia psittacina and Sarracenia purpurea, using Roche 454 pyrosequencing technology. We obtained 46 275 and 36 681 contigs by de novo assembly methods for S. psittacina and S. purpurea, respectively, and further identified 16 163 orthologous contigs between them. Estimation of synonymous substitution rates between orthologous and paralogous contigs indicates the events of genome duplication and speciation within the Sarracenia genus both occurred ∼2 million years ago. The ratios of synonymous and non-synonymous substitution rates indicated that 491 contigs have been under positive selection (K(a)/K(s) > 1). Significant proportions of these contigs were involved in functions related to binding activity. We also found that the greatest sequence similarity for both of these species was to Vitis vinifera, which is most consistent with a non-current classification of the order Ericales as an asterid. This study has provided new insights into pitcher plants and will contribute greatly to future research on this genus and its distinctive ecological adaptations.}, } @article {pmid21674231, year = {2011}, author = {Bengtsson, J and Eriksson, KM and Hartmann, M and Wang, Z and Shenoy, BD and Grelet, GA and Abarenkov, K and Petri, A and Rosenblad, MA and Nilsson, RH}, title = {Metaxa: a software tool for automated detection and discrimination among ribosomal small subunit (12S/16S/18S) sequences of archaea, bacteria, eukaryotes, mitochondria, and chloroplasts in metagenomes and environmental sequencing datasets.}, journal = {Antonie van Leeuwenhoek}, volume = {100}, number = {3}, pages = {471-475}, doi = {10.1007/s10482-011-9598-6}, pmid = {21674231}, issn = {1572-9699}, mesh = {Archaea/*genetics/isolation & purification ; Bacteria/*genetics/isolation & purification ; Chloroplasts/*genetics ; Databases, Nucleic Acid ; Eukaryota/*genetics/isolation & purification ; Metagenome ; Metagenomics/instrumentation/*methods ; Mitochondria/*genetics ; Phylogeny ; Ribosome Subunits, Small/*genetics ; Sequence Alignment ; *Software ; }, abstract = {The ribosomal small subunit (SSU) rRNA gene has emerged as an important genetic marker for taxonomic identification in environmental sequencing datasets. In addition to being present in the nucleus of eukaryotes and the core genome of prokaryotes, the gene is also found in the mitochondria of eukaryotes and in the chloroplasts of photosynthetic eukaryotes. These three sets of genes are conceptually paralogous and should in most situations not be aligned and analyzed jointly. To identify the origin of SSU sequences in complex sequence datasets has hitherto been a time-consuming and largely manual undertaking. However, the present study introduces Metaxa (http://microbiology.se/software/metaxa/), an automated software tool to extract full-length and partial SSU sequences from larger sequence datasets and assign them to an archaeal, bacterial, nuclear eukaryote, mitochondrial, or chloroplast origin. Using data from reference databases and from full-length organelle and organism genomes, we show that Metaxa detects and scores SSU sequences for origin with very low proportions of false positives and negatives. We believe that this tool will be useful in microbial and evolutionary ecology as well as in metagenomics.}, } @article {pmid21673095, year = {2011}, author = {Jiang, X and Fares, MA}, title = {Functional diversification of the twin-arginine translocation pathway mediates the emergence of novel ecological adaptations.}, journal = {Molecular biology and evolution}, volume = {28}, number = {11}, pages = {3183-3193}, doi = {10.1093/molbev/msr154}, pmid = {21673095}, issn = {1537-1719}, mesh = {Adaptation, Biological/*genetics/physiology ; Archaea/*genetics/metabolism ; Bacteria/*genetics/metabolism ; Cluster Analysis ; Computational Biology ; Escherichia coli Proteins/*genetics/physiology ; *Evolution, Molecular ; Likelihood Functions ; Membrane Transport Proteins/*genetics/physiology ; Models, Genetic ; Phylogeny ; Protein Structure, Secondary ; Species Specificity ; }, abstract = {Microorganisms occupy a myriad of ecological niches that show an astonishing diversity. The molecular mechanisms underlying microbes' ecological diversity remain a fundamental conundrum in evolutionary biology. Evidence points to that the secretion of a particular set of proteins mediates microbes' interaction with the environment. Several systems are involved in this secretion, including the Sec secretion system and the Tat pathway. Shifts in the functions of proteins from the secretion systems may condition the set of secreted proteins and can, therefore, mediate adaptations to new ecological niches. In this manuscript, we have investigated processes of functional divergence (FD)-a term used here to refer to the emergence of novel functions by the modification of ancestral ones-of Tat pathway proteins using a large set of microbes with different lifestyles. The application of a novel approach to identify FD allowed us to distinguish molecular changes in the three Tat proteins among different groups of archaea and bacteria. We found these changes as well as the composition of secreted proteins to be correlated with differences in microbe's lifestyles. We identified major signatures of FD in halophilic and thermophilic archaea as well as in pathogenic bacteria. The location of amino acids affected by FD in functionally important domains of Tat proteins made it possible to find the link between the molecular changes in Tat, the set of secreted proteins and the environmental features of the microbes. We present evidence that links specific molecular changes in secretion mediating proteins of microbes to their ecological adaptations.}, } @article {pmid21668940, year = {2011}, author = {Orsini, L and Jansen, M and Souche, EL and Geldof, S and De Meester, L}, title = {Single nucleotide polymorphism discovery from expressed sequence tags in the waterflea Daphnia magna.}, journal = {BMC genomics}, volume = {12}, number = {}, pages = {309}, pmid = {21668940}, issn = {1471-2164}, mesh = {Animals ; Daphnia/*genetics ; Databases, Genetic ; *Expressed Sequence Tags ; Gene Expression Regulation ; Pesticides/toxicity ; *Polymorphism, Single Nucleotide ; Sequence Analysis, DNA ; Stress, Physiological ; }, abstract = {BACKGROUND: Daphnia (Crustacea: Cladocera) plays a central role in standing aquatic ecosystems, has a well known ecology and is widely used in population studies and environmental risk assessments. Daphnia magna is, especially in Europe, intensively used to study stress responses of natural populations to pollutants, climate change, and antagonistic interactions with predators and parasites, which have all been demonstrated to induce micro-evolutionary and adaptive responses. Although its ecology and evolutionary biology is intensively studied, little is known on the functional genomics underpinning of phenotypic responses to environmental stressors. The aim of the present study was to find genes expressed in presence of environmental stressors, and target such genes for single nucleotide polymorphic (SNP) marker development.

RESULTS: We developed three expressed sequence tag (EST) libraries using clonal lineages of D. magna exposed to ecological stressors, namely fish predation, parasite infection and pesticide exposure. We used these newly developed ESTs and other Daphnia ESTs retrieved from NCBI GeneBank to mine for SNP markers targeting synonymous as well as non synonymous genetic variation. We validate the developed SNPs in six natural populations of D. magna distributed at regional scale.

CONCLUSIONS: A large proportion (47%) of the produced ESTs are Daphnia lineage specific genes, which are potentially involved in responses to environmental stress rather than to general cellular functions and metabolic activities, or reflect the arthropod's aquatic lifestyle. The characterization of genes expressed under stress and the validation of their SNPs for population genetic study is important for identifying ecologically responsive genes in D. magna.}, } @article {pmid21665319, year = {2011}, author = {Huang, X and Qiao, G}, title = {Biodiversity databases should gain support from journals.}, journal = {Trends in ecology & evolution}, volume = {26}, number = {8}, pages = {377-378}, doi = {10.1016/j.tree.2011.05.006}, pmid = {21665319}, issn = {1872-8383}, mesh = {*Biodiversity ; *Databases, Factual ; Ecology/methods/*standards ; Information Management/*methods/organization & administration ; Periodicals as Topic/standards ; Publishing ; Research/*standards ; }, } @article {pmid21664624, year = {2011}, author = {Kuss, O and Börgermann, J}, title = {Do higher-risk patients benefit from off-pump coronary artery bypass grafting? Evidence from an ecologic analysis of randomized trials.}, journal = {The Journal of thoracic and cardiovascular surgery}, volume = {142}, number = {3}, pages = {e117-22}, doi = {10.1016/j.jtcvs.2011.04.032}, pmid = {21664624}, issn = {1097-685X}, mesh = {Aged ; Aged, 80 and over ; Atrial Fibrillation/epidemiology ; *Coronary Artery Bypass, Off-Pump/statistics & numerical data ; Coronary Disease/epidemiology/*surgery ; Effect Modifier, Epidemiologic ; Female ; Humans ; Logistic Models ; Male ; Middle Aged ; Myocardial Infarction/epidemiology ; Patient Selection ; Randomized Controlled Trials as Topic ; Risk Factors ; Stroke/epidemiology ; Stroke Volume ; Treatment Outcome ; }, abstract = {OBJECTIVE: It is commonly believed that especially higher-risk patients benefit from off-pump coronary artery bypass grafting. However, analyses from several registries give different results. A common shortcoming of all those analyses is the fact that they concentrate on evidence from nonrandomized trials.

METHODS: In an ecologic analysis, we included all randomized trials comparing the on- and off-pump techniques until January 2011. By logistic regression, we investigated whether the effect of off-pump surgery on mortality, myocardial infarction, stroke, and atrial fibrillation is modified across the range of the 3 risk factors: age, proportion of women, and ejection fraction.

RESULTS: Eighty-six studies with a total population of 9906 patients reported on at least 1 risk factor and 1 outcome. We found a superiority of the off-pump technique in patients with lower ejection fraction values for the outcomes mortality and atrial fibrillation. No effect modification was seen for the risk factors age and proportion of women.

CONCLUSIONS: Our ecologic analysis of nearly 10,000 patients from 86 randomized trials found a superiority of the off-pump technique in patients with lower ejection fraction values, especially for the most valid outcome of mortality. As every ecologic analysis is prone to ecologic bias, a definite answer on the benefit of the off-pump technique in higher-risk patients can only be given by meta-analyses using individual patient data.}, } @article {pmid21657010, year = {2011}, author = {Zhou, R and Li, YH and Hu, YM and Su, HL and Wang, JN}, title = {[Spatiotemporal differentiation of construction land expansion in a typical town of south Jiangsu Province].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {22}, number = {3}, pages = {577-584}, pmid = {21657010}, issn = {1001-9332}, mesh = {China ; *City Planning ; Conservation of Natural Resources/*methods ; *Ecosystem ; Environmental Monitoring/methods ; Geographic Information Systems ; Satellite Communications ; *Urbanization ; }, abstract = {Choosing Xinzhuang Town in south Jiangsu Province as study area, and by using 1980, 1991, 2001, and 2009 high-resolution remote sensing images and GIS spatial analysis technology, an integrated expansion degree index model was established based on the existing indicators of construction land expansion, and the general and spatiotemporal differentiation characteristics of construction land expansion in the Town in three time periods of 1980-2009 were quantitatively analyzed. In 1980-2009, with the acceleration of rural urbanization and industrialization, the area of construction land in the Town increased significantly by 19.24 km2, and especially in 2001-2009, the expanded area, expanded contribution rate, and expansion intensity reached the maximum. The construction land expansion had an obvious spatial differentiation characteristic. In 1980-1991, the newly increased construction land mainly concentrated in town area. After 1991, the focus of construction land gradually spread to the villages with developed industries. Most of the increased construction lands were converted from paddy field and dry land, accounting for 88.1% of the total increased area, while the contribution from other land types was relatively small.}, } @article {pmid21654437, year = {2011}, author = {Bryngelson, A and Mittendorfer-Rutz, E and Fritzell, J and Asberg, M and Nygren, A}, title = {Reduction in personnel and long-term sickness absence for psychiatric disorders among employees in Swedish county councils: an ecological population-based study.}, journal = {Journal of occupational and environmental medicine}, volume = {53}, number = {6}, pages = {658-662}, doi = {10.1097/JOM.0b013e31821aa706}, pmid = {21654437}, issn = {1536-5948}, mesh = {*Absenteeism ; Adolescent ; Adult ; Databases, Factual ; Employment/psychology ; Female ; Government ; Humans ; Male ; Mental Disorders/*epidemiology ; Middle Aged ; Personnel Downsizing/*psychology ; Regression Analysis ; Sick Leave/*statistics & numerical data ; Sweden/epidemiology ; Workplace/psychology ; Young Adult ; }, abstract = {OBJECTIVE: The aim was to examine whether staff downsizing was related to long-term psychiatric sickness absence.

METHODS: We used aggregate data on sickness absence from AFA insurance, as well as information on staff numbers from the Swedish Association of Local Authorities and Regions. Bootstrap regression analyses were used to elucidate whether there was a relationship between reduction in personnel and changes in sickness rates.

RESULTS: A staff reduction of 1% increased the sickness rate, on average, by 9%. The associations were similar in men and women as well as in different age groups, although statistical significance was only reached in the groups of women and middle-aged employees.

CONCLUSIONS: Our findings suggest that downsizing may be related to subsequent increases in psychiatric sickness absence. The association appeared after a time-delay of several years.}, } @article {pmid21651688, year = {2012}, author = {Jansson, JK and Neufeld, JD and Moran, MA and Gilbert, JA}, title = {Omics for understanding microbial functional dynamics.}, journal = {Environmental microbiology}, volume = {14}, number = {1}, pages = {1-3}, doi = {10.1111/j.1462-2920.2011.02518.x}, pmid = {21651688}, issn = {1462-2920}, mesh = {Computational Biology ; Ecology/*methods ; Gene Expression Profiling ; *Genomics ; Metabolomics ; *Microbiological Phenomena ; *Proteomics ; Sequence Analysis, DNA/methods ; Sequence Analysis, RNA/methods ; }, } @article {pmid21647549, year = {2012}, author = {Xu, RY and Nan, P and Pan, H and Zhou, T and Chen, J}, title = {Molecular cloning, characterization and expression of a chalcone reductase gene from Astragalus membranaceus Bge. var. mongholicus (Bge.) Hsiao.}, journal = {Molecular biology reports}, volume = {39}, number = {3}, pages = {2275-2283}, pmid = {21647549}, issn = {1573-4978}, mesh = {Alcohol Oxidoreductases/*genetics/*metabolism ; Astragalus propinquus/*enzymology ; Base Sequence ; Blotting, Southern ; Cloning, Molecular ; Computational Biology ; DNA, Complementary/genetics ; Gene Expression Profiling ; Molecular Sequence Data ; Molecular Structure ; Sequence Analysis, DNA ; }, abstract = {A chalcone reductase (CHR) gene was isolated from Astragalus membranaceus Bge. var. mongholicus (Bge.) Hsiao (A. mongholicus). The full-length cDNA of A. mongholicus CHR, designated as Amchr (GenBank accession No. HM357239), was 1196 bp long. It had a 957 bp open reading frame encoding a 318-amino acid protein of 35 kDa, a 67 bp 5' non-coding region and a 172 bp 3'-untranslated region. The putative AmCHR protein showed striking similarity to CHR from other leguminous species. Two-dimensional structure modeling showed that AmCHR consisted of 45.28% α-helix, 10.38% extended strand and 44.34% random coil. Prediction showed that three-dimensional AmCHR was a global protein containing an aldo-ket-red domain, with a putative Asp-Tyr-Lys-His catalytic tetrad in the center. The AmCHR gene was 1251 bp long, consisting of three exons and two introns. Intron I was 125 bp and intron II was 169 bp long. Southern blot analysis indicated that Amchr belonged to a small multigene family. Under natural conditions, Amchr was expressed differentially in the root, stem and leaf tissues of A. mongholicus, with a preferential expression in the root. The recombinant AmCHR protein was successfully expressed in Escherichia coli strain BL21 with pET42a vector. The result showed that the expressed AmCHR protein had molecular weight of about 35 kDa, which matched the size of the predicted protein by bioinformatic analysis. This study opened avenues towards understanding of the function of AmCHR protein and the role of the Amchr gene in the calycosin-7-O-β-D: -glucoside branch pathway in A. mongholicus.}, } @article {pmid21647346, year = {2011}, author = {Bartell, SM and Lewandowski, TA}, title = {Administrative censoring in ecological analyses of autism and a Bayesian solution.}, journal = {Journal of environmental and public health}, volume = {2011}, number = {}, pages = {202783}, pmid = {21647346}, issn = {1687-9813}, mesh = {Autistic Disorder/*chemically induced/epidemiology ; *Bayes Theorem ; Child ; Child, Preschool ; Data Collection ; Data Interpretation, Statistical ; *Environmental Exposure ; Geography ; Humans ; Mercury/analysis/*toxicity ; *Models, Biological ; Prevalence ; Risk Assessment ; Socioeconomic Factors ; Texas/epidemiology ; Time Factors ; }, abstract = {Widely cited ecological analyses of autism have reported associations with mercury emissions, with precipitation, and race at the level of counties or school districts. However, state educational agencies often suppress any low numerical autism counts before releasing data--a phenomenon known as "administrative censoring." Previous analyses did not describe appropriate methods for censored data analysis; common substitution or exclusion methods are known to introduce bias and produce artificially narrow confidence intervals. We apply a Bayesian censored random effects Poisson model to reanalyze associations between 2001 Toxic Release Inventory reported mercury emissions and 2000-2001 autism counts in Texas. Relative risk estimates for autism decreased from 4.44 (95% CI: 4.16, 4.74) per thousand lbs. of air mercury emissions using a naive zero-substitution approach to 1.42 (95% CI: 1.09, 1.78) using the Bayesian approach. Inadequate attention to censoring poses a serious threat to the validity of ecological analyses of autism and other health outcomes.}, } @article {pmid21643960, year = {2012}, author = {Yang, H and Li, F and Kong, X and Yuan, X and Lian, G and Geng, M and Li, T and Yin, J and Yin, Y}, title = {Molecular cloning, tissue distribution and ontogenetic expression of Xiang pig chemerin and its involvement in regulating energy metabolism through Akt and ERK1/2 signaling pathways.}, journal = {Molecular biology reports}, volume = {39}, number = {2}, pages = {1887-1894}, pmid = {21643960}, issn = {1573-4978}, mesh = {Adipokines/*genetics/*metabolism/pharmacology ; Age Factors ; Analysis of Variance ; Animals ; Blotting, Western ; Cell Line, Tumor ; Chemotactic Factors/*genetics/*metabolism ; Cloning, Molecular ; Computational Biology ; Energy Metabolism/*drug effects/physiology ; *Gene Expression ; Gene Expression Profiling ; MAP Kinase Signaling System/physiology ; Mice ; Open Reading Frames/genetics ; Reverse Transcriptase Polymerase Chain Reaction ; Sus scrofa/*genetics ; }, abstract = {Chemerin, as a new member of adipokines family, is highly expressed in adipose tissue in rodent and its expression increases with obesity. Moreover, chemerin has been reported to have significant relationship with metabolic syndrome and insulin sensitivity. Here, the gene encoding chemerin from Xiang pig was cloned. The open reading frame of this cDNA encodes 163 deduced amino acid residues. The putative protein has a N-terminal signaling peptide and a nuclear localization signal profile which are highly conserved among the vertebrate orthologs. Both chemerin and chemerinR are highly expressed in lung, kidney and small intestine in adult Xiang pig. Besides these tissues, chemerin is abundant in liver and backfat, and chemerinR is abundant in spleen and skeletal muscle. We also investigated the age-dependent expression of chemerin in suckling Xiang piglets in various tissues, which showed an interaction between age and segments in abundance of chemerin and chemerinR from day 1 to day 21. For chemerinR, it was abundant in skeletal muscle of both adult and fetal Xiang pig. Further, we treated differentiated C2C12 cells with chemerin. The result showed that chemerin regulated energy metabolism partly through Akt and ERK1/2 signaling pathway. Taken together, our findings provide basic molecular information for the deeper investigation on the function of chemerin.}, } @article {pmid21636110, year = {2011}, author = {Burgert, S and Schäfer, RB and Foit, K and Kattwinkel, M and Metzeling, L and MacEwan, R and Kefford, BJ and Liess, M}, title = {Modelling aquatic exposure and effects of insecticides--application to south-eastern Australia.}, journal = {The Science of the total environment}, volume = {409}, number = {14}, pages = {2807-2814}, doi = {10.1016/j.scitotenv.2011.02.042}, pmid = {21636110}, issn = {1879-1026}, mesh = {Animals ; Aquatic Organisms ; Australia ; Environmental Exposure/analysis/*statistics & numerical data ; Geographic Information Systems ; Insecticides/*analysis ; Models, Biological ; *Models, Chemical ; Risk Assessment ; Rivers/chemistry ; Water Pollutants, Chemical/*analysis ; Water Pollution, Chemical/*statistics & numerical data ; }, abstract = {Agricultural pesticides are widely used and can affect freshwater organisms. We applied a spatially explicit exposure model, validated for central Europe, to estimate exposure to insecticides through runoff for streams in south-eastern Australia. The model allows the identification of streams potentially affected by insecticide runoff located in 10×10 km grid cells. The computation of runoff relies on key environmental factors such as land use, soil texture, slope and precipitation. Additionally, the model predicted the ecological effect of insecticides on the macroinvertebrate community. We predicted insecticide surface runoff that results in a moderate to poor ecological quality for streams in half of the grid cells containing agricultural land. These results are in good accordance with the results obtained by estimating pesticide stress with a biotic index (SPEAR(pesticides)) based on macroinvertebrate monitoring data. We conclude that the exposure and effect model can act as an effective and cost-saving tool to identify high risk areas of insecticide exposure and to support stream management.}, } @article {pmid21635644, year = {2011}, author = {Deichmeister, JM and Telang, A}, title = {Abundance of West Nile virus mosquito vectors in relation to climate and landscape variables.}, journal = {Journal of vector ecology : journal of the Society for Vector Ecology}, volume = {36}, number = {1}, pages = {75-85}, doi = {10.1111/j.1948-7134.2011.00143.x}, pmid = {21635644}, issn = {1948-7134}, mesh = {Aedes/growth & development/virology ; Animals ; Climate ; Culex/growth & development/virology ; Culicidae/*growth & development/*virology ; Geographic Information Systems ; Geography ; Insect Vectors/growth & development/virology ; Temperature ; West Nile virus/*physiology ; }, abstract = {It is currently unclear if the potential for West Nile virus transmission by mosquito vectors in the eastern United States is related to landscape or climate factors or both. We compared abundance of vector species between urban and suburban neighborhoods of Henrico County, VA, in relation to the following factors: temperature, precipitation, canopy cover, building footprint, and proximity to drainage infrastructure. Mosquitoes were collected throughout the 2005, 2006, and 2007 seasons and tested for West Nile virus (WNV) in pools of 10-50. Test results of mosquito pools were compared to average site abundance from 37 sites in Henrico County, VA; abundance was then examined in relation to ecological variables. Urban infrastructure was positively correlated with the abundance of Culex pipiens L./Cx. restuans, and our findings implicate combined sewer overflow systems as large contributors to Culex vector populations. No measure of urbanization examined in our study was correlated with Aedes albopictus abundance. Our study showed that certain landscape variables identified using Geographic Information Systems are valuable for predicting primary WNV vector abundance in Virginia, and that temperature along with low precipitation are strong predictors of population growth. Our results support other regional studies that found WNV proliferates under drought conditions.}, } @article {pmid21631506, year = {2011}, author = {Leuzinger, S and Quinn Thomas, R}, title = {How do we improve Earth system models? Integrating Earth system models, ecosystem models, experiments and long-term data. 1st INTERFACE workshop, Captiva Island, FL, USA, 28 February-3 March 2011.}, journal = {The New phytologist}, volume = {191}, number = {1}, pages = {15-18}, doi = {10.1111/j.1469-8137.2011.03778.x}, pmid = {21631506}, issn = {1469-8137}, mesh = {Carbon/chemistry ; Climate Change ; Data Interpretation, Statistical ; *Earth, Planet ; *Ecosystem ; Florida ; *Models, Theoretical ; Trees/physiology ; }, } @article {pmid21629788, year = {2011}, author = {Wagner, BD and Robertson, CE and Harris, JK}, title = {Application of two-part statistics for comparison of sequence variant counts.}, journal = {PloS one}, volume = {6}, number = {5}, pages = {e20296}, pmid = {21629788}, issn = {1932-6203}, support = {U01 HL081335/HL/NHLBI NIH HHS/United States ; 1U01HL081335-01/HL/NHLBI NIH HHS/United States ; }, mesh = {Humans ; *Models, Statistical ; Sequence Analysis/*methods ; }, abstract = {Investigation of microbial communities, particularly human associated communities, is significantly enhanced by the vast amounts of sequence data produced by high throughput sequencing technologies. However, these data create high-dimensional complex data sets that consist of a large proportion of zeros, non-negative skewed counts, and frequently, limited number of samples. These features distinguish sequence data from other forms of high-dimensional data, and are not adequately addressed by statistical approaches in common use. Ultimately, medical studies may identify targeted interventions or treatments, but lack of analytic tools for feature selection and identification of taxa responsible for differences between groups, is hindering advancement. The objective of this paper is to examine the application of a two-part statistic to identify taxa that differ between two groups. The advantages of the two-part statistic over common statistical tests applied to sequence count datasets are discussed. Results from the t-test, the Wilcoxon test, and the two-part test are compared using sequence counts from microbial ecology studies in cystic fibrosis and from cenote samples. We show superior performance of the two-part statistic for analysis of sequence data. The improved performance in microbial ecology studies was independent of study type and sequence technology used.}, } @article {pmid21627831, year = {2011}, author = {López-Giráldez, F and Townsend, JP}, title = {PhyDesign: an online application for profiling phylogenetic informativeness.}, journal = {BMC evolutionary biology}, volume = {11}, number = {}, pages = {152}, pmid = {21627831}, issn = {1471-2148}, mesh = {Databases, Genetic ; Genetic Loci ; *Phylogeny ; *Software ; }, abstract = {BACKGROUND: The rapid increase in number of sequenced genomes for species across of the tree of life is revealing a diverse suite of orthologous genes that could potentially be employed to inform molecular phylogenetic studies that encompass broader taxonomic sampling. Optimal usage of this diversity of loci requires user-friendly tools to facilitate widespread cost-effective locus prioritization for phylogenetic sampling. The Townsend (2007) phylogenetic informativeness provides a unique empirical metric for guiding marker selection. However, no software or automated methodology to evaluate sequence alignments and estimate the phylogenetic informativeness metric has been available.

RESULTS: Here, we present PhyDesign, a platform-independent online application that implements the Townsend (2007) phylogenetic informativeness analysis, providing a quantitative prediction of the utility of loci to solve specific phylogenetic questions. An easy-to-use interface facilitates uploading of alignments and ultrametric trees to calculate and depict profiles of informativeness over specified time ranges, and provides rankings of locus prioritization for epochs of interest.

CONCLUSIONS: By providing these profiles, PhyDesign facilitates locus prioritization increasing the efficiency of sequencing for phylogenetic purposes compared to traditional studies with more laborious and low capacity screening methods, as well as increasing the accuracy of phylogenetic studies. Together with a manual and sample files, the application is freely accessible at http://phydesign.townsend.yale.edu.}, } @article {pmid21627820, year = {2011}, author = {Lemke, S and Antonopoulos, DA and Meyer, F and Domanus, MH and Schmidt-Ott, U}, title = {BMP signaling components in embryonic transcriptomes of the hover fly Episyrphus balteatus (Syrphidae).}, journal = {BMC genomics}, volume = {12}, number = {}, pages = {278}, pmid = {21627820}, issn = {1471-2164}, mesh = {Animals ; Bone Morphogenetic Proteins/genetics/*metabolism ; Databases, Genetic ; Diptera/cytology/*embryology/*genetics ; Drosophila melanogaster/genetics ; Embryo, Nonmammalian/*metabolism ; Epithelium/metabolism ; Evolution, Molecular ; *Gene Expression Profiling ; Molecular Sequence Data ; Mothers ; Sequence Homology, Nucleic Acid ; Signal Transduction/*genetics ; }, abstract = {BACKGROUND: In animals, signaling of Bone Morphogenetic Proteins (BMPs) is essential for dorsoventral (DV) patterning of the embryo, but how BMP signaling evolved with changes in embryonic DV differentiation is largely unclear. Based on the extensive knowledge of BMP signaling in Drosophila melanogaster, the morphological diversity of extraembryonic tissues in different fly species provides a comparative system to address this question. The closest relatives of D. melanogaster with clearly distinct DV differentiation are hover flies (Diptera: Syrphidae). The syrphid Episyrphus balteatus is a commercial bio-agent against aphids and has been established as a model organism for developmental studies and chemical ecology. The dorsal blastoderm of E. balteatus gives rise to two extraembryonic tissues (serosa and amnion), whereas in D. melanogaster, the dorsal blastoderm differentiates into a single extraembryonic epithelium (amnioserosa). Recent studies indicate that several BMP signaling components of D. melanogaster, including the BMP ligand Screw (Scw) and other extracellular regulators, evolved in the dipteran lineage through gene duplication and functional divergence. These findings raise the question of whether the complement of BMP signaling components changed with the origin of the amnioserosa.

RESULTS: To search for BMP signaling components in E. balteatus, we generated and analyzed transcriptomes of freshly laid eggs (0-30 minutes) and late blastoderm to early germband extension stages (3-6 hours) using Roche/454 sequencing. We identified putative E. balteatus orthologues of 43% of all annotated D. melanogaster genes, including the genes of all BMP ligands and other BMP signaling components.

CONCLUSION: The diversification of several BMP signaling components in the dipteran linage of D. melanogaster preceded the origin of the amnioserosa.[Transcriptome sequence data from this study have been deposited at the NCBI Sequence Read Archive (SRP005289); individually assembled sequences have been deposited at GenBank (JN006969-JN006986).].}, } @article {pmid21627775, year = {2011}, author = {, and Austin, JD and Bertin, A and Bórquez, JP and Cárdenas, L and Cardoza, TB and Chapman, F and De Sousa, AC and De Souza, AP and Douglas, KC and Ellwood, SR and Ferriol, M and Garmendia, A and Gouin, N and Hargrove, J and Jasti, M and Keränen, I and Knott, KE and Konec, M and Kuitunen, K and Lima, MP and Linde, CC and Merle, H and Oliva, ME and Pérez, M and Saarinen, E and Samollow, PB and Scarpassa, VM and Segura, I and Smith, L and Trontelj, P and Valdivia, IM and Wallwork, H and Wellenreuther, M}, title = {Permanent genetic resources added to Molecular Ecology Resources Database 1 February 2011-31 March 2011.}, journal = {Molecular ecology resources}, volume = {11}, number = {4}, pages = {757-758}, doi = {10.1111/j.1755-0998.2011.03028.x}, pmid = {21627775}, issn = {1755-0998}, mesh = {Acanthaceae/genetics ; Animals ; Arthropods/genetics ; Ascomycota/genetics ; Chordata/genetics ; *Databases, Genetic ; *Microsatellite Repeats ; Molecular Sequence Data ; Plants/genetics ; Sequence Analysis, DNA ; Trematoda/genetics ; }, abstract = {This article documents the addition of 111 microsatellite marker loci to the Molecular Ecology Resources Database. Loci were developed for the following species: Acipenser oxyrinchus desotoi, Anopheles nuneztovari sensu lato, Asellus aquaticus, Calopteryx splendens, Calopteryx virgo, Centaurea aspera, Centaurea seridis, Chilina dombeyana, Proctoeces cf. lintoni and Pyrenophora teres f. teres.}, } @article {pmid21613283, year = {2011}, author = {Klaassen, RH and Alerstam, T and Carlsson, P and Fox, JW and Lindström, A}, title = {Great flights by great snipes: long and fast non-stop migration over benign habitats.}, journal = {Biology letters}, volume = {7}, number = {6}, pages = {833-835}, pmid = {21613283}, issn = {1744-957X}, mesh = {*Animal Migration ; Animals ; Charadriiformes/*physiology ; Environment ; *Flight, Animal ; Geographic Information Systems ; Male ; Time Factors ; }, abstract = {Migratory land birds perform extreme endurance flights when crossing ecological barriers, such as deserts, oceans and ice-caps. When travelling over benign areas, birds are expected to migrate by shorter flight steps, since carrying the heavy fuel loads needed for long non-stop flights comes at considerable cost. Here, we show that great snipes Gallinago media made long and fast non-stop flights (4300-6800 km in 48-96 h), not only over deserts and seas but also over wide areas of suitable habitats, which represents a previously unknown migration strategy among land birds. Furthermore, the great snipes achieved very high ground speeds (15-27 m s(-1)), which was not an effect of strong tailwind support, and we know of no other animal that travels this rapidly over such a long distance. Our results demonstrate that some migratory birds are prepared to accept extreme costs of strenuous exercise and large fuel loads, even when stopover sites are available along the route and there is little tailwind assistance. A strategy of storing a lot of energy before departure, even if migration is over benign habitats, may be advantageous owing to differential conditions of fuel deposition, predation or infection risk along the migration route.}, } @article {pmid21613235, year = {2011}, author = {Price, DR and Duncan, RP and Shigenobu, S and Wilson, AC}, title = {Genome expansion and differential expression of amino acid transporters at the aphid/Buchnera symbiotic interface.}, journal = {Molecular biology and evolution}, volume = {28}, number = {11}, pages = {3113-3126}, doi = {10.1093/molbev/msr140}, pmid = {21613235}, issn = {1537-1719}, mesh = {Amino Acid Transport Systems/*genetics/metabolism ; Animals ; Aphids/*genetics/*microbiology ; Bayes Theorem ; Buchnera/*genetics ; Chromosome Mapping ; Computational Biology ; *Evolution, Molecular ; Genes, Duplicate/genetics ; Likelihood Functions ; Models, Genetic ; Multigene Family/genetics ; *Phylogeny ; Real-Time Polymerase Chain Reaction ; Species Specificity ; *Symbiosis ; }, abstract = {In insects, some of the most ecologically important symbioses are nutritional symbioses that provide hosts with novel traits and thereby facilitate exploitation of otherwise inaccessible niches. One such symbiosis is the ancient obligate intracellular symbiosis of aphids with the γ-proteobacteria, Buchnera aphidicola. Although the nutritional basis of the aphid/Buchnera symbiosis is well understood, the processes and structures that mediate the intimate interactions of symbiotic partners remain uncharacterized. Here, using a de novo approach, we characterize the complement of 40 amino acid polyamine organocation (APC) superfamily member amino acid transporters (AATs) encoded in the genome of the pea aphid, Acyrthosiphon pisum. We find that the A. pisum APC superfamily is characterized by extensive gene duplications such that A. pisum has more APC superfamily transporters than other fully sequenced insects, including a ten paralog aphid-specific expansion of the APC transporter slimfast. Detailed expression analysis of 17 transporters selected on the basis of their phylogenetic relationship to five AATs identified in an earlier bacteriocyte expressed sequence tag study distinguished a subset of eight transporters that have been recruited for amino acid transport in bacteriocyte cells at the symbiotic interface. These eight transporters include transporters that are highly expressed and/or highly enriched in bacteriocytes and intriguingly, the four AATs that show bacteriocyte-enriched expression are all members of gene family expansions, whereas three of the four that are highly expressed but not enriched in bacteriocytes retain one-to-one orthology with transporters in other genomes. Finally, analysis of evolutionary rates within the large A. pisum slimfast expansion demonstrated increased rates of molecular evolution coinciding with two major shifts in expression: 1) a loss of gut expression and possibly a gain of bacteriocyte expression and 2) loss of expression in all surveyed tissues in asexual females. Taken together, our characterization of nutrient AATs at the aphid/Buchnera symbiotic interface provides the first examination of the processes and structures operating at the interface of an obligate intracellular insect nutritional symbiosis, offering unique insight into the types of genomic change that likely facilitated evolutionary maintenance of the symbiosis.}, } @article {pmid21613148, year = {2011}, author = {Cardinale, BJ and Matulich, KL and Hooper, DU and Byrnes, JE and Duffy, E and Gamfeldt, L and Balvanera, P and O'Connor, MI and Gonzalez, A}, title = {The functional role of producer diversity in ecosystems.}, journal = {American journal of botany}, volume = {98}, number = {3}, pages = {572-592}, doi = {10.3732/ajb.1000364}, pmid = {21613148}, issn = {1537-2197}, mesh = {*Biodiversity ; Databases as Topic ; *Food Chain ; Species Specificity ; }, abstract = {Over the past several decades, a rapidly expanding field of research known as biodiversity and ecosystem functioning has begun to quantify how the world's biological diversity can, as an independent variable, control ecological processes that are both essential for, and fundamental to, the functioning of ecosystems. Research in this area has often been justified on grounds that (1) loss of biological diversity ranks among the most pronounced changes to the global environment and that (2) reductions in diversity, and corresponding changes in species composition, could alter important services that ecosystems provide to humanity (e.g., food production, pest/disease control, water purification). Here we review over two decades of experiments that have examined how species richness of primary producers influences the suite of ecological processes that are controlled by plants and algae in terrestrial, marine, and freshwater ecosystems. Using formal meta-analyses, we assess the balance of evidence for eight fundamental questions and corresponding hypotheses about the functional role of producer diversity in ecosystems. These include questions about how primary producer diversity influences the efficiency of resource use and biomass production in ecosystems, how primary producer diversity influences the transfer and recycling of biomass to other trophic groups in a food web, and the number of species and spatial /temporal scales at which diversity effects are most apparent. After summarizing the balance of evidence and stating our own confidence in the conclusions, we outline several new questions that must now be addressed if this field is going to evolve into a predictive science that can help conserve and manage ecological processes in ecosystems.}, } @article {pmid21608266, year = {2011}, author = {Chen, WB and Carsjens, GJ}, title = {[Environmental impact assessment based on planning support system].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {22}, number = {2}, pages = {488-494}, pmid = {21608266}, issn = {1001-9332}, mesh = {China ; *City Planning ; *Conservation of Natural Resources ; Decision Making ; *Decision Support Techniques ; *Ecosystem ; Environment ; *Environment Design ; Humans ; }, abstract = {How to assess environmental impact is one of the keys in land use planning. This article described in detail the concepts of activities, impact zones, functions, and sensitivities, as well as the development of STEPP (strategic tool for integrating environmental aspects in planning procedures) based on Avenue, the secondary developing language of ArcView GIS. The system makes it convenient for planning practitioners exchanging information, and can spatially, visually and quantitatively describe environmental impact and its change. In this study, the urban-rural combination area located between EDE and Veenendaal of The Netherlands was taken as case, and the results indicated that the environment was incorporated well in the planning procedure based on the concepts, and could also demonstrate the effects of planning measures on environment spatially, explicitly, and in real-time, facilitating the participation of planning practitioners and decision-making. Some proposals of how to promote STEEP application in China were suggested.}, } @article {pmid21608261, year = {2011}, author = {Zhang, PF and Hu, YM and Xiong, ZP and Liu, M}, title = {[Variation pattern and its affecting factors of three-dimensional landscape in urban residential community of Shenyang].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {22}, number = {2}, pages = {453-459}, pmid = {21608261}, issn = {1001-9332}, mesh = {China ; Cities ; *City Planning ; *Ecosystem ; *Environment Design ; Environmental Monitoring/*methods ; Geographic Information Systems ; *Imaging, Three-Dimensional ; Satellite Communications ; }, abstract = {Based on the 1:10000 aerial photo in 1997 and the three QuickBird images in 2002, 2005, and 2008, and by using Barista software and GIS and RS techniques, the three-dimensional information of the residential community in Tiexi District of Shenyang was extracted, and the variation pattern of the three-dimensional landscape in the district during its reconstruction in 1997-2008 and related affecting factors were analyzed with the indices, ie. road density, greening rate, average building height, building height standard deviation, building coverage rate, floor area rate, building shape coefficient, population density, and per capita GDP. The results showed that in 1997-2008, the building area for industry decreased, that for commerce and other public affairs increased, and the area for residents, education, and medical cares basically remained stable. The building number, building coverage rate, and building shape coefficient decreased, while the floor area rate, average building height, height standard deviation, road density, and greening rate increased. Within the limited space of residential community, the containing capacity of population and economic activity increased, and the environment quality also improved to some extent. The variation degree of average building height increased, but the building energy consumption decreased. Population growth and economic development had positive correlations with floor area rate, road density, and greening rate, but negative correlation with building coverage rate.}, } @article {pmid21608260, year = {2011}, author = {Dai, SW and Yang, XG and Zhao, M and Li, Y and Wang, WF and Liu, ZJ}, title = {[Changes of China agricultural climate resources under the background of climate change. II. Spatiotemporal change characteristics of agricultural climate resources in Southwest China].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {22}, number = {2}, pages = {442-452}, pmid = {21608260}, issn = {1001-9332}, mesh = {China ; Climate Change/*statistics & numerical data ; Crops, Agricultural/*growth & development ; Ecology/methods ; *Ecosystem ; Environmental Monitoring/*methods ; Geographic Information Systems ; Rain ; Sunlight ; Temperature ; }, abstract = {Based on the 1961-2007 ground observation data from 88 meteorological stations in Southwest China, and by using statistical methods and GIS software, this paper analyzed the spatiotemporal change characteristics of agricultural climate resources in this region in the whole year and during temperature-defined growth period. In 1961-2007, the annual mean temperature in the region showed an increasing trend, with the increment averaged 0.18 degrees C x (10 a)(-1). The > or = 10 degrees C and > or = 15 degrees C accumulated temperature during temperature-defined growth period also showed an increasing trend, with the increment averaged 55.3 degrees C x d x (10 a)(-1) and 37 degrees C x d x (10 a)(-1), respectively. The annual sunshine hours decreased gradually from west to east, and the decreasing trend was more significant in eastern than in western region. The sunshine hours during temperature-defined growth period showed an overall increasing trend, and the spatial difference was great. The precipitation resource had an overall decrease, with the decrement in whole year and during temperature-defined growth period averaged 10 mm x (10 a)(-1) and 8 mm x (10 a)(-1), respectively. The annual reference crop evapotranspiration generally decreased, but the decrement was less than that of annual precipitation. The reference crop evapotranspiration during temperature-defined growth period within about 53% meteorological stations decreased.}, } @article {pmid21608242, year = {2011}, author = {Zhang, YD and Zhang, XH and Liu, SR}, title = {[Correlation analysis on normalized difference vegetation index (NDVI) of different vegetations and climatic factors in Southwest China].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {22}, number = {2}, pages = {323-330}, pmid = {21608242}, issn = {1001-9332}, mesh = {China ; *Climate ; *Ecosystem ; Geographic Information Systems ; Meteorological Concepts ; Population Dynamics ; Rain ; Satellite Communications ; Temperature ; Trees/classification/*growth & development ; }, abstract = {Based on the 1982-2006 NDVI remote sensing data and meteorological data of Southwest China, and by using GIS technology, this paper interpolated and extracted the mean annual temperature, annual precipitation, and drought index in the region, and analyzed the correlations of the annual variation of NDVI in different vegetation types (marsh, shrub, bush, grassland, meadow, coniferous forest, broad-leaved forest, alpine vegetation, and cultural vegetation) with corresponding climatic factors. In 1982-2006, the NDVI, mean annual temperature, and annual precipitation had an overall increasing trend, and the drought index decreased. Particularly, the upward trend of mean annual temperature was statistically significant. Among the nine vegetation types, the NDVI of bush and mash decreased, and the downward trend was significant for bush. The NDVI of the other seven vegetation types increased, and the upward trend was significant for coniferous forest, meadow, and alpine vegetation, and extremely significant for shrub. The mean annual temperature in the areas with all the nine vegetation types increased significantly, while the annual precipitation had no significant change. The drought index in the areas with marsh, bush, and cultural vegetation presented an increasing trend, that in the areas with meadow and alpine vegetation decreased significantly, and this index in the areas with other four vegetation types had an unobvious decreasing trend. The NDVI of shrub and coniferous forest had a significantly positive correlation with mean annual temperature, and that of shrub and meadow had significantly negative correlation with drought index. Under the conditions of the other two climatic factors unchanged, the NDVI of coniferous forest, broad-leaved forest, and alpine vegetation showed the strongest correlation with mean annual temperature, that of grass showed the strongest correlation with annual precipitation, and the NDVI of mash, shrub, grass, meadow, and cultural vegetation showed the strongest correlation with drought index. There existed definite correlations among the climatic factors. If the correlations among the climatic factors were ignored, the significant level of the correlations between NDVI and climatic factors would be somewhat reduced.}, } @article {pmid21606358, year = {2011}, author = {Dell, AI and Pawar, S and Savage, VM}, title = {Systematic variation in the temperature dependence of physiological and ecological traits.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {108}, number = {26}, pages = {10591-10596}, pmid = {21606358}, issn = {1091-6490}, mesh = {Animals ; Biodiversity ; Databases, Factual ; *Ecology ; Models, Theoretical ; *Temperature ; }, abstract = {To understand the effects of temperature on biological systems, we compile, organize, and analyze a database of 1,072 thermal responses for microbes, plants, and animals. The unprecedented diversity of traits (n = 112), species (n = 309), body sizes (15 orders of magnitude), and habitats (all major biomes) in our database allows us to quantify novel features of the temperature response of biological traits. In particular, analysis of the rising component of within-species (intraspecific) responses reveals that 87% are fit well by the Boltzmann-Arrhenius model. The mean activation energy for these rises is 0.66 ± 0.05 eV, similar to the reported across-species (interspecific) value of 0.65 eV. However, systematic variation in the distribution of rise activation energies is evident, including previously unrecognized right skewness around a median of 0.55 eV. This skewness exists across levels of organization, taxa, trophic groups, and habitats, and it is partially explained by prey having increased trait performance at lower temperatures relative to predators, suggesting a thermal version of the life-dinner principle-stronger selection on running for your life than running for your dinner. For unimodal responses, habitat (marine, freshwater, and terrestrial) largely explains the mean temperature at which trait values are optimal but not variation around the mean. The distribution of activation energies for trait falls has a mean of 1.15 ± 0.39 eV (significantly higher than rises) and is also right-skewed. Our results highlight generalities and deviations in the thermal response of biological traits and help to provide a basis to predict better how biological systems, from cells to communities, respond to temperature change.}, } @article {pmid21600936, year = {2011}, author = {Lee, SH and Cho, JC}, title = {Group-specific PCR primers for the phylum Acidobacteria designed based on the comparative analysis of 16S rRNA gene sequences.}, journal = {Journal of microbiological methods}, volume = {86}, number = {2}, pages = {195-203}, doi = {10.1016/j.mimet.2011.05.003}, pmid = {21600936}, issn = {1872-8359}, mesh = {Bacteria/classification/*genetics/*isolation & purification ; Bacteriological Techniques/*methods ; Cluster Analysis ; Computational Biology ; Consensus Sequence ; DNA Primers/*genetics ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Phylogeny ; Polymerase Chain Reaction/*methods ; RNA, Ribosomal, 16S/genetics ; Sensitivity and Specificity ; Sequence Analysis, DNA ; Soil Microbiology ; }, abstract = {We performed a comprehensive phylogenetic analysis of the phylum Acidobacteria and developed novel, group-specific PCR primers for Acidobacteria and its class-level subgroups. Acidobacterial 16S rRNA gene sequences deposited in the RDP database were used to construct a local database then subsequently analyzed. A total of 556 phylotypes were observed and the majority of the phylotypes belonged to five major subgroups (subgroups 1, 2, 3, 4, and 6), which comprised >80% of the acidobacterial sequences in the RDP database. Phylum-specific and subgroup-specific primers were designed from the consensus sequences of the phylotype sequences, and the specificities of the designed primers were evaluated both in silico and empirically for coverage and tolerance. The phylum-specific primer ACIDO, which was designed in this study, showed increased coverage for Acidobacteria, as compared to the previous phylum-specific primer 31F. However, the tolerance of the primer ACIDO for non-target sequences was slightly higher than that of the primer 31F. We also developed subgroup-specific PCR primers for the major subgroups of Acidobacteria, except for subgroup 4. Subgroup-specific primers S1, S2, and S3, which targeted subgroups 1, 2, and 3, respectively, showed high coverage for their target subgroups and low tolerance for non-target sequences. However, the primer S6 targeting subgroup 6 showed a lower specificity in its empirical evaluation than expected from the in silico results. The subgroup-specific primers, as well as the phylum-specific primer designed in this study, will be valuable tools in understanding the phylogenetic diversity and ecological niche of the phylum Acidobacteria and its subgroups.}, } @article {pmid21599235, year = {2011}, author = {Hasegawa, T and Konno, N and Masuda, N}, title = {Numerical study of a three-state host-parasite system on the square lattice.}, journal = {Physical review. E, Statistical, nonlinear, and soft matter physics}, volume = {83}, number = {4 Pt 2}, pages = {046102}, doi = {10.1103/PhysRevE.83.046102}, pmid = {21599235}, issn = {1550-2376}, mesh = {Algorithms ; Animals ; Behavior, Animal ; Computer Simulation ; Ecology ; Host-Parasite Interactions/*genetics/*physiology ; Models, Biological ; Models, Statistical ; Models, Theoretical ; Monte Carlo Method ; Population Dynamics ; Time Factors ; }, abstract = {We numerically study the phase diagram of a three-state host-parasite model on the square lattice motivated by population biology. The model is an extension of the contact process, and the three states correspond to an empty site, a host, and a parasite. We determine the phase diagram of the model by scaling analysis. In agreement with previous results, three phases are identified: the phase in which both hosts and parasites are extinct (S(0)), the phase in which hosts survive but parasites are extinct (S(01)), and the phase in which both hosts and parasites survive (S(012)). We argue that both the S(0)-S(01) and S(01)-S(012) boundaries belong to the directed percolation class. In this model, it has been suggested that an excessively large reproduction rate of parasites paradoxically extinguishes hosts and parasites and results in S(0). We show that this paradoxical extinction is a finite size effect; the corresponding parameter region is likely to disappear in the limit of infinite system size.}, } @article {pmid21596762, year = {2011}, author = {Te Grotenhuis, M and Eisinga, R and Subramanian, SV}, title = {Robinson's Ecological Correlations and the Behavior of Individuals: methodological corrections.}, journal = {International journal of epidemiology}, volume = {40}, number = {4}, pages = {1123-1125}, doi = {10.1093/ije/dyr081}, pmid = {21596762}, issn = {1464-3685}, mesh = {Black or African American/statistics & numerical data ; *Bias ; Censuses ; Data Interpretation, Statistical ; Educational Status ; *Epidemiologic Methods ; Humans ; United States ; White People/statistics & numerical data ; }, } @article {pmid21590668, year = {2011}, author = {Suwannatrai, A and Suwannatrai, K and Haruay, S and Piratae, S and Thammasiri, C and Khampoosa, P and Kulsantiwong, J and Prasopdee, S and Tarbsripair, P and Suwanwerakamtorn, R and Sukchan, S and Boonmars, T and Malone, JB and Kearney, MT and Tesana, S}, title = {Effect of soil surface salt on the density and distribution of the snail Bithynia siamensis goniomphalos in northeast Thailand.}, journal = {Geospatial health}, volume = {5}, number = {2}, pages = {183-190}, doi = {10.4081/gh.2011.170}, pmid = {21590668}, issn = {1970-7096}, mesh = {Animals ; Geographic Information Systems ; Host-Parasite Interactions ; Humans ; Models, Biological ; Opisthorchiasis/*epidemiology/parasitology ; Opisthorchis/*parasitology ; Population Density ; Seawater/chemistry ; Snails/*growth & development/parasitology ; Sodium Chloride/analysis ; Soil/*chemistry ; Thailand/epidemiology ; }, abstract = {Opisthorchis viverrini infection is associated with human cholangiocarcinoma and northeast Thailand has the highest incidence of this disease in the world. Bithynia siamensis goniomphalos is the major freshwater snail intermediate host of O. viverrini in this area and an analysis based on geographical information systems was used to determine the effect of variation in soil surface salt on the density and distribution of this snail. A malacological survey was carried out in 56 water bodies in the Khorat basin, northeast Thailand at locations with various soil surface salt levels. Mollusk samples were collected from 10 ecologically representative water body sites with 10-20 sampling stations in each. The shoreline of clear, shallow water bodies was found to be the preferred B. s. goniomphalos habitat. The snails were exclusively found in water with salinity levels ranging between 0.05 and 22.11 parts per thousand (ppt), which supports the notion that B. s. goniomphalos prefers water with some saline content over pure, freshwater. The highest snail population densities were in rice fields, ponds, road-side ditches and canals within a water salinity range of 2.5-5.0 ppt. However, the presence of B. s. goniomphalos was negatively correlated with water salinity (P ≤0.05), both with regard to density and distribution. The areas with the highest density of B. s. goniomphalos were those with less than 1% soil surface salt (potential index = 0.314), while the lowest densities were found in areas exceeding 50% soil surface salt (potential index = 0.015).}, } @article {pmid21590666, year = {2011}, author = {Delgado-Petrocelli, L and Camardiel, A and Aguilar, VH and Martinez, N and Córdova, K and Ramos, S}, title = {Geospatial tools for the identification of a malaria corridor in Estado Sucre, a Venezuelan north-eastern state.}, journal = {Geospatial health}, volume = {5}, number = {2}, pages = {169-176}, doi = {10.4081/gh.2011.168}, pmid = {21590666}, issn = {1970-7096}, mesh = {Analysis of Variance ; Animals ; Anopheles/*growth & development ; Climate Change ; Cluster Analysis ; Ecology/methods ; *Endemic Diseases ; Geographic Information Systems ; Humans ; Incidence ; Insect Vectors/growth & development ; Malaria/*epidemiology ; Models, Biological ; Venezuela/epidemiology ; *Wetlands ; }, abstract = {Landscape ecology research relies on frameworks based on geographical information systems (GIS), geostatistics and spatial-feature relationships. With regard to health, the approach consists of systems analysis using a set of powerful tools aimed at the reduction of community vulnerability through improved public policies. The north-oriental malaria focus, one of five such foci in Venezuela, situated in the north-eastern part of the Estado Sucre state, unites several social and environmental features and functions as an epidemiological corridor, i.e. an endemic zone characterised by permanent interaction between the mosquito vector and the human host allowing a continuous persistence of the malaria lifecycle. A GIS was developed based on official cartography with thematic overlays depicting malaria distribution, socio-economic conditions, basic environmental information and specific features associated with the natural wetlands present in the area. Generally, malaria foci are continuously active but when the malaria situation was modelled in the north-oriental focus, a differential, spatio-temporal distribution pattern situation was found, i.e. a situation oscillating between very active and dormant transmission. This pattern was displayed by spatial and statistical analysis based on the model generated in this study and the results were confirmed by municipal and county malaria records. Control of malaria, keeping the incidence at a permanently low level within the regional population, should be possible if these results are taken into account when designing and implementing epidemiological surveillance policies.}, } @article {pmid21590665, year = {2011}, author = {Machault, V and Vignolles, C and Borchi, F and Vounatsou, P and Pages, F and Briolant, S and Lacaux, JP and Rogier, C}, title = {The use of remotely sensed environmental data in the study of malaria.}, journal = {Geospatial health}, volume = {5}, number = {2}, pages = {151-168}, doi = {10.4081/gh.2011.167}, pmid = {21590665}, issn = {1970-7096}, mesh = {Animals ; Anopheles/*growth & development/parasitology ; Ecosystem ; Geographic Information Systems ; Humans ; Insect Vectors/*parasitology ; Malaria/*epidemiology/prevention & control/transmission ; Models, Biological ; Plasmodium/parasitology ; *Remote Sensing Technology ; Risk Assessment/methods ; Space-Time Clustering ; Urban Health ; Weather ; }, abstract = {Mapping and anticipating risk is a major issue in the fight against malaria, a disease causing an estimated one million deaths each year. Approximately half the world's population is at risk and it is of prime importance to evaluate the burden of malaria at the spatial as well as the temporal level. The role of the environment with regard to the determinants of transmission and burden of the disease are described followed by a discussion of special issues such as urban malaria, human population mapping and the detection of changes at the temporal scale. Risk maps at appropriate scales can provide valuable information for targeted control and the present review discusses the essentials of principles, methods, advantages and limitations of remote sensing along with a presentation of ecological, meteorological and climatologic data which rule the distribution of malaria. The panel of commonly used analytic methods is examined and the methodological limitations are highlighted. A review of the literature details the increasing interest in the use of remotely sensed data in the study of malaria, by mapping or modeling several malariometric indices such as prevalence, morbidity and mortality, which are discussed with reference to vector breeding, vector density and entomological inoculation rate, estimates of which constitute the foundation for understanding endemicity and epidemics.}, } @article {pmid21586382, year = {2011}, author = {Rigaud, AS and Pino, M and Wu, YH and DE Rotrou, J and Boulay, M and Seux, ML and Hugonot-Diener, L and DE Sant'anna, M and Moulin, F and LE Gouverneur, G and Cristancho-Lacroix, V and Lenoir, H}, title = {[Support for patients with Alzheimer's disease and their caregivers by gerontechnology].}, journal = {Geriatrie et psychologie neuropsychiatrie du vieillissement}, volume = {9}, number = {1}, pages = {91-100}, doi = {10.1684/pnv.2010.0248}, pmid = {21586382}, issn = {2115-8789}, mesh = {Accidental Falls/prevention & control ; Aged ; Alzheimer Disease/*psychology ; Automation ; Caregivers/*psychology ; Computer-Assisted Instruction ; *Cost of Illness ; France ; Geographic Information Systems ; Humans ; *Internet ; Randomized Controlled Trials as Topic ; Reminder Systems ; Remote Consultation ; Robotics ; *Self-Help Devices ; *Social Support ; }, abstract = {The increasing number of people suffering from Alzheimer's disease raises the question of their caring at home, especially when the disease causes disability and negative consequences in daily life such as isolation, falls, wandering, errors in drug taking. Furthermore, caregivers bear a substantial burden that can have adverse effects on their physical and mental health. New technologies of information could play an additional role as care providers without substituting family or professional caregivers help. A review of literature focused on the different technological solutions conceived for patients suffering from Alzheimer's disease and their carers shows that these appliances could help to provide reminders in daily life (drugs, tasks and appointments, meals cooking), to activate residual cognitive resources by computerized cognitive stimulation intervention, to reduce stress, anxiety and depressive symptoms in patients by visual contact with families and professionals (webconference), to contribute to patients safety by detecting falls and wandering, and to help families in the caring of patients with computerized information and counselling interventions. We also discuss the current limitations for a widespread use of these technologies and outline future research avenues. True needs of end-users are still poorly known and should be more clearly defined. Simplicity of the use of these appliances should be further improved. Demonstration of medical and social benefits for elderly people should be carried out in randomized, controlled studies. Ethical reflexion should be developed in conjunction with the use of these gerontechnologies. Finally, the economical model which would enable the providing of these appliances to the largest number of patients and caregivers should be implemented. Although these gerontechnologies are promising, research is still needed to tailor them properly to the needs of end-users, assess their benefit in ecological context of people with Alzheimer's disease in order to provide them with appropriate tools in daily life.}, } @article {pmid21586331, year = {2011}, author = {Ahmadlou, M and Adeli, H}, title = {Functional community analysis of brain: a new approach for EEG-based investigation of the brain pathology.}, journal = {NeuroImage}, volume = {58}, number = {2}, pages = {401-408}, doi = {10.1016/j.neuroimage.2011.04.070}, pmid = {21586331}, issn = {1095-9572}, mesh = {Adolescent ; Algorithms ; Attention Deficit Disorder with Hyperactivity/pathology ; Auditory Perception/physiology ; Brain/*pathology ; Brain Diseases/*pathology ; Child ; Cortical Synchronization ; Data Interpretation, Statistical ; Electroencephalography/*methods/statistics & numerical data ; Evoked Potentials/physiology ; Female ; Fuzzy Logic ; Humans ; Likelihood Functions ; Male ; Neural Pathways/*pathology ; Psychomotor Performance/physiology ; Reproducibility of Results ; Visual Perception/physiology ; }, abstract = {Analysis of structure of the brain functional connectivity (SBFC) is a fundamental issue for understanding of the brain cognition as well as the pathology of brain disorders. Analysis of communities among sub-parts of a system is increasingly used for social, ecological, and other networks. This paper presents a new methodology for investigation of the SBFC and understanding of the brain based on graph theory and community pattern analysis of functional connectivity graph of the brain obtained from encephalograms (EEGs). The methodology consists of three main parts: fuzzy synchronization likelihood (FSL), community partitioning, and decisions based on partitions. As an example application, the methodology is applied to analysis of brain of patients with attention deficit/hyperactivity disorder (ADHD) and the problem of discrimination of ADHD EEGs from healthy (non-ADHD) EEGs.}, } @article {pmid21586330, year = {2011}, author = {Dziobek, I and Preissler, S and Grozdanovic, Z and Heuser, I and Heekeren, HR and Roepke, S}, title = {Neuronal correlates of altered empathy and social cognition in borderline personality disorder.}, journal = {NeuroImage}, volume = {57}, number = {2}, pages = {539-548}, doi = {10.1016/j.neuroimage.2011.05.005}, pmid = {21586330}, issn = {1095-9572}, mesh = {Adult ; Borderline Personality Disorder/*physiopathology/psychology ; Brain/*physiopathology ; *Brain Mapping ; Cognition/physiology ; Emotions/physiology ; Empathy/physiology ; Female ; Humans ; Image Interpretation, Computer-Assisted ; Magnetic Resonance Imaging ; *Social Behavior ; Social Perception ; }, abstract = {Borderline personality disorder (BPD) is a severe psychiatric condition of undetermined brain underpinnings, which involves profound emotion regulation deficits and interpersonal impairment. To elucidate biopsychological markers of the disorder, we performed two studies: i.) assessing empathy and social cognition and ii.) measuring the psychophysical properties and functional brain correlates of empathic functioning in a total of fifty-one affected patients and 50 age- and gender-matched controls. In the behavioral study we applied the Multifaceted Empathy Test (MET), a new, ecologically valid measure to assess cognitive (i.e., social cognition) and emotional (i.e., empathic concern) empathy to a subset of participants. In the second study, functional Magnetic Resonance Imaging and skin conductance measurements were performed while participants took a scanner-adapted version of the MET. Patients with BPD showed impairments in cognitive and emotional empathy. Brain responses during cognitive empathy were significantly reduced in patients compared to controls in the left superior temporal sulcus and gyrus (STS/STG), where this reduction was associated with levels of intrusive symptomatology in the BPD group. During emotional empathy, patients with BPD exhibited greater brain activity than controls in the right middle insular cortex, a response that was associated with skin conductance responses in the patients. Results indicate that altered functioning of the STS/STG and insula represents pathophysiological mediators for reduced empathy in BPD, with an important role for intrusive symptomatology and levels of arousal. The findings thus support a conceptualization of BPD as involving deficits in both inferring others' mental states and being emotionally attuned to another person.}, } @article {pmid21585048, year = {2011}, author = {Xie, C and Suo, F and Zhou, Y and Wang, L and Xiang, L and Dong, L and Jia, G and Sun, C and Chen, S}, title = {[Quantitative study on ecological suitability of Chinese herbal medicine based on GIS].}, journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica}, volume = {36}, number = {3}, pages = {379-382}, pmid = {21585048}, issn = {1001-5302}, mesh = {Adaptation, Biological ; *Drugs, Chinese Herbal ; *Ecology ; Environment ; *Geographic Information Systems ; Models, Theoretical ; }, abstract = {The quality of Chinese herbal medicine is closely related to its producing region. In order to apply mathematical models to do a quantitative study on the suitability of Chinese herbal medicine, it is necessary to study on the ecological factors and the interpolation of climatic data, which influence the Chinese herbal medicine growth. The paper firstly studied the judgment standard of ecological index from the points of ecology and statistics, and how to calculate the optimum range values and the weight of each ecological factor. Secondly, meteorological element data is essential data in analyzing the suitable region of Chinese herbal medicine, and the spatial distribution of meteorological elements is closely related to terrain environment, so, in order to make the results close to true value by the greatest degree. The paper adopted multiple linear regression interpolation method which based on DEM. The paper distinguished the factor system of suitable region and interpolation on the point of datumization, and made a study on it about some key issues.}, } @article {pmid21585033, year = {2011}, author = {Zhang, X and Zhou, T and Guo, L and Zhu, S and Huang, L}, title = {[Ecology suitability of Polygonum capitatum in Guizhou province based on topographical conditions].}, journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica}, volume = {36}, number = {3}, pages = {311-315}, pmid = {21585033}, issn = {1001-5302}, mesh = {Adaptation, Biological ; China ; *Ecology ; Gallic Acid/analysis ; Geographic Information Systems ; Polygonum/chemistry/*physiology ; *Topography, Medical ; }, abstract = {OBJECTIVE: To study ecology suitability rank dividing of Polygonum capitatum for selecting artificial planting base and high-quality industrial raw material in Guizhou province.

METHOD: Based on the investigation of PCB and DEM data of Guizhou province, the relationship between the gallic acid content in P. capitatum and topographical conditions was analyzed by statistical analysis. The geographic information systems (GIS)-based assessment and landscape ecological principles were applied to assess ecology suitability areas of P. capitatum in Guizhou.

RESULT AND CONCLUSION: slope, aspect and altitude are main topographical factors that affect the content of gallic acid in P. capitatum. The gallic acid content of P. capitatum is higher in the lower altitude, shady slope and smaller slope areas. The gallic acid content is higher in the eastern areas of Guizhou province.}, } @article {pmid21573854, year = {2012}, author = {Jeong, SW and An, YJ}, title = {Construction of a chemical ranking system of soil pollution substances for screening of priority soil contaminants in Korea.}, journal = {Environmental monitoring and assessment}, volume = {184}, number = {4}, pages = {2193-2204}, pmid = {21573854}, issn = {1573-2959}, mesh = {Chemical Hazard Release ; Databases, Factual ; Ecotoxicology ; Environmental Exposure ; Republic of Korea ; Soil Pollutants/*analysis/*classification/poisoning ; }, abstract = {The Korean government recently proposed expanding the number of soil-quality standards to 30 by 2015. The objectives of our study were to construct a reasonable protocol for screening priority soil contaminants for inclusion in the planned soil quality standard expansion. The chemical ranking system of soil pollution substances (CROSS) was first developed to serve as an analytical tool in chemical scoring and ranking of possible soil pollution substances. CROSS incorporates important parameters commonly used in several previous chemical ranking and scoring systems and the new soil pollution parameters. CROSS uses soil-related parameters in its algorithm, including information related to the soil environment, such as soil ecotoxicological data, the soil toxic release inventory (TRI), and soil partitioning coefficients. Soil TRI and monitoring data were incorporated as local specific parameters. In addition, CROSS scores the transportability of chemicals in soil because soil contamination may result in groundwater contamination. Dermal toxicity was used in CROSS only to consider contact with soil. CROSS uses a certainty score to incorporate data uncertainty. CROSS scores the importance of each candidate substance and assigns rankings on the basis of total scores. Cadmium was the most highly ranked. Generally, metals were ranked higher than other substances. Pentachlorophenol, phenol, dieldrin, and methyl tert-butyl ether were ranked the highest among chlorinated compounds, aromatic compounds, pesticides, and others, respectively. The priority substance list generated from CROSS will be used in selecting substances for possible inclusion in the Korean soil quality standard expansion; it will also provide important information for designing a soil-environment management scheme.}, } @article {pmid21573169, year = {2011}, author = {van Gremberghe, I and Leliaert, F and Mergeay, J and Vanormelingen, P and Van der Gucht, K and Debeer, AE and Lacerot, G and De Meester, L and Vyverman, W}, title = {Lack of phylogeographic structure in the freshwater cyanobacterium Microcystis aeruginosa suggests global dispersal.}, journal = {PloS one}, volume = {6}, number = {5}, pages = {e19561}, pmid = {21573169}, issn = {1932-6203}, mesh = {Base Sequence ; DNA, Bacterial/chemistry/genetics ; DNA, Intergenic/genetics ; DNA, Ribosomal/genetics ; Databases, Nucleic Acid ; Fresh Water/*microbiology ; *Internationality ; Microcystis/*genetics/*physiology ; Models, Genetic ; Molecular Sequence Data ; Movement ; Nucleic Acid Conformation ; Operon/genetics ; *Phylogeography ; Sequence Alignment ; }, abstract = {BACKGROUND: Free-living microorganisms have long been assumed to have ubiquitous distributions with little biogeographic signature because they typically exhibit high dispersal potential and large population sizes. However, molecular data provide contrasting results and it is far from clear to what extent dispersal limitation determines geographic structuring of microbial populations. We aimed to determine biogeographical patterns of the bloom-forming freshwater cyanobacterium Microcystis aeruginosa. Being widely distributed on a global scale but patchily on a regional scale, this prokaryote is an ideal model organism to study microbial dispersal and biogeography.

The phylogeography of M. aeruginosa was studied based on a dataset of 311 rDNA internal transcribed spacer (ITS) sequences sampled from six continents. Richness of ITS sequences was high (239 ITS types were detected). Genetic divergence among ITS types averaged 4% (maximum pairwise divergence was 13%). Preliminary analyses revealed nearly completely unresolved phylogenetic relationships and a lack of genetic structure among all sequences due to extensive homoplasy at multiple hypervariable sites. After correcting for this, still no clear phylogeographic structure was detected, and no pattern of isolation by distance was found on a global scale. Concomitantly, genetic differentiation among continents was marginal, whereas variation within continents was high and was mostly shared with all other continents. Similarly, no genetic structure across climate zones was detected.

CONCLUSIONS/SIGNIFICANCE: The high overall diversity and wide global distribution of common ITS types in combination with the lack of phylogeographic structure suggest that intercontinental dispersal of M. aeruginosa ITS types is not rare, and that this species might have a truly cosmopolitan distribution.}, } @article {pmid21572512, year = {2011}, author = {He, BZ and Holloway, AK and Maerkl, SJ and Kreitman, M}, title = {Does positive selection drive transcription factor binding site turnover? A test with Drosophila cis-regulatory modules.}, journal = {PLoS genetics}, volume = {7}, number = {4}, pages = {e1002053}, pmid = {21572512}, issn = {1553-7404}, support = {R01 GM078381/GM/NIGMS NIH HHS/United States ; GM078381/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Binding Sites/*genetics ; Biological Evolution ; Databases, Genetic ; Drosophila/genetics/*metabolism ; Drosophila Proteins/genetics/*metabolism ; Drosophila melanogaster/genetics/*metabolism ; Gene Expression Regulation ; Models, Genetic ; Mutation ; Phylogeny ; Polymorphism, Genetic ; Protein Binding/*genetics ; *Selection, Genetic ; Sequence Analysis, DNA ; Species Specificity ; Transcription Factors/genetics/*metabolism ; }, abstract = {Transcription factor binding site(s) (TFBS) gain and loss (i.e., turnover) is a well-documented feature of cis-regulatory module (CRM) evolution, yet little attention has been paid to the evolutionary force(s) driving this turnover process. The predominant view, motivated by its widespread occurrence, emphasizes the importance of compensatory mutation and genetic drift. Positive selection, in contrast, although it has been invoked in specific instances of adaptive gene expression evolution, has not been considered as a general alternative to neutral compensatory evolution. In this study we evaluate the two hypotheses by analyzing patterns of single nucleotide polymorphism in the TFBS of well-characterized CRM in two closely related Drosophila species, Drosophila melanogaster and Drosophila simulans. An important feature of the analysis is classification of TFBS mutations according to the direction of their predicted effect on binding affinity, which allows gains and losses to be evaluated independently along the two phylogenetic lineages. The observed patterns of polymorphism and divergence are not compatible with neutral evolution for either class of mutations. Instead, multiple lines of evidence are consistent with contributions of positive selection to TFBS gain and loss as well as purifying selection in its maintenance. In discussion, we propose a model to reconcile the finding of selection driving TFBS turnover with constrained CRM function over long evolutionary time.}, } @article {pmid21569320, year = {2011}, author = {Cargo, M and Marks, E and Brimblecombe, J and Scarlett, M and Maypilama, E and Dhurrkay, JG and Daniel, M}, title = {Integrating an ecological approach into an Aboriginal community-based chronic disease prevention program: a longitudinal process evaluation.}, journal = {BMC public health}, volume = {11}, number = {}, pages = {299}, pmid = {21569320}, issn = {1471-2458}, mesh = {Australia ; Cardiovascular Diseases/*prevention & control ; *Community Networks ; Diabetes Mellitus, Type 2/*prevention & control ; Female ; Health Promotion/*methods ; Humans ; Interviews as Topic ; Longitudinal Studies ; Male ; }, abstract = {BACKGROUND: Public health promotes an ecological approach to chronic disease prevention, however, little research has been conducted to assess the integration of an ecological approach in community-based prevention programs. This study sought to contribute to the evidence base by assessing the extent to which an ecological approach was integrated into an Aboriginal community-based cardiovascular disease (CVD) and type 2 diabetes prevention program, across three-intervention years.

METHODS: Activity implementation forms were completed by interview with implementers and participant observation across three intervention years. A standardised ecological coding procedure was applied to assess participant recruitment settings, intervention targets, intervention strategy types, extent of ecologicalness and organisational partnering. Inter-rater reliability for two coders was assessed at Kappa = 0.76 (p < .0.001), 95% CI (0.58, 0.94).

RESULTS: 215 activities were implemented across three intervention years by the health program (HP) with some activities implemented in multiple years. Participants were recruited most frequently through organisational settings in years 1 and 2, and organisational and community settings in year 3. The most commonly utilised intervention targets were the individual (IND) as a direct target, and interpersonal (INT) and organisational (ORG) environments as indirect targets; policy (POL), and community (COM) were targeted least. Direct (HP→ IND) and indirect intervention strategies (i.e., HP→ INT→ IND, HP→ POL → IND) were used most often; networking strategies, which link at least two targets (i.e., HP→[ORG-ORG]→IND), were used the least. The program did not become more ecological over time.

CONCLUSIONS: The quantity of activities with IND, INT and ORG targets and the proportion of participants recruited through informal cultural networking demonstrate community commitment to prevention. Integration of an ecological approach would have been facilitated by greater inter-organisational collaboration and centralised planning. The upfront time required for community stakeholders to develop their capacity to mobilise around chronic disease is at odds with short-term funding cycles that emphasise organisational accountability.}, } @article {pmid21562085, year = {2011}, author = {Ness, AR and Griffiths, AE and Howe, LD and Leary, SD}, title = {Drawing causal inferences in epidemiologic studies of early life influences.}, journal = {The American journal of clinical nutrition}, volume = {94}, number = {6 Suppl}, pages = {1959S-1963S}, doi = {10.3945/ajcn.110.001461}, pmid = {21562085}, issn = {1938-3207}, mesh = {Bias ; Confounding Factors, Epidemiologic ; Data Interpretation, Statistical ; Epidemiologic Studies ; Female ; Follow-Up Studies ; Humans ; Obesity/*epidemiology ; Pregnancy ; *Prenatal Exposure Delayed Effects ; }, abstract = {Observational studies can describe associations between early life exposures and subsequent outcomes in human populations. It is challenging to draw causal inferences from these associations because exposures often occur many years before the outcome and are related to other early life exposures. An approach is required that combines traditional epidemiologic and statistical principles with the use of novel and sophisticated analytic methods. To minimize the bias in longitudinal studies of early origins, researchers need to do all they can to reduce losses to follow-up and to describe individuals who are lost to follow-up. To reduce the role of chance, researchers should concentrate on effect sizes and the strength of the evidence to support these effect sizes, and they should be cautious in their interpretation of subgroup analyses. More complex analytic approaches can and should be used to handle missing data and repeated measurements. Addressing the issue of confounding is not straightforward. Statistical adjustment for the confounders measured in a study may help, but a lack of attenuation does not guarantee that the association is not confounded. Ecologic studies, observational studies in populations with different confounding structures, and the follow-up of randomized trials (where these exist) can be informative. Genetic and nongenetic instrumental variable approaches (eg, Mendelian randomization) may also provide causal insights. These approaches to confounding often require the comparison of data from different populations or a combination of studies to ensure adequate power to provide robust estimates of the causal effect.}, } @article {pmid21556707, year = {2011}, author = {Li, H and Chen, Z and Hu, M and Wang, Z and Hua, H and Yin, C and Zeng, H}, title = {Different effects of night versus day high temperature on rice quality and accumulation profiling of rice grain proteins during grain filling.}, journal = {Plant cell reports}, volume = {30}, number = {9}, pages = {1641-1659}, pmid = {21556707}, issn = {1432-203X}, mesh = {Carbohydrate Metabolism ; Computational Biology ; Electrophoresis, Gel, Two-Dimensional ; Glycoside Hydrolases/metabolism ; *Hot Temperature ; Isoenzymes ; Oryza/enzymology/growth & development/*physiology ; Plant Proteins/analysis/*metabolism ; Pyruvate, Orthophosphate Dikinase/metabolism ; Seeds/enzymology/growth & development/*physiology ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/methods ; }, abstract = {High temperature has adverse effects on rice yield and quality. The different influences of night high temperature (NHT) and day high temperature (DHT) on rice quality and seed protein accumulation profiles during grain filling in indica rice '9311' were studied in this research. The treatment temperatures of the control, NHT, and DHT were 28°C/20°C, 27°C/35°C, and 35°C/27°C, respectively, and all the treatments were maintained for 20 days. The result of rice quality analysis indicated that compared with DHT, NHT exerted less effect on head rice rate and chalkiness, whereas greater effect on grain weight. Moreover, the dynamic accumulation change profiles of 61 protein spots, differentially accumulated and successfully identified under NHT and DHT conditions, were performed by proteomic approach. The results also showed that the different suppressed extent of accumulation amount of cyPPDKB might result in different grain chalkiness between NHT and DHT. Most identified isoforms of proteins, such as PPDK and pullulanase, displayed different accumulation change patterns between NHT and DHT. In addition, compared with DHT, NHT resulted in the unique accumulation patterns of stress and defense proteins. Taken together, the mechanisms of seed protein accumulation profiles induced by NHT and DHT during grain filling should be different in rice, and the potential molecular basis is discussed in this study.}, } @article {pmid21554669, year = {2011}, author = {Lurgi, M and Robertson, D}, title = {Automated experimentation in ecological networks.}, journal = {Automated experimentation}, volume = {3}, number = {1}, pages = {1}, pmid = {21554669}, issn = {1759-4499}, abstract = {BACKGROUND: In ecological networks, natural communities are studied from a complex systems perspective by representing interactions among species within them in the form of a graph, which is in turn analysed using mathematical tools. Topological features encountered in complex networks have been proved to provide the systems they represent with interesting attributes such as robustness and stability, which in ecological systems translates into the ability of communities to resist perturbations of different kinds. A focus of research in community ecology is on understanding the mechanisms by which these complex networks of interactions among species in a community arise. We employ an agent-based approach to model ecological processes operating at the species' interaction level for the study of the emergence of organisation in ecological networks.

RESULTS: We have designed protocols of interaction among agents in a multi-agent system based on ecological processes occurring at the interaction level between species in plant-animal mutualistic communities. Interaction models for agents coordination thus engineered facilitate the emergence of network features such as those found in ecological networks of interacting species, in our artificial societies of agents.

CONCLUSIONS: Agent based models developed in this way facilitate the automation of the design an execution of simulation experiments that allow for the exploration of diverse behavioural mechanisms believed to be responsible for community organisation in ecological communities. This automated way of conducting experiments empowers the study of ecological networks by exploiting the expressive power of interaction models specification in agent systems.}, } @article {pmid21554380, year = {2011}, author = {Thomas, MC and Thomas, DK and Selinger, LB and Inglis, GD}, title = {spyder, a new method for in silico design and assessment of 16S rRNA gene primers for molecular microbial ecology.}, journal = {FEMS microbiology letters}, volume = {320}, number = {2}, pages = {152-159}, doi = {10.1111/j.1574-6968.2011.02302.x}, pmid = {21554380}, issn = {1574-6968}, mesh = {Algorithms ; Amino Acid Sequence ; Base Sequence ; Computational Biology/*methods ; Computer-Aided Design ; *DNA Primers ; Databases, Nucleic Acid ; *Environmental Microbiology ; Escherichia coli/genetics ; *Genes, Bacterial ; Molecular Sequence Data ; RNA, Ribosomal, 16S/*genetics ; Sequence Alignment ; *Software ; }, abstract = {Molecular microbial ecology studies are heavily reliant on 'Universal' 16S rRNA gene primers for elucidating microbial community structure and composition, and yet primer design and optimization is often overlooked. Primers that exhibit minor biases due to primer-template mismatches can substantially alter the pool of amplicons from a community DNA sample, resulting in inaccurate conclusions. As a result, it is important that primers are critically evaluated against the most comprehensive data sets available before commencing molecular microbial community studies. We present a user-friendly, multi-platform (e.g. Windows, Linux, Mac) method named spyder for the in silico design and assessment of 16S rRNA gene primers. The method utilizes the Ribosomal Database Project's Probe Match feature coupled with a compact program (available at http://people.uleth.ca/~selibl/Spyder/Spyder.html) that aligns and identifies mismatches between primers and templates. To demonstrate the value of spyder, we assessed commonly used 'Universal' and phyla-specific primers and identified primer modifications that improved the coverage of target organisms by 5-42% as well as removed excessive degeneracies.}, } @article {pmid21554114, year = {2011}, author = {Watson, RA and Mills, R and Buckley, CL}, title = {Global adaptation in networks of selfish components: emergent associative memory at the system scale.}, journal = {Artificial life}, volume = {17}, number = {3}, pages = {147-166}, doi = {10.1162/artl_a_00029}, pmid = {21554114}, issn = {1064-5462}, mesh = {*Adaptation, Physiological ; *Association Learning ; Computational Biology ; Humans ; *Memory ; *Neural Networks, Computer ; Software ; }, abstract = {In some circumstances complex adaptive systems composed of numerous self-interested agents can self-organize into structures that enhance global adaptation, efficiency, or function. However, the general conditions for such an outcome are poorly understood and present a fundamental open question for domains as varied as ecology, sociology, economics, organismic biology, and technological infrastructure design. In contrast, sufficient conditions for artificial neural networks to form structures that perform collective computational processes such as associative memory/recall, classification, generalization, and optimization are well understood. Such global functions within a single agent or organism are not wholly surprising, since the mechanisms (e.g., Hebbian learning) that create these neural organizations may be selected for this purpose; but agents in a multi-agent system have no obvious reason to adhere to such a structuring protocol or produce such global behaviors when acting from individual self-interest. However, Hebbian learning is actually a very simple and fully distributed habituation or positive feedback principle. Here we show that when self-interested agents can modify how they are affected by other agents (e.g., when they can influence which other agents they interact with), then, in adapting these inter-agent relationships to maximize their own utility, they will necessarily alter them in a manner homologous with Hebbian learning. Multi-agent systems with adaptable relationships will thereby exhibit the same system-level behaviors as neural networks under Hebbian learning. For example, improved global efficiency in multi-agent systems can be explained by the inherent ability of associative memory to generalize by idealizing stored patterns and/or creating new combinations of subpatterns. Thus distributed multi-agent systems can spontaneously exhibit adaptive global behaviors in the same sense, and by the same mechanism, as with the organizational principles familiar in connectionist models of organismic learning.}, } @article {pmid21547815, year = {2011}, author = {Choi, M and Curriero, FC and Johantgen, M and Mills, ME and Sattler, B and Lipscomb, J}, title = {Association between ozone and emergency department visits: an ecological study.}, journal = {International journal of environmental health research}, volume = {21}, number = {3}, pages = {201-221}, doi = {10.1080/09603123.2010.533366}, pmid = {21547815}, issn = {1369-1619}, mesh = {Air Pollutants/*analysis/toxicity ; Demography ; Ecology/*methods/statistics & numerical data ; Emergency Service, Hospital/*statistics & numerical data ; Geographic Information Systems ; Humans ; Maryland/epidemiology ; Ozone/*analysis/toxicity ; Seasons ; Socioeconomic Factors ; Time Factors ; Weather ; }, abstract = {The objective of this study was to examine the association between the levels of ozone concentration and emergency department (ED) visits for respiratory and cardiovascular conditions in Maryland in the United States by considering temporal and spatial characteristics, including socioeconomic status (SES), as a covariate. This study used multiple large datasets derived from government agencies for data of ozone, weather, census, and ED visits to represent Maryland in the summer of 2002. Block kriging was used to estimate the daily ozone and weather factors by ZIP code-day level. Results from a negative binomial regression showed that a 10-ppb increment of the 8-hr ozone level as a three-day average was associated with increased respiratory ED visits by 2.4%, after adjusting for weather factors, SES, and day of the week. For cardiovascular ED visits, an increment of 10 ppb of the 8-hr ozone level as a five-day average increased by 3.5%.}, } @article {pmid21545586, year = {2011}, author = {Sawyer, H and Kauffman, MJ}, title = {Stopover ecology of a migratory ungulate.}, journal = {The Journal of animal ecology}, volume = {80}, number = {5}, pages = {1078-1087}, doi = {10.1111/j.1365-2656.2011.01845.x}, pmid = {21545586}, issn = {1365-2656}, mesh = {Animal Migration/*physiology ; Animals ; *Deer/physiology ; Ecosystem ; *Energy Intake ; *Feeding Behavior ; Female ; Geographic Information Systems ; *Herbivory ; Linear Models ; Models, Biological ; Remote Sensing Technology ; Seasons ; Time Factors ; }, abstract = {1. Birds that migrate long distances use stopover sites to optimize fuel loads and complete migration as quickly as possible. Stopover use has been predicted to facilitate a time-minimization strategy in land migrants as well, but empirical tests have been lacking, and alternative migration strategies have not been considered. 2. We used fine-scale movement data to evaluate the ecological role of stopovers in migratory mule deer Odocoileus hemionus- a land migrant whose fitness is strongly influenced by energy intake rather than migration speed. 3. Although deer could easily complete migrations (range 18-144 km) in several days, they took an average of 3 weeks and spent 95% of that time in a series of stopover sites that had higher forage quality than movement corridors. Forage quality of stopovers increased with elevation and distance from winter range. Mule deer use of stopovers corresponded with a narrow phenological range, such that deer occupied stopovers 44 days prior to peak green-up, when forage quality was presumed to be highest. Mule deer used one stopover for every 5·3 and 6·7 km travelled during spring and autumn migrations, respectively, and used the same stopovers in consecutive years. 4. Study findings indicate that stopovers play a key role in the migration strategy of mule deer by allowing individuals to migrate in concert with plant phenology and maximize energy intake rather than speed. Our results suggest that stopover use may be more common among non-avian taxa than previously thought and, although the underlying migration strategies of temperate ungulates and birds are quite different, stopover use is important to both. 5. Exploring the role of stopovers in land migrants broadens the scope of stopover ecology and recognizes that the applied and theoretical benefits of stopover ecology need not be limited to avian taxa.}, } @article {pmid21543903, year = {2011}, author = {Jiang, L and Wang, Y and Björn, LO and Li, S}, title = {Does cell cycle arrest occur in plant under solar UV-B radiation?.}, journal = {Plant signaling & behavior}, volume = {6}, number = {6}, pages = {892-894}, pmid = {21543903}, issn = {1559-2324}, mesh = {Arabidopsis/cytology/genetics/radiation effects ; Arabidopsis Proteins/genetics/metabolism ; Cell Cycle Checkpoints/genetics/*radiation effects ; Computational Biology ; Gene Expression Regulation, Plant/radiation effects ; Oligonucleotide Array Sequence Analysis ; Plant Cells/metabolism/*radiation effects ; *Ultraviolet Rays ; }, abstract = {UV-B radiation (280-315 nm) is an integral part of solar radiation and has many harmful effects on plant growth and development. However, the molecular mechanism for the inhibition of plant growth by UV-B remains largely unknown. UV-B radiation induces various responses such as growth inhibition, DNA damage and changes of gene expression. Recently, by using synchronous root tip culture, we found that UV-B modulates the expression of cell cycle regulatory genes through DNA damage. Western blotting analysis revealed that UV-B induced G1-to-S arrest did not correlate with the protein abundance of CDKB1;1 and CYCD3;1 gene regulating proteins, but may with the posttranslational control. We extended the expression analysis of cell cycle related genes based on the published microarray data and the results strengthen our assumption that cell cycle arrest could occur in plant under solar UV-B radiation. Further study is needed to elucidate the relationship between cell cycle regulation and protective pathway induced by low dose of UV-B radiation fundamental molecular mechanism for how plants respond to solar UV-B radiation.}, } @article {pmid21535428, year = {2011}, author = {Hrcek, J and Miller, SE and Quicke, DL and Smith, MA}, title = {Molecular detection of trophic links in a complex insect host-parasitoid food web.}, journal = {Molecular ecology resources}, volume = {11}, number = {5}, pages = {786-794}, doi = {10.1111/j.1755-0998.2011.03016.x}, pmid = {21535428}, issn = {1755-0998}, mesh = {Animals ; Base Sequence ; Cluster Analysis ; Computational Biology ; DNA Barcoding, Taxonomic ; DNA Primers/genetics ; Diptera/*genetics ; *Food Chain ; Host-Parasite Interactions/*genetics ; Hymenoptera/*genetics ; Larva/parasitology ; Lepidoptera/*genetics/*parasitology ; Molecular Sequence Data ; Papua New Guinea ; Phylogeny ; Sequence Analysis, DNA ; Species Specificity ; Tropical Climate ; }, abstract = {Previously, host-parasitoid links have been unveiled almost exclusively by time-intensive rearing, while molecular methods were used only in simple agricultural host-parasitoid systems in the form of species-specific primers. Here, we present a general method for the molecular detection of these links applied to a complex caterpillar-parasitoid food web from tropical rainforest of Papua New Guinea. We DNA barcoded hosts, parasitoids and their tissue remnants and matched the sequences to our extensive library of local species. We were thus able to match 87% of host sequences and 36% of parasitoid sequences to species and infer subfamily or family in almost all cases. Our analysis affirmed 93 hitherto unknown trophic links between 37 host species from a wide range of Lepidoptera families and 46 parasitoid species from Hymenoptera and Diptera by identifying DNA sequences for both the host and the parasitoid involved in the interaction. Molecular detection proved especially useful in cases where distinguishing host species in caterpillar stage was difficult morphologically, or when the caterpillar died during rearing. We have even detected a case of extreme parasitoid specialization in a pair of Choreutis species that do not differ in caterpillar morphology and ecology. Using the molecular approach outlined here leads to better understanding of parasitoid host specificity, opens new possibilities for rapid surveys of food web structure and allows inference of species associations not already anticipated.}, } @article {pmid21534940, year = {2011}, author = {Fewster, RM}, title = {Variance estimation for systematic designs in spatial surveys.}, journal = {Biometrics}, volume = {67}, number = {4}, pages = {1518-1531}, doi = {10.1111/j.1541-0420.2011.01604.x}, pmid = {21534940}, issn = {1541-0420}, mesh = {Animals ; Biometry/*methods ; *Censuses ; Computer Simulation ; *Data Interpretation, Statistical ; Ecology/*statistics & numerical data ; *Hyaenidae ; *Models, Statistical ; *Population Density ; Sample Size ; }, abstract = {In spatial surveys for estimating the density of objects in a survey region, systematic designs will generally yield lower variance than random designs. However, estimating the systematic variance is well known to be a difficult problem. Existing methods tend to overestimate the variance, so although the variance is genuinely reduced, it is over-reported, and the gain from the more efficient design is lost. The current approaches to estimating a systematic variance for spatial surveys are to approximate the systematic design by a random design, or approximate it by a stratified design. Previous work has shown that approximation by a random design can perform very poorly, while approximation by a stratified design is an improvement but can still be severely biased in some situations. We develop a new estimator based on modeling the encounter process over space. The new "striplet" estimator has negligible bias and excellent precision in a wide range of simulation scenarios, including strip-sampling, distance-sampling, and quadrat-sampling surveys, and including populations that are highly trended or have strong aggregation of objects. We apply the new estimator to survey data for the spotted hyena (Crocuta crocuta) in the Serengeti National Park, Tanzania, and find that the reported coefficient of variation for estimated density is 20% using approximation by a random design, 17% using approximation by a stratified design, and 11% using the new striplet estimator. This large reduction in reported variance is verified by simulation.}, } @article {pmid21531796, year = {2011}, author = {Chandler, JC and Molins, CR and Petersen, JM and Belisle, JT}, title = {Differential chitinase activity and production within Francisella species, subspecies, and subpopulations.}, journal = {Journal of bacteriology}, volume = {193}, number = {13}, pages = {3265-3275}, pmid = {21531796}, issn = {1098-5530}, support = {U54 AI065357/AI/NIAID NIH HHS/United States ; U54AI065357/AI/NIAID NIH HHS/United States ; }, mesh = {Chitin/metabolism ; Chitinases/genetics/*metabolism ; Computational Biology ; DNA, Bacterial/genetics ; Francisella/*enzymology/genetics ; Gene Knockout Techniques ; Genes, Bacterial ; }, abstract = {Genotyping of Francisella tularensis (A1a, A1b, A2, and type B) and Francisella novicida has identified multiple differences between species and among F. tularensis subspecies and subpopulations. Variations in virulence, geographic distribution, and ecology are also known to exist among this group of bacteria, despite the >95% nucleotide identity in their genomes. This study expands the description of phenotypic differences by evaluating the ability of F. tularensis and F. novicida to degrade chitin analogs and produce active chitinases. Endochitinase activities were observed to vary among F. tularensis and F. novicida strains. The activity observed for F. tularensis strains was predominantly associated with whole-cell lysates, while the chitinase activity of F. novicida localized to the culture supernatant. In addition, the overall level of chitinase activity differed among the subpopulations of F. tularensis and between the species. Bioinformatic analyses identified two new putative chitinase genes (chiC and chiD), as well as the previously described chiA and chiB. However, the presence of these four open reading frames as intact genes or pseudogenes was found to differ between Francisella species and F. tularensis subspecies and subpopulations. Recombinant production of the putative chitinases and enzymatic evaluations revealed ChiA, ChiB, ChiC, and ChiD possessed dissimilar chitinase activities. These biochemical studies coupled with bioinformatic analyses and the evaluation of chiA and chiC knockouts in F. tularensis A1 and A2 strains, respectively, provided a molecular basis to explain the differential chitinase activities observed among the species and subpopulations of Francisella.}, } @article {pmid21531037, year = {2012}, author = {Schädler, S and Morio, M and Bartke, S and Finkel, M}, title = {Integrated planning and spatial evaluation of megasite remediation and reuse options.}, journal = {Journal of contaminant hydrology}, volume = {127}, number = {1-4}, pages = {88-100}, doi = {10.1016/j.jconhyd.2011.03.003}, pmid = {21531037}, issn = {1873-6009}, mesh = {Berlin ; Conservation of Natural Resources ; Costs and Cost Analysis ; Environmental Restoration and Remediation/*economics ; Geographic Information Systems ; Groundwater/*chemistry ; Models, Theoretical ; Soil/chemistry ; Tetrachloroethylene/analysis ; Trichloroethylene/analysis ; Water Pollutants, Chemical/analysis ; }, abstract = {Redevelopment of large contaminated brownfields (megasites) is often hampered by a lack of communication and harmonization among diverse stakeholders with potentially conflicting interests. Decision support is required to provide integrative yet transparent evaluation of often complex spatial information to stakeholders with different areas of expertise. It is considered crucial for successful redevelopment to identify a shared vision of how the respective contaminated site could be remediated and redeveloped. We describe a framework of assessment methods and models that analyzes and visualizes site- and land use-specific spatial information at the screening level, with the aim to support the derivation of recommendable land use layouts and to initiate further and more detailed planning. The framework integrates a GIS-based identification of areas to be remediated, an estimation of associated clean-up costs, a spatially explicit market value appraisal, and an assessment of the planned future land use's contribution to sustainable urban and regional development. Case study results show that derived options are potentially favorable in both a sustainability and an economic sense and that iterative re-planning is facilitated by the evaluation and visualization of economic, ecological and socio-economic aspects. The framework supports an efficient early judgment about whether and how abandoned land may be assigned a sustainable and marketable land use.}, } @article {pmid23761246, year = {2011}, author = {Nebel, M and Pfabel, C and Stock, A and Dunthorn, M and Stoeck, T}, title = {Delimiting operational taxonomic units for assessing ciliate environmental diversity using small-subunit rRNA gene sequences.}, journal = {Environmental microbiology reports}, volume = {3}, number = {2}, pages = {154-158}, doi = {10.1111/j.1758-2229.2010.00200.x}, pmid = {23761246}, issn = {1758-2229}, abstract = {Delineating operational taxonomic units (OTUs) is a central element in any culture-independent analysis of environmental microbial eukaryotic diversity. Previous studies either have not justified their choice in sequence distance used to bin small-subunit ribosomal RNA (SSU rRNA) gene sequences amplified from environmental samples into OTUs, or have used a value based on the average across a broad sampling of microbial eukaryotes. Here, we analyse distances (320 922 pairwise comparisons) among sequences just from identified ciliates, and compare these with their taxonomic hierarchy. Our results show that no single sequence similarity value can always and unambiguously delineate species boundaries and higher taxa. Nevertheless, we suggest the use of 98% similarity to delineate ciliate OTUs because this threshold at least accounts for intra-specific polymorphism among multiple rRNA cistron copies. However, we suggest refraining from reconciling SSU rRNA gene-based OTUs and ciliate morphotypes; these OTUs should be used to analyse ciliate phylotype diversity, not ciliate species diversity.}, } @article {pmid22749547, year = {2011}, author = {Kracalik, I and Lukhnova, L and Aikimbayev, A and Pazilov, Y and Temiralyeva, G and Blackburn, JK}, title = {Incorporating retrospective clustering into a prospective Cusum methodology for anthrax: evaluating the effects of disease expectation.}, journal = {Spatial and spatio-temporal epidemiology}, volume = {2}, number = {1}, pages = {11-21}, doi = {10.1016/j.sste.2010.06.001}, pmid = {22749547}, issn = {1877-5853}, mesh = {Animals ; Anthrax/*epidemiology/veterinary ; Cluster Analysis ; Data Interpretation, Statistical ; Disease Outbreaks/*statistics & numerical data/veterinary ; Geography, Medical/methods/statistics & numerical data ; Kazakhstan/epidemiology ; Livestock ; Prospective Studies ; Retrospective Studies ; *Spatio-Temporal Analysis ; }, abstract = {We analysed livestock anthrax in Kazakhstan from 1960-2006, using a prospective CUSUM to examine the affects of expectation on the detection of spatio-temporal clusters. Three methods for deriving baselines were used for CUSUM; a standard z-score, AVG, a spatially-weighted z-score derived from Local Moran's I, LISA, and a moving-window average, MWA. LISA and AVG elicited alarm signals in the second year that did not return below threshold during the 47-year period, while MWA signaled an alarm at year four and relented at year fifteen. The number of spatial clusters elicited varied: LISA n=16, AVG n=11, and MWA n=3, although there were clusters present around Shymkent, in south-central Kazakhstan, in each method. The results illustrate that the selection of a baseline with an unknown background population has a significant effect on the ability to detect the onset of clusters in space and in time when employing a CUSUM methodology.}, } @article {pmid22696946, year = {2011}, author = {Bileva, T and Arnaudova, Zh}, title = {Mapping of nematode distribution and assessment of its ecological status using GIS techniques in Plovdiv region, Bulgaria.}, journal = {Communications in agricultural and applied biological sciences}, volume = {76}, number = {3}, pages = {347-353}, pmid = {22696946}, issn = {1379-1176}, mesh = {Animals ; Bulgaria ; Ecology ; *Geographic Information Systems ; Nematoda/classification/*isolation & purification ; Plant Diseases/parasitology ; Soil/chemistry/*parasitology ; Vitis/parasitology ; }, abstract = {The current investigation was carried out in selected vineyards in Plovdiv region, South Bulgaria. The GIS database was created including factors influenced on nematode distribution in the soil. The plant-parasitic nematodes from family Longidoridae associated with grapevine and soil type of the region were described. The impact of longidorids as virus vectors and some ecological aspects of their occurrence in vineyards in South Bulgaria are discussed.}, } @article {pmid22163432, year = {2010}, author = {Wang, K and Franklin, SE and Guo, X and Cattet, M}, title = {Remote sensing of ecology, biodiversity and conservation: a review from the perspective of remote sensing specialists.}, journal = {Sensors (Basel, Switzerland)}, volume = {10}, number = {11}, pages = {9647-9667}, pmid = {22163432}, issn = {1424-8220}, mesh = {*Biodiversity ; *Ecology ; Geographic Information Systems ; Remote Sensing Technology/*methods ; }, abstract = {Remote sensing, the science of obtaining information via noncontact recording, has swept the fields of ecology, biodiversity and conservation (EBC). Several quality review papers have contributed to this field. However, these papers often discuss the issues from the standpoint of an ecologist or a biodiversity specialist. This review focuses on the spaceborne remote sensing of EBC from the perspective of remote sensing specialists, i.e., it is organized in the context of state-of-the-art remote sensing technology, including instruments and techniques. Herein, the instruments to be discussed consist of high spatial resolution, hyperspectral, thermal infrared, small-satellite constellation, and LIDAR sensors; and the techniques refer to image classification, vegetation index (VI), inversion algorithm, data fusion, and the integration of remote sensing (RS) and geographic information system (GIS).}, } @article {pmid21594118, year = {2010}, author = {Taekul, C and Johnson, NF and Masner, L and Polaszek, A and Rajmohana K, }, title = {World species of the genus Platyscelio Kieffer (Hymenoptera: Platygastridae).}, journal = {ZooKeys}, volume = {}, number = {50}, pages = {97-126}, pmid = {21594118}, issn = {1313-2970}, abstract = {The genus Platyscelio Kieffer (Hymenoptera: Platygastridae, Scelioninae) is a widespread group in the Old World, found from West Africa to northern Queensland, Australia. The species concepts are revised and a key to world species is presented. The genus is comprised of 6 species, including 2 known species which are redescribed: Platyscelioafricanus Risbec (Benin, Cameroon, Central African Republic, Ghana, Guinea, Guinea-Bissau, Ivory Coast, Kenya, Mozambique, Nigeria, Sierra Leone, South Africa, Tanzania, Togo, Uganda, Yemen, Zimbabwe); and Platysceliopulchricornis Kieffer (Australia, Bangladesh, China, India, Indonesia, Japan, Malaysia, Papua New Guinea, Philippines, Solomon Islands, Taiwan, Thailand, Vanuatu, Vietnam). Five species-group names are considered to be junior synonyms of Platysceliopulchricornis: Platyscelioabnormis Crawford syn. n., Platysceliodunensis Mukerjee syn. n., Platysceliomirabilis Dodd syn. n., Platysceliopunctatus Kieffer syn. n., and Platysceliowilcoxi Fullaway. The following species are hypothesized and described as new taxa: Platyscelioarcuatus Taekul & Johnson, sp. n. (Western Australia); Platysceliomysterium Taekul & Johnson, sp. n. (Zimbabwe, Botswana, South Africa); Platysceliomzantsi Taekul & Johnson, sp. n. (South Africa); and Platysceliostriga Taekul & Johnson, sp. n. (Western Australia).}, } @article {pmid22423312, year = {2008}, author = {Hubert, N and Hanner, R and Holm, E and Mandrak, NE and Taylor, E and Burridge, M and Watkinson, D and Dumont, P and Curry, A and Bentzen, P and Zhang, J and April, J and Bernatchez, L}, title = {Identifying Canadian freshwater fishes through DNA barcodes.}, journal = {PloS one}, volume = {3}, number = {6}, pages = {e2490}, pmid = {22423312}, issn = {1932-6203}, mesh = {Animals ; Canada ; DNA/genetics ; DNA Barcoding, Taxonomic/*methods ; Databases, Genetic ; Fishes/classification/*genetics ; Fresh Water ; Genetic Variation ; }, abstract = {BACKGROUND: DNA barcoding aims to provide an efficient method for species-level identifications using an array of species specific molecular tags derived from the 5' region of the mitochondrial cytochrome c oxidase I (COI) gene. The efficiency of the method hinges on the degree of sequence divergence among species and species-level identifications are relatively straightforward when the average genetic distance among individuals within a species does not exceed the average genetic distance between sister species. Fishes constitute a highly diverse group of vertebrates that exhibit deep phenotypic changes during development. In this context, the identification of fish species is challenging and DNA barcoding provide new perspectives in ecology and systematics of fishes. Here we examined the degree to which DNA barcoding discriminate freshwater fish species from the well-known Canadian fauna, which currently encompasses nearly 200 species, some which are of high economic value like salmons and sturgeons.

We bi-directionally sequenced the standard 652 bp "barcode" region of COI for 1360 individuals belonging to 190 of the 203 Canadian freshwater fish species (95%). Most species were represented by multiple individuals (7.6 on average), the majority of which were retained as voucher specimens. The average genetic distance was 27 fold higher between species than within species, as K2P distance estimates averaged 8.3% among congeners and only 0.3% among concpecifics. However, shared polymorphism between sister-species was detected in 15 species (8% of the cases). The distribution of K2P distance between individuals and species overlapped and identifications were only possible to species group using DNA barcodes in these cases. Conversely, deep hidden genetic divergence was revealed within two species, suggesting the presence of cryptic species.

CONCLUSIONS/SIGNIFICANCE: The present study evidenced that freshwater fish species can be efficiently identified through the use of DNA barcoding, especially the species complex of small-sized species, and that the present COI library can be used for subsequent applications in ecology and systematics.}, } @article {pmid22320045, year = {2008}, author = {Stefanoff, P and Staszewska, E and Ustrnul, Z and Rogalska, J and Łankiewicz, A and Rosińska, M}, title = {[Ecologic study of the risk of tick-borne encephalitis in Poland--presentation of the method].}, journal = {Przeglad epidemiologiczny}, volume = {62 Suppl 1}, number = {0 1}, pages = {112-121}, pmid = {22320045}, issn = {0033-2100}, support = {R01 TW007248-01A2/TW/FIC NIH HHS/United States ; }, mesh = {Animals ; Encephalitis Viruses, Tick-Borne/*isolation & purification ; Encephalitis, Tick-Borne/diagnosis/*epidemiology/virology ; *Geographic Information Systems ; Humans ; Incidence ; Poland ; Seasons ; *Sentinel Surveillance ; Socioeconomic Factors ; Space-Time Clustering ; *Ticks ; Trees ; }, abstract = {W pracy omówiono metodologię aktualnie prowadzonych badań ekologicznych kleszczowego zapalenia mózgu (kzm) na terenie Polski. W celu oceny wpływu zróżnicowanych czynników środowiskowych, klimatycznych oraz społecznych na występowanie kzm w różnych regionach Polski zostanie przeprowadzona wieloczynnikoica analiza statystyczna na poziomie gmin dla lat 1999-2006.}, } @article {pmid22876793, year = {2007}, author = {Schaffer, WM and Bronnikova, TV}, title = {Parametric dependence in model epidemics. II: Non-contact rate-related parameters.}, journal = {Journal of biological dynamics}, volume = {1}, number = {3}, pages = {231-248}, doi = {10.1080/17513750701201364}, pmid = {22876793}, issn = {1751-3766}, mesh = {*Data Interpretation, Statistical ; *Epidemics ; *Models, Statistical ; Seasons ; }, abstract = {In a previous paper, we discussed the bifurcation structure of SEIR equations subject to seasonality. There, the focus was on parameters that affect transmission: the mean contact rate, β(0), and the magnitude of seasonality, ε(B). Using numerical continuation and brute force simulation, we characterized a global pattern of parametric dependence in terms of subharmonic resonances and period-doublings of the annual cycle. In the present paper, we extend this analysis and consider the effects of varying non-contact-related parameters: periods of latency, infection and immunity, and rates of mortality and reproduction, which, following the usual practice, are assumed to be equal. The emergence of several new forms of dynamical complexity notwithstanding, the pattern previously reported is preserved. More precisely, the principal effect of varying non-contact related parameters is to displace bifurcation curves in the β(0)-ε(B) parameter plane and to expand or contract the regions of resonance and period-doubling they delimit. Implications of this observation with respect to modeling real-world epidemics are considered.}, } @article {pmid24198016, year = {1996}, author = {Britton, GM and Meidinger, DV and Banner, A}, title = {The development of an ecological classification data management and analysis system for British Columbia.}, journal = {Environmental monitoring and assessment}, volume = {39}, number = {1-3}, pages = {365-372}, pmid = {24198016}, issn = {0167-6369}, abstract = {Since 1975, the British Columbia Ministry of Forests has been systematically developing an ecosystem classification of the province, an area covering 94 million hectares. This Biogeoclimatic Ecosystem Classification (BEC) system provides a framework for resource conservation and management. To date, approximately 250 person-years have been invested in the collection, analysis and synthesis of over 8000 ecological (vegetation and environmental data) plots, and in the production of ecological field guides.The development of a database and analysis system on the micro-computer platform to support a classification system of this magnitude was a complex procedure that required judicious planning and coordination. We have developed data-processing software that permits a user to select raw data from broad provincial or regional coverage to plot- and species-level summaries, and to export the data to a variety of output formats.This paper addresses key issues for handling ecological field data on the desktop computer with emphasis on standards, operator ease-of-use, and data access.}, } @article {pmid21525074, year = {2011}, author = {Harvey, SB and Glozier, N and Henderson, M and Allaway, S and Litchfield, P and Holland-Elliott, K and Hotopf, M}, title = {Depression and work performance: an ecological study using web-based screening.}, journal = {Occupational medicine (Oxford, England)}, volume = {61}, number = {3}, pages = {209-211}, doi = {10.1093/occmed/kqr020}, pmid = {21525074}, issn = {1471-8405}, mesh = {Adult ; Analysis of Variance ; Depressive Disorder/*diagnosis ; Diagnosis, Computer-Assisted/*methods ; Efficiency ; Employee Performance Appraisal/*methods ; Female ; Humans ; *Internet ; Male ; Mass Screening/*methods ; Mental Health Services/organization & administration ; Middle Aged ; Occupational Health Services/*methods ; Psychiatric Status Rating Scales ; United Kingdom ; }, abstract = {BACKGROUND: Depression is reported to be a major cause of illness-related sub-optimal work performance (presenteeism). However, the majority of studies examining presenteeism have relied on self-report measures of work performance. Furthermore, employers currently face a number of practical challenges in attempting to facilitate early identification of depression.

AIMS: To test whether a web-based screening tool for depression could be used successfully in the workplace and whether it was possible to detect an association between rates of depression and objective measures of impaired workgroup performance.

METHODS: All permanent employees of a telecommunications company with UK-based call centres were encouraged to complete a web-based psychological assessment using the Patient Health Questionnaire depression scale (PHQ-9). In addition to confidential individual level results, the tool was able to provide anonymized summary statistics for each workgroup. Four objective measures of work performance were collected for each workgroup.

RESULTS: During the study period, 1161 web-based PHQ-9 questionnaires were completed. There was a negative linear relationship between rates of depressive symptoms and the overall performance of a workgroup (P < 0.001). The linear relationship between depression and workgroup performance remained after controlling for gender balance, percent of temporary staff, employees' perceived level of engagement and satisfaction with their line manager (P < 0.01).

CONCLUSIONS: Workgroups with high levels of depressive symptoms tend to perform poorly. Computer-aided web-based screening for symptoms of depression is feasible in a work setting.}, } @article {pmid21524302, year = {2011}, author = {DeSantis, TZ and Keller, K and Karaoz, U and Alekseyenko, AV and Singh, NN and Brodie, EL and Pei, Z and Andersen, GL and Larsen, N}, title = {Simrank: Rapid and sensitive general-purpose k-mer search tool.}, journal = {BMC ecology}, volume = {11}, number = {}, pages = {11}, pmid = {21524302}, issn = {1472-6785}, support = {AI075410-01/AI/NIAID NIH HHS/United States ; U01-HG004866/HG/NHGRI NIH HHS/United States ; UH2/UH3CA140233/CA/NCI NIH HHS/United States ; }, mesh = {Computational Biology ; DNA ; *Databases, Bibliographic ; *Databases, Factual ; *Molecular Biology ; Proteins ; RNA ; *Software ; }, abstract = {BACKGROUND: Terabyte-scale collections of string-encoded data are expected from consortia efforts such as the Human Microbiome Project http://nihroadmap.nih.gov/hmp. Intra- and inter-project data similarity searches are enabled by rapid k-mer matching strategies. Software applications for sequence database partitioning, guide tree estimation, molecular classification and alignment acceleration have benefited from embedded k-mer searches as sub-routines. However, a rapid, general-purpose, open-source, flexible, stand-alone k-mer tool has not been available.

RESULTS: Here we present a stand-alone utility, Simrank, which allows users to rapidly identify database strings the most similar to query strings. Performance testing of Simrank and related tools against DNA, RNA, protein and human-languages found Simrank 10X to 928X faster depending on the dataset.

CONCLUSIONS: Simrank provides molecular ecologists with a high-throughput, open source choice for comparing large sequence sets to find similarity.}, } @article {pmid21518215, year = {2011}, author = {Burg, D and Ng, C and Ting, L and Cavicchioli, R}, title = {Proteomics of extremophiles.}, journal = {Environmental microbiology}, volume = {13}, number = {8}, pages = {1934-1955}, doi = {10.1111/j.1462-2920.2011.02484.x}, pmid = {21518215}, issn = {1462-2920}, mesh = {Archaea/*metabolism ; Bacteria/*metabolism ; Databases, Protein ; Gene Expression Profiling ; Mass Spectrometry ; Proteins/metabolism ; *Proteomics ; Sequence Analysis, Protein ; Staining and Labeling ; }, abstract = {Functional genomic approaches, such as proteomics, greatly enhance the value of genome sequences by providing a global level assessment of which genes are expressed, when genes are expressed and at what cellular levels gene products are synthesized. With over 1000 complete genome sequences of different microorganisms available, and DNA sequencing for environmental samples (metagenomes) producing vast amounts of gene sequence data, there is a real opportunity and a clear need to generate associated functional genomic data to learn about the source microorganisms. In contrast to the technological advances that have led to the accelerated rate and ease at which DNA sequence data can be generated, mass spectrometry based proteomics remains a technically sophisticated and exacting science. In recognition of the need to make proteomics more accessible to a growing number of environmental microbiologists so that the 'functional genomics gap' may be bridged, this review strives to demystify proteomic technologies and describe ways in which they have been applied, and more importantly, can be applied to study the physiology and ecology of extremophiles.}, } @article {pmid21513361, year = {2011}, author = {Gibbons, RD and Mann, JJ}, title = {Strategies for quantifying the relationship between medications and suicidal behaviour: what has been learned?.}, journal = {Drug safety}, volume = {34}, number = {5}, pages = {375-395}, pmid = {21513361}, issn = {1179-1942}, support = {R01 MH080122/MH/NIMH NIH HHS/United States ; MH062185/MH/NIMH NIH HHS/United States ; R01MH8012201/MH/NIMH NIH HHS/United States ; }, mesh = {Adult ; Adverse Drug Reaction Reporting Systems/statistics & numerical data ; Antidepressive Agents/adverse effects ; Child ; Data Interpretation, Statistical ; Depression/complications/drug therapy ; *Drug-Related Side Effects and Adverse Reactions ; Humans ; Pharmacoepidemiology/methods ; *Research Design ; Suicidal Ideation ; Suicide/psychology/*statistics & numerical data ; Suicide, Attempted/psychology/statistics & numerical data ; }, abstract = {In recent years there has been considerable concern that certain classes of drugs, for example antidepressants, may increase the risk of suicide. In this current opinion article, we examine the literature on methodological and statistical approaches to the design and analysis of suicidal event studies. Experimental, ecological and observational studies of the relationship between drugs and suicidal events (thoughts, attempts and completion) are discussed. Areas considered include analysis of spontaneous reporting system data, ecological trends in national and/or small area (e.g. county) suicide rates, meta-analyses of randomized clinical trials, and large-scale medical claims data. New statistical and experimental strategies for investigating possible associations between drugs and suicide are highlighted, and we suggest directions for future statistical/methodological research. To put this into context, we then review the most recent literature on the relationship between drugs (antidepressants, antiepileptics, varenicline, montelukast and antipsychotics) and suicidal events. Overall, there appears to be little evidence that drugs increase the risk of suicide and related behaviour. Numerous lines of evidence in adults clearly demonstrate that inadequate treatment of depression (pharmacotherapy and/or psychotherapy) is associated with increased risk of suicidal behaviour. In children, the results are less clear and further study is required to better delineate which children benefit from treatment and who may be at increased risk as a consequence of treatment. From a statistical and methodological perspective, the field of pharmacoepidemiology is a fertile area for statistical research, both in theory and in application. In general, methods have been adopted from other areas such as general epidemiology, despite the singular nature of many of the problems that are unique to drug safety in general, in particular the study of rare events. Finally, there is considerable debate concerning the communication of risk. For suicide, regulatory action has been taken largely on the basis of evidence suggesting increased risk of suicidal thoughts. However, suicidal thoughts are quite common, particularly among patients with depression, and may have little relationship to suicidal behaviour and/or completion.}, } @article {pmid21510177, year = {2011}, author = {Rosenheim, JA and Parsa, S and Forbes, AA and Krimmel, WA and Law, YH and Segoli, M and Segoli, M and Sivakoff, FS and Zaviezo, T and Gross, K}, title = {Ecoinformatics for integrated pest management: expanding the applied insect ecologist's tool-kit.}, journal = {Journal of economic entomology}, volume = {104}, number = {2}, pages = {331-342}, doi = {10.1603/ec10380}, pmid = {21510177}, issn = {0022-0493}, mesh = {Animals ; Biomass ; Ecology/*methods ; *Informatics ; *Insecta ; *Pest Control ; }, abstract = {Experimentation has been the cornerstone of much of integrated pest management (IPM) research. Here, we aim to open a discussion on the possible merits of expanding the use of observational studies, and in particular the use of data from farmers or private pest management consultants in "ecoinformatics" studies, as tools that might complement traditional, experimental research. The manifold advantages of experimentation are widely appreciated: experiments provide definitive inferences regarding causal relationships between key variables, can produce uniform and high-quality data sets, and are highly flexible in the treatments that can be evaluated. Perhaps less widely considered, however, are the possible disadvantages of experimental research. Using the yield-impact study to focus the discussion, we address some reasons why observational or ecoinformatics approaches might be attractive as complements to experimentation. A survey of the literature suggests that many contemporary yield-impact studies lack sufficient statistical power to resolve the small, but economically important, effects on crop yield that shape pest management decision-making by farmers. Ecoinformatics-based data sets can be substantially larger than experimental data sets and therefore hold out the promise of enhanced power. Ecoinformatics approaches also address problems at the spatial and temporal scales at which farming is conducted, can achieve higher levels of "external validity," and can allow researchers to efficiently screen many variables during the initial, exploratory phases of research projects. Experimental, observational, and ecoinformatics-based approaches may, if used together, provide more efficient solutions to problems in pest management than can any single approach, used in isolation.}, } @article {pmid21509511, year = {2012}, author = {Kristensen, EA and Baattrup-Pedersen, A and Andersen, HE}, title = {Prediction of stream fish assemblages from land use characteristics: implications for cost-effective design of monitoring programmes.}, journal = {Environmental monitoring and assessment}, volume = {184}, number = {3}, pages = {1435-1448}, pmid = {21509511}, issn = {1573-2959}, mesh = {Agriculture/statistics & numerical data ; Animals ; *Biodiversity ; Environmental Monitoring/*economics/instrumentation/methods ; Fishes/*classification/growth & development ; Geographic Information Systems ; Models, Statistical ; Rivers/chemistry ; *Statistics as Topic ; Trees/classification/growth & development ; Water Supply/statistics & numerical data ; }, abstract = {Increasing human impact on stream ecosystems has resulted in a growing need for tools helping managers to develop conservations strategies, and environmental monitoring is crucial for this development. This paper describes the development of models predicting the presence of fish assemblages in lowland streams using solely cost-effective GIS-derived land use variables. Three hundred thirty-five stream sites were separated into two groups based on size. Within each group, fish abundance data and cluster analysis were used to determine the composition of fish assemblages. The occurrence of assemblages was predicted using a dataset containing land use variables at three spatial scales (50 m riparian corridor, 500 m riparian corridor and the entire catchment) supplemented by a dataset on in-stream variables. The overall classification success varied between 66.1-81.1% and was only marginally better when using in-stream variables than when applying only GIS variables. Also, the prediction power of a model combining GIS and in-stream variables was only slightly better than prediction based solely on GIS variables. The possibility of obtaining precise predictions without using costly in-stream variables offers great potential in the design of monitoring programmes as the distribution of monitoring sites along a gradient in ecological quality can be done at a low cost.}, } @article {pmid21507217, year = {2011}, author = {Winskill, P and Rowland, M and Mtove, G and Malima, RC and Kirby, MJ}, title = {Malaria risk factors in north-east Tanzania.}, journal = {Malaria journal}, volume = {10}, number = {}, pages = {98}, pmid = {21507217}, issn = {1475-2875}, mesh = {Age Factors ; Child ; Child, Preschool ; Cluster Analysis ; Family Characteristics ; Female ; Geographic Information Systems ; Health Surveys ; Humans ; Infant ; *Insecticide-Treated Bednets ; Logistic Models ; Malaria, Falciparum/*epidemiology/parasitology/transmission ; Male ; Multivariate Analysis ; Plasmodium falciparum/*isolation & purification ; Prevalence ; Risk Factors ; Tanzania/epidemiology ; }, abstract = {BACKGROUND: Understanding the factors which determine a household's or individual's risk of malaria infection is important for targeting control interventions at all intensities of transmission. Malaria ecology in Tanzania appears to have reduced over recent years. This study investigated potential risk factors and clustering in face of changing infection dynamics.

METHODS: Household survey data were collected in villages of rural Muheza district. Children aged between six months and thirteen years were tested for presence of malaria parasites using microscopy. A multivariable logistic regression model was constructed to identify significant risk factors for children. Geographical information systems combined with global positioning data and spatial scan statistic analysis were used to identify clusters of malaria.

RESULTS: Using an insecticide-treated mosquito net of any type proved to be highly protective against malaria (OR 0.75, 95% CI 0.59-0.96). Children aged five to thirteen years were at higher risk of having malaria than those aged under five years (OR 1.71, 95% CI 1.01-2.91). The odds of malaria were less for females when compared to males (OR 0.62, 95% CI 0.39-0.98). Two spatial clusters of significantly increased malaria risk were identified in two out of five villages.

CONCLUSIONS: This study provides evidence that recent declines in malaria transmission and prevalence may shift the age groups at risk of malaria infection to older children. Risk factor analysis provides support for universal coverage and targeting of long-lasting insecticide-treated nets (LLINs) to all age groups. Clustering of cases indicates heterogeneity of risk. Improved targeting of LLINs or additional supplementary control interventions to high risk clusters may improve outcomes and efficiency as malaria transmission continues to fall under intensified control.}, } @article {pmid21506776, year = {2011}, author = {Ennen, JR and Qualls, CP}, title = {Distribution and habitat utilization of the gopher tortoise tick (Amblyomma tuberculatum) in Southern Mississippi.}, journal = {The Journal of parasitology}, volume = {97}, number = {2}, pages = {202-206}, doi = {10.1645/GE-2599.1}, pmid = {21506776}, issn = {1937-2345}, mesh = {Animals ; *Ecosystem ; Geographic Information Systems ; Host-Parasite Interactions ; Ixodidae/*physiology ; Mississippi/epidemiology ; Principal Component Analysis ; Tick Infestations/epidemiology/parasitology/*veterinary ; Turtles/*parasitology ; }, abstract = {The distribution of the gopher tortoise tick (Amblyomma tuberculatum) has been considered intrinsically linked to the distribution of its primary host, gopher tortoises (Gopherus polyphemus). However, the presence of G. polyphemus does not always equate to the presence of A. tuberculatum . There is a paucity of data on the ecology, habitat preferences, and distribution of A. tuberculatum . The goals of this study were to assess the distribution of A. tuberculatum in southern Mississippi and to determine which, if any, habitat parameters explain the distribution pattern of A. tuberculatum . During 2006-2007, we examined 13 G. polyphemus populations in southern Mississippi for the presence of A. tuberculatum , and we measured a suite of habitat parameters at each site. Only 23% of the G. polyphemus populations supported A. tuberculatum , suggesting a more restricted distribution than its host. The results of our multivariate analyses identified several habitat variables, e.g., depth of sand and percentage of sand in the topsoil and burrow apron, as being important in discriminating between sites with, and without, A. tuberculatum. Amblyomma tuberculatum was only found at sites with a mean sand depth of > 100 cm and a mean percentage of topsoil and burrow apron sand composition > 94.0 and 92.4, respectively. Thus, environmental factors, and not just its host's range, seem to influence the distribution of A. tuberculatum.}, } @article {pmid21504418, year = {2011}, author = {Dupuis, JA and Goulard, M}, title = {Estimating species richness from quadrat sampling data: a general approach.}, journal = {Biometrics}, volume = {67}, number = {4}, pages = {1489-1497}, doi = {10.1111/j.1541-0420.2011.01595.x}, pmid = {21504418}, issn = {1541-0420}, mesh = {Animals ; Biodiversity ; Biometry/*methods ; Birds/*classification ; *Censuses ; Computer Simulation ; *Data Interpretation, Statistical ; Ecology/*statistics & numerical data ; *Ecosystem ; *Models, Statistical ; Population Dynamics ; Sample Size ; }, abstract = {We consider the problem of estimating the number of species (denoted by S) of a biological community located in a region divided into n quadrats. To address this question, different hierarchical parametric approaches have been recently developed. Despite a detailed modeling of the underlying biological processes, they all have some limitations. Indeed, some assume that n is theoretically infinite; as a result, n and the sampling fraction are not a part of such models. Others require some prior information on S to be efficiently implemented. Our approach is more general in that it applies without limitation on the size of n, and it can be used in the presence, as well as in the absence, of prior information on S. Moreover, it can be viewed as an extension of the approach of Dorazio and Royle (2005, Journal of the American Statistical Association 100, 389-398) in that n is a part of the model and a prior distribution is placed on S. Despite serious computational difficulties, we have perfected an efficient Markov chain Monte Carlo algorithm, which allows us to obtain the Bayesian estimate of S. We illustrate our approach by estimating the number of species of a bird community located in a forest.}, } @article {pmid21500879, year = {2011}, author = {Wetter, DW and McClure, JB and Cofta-Woerpel, L and Costello, TJ and Reitzel, LR and Businelle, MS and Cinciripini, PM}, title = {A randomized clinical trial of a palmtop computer-delivered treatment for smoking relapse prevention among women.}, journal = {Psychology of addictive behaviors : journal of the Society of Psychologists in Addictive Behaviors}, volume = {25}, number = {2}, pages = {365-371}, pmid = {21500879}, issn = {1939-1501}, support = {R01 CA074517/CA/NCI NIH HHS/United States ; K01DP001120/DP/NCCDPHP CDC HHS/United States ; R01CA74517 S1/CA/NCI NIH HHS/United States ; K01 DP001120/DP/NCCDPHP CDC HHS/United States ; R01CA74517/CA/NCI NIH HHS/United States ; K07CA84603/CA/NCI NIH HHS/United States ; }, mesh = {Adolescent ; Adult ; Aged ; *Computers, Handheld ; Female ; Humans ; Middle Aged ; Secondary Prevention ; Smoking Cessation/*methods ; *Smoking Prevention ; Therapy, Computer-Assisted/*instrumentation ; Treatment Outcome ; }, abstract = {Relapse is the rule rather than the exception among smokers attempting to quit, and compared to men, women may have higher relapse rates. The current study was a randomized clinical trial testing a palmtop computer-delivered treatment (CDT) for smoking relapse prevention among women. The intervention was individualized based on key theoretical constructs that were measured using ecological momentary assessment (EMA). All participants (N = 302) received standard smoking cessation treatment consisting of nicotine replacement therapy and group counseling, and completed EMA procedures for one week after quitting. At the completion of the group counseling sessions and EMA procedures, participants were randomized to either CDT or no further computer-delivered treatment or assessment (EMA-Only). CDT participants received a palmtop computer-delivered relapse prevention treatment for one additional month. CDT did not improve abstinence rates relative to EMA-Only. Process analyses suggested that heavier smokers were more likely to use CDT and that greater use among CDT participants may be associated with more positive outcomes. The rapid pace of technological advances in mobile computer technology and the ubiquity of such devices provide a novel platform for developing new and potentially innovative treatments. However, the current study did not demonstrate the efficacy of such technology in improving treatment outcomes.}, } @article {pmid21498882, year = {2011}, author = {Zhang, X and Kupiec, M and Gophna, U and Tuller, T}, title = {Analysis of coevolving gene families using mutually exclusive orthologous modules.}, journal = {Genome biology and evolution}, volume = {3}, number = {}, pages = {413-423}, pmid = {21498882}, issn = {1759-6653}, mesh = {Aldehyde Oxidoreductases/metabolism ; Algorithms ; Amino Acid Oxidoreductases/metabolism ; Archaea/genetics ; Bacteria/genetics ; Carrier Proteins/metabolism ; Cell Lineage/genetics ; Computational Biology/*methods ; Environment ; Eukaryota/genetics ; *Evolution, Molecular ; Gene Duplication ; Multienzyme Complexes/metabolism ; *Multigene Family ; Multivariate Analysis ; Phylogeny ; Proteasome Endopeptidase Complex/genetics/metabolism ; Ribosomal Proteins/chemistry/*genetics/metabolism ; Signal Transduction ; Thymidylate Synthase/metabolism ; Transferases/metabolism ; }, abstract = {Coevolutionary networks can encapsulate information about the dynamics of presence and absence of gene families in organisms. Analysis of such networks should reveal fundamental principles underlying the evolution of cellular systems and the functionality of sets of genes. In this study, we describe a new approach for analyzing coevolutionary networks. Our method detects Mutually Exclusive Orthologous Modules (MEOMs). A MEOM is composed of two sets of gene families, each including gene families that tend to appear in the same organisms, such that the two sets tend to mutually exclude each other (if one set appears in a certain organism the second set does not). Thus, a MEOM reflects the evolutionary replacement of one set of genes by another due to reasons such as lineage/environmental specificity, incompatibility, or functional redundancy. We use our method to analyze a coevolutionary network that is based on 383 microorganisms from the three domains of life. As we demonstrate, our method is useful for detecting meaningful evolutionary clades of organisms as well as sets of proteins that interact with each other. Among our results, we report that: 1) MEOMs tend to include gene families whose cellular functions involve transport, energy production, metabolism, and translation, suggesting that changes in the metabolic environments that require adaptation to new sources of energy are central triggers of complex/pathway replacement in evolution. 2) Many MEOMs are related to outer membrane proteins, such proteins are involved in interaction with the environment and could thus be replaced as a result of adaptation. 3) MEOMs tend to separate organisms with large phylogenetic distance but they also separate organisms that live in different ecological niches. 4) Strikingly, although many MEOMs can be identified, there are much fewer cases where the two cliques in the MEOM completely mutually exclude each other, demonstrating the flexibility of protein evolution. 5) CO dehydrogenase and thymidylate synthase and the glycine cleavage genes mutually exclude each other in archaea; this may represent an alternative route for generation of methyl donors for thymidine synthesis.}, } @article {pmid21498766, year = {2011}, author = {Iwai, S and Johnson, TA and Chai, B and Hashsham, SA and Tiedje, JM}, title = {Comparison of the specificities and efficacies of primers for aromatic dioxygenase gene analysis of environmental samples.}, journal = {Applied and environmental microbiology}, volume = {77}, number = {11}, pages = {3551-3557}, pmid = {21498766}, issn = {1098-5336}, support = {P42 ES004911/ES/NIEHS NIH HHS/United States ; P42 ES004911-20/ES/NIEHS NIH HHS/United States ; }, mesh = {Computational Biology ; DNA Primers/*genetics ; Dioxygenases/*genetics/metabolism ; *Environmental Microbiology ; Genetic Variation ; Hydrocarbons, Aromatic/metabolism ; *Metagenomics ; Polymerase Chain Reaction/*methods ; }, abstract = {Aromatic dioxygenase genes have long been of interest for bioremediation and aromatic carbon cycling studies. To date, 115 primers and probes have been designed and used to analyze dioxygenase gene diversities in environmental samples. Here we analyze those primers' specificities, coverages, and PCR product lengths compared to known aromatic dioxygenase genes based on in silico analysis as well as summarize their differing advantages or effectiveness from over 50 reported experimental studies. We also provide some guidance for primer use in future studies.}, } @article {pmid21498690, year = {2011}, author = {Grosse-Wilde, E and Kuebler, LS and Bucks, S and Vogel, H and Wicher, D and Hansson, BS}, title = {Antennal transcriptome of Manduca sexta.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {108}, number = {18}, pages = {7449-7454}, pmid = {21498690}, issn = {1091-6490}, mesh = {Animals ; Computational Biology ; Female ; Gene Expression Profiling ; Image Processing, Computer-Assisted ; Male ; *Manduca ; Microarray Analysis ; Microscopy ; Multigene Family/*genetics ; Neuropil/*cytology/metabolism ; Polymerase Chain Reaction ; Receptors, Odorant/genetics/*metabolism ; Sex Factors ; }, abstract = {In recent years, considerable progress has been made in understanding the molecular mechanisms underlying olfaction in insects. Because of the diverse nature of the gene families involved, this process has largely relied on genomic data. As a consequence, studies have focused on a small subset of species with extensive genomic information. For Lepidoptera, a large order historically crucial to olfactory research, this circumstance has mostly limited advances to the domesticated species Bombyx mori, with some progress in the noctuid Heliothis virescens based on a nonpublic partial genome database. Because of the limited behavioral repertoire and nonexistent ecological importance of Bombyx, molecular data on the tobacco hornworm Manduca sexta are of utmost importance, especially with regards to its position as a classical olfactory model and its complex natural behavior. Here we present the use of transcriptomic and microarray data to identify members of the main olfactory gene families of Manduca. To assess the quality of our data, we correlate information on expressed receptor genes with detailed morphological data on the antennal lobe. Finally, we compare the expression of the near-complete transcript sets in male and female antennae.}, } @article {pmid21497273, year = {2011}, author = {Munoz, R and Yarza, P and Ludwig, W and Euzéby, J and Amann, R and Schleifer, KH and Glöckner, FO and Rosselló-Móra, R}, title = {Release LTPs104 of the All-Species Living Tree.}, journal = {Systematic and applied microbiology}, volume = {34}, number = {3}, pages = {169-170}, doi = {10.1016/j.syapm.2011.03.001}, pmid = {21497273}, issn = {1618-0984}, mesh = {Archaea/*classification/genetics ; Bacteria/*classification/genetics ; Computational Biology ; Databases, Nucleic Acid ; Eukaryota/*classification/genetics ; Phylogeny ; RNA, Ribosomal, 16S/*genetics ; RNA, Ribosomal, 23S/*genetics ; Ribotyping ; Sequence Alignment ; Sequence Analysis, RNA ; }, } @article {pmid21490533, year = {2011}, author = {Haneuse, S and Bartell, S}, title = {Designs for the combination of group- and individual-level data.}, journal = {Epidemiology (Cambridge, Mass.)}, volume = {22}, number = {3}, pages = {382-389}, pmid = {21490533}, issn = {1531-5487}, support = {R01 CA125081/CA/NCI NIH HHS/United States ; R01 CA125081-03/CA/NCI NIH HHS/United States ; NCI R-01 CA125081/CA/NCI NIH HHS/United States ; }, mesh = {*Bias ; Birth Weight ; Confounding Factors, Epidemiologic ; Data Collection ; Data Interpretation, Statistical ; *Effect Modifier, Epidemiologic ; *Epidemiologic Research Design ; Ethnicity/statistics & numerical data ; Female ; Humans ; *Infant, Low Birth Weight ; Infant, Newborn ; Male ; Models, Statistical ; North Carolina ; Risk Factors ; Sex Factors ; }, abstract = {BACKGROUND: Studies of ecologic or aggregate data suffer from a broad range of biases when scientific interest lies with individual-level associations. To overcome these biases, epidemiologists can choose from a range of designs that combine these group-level data with individual-level data. The individual-level data provide information to identify, evaluate, and control bias, whereas the group-level data are often readily accessible and provide gains in efficiency and power. Within this context, the literature on developing models, particularly multilevel models, is well-established, but little work has been published to help researchers choose among competing designs and plan additional data collection.

METHODS: We review recently proposed "combined" group- and individual-level designs and methods that collect and analyze data at 2 levels of aggregation. These include aggregate data designs, hierarchical related regression, two-phase designs, and hybrid designs for ecologic inference.

RESULTS: The various methods differ in (i) the data elements available at the group and individual levels and (ii) the statistical techniques used to combine the 2 data sources. Implementing these techniques requires care, and it may often be simpler to ignore the group-level data once the individual-level data are collected. A simulation study, based on birth-weight data from North Carolina, is used to illustrate the benefit of incorporating group-level information.

CONCLUSIONS: Our focus is on settings where there are individual-level data to supplement readily accessible group-level data. In this context, no single design is ideal. Choosing which design to adopt depends primarily on the model of interest and the nature of the available group-level data.}, } @article {pmid21489684, year = {2011}, author = {Thompson, MP and Calkin, DE}, title = {Uncertainty and risk in wildland fire management: a review.}, journal = {Journal of environmental management}, volume = {92}, number = {8}, pages = {1895-1909}, doi = {10.1016/j.jenvman.2011.03.015}, pmid = {21489684}, issn = {1095-8630}, mesh = {Conservation of Natural Resources/*methods ; *Decision Support Techniques ; *Environment ; Fires/*prevention & control ; Risk Assessment ; *Uncertainty ; }, abstract = {Wildland fire management is subject to manifold sources of uncertainty. Beyond the unpredictability of wildfire behavior, uncertainty stems from inaccurate/missing data, limited resource value measures to guide prioritization across fires and resources at risk, and an incomplete scientific understanding of ecological response to fire, of fire behavior response to treatments, and of spatiotemporal dynamics involving disturbance regimes and climate change. This work attempts to systematically align sources of uncertainty with the most appropriate decision support methodologies, in order to facilitate cost-effective, risk-based wildfire planning efforts. We review the state of wildfire risk assessment and management, with a specific focus on uncertainties challenging implementation of integrated risk assessments that consider a suite of human and ecological values. Recent advances in wildfire simulation and geospatial mapping of highly valued resources have enabled robust risk-based analyses to inform planning across a variety of scales, although improvements are needed in fire behavior and ignition occurrence models. A key remaining challenge is a better characterization of non-market resources at risk, both in terms of their response to fire and how society values those resources. Our findings echo earlier literature identifying wildfire effects analysis and value uncertainty as the primary challenges to integrated wildfire risk assessment and wildfire management. We stress the importance of identifying and characterizing uncertainties in order to better quantify and manage them. Leveraging the most appropriate decision support tools can facilitate wildfire risk assessment and ideally improve decision-making.}, } @article {pmid21488956, year = {2012}, author = {Seiferling, IS and Proulx, R and Peres-Neto, PR and Fahrig, L and Messier, C}, title = {Measuring protected-area isolation and correlations of isolation with land-use intensity and protection status.}, journal = {Conservation biology : the journal of the Society for Conservation Biology}, volume = {26}, number = {4}, pages = {610-618}, doi = {10.1111/j.1523-1739.2011.01674.x}, pmid = {21488956}, issn = {1523-1739}, mesh = {Conservation of Natural Resources/*methods ; Databases, Factual ; *Ecosystem ; Environment ; Geography ; Human Activities ; Humans ; Models, Statistical ; Plants ; }, abstract = {Protected areas cover over 12% of the terrestrial surface of Earth, and yet many fail to protect species and ecological processes as originally envisioned. Results of recent studies suggest that a critical reason for this failure is an increasing contrast between the protected lands and the surrounding matrix of often highly altered land cover. We measured the isolation of 114 protected areas distributed worldwide by comparing vegetation-cover heterogeneity inside protected areas with heterogeneity outside the protected areas. We quantified heterogeneity as the contagion of greenness on the basis of NDVI (normalized difference vegetation index) values, for which a higher value of contagion indicates less heterogeneous land cover. We then measured isolation as the difference between mean contagion inside the protected area and mean contagion in 3 buffer areas of increasing distance from the protected-area border. The isolation of protected areas was significantly positive in 110 of the 114 areas, indicating that vegetation cover was consistently more heterogeneous 10-20 km outside protected areas than inside their borders. Unlike previous researchers, we found that protected areas in which low levels of human activity are allowed were more isolated than areas in which high levels are allowed. Our method is a novel way to assess the isolation of protected areas in different environmental contexts and regions.}, } @article {pmid21483476, year = {2011}, author = {Eren, AM}, title = {PLoS Computational Biology conference postcard from PSB 2011.}, journal = {PLoS computational biology}, volume = {7}, number = {3}, pages = {e1002019}, doi = {10.1371/journal.pcbi.1002019}, pmid = {21483476}, issn = {1553-7358}, mesh = {Computational Biology/*methods ; Ecology ; Genes, Bacterial ; Software ; }, } @article {pmid21483212, year = {2011}, author = {Shah, A}, title = {Further evidence for epidemiological transition hypothesis for elderly suicides.}, journal = {Journal of injury & violence research}, volume = {3}, number = {1}, pages = {29-34}, pmid = {21483212}, issn = {2008-4072}, mesh = {Adolescent ; Adult ; Age Factors ; Data Interpretation, Statistical ; Female ; Gross Domestic Product/statistics & numerical data ; Humans ; Male ; Middle Aged ; Models, Theoretical ; Risk Factors ; Sex Factors ; Socioeconomic Factors ; Suicide/*statistics & numerical data ; Young Adult ; }, abstract = {BACKGROUND: A developmental model of epidemiological transition for elderly suicide rates with four sequential stages has been developed to simultaneously explain cross-national variations in elderly suicide rates, trends over time for elderly suicide rates and age-associated trends in suicides rates reported in the literature. This model was supported by demonstration of a curvilinear (inverted U-shaped curve) relationship between elderly suicide rates and socio-economic status fitting the quadratic equation Y = A + BX - CX2 (where Y is the suicide rate, X is the socio-economic status and A,B, and C are constants) in both sexes. However, this relationship was derived from a cross-sectional study and, therefore, only an association can be inferred. One way to substantiate this further would be to examine the above curvilinear relationship between suicide rates and socio-economic status in a series of younger age-bands because a large part of the epidemiological transition hypothesis was contingent upon the impact of socio-economic status, through a series of mechanisms, on life expectancy. It was hypothesized that the curvilinear (inverted U-shaped curve) relationship between suicide rates and socio-economic status would be absent in younger age-bands and may be present in the younger age-bands closer to the older age-bands (i.e. 45-54 years and 55-64 years).

METHODS: The curvilinear relationship between suicide rates in five age-bands 15-24 years to 55-64 years in both sexes and gross national domestic product (GDP), a measure of socio-economic status, fitting the above quadratic equation was examined with curve estimation regression model using data from the World Health Organization.

RESULTS: In males in the age-bands 35-44 years, 45-54 years and 55-64 years there was a statistically significant curvilinear (inverted U-shaped curve) relationship with GDP and fitted the quadratic equation Y = A + BX - CX2; this relationship was absent in males in the age-bands 15-24 years and 25-34 years. In females in the age-bands 45-54 years and 55-64 years there was a statistically significant curvilinear with GDP (inverted U-shaped curve) and fitted the quadratic equation Y = A + BX - CX2; this relationship was absent in females in the age-bands 15-24 years, 25-34 years and 35-44 years.

CONCLUSIONS: Although caution should be exercised in accepting the model of the epidemiological transition hypothesis for elderly suicide rates because it had been generated from cross-sectional data using an ecological design, the findings of the current study of suicide rates in younger age-bands provide support for this hypothesis. ‎}, } @article {pmid21481214, year = {2011}, author = {Tsai, YH}, title = {PhyloGeoViz: a web-based program that visualizes genetic data on maps.}, journal = {Molecular ecology resources}, volume = {11}, number = {3}, pages = {557-561}, doi = {10.1111/j.1755-0998.2010.02964.x}, pmid = {21481214}, issn = {1755-0998}, mesh = {Computational Biology/*methods ; Ecology/*methods ; Gene Frequency ; Genetics, Population/methods ; Geographic Information Systems ; *Internet ; Phylogeography/*methods ; Software ; }, abstract = {The first step of many population genetic studies is the simple visualization of allele frequencies on a landscape. This basic data exploration can be challenging without proprietary software, and the manual plotting of data is cumbersome and unfeasible at large sample sizes. I present an open source, web-based program that plots any kind of frequency or count data as pie charts in Google Maps (Google Inc., Mountain View, CA). Pie polygons are then exportable to Google Earth (Google Inc.), a free Geographic Information Systems platform. Import of genetic data into Google Earth allows phylogeographers access to a wealth of spatial information layers integral to forming hypotheses and understanding patterns in the data.}, } @article {pmid21476067, year = {2011}, author = {Peterson, MJ and Efroymson, RA and Adams, SM}, title = {Long-term biological monitoring of an impaired stream: synthesis and environmental management implications.}, journal = {Environmental management}, volume = {47}, number = {6}, pages = {1125-1140}, pmid = {21476067}, issn = {1432-1009}, mesh = {Animals ; Biodiversity ; Conservation of Natural Resources ; Cyprinidae ; Daphnia ; Environmental Monitoring/*methods ; Environmental Restoration and Remediation ; Population Density ; Rivers/*chemistry ; Tennessee ; Water Pollutants, Chemical/*analysis/toxicity ; Water Pollution, Chemical/statistics & numerical data ; }, abstract = {The long-term ecological recovery of an impaired stream in response to an industrial facility's pollution abatement actions and the implications of the biological monitoring effort to environmental management is the subject of this special issue of Environmental Management. This final article focuses on the synthesis of the biological monitoring program's components and methods, the efficacy of various biological monitoring techniques to environmental management, and the lessons learned from the program that might be applicable to the design and application of other programs. The focus of the 25-year program has been on East Fork Poplar Creek, an ecologically impaired stream in Oak Ridge, Tennessee with varied and complex stressors from a Department of Energy facility in its headwaters. Major components of the long-term program included testing and monitoring of invertebrate and fish toxicity, bioindicators of fish health, fish contaminant accumulation, and instream communities (including periphyton, benthic macroinvertebrate, and fish). Key parallel components of the program include water chemistry sampling and data management. Multiple lines of evidence suggested positive ecological responses during three major pollution abatement periods. Based on this case study and the related literature, effective environmental management of impaired streams starts with program design that is consistent across space and time, but also adaptable to changing conditions. The biological monitoring approaches used for the program provided a strong basis for assessments of recovery from remedial actions, and the likely causes of impairment. This case study provides a unique application of multidisciplinary and quantitative techniques to address multiple and complex regulatory and programmatic goals, environmental stressors, and remedial actions.}, } @article {pmid21466385, year = {2011}, author = {Pelecanos, AM and Ryan, PA and Gatton, ML}, title = {Spatial-temporal epidemiological analyses of two sympatric, co-endemic alphaviral diseases in Queensland, Australia.}, journal = {Vector borne and zoonotic diseases (Larchmont, N.Y.)}, volume = {11}, number = {4}, pages = {375-382}, doi = {10.1089/vbz.2009.0256}, pmid = {21466385}, issn = {1557-7759}, mesh = {Adolescent ; Adult ; Age Distribution ; Aged ; Alphavirus/*pathogenicity ; Alphavirus Infections/*epidemiology/transmission ; Animals ; Child ; Child, Preschool ; Culicidae/virology ; *Ecosystem ; Endemic Diseases ; Female ; Geographic Information Systems ; Geography ; Humans ; Incidence ; Infant ; Infant, Newborn ; Insect Vectors/virology ; Logistic Models ; Male ; Middle Aged ; Queensland/epidemiology ; Retrospective Studies ; Risk Factors ; Ross River virus/pathogenicity ; Seasons ; Young Adult ; }, abstract = {BACKGROUND: The two most reported mosquito-borne diseases in Queensland, a northern state of Australia, are Ross River virus (RRV) disease and Barmah Forest virus (BFV) disease. Both diseases are endemic in Queensland and have similar clinical symptoms and comparable transmission cycles involving a complex inter-relationship between human hosts, various mosquito vectors, and a range of nonhuman vertebrate hosts, including marsupial mammals that are unique to the Australasian region. Although these viruses are thought to share similar vectors and vertebrate hosts, RRV is four times more prevalent than BFV in Queensland.

METHODS: We performed a retrospective analysis of BFV and RRV human disease notification data collected from 1995 to 2007 in Queensland to ascertain whether there were differences in the incidence patterns of RRV and BFV disease. In particular, we compared the temporal incidence and spatial distribution of both diseases and considered the relationship between their disease dynamics. We also investigated whether a peak in BFV incidence during spring was indicative of the following RRV and BFV transmission season incidence levels.

RESULTS: Although there were large differences in the notification rates of the two diseases, they had similar annual temporal patterns, but there were regional variations between the length and magnitude of the transmission seasons. During periods of increased disease activity, however, there was no association between the dynamics of the two diseases.

CONCLUSIONS: The results from this study suggest that while RRV and BFV share similar mosquito vectors, there are significant differences in the ecology of these viruses that result in different epidemic patterns of disease incidence. Further investigation is required into the ecology of each virus to determine which factors are important in promoting RRV and BFV disease outbreaks.}, } @article {pmid21465285, year = {2011}, author = {Escobar-Sánchez, O and Galván-Magaña, F and Rosíles-Martínez, R}, title = {Biomagnification of mercury and selenium in blue shark Prionace glauca from the Pacific Ocean off Mexico.}, journal = {Biological trace element research}, volume = {144}, number = {1-3}, pages = {550-559}, doi = {10.1007/s12011-011-9040-y}, pmid = {21465285}, issn = {1559-0720}, mesh = {Aging/physiology ; Animals ; Body Size ; Brachyura ; Cephalopoda ; Data Interpretation, Statistical ; Environmental Monitoring ; Female ; Male ; Mercury/*metabolism ; Mexico ; Pacific Ocean ; Perciformes ; Reproducibility of Results ; Selenium/*metabolism ; Sex Characteristics ; Sharks/*metabolism ; Water Pollutants, Chemical ; }, abstract = {The aim of this study was to determine the biomagnification of mercury through the principal prey of the blue shark, Prionace glauca, off the western coast of Baja California Sur, Mexico, as well as the relationship between mercury and selenium in blue sharks. High levels of mercury were found in shark muscle tissues (1.39 ± 1.58 μg/g wet weight); these values are above the allowed 1.0 μg/g for human consumption. The mercury to selenium molar ratio was 1:0.2. We found a low correlation between mercury bioaccumulation and shark size. Juveniles have lower concentrations of mercury than adults. Regarding the analyzed prey, the main prey of the blue shark, pelagic red crab, Pleuroncodes planipes, bioaccumulated 0.04 ± 0.01 μg/g Hg wet weight, but the prey with higher bioaccumulation was the bullet fish Auxis spp. (0.20 ± 0.02 μg/g wet weight). In terms of volume, the red crab P. planipes can be the prey that provides high levels of mercury to the blue shark.}, } @article {pmid21460565, year = {2011}, author = {Mao, JF and Wang, XR}, title = {Distinct niche divergence characterizes the homoploid hybrid speciation of Pinus densata on the Tibetan plateau.}, journal = {The American naturalist}, volume = {177}, number = {4}, pages = {424-439}, doi = {10.1086/658905}, pmid = {21460565}, issn = {1537-5323}, mesh = {*Biological Evolution ; Demography ; *Ecosystem ; *Genetic Speciation ; Geographic Information Systems ; Pinus/*genetics/*physiology ; Ploidies ; Tibet ; }, abstract = {Ecological divergence and selection for novel adaptations to new habitats have been theoretically proposed to play important roles in promoting homoploid hybrid speciation (HHS). The successful establishment of Pinus densata on the Tibetan Plateau is one of the few known examples of HHS. In this study, we carried out extensive field expeditions to obtain representative coverage of occurrence sites of P. densata and its two putative parents. We then applied a series of geographic information system-based analyses to define the patterns of environmental variation within and among the three pine species, to remove potentially confounding effects of spatial autocorrelation in the environmental data due to allopatric ranges, and to build species distribution models. All results consistently indicated that the ecological preferences of P. densata and its parental species have diverged, and they identified candidate ecological factors associated with habitat-specific adaptation. Projections from niche modeling indicated that P. densata could extend across a vast range along the parallel valley systems of the southeastern Tibetan Plateau. Our findings provide evidence of a distinct niche shift in P. densata and support the hypothesis that local adaptation and geographic isolation help maintain and reinforce between-species differences and reproductive isolation in the species complex.}, } @article {pmid21457476, year = {2011}, author = {, and Agata, K and Alasaad, S and Almeida-Val, VM and Alvarez-Dios, JA and Barbisan, F and Beadell, JS and Beltrán, JF and Benítez, M and Bino, G and Bleay, C and Bloor, P and Bohlmann, J and Booth, W and Boscari, E and Caccone, A and Campos, T and Carvalho, BM and Climaco, GT and Clobert, J and Congiu, L and Cowger, C and Dias, G and Doadrio, I and Farias, IP and Ferrand, N and Freitas, PD and Fusco, G and Galetti, PM and Gallardo-Escárate, C and Gaunt, MW and Ocampo, ZG and Gonçalves, H and Gonzalez, EG and Haye, P and Honnay, O and Hyseni, C and Jacquemyn, H and Jowers, MJ and Kakezawa, A and Kawaguchi, E and Keeling, CI and Kwan, YS and La Spina, M and Lee, WO and Leśniewska, M and Li, Y and Liu, H and Liu, X and Lopes, S and Martínez, P and Meeus, S and Murray, BW and Nunes, AG and Okedi, LM and Ouma, JO and Pardo, BG and Parks, R and Paula-Silva, MN and Pedraza-Lara, C and Perera, OP and Pino-Querido, A and Richard, M and Rossini, BC and Samarasekera, NG and Sánchez, A and Sanchez, JA and Santos, CH and Shinohara, W and Soriguer, RC and Sousa, AC and Sousa, CF and Stevens, VM and Tejedo, M and Valenzuela-Bustamante, M and Van de Vliet, MS and Vandepitte, K and Vera, M and Wandeler, P and Wang, W and Won, YJ and Yamashiro, A and Yamashiro, T and Zhu, C}, title = {Permanent genetic resources added to Molecular Ecology Resources Database 1 December 2010-31 January 2011.}, journal = {Molecular ecology resources}, volume = {11}, number = {3}, pages = {586-589}, doi = {10.1111/j.1755-0998.2011.03004.x}, pmid = {21457476}, issn = {1755-0998}, mesh = {Animals ; *Databases, Genetic ; Fungi/*classification/genetics ; *Microsatellite Repeats ; Molecular Sequence Data ; Plants/*classification/genetics ; Sequence Analysis, DNA ; }, abstract = {This article documents the addition of 238 microsatellite marker loci to the Molecular Ecology Resources Database. Loci were developed for the following species: Alytes dickhilleni, Arapaima gigas, Austropotamobius italicus, Blumeria graminis f. sp. tritici, Cobitis lutheri, Dendroctonus ponderosae, Glossina morsitans morsitans, Haplophilus subterraneus, Kirengeshoma palmata, Lysimachia japonica, Macrolophus pygmaeus, Microtus cabrerae, Mytilus galloprovincialis, Pallisentis (Neosentis) celatus, Pulmonaria officinalis, Salminus franciscanus, Thais chocolata and Zootoca vivipara. These loci were cross-tested on the following species: Acanthina monodon, Alytes cisternasii, Alytes maurus, Alytes muletensis, Alytes obstetricans almogavarii, Alytes obstetricans boscai, Alytes obstetricans obstetricans, Alytes obstetricans pertinax, Cambarellus montezumae, Cambarellus zempoalensis, Chorus giganteus, Cobitis tetralineata, Glossina fuscipes fuscipes, Glossina pallidipes, Lysimachia japonica var. japonica, Lysimachia japonica var. minutissima, Orconectes virilis, Pacifastacus leniusculus, Procambarus clarkii, Salminus brasiliensis and Salminus hilarii.}, } @article {pmid21455706, year = {2011}, author = {Beyrem, H and Boufahja, F and Hedfi, A and Essid, N and Aïssa, P and Mahmoudi, E}, title = {Laboratory study on individual and combined effects of cobalt- and zinc-spiked sediment on meiobenthic nematodes.}, journal = {Biological trace element research}, volume = {144}, number = {1-3}, pages = {790-803}, doi = {10.1007/s12011-011-9032-y}, pmid = {21455706}, issn = {1559-0720}, mesh = {Analysis of Variance ; Animals ; Cobalt/*toxicity ; Data Interpretation, Statistical ; Dose-Response Relationship, Drug ; Geologic Sediments/*chemistry ; Mediterranean Sea ; Nematoda/classification/*metabolism ; Population ; Species Specificity ; Tunisia ; Zinc/*toxicity ; }, abstract = {Free-living nematodes are the most abundant taxa among the meiobenthos and the predominant prey for bottom-feeding fishes. They are able to accumulate toxicants from sediments which explain their use in this study as possible tools in nutritional quality assessment of fishes. Nematodes from sediments of Ghar El Melh lagoon (Tunisia) were subjected to cobalt and/or zinc enrichment in a microcosm experiment for 30 days. Three levels (low, medium, and high) of each treatment were used. Nematode abundance and diversity significantly decreased, and the taxonomic structure was altered. Results from multivariate analyses of the species abundance data revealed that all treatments were significantly different from the control. Both univariate and multivariate analyses of the data showed that the differential response occurred in all treatments, but the assemblages from microcosms contaminated with zinc alone were much more negatively affected compared with those exposed to cobalt alone. The presence of cobalt simultaneously with zinc seems to reduce its impact on nematode species composition. Such a result is suggestive of antagonistic interactions between these two metals. The responses of nematode species to the cobalt and zinc treatments were varied. Oncholaimellus mediterraneus, Oncholaimus campylocercoides, and Neochromadora trichophora were significantly affected with cobalt contamination but, they were not eliminated. Exposed to zinc, Hypodontolaimus colesi was eliminated and seemed to be an intolerant species versus this metal. Some of these species, "cobalt-sensitive" or "zinc-sensitive", were also affected by the metal combination even at low dose: O. mediterraneus, N. trichophora, and H. colesi. Differential sensitivity to cobalt and/or zinc may result in a subsequent competitive release of more tolerant species. A list of this kind of species was established to be used as a possible preventive tool versus contaminated fish. This was most evidently the case in Marylynnia stekhoveni and O. campylocercoides which increased at all doses of cobalt and zinc, respectively. These two resistant species have also the opportunity to dominate the nematode assemblage when the studied metals were added together. The level of health risk is probably higher for humans assimilating additional amount of cobalt and zinc, especially heavy smokers and/or patients using some medications including salts of these metals.}, } @article {pmid21429161, year = {2011}, author = {Abadía-Cardoso, A and Clemento, AJ and Garza, JC}, title = {Discovery and characterization of single-nucleotide polymorphisms in steelhead/rainbow trout, Oncorhynchus mykiss.}, journal = {Molecular ecology resources}, volume = {11 Suppl 1}, number = {}, pages = {31-49}, doi = {10.1111/j.1755-0998.2010.02971.x}, pmid = {21429161}, issn = {1755-0998}, mesh = {Animals ; Base Sequence ; Consensus Sequence ; Databases, Genetic ; Expressed Sequence Tags ; Gene Frequency ; Heterozygote ; Oncorhynchus mykiss/*genetics ; *Polymorphism, Single Nucleotide ; Rivers ; Sequence Analysis, DNA ; }, abstract = {Single-nucleotide polymorphisms (SNPs) have several advantages over other genetic markers, including lower mutation and genotyping error rates, ease of inter-laboratory standardization, and the prospect of high-throughput, low-cost genotyping. Nevertheless, their development and use has only recently moved beyond model organisms to groups such as salmonid fishes. Oncorhynchus mykiss is a salmonid native to the North Pacific rim that has now been introduced throughout the world for fisheries and aquaculture. The anadromous form of the species is known as steelhead. Native steelhead populations on the west coast of the United States have declined and many now have protected status. The nonanadromous, or resident, form of the species is termed rainbow, redband or golden trout. Additional life history and morphological variation, and interactions between the forms, make the species challenging to study, monitor and evaluate. Here, we describe the discovery, characterization and assay development for 139 SNP loci in steelhead/rainbow trout. We used EST sequences from existing genomic databases to design primers for 480 genes. Sanger-sequencing products from these genes provided 130 KB of consensus sequence in which variation was surveyed for 22 individuals from steelhead, rainbow and redband trout groups. The resulting TaqMan assays were surveyed in five steelhead populations and three rainbow trout stocks, where they had a mean minor allele frequency of 0.15-0.26 and observed heterozygosity of 0.18-0.35. Mean F(ST) was 0.204. The development of SNPs for O. mykiss will help to provide highly informative genetic tools for individual and stock identification, pedigree reconstruction, phylogeography and ecological investigation.}, } @article {pmid21447483, year = {2011}, author = {Wiens, JJ and Morrill, MC}, title = {Missing data in phylogenetic analysis: reconciling results from simulations and empirical data.}, journal = {Systematic biology}, volume = {60}, number = {5}, pages = {719-731}, doi = {10.1093/sysbio/syr025}, pmid = {21447483}, issn = {1076-836X}, mesh = {Animals ; Bayes Theorem ; Biological Evolution ; Computer Simulation ; Data Interpretation, Statistical ; Likelihood Functions ; *Models, Genetic ; *Phylogeny ; Urodela/*classification/genetics ; }, } @article {pmid21445229, year = {2011}, author = {Ernebjerg, M and Kishony, R}, title = {Dynamic phenotypic clustering in noisy ecosystems.}, journal = {PLoS computational biology}, volume = {7}, number = {3}, pages = {e1002017}, pmid = {21445229}, issn = {1553-7358}, support = {P50 GM068763/GM/NIGMS NIH HHS/United States ; R01 GM081617/GM/NIGMS NIH HHS/United States ; 5P50 GM068763-07/GM/NIGMS NIH HHS/United States ; }, mesh = {Algorithms ; Cluster Analysis ; Computational Biology/*methods ; *Ecosystem ; Microbial Interactions ; *Models, Biological ; Phenotype ; Soil Microbiology ; }, abstract = {In natural ecosystems, hundreds of species typically share the same environment and are connected by a dense network of interactions such as predation or competition for resources. Much is known about how fixed ecological niches can determine species abundances in such systems, but far less attention has been paid to patterns of abundances in randomly varying environments. Here, we study this question in a simple model of competition between many species in a patchy ecosystem with randomly fluctuating environmental conditions. Paradoxically, we find that introducing noise can actually induce ordered patterns of abundance-fluctuations, leading to a distinct periodic variation in the correlations between species as a function of the phenotypic distance between them; here, difference in growth rate. This is further accompanied by the formation of discrete, dynamic clusters of abundant species along this otherwise continuous phenotypic axis. These ordered patterns depend on the collective behavior of many species; they disappear when only individual or pairs of species are considered in isolation. We show that they arise from a balance between the tendency of shared environmental noise to synchronize species abundances and the tendency for competition among species to make them fluctuate out of step. Our results demonstrate that in highly interconnected ecosystems, noise can act as an ordering force, dynamically generating ecological patterns even in environments lacking explicit niches.}, } @article {pmid21442996, year = {2010}, author = {Zhang, PF and Hu, YM and He, HS and Xiong, ZP and Liu, M}, title = {[Dynamic changes of urban architecture landscape based on Barista: a case study in Tiexi District of Shenyang City].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {21}, number = {12}, pages = {3105-3112}, pmid = {21442996}, issn = {1001-9332}, mesh = {*Architecture ; China ; *City Planning ; *Facility Design and Construction ; Geographic Information Systems ; *Imaging, Three-Dimensional ; Satellite Communications ; *Software ; }, abstract = {In this paper, three-dimensional building information was extracted from high resolution satellite image based on Barista software. Combined with ArcGIS software, the dynamic changes of the building landscape in Tiexi District of Shenyang City during urban renewal process were analyzed from the conversion contribution rate, building density, average building height, and built-up area rate. It was found that during this urban renewal process, four dominant landscape types (vacant lot, residential building, industrial building, and road) were the main parts of the landscape changes. The areas of vacant lot, residential building, commercial building, and road increased, while that of industrial building decreased. The building density decreased, while the average building height increased. There was an obvious regional variation in building landscape. The building density in industrial district was higher than that in residential district, while the average building height was in adverse. The further from the city center, the lower the building density and building average height.}, } @article {pmid21439607, year = {2011}, author = {Lancelot, C and Thieu, V and Polard, A and Garnier, J and Billen, G and Hecq, W and Gypens, N}, title = {Cost assessment and ecological effectiveness of nutrient reduction options for mitigating Phaeocystis colony blooms in the Southern North Sea: an integrated modeling approach.}, journal = {The Science of the total environment}, volume = {409}, number = {11}, pages = {2179-2191}, doi = {10.1016/j.scitotenv.2011.02.023}, pmid = {21439607}, issn = {1879-1026}, mesh = {Agriculture ; Conservation of Natural Resources/*economics/methods ; Costs and Cost Analysis ; *Eutrophication ; Geographic Information Systems ; Haptophyta/*growth & development ; Models, Biological ; Models, Chemical ; Nitrogen/analysis ; North Sea ; Phosphorus/analysis ; Waste Disposal, Fluid/economics ; Waste Management/*economics/methods ; Water Pollutants, Chemical/analysis ; Water Pollution, Chemical/*prevention & control/statistics & numerical data ; }, abstract = {Nutrient reduction measures have been already taken by wealthier countries to decrease nutrient loads to coastal waters, in most cases however, prior to having properly assessed their ecological effectiveness and their economic costs. In this paper we describe an original integrated impact assessment methodology to estimate the direct cost and the ecological performance of realistic nutrient reduction options to be applied in the Southern North Sea watershed to decrease eutrophication, visible as Phaeocystis blooms and foam deposits on the beaches. The mathematical tool couples the idealized biogeochemical GIS-based model of the river system (SENEQUE-RIVERSTRAHLER) implemented in the Eastern Channel/Southern North Sea watershed to the biogeochemical MIRO model describing Phaeocystis blooms in the marine domain. Model simulations explore how nutrient reduction options regarding diffuse and/or point sources in the watershed would affect the Phaeocystis colony spreading in the coastal area. The reference and prospective simulations are performed for the year 2000 characterized by mean meteorological conditions, and nutrient reduction scenarios include and compare upgrading of wastewater treatment plants and changes in agricultural practices including an idealized shift towards organic farming. A direct cost assessment is performed for each realistic nutrient reduction scenario. Further the reduction obtained for Phaeocystis blooms is assessed by comparison with ecological indicators (bloom magnitude and duration) and the cost for reducing foam events on the beaches is estimated. Uncertainty brought by the added effect of meteorological conditions (rainfall) on coastal eutrophication is discussed. It is concluded that the reduction obtained by implementing realistic environmental measures on the short-term is costly and insufficient to restore well-balanced nutrient conditions in the coastal area while the replacement of conventional agriculture by organic farming might be an option to consider in the nearby future.}, } @article {pmid21438133, year = {2011}, author = {Ehrlich, G and Jöhncke, U and Drost, W and Schulte, C}, title = {Problems faced when evaluating the bioaccumulation potential of substances under REACH.}, journal = {Integrated environmental assessment and management}, volume = {7}, number = {4}, pages = {550-558}, doi = {10.1002/ieam.190}, pmid = {21438133}, issn = {1551-3793}, mesh = {Air ; Chemical Industry/*legislation & jurisprudence ; Data Interpretation, Statistical ; Ecotoxicology/*methods ; Environmental Pollutants/analysis/chemistry/*metabolism/*toxicity ; Environmental Pollution/analysis/*legislation & jurisprudence/prevention & control ; Europe ; Humans ; Hydrophobic and Hydrophilic Interactions ; Isotope Labeling ; *Social Control, Formal ; }, abstract = {The identification and regulation of substances that combine persistence, bioaccumulation potential, and toxicity ("PBT" substances) is one central aspect of the European chemical legislation REACH (Registration, Evaluation, Authorisation, and Restriction of Chemicals), because these substances may elicit adverse long-term effects after release to the environment. The determination of a substance that has persistence, bioaccumulation potential, and toxicity is based on a set of distinct cutoff criteria identified in Annex XIII of the REACH regulation. Regarding the bioaccumulation potential, the evaluation is focused on the substance's bioconcentration factor as single decisive criterion. In addition, the REACH guidelines provide a selection of standardized test procedures for measuring bioconcentration factor and guidance in appraising test results. However, alternative test results like bioaccumulation factors and biomagnification as well as additional indications for a bioaccumulation potential such as trophic magnification are only allowed for supporting evidence. The currently used test systems with aquatic exposure have been demonstrated to generate reliable results for the majority of neutral, lipophilic organic substances, which facilitate clear decision-making by means of the crucial bioconcentration factor cutoff criteria of Annex XIII. However, certain substance groups such as highly hydrophobic organic substances and amphiphilic and nonlipophilic compounds are difficult to evaluate with common test strategies due to inappropriate test systems or accumulation mechanisms not based on lipophilicity. Recent scientific progress has already been made to establish alternative test systems and to refine the bioaccumulation assessment by consideration of additive accumulation mechanisms and indications. This article gives an overview on actual shortcomings in the current bioaccumulation assessment under REACH and also provides suggestions for a refinement of evaluation.}, } @article {pmid21437252, year = {2011}, author = {Wu, D and Wu, M and Halpern, A and Rusch, DB and Yooseph, S and Frazier, M and Venter, JC and Eisen, JA}, title = {Stalking the fourth domain in metagenomic data: searching for, discovering, and interpreting novel, deep branches in marker gene phylogenetic trees.}, journal = {PloS one}, volume = {6}, number = {3}, pages = {e18011}, pmid = {21437252}, issn = {1932-6203}, mesh = {Bacterial Proteins/*genetics ; Base Sequence ; *Databases, Genetic ; *Evolution, Molecular ; *Metagenomics ; Multigene Family/genetics ; Oceans and Seas ; *Phylogeny ; RNA, Ribosomal/*genetics ; Rec A Recombinases/*genetics ; }, abstract = {BACKGROUND: Most of our knowledge about the ancient evolutionary history of organisms has been derived from data associated with specific known organisms (i.e., organisms that we can study directly such as plants, metazoans, and culturable microbes). Recently, however, a new source of data for such studies has arrived: DNA sequence data generated directly from environmental samples. Such metagenomic data has enormous potential in a variety of areas including, as we argue here, in studies of very early events in the evolution of gene families and of species.

We designed and implemented new methods for analyzing metagenomic data and used them to search the Global Ocean Sampling (GOS) expedition data set for novel lineages in three gene families commonly used in phylogenetic studies of known and unknown organisms: small subunit rRNA and the recA and rpoB superfamilies. Though the methods available could not accurately identify very deeply branched ss-rRNAs (largely due to difficulties in making robust sequence alignments for novel rRNA fragments), our analysis revealed the existence of multiple novel branches in the recA and rpoB gene families. Analysis of available sequence data likely from the same genomes as these novel recA and rpoB homologs was then used to further characterize the possible organismal source of the novel sequences.

CONCLUSIONS/SIGNIFICANCE: Of the novel recA and rpoB homologs identified in the metagenomic data, some likely come from uncharacterized viruses while others may represent ancient paralogs not yet seen in any cultured organism. A third possibility is that some come from novel cellular lineages that are only distantly related to any organisms for which sequence data is currently available. If there exist any major, but so-far-undiscovered, deeply branching lineages in the tree of life, we suggest that methods such as those described herein currently offer the best way to search for them.}, } @article {pmid21431606, year = {2011}, author = {Gürlebeck, K and Ji, X}, title = {Lotka-Volterra system with Volterra multiplier.}, journal = {Advances in experimental medicine and biology}, volume = {696}, number = {}, pages = {647-655}, doi = {10.1007/978-1-4419-7046-6_66}, pmid = {21431606}, issn = {0065-2598}, mesh = {Animals ; Computational Biology ; Ecology/*statistics & numerical data ; *Ecosystem ; Food Chain ; Mathematical Concepts ; Models, Biological ; Models, Statistical ; Predatory Behavior ; }, abstract = {With the aid of Volterra multiplier, we study ecological equations for both tree system and cycle system. We obtain a set of sufficient conditions for the ultimate boundedness to nonautonomous n-dimensional Lotka-Volterra tree systems with continuous time delay. The criteria are applicable to cooperative model, competition model, and predator-prey model. As to cycle system, we consider a three-dimensional predator-prey Lotka-Volterra system. In order to get a condition under which the system is globally asymptotic stable, we obtain a Volterra multiplier, so that in a parameter region the system is with the Volterra multiplier it is globally stable. We have also proved that in regions in which the condition is not satisfied, the system is unstable or at least it is not globally stable. Therefore, we say that the three-dimensional cycle system is with global bifurcation.}, } @article {pmid21429157, year = {2011}, author = {, and Agostini, C and Agudelo, PA and Bâ, K and Barber, PA and Bisol, PM and Brouat, C and Burgess, TI and Calves, I and Carrillo Avila, M and Chow, S and Cordes, L and Da Silva, D and Dalecky, A and De Meester, L and Doadrio, I and Dobigny, G and Duplantier, JM and Evison, SE and Ford, R and Fresneau, D and Galetti, PM and Gauthier, P and Geldof, S and Granjon, L and Guérin, F and St J Hardy, GE and Hernandez Escobar, C and Hima, K and Hu, J and Huang, L and Humeau, L and Jansen, B and Jaquemet, S and Jiang, ZQ and Jung, SJ and Kim, BS and Kim, CH and Kim, JO and Lai, CH and Laroche, J and Lavergne, E and Lawton-Rauh, A and Le Corre, M and Leach, MM and Lee, J and Leo, AE and Lichtenzveig, J and Lin, L and Linde, CC and Liu, SF and Marino, IA and McKeown, NJ and Nohara, K and Oh, MJ and Okamoto, H and Oliver, R and Olivera Angel, M and Ornelas-García, CP and Orsini, L and Ostos Alfonso, H and Othman, AS and Papetti, C and Patarnello, T and Pedraza-Lara, C and Piller, KR and Poteaux, C and Requier, JB and Roziana, MK and Semba, Y and Sembene, M and Shah, RM and Shahril, AR and Shao, A and Shaw, PW and Song, L and Souza Ferreira, R and Su, YQ and Suzuki, N and Tatard, C and Taylor, KM and Taylor, PW and Thiam, M and Valbuena, R and Wang, H and Yang, BG and Yuan, Q and Zajonz, U and Zane, L and Zhu, L and Zhuang, ZM and Zulaiha, AR}, title = {Permanent genetic resources added to Molecular Ecology Resources Database 1 October 2010-30 November 2010.}, journal = {Molecular ecology resources}, volume = {11}, number = {2}, pages = {418-421}, doi = {10.1111/j.1755-0998.2010.02970.x}, pmid = {21429157}, issn = {1755-0998}, mesh = {Animals ; *Databases, Genetic ; Eukaryota/*genetics ; Fungi/*genetics ; Microsatellite Repeats ; Molecular Sequence Data ; }, abstract = {This article documents the addition of 277 microsatellite marker loci to the Molecular Ecology Resources Database. Loci were developed for the following species: Ascochyta rabiei, Cambarellus chapalanus, Chionodraco hamatus, Coptis omeiensis, Cynoscion nebulosus, Daphnia magna, Gerbillus nigeriae, Isurus oxyrinchus, Lates calcarifer, Metacarcinus magister, Oplegnathus fasciatus, Pachycondyla verenae, Phaethon lepturus, Pimelodus grosskopfii, Rotylenchulus reniformis, Scomberomorus niphonius, Sepia esculenta, Terapon jarbua, Teratosphaeria cryptica and Thunnus obesus. These loci were cross-tested on the following species: Austropotamobius italicus, Cambarellus montezumae, Cambarellus puer, Cambarellus shufeldtii, Cambarellus texanus, Chionodraco myersi, Chionodraco rastrospinosus, Coptis chinensis, Coptis chinensis var. brevisepala, Coptis deltoidea, Coptis teeta, Orconectes virilis, Pacifastacus leniusculus, Pimelodus bochii, Procambarus clarkii, Pseudopimelodus bufonius, Rhamdia quelen, Sepia andreana, Sepiella maindroni, Thunnus alalunga, Thunnus albacares, Thunnus maccoyii, Thunnus orientalis, Thunnus thynnus and Thunnus tonggol.}, } @article {pmid21429127, year = {2011}, author = {, and Aggarwal, RK and Allainguillaume, J and Bajay, MM and Barthwal, S and Bertolino, P and Chauhan, P and Consuegra, S and Croxford, A and Dalton, DL and den Belder, E and Díaz-Ferguson, E and Douglas, MR and Drees, M and Elderson, J and Esselink, GD and Fernández-Manjarrés, JF and Frascaria-Lacoste, N and Gäbler-Schwarz, S and Garcia de Leaniz, C and Ginwal, HS and Goodisman, MA and Guo, B and Hamilton, MB and Hayes, PK and Hong, Y and Kajita, T and Kalinowski, ST and Keller, L and Koop, BF and Kotzé, A and Lalremruata, A and Leese, F and Li, C and Liew, WY and Martinelli, S and Matthews, EA and Medlin, LK and Messmer, AM and Meyer, EI and Monteiro, M and Moyer, GR and Nelson, RJ and Nguyen, TT and Omoto, C and Ono, J and Pavinato, VA and Pearcy, M and Pinheiro, JB and Power, LD and Rawat, A and Reusch, TB and Sanderson, D and Sannier, J and Sathe, S and Sheridan, CK and Smulders, MJ and Sukganah, A and Takayama, K and Tamura, M and Tateishi, Y and Vanhaecke, D and Vu, NV and Wickneswari, R and Williams, AS and Wimp, GM and Witte, V and Zucchi, MI}, title = {Permanent genetic resources added to Molecular Ecology Resources Database 1 August 2010-30 September 2010.}, journal = {Molecular ecology resources}, volume = {11}, number = {1}, pages = {219-222}, doi = {10.1111/j.1755-0998.2010.02944.x}, pmid = {21429127}, issn = {1755-0998}, mesh = {*Databases, Nucleic Acid ; Dictyostelium/genetics ; Epimedium/genetics ; Haptophyta/genetics ; Microsatellite Repeats ; Molecular Sequence Data ; }, abstract = {This article documents the addition of 229 microsatellite marker loci to the Molecular Ecology Resources Database. Loci were developed for the following species: Acacia auriculiformis × Acacia mangium hybrid, Alabama argillacea, Anoplopoma fimbria, Aplochiton zebra, Brevicoryne brassicae, Bruguiera gymnorhiza, Bucorvus leadbeateri, Delphacodes detecta, Tumidagena minuta, Dictyostelium giganteum, Echinogammarus berilloni, Epimedium sagittatum, Fraxinus excelsior, Labeo chrysophekadion, Oncorhynchus clarki lewisi, Paratrechina longicornis, Phaeocystis antarctica, Pinus roxburghii and Potamilus capax. These loci were cross-tested on the following species: Acacia peregrinalis, Acacia crassicarpa, Bruguiera cylindrica, Delphacodes detecta, Tumidagena minuta, Dictyostelium macrocephalum, Dictyostelium discoideum, Dictyostelium purpureum, Dictyostelium mucoroides, Dictyostelium rosarium, Polysphondylium pallidum, Epimedium brevicornum, Epimedium koreanum, Epimedium pubescens, Epimedium wushanese and Fraxinus angustifolia.}, } @article {pmid21429115, year = {2011}, author = {Vandergast, AG and Perry, WM and Lugo, RV and Hathaway, SA}, title = {Genetic Landscapes GIS Toolbox: tools to map patterns of genetic divergence and diversity.}, journal = {Molecular ecology resources}, volume = {11}, number = {1}, pages = {158-161}, doi = {10.1111/j.1755-0998.2010.02904.x}, pmid = {21429115}, issn = {1755-0998}, mesh = {*Evolution, Molecular ; *Genetic Variation ; Genetics, Population/*instrumentation ; Geographic Information Systems/*instrumentation ; Geography ; }, abstract = {The Landscape Genetics GIS Toolbox contains tools that run in the Geographic Information System software, ArcGIS(®), to map genetic landscapes and to summarize multiple genetic landscapes as average and variance surfaces. These tools can be used to visualize the distribution of genetic diversity across geographic space and to study associations between patterns of genetic diversity and geographic features or other geo-referenced environmental data sets. Together, these tools create genetic landscape surfaces directly from tables containing genetic distance or diversity data and sample location coordinates, greatly reducing the complexity of building and analyzing these raster surfaces in a Geographic Information System.}, } @article {pmid21429109, year = {2011}, author = {Wordley, C and Slate, J and Stapley, J}, title = {Mining online genomic resources in Anolis carolinensis facilitates rapid and inexpensive development of cross-species microsatellite markers for the Anolis lizard genus.}, journal = {Molecular ecology resources}, volume = {11}, number = {1}, pages = {126-133}, doi = {10.1111/j.1755-0998.2010.02863.x}, pmid = {21429109}, issn = {1755-0998}, mesh = {Animals ; Data Mining/economics/*methods ; *Databases, Nucleic Acid/economics ; Expressed Sequence Tags ; Genomics/economics/*methods ; Lizards/classification/*genetics ; *Microsatellite Repeats ; Online Systems/economics ; Species Specificity ; }, abstract = {Online sequence databases can provide valuable resources for the development of cross-species genetic markers. In particular, mining expressed tag sequences (EST) for microsatellites and developing conserved cross-species microsatellite markers can provide a rapid and relatively inexpensive method to develop new markers for a range of species. Here, we adopt this approach to develop cross-species microsatellite markers in Anolis lizards, which is a model genus in evolutionary biology and ecology. Using EST sequences from Anolis carolinensis, we identified 127 microsatellites that satisfied our criteria, and tested 49 of these in five species of Anolis (carolinensis, distichus, apletophallus, porcatus and sagrei). We identified between 8 and 25 new variable genetic markers for five Anolis species. These markers will be a valuable resource for studies of population genetics, comparative mapping, mating systems, behavioural ecology and adaptive radiations in this diverse lineage.}, } @article {pmid21426283, year = {2011}, author = {Baade, PD and Youlden, DR and Coory, MD and Gardiner, RA and Chambers, SK}, title = {Urban-rural differences in prostate cancer outcomes in Australia: what has changed?.}, journal = {The Medical journal of Australia}, volume = {194}, number = {6}, pages = {293-296}, doi = {10.5694/j.1326-5377.2011.tb02977.x}, pmid = {21426283}, issn = {1326-5377}, mesh = {Age Factors ; Aged ; Australia/epidemiology ; Confidence Intervals ; Databases, Factual ; Early Detection of Cancer/*statistics & numerical data ; Follow-Up Studies ; Health Services Accessibility/statistics & numerical data ; Healthcare Disparities/*statistics & numerical data ; Humans ; Male ; Middle Aged ; Needs Assessment ; Prostate-Specific Antigen/*blood ; Prostatectomy/methods/statistics & numerical data ; Prostatic Neoplasms/*mortality/*prevention & control/surgery ; Retrospective Studies ; Risk Assessment ; Rural Population/*statistics & numerical data ; Survival Analysis ; Treatment Outcome ; Urban Population/*statistics & numerical data ; }, abstract = {OBJECTIVE: To update our previous analysis of trends for prostate-specific antigen (PSA) testing, prostate cancer incidence, radical prostatectomy and prostate cancer mortality to assess whether men in rural and regional areas of Australia now have more equitable access to prostate cancer services, and improved outcomes.

Descriptive study using population-based data for Australian men aged 50-79 years from 1982 to the 2008-09 financial year (depending on data availability for each outcome measure).

MAIN OUTCOME MEASURES: Age-standardised rates per 100,000 men and 5-year survival rates.

RESULTS: Overall, rates of PSA screening and radical prostatectomy increased, accompanied by reductions in mortality and improvements in survival throughout Australia. Incidence rates were similar for men in urban and rural areas. However, in the last year of data collection, for men in rural areas compared with urban areas, rates of PSA screening (21,267/100,000 v 24,606/100,000; P < 0.01) and radical prostatectomy (182.2/100,000 v 239.2/100,000; P < 0.01) remained lower, mortality remained higher (56.9/100,000 v 45.8/100,000; P < 0.01), and survival outcomes continued to be poorer (5-year relative survival, 87.7% v 91.4%; P < 0.01).

CONCLUSIONS: With some limitations, these ecological data demonstrate that the use of diagnostic and treatment services among men living in rural areas of Australia remains lower than among their urban counterparts, their survival and mortality outcomes are poorer, and these differentials are continuing. There is an urgent need to explore further the reasons for these differences and to implement changes so these inequalities can be reduced.}, } @article {pmid21424229, year = {2011}, author = {Schmidt, G and Pesch, R and Schröder, W and Conrad, A and Kolossa-Gehring, M and Feigenspan, S and Dobler, L and Wiesmüller, GA and Birke, M and Utermann, J}, title = {The potential of spatial information in human biomonitoring by example of two German environmental epidemiology studies.}, journal = {Environmental geochemistry and health}, volume = {33}, number = {4}, pages = {399-408}, pmid = {21424229}, issn = {1573-2983}, mesh = {Adolescent ; Adult ; Child ; Child, Preschool ; Environmental Monitoring/*methods ; Environmental Pollutants/*analysis/metabolism/urine ; Epidemiologic Studies ; Epidemiological Monitoring ; Female ; *Geographic Information Systems ; Geologic Sediments/analysis/chemistry ; Germany/epidemiology ; Humans ; Male ; Rivers/chemistry ; Soil/analysis/chemistry ; Uranium/*analysis/metabolism/urine ; Water Supply/analysis ; }, abstract = {This study aimed at statistically investigating the association between the internal exposure of children and young adults to uranium (U) and epidemiologically relevant external determinants of exposure. The investigation was performed with data from two studies within the framework of the German health-related environmental monitoring program: The German Environmental Survey for Children (GerES IV) conducted by the Federal Environment Agency (Umweltbundesamt) with data on 1,780 children 3-14 years of age and their home environment and the German Environmental Specimen Bank (ESB, section: human specimens) with data on 2,253 students 20-29 years of age. Both studies provided data on the U levels in human urine for all probands. GerES IV furthermore provided an extensive environmental and demographic database on, e.g., U levels in drinking water. The data from GerES IV and ESB were linked by GIS to spatially relevant exposure information, including background values of U in stream sediments and in upper and lower soils, U levels in mosses and particulate matter in the lower atmosphere, precipitation and elevation as well as forest density. Bivariate correlation analysis and two decision tree models showed moderate but significant associations between U in human urine and U levels in drinking water, stream sediments and upper and lower soils. Future investigations considering additional epidemiologically relevant data sets may differentiate the results. Furthermore, the sample design of future environmental epidemiology studies should take the spatial evaluation of the data into greater account.}, } @article {pmid21414966, year = {2011}, author = {Maldonado, E and Dutheil, JY and da Fonseca, RR and Vasconcelos, V and Antunes, A}, title = {IMPACT: integrated multiprogram platform for analyses in ConTest.}, journal = {The Journal of heredity}, volume = {102}, number = {3}, pages = {366-369}, doi = {10.1093/jhered/esr003}, pmid = {21414966}, issn = {1465-7333}, mesh = {Amino Acid Sequence ; Computational Biology ; *Programming Languages ; Proteins/chemistry ; *User-Computer Interface ; }, abstract = {In this paper, we introduce a new Graphical User Interface that estimates evolutionary rates on protein sequences by assessing changes in biochemical constraints. We describe IMPACT, a platform-independent (tested in Linux, Windows, and MacOS), easy to install software written in Java. IMPACT integrates the use of a built-in multiple sequence alignment editor, with programs that perform phylogenetic and protein structure analyses (ConTest, PhyML, ATV, and Jmol) allowing the user to quickly and efficiently perform evolutionary analyses on protein sequences, including the detection of selection (negative and positive) signatures at the amino acid scale, which can provide fundamental insight about species evolution and ecological fitness. IMPACT provides the user with a working platform that combines a number of bioinformatics tools and utilities in one place, transferring information directly among the various programs and therefore increasing the overall performance of evolutionary analyses on proteins.}, } @article {pmid21411280, year = {2011}, author = {Fisher, DJ and Copas, AJ and Tierney, JF and Parmar, MK}, title = {A critical review of methods for the assessment of patient-level interactions in individual participant data meta-analysis of randomized trials, and guidance for practitioners.}, journal = {Journal of clinical epidemiology}, volume = {64}, number = {9}, pages = {949-967}, doi = {10.1016/j.jclinepi.2010.11.016}, pmid = {21411280}, issn = {1878-5921}, support = {//Medical Research Council/United Kingdom ; }, mesh = {Algorithms ; Bias ; Data Interpretation, Statistical ; Humans ; MEDLINE ; *Meta-Analysis as Topic ; *Models, Statistical ; Outcome Assessment, Health Care ; Randomized Controlled Trials as Topic/*methods/statistics & numerical data ; Research Design ; }, abstract = {OBJECTIVE: Treatments may be more effective in some patients than others, and individual participant data (IPD) meta-analysis of randomized trials provides perhaps the best method of investigating treatment-covariate interactions. Various methods are used; we provide a comprehensive critique and develop guidance on method selection.

STUDY DESIGN AND SETTING: We searched MEDLINE to identify all frequentist methods and appraised them for simplicity, risk of bias, and power. IPD data sets were reanalyzed.

RESULTS: Four methodological categories were identified: PWT: pooling of within-trial covariate interactions; OSM: "one-stage" model with a treatment-covariate interaction term; TDCS: testing for difference between covariate subgroups in their pooled treatment effects; and CWA: combining PWT with meta-regression. Distinguishing across- and within-trial information is important, as the former may be subject to ecological bias. A strategy is proposed for method selection in different circumstances; PWT or CWA are natural first steps. The OSM method allows for more complex analyses; TDCS should be avoided. Our reanalysis shows that different methods can lead to substantively different findings.

CONCLUSION: The choice of method for investigating interactions in IPD meta-analysis is driven mainly by whether across-trial information is considered for inclusion, a decision, which depends on balancing possible improvement in power with an increased risk of bias.}, } @article {pmid21407210, year = {2011}, author = {Raes, J and Letunic, I and Yamada, T and Jensen, LJ and Bork, P}, title = {Toward molecular trait-based ecology through integration of biogeochemical, geographical and metagenomic data.}, journal = {Molecular systems biology}, volume = {7}, number = {}, pages = {473}, pmid = {21407210}, issn = {1744-4292}, mesh = {Adaptation, Physiological ; Algorithms ; Biodiversity ; *Climate ; Data Interpretation, Statistical ; *Ecology ; *Ecosystem ; Genetic Loci/*genetics ; Geography ; Metabolic Networks and Pathways ; *Metagenomics ; Molecular Sequence Annotation ; Oceans and Seas ; Regression Analysis ; Seawater/*microbiology ; Species Specificity ; }, abstract = {Using metagenomic 'parts lists' to infer global patterns on microbial ecology remains a significant challenge. To deduce important ecological indicators such as environmental adaptation, molecular trait dispersal, diversity variation and primary production from the gene pool of an ecosystem, we integrated 25 ocean metagenomes with geographical, meteorological and geophysicochemical data. We find that climatic factors (temperature, sunlight) are the major determinants of the biomolecular repertoire of each sample and the main limiting factor on functional trait dispersal (absence of biogeographic provincialism). Molecular functional richness and diversity show a distinct latitudinal gradient peaking at 20° N and correlate with primary production. The latter can also be predicted from the molecular functional composition of an environmental sample. Together, our results show that the functional community composition derived from metagenomes is an important quantitative readout for molecular trait-based biogeography and ecology.}, } @article {pmid21404233, year = {2011}, author = {Matauschek, C and Roos, C and Heymann, EW}, title = {Mitochondrial phylogeny of tamarins (Saguinus, Hoffmannsegg 1807) with taxonomic and biogeographic implications for the S. nigricollis species group.}, journal = {American journal of physical anthropology}, volume = {144}, number = {4}, pages = {564-574}, doi = {10.1002/ajpa.21445}, pmid = {21404233}, issn = {1096-8644}, mesh = {Animals ; Cluster Analysis ; Complementarity Determining Regions ; Computational Biology ; Cytochromes b/genetics ; DNA, Mitochondrial/chemistry/*genetics ; Feces/chemistry ; Geography ; Models, Statistical ; Peru ; Phylogeny ; Saguinus/classification/*genetics ; Sequence Analysis, DNA ; }, abstract = {Tamarins of the genus Saguinus, subfamily Callitrichinae, represent one of the most diverse primate radiations. So far, about 35 taxa have been described, but detailed information about their taxonomy and phylogeny is still lacking. To further elucidate the phylogenetic relationships and the biogeographic history within the genus, and to contribute to a more reliable classification of its taxa, we sequenced the complete mitochondrial cytochrome b gene and the hypervariable region I of the D-loop. Therefore, we mainly used fecal samples from wild tamarins collected during two expeditions to the Peruvian Amazon, an area of high tamarin diversity. Our data suggest that the numerous taxa of the S. nigricollis species group are derived from a common ancestor that separated from the other representatives of the genus ~10 mya. Most taxa of the S. nigricollis group form monophyletic clusters, which mainly originated in a single rapid radiation ~2.9 mya. S. fuscicollis and S. nigricollis appear as polyphyletic taxa, but we could identify various clusters, which are mainly consistent with differences in coat coloration. We could confirm most of the existing taxa as distinct entities and suggest species status for fuscicollis, illigeri, lagonotus, leucogenys, nigricollis, nigrifrons, tripartitus, and weddelli. Our genetic data do not support a separate status for melanoleucus and graellsi, but due to differences in fur coloration, we give them subspecies status. The species group most likely originated in western Amazonia and diversified during the decline of the Acre wetland and the formation of the Amazonian river system.}, } @article {pmid21402946, year = {2011}, author = {Tseng, YY and Li, WH}, title = {Evolutionary approach to predicting the binding site residues of a protein from its primary sequence.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {108}, number = {13}, pages = {5313-5318}, pmid = {21402946}, issn = {1091-6490}, support = {R01 GM030998/GM/NIGMS NIH HHS/United States ; R37 GM030998/GM/NIGMS NIH HHS/United States ; GM30998/GM/NIGMS NIH HHS/United States ; }, mesh = {*Amino Acid Sequence ; Binding Sites ; *Biological Evolution ; Databases, Protein ; Models, Molecular ; Molecular Sequence Data ; Protein Folding ; Protein Structure, Tertiary ; Proteins/*chemistry/*genetics ; Sequence Analysis, Protein/*methods ; }, abstract = {Protein binding site residues, especially catalytic residues, play a central role in protein function. Because more than 99% of the ∼ 12 million protein sequences in the nonredundant protein database have no structural information, it is desirable to develop methods to predict the binding site residues of a protein from its primary sequence. This task is highly challenging, because the binding site residues constitute only a small portion of a protein. However, the binding site residues of a protein are clustered in its functional pocket(s), and their spatial patterns tend to be conserved in evolution. To take advantage of these evolutionary and structural principles, we constructed a database of ∼ 50,000 templates (called the pocket-containing segment database), each of which includes not only a sequence segment that contains a functional pocket but also the structural attributes of the pocket. To use this database, we designed a template-matching technique, termed residue-matching profiling, and established a criterion for selecting templates for a query sequence. Finally, we developed a probabilistic model for assigning spatial scores to matched residues between the template and query sequence in local alignments using a set of selected scoring matrices and for computing the binding likelihood of each matched residue in the query sequence. From the likelihoods, one can predict the binding site residues in the query sequence. An automated computational pipeline was developed for our method. A performance evaluation shows that our method achieves a 70% precision in predicting binding site residues at 60% sensitivity.}, } @article {pmid21401565, year = {2011}, author = {Cao, J and Wang, L and Xu, J}, title = {Robust estimation for ordinary differential equation models.}, journal = {Biometrics}, volume = {67}, number = {4}, pages = {1305-1313}, doi = {10.1111/j.1541-0420.2011.01577.x}, pmid = {21401565}, issn = {1541-0420}, mesh = {Animals ; Computer Simulation ; *Data Interpretation, Statistical ; Humans ; *Models, Biological ; *Models, Statistical ; *Numerical Analysis, Computer-Assisted ; }, abstract = {Applied scientists often like to use ordinary differential equations (ODEs) to model complex dynamic processes that arise in biology, engineering, medicine, and many other areas. It is interesting but challenging to estimate ODE parameters from noisy data, especially when the data have some outliers. We propose a robust method to address this problem. The dynamic process is represented with a nonparametric function, which is a linear combination of basis functions. The nonparametric function is estimated by a robust penalized smoothing method. The penalty term is defined with the parametric ODE model, which controls the roughness of the nonparametric function and maintains the fidelity of the nonparametric function to the ODE model. The basis coefficients and ODE parameters are estimated in two nested levels of optimization. The coefficient estimates are treated as an implicit function of ODE parameters, which enables one to derive the analytic gradients for optimization using the implicit function theorem. Simulation studies show that the robust method gives satisfactory estimates for the ODE parameters from noisy data with outliers. The robust method is demonstrated by estimating a predator-prey ODE model from real ecological data.}, } @article {pmid21401325, year = {2011}, author = {Carmichael, N and Bausen, M and Boobis, AR and Cohen, SM and Embry, M and Fruijtier-Pölloth, C and Greim, H and Lewis, R and Bette Meek, ME and Mellor, H and Vickers, C and Doe, J}, title = {Using mode of action information to improve regulatory decision-making: an ECETOC/ILSI RF/HESI workshop overview.}, journal = {Critical reviews in toxicology}, volume = {41}, number = {3}, pages = {175-186}, doi = {10.3109/10408444.2010.541225}, pmid = {21401325}, issn = {1547-6898}, mesh = {Academies and Institutes ; Animals ; *Consensus Development Conferences as Topic ; *Decision Support Techniques ; Ecotoxicology/legislation & jurisprudence ; Environmental Pollution/*legislation & jurisprudence ; Foundations ; *Government Regulation ; Hazardous Substances/*toxicity ; Humans ; Risk Assessment/methods ; }, abstract = {The European Centre for Ecotoxicology and Toxicology of Chemicals (ECETOC), the International Life Sciences Institute (ILSI) Research Foundation (RF), and the ILSI Health and Environmental Sciences Institute (HESI) hosted a workshop in November 2009 to review current practice in the application of mode of action (MOA) considerations in chemical risk assessment. The aim was to provide a rationale for a more general, but flexible approach and to propose steps to facilitate broader uptake and use of the MOA concept. There was consensus amongst the workshop participants that it will require substantial effort and cooperation from the multiple disciplines involved to embrace a common, consistent, and transparent approach. Setting up a repository of accepted MOAs and associated guidance concerning appropriate data to support specific MOAs for critical effects would facilitate categorization of chemicals and allow predictions of toxicity outcomes by read-across. This should in future contribute to the reduction of toxicity testing in animals. The workshop participants also acknowledged the value and importance of human data and the importance of integrating information from biological pathway analyses into current MOA/human relevance frameworks.}, } @article {pmid21395929, year = {2011}, author = {Bonfim, C and Alves, A and Costa, TR and Alencar, F and Pedroza, D and Portugal, JL and Medeiros, Z}, title = {Spatial analysis and privation index to identify urban areas with a high risk of lymphatic filariasis.}, journal = {Tropical medicine & international health : TM & IH}, volume = {16}, number = {6}, pages = {748-755}, doi = {10.1111/j.1365-3156.2011.02758.x}, pmid = {21395929}, issn = {1365-3156}, mesh = {Brazil/epidemiology ; Elephantiasis, Filarial/*epidemiology/prevention & control/transmission ; Epidemiologic Methods ; Geographic Information Systems ; Humans ; *Poverty Areas ; Socioeconomic Factors ; Urban Health/*statistics & numerical data ; }, abstract = {OBJECTIVE: To evaluate composite living conditions as indicators of urban areas with a higher risk of filariasis transmission.

METHODS: This was an ecological study in the municipality of Jaboatão dos Guararapes, in Brazil. The analysis units were census tracts. The study was divided into three phases. First, data gathered during an epidemiological investigation were analysed. Secondly, living condition indicators were drawn up and the relationship between these indicators and microfilaremia prevalence rates was analysed. Thirdly, positive cases were georeferenced with a view to identifying spatial concentration using kernel intensity estimates. Two composite living condition indicators were calculated: a socio-environmental risk index (in the form of scores) and a social deprivation index (through principal-component factor analysis).

RESULTS: Of 23,673 individuals examined, 1.4% had microfilaremia. According to the two indicators, greater prevalence was found in the high-risk strata, and this association was confirmed by the kernel intensity estimates.

CONCLUSIONS: Classification of census tracts into risk strata showed the relevance of socio-economic factors and environmental conditions in identifying priority areas in urban spaces for interventions by the surveillance services and in planning filariasis control. Spatial analysis also proved to be an important tool for building up a territorially based surveillance system. These indicators, used in association with spatial analysis, are an instrument to be used by the Global Programme to Eliminate Lymphatic Filariasis.}, } @article {pmid21395891, year = {2011}, author = {Barberán, A and Fernández-Guerra, A and Auguet, JC and Galand, PE and Casamayor, EO}, title = {Phylogenetic ecology of widespread uncultured clades of the Kingdom Euryarchaeota.}, journal = {Molecular ecology}, volume = {20}, number = {9}, pages = {1988-1996}, doi = {10.1111/j.1365-294X.2011.05057.x}, pmid = {21395891}, issn = {1365-294X}, mesh = {Biodiversity ; Databases, Genetic ; *Ecosystem ; Environment ; Euryarchaeota/*classification/*genetics ; Genes, rRNA/*genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Despite its widespread distribution and high levels of phylogenetic diversity, microbes are poorly understood creatures. We applied a phylogenetic ecology approach in the Kingdom Euryarchaeota (Archaea) to gain insight into the environmental distribution and evolutionary history of one of the most ubiquitous and largely unknown microbial groups. We compiled 16S rRNA gene sequences from our own sequence libraries and public genetic databases for two of the most widespread mesophilic Euryarchaeota clades, Lake Dagow Sediment (LDS) and Rice Cluster-V (RC-V). The inferred population history indicated that both groups have undergone specific nonrandom evolution within environments, with several noteworthy habitat transition events. Remarkably, the LDS and RC-V groups had enormous levels of genetic diversity when compared with other microbial groups, and proliferation of sequences within each single clade was accompanied by significant ecological differentiation. Additionally, the freshwater Euryarchaeota counterparts unexpectedly showed high phylogenetic diversity, possibly promoted by their environmental adaptability and the heterogeneous nature of freshwater ecosystems. The temporal phylogenetic diversification pattern of these freshwater Euryarchaeota was concentrated both in early times and recently, similarly to other much less diverse but deeply sampled archaeal groups, further stressing that their genetic diversity is a function of environment plasticity. For the vast majority of living beings on Earth (i.e. the uncultured microorganisms), how they differ in the genetic or physiological traits used to exploit the environmental resources is largely unknown. Inferring population history from 16S rRNA gene-based molecular phylogenies under an ecological perspective may shed light on the intriguing relationships between lineage, environment, evolution and diversity in the microbial world.}, } @article {pmid21393383, year = {2011}, author = {Christin, PA and Osborne, CP and Sage, RF and Arakaki, M and Edwards, EJ}, title = {C(4) eudicots are not younger than C(4) monocots.}, journal = {Journal of experimental botany}, volume = {62}, number = {9}, pages = {3171-3181}, doi = {10.1093/jxb/err041}, pmid = {21393383}, issn = {1460-2431}, mesh = {Biological Evolution ; Carbon Dioxide/metabolism ; Cell Respiration ; Databases, Genetic ; Ecosystem ; *Evolution, Molecular ; Genetic Variation ; Genome, Plant/genetics ; Magnoliopsida/classification/*genetics/physiology ; Models, Genetic ; Photosynthesis/*genetics ; Phylogeny ; Poaceae/classification/genetics/physiology ; Sequence Analysis, DNA ; Time Factors ; }, abstract = {C(4) photosynthesis is a plant adaptation to high levels of photorespiration. Physiological models predict that atmospheric CO(2) concentration selected for C(4) grasses only after it dropped below a critical threshold during the Oligocene (∼30 Ma), a hypothesis supported by phylogenetic and molecular dating analyses. However the same models predict that CO(2) should have reached much lower levels before selecting for C(4) eudicots, making C(4) eudicots younger than C(4) grasses. In this study, different phylogenetic datasets were combined in order to conduct the first comparative analysis of the age of C(4) origins in eudicots. Our results suggested that all lineages of C(4) eudicots arose during the last 30 million years, with the earliest before 22 Ma in Chenopodiaceae and Aizoaceae, and the latest probably after 2 Ma in Flaveria. C(4) eudicots are thus not globally younger than C(4) monocots. All lineages of C(4) plants evolved in a similar low CO(2) atmosphere that predominated during the last 30 million years. Independent C(4) origins were probably driven by different combinations of specific factors, including local ecological characteristics such as habitat openness, aridity, and salinity, as well as the speciation and dispersal history of each clade. Neither the lower number of C(4) species nor the frequency of C(3)-C(4) intermediates in eudicots can be attributed to a more recent origin, but probably result from variation in diversification and evolutionary rates among the different groups that evolved the C(4) pathway.}, } @article {pmid21392355, year = {2010}, author = {Miller, CS and Hebblewhite, M and Goodrich, JM and Miquelle, DG}, title = {Review of research methodologies for tigers: telemetry.}, journal = {Integrative zoology}, volume = {5}, number = {4}, pages = {378-389}, doi = {10.1111/j.1749-4877.2010.00216.x}, pmid = {21392355}, issn = {1749-4877}, mesh = {Animals ; Conservation of Natural Resources/*methods ; Demography ; Endangered Species ; Geographic Information Systems/instrumentation ; *Telemetry ; Tigers/*physiology ; }, abstract = {Over the past half century, wildlife research has relied on technological advances to gain additional insight into the secretive lives of animals. This revolution started in the 1960s with the development of radio telemetry and continues today with the use of Global Positioning System (GPS)-based research techniques. In the present paper we review the history of radio telemetry from its origins with grizzly bears in Yellowstone to its early applications in tiger research and conservation in Asia. We address the different types of data that are available using radio telemetry as opposed to using other research techniques, such as behavioral observations, camera trapping, DNA analysis and scat analysis. In the late 1990s, the rapid development of GPS collar technology revolutionized wildlife research. This new technology has enabled researchers to dramatically improve their ability to gather data on animal movements and ecology. Despite the ecological and conservation benefits of radio telemetry, there have been few telemetry studies of tigers in the wild, and most have been on the Bengal or Amur subspecies. We close with an assessment of the current tiger conservation efforts using GPS technology and discuss how this new information can help to preserve tigers for future generations.}, } @article {pmid21392325, year = {2010}, author = {Stenseth, NC}, title = {The biological consequences of global change.}, journal = {Integrative zoology}, volume = {5}, number = {2}, pages = {85-86}, doi = {10.1111/j.1749-4877.2010.00200.x}, pmid = {21392325}, issn = {1749-4877}, mesh = {*Climate Change ; Data Interpretation, Statistical ; *Ecosystem ; Introduced Species/*trends ; Population Dynamics ; Species Specificity ; }, } @article {pmid21392320, year = {2010}, author = {Ogilvie, SC and Ataria, JM and Waiwai, J and Doherty, J and Miller, A and Ross, JG and Eason, CT}, title = {Vertebrate pesticide risk assessment by indigenous communities in New Zealand.}, journal = {Integrative zoology}, volume = {5}, number = {1}, pages = {37-43}, doi = {10.1111/j.1749-4877.2010.00190.x}, pmid = {21392320}, issn = {1749-4877}, mesh = {Animals ; Databases, Factual ; Ferns/*drug effects/metabolism ; Fluoroacetates/pharmacokinetics/*toxicity ; Humans ; New Zealand ; Pest Control/*methods ; Pesticides/pharmacokinetics/*toxicity ; Population Groups ; Risk Assessment ; Rubiaceae/*drug effects/metabolism ; Time Factors ; Trichosurus/*metabolism ; }, abstract = {In New Zealand, the vertebrate pesticide sodium fluoroacetate (Compound 1080) is aerially applied in baits for control of the brush-tailed possum Trichosurus vulpecula (Kerr, 1792). Maori, the indigenous people of New Zealand, have raised concerns about 1080 impacts on culturally-important species. Here, we outline two steps taken to help Maori assess 1080 risk. First, field research was undertaken to determine if naturally-occurring plants utilized by a Maori community for food and medicine would take up 1080 from baits. Single baits were placed at the base of individual plants of two species, pikopiko (Asplenium bulbiferum) and karamuramu (Coprosma robusta). Plants were sampled at various times up to 56 days, and samples were analyzed for 1080 content. No 1080 was detected in any of the pikopiko samples, whereas 1080 was detected in karamuramu, at a maximum concentration of 5 ppb after seven days, and 2.5 ppb after 14 days. This concentration decreased to 0 at 28 days, indicating that 1080 was not persistent. The results of the present study suggest there is negligible risk of humans being poisoned by consuming plants that have taken up 1080 from baits. To allay community concerns that minute concentrations of 1080 might influence the medicinal properties of plants, it is suggested that a withholding period of 30 days after 1080 control operations could be adopted. Second, after further consultation we undertook a review of the scientific literature relating to 1080 impacts on additional non-target species of cultural importance to Maori. The information was presented on an interactive foodweb database that allowed the collection and presentation of a large volume of complex information about 1080 in a holistic and pictorial fashion. This database was presented to many Maori communities throughout New Zealand, and feedback was overwhelmingly positive. The database is likely to play a key role in informing these communities about 1080, and is seen as an important new tool to help these communities make their own risk assessments.}, } @article {pmid21385165, year = {2011}, author = {Li, J and Ban, J and Santiago, LS}, title = {Nonparametric tests for homogeneity of species assemblages: a data depth approach.}, journal = {Biometrics}, volume = {67}, number = {4}, pages = {1481-1488}, doi = {10.1111/j.1541-0420.2011.01573.x}, pmid = {21385165}, issn = {1541-0420}, mesh = {*Biodiversity ; Biometry/*methods ; Computer Simulation ; *Data Interpretation, Statistical ; Ecology/*statistics & numerical data ; *Ecosystem ; *Models, Statistical ; Population Dynamics ; Trees/*classification ; }, abstract = {Testing homogeneity of species assemblages has important applications in ecology. Due to the unique structure of abundance data often collected in ecological studies, most classical statistical tests cannot be applied directly. In this article, we propose two novel nonparametric tests for comparing species assemblages based on the concept of data depth. They can be considered as a natural generalization of the Kolmogorov-Smirnov and the Cramér-von Mises tests (KS and CM) in this species assemblage comparison context. Our simulation studies show that the proposed test is more powerful than other existing methods under various settings. A real example is used to demonstrate how the proposed method is applied to compare species assemblages using plant community data from a highly diverse tropical forest at Barro Colorado Island, Panama.}, } @article {pmid21382361, year = {2012}, author = {Pleil, JD and Sobus, JR and Sheppard, PR and Ridenour, G and Witten, ML}, title = {Strategies for evaluating the environment-public health interaction of long-term latency disease: the quandary of the inconclusive case-control study.}, journal = {Chemico-biological interactions}, volume = {196}, number = {3}, pages = {68-78}, doi = {10.1016/j.cbi.2011.02.020}, pmid = {21382361}, issn = {1872-7786}, mesh = {Case-Control Studies ; Child, Preschool ; Computer Simulation ; *Data Interpretation, Statistical ; *Disease Outbreaks ; *Environmental Exposure ; Humans ; Nevada/epidemiology ; Precursor Cell Lymphoblastic Leukemia-Lymphoma/chemically induced/*epidemiology/etiology ; Public Health/*methods ; Retrospective Studies ; }, abstract = {Environmental links to disease are difficult to uncover because environmental exposures are variable in time and space, contaminants occur in complex mixtures, and many diseases have a long time delay between exposure and onset. Furthermore, individuals in a population have different activity patterns (e.g., hobbies, jobs, and interests), and different genetic susceptibilities to disease. As such, there are many potential confounding factors to obscure the reasons that one individual gets sick and another remains healthy. An important method for deducing environmental associations with disease outbreak is the retrospective case-control study wherein the affected and control subject cohorts are studied to see what is different about their previous exposure history. Despite success with infectious diseases (e.g., food poisoning, and flu), case-control studies of cancer clusters rarely have an unambiguous outcome. This is attributed to the complexity of disease progression and the long-term latency between exposure and disease onset. In this article, we consider strategies for investigating cancer clusters and make some observations for improving statistical power through broader non-parametric approaches wherein sub-populations (i.e., whole towns), rather than individuals, are treated as the cases and controls, and the associated cancer rates are treated as the dependent variable. We subsequently present some ecological data for tungsten and cobalt from studies by University of Arizona researchers who document elevated levels of tungsten and cobalt in Fallon, NV. These results serve as candidates for future hybrid ecologic case-control investigations of childhood leukemia clusters.}, } @article {pmid21378367, year = {2011}, author = {Swanson, M and Studts, CR and Bardach, SH and Bersamin, A and Schoenberg, NE}, title = {Intergenerational energy balance interventions: a systematic literature review.}, journal = {Health education & behavior : the official publication of the Society for Public Health Education}, volume = {38}, number = {2}, pages = {171-197}, pmid = {21378367}, issn = {1552-6127}, support = {R01 DK081324/DK/NIDDK NIH HHS/United States ; UL1 TR001998/TR/NCATS NIH HHS/United States ; 1 R01 DK081324-01/DK/NIDDK NIH HHS/United States ; R01 DK081324-01/DK/NIDDK NIH HHS/United States ; UL1 RR033173/RR/NCRR NIH HHS/United States ; }, mesh = {Databases, Bibliographic ; Energy Intake/physiology ; Energy Metabolism/physiology ; Family Health ; *Health Behavior ; Health Promotion/*methods ; Humans ; *Intergenerational Relations ; Obesity/epidemiology/metabolism/*prevention & control ; }, abstract = {Many nations have witnessed a dramatic increase in the prevalence of obesity and overweight across their population. Recognizing the influence of the household environment on energy balance has led many researchers to suggest that intergenerational interventions hold promise for addressing this epidemic. Yet few comprehensive reviews of intergenerational energy balance interventions have been undertaken. Our review of the literature over the past decade revealed that intergenerational intervention approaches to enhance energy balance use a broad array of designs, target populations, and theoretical models, making results difficult to compare and "best practices" challenging to identify. Additional themes include variation in how interventions incorporate the intergenerational component; an increasing acknowledgment of the importance of ecological models; variations in the location of interventions delivery; diversity in the intervention flexibility/structure, intensity, and duration; and variation in outcomes and measures used across studies. We discuss implications and future directions of intergenerational energy balance approaches.}, } @article {pmid21377756, year = {2011}, author = {Chen, Y and Pang, Q and Dai, S and Wang, Y and Chen, S and Yan, X}, title = {Proteomic identification of differentially expressed proteins in Arabidopsis in response to methyl jasmonate.}, journal = {Journal of plant physiology}, volume = {168}, number = {10}, pages = {995-1008}, doi = {10.1016/j.jplph.2011.01.018}, pmid = {21377756}, issn = {1618-1328}, mesh = {Acetates/*pharmacology ; Arabidopsis/*drug effects/metabolism ; Arabidopsis Proteins/drug effects/*metabolism ; Cyclopentanes/*pharmacology ; Databases, Protein ; Down-Regulation/drug effects ; Electrophoresis, Gel, Two-Dimensional ; Glucosinolates/metabolism ; Oxylipins/*pharmacology ; Plant Growth Regulators/*pharmacology ; Plant Leaves/drug effects/metabolism ; Proteome/analysis/*drug effects ; Proteomics/*methods ; Signal Transduction ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ; Tandem Mass Spectrometry ; Time Factors ; Up-Regulation/drug effects ; }, abstract = {Jasmonates (JAs) are the well characterized fatty acid-derived cyclopentanone signals involved in the plant response to biotic and abiotic stresses. JAs have been shown to regulate many aspects of plant metabolism, including glucosinolate biosynthesis. Glucosinolates are natural plant products that function in defense against herbivores and pathogens. In this study, we applied a proteomic approach to gain insight into the physiological processes, including glucosinolate metabolism, in response to methyl jasmonate (MeJA). We identified 194 differentially expressed protein spots that contained proteins that participated in a wide range of physiological processes. Functional classification analysis showed that photosynthesis and carbohydrate anabolism were repressed after MeJA treatment, while carbohydrate catabolism was up-regulated. Additionally, proteins related to the JA biosynthesis pathway, stress and defense, and secondary metabolism were up-regulated. Among the differentially expressed proteins, many were involved in oxidative tolerance. The results indicate that MeJA elicited a defense response at the proteome level through a mechanism of redirecting growth-related metabolism to defense-related metabolism.}, } @article {pmid21371061, year = {2011}, author = {Linkov, I and Welle, P and Loney, D and Tkachuk, A and Canis, L and Kim, JB and Bridges, T}, title = {Use of multicriteria decision analysis to support weight of evidence evaluation.}, journal = {Risk analysis : an official publication of the Society for Risk Analysis}, volume = {31}, number = {8}, pages = {1211-1225}, doi = {10.1111/j.1539-6924.2011.01585.x}, pmid = {21371061}, issn = {1539-6924}, mesh = {*Decision Support Techniques ; Ecosystem ; Environmental Pollution/legislation & jurisprudence ; Environmental Restoration and Remediation/legislation & jurisprudence/methods/statistics & numerical data ; Humans ; Risk Assessment/*methods/statistics & numerical data ; United States ; United States Environmental Protection Agency ; }, abstract = {Weight of evidence (WOE) methods are key components of ecological and human health risk assessments. Most WOE applications rely on the qualitative integration of diverse lines of evidence (LOE) representing impact on ecological receptors and humans. Recent calls for transparency in assessments and justifiability of management decisions are pushing the community to consider quantitative methods for integrated risk assessment and management. This article compares and contrasts the type of information required for application of individual WOE techniques and the outcomes that they provide in ecological risk assessment and proposes a multicriteria decision analysis (MCDA) framework for integrating individual LOE in support of management decisions. The use of quantitative WOE techniques is illustrated for a hypothetical but realistic case study of selecting remedial alternatives at a contaminated aquatic site. Use of formal MCDA does not necessarily eliminate biases and judgment calls necessary for selecting remedial alternatives, but allows for transparent evaluation and fusion of individual LOE. It also provides justifiable methods for selecting remedial alternatives consistent with stakeholder and decision-maker values.}, } @article {pmid21366926, year = {2011}, author = {Pavlović-Lažetić, GM and Mitić, NS and Kovačević, JJ and Obradović, Z and Malkov, SN and Beljanski, MV}, title = {Bioinformatics analysis of disordered proteins in prokaryotes.}, journal = {BMC bioinformatics}, volume = {12}, number = {}, pages = {66}, pmid = {21366926}, issn = {1471-2105}, mesh = {Amino Acids/analysis ; Archaea/genetics/metabolism ; Archaeal Proteins/*analysis/chemistry ; Bacteria/genetics/metabolism ; Bacterial Proteins/*analysis/chemistry ; Base Composition ; Cluster Analysis ; Computational Biology/*methods ; Databases, Protein ; Genomics/methods ; Internet ; Protein Conformation ; Proteome/analysis ; }, abstract = {BACKGROUND: A significant number of proteins have been shown to be intrinsically disordered, meaning that they lack a fixed 3 D structure or contain regions that do not posses a well defined 3 D structure. It has also been proven that a protein's disorder content is related to its function. We have performed an exhaustive analysis and comparison of the disorder content of proteins from prokaryotic organisms (i.e., superkingdoms Archaea and Bacteria) with respect to functional categories they belong to, i.e., Clusters of Orthologous Groups of proteins (COGs) and groups of COGs-Cellular processes (Cp), Information storage and processing (Isp), Metabolism (Me) and Poorly characterized (Pc). We also analyzed the disorder content of proteins with respect to various genomic, metabolic and ecological characteristics of the organism they belong to. We used correlations and association rule mining in order to identify the most confident associations between specific modalities of the characteristics considered and disorder content.

RESULTS: Bacteria are shown to have a somewhat higher level of protein disorder than archaea, except for proteins in the Me functional group. It is demonstrated that the Isp and Cp functional groups in particular (L-repair function and N-cell motility and secretion COGs of proteins in specific) possess the highest disorder content, while Me proteins, in general, posses the lowest. Disorder fractions have been confirmed to have the lowest level for the so-called order-promoting amino acids and the highest level for the so-called disorder promoters. For each pair of organism characteristics, specific modalities are identified with the maximum disorder proteins in the corresponding organisms, e.g., high genome size-high GC content organisms, facultative anaerobic-low GC content organisms, aerobic-high genome size organisms, etc. Maximum disorder in archaea is observed for high GC content-low genome size organisms, high GC content-facultative anaerobic or aquatic or mesophilic organisms, etc. Maximum disorder in bacteria is observed for high GC content-high genome size organisms, high genome size-aerobic organisms, etc. Some of the most reliable association rules mined establish relationships between high GC content and high protein disorder, medium GC content and both medium and low protein disorder, anaerobic organisms and medium protein disorder, Gammaproteobacteria and low protein disorder, etc. A web site Prokaryote Disorder Database has been designed and implemented at the address http://bioinfo.matf.bg.ac.rs/disorder, which contains complete results of the analysis of protein disorder performed for 296 prokaryotic completely sequenced genomes.

CONCLUSIONS: Exhaustive disorder analysis has been performed by functional classes of proteins, for a larger dataset of prokaryotic organisms than previously done. Results obtained are well correlated to those previously published, with some extension in the range of disorder level and clear distinction between functional classes of proteins. Wide correlation and association analysis between protein disorder and genomic and ecological characteristics has been performed for the first time. The results obtained give insight into multi-relationships among the characteristics and protein disorder. Such analysis provides for better understanding of the evolutionary process and may be useful for taxon determination. The main drawback of the approach is the fact that the disorder considered has been predicted and not experimentally established.}, } @article {pmid21366814, year = {2011}, author = {Peng, C and Guiot, J and Wu, H and Jiang, H and Luo, Y}, title = {Integrating models with data in ecology and palaeoecology: advances towards a model-data fusion approach.}, journal = {Ecology letters}, volume = {14}, number = {5}, pages = {522-536}, doi = {10.1111/j.1461-0248.2011.01603.x}, pmid = {21366814}, issn = {1461-0248}, mesh = {Carbon/analysis ; Climate Change ; Data Interpretation, Statistical ; Ecology/*methods/trends ; Ecosystem ; Forecasting/methods ; *Models, Biological ; *Models, Statistical ; }, abstract = {It is increasingly being recognized that global ecological research requires novel methods and strategies in which to combine process-based ecological models and data in cohesive, systematic ways. Model-data fusion (MDF) is an emerging area of research in ecology and palaeoecology. It provides a new quantitative approach that offers a high level of empirical constraint over model predictions based on observations using inverse modelling and data assimilation (DA) techniques. Increasing demands to integrate model and data methods in the past decade has led to MDF utilization in palaeoecology, ecology and earth system sciences. This paper reviews key features and principles of MDF and highlights different approaches with regards to DA. After providing a critical evaluation of the numerous benefits of MDF and its current applications in palaeoecology (i.e., palaeoclimatic reconstruction, palaeovegetation and palaeocarbon storage) and ecology (i.e. parameter and uncertainty estimation, model error identification, remote sensing and ecological forecasting), the paper discusses method limitations, current challenges and future research direction. In the ongoing data-rich era of today's world, MDF could become an important diagnostic and prognostic tool in which to improve our understanding of ecological processes while testing ecological theory and hypotheses and forecasting changes in ecosystem structure, function and services.}, } @article {pmid21363983, year = {2011}, author = {MacMillan, K and Enscore, RE and Ogen-Odoi, A and Borchert, JN and Babi, N and Amatre, G and Atiku, LA and Mead, PS and Gage, KL and Eisen, RJ}, title = {Landscape and residential variables associated with plague-endemic villages in the West Nile region of Uganda.}, journal = {The American journal of tropical medicine and hygiene}, volume = {84}, number = {3}, pages = {435-442}, pmid = {21363983}, issn = {1476-1645}, mesh = {Animals ; Animals, Domestic ; Case-Control Studies ; Demography ; Disease Outbreaks ; Endemic Diseases ; Geographic Information Systems ; *Housing ; Humans ; Plague/*epidemiology ; Risk Factors ; Rivers ; Uganda/epidemiology ; }, abstract = {Plague, caused by the bacteria Yersinia pestis, is a severe, often fatal disease. This study focuses on the plague-endemic West Nile region of Uganda, where limited information is available regarding environmental and behavioral risk factors associated with plague infection. We conducted observational surveys of 10 randomly selected huts within historically classified case and control villages (four each) two times during the dry season of 2006 (N = 78 case huts and N = 80 control huts), which immediately preceded a large plague outbreak. By coupling a previously published landscape-level statistical model of plague risk with this observational survey, we were able to identify potential residence-based risk factors for plague associated with huts within historic case or control villages (e.g., distance to neighboring homestead and presence of pigs near the home) and huts within areas previously predicted as elevated risk or low risk (e.g., corn and other annual crops grown near the home, water storage in the home, and processed commercial foods stored in the home). The identified variables are consistent with current ecologic theories on plague transmission dynamics. This preliminary study serves as a foundation for future case control studies in the area.}, } @article {pmid21361015, year = {2010}, author = {Song, YQ and Cao, ML}, title = {[Landscape ecological security assessment of Beijing City based on RS and GIS].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {21}, number = {11}, pages = {2889-2895}, pmid = {21361015}, issn = {1001-9332}, mesh = {China ; *Conservation of Natural Resources ; Ecology/methods ; *Ecosystem ; Environment Design ; *Geographic Information Systems ; *Remote Sensing Technology ; Risk Assessment ; Safety ; Satellite Communications ; }, abstract = {By using RS, GIS, and landscape ecology methods, and based on the landscape structure, function, vitality, ecological sensitivity, and landscape pressure, an evaluation index system of landscape ecological security was constructed to analyze the landscape ecological security level and its spatiotemporal distribution pattern in Beijing City in 1988-2004. During the study period, the ecological service value of Beijing City was on a relatively high level, while the landscape vigor index and landscape pressure were on a relatively low level. The stability of landscape structure dropped, and the ecological sensitivity was also on a relatively low level. In 1998 and 2004, the landscape ecological security index of Beijing City was on a medium level, with the average value being 0.410 and 0.403, respectively, suggesting a slight deterioration in the landscape ecological security during the study period.}, } @article {pmid21359459, year = {2011}, author = {Moraes, AB and Zanini, RR and Giugliani, ER and Riboldi, J}, title = {[Trends in the proportion of low birth weight from 1994 to 2004 in Rio Grande do Sul State, Brazil: a multilevel analysis].}, journal = {Cadernos de saude publica}, volume = {27}, number = {2}, pages = {229-240}, doi = {10.1590/s0102-311x2011000200004}, pmid = {21359459}, issn = {1678-4464}, mesh = {Brazil/epidemiology ; Cesarean Section/statistics & numerical data ; Forecasting ; Humans ; Infant Mortality ; *Infant, Low Birth Weight ; Infant, Newborn ; Information Systems/statistics & numerical data ; Longitudinal Studies ; Multilevel Analysis ; Premature Birth/*epidemiology ; Socioeconomic Factors ; }, abstract = {The aim of this longitudinal ecological study was to analyze the trend in the proportion of low birth weight in Rio Grande do Sul State, Brazil, from 1994 to 2004 by panel data analysis and multilevel linear regression (two levels: by micro-region and time in years) to estimate risk factors associated with low birth weight. The proportion of low birth weight increased by 1.2% per year, and the multilevel model showed that the proportions differed between the micro-regions and increased over time, with the increase in the percentage of premature newborns, with the increase in the infant mortality rate, and with the increase in the cesarean rate. Among the micro-regions, the proportions of low birth weight varied positively with the urbanization rate and expenditures in the Unified National Health System and negatively with rate of participation in the workforce. According to the multilevel model, most of the variation in proportions of low birth weight was due to the effects of the micro-region of residence of the newborn's mother.}, } @article {pmid21359150, year = {2011}, author = {Charland, KM and Brownstein, JS and Verma, A and Brien, S and Buckeridge, DL}, title = {Socio-economic disparities in the burden of seasonal influenza: the effect of social and material deprivation on rates of influenza infection.}, journal = {PloS one}, volume = {6}, number = {2}, pages = {e17207}, pmid = {21359150}, issn = {1932-6203}, support = {R21 LM009263/LM/NLM NIH HHS/United States ; R21 AI073591-02/AI/NIAID NIH HHS/United States ; R21AI073591-01/AI/NIAID NIH HHS/United States ; R21 AI073591/AI/NIAID NIH HHS/United States ; CAT 86857/CAPMC/CIHR/Canada ; PAN-83152/CAPMC/CIHR/Canada ; R21LM009263-01/LM/NLM NIH HHS/United States ; }, mesh = {Adolescent ; Adult ; Aged ; Aged, 80 and over ; Child ; Child, Preschool ; *Cost of Illness ; Female ; *Health Status Disparities ; Healthcare Disparities/statistics & numerical data ; Humans ; Incidence ; Infant ; Infant, Newborn ; Influenza, Human/*economics/*epidemiology/etiology ; Male ; Middle Aged ; *Psychosocial Deprivation ; Quebec/epidemiology ; Risk Factors ; Seasons ; *Social Class ; Socioeconomic Factors ; Young Adult ; }, abstract = {BACKGROUND: There is little empirical evidence in support of a relationship between rates of influenza infection and level of material deprivation (i.e., lack of access to goods and services) and social deprivation (i.e. lack of social cohesion and support).

METHOD: Using validated population-level indices of material and social deprivation and medical billing claims for outpatient clinic and emergency department visits for influenza from 1996 to 2006, we assessed the relationship between neighbourhood rates of influenza and neighbourhood levels of deprivation using Bayesian ecological regression models. Then, by pooling data from neighbourhoods in the top decile (i.e., most deprived) and the bottom decile, we compared rates in the most deprived populations to the least deprived populations using age- and sex-standardized rate ratios.

RESULTS: Deprivation scores ranged from one to five with five representing the highest level of deprivation. We found a 21% reduction in rates for every 1 unit increase in social deprivation score (rate ratio [RR] 0.79, 95% Credible Interval [CrI] 0.66, 0.97). There was little evidence of a meaningful linear relationship with material deprivation (RR 1.06, 95% CrI 0.93, 1.24). However, relative to neighbourhoods with deprivation scores in the bottom decile, those in the top decile (i.e., most materially deprived) had substantially higher rates (RR 2.02, 95% Confidence Interval 1.99, 2.05).

CONCLUSION: Though it is hypothesized that social and material deprivation increase risk of acute respiratory infection, we found decreasing healthcare utilization rates for influenza with increasing social deprivation. This finding may be explained by the fewer social contacts and, thus, fewer influenza exposure opportunities of the socially deprived. Though there was no evidence of a linear relationship with material deprivation, when comparing the least to the most materially deprived populations, we observed higher rates in the most materially deprived populations.}, } @article {pmid21352934, year = {2011}, author = {Chan, LM and Brown, JL and Yoder, AD}, title = {Integrating statistical genetic and geospatial methods brings new power to phylogeography.}, journal = {Molecular phylogenetics and evolution}, volume = {59}, number = {2}, pages = {523-537}, doi = {10.1016/j.ympev.2011.01.020}, pmid = {21352934}, issn = {1095-9513}, mesh = {Animals ; Anura ; Central America ; Classification/*methods ; *Data Interpretation, Statistical ; *Demography ; Genetics, Population ; *Geographic Information Systems ; Heteroptera ; Lizards ; Madagascar ; Mexico ; *Models, Genetic ; Passeriformes ; *Phylogeny ; Population Dynamics ; }, abstract = {The field of phylogeography continues to grow in terms of power and accessibility. Initially uniting population genetics and phylogenetics, it now spans disciplines as diverse as geology, statistics, climatology, ecology, physiology, and bioinformatics to name a few. One major and recent integration driving the field forward is between "statistical phylogeography" and Geographic Information Systems (GIS) (Knowles, 2009). Merging genetic and geospatial data, and their associated methodological toolkits, is helping to bring explicit hypothesis testing to the field of phylogeography. Hypotheses derived from one approach can be reciprocally tested with data derived from the other field and the synthesis of these data can help place demographic events in an historical and spatial context, guide genetic sampling, and point to areas for further investigation. Here, we present three practical examples of empirical analysis that integrate statistical genetic and GIS tools to construct and test phylogeographic hypotheses. Insights into the evolutionary mechanisms underlying recent divergences can benefit from simultaneously considering diverse types of information to iteratively test and reformulate hypotheses. Our goal is to provide the reader with an introduction to the variety of available tools and their potential application to typical questions in phylogeography with the hope that integrative methods will be more broadly and commonly applied to other biological systems and data sets.}, } @article {pmid21341304, year = {2011}, author = {Wakefield, J and Haneuse, S and Dobra, A and Teeple, E}, title = {Bayes computation for ecological inference.}, journal = {Statistics in medicine}, volume = {30}, number = {12}, pages = {1381-1396}, pmid = {21341304}, issn = {1097-0258}, support = {R01 CA095994/CA/NCI NIH HHS/United States ; R01 CA095994-04/CA/NCI NIH HHS/United States ; R01 CA125081/CA/NCI NIH HHS/United States ; }, mesh = {*Bayes Theorem ; Computer Simulation ; *Data Interpretation, Statistical ; Diabetes Mellitus/epidemiology ; *Epidemiologic Methods ; Female ; Humans ; Markov Chains ; *Models, Statistical ; Monte Carlo Method ; *Numerical Analysis, Computer-Assisted ; }, abstract = {Ecological data are available at the level of the group, rather than at the level of the individual. The use of ecological data in spatial epidemiological investigations is particularly common. Although the computational methods described are more generally applicable, this paper concentrates on the situation in which the margins of 2 × 2 tables are observed in each of n geographical areas, with a Bayesian approach to inference. We consider auxiliary schemes that impute the missing data, and compare with a previously suggested normal approximation. The analysis of ecological data is subject to ecological bias, with the only reliable means of removing such bias being the addition of auxiliary individual-level information. Various schemes have been suggested for this supplementation, and we illustrate how the computational methods may be applied to the analysis of such enhanced data. The methods are illustrated using simulated data and two examples. In the first example, the ecological data are supplemented with a simple random sample of individual-level data, and in this example the normal approximation fails. In the second example case-control sampling provides the additional information.}, } @article {pmid21337020, year = {2011}, author = {Christensen, SW and Brandt, CC and McCracken, MK}, title = {Importance of data management in a long-term biological monitoring program.}, journal = {Environmental management}, volume = {47}, number = {6}, pages = {1112-1124}, pmid = {21337020}, issn = {1432-1009}, mesh = {Archives ; *Database Management Systems ; Electronic Data Processing ; Environmental Monitoring/*methods/standards ; Environmental Restoration and Remediation ; Information Storage and Retrieval ; Water Pollution, Chemical/statistics & numerical data ; }, abstract = {The long-term Biological Monitoring and Abatement Program (BMAP) has always needed to collect and retain high-quality data on which to base its assessments of ecological status of streams and their recovery after remediation. Its formal quality assurance, data processing, and data management components all contribute to meeting this need. The Quality Assurance Program comprehensively addresses requirements from various institutions, funders, and regulators, and includes a data management component. Centralized data management began a few years into the program when an existing relational database was adapted and extended to handle biological data. The database's main data tables and several key reference tables are described. One of the most important related activities supporting long-term analyses was the establishing of standards for sampling site names, taxonomic identification, flagging, and other components. The implemented relational database supports the transmittal of data to the Oak Ridge Environmental Information System (OREIS) as the permanent repository. We also discuss some limitations to our implementation. Some types of program data were not easily accommodated in the central systems, and many possible data-sharing and integration options are not easily accessible to investigators. From our experience we offer data management advice to other biologically oriented long-term environmental sampling and analysis programs.}, } @article {pmid21335835, year = {2011}, author = {Parsons, TD and Courtney, CG and Arizmendi, B and Dawson, M}, title = {Virtual Reality Stroop Task for neurocognitive assessment.}, journal = {Studies in health technology and informatics}, volume = {163}, number = {}, pages = {433-439}, pmid = {21335835}, issn = {0926-9630}, mesh = {*Computer Graphics ; Computer-Assisted Instruction/*methods ; Diagnosis, Computer-Assisted/*methods ; Humans ; Photic Stimulation/*methods ; *Stroop Test ; }, abstract = {Given the prevalence of traumatic brain injury (TBI), and the fact that many mild TBIs have no external marker of injury, there is a pressing need for innovative assessment technology. The demand for assessment that goes beyond traditional paper-and-pencil testing has resulted in the use of automated cognitive testing for increased precision and efficiency; and the use of virtual environment technology for enhanced ecological validity and increased function-based assessment. To address these issues, a Virtual Reality Stroop Task (VRST) that involves the subject being immersed in a virtual Humvee as Stroop stimuli appear on the windshield was developed. This study is an initial validation of the VRST as an assessment of neurocognitive functioning. When compared to the paper-and-pencil, as well as Automated Neuropsychological Assessment Metrics versions of the Stroop, the VRST appears to have enhanced capacity for providing an indication of a participant's reaction time and ability to inhibit a prepotent response while immersed in a military relevant simulation that presents psychophysiologically arousing high and low threat stimuli.}, } @article {pmid21330594, year = {2011}, author = {Hoerster, KD and Mayer, JA and Gabbard, S and Kronick, RG and Roesch, SC and Malcarne, VL and Zuniga, ML}, title = {Impact of individual-, environmental-, and policy-level factors on health care utilization among US farmworkers.}, journal = {American journal of public health}, volume = {101}, number = {4}, pages = {685-692}, pmid = {21330594}, issn = {1541-0048}, mesh = {Adult ; *Agriculture ; Female ; Geographic Information Systems ; Health Care Surveys ; Health Services/*statistics & numerical data ; *Health Services Accessibility ; Humans ; Logistic Models ; Male ; *Policy ; Risk ; *Social Class ; United States ; }, abstract = {OBJECTIVES: We examined individual-, environmental-, and policy-level correlates of US farmworker health care utilization, guided by the behavioral model for vulnerable populations and the ecological model.

METHODS: The 2006 and 2007 administrations of the National Agricultural Workers Survey (n = 2884) provided the primary data. Geographic information systems, the 2005 Uniform Data System, and rurality and border proximity indices provided environmental variables. To identify factors associated with health care use, we performed logistic regression using weighted hierarchical linear modeling.

RESULTS: Approximately half (55.3%) of farmworkers utilized US health care in the previous 2 years. Several factors were independently associated with use at the individual level (gender, immigration and migrant status, English proficiency, transportation access, health status, and non-US health care utilization), the environmental level (proximity to US-Mexico border), and the policy level (insurance status and workplace payment structure). County Federally Qualified Health Center resources were not independently associated.

CONCLUSIONS: We identified farmworkers at greatest risk for poor access. We made recommendations for change to farmworker health care access at all 3 levels of influence, emphasizing Federally Qualified Health Center service delivery.}, } @article {pmid21330308, year = {2011}, author = {Orozco, FA and Cole, DC and Ibrahim, S and Wanigaratne, S}, title = {Health promotion outcomes associated with a community-based program to reduce pesticide-related risks among small farm households.}, journal = {Health promotion international}, volume = {26}, number = {4}, pages = {432-446}, doi = {10.1093/heapro/dar006}, pmid = {21330308}, issn = {1460-2245}, mesh = {Adolescent ; Adult ; Aged ; *Agriculture ; *Community Networks ; Ecuador ; Environmental Exposure/*prevention & control ; Female ; Focus Groups ; Health Promotion/*organization & administration ; Humans ; Longitudinal Studies ; Male ; Middle Aged ; *Outcome Assessment, Health Care ; Pesticides/*toxicity ; Rural Population ; Surveys and Questionnaires ; Young Adult ; }, abstract = {A range of determinants at multiple socio-ecological levels operate in small farm households' use and handling of hazardous pesticides, suggesting the need for integrated health and agriculture promotion approaches. The aim is to assess changes in health promotion outcomes relevant to highly hazardous pesticide use associated with a multi-component community program. A longitudinal evaluation design using mixed methods was employed in 18 agricultural communities in Ecuador. Over a 7-month period, health education and agricultural interventions focused upon: health risks associated with hazardous pesticides, more adequate use and handling of pesticides, and better crop management techniques. Data collection included field forms, focus groups, structured observations and repeat surveys. In the qualitative analysis, communities were compared by extent of leadership and involvement with the interventions. For the quantitative analysis, hypothesized paths were constructed including factors relevant to pesticide-related practices and use. Testing involved gender-role stratified (household and crop manager) multivariable regression models. Information on pesticide health impacts and the pesticide use and handling, shared in focus groups, showed substantial improvement, as a result of health promotion activities though people were still observed to engage in risky practices in the field. In path models, community leadership and intervention intensity lead to changes in the household managers' pesticide-related knowledge and practices and to reduction in farm use of hazardous pesticides (both significant, p < 0.05). Integrated, community programs can promote pesticide-related risk reduction among small farm households. Changing practices in the use and management of pesticides among crop managers appears limited by deeper structural and cultural factors.}, } @article {pmid21326234, year = {2011}, author = {Rouxel, T and Grandaubert, J and Hane, JK and Hoede, C and van de Wouw, AP and Couloux, A and Dominguez, V and Anthouard, V and Bally, P and Bourras, S and Cozijnsen, AJ and Ciuffetti, LM and Degrave, A and Dilmaghani, A and Duret, L and Fudal, I and Goodwin, SB and Gout, L and Glaser, N and Linglin, J and Kema, GH and Lapalu, N and Lawrence, CB and May, K and Meyer, M and Ollivier, B and Poulain, J and Schoch, CL and Simon, A and Spatafora, JW and Stachowiak, A and Turgeon, BG and Tyler, BM and Vincent, D and Weissenbach, J and Amselem, J and Quesneville, H and Oliver, RP and Wincker, P and Balesdent, MH and Howlett, BJ}, title = {Effector diversification within compartments of the Leptosphaeria maculans genome affected by Repeat-Induced Point mutations.}, journal = {Nature communications}, volume = {2}, number = {}, pages = {202}, pmid = {21326234}, issn = {2041-1723}, support = {//Intramural NIH HHS/United States ; }, mesh = {Ascomycota/*genetics/*pathogenicity ; Base Composition/genetics ; Base Sequence ; Computational Biology ; DNA Transposable Elements/genetics ; *Genetic Variation ; Genome, Fungal/*genetics ; Molecular Sequence Annotation ; Molecular Sequence Data ; *Phylogeny ; Point Mutation/*genetics ; Sequence Analysis, DNA ; Transcription Factors/*genetics ; }, abstract = {Fungi are of primary ecological, biotechnological and economic importance. Many fundamental biological processes that are shared by animals and fungi are studied in fungi due to their experimental tractability. Many fungi are pathogens or mutualists and are model systems to analyse effector genes and their mechanisms of diversification. In this study, we report the genome sequence of the phytopathogenic ascomycete Leptosphaeria maculans and characterize its repertoire of protein effectors. The L. maculans genome has an unusual bipartite structure with alternating distinct guanine and cytosine-equilibrated and adenine and thymine (AT)-rich blocks of homogenous nucleotide composition. The AT-rich blocks comprise one-third of the genome and contain effector genes and families of transposable elements, both of which are affected by repeat-induced point mutation, a fungal-specific genome defence mechanism. This genomic environment for effectors promotes rapid sequence diversification and underpins the evolutionary potential of the fungus to adapt rapidly to novel host-derived constraints.}, } @article {pmid21326225, year = {2011}, author = {Crisp, MD and Burrows, GE and Cook, LG and Thornhill, AH and Bowman, DM}, title = {Flammable biomes dominated by eucalypts originated at the Cretaceous-Palaeogene boundary.}, journal = {Nature communications}, volume = {2}, number = {}, pages = {193}, pmid = {21326225}, issn = {2041-1723}, mesh = {Base Sequence ; Bayes Theorem ; *Biological Evolution ; Computational Biology ; DNA, Ribosomal Spacer/genetics ; *Ecosystem ; *Fires ; Models, Genetic ; Myrtaceae/anatomy & histology/genetics/*physiology ; Paleontology ; *Phylogeny ; Plant Stems/anatomy & histology/growth & development ; Sequence Alignment ; Sequence Analysis, DNA ; }, abstract = {Fire is a major modifier of communities, but the evolutionary origins of its prevalent role in shaping current biomes are uncertain. Australia is among the most fire-prone continents, with most of the landmass occupied by the fire-dependent sclerophyll and savanna biomes. In contrast to biomes with similar climates in other continents, Australia has a tree flora dominated by a single genus, Eucalyptus, and related Myrtaceae. A unique mechanism in Myrtaceae for enduring and recovering from fire damage likely resulted in this dominance. Here, we find a conserved phylogenetic relationship between post-fire resprouting (epicormic) anatomy and biome evolution, dating from 60 to 62 Ma, in the earliest Palaeogene. Thus, fire-dependent communities likely existed 50 million years earlier than previously thought. We predict that epicormic resprouting could make eucalypt forests and woodlands an excellent long-term carbon bank for reducing atmospheric CO(2) compared with biomes with similar fire regimes in other continents.}, } @article {pmid21320348, year = {2011}, author = {Ruijs, WL and Hautvast, JL and van der Velden, K and de Vos, S and Knippenberg, H and Hulscher, ME}, title = {Religious subgroups influencing vaccination coverage in the Dutch Bible belt: an ecological study.}, journal = {BMC public health}, volume = {11}, number = {}, pages = {102}, pmid = {21320348}, issn = {1471-2458}, mesh = {Databases as Topic ; Humans ; Immunization Programs/*statistics & numerical data ; Netherlands ; Regression Analysis ; *Religion and Medicine ; }, abstract = {BACKGROUND: The Netherlands has experienced epidemics of vaccine preventable diseases largely confined to the Bible belt, an area where -among others- orthodox protestant groups are living. Lacking information on the vaccination coverage in this minority, and its various subgroups, control of vaccine preventable diseases is focused on the geographical area of the Bible belt. However, the adequacy of this strategy is questionable. This study assesses the influence of presence of various orthodox protestant subgroups (orthodox protestant denominations, OPDs) on municipal vaccination coverage in the Bible belt.

METHODS: We performed an ecological study at municipality level. Data on number of inhabitants, urbanization level, socio-economical status, immigration and vaccination coverage were obtained from national databases. As religion is not registered in the Netherlands, membership numbers of the OPDs had to be obtained from church year books and via church offices. For all municipalities in the Netherlands, the effect of presence or absence of OPDs on vaccination coverage was assessed by comparing mean vaccination coverage. For municipalities where OPDs were present, the effect of each of them (measured as membership ratio, the number of members proportional to total number of inhabitants) on vaccination coverage was assessed by bivariate correlation and multiple regression analysis in a model containing the determinants immigration, socio-economical status and urbanization as well.

RESULTS: Mean vaccination coverage (93.5% ± 4.7) in municipalities with OPDs (n = 135) was significantly lower (p < 0.001) than in 297 municipalities without OPDs (96.9% ± 2.1). Multiple regression analyses showed that in municipalities with OPDs 84% of the variance in vaccination coverage was explained by the presence of these OPDs. Immigration had a significant, but small explanatory effect as well. Membership ratios of all OPDs were negatively related to vaccination coverage; this relationship was strongest for two very conservative OPDs.

CONCLUSION: As variance in municipal vaccination coverage in the Bible belt is largely explained by membership ratios of the various OPDs, control of vaccine preventable diseases should be focused on these specific risk groups. In current policy part of the orthodox protestant risk group is missed.}, } @article {pmid21318028, year = {2011}, author = {Zeng, C and Liu, Y and Liu, Y and Hu, J and Bai, X and Yang, X}, title = {An integrated approach for assessing aquatic ecological carrying capacity: a case study of Wujin District in the Tai Lake Basin, China.}, journal = {International journal of environmental research and public health}, volume = {8}, number = {1}, pages = {264-280}, pmid = {21318028}, issn = {1660-4601}, mesh = {Agriculture ; Biodiversity ; Biological Oxygen Demand Analysis ; China ; *Conservation of Natural Resources ; *Ecosystem ; Environmental Monitoring/*methods ; *Fresh Water ; Geographic Information Systems ; Industry ; Nitrogen/analysis ; Phosphorus/analysis ; Population Density ; Satellite Communications ; Water Pollution, Chemical/analysis ; Water Supply ; }, abstract = {Aquatic ecological carrying capacity is an effective method for analyzing sustainable development in regional water management. In this paper, an integrated approach is employed for assessing the aquatic ecological carrying capacity of Wujin District in the Tai Lake Basin, China. An indicator system is established considering social and economic development as well as ecological resilience perspectives. While calculating the ecological index, the normalized difference vegetation index (NDVI) is extracted from Moderate Resolution Imaging Spectroradiometer (MODIS) time-series images, followed by spatial and temporal analysis of vegetation cover. Finally, multi-index assessment of aquatic ecological carrying capacity is carried out for the period 2000 to 2008, including both static and dynamic variables. The results reveal that aquatic ecological carrying capacity presents a slight upward trend in the past decade and the intensity of human activities still exceeded the aquatic ecological carrying capacity in 2008. In terms of human activities, population has decreased, GDP has quadrupled, and fertilizer application and industrial wastewater discharge have declined greatly in the past decade. The indicators representing aquatic ecosystem conditions have the lowest scores, which are primarily attributed to the water eutrophication problem. Yet the terrestrial ecosystem is assessed to be in better condition since topographic backgrounds and landscape diversity are at higher levels. Based on the work carried out, it is suggested that pollutant emission be controlled to improve water quality and agricultural development around Ge Lake (the largest lake in Wujin District) be reduced.}, } @article {pmid21314775, year = {2011}, author = {Sills, MR and Hall, M and Simon, HK and Fieldston, ES and Walter, N and Levin, JE and Brogan, TV and Hain, PD and Goodman, DM and Fritch-Levens, DD and Fagbuyi, DB and Mundorff, MB and Libby, AM and Anderson, HO and Padula, WV and Shah, SS}, title = {Resource burden at children's hospitals experiencing surge volumes during the spring 2009 H1N1 influenza pandemic.}, journal = {Academic emergency medicine : official journal of the Society for Academic Emergency Medicine}, volume = {18}, number = {2}, pages = {158-166}, doi = {10.1111/j.1553-2712.2010.00992.x}, pmid = {21314775}, issn = {1553-2712}, support = {R03 HS016418/HS/AHRQ HHS/United States ; 5R03HS016418/HS/AHRQ HHS/United States ; K01 AI73729/AI/NIAID NIH HHS/United States ; }, mesh = {Adolescent ; Child ; Child, Preschool ; Chronic Disease/epidemiology ; Databases, Factual ; Health Care Rationing ; Hospitalization/*statistics & numerical data ; Hospitals, Pediatric/*statistics & numerical data ; Humans ; Infant ; Infant, Newborn ; Influenza A Virus, H1N1 Subtype ; Influenza, Human/epidemiology/*therapy ; Male ; Pandemics ; Regression Analysis ; Risk Factors ; Severity of Illness Index ; United States/epidemiology ; Young Adult ; }, abstract = {OBJECTIVES: The objective was to describe the emergency department (ED) resource burden of the spring 2009 H1N1 influenza pandemic at U.S. children's hospitals by quantifying observed-to-expected utilization.

METHODS: The authors performed an ecologic analysis for April through July 2009 using data from 23 EDs in the Pediatric Health Information System (PHIS), an administrative database of widely distributed U.S. children's hospitals. All ED visits during the study period were included, and data from the 5 prior years were used for establishing expected values. Primary outcome measures included observed-to-expected ratios for ED visits for all reasons and for influenza-related illness (IRI).

RESULTS: Overall, 390,983 visits, and 88,885 visits for IRI, were included for Calendar Weeks 16 through 29, when 2009 H1N1 influenza was circulating. The subset of 106,330 visits and 31,703 IRI visits made to the 14 hospitals experiencing the authors' definition of ED surge during Weeks 16 to 29 was also studied. During surge weeks, the 14 EDs experienced 29% more total visits and 51% more IRI visits than expected (p < 0.01 for both comparisons). Of ED IRI visits during surge weeks, only 4.8% were admitted to non-intensive care beds (70% of expected, p < 0.01), 0.19% were admitted to intensive care units (44% of expected, p < 0.01), and 0.01% received mechanical ventilation (5.0% of expected, p < 0.01). Factors associated with more-than-expected visits included ages 2-17 years, payer type, and asthma. No factors were associated with more-than-expected hospitalizations from the ED.

CONCLUSIONS: During the spring 2009 H1N1 influenza pandemic, pediatric EDs nationwide experienced a marked increase in visits, with far fewer than expected requiring nonintensive or intensive care hospitalization. The data in this study can be used for future pandemic planning.}, } @article {pmid21311587, year = {2011}, author = {, }, title = {A research agenda for malaria eradication: vector control.}, journal = {PLoS medicine}, volume = {8}, number = {1}, pages = {e1000401}, pmid = {21311587}, issn = {1549-1676}, support = {R01 AI056402/AI/NIAID NIH HHS/United States ; R01 AI056402-07/AI/NIAID NIH HHS/United States ; }, mesh = {Africa South of the Sahara/epidemiology ; Animals ; Anopheles/classification/genetics/growth & development/*parasitology ; Developing Countries ; Endemic Diseases ; Feeding Behavior ; Female ; Global Health ; Humans ; Insect Vectors/*parasitology ; Insecticide Resistance ; Insecticides ; Interdisciplinary Communication ; Knowledge Bases ; Malaria/epidemiology/*prevention & control/transmission ; *Mosquito Control/instrumentation/methods/organization & administration/statistics & numerical data ; Papua New Guinea/epidemiology ; Plasmodium/growth & development/physiology ; *Research ; Species Specificity ; }, abstract = {Different challenges are presented by the variety of malaria transmission environments present in the world today. In each setting, improved control for reduction of morbidity is a necessary first step towards the long-range goal of malaria eradication and a priority for regions where the disease burden is high. For many geographic areas where transmission rates are low to moderate, sustained and well-managed application of currently available tools may be sufficient to achieve local elimination. The research needs for these areas will be to sustain and perhaps improve the effectiveness of currently available tools. For other low-to-moderate transmission regions, notably areas where the vectors exhibit behaviours such as outdoor feeding and resting that are not well targeted by current strategies, new interventions that target predictable features of the biology/ecologies of the local vectors will be required. To achieve elimination in areas where high levels of transmission are sustained by very efficient vector species, radically new interventions that significantly reduce the vectorial capacity of wild populations will be needed. Ideally, such interventions should be implemented with a one-time application with a long-lasting impact, such as genetic modification of the vectorial capacity of the wild vector population.}, } @article {pmid21311007, year = {2011}, author = {Reichman, OJ and Jones, MB and Schildhauer, MP}, title = {Challenges and opportunities of open data in ecology.}, journal = {Science (New York, N.Y.)}, volume = {331}, number = {6018}, pages = {703-705}, doi = {10.1126/science.1197962}, pmid = {21311007}, issn = {1095-9203}, mesh = {*Access to Information ; Data Collection ; *Databases, Factual ; *Ecology ; *Information Dissemination ; Information Management ; *Information Storage and Retrieval ; *Information Systems ; Internet ; }, abstract = {Ecology is a synthetic discipline benefiting from open access to data from the earth, life, and social sciences. Technological challenges exist, however, due to the dispersed and heterogeneous nature of these data. Standardization of methods and development of robust metadata can increase data access but are not sufficient. Reproducibility of analyses is also important, and executable workflows are addressing this issue by capturing data provenance. Sociological challenges, including inadequate rewards for sharing data, must also be resolved. The establishment of well-curated, federated data repositories will provide a means to preserve data while promoting attribution and acknowledgement of its use.}, } @article {pmid21308377, year = {2011}, author = {Turner, DS and Richter, HE}, title = {Wet/dry mapping: using citizen scientists to monitor the extent of perennial surface flow in dryland regions.}, journal = {Environmental management}, volume = {47}, number = {3}, pages = {497-505}, pmid = {21308377}, issn = {1432-1009}, mesh = {Arizona ; Environmental Monitoring/*methods ; Fresh Water/*analysis ; Geographic Information Systems ; Humans ; Volunteers ; Water Movements ; Water Supply/*analysis/statistics & numerical data ; }, abstract = {Wet/dry mapping provides a low-cost, comprehensive snapshot for monitoring flow conditions in rivers with interrupted perennial (spatially intermittent) surface flow. When used in conjunction with more traditional point-specific stream flow or groundwater measurements, it provides a better understanding of hydrologic systems at the broad landscape or watershed scale. Through use of trained volunteers, we mapped reaches with surface water during the driest time of year to track annual variation in length and location of perennial flow. Data from 12 years of wet/dry mapping on the San Pedro River in Arizona, USA, showed 62 reaches with surface flow in every year, totaling 32% of the river length through the San Pedro Riparian National Conservation Area. They also show areas with high year-to-year variation in flow length, which indicate changes in local groundwater conditions and may provide early warning of ecological changes. Data and maps from this project have been useful for a wide variety of conservation, management, and research efforts.}, } @article {pmid21306664, year = {2011}, author = {Saadat, M}, title = {Association between healthy life expectancy at birth and consanguineous marriages in 63 countries.}, journal = {Journal of biosocial science}, volume = {43}, number = {4}, pages = {475-480}, doi = {10.1017/S0021932011000034}, pmid = {21306664}, issn = {1469-7599}, mesh = {*Consanguinity ; Data Interpretation, Statistical ; Female ; Humans ; Income/statistics & numerical data ; *Internationality ; Iran ; *Life Expectancy ; Male ; *Parturition ; Poverty/statistics & numerical data ; Socioeconomic Factors ; Statistics as Topic ; Statistics, Nonparametric ; }, abstract = {In order to investigate the association between mean inbreeding coefficient (α) and healthy life expectancy at birth (HALE; years) the present ecological study on 63 countries was done. Statistical analysis showed that HALE negatively and positively correlated with log(10)α and log(10)GNI per capita, respectively (p<0.001). It should be noted that log(10)α and log(10)GNI per capita were significantly correlated with each other (p<0.001). After controlling for log(10)GNI per capita, significant negative correlations between log(10)α and HALE were observed. The countries were stratified according to their GNI per capita into low- and high-income countries. In countries with high income, after controlling for log(10)GNI per capita, the correlation between HALE at birth and log(10)α was significant (for males r=-0.399, df=32, p=0.001; for females r=-0.683, df=32, p<0.001). In high-income Asian and African countries, where consanguineous marriage is common, after controlling for log(10)GNI per capita, the correlation between HALE at birth and log(10)α was significant (for males r=-0.819, df=8, p=0.004; for females r=-0.936, df=8, p<0.001). It seems that consanguinity influences HALE independent of country income.}, } @article {pmid21304960, year = {2011}, author = {Miloslavich, P and Klein, E and Díaz, JM and Hernández, CE and Bigatti, G and Campos, L and Artigas, F and Castillo, J and Penchaszadeh, PE and Neill, PE and Carranza, A and Retana, MV and Díaz de Astarloa, JM and Lewis, M and Yorio, P and Piriz, ML and Rodríguez, D and Yoneshigue-Valentin, Y and Gamboa, L and Martín, A}, title = {Marine biodiversity in the Atlantic and Pacific coasts of South America: knowledge and gaps.}, journal = {PloS one}, volume = {6}, number = {1}, pages = {e14631}, pmid = {21304960}, issn = {1932-6203}, mesh = {*Aquatic Organisms ; *Biodiversity ; Informatics/*methods ; Marine Biology/*methods ; South America ; }, abstract = {The marine areas of South America (SA) include almost 30,000 km of coastline and encompass three different oceanic domains--the Caribbean, the Pacific, and the Atlantic--ranging in latitude from 12∘N to 55∘S. The 10 countries that border these coasts have different research capabilities and taxonomic traditions that affect taxonomic knowledge. This paper analyzes the status of knowledge of marine biodiversity in five subregions along the Atlantic and Pacific coasts of South America (SA): the Tropical East Pacific, the Humboldt Current,the Patagonian Shelf, the Brazilian Shelves, and the Tropical West Atlantic, and it provides a review of ecosystem threats and regional marine conservation strategies. South American marine biodiversity is least well known in the tropical subregions (with the exception of Costa Rica and Panama). Differences in total biodiversity were observed between the Atlantic and Pacific oceans at the same latitude. In the north of the continent, the Tropical East Pacific is richer in species than the Tropical West Atlantic, however, when standardized by coastal length, there is very little difference among them. In the south, the Humboldt Current system is much richer than the Patagonian Shelf. An analysis of endemism shows that 75% of the species are reported within only one of the SA regions, while about 22% of the species of SA are not reported elsewhere in the world. National and regional initiatives focusing on new exploration, especially to unknown areas and ecosystems, as well as collaboration among countries are fundamental to achieving the goal of completing inventories of species diversity and distribution.These inventories will allow accurate interpretation of the biogeography of its two oceanic coasts and latitudinal trends,and will also provide relevant information for science based policies.}, } @article {pmid21303624, year = {2011}, author = {Weitzman, ER and Kaci, L and Quinn, M and Mandl, KD}, title = {Helping high-risk youth move through high-risk periods: personally controlled health records for improving social and health care transitions.}, journal = {Journal of diabetes science and technology}, volume = {5}, number = {1}, pages = {47-54}, pmid = {21303624}, issn = {1932-2968}, support = {1U54RR025224-01/RR/NCRR NIH HHS/United States ; P01HK000016/HK/PHITPO CDC HHS/United States ; P01HK000088-01/HK/PHITPO CDC HHS/United States ; R21 AA016638-01A1/AA/NIAAA NIH HHS/United States ; }, mesh = {Adolescent ; Adolescent Health Services/*organization & administration ; Adult ; Algorithms ; Chronic Disease ; Continuity of Patient Care/*organization & administration ; Diabetes Mellitus/etiology/*therapy ; *Health Records, Personal ; Humans ; Models, Biological ; Patient Transfer/methods/*organization & administration ; Risk ; *Social Adjustment ; Time Factors ; Young Adult ; }, abstract = {BACKGROUND: New patient-centered information technologies are needed to address risks associated with health care transitions for adolescents and young adults with diabetes, including systems that support individual and structural impediments to self- and clinical-care.

METHODS: We describe the personally controlled health record (PCHR) system platform and its key structural capabilities and assess its alignment with tenets of the chronic care model (CCM) and the social-behavioral and health care ecologies within which adolescents and young adults with diabetes mature.

RESULTS: Configured as Web-based platforms, PCHRs can support a new class of patient-facing applications that serve as monitoring and support systems for adolescents navigating complex social, developmental, and health care transitions. The approach can enable supportive interventions tailored to individual patient needs to boost adherence, self-management, and monitoring.

CONCLUSIONS: The PCHR platform is a paradigm shift for the organization of health information systems and is consistent with the CCM and conceptualizations of patient- and family-centered care for diabetes. Advancing the approach augers well for improvement around health care transitions for youth and also requires that we address (i) structural barriers impacting diabetes care for maturing youth; (ii) challenges around health and technology literacy; (iii) privacy and confidentiality issues, including sharing of health information within family and institutional systems; and (iv) needs for evaluation around uptake, impacts, and outcomes.}, } @article {pmid21298266, year = {2011}, author = {Arianoutsou, M and Koukoulas, S and Kazanis, D}, title = {Evaluating post-fire forest resilience using GIS and multi-criteria analysis: an example from Cape Sounion National Park, Greece.}, journal = {Environmental management}, volume = {47}, number = {3}, pages = {384-397}, pmid = {21298266}, issn = {1432-1009}, mesh = {Ecosystem ; Fires/*statistics & numerical data ; Forestry/*methods ; *Geographic Information Systems ; Greece ; Multivariate Analysis ; *Trees ; }, abstract = {Forest fires are one of the major causes of ecological disturbance in the mediterranean climate ecosystems of the world. Despite the fact that a lot of resources have been invested in fire prevention and suppression, the number of fires occurring in the Mediterranean Basin in the recent decades has continued to markedly increase. The understanding of the relationship between landscape and fire lies, among others, in the identification of the system's post-fire resilience. In our study, ecological and landscape data are integrated with decision-support techniques in a Geographic Information Systems (GIS) framework to evaluate the risk of losing post-fire resilience in Pinus halepensis forests, using Cape Sounion National Park, Central Greece, as a pilot case. The multi-criteria decision support approach has been used to synthesize both bio-indicators (woody cover, pine density, legume cover and relative species richness and annual colonizers) and geo-indicators (fire history, parent material, and slope inclination) in order to rank the landscape components. Judgments related to the significance of each factor were incorporated within the weights coefficients and then integrated into the multicriteria rule to map the risk index. Sensitivity analysis was very critical for assessing the contribution of each factor and the sensitivity to subjective weight judgments to the final output. The results of this study include a final ranking map of the risk of losing resilience, which is very useful in identifying the "risk hotspots", where post-fire management measures should be applied in priority.}, } @article {pmid21296383, year = {2011}, author = {Neal, C and Rowland, P and Scholefield, P and Vincent, C and Woods, C and Sleep, D}, title = {The Ribble/Wyre observatory: major, minor and trace elements in rivers draining from rural headwaters to the heartlands of the NW England historic industrial base.}, journal = {The Science of the total environment}, volume = {409}, number = {8}, pages = {1516-1529}, doi = {10.1016/j.scitotenv.2011.01.018}, pmid = {21296383}, issn = {1879-1026}, mesh = {Agriculture ; England ; Environmental Monitoring ; Geographic Information Systems ; Industry ; Rivers/*chemistry ; Trace Elements/*analysis ; Water Movements ; Water Pollutants, Chemical/*analysis ; Water Pollution, Chemical/statistics & numerical data ; Water Supply/analysis ; }, abstract = {Information on a new observatory study of the water quality of two major river basins in northwestern England (the Ribble and Wyre) is presented. It covers upland, intermediate and lowland environments of contrasting pollution history with sufficient detail to examine transitional gradients. The upland rivers drain acidic soils subjected to long-term acidic deposition. Nonetheless, the acidic runoff from the soils is largely neutralised by high alkalinity groundwaters, although the rivers retain, perhaps as colloids, elements such as Al and Fe that are mobilised under acid conditions. The lowland rivers are contaminated and have variable water quality due to variable urban/industrial point and diffuse inputs reflecting local and regional differences in historic and contemporary sources. For most determinands, pollutant concentrations are not a major cause for concern although phosphate levels remain high. Set against earlier studies for other regions, there may be a general decline in pollutant levels and this is most clearly observed for boron where effluent inputs have declined significantly due to reductions in household products that are flushed down the drain. High concentrations of sodium and chloride occurred briefly after a severe cold spell due to flushing of road salts. A major inventory for water quality within rural, urban, industrial and agricultural typologies is provided within data summary attachments for over 50 water quality determinands. Within the next year, the full dataset will be made available from the CEH website. This, with ongoing monitoring, represents a platform for water quality studies across a wide range of catchment typologies pertinent to environmental management of clean and impacted systems within the UK. The study provides a base of research "from source to sea" including extensions to the estuary and open sea for a semi-confined basin, the Irish Sea, where there are many issues of pollution inputs and contamination.}, } @article {pmid21292404, year = {2011}, author = {Rinaldi, L and Genchi, C and Musella, V and Genchi, M and Cringoli, G}, title = {Geographical information systems as a tool in the control of heartworm infections in dogs and cats.}, journal = {Veterinary parasitology}, volume = {176}, number = {4}, pages = {286-290}, doi = {10.1016/j.vetpar.2011.01.010}, pmid = {21292404}, issn = {1873-2550}, mesh = {Animals ; Cat Diseases/epidemiology/parasitology/*prevention & control ; Cats ; Data Collection ; Dirofilaria immitis/pathogenicity ; Dirofilaria repens/pathogenicity ; Dirofilariasis/epidemiology/parasitology/*prevention & control ; Dog Diseases/epidemiology/parasitology/*prevention & control ; Dogs ; Ecosystem ; Europe/epidemiology ; Forecasting ; Geographic Information Systems/*standards ; Population Surveillance ; Risk Assessment ; }, abstract = {Geospatial tools (e.g., geographical information systems, remote sensing, global positioning systems, and virtual globes) are very useful for the simultaneous visualization of health data with environmental data, which holds promise to understand environmental-health linkages and to generate new hypotheses to be tested in future research. Current epidemiological studies clearly show that the distribution patterns of vector-borne infections are changing; for example, in Europe, heartworm infection and subcutaneous dirofilariosis are spreading throughout areas that previously had little to no incidence of heartworm. In view of the changes of the distribution patterns of Dirofilaria immitis and Dirofilaria repens, geospatial tools are now more useful for mapping (including territorial sampling), monitoring, ecological analysis, risk assessment, forecasting (including the choose of the timing of treatment), early warning, and surveillance of both heartworm and subcutaneous dirofilariosis. All these issues have control of these infections as the ultimate goal.}, } @article {pmid21285367, year = {2011}, author = {Wang, L and Chen, S and Vergin, KL and Giovannoni, SJ and Chan, SW and DeMott, MS and Taghizadeh, K and Cordero, OX and Cutler, M and Timberlake, S and Alm, EJ and Polz, MF and Pinhassi, J and Deng, Z and Dedon, PC}, title = {DNA phosphorothioation is widespread and quantized in bacterial genomes.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {108}, number = {7}, pages = {2963-2968}, pmid = {21285367}, issn = {1091-6490}, support = {P30 ES002109/ES/NIEHS NIH HHS/United States ; }, mesh = {Base Sequence ; Chromatography, Liquid ; Cloning, Molecular ; Cluster Analysis ; Computational Biology ; DNA Primers/genetics ; DNA, Bacterial/*metabolism ; Gene Transfer, Horizontal/*genetics ; Genes, Bacterial/*genetics ; Genome, Bacterial/*genetics ; Genomics ; Molecular Sequence Data ; Phosphorothioate Oligonucleotides/*metabolism ; *Phylogeny ; Reverse Transcriptase Polymerase Chain Reaction ; Sequence Analysis, DNA ; Sulfur/metabolism ; Tandem Mass Spectrometry ; Vibrionaceae/*genetics ; }, abstract = {Phosphorothioate (PT) modification of DNA, with sulfur replacing a nonbridging phosphate oxygen, was recently discovered as a product of the dnd genes found in bacteria and archaea. Given our limited understanding of the biological function of PT modifications, including sequence context, genomic frequencies, and relationships to the diversity of dnd gene clusters, we undertook a quantitative study of PT modifications in prokaryotic genomes using a liquid chromatography-coupled tandem quadrupole mass spectrometry approach. The results revealed a diversity of unique PT sequence contexts and three discrete genomic frequencies in a wide range of bacteria. Metagenomic analyses of PT modifications revealed unique ecological distributions, and a phylogenetic comparison of dnd genes and PT sequence contexts strongly supports the horizontal transfer of dnd genes. These results are consistent with the involvement of PT modifications in a type of restriction-modification system with wide distribution in prokaryotes.}, } @article {pmid21283605, year = {2011}, author = {, }, title = {A research agenda for malaria eradication: modeling.}, journal = {PLoS medicine}, volume = {8}, number = {1}, pages = {e1000403}, pmid = {21283605}, issn = {1549-1676}, support = {/WT_/Wellcome Trust/United Kingdom ; 079091/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Animals ; Anopheles/genetics/parasitology ; Carrier State/parasitology ; Databases, Factual/standards ; Drug Resistance ; Feasibility Studies ; Global Health ; Health Policy ; Humans ; Insect Vectors/genetics/parasitology ; Insecticide Resistance ; Internet ; Malaria/economics/epidemiology/*prevention & control/transmission ; *Models, Theoretical ; Mosquito Control/economics/methods/organization & administration ; Planning Techniques ; Plasmodium/drug effects/growth & development/physiology ; *Research ; Resource Allocation ; Socioeconomic Factors ; User-Computer Interface ; }, abstract = {Malaria modeling can inform policy and guide research for malaria elimination and eradication from local implementation to global policy. A research and development agenda for malaria modeling is proposed, to support operations and to enhance the broader eradication research agenda. Models are envisioned as an integral part of research, planning, and evaluation, and modelers should ideally be integrated into multidisciplinary teams to update the models iteratively, communicate their appropriate use, and serve the needs of other research scientists, public health specialists, and government officials. A competitive and collaborative framework will result in policy recommendations from multiple, independently derived models and model systems that share harmonized databases. As planned, modeling results will be produced in five priority areas: (1) strategic planning to determine where and when resources should be optimally allocated to achieve eradication; (2) management plans to minimize the evolution of drug and pesticide resistance; (3) impact assessments of new and needed tools to interrupt transmission; (4) technical feasibility assessments to determine appropriate combinations of tools, an associated set of target intervention coverage levels, and the expected timelines for achieving a set of goals in different socio-ecological settings and different health systems; and (5) operational feasibility assessments to weigh the economic costs, capital investments, and human resource capacities required.}, } @article {pmid21282665, year = {2011}, author = {Wurm, Y and Wang, J and Riba-Grognuz, O and Corona, M and Nygaard, S and Hunt, BG and Ingram, KK and Falquet, L and Nipitwattanaphon, M and Gotzek, D and Dijkstra, MB and Oettler, J and Comtesse, F and Shih, CJ and Wu, WJ and Yang, CC and Thomas, J and Beaudoing, E and Pradervand, S and Flegel, V and Cook, ED and Fabbretti, R and Stockinger, H and Long, L and Farmerie, WG and Oakey, J and Boomsma, JJ and Pamilo, P and Yi, SV and Heinze, J and Goodisman, MA and Farinelli, L and Harshman, K and Hulo, N and Cerutti, L and Xenarios, I and Shoemaker, D and Keller, L}, title = {The genome of the fire ant Solenopsis invicta.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {108}, number = {14}, pages = {5679-5684}, pmid = {21282665}, issn = {1091-6490}, mesh = {Animals ; Ants/*genetics ; Base Sequence ; Computational Biology ; DNA Methylation ; *Evolution, Molecular ; Expressed Sequence Tags ; Genome, Insect/*genetics ; Genomics/*methods ; Hierarchy, Social ; Male ; Molecular Sequence Data ; *Phylogeny ; Receptors, Odorant/genetics ; Sequence Analysis, DNA ; Vitellogenins/genetics ; }, abstract = {Ants have evolved very complex societies and are key ecosystem members. Some ants, such as the fire ant Solenopsis invicta, are also major pests. Here, we present a draft genome of S. invicta, assembled from Roche 454 and Illumina sequencing reads obtained from a focal haploid male and his brothers. We used comparative genomic methods to obtain insight into the unique features of the S. invicta genome. For example, we found that this genome harbors four adjacent copies of vitellogenin. A phylogenetic analysis revealed that an ancestral vitellogenin gene first underwent a duplication that was followed by possibly independent duplications of each of the daughter vitellogenins. The vitellogenin genes have undergone subfunctionalization with queen- and worker-specific expression, possibly reflecting differential selection acting on the queen and worker castes. Additionally, we identified more than 400 putative olfactory receptors of which at least 297 are intact. This represents the largest repertoire reported so far in insects. S. invicta also harbors an expansion of a specific family of lipid-processing genes, two putative orthologs to the transformer/feminizer sex differentiation gene, a functional DNA methylation system, and a single putative telomerase ortholog. EST data indicate that this S. invicta telomerase ortholog has at least four spliceforms that differ in their use of two sets of mutually exclusive exons. Some of these and other unique aspects of the fire ant genome are likely linked to the complex social behavior of this species.}, } @article {pmid21272107, year = {2011}, author = {Grueber, CE and Nakagawa, S and Laws, RJ and Jamieson, IG}, title = {Multimodel inference in ecology and evolution: challenges and solutions.}, journal = {Journal of evolutionary biology}, volume = {24}, number = {4}, pages = {699-711}, doi = {10.1111/j.1420-9101.2010.02210.x}, pmid = {21272107}, issn = {1420-9101}, mesh = {*Biological Evolution ; Data Interpretation, Statistical ; Ecology/*methods ; Models, Biological ; }, abstract = {Information theoretic approaches and model averaging are increasing in popularity, but this approach can be difficult to apply to the realistic, complex models that typify many ecological and evolutionary analyses. This is especially true for those researchers without a formal background in information theory. Here, we highlight a number of practical obstacles to model averaging complex models. Although not meant to be an exhaustive review, we identify several important issues with tentative solutions where they exist (e.g. dealing with collinearity amongst predictors; how to compute model-averaged parameters) and highlight areas for future research where solutions are not clear (e.g. when to use random intercepts or slopes; which information criteria to use when random factors are involved). We also provide a worked example of a mixed model analysis of inbreeding depression in a wild population. By providing an overview of these issues, we hope that this approach will become more accessible to those investigating any process where multiple variables impact an evolutionary or ecological response.}, } @article {pmid21267469, year = {2011}, author = {Jeffers, ES and Bonsall, MB and Willis, KJ}, title = {Stability in ecosystem functioning across a climatic threshold and contrasting forest regimes.}, journal = {PloS one}, volume = {6}, number = {1}, pages = {e16134}, pmid = {21267469}, issn = {1932-6203}, mesh = {Climate ; *Climate Change ; Computational Biology ; Data Interpretation, Statistical ; *Ecosystem ; Forecasting ; Nitrogen/metabolism ; Nitrogen Cycle ; *Trees ; }, abstract = {Classical ecological theory predicts that changes in the availability of essential resources such as nitrogen should lead to changes in plant community composition due to differences in species-specific nutrient requirements. What remains unknown, however, is the extent to which climate change will alter the relationship between plant communities and the nitrogen cycle. During intervals of climate change, do changes in nitrogen cycling lead to vegetation change or do changes in community composition alter the nitrogen dynamics? We used long-term ecological data to determine the role of nitrogen availability in changes of forest species composition under a rapidly changing climate during the early Holocene (16k to 8k cal. yrs. BP). A statistical computational analysis of ecological data spanning 8,000 years showed that secondary succession from a coniferous to deciduous forest occurred independently of changes in the nitrogen cycle. As oak replaced pine under a warming climate, nitrogen cycling rates increased. Interestingly, the mechanism by which the species interacted with nitrogen remained stable across this threshold change in climate and in the dominant tree species. This suggests that changes in tree population density over successional time scales are not driven by nitrogen availability. Thus, current models of forest succession that incorporate the effects of available nitrogen may be over-estimating tree population responses to changes in this resource, which may result in biased predictions of future forest dynamics under climate warming.}, } @article {pmid21255926, year = {2011}, author = {He, G and Zhang, L and Lu, Y and Mol, AP}, title = {Managing major chemical accidents in China: towards effective risk information.}, journal = {Journal of hazardous materials}, volume = {187}, number = {1-3}, pages = {171-181}, doi = {10.1016/j.jhazmat.2011.01.017}, pmid = {21255926}, issn = {1873-3336}, mesh = {*Accidents ; *Chemical Industry ; China ; Risk Assessment ; }, abstract = {Chemical industries, from their very inception, have been controversial due to the high risks they impose on safety of human beings and the environment. Recent decades have witnessed increasing impacts of the accelerating expansion of chemical industries and chemical accidents have become a major contributor to environmental and health risks in China. This calls for the establishment of an effective chemical risk management system, which requires reliable, accurate and comprehensive data in the first place. However, the current chemical accident-related data system is highly fragmented and incomplete, as different responsible authorities adopt different data collection standards and procedures for different purposes. In building a more comprehensive, integrated and effective information system, this article: (i) reviews and assesses the existing data sources and data management, (ii) analyzes data on 976 recorded major hazardous chemical accidents in China over the last 40 years, and (iii) identifies the improvements required for developing integrated risk management in China.}, } @article {pmid21254845, year = {2011}, author = {Newman, CM and Cerutti, F and Anderson, TK and Hamer, GL and Walker, ED and Kitron, UD and Ruiz, MO and Brawn, JD and Goldberg, TL}, title = {Culex flavivirus and West Nile virus mosquito coinfection and positive ecological association in Chicago, United States.}, journal = {Vector borne and zoonotic diseases (Larchmont, N.Y.)}, volume = {11}, number = {8}, pages = {1099-1105}, pmid = {21254845}, issn = {1557-7759}, support = {T32 AI007414/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Case-Control Studies ; Chicago/epidemiology ; Culex/*virology ; Databases, Nucleic Acid ; Ecology ; Flavivirus/genetics/*isolation & purification ; Likelihood Functions ; Polymerase Chain Reaction ; RNA ; Reverse Transcriptase Polymerase Chain Reaction ; United States/epidemiology ; West Nile Fever/*epidemiology/transmission/*virology ; West Nile virus/genetics/isolation & purification ; }, abstract = {Culex flavivirus (CxFV) is an insect-specific flavivirus globally distributed in mosquitoes of the genus Culex. CxFV was positively associated with West Nile virus (WNV) infection in a case-control study of 268 mosquito pools from an endemic focus of WNV transmission in Chicago, United States. Specifically, WNV-positive Culex mosquito pools were four times more likely also to be infected with CxFV than were spatiotemporally matched WNV-negative pools. In addition, mosquito pools from residential sites characterized by dense housing and impermeable surfaces were more likely to be infected with CxFV than were pools from nearby urban green spaces. Further, 6/15 (40%) WNV-positive individual mosquitoes were also CxFV positive, demonstrating that both viruses can coinfect mosquitoes in nature. Phylogenetic analysis of CxFV from Chicago demonstrated a pattern similar to WNV, consisting of low global viral diversity and lack of geographic clustering. These results illustrate a positive ecological association between CxFV and WNV, and that coinfection of individual mosquitoes can occur naturally in areas of high flaviviral transmission. These conclusions represent a challenge to the hypothesis of super-infection exclusion in the CxFV/WNV system, whereby an established infection with one virus may interfere with secondary viral infection with a similar virus. This study suggests that infection with insect-specific flaviviruses such as CxFV may not exclude secondary infection with genetically distinct flaviviruses such as WNV, and that both viruses can naturally coinfect mosquitoes that are epidemic bridge vectors of WNV to humans.}, } @article {pmid21253602, year = {2011}, author = {Orozovic, G and Orozovic, K and Lennerstrand, J and Olsen, B}, title = {Detection of resistance mutations to antivirals oseltamivir and zanamivir in avian influenza A viruses isolated from wild birds.}, journal = {PloS one}, volume = {6}, number = {1}, pages = {e16028}, pmid = {21253602}, issn = {1932-6203}, mesh = {Animals ; Antiviral Agents/*pharmacology ; Computational Biology/methods ; Databases, Nucleic Acid ; Drug Resistance, Viral/*genetics ; Ducks ; Influenza A virus/drug effects/*genetics/isolation & purification ; Influenza in Birds/drug therapy/*virology ; *Mutation, Missense ; Oseltamivir/*pharmacology ; RNA, Viral/isolation & purification ; Sequence Analysis, DNA ; Swine ; Zanamivir/*pharmacology ; }, abstract = {The neuraminidase (NA) inhibitors oseltamivir and zanamivir are the first-line of defense against potentially fatal variants of influenza A pandemic strains. However, if resistant virus strains start to arise easily or at a high frequency, a new anti-influenza strategy will be necessary. This study aimed to investigate if and to what extent NA inhibitor-resistant mutants exist in the wild population of influenza A viruses that inhabit wild birds. NA sequences of all NA subtypes available from 5490 avian, 379 swine and 122 environmental isolates were extracted from NCBI databases. In addition, a dataset containing 230 virus isolates from mallard collected at Ottenby Bird Observatory (Öland, Sweden) was analyzed. Isolated NA RNA fragments from Ottenby were transformed to cDNA by RT-PCR, which was followed by sequencing. The analysis of genotypic profiles for NAs from both data sets in regard to antiviral resistance mutations was performed using bioinformatics tools. All 6221 sequences were scanned for oseltamivir- (I117V, E119V, D198N, I222V, H274Y, R292K, N294S and I314V) and zanamivir-related mutations (V116A, R118K, E119G/A/D, Q136K, D151E, R152K, R224K, E276D, R292K and R371K). Of the sequences from the avian NCBI dataset, 132 (2.4%) carried at least one, or in two cases even two and three, NA inhibitor resistance mutations. Swine and environmental isolates from the same data set had 18 (4.75%) and one (0.82%) mutant, respectively, with at least one mutation. The Ottenby sequences carried at least one mutation in 15 cases (6.52%). Therefore, resistant strains were more frequently found in Ottenby samples than in NCBI data sets. However, it is still uncertain if these mutations are the result of natural variations in the viruses or if they are induced by the selective pressure of xenobiotics (e.g., oseltamivir, zanamivir).}, } @article {pmid21250443, year = {2010}, author = {Li, WM and Li, XH and Cai, XY and Chen, JW and Qiao, XL and Kiwao, K and Daisuke, J and Toyomi, I}, title = {[Application of automated identification and quantification system with a database (AIQS-DB) to screen organic pollutants in surface waters from Yellow River and Yangtze River].}, journal = {Huan jing ke xue= Huanjing kexue}, volume = {31}, number = {11}, pages = {2627-2632}, pmid = {21250443}, issn = {0250-3301}, mesh = {China ; Databases, Factual ; Environmental Monitoring/*methods ; Fresh Water/analysis ; Gas Chromatography-Mass Spectrometry ; Organic Chemicals/*analysis ; Rivers/*chemistry ; Water Pollutants, Chemical/*analysis ; }, abstract = {Approximately 1 000 chemicals were screened in surface waters from downstreams of Yellow River and Yangtze River using GC-MS coupled with Automated Identification and Quantification System with a Database (AIQS-DB). 95 pollutants were detected in water samples from Yellow River in Shandong Province and 121 in those from Yangtze River in Jiangsu Province. The pollutants involved n-alkanes, PAHs, phenols, nitro compounds, phthalates esters (PAEs), pesticides and pharmaceuticals, etc. The average concentrations of n-alkanes, 16 priority PAHs and 6 priority PAEs were 1 806 ng/L, 27 ng/L, 77 ng/L in water samples from Yellow River and 720 ng/L, 30 ng/L, 2 166 ng/L in water samples from Yangtze River respectively. Besides, 9 and 11 pesticides were detected in water samples from Yellow River and Yangtze River respectively. The levels of pollutants showed stronger site dependence in samples from Yellow River than those from Yangtze River. Combination of GC-MS and AIQS-DB shows high efficiency in regional pollutants survey.}, } @article {pmid21245031, year = {2011}, author = {Fu, CH and Chen, YW and Hsiao, YY and Pan, ZJ and Liu, ZJ and Huang, YM and Tsai, WC and Chen, HH}, title = {OrchidBase: a collection of sequences of the transcriptome derived from orchids.}, journal = {Plant & cell physiology}, volume = {52}, number = {2}, pages = {238-243}, doi = {10.1093/pcp/pcq201}, pmid = {21245031}, issn = {1471-9053}, mesh = {Data Mining ; *Databases, Genetic ; Expressed Sequence Tags ; *Gene Expression Profiling ; Gene Library ; Internet ; Molecular Sequence Annotation ; Orchidaceae/*genetics ; Sequence Analysis, DNA ; User-Computer Interface ; }, abstract = {Orchids are one of the most ecological and evolutionarily significant plants, and the Orchidaceae is one of the most abundant families of the angiosperms. Genetic databases will be useful not only for gene discovery but also for future genomic annotation. For this purpose, OrchidBase was established from 37,979,342 sequence reads collected from 11 in-house Phalaenopsis orchid cDNA libraries. Among them, 41,310 expressed sequence tags (ESTs) were obtained by using Sanger sequencing, whereas 37,908,032 reads were obtained by using next-generation sequencing (NGS) including both Roche 454 and Solexa Illumina sequencers. These reads were assembled into 8,501 contigs and 76,116 singletons, resulting in 84,617 non-redundant transcribed sequences with an average length of 459 bp. The analysis pipeline of the database is an automated system written in Perl and C#, and consists of the following components: automatic pre-processing of EST reads, assembly of raw sequences, annotation of the assembled sequences and storage of the analyzed information in SQL databases. A web application was implemented with HTML and a Microsoft .NET Framework C# program for browsing and querying the database, creating dynamic web pages on the client side, analyzing gene ontology (GO) and mapping annotated enzymes to KEGG pathways. The online resources for putative annotation can be searched either by text or by using BLAST, and the results can be explored on the website and downloaded. Consequently, the establishment of OrchidBase will provide researchers with a high-quality genetic resource for data mining and facilitate efficient experimental studies on orchid biology and biotechnology. The OrchidBase database is freely available at http://lab.fhes.tn.edu.tw/est.}, } @article {pmid21210977, year = {2010}, author = {Antao, T}, title = {interPopula: a Python API to access the HapMap Project dataset.}, journal = {BMC bioinformatics}, volume = {11 Suppl 12}, number = {Suppl 12}, pages = {S10}, pmid = {21210977}, issn = {1471-2105}, mesh = {*Databases, Nucleic Acid ; Humans ; Molecular Sequence Annotation ; *Polymorphism, Single Nucleotide ; Population Groups/genetics ; *Software ; Systems Integration ; }, abstract = {BACKGROUND: The HapMap project is a publicly available catalogue of common genetic variants that occur in humans, currently including several million SNPs across 1115 individuals spanning 11 different populations. This important database does not provide any programmatic access to the dataset, furthermore no standard relational database interface is provided.

RESULTS: interPopula is a Python API to access the HapMap dataset. interPopula provides integration facilities with both the Python ecology of software (e.g. Biopython and matplotlib) and other relevant human population datasets (e.g. Ensembl gene annotation and UCSC Known Genes). A set of guidelines and code examples to address possible inconsistencies across heterogeneous data sources is also provided.

CONCLUSIONS: interPopula is a straightforward and flexible Python API that facilitates the construction of scripts and applications that require access to the HapMap dataset.}, } @article {pmid21233398, year = {2011}, author = {Andolfatto, P and Davison, D and Erezyilmaz, D and Hu, TT and Mast, J and Sunayama-Morita, T and Stern, DL}, title = {Multiplexed shotgun genotyping for rapid and efficient genetic mapping.}, journal = {Genome research}, volume = {21}, number = {4}, pages = {610-617}, pmid = {21233398}, issn = {1549-5469}, support = {P50 GM071508/GM/NIGMS NIH HHS/United States ; R01 GM063622/GM/NIGMS NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; GM063622-06A1/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Chromosome Breakpoints ; Chromosome Mapping/*methods ; Computational Biology ; Drosophila/genetics ; Female ; Genes, Dominant/genetics ; Genetic Markers ; Genotype ; Male ; Molecular Typing/*methods ; Phenotype ; Quantitative Trait Loci/genetics ; Recombination, Genetic/genetics ; Research Design ; Sequence Analysis, DNA/*methods ; }, abstract = {We present a new approach to genotyping based on multiplexed shotgun sequencing that can identify recombination breakpoints in a large number of individuals simultaneously at a resolution sufficient for most mapping purposes, such as quantitative trait locus (QTL) mapping and mapping of induced mutations. We first describe a simple library construction protocol that uses just 10 ng of genomic DNA per individual and makes the approach accessible to any laboratory with standard molecular biology equipment. Sequencing this library results in a large number of sequence reads widely distributed across the genomes of multiplexed bar-coded individuals. We develop a Hidden Markov Model to estimate ancestry at all genomic locations in all individuals using these data. We demonstrate the utility of the approach by mapping a dominant marker allele in D. simulans to within 105 kb of its true position using 96 F1-backcross individuals genotyped in a single lane on an Illumina Genome Analyzer. We further demonstrate the utility of our method by genetically mapping more than 400 previously unassembled D. simulans contigs to linkage groups and by evaluating the quality of targeted introgression lines. At this level of multiplexing and divergence between strains, our method allows estimation of recombination breakpoints to a median of 38-kb intervals. Our analysis suggests that higher levels of multiplexing and/or use of strains with lower levels of divergence are practicable.}, } @article {pmid21229596, year = {2011}, author = {Martyniuk, CJ and Griffitt, RJ and Denslow, ND}, title = {Omics in aquatic toxicology: not just another microarray.}, journal = {Environmental toxicology and chemistry}, volume = {30}, number = {2}, pages = {263-264}, doi = {10.1002/etc.428}, pmid = {21229596}, issn = {1552-8618}, mesh = {Animals ; Computational Biology/*methods ; Ecotoxicology/methods ; Hydrobiology/*methods ; *Microarray Analysis/methods ; Toxicogenetics/*methods ; }, } @article {pmid21228203, year = {2011}, author = {Philippides, A and Baddeley, B and Cheng, K and Graham, P}, title = {How might ants use panoramic views for route navigation?.}, journal = {The Journal of experimental biology}, volume = {214}, number = {Pt 3}, pages = {445-451}, doi = {10.1242/jeb.046755}, pmid = {21228203}, issn = {1477-9145}, support = {BB/F010052/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/H013644/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; Ants/*physiology ; Cues ; Desert Climate ; *Homing Behavior ; Locomotion ; Photography ; Space Perception ; Spatial Behavior ; Travel ; Vision, Ocular ; }, abstract = {Studies of insect navigation have demonstrated that insects possess an interesting and sophisticated repertoire of visual navigation behaviours. Ongoing research seeks to help us understand how these behaviours are controlled in natural complex environments. A necessary complement to behavioural studies is an understanding of the sensory ecology within which an animal behaves. To this end we have analysed ants'-perspective views of a habitat within which desert ant navigation is well studied. Results from our analysis suggest that: parsimonious visual strategies for homing and route guidance are effective over behaviourally useful distances even in cluttered environments; that these strategies can function effectively using only the skyline heights as input; and that the simplicity and efficacy of using stored views as a visual compass makes it a viable and robust mechanism for route guidance.}, } @article {pmid21222153, year = {2011}, author = {Okvat, HA and Zautra, AJ}, title = {Community gardening: a parsimonious path to individual, community, and environmental resilience.}, journal = {American journal of community psychology}, volume = {47}, number = {3-4}, pages = {374-387}, doi = {10.1007/s10464-010-9404-z}, pmid = {21222153}, issn = {1573-2770}, mesh = {Climate Change ; Community Networks/organization & administration ; Ecosystem ; Female ; *Gardening ; Humans ; Male ; *Personal Satisfaction ; Psychology, Social ; Public Health ; *Residence Characteristics ; *Resilience, Psychological ; Retrospective Studies ; Urban Population ; }, abstract = {The goal of this paper is to introduce community gardening as a promising method of furthering well-being and resilience on multiple levels: individual, social group, and natural environment. We examine empirical evidence for the benefits of gardening, and we advocate the development and testing of social ecological models of community resilience through examination of the impact of community gardens, especially in urban areas. The definition of community is extended beyond human social ties to include connections with other species and the earth itself, what Berry (1988) has called an Earth community. We discuss the potential contribution of an extensive network of community gardens to easing the global climate change crisis and address the role of community psychologists in community gardening research and policy-oriented action.}, } @article {pmid21220184, year = {2011}, author = {Du, Y and Xue, HP and Wu, SJ and Ling, F and Xiao, F and Wei, XH}, title = {Lake area changes in the middle Yangtze region of China over the 20th century.}, journal = {Journal of environmental management}, volume = {92}, number = {4}, pages = {1248-1255}, doi = {10.1016/j.jenvman.2010.12.007}, pmid = {21220184}, issn = {1095-8630}, mesh = {China ; Conservation of Natural Resources ; Ecology ; *Fresh Water ; Geographic Information Systems ; Geologic Sediments ; *Geological Phenomena ; Maps as Topic ; }, abstract = {The Jianghan Plain and the Dongting lake area, located in the middle reaches of the Yangtze River are famous for their abundant freshwater lakes. The lakes have undergone changes in size and number over thousands of years due to natural causes and human activities. The 20th century particularly, witnessed dramatic changes in the freshwater resources of this region. This paper traces and analyzes lake evolution in the middle reaches of the Yangtze River over the past century. Lakes greater than 0.1 km(2) in size are mapped using Geographic Information System. Data is acquired and integrated from drainage network maps, relief maps, historical maps and remotely sensed images for different time periods. The results indicate that while there has been little change in the number of lakes over the past century, the lake area has experienced a dramatic decrease of 58.06%. The paper also examines the natural processes and human activities that may have contributed to the decrease in lake area. The results show that the decrease in total lake area appears to coincide with periods of rapid land reclamation in the middle reaches of the Yangtze River. Moreover, uncontrolled land reclamation activities can create an increase in sediment deposition in lakes thereby further reducing the lake size. Reduction of the lake area directly affects flood-control and has a negative ecological impact on the environment and on human life and property.}, } @article {pmid21184865, year = {2010}, author = {D'Avolio, LW and Farwell, WR and Fiore, LD}, title = {Comparative effectiveness research and medical informatics.}, journal = {The American journal of medicine}, volume = {123}, number = {12 Suppl 1}, pages = {e32-7}, doi = {10.1016/j.amjmed.2010.10.006}, pmid = {21184865}, issn = {1555-7162}, mesh = {*Comparative Effectiveness Research/methods/organization & administration/standards/trends ; Humans ; *Medical Informatics ; Research Design ; United States ; *United States Department of Veterans Affairs ; }, abstract = {As is the case for environmental, ecological, astronomical, and other sciences, medical practice and research finds itself in a tsunami of data. This data deluge, due primarily to the introduction of digitalization in routine medical care and medical research, affords the opportunity for improved patient care and scientific discovery. Medical informatics is the subdiscipline of medicine created to make greater use of information in order to improve healthcare. The 4 areas of medical informatics research (information access, structure, analysis, and interaction) are used as a framework to discuss the overlap in information needs of comparative effectiveness research and potential contributions of medical informatics. Examples of progress from the medical informatics literature and the Veterans Affairs Healthcare System are provided.}, } @article {pmid21215865, year = {2011}, author = {Gröger, T and Zimmermann, R}, title = {Application of parallel computing to speed up chemometrics for GC×GC-TOFMS based metabolic fingerprinting.}, journal = {Talanta}, volume = {83}, number = {4}, pages = {1289-1294}, doi = {10.1016/j.talanta.2010.09.015}, pmid = {21215865}, issn = {1873-3573}, support = {5R01 ES013932/ES/NIEHS NIH HHS/United States ; }, mesh = {*Computers ; Gas Chromatography-Mass Spectrometry/*methods ; Informatics/*methods ; *Metabolome ; Metabolomics/*methods ; Software ; Time Factors ; }, abstract = {Parallel computing was tested regarding its ability to speed up chemometric operations for data analysis. A set of metabolic samples from a second hand smoke (SHS) experiment was analyzed with comprehensive two-dimensional gas chromatography time-of-flight mass spectrometry (GC×GC-TOFMS). Data was further preprocessed and analyzed. The preprocessing step comprises background correction, smoothing and alignment of the chromatographic signal. Data analysis was performed by applying t-test and partial least squares projection to latent structures discriminant analysis (PLS-DA). The optimization of the algorithm for parallel computing led to a substantial increase in performance. Metabolic fingerprinting showed a discrimination of the samples and indicates a metabolic effect of SHS.}, } @article {pmid21212231, year = {2011}, author = {Gompert, Z and Buerkle, CA}, title = {A hierarchical Bayesian model for next-generation population genomics.}, journal = {Genetics}, volume = {187}, number = {3}, pages = {903-917}, pmid = {21212231}, issn = {1943-2631}, mesh = {Bayes Theorem ; Computer Simulation ; *Data Interpretation, Statistical ; *Demography ; Genetic Association Studies ; Genetic Variation/*genetics ; Haplotypes/genetics ; Humans ; Metagenomics/*statistics & numerical data ; Models, Theoretical ; Polymorphism, Single Nucleotide/genetics ; Population/*genetics ; Selection, Genetic/*genetics ; }, abstract = {The demography of populations and natural selection shape genetic variation across the genome and understanding the genomic consequences of these evolutionary processes is a fundamental aim of population genetics. We have developed a hierarchical Bayesian model to quantify genome-wide population structure and identify candidate genetic regions affected by selection. This model improves on existing methods by accounting for stochastic sampling of sequences inherent in next-generation sequencing (with pooled or indexed individual samples) and by incorporating genetic distances among haplotypes in measures of genetic differentiation. Using simulations we demonstrate that this model has a low false-positive rate for classifying neutral genetic regions as selected genes (i.e., Φ(ST) outliers), but can detect recent selective sweeps, particularly when genetic regions in multiple populations are affected by selection. Nonetheless, selection affecting just a single population was difficult to detect and resulted in a high false-negative rate under certain conditions. We applied the Bayesian model to two large sets of human population genetic data. We found evidence of widespread positive and balancing selection among worldwide human populations, including many genetic regions previously thought to be under selection. Additionally, we identified novel candidate genes for selection, several of which have been linked to human diseases. This model will facilitate the population genetic analysis of a wide range of organisms on the basis of next-generation sequence data.}, } @article {pmid21210167, year = {2011}, author = {Ambily Nath, IV and Loka Bharathi, PA}, title = {Diversity in transcripts and translational pattern of stress proteins in marine extremophiles.}, journal = {Extremophiles : life under extreme conditions}, volume = {15}, number = {2}, pages = {129-153}, pmid = {21210167}, issn = {1433-4909}, mesh = {Chaperonin 60/metabolism ; DNA/genetics ; DNA Repair ; *Genetic Variation ; HSP70 Heat-Shock Proteins/metabolism ; Halobacteriales/*genetics ; Heat-Shock Proteins/*genetics ; Hot Temperature ; Hydrogen-Ion Concentration ; Oxidative Stress ; Pressure ; Protein Folding ; RNA, Messenger/*metabolism ; Species Specificity ; Temperature ; }, abstract = {Extremophiles occur in a diverse range of habitats, from the frigid waters of Antarctic to the superheated plumes of hydrothermal vents. Their in-depth study could provide important insights into the biochemical, ecological and evolutionary aspects of marine microbes. The cellular machinery of such extreme-lovers could be highly flexible to cope with such harsh environments. Extreme conditions of temperature, pressure, salinity, pH, oxidative stress, radiation, etc., above the physiological tolerance level can disrupt the natural conformation of proteins in the cell. The induction of stress proteins (heat/cold shock proteins/salt stress proteins/pressure-induced proteins) plays a vital role in the acclimatization of extremophiles. The present review focuses on the in vitro studies conducted on the transcripts and translational pattern of stress proteins in extremophiles. Though some proteins are unique, a commonality in stress resistance mechanism has been observed, for example, the universal occurrence of HSP60, 70 and the expression of metabolic and DNA repair proteins. The review highlights that among all the stressful conditions, salt/osmotic stress evokes the expression of highest number of transcripts/proteins while psychrophilic condition the least.}, } @article {pmid21209928, year = {2010}, author = {Wei, CL and Rowe, GT and Escobar-Briones, E and Boetius, A and Soltwedel, T and Caley, MJ and Soliman, Y and Huettmann, F and Qu, F and Yu, Z and Pitcher, CR and Haedrich, RL and Wicksten, MK and Rex, MA and Baguley, JG and Sharma, J and Danovaro, R and MacDonald, IR and Nunnally, CC and Deming, JW and Montagna, P and Lévesque, M and Weslawski, JM and Wlodarska-Kowalczuk, M and Ingole, BS and Bett, BJ and Billett, DS and Yool, A and Bluhm, BA and Iken, K and Narayanaswamy, BE}, title = {Global patterns and predictions of seafloor biomass using random forests.}, journal = {PloS one}, volume = {5}, number = {12}, pages = {e15323}, pmid = {21209928}, issn = {1932-6203}, mesh = {Algorithms ; Animals ; Artificial Intelligence ; Biodiversity ; *Biomass ; Carbon/chemistry ; Computational Biology/methods ; Ecosystem ; Marine Biology/*methods ; Models, Biological ; Oceans and Seas ; Regression Analysis ; }, abstract = {A comprehensive seafloor biomass and abundance database has been constructed from 24 oceanographic institutions worldwide within the Census of Marine Life (CoML) field projects. The machine-learning algorithm, Random Forests, was employed to model and predict seafloor standing stocks from surface primary production, water-column integrated and export particulate organic matter (POM), seafloor relief, and bottom water properties. The predictive models explain 63% to 88% of stock variance among the major size groups. Individual and composite maps of predicted global seafloor biomass and abundance are generated for bacteria, meiofauna, macrofauna, and megafauna (invertebrates and fishes). Patterns of benthic standing stocks were positive functions of surface primary production and delivery of the particulate organic carbon (POC) flux to the seafloor. At a regional scale, the census maps illustrate that integrated biomass is highest at the poles, on continental margins associated with coastal upwelling and with broad zones associated with equatorial divergence. Lowest values are consistently encountered on the central abyssal plains of major ocean basins The shift of biomass dominance groups with depth is shown to be affected by the decrease in average body size rather than abundance, presumably due to decrease in quantity and quality of food supply. This biomass census and associated maps are vital components of mechanistic deep-sea food web models and global carbon cycling, and as such provide fundamental information that can be incorporated into evidence-based management.}, } @article {pmid21209885, year = {2010}, author = {Arinaminpathy, N and Grenfell, B}, title = {Dynamics of glycoprotein charge in the evolutionary history of human influenza.}, journal = {PloS one}, volume = {5}, number = {12}, pages = {e15674}, pmid = {21209885}, issn = {1932-6203}, support = {R01 GM083983/GM/NIGMS NIH HHS/United States ; R01 GM083983-01/GM/NIGMS NIH HHS/United States ; }, mesh = {Computational Biology/methods ; Databases, Protein ; Epidemics ; Evolution, Molecular ; Glycoproteins/chemistry/*metabolism ; Glycosylation ; Hemagglutinin Glycoproteins, Influenza Virus/metabolism ; Humans ; Hydrogen-Ion Concentration ; Immune System ; Influenza A Virus, H3N2 Subtype/metabolism ; Influenza, Human/*epidemiology ; Neuraminidase/chemistry ; Phenotype ; Viruses/*genetics ; }, abstract = {BACKGROUND: Influenza viruses show a significant capacity to evade host immunity; this is manifest both as large occasional jumps in the antigenic phenotype of viral surface molecules and in gradual antigenic changes leading to annual influenza epidemics in humans. Recent mouse studies show that avidity for host cells can play an important role in polyclonal antibody escape, and further that electrostatic charge of the hemagglutinin glycoprotein can contribute to such avidity.

We test the role of glycoprotein charge on sequence data from the three major subtypes of influenza A in humans, using a simple method of calculating net glycoprotein charge. Of all subtypes, H3N2 in humans shows a striking pattern of increasing positive charge since its introduction in 1968. Notably, this trend applies to both hemagglutinin and neuraminidase glycoproteins. In the late 1980s hemagglutinin charge reached a plateau, while neuraminidase charge started to decline. We identify key groups of amino acid sites involved in this charge trend.

CONCLUSIONS/SIGNIFICANCE: To our knowledge these are the first indications that, for human H3N2, net glycoprotein charge covaries strongly with antigenic drift on a global scale. Further work is needed to elucidate how such charge interacts with other immune escape mechanisms, such as glycosylation, and we discuss important questions arising for future study.}, } @article {pmid21203831, year = {2011}, author = {Christens, BD and Speer, PW}, title = {Contextual influences on participation in community organizing: a multilevel longitudinal study.}, journal = {American journal of community psychology}, volume = {47}, number = {3-4}, pages = {253-263}, doi = {10.1007/s10464-010-9393-y}, pmid = {21203831}, issn = {1573-2770}, mesh = {Community Networks/*organization & administration ; Female ; Humans ; Longitudinal Studies ; Male ; United States ; *Volunteers ; }, abstract = {This article reports results from a study of contextual influences on participation among people involved in congregation-based community organizing. Data are drawn from 11,538 individual participants in 115 congregations taking part in one of five local organizing initiatives in different cities over a five-year period. Analyses used 3-level longitudinal models with binary indicators of participation/non-participation in group meetings each successive year as the criterion. Time-varying predictors at level-1 included prior participation in group meetings as a control, the types of group meetings that participants attended, the number of face-to-face meetings held between each participant and organizing staff of the local organizing initiatives, and a measure of the involvement of participants' affiliation networks. At level-2, demographic information was collected for a subset of participants (N = 461) and was included in a separate model. Neighborhood compositional characteristics were examined at level-3, including median income, economic heterogeneity, and residential stability. Study results found that characteristics of organizational settings (i.e., types of group meetings attended and frequency of face-to-face contact) predicted future participation in group meetings but that individual and neighborhood-level demographic characteristics were generally not predictive of future participation in community organizing activities.}, } @article {pmid21203829, year = {2011}, author = {Peirson, LJ and Boydell, KM and Ferguson, HB and Ferris, LE}, title = {An ecological process model of systems change.}, journal = {American journal of community psychology}, volume = {47}, number = {3-4}, pages = {307-321}, doi = {10.1007/s10464-010-9405-y}, pmid = {21203829}, issn = {1573-2770}, support = {//Canadian Institutes of Health Research/Canada ; }, mesh = {Community Networks/organization & administration ; *Diffusion of Innovation ; Health Policy ; Health Promotion/organization & administration ; *Models, Theoretical ; *Social Change ; }, abstract = {In June 2007 the American Journal of Community Psychology published a special issue focused on theories, methods and interventions for systems change which included calls from the editors and authors for theoretical advancement in this field. We propose a conceptual model of systems change that integrates familiar and fundamental community psychology principles (succession, interdependence, cycling of resources, adaptation) and accentuates a process orientation. To situate our framework we offer a definition of systems change and a brief review of the ecological perspective and principles. The Ecological Process Model of Systems Change is depicted, described and applied to a case example of policy driven systems level change in publicly funded social programs. We conclude by identifying salient implications for thinking and action which flow from the Model.}, } @article {pmid21203427, year = {2010}, author = {Hendrich, L and Pons, J and Ribera, I and Balke, M}, title = {Mitochondrial cox1 sequence data reliably uncover patterns of insect diversity but suffer from high lineage-idiosyncratic error rates.}, journal = {PloS one}, volume = {5}, number = {12}, pages = {e14448}, pmid = {21203427}, issn = {1932-6203}, mesh = {Animals ; Australia ; Classification ; Coleoptera ; Computational Biology/methods ; DNA, Mitochondrial/*genetics ; Electron Transport Complex IV/*genetics ; Electronic Data Processing ; Genetic Variation ; Insecta ; Likelihood Functions ; Mitochondria/*metabolism ; Phylogeny ; Reproducibility of Results ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: The demand for scientific biodiversity data is increasing, but taxonomic expertise is often limited or not available. DNA sequencing is a potential remedy to overcome this taxonomic impediment. Mitochondrial DNA is most commonly used, e.g., for species identification ("DNA barcoding"). Here, we present the first study in arthropods based on a near-complete species sampling of a family-level taxon from the entire Australian region. We aimed to assess how reliably mtDNA data can capture species diversity when many sister species pairs are included. Then, we contrasted phylogenetic subsampling with the hitherto more commonly applied geographical subsampling, where sister species are not necessarily captured.

We sequenced 800 bp cox1 for 1,439 individuals including 260 Australian species (78% species coverage). We used clustering with thresholds of 1 to 10% and general mixed Yule Coalescent (GMYC) analysis for the estimation of species richness. The performance metrics used were taxonomic accuracy and agreement between the morphological and molecular species richness estimation. Clustering (at the 3% level) and GMYC reliably estimated species diversity for single or multiple geographic regions, with an error for larger clades of lower than 10%, thus outperforming parataxonomy. However, the rates of error were higher for some individual genera, with values of up to 45% when very recent species formed nonmonophyletic clusters. Taxonomic accuracy was always lower, with error rates above 20% and a larger variation at the genus level (0 to 70%). Sørensen similarity indices calculated for morphospecies, 3% clusters and GMYC entities for different pairs of localities was consistent among methods and showed expected decrease over distance.

CONCLUSION/SIGNIFICANCE: Cox1 sequence data are a powerful tool for large-scale species richness estimation, with a great potential for use in ecology and β-diversity studies and for setting conservation priorities. However, error rates can be high in individual lineages.}, } @article {pmid21199026, year = {2011}, author = {Powell, JR and Monaghan, MT and Opik, M and Rillig, MC}, title = {Evolutionary criteria outperform operational approaches in producing ecologically relevant fungal species inventories.}, journal = {Molecular ecology}, volume = {20}, number = {3}, pages = {655-666}, doi = {10.1111/j.1365-294X.2010.04964.x}, pmid = {21199026}, issn = {1365-294X}, mesh = {*Biodiversity ; Biological Evolution ; Cluster Analysis ; Computational Biology/*methods ; DNA, Fungal/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Ecuador ; Estonia ; Fungi/*classification/*genetics ; Genetic Speciation ; Genetic Variation ; Likelihood Functions ; Models, Genetic ; Phylogeny ; RNA, Fungal/genetics ; RNA, Ribosomal, 18S/*genetics ; Sequence Analysis, DNA ; Species Specificity ; Time Factors ; }, abstract = {Analyses of the structure and function of microbial communities are highly constrained by the diversity of organisms present within most environmental samples. A common approach is to rely almost entirely on DNA sequence data for estimates of microbial diversity, but to date there is no objective method of clustering sequences into groups that is grounded in evolutionary theory of what constitutes a biological lineage. The general mixed Yule-coalescent (GMYC) model uses a likelihood-based approach to distinguish population-level processes within lineages from processes associated with speciation and extinction, thus identifying a distinct point where extant lineages became independent. Using two independent surveys of DNA sequences associated with a group of ubiquitous plant-symbiotic fungi, we compared estimates of species richness derived using the GMYC model to those based on operational taxonomic units (OTUs) defined by fixed levels of sequence similarity. The model predicted lower species richness in these surveys than did traditional methods of sequence similarity. Here, we show for the first time that groups delineated by the GMYC model better explained variation in the distribution of fungi in relation to putative niche-based variables associated with host species identity, edaphic factors, and aspects of how the sampled ecosystems were managed. Our results suggest the coalescent-based GMYC model successfully groups environmental sequences of fungi into clusters that are ecologically more meaningful than more arbitrary approaches for estimating species richness.}, } @article {pmid21191878, year = {2011}, author = {Golden, HE and Knightes, CD}, title = {Simulated watershed mercury and nitrate flux responses to multiple land cover conversion scenarios.}, journal = {Environmental toxicology and chemistry}, volume = {30}, number = {4}, pages = {773-786}, doi = {10.1002/etc.449}, pmid = {21191878}, issn = {1552-8618}, mesh = {Environmental Monitoring ; Geographic Information Systems ; Mercury/*analysis/chemistry ; Models, Chemical ; Nitrates/*analysis/chemistry ; Seasons ; Water Pollutants, Chemical/*analysis/chemistry ; Water Pollution, Chemical/statistics & numerical data ; Water Supply/*analysis ; }, abstract = {Water quality and toxic exposure science is transitioning towards analysis of multiple stressors rather than one particular environmental concern (e.g., mercury) or a group of similarly reacting chemicals (e.g., nutrients). However, two of the most important water quality constituents affecting both human and ecosystem health today, reactive nitrogen (N(r)) and methylmercury (MeHg), are often assessed separately for their independent effects on water quality. With the continued pressure of landscape modifications on water quality, a challenge remains in understanding the concurrent watershed flux response of both N(r) and MeHg to such physical stressors, particularly at the spatial scale (regional watersheds) and within the mixed land cover type systems that most decision-making processes are conducted. We simulate the annual average and monthly flux responses of Hg (MeHg and total mercury [HgT]), NO(3) -N, and runoff to four land cover change scenarios in the Haw River Watershed (NC, USA), a headwater system in the Cape Fear River Basin. Fluxes are simulated using a process-based, spatially explicit watershed Grid-Based Mercury Model (GBMM) and a NO(3) -N watershed flux model we developed to link to GBMM. Results suggest that annual NO(3) -N and Hg fluxes increase and decrease concomitantly to land cover change; however, the magnitude of the changes in NO(3) -N, MeHg, HgT, and water fluxes vary considerably between different land cover conversion scenarios. Converting pasture land to a suburbanized landscape elicited the greatest increase in runoff and MeHg, HgT, and NO(3) -N fluxes among all four conversion scenarios. Our findings provide insight for multi-stressor ecological exposure research and management of coastal eutrophication resulting from elevated N(r) loadings and exposure risk due to elevated concentrations of MeHg in fish tissue.}, } @article {pmid21189301, year = {2011}, author = {van Heerwaarden, J and Doebley, J and Briggs, WH and Glaubitz, JC and Goodman, MM and de Jesus Sanchez Gonzalez, J and Ross-Ibarra, J}, title = {Genetic signals of origin, spread, and introgression in a large sample of maize landraces.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {108}, number = {3}, pages = {1088-1092}, pmid = {21189301}, issn = {1091-6490}, mesh = {Databases, Genetic ; *Demography ; Gene Frequency ; Genetic Drift ; *Genetic Variation ; *Genetics, Population ; Genotype ; Geography ; Mexico ; Polymorphism, Single Nucleotide/*genetics ; Principal Component Analysis ; Species Specificity ; Zea mays/*genetics ; }, abstract = {The last two decades have seen important advances in our knowledge of maize domestication, thanks in part to the contributions of genetic data. Genetic studies have provided firm evidence that maize was domesticated from Balsas teosinte (Zea mays subspecies parviglumis), a wild relative that is endemic to the mid- to lowland regions of southwestern Mexico. An interesting paradox remains, however: Maize cultivars that are most closely related to Balsas teosinte are found mainly in the Mexican highlands where subspecies parviglumis does not grow. Genetic data thus point to primary diffusion of domesticated maize from the highlands rather than from the region of initial domestication. Recent archeological evidence for early lowland cultivation has been consistent with the genetics of domestication, leaving the issue of the ancestral position of highland maize unresolved. We used a new SNP dataset scored in a large number of accessions of both teosinte and maize to take a second look at the geography of the earliest cultivated maize. We found that gene flow between maize and its wild relatives meaningfully impacts our inference of geographic origins. By analyzing differentiation from inferred ancestral gene frequencies, we obtained results that are fully consistent with current ecological, archeological, and genetic data concerning the geography of early maize cultivation.}, } @article {pmid21179546, year = {2010}, author = {Cruz-Motta, JJ and Miloslavich, P and Palomo, G and Iken, K and Konar, B and Pohle, G and Trott, T and Benedetti-Cecchi, L and Herrera, C and Hernández, A and Sardi, A and Bueno, A and Castillo, J and Klein, E and Guerra-Castro, E and Gobin, J and Gómez, DI and Riosmena-Rodríguez, R and Mead, A and Bigatti, G and Knowlton, A and Shirayama, Y}, title = {Patterns of spatial variation of assemblages associated with intertidal rocky shores: a global perspective.}, journal = {PloS one}, volume = {5}, number = {12}, pages = {e14354}, pmid = {21179546}, issn = {1932-6203}, mesh = {Animals ; Biodiversity ; Bivalvia/metabolism ; Conservation of Natural Resources ; Databases, Factual ; Demography ; Ecology ; Ecosystem ; Environment ; Invertebrates/*physiology ; Marine Biology/methods ; Oceans and Seas ; Rhodophyta/metabolism ; Temperature ; Thoracica/metabolism ; }, abstract = {Assemblages associated with intertidal rocky shores were examined for large scale distribution patterns with specific emphasis on identifying latitudinal trends of species richness and taxonomic distinctiveness. Seventy-two sites distributed around the globe were evaluated following the standardized sampling protocol of the Census of Marine Life NaGISA project (www.nagisa.coml.org). There were no clear patterns of standardized estimators of species richness along latitudinal gradients or among Large Marine Ecosystems (LMEs); however, a strong latitudinal gradient in taxonomic composition (i.e., proportion of different taxonomic groups in a given sample) was observed. Environmental variables related to natural influences were strongly related to the distribution patterns of the assemblages on the LME scale, particularly photoperiod, sea surface temperature (SST) and rainfall. In contrast, no environmental variables directly associated with human influences (with the exception of the inorganic pollution index) were related to assemblage patterns among LMEs. Correlations of the natural assemblages with either latitudinal gradients or environmental variables were equally strong suggesting that neither neutral models nor models based solely on environmental variables sufficiently explain spatial variation of these assemblages at a global scale. Despite the data shortcomings in this study (e.g., unbalanced sample distribution), we show the importance of generating biological global databases for the use in large-scale diversity comparisons of rocky intertidal assemblages to stimulate continued sampling and analyses.}, } @article {pmid21175829, year = {2011}, author = {Scholz, AJ and Steinback, C and Kruse, SA and Mertens, M and Silverman, H}, title = {Incorporation of spatial and economic analyses of human-use data in the design of marine protected areas.}, journal = {Conservation biology : the journal of the Society for Conservation Biology}, volume = {25}, number = {3}, pages = {485-492}, doi = {10.1111/j.1523-1739.2010.01626.x}, pmid = {21175829}, issn = {1523-1739}, mesh = {Animals ; California ; Conservation of Natural Resources/*economics ; Data Interpretation, Statistical ; Environmental Policy/economics ; *Fisheries ; Geographic Information Systems ; Humans ; }, abstract = {Social, economic, and ecological criteria contribute to the successful design, implementation, and management of marine protected areas (MPAs). In the context of California's Marine Life Protection Act Initiative, we developed a set of methods for collecting, compiling, and analyzing data about the spatial extent and relative economic importance of commercial and recreational fishing. We interviewed 174 commercial fishers who represented the major fisheries in the initiative's north-central coast region, which extends from Point Arena south to Pigeon Point. These fishers provided data that we used to map the extent of each of the fishing grounds, to weight the relative importance of areas within the grounds, to characterize the operating costs of each fishery, and to analyze the potential economic losses associated with proposed marine protected areas. A regional stakeholder group used the maps and impact analyses in conjunction with other data sets to iteratively identify economic and ecological trade-offs in designations of different areas as MPAs at regional, port, and fishery extents. Their final proposed MPA network designated 20% of state waters as MPAs. Potential net economic loss ranged from 1.7% to 14.2% in the first round of network design and totaled 6.3% in the final round of design. This process is a case study in the application of spatial analysis to validate and integrate local stakeholder knowledge in marine planning.}, } @article {pmid21173280, year = {2010}, author = {Bodenstein, L}, title = {Regarding Anderegg et al. and climate change credibility.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {107}, number = {52}, pages = {E188; author reply E189}, pmid = {21173280}, issn = {1091-6490}, mesh = {*Climate ; Climate Change/*statistics & numerical data ; Databases, Factual ; Ecology/statistics & numerical data/trends ; Forecasting ; *Greenhouse Effect ; Humans ; Public Opinion ; Research Personnel/statistics & numerical data ; }, } @article {pmid21173219, year = {2011}, author = {Roura-Pascual, N and Hui, C and Ikeda, T and Leday, G and Richardson, DM and Carpintero, S and Espadaler, X and Gómez, C and Guénard, B and Hartley, S and Krushelnycky, P and Lester, PJ and McGeoch, MA and Menke, SB and Pedersen, JS and Pitt, JP and Reyes, J and Sanders, NJ and Suarez, AV and Touyama, Y and Ward, D and Ward, PS and Worner, SP}, title = {Relative roles of climatic suitability and anthropogenic influence in determining the pattern of spread in a global invader.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {108}, number = {1}, pages = {220-225}, pmid = {21173219}, issn = {1091-6490}, mesh = {Animals ; Ants/*growth & development ; *Climate ; Commerce ; Computer Simulation ; Databases, Factual ; Ecology/*methods ; *Ecosystem ; Geography ; Human Activities ; Humans ; Introduced Species/*trends ; *Models, Biological ; Regression Analysis ; }, abstract = {Because invasive species threaten the integrity of natural ecosystems, a major goal in ecology is to develop predictive models to determine which species may become widespread and where they may invade. Indeed, considerable progress has been made in understanding the factors that influence the local pattern of spread for specific invaders and the factors that are correlated with the number of introduced species that have become established in a given region. However, few studies have examined the relative importance of multiple drivers of invasion success for widespread species at global scales. Here, we use a dataset of >5,000 presence/absence records to examine the interplay between climatic suitability, biotic resistance by native taxa, human-aided dispersal, and human modification of habitats, in shaping the distribution of one of the world's most notorious invasive species, the Argentine ant (Linepithema humile). Climatic suitability and the extent of human modification of habitats are primarily responsible for the distribution of this global invader. However, we also found some evidence for biotic resistance by native communities. Somewhat surprisingly, and despite the often cited importance of propagule pressure as a crucial driver of invasions, metrics of the magnitude of international traded commodities among countries were not related to global distribution patterns. Together, our analyses on the global-scale distribution of this invasive species provide strong evidence for the interplay of biotic and abiotic determinants of spread and also highlight the challenges of limiting the spread and subsequent impact of highly invasive species.}, } @article {pmid21170326, year = {2010}, author = {Arnold, SE and Faruq, S and Savolainen, V and McOwan, PW and Chittka, L}, title = {FReD: the floral reflectance database--a web portal for analyses of flower colour.}, journal = {PloS one}, volume = {5}, number = {12}, pages = {e14287}, pmid = {21170326}, issn = {1932-6203}, support = {BBS/S/L/2005/12155A//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; Bees/physiology ; Color ; Databases, Factual ; Flowers/metabolism/*physiology ; Geography ; Internet ; Models, Biological ; Plant Physiological Phenomena ; Plants/metabolism ; Pollen/metabolism ; Pollination/*physiology ; Software ; User-Computer Interface ; }, abstract = {BACKGROUND: Flower colour is of great importance in various fields relating to floral biology and pollinator behaviour. However, subjective human judgements of flower colour may be inaccurate and are irrelevant to the ecology and vision of the flower's pollinators. For precise, detailed information about the colours of flowers, a full reflectance spectrum for the flower of interest should be used rather than relying on such human assessments.

The Floral Reflectance Database (FReD) has been developed to make an extensive collection of such data available to researchers. It is freely available at http://www.reflectance.co.uk. The database allows users to download spectral reflectance data for flower species collected from all over the world. These could, for example, be used in modelling interactions between pollinator vision and plant signals, or analyses of flower colours in various habitats. The database contains functions for calculating flower colour loci according to widely-used models of bee colour space, reflectance graphs of the spectra and an option to search for flowers with similar colours in bee colour space.

CONCLUSIONS/SIGNIFICANCE: The Floral Reflectance Database is a valuable new tool for researchers interested in the colours of flowers and their association with pollinator colour vision, containing raw spectral reflectance data for a large number of flower species.}, } @article {pmid21167615, year = {2011}, author = {Musella, V and Catelan, D and Rinaldi, L and Lagazio, C and Cringoli, G and Biggeri, A}, title = {Covariate selection in multivariate spatial analysis of ovine parasitic infection.}, journal = {Preventive veterinary medicine}, volume = {99}, number = {2-4}, pages = {69-77}, doi = {10.1016/j.prevetmed.2010.11.012}, pmid = {21167615}, issn = {1873-1716}, mesh = {Animals ; Bayes Theorem ; *Dairying ; Female ; Geographic Information Systems ; Intestinal Diseases, Parasitic/epidemiology/*veterinary ; Multivariate Analysis ; Poaceae/*parasitology ; Risk Factors ; Sheep ; Sheep Diseases/*epidemiology ; }, abstract = {Gastrointestinal (GI) strongyle and fluke infections remain one of the main constraints on health and productivity in sheep dairy production. A cross-sectional survey was conducted in 2004-2005 on ovine farms in the Campania region of southern Italy in order to evaluate the prevalence of Haemonchus contortus, Fasciola hepatica, Dicrocoelium dendriticum and Calicophoron daubneyi from among other parasitic infections. In the present work, we focused on the role of the ecological characteristics of the pasture environment while accounting for the underlying long range geographical risk pattern. Bayesian multivariate spatial statistical analysis was used. A systematic grid (10 km×10 km) sampling approach was used. Laboratory procedures were based on the FLOTAC technique to detect and count eggs of helminths. A Geographical Information System (GIS) was constructed by using environmental data layers. Data on each of these layers were then extracted for pasturing areas that were previously digitalized aerial images of the ovine farms. Bayesian multivariate statistical analyses, including improper multivariate conditional autoregressive models, were used to select covariates on a multivariate spatially structured risk surface. Out of the 121 tested farms, 109 were positive for H. contortus, 81 for D. dendriticum, 17 for C. daubneyi and 15 for F. hepatica. The statistical analysis highlighted a north-south long range spatially structured pattern. This geographical pattern is treated here as a confounder, because the main interest was in the causal role of ecological covariates at the level of each pasturing area. A high percentage of pasture and impermeable soil were strong predictors of F. hepatica risk and a high percentage of wood was a strong predictor of C. daubneyi. A high percentage of wood, rocks and arable soil with sparse trees explained the spatial distribution of D. dendriticum. Sparse vegetation, river, mixed soil and permeable soil explained the spatial distribution of the H. contortus. Bayesian multivariate spatial analysis of parasitic infections with covariates from remote sensing at a very small geographical level allowed us to identify relevant risk predictors. All the covariates selected are consistent with the life cycles of the helminths investigated. This research showed the utility of appropriate GIS-driven surveillance systems. Moreover, spatial features can be used to tailor sampling design where the sampling fraction can be a function of remote sensing covariables.}, } @article {pmid21163721, year = {2011}, author = {Goater, S and Derne, B and Weinstein, P}, title = {Critical issues in the development of health information systems in supporting environmental health: a case study of ciguatera.}, journal = {Environmental health perspectives}, volume = {119}, number = {5}, pages = {585-590}, pmid = {21163721}, issn = {1552-9924}, mesh = {Ciguatera Poisoning/*epidemiology ; *Environmental Health ; Foodborne Diseases/epidemiology ; Humans ; *Information Systems ; }, abstract = {BACKGROUND: Emerging environmental pressures resulting from climate change and globalization challenge the capacity of health information systems (HIS) in the Pacific to inform future policy and public health interventions. Ciguatera, a globally common marine food-borne illness, is used here to illustrate specific HIS challenges in the Pacific and how these might be overcome proactively to meet the changing surveillance needs resulting from environmental change.

OBJECTIVES: We review and highlight inefficiencies in the reactive nature of existing HIS in the Pacific to collect, collate, and communicate ciguatera fish poisoning data currently used to inform public health intervention. Further, we review the capacity of existing HIS to respond to new data needs associated with shifts in ciguatera disease burden likely to result from coral reef habitat disruption.

DISCUSSION: Improved knowledge on the ecological drivers of ciguatera prevalence at local and regional levels is needed, combined with enhanced surveillance techniques and data management systems, to capture environmental drivers as well as health outcomes data.

CONCLUSIONS: The capacity of public HIS to detect and prevent future outbreaks is largely dependent on the future development of governance strategies that promote proactive surveillance and health action. Accordingly, we present an innovative framework from which to stimulate scientific debate on how this might be achieved by using existing larger scale data sets and multidisciplinary collaborations.}, } @article {pmid21163040, year = {2010}, author = {Chen, XY and Zhang, CQ and Zhang, H and Liu, W and Wang, JY}, title = {[Analysis on the current use and trend of drugs for digestive system through comprehensive statistics index, in Hangzhou].}, journal = {Zhonghua liu xing bing xue za zhi = Zhonghua liuxingbingxue zazhi}, volume = {31}, number = {5}, pages = {572-575}, pmid = {21163040}, issn = {0254-6450}, mesh = {China ; Data Interpretation, Statistical ; Digestive System ; Drug Utilization/*statistics & numerical data ; Gastrointestinal Agents/*therapeutic use ; Humans ; }, abstract = {OBJECTIVE: To investigate the use and trend of drugs on digestive system in Hangzhou area, under the comprehensive statistics index (CSI).

METHODS: Using the analytical method related to the sum of consumption and CSI, the application of digestive system drugs of different manufacturers in Hangzhou from 2005 to 2007 was analyzed.

RESULTS: Other than H2 receptor antagonist, the total consumption of digestive system drugs increased yearly, in terms of the total consumption, the first 4 leading ones were proton pump inhibitors, micro ecology medicines, antiemetic drugs and gastroprokinetic agents. The Laspeyres index of drugs on digestive system increased to different extent. The Laspeyres indices of proton pump inhibitors, probiotics, antiemetic drugs and gastroprokinetic agents were 1.396 50, 1.020 42, 1.728 90, 1.148 50 in 2006 while 2.081 10, 1.217 55, 2.223 50, 1.156 60 in 2007, respectively.

CONCLUSION: Through CSI, the results showed the situation of use and trend of digestive system related drugs in Hangzhou. Factors as rationality, efficiency and costs of the drugs as well as the etiology of the disease were also explored to some degree.}, } @article {pmid21162723, year = {2010}, author = {Qiu, L and Yang, C and Tian, B and Yang, JB and Liu, A}, title = {Exploiting EST databases for the development and characterization of EST-SSR markers in castor bean (Ricinus communis L.).}, journal = {BMC plant biology}, volume = {10}, number = {}, pages = {278}, pmid = {21162723}, issn = {1471-2229}, mesh = {Ricinus communis/*genetics ; *Databases, Genetic ; *Expressed Sequence Tags ; *Genes, Plant ; *Microsatellite Repeats ; Polymerase Chain Reaction ; *Polymorphism, Genetic ; }, abstract = {BACKGROUND: The castor bean (Ricinus communis L.), a monotypic species in the spurge family (Euphorbiaceae, 2n = 20), is an important non-edible oilseed crop widely cultivated in tropical, sub-tropical and temperate countries for its high economic value. Because of the high level of ricinoleic acid (over 85%) in its seed oil, the castor bean seed derivatives are often used in aviation oil, lubricants, nylon, dyes, inks, soaps, adhesive and biodiesel. Due to lack of efficient molecular markers, little is known about the population genetic diversity and the genetic relationships among castor bean germplasm. Efficient and robust molecular markers are increasingly needed for breeding and improving varieties in castor bean. The advent of modern genomics has produced large amounts of publicly available DNA sequence data. In particular, expressed sequence tags (ESTs) provide valuable resources to develop gene-associated SSR markers.

RESULTS: In total, 18,928 publicly available non-redundant castor bean EST sequences, representing approximately 17.03 Mb, were evaluated and 7732 SSR sites in 5,122 ESTs were identified by data mining. Castor bean exhibited considerably high frequency of EST-SSRs. We developed and characterized 118 polymorphic EST-SSR markers from 379 primer pairs flanking repeats by screening 24 castor bean samples collected from different countries. A total of 350 alleles were identified from 118 polymorphic SSR loci, ranging from 2-6 per locus (A) with an average of 2.97. The EST-SSR markers developed displayed moderate gene diversity (He) with an average of 0.41. Genetic relationships among 24 germplasms were investigated using the genotypes of 350 alleles, showing geographic pattern of genotypes across genetic diversity centers of castor bean.

CONCLUSION: Castor bean EST sequences exhibited considerably high frequency of SSR sites, and were rich resources for developing EST-SSR markers. These EST-SSR markers would be particularly useful for both genetic mapping and population structure analysis, facilitating breeding and crop improvement of castor bean.}, } @article {pmid21159406, year = {2011}, author = {Whitlock, MC}, title = {Data archiving in ecology and evolution: best practices.}, journal = {Trends in ecology & evolution}, volume = {26}, number = {2}, pages = {61-65}, doi = {10.1016/j.tree.2010.11.006}, pmid = {21159406}, issn = {0169-5347}, mesh = {*Biological Evolution ; Databases, Factual ; Ecology/methods/*standards ; Information Management/*methods ; Periodicals as Topic/standards ; Publishing ; Research/*standards ; }, abstract = {Many ecology and evolution journals have recently adopted policies requiring that data from their papers be publicly archived. I present suggestions on how data generators, data re-users, and journals can maximize the fairness and scientific value of data archiving. Data should be archived with enough clarity and supporting information that they can be accurately interpreted by others. Re-users should respect their intellectual debt to the originators of data through citation both of the paper and of the data package. In addition, journals should consider requiring that all data for published papers be archived, just as DNA sequences must be deposited in GenBank. Data are another valuable part of the legacy of a scientific career and archiving them can lead to new scientific insights. Archiving also increases opportunities for credit to be given to the scientists who originally collected the data.}, } @article {pmid21159004, year = {2011}, author = {Bulatova, N and Jones, RM and White, TA and Shchipanov, NA and Pavlova, SV and Searle, JB}, title = {Natural hybridization between extremely divergent chromosomal races of the common shrew (Sorex araneus, Soricidae, Soricomorpha): hybrid zone in European Russia.}, journal = {Journal of evolutionary biology}, volume = {24}, number = {3}, pages = {573-586}, doi = {10.1111/j.1420-9101.2010.02191.x}, pmid = {21159004}, issn = {1420-9101}, mesh = {Animals ; Chromosomes, Mammalian/*genetics ; Demography ; Geographic Information Systems ; *Hybridization, Genetic ; Karyotyping ; Russia ; Shrews/*genetics ; }, abstract = {The Moscow and Seliger chromosomal races of the common shrew differ by Robertsonian fusions and possibly whole-arm reciprocal translocations (WARTs) such that their F1 hybrids produce a chain-of-eleven configuration at meiosis I and are expected to suffer substantial infertility. Of numerous hybrid zones that have been described in the common shrew, those between the Moscow and Seliger races involve the greatest chromosomal difference. We collected 211 individuals from this zone to generate a total dataset of 298 individuals from 187 unique global positioning system (GPS) locations within the vicinity of interracial contact. We used a geographic information system (GIS) to map the location of the hybrid zone, which follows a direct route between two lakes, as would be anticipated from tension zone theory. Even within the central area of the hybrid zone, there is a much higher frequency of pure race individuals than hybrid, making this a clear example of a bimodal zone in the sense of Jiggins & Mallet (2000). The zone runs through good habitat for common shrews, but nevertheless it is very narrow (standard cline widths: 3-4 km), as would be anticipated from low hybrid fitness. There is clear potential for an interruption to gene flow and build-up of reproductive isolation. As found in some other hybrid zones, there is a high frequency of novel genetic variants, in this case, new chromosomal rearrangements. Here, we report a de novo Robertsonian fission and a de novo reciprocal translocation, both for the first time in the common shrew. There is an extraordinarily high frequency of de novo mutations recorded in F1 hybrids in the zone and we discuss how chromosomal instability may be associated with such hybrids. The occurrence of a de novo Robertsonian fission is of considerable significance because it provides missing evidence that fissions are the basis of the novel acrocentric forms found and apparently selected for in certain common shrew hybrid zones.}, } @article {pmid21155023, year = {2010}, author = {Wei, W and Liu, L and Chen, J and Jin, K and Jiang, F and Liu, F and Fan, R and Cheng, Z and Shen, M and Xue, C and Cai, S and Xu, Y and Nan, P}, title = {Racial differences in MLH1 and MSH2 mutation: an analysis of yellow race and white race based on the InSiGHT database.}, journal = {Journal of bioinformatics and computational biology}, volume = {8 Suppl 1}, number = {}, pages = {111-125}, doi = {10.1142/s0219720010005154}, pmid = {21155023}, issn = {1757-6334}, mesh = {Adaptor Proteins, Signal Transducing/*genetics ; Asian People/*genetics ; Colorectal Neoplasms, Hereditary Nonpolyposis/genetics ; Computational Biology ; Databases, Genetic/statistics & numerical data ; Gene Frequency ; Humans ; MutL Protein Homolog 1 ; MutS Homolog 2 Protein/*genetics ; *Mutation ; Nuclear Proteins/*genetics ; White People/*genetics ; }, abstract = {MLH1 and MSH2 mutations underlie 90% of hereditary nonpolyposis colorectal cancer (HNPCC) mutations. The International Society of Gastrointestinal Hereditary Tumors (InSiGHT) has established an international database of mutations associated with HNPCC. Based on the InSiGHT database and the original references that reported the mutations, we analyzed the distributions of MLH1 and MSH2 mutations in yellow race and white race respectively and compared them subsequently. We found: (1) the distributions of mutation individuals in exon 1, 17 and 19 of MLH1 gene and in exon 2 of MSH2 gene showed significant differences between the two race groups (p < 0.05); (2) the distributions of mutation types in exon 2, 7 and 18 of MLH1 and exon 10 and 16 of MSH2 showed significant differences (p < 0.05); and (3) three mutations (c.649C > T, c.1625A > T and c.1721T > C) in MLH1 and five mutations (c.23C > T, c.187dupG, c.505A > G, c.1168C > T and c.2211-6T > C) in MSH2 have much higher frequency in yellow race than those in white race. Furthermore, three mutations (c.1453G > C, c.1742C > T and c.1758dupC) in MLH1 and two mutations (c.1255C > A and c.1886A > G) in MSH2 were only found in yellow race, which implies that specific mutations in yellow race need more attention when screening mutations in these two genes.}, } @article {pmid21155017, year = {2010}, author = {Shih, TH and Chen, CM and Wang, HW and Pai, TW and Chang, HT}, title = {BiMFG: bioinformatics tools for marine and freshwater species.}, journal = {Journal of bioinformatics and computational biology}, volume = {8 Suppl 1}, number = {}, pages = {17-32}, doi = {10.1142/s0219720010005105}, pmid = {21155017}, issn = {1757-6334}, mesh = {Algorithms ; Animals ; *Computational Biology ; *Databases, Genetic ; Fishes/genetics ; Fresh Water/microbiology ; Genetics, Microbial/statistics & numerical data ; Humans ; Internet ; Invertebrates/genetics ; Marine Biology/*statistics & numerical data ; Models, Molecular ; Protein Structure, Secondary ; Seawater/microbiology ; Sequence Alignment/statistics & numerical data ; Structural Homology, Protein ; }, abstract = {Biomolecule sequences and structures of land, air and water species are determined rapidly and the data entries are unevenly distributed for different organisms. It frequently leads to the BLAST results of homologous search containing undesirable entries from organisms living in different environments. To reduce irrelevant searching results, a separate database for comparative genomics is urgently required. A comprehensive bioinformatics tool set and an integrated database, named Bioinformatics tools for Marine and Freshwater Genomics (BiMFG), are constructed for comparative analyses among model species and underwater species. Novel matching techniques based on conserved motifs and/or secondary structure elements are designed for efficiently and effectively retrieving and aligning remote sequences through cross-species comparisons. It is especially helpful when sequences under analysis possess low similarities and unresolved structural information. In addition, the system provides core techniques of multiple sequence alignment, multiple second structure profile alignment and iteratively refined multiple structural alignments for biodiversity analysis and verification in marine and freshwater biology. The BiMFG web server is freely available for use at http://bimfg.cs.ntou.edu.tw/.}, } @article {pmid21153757, year = {2011}, author = {Vesco, U and Knap, N and Labruna, MB and Avšič-Županc, T and Estrada-Peña, A and Guglielmone, AA and Bechara, GH and Gueye, A and Lakos, A and Grindatto, A and Conte, V and De Meneghi, D}, title = {An integrated database on ticks and tick-borne zoonoses in the tropics and subtropics with special reference to developing and emerging countries.}, journal = {Experimental & applied acarology}, volume = {54}, number = {1}, pages = {65-83}, pmid = {21153757}, issn = {1572-9702}, mesh = {Animals ; Arachnid Vectors/*microbiology ; *Databases as Topic ; Developing Countries ; Geography ; Humans ; Tick-Borne Diseases/diagnosis/epidemiology/*microbiology ; Ticks/*microbiology ; Tropical Climate ; Zoonoses/epidemiology/*microbiology ; }, abstract = {Tick-borne zoonoses (TBZ) are emerging diseases worldwide. A large amount of information (e.g. case reports, results of epidemiological surveillance, etc.) is dispersed through various reference sources (ISI and non-ISI journals, conference proceedings, technical reports, etc.). An integrated database-derived from the ICTTD-3 project (http://www.icttd.nl)-was developed in order to gather TBZ records in the (sub-)tropics, collected both by the authors and collaborators worldwide. A dedicated website (http://www.tickbornezoonoses.org) was created to promote collaboration and circulate information. Data collected are made freely available to researchers for analysis by spatial methods, integrating mapped ecological factors for predicting TBZ risk. The authors present the assembly process of the TBZ database: the compilation of an updated list of TBZ relevant for (sub-)tropics, the database design and its structure, the method of bibliographic search, the assessment of spatial precision of geo-referenced records. At the time of writing, 725 records extracted from 337 publications related to 59 countries in the (sub-)tropics, have been entered in the database. TBZ distribution maps were also produced. Imported cases have been also accounted for. The most important datasets with geo-referenced records were those on Spotted Fever Group rickettsiosis in Latin-America and Crimean-Congo Haemorrhagic Fever in Africa. The authors stress the need for international collaboration in data collection to update and improve the database. Supervision of data entered remains always necessary. Means to foster collaboration are discussed. The paper is also intended to describe the challenges encountered to assemble spatial data from various sources and to help develop similar data collections.}, } @article {pmid21151577, year = {2010}, author = {Boerlijst, MC and van Ballegooijen, WM}, title = {Spatial pattern switching enables cyclic evolution in spatial epidemics.}, journal = {PLoS computational biology}, volume = {6}, number = {12}, pages = {e1001030}, pmid = {21151577}, issn = {1553-7358}, mesh = {Computational Biology ; *Disease Outbreaks ; *Evolution, Molecular ; Host-Pathogen Interactions ; *Models, Biological ; Mutation ; *Time Factors ; }, abstract = {Infectious diseases often spread as spatial epidemic outbreak waves. A number of model studies have shown that such spatial pattern formation can have important consequences for the evolution of pathogens. Here, we show that such spatial patterns can cause cyclic evolutionary dynamics in selection for the length of the infectious period. The necessary reversal in the direction of selection is enabled by a qualitative change in the spatial pattern from epidemic waves to irregular local outbreaks. The spatial patterns are an emergent property of the epidemic system, and they are robust against changes in specific model assumptions. Our results indicate that emergent spatial patterns can act as a rich source for complexity in pathogen evolution.}, } @article {pmid21142970, year = {2011}, author = {Gyuranecz, M and Rigó, K and Dán, A and Földvári, G and Makrai, L and Dénes, B and Fodor, L and Majoros, G and Tirják, L and Erdélyi, K}, title = {Investigation of the ecology of Francisella tularensis during an inter-epizootic period.}, journal = {Vector borne and zoonotic diseases (Larchmont, N.Y.)}, volume = {11}, number = {8}, pages = {1031-1035}, doi = {10.1089/vbz.2010.0091}, pmid = {21142970}, issn = {1557-7759}, mesh = {Animals ; Databases, Nucleic Acid ; Disease Reservoirs/*microbiology ; Ecology ; Ecosystem ; Female ; Francisella tularensis/genetics ; Hares/*microbiology ; Hungary/epidemiology ; Insect Vectors/microbiology ; Mammals ; Mice ; Real-Time Polymerase Chain Reaction ; Ruminants/blood/microbiology ; Siphonaptera/microbiology ; Ticks/*microbiology ; Tularemia/*epidemiology/*transmission ; }, abstract = {A 1-year study of the ecological cycle of Francisella tularensis was performed in an enzootic area during an inter-epizootic period. The study was based on multiple sampling of all major constituents of the disease cycle. Seroprevalence of tularemia in the European brown hare (Lepus europaeus) population was 5.1% (10/197) with low antibody titers (1/10 and 1/20), and F. tularensis ssp. holarctica was isolated from four hares. F. tularensis was not detected in the 38 common voles (Microtus arvalis), 110 yellow-necked mice (Apodemus flavicollis), or 15 stripped field mice (Apodemus agrarius) trapped during the study, or the by-catch of 8 Eurasian pygmy shrews (Sorex minutus) or 6 common shrews (Sorex araneus). A total of 1106 Ixodes ricinus and 476 Haemaphysalis concinna ticks were collected from vegetation, and 404 I. ricinus, 28 H. concinna ticks, and 15 Ctenophtalmus assimilis and 10 Nosopsyllus fasciatus fleas were combed off small mammals. One H. concinna female and one nymph collected from the vegetation was found infected with F. tularensis ssp. holarctica by TaqMan polymerase chain reaction, thus resulting a 0.42% (2/476) prevalence. F. tularensis-specific DNA was not detected in environmental water samples, and the examined 100 sheep, 50 cows, and 50 buffalos grazed at the study area were all seronegative. During inter-epizootic periods, F. tularensis ssp. holarctica seems to persist only in the European brown hare--H. concinna cycle at the studied habitat. H. concinna may not serve exclusively as an arthropod vector, but it may also harbor bacteria for 3-4 years through multiple life stages and act as an important reservoir of F. tularensis. Rodent species probably do not serve as true reservoir hosts of tularemia.}, } @article {pmid21139633, year = {2011}, author = {Ekblom, R and Galindo, J}, title = {Applications of next generation sequencing in molecular ecology of non-model organisms.}, journal = {Heredity}, volume = {107}, number = {1}, pages = {1-15}, pmid = {21139633}, issn = {1365-2540}, mesh = {Databases, Genetic ; Ecology/methods ; Gene Expression Profiling/methods ; Genome ; Genomics/*methods ; Sequence Analysis, DNA/*methods ; Sequence Analysis, RNA/*methods ; }, abstract = {As most biologists are probably aware, technological advances in molecular biology during the last few years have opened up possibilities to rapidly generate large-scale sequencing data from non-model organisms at a reasonable cost. In an era when virtually any study organism can 'go genomic', it is worthwhile to review how this may impact molecular ecology. The first studies to put the next generation sequencing (NGS) to the test in ecologically well-characterized species without previous genome information were published in 2007 and the beginning of 2008. Since then several studies have followed in their footsteps, and a large number are undoubtedly under way. This review focuses on how NGS has been, and can be, applied to ecological, population genetic and conservation genetic studies of non-model species, in which there is no (or very limited) genomic resources. Our aim is to draw attention to the various possibilities that are opening up using the new technologies, but we also highlight some of the pitfalls and drawbacks with these methods. We will try to provide a snapshot of the current state of the art for this rapidly advancing and expanding field of research and give some likely directions for future developments.}, } @article {pmid21129490, year = {2011}, author = {Vélez-Zuazo, X and Agnarsson, I}, title = {Shark tales: a molecular species-level phylogeny of sharks (Selachimorpha, Chondrichthyes).}, journal = {Molecular phylogenetics and evolution}, volume = {58}, number = {2}, pages = {207-217}, doi = {10.1016/j.ympev.2010.11.018}, pmid = {21129490}, issn = {1095-9513}, mesh = {Animals ; Bayes Theorem ; Biological Evolution ; Cell Nucleus/genetics ; DNA, Mitochondrial/genetics ; Data Mining ; *Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA ; Sharks/*classification/genetics ; }, abstract = {Sharks are a diverse and ecologically important group, including some of the ocean's largest predatory animals. Sharks are also commercially important, with many species suffering overexploitation and facing extinction. However, despite a long evolutionary history, commercial, and conservation importance, phylogenetic relationships within the sharks are poorly understood. To date, most studies have either focused on smaller clades within sharks, or sampled taxa sparsely across the group. A more detailed species-level phylogeny will offer further insights into shark taxonomy, provide a tool for comparative analyses, as well as facilitating phylogenetic estimates of conservation priorities. We used four mitochondrial and one nuclear gene to investigate the phylogenetic relationships of 229 species (all eight Orders and 31 families) of sharks, more than quadrupling the number of taxon sampled in any prior study. The resulting Bayesian phylogenetic hypothesis agrees with prior studies on the major relationships of the sharks phylogeny; however, on those relationships that have proven more controversial, it differs in several aspects from the most recent molecular studies. The phylogeny supports the division of sharks into two major groups, the Galeomorphii and Squalimorphii, rejecting the hypnosqualean hypothesis that places batoids within sharks. Within the squalimorphs the orders Hexanchiformes, Squatiniformes, Squaliformes, and Pristiophoriformes are broadly monophyletic, with minor exceptions apparently due to missing data. Similarly, within Galeomorphs, the orders Heterodontiformes, Lamniformes, Carcharhiniformes, and Orectolobiformes are broadly monophyletic, with a couple of species 'misplaced'. In contrast, many of the currently recognized shark families are not monophyletic according to our results. Our phylogeny offers some of the first clarification of the relationships among families of the order Squaliformes, a group that has thus far received relatively little phylogenetic attention. Our results suggest that the genus Echinorhinus is not a squaliform, but rather related to the saw sharks, a hypothesis that might be supported by both groups sharing 'spiny' snouts. In sum, our results offer the most detailed species-level phylogeny of sharks to date and a tool for comparative analyses.}, } @article {pmid21125307, year = {2010}, author = {McKenzie, VJ and Goulet, NE}, title = {Bird community composition linked to human West Nile virus cases along the Colorado front range.}, journal = {EcoHealth}, volume = {7}, number = {4}, pages = {439-447}, pmid = {21125307}, issn = {1612-9210}, mesh = {Altitude ; Animals ; Bird Diseases/epidemiology/transmission/virology ; Birds/classification/virology ; Colorado/epidemiology ; Crows/virology ; Culicidae/*virology ; Databases, Factual ; Disease Reservoirs/veterinary/virology ; Ecosystem ; Environmental Health ; Humans ; Insect Vectors/*virology ; Linear Models ; Public Health/statistics & numerical data ; Risk Assessment/methods ; Songbirds/virology ; Species Specificity ; West Nile Fever/epidemiology/*transmission/virology ; West Nile virus/*isolation & purification ; }, abstract = {In the present study, we examined whether bird community composition can predict the annual number of human West Nile virus (WNV) cases on a per county basis in the Colorado Front Range, a region that experienced high numbers of human cases during the early part of the North American epidemic. We analyzed data sets pertaining to birds and human WNV cases from multiple existing databases between the years 2002 and 2008. Based on previous studies that used amplification fractions to compare the relative competence of different bird species, ten bird species that are common in Colorado were selected and categorized as high amplification birds, such as the American Robin (Turdus migratorius), or low amplification birds, such as the American Crow (Corvus brachyrhynchos). A general linear modeling analysis was used with an information theoretic (AIC) model sorting approach to examine which of the models best predicted the number of human WNV cases per county. Candidate models included year as a covariate and one of several bird community descriptors (e.g., richness, diversity, total bird abundance, high amplification abundance, or low amplification abundance). Results demonstrated that high amplification birds were a significant predictor of human WNV cases between 2002 and 2008. Our results suggest that a small subset of the bird community with high amplification fractions may drive the dynamics of human disease risk for West Nile. This study has implications for surveillance of West Nile and may offer insight into disease risk associated with other vector-borne zoonotic diseases.}, } @article {pmid21121040, year = {2011}, author = {Bunge, J}, title = {Estimating the number of species with CatchAll.}, journal = {Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing}, volume = {}, number = {}, pages = {121-130}, doi = {10.1142/9789814335058_0014}, pmid = {21121040}, issn = {2335-6936}, mesh = {Algorithms ; *Biodiversity ; Computational Biology ; Databases, Factual/statistics & numerical data ; Ecosystem ; Finite Element Analysis ; Likelihood Functions ; Models, Statistical ; Seawater/microbiology ; *Software ; Species Specificity ; Statistics, Nonparametric ; }, abstract = {In many situations we are faced with the need to estimate the number of classes in a population from observed count data: this arises not only in biology, where we are interested in the number of taxa such as species, but also in many other fields such as public health, criminal justice, software engineering, etc. This problem has a rich history in theoretical statistics, dating back at least to 1943, and many approaches have been proposed and studied. However, to date only one approach has been implemented in readily available software, namely a relatively simple nonparametric method which, while straightforward to program, is not flexible and can be prone to information loss. Here we present CatchAll, a new, platform-independent, user-friendly, computationally optimized software package which calculates a powerful and flexible suite of parametric models (based on current statistical research) in addition to all existing nonparametric procedures. We briefly describe the software and its mathematical underpinnings (which are treated in depth elsewhere), and we work through an applied example from microbial ecology in detail.}, } @article {pmid21114113, year = {2010}, author = {Forkuo, EK}, title = {Digital elevation modelling using ASTER stereo imagery.}, journal = {Journal of environmental science & engineering}, volume = {52}, number = {2}, pages = {81-92}, pmid = {21114113}, mesh = {Altitude ; Ecology/*statistics & numerical data ; Engineering ; Geographic Information Systems/*statistics & numerical data ; Geography/*statistics & numerical data ; Maps as Topic ; Models, Statistical ; }, abstract = {Digital elevation model (DEM) in recent times has become an integral part of national spatial data infrastructure of many countries world-wide due to its invaluable importance. Although DEMs are mostly generated from contours maps, stereo aerial photographs and air-borne and terrestrial laser scanning, the stereo interpretation and auto-correlation from satellite image stereo-pairs such as with SPOT, IRS, and relatively new ASTER imagery is also an effective means of producing DEM data. In this study, terrain elevation data were derived by applying photogrammetric process to ASTER stereo imagery. Also, the quality ofDEMs produced from ASTER stereo imagery was analysed by comparing it with DEM produced from topographic map at a scale of 1:50,000. While analyzing the vertical accuracy of the generated ASTER DEM, fifty ground control points were extracted from the map and overlaid on the DEM. Results indicate that a root-mean-square error in elevation of +/- 14 m was achieved with ASTER stereo image data of good quality. The horizontal accuracy obtained from the ground control points was 14.77, which is within the acceptable range of +/- 7m to +/- 25 m. The generated (15 m) DEM was compared with a 20m, 25m, and a 30 m pixel DEM to the original map. In all, the results proved that, the 15 m DEM conform to the original map DEM than the others. Overall, this analysis proves that, the generated digital terrain model, DEM is acceptable.}, } @article {pmid21108798, year = {2010}, author = {Browne, P and Barret, M and O'Gara, F and Morrissey, JP}, title = {Computational prediction of the Crc regulon identifies genus-wide and species-specific targets of catabolite repression control in Pseudomonas bacteria.}, journal = {BMC microbiology}, volume = {10}, number = {}, pages = {300}, pmid = {21108798}, issn = {1471-2180}, mesh = {Bacterial Proteins/genetics/*metabolism ; *Catabolite Repression ; *Computational Biology ; *Gene Expression Regulation, Bacterial ; Pseudomonas/chemistry/classification/genetics/*metabolism ; *Regulon ; Repressor Proteins/genetics/*metabolism ; }, abstract = {BACKGROUND: Catabolite repression control (CRC) is an important global control system in Pseudomonas that fine tunes metabolism in order optimise growth and metabolism in a range of different environments. The mechanism of CRC in Pseudomonas spp. centres on the binding of a protein, Crc, to an A-rich motif on the 5' end of an mRNA resulting in translational down-regulation of target genes. Despite the identification of several Crc targets in Pseudomonas spp. the Crc regulon has remained largely unexplored.

RESULTS: In order to predict direct targets of Crc, we used a bioinformatics approach based on detection of A-rich motifs near the initiation of translation of all protein-encoding genes in twelve fully sequenced Pseudomonas genomes. As expected, our data predict that genes related to the utilisation of less preferred nutrients, such as some carbohydrates, nitrogen sources and aromatic carbon compounds are targets of Crc. A general trend in this analysis is that the regulation of transporters is conserved across species whereas regulation of specific enzymatic steps or transcriptional activators are often conserved only within a species. Interestingly, some nucleoid associated proteins (NAPs) such as HU and IHF are predicted to be regulated by Crc. This finding indicates a possible role of Crc in indirect control over a subset of genes that depend on the DNA bending properties of NAPs for expression or repression. Finally, some virulence traits such as alginate and rhamnolipid production also appear to be regulated by Crc, which links nutritional status cues with the regulation of virulence traits.

CONCLUSIONS: Catabolite repression control regulates a broad spectrum of genes in Pseudomonas. Some targets are genus-wide and are typically related to central metabolism, whereas other targets are species-specific, or even unique to particular strains. Further study of these novel targets will enhance our understanding of how Pseudomonas bacteria integrate nutritional status cues with the regulation of traits that are of ecological, industrial and clinical importance.}, } @article {pmid21104144, year = {2011}, author = {Mani, I and Kumar, R and Singh, M and Nagpure, NS and Kushwaha, B and Srivastava, PK and Rao, DS and Lakra, WS}, title = {Nucleotide variation and physical mapping of ribosomal genes using FISH in genus Tor (Pisces, Cyprinidae).}, journal = {Molecular biology reports}, volume = {38}, number = {4}, pages = {2637-2647}, pmid = {21104144}, issn = {1573-4978}, mesh = {Animals ; Chromomycin A3 ; Computational Biology ; Cyprinidae/*genetics ; DNA Primers/genetics ; DNA, Ribosomal/*genetics ; Fluorescent Dyes ; *Genetic Variation ; In Situ Hybridization, Fluorescence ; Microscopy, Fluorescence ; *Physical Chromosome Mapping ; Sequence Analysis, DNA ; Silver Staining ; Species Specificity ; }, abstract = {Molecular cytogenetic studies were carried out for localization of 18S and 5S ribosomal DNAs on chromosomes of three cyprinid fish species viz., T. khudree, T. mussullah and T. mosal mahanadicus using two color fluorescence in situ hybridization (FISH). All the species typically possessed 100 diploid chromosomes with minor variation in karyo-morphology. The 18S rDNA signals were observed on two pair of chromosomes in T. khudree and T. mussullah, and three pairs in T. mosal mahanadicus. The location of 18S signals also showed affinity to silver nitrate and chromomycin A3 staining. Similarly, variation in localization of 5S rDNA among the three species has been detected with the presence of FISH signals on one pair of chromosome in T. khudree and T. mussullah, and on two pairs in T. mosal mahanadicus. These molecular markers could be used as species specific markers for taxonomic identification and can further add in understanding the dynamics of genome organization and karyotypic evolution of these species. The 18S rDNA region was sequenced that generated 1811, 1810 and 1776 bp long 18S sequence in T. khudree, T. mussullah and T. mosal mahanadicus, respectively. The 18S rDNA sequence showed 95-98% identity among the subject species. Similarly, 5S sequencing generated 203 bp long fragments in these species with 100% identity in coding and 9.63% variability in non-transcribed spacer regions. The nucleotide sequence variations could be used for understanding the genetic diversity and will add new informative characters in comparative genomics. These results, in general, would enhance the value and interpretation of ecological assessment data for conservation of Tor species.}, } @article {pmid21098721, year = {2011}, author = {Bullaughey, K}, title = {Changes in selective effects over time facilitate turnover of enhancer sequences.}, journal = {Genetics}, volume = {187}, number = {2}, pages = {567-582}, pmid = {21098721}, issn = {1943-2631}, support = {R01 GM072861/GM/NIGMS NIH HHS/United States ; GM72861/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Computational Biology ; Drosophila/*genetics ; *Enhancer Elements, Genetic ; *Evolution, Molecular ; Gene Expression Profiling ; Genetic Drift ; Models, Genetic ; Mutation ; Selection, Genetic/*genetics ; }, abstract = {Correct gene expression is often critical and consequently stabilizing selection on expression is widespread. Yet few genes possess highly conserved regulatory DNA, and for the few enhancers that have been carefully characterized, substantial functional reorganization has often occurred. Given that natural selection removes mutations of even very small deleterious effect, how can transcription factor binding evolve so readily when it underlies a conserved phenotype? As a first step toward addressing this question, I combine a computational model for regulatory function that incorporates many aspects of our present biological knowledge with a model for the fitness effects of misexpression. I then use this model to study the evolution of enhancers. Several robust behaviors emerge: First, the selective effects of mutations at a site change dramatically over time due to substitutions elsewhere in the enhancer, and even the overall degree of constraint across the enhancer can change considerably. Second, many of the substitutions responsible for changes in binding occur at sites where previously the mutation would have been strongly deleterious, suggesting that fluctuations in selective effects at a site are important for functional turnover. Third, most substitutions contributing to the repatterning of binding and constraint are effectively neutral, highlighting the importance of genetic drift-even for enhancers underlying conserved phenotypes. These findings have important implications for phylogenetic inference of function and for interpretations of selection coefficients estimated for regulatory DNA.}, } @article {pmid21095920, year = {2010}, author = {Artemiadis, PK and Krebs, HI}, title = {On the control of the MIT-skywalker.}, journal = {Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference}, volume = {2010}, number = {}, pages = {1287-1291}, doi = {10.1109/IEMBS.2010.5626407}, pmid = {21095920}, issn = {2375-7477}, mesh = {Biofeedback, Psychology/*instrumentation ; Computer-Aided Design ; Equipment Design ; Equipment Failure Analysis ; Exercise Test/*instrumentation ; Feedback ; Gait Disorders, Neurologic/*rehabilitation ; Humans ; Physical Therapy Modalities/*instrumentation ; Robotics/*instrumentation ; Therapy, Computer-Assisted/*instrumentation ; }, abstract = {Walking impairments are a common sequela of neurological injury, severely affecting the quality of life of both adults and children. Gait therapy is the traditional approach to ameliorate the problem by re-training the nervous system and there have been some attempts to mechanize such approach. In this paper, we present a novel device to deliver gait therapy, which, in contrast to previous approaches, takes advantage of the concept of passive walkers and the natural dynamics of the lower extremity in order to deliver more "ecological" therapy. We also discuss the closed-loop control scheme, which enables safe and efficient operation of the device, and present the initial feasibility tests with unimpaired subjects.}, } @article {pmid21093016, year = {2011}, author = {Henegar, A and Mombelli, E and Pandard, P and Péry, AR}, title = {What can be learnt from an ecotoxicity database in the framework of the REACh regulation?.}, journal = {The Science of the total environment}, volume = {409}, number = {3}, pages = {489-494}, doi = {10.1016/j.scitotenv.2010.10.028}, pmid = {21093016}, issn = {1879-1026}, mesh = {Animals ; Chlorophyta/drug effects ; Daphnia/drug effects ; *Databases as Topic ; Ecotoxicology ; Education ; Environmental Policy ; Environmental Pollutants/toxicity ; Environmental Pollution/*legislation & jurisprudence ; European Union ; Fishes ; Food Chain ; Quantitative Structure-Activity Relationship ; Sensitivity and Specificity ; Toxicity Tests/*methods ; }, abstract = {Since REACh applies in all of EU, special emphasis has been put on the reduction of systematic ecotoxicity testing. In this context, it is important to extract a maximum of information from existing ecotoxicity databases in order to propose alternative methods aimed at replacing and reducing experimental testing. Consequently, we analyzed a database of new chemicals registered in France and Europe during the last twenty years reporting aquatic ecotoxicity data with respect to three trophic levels (i.e., Algae EC50 72 h, Daphnia EC50 48 h and Fish LC50 96 h). In order to ensure the relevance of the comparison between these three experimental tests, we performed a stringent data selection based on the pertinence and quality of available ecotoxicological information. At the end of this selection, less than 5% of the initial number of chemicals was retained for subsequent analysis. Such an analysis showed that fish was the least sensitive trophic level, whereas Daphnia had the highest sensitivity. Moreover, thanks to an analysis of the relative sensitivity of trophic levels, it was possible to establish that respective correction factors of 50 and 10 would be necessary if only one or two test values were available. From a physicochemical point of view, it was possible to characterize two significant correlations relating the sensitivity of the aforementioned trophic levels with the chemical structure of the retained substances. This analysis showed that algae displayed a higher sensitivity towards chemicals containing acid fragments whereas fish presented a higher sensitivity towards chemicals containing aromatic ether fragments. Overall, our work suggests that statistical analysis of historical data combined with data yielded by the REACh regulation should permit the derivation of robust safety factors, testing strategies and mathematical models. These alternative methods, in turn, could allow a replacement and reduction of ecotoxicological testing.}, } @article {pmid21092232, year = {2010}, author = {Ueno, S and Le Provost, G and Léger, V and Klopp, C and Noirot, C and Frigerio, JM and Salin, F and Salse, J and Abrouk, M and Murat, F and Brendel, O and Derory, J and Abadie, P and Léger, P and Cabane, C and Barré, A and de Daruvar, A and Couloux, A and Wincker, P and Reviron, MP and Kremer, A and Plomion, C}, title = {Bioinformatic analysis of ESTs collected by Sanger and pyrosequencing methods for a keystone forest tree species: oak.}, journal = {BMC genomics}, volume = {11}, number = {}, pages = {650}, pmid = {21092232}, issn = {1471-2164}, mesh = {Base Sequence ; Cluster Analysis ; Computational Biology/*methods ; Contig Mapping ; *Expressed Sequence Tags ; Gene Library ; Genes, Plant/genetics ; Microsatellite Repeats/genetics ; Peptides/genetics ; Polymorphism, Single Nucleotide/genetics ; Quercus/*genetics ; RNA, Messenger/genetics/metabolism ; Sequence Analysis, DNA/*methods ; Sequence Homology, Nucleic Acid ; Software ; Species Specificity ; *Temperature ; Trees/*genetics ; }, abstract = {BACKGROUND: The Fagaceae family comprises about 1,000 woody species worldwide. About half belong to the Quercus family. These oaks are often a source of raw material for biomass wood and fiber. Pedunculate and sessile oaks, are among the most important deciduous forest tree species in Europe. Despite their ecological and economical importance, very few genomic resources have yet been generated for these species. Here, we describe the development of an EST catalogue that will support ecosystem genomics studies, where geneticists, ecophysiologists, molecular biologists and ecologists join their efforts for understanding, monitoring and predicting functional genetic diversity.

RESULTS: We generated 145,827 sequence reads from 20 cDNA libraries using the Sanger method. Unexploitable chromatograms and quality checking lead us to eliminate 19,941 sequences. Finally a total of 125,925 ESTs were retained from 111,361 cDNA clones. Pyrosequencing was also conducted for 14 libraries, generating 1,948,579 reads, from which 370,566 sequences (19.0%) were eliminated, resulting in 1,578,192 sequences. Following clustering and assembly using TGICL pipeline, 1,704,117 EST sequences collapsed into 69,154 tentative contigs and 153,517 singletons, providing 222,671 non-redundant sequences (including alternative transcripts). We also assembled the sequences using MIRA and PartiGene software and compared the three unigene sets. Gene ontology annotation was then assigned to 29,303 unigene elements. Blast search against the SWISS-PROT database revealed putative homologs for 32,810 (14.7%) unigene elements, but more extensive search with Pfam, Refseq_protein, Refseq_RNA and eight gene indices revealed homology for 67.4% of them. The EST catalogue was examined for putative homologs of candidate genes involved in bud phenology, cuticle formation, phenylpropanoids biosynthesis and cell wall formation. Our results suggest a good coverage of genes involved in these traits. Comparative orthologous sequences (COS) with other plant gene models were identified and allow to unravel the oak paleo-history. Simple sequence repeats (SSRs) and single nucleotide polymorphisms (SNPs) were searched, resulting in 52,834 SSRs and 36,411 SNPs. All of these are available through the Oak Contig Browser http://genotoul-contigbrowser.toulouse.inra.fr:9092/Quercus_robur/index.html.

CONCLUSIONS: This genomic resource provides a unique tool to discover genes of interest, study the oak transcriptome, and develop new markers to investigate functional diversity in natural populations.}, } @article {pmid21090508, year = {2010}, author = {Kang, YJ and Cheng, J and Mei, LJ and Hu, J and Piao, Z and Yin, SX}, title = {Multiple copies of 16s rRNA gene affect the restriction patterns and DGGE profile as revealed by analysis of genome database.}, journal = {Mikrobiologiia}, volume = {79}, number = {5}, pages = {664-671}, pmid = {21090508}, issn = {0026-3656}, mesh = {Bacteria/*genetics/isolation & purification ; Databases, Genetic ; *Denaturing Gradient Gel Electrophoresis ; *Gene Dosage ; *Genes, rRNA ; Genome, Bacterial ; *Polymorphism, Restriction Fragment Length ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/*genetics ; Sensitivity and Specificity ; }, abstract = {The use of 16S rRNA gene has been a "golden" method to determine the diversity of microbial communities in environmental samples, phylogenetic relationships of prokaryotes and taxonomic position of newly isolated organisms. However due to the presence of multiple heterogeneous 16S rRNA gene copies in many strains, the interpretation of microbial ecology via 16S rRNA sequences is complicated. Purpose of present paper is to demonstrate the extent to which the multiple heterogeneous 16S rRNA gene copies affect RFLP patterns and DGG E profiles by using the genome database. In present genome database, there are 782 bacterial strains in total whose genomes have been completely sequenced and annotated. Among the total strains, 639 strains (82%) possess multiple 16S rRNA gene copies, 415 strains (53%) whose multiple copies are heterogeneous in sequences as revealed by alignment, 236 strains (30%) whose multiple copies show different restrict patterns by CSP61 + Hinfl, MspI + Rsal or HhaI as analyzed in silico. Polymorphisms of the multiple copies in certain strains were further characterized by G + C% and phylogentic distances based on the sequences of V3 region, which are linked to DGGE patters. Polymorphisms of a few strains were shown as examples. Using artificial communities, it is demonstrated that the presence of multiple heterogeneous 16S rRNA gene copies potentially leads to over-estimation of the diversity of a community. It is suggested that care must be taken when interpreting 16S rRNA-based RFLP and DGGE data and profiling an environmental community.}, } @article {pmid21085582, year = {2010}, author = {Stern, RF and Horak, A and Andrew, RL and Coffroth, MA and Andersen, RA and Küpper, FC and Jameson, I and Hoppenrath, M and Véron, B and Kasai, F and Brand, J and James, ER and Keeling, PJ}, title = {Environmental barcoding reveals massive dinoflagellate diversity in marine environments.}, journal = {PloS one}, volume = {5}, number = {11}, pages = {e13991}, pmid = {21085582}, issn = {1932-6203}, mesh = {Animals ; Atlantic Ocean ; *Biodiversity ; Caribbean Region ; Cluster Analysis ; DNA, Mitochondrial/chemistry/genetics ; Databases, Nucleic Acid ; Dinoflagellida/classification/*genetics/*growth & development ; Electron Transport Complex IV/genetics ; *Genetic Variation ; Molecular Sequence Data ; Pacific Ocean ; Phylogeny ; Protozoan Proteins/genetics ; Seawater/microbiology ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {BACKGROUND: Dinoflagellates are an ecologically important group of protists with important functions as primary producers, coral symbionts and in toxic red tides. Although widely studied, the natural diversity of dinoflagellates is not well known. DNA barcoding has been utilized successfully for many protist groups. We used this approach to systematically sample known "species", as a reference to measure the natural diversity in three marine environments.

In this study, we assembled a large cytochrome c oxidase 1 (COI) barcode database from 8 public algal culture collections plus 3 private collections worldwide resulting in 336 individual barcodes linked to specific cultures. We demonstrate that COI can identify to the species level in 15 dinoflagellate genera, generally in agreement with existing species names. Exceptions were found in species belonging to genera that were generally already known to be taxonomically challenging, such as Alexandrium or Symbiodinium. Using this barcode database as a baseline for cultured dinoflagellate diversity, we investigated the natural diversity in three diverse marine environments (Northeast Pacific, Northwest Atlantic, and Caribbean), including an evaluation of single-cell barcoding to identify uncultivated groups. From all three environments, the great majority of barcodes were not represented by any known cultured dinoflagellate, and we also observed an explosion in the diversity of genera that previously contained a modest number of known species, belonging to Kareniaceae. In total, 91.5% of non-identical environmental barcodes represent distinct species, but only 51 out of 603 unique environmental barcodes could be linked to cultured species using a conservative cut-off based on distances between cultured species.

CONCLUSIONS/SIGNIFICANCE: COI barcoding was successful in identifying species from 70% of cultured genera. When applied to environmental samples, it revealed a massive amount of natural diversity in dinoflagellates. This highlights the extent to which we underestimate microbial diversity in the environment.}, } @article {pmid21083923, year = {2010}, author = {Tuck, DP and Miranker, W}, title = {Modeling the clonal heterogeneity of stem cells.}, journal = {Theoretical biology & medical modelling}, volume = {7}, number = {}, pages = {44}, pmid = {21083923}, issn = {1742-4682}, mesh = {Clone Cells/cytology ; Computer Simulation ; Humans ; *Models, Biological ; Stem Cells/*cytology ; }, abstract = {Recent experimental studies suggest that tissue stem cell pools are composed of functionally diverse clones. Metapopulation models in ecology concentrate on collections of populations and their role in stabilizing coexistence and maintaining selected genetic or epigenetic variation. Such models are characterized by expansion and extinction of spatially distributed populations. We develop a mathematical framework derived from the multispecies metapopulation model of Tilman et al (1994) to study the dynamics of heterogeneous stem cell metapopulations. In addition to normal stem cells, the model can be applied to cancer cell populations and their response to treatment. In our model disturbances may lead to expansion or contraction of cells with distinct properties, reflecting proliferation, apoptosis, and clonal competition. We first present closed-form expressions for the basic model which defines clonal dynamics in the presence of exogenous global disturbances. We then extend the model to include disturbances which are periodic and which may affect clones differently. Within the model framework, we propose a method to devise an optimal strategy of treatments to regulate expansion, contraction, or mutual maintenance of cells with specific properties.}, } @article {pmid21080328, year = {2010}, author = {Livingston, M}, title = {The ecology of domestic violence: the role of alcohol outlet density.}, journal = {Geospatial health}, volume = {5}, number = {1}, pages = {139-149}, doi = {10.4081/gh.2010.194}, pmid = {21080328}, issn = {1970-7096}, mesh = {Alcohol Drinking/*economics/epidemiology ; Commerce/*economics/statistics & numerical data ; Confidence Intervals ; Cross-Sectional Studies ; Demography ; Domestic Violence/*statistics & numerical data ; Ethanol/economics/*supply & distribution ; Geographic Information Systems ; Humans ; Income/statistics & numerical data ; Linear Models ; Models, Statistical ; Risk Assessment ; Socioeconomic Factors ; Statistics as Topic ; Victoria/epidemiology ; }, abstract = {Studies have consistently found positive associations between the density of alcohol outlets and levels of violence in areas. Few studies have examined whether this relationship holds for domestic violence. This study assesses whether alcohol outlet density is related to domestic violence and whether this relationship is due to alcohol availability or to co-occurring economic disadvantage and social disorganisation. Cross-sectional data on family incidents, liquor outlets and socio-demographic characteristics were obtained for 217 postcodes in Melbourne, Australia. These data were used to construct models assessing the association between alcohol outlet density and domestic violence, both with and without controlling for socio-demographic factors. Models were tested for spatial autocorrelation, and spatial- error models were developed to control for its influence. Outlet density was significantly associated with rates of domestic violence, even controlling for socio-demographic factors. The density of hotels (pubs) was positively associated with domestic violence rates and the density of restaurants and bars was negatively associated with domestic violence. Socio-economic disadvantage was also associated with domestic violence rates. The density of packaged liquor outlets was not associated with rates of domestic violence. The results present a mixed picture, and further study is required to develop a clearer understanding of the links between alcohol availability and domestic violence.}, } @article {pmid21080322, year = {2010}, author = {Salahi-Moghaddam, A and Mohebali, M and Moshfae, A and Habibi, M and Zarei, Z}, title = {Ecological study and risk mapping of visceral leishmaniasis in an endemic area of Iran based on a geographical information systems approach.}, journal = {Geospatial health}, volume = {5}, number = {1}, pages = {71-77}, doi = {10.4081/gh.2010.188}, pmid = {21080322}, issn = {1970-7096}, mesh = {Analysis of Variance ; Animals ; *Climate ; Cross-Sectional Studies ; Dogs ; Ecosystem ; *Geographic Information Systems ; Geography ; Humans ; Humidity ; Iran/epidemiology ; Leishmaniasis, Visceral/*epidemiology/transmission ; Regression Analysis ; Risk Assessment/methods ; Risk Factors ; Rural Population ; Statistics as Topic ; Temperature ; }, abstract = {Between 1998 and 2001, a total of 1,062 human cases of visceral leishmaniasis were reported from the rural district of Meshkin-Shahr in the mountainous, north-western Iranian province of Ardabil. In the summer of 2008, a cross-sectional study of dogs was conducted in this endemic area by randomly selecting 384 animals from 21 villages and testing them serologically for leishmaniasis. Villages, in which more than 10% of investigated dogs showed anti- Leishmania titres ≥ 1/320, were considered to be high-risk environments. Regression analysis showed no statistically significant correlation between topographic conditions and the prevalence of positive cases. However, when the results were compared with past meteorological records, a statistically significant positive correlation (P = 0.007) was found between the number of infected dogs with anti-Leishmania titres ≥ 1/640 and the number of days in a year with temperatures below 0 °C. While humidity showed an inverse correlation (P = 0.009) with the anti-Leishmania titres, a positive correlation (P <0.001) was found in relation to the amount of rainfall. Mapping of the areas at risk for kala-azar in the Meshkin-Shahr district supports the impression that the low temperatures prevalent in the Ardebil province constitute an important factor influencing the distribution of leishmaniasis there.}, } @article {pmid21080319, year = {2010}, author = {Kakani, S and LaBeaud, AD and King, CH}, title = {Planning for Rift Valley fever virus: use of geographical information systems to estimate the human health threat of white-tailed deer (Odocoileus virginianus)-related transmission.}, journal = {Geospatial health}, volume = {5}, number = {1}, pages = {33-43}, pmid = {21080319}, issn = {1970-7096}, support = {U01 AI045473/AI/NIAID NIH HHS/United States ; U01 AI045473-04/AI/NIAID NIH HHS/United States ; U54 AI057160/AI/NIAID NIH HHS/United States ; U01 AI45473-S1/AI/NIAID NIH HHS/United States ; }, mesh = {Aerosols ; Animals ; Bioterrorism ; *Culicidae ; Deer/*parasitology ; Disease Outbreaks/statistics & numerical data ; Disease Reservoirs ; Epidemiologic Methods ; Geographic Information Systems/*instrumentation ; Humans ; Insect Vectors/*parasitology ; New England/epidemiology ; Rift Valley Fever/epidemiology/*transmission ; Risk Assessment/methods ; Zoonoses/epidemiology/*transmission ; }, abstract = {Rift Valley fever (RVF) virus is a mosquito-borne phlebovirus of the Bunyaviridae family that causes frequent outbreaks of severe animal and human disease in sub-Saharan Africa, Egypt and the Arabian Peninsula. Based on its many known competent vectors, its potential for transmission via aerosolization, and its progressive spread from East Africa to neighbouring regions, RVF is considered a high-priority, emerging health threat for humans, livestock and wildlife in all parts of the world. Introduction of West Nile virus to North America has shown the potential for "exotic" viral pathogens to become embedded in local ecological systems. While RVF is known to infect and amplify within domestic livestock, such as taurine cattle, sheep and goats, if RVF virus is accidentally or intentionally introduced into North America, an important unknown factor will be the role of local wildlife in the maintenance or propagation of virus transmission. We examined the potential impact of RVF transmission via white-tailed deer (Odocoileus virginianus) in a typical north-eastern United States urban-suburban landscape, where livestock are rare but where these potentially susceptible, ungulate wildlife are highly abundant. Model results, based on overlap of mosquito, human and projected deer densities, indicate that a significant proportion (497/1186 km(2), i.e. 42%) of the urban and peri-urban landscape could be affected by RVF transmission during the late summer months. Deer population losses, either by intervention for herd reduction or by RVF-related mortality, would substantially reduce these likely transmission zones to 53.1 km(2), i.e. by 89%.}, } @article {pmid21078327, year = {2011}, author = {Terenius, O and Papanicolaou, A and Garbutt, JS and Eleftherianos, I and Huvenne, H and Kanginakudru, S and Albrechtsen, M and An, C and Aymeric, JL and Barthel, A and Bebas, P and Bitra, K and Bravo, A and Chevalier, F and Collinge, DP and Crava, CM and de Maagd, RA and Duvic, B and Erlandson, M and Faye, I and Felföldi, G and Fujiwara, H and Futahashi, R and Gandhe, AS and Gatehouse, HS and Gatehouse, LN and Giebultowicz, JM and Gómez, I and Grimmelikhuijzen, CJ and Groot, AT and Hauser, F and Heckel, DG and Hegedus, DD and Hrycaj, S and Huang, L and Hull, JJ and Iatrou, K and Iga, M and Kanost, MR and Kotwica, J and Li, C and Li, J and Liu, J and Lundmark, M and Matsumoto, S and Meyering-Vos, M and Millichap, PJ and Monteiro, A and Mrinal, N and Niimi, T and Nowara, D and Ohnishi, A and Oostra, V and Ozaki, K and Papakonstantinou, M and Popadic, A and Rajam, MV and Saenko, S and Simpson, RM and Soberón, M and Strand, MR and Tomita, S and Toprak, U and Wang, P and Wee, CW and Whyard, S and Zhang, W and Nagaraju, J and Ffrench-Constant, RH and Herrero, S and Gordon, K and Swevers, L and Smagghe, G}, title = {RNA interference in Lepidoptera: an overview of successful and unsuccessful studies and implications for experimental design.}, journal = {Journal of insect physiology}, volume = {57}, number = {2}, pages = {231-245}, doi = {10.1016/j.jinsphys.2010.11.006}, pmid = {21078327}, issn = {1879-1611}, mesh = {Animals ; Databases, Genetic ; Epidermis/growth & development ; *Gene Expression Regulation ; Gene Silencing ; Immunity, Innate ; Insect Proteins/drug effects/genetics/immunology ; Lepidoptera/drug effects/*genetics/growth & development/*immunology ; *RNA Interference ; RNA, Double-Stranded/drug effects ; Research Design ; }, abstract = {Gene silencing through RNA interference (RNAi) has revolutionized the study of gene function, particularly in non-model insects. However, in Lepidoptera (moths and butterflies) RNAi has many times proven to be difficult to achieve. Most of the negative results have been anecdotal and the positive experiments have not been collected in such a way that they are possible to analyze. In this review, we have collected detailed data from more than 150 experiments including all to date published and many unpublished experiments. Despite a large variation in the data, trends that are found are that RNAi is particularly successful in the family Saturniidae and in genes involved in immunity. On the contrary, gene expression in epidermal tissues seems to be most difficult to silence. In addition, gene silencing by feeding dsRNA requires high concentrations for success. Possible causes for the variability of success in RNAi experiments in Lepidoptera are discussed. The review also points to a need to further investigate the mechanism of RNAi in lepidopteran insects and its possible connection to the innate immune response. Our general understanding of RNAi in Lepidoptera will be further aided in the future as our public database at http://insectacentral.org/RNAi will continue to gather information on RNAi experiments.}, } @article {pmid21076313, year = {2011}, author = {Graves, BA}, title = {Geographic analysis of cardiac interventional services in Alabama.}, journal = {The Journal of cardiovascular nursing}, volume = {26}, number = {4}, pages = {E1-11}, doi = {10.1097/JCN.0b013e3181ecaacb}, pmid = {21076313}, issn = {1550-5049}, mesh = {Adult ; Black or African American ; Aged ; Alabama ; Cardiac Care Facilities/*supply & distribution ; Female ; Geographic Information Systems ; *Health Services Accessibility ; *Healthcare Disparities ; Humans ; Male ; Myocardial Infarction/*therapy ; Poverty Areas ; *Residence Characteristics ; Small-Area Analysis ; Time Factors ; }, abstract = {BACKGROUND: Cardiovascular disease is the leading cause of death in the state of Alabama. The purpose of this study was to explore the geographical accessibility of the Alabama population to cardiac interventional services (CISs) for the treatment of acute myocardial infarction.

METHODS: A descriptive ecological study design was used. Census tract-level population census data were used to describe access to CIS in Alabama. Descriptive analysis was conducted within a geographical information system (GIS) and provided empirical measures of travel time, calculated population proportions, and generated maps for visual identification of areas of low access. Descriptive statistics are reported as proportions (percentages) of the population with access by travel time.

FINDINGS: The GIS analysis revealed that 58.2%, 85.9%, and 96.0% of the total Alabama population were within 30-, 60-, or 90-minute travel time, respectively, of a hospital with CIS. Maps provided visualization of CIS coverage areas for Alabama. One distinct area within the Alabama Black Belt was at greater than 90 minutes from a hospital with CIS. This area is known as a mostly black, impoverished population subject to health disparities.

CONCLUSIONS: The GIS showed that 96% of the Alabama population is within 90-minute travel time of a hospital with CIS. For the best outcomes to occur allowing adequate time for symptom recognition, travel time, and 30-minute door-to-needle time, only 85.9% and 58.2% are within 60- and 30-minute travel time, respectively.}, } @article {pmid21075411, year = {2011}, author = {Luque Fernández, MÁ and Mason, PR and Gray, H and Bauernfeind, A and Fesselet, JF and Maes, P}, title = {Descriptive spatial analysis of the cholera epidemic 2008-2009 in Harare, Zimbabwe: a secondary data analysis.}, journal = {Transactions of the Royal Society of Tropical Medicine and Hygiene}, volume = {105}, number = {1}, pages = {38-45}, doi = {10.1016/j.trstmh.2010.10.001}, pmid = {21075411}, issn = {1878-3503}, mesh = {Adolescent ; Adult ; Child ; Child, Preschool ; Cholera/*epidemiology/transmission ; Disease Outbreaks/*statistics & numerical data ; Female ; Geographic Information Systems ; Humans ; Incidence ; Infant ; Infant, Newborn ; Male ; Middle Aged ; Poisson Distribution ; Population Surveillance ; Regression Analysis ; Risk Factors ; Sanitation/*standards ; Space-Time Clustering ; Young Adult ; Zimbabwe/epidemiology ; }, abstract = {This ecological study describes the cholera epidemic in Harare during 2008-2009 and identifies patterns that may explain transmission. Rates ratios of cholera cases by suburb were calculated by a univariate regression Poisson model and then, through an Empirical Bayes modelling, smoothed rate ratios were estimated and represented geographically. Mbare and southwest suburbs of Harare presented higher rate ratios. Suburbs attack rates ranged from 1.2 (95% Cl = 0.7-1.6) cases per 1000 people in Tynwald to 90.3 (95% Cl = 82.8-98.2) in Hopley. The identification of this spatial pattern in the spread, characterised by low risk in low density residential housing, and a higher risk in high density south west suburbs and Mbare, could be used to advocate for improving water and sanitation conditions and specific preparedness measures in the most affected areas.}, } @article {pmid21072840, year = {2011}, author = {Garcia-Reyero, N and Perkins, EJ}, title = {Systems biology: leading the revolution in ecotoxicology.}, journal = {Environmental toxicology and chemistry}, volume = {30}, number = {2}, pages = {265-273}, doi = {10.1002/etc.401}, pmid = {21072840}, issn = {1552-8618}, mesh = {Animals ; Computational Biology/*methods/trends ; Ecotoxicology/*methods/trends ; Hydrobiology/methods/trends ; Systems Biology/*methods/trends ; }, abstract = {The rapid development of new technologies such as transcriptomics, proteomics, and metabolomics (Omics) are changing the way ecotoxicology is practiced. The data deluge has begun with genomes of over 65 different aquatic species that are currently being sequenced, and many times that number with at least some level of transcriptome sequencing. Integrating these top-down methodologies is an essential task in the field of systems biology. Systems biology is a biology-based interdisciplinary field that focuses on complex interactions in biological systems, with the intent to model and discover emergent properties of the system. Recent studies demonstrate that Omics technologies provide valuable insight into ecotoxicity, both in laboratory exposures with model organisms and with animals exposed in the field. However, these approaches require a context of the whole animal and population to be relevant. Powerful approaches using reverse engineering to determine interacting networks of genes, proteins, or biochemical reactions are uncovering unique responses to toxicants. Modeling efforts in aquatic animals are evolving to interrelate the interacting networks of a system and the flow of information linking these elements. Just as is happening in medicine, systems biology approaches that allow the integration of many different scales of interaction and information are already driving a revolution in understanding the impacts of pollutants on aquatic systems.}, } @article {pmid21072585, year = {2011}, author = {Kim, K and Yoo, K and Ki, D and Son, IS and Oh, KJ and Park, J}, title = {Decision-Tree-based data mining and rule induction for predicting and mapping soil bacterial diversity.}, journal = {Environmental monitoring and assessment}, volume = {178}, number = {1-4}, pages = {595-610}, pmid = {21072585}, issn = {1573-2959}, mesh = {Bacteria/*classification ; *Biodiversity ; Data Mining/*methods ; *Decision Trees ; Geographic Information Systems ; Geography ; Models, Biological ; *Soil Microbiology ; }, abstract = {Soilmicrobial ecology plays a significant role in global ecosystems. Nevertheless, methods of model prediction and mapping have yet to be established for soil microbial ecology. The present study was undertaken to develop an artificial-intelligence- and geographical information system (GIS)-integrated framework for predicting and mapping soil bacterial diversity using pre-existing environmental geospatial database information, and to further evaluate the applicability of soil bacterial diversity mapping for planning construction of eco-friendly roads. Using a stratified random sampling, soil bacterial diversity was measured in 196 soil samples in a forest area where construction of an eco-friendly road was planned. Model accuracy, coherence analyses, and tree analysis were systematically performed, and four-class discretized decision tree (DT) with ordinary pair-wise partitioning (OPP) was selected as the optimal model among tested five DT model variants. GIS-based simulations of the optimal DT model with varying weights assigned to soil ecological quality showed that the inclusion of soil ecology in environmental components, which are considered in environmental impact assessment, significantly affects the spatial distributions of overall environmental quality values as well as the determination of an environmentally optimized road route. This work suggests a guideline to use systematic accuracy, coherence, and tree analyses in selecting an optimal DT model from multiple candidate model variants, and demonstrates the applicability of the OPP-improved DT integrated with GIS in rule induction for mapping bacterial diversity. These findings also provide implication on the significance of soil microbial ecology in environmental impact assessment and eco-friendly construction planning.}, } @article {pmid21071124, year = {2011}, author = {Kozlov, MV and Zvereva, EL}, title = {A second life for old data: global patterns in pollution ecology revealed from published observational studies.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {159}, number = {5}, pages = {1067-1075}, doi = {10.1016/j.envpol.2010.10.028}, pmid = {21071124}, issn = {1873-6424}, mesh = {Air Pollution/*adverse effects/statistics & numerical data ; Climate ; Databases as Topic ; *Ecosystem ; }, abstract = {A synthesis of research on the responses of terrestrial biota (1095 effect sizes) to industrial pollution (206 point emission sources) was conducted to reveal regional and global patterns from small-scale observational studies. A meta-analysis, in combination with other statistical methods, showed that the effects of pollution depend on characteristics of the specific polluter (type, amount of emission, duration of impact on biota), the affected organism (trophic group, life history), the level at which the response was measured (organism, population, community), and the environment (biome, climate). In spite of high heterogeneity in responses, we have detected several general patterns. We suggest that the development of evolutionary adaptations to pollution is a common phenomenon and that the harmful effects of pollution on terrestrial ecosystems are likely to increase as the climate warms. We argue that community- and ecosystem-level responses to pollution should be explored directly, rather than deduced from organism-level studies.}, } @article {pmid21070223, year = {2011}, author = {Fairbairn, DJ}, title = {The advent of mandatory data archiving.}, journal = {Evolution; international journal of organic evolution}, volume = {65}, number = {1}, pages = {1-2}, doi = {10.1111/j.1558-5646.2010.01182.x}, pmid = {21070223}, issn = {1558-5646}, mesh = {Access to Information ; Archives ; Biological Evolution ; *Biology ; *Databases, Factual ; Ecology ; *Editorial Policies ; *Periodicals as Topic ; }, } @article {pmid21059910, year = {2010}, author = {Lanfear, R and Ho, SY and Love, D and Bromham, L}, title = {Mutation rate is linked to diversification in birds.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {107}, number = {47}, pages = {20423-20428}, pmid = {21059910}, issn = {1091-6490}, mesh = {Age Factors ; Animals ; Base Sequence ; *Biodiversity ; Birds/*genetics ; Body Size ; Computational Biology ; *Evolution, Molecular ; *Genetic Speciation ; Linear Models ; Mutation/*genetics ; *Phylogeny ; Population Density ; Sequence Alignment ; Sex Characteristics ; }, abstract = {How does genome evolution affect the rate of diversification of biological lineages? Recent studies have suggested that the overall rate of genome evolution is correlated with the rate of diversification. If true, this claim has important consequences for understanding the process of diversification, and implications for the use of DNA sequence data to reconstruct evolutionary history. However, the generality and cause of this relationship have not been established. Here, we test the relationship between the rate of molecular evolution and net diversification with a 19-gene, 17-kb DNA sequence dataset from 64 families of birds. We show that rates of molecular evolution are positively correlated to net diversification in birds. Using a 7.6-kb dataset of protein-coding DNA, we show that the synonymous substitution rate, and therefore the mutation rate, is correlated to net diversification. Further analysis shows that the link between mutation rates and net diversification is unlikely to be the indirect result of correlations with life-history variables that may influence both quantities, suggesting that there might be a causal link between mutation rates and net diversification.}, } @article {pmid21059871, year = {2011}, author = {Zimmerman, MA and Stewart, SE and Morrel-Samuels, S and Franzen, S and Reischl, TM}, title = {Youth Empowerment Solutions for Peaceful Communities: combining theory and practice in a community-level violence prevention curriculum.}, journal = {Health promotion practice}, volume = {12}, number = {3}, pages = {425-439}, doi = {10.1177/1524839909357316}, pmid = {21059871}, issn = {1524-8399}, support = {U49 CE000348/CE/NCIPC CDC HHS/United States ; }, mesh = {Adolescent ; Adolescent Behavior/*psychology ; Adult ; Community Networks/*organization & administration ; Community-Institutional Relations ; Curriculum ; Female ; Humans ; Intergenerational Relations ; Leadership ; Male ; Models, Educational ; Power, Psychological ; Program Development/methods ; Program Evaluation/methods ; *Social Change ; Violence/*prevention & control ; }, abstract = {This article describes the development and evaluation of an after-school curriculum designed to prepare adolescents to prevent violence through community change. This curriculum, part of the Youth Empowerment Solutions for Peaceful Communities (YES) program, is guided by empowerment and ecological theories within a positive youth development context. YES is designed to enhance the capacity of adolescents and adults to work together to plan and implement community change projects. The youth curriculum is organized around six themed units: (a) Youth as Leaders, (b) Learning about Our Community, (c) Improving Our Community, (d) Building Intergenerational Partnerships, (e) Planning for Change, and (f) Action and Reflection. The curriculum was developed through an iterative process. Initially, program staff members documented their activities with youth. These outlines were formalized as curriculum sessions. Each session was reviewed by the program and research staff and revised based on underlying theory and practical application. The curriculum process evaluation includes staff and youth feedback. This theoretically based, field-tested curriculum is designed to be easily adapted and implemented in a diverse range of communities.}, } @article {pmid21055855, year = {2010}, author = {Coldefy, M and Curtis, SE}, title = {The geography of institutional psychiatric care in France 1800-2000: historical analysis of the spatial diffusion of specialised facilities for institutional care of mental illness.}, journal = {Social science & medicine (1982)}, volume = {71}, number = {12}, pages = {2117-2129}, pmid = {21055855}, issn = {1873-5347}, mesh = {Databases as Topic ; *Diffusion of Innovation ; France ; History, 19th Century ; History, 20th Century ; Hospitals, Psychiatric/*history/supply & distribution ; Humans ; Mental Disorders/*history/therapy ; Mental Health Services/*history/supply & distribution ; }, abstract = {As in other European countries, specialised psychiatric hospitals were established throughout France during the 19th Century. The construction of these hospitals can be considered as the concrete expression of a therapeutic innovation which recognized insanity as an illness that could be treated in such specialised institutions. The spatial diffusion of these innovative institutions through 19th and 20th century France is analysed and we explore how far this can be understood through theories of diffusion of innovations including geographical models of hierarchical and expansion diffusion (or whether other conceptual models are more appropriate). The research reported here particularly focuses on the period 1800-1961. It involved the construction of an original historical database of both psychiatric hospitals and information on the cities where these institutions were located. This was used to examine and interpret the different phases of development of psychiatric institutions and the parts of the country and types of geographical setting where they were concentrated. A multiple correspondence analysis was then performed to examine the connections between different aspects of the diffusion process. The study shows the limitations of classical models of spatial diffusion, which are found to be consistent with some, but not all aspects of the development of psychiatric institutions in France. An alternative political ecology approach seems more appropriate to conceptualise the various processes involved; national policies, social representations, medicalisation of care of mental illness, and urban and economic growth all seem to be associated with the emergence of a variable and complex pattern. This paper also opens a large field of research. Compared with other western countries, the geography of French psychiatric care is relatively under-researched, although there has been a strong spatial dimension to mental health policy in the country. This analysis provides a context for studies of more contemporary processes of French deinstitutionalisation, which is strongly structured by the past heritage of these large asylum facilities.}, } @article {pmid21048761, year = {2010}, author = {Yooseph, S and Nealson, KH and Rusch, DB and McCrow, JP and Dupont, CL and Kim, M and Johnson, J and Montgomery, R and Ferriera, S and Beeson, K and Williamson, SJ and Tovchigrechko, A and Allen, AE and Zeigler, LA and Sutton, G and Eisenstadt, E and Rogers, YH and Friedman, R and Frazier, M and Venter, JC}, title = {Genomic and functional adaptation in surface ocean planktonic prokaryotes.}, journal = {Nature}, volume = {468}, number = {7320}, pages = {60-66}, pmid = {21048761}, issn = {1476-4687}, mesh = {Aquatic Organisms/classification/*genetics/isolation & purification/virology ; Biodiversity ; Biomass ; Databases, Protein ; Genome, Bacterial/genetics ; *Genomics ; *Metagenome ; Models, Biological ; Oceans and Seas ; Phylogeny ; Plankton/*genetics/growth & development/isolation & purification/metabolism ; Prokaryotic Cells/classification/*metabolism/virology ; RNA, Ribosomal, 16S/genetics ; Water Microbiology ; }, abstract = {The understanding of marine microbial ecology and metabolism has been hampered by the paucity of sequenced reference genomes. To this end, we report the sequencing of 137 diverse marine isolates collected from around the world. We analysed these sequences, along with previously published marine prokaryotic genomes, in the context of marine metagenomic data, to gain insights into the ecology of the surface ocean prokaryotic picoplankton (0.1-3.0 μm size range). The results suggest that the sequenced genomes define two microbial groups: one composed of only a few taxa that are nearly always abundant in picoplanktonic communities, and the other consisting of many microbial taxa that are rarely abundant. The genomic content of the second group suggests that these microbes are capable of slow growth and survival in energy-limited environments, and rapid growth in energy-rich environments. By contrast, the abundant and cosmopolitan picoplanktonic prokaryotes for which there is genomic representation have smaller genomes, are probably capable of only slow growth and seem to be relatively unable to sense or rapidly acclimate to energy-rich conditions. Their genomic features also lead us to propose that one method used to avoid predation by viruses and/or bacterivores is by means of slow growth and the maintenance of low biomass.}, } @article {pmid21045053, year = {2011}, author = {Sun, S and Chen, J and Li, W and Altintas, I and Lin, A and Peltier, S and Stocks, K and Allen, EE and Ellisman, M and Grethe, J and Wooley, J}, title = {Community cyberinfrastructure for Advanced Microbial Ecology Research and Analysis: the CAMERA resource.}, journal = {Nucleic acids research}, volume = {39}, number = {Database issue}, pages = {D546-51}, pmid = {21045053}, issn = {1362-4962}, support = {R01 RR025030-02/RR/NCRR NIH HHS/United States ; R01 RR025030-03/RR/NCRR NIH HHS/United States ; R01 RR025030/RR/NCRR NIH HHS/United States ; R01 RR025030-01/RR/NCRR NIH HHS/United States ; R01RR025030/RR/NCRR NIH HHS/United States ; }, mesh = {*Databases, Genetic ; Environment ; *Metagenome ; Metagenomics ; Software ; }, abstract = {The Community Cyberinfrastructure for Advanced Microbial Ecology Research and Analysis (CAMERA, http://camera.calit2.net/) is a database and associated computational infrastructure that provides a single system for depositing, locating, analyzing, visualizing and sharing data about microbial biology through an advanced web-based analysis portal. CAMERA collects and links metadata relevant to environmental metagenome data sets with annotation in a semantically-aware environment allowing users to write expressive semantic queries against the database. To meet the needs of the research community, users are able to query metadata categories such as habitat, sample type, time, location and other environmental physicochemical parameters. CAMERA is compliant with the standards promulgated by the Genomic Standards Consortium (GSC), and sustains a role within the GSC in extending standards for content and format of the metagenomic data and metadata and its submission to the CAMERA repository. To ensure wide, ready access to data and annotation, CAMERA also provides data submission tools to allow researchers to share and forward data to other metagenomics sites and community data archives such as GenBank. It has multiple interfaces for easy submission of large or complex data sets, and supports pre-registration of samples for sequencing. CAMERA integrates a growing list of tools and viewers for querying, analyzing, annotating and comparing metagenome and genome data.}, } @article {pmid21040513, year = {2010}, author = {Xie, G and Chain, PS and Lo, CC and Liu, KL and Gans, J and Merritt, J and Qi, F}, title = {Community and gene composition of a human dental plaque microbiota obtained by metagenomic sequencing.}, journal = {Molecular oral microbiology}, volume = {25}, number = {6}, pages = {391-405}, pmid = {21040513}, issn = {2041-1014}, support = {Y01 DE006006/DE/NIDCR NIH HHS/United States ; Y01 DE006006-01/DE/NIDCR NIH HHS/United States ; Y1-DE-6006-02/DE/NIDCR NIH HHS/United States ; }, mesh = {Actinobacteria/classification ; Bacteria/classification ; Bacterial Proteins/genetics ; Bacteroidetes/classification ; Chromosome Mapping ; Contig Mapping/methods ; Cyanobacteria/classification ; Databases, Nucleic Acid ; Dental Plaque/*microbiology ; Drug Resistance, Bacterial/genetics ; Ecosystem ; Fibrobacter/classification ; Fusobacteria/classification ; Gastrointestinal Tract/microbiology ; Genome, Bacterial/*genetics ; Humans ; Metagenome/*genetics ; Metagenomics/methods ; Proteobacteria/classification ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; *Sequence Analysis, DNA ; Spirochaetaceae/classification ; }, abstract = {Human dental plaque is a complex microbial community containing an estimated 700 to 19,000 species/phylotypes. Despite numerous studies analysing species richness in healthy and diseased human subjects, the true genomic composition of the human dental plaque microbiota remains unknown. Here we report a metagenomic analysis of a healthy human plaque sample using a combination of second-generation sequencing platforms. A total of 860 million base pairs of non-human sequences were generated. Various analysis tools revealed the presence of 12 well-characterized phyla, members of the TM-7 and BRC1 clade, and sequences that could not be classified. Both pathogens and opportunistic pathogens were identified, supporting the ecological plaque hypothesis for oral diseases. Mapping the metagenomic reads to sequenced reference genomes demonstrated that 4% of the reads could be assigned to the sequenced species. Preliminary annotation identified genes belonging to all known functional categories. Interestingly, although 73% of the total assembled contig sequences were predicted to code for proteins, only 51% of them could be assigned a functional role. Furthermore, ~2.8% of the total predicted genes coded for proteins involved in resistance to antibiotics and toxic compounds, suggesting that the oral cavity is an important reservoir for antimicrobial resistance.}, } @article {pmid21035855, year = {2011}, author = {Wang, M and Riffel, M}, title = {Making the right conclusions based on wrong results and small sample sizes: interpretation of statistical tests in ecotoxicology.}, journal = {Ecotoxicology and environmental safety}, volume = {74}, number = {4}, pages = {684-692}, doi = {10.1016/j.ecoenv.2010.10.019}, pmid = {21035855}, issn = {1090-2414}, mesh = {Animals ; Bees/drug effects ; Biomass ; Data Interpretation, Statistical ; Ecotoxicology ; Environmental Pollutants/*toxicity ; Environmental Pollution/statistics & numerical data ; Mice ; Monte Carlo Method ; Oligochaeta/drug effects ; Pesticides/*toxicity ; Research Design ; Risk Assessment/methods ; Sample Size ; Statistics, Nonparametric ; Toxicity Tests/*methods/statistics & numerical data ; }, abstract = {In environmental risk assessments statistical tests are a standard tool to evaluate the significance of effects by pesticides. While it has rarely been assessed how likely it is to detect effects given a specific sample size, it was never analysed how reliable results are if the test preconditions, particularly of parametric tests, are not fulfilled or how likely it is to detect deviations from these preconditions. Therefore, we analyse the performance of a parametric and a non-parametric test using Monte Carlo simulation, focussing on typical data used in ecotoxicological risk assessments. We show that none of the data distributions are normal and that for typical sample sizes of N<20 it is very unlikely to detect deviations from normality. Non-parametric tests performed markedly better than parametric tests, except when data were in fact normally distributed. We finally discuss the impact of using different tests on pesticide risk assessments.}, } @article {pmid21033636, year = {2010}, author = {Ahgren, B}, title = {Mutualism and antagonism within organisations of integrated health care.}, journal = {Journal of health organization and management}, volume = {24}, number = {4}, pages = {396-411}, doi = {10.1108/14777261011065002}, pmid = {21033636}, issn = {1477-7266}, mesh = {Community Health Services ; Databases, Factual ; Delivery of Health Care, Integrated/*organization & administration/trends ; Meta-Analysis as Topic ; Models, Theoretical ; *Organizational Culture ; Sweden ; }, abstract = {PURPOSE: The purpose of this paper is to explore the concepts of Swedish integrated health care, their state of development and interdependence, and, furthermore, evaluate whether the theoretical framework used improves the comprehension of why integrated health care arrangements endure or cease.

DESIGN/METHODOLOGY/APPROACH: The study is founded on descriptive data gathered from a literature search on integrated health care in Sweden. With inspiration from ecology theory, these data were analysed guided by a theoretical model based on a continuum of symbiotic effects, from antagonism to mutualism.

FINDINGS: The era of Swedish integrated health care started in the 1990s, when a kind of clinical network called chains of care was launched. At the beginning the chain of care development was predominantly surrounded by non-integrative conditions, which had a restraining effect on these efforts. Even so, it seems that chains of care are here to stay. This faith in chains of care can to some extent be explained by the crucial role they have as connectors in the emerging local health care systems. Thus, these systems need chains of care to evolve and chains of care seem to require the integrative framework of local health care to progress and endure. Integrated health care performance could be troublesome, unless such mutualistic conditions are in place. States of commensalism may also be promoted, but the advantages are unilateral and therefore there is a risk of disloyalty by the unaffected part, which, in turn, can create a breeding-ground for an antagonistic liaison.

ORIGINALITY/VALUE: A theoretical approach founded on what may be called "Health Care System Ecology" appears to enhance the understanding of the complex logic of integrated health care.}, } @article {pmid21029850, year = {2010}, author = {Moore, JH}, title = {Detecting, characterizing, and interpreting nonlinear gene-gene interactions using multifactor dimensionality reduction.}, journal = {Advances in genetics}, volume = {72}, number = {}, pages = {101-116}, doi = {10.1016/B978-0-12-380862-2.00005-9}, pmid = {21029850}, issn = {0065-2660}, support = {AI59694/AI/NIAID NIH HHS/United States ; LM009012/LM/NLM NIH HHS/United States ; LM010098/LM/NLM NIH HHS/United States ; }, mesh = {Algorithms ; Artificial Intelligence ; Computational Biology/methods ; Data Mining ; Disease/*genetics ; *Epistasis, Genetic ; Genetics, Medical ; Humans ; *Models, Genetic ; }, abstract = {Human health is a complex process that is dependent on many genes, many environmental factors and chance events that are perhaps not measurable with current technology or are simply unknowable. Success in the design and execution of population-based association studies to identify those genetic and environmental factors that play an important role in human disease will depend on our ability to embrace, rather that ignore, complexity in the genotype to phenotype mapping relationship for any given human ecology. We review here three general computational challenges that must be addressed. First, data mining and machine learning methods are needed to model nonlinear interactions between multiple genetic and environmental factors. Second, filter and wrapper methods are needed to identify attribute interactions in large and complex solution landscapes. Third, visualization methods are needed to help interpret computational models and results. We provide here an overview of the multifactor dimensionality reduction (MDR) method that was developed for addressing each of these challenges.}, } @article {pmid20981026, year = {2010}, author = {Fonseca, VG and Carvalho, GR and Sung, W and Johnson, HF and Power, DM and Neill, SP and Packer, M and Blaxter, ML and Lambshead, PJ and Thomas, WK and Creer, S}, title = {Second-generation environmental sequencing unmasks marine metazoan biodiversity.}, journal = {Nature communications}, volume = {1}, number = {7}, pages = {98}, pmid = {20981026}, issn = {2041-1723}, support = {MR/K001744/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Animals ; *Biodiversity ; Computational Biology ; Marine Biology ; Phylogeny ; Polymerase Chain Reaction ; Sequence Analysis, DNA/*methods ; }, abstract = {Biodiversity is of crucial importance for ecosystem functioning, sustainability and resilience, but the magnitude and organization of marine diversity at a range of spatial and taxonomic scales are undefined. In this paper, we use second-generation sequencing to unmask putatively diverse marine metazoan biodiversity in a Scottish temperate benthic ecosystem. We show that remarkable differences in diversity occurred at microgeographical scales and refute currently accepted ecological and taxonomic paradigms of meiofaunal identity, rank abundance and concomitant understanding of trophic dynamics. Richness estimates from the current benchmarked Operational Clustering of Taxonomic Units from Parallel UltraSequencing analyses are broadly aligned with those derived from morphological assessments. However, the slope of taxon rarefaction curves for many phyla remains incomplete, suggesting that the true alpha diversity is likely to exceed current perceptions. The approaches provide a rapid, objective and cost-effective taxonomic framework for exploring links between ecosystem structure and function of all hitherto intractable, but ecologically important, communities.}, } @article {pmid20980316, year = {2010}, author = {Lyons, SK and Wagner, PJ and Dzikiewicz, K}, title = {Ecological correlates of range shifts of Late Pleistocene mammals.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {365}, number = {1558}, pages = {3681-3693}, pmid = {20980316}, issn = {1471-2970}, mesh = {Adaptation, Biological/*physiology ; Animals ; Body Size ; *Climate Change ; Databases, Factual ; *Demography ; *Fossils ; Geography ; Mammals/*physiology ; *Phylogeny ; Statistics, Nonparametric ; United States ; }, abstract = {Understanding and predicting how species' distributions will shift as climate changes are central questions in ecology today. The late Quaternary of North America represents a natural experiment in which we can evaluate how species responded during the expansion and contraction of the glaciers. Here, we ask whether species' range shifts differ because of taxonomic affinity, life-history traits, body size or topographic heterogeneity and whether the species survived the megafaunal extinction. There was no difference in range shifts between victims and survivors of the megafaunal extinction. In general, the change in the size of a species' range is not well correlated with any of the ecological or life-history traits evaluated. However, there are significant relationships between some variables and the movements of the centroids of ranges. Differences in the distances shifted exist among orders, although this is probably a result of body size differences as larger bodied species show larger shifts. Although there are a few exceptions, the distance that species shifted their range was weakly correlated with life-history traits. Finally, species in more topographically heterogeneous areas show smaller shifts than species in less-diverse areas. Overall, these results indicate that when trying to predict species range shifts in the future, body size, lifespan and the topographic relief of the landscape should be taken into account.}, } @article {pmid20980087, year = {2011}, author = {McEniry, M}, title = {Infant mortality, season of birth and the health of older Puerto Rican adults.}, journal = {Social science & medicine (1982)}, volume = {72}, number = {6}, pages = {1004-1015}, pmid = {20980087}, issn = {1873-5347}, support = {K25 AG027239-05/AG/NIA NIH HHS/United States ; R24 HD041028/HD/NICHD NIH HHS/United States ; P30 AG017266/AG/NIA NIH HHS/United States ; K25 AG027239/AG/NIA NIH HHS/United States ; R24 HD47873/HD/NICHD NIH HHS/United States ; R24 HD047873/HD/NICHD NIH HHS/United States ; }, mesh = {Age of Onset ; Aged ; Databases, Factual ; Diabetes Mellitus/epidemiology/etiology ; Female ; Health Behavior ; *Health Status ; Heart Diseases/epidemiology/etiology ; Humans ; Infant Mortality/*trends ; Infant, Newborn ; Interviews as Topic ; Male ; Middle Aged ; Puerto Rico/epidemiology ; *Seasons ; Social Class ; }, abstract = {The increasing prevalence of heart disease and diabetes among aging populations in low and middle income countries leads to questions regarding the degree to which endogenous early life exposures (exposures in utero) are important determinants of these health conditions. We devised a test using infant mortality (IMR) to verify if season of birth is a good indicator of early life (in utero) conditions that precipitate adult onset of disease. We linked annual IMR at the municipality (municipio) level from the late 1920s to early 1940s with individual birth year and place using a representative sample of older Puerto Rican adults (n = 1447) from the Puerto Rican Elderly: Health Conditions (PREHCO) study. We estimated the effects of season of birth on adult heart disease and diabetes for all respondents and then for respondents according to whether they were born when IMR was lower or higher, controlling for age, gender, obesity, respondent's educational level, adult behavior (smoking and exercise) and other early life exposures (childhood health, knee height and childhood socioeconomic status (SES)). The pattern of effects suggests that season of birth reflects endogenous causes: (1) odds of heart disease and diabetes were strong and significant for those born during the lean season in years when IMR was lower; (2) effects remained consistent even after controlling for other childhood conditions and adult behavior; but (3) no seasonality effects on adult health for adults born when IMR was higher. We conclude that in this population of older Puerto Rican adults there is continued support that the timing of adverse endogenous (in utero) conditions such as poor nutrition and infectious diseases is associated with adult heart disease and diabetes. It will be important to test the validity of these findings in other similar populations in the developing world.}, } @article {pmid20976956, year = {2010}, author = {Urban, E}, title = {[Domestic violence--problem of public health].}, journal = {Przeglad epidemiologiczny}, volume = {64}, number = {3}, pages = {421-424}, pmid = {20976956}, issn = {0033-2100}, mesh = {Community Networks/*organization & administration ; Cooperative Behavior ; Domestic Violence/*prevention & control ; Europe ; Health Promotion/*organization & administration ; *Helping Behavior ; Humans ; Poland ; Primary Prevention/*organization & administration ; Public Health ; *Public Health Practice ; Spouse Abuse/*prevention & control ; World Health Organization ; }, abstract = {In 1996 international declaration was created and it consider a violence as one of the main problems of public health. Report of World Health Organization explain problem of the violence by the ecological model. It helps in distinguish factors which influence on behavior and rises a risk to be a perpetrator or victim of a violence. Domestic violence is a kind of interpersonal violence. It touch many people. There is no integrated system of counteraction against violence in Poland. There is also lack of data's monitorising this phenomenon.}, } @article {pmid20975936, year = {2010}, author = {Menden-Deuer, S}, title = {Inherent high correlation of individual motility enhances population dispersal in a heterotrophic, planktonic protist.}, journal = {PLoS computational biology}, volume = {6}, number = {10}, pages = {e1000942}, pmid = {20975936}, issn = {1553-7358}, mesh = {Analysis of Variance ; Cell Movement/*physiology ; Computational Biology/*methods ; Dinoflagellida/cytology/*physiology ; Image Processing, Computer-Assisted ; Markov Chains ; Microscopy, Video ; *Models, Biological ; Plankton/cytology/*physiology ; Reproducibility of Results ; }, abstract = {Quantitative linkages between individual organism movements and the resulting population distributions are fundamental to understanding a wide range of ecological processes, including rates of reproduction, consumption, and mortality, as well as the spread of diseases and invasions. Typically, quantitative data are collected on either movement behaviors or population distributions, rarely both. This study combines empirical observations and model simulations to gain a mechanistic understanding and predictive ability of the linkages between both individual movement behaviors and population distributions of a single-celled planktonic herbivore. In the laboratory, microscopic 3D movements and macroscopic population distributions were simultaneously quantified in a 1L tank, using automated video- and image-analysis routines. The vertical velocity component of cell movements was extracted from the empirical data and used to motivate a series of correlated random walk models that predicted population distributions. Validation of the model predictions with empirical data was essential to distinguish amongst a number of theoretically plausible model formulations. All model predictions captured the essence of the population redistribution (mean upward drift) but only models assuming long correlation times (minute), captured the variance in population distribution. Models assuming correlation times of 8 minutes predicted the least deviation from the empirical observations. Autocorrelation analysis of the empirical data failed to identify a de-correlation time in the up to 30-second-long swimming trajectories. These minute-scale estimates are considerably greater than previous estimates of second-scale correlation times. Considerable cell-to-cell variation and behavioral heterogeneity were critical to these results. Strongly correlated random walkers were predicted to have significantly greater dispersal distances and more rapid encounters with remote targets (e.g. resource patches, predators) than weakly correlated random walkers. The tendency to disperse rapidly in the absence of aggregative stimuli has important ramifications for the ecology and biogeography of planktonic organisms that perform this kind of random walk.}, } @article {pmid20971988, year = {2010}, author = {Papanicolaou, A and Heckel, DG}, title = {The GMOD Drupal bioinformatic server framework.}, journal = {Bioinformatics (Oxford, England)}, volume = {26}, number = {24}, pages = {3119-3124}, pmid = {20971988}, issn = {1367-4811}, mesh = {*Computational Biology ; Database Management Systems ; Databases, Factual ; Internet ; RNA Interference ; *Software ; User-Computer Interface ; }, abstract = {MOTIVATION: Next-generation sequencing technologies have led to the widespread use of -omic applications. As a result, there is now a pronounced bioinformatic bottleneck. The general model organism database (GMOD) tool kit (http://gmod.org) has produced a number of resources aimed at addressing this issue. It lacks, however, a robust online solution that can deploy heterogeneous data and software within a Web content management system (CMS).

RESULTS: We present a bioinformatic framework for the Drupal CMS. It consists of three modules. First, GMOD-DBSF is an application programming interface module for the Drupal CMS that simplifies the programming of bioinformatic Drupal modules. Second, the Drupal Bioinformatic Software Bench (biosoftware_bench) allows for a rapid and secure deployment of bioinformatic software. An innovative graphical user interface (GUI) guides both use and administration of the software, including the secure provision of pre-publication datasets. Third, we present genes4all_experiment, which exemplifies how our work supports the wider research community.

CONCLUSION: Given the infrastructure presented here, the Drupal CMS may become a powerful new tool set for bioinformaticians. The GMOD-DBSF base module is an expandable community resource that decreases development time of Drupal modules for bioinformatics. The biosoftware_bench module can already enhance biologists' ability to mine their own data. The genes4all_experiment module has already been responsible for archiving of more than 150 studies of RNAi from Lepidoptera, which were previously unpublished.

Implemented in PHP and Perl. Freely available under the GNU Public License 2 or later from http://gmod-dbsf.googlecode.com.}, } @article {pmid20971549, year = {2011}, author = {Jaenicke, J and Englhart, S and Siegert, F}, title = {Monitoring the effect of restoration measures in Indonesian peatlands by radar satellite imagery.}, journal = {Journal of environmental management}, volume = {92}, number = {3}, pages = {630-638}, doi = {10.1016/j.jenvman.2010.09.029}, pmid = {20971549}, issn = {1095-8630}, mesh = {Environmental Restoration and Remediation/*methods ; *Geographic Information Systems ; Indonesia ; *Soil ; }, abstract = {In the context of the ongoing climate change discussions the importance of peatlands as carbon stores is increasingly recognised in the public. Drainage, deforestation and peat fires are the main reasons for the release of huge amounts of carbon from peatlands. Successful restoration of degraded tropical peatlands is of high interest due to their huge carbon store and sequestration potential. The blocking of drainage canals by dam building has become one of the most important measures to restore the hydrology and the ecological function of the peat domes. This study investigates the capability of using multitemporal radar remote sensing imagery for monitoring the hydrological effects of these measures. The study area is the former Mega Rice Project area in Central Kalimantan, Indonesia, where peat drainage and forest degradation is especially intense. Restoration measures started in July 2004 by building 30 large dams until June 2008. We applied change detection analysis with more than 80 ENVISAT ASAR and ALOS PALSAR images, acquired between 2004 and 2009. Radar signal increases of up to 1.36 dB show that high frequency multitemporal radar satellite imagery can be used to detect an increase in peat soil moisture after dam construction, especially in deforested areas with a high density of dams. Furthermore, a strong correlation between cross-polarised radar backscatter coefficients and groundwater levels above -50 cm was found. Monitoring peatland rewetting and quantifying groundwater level variations is important information for vegetation re-establishment, fire hazard warning and making carbon emission mitigation tradable under the voluntary carbon market or REDD (Reducing Emissions from Deforestation and Degradation) mechanism.}, } @article {pmid20964363, year = {2010}, author = {MacLeod, M and Scheringer, M and McKone, TE and Hungerbuhler, K}, title = {The State of Multimedia Mass-Balance Modeling in Environmental science and decision-making.}, journal = {Environmental science & technology}, volume = {44}, number = {22}, pages = {8360-8364}, doi = {10.1021/es103297w}, pmid = {20964363}, issn = {1520-5851}, mesh = {Atmosphere/chemistry ; *Decision Support Techniques ; Ecological and Environmental Phenomena ; Environment ; Environmental Pollutants/analysis/chemistry ; *Models, Chemical ; Plants/chemistry ; Soil/chemistry ; }, } @article {pmid20962214, year = {2010}, author = {Chandrasekaran, C and Turesson, HK and Brown, CH and Ghazanfar, AA}, title = {The influence of natural scene dynamics on auditory cortical activity.}, journal = {The Journal of neuroscience : the official journal of the Society for Neuroscience}, volume = {30}, number = {42}, pages = {13919-13931}, pmid = {20962214}, issn = {1529-2401}, support = {R01 NS054898/NS/NINDS NIH HHS/United States ; R01 NS054898-03/NS/NINDS NIH HHS/United States ; R90 DA023419/DA/NIDA NIH HHS/United States ; R01NS054898/NS/NINDS NIH HHS/United States ; }, mesh = {Acoustic Stimulation ; Animals ; Auditory Cortex/*physiology ; Data Interpretation, Statistical ; Ecosystem ; *Environment ; Evoked Potentials, Auditory/physiology ; Macaca fascicularis ; Photic Stimulation ; }, abstract = {The efficient cortical encoding of natural scenes is essential for guiding adaptive behavior. Because natural scenes and network activity in cortical circuits share similar temporal scales, it is necessary to understand how the temporal structure of natural scenes influences network dynamics in cortical circuits and spiking output. We examined the relationship between the structure of natural acoustic scenes and its impact on network activity [as indexed by local field potentials (LFPs)] and spiking responses in macaque primary auditory cortex. Natural auditory scenes led to a change in the power of the LFP in the 2-9 and 16-30 Hz frequency ranges relative to the ongoing activity. In contrast, ongoing rhythmic activity in the 9-16 Hz range was essentially unaffected by the natural scene. Phase coherence analysis showed that scene-related changes in LFP power were at least partially attributable to the locking of the LFP and spiking activity to the temporal structure in the scene, with locking extending up to 25 Hz for some scenes and cortical sites. Consistent with distributed place and temporal coding schemes, a key predictor of phase locking and power changes was the overlap between the spectral selectivity of a cortical site and the spectral structure of the scene. Finally, during the processing of natural acoustic scenes, spikes were locked to LFP phase at frequencies up to 30 Hz. These results are consistent with an idea that the cortical representation of natural scenes emerges from an interaction between network activity and stimulus dynamics.}, } @article {pmid20961650, year = {2010}, author = {Ewers, RM and Marsh, CJ and Wearn, OR}, title = {Making statistics biologically relevant in fragmented landscapes.}, journal = {Trends in ecology & evolution}, volume = {25}, number = {12}, pages = {699-704}, doi = {10.1016/j.tree.2010.09.008}, pmid = {20961650}, issn = {0169-5347}, mesh = {Animals ; Birds ; *Ecosystem ; Environment ; *Environmental Monitoring ; Geographic Information Systems ; Insecta ; Mice ; Models, Biological ; Population Dynamics ; Species Specificity ; Statistics as Topic/*methods ; }, abstract = {The biological impacts of habitat fragmentation are routinely assessed using standard statistical modelling techniques that are used across many ecological disciplines. However, to assess the biological relevance of fragmentation impacts, we must consider an extra, spatial dimension to the standard statistical model: the biological importance of a significant and well supported model with large effect sizes crucially depends on the configuration of habitat within the study area. We argue that mapping the outputs from statistical models across a study area generates biologically meaningful estimates of fragmentation impacts. Integrating traditional statistical approaches with geographic information systems will facilitate rigorous comparisons of fragmentation impacts between taxa, studies and ecosystems.}, } @article {pmid20961649, year = {2010}, author = {Patterson, DJ and Cooper, J and Kirk, PM and Pyle, RL and Remsen, DP}, title = {Names are key to the big new biology.}, journal = {Trends in ecology & evolution}, volume = {25}, number = {12}, pages = {686-691}, doi = {10.1016/j.tree.2010.09.004}, pmid = {20961649}, issn = {0169-5347}, mesh = {Animals ; *Classification ; Databases as Topic ; Humans ; Informatics ; Internet ; *Terminology as Topic ; }, abstract = {Those who seek answers to big, broad questions about biology, especially questions emphasizing the organism (taxonomy, evolution and ecology), will soon benefit from an emerging names-based infrastructure. It will draw on the almost universal association of organism names with biological information to index and interconnect information distributed across the Internet. The result will be a virtual data commons, expanding as further data are shared, allowing biology to become more of a 'big science'. Informatics devices will exploit this 'big new biology', revitalizing comparative biology with a broad perspective to reveal previously inaccessible trends and discontinuities, so helping us to reveal unfamiliar biological truths. Here, we review the first components of this freely available, participatory and semantic Global Names Architecture.}, } @article {pmid20958978, year = {2010}, author = {Lin, Z and Wu, WS and Liang, H and Woo, Y and Li, WH}, title = {The spatial distribution of cis regulatory elements in yeast promoters and its implications for transcriptional regulation.}, journal = {BMC genomics}, volume = {11}, number = {}, pages = {581}, pmid = {20958978}, issn = {1471-2164}, support = {GM081724/GM/NIGMS NIH HHS/United States ; GM30998/GM/NIGMS NIH HHS/United States ; }, mesh = {5' Untranslated Regions/genetics ; Base Pairing/genetics ; Binding Sites ; Databases, Genetic ; Gene Expression Profiling ; *Gene Expression Regulation, Fungal ; Genes, Fungal/genetics ; Nucleosomes/metabolism ; Polymorphism, Single Nucleotide/genetics ; Promoter Regions, Genetic/*genetics ; Regulon/genetics ; Saccharomyces/*genetics ; Selection, Genetic/genetics ; TATA Box/genetics ; Transcription Factors/metabolism ; Transcription Initiation Site ; *Transcription, Genetic ; }, abstract = {BACKGROUND: How the transcription factor binding sites (TFBSs) are distributed in the promoter region have implications for gene regulation. Previous studies used the translation start codon as the reference point to infer the TFBS distribution. However, it is biologically more relevant to use the transcription start site (TSS) as the reference point. In this study, we reexamined the spatial distribution of TFBSs, investigated various promoter features that may affect the distribution, and studied the effect of TFBS distribution on transcriptional regulation.

RESULTS: We found a sharp peak for the distribution of TFBSs at ~115 bp upstream of the TSS, but no clear peak when the translation start codon was used as the reference point. Our analysis of sequence variation data among 63 yeast strains revealed very low deletion polymorphisms in the region between the distribution peak and the TSS, suggesting that the distances between TFBSs and the TSS have been selectively constrained in evolution. As in previous studies, we found that the nucleosome occupancy and the presence/absence of TATA-box in the promoter region affect the TFBS distribution pattern. In addition, we found that there exists a correlation between the 5'UTR length and the TFBS distribution pattern and we showed that the TFBS distribution pattern affects gene transcription level and plasticity.

CONCLUSIONS: The spatial distribution of TFBSs obtained using the TSS as the reference point shows a much sharper peak than does the distribution obtained using the translation start codon as the reference point. The TFBS distribution pattern is affected by nucleosome occupancy and presence of TATA-box and it affects the transcription level and transcription plasticity of the gene.}, } @article {pmid20956371, year = {2010}, author = {Barton, CM and Ullah, II and Bergin, S}, title = {Land use, water and Mediterranean landscapes: modelling long-term dynamics of complex socio-ecological systems.}, journal = {Philosophical transactions. Series A, Mathematical, physical, and engineering sciences}, volume = {368}, number = {1931}, pages = {5275-5297}, doi = {10.1098/rsta.2010.0193}, pmid = {20956371}, issn = {1364-503X}, mesh = {Agriculture/trends ; Archaeology/methods/trends ; Climate ; Computational Biology/methods ; Ecosystem ; Humans ; Mediterranean Region ; Ownership/trends ; Social Behavior ; *Water Supply ; Wind ; }, abstract = {The evolution of Mediterranean landscapes during the Holocene has been increasingly governed by the complex interactions of water and human land use. Different land-use practices change the amount of water flowing across the surface and infiltrating the soil, and change water's ability to move surface sediments. Conversely, water amplifies the impacts of human land use and extends the ecological footprint of human activities far beyond the borders of towns and fields. Advances in computational modelling offer new tools to study the complex feedbacks between land use, land cover, topography and surface water. The Mediterranean Landscape Dynamics project (MedLand) is building a modelling laboratory where experiments can be carried out on the long-term impacts of agropastoral land use, and whose results can be tested against the archaeological record. These computational experiments are providing new insights into the socio-ecological consequences of human decisions at varying temporal and spatial scales.}, } @article {pmid20953937, year = {2010}, author = {Wang, H and Guo, S and Huang, M and Thorsten, LH and Wei, J}, title = {Ascomycota has a faster evolutionary rate and higher species diversity than Basidiomycota.}, journal = {Science China. Life sciences}, volume = {53}, number = {10}, pages = {1163-1169}, doi = {10.1007/s11427-010-4063-8}, pmid = {20953937}, issn = {1869-1889}, mesh = {Ascomycota/*classification/*genetics ; Basidiomycota/*classification/*genetics ; DNA, Fungal/genetics ; Databases, Nucleic Acid ; *Evolution, Molecular ; Fungal Proteins/genetics ; Genes, Fungal ; Genetic Variation ; Species Specificity ; Time Factors ; }, abstract = {Differences in rates of nucleotide or amino acid substitutions among major groups of organisms are repeatedly found and well documented. A growing body of evidence suggests a link between the rate of neutral molecular change within populations and the evolution of species diversity. More than 98% of terrestrial fungi belong to the phyla Ascomycota or Basidiomycota. The former is considerably richer in number of species than the latter. We obtained DNA sequences of 21 protein-coding genes from the lichenized fungus Rhizoplaca chrysoleuca and used them together with sequences from GenBank for subsequent analyses. Three datasets were used to test rate discrepancies between Ascomycota and Basidiomycota and that within Ascomycota: (i) 13 taxa including 105 protein-coding genes, (ii) nine taxa including 21 protein-coding genes, and (iii) nuclear LSU rDNA of 299 fungal species. Based on analyses of the 105 protein-coding genes and nuclear LSU rDNA datasets, we found that the evolutionary rate was higher in Ascomycota than in Basidiomycota. The differences in substitution rates between Ascomycota and Basidiomycota were significant. Within Ascomycota, the species-rich Sordariomycetes has the fastest evolutionary rate, while Leotiomycetes has the slowest. Our results indicate that the main contribution to the higher substitution rates in Ascomycota does not come from mutualism, ecological conditions, sterility, metabolic rate or shorter generation time, but is possibly caused by the founder effect. This is another example of the correlation between species number and evolutionary rates, which is consistent with the hypothesis that the founder effect is responsible for accelerated substitution rates in diverse clades.}, } @article {pmid20950475, year = {2010}, author = {Durand, J and Bodénès, C and Chancerel, E and Frigerio, JM and Vendramin, G and Sebastiani, F and Buonamici, A and Gailing, O and Koelewijn, HP and Villani, F and Mattioni, C and Cherubini, M and Goicoechea, PG and Herrán, A and Ikaran, Z and Cabané, C and Ueno, S and Alberto, F and Dumoulin, PY and Guichoux, E and de Daruvar, A and Kremer, A and Plomion, C}, title = {A fast and cost-effective approach to develop and map EST-SSR markers: oak as a case study.}, journal = {BMC genomics}, volume = {11}, number = {}, pages = {570}, pmid = {20950475}, issn = {1471-2164}, mesh = {Chromosome Mapping/*economics/*methods ; Cost-Benefit Analysis ; Data Mining ; *Expressed Sequence Tags ; *Genetic Markers ; Genome, Plant/genetics ; Microsatellite Repeats/genetics ; Minisatellite Repeats/*genetics ; Polymorphism, Genetic ; Quercus/*genetics ; }, abstract = {BACKGROUND: Expressed Sequence Tags (ESTs) are a source of simple sequence repeats (SSRs) that can be used to develop molecular markers for genetic studies. The availability of ESTs for Quercus robur and Quercus petraea provided a unique opportunity to develop microsatellite markers to accelerate research aimed at studying adaptation of these long-lived species to their environment. As a first step toward the construction of a SSR-based linkage map of oak for quantitative trait locus (QTL) mapping, we describe the mining and survey of EST-SSRs as well as a fast and cost-effective approach (bin mapping) to assign these markers to an approximate map position. We also compared the level of polymorphism between genomic and EST-derived SSRs and address the transferability of EST-SSRs in Castanea sativa (chestnut).

RESULTS: A catalogue of 103,000 Sanger ESTs was assembled into 28,024 unigenes from which 18.6% presented one or more SSR motifs. More than 42% of these SSRs corresponded to trinucleotides. Primer pairs were designed for 748 putative unigenes. Overall 37.7% (283) were found to amplify a single polymorphic locus in a reference full-sib pedigree of Quercus robur. The usefulness of these loci for establishing a genetic map was assessed using a bin mapping approach. Bin maps were constructed for the male and female parental tree for which framework linkage maps based on AFLP markers were available. The bin set consisting of 14 highly informative offspring selected based on the number and position of crossover sites. The female and male maps comprised 44 and 37 bins, with an average bin length of 16.5 cM and 20.99 cM, respectively. A total of 256 EST-SSRs were assigned to bins and their map position was further validated by linkage mapping. EST-SSRs were found to be less polymorphic than genomic SSRs, but their transferability rate to chestnut, a phylogenetically related species to oak, was higher.

CONCLUSION: We have generated a bin map for oak comprising 256 EST-SSRs. This resource constitutes a first step toward the establishment of a gene-based map for this genus that will facilitate the dissection of QTLs affecting complex traits of ecological importance.}, } @article {pmid20950449, year = {2010}, author = {Ribeiro, MC and Pereira, MJ and Soares, A and Branquinho, C and Augusto, S and Llop, E and Fonseca, S and Nave, JG and Tavares, AB and Dias, CM and Silva, A and Selemane, I and de Toro, J and Santos, MJ and Santos, F}, title = {A study protocol to evaluate the relationship between outdoor air pollution and pregnancy outcomes.}, journal = {BMC public health}, volume = {10}, number = {}, pages = {613}, pmid = {20950449}, issn = {1471-2458}, mesh = {Air Pollutants/*adverse effects/analysis ; Cohort Studies ; Environmental Monitoring/methods ; Female ; Geographic Information Systems ; Humans ; Medical Audit ; Portugal ; Pregnancy ; *Pregnancy Outcome ; Research Design ; Retrospective Studies ; Surveys and Questionnaires ; Uncertainty ; }, abstract = {BACKGROUND: The present study protocol is designed to assess the relationship between outdoor air pollution and low birth weight and preterm births outcomes performing a semi-ecological analysis. Semi-ecological design studies are widely used to assess effects of air pollution in humans. In this type of analysis, health outcomes and covariates are measured in individuals and exposure assignments are usually based on air quality monitor stations. Therefore, estimating individual exposures are one of the major challenges when investigating these relationships with a semi-ecologic design.

METHODS/DESIGN: Semi-ecologic study consisting of a retrospective cohort study with ecologic assignment of exposure is applied. Health outcomes and covariates are collected at Primary Health Care Center. Data from pregnant registry, clinical record and specific questionnaire administered orally to the mothers of children born in period 2007-2010 in Portuguese Alentejo Litoral region, are collected by the research team. Outdoor air pollution data are collected with a lichen diversity biomonitoring program, and individual pregnancy exposures are assessed with spatial geostatistical simulation, which provides the basis for uncertainty analysis of individual exposures. Awareness of outdoor air pollution uncertainty will improve validity of individual exposures assignments for further statistical analysis with multivariate regression models.

DISCUSSION: Exposure misclassification is an issue of concern in semi-ecological design. In this study, personal exposures are assigned to each pregnant using geocoded addresses data. A stochastic simulation method is applied to lichen diversity values index measured at biomonitoring survey locations, in order to assess spatial uncertainty of lichen diversity value index at each geocoded address. These methods assume a model for spatial autocorrelation of exposure and provide a distribution of exposures in each study location. We believe that variability of simulated exposure values at geocoded addresses will improve knowledge on variability of exposures, improving therefore validity of individual exposures to input in posterior statistical analysis.}, } @article {pmid20950425, year = {2010}, author = {Fernàndez-Guerra, A and Buchan, A and Mou, X and Casamayor, EO and González, JM}, title = {T-RFPred: a nucleotide sequence size prediction tool for microbial community description based on terminal-restriction fragment length polymorphism chromatograms.}, journal = {BMC microbiology}, volume = {10}, number = {}, pages = {262}, pmid = {20950425}, issn = {1471-2180}, mesh = {Amplified Fragment Length Polymorphism Analysis/*methods ; Bacteria/*classification/genetics ; Computational Biology/*methods ; DNA Fingerprinting/*methods ; DNA, Bacterial/analysis ; Gene Library ; Phylogeny ; Polymerase Chain Reaction ; *Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S ; Restriction Mapping/*methods ; Seawater/*microbiology ; Sequence Analysis, RNA ; Software ; Water Microbiology ; }, abstract = {BACKGROUND: Terminal-Restriction Fragment Length Polymorphism (T-RFLP) is a technique used to analyze complex microbial communities. It allows for the quantification of unique or numerically dominant phylotypes in amplicon pools and it has been used primarily for comparisons between different communities. T-RFPred, Terminal-Restriction Fragment Prediction, was developed to identify and assign taxonomic information to chromatogram peaks of a T-RFLP fingerprint for a more comprehensive description of microbial communities. The program estimates the expected fragment size of representative 16S rRNA gene sequences (either from a complementary clone library or from public databases) for a given primer and restriction enzyme(s) and provides candidate taxonomic assignments.

RESULTS: To show the accuracy of the program, T-RFLP profiles of a marine bacterial community were described using artificial bacterioplankton clone libraries of sequences obtained from public databases. For all valid chromatogram peaks, a phylogenetic group could be assigned.

CONCLUSIONS: T-RFPred offers enhanced functionality of T-RFLP profile analysis over current available programs. In particular, it circumvents the need for full-length 16S rRNA gene sequences during taxonomic assignments of T-RF peaks. Thus, large 16S rRNA gene datasets from environmental studies, including metagenomes, or public databases can be used as the reference set. Furthermore, T-RFPred is useful in experimental design for the selection of primers as well as the type and number of restriction enzymes that will yield informative chromatograms from natural microbial communities.}, } @article {pmid20940022, year = {2011}, author = {Gantner, S and Andersson, AF and Alonso-Sáez, L and Bertilsson, S}, title = {Novel primers for 16S rRNA-based archaeal community analyses in environmental samples.}, journal = {Journal of microbiological methods}, volume = {84}, number = {1}, pages = {12-18}, doi = {10.1016/j.mimet.2010.10.001}, pmid = {20940022}, issn = {1872-8359}, mesh = {Archaea/*classification/*genetics ; *Biodiversity ; Computational Biology ; DNA Primers/*genetics ; DNA, Archaeal/chemistry/genetics ; *Environmental Microbiology ; High-Throughput Nucleotide Sequencing/methods ; Metagenomics/*methods ; Molecular Sequence Data ; Polymerase Chain Reaction/methods ; RNA, Archaeal/genetics ; RNA, Ribosomal, 16S/*genetics ; Sensitivity and Specificity ; }, abstract = {Next generation sequencing technologies for in depth analyses of complex microbial communities rely on rational primer design based on up-to-date reference databases. Most of the 16S rRNA-gene based analyses of environmental Archaea community composition use PCR primers developed from small data sets several years ago, making an update long overdue. Here we present a new set of archaeal primers targeting the 16S rRNA gene designed from 8500 aligned archaeal sequences in the SILVA database. The primers 340F-1000R showed a high archaeal specificity (<1% bacteria amplification) covering 93 and 97% of available sequences for Crenarchaeota and Euryarchaeota respectively. In silico tests of the primers revealed at least 38% higher coverage for Archaea compared to other commonly used primers. Empirical tests with clone libraries confirmed the high specificity of the primer pair to Archaea in three biomes: surface waters in the Arctic Ocean, the pelagic zone of a temperate lake and a methanogenic bioreactor. The clone libraries featured both Euryarchaeota and Crenarchaeota in variable proportions and revealed dramatic differences in the archaeal community composition and minimal phylogenetic overlap between samples.}, } @article {pmid20931194, year = {2011}, author = {Lynch, AJ}, title = {The usefulness of a threat and disturbance categorization developed for Queensland wetlands to environmental management, monitoring, and evaluation.}, journal = {Environmental management}, volume = {47}, number = {1}, pages = {40-55}, pmid = {20931194}, issn = {1432-1009}, mesh = {*Conservation of Natural Resources ; Databases, Factual ; Environmental Monitoring/*methods ; Information Services ; Queensland ; *Wetlands ; }, abstract = {There is no comprehensive system of describing threats and disturbances currently used in Australia, despite the widespread impacts of human activities on natural ecosystems. Yet a detailed categorization would facilitate the collation of threatening process information into information systems; enable standardized collection and availability of data; and enable comparative analyses of ecosystem condition between stakeholders, agencies, states, and nations, particularly for environmental reporting and evaluation mechanisms such as State of the Environment. As part of the Queensland Wetlands Programme (QWP), a threat and disturbance framework was developed, focused on the pressure and impacts components of the DPSIR (driver-pressure-state-impacts-response) framework. A wetland inventory database was developed also that included a detailed threat and disturbance categorization using the QWP framework. The categorization encompasses a broad range of anthropogenic and natural processes, and is hierarchical to accommodate varying levels of detail or knowledge. By incorporating detailed qualitative and quantitative information, a comprehensive threats and disturbances categorization can contribute to conceptual or spatially explicit knowledge and management assessments. The application of the framework and categorization to several threatening processes is demonstrated, and its relationship to current natural resource condition indicators is discussed. Threat evaluation is an essential component of ecological assessment and environmental management, and a standardized categorization enables consistency in attributing processes, impacts and their short- to long-term consequences. Such a systematic framework and categorization demonstrates the importance and usefulness of comprehensive approaches, and this approach can be readily adapted to management, monitoring and evaluation of other target ecosystems and biota.}, } @article {pmid20925445, year = {2010}, author = {Landsiedel, R and Ma-Hock, L and Van Ravenzwaay, B and Schulz, M and Wiench, K and Champ, S and Schulte, S and Wohlleben, W and Oesch, F}, title = {Gene toxicity studies on titanium dioxide and zinc oxide nanomaterials used for UV-protection in cosmetic formulations.}, journal = {Nanotoxicology}, volume = {4}, number = {}, pages = {364-381}, doi = {10.3109/17435390.2010.506694}, pmid = {20925445}, issn = {1743-5404}, mesh = {Administration, Inhalation ; Animals ; Body Weight/drug effects ; Bone Marrow Cells/drug effects ; Cell Line ; Cosmetics/chemistry/toxicity ; Cricetinae ; Data Interpretation, Statistical ; Macrophages, Alveolar/drug effects ; Male ; Mice ; Micronuclei, Chromosome-Defective/drug effects ; Mutagenicity Tests/methods ; Nanostructures/administration & dosage/chemistry/*toxicity ; Rats ; Rats, Wistar ; Salmonella ; Sunscreening Agents/administration & dosage/chemistry/*toxicity ; Titanium/administration & dosage/chemistry/*toxicity ; Zinc Oxide/administration & dosage/chemistry/*toxicity ; }, abstract = {Titanium dioxide and zinc oxide nanomaterials, used as UV protecting agents in sunscreens, were investigated for their potential genotoxicity in in vitro and in vivo test systems. Since standard OECD test methods are designed for soluble materials and genotoxicity testing for nanomaterials is still under revision, a battery of standard tests was used, covering different endpoints. Additionally, a procedure to disperse the nanomaterials in the test media and careful characterization of the dispersed test item was added to the testing methods. No genotoxicity was observed in vitro (Ames' Salmonella gene mutation test and V79 micronucleus chromosome mutation test) or in vivo (mouse bone marrow micronucleus test and Comet DNA damage assay in lung cells from rats exposed by inhalation). These results add to the still limited data base on genotoxicity test results with nanomaterials and provide congruent results of a battery of standard OECD test methods applied to nanomaterials.}, } @article {pmid20924579, year = {2010}, author = {Fürst, C and Volk, M and Pietzsch, K and Makeschin, F}, title = {Pimp your landscape: a tool for qualitative evaluation of the effects of regional planning measures on ecosystem services.}, journal = {Environmental management}, volume = {46}, number = {6}, pages = {953-968}, pmid = {20924579}, issn = {1432-1009}, mesh = {Agriculture ; Conservation of Natural Resources/*methods ; Decision Support Techniques ; *Ecosystem ; Environment ; Environmental Monitoring ; *Geographic Information Systems ; Planning Techniques ; Policy Making ; Water Supply ; }, abstract = {The article presents the platform "Pimp your landscape" (PYL), which aims firstly at the support of planners by simulating alternative land-use scenarios and by an evaluation of benefits or risks for regionally important ecosystem services. Second, PYL supports an integration of information on environmental and landscape conditions into impact assessment. Third, PYL supports the integration of impacts of planning measures on ecosystem services. PYL is a modified 2-D cellular automaton with GIS features. The cells have the major attribute "land-use type" and can be supplemented with additional information, such as specifics regarding geology, topography and climate. The GIS features support the delineation of non-cellular infrastructural elements, such as roads or water bodies. An evaluation matrix represents the core element of the system. In this matrix, values in a relative scale from 0 (lowest value) to 100 (highest value) are assigned to the land-use types and infrastructural elements depending on their effect on ecosystem services. The option to configure rules for describing the impact of environmental attributes and proximity effects on cell values and land-use transition probabilities is of particular importance. User interface and usage of the platform are demonstrated by an application case. Constraints and limits of the recent version are discussed, including the need to consider in the evaluation, landscape-structure aspects such as patch size, fragmentation and spatial connectivity. Regarding the further development, it is planned to include the impact of land management practices to support climate change adaptation and mitigation strategies in regional planning.}, } @article {pmid20919633, year = {2010}, author = {Pfrender, ME and Hawkins, CP and Bagley, M and Courtney, GW and Creutzburg, BR and Epler, JH and Fend, S and Schindel, D and Ferrington, LC and Hartzell, PL and Jackson, S and Larsen, DP and Lévesque, A and Morse, JC and Petersen, MJ and Ruiter, D and Whiting, M}, title = {Assessing macroinvertebrate biodiversity in freshwater ecosystems: advances and challenges in DNA-based approaches.}, journal = {The Quarterly review of biology}, volume = {85}, number = {3}, pages = {319-340}, doi = {10.1086/655118}, pmid = {20919633}, issn = {0033-5770}, mesh = {Animals ; Biodiversity ; Computational Biology ; DNA/*genetics ; *Ecosystem ; Fresh Water ; Invertebrates/genetics ; Marine Biology ; Polymerase Chain Reaction ; }, abstract = {Assessing the biodiversity of macroinvertebrate fauna in freshwater ecosystems is an essential component of both basic ecological inquiry and applied ecological assessments. Aspects of taxonomic diversity and composition in freshwater communities are widely used to quantify water quality and measure the efficacy of remediation and restoration efforts. The accuracy and precision of biodiversity assessments based on standard morphological identifications are often limited by taxonomic resolution and sample size. Morphologically based identifications are laborious and costly, significantly constraining the sample sizes that can be processed. We suggest that the development of an assay platform based on DNA signatures will increase the precision and ease of quantifying biodiversity in freshwater ecosystems. Advances in this area will be particularly relevant for benthic and planktonic invertebrates, which are often monitored by regulatory agencies. Adopting a genetic assessment platform will alleviate some of the current limitations to biodiversity assessment strategies. We discuss the benefits and challenges associated with DNA-based assessments and the methods that are currently available. As recent advances in microarray and next-generation sequencing technologies will facilitate a transition to DNA-based assessment approaches, future research efforts should focus on methods for data collection, assay platform development, establishing linkages between DNA signatures and well-resolved taxonomies, and bioinformatics.}, } @article {pmid20919581, year = {2010}, author = {Hoberg, EP}, title = {Invasive processes, mosaics and the structure of helminth parasite faunas.}, journal = {Revue scientifique et technique (International Office of Epizootics)}, volume = {29}, number = {2}, pages = {255-272}, pmid = {20919581}, issn = {0253-1933}, mesh = {Animals ; Animals, Domestic/parasitology ; Climate Change ; Ecosystem ; Helminthiasis, Animal/parasitology/*transmission ; Helminths/*physiology ; Host-Parasite Interactions ; Humans ; *Introduced Species ; Vertebrates/*parasitology ; }, abstract = {The biosphere in evolutionary and ecological time has been structured by episodes of geographic and host colonisation that have determined distributions of complex assemblages of microparasites and macroparasites, including helminths circulating among vertebrates. Biological invasion is an intricate phenomenon often involving 'extra-range dispersal' and establishment of exotic (non-indigenous) species and populations substantially beyond their native range. Invasion may also involve the expansion or shifting of host and geographic distributions of an endemic (indigenous) species or fauna under changing environmental conditions. Invasions result in faunal interchange occurring under influences from both natural and anthropogenic forces where expansion on spatial/temporal continua bridges continents, regions and landscapes. Drivers for invasion are idiosyncratic, multifactorial, interactive, and opportunistic, with a powerful role for historical contingency. The life history patterns of helminths interact with invasion pathways to determine the potential for introduction. Human-mediated events, such as the global expansion of pathogens linked to development of agriculture, domestication of food animals, and European exploration have had a pervasive influence on the distribution of helminths. Globalisation, broad transport networks and environmental perturbation linked to climate change, along with other drivers, have accelerated these processes. A consequence of invasion and establishment of exotic species is that faunal structure will be a mosaic that includes admixtures of indigenous and non-indigenous species and populations; exemplified by helminth faunas among domestic and free-ranging ungulates and a diversity of host-parasite systems among vertebrates. Contemporary mosaics are evident where human-mediated events have brought assemblages of new invaders and relatively old endemic species into sympatry, highlighting interactions at ecotones, particularly those at borderlands between managed and natural ecosystems. Understanding the historical origins and complex components of mosaics is essential in formulating predictions about future responses to environmental change. Powerful tools are available which support the study of invasive species, the most important being systematics and our capacity to accurately identify parasites and to define evolutionary and biogeographic history. Faunal baselines derived from arrays of biological specimens, integrated surveys and informatics are a permanent record of the biosphere when archived in museum collections. The absence of comprehensive taxonomic inventories of parasites, including molecular-genetic data, limits our ability to recognise the introduction of non-indigenous parasites, and to document patterns of expansion for local faunas under a regime of environmental perturbation.}, } @article {pmid20889857, year = {2010}, author = {Maher, SP and Ellis, C and Gage, KL and Enscore, RE and Peterson, AT}, title = {Range-wide determinants of plague distribution in North America.}, journal = {The American journal of tropical medicine and hygiene}, volume = {83}, number = {4}, pages = {736-742}, pmid = {20889857}, issn = {1476-1645}, mesh = {Animals ; Databases, Factual ; Demography ; Disease Reservoirs ; *Ecosystem ; Host-Pathogen Interactions ; Humans ; Insect Vectors/physiology ; *Mammals ; Models, Biological ; North America/epidemiology ; Plague/*epidemiology/transmission ; Siphonaptera/physiology ; Species Specificity ; }, abstract = {Plague, caused by the bacterium Yersinia pestis, is established across western North America, and yet little is known of what determines the broad-scale dimensions of its overall range. We tested whether its North American distribution represents a composite of individual host-plague associations (the "Host Niche Hypothesis"), or whether mammal hosts become infected only at sites overlapping ecological conditions appropriate for plague transmission and maintenance (the "Plague Niche Hypothesis"). We took advantage of a novel data set summarizing plague records in wild mammals newly digitized from paper-based records at the Centers for Disease Control and Prevention to develop range-wide tests of ecological niche similarity between mammal host niches and plague-infected host niches. Results indicate that plague infections occur under circumstances distinct from the broader ecological distribution of hosts, and that plague-infected niches are similar among hosts; hence, evidence coincides with the predictions of the Plague Niche Hypothesis, and contrasts with those of the Host Niche Hypothesis. The "plague niche" is likely driven by ecological requirements of vector flea species.}, } @article {pmid20888613, year = {2010}, author = {Dogan, HM and Cetin, I and Egri, M}, title = {Spatiotemporal change and ecological modelling of malaria in Turkey by means of geographic information systems.}, journal = {Transactions of the Royal Society of Tropical Medicine and Hygiene}, volume = {104}, number = {11}, pages = {726-732}, doi = {10.1016/j.trstmh.2010.08.003}, pmid = {20888613}, issn = {1878-3503}, mesh = {Disease Reservoirs ; Ecosystem ; Female ; Forecasting ; *Geographic Information Systems ; Humans ; Incidence ; Logistic Models ; Malaria, Vivax/*epidemiology/transmission ; Male ; Plasmodium vivax/*pathogenicity ; Space-Time Clustering ; Turkey/epidemiology ; }, abstract = {We described the spatiotemporal change of malaria (Plasmodium vivax) in Turkey over 34 years (1975-2008), and assessed the role of environmental variables in this change. We developed seven 5-year-period raster maps by using geo-referenced malaria case data from the centres of 81 provinces and the kriging method with a spherical variogram model in a geographic information systems (GIS) model. We also modelled malaria incidence in GIS by using our average malaria incidence raster map, and complementary spatial database including the raster map layers of 14 environmental variables. We chose linear regression analysis with backward method to investigate relationships among variables and develop a model. The model was run in GIS to obtain a model incidence raster map. We tested the reliability of the model map by residual statistics, and found the model map dependable. Five-year-period maps revealed that the distribution of malaria cases moved from the East Mediterranean region to the Southeast Anatolia region due to changing human activities. The latitude, minimum temperature, distance to seas and elevation variables were found to have significant impacts on malaria. Consequently, the model incidence map established a good background for early warning systems to predict epidemics of malaria following environmental changes.}, } @article {pmid20886047, year = {2010}, author = {Kot, CY and Fujioka, E and Hazen, LJ and Best, BD and Read, AJ and Halpin, PN}, title = {Spatio-temporal gap analysis of OBIS-SEAMAP project data: assessment and way forward.}, journal = {PloS one}, volume = {5}, number = {9}, pages = {e12990}, pmid = {20886047}, issn = {1932-6203}, mesh = {Animals ; *Databases, Factual/trends ; *Ecosystem ; Endangered Species/trends ; *Marine Biology/trends ; Oceans and Seas ; *Program Evaluation ; }, abstract = {The OBIS-SEAMAP project has acquired and served high-quality marine mammal, seabird, and sea turtle data to the public since its inception in 2002. As data accumulated, spatial and temporal biases resulted and a comprehensive gap analysis was needed in order to assess coverage to direct data acquisition for the OBIS-SEAMAP project and for taxa researchers should true gaps in knowledge exist. All datasets published on OBIS-SEAMAP up to February 2009 were summarized spatially and temporally. Seabirds comprised the greatest number of records, compared to the other two taxa, and most records were from shipboard surveys, compared to the other three platforms. Many of the point observations and polyline tracklines were located in northern and central Atlantic and the northeastern and central-eastern Pacific. The Southern Hemisphere generally had the lowest representation of data, with the least number of records in the southern Atlantic and western Pacific regions. Temporally, records of observations for all taxa were the lowest in fall although the number of animals sighted was lowest in the winter. Oceanographic coverage of observations varied by platform for each taxa, which showed that using two or more platforms represented habitat ranges better than using only one alone. Accessible and published datasets not already incorporated do exist within spatial and temporal gaps identified. Other related open-source data portals also contain data that fill gaps, emphasizing the importance of dedicated data exchange. Temporal and spatial gaps were mostly a result of data acquisition effort, development of regional partnerships and collaborations, and ease of field data collection. Future directions should include fostering partnerships with researchers in the Southern Hemisphere while targeting datasets containing species with limited representation. These results can facilitate prioritizing datasets needed to be represented and for planning research for true gaps in space and time.}, } @article {pmid20884961, year = {2010}, author = {Riordan, DV and Stark, C}, title = {Interpretation of ecological data.}, journal = {The British journal of psychiatry : the journal of mental science}, volume = {197}, number = {4}, pages = {332; author reply 332}, doi = {10.1192/bjp.197.4.332}, pmid = {20884961}, issn = {1472-1465}, mesh = {Child, Preschool ; Data Interpretation, Statistical ; *Family Characteristics ; Female ; Humans ; Suicide/*statistics & numerical data ; Young Adult ; }, } @article {pmid20879541, year = {2010}, author = {Cao, JJ and Liu, YJ}, title = {[Ecological sensitivity of Shanghai City based on GIS spatial analysis].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {21}, number = {7}, pages = {1805-1812}, pmid = {20879541}, issn = {1001-9332}, mesh = {China ; *Cities ; Conservation of Natural Resources/*economics ; *Ecosystem ; *Environmental Monitoring/methods ; *Geographic Information Systems ; Human Activities ; Models, Theoretical ; }, abstract = {In this paper, five sensitivity factors affecting the eco-environment of Shanghai City, i.e., rivers and lakes, historical relics and forest parks, geological disasters, soil pollution, and land use, were selected, and their weights were determined by analytic hierarchy process. Combining with GIS spatial analysis technique, the sensitivities of these factors were classified into four grades, i.e., highly sensitive, moderately sensitive, low sensitive, and insensitive, and the spatial distribution of the ecological sensitivity of Shanghai City was figured out. There existed a significant spatial differentiation in the ecological sensitivity of the City, and the insensitive, low sensitive, moderately sensitive, and highly sensitive areas occupied 37.07%, 5.94%, 38.16%, and 18.83%, respectively. Some suggestions on the City's zoning protection and construction were proposed. This study could provide scientific references for the City's environmental protection and economic development.}, } @article {pmid20879181, year = {2010}, author = {Shihadeh, ES and Winters, L}, title = {Church, place, and crime: Latinos and homicide in new destinations.}, journal = {Sociological inquiry}, volume = {80}, number = {4}, pages = {628-649}, doi = {10.1111/j.1475-682x.2010.00355.x}, pmid = {20879181}, issn = {0038-0245}, mesh = {Community Networks/economics/history ; *Crime/economics/ethnology/history/legislation & jurisprudence/psychology ; Criminals/education/history/legislation & jurisprudence/psychology ; *Hispanic or Latino/education/ethnology/history/legislation & jurisprudence/psychology ; History, 20th Century ; History, 21st Century ; *Homicide/economics/ethnology/history/legislation & jurisprudence/psychology ; *Population Dynamics/history ; *Religion/history ; Social Justice/economics/education/history/legislation & jurisprudence/psychology ; Social Mobility/economics/history ; Social Problems/economics/ethnology/history/legislation & jurisprudence/psychology ; Violence/economics/ethnology/history/legislation & jurisprudence/psychology ; }, abstract = {Latinos are moving beyond traditional areas and settling in new, potentially disorganized destinations. Without an established immigrant community, new destinations appear to rely more on the local religious ecology to regulate community life and to keep crime low. We examine the link between religious ecology and Latino homicide victimization for traditional and new destination counties. We observe four findings. (1) A Catholic presence has no effect on Latino violence in the old and well-organized traditional settlement areas. But in new Latino settlement areas, a Catholic presence substantially lowers violence against Latinos. In contrast, mainline Protestantism is linked to high levels of violence against Latinos in new destinations. (2) Previous claims that Latino communities are safe do not apply to new destinations, where Latinos are murdered at a high rate. (3) Previous claims that areas with high Latino immigration are safe for Latinos are not true for new destinations. (4) New Latino destinations offer little insulation from the effects of economic deprivation on violence. We discuss the implications of the findings.}, } @article {pmid20874809, year = {2011}, author = {Dieleman, WI and Janssens, IA}, title = {Can publication bias affect ecological research? A case study on soil respiration under elevated CO2.}, journal = {The New phytologist}, volume = {190}, number = {3}, pages = {517-521}, doi = {10.1111/j.1469-8137.2010.03499.x}, pmid = {20874809}, issn = {1469-8137}, mesh = {Aerobiosis/drug effects ; Atmosphere/chemistry ; Carbon Dioxide/*pharmacology ; Databases as Topic ; *Ecology ; *Publication Bias ; Regression Analysis ; *Research ; Soil/*chemistry ; }, } @article {pmid20872652, year = {2010}, author = {Hope, BK and Stone, D and Fuji, T and Gensemer, RW and Jenkins, J}, title = {Meeting the challenge of identifying persistent pollutants at the state level.}, journal = {Integrated environmental assessment and management}, volume = {6}, number = {4}, pages = {735-748}, doi = {10.1002/ieam.94}, pmid = {20872652}, issn = {1551-3793}, mesh = {Animals ; Databases, Factual ; Ecotoxicology/*methods ; Oregon ; Water Pollutants, Chemical/*analysis/toxicity ; }, abstract = {In 2007, the State of Oregon enacted legislation aimed at identifying persistent pollutants that could pose a threat to waters of the State and then reducing their discharge by means of a comprehensive pollution prevention program. This legislation defined a persistent pollutant as one that is toxic and persistent or bioaccumulative; a broad definition that required evaluation of an extensive number and variety of chemicals. The Oregon Department of Environmental Quality, in consultation with a science workgroup, implemented a 12-step process for identifying and prioritizing persistent pollutants consistent with this definition. This process is characterized by (a) maximum overall transparency in its conduct, including extensive public involvement, (b) 3 levels of objective and predefined criteria for categorization of a chemical as a persistent pollutant, (c) full disclosure of values and sources for all physicochemical data used for comparison with these criteria, and (d) clear acknowledgement when a chemical was identified as a persistent pollutant for reasons other than these criteria alone. This process was used to identify those chemicals relevant as persistent pollutants and to then prioritize them in terms of their relative ability to adversely impact waters of the state, with special emphasis on impacts to aquatic receptors. An initial list of 2130 chemicals was compiled from existing lists. Criteria for toxicity, persistence, and bioaccumulative potential were defined and then used with 2 different chemical property evaluation models (PBT Profiler and EPISuite) to produce a final list of 118 chemicals. The final list includes several legacy pollutants but also contains numerous current-use pharmaceuticals, personal care products, and pesticides, approximately half of which appear only once or not at all on lists compiled by others. Although it drew from the experience of others, assembling this list proved to be an exemplar of science in the service of policy.}, } @article {pmid20849277, year = {2011}, author = {Jameson, LJ and Medlock, JM}, title = {Tick surveillance in Great Britain.}, journal = {Vector borne and zoonotic diseases (Larchmont, N.Y.)}, volume = {11}, number = {4}, pages = {403-412}, doi = {10.1089/vbz.2010.0079}, pmid = {20849277}, issn = {1557-7759}, mesh = {Animals ; Databases, Factual ; Disease Reservoirs/*parasitology ; Female ; Geographic Information Systems ; *Host-Parasite Interactions ; Humans ; Insect Vectors/*physiology ; Male ; Population Surveillance ; Tick Infestations ; Ticks/classification/*physiology ; United Kingdom ; }, abstract = {The ability for public/veterinary health agencies to assess the risks posed by tick-borne pathogens is reliant on an understanding of the main tick vector species. Crucially, the status, distribution, and changing trends in tick distribution and abundance are implicit requirements of any risk assessment; however, this is contingent on the quality of tick distribution data. Since 2005 the Health Protection Agency has promoted an enhanced tick surveillance program. Through engagement with a variety of public and veterinary health agencies and practitioners (e.g., clinicians and veterinarians), wildlife groups (deer society, zoos, animal refuge centers, and academics), and amateur entomologists, >4000 ticks from 900 separate records across Great Britain have been submitted, representing 14 tick species (Ixodes ricinus, Ixodes hexagonus, Ixodes acuminatus, Ixodes arboricola, Ixodes canisuga, Ixodes frontalis, Ixodes lividus, Ixodes trianguliceps, Ixodes ventalloi, Carios vespertilionis, Dermacentor reticulatus, Haemaphysalis punctata, Hyalomma marginatum, and Amblyomma species). The majority of ticks submitted were I. ricinus (81%), followed by I. hexagonus (10%) and I. frontalis (2.5%). Predominant host groups include companion animals (411 records), humans (198 records), wild birds (111 records), and large wild mammals (88 records), with records also from small/medium wild mammals, livestock, the environment and domestic/aviary birds. The scheme has elucidated the detection of two nonnative tick species, the expansion of previously geographically restricted D. reticulatus and produced ground data on the spread of I. ricinus in southwest England. It has also provided a forum for submission of ticks from the concerned public and particularly those infected with Lyme borreliosis, thus raising awareness among public health agencies of the increased peri-urban tick problem in Britain. Our results demonstrate that it is possible to run a cost-effective nationwide surveillance program to successfully monitor endemic tick species, identify subtle changes in their distribution, and detect the arrival and presence of exotic species.}, } @article {pmid20843852, year = {2011}, author = {Myers, CE and Lieberman, BS}, title = {Sharks that pass in the night: using Geographical Information Systems to investigate competition in the Cretaceous Western Interior Seaway.}, journal = {Proceedings. Biological sciences}, volume = {278}, number = {1706}, pages = {681-689}, pmid = {20843852}, issn = {1471-2954}, mesh = {Animals ; Demography ; *Ecosystem ; *Fossils ; *Geographic Information Systems ; Population Dynamics ; Sharks/*physiology ; }, abstract = {One way the effects of both ecology and environment on species can be observed in the fossil record is as changes in geographical distribution and range size. The prevalence of competitive interactions and species replacements in the fossil record has long been investigated and many evolutionary perspectives, including those of Darwin, have emphasized the importance of competitive interactions that ultimately lead one species to replace another. However, evidence for such phenomena in the fossil record is not always manifest. Here we use new quantitative analytical techniques based on Geographical Information Systems and PaleoGIS tectonic reconstructions to consider this issue in greater detail. The abundant, well-preserved fossil marine vertebrates of the Late Cretaceous Western Interior Seaway of North America provide the component data for this study. Statistical analysis of distributional and range size changes in taxa confirms earlier ideas that the relative frequency of competitive replacement in the fossil record is limited to non-existent. It appears that typically, environmental gradients played the primary role in determining species distributions, with competitive interactions playing a more minor role.}, } @article {pmid20840751, year = {2010}, author = {Linard, C and Alegana, VA and Noor, AM and Snow, RW and Tatem, AJ}, title = {A high resolution spatial population database of Somalia for disease risk mapping.}, journal = {International journal of health geographics}, volume = {9}, number = {}, pages = {45}, pmid = {20840751}, issn = {1476-072X}, support = {079080/WT_/Wellcome Trust/United Kingdom ; 081829/WT_/Wellcome Trust/United Kingdom ; 079081/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Communicable Diseases ; *Databases, Factual ; Delivery of Health Care ; *Geography ; Humans ; *Population Density ; Risk Assessment/*methods ; Somalia/epidemiology ; }, abstract = {BACKGROUND: Millions of Somali have been deprived of basic health services due to the unstable political situation of their country. Attempts are being made to reconstruct the health sector, in particular to estimate the extent of infectious disease burden. However, any approach that requires the use of modelled disease rates requires reasonable information on population distribution. In a low-income country such as Somalia, population data are lacking, are of poor quality, or become outdated rapidly. Modelling methods are therefore needed for the production of contemporary and spatially detailed population data.

RESULTS: Here land cover information derived from satellite imagery and existing settlement point datasets were used for the spatial reallocation of populations within census units. We used simple and semi-automated methods that can be implemented with free image processing software to produce an easily updatable gridded population dataset at 100 × 100 meters spatial resolution. The 2010 population dataset was matched to administrative population totals projected by the UN. Comparison tests between the new dataset and existing population datasets revealed important differences in population size distributions, and in population at risk of malaria estimates. These differences are particularly important in more densely populated areas and strongly depend on the settlement data used in the modelling approach.

CONCLUSIONS: The results show that it is possible to produce detailed, contemporary and easily updatable settlement and population distribution datasets of Somalia using existing data. The 2010 population dataset produced is freely available as a product of the AfriPop Project and can be downloaded from: http://www.afripop.org.}, } @article {pmid20839850, year = {2010}, author = {Desvaux, M and Dumas, E and Chafsey, I and Chambon, C and Hébraud, M}, title = {Comprehensive appraisal of the extracellular proteins from a monoderm bacterium: theoretical and empirical exoproteomes of Listeria monocytogenes EGD-e by secretomics.}, journal = {Journal of proteome research}, volume = {9}, number = {10}, pages = {5076-5092}, doi = {10.1021/pr1003642}, pmid = {20839850}, issn = {1535-3907}, mesh = {Bacterial Proteins/*analysis/*metabolism ; Computational Biology/methods ; Electrophoresis, Gel, Two-Dimensional ; Extracellular Space/metabolism ; Gram-Positive Bacteria/metabolism ; Listeria monocytogenes/*metabolism ; Proteomics/*methods ; }, abstract = {Defined as proteins actively transported via secretion systems, secreted proteins can have radically different subcellular destinations in monoderm (Gram-positive) bacteria. From degradative enzymes in saprophytes to virulence factors in pathogens, secreted proteins are the main tools used by bacteria to interact with their surroundings. The etiological agent of listeriosis, Listeria monocytogenes, is a Gram-positive facultative intracellular foodborne pathogen, whose ecological niche is the soil and as such should be primarily considered as a ubiquitous saprophyte. Recent advances on protein secretion systems in this species prompted us to investigate the exoproteome. First, an original and rational bioinformatic strategy was developed to mimic the protein exportation steps leading to the extracellular localization of secreted proteins; 79 exoproteins were predicted as secreted via Sec, 1 exoprotein via Tat, 4 bacteriocins via ABC exporters, 3 exoproteins via holins, and 3 exoproteins via the WXG100 system. This bioinformatic analysis allowed for defining a databank of the mature protein set in L. monocytogenes, which was used for generating the theoretical exoproteome and for subsequent protein identification by proteomics. 2-DE proteomic analyses were performed over a wide pI range to experimentally cover the largest protein spectrum possible. A total of 120 spots could be resolved and identified, which corresponded to 50 distinct proteins. These exoproteins were essentially virulence factors, degradative enzymes, and proteins of unknown functions, which exportation would essentially rely on the Sec pathway or nonclassical secretion. This investigation resulted in the first comprehensive appraisal of the exoproteome of L. monocytogenes EGD-e based on theoretical and experimental secretomic analyses, which further provided indications on listerial physiology in relation with its habitat and lifestyle. The novel and rational strategy described here is generic and has been purposely designed for the prediction of proteins localized extracellularly in monoderm bacteria.}, } @article {pmid20838793, year = {2010}, author = {Poor, CJ and Ullman, JL}, title = {Using regression tree analysis to improve predictions of low-flow nitrate and chloride in Willamette River Basin watersheds.}, journal = {Environmental management}, volume = {46}, number = {5}, pages = {771-780}, pmid = {20838793}, issn = {1432-1009}, mesh = {Chlorides/*analysis ; Data Mining ; Decision Support Techniques ; Decision Trees ; Environmental Monitoring/*methods ; Forecasting ; Models, Chemical ; Nitrates/*analysis ; Oregon ; Regression Analysis ; Rivers/chemistry ; Water Pollutants, Chemical/*analysis ; Water Pollution, Chemical/*statistics & numerical data ; Water Supply/analysis/statistics & numerical data ; }, abstract = {The use of regression tree analysis is examined as a tool to evaluate hydrologic and land use factors that affect nitrate and chloride stream concentrations during low-flow conditions. Although this data mining technique has been used to assess a range of ecological parameters, it has not previously been used for stream water quality analysis. Regression tree analysis was conducted on nitrate and chloride data from 71 watersheds in the Willamette River Basin to determine whether this method provides a greater predictive ability compared to standard multiple linear regression, and to elucidate the potential roles of controlling mechanisms. Metrics used in the models included a variety of watershed-scale landscape indices and land use classifications. Regression tree analysis significantly enhanced model accuracy over multiple linear regression, increasing nitrate R[2] values from 0.38 to 0.75 and chloride R[2] values from 0.64 to 0.85 and as indicated by the ΔAIC value. These improvements are primarily attributed to the ability for regression trees to more effectively handle interactions and manage non-linear functions associated with watershed heterogeneity within the basin. Whereas hydrologic factors governed the conservative chloride tracer in the model, land use dominated control of nitrate concentrations. Watersheds containing higher agricultural activity did not necessarily yield high nitrate concentrations, but agricultural areas combined with either small proportions of forested land or greater urbanization generated nitrate levels far exceeding water quality standards. Although further refinements are recommended, we conclude that regression tree analysis presents water resource managers a promising tool that improves on the predictive ability of standard statistical methods, provides insight into controlling mechanisms, and helps identify catchment characteristics associated with water quality impairment.}, } @article {pmid20833198, year = {2011}, author = {Al-Yahya, E and Dawes, H and Smith, L and Dennis, A and Howells, K and Cockburn, J}, title = {Cognitive motor interference while walking: a systematic review and meta-analysis.}, journal = {Neuroscience and biobehavioral reviews}, volume = {35}, number = {3}, pages = {715-728}, doi = {10.1016/j.neubiorev.2010.08.008}, pmid = {20833198}, issn = {1873-7528}, mesh = {Cognition/*physiology ; Databases, Factual/statistics & numerical data ; Gait/physiology ; Humans ; Neuropsychological Tests ; Psychomotor Performance/*physiology ; Regression Analysis ; Walking/*physiology ; }, abstract = {Dual-task methodology has been increasingly used to assess cognitive motor interference while walking. However, whether the observed dual-task-related gait changes are systematically related to methodological variations remains unclear and researchers still lack knowledge of what cognitive task to use in different groups for clinical purposes or for research. We systematically reviewed experimental studies that measured gait performance with and without performing concurrent cognitive task. Our results suggest that cognitive tasks that involve internal interfering factors seem to disturb gait performance more than those involving external interfering factors. Meta-analysis results show that the overall effect of different cognitive tasks was prominent in gait speed. In healthy participants, meta-regression analysis suggests strong associations between age and speed reduction under dual-task conditions and between the level of cognitive state and speed reduction under dual-task conditions. Standardizing research methodologies, as well as improving their ecological validity, enables better understanding of dual-task-related gait changes in different populations and improves, in turn, our understanding of neural mechanisms and gait control in general in content.}, } @article {pmid20828916, year = {2011}, author = {Ryu, J and Leschine, TM and Nam, J and Chang, WK and Dyson, K}, title = {A resilience-based approach for comparing expert preferences across two large-scale coastal management programs.}, journal = {Journal of environmental management}, volume = {92}, number = {1}, pages = {92-101}, doi = {10.1016/j.jenvman.2010.08.020}, pmid = {20828916}, issn = {1095-8630}, mesh = {Conservation of Natural Resources/*legislation & jurisprudence ; Decision Support Techniques ; Ecology ; Environment ; Republic of Korea ; *Social Conditions ; Washington ; }, abstract = {This report proposes a method for assessing resilience-building components in coastal social-ecological systems. Using the proposed model, the preferences of experts in Masan Bay (South Korea) and Puget Sound (USA) are compared. A total of 30 management objectives were determined and used to build a hierarchic tree designed using the principles of the Analytic Hierarchy Process (AHP). Surveys were performed with 35 Puget Sound experts using face-to-face interviews and with 28 Masan Bay experts by mail. The results demonstrate that the legal objective, which enables legislation, was the highest preferred component in both regions. The knowledge translation variable was also given a high preference score in both regions. An analysis of variance (ANOVA) showed that the Puget Sound experts significantly favored attention to education, habitat restoration and species protection objectives in comparison to the Masan Bay experts. The Masan Bay experts placed greater emphasis on legislation and the type of institutional design than did the Puget Sound experts. Using cluster analysis, four distinct groups of respondents were independently identified in Puget Sound and three groups were identified in Masan Bay. One unique subgroup in the Puget Sound experts group, which was characterized by its high preferences for habitat restoration and species protection, was not observed in Masan Bay. Demographic variables (length of career and role in coastal issue) failed to account for the differences in groupings and preferences in either region, except for the variable 'favoring information source' in the Puget Sound group. This finding implies that the demographic information was not related to differences in group opinions in both regions. The analysis framework presented here was effective in identifying expert preferences regarding the overall structure and emphasis in coastal management programs. Thus, this framework can be applied towards coastal policy development.}, } @article {pmid20827984, year = {2010}, author = {Wei, YX and Wang, LW}, title = {[Progress in research on land cover products of MODIS].}, journal = {Guang pu xue yu guang pu fen xi = Guang pu}, volume = {30}, number = {7}, pages = {1848-1852}, pmid = {20827984}, issn = {1000-0593}, mesh = {Environment ; *Environmental Monitoring ; *Geographic Information Systems ; *Remote Sensing Technology ; }, abstract = {Remote sensing technology has been rapidly developed in recent decades, and has been widely used in ecology and environment field. MODIS is a new data source, and in its many products, land cover product is an important product, and it has often been used in global and regional models. In the present review, the procedure of producing land cover product is clearly discussed, and the feature of the classification based network or decision tree is introduced. The paper emphasized the importance of direction information in classification, detailed introduction of change vector analysis methods and land cover change detection based artificial nerve network, analyzed global 17 land cover types defined by IGBP, and compared with other 3 classification systems.}, } @article {pmid20827581, year = {2010}, author = {Tenbrook, PL and Palumbo, AJ and Fojut, TL and Hann, P and Karkoski, J and Tjeerdema, RS}, title = {The University of California-Davis methodology for deriving aquatic life pesticide water quality criteria.}, journal = {Reviews of environmental contamination and toxicology}, volume = {209}, number = {}, pages = {1-155}, doi = {10.1007/978-1-4419-6883-8_1}, pmid = {20827581}, issn = {0179-5953}, mesh = {Animals ; Biological Availability ; Data Interpretation, Statistical ; Ecotoxicology ; Endpoint Determination ; Environmental Monitoring ; Pesticides/*toxicity ; Quantitative Structure-Activity Relationship ; Water Pollutants, Chemical/*toxicity ; }, } @article {pmid20827291, year = {2011}, author = {Lozupone, C and Lladser, ME and Knights, D and Stombaugh, J and Knight, R}, title = {UniFrac: an effective distance metric for microbial community comparison.}, journal = {The ISME journal}, volume = {5}, number = {2}, pages = {169-172}, pmid = {20827291}, issn = {1751-7370}, support = {T15 LM009451/LM/NLM NIH HHS/United States ; 5T15 LM009451-03/LM/NLM NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; }, mesh = {Animals ; Bacteria/classification/genetics ; *Data Interpretation, Statistical ; Ecology/*methods ; *Ecosystem ; Humans ; Phylogeny ; Software/*standards ; }, } @article {pmid20824127, year = {2010}, author = {Sueur, C and Deneubourg, JL and Petit, O and Couzin, ID}, title = {Differences in nutrient requirements imply a non-linear emergence of leaders in animal groups.}, journal = {PLoS computational biology}, volume = {6}, number = {9}, pages = {e1000917}, pmid = {20824127}, issn = {1553-7358}, mesh = {Algorithms ; Animals ; Behavior, Animal/*physiology ; Body Weight ; Computational Biology/methods ; Computer Simulation ; Female ; Leadership ; Macaca mulatta ; Male ; Nonlinear Dynamics ; *Nutritional Requirements ; *Social Dominance ; Statistics, Nonparametric ; }, abstract = {Collective decision making and especially leadership in groups are among the most studied topics in natural, social, and political sciences. Previous studies have shown that some individuals are more likely to be leaders because of their social power or the pertinent information they possess. One challenge for all group members, however, is to satisfy their needs. In many situations, we do not yet know how individuals within groups distribute leadership decisions between themselves in order to satisfy time-varying individual requirements. To gain insight into this problem, we build a dynamic model where group members have to satisfy different needs but are not aware of each other's needs. Data about needs of animals come from real data observed in macaques. Several studies showed that a collective movement may be initiated by a single individual. This individual may be the dominant one, the oldest one, but also the one having the highest physiological needs. In our model, the individual with the lowest reserve initiates movements and decides for all its conspecifics. This simple rule leads to a viable decision-making system where all individuals may lead the group at one moment and thus suit their requirements. However, a single individual becomes the leader in 38% to 95% of cases and the leadership is unequally (according to an exponential law) distributed according to the heterogeneity of needs in the group. The results showed that this non-linearity emerges when one group member reaches physiological requirements, mainly the nutrient ones - protein, energy and water depending on weight - superior to those of its conspecifics. This amplification may explain why some leaders could appear in animal groups without any despotism, complex signalling, or developed cognitive ability.}, } @article {pmid20824122, year = {2010}, author = {Laneri, K and Bhadra, A and Ionides, EL and Bouma, M and Dhiman, RC and Yadav, RS and Pascual, M}, title = {Forcing versus feedback: epidemic malaria and monsoon rains in northwest India.}, journal = {PLoS computational biology}, volume = {6}, number = {9}, pages = {e1000898}, pmid = {20824122}, issn = {1553-7358}, mesh = {Animals ; Computer Simulation ; Culicidae ; Databases, Factual ; *Epidemics ; Feedback, Physiological ; Host-Parasite Interactions ; Humans ; India/epidemiology ; Insect Vectors ; Malaria, Falciparum/*epidemiology/transmission ; *Models, Biological ; Models, Statistical ; Plasmodium falciparum/*growth & development ; *Rain ; Seasons ; Systems Biology/methods ; }, abstract = {Malaria epidemics in regions with seasonal windows of transmission can vary greatly in size from year to year. A central question has been whether these interannual cycles are driven by climate, are instead generated by the intrinsic dynamics of the disease, or result from the resonance of these two mechanisms. This corresponds to the more general inverse problem of identifying the respective roles of external forcings vs. internal feedbacks from time series for nonlinear and noisy systems. We propose here a quantitative approach to formally compare rival hypotheses on climate vs. disease dynamics, or external forcings vs. internal feedbacks, that combines dynamical models with recently developed, computational inference methods. The interannual patterns of epidemic malaria are investigated here for desert regions of northwest India, with extensive epidemiological records for Plasmodium falciparum malaria for the past two decades. We formulate a dynamical model of malaria transmission that explicitly incorporates rainfall, and we rely on recent advances on parameter estimation for nonlinear and stochastic dynamical systems based on sequential Monte Carlo methods. Results show a significant effect of rainfall in the inter-annual variability of epidemic malaria that involves a threshold in the disease response. The model exhibits high prediction skill for yearly cases in the malaria transmission season following the monsoonal rains. Consideration of a more complex model with clinical immunity demonstrates the robustness of the findings and suggests a role of infected individuals that lack clinical symptoms as a reservoir for transmission. Our results indicate that the nonlinear dynamics of the disease itself play a role at the seasonal, but not the interannual, time scales. They illustrate the feasibility of forecasting malaria epidemics in desert and semi-arid regions of India based on climate variability. This approach should be applicable to malaria in other locations, to other infectious diseases, and to other nonlinear systems under forcing.}, } @article {pmid20821712, year = {2010}, author = {Fox, DR}, title = {Statistics and ecotoxicology: shotgun marriage or enduring partnership?.}, journal = {Integrated environmental assessment and management}, volume = {6}, number = {3}, pages = {501-502}, doi = {10.1002/ieam.81}, pmid = {20821712}, issn = {1551-3793}, mesh = {Data Interpretation, Statistical ; Ecotoxicology/*methods ; Research Design ; *Statistics as Topic ; }, } @article {pmid20821701, year = {2010}, author = {Crane, M and Gross, M and Matthiessen, P and Ankley, GT and Axford, S and Bjerregaard, P and Brown, R and Chapman, P and Dorgeloh, M and Galay-Burgos, M and Green, J and Hazlerigg, C and Janssen, J and Lorenzen, K and Parrott, J and Rufli, H and Schäfers, C and Seki, M and Stolzenberg, HC and van der Hoeven, N and Vethaak, D and Winfield, IJ and Zok, S and Wheeler, J}, title = {Multi-criteria decision analysis of test endpoints for detecting the effects of endocrine active substances in fish full life cycle tests.}, journal = {Integrated environmental assessment and management}, volume = {6}, number = {3}, pages = {378-389}, doi = {10.1002/ieam.43}, pmid = {20821701}, issn = {1551-3793}, mesh = {Animals ; *Decision Support Techniques ; Ecotoxicology/*methods ; Endocrine Disruptors/*toxicity ; Endpoint Determination/*methods ; Female ; Fishes/*growth & development ; Life Cycle Stages/*drug effects ; Male ; Toxicity Tests/*methods ; }, abstract = {Fish full life cycle (FFLC) tests are increasingly required in the ecotoxicological assessment of endocrine active substances. However, FFLC tests have not been internationally standardized or validated, and it is currently unclear how such tests should best be designed to provide statistically sound and ecologically relevant results. This study describes how the technique of multi-criteria decision analysis (MCDA) was used to elicit the views of fish ecologists, aquatic ecotoxicologists and statisticians on optimal experimental designs for assessing the effects of endocrine active chemicals on fish. In MCDA qualitative criteria (that can be valued, but not quantified) and quantitative criteria can be used in a structured decision-making process. The aim of the present application of MCDA is to present a logical means of collating both data and expert opinions on the best way to focus FFLC tests on endocrine active substances. The analyses are presented to demonstrate how MCDA can be used in this context. Each of 3 workgroups focused on 1 of 3 species: fathead minnow (Pimephales promelas), Japanese medaka (Oryzias latipes), and zebrafish (Danio rerio). Test endpoints (e.g., fecundity, growth, gonadal histopathology) were scored for each species for various desirable features such as statistical power and ecological relevance, with the importance of these features determined by assigning weights to them, using a swing weighting procedure. The endpoint F1 fertilization success consistently emerged as a preferred option for all species. In addition, some endpoints scored highly in particular species, such as development of secondary sexual characteristics (fathead minnow) and sex ratio (zebrafish). Other endpoints such as hatching success ranked relatively highly and should be considered as useful endpoints to measure in tests with any of the fish species. MCDA also indicated relatively less preferred endpoints in fish life cycle tests. For example, intensive histopathology consistently ranked low, as did measurement of diagnostic biomarkers, such as vitellogenin, most likely due to the high costs of these methods or their limited ecological relevance. Life cycle tests typically do not focus on identifying toxic modes and/or mechanisms of action, but rather, single chemical concentration-response relationships for endpoints (e.g., survival, growth, reproduction) that can be translated into evaluation of risk. It is, therefore, likely to be an inefficient use of limited resources to measure these mechanism-specific endpoints in life cycle tests, unless the value of such endpoints for answering particular questions justifies their integration in specific case studies.}, } @article {pmid20817633, year = {2010}, author = {Strack, RW and Lovelace, KA and Jordan, TD and Holmes, AP}, title = {Framing photovoice using a social-ecological logic model as a guide.}, journal = {Health promotion practice}, volume = {11}, number = {5}, pages = {629-636}, doi = {10.1177/1524839909355519}, pmid = {20817633}, issn = {1524-8399}, mesh = {Community Networks/*organization & administration ; Community-Based Participatory Research/*organization & administration ; Health Promotion/*organization & administration ; Humans ; Smoking Prevention ; *Social Change ; }, abstract = {Photovoice is a community-based participatory action research method designed to uncover the root causes of community problems and to collectively address them. Individual change and empowerment are desired outcomes of the photovoice process, but more importantly, the process seeks to engage groups and whole communities to foster positive systems change. This article presents a logic model informed by the social-ecological model of health to guide photovoice planners and participants in planning activities that produce individual-and community-level change. The model presented here should help planners and participants plan, implement, and evaluate other photovoice efforts and provide them a visual guide to ensure that all parties are on the same conceptual page and increase the intentionality of their efforts.}, } @article {pmid20817437, year = {2010}, author = {Yarza, P and Ludwig, W and Euzéby, J and Amann, R and Schleifer, KH and Glöckner, FO and Rosselló-Móra, R}, title = {Update of the All-Species Living Tree Project based on 16S and 23S rRNA sequence analyses.}, journal = {Systematic and applied microbiology}, volume = {33}, number = {6}, pages = {291-299}, doi = {10.1016/j.syapm.2010.08.001}, pmid = {20817437}, issn = {1618-0984}, mesh = {Archaea/*classification/genetics ; Bacteria/*classification/genetics ; *Databases, Genetic ; *Phylogeny ; RNA, Ribosomal, 16S/*genetics ; RNA, Ribosomal, 23S/*genetics ; }, abstract = {The "All-Species Living Tree Project" (LTP) provides the scientific community with a useful taxonomic tool consisting of a curated database of type strain sequences, a universal and optimized alignment and a single phylogenetic tree harboring all the type strains of the hitherto classified species. On the website http://www.arb-silva.de/projects/living-tree an update has been regularly maintained by including the 1301 new descriptions that have appeared in the validation and notification lists of the IJSEM journal. The topology of the 16S rRNA-based tree was validated with a detailed comparison against a collection of taxa-specific and broad-range trees made using different approaches, subsets of sequences and alignments. Seven percent of the classified species is still missing, as their type strains do not have a good quality SSU sequence. In addition, a new database of type strains for which adequate 23S rRNA entries existed in public repositories was built. Among the 8602 species with validly published names until February 2010, we were able to find good quality LSU representatives for 792 type strains, whereas around 91% of the complete catalogue still remains unsequenced. Despite the scarce representation of some groups in LSU databases, we have devised a highly optimized alignment and a reliable LSU tree in order to set up a stable phylogenetic starting point for taxonomic purposes. The current release corresponds to the fourth update of the project (LTPs102), and contains additional features which increase usability and compatibility. Use the contact address living-tree@arb-silva.de to provide additional input for the development of this taxonomic tool.}, } @article {pmid20814715, year = {2010}, author = {Raine, KD and Plotnikoff, R and Nykiforuk, C and Deegan, H and Hemphill, E and Storey, K and Schopflocher, D and Veugelers, P and Wild, TC and Ohinmaa, A}, title = {Reflections on community-based population health intervention and evaluation for obesity and chronic disease prevention: the Healthy Alberta Communities project.}, journal = {International journal of public health}, volume = {55}, number = {6}, pages = {679-686}, pmid = {20814715}, issn = {1661-8564}, support = {//Canadian Institutes of Health Research/Canada ; }, mesh = {Alberta ; Chronic Disease/*prevention & control ; Community Networks/economics/*organization & administration ; Humans ; Obesity/*prevention & control ; *Research Design ; }, abstract = {OBJECTIVES: To reflect upon a population health intervention for obesity and chronic disease prevention, with specific attention to the processes of change and developing, implementing and evaluating an intervention in a community-university-government partnership context.

METHODS: To capture the value, process and context of our interventions, we employed a multi-layered, mixed methods research and evaluation design. Guided by assumptions of community-based participatory research, and using a validated capacity-building tool, the investigators described and reflected critically upon the level and nature of capacity built (for both research and intervention) as indicators of the process and contextual influences on intervention success.

RESULTS: Capacity was built in communities through collaborative approaches. We captured complexity of change in social context to advance understanding of how to intervene to transform environments. Developing novel community evaluation strategies can help to advance understanding of how environmental interventions affect health before health outcomes data demonstrate change.

CONCLUSIONS: Our experience provides an example of operationalizing an ecological framework. As a community-university-government partnership, Healthy Alberta Communities provides an opportunity for developing promising practices for the health of communities, as well as a unique research platform for evaluating the process and establishing effectiveness of population health interventions.}, } @article {pmid20813951, year = {2010}, author = {Alroy, J}, title = {The shifting balance of diversity among major marine animal groups.}, journal = {Science (New York, N.Y.)}, volume = {329}, number = {5996}, pages = {1191-1194}, doi = {10.1126/science.1189910}, pmid = {20813951}, issn = {1095-9203}, mesh = {Adaptation, Biological ; Animals ; Anthozoa ; *Biodiversity ; Biological Evolution ; Data Interpretation, Statistical ; *Databases, Factual ; Extinction, Biological ; *Fossils ; *Invertebrates ; Marine Biology ; Models, Biological ; *Mollusca ; Oceans and Seas ; Paleontology ; Population Dynamics ; Statistics as Topic ; Time ; }, abstract = {The fossil record demonstrates that each major taxonomic group has a consistent net rate of diversification and a limit to its species richness. It has been thought that long-term changes in the dominance of major taxonomic groups can be predicted from these characteristics. However, new analyses show that diversity limits may rise or fall in response to adaptive radiations or extinctions. These changes are idiosyncratic and occur at different times in each taxa. For example, the end-Permian mass extinction permanently reduced the diversity of important, previously dominant groups such as brachiopods and crinoids. The current global crisis may therefore permanently alter the biosphere's taxonomic composition by changing the rules of evolution.}, } @article {pmid20813942, year = {2010}, author = {Marshall, CR}, title = {Paleontology. Marine biodiversity dynamics over deep time.}, journal = {Science (New York, N.Y.)}, volume = {329}, number = {5996}, pages = {1156-1157}, doi = {10.1126/science.1194924}, pmid = {20813942}, issn = {1095-9203}, mesh = {Animals ; *Biodiversity ; Data Interpretation, Statistical ; *Databases, Factual ; *Ecosystem ; Extinction, Biological ; *Fossils ; Geography ; *Invertebrates ; Marine Biology ; Oceans and Seas ; *Paleontology ; Population Dynamics ; Time ; }, } @article {pmid20813425, year = {2010}, author = {Edwards, M and Beaugrand, G and Hays, GC and Koslow, JA and Richardson, AJ}, title = {Multi-decadal oceanic ecological datasets and their application in marine policy and management.}, journal = {Trends in ecology & evolution}, volume = {25}, number = {10}, pages = {602-610}, doi = {10.1016/j.tree.2010.07.007}, pmid = {20813425}, issn = {0169-5347}, mesh = {Animals ; Climate Change ; Conservation of Energy Resources ; *Databases, Factual ; Environmental Policy ; Fisheries ; *Marine Biology ; Oceans and Seas ; Plankton ; Time Factors ; }, abstract = {Long-term biological time-series in the oceans are relatively rare. Using the two longest of these we show how the information value of such ecological time-series increases through space and time in terms of their potential policy value. We also explore the co-evolution of these oceanic biological time-series with changing marine management drivers. Lessons learnt from reviewing these sequences of observations provide valuable context for the continuation of existing time-series and perspective for the initiation of new time-series in response to rapid global change. Concluding sections call for a more integrated approach to marine observation systems and highlight the future role of ocean observations in adaptive marine management.}, } @article {pmid20807970, year = {2010}, author = {Niederkrotenthaler, T and Voracek, M and Herberth, A and Till, B and Strauss, M and Etzersdorfer, E and Eisenwort, B and Sonneck, G}, title = {Role of media reports in completed and prevented suicide: Werther v. Papageno effects.}, journal = {The British journal of psychiatry : the journal of mental science}, volume = {197}, number = {3}, pages = {234-243}, doi = {10.1192/bjp.bp.109.074633}, pmid = {20807970}, issn = {1472-1465}, mesh = {Austria/epidemiology ; Data Interpretation, Statistical ; Humans ; *Imitative Behavior ; Language ; Mass Media/*statistics & numerical data ; *Models, Statistical ; Newspapers as Topic/*statistics & numerical data ; Qualitative Research ; Risk Factors ; Suicide/psychology/*statistics & numerical data ; Suicide, Attempted/prevention & control/psychology/statistics & numerical data ; Suicide Prevention ; }, abstract = {BACKGROUND: Media reporting of suicide has repeatedly been shown to trigger suicidal behaviour. Few studies have investigated the associations between specific media content and suicide rates. Even less is known about the possible preventive effects of suicide-related media content.

AIMS: To test the hypotheses that certain media content is associated with an increase in suicide, suggesting a so-called Werther effect, and that other content is associated with a decrease in suicide, conceptualised as a Papageno effect. Further, to identify classes of media articles with similar reporting profiles and to test for associations between these classes and suicide.

METHOD: Content analysis and latent class analysis (LCA) of 497 suicide-related print media reports published in Austria between 1 January and 30 June 2005. Ecological study to identify associations between media item content and short-term changes in suicide rates.

RESULTS: Repetitive reporting of the same suicide and the reporting of suicide myths were positively associated with suicide rates. Coverage of individual suicidal ideation not accompanied by suicidal behaviour was negatively associated with suicide rates. The LCA yielded four classes of media reports, of which the mastery of crisis class (articles on individuals who adopted coping strategies other than suicidal behaviour in adverse circumstances) was negatively associated with suicide, whereas the expert opinion class and the epidemiological facts class were positively associated with suicide.

CONCLUSIONS: The impact of suicide reporting may not be restricted to harmful effects; rather, coverage of positive coping in adverse circumstances, as covered in media items about suicidal ideation, may have protective effects.}, } @article {pmid20800072, year = {2010}, author = {Cole, DJ and Morgan, BJ and Titterington, DM}, title = {Determining the parametric structure of models.}, journal = {Mathematical biosciences}, volume = {228}, number = {1}, pages = {16-30}, doi = {10.1016/j.mbs.2010.08.004}, pmid = {20800072}, issn = {1879-3134}, mesh = {Algorithms ; Bayes Theorem ; Computational Biology/*methods ; Ecosystem ; Likelihood Functions ; Linear Models ; *Models, Biological ; *Models, Statistical ; *Nonlinear Dynamics ; Oxygen/metabolism ; Sewage/microbiology ; }, abstract = {In this paper we develop a comprehensive approach to determining the parametric structure of models. This involves considering whether a model is parameter redundant or not and investigating model identifiability. The approach adopted makes use of exhaustive summaries, quantities that uniquely define the model. We review and generalise previous work on evaluating the symbolic rank of an appropriate derivative matrix to detect parameter redundancy, and then develop further tools for use within this framework, based on a matrix decomposition. Complex models, where the symbolic rank is difficult to calculate, may be simplified structurally using reparameterisation and by finding a reduced-form exhaustive summary. The approach of the paper is illustrated using examples from ecology, compartment modelling and Bayes networks. This work is topical as models in the biosciences and elsewhere are becoming increasingly complex.}, } @article {pmid20734854, year = {2010}, author = {Karamova, LM and Larionova, TK and Basharova, GR}, title = {[Criteria of ecologic safety for serum levels of heavy metals in humans].}, journal = {Meditsina truda i promyshlennaia ekologiia}, volume = {}, number = {6}, pages = {21-23}, pmid = {20734854}, issn = {1026-9428}, mesh = {Adult ; Cholesterol/blood ; Data Interpretation, Statistical ; Ecology ; Environmental Monitoring ; Environmental Pollutants/*blood/toxicity ; Female ; Hair/chemistry ; Hemostasis ; Homeostasis ; Humans ; Male ; Maximum Allowable Concentration ; Metals, Heavy/*blood/toxicity ; Russia ; Safety ; Triglycerides/blood ; }, abstract = {To evaluate ecologically allowable level of serum metals content in humans for making regional background normal level, the number of heavy metal ions should be determined in healthy human serum and simultaneously homeostasis parameters (hemolysis, biochemistry, immunologic) should be measured--clinically normal limits of these parameters are responsible for safe levels of of the heavy metals in human body. The suggested levels of metals in healthy human serum could serve as clinical MACs.}, } @article {pmid20729613, year = {2010}, author = {Edberg, M and Cleary, SD and Andrade, E and Leiva, R and Bazurto, M and Rivera, MI and Montero, L and Calderon, M}, title = {SAFER Latinos: a community partnership to address contributing factors for Latino youth violence.}, journal = {Progress in community health partnerships : research, education, and action}, volume = {4}, number = {3}, pages = {221-233}, doi = {10.1353/cpr.2010.0009}, pmid = {20729613}, issn = {1557-0541}, support = {P20 MD006898/MD/NIMHD NIH HHS/United States ; 5U49CE000771/CE/NCIPC CDC HHS/United States ; }, mesh = {Adolescent ; *Community Networks ; Health Promotion ; Health Status Disparities ; *Hispanic or Latino ; Humans ; Maryland ; Models, Theoretical ; Risk Factors ; Social Class ; Violence/*ethnology/*prevention & control ; }, abstract = {BACKGROUND: This paper describes a multilevel youth violence prevention effort called SAFER Latinos (Seguridad, Apoyo, Familia, Educacion, y Recursos), a collaboration between The George Washington University School of Public Health and Health Services (GWU) and two key Latino community organizations.

OBJECTIVES: To implement and evaluate an intervention addressing factors within the social ecology of an immigrant Latino community.

METHODS: The intervention includes (1) Social promotores for family outreach and problem resolution; (2) Youth peer advocates at the high school level; (3) a drop-in center with support services for families and youth; and (4) community events, capacity building, and messages. Evaluation includes a baseline and follow-up surveys (N = 1,400) and focus groups.

LESSONS LEARNED: (1) Community circumstances change, requiring regular program adaptation. (2) Community interventions with research face potential contradictions in purpose impacting management of the collaboration and model fidelity. (3) Etiological models tied to interventions may have to be revisited owing to changes in the character and dynamics of the immigrant community.}, } @article {pmid20723060, year = {2010}, author = {Eckert, AJ and Bower, AD and González-Martínez, SC and Wegrzyn, JL and Coop, G and Neale, DB}, title = {Back to nature: ecological genomics of loblolly pine (Pinus taeda, Pinaceae).}, journal = {Molecular ecology}, volume = {19}, number = {17}, pages = {3789-3805}, doi = {10.1111/j.1365-294X.2010.04698.x}, pmid = {20723060}, issn = {1365-294X}, mesh = {Adaptation, Physiological/genetics ; Bayes Theorem ; Climate ; DNA, Plant/genetics ; Ecology/methods ; Gene Frequency ; Genes, Plant ; *Genetic Variation ; *Genetics, Population ; Genomics/methods ; Genotype ; Geographic Information Systems ; Geography ; Linear Models ; Models, Genetic ; Pinus taeda/*genetics ; Polymorphism, Single Nucleotide ; Principal Component Analysis ; Sequence Analysis, DNA ; }, abstract = {Genetic variation is often arrayed in latitudinal or altitudinal clines, reflecting either adaptation along environmental gradients, migratory routes, or both. For forest trees, climate is one of the most important drivers of adaptive phenotypic traits. Correlations of single and multilocus genotypes with environmental gradients have been identified for a variety of forest trees. These correlations are interpreted normally as evidence of natural selection. Here, we use a genome-wide dataset of single nucleotide polymorphisms (SNPs) typed from 1730 loci in 682 loblolly pine (Pinus taeda L.) trees sampled from 54 local populations covering the full-range of the species to examine allelic correlations to five multivariate measures of climate. Applications of a Bayesian generalized linear mixed model, where the climate variable was a fixed effect and an estimated variance-covariance matrix controlled random effects due to shared population history, identified several well-supported SNPs associating to principal components corresponding to geography, temperature, growing degree-days, precipitation and aridity. Functional annotation of those genes with putative orthologs in Arabidopsis revealed a diverse set of abiotic stress response genes ranging from transmembrane proteins to proteins involved in sugar metabolism. Many of these SNPs also had large allele frequency differences among populations (F(ST) = 0.10-0.35). These results illustrate a first step towards a ecosystem perspective of population genomics for non-model organisms, but also highlight the need for further integration of the methodologies employed in spatial statistics, population genetics and climate modeling during scans for signatures of natural selection from genomic data.}, } @article {pmid20723051, year = {2010}, author = {Anderson, CD and Epperson, BK and Fortin, MJ and Holderegger, R and James, PM and Rosenberg, MS and Scribner, KT and Spear, S}, title = {Considering spatial and temporal scale in landscape-genetic studies of gene flow.}, journal = {Molecular ecology}, volume = {19}, number = {17}, pages = {3565-3575}, doi = {10.1111/j.1365-294X.2010.04757.x}, pmid = {20723051}, issn = {1365-294X}, mesh = {Ecology/methods ; *Environment ; *Gene Flow ; Genetic Markers ; *Genetics, Population ; Genotype ; *Models, Genetic ; Models, Statistical ; }, abstract = {Landscape features exist at multiple spatial and temporal scales, and these naturally affect spatial genetic structure and our ability to make inferences about gene flow. This article discusses how decisions about sampling of genotypes (including choices about analytical methods and genetic markers) should be driven by the scale of spatial genetic structure, the time frame that landscape features have existed in their current state, and all aspects of a species' life history. Researchers should use caution when making inferences about gene flow, especially when the spatial extent of the study area is limited. The scale of sampling of the landscape introduces different features that may affect gene flow. Sampling grain should be smaller than the average home-range size or dispersal distance of the study organism and, for raster data, existing research suggests that simplifying the thematic resolution into discrete classes may result in low power to detect effects on gene flow. Therefore, the methods used to characterize the landscape between sampling sites may be a primary determinant for the spatial scale at which analytical results are applicable, and the use of only one sampling scale for a particular statistical method may lead researchers to overlook important factors affecting gene flow. The particular analytical technique used to correlate landscape data and genetic data may also influence results; common landscape-genetic methods may not be suitable for all study systems, particularly when the rate of landscape change is faster than can be resolved by common molecular markers.}, } @article {pmid20714642, year = {2010}, author = {Pang, E and Lin, K}, title = {Yeast protein-protein interaction binding sites: prediction from the motif-motif, motif-domain and domain-domain levels.}, journal = {Molecular bioSystems}, volume = {6}, number = {11}, pages = {2164-2173}, doi = {10.1039/c0mb00038h}, pmid = {20714642}, issn = {1742-2051}, mesh = {Binding Sites ; Databases, Protein ; Mutation/genetics ; Predictive Value of Tests ; Protein Binding ; *Protein Interaction Domains and Motifs ; Protein Interaction Mapping/*methods ; Reproducibility of Results ; Saccharomyces cerevisiae/*metabolism ; }, abstract = {Interacting proteins can contact with each other at three different levels: by a domain binding to another domain, by a domain binding to a short protein motif, or by a motif binding to another motif. In our previous work, we proposed an approach to predict motif-motif binding sites for the yeast interactome by contrasting high-quality positive interactions and high-quality non-interactions using a simple statistical analysis. Here, we extend this idea to more comprehensively infer binding sites, including domain-domain, domain-motif, and motif-motif interactions. In this study, we integrated 2854 yeast proteins that undergo 13 531 high-quality interactions and 3491 yeast proteins undergoing 578 459 high-quality non-interactions. Overall, we found 6315 significant binding site pairs involving 2371 domains and 637 motifs. Benchmarked using the iPfam, DIP CORE, and MIPS, our inferred results are reliable. Interestingly, some of our predicted binding site pairs may, at least in the yeast genome, guide researchers to assay novel protein-protein interactions by mutagenesis or other experiments. Our work demonstrates that by inferring significant protein-protein binding sites at an aggregate level combining domain-domain, domain-motif and motif-motif levels based on high-quality positive and negative datasets, this method may be capable of identifying the binding site pairs that mediate protein-protein interactions.}, } @article {pmid20711777, year = {2011}, author = {Rubach, MN and Crum, SJ and Van den Brink, PJ}, title = {Variability in the dynamics of mortality and immobility responses of freshwater arthropods exposed to chlorpyrifos.}, journal = {Archives of environmental contamination and toxicology}, volume = {60}, number = {4}, pages = {708-721}, pmid = {20711777}, issn = {1432-0703}, mesh = {Animals ; Arthropods/*drug effects/growth & development ; Chlorpyrifos/*toxicity ; Data Interpretation, Statistical ; Dose-Response Relationship, Drug ; Endpoint Determination ; Fresh Water/*chemistry ; Lethal Dose 50 ; Motor Activity/*drug effects ; Species Specificity ; *Toxicity Tests/methods/standards ; Water Pollutants, Chemical/*toxicity ; }, abstract = {The species sensitivity distribution (SSD) concept is an important probabilistic tool for environmental risk assessment (ERA) and accounts for differences in species sensitivity to different chemicals. The SSD model assumes that the sensitivity of the species included is randomly distributed. If this assumption is violated, indicator values, such as the 50% hazardous concentration, can potentially change dramatically. Fundamental research, however, has discovered and described specific mechanisms and factors influencing toxicity and sensitivity for several model species and chemical combinations. Further knowledge on how these mechanisms and factors relate to toxicologic standard end points would be beneficial for ERA. For instance, little is known about how the processes of toxicity relate to the dynamics of standard toxicity end points and how these may vary across species. In this article, we discuss the relevance of immobilization and mortality as end points for effects of the organophosphate insecticide chlorpyrifos on 14 freshwater arthropods in the context of ERA. For this, we compared the differences in response dynamics during 96 h of exposure with the two end points across species using dose response models and SSDs. The investigated freshwater arthropods vary less in their immobility than in their mortality response. However, differences in observed immobility and mortality were surprisingly large for some species even after 96 h of exposure. As expected immobility was consistently the more sensitive end point and less variable across the tested species and may therefore be considered as the relevant end point for population of SSDs and ERA, although an immobile animal may still potentially recover. This is even more relevant because an immobile animal is unlikely to survive for long periods under field conditions. This and other such considerations relevant to the decision-making process for a particular end point are discussed.}, } @article {pmid20707227, year = {2010}, author = {Horton, S and Miloff, A}, title = {Iodine status and availability of iodized salt: an across-country analysis.}, journal = {Food and nutrition bulletin}, volume = {31}, number = {2}, pages = {214-220}, doi = {10.1177/156482651003100204}, pmid = {20707227}, issn = {0379-5721}, mesh = {Child ; Cross-Sectional Studies ; Databases, Factual ; Developed Countries/statistics & numerical data ; Developing Countries/statistics & numerical data ; Family Characteristics ; *Global Health ; Humans ; Iodine/*administration & dosage/analysis/deficiency/supply & distribution/urine ; Models, Statistical ; Nutrition Policy ; *Nutritional Status ; Sodium Chloride, Dietary/*supply & distribution ; Soil/analysis ; }, abstract = {BACKGROUND: Iodine deficiency has serious consequences, and the Universal Salt iodization initiative has attempted to reduce the extent of deficiency.

OBJECTIVE: We aim to see how far across-country variations in urinary iodine in school-age children can be explained by environmental factors, particularly soil iodine and the availability of iodized salt.

METHODS: We use simple multivariate regression for two separate datasets, one for 30 developing countries, and one for 13 developed countries, using data on availability of iodized salt and soil iodine levels.

RESULTS: Median urinary iodine excretion is significantly and positively related to household availability of iodized salt (elasticity, 0.73) for developing countries, but the soil coefficient is not significant, probably because the dummy variable is not well measured. For the developed countries, there is a positive and significant effect of salt penetration rates (elasticity, 0.83) and a positive and significant effect of soil iodine (elasticity, 0.77). There is also a suggestion that countries with more serious soil deficits are more likely to iodize salt, so that univariate regressions of urinary iodine excretion on salt availability or penetration rates underestimate the beneficial effects of iodized salt availability on iodine nutrition.

CONCLUSIONS: There are limitations to cross-sectional (ecologic) studies such as this, and the data are not perfect. Nevertheless, the results provide support for policies to iodize salt, given the widespread deficiency of iodine in diets worldwide.}, } @article {pmid20707097, year = {2010}, author = {Zhang, MY and Wang, KL and Liu, HY and Chen, HS and Zhang, CH and Yue, YM}, title = {[Responses of ecosystem service values to landscape pattern change in typical Karst area of northwest Guangxi, China].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {21}, number = {5}, pages = {1174-1179}, pmid = {20707097}, issn = {1001-9332}, mesh = {Altitude ; China ; *Ecosystem ; *Environment Design ; Environmental Monitoring/methods ; Geographic Information Systems ; Poaceae/*growth & development ; Satellite Communications ; Trees/*growth & development ; }, abstract = {Based on 3S technique, this paper examined the responses of ecosystem service values (ESVs) to the landscape pattern change in the typical Karst area of northwest Guangxi, China in 1985, 1990, 2000 and 2005. The ESVs in the study area had close relations to landscape area, fragmentation degree, complexity of patch shape, areas of critical type, patch connectivity, and patch richness. It was linearly positively correlated with landscape area and had curvilinear positive correlations with patch index (LPI), contagion index (CONTAG), aggregative index (AI), effective mesh (MESH), proportion of like adjacencies (PLADJ), and tended to be increased with increasing patch area and patch connectivity of critical landscape type. The ESVs had curvilinear negative correlations with division index (DIVISION), split index (SPLIT), and patch richness (PRD), and decreased with increasing patch fragmentation and shrinking patch size. Therefore, it would be important to protect the critical landscape types such as woodland, shrub, and grassland, and to increase the patch size and connectivity to 'avoid further fragmentation. Moreover, it would be necessary to reduce the frequency and severity of disturbances to ensure the ESVs growth and the sustainable development of the study area.}, } @article {pmid20703226, year = {2010}, author = {Wood, SN}, title = {Statistical inference for noisy nonlinear ecological dynamic systems.}, journal = {Nature}, volume = {466}, number = {7310}, pages = {1102-1104}, pmid = {20703226}, issn = {1476-4687}, mesh = {Animals ; Computer Simulation ; *Data Interpretation, Statistical ; Diptera/physiology ; Ecology/methods ; *Models, Biological ; Population Density ; }, abstract = {Chaotic ecological dynamic systems defy conventional statistical analysis. Systems with near-chaotic dynamics are little better. Such systems are almost invariably driven by endogenous dynamic processes plus demographic and environmental process noise, and are only observable with error. Their sensitivity to history means that minute changes in the driving noise realization, or the system parameters, will cause drastic changes in the system trajectory. This sensitivity is inherited and amplified by the joint probability density of the observable data and the process noise, rendering it useless as the basis for obtaining measures of statistical fit. Because the joint density is the basis for the fit measures used by all conventional statistical methods, this is a major theoretical shortcoming. The inability to make well-founded statistical inferences about biological dynamic models in the chaotic and near-chaotic regimes, other than on an ad hoc basis, leaves dynamic theory without the methods of quantitative validation that are essential tools in the rest of biological science. Here I show that this impasse can be resolved in a simple and general manner, using a method that requires only the ability to simulate the observed data on a system from the dynamic model about which inferences are required. The raw data series are reduced to phase-insensitive summary statistics, quantifying local dynamic structure and the distribution of observations. Simulation is used to obtain the mean and the covariance matrix of the statistics, given model parameters, allowing the construction of a 'synthetic likelihood' that assesses model fit. This likelihood can be explored using a straightforward Markov chain Monte Carlo sampler, but one further post-processing step returns pure likelihood-based inference. I apply the method to establish the dynamic nature of the fluctuations in Nicholson's classic blowfly experiments.}, } @article {pmid20702025, year = {2010}, author = {Luo, W and Lu, Y and Zhang, Y and Fu, W and Wang, B and Jiao, W and Wang, G and Tong, X and Giesy, JP}, title = {Watershed-scale assessment of arsenic and metal contamination in the surface soils surrounding Miyun Reservoir, Beijing, China.}, journal = {Journal of environmental management}, volume = {91}, number = {12}, pages = {2599-2607}, doi = {10.1016/j.jenvman.2010.07.023}, pmid = {20702025}, issn = {1095-8630}, mesh = {Arsenic/*analysis ; China ; Geographic Information Systems ; Multivariate Analysis ; Principal Component Analysis ; Risk Assessment ; Soil/*analysis ; Soil Pollutants/*analysis ; Water Pollution, Chemical ; Water Supply/standards ; }, abstract = {Concentrations of As and selected metals were determined in surface soils of the Miyun Reservoir watershed of Beijing, China. The degree to which concentrations of As and metals exceeded the corresponding background concentration of soils was: Cr>Cu>Zn>As>Ni with no apparent anthropogenic contamination with Cd and Pb. Based on the results of a combination of multivariate statistics and geostatistical analysis, greater concentrations of Cr and Ni in soils were determined to be primarily from iron ore mining near where the Chaohe River enters the northeast portion of the reservoir. Agricultural activities were responsible for the observed elevated concentrations of Cu and Zn in soils. Relatively great concentrations of As were found in soils near the upstream regions of the Baihe River in Chicheng County where small gold mining activities have taken place. The greatest potential for adverse effects of Cr and Cu occurred along the eastern shore of Miyun Reservoir.}, } @article {pmid20701696, year = {2010}, author = {Ranganathan, Y and Borges, RM}, title = {Reducing the babel in plant volatile communication: using the forest to see the trees.}, journal = {Plant biology (Stuttgart, Germany)}, volume = {12}, number = {5}, pages = {735-742}, doi = {10.1111/j.1438-8677.2009.00278.x}, pmid = {20701696}, issn = {1438-8677}, mesh = {*Algorithms ; *Artificial Intelligence ; Computational Biology/*methods ; Ficus/*chemistry ; Principal Component Analysis ; Volatile Organic Compounds/*chemistry/classification ; }, abstract = {While plants of a single species emit a diversity of volatile organic compounds (VOCs) to attract or repel interacting organisms, these specific messages may be lost in the midst of the hundreds of VOCs produced by sympatric plants of different species, many of which may have no signal content. Receivers must be able to reduce the babel or noise in these VOCs in order to correctly identify the message. For chemical ecologists faced with vast amounts of data on volatile signatures of plants in different ecological contexts, it is imperative to employ accurate methods of classifying messages, so that suitable bioassays may then be designed to understand message content. We demonstrate the utility of 'Random Forests' (RF), a machine-learning algorithm, for the task of classifying volatile signatures and choosing the minimum set of volatiles for accurate discrimination, using data from sympatric Ficus species as a case study. We demonstrate the advantages of RF over conventional classification methods such as principal component analysis (PCA), as well as data-mining algorithms such as support vector machines (SVM), diagonal linear discriminant analysis (DLDA) and k-nearest neighbour (KNN) analysis. We show why a tree-building method such as RF, which is increasingly being used by the bioinformatics, food technology and medical community, is particularly advantageous for the study of plant communication using volatiles, dealing, as it must, with abundant noise.}, } @article {pmid20700466, year = {2010}, author = {Menge, DN and DeNoyer, JL and Lichstein, JW}, title = {Phylogenetic constraints do not explain the rarity of nitrogen-fixing trees in late-successional temperate forests.}, journal = {PloS one}, volume = {5}, number = {8}, pages = {e12056}, pmid = {20700466}, issn = {1932-6203}, mesh = {Databases, Factual ; Ecology ; Evolution, Molecular ; *Nitrogen Fixation ; *Phylogeny ; Trees/genetics/*metabolism/physiology ; }, abstract = {BACKGROUND: Symbiotic nitrogen (N)-fixing trees are rare in late-successional temperate forests, even though these forests are often N limited. Two hypotheses could explain this paradox. The 'phylogenetic constraints hypothesis' states that no late-successional tree taxa in temperate forests belong to clades that are predisposed to N fixation. Conversely, the 'selective constraints hypothesis' states that such taxa are present, but N-fixing symbioses would lower their fitness. Here we test the phylogenetic constraints hypothesis.

Using U.S. forest inventory data, we derived successional indices related to shade tolerance and stand age for N-fixing trees, non-fixing trees in the 'potentially N-fixing clade' (smallest angiosperm clade that includes all N fixers), and non-fixing trees outside this clade. We then used phylogenetically independent contrasts (PICs) to test for associations between these successional indices and N fixation. Four results stand out from our analysis of U.S. trees. First, N fixers are less shade-tolerant than non-fixers both inside and outside of the potentially N-fixing clade. Second, N fixers tend to occur in younger stands in a given geographical region than non-fixers both inside and outside of the potentially N-fixing clade. Third, the potentially N-fixing clade contains numerous late-successional non-fixers. Fourth, although the N fixation trait is evolutionarily conserved, the successional traits are relatively labile.

CONCLUSIONS/SIGNIFICANCE: These results suggest that selective constraints, not phylogenetic constraints, explain the rarity of late-successional N-fixing trees in temperate forests. Because N-fixing trees could overcome N limitation to net primary production if they were abundant, this study helps to understand the maintenance of N limitation in temperate forests, and therefore the capacity of this biome to sequester carbon.}, } @article {pmid20698918, year = {2011}, author = {Elwyn, G and Stiel, M and Durand, MA and Boivin, J}, title = {The design of patient decision support interventions: addressing the theory-practice gap.}, journal = {Journal of evaluation in clinical practice}, volume = {17}, number = {4}, pages = {565-574}, doi = {10.1111/j.1365-2753.2010.01517.x}, pmid = {20698918}, issn = {1365-2753}, mesh = {*Decision Support Techniques ; Humans ; *Models, Theoretical ; *Patient Participation ; }, abstract = {BACKGROUND: Although an increasing number of decision support interventions for patients (including decision aids) are produced, few make explicit use of theory. We argue the importance of using theory to guide design. The aim of this work was to address this theory-practice gap and to examine how a range of selected decision-making theories could inform the design and evaluation of decision support interventions.

METHODS: We reviewed the decision-making literature and selected relevant theories. We assessed their key principles, theoretical pathways and predictions in order to determine how they could inform the design of two core components of decision support interventions, namely, information and deliberation components and to specify theory-based outcome measures.

RESULTS: Eight theories were selected: (1) the expected utility theory; (2) the conflict model of decision making; (3) prospect theory; (4) fuzzy-trace theory; (5) the differentiation and consolidation theory; (6) the ecological rationality theory; (7) the rational-emotional model of decision avoidance; and finally, (8) the Attend, React, Explain, Adapt model of affective forecasting. Some theories have strong relevance to the information design (e.g. prospect theory); some are more relevant to deliberation processes (conflict theory, differentiation theory and ecological validity). None of the theories in isolation was sufficient to inform the design of all the necessary components of decision support interventions. It was also clear that most work in theory-building has focused on explaining or describing how humans think rather than on how tools could be designed to help humans make good decisions. It is not surprising therefore that a large theory-practice gap exists as we consider decision support for patients. There was no relevant theory that integrated all the necessary contributions to the task of making good decisions in collaborative interactions.

DISCUSSION: Initiatives such as the International Patient Decision Aids Standards Collaboration influence standards for the design of decision support interventions. However, this analysis points to the need to undertake more work in providing theoretical foundations for these interventions.}, } @article {pmid20697878, year = {2010}, author = {Kwak, DA and Lee, WK and Kafatos, M and Son, Y and Cho, HK and Lee, SH}, title = {Estimation of effective plant area index for South Korean forests using LiDAR system.}, journal = {Science China. Life sciences}, volume = {53}, number = {7}, pages = {898-908}, doi = {10.1007/s11427-010-4019-z}, pmid = {20697878}, issn = {1869-1889}, mesh = {*Geographic Information Systems ; Republic of Korea ; *Trees ; }, abstract = {Light Detection and Ranging (LiDAR) systems can be used to estimate both vertical and horizontal forest structure. Woody components, the leaves of trees and the understory can be described with high precision, using geo-registered 3D-points. Based on this concept, the Effective Plant Area Indices (PAI(e)) for areas of Korean Pine (Pinus koraiensis), Japanese Larch (Larix leptolepis) and Oak (Quercus spp.) were estimated by calculating the ratio of intercepted and incident LIDAR laser rays for the canopies of the three forest types. Initially, the canopy gap fraction (G (LiDAR)) was generated by extracting the LiDAR data reflected from the canopy surface, or inner canopy area, using k-means statistics. The LiDAR-derived PAI(e) was then estimated by using G (LIDAR) with the Beer-Lambert law. A comparison of the LiDAR-derived and field-derived PAI(e) revealed the coefficients of determination for Korean Pine, Japanese Larch and Oak to be 0.82, 0.64 and 0.59, respectively. These differences between field-based and LIDAR-based PAI(e) for the different forest types were attributed to the amount of leaves and branches in the forest stands. The absence of leaves, in the case of both Larch and Oak, meant that the LiDAR pulses were only reflected from branches. The probability that the LiDAR pulses are reflected from bare branches is low as compared to the reflection from branches with a high leaf density. This is because the size of the branch is smaller than the resolution across and along the 1 meter LIDAR laser track. Therefore, a better predictive accuracy would be expected for the model if the study would be repeated in late spring when the shoots and leaves of the deciduous trees begin to appear.}, } @article {pmid20697877, year = {2010}, author = {Kim, SR and Kwak, DA and Lee, WK and Son, Y and Bae, SW and Kim, C and Yoo, S}, title = {Estimation of carbon storage based on individual tree detection in Pinus densiflora stands using a fusion of aerial photography and LiDAR data.}, journal = {Science China. Life sciences}, volume = {53}, number = {7}, pages = {885-897}, doi = {10.1007/s11427-010-4017-1}, pmid = {20697877}, issn = {1869-1889}, mesh = {Carbon/*metabolism ; Geographic Information Systems ; *Photography ; Pinus/*metabolism ; Republic of Korea ; }, abstract = {The objective of this study was to estimate the carbon storage capacity of Pinus densiflora stands using remotely sensed data by combining digital aerial photography with light detection and ranging (LiDAR) data. A digital canopy model (DCM), generated from the LiDAR data, was combined with aerial photography for segmenting crowns of individual trees. To eliminate errors in over and under-segmentation, the combined image was smoothed using a Gaussian filtering method. The processed image was then segmented into individual trees using a marker-controlled watershed segmentation method. After measuring the crown area from the segmented individual trees, the individual tree diameter at breast height (DBH) was estimated using a regression function developed from the relationship observed between the field-measured DBH and crown area. The above ground biomass of individual trees could be calculated by an image-derived DBH using a regression function developed by the Korea Forest Research Institute. The carbon storage, based on individual trees, was estimated by simple multiplication using the carbon conversion index (0.5), as suggested in guidelines from the Intergovernmental Panel on Climate Change. The mean carbon storage per individual tree was estimated and then compared with the field-measured value. This study suggested that the biomass and carbon storage in a large forest area can be effectively estimated using aerial photographs and LiDAR data.}, } @article {pmid20697873, year = {2010}, author = {Ma, W and Fang, J and Yang, Y and Mohammat, A}, title = {Biomass carbon stocks and their changes in northern China's grasslands during 1982-2006.}, journal = {Science China. Life sciences}, volume = {53}, number = {7}, pages = {841-850}, doi = {10.1007/s11427-010-4020-6}, pmid = {20697873}, issn = {1869-1889}, mesh = {*Biomass ; *Carbon ; China ; Climate ; Data Collection ; Geographic Information Systems ; *Poaceae ; }, abstract = {Grassland covers approximately one-third of the area of China and plays an important role in the global terrestrial carbon (C) cycle. However, little is known about biomass C stocks and dynamics in these grasslands. During 2001-2005, we conducted five consecutive field sampling campaigns to investigate above-and below-ground biomass for northern China's grasslands. Using measurements obtained from 341 sampling sites, together with a NDVI (normalized difference vegetation index) time series dataset over 1982-2006, we examined changes in biomass C stock during the past 25 years. Our results showed that biomass C stock in northern China's grasslands was estimated at 557.5 Tg C (1 Tg=10(12) g), with a mean density of 39.5 g C m(-2) for above-ground biomass and 244.6 g C m(-2) for below-ground biomass. An increasing rate of 0.2 Tg C yr(-1) has been observed over the past 25 years, but grassland biomass has not experienced a significant change since the late 1980s. Seasonal rainfall (January-July) was the dominant factor driving temporal dynamics in biomass C stock; however, the responses of grassland biomass to climate variables differed among various grassland types. Biomass in arid grasslands (i.e., desert steppe and typical steppe) was significantly associated with precipitation, while biomass in humid grasslands (i.e., alpine meadow) was positively correlated with mean January-July temperatures. These results suggest that different grassland ecosystems in China may show diverse responses to future climate changes.}, } @article {pmid20696667, year = {2011}, author = {Blair, C and Murphy, RW}, title = {Recent trends in molecular phylogenetic analysis: where to next?.}, journal = {The Journal of heredity}, volume = {102}, number = {1}, pages = {130-138}, doi = {10.1093/jhered/esq092}, pmid = {20696667}, issn = {1465-7333}, mesh = {Algorithms ; *Databases, Genetic ; Evolution, Molecular ; Genetic Loci ; Models, Biological ; *Phylogeny ; Sequence Alignment/*trends ; Sequence Analysis, DNA/*trends ; Species Specificity ; }, abstract = {The acquisition of large multilocus sequence data is providing researchers with an unprecedented amount of information to resolve difficult phylogenetic problems. With these large quantities of data comes the increasing challenge regarding the best methods of analysis. We review the current trends in molecular phylogenetic analysis, focusing specifically on the topics of multiple sequence alignment and methods of tree reconstruction. We suggest that traditional methods are inadequate for these highly heterogeneous data sets and that researchers employ newer more sophisticated search algorithms in their analyses. If we are to best extract the information present in these data sets, a sound understanding of basic phylogenetic principles combined with modern methodological techniques are necessary.}, } @article {pmid20694529, year = {2010}, author = {Samecka-Cymerman, A and Stankiewicz, A and Kolon, K and Kempers, AJ and Leuven, RS}, title = {Market Basket Analysis: a new tool in ecology to describe chemical relations in the environment--a case study of the fern Athyrium distentifolium in the Tatra National Park in Poland.}, journal = {Journal of chemical ecology}, volume = {36}, number = {9}, pages = {1029-1034}, pmid = {20694529}, issn = {1573-1561}, mesh = {Data Mining/*methods ; Ecology/*methods ; *Environment ; Ferns/*chemistry ; Geologic Sediments/chemistry ; Poland ; Principal Component Analysis ; }, abstract = {In this study, the novel data mining technique Market Basket Analysis (MBA) was applied for the first time in biogeochemical and ecological investigations. The method was tested on the fern Athyrium distentifolium, in which we measured concentrations of the elements Ca, Cd, Cr, Cu, Fe, K, Mg, Mn, Na, Ni, Pb, and Zn. Plants were sampled from sites with different types of bedrock in the Tatra National Park in Poland. MBA was used to investigate whether specimens of Athyrium distentifolium that contain elevated levels of certain elements occur more frequently on a specific type of bedrock and to identify relationships between the type of bedrock and the concentrations of the elements in this fern. The results were compared with those of the commonly used principal component and classification analysis (PCCA) technique. MBA and PCCA ordination both yielded distinct groups of ferns growing on different types of bedrock. Although the results of MBA and PCCA were similar, MBA has the advantage of being independent of the size of the data set. In addition, MBA revealed not only dominant elements but, in the case of limestone bedrock, also showed very low concentrations of Cd, Fe, Mn, and Pb in ferns growing on this type of parent material. MBA, thus, appeared to be a promising data mining method to reveal chemical relations in the environment as well as the accumulation of chemical elements in bioindicators. This technique can be used to reveal associations and correlations among items in large data sets collected on a national or even larger scale.}, } @article {pmid20689854, year = {2010}, author = {Rittenhouse, CD and Pidgeon, AM and Albright, TP and Culbert, PD and Clayton, MK and Flather, CH and Huang, C and Masek, JG and Stewart, SI and Radeloff, VC}, title = {Conservation of forest birds: evidence of a shifting baseline in community structure.}, journal = {PloS one}, volume = {5}, number = {8}, pages = {e11938}, pmid = {20689854}, issn = {1932-6203}, mesh = {Animals ; Biodiversity ; *Birds ; Conservation of Natural Resources/*methods ; Databases, Factual ; *Trees ; }, abstract = {BACKGROUND: Quantifying changes in forest bird diversity is an essential task for developing effective conservation actions. When subtle changes in diversity accumulate over time, annual comparisons may offer an incomplete perspective of changes in diversity. In this case, progressive change, the comparison of changes in diversity from a baseline condition, may offer greater insight because changes in diversity are assessed over longer periods of times. Our objectives were to determine how forest bird diversity has changed over time and whether those changes were associated with forest disturbance.

We used North American Breeding Bird Survey data, a time series of Landsat images classified with respect to land cover change, and mixed-effects models to associate changes in forest bird community structure with forest disturbance, latitude, and longitude in the conterminous United States for the years 1985 to 2006. We document a significant divergence from the baseline structure for all birds of similar migratory habit and nest location, and all forest birds as a group from 1985 to 2006. Unexpectedly, decreases in progressive similarity resulted from small changes in richness (<1 species per route for the 22-year study period) and modest losses in abundance (-28.7 - -10.2 individuals per route) that varied by migratory habit and nest location. Forest disturbance increased progressive similarity for Neotropical migrants, permanent residents, ground nesting, and cavity nesting species. We also documented highest progressive similarity in the eastern United States.

CONCLUSIONS/SIGNIFICANCE: Contemporary forest bird community structure is changing rapidly over a relatively short period of time (e.g., approximately 22 years). Forest disturbance and forest regeneration are primary factors associated with contemporary forest bird community structure, longitude and latitude are secondary factors, and forest loss is a tertiary factor. Importantly, these findings suggest some regions of the United States may already fall below the habitat amount threshold where fragmentation effects become important predictors of forest bird community structure.}, } @article {pmid20689845, year = {2010}, author = {Webb, TJ and Vanden Berghe, E and O'Dor, R}, title = {Biodiversity's big wet secret: the global distribution of marine biological records reveals chronic under-exploration of the deep pelagic ocean.}, journal = {PloS one}, volume = {5}, number = {8}, pages = {e10223}, pmid = {20689845}, issn = {1932-6203}, mesh = {*Biodiversity ; Databases, Factual ; Marine Biology/*statistics & numerical data ; Oceans and Seas ; *Records ; Time Factors ; }, abstract = {BACKGROUND: Understanding the distribution of marine biodiversity is a crucial first step towards the effective and sustainable management of marine ecosystems. Recent efforts to collate location records from marine surveys enable us to assemble a global picture of recorded marine biodiversity. They also effectively highlight gaps in our knowledge of particular marine regions. In particular, the deep pelagic ocean--the largest biome on Earth--is chronically under-represented in global databases of marine biodiversity.

We use data from the Ocean Biogeographic Information System to plot the position in the water column of ca 7 million records of marine species occurrences. Records from relatively shallow waters dominate this global picture of recorded marine biodiversity. In addition, standardising the number of records from regions of the ocean differing in depth reveals that regardless of ocean depth, most records come either from surface waters or the sea bed. Midwater biodiversity is drastically under-represented.

CONCLUSIONS/SIGNIFICANCE: The deep pelagic ocean is the largest habitat by volume on Earth, yet it remains biodiversity's big wet secret, as it is hugely under-represented in global databases of marine biological records. Given both its value in the provision of a range of ecosystem services, and its vulnerability to threats including overfishing and climate change, there is a pressing need to increase our knowledge of Earth's largest ecosystem.}, } @article {pmid20687027, year = {2010}, author = {Zeichner, BC and Adams, SD}, title = {Using geographic information systems to maximize environmental surveillance efforts and impact.}, journal = {U.S. Army Medical Department journal}, volume = {}, number = {}, pages = {29-35}, pmid = {20687027}, issn = {1524-0436}, mesh = {Animals ; Coleoptera ; Ecology ; *Environmental Monitoring ; *Geographic Information Systems ; *Insecta ; Mosquito Control ; Ticks ; }, abstract = {There has been tremendous advancement in geographic information systems (GIS) software and hardware over the last 2 decades. This article illustrates how these advancements can be used to greatly increase the ease and efficiency of collecting environmental samples and demonstrate how environmental data collected within a GIS is more valuable because of the visualization, analysis, and historical capabilities of GIS. This article reviews 6 actual field surveys conducted using desktop GIS and field GIS by entomologists with the US Army Public Health Command (Provisional). While these examples entail entomological data, the techniques and procedures are applicable to any type of environmental data.}, } @article {pmid20679517, year = {2010}, author = {Lexer, C and Joseph, JA and van Loo, M and Barbará, T and Heinze, B and Bartha, D and Castiglione, S and Fay, MF and Buerkle, CA}, title = {Genomic admixture analysis in European Populus spp. reveals unexpected patterns of reproductive isolation and mating.}, journal = {Genetics}, volume = {186}, number = {2}, pages = {699-712}, pmid = {20679517}, issn = {1943-2631}, mesh = {Adaptation, Biological/*genetics ; Alleles ; Base Sequence ; Bayes Theorem ; *Biological Evolution ; Chromosome Mapping ; Crosses, Genetic ; Data Interpretation, Statistical ; Epistasis, Genetic ; Genetic Drift ; Genetic Linkage ; Genetic Markers ; Genetic Speciation ; Genetic Variation ; Genotype ; *Hybridization, Genetic ; Polymorphism, Genetic ; Populus/*genetics/*physiology ; Reproduction/genetics ; Sequence Analysis, DNA ; }, abstract = {Admixture between genetically divergent populations facilitates genomic studies of the mechanisms involved in adaptation, reproductive isolation, and speciation, including mapping of the loci involved in these phenomena. Little is known about how pre- and postzygotic barriers will affect the prospects of "admixture mapping" in wild species. We have studied 93 mapped genetic markers (microsatellites, indels, and sequence polymorphisms, ∼60,000 data points) to address this topic in hybrid zones of Populus alba and P. tremula, two widespread, ecologically important forest trees. Using genotype and linkage information and recently developed analytical tools we show that (1) reproductive isolation between these species is much stronger than previously assumed but this cannot prevent the introgression of neutral or advantageous alleles, (2) unexpected genotypic gaps exist between recombinant hybrids and their parental taxa, (3) these conspicuous genotypic patterns are due to assortative mating and strong postzygotic barriers, rather than recent population history. We discuss possible evolutionary trajectories of hybrid lineages between these species and outline strategies for admixture mapping in hybrid zones between highly divergent populations. Datasets such as this one are still rare in studies of natural hybrid zones but should soon become more common as high throughput genotyping and resequencing become feasible in nonmodel species.}, } @article {pmid20678856, year = {2010}, author = {Stubelj Ars, M and Bohanec, M}, title = {Towards the ecotourism: a decision support model for the assessment of sustainability of mountain huts in the Alps.}, journal = {Journal of environmental management}, volume = {91}, number = {12}, pages = {2554-2564}, doi = {10.1016/j.jenvman.2010.07.006}, pmid = {20678856}, issn = {1095-8630}, mesh = {*Decision Support Techniques ; Decision Trees ; *Ecosystem ; Housing ; *Mountaineering ; Slovenia ; }, abstract = {This paper studies mountain hut infrastructure in the Alps as an important element of ecotourism in the Alpine region. To improve the decision-making process regarding the implementation of future infrastructure and improvement of existing infrastructure in the vulnerable natural environment of mountain ecosystems, a new decision support model has been developed. The methodology is based on qualitative multi-attribute modelling supported by the DEXi software. The integrated rule-based model is hierarchical and consists of two submodels that cover the infrastructure of the mountain huts and that of the huts' surroundings. The final goal for the designed tool is to help minimize the ecological footprint of tourists in environmentally sensitive and undeveloped mountain areas and contribute to mountain ecotourism. The model has been tested in the case study of four mountain huts in Triglav National Park in Slovenia. Study findings provide a new empirical approach to evaluating existing mountain infrastructure and predicting improvements for the future. The assessment results are of particular interest for decision makers in protected areas, such as Alpine national parks managers and administrators. In a way, this model proposes an approach to the management assessment of mountain huts with the main aim of increasing the quality of life of mountain environment visitors as well as the satisfaction of tourists who may eventually become ecotourists.}, } @article {pmid20673967, year = {2010}, author = {Jarva, J and Tarvainen, T and Reinikainen, J and Eklund, M}, title = {TAPIR--Finnish national geochemical baseline database.}, journal = {The Science of the total environment}, volume = {408}, number = {20}, pages = {4385-4395}, doi = {10.1016/j.scitotenv.2010.06.050}, pmid = {20673967}, issn = {1879-1026}, mesh = {*Databases, Factual ; Environmental Monitoring ; Environmental Pollution/statistics & numerical data ; Finland ; Metals, Heavy/analysis/standards ; Soil/analysis/standards ; Soil Pollutants/analysis/*standards ; }, abstract = {In Finland, a Government Decree on the Assessment of Soil Contamination and Remediation Needs has generated a need for reliable and readily accessible data on geochemical baseline concentrations in Finnish soils. According to the Decree, baseline concentrations, referring both to the natural geological background concentrations and the diffuse anthropogenic input of substances, shall be taken into account in the soil contamination assessment process. This baseline information is provided in a national geochemical baseline database, TAPIR, that is publicly available via the Internet. Geochemical provinces with elevated baseline concentrations were delineated to provide regional geochemical baseline values. The nationwide geochemical datasets were used to divide Finland into geochemical provinces. Several metals (Co, Cr, Cu, Ni, V, and Zn) showed anomalous concentrations in seven regions that were defined as metal provinces. Arsenic did not follow a similar distribution to any other elements, and four arsenic provinces were separately determined. Nationwide geochemical datasets were not available for some other important elements such as Cd and Pb. Although these elements are included in the TAPIR system, their distribution does not necessarily follow the ones pre-defined for metal and arsenic provinces. Regional geochemical baseline values, presented as upper limit of geochemical variation within the region, can be used as trigger values to assess potential soil contamination. Baseline values have also been used to determine upper and lower guideline values that must be taken into account as a tool in basic risk assessment. If regional geochemical baseline values are available, the national guideline values prescribed in the Decree based on ecological risks can be modified accordingly. The national geochemical baseline database provides scientifically sound, easily accessible and generally accepted information on the baseline values, and it can be used in various environmental applications.}, } @article {pmid20673367, year = {2010}, author = {Sainz-Elipe, S and Latorre, JM and Escosa, R and Masià, M and Fuentes, MV and Mas-Coma, S and Bargues, MD}, title = {Malaria resurgence risk in southern Europe: climate assessment in an historically endemic area of rice fields at the Mediterranean shore of Spain.}, journal = {Malaria journal}, volume = {9}, number = {}, pages = {221}, pmid = {20673367}, issn = {1475-2875}, mesh = {Agriculture ; Animals ; Anopheles/*growth & development/parasitology ; Climate ; Ecology ; Environmental Monitoring ; Epidemiological Monitoring ; Geographic Information Systems ; Humans ; Insect Vectors/*growth & development/parasitology ; Malaria/transmission ; Malaria, Falciparum/*epidemiology/parasitology/transmission ; Malaria, Vivax/*epidemiology/parasitology/transmission ; Oryza ; Plasmodium falciparum ; Plasmodium vivax ; Risk ; Seasons ; Spain/epidemiology ; Temperature ; }, abstract = {BACKGROUND: International travel and immigration have been related with an increase of imported malaria cases. This fact and climate change, prolonging the period favouring vector development, require an analysis of the malaria transmission resurgence risk in areas of southern Europe. Such a study is made for the first time in Spain. The Ebro Delta historically endemic area was selected due to its rice field landscape, the presence of only one vector, Anopheles atroparvus, with densities similar to those it presented when malaria was present, in a situation which pronouncedly differs from already assessed potential resurgence areas in other Mediterranean countries, such as France and Italy, where many different Anopheles species coexist and a different vector species dominates.

METHODS: The transmission risk was assessed analysing: 1) climate diagrams including the minimum temperature for Plasmodium falciparum and Plasmodium vivax development; 2) monthly evolution of the Gradient Model Risk (GMR) index, specifying transmission risk period and number of potential Plasmodium generations; 3) ecological characteristics using remote sensing images with the Eurasia Land Cover characteristics database and the monthly evolution of the Normalized Difference Vegetation Index (NDVI); 4) evaluation of A. atroparvus population dynamics.

RESULTS: Climatological analyses and GMR index show that a transmission risk presently exists, lasting from May until September for P. falciparum, and from May until October for P. vivax. The GMR index shows that the temperature increase does not actually mean a transmission risk increase if accompanied by a precipitation decrease reducing the number of parasite generations and transmission period. Nevertheless, this limitation is offset by the artificial flooding of the rice fields. Maximum NDVI values and A. atroparvus maximum abundance correspond to months with maximum growth of the rice fields.

CONCLUSIONS: The Ebro Delta presents the ecological characteristics that favour transmission. The temperature increase has favoured a widening of the monthly potential transmission window with respect to when malaria was endemic. The combined application of modified climate diagrams and GMR index, together with spatial characterization conforms a useful tool for assessing potential areas at risk of malaria resurgence. NDVI is a good marker when dealing with a rice field area.}, } @article {pmid20660497, year = {2010}, author = {Yamashita, G and Miller, H and Goddard, A and Norton, C}, title = {A model for Bioinformatics training: the marine biological laboratory.}, journal = {Briefings in bioinformatics}, volume = {11}, number = {6}, pages = {610-615}, doi = {10.1093/bib/bbq029}, pmid = {20660497}, issn = {1477-4054}, mesh = {Computational Biology/education ; Marine Biology/*education ; Medical Informatics/education ; *Models, Educational ; }, abstract = {Many areas of science such as biology, medicine and oceanography are becoming increasingly data-rich and most programs that train scientists do not address informatics techniques or technologies that are necessary for managing and analysing large amounts of data. Educational resources for scientists in informatics are scarce, yet scientists need the skills and knowledge to work with informaticians and manage graduate students and post-docs in informatics projects. The Marine Biological Laboratory houses a world-renowned library and is involved in a number of informatics projects in the sciences. The MBL has been home to the National Library of Medicine's BioMedical Informatics Course for nearly two decades and is committed to educating scientists and other scholars in informatics. In an innovative, immersive learning experience, G.Y., a biologist and post-doc at Arizona State University, visited the Science Informatics Group at the MBL to learn first hand how informatics is done and how informatics teams work. Hands-on work with developers, systems administrators, librarians and other scientists provided an invaluable education in informatics and is a model for future science informatics training.}, } @article {pmid20656855, year = {2010}, author = {Depkat-Jakob, PS and Hilgarth, M and Horn, MA and Drake, HL}, title = {Effect of earthworm feeding guilds on ingested dissimilatory nitrate reducers and denitrifiers in the alimentary canal of the earthworm.}, journal = {Applied and environmental microbiology}, volume = {76}, number = {18}, pages = {6205-6214}, pmid = {20656855}, issn = {1098-5336}, mesh = {Actinobacteria/genetics/metabolism ; Animals ; Base Sequence ; Cloning, Molecular ; Cluster Analysis ; Computational Biology ; DNA Primers/genetics ; Denitrification/*genetics ; Digestive System/*microbiology ; Feeding Behavior/*physiology ; Germany ; Molecular Sequence Data ; Nitrate Reductase/*genetics/metabolism ; Nitrates/*metabolism ; Oligochaeta/enzymology/microbiology/*physiology ; Phylogeny ; Polymorphism, Restriction Fragment Length ; Proteobacteria/genetics/metabolism ; Sequence Analysis, DNA ; *Soil Microbiology ; }, abstract = {The earthworm gut is an anoxic nitrous oxide (N(2)O)-emitting microzone in aerated soils. In situ conditions of the gut might stimulate ingested nitrate-reducing soil bacteria linked to this emission. The objective of this study was to determine if dissimilatory nitrate reducers and denitrifiers in the alimentary canal were affected by feeding guilds (epigeic [Lumbricus rubellus], anecic [Lumbricus terrestris], and endogeic [Aporrectodea caliginosa]). Genes and gene transcripts of narG (encodes a subunit of nitrate reductase and targets both dissimilatory nitrate reducers and denitrifiers) and nosZ (encodes a subunit of N(2)O reductase and targets denitrifiers) were detected in guts and soils. Gut-derived sequences were similar to those of cultured and uncultured soil bacteria and to soil-derived sequences obtained in this study. Gut-derived narG sequences and narG terminal restriction fragments (TRFs) were affiliated mainly with Gram-positive organisms (Actinobacteria). The majority of gut- and uppermost-soil-derived narG transcripts were affiliated with Mycobacterium (Actinobacteria). In contrast, narG sequences indicative of Gram-negative organisms (Proteobacteria) were dominant in mineral soil. Most nosZ sequences and nosZ TRFs were affiliated with Bradyrhizobium (Alphaproteobacteria) and uncultured soil bacteria. TRF profiles indicated that nosZ transcripts were more affected by earthworm feeding guilds than were nosZ genes, whereas narG transcripts were less affected by earthworm feeding guilds than were narG genes. narG and nosZ transcripts were different and less diverse in the earthworm gut than in mineral soil. The collective results indicate that dissimilatory nitrate reducers and denitrifiers in the earthworm gut are soil derived and that ingested narG- and nosZ-containing taxa were not uniformly stimulated in the guts of worms from different feeding guilds.}, } @article {pmid20656371, year = {2010}, author = {Magurran, AE and Baillie, SR and Buckland, ST and Dick, JM and Elston, DA and Scott, EM and Smith, RI and Somerfield, PJ and Watt, AD}, title = {Long-term datasets in biodiversity research and monitoring: assessing change in ecological communities through time.}, journal = {Trends in ecology & evolution}, volume = {25}, number = {10}, pages = {574-582}, doi = {10.1016/j.tree.2010.06.016}, pmid = {20656371}, issn = {0169-5347}, support = {250189/ERC_/European Research Council/International ; }, mesh = {Animals ; *Biodiversity ; Databases, Factual ; Ecology/*methods ; Humans ; Time Factors ; }, abstract = {The growing need for baseline data against which efforts to reduce the rate of biodiversity loss can be judged highlights the importance of long-term datasets, some of which are as old as ecology itself. We review methods of evaluating change in biodiversity at the community level using these datasets, and contrast whole-community approaches with those that combine information from different species and habitats. As all communities experience temporal turnover, one of the biggest challenges is distinguishing change that can be attributed to external factors, such as anthropogenic activities, from underlying natural change. We also discuss methodological issues, such as false alerts and modifications in design, of which users of these data sets need to be aware.}, } @article {pmid20648747, year = {2010}, author = {Epps, MJ and Arnold, AE}, title = {Diversity, abundance and community network structure in sporocarp-associated beetle communities of the central Appalachian Mountains.}, journal = {Mycologia}, volume = {102}, number = {4}, pages = {785-802}, doi = {10.3852/09-161}, pmid = {20648747}, issn = {0027-5514}, mesh = {Animals ; Biodiversity ; Coleoptera/*microbiology ; *Community Networks ; Fungi/*isolation & purification ; }, abstract = {Although arthropods are abundant and diverse in and on macrofungal sporocarps, their associations with fungi seldom have been described at a community level. We examined sporocarp-associated beetle communities in two primary sites in the Appalachian Mountains and foothills, assessing beetle diversity and abundance in relation to study site, sampling season (early vs. late summer), and sporocarp characteristics such as taxonomic position, dry mass and age. From 758 sporocarps representing >180 species we recovered 15404 adult beetles representing 72 species and 15 families, primarily Staphylinidae (> 98% of individuals and of 64% morphospecies). The probability of sporocarp colonization by beetles, beetle abundance and diversity differed among fungal species and were positively associated with sporocarp dry mass. Sporocarp age was positively correlated with beetle diversity and abundance (as measured in a focal species, Megacollybia platyphylla, Tricholomataceae), and its effects were independent of dry mass. Many beetle species were generalists, visiting a wide breadth of fungi in both the Agaricales and Polyporales; however, several beetle taxa showed evidence of specialization on particular fungal hosts. Host association data were used to examine the structure underlying sporocarp-beetle associations. Here we present the first evidence of nested community structure in the sporocarp-beetle interaction network.}, } @article {pmid20640838, year = {2009}, author = {Yang, G and Xing, C and Liu, CB and Fu, YJ and Zhou, LJ and Zu, YG}, title = {First-principle conformational analysis of glycine residues in the alphabeta-tubulin dimer.}, journal = {Interdisciplinary sciences, computational life sciences}, volume = {1}, number = {3}, pages = {196-203}, doi = {10.1007/s12539-009-0021-1}, pmid = {20640838}, issn = {1913-2751}, mesh = {Algorithms ; Amino Acid Sequence ; Cluster Analysis ; Computational Biology/methods ; Computers ; Dimerization ; Gases ; Glycine/*chemistry ; Hydrogen Bonding ; Models, Molecular ; Molecular Conformation ; Molecular Sequence Data ; Proteins/chemistry ; Tubulin/*chemistry ; }, abstract = {Amino acids, especially glycine, have been extensively studied whereas their conformational behaviors in proteins are rather limited. In this work, all the polypeptides containing glycine residues are truncated from the alphabeta-tubulin dimer and refined with the partial optimization technique, where the backbone atoms of the previous and posterior residues to the glycine residues are fixed at the experimental Cartesian positions whereas the others fully relaxed. The combination of the polypeptide models and partial optimization technique is validated by twolayer ONIOM calculations, being effective to retain the local structures of proteins and meanwhile optimizing the concerned glycine residues towards energy minima. Owing to the lack of side chains, various types of hydrogen bonding interactions are detected in the glycine residues. The conformational analyses of proteins are mainly based on the dihedrals. Theta(1)(angleH(5)C(2)C(3)O(4)), Theta(2)(angleH(6)C(2)C(3)O(4)) and Theta(3)(angleN(1)C(2)C(3)O(4)) are the three key dihedrals to determine the glycine conformations, which were found to change synchronously and correlate with each other by four linear equations. It thus provided the first evidence of the correlation of intra-dihedrals for the amino acid residues in proteins. In addition, the three dihedrals of the gas-phase glycine conformations were also found to suit well with these linear equations, elucidating the rationality of using amino acids as the computational models of proteins.}, } @article {pmid20638846, year = {2010}, author = {Kretzschmar, M and Gomes, MG and Coutinho, RA and Koopman, JS}, title = {Unlocking pathogen genotyping information for public health by mathematical modeling.}, journal = {Trends in microbiology}, volume = {18}, number = {9}, pages = {406-412}, doi = {10.1016/j.tim.2010.06.008}, pmid = {20638846}, issn = {1878-4380}, mesh = {Bacteria/classification/*genetics ; Communicable Disease Control/*methods ; Communicable Diseases/*epidemiology/*microbiology/transmission/virology ; Computational Biology ; Disease Notification ; Europe ; Evolution, Molecular ; Genotype ; Humans ; Models, Biological ; Models, Statistical ; Models, Theoretical ; Molecular Epidemiology/*methods ; Netherlands ; *Public Health ; Viruses/classification/*genetics ; }, abstract = {Molecular typing and mathematical modeling have gone through rapid development in the past decade. Both offer new insights into the epidemiology of infectious diseases, thereby contributing to a better understanding of transmission dynamics. Infectious disease surveillance and control benefit from the optimum use of these techniques. In this paper, we review recent developments and propose methods to integrate pathogen ecology and molecular evolution based on their common dependence on the underlying host contact patterns.}, } @article {pmid20637598, year = {2010}, author = {Carlson, RP and Taffs, RL}, title = {Molecular-level tradeoffs and metabolic adaptation to simultaneous stressors.}, journal = {Current opinion in biotechnology}, volume = {21}, number = {5}, pages = {670-676}, pmid = {20637598}, issn = {1879-0429}, support = {P20 RR024237/RR/NCRR NIH HHS/United States ; R01 EB006532/EB/NIBIB NIH HHS/United States ; EB006532/EB/NIBIB NIH HHS/United States ; }, mesh = {*Adaptation, Physiological ; Computational Biology/methods ; Ecology ; Systems Biology/methods ; }, abstract = {Life is a dynamic process driven by the complex interplay between physical constraints and selection pressures, ranging from nutrient limitation to inhibitory substances to predators. These stressors are not mutually exclusive; microbes have faced concurrent challenges for eons. Genome-enabled systems biology approaches are adapting economic and ecological concepts like tradeoff curves and strategic resource allocation theory to analyze metabolic adaptations to simultaneous stressors. These methodologies can accurately describe and predict metabolic adaptations to concurrent stresses by considering the tradeoff between investment of limiting resources into enzymatic machinery and the resulting cellular function. The approaches represent promising links between computational biology and well-established economic and ecological methodologies for analyzing the interplay between physical constraints and microbial fitness.}, } @article {pmid20637073, year = {2010}, author = {Ficetola, GF and Coissac, E and Zundel, S and Riaz, T and Shehzad, W and Bessière, J and Taberlet, P and Pompanon, F}, title = {An in silico approach for the evaluation of DNA barcodes.}, journal = {BMC genomics}, volume = {11}, number = {}, pages = {434}, pmid = {20637073}, issn = {1471-2164}, mesh = {Animals ; *Computational Biology ; DNA Fingerprinting/*methods/standards ; DNA Primers/genetics ; Databases, Genetic ; Humans ; Mice ; Polymerase Chain Reaction ; Quality Control ; Reproducibility of Results ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: DNA barcoding is a key tool for assessing biodiversity in both taxonomic and environmental studies. Essential features of barcodes include their applicability to a wide spectrum of taxa and their ability to identify even closely related species. Several DNA regions have been proposed as barcodes and the region selected strongly influences the output of a study. However, formal comparisons between barcodes remained limited until now. Here we present a standard method for evaluating barcode quality, based on the use of a new bioinformatic tool that performs in silico PCR over large databases. We illustrate this approach by comparing the taxonomic coverage and the resolution of several DNA regions already proposed for the barcoding of vertebrates. To assess the relationship between in silico and in vitro PCR, we also developed specific primers amplifying different species of Felidae, and we tested them using both kinds of PCR RESULTS: Tests on specific primers confirmed the correspondence between in silico and in vitro PCR. Nevertheless, results of in silico and in vitro PCRs can be somehow different, also because tuning PCR conditions can increase the performance of primers with limited taxonomic coverage. The in silico evaluation of DNA barcodes showed a strong variation of taxonomic coverage (i.e., universality): barcodes based on highly degenerated primers and those corresponding to the conserved region of the Cyt-b showed the highest coverage. As expected, longer barcodes had a better resolution than shorter ones, which are however more convenient for ecological studies analysing environmental samples.

CONCLUSIONS: In silico PCR could be used to improve the performance of a study, by allowing the preliminary comparison of several DNA regions in order to identify the most appropriate barcode depending on the study aims.}, } @article {pmid20636132, year = {2010}, author = {Anthes, N and David, P and Auld, JR and Hoffer, JN and Jarne, P and Koene, JM and Kokko, H and Lorenzi, MC and Pélissié, B and Sprenger, D and Staikou, A and Schärer, L}, title = {Bateman gradients in hermaphrodites: an extended approach to quantify sexual selection.}, journal = {The American naturalist}, volume = {176}, number = {3}, pages = {249-263}, doi = {10.1086/655218}, pmid = {20636132}, issn = {1537-5323}, mesh = {Animals ; Biomphalaria/physiology ; *Data Interpretation, Statistical ; Disorders of Sex Development ; Female ; Male ; Mating Preference, Animal/*physiology ; }, abstract = {Sexual selection is often quantified using Bateman gradients, which represent sex-specific regression slopes of reproductive success on mating success and thus describe the expected fitness returns from mating more often. Although the analytical framework for Bateman gradients aimed at covering all sexual systems, empirical studies are biased toward separate-sex organisms, probably because important characteristics of other systems remain incompletely treated. Our synthesis complements the existing Bateman gradient approach with three essential reproductive features of simultaneous hermaphrodites. First, mating in one sex may affect fitness via the opposite sex, for example, through energetic trade-offs. We integrate cross-sex selection effects and show how they help characterizing sexually mutualistic versus antagonistic selection. Second, male and female mating successes may be correlated, complicating the interpretation of Bateman gradients. We show how to quantify the impact of this correlation on sexual selection and propose a principal component analysis on male and female mating success to facilitate interpretation. Third, self-fertilization is accounted for by adding selfed progeny as a separate category of reproductive success to analyses of Bateman gradients. Finally, using a worked example from the snail Biomphalaria glabrata, we illustrate how the extended analytical framework can enhance our understanding of sexual selection in hermaphroditic animals and plants.}, } @article {pmid20633615, year = {2010}, author = {Hulzebos, E and Gunnarsdottir, S and Rila, JP and Dang, Z and Rorije, E}, title = {An Integrated Assessment Scheme for assessing the adequacy of (eco)toxicological data under REACH.}, journal = {Toxicology letters}, volume = {198}, number = {2}, pages = {255-262}, doi = {10.1016/j.toxlet.2010.07.004}, pmid = {20633615}, issn = {1879-3169}, mesh = {Animals ; *Databases, Factual ; *Ecotoxicology/legislation & jurisprudence/methods/standards ; Endpoint Determination ; European Union ; Government Regulation ; Guidelines as Topic ; *Hazardous Substances/classification/toxicity ; Quantitative Structure-Activity Relationship ; Reproducibility of Results ; Risk Assessment/legislation & jurisprudence/methods/standards ; }, abstract = {REACH requires all available (eco)toxicological information, whether protocol studies, other experiments, or non-testing approaches such as read-across or (Q)SAR, to be collected and evaluated. However, guidance documents only limitedly address how adequacy of (eco)toxicological information can be assessed consistently and transparently. We propose an Integrated Assessment Scheme (IAS) for the evaluation of (eco)toxicological data. The IAS consists of three modules: (i) the reliability of the data; (ii) the validity of the methods the data are generated from and; (iii) the regulatory need of the data. Each module is assessed and documented using adjusted OECD principles for the validation of (Q)SARs. These adjusted principles provide a harmonised set of criteria for the evaluation of all types of (eco)toxicological data. Assessment codes, similar to Klimisch codes, are assigned to the evaluated information in each module. The coherent combination of the assessment codes of all three modules determines the overall adequacy of information for fulfilling the information requirement in REACH, and can serve as a weight in a Weight of Evidence procedure as mentioned in REACH Annex XI.}, } @article {pmid20623014, year = {2010}, author = {Merem, E and Robinson, B and Wesley, JM and Yerramilli, S and Twumasi, YA}, title = {Using GIS in ecological management: green assessment of the impacts of petroleum activities in the state of Texas.}, journal = {International journal of environmental research and public health}, volume = {7}, number = {5}, pages = {2101-2130}, pmid = {20623014}, issn = {1660-4601}, mesh = {*Conservation of Natural Resources ; *Ecology ; *Geographic Information Systems ; *Petroleum ; Texas ; }, abstract = {Geo-information technologies are valuable tools for ecological assessment in stressed environments. Visualizing natural features prone to disasters from the oil sector spatially not only helps in focusing the scope of environmental management with records of changes in affected areas, but it also furnishes information on the pace at which resource extraction affects nature. Notwithstanding the recourse to ecosystem protection, geo-spatial analysis of the impacts remains sketchy. This paper uses GIS and descriptive statistics to assess the ecological impacts of petroleum extraction activities in Texas. While the focus ranges from issues to mitigation strategies, the results point to growth in indicators of ecosystem decline.}, } @article {pmid20619942, year = {2010}, author = {Brulle, F and Morgan, AJ and Cocquerelle, C and Vandenbulcke, F}, title = {Transcriptomic underpinning of toxicant-mediated physiological function alterations in three terrestrial invertebrate taxa: a review.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {158}, number = {9}, pages = {2793-2808}, doi = {10.1016/j.envpol.2010.06.019}, pmid = {20619942}, issn = {1873-6424}, mesh = {Agrochemicals/toxicity ; Animals ; Arthropods/*drug effects/genetics/metabolism ; Gene Expression/*drug effects ; Gene Expression Profiling ; Metals/toxicity ; Nematoda/*drug effects/genetics/metabolism ; Oligochaeta/*drug effects/genetics/metabolism ; Polycyclic Aromatic Hydrocarbons/toxicity ; Soil Pollutants/*toxicity ; }, abstract = {Diverse anthropogenic activities often lead to the accumulation of inorganic and organic residues in topsoils. Biota living in close contact with contaminated soils may experience stress at different levels of biological organisation throughout the continuum from the molecular-genetic to ecological and community levels. To date, the relationship between changes at the molecular (mRNA expression) and biochemical/physiological levels evoked by exposures to chemical compounds has been partially established in a limited number of terrestrial invertebrate species. Recently, the advent of a family of transcriptomic tools (e.g. Real-time PCR, Subtractive Suppressive Hybridization, Expressed Sequence Tag sequencing, pyro-sequencing technologies, Microarray chips), together with supporting informatic and statistical procedures, have permitted the robust analyses of global gene expression changes within an ecotoxicological context. This review focuses on how transcriptomics is enlightening our understanding of the molecular-genetic responses of three contrasting terrestrial macroinvertebrate taxa (nematodes, earthworms, and springtails) to inorganics, organics, and agrochemicals.}, } @article {pmid20618961, year = {2010}, author = {Rho, M and Schaack, S and Gao, X and Kim, S and Lynch, M and Tang, H}, title = {LTR retroelements in the genome of Daphnia pulex.}, journal = {BMC genomics}, volume = {11}, number = {}, pages = {425}, pmid = {20618961}, issn = {1471-2164}, support = {F32GM083550/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Daphnia/*genetics ; Female ; Genome/*genetics ; Laboratories ; Male ; Retroelements/*genetics ; Terminal Repeat Sequences/*genetics ; Transcription, Genetic ; }, abstract = {BACKGROUND: Long terminal repeat (LTR) retroelements represent a successful group of transposable elements (TEs) that have played an important role in shaping the structure of many eukaryotic genomes. Here, we present a genome-wide analysis of LTR retroelements in Daphnia pulex, a cyclical parthenogen and the first crustacean for which the whole genomic sequence is available. In addition, we analyze transcriptional data and perform transposon display assays of lab-reared lineages and natural isolates to identify potential influences on TE mobility and differences in LTR retroelements loads among individuals reproducing with and without sex.

RESULTS: We conducted a comprehensive de novo search for LTR retroelements and identified 333 intact LTR retroelements representing 142 families in the D. pulex genome. While nearly half of the identified LTR retroelements belong to the gypsy group, we also found copia (95), BEL/Pao (66) and DIRS (19) retroelements. Phylogenetic analysis of reverse transcriptase sequences showed that LTR retroelements in the D. pulex genome form many lineages distinct from known families, suggesting that the majority are novel. Our investigation of transcriptional activity of LTR retroelements using tiling array data obtained from three different experimental conditions found that 71 LTR retroelements are actively transcribed. Transposon display assays of mutation-accumulation lines showed evidence for putative somatic insertions for two DIRS retroelement families. Losses of presumably heterozygous insertions were observed in lineages in which selfing occurred, but never in asexuals, highlighting the potential impact of reproductive mode on TE abundance and distribution over time. The same two families were also assayed across natural isolates (both cyclical parthenogens and obligate asexuals) and there were more retroelements in populations capable of reproducing sexually for one of the two families assayed.

CONCLUSIONS: Given the importance of LTR retroelements activity in the evolution of other genomes, this comprehensive survey provides insight into the potential impact of LTR retroelements on the genome of D. pulex, a cyclically parthenogenetic microcrustacean that has served as an ecological model for over a century.}, } @article {pmid20616861, year = {2010}, author = {Herrmann, D and Poncet, BN and Manel, S and Rioux, D and Gielly, L and Taberlet, P and Gugerli, F}, title = {Selection criteria for scoring amplified fragment length polymorphisms (AFLPs) positively affect the reliability of population genetic parameter estimates.}, journal = {Genome}, volume = {53}, number = {4}, pages = {302-310}, doi = {10.1139/g10-006}, pmid = {20616861}, issn = {1480-3321}, mesh = {*Algorithms ; Amplified Fragment Length Polymorphism Analysis/*methods/standards ; Arabis/genetics ; Computational Biology/*methods ; DNA, Plant/genetics ; Genetic Markers/genetics ; Genetics, Population/*methods/standards ; Polymerase Chain Reaction ; Reproducibility of Results ; }, abstract = {A reliable data set is a fundamental prerequisite for consistent results and conclusions in population genetic studies. However, marker scoring of genetic fingerprints such as amplified fragment length polymorphisms (AFLPs) is a highly subjective procedure, inducing inconsistencies owing to personal or laboratory-specific criteria. We applied two alternative marker selection algorithms, the newly developed script scanAFLP and the recently published AFLPScore, to a large AFLP genome scan to test how population genetic parameters and error rates were affected. These results were confronted with replicated random selections of marker subsets. We show that the newly developed marker selection criteria reduced the mismatch error rate and had a notable influence on estimates of genetic diversity and differentiation. Both effects are likely to influence biological inference. For example, genetic diversity (HS) was 29% lower while genetic differentiation (FST) was 8% higher when applying scanAFLP compared with AFLPScore. Likewise, random selections of markers resulted in substantial deviations of population genetic parameters compared with the data sets including specific selection criteria. These randomly selected marker sets showed surprisingly low variance among replicates. We conclude that stringent marker selection and phenotype calling reduces noise in the data set while retaining patterns of population genetic structure.}, } @article {pmid20603756, year = {2010}, author = {Jakes, SS and DeBord, K}, title = {The interface of family, school, and community factors for the positive development of children and youth.}, journal = {Journal of prevention & intervention in the community}, volume = {38}, number = {3}, pages = {177-182}, doi = {10.1080/10852352.2010.486293}, pmid = {20603756}, issn = {1540-7330}, mesh = {Adolescent ; Child ; *Child Development ; *Community Networks ; *Family ; Humans ; *Schools ; Young Adult ; }, abstract = {In this issue, we examine the application of the ecological elements of family, school, and community on the developmental outcomes of children and youth. Five empirical articles then provide insight into the interaction of individual development, intelligence, and risk with contextual factors such as involvement, expectations, relationships, peers, and community. We conclude that individual child and youth outcomes are powerfully influenced by family involvement at a young age, but as age increases, this involvement becomes less salient. In youth considered "high risk," family and community protective factors were not able to significantly improve child outcomes. We specifically recommend that practitioners target interventions for high risk audiences that are guided by assessments of the child's developmental and risk profiles.}, } @article {pmid20600991, year = {2010}, author = {Szameitat, DP and Kreifelts, B and Alter, K and Szameitat, AJ and Sterr, A and Grodd, W and Wildgruber, D}, title = {It is not always tickling: distinct cerebral responses during perception of different laughter types.}, journal = {NeuroImage}, volume = {53}, number = {4}, pages = {1264-1271}, doi = {10.1016/j.neuroimage.2010.06.028}, pmid = {20600991}, issn = {1095-9572}, support = {G0200128/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Adult ; Auditory Perception/*physiology ; Brain/anatomy & histology/*physiology ; *Brain Mapping ; Emotions/physiology ; Female ; Humans ; Image Interpretation, Computer-Assisted ; Laughter/*physiology ; Magnetic Resonance Imaging ; Male ; }, abstract = {Laughter is highly relevant for social interaction in human beings and non-human primates. In humans as well as in non-human primates laughter can be induced by tickling. Human laughter, however, has further diversified and encompasses emotional laughter types with various communicative functions, e.g. joyful and taunting laughter. Here, it was evaluated if this evolutionary diversification of ecological functions is associated with distinct cerebral responses underlying laughter perception. Functional MRI revealed a double-dissociation of cerebral responses during perception of tickling laughter and emotional laughter (joy and taunt) with higher activations in the anterior rostral medial frontal cortex (arMFC) when emotional laughter was perceived, and stronger responses in the right superior temporal gyrus (STG) during appreciation of tickling laughter. Enhanced activation of the arMFC for emotional laughter presumably reflects increasing demands on social cognition processes arising from the greater social salience of these laughter types. Activation increase in the STG for tickling laughter may be linked to the higher acoustic complexity of this laughter type. The observed dissociation of cerebral responses for emotional laughter and tickling laughter was independent of task-directed focusing of attention. These findings support the postulated diversification of human laughter in the course of evolution from an unequivocal play signal to laughter with distinct emotional contents subserving complex social functions.}, } @article {pmid20594819, year = {2010}, author = {Sener, S and Sener, E and Nas, B and Karagüzel, R}, title = {Combining AHP with GIS for landfill site selection: a case study in the Lake Beyşehir catchment area (Konya, Turkey).}, journal = {Waste management (New York, N.Y.)}, volume = {30}, number = {11}, pages = {2037-2046}, doi = {10.1016/j.wasman.2010.05.024}, pmid = {20594819}, issn = {1879-2456}, mesh = {Conservation of Natural Resources ; Decision Support Techniques ; Ecology ; Environment ; Environmental Monitoring/*methods ; Equipment Design ; Geographic Information Systems ; Geography ; Models, Statistical ; Refuse Disposal/*instrumentation/*methods ; Turkey ; }, abstract = {Landfills are the most common method for the disposal of municipal solid waste (MSW) in Turkey. However, determining the location of landfill sites is a difficult and complex process because it must combine social, environmental and technical parameters. Additionally, it depends on several criteria and regulations. The main objective of this study was to select of a landfill site for the Lake Beyşehir catchment area. The Beyşehir Lake is the largest freshwater lake and drinking water reservoir in Turkey, but there is no controlled landfill site in the region. Therefore, the landfill site should be determined such that the lake is protected. To determine the most suitable landfill site, an analytical hierarchy process (AHP) was combined with a geographic information system (GIS) to examine several criteria, such as geology/hydrogeology, land use, slope, height, aspect and distance from settlements, surface waters, roads, and protected areas (ecologic, scientific or historic). Each criterion was evaluated with the aid of AHP and mapped by GIS. Data were assorted into four suitability classes within the study area, i.e., high, moderate, low and very low suitability areas, which represented 3.24%, 7.55%, 12.70% and 2.81%, of the study area, respectively. Additionally, 73.70% was determined to be completely unsuitable for a landfill site. As a result, two candidate landfill sites are suggested and discussed. The final decision for landfill site selection will require more detailed field studies.}, } @article {pmid20591175, year = {2010}, author = {Hankeln, W and Buttigieg, PL and Fink, D and Kottmann, R and Yilmaz, P and Glöckner, FO}, title = {MetaBar - a tool for consistent contextual data acquisition and standards compliant submission.}, journal = {BMC bioinformatics}, volume = {11}, number = {}, pages = {358}, pmid = {20591175}, issn = {1471-2105}, mesh = {Base Sequence ; *Databases, Genetic ; *Genomics ; Information Storage and Retrieval/*methods ; Internet ; Programming Languages ; *Software ; User-Computer Interface ; Workflow ; }, abstract = {BACKGROUND: Environmental sequence datasets are increasing at an exponential rate; however, the vast majority of them lack appropriate descriptors like sampling location, time and depth/altitude: generally referred to as metadata or contextual data. The consistent capture and structured submission of these data is crucial for integrated data analysis and ecosystems modeling. The application MetaBar has been developed, to support consistent contextual data acquisition.

RESULTS: MetaBar is a spreadsheet and web-based software tool designed to assist users in the consistent acquisition, electronic storage, and submission of contextual data associated to their samples. A preconfigured Microsoft Excel spreadsheet is used to initiate structured contextual data storage in the field or laboratory. Each sample is given a unique identifier and at any stage the sheets can be uploaded to the MetaBar database server. To label samples, identifiers can be printed as barcodes. An intuitive web interface provides quick access to the contextual data in the MetaBar database as well as user and project management capabilities. Export functions facilitate contextual and sequence data submission to the International Nucleotide Sequence Database Collaboration (INSDC), comprising of the DNA DataBase of Japan (DDBJ), the European Molecular Biology Laboratory database (EMBL) and GenBank. MetaBar requests and stores contextual data in compliance to the Genomic Standards Consortium specifications. The MetaBar open source code base for local installation is available under the GNU General Public License version 3 (GNU GPL3).

CONCLUSION: The MetaBar software supports the typical workflow from data acquisition and field-sampling to contextual data enriched sequence submission to an INSDC database. The integration with the megx.net marine Ecological Genomics database and portal facilitates georeferenced data integration and metadata-based comparisons of sampling sites as well as interactive data visualization. The ample export functionalities and the INSDC submission support enable exchange of data across disciplines and safeguarding contextual data.}, } @article {pmid20585972, year = {2010}, author = {Hogerwerf, L and Wallace, RG and Ottaviani, D and Slingenbergh, J and Prosser, D and Bergmann, L and Gilbert, M}, title = {Persistence of highly pathogenic avian influenza H5N1 virus defined by agro-ecological niche.}, journal = {EcoHealth}, volume = {7}, number = {2}, pages = {213-225}, pmid = {20585972}, issn = {1612-9210}, support = {R01TW00786901/TW/FIC NIH HHS/United States ; }, mesh = {Agriculture ; Animals ; Chickens/virology ; China/epidemiology ; Databases, Factual ; Ducks/virology ; *Ecosystem ; Geography ; Humans ; India/epidemiology ; Indonesia/epidemiology ; Influenza A Virus, H5N1 Subtype/*pathogenicity ; Influenza, Human/*epidemiology/*virology ; Logistic Models ; Population Density ; Poultry Diseases/virology ; Risk Factors ; Socioeconomic Factors ; }, abstract = {The highly pathogenic avian influenza (HPAI) H5N1 virus has spread across Eurasia and into Africa. Its persistence in a number of countries continues to disrupt poultry production, impairs smallholder livelihoods, and raises the risk a genotype adapted to human-to-human transmission may emerge. While previous studies identified domestic duck reservoirs as a primary risk factor associated with HPAI H5N1 persistence in poultry in Southeast Asia, little is known of such factors in countries with different agro-ecological conditions, and no study has investigated the impact of such conditions on HPAI H5N1 epidemiology at the global scale. This study explores the patterns of HPAI H5N1 persistence worldwide, and for China, Indonesia, and India includes individual provinces that have reported HPAI H5N1 presence during the 2004-2008 period. Multivariate analysis of a set of 14 agricultural, environmental, climatic, and socio-economic factors demonstrates in quantitative terms that a combination of six variables discriminates the areas with human cases and persistence: agricultural population density, duck density, duck by chicken density, chicken density, the product of agricultural population density and chicken output/input ratio, and purchasing power per capita. The analysis identifies five agro-ecological clusters, or niches, representing varying degrees of disease persistence. The agro-ecological distances of all study areas to the medoid of the niche with the greatest number of human cases are used to map HPAI H5N1 risk globally. The results indicate that few countries remain where HPAI H5N1 would likely persist should it be introduced.}, } @article {pmid20576761, year = {2010}, author = {Evans, NM and Holder, MT and Barbeitos, MS and Okamura, B and Cartwright, P}, title = {The phylogenetic position of Myxozoa: exploring conflicting signals in phylogenomic and ribosomal data sets.}, journal = {Molecular biology and evolution}, volume = {27}, number = {12}, pages = {2733-2746}, doi = {10.1093/molbev/msq159}, pmid = {20576761}, issn = {1537-1719}, mesh = {Animals ; Base Sequence ; Cnidaria/classification/genetics ; DNA, Ribosomal/genetics ; *Databases, Genetic ; Myxozoa/*classification/genetics ; *Phylogeny ; RNA, Ribosomal, 18S/*genetics ; RNA, Ribosomal, 28S/*genetics ; Ribosomes/genetics ; }, abstract = {Myxozoans are a diverse group of microscopic endoparasites that have been the focus of much controversy regarding their phylogenetic position. Two dramatically different hypotheses have been put forward regarding the placement of Myxozoa within Metazoa. One hypothesis, supported by ribosomal DNA (rDNA) data, place Myxozoa as a sister taxon to Bilateria. The alternative hypothesis, supported by phylogenomic data and morphology, place Myxozoa within Cnidaria. Here, we investigate these conflicting hypotheses and explore the effects of missing data, model choice, and inference methods, all of which can have an effect in placing highly divergent taxa. In addition, we identify subsets of the data that most influence the placement of Myxozoa and explore their effects by removing them from the data sets. Assembling the largest taxonomic sampling of myxozoans and cnidarians to date, with a comprehensive sampling of other metazoans for 18S and 28S nuclear rDNA sequences, we recover a well-supported placement of Myxozoa as an early diverging clade of Bilateria. By conducting parametric bootstrapping, we find that the bilaterian placement of Buddenbrockia could not alone be explained by long-branch attraction. After trimming a published phylogenomic data set, to circumvent problems of missing data, we recover the myxozoan Buddenbrockia plumatellae as a medusozoan cnidarian. In further explorations of these data sets, we find that removal of just a few identified sites under a maximum likelihood criterion employing the Whelan and Goldman amino acid substitution model changes the placement of Buddenbrockia from within Cnidaria to the alternative hypothesis at the base of Bilateria. Under a Bayesian criterion employing the CAT model, the cnidarian placement is more resilient to data removal, but under one test, a well-supported early diverging bilaterian position for Buddenbrockia is recovered. Our results confirm the existence of two relatively stable placements for myxozoans and demonstrate that conflicting signal exists not only between the two types of data but also within the phylogenomic data set. These analyses underscore the importance of careful model selection, taxon and data sampling, and in-depth data exploration when investigating the phylogenetic placement of highly divergent taxa.}, } @article {pmid20570961, year = {2011}, author = {Luque Fernández, MÁ and Gutiérrez Garitano, I and Cavanillas, AB}, title = {Increased risk of maternal deaths associated with foreign origin in Spain: a population based case-control study.}, journal = {European journal of public health}, volume = {21}, number = {3}, pages = {292-294}, doi = {10.1093/eurpub/ckp245}, pmid = {20570961}, issn = {1464-360X}, mesh = {Adolescent ; Adult ; Case-Control Studies ; Databases, Factual ; *Developing Countries ; *Emigrants and Immigrants ; Female ; Humans ; Maternal Age ; Maternal Mortality/*ethnology ; Risk Assessment ; Spain/epidemiology ; Young Adult ; }, abstract = {In Europe, different studies have identified immigrant women coming from developing countries as a risk group for maternal death. In Spain, an ecological study showed higher maternal mortality rates among foreign mothers compared with Spanish mothers during 2003-04. To examine whether the maternal death risk among foreign mothers in Spain is increased, we performed a population-based matched case-control study. Each case of maternal death during 1999-2006 was matched with four mothers who had given birth during the same year the case occurred. The National Statistics Institute provided the data. The variables in the study were maternal age and country of origin. We used a conditional logistic regression analysis. Adjusted by age, the risk of maternal death was 87% higher among foreign mothers. This study confirms that there is an increased risk of maternal death among foreign mothers in Spain. It would be desirable to analyse the socio-economic and healthcare circumstances surrounding the deaths.}, } @article {pmid20566872, year = {2010}, author = {Anderegg, WR and Prall, JW and Harold, J and Schneider, SH}, title = {Expert credibility in climate change.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {107}, number = {27}, pages = {12107-12109}, pmid = {20566872}, issn = {1091-6490}, mesh = {*Climate ; Climate Change/*statistics & numerical data ; Databases, Factual ; Ecology/statistics & numerical data/trends ; Forecasting ; *Greenhouse Effect ; Humans ; Public Opinion ; Research Personnel/statistics & numerical data ; }, abstract = {Although preliminary estimates from published literature and expert surveys suggest striking agreement among climate scientists on the tenets of anthropogenic climate change (ACC), the American public expresses substantial doubt about both the anthropogenic cause and the level of scientific agreement underpinning ACC. A broad analysis of the climate scientist community itself, the distribution of credibility of dissenting researchers relative to agreeing researchers, and the level of agreement among top climate experts has not been conducted and would inform future ACC discussions. Here, we use an extensive dataset of 1,372 climate researchers and their publication and citation data to show that (i) 97-98% of the climate researchers most actively publishing in the field surveyed here support the tenets of ACC outlined by the Intergovernmental Panel on Climate Change, and (ii) the relative climate expertise and scientific prominence of the researchers unconvinced of ACC are substantially below that of the convinced researchers.}, } @article {pmid20566506, year = {2010}, author = {Hebblewhite, M and Haydon, DT}, title = {Distinguishing technology from biology: a critical review of the use of GPS telemetry data in ecology.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {365}, number = {1550}, pages = {2303-2312}, pmid = {20566506}, issn = {1471-2970}, mesh = {Animals ; *Animals, Wild ; Conservation of Natural Resources/*methods ; Ecology/*methods ; *Ecosystem ; *Geographic Information Systems ; }, abstract = {In the past decade, ecologists have witnessed vast improvements in our ability to collect animal movement data through animal-borne technology, such as through GPS or ARGOS systems. However, more data does not necessarily yield greater knowledge in understanding animal ecology and conservation. In this paper, we provide a review of the major benefits, problems and potential misuses of GPS/Argos technology to animal ecology and conservation. Benefits are obvious, and include the ability to collect fine-scale spatio-temporal location data on many previously impossible to study animals, such as ocean-going fish, migratory songbirds and long-distance migratory mammals. These benefits come with significant problems, however, imposed by frequent collar failures and high cost, which often results in weaker study design, reduced sample sizes and poorer statistical inference. In addition, we see the divorcing of biologists from a field-based understanding of animal ecology to be a growing problem. Despite these difficulties, GPS devices have provided significant benefits, particularly in the conservation and ecology of wide-ranging species. We conclude by offering suggestions for ecologists on which kinds of ecological questions would currently benefit the most from GPS/Argos technology, and where the technology has been potentially misused. Significant conceptual challenges remain, however, including the links between movement and behaviour, and movement and population dynamics.}, } @article {pmid20566505, year = {2010}, author = {Morales, JM and Moorcroft, PR and Matthiopoulos, J and Frair, JL and Kie, JG and Powell, RA and Merrill, EH and Haydon, DT}, title = {Building the bridge between animal movement and population dynamics.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {365}, number = {1550}, pages = {2289-2301}, pmid = {20566505}, issn = {1471-2970}, mesh = {*Animal Migration ; Animals ; *Animals, Wild ; *Ecosystem ; *Geographic Information Systems ; *Models, Biological ; Population Dynamics ; }, abstract = {While the mechanistic links between animal movement and population dynamics are ecologically obvious, it is much less clear when knowledge of animal movement is a prerequisite for understanding and predicting population dynamics. GPS and other technologies enable detailed tracking of animal location concurrently with acquisition of landscape data and information on individual physiology. These tools can be used to refine our understanding of the mechanistic links between behaviour and individual condition through 'spatially informed' movement models where time allocation to different behaviours affects individual survival and reproduction. For some species, socially informed models that address the movements and average fitness of differently sized groups and how they are affected by fission-fusion processes at relevant temporal scales are required. Furthermore, as most animals revisit some places and avoid others based on their previous experiences, we foresee the incorporation of long-term memory and intention in movement models. The way animals move has important consequences for the degree of mixing that we expect to find both within a population and between individuals of different species. The mixing rate dictates the level of detail required by models to capture the influence of heterogeneity and the dynamics of intra- and interspecific interaction.}, } @article {pmid20566503, year = {2010}, author = {Owen-Smith, N and Fryxell, JM and Merrill, EH}, title = {Foraging theory upscaled: the behavioural ecology of herbivore movement.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {365}, number = {1550}, pages = {2267-2278}, pmid = {20566503}, issn = {1471-2970}, mesh = {*Animal Migration ; Animals ; *Animals, Wild ; *Behavior, Animal ; *Ecosystem ; *Feeding Behavior ; *Geographic Information Systems ; }, abstract = {We outline how principles of optimal foraging developed for diet and food patch selection might be applied to movement behaviour expressed over larger spatial and temporal scales. Our focus is on large mammalian herbivores, capable of carrying global positioning system (GPS) collars operating through the seasonal cycle and dependent on vegetation resources that are fixed in space but seasonally variable in availability and nutritional value. The concept of intermittent movement leads to the recognition of distinct movement modes over a hierarchy of spatio-temporal scales. Over larger scales, periods with relatively low displacement may indicate settlement within foraging areas, habitat units or seasonal ranges. Directed movements connect these patches or places used for other activities. Selection is expressed by switches in movement mode and the intensity of utilization by the settlement period relative to the area covered. The type of benefit obtained during settlement periods may be inferred from movement patterns, local environmental features, or the diel activity schedule. Rates of movement indicate changing costs in time and energy over the seasonal cycle, between years and among regions. GPS telemetry potentially enables large-scale movement responses to changing environmental conditions to be linked to population performance.}, } @article {pmid20566502, year = {2010}, author = {Gaillard, JM and Hebblewhite, M and Loison, A and Fuller, M and Powell, R and Basille, M and Van Moorter, B}, title = {Habitat-performance relationships: finding the right metric at a given spatial scale.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {365}, number = {1550}, pages = {2255-2265}, pmid = {20566502}, issn = {1471-2970}, mesh = {Animals ; *Animals, Wild ; *Behavior, Animal ; *Ecosystem ; *Geographic Information Systems ; *Population Dynamics ; Seasons ; }, abstract = {The field of habitat ecology has been muddled by imprecise terminology regarding what constitutes habitat, and how importance is measured through use, selection, avoidance and other bio-statistical terminology. Added to the confusion is the idea that habitat is scale-specific. Despite these conceptual difficulties, ecologists have made advances in understanding 'how habitats are important to animals', and data from animal-borne global positioning system (GPS) units have the potential to help this clarification. Here, we propose a new conceptual framework to connect habitats with measures of animal performance itself--towards assessing habitat-performance relationship (HPR). Long-term studies will be needed to estimate consequences of habitat selection for animal performance. GPS data from wildlife can provide new approaches for studying useful correlates of performance that we review. Recent examples include merging traditional resource selection studies with information about resources used at different critical life-history events (e.g. nesting, calving, migration), uncovering habitats that facilitate movement or foraging and, ultimately, comparing resources used through different life-history strategies with those resulting in death. By integrating data from GPS receivers with other animal-borne technologies and combining those data with additional life-history information, we believe understanding the drivers of HPRs will inform animal ecology and improve conservation.}, } @article {pmid20566499, year = {2010}, author = {Kie, JG and Matthiopoulos, J and Fieberg, J and Powell, RA and Cagnacci, F and Mitchell, MS and Gaillard, JM and Moorcroft, PR}, title = {The home-range concept: are traditional estimators still relevant with modern telemetry technology?.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {365}, number = {1550}, pages = {2221-2231}, pmid = {20566499}, issn = {1471-2970}, mesh = {Animals ; *Animals, Wild ; *Data Interpretation, Statistical ; *Ecosystem ; *Geographic Information Systems ; *Homing Behavior ; *Models, Statistical ; Telemetry ; }, abstract = {Recent advances in animal tracking and telemetry technology have allowed the collection of location data at an ever-increasing rate and accuracy, and these advances have been accompanied by the development of new methods of data analysis for portraying space use, home ranges and utilization distributions. New statistical approaches include data-intensive techniques such as kriging and nonlinear generalized regression models for habitat use. In addition, mechanistic home-range models, derived from models of animal movement behaviour, promise to offer new insights into how home ranges emerge as the result of specific patterns of movements by individuals in response to their environment. Traditional methods such as kernel density estimators are likely to remain popular because of their ease of use. Large datasets make it possible to apply these methods over relatively short periods of time such as weeks or months, and these estimates may be analysed using mixed effects models, offering another approach to studying temporal variation in space-use patterns. Although new technologies open new avenues in ecological research, our knowledge of why animals use space in the ways we observe will only advance by researchers using these new technologies and asking new and innovative questions about the empirical patterns they observe.}, } @article {pmid20566498, year = {2010}, author = {Boyce, MS and Pitt, J and Northrup, JM and Morehouse, AT and Knopff, KH and Cristescu, B and Stenhouse, GB}, title = {Temporal autocorrelation functions for movement rates from global positioning system radiotelemetry data.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {365}, number = {1550}, pages = {2213-2219}, pmid = {20566498}, issn = {1471-2970}, mesh = {Alberta ; *Animal Migration ; Animals ; *Animals, Wild ; *Data Interpretation, Statistical ; Female ; *Geographic Information Systems ; Seasons ; Telemetry ; }, abstract = {Autocorrelation has been viewed as a problem in telemetry studies because sequential observations are not independent in time or space, therefore violating assumptions for statistical inference. Yet nearly all ecological and behavioural data are autocorrelated in both space and time. We argue that there is much to learn about the structure of ecological and behavioural data from patterns of autocorrelation. Such patterns include periodicity in movement and patchiness in spatial data, which can be characterized by an autocorrelogram, semivariogram or spectrum. We illustrate the utility of temporal autocorrelation functions (ACFs) for analysing step-length data from GPS telemetry of wolves (Canis lupus), cougars (Puma concolor), grizzly bears (Ursus arctos) and elk (Cervus elaphus) in western Alberta. ACFs often differ by season, reflecting differences in foraging behaviour. In wilderness landscapes, step-length ACFs for predators decay slowly to apparently random patterns, but sometimes display strong daily rhythms in areas of human disturbance. In contrast, step lengths of elk are consistently periodic, reflecting crepuscular activity.}, } @article {pmid20566497, year = {2010}, author = {Smouse, PE and Focardi, S and Moorcroft, PR and Kie, JG and Forester, JD and Morales, JM}, title = {Stochastic modelling of animal movement.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {365}, number = {1550}, pages = {2201-2211}, pmid = {20566497}, issn = {1471-2970}, mesh = {*Animal Migration ; Animals ; *Animals, Wild ; Data Interpretation, Statistical ; *Geographic Information Systems ; *Models, Statistical ; Stochastic Processes ; }, abstract = {Modern animal movement modelling derives from two traditions. Lagrangian models, based on random walk behaviour, are useful for multi-step trajectories of single animals. Continuous Eulerian models describe expected behaviour, averaged over stochastic realizations, and are usefully applied to ensembles of individuals. We illustrate three modern research arenas. (i) Models of home-range formation describe the process of an animal 'settling down', accomplished by including one or more focal points that attract the animal's movements. (ii) Memory-based models are used to predict how accumulated experience translates into biased movement choices, employing reinforced random walk behaviour, with previous visitation increasing or decreasing the probability of repetition. (iii) Lévy movement involves a step-length distribution that is over-dispersed, relative to standard probability distributions, and adaptive in exploring new environments or searching for rare targets. Each of these modelling arenas implies more detail in the movement pattern than general models of movement can accommodate, but realistic empiric evaluation of their predictions requires dense locational data, both in time and space, only available with modern GPS telemetry.}, } @article {pmid20566496, year = {2010}, author = {Frair, JL and Fieberg, J and Hebblewhite, M and Cagnacci, F and DeCesare, NJ and Pedrotti, L}, title = {Resolving issues of imprecise and habitat-biased locations in ecological analyses using GPS telemetry data.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {365}, number = {1550}, pages = {2187-2200}, pmid = {20566496}, issn = {1471-2970}, mesh = {Animals ; *Animals, Wild ; *Behavior, Animal ; Ecology/*methods ; *Ecosystem ; *Geographic Information Systems ; Reproducibility of Results ; Telemetry ; }, abstract = {Global positioning system (GPS) technologies collect unprecedented volumes of animal location data, providing ever greater insight into animal behaviour. Despite a certain degree of inherent imprecision and bias in GPS locations, little synthesis regarding the predominant causes of these errors, their implications for ecological analysis or solutions exists. Terrestrial deployments report 37 per cent or less non-random data loss and location precision 30 m or less on average, with canopy closure having the predominant effect, and animal behaviour interacting with local habitat conditions to affect errors in unpredictable ways. Home-range estimates appear generally robust to contemporary levels of location imprecision and bias, whereas movement paths and inferences of habitat selection may readily become misleading. There is a critical need for greater understanding of the additive or compounding effects of location imprecision, fix-rate bias, and, in the case of resource selection, map error on ecological insights. Technological advances will help, but at present analysts have a suite of ad hoc statistical corrections and modelling approaches available-tools that vary greatly in analytical complexity and utility. The success of these solutions depends critically on understanding the error-inducing mechanisms, and the biggest gap in our current understanding involves species-specific behavioural effects on GPS performance.}, } @article {pmid20566495, year = {2010}, author = {Urbano, F and Cagnacci, F and Calenge, C and Dettki, H and Cameron, A and Neteler, M}, title = {Wildlife tracking data management: a new vision.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {365}, number = {1550}, pages = {2177-2185}, pmid = {20566495}, issn = {1471-2970}, mesh = {Animals ; *Animals, Wild ; *Behavior, Animal ; Database Management Systems/*instrumentation ; Ecology/instrumentation/*methods ; Geographic Information Systems/*instrumentation ; Information Storage and Retrieval/*methods ; Models, Theoretical ; }, abstract = {To date, the processing of wildlife location data has relied on a diversity of software and file formats. Data management and the following spatial and statistical analyses were undertaken in multiple steps, involving many time-consuming importing/exporting phases. Recent technological advancements in tracking systems have made large, continuous, high-frequency datasets of wildlife behavioural data available, such as those derived from the global positioning system (GPS) and other animal-attached sensor devices. These data can be further complemented by a wide range of other information about the animals' environment. Management of these large and diverse datasets for modelling animal behaviour and ecology can prove challenging, slowing down analysis and increasing the probability of mistakes in data handling. We address these issues by critically evaluating the requirements for good management of GPS data for wildlife biology. We highlight that dedicated data management tools and expertise are needed. We explore current research in wildlife data management. We suggest a general direction of development, based on a modular software architecture with a spatial database at its core, where interoperability, data model design and integration with remote-sensing data sources play an important role in successful GPS data handling.}, } @article {pmid20566494, year = {2010}, author = {Tomkiewicz, SM and Fuller, MR and Kie, JG and Bates, KK}, title = {Global positioning system and associated technologies in animal behaviour and ecological research.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {365}, number = {1550}, pages = {2163-2176}, pmid = {20566494}, issn = {1471-2970}, mesh = {Animals ; *Animals, Wild ; *Behavior, Animal ; Ecology/*methods ; Geographic Information Systems/*instrumentation ; Satellite Communications/*instrumentation ; }, abstract = {Biologists can equip animals with global positioning system (GPS) technology to obtain accurate (less than or equal to 30 m) locations that can be combined with sensor data to study animal behaviour and ecology. We provide the background of GPS techniques that have been used to gather data for wildlife studies. We review how GPS has been integrated into functional systems with data storage, data transfer, power supplies, packaging and sensor technologies to collect temperature, activity, proximity and mortality data from terrestrial species and birds. GPS 'rapid fixing' technologies combined with sensors provide location, dive frequency and duration profiles, and underwater acoustic information for the study of marine species. We examine how these rapid fixing technologies may be applied to terrestrial and avian applications. We discuss positional data quality and the capability for high-frequency sampling associated with GPS locations. We present alternatives for storing and retrieving data by using dataloggers (biologging), radio-frequency download systems (e.g. very high frequency, spread spectrum), integration of GPS with other satellite systems (e.g. Argos, Globalstar) and potential new data recovery technologies (e.g. network nodes). GPS is one component among many rapidly evolving technologies. Therefore, we recommend that users and suppliers interact to ensure the availability of appropriate equipment to meet animal research objectives.}, } @article {pmid20566493, year = {2010}, author = {Cagnacci, F and Boitani, L and Powell, RA and Boyce, MS}, title = {Animal ecology meets GPS-based radiotelemetry: a perfect storm of opportunities and challenges.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {365}, number = {1550}, pages = {2157-2162}, pmid = {20566493}, issn = {1471-2970}, mesh = {*Animal Migration ; Animals ; Behavior, Animal ; Ecology/*methods ; *Ecosystem ; *Geographic Information Systems ; Population Dynamics ; Telemetry/*methods ; }, abstract = {Global positioning system (GPS) telemetry technology allows us to monitor and to map the details of animal movement, securing vast quantities of such data even for highly cryptic organisms. We envision an exciting synergy between animal ecology and GPS-based radiotelemetry, as for other examples of new technologies stimulating rapid conceptual advances, where research opportunities have been paralleled by technical and analytical challenges. Animal positions provide the elemental unit of movement paths and show where individuals interact with the ecosystems around them. We discuss how knowing where animals go can help scientists in their search for a mechanistic understanding of key concepts of animal ecology, including resource use, home range and dispersal, and population dynamics. It is probable that in the not-so-distant future, intense sampling of movements coupled with detailed information on habitat features at a variety of scales will allow us to represent an animal's cognitive map of its environment, and the intimate relationship between behaviour and fitness. An extended use of these data over long periods of time and over large spatial scales can provide robust inferences for complex, multi-factorial phenomena, such as meta-analyses of the effects of climate change on animal behaviour and distribution.}, } @article {pmid20566492, year = {2010}, author = {Cagnacci, F and Boitani, L and Powell, RA and Boyce, MS}, title = {Challenges and opportunities of using GPS-based location data in animal ecology.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {365}, number = {1550}, pages = {2155}, doi = {10.1098/rstb.2010.0098}, pmid = {20566492}, issn = {1471-2970}, mesh = {*Animal Migration ; Animals ; Ecology/*methods ; *Geographic Information Systems ; *Telemetry ; }, } @article {pmid20565830, year = {2010}, author = {Peng, Z and Lu, T and Li, L and Liu, X and Gao, Z and Hu, T and Yang, X and Feng, Q and Guan, J and Weng, Q and Fan, D and Zhu, C and Lu, Y and Han, B and Jiang, Z}, title = {Genome-wide characterization of the biggest grass, bamboo, based on 10,608 putative full-length cDNA sequences.}, journal = {BMC plant biology}, volume = {10}, number = {}, pages = {116}, pmid = {20565830}, issn = {1471-2229}, mesh = {Alternative Splicing/genetics ; Base Composition ; Base Sequence ; DNA Transposable Elements/genetics ; DNA, Complementary/chemistry/*genetics ; Databases, Genetic ; Expressed Sequence Tags ; Genome, Plant/*genetics ; Lignin/biosynthesis ; Minisatellite Repeats/genetics ; Molecular Sequence Data ; Phylogeny ; Poaceae/classification/*genetics ; }, abstract = {BACKGROUND: With the availability of rice and sorghum genome sequences and ongoing efforts to sequence genomes of other cereal and energy crops, the grass family (Poaceae) has become a model system for comparative genomics and for better understanding gene and genome evolution that underlies phenotypic and ecological divergence of plants. While the genomic resources have accumulated rapidly for almost all major lineages of grasses, bamboo remains the only large subfamily of Poaceae with little genomic information available in databases, which seriously hampers our ability to take a full advantage of the wealth of grass genomic data for effective comparative studies.

RESULTS: Here we report the cloning and sequencing of 10,608 putative full length cDNAs (FL-cDNAs) primarily from Moso bamboo, Phyllostachys heterocycla cv. pubescens, a large woody bamboo with the highest ecological and economic values of all bamboos. This represents the third largest FL-cDNA collection to date of all plant species, and provides the first insight into the gene and genome structures of bamboos. We developed a Moso bamboo genomic resource database that so far contained the sequences of 10,608 putative FL-cDNAs and nearly 38,000 expressed sequence tags (ESTs) generated in this study.

CONCLUSION: Analysis of FL-cDNA sequences show that bamboo diverged from its close relatives such as rice, wheat, and barley through an adaptive radiation. A comparative analysis of the lignin biosynthesis pathway between bamboo and rice suggested that genes encoding caffeoyl-CoA O-methyltransferase may serve as targets for genetic manipulation of lignin content to reduce pollutants generated from bamboo pulping.}, } @article {pmid20561207, year = {2010}, author = {Opik, M and Vanatoa, A and Vanatoa, E and Moora, M and Davison, J and Kalwij, JM and Reier, U and Zobel, M}, title = {The online database MaarjAM reveals global and ecosystemic distribution patterns in arbuscular mycorrhizal fungi (Glomeromycota).}, journal = {The New phytologist}, volume = {188}, number = {1}, pages = {223-241}, doi = {10.1111/j.1469-8137.2010.03334.x}, pmid = {20561207}, issn = {1469-8137}, mesh = {Cluster Analysis ; *Databases, Genetic ; *Ecosystem ; Geography ; Glomeromycota/*classification/*genetics ; *Internet ; Mycorrhizae/*classification/*genetics ; Phylogeny ; Ribosome Subunits, Small/genetics ; }, abstract = {• Here, we describe a new database, MaarjAM, that summarizes publicly available Glomeromycota DNA sequence data and associated metadata. The goal of the database is to facilitate the description of distribution and richness patterns in this group of fungi. • Small subunit (SSU) rRNA gene sequences and available metadata were collated from all suitable taxonomic and ecological publications. These data have been made accessible in an open-access database (http://maarjam.botany.ut.ee). • Two hundred and eighty-two SSU rRNA gene virtual taxa (VT) were described based on a comprehensive phylogenetic analysis of all collated Glomeromycota sequences. Two-thirds of VT showed limited distribution ranges, occurring in single current or historic continents or climatic zones. Those VT that associated with a taxonomically wide range of host plants also tended to have a wide geographical distribution, and vice versa. No relationships were detected between VT richness and latitude, elevation or vascular plant richness. • The collated Glomeromycota molecular diversity data suggest limited distribution ranges in most Glomeromycota taxa and a positive relationship between the width of a taxon's geographical range and its host taxonomic range. Inconsistencies between molecular and traditional taxonomy of Glomeromycota, and shortage of data from major continents and ecosystems, are highlighted.}, } @article {pmid20560329, year = {2010}, author = {Xi, FM and He, HS and Hu, YM and Wu, XQ and Chang, Y and Liu, M and Shi, TM and Wang, JN}, title = {[Spatiotemporal pattern of urban growth and its driving forces in urban agglomeration of central Liaoning Province, China].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {21}, number = {3}, pages = {707-713}, pmid = {20560329}, issn = {1001-9332}, mesh = {China ; Cities ; *City Planning ; Conservation of Natural Resources/methods ; *Ecosystem ; Environmental Monitoring/*methods ; Geographic Information Systems ; Satellite Communications ; *Urbanization ; }, abstract = {Based on the five temporal Landsat TM remote sensing data of 1988, 1992, 1997, 2000, and 2004, and by using GIS spatial analysis and landscape pattern analysis, this paper analyzed the spatiotemporal pattern of urban growth and its driving forces in the urban agglomeration of central Liaoning Province (UACLP). From 1988 to 2004, the urban area in the UACLP had being increased from 812.55 km2 to 1345.86 km2, with an average growth rate of 32.96 km2 per year. The urban growth rate increased rapidly after 1997, and the urban growth intensity was up to the peak in 1997-2000. The urban growth was mainly concentrated in the central dense belt of the UACLP. From 1988 to 1997, the urban growth was relatively slow, its spatial pattern was compact, and edge growth and filling were the main urban growth types. From 1997 to 2004, the urban growth became faster with diffused spatial pattern and complex patch shape, and "frog leap" and diffusion were the main urban growth types. Non-agricultural population growth, economic growth, urban spatial mutual attraction, industrial development, and development zones construction policies were the main driving forces of urban growth in the UACLP.}, } @article {pmid20553933, year = {2010}, author = {Tachovsky, JA and Urban, JD and Wikoff, DS and Haws, LC and Harris, MA}, title = {Reduction of a large fish tissue analyte database: identifying and assessing data specific to a remediation site for risk assessment application.}, journal = {Chemosphere}, volume = {80}, number = {5}, pages = {481-488}, doi = {10.1016/j.chemosphere.2010.04.072}, pmid = {20553933}, issn = {1879-1298}, mesh = {Animals ; Benzofurans/metabolism ; Databases, Factual ; Environmental Exposure/analysis ; Environmental Monitoring/*methods ; Environmental Restoration and Remediation ; Fishes/*metabolism ; Polychlorinated Biphenyls/metabolism ; Polychlorinated Dibenzodioxins/analogs & derivatives/metabolism ; Polymers/metabolism ; Risk Assessment ; Rivers/chemistry ; Water Pollutants, Chemical/*metabolism ; Water Pollution, Chemical/statistics & numerical data ; }, abstract = {The Lower Passaic River (LPR) is one of the most heavily industrialized waterways in the US with both historical and continuing discharges of chemicals from point and non-point sources. Significant efforts have been initiated on behalf of public, private, and regulatory entities to restore this degraded urban river. Considerable attention has been devoted to characterizing environmental media with respect to human and ecological risk. As part of these efforts, a wealth of environmental data have been collected and analyzed for a variety of metals, pesticides, organic compounds, polycyclic aromatic hydrocarbons (PAHs), polychlorinated biphenyls (PCBs), polychlorinated dibenzodioxins/furans (PCDD/Fs), and dioxin-like compounds. The objectives of the study described in this paper were two-fold: (1) to generate LPR-specific data for use in human health risk assessment by characterizing concentrations of contaminants in LPR fish tissue samples based on publicly available data using a methodical and transparent approach, and (2) using the resulting data, to calculate the contaminant concentrations in a "Representative Fish," which is a representation of proportional fish tissue concentrations calculated based upon consumption patterns of LPR anglers. The data reduction, processing, and analyses described provide a representative dataset for the conduct of a human health assessment associated with fish consumption from the LPR.}, } @article {pmid20551039, year = {2010}, author = {Studer, RA and Robinson-Rechavi, M}, title = {Large-scale analysis of orthologs and paralogs under covarion-like and constant-but-different models of amino acid evolution.}, journal = {Molecular biology and evolution}, volume = {27}, number = {11}, pages = {2618-2627}, pmid = {20551039}, issn = {1537-1719}, mesh = {Amino Acids/*genetics ; Animals ; Databases, Nucleic Acid ; *Evolution, Molecular ; Gene Duplication/genetics ; Humans ; *Models, Genetic ; Selection, Genetic ; *Sequence Homology, Amino Acid ; }, abstract = {Functional divergence between homologous proteins is expected to affect amino acid sequences in two main ways, which can be considered as proxies of biochemical divergence: a "covarion-like" pattern of correlated changes in evolutionary rates, and switches in conserved residues ("conserved but different"). Although these patterns have been used in case studies, a large-scale analysis is needed to estimate their frequency and distribution. We use a phylogenomic framework of animal genes to answer three questions: 1) What is the prevalence of such patterns? 2) Can we link such patterns at the amino acid level with selection inferred at the codon level? 3) Are patterns different between paralogs and orthologs? We find that covarion-like patterns are more frequently detected than "constant but different," but that only the latter are correlated with signal for positive selection. Finally, there is no obvious difference in patterns between orthologs and paralogs.}, } @article {pmid20548941, year = {2010}, author = {Gavrilets, S}, title = {Rapid transition towards the Division of Labor via evolution of developmental plasticity.}, journal = {PLoS computational biology}, volume = {6}, number = {6}, pages = {e1000805}, pmid = {20548941}, issn = {1553-7358}, support = {R01 GM056693/GM/NIGMS NIH HHS/United States ; GM56693/GM/NIGMS NIH HHS/United States ; }, mesh = {Algorithms ; Animals ; Cell Differentiation/*physiology ; Cell Survival ; Computational Biology/methods ; Evolution, Molecular ; Fertility ; Germ Cells/*growth & development ; Insecta ; *Models, Biological ; }, abstract = {A crucial step in several major evolutionary transitions is the division of labor between components of the emerging higher-level evolutionary unit. Examples include the separation of germ and soma in simple multicellular organisms, appearance of multiple cell types and organs in more complex organisms, and emergence of casts in eusocial insects. How the division of labor was achieved in the face of selfishness of lower-level units is controversial. I present a simple mathematical model describing the evolutionary emergence of the division of labor via developmental plasticity starting with a colony of undifferentiated cells and ending with completely differentiated multicellular organisms. I explore how the plausibility and the dynamics of the division of labor depend on its fitness advantage, mutation rate, costs of developmental plasticity, and the colony size. The model shows that the transition to differentiated multicellularity, which has happened many times in the history of life, can be achieved relatively easily. My approach is expandable in a number of directions including the emergence of multiple cell types, complex organs, or casts of eusocial insects.}, } @article {pmid20543491, year = {2010}, author = {Campbell-Voytal, K}, title = {Phases of "pre-engagement" capacity building: discovery, exploration, and trial alliance.}, journal = {Progress in community health partnerships : research, education, and action}, volume = {4}, number = {2}, pages = {155-162}, doi = {10.1353/cpr.0.0118}, pmid = {20543491}, issn = {1557-0541}, mesh = {Black or African American ; Aged ; Attitude to Health/*ethnology ; Child, Preschool ; Community Networks/*organization & administration ; Community-Based Participatory Research/*methods ; *Community-Institutional Relations ; Female ; Health Promotion/*organization & administration ; Humans ; Male ; Mexican Americans ; Obesity/prevention & control ; *Organizational Case Studies ; }, abstract = {BACKGROUND: Academic prevention researchers who engage limited-resource communities may find that organizational or community capacity for prevention is low. Community organizations, neighborhoods, and academic partners may lack shared issue awareness, mutual interests, and interactive skills necessary for collaborative intervention. Existing capacity building models either ignore a 'pre-engagement' phase or acknowledge it without offering strategic detail. An exploratory or developmental phase before active engagement can be achieved through co-located work in a community setting. The construct, "ecology of practice," provides conceptual background for examining how "shared work" introduces and prepares partners for future collaboration consistent with community-based participatory research (CBPR) principles.

OBJECTIVE: This paper presents two case studies where pre-engagement capacity building involved partners who were initially unaware, disinterested, or unable to engage in preventive interventions. These cases illustrate how mutual participation in shared "ecologies of practice" enabled an exchange of cultural knowledge, skill, and language that laid the groundwork for future preventive intervention.

METHODS: A trajectory of developmental work in each case occurred over 5 years. Historical timelines, interviews, and personal communications between community and academic leaders were reviewed and common themes identified. A model of "pre-capacity building" emerged.

CONCLUSION: Capacity-building models that detail strategies for developing equitable engagement in under-resourced settings will more effectively move best practices into vulnerable communities. Preventive interventions must be translated equitably if health disparities are to be reduced.}, } @article {pmid20540779, year = {2010}, author = {Hartman, AL and Riddle, S and McPhillips, T and Ludäscher, B and Eisen, JA}, title = {Introducing W.A.T.E.R.S.: a workflow for the alignment, taxonomy, and ecology of ribosomal sequences.}, journal = {BMC bioinformatics}, volume = {11}, number = {}, pages = {317}, pmid = {20540779}, issn = {1471-2105}, mesh = {Base Sequence ; Genes, rRNA ; Genomics/*methods ; Phylogeny ; Ribosomes/*genetics ; Sequence Alignment/*methods ; Sequence Analysis, RNA ; *Software ; }, abstract = {BACKGROUND: For more than two decades microbiologists have used a highly conserved microbial gene as a phylogenetic marker for bacteria and archaea. The small-subunit ribosomal RNA gene, also known as 16 S rRNA, is encoded by ribosomal DNA, 16 S rDNA, and has provided a powerful comparative tool to microbial ecologists. Over time, the microbial ecology field has matured from small-scale studies in a select number of environments to massive collections of sequence data that are paired with dozens of corresponding collection variables. As the complexity of data and tool sets have grown, the need for flexible automation and maintenance of the core processes of 16 S rDNA sequence analysis has increased correspondingly.

RESULTS: We present WATERS, an integrated approach for 16 S rDNA analysis that bundles a suite of publicly available 16 S rDNA analysis software tools into a single software package. The "toolkit" includes sequence alignment, chimera removal, OTU determination, taxonomy assignment, phylogentic tree construction as well as a host of ecological analysis and visualization tools. WATERS employs a flexible, collection-oriented 'workflow' approach using the open-source Kepler system as a platform.

CONCLUSIONS: By packaging available software tools into a single automated workflow, WATERS simplifies 16 S rDNA analyses, especially for those without specialized bioinformatics, programming expertise. In addition, WATERS, like some of the newer comprehensive rRNA analysis tools, allows researchers to minimize the time dedicated to carrying out tedious informatics steps and to focus their attention instead on the biological interpretation of the results. One advantage of WATERS over other comprehensive tools is that the use of the Kepler workflow system facilitates result interpretation and reproducibility via a data provenance sub-system. Furthermore, new "actors" can be added to the workflow as desired and we see WATERS as an initial seed for a sizeable and growing repository of interoperable, easy-to-combine tools for asking increasingly complex microbial ecology questions.}, } @article {pmid20538728, year = {2010}, author = {Zhang, Z and López-Giráldez, F and Townsend, JP}, title = {LOX: inferring Level Of eXpression from diverse methods of census sequencing.}, journal = {Bioinformatics (Oxford, England)}, volume = {26}, number = {15}, pages = {1918-1919}, pmid = {20538728}, issn = {1367-4811}, support = {P01 GM068087-06/GM/NIGMS NIH HHS/United States ; P01 GM068087/GM/NIGMS NIH HHS/United States ; RR19895/RR/NCRR NIH HHS/United States ; P01 GM068087-06S1/GM/NIGMS NIH HHS/United States ; P01 GM 068087/GM/NIGMS NIH HHS/United States ; P01 GM068087-08/GM/NIGMS NIH HHS/United States ; P01 GM068087-07/GM/NIGMS NIH HHS/United States ; }, mesh = {Computational Biology/*methods ; Expressed Sequence Tags ; Gene Expression Profiling/*methods ; Gene Expression Regulation, Fungal ; Oligonucleotide Array Sequence Analysis/methods ; *Software ; }, abstract = {SUMMARY: We present LOX (Level Of eXpression) that estimates the Level Of gene eXpression from high-throughput-expressed sequence datasets with multiple treatments or samples. Unlike most analyses, LOX incorporates a gene bias model that facilitates integration of diverse transcriptomic sequencing data that arises when transcriptomic data have been produced using diverse experimental methodologies. LOX integrates overall sequence count tallies normalized by total expressed sequence count to provide expression levels for each gene relative to all treatments as well as Bayesian credible intervals.

AVAILABILITY: http://www.yale.edu/townsend/software.html}, } @article {pmid20535611, year = {2010}, author = {Lorz, C and Fürst, C and Galic, Z and Matijasic, D and Podrazky, V and Potocic, N and Simoncic, P and Strauch, M and Vacik, H and Makeschin, F}, title = {GIS-based probability assessment of natural hazards in forested landscapes of Central and South-Eastern Europe.}, journal = {Environmental management}, volume = {46}, number = {6}, pages = {920-930}, pmid = {20535611}, issn = {1432-1009}, mesh = {Climate Change ; Conservation of Natural Resources/*methods ; Disasters/statistics & numerical data ; Droughts/statistics & numerical data ; Ecosystem ; Europe, Eastern ; Fires/statistics & numerical data ; Forestry/*methods ; *Geographic Information Systems ; Probability ; Proportional Hazards Models ; Safety Management ; *Trees ; Wind ; }, abstract = {We assessed the probability of three major natural hazards--windthrow, drought, and forest fire--for Central and South-Eastern European forests which are major threats for the provision of forest goods and ecosystem services. In addition, we analyzed spatial distribution and implications for a future oriented management of forested landscapes. For estimating the probability of windthrow, we used rooting depth and average wind speed. Probabilities of drought and fire were calculated from climatic and total water balance during growing season. As an approximation to climate change scenarios, we used a simplified approach with a general increase of pET by 20%. Monitoring data from the pan-European forests crown condition program and observed burnt areas and hot spots from the European Forest Fire Information System were used to test the plausibility of probability maps. Regions with high probabilities of natural hazard are identified and management strategies to minimize probability of natural hazards are discussed. We suggest future research should focus on (i) estimating probabilities using process based models (including sensitivity analysis), (ii) defining probability in terms of economic loss, (iii) including biotic hazards, (iv) using more detailed data sets on natural hazards, forest inventories and climate change scenarios, and (v) developing a framework of adaptive risk management.}, } @article {pmid20532847, year = {2010}, author = {Wayland, MT}, title = {Proboscis profiler: a tool for detecting acanthocephalan morphotypes.}, journal = {Systematic parasitology}, volume = {76}, number = {3}, pages = {159-167}, pmid = {20532847}, issn = {1573-5192}, mesh = {Acanthocephala/*anatomy & histology/*classification ; Animal Structures/anatomy & histology ; Animals ; Computational Biology/*methods ; Parasitology/*methods ; Software ; }, abstract = {Molecular studies conducted over the past 25 years have revealed previously unrecognised diversity in the phylum Acanthocephala. Several nominal species have been shown to represent complexes of morphologically cryptic biological species, a situation potentially confounding the analysis of ecological data. A software tool, 'Proboscis profiler', was developed to detect morphological heterogeneity in collections of superficially similar acanthocephalan worms based on the multivariate statistical analysis of proboscis hook dimensions. Proboscis profiler identifies objective, natural groups in a collection of acanthocephalans which may correspond to distinct biological species or populations. Initial trials demonstrate that Proboscis profiler can discriminate biological acanthocephalan species of the Echinorhynchus gadi Zoega in Müller, 1776 complex and differentiate between dorsal and ventral hook rows from the proboscis of E. salmonis Müller, 1784. Proboscis profiler is free software and can be downloaded from http://acanthocephala.sourceforge.net.}, } @article {pmid20528857, year = {2011}, author = {Warton, DI}, title = {Regularized sandwich estimators for analysis of high-dimensional data using generalized estimating equations.}, journal = {Biometrics}, volume = {67}, number = {1}, pages = {116-123}, doi = {10.1111/j.1541-0420.2010.01438.x}, pmid = {20528857}, issn = {1541-0420}, mesh = {*Algorithms ; Animals ; Biometry/*methods ; Computer Simulation ; *Data Interpretation, Statistical ; *Ecosystem ; *Models, Statistical ; Nematoda/*growth & development ; *Population Growth ; }, abstract = {A modification of generalized estimating equations (GEEs) methodology is proposed for hypothesis testing of high-dimensional data, with particular interest in multivariate abundance data in ecology, an important application of interest in thousands of environmental science studies. Such data are typically counts characterized by high dimensionality (in the sense that cluster size exceeds number of clusters, n>K) and over-dispersion relative to the Poisson distribution. Usual GEE methods cannot be applied in this setting primarily because sandwich estimators become numerically unstable as n increases. We propose instead using a regularized sandwich estimator that assumes a common correlation matrix R, and shrinks the sample estimate of R toward the working correlation matrix to improve its numerical stability. It is shown via theory and simulation that this substantially improves the power of Wald statistics when cluster size is not small. We apply the proposed approach to study the effects of nutrient addition on nematode communities, and in doing so discuss important issues in implementation, such as using statistics that have good properties when parameter estimates approach the boundary (), and using resampling to enable valid inference that is robust to high dimensionality and to possible model misspecification.}, } @article {pmid20525623, year = {2010}, author = {Marshall, DC}, title = {Cryptic failure of partitioned Bayesian phylogenetic analyses: lost in the land of long trees.}, journal = {Systematic biology}, volume = {59}, number = {1}, pages = {108-117}, doi = {10.1093/sysbio/syp080}, pmid = {20525623}, issn = {1076-836X}, mesh = {*Bayes Theorem ; Classification/*methods ; Computational Biology/*methods ; *Data Collection ; *Evolution, Molecular ; Markov Chains ; Monte Carlo Method ; *Phylogeny ; Reproducibility of Results ; }, abstract = {Partitioned Bayesian phylogenetic analyses of routine genetic data sets, constructed using MrBayes (Ronquist and Huelsenbeck 2003), can become trapped in regions of parameter space characterized by unrealistically long trees and distorted partition rate multipliers. Such analyses commonly fail to reach stationarity during hundreds of millions of generations of sampling-many times longer than most published analyses. Some data sets are so prone to this problem that paired MrBayes runs begun from different starting trees repeatedly find the same incorrect long-tree solutions and consequently pass the most commonly employed tests of stationarity, including the average standard deviation of split frequencies (ASDSF) and the potential scale reduction factor (PSRF) statistics offered by MrBayes (Gelman and Rubin 1992). In these situations, failure to reach stationarity is recognizable only in light of prior knowledge of model parameters, such as the expectation that third-codon-position sites usually evolve fastest in protein-coding genes. The conditions that lead to the long-tree problem are frequently encountered in phylogenetic studies today, and I present 6 demonstration examples from the literature. Although the effects on tree length (TL) are often dramatic, effects on topology appear to be subtle. Susceptibility to the problem is sometimes predicted by the difference between the true TL and the starting TL. In some cases, the problems described here can be avoided or reduced by manipulation of the starting TL and/or by adjustments to the prior on branch lengths. In more difficult situations, accurate branch length estimation may not be possible with Bayesian methods because of dependence of the solution on the branch length prior.}, } @article {pmid20525619, year = {2010}, author = {Thomson, RC and Shaffer, HB}, title = {Sparse supermatrices for phylogenetic inference: taxonomy, alignment, rogue taxa, and the phylogeny of living turtles.}, journal = {Systematic biology}, volume = {59}, number = {1}, pages = {42-58}, doi = {10.1093/sysbio/syp075}, pmid = {20525619}, issn = {1076-836X}, mesh = {Animals ; Classification/*methods ; Computational Biology/*methods ; *Data Collection ; *Phylogeny ; Sequence Alignment/*methods ; Turtles/*classification/*genetics ; }, abstract = {As phylogenetic data sets grow in size and number, objective methods to summarize this information are becoming increasingly important. Supermatrices can combine existing data directly and in principle provide effective syntheses of phylogenetic information that may reveal new relationships. However, several serious difficulties exist in the construction of large supermatrices that must be overcome before these approaches will enjoy broad utility. We present analyses that examine the performance of sparse supermatrices constructed from large sequence databases for the reconstruction of species-level phylogenies. We develop a largely automated informatics pipeline that allows for the construction of sparse supermatrices from GenBank data. In doing so, we develop strategies for alleviating some of the outstanding impediments to accurate phylogenetic inference using these approaches. These include taxonomic standardization, automated alignment, and the identification of rogue taxa. We use turtles as an exemplar clade and present a well-supported species-level phylogeny for two-thirds of all turtle species based on a approximately 50 kb supermatrix consisting of 93% missing data. Finally, we discuss some of the remaining pitfalls and concerns associated with supermatrix analyses, provide comparisons to supertree approaches, and suggest areas for future research.}, } @article {pmid20525606, year = {2009}, author = {Huang, H and Knowles, LL}, title = {What is the danger of the anomaly zone for empirical phylogenetics?.}, journal = {Systematic biology}, volume = {58}, number = {5}, pages = {527-536}, doi = {10.1093/sysbio/syp047}, pmid = {20525606}, issn = {1076-836X}, mesh = {Classification/*methods ; Computational Biology/*methods ; Computer Simulation ; *Evolution, Molecular ; Genes/*genetics ; *Models, Genetic ; Mutation/genetics ; *Phylogeny ; Species Specificity ; }, abstract = {The increasing number of observations of gene trees with discordant topologies in phylogenetic studies has raised awareness about the problems of incongruence between species trees and gene trees. Moreover, theoretical treatments focusing on the impact of coalescent variance on phylogenetic study have also identified situations where the most probable gene trees are ones that do not match the underlying species tree (i.e., anomalous gene trees [AGTs]). However, although the theoretical proof of the existence of AGTs is alarming, the actual risk that AGTs pose to empirical phylogenetic study is far from clear. Establishing the conditions (i.e., the branch lengths in a species tree) for which AGTs are possible does not address the critical issue of how prevalent they might be. Furthermore, theoretical characterization of the species trees for which AGTs may pose a problem (i.e., the anomaly zone or the species histories for which AGTs are theoretically possible) is based on consideration of just one source of variance that contributes to species tree and gene tree discord-gene lineage coalescence. Yet, empirical data contain another important stochastic component-mutational variance. Estimated gene trees will differ from the underlying gene trees (i.e., the actual genealogy) because of the random process of mutation. Here, we take a simulation approach to investigate the prevalence of AGTs, among estimated gene trees, thereby characterizing the boundaries of the anomaly zone taking into account both coalescent and mutational variances. We also determine the frequency of realized AGTs, which is critical to putting the theoretical work on AGTs into a realistic biological context. Two salient results emerge from this investigation. First, our results show that mutational variance can indeed expand the parameter space (i.e., the relative branch lengths in a species tree) where AGTs might be observed in empirical data. By exploring the underlying cause for the expanded anomaly zone, we identify aspects of empirical data relevant to avoiding the problems that AGTs pose for species tree inference from multilocus data. Second, for the empirical species histories where AGTs are possible, unresolved trees-not AGTs-predominate the pool of estimated gene trees. This result suggests that the risk of AGTs, while they exist in theory, may rarely be realized in practice. By considering the biological realities of both mutational and coalescent variances, the study has refined, and redefined, what the actual challenges are for empirical phylogenetic study of recently diverged taxa that have speciated rapidly-AGTs themselves are unlikely to pose a significant danger to empirical phylogenetic study.}, } @article {pmid20525604, year = {2009}, author = {McCormack, JE and Huang, H and Knowles, LL}, title = {Maximum likelihood estimates of species trees: how accuracy of phylogenetic inference depends upon the divergence history and sampling design.}, journal = {Systematic biology}, volume = {58}, number = {5}, pages = {501-508}, doi = {10.1093/sysbio/syp045}, pmid = {20525604}, issn = {1076-836X}, mesh = {Classification/*methods ; Computational Biology/*methods ; Computer Simulation ; *Evolution, Molecular ; Genes/*genetics ; Genetic Speciation ; *Likelihood Functions ; *Models, Genetic ; *Phylogeny ; *Research Design ; }, abstract = {The understanding that gene trees are often in discord with each other and with the species trees that contain them has led researchers to methods that incorporate the inherent stochasticity of genetic processes in the phylogenetic estimation procedure. Recently developed methods for species-tree estimation that not only consider the retention and sorting of ancestral polymorphism but also quantify the actual probabilities of incomplete lineage sorting are expected to provide an improvement over earlier summary-statistic based approaches that discard much of the information content of gene trees. However, these new methods have yet to be tested on truly challenging evolutionary histories such as those marked by recent rapid speciation where high levels of incomplete lineage sorting and discord among gene trees predominate. Here, we test a new maximum-likelihood method that incorporates stochastic models of both nucleotide substitution and lineage sorting for species-tree estimation. Using a simulation approach, we consider a broad range of species-tree topologies under 2 scenarios representing moderate and severe incomplete lineage sorting. We show that the maximum-likelihood method results in more accurate species trees than a summary-statistic based approach, demonstrating that information contained in discordant gene trees can be effectively extracted using a full probabilistic model. Moreover, we demonstrate that the shape of the original species tree (i.e., the relative lengths of internal branches) has a significant impact on whether the species tree is estimated accurately. In the speciation histories explored here, it is not just the recent origin of species that affects the accuracy of the estimates but the variance in relative species divergence times as well. Additionally, we show that sampling effort (number of individuals and/or loci) and sampling design (ratio of individuals to loci) are both important factors affecting the accuracy of species-tree estimates, which is again affected by the relative timing of divergence among species. The inherent difficulties of estimating relationships when species have undergone a recent radiation are discussed, and in particular, the limitations with maximum-likelihood estimates of species trees that do not consider uncertainty in the estimated gene trees of individual loci. Thus, despite substantial improvements over current summary-statistic based approaches, and the increased sophistication of procedures that incorporate the process of gene lineage coalescence, recent radiations still appear to pose daunting challenges for phylogenetics.}, } @article {pmid20525603, year = {2009}, author = {Cranston, KA and Hurwitz, B and Ware, D and Stein, L and Wing, RA}, title = {Species trees from highly incongruent gene trees in rice.}, journal = {Systematic biology}, volume = {58}, number = {5}, pages = {489-500}, doi = {10.1093/sysbio/syp054}, pmid = {20525603}, issn = {1076-836X}, mesh = {Base Sequence ; *Bayes Theorem ; Classification/*methods ; Computational Biology/*methods ; Genes/*genetics ; *Models, Genetic ; Oryza/*genetics ; *Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA ; Software ; }, abstract = {Several methods have recently been developed to infer multilocus phylogenies by incorporating information from topological incongruence of the individual genes. In this study, we investigate 2 such methods, Bayesian concordance analysis and Bayesian estimation of species trees. Our test data are a collection of genes from cultivated rice (genus Oryza) and the most closely related wild species, generated using a high-throughput sequencing protocol and bioinformatics pipeline. Trees inferred from independent genes display levels of topological incongruence that far exceed that seen in previous data sets analyzed with these species tree methods. We identify differences in phylogenetic results between inference methods that incorporate gene tree incongruence. Finally, we discuss the challenges of scaling these analyses for data sets with thousands of gene trees and extensive levels of missing data.}, } @article {pmid20523898, year = {2010}, author = {Bedford, T and Cobey, S and Beerli, P and Pascual, M}, title = {Global migration dynamics underlie evolution and persistence of human influenza A (H3N2).}, journal = {PLoS pathogens}, volume = {6}, number = {5}, pages = {e1000918}, pmid = {20523898}, issn = {1553-7374}, support = {R01 GM078985/GM/NIGMS NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; R01 GM 078985/GM/NIGMS NIH HHS/United States ; }, mesh = {Asia/epidemiology ; Emigration and Immigration/*statistics & numerical data ; *Evolution, Molecular ; Genetic Variation ; Geographic Information Systems ; Global Health ; Humans ; Influenza A Virus, H3N2 Subtype/*genetics/growth & development ; Influenza, Human/*epidemiology/transmission/*virology ; Pedigree ; United States/epidemiology ; }, abstract = {The global migration patterns of influenza viruses have profound implications for the evolutionary and epidemiological dynamics of the disease. We developed a novel approach to reconstruct the genetic history of human influenza A (H3N2) collected worldwide over 1998 to 2009 and used it to infer the global network of influenza transmission. Consistent with previous models, we find that China and Southeast Asia lie at the center of this global network. However, we also find that strains of influenza circulate outside of Asia for multiple seasons, persisting through dynamic migration between northern and southern regions. The USA acts as the primary hub of temperate transmission and, together with China and Southeast Asia, forms the trunk of influenza's evolutionary tree. These findings suggest that antiviral use outside of China and Southeast Asia may lead to the evolution of long-term local and potentially global antiviral resistance. Our results might also aid the design of surveillance efforts and of vaccines better tailored to different geographic regions.}, } @article {pmid20521067, year = {2011}, author = {Rakocevic, M and Martim, SF}, title = {Time series in analysis of yerba-mate biennial growth modified by environment.}, journal = {International journal of biometeorology}, volume = {55}, number = {2}, pages = {161-171}, pmid = {20521067}, issn = {1432-1254}, mesh = {Computer Simulation ; *Data Interpretation, Statistical ; *Ecosystem ; Ilex paraguariensis/*growth & development ; *Models, Biological ; *Models, Statistical ; *Seasons ; }, abstract = {To assess differences in the lag-effect pattern in the relationship between yerba-mate biennial growth and environmental factors, a time-series analysis was performed. A generalized Poisson regression model was used to control time trends, temperature, growing degree days (GDD), rainfalls and night length (NL). It was hypothesized that the active growth and growth pauses in yerba-mate are controlled endogenously and modified by environment, and that genders would respond differently to environmental modifications. The patterns in the lag effect from the distributed-lag models were similar to those of time-series models with meteorological data means with lag = 0. GDD and NL were principal factors affecting biennial yerba-mate shoot elongation and the number of green leaves of females grown in monoculture, besides their significant effects on metamer emission and leaf area in males grown in monoculture. NL also had a significant influence on shoot elongation and leaf area of both genders grown in forest understorey (FUS), indicating that yerba-mate growth is synchronized by an internal clock sensitive to temperature adjustments. The morphological plasticity and the adaptation efforts of yerba-mate were more pronounced in monoculture than in FUS. Sexual dimorphism was expressed-males were more sensitive to environmental changes than females, especially in monoculture. Growth modifications were much more intense when plants were grown in a cultivation system that is less like yerba-mate natural habitat (monoculture) than in one resembling its natural habitat (FUS). Our data support the ecological specialization theory.}, } @article {pmid20519284, year = {2010}, author = {Parmentier, G and Bastian, FB and Robinson-Rechavi, M}, title = {Homolonto: generating homology relationships by pairwise alignment of ontologies and application to vertebrate anatomy.}, journal = {Bioinformatics (Oxford, England)}, volume = {26}, number = {14}, pages = {1766-1771}, pmid = {20519284}, issn = {1367-4811}, mesh = {*Algorithms ; Animals ; Databases, Factual ; Gene Expression ; Humans ; Sequence Alignment/methods ; Software ; Vertebrates/*anatomy & histology/genetics ; }, abstract = {MOTIVATION: The anatomy of model species is described in ontologies, which are used to standardize the annotations of experimental data, such as gene expression patterns. To compare such data between species, we need to establish relations between ontologies describing different species.

RESULTS: We present a new algorithm, and its implementation in the software Homolonto, to create new relationships between anatomical ontologies, based on the homology concept. Homolonto uses a supervised ontology alignment approach. Several alignments can be merged, forming homology groups. We also present an algorithm to generate relationships between these homology groups. This has been used to build a multi-species ontology, for the database of gene expression evolution Bgee.

AVAILABILITY: download section of the Bgee website http://bgee.unil.ch/}, } @article {pmid20515493, year = {2010}, author = {Lancaster, LT}, title = {Molecular evolutionary rates predict both extinction and speciation in temperate angiosperm lineages.}, journal = {BMC evolutionary biology}, volume = {10}, number = {}, pages = {162}, pmid = {20515493}, issn = {1471-2148}, mesh = {DNA, Plant/genetics ; DNA, Ribosomal Spacer/genetics ; Databases, Genetic ; *Evolution, Molecular ; *Extinction, Biological ; *Genetic Speciation ; Magnoliopsida/*classification/genetics ; *Models, Genetic ; Phylogeny ; }, abstract = {BACKGROUND: A positive relationship between diversification (i.e., speciation) and nucleotide substitution rates is commonly reported for angiosperm clades. However, the underlying cause of this relationship is often unknown because multiple intrinsic and extrinsic factors can affect the relationship, and these have confounded previous attempts infer causation. Determining which factor drives this oft-reported correlation can lend insight into the macroevolutionary process.

RESULTS: Using a new database of 13 time-calibrated angiosperm phylogenies based on internal transcribed spacer (ITS) sequences, and controlling for extrinsic variables of life history and habitat, I evaluated several potential intrinsic causes of this correlation. Speciation rates (lambda) and relative extinction rates (epsilon) were positively correlated with mean substitution rates, but were uncorrelated with substitution rate heterogeneity. It is unlikely that the positive diversification-substitution correlation is due to accelerated molecular evolution during speciation (e.g., via enhanced selection or drift), because punctuated increases in ITS rate (i.e., greater mean and variation in ITS rate for rapidly speciating clades) were not observed. Instead, fast molecular evolution likely increases speciation rate (via increased mutational variation as a substrate for selection and reproductive isolation) but also increases extinction (via mutational genetic load).

CONCLUSIONS: In general, these results predict that clades with higher background substitution rates may undergo successful diversification under new conditions while clades with lower substitution rates may experience decreased extinction during environmental stasis.}, } @article {pmid20515448, year = {2010}, author = {Tamames, J and de Lorenzo, V}, title = {EnvMine: a text-mining system for the automatic extraction of contextual information.}, journal = {BMC bioinformatics}, volume = {11}, number = {}, pages = {294}, pmid = {20515448}, issn = {1471-2105}, mesh = {Bayes Theorem ; Data Mining/*methods ; Databases, Factual ; Information Storage and Retrieval/*methods ; Pattern Recognition, Automated/methods ; Periodicals as Topic ; }, abstract = {BACKGROUND: For ecological studies, it is crucial to count on adequate descriptions of the environments and samples being studied. Such a description must be done in terms of their physicochemical characteristics, allowing a direct comparison between different environments that would be difficult to do otherwise. Also the characterization must include the precise geographical location, to make possible the study of geographical distributions and biogeographical patterns. Currently, there is no schema for annotating these environmental features, and these data have to be extracted from textual sources (published articles). So far, this had to be performed by manual inspection of the corresponding documents. To facilitate this task, we have developed EnvMine, a set of text-mining tools devoted to retrieve contextual information (physicochemical variables and geographical locations) from textual sources of any kind.

RESULTS: EnvMine is capable of retrieving the physicochemical variables cited in the text, by means of the accurate identification of their associated units of measurement. In this task, the system achieves a recall (percentage of items retrieved) of 92% with less than 1% error. Also a Bayesian classifier was tested for distinguishing parts of the text describing environmental characteristics from others dealing with, for instance, experimental settings.Regarding the identification of geographical locations, the system takes advantage of existing databases such as GeoNames to achieve 86% recall with 92% precision. The identification of a location includes also the determination of its exact coordinates (latitude and longitude), thus allowing the calculation of distance between the individual locations.

CONCLUSION: EnvMine is a very efficient method for extracting contextual information from different text sources, like published articles or web pages. This tool can help in determining the precise location and physicochemical variables of sampling sites, thus facilitating the performance of ecological analyses. EnvMine can also help in the development of standards for the annotation of environmental features.}, } @article {pmid20512594, year = {2010}, author = {Risch, AC and Wirthner, S and Busse, MD and Page-Dumroese, DS and Schütz, M}, title = {Grubbing by wild boars (Sus scrofa L.) and its impact on hardwood forest soil carbon dioxide emissions in Switzerland.}, journal = {Oecologia}, volume = {164}, number = {3}, pages = {773-784}, pmid = {20512594}, issn = {1432-1939}, mesh = {Animals ; Carbon Dioxide/*analysis ; *Feeding Behavior ; Geographic Information Systems ; *Soil ; Soil Microbiology ; Sus scrofa/*physiology ; Switzerland ; Temperature ; Trees ; }, abstract = {Interest in soil C storage and release has increased in recent years. In addition to factors such as climate/land-use change, vertebrate animals can have a considerable impact on soil CO(2) emissions. To date, most research has considered herbivores, while the impact of omnivorous animals has rarely been investigated. Our goal was to determine how European wild boars (Sus scrofa L.), large omnivores that consume soil-inhabiting animals and belowground plant parts by grubbing in the soil, affect soil C dynamics. We measured soil respiration (CO(2)), temperature, and moisture on paired grubbed and non-grubbed plots in six hardwood forest stands for a 3-year period and sampled fine root and microbial biomass at the beginning and after 2 years of the study. We also measured the percentage of freshly disturbed forest soil within the larger surroundings of each stand and used this information together with hunting statistics and forest cover data to model the total amount of CO(2) released from Swiss forest soils due to grubbing during 1 year. Soil CO(2) emissions were significantly higher on grubbed compared to non-grubbed plots during the study. On average 23.1% more CO(2) was released from these plots, which we associated with potential alterations in CO(2) diffusion rates, incorporation of litter into the mineral soil and higher fine root/microbial biomass. Thus, wild boars considerably increased the small-scale heterogeneity of soil properties. Roughly 1% of Switzerland's surface area is similar to our sites (boar density/forest cover). Given the range of forest soil disturbance of 27-54% at our sites, the geographic information system model predicted that boar grubbing would lead to the release of an additional 49,731.10-98,454.74 t CO(2) year(-1). These values are relatively small compared to total soil emissions estimated for Swiss hardwood forests and suggest that boars will have little effect on large-scale emissions unless their numbers increase and their range expands dramatically.}, } @article {pmid20508122, year = {2010}, author = {Schneps, MH and Griswold, A and Finkelstein, N and McLeod, M and Schrag, DP}, title = {SPORE series winner. Using video to build learning contexts online.}, journal = {Science (New York, N.Y.)}, volume = {328}, number = {5982}, pages = {1119-1120}, doi = {10.1126/science.1186934}, pmid = {20508122}, issn = {1095-9203}, mesh = {*Computer-Assisted Instruction ; Ecology/*education ; Humans ; *Internet ; Learning ; Online Systems ; *Video Recording ; }, } @article {pmid20503184, year = {2010}, author = {Ocaña-Riola, R}, title = {Common errors in disease mapping.}, journal = {Geospatial health}, volume = {4}, number = {2}, pages = {139-154}, doi = {10.4081/gh.2010.196}, pmid = {20503184}, issn = {1970-7096}, mesh = {Bayes Theorem ; Data Interpretation, Statistical ; Decision Making ; *Epidemiologic Studies ; Geographic Information Systems ; Geography ; Health Policy ; Humans ; Incidence ; *Observer Variation ; *Research Design ; Risk ; }, abstract = {Many morbid-mortality atlases and small-area studies have been carried out over the last decade. However, the methods used to draw up such research, the interpretation of results and the conclusions published are often inaccurate. Often, the proliferation of this practice has led to inefficient decision-making, implementation of inappropriate health policies and negative impact on the advancement of scientific knowledge. This paper reviews the most frequent errors in the design, analysis and interpretation of small-area epidemiological studies and proposes a diagnostic evaluation test that should enable the scientific quality of published papers to be ascertained. Nine common mistakes in disease mapping methods are discussed. From this framework, and following the theory of diagnostic evaluation, a standardised test to evaluate the scientific quality of a small-area epidemiology study has been developed. Optimal quality is achieved with the maximum score (16 points), average with a score between 8 and 15 points, and low with a score of 7 or below. A systematic evaluation of scientific papers, together with an enhanced quality in future research, will contribute towards increased efficacy in epidemiological surveillance and in health planning based on the spatio-temporal analysis of ecological information.}, } @article {pmid20500873, year = {2010}, author = {Sanderson, MJ and McMahon, MM and Steel, M}, title = {Phylogenomics with incomplete taxon coverage: the limits to inference.}, journal = {BMC evolutionary biology}, volume = {10}, number = {}, pages = {155}, pmid = {20500873}, issn = {1471-2148}, mesh = {Computational Biology/*methods ; Data Mining ; Databases, Genetic ; Genomic Library ; Genomics/*methods ; Models, Genetic ; *Phylogeny ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: Phylogenomic studies based on multi-locus sequence data sets are usually characterized by partial taxon coverage, in which sequences for some loci are missing for some taxa. The impact of missing data has been widely studied in phylogenetics, but it has proven difficult to distinguish effects due to error in tree reconstruction from effects due to missing data per se. We approach this problem using a explicitly phylogenomic criterion of success, decisiveness, which refers to whether the pattern of taxon coverage allows for uniquely defining a single tree for all taxa.

RESULTS: We establish theoretical bounds on the impact of missing data on decisiveness. Results are derived for two contexts: a fixed taxon coverage pattern, such as that observed from an already assembled data set, and a randomly generated pattern derived from a process of sampling new data, such as might be observed in an ongoing comparative genomics sequencing project. Lower bounds on how many loci are needed for decisiveness are derived for the former case, and both lower and upper bounds for the latter. When data are not decisive for all trees, we estimate the probability of decisiveness and the chances that a given edge in the tree will be distinguishable. Theoretical results are illustrated using several empirical examples constructed by mining sequence databases, genomic libraries such as ESTs and BACs, and complete genome sequences.

CONCLUSION: Partial taxon coverage among loci can limit phylogenomic inference by making it impossible to distinguish among multiple alternative trees. However, even though lack of decisiveness is typical of many sparse phylogenomic data sets, it is often still possible to distinguish a large fraction of edges in the tree.}, } @article {pmid20497209, year = {2010}, author = {Kuhnert, PM and Martin, TG and Griffiths, SP}, title = {A guide to eliciting and using expert knowledge in Bayesian ecological models.}, journal = {Ecology letters}, volume = {13}, number = {7}, pages = {900-914}, doi = {10.1111/j.1461-0248.2010.01477.x}, pmid = {20497209}, issn = {1461-0248}, mesh = {*Bayes Theorem ; *Ecology ; *Models, Theoretical ; }, abstract = {Expert knowledge in ecology is gaining momentum as a tool for conservation decision-making where data are lacking. Yet, little information is available to help a researcher decide whether expert opinion is useful for their model, how an elicitation should be conducted, what the most relevant method for elicitation is and how this can be translated into prior distributions for analysis in a Bayesian model. In this study, we provide guidance in using expert knowledge in a transparent and credible manner to inform ecological models and ultimately natural resource and conservation decision-making. We illustrate the decisions faced when considering the use of expert knowledge in a model with the help of two real ecological case studies. These examples are explored further to examine the impact of expert knowledge through 'priors' in Bayesian modeling and specifically how to minimize potential bias. Finally, we make recommendations on the use of expert opinion in ecology. We believe if expert knowledge is elicited and incorporated into ecological models with the same level of rigour provided in the collection and use of empirical data, expert knowledge can increase the precision of models and facilitate informed decision-making in a cost-effective manner.}, } @article {pmid20486927, year = {2011}, author = {McCrea, RS and Morgan, BJ}, title = {Multistate mark-recapture model selection using score tests.}, journal = {Biometrics}, volume = {67}, number = {1}, pages = {234-241}, doi = {10.1111/j.1541-0420.2010.01421.x}, pmid = {20486927}, issn = {1541-0420}, mesh = {*Algorithms ; *Animal Migration ; Animals ; Biometry/*methods ; *Censuses ; Computer Simulation ; *Data Interpretation, Statistical ; *Models, Biological ; *Population Dynamics ; }, abstract = {Although multistate mark-recapture models are recognized as important, they lack a simple model-selection procedure. This article proposes and evaluates a step-up approach to select appropriate models for multistate mark-recapture data using score tests. Only models supported by the data require fitting, so that over-complicated model structures with too many parameters do not need to be considered. Typically only a small number of models are fitted, and the procedure is also able to identify parameter-redundant and near-redundant models. The good performance of the technique is demonstrated using simulation, and the approach is illustrated on a three-region Canada goose data set. In this case, it identifies a new model that is much simpler than the best model previously considered for this application.}, } @article {pmid20481408, year = {2009}, author = {Keating, N and Dosman, D}, title = {Social capital and the care networks of frail seniors.}, journal = {Canadian review of sociology = Revue canadienne de sociologie}, volume = {46}, number = {4}, pages = {301-318}, doi = {10.1111/j.1755-618x.2009.01216.x}, pmid = {20481408}, issn = {1755-6171}, mesh = {Adult ; Aged ; *Caregivers ; Cluster Analysis ; Community Networks ; Data Collection ; *Family ; Female ; *Frail Elderly ; Humans ; *Intergenerational Relations ; Male ; Middle Aged ; Quality of Life ; *Social Support ; }, abstract = {Social capital has been a key framework in conceptualizing the place of social ties in quality of life. Families have not been among groups of interest in social capital research. Yet within the context of research and public policy on aging, the contemporary discourse on families and care is congruent with social capital assumptions. In this paper, we draw on social capital literature to frame our understanding of the social capital inherent in families of frail older adults, and hypothesize their abilities to benefit family members. Data are drawn from Statistics Canada 2002 General Social Survey on Aging and Social Support.}, } @article {pmid20479502, year = {2011}, author = {Hickey, G and Blanchette, M and Carmi, P and Maheshwari, A and Zeh, N}, title = {An approximation algorithm for the Noah's Ark problem with random feature loss.}, journal = {IEEE/ACM transactions on computational biology and bioinformatics}, volume = {8}, number = {2}, pages = {551-556}, doi = {10.1109/TCBB.2010.37}, pmid = {20479502}, issn = {1557-9964}, mesh = {*Algorithms ; *Biodiversity ; Computational Biology/*methods ; Phylogeny ; }, abstract = {The phylogenetic diversity (PD) of a set of species is a measure of their evolutionary distinctness based on a phylogenetic tree. PD is increasingly being adopted as an index of biodiversity in ecological conservation projects. The Noah's Ark Problem (NAP) is an NP-Hard optimization problem that abstracts a fundamental conservation challenge in asking to maximize the expected PD of a set of taxa given a fixed budget, where each taxon is associated with a cost of conservation and a probability of extinction. Only simplified instances of the problem, where one or more parameters are fixed as constants, have as of yet been addressed in the literature. Furthermore, it has been argued that PD is not an appropriate metric for models that allow information to be lost along paths in the tree. We therefore generalize the NAP to incorporate a proposed model of feature loss according to an exponential distribution and term this problem NAP with Loss (NAPL). In this paper, we present a pseudopolynomial time approximation scheme for NAPL.}, } @article {pmid20479258, year = {2010}, author = {Sallan, LC and Coates, MI}, title = {End-Devonian extinction and a bottleneck in the early evolution of modern jawed vertebrates.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {107}, number = {22}, pages = {10131-10135}, pmid = {20479258}, issn = {1091-6490}, mesh = {Animals ; Biodiversity ; *Biological Evolution ; Databases, Factual ; Ecosystem ; *Extinction, Biological ; Fossils ; History, Ancient ; Marine Biology ; Models, Genetic ; Phylogeny ; Time Factors ; Vertebrates/*classification/*genetics ; }, abstract = {The Devonian marks a critical stage in the early evolution of vertebrates: It opens with an unprecedented diversity of fishes and closes with the earliest evidence of limbed tetrapods. However, the latter part of the Devonian has also been characterized as a period of global biotic crisis marked by two large extinction pulses: a "Big Five" mass extinction event at the Frasnian-Famennian stage boundary (374 Ma) and the less well-documented Hangenberg event some 15 million years later at the Devonian-Carboniferous boundary (359 Ma). Here, we report the results of a wide-ranging analysis of the impact of these events on early vertebrate evolution, which was obtained from a database of vertebrate occurrences sampling over 1,250 taxa from 66 localities spanning Givetian to Serpukhovian stages (391 to 318 Ma). We show that major vertebrate clades suffered acute and systematic effects centered on the Hangenberg extinction involving long-term losses of over 50% of diversity and the restructuring of vertebrate ecosystems worldwide. Marine and nonmarine faunas were equally affected, precluding the existence of environmental refugia. The subsequent recovery of previously diverse groups (including placoderms, sarcopterygian fish, and acanthodians) was minimal. Tetrapods, actinopterygians, and chondrichthyans, all scarce within the Devonian, undergo large diversification events in the aftermath of the extinction, dominating all subsequent faunas. The Hangenberg event represents a previously unrecognized bottleneck in the evolutionary history of vertebrates as a whole and a historical contingency that shaped the roots of modern biodiversity.}, } @article {pmid20478548, year = {2010}, author = {Zhang, X and Joseph, KS and Kramer, MS}, title = {Decreased term and postterm birthweight in the United States: impact of labor induction.}, journal = {American journal of obstetrics and gynecology}, volume = {203}, number = {2}, pages = {124.e1-7}, doi = {10.1016/j.ajog.2010.03.044}, pmid = {20478548}, issn = {1097-6868}, support = {//Canadian Institutes of Health Research/Canada ; }, mesh = {Adult ; *Birth Weight ; Cesarean Section/adverse effects/statistics & numerical data ; Confidence Intervals ; Databases, Factual ; Female ; *Gestational Age ; Humans ; Incidence ; Infant Mortality/trends ; Infant, Newborn ; *Infant, Postmature ; Labor, Induced/adverse effects/*statistics & numerical data ; Linear Models ; Maternal Age ; Multivariate Analysis ; Parity ; Pregnancy ; Premature Birth ; Retrospective Studies ; Risk Assessment ; *Term Birth ; United States/epidemiology ; Vital Statistics ; White People/statistics & numerical data ; Young Adult ; }, abstract = {OBJECTIVE: We sought to assess recent trends in falling mean birthweight (BW) and gestational age (GA) among US non-Hispanic white singleton live births >or=37 weeks of gestation and the contribution of increased rates of induction to these trends.

STUDY DESIGN: This was an ecological study based on US vital statistics from 1992 through 2003.

RESULTS: From 1992 through 2003, mean BW fell by 37 g, mean GA by 3 days, and macrosomia rates by 25%. Rates of induction nearly doubled from 14% to 27%. Our ecological state-level analysis showed that the increased rate of induction was significantly associated with reduced mean BW (r = -0.54; 95% confidence interval [CI], -0.71 to -0.29), mean GA (r = -0.44; 95% CI, -0.65 to -0.17), and rate of macrosomia (r = -0.55; 95% CI, -0.74 to -0.32).

CONCLUSION: Increasing use of induction is a likely cause of the observed recent declines in BW and GA. The impact of these trends on infant and long-term health warrants attention and investigation.}, } @article {pmid20473629, year = {2011}, author = {Tsumura, Y and Kado, T and Yoshida, K and Abe, H and Ohtani, M and Taguchi, Y and Fukue, Y and Tani, N and Ueno, S and Yoshimura, K and Kamiya, K and Harada, K and Takeuchi, Y and Diway, B and Finkeldey, R and Na'iem, M and Indrioko, S and Ng, KK and Muhammad, N and Lee, SL}, title = {Molecular database for classifying Shorea species (Dipterocarpaceae) and techniques for checking the legitimacy of timber and wood products.}, journal = {Journal of plant research}, volume = {124}, number = {1}, pages = {35-48}, pmid = {20473629}, issn = {1618-0860}, mesh = {Base Sequence ; *Databases, Nucleic Acid ; Dipterocarpaceae/*classification/*genetics ; Fatty Acids, Unsaturated/genetics ; Genetic Variation ; Molecular Sequence Data ; Nucleotides/genetics ; Phylogeny ; Sequence Analysis, DNA/*methods ; Species Specificity ; Wood/anatomy & histology/*genetics ; }, abstract = {The extent of tropical forest has been declining, due to over-exploitation and illegal logging activities. Large quantities of unlawfully extracted timber and other wood products have been exported, mainly to developed countries. As part of the export monitoring effort, we have developed methods for extracting and analyzing DNA from wood products, such as veneers and sawn timbers made from dipterocarps, in order to identify the species from which they originated. We have also developed a chloroplast DNA database for classifying Shorea species, which are both ecologically and commercially important canopy tree species in the forests of Southeast Asia. We are able to determine the candidate species of wood samples, based on DNA sequences and anatomical data. The methods for analyzing DNA from dipterocarp wood products may have strong deterrent effects on international trade of illegitimate dipterocarp products. However, the method for analyzing DNA from wood is not perfect for all wood products and need for more improvement, especially for plywood sample. Consequently, there may be benefits for the conservation of tropical forests in Southeast Asia.}, } @article {pmid20464894, year = {2010}, author = {Bottari, CL and Dassa, C and Rainville, CM and Dutil, E}, title = {The IADL profile: development, content validity, intra- and interrater agreement.}, journal = {Canadian journal of occupational therapy. Revue canadienne d'ergotherapie}, volume = {77}, number = {2}, pages = {90-100}, doi = {10.2182/cjot.2010.77.2.5}, pmid = {20464894}, issn = {0008-4174}, mesh = {*Activities of Daily Living ; Acute Disease ; Adolescent ; Adult ; Brain Injuries/diagnosis/*rehabilitation ; *Cognition ; Data Interpretation, Statistical ; Glasgow Coma Scale ; Humans ; Middle Aged ; Pilot Projects ; Psychometrics ; Reproducibility of Results ; Validation Studies as Topic ; Video Recording ; }, abstract = {BACKGROUND: Occupational therapists are frequently asked to document the interplay between individuals' neuropsychological deficits and the requirements of their daily lives.

PURPOSE: The present study was designed to develop and validate a measure of independence in everyday functioning that considers recent advances in research regarding the ecological assessment of executive functions.

METHOD: Experts (n=8) judged the IADL Profile's content validity and the tool was pilot tested with the target population (n=8). To document the tool's reliability, 30 patients aged 16 to 65 with moderate or severe TBI were recruited. A trained examiner administered the IADL Profile, and three trained judges rated video recordings on two occasions.

RESULTS: An eight-task (29-item) test was developed. Comparing ratings of four raters, 95 percent of kappa coefficients indicated moderate to almost perfect agreement, and 94% showed almost perfect intrarater agreement.

IMPLICATIONS: The IADL Profile provides occupational therapists with a set of measures of IADL independence with strong preliminary evidence of reliability.}, } @article {pmid20463896, year = {2010}, author = {Pfister, CA and Meyer, F and Antonopoulos, DA}, title = {Metagenomic profiling of a microbial assemblage associated with the California mussel: a node in networks of carbon and nitrogen cycling.}, journal = {PloS one}, volume = {5}, number = {5}, pages = {e10518}, pmid = {20463896}, issn = {1932-6203}, mesh = {Animals ; Archaea/genetics/metabolism ; Bacteria/classification/*genetics/metabolism ; Bacterial Proteins/metabolism ; Base Sequence ; Bivalvia/*microbiology ; Carbon/*metabolism ; Carbon Dioxide/metabolism ; Databases, Genetic ; Gene Expression Profiling/*methods ; Metagenomics/*methods ; Nitrogen/*metabolism ; Phylogeny ; Surface Properties ; Water Movements ; }, abstract = {Mussels are conspicuous and often abundant members of rocky shores and may constitute an important site for the nitrogen cycle due to their feeding and excretion activities. We used shotgun metagenomics of the microbial community associated with the surface of mussels (Mytilus californianus) on Tatoosh Island in Washington state to test whether there is a nitrogen-based microbial assemblage associated with mussels. Analyses of both tidepool mussels and those on emergent benches revealed a diverse community of Bacteria and Archaea with approximately 31 million bp from 6 mussels in each habitat. Using MG-RAST, between 22.5-25.6% were identifiable using the SEED non-redundant database for proteins. Of those fragments that were identifiable through MG-RAST, the composition was dominated by Cyanobacteria and Alpha- and Gamma-proteobacteria. Microbial composition was highly similar between the tidepool and emergent bench mussels, suggesting similar functions across these different microhabitats. One percent of the proteins identified in each sample were related to nitrogen cycling. When normalized to protein discovery rate, the high diversity and abundance of enzymes related to the nitrogen cycle in mussel-associated microbes is as great or greater than that described for other marine metagenomes. In some instances, the nitrogen-utilizing profile of this assemblage was more concordant with soil metagenomes in the Midwestern U.S. than for open ocean system. Carbon fixation and Calvin cycle enzymes further represented 0.65 and 1.26% of all proteins and their abundance was comparable to a number of open ocean marine metagenomes. In sum, the diversity and abundance of nitrogen and carbon cycle related enzymes in the microbes occupying the shells of Mytilus californianus suggest these mussels provide a node for microbial populations and thus biogeochemical processes.}, } @article {pmid20463048, year = {2010}, author = {Burri, R and Salamin, N and Studer, RA and Roulin, A and Fumagalli, L}, title = {Adaptive divergence of ancient gene duplicates in the avian MHC class II beta.}, journal = {Molecular biology and evolution}, volume = {27}, number = {10}, pages = {2360-2374}, doi = {10.1093/molbev/msq120}, pmid = {20463048}, issn = {1537-1719}, mesh = {Adaptation, Biological/*genetics ; Amino Acid Sequence ; Animals ; Bayes Theorem ; Birds/*genetics ; Computational Biology ; Computer Simulation ; *Evolution, Molecular ; Exons/genetics ; Genes, Duplicate/*genetics ; Genes, MHC Class II/*genetics ; Likelihood Functions ; Models, Genetic ; *Phylogeny ; *Selection, Genetic ; Sequence Alignment ; }, abstract = {Gene duplication and neofunctionalization are known to be important processes in the evolution of phenotypic complexity. They account for important evolutionary novelties that confer ecological adaptation, such as the major histocompatibility complex (MHC), a multigene family crucial to the vertebrate immune system. In birds, two MHC class II β (MHCIIβ) exon 3 lineages have been recently characterized, and two hypotheses for the evolutionary history of MHCIIβ lineages were proposed. These lineages could have arisen either by 1) an ancient duplication and subsequent divergence of one paralog or by 2) recent parallel duplications followed by functional convergence. Here, we compiled a data set consisting of 63 MHCIIβ exon 3 sequences from six avian orders to distinguish between these hypotheses and to understand the role of selection in the divergent evolution of the two avian MHCIIβ lineages. Based on phylogenetic reconstructions and simulations, we show that a unique duplication event preceding the major avian radiations gave rise to two ancestral MHCIIβ lineages that were each likely lost once later during avian evolution. Maximum likelihood estimation shows that following the ancestral duplication, positive selection drove a radical shift from basic to acidic amino acid composition of a protein domain facing the α-chain in the MHCII α β-heterodimer. Structural analyses of the MHCII α β-heterodimer highlight that three of these residues are potentially involved in direct interactions with the α-chain, suggesting that the shift following duplication may have been accompanied by coevolution of the interacting α- and β-chains. These results provide new insights into the long-term evolutionary relationships among avian MHC genes and open interesting perspectives for comparative and population genomic studies of avian MHC evolution.}, } @article {pmid20462111, year = {2010}, author = {Greenacre, M}, title = {Correspondence analysis of raw data.}, journal = {Ecology}, volume = {91}, number = {4}, pages = {958-963}, doi = {10.1890/09-0239.1}, pmid = {20462111}, issn = {0012-9658}, mesh = {Animals ; *Data Interpretation, Statistical ; Ecology/*methods ; Ecosystem ; Models, Biological ; North Sea ; Population Dynamics ; }, abstract = {Correspondence analysis has found extensive use in ecology, archaeology, linguistics, and the social sciences as a method for visualizing the patterns of association in a table of frequencies or nonnegative ratio-scale data. Inherent to the method is the expression of the data in each row or each column relative to their respective totals, and it is these sets of relative values (called profiles) that are visualized. This "relativization" of the data makes perfect sense when the margins of the table represent samples from subpopulations of inherently different sizes. But in some ecological applications sampling is performed on equal areas or equal volumes so that the absolute levels of the observed occurrences may be of relevance, in which case relativization may not be required. In this paper, I define the correspondence analysis of the raw "unrelativized" data and discuss its properties, comparing this new method to regular correspondence analysis and to a related variant of nonsymmetric correspondence analysis.}, } @article {pmid20462014, year = {2010}, author = {Li, XL and Zeng, GM and Shi, L and Liang, J and Cai, Q}, title = {[Urban ecological land in Changsha City: its quantitative analysis and optimization].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {21}, number = {2}, pages = {415-421}, pmid = {20462014}, issn = {1001-9332}, mesh = {China ; Cities ; City Planning/*statistics & numerical data ; *Ecosystem ; Environment Design/*statistics & numerical data ; Geographic Information Systems ; Models, Statistical ; Poaceae/growth & development ; Trees/*growth & development ; }, abstract = {In this paper, a hierarchy index system suitable for catastrophe progression method was constructed to comprehensively analyze and evaluate the status of ecological land construction in Changsha City in 2007. Based on the evaluation results, the irrationalities of the distribution pattern of Changsha urban ecological land were discussed. With the support of geographic information system (GIS), the ecological corridors of the urban ecological land were constructed by using the 'least-cost' modeling, and, in combining with conflict analysis, the optimum project of the urban ecological land was put forward, forming an integrated evaluation system. The results indicated that the ecological efficiency of urban ecological land in Changsha in 2007 was at medium level, with an evaluation value being 0.9416, and the quantitative index being relatively high but the coordination index being relatively low. The analysis and verification with software Fragstats showed that the ecological efficiency of the urban ecological land after optimization was higher, with the evaluation value being 0.9618, and the SHDI, CONTAG, and other indices also enhanced.}, } @article {pmid20462012, year = {2010}, author = {Zhou, DC and Luo, GP and Xu, WQ and Feng, YX}, title = {[Dynamics of ecosystem services value in Aksu River watershed in 1960 -2008].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {21}, number = {2}, pages = {399-408}, pmid = {20462012}, issn = {1001-9332}, mesh = {China ; Conservation of Natural Resources/*economics ; Crops, Agricultural/*growth & development ; Ecology/economics ; Geographic Information Systems ; Poaceae/growth & development ; Rivers ; Satellite Communications ; Trees/*growth & development ; *Wetlands ; }, abstract = {By using GIS-RS techniques and the table 'Equivalent weight of China terrestrial ecosystems services value', in combining with the local grain yield and grain purchasing price, this paper analyzed the changes of ecosystem services value in Aksu River watershed in 1960-2008, and explored the responses of ecosystem services value change in arid trans-boundary river watershed to land use/cover change. Overall, the ecosystem services value in Aksu River watershed in 1960-2008 changed slightly, with the total value increased after an initial decrease. The main cause of the initial decrease was the area decrease of wetland, woodland, and grassland. The area increase of cropland and water body partly offset the loss of the total value, but the loss was still larger than the gain. The contribution of each ecosystem service value to the total ecosystem services value had less change, and the service value from soil formation and protection together with waste treatment contributed most. There was a significant spatial heterogeneity in the magnitude and the variation of ecosystem services value, with the downstream of the watershed changed significantly. Sensitivity analysis indicated that the estimated total ecosystem services value in the study area was inelastic to the services value coefficients, and the results shown in this paper were robust.}, } @article {pmid20461554, year = {2011}, author = {Hepcan, CC and Ozkan, MB}, title = {Establishing ecological networks for habitat conservation in the case of Çeşme-Urla Peninsula, Turkey.}, journal = {Environmental monitoring and assessment}, volume = {174}, number = {1-4}, pages = {157-170}, pmid = {20461554}, issn = {1573-2959}, mesh = {*Conservation of Natural Resources ; *Ecosystem ; Geographic Information Systems ; Turkey ; }, abstract = {The study involves the Çeşme-Urla Peninsula, where habitat fragmentation and loss, which threaten biological diversity, have become an urgent matter of concern in recent decades. The study area has been subjected to anthropogenic pressures and alterations due to ongoing and impending land uses. Therefore, ecological networks, as an appropriate way to deal with habitat fragmentation and loss and to improve ecological quality, were identified in the study area as one of the early attempts in the country to maintain its rich biodiversity. In this sense, core areas and ecological linkages as primary components of ecological networks were established on the basis of sustaining natural habitats. A GIS-based model was created to identify core areas and to facilitate the ecological connectivity. The modeling process for core areas and corridors combined 14 and 21 different variables, respectively. The variables were used as environmental inputs in the model, and all analyses were materialized in ArcGIS 9.2 using grid functions of image analysis and spatial analyst modules. As a result, six core areas and 36 corridor alternatives were materialized. Furthermore, some recommendations for the implementation and management of the proposed ecological networks were revealed and discussed.}, } @article {pmid20457552, year = {2010}, author = {Beale, L and Hodgson, S and Abellan, JJ and Lefevre, S and Jarup, L}, title = {Evaluation of spatial relationships between health and the environment: the rapid inquiry facility.}, journal = {Environmental health perspectives}, volume = {118}, number = {9}, pages = {1306-1312}, pmid = {20457552}, issn = {1552-9924}, support = {N01PC35141/PC/NCI NIH HHS/United States ; N01-PC-35141/PC/NCI NIH HHS/United States ; G0801056/MRC_/Medical Research Council/United Kingdom ; U38 EH000182/EH/NCEH CDC HHS/United States ; 1-U38-EH000182/EH/NCEH CDC HHS/United States ; }, mesh = {Environmental Exposure/adverse effects ; Environmental Health/*methods ; Epidemiology ; Geographic Information Systems ; Public Health/*methods ; Risk Factors ; United Kingdom ; United States ; }, abstract = {BACKGROUND: The initiation of environmental public health tracking systems in the United States and the United Kingdom provided an opportunity to advance techniques and tools available for spatial epidemiological analysis integrating both health and environmental data.

OBJECTIVE: The Rapid Inquiry Facility (RIF) allows users to calculate adjusted and unadjusted standardized rates and risks. The RIF is embedded in ArcGIS so that further geographical information system (GIS) spatial functionality can be exploited or results can be exported to statistical packages for further tailored analyses where required. The RIF also links directly to several statistical packages and displays the results in the GIS.

METHODS: The value of the RIF is illustrated here with two case studies: risk of leukemia in areas surrounding oil refineries in the State of Utah (USA) and an analysis of the geographical variation of risk of esophageal cancer in relation to zinc cadmium sulfide exposure in Norwich (United Kingdom).

RESULTS: The risk analysis study in Utah did not suggest any evidence of increased relative risk of leukemia, multiple myeloma, or Hodgkin's lymphoma in the populations around the five oil-refining facilities but did reveal an excess risk of non-Hodgkin's lymphoma that might warrant further investigation. The disease-mapping study in Norwich did not reveal any areas with higher relative risks of esophageal cancer common to both males and females, suggesting that a common geographically determined exposure was unlikely to be influencing cancer risk in the area.

CONCLUSION: The RIF offers a tool that allows epidemiologists to quickly carry out ecological environmental epidemiological analysis such as risk assessment or disease mapping.}, } @article {pmid20454662, year = {2010}, author = {Boni, MF and de Jong, MD and van Doorn, HR and Holmes, EC}, title = {Guidelines for identifying homologous recombination events in influenza A virus.}, journal = {PloS one}, volume = {5}, number = {5}, pages = {e10434}, pmid = {20454662}, issn = {1932-6203}, support = {G0600718/MRC_/Medical Research Council/United Kingdom ; GM080533/GM/NIGMS NIH HHS/United States ; 077078/Z/05/Z/WT_/Wellcome Trust/United Kingdom ; R01 GM080533/GM/NIGMS NIH HHS/United States ; /WT_/Wellcome Trust/United Kingdom ; 081613/Z/06/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Algorithms ; Base Sequence ; Computer Simulation ; Databases, Genetic ; Genetic Techniques/*standards ; Influenza A virus/*genetics ; Likelihood Functions ; Phylogeny ; *Recombination, Genetic ; }, abstract = {The rapid evolution of influenza viruses occurs both clonally and non-clonally through a variety of genetic mechanisms and selection pressures. The non-clonal evolution of influenza viruses comprises relatively frequent reassortment among gene segments and a more rarely reported process of non-homologous RNA recombination. Homologous RNA recombination within segments has been proposed as a third such mechanism, but to date the evidence for the existence of this process among influenza viruses has been both weak and controversial. As homologous recombination has not yet been demonstrated in the laboratory, supporting evidence, if it exists, may come primarily from patterns of phylogenetic incongruence observed in gene sequence data. Here, we review the necessary criteria related to laboratory procedures and sample handling, bioinformatic analysis, and the known ecology and evolution of influenza viruses that need to be met in order to confirm that a homologous recombination event occurred in the history of a set of sequences. To determine if these criteria have an effect on recombination analysis, we gathered 8307 publicly available full-length sequences of influenza A segments and divided them into those that were sequenced via the National Institutes of Health Influenza Genome Sequencing Project (IGSP) and those that were not. As sample handling and sequencing are executed to a very high standard in the IGSP, these sequences should be less likely to be exposed to contamination by other samples or by laboratory strains, and thus should not exhibit laboratory-generated signals of homologous recombination. Our analysis shows that the IGSP data set contains only two phylogenetically-supported single recombinant sequences and no recombinant clades. In marked contrast, the non-IGSP data show a very large amount of potential recombination. We conclude that the presence of false positive signals in the non-IGSP data is more likely than false negatives in the IGSP data, and that given the evidence to date, homologous recombination seems to play little or no role in the evolution of influenza A viruses.}, } @article {pmid20452420, year = {2010}, author = {Mocali, S and Benedetti, A}, title = {Exploring research frontiers in microbiology: the challenge of metagenomics in soil microbiology.}, journal = {Research in microbiology}, volume = {161}, number = {6}, pages = {497-505}, doi = {10.1016/j.resmic.2010.04.010}, pmid = {20452420}, issn = {1769-7123}, mesh = {Biodiversity ; Databases, Genetic ; Gene Library ; Industrial Microbiology ; Internationality ; *Metagenomics/trends ; Phylogeny ; Soil/analysis ; *Soil Microbiology ; }, abstract = {Soil is one of the most complex and challenging environments for microbiologists. In fact, although it contains the largest microbial diversity on the planet, the majority of these microbes are still uncharacterized and represent an enormous unexplored reservoir of genetic and metabolic diversity. Metagenomics, the study of the entire genome of soil biota, currently represents a powerful tool for assessing the diversity of complex microbial communities, providing access to a number of new species, genes or novel molecules that are relevant for biotechnology and agricultural applications. In this paper, the onset of new high-throughput metagenomic approaches and new perspectives in soil microbial ecology and data handling are discussed.}, } @article {pmid20449595, year = {2010}, author = {Jackson, ME and Asi, NS and Fullard, JH}, title = {Auditory sensitivity and ecological relevance: the functional audiogram as modelled by the bat detecting moth ear.}, journal = {Journal of comparative physiology. A, Neuroethology, sensory, neural, and behavioral physiology}, volume = {196}, number = {7}, pages = {453-462}, pmid = {20449595}, issn = {1432-1351}, mesh = {Acoustic Stimulation/methods ; Animals ; Auditory Threshold/physiology ; Chiroptera ; Cochlear Nerve/*physiology ; *Ecology ; Evoked Potentials, Auditory/*physiology ; Hearing/*physiology ; In Vitro Techniques ; Moths/*physiology ; Online Systems ; Psychoacoustics ; Reaction Time/physiology ; }, abstract = {Auditory sensitivity has often been measured by identifying neural threshold in real-time (online) which can introduce bias in the audiograms that are produced. We tested this by recording auditory nerve activity of the notodontid moth Nadata gibbosa elicited by bat-like ultrasound and analysing the response offline. We compared this audiogram with a published online audiogram showing that the bias introduced can result in a difference in the audiogram shape. In the second part of our study we compared offline audiograms using spike number as threshold with others that used spike period and stimulus/spike latency, variables that have been suggested as providing behaviourally functional criteria. These comparisons reveal that functional audiograms are more flatly tuned than simple spike audiograms. The shapes of behavioural audiograms are discussed in the context of the selection pressure that maintains their shape, bat predation. Finally, we make predictions on the distance from bats at which notodontid moths use negative phonotaxis or the acoustic startle response.}, } @article {pmid20444722, year = {2010}, author = {De Leo, FC and Smith, CR and Rowden, AA and Bowden, DA and Clark, MR}, title = {Submarine canyons: hotspots of benthic biomass and productivity in the deep sea.}, journal = {Proceedings. Biological sciences}, volume = {277}, number = {1695}, pages = {2783-2792}, pmid = {20444722}, issn = {1471-2954}, mesh = {Animals ; *Biomass ; *Ecosystem ; Fishes/*physiology ; Geographic Information Systems ; Geologic Sediments ; Invertebrates/classification/*physiology ; New Zealand ; Oceans and Seas ; Polychaeta/physiology ; Seawater ; }, abstract = {Submarine canyons are dramatic and widespread topographic features crossing continental and island margins in all oceans. Canyons can be sites of enhanced organic-matter flux and deposition through entrainment of coastal detrital export, dense shelf-water cascade, channelling of resuspended particulate material and focusing of sediment deposition. Despite their unusual ecological characteristics and global distribution along oceanic continental margins, only scattered information is available about the influence of submarine canyons on deep-sea ecosystem structure and productivity. Here, we show that deep-sea canyons such as the Kaikoura Canyon on the eastern New Zealand margin (42 degrees 01' S, 173 degrees 03' E) can sustain enormous biomasses of infaunal megabenthic invertebrates over large areas. Our reported biomass values are 100-fold higher than those previously reported for deep-sea (non-chemosynthetic) habitats below 500 m in the ocean. We also present evidence from deep-sea-towed camera images that areas in the canyon that have the extraordinary benthic biomass also harbour high abundances of macrourid (rattail) fishes likely to be feeding on the macro- and megabenthos. Bottom-trawl catch data also indicate that the Kaikoura Canyon has dramatically higher abundances of benthic-feeding fishes than adjacent slopes. Our results demonstrate that the Kaikoura Canyon is one of the most productive habitats described so far in the deep sea. A new global inventory suggests there are at least 660 submarine canyons worldwide, approximately 100 of which could be biomass hotspots similar to the Kaikoura Canyon. The importance of such deep-sea canyons as potential hotspots of production and commercial fisheries yields merits substantial further study.}, } @article {pmid20437969, year = {2010}, author = {North, EW and King, DM and Xu, J and Hood, RR and Newell, RI and Paynter, K and Kellogg, ML and Liddel, MK and Boesch, DF}, title = {Linking optimization and ecological models in a decision support tool for oyster restoration and management.}, journal = {Ecological applications : a publication of the Ecological Society of America}, volume = {20}, number = {3}, pages = {851-866}, doi = {10.1890/08-1733.1}, pmid = {20437969}, issn = {1051-0761}, mesh = {Animals ; *Crassostrea ; *Decision Support Techniques ; *Ecosystem ; *Environmental Restoration and Remediation ; *Fisheries ; Humans ; Maryland ; Models, Biological ; Models, Economic ; Virginia ; }, abstract = {Restoration of ecologically important marine species and habitats is restricted by funding constraints and hindered by lack of information about trade-offs among restoration goals and the effectiveness of alternative restoration strategies. Because ecosystems provide diverse human and ecological benefits, achieving one restoration benefit may take place at the expense of other benefits. This poses challenges when attempting to allocate limited resources to optimally achieve multiple benefits, and when defining measures of restoration success. We present a restoration decision-support tool that links ecosystem prediction and human use in a flexible "optimization" framework that clarifies important restoration trade-offs, makes location-specific recommendations, predicts benefits, and quantifies the associated costs (in the form of lost opportunities). The tool is illustrated by examining restoration options related to the eastern oyster, Crassostrea virginica, which supported an historically important fishery in Chesapeake Bay and provides a range of ecosystem services such as removing seston, enhancing water clarity, and creating benthic habitat. We use an optimization approach to identify the locations where oyster restoration efforts are most likely to maximize one or more benefits such as reduction in seston, increase in light penetration, spawning stock enhancement, and harvest, subject to funding constraints and other limitations. This proof-of-concept Oyster Restoration Optimization model (ORO) incorporates predictions from three-dimensional water quality (nutrients-phytoplankton zooplankton-detritus [NPZD] with oyster filtration) and larval transport models; calculates size- and salinity-dependent growth, mortality, and fecundity of oysters; and includes economic costs of restoration efforts. Model results indicate that restoration of oysters in different regions of the Chesapeake Bay would maximize different suites of benefits due to interactions between the physical characteristics of a system and nonlinear biological processes. For example, restoration locations that maximize harvest are not the same as those that would maximize spawning stock enhancement. Although preliminary, the ORO model demonstrates that our understanding of circulation patterns, single-species population dynamics and their interactions with the ecosystem can be integrated into one quantitative framework that optimizes spending allocations and provides explicit advice along with testable predictions. The ORO model has strengths and constraints as a tool to support restoration efforts and ecosystem approaches to fisheries management.}, } @article {pmid20435726, year = {2010}, author = {Pitt, FD and Mazard, S and Humphreys, L and Scanlan, DJ}, title = {Functional characterization of Synechocystis sp. strain PCC 6803 pst1 and pst2 gene clusters reveals a novel strategy for phosphate uptake in a freshwater cyanobacterium.}, journal = {Journal of bacteriology}, volume = {192}, number = {13}, pages = {3512-3523}, pmid = {20435726}, issn = {1098-5530}, mesh = {Bacterial Proteins/metabolism/*physiology ; Biological Transport/genetics/physiology ; Computational Biology ; Flow Cytometry ; Fresh Water/*microbiology ; Gene Expression Regulation, Bacterial/genetics/physiology ; Kinetics ; Multigene Family/genetics/*physiology ; Mutagenesis ; Phosphates/*metabolism ; Phylogeny ; Polymerase Chain Reaction ; Synechocystis/genetics/*metabolism ; }, abstract = {Synechocystis sp. strain PCC 6803 possesses two putative ABC-type inorganic phosphate (P(i)) transporters with three associated P(i)-binding proteins (PBPs), SphX (encoded by sll0679), PstS1 (encoded by sll0680), and PstS2 (encoded by slr1247), organized in two spatially discrete gene clusters, pst1 and pst2. We used a combination of mutagenesis, gene expression, and radiotracer uptake analyses to functionally characterize the role of these PBPs and associated gene clusters. Quantitative PCR (qPCR) demonstrated that pstS1 was expressed at a high level in P(i)-replete conditions compared to sphX or pstS2. However, a P(i) stress shift increased expression of pstS2 318-fold after 48 h, compared to 43-fold for pstS1 and 37-fold for sphX. A shift to high-light conditions caused a transient increase of all PBPs, whereas N stress primarily increased expression of sphX. Interposon mutagenesis of each PBP demonstrated that disruption of pstS1 alone caused constitutive expression of pho regulon genes, implicating PstS1 as a major component of the P(i) sensing machinery. The pstS1 mutant was also transformation incompetent. (32)P(i) radiotracer uptake experiments using pst1 and pst2 deletion mutants showed that Pst1 acts as a low-affinity, high-velocity transporter (K(s), 3.7 + or - 0.7 microM; V(max), 31.18 + or - 3.96 fmol cell(-1) min(-1)) and Pst2 acts as a high-affinity, low-velocity system (K(s), 0.07 + or - 0.01 microM; V(max), 0.88 + or - 0.11 fmol cell(-1) min(-1)). These P(i) ABC transporters thus exhibit differences in both kinetic and regulatory properties, the former trait potentially dramatically increasing the dynamic range of P(i) transport into the cell, which has potential implications for our understanding of the ecological success of this key microbial group.}, } @article {pmid20431144, year = {2010}, author = {Raiford, DW and Krane, DE and Doom, TE and Raymer, ML}, title = {Automated isolation of translational efficiency bias that resists the confounding effect of GC(AT)-content.}, journal = {IEEE/ACM transactions on computational biology and bioinformatics}, volume = {7}, number = {2}, pages = {238-250}, doi = {10.1109/TCBB.2008.65}, pmid = {20431144}, issn = {1557-9964}, mesh = {Algorithms ; Bacteria/genetics ; Base Composition/*genetics ; Codon/*genetics/metabolism ; Databases, Genetic ; Genes, Bacterial ; Genomics/*methods ; Oligonucleotide Array Sequence Analysis ; Principal Component Analysis ; *Protein Biosynthesis ; Sequence Analysis, DNA/methods ; Statistics, Nonparametric ; }, abstract = {Genomic sequencing projects are an abundant source of information for biological studies ranging from the molecular to the ecological in scale; however, much of the information present may yet be hidden from casual analysis. One such information domain, trends in codon usage, can provide a wealth of information about an organism's genes and their expression. Degeneracy in the genetic code allows more than one triplet codon to code for the same amino acid, and usage of these codons is often biased such that one or more of these synonymous codons are preferred. Detection of this bias is an important tool in the analysis of genomic data, particularly as a predictor of gene expressivity. Methods for identifying codon usage bias in genomic data that rely solely on genomic sequence data are susceptible to being confounded by the presence of several factors simultaneously influencing codon selection. Presented here is a new technique for removing the effects of one of the more common confounding factors, GC(AT)-content, and of visualizing the search-space for codon usage bias through the use of a solution landscape. This technique successfully isolates expressivity-related codon usage trends, using only genomic sequence information, where other techniques fail due to the presence of GC(AT)-content confounding influences.}, } @article {pmid20428711, year = {2010}, author = {Soares, PA and Nascimento, LF}, title = {Spatial analysis of hospitalization for heart diseases in Vale do Paraíba.}, journal = {Arquivos brasileiros de cardiologia}, volume = {94}, number = {6}, pages = {747-753}, doi = {10.1590/s0066-782x2010005000038}, pmid = {20428711}, issn = {1678-4170}, mesh = {Adult ; Age Distribution ; Brazil/epidemiology ; Cluster Analysis ; Female ; Geographic Information Systems ; Hospitalization/*statistics & numerical data ; Humans ; Male ; Middle Aged ; Myocardial Infarction/*epidemiology ; Myocardial Ischemia/*epidemiology ; Residence Characteristics/statistics & numerical data ; Retrospective Studies ; Risk Factors ; Sex Distribution ; Socioeconomic Factors ; }, abstract = {BACKGROUND: Ischemic heart diseases (IHD) are important causes of death in the Vale do Paraíba paulista.

OBJECTIVE: To identify patterns of spatial distribution of hospitalizations for acute myocardial infarction (AMI) and IHD in the Vale do Paraíba paulista.

METHODS: This was an ecological study using exploratory spatial analysis of hospitalization data for acute myocardial infarction and ischemic heart disease in the Vale do Paraíba between 2004 and 2005. The statistical analysis used spatial georeferenced databases of 35 municipalities and spatial statistics routines. The admission data were obtained from the Portal Datasus of the Ministry of Health. The variables were the number of admissions for males and females aged over 30 years. To evaluate the spatial dependence we used the autocorrelation coefficients of Global Moran and Local Moran's index. We also analyzed the correlations between variables, using the TerraView program. The level of significance was 5%.

RESULTS: Among 6,287 admissions, the rates were 161.66/100 thousand. Of the total of 35 municipalities, 31.4% had rates above average. The coefficient of Moran (global) showed a statistical significance. Local indexes showed clusters, indicating a cluster of 9 municipalities in which there was spatial dependence with their own dynamics.

CONCLUSION: In the mid Vale do Paraíba paulista, the spatial analysis identified spatial clusters of hospitalizations due to acute myocardial infarction and ischemic heart disease, allowing intervention to reduce rates. (Arq Bras Cardiol 2007;88(6):624-628).}, } @article {pmid20426792, year = {2010}, author = {Vandenkoornhuyse, P and Dufresne, A and Quaiser, A and Gouesbet, G and Binet, F and Francez, AJ and Mahé, S and Bormans, M and Lagadeuc, Y and Couée, I}, title = {Integration of molecular functions at the ecosystemic level: breakthroughs and future goals of environmental genomics and post-genomics.}, journal = {Ecology letters}, volume = {13}, number = {6}, pages = {776-791}, pmid = {20426792}, issn = {1461-0248}, mesh = {Animals ; Computational Biology ; *Ecosystem ; *Environment ; Gene Expression ; *Metagenomics ; Proteomics ; }, abstract = {Environmental genomics and genome-wide expression approaches deal with large-scale sequence-based information obtained from environmental samples, at organismal, population or community levels. To date, environmental genomics, transcriptomics and proteomics are arguably the most powerful approaches to discover completely novel ecological functions and to link organismal capabilities, organism-environment interactions, functional diversity, ecosystem processes, evolution and Earth history. Thus, environmental genomics is not merely a toolbox of new technologies but also a source of novel ecological concepts and hypotheses. By removing previous dichotomies between ecophysiology, population ecology, community ecology and ecosystem functioning, environmental genomics enables the integration of sequence-based information into higher ecological and evolutionary levels. However, environmental genomics, along with transcriptomics and proteomics, must involve pluridisciplinary research, such as new developments in bioinformatics, in order to integrate high-throughput molecular biology techniques into ecology. In this review, the validity of environmental genomics and post-genomics for studying ecosystem functioning is discussed in terms of major advances and expectations, as well as in terms of potential hurdles and limitations. Novel avenues for improving the use of these approaches to test theory-driven ecological hypotheses are also explored.}, } @article {pmid20426325, year = {2010}, author = {Piao, S and Luyssaert, S and Ciais, P and Janssens, IA and Chen, A and Cao, C and Fang, J and Friedlingstein, P and Luo, Y and Wang, S}, title = {Forest annual carbon cost: a global-scale analysis of autotrophic respiration.}, journal = {Ecology}, volume = {91}, number = {3}, pages = {652-661}, doi = {10.1890/08-2176.1}, pmid = {20426325}, issn = {0012-9658}, mesh = {Autotrophic Processes/*physiology ; Biomass ; Carbon/*metabolism ; Databases, Factual ; *Ecosystem ; Energy Metabolism ; Models, Biological ; Oxygen Consumption ; Temperature ; Trees/*metabolism ; }, abstract = {Forest autotrophic respiration (R(a)) plays an important role in the carbon balance of forest ecosystems. However, its drivers at the global scale are not well known. Based on a global forest database, we explore the relationships of annual R(a) with mean annual temperature (MAT) and biotic factors including net primary productivity (NPP), total biomass, stand age, mean tree height, and maximum leaf area index (LAI). The results show that the spatial patterns of forest annual R(a) at the global scale are largely controlled by temperature. R(a) is composed of growth (R(g)) and maintenance respiration (R(m)). We used a modified Arrhenius equation to express the relationship between R(a) and MAT. This relationship was calibrated with our data and shows that a 10 degrees C increase in MAT will result in an increase of annual R(m) by a factor of 1.9-2.5 (Q10). We also found that the fraction of total assimilation (gross primary production, GPP) used in R(a) is lowest in the temperate regions characterized by a MAT of approximately 11 degrees C. Although we could not confirm a relationship between the ratio of R(a) to GPP and age across all forest sites, the R(a) to GPP ratio tends to significantly increase in response to increasing age for sites with MAT between 8 degrees and 12 degrees C. At the plant scale, direct up-scaled R(a) estimates were found to increase as a power function with forest total biomass; however, the coefficient of the power function (0.2) was much smaller than that expected from previous studies (0.75 or 1). At the ecosystem scale, R(a) estimates based on both GPP - NPP and TER - R(h) (total ecosystem respiration - heterotrophic respiration) were not significantly correlated with forest total biomass (P > 0.05) with either a linear or a power function, implying that the previous individual-based metabolic theory may be not suitable for the application at ecosystem scale.}, } @article {pmid20426324, year = {2010}, author = {Peterson, EE and Ver Hoef, JM}, title = {A mixed-model moving-average approach to geostatistical modeling in stream networks.}, journal = {Ecology}, volume = {91}, number = {3}, pages = {644-651}, doi = {10.1890/08-1668.1}, pmid = {20426324}, issn = {0012-9658}, mesh = {Ecosystem ; Geography ; *Models, Statistical ; *Rivers ; *Water Movements ; }, abstract = {Spatial autocorrelation is an intrinsic characteristic in freshwater stream environments where nested watersheds and flow connectivity may produce patterns that are not captured by Euclidean distance. Yet, many common autocovariance functions used in geostatistical models are statistically invalid when Euclidean distance is replaced with hydrologic distance. We use simple worked examples to illustrate a recently developed moving-average approach used to construct two types of valid autocovariance models that are based on hydrologic distances. These models were designed to represent the spatial configuration, longitudinal connectivity, discharge, and flow direction in a stream network. They also exhibit a different covariance structure than Euclidean models and represent a true difference in the way that spatial relationships are represented. Nevertheless, the multi-scale complexities of stream environments may not be fully captured using a model based on one covariance structure. We advocate using a variance component approach, which allows a mixture of autocovariance models (Euclidean and stream models) to be incorporated into a single geostatistical model. As an example, we fit and compare "mixed models," based on multiple covariance structures, for a biological indicator. The mixed model proves to be a flexible approach because many sources of information can be incorporated into a single model.}, } @article {pmid20421198, year = {2010}, author = {Sukumaran, J and Holder, MT}, title = {DendroPy: a Python library for phylogenetic computing.}, journal = {Bioinformatics (Oxford, England)}, volume = {26}, number = {12}, pages = {1569-1571}, doi = {10.1093/bioinformatics/btq228}, pmid = {20421198}, issn = {1367-4811}, mesh = {Algorithms ; Computational Biology/*methods ; Databases, Factual ; *Phylogeny ; Programming Languages ; *Software ; }, abstract = {UNLABELLED: DendroPy is a cross-platform library for the Python programming language that provides for object-oriented reading, writing, simulation and manipulation of phylogenetic data, with an emphasis on phylogenetic tree operations. DendroPy uses a splits-hash mapping to perform rapid calculations of tree distances, similarities and shape under various metrics. It contains rich simulation routines to generate trees under a number of different phylogenetic and coalescent models. DendroPy's data simulation and manipulation facilities, in conjunction with its support of a broad range of phylogenetic data formats (NEXUS, Newick, PHYLIP, FASTA, NeXML, etc.), allow it to serve a useful role in various phyloinformatics and phylogeographic pipelines.

AVAILABILITY: The stable release of the library is available for download and automated installation through the Python Package Index site (http://pypi.python.org/pypi/DendroPy), while the active development source code repository is available to the public from GitHub (http://github.com/jeetsukumaran/DendroPy).}, } @article {pmid20417548, year = {2010}, author = {Wang, X and Mannaerts, CM and Yang, S and Gao, Y and Zheng, D}, title = {Evaluation of soil nitrogen emissions from riparian zones coupling simple process-oriented models with remote sensing data.}, journal = {The Science of the total environment}, volume = {408}, number = {16}, pages = {3310-3318}, doi = {10.1016/j.scitotenv.2010.03.026}, pmid = {20417548}, issn = {1879-1026}, mesh = {*Geographic Information Systems ; Models, Theoretical ; Nitrogen/*analysis ; Soil/*analysis ; }, abstract = {Riparian ecosystems have critical impacts on controlling the non-point source pollution and maintaining the health of aquatic ecosystems. In this study, a process oriented soil denitrification model was extended with algorithms from a simple nitrogen (N) cycle model and coupled to land surface remote sensing data to enhance its performance in spatial and temporal prediction of gaseous N emissions from soils in the riparian buffer zone surrounding the Guanting reservoir (China). The N emission model is based on chemical and physical relationships that govern the heat budget, soil moisture variations and nitrogen movement in soils. Besides soil water and heat processes, it includes nitrification, denitrification and ammonia (NH(3)) volatilization. SPOT-5 and Landsat-5 TM satellite data were used to derive spatial land surface information and the temporal variation in land cover parameters was also used to drive the model. A laboratory-scale anaerobic incubation experiment was used to estimate the soil denitrification model parameters for the different soil types. An in situ field-scale experiment was conducted to calibrate and validate the soil temperature, moisture and nitrogen sub-models. An indirect method was used to verify simulated N emissions, resulting in a coefficient of determination of R(2)=0.83 between simulated and observed values. Then the model was applied to the whole riparian buffer zone catchment, using the spatial resolution (10m) of the SPOT-5 image. Model sensitivity analysis showed that soil moisture was the most sensitive parameter for gaseous N emissions and soil denitrification was the main process affecting N losses to the atmosphere in the riparian area. From the aspect of land use management around the Guanting reservoir, the spatial structure and distribution of land cover and land use types in the riparian area should be adapted, to enhance faster ecological restoration of the wetland ecological system surrounding this strategically important water resource.}, } @article {pmid20413212, year = {2010}, author = {Gasparatos, A}, title = {Embedded value systems in sustainability assessment tools and their implications.}, journal = {Journal of environmental management}, volume = {91}, number = {8}, pages = {1613-1622}, doi = {10.1016/j.jenvman.2010.03.014}, pmid = {20413212}, issn = {1095-8630}, mesh = {*Conservation of Natural Resources ; Cost-Benefit Analysis ; Decision Making ; *Decision Support Techniques ; Ecology ; Environment ; Environmental Health/*methods ; Humans ; Program Evaluation/*methods ; Risk Assessment/*methods ; United States ; United States Environmental Protection Agency ; }, abstract = {This paper explores the implications that arise with the selection of specific sustainability evaluation tools. Sustainability evaluation tools are conceptualized in this paper as value articulating institutions and as such their choice is a far from a trivial matter. In fact their choice can entail various ethical and practical repercussions. However, in most cases the choice of the evaluation tool is made by the analyst(s) without taking into consideration the values of the affected stakeholders. By choosing the analytical tool the analyst essentially "subscribes to" and ultimately "enforces" a particular worldview as the legitimate yardstick to evaluate the sustainability of a particular project (or policy). Instead, this paper argues that the selection of evaluation tools should be consistent with the values of the affected stakeholders. With this in mind, different sustainability evaluation tools' assumptions are critically reviewed and a number of suggestions that could facilitate the choice of the most appropriate tool according to the context of the sustainability evaluation are provided. It is expected that conscious evaluation tool selection, following the suggestions made in this paper, will reduce the risk of providing distorted sustainability evaluations.}, } @article {pmid20411118, year = {2010}, author = {Kennedy, J and Flemer, B and Jackson, SA and Lejon, DP and Morrissey, JP and O'Gara, F and Dobson, AD}, title = {Marine metagenomics: new tools for the study and exploitation of marine microbial metabolism.}, journal = {Marine drugs}, volume = {8}, number = {3}, pages = {608-628}, pmid = {20411118}, issn = {1660-3397}, mesh = {Bacteria/enzymology/*genetics/*metabolism ; Biotechnology ; Data Mining ; Marine Biology ; *Metagenomics/methods ; Seawater/*microbiology ; *Water Microbiology ; }, abstract = {The marine environment is extremely diverse, with huge variations in pressure and temperature. Nevertheless, life, especially microbial life, thrives throughout the marine biosphere and microbes have adapted to all the divergent environments present. Large scale DNA sequence based approaches have recently been used to investigate the marine environment and these studies have revealed that the oceans harbor unprecedented microbial diversity. Novel gene families with representatives only within such metagenomic datasets represent a large proportion of the ocean metagenome. The presence of so many new gene families from these uncultured and highly diverse microbial populations represents a challenge for the understanding of and exploitation of the biology and biochemistry of the ocean environment. The application of new metagenomic and single cell genomics tools offers new ways to explore the complete metabolic diversity of the marine biome.}, } @article {pmid20407998, year = {2010}, author = {Friesen, MN and Krassikouva-Enns, O and Ringaert, L and Isfeld, H}, title = {Community support systems for farmers who live with disability.}, journal = {Journal of agromedicine}, volume = {15}, number = {2}, pages = {166-174}, doi = {10.1080/10599241003630569}, pmid = {20407998}, issn = {1545-0813}, mesh = {Agriculture ; *Community Health Services ; *Community Networks ; Disabled Persons/*rehabilitation ; Financial Support ; Health Personnel ; Health Services Accessibility ; Health Services Needs and Demand ; Health Services Research ; Humans ; Occupational Diseases ; Occupational Health ; Qualitative Research ; *Rehabilitation, Vocational/economics/statistics & numerical data ; Spouses ; }, abstract = {To return to farming following the onset of a disabling injury or health condition is predicated on a supportive environment for the farm owner-operator. The purpose of this study was to examine barriers and facilitators of returning to work after an injury or acquired disability, and to identify community supports (formal and informal) needed and available to farmers. This was a qualitative study using a participatory action research approach that involved a research team, an advisory group of seven stakeholder participants and semistructured interviews with farmers, their spouses, and service providers in the study communities. A total of 11 farmers and 17 service providers took part in a focus group or were interviewed individually with or without the spouse present. Focus group discussions and interviews were transcribed and analyzed using constant comparison method and team consensus of findings. Themes of barriers and facilitators for return to farming were identified as health care services, financial and economic issues, and "hands-on" assistance. Themes were organized into an ecological conceptual diagram depicting barriers and facilitators in the microsystem of the farm family, the mesosystem of the local farming community and regional health jurisdictions, and the macrosystem of the province and/or nation's social, legislative, and economic realities. Enhancing community support systems for farmers who become disabled as a result of injury or illness will require a multilevel system approach that involves health, financial, and labor resources.}, } @article {pmid20399012, year = {2010}, author = {Kumar, A and Clement, S and Agrawal, VP}, title = {Structural modeling and analysis of an effluent treatment process for electroplating--a graph theoretic approach.}, journal = {Journal of hazardous materials}, volume = {179}, number = {1-3}, pages = {748-761}, doi = {10.1016/j.jhazmat.2010.03.066}, pmid = {20399012}, issn = {1873-3336}, mesh = {Algorithms ; Computer Simulation ; Decision Trees ; *Electroplating ; Industrial Waste/*analysis ; Information Storage and Retrieval ; *Models, Structural ; Waste Disposal, Fluid/*methods ; }, abstract = {An attempt is made to address a few ecological and environment issues by developing different structural models for effluent treatment system for electroplating. The effluent treatment system is defined with the help of different subsystems contributing to waste minimization. Hierarchical tree and block diagram showing all possible interactions among subsystems are proposed. These non-mathematical diagrams are converted into mathematical models for design improvement, analysis, comparison, storage retrieval and commercially off-the-shelf purchases of different subsystems. This is achieved by developing graph theoretic model, matrix models and variable permanent function model. Analysis is carried out by permanent function, hierarchical tree and block diagram methods. Storage and retrieval is done using matrix models. The methodology is illustrated with the help of an example. Benefits to the electroplaters/end user are identified.}, } @article {pmid20398318, year = {2010}, author = {Kamanga, A and Moono, P and Stresman, G and Mharakurwa, S and Shiff, C}, title = {Rural health centres, communities and malaria case detection in Zambia using mobile telephones: a means to detect potential reservoirs of infection in unstable transmission conditions.}, journal = {Malaria journal}, volume = {9}, number = {}, pages = {96}, pmid = {20398318}, issn = {1475-2875}, mesh = {Antimalarials/therapeutic use ; *Cell Phone ; Data Collection ; Diagnostic Tests, Routine/instrumentation/*methods ; *Disease Reservoirs ; Geographic Information Systems ; Health Workforce/organization & administration ; Humans ; Incidence ; Malaria/*diagnosis/epidemiology/transmission ; Reagent Kits, Diagnostic/*economics/standards ; Rural Health ; Rural Health Services ; Seasons ; Time Factors ; Zambia/epidemiology ; }, abstract = {BACKGROUND: Effective malaria control depends on timely acquisition of information on new cases, their location and their frequency so as to deploy supplies, plan interventions or focus attention on specific locations appropriately to intervene and prevent an upsurge in transmission. The process is known as active case detection, but because the information is time sensitive, it is difficult to carry out. In Zambia, the rural health services are operating effectively and for the most part are provided with adequate supplies of rapid diagnostic tests (RDT) as well as effective drugs for the diagnosis and treatment of malaria. The tests are administered to all prior to treatment and appropriate records are kept. Data are obtained in a timely manner and distribution of this information is important for the effective management of malaria control operations. The work reported here involves combining the process of positive diagnoses in rural health centres (passive case detection) to help detect potential outbreaks of malaria and target interventions to foci where parasite reservoirs are likely to occur.

METHODS: Twelve rural health centres in the Choma and Namwala Districts were recruited to send weekly information of rapid malaria tests used and number of positive diagnoses to the Malaria Institute at Macha using mobile telephone SMS. Data were entered in excel, expressed as number of cases per rural health centre and distributed weekly to interested parties.

RESULTS: These data from each of the health centres which were mapped using geographical positioning system (GPS) coordinates were used in a time sensitive manner to plot the patterns of malaria case detection in the vicinity of each location. The data were passed on to the appropriate authorities. The seasonal pattern of malaria transmission associated with local ecological conditions can be seen in the distribution of cases diagnosed.

CONCLUSIONS: Adequate supplies of RDT are essential in health centres and the system can be expanded throughout the country to support strategic targeting of interventions by the National Malaria Control Programme. Participation by the health centre staff was excellent.}, } @article {pmid20398280, year = {2010}, author = {Gilardoni, PA and Schuck, S and Jüngling, R and Rotter, B and Baldwin, IT and Bonaventure, G}, title = {SuperSAGE analysis of the Nicotiana attenuata transcriptome after fatty acid-amino acid elicitation (FAC): identification of early mediators of insect responses.}, journal = {BMC plant biology}, volume = {10}, number = {}, pages = {66}, pmid = {20398280}, issn = {1471-2229}, mesh = {Amino Acids/*metabolism ; Animals ; Databases, Genetic ; Expressed Sequence Tags ; Fatty Acids/*metabolism ; *Gene Expression Profiling ; *Gene Expression Regulation, Plant ; Gene Library ; Gene Silencing ; Manduca/*physiology ; Molecular Sequence Data ; Phosphatidate Phosphatase/metabolism ; Plant Leaves/parasitology ; Polymerase Chain Reaction ; RNA, Messenger/genetics/metabolism ; Reproducibility of Results ; Nicotiana/enzymology/*genetics/*parasitology ; }, abstract = {BACKGROUND: Plants trigger and tailor defense responses after perception of the oral secretions (OS) of attacking specialist lepidopteran larvae. Fatty acid-amino acid conjugates (FACs) in the OS of the Manduca sexta larvae are necessary and sufficient to elicit the herbivory-specific responses in Nicotiana attenuata, an annual wild tobacco species. How FACs are perceived and activate signal transduction mechanisms is unknown.

RESULTS: We used SuperSAGE combined with 454 sequencing to quantify the early transcriptional changes elicited by the FAC N-linolenoyl-glutamic acid (18:3-Glu) and virus induced gene silencing (VIGS) to examine the function of candidate genes in the M. sexta-N. attenuata interaction. The analysis targeted mRNAs encoding regulatory components: rare transcripts with very rapid FAC-elicited kinetics (increases within 60 and declines within 120 min). From 12,744 unique Tag sequences identified (UniTags), 430 and 117 were significantly up- and down-regulated >or= 2.5-fold, respectively, after 18:3-Glu elicitation compared to wounding. Based on gene ontology classification, more than 25% of the annotated UniTags corresponded to putative regulatory components, including 30 transcriptional regulators and 22 protein kinases. Quantitative PCR analysis was used to analyze the FAC-dependent regulation of a subset of 27 of these UniTags and for most of them a rapid and transient induction was confirmed. Six FAC-regulated genes were functionally characterized by VIGS and two, a putative lipid phosphate phosphatase (LPP) and a protein of unknown function, were identified as important mediators of the M. sexta-N. attenuata interaction.

CONCLUSIONS: The analysis of the early changes in the transcriptome of N. attenuata after FAC elicitation using SuperSAGE/454 has identified regulatory genes involved in insect-specific mediated responses in plants. Moreover, it has provided a foundation for the identification of additional novel regulators associated with this process.}, } @article {pmid20391055, year = {2010}, author = {Arcidiacono, C and Procentese, F and Baldi, S}, title = {Participatory planning and community development: an e-learning training program.}, journal = {Journal of prevention & intervention in the community}, volume = {38}, number = {1}, pages = {70-83}, doi = {10.1080/10852350903393475}, pmid = {20391055}, issn = {1540-7330}, mesh = {Adult ; Community Networks/*organization & administration ; Cooperative Behavior ; Guidelines as Topic ; Humans ; Inservice Training/*methods/organization & administration ; *Internet ; Italy ; Program Development ; Psychology ; *Social Planning ; Young Adult ; }, abstract = {The main goal of this article is to provide guidelines for all community actors on the acquisition of participatory planning tools. There is a growing need for experts capable of participatory interventions to act as social catalysts to promote local well-being and empowerment. Thus, under an ecological approach, 21 young graduates from different fields (architecture, psychology, environmental planning), public administration officers and social organization managers, all residing in Southern Italy, were offered individual and group empowerment training modules through a multidisciplinary training experience with e-learning features. These consisted of 1,500 hours of didactic activities including online cooperative experiences and field interactions directed toward acquiring participatory planning and community mediation tools. Our experience indicates that it is possible to promote participation and acquire skills through online training. Online training has shown itself to be a useful and successful tool for promoting skills in the field of social planning.}, } @article {pmid20381096, year = {2010}, author = {Andersen, JH and Murray, C and Kaartokallio, H and Axe, P and Molvaer, J}, title = {A simple method for confidence rating of eutrophication status classifications.}, journal = {Marine pollution bulletin}, volume = {60}, number = {6}, pages = {919-924}, doi = {10.1016/j.marpolbul.2010.03.020}, pmid = {20381096}, issn = {1879-3363}, mesh = {Classification/*methods ; Data Interpretation, Statistical ; Environmental Monitoring/*methods/statistics & numerical data ; *Eutrophication ; Oceans and Seas ; *Research Design ; }, abstract = {We report the development of a methodology for assessing confidence in ecological status classifications. The method presented here can be considered as a secondary assessment, supporting the primary assessment of eutrophication or ecological status. The confidence assessment is based on scoring the quality of the indicators on which the primary assessment is made. This represents a first step towards linking status classification with information regarding their accuracy and precision. Applied to an existing data set used for assessment of eutrophication status of the Baltic Sea (including the Kattegat and Danish Straits) we demonstrate that confidence in the assessment is Good or High in 149 out of 189 areas assessed (79%). Contrary to our expectations, assessments of the open parts of the Baltic Sea have a higher confidence than assessments of coastal waters. We also find that in open waters of the Baltic Sea, some biological indicators have a higher confidence than indicators representing physical-chemical conditions. In coastal waters, phytoplankton, submerged aquatic vegetation and indicators of physical-chemical conditions have a higher confidence than indicators of the quality of benthic invertebrate communities. Our analyses also show that the perceived weaknesses of eutrophication assessments are due more to Low confidence in reference conditions and acceptable deviations, rather than in the monitoring data.}, } @article {pmid20380436, year = {2010}, author = {Ducrot, V and Billoir, E and Péry, AR and Garric, J and Charles, S}, title = {From individual to population level effects of toxicants in the tubicifid Branchiura sowerbyi using threshold effect models in a Bayesian framework.}, journal = {Environmental science & technology}, volume = {44}, number = {9}, pages = {3566-3571}, doi = {10.1021/es903860w}, pmid = {20380436}, issn = {0013-936X}, mesh = {Animals ; Annelida/*drug effects ; Bayes Theorem ; Calibration ; Data Interpretation, Statistical ; Environmental Monitoring/methods ; Environmental Pollutants/pharmacology/toxicity ; Hazardous Substances/*toxicity ; Models, Statistical ; Models, Theoretical ; Risk Assessment ; Time Factors ; Zinc/toxicity ; }, abstract = {Effects of zinc were studied in the freshwater worm Branchiura sowerbyi using partial and full life-cycle tests. Only newborn and juveniles were sensitive to zinc, displaying effects on survival, growth, and age at first brood at environmentally relevant concentrations. Threshold effect models were proposed to assess toxic effects on individuals. They were fitted to life-cycle test data using Bayesian inference and adequately described life-history trait data in exposed organisms. The daily asymptotic growth rate of theoretical populations was then simulated with a matrix population model, based upon individual-level outputs. Population-level outputs were in accordance with existing literature for controls. Working in a Bayesian framework allowed incorporating parameter uncertainty in the simulation of the population-level response to zinc exposure, thus increasing the relevance of test results in the context of ecological risk assessment.}, } @article {pmid20380216, year = {2010}, author = {Patterson, TA and McConnell, BJ and Fedak, MA and Bravington, MV and Hindell, MA}, title = {Using GPS data to evaluate the accuracy of state-space methods for correction of Argos satellite telemetry error.}, journal = {Ecology}, volume = {91}, number = {1}, pages = {273-285}, doi = {10.1890/08-1480.1}, pmid = {20380216}, issn = {0012-9658}, mesh = {Animal Identification Systems ; Animals ; Computer Simulation ; *Geographic Information Systems ; Microsatellite Instability ; Seals, Earless/*physiology ; *Spacecraft ; *Telemetry ; }, abstract = {Recent studies have applied state-space models to satellite telemetry data in order to remove noise from raw location estimates and infer the true tracks of animals. However, while the resulting tracks may appear plausible, it is difficult to determine the accuracy of the estimated positions, especially for position estimates interpolated to times between satellite locations. In this study, we use data from two gray seals (Halichoerus grypus) carrying tags that transmitted Fastloc GPS positions via Argos satellites. This combination of Service Argos data and highly accurate GPS data allowed examination of the accuracy of state-space position estimates and their uncertainty derived from satellite telemetry data. After applying a speed filter to remove aberrant satellite telemetry locations, we fit a continuous-time Kalman filter to estimate the parameters of a random walk, used Kalman smoothing to infer positions at the times of the GPS measurements, and then compared the filtered telemetry estimates with the actual GPS measurements. We investigated the effect of varying maximum speed thresholds in the speed-filtering algorithm on the root mean-square error (RMSE) estimates and used minimum RMSE as a criterion to guide the final choice of speed threshold. The optimal speed thresholds differed between the two animals (1.1 m/s and 2.5 m/s) and retained 50% and 65% of the data for each seal. However, using a speed filter of 1.1 m/s resulted in very similar RMSE for both animals. For the two seals, the RMSE of the Kalman-filtered estimates of location were 5.9 and 12.76 km, respectively, and 75% of the modeled positions had errors less than 6.25 km and 11.7 km for each seal. Confidence interval coverage was close to correct at typical levels (80-95%), although it tended to be overly generous at smaller sizes. The reliability of uncertainty estimates was also affected by the chosen speed threshold. The combination of speed and Kalman filtering allows for effective calculation of location and also indicates the limits of accuracy when correcting service Argos locations and linking satellite telemetry data to spatial covariate and habitat data.}, } @article {pmid20378597, year = {2010}, author = {Nelson, A and Abbott, R and Macdonald, D}, title = {Indigenous Austalians and physical activity: using a social-ecological model to review the literature.}, journal = {Health education research}, volume = {25}, number = {3}, pages = {498-509}, doi = {10.1093/her/cyq025}, pmid = {20378597}, issn = {1465-3648}, mesh = {Australia ; Cultural Characteristics ; *Cultural Competency ; Databases, Bibliographic ; *Epidemiologic Research Design ; *Health Status Disparities ; Humans ; *Motor Activity ; Social Values ; }, abstract = {This paper aims to present what is currently known about Indigenous Australians and their engagement in physical activity and to then challenge some of the 'taken-for-granted' ways of thinking about promoting or researching physical activity with Indigenous Australians. Major health, education and sport databases, as well as government websites were searched using the key terms of physical activity, sport, leisure, recreation, Indigenous and Aboriginal/Aborigine. A social-ecological model of health was adapted and used as an organizing framework to synthesize the literature. It is concluded that socioecological models can be valuable tools for understanding and promoting issues related to physical activity engagement for a range of populations but they may require complementary critical insights, including those from Indigenous perspectives. Productive theoretical spaces where Western and Indigenous knowledges come together can assist health educators to consider the complexity and diversity of Indigenous people's lived experiences when planning and implementing programs.}, } @article {pmid20375075, year = {2010}, author = {Walters, JR and Harrison, RG}, title = {Combined EST and proteomic analysis identifies rapidly evolving seminal fluid proteins in Heliconius butterflies.}, journal = {Molecular biology and evolution}, volume = {27}, number = {9}, pages = {2000-2013}, doi = {10.1093/molbev/msq092}, pmid = {20375075}, issn = {1537-1719}, mesh = {Animals ; Butterflies/genetics/*metabolism ; Computational Biology ; Evolution, Molecular ; *Expressed Sequence Tags ; Insect Proteins/genetics/*metabolism ; Male ; Proteomics/*methods ; Seminal Plasma Proteins/genetics ; }, abstract = {Seminal fluid proteins (SFPs) directly influence a wide range of reproductive processes, including fertilization, sperm storage, egg production, and immune response. Like many other reproductive proteins, the molecular evolution of SFPs is generally characterized by rapid and frequently adaptive evolution. However, the evolutionary processes underlying this often-documented pattern have not yet been confidently determined. A robust understanding of the processes governing SFP evolution will ultimately require identifying SFPs and characterizing their evolution in many different taxa, often where only limited genomic resources are available. Here, we report the first comprehensive molecular genetic and evolutionary analysis of SFPs conducted in Lepidoptera (moths and butterflies). We have identified 51 novel SFPs from two species of Heliconius butterflies (Heliconius erato and Heliconius melpomene) by combining "indirect" bioinformatic and expression analyses of expressed sequence tags from male accessory gland and wing tissues with "direct" proteomic analyses of spermatophores. Proteomic analyses identified fewer SFPs than the indirect criteria but gave consistent results. Of 51 SFPs, 40 were identified in both species but fewer than half could be functionally annotated via similarity searches (Blast, IPRscan, etc.). The majority of annotated Heliconius SFPs were predicted to be chymotrypsins. Comparisons of Heliconius SFPs with those from fruit fly, mosquito, honeybee, and cricket suggest that gene turnover is high among these proteins and that SFPs are rarely conserved across insect orders. Pairwise estimates of evolutionary rates between SFPs and nonreproductive proteins show that, on average, Heliconius SFPs are evolving rapidly. At least one of these SFPs is evolving adaptively (dN/dS > 1), implicating a role for positive selection in this rapid evolution. This work establishes a strong precedent for future research on the causes and consequences of reproductive protein evolution in the Lepidoptera. Butterflies and moths have an extremely rich history of organismal research, which will provide an informative ecological context for further molecular evolutionary investigations.}, } @article {pmid20369009, year = {2010}, author = {Gething, PW and Patil, AP and Hay, SI}, title = {Quantifying aggregated uncertainty in Plasmodium falciparum malaria prevalence and populations at risk via efficient space-time geostatistical joint simulation.}, journal = {PLoS computational biology}, volume = {6}, number = {4}, pages = {e1000724}, pmid = {20369009}, issn = {1553-7358}, support = {079091/WT_/Wellcome Trust/United Kingdom ; #079080/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Algorithms ; Computational Biology/*methods ; Computer Simulation ; Humans ; Malaria, Falciparum/*epidemiology ; *Models, Biological ; *Plasmodium falciparum ; Prevalence ; Reproducibility of Results ; Risk ; Topography, Medical/*methods ; }, abstract = {Risk maps estimating the spatial distribution of infectious diseases are required to guide public health policy from local to global scales. The advent of model-based geostatistics (MBG) has allowed these maps to be generated in a formal statistical framework, providing robust metrics of map uncertainty that enhances their utility for decision-makers. In many settings, decision-makers require spatially aggregated measures over large regions such as the mean prevalence within a country or administrative region, or national populations living under different levels of risk. Existing MBG mapping approaches provide suitable metrics of local uncertainty--the fidelity of predictions at each mapped pixel--but have not been adapted for measuring uncertainty over large areas, due largely to a series of fundamental computational constraints. Here the authors present a new efficient approximating algorithm that can generate for the first time the necessary joint simulation of prevalence values across the very large prediction spaces needed for global scale mapping. This new approach is implemented in conjunction with an established model for P. falciparum allowing robust estimates of mean prevalence at any specified level of spatial aggregation. The model is used to provide estimates of national populations at risk under three policy-relevant prevalence thresholds, along with accompanying model-based measures of uncertainty. By overcoming previously unchallenged computational barriers, this study illustrates how MBG approaches, already at the forefront of infectious disease mapping, can be extended to provide large-scale aggregate measures appropriate for decision-makers.}, } @article {pmid20365019, year = {2009}, author = {Houchmandzadeh, B}, title = {Theory of neutral clustering for growing populations.}, journal = {Physical review. E, Statistical, nonlinear, and soft matter physics}, volume = {80}, number = {5 Pt 1}, pages = {051920}, doi = {10.1103/PhysRevE.80.051920}, pmid = {20365019}, issn = {1550-2376}, mesh = {Animals ; Cluster Analysis ; Computer Simulation ; *Data Interpretation, Statistical ; Humans ; *Models, Biological ; *Models, Statistical ; *Population Growth ; }, abstract = {The spatial distribution of most species in nature is nonuniform. We have shown recently [B. Houchmandzadeh, Phys. Rev. Lett. 101, 078103 (2008)] on an experimental ecological community of amoeba that the most basic facts of life--birth and death--are enough to cause considerable aggregation which cannot be smoothened by random movements of the organisms. This clustering, termed neutral and always present, is independent of external causes and social interaction. We develop here the theoretical groundwork of this phenomenon by explicitly computing the pair-correlation function and the variance to mean ratio of the above neutral model and its comparison to numerical simulations.}, } @article {pmid20363539, year = {2010}, author = {Lavoie, RA and Champoux, L and Rail, JF and Lean, DR}, title = {Organochlorines, brominated flame retardants and mercury levels in six seabird species from the Gulf of St. Lawrence (Canada): relationships with feeding ecology, migration and molt.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {158}, number = {6}, pages = {2189-2199}, doi = {10.1016/j.envpol.2010.02.016}, pmid = {20363539}, issn = {1873-6424}, mesh = {Animal Migration/*physiology ; Animals ; Birds/*growth & development/metabolism/physiology ; Canada ; Data Interpretation, Statistical ; *Environmental Monitoring ; Environmental Pollutants/*analysis ; Feeding Behavior/*physiology ; Flame Retardants/analysis ; Hydrocarbons, Brominated/analysis ; Hydrocarbons, Chlorinated/analysis ; Methylmercury Compounds/analysis ; Molting/*physiology ; Ovum/chemistry/drug effects ; Species Specificity ; }, abstract = {Concentrations of organochlorines (OCs), brominated flame retardants (BFRs) and mercury (Hg) were measured in eggs of six seabird species breeding in the Gulf of St. Lawrence, Canada. Stable nitrogen (delta15N) and carbon (delta13C) isotopes were used as ecological tracers to measure trophic level and connectivity with benthos, respectively. Concentrations, patterns as well as ecological tracers varied significantly between species. The sum of polychlorinated biphenyls (SigmaPCBs) was the most important group measured in all seabird species based on concentration followed generally by the sum of chlorinated pesticides (SigmaCPs), the sum of brominated flame retardants (SigmaBFRs) and finally total Hg (THg). SigmaPCBs, SigmaCPs and SigmaBFRs increased with trophic level, whereas THg did not. Only SigmaBFRs increased with a higher connectivity with the benthos. Seabird species resident to the Great Lakes-St. Lawrence ecosystem showed higher Hg and BFR levels than migratory species. Molt patterns were used to explain variations of contaminant levels.}, } @article {pmid20331786, year = {2010}, author = {Haubold, B and Pfaffelhuber, P and Lynch, M}, title = {mlRho - a program for estimating the population mutation and recombination rates from shotgun-sequenced diploid genomes.}, journal = {Molecular ecology}, volume = {19 Suppl 1}, number = {Suppl 1}, pages = {277-284}, pmid = {20331786}, issn = {1365-294X}, support = {R01 GM036827/GM/NIGMS NIH HHS/United States ; R01 GM101672/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Ciona intestinalis/genetics ; Computational Biology/methods ; Computer Simulation ; DNA Mutational Analysis/*methods ; Daphnia/genetics ; Diploidy ; *Genetics, Population ; Genome ; Genomics/*methods ; Likelihood Functions ; Models, Genetic ; *Recombination, Genetic ; *Software ; }, abstract = {Improvements in sequencing technology over the past 5 years are leading to routine application of shotgun sequencing in the fields of ecology and evolution. However, the theory to estimate evolutionary parameters from these data is still being worked out. Here we present an extension and implementation of part of this theory, mlRho. This program can efficiently compute the following three maximum likelihood estimators based on shotgun sequence data obtained from single diploid individuals: the population mutation rate (4N(e)mu), the sequencing error rate, and the population recombination rate (4N(e)c). We demonstrate the accuracy of mlRho by applying it to simulated data sets. In addition, we analyse the genomes of the sea squirt Ciona intestinalis and the water flea Daphnia pulex. Ciona intestinalis is an obligate outcrosser, while D. pulex is a cyclic parthenogen, and we discuss how these contrasting life histories are reflected in our parameter estimates. The program mlRho is freely available from http://guanine.evolbio.mpg.de/mlRho.}, } @article {pmid20331771, year = {2010}, author = {Coolon, JD and Jones, KL and Narayanan, S and Wisely, SM}, title = {Microbial ecological response of the intestinal flora of Peromyscus maniculatus and P. leucopus to heavy metal contamination.}, journal = {Molecular ecology}, volume = {19 Suppl 1}, number = {}, pages = {67-80}, doi = {10.1111/j.1365-294X.2009.04485.x}, pmid = {20331771}, issn = {1365-294X}, mesh = {Animals ; Bacteria/classification/drug effects/*genetics ; Biodegradation, Environmental ; Body Size ; Computational Biology ; DNA, Bacterial/genetics ; Ecosystem ; Environmental Monitoring/methods ; Intestines/*microbiology ; Metals, Heavy/*toxicity ; Mining ; Peromyscus/*microbiology ; RNA, Ribosomal, 16S/genetics ; *Soil Microbiology ; Soil Pollutants/toxicity ; }, abstract = {Heavy metal contamination negatively affects natural systems including plants, birds, fish and bacteria by reducing biodiversity at contaminated sites. At the Tri-State Mining District, efforts have been made to remediate sites to mitigate the detrimental effects that contamination has caused on human health. While the remediation effort has returned the site to within federal safety standards, it is unclear if this effort is sufficient to restore floral and faunal communities. Intrinsic to ecosystem and organism health is the biodiversity and composition of microbial communities. We have taken advantage of recent advances in sequencing technology and surveyed the bacterial community of remediated and reference soils as well as the intestinal microbial community of two ubiquitous rodent species to provide insight on the impacts of residual heavy metal contamination on the ecosystem. Rodents found on the remediated site had reduced body mass, smaller body size and lower body fat than animals on reference sites. Using bar-coded, massively parallel sequencing, we found that bacterial communities in both the soil and Peromyscus spp. gastrointestinal tracts had no difference in diversity between reference and remediated sites but assemblages differed in response to contamination. These results suggest that niche voids left by microbial taxa that were unable to deal with the remnant levels of heavy metals on remediated sites were replaced by taxa that could persist in this environment. Whether this replacement provided similar ecosystem services as ancestral bacterial communities is unknown.}, } @article {pmid20331767, year = {2010}, author = {Stoeck, T and Bass, D and Nebel, M and Christen, R and Jones, MD and Breiner, HW and Richards, TA}, title = {Multiple marker parallel tag environmental DNA sequencing reveals a highly complex eukaryotic community in marine anoxic water.}, journal = {Molecular ecology}, volume = {19 Suppl 1}, number = {}, pages = {21-31}, doi = {10.1111/j.1365-294X.2009.04480.x}, pmid = {20331767}, issn = {1365-294X}, mesh = {*Biodiversity ; Cluster Analysis ; Computational Biology ; DNA, Ribosomal/*analysis/genetics/isolation & purification ; Dinoflagellida/classification/genetics ; Gene Library ; Seawater/*microbiology ; Sequence Analysis, DNA/*methods ; Sequence Tagged Sites ; *Water Microbiology ; }, abstract = {Sequencing of ribosomal DNA clone libraries amplified from environmental DNA has revolutionized our understanding of microbial eukaryote diversity and ecology. The results of these analyses have shown that protist groups are far more genetically heterogeneous than their morphological diversity suggests. However, the clone library approach is labour-intensive, relatively expensive, and methodologically biased. Therefore, even the most intensive rDNA library analyses have recovered only small samples of much larger assemblages, indicating that global environments harbour a vast array of unexplored biodiversity. High-throughput parallel tag 454 sequencing offers an unprecedented scale of sampling for molecular detection of microbial diversity. Here, we report a 454 protocol for sampling and characterizing assemblages of eukaryote microbes. We use this approach to sequence two SSU rDNA diversity markers-the variable V4 and V9 regions-from 10 L of anoxic Norwegian fjord water. We identified 38 116 V4 and 15 156 V9 unique sequences. Both markers detect a wide range of taxonomic groups but in both cases the diversity detected was dominated by dinoflagellates and close relatives. Long-tailed rank abundance curves suggest that the 454 sequencing approach provides improved access to rare genotypes. Most tags detected represent genotypes not currently in GenBank, although many are similar to database sequences. We suggest that current understanding of the ecological complexity of protist communities, genetic diversity, and global species richness are severely limited by the sequence data hitherto available, and we discuss the biological significance of this high amplicon diversity.}, } @article {pmid20331766, year = {2010}, author = {Creer, S and Fonseca, VG and Porazinska, DL and Giblin-Davis, RM and Sung, W and Power, DM and Packer, M and Carvalho, GR and Blaxter, ML and Lambshead, PJ and Thomas, WK}, title = {Ultrasequencing of the meiofaunal biosphere: practice, pitfalls and promises.}, journal = {Molecular ecology}, volume = {19 Suppl 1}, number = {}, pages = {4-20}, doi = {10.1111/j.1365-294X.2009.04473.x}, pmid = {20331766}, issn = {1365-294X}, support = {G0900740/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Animals ; *Biodiversity ; Computational Biology ; DNA/isolation & purification ; Ecosystem ; Evolution, Molecular ; Metagenomics/*methods ; *Phylogeny ; Polymerase Chain Reaction/methods ; RNA, Ribosomal, 18S/genetics ; Ribosome Subunits, Small, Eukaryotic ; Sequence Analysis, DNA/*methods ; }, abstract = {Biodiversity assessment is the key to understanding the relationship between biodiversity and ecosystem functioning, but there is a well-acknowledged biodiversity identification gap related to eukaryotic meiofaunal organisms. Meiofaunal identification is confounded by the small size of taxa, morphological convergence and intraspecific variation. However, the most important restricting factor in meiofaunal ecological research is the mismatch between diversity and the number of taxonomists that are able to simultaneously identify and catalogue meiofaunal diversity. Accordingly, a molecular operational taxonomic unit (MOTU)-based approach has been advocated for en mass meiofaunal biodiversity assessment, but it has been restricted by the lack of throughput afforded by chain termination sequencing. Contemporary pyrosequencing offers a solution to this problem in the form of environmental metagenetic analyses, but this represents a novel field of biodiversity assessment. Here, we provide an overview of meiofaunal metagenetic analyses, ranging from sample preservation and DNA extraction to PCR, sequencing and the bioinformatic interrogation of multiple, independent samples using 454 Roche sequencing platforms. We report two examples of environmental metagenetic nuclear small subunit 18S (nSSU) analyses of marine and tropical rainforest habitats and provide critical appraisals of the level of putative recombinant DNA molecules (chimeras) in metagenetic data sets. Following stringent quality control measures, environmental metagenetic analyses achieve MOTU formation across the eukaryote domain of life at a fraction of the time and cost of traditional approaches. The effectiveness of Roche 454 sequencing brings substantial advantages to studies aiming to elucidate the molecular genetic richness of not only meiofaunal, but also all complex eukaryotic communities.}, } @article {pmid20353452, year = {2010}, author = {Chen, X and Hodges, JS and Shuman, SK and Gatewood, LC and Xu, J}, title = {Predicting tooth loss for older adults with special needs.}, journal = {Community dentistry and oral epidemiology}, volume = {38}, number = {3}, pages = {235-243}, doi = {10.1111/j.1600-0528.2009.00527.x}, pmid = {20353452}, issn = {1600-0528}, mesh = {Aged ; Female ; Health Status ; Humans ; Long-Term Care ; Male ; Minnesota/epidemiology ; Oral Health ; Predictive Value of Tests ; Retrospective Studies ; *Risk Assessment ; Risk Factors ; Tooth Loss/*epidemiology/*etiology ; }, abstract = {OBJECTIVES: Older Adults with Special Needs (OASN) have more oral health needs compared with healthy, independent elders. Currently, little is known about tooth loss, a key indicator of oral function loss, among OASN. Risk assessment is primarily based on clinical experience rather than scientific evidence, raising concerns for quality of care. The study's objective was to develop an evidence-based model to quantitatively predict tooth loss for OASN.

METHODS: Four hundred ninety-one dentate older adults, including 235 from long-term care facilities, were retrospectively recruited. Subjects were treated and brought to a state of oral health before enrollment. Medical and dental assessments were abstracted from dental records and used to predict risk of tooth loss. Tooth loss events were recorded for subjects during follow-up. Multivariate negative-binomial regression was used, starting with 27 risk factors and removing variables using Akaike's Information Criterion. Pearson's correlation was then conducted to evaluate the overall fit of the final fitted model.

RESULTS: The final fitted model included eight predictors. Among them, age, number of decayed/broken teeth at arrival, anticholinergic burden of medications and physical mobility were associated with risk of tooth loss in OASN (P ≤ 0.05). Internal validation indicated satisfactory fit of the final fitted model.

CONCLUSION: An evidence-based model with eight predictors was developed to quantitatively predict risk of tooth loss for OASN at the individual level.}, } @article {pmid20345399, year = {2010}, author = {Urbina-Cardona, JN and Flores-Villela, O}, title = {Ecological-niche modeling and prioritization of conservation-area networks for Mexican herpetofauna.}, journal = {Conservation biology : the journal of the Society for Conservation Biology}, volume = {24}, number = {4}, pages = {1031-1041}, doi = {10.1111/j.1523-1739.2009.01432.x}, pmid = {20345399}, issn = {1523-1739}, mesh = {Amphibians/*physiology ; Animals ; Conservation of Natural Resources/*methods ; Databases, Factual ; *Demography ; *Ecosystem ; Geography ; Mexico ; *Models, Theoretical ; Planning Techniques ; Reptiles/*physiology ; Species Specificity ; }, abstract = {One of the most important tools in conservation biology is information on the geographic distribution of species and the variables determining those patterns. We used maximum-entropy niche modeling to run distribution models for 222 amphibian and 371 reptile species (49% endemics and 27% threatened) for which we had 34,619 single geographic records. The planning region is in southeastern Mexico, is 20% of the country's area, includes 80% of the country's herpetofauna, and lacks an adequate protected-area system. We used probabilistic data to build distribution models of herpetofauna for use in prioritizing conservation areas for three target groups (all species and threatened and endemic species). The accuracy of species-distribution models was better for endemic and threatened species than it was for all species. Forty-seven percent of the region has been deforested and additional conservation areas with 13.7% to 88.6% more native vegetation (76% to 96% of the areas are outside the current protected-area system) are needed. There was overlap in 26 of the main selected areas in the conservation-area network prioritized to preserve the target groups, and for all three target groups the proportion of vegetation types needed for their conservation was constant: 30% pine and oak forests, 22% tropical evergreen forest, 17% low deciduous forest, and 8% montane cloud forests. The fact that different groups of species require the same proportion of habitat types suggests that the pine and oak forests support the highest proportion of endemic and threatened species and should therefore be given priority over other types of vegetation for inclusion in the protected areas of southeastern Mexico.}, } @article {pmid20336296, year = {2010}, author = {Lauer, M and Aswani, S}, title = {Indigenous knowledge and long-term ecological change: detection, interpretation, and responses to changing ecological conditions in Pacific Island communities.}, journal = {Environmental management}, volume = {45}, number = {5}, pages = {985-997}, pmid = {20336296}, issn = {1432-1009}, mesh = {Conservation of Natural Resources/legislation & jurisprudence/*methods ; *Ecosystem ; Environmental Monitoring/legislation & jurisprudence/*methods ; Geographic Information Systems ; *Health Knowledge, Attitudes, Practice ; *Marine Biology ; Ownership ; Pacific Islands ; Rural Population ; Satellite Communications ; Seaweed/growth & development ; Surveys and Questionnaires ; }, abstract = {When local resource users detect, understand, and respond to environmental change they can more effectively manage environmental resources. This article assesses these abilities among artisanal fishers in Roviana Lagoon, Solomon Islands. In a comparison of two villages, it documents local resource users' abilities to monitor long-term ecological change occurring to seagrass meadows near their communities, their understandings of the drivers of change, and their conceptualizations of seagrass ecology. Local observations of ecological change are compared with historical aerial photography and IKONOS satellite images that show 56 years of actual changes in seagrass meadows from 1947 to 2003. Results suggest that villagers detect long-term changes in the spatial cover of rapidly expanding seagrass meadows. However, for seagrass meadows that showed no long-term expansion or contraction in spatial cover over one-third of respondents incorrectly assumed changes had occurred. Examples from a community-based management initiative designed around indigenous ecological knowledge and customary sea tenure governance show how local observations of ecological change shape marine resource use and practices which, in turn, can increase the management adaptability of indigenous or hybrid governance systems.}, } @article {pmid20305019, year = {2010}, author = {Pycke, BF and Crabbé, A and Verstraete, W and Leys, N}, title = {Characterization of triclosan-resistant mutants reveals multiple antimicrobial resistance mechanisms in Rhodospirillum rubrum S1H.}, journal = {Applied and environmental microbiology}, volume = {76}, number = {10}, pages = {3116-3123}, pmid = {20305019}, issn = {1098-5336}, mesh = {Anti-Bacterial Agents/*pharmacology ; Computational Biology ; Drug Resistance, Bacterial/*genetics ; Enoyl-(Acyl-Carrier-Protein) Reductase (NADH)/genetics ; Microbial Sensitivity Tests ; Mutation/genetics ; Rhodospirillum rubrum/*drug effects/*genetics/growth & development/metabolism ; Triclosan/*pharmacology ; }, abstract = {Antimicrobial resistance mechanisms were identified in 11 spontaneous high- and low-level triclosan resistance (Tcs(r)) mutants of Rhodospirillum rubrum S1H by genotyping complemented with transcriptional analyses, antibiotic resistance screening, and membrane permeability analyses. High-end Tcs(r) (MIC = 8 mg/liter) was the result of a FabI1(G98V) mutation. This point mutation led to an even higher level of Tcs(r) (MIC > or = 16 mg/liter) in combination with constitutive upregulation of mexB and mexF efflux pump homologs. Hence, a mechanistic synergy of constitutive efflux pump expression and a FabI1 point mutation could prevent TCS-induced cell permeabilization, which was shown to occur between 4 and 8 mg/liter TCS in the R. rubrum S1H parent strain. Low-level Tcs(r) mutants constitutively upregulated the emrAB, mexAB, and/or mexF homolog. The mutants that overexpressed emrAB also derepressed the micropollutant-upregulated factors mufA1 and mufM. In some cases, low-level Tcs(r) decreased innate resistance to ampicillin and tetracycline, while in others, a triclosan-induced antibiotic cross-resistance was shown for chloramphenicol and carbenicillin. This study showed that the TCS resistance degree is dependent of the initial exposure concentration in Rhodospirillum rubrum S1H and that similar resistance degrees can be the result of different defense mechanisms, which all have distinct antibiotic cross-resistance profiles.}, } @article {pmid20300936, year = {2010}, author = {Zhu, X and Pfueller, S and Whitelaw, P and Winter, C}, title = {Spatial differentiation of landscape values in the Murray River region of Victoria, Australia.}, journal = {Environmental management}, volume = {45}, number = {5}, pages = {896-911}, pmid = {20300936}, issn = {1432-1009}, mesh = {Conservation of Natural Resources/economics/*methods/statistics & numerical data ; *Ecosystem ; *Geographic Information Systems ; Geography ; Research ; *Rivers ; Social Values ; Socioeconomic Factors ; Surveys and Questionnaires ; Victoria ; }, abstract = {This research advances the understanding of the location of perceived landscape values through a statistically based approach to spatial analysis of value densities. Survey data were obtained from a sample of people living in and using the Murray River region, Australia, where declining environmental quality prompted a reevaluation of its conservation status. When densities of 12 perceived landscape values were mapped using geographic information systems (GIS), valued places clustered along the entire river bank and in associated National/State Parks and reserves. While simple density mapping revealed high value densities in various locations, it did not indicate what density of a landscape value could be regarded as a statistically significant hotspot or distinguish whether overlapping areas of high density for different values indicate identical or adjacent locations. A spatial statistic Getis-Ord Gi* was used to indicate statistically significant spatial clusters of high value densities or "hotspots". Of 251 hotspots, 40% were for single non-use values, primarily spiritual, therapeutic or intrinsic. Four hotspots had 11 landscape values. Two, lacking economic value, were located in ecologically important river red gum forests and two, lacking wilderness value, were near the major towns of Echuca-Moama and Albury-Wodonga. Hotspots for eight values showed statistically significant associations with another value. There were high associations between learning and heritage values while economic and biological diversity values showed moderate associations with several other direct and indirect use values. This approach may improve confidence in the interpretation of spatial analysis of landscape values by enhancing understanding of value relationships.}, } @article {pmid20237650, year = {2010}, author = {Galperin, MY and Higdon, R and Kolker, E}, title = {Interplay of heritage and habitat in the distribution of bacterial signal transduction systems.}, journal = {Molecular bioSystems}, volume = {6}, number = {4}, pages = {721-728}, pmid = {20237650}, issn = {1742-2051}, support = {Z99 LM999999/ImNIH/Intramural NIH HHS/United States ; U01 DK072473/DK/NIDDK NIH HHS/United States ; ZIA LM000073-15/ImNIH/Intramural NIH HHS/United States ; R01 GM076680/GM/NIGMS NIH HHS/United States ; ZIA LM000073/ImNIH/Intramural NIH HHS/United States ; R01 GM076680-02/GM/NIGMS NIH HHS/United States ; UO1 DK072473/DK/NIDDK NIH HHS/United States ; }, mesh = {Adaptation, Physiological ; Bacteria/classification/*genetics/*metabolism ; Bacterial Proteins/genetics/metabolism ; Databases, Genetic ; Ecosystem ; Genome, Bacterial ; Models, Biological ; Phylogeny ; Signal Transduction/*genetics/*physiology ; Systems Biology ; }, abstract = {Comparative analysis of the complete genome sequences from a variety of poorly studied organisms aims at predicting ecological and behavioral properties of these organisms and helping in characterizing their habitats. This task requires finding appropriate descriptors that could be correlated with the core traits of each system and would allow meaningful comparisons. Using the relatively simple bacterial models, first attempts have been made to introduce suitable metrics to describe the complexity of organism's signaling machinery, which included introducing the "bacterial IQ" score. Here, we use an updated census of prokaryotic signal transduction systems to improve this parameter and evaluate its consistency within selected bacterial phyla. We also introduce a more elaborate descriptor, a set of profiles of relative abundance of members of each family of signal transduction proteins encoded in each genome. We show that these family profiles are well conserved within each genus and are often consistent within families of bacteria. Thus, they reflect evolutionary relationships between organisms as well as individual adaptations of each organism to its specific ecological niche.}, } @article {pmid20237475, year = {2010}, author = {Vonholdt, BM and Pollinger, JP and Lohmueller, KE and Han, E and Parker, HG and Quignon, P and Degenhardt, JD and Boyko, AR and Earl, DA and Auton, A and Reynolds, A and Bryc, K and Brisbin, A and Knowles, JC and Mosher, DS and Spady, TC and Elkahloun, A and Geffen, E and Pilot, M and Jedrzejewski, W and Greco, C and Randi, E and Bannasch, D and Wilton, A and Shearman, J and Musiani, M and Cargill, M and Jones, PG and Qian, Z and Huang, W and Ding, ZL and Zhang, YP and Bustamante, CD and Ostrander, EA and Novembre, J and Wayne, RK}, title = {Genome-wide SNP and haplotype analyses reveal a rich history underlying dog domestication.}, journal = {Nature}, volume = {464}, number = {7290}, pages = {898-902}, pmid = {20237475}, issn = {1476-4687}, support = {ZIC HG200365-03/ImNIH/Intramural NIH HHS/United States ; R01 GM083606-03/GM/NIGMS NIH HHS/United States ; R01 GM083606/GM/NIGMS NIH HHS/United States ; ZIC HG200365/ImNIH/Intramural NIH HHS/United States ; ZIC HG200365-02/ImNIH/Intramural NIH HHS/United States ; ZIC HG200365-01/ImNIH/Intramural NIH HHS/United States ; T32 HG002536/HG/NHGRI NIH HHS/United States ; }, mesh = {Animals ; Animals, Domestic/classification/*genetics ; Animals, Wild/classification/genetics ; Breeding ; Computational Biology ; Dogs/classification/*genetics ; Evolution, Molecular ; Asia, Eastern/ethnology ; Genome/*genetics ; Haplotypes/*genetics ; Middle East/ethnology ; Phenotype ; Phylogeny ; Polymorphism, Single Nucleotide/*genetics ; Wolves/classification/genetics ; }, abstract = {Advances in genome technology have facilitated a new understanding of the historical and genetic processes crucial to rapid phenotypic evolution under domestication. To understand the process of dog diversification better, we conducted an extensive genome-wide survey of more than 48,000 single nucleotide polymorphisms in dogs and their wild progenitor, the grey wolf. Here we show that dog breeds share a higher proportion of multi-locus haplotypes unique to grey wolves from the Middle East, indicating that they are a dominant source of genetic diversity for dogs rather than wolves from east Asia, as suggested by mitochondrial DNA sequence data. Furthermore, we find a surprising correspondence between genetic and phenotypic/functional breed groupings but there are exceptions that suggest phenotypic diversification depended in part on the repeated crossing of individuals with novel phenotypes. Our results show that Middle Eastern wolves were a critical source of genome diversity, although interbreeding with local wolf populations clearly occurred elsewhere in the early history of specific lineages. More recently, the evolution of modern dog breeds seems to have been an iterative process that drew on a limited genetic toolkit to create remarkable phenotypic diversity.}, } @article {pmid20231481, year = {2010}, author = {Diefendorf, AF and Mueller, KE and Wing, SL and Koch, PL and Freeman, KH}, title = {Global patterns in leaf 13C discrimination and implications for studies of past and future climate.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {107}, number = {13}, pages = {5738-5743}, pmid = {20231481}, issn = {1091-6490}, mesh = {Altitude ; Carbon Isotopes/*metabolism ; *Climate Change/history ; Databases, Factual ; Ecosystem ; History, Ancient ; Models, Biological ; Plant Leaves/*metabolism ; Rain ; Trees/metabolism ; }, abstract = {Fractionation of carbon isotopes by plants during CO(2) uptake and fixation (Delta(leaf)) varies with environmental conditions, but quantitative patterns of Delta(leaf) across environmental gradients at the global scale are lacking. This impedes interpretation of variability in ancient terrestrial organic matter, which encodes climatic and ecological signals. To address this problem, we converted 3,310 published leaf delta(13)C values into mean Delta(leaf) values for 334 woody plant species at 105 locations (yielding 570 species-site combinations) representing a wide range of environmental conditions. Our analyses reveal a strong positive correlation between Delta(leaf) and mean annual precipitation (MAP; R(2) = 0.55), mirroring global trends in gross primary production and indicating stomatal constraints on leaf gas-exchange, mediated by water supply, are the dominant control of Delta(leaf) at large spatial scales. Independent of MAP, we show a lesser, negative effect of altitude on Delta(leaf) and minor effects of temperature and latitude. After accounting for these factors, mean Delta(leaf) of evergreen gymnosperms is lower (by 1-2.7 per thousand) than for other woody plant functional types (PFT), likely due to greater leaf-level water-use efficiency. Together, environmental and PFT effects contribute to differences in mean Delta(leaf) of up to 6 per thousand between biomes. Coupling geologic indicators of ancient precipitation and PFT (or biome) with modern Delta(leaf) patterns has potential to yield more robust reconstructions of atmospheric delta(13)C values, leading to better constraints on past greenhouse-gas perturbations. Accordingly, we estimate a 4.6 per thousand decline in the delta(13)C of atmospheric CO(2) at the onset of the Paleocene-Eocene Thermal Maximum, an abrupt global warming event approximately 55.8 Ma.}, } @article {pmid20221265, year = {2010}, author = {Sunagawa, S and Woodley, CM and Medina, M}, title = {Threatened corals provide underexplored microbial habitats.}, journal = {PloS one}, volume = {5}, number = {3}, pages = {e9554}, pmid = {20221265}, issn = {1932-6203}, mesh = {Animals ; Anthozoa/genetics/*physiology ; Bacteria/*genetics ; Cluster Analysis ; Computational Biology/methods ; Coral Reefs ; Ecosystem ; Endangered Species ; Genetic Variation ; Phylogeny ; RNA, Ribosomal, 16S/*genetics ; Seawater/microbiology ; }, abstract = {Contemporary in-depth sequencing of environmental samples has provided novel insights into microbial community structures, revealing that their diversity had been previously underestimated. Communities in marine environments are commonly composed of a few dominant taxa and a high number of taxonomically diverse, low-abundance organisms. However, studying the roles and genomic information of these "rare" organisms remains challenging, because little is known about their ecological niches and the environmental conditions to which they respond. Given the current threat to coral reef ecosystems, we investigated the potential of corals to provide highly specialized habitats for bacterial taxa including those that are rarely detected or absent in surrounding reef waters. The analysis of more than 350,000 small subunit ribosomal RNA (16S rRNA) sequence tags and almost 2,000 nearly full-length 16S rRNA gene sequences revealed that rare seawater biosphere members are highly abundant or even dominant in diverse Caribbean corals. Closely related corals (in the same genus/family) harbored similar bacterial communities. At higher taxonomic levels, however, the similarities of these communities did not correlate with the phylogenetic relationships among corals, opening novel questions about the evolutionary stability of coral-microbial associations. Large proportions of OTUs (28.7-49.1%) were unique to the coral species of origin. Analysis of the most dominant ribotypes suggests that many uncovered bacterial taxa exist in coral habitats and await future exploration. Our results indicate that coral species, and by extension other animal hosts, act as specialized habitats of otherwise rare microbes in marine ecosystems. Here, deep sequencing provided insights into coral microbiota at an unparalleled resolution and revealed that corals harbor many bacterial taxa previously not known. Given that two of the coral species investigated are listed as threatened under the U.S. Endangered Species Act, our results add an important microbial diversity-based perspective to the significance of conserving coral reefs.}, } @article {pmid20206436, year = {2010}, author = {Balana, BB and Mathijs, E and Muys, B}, title = {Assessing the sustainability of forest management: an application of multi-criteria decision analysis to community forests in northern Ethiopia.}, journal = {Journal of environmental management}, volume = {91}, number = {6}, pages = {1294-1304}, doi = {10.1016/j.jenvman.2010.02.005}, pmid = {20206436}, issn = {1095-8630}, mesh = {*Decision Support Techniques ; Ethiopia ; *Trees ; }, abstract = {Continuous deterioration of the natural resource base has become a serious threat to both the ecological systems and economic production in Ethiopia. Many of these problems have been attributed directly or indirectly to the rapid dwindling of the country's forest cover which is associated with unsustainable forest use and management. Closing community woodlands from human and livestock intervention to promote natural regeneration of forests has been one of the environmental restoration strategies pursued in the degraded highland areas of northern Ethiopia. However, local pressure to use reforested community lands for economic benefit has become a major threat to forest sustainability. Using locally identified sets of criteria and indicators for sustainable community forest management, this paper applies a multi-criteria decision analysis tool to evaluate forest management problems in the northern province of Tigray, Ethiopia. Three MCA methods - ranking, pair-wise comparison, and scoring - were used in evaluating the sets of criteria and indicators and alternative forest management scenarios. Results from the study indicate a number of noteworthy points: 1) MCA techniques both for identifying local level sustainability criteria and indicators and evaluating management schemes in a participatory decision environment appear to be effective tools to address local resource management problems; 2) Evaluated against the selected sets of criteria and indicators, the current forest management regime in the study area is not on a sustainable path; 3) Acquainting local people with adequate environmental knowledge and raising local awareness about the long-term consequences of environmental degradation ranked first among the set of sustainability criteria; and 4) In order to harmonize both environmental and economic objectives, the present 'ecological-biased' forest management regime needs to be substituted by an appropriate holistic scheme that takes into account stakeholders' multiple preferences and priority rankings.}, } @article {pmid20205726, year = {2010}, author = {Lukacs, MF and Harstad, H and Bakke, HG and Beetz-Sargent, M and McKinnel, L and Lubieniecki, KP and Koop, BF and Grimholt, U}, title = {Comprehensive analysis of MHC class I genes from the U-, S-, and Z-lineages in Atlantic salmon.}, journal = {BMC genomics}, volume = {11}, number = {}, pages = {154}, pmid = {20205726}, issn = {1471-2164}, mesh = {Alleles ; Amino Acid Sequence ; Animals ; Betahistine ; Chromosome Mapping ; Chromosomes, Artificial, Bacterial ; Computational Biology ; Fish Proteins/*genetics ; Gene Expression Profiling ; Gene Order ; *Genes, MHC Class I ; Genetic Linkage ; Genomic Library ; Genomics/methods ; Molecular Sequence Data ; Phylogeny ; Salmo salar/*genetics/immunology ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: We have previously sequenced more than 500 kb of the duplicated MHC class I regions in Atlantic salmon. In the IA region we identified the loci for the MHC class I gene Sasa-UBA in addition to a soluble MHC class I molecule, Sasa-ULA. A pseudolocus for Sasa-UCA was identified in the nonclassical IB region. Both regions contained genes for antigen presentation, as wells as orthologues to other genes residing in the human MHC region.

RESULTS: The genomic localisation of two MHC class I lineages (Z and S) has been resolved. 7 BACs were sequenced using a combination of standard Sanger and 454 sequencing. The new sequence data extended the IA region with 150 kb identifying the location of one Z-lineage locus, ZAA. The IB region was extended with 350 kb including three new Z-lineage loci, ZBA, ZCA and ZDA in addition to a UGA locus. An allelic version of the IB region contained a functional UDA locus in addition to the UCA pseudolocus. Additionally a BAC harbouring two MHC class I genes (UHA) was placed on linkage group 14, while a BAC containing the S-lineage locus SAA (previously known as UAA) was placed on LG10. Gene expression studies showed limited expression range for all class I genes with exception of UBA being dominantly expressed in gut, spleen and gills, and ZAA with high expression in blood.

CONCLUSION: Here we describe the genomic organization of MHC class I loci from the U-, Z-, and S-lineages in Atlantic salmon. Nine of the described class I genes are located in the extension of the duplicated IA and IB regions, while three class I genes are found on two separate linkage groups. The gene organization of the two regions indicates that the IB region is evolving at a different pace than the IA region. Expression profiling, polymorphic content, peptide binding properties and phylogenetic relationship show that Atlantic salmon has only one MHC class Ia gene (UBA), in addition to a multitude of nonclassical MHC class I genes from the U-, S- and Z-lineages.}, } @article {pmid20202199, year = {2010}, author = {Okara, RM and Sinka, ME and Minakawa, N and Mbogo, CM and Hay, SI and Snow, RW}, title = {Distribution of the main malaria vectors in Kenya.}, journal = {Malaria journal}, volume = {9}, number = {}, pages = {69}, pmid = {20202199}, issn = {1475-2875}, support = {079091//Wellcome Trust/United Kingdom ; 079080//Wellcome Trust/United Kingdom ; 083124//Wellcome Trust/United Kingdom ; 083534//Wellcome Trust/United Kingdom ; }, mesh = {Animals ; Anopheles/*classification/parasitology ; *Databases, Factual ; Ecology ; Geographic Information Systems ; Geography ; Humans ; Insect Vectors/*classification/parasitology ; Kenya ; Malaria, Falciparum/epidemiology/parasitology/*transmission ; Population Density ; Species Specificity ; }, abstract = {BACKGROUND: A detailed knowledge of the distribution of the main Anopheles malaria vectors in Kenya should guide national vector control strategies. However, contemporary spatial distributions of the locally dominant Anopheles vectors including Anopheles gambiae, Anopheles arabiensis, Anopheles merus, Anopheles funestus, Anopheles pharoensis and Anopheles nili are lacking. The methods and approaches used to assemble contemporary available data on the present distribution of the dominant malaria vectors in Kenya are presented here.

METHOD: Primary empirical data from published and unpublished sources were identified for the period 1990 to 2009. Details recorded for each source included the first author, year of publication, report type, survey location name, month and year of survey, the main Anopheles species reported as present and the sampling and identification methods used. Survey locations were geo-positioned using national digital place name archives and on-line geo-referencing resources. The geo-located species-presence data were displayed and described administratively, using first-level administrative units (province), and biologically, based on the predicted spatial margins of Plasmodium falciparum transmission intensity in Kenya for the year 2009. Each geo-located survey site was assigned an urban or rural classification and attributed an altitude value.

RESULTS: A total of 498 spatially unique descriptions of Anopheles vector species across Kenya sampled between 1990 and 2009 were identified, 53% were obtained from published sources and further communications with authors. More than half (54%) of the sites surveyed were investigated since 2005. A total of 174 sites reported the presence of An. gambiae complex without identification of sibling species. Anopheles arabiensis and An. funestus were the most widely reported at 244 and 265 spatially unique sites respectively with the former showing the most ubiquitous distribution nationally. Anopheles gambiae, An. arabiensis, An. funestus and An. pharoensis were reported at sites located in all the transmission intensity classes with more reports of An. gambiae in the highest transmission intensity areas than the very low transmission areas.

CONCLUSION: A contemporary, spatially defined database of the main malaria vectors in Kenya provides a baseline for future compilations of data and helps identify areas where information is currently lacking. The data collated here are published alongside this paper where it may help guide future sampling location decisions, help with the planning of vector control suites nationally and encourage broader research inquiry into vector species niche modeling.}, } @article {pmid20199681, year = {2010}, author = {Boulos, MN and Warren, J and Gong, J and Yue, P}, title = {Web GIS in practice VIII: HTML5 and the canvas element for interactive online mapping.}, journal = {International journal of health geographics}, volume = {9}, number = {}, pages = {14}, pmid = {20199681}, issn = {1476-072X}, mesh = {Computer Graphics ; Data Display ; Databases, Factual ; *Geographic Information Systems ; Humans ; Information Storage and Retrieval/*methods ; *Internet ; Maps as Topic ; Programming Languages ; }, abstract = {HTML5 is being developed as the next major revision of HTML (Hypertext Markup Language), the core markup language of the World Wide Web. It aims at reducing the need for proprietary, plug-in-based rich Internet application (RIA) technologies such as Adobe Flash. The canvas element is part of HTML5 and is used to draw graphics using scripting (e.g., JavaScript). This paper introduces Cartagen, an open-source, vector-based, client-side framework for rendering plug-in-free, offline-capable, interactive maps in native HTML5 on a wide range of Web browsers and mobile phones. Cartagen was developed at MIT Media Lab's Design Ecology group. Potential applications of the technology as an enabler for participatory online mapping include mapping real-time air pollution, citizen reporting, and disaster response, among many other possibilities.}, } @article {pmid20197794, year = {2011}, author = {Tabor, JA and O'rourke, MK and Lebowitz, MD and Harris, RB}, title = {Landscape-epidemiological study design to investigate an environmentally based disease.}, journal = {Journal of exposure science & environmental epidemiology}, volume = {21}, number = {2}, pages = {197-211}, doi = {10.1038/jes.2009.67}, pmid = {20197794}, issn = {1559-064X}, mesh = {Arizona/epidemiology ; Coccidioidomycosis/diagnosis/*epidemiology/ethnology/transmission ; Cross-Sectional Studies ; Demography ; Environmental Exposure/*analysis ; Epidemiologic Studies ; Female ; *Geographic Information Systems ; Humans ; Male ; Risk Factors ; Telephone ; }, abstract = {Cost-effective approaches for identifying and enrolling subjects in community-based epidemiological studies face many challenges. Additional challenges arise when a neighborhood scale of analysis is required to distinguish between individual- and group-level risk factors with strong environmental determinants. A stratified, two-stage, cross-sectional, address-based telephone survey of Greater Tucson, Arizona, was conducted in 2002-2003. Subjects were recruited from direct marketing data at neighborhood resolution using a geographic information system (GIS). Three geomorphic strata were divided into two demographic units. Households were randomly selected within census block groups, selected using the probability proportional to size technique. Purchased direct marketing lists represented 45.2% of Census 2000 households in the surveyed block groups. Survey design effect (1.6) on coccidioidomycosis prevalence (88 per 100,000 per year) was substantially reduced in four of the six strata (0.3-0.9). Race-ethnicity was more robust than age and gender to compensate for significant selection bias using poststratification. Clustered, address-based telephone surveys provide a cost-effective, valid method for recruiting populations from address-based lists using a GIS to design surveys and population survey statistical methods for analysis. Landscape ecology provides effective methods for identifying scales of analysis and units for stratification that will improve sampling efficiency when environmental variables of interest are strong predictors.}, } @article {pmid20195499, year = {2010}, author = {Wooley, JC and Godzik, A and Friedberg, I}, title = {A primer on metagenomics.}, journal = {PLoS computational biology}, volume = {6}, number = {2}, pages = {e1000667}, pmid = {20195499}, issn = {1553-7358}, mesh = {Computational Biology ; *Metagenomics ; Sequence Analysis, DNA ; }, abstract = {Metagenomics is a discipline that enables the genomic study of uncultured microorganisms. Faster, cheaper sequencing technologies and the ability to sequence uncultured microbes sampled directly from their habitats are expanding and transforming our view of the microbial world. Distilling meaningful information from the millions of new genomic sequences presents a serious challenge to bioinformaticians. In cultured microbes, the genomic data come from a single clone, making sequence assembly and annotation tractable. In metagenomics, the data come from heterogeneous microbial communities, sometimes containing more than 10,000 species, with the sequence data being noisy and partial. From sampling, to assembly, to gene calling and function prediction, bioinformatics faces new demands in interpreting voluminous, noisy, and often partial sequence data. Although metagenomics is a relative newcomer to science, the past few years have seen an explosion in computational methods applied to metagenomic-based research. It is therefore not within the scope of this article to provide an exhaustive review. Rather, we provide here a concise yet comprehensive introduction to the current computational requirements presented by metagenomics, and review the recent progress made. We also note whether there is software that implements any of the methods presented here, and briefly review its utility. Nevertheless, it would be useful if readers of this article would avail themselves of the comment section provided by this journal, and relate their own experiences. Finally, the last section of this article provides a few representative studies illustrating different facets of recent scientific discoveries made using metagenomics.}, } @article {pmid20195496, year = {2010}, author = {Freilich, S and Kreimer, A and Borenstein, E and Gophna, U and Sharan, R and Ruppin, E}, title = {Decoupling Environment-Dependent and Independent Genetic Robustness across Bacterial Species.}, journal = {PLoS computational biology}, volume = {6}, number = {2}, pages = {e1000690}, pmid = {20195496}, issn = {1553-7358}, support = {R01 GM028016/GM/NIGMS NIH HHS/United States ; GM28016/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacteria/*genetics ; *Bacterial Physiological Phenomena ; Computational Biology/*methods ; Computer Simulation ; Environment ; Genetic Variation ; Metabolic Networks and Pathways ; *Models, Genetic ; Selection, Genetic ; Systems Biology/*methods ; }, abstract = {The evolutionary origins of genetic robustness are still under debate: it may arise as a consequence of requirements imposed by varying environmental conditions, due to intrinsic factors such as metabolic requirements, or directly due to an adaptive selection in favor of genes that allow a species to endure genetic perturbations. Stratifying the individual effects of each origin requires one to study the pertaining evolutionary forces across many species under diverse conditions. Here we conduct the first large-scale computational study charting the level of robustness of metabolic networks of hundreds of bacterial species across many simulated growth environments. We provide evidence that variations among species in their level of robustness reflect ecological adaptations. We decouple metabolic robustness into two components and quantify the extents of each: the first, environmental-dependent, is responsible for at least 20% of the non-essential reactions and its extent is associated with the species' lifestyle (specialized/generalist); the second, environmental-independent, is associated (correlation = approximately 0.6) with the intrinsic metabolic capacities of a species-higher robustness is observed in fast growers or in organisms with an extensive production of secondary metabolites. Finally, we identify reactions that are uniquely susceptible to perturbations in human pathogens, potentially serving as novel drug-targets.}, } @article {pmid20194113, year = {2010}, author = {Freilich, S and Kreimer, A and Meilijson, I and Gophna, U and Sharan, R and Ruppin, E}, title = {The large-scale organization of the bacterial network of ecological co-occurrence interactions.}, journal = {Nucleic acids research}, volume = {38}, number = {12}, pages = {3857-3868}, pmid = {20194113}, issn = {1362-4962}, mesh = {Bacteria/growth & development/metabolism ; *Bacterial Physiological Phenomena ; Data Mining ; *Ecosystem ; *Environmental Microbiology ; *Microbial Interactions ; PubMed ; }, abstract = {In their natural environments, microorganisms form complex systems of interactions. Understating the structure and organization of bacterial communities is likely to have broad medical and ecological consequences, yet a comprehensive description of the network of environmental interactions is currently lacking. Here, we mine co-occurrences in the scientific literature to construct such a network and demonstrate an expected pattern of association between the species' lifestyle and the recorded number of co-occurring partners. We further focus on the well-annotated gut community and show that most co-occurrence interactions of typical gut bacteria occur within this community. The network is then clustered into species-groups that significantly correspond with natural occurring communities. The relationships between resource competition, metabolic yield and growth rate within the clusters correspond with the r/K selection theory. Overall, these results support the constructed clusters as a first approximation of a bacterial ecosystem model. This comprehensive collection of predicted communities forms a new data resource for further systematic characterization of the ecological design principals shaping communities. Here, we demonstrate its utility for predicting cooperation and inhibition within communities.}, } @article {pmid20194080, year = {2010}, author = {Graber, LK and Asher, D and Anandaraja, N and Bopp, RF and Merrill, K and Cullen, MR and Luboga, S and Trasande, L}, title = {Childhood lead exposure after the phaseout of leaded gasoline: an ecological study of school-age children in Kampala, Uganda.}, journal = {Environmental health perspectives}, volume = {118}, number = {6}, pages = {884-889}, pmid = {20194080}, issn = {1552-9924}, mesh = {Child ; Cities ; Cross-Sectional Studies ; Dust/*analysis ; Environmental Exposure/*analysis ; Environmental Monitoring/*statistics & numerical data ; Environmental Pollutants/*blood ; Female ; Gasoline/analysis ; Geographic Information Systems ; Humans ; Lead/*blood ; Male ; Refuse Disposal/statistics & numerical data ; Regression Analysis ; Surveys and Questionnaires ; Uganda ; }, abstract = {BACKGROUND: Tetraethyl lead was phased out of gasoline in Uganda in 2005. Recent mitigation of an important source of lead exposure suggests examination and re-evaluation of the prevalence of childhood lead poisoning in this country. Ongoing concerns persist about exposure from the Kiteezi landfill in Kampala, the country's capital.

OBJECTIVES: We determined blood lead distributions among Kampala schoolchildren and identified risk factors for elevated blood lead levels (EBLLs; >or= 10 microg/dL). Analytical approach: Using a stratified, cross-sectional design, we obtained blood samples, questionnaire data, and soil and dust samples from the homes and schools of 163 4- to 8-year-old children representing communities with different risks of exposure.

RESULTS: The mean blood lead level (BLL) was 7.15 microg/dL; 20.5% of the children were found to have EBLL. Multivariable analysis found participants whose families owned fewer household items, ate canned food, or used the community water supply as their primary water source to have higher BLLs and likelihood of EBLLs. Distance < 0.5 mi from the landfill was the factor most strongly associated with increments in BLL (5.51 microg/dL, p < 0.0001) and likelihood of EBLL (OR = 4.71, p = 0.0093). Dust/soil lead was not significantly predictive of BLL/EBLL.

CONCLUSIONS: Lead poisoning remains highly prevalent among school-age children in Kampala. Confirmatory studies are needed, but further efforts are indicated to limit lead exposure from the landfill, whether through water contamination or through another mechanism. Although African nations are to be lauded for the removal of lead from gasoline, this study serves as a reminder that other sources of exposure to this potent neurotoxicant merit ongoing attention.}, } @article {pmid20188104, year = {2010}, author = {Ganswindt, A and Muenscher, S and Henley, M and Henley, S and Heistermann, M and Palme, R and Thompson, P and Bertschinger, H}, title = {Endocrine correlates of musth and the impact of ecological and social factors in free-ranging African elephants (Loxodonta africana).}, journal = {Hormones and behavior}, volume = {57}, number = {4-5}, pages = {506-514}, doi = {10.1016/j.yhbeh.2010.02.009}, pmid = {20188104}, issn = {1095-6867}, mesh = {Androgens/*metabolism ; Animals ; Animals, Wild ; Animals, Zoo ; Data Interpretation, Statistical ; Elephants/*physiology ; *Environment ; Feces/chemistry ; Female ; Glucocorticoids/*metabolism ; Male ; Seasons ; Sexual Behavior, Animal/*physiology ; *Social Environment ; }, abstract = {Sexual activity in mature male African elephants is predominantly associated with the occurrence of musth, a state or condition which refers to a set of physical, physiological and behavioral characteristics, including an elevation in androgen levels. Although musth appears to be energetically costly, the degree to which it is associated with changes in adrenal endocrine function (e.g., glucocorticoid output) is still unclear. To investigate the possible effect of musth on adrenocortical function, and the impact of socioecological changes on androgen and glucocorticoid levels, six adult African elephant bulls were followed for 13months in the Kruger National Park, South Africa, and observations and fecal sample collection for endocrine monitoring was carried out about twice weekly. Our data showed that the occurrence of musth was associated with reduced glucocorticoid output, suggesting that musth does not represent a physiological stress mediated by the hypothalamic-pituitary-adrenal axis. This confirms previous findings in captive-housed animals, providing evidence for a suppressive effect of the musth condition on adrenocortical activity. Furthermore, a seasonal effect on androgen and glucocorticoid levels was found, which appears to vary depending on the reproductive status of the animal. The results also indicate a relationship between the presence or absence of social partners and changes in testicular and adrenal endocrine activity. Finally, the data confirm previous findings in captive-housed elephants, that an elevation in androgen concentrations usually occurs before the onset of physical musth signs, and therefore support the idea that the change in androgen levels represents the initial stimulus for the musth condition.}, } @article {pmid20184658, year = {2010}, author = {Staus, NL and Strittholt, JR and Dellasala, DA}, title = {Evaluating areas of high conservation value in Western Oregon with a decision-support model.}, journal = {Conservation biology : the journal of the Society for Conservation Biology}, volume = {24}, number = {3}, pages = {711-720}, doi = {10.1111/j.1523-1739.2010.01445.x}, pmid = {20184658}, issn = {1523-1739}, mesh = {Animals ; *Conservation of Natural Resources ; *Decision Support Techniques ; *Ecosystem ; Environmental Monitoring ; Oregon ; Strigiformes ; }, abstract = {The Northwest Forest Plan was implemented in 1994 to protect habitat for species associated with old-growth forests, including Northern Spotted Owls (Strix occidentailis caurina) in Washington, Oregon, and northern California (U.S.A.). Nevertheless, 10-year monitoring data indicate mixed success in meeting the ecological goals of the plan. We used the ecosystem management decision-support model to evaluate terrestrial and aquatic habitats across the landscape on the basis of ecological objectives of the Northwest Forest Plan, which included maintenance of late-successional and old-growth forest, recovery, and maintenance of Pacific salmon (Oncorhynchus spp.), and viability of Northern Spotted Owls. Areas of the landscape that contained habitat characteristics that supported these objectives were considered of high conservation value. We used the model to evaluate ecological condition of each of the 36, 180 township and range sections of the study area. Eighteen percent of the study area was identified as habitat of high conservation value. These areas were mostly on public lands. Many of the sections that contained habitat of exceptional conservation value were on Bureau of Land Management land that has been considered for management-plan revisions to increase timber harvests. The results of our model can be used to guide future land management in the Northwest Forest Plan area, and illustrate how decision-support models can help land managers develop strategies to better meet their goals.}, } @article {pmid20184652, year = {2010}, author = {Howes, AL and Maron, M and McAlpine, CA}, title = {Bayesian networks and adaptive management of wildlife habitat.}, journal = {Conservation biology : the journal of the Society for Conservation Biology}, volume = {24}, number = {4}, pages = {974-983}, doi = {10.1111/j.1523-1739.2010.01451.x}, pmid = {20184652}, issn = {1523-1739}, mesh = {Animals ; Bayes Theorem ; Conservation of Natural Resources/*methods ; Data Collection ; *Decision Support Techniques ; *Ecosystem ; Passeriformes/*physiology ; Population Dynamics ; Queensland ; Sensitivity and Specificity ; }, abstract = {Adaptive management is an iterative process of gathering new knowledge regarding a system's behavior and monitoring the ecological consequences of management actions to improve management decisions. Although the concept originated in the 1970s, it is rarely actively incorporated into ecological restoration. Bayesian networks (BNs) are emerging as efficient ecological decision-support tools well suited to adaptive management, but examples of their application in this capacity are few. We developed a BN within an adaptive-management framework that focuses on managing the effects of feral grazing and prescribed burning regimes on avian diversity within woodlands of subtropical eastern Australia. We constructed the BN with baseline data to predict bird abundance as a function of habitat structure, grazing pressure, and prescribed burning. Results of sensitivity analyses suggested that grazing pressure increased the abundance of aggressive honeyeaters, which in turn had a strong negative effect on small passerines. Management interventions to reduce pressure of feral grazing and prescribed burning were then conducted, after which we collected a second set of field data to test the response of small passerines to these measures. We used these data, which incorporated ecological changes that may have resulted from the management interventions, to validate and update the BN. The network predictions of small passerine abundance under the new habitat and management conditions were very accurate. The updated BN concluded the first iteration of adaptive management and will be used in planning the next round of management interventions. The unique belief-updating feature of BNs provides land managers with the flexibility to predict outcomes and evaluate the effectiveness of management interventions.}, } @article {pmid20171753, year = {2010}, author = {McMeekin, TA and Hill, C and Wagner, M and Dahl, A and Ross, T}, title = {Ecophysiology of food-borne pathogens: Essential knowledge to improve food safety.}, journal = {International journal of food microbiology}, volume = {139 Suppl 1}, number = {}, pages = {S64-78}, doi = {10.1016/j.ijfoodmicro.2010.01.041}, pmid = {20171753}, issn = {1879-3460}, mesh = {Bacteria/chemistry ; *Bacterial Physiological Phenomena ; *Consumer Product Safety ; Food Analysis/*methods ; Foodborne Diseases/*microbiology ; Humans ; Knowledge ; }, abstract = {The term ecophysiology suggests that a natural connection exists between microbial ecology and microbial physiology, the former being concerned with the responses of microbial populations to environmental influences, and the latter with activities within individual cells. In this contribution we choose to integrate these as far as possible and also indicate how understanding of both is benefiting from advances in molecular biology and informatics. We consider how microbial dispersal relates to microbial survival, recovery and proliferation, including the significance of random factors (stochasticity) in continuation of bacterial lineages, observing that minor environmental changes, can greatly influence the potential for food-borne disease. Homeostasis and membrane transport are identified as potential targets to control food-borne pathogens and the role of compatible solutes in stress protection is presented. Phenotypic variation in genetically homogeneous populations is highlighted as a major component of the overall microbial survival strategy. The marked influence and potential of predictive microbiology as an aid to food safety management is discussed, as is the need for greater knowledge of the ecophysiology of microbes in the growth/no growth region. The application of fundamental scientific principles, including thermodynamics, chemistry and microbial physiology is advocated as the basis for development of theory underpinning microbial ecophysiology. Advancing microbial food safety continues to require development of rapid, quantitative methods as an early warning system and mechanism to curtail microbial food-borne disease outbreaks. However, advances made by technologists and molecular biologists must be combined with knowledge of ecophysiology: e.g. biological rates will continue to constrain resolution of the recalcitrant problem of reducing the time required for enrichment processes. The discussion presented leads to the conclusion that microbial and molecular methods are appropriate for enumeration and prevalence studies but that predictive model development should continue for the purposes of comparative process control and to support the risk assessment paradigm. We conclude also that contributions of human error or complacency to microbial food-borne illness will continue to thwart the best efforts of microbiologists and technologists to reduce its incidence. Decision-support technologies reporting in real-time appear to have potential to make objective food safety decisions thereby reducing the impact of human indifference to the application of simple, but effective, food hygiene rules.}, } @article {pmid20171531, year = {2010}, author = {Mohr, SB and Garland, CF and Gorham, ED and Grant, WB and Garland, FC}, title = {Ultraviolet B irradiance and incidence rates of bladder cancer in 174 countries.}, journal = {American journal of preventive medicine}, volume = {38}, number = {3}, pages = {296-302}, doi = {10.1016/j.amepre.2009.10.044}, pmid = {20171531}, issn = {1873-2607}, mesh = {Databases, Factual ; Health Expenditures/statistics & numerical data ; Humans ; Incidence ; Regression Analysis ; Risk Factors ; Smoking/epidemiology ; Sunlight/adverse effects ; Ultraviolet Rays/*adverse effects ; Urinary Bladder Neoplasms/*epidemiology/etiology ; Vitamin D/*analogs & derivatives/blood ; }, abstract = {BACKGROUND: Although nearly half of bladder cancer cases are due to smoking, the cause of nearly half is unexplained.

PURPOSE: This study aims to determine whether an inverse association exists between ultraviolet B (UVB) irradiance and incidence rates of bladder cancer worldwide.

METHODS: This study used an ecologic approach. Age-adjusted incidence rates of bladder cancer from 2002 were obtained for all 174 countries in GLOBOCAN, a database of the International Agency for Research on Cancer. The relationship of latitude and estimated serum 25-hydroxyvitamin D [25(OH)D] with incidence rates was determined. The independent contributions to incidence rates of bladder cancer of UVB, per capita cigarette consumption in 1980, and per capita health expenditure for 2001 were assessed using multiple regression. The analyses were performed in July 2008.

RESULTS: Bladder cancer incidence rates were higher in countries at higher latitudes than those nearer to the equator (r=-0.66, 95% CI=-0.74, -0.57, p<0.01). Ultraviolet B irradiance was independently inversely associated with incidence rates of bladder cancer after controlling for per capita cigarette consumption (beta=-0.28, 95% CI=-0.51, -0.05; R(2) for model=0.38, p<0.0001). Further, UVB irradiance was also inversely associated with incidence rates after controlling for per capita health expenditure (beta=-0.23, 95% CI=-0.36, -0.01; R(2) for model=0.49, p<0.0001) in a separate regression model.

CONCLUSIONS: Further investigation is needed to confirm the associations identified in this study using observational studies of individuals. The focus of this research should include the association of serum 25(OH)D levels with risk of bladder cancer.}, } @article {pmid20167824, year = {2010}, author = {McDonald, E and Bailie, R and Grace, J and Brewster, D}, title = {An ecological approach to health promotion in remote Australian Aboriginal communities.}, journal = {Health promotion international}, volume = {25}, number = {1}, pages = {42-53}, doi = {10.1093/heapro/daq004}, pmid = {20167824}, issn = {1460-2245}, mesh = {Adolescent ; Adult ; Child ; Child, Preschool ; Community Networks ; *Ecology ; Family Characteristics ; Female ; Focus Groups ; Health Knowledge, Attitudes, Practice ; Health Promotion/*methods/organization & administration ; Housing ; Humans ; Hygiene ; Interviews as Topic ; Male ; Northern Territory ; Poverty ; Program Development ; Review Literature as Topic ; Rural Population ; Young Adult ; }, abstract = {Poor environmental conditions and poor child health in remote Australian Aboriginal communities are a symptom of a disjuncture in the cultures of a disadvantaged (and only relatively recently enfranchised) minority population and a proportionally large, wealthy dominant immigrant population, problematic social policies and the legacy of colonialism. Developing effective health promotion interventions in this environment is a challenge. Taking an ecological approach, the objective of this study was to identify the key social, economic, cultural and environmental factors that contribute to poor hygiene in remote Aboriginal communities, and to determine approaches that will improve hygiene and reduce the burden of infection among children. The methods included a mix of quantitative and qualitative community-based studies and literature reviews. Study findings showed that a combination of crowding, non-functioning health hardware and poor standards of personal and domestic hygiene underlie the high burden of infection experienced by children. Also, models of health promotion drawn from developed and developing countries can be adapted for use in remote Australian Aboriginal community contexts. High levels of disadvantage in relation to social determinants of health underlie the problem of poor environmental conditions and poor child health in remote Australian Aboriginal communities. Measures need to be taken to address the immediate problems that impact on children's health-for example, by ensuring the availability of functional and adequate water and sanitation facilities-but these interventions are unlikely to have a major effect unless the underlying issues are also addressed.}, } @article {pmid20161718, year = {2010}, author = {Hay, SI and Sinka, ME and Okara, RM and Kabaria, CW and Mbithi, PM and Tago, CC and Benz, D and Gething, PW and Howes, RE and Patil, AP and Temperley, WH and Bangs, MJ and Chareonviriyaphap, T and Elyazar, IR and Harbach, RE and Hemingway, J and Manguin, S and Mbogo, CM and Rubio-Palis, Y and Godfray, HC}, title = {Developing global maps of the dominant anopheles vectors of human malaria.}, journal = {PLoS medicine}, volume = {7}, number = {2}, pages = {e1000209}, pmid = {20161718}, issn = {1549-1676}, support = {#079091/WT_/Wellcome Trust/United Kingdom ; 079091/WT_/Wellcome Trust/United Kingdom ; #083534/WT_/Wellcome Trust/United Kingdom ; #083124/WT_/Wellcome Trust/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; }, mesh = {Animals ; Anopheles/*parasitology/*physiology ; Databases, Factual ; Ecology ; Humans ; Insect Vectors/*parasitology/*physiology ; Malaria/epidemiology/parasitology/*transmission ; }, abstract = {Simon Hay and colleagues describe how the Malaria Atlas Project has collated anopheline occurrence data to map the geographic distributions of the dominant mosquito vectors of human malaria.}, } @article {pmid20156125, year = {2010}, author = {Yellowlees, PM and Chorba, K and Burke Parish, M and Wynn-Jones, H and Nafiz, N}, title = {Telemedicine can make healthcare greener.}, journal = {Telemedicine journal and e-health : the official journal of the American Telemedicine Association}, volume = {16}, number = {2}, pages = {229-232}, doi = {10.1089/tmj.2009.0105}, pmid = {20156125}, issn = {1556-3669}, mesh = {Conservation of Natural Resources/economics/*methods ; Ecology ; *Environmental Policy ; Health Care Sector/economics/*organization & administration ; Health Policy/*economics ; Humans ; Information Systems/economics/*organization & administration ; Politics ; Telemedicine/economics/*methods/organization & administration ; United States ; }, abstract = {The American healthcare industry is generally lacking environmentally sustainable practices. The environmental impact of healthcare practices in the country has been largely disregarded due to ambivalence, ignorance, and fears of additional costs and regulations. The current practices continue to pollute the environment by requiring large amounts of travel and paperwork by both the patient and the clinician. Telemedicine and health information technology help save time, energy, raw materials (such as paper and plastic), and fuel, thereby lowering the carbon footprint of the health industry. By implementing green practices, for instance, by engaging in carbon credit programs, the health industry could benefit financially as well as reduce its negative impact on the health of our planet. Companies that reduce their carbon emissions by implementing energy-saving practices can sell their carbon credits to companies that emit more carbon than permissible by their legally binding commitment. These carbon profits can then be used for healthcare research or to provide healthcare to the underserved. Alternatively, the savings could be used for green purchasing and to implement other carbon-reducing activities. This report reviews the numerous possible options for the American health industry to become greener and lower its carbon footprint while at the same time becoming more time- and cost efficient.}, } @article {pmid20154520, year = {2010}, author = {Perron, A and O'Grady, KA}, title = {Applying Dixon and Dixon's Integrative Model for Environmental Health Research toward a critical analysis of childhood lead poisoning in Canada.}, journal = {ANS. Advances in nursing science}, volume = {33}, number = {1}, pages = {E1-16}, doi = {10.1097/ANS.0b013e3181cd834d}, pmid = {20154520}, issn = {1550-5014}, mesh = {Canada/epidemiology ; Child ; *Child Welfare/statistics & numerical data ; Data Interpretation, Statistical ; Ecology ; Ecosystem ; Environmental Exposure/prevention & control/statistics & numerical data ; Environmental Health/*organization & administration ; Health Services Needs and Demand ; Housing ; Humans ; Knowledge ; Lead Poisoning/epidemiology/*prevention & control ; *Models, Nursing ; Nursing Research/*organization & administration ; Primary Prevention ; Research Design ; Risk Assessment ; United States/epidemiology ; Vulnerable Populations ; }, abstract = {Occurrences of childhood lead poisoning resulting from exposure to residential sources of lead is an underresearched area in Canada. Dixon and Dixon's Integrative Model for Environmental Health Research substantiates this claim by grouping Canadian research on this health topic into the model's 4 domains: physiological, vulnerability, epistemological, and health protection. This process is useful not only for identifying research gaps within the Canadian context but also in setting the groundwork for a future critical analysis to illuminate the sociopolitical and economic influences that shape healthcare knowledge, and ultimately, influence how healthcare providers and policy makers produce and use this information.}, } @article {pmid20150743, year = {2010}, author = {de Marco, R and Accordini, S and Antonicelli, L and Bellia, V and Bettin, MD and Bombieri, C and Bonifazi, F and Bugiani, M and Carosso, A and Casali, L and Cazzoletti, L and Cerveri, I and Corsico, AG and Ferrari, M and Fois, AG and Lo Cascio, V and Marcon, A and Marinoni, A and Olivieri, M and Perbellini, L and Pignatti, P and Pirina, P and Poli, A and Rolla, G and Trabetti, E and Verlato, G and Villani, S and Zanolin, ME and , }, title = {The Gene-Environment Interactions in Respiratory Diseases (GEIRD) Project.}, journal = {International archives of allergy and immunology}, volume = {152}, number = {3}, pages = {255-263}, doi = {10.1159/000283034}, pmid = {20150743}, issn = {1423-0097}, mesh = {Asthma/epidemiology/genetics ; Bias ; Case-Control Studies ; Data Collection ; Data Interpretation, Statistical ; Databases, Factual ; *Environment ; Environmental Pollution ; *Epidemiologic Research Design ; Female ; Housing ; Humans ; Italy/epidemiology ; Longitudinal Studies ; Male ; Nutrition Surveys ; Phenotype ; Public Sector ; Pulmonary Disease, Chronic Obstructive/epidemiology/genetics ; Respiratory Tract Diseases/*epidemiology/*genetics ; Rhinitis, Allergic, Perennial/epidemiology/genetics ; Rhinitis, Allergic, Seasonal/epidemiology/genetics ; Surveys and Questionnaires ; }, abstract = {The role of genetic and environmental factors, as well as their interaction, in the natural history of asthma, allergic rhinitis and chronic obstructive pulmonary disease (COPD) is largely unknown. This is mainly due to the lack of large-scale analytical epidemiological/genetic studies aimed at investigating these 3 respiratory conditions simultaneously. The GEIRD project is a collaborative initiative designed to collect information on biomarkers of inflammation and oxidative stress, individual and ecological exposures, diet, early-life factors, smoking habits, genetic traits and medication use in large and accurately defined series of asthma, allergic rhinitis and COPD phenotypes. It is a population-based multicase-control design, where cases and controls are identified through a 2-stage screening process (postal questionnaire and clinical examination) in pre-existing cohorts or new samples of subjects. It is aimed at elucidating the role that modifiable and genetic factors play in the occurrence, persistence, severity and control of inflammatory airway diseases, by way of the establishment of a historical multicentre standardized databank of phenotypes, contributed by and openly available to international epidemiologists. Researchers conducting population-based surveys with standardized methods may contribute to the public-domain case-control database, and use the resulting increased power to answer their own scientific questions.}, } @article {pmid20147900, year = {2010}, author = {Regier, JC and Shultz, JW and Zwick, A and Hussey, A and Ball, B and Wetzer, R and Martin, JW and Cunningham, CW}, title = {Arthropod relationships revealed by phylogenomic analysis of nuclear protein-coding sequences.}, journal = {Nature}, volume = {463}, number = {7284}, pages = {1079-1083}, pmid = {20147900}, issn = {1476-4687}, mesh = {Animals ; Arthropods/chemistry/*classification/*genetics ; Bayes Theorem ; Cell Nucleus/*genetics ; Computational Biology ; Crustacea/classification ; Genes/*genetics ; Insecta/classification ; Likelihood Functions ; Open Reading Frames/genetics ; *Phylogeny ; Proteins/*genetics ; Sequence Alignment ; Species Specificity ; }, abstract = {The remarkable antiquity, diversity and ecological significance of arthropods have inspired numerous attempts to resolve their deep phylogenetic history, but the results of two decades of intensive molecular phylogenetics have been mixed. The discovery that terrestrial insects (Hexapoda) are more closely related to aquatic Crustacea than to the terrestrial centipedes and millipedes (Myriapoda) was an early, if exceptional, success. More typically, analyses based on limited samples of taxa and genes have generated results that are inconsistent, weakly supported and highly sensitive to analytical conditions. Here we present strongly supported results from likelihood, Bayesian and parsimony analyses of over 41 kilobases of aligned DNA sequence from 62 single-copy nuclear protein-coding genes from 75 arthropod species. These species represent every major arthropod lineage, plus five species of tardigrades and onychophorans as outgroups. Our results strongly support Pancrustacea (Hexapoda plus Crustacea) but also strongly favour the traditional morphology-based Mandibulata (Myriapoda plus Pancrustacea) over the molecule-based Paradoxopoda (Myriapoda plus Chelicerata). In addition to Hexapoda, Pancrustacea includes three major extant lineages of 'crustaceans', each spanning a significant range of morphological disparity. These are Oligostraca (ostracods, mystacocarids, branchiurans and pentastomids), Vericrustacea (malacostracans, thecostracans, copepods and branchiopods) and Xenocarida (cephalocarids and remipedes). Finally, within Pancrustacea we identify Xenocarida as the long-sought sister group to the Hexapoda, a result confirming that 'crustaceans' are not monophyletic. These results provide a statistically well-supported phylogenetic framework for the largest animal phylum and represent a step towards ending the often-heated, century-long debate on arthropod relationships.}, } @article {pmid20147313, year = {2010}, author = {Pichegru, L and Grémillet, D and Crawford, RJ and Ryan, PG}, title = {Marine no-take zone rapidly benefits endangered penguin.}, journal = {Biology letters}, volume = {6}, number = {4}, pages = {498-501}, pmid = {20147313}, issn = {1744-957X}, mesh = {Animals ; *Biodiversity ; Conservation of Natural Resources/methods/*statistics & numerical data ; Fisheries/*legislation & jurisprudence/*statistics & numerical data ; Geographic Information Systems ; Marine Biology/*methods ; Oceans and Seas ; Predatory Behavior/physiology ; South Africa ; Spheniscidae/*physiology ; }, abstract = {No-take zones may protect populations of targeted marine species and restore the integrity of marine ecosystems, but it is unclear whether they benefit top predators that rely on mobile pelagic fishes. In South Africa, foraging effort of breeding African penguins decreased by 30 per cent within three months of closing a 20 km zone to the competing purse-seine fisheries around their largest colony. After the fishing ban, most of the penguins from this island had shifted their feeding effort inside the closed area. Birds breeding at another colony situated 50 km away, whose fishing grounds remained open to fishing, increased their foraging effort during the same period. This demonstrates the immediate benefit of a relatively small no-take zone for a marine top predator relying on pelagic prey. Selecting such small protected areas may be an important first conservation step, minimizing stakeholder conflicts and easing compliance, while ensuring benefit for the ecosystems within these habitats.}, } @article {pmid20147218, year = {2009}, author = {Daims, H}, title = {Use of fluorescence in situ hybridization and the daime image analysis program for the cultivation-independent quantification of microorganisms in environmental and medical samples.}, journal = {Cold Spring Harbor protocols}, volume = {2009}, number = {7}, pages = {pdb.prot5253}, doi = {10.1101/pdb.prot5253}, pmid = {20147218}, issn = {1559-6095}, mesh = {Bacteria/genetics ; Biofilms ; Biomass ; Computational Biology/methods ; Ecology ; Image Processing, Computer-Assisted ; In Situ Hybridization, Fluorescence/*methods ; *Microbiological Techniques ; Plankton/metabolism ; RNA, Ribosomal/genetics/metabolism ; Software ; }, abstract = {Conventional cultivation-based methods to measure microbial abundance are unsuitable for quantifying uncultured microorganisms that constitute the majority of microbial life in most environmental or medical samples. This problem is solved by the quantification approach described here, which combines fluorescence in situ hybridization (FISH) with rRNA-targeted probes and digital image analysis. By measuring the areas of probe-labeled biomass in randomly recorded image pairs, an unbiased estimate of the relative biovolume of the population of interest can be obtained. This approach expresses abundance as "biovolume fraction" (relative to the total biovolume of the whole microbial community). This value equals the share of biochemical reaction space occupied by the quantified population and thus can be more relevant ecologically than absolute cell numbers (e.g., a few large cells can contain the same biovolume as many small cells). Another advantage lies in the complete independence of this method from the morphology of the quantified organisms. Regardless of whether the target microbes occur as single cells in plankton samples, as filaments, or as dense aggregates in biofilms, this cultivation-independent method allows the composition of complex microbial communities to be determined.}, } @article {pmid20135692, year = {2010}, author = {Valdespino, C and Rico-Hernández, G and Mandujano, S}, title = {Gastrointestinal parasites of Howler monkeys (Alouatta palliata) inhabiting the fragmented landscape of the Santa Marta mountain range, Veracruz, Mexico.}, journal = {American journal of primatology}, volume = {72}, number = {6}, pages = {539-548}, doi = {10.1002/ajp.20808}, pmid = {20135692}, issn = {1098-2345}, mesh = {Alouatta/*parasitology ; Animals ; Databases, Factual ; Dicrocoeliidae/classification/isolation & purification ; Ecosystem ; Eimeriida/classification/*isolation & purification ; Endangered Species ; Feces/parasitology ; Gastrointestinal Tract/*parasitology ; Helminths/classification/*isolation & purification ; Oxyurida/classification/isolation & purification ; Parasitic Diseases, Animal/*classification/prevention & control ; }, abstract = {In recent years populations of howler monkeys (Alouatta palliata) in southeastern Mexico have decreased substantially due to the transformation and loss of natural habitats. This is especially evident in the Santa Marta mountain range, Veracruz, Mexico where several studies have evaluated the impact of fragmentation on howler monkey populations in order to propose management programs for their conservation. The conditions generated by fragmentation likely change the rates of parasitic infection and could decrease howler survival. In this study, gastrointestinal parasite species richness, prevalence, and egg density of infection were determined in howler groups inhabiting five forest fragments at the Santa Marta mountain range. Two hundred and seventy-eight fresh fecal samples were collected between October 2002 and April 2003. Three parasite species were found during the dry and the wet season in all forest fragments sampled: one unidentified species of Eimeriidae; Trypanoxyuris minutus (Oxyuridae); and Controrchis biliophilus (Dicrocoeliidae). Both the prevalence of T. minutus and infection density for all parasites differed between seasons and fragments (the largest fragment consistently differed from other fragments). Host density, distance to the nearest town, fragment size, fragment shape, and total basal area of food trees explained parasite prevalence, but each species had a different pattern. Although parasite richness was lower, prevalence and density were higher than values reported for howlers in conserved forests. These results suggest that the establishment of biological corridors and animal translocation programs must take into account the parasite ecology of each fragment to avoid higher infection rates and preclude potential consequent mortality.}, } @article {pmid20134078, year = {2010}, author = {Memon, FN and Owen, AM and Sanchez-Graillet, O and Upton, GJ and Harrison, AP}, title = {Identifying the impact of G-quadruplexes on Affymetrix 3' arrays using cloud computing.}, journal = {Journal of integrative bioinformatics}, volume = {7}, number = {2}, pages = {111}, doi = {10.2390/biecoll-jib-2010-111}, pmid = {20134078}, issn = {1613-4516}, support = {BB/E001742/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Computational Biology/methods ; DNA/chemistry ; Databases, Genetic ; *G-Quadruplexes ; Guanine/*chemistry ; Oligonucleotide Array Sequence Analysis/*methods ; RNA/chemistry ; }, abstract = {A tetramer quadruplex structure is formed by four parallel strands of DNA/ RNA containing runs of guanine. These quadruplexes are able to form because guanine can Hoogsteen hydrogen bond to other guanines, and a tetrad of guanines can form a stable arrangement. Recently we have discovered that probes on Affymetrix GeneChips that contain runs of guanine do not measure gene expression reliably. We associate this finding with the likelihood that quadruplexes are forming on the surface of GeneChips. In order to cope with the rapidly expanding size of GeneChip array datasets in the public domain, we are exploring the use of cloud computing to replicate our experiments on 3' arrays to look at the effect of the location of G-spots (runs of guanines). Cloud computing is a recently introduced high-performance solution that takes advantage of the computational infrastructure of large organisations such as Amazon and Google. We expect that cloud computing will become widely adopted because it enables bioinformaticians to avoid capital expenditure on expensive computing resources and to only pay a cloud computing provider for what is used. Moreover, as well as financial efficiency, cloud computing is an ecologically-friendly technology, it enables efficient data-sharing and we expect it to be faster for development purposes. Here we propose the advantageous use of cloud computing to perform a large data-mining analysis of public domain 3' arrays.}, } @article {pmid20133356, year = {2010}, author = {Friedman, M}, title = {Explosive morphological diversification of spiny-finned teleost fishes in the aftermath of the end-Cretaceous extinction.}, journal = {Proceedings. Biological sciences}, volume = {277}, number = {1688}, pages = {1675-1683}, pmid = {20133356}, issn = {1471-2954}, mesh = {Animals ; *Biodiversity ; *Biological Evolution ; Body Size ; Databases, Factual ; Extinction, Biological ; Fishes/*anatomy & histology/*classification/genetics ; Fossils ; Species Specificity ; }, abstract = {The spiny-finned teleost fishes (Acanthomorpha) include nearly one-third of all living vertebrate species and assume a bewildering array of bodyplans, but the macroevolutionary assembly of modern acanthomorph biodiversity remains largely unexplored. Here, I reconstruct the trajectory of morphological diversification in this major radiation from its first appearance in the Late Cretaceous to the Miocene using a geometric morphometric database comprising more than 600 extinct species known from complete body fossils. The anatomical diversity (disparity) of acanthomorphs is low throughout the Cretaceous, increases sharply and significantly in the wake of the Cretaceous-Palaeogene (K-P) extinction, and shows little change throughout subsequent Cenozoic intervals. This pattern of morphological diversification appears robust to two potential biasing factors: the 'Lagerstätten effect', and the non-random segregation of rare and common taxa along phenotypic axes. Dissecting the trajectory of acanthomorph radiation along phylogenetic lines reveals that the abrupt post-extinction increase in disparity is driven largely by the proliferation of trophically diverse modern groups within Percomorpha, a spiny-fin subclade containing more than 15 000 living species and identified as showing a substantially elevated diversification rate relative to background vertebrate levels. A major component of the Palaeogene acanthomorph radiation reflects colonization of morphospace previously occupied by non-acanthomorph victims of the K-P. However, other aspects of morphological diversification cannot be explained by this simple ecological release model, suggesting that multiple factors contributed to the prolific anatomical radiation of acanthomorphs.}, } @article {pmid20130030, year = {2010}, author = {Parks, DH and Beiko, RG}, title = {Identifying biologically relevant differences between metagenomic communities.}, journal = {Bioinformatics (Oxford, England)}, volume = {26}, number = {6}, pages = {715-721}, doi = {10.1093/bioinformatics/btq041}, pmid = {20130030}, issn = {1367-4811}, mesh = {Base Sequence ; Computational Biology/methods ; Databases, Genetic ; Genome, Bacterial ; *Metagenome ; Metagenomics/*methods ; Molecular Sequence Data ; Sequence Analysis, DNA ; }, abstract = {MOTIVATION: Metagenomics is the study of genetic material recovered directly from environmental samples. Taxonomic and functional differences between metagenomic samples can highlight the influence of ecological factors on patterns of microbial life in a wide range of habitats. Statistical hypothesis tests can help us distinguish ecological influences from sampling artifacts, but knowledge of only the P-value from a statistical hypothesis test is insufficient to make inferences about biological relevance. Current reporting practices for pairwise comparative metagenomics are inadequate, and better tools are needed for comparative metagenomic analysis.

RESULTS: We have developed a new software package, STAMP, for comparative metagenomics that supports best practices in analysis and reporting. Examination of a pair of iron mine metagenomes demonstrates that deeper biological insights can be gained using statistical techniques available in our software. An analysis of the functional potential of 'Candidatus Accumulibacter phosphatis' in two enhanced biological phosphorus removal metagenomes identified several subsystems that differ between the A.phosphatis stains in these related communities, including phosphate metabolism, secretion and metal transport.

AVAILABILITY: Python source code and binaries are freely available from our website at http://kiwi.cs.dal.ca/Software/STAMP CONTACT: beiko@cs.dal.ca

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, } @article {pmid20128693, year = {2010}, author = {Almeida, NF and Yan, S and Cai, R and Clarke, CR and Morris, CE and Schaad, NW and Schuenzel, EL and Lacy, GH and Sun, X and Jones, JB and Castillo, JA and Bull, CT and Leman, S and Guttman, DS and Setubal, JC and Vinatzer, BA}, title = {PAMDB, a multilocus sequence typing and analysis database and website for plant-associated microbes.}, journal = {Phytopathology}, volume = {100}, number = {3}, pages = {208-215}, doi = {10.1094/PHYTO-100-3-0208}, pmid = {20128693}, issn = {0031-949X}, mesh = {Bacteria/*genetics ; Computational Biology ; *Databases, Factual ; *Internet ; Phylogeny ; Plant Diseases/*microbiology ; Plants/*microbiology ; }, abstract = {Although there are adequate DNA sequence differences among plant-associated and plant-pathogenic bacteria to facilitate molecular approaches for their identification, identification at a taxonomic level that is predictive of their phenotype is a challenge. The problem is the absence of a taxonomy that describes genetic variation at a biologically relevant resolution and of a database containing reference strains for comparison. Moreover, molecular evolution, population genetics, ecology, and epidemiology of many plant-pathogenic and plant-associated bacteria are still poorly understood. To address these challenges, a database with web interface was specifically designed for plant-associated and plant-pathogenic microorganisms. The Plant-Associated Microbes Database (PAMDB) comprises, thus far, data from multilocus sequence typing and analysis (MLST/MLSA) studies of Acidovorax citrulli, Pseudomonas syringae, Ralstonia solanacearum, and Xanthomonas spp. Using data deposited in PAMDB, a robust phylogeny of Xanthomonas axonopodis and related bacteria has been inferred, and the diversity existing in the Xanthomonas genus and in described Xanthomonas spp. has been compared with the diversity in P. syringae and R. solanacearum. Moreover, we show how PAMDB makes it easy to distinguish between different pathogens that cause almost identical diseases. The scalable design of PAMDB will make it easy to add more plant pathogens in the future.}, } @article {pmid20123619, year = {2010}, author = {Breen, MS and Breen, M and Terasaki, N and Yamazaki, M and Conolly, RB}, title = {Computational model of steroidogenesis in human H295R cells to predict biochemical response to endocrine-active chemicals: model development for metyrapone.}, journal = {Environmental health perspectives}, volume = {118}, number = {2}, pages = {265-272}, pmid = {20123619}, issn = {1552-9924}, mesh = {Adrenal Glands/*drug effects/metabolism ; Cell Line, Tumor ; Computational Biology/methods ; Endocrine Disruptors/*pharmacology ; Humans ; Metyrapone/*pharmacology ; Models, Theoretical ; Steroids/*metabolism ; }, abstract = {BACKGROUND: An in vitro steroidogenesis assay using the human adrenocortical carcinoma cell line H295R is being evaluated as a possible screening assay to detect and assess the impact of endocrine-active chemicals (EACs) capable of altering steroid biosynthesis. Data interpretation and their quantitative use in human and ecological risk assessments can be enhanced with mechanistic computational models to help define mechanisms of action and improve understanding of intracellular concentration-response behavior.

OBJECTIVES: The goal of this study was to develop a mechanistic computational model of the metabolic network of adrenal steroidogenesis to estimate the synthesis and secretion of adrenal steroids in human H295R cells and their biochemical response to steroidogenesis-disrupting EAC.

METHODS: We developed a deterministic model that describes the biosynthetic pathways for the conversion of cholesterol to adrenal steroids and the kinetics for enzyme inhibition by metryrapone (MET), a model EAC. Using a nonlinear parameter estimation method, the model was fitted to the measurements from an in vitro steroidogenesis assay using H295R cells.

RESULTS: Model-predicted steroid concentrations in cells and culture medium corresponded well to the time-course measurements from control and MET-exposed cells. A sensitivity analysis indicated the parameter uncertainties and identified transport and metabolic processes that most influenced the concentrations of primary adrenal steroids, aldosterone and cortisol.

CONCLUSIONS: Our study demonstrates the feasibility of using a computational model of steroidogenesis to estimate steroid concentrations in vitro. This capability could be useful to help define mechanisms of action for poorly characterized chemicals and mixtures in support of predictive hazard and risk assessments with EACs.}, } @article {pmid20122796, year = {2010}, author = {Lim, SR and Lam, CW and Schoenung, JM}, title = {Quantity-based and toxicity-based evaluation of the U.S. Toxics Release Inventory.}, journal = {Journal of hazardous materials}, volume = {178}, number = {1-3}, pages = {49-56}, doi = {10.1016/j.jhazmat.2010.01.041}, pmid = {20122796}, issn = {1873-3336}, mesh = {Carcinogens/analysis ; Databases, Factual ; Environmental Monitoring/*statistics & numerical data ; Environmental Pollutants/*analysis/*toxicity ; Equipment and Supplies ; Health ; Humans ; Industrial Waste/analysis ; Industry/statistics & numerical data ; Metals/analysis/toxicity ; Noxae/*analysis/*toxicity ; United States ; United States Environmental Protection Agency ; Water Pollutants, Chemical/analysis ; }, abstract = {The U.S. EPA Toxics Release Inventory (TRI) represents an extensive, publicly available dataset on toxics and, as such, has contributed to reducing the releases and disposal of toxic chemicals. The TRI, however, reports on a wide range of releases from different sources, some of which are less likely to generate a human or ecological hazard. Furthermore, the TRI is quantity based and does not take into account the relative toxicity of chemicals. In an effort to utilize the TRI more effectively to guide environmental management and policy, this work provides an in-depth analysis of the quantity-based TRI data for year 2007 at industry sector, state, and chemical levels and couples it with toxicity potentials. These toxicity potentials are derived from the U.S. EPA's TRACI (Tool for the Reduction and Assessment of Chemical and other environmental Impacts) characterization factors for cancer, non-cancer and ecotoxicity. The combination of quantity-based and toxicity-based analysis allows a more robust evaluation of toxics use and priorities. Results show, for instance, that none of the highest priority chemicals identified through the toxicity-based evaluation would have been identified if only quantity-based evaluation had been used. As the chemicals are aggregated to the state and industry sector levels, the discrepancies between the evaluation methods are less significant.}, } @article {pmid20120823, year = {2009}, author = {De Cáceres, M and Legendre, P}, title = {Associations between species and groups of sites: indices and statistical inference.}, journal = {Ecology}, volume = {90}, number = {12}, pages = {3566-3574}, doi = {10.1890/08-1823.1}, pmid = {20120823}, issn = {0012-9658}, mesh = {Animals ; Data Interpretation, Statistical ; *Ecosystem ; Environmental Monitoring ; *Models, Biological ; *Models, Statistical ; Species Specificity ; }, abstract = {Ecologists often face the task of studying the association between single species and one or several groups of sites representing habitat types, community types, or other categories. Besides characterizing the ecological preference of the species, the strength of the association usually presents a lot of interest for conservation biology, landscape mapping and management, and natural reserve design, among other applications. The indices most frequently employed to assess these relationships are the phi coefficient of association and the indicator value index (IndVal). We compare these two approaches by putting them into a broader framework of related measures, which includes several new indices. We present permutation tests to assess the statistical significance of species-site group associations and bootstrap methods for obtaining confidence intervals. Correlation measures, such as the phi coefficient, are more context-dependent than indicator values but allow focusing on the preference of the species. In contrast, the two components of an indicator value index directly assess the value of the species as a bioindicator because they can be interpreted as its positive predictive value and sensitivity. Ecologists should select the most appropriate index of association strength according to their objective and then compute confidence intervals to determine the precision of the estimate.}, } @article {pmid20120822, year = {2009}, author = {Forester, JD and Im, HK and Rathouz, PJ}, title = {Accounting for animal movement in estimation of resource selection functions: sampling and data analysis.}, journal = {Ecology}, volume = {90}, number = {12}, pages = {3554-3565}, doi = {10.1890/08-0874.1}, pmid = {20120822}, issn = {0012-9658}, mesh = {Animals ; Behavior, Animal/*physiology ; *Data Interpretation, Statistical ; Deer/physiology ; Ecosystem ; Feeding Behavior/*physiology ; Likelihood Functions ; Models, Biological ; *Models, Statistical ; *Movement ; Spatial Behavior/*physiology ; }, abstract = {Patterns of resource selection by animal populations emerge as a result of the behavior of many individuals. Statistical models that describe these population-level patterns of habitat use can miss important interactions between individual animals and characteristics of their local environment; however, identifying these interactions is difficult. One approach to this problem is to incorporate models of individual movement into resource selection models. To do this, we propose a model for step selection functions (SSF) that is composed of a resource-independent movement kernel and a resource selection function (RSF). We show that standard case-control logistic regression may be used to fit the SSF; however, the sampling scheme used to generate control points (i.e., the definition of availability) must be accommodated. We used three sampling schemes to analyze simulated movement data and found that ignoring sampling and the resource-independent movement kernel yielded biased estimates of selection. The level of bias depended on the method used to generate control locations, the strength of selection, and the spatial scale of the resource map. Using empirical or parametric methods to sample control locations produced biased estimates under stronger selection; however, we show that the addition of a distance function to the analysis substantially reduced that bias. Assuming a uniform availability within a fixed buffer yielded strongly biased selection estimates that could be corrected by including the distance function but remained inefficient relative to the empirical and parametric sampling methods. As a case study, we used location data collected from elk in Yellowstone National Park, USA, to show that selection and bias may be temporally variable. Because under constant selection the amount of bias depends on the scale at which a resource is distributed in the landscape, we suggest that distance always be included as a covariate in SSF analyses. This approach to modeling resource selection is easily implemented using common statistical tools and promises to provide deeper insight into the movement ecology of animals.}, } @article {pmid20120821, year = {2009}, author = {Plank, MJ and Codling, EA}, title = {Sampling rate and misidentification of Lévy and non-Lévy movement paths.}, journal = {Ecology}, volume = {90}, number = {12}, pages = {3546-3553}, doi = {10.1890/09-0079.1}, pmid = {20120821}, issn = {0012-9658}, mesh = {Animals ; *Behavior, Animal ; *Data Interpretation, Statistical ; Ecosystem ; *Feeding Behavior ; Flight, Animal ; Models, Biological ; *Movement ; Spatial Behavior/*physiology ; }, abstract = {A large number of empirical studies have attributed Lévy search patterns to the foraging movements of animals. Typically, this is done by fitting a power-law distribution with an exponent of 1 < mu < or = 3 to the observed step lengths. Most studies record the animal's location at equally spaced time intervals, which are sometimes significantly longer than the natural time scale of the animal's movements. The collected data thus represent a subsample of the animal's movement. In this paper, the effect of subsampling on the observed properties of both Lévy and non-Lévy simulated movement paths is investigated. We find that the apparent properties of the observed movement path can be sensitive to the sampling rate even though Lévy search patterns are supposedly scale-independent. We demonstrate that, in certain contexts and dependent on the sampling rate used in observation, it is possible to misidentify a non-Lévy movement path as being a Lévy path. We also demonstrate that a Lévy movement path can be misidentified as a non-Lévy path, but this is dependent on the value of mu of the original simulated path, with the greatest uncertainty for mu = 2. We discuss the implications of these results in the context of studies of animal movements and foraging behavior.}, } @article {pmid20118191, year = {2010}, author = {Wegmann, D and Excoffier, L}, title = {Bayesian inference of the demographic history of chimpanzees.}, journal = {Molecular biology and evolution}, volume = {27}, number = {6}, pages = {1425-1435}, doi = {10.1093/molbev/msq028}, pmid = {20118191}, issn = {1537-1719}, mesh = {Animals ; *Bayes Theorem ; Databases, Genetic ; *Evolution, Molecular ; Markov Chains ; Microsatellite Repeats ; *Models, Genetic ; Monte Carlo Method ; Pan paniscus/*genetics ; Pan troglodytes/*genetics ; Reproducibility of Results ; Sequence Analysis, DNA ; }, abstract = {Due to an almost complete absence of fossil record, the evolutionary history of chimpanzees has only been studied recently on the basis of genetic data. Although the general topology of the chimpanzee phylogeny is well established, uncertainties remain concerning the size of current and past populations, the occurrence of bottlenecks or population expansions, or about divergence times and migrations rates between subspecies. Here, we present a novel attempt at globally inferring the detailed evolution of the Pan genus based on approximate Bayesian computation, an approach preferentially applied to complex models where the likelihood cannot be computed analytically. Based on two microsatellite and DNA sequence data sets and adjusting simulated data for local levels of inbreeding and patterns of missing data, we find support for several new features of chimpanzee evolution as compared with previous studies based on smaller data sets and simpler evolutionary models. We find that the central chimpanzees are certainly the oldest population of all P. troglodytes subspecies and that the other two P. t. subspecies diverged from the central chimpanzees by founder events. We also find an older divergence time (1.6 million years [My]) between common chimpanzee and Bonobos than previous studies (0.9-1.3 My), but this divergence appears to have been very progressive with the maintenance of relatively high levels of gene flow between the ancestral chimpanzee population and the Bonobos. Finally, we could also confirm the existence of strong unidirectional gene flow from the western into the central chimpanzee. These results show that interesting and innovative features of chimpanzee history emerge when considering their whole evolutionary history in a single analysis, rather than relying on simpler models involving several comparisons of pairs of populations.}, } @article {pmid20098655, year = {2010}, author = {Homan, JM}, title = {Eyes on the prize: reflections on the impact of the evolving digital ecology on the librarian as expert intermediary and knowledge coach, 1969-2009.}, journal = {Journal of the Medical Library Association : JMLA}, volume = {98}, number = {1}, pages = {49-56}, pmid = {20098655}, issn = {1558-9439}, mesh = {Decision Making ; History, 20th Century ; History, 21st Century ; Humans ; Knowledge ; *Librarians/history ; Libraries, Digital/history/*organization & administration ; Libraries, Medical/history/*organization & administration ; Medical Informatics/history/trends ; *Professional Role/history ; }, abstract = {OBJECTIVE: The 2009 Janet Doe Lecture reflects on the continuing value and increasing return on investment of librarian-mediated services in the constantly evolving digital ecology and complex knowledge environment of the health sciences.

SETTING: The interrelationship of knowledge, decision making based on knowledge, technology used to access and retrieve knowledge, and the important linkage roles of expert librarian intermediaries is examined.

METHODOLOGY: Professional experiences from 1969 to 2009, occurring during a time of unprecedented changes in the digital ecology of librarianship, are the base on which the evolving role and value of librarians as knowledge coaches and expert intermediaries are examined.

CONCLUSION: Librarian-mediated services linking knowledge and critical decision making in health care have become more valuable than ever as technology continues to reshape an increasingly complex knowledge environment.}, } @article {pmid20090942, year = {2010}, author = {Costa, DP and Robinson, PW and Arnould, JP and Harrison, AL and Simmons, SE and Hassrick, JL and Hoskins, AJ and Kirkman, SP and Oosthuizen, H and Villegas-Amtmann, S and Crocker, DE}, title = {Accuracy of ARGOS locations of Pinnipeds at-sea estimated using Fastloc GPS.}, journal = {PloS one}, volume = {5}, number = {1}, pages = {e8677}, pmid = {20090942}, issn = {1932-6203}, mesh = {*Animal Migration ; Animals ; Caniformia/classification/*physiology ; *Geographic Information Systems ; Species Specificity ; }, abstract = {BACKGROUND: ARGOS satellite telemetry is one of the most widely used methods to track the movements of free-ranging marine and terrestrial animals and is fundamental to studies of foraging ecology, migratory behavior and habitat-use. ARGOS location estimates do not include complete error estimations, and for many marine organisms, the most commonly acquired locations (Location Class 0, A, B, or Z) are provided with no declared error estimate.

We compared the accuracy of ARGOS Locations to those obtained using Fastloc GPS from the same electronic tags on five species of pinnipeds: 9 California sea lions (Zalophus californianus), 4 Galapagos sea lions (Zalophus wollebaeki), 6 Cape fur seals (Arctocephalus pusillus pusillus), 3 Australian fur seals (A. p. doriferus) and 5 northern elephant seals (Mirounga angustirostris). These species encompass a range of marine habitats (highly pelagic vs coastal), diving behaviors (mean dive durations 2-21 min) and range of latitudes (equator to temperate). A total of 7,318 ARGOS positions and 27,046 GPS positions were collected. Of these, 1,105 ARGOS positions were obtained within five minutes of a GPS position and were used for comparison. The 68(th) percentile ARGOS location errors as measured in this study were LC-3 0.49 km, LC-2 1.01 km, LC-1 1.20 km, LC-0 4.18 km, LC-A 6.19 km, LC-B 10.28 km.

CONCLUSIONS/SIGNIFICANCE: The ARGOS errors measured here are greater than those provided by ARGOS, but within the range of other studies. The error was non-normally distributed with each LC highly right-skewed. Locations of species that make short duration dives and spend extended periods on the surface (sea lions and fur seals) had less error than species like elephant seals that spend more time underwater and have shorter surface intervals. Supplemental data (S1) are provided allowing the creation of density distributions that can be used in a variety of filtering algorithms to improve the quality of ARGOS tracking data.}, } @article {pmid20085309, year = {2010}, author = {Izumikawa, M and Khan, ST and Takagi, M and Shin-ya, K}, title = {Sponge-derived Streptomyces producing isoprenoids via the mevalonate pathway.}, journal = {Journal of natural products}, volume = {73}, number = {2}, pages = {208-212}, doi = {10.1021/np900747t}, pmid = {20085309}, issn = {1520-6025}, mesh = {Animals ; Erythritol/analogs & derivatives/metabolism ; Hydroxymethylglutaryl-CoA-Reductases, NADP-dependent/*metabolism ; Marine Biology ; Mevalonic Acid/*metabolism ; Molecular Structure ; Porifera/*microbiology ; Sequence Homology, Nucleic Acid ; Streptomyces/*chemistry/enzymology/genetics ; Sugar Phosphates/metabolism ; Terpenes/chemistry/*isolation & purification/metabolism ; }, abstract = {In the course of our screening program for isoprenoids of marine actinobacterial origin, 523 actinobacterial strains were isolated from marine samples. Actinobacteria usually use the 2-C-methyl-d-erythritol 4-phosphate pathway for the production of primary metabolites, but some have been reported to use the mevalonate (MVA) pathway for the production of isoprenoids as secondary metabolites. 3-Hydroxy-3-methyl glutaryl coenzyme A reductase (HMGR) is a key enzyme and plays an important role in the MVA pathway. Therefore, we screened strains possessing the HMGR gene from the 523 strains mentioned above and also investigated isoprenoid compounds from cultures of strains possessing HMGR genes. As a result, Streptomyces sp. SpC080624SC-11 isolated from a marine sponge, Cinachyra sp., was shown to possess the HMGR gene and produce novel isoprenoids, JBIR-46 (1), -47 (2), and -48 (3). On the basis of extensive NMR and MS analyses, the structures of 1-3 were determined to be phenazine derivatives harboring dimethylallyl moieties. Furthermore, the isoprene units of 2 and 3 were confirmed to be synthesized via the MVA pathway in a feeding experiment using [1-(13)C]acetate.}, } @article {pmid20082675, year = {2010}, author = {An, GC}, title = {Translational systems biology using an agent-based approach for dynamic knowledge representation: An evolutionary paradigm for biomedical research.}, journal = {Wound repair and regeneration : official publication of the Wound Healing Society [and] the European Tissue Repair Society}, volume = {18}, number = {1}, pages = {8-12}, doi = {10.1111/j.1524-475X.2009.00568.x}, pmid = {20082675}, issn = {1524-475X}, mesh = {Animals ; Burns/therapy ; Computational Biology ; Humans ; *Models, Biological ; *Systems Biology ; *Translational Research, Biomedical ; }, abstract = {The greatest challenge facing the biomedical research community is the effective translation of basic mechanistic knowledge into clinically effective therapeutics. This challenge is most evident in attempts to understand and modulate "systems" processes/disorders, such as sepsis, cancer, and wound healing. Formulating an investigatory strategy for these issues requires the recognition that these are dynamic processes. Representation of the dynamic behavior of biological systems can aid in the investigation of complex pathophysiological processes by augmenting existing discovery procedures by integrating disparate information sources and knowledge. This approach is termed Translational Systems Biology. Focusing on the development of computational models capturing the behavior of mechanistic hypotheses provides a tool that bridges gaps in the understanding of a disease process by visualizing "thought experiments" to fill those gaps. Agent-based modeling is a computational method particularly well suited to the translation of mechanistic knowledge into a computational framework. Utilizing agent-based models as a means of dynamic hypothesis representation will be a vital means of describing, communicating, and integrating community-wide knowledge. The transparent representation of hypotheses in this dynamic fashion can form the basis of "knowledge ecologies," where selection between competing hypotheses will apply an evolutionary paradigm to the development of community knowledge.}, } @article {pmid20082009, year = {2010}, author = {Sofonia, JJ and Unsworth, RK}, title = {Development of water quality thresholds during dredging for the protection of benthic primary producer habitats.}, journal = {Journal of environmental monitoring : JEM}, volume = {12}, number = {1}, pages = {159-163}, doi = {10.1039/b904986j}, pmid = {20082009}, issn = {1464-0333}, mesh = {Animals ; Australia ; Data Interpretation, Statistical ; *Ecosystem ; Environmental Monitoring/*methods/standards ; Environmental Pollution/analysis/legislation & jurisprudence/*prevention & control ; Geologic Sediments/*analysis ; Government Regulation ; Invertebrates/*physiology ; Marine Biology ; Nephelometry and Turbidimetry ; Photosynthesis ; Time Factors ; Water Pollutants/*analysis ; }, abstract = {Given the potential for adverse effects of ocean dredging on marine organisms, particularly benthic primary producer communities, the management and monitoring of those activities which cause elevated turbidity and sediment loading is critical. In practice, however, this has proven challenging as the development of water quality threshold values, upon which management responses are based, are subject to a large number of physical and biological parameters that are spatially and temporally specific. As a consequence, monitoring programs to date have taken a wide range of different approaches, most focusing on measures of turbidity reported as nephelometric turbidity units (NTU). This paper presents a potential approach in the determination of water quality thresholds which utilises data gathered through the long-term deployment of in situ water instruments, but suggests a focus on photosynthetic active radiation (PAR) rather than NTU as it is more relevant biologically and inclusive of other site conditions. A simple mathematical approach to data interpretation is also presented which facilitates threshold value development, not individual values of concentrations over specific intervals, but as an equation which may be utilized in numerical modelling.}, } @article {pmid20077707, year = {2009}, author = {Ye, HF and Guo, SH and Wu, B and Wang, YH}, title = {[Differential geometry expression and analysis of regionalized variables of typical pollutants concentration in terrestrial environment].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {20}, number = {10}, pages = {2475-2480}, pmid = {20077707}, issn = {1001-9332}, mesh = {Data Interpretation, Statistical ; Ecology/*methods/*statistics & numerical data ; Ecosystem ; Environmental Monitoring ; Environmental Pollutants/*analysis ; *Models, Theoretical ; Statistics as Topic ; }, abstract = {Based on the basic concepts of differential geometry in analyzing environmental data and establishing related models, the methodology for differential geometry expression and analysis of pollutants concentration in terrestrial environment was presented. As a kind of regionalized variables, the spatial distribution pattern of the pollutants concentration was transformed into 3-dimension form, and fitted with conicoid. This approach made it possible to analyze the quantitative relationships between the regionalized variables and their spatial structural attributes. For illustration purpose, several sorts of typical space fabrics, such as convexity, concavity, ridge, ravine, saddle, and slope, were calculated and characterized. It was suggested that this approach was feasible for analyzing the regionalized variables of pollutants concentration in terrestrial environment.}, } @article {pmid20077704, year = {2009}, author = {Pan, Y and Xiao, H and Yu, ZR}, title = {[Spatial evaluation on ecological and aesthetic quality of Beijing agricultural landscape].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {20}, number = {10}, pages = {2455-2460}, pmid = {20077704}, issn = {1001-9332}, mesh = {China ; City Planning ; Conservation of Natural Resources/*methods ; Crops, Agricultural/*growth & development ; *Ecosystem ; Environmental Monitoring/*methods ; Geographic Information Systems ; Satellite Communications ; }, abstract = {A total of ten single indices mainly reflecting the ecological and aesthetic quality of agricultural landscape, including ecosystem function, naturalness, openness and diversity, contamination probability, and orderliness were selected, their different weights were given based on field survey and expert system, and an integrated evaluation index system of agricultural landscape quality was constructed. In the meantime, the land use data provided by GIS and the remote sensing data of vegetation index were used to evaluate the Beijing agricultural landscape quality and its spatial variation. There was a great spatial variation in the agricultural landscape quality of Beijing, being worse at the edges of urban area and towns, but better in suburbs. The agricultural landscape quality was mainly related to topography and human activity. To construct a large-scale integrated index system based on remote sensing data and landscape indices would have significance in evaluating the spatial variation of agricultural landscape quality.}, } @article {pmid20077703, year = {2009}, author = {Zhou, R and Li, YH and Hu, YM and Xi, FM and Shan, T and He, HS and Liu, M and Wang, JN}, title = {[Spatiotemporal expansion of urban and rural built-up areas in Shenyang City: an analysis based on remote sensing and GIS technology].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {20}, number = {10}, pages = {2446-2454}, pmid = {20077703}, issn = {1001-9332}, mesh = {China ; *City Planning ; Conservation of Natural Resources/*methods ; *Ecosystem ; Environmental Monitoring/*methods ; Geographic Information Systems ; Satellite Communications ; *Social Planning ; }, abstract = {By using 1985, 1995, 1997, 2000 and 2004 satellite images and GIS technology, three indices including built-up area density, expansion intensity index, and fractal dimension were chosen to analyze the spatiotemporal characteristics, spatial differentiation, and morphological changes of urban and rural built-up areas in Shenyang City in 1985-2004, with the main driving factors discussed. In the study period, the high-density area of urban built-up area in the City increased year by year, and that of rural built-up area changed slightly before 1997 but increased gradually thereafter. The increased area, expansion speed, and expansion intensity of built-up area were evidently greater in urban than in rural area. An obvious spatial differentiation was observed in the expansion of built-up area between urban and rural areas, with the high-speed expansion mainly concentrated in urban area. The fractal dimension in urban area increased gradually, which meant that the integrated configuration of urban area became more and more complex, while that in rural area changed irregularly, because of the lack of reasonable planning and construction. Economic development, population growth, transportation, natural environment, policy-guiding, and urban planning were the main driving forces of the expansion of built-up areas in Shenyang City.}, } @article {pmid20077235, year = {2009}, author = {Awkerman, JA and Raimondo, S and Barron, MG}, title = {Estimation of wildlife hazard levels using interspecies correlation models and standard laboratory rodent toxicity data.}, journal = {Journal of toxicology and environmental health. Part A}, volume = {72}, number = {24}, pages = {1604-1609}, doi = {10.1080/15287390903232491}, pmid = {20077235}, issn = {1528-7394}, mesh = {Animals ; *Animals, Laboratory ; *Animals, Wild ; Data Interpretation, Statistical ; Ecosystem ; Environmental Pollutants/*analysis/metabolism/*toxicity ; Hazardous Substances/*analysis/metabolism/*toxicity ; Inorganic Chemicals/analysis/metabolism/toxicity ; Lethal Dose 50 ; Mice ; Organic Chemicals/analysis/metabolism/toxicity ; Rats ; Risk Assessment ; Rodentia ; Species Specificity ; }, abstract = {Toxicity data from laboratory rodents are widely available and frequently used in human health assessments as animal model data. This study explores the possibility of using single rodent acute toxicity values to predict chemical toxicity to a diversity of wildlife species and estimate hazard levels from modeled species sensitivity distributions (SSD). Interspecies correlation estimation (ICE) models predict toxicity values for untested species using the sensitivity relationship between measured toxicity values of two species. Predicted toxicity values can subsequently populate SSD for application in ecological risk assessments. Laboratory mouse and rat toxicity values were used to estimate toxicity to wildlife and the predicted values then were used to derive SSD hazard dose levels. Toxicity values were predicted within fivefold of measured toxicity values for 78% of ICE models using laboratory rat or mouse toxicity as a surrogate value. Hazard dose levels (HD5) were within fivefold of measured estimates for 72% of SSD developed using laboratory rodent ICE models. Rodents were most often in the least sensitive quartile of species sensitivity distributions, and therefore toxicity values alone may not adequately represent the toxicity to many species of concern without appropriate safety or assessment factors. Laboratory rodent toxicity data offer an additional source of information that can be used to predict hazard levels for wildlife species, and thus offer a starting point for both health and ecological risk assessment.}, } @article {pmid20074338, year = {2010}, author = {Vogel, H and Heidel, AJ and Heckel, DG and Groot, AT}, title = {Transcriptome analysis of the sex pheromone gland of the noctuid moth Heliothis virescens.}, journal = {BMC genomics}, volume = {11}, number = {}, pages = {29}, pmid = {20074338}, issn = {1471-2164}, mesh = {Amino Acid Sequence ; Animals ; Conserved Sequence ; Databases, Nucleic Acid ; Databases, Protein ; Expressed Sequence Tags ; Gene Expression Profiling/*methods ; Humans ; Molecular Sequence Data ; Moths/anatomy & histology/*chemistry/genetics/metabolism ; Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA/*methods ; Sex Attractants/*analysis/biosynthesis/chemistry/genetics ; }, abstract = {BACKGROUND: The chemical components of sex pheromones have been determined for more than a thousand moth species, but so far only a handful of genes encoding enzymes responsible for the biosynthesis of these compounds have been identified. For understanding the evolution of moth sexual communication, it is essential to know which genes are involved in the production of specific pheromone components and what controls the variation in their relative frequencies in the pheromone blend. We used a transcriptomic approach to characterize the pheromone gland of the Noctuid moth Heliothis virescens, an important agricultural pest, in order to obtain substantial general sequence information and to identify a range of candidate genes involved in the pheromone biosynthetic pathway.

RESULTS: To facilitate identifying sets of genes involved in a broad range of processes and to capture rare transcripts, we developed our majority of ESTs from a normalized cDNA library of Heliothis virescens pheromone glands (PG). Combining these with a non-normalized library yielded a total of 17,233 ESTs, which assembled into 2,082 contigs and 6,228 singletons. Using BLAST searches of the NR and Swissprot databases we were able to identify a large number of putative unique gene elements (unigenes), which we compared to those derived from previous transcriptomic surveys of the larval stage of Heliothis virescens. The distribution of unigenes among GO Biological Process functional groups shows an overall similarity between PG and larval transcriptomes, but with distinct enrichment of specific pathways in the PG. In addition, we identified a large number of candidate genes in the pheromone biosynthetic pathways.

CONCLUSION: These data constitute one of the first large-scale EST-projects for Noctuidae, a much-needed resource for exploring these pest species. Our analysis shows a surprisingly complex transcriptome and we identified a large number of potential pheromone biosynthetic pathway and immune-related genes that can be applied to population and systematic studies of Heliothis virescens and other Noctuidae.}, } @article {pmid20067528, year = {2010}, author = {Khan, ST and Izumikawa, M and Motohashi, K and Mukai, A and Takagi, M and Shin-Ya, K}, title = {Distribution of the 3-hydroxyl-3-methylglutaryl coenzyme A reductase gene and isoprenoid production in marine-derived Actinobacteria.}, journal = {FEMS microbiology letters}, volume = {304}, number = {1}, pages = {89-96}, doi = {10.1111/j.1574-6968.2009.01886.x}, pmid = {20067528}, issn = {1574-6968}, mesh = {Actinobacteria/classification/enzymology/*genetics/isolation & purification ; Animals ; Geologic Sediments/microbiology ; HL-60 Cells/drug effects ; Humans ; Hydroxymethylglutaryl CoA Reductases/*genetics/metabolism ; Japan ; *Marine Biology ; Molecular Sequence Data ; Phylogeny ; Porifera/microbiology ; Sequence Analysis, DNA ; Terpenes/chemistry/*metabolism/pharmacology ; Urochordata/microbiology ; }, abstract = {During the course of our screening program to isolate isoprenoids from marine Actinobacteria, 523 actinobacterial strains were isolated from 18 marine sponges, a tunicate, and two marine sediments. These strains belonged to 21 different genera, but most were members of Streptomyces, Nocardia, Rhodococcus, and Micromonospora. Some Actinobacteria have been reported to use the mevalonate pathway for the production of isoprenoids as secondary metabolites. Therefore, we investigated whether these strains possessed the 3-hydroxyl-3-methylglutaryl coenzyme A reductase (hmgr) gene, which indicates the presence of the mevalonate pathway. As a result, six strains belonging to the genera Streptomyces (SpC080624SC-11, SpA080624GE-02, and Sp080513GE-23), Nocardia (Sp080513SC-18), and Micromonospora (Se080624GE-07 and SpC080624GE-05) were found to possess the hmgr gene, and these genes were highly similar to hmgr genes in isoprenoid biosynthetic gene clusters. Among the six strains, the two strains SpC080624SC-11 and SpA080624GE-02 produced the novel isoprenoids, JBIR-46, -47, and -48, which consisted of phenazine chromophores, and Sp080513GE-23 produced a known isoprenoid, fumaquinone. Furthermore, these compounds showed cytotoxic activity against human acute myelogenous leukemia HL-60 cells.}, } @article {pmid20063769, year = {2009}, author = {Sheremet'ev, SN and Gamaleĭ, IuV}, title = {[Trends of the grass ecological evolution].}, journal = {Zhurnal obshchei biologii}, volume = {70}, number = {6}, pages = {459-483}, pmid = {20063769}, issn = {0044-4596}, mesh = {Adaptation, Biological ; *Biological Evolution ; *Climate Change ; Databases, Factual ; *Ecology ; Phylogeny ; Poaceae/classification/*growth & development/metabolism ; Time Factors ; Water/metabolism ; }, abstract = {The results of an analytic research show that the evolution of leaf structure and water balance are completely coincident with the global changes of the planet climate and hydrology. Taxic diversity of herbs and herbaceous biomes is a function of the paleoclimate variability and the plant adaptations to it. The correlation between the plant organization and climate changes allow to reconstruct both the climate changes chronicle and the geological ages of plant taxa based on the structure and function of the plant species. Two global trends of ecological evolution can be recognized differing mutually by the composition of herbaceous adaptive types: (a) the evolutionary line of herbs of chilling plains with domination of the plant species with C3 apoplastic syndrome formed under cold climate condition, and (b) the evolutionary line of herbs of hot plains with domination of plant species with C4 apoplastic syndrome. Both trends include the monocots and dicots, and both are the results of climate changes in the Cenozoic. C3 herbs of chilling plains and the steppe and meadow phytocoenoses formed by them arose as an answer to the temperature decrease in the significant areas of high latitudes. The apoplastic syndrome (transfer from symplastic transport of assimilates suppressed by cold to their apoplastic transport) is a diagnostic feature for this group of herbs. The C4 herbs of hot plains and the savannas, deserts and the saline land plant vegetation are an adaptive answer to iridizations of low latitude areas. The C4 syndrome (compensation of stomata closure by the mechanism of CO2 concentration in the leaf tissues) is a special character of this group of herbs. Both types of herbaceous biomes come to change forest biomes which were strongly decreased in both areas at low and high latitudes. This tendency is continued in parallel with the climate tendency to the continent dessication and cooling.}, } @article {pmid20060570, year = {2010}, author = {Lahr, J and Münier, B and De Lange, HJ and Faber, JF and Sørensen, PB}, title = {Wildlife vulnerability and risk maps for combined pollutants.}, journal = {The Science of the total environment}, volume = {408}, number = {18}, pages = {3891-3898}, doi = {10.1016/j.scitotenv.2009.11.018}, pmid = {20060570}, issn = {1879-1026}, mesh = {Animals ; Cadmium/analysis/toxicity ; Chlorpyrifos/analysis/toxicity ; Copper/analysis/toxicity ; Denmark ; Ecosystem ; Environmental Exposure/analysis/statistics & numerical data ; Environmental Monitoring/*methods ; Environmental Pollutants/*analysis ; Environmental Pollution/statistics & numerical data ; Geographic Information Systems ; Geography ; Insecticides/*analysis/toxicity ; Metals/*analysis/toxicity ; Nickel/analysis/toxicity ; Risk Assessment/methods ; Risk Factors ; Zinc/analysis/toxicity ; }, abstract = {Ecological risk and vulnerability maps can be used to improve the analysis of pollutant risks and communication to stakeholders. Often, such maps are made for one pollutant at the time. We used the results of wildlife vulnerability analysis, a novel trait-based risk assessment approach, to map overall vulnerability of habitats in Denmark to various metals and one insecticide. These maps were combined with maps of estimated soil concentrations for the same compounds divided by their Maximum Permissible Concentrations. This combination yielded relative risk maps that can be used to assess where the highest risk conditions to wildlife from these individual pollutants in Denmark occur (hot spot identification). In order to show how cumulative risk maps can be made, the maps of the individual pollutants were combined assuming different mechanisms of joint toxicity: no addition, concentration addition, antagonism and synergism. The study demonstrated that with an accurate set of geographical and ecological data one can use the results of vulnerability analysis to make relevant ecological risk maps that show hot spot areas for risks of single or cumulative risks from soil pollutants.}, } @article {pmid20050907, year = {2010}, author = {Rausher, MD and McPeek, MA and Moore, AJ and Rieseberg, L and Whitlock, MC}, title = {Data archiving.}, journal = {Evolution; international journal of organic evolution}, volume = {64}, number = {3}, pages = {603-604}, doi = {10.1111/j.1558-5646.2009.00940.x}, pmid = {20050907}, issn = {1558-5646}, mesh = {*Archives ; Biological Evolution ; *Databases, Factual ; Ecology ; Publishing ; }, } @article {pmid20049244, year = {2009}, author = {Arboleda, S and Jaramillo-O, N and Peterson, AT}, title = {Mapping environmental dimensions of dengue fever transmission risk in the Aburrá Valley, Colombia.}, journal = {International journal of environmental research and public health}, volume = {6}, number = {12}, pages = {3040-3055}, pmid = {20049244}, issn = {1660-4601}, mesh = {Algorithms ; Colombia/epidemiology ; Demography ; Dengue/epidemiology/*transmission ; Densovirinae ; *Geographic Information Systems ; Humans ; Models, Statistical ; Models, Theoretical ; Risk Assessment ; Risk Factors ; Topography, Medical ; }, abstract = {Dengue fever (DF) is endemic in Medellín, the second largest Colombian city, and surrounding municipalities. We used DF case and satellite environmental data to investigate conditions associated with suitable areas for DF occurrence in 2008 in three municipalities (Bello, Medellín and Itagüí). We develop spatially stratified tests of ecological niche models, and found generally good predictive ability, with all model tests yielding results significantly better than random expectations. We concluded that Bello and Medellín present ecological conditions somewhat different from, and more suitable for DF than, those of Itagüí. We suggest that areas predicted by our models as suitable for DF could be considered as at-risk, and could be used to guide campaigns for DF prevention in these municipalities.}, } @article {pmid20049243, year = {2009}, author = {Yang, X and Ma, H}, title = {Natural environment suitability of China and its relationship with population distributions.}, journal = {International journal of environmental research and public health}, volume = {6}, number = {12}, pages = {3025-3039}, pmid = {20049243}, issn = {1660-4601}, mesh = {China ; Conservation of Natural Resources/*statistics & numerical data ; Demography ; Geographic Information Systems ; Gross Domestic Product/statistics & numerical data ; Humans ; Models, Statistical ; Models, Theoretical ; *Population Growth ; Statistics as Topic ; }, abstract = {The natural environment factor is one of the main indexes for evaluating human habitats, sustained economic growth and ecological health status. Based on Geographic Information System (GIS) technology and an analytic hierarchy process method, this article presents the construction of the Natural Environment Suitability Index (NESI) model of China by using natural environment data including climate, hydrology, surface configuration and ecological conditions. The NESI value is calculated in grids of 1 km by 1 km through ArcGIS. The spatial regularity of NESI is analyzed according to its spatial distribution and proportional structure. The relationship of NESI with population distribution and economic growth is also discussed by analyzing NESI results with population distribution data and GDP data in 1 km by 1 km grids. The study shows that: (1) the value of NESI is higher in the East and lower in the West in China; The best natural environment area is the Yangtze River Delta region and the worst are the northwest of Tibet and southwest of Xinjiang. (2) There is a close correlation among natural environment, population distribution and economic growth; the best natural environment area, the Yangtze River Delta region, is also the region with higher population density and richer economy. The worst natural environment areas, Northwest and Tibetan Plateau, are also regions with lower population density and poorer economies.}, } @article {pmid21452522, year = {2010}, author = {Lonc, E and Rydzanicz, K and Jawień, P}, title = {[Ecological aspects of mosquito biocontrol with implementation of GPS/GIS].}, journal = {Wiadomosci parazytologiczne}, volume = {56}, number = {4}, pages = {297-303}, pmid = {21452522}, issn = {0043-5163}, mesh = {Animals ; Culicidae ; *Geographic Information Systems ; Mosquito Control/*methods ; Pest Control, Biological/*methods ; Poland ; }, abstract = {Mosquitoes bionomics and vector role as well as integrated control methods with GPS/GIS techniques were presented. Special attention was put on GIS which enables analysis of biological and environmental data generated by GPS (Global Positioning System). Combined with data from surveillance and management activities, those techniques provide a powerful tool for the precise analysis of mosquito development, breeding sites, and effective biocontrol effects on maps.}, } @article {pmid20040079, year = {2009}, author = {Heinz, E and Tischler, P and Rattei, T and Myers, G and Wagner, M and Horn, M}, title = {Comprehensive in silico prediction and analysis of chlamydial outer membrane proteins reflects evolution and life style of the Chlamydiae.}, journal = {BMC genomics}, volume = {10}, number = {}, pages = {634}, pmid = {20040079}, issn = {1471-2164}, mesh = {Bacterial Outer Membrane Proteins/genetics/*metabolism ; Chlamydia/classification/genetics/*metabolism/physiology ; Chlamydia muridarum/classification/genetics/metabolism/physiology ; Chlamydia trachomatis/classification/genetics/metabolism/physiology ; Computational Biology/*methods ; *Evolution, Molecular ; Lipoproteins/genetics/*metabolism ; Software ; }, abstract = {BACKGROUND: Chlamydiae are obligate intracellular bacteria comprising some of the most important bacterial pathogens of animals and humans. Although chlamydial outer membrane proteins play a key role for attachment to and entry into host cells, only few have been described so far. We developed a comprehensive, multiphasic in silico approach, including the calculation of clusters of orthologues, to predict outer membrane proteins using conservative criteria. We tested this approach using Escherichia coli (positive control) and Bacillus subtilis (negative control), and applied it to five chlamydial species; Chlamydia trachomatis, Chlamydia muridarum, Chlamydia (a.k.a. Chlamydophila) pneumoniae, Chlamydia (a.k.a. Chlamydophila) caviae, and Protochlamydia amoebophila.

RESULTS: In total, 312 chlamydial outer membrane proteins and lipoproteins in 88 orthologous clusters were identified, including 238 proteins not previously recognized to be located in the outer membrane. Analysis of their taxonomic distribution revealed an evolutionary conservation among Chlamydiae, Verrucomicrobia, Lentisphaerae and Planctomycetes as well as lifestyle-dependent conservation of the chlamydial outer membrane protein composition.

CONCLUSION: This analysis suggested a correlation between the outer membrane protein composition and the host range of chlamydiae and revealed a common set of outer membrane proteins shared by these intracellular bacteria. The collection of predicted chlamydial outer membrane proteins is available at the online database pCOMP http://www.microbial-ecology.net/pcomp and might provide future guidance in the quest for anti-chlamydial vaccines.}, } @article {pmid20038629, year = {2010}, author = {Wang, PP and Ruvinsky, I}, title = {Computational prediction of Caenorhabditis box H/ACA snoRNAs using genomic properties of their host genes.}, journal = {RNA (New York, N.Y.)}, volume = {16}, number = {2}, pages = {290-298}, pmid = {20038629}, issn = {1469-9001}, mesh = {Algorithms ; Animals ; Bayes Theorem ; Caenorhabditis/*genetics ; Caenorhabditis elegans/genetics ; Computational Biology ; Genome, Helminth ; Introns ; Operon ; Phylogeny ; RNA Splice Sites ; RNA, Helminth/classification/*genetics ; RNA, Small Nucleolar/classification/*genetics ; Species Specificity ; }, abstract = {Identification of small nucleolar RNAs (snoRNAs) in genomic sequences has been challenging due to the relative paucity of sequence features. Many current prediction algorithms rely on detection of snoRNA motifs complementary to target sites in snRNAs and rRNAs. However, recent discovery of snoRNAs without apparent targets requires development of alternative prediction methods. We present an approach that combines rule-based filters and a Bayesian Classifier to identify a class of snoRNAs (H/ACA) without requiring target sequence information. It takes advantage of unique attributes of their genomic organization and improved species-specific motif characterization to predict snoRNAs that may otherwise be difficult to discover. Searches in the genomes of Caenorhabditis elegans and the closely related Caenorhabditis briggsae suggest that our method performs well compared to recent benchmark algorithms. Our results illustrate the benefits of training gene discovery engines on features restricted to particular phylogenetic groups and the utility of incorporating diverse data types in gene prediction.}, } @article {pmid20034392, year = {2009}, author = {Papanicolaou, A and Stierli, R and Ffrench-Constant, RH and Heckel, DG}, title = {Next generation transcriptomes for next generation genomes using est2assembly.}, journal = {BMC bioinformatics}, volume = {10}, number = {}, pages = {447}, pmid = {20034392}, issn = {1471-2105}, support = {BB/E011845/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; Databases, Genetic ; Drosophila ; *Expressed Sequence Tags ; Gene Expression Profiling/*methods ; *Genome ; Genomics/*methods ; Sequence Analysis, DNA/methods ; }, abstract = {BACKGROUND: The decreasing costs of capillary-based Sanger sequencing and next generation technologies, such as 454 pyrosequencing, have prompted an explosion of transcriptome projects in non-model species, where even shallow sequencing of transcriptomes can now be used to examine a range of research questions. This rapid growth in data has outstripped the ability of researchers working on non-model species to analyze and mine transcriptome data efficiently.

RESULTS: Here we present a semi-automated platform 'est2assembly' that processes raw sequence data from Sanger or 454 sequencing into a hybrid de-novo assembly, annotates it and produces GMOD compatible output, including a SeqFeature database suitable for GBrowse. Users are able to parameterize assembler variables, judge assembly quality and determine the optimal assembly for their specific needs. We used est2assembly to process Drosophila and Bicyclus public Sanger EST data and then compared them to published 454 data as well as eight new insect transcriptome collections.

CONCLUSIONS: Analysis of such a wide variety of data allows us to understand how these new technologies can assist EST project design. We determine that assembler parameterization is as essential as standardized methods to judge the output of ESTs projects. Further, even shallow sequencing using 454 produces sufficient data to be of wide use to the community. est2assembly is an important tool to assist manual curation for gene models, an important resource in their own right but especially for species which are due to acquire a genome project using Next Generation Sequencing.}, } @article {pmid20033686, year = {2010}, author = {Volk, M and Lautenbach, S and van Delden, H and Newham, LT and Seppelt, R}, title = {How can we make progress with decision support systems in landscape and river basin management? Lessons learned from a comparative analysis of four different decision support systems.}, journal = {Environmental management}, volume = {46}, number = {6}, pages = {834-849}, pmid = {20033686}, issn = {1432-1009}, mesh = {Conservation of Natural Resources/*methods ; Decision Making, Computer-Assisted ; *Decision Support Techniques ; Environment ; Environmental Policy ; Models, Theoretical ; Rivers ; Water Supply/analysis ; }, abstract = {This article analyses the benefits and shortcomings of the recently developed decision support systems (DSS) FLUMAGIS, Elbe-DSS, CatchMODS, and MedAction. The analysis elaborates on the following aspects: (i) application area/decision problem, (ii) stakeholder interaction/users involved, (iii) structure of DSS/model structure, (iv) usage of the DSS, and finally (v) most important shortcomings. On the basis of this analysis, we formulate four criteria that we consider essential for the successful use of DSS in landscape and river basin management. The criteria relate to (i) system quality, (ii) user support and user training, (iii) perceived usefulness and (iv) user satisfaction. We can show that the availability of tools and technologies for DSS in landscape and river basin management is good to excellent. However, our investigations indicate that several problems have to be tackled. First of all, data availability and homogenisation, uncertainty analysis and uncertainty propagation and problems with model integration require further attention. Furthermore, the appropriate and methodological stakeholder interaction and the definition of 'what end-users really need and want' have been documented as general shortcomings of all four examples of DSS. Thus, we propose an iterative development process that enables social learning of the different groups involved in the development process, because it is easier to design a DSS for a group of stakeholders who actively participate in an iterative process. We also identify two important lines of further development in DSS: the use of interactive visualization tools and the methodology of optimization to inform scenario elaboration and evaluate trade-offs among environmental measures and management alternatives.}, } @article {pmid20032004, year = {2010}, author = {Helsel, D}, title = {Much ado about next to nothing: incorporating nondetects in science.}, journal = {The Annals of occupational hygiene}, volume = {54}, number = {3}, pages = {257-262}, doi = {10.1093/annhyg/mep092}, pmid = {20032004}, issn = {1475-3162}, mesh = {Data Interpretation, Statistical ; Ecology/*statistics & numerical data ; Environmental Monitoring ; Environmental Pollutants/analysis ; Environmental Pollution/statistics & numerical data ; Humans ; Limit of Detection ; Statistics as Topic/*methods ; }, abstract = {A great many papers and one textbook have been published on the topic of how to incorporate 'nondetects', low-level values reported only as below a detection limit, into statistical analyses. This is of interest not only in occupational hygiene but also in environmental sciences and astronomy, among other fields. Here, the literature is reviewed from the earliest known publication on the topic >40 years ago and recommendations contrasted. I have tried to pull some unifying conclusions out of the mix, ending with four suggestions I believe all can agree on. See if you agree with me.}, } @article {pmid20029898, year = {2009}, author = {Georgescu, V and Soubeyrand, S and Kretzschmar, A and Laine, AL}, title = {Exploring spatial and multitype assemblages of species abundances.}, journal = {Biometrical journal. Biometrische Zeitschrift}, volume = {51}, number = {6}, pages = {979-995}, doi = {10.1002/bimj.200900055}, pmid = {20029898}, issn = {1521-4036}, mesh = {Biometry/*methods ; Computer Simulation ; *Data Interpretation, Statistical ; *Ecosystem ; *Models, Biological ; *Population Dynamics ; *Species Specificity ; }, abstract = {The ecological theory of the existence of multiple stable states between species, or the spatial heterogeneity of some unobserved environmental factor, supports the idea of multitype interactions between species. These multitype interactions can lead to different assemblages of species abundances. An exploratory tool for the detection of these species assemblages and for their spatial analysis is presented in this article. A two-stage analysis is proposed. First, a classification into types of species assemblages using only the species abundances at each site, regardless of their spatial location, is performed. The clustering procedure is based on multivariate normal mixtures and provides a measure of the classification uncertainty. Second, some tools for the study of the spatial structure of these types of assemblages are presented. We transfer the classification uncertainty to the spatial analysis of the classes in order to draw more accurate conclusions. This classification and spatial analysis method is used to point out a spatial gradient of infection in a host-pathogen system in the Aland Islands in Finland. It can be a useful preliminary tool for ecological studies involving the spatial distributions of several species.}, } @article {pmid20028030, year = {2010}, author = {Nakamura, K and Tachikawa, Y and Ohno, O and Kitamura, M and Suganuma, M and Uemura, D}, title = {Neocomplanines A and B, a complanine family isolated from the marine fireworm.}, journal = {Journal of natural products}, volume = {73}, number = {3}, pages = {303-305}, doi = {10.1021/np900694j}, pmid = {20028030}, issn = {1520-6025}, mesh = {Alkenes/chemistry ; Animals ; Marine Biology ; Molecular Structure ; Polychaeta/*chemistry ; Protein Kinase C/*drug effects/metabolism ; Quaternary Ammonium Compounds/chemistry/*isolation & purification ; }, abstract = {Two new members of the complanine family, neocomplanines A (2) and B (3), were isolated as minor components of the methanolic extract of the "marine fireworm" Eurythoe complanata. The structures of the neocomplanines were revealed spectroscopically to be a trimethylammonium unit with a saturated carbon chain. The planar structures of neocomplanines A and B were confirmed successfully through total syntheses that used epichlorohydrin as a starting material. The neocomplanines show inflammatory activity and also enhanced PKC activity in combination with TPA in the presence of Ca(2+) in vitro; both are similar to the effects of complanine (1). The molecular mechanism of the effects of complanine-related compounds is discussed.}, } @article {pmid20027645, year = {2010}, author = {Cozzi, B and Panin, M and Butti, C and Podestà, M and Zotti, A}, title = {Bone density distribution patterns in the rostrum of delphinids and beaked whales: evidence of family-specific evolutive traits.}, journal = {Anatomical record (Hoboken, N.J. : 2007)}, volume = {293}, number = {2}, pages = {235-242}, doi = {10.1002/ar.21044}, pmid = {20027645}, issn = {1932-8494}, mesh = {Absorptiometry, Photon/statistics & numerical data ; Animals ; Biological Evolution ; *Bone Density/genetics ; Cartilage/*anatomy & histology/diagnostic imaging ; Data Interpretation, Statistical ; Dolphins/*anatomy & histology/genetics ; Facial Bones/*anatomy & histology/diagnostic imaging ; Inheritance Patterns ; Species Specificity ; Whales/*anatomy & histology/genetics ; }, abstract = {Toothed whales have undergone a profound telescopic rearrangement of the skull, with elongation of facial bones and formation of a hollow rostrum, filled in vivo by the mesorostral cartilage. In most species of the family Ziphiidae, this latter cartilage becomes secondarily ossified, producing in some cases the densest bone existing in nature. Starting from this observation, we wanted to investigate the patterns of distribution of bone mineral density (BMD) in the rostrum of two families of toothed whales with different ecological and behavioral traits: Delphinidae and Ziphiidae. We analyzed BMD non invasively by means of the dual energy X-ray absorptiometry technology, and found two different density distribution patterns that distinctly set the two families apart. Namely, BMD values decrease from the proximal to the distal region of the rostrum in delphinids, whereas the beaked whales show a BMD peak in the central region. Possible functions such as ballast or protection against clashes might be likely, although more data about the species of both families is needed to give better evidence.}, } @article {pmid20025988, year = {2010}, author = {Zhang, Z and Townsend, JP}, title = {The filamentous fungal gene expression database (FFGED).}, journal = {Fungal genetics and biology : FG & B}, volume = {47}, number = {3}, pages = {199-204}, pmid = {20025988}, issn = {1096-0937}, support = {P01 GM068087-06/GM/NIGMS NIH HHS/United States ; P01 GM068087/GM/NIGMS NIH HHS/United States ; P01 GM068087-01A10001/GM/NIGMS NIH HHS/United States ; P01 GM068087-08/GM/NIGMS NIH HHS/United States ; P01 GM068087-07/GM/NIGMS NIH HHS/United States ; GM068087/GM/NIGMS NIH HHS/United States ; P01 GM068087-06S1/GM/NIGMS NIH HHS/United States ; }, mesh = {Algorithms ; Chromosome Mapping ; Computational Biology/methods ; Computer Graphics ; Database Management Systems ; *Databases, Genetic ; *Gene Expression ; Gene Expression Profiling/methods ; Gene Expression Regulation, Fungal ; *Genes, Fungal ; Genome, Fungal ; Internet ; Models, Genetic ; Models, Statistical ; Oligonucleotide Array Sequence Analysis/methods ; Saccharomyces cerevisiae/genetics ; Sequence Alignment ; Software ; Systems Integration ; User-Computer Interface ; }, abstract = {Filamentous fungal gene expression assays provide essential information for understanding systemic cellular regulation. To aid research on fungal gene expression, we constructed a novel, comprehensive, free database, the filamentous fungal gene expression database (FFGED), available at http://bioinfo.townsend.yale.edu. FFGED features user-friendly management of gene expression data, which are assorted into experimental metadata, experimental design, raw data, normalized details, and analysis results. Data may be submitted in the process of an experiment, and any user can submit multiple experiments, thus classifying the FFGED as an "active experiment" database. Most importantly, FFGED functions as a collective and collaborative platform, by connecting each experiment with similar related experiments made public by other users, maximizing data sharing among different users, and correlating diverse gene expression levels under multiple experimental designs within different experiments. A clear and efficient web interface is provided with enhancement by AJAX (Asynchronous JavaScript and XML) and through a collection of tools to effectively facilitate data submission, sharing, retrieval and visualization.}, } @article {pmid20024654, year = {2010}, author = {Wolfslehner, B and Seidl, R}, title = {Harnessing ecosystem models and multi-criteria decision analysis for the support of forest management.}, journal = {Environmental management}, volume = {46}, number = {6}, pages = {850-861}, pmid = {20024654}, issn = {1432-1009}, mesh = {Biodiversity ; *Decision Support Techniques ; Ecosystem ; Forestry/*methods ; Information Management ; *Models, Biological ; Weights and Measures ; }, abstract = {The decision-making environment in forest management (FM) has changed drastically during the last decades. Forest management planning is facing increasing complexity due to a widening portfolio of forest goods and services, a societal demand for a rational, transparent decision process and rising uncertainties concerning future environmental conditions (e.g., climate change). Methodological responses to these challenges include an intensified use of ecosystem models to provide an enriched, quantitative information base for FM planning. Furthermore, multi-criteria methods are increasingly used to amalgamate information, preferences, expert judgments and value expressions, in support of the participatory and communicative dimensions of modern forestry. Although the potential of combining these two approaches has been demonstrated in a number of studies, methodological aspects in interfacing forest ecosystem models (FEM) and multi-criteria decision analysis (MCDA) are scarcely addressed explicitly. In this contribution we review the state of the art in FEM and MCDA in the context of FM planning and highlight some of the crucial issues when combining ecosystem and preference modeling. We discuss issues and requirements in selecting approaches suitable for supporting FM planning problems from the growing body of FEM and MCDA concepts. We furthermore identify two major challenges in a harmonized application of FEM-MCDA: (i) the design and implementation of an indicator-based analysis framework capturing ecological and social aspects and their interactions relevant for the decision process, and (ii) holistic information management that supports consistent use of different information sources, provides meta-information as well as information on uncertainties throughout the planning process.}, } @article {pmid20021585, year = {2009}, author = {Greenhalgh, T and Potts, HW and Wong, G and Bark, P and Swinglehurst, D}, title = {Tensions and paradoxes in electronic patient record research: a systematic literature review using the meta-narrative method.}, journal = {The Milbank quarterly}, volume = {87}, number = {4}, pages = {729-788}, pmid = {20021585}, issn = {1468-0009}, support = {RDA/03/07/076/DH_/Department of Health/United Kingdom ; 07/133/MRC_/Medical Research Council/United Kingdom ; CFHEP 002/DH_/Department of Health/United Kingdom ; CFHEP 007/DH_/Department of Health/United Kingdom ; }, mesh = {Access to Information ; *Diffusion of Innovation ; England ; *Health Services Research ; Hospital Information Systems/organization & administration ; Humans ; MEDLINE ; Medical Records Systems, Computerized/*organization & administration ; Risk Factors ; }, abstract = {CONTEXT: The extensive research literature on electronic patient records (EPRs) presents challenges to systematic reviewers because it covers multiple research traditions with different underlying philosophical assumptions and methodological approaches.

METHODS: Using the meta-narrative method and searching beyond the Medline-indexed literature, this review used "conflicting" findings to address higher-order questions about how researchers had differently conceptualized and studied the EPR and its implementation.

FINDINGS: Twenty-four previous systematic reviews and ninety-four further primary studies were considered. Key tensions in the literature centered on (1) the EPR ("container" or "itinerary"); (2) the EPR user ("information-processer" or "member of socio-technical network"); (3) organizational context ("the setting within which the EPR is implemented" or "the EPR-in-use"); (4) clinical work ("decision making" or "situated practice"); (5) the process of change ("the logic of determinism" or "the logic of opposition"); (6) implementation success ("objectively defined" or "socially negotiated"); and (7) complexity and scale ("the bigger the better" or "small is beautiful").

CONCLUSIONS: The findings suggest that EPR use will always require human input to recontextualize knowledge; that even though secondary work (audit, research, billing) may be made more efficient by the EPR, primary clinical work may be made less efficient; that paper may offer a unique degree of ecological flexibility; and that smaller EPR systems may sometimes be more efficient and effective than larger ones. We suggest an agenda for further research.}, } @article {pmid20018774, year = {2009}, author = {Cohen, JE and Schittler, DN and Raffaelli, DG and Reuman, DC}, title = {Food webs are more than the sum of their tritrophic parts.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {106}, number = {52}, pages = {22335-22340}, pmid = {20018774}, issn = {1091-6490}, mesh = {Animals ; Body Size ; Databases, Factual ; Ecosystem ; *Food Chain ; Fresh Water ; Marine Biology ; Michigan ; Models, Biological ; Population Density ; Scotland ; Seawater ; }, abstract = {Many studies have aimed to understand food webs by investigating components such as trophic links (one consumer taxon eats one resource taxon), tritrophic interactions (one consumer eats an intermediate taxon, which eats a resource), or longer chains of links. We show here that none of these components (links, tritrophic interactions, and longer chains), individually or as an ensemble, accounts fully for the properties of the next higher level of organization. As a cell is more than its molecules, as an organ is more than its cells, and as an organism is more than its organs, in a food web, new structure emerges at every organizational level up to and including the whole web. We demonstrate the emergence of properties at progressively higher levels of structure by using all of the directly observed, appropriately organized, publicly available food web datasets with relatively complete trophic link data and with average body mass and population density data for each taxon. There are only three such webs, those of Tuesday Lake, Michigan, in 1984 and 1986, and Ythan Estuary, Scotland. We make the data freely available online with this report. Differences in web patterns between Tuesday Lake and Ythan Estuary, and similarities of Tuesday Lake in 1984 and 1986 despite 50% turnover of species, suggest that the patterns we describe respond to major differences between ecosystem types.}, } @article {pmid20018454, year = {2010}, author = {Vocht, Fd and Burstyn, I}, title = {Historical "evidence" that electrification caused the 20th century epidemic of diseases of civilization and the ecological fallacy.}, journal = {Medical hypotheses}, volume = {74}, number = {5}, pages = {957-958}, doi = {10.1016/j.mehy.2009.11.034}, pmid = {20018454}, issn = {1532-2777}, mesh = {Age Factors ; Causality ; Chronic Disease/*epidemiology ; *Civilization ; Data Interpretation, Statistical ; Electricity/*adverse effects/history ; History, 20th Century ; Humans ; Socioeconomic Factors ; United States/epidemiology ; }, } @article {pmid20016844, year = {2009}, author = {Holland, RA and Wikelski, M and Kümmeth, F and Bosque, C}, title = {The secret life of oilbirds: new insights into the movement ecology of a unique avian frugivore.}, journal = {PloS one}, volume = {4}, number = {12}, pages = {e8264}, pmid = {20016844}, issn = {1932-6203}, mesh = {Animal Migration/*physiology ; Animals ; Birds/*physiology ; *Ecological and Environmental Phenomena ; Ecosystem ; Feeding Behavior/*physiology ; Flight, Animal/physiology ; *Fruit ; Geographic Information Systems ; Nesting Behavior/physiology ; }, abstract = {BACKGROUND: Steatornis caripensis (the oilbird) is a very unusual bird. It supposedly never sees daylight, roosting in huge aggregations in caves during the day and bringing back fruit to the cave at night. As a consequence a large number of the seeds from the fruit they feed upon germinate in the cave and spoil.

Here we use newly developed GPS/acceleration loggers with remote UHF readout to show that several assumptions about the behaviour of Steatornis caripensis need to be revised. On average, they spend only every 3(rd) day in a cave, individuals spent most days sitting quietly in trees in the rainforest where they regurgitate seeds.

CONCLUSIONS/SIGNIFICANCE: This provides new data on the extent of seed dispersal and the movement ecology of Steatornis caripensis. It suggests that Steatornis caripensis is perhaps the most important long-distance seed disperser in Neotropical forests. We also show that colony-living comes with high activity costs to individuals.}, } @article {pmid20015547, year = {2010}, author = {Leroy, D and Haubruge, E and De Pauw, E and Thomé, JP and Francis, F}, title = {Development of ecotoxicoproteomics on the freshwater amphipod Gammarus pulex: identification of PCB biomarkers in glycolysis and glutamate pathways.}, journal = {Ecotoxicology and environmental safety}, volume = {73}, number = {3}, pages = {343-352}, doi = {10.1016/j.ecoenv.2009.11.006}, pmid = {20015547}, issn = {1090-2414}, mesh = {Amphipoda/chemistry/*drug effects/metabolism ; Animals ; Arginine Kinase/metabolism ; Biomarkers/metabolism ; Chromatography, Gas ; Databases, Protein ; *Ecosystem ; Electrophoresis, Polyacrylamide Gel ; Fresh Water/chemistry ; Glutamates/metabolism ; Glyceraldehyde-3-Phosphate Dehydrogenases/metabolism ; Glycolysis/physiology ; Longevity/drug effects ; Phosphopyruvate Hydratase/metabolism ; Polychlorinated Biphenyls/*metabolism/toxicity ; Protein Array Analysis ; Proteomics/*methods ; Water Pollutants, Chemical/*metabolism/toxicity ; }, abstract = {PCBs are persistent organic pollutants largely distributed in the biosphere. Although their effects on vertebrates are well described, little is known about their action on freshwater invertebrate's metabolism. Gammarus pulex (Linné) was selected as an indicator model to develop a proteomic approach in order to characterize the effects of PCBs on the protein profile of this freshwater crustacean. Sublethal coplanar PCBs exposition and related 2D gel were performed. More than 560 spots were detected and a total of 21 proteins exhibiting significant expression differences in PCB exposed to G. pulex were identified by mass spectrometry. Database searches were conducted to relate the results to well-known metabolic pathways (pentose phosphate, cytoskeleton, energy, etc.). In particular, glyceraldehyde 3-phosphate dehydrogenase and arginine kinase were found to be sensitive to the PCB exposition of G. pulex. The aim of the present study was to assess the biochemical responses and the metabolic changes in G. pulex following intoxication to coplanar PCB congeners CB77 and CB169 by a proteomic approach. This approach allowed us, by the identification of key proteins, to highlight important biochemical mechanisms disturbed by the presence of these contaminants in G. pulex.}, } @article {pmid20014586, year = {2009}, author = {Gardner, JB and Drinkwater, LE}, title = {The fate of nitrogen in grain cropping systems: a meta-analysis of 15N field experiments.}, journal = {Ecological applications : a publication of the Ecological Society of America}, volume = {19}, number = {8}, pages = {2167-2184}, doi = {10.1890/08-1122.1}, pmid = {20014586}, issn = {1051-0761}, mesh = {*Agriculture ; Climate ; Databases, Factual ; Ecosystem ; Edible Grain/*growth & development/*metabolism ; Environmental Monitoring/*methods ; Fertilizers ; Nitrogen/*metabolism ; Nitrogen Isotopes ; }, abstract = {Intensively managed grain farms are saturated with large inputs of nitrogen (N) fertilizer, leading to N losses and environmental degradation. Despite decades of research directed toward reducing N losses from agroecosystems, progress has been minimal, and the currently promoted best management practices are not necessarily the most effective. We investigated the fate of N additions to temperate grain agroecosystems using a meta-analysis of 217 field-scale studies that followed the stable isotope 15N in crops and soil. We compared management practices that alter inorganic fertilizer additions, such as application timing or reduced N fertilizer rates, to practices that re-couple the biogeochemical cycles of carbon (C) and N, such as organic N sources and diversified crop rotations, and analyzed the following response variables: 15N recovery in crops, total recovery of 15N in crops and soil, and crop yield. More of the literature (94%) emphasized crop recovery of 15N than total 15N recovery in crops and soil (58%), though total recovery is a more ecologically appropriate indicator for assessing N losses. Findings show wide differences in the ability of management practices to improve N use efficiency. Practices that aimed to increase crop uptake of commercial fertilizer had a lower impact on total 15N recovery (3-21% increase) than practices that re-coupled C and N cycling (30-42% increase). A majority of studies (66%) were only one growing season long, which poses a particular problem when organic N sources are used because crops recover N from these sources over several years. These short-term studies neglect significant ecological processes that occur over longer time scales. Field-scale mass balance calculations using the 15N data set show that, on average, 43 kg N x ha(-1) x yr(-1) was unaccounted for at the end of one growing season out of 114 kg N x ha(-1) x yr(-1), representing approximately 38% of the total 15N applied. This comprehensive assessment of stable-isotope research on agroecosystem N management can inform the development of policies to mitigate nonpoint source pollution. Nitrogen management practices that most effectively increase N retention are not currently being promoted and are rare on the landscape in the United States.}, } @article {pmid20011594, year = {2009}, author = {Schloss, PD}, title = {A high-throughput DNA sequence aligner for microbial ecology studies.}, journal = {PloS one}, volume = {4}, number = {12}, pages = {e8230}, pmid = {20011594}, issn = {1932-6203}, mesh = {Algorithms ; Bacteria/*genetics ; Base Sequence ; Databases, Nucleic Acid ; *Ecological and Environmental Phenomena ; High-Throughput Screening Assays/*instrumentation ; Molecular Sequence Data ; Sequence Alignment/*instrumentation ; Sequence Analysis, DNA/*instrumentation ; }, abstract = {As the scope of microbial surveys expands with the parallel growth in sequencing capacity, a significant bottleneck in data analysis is the ability to generate a biologically meaningful multiple sequence alignment. The most commonly used aligners have varying alignment quality and speed, tend to depend on a specific reference alignment, or lack a complete description of the underlying algorithm. The purpose of this study was to create and validate an aligner with the goal of quickly generating a high quality alignment and having the flexibility to use any reference alignment. Using the simple nearest alignment space termination algorithm, the resulting aligner operates in linear time, requires a small memory footprint, and generates a high quality alignment. In addition, the alignments generated for variable regions were of as high a quality as the alignment of full-length sequences. As implemented, the method was able to align 18 full-length 16S rRNA gene sequences and 58 V2 region sequences per second to the 50,000-column SILVA reference alignment. Most importantly, the resulting alignments were of a quality equal to SILVA-generated alignments. The aligner described in this study will enable scientists to rapidly generate robust multiple sequences alignments that are implicitly based upon the predicted secondary structure of the 16S rRNA molecule. Furthermore, because the implementation is not connected to a specific database it is easy to generalize the method to reference alignments for any DNA sequence.}, } @article {pmid20011052, year = {2009}, author = {Kolaczkowski, B and Thornton, JW}, title = {Long-branch attraction bias and inconsistency in Bayesian phylogenetics.}, journal = {PloS one}, volume = {4}, number = {12}, pages = {e7891}, pmid = {20011052}, issn = {1932-6203}, support = {R01 GM062351/GM/NIGMS NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; R01-GM62351/GM/NIGMS NIH HHS/United States ; }, mesh = {Bayes Theorem ; Bias ; Computer Simulation ; Databases, Genetic ; Humans ; Likelihood Functions ; Models, Genetic ; *Phylogeny ; }, abstract = {Bayesian inference (BI) of phylogenetic relationships uses the same probabilistic models of evolution as its precursor maximum likelihood (ML), so BI has generally been assumed to share ML's desirable statistical properties, such as largely unbiased inference of topology given an accurate model and increasingly reliable inferences as the amount of data increases. Here we show that BI, unlike ML, is biased in favor of topologies that group long branches together, even when the true model and prior distributions of evolutionary parameters over a group of phylogenies are known. Using experimental simulation studies and numerical and mathematical analyses, we show that this bias becomes more severe as more data are analyzed, causing BI to infer an incorrect tree as the maximum a posteriori phylogeny with asymptotically high support as sequence length approaches infinity. BI's long branch attraction bias is relatively weak when the true model is simple but becomes pronounced when sequence sites evolve heterogeneously, even when this complexity is incorporated in the model. This bias--which is apparent under both controlled simulation conditions and in analyses of empirical sequence data--also makes BI less efficient and less robust to the use of an incorrect evolutionary model than ML. Surprisingly, BI's bias is caused by one of the method's stated advantages--that it incorporates uncertainty about branch lengths by integrating over a distribution of possible values instead of estimating them from the data, as ML does. Our findings suggest that trees inferred using BI should be interpreted with caution and that ML may be a more reliable framework for modern phylogenetic analysis.}, } @article {pmid20007768, year = {2010}, author = {Scheckenbach, F and Hausmann, K and Wylezich, C and Weitere, M and Arndt, H}, title = {Large-scale patterns in biodiversity of microbial eukaryotes from the abyssal sea floor.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {107}, number = {1}, pages = {115-120}, pmid = {20007768}, issn = {1091-6490}, mesh = {Animals ; *Biodiversity ; Databases, Factual ; *Ecosystem ; *Environment ; *Eukaryota/classification/genetics ; Genetic Variation ; Likelihood Functions ; Molecular Sequence Data ; Oceans and Seas ; Parasites/classification/genetics ; Phylogeny ; Population Density ; }, abstract = {Eukaryotic microbial life at abyssal depths remains "uncharted territory" in eukaryotic microbiology. No phylogenetic surveys have focused on the largest benthic environment on this planet, the abyssal plains. Moreover, knowledge of the spatial patterns of deep-sea community structure is scanty, and what little is known originates primarily from morphology-based studies of foraminiferans. Here we report on the great phylogenetic diversity of microbial eukaryotic communities of all 3 abyssal plains of the southeastern Atlantic Ocean--the Angola, Cape, and Guinea Abyssal Plains--from depths of 5,000 m. A high percentage of retrieved clones had no close representatives in genetic databases. Many clones were affiliated with parasitic species. Furthermore, differences between the communities of the Cape Abyssal Plain and the other 2 abyssal plains point to environmental gradients apparently shaping community structure at the landscape level. On a regional scale, local species diversity showed much less variation. Our study provides insight into the community composition of microbial eukaryotes on larger scales from the wide abyssal sea floor realm and marks a direction for more detailed future studies aimed at improving our understanding of deep-sea microbes at the community and ecosystem levels, as well as the ecological principles at play.}, } @article {pmid20007739, year = {2010}, author = {Horton, M and Bodenhausen, N and Bergelson, J}, title = {MARTA: a suite of Java-based tools for assigning taxonomic status to DNA sequences.}, journal = {Bioinformatics (Oxford, England)}, volume = {26}, number = {4}, pages = {568-569}, doi = {10.1093/bioinformatics/btp682}, pmid = {20007739}, issn = {1367-4811}, mesh = {Base Sequence/*genetics ; Databases, Genetic ; Genomics/*methods ; *Programming Languages ; *Software ; }, abstract = {We have created a suite of Java-based software to better provide taxonomic assignments to DNA sequences. We anticipate that the program will be useful for protistologists, virologists, mycologists and other microbial ecologists. The program relies on NCBI utilities including the BLAST software and Taxonomy database and is easily manipulated at the command-line to specify a BLAST candidate's query-coverage or percent identity requirements; other options include the ability to set minimal consensus requirements (%) for each of the eight major taxonomic ranks (Domain, Kingdom, Phylum, ...) and whether to consider lower scoring candidates when the top-hit lacks taxonomic classification.}, } @article {pmid20001097, year = {2010}, author = {Maloney, J and Newsome, A and Huang, J and Kirby, J and Kranz, M and Wateska, A and Dunlap, B and Yabsley, MJ and Dunn, JR and Jones, TF and Moncayo, AC}, title = {Seroprevalence of Trypanosoma cruzi in raccoons from Tennessee.}, journal = {The Journal of parasitology}, volume = {96}, number = {2}, pages = {353-358}, doi = {10.1645/GE-2312.1}, pmid = {20001097}, issn = {1937-2345}, mesh = {Age Factors ; Animals ; Antibodies, Protozoan/*blood ; Chagas Disease/epidemiology/*veterinary ; Ecosystem ; Female ; Fluorescent Antibody Technique, Indirect/veterinary ; Geographic Information Systems ; Male ; Raccoons/*parasitology ; Rural Health ; Seroepidemiologic Studies ; Sex Factors ; Suburban Health ; Tennessee/epidemiology ; Trypanosoma cruzi/*immunology ; }, abstract = {Trypanosoma cruzi is the etiologic agent of Chagas' disease. Autochthonous human and canine transmission of T. cruzi has been documented in Tennessee, but little is known about its ecology, including the prevalence of T. cruzi among wildlife in Tennessee. Serum samples from 706 raccoons (Procyon lotor) from 10 counties in the Ridge and Valley and Blue Ridge Mountains ecoregions of eastern Tennessee were tested for antibodies reactive with T. cruzi using the indirect fluorescent antibody assay. Two hundred six (29.2%) samples were seropositive, with 9 counties yielding positive samples (range 14.6-63.6%). Significantly more raccoons from rural habitats (35.1%) were found positive for T. cruzi exposure than were those from suburban habitats (23.1%, P < 0.001). Land cover class was not associated with seropositivity status (P = 0.441), even though deciduous forest was the most common site from where raccoons were trapped and the most common site of positive raccoons in rural areas (42%). Interestingly, age was positively associated with seropositivity. Raccoons older than 1 yr (adults) were 40.1% seropositive compared to 12.2% of those less than 1 yr (juveniles; P < 0.001). Female adults were significantly more likely to be exposed to T. cruzi than were male adult raccoons (P < 0.001). No significant seroprevalence difference was seen among male and female juveniles. This study contributes to understanding the dynamics of T. cruzi exposure within raccoon populations in Tennessee. The importance of habitat (rural vs. suburban) and microhabitat (dens) in risk of exposure to these populations is also discussed.}, } @article {pmid19967255, year = {2009}, author = {Barcellos, C and Acosta, LM and Lisboa, E and Bastos, FI}, title = {Surveillance of mother-to-child HIV transmission: socioeconomic and health care coverage indicators.}, journal = {Revista de saude publica}, volume = {43}, number = {6}, pages = {1006-1014}, doi = {10.1590/s0034-89102009005000070}, pmid = {19967255}, issn = {1518-8787}, support = {1D43TW05799/TW/FIC NIH HHS/United States ; }, mesh = {Brazil/epidemiology ; Cluster Analysis ; Female ; Geographic Information Systems ; HIV Infections/epidemiology/*transmission ; Health Services Accessibility/*statistics & numerical data ; *Health Status Indicators ; Humans ; Infant, Newborn ; Infectious Disease Transmission, Vertical/prevention & control/*statistics & numerical data ; Live Birth/epidemiology ; Poverty/statistics & numerical data ; Pregnancy ; Prenatal Care/statistics & numerical data ; Primary Health Care/*standards ; *Sentinel Surveillance ; Socioeconomic Factors ; Statistics, Nonparametric ; }, abstract = {OBJECTIVE: To identify clustering areas of infants exposed to HIV during pregnancy and their association with indicators of primary care coverage and socioeconomic condition.

METHODS: Ecological study where the unit of analysis was primary care coverage areas in the city of Porto Alegre, Southern Brazil, in 2003. Geographical Information System and spatial analysis tools were used to describe indicators of primary care coverage areas and socioeconomic condition, and estimate the prevalence of liveborn infants exposed to HIV during pregnancy and delivery. Data was obtained from Brazilian national databases. The association between different indicators was assessed using Spearman's nonparametric test.

RESULTS: There was found an association between HIV infection and high birth rates (r=0.22, p<0.01) and lack of prenatal care (r=0.15, p<0.05). The highest HIV infection rates were seen in areas with poor socioeconomic conditions and difficult access to health services (r=0.28, p<0.01). The association found between higher rate of prenatal care among HIV-infected women and adequate immunization coverage (r=0.35, p<0.01) indicates that early detection of HIV infection is effective in those areas with better primary care services.

CONCLUSIONS: Urban poverty is a strong determinant of mother-to-child HIV transmission but this trend can be fought with health surveillance at the primary care level.}, } @article {pmid19963957, year = {2009}, author = {Taffoni, F and Formica, D and Campolo, D and Keller, F and Guglielmelli, E}, title = {Block-box instrumented toy: a new platform for assessing spatial cognition in infants.}, journal = {Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference}, volume = {2009}, number = {}, pages = {210-213}, doi = {10.1109/IEMBS.2009.5333127}, pmid = {19963957}, issn = {2375-7477}, mesh = {Child Development ; Cognition/*physiology ; Diagnosis, Computer-Assisted/*instrumentation ; Equipment Design ; Equipment Failure Analysis ; Humans ; Infant ; Infant Behavior/*physiology ; Infant, Newborn ; Neuropsychological Tests ; *Play and Playthings ; Reproducibility of Results ; Sensitivity and Specificity ; Space Perception/*physiology ; Spatial Behavior/*physiology ; Transducers ; }, abstract = {This paper describes an interdisciplinary approach to the assessment on infants' behavior, with a focus on the technology. The goal is an objective, quantitative analysis of concurrent maturation of sensory, motor and cognitive abilities in young children, in relation to the achievement of developmental milestones. An instrumented block-box toy specifically developed to assess the ability to insert objects into holes is presented. The functional specifications are derived from experimental protocols devised by neuroscientists to assess spatial cognition skills. Technological choices are emphasized with respect to ecological requirements. An ad-hoc calibration procedure is also presented which is suitable to unstructured environments. Finally, preliminary tests carried out at a local day-care with 12-24 months old infants are presented which prove the in-field usability of the proposed technology.}, } @article {pmid19963310, year = {2010}, author = {Rainham, D and McDowell, I and Krewski, D and Sawada, M}, title = {Conceptualizing the healthscape: contributions of time geography, location technologies and spatial ecology to place and health research.}, journal = {Social science & medicine (1982)}, volume = {70}, number = {5}, pages = {668-676}, doi = {10.1016/j.socscimed.2009.10.035}, pmid = {19963310}, issn = {1873-5347}, mesh = {Environment ; Environment Design ; Geographic Information Systems ; *Geography ; Humans ; Interpersonal Relations ; *Models, Theoretical ; Movement ; *Sociology, Medical ; Time ; }, abstract = {Geomatics and related technologies allow for the application of integrated approaches to the analysis of individual spatial and temporal activities in the context of place and health research. The ability to track individuals as they make decisions and negotiate space may provide a fundamental advance. This paper introduces the need to move beyond conventional place-based perspectives in health research, and invokes the theoretical contributions of time geography and spatial ecology as opportunities to integrate human agency into contextual models of health. Issues around the geographical representation of place are reviewed, and the concept of the healthscape is introduced as an approach to operationalizing context as expressed by the spatial and temporal activities of individuals. We also discuss how these concepts have the potential to influence and contribute to empirical place and health research.}, } @article {pmid19962450, year = {2010}, author = {Ware, JL and Grimaldi, DA and Engel, MS}, title = {The effects of fossil placement and calibration on divergence times and rates: an example from the termites (Insecta: Isoptera).}, journal = {Arthropod structure & development}, volume = {39}, number = {2-3}, pages = {204-219}, doi = {10.1016/j.asd.2009.11.003}, pmid = {19962450}, issn = {1873-5495}, mesh = {Animals ; Biological Evolution ; Databases, Genetic ; *Fossils ; Isoptera/*classification/*genetics ; Models, Anatomic ; Models, Genetic ; Paleontology/methods ; Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA ; Time Factors ; }, abstract = {Among insects, eusocial behavior occurs in termites, ants, some bees and wasps. Isoptera and Hymenoptera convergently share social behavior, and for both taxa its evolution remains poorly understood. While dating analyses provide researchers with the opportunity to date the origin of eusociality, fossil calibration methodology may mislead subsequent ecological interpretations. Using a comprehensive termite dataset, we explored the effect of fossil placement and calibration methodology. A combined molecular and morphological dataset for 42 extant termite lineages was used, and a second dataset including these 42 taxa, plus an additional 39 fossil lineages for which we had only morphological data. MrBayes doublet-model analyses recovered similar topologies, with one minor exception (Stolotermitidae is sister to the Hodotermitidae, s.s., in the 42-taxon analysis but is in a polytomy with Hodotermitidae and (Kalotermitidae + Neoisoptera) in the 81-taxon analysis). Analyses using the r8s program on these topologies were run with either minimum/maximum constraints (analysis a = 42-taxon and analysis c = 81-taxon analyses) or with the fossil taxon ages fixed (ages fixed to be the geological age of the deposit from which they came, analysis b = 81-taxon analysis). Confidence intervals were determined for the resulting ultrametric trees, and for most major clades there was significant overlap between dates recovered for analyses A and C (with exceptions, such as the nodes Neoisoptera, and Euisoptera). With the exception of isopteran and eusiopteran node ages, however, none of the major clade ages overlapped when analysis B is compared with either analysis A or C. Future studies on Dictyoptera should note that the age of Kalotermitidae was underestimated in absence of kalotermitid fossils with fixed ages.}, } @article {pmid19960939, year = {2009}, author = {Meng, XC and Sun, CZ and Chen, SL and Xie, CX and Sun, H and Wang, XJ}, title = {[Study on suitability regionalization producing area of vulnerable species Acanthopanax senticosus based on TCMGIS].}, journal = {Zhong yao cai = Zhongyaocai = Journal of Chinese medicinal materials}, volume = {32}, number = {8}, pages = {1195-1198}, pmid = {19960939}, issn = {1001-4454}, mesh = {China ; Climate ; Conservation of Natural Resources ; Ecosystem ; Eleutherococcus/*growth & development ; *Geographic Information Systems ; Geography ; Plants, Medicinal/*growth & development ; Soil ; }, abstract = {OBJECTIVE: To determine the suitable regions of Acanthopanax senticosus and provide the basis for its resource census, reservation, wild nature and cultivation.

METHODS: The traditional Chinese medicine geographic information system (TCMGIS) was used to select the suitable producing areas.

RESULTS: The ecological environments of 269 counties in 11 province or directly governed city region were suitable for Acanthopanax senticosus. They were located in Xiaoxing'anling, Changbai Mountain, Daxing' anling, Yanshan Mountains, Taihang Mountains and Qinling, among which Heilongjiang accounted for 49.3% and Inner Mongolia reached 22.4%, Jilin reached 16.5%, Liaoning reached 4.3%, the total of Hebei, Beijing, Henan, Shanxi, Sichuan and Gansu was 7.4%.}, } @article {pmid19958050, year = {2010}, author = {Bruins, RJ and Munns, WR and Botti, SJ and Brink, S and Cleland, D and Kapustka, L and Lee, D and Luzadis, V and McCarthy, LF and Rana, N and Rideout, DB and Rollins, M and Woodbury, P and Zupko, M}, title = {A new process for organizing assessments of social, economic, and environmental outcomes: case study of wildland fire management in the USA.}, journal = {Integrated environmental assessment and management}, volume = {6}, number = {3}, pages = {469-483}, doi = {10.1897/IEAM_2009-075.1}, pmid = {19958050}, issn = {1551-3793}, mesh = {Decision Support Techniques ; Endpoint Determination ; *Environment ; Fires/*economics/prevention & control ; Goals ; Government Agencies ; Models, Theoretical ; Planning Techniques ; Problem Solving ; Risk Assessment ; *Societies ; Systems Integration ; United States ; }, abstract = {Ecological risk assessments typically are organized using the processes of planning (a discussion among managers, stakeholders, and analysts to clarify ecosystem management goals and assessment scope) and problem formulation (evaluation of existing information to generate hypotheses about adverse ecological effects, select assessment endpoints, and develop an analysis plan). These processes require modification to be applicable for integrated assessments that evaluate ecosystem management alternatives in terms of their ecological, economic, and social consequences.We present 8 questions that define the steps of a new process we term integrated problem formulation (IPF), and we illustrate the use of IPF through a retrospective case study comparing 2 recent phases of development of the Fire Program Analysis (FPA) system, a planning and budgeting system for the management of wildland fire throughout publicly managed lands in the United States. IPF extends traditional planning and problem formulation by including the explicit comparison of management alternatives, the valuation of ecological, economic and social endpoints, and the combination or integration of those endpoints. The phase 1, limited prototype FPA system used a set of assessment endpoints of common form (i.e., probabilities of given flame heights over acres of selected land-resource types), which were specified and assigned relative weights at the local level in relation to a uniform national standard. This approach was chosen to permit system-wide optimization of fire management budget allocations according to a cost-effectiveness criterion. Before full development, however, the agencies abandoned this approach in favor of a phase 2 system that examined locally specified (rather than system-optimized) allocation alternatives and was more permissive as to endpoint form. We demonstrate how the IPF process illuminates the nature, rationale, and consequences of these differences, and argue that its early use for the FPA system may have enabled a smoother development path.}, } @article {pmid19900299, year = {2009}, author = {Hill, AW and Guralnick, R and Flemons, P and Beaman, R and Wieczorek, J and Ranipeta, A and Chavan, V and Remsen, D}, title = {Location, location, location: utilizing pipelines and services to more effectively georeference the world's biodiversity data.}, journal = {BMC bioinformatics}, volume = {10 Suppl 14}, number = {Suppl 14}, pages = {S3}, pmid = {19900299}, issn = {1471-2105}, mesh = {*Biodiversity ; Computational Biology/*methods ; Databases, Factual ; Humans ; }, abstract = {BACKGROUND: Increasing the quantity and quality of data is a key goal of biodiversity informatics, leading to increased fitness for use in scientific research and beyond. This goal is impeded by a legacy of geographic locality descriptions associated with biodiversity records that are often heterogeneous and not in a map-ready format. The biodiversity informatics community has developed best practices and tools that provide the means to do retrospective georeferencing (e.g., the BioGeomancer toolkit), a process that converts heterogeneous descriptions into geographic coordinates and a measurement of spatial uncertainty. Even with these methods and tools, data publishers are faced with the immensely time-consuming task of vetting georeferenced localities. Furthermore, it is likely that overlap in georeferencing effort is occurring across data publishers. Solutions are needed that help publishers more effectively georeference their records, verify their quality, and eliminate the duplication of effort across publishers.

RESULTS: We have developed a tool called BioGeoBIF, which incorporates the high throughput and standardized georeferencing methods of BioGeomancer into a beginning-to-end workflow. Custodians who publish their data to the Global Biodiversity Information Facility (GBIF) can use this system to improve the quantity and quality of their georeferences. BioGeoBIF harvests records directly from the publishers' access points, georeferences the records using the BioGeomancer web-service, and makes results available to data managers for inclusion at the source. Using a web-based, password-protected, group management system for each data publisher, we leave data ownership, management, and vetting responsibilities with the managers and collaborators of each data set. We also minimize the georeferencing task, by combining and storing unique textual localities from all registered data access points, and dynamically linking that information to the password protected record information for each publisher.

CONCLUSION: We have developed one of the first examples of services that can help create higher quality data for publishers mediated through the Global Biodiversity Information Facility and its data portal. This service is one step towards solving many problems of data quality in the growing field of biodiversity informatics. We envision future improvements to our service that include faster results returns and inclusion of more georeferencing engines.}, } @article {pmid19947224, year = {2009}, author = {Zhang, R and Zhu, MM and Ma, JH and Wang, F}, title = {[Suitable habitat of Therioaphis trifolii population on arable lands of southern Ningxia based on GIS].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {20}, number = {8}, pages = {1998-2004}, pmid = {19947224}, issn = {1001-9332}, mesh = {Altitude ; Animals ; China ; Climate ; *Ecosystem ; Geographic Information Systems/*statistics & numerical data ; Insecta/*growth & development ; Medicago sativa/growth & development/*parasitology ; Population Density ; }, abstract = {Based on GIS techniques, the interpolation maps of Therioaphis trifolii population on the arable lands in Yuanzhou District of Guyuan City in different periods were overlapped with the ecological regionalization map and digital altitude map, aimed to analyze the relations of T. trifolii population density with its ecological environment and geographical distribution. In the study area, the occurrence and distribution of T. trifolii had close relations with climate, geomorphology, and altitude. The suitable habitat of T. trifolii in the District was located in the semi-arid plain area and semi-arid holly area at the altitude 1440-2000 m, while the most possible occurrence area was the semi-arid plain at the altitude 1600-1800 m. By combining the suitable habitat with the interpolation maps of T. trifolii population in different periods, the spatial dynamics of T. trifolii population in variety of ecological areas could be analyzed quantitatively.}, } @article {pmid21352770, year = {2009}, author = {Peterson, AT and Andersen, MJ and Bodbyl-Roels, S and Hosner, P and Nyári, A and Oliveros, C and Papeş, M}, title = {A prototype forecasting system for bird-borne disease spread in North America based on migratory bird movements.}, journal = {Epidemics}, volume = {1}, number = {4}, pages = {240-249}, doi = {10.1016/j.epidem.2009.11.003}, pmid = {21352770}, issn = {1878-0067}, mesh = {Algorithms ; *Animal Migration ; Animals ; Bird Diseases/*epidemiology/*transmission ; Birds ; Databases, Factual ; Ecology ; Geographic Information Systems ; North America/epidemiology ; Seasons ; West Nile Fever/epidemiology/transmission ; West Nile virus ; }, abstract = {The past two decades have seen major outbreaks of influenza viruses and flaviviruses that are spread at least in part by migratory birds. Although much new information has accumulated on the natural history of the viruses, and on the geography of migration by individual bird species, no synthesis has been achieved regarding likely patterns of spread of such pathogens by migratory birds, which constitutes a large-scale challenge in understanding the geography of bird migration. We here present a first step in this direction: a summary of seasonal (breeding, wintering) distributions of all 392 North American bird species that show marked seasonal migratory movements and that meet a series of conditions for inclusion in our analyses. We use species-level interseasonal connectivity among distributional areas to make initial forecasts of patterns of spread of bird-borne diseases via bird migration. We identify key next steps towards improved forecasting of spread patterns of bird-borne pathogens in North America, which will require substantial improvements in knowledge of the geography of bird migration.}, } @article {pmid19944930, year = {2009}, author = {Bors, P and Dessauer, M and Bell, R and Wilkerson, R and Lee, J and Strunk, SL}, title = {The Active Living by Design national program: community initiatives and lessons learned.}, journal = {American journal of preventive medicine}, volume = {37}, number = {6 Suppl 2}, pages = {S313-21}, doi = {10.1016/j.amepre.2009.09.027}, pmid = {19944930}, issn = {1873-2607}, mesh = {Community Networks/*organization & administration ; *Environment Design ; *Exercise ; Health Education/organization & administration ; Health Policy ; Health Promotion/methods/*organization & administration ; Humans ; Interinstitutional Relations ; Leadership ; Poverty ; Program Development ; Social Support ; }, abstract = {Public health advocates have increasingly highlighted the importance of implementing comprehensive physical activity interventions that use an ecologic framework. Such a framework can broadly address physical activity barriers, such as the lack of opportunities, social support, policies, built environments, and community awareness. The Active Living by Design (ALbD) was a community grant program of the Robert Wood Johnson Foundation (RWJF), which was established to help 25 communities create environments that support active living. Each funded site established a multidisciplinary community partnership and implemented the 5P strategies: preparation, promotions, programs, policy, and physical projects. The community partnerships worked within neighborhoods, schools, worksites, and other organizations to increase physical and social supports for physical activity. Ten community examples illustrate the 5Ps. Throughout the 5-year grant, the ALbD national program office provided community partnerships with group and individualized learning opportunities. Technical assistance and peer-to-peer learning was facilitated by ALbD project officers, who also coached each community partnership via site visits, regular phone calls, and electronic communications. The ALbD grant program provided valuable lessons for communities, technical assistance organizations, and funders. Community partnerships experienced success in a variety of settings and their collaborative approaches encouraged multiple organizations, including funders, to participate in improving conditions for active living. Strong local leadership was a key to success and community partnerships benefited considerably from peer-to-peer learning. The 5P model, while challenging to implement comprehensively, proved to be a useful model for community change.}, } @article {pmid19943108, year = {2010}, author = {Choueri, RB and Cesar, A and Abessa, DM and Torres, RJ and Riba, I and Pereira, CD and Nascimento, MR and Morais, RD and Mozeto, AA and DelValls, TA}, title = {Harmonised framework for ecological risk assessment of sediments from ports and estuarine zones of North and South Atlantic.}, journal = {Ecotoxicology (London, England)}, volume = {19}, number = {4}, pages = {678-696}, pmid = {19943108}, issn = {1573-3017}, mesh = {Amphipoda/drug effects ; Animals ; Atlantic Ocean ; Brazil ; Decision Support Techniques ; *Ecosystem ; Environmental Monitoring/*methods/standards ; Factor Analysis, Statistical ; Geologic Sediments/*chemistry ; Guidelines as Topic ; Larva/drug effects ; Principal Component Analysis ; Quality Control ; Risk Assessment ; Sea Urchins/drug effects/embryology ; Seawater/chemistry ; Spain ; *Toxicity Tests/standards ; Water Pollutants, Chemical/*analysis/toxicity ; }, abstract = {This paper presents a harmonised framework of sediment quality assessment and dredging material characterisation for estuaries and port zones of North and South Atlantic. This framework, based on the weight-of-evidence approach, provides a structure and a process for conducting sediment/dredging material assessment that leads to a decision. The main structure consists of "step 1" (examination of available data); "step 2" (chemical characterisation and toxicity assessment); "decision 1" (any chemical level higher than reference values? are sediments toxic?); "step 3" (assessment of benthic community structure); "step 4" (integration of the results); "decision 2" (are sediments toxic or benthic community impaired?); "step 5" (construction of the decision matrix) and "decision 3" (is there environmental risk?). The sequence of assessments may be interrupted when the information obtained is judged to be sufficient for a correct characterisation of the risk posed by the sediments/dredging material. This framework brought novel features compared to other sediment/dredging material risk assessment frameworks: data integration through multivariate analysis allows the identification of which samples are toxic and/or related to impaired benthic communities; it also discriminates the chemicals responsible for negative biological effects; and the framework dispenses the use of a reference area. We demonstrated the successful application of this framework in different port and estuarine zones of the North (Gulf of Cádiz) and South Atlantic (Santos and Paranaguá Estuarine Systems).}, } @article {pmid19941672, year = {2009}, author = {Skerker, JM and Lucks, JB and Arkin, AP}, title = {Evolution, ecology and the engineered organism: lessons for synthetic biology.}, journal = {Genome biology}, volume = {10}, number = {11}, pages = {114}, pmid = {19941672}, issn = {1474-760X}, mesh = {Archaea/genetics ; Bacteria/genetics ; Computational Biology/*methods ; DNA/genetics ; Ecology ; Escherichia coli/genetics ; *Evolution, Molecular ; Genetic Engineering/*methods ; Humans ; Models, Genetic ; }, abstract = {As the scope and complexity of synthetic biology grows, an understanding of evolution and ecology will be critical to its success.}, } @article {pmid19941637, year = {2009}, author = {Kelly-Hope, LA and Hemingway, J and McKenzie, FE}, title = {Environmental factors associated with the malaria vectors Anopheles gambiae and Anopheles funestus in Kenya.}, journal = {Malaria journal}, volume = {8}, number = {}, pages = {268}, pmid = {19941637}, issn = {1475-2875}, mesh = {Animals ; Anopheles/classification/*growth & development ; *Ecosystem ; Environment ; Feeding Behavior ; Geographic Information Systems ; Insect Bites and Stings ; Insect Vectors/classification/*growth & development ; Kenya ; Malaria, Falciparum/*transmission ; Plasmodium falciparum/*growth & development/isolation & purification ; Seasons ; Statistics, Nonparametric ; Water ; }, abstract = {BACKGROUND: The Anopheles gambiae and Anopheles funestus mosquito species complexes are the primary vectors of Plasmodium falciparum malaria in sub-Saharan Africa. To better understand the environmental factors influencing these species, the abundance, distribution and transmission data from a south-eastern Kenyan study were retrospectively analysed, and the climate, vegetation and elevation data in key locations compared.

METHODS: Thirty villages in Malindi, Kilifi and Kwale Districts with data on An. gambiae sensu strict, Anopheles arabiensis and An. funestus entomological inoculation rates (EIRs), were used as focal points for spatial and environmental analyses. Transmission patterns were examined for spatial autocorrelation using the Moran's I statistic, and for the clustering of high or low EIR values using the Getis-Ord Gi* statistic. Environmental data were derived from remote-sensed satellite sources of precipitation, temperature, specific humidity, Normalized Difference Vegetation Index (NDVI), and elevation. The relationship between transmission and environmental measures was examined using bivariate correlations, and by comparing environmental means between locations of high and low clustering using the Mann-Whitney U test.

RESULTS: Spatial analyses indicated positive autocorrelation of An. arabiensis and An. funestus transmission, but not of An. gambiae s.s., which was found to be widespread across the study region. The spatial clustering of high EIR values for An. arabiensis was confined to the lowland areas of Malindi, and for An. funestus to the southern districts of Kilifi and Kwale. Overall, An. gambiae s.s. and An. arabiensis had similar spatial and environmental trends, with higher transmission associated with higher precipitation, but lower temperature, humidity and NDVI measures than those locations with lower transmission by these species and/or in locations where transmission by An. funestus was high. Statistical comparisons indicated that precipitation and temperatures were significantly different between the An. arabiensis and An. funestus high and low transmission locations.

CONCLUSION: These finding suggest that the abundance, distribution and malaria transmission of different malaria vectors are driven by different environmental factors. A better understanding of the specific ecological parameters of each malaria mosquito species will help define their current distributions, and how they may currently and prospectively be affected by climate change, interventions and other factors.}, } @article {pmid19932465, year = {2009}, author = {Paquette, SR and Lapointe, FJ}, title = {A statistical procedure to assess the significance level of barriers to gene flow.}, journal = {Journal of genetics and genomics = Yi chuan xue bao}, volume = {36}, number = {11}, pages = {685-693}, doi = {10.1016/S1673-8527(08)60161-7}, pmid = {19932465}, issn = {1673-8527}, mesh = {Algorithms ; Animals ; Computer Simulation ; Data Interpretation, Statistical ; Fishes/genetics ; *Gene Flow ; Genetics, Population ; *Mathematical Computing ; Models, Genetic ; }, abstract = {Although several methods are available to study the extent of isolation by distance (IBD) among natural populations, comparatively few exist to detect the presence of sharp genetic breaks in genetic distance datasets. In recent years, Monmonier's maximum-difference algorithm has been increasingly used by population geneticists. However, this method does not provide means to measure the statistical significance of such barriers, nor to determine their relative contribution to population differentiation with respect to IBD. Here, we propose an approach to assess the significance of genetic boundaries. The method is based on the calculation of a multiple regression from distance matrices, where binary matrices represent putative genetic barriers to test, in addition to geographic and genetic distances. Simulation results suggest that this method reliably detects the presence of genetic barriers, even in situations where IBD is also significant. We also illustrate the methodology by analyzing previously published datasets. Conclusions about the importance of genetic barriers can be misleading if one does not take into consideration their relative contribution to the overall genetic structure of species.}, } @article {pmid19930445, year = {2010}, author = {Poretsky, RS and Sun, S and Mou, X and Moran, MA}, title = {Transporter genes expressed by coastal bacterioplankton in response to dissolved organic carbon.}, journal = {Environmental microbiology}, volume = {12}, number = {3}, pages = {616-627}, pmid = {19930445}, issn = {1462-2920}, mesh = {Animals ; Bacteria/*genetics/metabolism ; Bacterial Proteins/*genetics/metabolism ; Carbon/chemistry/*metabolism ; Carrier Proteins/*genetics ; Databases, Genetic ; Genomics/methods ; Molecular Sequence Data ; Oceans and Seas ; Plankton/*genetics/metabolism ; Seawater/*chemistry/*microbiology ; Water Microbiology ; }, abstract = {Coastal ocean bacterioplankton control the flow of dissolved organic carbon (DOC) from terrestrial and oceanic sources into the marine food web, and regulate the release of inorganic carbon to atmospheric and offshore reservoirs. While the fate of the chemically complex coastal DOC reservoir has long been recognized as a critical feature of the global carbon budget, it has been problematic to identify both the compounds that serve as major conduits for carbon flux and the roles of individual bacterioplankton taxa in mediating that flux. Here we analyse random libraries of expressed genes from a coastal bacterial community to identify sequences representing DOC-transporting proteins. Predicted substrates of expressed transporter genes indicated that carboxylic acids, compatible solutes, polyamines and lipids may be key components of the biologically labile DOC pool in coastal waters, in addition to canonical bacterial substrates such as amino acids, oligopeptides and carbohydrates. Half of the expressed DOC transporter sequences in this coastal ocean appeared to originate from just eight taxa: Roseobacter, SAR11, Flavobacteriales and five orders of gamma-Proteobacteria. While all major taxa expressed transporter genes for some DOC components (e.g. amino acids), there were indications of specialization within the bacterioplankton community for others (e.g. carbohydrates, carboxylic acids and polyamines). Experimental manipulations of the natural DOC pool that increased the concentration of phytoplankton- or vascular plant-derived compounds invoked a readily measured response in bacterial transporter gene expression. This highly resolved view of the potential for carbon flux into heterotrophic bacterioplankton cells identifies possible bioreactive components of the coastal DOC pool and highlights differing ecological roles in carbon turnover for the resident bacterial taxa.}, } @article {pmid19929115, year = {2009}, author = {Koehnle, TJ and Schank, JC}, title = {An ancient black art.}, journal = {Journal of comparative psychology (Washington, D.C. : 1983)}, volume = {123}, number = {4}, pages = {452-458}, doi = {10.1037/a0017435}, pmid = {19929115}, issn = {1939-2087}, mesh = {Analysis of Variance ; Animals ; *Behavior, Animal ; Bias ; Data Interpretation, Statistical ; *Ecology ; Humans ; Models, Statistical ; Monte Carlo Method ; Probability Theory ; Random Allocation ; *Reproducibility of Results ; Research Design/*statistics & numerical data ; }, abstract = {The doctrine of pseudoreplication (DP) offers specific advice on how to ensure statistical independence and compute F-ratios properly when testing a null hypothesis. Our target article showed that this advice can lead to problems in experimental design and analysis. Though a few commenters attempt to defend DP, none offered substantive evidence that our modeling results were incorrect. In our response, we further highlight the complications surrounding definitions of experimental units. In particular, we show that the definition of independence assumed in DP is inconsistent with independence as defined in probability theory. We show that interconnectedness across levels of analysis is pervasive, and that no simple set of rules or procedures can help experimenters avoid this problem. We argue that the relevance or interference of a particular level of analysis can be determined only after an experiment is done. In our view, analytical methods must be designed to match experiments, the opposite of the advice offered in DP. Finally, we emphasize the weakness of null testing and the inability of p values to predict whether a result will generalize or be replicated.}, } @article {pmid19926862, year = {2009}, author = {Luo, H and Benner, R and Long, RA and Hu, J}, title = {Subcellular localization of marine bacterial alkaline phosphatases.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {106}, number = {50}, pages = {21219-21223}, pmid = {19926862}, issn = {1091-6490}, mesh = {Alkaline Phosphatase/analysis/genetics/*metabolism ; Bacteria/enzymology ; Bacterial Proteins/analysis/genetics ; Biodiversity ; Biological Transport ; Computational Biology ; Cytosol/chemistry ; Databases, Nucleic Acid ; *Ecosystem ; Extracellular Matrix/chemistry ; Marine Biology ; Oceans and Seas ; Phosphates/*metabolism ; }, abstract = {Bacterial alkaline phosphatases (APases) are important enzymes in organophosphate utilization in the ocean. The subcellular localization of APases has significant ecological implications for marine biota but is largely unknown. The extensive metagenomic sequence databases from the Global Ocean Sampling Expedition provide an opportunity to address this question. A bioinformatics pipeline was developed to identify marine bacterial APases from the metagenomic databases, and a consensus classification algorithm was designed to predict their subcellular localizations. We identified 3,733 bacterial APase sequences (including PhoA, PhoD, and PhoX) and found that cytoplasmic (41%) and extracellular (30%) APases exceed their periplasmic (17%), outer membrane (12%), and inner membrane (0.9%) counterparts. The unexpectedly high abundance of cytoplasmic APases suggests that the transport and intracellular hydrolysis of small organophosphate molecules is an important mechanism for bacterial acquisition of phosphorus (P) in the surface ocean. On average, each marine bacterium possessed at least one suite of uptake of glycerol phosphate (ugp) genes (e.g., ugpA, ugpB, ugpC, ugpE) for dissolved organic phosphorus (DOP) transport, but only half of them had ugpQ, which hydrolyzes transported DOP, indicating that cytoplasmic APases play a role in hydrolyzing transported DOP. The most abundant heterotrophic marine bacteria, alpha- and gamma-Proteobacteria, might hydrolyze DOP outside the cytoplasmic membrane, but the former could also transport and hydrolyze DOP in the cytoplasm. The abundant extracellular APases could provide bioavailable P for organisms that cannot directly access organophosphates, and thereby increase marine biological productivity and diversity.}, } @article {pmid19914921, year = {2010}, author = {Caporaso, JG and Bittinger, K and Bushman, FD and DeSantis, TZ and Andersen, GL and Knight, R}, title = {PyNAST: a flexible tool for aligning sequences to a template alignment.}, journal = {Bioinformatics (Oxford, England)}, volume = {26}, number = {2}, pages = {266-267}, pmid = {19914921}, issn = {1367-4811}, support = {1U01HG004866-01/HG/NHGRI NIH HHS/United States ; T15LM009451/LM/NLM NIH HHS/United States ; UH2CA140233/CA/NCI NIH HHS/United States ; UH2DK083981/DK/NIDDK NIH HHS/United States ; }, mesh = {Algorithms ; Databases, Genetic ; Sequence Alignment/*methods ; Sequence Analysis, RNA/methods ; *Software ; User-Computer Interface ; }, abstract = {MOTIVATION: The Nearest Alignment Space Termination (NAST) tool is commonly used in sequence-based microbial ecology community analysis, but due to the limited portability of the original implementation, it has not been as widely adopted as possible. Python Nearest Alignment Space Termination (PyNAST) is a complete reimplementation of NAST, which includes three convenient interfaces: a Mac OS X GUI, a command-line interface and a simple application programming interface (API).

RESULTS: The availability of PyNAST will make the popular NAST algorithm more portable and thereby applicable to datasets orders of magnitude larger by allowing users to install PyNAST on their own hardware. Additionally because users can align to arbitrary template alignments, a feature not available via the original NAST web interface, the NAST algorithm will be readily applicable to novel tasks outside of microbial community analysis.

AVAILABILITY: PyNAST is available at http://pynast.sourceforge.net.}, } @article {pmid19912534, year = {2009}, author = {Dalziel, AC and Rogers, SM and Schulte, PM}, title = {Linking genotypes to phenotypes and fitness: how mechanistic biology can inform molecular ecology.}, journal = {Molecular ecology}, volume = {18}, number = {24}, pages = {4997-5017}, doi = {10.1111/j.1365-294X.2009.04427.x}, pmid = {19912534}, issn = {1365-294X}, mesh = {Databases, Genetic ; Evolution, Molecular ; *Genetic Fitness ; Genetic Variation ; *Genetics, Population ; Genomics/*methods ; *Genotype ; *Phenotype ; }, abstract = {The accessibility of new genomic resources, high-throughput molecular technologies and analytical approaches such as genome scans have made finding genes contributing to fitness variation in natural populations an increasingly feasible task. Once candidate genes are identified, we argue that it is necessary to take a mechanistic approach and work up through the levels of biological organization to fully understand the impacts of genetic variation at these candidate genes. We demonstrate how this approach provides testable hypotheses about the causal links among levels of biological organization, and assists in designing relevant experiments to test the effects of genetic variation on phenotype, whole-organism performance capabilities and fitness. We review some of the research programs that have incorporated mechanistic approaches when examining naturally occurring genetic and phenotypic variation and use these examples to highlight the value of developing a comprehensive understanding of the relationship between genotype and fitness. We give suggestions to guide future research aimed at uncovering and understanding the genetic basis of adaptation and argue that further integration of mechanistic approaches will help molecular ecologists better understand the evolution of natural populations.}, } @article {pmid19910112, year = {2010}, author = {Morais, SA and Delerue-Matos, C}, title = {A perspective on LCA application in site remediation services: critical review of challenges.}, journal = {Journal of hazardous materials}, volume = {175}, number = {1-3}, pages = {12-22}, doi = {10.1016/j.jhazmat.2009.10.041}, pmid = {19910112}, issn = {1873-3336}, mesh = {Conservation of Natural Resources ; Decision Making ; Decision Support Techniques ; Ecology ; Ecosystem ; Environment ; Environmental Monitoring/*methods ; Environmental Restoration and Remediation/*methods ; Risk Assessment/methods ; Soil/analysis ; Soil Pollutants/chemistry ; Water Pollutants/chemistry ; Water Purification ; }, abstract = {The remediation of contaminated sites supports the goal of sustainable development but may also have environmental impacts at a local, regional and global scale. Life cycle assessment (LCA) has increasingly been used in order to support site remediation decision-making. This review article discusses existing LCA methods and proposed models focusing on critical decisions and assumptions of the LCA application to site remediation activities. It is concluded that LCA has limitations as an adequate holistic decision-making tool since spatial and temporal differentiation of non-global impacts assessment is a major hurdle in site remediation LCA. Moreover, a consequential LCA perspective should be adopted when the different remediation services to be compared generate different site's physical states, displacing alternative post-remediation scenarios. The environmental effects of the post-remediation stage of the site is generally disregarded in the past site remediation LCA studies and such exclusion may produce misleading conclusions and misdirected decision-making. In addition, clear guidance accepted by all stakeholders on remediation capital equipment exclusion and on dealing with multifunctional processes should be developed for site remediation LCA applications.}, } @article {pmid19908400, year = {2010}, author = {Sterk, P and Hirschman, L and Field, D and Wooley, J}, title = {Genomic standards consortium workshop: metagenomics, metadata and metaanalysis (M3).}, journal = {Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing}, volume = {}, number = {}, pages = {481-484}, pmid = {19908400}, issn = {2335-6936}, mesh = {Computational Biology ; Data Interpretation, Statistical ; Meta-Analysis as Topic ; Metagenome ; Metagenomics/*standards/statistics & numerical data ; }, abstract = {The M3 workshop has, as its primary focus, the rapidly growing area of metagenomics, including the metadata standards and the meta-analysis approaches needed to organize, process and interpret metagenomics data. The PSB Workshop builds on the first M3 meeting, a Special Interest Group (SIG) meeting at ISMB 2009, organized by the Genomics Standards Consortium.}, } @article {pmid19902371, year = {2010}, author = {Ilić, I and Zivković, D and Vusović, N and Bogdanović, D}, title = {Optimizing the SO2 total emission control strategy: case study-Bor (Serbia).}, journal = {Environmental monitoring and assessment}, volume = {169}, number = {1-4}, pages = {587-596}, pmid = {19902371}, issn = {1573-2959}, mesh = {Air Pollutants/*analysis ; Air Pollution/*prevention & control ; *Environmental Monitoring ; Geographic Information Systems ; Models, Chemical ; Serbia ; Sulfur Dioxide/*analysis ; }, abstract = {A geographic information system (GIS)--based on spatial analysis--was developed for optimizing the SO(2) total emission cut scheme on air pollution in Bor (Serbia), combined with Models-3 modeling system and linear programming model. GIS is mainly used for establishing a multifactor assessment model to quantitatively divide environmental functional zone and also used for selecting control sites in linear programming model. A linear programming model was developed to optimize the emission determined by SO(2) control measures. According to the obtained results, some large emissions need to be cut for about 50%. The improvement of the ecological environment is urgently needed for controlling the background SO(2) pollution in Bor.}, } @article {pmid19902368, year = {2010}, author = {Yates, AG and Bailey, RC}, title = {Selecting objectively defined reference sites for stream bioassessment programs.}, journal = {Environmental monitoring and assessment}, volume = {170}, number = {1-4}, pages = {129-140}, pmid = {19902368}, issn = {1573-2959}, mesh = {*Decision Support Techniques ; Environmental Monitoring/*methods ; Geographic Information Systems ; Reference Standards ; Rivers/*chemistry ; Water Pollutants/*analysis/standards ; Water Pollution/analysis ; }, abstract = {Our study develops and demonstrates an objective method for selecting reference sites for the assessment of ecological condition in freshwater ecosystems. The method uses widely available GIS data to group potential sites based on their natural environments. It then establishes the degree and types of human activities each site is exposed to prior to scoring the sites in each group by the relative amount of human activity present. Finally, the sites in each group with the least amount of human activity are categorized as reference sites, with the boundary between reference and test sites defined to maximize the distinctiveness of the two categories with respect to human activity. Application of this technique for the purpose of identifying headwater reference basins in rural areas of southwestern Ontario resulted in the classification of basins into six natural groups based on the dominant texture of the surface geology. Development of a human activity gradient indicated that basins varied according to the amount of exposure to agricultural activities with most basins having at least moderate exposure. Establishment of the reference test boundary indicated that the selected reference basins exhibited substantively lower extents of agricultural activity than test sites for most groups. Because this method uses only widely available GIS data, it enables rapid and cost-effective identification of candidate reference sites, even for large, remote, and understudied regions.}, } @article {pmid19897828, year = {2009}, author = {Lim, YY and Prang, KH and Cysique, L and Pietrzak, RH and Snyder, PJ and Maruff, P}, title = {A method for cross-cultural adaptation of a verbal memory assessment.}, journal = {Behavior research methods}, volume = {41}, number = {4}, pages = {1190-1200}, doi = {10.3758/BRM.41.4.1190}, pmid = {19897828}, issn = {1554-3528}, mesh = {Adult ; China ; *Cross-Cultural Comparison ; Data Interpretation, Statistical ; Executive Function/*physiology ; Female ; France ; Humans ; Language ; Malaysia ; Male ; Multilingualism ; *Neuropsychological Tests ; United States ; *Verbal Learning ; Young Adult ; }, abstract = {Verbal memory tests-although important to the neuropsychological assessment of memory-are biased to many cultures. In the present article, we highlighted the limitations associated with the direct translation of tests and word matching, as well as the lack of ecological validity and cultural appropriateness when tests developed in one culture are used in another. To overcome these limitations, a verbal memory paradigm was developed that framed the memory assessment with a shopping-list format, but that developed culturally specific stimuli for the different language groups. The aim of the present study was to determine the equivalence of this shopping list memory test in different cultural and language groups. Eighty-three adults from English-, French-, Malay-, and Chinese-speaking cultures participated in four experiments. The results of all the experiments indicated that performance of verbal list learning is equivalent, irrespective of the language used. These results support the use of this methodology for minimizing cross-cultural test bias, and have important implications for testing culturally and linguistically diverse individuals.}, } @article {pmid19894124, year = {2010}, author = {López, I and Gámez, M and Garay, J and Standovár, T and Varga, Z}, title = {Application of change-point problem to the detection of plant patches.}, journal = {Acta biotheoretica}, volume = {58}, number = {1}, pages = {51-63}, doi = {10.1007/s10441-009-9093-x}, pmid = {19894124}, issn = {1572-8358}, mesh = {Algorithms ; Artificial Intelligence ; Computer Graphics ; Computer Simulation ; Ecology ; Image Interpretation, Computer-Assisted ; Likelihood Functions ; Models, Theoretical ; Pattern Recognition, Automated ; Plant Physiological Phenomena ; Plants/*metabolism ; Systems Biology ; }, abstract = {In ecology, if the considered area or space is large, the spatial distribution of individuals of a given plant species is never homogeneous; plants form different patches. The homogeneity change in space or in time (in particular, the related change-point problem) is an important research subject in mathematical statistics. In the paper, for a given data system along a straight line, two areas are considered, where the data of each area come from different discrete distributions, with unknown parameters. In the paper a method is presented for the estimation of the distribution change-point between both areas and an estimate is given for the distributions separated by the obtained change-point. The solution of this problem will be based on the maximum likelihood method. Furthermore, based on an adaptation of the well-known bootstrap resampling, a method for the estimation of the so-called change-interval is also given. The latter approach is very general, since it not only applies in the case of the maximum-likelihood estimation of the change-point, but it can be also used starting from any other change-point estimation known in the ecological literature. The proposed model is validated against typical ecological situations, providing at the same time a verification of the applied algorithms.}, } @article {pmid19886504, year = {2009}, author = {Nielson, RM and Manly, BF and McDonald, LL and Sawyer, H and McDonald, TL}, title = {Estimating habitat selection when GPS fix success is less than 100%.}, journal = {Ecology}, volume = {90}, number = {10}, pages = {2956-2962}, doi = {10.1890/08-1562.1}, pmid = {19886504}, issn = {0012-9658}, mesh = {Animal Identification Systems/*instrumentation ; Animal Migration ; Animals ; Deer/*physiology ; Ecosystem ; Female ; *Geographic Information Systems ; *Models, Biological ; }, abstract = {Inferences about habitat selection by animals derived from sequences of relocations obtained with global positioning system (GPS) collars can be influenced by GPS fix success. Environmental factors such as dense canopy cover or rugged terrain can reduce GPS fix success, making subsequent modeling problematic if fix success depends on the selected habitat. Ignoring failed fix attempts may affect estimates of model coefficients and lead to incorrect conclusions about habitat selection. Here, we present a habitat selection model that accounts for missing locations due to habitat-induced data losses, called a resource selection function (RSF) for GPS fix success. The model's formulation is similar to adjusting estimates of probability of occupancy when detection is less than 100% in patch occupancy sampling. We demonstrate use of the model with GPS data collected from an adult female mule deer (Odocoileus hemionus) and discuss how to analyze data from multiple animals. In the simulations presented, our habitat selection model was generally unbiased for GPS data sets missing up to 50% of the locations.}, } @article {pmid19880384, year = {2010}, author = {Tseng, YY and Chen, ZJ and Li, WH}, title = {fPOP: footprinting functional pockets of proteins by comparative spatial patterns.}, journal = {Nucleic acids research}, volume = {38}, number = {Database issue}, pages = {D288-95}, pmid = {19880384}, issn = {1362-4962}, support = {GM30998/GM/NIGMS NIH HHS/United States ; }, mesh = {Algorithms ; Animals ; Bacterial Proteins/chemistry ; Binding Sites ; Computational Biology/*methods/trends ; Computer Simulation ; *Databases, Genetic ; *Databases, Protein ; Humans ; Information Storage and Retrieval/methods ; Internet ; Protein Conformation ; Protein Structure, Tertiary ; Proteins/*chemistry ; Software ; }, abstract = {fPOP (footprinting Pockets Of Proteins, http://pocket.uchicago.edu/fpop/) is a relational database of the protein functional surfaces identified by analyzing the shapes of binding sites in approximately 42,700 structures, including both holo and apo forms. We previously used a purely geometric method to extract the spatial patterns of functional surfaces (split pockets) in approximately 19,000 bound structures and constructed a database, SplitPocket (http://pocket.uchicago.edu/). These functional surfaces are now used as spatial templates to predict the binding surfaces of unbound structures. To conduct a shape comparison, we use the Smith-Waterman algorithm to footprint an unbound pocket fragment with those of the functional surfaces in SplitPocket. The pairwise alignment of the unbound and bound pocket fragments is used to evaluate the local structural similarity via geometric matching. The final results of our large-scale computation, including approximately 90,000 identified or predicted functional surfaces, are stored in fPOP. This database provides an easily accessible resource for studying functional surfaces, assessing conformational changes between bound and unbound forms and analyzing functional divergence. Moreover, it may facilitate the exploration of the physicochemical textures of molecules and the inference of protein function. Finally, our approach provides a framework for classification of proteins into families on the basis of their functional surfaces.}, } @article {pmid19879976, year = {2010}, author = {Lopes, JS and Beaumont, MA}, title = {ABC: a useful Bayesian tool for the analysis of population data.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {10}, number = {6}, pages = {826-833}, doi = {10.1016/j.meegid.2009.10.010}, pmid = {19879976}, issn = {1567-7257}, mesh = {Algorithms ; *Bayes Theorem ; Communicable Diseases/epidemiology/genetics ; Computer Simulation ; Data Interpretation, Statistical ; *Epidemiologic Studies ; Genetics, Population/*statistics & numerical data ; Humans ; Likelihood Functions ; Markov Chains ; *Models, Statistical ; Monte Carlo Method ; }, abstract = {Approximate Bayesian computation (ABC) is a recently developed technique for solving problems in Bayesian inference. Although typically less accurate than, for example, the frequently used Markov Chain Monte Carlo (MCMC) methods, they have greater flexibility because they do not require the specification of a likelihood function. For this reason considerable amounts of data can be analysed and more complex models can be used providing, thereby, a potential better fit of the model to the data. Since its first applications in the late 1990s its usage has been steadily increasing. The framework was originally developed to solve problems in population genetics. However, as its efficiency was recognized its popularity increased and, consequently, it started to be used in fields as diverse as phylogenetics, ecology, conservation, molecular evolution and epidemiology. While the ABC algorithm is still being greatly studied and alterations to it are being proposed, the statistical approach has already reached a level of maturity well demonstrated by the number of related computer packages that are being developed. As improved ABC algorithms are proposed, the expansion of the use of this method can only increase. In this paper we are going to depict the context that led to the development of ABC focusing on the field of infectious disease epidemiology. We are then going to describe its current usage in such field and present its most recent developments.}, } @article {pmid19878454, year = {2009}, author = {Guillot, G and Leblois, R and Coulon, A and Frantz, AC}, title = {Statistical methods in spatial genetics.}, journal = {Molecular ecology}, volume = {18}, number = {23}, pages = {4734-4756}, doi = {10.1111/j.1365-294X.2009.04410.x}, pmid = {19878454}, issn = {1365-294X}, mesh = {Cluster Analysis ; *Genetic Variation ; *Genetics, Population ; *Models, Genetic ; *Models, Statistical ; }, abstract = {The joint analysis of spatial and genetic data is rapidly becoming the norm in population genetics. More and more studies explicitly describe and quantify the spatial organization of genetic variation and try to relate it to underlying ecological processes. As it has become increasingly difficult to keep abreast with the latest methodological developments, we review the statistical toolbox available to analyse population genetic data in a spatially explicit framework. We mostly focus on statistical concepts but also discuss practical aspects of the analytical methods, highlighting not only the potential of various approaches but also methodological pitfalls.}, } @article {pmid19875154, year = {2009}, author = {Gutiérrez, S and Fernandez, C and Barata, C and Tarazona, JV}, title = {Forecasting risk along a river basin using a probabilistic and deterministic model for environmental risk assessment of effluents through ecotoxicological evaluation and GIS.}, journal = {The Science of the total environment}, volume = {408}, number = {2}, pages = {294-303}, doi = {10.1016/j.scitotenv.2009.09.053}, pmid = {19875154}, issn = {1879-1026}, mesh = {Animals ; Ecotoxicology/*methods ; Gas Chromatography-Mass Spectrometry ; *Geographic Information Systems ; *Models, Statistical ; Risk Assessment/*methods ; Rivers/*chemistry ; Solid Phase Microextraction ; Water Pollutants, Chemical/*analysis ; }, abstract = {This work presents a computer model for Risk Assessment of Basins by Ecotoxicological Evaluation (RABETOX). The model is based on whole effluent toxicity testing and water flows along a specific river basin. It is capable of estimating the risk along a river segment using deterministic and probabilistic approaches. The Henares River Basin was selected as a case study to demonstrate the importance of seasonal hydrological variations in Mediterranean regions. As model inputs, two different ecotoxicity tests (the miniaturized Daphnia magna acute test and the D.magna feeding test) were performed on grab samples from 5 waste water treatment plant effluents. Also used as model inputs were flow data from the past 25 years, water velocity measurements and precise distance measurements using Geographical Information Systems (GIS). The model was implemented into a spreadsheet and the results were interpreted and represented using GIS in order to facilitate risk communication. To better understand the bioassays results, the effluents were screened through SPME-GC/MS analysis. The deterministic model, performed each month during one calendar year, showed a significant seasonal variation of risk while revealing that September represents the worst-case scenario with values up to 950 Risk Units. This classifies the entire area of study for the month of September as "sublethal significant risk for standard species". The probabilistic approach using Monte Carlo analysis was performed on 7 different forecast points distributed along the Henares River. A 0% probability of finding "low risk" was found at all forecast points with a more than 50% probability of finding "potential risk for sensitive species". The values obtained through both the deterministic and probabilistic approximations reveal the presence of certain substances, which might be causing sublethal effects in the aquatic species present in the Henares River.}, } @article {pmid19865479, year = {2009}, author = {Emerson, GL and Li, Y and Frace, MA and Olsen-Rasmussen, MA and Khristova, ML and Govil, D and Sammons, SA and Regnery, RL and Karem, KL and Damon, IK and Carroll, DS}, title = {The phylogenetics and ecology of the orthopoxviruses endemic to North America.}, journal = {PloS one}, volume = {4}, number = {10}, pages = {e7666}, pmid = {19865479}, issn = {1932-6203}, mesh = {DNA, Mitochondrial/genetics ; DNA, Viral/genetics ; Databases, Factual ; Ecology ; Ecosystem ; Evolution, Molecular ; Genetic Speciation ; Geography ; North America ; Orthopoxvirus/*classification/*genetics ; Phylogeny ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {The data presented herein support the North American orthopoxviruses (NA OPXV) in a sister relationship to all other currently described Orthopoxvirus (OPXV) species. This phylogenetic analysis reaffirms the identification of the NA OPXV as close relatives of "Old World" (Eurasian and African) OPXV and presents high support for deeper nodes within the Chordopoxvirinae family. The natural reservoir host(s) for many of the described OPXV species remains unknown although a clear virus-host association exists between the genus OPXV and several mammalian taxa. The hypothesized host associations and the deep divergence of the OPXV/NA OPXV clades depicted in this study may reflect the divergence patterns of the mammalian faunas of the Old and New World and reflect a more ancient presence of OPXV on what are now the American continents. Genes from the central region of the poxvirus genome are generally more conserved than genes from either end of the linear genome due to functional constraints imposed on viral replication abilities. The relatively slower evolution of these genes may more accurately reflect the deeper history among the poxvirus group, allowing for robust placement of the NA OPXV within Chordopoxvirinae. Sequence data for nine genes were compiled from three NA OPXV strains plus an additional 50 genomes collected from Genbank. The current, gene sequence based phylogenetic analysis reaffirms the identification of the NA OPXV as the nearest relatives of "Old World" OPXV and presents high support for deeper nodes within the Chordopoxvirinae family. Additionally, the substantial genetic distances that separate the currently described NA OPXV species indicate that it is likely that many more undescribed OPXV/NA OPXV species may be circulating among wild animals in North America.}, } @article {pmid19862777, year = {2010}, author = {Amsler, SJ}, title = {Energetic costs of territorial boundary patrols by wild chimpanzees.}, journal = {American journal of primatology}, volume = {72}, number = {2}, pages = {93-103}, doi = {10.1002/ajp.20757}, pmid = {19862777}, issn = {1098-2345}, mesh = {Animals ; Behavior, Animal/*physiology ; Eating/physiology ; Energy Metabolism/*physiology ; Geographic Information Systems ; Male ; Pan troglodytes/metabolism/*physiology ; *Territoriality ; Travel ; }, abstract = {Chimpanzees are well known for their territorial behavior. Males who belong to the same community routinely patrol their territories, occasionally making deep incursions into those of their neighbors. Male chimpanzees may obtain several fitness benefits by participating in territorial boundary patrols, but patrolling is also likely to involve fitness costs. Patrollers risk injury or even death, and patrols may be energetically costly and may involve opportunity costs. Although territorial patrols have been reported at all long-term chimpanzee study sites, quantitative data on their energetic costs have not previously been available. I evaluated the energy costs of patrolling for male chimpanzees at Ngogo, Kibale National Park, Uganda during 14 months of observation. In 29 patrols and matched control periods, I recorded the distances covered and time spent traveling and feeding by chimpanzees. I found that male chimpanzees covered longer distances, spent more time traveling, and spent less time feeding during patrols than during control periods. These results support the hypothesis that chimpanzees incur energetic costs while patrolling and suggest that ecological factors may constrain the ability of chimpanzees to patrol.}, } @article {pmid19862322, year = {2009}, author = {Young, LC and Vanderlip, C and Duffy, DC and Afanasyev, V and Shaffer, SA}, title = {Bringing home the trash: do colony-based differences in foraging distribution lead to increased plastic ingestion in Laysan albatrosses?.}, journal = {PloS one}, volume = {4}, number = {10}, pages = {e7623}, pmid = {19862322}, issn = {1932-6203}, mesh = {Animals ; Behavior, Animal ; Birds/*physiology ; *Environmental Pollutants ; *Flight, Animal ; Geographic Information Systems ; Geography ; Nesting Behavior ; Pacific Ocean ; *Plastics ; Refuse Disposal ; }, abstract = {When searching for prey, animals should maximize energetic gain, while minimizing energy expenditure by altering their movements relative to prey availability. However, with increasing amounts of marine debris, what once may have been 'optimal' foraging strategies for top marine predators, are leading to sub-optimal diets comprised in large part of plastic. Indeed, the highly vagile Laysan albatross (Phoebastria immutabilis) which forages throughout the North Pacific, are well known for their tendency to ingest plastic. Here we examine whether Laysan albatrosses nesting on Kure Atoll and Oahu Island, 2,150 km apart, experience different levels of plastic ingestion. Twenty two geolocators were deployed on breeding adults for up to two years. Regurgitated boluses of undigestable material were also collected from chicks at each site to compare the amount of plastic vs. natural foods. Chicks from Kure Atoll were fed almost ten times the amount of plastic compared to chicks from Oahu despite boluses from both colonies having similar amounts of natural food. Tracking data indicated that adults from either colony did not have core overlapping distributions during the early half of the breeding period and that adults from Kure had a greater overlap with the putative range of the Western Garbage Patch corroborating our observation of higher plastic loads at this colony. At-sea distributions also varied throughout the year suggesting that Laysan albatrosses either adjusted their foraging behavior according to constraints on time away from the nest or to variation in resources. However, in the non-breeding season, distributional overlap was greater indicating that the energy required to reach the foraging grounds was less important than the total energy available. These results demonstrate how a marine predator that is not dispersal limited alters its foraging strategy throughout the reproductive cycle to maximize energetic gain and how this has led to differences in plastic ingestion.}, } @article {pmid19858098, year = {2010}, author = {Kottmann, R and Kostadinov, I and Duhaime, MB and Buttigieg, PL and Yilmaz, P and Hankeln, W and Waldmann, J and Glöckner, FO}, title = {Megx.net: integrated database resource for marine ecological genomics.}, journal = {Nucleic acids research}, volume = {38}, number = {Database issue}, pages = {D391-5}, pmid = {19858098}, issn = {1362-4962}, mesh = {Animals ; Computational Biology/*methods/trends ; *Databases, Genetic ; *Databases, Nucleic Acid ; *Databases, Protein ; Ecology ; Environment ; Genome, Bacterial ; Geography ; Humans ; Information Storage and Retrieval/methods ; Internet ; Oceans and Seas ; Protein Structure, Tertiary ; Software ; }, abstract = {Megx.net is a database and portal that provides integrated access to georeferenced marker genes, environment data and marine genome and metagenome projects for microbial ecological genomics. All data are stored in the Microbial Ecological Genomics DataBase (MegDB), which is subdivided to hold both sequence and habitat data and global environmental data layers. The extended system provides access to several hundreds of genomes and metagenomes from prokaryotes and phages, as well as over a million small and large subunit ribosomal RNA sequences. With the refined Genes Mapserver, all data can be interactively visualized on a world map and statistics describing environmental parameters can be calculated. Sequence entries have been curated to comply with the proposed minimal standards for genomes and metagenomes (MIGS/MIMS) of the Genomic Standards Consortium. Access to data is facilitated by Web Services. The updated megx.net portal offers microbial ecologists greatly enhanced database content, and new features and tools for data analysis, all of which are freely accessible from our webpage http://www.megx.net.}, } @article {pmid19844050, year = {2009}, author = {Benedetti, L and Prat, P and Nopens, I and Poch, M and Poch, M and Turon, C and De Baets, B and Comas, J}, title = {A new rule generation method to develop a decision support system for integrated management at river basin scale.}, journal = {Water science and technology : a journal of the International Association on Water Pollution Research}, volume = {60}, number = {8}, pages = {2035-2040}, doi = {10.2166/wst.2009.522}, pmid = {19844050}, issn = {0273-1223}, mesh = {Computer Simulation ; Conservation of Natural Resources/*methods ; *Decision Support Techniques ; *Rivers ; Weather ; }, abstract = {The Besòs River Basin authority is working towards the implementation of integrated river basin management, as required by the Water Framework Directive (WFD), to achieve a good ecological and chemical status of all water bodies by 2015. The studied system is constituted by two communities (La Garriga and Granollers), their corresponding draining catchments, sewer systems and two WWTPs, which discharge treated water at different locations of the same river. Within this context, the realisation of an integrated model of the river stretch and of the two WWTPs with their sewer systems and draining catchments was necessary. Such a model allows to efficiently simulate and analyse the behaviour of the integrated system and to optimize its performance holistically. In this article, a method is presented to generate rules to be implemented in a supervisory system for automatic management of the Integrated Urban Wastewater System (IUWS) in dry and storm weather. This is achieved by identifying, with the help of Monte Carlo simulations, the most performing operational parameters-according to environmental and economic criteria-for the two weather conditions.}, } @article {pmid19837657, year = {2010}, author = {Ingvarsson, PK}, title = {Natural selection on synonymous and nonsynonymous mutations shapes patterns of polymorphism in Populus tremula.}, journal = {Molecular biology and evolution}, volume = {27}, number = {3}, pages = {650-660}, doi = {10.1093/molbev/msp255}, pmid = {19837657}, issn = {1537-1719}, mesh = {Adaptation, Biological ; Bayes Theorem ; Codon/genetics ; Computational Biology/*methods ; *Evolution, Molecular ; *Mutation ; Nonlinear Dynamics ; Populus/*genetics ; *Selection, Genetic ; }, abstract = {One important goal of population genetics is to understand the relative importance of different evolutionary processes for shaping variation in natural populations. Here, I use multilocus data to show that natural selection on both synonymous and nonsynonymous mutations plays an important role in shaping levels of synonymous polymorphism in European aspen (Populus tremula). Previous studies have documented a preferential fixation of synonymous mutations encoding preferred codons in P. tremula. The results presented here show that this has resulted in an increase in codon bias in P. tremula, consistent with stronger selection acting on synonymous codon usage. In addition, positive selection on nonsynonymous mutations appears to be common in P. tremula, with approximately 30% of all mutations having been fixed by positive selection. In addition, the recurrent fixation of beneficial mutations also reduces standing levels of polymorphism as evidenced by a significantly negative relationship between the rate of protein evolution synonymous site diversity and silent site diversity. Finally, I use approximate Bayesian methods to estimate the strength of selection acting on beneficial substitutions. These calculations show that recurrent hitchhiking reduces polymorphism by, on average, 30%. The product of strength of selection acting on beneficial mutations and the rate by which these occur across the genome (2N(e)lambdas) equals 1.54x10(- 7), which is in line with estimates from Drosophila where recurrent hitchhiking has also been shown to have significant effects on standing levels of polymorphism.}, } @article {pmid19834728, year = {2010}, author = {Wang, SI and Lee, LT and Zou, ML and Fan, CW and Yaung, CL}, title = {Pregnancy outcome of women in the vicinity of nuclear power plants in Taiwan.}, journal = {Radiation and environmental biophysics}, volume = {49}, number = {1}, pages = {57-65}, pmid = {19834728}, issn = {1432-2099}, mesh = {Adult ; Databases, Factual ; Environmental Exposure/*statistics & numerical data ; Female ; Humans ; Infant, Newborn ; Labor, Obstetric ; *Nuclear Power Plants ; Policy Making ; Pregnancy ; Pregnancy Outcome/*epidemiology ; Pregnancy Trimesters ; Public Health ; Risk ; Taiwan/epidemiology ; Time Factors ; Young Adult ; }, abstract = {The purpose of the study was to investigate whether proximity to nuclear power plants may increase the risk of abnormal pregnant outcomes among the resident women. In this ecological study, data were used from the Health Services Birth Reports Database established by the Bureau of Health Promotion, National Department of Health, Taiwan, in 2001-2004. Chi-square-tests were carried out to investigate the "Plant-vicinity" and "Non plant-vicinity" group in terms of pregnancy outcome. Additionally, logistic regression was performed to investigate whether residence in the vicinity of a nuclear power plant was related to any abnormal pregnancy results. Based on data from 5,679 included subjects, no difference was observed between pregnancy outcomes of the "Plant-vicinity" and "Non plant-vicinity" groups. After accounting for possible confounders, the adjusted odds ratios were 1.20 (95% CI = 0.56-2.56) for stillbirth, 1.21 (95% CI = 0.95-1.53) for premature birth, 1.04 (95% CI = 0.79-1.37) for low birth weight, and 1.58 (95% CI = 0.85-2.93) for congenital deficiencies, respectively, when comparing the "Plant-vicinity" with the "Non plant-vicinity" group. The results of the study indicate that residence in the vicinity of a nuclear power plant is not a significant factor which will cause abnormal health situations during pregnancy.}, } @article {pmid19834481, year = {2009}, author = {Rodriguez-Valera, F and Martin-Cuadrado, AB and Rodriguez-Brito, B and Pasić, L and Thingstad, TF and Rohwer, F and Mira, A}, title = {Explaining microbial population genomics through phage predation.}, journal = {Nature reviews. Microbiology}, volume = {7}, number = {11}, pages = {828-836}, pmid = {19834481}, issn = {1740-1534}, mesh = {Bacteria/classification/*genetics/*virology ; Bacteriophages/genetics/*physiology ; Computational Biology ; *Genome, Bacterial/genetics ; *Genomics ; Models, Biological ; *Population Dynamics ; Selection, Genetic ; Species Specificity ; }, abstract = {The remarkable differences that have been detected by metagenomics in the genomes of strains of the same bacterial species are difficult to reconcile with the widely accepted paradigm that periodic selection within bacterial populations will regularly purge genomic diversity by clonal replacement. We have found that many of the genes that differ between strains affect regions that are potential phage recognition targets. We therefore propose the constant-diversity dynamics model, in which the diversity of prokaryotic populations is preserved by phage predation. We provide supporting evidence for this model from metagenomics, mathematical analysis and computer simulations. Periodic selection and phage predation dynamics are not mutually exclusive; we compare their predictions to shed light on the ecological circumstances under which each type of dynamics could predominate.}, } @article {pmid19823684, year = {2009}, author = {Sumner, MD and Wotherspoon, SJ and Hindell, MA}, title = {Bayesian estimation of animal movement from archival and satellite tags.}, journal = {PloS one}, volume = {4}, number = {10}, pages = {e7324}, pmid = {19823684}, issn = {1932-6203}, mesh = {*Animal Migration ; Animals ; Bayes Theorem ; Behavior, Animal ; Ecology ; Environmental Monitoring ; *Geographic Information Systems ; *Microsatellite Repeats ; Models, Statistical ; Monte Carlo Method ; Satellite Communications ; Species Specificity ; Telemetry/instrumentation ; }, abstract = {The reliable estimation of animal location, and its associated error is fundamental to animal ecology. There are many existing techniques for handling location error, but these are often ad hoc or are used in isolation from each other. In this study we present a Bayesian framework for determining location that uses all the data available, is flexible to all tagging techniques, and provides location estimates with built-in measures of uncertainty. Bayesian methods allow the contributions of multiple data sources to be decomposed into manageable components. We illustrate with two examples for two different location methods: satellite tracking and light level geo-location. We show that many of the problems with uncertainty involved are reduced and quantified by our approach. This approach can use any available information, such as existing knowledge of the animal's potential range, light levels or direct location estimates, auxiliary data, and movement models. The approach provides a substantial contribution to the handling uncertainty in archival tag and satellite tracking data using readily available tools.}, } @article {pmid19818005, year = {2009}, author = {Stephens, PR and Wiens, JJ}, title = {Bridging the gap between community ecology and historical biogeography: niche conservatism and community structure in emydid turtles.}, journal = {Molecular ecology}, volume = {18}, number = {22}, pages = {4664-4679}, doi = {10.1111/j.1365-294X.2009.04378.x}, pmid = {19818005}, issn = {1365-294X}, mesh = {Animals ; Cell Nucleus/genetics ; Climate ; DNA, Mitochondrial/genetics ; *Ecosystem ; Geographic Information Systems ; Geography ; Logistic Models ; Models, Biological ; North America ; *Phylogeny ; Sequence Analysis, DNA ; Turtles/classification/*genetics ; }, abstract = {Historical (phylogenetic) biogeography and community ecology were once integrated as part of the broader study of organismal diversity, but in recent decades have become largely separate disciplines. This is unfortunate because many patterns studied by community ecologists may originate through processes studied by historical biogeographers and vice versa. In this study, we explore the causes of a geographic pattern of community structure (habitat use) in the emydid turtle assemblages of eastern North America, with more semi-terrestrial species of the subfamily Emydinae in the north and more aquatic species of Deirochelyinae in the south. Specifically, we address the factors that prevent northern emydines from invading southern communities. We test for competitive exclusion by examining patterns of range overlap, and test for the role of niche conservatism using analyses of climatic and physiological data based on a multilocus molecular phylogeny. We find no support for competitive exclusion, whereas several lines of evidence support the idea that niche conservatism has prevented northern emydines from dispersing into southern communities. Our results show how understanding the causes of patterns of historical biogeography may help explain patterns of community structure.}, } @article {pmid19816910, year = {2009}, author = {Goulart, VD and Azevedo, PG and van de Schepop, JA and Teixeira, CP and Barçante, L and Azevedo, CS and Young, RJ}, title = {GAPs in the study of zoo and wild animal welfare.}, journal = {Zoo biology}, volume = {28}, number = {6}, pages = {561-573}, doi = {10.1002/zoo.20285}, pmid = {19816910}, issn = {1098-2361}, mesh = {Animal Welfare/*history/*standards/trends ; Animals ; *Animals, Wild ; *Animals, Zoo ; *Bibliometrics ; Databases, Bibliographic ; History, 20th Century ; History, 21st Century ; Journal Impact Factor ; }, abstract = {To investigate the science of animal welfare for zoo and wild animals in the period from 1966 to 2007, we conducted a bibliometric analysis of abstracts downloaded from The Web of Science((c)) database using the keyword combination "Animal welfare, Zoo* and wild" in the topic field. In total we downloaded 1,125 abstracts, which were classified into the following categories: year of publication; environment of the study (e.g., zoo) or theoretical; area of knowledge (e.g., conservation in situ); number of experimental animals used; species; addresses of authors; taxonomic classification; publication language; journal name; number of citations received. Since 1990, there has been a rapid increase in the number of articles published in this area of animal welfare. One worrying result was that published articles were predominately of a theoretical nature (58.65%, N=563). Most of the articles were published by authors either in Europe (47.43%, N=480) or North America (37.65%, N=381) and written in English (87.71%, N=971). The majority of experimental studies were conducted with mammals (75.92%, N=391), and had small sample sizes (N=7 for zoo-based studies). In terms of impact factor (IF), the journals in this study had a median factor equivalent to that for the area of biological sciences (median IF=1.013). Little knowledge cross-over from farm animal welfare was found (only four articles) in this study. In conclusion, zoo and wild animal welfare as a science may benefit from a greater interaction with farm animal welfare.}, } @article {pmid19816576, year = {2009}, author = {Sims, DW and Queiroz, N and Humphries, NE and Lima, FP and Hays, GC}, title = {Long-term GPS tracking of ocean sunfish Mola mola offers a new direction in fish monitoring.}, journal = {PloS one}, volume = {4}, number = {10}, pages = {e7351}, pmid = {19816576}, issn = {1932-6203}, mesh = {Animal Migration ; Animals ; Climate ; Conservation of Natural Resources/*methods ; Ecosystem ; Environmental Monitoring/*instrumentation/methods ; *Geographic Information Systems ; Geography/methods ; Marine Biology/*methods ; Perciformes/*physiology ; Portugal ; Predatory Behavior ; Satellite Communications ; }, abstract = {Satellite tracking of large pelagic fish provides insights on free-ranging behaviour, distributions and population structuring. Up to now, such fish have been tracked remotely using two principal methods: direct positioning of transmitters by Argos polar-orbiting satellites, and satellite relay of tag-derived light-level data for post hoc track reconstruction. Error fields associated with positions determined by these methods range from hundreds of metres to hundreds of kilometres. However, low spatial accuracy of tracks masks important details, such as foraging patterns. Here we use a fast-acquisition global positioning system (Fastloc GPS) tag with remote data retrieval to track long-term movements, in near real time and position accuracy of <70 m, of the world's largest bony fish, the ocean sunfish Mola mola. Search-like movements occurred over at least three distinct spatial scales. At fine scales, sunfish spent longer in highly localised areas with faster, straighter excursions between them. These 'stopovers' during long-distance movement appear consistent with finding and exploiting food patches. This demonstrates the feasibility of GPS tagging to provide tracks of unparalleled accuracy for monitoring movements of large pelagic fish, and with nearly four times as many locations obtained by the GPS tag than by a conventional Argos transmitter. The results signal the potential of GPS-tagged pelagic fish that surface regularly to be detectors of resource 'hotspots' in the blue ocean and provides a new capability for understanding large pelagic fish behaviour and habitat use that is relevant to ocean management and species conservation.}, } @article {pmid19815759, year = {2009}, author = {Field, D and Sansone, SA and Collis, A and Booth, T and Dukes, P and Gregurick, SK and Kennedy, K and Kolar, P and Kolker, E and Maxon, M and Millard, S and Mugabushaka, AM and Perrin, N and Remacle, JE and Remington, K and Rocca-Serra, P and Taylor, CF and Thorley, M and Tiwari, B and Wilbanks, J}, title = {Megascience. 'Omics data sharing.}, journal = {Science (New York, N.Y.)}, volume = {326}, number = {5950}, pages = {234-236}, pmid = {19815759}, issn = {1095-9203}, support = {/WT_/Wellcome Trust/United Kingdom ; 000001/WT_/Wellcome Trust/United Kingdom ; BB/E025080/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {*Computational Biology ; *Genomics ; Guidelines as Topic ; *Information Dissemination ; *Metabolomics ; Public Policy ; }, } @article {pmid19809132, year = {2009}, author = {Wienand, I and Nolting, U and Kistemann, T}, title = {Using Geographical Information Systems (GIS) as an instrument of water resource management: a case study from a GIS-based Water Safety Plan in Germany.}, journal = {Water science and technology : a journal of the International Association on Water Pollution Research}, volume = {60}, number = {7}, pages = {1691-1699}, doi = {10.2166/wst.2009.501}, pmid = {19809132}, issn = {0273-1223}, mesh = {*Environmental Monitoring ; *Geographic Information Systems ; Germany ; Rivers ; Water Movements ; *Water Pollutants, Chemical ; Water Pollution, Chemical/prevention & control ; *Water Supply ; }, abstract = {Following international developments and the new WHO Drinking Water Guidelines (WHO 2004) a process-orientated concept for risk, monitoring and incident management has been developed and implemented in this study. The concept will be reviewed with special consideration for resource protection (first barrier of the multi-barrier system) and in turn, for the Water Safety Plan (WSP) which adequately considers-beyond the current framework of legal requirements-possible new hygienic-microbiologically relevant risks (especially emerging pathogens) for the drinking water supply. The development of a WSP within the framework of risk, monitoring and incident management includes the application of Geographical Information Systems (GIS). In the present study, GIS was used for visualization and spatial analysis in decisive steps in the WSP. The detailed process of GIS-supported implementation included the identification of local participants and their tasks and interactions as an essential part of risk management. A detailed ecological investigation of drinking water conditions in the catchment area was conducted in addition to hazard identification, risk assessment and the monitoring of control measures. The main task of our study was to find out in which steps of the WSP the implementation of GIS could be integrated as a useful, and perhaps even an essential tool.}, } @article {pmid19803171, year = {2009}, author = {Xu, X and Wang, XM and Wang, TH and Liu, YN and Wang, KY}, title = {[Application of "overlay-maps" model in prior period research of ecological planning of Shanghai Expo area].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {20}, number = {5}, pages = {1132-1139}, pmid = {19803171}, issn = {1001-9332}, mesh = {China ; *City Planning ; *Ecosystem ; *Environment Design ; Geographic Information Systems ; Models, Theoretical ; Poaceae/growth & development ; Trees/growth & development ; }, abstract = {An ecological planning approach for Shanghai Expo 2010 was constructed based on "overlay-maps" model, and the ecological elements and GIS visualization in Shanghai Expo 2010 area were investigated and analyzed from the aspects of human comfort degree, life health, and sustainable utilization of resources. This approach included the determination of objectives for ecological planning, the selection and in situ investigation of ecological elements, the construction of eco-database, and the integrative analysis of GIS visualization, being indispensable for the prior period research of ecological planning of Expo area. Based on the present situation of soil pollution in the Expo area, a tentative scheme of soil restoration and utilization was brought forward, with the concerns of green space demand and soil secondary pollution avoidance. To protect the wild life habitats in Expo area, a demarcation of conservation areas for plants and original landscape was made. A conception of using landscape elements to optimize air temperature, humidity, and ventilation in the process of urban design was proposed, aimed to promote the human comfort degree under tropical monsoon conditions.}, } @article {pmid19801441, year = {2009}, author = {Johansson, LC and Hedenström, A}, title = {The vortex wake of blackcaps (Sylvia atricapilla L.) measured using high-speed digital particle image velocimetry (DPIV).}, journal = {The Journal of experimental biology}, volume = {212}, number = {Pt 20}, pages = {3365-3376}, doi = {10.1242/jeb.034454}, pmid = {19801441}, issn = {1477-9145}, mesh = {Animals ; Biomechanical Phenomena ; Flight, Animal/*physiology ; Image Interpretation, Computer-Assisted/instrumentation/*methods ; Models, Biological ; Passeriformes/*anatomy & histology/physiology ; Rheology/instrumentation/*methods ; Tail/anatomy & histology ; Wings, Animal/anatomy & histology ; }, abstract = {Reconstructing the vortex wake of freely flying birds is challenging, but in the past few years, direct measurements of the wake circulation have become available for a number of species. Streamwise circulation has been measured at different positions along the span of the birds, but no measurements have been performed in the transverse plane. Recent findings from studies of bat wakes have pointed to the importance of transverse plane data for reconstructing the wake topology because important structures may be missed otherwise. We present results of high-speed DPIV measurements in the transverse plane behind freely flying blackcaps. We found novel wake structures previously not shown in birds, including wing root vortices of opposite as well as the same sign as the wing tip vortices. This suggests a more complex wake structure in birds than previously assumed and calls for more detailed studies of the flow over the wings and body, respectively. Based on measurements on birds with and without a tail we also tested hypotheses regarding the function of the tail during steady flight. We were unable to detect any differences in the wake pattern between birds with and without a tail. We conclude that the birds do not use their tail to exploit vortices shed at the wing root during the downstroke. Neither did we find support for the hypothesis that the tail should reduce the drag of the bird. The function of the tail during steady flight thus remains unclear and calls for further investigation in future studies.}, } @article {pmid19800066, year = {2009}, author = {Begon, M and Colloud, F and Fohanno, V and Bahuaud, P and Monnet, T}, title = {Computation of the 3D kinematics in a global frame over a 40m-long pathway using a rolling motion analysis system.}, journal = {Journal of biomechanics}, volume = {42}, number = {16}, pages = {2649-2653}, doi = {10.1016/j.jbiomech.2009.08.020}, pmid = {19800066}, issn = {1873-2380}, mesh = {Biomechanical Phenomena/physiology ; Equipment Design ; Equipment Failure Analysis ; Humans ; Image Interpretation, Computer-Assisted/*instrumentation ; Imaging, Three-Dimensional/*instrumentation ; Locomotion/*physiology ; Male ; Monitoring, Ambulatory/*instrumentation ; Whole Body Imaging/*instrumentation/methods ; Young Adult ; }, abstract = {A rolling motion analysis system has been purpose-built to acquire an accurate three-dimensional kinematics of human motion with large displacement. Using this device, the kinematics is collected in a local frame associated with the rolling motion analysis system. The purpose of this paper is to express the local kinematics of a subject walking on a 40 m-long pathway in a global system of co-ordinates. One participant performed five trials of walking while he was followed by a rolling eight camera optoelectronic motion analysis system. The kinematics of the trials were reconstructed in the global frame using two different algorithms and 82 markers placed on the floor organized in two parallel and horizontal lines. The maximal error ranged from 0.033 to 0.187 m (<0.5% of the volume diagonal). As a result, this device is accurate enough for acquiring the kinematics of cyclic activities with large displacements in ecological environment.}, } @article {pmid19798411, year = {2009}, author = {Nan, J and Brostromer, E and Liu, XY and Kristensen, O and Su, XD}, title = {Bioinformatics and structural characterization of a hypothetical protein from Streptococcus mutans: implication of antibiotic resistance.}, journal = {PloS one}, volume = {4}, number = {10}, pages = {e7245}, pmid = {19798411}, issn = {1932-6203}, mesh = {Amino Acid Sequence ; Bacterial Proteins/*chemistry/metabolism ; Computational Biology/*methods ; Crystallography, X-Ray/methods ; Databases, Protein ; Dental Caries/microbiology ; *Drug Resistance, Microbial ; Gene Transfer, Horizontal ; Humans ; Ligands ; Models, Molecular ; Molecular Sequence Data ; Phylogeny ; Protein Structure, Secondary ; Sequence Homology, Amino Acid ; Streptococcus mutans/*metabolism ; }, abstract = {As an oral bacterial pathogen, Streptococcus mutans has been known as the aetiologic agent of human dental caries. Among a total of 1960 identified proteins within the genome of this organism, there are about 500 without any known functions. One of these proteins, SMU.440, has very few homologs in the current protein databases and it does not fall into any protein functional families. Phylogenetic studies showed that SMU.440 is related to a particular ecological niche and conserved specifically in some oral pathogens, due to lateral gene transfer. The co-occurrence of a MarR protein within the same operon among these oral pathogens suggests that SMU.440 may be associated with antibiotic resistance. The structure determination of SMU.440 revealed that it shares the same fold and a similar pocket as polyketide cyclases, which indicated that it is very likely to bind some polyketide-like molecules. From the interlinking structural and bioinformatics studies, we have concluded that SMU.440 could be involved in polyketide-like antibiotic resistance, providing a better understanding of this hypothetical protein. Besides, the combination of multiple methods in this study can be used as a general approach for functional studies of a protein with unknown function.}, } @article {pmid19795653, year = {2009}, author = {Liu, X and Guo, QX}, title = {[Landscape pattern in Northeast China based on moving window method].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {20}, number = {6}, pages = {1415-1422}, pmid = {19795653}, issn = {1001-9332}, mesh = {China ; *Conservation of Natural Resources ; Crops, Agricultural/*growth & development ; *Ecosystem ; Environmental Monitoring/*methods ; Geographic Information Systems ; Geography ; Human Activities ; Rivers ; Temperature ; Trees/*growth & development ; Water/analysis ; }, abstract = {Based on GIS technology and by using moving window method, the characteristics of landscape pattern in Northeast China in 2006 and the relationships between these characteristics and environmental factors such as precipitation, air temperature, altitude and human activities were studied. In the study area in 2006, forest land had the largest proportion, followed by the cultivated land, occupying 61.69% and 25.11% of the total respectively, and the landscape diversity had the characteristics of circle-zoning structure, which provided a buffer region for fragmented and sensitive regions, making the adverse ecological consequences be reduced to or restricted in a definite scale. The correlation coefficients of landscape indices with precipitation and air temperature were less than 0.4, and those with altitude were less than 0.07, illustrating that the heterogeneity of landscape pattern in study area was not dependent on single natural factors.}, } @article {pmid19795652, year = {2009}, author = {Zhang, HF and Ouyang, ZY and Zheng, H and Xu, WH}, title = {[Landscape pattern change and its ecological effect in Manas River Basin of Xinjiang, China].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {20}, number = {6}, pages = {1408-1414}, pmid = {19795652}, issn = {1001-9332}, mesh = {*Agriculture/methods ; China ; *Conservation of Natural Resources ; *Ecosystem ; Environment Design ; Environmental Monitoring/*methods ; Geographic Information Systems ; Geography ; Rivers ; Satellite Communications/instrumentation ; }, abstract = {Based on the 1976, 1989, 2000 and 2005 remote sensing images and related meteorological data, the landscape pattern change and its ecological effect in Manas River Basin of Xinjiang in 1976-2005 were analyzed with GIS and FRAGSTATES. In the study period, the landscape pattern change in the Basin mainly manifested in the increase of farmland, grassland, and residential area while the decrease of forestland, wetland, desert, and snow and ice coverage. At landscape level, the patch number, landscape shape index, and contagion index increased, while Shannon's diversity index decreased; at class level, there was a greater difference in the heterogeneity index among different kinds of landscape, indicating a complexity of the landscape ecosystem. The landscape pattern change caused the negative ecological effect of wetland area shrinking, but some positive effects such as the decrease of evaporation and the increase of relative humidity. From 1976 to 2005, the wetland area decreased from 415.7 km2 to 297.4 km2, with a decrement of 28%, evaporation decreased by 0.91 mm x a(-1), and relative humidity increased by 0.037% x a(-1).}, } @article {pmid19789985, year = {2010}, author = {Skoracka, A and Smith, L and Oldfield, G and Cristofaro, M and Amrine, JW}, title = {Host-plant specificity and specialization in eriophyoid mites and their importance for the use of eriophyoid mites as biocontrol agents of weeds.}, journal = {Experimental & applied acarology}, volume = {51}, number = {1-3}, pages = {93-113}, pmid = {19789985}, issn = {1572-9702}, mesh = {Animals ; Databases as Topic ; Mites/*growth & development ; Pest Control, Biological/*methods ; Plants/*parasitology ; Regression Analysis ; Species Specificity ; }, abstract = {Eriophyoid mites, which are among the smallest plant feeders, are characterized by the intimate relationships they have with their hosts and the restricted range of plants upon which they can reproduce. The knowledge of their true host ranges and mechanisms causing host specificity is fundamental to understanding mite-host interactions, potential mite-host coevolution, and diversity of this group, as well as to apply effective control strategies or to use them as effective biological control agents. The aim of this paper is to review current knowledge on host specificity and specialization in eriophyoid mites, and to point out knowledge gaps and doubts. Using available data on described species and recorded hosts we showed that: (1) 80% of eriophyoids have been reported on only one host species, 95% on one host genus, and 99% on one host family; (2) Diptilomiopidae has the highest proportion of monophagous species and Phytoptidae has the fewest; (3) non-monophagous eriophyoids show the tendency to infest closely related hosts; 4) vagrant eriophyoids have a higher proportion of monophagous species than refuge-seeking and refuge-inducing species; (5) the proportions of monophagous species infesting annual and perennial hosts are similar; however, many species infesting annual hosts have wider host ranges than those infesting perennial hosts; (6) the proportions of species that are monophagous infesting evergreen and deciduous plants are similar; (7) non-monophagous eriophyoid species have wider geographic distribution than monophagous species. Field and laboratory host-specificity tests for several eriophyoid species and their importance for biological control of weeds are described. Testing the actual host range of a given eriophyoid species, searching for ecological data, genetic differentiation analysis, and recognizing factors and mechanisms that contribute to host specificity of eriophyoid mites are suggested as future directions for research.}, } @article {pmid19787059, year = {2009}, author = {Not, F and del Campo, J and Balagué, V and de Vargas, C and Massana, R}, title = {New insights into the diversity of marine picoeukaryotes.}, journal = {PloS one}, volume = {4}, number = {9}, pages = {e7143}, pmid = {19787059}, issn = {1932-6203}, mesh = {Animals ; *Biodiversity ; Ciliophora/physiology ; Cloning, Molecular ; Computational Biology ; DNA, Ribosomal/analysis/*genetics ; Environment ; Eukaryota ; Genetic Variation ; Marine Biology/*methods ; Phylogeny ; Polymerase Chain Reaction ; RNA, Ribosomal, 18S/*genetics ; Seawater ; Sequence Analysis, DNA ; }, abstract = {Over the last decade, culture-independent surveys of marine picoeukaryotic diversity based on 18S ribosomal DNA clone libraries have unveiled numerous sequences of novel high-rank taxa. This newfound diversity has significantly altered our understanding of marine microbial food webs and the evolution of eukaryotes. However, the current picture of marine eukaryotic biodiversity may be significantly skewed by PCR amplification biases, occurrence of rDNA genes in multiple copies within a single cell, and the capacity of DNA to persist as extracellular material. In this study we performed an analysis of the metagenomic dataset from the Global Ocean Survey (GOS) expedition, seeking eukaryotic ribosomal signatures. This PCR-free approach revealed similar phylogenetic patterns to clone library surveys, suggesting that PCR steps do not impose major biases in the exploration of environmental DNA. The different cell size fractions within the GOS dataset, however, displayed a distinct picture. High protistan diversity in the <0.8 microm size fraction, in particular sequences from radiolarians and ciliates (and their absence in the 0.8-3 microm fraction), suggest that most of the DNA in this fraction comes from extracellular material from larger cells. In addition, we compared the phylogenetic patterns from rDNA and reverse transcribed rRNA 18S clone libraries from the same sample harvested in the Mediterranean Sea. The libraries revealed major differences, with taxa such as pelagophytes or picobiliphytes only detected in the 18S rRNA library. MAST (Marine Stramenopiles) appeared as potentially prominent grazers and we observed a significant decrease in the contribution of alveolate and radiolarian sequences, which overwhelmingly dominated rDNA libraries. The rRNA approach appears to be less affected by taxon-specific rDNA copy number and likely better depicts the biogeochemical significance of marine protists.}, } @article {pmid19787045, year = {2009}, author = {Djikeng, A and Kuzmickas, R and Anderson, NG and Spiro, DJ}, title = {Metagenomic analysis of RNA viruses in a fresh water lake.}, journal = {PloS one}, volume = {4}, number = {9}, pages = {e7264}, pmid = {19787045}, issn = {1932-6203}, mesh = {Databases, Genetic ; Ecology ; Fresh Water/*virology ; Genetic Techniques ; Genetic Variation ; Genome, Viral ; Maryland ; Phylogeny ; RNA Viruses/*genetics ; Sequence Alignment ; Software ; *Water Microbiology ; }, abstract = {Freshwater lakes and ponds present an ecological interface between humans and a variety of host organisms. They are a habitat for the larval stage of many insects and may serve as a medium for intraspecies and interspecies transmission of viruses such as avian influenza A virus. Furthermore, freshwater bodies are already known repositories for disease-causing viruses such as Norwalk Virus, Coxsackievirus, Echovirus, and Adenovirus. While RNA virus populations have been studied in marine environments, to this date there has been very limited analysis of the viral community in freshwater. Here we present a survey of RNA viruses in Lake Needwood, a freshwater lake in Maryland, USA. Our results indicate that just as in studies of other aquatic environments, the majority of nucleic acid sequences recovered did not show any significant similarity to known sequences. The remaining sequences are mainly from viral types with significant similarity to approximately 30 viral families. We speculate that these novel viruses may infect a variety of hosts including plants, insects, fish, domestic animals and humans. Among these viruses we have discovered a previously unknown dsRNA virus closely related to Banna Virus which is responsible for a febrile illness and is endemic to Southeast Asia. Moreover we found multiple viral sequences distantly related to Israeli Acute Paralysis virus which has been implicated in honeybee colony collapse disorder. Our data suggests that due to their direct contact with humans, domestic and wild animals, freshwater ecosystems might serve as repositories of a wide range of viruses (both pathogenic and non-pathogenic) and possibly be involved in the spread of emerging and pandemic diseases.}, } @article {pmid19783629, year = {2009}, author = {Nunes, A and Borrego, MJ and Nunes, B and Florindo, C and Gomes, JP}, title = {Evolutionary dynamics of ompA, the gene encoding the Chlamydia trachomatis key antigen.}, journal = {Journal of bacteriology}, volume = {191}, number = {23}, pages = {7182-7192}, pmid = {19783629}, issn = {1098-5530}, mesh = {Amino Acid Sequence ; Antigens, Bacterial/chemistry/classification/genetics/*metabolism ; Bacterial Outer Membrane Proteins/chemistry/classification/genetics/*metabolism ; Chlamydia trachomatis/genetics/*metabolism ; Computational Biology ; *Evolution, Molecular ; Genomics ; Genotype ; Molecular Sequence Data ; Phylogeny ; Sequence Homology, Amino Acid ; }, abstract = {Chlamydia trachomatis is the trachoma agent and causes most bacterial sexually transmitted infections worldwide. Its major outer membrane protein (MOMP) is a well-known porin and adhesin and is the dominant antigen. So far, investigation of MOMP variability has been focused mainly on molecular epidemiological surveys. In contrast, we aimed to evaluate the impact of the host pressure on this key antigen by analyzing its evolutionary dynamics in 795 isolates from urogenital infections, taking into account the MOMP secondary structure and the sizes/positions of antigenic regions. One-third of the specimens showed a mutational drift from the corresponding genotype, where approximately 42% of the mutations had never been described. Amino acid alterations were sixfold more frequent within B-cell epitopes than in the remaining protein (P = 0.027), and some mutations were also found within or close to T-cell antigenic clusters. Interestingly, the two most ecologically successful genotypes, E and F, showed a mutation rate 60.3-fold lower than that of the other genotypes (P < 10(-8)), suggesting that their efficacy may be the result of a better fitness in dealing with the host immune system rather than of specific virulence factors. Furthermore, the variability exhibited by some genetic variants involved residues that are known to play a critical role during the membrane mechanical movements, contributing to a more stable and flexible porin conformation, which suggests some plasticity to deal with environmental pressure. Globally, these MOMP mutational trends yielded no mosaic structures or important phylogenetic changes, but instead yielded point mutations on specific protein domains, which may enhance pathogen's infectivity, persistence, and transmission.}, } @article {pmid19776167, year = {2009}, author = {Barrick, JE and Lenski, RE}, title = {Genome-wide mutational diversity in an evolving population of Escherichia coli.}, journal = {Cold Spring Harbor symposia on quantitative biology}, volume = {74}, number = {}, pages = {119-129}, pmid = {19776167}, issn = {1943-4456}, support = {K99 GM087550/GM/NIGMS NIH HHS/United States ; K99 GM087550-01/GM/NIGMS NIH HHS/United States ; R00 GM087550/GM/NIGMS NIH HHS/United States ; GM-087550/GM/NIGMS NIH HHS/United States ; }, mesh = {DNA, Bacterial/genetics ; Databases, Nucleic Acid ; Escherichia coli/*genetics/physiology ; *Evolution, Molecular ; Genetic Variation ; Genome, Bacterial ; Models, Genetic ; Mutation ; Phenotype ; Polymorphism, Single Nucleotide ; Time Factors ; }, abstract = {The level of genetic variation in a population is the result of a dynamic tension between evolutionary forces. Mutations create variation, certain frequency-dependent interactions may preserve diversity, and natural selection purges variation. New sequencing technologies offer unprecedented opportunities to discover and characterize the diversity present in evolving microbial populations on a whole-genome scale. By sequencing mixed-population samples, we have identified single-nucleotide polymorphisms (SNPs) present at various points in the history of an Escherichia coli population that has evolved for almost 20 years from a founding clone. With 50-fold genome coverage, we were able to catch beneficial mutations as they swept to fixation, discover contending beneficial alleles that were eliminated by clonal interference, and detect other minor variants possibly adapted to a new ecological niche. Additionally, there was a dramatic increase in genetic diversity late in the experiment after a mutator phenotype evolved. Still finer-resolution details of the structure of genetic variation and how it changes over time in microbial evolution experiments will enable new applications and quantitative tests of population genetic theory.}, } @article {pmid19776064, year = {2010}, author = {Stewart, G}, title = {Meta-analysis in applied ecology.}, journal = {Biology letters}, volume = {6}, number = {1}, pages = {78-81}, pmid = {19776064}, issn = {1744-957X}, mesh = {Bayes Theorem ; Conservation of Natural Resources/*methods ; *Data Interpretation, Statistical ; Decision Support Techniques ; Ecology/*methods ; *Meta-Analysis as Topic ; *Uncertainty ; }, abstract = {This overview examines research synthesis in applied ecology and conservation. Vote counting and pooling unweighted averages are widespread despite the superiority of syntheses based on weighted combination of effects. Such analyses allow exploration of methodological uncertainty in addition to consistency of effects across species, space and time, but exploring heterogeneity remains controversial. Meta-analyses are required to generalize in ecology, and to inform evidence-based decision-making, but the more sophisticated statistical techniques and registers of research used in other disciplines must be employed in ecology to fully realize their benefits.}, } @article {pmid19775728, year = {2009}, author = {Poh-Chin, L and Martin, W and Ming-Houng, C and Wing-Cheung, W and Chien-Tat, L}, title = {An ecological study of physical environmental risk factors for elderly falls in an urban setting of Hong Kong.}, journal = {The Science of the total environment}, volume = {407}, number = {24}, pages = {6157-6165}, doi = {10.1016/j.scitotenv.2009.08.042}, pmid = {19775728}, issn = {1879-1026}, mesh = {Accidental Falls/*statistics & numerical data ; Aged ; Cities ; Geographic Information Systems ; Hong Kong ; Humans ; Risk Factors ; }, abstract = {Elderly fall has become an issue of great public health concern and typically important to the aging population in Hong Kong because it carries a great burden to the individuals and the society. More accurate information about environmental risk factors to falls among the elderly could alleviate if not overcome the situation. Conventional approaches to elderly falls were mainly conducted using statistical methods and clinical tests on falls. This study employs ecological and associative analysis using the geographic information systems (GIS) technology to visualize spatial association of falls and environmental factors. The study identified eleven hot spots of elderly falls with unique environmental characteristics. Amongst various environmental attributes, busy streets and junctions, outdoor markets, and refuse collection points, exhibit a strong spatial relationship with the hot spots. The results have demonstrated that GIS can offer an excellent synergic platform to explore the role of space and pattern in fall occurrences.}, } @article {pmid19769997, year = {2010}, author = {Huberty, JL and Balluff, M and O'Dell, M and Peterson, K}, title = {From good ideas to actions: a model-driven community collaborative to prevent childhood obesity.}, journal = {Preventive medicine}, volume = {50 Suppl 1}, number = {}, pages = {S36-43}, doi = {10.1016/j.ypmed.2009.08.013}, pmid = {19769997}, issn = {1096-0260}, mesh = {Child ; Community Networks/*organization & administration ; Community-Institutional Relations ; Health Promotion/methods/*organization & administration ; Humans ; Models, Organizational ; Obesity/*prevention & control ; Program Development ; }, abstract = {OBJECTIVE: Activate Omaha Kids, a community collaborative, was designed, implemented, and evaluated with the aim of preventing childhood obesity in the Omaha community. Activate Omaha Kids brought together key stakeholders and community leaders to create a community coalition. The coalition's aim was to oversee a long-term sustainable approach to preventing obesity. Following a planning phase, a business plan was developed that prioritized best practices to be implemented in Omaha.

METHODS: The business plan was developed using the Ecological Model, Health Policy Model, and Robert Wood Johnson Foundation Active Living by Design 5P model. The three models helped the community identify target populations and activities that then created a single model for sustainable change.

RESULTS: Twenty-four initiatives were identified, over one million dollars in funding was secured, and evaluation strategies were identified.

CONCLUSION: By using the models from the initial steps through evaluation, a clear facilitation of the process was possible, and the result was a comprehensive, feasible plan. The use of the models to design a strategic plan was pivotal in building a sustainable coalition to achieve measurable improvements in the health of children and prove replicable over time.}, } @article {pmid19769125, year = {2009}, author = {Bar-David, S and Bar-David, I and Cross, PC and Ryan, SJ and Knechtel, CU and Getz, WM}, title = {Methods for assessing movement path recursion with application to African buffalo in South Africa.}, journal = {Ecology}, volume = {90}, number = {9}, pages = {2467-2479}, pmid = {19769125}, issn = {0012-9658}, support = {R01 GM083863-02/GM/NIGMS NIH HHS/United States ; R01 GM083863-04/GM/NIGMS NIH HHS/United States ; R01 GM083863-01/GM/NIGMS NIH HHS/United States ; R01 GM083863/GM/NIGMS NIH HHS/United States ; R01 GM083863-03/GM/NIGMS NIH HHS/United States ; }, mesh = {Animal Migration/*physiology ; Animals ; Buffaloes/*physiology ; Demography ; *Ecosystem ; Feeding Behavior ; Geographic Information Systems ; Models, Biological ; South Africa ; Time Factors ; }, abstract = {Recent developments of automated methods for monitoring animal movement, e.g., global positioning systems (GPS) technology, yield high-resolution spatiotemporal data. To gain insights into the processes creating movement patterns, we present two new techniques for extracting information from these data on repeated visits to a particular site or patch ("recursions"). Identification of such patches and quantification of recursion pathways, when combined with patch-related ecological data, should contribute to our understanding of the habitat requirements of large herbivores, of factors governing their space-use patterns, and their interactions with the ecosystem. We begin by presenting output from a simple spatial model that simulates movements of large-herbivore groups based on minimal parameters: resource availability and rates of resource recovery after a local depletion. We then present the details of our new techniques of analyses (recursion analysis and circle analysis) and apply them to data generated by our model, as well as two sets of empirical data on movements of African buffalo (Syncerus caffer): the first collected in Klaserie Private Nature Reserve and the second in Kruger National Park, South Africa. Our recursion analyses of model outputs provide us with a basis for inferring aspects of the processes governing the production of buffalo recursion patterns, particularly the potential influence of resource recovery rate. Although the focus of our simulations was a comparison of movement patterns produced by different resource recovery rates, we conclude our paper with a comprehensive discussion of how recursion analyses can be used when appropriate ecological data are available to elucidate various factors influencing movement. Inter alia, these include the various limiting and preferred resources, parasites, and topographical and landscape factors.}, } @article {pmid19766661, year = {2010}, author = {Ross, JV}, title = {Computationally exact methods for stochastic periodic dynamics: Spatiotemporal dispersal and temporally forced transmission.}, journal = {Journal of theoretical biology}, volume = {262}, number = {1}, pages = {14-22}, doi = {10.1016/j.jtbi.2009.09.014}, pmid = {19766661}, issn = {1095-8541}, mesh = {Adaptation, Biological/physiology ; Aerosols ; Animal Migration/physiology ; Animals ; Birds/physiology ; Computational Biology/*methods ; Computer Simulation ; *Demography ; Disease Transmission, Infectious/*statistics & numerical data ; Ecosystem ; Extinction, Biological ; Humans ; *Periodicity ; Population Dynamics ; Sample Size ; Seasons ; *Stochastic Processes ; Time Factors ; }, abstract = {The dynamics of many diseases and populations possess distinct recurring phases. For example, many species breed only during a subset of the year and the infection dynamics of many pathogens have transmission rates that vary with season. Here I investigate computational methods for studying transient and long-term behaviour of stochastic models which have periodic phases-several different potential techniques for studying long-term behaviour will be contrasted. I illustrate the results with two studies: The first is of a spatially realistic metapopulation model of malleefowl (Leipoa ocellata), a species which disperses only during a quarter of the year; this model is used to highlight the advantages and disadvantages of the particular methods presented. The second study is of a model for disease dynamics which incorporates seasonality in both the rate of within-population transmission and also in the rate of transmission effected via aerosol importation. This model has applications to studying disease invasion and persistence in captive-breeding populations. We demonstrate, via comparison to appropriately matched models with constant transmission rates and also no aerosol transmission, that seasonality and aerosol importation may alter control choices, with possibly an increase in the threshold population size for local control surveillance, transfer of importance to limiting aerosol transmission, and the use of temporally targetted surveillance. The methodology presented is the gold-standard for dealing with many phased processes in ecology and epidemiology, but its application is limited to systems of small size.}, } @article {pmid19765038, year = {2009}, author = {Greenwald, KR and Gibbs, HL and Waite, TA}, title = {Efficacy of land-cover models in predicting isolation of marbled salamander populations in a fragmented landscape.}, journal = {Conservation biology : the journal of the Society for Conservation Biology}, volume = {23}, number = {5}, pages = {1232-1241}, doi = {10.1111/j.1523-1739.2009.01204.x}, pmid = {19765038}, issn = {1523-1739}, mesh = {Animals ; Conservation of Natural Resources ; Geographic Information Systems ; *Models, Theoretical ; Polymorphism, Genetic ; *Urodela/genetics ; }, abstract = {Amphibians worldwide are facing rapid declines due to habitat loss and fragmentation, disease, and other causes. Where habitat alteration is implicated, there is a need for spatially explicit conservation plans. Models built with geographic information systems (GIS) are frequently used to inform such planning. We explored the potential for using GIS models of functional landscape connectivity as a reliable proxy for genetically derived measures of population isolation. We used genetic assignment tests to characterize isolation of marbled salamander populations and evaluated whether the relative amount of modified habitat around breeding ponds was a reliable indicator of population isolation. Using a resampling analysis, we determined whether certain land-cover variables consistently described population isolation. We randomly drew half the data for model building and tested the performance of the best models on the other half 100 times. Deciduous forest was consistently associated with lower levels of population isolation, whereas salamander populations in regions of agriculture and anthropogenic development were more isolated. Models that included these variables and pond size explained 65-70% of variation in genetically inferred isolation across sites. The resampling analysis confirmed that these habitat variables were consistently good predictors of isolation. Used judiciously, simple GIS models with key land-cover variables can be used to estimate population isolation if field sampling and genetic analysis are not possible.}, } @article {pmid19762642, year = {2009}, author = {Cermeño, P and Falkowski, PG}, title = {Controls on diatom biogeography in the ocean.}, journal = {Science (New York, N.Y.)}, volume = {325}, number = {5947}, pages = {1539-1541}, doi = {10.1126/science.1174159}, pmid = {19762642}, issn = {1095-9203}, mesh = {*Biodiversity ; Biological Evolution ; Climatic Processes ; Databases, Factual ; *Diatoms/classification/genetics/physiology ; *Ecosystem ; *Fossils ; Genetic Speciation ; Geography ; Geologic Sediments/*microbiology ; Oceans and Seas ; *Phytoplankton/classification/genetics/physiology ; Seawater/*microbiology ; }, abstract = {The extent to which the spatial distribution of marine planktonic microbes is controlled by local environmental selection or dispersal is poorly understood. Our ability to separate the effects of these two biogeographic controls is limited by the enormous environmental variability both in space and through time. To circumvent this limitation, we analyzed fossil diatom assemblages over the past ~1.5 million years from the world oceans and show that these eukaryotic microbes are not limited by dispersal. The lack of dispersal limitation in marine diatoms suggests that the biodiversity at the microbial level fundamentally differs from that of macroscopic animals and plants for which geographic isolation is a common component of speciation.}, } @article {pmid19762632, year = {2009}, author = {Patterson, DJ}, title = {Ecology. Seeing the big picture on microbe distribution.}, journal = {Science (New York, N.Y.)}, volume = {325}, number = {5947}, pages = {1506-1507}, doi = {10.1126/science.1179690}, pmid = {19762632}, issn = {1095-9203}, mesh = {Arctic Regions ; *Bacteria/classification ; Bacterial Physiological Phenomena ; Biodiversity ; *Diatoms ; *Ecosystem ; Geologic Sediments/*microbiology ; Seawater/*microbiology ; }, } @article {pmid19759036, year = {2009}, author = {Hejnol, A and Obst, M and Stamatakis, A and Ott, M and Rouse, GW and Edgecombe, GD and Martinez, P and Baguñà, J and Bailly, X and Jondelius, U and Wiens, M and Müller, WE and Seaver, E and Wheeler, WC and Martindale, MQ and Giribet, G and Dunn, CW}, title = {Assessing the root of bilaterian animals with scalable phylogenomic methods.}, journal = {Proceedings. Biological sciences}, volume = {276}, number = {1677}, pages = {4261-4270}, pmid = {19759036}, issn = {1471-2954}, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; *Biological Evolution ; Computational Biology ; Likelihood Functions ; Models, Genetic ; Molecular Sequence Data ; *Phylogeny ; Sequence Analysis, DNA ; Sequence Homology ; Turbellaria/*classification/*genetics ; }, abstract = {A clear picture of animal relationships is a prerequisite to understand how the morphological and ecological diversity of animals evolved over time. Among others, the placement of the acoelomorph flatworms, Acoela and Nemertodermatida, has fundamental implications for the origin and evolution of various animal organ systems. Their position, however, has been inconsistent in phylogenetic studies using one or several genes. Furthermore, Acoela has been among the least stable taxa in recent animal phylogenomic analyses, which simultaneously examine many genes from many species, while Nemertodermatida has not been sampled in any phylogenomic study. New sequence data are presented here from organisms targeted for their instability or lack of representation in prior analyses, and are analysed in combination with other publicly available data. We also designed new automated explicit methods for identifying and selecting common genes across different species, and developed highly optimized supercomputing tools to reconstruct relationships from gene sequences. The results of the work corroborate several recently established findings about animal relationships and provide new support for the placement of other groups. These new data and methods strongly uphold previous suggestions that Acoelomorpha is sister clade to all other bilaterian animals, find diminishing evidence for the placement of the enigmatic Xenoturbella within Deuterostomia, and place Cycliophora with Entoprocta and Ectoprocta. The work highlights the implications that these arrangements have for metazoan evolution and permits a clearer picture of ancestral morphologies and life histories in the deep past.}, } @article {pmid19756840, year = {2009}, author = {Bu, L and Xiao, J and Lu, L and Xu, G and Li, J and Zhao, F and Li, X and Wu, J}, title = {The repertoire and evolution of ATP-binding cassette systems in Synechococcus and Prochlorococcus.}, journal = {Journal of molecular evolution}, volume = {69}, number = {4}, pages = {300-310}, pmid = {19756840}, issn = {1432-1432}, mesh = {ATP-Binding Cassette Transporters/chemistry/*genetics ; Bacterial Proteins/chemistry/*genetics ; *Evolution, Molecular ; Fresh Water/microbiology ; Phylogeny ; Prochlorococcus/*genetics ; Protein Structure, Tertiary ; Seawater/microbiology ; Synechococcus/*genetics ; }, abstract = {Synechococcus and Prochlorococcus have made great contributions to earth's photosynthetic biomass. ATP-binding cassette (ABC) protein systems have been characterized to play important roles in various physiological functions, including carbon fixation, phosphate assimilation, and vitamin B(12) metabolism. In this study, the repertoire and domain architectures of ABC systems in Synechococcus and Prochlorococcus, as well as their potential evolutionary mechanism, have been surveyed extensively. Comparative analysis revealed an uneven phylogenetic distribution of the ABC systems in these organisms, and in particular that fresh-water Synechococcus strains contain more ABC systems than those of marine ones. Phylogenetic analysis indicated that lineage-specific gene expansion and duplication may be the important forces driving the variability of ABC systems in fresh-water Synechococcus and such an expansion was likely to be relevant to their ecological tolerance. At the domain level, ATP-binding domains in several ABC systems were found to fuse with many additional domains after the divergence from their common ancestor, indicating the versatile functions of ABC systems in cyanobacteria. Subsequently, 19 ABC system families were deduced to be the core set of ABC systems conserved in all marine-living Synechococcus and Prochlorococcus. In conclusion, the comprehensive survey of ABC systems in Synechococcus and Prochlorococcus provides novel insights into their potential evolutionary mechanism and the basis for further investigation of their physiological roles.}, } @article {pmid19756138, year = {2009}, author = {Aanensen, DM and Huntley, DM and Feil, EJ and al-Own, F and Spratt, BG}, title = {EpiCollect: linking smartphones to web applications for epidemiology, ecology and community data collection.}, journal = {PloS one}, volume = {4}, number = {9}, pages = {e6968}, pmid = {19756138}, issn = {1932-6203}, support = {/WT_/Wellcome Trust/United Kingdom ; 089472/WT_/Wellcome Trust/United Kingdom ; }, mesh = {*Cell Phone ; Computational Biology/*instrumentation/methods ; Computers ; Data Collection/*instrumentation/methods ; Database Management Systems ; Ecology/*instrumentation ; Epidemiology/*instrumentation ; Geography ; Humans ; Information Dissemination ; Internet ; Programming Languages ; Software ; }, abstract = {BACKGROUND: Epidemiologists and ecologists often collect data in the field and, on returning to their laboratory, enter their data into a database for further analysis. The recent introduction of mobile phones that utilise the open source Android operating system, and which include (among other features) both GPS and Google Maps, provide new opportunities for developing mobile phone applications, which in conjunction with web applications, allow two-way communication between field workers and their project databases.

METHODOLOGY: Here we describe a generic framework, consisting of mobile phone software, EpiCollect, and a web application located within www.spatialepidemiology.net. Data collected by multiple field workers can be submitted by phone, together with GPS data, to a common web database and can be displayed and analysed, along with previously collected data, using Google Maps (or Google Earth). Similarly, data from the web database can be requested and displayed on the mobile phone, again using Google Maps. Data filtering options allow the display of data submitted by the individual field workers or, for example, those data within certain values of a measured variable or a time period.

CONCLUSIONS: Data collection frameworks utilising mobile phones with data submission to and from central databases are widely applicable and can give a field worker similar display and analysis tools on their mobile phone that they would have if viewing the data in their laboratory via the web. We demonstrate their utility for epidemiological data collection and display, and briefly discuss their application in ecological and community data collection. Furthermore, such frameworks offer great potential for recruiting 'citizen scientists' to contribute data easily to central databases through their mobile phone.}, } @article {pmid19751076, year = {2009}, author = {Shiffman, S}, title = {How many cigarettes did you smoke? Assessing cigarette consumption by global report, Time-Line Follow-Back, and ecological momentary assessment.}, journal = {Health psychology : official journal of the Division of Health Psychology, American Psychological Association}, volume = {28}, number = {5}, pages = {519-526}, pmid = {19751076}, issn = {1930-7810}, support = {R01 DA006084-09/DA/NIDA NIH HHS/United States ; DA 02074/DA/NIDA NIH HHS/United States ; DA 06084/DA/NIDA NIH HHS/United States ; }, mesh = {Adult ; Bias ; Breath Tests ; Carbon Monoxide/analysis ; *Computers, Handheld ; Cotinine/analysis ; Cross-Sectional Studies ; Data Collection/statistics & numerical data ; Data Interpretation, Statistical ; Female ; *Global Health ; Health Surveys ; Humans ; Male ; *Mental Recall ; Middle Aged ; Saliva/chemistry ; Smoking/*epidemiology ; Smoking Cessation/statistics & numerical data ; *Social Environment ; }, abstract = {OBJECTIVE: This study evaluated and compared several methods of assessing daily cigarette consumption.

DESIGN: Comparison of measures of daily cigarette consumption from several sources, from 232 smokers entering a smoking cessation program.

MAIN OUTCOME MEASURES: Global reports of average smoking, Time-Line Follow-Back (TLFB) recall for the week preceding the study (premonitoring TLFB), 2 weeks' cigarette recordings using electronic diaries and ecological momentary assessment (EMA), and TLFB recall of smoking during EMA (monitored TLFB).

RESULTS: Global reports and premonitoring TLFB showed severe digit bias: six times as many values as expected were rounded at 10. Monitored TLFB also showed substantial digit bias (four times). EMA data showed none. EMA averaged 2.6 cigarettes lower than monitored TLFB, but exceeded TLFB on 32% of days. Across days, EMA and TLFB only correlated 0.29. Daily variations in TLFB did not correlate with variations in carbon monoxide (CO) measures taken on 3 days, but EMA measures did; among participants whose CO varied, r = .69. CO correlated with EMA cigarettes recorded in the preceding 2 hours, suggesting timely recording of cigarettes.

CONCLUSION: TLFB measures are limited for precise assessment of cigarette consumption. EMA measures appear to be useful for tracking smoking, and likely other health-relevant events.}, } @article {pmid19740877, year = {2009}, author = {Powell, JR and Parrent, JL and Hart, MM and Klironomos, JN and Rillig, MC and Maherali, H}, title = {Phylogenetic trait conservatism and the evolution of functional trade-offs in arbuscular mycorrhizal fungi.}, journal = {Proceedings. Biological sciences}, volume = {276}, number = {1676}, pages = {4237-4245}, pmid = {19740877}, issn = {1471-2954}, mesh = {Base Sequence ; Bayes Theorem ; *Biological Evolution ; Biomass ; Computational Biology ; *Ecosystem ; Models, Genetic ; Molecular Sequence Data ; Mycorrhizae/*genetics/*physiology ; Ontario ; *Phenotype ; Phosphorus/analysis ; *Phylogeny ; Plant Roots/microbiology ; Plant Shoots/chemistry/microbiology ; Plantago/microbiology ; Poa/microbiology ; RNA, Ribosomal, 18S/genetics ; Sequence Analysis, DNA ; Soil Microbiology ; Species Specificity ; *Symbiosis ; }, abstract = {The diversity of functional and life-history traits of organisms depends on adaptation as well as the legacy of shared ancestry. Although the evolution of traits in macro-organisms is well studied, relatively little is known about character evolution in micro-organisms. Here, we surveyed an ancient and ecologically important group of microbial plant symbionts, the arbuscular mycorrhizal (AM) fungi, and tested hypotheses about the evolution of functional and life-history traits. Variation in the extent of root and soil colonization by AM fungi is constrained to a few nodes basal to the most diverse groups within the phylum, with relatively little variation associated with recent divergences. We found no evidence for a trade-off in biomass allocated to root versus soil colonization in three published glasshouse experiments; rather these traits were positively correlated. Partial support was observed for correlated evolution between fungal colonization strategies and functional benefits of the symbiosis to host plants. The evolution of increased soil colonization was positively correlated with total plant biomass and shoot phosphorus content. Although the effect of AM fungi on infection by root pathogens was phylogenetically conserved, there was no evidence for correlated evolution between the extent of AM fungal root colonization and pathogen infection. Variability in colonization strategies evolved early in the diversification of AM fungi, and we propose that these strategies were influenced by functional interactions with host plants, resulting in an evolutionary stasis resembling trait conservatism.}, } @article {pmid19731679, year = {2009}, author = {Mutel, CL and Hellweg, S}, title = {Regionalized life cycle assessment: computational methodology and application to inventory databases.}, journal = {Environmental science & technology}, volume = {43}, number = {15}, pages = {5797-5803}, doi = {10.1021/es803002j}, pmid = {19731679}, issn = {0013-936X}, mesh = {Air Pollutants/analysis ; *Databases, Factual ; Ecology ; Ecosystem ; Electricity ; Environment ; Environmental Monitoring/*methods ; Environmental Pollutants/analysis ; Environmental Pollution ; Europe ; Geographic Information Systems ; Risk Assessment ; Software ; }, abstract = {Life cycle assessment (LCA) studies have shown that site-dependent impact assessment for categories like acidification and eutrophication give more accurate and realistic results than site-generic assessments. To date, existing geography-specific, or regionalized, impact assessment factors have not been applied to LCA databases and software tools. We describe a simple, generic methodology to couple existing regionalized characterization factors with large life cycle inventory databases. This approach allows for detailed geographic life cycle impact assessment results. Case-study results for European country-specific electricity mixes are calculated using the Ecoinvent 2.01 database and the EDIP 2003 and Accumulated Exceedance impact assessment methods and CASES project external energy cost characterization factors. In most cases, regionalization shows different total scores, different processes of high importance, and varying geographic distributions of environmental impacts. As the methodology requires no additional input other than the geographic information already in existing LCA databases, it can be used routinely. Better and more consistent geographic information in life cycle inventory databases and impact assessment methods, tailored to the specific spatial range of all environmental effects considered, would be beneficial.}, } @article {pmid19727932, year = {2010}, author = {Fürst, C and Lorz, C and Vacik, H and Potocic, N and Makeschin, F}, title = {How to support forest management in a world of change: results of some regional studies.}, journal = {Environmental management}, volume = {46}, number = {6}, pages = {941-952}, pmid = {19727932}, issn = {1432-1009}, mesh = {Communication ; Decision Support Techniques ; Forestry/*methods/organization & administration ; Information Dissemination ; Marketing ; Planning Techniques ; Trees ; }, abstract = {This article presents results of several studies in Middle, Eastern and Southeastern Europe on needs and application areas, desirable attributes and marketing potentials of forest management support tools. By comparing present and future application areas, a trend from sectoral planning towards landscape planning and integration of multiple stakeholder needs is emerging. In terms of conflicts, where management support tools might provide benefit, no clear tendencies were found, neither on local nor on regional level. In contrast, on national and European levels, support of the implementation of laws, directives, and regulations was found to be of highest importance. Following the user-requirements analysis, electronic tools supporting communication are preferred against paper-based instruments. The users identified most important attributes of optimized management support tools: (i) a broad accessibility for all users at any time should be guaranteed, (ii) the possibility to integrate iteratively experiences from case studies and from regional experts into the knowledge base (learning system) should be given, and (iii) a self-explanatory user interface is demanded, which is also suitable for users rather inexperienced with electronic tools. However, a market potential analysis revealed that the willingness to pay for management tools is very limited, although the participants specified realistic ranges of maximal amounts of money, which would be invested if the products were suitable and payment inevitable. To bridge the discrepancy between unwillingness to pay and the need to use management support tools, optimized financing or cooperation models between practice and science must be found.}, } @article {pmid19720861, year = {2009}, author = {Jiang, ZF and Machado, CA}, title = {Evolution of sex-dependent gene expression in three recently diverged species of Drosophila.}, journal = {Genetics}, volume = {183}, number = {3}, pages = {1175-1185}, pmid = {19720861}, issn = {1943-2631}, mesh = {Animals ; Computational Biology/methods ; Drosophila/classification/*genetics ; *Evolution, Molecular ; Female ; Gene Expression Profiling/*methods ; Genes, Insect/genetics ; Genetic Speciation ; Genetic Variation ; Male ; Monte Carlo Method ; Oligonucleotide Array Sequence Analysis/*methods ; Phylogeny ; Sequence Analysis, DNA/methods ; Sex Factors ; Species Specificity ; }, abstract = {Sexual dimorphism in morphological, physiological, and behavioral traits is pervasive in animals, as is the observation of strong sexual dimorphism in genomewide patterns of gene expression in the few species where this has been studied. Studies of transcriptome divergence show that most interspecific transcriptional divergence is highly sex dependent, an observation consistent with the action of sex-dependent natural selection during species divergence. However, few transcriptome evolution studies have been conducted between recently diverged species (<1 MY). Here, we present analyses of sex-biased transcriptome divergence in sexually mature adults of three recently diverged species of Drosophila: Drosophila pseudoobscura, D. persimilis, and D. pseudoobscura bogotana. Data were collected using a custom designed Agilent oligonucleotide. Expression was detected in 12,507 genes. About 80% of the expressed genes show sex-biased expression in each species. Across species, 21% of the transcriptome shows switches between nonsex bias and sex bias, and just 0.9% of the transcriptome shows reversals of sex-biased expression. Over 80% of the expression divergence between species is due to changes in one sex only. About 15% of the expression divergence between species is due to changes in the same direction in both sexes and just 2% is due to changes in both sexes but in opposite directions. In agreement with previous studies, we observe a high level of sex-dependent transcriptome divergence and strong demasculinization of the two arms of the X chromosome in all species. However, in contrast to previous studies we find that male-biased genes do not have higher levels of expression divergence than non-sex-biased genes, and sex-biased genes show higher levels of expression divergence in the alternate sex, suggesting that sex-biased genes endure stronger selection when expressed in the alternate sex.}, } @article {pmid19720105, year = {2009}, author = {Molander, L and Gerstrand, M and Rudén, C}, title = {WikiPharma - a freely available, easily accessible, interactive and comprehensive database for environmental effect data for pharmaceuticals.}, journal = {Regulatory toxicology and pharmacology : RTP}, volume = {55}, number = {3}, pages = {367-371}, doi = {10.1016/j.yrtph.2009.08.009}, pmid = {19720105}, issn = {1096-0295}, mesh = {*Databases, Factual ; *Drug-Related Side Effects and Adverse Reactions ; Environmental Exposure/adverse effects ; Environmental Pollutants/*toxicity ; Humans ; Sweden ; Water Pollutants, Chemical/adverse effects ; }, abstract = {A significant number of Active Pharmaceutical Ingredients (APIs) have been identified in the environment and in surface waters. Data on the environmental hazards associated with these substances are emerging but are still scarce. We have compiled publicly available ecotoxicity data for APIs into a database called WikiPharma. The use of the database is free of charge. It can be accessed and updated continuously as a "wiki". The aim of WikiPharma is to provide an easily accessible, comprehensive and up-to-date overview of effects caused by pharmaceuticals on non-target organisms. The database currently contains basic information, i.e. substance name, ATC code(s) and pharmaceutical group(s), for 831 APIs representing 35 different drug classes. Effect data have been identified and included for 116 of these substances. These ecotoxicity test data have been extracted from 156 different sources. The development of a comprehensive database on ecological hazard of APIs can facilitate identification of data gaps and promote environmental risk assessment of these substances. The database is available at www.wikipharma.org.}, } @article {pmid19719021, year = {2009}, author = {Stagner, MW and Lansing, J}, title = {Progress toward a prevention perspective.}, journal = {The Future of children}, volume = {19}, number = {2}, pages = {19-38}, doi = {10.1353/foc.0.0036}, pmid = {19719021}, issn = {1054-8289}, mesh = {Child ; Child Abuse/*prevention & control ; Child, Preschool ; Community Networks ; Humans ; Models, Theoretical ; Parent-Child Relations ; Preventive Health Services/*methods/*organization & administration/trends ; Professional-Family Relations ; Risk Factors ; Social Support ; }, abstract = {Matthew Stagner and Jiffy Lansing chart developments in the field of child maltreatment and propose a new framework for preventing child abuse and neglect. They begin by describing the concept of investment-prevention as it has been applied recently in fields such as health care and welfare. They then explain how the new framework applies to maltreatment prevention, noting in particular how it differs from the traditional child protective services response to maltreatment. Whereas the traditional response aims to prevent a recurrence of maltreatment once it has already taken place, the new framework focuses on preventing maltreatment from occurring at all. Rather than identifying risk factors for maltreatment and addressing the problems and deficiencies of the primary caretaker, the new framework focuses on strengthening protective factors and building family and social networks to reinforce the ability of parents to care for their children. Whereas the orientation of the traditional child welfare service approach is legal and medical, the new framework has a more developmental and ecological orientation. It aims to build on the strengths children have at particular points of the life stage and enhance the social context of the child. Rather than putting families into the hands of unknown professionals who shuffle them from one program to another, including foster care, the investment-prevention model seeks to integrate professionals and paraprofessionals from the family's community into their everyday life, as well as to ensure an interconnected system of services. Finally, rather than seeking to minimize harm to the child, it aims to maximize potential--to strengthen the capacity of parents and communities to care for their children in ways that promote well-being. Researchers have struggled to define maltreatment, identify its causes, and assess its consequences and costs. In recent years, however, researchers have clarified the severe consequences of child maltreatment and highlighted several risk factors. They have also developed new prevention interventions based on a variety of theories explaining why maltreatment takes place. Stagner and Lansing conclude with a brief survey of these new prevention interventions. The task for researchers now, they say, is to conduct rigorous evaluations of the interventions to demonstrate the benefits of prevention.}, } @article {pmid19716379, year = {2010}, author = {Bastani, R and Glenn, BA and Taylor, VM and Chen, MS and Nguyen, TT and Stewart, SL and Maxwell, AE}, title = {Integrating theory into community interventions to reduce liver cancer disparities: The Health Behavior Framework.}, journal = {Preventive medicine}, volume = {50}, number = {1-2}, pages = {63-67}, pmid = {19716379}, issn = {1096-0260}, support = {P01 CA109091-01A1/CA/NCI NIH HHS/United States ; P01 CA109091/CA/NCI NIH HHS/United States ; U01 CA114640/CA/NCI NIH HHS/United States ; U01 CA 114640/CA/NCI NIH HHS/United States ; P01 CA109091-040003/CA/NCI NIH HHS/United States ; }, mesh = {Asia, Southeastern/ethnology ; Asian ; California ; *Community Networks ; *Health Status Disparities ; Hepatitis B/prevention & control ; Humans ; Liver Neoplasms/ethnology/*prevention & control ; Mass Screening ; *Models, Theoretical ; Program Development ; *Risk Reduction Behavior ; }, abstract = {Mitigating the unequal burden of cancer often involves conducting community-based trials to develop effective intervention strategies to promote cancer-related health behaviors. However, this is challenging due to the simultaneous influence of numerous factors, at multiple levels in the socio-ecological context, on health behavior. A sound conceptual framework can bring order to this complex environment and provide a roadmap for systematically addressing the multiple determinants of the behavior in question. This paper describes the application of The Health Behavior Framework, an integrative conceptual model, in an ongoing Program Project, "Liver Cancer Control Interventions for Asian-Americans." The Framework has been integral to shaping all aspects of the three component research trials from selection of the study designs to development of the interventions and data collection instruments. We advocate universal adoption of theory into community-based intervention research as a way to accelerate our ability to develop effective interventions and facilitate synthesis of study results across populations and behavioral outcomes: critical steps in advancing the field of health disparities research.}, } @article {pmid19706155, year = {2009}, author = {Rounge, TB and Rohrlack, T and Nederbragt, AJ and Kristensen, T and Jakobsen, KS}, title = {A genome-wide analysis of nonribosomal peptide synthetase gene clusters and their peptides in a Planktothrix rubescens strain.}, journal = {BMC genomics}, volume = {10}, number = {}, pages = {396}, pmid = {19706155}, issn = {1471-2164}, mesh = {Computational Biology ; Cyanobacteria/*genetics/metabolism ; DNA, Bacterial/genetics ; Evolution, Molecular ; Genes, Bacterial ; Genome, Bacterial ; *Genome-Wide Association Study ; *Multigene Family ; Oligopeptides/biosynthesis ; Peptide Synthases/*genetics ; Phylogeny ; Sequence Analysis, DNA/methods ; }, abstract = {BACKGROUND: Cyanobacteria often produce several different oligopeptides, with unknown biological functions, by nonribosomal peptide synthetases (NRPS). Although some cyanobacterial NRPS gene cluster types are well described, the entire NRPS genomic content within a single cyanobacterial strain has never been investigated. Here we have combined a genome-wide analysis using massive parallel pyrosequencing ("454") and mass spectrometry screening of oligopeptides produced in the strain Planktothrix rubescens NIVA CYA 98 in order to identify all putative gene clusters for oligopeptides.

RESULTS: Thirteen types of oligopeptides were uncovered by mass spectrometry (MS) analyses. Microcystin, cyanopeptolin and aeruginosin synthetases, highly similar to already characterized NRPS, were present in the genome. Two novel NRPS gene clusters were associated with production of anabaenopeptins and microginins, respectively. Sequence-depth of the genome and real-time PCR data revealed three copies of the microginin gene cluster. Since NRPS gene cluster candidates for microviridin and oscillatorin synthesis could not be found, putative (gene encoded) precursor peptide sequences to microviridin and oscillatorin were found in the genes mdnA and oscA, respectively. The genes flanking the microviridin and oscillatorin precursor genes encode putative modifying enzymes of the precursor oligopeptides. We therefore propose ribosomal pathways involving modifications and cyclisation for microviridin and oscillatorin. The microviridin, anabaenopeptin and cyanopeptolin gene clusters are situated in close proximity to each other, constituting an oligopeptide island.

CONCLUSION: Altogether seven nonribosomal peptide synthetase (NRPS) gene clusters and two gene clusters putatively encoding ribosomal oligopeptide biosynthetic pathways were revealed. Our results demonstrate that whole genome shotgun sequencing combined with MS-directed determination of oligopeptides successfully can identify NRPS gene clusters and the corresponding oligopeptides. The analyses suggest independent evolution of all NRPS gene clusters as functional units. Our data indicate that the Planktothrix genome displays evolution of dual pathways (NRPS and ribosomal) for production of oligopeptides in order to maximize the diversity of oligopeptides with similar but functional discrete bioactivities.}, } @article {pmid19695137, year = {2009}, author = {Flauzino, RF and Souza-Santos, R and Oliveira, RM}, title = {[Dengue, geoprocessing, and socioeconomic and environmental indicators: a review].}, journal = {Revista panamericana de salud publica = Pan American journal of public health}, volume = {25}, number = {5}, pages = {456-461}, doi = {10.1590/s1020-49892009000500012}, pmid = {19695137}, issn = {1020-4989}, mesh = {Dengue/*epidemiology ; Environment ; Geographic Information Systems ; Humans ; Latin America/epidemiology ; Socioeconomic Factors ; }, abstract = {OBJECTIVE: To further understand the disease behavior of dengue by analyzing studies on dengue and geoprocessing, as well as socioeconomic and environmental indicators.

METHOD: MEDLINE, SciELO, and Lilacs databases, as well as the CAPES dissertation databank, were searched using the following key words: dengue, geographic information system, spatial analysis, geoprocessing, remote sensing, and socioenvironmental indicators. A manual search of the bibliographies of select articles was also performed. All studies published in English, Portuguese, or Spanish, through December 2007, that focused on dengue, geoprocessing, and socioeconomic and environmental indicators were included. The relevant articles were grouped according to type (serologic surveys or secondary data analyses) and spatial analysis unit (municipality, health district, neighborhood, administrative region, census tracts, and city blocks).

RESULTS: Twenty-two studies from Latin America (19 from Brazil) were evaluated. Six were serologic surveys and 16 employed secondary data. Geographic information systems were employed in one survey, and 11 used secondary data analyses. Spatial clustering was similar in both types of studies. Poverty was not a major risk factor for the disease. Spatial heterogeneity of living conditions and incidence was reported by 15 of 16 studies with secondary data.

CONCLUSIONS: Since the complexity of dengue is closely tied to the ecological characteristics of the environment, studies based on spatial clusters plus local environmental determinants provide a more comprehensive view of the disease. These studies also allow for the identification of spatial heterogeneity, shown to be a key to understanding how dengue epidemics develop.}, } @article {pmid19691615, year = {2009}, author = {Norman, C and Zarrinkoub, R and Hasselström, J and Godman, B and Granath, F and Wettermark, B}, title = {Potential savings without compromising the quality of care.}, journal = {International journal of clinical practice}, volume = {63}, number = {9}, pages = {1320-1326}, doi = {10.1111/j.1742-1241.2009.02129.x}, pmid = {19691615}, issn = {1742-1241}, mesh = {Angiotensin-Converting Enzyme Inhibitors/economics/therapeutic use ; Anticholesteremic Agents/*economics/therapeutic use ; Antihypertensive Agents/*economics/therapeutic use ; Cost Savings ; Cross-Sectional Studies ; Diabetes Mellitus/drug therapy/*economics ; Guideline Adherence ; Health Expenditures ; Humans ; Hydroxymethylglutaryl-CoA Reductase Inhibitors/economics/therapeutic use ; Hypercholesterolemia/drug therapy/*economics ; Hypertension/drug therapy/*economics ; Hypoglycemic Agents/*economics/therapeutic use ; Practice Guidelines as Topic ; Primary Health Care/economics ; Quality of Health Care ; Simvastatin/economics/therapeutic use ; Sweden ; }, abstract = {AIMS: This study was designed to analyse the association between adherence to guidelines for rational drug use and surrogate outcome markers for hypertension, diabetes and hypercholesterolaemia.

METHODS: The study used a cross-sectional ecological design. Data from dispensed prescriptions and medical records were analysed from 24 primary healthcare centres with a combined registered population of 330,000 patients in 2006. Guideline adherence was determined calculating the proportion of the prescribed volume of antidiabetic agents, antihypertensives and lipid-lowering agents representing the 14 different drugs included in the guidelines for these three areas. Patient outcome was assessed using surrogate marker data on HbA1C, blood pressure (BP) and s-cholesterol. The association between the guidelines adherence and outcomes measures was analysed by logistic regression.

RESULTS: The proportion of guideline antidiabetic drugs in relation to all antidiabetic drugs prescribed varied between 80% and 97% among the practices, the ratio of angiotensin converting enzyme (ACE)-inhibitors to all renin-angiotensin drugs 40-77% and the ratio of simvastatin to all statins 58-90%. The proportion of patients reaching targets for HbA1C, BP and s-cholesterol varied between 34% and 66%, 36% and 57% and 46% and 71% respectively. No significant associations were found between adherence to the guidelines and outcome. The expenditures for antihypertensives and lipid-lowering drugs could potentially be reduced by 10% and 50% respectively if all practices adhered to the guidelines as the top performing practices.

CONCLUSION: A substantial amount of money can be saved in primary care without compromising the quality of care by using recommended first-line drugs for the treatment diabetes, hypertension and hypercholesterolaemia.}, } @article {pmid19688917, year = {2009}, author = {Martin, J and Runge, MC and Nichols, JD and Lubow, BC and Kendall, WL}, title = {Structured decision making as a conceptual framework to identify thresholds for conservation and management.}, journal = {Ecological applications : a publication of the Ecological Society of America}, volume = {19}, number = {5}, pages = {1079-1090}, doi = {10.1890/08-0255.1}, pmid = {19688917}, issn = {1051-0761}, mesh = {*Conservation of Natural Resources ; *Decision Making ; Decision Support Techniques ; Models, Theoretical ; }, abstract = {Thresholds and their relevance to conservation have become a major topic of discussion in the ecological literature. Unfortunately, in many cases the lack of a clear conceptual framework for thinking about thresholds may have led to confusion in attempts to apply the concept of thresholds to conservation decisions. Here, we advocate a framework for thinking about thresholds in terms of a structured decision making process. The purpose of this framework is to promote a logical and transparent process for making informed decisions for conservation. Specification of such a framework leads naturally to consideration of definitions and roles of different kinds of thresholds in the process. We distinguish among three categories of thresholds. Ecological thresholds are values of system state variables at which small changes bring about substantial changes in system dynamics. Utility thresholds are components of management objectives (determined by human values) and are values of state or performance variables at which small changes yield substantial changes in the value of the management outcome. Decision thresholds are values of system state variables at which small changes prompt changes in management actions in order to reach specified management objectives. The approach that we present focuses directly on the objectives of management, with an aim to providing decisions that are optimal with respect to those objectives. This approach clearly distinguishes the components of the decision process that are inherently subjective (management objectives, potential management actions) from those that are more objective (system models, estimates of system state). Optimization based on these components then leads to decision matrices specifying optimal actions to be taken at various values of system state variables. Values of state variables separating different actions in such matrices are viewed as decision thresholds. Utility thresholds are included in the objectives component, and ecological thresholds may be embedded in models projecting consequences of management actions. Decision thresholds are determined by the above-listed components of a structured decision process. These components may themselves vary over time, inducing variation in the decision thresholds inherited from them. These dynamic decision thresholds can then be determined using adaptive management. We provide numerical examples (that are based on patch occupancy models) of structured decision processes that include all three kinds of thresholds.}, } @article {pmid19687804, year = {2009}, author = {Holsinger, KE and Weir, BS}, title = {Genetics in geographically structured populations: defining, estimating and interpreting F(ST).}, journal = {Nature reviews. Genetics}, volume = {10}, number = {9}, pages = {639-650}, pmid = {19687804}, issn = {1471-0064}, support = {R01 GM068449/GM/NIGMS NIH HHS/United States ; R01 GM075091/GM/NIGMS NIH HHS/United States ; 1 R01 GM 068449-01A1/GM/NIGMS NIH HHS/United States ; 1 R01 GM 075091/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; *Data Interpretation, Statistical ; Gene Frequency ; Genetic Variation ; Genetics, Population/methods/*statistics & numerical data ; Geography ; Humans ; Population Groups/*genetics/statistics & numerical data ; Statistics as Topic ; }, abstract = {Wright's F-statistics, and especially F(ST), provide important insights into the evolutionary processes that influence the structure of genetic variation within and among populations, and they are among the most widely used descriptive statistics in population and evolutionary genetics. Estimates of F(ST) can identify regions of the genome that have been the target of selection, and comparisons of F(ST) from different parts of the genome can provide insights into the demographic history of populations. For these reasons and others, F(ST) has a central role in population and evolutionary genetics and has wide applications in fields that range from disease association mapping to forensic science. This Review clarifies how F(ST) is defined, how it should be estimated, how it is related to similar statistics and how estimates of F(ST) should be interpreted.}, } @article {pmid19686400, year = {2009}, author = {Baisch, MJ}, title = {Community health: an evolutionary concept analysis.}, journal = {Journal of advanced nursing}, volume = {65}, number = {11}, pages = {2464-2476}, doi = {10.1111/j.1365-2648.2009.05068.x}, pmid = {19686400}, issn = {1365-2648}, mesh = {*Community Health Nursing ; *Community Networks ; Community Participation/psychology ; *Concept Formation ; *Cooperative Behavior ; *Health Promotion ; *Health Services Needs and Demand ; Humans ; Socioeconomic Factors ; }, abstract = {TITLE: Community health: an evolutionary concept analysis.

AIM: This paper is a report of a concept analysis of community health.

BACKGROUND: Community health is a term that has been broadly used in both research and practice. Although local communities are invested in community health improvement, this process often occurs without a clear definition of the concept of community health.

DATA SOURCES: Data sources included a sample of 537 papers covering the period 1990 to 2004 and representing the disciplines of nursing, public health, medicine and sociology and landmark works concerning community health, six community health assessment instruments and interviews with seven key community health informants.

REVIEW METHODS: Rodgers' Evolutionary Method of Concept Analysis was used to design the study and analyse the data. The professional literature was analysed and compared with the use of the concept of community health in community health assessment instruments and by key informants.

RESULTS: Dynamic and contextual, community health is achieved through participatory, community development processes based upon ecological models that address broad determinants of health. The primary focus of this collaborative work is population-based health promotion and disease prevention.

CONCLUSION: The definition derived from the concept analysis of community health makes explicit the importance of community-based participatory action in local health improvement processes. Identification of the attributes of community health will enhance communication across disciplines involved in community health practice, research and education.}, } @article {pmid19684980, year = {2009}, author = {Nasser, JT and Donalisio, MR and Vasconcelos, CH}, title = {[Spatial distribution of American tegumentary leishmaniasis cases in Campinas, State of São Paulo, between 1992 and 2003].}, journal = {Revista da Sociedade Brasileira de Medicina Tropical}, volume = {42}, number = {3}, pages = {309-314}, doi = {10.1590/s0037-86822009000300013}, pmid = {19684980}, issn = {1678-9849}, mesh = {Adolescent ; Adult ; Animals ; Brazil/epidemiology ; Female ; *Geographic Information Systems ; Humans ; Insect Vectors ; Leishmaniasis, Cutaneous/*epidemiology/transmission ; Male ; Middle Aged ; Psychodidae ; Retrospective Studies ; Socioeconomic Factors ; Space-Time Clustering ; Young Adult ; }, abstract = {This is a retrospective study with ecological features that describes the epidemiological pattern and geographical distribution of American tegumentary leishmaniasis cases in Campinas, São Paulo, between 1992 and 2003. The probable infection locations were georeferenced by means of Global Position System and spatially described using Spring 4.01 Beta software from the Brazilian National Space Research Institute. A kernel estimator was applied to identify areas of case concentration, three epidemic areas with higher case intensity were found in the municipal area in 1993/1995 and 2002/2003. Socio-demographic (gender, age, occupation, residence time), closeness of domicile to forest, and clinical form of the disease were studied. Although socio-environment characteristics of the areas were different, epidemics profiles were similar. Age, sex and occupational distribution suggest peri-domestic transmission. Proximity to forest has been a risk factor.}, } @article {pmid19682285, year = {2009}, author = {Wilkins, O and Waldron, L and Nahal, H and Provart, NJ and Campbell, MM}, title = {Genotype and time of day shape the Populus drought response.}, journal = {The Plant journal : for cell and molecular biology}, volume = {60}, number = {4}, pages = {703-715}, doi = {10.1111/j.1365-313X.2009.03993.x}, pmid = {19682285}, issn = {1365-313X}, mesh = {Databases, Genetic ; *Droughts ; Gene Expression Profiling ; Gene Expression Regulation, Plant ; *Genotype ; Oligonucleotide Array Sequence Analysis ; *Photoperiod ; Plant Stomata/physiology ; Plant Transpiration ; Populus/*genetics/*physiology ; RNA, Plant/genetics ; Trees/genetics ; Water/metabolism ; }, abstract = {As exposure to episodic drought can impinge significantly on forest health and the establishment of productive tree plantations, there is great interest in understanding the mechanisms of drought response in trees. The ecologically dominant and economically important genus Populus, with its sequenced genome, provides an ideal opportunity to examine transcriptome level changes in trees in response to a drought stimulus. The transcriptome level drought response of two commercially important Populus clones (P. deltoides x P. nigra, DN34, and P. nigra x P. maximowiczii, NM6) was characterized over a diurnal period using a 4 x 2 x 2 complete randomized factorial anova experimental design (four time points, two genotypes and two treatment conditions), using Affymetrix Poplar GeneChip microarrays. Notably, the specific genes that exhibited changes in transcript abundance in response to drought differed between the genotypes and/or the time of day that they exhibited their greatest differences. This study emphasizes the fact that it is not possible to draw simple, generalized conclusions about the drought response of the genus Populus on the basis of one species, nor on the basis of results collected at a single time point. The data derived from our studies provide insights into the variety of genetic mechanisms underpinning the Populus drought response, and provide candidates for future experiments aimed at understanding this response across this economically and ecologically important genus.}, } @article {pmid19674334, year = {2009}, author = {Hallik, L and Niinemets, Ü and Wright, IJ}, title = {Are species shade and drought tolerance reflected in leaf-level structural and functional differentiation in Northern Hemisphere temperate woody flora?.}, journal = {The New phytologist}, volume = {184}, number = {1}, pages = {257-274}, doi = {10.1111/j.1469-8137.2009.02918.x}, pmid = {19674334}, issn = {1469-8137}, mesh = {*Adaptation, Physiological ; Biomass ; Databases as Topic ; *Droughts ; *Ecosystem ; Photosynthesis ; Plant Leaves/*anatomy & histology/*physiology ; *Plant Physiological Phenomena ; Quantitative Trait, Heritable ; Regression Analysis ; Species Specificity ; Wood ; }, abstract = {Leaf-level determinants of species environmental stress tolerance are still poorly understood. Here, we explored dependencies of species shade (T(shade)) and drought (T(drought)) tolerance scores on key leaf structural and functional traits in 339 Northern Hemisphere temperate woody species. In general, T(shade) was positively associated with leaf life-span (L(L)), and negatively with leaf dry mass (M(A)), nitrogen content (N(A)), and photosynthetic capacity (A(A)) per area, while opposite relationships were observed with drought tolerance. Different trait combinations responsible for T(shade) and T(drought) were observed among the key plant functional types: deciduous and evergreen broadleaves and evergreen conifers. According to principal component analysis, resource-conserving species with low N content and photosynthetic capacity, and high L(L) and M(A), had higher T(drought), consistent with the general stress tolerance strategy, whereas variation in T(shade) did not concur with the postulated stress tolerance strategy. As drought and shade often interact in natural communities, reverse effects of foliar traits on these key environmental stress tolerances demonstrate that species niche differentiation is inherently constrained in temperate woody species. Different combinations of traits among key plant functional types further explain the contrasting bivariate correlations often observed in studies seeking functional explanation of variation in species environmental tolerances.}, } @article {pmid19673500, year = {2009}, author = {Zhao, XM and Zhang, XW and Tang, WH and Chen, L}, title = {FPPI: Fusarium graminearum protein-protein interaction database.}, journal = {Journal of proteome research}, volume = {8}, number = {10}, pages = {4714-4721}, doi = {10.1021/pr900415b}, pmid = {19673500}, issn = {1535-3907}, mesh = {Databases, Protein ; Fungal Proteins/*chemistry/metabolism ; Fusarium/*chemistry/pathogenicity ; Plant Diseases/microbiology ; Poaceae ; Protein Binding ; Protein Interaction Domains and Motifs ; Protein Interaction Mapping/*methods ; Proteomics/*methods ; Reproducibility of Results ; Research Design ; Two-Hybrid System Techniques ; }, abstract = {The fungal pathogen Fusarium graminearum (telomorph Gibberella zeae) is the causal agent of several destructive crop diseases. Identifying interactions among F. graminearum proteins and understanding their functions can provide insights into pathogenic mechanisms underlying F. graminearum-host interactions. F. graminearum protein-protein interaction (FPPI) database provides comprehensive information of protein-protein interactions (PPIs) of F. graminearum predicted based on both interologs from several PPI databases of seven species and domain-domain interactions experimentally determined based on protein structures. FPPI contains 223,166 interactions among 7406 proteins for F. graminearum. To the best of our knowledge, it is the first PPI map for this destructive fungus, which is thereby expected to shed light on biological functions of F. graminearum proteins. The predicted interactome covers about 52% of the whole F. graminearum proteome, and each interaction is assigned a score as the confidence for the predicted PPI. In particular, we constructed a core PPI data set with high confidence that consists of 27,102 interactions and 3745 proteins. To verify the reliability of the predicted interactome, we conducted yeast two-hybrid experiments over 3 randomly selected predictions from the core PPI data set, among which one pair of proteins was confirmed to indeed interact with each other, thereby proving high confidence on the core PPI data set. In addition, FPPI contains other functional information for F. graminearum genes, including homologues in other species deposited in different databases and the inferred functional characteristics, and so on. We further constructed an intuitive query interface for the database that provides easy access to the important features of proteins. In summary, FPPI is a rich source of information for system-level understanding of gene functions and biological processes in F. graminearum. Public access to the FPPI database is available at http://csb.shu.edu.cn/fppi.}, } @article {pmid19671163, year = {2009}, author = {Knudsen, B and Miyamoto, MM}, title = {Accurate and fast methods to estimate the population mutation rate from error prone sequences.}, journal = {BMC bioinformatics}, volume = {10}, number = {}, pages = {247}, pmid = {19671163}, issn = {1471-2105}, mesh = {Algorithms ; Computational Biology/*methods ; *Genetics, Population ; *Mutation ; Population Density ; Sequence Alignment ; }, abstract = {BACKGROUND: The population mutation rate (theta) remains one of the most fundamental parameters in genetics, ecology, and evolutionary biology. However, its accurate estimation can be seriously compromised when working with error prone data such as expressed sequence tags, low coverage draft sequences, and other such unfinished products. This study is premised on the simple idea that a random sequence error due to a chance accident during data collection or recording will be distributed within a population dataset as a singleton (i.e., as a polymorphic site where one sampled sequence exhibits a unique base relative to the common nucleotide of the others). Thus, one can avoid these random errors by ignoring the singletons within a dataset.

RESULTS: This strategy is implemented under an infinite sites model that focuses on only the internal branches of the sample genealogy where a shared polymorphism can arise (i.e., a variable site where each alternative base is represented by at least two sequences). This approach is first used to derive independently the same new Watterson and Tajima estimators of theta, as recently reported by Achaz 1 for error prone sequences. It is then used to modify the recent, full, maximum-likelihood model of Knudsen and Miyamoto 2, which incorporates various factors for experimental error and design with those for coalescence and mutation. These new methods are all accurate and fast according to evolutionary simulations and analyses of a real complex population dataset for the California seahare.

CONCLUSION: In light of these results, we recommend the use of these three new methods for the determination of theta from error prone sequences. In particular, we advocate the new maximum likelihood model as a starting point for the further development of more complex coalescent/mutation models that also account for experimental error and design.}, } @article {pmid19661405, year = {2009}, author = {Sanchez, PA and Ahamed, S and Carré, F and Hartemink, AE and Hempel, J and Huising, J and Lagacherie, P and McBratney, AB and McKenzie, NJ and Mendonça-Santos, Mde L and Minasny, B and Montanarella, L and Okoth, P and Palm, CA and Sachs, JD and Shepherd, KD and Vågen, TG and Vanlauwe, B and Walsh, MG and Winowiecki, LA and Zhang, GL}, title = {Environmental science. Digital soil map of the world.}, journal = {Science (New York, N.Y.)}, volume = {325}, number = {5941}, pages = {680-681}, doi = {10.1126/science.1175084}, pmid = {19661405}, issn = {1095-9203}, mesh = {Agriculture ; Climate ; *Databases, Factual ; *Ecology ; Ecosystem ; Environment ; Humans ; *Soil/analysis ; }, } @article {pmid19656373, year = {2009}, author = {Patil, AP and Okiro, EA and Gething, PW and Guerra, CA and Sharma, SK and Snow, RW and Hay, SI}, title = {Defining the relationship between Plasmodium falciparum parasite rate and clinical disease: statistical models for disease burden estimation.}, journal = {Malaria journal}, volume = {8}, number = {}, pages = {186}, pmid = {19656373}, issn = {1475-2875}, support = {#079091/WT_/Wellcome Trust/United Kingdom ; 079091/WT_/Wellcome Trust/United Kingdom ; #079080/WT_/Wellcome Trust/United Kingdom ; 079080/WT_/Wellcome Trust/United Kingdom ; #086166/WT_/Wellcome Trust/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; }, mesh = {Animals ; Cost of Illness ; Databases, Factual ; Endemic Diseases/*statistics & numerical data ; Humans ; Incidence ; Malaria, Falciparum/*epidemiology/parasitology ; Models, Biological ; *Models, Statistical ; Normal Distribution ; Plasmodium falciparum/isolation & purification/pathogenicity ; Prevalence ; }, abstract = {BACKGROUND: Clinical malaria has proven an elusive burden to enumerate. Many cases go undetected by routine disease recording systems. Epidemiologists have, therefore, frequently defaulted to actively measuring malaria in population cohorts through time. Measuring the clinical incidence of malaria longitudinally is labour-intensive and impossible to undertake universally. There is a need, therefore, to define a relationship between clinical incidence and the easier and more commonly measured index of infection prevalence: the "parasite rate". This relationship can help provide an informed basis to define malaria burdens in areas where health statistics are inadequate.

METHODS: Formal literature searches were conducted for Plasmodium falciparum malaria incidence surveys undertaken prospectively through active case detection at least every 14 days. The data were abstracted, standardized and geo-referenced. Incidence surveys were time-space matched with modelled estimates of infection prevalence derived from a larger database of parasite prevalence surveys and modelling procedures developed for a global malaria endemicity map. Several potential relationships between clinical incidence and infection prevalence were then specified in a non-parametric Gaussian process model with minimal, biologically informed, prior constraints. Bayesian inference was then used to choose between the candidate models.

RESULTS: The suggested relationships with credible intervals are shown for the Africa and a combined America and Central and South East Asia regions. In both regions clinical incidence increased slowly and smoothly as a function of infection prevalence. In Africa, when infection prevalence exceeded 40%, clinical incidence reached a plateau of 500 cases per thousand of the population per annum. In the combined America and Central and South East Asia regions, this plateau was reached at 250 cases per thousand of the population per annum. A temporal volatility model was also incorporated to facilitate a closer description of the variance in the observed data.

CONCLUSION: It was possible to model a relationship between clinical incidence and P. falciparum infection prevalence but the best-fit models were very noisy reflecting the large variance within the observed opportunistic data sample. This continuous quantification allows for estimates of the clinical burden of P. falciparum of known confidence from wherever an estimate of P. falciparum prevalence is available.}, } @article {pmid19650732, year = {2009}, author = {Daniels, TJ and Falco, RC and McHugh, EE and Vellozzi, J and Boccia, T and Denicola, AJ and Pound, JM and Miller, JA and George, JE and Fish, D}, title = {Acaricidal treatment of white-tailed deer to control Ixodes scapularis (Acari: Ixodidae) in a New York Lyme disease-endemic community.}, journal = {Vector borne and zoonotic diseases (Larchmont, N.Y.)}, volume = {9}, number = {4}, pages = {381-387}, doi = {10.1089/vbz.2008.0197}, pmid = {19650732}, issn = {1557-7759}, mesh = {Acaricides/*administration & dosage ; Analysis of Variance ; Animal Feed ; Animals ; Arachnid Vectors/growth & development ; Deer/*parasitology ; Endemic Diseases/prevention & control ; Geographic Information Systems ; Humans ; *Ixodes/growth & development ; Lyme Disease/*prevention & control ; New York ; Tick Control/*methods/statistics & numerical data ; Tick Infestations/prevention & control/*veterinary ; Zea mays ; }, abstract = {The efficacy of topically treating white-tailed deer with an acaricide was evaluated in a Lyme disease-endemic community of southern New York State. Twenty-four 4-Poster feeders were placed in a 5.2 km(2) treatment area in Bedford, NY, while a site in Lewisboro, NY, 4.8 km distant, served as control. Treatment periods ran from 15 September to 15 December each fall from 1997 to 2001, and from 15 March to 15 May each spring from 1998 to 2002. Corn consumption averaged 15,779 kg in fall sessions and 9054 kg in spring sessions, and a mean of 89.6% of deer in the study area showed evidence of using the feeders. Deer densities, estimated by aerial snow counts, averaged 22 and 28 deer per km(2) in Bedford and Lewisboro, respectively, over a 3-year period. Significant reductions in tick numbers on deer captured in the treatment area were noted in fall 1999 compared to deer captured at the control site. Drag sampling for nymphal host-seeking ticks indicated 63.6% control in 2001, which dropped to 54.8% the following year, but reached 80% in 2003. Higher-than-normal acorn production in 2001 that likely caused a drop in deer visitation to the feeders may have reduced efficacy against larval ticks in 2002. The 4-Poster effectively reduced the density of Ixodes scapularis, though the level of control is dependent on environmental factors that affect feeding behavior of white-tailed deer.}, } @article {pmid19647082, year = {2009}, author = {Zhou, L and Bai, R and Tian, J and Liu, X and Lu, D and Zhu, P and Liu, Y and Zeng, L and Luo, W and Zhang, Y and Wang, A}, title = {Bioinformatic comparisons and tissue expression of the neuronal nitric oxide synthase (nNOS) gene from the red drum (Sciaenops ocellatus).}, journal = {Fish & shellfish immunology}, volume = {27}, number = {4}, pages = {577-584}, doi = {10.1016/j.fsi.2009.07.010}, pmid = {19647082}, issn = {1095-9947}, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Computational Biology ; DNA, Complementary/genetics ; Gene Expression Regulation, Enzymologic/*physiology ; Molecular Sequence Data ; Nitric Oxide Synthase Type I/genetics/*metabolism ; Perciformes/*metabolism ; Phylogeny ; Tissue Distribution ; }, abstract = {The full length cDNA sequence for neuronal nitric oxide synthase (nNOS) gene from red drum (Sciaenops ocellatus) has been cloned, subjected to bioinformatic analysis, and examined for expression in different tissues. Red drum nNOS showed high identity to nNOS of mammals and other fish species. Notably, a unique 7-aa insertion was found in the important catalytic sites of the NO synthase domain, possibly affecting the function of red drum nNOS. Furthermore, this nNOS was expressed not only in brain but also in most of the internal organs including liver, intestine, spleen, head kidney and thymus.}, } @article {pmid19646234, year = {2009}, author = {Probst, JC and Laditka, JN and Laditka, SB}, title = {Association between community health center and rural health clinic presence and county-level hospitalization rates for ambulatory care sensitive conditions: an analysis across eight US states.}, journal = {BMC health services research}, volume = {9}, number = {}, pages = {134}, pmid = {19646234}, issn = {1472-6963}, support = {U1CRH03711-03//PHS HHS/United States ; }, mesh = {Adolescent ; Adult ; Aged ; Ambulatory Care/*statistics & numerical data ; Child ; Child, Preschool ; Community Health Centers/*supply & distribution ; Cross-Sectional Studies ; Databases as Topic ; Health Services Accessibility ; Hospitalization/*trends ; Humans ; Infant ; Infant, Newborn ; Middle Aged ; Patient Discharge/statistics & numerical data ; Poisson Distribution ; Rural Health Services/*supply & distribution ; United States ; Young Adult ; }, abstract = {BACKGROUND: Federally qualified community health centers (CHCs) and rural health clinics (RHCs) are intended to provide access to care for vulnerable populations. While some research has explored the effects of CHCs on population health, little information exists regarding RHC effects. We sought to clarify the contribution that CHCs and RHCs may make to the accessibility of primary health care, as measured by county-level rates of hospitalization for ambulatory care sensitive (ACS) conditions.

METHODS: We conducted an ecologic analysis of the relationship between facility presence and county-level hospitalization rates, using 2002 discharge data from eight states within the US (579 counties). Counties were categorized by facility availability: CHC(s) only, RHC(s) only, both (CHC and RHC), and neither. US Agency for Healthcare Research and Quality definitions were used to identify ACS diagnoses. Discharge rates were based on the individual's county of residence and were obtained by dividing ACS hospitalizations by the relevant county population. We calculated ACS rates separately for children, working age adults, and older individuals, and for uninsured children and working age adults. To ensure stable rates, we excluded counties having fewer than 1,000 residents in the child or working age adult categories, or 500 residents among those 65 and older. Multivariate Poisson analysis was used to calculate adjusted rate ratios.

RESULTS: Among working age adults, rate ratio (RR) comparing ACS hospitalization rates for CHC-only counties to those of counties with neither facility was 0.86 (95% Confidence Interval, CI, 0.78-0.95). Among older adults, the rate ratio for CHC-only counties compared to counties with neither facility was 0.84 (CI 0.81-0.87); for counties with both CHC and RHC present, the RR was 0.88 (CI 0.84-0.92). No CHC/RHC effects were found for children. No effects were found on estimated hospitalization rates among uninsured populations.

CONCLUSION: Our results suggest that CHCs and RHCs may play a useful role in providing access to primary health care. Their presence in a county may help to limit the county's rate of hospitalization for ACS diagnoses, particularly among older people.}, } @article {pmid19645273, year = {2009}, author = {Foley, DH and Wilkerson, RC and Rueda, LM}, title = {Importance of the "what," "when," and "where" of mosquito collection events.}, journal = {Journal of medical entomology}, volume = {46}, number = {4}, pages = {717-722}, doi = {10.1603/033.046.0401}, pmid = {19645273}, issn = {0022-2585}, mesh = {Animals ; Biodiversity ; *Culicidae ; Databases, Factual ; *Geographic Information Systems ; Internet ; *Mosquito Control ; Population Density ; }, abstract = {There is increasing need to apply established standards for recording data on mosquito collection events, because of the diversity of potential data providers, and the growth and interoperability of online databases designed to host these collection records. In particular, adequate taxonomic and georeference data are needed for geodatabases such as Mosquitomap (http://www. mosquitomap.org/) that map and compare these collection points with other spatial information in a geographical information system (GIS) setting. Accurately georeferenced collection data are crucial for understanding mosquito biogeography, ecology, and the impact of environmental changes, as well as for species distribution modeling, planning mosquito surveys, and for determining disease risk. We sampled representative published reports of new mosquito species records from 1980 in North America to the present to ascertain the quality of georeference information. Our results show that authors have increased the frequency of reporting georeferences but that they vary in the precision of the georeference, and some information, such as the source, date, and datum of the georeference, are usually not given. We discuss recently established standards for recording collection events, some relevant online resources available to researchers to assist them in their georeferencing, and the data input schema developed for the Mosquitomap database. We propose that the mosquito research community adopt data standards for recording and reporting the results of mosquito collection events to increase the value of these data. In particular, we recommend authors lodge voucher specimens and use a GPS set to the WGS84 datum.}, } @article {pmid19640306, year = {2009}, author = {Fleury, E and Huvet, A and Lelong, C and de Lorgeril, J and Boulo, V and Gueguen, Y and Bachère, E and Tanguy, A and Moraga, D and Fabioux, C and Lindeque, P and Shaw, J and Reinhardt, R and Prunet, P and Davey, G and Lapègue, S and Sauvage, C and Corporeau, C and Moal, J and Gavory, F and Wincker, P and Moreews, F and Klopp, C and Mathieu, M and Boudry, P and Favrel, P}, title = {Generation and analysis of a 29,745 unique Expressed Sequence Tags from the Pacific oyster (Crassostrea gigas) assembled into a publicly accessible database: the GigasDatabase.}, journal = {BMC genomics}, volume = {10}, number = {}, pages = {341}, pmid = {19640306}, issn = {1471-2164}, mesh = {Animals ; Crassostrea/*genetics ; *Databases, Genetic ; *Expressed Sequence Tags ; Gene Expression Profiling ; Gene Library ; Genome ; Genomics/methods ; Microsatellite Repeats ; Polymorphism, Single Nucleotide ; Sequence Analysis, DNA ; User-Computer Interface ; }, abstract = {BACKGROUND: Although bivalves are among the most-studied marine organisms because of their ecological role and economic importance, very little information is available on the genome sequences of oyster species. This report documents three large-scale cDNA sequencing projects for the Pacific oyster Crassostrea gigas initiated to provide a large number of expressed sequence tags that were subsequently compiled in a publicly accessible database. This resource allowed for the identification of a large number of transcripts and provides valuable information for ongoing investigations of tissue-specific and stimulus-dependant gene expression patterns. These data are crucial for constructing comprehensive DNA microarrays, identifying single nucleotide polymorphisms and microsatellites in coding regions, and for identifying genes when the entire genome sequence of C. gigas becomes available.

DESCRIPTION: In the present paper, we report the production of 40,845 high-quality ESTs that identify 29,745 unique transcribed sequences consisting of 7,940 contigs and 21,805 singletons. All of these new sequences, together with existing public sequence data, have been compiled into a publicly-available Website http://public-contigbrowser.sigenae.org:9090/Crassostrea_gigas/index.html. Approximately 43% of the unique ESTs had significant matches against the SwissProt database and 27% were annotated using Gene Ontology terms. In addition, we identified a total of 208 in silico microsatellites from the ESTs, with 173 having sufficient flanking sequence for primer design. We also identified a total of 7,530 putative in silico, single-nucleotide polymorphisms using existing and newly-generated EST resources for the Pacific oyster.

CONCLUSION: A publicly-available database has been populated with 29,745 unique sequences for the Pacific oyster Crassostrea gigas. The database provides many tools to search cleaned and assembled ESTs. The user may input and submit several filters, such as protein or nucleotide hits, to select and download relevant elements. This database constitutes one of the most developed genomic resources accessible among Lophotrochozoans, an orphan clade of bilateral animals. These data will accelerate the development of both genomics and genetics in a commercially-important species with the highest annual, commercial production of any aquatic organism.}, } @article {pmid19637608, year = {2009}, author = {Zhou, R and Li, YH and Hu, YM and Zhang, JH and Liu, M}, title = {[Protection regionalization of Houshi Forest Park based on landscape sensitivity].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {20}, number = {3}, pages = {665-672}, pmid = {19637608}, issn = {1001-9332}, mesh = {China ; *Conservation of Natural Resources ; *Ecology ; *Environment Design ; Forestry ; Geographic Information Systems ; Trees/*growth & development ; }, abstract = {By using GIS technology, and selecting slope, relative distance to viewpoints, relative distance to tourism roads, visual probability of viewpoints, and visual probability of tourism roads as the indices, the landscape sensitivity of Houshi Forest Park was assessed, and an integrated assessment model was established. The AHP method was utilized to determine the weights of the indices, and further, to identify the integrated sensitivity class of the areas in the Park. Four classes of integrated sensitivity area were divided. Class I had an area of 297.24 hm2, occupying 22.9% of the total area of the Park, which should be strictly protected to maintain natural landscape, and prohibited any exploitation or construction. Class II had an area of 359.72 hm2, accounting for 27.8% of the total. The hills in this area should be kept from destroying to protect vegetation and water, but the simple byway and stone path could be built. Class III had an area reached up to 495.80 hm2, occupying 38.3% of the total, which could be moderately exploited, and artificial landscape was advocated to beautify and set off natural landscape. Class IV had the smallest area (142.80 hm2) accounting for 11% of the total, which had the greatest potential of exploitation, being possible to build large-scale integrated tourism facilities and travelling roads.}, } @article {pmid19635847, year = {2009}, author = {Parks, DH and Porter, M and Churcher, S and Wang, S and Blouin, C and Whalley, J and Brooks, S and Beiko, RG}, title = {GenGIS: A geospatial information system for genomic data.}, journal = {Genome research}, volume = {19}, number = {10}, pages = {1896-1904}, pmid = {19635847}, issn = {1549-5469}, mesh = {Africa ; Biodiversity ; Classification ; DNA, Mitochondrial/analysis/genetics ; *Databases, Genetic ; Genetic Variation ; Genomics/*methods ; *Geographic Information Systems ; HIV-1/classification/genetics/metabolism ; Humans ; Oceans and Seas ; Phylogeny ; *Software ; Specimen Handling/methods ; }, abstract = {The increasing availability of genetic sequence data associated with explicit geographic and ecological information is offering new opportunities to study the processes that shape biodiversity. The generation and testing of hypotheses using these data sets requires effective tools for mathematical and visual analysis that can integrate digital maps, ecological data, and large genetic, genomic, or metagenomic data sets. GenGIS is a free and open-source software package that supports the integration of digital map data with genetic sequences and environmental information from multiple sample sites. Essential bioinformatic and statistical tools are integrated into the software, allowing the user a wide range of analysis options for their sequence data. Data visualizations are combined with the cartographic display to yield a clear view of the relationship between geography and genomic diversity, with a particular focus on the hierarchical clustering of sites based on their similarity or phylogenetic proximity. Here we outline the features of GenGIS and demonstrate its application to georeferenced microbial metagenomic, HIV-1, and human mitochondrial DNA data sets.}, } @article {pmid19629735, year = {2010}, author = {Huang, PH and Tsai, JS and Lin, WT}, title = {Using multiple-criteria decision-making techniques for eco-environmental vulnerability assessment: a case study on the Chi-Jia-Wan Stream watershed, Taiwan.}, journal = {Environmental monitoring and assessment}, volume = {168}, number = {1-4}, pages = {141-158}, pmid = {19629735}, issn = {1573-2959}, mesh = {Conservation of Natural Resources ; *Decision Making, Computer-Assisted ; Ecosystem ; *Environment ; Environmental Monitoring/*methods ; Geographic Information Systems ; Geological Phenomena ; Multivariate Analysis ; Rivers/*chemistry ; Taiwan ; Water Pollutants ; Water Pollution/*analysis/statistics & numerical data ; }, abstract = {The Chi-Jia-Wan Stream watershed, located in the area of the upstream Da-Chia River in central Taiwan, is famous for slopeland agriculture and the land-locked salmon. Improper agricultural activities have caused apparent ecosystem vulnerability and sensitivity. In this study, a system that combined three watershed-based environmental indicators with multiple-criteria decision-making techniques, the Analytical Hierarchy Process, and the Preference Ranking Organization METHod for Enrichment Evaluations was developed to assess eco-environmental vulnerability. The composite evaluation index system was set up including sediment, runoff, and nutrient factors. Supported by geographic information system and K-means clustering and taking the subwatershed as the evaluation unit, the vulnerability is classified into four levels: potential, low, moderate, and high. The evaluated results show that 8.82% of subwatersheds (six subwatersheds) are in the moderately and highly vulnerable zones. These subwatersheds represent vertical-belt distribution, mainly concentrated in the right side of the studied area and near the riparian zone along the Chi-Jia-Wan Stream. The exploited farmland in the moderately and highly vulnerable zones is about 142.21 ha, occupying 75.38% of the total farmland in the studied watershed. These seriously vulnerable zones that have caused degradation in the quality of the eco-environment should be treated with more best management practices for eco-environmental rehabilitation. Additionally, the proposed model can effectively evaluate the eco-environmental vulnerability grade for reference in policy planning and ecological restoration in this area.}, } @article {pmid19627627, year = {2009}, author = {Simoonga, C and Utzinger, J and Brooker, S and Vounatsou, P and Appleton, CC and Stensgaard, AS and Olsen, A and Kristensen, TK}, title = {Remote sensing, geographical information system and spatial analysis for schistosomiasis epidemiology and ecology in Africa.}, journal = {Parasitology}, volume = {136}, number = {13}, pages = {1683-1693}, pmid = {19627627}, issn = {1469-8161}, support = {/WT_/Wellcome Trust/United Kingdom ; 081673/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Africa/epidemiology ; Animals ; Bayes Theorem ; Ecosystem ; *Geographic Information Systems ; Humans ; Models, Biological ; Population Surveillance/*methods ; Satellite Communications ; Schistosomiasis/*epidemiology ; Snails ; }, abstract = {Beginning in 1970, the potential of remote sensing (RS) techniques, coupled with geographical information systems (GIS), to improve our understanding of the epidemiology and control of schistosomiasis in Africa, has steadily grown. In our current review, working definitions of RS, GIS and spatial analysis are given, and applications made to date with RS and GIS for the epidemiology and ecology of schistosomiasis in Africa are summarised. Progress has been made in mapping the prevalence of infection in humans and the distribution of intermediate host snails. More recently, Bayesian geostatistical modelling approaches have been utilized for predicting the prevalence and intensity of infection at different scales. However, a number of challenges remain; hence new research is needed to overcome these limitations. First, greater spatial and temporal resolution seems important to improve risk mapping and understanding of transmission dynamics at the local scale. Second, more realistic risk profiling can be achieved by taking into account information on people's socio-economic status; furthermore, future efforts should incorporate data on domestic access to clean water and adequate sanitation, as well as behavioural and educational issues. Third, high-quality data on intermediate host snail distribution should facilitate validation of infection risk maps and modelling transmission dynamics. Finally, more emphasis should be placed on risk mapping and prediction of multiple species parasitic infections in an effort to integrate disease risk mapping and to enhance the cost-effectiveness of their control.}, } @article {pmid19625306, year = {2010}, author = {Rowe, W and Platt, M and Wedge, DC and Day, PJ and Kell, DB and Knowles, J}, title = {Analysis of a complete DNA-protein affinity landscape.}, journal = {Journal of the Royal Society, Interface}, volume = {7}, number = {44}, pages = {397-408}, pmid = {19625306}, issn = {1742-5662}, support = {BB/D017432/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; PBB/D000203/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Adaptation, Biological/genetics ; Aptamers, Nucleotide/*metabolism ; Computational Biology ; DNA-Binding Proteins/*metabolism ; Evolution, Molecular ; Models, Genetic ; Phycocyanin/chemistry/genetics/*metabolism ; }, abstract = {Properties of biological fitness landscapes are of interest to a wide sector of the life sciences, from ecology to genetics to synthetic biology. For biomolecular fitness landscapes, the information we currently possess comes primarily from two sources: sparse samples obtained from directed evolution experiments; and more fine-grained but less authentic information from 'in silico' models (such as NK-landscapes). Here we present the entire protein-binding profile of all variants of a nucleic acid oligomer 10 bases in length, which we have obtained experimentally by a series of highly parallel on-chip assays. The resulting complete landscape of sequence-binding pairs, comprising more than one million binding measurements in duplicate, has been analysed statistically using a number of metrics commonly applied to synthetic landscapes. These metrics show that the landscape is rugged, with many local optima, and that this arises from a combination of experimental variation and the natural structural properties of the oligonucleotides.}, } @article {pmid19622670, year = {2009}, author = {Zhao, Y and Wei, W and Lee, IM and Shao, J and Suo, X and Davis, RE}, title = {Construction of an interactive online phytoplasma classification tool, iPhyClassifier, and its application in analysis of the peach X-disease phytoplasma group (16SrIII).}, journal = {International journal of systematic and evolutionary microbiology}, volume = {59}, number = {Pt 10}, pages = {2582-2593}, pmid = {19622670}, issn = {1466-5026}, mesh = {Bacterial Typing Techniques ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; *Internet ; Molecular Sequence Data ; Online Systems ; Phylogeny ; Phytoplasma/*classification/*genetics/isolation & purification ; Plant Diseases/*microbiology ; Polymorphism, Restriction Fragment Length ; Prunus/*microbiology ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Software ; }, abstract = {Phytoplasmas, the causal agents of numerous plant diseases, are insect-vector-transmitted, cell-wall-less bacteria descended from ancestral low-G+C-content Gram-positive bacteria in the Bacillus-Clostridium group. Despite their monophyletic origin, widely divergent phytoplasma lineages have evolved in adaptation to specific ecological niches. Classification and taxonomic assignment of phytoplasmas have been based primarily on molecular analysis of 16S rRNA gene sequences because of the inaccessibility of measurable phenotypic characters suitable for conventional microbial characterization. In the present study, an interactive online tool, iPhyClassifier, was developed to expand the efficacy and capacity of the current 16S rRNA gene sequence-based phytoplasma classification system. iPhyClassifier performs sequence similarity analysis, simulates laboratory restriction enzyme digestions and subsequent gel electrophoresis and generates virtual restriction fragment length polymorphism (RFLP) profiles. Based on calculated RFLP pattern similarity coefficients and overall sequence similarity scores, iPhyClassifier makes instant suggestions on tentative phytoplasma 16Sr group/subgroup classification status and 'Candidatus Phytoplasma' species assignment. Using iPhyClassifier, we revised and updated the classification of strains affiliated with the peach X-disease phytoplasma group. The online tool can be accessed at http://www.ba.ars.usda.gov/data/mppl/iPhyClassifier.html.}, } @article {pmid19621796, year = {2009}, author = {Potemkina, NS}, title = {[Human ecology, nutrition culture and modern information technologies].}, journal = {Aviakosmicheskaia i ekologicheskaia meditsina = Aerospace and environmental medicine}, volume = {43}, number = {2}, pages = {13-16}, pmid = {19621796}, issn = {0233-528X}, mesh = {*Ecosystem ; Feeding Behavior/*psychology ; *Health Status ; Humans ; Medical Informatics/*trends ; }, abstract = {Extensive use of information technologies in advertising and teaching healthy dietary habits could foster the culture of nutrition within the domain of consumption culture and have effect on the global agriculture and foods industry. Besides, it could implant in the public mind careful and respectful attitude to the planetary resources, personal health as a national wealth and substrate for intellectual growth, and awareness that nutrition is one of the most important links of humans to nature.}, } @article {pmid19619890, year = {2009}, author = {Linkov, I and Loney, D and Cormier, S and Satterstrom, FK and Bridges, T}, title = {Weight-of-evidence evaluation in environmental assessment: review of qualitative and quantitative approaches.}, journal = {The Science of the total environment}, volume = {407}, number = {19}, pages = {5199-5205}, doi = {10.1016/j.scitotenv.2009.05.004}, pmid = {19619890}, issn = {1879-1026}, mesh = {Decision Support Techniques ; *Ecotoxicology ; Environmental Medicine/*methods ; Health Status ; Humans ; Risk Assessment/methods ; }, abstract = {Assessments of human health and ecological risk draw upon multiple types and sources of information, requiring the integration of multiple lines of evidence before conclusions may be reached. Risk assessors often make use of weight-of-evidence (WOE) approaches to perform the integration, whether integrating evidence concerning potential carcinogenicity, toxicity, and exposure from chemicals at a contaminated site, or evaluating processes concerned with habitat loss or modification when managing a natural resource. Historically, assessors have relied upon qualitative WOE approaches, such as professional judgment, or limited quantitative methods, such as direct scoring, to develop conclusions from multiple lines of evidence. Current practice often lacks transparency resulting in risk estimates lacking quantified uncertainty. This paper reviews recent applications of weight of evidence used in human health and ecological risk assessment. Applications are sorted based on whether the approach relies on qualitative and quantitative methods in order to reveal trends in the use of the term weight of evidence, especially as a means to facilitate structured and transparent development of risk conclusions from multiple lines of evidence.}, } @article {pmid19619336, year = {2009}, author = {Williams, RA and Peterson, AT}, title = {Ecology and geography of avian influenza (HPAI H5N1) transmission in the Middle East and northeastern Africa.}, journal = {International journal of health geographics}, volume = {8}, number = {}, pages = {47}, pmid = {19619336}, issn = {1476-072X}, mesh = {Africa, Northern/epidemiology ; Animals ; Birds ; *Demography ; Ecology/*trends ; Geographic Information Systems ; Humans ; *Influenza A Virus, H5N1 Subtype ; Influenza in Birds/epidemiology/*transmission ; Middle East/epidemiology ; Species Specificity ; }, abstract = {BACKGROUND: The emerging highly pathogenic avian influenza strain H5N1 ("HPAI-H5N1") has spread broadly in the past decade, and is now the focus of considerable concern. We tested the hypothesis that spatial distributions of HPAI-H5N1 cases are related consistently and predictably to coarse-scale environmental features in the Middle East and northeastern Africa.We used ecological niche models to relate virus occurrences to 8 km resolution digital data layers summarizing parameters of monthly surface reflectance and landform. Predictive challenges included a variety of spatial stratification schemes in which models were challenged to predict case distributions in broadly unsampled areas.

RESULTS: In almost all tests, HPAI-H5N1 cases were indeed occurring under predictable sets of environmental conditions, generally predicted absent from areas with low NDVI values and minimal seasonal variation, and present in areas with a broad range of and appreciable seasonal variation in NDVI values. Although we documented significant predictive ability of our models, even between our study region and West Africa, case occurrences in the Arabian Peninsula appear to follow a distinct environmental regime.

CONCLUSION: Overall, we documented a variable environmental "fingerprint" for areas suitable for HPAI-H5N1 transmission.}, } @article {pmid19617385, year = {2009}, author = {Zinger, L and Coissac, E and Choler, P and Geremia, RA}, title = {Assessment of microbial communities by graph partitioning in a study of soil fungi in two Alpine meadows.}, journal = {Applied and environmental microbiology}, volume = {75}, number = {18}, pages = {5863-5870}, pmid = {19617385}, issn = {1098-5336}, mesh = {Animals ; *Biodiversity ; *Cluster Analysis ; Computational Biology/*methods ; DNA, Fungal/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Fungi/*classification/*genetics/isolation & purification ; Genes, rRNA ; Molecular Sequence Data ; Phylogeny ; RNA, Fungal/genetics ; RNA, Ribosomal/genetics ; Sequence Analysis, DNA ; *Soil Microbiology ; }, abstract = {Understanding how microbial community structure and diversity respond to environmental conditions is one of the main challenges in environmental microbiology. However, there is often confusion between determining the phylogenetic structure of microbial communities and assessing the distribution and diversity of molecular operational taxonomic units (MOTUs) in these communities. This has led to the use of sequence analysis tools such as multiple alignments and hierarchical clustering that are not adapted to the analysis of large and diverse data sets and not always justified for characterization of MOTUs. Here, we developed an approach combining a pairwise alignment algorithm and graph partitioning by using MCL (Markov clustering) in order to generate discrete groups for nuclear large-subunit rRNA gene and internal transcript spacer 1 sequence data sets obtained from a yearly monitoring study of two spatially close but ecologically contrasting alpine soils (namely, early and late snowmelt locations). We compared MCL with a classical single-linkage method (Ccomps) and showed that MCL reduced bias such as the chaining effect. Using MCL, we characterized fungal communities in early and late snowmelt locations. We found contrasting distributions of MOTUs in the two soils, suggesting that there is a high level of habitat filtering in the assembly of alpine soil fungal communities. However, few MOTUs were specific to one location.}, } @article {pmid19617370, year = {2009}, author = {Caro-Quintero, A and Rodriguez-Castaño, GP and Konstantinidis, KT}, title = {Genomic insights into the convergence and pathogenicity factors of Campylobacter jejuni and Campylobacter coli species.}, journal = {Journal of bacteriology}, volume = {191}, number = {18}, pages = {5824-5831}, pmid = {19617370}, issn = {1098-5530}, mesh = {Bacterial Proteins/genetics ; Campylobacter coli/genetics/*pathogenicity ; Campylobacter jejuni/genetics/*pathogenicity ; Databases, Genetic ; *Evolution, Molecular ; Gene Flow ; *Gene Transfer, Horizontal ; Genetic Speciation ; Genome, Bacterial ; *Genomics ; Sequence Analysis, DNA/*methods ; }, abstract = {Whether or not bacteria form coherent evolutionary groups via means of genetic exchange and, hence, elicit distinct species boundaries remains an unsettled issue. A recent report implied that not only may the former be true but also, in fact, the clearly distinct Campylobacter jejuni and Campylobacter coli species may be converging as a consequence of increased interspecies gene flow fostered, presumably, by the recent invasion of an overlapping ecological niche (S. K. Sheppard, N. D. McCarthy, D. Falush, and M. C. Maiden, Science 320:237-239, 2008). We have reanalyzed the Campylobacter multilocus sequence typing database used in the previous study and found that the number of interspecies gene transfer events may actually be too infrequent to account, unequivocally, for species convergence. For instance, only 1 to 2% of the 4,507 Campylobacter isolates examined appeared to have imported gene alleles from another Campylobacter species. Furthermore, by analyzing the available Campylobacter genomic sequences, we show that although there seems to be a slightly higher number of exchanged genes between C. jejuni and C. coli relative to other comparable species (approximately 10% versus 2 to 3% of the total genes in the genome, respectively), the function and spatial distribution in the genome of the exchanged genes are far from random, and hence, inconsistent with the species convergence hypothesis. In fact, the exchanged genes appear to be limited to a few environmentally selected cellular functions. Accordingly, these genes may represent important pathogenic determinants of pathogenic Campylobacter, and convergence of (any) two bacterial species remains to be seen.}, } @article {pmid19615855, year = {2009}, author = {Schliebs, S and Defoin-Platel, M and Worner, S and Kasabov, N}, title = {Integrated feature and parameter optimization for an evolving spiking neural network: exploring heterogeneous probabilistic models.}, journal = {Neural networks : the official journal of the International Neural Network Society}, volume = {22}, number = {5-6}, pages = {623-632}, doi = {10.1016/j.neunet.2009.06.038}, pmid = {19615855}, issn = {1879-2782}, mesh = {*Action Potentials ; Algorithms ; Animals ; *Artificial Intelligence ; Bayes Theorem ; Ceratitis capitata ; Databases, Factual ; Ecosystem ; Humans ; *Models, Statistical ; *Neural Networks, Computer ; Neurons/physiology ; Normal Distribution ; Software ; Time Factors ; }, abstract = {This study introduces a quantum-inspired spiking neural network (QiSNN) as an integrated connectionist system, in which the features and parameters of an evolving spiking neural network are optimized together with the use of a quantum-inspired evolutionary algorithm. We propose here a novel optimization method that uses different representations to explore the two search spaces: A binary representation for optimizing feature subsets and a continuous representation for evolving appropriate real-valued configurations of the spiking network. The properties and characteristics of the improved framework are studied on two different synthetic benchmark datasets. Results are compared to traditional methods, namely a multi-layer-perceptron and a naïve Bayesian classifier (NBC). A previously used real world ecological dataset on invasive species establishment prediction is revisited and new results are obtained and analyzed by an ecological expert. The proposed method results in a much faster convergence to an optimal solution (or a close to it), in a better accuracy, and in a more informative set of features selected.}, } @article {pmid19609599, year = {2010}, author = {Morrison, M and Daugherty, SC and Nelson, WC and Davidsen, T and Nelson, KE and , }, title = {The FibRumBa database: a resource for biologists with interests in gastrointestinal microbial ecology, plant biomass degradation, and anaerobic microbiology.}, journal = {Microbial ecology}, volume = {59}, number = {2}, pages = {212-213}, doi = {10.1007/s00248-009-9562-4}, pmid = {19609599}, issn = {1432-184X}, mesh = {Animals ; *Databases, Genetic ; Fibrobacter/*genetics ; Genome, Bacterial ; Genomic Library ; Rumen/*microbiology/physiology ; }, } @article {pmid19593896, year = {2009}, author = {Hoberg, EP and Pilitt, PA and Galbreath, KE}, title = {Why museums matter: a tale of pinworms (Oxyuroidea: Heteroxynematidae) among pikas (Ochotona princeps and O. collaris) in the American west.}, journal = {The Journal of parasitology}, volume = {95}, number = {2}, pages = {490-501}, doi = {10.1645/GE-1823.1}, pmid = {19593896}, issn = {0022-3395}, mesh = {Animals ; Female ; Lagomorpha/*parasitology ; Male ; Microscopy, Interference/veterinary ; *Museums ; Oxyuriasis/parasitology/*veterinary ; Oxyuroidea/anatomy & histology/*classification ; United States ; }, abstract = {Permanent and well-supported museum or natural history collections provide a solid foundation for the process of systematics research through creation of an empirical record which validates our understanding of the biosphere. We explore the role of museums in ongoing studies of the complex helminth fauna characteristic of pikas (Ochotona spp.) in the American west. These studies address the taxonomy for pinworms of the Labiostomatinae and the problems associated with the absence of adequate type series and vouchers and with misidentifications in original descriptions. We demonstrate that the types for Labiostomum (Labiostomum) coloradensis are identical to some specimens in the syntype series representing L. (Eugenuris) utahensis, although the published descriptions are in disagreement. Both are identical to L. (Eugenuris) talkeetnaeuris and, as a consequence, are reduced as junior synonyms. Only 2 species of large pinworms, namely L. (Labiostomum) rauschi and L. (Eugenuris) talkeetnaeuris, are widely distributed in Ochotona collaris and O. princeps. Although this serves to clarify the taxonomy for species in these genera, prior records remain confused, as representative voucher specimens from all major surveys in North America were never submitted to museum collections. We strongly suggest that type and voucher series should not be held in private or personal collections, where such are eventually lost, discarded, or destroyed through neglect due to inattention and the absence of curation. The potential to accumulate meaningful baselines for assessment of environmental change is jeopardized if materials from survey and inventory are not routinely submitted to museum collections. The capacity of museum repositories, as a focus for systematics, ecology, and evolutionary studies and for the development of resources for biodiversity informatics, continues to be undervalued and poorly utilized by a cadre of scientists who are dependant on accurate and definitive information that transcends specific disciplines.}, } @article {pmid19593066, year = {2009}, author = {Knoch, TA and Baumgärtner, V and de Zeeuw, LV and Grosveld, FG and Egger, K}, title = {e-Human Grid Ecology - understanding and approaching the inverse tragedy of the commons in the e-Grid society.}, journal = {Studies in health technology and informatics}, volume = {147}, number = {}, pages = {269-276}, pmid = {19593066}, issn = {0926-9630}, mesh = {Databases as Topic/*organization & administration ; *Efficiency, Organizational ; Humans ; Information Dissemination ; *Information Storage and Retrieval ; *Information Systems ; }, abstract = {With ever-new technologies emerging also the amount of information to be stored and processed is growing exponentially and is believed to be always at the limit. In contrast, however, huge resources are available in the IT sector alike e.g. the renewable energy sector, which are often even not at all used. This under-usage bares any rational especially in the IT sector where e.g. virtualisation and grid approaches could be fast implemented due to the great technical and fast turnover opportunities. Here, we describe this obvious paradox for the first time as the Inverse Tragedy of the Commons, in contrast to the Classical Tragedy of the Commons where resources are overexploited. From this perspective the grid IT sector attempting to share resources for better efficiency, reveals two challenges leading to the heart of the paradox: i) From a macro perspective all grid infrastructures involve not only mere technical solutions but also dominantly all of the autopoietic social sub-systems ranging from religion to policy. ii) On the micro level the individual players and their psychology and risk behaviour are of major importance for acting within the macro autopoietic framework. Thus, the challenges of grid implementation are similar to those of e.g. climate protection. This is well described by the classic Human Ecology triangle and our extension to a rectangle: invironment-individual-society-environment. Extension of this classical interdisciplinary field of basic and applied research to an e-Human Grid Ecology rational, allows the Inverse Tragedy of the Commons of the grid sector to be understood and approached better and implies obvious guidelines in the day-to-day management for grid and other (networked) resources, which is of importance for many fields with similar paradoxes as in (e-)society.}, } @article {pmid19592531, year = {2009}, author = {Moro, CV and Crouzet, O and Rasconi, S and Thouvenot, A and Coffe, G and Batisson, I and Bohatier, J}, title = {New design strategy for development of specific primer sets for PCR-based detection of Chlorophyceae and Bacillariophyceae in environmental samples.}, journal = {Applied and environmental microbiology}, volume = {75}, number = {17}, pages = {5729-5733}, pmid = {19592531}, issn = {1098-5336}, mesh = {Chlorophyta/genetics/*isolation & purification ; Computational Biology ; Computer Simulation ; DNA Primers/*genetics ; DNA, Algal/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Diatoms/genetics/*isolation & purification ; *Environmental Microbiology ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction/*methods ; RNA, Algal/genetics ; RNA, Ribosomal, 18S/genetics ; Sensitivity and Specificity ; Sequence Analysis, DNA ; Sequence Homology ; }, abstract = {Studying aquatic microalgae is essential for monitoring biodiversity and water quality. We designed new sets of 18S rRNA PCR primers for Chlorophyceae and Bacillariophyceae by using the ARB software and implementing a virtual PCR program. The results of specificity analysis showed that most of the targeted algal families were identified and nontargeted organisms, such as fungi or ciliates, were excluded. These newly developed PCR primer sets were also able to amplify microalgal rRNA genes from environmental samples with accurate specificity. These tools could be of great interest for studying freshwater microalgal ecology and for developing bioindicators of the health status of aquatic environments.}, } @article {pmid19592529, year = {2009}, author = {Caron, DA and Countway, PD and Savai, P and Gast, RJ and Schnetzer, A and Moorthi, SD and Dennett, MR and Moran, DM and Jones, AC}, title = {Defining DNA-based operational taxonomic units for microbial-eukaryote ecology.}, journal = {Applied and environmental microbiology}, volume = {75}, number = {18}, pages = {5797-5808}, pmid = {19592529}, issn = {1098-5336}, mesh = {Atlantic Ocean ; Classification/*methods ; Computational Biology/*methods ; DNA, Ribosomal/*genetics ; *Ecosystem ; Eukaryotic Cells/*classification ; Molecular Sequence Data ; Pacific Ocean ; RNA, Ribosomal, 18S/*genetics ; Seawater/microbiology ; Sequence Analysis, DNA ; }, abstract = {DNA sequence information has increasingly been used in ecological research on microbial eukaryotes. Sequence-based approaches have included studies of the total diversity of selected ecosystems, studies of the autecology of ecologically relevant species, and identification and enumeration of species of interest for human health. It is still uncommon, however, to delineate protistan species based on their genetic signatures. The reluctance to assign species-level designations based on DNA sequences is in part a consequence of the limited amount of sequence information presently available for many free-living microbial eukaryotes and in part a consequence of the problematic nature of and debate surrounding the microbial species concept. Despite the difficulties inherent in assigning species names to DNA sequences, there is a growing need to attach meaning to the burgeoning amount of sequence information entering the literature, and there is a growing desire to apply this information in ecological studies. We describe a computer-based tool that assigns DNA sequences from environmental databases to operational taxonomic units at approximately species-level distinctions. This approach provides a practical method for ecological studies of microbial eukaryotes (primarily protists) by enabling semiautomated analysis of large numbers of samples spanning great taxonomic breadth. Derivation of the algorithm was based on an analysis of complete small-subunit (18S) rRNA gene sequences and partial gene sequences obtained from the GenBank database for morphologically described protistan species. The program was tested using environmental 18S rRNA data sets for two oceanic ecosystems. A total of 388 operational taxonomic units were observed for 2,207 sequences obtained from samples collected in the western North Atlantic and eastern North Pacific oceans.}, } @article {pmid19592430, year = {2010}, author = {Shah, A}, title = {The relationship between elderly suicide rates and the internet: a cross-national study.}, journal = {The International journal of social psychiatry}, volume = {56}, number = {3}, pages = {214-219}, doi = {10.1177/0020764009105645}, pmid = {19592430}, issn = {1741-2854}, mesh = {Aged ; Databases, Factual ; Female ; Humans ; Internet/*statistics & numerical data ; Male ; Suicide/*trends ; United Nations ; United States ; World Health Organization ; }, abstract = {BACKGROUND: Suicide rates generally increase with age. Internet websites and chat rooms have been reported both to promote suicides and to have a positive beneficial effect on suicidal individuals. The role of the internet in elderly suicides has not been studied.

METHODS: The relationship between elderly suicide rates and the prevalence of internet users was examined in a cross-national study using data from the World Health Organization and the United Nations website.

RESULTS: The prevalence of internet users was significantly and positively correlated with suicide rates in both genders in the age bands 65-74 years and 75+ years. On multiple regression analysis the prevalence of internet users was independently associated with suicide rates in both genders in both age bands.

CONCLUSION: Caution should be exercised in the attribution of a causal relationship and the direction of this relationship because of the cross-sectional and ecological study design whereby the findings are subject to ecological fallacy. However, the findings identify and support a need for further research.}, } @article {pmid19589163, year = {2009}, author = {deLemos, JL and Brugge, D and Cajero, M and Downs, M and Durant, JL and George, CM and Henio-Adeky, S and Nez, T and Manning, T and Rock, T and Seschillie, B and Shuey, C and Lewis, J}, title = {Development of risk maps to minimize uranium exposures in the Navajo Churchrock mining district.}, journal = {Environmental health : a global access science source}, volume = {8}, number = {}, pages = {29}, pmid = {19589163}, issn = {1476-069X}, support = {P30 ES012072/ES/NIEHS NIH HHS/United States ; R01 ES014565/ES/NIEHS NIH HHS/United States ; R25 ES013208/ES/NIEHS NIH HHS/United States ; }, mesh = {Environment ; Environmental Exposure/*analysis ; Environmental Monitoring ; Geographic Information Systems/instrumentation ; Geography/methods ; Geologic Sediments/chemistry ; Humans ; *Indians, North American ; Information Dissemination ; *Maps as Topic ; *Mining ; New Mexico ; Risk Factors ; Soil Pollutants, Radioactive/*analysis ; Uranium/*analysis ; Water Pollutants, Radioactive/analysis ; Water Supply/analysis ; }, abstract = {BACKGROUND: Decades of improper disposal of uranium-mining wastes on the Navajo Nation has resulted in adverse human and ecological health impacts as well as socio-cultural problems. As the Navajo people become increasingly aware of the contamination problems, there is a need to develop a risk-communication strategy to properly inform tribal members of the extent and severity of the health risks. To be most effective, this strategy needs to blend accepted risk-communication techniques with Navajo perspectives such that the strategy can be used at the community level to inform culturally- and toxicologically-relevant decisions about land and water use as well as mine-waste remediation.

OBJECTIVE: The objective of this study was to develop GIS-based thematic maps as communication tools to clearly identify high risk exposure areas and offer alternatives to minimize public and ecological health impacts.

METHODS: Thematic maps were produced that incorporated data derived from environmental sampling and public health surveys. The maps show the location and quality of unregulated water resources and identify regulated water sources that could be used as alternatives. In addition, the maps show the location of contaminated soil and sediment areas in which disturbance of surface deposits should be avoided. Preliminary feedback was collected from an informal Navajo working group to assess the clarity and efficacy of this proposed communication method.

RESULTS: The working group found the maps to be both clear and effective, and made suggestions for improvements, such as the addition of more map features. The working group predicted that once the maps are presented to the public, water hauling and soil use behaviors will change, and dialogue with chapter officials will be initiated to accelerate further risk reduction efforts.

IMPLICATIONS: Because risk communication is complicated by language barriers, lack of infrastructure, and historical mistrust of non-Navajo researchers, mapping provides an easily interpretable medium that can be objectively viewed by community members and decision makers to evaluate activities that affect toxicant exposures.}, } @article {pmid19587772, year = {2009}, author = {Gomez-Alvarez, V and Teal, TK and Schmidt, TM}, title = {Systematic artifacts in metagenomes from complex microbial communities.}, journal = {The ISME journal}, volume = {3}, number = {11}, pages = {1314-1317}, doi = {10.1038/ismej.2009.72}, pmid = {19587772}, issn = {1751-7370}, mesh = {Base Sequence ; Databases, Genetic/*standards ; *Metagenome ; Metagenomics/*standards ; Molecular Sequence Data ; Sequence Alignment ; Sequence Analysis, DNA/standards ; *Soil Microbiology ; }, abstract = {Metagenomics is providing an unprecedented view of the taxonomic diversity, metabolic potential and ecological role of microbial communities in biomes as diverse as the mammalian gastrointestinal tract, the marine water column and soils. However, we have found a systematic error in metagenomes generated by 454-based pyrosequencing that leads to an overestimation of gene and taxon abundance; between 11% and 35% of sequences in a typical metagenome are artificial replicates. Here we document the error in several published and original datasets and offer a web-based solution (http://microbiomes.msu.edu/replicates) for identifying and removing these artifacts.}, } @article {pmid19585244, year = {2009}, author = {McAlexander, KM and Banda, JA and McAlexander, JW and Lee, RE}, title = {Physical activity resource attributes and obesity in low-income African Americans.}, journal = {Journal of urban health : bulletin of the New York Academy of Medicine}, volume = {86}, number = {5}, pages = {696-707}, pmid = {19585244}, issn = {1468-2869}, mesh = {Adolescent ; Adult ; Black or African American/*statistics & numerical data ; Aged ; Aged, 80 and over ; Body Mass Index ; Cross-Sectional Studies ; *Environment Design ; Female ; Geographic Information Systems ; *Health Knowledge, Attitudes, Practice ; Humans ; Male ; Middle Aged ; *Motor Activity ; Obesity/economics/*ethnology ; Poverty/ethnology/statistics & numerical data ; *Residence Characteristics ; Social Class ; Texas ; Urban Health ; Young Adult ; }, abstract = {More than two thirds of Americans are overweight or obese, and African Americans are particularly vulnerable to obesity when compared to Caucasians. Ecological models of health suggest that lower individual and environmental socioeconomic status and the built environment may be related to health attitudes and behaviors that contribute to obesity. This cross-sectional study measured the direct associations of neighborhood physical activity resource attributes with body mass index (BMI) and body fat among low-income 216 African Americans (Mean (M) age = 43.5 years, 63.9% female) residing in 12 public housing developments. The Physical Activity Resource Assessment instrument measured accessibility, incivilities, and the quality of features and amenities of each physical activity resource within an 800-m radius around each housing development. Sidewalk connectivity was measured using the Pedestrian Environment Data Scan instrument. Ecological multivariate regression models analyzed the associations between the built environment attributes and resident BMI and body fat at the neighborhood level. Sidewalk connectivity was associated with BMI (M = 31.3 kg/m(2); p < 0.05). Sidewalk connectivity and resource accessibility were associated with body fat percentage (M = 34.8%, p < 0.05). Physical activity resource attributes and neighborhood sidewalk connectivity were related to BMI and body fat among low-income African Americans living in housing developments.}, } @article {pmid19583871, year = {2009}, author = {Thornton, KR}, title = {Automating approximate Bayesian computation by local linear regression.}, journal = {BMC genetics}, volume = {10}, number = {}, pages = {35}, pmid = {19583871}, issn = {1471-2156}, mesh = {Algorithms ; Animals ; *Bayes Theorem ; Computational Biology/*methods ; Computer Simulation ; Drosophila melanogaster/genetics ; Genetics, Population/methods ; *Linear Models ; *Software ; }, abstract = {BACKGROUND: In several biological contexts, parameter inference often relies on computationally-intensive techniques. "Approximate Bayesian Computation", or ABC, methods based on summary statistics have become increasingly popular. A particular flavor of ABC based on using a linear regression to approximate the posterior distribution of the parameters, conditional on the summary statistics, is computationally appealing, yet no standalone tool exists to automate the procedure. Here, I describe a program to implement the method.

RESULTS: The software package ABCreg implements the local linear-regression approach to ABC. The advantages are: 1. The code is standalone, and fully-documented. 2. The program will automatically process multiple data sets, and create unique output files for each (which may be processed immediately in R), facilitating the testing of inference procedures on simulated data, or the analysis of multiple data sets. 3. The program implements two different transformation methods for the regression step. 4. Analysis options are controlled on the command line by the user, and the program is designed to output warnings for cases where the regression fails. 5. The program does not depend on any particular simulation machinery (coalescent, forward-time, etc.), and therefore is a general tool for processing the results from any simulation. 6. The code is open-source, and modular.Examples of applying the software to empirical data from Drosophila melanogaster, and testing the procedure on simulated data, are shown.

CONCLUSION: In practice, the ABCreg simplifies implementing ABC based on local-linear regression.}, } @article {pmid19579687, year = {2009}, author = {Bos, MJ and Koolstra, CM and Willems, JT}, title = {Adolescent responses toward a new technology: first associations, information seeking and affective responses to ecogenomics.}, journal = {Public understanding of science (Bristol, England)}, volume = {18}, number = {2}, pages = {243-253}, doi = {10.1177/0963662507087306}, pmid = {19579687}, issn = {0963-6625}, mesh = {Adolescent ; *Adolescent Behavior ; Age Factors ; *Attitude to Computers ; Awareness ; Biodiversity ; Biotechnology/*education ; Child ; Communication ; Educational Measurement ; Educational Status ; Female ; *Genomics ; Humans ; Information Storage and Retrieval ; Male ; Marine Biology ; }, abstract = {This paper reports on an exploratory study among adolescents (N = 752) who were introduced to the emerging technology of ecogenomics for the first time. An online survey focused on their associations with the term ecogenomics, their planned information seeking behaviors if they were to acquire information about the new technology, and their first affective responses toward ecogenomics after having read some introductory information about it. Adolescents were found to associate ecogenomics most frequently with economy. Although the Internet was the most popular medium to be used in their planned information seeking behaviors, books and science communication professionals were judged as the most trustworthy information sources. After having read the introductory information about ecogenomics most adolescents reported positive affective responses toward the new technology.}, } @article {pmid19578575, year = {2009}, author = {Cerbino Neto, J and Werneck, GL and Costa, CH}, title = {Factors associated with the incidence of urban visceral leishmaniasis: an ecological study in Teresina, Piauí State, Brazil.}, journal = {Cadernos de saude publica}, volume = {25}, number = {7}, pages = {1543-1551}, doi = {10.1590/s0102-311x2009000700012}, pmid = {19578575}, issn = {1678-4464}, mesh = {Animals ; Brazil/epidemiology ; *Ecosystem ; *Geographic Information Systems ; Humans ; Incidence ; Leishmaniasis, Visceral/*epidemiology ; Risk Factors ; Socioeconomic Factors ; Urban Population ; }, abstract = {The objective of this study was to identify socioeconomic and environmental factors associated with the incidence of visceral leishmaniasis in the city of Teresina, Piauí State, Brazil. This was an ecological study based on 1,744 cases reported from 1991 to 2000, and the city's neighborhoods served as the unit of analysis. Mean annual incidence rates were related to socioeconomic and demographic indicators and a vegetation index derived from remote sensing images by means of spatial multiple linear regression models. The neighborhoods with the highest incidence rates were mostly located in the city's peripheral areas. Multivariate analysis identified an interaction between population growth and the vegetation index, so that areas with high population growth and abundant vegetation showed the highest incidence rates. The percentage of households with piped water was inversely associated with visceral leishmaniasis incidence. Spatial distribution of visceral leishmaniasis in Teresina during the 1990s was heterogeneous, and incidence of the disease was associated with the peripheral neighborhoods with the heaviest vegetation cover, subject to rapid occupation and lack of adequate sanitation infrastructure.}, } @article {pmid19577353, year = {2009}, author = {Fujisawa, Y and Hamano, T and Takegawa, S}, title = {Social capital and perceived health in Japan: an ecological and multilevel analysis.}, journal = {Social science & medicine (1982)}, volume = {69}, number = {4}, pages = {500-505}, doi = {10.1016/j.socscimed.2009.05.046}, pmid = {19577353}, issn = {1873-5347}, mesh = {Adult ; Aged ; Female ; *Health Status ; Health Surveys ; Helping Behavior ; Humans ; Japan ; Male ; Middle Aged ; Multilevel Analysis ; Regression Analysis ; Residence Characteristics/statistics & numerical data ; *Social Support ; Socioeconomic Factors ; }, abstract = {Numerous empirical studies, largely conducted in Western societies, have linked social capital to health outcomes. However, few studies thus far have been conducted in northeastern Asian countries, particularly Japan. Therefore, whether social capital is a determinant of health in Japanese society remains unclear. This study attempted to provide new evidence for the impact of social capital on health in Japan by analyzing original survey data with two different statistical models. In total, 1910 subjects were randomly selected from 210 enumeration districts (EDs) considered in the 2000 population census. In the present study, after excluding missing data on the outcome and predictor variables, we conducted an analysis of 1157 individuals nested within 206 EDs. Ecological and multilevel regression analyses were performed to examine the association between social capital and health, measured by the General Health (GH) perception item (a subcategory of Short Form 36 (SF-36)), and to estimate the impact of aggregated indicators of social capital on health. We developed an original Japanese version of three social capital items (perceived helpfulness, kindness, and greeting) based on previous studies and expert opinions and prepared a social cohesion index that integrated these three social capital items. The ecological model, after adjusting for sociodemographic factors, revealed that perceived helpfulness and greeting, along with the social cohesion index, were observed to have statistically significant associations with GH. The multilevel model, after adjusting for individual social capital perceptions, indicated that the two aggregated indicators of community social capital (kindness and greeting), along with the social cohesion index, showed a statistically significant association with GH. These results showed the existence of a contextual effect of social capital on health outcomes, although individual differences in social capital perceptions in Japan were considered.}, } @article {pmid19576779, year = {2009}, author = {Chibucos, MC and Tseng, TT and Setubal, JC}, title = {Describing commonalities in microbial effector delivery using the Gene Ontology.}, journal = {Trends in microbiology}, volume = {17}, number = {7}, pages = {312-319}, doi = {10.1016/j.tim.2009.05.001}, pmid = {19576779}, issn = {1878-4380}, mesh = {Animals ; Bacteria/genetics ; Computational Biology/*methods ; Fungi/genetics ; Membrane Transport Proteins/*genetics/*physiology ; Nematoda/genetics ; Oomycetes/genetics ; Protein Transport ; Virulence Factors/*genetics/*metabolism ; *Vocabulary, Controlled ; }, abstract = {Myriad symbiotic microbes, ranging from mutualistic through to pathogenic, deliver 'effector' molecules into the cytoplasm or cellular milieu of their hosts to facilitate colonization. Among ecologically and evolutionarily diverse taxa, analogous processes and structures exist to facilitate effector delivery. These include syringe-like injection (bacteria and nematodes), common host-targeting signals (oomycetes and protozoans) and specialized intercellular structures (fungi and oomycetes). Here, we briefly introduce readers to the Gene Ontology (GO), a controlled vocabulary to facilitate comparative genomics of diverse taxa. We also summarize and compare selected mechanisms of effector delivery from various organisms and show how careful annotation of gene products with GO can reveal underlying similarities among diverse taxa.}, } @article {pmid19568419, year = {2009}, author = {Yang, JC and Madupu, R and Durkin, AS and Ekborg, NA and Pedamallu, CS and Hostetler, JB and Radune, D and Toms, BS and Henrissat, B and Coutinho, PM and Schwarz, S and Field, L and Trindade-Silva, AE and Soares, CA and Elshahawi, S and Hanora, A and Schmidt, EW and Haygood, MG and Posfai, J and Benner, J and Madinger, C and Nove, J and Anton, B and Chaudhary, K and Foster, J and Holman, A and Kumar, S and Lessard, PA and Luyten, YA and Slatko, B and Wood, N and Wu, B and Teplitski, M and Mougous, JD and Ward, N and Eisen, JA and Badger, JH and Distel, DL}, title = {The complete genome of Teredinibacter turnerae T7901: an intracellular endosymbiont of marine wood-boring bivalves (shipworms).}, journal = {PloS one}, volume = {4}, number = {7}, pages = {e6085}, pmid = {19568419}, issn = {1932-6203}, mesh = {Animals ; Bivalvia/metabolism/*microbiology ; Computational Biology ; *Genome, Bacterial ; *Marine Biology ; Nitrogen/metabolism ; Phylogeny ; Polysaccharides/metabolism ; Proteobacteria/classification/enzymology/*genetics/physiology ; Quorum Sensing ; Spectrometry, Mass, Electrospray Ionization ; *Symbiosis ; Tandem Mass Spectrometry ; *Wood ; }, abstract = {Here we report the complete genome sequence of Teredinibacter turnerae T7901. T. turnerae is a marine gamma proteobacterium that occurs as an intracellular endosymbiont in the gills of wood-boring marine bivalves of the family Teredinidae (shipworms). This species is the sole cultivated member of an endosymbiotic consortium thought to provide the host with enzymes, including cellulases and nitrogenase, critical for digestion of wood and supplementation of the host's nitrogen-deficient diet. T. turnerae is closely related to the free-living marine polysaccharide degrading bacterium Saccharophagus degradans str. 2-40 and to as yet uncultivated endosymbionts with which it coexists in shipworm cells. Like S. degradans, the T. turnerae genome encodes a large number of enzymes predicted to be involved in complex polysaccharide degradation (>100). However, unlike S. degradans, which degrades a broad spectrum (>10 classes) of complex plant, fungal and algal polysaccharides, T. turnerae primarily encodes enzymes associated with deconstruction of terrestrial woody plant material. Also unlike S. degradans and many other eubacteria, T. turnerae dedicates a large proportion of its genome to genes predicted to function in secondary metabolism. Despite its intracellular niche, the T. turnerae genome lacks many features associated with obligate intracellular existence (e.g. reduced genome size, reduced %G+C, loss of genes of core metabolism) and displays evidence of adaptations common to free-living bacteria (e.g. defense against bacteriophage infection). These results suggest that T. turnerae is likely a facultative intracellular ensosymbiont whose niche presently includes, or recently included, free-living existence. As such, the T. turnerae genome provides insights into the range of genomic adaptations associated with intracellular endosymbiosis as well as enzymatic mechanisms relevant to the recycling of plant materials in marine environments and the production of cellulose-derived biofuels.}, } @article {pmid19565774, year = {2009}, author = {Le, L and Qi, W and Zhang, XH and Qu, YB}, title = {[Neighborhood relationships of land use spatial pattern in Qixia City].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {20}, number = {4}, pages = {909-915}, pmid = {19565774}, issn = {1001-9332}, mesh = {China ; *City Planning ; *Conservation of Natural Resources ; Crops, Agricultural/*growth & development ; Ecosystem ; Fruit/growth & development ; Geographic Information Systems ; Poaceae/growth & development ; Trees/*growth & development ; }, abstract = {By using the modules of neighborhood statistics and spatial analysis in ArcGIS software, an analysis was conducted with neighborhood factors on the spatiotemporal variation trend of the neighborhood relationships among main land use types in Qixia City of Shandong Province from 1987 to 2003. The results indicated that the neighborhood relationships between different land use types increased with increasing neighborhood distance, while those among the same land use types manifested congregation, which decreased with increasing neighborhood distance. From 1987 to 2003, the neighborhood relationships between construction land and orchard land, and between woodland and orchard land presented decreasing trend, while those of construction land with woodland and grassland were in adverse. Some measures such as controlling construction land area, protecting cultivated land, and decreasing the disturbances of human activities on woodland and grassland should be carried out to realize the harmonious development of economic and ecological benefits in Qixia City.}, } @article {pmid19565773, year = {2009}, author = {Liu, CY and Zhang, SQ and Jiang, HX and Wang, H}, title = {[Spatiotemporal dynamics and landscape pattern of alien species Spartina alterniflora in Yancheng coastal wetlands of Jiangsu Province, China].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {20}, number = {4}, pages = {901-908}, pmid = {19565773}, issn = {1001-9332}, mesh = {Biodiversity ; China ; *Ecosystem ; Geographic Information Systems ; Oceans and Seas ; Poaceae/classification/*growth & development ; Satellite Communications ; *Wetlands ; }, abstract = {Based on the 1992-2007 remote sensing images and field survey data, and by using the landscape ecology theories and the method of conversion matrix, the spatiotemporal dynamics and landscape pattern of Spartina alterniflora in Yancheng coastal wetlands were analyzed by GIS. The results showed that the total area of S. alterniflora along the whole coastal beaches of Yancheng increased from 3561 hm2 in 1992 to 14491 hm2 in 2007, with a growth rate of 306.94%. In 1992-2007, the total area of S. alterniflora conversion-in and conversion-out was 26291 hm2 and 15361 hm2, respectively, and the S. alterniflora community in the core area of Yancheng National Nature Reserve expanded from 597 hm2 to 2814 hm2, with an annual growth rate of 24.74%. The S. alterniflora community transformed from scattered patches in estuarine regions into continuous belt pattern mainly distributed in the periphery of coastal wetlands from Sheyang River to Liangduo River. Its centroid moved to the southeast, with a distance of 2.92 km. The average area of patches increased from 1992 to 2002, and then decreased from 2002 to 2007. The largest patch index and area-weighted contiguity index increased year by year, and the shape of patches tended to be more regular.}, } @article {pmid19559481, year = {2010}, author = {Cook, JR and Kilmer, RP}, title = {Defining the scope of systems of care: an ecological perspective.}, journal = {Evaluation and program planning}, volume = {33}, number = {1}, pages = {18-20}, doi = {10.1016/j.evalprogplan.2009.05.006}, pmid = {19559481}, issn = {1873-7870}, mesh = {Adolescent ; Adolescent Health Services/*organization & administration ; Child ; Child Health Services/*organization & administration ; Community Networks/*organization & administration ; Delivery of Health Care/*organization & administration ; Health Planning/*organization & administration ; Health Services Needs and Demand ; Humans ; Mental Health Services/*organization & administration ; Organizational Objectives ; Quality Assurance, Health Care ; Social Change ; }, abstract = {The definition of a system of care (SOC) can guide those intending to develop and sustain SOCs. Hodges, Ferreira, Israel, and Mazza [Hodges, S., Ferreira, K., Israel, N., & Mazza, J. (in press). Systems of care, featherless bipeds, and the measure of all things. Evaluation and Program Planning] have emphasized contexts in which services are provided to families, plus the adaptive, dynamic, complex nature of systems and multiple components that comprise SOCs. However, two areas need additional clarification: (1) the nature of the "system" of concern in a "system of care," and how it should differ from a "service delivery system"; and (2) the degree to which intended, or desired, outcomes of a SOC extend beyond increased access to "necessary" services and supports. These prime issues in the conceptualization of SOCs are addressed, drawing on ecological theory to underscore the need for broader systems--including factors in the proximal and distal contexts of children and families--to be engaged in the process of promoting well-being and helping children and families function and participate fully in their communities. A revised definition is proposed, with implications for the implementation of SOCs.}, } @article {pmid19558712, year = {2009}, author = {Wall, M and Hayes, R and Moore, D and Petticrew, M and Clow, A and Schmidt, E and Draper, A and Lock, K and Lynch, R and Renton, A}, title = {Evaluation of community level interventions to address social and structural determinants of health: a cluster randomised controlled trial.}, journal = {BMC public health}, volume = {9}, number = {}, pages = {207}, pmid = {19558712}, issn = {1471-2458}, support = {G0700837/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Adolescent ; Adult ; *Attitude to Health/ethnology ; Cluster Analysis ; Community Health Services/*methods ; Data Interpretation, Statistical ; Ethnicity ; Health Promotion/*methods ; Health Services Research/*methods ; *Health Status Indicators ; Health Surveys ; Humans ; London ; Longitudinal Studies ; Socioeconomic Factors ; }, abstract = {BACKGROUND: In London and the rest of the UK, diseases associated with poor diet, inadequate physical activity and mental illness account for a large proportion of area based health inequality. There is a lack of evidence on interventions promoting healthier behaviours especially in marginalised populations, at a structural or ecological level and utilising a community development approach.The Well London project financed by the Big Lottery 'Wellbeing' Fund and implemented by a consortium of London based agencies led by the Greater London Authority and the London Health Commission is implementing a set of complex interventions across 20 deprived areas of London. The interventions focus on healthy eating, healthy physical activity and mental health and wellbeing and are designed and executed with community participation complementing existing facilities and services.

METHODS/DESIGN: The programme will be evaluated through a cluster randomised controlled trial. Forty areas across London were chosen based on deprivation scores. Areas were characterised by high proportion of Black and Minority Ethnic residents, worklessness, ill-health and poor physical environments. Twenty areas were randomly assigned to the intervention arm of Well London project and twenty 'matched' areas assigned as controls. Measures of physical activity, diet and mental health are collected at start and end of the project and compared to assess impact.The quantitative element will be complemented by a longitudinal qualitative study elucidating pathways of influence between intervention activities and health outcomes. A related element of the study investigates the health-related aspects of the structural and ecological characteristics of the project areas. The project 'process' will also be evaluated.

DISCUSSION: The size of the project and the fact that the interventions are 'complex' in the sense that firstly, there are a number of interacting components with a wide range of groups and organisational levels targeted by the intervention, and secondly, a degree of flexibility or tailoring of the intervention, makes this trial potentially very useful in providing evidence of the types of activities that can be used to address chronic health problems in communities suffering from multiple deprivation.

TRIAL REGISTRATION: Current Controlled Trials ISRCTN68175121.}, } @article {pmid19558202, year = {2010}, author = {Power, BA and Tinholt, MJ and Hill, RA and Fikart, A and Wilson, RM and Stewart, GG and Sinnett, GD and Runnells, JL}, title = {A risk-ranking methodology for prioritizing historic, potentially contaminated mine sites in British Columbia.}, journal = {Integrated environmental assessment and management}, volume = {6}, number = {1}, pages = {145-154}, doi = {10.1897/IEAM_2009-016.1}, pmid = {19558202}, issn = {1551-3793}, mesh = {British Columbia ; *Decision Support Techniques ; Environmental Monitoring/methods ; Humans ; *Mining ; Risk Assessment/*methods ; Water Pollutants, Chemical/analysis ; }, abstract = {The Crown Land Restoration Branch (CLRB) of the British Columbia Ministry of Agriculture and Lands is responsible for managing thousands of historic and abandoned mine sites on provincial lands (referred to as Crown Contaminated Sites). For most of these sites, there is limited information available regarding the extent of potential contamination or potential human health and ecological risks. Given the large number of sites, the CLRB sought a system for prioritizing investigation and management efforts among them. We developed a Risk-Ranking Methodology (RRM) to meet this objective, which was implemented in 2007/2008 with an emphasis on historic mine sites because of the significant number of sites and related potential risk. The RRM uses a risk-based Preliminary Site Investigation to gather key information about the sites. The information for each site is analyzed and summarized according to several attributes aimed at characterizing potential health and ecological risks. The summary information includes, but is not limited to, generic comparisons of exposure with effects levels (screening quotients) for human and ecological exposure pathways. The summary information (more than 25 attributes) is then used in a workshop setting to evaluate relative rankings among sites, and also to identify subsequent management actions for each site. Application of the RRM in 2007/2008 was considered successful, because there was confidence in the process, the content and the outputs. A key challenge was keeping the number of attributes to a manageable level. Ranking was based on discussion and consensus, which was a feasible approach given the relatively small number of sites that need to be ranked each year, and facilitated transparency in the ranking process. We do not rule out the future possibility of developing a quantitative function to capture trade-offs among attributes.}, } @article {pmid19557160, year = {2009}, author = {Zhang, Z and Townsend, JP}, title = {Maximum-likelihood model averaging to profile clustering of site types across discrete linear sequences.}, journal = {PLoS computational biology}, volume = {5}, number = {6}, pages = {e1000421}, pmid = {19557160}, issn = {1553-7358}, support = {S10 RR019895/RR/NCRR NIH HHS/United States ; RR19895/RR/NCRR NIH HHS/United States ; }, mesh = {Alcohol Dehydrogenase/chemistry/genetics ; Algorithms ; *Amino Acid Sequence ; Animals ; *Base Sequence ; *Cluster Analysis ; Computational Biology/*methods ; Computer Simulation ; Drosophila/enzymology/genetics ; Drosophila Proteins/chemistry/genetics ; *Likelihood Functions ; Models, Genetic ; Sequence Analysis/*methods ; }, abstract = {A major analytical challenge in computational biology is the detection and description of clusters of specified site types, such as polymorphic or substituted sites within DNA or protein sequences. Progress has been stymied by a lack of suitable methods to detect clusters and to estimate the extent of clustering in discrete linear sequences, particularly when there is no a priori specification of cluster size or cluster count. Here we derive and demonstrate a maximum likelihood method of hierarchical clustering. Our method incorporates a tripartite divide-and-conquer strategy that models sequence heterogeneity, delineates clusters, and yields a profile of the level of clustering associated with each site. The clustering model may be evaluated via model selection using the Akaike Information Criterion, the corrected Akaike Information Criterion, and the Bayesian Information Criterion. Furthermore, model averaging using weighted model likelihoods may be applied to incorporate model uncertainty into the profile of heterogeneity across sites. We evaluated our method by examining its performance on a number of simulated datasets as well as on empirical polymorphism data from diverse natural alleles of the Drosophila alcohol dehydrogenase gene. Our method yielded greater power for the detection of clustered sites across a breadth of parameter ranges, and achieved better accuracy and precision of estimation of clusters, than did the existing empirical cumulative distribution function statistics.}, } @article {pmid19546840, year = {2009}, author = {Jardine, A and Menzies, RI and Deeks, SL and Patel, MS and McIntyre, PB}, title = {The impact of pneumococcal conjugate vaccine on rates of myringotomy with ventilation tube insertion in Australia.}, journal = {The Pediatric infectious disease journal}, volume = {28}, number = {9}, pages = {761-765}, doi = {10.1097/INF.0b013e31819e9bc5}, pmid = {19546840}, issn = {1532-0987}, mesh = {Age Factors ; Australia/epidemiology ; Child ; Child, Preschool ; Data Collection/methods ; Databases, Factual ; Female ; Heptavalent Pneumococcal Conjugate Vaccine ; Humans ; Incidence ; Infant ; Infant, Newborn ; Male ; Middle Ear Ventilation/*statistics & numerical data ; Models, Statistical ; Otitis Media/*epidemiology/prevention & control/*surgery ; Pneumococcal Infections/*epidemiology/prevention & control/*surgery ; Pneumococcal Vaccines/*administration & dosage/*immunology ; Product Surveillance, Postmarketing ; }, abstract = {BACKGROUND: In randomized controlled trials and postmarketing studies the heptavalent pneumococcal conjugate vaccine (7vPCV) has been shown to reduce myringotomy with ventilation tube insertion (MVTI) procedures in a 4-dose schedule. In Australia, a 3-dose schedule at 2, 4, and 6 months of age is routinely used in non-Indigenous children. Our aim was to determine if a reduction in MVTI comparable to that documented in the United States occurred in Australia despite the absence of the booster dose.

METHODS: All episodes of MVTI in Australia from July 1998 to June 2007 among children aged
RESULTS: A total of 238,634 hospital separations were identified. In the 2.5 years after routine 7vPCV introduction, there was a significant adjusted reduction in MVTI in children aged <1, 1, and 2 years of 23%, 16%, and 6%, respectively. A nonsignificant reduction was observed in those aged 3 and 4 years, while a significant increase of 5% was observed for the 5- to 9-year age group.

CONCLUSIONS: Although ecologic data such as this have limitations, the significant differential effects observed by time period and age group are suggestive of a vaccine effect of similar magnitude to that documented by postmarketing surveillance in the United States. The rapid uptake of 7vPCV in Australia, including catch up to 2 years of age, is an important difference to the United States and it is possible that an even greater effect would have been observed with a booster dose in the second year of life. Longer term data will be needed to fully assess the role of a booster dose.}, } @article {pmid19540288, year = {2009}, author = {Brown, E and Dury, S and Holdsworth, M}, title = {Motivations of consumers that use local, organic fruit and vegetable box schemes in Central England and Southern France.}, journal = {Appetite}, volume = {53}, number = {2}, pages = {183-188}, doi = {10.1016/j.appet.2009.06.006}, pmid = {19540288}, issn = {1095-8304}, mesh = {Adolescent ; Adult ; Community Networks ; Conservation of Natural Resources ; *Consumer Behavior ; England ; Food, Organic/*statistics & numerical data ; France ; *Fruit ; Humans ; Middle Aged ; Motivation ; Seasons ; Socioeconomic Factors ; Surveys and Questionnaires ; *Vegetables ; }, abstract = {Commercial fruit and vegetable box schemes are rapidly growing initiatives that allow customers to make local, organic food choices. This study investigated the socio-demographic profile of consumers using local commercial box schemes, and investigated the barriers and motivations of customers. Cross-sectional surveys using identical questionnaires were conducted in Montpellier, France and Nottingham, England. Box scheme users in both countries were primarily rather affluent professionals. The English reported access to local produce that has travelled less food miles (a more altruistic reason) to be the most important motive to purchasing from the box scheme, whereas the French stated quality of produce (a more hedonistic reason) to be key. Both countries ranked ecological commitment and access to organic food as the next most important influences on their participation. The findings reinforce the importance of food quality and pleasure for the French generally, although once this fundamental criterion has been fulfilled, French box scheme users appear equally motivated by contributing positively to the ecosystem. In England, the desire to eat out of season food was cited as the main barrier to making more sustainable food choices. Cost was an important obstacle to increasing consumption of food from sustainable sources in both countries.}, } @article {pmid19533342, year = {2009}, author = {Raimondo, S and Vivian, DN and Barron, MG}, title = {Standardizing acute toxicity data for use in ecotoxicology models: influence of test type, life stage, and concentration reporting.}, journal = {Ecotoxicology (London, England)}, volume = {18}, number = {7}, pages = {918-928}, pmid = {19533342}, issn = {1573-3017}, mesh = {Animals ; Databases as Topic ; Databases, Factual ; Ecotoxicology/*standards ; Larva/drug effects ; Life Cycle Stages/*drug effects ; Models, Statistical ; Risk Assessment ; Toxicity Tests, Acute/*standards ; Water Pollutants, Chemical/analysis/*toxicity ; }, abstract = {Ecotoxicological models generally have large data requirements and are frequently based on existing information from diverse sources. Standardizing data for toxicological models may be necessary to reduce extraneous variation and to ensure models reflect intrinsic relationships. However, the extent to which data standardization is necessary remains unclear, particularly when data transformations are used in model development. An extensive acute toxicity database was compiled for aquatic species to comprehensively assess the variation associated with acute toxicity test type (e.g., flow-through, static), reporting concentrations as nominal or measured, and organism life stage. Three approaches were used to assess the influence of these factors on log-transformed acute toxicity: toxicity ratios, log-linear models of factor groups, and comparison of interspecies correlation estimation (ICE) models developed using either standardized test types or reported concentration type. In general, median ratios were generally less than 2.0, the slopes of log-linear models were approximately one for well-represented comparisons, and ICE models developed using data from standardized test types or reported concentrations did not differ substantially. These results indicate that standardizing test data by acute test type, reported concentration type, or life stage may not be critical for developing ecotoxicological models using large datasets of log-transformed values.}, } @article {pmid19522587, year = {2009}, author = {Skelsey, P and Rossing, WA and Kessel, GJ and van der Werf, W}, title = {Scenario approach for assessing the utility of dispersal information in decision support for aerially spread plant pathogens, applied to Phytophthora infestans.}, journal = {Phytopathology}, volume = {99}, number = {7}, pages = {887-895}, doi = {10.1094/PHYTO-99-7-0887}, pmid = {19522587}, issn = {0031-949X}, mesh = {*Air Microbiology ; Biomass ; *Decision Support Techniques ; Fungicides, Industrial/*pharmacology ; *Information Dissemination ; Models, Biological ; Phytophthora infestans/drug effects/*physiology ; Plant Diseases/microbiology ; Solanum tuberosum/drug effects/growth & development/microbiology ; Spores, Fungal/drug effects/physiology ; }, abstract = {Opportunities exist to improve decision support systems through the use of dispersal information gained from epidemiological research. However, dispersal and demographic information is often fragmentary in plant pathology, and this uncertainty creates a risk of inappropriate action whenever such information is used as a basis for decision making. In this article, a scenario-based simulation approach is used to evaluate crop and economic risks and benefits in the use of dispersal information for decision making using the potato late blight pathosystem (Phytophthora infestans-Solanum tuberosum) as a case study. A recently validated spatiotemporal potato late blight model was coupled to submodels for crop growth, tuber dry matter production, and fungicide efficacy. The yield response of a range of management scenarios to a single influx of primary inoculum (the initial spore load) was calculated. Damage curves (relative yield loss versus initial spore load) from a range of combinations of varietal susceptibility and fungicide treatments were used to classify the various management scenarios as either sensitive to initial spore load or tolerant to initial spore load, thus identifying where a high degree of accuracy would be required in dispersal information for appropriate decision making, and where a greater degree of uncertainty could be tolerated. General epidemics, resulting from spatially homogeneous initial spore loads, responded more strongly to the size of the initial spore load than focal epidemics, resulting from an initial spot infection. Susceptible cultivars responded with sizeable yield losses even at low levels of initial spore load, regardless of the fungicide management regime used. These results indicated that, for susceptible cultivars (late cultivars in particular), the degree of accuracy that would be required in dispersal information for appropriate decision making is unlikely to be practically attainable. The results also indicated that, contrary to "folk wisdom," spore loads of a few hundred spores per square meter do not lead to appreciable crop loss in resistant cultivars and are therefore acceptable. We conclude that scope exists for including dispersal information in decision making for potato late blight with resistant potato cultivars but not for susceptible cultivars. The modeling framework used in this study can be extended to investigate the scope for inclusion of dispersal information in decision support for other aerially transmitted pathogens.}, } @article {pmid19516897, year = {2009}, author = {Maughan, H and Redfield, RJ}, title = {Tracing the evolution of competence in Haemophilus influenzae.}, journal = {PloS one}, volume = {4}, number = {6}, pages = {e5854}, pmid = {19516897}, issn = {1932-6203}, support = {F32 GM078861/GM/NIGMS NIH HHS/United States ; 5 F32 GM078861-03/GM/NIGMS NIH HHS/United States ; }, mesh = {Bayes Theorem ; Computational Biology/methods ; DNA Repair ; DNA, Bacterial/genetics/metabolism ; Ecology ; Evolution, Molecular ; Genes, Bacterial ; Genome ; Genome, Bacterial ; Haemophilus influenzae/*genetics ; Models, Genetic ; Phenotype ; Phylogeny ; Recombination, Genetic ; Species Specificity ; }, abstract = {Natural competence is the genetically encoded ability of some bacteria to take up DNA from the environment. Although most of the incoming DNA is degraded, occasionally intact homologous fragments can recombine with the chromosome, displacing one resident strand. This potential to use DNA as a source of both nutrients and genetic novelty has important implications for the ecology and evolution of competent bacteria. However, it is not known how frequently competence changes during evolution, or whether non-competent strains can persist for long periods of time. We have previously studied competence in H. influenzae and found that both the amount of DNA taken up and the amount recombined varies extensively between different strains. In addition, several strains are unable to become competent, suggesting that competence has been lost at least once. To investigate how many times competence has increased or decreased during the divergence of these strains, we inferred the evolutionary relationships of strains using the largest datasets currently available. However, despite the use of three datasets and multiple inference methods, few nodes were resolved with high support, perhaps due to extensive mixing by recombination. Tracing the evolution of competence in those clades that were well supported identified changes in DNA uptake and/or transformation in most strains. The recency of these events suggests that competence has changed frequently during evolution but the poor support of basal relationships precludes the determination of whether non-competent strains can persist for long periods of time. In some strains, changes in transformation have occurred that cannot be due to changes in DNA uptake, suggesting that selection can act on transformation independent of DNA uptake.}, } @article {pmid19502444, year = {2009}, author = {Palmer, K and Drake, HL and Horn, MA}, title = {Genome-derived criteria for assigning environmental narG and nosZ sequences to operational taxonomic units of nitrate reducers.}, journal = {Applied and environmental microbiology}, volume = {75}, number = {15}, pages = {5170-5174}, pmid = {19502444}, issn = {1098-5336}, mesh = {Bacteria/*classification/*genetics ; Bacterial Proteins/*genetics ; Cluster Analysis ; Computational Biology/*methods ; DNA, Ribosomal/genetics ; *Environmental Microbiology ; Nitrate Reductase/*genetics ; Oxidoreductases/*genetics ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Homology, Nucleic Acid ; }, abstract = {Ninety percent of cultured bacterial nitrate reducers with a 16S rRNA gene similarity of > or =97% had a narG or nosZ similarity of > or =67% or > or =80%, respectively, suggesting that 67% and 80% could be used as standardized, conservative threshold similarity values for narG and nosZ, respectively (i.e., any two sequences that are less similar than the threshold similarity value have a very high probability of belonging to different species), for estimating species-level operational taxonomic units. Genus-level tree topologies of narG and nosZ were generally similar to those of the corresponding 16S rRNA genes. Although some genomes contained multiple copies of narG, recent horizontal gene transfer of narG was not apparent.}, } @article {pmid19502381, year = {2009}, author = {Kuo, CH and Moran, NA and Ochman, H}, title = {The consequences of genetic drift for bacterial genome complexity.}, journal = {Genome research}, volume = {19}, number = {8}, pages = {1450-1454}, pmid = {19502381}, issn = {1088-9051}, support = {R01 GM056120/GM/NIGMS NIH HHS/United States ; R01 GM074738/GM/NIGMS NIH HHS/United States ; GM74738/GM/NIGMS NIH HHS/United States ; GM56120/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacteria/classification/*genetics ; Computational Biology ; Databases, Genetic ; *Evolution, Molecular ; Genes, Bacterial/genetics ; *Genetic Drift ; Genome, Bacterial/*genetics ; Models, Genetic ; Mutation ; Species Specificity ; }, abstract = {Genetic drift, which is particularly effective within small populations, can shape the size and complexity of genomes by affecting the fixation of deleterious mutations. In Bacteria, assessing the contribution of genetic drift to genome evolution is problematic because the usual methods, based on intraspecific polymorphisms, can be thwarted by difficulties in delineating species' boundaries. The increased availability of sequenced bacterial genomes allows application of an alternative estimator of drift, the genome-wide ratio of replacement to silent substitutions in protein-coding sequences. This ratio, which reflects the action of purifying selection across the entire genome, shows a strong inverse relationship with genome size, indicating that drift promotes genome reduction in bacteria.}, } @article {pmid19497664, year = {2009}, author = {Wei, S and Hu, Y and Srivastava, M and Zhou, Q and Niu, R and Li, Y and Wu, Z and Sun, T}, title = {Seed germination of a newly discovered hyperaccumulator Solanum nigrum L. affected by illumination and seed-soaking reagent.}, journal = {Journal of hazardous materials}, volume = {170}, number = {2-3}, pages = {1256-1259}, doi = {10.1016/j.jhazmat.2009.05.014}, pmid = {19497664}, issn = {1873-3336}, mesh = {Darkness ; Data Interpretation, Statistical ; Germination/drug effects/*physiology/*radiation effects ; Gibberellins/pharmacology ; Hydrogen Peroxide/pharmacology ; Indicators and Reagents ; Light ; Nitrates/pharmacology ; Potassium Compounds/pharmacology ; Seeds/*drug effects/growth & development/*radiation effects ; Solanum nigrum/*growth & development ; }, abstract = {Solanum nigrum is a newly found Cd-hyperaccumulator which showed very high remediation efficiency in polluted soil. Seed germination experiments with different illumination and seed-soaking reagents were conducted in constant temperature box and greenhouse with soil as burgeon base. The results showed that the germination rate with alternating light/dark photoperiod was about twice of that without lighting (p < 0.05), suggesting that illumination is one of the important conditions for seed germination of S. nigrum. All treatments with seed-soaking reagents significantly increased the seed germination rate of S. nigrum (p < 0.05). Treatment with H2O2 (0.1%) had the shortest germination time. The germination rate of seeds that were not washed in water following soaking was 2-3 times higher than that of seeds that were washed after soaking.}, } @article {pmid19497657, year = {2009}, author = {Reiter, MA and Saintil, M and Yang, Z and Pokrajac, D}, title = {Derivation of a GIS-based watershed-scale conceptual model for the St. Jones River Delaware from habitat-scale conceptual models.}, journal = {Journal of environmental management}, volume = {90}, number = {11}, pages = {3253-3265}, doi = {10.1016/j.jenvman.2009.04.018}, pmid = {19497657}, issn = {1095-8630}, mesh = {Conservation of Natural Resources ; Ecosystem ; Environmental Monitoring/*methods ; *Geographic Information Systems ; *Models, Theoretical ; Rivers ; }, abstract = {Conceptual modeling is a useful tool for identifying pathways between drivers, stressors, Valued Ecosystem Components (VECs), and services that are central to understanding how an ecosystem operates. The St. Jones River watershed, DE is a complex ecosystem, and because management decisions must include ecological, social, political, and economic considerations, a conceptual model is a good tool for accommodating the full range of inputs. In 2002, a Four-Component, Level 1 conceptual model was formed for the key habitats of the St. Jones River watershed, but since the habitat level of resolution is too fine for some important watershed-scale issues we developed a functional watershed-scale model using the existing narrowed habitat-scale models. The narrowed habitat-scale conceptual models and associated matrices developed by Reiter et al. (2006) were combined with data from the 2002 land use/land cover (LULC) GIS-based maps of Kent County in Delaware to assemble a diagrammatic and numerical watershed-scale conceptual model incorporating the calculated weight of each habitat within the watershed. The numerical component of the assembled watershed model was subsequently subjected to the same Monte Carlo narrowing methodology used for the habitat versions to refine the diagrammatic component of the watershed-scale model. The narrowed numerical representation of the model was used to generate forecasts for changes in the parameters "Agriculture" and "Forest", showing that land use changes in these habitats propagated through the results of the model by the weighting factor. Also, the narrowed watershed-scale conceptual model identified some key parameters upon which to focus research attention and management decisions at the watershed scale. The forecast and simulation results seemed to indicate that the watershed-scale conceptual model does lead to different conclusions than the habitat-scale conceptual models for some issues at the larger watershed scale.}, } @article {pmid19495966, year = {2009}, author = {Sonderegger, DL and Wang, H and Huang, Y and Clements, WH}, title = {Effects of measurement error on the strength of concentration-response relationships in aquatic toxicology.}, journal = {Ecotoxicology (London, England)}, volume = {18}, number = {7}, pages = {824-828}, doi = {10.1007/s10646-009-0325-2}, pmid = {19495966}, issn = {1573-3017}, mesh = {Animals ; Bias ; Colorado ; Computer Simulation ; Data Interpretation, Statistical ; Diptera/*drug effects/physiology ; Dose-Response Relationship, Drug ; Ecotoxicology ; Environmental Monitoring/*statistics & numerical data ; Environmental Restoration and Remediation ; Life Cycle Stages/drug effects/physiology ; Metals, Heavy/analysis/*toxicity ; Models, Statistical ; Predictive Value of Tests ; Reproducibility of Results ; Risk Assessment ; Rivers/chemistry ; Water Pollutants, Chemical/analysis/*toxicity ; }, abstract = {The effect that measurement error of predictor variables has on regression inference is well known in the statistical literature. However, the influence of measurement error on the ability to quantify relationships between chemical stressors and biological responses has received little attention in ecotoxicology. We present a common data-collection scenario and demonstrate that the relationship between explanatory and response variables is consistently underestimated when measurement error is ignored. A straightforward extension of the regression calibration method is to use a nonparametric method to smooth the predictor variable with respect to another covariate (e.g., time) and using the smoothed predictor to estimate the response variable. We conducted a simulation study to compare the effectiveness of the proposed method to the naive analysis that ignores measurement error. We conclude that the method satisfactorily addresses the problem when measurement error is moderate to large, and does not result in a noticeable loss of power in the case where measurement error is absent.}, } @article {pmid19495862, year = {2009}, author = {Diefenderfer, HL and Sobocinski, KL and Thom, RM and May, CW and Borde, AB and Southard, SL and Vavrinec, J and Sather, NK}, title = {Multiscale analysis of restoration priorities for marine shoreline planning.}, journal = {Environmental management}, volume = {44}, number = {4}, pages = {712-731}, pmid = {19495862}, issn = {1432-1009}, mesh = {*Conservation of Natural Resources ; Ecosystem ; Environmental Pollutants ; Geographic Information Systems ; *Models, Theoretical ; Seawater ; *Wetlands ; }, abstract = {Planners are being called on to prioritize marine shorelines for conservation status and restoration action. This study documents an approach to determining the management strategy most likely to succeed based on current conditions at local and landscape scales. The conceptual framework based in restoration ecology pairs appropriate restoration strategies with sites based on the likelihood of producing long-term resilience given the condition of ecosystem structures and processes at three scales: the shorezone unit (site), the drift cell reach (nearshore marine landscape), and the watershed (terrestrial landscape). The analysis is structured by a conceptual ecosystem model that identifies anthropogenic impacts on targeted ecosystem functions. A scoring system, weighted by geomorphic class, is applied to available spatial data for indicators of stress and function using geographic information systems. This planning tool augments other approaches to prioritizing restoration, including historical conditions and change analysis and ecosystem valuation.}, } @article {pmid19485768, year = {2009}, author = {Di Luca, M and Boccolini, D and Severini, F and Toma, L and Barbieri, FM and Massa, A and Romi, R}, title = {A 2-year entomological study of potential malaria vectors in central Italy.}, journal = {Vector borne and zoonotic diseases (Larchmont, N.Y.)}, volume = {9}, number = {6}, pages = {703-711}, doi = {10.1089/vbz.2008.0129}, pmid = {19485768}, issn = {1557-7759}, mesh = {Animals ; Anopheles/genetics/parasitology/*physiology ; Culicidae/growth & development ; Databases, Nucleic Acid ; *Ecosystem ; Entomology ; Female ; Geography ; Humans ; Insect Vectors/genetics/parasitology/*physiology ; Italy ; Longitudinal Studies ; Malaria/parasitology/transmission ; Polymerase Chain Reaction/veterinary ; Population Density ; }, abstract = {Europe was officially declared free from malaria in 1975; nevertheless, this disease remains a potential problem related to the presence of former vectors, belonging to the Anopheles maculipennis complex. Autochthonous-introduced malaria cases, recently reported in European countries, together with the predicted climatic and environmental changes, have increased the concern of health authorities over the possible resurgence of this disease in the Mediterranean Basin. In Italy, to study the distribution and bionomics of indigenous anopheline populations and to assess environmental parameters that could influence their dynamics, an entomological study was carried out in 2005-2006 in an at-risk study area. This model area is represented by the geographical region named the Maremma, a Tyrrhenian costal plain in Central Italy, where malaria was hyperendemic up to the 1950s. Fortnightly, entomological surveys (April-October) were carried out in four selected sites with different ecological features. Morphological and molecular characterization, blood meal identification, and parity rate assessment of the anophelines were performed. In total, 8274 mosquitoes were collected, 7691 of which were anophelines. Six Anopheles species were recorded, the most abundant of which were Anopheles labranchiae and An. maculipennis s.s. An. labranchiae is predominant in the coastal plain, where it is present in scattered foci. However, this species exhibits a wider than expected range: in fact it has been recorded, for the first time, inland where An. maculipennis s.s. is the most abundant species. Both species fed on a wide range of animal hosts, also showing a marked aggressiveness on humans, when available. Our findings demonstrated the high receptivity of the Maremma area, where the former malaria vector, An. labranchiae, occurs at different densities related to the kind of environment, climatic parameters, and anthropic activities.}, } @article {pmid19485627, year = {2009}, author = {Cooper, H and Patall, EA}, title = {The relative benefits of meta-analysis conducted with individual participant data versus aggregated data.}, journal = {Psychological methods}, volume = {14}, number = {2}, pages = {165-176}, doi = {10.1037/a0015565}, pmid = {19485627}, issn = {1082-989X}, mesh = {Data Collection/*methods ; Data Interpretation, Statistical ; Humans ; *Meta-Analysis as Topic ; Models, Statistical ; }, abstract = {The authors describe the relative benefits of conducting meta-analyses with (a) individual participant data (IPD) gathered from the constituent studies and (b) aggregated data (AD), or the group-level statistics (in particular, effect sizes) that appear in reports of a study's results. Given that both IPD and AD are equally available, meta-analysis of IPD is superior to meta-analysis of AD. IPD meta-analysis permits synthesists to perform subgroup analyses not conducted by the original collectors of the data, to check the data and analyses in the original studies, to add new information to the data sets, and to use different statistical methods. However, the cost of IPD meta-analysis and the lack of available IPD data sets suggest that the best strategy currently available is to use both approaches in a complementary fashion such that the first step in conducting an IPD meta-analysis would be to conduct an AD meta-analysis. Regardless of whether a meta-analysis is conducted with IPD or AD, synthesists must remain vigilant in how they interpret their results. They must avoid ecological fallacies, Simpson's paradox, and interpretation of synthesis-generated evidence as supporting causal inferences.}, } @article {pmid21392287, year = {2009}, author = {Evangelista, P and Engeman, R and Tallents, L}, title = {Testing a passive tracking index for monitoring the endangered Ethiopian wolf.}, journal = {Integrative zoology}, volume = {4}, number = {2}, pages = {172-178}, doi = {10.1111/j.1749-4877.2009.00147.x}, pmid = {21392287}, issn = {1749-4877}, mesh = {Analysis of Variance ; *Animal Migration ; Animals ; *Data Interpretation, Statistical ; *Endangered Species ; Ethiopia ; Female ; Male ; *Wolves ; }, abstract = {The endangered Ethiopian wolf is considered the rarest canid in Africa. The species faces many threats and is particularly vulnerable to diseases such as rabies. A simple, low-technology means to monitor populations would greatly facilitate conservation efforts, through early detection of population changes and behavior, and signaling a need for intervention. We tested a passive tracking index methodology, which has been a valuable tool for indexing canids and other species around the world. The method uses counts of track intrusions into plots placed in the animals' routes of travel as the basis for calculating an index. Unlike for other species, for which the placement of tracking plots on dirt roads has been extremely successful, we found in our first trial that this approach did not adequately intersect the wolves' activity patterns. The low vegetation associated with Afro-alpine habitats offered little benefit for the wolves to travel roads. However, in our second trial among molerat colonies, a focus of wolf foraging activity, we found plot placement on molerat mounds was efficient for collecting Ethiopian wolf plot intrusions for index calculations. This plot placement method coupled with the passive tracking index calculations might offer resource managers a cost efficient tool that requires minimal equipment to monitor Ethiopian wolf populations on the Sanetti Plateau and other Afro-alpine habitats. Plot placement on roads in other Ethiopian wolf habitats where cross-country travel is more difficult might still be a viable means to collect track data, but would require further testing.}, } @article {pmid21392286, year = {2009}, author = {Ren, B and Li, M and Long, Y and Wu, R and Wei, F}, title = {Home range and seasonality of Yunnan snub-nosed monkeys.}, journal = {Integrative zoology}, volume = {4}, number = {2}, pages = {162-171}, doi = {10.1111/j.1749-4877.2009.00153.x}, pmid = {21392286}, issn = {1749-4877}, mesh = {Animal Migration/physiology ; Animals ; Behavior, Animal/physiology ; China ; Colobinae/*physiology ; Geographic Information Systems ; Homing Behavior/*physiology ; Male ; *Seasons ; }, abstract = {Home range studies are essential for understanding an animal's behavioral ecology and for making wildlife conservation efficient. The home range of a group of Yunnan snub-nosed monkeys (Rhinopithecus bieti Milne-Edwards, 1897) was estimated using a global positioning system collar from December 2003 to October 2004 in northern Yunnan Province, China. To measure the ranging area of the study group 1291 animal locations were fixed. Based on the 100% minimum convex polygon method, the home range size was approximately 32.8 km(2) ; based on the grid-cell method it was approximately 17.8 km(2) using a 250-m grid and 23.3 km(2) using a 500-m grid. We assessed seasonal changes in the home range of this monkey population and found a different ranging pattern of from earlier studies. Daily range size was calculated as 4.80 ± 5.81 ha (mean ± standard deviation), with a range of 45.66 ha (0.01-45.67 ha).}, } @article {pmid20836814, year = {2009}, author = {Schäfer, ML and Lundström, JO}, title = {The present distribution and predicted geographic expansion of the floodwater mosquito Aedes sticticus in Sweden.}, journal = {Journal of vector ecology : journal of the Society for Vector Ecology}, volume = {34}, number = {1}, pages = {141-147}, doi = {10.1111/j.1948-7134.2009.00017.x}, pmid = {20836814}, issn = {1948-7134}, mesh = {Aedes/*physiology ; Animals ; Climate ; Climate Change ; Geographic Information Systems ; *Geography ; Models, Biological ; Population Density ; Sweden ; Temperature ; }, abstract = {The mass emergence of floodwater mosquitoes, in particular Aedes sticticus and Aedes vexans, causes substantial nuisance and reduces life quality for inhabitants of infested areas and can have a negative impact on the socio-economic conditions of a region. We compared the previous, present, and predicted geographic distribution of Ae. sticticus in Sweden. Previous records from the literature until 1990 list the species in three out of 21 Swedish counties. Beginning in 1998, studies show that the present distribution of the species covers 11 counties, with highest abundances in an east-west belt in Central Sweden. Using climate data from the present and predicted climate scenarios, the expected distribution of Ae. sticticus in 2020, 2050, and 2080 could be modelled using GIS. As variables, mean temperatures and cumulative precipitation between May and August and degree slope were chosen. The predicted geographic distribution of Ae. sticticus will continue to increase and include 20 out of 21 Swedish counties. The expected temperature rise will increase the suitable area towards the northern part of Sweden by 2050. Some non-suitable areas can be found along the south-east coast due to insufficient amount of precipitation in 2050 and 2080. Modelling the expected distribution of a species using predicted climate change scenarios provides a valuable tool for risk assessments and early-warning systems that is easily applied to different species and scenarios.}, } @article {pmid19478138, year = {2009}, author = {Hollister, JD and Gaut, BS}, title = {Epigenetic silencing of transposable elements: a trade-off between reduced transposition and deleterious effects on neighboring gene expression.}, journal = {Genome research}, volume = {19}, number = {8}, pages = {1419-1428}, pmid = {19478138}, issn = {1088-9051}, mesh = {Arabidopsis/*genetics ; DNA Methylation ; DNA Transposable Elements/*genetics ; Databases, Genetic ; *Epigenesis, Genetic ; Evolution, Molecular ; Gene Expression Profiling ; Gene Expression Regulation, Plant ; *Gene Silencing ; Genome, Plant ; Models, Genetic ; Mutagenesis, Insertional ; RNA, Small Interfering/genetics ; }, abstract = {Transposable elements (TEs) are ubiquitous genomic parasites. The deleterious consequences of the presence and activity of TEs have fueled debate about the evolutionary forces countering their expansion. Purifying selection is thought to purge TE insertions from the genome, and TE sequences are targeted by hosts for epigenetic silencing. However, the interplay between epigenetic and evolutionary forces countering TE expansion remains unexplored. Here we analyze genomic, epigenetic, and population genetic data from Arabidopsis thaliana to yield three observations. First, gene expression is negatively correlated with the density of methylated TEs. Second, the signature of purifying selection is detectable for methylated TEs near genes but not for unmethylated TEs or for TEs far from genes. Third, TE insertions are distributed by age and methylation status, such that older, methylated TEs are farther from genes. Based on these observations, we present a model in which host silencing of TEs near genes has deleterious effects on neighboring gene expression, resulting in the preferential loss of methylated TEs from gene-rich chromosomal regions. This mechanism implies an evolutionary tradeoff in which the benefit of TE silencing imposes a fitness cost via deleterious effects on the expression of nearby genes.}, } @article {pmid19475485, year = {2010}, author = {Zhang, J and Ma, K and Fu, B}, title = {Wetland loss under the impact of agricultural development in the Sanjiang Plain, NE China.}, journal = {Environmental monitoring and assessment}, volume = {166}, number = {1-4}, pages = {139-148}, pmid = {19475485}, issn = {1573-2959}, mesh = {*Agriculture ; China ; *Conservation of Natural Resources ; Environment ; Geographic Information Systems ; Geological Phenomena ; *Wetlands ; }, abstract = {Wetland loss has been the major environmental problem in Sanjiang Plain, NE China in recent years because of the dramatic agricultural development. We determined the spatial associations of the wetland loss rates in an 11,000-km(2) study area for two intervals of period 1 (1975-1989) and period 2 (1989-2004) spanning 30 years by using geographic information systems. The landscape of this area was simple with five categories, composed of ten types, and including three natural wetland types--open water, marsh, and wet meadow. Extensive agriculture was the principal cultivation form in terms of large size farm units in the area. Agriculture has become the principal land use category replacing natural wetlands over the 30-year period. It has changed the whole landscape of the region and the landscape pattern, causing wetland loss and fragmentation. The wetland loss rate of the area was very different between the two intervals, while wetland loss was not uniform throughout the region and was influenced by the landscape characteristics, such as topography, geomorphology, and the location of the wetlands in the watershed. Despite the remarkable land use changes, the wetlands distribution in the landscapes was similar compared to their original pattern. These results indicated that agricultural development affected the areas more than the distribution pattern of the wetlands in this region.}, } @article {pmid19473217, year = {2009}, author = {Cavender-Bares, J and Kozak, KH and Fine, PV and Kembel, SW}, title = {The merging of community ecology and phylogenetic biology.}, journal = {Ecology letters}, volume = {12}, number = {7}, pages = {693-715}, doi = {10.1111/j.1461-0248.2009.01314.x}, pmid = {19473217}, issn = {1461-0248}, mesh = {Biodiversity ; Computational Biology ; *Ecology ; *Ecosystem ; Extinction, Biological ; Gene Flow ; Genetic Speciation ; *Phylogeny ; Population Dynamics ; }, abstract = {The increasing availability of phylogenetic data, computing power and informatics tools has facilitated a rapid expansion of studies that apply phylogenetic data and methods to community ecology. Several key areas are reviewed in which phylogenetic information helps to resolve long-standing controversies in community ecology, challenges previous assumptions, and opens new areas of investigation. In particular, studies in phylogenetic community ecology have helped to reveal the multitude of processes driving community assembly and have demonstrated the importance of evolution in the assembly process. Phylogenetic approaches have also increased understanding of the consequences of community interactions for speciation, adaptation and extinction. Finally, phylogenetic community structure and composition holds promise for predicting ecosystem processes and impacts of global change. Major challenges to advancing these areas remain. In particular, determining the extent to which ecologically relevant traits are phylogenetically conserved or convergent, and over what temporal scale, is critical to understanding the causes of community phylogenetic structure and its evolutionary and ecosystem consequences. Harnessing phylogenetic information to understand and forecast changes in diversity and dynamics of communities is a critical step in managing and restoring the Earth's biota in a time of rapid global change.}, } @article {pmid19472063, year = {2010}, author = {Vadrevu, KP and Eaturu, A and Badarinath, KV}, title = {Fire risk evaluation using multicriteria analysis--a case study.}, journal = {Environmental monitoring and assessment}, volume = {166}, number = {1-4}, pages = {223-239}, pmid = {19472063}, issn = {1573-2959}, mesh = {Decision Making, Computer-Assisted ; *Fires ; Geographic Information Systems ; Multivariate Analysis ; Risk Assessment ; *Trees ; }, abstract = {Forest fires are one of the major causes of ecological disturbance and environmental concerns in tropical deciduous forests of south India. In this study, we use fuzzy set theory integrated with decision-making algorithm in a Geographic Information Systems (GIS) framework to map forest fire risk. Fuzzy set theory implements classes or groupings of data with boundaries that are not sharply defined (i.e., fuzzy) and consists of a rule base, membership functions, and an inference procedure. We used satellite remote sensing datasets in conjunction with topographic, vegetation, climate, and socioeconomic datasets to infer the causative factors of fires. Spatial-level data on these biophysical and socioeconomic parameters have been aggregated at the district level and have been organized in a GIS framework. A participatory multicriteria decision-making approach involving Analytical Hierarchy Process has been designed to arrive at a decision matrix that identified the important causative factors of fires. These expert judgments were then integrated using spatial fuzzy decision-making algorithm to map the forest fire risk. Results from this study were quite useful in identifying potential "hotspots" of fire risk, where forest fire protection measures can be taken in advance. Further, this study also demonstrates the potential of multicriteria analysis integrated with GIS as an effective tool in assessing "where and when" forest fires will most likely occur.}, } @article {pmid19467285, year = {2009}, author = {Hrovat, M and Segner, H and Jeram, S}, title = {Variability of in vivo fish acute toxicity data.}, journal = {Regulatory toxicology and pharmacology : RTP}, volume = {54}, number = {3}, pages = {294-300}, doi = {10.1016/j.yrtph.2009.05.013}, pmid = {19467285}, issn = {1096-0295}, mesh = {Animals ; Databases, Factual ; Fishes ; Hazardous Substances/analysis/*toxicity ; Hydrogen-Ion Concentration ; Lethal Dose 50 ; Reproducibility of Results ; Species Specificity ; Temperature ; Toxicity Tests, Acute/*methods ; }, abstract = {The variability of toxicity data contained within databases was investigated using the widely used US EPA ECOTOX database as an example. Fish acute lethality (LC50) values for 44 compounds (for which at least 10 data entries existed) were extracted from the ECOTOX database yielding a total of 4654 test records. Significant variability of LC50 test results was observed, exceeding several orders of magnitude. In an attempt to systematically explore potential causes of the data variability, the influence of biological factors (such as test species or life stages) and physical factors (such as water temperature, pH or water hardness) were examined. Even after eliminating the influence of these inherent factors, considerable data variability remained, suggesting an important role of factors relating to technical and measurement procedures. The analysis, however, was limited by pronounced gaps in the test documentation. Of the 4654 extracted test reports, 66.5% provided no information on the fish life stage used for testing. Likewise, water temperature, hardness or pH were not recorded in 19.6%, 48.2% and 41.2% of the data entries, respectively. From these findings, we recommend the rigorous control of data entries ensuring complete recording of testing conditions. A more consistent database will help to better discriminate between technical and natural variability of the test data, which is of importance in ecological risk assessment for extrapolation from laboratory tests to the field, and also might help to develop correction factors that account for systematic differences in test results caused by species, life stage or test conditions.}, } @article {pmid19461231, year = {2009}, author = {Pavlish, C and Ho, A}, title = {Pathway to social justice: research on human rights and gender-based violence in a Rwandan refugee cAMP.}, journal = {ANS. Advances in nursing science}, volume = {32}, number = {2}, pages = {144-157}, doi = {10.1097/ANS.0b013e3181a3b0c4}, pmid = {19461231}, issn = {1550-5014}, mesh = {Anthropology, Cultural ; Attitude to Health/*ethnology ; Community Networks ; Family/ethnology ; Female ; Focus Groups ; Gender Identity ; Health Knowledge, Attitudes, Practice ; Health Services Needs and Demand ; Human Rights Abuses/ethnology/*prevention & control/statistics & numerical data ; Humans ; Leadership ; Male ; Nursing Methodology Research ; Power, Psychological ; Refugees/*psychology/statistics & numerical data ; Rwanda ; *Social Justice ; Surveys and Questionnaires ; Violence/ethnology/*prevention & control/statistics & numerical data ; Vulnerable Populations/ethnology/statistics & numerical data ; Women's Health/*ethnology ; }, abstract = {Gender-based violence persists in postconflict settings. Implementing an ethnographic study with Congolese refugees in Rwanda, we investigated community perspectives on justice and human rights. As core concepts, participants described the right to equal value as human beings and the corresponding responsibility to respect human rights as the basis for justice. Three factors that impede human rights include cultural ideology, social distance, and lack of a rights-enabling environment. Men described gender similarities while women emphasized gender differences in human rights. Ecological perspectives and rights-based approaches to achieving social justice seem warranted.}, } @article {pmid19460914, year = {2009}, author = {Ward, MM}, title = {Access to care and the incidence of end-stage renal disease due to diabetes.}, journal = {Diabetes care}, volume = {32}, number = {6}, pages = {1032-1036}, pmid = {19460914}, issn = {1935-5548}, support = {//Intramural NIH HHS/United States ; }, mesh = {Adult ; Budgets ; Databases, Factual/statistics & numerical data ; Diabetic Nephropathies/*epidemiology/therapy ; Health Services Accessibility/*statistics & numerical data ; Hospitalization/statistics & numerical data ; Humans ; Incidence ; Income/statistics & numerical data ; Kidney Failure, Chronic/*epidemiology/therapy ; Medicaid/statistics & numerical data ; Medically Uninsured/statistics & numerical data ; Medicare/statistics & numerical data ; Poverty/statistics & numerical data ; Rural Population/statistics & numerical data ; Socioeconomic Factors ; United States/epidemiology ; Young Adult ; }, abstract = {OBJECTIVE: Low socioeconomic status (SES) is associated with an increased risk of end-stage renal disease (ESRD) due to diabetes. Because ESRD is a preventable complication of diabetes, the association with SES may be related to limited access to treatment.

RESEARCH DESIGN AND METHODS: In this population-based ecological study, I examined the association between the incidence of ESRD attributed to diabetes and the proportion of hospitalizations with no insurance, Medicaid, or managed care insurance; residence in a primary care provider shortage area or rural area; and rate of hospitalizations for hyperglycemic complications, by ZIP code in California in 2001-2004.

RESULTS: The incidence of ESRD attributed to diabetes was higher in ZIP codes with higher proportions of hospitalizations with no insurance (r = 0.45; P < 0.0001) or Medicaid (r = 0.69; P < 0.0001) and in ZIP codes with higher rates of hospitalizations for hyperglycemic complications (r = 0.27; P < 0.0001). The incidence was lower in ZIP codes with higher proportions of hospitalizations with managed care insurance (r = -0.37; P < 0.0001) and was lower in primary care provider shortage areas and rural locations. In contrast, there were only weak associations between measures of access to care and the incidence of ESRD attributed to polycystic kidney disease, a condition that is not treatable.

CONCLUSIONS: The incidence of ESRD attributed to diabetes is strongly associated with area-based measures of access to care, suggesting that access to treatment partly mediates the association between SES and the incidence of ESRD.}, } @article {pmid19460146, year = {2009}, author = {Simard, F and Ayala, D and Kamdem, GC and Pombi, M and Etouna, J and Ose, K and Fotsing, JM and Fontenille, D and Besansky, NJ and Costantini, C}, title = {Ecological niche partitioning between Anopheles gambiae molecular forms in Cameroon: the ecological side of speciation.}, journal = {BMC ecology}, volume = {9}, number = {}, pages = {17}, pmid = {19460146}, issn = {1472-6785}, support = {R01 AI063508/AI/NIAID NIH HHS/United States ; R01-AI 063508/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Anopheles/classification/*genetics ; Bayes Theorem ; Cameroon ; Chromosome Inversion ; Cluster Analysis ; Ecology ; *Ecosystem ; Evolution, Molecular ; *Genetic Speciation ; Genetics, Population ; Geographic Information Systems ; Karyotyping ; *Models, Genetic ; Polymorphism, Genetic ; Species Specificity ; }, abstract = {BACKGROUND: Speciation among members of the Anopheles gambiae complex is thought to be promoted by disruptive selection and ecological divergence acting on sets of adaptation genes protected from recombination by polymorphic paracentric chromosomal inversions. However, shared chromosomal polymorphisms between the M and S molecular forms of An. gambiae and insufficient information about their relationship with ecological divergence challenge this view. We used Geographic Information Systems, Ecological Niche Factor Analysis, and Bayesian multilocus genetic clustering to explore the nature and extent of ecological and chromosomal differentiation of M and S across all the biogeographic domains of Cameroon in Central Africa, in order to understand the role of chromosomal arrangements in ecological specialisation within and among molecular forms.

RESULTS: Species distribution modelling with presence-only data revealed differences in the ecological niche of both molecular forms and the sibling species, An. arabiensis. The fundamental environmental envelope of the two molecular forms, however, overlapped to a large extent in the rainforest, where they occurred in sympatry. The S form had the greatest niche breadth of all three taxa, whereas An. arabiensis and the M form had the smallest niche overlap. Correspondence analysis of M and S karyotypes confirmed that molecular forms shared similar combinations of chromosomal inversion arrangements in response to the eco-climatic gradient defining the main biogeographic domains occurring across Cameroon. Savanna karyotypes of M and S, however, segregated along the smaller-scale environmental gradient defined by the second ordination axis. Population structure analysis identified three chromosomal clusters, each containing a mixture of M and S specimens. In both M and S, alternative karyotypes were segregating in contrasted environments, in agreement with a strong ecological adaptive value of chromosomal inversions.

CONCLUSION: Our data suggest that inversions on the second chromosome of An. gambiae are not causal to the evolution of reproductive isolation between the M and S forms. Rather, they are involved in ecological specialization to a similar extent in both genetic backgrounds, and most probably predated lineage splitting between molecular forms. However, because chromosome-2 inversions promote ecological divergence, resulting in spatial and/or temporal isolation between ecotypes, they might favour mutations in other ecologically significant genes to accumulate in unlinked chromosomal regions. When such mutations occur in portions of the genome where recombination is suppressed, such as the pericentromeric regions known as speciation islands in An. gambiae, they would contribute further to the development of reproductive isolation.}, } @article {pmid19459840, year = {2010}, author = {Johnson, DS and Laake, JL and Ver Hoef, JM}, title = {A model-based approach for making ecological inference from distance sampling data.}, journal = {Biometrics}, volume = {66}, number = {1}, pages = {310-318}, doi = {10.1111/j.1541-0420.2009.01265.x}, pmid = {19459840}, issn = {1541-0420}, mesh = {Biometry/*methods ; Computer Simulation ; *Data Interpretation, Statistical ; *Ecosystem ; Environmental Monitoring/*methods ; *Models, Statistical ; *Population Density ; *Sample Size ; }, abstract = {We consider a fully model-based approach for the analysis of distance sampling data. Distance sampling has been widely used to estimate abundance (or density) of animals or plants in a spatially explicit study area. There is, however, no readily available method of making statistical inference on the relationships between abundance and environmental covariates. Spatial Poisson process likelihoods can be used to simultaneously estimate detection and intensity parameters by modeling distance sampling data as a thinned spatial point process. A model-based spatial approach to distance sampling data has three main benefits: it allows complex and opportunistic transect designs to be employed, it allows estimation of abundance in small subregions, and it provides a framework to assess the effects of habitat or experimental manipulation on density. We demonstrate the model-based methodology with a small simulation study and analysis of the Dubbo weed data set. In addition, a simple ad hoc method for handling overdispersion is also proposed. The simulation study showed that the model-based approach compared favorably to conventional distance sampling methods for abundance estimation. In addition, the overdispersion correction performed adequately when the number of transects was high. Analysis of the Dubbo data set indicated a transect effect on abundance via Akaike's information criterion model selection. Further goodness-of-fit analysis, however, indicated some potential confounding of intensity with the detection function.}, } @article {pmid19458656, year = {2009}, author = {Shapiro, BJ and Alm, E}, title = {The slow:fast substitution ratio reveals changing patterns of natural selection in gamma-proteobacterial genomes.}, journal = {The ISME journal}, volume = {3}, number = {10}, pages = {1180-1192}, doi = {10.1038/ismej.2009.51}, pmid = {19458656}, issn = {1751-7370}, mesh = {Cluster Analysis ; Computational Biology/methods ; DNA, Bacterial/*genetics ; *Evolution, Molecular ; Gammaproteobacteria/*genetics ; *Genes, Bacterial ; *Genome, Bacterial ; *Mutation ; *Selection, Genetic ; }, abstract = {Different microbial species are thought to occupy distinct ecological niches, subjecting each species to unique selective constraints, which may leave a recognizable signal in their genomes. Thus, it may be possible to extract insight into the genetic basis of ecological differences among lineages by identifying unusual patterns of substitutions in orthologous gene or protein sequences. We used the ratio of substitutions in slow- versus fast-evolving sites (nucleotides in DNA, or amino acids in protein sequence) to quantify deviations from the typical pattern of selective constraint observed across bacterial lineages. We propose that elevated S:F in one branch (an excess of slow-site substitutions) can indicate a functionally relevant change, due to either positive selection or relaxed evolutionary constraint. In a genome-wide comparative study of gamma-proteobacterial proteins, we find that cell-surface proteins involved with motility and secretion functions often have high S:F ratios, whereas information-processing genes do not. Change in evolutionary constraints in some species is evidenced by increased S:F ratios within functionally related sets of genes (for example, energy production in Pseudomonas fluorescens), whereas other species apparently evolve mostly by drift (for example, uniformly elevated S:F across most genes in Buchnera spp.). Overall, S:F reveals several species-specific, protein-level changes with potential functional/ecological importance. As microbial genome projects yield more species-rich gene trees, the S:F ratio will become an increasingly powerful tool for uncovering functional genetic differences among species.}, } @article {pmid19457198, year = {2009}, author = {Egg, M and Höckner, M and Brandstätter, A and Schuler, D and Dallinger, R}, title = {Structural and bioinformatic analysis of the Roman snail Cd-Metallothionein gene uncovers molecular adaptation towards plasticity in coping with multifarious environmental stress.}, journal = {Molecular ecology}, volume = {18}, number = {11}, pages = {2426-2443}, doi = {10.1111/j.1365-294X.2009.04191.x}, pmid = {19457198}, issn = {1365-294X}, mesh = {Adaptation, Physiological/*genetics ; Amino Acid Sequence ; Animals ; Base Sequence ; Binding Sites ; Cadmium/metabolism ; Computational Biology/*methods ; Environmental Pollutants/analysis ; Metallothionein/*genetics ; Molecular Sequence Data ; Promoter Regions, Genetic ; Response Elements ; Sequence Analysis, DNA ; Snails/*genetics/metabolism ; Stress, Physiological ; Transcription Factors/genetics/metabolism ; }, abstract = {Metallothioneins (MTs) are a family of multifunctional proteins involved, among others, in stress response. The Cadmium (Cd)-MT gene of the Roman snail (Helix pomatia), for example, encodes for a protein induced upon cadmium exposure. While our previous studies have demonstrated that the expressed Cd-MT isoform of Roman snails assists detoxification of cadmium, the present work focuses on the potential plasticity of this gene in response to a variety of environmental stressors playing a crucial role in the specific ecological niche of H. pomatia. Our hypothesis is based on a bioinformatic approach involving gene sequencing, structural and in silico analysis of transcription factor binding sites (TFBs), and a comparison of these features with other MT genes. Our results show that the Roman snail's Cd-MT gene not only is the largest known MT gene, but also contains--apart from the regulatory promoter region--several intronic repeat cassettes of putative TFBs suggested to be involved in environmental stress response, immune competence, and regulation of gene expression. Moreover, intronic scaffold/matrix attachment regions (S/MARs) and stress-induced duplex destabilization sites confer a high potential for epigenetic gene regulation. This suggested regulatory plasticity is also supported by physiological data showing that Cd-MT in Roman snails can be induced differentially not only after cadmium exposure, but also in response to nonmetallic environmental stressors. It is concluded that structural analysis combined with bioinformatic screening may constitute valuable tools for predicting the potential for plasticity and niche-specific adaptation of stress-responsive genes in populations living under rapidly changing environmental conditions.}, } @article {pmid19454530, year = {2009}, author = {French, CE}, title = {Synthetic biology and biomass conversion: a match made in heaven?.}, journal = {Journal of the Royal Society, Interface}, volume = {6 Suppl 4}, number = {Suppl 4}, pages = {S547-58}, pmid = {19454530}, issn = {1742-5662}, mesh = {Bacteria/metabolism ; *Biodegradation, Environmental ; *Biomass ; Biotechnology/*methods ; Cellulose/chemistry ; Computational Biology/*methods ; Ecology ; *Energy-Generating Resources ; Ethanol/chemistry ; Fermentation ; Genetic Engineering/methods ; Ketones/chemistry ; Microbiology ; Models, Genetic ; Systems Biology/*methods ; }, abstract = {To move our economy onto a sustainable basis, it is essential that we find a replacement for fossil carbon as a source of liquid fuels and chemical industry feedstocks. Lignocellulosic biomass, available in enormous quantities, is the only feasible replacement. Many micro-organisms are capable of rapid and efficient degradation of biomass, employing a battery of specialized enzymes, but do not produce useful products. Attempts to transfer biomass-degrading capability to industrially useful organisms by heterologous expression of one or a few biomass-degrading enzymes have met with limited success. It seems probable that an effective biomass-degradation system requires the synergistic action of a large number of enzymes, the individual and collective actions of which are poorly understood. By offering the ability to combine any number of transgenes in a modular, combinatorial way, synthetic biology offers a new approach to elucidating the synergistic action of combinations of biomass-degrading enzymes in vivo and may ultimately lead to a transferable biomass-degradation system. Also, synthetic biology offers the potential for assembly of novel product-formation pathways, as well as mechanisms for increased solvent tolerance. Thus, synthetic biology may finally lead to cheap and effective processes for conversion of biomass to useful products.}, } @article {pmid19453656, year = {2009}, author = {Arroyo, TP and Olson, ME and García-Mendoza, A and Solano, E}, title = {A GIS-based comparison of the Mexican national and IUCN methods for determining extinction risk.}, journal = {Conservation biology : the journal of the Society for Conservation Biology}, volume = {23}, number = {5}, pages = {1156-1166}, doi = {10.1111/j.1523-1739.2009.01241.x}, pmid = {19453656}, issn = {1523-1739}, mesh = {*Asparagaceae/classification ; Ecosystem ; *Extinction, Biological ; *Geographic Information Systems ; Mexico ; Species Specificity ; }, abstract = {The national systems used in the evaluation of extinction risk are often touted as more readily applied and somehow more regionally appropriate than the system of the International Union for Conservation of Nature (IUCN). We compared risk assessments of the Mexican national system (method for evaluation of risk of extinction of wild species [MER]) with the IUCN system for the 16 Polianthes taxa (Agavaceae), a genus of plants with marked variation in distribution sizes. We used a novel combination of herbarium data, geographic information systems (GIS), and species distribution models to provide rapid, repeatable estimates of extinction risk. Our GIS method showed that the MER and the IUCN system use similar data. Our comparison illustrates how the IUCN method can be applied even when all desirable data are not available, and that the MER offers no special regional advantage with respect to the IUCN regional system. Instead, our results coincided, with both systems identifying 14 taxa of conservation concern and the remaining two taxa of low risk, largely because both systems use similar information. An obstacle for the application of the MER is that there are no standards for quantifying the criteria of habitat condition and intrinsic biological vulnerability. If these impossible-to-quantify criteria are left out, what are left are geographical distribution and the impact of human activity, essentially the considerations we were able to assess for the IUCN method. Our method has the advantage of making the IUCN criteria easy to apply, and because each step can be standardized between studies, it ensures greater comparability of extinction risk estimates among taxa.}, } @article {pmid19446015, year = {2010}, author = {Manno, M and Viau, C and , and Cocker, J and Colosio, C and Lowry, L and Mutti, A and Nordberg, M and Wang, S}, title = {Biomonitoring for occupational health risk assessment (BOHRA).}, journal = {Toxicology letters}, volume = {192}, number = {1}, pages = {3-16}, doi = {10.1016/j.toxlet.2009.05.001}, pmid = {19446015}, issn = {1879-3169}, mesh = {Data Interpretation, Statistical ; Ecotoxicology ; Environmental Monitoring/*methods ; Humans ; Occupational Exposure/*analysis ; Occupational Health ; Public Health ; Risk Assessment/*methods ; }, abstract = {Biological monitoring (BM or biomonitoring) deals with the assessment of individual human exposure, effect and susceptibility to occupational risk factors. It is a fundamental tool in occupational health risk assessment (OHRA) and occupational health practice (OHP) and it has become one of the most, if not the most active area in occupational health (OH) research today. From the few hundred BM papers published in the 80s, there are now several tens of thousand papers published in the peer review literature each year, and the trend is still rising exponentially. As a result, BM has become a priority for the Scientific Committee on Occupational Toxicology (SCOT) of the International Commission on Occupational Health (ICOH). Moreover, there has been a long-term interest in biological monitoring by other SCs of ICOH such as the Scientific Committees on Toxicology of Metals (SCTM) and on Rural Health (SCRH). Despite its current popularity, though, BM is not always correctly used or interpreted by those involved in OHRA or OHP. The present review has been prepared to fill this gap and to help preventing misuse and misinterpretation of data. Although the document is meant to be a reference primarily for those involved in OH research and/or practice, it might become of interest for a wider audience within and outside ICOH, including scientists, occupational physicians, industrial hygienists and occupational or public health professionals in general, involved in chemical risk assessment for occupational health. The mission of SCOT and also of other SCs of ICOH, such as SCTM and SCRH, is indeed to promote the advancement and diffusion of knowledge on biological monitoring and other relevant occupational toxicology aspects and to make them available and useful to the entire OH scientific community. All articles retrieved as of 3 January, 2007 as "Review" with the combined key words "biological monitoring" in PubMed from 2000 to 2007 have been scanned individually. This yielded a total of 1400 articles from a grand total of 2486 (excluding limitation on year of publication). When the title was related to human occupational biological monitoring, the abstract was read and its content was included. Articles outside the 2000-2007 time frame or that are not classified as "Review" in PubMed have also been included, when relevant. The review is in four parts: (a) the introduction, containing the basic principles and definitions of BM and the different types of biomarkers (BMK), their toxicological significance, practical use and limitations, (b) the methodological and analytical aspects of BM in exposed workers, (c) the interpretation and management of BM data, including a number of recommendations to be considered when planning, performing and interpreting BM results and, finally, (d) the ethical aspects of BM. A list of key references to relevant papers or documents has been included. The BM of specific chemicals or groups of chemicals is outside the purpose of the review. The document is aimed to represent the state of the art on biological monitoring in occupational risk assessment. We expect that reference to its content will be made, whenever appropriate, by those involved in occupational health practice and research when dealing with BM issues. The document is not meant, though, to represent a rigid nor a permanent set of rules and it will be periodically updated according to new developments and any significant advance in BM science. Any part of the document, therefore, is open to suggestions by scientifically qualified persons or institutions officially involved in BM and comments should be sent directly to the authors. A preliminary draft of the document has been presented at the 7th International Symposium on Biological Monitoring, Beijing, 10-12 September, 2007.}, } @article {pmid19445709, year = {2009}, author = {Tzahor, S and Man-Aharonovich, D and Kirkup, BC and Yogev, T and Berman-Frank, I and Polz, MF and Béjà, O and Mandel-Gutfreund, Y}, title = {A supervised learning approach for taxonomic classification of core-photosystem-II genes and transcripts in the marine environment.}, journal = {BMC genomics}, volume = {10}, number = {}, pages = {229}, pmid = {19445709}, issn = {1471-2164}, mesh = {Bacteriophages/classification/*genetics ; Cluster Analysis ; Computational Biology/*methods ; Genes, Bacterial ; Genes, Viral ; Genome, Bacterial ; Genome, Viral ; Genomics/methods ; Mediterranean Sea ; Photosystem II Protein Complex/*classification/genetics ; Principal Component Analysis ; Prochlorococcus/classification/*genetics ; Seawater/microbiology ; Sequence Analysis, DNA ; Synechococcus/classification/*genetics ; }, abstract = {BACKGROUND: Cyanobacteria of the genera Synechococcus and Prochlorococcus play a key role in marine photosynthesis, which contributes to the global carbon cycle and to the world oxygen supply. Recently, genes encoding the photosystem II reaction center (psbA and psbD) were found in cyanophage genomes. This phenomenon suggested that the horizontal transfer of these genes may be involved in increasing phage fitness. To date, a very small percentage of marine bacteria and phages has been cultured. Thus, mapping genomic data extracted directly from the environment to its taxonomic origin is necessary for a better understanding of phage-host relationships and dynamics.

RESULTS: To achieve an accurate and rapid taxonomic classification, we employed a computational approach combining a multi-class Support Vector Machine (SVM) with a codon usage position specific scoring matrix (cuPSSM). Our method has been applied successfully to classify core-photosystem-II gene fragments, including partial sequences coming directly from the ocean, to seven different taxonomic classes. Applying the method on a large set of DNA and RNA psbA clones from the Mediterranean Sea, we studied the distribution of cyanobacterial psbA genes and transcripts in their natural environment. Using our approach, we were able to simultaneously examine taxonomic and ecological distributions in the marine environment.

CONCLUSION: The ability to accurately classify the origin of individual genes and transcripts coming directly from the environment is of great importance in studying marine ecology. The classification method presented in this paper could be applied further to classify other genes amplified from the environment, for which training data is available.}, } @article {pmid19440854, year = {2009}, author = {Fuchs, C and Bichler, RM and Raffl, C}, title = {Cyberethics and co-operation in the information society.}, journal = {Science and engineering ethics}, volume = {15}, number = {4}, pages = {447-466}, doi = {10.1007/s11948-009-9138-1}, pmid = {19440854}, issn = {1471-5546}, mesh = {Capitalism ; Computers/ethics ; *Cooperative Behavior ; Humans ; Informatics/*ethics ; Information Dissemination/*ethics ; Internet/*ethics ; Social Class ; }, abstract = {The task of this paper is to ground the notion of cyberethics of co-operation. The evolution of modern society has resulted in a shift from industrial society towards informational capitalism. This transformation is a multidimensional shift that affects all aspects of society. Hence also the ethical system of society is penetrated by the emergence of the knowledge society and ethical guidelines for the information age are needed. Ethical issues and conflicts in the knowledge society are connected to topics of ecological and social sustainability. For information ethics and cyberethics, the sustainable design of society, social, and socio-technological systems is important. In this context the notions of sustainability and co-operation are discussed. Based on these categories, the approach of cyberethics of co-operation can be theoretically grounded.}, } @article {pmid19433131, year = {2009}, author = {Sihtmäe, M and Dubourguier, HC and Kahru, A}, title = {Toxicological information on chemicals published in the Russian language: Contribution to REACH and 3Rs.}, journal = {Toxicology}, volume = {262}, number = {1}, pages = {27-37}, doi = {10.1016/j.tox.2009.05.001}, pmid = {19433131}, issn = {1879-3185}, mesh = {Animals ; Chemical Warfare Agents/toxicity ; Databases, Factual ; *Ecotoxicology ; Estonia ; Hazardous Substances/*toxicity ; Humans ; Internet ; Libraries ; *Public Sector ; Publishing ; Quantitative Structure-Activity Relationship ; Russia ; Toxicity Tests/methods ; *Toxicology ; }, abstract = {This review is reporting on the current situation of publicly available toxicological and ecotoxicological information on chemicals published in Russian language in various libraries, databases as well as in the Internet. This information can be beneficial for the new EU chemical policy REACH and for the development of intelligent testing strategies (involving also QSAR and QAAR) that enable a significant increase in the use of non-testing information for regulatory decision making, thus minimizing the need for animal testing according to the 3R's strategy. Currently, the access to this information is limited due to the language barrier and low level of digitalization of respective journals and books. Fortunately, on-line translation services are overcoming language barriers already now.}, } @article {pmid19432793, year = {2010}, author = {Buckland, ST and Laake, JL and Borchers, DL}, title = {Double-observer line transect methods: levels of independence.}, journal = {Biometrics}, volume = {66}, number = {1}, pages = {169-177}, doi = {10.1111/j.1541-0420.2009.01239.x}, pmid = {19432793}, issn = {1541-0420}, mesh = {*Algorithms ; Animals ; Biometry/*methods ; *Data Interpretation, Statistical ; *Models, Statistical ; *Population Dynamics ; *Whales ; }, abstract = {Double-observer line transect methods are becoming increasingly widespread, especially for the estimation of marine mammal abundance from aerial and shipboard surveys when detection of animals on the line is uncertain. The resulting data supplement conventional distance sampling data with two-sample mark-recapture data. Like conventional mark-recapture data, these have inherent problems for estimating abundance in the presence of heterogeneity. Unlike conventional mark-recapture methods, line transect methods use knowledge of the distribution of a covariate, which affects detection probability (namely, distance from the transect line) in inference. This knowledge can be used to diagnose unmodeled heterogeneity in the mark-recapture component of the data. By modeling the covariance in detection probabilities with distance, we show how the estimation problem can be formulated in terms of different levels of independence. At one extreme, full independence is assumed, as in the Petersen estimator (which does not use distance data); at the other extreme, independence only occurs in the limit as detection probability tends to one. Between the two extremes, there is a range of models, including those currently in common use, which have intermediate levels of independence. We show how this framework can be used to provide more reliable analysis of double-observer line transect data. We test the methods by simulation, and by analysis of a dataset for which true abundance is known. We illustrate the approach through analysis of minke whale sightings data from the North Sea and adjacent waters.}, } @article {pmid19432789, year = {2010}, author = {Foster, SD and Dunstan, PK}, title = {The analysis of biodiversity using rank abundance distributions.}, journal = {Biometrics}, volume = {66}, number = {1}, pages = {186-195}, doi = {10.1111/j.1541-0420.2009.01263.x}, pmid = {19432789}, issn = {1541-0420}, mesh = {*Algorithms ; Animals ; *Biodiversity ; Biometry/*methods ; Computer Simulation ; *Data Interpretation, Statistical ; Epidemiologic Methods ; *Models, Statistical ; *Population Dynamics ; }, abstract = {Biodiversity is an important topic of ecological research. A common form of data collected to investigate patterns of biodiversity is the number of individuals of each species at a series of locations. These data contain information on the number of individuals (abundance), the number of species (richness), and the relative proportion of each species within the sampled assemblage (evenness). If there are enough sampled locations across an environmental gradient then the data should contain information on how these three attributes of biodiversity change over gradients. We show that the rank abundance distribution (RAD) representation of the data provides a convenient method for quantifying these three attributes constituting biodiversity. We present a statistical framework for modeling RADs and allow their multivariate distribution to vary according to environmental gradients. The method relies on three models: a negative binomial model, a truncated negative binomial model, and a novel model based on a modified Dirichlet-multinomial that allows for a particular type of heterogeneity observed in RAD data. The method is motivated by, and applied to, a large-scale marine survey off the coast of Western Australia, Australia. It provides a rich description of biodiversity and how it changes with environmental conditions.}, } @article {pmid19432506, year = {2009}, author = {De Lange, HJ and Lahr, J and Van der Pol, JJ and Wessels, Y and Faber, JH}, title = {Ecological vulnerability in wildlife: an expert judgment and multicriteria analysis tool using ecological traits to assess relative impact of pollutants.}, journal = {Environmental toxicology and chemistry}, volume = {28}, number = {10}, pages = {2233-2240}, doi = {10.1897/08-626.1}, pmid = {19432506}, issn = {0730-7268}, mesh = {Animals ; Animals, Wild/*physiology ; Cadmium/analysis/toxicity ; Chlorpyrifos/analysis/toxicity ; Copper/analysis/toxicity ; DDT/analysis/toxicity ; Decision Support Techniques ; Ecotoxicology/*methods ; Environmental Monitoring ; Environmental Pollution/*adverse effects/*analysis ; Geologic Sediments/analysis ; Ivermectin/analysis/toxicity ; Risk Assessment ; Species Specificity ; Zinc/analysis/toxicity ; }, abstract = {Nature development in The Netherlands often is planned on contaminated soils and sediments of former agricultural land and in floodplain areas; however, this contamination may present a risk to wildlife species desired at those nature development sites. Specific risk assessment methods are needed, because toxicological information is lacking for most wildlife species. The vulnerability of a species is a combination of its potential exposure, sensitivity to the type of pollutant, and recovery capacity. We developed a new method to predict ecological vulnerability in wildlife using autecological information. The analysis results in an ordinal ranking of vulnerable species. The method was applied to six representative contaminants: copper and zinc (essential metals, low to medium toxicity), cadmium (nonessential metal, high toxicity), DDT (persistent organic pesticide, high toxicity), chlorpyrifos (persistent organophosphate insecticide, high toxicity), and ivermectin (persistent veterinary pharmaceutical, low to medium toxicity). High vulnerability to the essential metals copper and zinc was correlated with soil and sediment habitat preference of a species and with r-strategy (opportunistic strategy suited for unstable environments). Increased vulnerability to the bioaccumulating substances cadmium and DDT was correlated with higher position of a species in the food web and with life span and K-strategy (equilibrium strategy suited for stable environments). Vulnerability to chlorpyrifos and ivermectin was high for species with a preference for soil habitats. The ecological vulnerability analysis has potential to further our abilities in risk assessment.}, } @article {pmid19431938, year = {2009}, author = {Thiele, J and Kollmann, J and Andersen, UR}, title = {Ecological and socioeconomic correlates of plant invasions in Denmark: the utility of environmental assessment data.}, journal = {Ambio}, volume = {38}, number = {2}, pages = {89-94}, doi = {10.1579/0044-7447-38.2.89}, pmid = {19431938}, issn = {0044-7447}, mesh = {Biodiversity ; Denmark ; Ecosystem ; Geographic Information Systems ; *Plant Development ; *Socioeconomic Factors ; }, abstract = {Control of plant invasions requires regional knowledge of invasive species' distribution and the factors that promote their spread. We studied the distribution of invasive alien plants in Denmark at 2 spatial scales ("site" and "municipality") based on habitat descriptions and species lists from 2343 sites recorded within environmental assessments for planned infrastructure projects and conservation management. We created a Geographic Information System database of the sites and supplemented the field data with information on traffic routes, water courses, and socioeconomic indicators from the respective municipalities. The percentage of invaded sites within a municipality decreased with increasing tax percentage and it increased with (sub-)urbanity. The number of invasive species at the sites was positively correlated with resident plant diversity, disturbance, and proximity to traffic routes. We conclude that current plant invasions in Denmark are mainly an anthropogenic (sub-)urban phenomenon. The results are discussed with respect to the utility of environmental assessment data for studying plant invasions and improving control of invasive species.}, } @article {pmid19431292, year = {2009}, author = {Schulz, R and Stehle, S and Elsaesser, D and Matezki, S and Müller, A and Neumann, M and Ohliger, R and Wogram, J and Zenker, K}, title = {Geodata-based probabilistic risk assessment and management of pesticides in Germany: a conceptual framework.}, journal = {Integrated environmental assessment and management}, volume = {5}, number = {1}, pages = {69-79}, doi = {10.1897/ieam_2008-032.1}, pmid = {19431292}, issn = {1551-3777}, mesh = {Conservation of Energy Resources ; Environmental Exposure ; *Geographic Information Systems ; Germany ; Models, Statistical ; Pesticides/*chemistry/*toxicity ; *Risk Assessment ; Rivers/*chemistry ; Water Movements ; Water Pollutants, Chemical/*chemistry/*toxicity ; Water Pollution, Chemical ; }, abstract = {The procedure for the risk assessment of pesticides in Germany is currently further developed from a deterministic to a geodata-based probabilistic risk assessment (GeoPRA) approach. As the initial step, the exposure assessment for spray drift in permanent crops, such as vineyards, fruit orchards, and hops, is considered. In our concept, geoinformation tools are used to predict distribution functions for exposure concentrations based mainly on spatial information regarding the neighbourhood of crops and surface waters. A total number of 23 factors affecting the drift into surface waters were assessed and suggestions for their inclusion into the approach developed. The main objectives are to base the exposure estimation on a realistic representation of local landscape characteristics and on empirical results for the impact of each feature on the drift deposition. A framework for the identification of high-risk sites (active management areas [AMAs]) based on protection goals and ecological considerations was developed in order to implement suitable risk mitigation measures. The inclusion of active mitigation measures at sites with identified and verified risk is considered a central and important part of the overall assessment strategy. The suggested GeoPRA procedure itself is comprised of the following 4 steps, including elements of the extensive preliminary work conducted so far: 1) nationwide risk assessment, preferably based only on geodata-based factors; 2) identification of AMAs, including the spatial extension of contamination, the level of contamination, and the tolerable effect levels; 3) refined exposure assessment, using aerial photographs and field surveys; and 4) mitigation measures, with a focus on landscape-level active mitigation measures leading to effective risk reductions. The suggested GeoPRA procedure offers the possibility to actively involve the farming community in the process of pesticide management. Overall, the new procedure will aim at increased flexibility of pesticide application regulations and a high level of protection of surface waters.}, } @article {pmid19429249, year = {2009}, author = {Sanderson, H and Thomsen, M}, title = {Comparative analysis of pharmaceuticals versus industrial chemicals acute aquatic toxicity classification according to the United Nations classification system for chemicals. Assessment of the (Q)SAR predictability of pharmaceuticals acute aquatic toxicity and their predominant acute toxic mode-of-action.}, journal = {Toxicology letters}, volume = {187}, number = {2}, pages = {84-93}, doi = {10.1016/j.toxlet.2009.02.003}, pmid = {19429249}, issn = {0378-4274}, mesh = {Animals ; Databases as Topic ; Drug-Related Side Effects and Adverse Reactions/*classification ; *Ecotoxicology ; Industry ; Pharmaceutical Preparations/chemistry ; Quantitative Structure-Activity Relationship ; United Nations ; Water Pollutants, Chemical/classification/*toxicity ; }, abstract = {Pharmaceuticals have been reported to be ubiquitously present in surface waters prompting concerns of effects of these bioactive substances. Meanwhile, there is a general scarcity of publicly available ecotoxicological data concerning pharmaceuticals. The aim of this paper was to compile a comprehensive database based on OECD's standardized measured ecotoxicological data and to evaluate if there is generally cause of greater concern with regards to pharmaceutical aquatic toxicological profiles relative to industrial chemicals. Comparisons were based upon aquatic ecotoxicity classification under the United Nations Global Harmonized System for classification and labeling of chemicals (GHS). Moreover, we statistically explored whether the predominant mode-of-action (MOA) for pharmaceuticals is narcosis. We found 275 pharmaceuticals with 569 acute aquatic effect data; 23 pharmaceuticals had chronic data. Pharmaceuticals were found to be more frequent than industrial chemicals in GHS category III. Acute toxicity was predictable (>92%) using a generic (Q)SAR ((Quantitative) Structure Activity Relationship) suggesting a narcotic MOA. Analysis of model prediction error suggests that 68% of the pharmaceuticals have a non-specific MOA. Additionally, the acute-to-chronic ratio (ACR) for 70% of the analyzed pharmaceuticals was below 25 further suggesting a non-specific MOA. Sub-lethal receptor-mediated effects may however have a more specific MOA.}, } @article {pmid19425418, year = {2009}, author = {Hoeting, JA}, title = {The importance of accounting for spatial and temporal correlation in analyses of ecological data.}, journal = {Ecological applications : a publication of the Ecological Society of America}, volume = {19}, number = {3}, pages = {574-577}, doi = {10.1890/08-0836.1}, pmid = {19425418}, issn = {1051-0761}, mesh = {Animals ; Bayes Theorem ; Data Interpretation, Statistical ; *Ecosystem ; Geographic Information Systems ; Humans ; *Models, Statistical ; Time Factors ; }, } @article {pmid19422959, year = {2009}, author = {Milner, FA}, title = {Predator-prey interactions, agricultural ecology, demography, aquatic ecology, epidemiology of infectious diseases, cancer, molecular and cell biology, and genetics--from CMPD2, The Second Conference on Computational and Mathematical Population Dynamics, Campinas, Brazil.}, journal = {Journal of theoretical biology}, volume = {258}, number = {3}, pages = {337-338}, doi = {10.1016/j.jtbi.2009.04.012}, pmid = {19422959}, issn = {1095-8541}, mesh = {Animals ; *Computational Biology ; Humans ; Models, Biological ; *Models, Theoretical ; *Population Dynamics ; }, } @article {pmid19419650, year = {2009}, author = {Bartsch, D}, title = {Response to Wilkinson & Tepfer's "Fitness and beyond: preparing for the arrival of GM crops with ecologically important novel characters".}, journal = {Environmental biosafety research}, volume = {8}, number = {1}, pages = {17-18}, doi = {10.1051/ebr/2009002}, pmid = {19419650}, issn = {1635-7922}, mesh = {Consumer Product Safety ; Crops, Agricultural/*genetics/growth & development/physiology ; Decision Making ; Decision Support Techniques ; *Food, Genetically Modified ; Gene Flow ; Humans ; *Models, Biological ; Phenotype ; Plants, Genetically Modified/growth & development/*physiology ; Risk Assessment ; Transgenes ; }, } @article {pmid19419649, year = {2009}, author = {Harwood, T}, title = {Response to Wilkinson & Tepfer's "Fitness and beyond: preparing for the arrival of GM crops with ecologically important novel characters". Fuzzy reasoning and unacceptable change: defining and assessing an ambiguous endpoint.}, journal = {Environmental biosafety research}, volume = {8}, number = {1}, pages = {15-16}, doi = {10.1051/ebr/2009004}, pmid = {19419649}, issn = {1635-7922}, mesh = {Consumer Product Safety ; Crops, Agricultural/*genetics ; Decision Making ; *Decision Support Techniques ; *Food, Genetically Modified ; *Fuzzy Logic ; Gene Flow ; Humans ; *Models, Biological ; *Plants, Genetically Modified ; Risk Assessment ; Transgenes ; }, } @article {pmid19410410, year = {2010}, author = {Onofrejová, L and Vasícková, J and Klejdus, B and Stratil, P and Misurcová, L and Krácmar, S and Kopecký, J and Vacek, J}, title = {Bioactive phenols in algae: the application of pressurized-liquid and solid-phase extraction techniques.}, journal = {Journal of pharmaceutical and biomedical analysis}, volume = {51}, number = {2}, pages = {464-470}, doi = {10.1016/j.jpba.2009.03.027}, pmid = {19410410}, issn = {1873-264X}, mesh = {Antioxidants/*analysis/chemistry ; Benzoic Acid/analysis/chemistry ; Chromatography, High Pressure Liquid/*methods ; Cinnamates/analysis/chemistry ; Eukaryota/*chemistry ; Freshwater Biology/methods ; *Online Systems ; Phenols/*analysis/chemistry ; Reference Standards ; Seawater/chemistry ; Solid Phase Extraction/*methods ; }, abstract = {A new extraction technique based on the off-line combination of pressurized-liquid with solid-phase extraction (PLE-SPE) is described. The method was used for the extraction of bioactive phenolic acids (protocatechuic, p-hydroxybenzoic, 2,3-dihydroxybenzoic, chlorogenic, vanillic, caffeic, p-coumaric, salicylic acid), cinnamic acid and hydroxybenzaldehydes (p-hydroxybenzaldehyde, 3,4-dihydroxybenzaldehyde, vanillin) from in vitro culture of two freshwater algae (Anabaena doliolum and Spongiochloris spongiosa) and from food products of marine macroalgae Porphyra tenera (nori) and Undaria pinnatifida (wakame). For the identification and quantification of the compounds the molecular ions [M-H](-) and specific fragments were analyzed by quadrupole mass spectrometry analyzer connected on-line with a reversed-phase HPLC system. Our analysis showed that the freshwater algae and marine algal products contained submicrogram or microgram level of above-mentioned phenols per gram of lyophilized sample. In addition, the total phenol content (Folin-Ciocalteu assay) and antioxidant activity (TEAC assay, Trolox equivalent antioxidant capacity assay) of the PLE-SPE extracts were determined and discussed.}, } @article {pmid19409075, year = {2009}, author = {Rapp, RA and Udall, JA and Wendel, JF}, title = {Genomic expression dominance in allopolyploids.}, journal = {BMC biology}, volume = {7}, number = {}, pages = {18}, pmid = {19409075}, issn = {1741-7007}, mesh = {Computational Biology ; Diploidy ; *Gene Expression Regulation, Plant ; Genome, Plant/*genetics ; Gossypium/*genetics ; *Polyploidy ; }, abstract = {BACKGROUND: Allopolyploid speciation requires rapid evolutionary reconciliation of two diverged genomes and gene regulatory networks. Here we describe global patterns of gene expression accompanying genomic merger and doubling in inter-specific crosses in the cotton genus (Gossypium L.).

RESULTS: Employing a micro-array platform designed against 40,430 unigenes, we assayed gene expression in two sets of parental diploids and their colchicine-doubled allopolyploid derivatives. Up to half of all genes were differentially expressed among diploids, a striking level of expression evolution among congeners. In the allopolyploids, most genes were expressed at mid-parent levels, but this was achieved via a phenomenon of genome-wide expression dominance, whereby gene expression was either up- or down-regulated to the level of one of the two parents, independent of the magnitude of gene expression. This massive expression dominance was approximately equal with respect to direction (up- or down-regulation), and the same diploid parent could be either the dominant or the recessive genome depending on the specific genomic combination. Transgressive up- and down-regulation were also common in the allopolyploids, both for genes equivalently or differentially expressed between the parents.

CONCLUSION: Our data provide novel insights into the architecture of gene expression in the allopolyploid nucleus, raise questions regarding the responsible underlying mechanisms of genome dominance, and provide clues into the enigma of the evolutionary prevalence of allopolyploids.}, } @article {pmid19402760, year = {2009}, author = {Papa, A and Velo, E and Papadimitriou, E and Cahani, G and Kota, M and Bino, S}, title = {Ecology of the Crimean-Congo hemorrhagic fever endemic area in Albania.}, journal = {Vector borne and zoonotic diseases (Larchmont, N.Y.)}, volume = {9}, number = {6}, pages = {713-716}, doi = {10.1089/vbz.2008.0141}, pmid = {19402760}, issn = {1557-7759}, mesh = {Albania/epidemiology ; Animals ; Antibodies, Viral ; Arachnid Vectors/genetics/*virology ; Birds/blood/virology ; Cattle ; Databases, Nucleic Acid ; *Ecosystem ; Endemic Diseases ; Female ; Goats/blood/virology ; Hares/blood/virology ; Hemorrhagic Fever Virus, Crimean-Congo/*isolation & purification ; Hemorrhagic Fever, Crimean/epidemiology ; Humans ; Immunoglobulin G/blood ; Polymerase Chain Reaction/veterinary ; Ticks/genetics/*virology ; Viral Load ; }, abstract = {Crimean-Congo hemorrhagic fever virus (CCHFV) is endemic in Albania. Ticks collected from cattle grazing in the endemic areas of Albania were tested for presence of CCHFV RNA, while serum samples collected from goats, cattle, hares, and birds were tested for the presence of specific IgG antibodies to CCHFV. One of the 31 pools prepared, consisting of four female Hyalomma spp. ticks, was found to carry CCHFV RNA with 99.2-100% homology to sequences detected in patients from the same region. Antibodies were not detected in cattle, hares, and birds, but 2/10 goats presented high titers of IgG antibodies. The shepherd of that flock was a member of a family affected by CCHF 10 days before the collection of goats' sera, and he presented a mild form of the disease.}, } @article {pmid19402130, year = {2009}, author = {Near, TJ}, title = {Conflict and resolution between phylogenies inferred from molecular and phenotypic data sets for hagfish, lampreys, and gnathostomes.}, journal = {Journal of experimental zoology. Part B, Molecular and developmental evolution}, volume = {312}, number = {7}, pages = {749-761}, doi = {10.1002/jez.b.21293}, pmid = {19402130}, issn = {1552-5015}, mesh = {Amino Acids/analysis ; Animals ; Bayes Theorem ; Computational Biology ; *Evolution, Molecular ; Hagfishes/classification/*genetics ; Lampreys/classification/*genetics ; *Phylogeny ; RNA, Ribosomal ; Vertebrates/classification/*genetics ; }, abstract = {One of the most problematic issues in vertebrate phylogenetics is the disagreement between phenotypic and molecular inferences regarding the relationships among hagfishes, lampreys, and gnathostomes. Phenotypic characters support monophyly of lampreys and gnathostomes, whereas nearly all published analyses of molecular data sets support monophyly of hagfishes and lampreys. In this study I present results of phylogenetic analyses of combined phenotypic and molecular data sets that focus on relationships among hagfishes, lampreys, and gnathostomes. Maximum parsimony analyses of 115 phenotypic characters combined with 4,638 rRNA sites and more than 10,000 amino acids each result in monophyly of lampreys and gnathostomes, demonstrating that the addition of relatively few phenotypic characters can alter phylogenetic inferences from large molecular data sets. On the other hand, Bayesian analyses of the combined data sets support monophyly of hagfish and lampreys, indicating that model-based analyses may be prone to data "swamping," where the phylogenetic signal of the larger molecular data sets overwhelm the signal present in the much smaller phenotypic data set. Nodes that relate hagfish and lampreys were recovered at a low frequency in parametric bootstrapping analyses, indicating that the timing of diversification among hagfishes, lampreys, and gnathostomes has created a difficult phylogenetic problem for molecular data. The fact that addition of relatively few phenotypic characters can alter phylogenetic inferences of cyclostome monophyly obtained from molecular data sets, and the inability of simulated data sets to recover key nodes in the craniate phylogeny provide reasons to view the strong support for cyclostome monophyly inferred from molecular data sets with a measured degree of skepticism.}, } @article {pmid19401414, year = {2009}, author = {Takeuchi, F and Serizawa, M and Yamamoto, K and Fujisawa, T and Nakashima, E and Ohnaka, K and Ikegami, H and Sugiyama, T and Katsuya, T and Miyagishi, M and Nakashima, N and Nawata, H and Nakamura, J and Kono, S and Takayanagi, R and Kato, N}, title = {Confirmation of multiple risk Loci and genetic impacts by a genome-wide association study of type 2 diabetes in the Japanese population.}, journal = {Diabetes}, volume = {58}, number = {7}, pages = {1690-1699}, pmid = {19401414}, issn = {1939-327X}, mesh = {Cyclin-Dependent Kinase 5/genetics ; Cyclin-Dependent Kinase Inhibitor p15/genetics ; Cyclin-Dependent Kinase Inhibitor p16/genetics ; Diabetes Mellitus, Type 2/*genetics ; Ethnicity/genetics ; Genetic Predisposition to Disease/genetics ; *Genetic Variation ; *Genome-Wide Association Study ; Genotype ; Humans ; Japan ; KCNQ1 Potassium Channel/genetics ; Meta-Analysis as Topic ; Racial Groups/genetics ; Risk Assessment ; tRNA Methyltransferases ; }, abstract = {OBJECTIVE: To identify novel type 2 diabetes gene variants and confirm previously identified ones, a three-staged genome-wide association study was performed in the Japanese population.

RESEARCH DESIGN AND METHODS: In the stage 1 scan, we genotyped 519 case and 503 control subjects with 482,625 single nucleotide polymorphism (SNP) markers; in the stage 2 panel comprising 1,110 case subjects and 1,014 control subjects, we assessed 1,456 SNPs (P < 0.0025, stage 1); additionally to direct genotyping, 964 healthy control subjects formed the in silico control panel. Along with genome-wide exploration, we aimed to replicate the disease association of 17 SNPs from 16 candidate loci previously identified in Europeans. The associated and/or replicated loci (23 SNPs; P < 7 x 10(-5) for genome-wide exploration and P < 0.05 for replication) were examined in the stage 3 panel comprising 4,000 case subjects and 12,569 population-based samples, from which 4,889 nondiabetic control subjects were preselected. The 12,569 subjects were used for overall risk assessment in the general population.

RESULTS: Four loci-1 novel with suggestive evidence (PEPD on 19q13, P = 1.4 x 10(-5)) and three previously reported-were identified; the association of CDKAL1, CDKN2A/CDKN2B, and KCNQ1 were confirmed (P < 10(-19)). Moreover, significant associations were replicated in five other candidate loci: TCF7L2, IGF2BP2, SLC30A8, HHEX, and KCNJ11. There was substantial overlap of type 2 diabetes susceptibility genes between the two populations, whereas effect size and explained variance tended to be higher in the Japanese population.

CONCLUSIONS: The strength of association was more prominent in the Japanese population than in Europeans for more than half of the confirmed type 2 diabetes loci.}, } @article {pmid19397587, year = {2010}, author = {Wulfsohn, D and Sciortino, M and Aaslyng, JM and García-Fiñana, M}, title = {Nondestructive, stereological estimation of canopy surface area.}, journal = {Biometrics}, volume = {66}, number = {1}, pages = {159-168}, doi = {10.1111/j.1541-0420.2009.01237.x}, pmid = {19397587}, issn = {1541-0420}, mesh = {*Algorithms ; Biometry/*methods ; Chrysanthemum/*growth & development ; *Data Interpretation, Statistical ; *Models, Biological ; *Models, Statistical ; Plant Leaves/*growth & development ; }, abstract = {We describe a stereological procedure to estimate the total leaf surface area of a plant canopy in vivo, and address the problem of how to predict the variance of the corresponding estimator. The procedure involves three nested systematic uniform random sampling stages: (i) selection of plants from a canopy using the smooth fractionator, (ii) sampling of leaves from the selected plants using the fractionator, and (iii) area estimation of the sampled leaves using point counting. We apply this procedure to estimate the total area of a chrysanthemum (Chrysanthemum morifolium L.) canopy and evaluate both the time required and the precision of the estimator. Furthermore, we compare the precision of point counting for three different grid intensities with that of several standard leaf area measurement techniques. Results showed that the precision of the plant leaf area estimator based on point counting is high. Using a grid intensity of 1.76 cm(2)/point we estimated plant and canopy surface areas with accuracies similar to or better than those obtained using image analysis and a commercial leaf area meter. For canopy surface areas of approximately 1 m(2) (10 plants), the fractionator leaf approach with sampling fraction equal to 1/9 followed by point counting using a 4.3 cm(2)/point grid produced a coefficient of error of less than 7%. The smooth fractionator can be used to ensure that the additional contribution to the estimator variance due to between-plant variability is small.}, } @article {pmid19393086, year = {2009}, author = {Hooper, SD and Mavromatis, K and Kyrpides, NC}, title = {Microbial co-habitation and lateral gene transfer: what transposases can tell us.}, journal = {Genome biology}, volume = {10}, number = {4}, pages = {R45}, pmid = {19393086}, issn = {1474-760X}, mesh = {Bacillus cereus/genetics/growth & development ; Bacteria/classification/*genetics/growth & development ; Bacterial Proteins/genetics ; Databases, Genetic ; *Ecosystem ; Escherichia coli/genetics/growth & development ; Fresh Water/microbiology ; Gene Transfer, Horizontal/*genetics ; Phylogeny ; Proteobacteria/genetics/growth & development ; Salmonella enterica/genetics/growth & development ; Seawater/microbiology ; Soil Microbiology ; Transposases/genetics ; Water Microbiology ; }, abstract = {BACKGROUND: Determining the habitat range for various microbes is not a simple, straightforward matter, as habitats interlace, microbes move between habitats, and microbial communities change over time. In this study, we explore an approach using the history of lateral gene transfer recorded in microbial genomes to begin to answer two key questions: where have you been and who have you been with?

RESULTS: All currently sequenced microbial genomes were surveyed to identify pairs of taxa that share a transposase that is likely to have been acquired through lateral gene transfer. A microbial interaction network including almost 800 organisms was then derived from these connections. Although the majority of the connections are between closely related organisms with the same or overlapping habitat assignments, numerous examples were found of cross-habitat and cross-phylum connections.

CONCLUSIONS: We present a large-scale study of the distributions of transposases across phylogeny and habitat, and find a significant correlation between habitat and transposase connections. We observed cases where phylogenetic boundaries are traversed, especially when organisms share habitats; this suggests that the potential exists for genetic material to move laterally between diverse groups via bridging connections. The results presented here also suggest that the complex dynamics of microbial ecology may be traceable in the microbial genomes.}, } @article {pmid19383629, year = {2009}, author = {Casey, EA and Lindhorst, TP}, title = {Toward a multi-level, ecological approach to the primary prevention of sexual assault: prevention in peer and community contexts.}, journal = {Trauma, violence & abuse}, volume = {10}, number = {2}, pages = {91-114}, doi = {10.1177/1524838009334129}, pmid = {19383629}, issn = {1524-8380}, support = {K01 MH072827/MH/NIMH NIH HHS/United States ; R24 HD042828/HD/NICHD NIH HHS/United States ; K01 MH072827-04/MH/NIMH NIH HHS/United States ; R24 HD042828-10/HD/NICHD NIH HHS/United States ; }, mesh = {Community Health Services/*organization & administration ; *Community Networks ; Domestic Violence/prevention & control ; Female ; Health Promotion/organization & administration ; Humans ; Male ; Peer Group ; Primary Prevention/*organization & administration ; Rape/*prevention & control ; Social Environment ; Social Values ; Spouse Abuse/*prevention & control ; }, abstract = {Although sexual assault prevention programs have been increasingly successful at improving knowledge about sexual violence and decreasing rape-supportive attitudes and beliefs among participants, reducing sexually assaultive conduct itself remains an elusive outcome. This review considers efforts to support change for individuals by creating prevention strategies that target peer network and community-level factors that support sexual violence. To this end, the article examines successful ecological prevention models from other prevention fields, identifies the components of multilevel prevention that appear critical to efficacy and discusses their application to existing and emerging sexual violence prevention strategies.}, } @article {pmid19383153, year = {2009}, author = {Fröhlich, T and Arnold, GJ and Fritsch, R and Mayr, T and Laforsch, C}, title = {LC-MS/MS-based proteome profiling in Daphnia pulex and Daphnia longicephala: the Daphnia pulex genome database as a key for high throughput proteomics in Daphnia.}, journal = {BMC genomics}, volume = {10}, number = {}, pages = {171}, pmid = {19383153}, issn = {1471-2164}, mesh = {Animals ; Chromatography, Liquid ; Daphnia/*chemistry ; *Databases, Protein ; Electrophoresis, Polyacrylamide Gel ; Genome ; Peptides/*chemistry/genetics ; Proteome/*chemistry ; Proteomics/*methods ; Tandem Mass Spectrometry ; }, abstract = {BACKGROUND: Daphniids, commonly known as waterfleas, serve as important model systems for ecology, evolution and the environmental sciences. The sequencing and annotation of the Daphnia pulex genome both open future avenues of research on this model organism. As proteomics is not only essential to our understanding of cell function, and is also a powerful validation tool for predicted genes in genome annotation projects, a first proteomic dataset is presented in this article.

RESULTS: A comprehensive set of 701,274 peptide tandem-mass-spectra, derived from Daphnia pulex, was generated, which lead to the identification of 531 proteins. To measure the impact of the Daphnia pulex filtered models database for mass spectrometry based Daphnia protein identification, this result was compared with results obtained with the Swiss-Prot and the Drosophila melanogaster database. To further validate the utility of the Daphnia pulex database for research on other Daphnia species, additional 407,778 peptide tandem-mass-spectra, obtained from Daphnia longicephala, were generated and evaluated, leading to the identification of 317 proteins.

CONCLUSION: Peptides identified in our approach provide the first experimental evidence for the translation of a broad variety of predicted coding regions within the Daphnia genome. Furthermore it could be demonstrated that identification of Daphnia longicephala proteins using the Daphnia pulex protein database is feasible but shows a slightly reduced identification rate. Data provided in this article clearly demonstrates that the Daphnia genome database is the key for mass spectrometry based high throughput proteomics in Daphnia.}, } @article {pmid19383151, year = {2009}, author = {Sturm, A and Cunningham, P and Dean, M}, title = {The ABC transporter gene family of Daphnia pulex.}, journal = {BMC genomics}, volume = {10}, number = {}, pages = {170}, pmid = {19383151}, issn = {1471-2164}, support = {//Intramural NIH HHS/United States ; }, mesh = {ATP-Binding Cassette Transporters/*genetics ; Animals ; Computational Biology/methods ; Daphnia/classification/*genetics ; Genome ; Genomics/methods ; *Multigene Family ; Phylogeny ; }, abstract = {BACKGROUND: The large gene superfamily of ABC (ATP-binding cassette) transporters encodes membrane proteins involved in trafficking processes across biological membranes and further essential cell biological functions. ABC transporters are evolutionary ancient and involved in the biochemical defence against toxicants. We report here a genome-wide survey of ABC proteins of Daphnia pulex, providing for the first time information on ABC proteins in crustacea, a primarily aquatic arthropod subphylum of high ecological and economical importance.

RESULTS: We identified 64 ABC proteins in the Daphnia genome, which possesses members of all current ABC subfamilies A to H. To unravel phylogenetic relationships, ABC proteins of Daphnia were compared to those from yeast, worm, fruit fly and human. A high conservation of Daphnia of ABC transporters was observed for proteins involved in fundamental cellular processes, including the mitochondrial half transporters of the ABCB subfamily, which function in iron metabolism and transport of Fe/S protein precursors, and the members of subfamilies ABCD, ABCE and ABCF, which have roles in very long chain fatty acid transport, initiation of gene transcription and protein translation, respectively. A number of Daphnia proteins showed one-to-one orthologous relationships to Drosophila ABC proteins including the sulfonyl urea receptor (SUR), the ecdysone transporter ET23, and the eye pigment precursor transporter scarlet. As the fruit fly, Daphnia lacked homologues to the TAP protein, which plays a role in antigene processing, and the cystic fibrosis transmembrane conductance regulator (CFTR), which functions as a chloride channel. Daphnia showed two proteins homologous to MDR (multidrug resistance) P-glycoproteins (ABCB subfamily) and six proteins homologous to MRPs (multidrug resistance-associated proteins) (ABCC subfamily). However, lineage specific gene duplications in the ABCB and ABCC subfamilies complicated the inference of function. A particularly high number of gene duplications were observed in the ABCG and ABCH subfamilies, which have 23 and 15 members, respectively.

CONCLUSION: The in silico characterisation of ABC transporters in the Daphnia pulex genome revealed that the complement of ABC transporters is as complex in crustaceans as that other metazoans. Not surprisingly, among currently available genomes, Daphnia ABC transporters most closely resemble those of the fruit fly, another arthropod.}, } @article {pmid19383108, year = {2009}, author = {Hughes, KW and Petersen, RH and Lickey, EB}, title = {Using heterozygosity to estimate a percentage DNA sequence similarity for environmental species' delimitation across basidiomycete fungi.}, journal = {The New phytologist}, volume = {182}, number = {4}, pages = {795-798}, doi = {10.1111/j.1469-8137.2009.02802.x}, pmid = {19383108}, issn = {1469-8137}, mesh = {Base Sequence ; Basidiomycota/*genetics ; Biodiversity ; DNA, Fungal/*genetics ; DNA, Intergenic/genetics ; Databases, Genetic ; *Environmental Microbiology ; Fruiting Bodies, Fungal/genetics ; *Genetic Variation ; *Heterozygote ; *Sequence Homology, Nucleic Acid ; Species Specificity ; }, } @article {pmid19370008, year = {2009}, author = {Danis, B and Griffiths, H}, title = {Polar science: bid for freely accessible biodiversity archive.}, journal = {Nature}, volume = {458}, number = {7240}, pages = {830}, pmid = {19370008}, issn = {1476-4687}, mesh = {Animals ; Antarctic Regions ; *Archives ; *Biodiversity ; Databases, Factual ; *Internet ; *Marine Biology ; Oceans and Seas ; }, } @article {pmid19365077, year = {2009}, author = {Cerling, TE and Wittemyer, G and Ehleringer, JR and Remien, CH and Douglas-Hamilton, I}, title = {History of Animals using Isotope Records (HAIR): a 6-year dietary history of one family of African elephants.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {106}, number = {20}, pages = {8093-8100}, pmid = {19365077}, issn = {1091-6490}, mesh = {*Animal Migration ; Animals ; Carbon Isotopes/analysis ; Climate ; Deuterium/analysis ; Ecosystem ; Elephants/*physiology ; *Feeding Behavior ; Fertilization ; Geographic Information Systems ; Hair/chemistry ; Isotopes/*analysis ; Kenya ; Nitrogen Isotopes/analysis ; }, abstract = {The dietary and movement history of individual animals can be studied using stable isotope records in animal tissues, providing insight into long-term ecological dynamics and a species niche. We provide a 6-year history of elephant diet by examining tail hair collected from 4 elephants in the same social family unit in northern Kenya. Sequential measurements of carbon, nitrogen, and hydrogen isotope rations in hair provide a weekly record of diet and water resources. Carbon isotope ratios were well correlated with satellite-based measurements of the normalized difference vegetation index (NDVI) of the region occupied by the elephants as recorded by the global positioning system (GPS) movement record; the absolute amount of C(4) grass consumption is well correlated with the maximum value of NDVI during individual wet seasons. Changes in hydrogen isotope ratios coincided very closely in time with seasonal fluctuations in rainfall and NDVI whereas diet shifts to relatively high proportions of grass lagged seasonal increases in NDVI by approximately 2 weeks. The peak probability of conception in the population occurred approximately 3 weeks after peak grazing. Spatial and temporal patterns of resource use show that the only period of pure browsing by the focal elephants was located in an over-grazed, communally managed region outside the protected area. The ability to extract time-specific longitudinal records on animal diets, and therefore the ecological history of an organism and its environment, provides an avenue for understanding the impact of climate dynamics and land-use change on animal foraging behavior and habitat relations.}, } @article {pmid19361902, year = {2009}, author = {Davis, HT and Aelion, CM and McDermott, S and Lawson, AB}, title = {Identifying natural and anthropogenic sources of metals in urban and rural soils using GIS-based data, PCA, and spatial interpolation.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {157}, number = {8-9}, pages = {2378-2385}, pmid = {19361902}, issn = {1873-6424}, support = {R01 ES012895/ES/NIEHS NIH HHS/United States ; R01 ES012895-01A1/ES/NIEHS NIH HHS/United States ; }, mesh = {Cities ; Environmental Monitoring/instrumentation/*methods ; Environmental Pollution/statistics & numerical data ; *Geographic Information Systems ; Metals, Heavy/*analysis ; Principal Component Analysis ; Soil/*chemistry ; Soil Pollutants/*analysis ; }, abstract = {Determining sources of neurotoxic metals in rural and urban soils is important for mitigating human exposure. Surface soil from four areas with significant clusters of mental retardation and developmental delay (MR/DD) in children, and one control site were analyzed for nine metals and characterized by soil type, climate, ecological region, land use and industrial facilities using readily available GIS-based data. Kriging, principal component analysis (PCA) and cluster analysis (CA) were used to identify commonalities of metal distribution. Three MR/DD areas (one rural and two urban) had similar soil types and significantly higher soil metal concentrations. PCA and CA results suggested that Ba, Be and Mn were consistently from natural sources; Pb and Hg from anthropogenic sources; and As, Cr, Cu, and Ni from both sources. Arsenic had low commonality estimates, was highly associated with a third PCA factor, and had a complex distribution, complicating mitigation strategies to minimize concentrations and exposures.}, } @article {pmid19358738, year = {2009}, author = {Jovelin, R and Phillips, PC}, title = {Evolutionary rates and centrality in the yeast gene regulatory network.}, journal = {Genome biology}, volume = {10}, number = {4}, pages = {R35}, pmid = {19358738}, issn = {1474-760X}, support = {R03 AG029377/AG/NIA NIH HHS/United States ; AG029377/AG/NIA NIH HHS/United States ; }, mesh = {Databases, Genetic ; *Evolution, Molecular ; Gene Expression Regulation, Fungal ; *Gene Regulatory Networks ; Genome, Fungal ; Protein Binding ; Saccharomyces/*genetics/metabolism ; Saccharomyces cerevisiae/genetics/metabolism ; Saccharomyces cerevisiae Proteins/*genetics/metabolism ; Transcription Factors/*genetics/metabolism ; Transcription, Genetic ; }, abstract = {BACKGROUND: Transcription factors play a fundamental role in regulating physiological responses and developmental processes. Here we examine the evolution of the yeast transcription factors in the context of the structure of the gene regulatory network.

RESULTS: In contrast to previous results for the protein-protein interaction and metabolic networks, we find that the position of a gene within the transcription network affects the rate of protein evolution such that more central transcription factors tend to evolve faster. Centrality is also positively correlated with expression variability, suggesting that the higher rate of divergence among central transcription factors may be due to their role in controlling information flow and may be the result of adaptation to changing environmental conditions. Alternatively, more central transcription factors could be more buffered against environmental perturbations and, therefore, less subject to strong purifying selection. Importantly, the relationship between centrality and evolutionary rates is independent of expression level, expression variability and gene essentiality.

CONCLUSIONS: Our analysis of the transcription network highlights the role of network structure on protein evolutionary rate. Further, the effect of network centrality on nucleotide divergence is different among the metabolic, protein-protein and transcriptional networks, suggesting that the effect of gene position is dependant on the function of the specific network under study. A better understanding of how these three cellular networks interact with one another may be needed to fully examine the impact of network structure on the function and evolution of biological systems.}, } @article {pmid19354065, year = {2009}, author = {Van Dole, KB and Swern, AS and Newcomb, K and Nelsen, L}, title = {Seasonal patterns in health care use and pharmaceutical claims for asthma prescriptions for preschool- and school-aged children.}, journal = {Annals of allergy, asthma & immunology : official publication of the American College of Allergy, Asthma, & Immunology}, volume = {102}, number = {3}, pages = {198-204}, doi = {10.1016/S1081-1206(10)60081-6}, pmid = {19354065}, issn = {1081-1206}, mesh = {Age Factors ; Ambulatory Care/statistics & numerical data ; Anti-Asthmatic Agents/*therapeutic use ; Asthma/*drug therapy/*epidemiology ; Child ; Child, Preschool ; Databases, Factual ; Delivery of Health Care/*statistics & numerical data ; Emergency Medical Services/statistics & numerical data ; Health Care Surveys ; Hospitalization/statistics & numerical data ; Humans ; Prescriptions/*statistics & numerical data ; *Seasons ; United States/epidemiology ; }, abstract = {BACKGROUND: In children, hospitalization for asthma is reported to have a distinct seasonal pattern with peaks coincident with the start of school. Although guidelines indicate that asthma controller medications should be used daily, there is limited information on actual seasonal patterns of medication use.

OBJECTIVE: To describe seasonal patterns of asthma-related health care use and asthma controller and reliever medication claims in children.

METHODS: An ecological analysis was conducted of data collected from records for children aged 2 to 12 years from 2002 through 2004 from an automated research database of insurance claims from a large US health care plan. Seasonal patterns for health care use and estimates of prescription asthma controller and reliever use were determined for preschool-aged children (aged 2-5 years) and school-aged children (aged 6-12 years). Rates were constructed by week; deviations from annual mean rates were used to determine peaks in use. Results were confirmed using Poisson regression models, modeling for rates within age group, with factors for week, year, and regions.

RESULTS: Emergency department and outpatient visits and hospitalizations were lowest during summer; rates increased beginning in September, peaking in October or November. Asthma controller and reliever medication claims increased beginning in September, peaking in December. Rates also were elevated in February.

CONCLUSIONS: The data suggest that children who reduce their asthma medications during the summer do not resume taking medications until signs or symptoms of asthma worsen. The summer hiatus and other factors may contribute to seasonal increases in health care use and in asthma medication prescriptions, particularly in the fall.}, } @article {pmid19349283, year = {2009}, author = {Abrusán, G and Grundmann, N and DeMester, L and Makalowski, W}, title = {TEclass--a tool for automated classification of unknown eukaryotic transposable elements.}, journal = {Bioinformatics (Oxford, England)}, volume = {25}, number = {10}, pages = {1329-1330}, doi = {10.1093/bioinformatics/btp084}, pmid = {19349283}, issn = {1367-4811}, mesh = {Computational Biology/*methods ; *DNA Transposable Elements ; Eukaryotic Cells ; Repetitive Sequences, Nucleic Acid ; Short Interspersed Nucleotide Elements ; *Software ; Terminal Repeat Sequences ; }, abstract = {MOTIVATION: The large number of sequenced genomes required the development of software that reconstructs the consensus sequences of transposons and other repetitive elements. However, the available tools usually focus on the accurate identification of raw repeats and provide no information about the taxonomic position of the reconstructed consensi. TEclass is a tool to classify unknown transposable elements into their four main functional categories, which reflect their mode of transposition: DNA transposons, long terminal repeats (LTRs), long interspersed nuclear elements (LINEs) and short interspersed nuclear elements (SINEs). TEclass uses machine learning support vector machine (SVM) for classification based on oligomer frequencies. It achieves 90-97% accuracy in the classification of novel DNA and LTR repeats, and 75% for LINEs and SINEs.

AVAILABILITY: http://www.compgen.uni-muenster.de/teclass, stand alone program upon request.}, } @article {pmid19339258, year = {2009}, author = {Wakefield, J}, title = {Multi-level modelling, the ecologic fallacy, and hybrid study designs.}, journal = {International journal of epidemiology}, volume = {38}, number = {2}, pages = {330-336}, pmid = {19339258}, issn = {1464-3685}, support = {R01 CAO95994//PHS HHS/United States ; }, mesh = {*Bias ; Data Interpretation, Statistical ; Humans ; *Models, Statistical ; Research Design ; }, } @article {pmid19337514, year = {2009}, author = {Martin, MT and Judson, RS and Reif, DM and Kavlock, RJ and Dix, DJ}, title = {Profiling chemicals based on chronic toxicity results from the U.S. EPA ToxRef Database.}, journal = {Environmental health perspectives}, volume = {117}, number = {3}, pages = {392-399}, pmid = {19337514}, issn = {1552-9924}, mesh = {Computational Biology/*methods ; *Databases, Factual ; Ecotoxicology/*methods ; Environmental Pollutants/*classification/toxicity ; Pesticides/*classification/toxicity ; United States ; United States Environmental Protection Agency ; }, abstract = {BACKGROUND: Thirty years of pesticide registration toxicity data have been historically stored as hardcopy and scanned documents by the U.S. Environmental Protection Agency (EPA). A significant portion of these data have now been processed into standardized and structured toxicity data within the EPA's Toxicity Reference Database (ToxRefDB), including chronic, cancer, developmental, and reproductive studies from laboratory animals. These data are now accessible and mineable within ToxRefDB and are serving as a primary source of validation for U.S. EPA's ToxCast research program in predictive toxicology.

OBJECTIVES: We profiled in vivo toxicities across 310 chemicals as a model application of ToxRefDB, meeting the need for detailed anchoring end points for development of ToxCast predictive signatures.

METHODS: Using query and structured data-mining approaches, we generated toxicity profiles from ToxRefDB based on long-term rodent bioassays. These chronic/cancer data were analyzed for suitability as anchoring end points based on incidence, target organ, severity, potency, and significance.

RESULTS: Under conditions of the bioassays, we observed pathologies for 273 of 310 chemicals, with greater preponderance (>90%) occurring in the liver, kidney, thyroid, lung, testis, and spleen. We observed proliferative lesions for 225 chemicals, and 167 chemicals caused progression to cancer-related pathologies.

CONCLUSIONS: Based on incidence, severity, and potency, we selected 26 primarily tissue-specific pathology end points to uniformly classify the 310 chemicals. The resulting toxicity profile classifications demonstrate the utility of structuring legacy toxicity information and facilitating the computation of these data within ToxRefDB for ToxCast and other applications.}, } @article {pmid19335877, year = {2009}, author = {Holzer, B and Keller, L and Chapuisat, M}, title = {Genetic clusters and sex-biased gene flow in a unicolonial Formica ant.}, journal = {BMC evolutionary biology}, volume = {9}, number = {}, pages = {69}, pmid = {19335877}, issn = {1471-2148}, mesh = {Animals ; Ants/*genetics ; Behavior, Animal ; Computational Biology ; DNA, Mitochondrial/genetics ; *Gene Flow ; Genes, Insect ; Genetic Markers ; *Genetics, Population ; Haplotypes ; Male ; Microsatellite Repeats ; Polymorphism, Genetic ; Sequence Analysis, DNA ; Social Behavior ; }, abstract = {BACKGROUND: Animal societies are diverse, ranging from small family-based groups to extraordinarily large social networks in which many unrelated individuals interact. At the extreme of this continuum, some ant species form unicolonial populations in which workers and queens can move among multiple interconnected nests without eliciting aggression. Although unicoloniality has been mostly studied in invasive ants, it also occurs in some native non-invasive species. Unicoloniality is commonly associated with very high queen number, which may result in levels of relatedness among nestmates being so low as to raise the question of the maintenance of altruism by kin selection in such systems. However, the actual relatedness among cooperating individuals critically depends on effective dispersal and the ensuing pattern of genetic structuring. In order to better understand the evolution of unicoloniality in native non-invasive ants, we investigated the fine-scale population genetic structure and gene flow in three unicolonial populations of the wood ant F. paralugubris.

RESULTS: The analysis of geo-referenced microsatellite genotypes and mitochondrial haplotypes revealed the presence of cryptic clusters of genetically-differentiated nests in the three populations of F. paralugubris. Because of this spatial genetic heterogeneity, members of the same clusters were moderately but significantly related. The comparison of nuclear (microsatellite) and mitochondrial differentiation indicated that effective gene flow was male-biased in all populations.

CONCLUSION: The three unicolonial populations exhibited male-biased and mostly local gene flow. The high number of queens per nest, exchanges among neighbouring nests and restricted long-distance gene flow resulted in large clusters of genetically similar nests. The positive relatedness among clustermates suggests that kin selection may still contribute to the maintenance of altruism in unicolonial populations if competition occurs among clusters.}, } @article {pmid19325912, year = {2009}, author = {Liu, S and Ji, K and Chen, J and Tai, D and Jiang, W and Hou, G and Chen, J and Li, J and Huang, B}, title = {Panorama phylogenetic diversity and distribution of Type A influenza virus.}, journal = {PloS one}, volume = {4}, number = {3}, pages = {e5022}, pmid = {19325912}, issn = {1932-6203}, mesh = {Biodiversity ; Databases, Nucleic Acid ; Hemagglutinins ; Influenza A virus/*classification/*genetics ; Neuraminidase ; *Phylogeny ; }, abstract = {BACKGROUND: Type A influenza virus is one of important pathogens of various animals, including humans, pigs, horses, marine mammals and birds. Currently, the viral type has been classified into 16 hemagglutinin and 9 neuraminidase subtypes, but the phylogenetic diversity and distribution within the viral type largely remain unclear from the whole view.

The panorama phylogenetic trees of influenza A viruses were calculated with representative sequences selected from approximately 23,000 candidates available in GenBank using web servers in NCBI and the software MEGA 4.0. Lineages and sublineages were classified according to genetic distances, topology of the phylogenetic trees and distributions of the viruses in hosts, regions and time.

CONCLUSIONS/SIGNIFICANCE: Here, two panorama phylogenetic trees of type A influenza virus covering all the 16 hemagglutinin subtypes and 9 neuraminidase subtypes, respectively, were generated. The trees provided us whole views and some novel information to recognize influenza A viruses including that some subtypes of avian influenza viruses are more complicated than Eurasian and North American lineages as we thought in the past. They also provide us a framework to generalize the history and explore the future of the viral circulation and evolution in different kinds of hosts. In addition, a simple and comprehensive nomenclature system for the dozens of lineages and sublineages identified within the viral type was proposed, which if universally accepted, will facilitate communications on the viral evolution, ecology and epidemiology.}, } @article {pmid19324737, year = {2009}, author = {Blanchet, S and Leprieur, F and Beauchard, O and Staes, J and Oberdorff, T and Brosse, S}, title = {Broad-scale determinants of non-native fish species richness are context-dependent.}, journal = {Proceedings. Biological sciences}, volume = {276}, number = {1666}, pages = {2385-2394}, pmid = {19324737}, issn = {0962-8452}, mesh = {Animals ; *Biodiversity ; Conservation of Natural Resources ; Databases, Factual ; Fishes/*physiology ; Fresh Water ; Geography ; Humans ; }, abstract = {Identifying the factors determining the non-native species richness (NNSR) in a given area is essential for preventing species invasions. The relative importance of human-related and natural factors considered for explaining NNSR might depend upon both the spatial scale (i.e. the extent of the gradients sampled) and the historical context of the area surveyed. Here, using a worldwide database of freshwater fish occurrences, we tested whether the relative influence of human and ecological determinants of non-native fish species establishment at the scale of the biogeographic realm was consistent (i) with that observed worldwide, and (ii) among the different biogeographical realms. The prominent role of human activity in shaping the global (i.e. worldwide) pattern of NNSR cannot be directly extrapolated to the biogeographic realms. Furthermore, the relationships between human and ecological determinants and NNSR vary strikingly across biogeographic realms, revealing a strong context dependency of the determinants of NNSR. In particular, the human-related factors play a predominant role in explaining the establishment of non-native species in economically developed realms, while in the other realms environmental characteristics of the river basins best explained geographical patterns of NNSR. In the face of future biological invasions, considering both the spatial scale and the historical context of the surveyed area is crucial to adopt effective conservation strategies.}, } @article {pmid19323614, year = {2009}, author = {Leroy, EM and Epelboin, A and Mondonge, V and Pourrut, X and Gonzalez, JP and Muyembe-Tamfum, JJ and Formenty, P}, title = {Human Ebola outbreak resulting from direct exposure to fruit bats in Luebo, Democratic Republic of Congo, 2007.}, journal = {Vector borne and zoonotic diseases (Larchmont, N.Y.)}, volume = {9}, number = {6}, pages = {723-728}, doi = {10.1089/vbz.2008.0167}, pmid = {19323614}, issn = {1557-7759}, mesh = {Animal Migration ; Animals ; Chiroptera/*virology ; Democratic Republic of the Congo/epidemiology ; Disease Outbreaks ; Disease Reservoirs/*virology ; Ebolavirus ; Female ; Geographic Information Systems ; Geography ; Hemorrhagic Fever, Ebola/*epidemiology/*transmission/virology ; Humans ; Interviews as Topic ; Male ; Zoonoses/epidemiology/*transmission/virology ; }, abstract = {Twelve years after the Kikwit Ebola outbreak in 1995, Ebola virus reemerged in the Occidental Kasaï province of the Democratic Republic of Congo (DRC) between May and November 2007, affecting more than 260 humans and causing 186 deaths. During this latter outbreak we conducted several epidemiological investigations to identify the underlying ecological conditions and animal sources. Qualitative social and environmental data were collected through interviews with villagers and by direct observation. The local populations reported no unusual morbidity or mortality among wild or domestic animals, but they described a massive annual fruit bat migration toward the southeast, up the Lulua River. Migrating bats settled in the outbreak area for several weeks, between April and May, nestling in the numerous fruit trees in Ndongo and Koumelele islands as well as in palm trees of a largely abandoned plantation. They were massively hunted by villagers, for whom they represented a major source of protein. By tracing back the initial human-human transmission events, we were able to show that, in May, the putative first human victim bought freshly killed bats from hunters to eat. We were able to reconstruct the likely initial human-human transmission events that preceded the outbreak. This study provides the most likely sequence of events linking a human Ebola outbreak to exposure to fruit bats, a putative virus reservoir. These findings support the suspected role of bats in the natural cycle of Ebola virus and indicate that the massive seasonal fruit bat migrations should be taken into account in operational Ebola risk maps and seasonal alerts in the DRC.}, } @article {pmid19320669, year = {2009}, author = {Vahabzadeh, M and Lin, JL and Mezghanni, M and Epstein, DH and Preston, KL}, title = {Automation in an addiction treatment research clinic: computerised contingency management, ecological momentary assessment and a protocol workflow system.}, journal = {Drug and alcohol review}, volume = {28}, number = {1}, pages = {3-11}, pmid = {19320669}, issn = {1465-3362}, support = {Z01 DA000175-13/ImNIH/Intramural NIH HHS/United States ; Z01 DA000499-01/ImNIH/Intramural NIH HHS/United States ; Z01 DA000500-01/ImNIH/Intramural NIH HHS/United States ; Z99 DA999999/ImNIH/Intramural NIH HHS/United States ; }, mesh = {Ambulatory Care/organization & administration ; Automation/methods ; Behavior Therapy/methods ; Communication ; Decision Support Systems, Clinical ; Efficiency, Organizational ; Humans ; *Information Systems ; Research Design/legislation & jurisprudence ; Substance Abuse Detection/methods ; Substance Abuse Treatment Centers/*organization & administration ; Substance-Related Disorders/*rehabilitation ; Time Factors ; }, abstract = {INTRODUCTION AND AIMS: A challenge in treatment research is the necessity of adhering to protocol and regulatory strictures while maintaining flexibility to meet patients' treatment needs and to accommodate variations among protocols. Another challenge is the acquisition of large amounts of data in an occasionally hectic environment, along with the provision of seamless methods for exporting, mining and querying the data.

DESIGN AND METHODS: We have automated several major functions of our outpatient treatment research clinic for studies in drug abuse and dependence. Here we describe three such specialised applications: the Automated Contingency Management (ACM) system for the delivery of behavioural interventions, the transactional electronic diary (TED) system for the management of behavioural assessments and the Protocol Workflow System (PWS) for computerised workflow automation and guidance of each participant's daily clinic activities. These modules are integrated into our larger information system to enable data sharing in real time among authorised staff.

RESULTS: ACM and the TED have each permitted us to conduct research that was not previously possible. In addition, the time to data analysis at the end of each study is substantially shorter. With the implementation of the PWS, we have been able to manage a research clinic with an 80 patient capacity, having an annual average of 18,000 patient visits and 7300 urine collections with a research staff of five. Finally, automated data management has considerably enhanced our ability to monitor and summarise participant safety data for research oversight.

DISCUSSION AND CONCLUSIONS: When developed in consultation with end users, automation in treatment research clinics can enable more efficient operations, better communication among staff and expansions in research methods.}, } @article {pmid19307881, year = {2009}, author = {Hansell, AL and Best, NG and Rushton, L}, title = {Lessons from ecological and spatial studies in relation to occupational lung disease.}, journal = {Current opinion in allergy and clinical immunology}, volume = {9}, number = {2}, pages = {87-92}, pmid = {19307881}, issn = {1473-6322}, support = {075883/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Air Pollutants ; *Ecology ; Humans ; *Information Systems ; Lung Diseases/epidemiology/*immunology ; Occupational Diseases/epidemiology/*immunology ; Research ; }, abstract = {PURPOSE OF REVIEW: The majority of epidemiological research into occupational lung disease has been advanced by the study of individuals, typically in a workplace setting. This review examines how recent advances in ecological and spatial study methodology and in the information held in routine databases could be used to enhance occupational health studies.

RECENT FINDINGS: Ecological studies often use routinely collected data, and this is becoming much more extensive and better validated with potential for increasing use in occupational health research. Improvements in computing power and statistical and geographical information systems methodology have led to more sophisticated mapping techniques and greater use of spatial information when investigating lung diseases usually related to occupational exposures. Ecological study methodology is experiencing a radical overhaul with supplementation of group-level data with information from small-scale individual-level studies. This hybrid design can be used to reduce bias and increase power and is directly applicable to the enhancement of aggregate information from job exposure matrices.

SUMMARY: Studies of occupational lung disease can be enhanced by incorporating methodological innovations from ecological and spatial studies.}, } @article {pmid19304329, year = {2009}, author = {Jamers, A and Blust, R and De Coen, W}, title = {Omics in algae: paving the way for a systems biological understanding of algal stress phenomena?.}, journal = {Aquatic toxicology (Amsterdam, Netherlands)}, volume = {92}, number = {3}, pages = {114-121}, doi = {10.1016/j.aquatox.2009.02.012}, pmid = {19304329}, issn = {1879-1514}, mesh = {*Computational Biology ; Eukaryota/genetics/*physiology ; Gene Expression Profiling ; Genomics ; Metabolomics ; Metals, Heavy/toxicity ; Proteomics ; Stress, Physiological/genetics/*physiology ; *Systems Biology ; }, abstract = {The last decade, the biological and biomedical scientific landscape has seen the increase in use and applications of "omics" technologies. These technologies provide methods that allow for a comprehensive description of nearly all components within the cell. Microalgae not only play an important ecological role, but are also of commercial importance and therefore call for an in depth knowledge of basic biological functions. Knowledge of separate algal subsystems has gradually become available, but the challenge remains to integrate data obtained from these subsystems and from different levels of biological organization. Systems biology is a discipline that aims at this integration. In this paper, the current status of "omics" in algae is reviewed. At the lowest level, genome studies and the use of microarrays seem to have found widespread acceptance in algal research. At higher level such as the proteome and metabolome, however, very few omic studies have been carried out in algae so far. Moreover, the need arises for the construction of computer databases to store obtained information in a systematic way. To illustrate the use and especially the future needs of algal "omics" in a systems biological context, a case study is presented in which a freshwater alga was subjected to heavy metal stress and toxicity endpoints were monitored on different levels of biological organization.}, } @article {pmid19302541, year = {2009}, author = {Willner, D and Thurber, RV and Rohwer, F}, title = {Metagenomic signatures of 86 microbial and viral metagenomes.}, journal = {Environmental microbiology}, volume = {11}, number = {7}, pages = {1752-1766}, doi = {10.1111/j.1462-2920.2009.01901.x}, pmid = {19302541}, issn = {1462-2920}, mesh = {Cluster Analysis ; Computational Biology/methods ; *Environmental Microbiology ; *Metagenome ; Metagenomics/*methods ; Microbiological Techniques/*methods ; Phylogeny ; }, abstract = {Previous studies have shown that dinucleotide abundances capture the majority of variation in genome signatures and are useful for quantifying lateral gene transfer and building molecular phylogenies. Metagenomes contain a mixture of individual genomes, and might be expected to lack compositional signatures. In many metagenomic data sets the majority of sequences have no significant similarities to known sequences and are effectively excluded from subsequent analyses. To circumvent this limitation, di-, tri- and tetranucleotide abundances of 86 microbial and viral metagenomes consisting of short pyrosequencing reads were analysed to provide a method which includes all sequences that can be used in combination with other analysis to increase our knowledge about microbial and viral communities. Both principal component analysis and hierarchical clustering showed definitive groupings of metagenomes drawn from similar environments. Together these analyses showed that dinucleotide composition, as opposed to tri- and tetranucleotides, defines a metagenomic signature which can explain up to 80% of the variance between biomes, which is comparable to that obtained by functional genomics. Metagenomes with anomalous content were also identified using dinucleotide abundances. Subsequent analyses determined that these metagenomes were contaminated with exogenous DNA, suggesting that this approach is a useful metric for quality control. The predictive strength of the dinucleotide composition also opens the possibility of assigning ecological classifications to unknown fragments. Environmental selection may be responsible for this dinucleotide signature through direct selection of specific compositional signals; however, simulations suggest that the environment may select indirectly by promoting the increased abundance of a few dominant taxa.}, } @article {pmid19301943, year = {2009}, author = {Smolders, E and Oorts, K and Van Sprang, P and Schoeters, I and Janssen, CR and McGrath, SP and McLaughlin, MJ}, title = {Toxicity of trace metals in soil as affected by soil type and aging after contamination: using calibrated bioavailability models to set ecological soil standards.}, journal = {Environmental toxicology and chemistry}, volume = {28}, number = {8}, pages = {1633-1642}, doi = {10.1897/08-592.1}, pmid = {19301943}, issn = {0730-7268}, support = {BBS/E/C/00004981/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; Bacteria/drug effects/metabolism ; Biological Availability ; Data Interpretation, Statistical ; Environmental Monitoring/methods ; Invertebrates/drug effects ; Metals/*chemistry ; Plants/drug effects ; Soil/*analysis ; Soil Pollutants/*chemistry/*standards ; Time Factors ; Trace Elements ; }, abstract = {Total concentrations of metals in soil are poor predictors of toxicity. In the last decade, considerable effort has been made to demonstrate how metal toxicity is affected by the abiotic properties of soil. Here this information is collated and shows how these data have been used in the European Union for defining predicted-no-effect concentrations (PNECs) of Cd, Cu, Co, Ni, Pb, and Zn in soil. Bioavailability models have been calibrated using data from more than 500 new chronic toxicity tests in soils amended with soluble metal salts, in experimentally aged soils, and in field-contaminated soils. In general, soil pH was a good predictor of metal solubility but a poor predictor of metal toxicity across soils. Toxicity thresholds based on the free metal ion activity were generally more variable than those expressed on total soil metal, which can be explained, but not predicted, using the concept of the biotic ligand model. The toxicity thresholds based on total soil metal concentrations rise almost proportionally to the effective cation exchange capacity of soil. Total soil metal concentrations yielding 10% inhibition in freshly amended soils were up to 100-fold smaller (median 3.4-fold, n = 110 comparative tests) than those in corresponding aged soils or field-contaminated soils. The change in isotopically exchangeable metal in soil proved to be a conservative estimate of the change in toxicity upon aging. The PNEC values for specific soil types were calculated using this information. The corrections for aging and for modifying effects of soil properties in metal-salt-amended soils are shown to be the main factors by which PNEC values rise above the natural background range.}, } @article {pmid19296854, year = {2009}, author = {Yin, Y and Martin, J and Abubucker, S and Wang, Z and Wyrwicz, L and Rychlewski, L and McCarter, JP and Wilson, RK and Mitreva, M}, title = {Molecular determinants archetypical to the phylum Nematoda.}, journal = {BMC genomics}, volume = {10}, number = {}, pages = {114}, pmid = {19296854}, issn = {1471-2164}, mesh = {Animals ; Cluster Analysis ; Computational Biology ; Genomics ; Multigene Family/*genetics ; Nematoda/*genetics ; Peptides/*genetics ; Protein Structure, Tertiary/*genetics ; Sequence Homology ; Species Specificity ; }, abstract = {BACKGROUND: Nematoda diverged from other animals between 600-1,200 million years ago and has become one of the most diverse animal phyla on earth. Most nematodes are free-living animals, but many are parasites of plants and animals including humans, posing major ecological and economical challenges around the world.

RESULTS: We investigated phylum-specific molecular characteristics in Nematoda by exploring over 214,000 polypeptides from 32 nematode species including 27 parasites. Over 50,000 nematode protein families were identified based on primary sequence, including approximately 10% with members from at least three different species. Nearly 1,600 of the multi-species families did not share homology to Pfam domains, including a total of 758 restricted to Nematoda. Majority of the 462 families that were conserved among both free-living and parasitic species contained members from multiple nematode clades, yet approximately 90% of the 296 parasite-specific families originated only from a single clade. Features of these protein families were revealed through extrapolation of essential functions from observed RNAi phenotypes in C. elegans, bioinformatics-based functional annotations, identification of distant homology based on protein folds, and prediction of expression at accessible nematode surfaces. In addition, we identified a group of nematode-restricted sequence features in energy-generating electron transfer complexes as potential targets for new chemicals with minimal or no toxicity to the host.

CONCLUSION: This study identified and characterized the molecular determinants that help in defining the phylum Nematoda, and therefore improved our understanding of nematode protein evolution and provided novel insights for the development of next generation parasite control strategies.}, } @article {pmid19296715, year = {2009}, author = {Schwöbel, J and Ebert, RU and Kühne, R and Schüürmann, G}, title = {Prediction of the intrinsic hydrogen bond acceptor strength of organic compounds by local molecular parameters.}, journal = {Journal of chemical information and modeling}, volume = {49}, number = {4}, pages = {956-962}, doi = {10.1021/ci900040z}, pmid = {19296715}, issn = {1549-9596}, mesh = {Algorithms ; Calibration ; Computer Simulation ; Databases, Factual ; Forecasting ; *Hydrogen Bonding ; Models, Chemical ; Organic Chemicals/*chemistry ; Reproducibility of Results ; }, abstract = {A quantum chemical model has been developed for predicting the hydrogen bond (HB) acceptor strength of monofunctional organic compounds from electronic ground-state properties of the single molecules. Local molecular parameters are used to quantify electrostatic, polarizability, and charge transfer components to hydrogen bonding, employing the ab initio and density functional theory levels HF/6-31G** and B3LYP/6-31G**. The model can handle lone pairs of intermediate and strong HB acceptor heteroatoms (N, O, S) as well as of weak HB acceptor halogens (F, Cl, Br) and includes also olefinic, alkyne, and aromatic pi-bonds as weak HB acceptor sites. The model calibration with 403 compounds and experimental values for the Abraham HB acceptor strength B yielded squared correlation coefficients r(2) around 0.95, outperforming existing fragment-based schemes. Model validation was performed applying a leave-50%-out procedure, yielding predictive squared correlation coefficients q(2) of around 0.95 for the subsets that both cover the whole chemical domain as well as (almost) the whole target value range of the data set.}, } @article {pmid19284552, year = {2009}, author = {Soli, R and Kaabi, B and Barhoumi, M and El-Ayeb, M and Srairi-Abid, N}, title = {Bioinformatic characterizations and prediction of K+ and Na+ ion channels effector toxins.}, journal = {BMC pharmacology}, volume = {9}, number = {}, pages = {4}, pmid = {19284552}, issn = {1471-2210}, mesh = {Amino Acid Motifs ; Animals ; *Computational Biology ; Models, Statistical ; Molecular Sequence Data ; Phylogeny ; Potassium Channels/*drug effects ; Protein Structure, Tertiary ; Scorpion Venoms/chemistry/classification/*pharmacology ; Sequence Homology, Amino Acid ; Sodium Channels/*drug effects ; }, abstract = {BACKGROUND: K+ and Na+ channel toxins constitute a large set of polypeptides, which interact with their ion channel targets. These polypeptides are classified in two different structural groups. Recently a new structural group called birtoxin-like appeared to contain both types of toxins has been described. We hypothesized that peptides of this group may contain two conserved structural motifs in K+ and/or Na+ channels scorpion toxins, allowing these birtoxin-like peptides to be active on K+ and/or Na+ channels.

RESULTS: Four multilevel motifs, overrepresented and specific to each group of K+ and/or Na+ ion channel toxins have been identified, using GIBBS and MEME and based on a training dataset of 79 sequences judged as representative of K+ and Na+ toxins.Unexpectedly birtoxin-like peptides appeared to present a new structural motif distinct from those present in K+ and Na+ channels Toxins. This result, supported by previous experimental data, suggests that birtoxin-like peptides may exert their activity on different sites than those targeted by classic K+ or Na+ toxins.Searching, the nr database with these newly identified motifs using MAST, retrieved several sequences (116 with e-value < 1) from various scorpion species (test dataset). The filtering process left 30 new and highly likely ion channel effectors.Phylogenetic analysis was used to classify the newly found sequences. Alternatively, classification tree analysis, using CART algorithm adjusted with the training dataset, using the motifs and their 2D structure as explanatory variables, provided a model for prediction of the activity of the new sequences.

CONCLUSION: The phylogenetic results were in perfect agreement with those obtained by the CART algorithm.Our results may be used as criteria for a new classification of scorpion toxins based on functional motifs.}, } @article {pmid19281304, year = {2009}, author = {Pulliam, JR and Dushoff, J}, title = {Ability to replicate in the cytoplasm predicts zoonotic transmission of livestock viruses.}, journal = {The Journal of infectious diseases}, volume = {199}, number = {4}, pages = {565-568}, pmid = {19281304}, issn = {0022-1899}, support = {P50 GM071508/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Animals, Domestic/virology ; Artiodactyla/*virology ; Cytoplasm/*virology ; Databases, Genetic ; Humans ; Logistic Models ; Virus Diseases/*transmission/veterinary/virology ; *Virus Replication ; Viruses/*growth & development ; *Zoonoses ; }, abstract = {Understanding viral factors that promote cross-species transmission is important for evaluating the risk of zoonotic emergence. We constructed a database of viruses of domestic artiodactyls and examined the correlation between traits linked in the literature to cross-species transmission and the ability of viruses to infect humans. Among these traits--genomic material, genome segmentation, and replication without nuclear entry--the last is the strongest predictor of cross-species transmission. This finding highlights nuclear entry as a barrier to transmission and suggests that the ability to complete replication in the cytoplasm may prove to be a useful indicator of the threat of cross-species transmission.}, } @article {pmid19279070, year = {2009}, author = {Lacerda, CM and Reardon, KF}, title = {Environmental proteomics: applications of proteome profiling in environmental microbiology and biotechnology.}, journal = {Briefings in functional genomics & proteomics}, volume = {8}, number = {1}, pages = {75-87}, doi = {10.1093/bfgp/elp005}, pmid = {19279070}, issn = {1477-4062}, mesh = {Bacteria/*genetics ; Bacterial Physiological Phenomena ; Bacterial Proteins/genetics/*metabolism ; Biotechnology/*methods ; Computational Biology/*methods ; Ecology ; *Environmental Microbiology ; Genome, Bacterial ; Protein Engineering ; Proteome/genetics/*metabolism ; Proteomics/*methods/trends ; Water Microbiology ; Water Purification ; }, abstract = {In this review, we present the use of proteomics to advance knowledge in the field of environmental biotechnology, including studies of bacterial physiology, metabolism and ecology. Bacteria are widely applied in environmental biotechnology for their ability to catalyze dehalogenation, methanogenesis, denitrification and sulfate reduction, among others. Their tolerance to radiation and toxic compounds is also of importance. Proteomics has an important role in helping uncover the pathways behind these cellular processes. Environmental samples are often highly complex, which makes proteome studies in this field especially challenging. Some of these challenges are the lack of genome sequences for the vast majority of environmental bacteria, difficulties in isolating bacteria and proteins from certain environments, and the presence of complex microbial communities. Despite these challenges, proteomics offers a unique dynamic view into cellular function. We present examples of environmental proteomics of model organisms, and then discuss metaproteomics (microbial community proteomics), which has the potential to provide insights into the function of a community without isolating organisms. Finally, the environmental proteomics literature is summarized as it pertains to the specific application areas of wastewater treatment, metabolic engineering, microbial ecology and environmental stress responses.}, } @article {pmid19277436, year = {2009}, author = {Kelly, BD and Davoren, M and Mhaoláin, AN and Breen, EG and Casey, P}, title = {Social capital and suicide in 11 European countries: an ecological analysis.}, journal = {Social psychiatry and psychiatric epidemiology}, volume = {44}, number = {11}, pages = {971-977}, pmid = {19277436}, issn = {1433-9285}, mesh = {Adult ; Attitude to Health ; Community Networks/*organization & administration/statistics & numerical data ; Cross-Cultural Comparison ; Europe/epidemiology ; Female ; Health Status ; Humans ; *Interpersonal Relations ; Male ; Middle Aged ; Social Behavior ; Social Class ; Social Medicine ; Social Support ; Socioeconomic Factors ; Suicide/psychology/*statistics & numerical data ; Surveys and Questionnaires ; Trust/*psychology ; Urban Population/statistics & numerical data ; Suicide Prevention ; }, abstract = {BACKGROUND: "Social capital" refers to the existence of voluntary community networks and relationships based on trust, and the use of these networks and relationships to enable positive social action. Social capital is positively associated with selected indices of mental health.

METHODS: We performed an ecological investigation of the relationship between social trust (as one component of social capital) and national suicide rates in 11 European countries (n=22,227).

RESULTS: There was an inverse relationship between social trust and national suicide rates (i.e. the higher the social trust, the lower was the suicide rate), after controlling for gender, age, marriage rates, standardised income and reported sadness.

CONCLUSIONS: Social capital may have a protective effect against suicide at the national level. Multi-level analysis, taking into account both group-level and individual-level variables, would help clarify this relationship further and guide appropriate interventions at both the group and individual levels.}, } @article {pmid19276153, year = {2009}, author = {de Jong, D and Eitel, M and Jakob, W and Osigus, HJ and Hadrys, H and Desalle, R and Schierwater, B}, title = {Multiple dicer genes in the early-diverging metazoa.}, journal = {Molecular biology and evolution}, volume = {26}, number = {6}, pages = {1333-1340}, doi = {10.1093/molbev/msp042}, pmid = {19276153}, issn = {1537-1719}, mesh = {Animals ; Anthozoa/enzymology/*genetics ; Bayes Theorem ; DEAD-box RNA Helicases/*genetics ; Databases, Genetic ; Evolution, Molecular ; Gene Duplication ; *Genetic Speciation ; Models, Genetic ; Phylogeny ; Placozoa/*genetics ; Ribonuclease III/*genetics ; }, abstract = {Dicer proteins are highly conserved, are present in organisms ranging from plants to metazoans, and are essential components of the RNA interference pathway. Although the complement of Dicer proteins has been investigated in many "higher" metazoans, there has been no corresponding characterization of Dicer proteins in any early-branching metazoan. We cloned partial cDNAs of genes belonging to the Dicer family from the anthozoan cnidarian Nematostella vectensis and two distantly related haplotypes (species lineages) of the Placozoa (Trichoplax adhaerens 16S haplotype 1 [H1] and Placozoa sp. [H2]). We also identified Dicer genes in the hydrozoan Hydra magnipapillata and the demosponge Amphimedon queenslandica with the use of publicly available sequence databases. Two Dicer genes are present in each cnidarian species, whereas five Dicer genes each are found in the Porifera and Placozoa. Phylogenetic analyses comparing these and other metazoan Dicers suggest an ancient duplication event of a "Proto-Dicer" gene. We show that the Placozoa is the only known metazoan phylum which contains both representatives of this duplication event and that the multiple Dicer genes of the "basal" metazoan phyla represent lineage-specific duplications. There is a striking diversity of Dicer genes in basal metazoans, in stark contrast to the single Dicer gene found in most higher metazoans. This new data has allowed us to formulate new hypotheses regarding the evolution of metazoan Dicer proteins and their possible functions in the early diverging metazoan phyla. We theorize that the multiple placozoan Dicer genes fulfill a specific biological requirement, such as an immune defense strategy against viruses.}, } @article {pmid19276111, year = {2009}, author = {Ionita-Laza, I and Lange, C and M Laird, N}, title = {Estimating the number of unseen variants in the human genome.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {106}, number = {13}, pages = {5008-5013}, pmid = {19276111}, issn = {1091-6490}, support = {R01 MH059532/MH/NIMH NIH HHS/United States ; R01 MH59532/MH/NIMH NIH HHS/United States ; }, mesh = {Databases, Genetic ; Ecology ; *Genetic Variation ; Genetics, Population ; Genome, Human/*genetics ; Humans ; *Models, Genetic ; Polymorphism, Single Nucleotide ; Population Groups/*genetics ; Sample Size ; }, abstract = {The different genetic variation discovery projects (The SNP Consortium, the International HapMap Project, the 1000 Genomes Project, etc.) aim to identify as much as possible of the underlying genetic variation in various human populations. The question we address in this article is how many new variants are yet to be found. This is an instance of the species problem in ecology, where the goal is to estimate the number of species in a closed population. We use a parametric beta-binomial model that allows us to calculate the expected number of new variants with a desired minimum frequency to be discovered in a new dataset of individuals of a specified size. The method can also be used to predict the number of individuals necessary to sequence in order to capture all (or a fraction of) the variation with a specified minimum frequency. We apply the method to three datasets: the ENCODE dataset, the SeattleSNPs dataset, and the National Institute of Environmental Health Sciences SNPs dataset. Consistent with previous descriptions, our results show that the African population is the most diverse in terms of the number of variants expected to exist, the Asian populations the least diverse, with the European population in-between. In addition, our results show a clear distinction between the Chinese and the Japanese populations, with the Japanese population being the less diverse. To find all common variants (frequency at least 1%) the number of individuals that need to be sequenced is small (approximately 350) and does not differ much among the different populations; our data show that, subject to sequence accuracy, the 1000 Genomes Project is likely to find most of these common variants and a high proportion of the rarer ones (frequency between 0.1 and 1%). The data reveal a rule of diminishing returns: a small number of individuals (approximately 150) is sufficient to identify 80% of variants with a frequency of at least 0.1%, while a much larger number (> 3,000 individuals) is necessary to find all of those variants. Finally, our results also show a much higher diversity in environmental response genes compared with the average genome, especially in African populations.}, } @article {pmid19276106, year = {2009}, author = {Friedman, M}, title = {Ecomorphological selectivity among marine teleost fishes during the end-Cretaceous extinction.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {106}, number = {13}, pages = {5218-5223}, pmid = {19276106}, issn = {1091-6490}, mesh = {Animals ; Body Size ; Databases, Factual ; *Extinction, Biological ; Fishes/*genetics ; Jaw ; *Marine Biology ; Phylogeny ; Selection, Genetic ; }, abstract = {Despite the attention focused on mass extinction events in the fossil record, patterns of extinction in the dominant group of marine vertebrates-fishes-remain largely unexplored. Here, I demonstrate ecomorphological selectivity among marine teleost fishes during the end-Cretaceous extinction, based on a genus-level dataset that accounts for lineages predicted on the basis of phylogeny but not yet sampled in the fossil record. Two ecologically relevant anatomical features are considered: body size and jaw-closing lever ratio. Extinction intensity is higher for taxa with large body sizes and jaws consistent with speed (rather than force) transmission; resampling tests indicate that victims represent a nonrandom subset of taxa present in the final stage of the Cretaceous. Logistic regressions of the raw data reveal that this nonrandom distribution stems primarily from the larger body sizes of victims relative to survivors. Jaw mechanics are also a significant factor for most dataset partitions but are always less important than body size. When data are corrected for phylogenetic nonindependence, jaw mechanics show a significant correlation with extinction risk, but body size does not. Many modern large-bodied, predatory taxa currently suffering from overexploitation, such billfishes and tunas, first occur in the Paleocene, when they appear to have filled the functional space vacated by some extinction victims.}, } @article {pmid19272611, year = {2009}, author = {Cain, AE and Depp, CA and Jeste, DV}, title = {Ecological momentary assessment in aging research: a critical review.}, journal = {Journal of psychiatric research}, volume = {43}, number = {11}, pages = {987-996}, pmid = {19272611}, issn = {1879-1379}, support = {P30 MH066248/MH/NIMH NIH HHS/United States ; P30MH066248/MH/NIMH NIH HHS/United States ; K23 MH077225/MH/NIMH NIH HHS/United States ; K23MH077225/MH/NIMH NIH HHS/United States ; R34 MH091260/MH/NIMH NIH HHS/United States ; }, mesh = {Aged ; *Aging/physiology/psychology ; Compliance ; Databases, Bibliographic/statistics & numerical data ; Ecology/*methods ; *Geriatric Assessment ; Humans ; Reproducibility of Results ; *Research ; Time Factors ; }, abstract = {Ecological momentary assessment (EMA) gathers respondent data on affective, behavioral, and contextual experiences as close in time to those experiences as possible. Potential advantages of EMA in aging research include reducing memory biases and gathering intra-individual data, yet there is little understanding about implementation. The goal of this critical review was to assess the feasibility and applications of EMA in psychological and behavioral research on aging. Through a comprehensive search of the online electronic databases, Psycinfo and Pubmed, for English-language peer-reviewed journals published between 1990 and 2007, we identified 40 articles using EMA methods in older adults. Studies sampled participants between five times per day over one day to once a week for 210 days. Samples were generally not cognitively impaired, evenly split between healthy and clinical populations, and only 6 of 40 studies focused on psychiatric diagnoses. The most common assessment content solicited ratings on affect (n=15), activities of daily living (n=12), physical activities (n=10), and social exchanges (n=8). A total of 90% of the studies that reported compliance reported rates over 80%. Uses of EMA varied widely, with research goals including validation of global measures, detection of subtle treatment effects, and for testing hypotheses about causal intra-individual relationships. Although these measures appear feasible and useful in aging research, recommendations for future studies include adapting measures to enable data collection among older participants with cognitive impairments and/or psychopathology, along with greater use of electronic data capture to improve compliance and increase ease of implementation.}, } @article {pmid19263891, year = {2008}, author = {Lindenmayer, DB and Wood, JT and Cunningham, RB and MacGregor, C and Crane, M and Michael, D and Montague-Drake, R and Brown, D and Muntz, R and Gill, AM}, title = {Testing hypotheses associated with bird responses to wildfire.}, journal = {Ecological applications : a publication of the Ecological Society of America}, volume = {18}, number = {8}, pages = {1967-1983}, doi = {10.1890/07-1943.1}, pmid = {19263891}, issn = {1051-0761}, mesh = {Animals ; Australia ; *Behavior, Animal ; *Biodiversity ; Birds/*physiology ; *Fires ; Geographic Information Systems ; Population Density ; Population Dynamics ; Time Factors ; }, abstract = {Disturbance is a key ecological process influencing the distribution and abundance of many elements of the earth's biota. Predicting the response of biota to disturbance is therefore important, but it nevertheless remains difficult to make accurate forecasts of response. We tested predictions from disturbance-related theories and concepts in 10 vegetation types at Booderee National Park (southeastern Australia) using a retrospective study of bird responses to fire history (over 35 years) on 110 sites and a prospective study following a single wildfire event in 2003 at 59 of these sites. Our data did not support predictions from the intermediate-disturbance hypothesis; observed bird species richness at a site was significantly (F(1,99) = 6.30, P = 0.014) negatively related to the number of fires since 1972 and was 8.7% lower (95% CI, 1.8-15.1%) for each additional fire. In contrast to fire history effects, we found that after the 2003 fire, the vast majority of individual species and the bird assemblage per se in most vegetation types recovered within two years. Thus, recovery after a single fire did not reflect long-term effects of multiple fires on overall bird species richness at a site. We postulated that the recovery of bird species richness and bird assemblage composition after the 2003 fire would be fastest in structurally simple vegetation types and slowest in structurally complex vegetation, but observed the opposite. Although observed bird species richness in vertically heterogeneous forest and woodland had returned to prefire levels by 2006, bird species richness in structurally simple vegetation types (e.g., sedgeland) had not. Postfire vegetation regeneration, together with a paucity of early-successional specialists, would explain the speed of recovery of the bird assemblage and why it changed relatively little during our investigation.}, } @article {pmid19262741, year = {2009}, author = {Zhang, Y and Zhou, X and Ge, X and Jiang, J and Li, M and Jia, S and Yang, X and Kan, Y and Miao, X and Zhao, G and Li, F and Huang, Y}, title = {Insect-Specific microRNA Involved in the Development of the Silkworm Bombyx mori.}, journal = {PloS one}, volume = {4}, number = {3}, pages = {e4677}, pmid = {19262741}, issn = {1932-6203}, mesh = {Algorithms ; Animals ; Bombyx/genetics/*growth & development ; Computational Biology ; Genes ; Genome ; Insecta ; MicroRNAs/genetics/*physiology ; Species Specificity ; }, abstract = {MicroRNAs (miRNAs) are endogenous non-coding genes that participate in post-transcription regulation by either degrading mRNA or blocking its translation. It is considered to be very important in regulating insect development and metamorphosis. We conducted a large-scale screening for miRNA genes in the silkworm Bombyx mori using sequence-by-synthesis (SBS) deep sequencing of mixed RNAs from egg, larval, pupal, and adult stages. Of 2,227,930 SBS tags, 1,144,485 ranged from 17 to 25 nt, corresponding to 256,604 unique tags. Among these non-redundant tags, 95,184 were matched to the silkworm genome. We identified 3,750 miRNA candidate genes using a computational pipeline combining RNAfold and TripletSVM algorithms. We confirmed 354 miRNA genes using miRNA microarrays and then performed expression profile analysis on these miRNAs for all developmental stages. While 106 miRNAs were expressed in all stages, 248 miRNAs were egg- and pupa-specific, suggesting that insect miRNAs play a significant role in embryogenesis and metamorphosis. We selected eight miRNAs for quantitative RT-PCR analysis; six of these were consistent with our microarray results. In addition, we searched for orthologous miRNA genes in mammals, a nematode, and other insects and found that most silkworm miRNAs are conserved in insects, whereas only a small number of silkworm miRNAs has orthologs in mammals and the nematode. These results suggest that there are many miRNAs unique to insects.}, } @article {pmid19260347, year = {2009}, author = {Wang, C and van der Meer, P and Peng, M and Douven, W and Hessel, R and Dang, C}, title = {Ecosystem services assessment of two watersheds of Lancang River in Yunnan, China with a decision tree approach.}, journal = {Ambio}, volume = {38}, number = {1}, pages = {47-54}, doi = {10.1579/0044-7447-38.1.47}, pmid = {19260347}, issn = {0044-7447}, mesh = {Biodiversity ; China ; Conservation of Natural Resources ; *Decision Support Techniques ; *Ecosystem ; Geography ; *Water Supply ; }, abstract = {In the Langcang (Upper-Mekong) watershed, degraded watershed ecosystems in upland areas threaten cultivation practices, water resources, and dam development downstream. Assessment of ecosystem services and the factors that threaten them is an important first step to support watershed management. This, however, requires detailed information that is often missing in mountainous regions. To overcome this, in this paper, we adopt a decision tree approach to assess protection, biodiversity, and production services in two mountainous watersheds (Fengqing and Xiaojie) of the Lancang River Basin. Decision tree rules were built on the basis of field surveys, available references, ecosystem maps derived from remote sensing, expert knowledge, basic topographic information, and community interviews. Decision tree results showed that forest cover and agro-forestry practices contribute greatly to improved ecosystem functioning in the Fengqing Catchment compared to the Xiaojie Catchment. The results were consistent with field observations. The decision tree method proved to be a suitable and flexible tool for the rapid assessment of watershed ecosystem services, for highlighting those areas that need more in-depth research, and for guiding watershed and ecosystem management.}, } @article {pmid19252401, year = {2009}, author = {Werner, P and Rabinowitz, S and Klinger, E and Korczyn, AD and Josman, N}, title = {Use of the virtual action planning supermarket for the diagnosis of mild cognitive impairment: a preliminary study.}, journal = {Dementia and geriatric cognitive disorders}, volume = {27}, number = {4}, pages = {301-309}, doi = {10.1159/000204915}, pmid = {19252401}, issn = {1421-9824}, mesh = {*Activities of Daily Living ; Aged ; Cognition Disorders/*diagnosis/psychology ; Computer Graphics ; Computer Simulation ; Data Interpretation, Statistical ; Feedback, Psychological ; Female ; Humans ; Male ; Middle Aged ; *Neuropsychological Tests ; Psychomotor Performance/physiology ; Reproducibility of Results ; Socioeconomic Factors ; }, abstract = {BACKGROUND: Although executive functioning (EF) was found to be associated with cognitive deterioration, the majority of the tests for assessing EF lack ecological validity.

AIMS: To examine the feasibility and the validity of the virtual action planning supermarket (VAP-S) for the diagnosis of patients with mild cognitive impairment (MCI).

METHODS: Thirty MCI patients (mean age = 69.5 years) were compared to 30 healthy elderly persons (mean age = 69.2 years) in their performance of the VAP-S.

RESULTS: Significant differences were found between the groups in the majority of the measures of the VAP-S. The combination of the MMSE and the trajectory duration provided the best predictive classification for the groups.

CONCLUSION: MCI patients have EF deficits, and the VAP-S is a viable tool to assess EF deficits in patients with MCI and healthy elderly.}, } @article {pmid19251847, year = {2009}, author = {Slater, SC and Goldman, BS and Goodner, B and Setubal, JC and Farrand, SK and Nester, EW and Burr, TJ and Banta, L and Dickerman, AW and Paulsen, I and Otten, L and Suen, G and Welch, R and Almeida, NF and Arnold, F and Burton, OT and Du, Z and Ewing, A and Godsy, E and Heisel, S and Houmiel, KL and Jhaveri, J and Lu, J and Miller, NM and Norton, S and Chen, Q and Phoolcharoen, W and Ohlin, V and Ondrusek, D and Pride, N and Stricklin, SL and Sun, J and Wheeler, C and Wilson, L and Zhu, H and Wood, DW}, title = {Genome sequences of three agrobacterium biovars help elucidate the evolution of multichromosome genomes in bacteria.}, journal = {Journal of bacteriology}, volume = {191}, number = {8}, pages = {2501-2511}, pmid = {19251847}, issn = {1098-5530}, support = {52005125//Howard Hughes Medical Institute/United States ; }, mesh = {Computational Biology/methods ; Conserved Sequence ; DNA, Bacterial/chemistry/*genetics ; *Evolution, Molecular ; Gene Order ; *Genome, Bacterial ; Molecular Sequence Data ; Phylogeny ; Rhizobium/*genetics ; Sequence Analysis, DNA ; Synteny ; }, abstract = {The family Rhizobiaceae contains plant-associated bacteria with critical roles in ecology and agriculture. Within this family, many Rhizobium and Sinorhizobium strains are nitrogen-fixing plant mutualists, while many strains designated as Agrobacterium are plant pathogens. These contrasting lifestyles are primarily dependent on the transmissible plasmids each strain harbors. Members of the Rhizobiaceae also have diverse genome architectures that include single chromosomes, multiple chromosomes, and plasmids of various sizes. Agrobacterium strains have been divided into three biovars, based on physiological and biochemical properties. The genome of a biovar I strain, A. tumefaciens C58, has been previously sequenced. In this study, the genomes of the biovar II strain A. radiobacter K84, a commercially available biological control strain that inhibits certain pathogenic agrobacteria, and the biovar III strain A. vitis S4, a narrow-host-range strain that infects grapes and invokes a hypersensitive response on nonhost plants, were fully sequenced and annotated. Comparison with other sequenced members of the Alphaproteobacteria provides new data on the evolution of multipartite bacterial genomes. Primary chromosomes show extensive conservation of both gene content and order. In contrast, secondary chromosomes share smaller percentages of genes, and conserved gene order is restricted to short blocks. We propose that secondary chromosomes originated from an ancestral plasmid to which genes have been transferred from a progenitor primary chromosome. Similar patterns are observed in select Beta- and Gammaproteobacteria species. Together, these results define the evolution of chromosome architecture and gene content among the Rhizobiaceae and support a generalized mechanism for second-chromosome formation among bacteria.}, } @article {pmid19251346, year = {2009}, author = {Irene Wong, YL and Stanhope, V}, title = {Conceptualizing community: a comparison of neighborhood characteristics of supportive housing for persons with psychiatric and developmental disabilities.}, journal = {Social science & medicine (1982)}, volume = {68}, number = {8}, pages = {1376-1387}, doi = {10.1016/j.socscimed.2009.01.046}, pmid = {19251346}, issn = {0277-9536}, support = {H133BO31109/BO/FDA HHS/United States ; R24 MH63220/MH/NIMH NIH HHS/United States ; }, mesh = {Adolescent ; Adult ; Databases, Factual ; *Developmental Disabilities ; *Disabled Persons ; Female ; Humans ; Male ; Models, Organizational ; Models, Statistical ; Pennsylvania ; Persons with Mental Disabilities ; *Residence Characteristics ; Residential Facilities/*organization & administration ; }, abstract = {Housing and services for persons with developmental disabilities (DD) have been shaped by the normalization approach, a commitment to full integration within the general community. In contrast, housing and services for persons with psychiatric disabilities (PD) have had various and sometimes conflicting goals, including provision of custodial care, promotion of therapeutic community, and community integration. This cross-field study compares the neighborhood characteristics of publicly-funded housing for the PD and DD populations in a metropolitan community. The aim of the study was to examine whether the contrasting housing approaches are reflected at an ecological level and to consider how these findings relate to the goal of community integration for people with PD and DD. Administrative databases provided residential addresses of 1932 residents with PD living in 297 locations and 1716 residents with DD living in 749 locations in the city of Philadelphia. The 2000 U.S. Census and city's police department database provided information on neighborhood characteristics. Geographic information system (GIS) methodology generated maps displaying the distribution of housing locations in relation to spatial dispersion, distress, stability, safety, and race/ethnic diversity. Statistical analyses compared neighborhood characteristics of the DD and PD populations. Findings indicated that the DD population in supportive housing was more spatially dispersed, and lived in less distressed, less unstable, more secure, but equally racially/ethnically diverse neighborhoods when compared to the PD population in supportive housing. Greater geographic dispersal among persons with DD may be the result of more emphasis on normalization within policies and programs determining the location of their housing. The higher funding levels for housing and residential support for persons with DD also provided programs with the option of placing people in higher income neighborhoods. Given that community integration has emerged as an organizing principle within mental health services over other models, policymakers in the field of psychiatric disabilities may have much to learn from the normalization movement for people with developmental disabilities.}, } @article {pmid19240807, year = {2009}, author = {Bibby, TS and Zhang, Y and Chen, M}, title = {Biogeography of photosynthetic light-harvesting genes in marine phytoplankton.}, journal = {PloS one}, volume = {4}, number = {2}, pages = {e4601}, pmid = {19240807}, issn = {1932-6203}, mesh = {Animals ; Bacterial Proteins/genetics ; Base Sequence ; Chlorophyll/analysis ; Computational Biology ; Cyanobacteria/*genetics ; Databases, Nucleic Acid ; Ecosystem ; Environment ; Genes, Bacterial ; Iron/metabolism ; Light-Harvesting Protein Complexes/*genetics ; Photosynthesis/*genetics ; Phycobilins/genetics ; Phycobilisomes/genetics ; Phytoplankton/*genetics ; Seawater ; }, abstract = {BACKGROUND: Photosynthetic light-harvesting proteins are the mechanism by which energy enters the marine ecosystem. The dominant prokaryotic photoautotrophs are the cyanobacterial genera Prochlorococcus and Synechococcus that are defined by two distinct light-harvesting systems, chlorophyll-bound protein complexes or phycobilin-bound protein complexes, respectively. Here, we use the Global Ocean Sampling (GOS) Project as a unique and powerful tool to analyze the environmental diversity of photosynthetic light-harvesting genes in relation to available metadata including geographical location and physical and chemical environmental parameters.

METHODS: All light-harvesting gene fragments and their metadata were obtained from the GOS database, aligned using ClustalX and classified phylogenetically. Each sequence has a name indicative of its geographic location; subsequent biogeographical analysis was performed by correlating light-harvesting gene budgets for each GOS station with surface chlorophyll concentration.

CONCLUSION/SIGNIFICANCE: Using the GOS data, we have mapped the biogeography of light-harvesting genes in marine cyanobacteria on ocean-basin scales and show that an environmental gradient exists in which chlorophyll concentration is correlated to diversity of light-harvesting systems. Three functionally distinct types of light-harvesting genes are defined: (1) the phycobilisome (PBS) genes of Synechococcus; (2) the pcb genes of Prochlorococcus; and (3) the iron-stress-induced (isiA) genes present in some marine Synechococcus. At low chlorophyll concentrations, where nutrients are limited, the Pcb-type light-harvesting system shows greater genetic diversity; whereas at high chlorophyll concentrations, where nutrients are abundant, the PBS-type light-harvesting system shows higher genetic diversity. We interpret this as an environmental selection of specific photosynthetic strategy. Importantly, the unique light-harvesting system isiA is found in the iron-limited, high-nutrient low-chlorophyll region of the equatorial Pacific. This observation demonstrates the ecological importance of isiA genes in enabling marine Synechococcus to acclimate to iron limitation and suggests that the presence of this gene can be a natural biomarker for iron limitation in oceanic environments.}, } @article {pmid19238849, year = {2008}, author = {Gao, JB and Zhao, ZQ and Li, SC}, title = {[Evaluation of ecosystem resilience in the regions across Qinghai-Tibet railway based on GIS].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {19}, number = {11}, pages = {2473-2479}, pmid = {19238849}, issn = {1001-9332}, mesh = {Altitude ; *Ecosystem ; *Environment Design ; Environmental Monitoring ; Evaluation Studies as Topic ; *Facility Design and Construction ; *Geographic Information Systems ; *Railroads ; Tibet ; }, abstract = {Based on GIS technique and the methods of mean-squared deviation weight decision and catastrophe progression, a more clear definition and associated evaluation for ecosystem resilience were given, with a case study in the regions across Qinghai-Tibet railway by using the indices of plant community coverage, species diversity, and biomass. It was shown that the areas with high ecosystem resilience were mainly located in the Qilian Mountain meadow grassland, Huangshui Valley needle-leaved and deciduous broad-leaved forest, and south Tanggula Mountain kobresia swamp meadow, while those with the lowest resilience were in the central part of Qaidam Basin, and the Kunlun Mountains. Most areas in the regions had higher or medium ecosystem resilience, with a trend of that in the south of Kunlun Mountains, the resilience in the north of the railway was lower, while in the east of Qaidam Basin (especially in the Qinghai Lake area), the resilience was lower in the south than in the north of the railway. Through the evaluation of ecosystem resilience, the key issues in the process of ecological resilience could be found, and corresponding effective measures would be pointed out to manage alpine ecosystems. Moreover, combining with the evaluation of vulnerability, scientific basis for regional development could be provided to avoid or mitigate the negative effects of human activities on eco-environment.}, } @article {pmid19238847, year = {2008}, author = {Zhou, R and Li, YH and Hu, YM and Liu, M}, title = {[Evaluation of view points in forest park based on landscape sensitivity].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {19}, number = {11}, pages = {2460-2466}, pmid = {19238847}, issn = {1001-9332}, mesh = {China ; *Conservation of Natural Resources ; *Ecology ; *Environment Design ; Evaluation Studies as Topic ; Forestry ; Geographic Information Systems ; Trees/*growth & development ; }, abstract = {Based on topographical characteristics, five factors including comparative slope, comparative distance, mutual visibility, vision probability, and striking degree were chosen to assess the landscape sensitivity of major view points in Houshi National Forest Park. Spatial analysis in GIS was used for exploring the theory and method of landscape sensitivity of view points. The results showed that in the Park, there were totally 23 view points, but none of them reached up to class I. Among the 23 points, 10 were of class II , accounting for 43.5% of the total, 8 were of class III, accounting for 34.8%, and 5 were of classes IV and V, accounting for 21.7%. Around the view points of class II, the landscape should be strictly protected to maintain their natural feature; around the view points of class III, human-made landscape points should be developed according to the natural landscape feature, and wide tourism roads and small-size buildings could be constructed but the style of the buildings should be harmonious with surrounding nature landscape; while around the view points of classes IV and V, large-size multifunctional items and roads could be built to perfect the natural landscape. Through the multi-perspective and quantitative evaluation of landscape sensitivity, this study enriched the theory of landscape visual assessment and landscape apperception, and provided scientific base and direction for the planning and management of forest parks and other tourism areas.}, } @article {pmid19197475, year = {2008}, author = {Padial, AA and Bini, LM and Thomaz, SM}, title = {The study of aquatic macrophytes in Neotropics: a scientometrical view of the main trends and gaps.}, journal = {Brazilian journal of biology = Revista brasleira de biologia}, volume = {68}, number = {4 Suppl}, pages = {1051-1059}, doi = {10.1590/s1519-69842008000500012}, pmid = {19197475}, issn = {1678-4375}, mesh = {Animals ; Argentina ; *Bibliometrics ; Biomedical Research/*statistics & numerical data ; Brazil ; Chile ; Conservation of Natural Resources ; Databases, Bibliographic ; Fresh Water ; Mexico ; Periodicals as Topic ; *Plants ; Research Personnel ; *Tropical Climate ; }, abstract = {Aquatic macrophytes comprises a diverse group of organisms including angiosperms, ferns, mosses, liverworts and some macroalgae that occur in seasonally or permanently wet environments. Among other implications, aquatic macrophytes are highly productive and with an important structuring role on aquatic environments. Ecological studies involving aquatic plants substantially increased in the last years. However, a precise view of researches devoted to aquatic macrophytes in Neotropics is necessary to reach a reliable evaluation of the scientific production. In the current study, we performed a scientometrics analysis of the scientific production devoted to Neotropical macrophytes in an attempt to find the main trends and gaps of researches concerning this group. The publication devoted to macrophytes in Neotropics increased conspicuously in the last two decades. Brazil, Argentina, Mexico and Chile were the most productive among Neotropical countries. Our analyses showed that the studies dealt mostly with the influences of aquatic macrophytes on organisms and abiotic features. Studies with a predictive approach or aiming to test ecological hypothesis are scarce. In addition, researches aiming to describe unknown species are still necessary. This is essential to support conservation efforts and to subsidize further investigations testing ecological hypotheses.}, } @article {pmid19219053, year = {2009}, author = {VerBerkmoes, NC and Denef, VJ and Hettich, RL and Banfield, JF}, title = {Systems biology: Functional analysis of natural microbial consortia using community proteomics.}, journal = {Nature reviews. Microbiology}, volume = {7}, number = {3}, pages = {196-205}, pmid = {19219053}, issn = {1740-1534}, mesh = {Bacteria/*genetics/*metabolism ; Chromatography, Liquid ; *Ecosystem ; Electrophoresis, Gel, Two-Dimensional ; *Environmental Microbiology ; *Genomics/trends ; Mass Spectrometry ; *Proteomics/trends ; }, abstract = {We know very little about the metabolic functioning and evolutionary dynamics of microbial communities. Recent advances in comprehensive, sequencing-based methods, however, are laying a molecular foundation for new insights into how microbial communities shape the Earth's biosphere. Here we explore the convergence of microbial ecology, genomics, biological mass spectrometry and informatics that form the new field of microbial community proteogenomics. We discuss the first applications of proteogenomics and its potential for studying the physiology, ecology and evolution of microbial populations and communities.}, } @article {pmid19217145, year = {2009}, author = {Howden, NJ and Bowes, MJ and Clark, AD and Humphries, N and Neal, C}, title = {Water quality, nutrients and the European union's Water Framework Directive in a lowland agricultural region: Suffolk, south-east England.}, journal = {The Science of the total environment}, volume = {407}, number = {8}, pages = {2966-2979}, doi = {10.1016/j.scitotenv.2008.12.040}, pmid = {19217145}, issn = {0048-9697}, mesh = {Agriculture ; England ; Environmental Monitoring ; European Union ; Geographic Information Systems ; Geography ; Phosphorus/*analysis/chemistry ; Rivers/*chemistry ; Water Movements ; Water Pollutants, Chemical/*analysis/chemistry ; Water Pollution/*legislation & jurisprudence ; }, abstract = {The water quality of 13 rivers in the lowland, agricultural county of Suffolk is investigated using routine monitoring data for the period 1981 to 2006 collected by the Environment Agency of England and Wales (EA), and its predecessors, with particular emphasis on phosphorus (as total reactive phosphorus, TRP) and total (dissolved and particulate) oxidised nitrogen (TOxN--predominantly nitrate NO3). Major ion and flow data are used to outline fundamental hydrochemical characteristics related to the groundwater provenance of base-flow waters. Relative load contributions from point and diffuse sources are approximated using Load Apportionment Modelling for both TRP and TOxN where concurrent flow and concentration data are available. Analyses indicate a mixture of point and diffuse sources of TRP, with the former being dominant during low flow periods, while for TOxN diffuse sources dominate. Out of 59 sites considered, 53 (90%) were found to have annual average TRP concentrations greater than 0.05 mg P l(-1), and 36 (61%) had average concentrations over 0.120 mg P l(-1), the upper thresholds for 'High' and 'Good' ecological status, respectively. Correspondingly, for TOxN, most of the rivers are already within 70% of the 11.3 mg N l(-1) threshold, with two rivers (Wang and Ore) being consistently greater than this. It is suggested that the major challenge is to characterise and control point-source TRP inputs which, being predominant during the late spring and summer low-flow period, coincide with the peak of primary biological production, thus presenting the major challenge to achieving 'good' ecological status under the Water Framework Directive. Results show that considerable effort is still required to ensure appropriate management and develop tools for decision-support.}, } @article {pmid19215984, year = {2009}, author = {Flynn, K and Spellman, T}, title = {Environmental levels of atrazine decrease spatial aggregation in the freshwater mussel, Elliptio complanata.}, journal = {Ecotoxicology and environmental safety}, volume = {72}, number = {4}, pages = {1228-1233}, doi = {10.1016/j.ecoenv.2008.02.013}, pmid = {19215984}, issn = {1090-2414}, mesh = {Analysis of Variance ; Animals ; Atrazine/pharmacokinetics/*toxicity ; Bivalvia/drug effects/*growth & development ; Data Interpretation, Statistical ; Estradiol/metabolism ; Fresh Water ; Half-Life ; Herbicides/pharmacokinetics/*toxicity ; }, abstract = {The commonly used herbicide atrazine (ATR), may cause estrogen-like alterations and, like other xenoestrogens, may alter behavior. Here effects on animal aggregation were tested in freshwater mussels exposed short-term to ecologically relevant ATR concentrations between 1.5 and 150microg/L. The aggregation index (AI), the fraction of mussels in the most densely populated tank section, was evaluated and showed higher AI at later times in both 6- and 72-h trials (p<0.001). After 72h, there was also less aggregation in estradiol- and mid-ATR-treated animals, 26% and 24% less than control, respectively (p<0.04). These data suggest that freshwater mussels tend to aggregate, that 72-h exposure to ecologically relevant ATR concentrations decreases aggregation, and that estradiol exposure has a similar effect. Given that bivalve aggregation may be related to reproduction, the results suggest that low concentrations of ATR may have ecological consequences on animal populations in this species.}, } @article {pmid19213207, year = {2008}, author = {Aguayo-Alckaraz, G and Jiménez-Pérez, LM and Celis-de la Rosa, A and Canales-Muñoz, JL}, title = {[Breast cancer mortality. Trend and geographical distribution, 1981-2001].}, journal = {Revista medica del Instituto Mexicano del Seguro Social}, volume = {46}, number = {4}, pages = {367-374}, pmid = {19213207}, issn = {0443-5117}, mesh = {Breast Neoplasms/*mortality ; Female ; Humans ; Mexico/epidemiology ; Young Adult ; }, abstract = {OBJECTIVE: to describe trend and geographical distribution of breast cancer mortality, in Mexico.

METHODS: it was done an ecological and tendency study from 1981 to 2001, 52,739 deaths by breast cancer in women > or = 20-year-old. Mortality was studied according to the International Classification of Diseases. The data were obtained from the National Institute of Statistics, Geography and Informatics and from the General Census of Population. The period studied was three-yearly. Adjusted rates were calculated with the direct method. It was utilized a lineal regression model for the analysis of mortality tendencies. Map was built from the distribution of the mortality along the country.

RESULTS: the mortality tendency was increased in the first decade and in the second it was maintained stable, with an important drop in four states (p<0.05). The 66% of the states had rates over the national adjusted rate, all of them in the north of the country. Nayarit, Guerrero, and Mexico State had an increment of 300%.

CONCLUSIONS: the ascending tendency and stabilization of the mortality is similar to other countries. The north states had the greater rate of mortality, intermediate rates in the middle of country and drops in the south. It is possible that these changes were secondary to environmental, social and medical care factors.}, } @article {pmid19209379, year = {2009}, author = {Li, N and Lv, J and Niu, DK}, title = {Low contents of carbon and nitrogen in highly abundant proteins: evidence of selection for the economy of atomic composition.}, journal = {Journal of molecular evolution}, volume = {68}, number = {3}, pages = {248-255}, pmid = {19209379}, issn = {1432-1432}, mesh = {Amino Acid Sequence ; Amino Acids/metabolism ; Carbon/*metabolism ; Chi-Square Distribution ; Databases, Protein ; Escherichia coli K12/genetics ; *Escherichia coli Proteins/chemistry/genetics/metabolism ; *Evolution, Molecular ; Kinetics ; Nitrogen/*metabolism ; Saccharomyces cerevisiae/genetics ; *Saccharomyces cerevisiae Proteins/chemistry/genetics/metabolism ; Schizosaccharomyces/genetics ; *Schizosaccharomyces pombe Proteins/chemistry/genetics/metabolism ; Statistics, Nonparametric ; Thermodynamics ; }, abstract = {Proteins that assimilate particular elements were found to avoid using amino acids containing the element, which indicates that the metabolic constraints of amino acids may influence the evolution of proteins. We suspected that low contents of carbon, nitrogen, and sulfur may also be selected for economy in highly abundant proteins that consume large amounts of the resources of cells. By analyzing recently available proteomic data in Escherichia coli, Saccharomyces cerevisiae, and Schizosaccharomyces pombe, we found that at least the carbon and nitrogen contents in amino acid side chains are negatively correlated with protein abundance. An amino acid with a high number of carbon atoms in its side chain generally requires relatively more energy for its synthesis. Thus, it may be selected against in highly abundant proteins either because of economy in building blocks or because of economy in energy. Previous studies showed that highly abundant proteins preferentially use cheap (in terms of energy) amino acids. We found that the carbon content is still negatively correlated with protein abundance after controlling for the energetic cost of the amino acids. However, the negative correlation between protein abundance and energetic cost disappeared after controlling for carbon content. Building blocks seem to be more restricted than energy. It seems that the amino acid sequences of highly abundant proteins have to compromise between optimization for their biological functions and reducing the consumption of limiting resources. By contrast, the amino acid sequences of weakly expressed proteins are more likely to be optimized for their biological functions.}, } @article {pmid19208993, year = {2009}, author = {Boyle, SA and Lourenço, WC and da Silva, LR and Smith, AT}, title = {Home range estimates vary with sample size and methods.}, journal = {Folia primatologica; international journal of primatology}, volume = {80}, number = {1}, pages = {33-42}, doi = {10.1159/000201092}, pmid = {19208993}, issn = {1421-9980}, mesh = {Animals ; Brazil ; *Data Interpretation, Statistical ; *Homing Behavior ; *Pitheciidae ; Sample Size ; }, abstract = {Accurate estimates of a primate's home range are important, yet methods vary greatly. This paper examines the accuracy of minimum convex polygon (MCP), adaptive kernel (AK) and fixed kernel (FK) estimators by comparing home range estimates of northern bearded saki monkeys (Chiropotes satanas chiropotes) living in forest fragments and continuous forest in the Brazilian Amazon area. MCP was more accurate than AK and FK in calculating home and day range when sample size was small, and AK overestimated range most frequently. It is important to consider the various home range methods, as the appropriate method may depend on sample size and the species' behavioral ecology.}, } @article {pmid19205913, year = {2010}, author = {Dengiz, O and Ozcan, H and Koksal, ES and Baskan, O and Kosker, Y}, title = {Sustainable natural resource management and environmental assessment in the Salt Lake (Tuz Golu) Specially Protected Area.}, journal = {Environmental monitoring and assessment}, volume = {161}, number = {1-4}, pages = {327-342}, pmid = {19205913}, issn = {1573-2959}, mesh = {Conservation of Natural Resources/*methods ; Environmental Monitoring/*methods ; Geographic Information Systems ; Geography ; Turkey ; }, abstract = {The Salt Lake Specially Protected Area is a unique ecosystem for both agricultural activities and natural life in Turkey. In the present study, an attempt was made to develop a conceptual land use strategy and methodology, taking into account ecological factors for regional development in the Salt Lake Specially Protected Area. A detailed Geographic Information System (GIS) analysis was done to create a comprehensive database including land use, land suitability, and environmental factors (soil, climate, water quality, fertilizing status, and heavy metal and pesticide pollution). The results of the land suitability survey for agricultural use showed that, while 62.6% of the study area soils were classified as best and relatively good, about 15% were classified as problematic and restricted lands, only 22.2% of the study area soils were not suitable for agricultural uses. However, this is not enough to derive maximum benefit with minimum degradation. Therefore, environmental factors and ecological conditions were combined to support this aim and to protect the ecosystem. Excessive irrigation practices, fertilizer and pesticide application, and incorrect management practices all accelerate salinization and degradation. In addition to this, it was found that a multi-layer GIS analysis made it easy to develop a framework for optimum land use and could increase the production yield preserving the environmental conditions. Finally, alternative management and crop patterns were undertaken to sustain this unique ecosystem, considering water, soil, climate, land use characteristics, and to provide guidance for planners or decision makers.}, } @article {pmid19205911, year = {2009}, author = {Mobley, LR and Kuo, TM and Clayton, LJ and Evans, WD}, title = {Mammography facilities are accessible, so why is utilization so low?.}, journal = {Cancer causes & control : CCC}, volume = {20}, number = {6}, pages = {1017-1028}, pmid = {19205911}, issn = {1573-7225}, support = {R01 CA126858/CA/NCI NIH HHS/United States ; R01 CA126858-02/CA/NCI NIH HHS/United States ; R21 CA117869/CA/NCI NIH HHS/United States ; 5 R21 CA117869-02/CA/NCI NIH HHS/United States ; }, mesh = {Aged ; Aged, 80 and over ; Breast Neoplasms/diagnosis ; California ; *Community Networks ; Female ; Geography ; *Health Services Accessibility ; *Healthcare Disparities ; Humans ; Mammography/*statistics & numerical data ; Models, Statistical ; *Preventive Medicine ; SEER Program ; Socioeconomic Factors ; }, abstract = {OBJECTIVE: This study examines new socio-ecological variables reflecting community context as predictors of mammography use.

METHODS: The conceptual model is a hybrid of traditional health-behavioral and socio-ecological constructs with an emphasis on spatial interaction among women and their environments, differentiating between several levels of influence for community context. Multilevel probability models of mammography use are estimated. The study sample includes 70,129 women with traditional Medicare fee-for-service coverage for inpatient and outpatient services, drawn from the SEER-Medicare linked data. The study population lives in heterogeneous California, where mammography facilities are dense but utilization rates are low.

RESULTS: Several contextual effects have large significant impacts on the probability of mammography use. Women living in areas with higher proportions of elderly in poverty are 33% less likely to use mammography. However, dually eligible women living in these poor areas are 2% more likely to use mammography than those without extra assistance living in these areas. Living in areas with higher commuter intensity, higher violent crime rates, greater land use mix (urbanicity), or more segregated Hispanic communities exhibit -14%, -1%, -6%, and -3% (lower) probability of use, respectively. Women living in segregated American Indian communities or in communities where more elderly women live alone exhibit 16% and 12% (higher) probability of use, respectively. Minority women living in more segregated communities by their minority are more likely to use mammography, suggesting social support, but this is significant for Native Americans only. Women with disability as their original reason for entitlement are found 40% more likely to use mammography when they reside in communities with high commuter intensity, suggesting greater ease of transportation for them in these environments.

CONCLUSIONS: Socio-ecological variables reflecting community context are important predictors of mammography use in insured elderly populations, often with larger magnitudes of effect than personal characteristics such as race or ethnicity (-3% to -7%), age (-2%), recent address change (-7%), disability (-5%) or dual eligibility status (-1%). Better understanding of community factors can enhance cancer control efforts.}, } @article {pmid19205254, year = {2009}, author = {Yoon, I}, title = {A mixed-method study of Princeville's rebuilding from the flood of 1999: lessons on the importance of invisible community assets.}, journal = {Social work}, volume = {54}, number = {1}, pages = {19-28}, doi = {10.1093/sw/54.1.19}, pmid = {19205254}, issn = {0037-8046}, mesh = {Community Networks/*organization & administration ; *Cooperative Behavior ; Data Collection ; *Facility Design and Construction ; *Floods ; Interviews as Topic ; North Carolina ; Organizational Case Studies ; }, abstract = {Guided by previous studies and the community assets perspective, a concurrent mixed-method case study was conducted five years after a devastating flood to investigate how invisible community assets played a role in Princeville's rebuilding process from the flood of 1999. The independent variables in this study included retrospectively assessed elected leadership, community cohesion, and depression. The dependent variables were the perceived financial recovery to the pre-disaster level and the current emotional status. The quantitative method (n=127) indicates a statistically significant relationship between the retrospectively assessed depression and the financial recovery (Spearman's rho=.327, p<.001). Chi-square coefficient reveals that elected leaders' ability to mobilize needed resources was also significantly related to the financial recovery (Cramers' V=.350, p=.013). Qualitative methods identified the community's symbolic meaning and unique needs of being an aged community as the most precious internal assets of the community during the rebuilding process. Major implications are discussed.}, } @article {pmid19205174, year = {2008}, author = {Robbins, AM and Eckelmann, CM and Quiñones, M}, title = {Forest fires in the insular Caribbean.}, journal = {Ambio}, volume = {37}, number = {7-8}, pages = {528-534}, doi = {10.1579/0044-7447-37.7.528}, pmid = {19205174}, issn = {0044-7447}, mesh = {Caribbean Region ; Conservation of Natural Resources/*methods ; Disasters/prevention & control ; Ecosystem ; *Fires/prevention & control ; Geographic Information Systems ; Satellite Communications ; *Trees ; Tropical Climate ; }, abstract = {This paper presents a summary of the forest fire reports in the insular Caribbean derived from both management reports and an analysis of publicly available Moderate Resolution Imaging Spectrodiometer (MODIS) satellite active fire products from the region. A vast difference between the amount of fires reported by land managers and fire points in the MODIS Fire Information for Resource Management System data can be observed. Future research is recommended to better understand the nature of these differences. While there is a general lack of available statistical data on forest fires in the Caribbean, a few general observations can be made: Forest fires occur mainly in dry forest types (500 to 1000 mm of mean annual rainfall). These are also the areas where most human settlements are located. Lowland high forests and montane forests with higher rainfall (1000 and more mm y(-1)) are less susceptible to forest fire, but they can burn in exceptionally dry years. Most of the dry forest ecosystems in the Caribbean can be considered to be fire-sensitive ecosystems, while the pine forests in the Caribbean (Cuba, Dominican Republic, and the Bahamas) are maintained by wildfires. In fire-sensitive ecosystems, uncontrolled burning often encourages the spread of alien invasive species. A Caribbean Fire Management Cooperation Strategy was developed between 2005 and 2006 under auspices of the Food and Agriculture Organization of the United Nations. This regional strategy aims to strengthen Caribbean fire management networking by encouraging closer collaboration among countries with similar ecological conditions. The strategy for the Caribbean identifies a number of research, training, and management activities to improve wildfire management capacity in the Caribbean.}, } @article {pmid19203376, year = {2009}, author = {Venier, P and De Pittà, C and Bernante, F and Varotto, L and De Nardi, B and Bovo, G and Roch, P and Novoa, B and Figueras, A and Pallavicini, A and Lanfranchi, G}, title = {MytiBase: a knowledgebase of mussel (M. galloprovincialis) transcribed sequences.}, journal = {BMC genomics}, volume = {10}, number = {}, pages = {72}, pmid = {19203376}, issn = {1471-2164}, mesh = {Animals ; Cluster Analysis ; Computational Biology ; *Databases, Genetic ; *Expressed Sequence Tags ; Gene Library ; Genetic Markers ; *Knowledge Bases ; Microsatellite Repeats ; Mytilus/*genetics ; Sequence Analysis, DNA ; User-Computer Interface ; }, abstract = {BACKGROUND: Although bivalves are among the most studied marine organisms due to their ecological role, economic importance and use in pollution biomonitoring, very little information is available on the genome sequences of mussels. This study reports the functional analysis of a large-scale Expressed Sequence Tag (EST) sequencing from different tissues of Mytilus galloprovincialis (the Mediterranean mussel) challenged with toxic pollutants, temperature and potentially pathogenic bacteria.

RESULTS: We have constructed and sequenced seventeen cDNA libraries from different Mediterranean mussel tissues: gills, digestive gland, foot, anterior and posterior adductor muscle, mantle and haemocytes. A total of 24,939 clones were sequenced from these libraries generating 18,788 high-quality ESTs which were assembled into 2,446 overlapping clusters and 4,666 singletons resulting in a total of 7,112 non-redundant sequences. In particular, a high-quality normalized cDNA library (Nor01) was constructed as determined by the high rate of gene discovery (65.6%). Bioinformatic screening of the non-redundant M. galloprovincialis sequences identified 159 microsatellite-containing ESTs. Clusters, consensuses, related similarities and gene ontology searches have been organized in a dedicated, searchable database http://mussel.cribi.unipd.it.

CONCLUSION: We defined the first species-specific catalogue of M. galloprovincialis ESTs including 7,112 unique transcribed sequences. Putative microsatellite markers were identified. This annotated catalogue represents a valuable platform for expression studies, marker validation and genetic linkage analysis for investigations in the biology of Mediterranean mussels.}, } @article {pmid19197672, year = {2009}, author = {Mason, M and Cheung, I and Walker, L}, title = {Creating a geospatial database of risks and resources to explore urban adolescent substance use.}, journal = {Journal of prevention & intervention in the community}, volume = {37}, number = {1}, pages = {21-34}, doi = {10.1080/10852350802498391}, pmid = {19197672}, issn = {1540-7330}, support = {TI15433/TI/CSAT SAMHSA HHS/United States ; }, mesh = {Adolescent ; Adolescent Behavior ; Cognitive Behavioral Therapy ; Databases, Factual ; District of Columbia/epidemiology ; Female ; *Geographic Information Systems ; Humans ; Interviews as Topic ; Male ; *Research Design ; *Residence Characteristics ; Risk ; *Social Environment ; *Substance-Related Disorders/epidemiology/therapy ; *Urban Population/statistics & numerical data ; }, abstract = {This article illustrates the methodology of creating a comprehensive geospatial database in order to systematically understand the social ecology of risk and protection for urban youth. The challenges and future opportunities involved with this complex work were reviewed, and specific examples were provided to guide researchers. Data were collected from a Washington, DC adolescent substance abuse treatment sample to construct a geospatial database to evaluate urban youths' social environmental risk and resources. A geographic information systems (GIS) approach was adopted to integrate a large array of variables at different levels of geography. For example, risk factors included proximity to crime hotspots, and other known potential establishments with negative influence (such as liquor stores). We also used GIS to assess the subjects' accessibility to protective resources such as public libraries, recreational, parks, and police stations. Unique to our method was the collecting and mapping of each teen's activity locations (places they typically frequent). These data form "risk and protection exposure" estimates for each teen. Finally, we illustrated the specific methods for creating a dynamic geospatial database for urban youth and present future analytical approaches and challenges with these type of data.}, } @article {pmid19192828, year = {2008}, author = {Billoir, E and Delignette-Muller, ML and Péry, AR and Charles, S}, title = {A Bayesian approach to analyzing ecotoxicological data.}, journal = {Environmental science & technology}, volume = {42}, number = {23}, pages = {8978-8984}, doi = {10.1021/es801418x}, pmid = {19192828}, issn = {0013-936X}, mesh = {Animals ; *Bayes Theorem ; Copper/toxicity ; Daphnia/drug effects/physiology ; *Databases as Topic ; *Ecotoxicology ; Models, Biological ; Reproduction/drug effects ; Zinc/toxicity ; }, abstract = {Standardized chronic toxicity tests are usually analyzed using a NOEC (no observed effect concentration) or ECx (x% effect concentration) calculation. However,these methods provide very little information for the material cost they entail. It has been proposed that biology-based methods, such as the DEBtox approach, would make better use of the data available. DEBtox deals with the energy balance between physiological processes, and gives insight on how a compound disturbs it. We propose that data analysis can be further improved by estimating the DEBtox parameters using the considerable expertise available in laboratories and/or the literature. The Bayesian inference appears to be an appropriate estimation method for this purpose, as this technique takes expertise into account as prior probability distribution for each parameter, and provides the corresponding posterior distributions given the data. From these posterior distributions, point estimates can easily be deduced, but also credible intervals which are ideal for use in risk assessment. In this paper, we demonstrate this approach through the analysis of two 21-day Daphnia reproduction tests.}, } @article {pmid19188209, year = {2009}, author = {Vardavas, CI and Connolly, GN and Kafatos, AG}, title = {Geographical information systems as a tool for monitoring tobacco industry advertising.}, journal = {Tobacco control}, volume = {18}, number = {3}, pages = {190-196}, doi = {10.1136/tc.2008.026856}, pmid = {19188209}, issn = {1468-3318}, mesh = {Adolescent ; Advertising/*statistics & numerical data ; Child ; Female ; *Geographic Information Systems ; Greece/epidemiology ; Humans ; Male ; Schools ; Smoking/*epidemiology ; Smoking Prevention ; Tobacco Industry/*methods ; }, abstract = {BACKGROUND: Although the use of a geographical information systems (GIS) approach is usually applied to epidemiological disease outbreaks and environmental exposure mapping, it has significant potential as a tobacco control research tool in monitoring point-of-purchase (POP) tobacco advertising.

DESIGN: An ecological study design approach was applied so as to primarily evaluate and interpret the spatial density and intensity of POP and tobacco industry advertisements within <300 m to high schools in Greece with the application of GIS methodology combining mapping, photographing and global positioning data.

RESULTS: The GIS approach identified 133 POP and 44 billboards within 300 m of the school gates of Heraklion schools. On average 13 POP (range 4-21) and 4.4 billboards (range 1-9) were located per school, and all had at least 1 POP within 20 m of the school gate. On average (SD) 9 (6) tobacco advertisements per POP (range 0-25) were noted, and 80% of them were below child height. The GIS protocol identified that kiosks, that were excepted from the Greek ban on tobacco advertising, in comparison to other POP, were found not only to be closer and visible from the school gates (44.1% vs 10.8%, p<0.001) but were also found to have more external advertisements (8 (5) vs 5 (3), p<0.001).

CONCLUSIONS: This study demonstrates the effectiveness of a GIS system in monitoring tobacco industry advertising on a large population-based scale and implies its use as a standardised method for monitoring tobacco industry strategies and tobacco control efforts.}, } @article {pmid19185386, year = {2009}, author = {Bolker, BM and Brooks, ME and Clark, CJ and Geange, SW and Poulsen, JR and Stevens, MH and White, JS}, title = {Generalized linear mixed models: a practical guide for ecology and evolution.}, journal = {Trends in ecology & evolution}, volume = {24}, number = {3}, pages = {127-135}, doi = {10.1016/j.tree.2008.10.008}, pmid = {19185386}, issn = {0169-5347}, mesh = {Bayes Theorem ; *Biological Evolution ; Data Interpretation, Statistical ; *Ecology ; Likelihood Functions ; *Linear Models ; Software ; }, abstract = {How should ecologists and evolutionary biologists analyze nonnormal data that involve random effects? Nonnormal data such as counts or proportions often defy classical statistical procedures. Generalized linear mixed models (GLMMs) provide a more flexible approach for analyzing nonnormal data when random effects are present. The explosion of research on GLMMs in the last decade has generated considerable uncertainty for practitioners in ecology and evolution. Despite the availability of accurate techniques for estimating GLMM parameters in simple cases, complex GLMMs are challenging to fit and statistical inference such as hypothesis testing remains difficult. We review the use (and misuse) of GLMMs in ecology and evolution, discuss estimation and inference and summarize 'best-practice' data analysis procedures for scientists facing this challenge.}, } @article {pmid19183487, year = {2009}, author = {Levine, RS and Yorita, KL and Walsh, MC and Reynolds, MG}, title = {A method for statistically comparing spatial distribution maps.}, journal = {International journal of health geographics}, volume = {8}, number = {}, pages = {7}, pmid = {19183487}, issn = {1476-072X}, mesh = {Africa/epidemiology ; Ecology/*statistics & numerical data ; Environment ; Geographic Information Systems/*statistics & numerical data ; Humans ; *Models, Statistical ; Mpox (monkeypox)/*epidemiology ; Predictive Value of Tests ; Species Specificity ; }, abstract = {BACKGROUND: Ecological niche modeling is a method for estimation of species distributions based on certain ecological parameters. Thus far, empirical determination of significant differences between independently generated distribution maps for a single species (maps which are created through equivalent processes, but with different ecological input parameters), has been challenging.

RESULTS: We describe a method for comparing model outcomes, which allows a statistical evaluation of whether the strength of prediction and breadth of predicted areas is measurably different between projected distributions. To create ecological niche models for statistical comparison, we utilized GARP (Genetic Algorithm for Rule-Set Production) software to generate ecological niche models of human monkeypox in Africa. We created several models, keeping constant the case location input records for each model but varying the ecological input data. In order to assess the relative importance of each ecological parameter included in the development of the individual predicted distributions, we performed pixel-to-pixel comparisons between model outcomes and calculated the mean difference in pixel scores. We used a two sample Student's t-test, (assuming as null hypothesis that both maps were identical to each other regardless of which input parameters were used) to examine whether the mean difference in corresponding pixel scores from one map to another was greater than would be expected by chance alone. We also utilized weighted kappa statistics, frequency distributions, and percent difference to look at the disparities in pixel scores. Multiple independent statistical tests indicated precipitation as the single most important independent ecological parameter in the niche model for human monkeypox disease.

CONCLUSION: In addition to improving our understanding of the natural factors influencing the distribution of human monkeypox disease, such pixel-to-pixel comparison tests afford users the ability to empirically distinguish the significance of each of the diverse environmental parameters included in the modeling process. This method will be particularly useful in situations where the outcomes (maps) appear similar upon visual inspection (as are generated with other modeling programs such as MAXENT), as it allows an investigator the capacity to explore subtle differences among ecological parameters and to demonstrate the individual importance of these factors within an overall model.}, } @article {pmid20525569, year = {2009}, author = {Baum, DA}, title = {Species as ranked taxa.}, journal = {Systematic biology}, volume = {58}, number = {1}, pages = {74-86}, doi = {10.1093/sysbio/syp011}, pmid = {20525569}, issn = {1076-836X}, mesh = {Animals ; *Classification ; Fossils ; Genetic Speciation ; Humans ; Hybridization, Genetic ; Phylogeny ; }, abstract = {Because species names play an important role in scientific communication, it is more important that species be understood to be taxa than that they be equated with functional ecological or evolutionary entities. Although most biologists would agree that taxa are composed of organisms that share a unique common history, 2 major challenges remain in developing a species-as-taxa concept. First, grouping: in the face of genealogical discordance at all levels in the taxonomic hierarchy, how can we understand the nature of taxa? Second, ranking: what criteria should be used to designate certain taxa in a nested series as being species? The grouping problem can be solved by viewing taxa as exclusive groups of organisms- sets of organisms that form a clade for a plurality of the genome (more than any conflicting set). However, no single objective criterion of species rank can be proposed. Instead, the species rank should be assigned by practitioners based on the semisubjective application of a set of species-ranking criteria. Although these criteria can be designed to yield species taxa that approximately match the ecological, evolutionary, and morphological entities that taxonomists have traditionally associated with the species rank, such a correspondence cannot be enforced without undermining the assumption that species are taxa. The challenge and art of monography is to use genealogical and other kinds of data to assign all organisms to one and only one species-ranked taxon. Various implications of the species-as-ranked-taxa view are discussed, including the synchronic nature of taxa, fossil species, the treatment of hybrids, and species nomenclature. I conclude that, although challenges remain, adopting the view that species are ranked taxa will facilitate a much-needed revolution in taxonomy that will allow it to better serve the biodiversity informatic needs of the 21st century.}, } @article {pmid19180702, year = {2009}, author = {Kent, C}, title = {Clement Kent.}, journal = {Current biology : CB}, volume = {19}, number = {2}, pages = {R54-5}, doi = {10.1016/j.cub.2008.10.041}, pmid = {19180702}, issn = {1879-0445}, mesh = {*Computational Biology ; Ecology ; Humans ; Models, Theoretical ; Research ; *Research Personnel ; }, } @article {pmid19179348, year = {2009}, author = {Subramanian, SV and Jones, K and Kaddour, A and Krieger, N}, title = {Revisiting Robinson: the perils of individualistic and ecologic fallacy.}, journal = {International journal of epidemiology}, volume = {38}, number = {2}, pages = {342-60; author reply 370-3}, pmid = {19179348}, issn = {1464-3685}, support = {K25 HL081275/HL/NHLBI NIH HHS/United States ; }, mesh = {*Bias ; *Data Interpretation, Statistical ; Education/history/legislation & jurisprudence ; Educational Status ; Ethnicity/psychology/statistics & numerical data ; History, 20th Century ; Humans ; Individuality ; Prejudice ; Social Conditions ; United States ; }, abstract = {BACKGROUND: W S Robinson made a seminal contribution by demonstrating that correlations for the same two variables can be different at the individual and ecologic level. This study reanalyzes and historically situates Robinson's influential study that laid the foundation for the primacy of analyzing data at only the individual level.

METHODS: We applied a binomial multilevel logistic model to analyse variation in illiteracy as enumerated by the 1930 US. Census (the same data as used by Robinson). The outcome was log odds of being illiterate, while predictors were race/nativity ('native whites', 'foreign-born whites' and 'negroes') at the individual-level, and presence of Jim Crow segregation laws for education at the state-level. We conducted historical research to identify the social and scientific context within which Robinson's study was produced and favourably received.

RESULTS: Empirically, the substantial state variations in illiteracy could not be accounted by the states' race/nativity composition. Different approaches to modelling state-effects yielded considerably attenuated associations at the individual-level between illiteracy and race/nativity. Furthermore, state variation in illiteracy was different across the race/nativity groups, with state variation being largest for whites and least for foreign-born whites. Strong effects of Jim Crow education laws on illiteracy were observed with the effect being strongest for blacks. Historically, Robinson's study was consonant with the post-World War II ascendancy of methodological individualism.

CONCLUSION: Applying a historically informed multilevel perspective to Robinson's profoundly influential study, we demonstrate that meaningful analysis of individual-level relationships requires attention to substantial heterogeneity in state characteristics. The implication is that perils are posed by not only ecological fallacy but also individualistic fallacy. Multilevel thinking, grounded in historical and spatiotemporal context, is thus a necessity, not an option.}, } @article {pmid19179345, year = {2009}, author = {Firebaugh, G}, title = {Commentary: 'Is the social world flat? W.S. Robinson and the ecologic fallacy'.}, journal = {International journal of epidemiology}, volume = {38}, number = {2}, pages = {368-70; author reply 370-3}, doi = {10.1093/ije/dyn355}, pmid = {19179345}, issn = {1464-3685}, mesh = {*Bias ; Black People/psychology/statistics & numerical data ; Data Interpretation, Statistical ; Humans ; Politics ; *Social Conditions ; }, } @article {pmid19178139, year = {2009}, author = {Borenstein, E and Feldman, MW}, title = {Topological signatures of species interactions in metabolic networks.}, journal = {Journal of computational biology : a journal of computational molecular cell biology}, volume = {16}, number = {2}, pages = {191-200}, pmid = {19178139}, issn = {1557-8666}, support = {R01 GM028016/GM/NIGMS NIH HHS/United States ; R01 GM028016-28/GM/NIGMS NIH HHS/United States ; GM28016/GM/NIGMS NIH HHS/United States ; }, mesh = {*Algorithms ; Animals ; Bacteria/classification/genetics/*metabolism ; Computational Biology/methods ; Ecosystem ; *Host-Parasite Interactions ; Humans ; *Metabolic Networks and Pathways ; Metabolomics/methods ; *Models, Biological ; Phylogeny ; Protein Interaction Mapping ; }, abstract = {The topology of metabolic networks can provide insight not only into the metabolic processes that occur within each species, but also into interactions between different species. Here, we introduce a novel pair-wise, topology-based measure of biosynthetic support, reflecting the extent to which the nutritional requirements of one species could be satisfied by the biosynthetic capacity of another. To evaluate the biosynthetic support for a given pair of species, we use a graph-based algorithm to identify the set of exogenously acquired compounds in the metabolic network of the first species, and calculate the fraction of this set that occurs in the metabolic network of the second species. Reconstructing the metabolic network of 569 bacterial species and several eukaryotes, and calculating the biosynthetic support score for all bacterial-eukaryotic pairs, we show that this measure indeed reflects host-parasite interactions and facilitates a successful prediction of such interactions on a large-scale. Integrating this method with phylogenetic analysis and calculating the biosynthetic support of ancestral species in the Firmicutes division (as well as other bacterial divisions) further reveals a large-scale evolutionary trend of biosynthetic capacity loss in parasites. The inference of ecological features from genomic-based data presented here lays the foundations for an exciting "reverse ecology" framework for studying the complex web of interactions characterizing various ecosystems.}, } @article {pmid19174924, year = {2008}, author = {Kapo, KE and Burton, GA and de Zwart, D and Posthuma, L and Dyer, SD}, title = {Quantitative lines of evidence for screening-level diagnostic assessment of regional fish community impacts: a comparison of spatial database evaluation methods.}, journal = {Environmental science & technology}, volume = {42}, number = {24}, pages = {9412-9418}, doi = {10.1021/es702998r}, pmid = {19174924}, issn = {0013-936X}, mesh = {Animals ; *Ecosystem ; Fishes/*physiology ; Geographic Information Systems ; Geography ; Logistic Models ; Ohio ; *Stress, Physiological ; }, abstract = {Determination of local ecological impacts and stressor identification in aquatic ecosystems is increasingly needed and required for designing effective watershed management plans in various jurisdictions. Spatial database evaluation methods applied to available environmental data resources can provide screening-level, geographically based stressor identification hypotheses. Cross-comparison of the output of independent methods is a critical step to address common concerns with the interpretation of output, identify strengths and weaknesses, and reduce uncertainty. Two current approaches were compared in this study: (1) the "Effect and Probable Cause" (EPC) method and (2) a GIS "Weights-of-Evidence/Weighted Logistic Regression" (WOE/WLR) method. The methods were applied to the same Ohio (U.S.) spatial data resources to link impacts on local fish assemblages with various natural and anthropogenic stressors. The methods generally yielded significantly similar results in the identification of stressors and their relative influence. However, key differences were also observed between the methods which reflected the distinctive objectives and sensitivities of each. The findings show that scientific interpretation of analysis output requires an understanding of method characteristics, and suggests the potential value of utilizing multiple methods as quantitative lines of evidence in screening-level regional diagnostic assessment.}, } @article {pmid19174541, year = {2009}, author = {Oakes, JM}, title = {Commentary: Individual, ecological and multilevel fallacies.}, journal = {International journal of epidemiology}, volume = {38}, number = {2}, pages = {361-8; author reply 370-3}, doi = {10.1093/ije/dyn356}, pmid = {19174541}, issn = {1464-3685}, mesh = {*Bias ; *Data Interpretation, Statistical ; Education/history/legislation & jurisprudence ; Educational Status ; History, 20th Century ; Humans ; Individuality ; Models, Statistical ; Prejudice ; Social Conditions ; United States ; }, } @article {pmid19172194, year = {2008}, author = {Mukherjee, J and Llewellyn, LE and Evans-Illidge, EA}, title = {A tropical marine microbial natural products geobibliography as an example of desktop exploration of current research using web visualisation tools.}, journal = {Marine drugs}, volume = {6}, number = {4}, pages = {550-577}, pmid = {19172194}, issn = {1660-3397}, mesh = {Animals ; Biodiversity ; *Biological Products ; *Databases, Bibliographic ; Drug Discovery/methods ; *Geographic Information Systems ; Internet ; Marine Biology/*methods ; Software ; Tropical Climate ; }, abstract = {Microbial marine biodiscovery is a recent scientific endeavour developing at a time when information and other technologies are also undergoing great technical strides. Global visualisation of datasets is now becoming available to the world through powerful and readily available software such as Worldwind, ArcGIS Explorer and Google Earth. Overlaying custom information upon these tools is within the hands of every scientist and more and more scientific organisations are making data available that can also be integrated into these global visualisation tools. The integrated global view that these tools enable provides a powerful desktop exploration tool. Here we demonstrate the value of this approach to marine microbial biodiscovery by developing a geobibliography that incorporates citations on tropical and near-tropical marine microbial natural products research with Google Earth and additional ancillary global data sets. The tools and software used are all readily available and the reader is able to use and install the material described in this article.}, } @article {pmid19164513, year = {2009}, author = {Johnson, CK and Tinker, MT and Estes, JA and Conrad, PA and Staedler, M and Miller, MA and Jessup, DA and Mazet, JA}, title = {Prey choice and habitat use drive sea otter pathogen exposure in a resource-limited coastal system.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {106}, number = {7}, pages = {2242-2247}, pmid = {19164513}, issn = {1091-6490}, mesh = {Animal Nutrition Sciences ; Animals ; California ; Choice Behavior ; Conservation of Natural Resources ; Databases, Factual ; Diet ; Ecology ; Ecosystem ; Food Chain ; Otters/immunology/*parasitology/*physiology ; Sarcocystis/metabolism ; Toxoplasma/metabolism ; Toxoplasmosis, Animal/epidemiology/immunology ; }, abstract = {The processes promoting disease in wild animal populations are highly complex, yet identifying these processes is critically important for conservation when disease is limiting a population. By combining field studies with epidemiologic tools, we evaluated the relationship between key factors impeding southern sea otter (Enhydra lutris nereis) population growth: disease and resource limitation. This threatened population has struggled to recover despite protection, so we followed radio-tagged sea otters and evaluated infection with 2 disease-causing protozoal pathogens, Toxoplasma gondii and Sarcocystis neurona, to reveal risks that increased the likelihood of pathogen exposure. We identified patterns of pathogen infection that are linked to individual animal behavior, prey choice, and habitat use. We detected a high-risk spatial cluster of S. neurona infections in otters with home ranges in southern Monterey Bay and a coastal segment near San Simeon and Cambria where otters had high levels of infection with T. gondii. We found that otters feeding on abalone, which is the preferred prey in a resource-abundant marine ecosystem, had a very low risk of infection with either pathogen, whereas otters consuming small marine snails were more likely to be infected with T. gondii. Individual dietary specialization in sea otters is an adaptive mechanism for coping with limited food resources along central coastal California. High levels of infection with protozoal pathogens may be an adverse consequence of dietary specialization in this threatened species, with both depleted resources and disease working synergistically to limit recovery.}, } @article {pmid19161432, year = {2009}, author = {Urban, DL and Minor, ES and Treml, EA and Schick, RS}, title = {Graph models of habitat mosaics.}, journal = {Ecology letters}, volume = {12}, number = {3}, pages = {260-273}, doi = {10.1111/j.1461-0248.2008.01271.x}, pmid = {19161432}, issn = {1461-0248}, mesh = {Conservation of Natural Resources ; *Ecosystem ; Geographic Information Systems ; *Models, Biological ; Population Dynamics ; }, abstract = {Graph theory is a body of mathematics dealing with problems of connectivity, flow, and routing in networks ranging from social groups to computer networks. Recently, network applications have erupted in many fields, and graph models are now being applied in landscape ecology and conservation biology, particularly for applications couched in metapopulation theory. In these applications, graph nodes represent habitat patches or local populations and links indicate functional connections among populations (i.e. via dispersal). Graphs are models of more complicated real systems, and so it is appropriate to review these applications from the perspective of modelling in general. Here we review recent applications of network theory to habitat patches in landscape mosaics. We consider (1) the conceptual model underlying these applications; (2) formalization and implementation of the graph model; (3) model parameterization; (4) model testing, insights, and predictions available through graph analyses; and (5) potential implications for conservation biology and related applications. In general, and for a variety of ecological systems, we find the graph model a remarkably robust framework for applications concerned with habitat connectivity. We close with suggestions for further work on the parameterization and validation of graph models, and point to some promising analytic insights.}, } @article {pmid19155068, year = {2009}, author = {Schäfers, C and Boshof, U and Jürling, H and Belanger, SE and Sanderson, H and Dyer, SD and Nielsen, AM and Willing, A and Gamon, K and Kasai, Y and Eadsforth, CV and Fisk, PR and Girling, AE}, title = {Environmental properties of long-chain alcohols. Part 2: Structure-activity relationship for chronic aquatic toxicity of long-chain alcohols.}, journal = {Ecotoxicology and environmental safety}, volume = {72}, number = {4}, pages = {996-1005}, doi = {10.1016/j.ecoenv.2008.07.019}, pmid = {19155068}, issn = {1090-2414}, mesh = {Animals ; Daphnia ; Data Interpretation, Statistical ; Environmental Monitoring ; Fatty Alcohols/*toxicity ; Growth/drug effects ; Quantitative Structure-Activity Relationship ; Reproducibility of Results ; Reproduction ; Risk Assessment ; Solutions/analysis ; Survival ; Water/chemistry ; Water Pollutants, Chemical/*toxicity ; }, abstract = {Daphnia magna reproduction tests were performed with C(10), C(12), C(14) and C(15) alcohols to establish a structure-activity relationship of chronic effects of long-chain alcohols. The data generation involved substantial methodological efforts due to the exceptionally rapid biodegradability of the test substances and the need to test as close as possible to their water solubility limits. Test concentrations were determined by GC-MS before and after test solution renewal. Whereas apparent toxicity based on survival and reproduction increased with increasing C-chain lengths up to C(14), observations of toxicity to C(15) alcohol were not in line with lower chain lengths due to the lack of toxicity below the level of water solubility. When omitting C(15), the slope of most (Q)SARs approach -1, being consistent with the expectation of a non-polar narcotic mode of action. Further testing at higher chain lengths is not sensible due to progressively lower solubility, at remaining biodegradability. Effects on mortality and reproduction are not expected below the level of water solubility.}, } @article {pmid19151444, year = {2008}, author = {Merem, EC and Twumasi, YA}, title = {Using spatial information technologies as monitoring devices in international watershed conservation along the Senegal River Basin of West Africa.}, journal = {International journal of environmental research and public health}, volume = {5}, number = {5}, pages = {464-476}, pmid = {19151444}, issn = {1660-4601}, mesh = {Africa ; Conservation of Natural Resources/*methods ; Ecosystem ; Employment ; *Geographic Information Systems ; Humans ; International Cooperation ; Maps as Topic ; *Rivers ; Spacecraft ; Time Factors ; *Water Movements ; }, abstract = {In this paper, we present the applications of spatial technologies-Geographic Information Systems (GIS) and remote sensing-in the international monitoring of river basins particularly analyzing the ecological, hydrological, and socio-economic issues along the Senegal River. The literature on multinational water crisis has for decades focused on mediation aspects of trans-boundary watershed management resulting in limited emphasis placed on the application of advances in geo-spatial information technologies in multinational watershed conservation in the arid areas of the West African sub-region within the Senegal River Basin for decision-making and monitoring. While the basin offers life support in a complex ecosystem that stretches across different nations in a mostly desert region characterized by water scarcity and subsistence economies, there exists recurrent environmental stress induced by both socio-economic and physical factors. Part of the problems consists of flooding, drought and limited access to sufficient quantities of water. These remain particularly sensitive issues that are crucial for the health of a rapidly growing population and the economy. The problems are further compounded due to the threats of climate change and the resultant degradation of almost the region's entire natural resources base. While the pace at which the institutional framework for managing the waters offers opportunities for hydro electricity and irrigated agriculture through the proliferation of dams, it has raised other serious concerns in the region. Even where data exists for confronting these issues, some of them are incompatible and dispersed among different agencies. This not only widens the geo-spatial data gaps, but it hinders the ability to monitor water problems along the basin. This study will fill that gap in research through mix scale methods built on descriptive statistics, GIS and remote sensing techniques by generating spatially referenced data to supplement the existing ones for the management of the Senegal River Basin. The results show the incidence of change predicated on pressures from demography, natural forces and the proliferation of river basin development which resulted in more irrigated areas to meet the needs of the inhabitants of the basin. With the substantial increase in bare surface areas, the basin faces growing exposure to the threats of desertification.}, } @article {pmid19148634, year = {2009}, author = {Pacharawongsakda, E and Yokwai, S and Ingsriswang, S}, title = {Potential natural product discovery from microbes through a diversity-guided computational framework.}, journal = {Applied microbiology and biotechnology}, volume = {82}, number = {3}, pages = {579-586}, doi = {10.1007/s00253-008-1847-x}, pmid = {19148634}, issn = {1432-0614}, mesh = {Bacteria/*chemistry/classification/genetics/metabolism ; *Biodiversity ; Biological Products/chemistry/genetics/metabolism ; Computational Biology/*methods ; Drug Discovery/*methods ; Internet ; Phylogeny ; Software ; }, abstract = {As the occurrence of natural compounds is related to the spatial distribution and evolution of microorganisms for biological and ecological relevance, the data integration of chemistry, geography, and phylogeny within an analytical framework is needed to make better decisions on sourcing the microbes for drug discovery. Such a framework should help researcher to decide on (a) which microorganisms are capable to produce the structurally diverse-bioactive compounds and (b) where those microbes could be found. Here, we present GIST (Geospatial Integrated Species, sites and bioactive compound relationships Tracking tool), a computational framework that could describe and compare how the chemical and genetic diversity varied among microbes in different areas. GIST mainly exploits the measures of bioactive diversity (BD) and phylogenetic diversity (PD), derived from the branch length of bioactive dendrogram and phylogenetic tree, respectively. Based on BD and PD, our framework could provide guidance and tools for measuring, monitoring, and evaluating of patterns and changes in biodiversity of microorganisms to improve the success rate of drug discovery.}, } @article {pmid19144393, year = {2009}, author = {Shih, YC and Chou, CL and Chiau, WY}, title = {Geographic information system applied to measuring benthic environmental impact with chemical measures on mariculture at Penghu Islet in Taiwan.}, journal = {The Science of the total environment}, volume = {407}, number = {6}, pages = {1824-1833}, doi = {10.1016/j.scitotenv.2008.11.064}, pmid = {19144393}, issn = {0048-9697}, mesh = {Animals ; Aquaculture/*methods ; *Environment ; Geographic Information Systems ; Geologic Sediments/*analysis ; Oxidation-Reduction ; Perciformes/*growth & development ; Taiwan ; }, abstract = {Cobia, Rachycentron canadum, is currently grown by marine aquaculture in Taiwan, particularly on Penghu Islet. Although the effect of marine aquaculture on the environment has been the subject of many studies, an understanding of its environmental impact has yet to be attained, and the continuing expansion of cage farming has caused noticeable ecological declines. Nevertheless, useful tools to measure this environmental degradation are scant. The results of this study suggest that the combination of a geographic information system (GIS) with redox potential and sulfide measurements can be used to definitively assess the condition of the benthic environment near cobia aquaculture sites and to help develop environmental monitoring programs. These applications could easily be adopted to assess multiple marine environmental conditions.}, } @article {pmid19137735, year = {2008}, author = {Ignjatović-Micić, D and Drinić, SM and Nikolić, A and Lazić-Jancić, V}, title = {Ssr analysis for genetic structure and diversity determination of maize local populations from former Yugoslavia territories.}, journal = {Genetika}, volume = {44}, number = {11}, pages = {1517-1524}, pmid = {19137735}, issn = {0016-6758}, mesh = {DNA Fingerprinting/methods ; DNA, Plant/*metabolism ; Databases, Genetic ; Genetic Markers/genetics ; *Polymorphism, Genetic ; Yugoslavia ; Zea mays/*genetics ; }, abstract = {A collection of 2178 local populations from ex-Yugoslavia territories is maintained in Maize Research Institute (MRI) gene bank. These populations were characterized mainly by morphological markers. In this work 21 local populations belonging to seven different agro-ecological groups have been subjected to SSR analysis using a DNA-pooling strategy. The objective of this work was to develop genetic fingerprints for characterization, identification and classification of the populations, as well as for estimation of their genetic diversity. Also, a DNA-pooling strategy was employed with the aim to certify if it could be applied for population analysis with SSR markers. Statistical analysis of 25 informative SSR primers revealing 224 alleles (bands) showed that the average within-population mean number of alleles was 2.55, the average values for total and within-population diversity were 0.784 and 0.502, respectively and G(ST) value was 0.360. Genetic distance values calculated using Modified Rogers' Distance were in the range from 0.35 to 0.60. The silver staining method of DNA used for bulked samples showed some weakness that could be overcome with a more sensitive staining method. Nevertheless, the results in this work indicate that the SSR analysis of bulks could be used for characterizing a large number of populations in gene banks.}, } @article {pmid19132821, year = {2009}, author = {von der Ohe, PC and De Deckere, E and Prüss, A and Muñoz, I and Wolfram, G and Villagrasa, M and Ginebreda, A and Hein, M and Brack, W}, title = {Toward an integrated assessment of the ecological and chemical status of European river basins.}, journal = {Integrated environmental assessment and management}, volume = {5}, number = {1}, pages = {50-61}, doi = {10.1897/IEAM_2008-043.1}, pmid = {19132821}, issn = {1551-3777}, mesh = {Databases, Factual ; *Ecosystem ; Environmental Monitoring/*methods ; Europe ; European Union ; Government Regulation ; Models, Theoretical ; Risk Assessment ; Rivers/*chemistry ; Water Movements ; Water Pollutants, Chemical/*chemistry/toxicity ; Water Pollution, Chemical/prevention & control ; }, abstract = {Here, recommendations to improve ecological and chemical status assessments in accordance with the European Water Framework Directive (WFD) are made on the basis of experience gained from the MODELKEY project database, linking existing biological and chemical monitoring data of 3 case study river basins (Elbe, Scheldt, and Llobregat). The data analysis within and across river basins revealed major obstacles to be tackled, including scarcity of matching ecological and chemical monitoring sites for cause-effect relationships as well as a general lack of stressor-specific metrics for single biological quality elements (BQE) to enable a comprehensive risk assessment of all predominant stressors, including toxicity. An example of such a metric, which is recommended for the BQE of benthic macroinvertebrates, is the trait-based species-at-risk index (SPEAR) that correlated well with a respective measure for toxic stress, referred to as toxic units, based on simple mixture toxicity concepts. Surprisingly, the assessment of chemical status of a total of 695 monitoring sites for 2000 to 2004 showed that environmental quality standards (EQSs) were exceeded for at least 1 of the currently 41 priority pollutants (PPs) in 92% to 98% of the cases in all 3 of the river basins, which, according to definition, indicates potential effects on ecological status. A comparison of compliance with EQSs for 41 PPs with a respective effect threshold (derived for benthic macroinvertebrates) revealed that the rather conservative concept of chemical status is most likely not protective in all cases. Furthermore, to account for the many other compounds that are detected frequently in European surface waters and that may also have ecotoxicological effects, we introduced a provisional predicted no-effect concentration that is in accordance with the EQS methodology and is suggested to identify potential emerging compounds for which no or insufficient toxicity data exist. In conclusion, this study aims to support the implementation of the WFD by drawing conclusions from the analysis of heterogeneous data sets of various member states and by introducing new tools to move toward an integrated European assessment of ecological and chemical status.}, } @article {pmid19132081, year = {2009}, author = {Wang, Z and Zhang, J}, title = {Why is the correlation between gene importance and gene evolutionary rate so weak?.}, journal = {PLoS genetics}, volume = {5}, number = {1}, pages = {e1000329}, pmid = {19132081}, issn = {1553-7404}, mesh = {Algorithms ; *Computational Biology ; Computer Simulation ; Conserved Sequence/genetics ; *Evolution, Molecular ; *Genes, Fungal ; Metabolic Networks and Pathways/genetics ; Models, Genetic ; Mutation ; Saccharomyces cerevisiae/*genetics ; Saccharomyces cerevisiae Proteins/genetics ; Statistics, Nonparametric ; }, abstract = {One of the few commonly believed principles of molecular evolution is that functionally more important genes (or DNA sequences) evolve more slowly than less important ones. This principle is widely used by molecular biologists in daily practice. However, recent genomic analysis of a diverse array of organisms found only weak, negative correlations between the evolutionary rate of a gene and its functional importance, typically measured under a single benign lab condition. A frequently suggested cause of the above finding is that gene importance determined in the lab differs from that in an organism's natural environment. Here, we test this hypothesis in yeast using gene importance values experimentally determined in 418 lab conditions or computationally predicted for 10,000 nutritional conditions. In no single condition or combination of conditions did we find a much stronger negative correlation, which is explainable by our subsequent finding that always-essential (enzyme) genes do not evolve significantly more slowly than sometimes-essential or always-nonessential ones. Furthermore, we verified that functional density, approximated by the fraction of amino acid sites within protein domains, is uncorrelated with gene importance. Thus, neither the lab-nature mismatch nor a potentially biased among-gene distribution of functional density explains the observed weakness of the correlation between gene importance and evolutionary rate. We conclude that the weakness is factual, rather than artifactual. In addition to being weakened by population genetic reasons, the correlation is likely to have been further weakened by the presence of multiple nontrivial rate determinants that are independent from gene importance. These findings notwithstanding, we show that the principle of slower evolution of more important genes does have some predictive power when genes with vastly different evolutionary rates are compared, explaining why the principle can be practically useful despite the weakness of the correlation.}, } @article {pmid19129846, year = {2009}, author = {Rabosky, DL and Sorhannus, U}, title = {Diversity dynamics of marine planktonic diatoms across the Cenozoic.}, journal = {Nature}, volume = {457}, number = {7226}, pages = {183-186}, pmid = {19129846}, issn = {1476-4687}, mesh = {*Biodiversity ; *Biological Evolution ; Databases, Factual ; Diatoms/classification/*physiology ; Fossils ; History, Ancient ; Phytoplankton/classification/*physiology ; Poaceae ; Time Factors ; }, abstract = {Diatoms are the dominant group of phytoplankton in the modern ocean. They account for approximately 40% of oceanic primary productivity and over 50% of organic carbon burial in marine sediments. Owing to their role as a biological carbon pump and effects on atmospheric CO(2) levels, there is great interest in elucidating factors that influenced the rapid rise in diatom diversity during the past 40 million years. Two biotic controls on diversification have been proposed to explain this diversity increase: (1) geochemical coupling between terrestrial grasslands and marine ecosystems through the global silicon cycle; and (2) competitive displacement of other phytoplankton lineages. However, these hypotheses have not been tested using sampling-standardized fossil data. Here we show that reconstructions of species diversity in marine phytoplankton reject these proposed controls and suggest a new pattern for oceanic diatom diversity across the Cenozoic. Peak species diversity in marine planktonic diatoms occurred at the Eocene-Oligocene boundary and was followed by a pronounced decline, from which diversity has not recovered. Although the roles of abiotic and biotic drivers of diversification remain unclear, major features of oceanic diatom evolution are decoupled from both grassland expansion and competition among phytoplankton groups.}, } @article {pmid19128526, year = {2009}, author = {Mahone, EM and Martin, R and Kates, WR and Hay, T and Horská, A}, title = {Neuroimaging correlates of parent ratings of working memory in typically developing children.}, journal = {Journal of the International Neuropsychological Society : JINS}, volume = {15}, number = {1}, pages = {31-41}, pmid = {19128526}, issn = {1469-7661}, support = {HD-24061/HD/NICHD NIH HHS/United States ; R01 NS042851/NS/NINDS NIH HHS/United States ; UL1 RR025005/RR/NCRR NIH HHS/United States ; P30 HD024061/HD/NICHD NIH HHS/United States ; P50 HD052121/HD/NICHD NIH HHS/United States ; M01 RR000052/RR/NCRR NIH HHS/United States ; R01 NS04285/NS/NINDS NIH HHS/United States ; M01 RR000052-466626/RR/NCRR NIH HHS/United States ; P50 HD052121-016297/HD/NICHD NIH HHS/United States ; P30 HD024061-21/HD/NICHD NIH HHS/United States ; R01 NS042851-04/NS/NINDS NIH HHS/United States ; }, mesh = {Adolescent ; Brain/*anatomy & histology ; Child ; Child, Preschool ; Data Interpretation, Statistical ; Female ; Humans ; *Magnetic Resonance Imaging ; Male ; Memory, Short-Term/*physiology ; Neuropsychological Tests ; *Parents ; Psychomotor Performance/*physiology ; Vocabulary ; }, abstract = {The purpose of the present study was to investigate construct validity of parent ratings of working memory in children, using a multi-trait/multi-method design including neuroimaging, rating scales, and performance-based measures. Thirty-five typically developing children completed performance-based tests of working memory and nonexecutive function (EF) skills, received volumetric MRI, and were rated by parents on both EF-specific and broad behavior rating scales. After controlling for total cerebral volume and age, parent ratings of working memory were significantly correlated with frontal gray, but not temporal, parietal, or occipital gray, or any lobar white matter volumes. Performance-based measures of working memory were also moderately correlated with frontal lobe gray matter volume; however, non-EF parent ratings and non-EF performance-based measures were not correlated with frontal lobe volumes. Results provide preliminary support for the convergent and discriminant validity of parent ratings of working memory, and emphasize their utility in exploring brain-behavior relationships in children. Rating scales that directly examine EF skills may potentially have ecological validity, not only for "everyday" function, but also as correlates of brain volume. (JINS, 2009, 15, 31-41.).}, } @article {pmid19126223, year = {2009}, author = {Wurm, Y and Uva, P and Ricci, F and Wang, J and Jemielity, S and Iseli, C and Falquet, L and Keller, L}, title = {Fourmidable: a database for ant genomics.}, journal = {BMC genomics}, volume = {10}, number = {}, pages = {5}, pmid = {19126223}, issn = {1471-2164}, mesh = {Animals ; Ants/*genetics ; Computational Biology/methods ; *Databases, Genetic ; Expressed Sequence Tags ; Genomics/*methods ; Oligonucleotide Array Sequence Analysis ; }, abstract = {BACKGROUND: Fourmidable is an infrastructure to curate and share the emerging genetic, molecular, and functional genomic data and protocols for ants.

DESCRIPTION: The Fourmidable assembly pipeline groups nucleotide sequences into clusters before independently assembling each cluster. Subsequently, assembled sequences are annotated via Interproscan and BLAST against general and insect-specific databases. Gene-specific information can be retrieved using gene identifiers, searching for similar sequences or browsing through inferred Gene Ontology annotations. The database will readily scale as ultra-high throughput sequence data and sequences from additional species become available.

CONCLUSION: Fourmidable currently houses EST data from two ant species and microarray gene expression data for one of these. Fourmidable is publicly available at http://fourmidable.unil.ch.}, } @article {pmid19120176, year = {2008}, author = {Holzmuller, P and Grébaut, P and Brizard, JP and Berthier, D and Chantal, I and Bossard, G and Bucheton, B and Vezilier, F and Chuchana, P and Bras-Gonçalves, R and Lemesre, JL and Vincendeau, P and Cuny, G and Frutos, R and Biron, DG}, title = {"Pathogeno-proteomics".}, journal = {Annals of the New York Academy of Sciences}, volume = {1149}, number = {}, pages = {66-70}, doi = {10.1196/annals.1428.061}, pmid = {19120176}, issn = {1749-6632}, mesh = {Computational Biology ; *Proteomics ; }, abstract = {Many scientists working on pathogens (viruses, bacteria, fungi, parasites) are betting heavily on data generated by longitudinal genomic-transcriptomic-proteomic studies to explain biochemical host-vector-pathogen interactions and thus to contribute to disease control. Availability of genome sequences of various organisms, from viruses to complex metazoans, led to the discovery of the functions of the genes themselves. The postgenomic era stimulated the development of proteomic and bioinformatics tools to identify the locations, functions, and interactions of the gene products in tissues and/or cells of living organisms. Because of the diversity of available methods and the level of integration they promote, proteomics tools are potentially able to resolve interesting issues specific not only to host-vector-pathogen interactions in cell immunobiology, but also to ecology and evolution, population biology, and adaptive processes. These new analytical tools, as all new tools, contain pitfalls directly related to experimental design, statistical treatment, and protein identification. Nevertheless, they offer the potency of building large protein-protein interaction networks for in silico analysis of novel biological entities named "interactomes," a way of modeling host-vector-pathogen interactions to define new interference strategies.}, } @article {pmid19119995, year = {2009}, author = {Libeskind-Hadas, R and Charleston, MA}, title = {On the computational complexity of the reticulate cophylogeny reconstruction problem.}, journal = {Journal of computational biology : a journal of computational molecular cell biology}, volume = {16}, number = {1}, pages = {105-117}, doi = {10.1089/cmb.2008.0084}, pmid = {19119995}, issn = {1557-8666}, mesh = {Algorithms ; *Biological Evolution ; Computational Biology/*methods ; Models, Theoretical ; *Phylogeny ; Time Factors ; }, abstract = {The cophylogeny reconstruction problem is that of finding minimal cost explanations of differences between evolutionary histories of ecologically linked groups of biological organisms. We present a proof that shows that the general problem of reconciling evolutionary histories is NP-complete and provide a sharp boundary where this intractability begins. We also show that a related problem, that of finding Pareto optimal solutions, is NP-hard. As a byproduct of our results, we give a framework by which meta-heuristics can be applied to find good solutions to this problem.}, } @article {pmid20351942, year = {2009}, author = {Weiss, JB and Lorenzi, NM}, title = {Building a shared vision for an online cancer survivorship community.}, journal = {AMIA ... Annual Symposium proceedings. AMIA Symposium}, volume = {2009}, number = {}, pages = {690-694}, pmid = {20351942}, issn = {1942-597X}, support = {T15 LM007450/LM/NLM NIH HHS/United States ; 5 T15 LM007450-07/LM/NLM NIH HHS/United States ; }, mesh = {Community Networks ; Cooperative Behavior ; Humans ; Information Services ; *Neoplasms/psychology ; *Online Systems ; Patient Participation ; *Self-Help Groups ; Social Support ; *Survivors ; }, abstract = {In order to achieve comprehensive, closed-loop care for cancer survivors, new strategies are needed to bring together patients, providers, and support services in local communities. To address this challenge, an online community for cancer survivorship was envisioned and designed collaboratively by cancer survivors, family members, community professionals, and informatics researchers in middle Tennessee. The vision developed by the community members serves as a foundation for medical informatics systems to build capacity in local communities to improve cancer care and social support. Using ecological systems theory and social capital as theoretical frameworks, key themes are identified for the future of communication and collaboration in cancer survivorship.}, } @article {pmid19110939, year = {2009}, author = {TenBrook, PL and Tjeerdema, RS and Hann, P and Karkoski, J}, title = {Methods for deriving pesticide aquatic life criteria.}, journal = {Reviews of environmental contamination and toxicology}, volume = {199}, number = {}, pages = {19-109}, pmid = {19110939}, issn = {0179-5953}, mesh = {Animals ; Data Interpretation, Statistical ; Databases, Factual ; Fresh Water ; Humans ; Pesticide Residues/*analysis/*toxicity ; Water Pollutants, Chemical/*analysis/*toxicity ; }, abstract = {Environmental regulators charged with protecting water quality must have scientifically defensible water quality goals. For protection of aquatic life, regulators need to know what levels of contaminants a water body can tolerate, without producing adverse effects. The USEPA has developed water quality criteria for many chemicals, but few are for current-use pesticides. Other countries also derive aquatic life criteria utilizing a variety of methodologies. As a prelude to developing a new criteria derivation methodology, this chapter explores the current state of aquatic life criteria derivation around the world. Rather than discussing each methodology independently, this review is organized according to critical elements that must be part of a scientifically defensible methodology. All of the reviewed methodologies rely on effects data to derive aquatic life criteria. Water quality criteria may be derived from single-species toxicity data by statistical extrapolation procedures (for adequate data sets), or by use of empirically based AFs (for data sets of any size). Assessment factor methods are conservative and have a low probability of underestimating risk, with a concomitant high probability of overestimating risk. Extrapolation methods may also under-, or overestimate risk, but uncertainty is quantifiable and is reduced when larger data sets are used. Although less common, methods are also available for criteria derivation using multispecies toxicity data. Environmental toxicity of chemicals is affected by several factors. Some of these factors can be addressed in criteria derivation, and some cannot. For example, factors such as magnitude, duration and frequency of exposure may be incorporated into criteria, either through use of time-to-event and population models or by derivation of both acute and chronic criteria that have duration and frequency components. Aquatic species may be exposed to hydrophobic organic chemicals by multiple routes. They may take up residues directly from water, or may be exposed dietarily, or combinations of both. Unfortunately, to properly address such multiple routes in criteria derivation, food web models are needed that work for chemicals that have specific modes of action. Similarly, both bioavailability and toxicity parameters may contribute to derivation of criteria, providing sufficient data are available. Ecotoxicological effects and physical-chemical data are needed for criteria derivation. The quality and quantity of required data are clearly stated in existing methodologies; some guidelines provide very specific data quality requirements. The level of detail provided by guidelines varies among methodologies. Most helpful are those that provide lists of acceptable data sources, descriptions of adequate data searches, schemes for rating ecotoxicity data, specifications of required data types (e.g., acute vs chronic), and instructions for data reduction. Many methodologies present procedures for deriving criteria from both large and small data sets. Very small data sets may be supplemented through the use of QSARs for selected pesticides, and through the use of models such as ICE (for prediction of toxicity to under-tested species), and ACE (for estimation of chronic toxicity from acute data). The toxicity of mixtures is addressed by several existing methodologies. In some cases, additional AFs are applied to criteria to account for exposure to mixtures, whereas in others, concentration addition models are used to assess compliance. Multiple stressors and bioaccumulation are also addressed in some methodologies, by providing for application of additional safety factors. Methods are also available for translating dietary exposure limits for humans or other fish-eating animals into water concentrations. Options for addressing the safety of TES exist, and rely heavily on data from surrogate species to derive criteria. Utilizing partition coefficients, criteria may be harmonized across media to ensure that levels set to protect one compartment do not result in unacceptable levels in other compartments. Several methodologies derive criteria from entire data sets through the use of statistical extrapolations; other methods utilize only the lowest (most sensitive) data point or points. Utilization of entire data sets allows derivation of confidence limits for criteria, and encourages data generation. Criteria derivation methodologies have improved over the past two decades as they have incorporated more ecological risk assessment techniques. No single existing methodology is ideal, but elements of several may be combined, and when used with newer risk assessment tools, will produce more usable and flexible criteria derivation procedures that are protective.}, } @article {pmid19108043, year = {2008}, author = {Barron, MG and Raimondo, S and Russom, C and Vivian, DN and Yee, SH}, title = {Accuracy of chronic aquatic toxicity estimates determined from acute toxicity data and two time-response models.}, journal = {Environmental toxicology and chemistry}, volume = {27}, number = {10}, pages = {2196-2205}, doi = {10.1897/08-004.1}, pmid = {19108043}, issn = {0730-7268}, mesh = {Algorithms ; Animals ; Animals, Wild ; Data Interpretation, Statistical ; Linear Models ; *Models, Statistical ; No-Observed-Adverse-Effect Level ; Reproduction/drug effects ; Survival Analysis ; Time Factors ; Toxicity Tests ; Water Pollutants, Chemical/chemistry/*toxicity ; }, abstract = {Traditionally, chronic toxicity in aquatic organisms and wildlife has been determined from either toxicity test data, acute to chronic ratios, or application of safety factors. A more recent alternative approach has been to estimate chronic toxicity by modeling the time course of mortality as determined in standard acute toxicity tests, but these approaches have received limited validation. The accuracy of chronic toxicity estimates from two time-response models, linear regression analysis (LRA) and accelerated life testing (ALT), was investigated using a dataset of more than 150 matched species pairs of standard acute toxicity test data and measured chronic no-observed-effect concentrations (NOECs). Chronic survival was more accurately modeled by both ALT (accuracy, 69%) and LRA (accuracy, 76%) than was reproduction, growth, or the most sensitive endpoint (accuracy, 50-60%). In general, LRA estimates of chronic toxicity were less conservative than ALT estimates, with 66 to 79% of LRA estimates being greater than the measured NOEC. Acute datasets with early mortality produced estimates of chronic survival that were more accurate (ALT, 92%; LRA, 89%) compared to all datasets but were less conservative (84% of ALT estimates were overestimated vs 93% of LRA estimates). Acute datasets with late mortality resulted in poor ALT and LRA estimates of chronic toxicity for all endpoints. Additional survival time measurements did not improve the accuracy of ALT or LRA estimates of chronic toxicity over the standard four acute measurement times (24, 48, 72, and 96 h). The time course of mortality should be considered when applying time-response models to estimate chronic aquatic toxicity, with greater accuracy likely for chronic survival than for growth or reproduction.}, } @article {pmid19108041, year = {2008}, author = {Forbes, VE and Calow, P and Sibly, RM}, title = {The extrapolation problem and how population modeling can help.}, journal = {Environmental toxicology and chemistry}, volume = {27}, number = {10}, pages = {1987-1994}, doi = {10.1897/08-029.1}, pmid = {19108041}, issn = {0730-7268}, mesh = {Data Interpretation, Statistical ; Ecotoxicology/*statistics & numerical data ; Environmental Pollutants/*toxicity ; Environmental Pollution/statistics & numerical data ; *Models, Statistical ; *Population ; Quantitative Structure-Activity Relationship ; }, abstract = {We argue that population modeling can add value to ecological risk assessment by reducing uncertainty when extrapolating from ecotoxicological observations to relevant ecological effects. We review other methods of extrapolation, ranging from application factors to species sensitivity distributions to suborganismal (biomarker and "-omics") responses to quantitative structure-activity relationships and model ecosystems, drawing attention to the limitations of each. We suggest a simple classification of population models and critically examine each model in an extrapolation context. We conclude that population models have the potential for adding value to ecological risk assessment by incorporating better understanding of the links between individual responses and population size and structure and by incorporating greater levels of ecological complexity. A number of issues, however, need to be addressed before such models are likely to become more widely used. In a science context, these involve challenges in parameterization, questions about appropriate levels of complexity, issues concerning how specific or general the models need to be, and the extent to which interactions through competition and trophic relationships can be easily incorporated.}, } @article {pmid19104943, year = {2009}, author = {Gross, KS and McDermott, PA}, title = {Use of city-archival data to inform dimensional structure of neighborhoods.}, journal = {Journal of urban health : bulletin of the New York Academy of Medicine}, volume = {86}, number = {2}, pages = {161-182}, pmid = {19104943}, issn = {1468-2869}, mesh = {Adolescent ; *Archives ; *Censuses ; Child ; Child Welfare ; Child, Preschool ; City Planning ; Crime/statistics & numerical data ; Ecology ; Factor Analysis, Statistical ; Geographic Information Systems ; Humans ; *Residence Characteristics ; Social Environment ; Stress, Psychological ; United States ; }, abstract = {A growing body of research has explored the impact of neighborhood residence on child and adolescent health and well-being. Most previous research has used the US Census variables as the measures of neighborhood ecology, although informative census data are not designed to represent the sociological and structural features that characterize neighborhoods. Alternatively, this study explored the use of large-city administrative data and geographical information systems to develop more uniquely informative empirical dimensions of neighborhood context. Exploratory and confirmatory structural analyses of geographically referenced administrative data aggregated to the census-block group identified three latent dimensions: social stress, structural decline, and neighborhood crime. Resultant dimensions were compared through canonical regression to those derived from US Census data. The relative explanatory capacity of the city-archival and census dimensions was assessed through multilevel linear modeling to predict standardized reading and mathematics achievement of 31,742 fifth- and 28,922 eight-grade children. Results indicated that the city-archival dimensions uniquely augmented predictions, and the combination of city and census dimensions explained significantly more neighborhood effects on achievement than did either source of neighborhood information independently.}, } @article {pmid19103235, year = {2009}, author = {Becker, A and Barnett, MJ and Capela, D and Dondrup, M and Kamp, PB and Krol, E and Linke, B and Rüberg, S and Runte, K and Schroeder, BK and Weidner, S and Yurgel, SN and Batut, J and Long, SR and Pühler, A and Goesmann, A}, title = {A portal for rhizobial genomes: RhizoGATE integrates a Sinorhizobium meliloti genome annotation update with postgenome data.}, journal = {Journal of biotechnology}, volume = {140}, number = {1-2}, pages = {45-50}, pmid = {19103235}, issn = {1873-4863}, support = {R37 GM030962-21/GM/NIGMS NIH HHS/United States ; GM30962/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacterial Proteins/genetics ; *Databases, Genetic ; *Genome, Bacterial ; *Information Management ; Information Storage and Retrieval ; Internet ; Medicago truncatula ; Microarray Analysis ; Sinorhizobium meliloti/*genetics ; User-Computer Interface ; }, abstract = {Sinorhizobium meliloti is a symbiotic soil bacterium of the alphaproteobacterial subdivision. Like other rhizobia, S. meliloti induces nitrogen-fixing root nodules on leguminous plants. This is an ecologically and economically important interaction, because plants engaged in symbiosis with rhizobia can grow without exogenous nitrogen fertilizers. The S. meliloti-Medicago truncatula (barrel medic) association is an important symbiosis model. The S. meliloti genome was published in 2001, and the M. truncatula genome currently is being sequenced. Many new resources and data have been made available since the original S. meliloti genome annotation and an update was needed. In June 2008, we submitted our annotation update to the EMBL and NCBI databases. Here we describe this new annotation and a new web-based portal RhizoGATE. About 1000 annotation updates were made; these included assigning functions to 313 putative proteins, assigning EC numbers to 431 proteins, and identifying 86 new putative genes. RhizoGATE incorporates the new annotion with the S. meliloti GenDB project, a platform that allows annotation updates in real time. Locations of transposon insertions, plasmid integrations, and array probe sequences are available in the GenDB project. RhizoGATE employs the EMMA platform for management and analysis of transcriptome data and the IGetDB data warehouse to integrate a variety of heterogeneous external data sources.}, } @article {pmid19102300, year = {2008}, author = {Wen, ZM and Jiao, F and Jiao, JY}, title = {[Prediction and mapping of potential vegetation distribution in Yanhe River catchment in hilly area of Loess Plateau].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {19}, number = {9}, pages = {1897-1904}, pmid = {19102300}, issn = {1001-9332}, mesh = {China ; Conservation of Natural Resources/methods/trends ; *Ecosystem ; Forecasting ; Geographic Information Systems ; *Models, Theoretical ; *Rivers ; Trees/classification/*growth & development ; }, abstract = {The prediction and mapping of potential vegetation distribution is of instructive to the ecological restoration planning. By using generalized additive model (GAM) and in combining with GIS spatial analyst and environmental stratification sampling techniques, a distribution model for 24 dominant species in Yanhe River catchment was developed, and, based on the interspecific relationships in plant communities and the distribution probability, the spatial distribution of plant species was calculated, and the distribution of 37 plant communities and of the potential vegetation in Yanhe River catchment was predicted. The results showed that there were no significant differences between predictive values and actual data, and the predictive spatial distribution of vegetation could actually reflect the distribution of potential vegetation in Yanhe River catchment, suggesting that the established model had good ability for the vegetation distribution prediction, which was of significance to the goal-setting and planning of vegetation restoration.}, } @article {pmid19102299, year = {2008}, author = {Liu, ZH and Chang, Y and Chen, HW}, title = {[Estimation of forest volume in Huzhong forest area based on RS, GIS and ANN].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {19}, number = {9}, pages = {1891-1896}, pmid = {19102299}, issn = {1001-9332}, mesh = {Biomass ; China ; Conservation of Natural Resources/*methods ; Environmental Monitoring ; *Geographic Information Systems ; *Neural Networks, Computer ; Satellite Communications ; Trees/*growth & development ; }, abstract = {Based on remote sensing (RS) which has integrated and realistic characteristics, geographic information system (GIS) which has powerful spatial analysis ability, and artificial neutral network (ANN) which can optimize nonlinear complex systems, the forest volume in Huzhong forest area was estimated. The results showed that there was an obvious negative correlation between the forest volume and infrared band, indicating that infrared band had definite potential in estimating forest volume. The forest volume also negatively correlated with visible band and PC1. Among the topographic factors, altitude exerted more influence than aspect and slope on the estimation of forest volume. The correlation coefficient of predicted value and actual value reached to 0.973, when the optimal ANN parameter, suitable GIS information, and RS bands were adopted. After principal component transformation, the amount of observation data was effectively reduced, while the predicted precision only had a small decline (R2 = 0.934).}, } @article {pmid19100655, year = {2009}, author = {Valentini, A and Pompanon, F and Taberlet, P}, title = {DNA barcoding for ecologists.}, journal = {Trends in ecology & evolution}, volume = {24}, number = {2}, pages = {110-117}, doi = {10.1016/j.tree.2008.09.011}, pmid = {19100655}, issn = {0169-5347}, mesh = {Animals ; Biodiversity ; Classification/methods ; DNA/chemistry ; Databases, Genetic ; Diet ; Ecology/*trends ; Food Chain ; Sequence Analysis, DNA/*methods ; Species Specificity ; }, abstract = {DNA barcoding - taxon identification using a standardized DNA region - has received much attention recently, and is being further developed through an international initiative. We anticipate that DNA barcoding techniques will be increasingly used by ecologists. They will be able to not only identify a single species from a specimen or an organism's remains but also determine the species composition of environmental samples. Short DNA fragments persist in the environment and might allow an assessment of local biodiversity from soil or water. Even DNA-based diet composition can be estimated using fecal samples. Here we review the new avenues offered to ecologists by DNA barcoding, particularly in the context of new sequencing technologies.}, } @article {pmid19100270, year = {2009}, author = {Bahrndorff, S and Tunnacliffe, A and Wise, MJ and McGee, B and Holmstrup, M and Loeschcke, V}, title = {Bioinformatics and protein expression analyses implicate LEA proteins in the drought response of Collembola.}, journal = {Journal of insect physiology}, volume = {55}, number = {3}, pages = {210-217}, doi = {10.1016/j.jinsphys.2008.11.010}, pmid = {19100270}, issn = {1879-1611}, support = {//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Adaptation, Biological/*genetics ; Animals ; Base Sequence ; Blotting, Western ; Computational Biology/methods ; DNA Primers/genetics ; *Droughts ; *Expressed Sequence Tags ; HSP70 Heat-Shock Proteins/metabolism ; Insect Proteins/chemistry/metabolism/*physiology ; Insecta/genetics/*physiology ; Molecular Sequence Data ; Plant Proteins/genetics ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {Humidity has a large impact on the distribution and abundance of terrestrial invertebrates, but the molecular mechanisms governing drought resistance are not fully understood. Some attention has been given to the role of the heat shock response as a component of desiccation tolerance, but recent focus has been on the chaperone-like LEA (late embryogenesis abundant) proteins in anhydrobiotic animals. This study investigates the expression of putative LEA proteins as well as the heat shock protein Hsp70 during drought stress in soil and surface dwelling species of Collembola (springtails). In silico analysis of four EST candidates from two species of Collembola showed the presence of a Group 3 LEA protein in Megaphorura arctica. In common with other Group 3 LEA proteins, the new sequence is predicted to be 100% natively unfolded, with a strong degree of lysine and alanine periodicity and with a negative average hydrophobicity of -1.273. The sequence clusters with members of the Group 3 LEA in plants. Furthermore, cross-species Western blotting showed drought-induced expression of putative LEA proteins in six species of Collembola. In the surface dwelling species, Orchesella cincta, degree of dehydration and length of exposure correlated with level of putative LEA protein. Hsp70 was also found to increase in individuals of O. cincta and Folsomia candida that had been exposed to drought conditions for 6 days. These results show the presence of a LEA protein-coding region in Collembola, but also indicate that several proteins are involved in response to dehydration stress, including Hsp70.}, } @article {pmid19097645, year = {2009}, author = {Allert, AL and Fairchild, JF and Distefano, RJ and Schmitt, CJ and Brumbaugh, WG and Besser, JM}, title = {Ecological effects of lead mining on Ozark streams: In-situ toxicity to woodland crayfish (Orconectes hylas).}, journal = {Ecotoxicology and environmental safety}, volume = {72}, number = {4}, pages = {1207-1219}, doi = {10.1016/j.ecoenv.2008.08.005}, pmid = {19097645}, issn = {1090-2414}, mesh = {Animals ; Astacoidea/*physiology ; Biomass ; Data Interpretation, Statistical ; Diet ; Female ; Fishes ; Fresh Water/analysis ; Hydrogen-Ion Concentration ; *Industrial Waste ; Invertebrates ; Lead/analysis/*toxicity ; Male ; Mass Spectrometry ; Metals/analysis/toxicity ; Metals, Heavy/analysis/toxicity ; *Mining ; Missouri ; Population ; Temperature ; Water Pollutants, Chemical/analysis/*toxicity ; }, abstract = {The Viburnum Trend mining district in southeast Missouri, USA is one of the largest producers of lead-zinc ore in the world. Previous stream surveys found evidence of increased metal exposure and reduced population densities of crayfish immediately downstream of mining sites. We conducted an in-situ 28-d exposure to assess toxicity of mining-derived metals to the woodland crayfish (Orconectes hylas). Crayfish survival and biomass were significantly lower at mining sites than at reference and downstream sites. Metal concentrations in water, detritus, macroinvertebrates, fish, and crayfish were significantly higher at mining sites, and were negatively correlated with caged crayfish survival. These results support previous field and laboratory studies that showed mining-derived metals negatively affect O. hylas populations in streams draining the Viburnum Trend, and that in-situ toxicity testing was a valuable tool for assessing the impacts of mining on crayfish populations.}, } @article {pmid19091334, year = {2009}, author = {Odisho, AY and Fradet, V and Cooperberg, MR and Ahmad, AE and Carroll, PR}, title = {Geographic distribution of urologists throughout the United States using a county level approach.}, journal = {The Journal of urology}, volume = {181}, number = {2}, pages = {760-5; discussion 765-6}, doi = {10.1016/j.juro.2008.10.034}, pmid = {19091334}, issn = {1527-3792}, support = {UL1 RR024131/RR/NCRR NIH HHS/United States ; }, mesh = {Adult ; Career Choice ; Confidence Intervals ; Databases, Factual ; Health Care Surveys ; Humans ; Logistic Models ; Male ; Middle Aged ; Needs Assessment ; Odds Ratio ; Physicians/*supply & distribution ; Probability ; Professional Practice Location/*statistics & numerical data ; Rural Health Services/*statistics & numerical data ; United States ; Urban Health Services/*statistics & numerical data ; *Urology ; Workforce ; }, abstract = {PURPOSE: The adequacy of the urologist work force in absolute numbers and relative distribution is unclear. To develop effective policies addressing the needs of an aging population we must better understand the urologist work force. We assessed the geographic distribution of urologists throughout the United States at the county level and determined the county characteristics associated with increased urologist density.

MATERIALS AND METHODS: County level data from the Department of Health and Human Services Area Resource File and the United States Census were analyzed in this ecological study. Logistic regression and ordinal logistic regression models were built to identify predictors of urologist density, defined as the number of urologists per 100,000 individuals. National patterns of urologist density were mapped graphically at the county level.

RESULTS: Overall 63% of the counties in the United States lack a urologist. Based on multivariate models urologists were less likely to be found in nonmetropolitan counties (OR 0.57, 95% CI 0.46-0.72) and rural counties (OR 0.03, 95% CI 0.02-0.06) than in metropolitan counties, which confirmed visually mapped models. Patterns of urologist density also appeared to be influenced by climate and county education levels rather than by traditional socioeconomic measures. Urologists younger than 45 years old were 3 times less likely to be located in nonmetropolitan and rural counties than their older counterparts.

CONCLUSIONS: The uneven distribution of urologists throughout the United States is likely to worsen as younger physicians continue to cluster in urban areas. Governing bodies must consider this distribution in their calls for increasing the number of training positions.}, } @article {pmid19087948, year = {2009}, author = {Walker, AM and Bruin, RP and Dove, MT and White, TO and Kleese van Dam, K and Tyer, RP}, title = {Integrating computing, data and collaboration grids: the RMCS tool.}, journal = {Philosophical transactions. Series A, Mathematical, physical, and engineering sciences}, volume = {367}, number = {1890}, pages = {1047-1050}, doi = {10.1098/rsta.2008.0159}, pmid = {19087948}, issn = {1364-503X}, mesh = {Computer Simulation ; *Cooperative Behavior ; Database Management Systems/*trends ; Databases, Factual/*trends ; Ecology/*methods/trends ; Information Dissemination/methods ; Information Storage and Retrieval/*trends ; *Internet ; *Models, Theoretical ; *Software ; Systems Integration ; User-Computer Interface ; }, abstract = {We describe RMCS as one of the first tools for grid computing that integrates data and metadata management into a single job submission system. The system is easy to use, with client tools that are easy to install. Although the RMCS system was developed as a prototype, it is now in production use and a number of scientific studies have been completed using it.}, } @article {pmid19087947, year = {2009}, author = {Martin, CJ and Haji, MH and Dew, PM and Pilling, MJ and Jimack, PK}, title = {Semantically enhanced provenance capture for chamber model development with a master chemical mechanism.}, journal = {Philosophical transactions. Series A, Mathematical, physical, and engineering sciences}, volume = {367}, number = {1890}, pages = {987-990}, doi = {10.1098/rsta.2008.0168}, pmid = {19087947}, issn = {1364-503X}, mesh = {Atmosphere/*chemistry ; Computer Simulation ; *Databases, Factual ; Ecology/*methods/trends ; Information Dissemination/*methods ; *Internet ; *Models, Chemical ; Semantics ; *Software ; }, abstract = {The development and maintenance of benchmark databases within scientific communities is reliant on interactions with database users. We explore the role of semantically enhanced provenance for computational modelling processes that make use of one such database: the master chemical mechanism, a key resource within the atmospheric chemistry community.}, } @article {pmid19087946, year = {2009}, author = {White, TO and Bruin, RP and Chiang, GT and Dove, MT and Tyer, RP and Walker, AM}, title = {Lessons in scientific data interoperability: XML and the eMinerals project.}, journal = {Philosophical transactions. Series A, Mathematical, physical, and engineering sciences}, volume = {367}, number = {1890}, pages = {1041-1046}, doi = {10.1098/rsta.2008.0175}, pmid = {19087946}, issn = {1364-503X}, mesh = {Computer Simulation ; Database Management Systems/*trends ; Databases, Factual/*trends ; Ecology/*methods/trends ; Information Dissemination/methods ; Information Storage and Retrieval/*trends ; *Internet ; Minerals/*chemistry ; *Models, Chemical ; *Software ; User-Computer Interface ; }, abstract = {A collaborative environmental eScience project produces a broad range of data, notable as much for its diversity, in source and format, as its quantity. We find that extensible markup language (XML) and associated technologies are invaluable in managing this deluge of data. We describe Fo X, a toolkit for allowing Fortran codes to read and write XML, thus allowing existing scientific tools to be easily re-used in an XML-centric workflow.}, } @article {pmid19087942, year = {2009}, author = {Blower, JD and Haines, K and Santokhee, A and Liu, CL}, title = {GODIVA2: interactive visualization of environmental data on the Web.}, journal = {Philosophical transactions. Series A, Mathematical, physical, and engineering sciences}, volume = {367}, number = {1890}, pages = {1035-1039}, doi = {10.1098/rsta.2008.0180}, pmid = {19087942}, issn = {1364-503X}, mesh = {Computer Simulation ; Database Management Systems/trends ; Databases, Factual/*trends ; Ecology/*methods/trends ; Information Dissemination/methods ; Information Storage and Retrieval/*trends ; *Internet ; *Models, Theoretical ; *Software ; *User-Computer Interface ; }, abstract = {GODIVA2 is a dynamic website that provides visual access to several terabytes of physically distributed, four-dimensional environmental data. It allows users to explore large datasets interactively without the need to install new software or download and understand complex data. Through the use of open international standards, GODIVA2 maintains a high level of interoperability with third-party systems, allowing diverse datasets to be mutually compared. Scientists can use the system to search for features in large datasets and to diagnose the output from numerical simulations and data processing algorithms. Data providers around Europe have adopted GODIVA2 as an INSPIRE-compliant dynamic quick-view system for providing visual access to their data.}, } @article {pmid19087938, year = {2009}, author = {Dozier, J and Frew, J}, title = {Computational provenance in hydrologic science: a snow mapping example.}, journal = {Philosophical transactions. Series A, Mathematical, physical, and engineering sciences}, volume = {367}, number = {1890}, pages = {1021-1033}, doi = {10.1098/rsta.2008.0187}, pmid = {19087938}, issn = {1364-503X}, mesh = {Computer Simulation ; Database Management Systems/*trends ; Databases, Factual/*trends ; Ecology/*methods/trends ; Information Dissemination/methods ; Information Storage and Retrieval/*trends ; *Internet ; *Models, Theoretical ; *Snow ; Software ; User-Computer Interface ; }, abstract = {Computational provenance--a record of the antecedents and processing history of digital information--is key to properly documenting computer-based scientific research. To support investigations in hydrologic science, we produce the daily fractional snow-covered area from NASA's moderate-resolution imaging spectroradiometer (MODIS). From the MODIS reflectance data in seven wavelengths, we estimate the fraction of each 500 m pixel that snow covers. The daily products have data gaps and errors because of cloud cover and sensor viewing geometry, so we interpolate and smooth to produce our best estimate of the daily snow cover. To manage the data, we have developed the Earth System Science Server (ES3), a software environment for data-intensive Earth science, with unique capabilities for automatically and transparently capturing and managing the provenance of arbitrary computations. Transparent acquisition avoids the scientists having to express their computations in specific languages or schemas in order for provenance to be acquired and maintained. ES3 models provenance as relationships between processes and their input and output files. It is particularly suited to capturing the provenance of an evolving algorithm whose components span multiple languages and execution environments.}, } @article {pmid19087936, year = {2009}, author = {Frame, I and Austen, KF and Calleja, M and Dove, MT and White, TO and Wilson, DJ}, title = {New tools to support collaboration and virtual organizations.}, journal = {Philosophical transactions. Series A, Mathematical, physical, and engineering sciences}, volume = {367}, number = {1890}, pages = {1051-1056}, doi = {10.1098/rsta.2008.0193}, pmid = {19087936}, issn = {1364-503X}, mesh = {Computer Simulation ; *Cooperative Behavior ; Database Management Systems/*trends ; Databases, Factual/*trends ; Ecology/*methods/trends ; Information Dissemination/methods ; Information Storage and Retrieval/*trends ; *Internet ; *Models, Theoretical ; *Software ; *User-Computer Interface ; }, abstract = {We describe the use of new eScience tools to support collaboration, including the use of XML data representations to support shared viewing of the information content of data, metadata tools for documenting data and Web 2.0 social networking tools for documenting ideas and the collaboration process. This latter work has led to the development of the http://SciSpace.net Web resource.}, } @article {pmid19087932, year = {2009}, author = {Lawrence, BN and Lowry, R and Miller, P and Snaith, H and Woolf, A}, title = {Information in environmental data grids.}, journal = {Philosophical transactions. Series A, Mathematical, physical, and engineering sciences}, volume = {367}, number = {1890}, pages = {1003-1014}, doi = {10.1098/rsta.2008.0237}, pmid = {19087932}, issn = {1364-503X}, mesh = {Computer Simulation ; Database Management Systems/*trends ; Databases, Factual/*trends ; Ecology/*methods/trends ; Information Dissemination/methods ; Information Storage and Retrieval/*trends ; *Internet ; *Models, Theoretical ; *Software ; User-Computer Interface ; }, abstract = {Providing homogeneous access ('services') to heterogeneous environmental data distributed across heterogeneous computing systems on a wide area network requires a robust information paradigm that can mediate between differing storage and information formats. While there are a number of ISO standards that provide some guidance on how to do this, the information landscape within domains is not well described. In this paper, we present an information taxonomy and two information components, which have been built for a specific application. These two components, one to aid data understanding and the other to aid data manipulation, are both deployed in the UK NERC DataGrid as described elsewhere.}, } @article {pmid19087931, year = {2009}, author = {Latham, SE and Cramer, R and Grant, M and Kershaw, P and Lawrence, BN and Lowry, R and Lowe, D and O'Neill, K and Miller, P and Pascoe, S and Pritchard, M and Snaith, H and Woolf, A}, title = {The NERC DataGrid services.}, journal = {Philosophical transactions. Series A, Mathematical, physical, and engineering sciences}, volume = {367}, number = {1890}, pages = {1015-1019}, doi = {10.1098/rsta.2008.0238}, pmid = {19087931}, issn = {1364-503X}, support = {MC_U120063239/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Computer Simulation ; Database Management Systems/*trends ; Databases, Factual/*trends ; Ecology/*methods/trends ; Information Dissemination/methods ; Information Storage and Retrieval/*trends ; *Internet ; *Models, Theoretical ; *Software ; User-Computer Interface ; }, abstract = {This short paper outlines the key components of the NERC DataGrid: a discovery service, a vocabulary service and a software stack deployed both centrally to provide a data discovery portal, and at data providers to provide local portals and data and metadata services.}, } @article {pmid19087179, year = {2009}, author = {Kelly, JK}, title = {Connecting QTLS to the g-matrix of evolutionary quantitative genetics.}, journal = {Evolution; international journal of organic evolution}, volume = {63}, number = {4}, pages = {813-825}, pmid = {19087179}, issn = {1558-5646}, support = {R01 GM073990/GM/NIGMS NIH HHS/United States ; GM073990/GM/NIGMS NIH HHS/United States ; }, mesh = {*Biological Evolution ; Data Interpretation, Statistical ; Gene Frequency ; Genetic Variation ; *Genetics, Population ; *Quantitative Trait Loci ; *Selection, Genetic ; }, abstract = {Evolutionary quantitative genetics has recently advanced in two distinct streams. Many biologists address evolutionary questions by estimating phenotypic selection and genetic (co)variances (G matrices). Simultaneously, an increasing number of studies have applied quantitative trait locus (QTL) mapping methods to dissect variation. Both conceptual and practical difficulties have isolated these two foci of quantitative genetics. A conceptual integration follows from the recognition that QTL allele frequencies are the essential variables relating the G-matrix to marker-based mapping experiments. Breeding designs initiated from randomly selected parental genotypes can be used to estimate QTL-specific genetic (co)variances. These statistics appropriately distill allelic variation and provide an explicit population context for QTL mapping estimates. Within this framework, one can parse the G-matrix into a set of mutually exclusive genomic components and ask whether these parts are similar or dissimilar in their respective features, for example the magnitude of phenotypic effects and the extent and nature of pleiotropy. As these features are critical determinants of sustained response to selection, the integration of QTL mapping methods into G-matrix estimation can provide a concrete, genetically based experimental program to investigate the evolutionary potential of natural populations.}, } @article {pmid19087109, year = {2009}, author = {Flynn, DF and Gogol-Prokurat, M and Nogeire, T and Molinari, N and Richers, BT and Lin, BB and Simpson, N and Mayfield, MM and DeClerck, F}, title = {Loss of functional diversity under land use intensification across multiple taxa.}, journal = {Ecology letters}, volume = {12}, number = {1}, pages = {22-33}, doi = {10.1111/j.1461-0248.2008.01255.x}, pmid = {19087109}, issn = {1461-0248}, mesh = {Adaptation, Biological/*physiology ; *Agriculture ; Animals ; *Biodiversity ; Birds/*physiology ; Central America ; Databases, Factual ; Mammals/*physiology ; *Models, Biological ; North America ; *Plant Physiological Phenomena ; Population Dynamics ; Species Specificity ; }, abstract = {Land use intensification can greatly reduce species richness and ecosystem functioning. However, species richness determines ecosystem functioning through the diversity and values of traits of species present. Here, we analyze changes in species richness and functional diversity (FD) at varying agricultural land use intensity levels. We test hypotheses of FD responses to land use intensification in plant, bird, and mammal communities using trait data compiled for 1600+ species. To isolate changes in FD from changes in species richness we compare the FD of communities to the null expectations of FD values. In over one-quarter of the bird and mammal communities impacted by agriculture, declines in FD were steeper than predicted by species number. In plant communities, changes in FD were indistinguishable from changes in species richness. Land use intensification can reduce the functional diversity of animal communities beyond changes in species richness alone, potentially imperiling provisioning of ecosystem services.}, } @article {pmid19084541, year = {2009}, author = {De Lara, M and Martinet, V}, title = {Multi-criteria dynamic decision under uncertainty: a stochastic viability analysis and an application to sustainable fishery management.}, journal = {Mathematical biosciences}, volume = {217}, number = {2}, pages = {118-124}, doi = {10.1016/j.mbs.2008.11.003}, pmid = {19084541}, issn = {0025-5564}, mesh = {Animals ; Conservation of Natural Resources ; Decision Support Techniques ; *Ecosystem ; Fisheries/economics/*methods ; Fishes/*growth & development ; *Models, Biological ; Stochastic Processes ; }, abstract = {Managing natural resources in a sustainable way is a hard task, due to uncertainties, dynamics and conflicting objectives (ecological, social, and economical). We propose a stochastic viability approach to address such problems. We consider a discrete-time control dynamical model with uncertainties, representing a bioeconomic system. The sustainability of this system is described by a set of constraints, defined in practice by indicators - namely, state, control and uncertainty functions - together with thresholds. This approach aims at identifying decision rules such that a set of constraints, representing various objectives, is respected with maximal probability. Under appropriate monotonicity properties of dynamics and constraints, having economic and biological content, we characterize an optimal feedback. The connection is made between this approach and the so-called Management Strategy Evaluation for fisheries. A numerical application to sustainable management of Bay of Biscay nephrops-hakes mixed fishery is given.}, } @article {pmid19083113, year = {2009}, author = {Munoz, B and Lesser, VM and Dorney, JR and Savage, R}, title = {A proposed methodology to determine accuracy of location and extent of geographically isolated wetlands.}, journal = {Environmental monitoring and assessment}, volume = {150}, number = {1-4}, pages = {53-64}, doi = {10.1007/s10661-008-0672-0}, pmid = {19083113}, issn = {1573-2959}, mesh = {Animals ; Conservation of Natural Resources/methods ; Data Collection/*methods ; Ecosystem ; Environmental Monitoring/*methods ; *Geographic Information Systems ; North Carolina ; Rivers ; Seawater ; Water Supply ; *Wetlands ; }, abstract = {Wetlands can provide significant environmental benefits such as assimilation of pollutants, flood water storage, groundwater recharge, and fish and wildlife habitat. Geographically isolated wetlands (IWs) can provide the same benefits as other wetlands, but are particularly vulnerable to losses from urbanization and agriculture since they are isolated, often smaller, and not equal to other wetlands in regulatory protection. There is a need for a reliable assessment of the total number and area of IWs. Access to this information can provide the foundation to monitor IW loss, and can assist in understanding the ecological effects of such loss as well as help to address regulatory shortcomings. A probability sampling survey methodology that balances statistical considerations, expert opinion, and operational considerations is discussed for assessing the accuracy of IW maps. A simulation exercise was used to illustrate how the proposed sampling methodology will produce reliable results in map accuracy assessment. A wetland map for the Lockwood Folly River watershed, in Brunswick County, NC, was created using historical and recent data and used as the sampling frame in the simulation exercise. An updated wetland map for the same watershed, showing exact locations of wetlands, was used to provide "ground-truth" observations based on wetland delineations approved by the U.S. Army Corps of Engineers. Survey-based accuracy estimates were calculated by comparing site classification differences obtained by using both the original and updated wetland maps.}, } @article {pmid19082749, year = {2009}, author = {Brooks, R and McKenney-Easterling, M and Brinson, M and Rheinhardt, R and Havens, K and O'Brien, D and Bishop, J and Rubbo, J and Armstrong, B and Hite, J}, title = {A Stream-Wetland-Riparian (SWR) index for assessing condition of aquatic ecosystems in small watersheds along the Atlantic slope of the eastern U.S.}, journal = {Environmental monitoring and assessment}, volume = {150}, number = {1-4}, pages = {101-117}, pmid = {19082749}, issn = {1573-2959}, mesh = {Animals ; Conservation of Natural Resources/methods ; *Ecosystem ; Environmental Monitoring/*methods ; Geographic Information Systems ; *Rivers ; Satellite Communications ; United States ; Water Movements ; Water Supply ; *Wetlands ; }, abstract = {As part of a regional study by the Atlantic Slope Consortium (ASC) to develop ecological and socioeconomic indicators of aquatic ecosystem condition, we developed and tested a protocol for rapidly assessing condition of the stream, wetland, and riparian components of freshwater aquatic ecosystems. Aspects of hydrology, vegetation, in-stream and wetland characteristics, and on-site stressors were measured in the field. The resulting metrics were used to develop an index of overall condition, termed the Stream-Wetland-Riparian (SWR) Index. Values of this Index were compared to existing biotic indices and chemical measures, and to a Landscape Index created using satellite-based land cover data and a geographic information system (GIS). Comparisons were made at several levels of spatial aggregation and resolution, from site to small watershed. The SWR Index and associated Landscape Indices were shown to correlate highly with biological indicators of stream condition at the site level and for small contributing areas. The landscape patterns prevalent throughout the entire watershed do not necessarily match the patterns found adjacent to the stream network. We suggest a top-down approach that managers can use to sequentially apply these methods, to first prioritize watersheds based on a relative condition measure provided by the Landscape Index, and then assess condition and diagnose stressors of aquatic resources at the subwatershed and site level.}, } @article {pmid19074238, year = {2008}, author = {Bell, N and Schuurman, N and Hameed, SM}, title = {Are injuries spatially related? Join-count spatial autocorrelation for small-area injury analysis.}, journal = {Injury prevention : journal of the International Society for Child and Adolescent Injury Prevention}, volume = {14}, number = {6}, pages = {346-353}, doi = {10.1136/ip.2008.018903}, pmid = {19074238}, issn = {1475-5785}, mesh = {Adolescent ; Adult ; Aged ; British Columbia/epidemiology ; Female ; Geographic Information Systems ; Hospitalization/statistics & numerical data ; Humans ; Male ; Middle Aged ; Poverty Areas ; Registries ; Residence Characteristics/statistics & numerical data ; Self-Injurious Behavior/epidemiology/prevention & control ; Small-Area Analysis ; Social Class ; Urban Health/statistics & numerical data ; Violence/statistics & numerical data ; Wounds and Injuries/*epidemiology/etiology/prevention & control ; Young Adult ; }, abstract = {OBJECTIVE: To present a geographic information systems (GIS) method for exploring the spatial pattern of injuries and to demonstrate the utility of using this method in conjunction with classic ecological models of injury patterns.

DESIGN: Profiles of patients' socioeconomic status (SES) were constructed by linking their postal code of residence to the census dissemination area that encompassed its location. Data were then integrated into a GIS, enabling the analysis of neighborhood contiguity and SES on incidence of injury.

SETTING: Data for this analysis (2001-2006) were obtained from the British Columbia Trauma Registry. Neighborhood SES was calculated using the Vancouver Area Neighborhood Deprivation Index. Spatial analysis was conducted using a join-count spatial autocorrelation algorithm.

PATIENTS: Male and female patients over the age of 18 and hospitalized from severe injury (Injury Severity Score >12) resulting from an assault or intentional self-harm and included in the British Columbia Trauma Registry were analyzed.

RESULTS: Male patients injured by assault and who resided in adjoining census areas were observed 1.3 to 5 times more often than would be expected under a random spatial pattern. Adjoining neighborhood clustering was less visible for residential patterns of patients hospitalized with injuries sustained from self-harm. A social gradient in assault injury rates existed separately for men and neighborhood SES, but less than would be expected when stratified by age, gender, and neighborhood. No social gradient between intentional injury from self-harm and neighborhood SES was observed.

CONCLUSIONS: This study demonstrates the added utility of integrating GIS technology into injury prevention research. Crucial information on the associated social and environmental influences of intentional injury patterns may be under-recognized if a spatial analysis is not also conducted. The join-count spatial autocorrelation is an ideal approach for investigating the interconnectedness of injury patterns that are rare and occur in only a small percentage of the population.}, } @article {pmid19068665, year = {2008}, author = {Li, J and Lü, YL and He, GZ and Wang, TY and Luo, W and Shi, YJ}, title = {[Spatial and temporal changes of emerging environmental pollution accidents and impact factors in China].}, journal = {Huan jing ke xue= Huanjing kexue}, volume = {29}, number = {9}, pages = {2684-2688}, pmid = {19068665}, issn = {0250-3301}, mesh = {China ; Ecology/methods/trends ; Environmental Monitoring/*methods ; Environmental Pollution/analysis/*statistics & numerical data ; Forecasting ; *Geographic Information Systems ; }, abstract = {Based on environmental statistics data from 1993 to 2005, spatial distribution and temporal tendency of the environmental pollution and destruction accidents and their external causes were analyzed by using GIS and non-parametric correlation methods. It was concluded that (1) during the study period, annual environmental pollution accidents was maximally 3001 times in 1994 and minimally 1406 in 2005, while the frequency decreased in general. In addition, water and air accidents occupied the most; (2) environmental pollution and destruction accidents centralized in southeast and middle parts of China, mainly in Hunan, Sichuan, and Guangxi; (3) factors including population, GDP, company number and industrial waste water discharge had positive impacts on frequency of environmental pollution and destruction accidents, while in developed provinces the frequency was only correlated with company number.}, } @article {pmid19067801, year = {2008}, author = {Kane, NC and Cronk, Q}, title = {Botany without borders: barcoding in focus.}, journal = {Molecular ecology}, volume = {17}, number = {24}, pages = {5175-5176}, doi = {10.1111/j.1365-294X.2008.03972.x}, pmid = {19067801}, issn = {1365-294X}, mesh = {Computational Biology/methods ; DNA, Plant/*genetics ; Genes, Plant ; *Genetic Markers ; Genome, Plant ; Plants/classification/*genetics ; Sequence Analysis, DNA ; }, abstract = {This recent meeting, held on the campus of the University of British Columbia, attracted 1200 delegates and a vast array of talks, but was notable for a remarkable showing of talks and posters on DNA barcoding in plants, spread through many sessions. The Canadian Centre for DNA Barcoding defines barcoding as 'species identification and discovery through the analysis of short, standardized gene regions known as DNA barcodes'. This approach is somewhat controversial in animals (Rubinoff et al., 2006), although it has been shown to be useful and reliable in many metazoan taxa (Meyer & Paulay 2005; Hajibabaei et al., 2007), in which the mitochondrial cytochrome oxidase I (COI) gene is used. However, in land plants, COI evolves far too slowly to be useful, and there is no obvious single universal alternative (Fazekas et al., 2008).Genes that work well in one taxon may perform poorly in other taxa. Additionally, some perfectly good plant species,reproductively isolated and morphologically and ecologically distinct, are too young to show much sequence divergence at most loci. Nevertheless, as we saw at this conference, progress has been made towards identifying genes that serve many of the functions of DNA barcodes, at least in some plant taxa.}, } @article {pmid19065264, year = {2008}, author = {Thomas, B and Holland, JD and Minot, EO}, title = {Elephant (Loxodonta africana) home ranges in Sabi Sand Reserve and Kruger National Park: a five-year satellite tracking study.}, journal = {PloS one}, volume = {3}, number = {12}, pages = {e3902}, doi = {10.1371/journal.pone.0003902}, pmid = {19065264}, issn = {1932-6203}, mesh = {Africa ; Animals ; *Ecosystem ; *Elephants ; Female ; *Geographic Information Systems ; Geography ; Poaceae ; Satellite Communications ; Temperature ; Time Factors ; Trees ; Water ; }, abstract = {During a five-year GPS satellite tracking study in Sabi Sand Reserve (SSR) and Kruger National Park (KNP) we monitored the daily movements of an elephant cow (Loxodonta africana) from September 2003 to August 2008. The study animal was confirmed to be part of a group of seven elephants therefore her position is representative of the matriarchal group. We found that the study animal did not use habitat randomly and confirmed strong seasonal fidelity to its summer and winter five-year home ranges. The cow's summer home range was in KNP in an area more than four times that of her SSR winter home range. She exhibited clear park habitation with up to three visits per year travelling via a well-defined northern or southern corridor. There was a positive correlation between the daily distance the elephant walked and minimum daily temperature and the elephant was significantly closer to rivers and artificial waterholes than would be expected if it were moving randomly in KNP and SSR. Transect lines established through the home ranges were surveyed to further understand the fine scale of the landscape and vegetation representative of the home ranges.}, } @article {pmid19063760, year = {2009}, author = {Patiny, S and Michez, D and Kuhlmann, M and Pauly, A and Barbier, Y}, title = {Factors limiting the species richness of bees in Saharan Africa.}, journal = {Bulletin of entomological research}, volume = {99}, number = {4}, pages = {337-346}, doi = {10.1017/S0007485308006433}, pmid = {19063760}, issn = {1475-2670}, mesh = {Africa, Northern ; Animals ; Bees/*physiology ; *Biodiversity ; *Demography ; Fresh Water ; Geographic Information Systems ; Geography ; Multivariate Analysis ; }, abstract = {There is a severe shortage of knowledge of bee biogeography. Some former studies have highlighted a link between bee diversity and xeric ecosystems, but we know practically nothing of the macro-ecological factors driving bee diversity. The present study aims to analyse the main macro-ecological factors driving bee species-richness in the Saharan region. Our dataset includes 25,000+ records for localities in Africa, between 37 degrees and 10 degrees N. Maps and GIS were used to get a first overview of the distribution of the studied taxa. Partial least squares analysis (PLS) was used to study the impact of a set of ecological factors on the bee species richness (SR). The mapping highlighted the clustering of the highest bee SR values in some parts of the Saharan area (e.g. Maghreb, western Africa). In Central Sahara, there is an obvious topological coincidence of the high SR, the local mountain chains and the inland waters. The PLS helped to quantify the relationships between bee SR and a set of eco-climatic variables. It also highlighted a residual variance not explained by the considered descriptors. Our results recover the tight link between bee SR and xeric ecosystems. They also suggest that, within these ecosystems, bee SR is driven by an optimum of the energy-water balance (on which adjustment is allowed by the above gradients).}, } @article {pmid19061501, year = {2008}, author = {Wu, WS and Li, WH}, title = {Systematic identification of yeast cell cycle transcription factors using multiple data sources.}, journal = {BMC bioinformatics}, volume = {9}, number = {}, pages = {522}, pmid = {19061501}, issn = {1471-2105}, support = {GM30998/GM/NIGMS NIH HHS/United States ; R01 GM081724/GM/NIGMS NIH HHS/United States ; GM081724/GM/NIGMS NIH HHS/United States ; R37 GM030998/GM/NIGMS NIH HHS/United States ; R01 GM030998/GM/NIGMS NIH HHS/United States ; }, mesh = {Cell Cycle/*genetics/physiology ; Computational Biology/*methods ; Gene Expression Regulation, Fungal/*genetics ; Models, Genetic ; Oligonucleotide Array Sequence Analysis ; Transcription Factors/*genetics ; Yeasts/*genetics/physiology ; }, abstract = {BACKGROUND: Eukaryotic cell cycle is a complex process and is precisely regulated at many levels. Many genes specific to the cell cycle are regulated transcriptionally and are expressed just before they are needed. To understand the cell cycle process, it is important to identify the cell cycle transcription factors (TFs) that regulate the expression of cell cycle-regulated genes.

RESULTS: We developed a method to identify cell cycle TFs in yeast by integrating current ChIP-chip, mutant, transcription factor binding site (TFBS), and cell cycle gene expression data. We identified 17 cell cycle TFs, 12 of which are known cell cycle TFs, while the remaining five (Ash1, Rlm1, Ste12, Stp1, Tec1) are putative novel cell cycle TFs. For each cell cycle TF, we assigned specific cell cycle phases in which the TF functions and identified the time lag for the TF to exert regulatory effects on its target genes. We also identified 178 novel cell cycle-regulated genes, among which 59 have unknown functions, but they may now be annotated as cell cycle-regulated genes. Most of our predictions are supported by previous experimental or computational studies. Furthermore, a high confidence TF-gene regulatory matrix is derived as a byproduct of our method. Each TF-gene regulatory relationship in this matrix is supported by at least three data sources: gene expression, TFBS, and ChIP-chip or/and mutant data. We show that our method performs better than four existing methods for identifying yeast cell cycle TFs. Finally, an application of our method to different cell cycle gene expression datasets suggests that our method is robust.

CONCLUSION: Our method is effective for identifying yeast cell cycle TFs and cell cycle-regulated genes. Many of our predictions are validated by the literature. Our study shows that integrating multiple data sources is a powerful approach to studying complex biological systems.}, } @article {pmid19060207, year = {2008}, author = {Wittemyer, G and Polansky, L and Douglas-Hamilton, I and Getz, WM}, title = {Disentangling the effects of forage, social rank, and risk on movement autocorrelation of elephants using Fourier and wavelet analyses.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {105}, number = {49}, pages = {19108-19113}, pmid = {19060207}, issn = {1091-6490}, mesh = {*Animal Migration ; Animals ; Ecology/*methods ; Elephants/*physiology ; Feeding Behavior/*physiology ; Female ; Fourier Analysis ; Geographic Information Systems ; Male ; *Models, Biological ; Movement ; *Social Dominance ; }, abstract = {The internal state of an individual-as it relates to thirst, hunger, fear, or reproductive drive-can be inferred by referencing points on its movement path to external environmental and sociological variables. Using time-series approaches to characterize autocorrelative properties of step-length movements collated every 3 h for seven free-ranging African elephants, we examined the influence of social rank, predation risk, and seasonal variation in resource abundance on periodic properties of movement. The frequency domain methods of Fourier and wavelet analyses provide compact summaries of temporal autocorrelation and show both strong diurnal and seasonal based periodicities in the step-length time series. This autocorrelation is weaker during the wet season, indicating random movements are more common when ecological conditions are good. Periodograms of socially dominant individuals are consistent across seasons, whereas subordinate individuals show distinct differences diverging from that of dominants during the dry season. We link temporally localized statistical properties of movement to landscape features and find that diurnal movement correlation is more common within protected wildlife areas, and multiday movement correlations found among lower ranked individuals are typically outside of protected areas where predation risks are greatest. A frequency-related spatial analysis of movement-step lengths reveal that rest cycles related to the spatial distribution of critical resources (i.e., forage and water) are responsible for creating the observed patterns. Our approach generates unique information regarding the spatial-temporal interplay between environmental and individual characteristics, providing an original approach for understanding the movement ecology of individual animals and the spatial organization of animal populations.}, } @article {pmid19060195, year = {2008}, author = {Mandel, JT and Bildstein, KL and Bohrer, G and Winkler, DW}, title = {Movement ecology of migration in turkey vultures.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {105}, number = {49}, pages = {19102-19107}, pmid = {19060195}, issn = {1091-6490}, mesh = {*Animal Migration ; Animals ; Birds/*physiology ; Ecology/*methods ; Flight, Animal ; *Geographic Information Systems ; Linear Models ; *Models, Biological ; Movement ; }, abstract = {We develop individual-based movement ecology models (MEM) to explore turkey vulture (Cathartes aura) migration decisions at both hourly and daily scales. Vulture movements in 10 migration events were recorded with satellite-reporting GPS sensors, and flight behavior was observed visually, aided by on-the-ground VHF radio-tracking. We used the North American Regional Reanalysis dataset to obtain values for wind speed, turbulent kinetic energy (TKE), and cloud height and used a digital elevation model for a measure of terrain ruggedness. A turkey vulture fitted with a heart-rate logger during 124 h of flight during 38 contiguous days showed only a small increase in mean heart rate as distance traveled per day increased, which suggests that, unlike flapping, soaring flight does not lead to greatly increased metabolic costs. Data from 10 migrations for 724 hourly segments and 152 daily segments showed that vultures depended heavily upon high levels of TKE in the atmospheric boundary layer to increase flight distances and maintain preferred bearings at both hourly and daily scales. We suggest how the MEM can be extended to other spatial and temporal scales of avian migration. Our success in relating model-derived atmospheric variables to migration indicates the potential of using regional reanalysis data, as here, and potentially other regional, higher-resolution, atmospheric models in predicting changing movement patterns of soaring birds under various scenarios of climate and land use change.}, } @article {pmid19057643, year = {2008}, author = {Wimberly, MC and Hildreth, MB and Boyte, SP and Lindquist, E and Kightlinger, L}, title = {Ecological niche of the 2003 west nile virus epidemic in the northern great plains of the United States.}, journal = {PloS one}, volume = {3}, number = {12}, pages = {e3744}, pmid = {19057643}, issn = {1932-6203}, support = {R01 AI079411/AI/NIAID NIH HHS/United States ; R01 AI079411-01/AI/NIAID NIH HHS/United States ; R01-AI79411/AI/NIAID NIH HHS/United States ; }, mesh = {*Disease Outbreaks ; Geographic Information Systems ; Humans ; Midwestern United States/epidemiology ; Models, Statistical ; Northwestern United States/epidemiology ; West Nile Fever/*epidemiology/transmission ; West Nile virus/pathogenicity ; }, abstract = {BACKGROUND: The incidence of West Nile virus (WNv) has remained high in the northern Great Plains compared to the rest of the United States. However, the reasons for the sustained high risk of WNv transmission in this region have not been determined. To assess the environmental drivers of WNv in the northern Great Plains, we analyzed the county-level spatial pattern of human cases during the 2003 epidemic across a seven-state region.

County-level data on WNv cases were examined using spatial cluster analysis, and were used to fit statistical models with weather, climate, and land use variables as predictors. In 2003 there was a single large cluster of elevated WNv risk encompassing North Dakota, South Dakota, and Nebraska along with portions of eastern Montana and Wyoming. The relative risk of WNv remained high within the boundaries of this cluster from 2004-2007. WNv incidence during the 2003 epidemic was found to have a stronger relationship with long-term climate patterns than with annual weather in either 2002 or 2003. WNv incidence increased with mean May-July temperature and had a unimodal relationship with total May-July precipitation. WNv incidence also increased with the percentage of irrigated cropland and with the percentage of the human population living in rural areas.

CONCLUSIONS/SIGNIFICANCE: The spatial pattern of WNv cases during the 2003 epidemic in the northern Great Plains was associated with both climatic gradients and land use patterns. These results were interpreted as evidence that environmental conditions across much of the northern Great Plains create a favorable ecological niche for Culex tarsalis, a particularly efficient vector of WNv. Further research is needed to determine the proximal causes of sustained WNv transmission and to enhance strategies for disease prevention.}, } @article {pmid19052320, year = {2008}, author = {Kunin, V and Copeland, A and Lapidus, A and Mavromatis, K and Hugenholtz, P}, title = {A bioinformatician's guide to metagenomics.}, journal = {Microbiology and molecular biology reviews : MMBR}, volume = {72}, number = {4}, pages = {557-78, Table of Contents}, pmid = {19052320}, issn = {1098-5557}, mesh = {*Database Management Systems ; Databases, Genetic ; Environmental Microbiology ; Genome/*genetics ; Genomics/*methods/standards ; Information Storage and Retrieval/*methods ; Sequence Analysis, DNA ; }, abstract = {As random shotgun metagenomic projects proliferate and become the dominant source of publicly available sequence data, procedures for the best practices in their execution and analysis become increasingly important. Based on our experience at the Joint Genome Institute, we describe the chain of decisions accompanying a metagenomic project from the viewpoint of the bioinformatic analysis step by step. We guide the reader through a standard workflow for a metagenomic project beginning with presequencing considerations such as community composition and sequence data type that will greatly influence downstream analyses. We proceed with recommendations for sampling and data generation including sample and metadata collection, community profiling, construction of shotgun libraries, and sequencing strategies. We then discuss the application of generic sequence processing steps (read preprocessing, assembly, and gene prediction and annotation) to metagenomic data sets in contrast to genome projects. Different types of data analyses particular to metagenomes are then presented, including binning, dominant population analysis, and gene-centric analysis. Finally, data management issues are presented and discussed. We hope that this review will assist bioinformaticians and biologists in making better-informed decisions on their journey during a metagenomic project.}, } @article {pmid19051047, year = {2009}, author = {Hale, SS and Hollister, JW}, title = {Beyond data management: how ecoinformatics can benefit environmental monitoring programs.}, journal = {Environmental monitoring and assessment}, volume = {150}, number = {1-4}, pages = {227-235}, pmid = {19051047}, issn = {1573-2959}, mesh = {Animals ; *Computational Biology ; Conservation of Natural Resources/methods ; *Ecosystem ; Environmental Monitoring/*methods ; Fresh Water ; *Models, Biological ; Seawater ; United States ; United States Environmental Protection Agency ; }, abstract = {We review ways in which the new discipline of ecoinformatics is changing how environmental monitoring data are managed, synthesized, and analyzed. Rapid improvements in information technology and strong interest in biodiversity and sustainable ecosystems are driving a vigorous phase of development in ecological databases. Emerging data standards and protocols enable these data to be shared in ways that have previously been difficult. We use the U.S. Environmental Protection Agency's National Coastal Assessment (NCA) as an example. The NCA has collected biological, chemical, and physical data from thousands of stations around the U.S. coasts since 1990. NCA data that were collected primarily to assess the ecological condition of the U.S. coasts can be used in innovative ways, such as biogeographical studies to analyze species invasions. NCA application of ecoinformatics tools leads to new possibilities for integrating the hundreds of thousands of NCA species records with other databases to address broad-scale and long-term questions such as environmental impacts, global climate change, and species invasions.}, } @article {pmid19049261, year = {2009}, author = {Noble, RB and Bailer, AJ and Noe, DA}, title = {Comparing methods for analyzing overdispersed binary data in aquatic toxicology.}, journal = {Environmental toxicology and chemistry}, volume = {28}, number = {5}, pages = {997-1006}, doi = {10.1897/08-221.1}, pmid = {19049261}, issn = {0730-7268}, mesh = {Computer Simulation ; *Data Interpretation, Statistical ; Ecotoxicology/*methods ; Environmental Pollutants ; *Models, Chemical ; *Models, Statistical ; Water/chemistry ; *Water Pollutants ; }, abstract = {Historically, death is the most commonly studied effect in aquatic toxicity tests. These tests typically employ a gradient of concentrations and exposure with more than one organism in a series of replicate chambers in each concentration. Whereas a binomial distribution commonly is employed for such effects, variability may exceed that predicted by binomial probability models. This additional variability could result from heterogeneity in the probabilities across the chambers in which the organisms are housed and subsequently exposed to concentrations of toxins. Incorrectly assuming a binomial distribution for the statistical analysis may lead to incorrect statistical inference. We consider the analysis of grouped binary data, here motivated by the study of survival. We use a computer simulation study to examine the impact of overdispersion or outliers on the analysis of binary data. We compare methods that assume binomial or generalizations that accommodate this potential overdispersion. These generalizations include adjusting the standard probit model for clustering/correlation or using alternative estimation methods, generalized estimating equations, or generalized linear mixed models (GLMM). When data were binomial or overdispersed binomial, none of the models exhibited any significant bias when estimating regression coefficients. When the data were truly binomial, the probit model controlled type I errors, as did the Donald and Donner method and the GLMM method. When data were overdispersed, the probit model no longer controlled type I error, and the standard errors were too small. In general, the Donald and Donner and the GLMM methods performed reasonably based on this study, although all procedures suffered some impact in the presence of potential outliers.}, } @article {pmid19046359, year = {2008}, author = {Crain, CM and Kroeker, K and Halpern, BS}, title = {Interactive and cumulative effects of multiple human stressors in marine systems.}, journal = {Ecology letters}, volume = {11}, number = {12}, pages = {1304-1315}, doi = {10.1111/j.1461-0248.2008.01253.x}, pmid = {19046359}, issn = {1461-0248}, mesh = {Animals ; Conservation of Natural Resources ; Databases, Factual ; *Ecosystem ; Humans ; Marine Biology ; Oceans and Seas ; Stress, Physiological/*physiology ; }, abstract = {Humans impact natural systems in a multitude of ways, yet the cumulative effect of multiple stressors on ecological communities remains largely unknown. Here we synthesized 171 studies that manipulated two or more stressors in marine and coastal systems and found that cumulative effects in individual studies were additive (26%), synergistic (36%), and antagonistic (38%). The overall interaction effect across all studies was synergistic, but interaction type varied by response level (community: antagonistic, population: synergistic), trophic level (autotrophs: antagonistic, heterotrophs: synergistic), and specific stressor pair (seven pairs additive, three pairs each synergistic and antagonistic). Addition of a third stressor changed interaction effects significantly in two-thirds of all cases and doubled the number of synergistic interactions. Given that most studies were performed in laboratories where stressor effects can be carefully isolated, these three-stressor results suggest that synergies may be quite common in nature where more than two stressors almost always coexist. While significant gaps exist in multiple stressor research, our results suggest an immediate need to account for stressor interactions in ecological studies and conservation planning.}, } @article {pmid19043583, year = {2008}, author = {Irwin, AJ and Finkel, ZV}, title = {Mining a sea of data: deducing the environmental controls of ocean chlorophyll.}, journal = {PloS one}, volume = {3}, number = {11}, pages = {e3836}, pmid = {19043583}, issn = {1932-6203}, mesh = {*Biomass ; Chlorophyll/analysis/*metabolism ; Climate ; Computational Biology ; *Ecosystem ; Food ; Light ; *Models, Biological ; Models, Statistical ; Nitrates ; Oceans and Seas ; Phytoplankton/metabolism ; }, abstract = {Chlorophyll biomass in the surface ocean is regulated by a complex interaction of physiological, oceanographic, and ecological factors and in turn regulates the rates of primary production and export of organic carbon to the deep ocean. Mechanistic models of phytoplankton responses to climate change require the parameterization of many processes of which we have limited knowledge. We develop a statistical approach to estimate the response of remote-sensed ocean chlorophyll to a variety of physical and chemical variables. Irradiance over the mixed layer depth, surface nitrate, sea-surface temperature, and latitude and longitude together can predict 83% of the variation in log chlorophyll in the North Atlantic. Light and nitrate regulate biomass through an empirically determined minimum function explaining nearly 50% of the variation in log chlorophyll by themselves and confirming that either light or macronutrients are often limiting and that much of the variation in chlorophyll concentration is determined by bottom-up mechanisms. Assuming the dynamics of the future ocean are governed by the same processes at work today, we should be able to apply these response functions to future climate change scenarios, with changes in temperature, nutrient distributions, irradiance, and ocean physics.}, } @article {pmid21448367, year = {2008}, author = {Strauch, AM and Muller, JM and Almedom, AM}, title = {Exploring the dynamics of social-ecological resilience in East and West Africa: Preliminary evidence from Tanzania and Niger.}, journal = {African health sciences}, volume = {8 Suppl 1}, number = {Suppl 1}, pages = {S28-35}, pmid = {21448367}, issn = {1729-0503}, mesh = {Adaptation, Psychological ; Agriculture ; Community Networks ; Community-Based Participatory Research ; *Conservation of Natural Resources ; Culture ; *Ecology ; *Ecosystem ; Humans ; Knowledge ; Niger ; Qualitative Research ; *Resilience, Psychological ; Social Conditions ; Tanzania ; Water Supply ; }, abstract = {BACKGROUND: Social-ecological resilience refers to the dynamic process of adaptive learning, reorganization and meaning-making demonstrated in linked human, animal, and plant ecosystems often organized in formal and/or informal social institutions, as they anticipate, withstand and/or judiciously engage with adversity while maintaining function without fundamentally losing their identity.

OBJECTIVE: To present two sets of examples that illustrate the complex ways in which transformation and persistence, two key aspects of the adaptive cycle may work together to preserve established patterns of human and/or animal uses of water resources and food plant species, in rural East and West Africa, respectively around the Serengeti National Park (Tanzania), and "Park W" (Niger), with the aim of identifying possible indicators of social-ecological resilience.

METHODS: Selective combinations of ecological and anthropological, quantitative and qualitative methods, including participatory tools of investigation and analysis.

RESULTS AND DISCUSSION: Our preliminary results are presented with minimal commentary and discussion in order to avoid hasty and/or unwarranted interpretation of the ongoing purposely iterative processes of investigation and analysis in the two study sites. Nevertheless we have identified a number of possible indicators of social-ecological resilience that may be tested in other localities in Africa and elsewhere.}, } @article {pmid19036133, year = {2008}, author = {Lu, T and Huang, X and Zhu, C and Huang, T and Zhao, Q and Xie, K and Xiong, L and Zhang, Q and Han, B}, title = {RICD: a rice indica cDNA database resource for rice functional genomics.}, journal = {BMC plant biology}, volume = {8}, number = {}, pages = {118}, pmid = {19036133}, issn = {1471-2229}, mesh = {Chromosomes, Plant ; Clone Cells ; DNA, Complementary/*genetics ; *Databases, Genetic ; *Genomics ; Internet ; Oryza/*genetics ; Sequence Analysis ; }, abstract = {BACKGROUND: The Oryza sativa L. indica subspecies is the most widely cultivated rice. During the last few years, we have collected over 20,000 putative full-length cDNAs and over 40,000 ESTs isolated from various cDNA libraries of two indica varieties Guangluai 4 and Minghui 63. A database of the rice indica cDNAs was therefore built to provide a comprehensive web data source for searching and retrieving the indica cDNA clones.

RESULTS: Rice Indica cDNA Database (RICD) is an online MySQL-PHP driven database with a user-friendly web interface. It allows investigators to query the cDNA clones by keyword, genome position, nucleotide or protein sequence, and putative function. It also provides a series of information, including sequences, protein domain annotations, similarity search results, SNPs and InDels information, and hyperlinks to gene annotation in both The Rice Annotation Project Database (RAP-DB) and The TIGR Rice Genome Annotation Resource, expression atlas in RiceGE and variation report in Gramene of each cDNA.

CONCLUSION: The online rice indica cDNA database provides cDNA resource with comprehensive information to researchers for functional analysis of indica subspecies and for comparative genomics. The RICD database is available through our website http://www.ncgr.ac.cn/ricd.}, } @article {pmid19031100, year = {2009}, author = {Bencko, V and Rames, J and Fabiánová, E and Pesek, J and Jakubis, M}, title = {Ecological and human health risk aspects of burning arsenic-rich coal.}, journal = {Environmental geochemistry and health}, volume = {31 Suppl 1}, number = {}, pages = {239-243}, pmid = {19031100}, issn = {1573-2983}, mesh = {Age Distribution ; Air Pollutants/analysis/*poisoning ; Arsenic/analysis/toxicity ; Arsenic Poisoning/epidemiology/*physiopathology ; Coal ; Databases, Factual ; Environmental Exposure/*adverse effects ; Environmental Monitoring/methods ; Epidemiological Monitoring ; Female ; Hair/chemistry ; Humans ; Incidence ; Male ; Power Plants ; Risk Assessment ; Sex Factors ; Skin Neoplasms/*chemically induced/epidemiology ; Slovakia/epidemiology ; Time Factors ; }, abstract = {The subject of the study was the ecological and human health consequences of environmental pollution from emissions arising from burning local coal with an arsenic content ranging from 900 to 1,500 g/tonne of dry substance. The first indication of environmental pollution by arsenic-containing emissions was the mass extinction of honeybee colonies. The neurotoxic and carcinogenic aspects of arsenic exposure were followed. On using a group diagnostics approach, significant hearing losses were detected in exposed children in both air and bone conduction audiometry at high frequency range (4,000 and 8,000 Hz, respectively). Exposure assessment of the local population of the Prievidza district, Central Slovakia, was based on biological monitoring. The criterion of higher exposure was arsenic content in hair exceeding concentrations of 3 microg/g of hair. In a 7.5-km radius of the exposed region, live about two-tenths of the district population who were considered as "exposed" and rest of the district served as the "reference" population. The subject of our analysis was a database of 1,503 non-melanoma skin cancer (NMSC) cases (756 in men and 747 in women) collected from 1977 to 1996 in the Prievidza district, Central Slovakia (population approximately 125,000). The age standardized incidence of NMSC (each confirmed by histological examination) in non-occupational settings ranged from 45.9 to 93.9 in men and from 34.6 to 81.4 in women. Analysis of our data demonstrates a positive correlation between human cumulative exposure to arsenic and incidence of NMSC.}, } @article {pmid19029140, year = {2009}, author = {Maheswari, U and Mock, T and Armbrust, EV and Bowler, C}, title = {Update of the Diatom EST Database: a new tool for digital transcriptomics.}, journal = {Nucleic acids research}, volume = {37}, number = {Database issue}, pages = {D1001-5}, pmid = {19029140}, issn = {1362-4962}, mesh = {*Databases, Genetic ; Diatoms/*genetics/metabolism ; Expressed Sequence Tags/*metabolism ; Gene Expression Profiling ; Internet ; User-Computer Interface ; }, abstract = {The Diatom Expressed Sequence Tag (EST) Database was constructed to provide integral access to ESTs from these ecologically and evolutionarily interesting microalgae. It has now been updated with 130,000 Phaeodactylum tricornutum ESTs from 16 cDNA libraries and 77,000 Thalassiosira pseudonana ESTs from seven libraries, derived from cells grown in different nutrient and stress regimes. The updated relational database incorporates results from statistical analyses such as log-likelihood ratios and hierarchical clustering, which help to identify differentially expressed genes under different conditions, and allow similarities in gene expression in different libraries to be investigated in a functional context. The database also incorporates links to the recently sequenced genomes of P. tricornutum and T. pseudonana, enabling an easy cross-talk between the expression pattern of diatom orthologs and the genome browsers. These improvements will facilitate exploration of diatom responses to conditions of ecological relevance and will aid gene function identification of diatom-specific genes and in silico gene prediction in this largely unexplored class of eukaryotes. The updated Diatom EST Database is available at http://www.biologie.ens.fr/diatomics/EST3.}, } @article {pmid19022554, year = {2009}, author = {Bohlen, C and Lewis, LY}, title = {Examining the economic impacts of hydropower dams on property values using GIS.}, journal = {Journal of environmental management}, volume = {90 Suppl 3}, number = {}, pages = {S258-69}, doi = {10.1016/j.jenvman.2008.07.026}, pmid = {19022554}, issn = {1095-8630}, mesh = {*Geographic Information Systems ; Housing/*economics ; Rivers ; *Social Change ; *Water Supply ; }, abstract = {While the era of dam building is largely over in the United States, globally dams are still being proposed and constructed. The articles in this special issue consider many aspects and impacts of dams around the world. This paper examines dam removal and the measurement of the impacts of dams on local community property values. Valuable lessons may be found. In the United States, hundreds of small hydropower dams will come up for relicensing in the coming decade. Whether or not the licenses are renewed and what happens to the dams if the licenses expires is a subject of great debate. Dams are beginning to be removed for river restoration and fisheries restoration and these "end-of-life" decisions may offer lessons for countries proposing or currently building small (and large) hydropower dams. What can these restoration stories tell us? In this paper, we examine the effects of dams along the Penobscot River in Maine (USA) on residential property values. We compare the results to findings from a similar (but ex post dam removal) data set for properties along the Kennebec river in Maine, where the Edwards Dam was removed in 1999. The Penobscot River Restoration Project, an ambitious basin-wide restoration effort, includes plans to remove two dams and decommission a third along the Penobscot River. Dam removal has significant effects on the local environment, and it is reasonable to anticipate that environmental changes will themselves be reflected in changes in property values. Here we examine historical real estate transaction data to examine whether landowners pay a premium or penalty to live near the Penobscot River or near a hydropower generating dam. We find that waterfront landowners on the Penobscot or other water bodies in our study area pay approximately a 16% premium for the privilege of living on the water. Nevertheless, landowners pay LESS to live near the Penobscot River than they do to live further away, contrary to the expectation that bodies of water function as real estate amenities and boost local property values. Results with respect to the effect of proximity to hydropower generating plants are equivocal. Homeowners pay a small premium for houses close to hydropower dams in our region, but the statistical significance of that result depends on the specific model form used to estimate the effect. Consideration of the social and economic impacts of dam removal-based river restoration can complement studies of the ecological impacts of the practice. Such studies help us understand the extent to which human society's subjective perception of value of aquatic ecosystems relates to objective measures of ecosystem health. The paper also illustrates how geographic information systems (GIS) can help inform these analyses.}, } @article {pmid19021110, year = {2008}, author = {Tourre, YM and Lacaux, JP and Vignolles, C and Ndione, JA and Lafaye, M}, title = {Mapping of zones potentially occupied by Aedes vexans and Culex poicilipes mosquitoes, the main vectors of Rift Valley fever in Senegal.}, journal = {Geospatial health}, volume = {3}, number = {1}, pages = {69-79}, doi = {10.4081/gh.2008.233}, pmid = {19021110}, issn = {1970-7096}, mesh = {Aedes/*physiology/virology ; Animals ; Culex/*physiology/virology ; Demography ; *Ecology ; Fresh Water/parasitology ; Geographic Information Systems ; Insect Vectors/*physiology/virology ; Population Density ; Population Dynamics ; Rain ; Rift Valley Fever/epidemiology/transmission/virology ; Rift Valley fever virus/*physiology ; Satellite Communications ; Seasons ; Senegal/epidemiology ; Species Specificity ; Time Factors ; }, abstract = {A necessary condition for Rift Valley fever (RVF) emergence is the presence of Aedes (Aedimorphus) vexans and Culex (Culex) poicilipes mosquitoes carrying the arbovirus and responsible for the infection. This paper presents a detailed mapping in the Sahelian region of Senegal of zones potentially occupied by these mosquitoes (ZPOMs) whose population density is directly linked to ecozones in the vicinity of small ponds. The vectors habitats and breeding sites have been characterized through an integrated approach combining remote sensing technology, geographical information systems, geographical positioning systems and field observations for proper geo-referencing. From five SPOT-5 images (approximately 10 m spatial resolution) with appropriate channels, a meridional composite transect of 290 x 60 km was first constructed at the height of the summer monsoon. Subsequent ZPOMs covered major ecozones from north to south with different hydrological environments and different patterns pond distributions. It was found that an overall area of 12,817 ha +/- 10% (about 0.8% of the transect) is occupied by ponds with an average ZPOM 17 times larger than this (212,813 ha +/- 10% or about 14% of the transect). By comparing the very humid year of 2003 with 2006 which had just below normal rainfall, the ZPOMs inter-annual variability was analyzed in a sandy-clayey ecozone with an important hydrofossil riverbed within the Ferlo region of Senegal. Very probably contributing to an increased abundance of vectors by the end of August 2003, it was shown that the aggregate pond area was already about 22 times larger than in August 2006, corresponding to an approximately five times larger total ZPOM. The results show the importance of pin-pointing small ponds (sizes down to 0.1 ha) and their geographical distribution in order to assess animal exposure to the RVF vectors.}, } @article {pmid19021109, year = {2008}, author = {Simoonga, C and Kazembe, LN and Kristensen, TK and Olsen, A and Appleton, CC and Mubita, P and Mubila, L}, title = {The epidemiology and small-scale spatial heterogeneity of urinary schistosomiasis in Lusaka province, Zambia.}, journal = {Geospatial health}, volume = {3}, number = {1}, pages = {57-67}, doi = {10.4081/gh.2008.232}, pmid = {19021109}, issn = {1970-7096}, mesh = {Adolescent ; Animals ; Child ; Cross-Sectional Studies ; Demography ; Disease Vectors ; Ecology ; Female ; Geographic Information Systems ; Humans ; Logistic Models ; Male ; Parasite Egg Count ; Prevalence ; Risk Factors ; Schistosoma haematobium/*isolation & purification/parasitology ; Schistosoma mansoni/*isolation & purification/parasitology ; Schistosomiasis haematobia/*epidemiology/parasitology/prevention & control ; Schools ; Snails/parasitology ; Socioeconomic Factors ; Water/parasitology ; Zambia/epidemiology ; }, abstract = {In line with the aims of the "National Bilharzia Control Programme" and the "School Health and Nutrition Programme" in Zambia, a study on urinary schistosomiasis was conducted in 20 primary schools of Lusaka province to further our understanding of the epidemiology of the infection, and to enhance spatial targeting of control. We investigated risk factors associated with urinary schistosomiasis, and examined small-scale spatial heterogeneity in prevalence, using data collected from 1,912 schoolchildren, 6 to 15-year-old, recruited from 20 schools in Kafue and Luangwa districts. The risk factors identified included geographical location, altitude, normalized difference vegetation index (NDVI), maximum temperature, age, sex of the child and intermediate host snail abundance. Three logistic regression models were fitted assuming different random effects to allow for spatial structuring. The mean prevalence rate was 9.6%, with significance difference between young and older children (odds ratio (OR) = 0.71; 95% confidence interval (CI) = 0.51-0.96). The risk of infection was related to intermediate host snail abundance (OR = 1.03; 95% CI = 1.00-1.05) and vegetation cover (OR = 1.04; 95% CI = 1.00-1.07). Schools located either on the plateau and the valley also differed in prevalence and intensity of infection for moderate infection to none (OR = 1.64; 95% CI = 1.36- 1.96). The overall predictive performance of the spatial random effects model was higher than the ordinary logistic regression. In addition, evidence of heterogeneity of the infection risk was found at the micro-geographical level. A sound understanding of small-scale heterogeneity, caused by spatial aggregation of schoolchildren, is important to inform health planners for implementing control schistosomiasis interventions.}, } @article {pmid19021106, year = {2008}, author = {Zendejas-Martínez, H and Townsend Peterson, A and Milián-Suazo, F}, title = {Coarse-scale spatial and ecological analysis of tuberculosis in cattle: an investigation in Jalisco, Mexico.}, journal = {Geospatial health}, volume = {3}, number = {1}, pages = {29-38}, doi = {10.4081/gh.2008.229}, pmid = {19021106}, issn = {1970-7096}, mesh = {*Animal Husbandry ; Animals ; Cattle/classification/microbiology ; *Dairying ; Demography ; *Ecology ; *Environment ; Geographic Information Systems ; Mexico/epidemiology ; Mycobacterium bovis/growth & development/*isolation & purification ; Prevalence ; Tuberculin Test/veterinary ; Tuberculosis, Bovine/*epidemiology/microbiology ; }, abstract = {We have tested the hypothesis that coarse-scale environmental features are associated with spatial variation in bovine tuberculosis (BTB) prevalence, based on extensive sampling and testing of cattle in the state of Jalisco, Mexico. Ecological niche models were developed to summarize relationships between BTB occurrences and aspects of climate, topography and surface. Model predictions, however, reflected the distributions of dairy cattle versus beef cattle, and the non-random nature of sampling any cattle, but did not succeed in detecting environmental correlates at spatial resolutions of 1 km. Given that the tests employed seek any predictivity better than random expectations, making the finding of no environmental associations conservative, we conclude that BTB prevalence is independent of coarsescale environmental features.}, } @article {pmid19021104, year = {2008}, author = {Cecchi, G and Ilemobade, A and Le Brun, Y and Hogerwerf, L and Slingenbergh, J}, title = {Agro-ecological features of the introduction and spread of the highly pathogenic avian influenza (HPAI) H5N1 in northern Nigeria.}, journal = {Geospatial health}, volume = {3}, number = {1}, pages = {7-16}, doi = {10.4081/gh.2008.227}, pmid = {19021104}, issn = {1970-7096}, mesh = {*Animal Husbandry ; Animal Migration ; Animals ; Animals, Wild/virology ; Birds/virology ; Chickens/virology ; Communicable Diseases, Emerging/*epidemiology/veterinary/virology ; Demography ; Disease Outbreaks/*veterinary ; Ducks/virology ; Ecology ; Influenza A Virus, H5N1 Subtype/*pathogenicity ; Influenza in Birds/*epidemiology ; Nigeria/epidemiology ; Poultry/classification/virology ; Poultry Diseases/*epidemiology/virology ; Public Health Informatics ; Rain ; Retrospective Studies ; Seasons ; Wetlands ; }, abstract = {Nigeria was the first African country to report highly pathogenic avian influenza (HPAI) H5N1 virus outbreaks in February 2006 and has since been the most severely hit country in sub-Saharan Africa. A retrospective survey carried out towards the end of 2007, coupled with follow-up spatial analysis, support the notion that the H5N1 virus may have spread from rural areas of northern Nigeria near wetlands frequented by palaearctic migratory birds. Possibly, this could have happened already during November to December 2005, one or two months prior to the first officially reported outbreak in a commercial poultry farm (Kaduna state). It is plausible that backyard poultry played a more important role in the H5N1 propagation than thought previously. Farming landscapes with significant numbers of domestic ducks may have helped to bridge the geographical and ecological gap between the waterfowl in the wetlands and the densely populated poultry rich states in north-central Nigeria, where the virus had more sizeable, visible impact.}, } @article {pmid19020986, year = {2009}, author = {Woodford, MH}, title = {Veterinary aspects of ecological monitoring: the natural history of emerging infectious diseases of humans, domestic animals and wildlife.}, journal = {Tropical animal health and production}, volume = {41}, number = {7}, pages = {1023-1033}, pmid = {19020986}, issn = {1573-7438}, mesh = {Animals ; *Animals, Domestic ; *Animals, Wild ; Climate ; Communicable Diseases, Emerging/transmission/*veterinary ; *Disease Vectors ; *Environment ; Environmental Monitoring/*methods ; Geographic Information Systems ; Humans ; Veterinary Medicine/*methods ; *Zoonoses ; }, abstract = {Proliferation of disease pathogens capable of affecting humans, domestic livestock and wildlife increasingly threatens environmental security and biodiversity. Livestock and wild animals in proximity to human beings are often in the chain of transmission and infection. Globalization of industrial livestock production (especially poultry upon which so much of the burgeoning human population depends) often permits transcontinental disease spread. Rapidly expanding (and often illegal) international trade in wild and domestic animals and their products are increasingly involved in the emergence of new diseases that may have the ability to transmit among humans, livestock and wildlife. Rapidly increasing urbanization has led in many places to overcrowded townships that rely on "bushmeat" for sustenance and has contributed to the emergence of virulent zoonotic pathogens. The emergence and proliferation of pathogens are exacerbated by anthropogenic transformation of natural landscapes in order to increase agricultural and livestock production. This paper posits that data gathered by veterinary ecologists should be interpreted and used by other disciplines. The importance of a thorough knowledge of the "natural history" (ecology) of the disease agent and its human, domestic and wild hosts is stressed.}, } @article {pmid19020927, year = {2009}, author = {Swett, RA and Listowski, C and Fry, D and Boutelle, S and Fann, D}, title = {A regional waterway management system for balancing recreational boating and resource protection.}, journal = {Environmental management}, volume = {43}, number = {6}, pages = {962-971}, doi = {10.1007/s00267-008-9231-2}, pmid = {19020927}, issn = {1432-1009}, mesh = {Conservation of Natural Resources/*methods ; Data Collection/methods ; Environment Design ; Florida ; Geographic Information Systems ; Geography ; Location Directories and Signs/classification ; Oceans and Seas ; *Recreation/economics ; Rivers ; *Ships/economics/legislation & jurisprudence ; Urbanization ; }, abstract = {Florida's coasts have been transformed over the past three decades as population growth and unprecedented demand for individual shore access to bays and estuaries led to the creation of residential canal developments. Thousands of miles of channels and basins were dredged as a by-product of this urbanization process. The navigable waterways that resulted are now being stressed by increasing boat traffic and canal-side activities. Recognizing their common goal to preserve the recreational and ecological value of southwest Florida waterways, the Florida Department of Environmental Protection, the four-county West Coast Inland Navigation District, and the University of Florida Sea Grant College Program signed a Memorandum of Agreement. The signatories agreed to develop a science-based Regional Waterway Management System (RWMS), which is a new approach to waterway planning and permitting based on carefully mapped channel depths, a census of actual boat populations, and the spatial extent of natural resources. The RWMS provides a comprehensive, regional overview of channel conditions and the geographic distribution and severity of existing impediments to safe navigation and resource protection. RWMS information and analyses result in regional-scale permitting to accommodate water-dependent uses while minimizing environmental impacts and reducing public expenditures. Compared with traditional approaches to waterway management, the science-based RWMS is relatively unbiased, objective, transparent, ecologically sound, and fiscally prudent.}, } @article {pmid19019436, year = {2009}, author = {Shannon, LM and Walker, R and Blevins, M}, title = {Developing a new system to measure outcomes in a service coordination program for youth with severe emotional disturbance.}, journal = {Evaluation and program planning}, volume = {32}, number = {2}, pages = {109-118}, doi = {10.1016/j.evalprogplan.2008.09.006}, pmid = {19019436}, issn = {1873-7870}, mesh = {Adolescent ; *Adolescent Health Services ; Affective Symptoms/*rehabilitation ; Age Factors ; Case Management ; *Community Mental Health Services ; Community Networks ; Computers, Handheld ; Data Collection ; Humans ; *Models, Organizational ; *Outcome Assessment, Health Care ; Program Development ; *Program Evaluation ; United States ; }, abstract = {This paper presents information on re-developing an outcome evaluation for a state-funded program providing service coordination utilizing wraparound to youth with severe emotional disturbance (SED) and their families. Originally funded by the Robert Wood Johnson Foundation, the Kentucky IMPACT program has existed statewide since 1990. Changing data needs and limitations of the original evaluation required revamping the program's data collection system. The new evaluation uses the extant knowledge base to improve: (1) design, (2) measures, and (3) utility. A pre-post design with multiple follow-ups provides the framework for data collection. An ecological framework provides a conceptual structure for selecting measures focusing on both the service recipients and their environment. Data collection via a personal digital assistant (PDA) ensures utility of the data for both consumers and researchers. Issues ranging from conceptualization to implementation of the project as well as lessons learned are discussed.}, } @article {pmid19015828, year = {2009}, author = {Chen, CH and Wu, RS and Liu, WL and Su, WR and Chang, YM}, title = {Development of a methodology for strategic environmental assessment: application to the assessment of golf course installation policy in Taiwan.}, journal = {Environmental management}, volume = {43}, number = {1}, pages = {166-188}, pmid = {19015828}, issn = {1432-1009}, mesh = {Conservation of Natural Resources/*methods ; *Environment ; *Environment Design ; Geographic Information Systems ; *Golf ; Information Management/methods ; *Policy Making ; Taiwan ; }, abstract = {Some countries, including Taiwan, have adopted strategic environmental assessment (SEA) to assess and modify proposed policies, plans, and programs (PPPs) in the planning phase for pursuing sustainable development. However, there were only some sketchy steps focusing on policy assessment in the system of Taiwan. This study aims to develop a methodology for SEA in Taiwan to enhance the effectiveness associated with PPPs. The proposed methodology comprises an SEA procedure involving PPP management and assessment in various phases, a sustainable assessment framework, and an SEA management system. The SEA procedure is devised based on the theoretical considerations by systems thinking and the regulative requirements in Taiwan. The positive and negative impacts on ecology, society, and economy are simultaneously considered in the planning (including policy generation and evaluation), implementation, and control phases of the procedure. This study used the analytic hierarchy process, Delphi technique, and systems analysis to develop a sustainable assessment framework. An SEA management system was built based on geographic information system software to process spatial, attribute, and satellite image data during the assessment procedure. The proposed methodology was applied in the SEA of golf course installation policy in 2001 as a case study, which was the first SEA in Taiwan. Most of the 82 existing golf courses in 2001 were installed on slope lands and caused a serious ecological impact. Assessment results indicated that 15 future golf courses installed on marginal lands (including buffer zones, remedied lands, and wastelands) were acceptable because the comprehensive environmental (ecological, social, and economic) assessment value was better based on environmental characteristics and management regulations of Taiwan. The SEA procedure in the planning phase for this policy was completed but the implementation phase of this policy was not begun because the related legislation procedure could not be arranged due to a few senators' resistance. A self-review of the control phase was carried out in 2006 using this methodology. Installation permits for 12 courses on slope lands were terminated after 2001 and then 27 future courses could be installed on marginal lands. The assessment value of this policy using the data on ecological, social, and economic conditions from 2006 was higher than that using the data from 2001. The analytical results illustrate that the proposed methodology can be used to effectively and efficiently assist the related authorities for SEA.}, } @article {pmid19015827, year = {2009}, author = {Meyer, BC and Lescot, JM and Laplana, R}, title = {Comparison of two spatial optimization techniques: a framework to solve multiobjective land use distribution problems.}, journal = {Environmental management}, volume = {43}, number = {2}, pages = {264-281}, pmid = {19015827}, issn = {1432-1009}, mesh = {Agriculture/methods ; Conservation of Natural Resources/*methods ; *Ecosystem ; France ; Geographic Information Systems ; Geography ; *Models, Theoretical ; Planning Techniques ; *Policy Making ; *Rivers ; }, abstract = {Two spatial optimization approaches, developed from the opposing perspectives of ecological economics and landscape planning and aimed at the definition of new distributions of farming systems and of land use elements, are compared and integrated into a general framework. The first approach, applied to a small river catchment in southwestern France, uses SWAT (Soil and Water Assessment Tool) and a weighted goal programming model in combination with a geographical information system (GIS) for the determination of optimal farming system patterns, based on selected objective functions to minimize deviations from the goals of reducing nitrogen and maintaining income. The second approach, demonstrated in a suburban landscape near Leipzig, Germany, defines a GIS-based predictive habitat model for the search of unfragmented regions suitable for hare populations (Lepus europaeus), followed by compromise optimization with the aim of planning a new habitat structure distribution for the hare. The multifunctional problem is solved by the integration of the three landscape functions ("production of cereals," "resistance to soil erosion by water," and "landscape water retention"). Through the comparison, we propose a framework for the definition of optimal land use patterns based on optimization techniques. The framework includes the main aspects to solve land use distribution problems with the aim of finding the optimal or best land use decisions. It integrates indicators, goals of spatial developments and stakeholders, including weighting, and model tools for the prediction of objective functions and risk assessments. Methodological limits of the uncertainty of data and model outcomes are stressed. The framework clarifies the use of optimization techniques in spatial planning.}, } @article {pmid19013534, year = {2009}, author = {Dixon, CJ and Schönswetter, P and Suda, J and Wiedermann, MM and Schneeweiss, GM}, title = {Reciprocal Pleistocene origin and postglacial range formation of an allopolyploid and its sympatric ancestors (Androsace adfinis group, Primulaceae).}, journal = {Molecular phylogenetics and evolution}, volume = {50}, number = {1}, pages = {74-83}, doi = {10.1016/j.ympev.2008.10.009}, pmid = {19013534}, issn = {1095-9513}, mesh = {DNA, Plant/genetics ; Databases, Nucleic Acid ; Europe ; *Phylogeny ; Ploidies ; *Polyploidy ; Primulaceae/*classification/*genetics ; Time Factors ; }, abstract = {The biogeographic history of polyploids and their lower-ploid ancestors is an important feature to achieve a better understanding of polyploid evolution. This is exemplified here using the ecologically congruent members of the Androsace adfinis group (Primulaceae) endemic to the southwestern European Alps. Employing relative genome size, AFLP fingerprint and chloroplast sequence haplotype data, we show that Androsace brigantiaca is a recent (probably no more than 0.2 million years) allopolyploid derivative of the geographically close A. adfinis and A. puberula, which formed reciprocally in a comparatively restricted area in the southern Southwestern Alps. Bayesian admixture analysis--also of artificial additive AFLP profiles--shows that the nuclear genome of A. brigantiaca is significantly biased towards the puberula-genome irrespective of maternal parentage. Nevertheless, there is no evidence for genetic interaction (hybridization, introgression) of A. brigantiaca with either of its ancestors, including the widely sympatric A. puberula. Sympatry might be facilitated by ecological displacement on a local scale or might be a transitory phase on the way to competitive replacement via, for instance, polyploid superiority.}, } @article {pmid19008248, year = {2009}, author = {Carlson, RP}, title = {Decomposition of complex microbial behaviors into resource-based stress responses.}, journal = {Bioinformatics (Oxford, England)}, volume = {25}, number = {1}, pages = {90-97}, pmid = {19008248}, issn = {1367-4811}, support = {EB006532/EB/NIBIB NIH HHS/United States ; }, mesh = {Adaptation, Physiological ; Computational Biology ; Ecosystem ; Escherichia coli/*physiology ; Least-Squares Analysis ; Metabolic Networks and Pathways ; Models, Biological ; *Stress, Physiological ; }, abstract = {MOTIVATION: Highly redundant metabolic networks and experimental data from cultures likely adapting simultaneously to multiple stresses can complicate the analysis of cellular behaviors. It is proposed that the explicit consideration of these factors is critical to understanding the competitive basis of microbial strategies.

RESULTS: Wide ranging, seemingly unrelated Escherichia coli physiological fluxes can be simply and accurately described as linear combinations of a few ecologically relevant stress adaptations. These strategies were identified by decomposing the central metabolism of E.coli into elementary modes (mathematically defined biochemical pathways) and assessing the resource investment cost-benefit properties for each pathway. The approach capitalizes on the inherent tradeoffs related to investing finite resources like nitrogen into different pathway enzymes when the pathways have varying metabolic efficiencies. The subset of ecologically competitive pathways represented 0.02% of the total permissible pathways. The biological relevance of the assembled strategies was tested against 10 000 randomly constructed pathway subsets. None of the randomly assembled collections were able to describe all of the considered experimental data as accurately as the cost-based subset. The results suggest these metabolic strategies are biologically significant. The current descriptions were compared with linear programming (LP)-based flux descriptions using the Euclidean distance metric. The current study's pathway subset described the experimental fluxes with better accuracy than the LP results without having to test multiple objective functions or constraints and while providing additional ecological insight into microbial behavior. The assembled pathways seem to represent a generalized set of strategies that can describe a wide range of microbial responses and hint at evolutionary processes where a handful of successful metabolic strategies are utilized simultaneously in different combinations to adapt to diverse conditions.}, } @article {pmid19006977, year = {2008}, author = {Mongoh, MN and Dyer, NW and Stoltenow, CL and Khaitsa, ML}, title = {Risk factors associated with anthrax outbreak in animals in North Dakota, 2005: a retrospective case-control study.}, journal = {Public health reports (Washington, D.C. : 1974)}, volume = {123}, number = {3}, pages = {352-359}, pmid = {19006977}, issn = {0033-3549}, mesh = {Animal Diseases/*epidemiology/*microbiology/prevention & control ; Animals ; Anthrax/*epidemiology/prevention & control/*veterinary ; Anthrax Vaccines/administration & dosage ; Anti-Bacterial Agents/administration & dosage ; Bacillus anthracis/isolation & purification ; Chi-Square Distribution ; Disease Outbreaks/*prevention & control/*veterinary ; Ecosystem ; Geographic Information Systems ; Horses ; North Dakota/epidemiology ; Polymerase Chain Reaction ; Public Health/*methods ; Risk Assessment/*methods ; Risk Factors ; Ruminants ; Sentinel Surveillance ; Swine ; Veterinary Medicine/*methods ; }, abstract = {OBJECTIVE: We identified the risk factors associated with the anthrax outbreak Of 2005 in animals in North Dakota.

METHODS: Medical records of the 2005 anthrax outbreak were obtained from the Veterinary Diagnostic Laboratory at North Dakota State University. Additional data were obtained from the North Dakota state veterinarian's office, and supplemental questionnaires were administered to producers. The data obtained included ecological and environmental factors, animal health factors, and management factors.

RESULTS: Anthrax occurred from July 1 to October 12, 2005. The cases were located in eastern North Dakota around the Red River Basin. Ransom, LaMoure, and Barnes counties reported most cases (71%). Species affected included cattle, bison, horses, sheep, elk, deer, pigs, and llamas. The predominant symptom was sudden death (38%) followed by bleeding from orifices (17%). Chi-square analysis indicated significant differences between case and control premises on the following variables: death reported on neighboring pasture, vaccination period, dry conditions, wet conditions, antibiotic use, multiple vaccination, and type of predator (coyote). Factors that significantly (p<0.05) predicted anthrax occurrences on the final logistic regression model were vaccination, use of antibiotics during an outbreak, and period of vaccine administration (before or during the outbreak).

CONCLUSIONS: The characteristics of the anthrax outbreak regarding time and place of occurrence, animals affected, clinical signs reported, and mortality rate were consistent with previous reports of natural anthrax outbreaks in animals. A number of factors that significantly predicted anthrax occurrence in animals in the 2005 outbreak in North Dakota were identified. This information is important in planning appropriate control and prevention measures for anthrax, including recommending the right vaccination and treatment regimens in managing future anthrax outbreaks.}, } @article {pmid19004872, year = {2009}, author = {Cole, JR and Wang, Q and Cardenas, E and Fish, J and Chai, B and Farris, RJ and Kulam-Syed-Mohideen, AS and McGarrell, DM and Marsh, T and Garrity, GM and Tiedje, JM}, title = {The Ribosomal Database Project: improved alignments and new tools for rRNA analysis.}, journal = {Nucleic acids research}, volume = {37}, number = {Database issue}, pages = {D141-5}, pmid = {19004872}, issn = {1362-4962}, support = {P42 ES004911/ES/NIEHS NIH HHS/United States ; P42ES04911/ES/NIEHS NIH HHS/United States ; }, mesh = {Computer Graphics ; *Databases, Nucleic Acid ; Internet ; RNA, Archaeal/*chemistry/classification ; RNA, Bacterial/*chemistry/classification ; RNA, Ribosomal/*chemistry/classification ; Sequence Alignment ; *Sequence Analysis, RNA ; Software ; }, abstract = {The Ribosomal Database Project (RDP) provides researchers with quality-controlled bacterial and archaeal small subunit rRNA alignments and analysis tools. An improved alignment strategy uses the Infernal secondary structure aware aligner to provide a more consistent higher quality alignment and faster processing of user sequences. Substantial new analysis features include a new Pyrosequencing Pipeline that provides tools to support analysis of ultra high-throughput rRNA sequencing data. This pipeline offers a collection of tools that automate the data processing and simplify the computationally intensive analysis of large sequencing libraries. In addition, a new Taxomatic visualization tool allows rapid visualization of taxonomic inconsistencies and suggests corrections, and a new class Assignment Generator provides instructors with a lesson plan and individualized teaching materials. Details about RDP data and analytical functions can be found at http://rdp.cme.msu.edu/.}, } @article {pmid19004752, year = {2009}, author = {Kleynhans, E and Terblanche, JS}, title = {The evolution of water balance in Glossina (Diptera: Glossinidae): correlations with climate.}, journal = {Biology letters}, volume = {5}, number = {1}, pages = {93-96}, pmid = {19004752}, issn = {1744-9561}, mesh = {Adaptation, Physiological ; Animals ; *Biological Evolution ; *Climate ; Geographic Information Systems ; Geography ; Homeostasis ; Phylogeny ; Pupa/classification/metabolism/physiology ; Rain ; Tsetse Flies/classification/metabolism/*physiology ; Water/*metabolism ; }, abstract = {The water balance of tsetse flies (Diptera: Glossinidae) has significant implications for understanding biogeography and climate change responses in these African disease vectors. Although moisture is important for tsetse population dynamics, evolutionary responses of Glossina water balance to climate have been relatively poorly explored and earlier studies may have been confounded by several factors. Here, using a physiological and GIS climate database, we investigate potential interspecific relationships between traits of water balance and climate. We do so in conventional and phylogenetically independent approaches for both adults and pupae. Results showed that water loss rates (WLR) were significantly positively related to precipitation in pupae even after phylogenetic adjustment. Adults showed no physiology-climate correlations. Ancestral trait reconstruction suggests that a reduction in WLR and increased size probably evolved from an intermediate ancestral state and may have facilitated survival in xeric environments. The results of this study therefore suggest an important role for water balance physiology of pupae in determining interspecific variation and lend support to conclusions reached by early studies of tsetse physiology.}, } @article {pmid19004334, year = {2008}, author = {Ponomareva, IS}, title = {[Biological cycle of radionuclides and dynamics of cattle leukemia in the Orenburg region].}, journal = {Radiatsionnaia biologiia, radioecologiia}, volume = {48}, number = {5}, pages = {606-610}, pmid = {19004334}, issn = {0869-8031}, mesh = {*Animal Feed/analysis/standards ; Animals ; Cattle ; Data Interpretation, Statistical ; Enzootic Bovine Leukosis/epidemiology/*etiology ; Leukemia Virus, Bovine/isolation & purification ; Radiation Monitoring/*methods ; Radioisotopes/*analysis/toxicity ; Russia/epidemiology ; Soil Pollutants, Radioactive/*analysis/toxicity ; }, abstract = {Global technogenic radionuclides pollution of environment, migration of radionuclides from soil into animal feeds stimulate additional contamination doses. Concentration of natural and of technogenic radionuclides in the investigated objects was determined as result of radiochemical and radiometric studies. It was established that maximum concentrations of 40K, 232Th, 226Ra (Bk/kg) radionuclides in the soil of the eastern zone was 391.6 +/- 77.64; 20.8 +/- 0.71; 16.7 +/- 0.8 (respectively) without exceeding permissable levels. It is also found that the density of soil pollution with 137Cs in the western zone is 0.28 +/- 0.075 mBk/m2 (76.8 +/- 20.4 mKi/km2), such soils are to be considered as locally polluted soils. The number of cattle infected with cattle leucosis is obviously higher in ecologically unsafe areas: 19.3% on the western farms, 12.95% in the central areas and 9.70% on the farms of the eastern zone. Long-term exposure to ecologically unsafe conditions may lead to the reduction of populations immune status expressed in lower disease resistance and in incidence of carcinogenic pathology.}, } @article {pmid19000519, year = {2008}, author = {Luque Fernández, MA}, title = {[Trends in the risk of late fetal mortality, prematurity and low birth weight associated with advanced maternal age in Spain [1996-2005]].}, journal = {Gaceta sanitaria}, volume = {22}, number = {5}, pages = {396-403}, doi = {10.1157/13126919}, pmid = {19000519}, issn = {0213-9111}, mesh = {Adult ; Age Factors ; Data Interpretation, Statistical ; Female ; Fetal Mortality/*trends ; Humans ; *Infant, Low Birth Weight ; Infant, Newborn ; *Infant, Premature ; *Maternal Age ; Middle Aged ; Poisson Distribution ; Pregnancy ; Prevalence ; *Reproductive Techniques, Assisted ; Risk Factors ; Spain ; }, abstract = {OBJECTIVES: To describe trends in fertility, fetal death rate, prematurity and low birth weight, as well as their association with advanced maternal age, in Spain from 1996 to 2005.

METHODS: We performed an ecological study. The association between low birth weight and prematurity with maternal age was analyzed through contingency tables. The pattern of fetal mortality rate was analyzed through direct standardization. To study the risk of late fetal mortality, adjusted by age and prematurity, a Poisson regression model was used.

RESULTS: The rates of fertility and late fetal mortality increased in women aged more than 35 years, especially in women aged more than 45 years. The risk of late fetal mortality was 2.7 times higher in women aged 45 years and above (rate ratio, 2.7; 95%CI: 1.8-3), with an etiological fraction of exposure of 69% (95%CI: 55.2-78.6). The prevalence rate of prematurity and low birth weight was three times higher in this age group, with a prevalence rate of prematurity of 2.9 (95%CI: 2.7-3.1) and of low birth weight of 3.1 (95%CI: 2.9-3.3).

CONCLUSIONS: The high risk found in women aged more than 45 years is explained by the increase in the proportion of pregnancies within this age group during the period analyzed. Further studies in perinatal epidemiology that analyze the impact of assisted reproduction techniques in pregnancies in older women are required, as well as a national registry of assisted reproduction techniques.}, } @article {pmid18999291, year = {2008}, author = {Rubin, MA and Mayer, J and Greene, T and Sauer, BC and Hota, B and Trick, W and Jernigan, JA and Samore, MH}, title = {An agent-based model for evaluating surveillance methods for catheter-related bloodstream infection.}, journal = {AMIA ... Annual Symposium proceedings. AMIA Symposium}, volume = {2008}, number = {}, pages = {631-635}, pmid = {18999291}, issn = {1942-597X}, mesh = {*Artificial Intelligence ; Catheter-Related Infections/*diagnosis ; Computer Simulation ; *Decision Support Systems, Clinical ; Diagnosis, Computer-Assisted/*methods ; Humans ; *Models, Theoretical ; Pattern Recognition, Automated/*methods ; Population Surveillance/*methods ; Reproducibility of Results ; Sensitivity and Specificity ; }, abstract = {Surveillance for catheter-related bloodstream infections (CRBSI) is hindered by the fact that clinical case criteria are complex and subjective. Simplified objective criteria, based only on microbiologic data, may be a less valid, but potentially more reliable system for estimating and comparing institutional infection rates. We developed an agent-based simulation model to examine the impact of these two different criteria on the measurement of CRBSI in a simulated 12-bed hospital intensive care unit (ICU). We found that, on average, the clinical criteria was more accurate at estimating the true CRBSI rate than the simple criteria (3.36+/-1.11 vs. 5.41+/-1.36 infections/1000 catheter-days, compared with a true rate of 3.54+/-1.60). However, ecologic correlation (i.e., the accurate ranking of CRBSI rates across institutions) was higher for simple criteria than clinical criteria. Thus, simplified objective criteria are potentially superior to clinical criteria in identifying the true differences in CRBSI rates between institutions.}, } @article {pmid18998775, year = {2008}, author = {Brown, MJ and Shaw, NT and Mador, RL}, title = {Mapping the sociotechnical healthcare ecosystem: expanding the horizons of sociotechnical inquiry.}, journal = {AMIA ... Annual Symposium proceedings. AMIA Symposium}, volume = {}, number = {}, pages = {1233-1235}, pmid = {18998775}, issn = {1942-597X}, mesh = {Canada ; Delivery of Health Care/*organization & administration ; *Ecosystem ; Information Dissemination/*methods ; *Medical Informatics ; *Models, Theoretical ; *Sociology, Medical ; }, abstract = {In recent years, sociotechnical approaches have become increasingly popular for understanding the design, implementation and evaluation of information technology in health informatics. On the whole, these approaches have sought to unite essential knowledge from the domains of the social sciences and information technology in the study of health informatics, with the central assertion that health information technology cannot be properly understood apart from its social and systemic contexts. This perspective has been enormously beneficial, as it has provided a solid and sophisticated theoretical basis from which health informatics researchers have begun to describe, study, and understand human-IT interactions and their consequences at a microsystemic level. As this theory continues to be applied, however, it has become increasingly clear that these human-IT microsystems are themselves imbedded within larger systemic contexts, and that both these contexts--as well as the interactions and change processes both between and among them--need to be clearly conceptualized and explored in greater detail. In this workshop, sponsored by the AMIA Working Group on People and Organizational Issues, we present human ecological theory as means for facilitating this theoretical growth and invite health informaticians from all disciplines to actively explore the emerging Sociotechnical Healthcare Ecosystem.}, } @article {pmid18992827, year = {2009}, author = {Che, J and Hu, JS and Zhou, WW and Murphy, RW and Papenfuss, TJ and Chen, MY and Rao, DQ and Li, PP and Zhang, YP}, title = {Phylogeny of the Asian spiny frog tribe Paini (Family Dicroglossidae) sensu Dubois.}, journal = {Molecular phylogenetics and evolution}, volume = {50}, number = {1}, pages = {59-73}, doi = {10.1016/j.ympev.2008.10.007}, pmid = {18992827}, issn = {1095-9513}, mesh = {Animals ; Anura/anatomy & histology/*classification/*genetics ; Asia ; Base Sequence ; Cell Nucleus/genetics ; DNA/genetics ; Databases, Nucleic Acid ; Mitochondria/genetics ; *Phylogeny ; }, abstract = {The anuran tribe Paini, family Dicroglossidae, is known in this group only from Asia. The phylogenetic relationships and often the taxonomic recognition of species are controversial. In order to stabilize the classification, we used approximately 2100 bp of nuclear (rhodopsin, tyrosinase) and mitochondrial (12S, 16S rRNA) DNA sequence data to infer the phylogenetic relationships of these frogs. Phylogenetic trees reconstructed using Bayesian inference and maximum parsimony methods supported a monophyletic tribe Paini. Two distinct groups (I,II) were recovered with the mtDNA alone and the total concatenated data (mtDNA+nuDNA). The recognition of two genera, Quasipaa and Nanorana, was supported. Group I, Quasipaa, is widespread east of the Hengduan Mountain Ranges and consists of taxa from relatively low elevations in southern China, Vietnam and Laos. Group II, Nanorana, contains a mix of species occurring from high to low elevation predominantly in the Qinghai-Tibetan Plateau and Hengduan Mountain Ranges. The occurrence of frogs at high elevations appears to be a derived ecological condition. The composition of some major species groups based on morphological characteristics strongly conflicts with the molecular analysis. Some possible cryptic species are indicated by the molecular analyses. The incorporation of genetic data from type localities helped to resolve some of the taxonomic problems, although further combined analyses of morphological data from type specimens are required. The two nuDNA gene segments proved to be very informative for resolving higher phylogenetic relationships and more nuclear data should be explored to be more confident in the relationships.}, } @article {pmid18986595, year = {2009}, author = {Naska, A and Berg, MA and Cuadrado, C and Freisling, H and Gedrich, K and Gregoric, M and Kelleher, C and Leskova, E and Nelson, M and Pace, L and Remaut, AM and Rodrigues, S and Sekula, W and Sjöstrom, M and Trygg, K and Turrini, A and Volatier, JL and Zajkas, G and Trichopoulou, A and , }, title = {Food balance sheet and household budget survey dietary data and mortality patterns in Europe.}, journal = {The British journal of nutrition}, volume = {102}, number = {1}, pages = {166-171}, doi = {10.1017/S000711450809466X}, pmid = {18986595}, issn = {1475-2662}, mesh = {Animals ; Cardiovascular Diseases/*mortality ; *Data Interpretation, Statistical ; Diet/*economics ; Diet Surveys ; Europe/epidemiology ; Feeding Behavior ; Fishes ; Food/*economics ; Food Supply/economics/statistics & numerical data ; Fruit ; Humans ; Neoplasms/*mortality ; Olive Oil ; Plant Oils ; Seafood ; Smoking ; Vegetables ; }, abstract = {Worldwide dietary data for nutrition monitoring and surveillance are commonly derived from food balance sheets (FBS) and household budget surveys (HBS). We have compared food supply from FBS and food availability data from HBS among eighteen European countries and have estimated the extent to which they correlate, focusing on food groups which are comparably captured by FBS and HBS and for which there is epidemiological evidence that they can have a noticeable impact on population mortality. Spearman's correlation coefficient was +0.78 (P < 10- 3) for vegetables (including legumes),+0.76 (P < 10- 3) for fruits, +0.69 (P < 10- 3) for fish and seafood and +0.93 (P < 10- 3) for olive oil. With respect to meat and meat products, the coefficient was lower at +0.39 (P = 0.08). Moreover, we have examined whether the supply (FBS) or the availability (HBS) of food groups known or presumed to have beneficial effect on the occurrence of CHD and total cancer can predict overall, coronary and cancer mortality in ecological analyses. After controlling for purchasing power parity-adjusted gross domestic product and tobacco smoking we found that for vegetables, fruits, fish and seafood, as well as for olive oil, both the FBS and the HBS estimates were inversely associated with all three indicators of mortality, although the number of countries with complete information on all study variables hindered formal statistical documentation (P>0.05 in some instances). FBS and HBS have their own strengths and weaknesses, but they may complement each other in dietary assessments at the population level.}, } @article {pmid18985077, year = {2010}, author = {Cohen Hubal, EA and Richard, AM and Shah, I and Gallagher, J and Kavlock, R and Blancato, J and Edwards, SW}, title = {Exposure science and the U.S. EPA National Center for Computational Toxicology.}, journal = {Journal of exposure science & environmental epidemiology}, volume = {20}, number = {3}, pages = {231-236}, doi = {10.1038/jes.2008.70}, pmid = {18985077}, issn = {1559-064X}, mesh = {Computational Biology/*methods/trends ; Ecotoxicology/*methods/trends ; Environmental Exposure/adverse effects/*analysis ; Environmental Pollutants/*analysis/toxicity ; Humans ; National Institute of Environmental Health Sciences (U.S.) ; United States ; *United States Environmental Protection Agency ; }, abstract = {The emerging field of computational toxicology applies mathematical and computer models and molecular biological and chemical approaches to explore both qualitative and quantitative relationships between sources of environmental pollutant exposure and adverse health outcomes. The integration of modern computing with molecular biology and chemistry will allow scientists to better prioritize data, inform decision makers on chemical risk assessments and understand a chemical's progression from the environment to the target tissue within an organism and ultimately to the key steps that trigger an adverse health effect. In this paper, several of the major research activities being sponsored by Environmental Protection Agency's National Center for Computational Toxicology are highlighted. Potential links between research in computational toxicology and human exposure science are identified. As with the traditional approaches for toxicity testing and hazard assessment, exposure science is required to inform design and interpretation of high-throughput assays. In addition, common themes inherent throughout National Center for Computational Toxicology research activities are highlighted for emphasis as exposure science advances into the 21st century.}, } @article {pmid18983655, year = {2008}, author = {Ingvarsson, PK}, title = {Molecular evolution of synonymous codon usage in Populus.}, journal = {BMC evolutionary biology}, volume = {8}, number = {}, pages = {307}, pmid = {18983655}, issn = {1471-2148}, mesh = {Base Composition ; *Codon ; Computational Biology ; DNA, Plant/genetics ; *Evolution, Molecular ; Expressed Sequence Tags ; Gene Expression ; Gene Expression Profiling ; *Genetics, Population ; Genome, Plant ; Likelihood Functions ; Models, Genetic ; Mutation ; Phylogeny ; Polymorphism, Genetic ; Populus/*genetics ; Selection, Genetic ; Sequence Alignment ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: Evolution of synonymous codon usage is thought to be determined by a balance between mutation, genetic drift and natural selection on translational efficiency. However, natural selection on codon usage is considered to be a weak evolutionary force and selection on codon usage is expected to be strongest in species with large effective population sizes.

RESULTS: I examined the evolution of synonymous codons using EST data from five species of Populus. Data on relative synonymous codon usage in genes with high and low gene expression were used to identify 25 codons from 18 different amino acids that were deemed to be preferred codons across all five species. All five species show significant correlations between codon bias and gene expression, independent of base composition, thus indicating that translational selection has shaped synonymous codon usage. Using a set of 158 orthologous genes I detected an excess of unpreferred to preferred (U --> P) mutations in two lineages, P. tremula and P. deltoides. Maximum likelihood estimates of the strength of selection acting on synonymous codons was also significantly greater than zero in P. tremula, with the ML estimate of 4Nes = 0.720.

CONCLUSION: The data is consistent with weak selection on preferred codons in all five species. There is also evidence suggesting that selection on synonymous codons has increased in P. tremula. Although the reasons for the increase in selection on codon usage in the P. tremula lineage are not clear, one possible explanation is an increase in the effective population size in P. tremula.}, } @article {pmid18974852, year = {2008}, author = {Wegmann, D and Dupanloup, I and Excoffier, L}, title = {Width of gene expression profile drives alternative splicing.}, journal = {PloS one}, volume = {3}, number = {10}, pages = {e3587}, pmid = {18974852}, issn = {1932-6203}, mesh = {Alternative Splicing/*genetics ; Animals ; Chromosome Mapping ; Conserved Sequence ; Databases, Genetic ; Evolution, Molecular ; *Gene Expression Profiling ; Gene Expression Regulation/*physiology ; Gene Frequency ; Genes/physiology ; Genome, Human ; Humans ; Mice ; Models, Genetic ; Organ Specificity/genetics ; Protein Isoforms/genetics ; RNA Splice Sites/genetics ; }, abstract = {Alternative splicing generates an enormous amount of functional and proteomic diversity in metazoan organisms. This process is probably central to the macromolecular and cellular complexity of higher eukaryotes. While most studies have focused on the molecular mechanism triggering and controlling alternative splicing, as well as on its incidence in different species, its maintenance and evolution within populations has been little investigated. Here, we propose to address these questions by comparing the structural characteristics as well as the functional and transcriptional profiles of genes with monomorphic or polymorphic splicing, referred to as MS and PS genes, respectively. We find that MS and PS genes differ particularly in the number of tissues and cell types where they are expressed.We find a striking deficit of PS genes on the sex chromosomes, particularly on the Y chromosome where it is shown not to be due to the observed lower breadth of expression of genes on that chromosome. The development of a simple model of evolution of cis-regulated alternative splicing leads to predictions in agreement with these observations. It further predicts the conditions for the emergence and the maintenance of cis-regulated alternative splicing, which are both favored by the tissue specific expression of splicing variants. We finally propose that the width of the gene expression profile is an essential factor for the acquisition of new transcript isoforms that could later be maintained by a new form of balancing selection.}, } @article {pmid18959306, year = {2008}, author = {Campos-Arceiz, A and Larrinaga, AR and Weerasinghe, UR and Takatsuki, S and Pastorini, J and Leimgruber, P and Fernando, P and Santamaría, L}, title = {Behavior rather than diet mediates seasonal differences in seed dispersal by Asian elephants.}, journal = {Ecology}, volume = {89}, number = {10}, pages = {2684-2691}, doi = {10.1890/07-1573.1}, pmid = {18959306}, issn = {0012-9658}, mesh = {Animal Feed ; Animals ; Behavior, Animal/*physiology ; Elephants/*metabolism ; Feces/*chemistry ; Feeding Behavior/*physiology ; Gastrointestinal Transit ; Geographic Information Systems ; Germination/*physiology ; Motor Activity ; Myanmar ; Seasons ; Seeds/*growth & development ; Sri Lanka ; Trees ; }, abstract = {Digestive physiology and movement patterns of animal dispersers determine deposition patterns for endozoochorously dispersed seeds. We combined data from feeding trials, germination tests, and GPS telemetry of Asian elephants (Elephas maximus) to (1) describe the spatial scale at which Asian elephants disperse seeds; (2) assess whether seasonal differences in diet composition and ranging behavior translate into differences in seed shadows; and (3) evaluate whether scale and seasonal patterns vary between two ecologically distinct areas: Sri Lanka's dry monsoon forests and Myanmar's (Burma) mixed-deciduous forests. The combination of seed retention times (mean 39.5 h, maximum 114 h) and elephant displacement rates (average 1988 m in 116 hours) resulted in 50% of seeds dispersed over 1.2 km (mean 1222-2105 m, maximum 5772 m). Shifts in diet composition did not affect gut retention time and germination of ingested seeds. Elephant displacements were slightly longer, with stronger seasonal variation in Myanmar. As a consequence, seed dispersal curves varied seasonally with longer distances during the dry season in Myanmar but not in Sri Lanka. Seasonal and geographic variation in seed dispersal curves was the result of variation in elephant movement patterns, rather than the effect of diet changes on the fate of ingested seeds.}, } @article {pmid18957598, year = {2008}, author = {Druzhinina, IS and Komoń-Zelazowska, M and Kredics, L and Hatvani, L and Antal, Z and Belayneh, T and Kubicek, CP}, title = {Alternative reproductive strategies of Hypocrea orientalis and genetically close but clonal Trichoderma longibrachiatum, both capable of causing invasive mycoses of humans.}, journal = {Microbiology (Reading, England)}, volume = {154}, number = {Pt 11}, pages = {3447-3459}, doi = {10.1099/mic.0.2008/021196-0}, pmid = {18957598}, issn = {1350-0872}, mesh = {Humans ; Hypocrea/classification/*genetics/isolation & purification ; Molecular Sequence Data ; Mycoses/*microbiology ; Phylogeny ; Soil Microbiology ; Trichoderma/classification/*genetics/isolation & purification ; }, abstract = {The common soil fungus Trichoderma (teleomorph Hypocrea, Ascomycota) shows increasing medical importance as an opportunistic human pathogen, particularly in immunocompromised and immunosuppressed patients. Regardless of the disease type and the therapy used, the prognosis for Trichoderma infection is usually poor. Trichoderma longibrachiatum has been identified as the causal agent in the majority of reported Trichoderma mycoses. As T. longibrachiatum is very common in environmental samples from all over the world, the relationship between its clinical and wild strains remains unclear. Here we performed a multilocus (ITS1 and 2, tef1, cal1 and chit18-5) phylogenetic analysis of all available clinical isolates (15) and 36 wild-type strains of the fungus including several cultures of its putative teleomorph Hypocrea orientalis. The concordance of gene genealogies recognized T. longibrachiatum and H. orientalis to be different phylogenetic species, which are reproductively isolated from each other. The majority of clinical strains (12) were attributed to T. longibrachiatum but three isolates belonged to H. orientalis, which broadens the phylogenetic span of human opportunists in the genus. Despite their genetic isolation, T. longibrachiatum and H. orientalis were shown to be cosmopolitan sympatric species with no bias towards certain geographical locations. The analysis of haplotype association, incongruence of tree topologies and the split decomposition method supported the conclusion that H. orientalis is sexually recombining whereas strict clonality prevails in T. longibrachiatum. This is a rare case of occurrence of sexual reproduction in opportunistic pathogenic fungi. The discovery of the different reproduction strategies in these two closely related species is medically relevant because it is likely that they would also differ in virulence and/or drug resistance. Genetic identity of environmental and clinical isolates of T. longibrachiatum and H. orientalis suggests the danger of nosocomial infections by Hypocrea/Trichoderma and highlights the need for ecological studies of spore dispersal as source of invasive human mycoses.}, } @article {pmid18957445, year = {2009}, author = {Proux, E and Studer, RA and Moretti, S and Robinson-Rechavi, M}, title = {Selectome: a database of positive selection.}, journal = {Nucleic acids research}, volume = {37}, number = {Database issue}, pages = {D404-7}, pmid = {18957445}, issn = {1362-4962}, mesh = {*Databases, Genetic ; *Genes ; Phylogeny ; Proteins/classification/*genetics ; *Selection, Genetic ; Sequence Homology, Amino Acid ; User-Computer Interface ; }, abstract = {Genome wide scans have shown that positive selection is relatively frequent at the molecular level. It is of special interest to identify which protein sites and which phylogenetic branches are affected. We present Selectome, a database which provides the results of a rigorous branch-site specific likelihood test for positive selection. The Web interface presents test results mapped both onto phylogenetic trees and onto protein alignments. It allows rapid access to results by keyword, gene name, or taxonomy based queries. Selectome is freely available at http://bioinfo.unil.ch/selectome/.}, } @article {pmid18957118, year = {2008}, author = {Bohnebeck, U and Lombardot, T and Kottmann, R and Glöckner, FO}, title = {MetaMine--a tool to detect and analyse gene patterns in their environmental context.}, journal = {BMC bioinformatics}, volume = {9}, number = {}, pages = {459}, pmid = {18957118}, issn = {1471-2105}, mesh = {*Algorithms ; Computational Biology/*methods ; *Databases, Genetic ; *Ecosystem ; Multigene Family/*genetics ; Pattern Recognition, Automated ; *Software ; }, abstract = {BACKGROUND: Modern sequencing technologies allow rapid sequencing and bioinformatic analysis of genomes and metagenomes. With every new sequencing project a vast number of new proteins become available with many genes remaining functionally unclassified based on evidences from sequence similarities alone. Extending similarity searches with gene pattern approaches, defined as genes sharing a distinct genomic neighbourhood, have shown to significantly improve the number of functional assignments. Further functional evidences can be gained by correlating these gene patterns with prevailing environmental parameters. MetaMine was developed to approach the large pool of unclassified proteins by searching for recurrent gene patterns across habitats based on key genes.

RESULTS: MetaMine is an interactive data mining tool which enables the detection of gene patterns in an environmental context. The gene pattern search starts with a user defined environmentally interesting key gene. With this gene a BLAST search is carried out against the Microbial Ecological Genomics DataBase (MEGDB) containing marine genomic and metagenomic sequences. This is followed by the determination of all neighbouring genes within a given distance and a search for functionally equivalent genes. In the final step a set of common genes present in a defined number of distinct genomes is determined. The gene patterns found are associated with their individual pattern instances describing gene order and directions. They are presented together with information about the sample and the habitat. MetaMine is implemented in Java and provided as a client/server application with a user-friendly graphical user interface. The system was evaluated with environmentally relevant genes related to the methane-cycle and carbon monoxide oxidation.

CONCLUSION: MetaMine offers a targeted, semi-automatic search for gene patterns based on expert input. The graphical user interface of MetaMine provides a user-friendly overview of the computed gene patterns for further inspection in an ecological context. Prevailing biological processes associated with a key gene can be used to infer new annotations and shape hypotheses to guide further analyses. The use-cases demonstrate that meaningful gene patterns can be quickly detected using MetaMine.MetaMine is freely available for academic use from http://www.megx.net/metamine.}, } @article {pmid18954136, year = {2008}, author = {Schüürmann, G and Ebert, RU and Chen, J and Wang, B and Kühne, R}, title = {External validation and prediction employing the predictive squared correlation coefficient test set activity mean vs training set activity mean.}, journal = {Journal of chemical information and modeling}, volume = {48}, number = {11}, pages = {2140-2145}, doi = {10.1021/ci800253u}, pmid = {18954136}, issn = {1549-9596}, mesh = {Databases, Factual ; Informatics ; Models, Chemical ; *Quantitative Structure-Activity Relationship ; Regression Analysis ; }, abstract = {The external prediction capability of quantitative structure-activity relationship (QSAR) models is often quantified using the predictive squared correlation coefficient, q (2). This index relates the predictive residual sum of squares, PRESS, to the activity sum of squares, SS, without postprocessing of the model output, the latter of which is automatically done when calculating the conventional squared correlation coefficient, r (2). According to the current OECD guidelines, q (2) for external validation should be calculated with SS referring to the training set activity mean. Our present findings including a mathematical proof demonstrate that this approach yields a systematic overestimation of the prediction capability that is triggered by the difference between the training and test set activity means. Example calculations with three regression models and data sets taken from literature show further that for external test sets, q (2) based on the training set activity mean may become even larger than r (2). As a consequence, we suggest to always use the test set activity mean when quantifying the external prediction capability through q (2) and to revise the respective OECD guidance document accordingly. The discussion includes a comparison between r (2) and q (2) value ranges and the q (2) statistics for cross-validation.}, } @article {pmid18952839, year = {2008}, author = {Makarieva, AM and Gorshkov, VG and Li, BL and Chown, SL and Reich, PB and Gavrilov, VM}, title = {Mean mass-specific metabolic rates are strikingly similar across life's major domains: Evidence for life's metabolic optimum.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {105}, number = {44}, pages = {16994-16999}, pmid = {18952839}, issn = {1091-6490}, mesh = {Animals ; Biological Evolution ; Body Weight ; Databases, Factual ; Energy Metabolism/*physiology ; Humans ; Metabolic Networks and Pathways ; Selection, Genetic ; Systems Biology ; }, abstract = {A fundamental but unanswered biological question asks how much energy, on average, Earth's different life forms spend per unit mass per unit time to remain alive. Here, using the largest database to date, for 3,006 species that includes most of the range of biological diversity on the planet-from bacteria to elephants, and algae to sapling trees-we show that metabolism displays a striking degree of homeostasis across all of life. We demonstrate that, despite the enormous biochemical, physiological, and ecological differences between the surveyed species that vary over 10(20)-fold in body mass, mean metabolic rates of major taxonomic groups displayed at physiological rest converge on a narrow range from 0.3 to 9 W kg(-1). This 30-fold variation among life's disparate forms represents a remarkably small range compared with the 4,000- to 65,000-fold difference between the mean metabolic rates of the smallest and largest organisms that would be observed if life as a whole conformed to universal quarter-power or third-power allometric scaling laws. The observed broad convergence on a narrow range of basal metabolic rates suggests that organismal designs that fit in this physiological window have been favored by natural selection across all of life's major kingdoms, and that this range might therefore be considered as optimal for living matter as a whole.}, } @article {pmid18950472, year = {2009}, author = {Murray-Smith, C and Brummitt, NA and Oliveira-Filho, AT and Bachman, S and Moat, J and Lughadha, EM and Lucas, EJ}, title = {Plant diversity hotspots in the Atlantic coastal forests of Brazil.}, journal = {Conservation biology : the journal of the Society for Conservation Biology}, volume = {23}, number = {1}, pages = {151-163}, doi = {10.1111/j.1523-1739.2008.01075.x}, pmid = {18950472}, issn = {1523-1739}, mesh = {*Biodiversity ; Brazil ; Conservation of Natural Resources/*methods ; Demography ; Geographic Information Systems ; Geography ; Myrtaceae/*physiology ; *Trees ; }, abstract = {Plant-diversity hotspots on a global scale are well established, but smaller local hotspots within these must be identified for effective conservation of plants at the global and local scales. We used the distributions of endemic and endemic-threatened species of Myrtaceae to indicate areas of plant diversity and conservation importance within the Atlantic coastal forests (Mata Atlântica) of Brazil. We applied 3 simple, inexpensive geographic information system (GIS) techniques to a herbarium specimen database: predictive species-distribution modeling (Maxent); complementarity analysis (DIVA-GIS); and mapping of herbarium specimen collection locations. We also considered collecting intensity, which is an inherent limitation of use of natural history records for biodiversity studies. Two separate areas of endemism were evident: the Serra do Mar mountain range from Paraná to Rio de Janeiro and the coastal forests of northern Espírito Santo and southern Bahia. We identified 12 areas of approximately 35 km(2) each as priority areas for conservation. These areas had the highest species richness and were highly threatened by urban and agricultural expansion. Observed species occurrences, species occurrences predicted from the model, and results of our complementarity analysis were congruent in identifying those areas with the most endemic species. These areas were then prioritized for conservation importance by comparing ecological data for each.}, } @article {pmid18947443, year = {2009}, author = {Chang, M and Groseclose, SL and Zaidi, AA and Braden, CR}, title = {An ecological analysis of sociodemographic factors associated with the incidence of salmonellosis, shigellosis, and E. coli O157:H7 infections in US counties.}, journal = {Epidemiology and infection}, volume = {137}, number = {6}, pages = {810-820}, doi = {10.1017/S0950268808001477}, pmid = {18947443}, issn = {0950-2688}, mesh = {Adolescent ; Adult ; Age Distribution ; Aged ; Child ; Child, Preschool ; Dysentery, Bacillary/economics/*epidemiology ; Ecosystem ; Escherichia coli Infections/economics/*epidemiology/microbiology ; *Escherichia coli O157 ; Female ; Humans ; Male ; Middle Aged ; Racial Groups ; Salmonella Infections/economics/*epidemiology ; Socioeconomic Factors ; United States/epidemiology ; Young Adult ; }, abstract = {Identifying county-level sociodemographic and economic factors associated with the incidence of enteric disease may provide new insights concerning the dynamics of community transmission of these diseases as well as opportunities for prevention. We used data from the National Notifiable Diseases Surveillance System, the U.S. Census Bureau, and the Health Resources and Services Administration to conduct an ecological analysis of 26 sociodemographic and economic factors associated with the incidence of salmonellosis, shigellosis, and E. coli O157:H7 infections in US counties for the period 1993 to 2002. Our study indicates that race, ethnicity, place of residence, age, educational attainment, and poverty may affect the risk of acquiring one of these enteric bacterial diseases. The lack of specificity of information regarding salmonellae and shigellae serotypes may have led to less specific associations between community-level determinants and reported incidence of those diseases. Future ecological analyses should use serotype-specific data on incidence, which may be available from laboratory-based surveillance systems.}, } @article {pmid18945191, year = {2009}, author = {Carpi, G and Bertolotti, L and Pecchioli, E and Cagnacci, F and Rizzoli, A}, title = {Anaplasma phagocytophilum groEL gene heterogeneity in Ixodes ricinus larvae feeding on roe deer in Northeastern Italy.}, journal = {Vector borne and zoonotic diseases (Larchmont, N.Y.)}, volume = {9}, number = {2}, pages = {179-184}, doi = {10.1089/vbz.2008.0068}, pmid = {18945191}, issn = {1557-7759}, mesh = {Anaplasma phagocytophilum/*genetics/*isolation & purification ; Animals ; Arachnid Vectors/*microbiology ; Chaperonin 60/genetics ; Databases, Nucleic Acid ; *Deer/microbiology/parasitology ; Disease Reservoirs/microbiology/veterinary ; Ehrlichiosis/transmission/veterinary ; Italy ; Ixodes/*microbiology ; Larva/microbiology ; Phylogeny ; Polymerase Chain Reaction/veterinary ; Prevalence ; }, abstract = {Anaplasma phagocytophilum is an emerging tick-borne pathogen with both veterinary and human health implications. The role of wildlife hosts for this pathogen are not well defined, even thought roe deer (Capreolus capreolus) has been suggested to contribute to the occurrence of this tick-borne diseases in Europe. Therefore the aim of the present study was to investigate the potential role of this ungulate species as a reservoir of human pathogenic strains of A. phagocytophilum in a tick-borne diseases endemic area in Northeastern Italy. Ixodes ricinus feeding on roe deer were collected and analyzed for the presence for A. phagocytophilum by a molecular approach targeting 16S rRNA and groEL genes. The mean prevalence of A. phagocytophilum recorded was 5.11%, highlighting the ability of roe deer to infect the I. ricinus larval stage. The results of further genetic characterization of the strains of A. phagocytophilum herein isolated, based on phylogenetic information contained in groEL gene sequences, showed substantial heterogeneity among sequences analyzed. Nevertheless, these findings suggest that the roe deer population of the Trentino region of Italy harbors strains of A. phagocytophilum of unknown pathogenicity for humans.}, } @article {pmid18941816, year = {2009}, author = {Verta, M and Kiviranta, H and Salo, S and Malve, O and Korhonen, M and Verkasalo, PK and Ruokojärvi, P and Rossi, E and Hanski, A and Päätalo, K and Vartiainen, T}, title = {A decision framework for possible remediation of contaminated sediments in the River Kymijoki, Finland.}, journal = {Environmental science and pollution research international}, volume = {16}, number = {1}, pages = {95-105}, pmid = {18941816}, issn = {0944-1344}, mesh = {Animals ; Chironomidae/drug effects ; Decision Support Techniques ; Ecosystem ; Environmental Exposure ; Environmental Restoration and Remediation/*methods ; Female ; Finland ; Geologic Sediments/*chemistry ; Humans ; Lipids/blood ; Milk, Human/chemistry ; Public Health ; Risk Factors ; Rivers/*chemistry ; *Water Pollutants, Chemical/chemistry/toxicity ; }, abstract = {BACKGROUND, AIM, AND SCOPE: The paper describes the spatial contamination of the River Kymijoki, South-Eastern Finland, and the coastal region of the Gulf of Finland with PCDD/Fs and mercury. The findings of ecotoxicologial and human health studies are also reported, including environmental and human risk assessments. Sediments from the River Kymijoki, draining into the Gulf of Finland, have been heavily polluted by the pulp and paper industry and by chemical industries. A wood preservative, known as Ky-5, was manufactured in the upper reaches of the river between 1940 and 1984 causing severe pollution of river sediments with polychlorinated dibenzo-p-dioxins (PCDD) and dibenzofurans (PCDF). Moreover, the sediments have been polluted with mercury (Hg) from chlor-alkali production and the use of Hg as a slimicide in pulp and paper manufacturing.

MATERIALS AND METHODS: An extensive sediment survey was conducted as well as sediment transport modeling, toxicity screening of sediment invertebrates, and a survey of contaminant bioaccumulation in invertebrates and fish. Studies on human exposure to PCDD/Fs and the possible effects on hypermineralization of teeth as well as an epidemiological study to reveal increased cancer risk were also conducted. An assessment of the ecological and human health risks with a null hypothesis (no remediation) was undertaken.

RESULTS: The sediment survey revealed severe contamination of river and coastal sediments with PCDD/Fs and Hg. The total volume of contaminated sediments was estimated to reach 5x10(6) m3 and hot spots with extremely high concentrations (max 292,000 ng g(-1) or 1,060 ng I-TEQ g(-1) d.w.) were located immediately downstream from the pollution source (approximately 90,000 m3). Sediment contamination was accompanied by changes in benthic assemblages, but direct effects were masked by many factors. The fish showed only slightly elevated PCDD/F levels in muscle, but orders of magnitude higher in the liver compared with reference freshwater sites and the Baltic Sea. The concentrations in human fat did not reveal high human exposure in the Kymijoki area in general and was lower than in sea fishermen. The relative risk for total cancer among farmers was marginally higher (RR=1.13) among those living close to the river, compared with farmers living further away, and the possibility of increased cancer risk cannot be ruled out. A conservative risk assessment revealed that the present probability of exceeding the WHO upper exposure limit of 4 pg WHO-TEQ kg(-1) d(-1) for PCDD/Fs and DL-PCBs was 6%. The probability of exceeding the WHO limit value of 0.23 mug kg(-1) d(-1) for methyl mercury was estimated to be notably higher at 62%. Based on these studies and the estimated risks connected with different remediation techniques a general remediation plan with cost benefit analysis was generated for several sub-regions in the river. Dredging, on-site treatment, and a close disposal of the most contaminated sediments (90,000 m3) was suggested as the first phase of the remediation. The decision regarding the start of remediation will be made during autumn 2008.

CONCLUSIONS: The sediments in the River Kymijoki are heavily polluted with PCDD/Fs and mercury from earlier chlorophenol, chlor-alkali, and pulp and paper manufacturing. A continuous transport of contaminants is taking place to the Gulf of Finland in the Baltic Sea. The highly increased PCDD/F and Hg levels in river sediments pose an ecotoxicological risk to benthic fauna, to fish-eating predators and probably to human health. The risks posed by mercury exceed those from PCDD/Fs and need to be evaluated for (former) chlor-alkali sites and other mercury releasing industries as one basis for remediation decision making.

The studies form the basis of a risk management strategy and a plan for possible remediation of contaminated sediments currently under consideration in the Southeast Finland Regional Environment Centre. It is recommended that a detailed restoration plan for the most seriously contaminated areas should be undertaken. Based on current knowledge, the restoration of the whole river is not feasible, considering the current risk caused by the contaminated sediment in the river and the costs of an extensive restoration project. The experiences gained in the present case should be utilized in the evaluation of PCDD/F- and mercury-contaminated sites in other countries. The case demonstrates that the historic reservoirs are of contemporary relevance and should be addressed, e.g., in the national implementation plans of the Stockholm Convention.}, } @article {pmid18931921, year = {2010}, author = {Wheat, CW}, title = {Rapidly developing functional genomics in ecological model systems via 454 transcriptome sequencing.}, journal = {Genetica}, volume = {138}, number = {4}, pages = {433-451}, pmid = {18931921}, issn = {1573-6857}, mesh = {Animals ; Butterflies/genetics ; Databases, Genetic ; *Ecology ; *Gene Expression Profiling ; Genetic Markers ; Genetics, Population ; Genome ; Genomics/*methods ; Oligonucleotide Array Sequence Analysis ; Sequence Alignment ; Sequence Analysis, DNA/*methods ; }, abstract = {Next generation sequencing technology affords new opportunities in ecological genetics. This paper addresses how an ecological genetics research program focused on a phenotype of interest can quickly move from no genetic resources to having various functional genomic tools. 454 sequencing and its error rates are discussed, followed by a review of de novo transcriptome assemblies focused on the first successful de novo assembly which happens to be in an ecological model system (the Glanville fritillary butterfly). The potential future developments in 454 sequencing are also covered. Particular attention is paid to the difficulties ecological geneticists are likely to encounter through reviewing relevant studies in both model and non-model systems. Various post-sequencing issues and applications of 454 generated data are presented (e.g. database management, microarray construction, molecular marker and candidate gene development). How to use species with genomic resources to inform study of those without is also discussed. In closing, some of the drawbacks of 454 sequencing are presented along with future prospects of this technology.}, } @article {pmid18926617, year = {2009}, author = {Reger, B and Mattern, T and Otte, A and Waldhardt, R}, title = {Assessing the spatial distribution of grassland age in a marginal European landscape.}, journal = {Journal of environmental management}, volume = {90}, number = {9}, pages = {2900-2909}, doi = {10.1016/j.jenvman.2007.10.015}, pmid = {18926617}, issn = {1095-8630}, mesh = {*Ecosystem ; Environment ; Europe ; Geographic Information Systems/instrumentation ; Geography/classification/*methods ; Poaceae/*growth & development ; }, abstract = {Grassland age is increasingly recognised to be an indicator for present-day biodiversity, e.g. plant species richness, and is also important for other landscape functions. We developed a methodological approach to systematically assess the spatial distribution of grassland age in marginal European landscapes. This approach - applied to the Lahn-Dill Highlands (1270 km(2)), a marginal landscape in Hesse, Germany - comprises three steps: (1) in a two-stage stratification process, we pre-stratified the study area according to recent land-cover patterns and their changes between 1955 and 1995 (stratification I) and classified grassland types by combining data on soil moisture, base-richness, and elevation (stratification II). From 50 grassland types, we randomly selected 1000 representative grassland patches. (2) We determined the age of these patches by means of aerial photograph interpretation of a chronosequence dating back to 1953 and classified each patch with respect to the age classes young (<18 years), mid-aged (18-47 years), and old (>47 years). (3) Based on this information, we calculated grassland type-specific probabilities for grassland patches to belong to the respective age classes. These probabilities were projected to districts by direct extrapolation. An exemplary validation of extrapolation results for two test areas was performed. The results revealed that 49% of the investigated patches were old grassland. The remaining patches were mid-aged (36%) or young grassland (15%). The extrapolation results indicated accordingly a predominance of old grassland at the district scale. Occurrences of mid-aged grassland were concentrated in districts with a pronounced land-cover change, whereas young grassland is apparently evenly distributed across the study area. Validation results suggest that our approach is suitable for a realistic estimation of grassland age in marginal European landscapes. The method may be applied in landscape models of various disciplines that rely on large-scale information on grassland age.}, } @article {pmid18923872, year = {2008}, author = {Sainsbury, AW and Deaville, R and Lawson, B and Cooley, WA and Farelly, SS and Stack, MJ and Duff, P and McInnes, CJ and Gurnell, J and Russell, PH and Rushton, SP and Pfeiffer, DU and Nettleton, P and Lurz, PW}, title = {Poxviral disease in red squirrels Sciurus vulgaris in the UK: spatial and temporal trends of an emerging threat.}, journal = {EcoHealth}, volume = {5}, number = {3}, pages = {305-316}, pmid = {18923872}, issn = {1612-9210}, mesh = {Animals ; Disease Outbreaks ; Disease Reservoirs ; Environmental Monitoring/methods ; Enzyme-Linked Immunosorbent Assay ; Epidemiological Monitoring ; Female ; Geographic Information Systems ; Male ; Microscopy, Electron, Transmission ; Poxviridae Infections/epidemiology/transmission/*veterinary ; Sciuridae/*virology ; Sex Distribution ; United Kingdom/epidemiology ; }, abstract = {The squirrel poxvirus (SQPV) is the probable mediator of apparent competition between the introduced invading gray squirrel (Sciurus carolinensis) and the red squirrel (Sciurus vulgaris) in the UK, and modeling studies have shown that this viral disease has had a significant impact on the decline of the red squirrel in the UK. However, given our limited understanding of the epidemiology of the disease, and more generally the effects of invasive species on parasite ecology, there is a need to investigate the transmission dynamics and the relative pathogenicity of the virus between species. We aimed to increase our knowledge of these processes through an empirical study in which we: (i) used pathological signs and transmission electron microscopy (TEM) to diagnose SQPV disease in red squirrels found dead during scanning surveillance between 1993 and 2005; (ii) detected antibody to SQPV using an enzyme-linked immunosorbent assay (ELISA) in the same animals; and (iii) mapped cases of the disease, and the gray squirrel distribution, using a geographical information system. We analyzed the distribution of cases of SQPV disease according to woodland type, a measure of squirrel density. SQPV disease occurred only in areas of England also inhabited by seropositive gray squirrels, and as the geographical range of gray squirrels expanded, SQPV disease occurred in these new gray squirrel habitats, supporting a role for the gray squirrel as a reservoir host of the virus. There was a delay between the establishment of invading gray squirrels and cases of the disease in red squirrels which implies gray squirrels must reach a threshold number or density before the virus is transmitted to red squirrels. The spatial and temporal trend in SQPV disease outbreaks suggested that SQPV disease will have a significant effect on Scottish populations of red squirrels within 25 years. The even spread of cases of disease across months suggested a direct rather than vector-borne transmission route is more likely. Eight juvenile and sub-adult free-living red squirrels apparently survived exposure to SQPV by mounting an immune response, the first evidence of immunity to SQPV in free-living red squirrels, which possibly suggests a changing host-parasite relationship and that the use of a vaccine may be an effective management tool to protect remnant red squirrel populations.}, } @article {pmid18922366, year = {2008}, author = {Amaral-Zettler, L and Peplies, J and Ramette, A and Fuchs, B and Ludwig, W and Glöckner, FO}, title = {Proceedings of the international workshop on Ribosomal RNA technology, April 7-9, 2008, Bremen, Germany.}, journal = {Systematic and applied microbiology}, volume = {31}, number = {4}, pages = {258-268}, doi = {10.1016/j.syapm.2008.08.004}, pmid = {18922366}, issn = {0723-2020}, mesh = {Archaea/classification/genetics ; Bacteria/classification/genetics ; Computational Biology/trends ; Databases, Nucleic Acid/trends ; Environmental Microbiology ; Genes, rRNA ; *Phylogeny ; RNA, Archaeal/genetics ; RNA, Bacterial/genetics ; RNA, Ribosomal/*genetics ; Ribotyping/*trends ; Sequence Analysis, RNA/*trends ; Software/trends ; }, abstract = {Thirty years have passed since Carl Woese proposed three primary domains of life based on the phylogenetic analysis of ribosomal RNA (rRNA) genes. Adopted by researchers worldwide, rRNA has become the "gold-standard" for molecular taxonomy, biodiversity analysis and the identification of microorganisms. The more than 700,000 rRNA sequences in public databases constitute an unprecedented hallmark of the richness of microbial biodiversity on earth. The International Workshop on Ribosomal RNA Technology convened on April 7-9, 2008 in Bremen, Germany (http://www.arb-silva.de/rrna-workshop) to summarize the current status of the field and strategize on the best ways of proceeding on both biological and technological fronts. In five sessions, 26 leading international speakers and approximately 120 participants representing diverse disciplines discussed new technological approaches to address three basic ecological questions: "Who is out there?" "How many are there?" and "What are they doing?".}, } @article {pmid18922166, year = {2008}, author = {Roche, B and Guégan, JF and Bousquet, F}, title = {Multi-agent systems in epidemiology: a first step for computational biology in the study of vector-borne disease transmission.}, journal = {BMC bioinformatics}, volume = {9}, number = {}, pages = {435}, pmid = {18922166}, issn = {1471-2105}, mesh = {Algorithms ; Animals ; Biological Evolution ; Computational Biology/*methods ; *Disease Transmission, Infectious ; *Disease Vectors ; Ecosystem ; *Epidemiologic Methods ; Geographic Information Systems ; Host-Parasite Interactions ; Models, Theoretical ; *Software ; Unified Medical Language System ; }, abstract = {BACKGROUND: Computational biology is often associated with genetic or genomic studies only. However, thanks to the increase of computational resources, computational models are appreciated as useful tools in many other scientific fields. Such modeling systems are particularly relevant for the study of complex systems, like the epidemiology of emerging infectious diseases. So far, mathematical models remain the main tool for the epidemiological and ecological analysis of infectious diseases, with SIR models could be seen as an implicit standard in epidemiology. Unfortunately, these models are based on differential equations and, therefore, can become very rapidly unmanageable due to the too many parameters which need to be taken into consideration. For instance, in the case of zoonotic and vector-borne diseases in wildlife many different potential host species could be involved in the life-cycle of disease transmission, and SIR models might not be the most suitable tool to truly capture the overall disease circulation within that environment. This limitation underlines the necessity to develop a standard spatial model that can cope with the transmission of disease in realistic ecosystems.

RESULTS: Computational biology may prove to be flexible enough to take into account the natural complexity observed in both natural and man-made ecosystems. In this paper, we propose a new computational model to study the transmission of infectious diseases in a spatially explicit context. We developed a multi-agent system model for vector-borne disease transmission in a realistic spatial environment.

CONCLUSION: Here we describe in detail the general behavior of this model that we hope will become a standard reference for the study of vector-borne disease transmission in wildlife. To conclude, we show how this simple model could be easily adapted and modified to be used as a common framework for further research developments in this field.}, } @article {pmid18848634, year = {2008}, author = {Hull, JM and Strobel, BN and Boal, CW and Hull, AC and Dykstra, CR and Irish, AM and Fish, AM and Ernest, HB}, title = {Comparative phylogeography and population genetics within Buteo lineatus reveals evidence of distinct evolutionary lineages.}, journal = {Molecular phylogenetics and evolution}, volume = {49}, number = {3}, pages = {988-996}, doi = {10.1016/j.ympev.2008.09.010}, pmid = {18848634}, issn = {1095-9513}, mesh = {Alleles ; Animals ; Bayes Theorem ; Computational Biology ; Conservation of Natural Resources ; DNA, Mitochondrial/genetics ; Evolution, Molecular ; Gene Frequency ; *Genetic Speciation ; Genetic Variation ; *Genetics, Population ; *Geography ; Haplotypes ; Hawks/classification/*genetics ; Microsatellite Repeats ; Mitochondria/genetics ; North America ; Phylogeny ; Population Dynamics ; Sequence Analysis, DNA ; }, abstract = {Traditional subspecies classifications may suggest phylogenetic relationships that are discordant with evolutionary history and mislead evolutionary inference. To more accurately describe evolutionary relationships and inform conservation efforts, we investigated the genetic relationships and demographic histories of Buteo lineatus subspecies in eastern and western North America using 21 nuclear microsatellite loci and 375-base pairs of mitochondrial control region sequence. Frequency based analyses of mitochondrial sequence data support significant population distinction between eastern (B. l. lineatus/alleni/texanus) and western (B. l.elegans) subspecies of B. lineatus. This distinction was further supported by frequency and Bayesian analyses of the microsatellite data. We found evidence of differing demographic histories between regions; among eastern sites, mitochondrial data suggested that rapid population expansion occurred following the end of the last glacial maximum, with B. l. texanus population expansion preceding that of B. l. lineatus/alleni. No evidence of post-glacial population expansion was detected among western samples (B. l.elegans). Rather, microsatellite data suggest that the western population has experienced a recent bottleneck, presumably associated with extensive anthropogenic habitat loss during the 19th and 20th centuries. Our data indicate that eastern and western populations of B. lineatus are genetically distinct lineages, have experienced very different demographic histories, and suggest management as separate conservation units may be warranted.}, } @article {pmid18847443, year = {2008}, author = {Beier, CM}, title = {Influence of political opposition and compromise on conservation outcomes in the Tongass National Forest, Alaska.}, journal = {Conservation biology : the journal of the Society for Conservation Biology}, volume = {22}, number = {6}, pages = {1485-1496}, doi = {10.1111/j.1523-1739.2008.01045.x}, pmid = {18847443}, issn = {1523-1739}, mesh = {Alaska ; Conservation of Natural Resources/*economics/*legislation & jurisprudence ; *Ecosystem ; Geographic Information Systems ; *Negotiating ; *Politics ; *Public Policy ; }, abstract = {To understand how a highly contentious policy process influenced a major conservation effort, I examined the origins, compromises, and outcomes of the Alaska National Interest Lands Conservation Act of 1980 (ANILCA) for the Tongass National Forest. Tongass wilderness designation was among the most controversial issues in the ANILCA debate, and it faced strong opposition from influential lawmakers, land managers, and Alaska residents. To investigate the influence of this opposition on Tongass conservation outcomes, I conducted a gap analysis of Tongass reserves and a policy analysis of the ANILCA debate and traced the influence of specific interests through the amendments, negotiations, and resulting compromises needed to enact ANILCA. Overall, I found that Tongass reserves comprise a broadly representative cross-section of ecosystems and species habitats in southeastern Alaska. Redrawn reserve boundaries, industry subsidies, and special access regulations reflected compromises to minimize the impact of wilderness conservation on mining, timber, and local stakeholder interests, respectively. Fragmentation of the Admiralty Island National Monument-the most ecologically valuable and politically controversial reserve-resulted from compromises with Alaskan Native (indigenous peoples of Alaska) corporations and timber interests. Despite language to accommodate "reasonable access" to wilderness reserves, ongoing access limitations highlight the concerns of Alaska residents that opposed ANILCA several decades ago. More broadly, the Tongass case suggests that early and ambitious conservation action may offset strong political opposition; compromises needed to establish key reserves often exacerbate development impacts in unprotected areas; and efforts to minimize social conflicts are needed to safeguard the long-term viability of conservation measures.}, } @article {pmid18845749, year = {2008}, author = {Schipper, J and Chanson, JS and Chiozza, F and Cox, NA and Hoffmann, M and Katariya, V and Lamoreux, J and Rodrigues, AS and Stuart, SN and Temple, HJ and Baillie, J and Boitani, L and Lacher, TE and Mittermeier, RA and Smith, AT and Absolon, D and Aguiar, JM and Amori, G and Bakkour, N and Baldi, R and Berridge, RJ and Bielby, J and Black, PA and Blanc, JJ and Brooks, TM and Burton, JA and Butynski, TM and Catullo, G and Chapman, R and Cokeliss, Z and Collen, B and Conroy, J and Cooke, JG and da Fonseca, GA and Derocher, AE and Dublin, HT and Duckworth, JW and Emmons, L and Emslie, RH and Festa-Bianchet, M and Foster, M and Foster, S and Garshelis, DL and Gates, C and Gimenez-Dixon, M and Gonzalez, S and Gonzalez-Maya, JF and Good, TC and Hammerson, G and Hammond, PS and Happold, D and Happold, M and Hare, J and Harris, RB and Hawkins, CE and Haywood, M and Heaney, LR and Hedges, S and Helgen, KM and Hilton-Taylor, C and Hussain, SA and Ishii, N and Jefferson, TA and Jenkins, RK and Johnston, CH and Keith, M and Kingdon, J and Knox, DH and Kovacs, KM and Langhammer, P and Leus, K and Lewison, R and Lichtenstein, G and Lowry, LF and Macavoy, Z and Mace, GM and Mallon, DP and Masi, M and McKnight, MW and Medellín, RA and Medici, P and Mills, G and Moehlman, PD and Molur, S and Mora, A and Nowell, K and Oates, JF and Olech, W and Oliver, WR and Oprea, M and Patterson, BD and Perrin, WF and Polidoro, BA and Pollock, C and Powel, A and Protas, Y and Racey, P and Ragle, J and Ramani, P and Rathbun, G and Reeves, RR and Reilly, SB and Reynolds, JE and Rondinini, C and Rosell-Ambal, RG and Rulli, M and Rylands, AB and Savini, S and Schank, CJ and Sechrest, W and Self-Sullivan, C and Shoemaker, A and Sillero-Zubiri, C and De Silva, N and Smith, DE and Srinivasulu, C and Stephenson, PJ and van Strien, N and Talukdar, BK and Taylor, BL and Timmins, R and Tirira, DG and Tognelli, MF and Tsytsulina, K and Veiga, LM and Vié, JC and Williamson, EA and Wyatt, SA and Xie, Y and Young, BE}, title = {The status of the world's land and marine mammals: diversity, threat, and knowledge.}, journal = {Science (New York, N.Y.)}, volume = {322}, number = {5899}, pages = {225-230}, doi = {10.1126/science.1165115}, pmid = {18845749}, issn = {1095-9203}, mesh = {Animals ; *Biodiversity ; Body Size ; Conservation of Natural Resources ; Databases, Factual ; Ecosystem ; *Extinction, Biological ; *Mammals/anatomy & histology/classification/physiology ; Marine Biology ; Phylogeny ; Population Dynamics ; Seawater ; }, abstract = {Knowledge of mammalian diversity is still surprisingly disparate, both regionally and taxonomically. Here, we present a comprehensive assessment of the conservation status and distribution of the world's mammals. Data, compiled by 1700+ experts, cover all 5487 species, including marine mammals. Global macroecological patterns are very different for land and marine species but suggest common mechanisms driving diversity and endemism across systems. Compared with land species, threat levels are higher among marine mammals, driven by different processes (accidental mortality and pollution, rather than habitat loss), and are spatially distinct (peaking in northern oceans, rather than in Southeast Asia). Marine mammals are also disproportionately poorly known. These data are made freely available to support further scientific developments and conservation action.}, } @article {pmid18845720, year = {2008}, author = {Pennisi, E}, title = {Ecology. Comprehensive conservation database details threats to mammals.}, journal = {Science (New York, N.Y.)}, volume = {322}, number = {5899}, pages = {178-179}, doi = {10.1126/science.322.5899.178b}, pmid = {18845720}, issn = {1095-9203}, mesh = {Animals ; Biodiversity ; *Conservation of Natural Resources ; *Databases, Factual ; *Ecosystem ; *Extinction, Biological ; *Mammals/classification ; Marine Biology ; Population Density ; }, } @article {pmid18842678, year = {2009}, author = {Zhang, Z and Cheung, KH and Townsend, JP}, title = {Bringing Web 2.0 to bioinformatics.}, journal = {Briefings in bioinformatics}, volume = {10}, number = {1}, pages = {1-10}, pmid = {18842678}, issn = {1477-4054}, support = {P01 GM068087/GM/NIGMS NIH HHS/United States ; GM068087/GM/NIGMS NIH HHS/United States ; P01 DC04732/DC/NIDCD NIH HHS/United States ; U24 NS051869/NS/NINDS NIH HHS/United States ; }, mesh = {*Computational Biology ; Computer-Assisted Instruction ; Cooperative Behavior ; Database Management Systems ; Databases, Factual ; Humans ; *Information Dissemination/methods ; Internet/*trends ; Research ; User-Computer Interface ; }, abstract = {Enabling deft data integration from numerous, voluminous and heterogeneous data sources is a major bioinformatic challenge. Several approaches have been proposed to address this challenge, including data warehousing and federated databasing. Yet despite the rise of these approaches, integration of data from multiple sources remains problematic and toilsome. These two approaches follow a user-to-computer communication model for data exchange, and do not facilitate a broader concept of data sharing or collaboration among users. In this report, we discuss the potential of Web 2.0 technologies to transcend this model and enhance bioinformatics research. We propose a Web 2.0-based Scientific Social Community (SSC) model for the implementation of these technologies. By establishing a social, collective and collaborative platform for data creation, sharing and integration, we promote a web services-based pipeline featuring web services for computer-to-computer data exchange as users add value. This pipeline aims to simplify data integration and creation, to realize automatic analysis, and to facilitate reuse and sharing of data. SSC can foster collaboration and harness collective intelligence to create and discover new knowledge. In addition to its research potential, we also describe its potential role as an e-learning platform in education. We discuss lessons from information technology, predict the next generation of Web (Web 3.0), and describe its potential impact on the future of bioinformatics studies.}, } @article {pmid18841204, year = {2008}, author = {Richter, DC and Ott, F and Auch, AF and Schmid, R and Huson, DH}, title = {MetaSim: a sequencing simulator for genomics and metagenomics.}, journal = {PloS one}, volume = {3}, number = {10}, pages = {e3373}, pmid = {18841204}, issn = {1932-6203}, mesh = {*Databases, Genetic ; *Genomics ; Models, Theoretical ; User-Computer Interface ; }, abstract = {BACKGROUND: The new research field of metagenomics is providing exciting insights into various, previously unclassified ecological systems. Next-generation sequencing technologies are producing a rapid increase of environmental data in public databases. There is great need for specialized software solutions and statistical methods for dealing with complex metagenome data sets.

To facilitate the development and improvement of metagenomic tools and the planning of metagenomic projects, we introduce a sequencing simulator called MetaSim. Our software can be used to generate collections of synthetic reads that reflect the diverse taxonomical composition of typical metagenome data sets. Based on a database of given genomes, the program allows the user to design a metagenome by specifying the number of genomes present at different levels of the NCBI taxonomy, and then to collect reads from the metagenome using a simulation of a number of different sequencing technologies. A population sampler optionally produces evolved sequences based on source genomes and a given evolutionary tree.

CONCLUSIONS/SIGNIFICANCE: MetaSim allows the user to simulate individual read datasets that can be used as standardized test scenarios for planning sequencing projects or for benchmarking metagenomic software.}, } @article {pmid18840282, year = {2008}, author = {Frank, DN}, title = {XplorSeq: a software environment for integrated management and phylogenetic analysis of metagenomic sequence data.}, journal = {BMC bioinformatics}, volume = {9}, number = {}, pages = {420}, pmid = {18840282}, issn = {1471-2105}, mesh = {Artificial Intelligence ; Base Sequence ; *Database Management Systems ; Genes, rRNA ; *Genome ; Information Storage and Retrieval ; Meta-Analysis as Topic ; *Phylogeny ; Sequence Analysis, DNA/*methods ; Systems Integration ; *User-Computer Interface ; }, abstract = {BACKGROUND: Advances in automated DNA sequencing technology have accelerated the generation of metagenomic DNA sequences, especially environmental ribosomal RNA gene (rDNA) sequences. As the scale of rDNA-based studies of microbial ecology has expanded, need has arisen for software that is capable of managing, annotating, and analyzing the plethora of diverse data accumulated in these projects.

RESULTS: XplorSeq is a software package that facilitates the compilation, management and phylogenetic analysis of DNA sequences. XplorSeq was developed for, but is not limited to, high-throughput analysis of environmental rRNA gene sequences. XplorSeq integrates and extends several commonly used UNIX-based analysis tools by use of a Macintosh OS-X-based graphical user interface (GUI). Through this GUI, users may perform basic sequence import and assembly steps (base-calling, vector/primer trimming, contig assembly), perform BLAST (Basic Local Alignment and Search Tool; 123) searches of NCBI and local databases, create multiple sequence alignments, build phylogenetic trees, assemble Operational Taxonomic Units, estimate biodiversity indices, and summarize data in a variety of formats. Furthermore, sequences may be annotated with user-specified meta-data, which then can be used to sort data and organize analyses and reports. A document-based architecture permits parallel analysis of sequence data from multiple clones or amplicons, with sequences and other data stored in a single file.

CONCLUSION: XplorSeq should benefit researchers who are engaged in analyses of environmental sequence data, especially those with little experience using bioinformatics software. Although XplorSeq was developed for management of rDNA sequence data, it can be applied to most any sequencing project. The application is available free of charge for non-commercial use at http://vent.colorado.edu/phyloware.}, } @article {pmid18837585, year = {2007}, author = {Masters, RD}, title = {Historical change and evolutionary theory.}, journal = {Politics and the life sciences : the journal of the Association for Politics and the Life Sciences}, volume = {26}, number = {2}, pages = {46-74}, doi = {10.2990/26_2_46}, pmid = {18837585}, issn = {0730-9384}, mesh = {*Altruism ; *Biological Evolution ; Economics ; Ethnicity ; Game Theory ; *Government ; Humans ; Information Systems ; Jurisprudence ; Leadership ; Politics ; Religion ; Social Behavior ; *Social Change ; Warfare ; }, abstract = {Despite advances in fields like genetics, evolutionary psychology, and human behavior and evolution--which generally focus on individual or small group behavior from a biological perspective--evolutionary biology has made little impact on studies of political change and social history. Theories of natural selection often seem inapplicable to human history because our social behavior is embedded in language (which makes possible the concepts of time and social identity on which what we call "history" depends). Peter Corning's Holistic Darwinism reconceptualizes evolutionary biology, making it possible to go beyond the barriers separating the social and natural sciences. Corning focuses on two primary processes: "synergy" (complex multivariate interactions at multiple levels between a species and its environment) and "cybernetics" (the information systems permitting communication between individuals and groups over time). Combining this frame of reference with inclusive fitness theory, it is possible to answer the most important (and puzzling) question in human history: How did a species that lived for millennia in hunter-gatherer bands form centralized states governing large populations of non-kin (including multi-ethnic empires as well as modern nation-states)? The fragility and contemporary ethnic violence in Kenya and the Congo should suffice as evidence that these issues need to be taken seriously. To explain the rise and fall of states as well as changes in human laws and customs--the core of historical research--it is essential to show how the provision of collective goods can overcome the challenge of self-interest and free-riding in some instances, yet fail to do so in others. To this end, it is now possible to consider how a state providing public goods can--under circumstances that often include effective leadership--contribute to enhanced inclusive fitness of virtually all its members. Because social behavior needs to adapt to ecology, but ecological systems are constantly transformed by human technology and social behavior, multilevel evolutionary processes can explain two central features of human history: the rise, transformations, and ultimate fall of centralized governments (the "stuff" of history); and the biological uniqueness of Homo sapiens as the mammalian species that colonized--and became top carnivore--in virtually every habitable environment on the earth's surface. Once scholars admit the necessity of linking processes of natural selection with human transformations of the natural world, it will seem anomalous that it has taken so long to integrate Darwinian biology and the social sciences.}, } @article {pmid18837308, year = {2008}, author = {Suo, FM and Chen, SL and Zhang, Z and Xie, CX}, title = {[Ecological evaluation of suitable area for production of Phellodendron amurense based on TCMGIS- I].}, journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica}, volume = {33}, number = {13}, pages = {1536-1539}, pmid = {18837308}, issn = {1001-5302}, mesh = {Acclimatization ; China ; *Ecosystem ; Geographic Information Systems ; *Medicine, Chinese Traditional ; Phellodendron/*growth & development/physiology ; }, abstract = {The TCMGIS- I (Suitability evaluation geographic information system of traditional Chinese medicine producing area) was developed and used to analyze the appropriate producing area of Phellodendron amurense in China. Taoshan county of Heilongjiang province, one of the main producing areas of the geo-authentic crude drug, was selected as the analytical basal place. The results show that besides traditional producing area in Taoshan county of Heilongjiang province, 131 counties of the provinces of Heilongjiang, Jilin, Liaoning and Innermongolia are also alternative areas according to the eco-soil condition that the medicinal plants needed, and the sum area are 567 989. 3 m2, the results also indicate some condign regions in Innermongolia municipality. The system is much valuable to the division of adaptive area, introduction and acclimatization of medicinal materials.}, } @article {pmid18831157, year = {2008}, author = {De Valpine, P and Cuddington, K and Hoopes, MF and Lockwood, JL}, title = {Is spread of invasive species regulated? Using ecological theory to interpret statistical analysis.}, journal = {Ecology}, volume = {89}, number = {9}, pages = {2377-2383}, doi = {10.1890/07-0090.1}, pmid = {18831157}, issn = {0012-9658}, mesh = {Animals ; Conservation of Natural Resources ; *Data Interpretation, Statistical ; Demography ; Ecology/*methods ; Ecosystem ; Models, Biological ; Models, Statistical ; }, abstract = {We investigate a recent proposal that invasive species display patterns of spatial "spread regulation" analogous to density-dependent regulation of population abundances. While invasive species do offer valuable tests of ecological theories about spatial spread, we argue that the statistical approach used in the study is not useful, and that the proposed definition of "spread regulation" is likely to be confusing. While concepts of negative feedbacks in spatial spread may be reasonable, the proposed definition of "spread regulation" encompasses accelerating, constant, or decelerating spread. There is no compelling biological or practical reason to adopt such a definition. Moreover, we show that the statistical patterns (from time series of ratios of newly to recently invaded sites) proposed as evidence of spread regulation are predictable from basic diffusion models or other common models of constant spread with some stochasticity in dynamics and/or observations. Because such a wide range of processes would generate the observed patterns, no clear biological conclusions emerge from the proposed approach to spread analysis. When regarded in the context of the impacts and management of invasive species, the proposed regulation concept has the potential to create costly misunderstandings.}, } @article {pmid18830741, year = {2008}, author = {Marttunen, M and Hämäläinen, RP}, title = {The decision analysis interview approach in the collaborative management of a large regulated water course.}, journal = {Environmental management}, volume = {42}, number = {6}, pages = {1026-1042}, pmid = {18830741}, issn = {0364-152X}, mesh = {*Community Participation ; Conservation of Natural Resources/*legislation & jurisprudence/*methods ; *Decision Making ; Decision Support Techniques ; Finland ; Fresh Water ; Interviews as Topic ; Uncertainty ; *Water Supply/legislation & jurisprudence ; }, abstract = {There are always conflicting goals in the management of large water courses. However, by involving stakeholders actively in the planning and decision-making processes, it is possible to work together toward commonly acceptable solutions. In this article, we describe how we applied interactive multicriteria decision analysis (MCDA) in a collaborative process which aimed at an ecologically, socially, and economically sustainable water course regulation policy. The stakeholders' opinions about the alternative regulation schemes and the relative importance of their impacts were elicited with the HIPRE software. Altogether, 20 personal interactive decision analysis interviews (DAIs) were carried out with the stakeholders. Our experience suggests that the DAIs can considerably improve the quality and efficiency of the collaborative planning process. By improving communication and understanding of the decision situation in the steering group, the approach helped to develop a consensus solution in a case having strong conflicts of interest. In order to gain the full benefits of the MCDA approach, interactive preference elicitation is vital. It is also essential to integrate the approach tightly into the planning and decision-making process. The project's home pages are available to the public at http://www.paijanne.hut.fi/.}, } @article {pmid18829120, year = {2008}, author = {Schirmer, K and Tanneberger, K and Kramer, NI and Völker, D and Scholz, S and Hafner, C and Lee, LE and Bols, NC and Hermens, JL}, title = {Developing a list of reference chemicals for testing alternatives to whole fish toxicity tests.}, journal = {Aquatic toxicology (Amsterdam, Netherlands)}, volume = {90}, number = {2}, pages = {128-137}, doi = {10.1016/j.aquatox.2008.08.005}, pmid = {18829120}, issn = {1879-1514}, mesh = {*Animal Testing Alternatives ; Animals ; Cell Line ; *Databases, Factual ; Ecotoxicology/*methods ; Inhibitory Concentration 50 ; Lethal Dose 50 ; *Organic Chemicals ; Reference Values ; United States ; United States Environmental Protection Agency ; }, abstract = {This paper details the derivation of a list of 60 reference chemicals for the development of alternatives to animal testing in ecotoxicology with a particular focus on fish. The chemicals were selected as a prerequisite to gather mechanistic information on the performance of alternative testing systems, namely vertebrate cell lines and fish embryos, in comparison to the fish acute lethality test. To avoid the need for additional experiments with fish, the U.S. EPA fathead minnow database was consulted as reference for whole organism responses. This database was compared to the Halle Registry of Cytotoxicity and a collation of data by the German EPA (UBA) on acute toxicity data derived from zebrafish embryos. Chemicals that were present in the fathead minnow database and in at least one of the other two databases were subject to selection. Criteria included the coverage of a wide range of toxicity and physico-chemical parameters as well as the determination of outliers of the in vivo/in vitro correlations. While the reference list of chemicals now guides our research for improving cell line and fish embryo assays to make them widely applicable, the list could be of benefit to search for alternatives in ecotoxicology in general. One example would be the use of this list to validate structure-activity prediction models, which in turn would benefit from a continuous extension of this list with regard to physico-chemical and toxicological data.}, } @article {pmid18822444, year = {2008}, author = {Gillund, F and Kjølberg, KA and von Krauss, MK and Myhr, AI}, title = {Do uncertainty analyses reveal uncertainties? Using the introduction of DNA vaccines to aquaculture as a case.}, journal = {The Science of the total environment}, volume = {407}, number = {1}, pages = {185-196}, doi = {10.1016/j.scitotenv.2008.08.001}, pmid = {18822444}, issn = {0048-9697}, mesh = {Animals ; *Aquaculture/methods/statistics & numerical data ; Autoimmunity/drug effects ; *Decision Support Techniques ; Fish Diseases/immunology/*prevention & control ; Fishes/growth & development/immunology ; Risk Assessment ; *Uncertainty ; *Vaccines, DNA/administration & dosage/adverse effects/therapeutic use ; *Water Pollution/adverse effects/analysis ; }, abstract = {The Walker and Harremoës (W&H) uncertainty framework is a tool to systematically identify scientific uncertainty. We applied the W&H uncertainty framework to elicit scientists' judgements of potential sources of uncertainty associated with the use of DNA vaccination in aquaculture. DNA vaccination is considered a promising solution to combat pathological fish diseases. There is, however, lack of knowledge regarding its ecological and social implications. Our findings indicate that scientists are open and aware of a number of uncertainties associated with DNA vaccination e.g. with regard to immune response, degradation and distribution of the DNA plasmid after injection and environmental release, and consider most of these uncertainties to be adequately reduced through more research. We proceed to discuss our experience of using the W&H uncertainty framework. Some challenges related to the application of the framework were recognised. This was especially related to the respondents' unfamiliarity with the concepts used and their lack of experience in discussing qualitative aspects of uncertainties. As we see it, the W&H framework should be considered as a useful tool to stimulate reflection on uncertainty and an important first step in a more extensive process of including and properly dealing with uncertainties in science and policymaking.}, } @article {pmid18818648, year = {2008}, author = {Hugenholtz, P and Tyson, GW}, title = {Microbiology: metagenomics.}, journal = {Nature}, volume = {455}, number = {7212}, pages = {481-483}, doi = {10.1038/455481a}, pmid = {18818648}, issn = {1476-4687}, mesh = {Biodiversity ; Computational Biology/trends ; *Ecosystem ; *Environmental Microbiology ; Eukaryotic Cells/metabolism ; Evolution, Molecular ; *Genetics, Microbial/methods ; Genome/genetics ; *Genomics/economics/methods/trends ; Humans ; Marine Biology ; Prokaryotic Cells/metabolism ; Sequence Analysis, DNA/economics ; Time Factors ; Viruses/genetics ; }, } @article {pmid18800865, year = {2009}, author = {Kjos, SA and Snowden, KF and Olson, JK}, title = {Biogeography and Trypanosoma cruzi infection prevalence of Chagas disease vectors in Texas, USA.}, journal = {Vector borne and zoonotic diseases (Larchmont, N.Y.)}, volume = {9}, number = {1}, pages = {41-50}, doi = {10.1089/vbz.2008.0026}, pmid = {18800865}, issn = {1557-7759}, mesh = {Animals ; Chagas Disease/epidemiology/parasitology/*transmission ; DNA, Protozoan/genetics ; Demography ; Ecosystem ; Environment ; Geographic Information Systems ; Humans ; Insect Vectors/*classification/genetics/parasitology ; Prevalence ; Texas/epidemiology ; Triatoma/*classification/parasitology ; Trypanosoma cruzi/*genetics ; }, abstract = {Data were pooled from multiple sources including newly collected triatomine specimens, preserved specimens, government reports, and scientific articles to create a biogeographical profile of triatomine vector species found in Texas. Triatomine specimens were documented in 97 of 254 counties, and Trypanosoma cruzi-infected specimens were reported from 48 counties. Triatomine specimens were distributed in 11 of the 12 ecoregions in Texas, with all but one species found in multiple ecoregions. Of the 241 newly collected specimens, 50.74% were infected with T. cruzi. Triatoma gerstaeckeri was the most frequently collected and most geographically dispersed species followed by T. sanguisuga. Three species, T. gerstaeckeri, T. sanguisuga, and T. lecticularia, were associated with human dwellings, and over half of the new specimens found inside or near houses were infected with T. cruzi. Chagas disease vectors in Texas are widely distributed and have adapted to ecologically diverse settings. The high T. cruzi infection prevalence of specimens found in close proximity to human settings suggests the presence of an active peridomestic Chagas disease transmission cycle.}, } @article {pmid18789760, year = {2008}, author = {Surek, B}, title = {Meeting Report: Algal Culture Collections 2008. An International Meeting at the Culture Collection of Algae and Protozoa (CCAP), Dunstaffnage Marine Laboratory, Dunbeg, Oban, United Kingdom; June 8-11, 2008.}, journal = {Protist}, volume = {159}, number = {4}, pages = {509-517}, doi = {10.1016/j.protis.2008.08.001}, pmid = {18789760}, issn = {1434-4610}, mesh = {Animals ; Biological Products/biosynthesis/isolation & purification ; *Biological Specimen Banks ; *Cell Line ; Computational Biology ; *Cryopreservation ; DNA Fingerprinting ; *Eukaryota/classification/cytology/genetics/metabolism ; *Marine Biology ; Scotland ; }, } @article {pmid18787917, year = {2008}, author = {Zhu, HM and Xiang, S and Yang, K and Wu, XH and Zhou, XN}, title = {Three Gorges Dam and its impact on the potential transmission of schistosomiasis in regions along the Yangtze River.}, journal = {EcoHealth}, volume = {5}, number = {2}, pages = {137-148}, pmid = {18787917}, issn = {1612-9210}, mesh = {Animals ; China ; *Ecosystem ; Endemic Diseases ; *Environment Design ; Environmental Monitoring ; Epidemiological Monitoring ; Geographic Information Systems ; Geography ; Human Activities ; Humans ; Rivers/*parasitology ; Schistosoma japonicum/*growth & development ; Schistosomiasis japonica/epidemiology/*transmission ; Snails/classification/*parasitology ; Water Supply/*analysis ; Weather ; }, abstract = {Large-scale hydroprojects have a propensity for incurring schistosomiasis epidemics by altering the environments of their vicinities. As the construction of the Three Gorges Dam, one of the world's largest hydroprojects to date, draws near its conclusion, an assessment of the dam's capacity in causing schistosomiasis becomes more urgent and pressing. This article reviews recent investigations into the possible effects of the dam on schistosomiasis in the Three Gorges region and areas along the Yangtze downstream from the dam. Data used in this article were extracted from peer-reviewed papers found in PubMed, Chinese Journal of Parasitology and Parasitic Diseases, and Chinese Journal of Schistosomiasis Control. Results indicate that the Three Gorges Dam is capable of inducing a wide variety of environmental and ecological changes both within the Three Gorges region and in downstream areas. These changes, however, carry ambivalent implications for the reproduction of Oncomelania snails and the spreading of schistosome infections. Furthermore, major changes in the demographics and agricultural practices of the Three Gorges and downstream Yangtze areas caused by the dam could also exert significant influence on the transmission of schistosomiasis in these regions. Major conclusions of this review include the need for further ecological simulations of the Three Gorges Dam and the need for deploying monitoring and intervention systems to provide successful prophylaxis of the Three Gorges Dam-associated schistosomiasis emergence.}, } @article {pmid18787916, year = {2008}, author = {Suo, AN and Xiong, YC and Wang, TM and Yue, DX and Ge, JP}, title = {Ecosystem health assessment of the Jinghe River Watershed on the Huangtu Plateau.}, journal = {EcoHealth}, volume = {5}, number = {2}, pages = {127-136}, pmid = {18787916}, issn = {1612-9210}, mesh = {Animals ; China ; *Conservation of Natural Resources ; Crops, Agricultural/growth & development ; *Ecosystem ; Environmental Monitoring/methods ; Geographic Information Systems ; Geography ; Human Activities ; Humans ; Models, Theoretical ; Plant Development ; *Rivers ; Satellite Communications ; Soil/*analysis/standards ; Trees/*growth & development ; }, abstract = {An improved Costanza model was developed to assess the health of the Jinhe River Watershed ecosystem. The watershed is located at the center of the Huangtu Plateau in China and has suffered a severe disturbance in the last few decades. Three indicators including vigor, organization, and resilience were calculated respectively by merging ground-based observations with remotely sensed data on a watershed scale. Health indices of 12 topographic sub-watersheds were calculated using a modified Costanza formula. Health evaluated results indicated that sub-watersheds in the Huangtu mountain region were relatively healthy ecosystems with scores over 0.673. The sub-watersheds in the loess mountain and the loess gully regions, e.g., Jinghe, Heihe, and Honghe regions, scored moderately; their evaluated value ranged from 0.505 to 0.606. The two sub-watersheds in the loess gully region and all sub-watersheds in the loess hilly region scored the lowest, less than 0.50 and were considered unhealthy ecosystems. It can be argued that the loess hilly region and the loess gully regions should be in primary consideration for ecological protection and rehabilitation. This study provided a possible quantitative model for ecological planning and landscape management with respect to topographic conditions in this area.}, } @article {pmid18776637, year = {2008}, author = {Mueller, LD}, title = {Can simple population genetic models reconcile partial match frequencies observed in large forensic databases?.}, journal = {Journal of genetics}, volume = {87}, number = {2}, pages = {101-108}, pmid = {18776637}, issn = {0022-1333}, mesh = {Computer Simulation ; Confidence Intervals ; *Databases, Genetic ; Ethnicity/genetics ; *Forensic Medicine ; *Genetics, Population ; Humans ; *Models, Genetic ; Parents ; Siblings ; }, abstract = {A recent study of partial matches in the Arizona offender database of DNA profiles has revealed a large number of nine and ten locus matches. I use simple models that incorporate the product rule, population substructure, and relatedness to predict the expected number of matches in large databases. I find that there is a relatively narrow window of parameter values that can plausibly describe the Arizona results. Further research could help determine if the Arizona samples are congruent with some of the models presented here or whether fundamental assumptions for predicting these match frequencies requires adjustments.}, } @article {pmid18774905, year = {2008}, author = {Xia, A and Sharakhova, MV and Sharakhov, IV}, title = {Reconstructing ancestral autosomal arrangements in the Anopheles gambiae complex.}, journal = {Journal of computational biology : a journal of computational molecular cell biology}, volume = {15}, number = {8}, pages = {965-980}, doi = {10.1089/cmb.2008.0076}, pmid = {18774905}, issn = {1557-8666}, mesh = {Algorithms ; Animals ; Anopheles/classification/*genetics ; *Chromosome Inversion ; *Chromosome Mapping ; Chromosomes/*genetics ; Computational Biology ; Evolution, Molecular ; Humans ; Karyotyping ; Models, Genetic ; Molecular Sequence Data ; Phylogeny ; }, abstract = {Members of the Anopheles gambiae complex have remarkably distinct ecological adaptations, behaviors, and degrees of vectorial capacity. Inferring phylogenetic relationships in the complex is crucial for identifying the genomic changes associated with the origin and loss of epidemiologically important traits. However, the high level of sequence similarity, genetic introgression, and shared molecular ancestral polymorphisms makes reconstruction of the A. gambiae complex phylogeny difficult. Phylogenetic relationships among the members of species complexes can be inferred from the distribution of fixed chromosomal inversions if outgroup arrangements are known. The aim of this work is to test a possibility of determining ancestral autosomal arrangements in the A. gambiae complex using outgroup chromosomes and a combination of bioinformatic and cytogenetic approaches. The minimum number of inversions between members of the A. gambiae complex and the outgroup species A. funestus and A. stephensi was calculated using the Multiple Genome Rearrangements (MGR) and Sorting Permutation by Reversals and block-INterchanGes (SPRING) programs. The physical mapping of A. merus chromosomes identified molecular coordinates of the proximal 2Ro+ inversion breakpoint in A. gambiae. DNA probes from 2La+ and 2Ro+ inversion breakpoints of the A. gambiae were mapped to the A. stephensi chromosomes. Assuming monophyletic origin of the inversions, this study concludes that physical mapping of ingroup and outgroup species can be used for identifying inversion breakpoints and ancestral autosomal arrangements within species complexes. Molecular characterization of the breakpoints in both ingroup and outgroup species will provide a solid basis for reconstructing the inversion history in the A. gambiae complex.}, } @article {pmid18767964, year = {2008}, author = {Rannala, B and Yang, Z}, title = {Phylogenetic inference using whole genomes.}, journal = {Annual review of genomics and human genetics}, volume = {9}, number = {}, pages = {217-231}, doi = {10.1146/annurev.genom.9.081307.164407}, pmid = {18767964}, issn = {1527-8204}, mesh = {Animals ; Data Interpretation, Statistical ; Databases, Genetic/statistics & numerical data ; Gene Transfer, Horizontal ; Genome ; Genomics/*statistics & numerical data ; Humans ; *Phylogeny ; Polymorphism, Genetic ; Recombination, Genetic ; Sequence Alignment/statistics & numerical data ; Software ; }, abstract = {The availability of genome-wide data provides unprecedented opportunities for resolving difficult phylogenetic relationships and for studying population genetic processes of mutation, selection, and recombination on a genomic scale. The use of appropriate statistical models becomes increasingly important when we are faced with very large datasets, which can lead to improved precision but not necessarily improved accuracy if the analytical methods have systematic biases. This review provides a critical examination of methods for analyzing genomic datasets from multiple loci, including concatenation, separate gene-by-gene analyses, and statistical models that accommodate heterogeneity in different aspects of the evolutionary process among data partitions. We discuss factors that may cause the gene tree to differ from the species tree, as well as strategies for estimating species phylogenies in the presence of gene tree conflicts. Genomic datasets provide computational and statistical challenges that are likely to be a focus of research for years to come.}, } @article {pmid18767725, year = {2008}, author = {Osakabe, M and Kotsubo, Y and Tajima, R and Hinomoto, N}, title = {Restriction fragment length polymorphism catalog for molecular identification of Japanese Tetranychus spider mites (Acari: Tetranychidae).}, journal = {Journal of economic entomology}, volume = {101}, number = {4}, pages = {1167-1175}, doi = {10.1603/0022-0493(2008)101[1167:rflpcf]2.0.co;2}, pmid = {18767725}, issn = {0022-0493}, mesh = {Animals ; *Databases, Nucleic Acid ; Female ; Japan ; *Polymorphism, Restriction Fragment Length ; Tetranychidae/*classification/genetics ; }, abstract = {Species identification is a basic issue in biosecurity. Polymerase chain reaction (PCR) followed by restriction fragment length polymorphism (RFLP) is a useful molecular diagnostic tool for species identification. However, the lack of transferability of data has been a serious shortcoming of this method. A RFLP catalog, i.e., a graph of PCR-RFLP patterns expected from sequence data, was devised as a tool to facilitate PCR-RFLP data sharing among laboratories. Twelve species of Tetranychus spider mites have been recorded in Japan to date. In this study, we analyzed DNA sequences of the internal transcribed spacer (ITS) region in nuclear ribosomal DNA of 11 Tetranychus species. For the species identification using PCR-RFLP, we chose six candidates from 131 restriction endonucleases and developed an RFLP catalog of all known Japanese Tetranychus species except Tetranychus neocaledonicus André. The RFLP catalog revealed that most Tetranychus species had diagnostic restriction fragments. The RFLP catalog is transferable and simple molecular diagnostic tool, and it has the ability to add more species and newly found intraspecific variations. Therefore, we believe that the RFLP catalog will contribute to biosecurity as a practical diagnostic tool for species identification of spider mites.}, } @article {pmid18765756, year = {2008}, author = {Simmons, ME and Wu, XB and Knight, SL and Lopez, RR}, title = {Assessing the influence of field- and GIS-based inquiry on student attitude and conceptual knowledge in an undergraduate ecology lab.}, journal = {CBE life sciences education}, volume = {7}, number = {3}, pages = {338-345}, pmid = {18765756}, issn = {1931-7913}, mesh = {*Attitude ; Data Collection ; Ecology/*education ; Ecosystem ; *Geographic Information Systems ; *Knowledge ; *Laboratories ; *Students ; Teaching/*methods ; }, abstract = {Combining field experience with use of information technology has the potential to create a problem-based learning environment that engages learners in authentic scientific inquiry. This study, conducted over a 2-yr period, determined differences in attitudes and conceptual knowledge between students in a field lab and students with combined field and geographic information systems (GIS) experience. All students used radio-telemetry equipment to locate fox squirrels, while one group of students was provided an additional data set in a GIS to visualize and quantify squirrel locations. Pre/postsurveys and tests revealed that attitudes improved in year 1 for both groups of students, but differences were minimal between groups. Attitudes generally declined in year 2 due to a change in the authenticity of the field experience; however, attitudes for students that used GIS declined less than those with field experience only. Conceptual knowledge also increased for both groups in both years. The field-based nature of this lab likely had a greater influence on student attitude and conceptual knowledge than did the use of GIS. Although significant differences were limited, GIS did not negatively impact student attitude or conceptual knowledge but potentially provided other benefits to learners.}, } @article {pmid18761096, year = {2008}, author = {Thomson, RC and Shedlock, AM and Edwards, SV and Shaffer, HB}, title = {Developing markers for multilocus phylogenetics in non-model organisms: A test case with turtles.}, journal = {Molecular phylogenetics and evolution}, volume = {49}, number = {2}, pages = {514-525}, doi = {10.1016/j.ympev.2008.08.006}, pmid = {18761096}, issn = {1095-9513}, mesh = {Algorithms ; Animals ; Bayes Theorem ; Chromosomes, Artificial, Bacterial ; Computational Biology/*methods ; DNA Primers ; Databases, Nucleic Acid ; Gene Library ; Genetic Markers ; Likelihood Functions ; Long Interspersed Nucleotide Elements ; Microsatellite Repeats ; Models, Genetic ; *Phylogeny ; Sequence Analysis, DNA ; Turtles/*classification/*genetics ; }, abstract = {We present a strategy for phylogenetic marker development in non-model systems. Rather than using the traditional approach of comparing distantly related taxa to develop conserved primers for unknown species, we explore an alternative strategy that builds primers directly from a single, relatively well characterized species and applies those primers to increasingly distantly related taxa. We develop and test our protocol with turtles. Using a single BAC end-sequence library consisting of 3461 sequences totaling 2.43 million base pairs of data, we outline a procedure to flag repeat elements, followed by a BLAST approach to categorize sequences into high, low, and no similarity compartments compared to GenBank sequences. We developed and tested a panel of 96 primer pairs with a set of turtle tissues that forms a series of increasingly distantly related taxa with respect to the BAC reference species. Finally, we sequenced 11 of these newly discovered markers across a diverse set of 18 turtle species that spans the 210 million years of chelonian crown-group history and that includes representatives of most of the major clades of extant turtles. Our results indicate that large numbers of new, phylogenetically informative markers can be developed quickly and inexpensively from a single BAC, EST, or similar genomic resource, and that those markers provide reliable phylogenetic information across both shallow and deep levels of phylogenetic history. Our results also highlight the importance of screening for and managing repetitive elements found in randomly sequenced DNA fragments. We presume that our strategy should work well across any similarly divergent clade, suggesting that many-marker datasets can be developed quickly and efficiently for phylogenetic analysis.}, } @article {pmid18759851, year = {2009}, author = {Ward, G and Hastie, T and Barry, S and Elith, J and Leathwick, JR}, title = {Presence-only data and the em algorithm.}, journal = {Biometrics}, volume = {65}, number = {2}, pages = {554-563}, doi = {10.1111/j.1541-0420.2008.01116.x}, pmid = {18759851}, issn = {1541-0420}, support = {R01 EB001988/EB/NIBIB NIH HHS/United States ; }, mesh = {Algorithms ; Biometry/*methods ; Computer Simulation ; Data Interpretation, Statistical ; *Epidemiologic Research Design ; *Likelihood Functions ; *Models, Biological ; *Models, Statistical ; Pattern Recognition, Automated ; *Population Dynamics ; Reproducibility of Results ; Risk Assessment/*methods ; Sample Size ; Sensitivity and Specificity ; }, abstract = {In ecological modeling of the habitat of a species, it can be prohibitively expensive to determine species absence. Presence-only data consist of a sample of locations with observed presences and a separate group of locations sampled from the full landscape, with unknown presences. We propose an expectation-maximization algorithm to estimate the underlying presence-absence logistic model for presence-only data. This algorithm can be used with any off-the-shelf logistic model. For models with stepwise fitting procedures, such as boosted trees, the fitting process can be accelerated by interleaving expectation steps within the procedure. Preliminary analyses based on sampling from presence-absence records of fish in New Zealand rivers illustrate that this new procedure can reduce both deviance and the shrinkage of marginal effect estimates that occur in the naive model often used in practice. Finally, it is shown that the population prevalence of a species is only identifiable when there is some unrealistic constraint on the structure of the logistic model. In practice, it is strongly recommended that an estimate of population prevalence be provided.}, } @article {pmid18757984, year = {2008}, author = {Walters, P and Ashworth, M and Tylee, A}, title = {Ethnic density, physical illness, social deprivation and antidepressant prescribing in primary care: ecological study.}, journal = {The British journal of psychiatry : the journal of mental science}, volume = {193}, number = {3}, pages = {235-239}, doi = {10.1192/bjp.bp.107.038299}, pmid = {18757984}, issn = {0007-1250}, mesh = {Antidepressive Agents/*administration & dosage ; *Ethnicity ; Family Practice/statistics & numerical data ; Female ; Health Care Surveys ; Health Services Accessibility ; Humans ; Male ; Population Density ; Practice Patterns, Physicians'/*statistics & numerical data ; *Primary Health Care/statistics & numerical data ; Quality Indicators, Health Care ; Socioeconomic Factors ; Vulnerable Populations/ethnology ; }, abstract = {BACKGROUND: Antidepressant prescribing should reflect need. The Quality and Outcomes Framework has provided an opportunity to explore factors affecting antidepressant prescribing in UK general practice.

AIMS: To explore the relationship between physical illness, social deprivation, ethnicity, practice characteristics and the volume of antidepressants prescribed in primary care.

METHOD: This was an ecological study using data derived from the Quality and Outcomes Framework, the Informatics Collaboratory of the Social Sciences, and Prescribing Analyses and CosT data for 2004-2005. Associations were examined using linear regression modelling.

RESULTS: Socio-economic status, ethnic density, asthma, chronic obstructive pulmonary disease and epilepsy explained 44% of the variance in the volume of antidepressants prescribed.

CONCLUSIONS: Lower volumes of antidepressants are prescribed in areas with high densities of Black or Asian people. This may suggest disparities in provision of care. Chronic respiratory disease and epilepsy may have a more important association with depression in primary care than previously thought.}, } @article {pmid18755027, year = {2008}, author = {Park, J and Lee, S and Choi, J and Ahn, K and Park, B and Park, J and Kang, S and Lee, YH}, title = {Fungal cytochrome P450 database.}, journal = {BMC genomics}, volume = {9}, number = {}, pages = {402}, pmid = {18755027}, issn = {1471-2164}, mesh = {Computational Biology ; Cytochrome P-450 Enzyme System/classification/*genetics ; Database Management Systems ; *Databases, Genetic ; Evolution, Molecular ; Fungal Proteins/classification/genetics ; Fungi/classification/enzymology/*genetics ; Genes, Fungal ; *Genome, Fungal ; Phylogeny ; }, abstract = {BACKGROUND: Cytochrome P450 enzymes play critical roles in fungal biology and ecology. To support studies on the roles and evolution of cytochrome P450 enzymes in fungi based on rapidly accumulating genome sequences from diverse fungal species, an efficient bioinformatics platform specialized for this super family of proteins is highly desirable.

RESULTS: The Fungal Cytochrome P450 Database (FCPD) archives genes encoding P450s in the genomes of 66 fungal and 4 oomycete species (4,538 in total) and supports analyses of their sequences, chromosomal distribution pattern, and evolutionary histories and relationships. The archived P450s were classified into 16 classes based on InterPro terms and clustered into 141 groups using tribe-MCL. The proportion of P450s in the total proteome and class distribution in individual species exhibited certain taxon-specific characteristics.

CONCLUSION: The FCPD will facilitate systematic identification and multifaceted analyses of P450s at multiple taxon levels via the web. All data and functions are available at the web site http://p450.riceblast.snu.ac.kr/.}, } @article {pmid18752601, year = {2008}, author = {Li, YF and Costello, JC and Holloway, AK and Hahn, MW}, title = {"Reverse ecology" and the power of population genomics.}, journal = {Evolution; international journal of organic evolution}, volume = {62}, number = {12}, pages = {2984-2994}, pmid = {18752601}, issn = {1558-5646}, support = {R01-GM076643A/GM/NIGMS NIH HHS/United States ; R01 GM076643-01A1/GM/NIGMS NIH HHS/United States ; R01 GM071926/GM/NIGMS NIH HHS/United States ; R01 GM076643-03/GM/NIGMS NIH HHS/United States ; R01 GM076643/GM/NIGMS NIH HHS/United States ; GM071926/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Base Sequence ; *Data Interpretation, Statistical ; Drosophila/genetics ; *Genetics, Population ; Genomics/*methods ; Humans ; Molecular Sequence Data ; Saccharomyces cerevisiae/genetics ; *Selection, Genetic ; Sequence Analysis, DNA ; }, abstract = {Rapid and inexpensive sequencing technologies are making it possible to collect whole genome sequence data on multiple individuals from a population. This type of data can be used to quickly identify genes that control important ecological and evolutionary phenotypes by finding the targets of adaptive natural selection, and we therefore refer to such approaches as "reverse ecology." To quantify the power gained in detecting positive selection using population genomic data, we compare three statistical methods for identifying targets of selection: the McDonald-Kreitman test, the mkprf method, and a likelihood implementation for detecting d(N)/d(S) > 1. Because the first two methods use polymorphism data we expect them to have more power to detect selection. However, when applied to population genomic datasets from human, fly, and yeast, the tests using polymorphism data were actually weaker in two of the three datasets. We explore reasons why the simpler comparative method has identified more genes under selection, and suggest that the different methods may really be detecting different signals from the same sequence data. Finally, we find several statistical anomalies associated with the mkprf method, including an almost linear dependence between the number of positively selected genes identified and the prior distributions used. We conclude that interpreting the results produced by this method should be done with some caution.}, } @article {pmid18752600, year = {2008}, author = {Moyle, LC}, title = {Ecological and evolutionary genomics in the wild tomatoes (Solanum sect. Lycopersicon).}, journal = {Evolution; international journal of organic evolution}, volume = {62}, number = {12}, pages = {2995-3013}, doi = {10.1111/j.1558-5646.2008.00487.x}, pmid = {18752600}, issn = {1558-5646}, mesh = {Adaptation, Biological/*genetics ; *Biodiversity ; Demography ; *Evolution, Molecular ; *Genetic Speciation ; Genomics/*methods ; Geographic Information Systems ; Geography ; Solanum lycopersicum/*genetics ; *Phenotype ; Reproduction/genetics ; Species Specificity ; }, abstract = {The plant group Solanum section Lycopersicon (the clade containing the domesticated tomato and its wild relatives) is ideal for integrating genomic tools and approaches into ecological and evolutionary research. Wild species within Lycopersicon span broad morphological, physiological, life history, mating system, and biochemical variation, and are separated by substantial, but incomplete postmating reproductive barriers, making this an ideal system for genetic analyses of these traits. This ecological and evolutionary diversity is matched by many logistical advantages, including extensive historical occurrence records for all species in the group, publicly available germplasm for hundreds of known wild accessions, demonstrated experimental tractability, and extensive genetic, genomic, and functional tools and information from the tomato research community. Here I introduce the numerous advantages of this system for Ecological and Evolutionary Functional Genomics (EEFG), and outline several ecological and evolutionary phenotypes and questions that can be fruitfully tackled in this system. These include biotic and abiotic adaptation, reproductive trait evolution, and the genetic basis of speciation. With the modest enhancement of some research strengths, this system is poised to join the best of our currently available model EEFG systems.}, } @article {pmid18717693, year = {2008}, author = {Sadovy De Mitcheson, Y and Cornish, A and Domeier, M and Colin, PL and Russell, M and Lindeman, KC}, title = {A global baseline for spawning aggregations of reef fishes.}, journal = {Conservation biology : the journal of the Society for Conservation Biology}, volume = {22}, number = {5}, pages = {1233-1244}, doi = {10.1111/j.1523-1739.2008.01020.x}, pmid = {18717693}, issn = {1523-1739}, mesh = {Animals ; Asia ; Conservation of Natural Resources/methods/*statistics & numerical data ; Databases, Factual ; Fisheries/*statistics & numerical data ; Fishes/*physiology ; Interviews as Topic ; Oceans and Seas ; Population Dynamics ; Sexual Behavior, Animal/*physiology ; *Social Behavior ; }, abstract = {Species that periodically and predictably congregate on land or in the sea can be extremely vulnerable to overexploitation. Many coral reef fishes form spawning aggregations that are increasingly the target of fishing. Although serious declines are well known for a few species, the extent of this behavior among fishes and the impacts of aggregation fishing are not appreciated widely. To profile aggregating species globally, establish a baseline for future work, and strengthen the case for protection, we (as members of the Society for the Conservation of Reef Fish Aggregations) developed a global database on the occurrence, history, and management of spawning aggregations. We complemented the database with information from interviews with over 300 fishers in Asia and the western Pacific. Sixty-seven species, mainly commercial, in 9 families aggregate to spawn in the 29 countries or territories considered in the database. Ninety percent of aggregation records were from reef pass channels, promontories, and outer reef-slope drop-offs. Multispecies aggregation sites were common, and spawning seasons of most species typically lasted <3 months. The best-documented species in the database, the Nassau grouper (Epinephelus striatus), has undergone substantial declines in aggregations throughout its range and is now considered threatened. Our findings have important conservation and management implications for aggregating species given that exploitation pressures on them are increasing, there is little effective management, and 79% of those aggregations sufficiently well documented were reported to be in decline. Nonetheless, a few success stories demonstrate the benefits of aggregation management. A major shift in perspective on spawning aggregations of reef fish, from being seen as opportunities for exploitation to acknowledging them as important life-history phenomena in need of management, is urgently needed.}, } @article {pmid18619410, year = {2008}, author = {Stokols, D and Misra, S and Moser, RP and Hall, KL and Taylor, BK}, title = {The ecology of team science: understanding contextual influences on transdisciplinary collaboration.}, journal = {American journal of preventive medicine}, volume = {35}, number = {2 Suppl}, pages = {S96-115}, doi = {10.1016/j.amepre.2008.05.003}, pmid = {18619410}, issn = {0749-3797}, support = {15R13DK69500-03/DK/NIDDK NIH HHS/United States ; }, mesh = {Community Networks/organization & administration ; Computer Communication Networks/organization & administration ; *Cooperative Behavior ; Empirical Research ; *Group Processes ; Health Promotion/organization & administration ; Humans ; Institutional Management Teams/organization & administration ; *Interdisciplinary Communication ; *Models, Organizational ; Outcome and Process Assessment, Health Care ; Research Personnel/*organization & administration ; Science/organization & administration ; }, abstract = {Increased public and private investments in large-scale team science initiatives over the past two decades have underscored the need to better understand how contextual factors influence the effectiveness of transdisciplinary scientific collaboration. Toward that goal, the findings from four distinct areas of research on team performance and collaboration are reviewed: (1) social psychological and management research on the effectiveness of teams in organizational and institutional settings; (2) studies of cyber-infrastructures (i.e., computer-based infrastructures) designed to support transdisciplinary collaboration across remote research sites; (3) investigations of community-based coalitions for health promotion; and (4) studies focusing directly on the antecedents, processes, and outcomes of scientific collaboration within transdisciplinary research centers and training programs. The empirical literature within these four domains reveals several contextual circumstances that either facilitate or hinder team performance and collaboration. A typology of contextual influences on transdisciplinary collaboration is proposed as a basis for deriving practical guidelines for designing, managing, and evaluating successful team science initiatives.}, } @article {pmid18619402, year = {2008}, author = {Mabry, PL and Olster, DH and Morgan, GD and Abrams, DB}, title = {Interdisciplinarity and systems science to improve population health: a view from the NIH Office of Behavioral and Social Sciences Research.}, journal = {American journal of preventive medicine}, volume = {35}, number = {2 Suppl}, pages = {S211-24}, pmid = {18619402}, issn = {0749-3797}, support = {Z99 OD999999/ImNIH/Intramural NIH HHS/United States ; }, mesh = {Behavioral Medicine/organization & administration ; Behavioral Research ; Humans ; *Interdisciplinary Communication ; National Institutes of Health (U.S.)/organization & administration ; Organizational Objectives ; Public Health/*methods ; Science/*methods/organization & administration/trends ; Social Sciences/organization & administration ; *Systems Theory ; United States ; }, abstract = {Fueled by the rapid pace of discovery, humankind's ability to understand the ultimate causes of preventable common disease burdens and to identify solutions is now reaching a revolutionary tipping point. Achieving optimal health and well-being for all members of society lies as much in the understanding of the factors identified by the behavioral, social, and public health sciences as by the biological ones. Accumulating advances in mathematical modeling, informatics, imaging, sensor technology, and communication tools have stimulated several converging trends in science: an emerging understanding of epigenomic regulation; dramatic successes in achieving population health-behavior changes; and improved scientific rigor in behavioral, social, and economic sciences. Fostering stronger interdisciplinary partnerships to bring together the behavioral-social-ecologic models of multilevel "causes of the causes" and the molecular, cellular, and, ultimately, physiological bases of health and disease will facilitate breakthroughs to improve the public's health. The strategic vision of the Office of Behavioral and Social Sciences Research (OBSSR) at the National Institutes of Health (NIH) is rooted in a collaborative approach to addressing the complex and multidimensional issues that challenge the public's health. This paper describes OBSSR's four key programmatic directions (next-generation basic science, interdisciplinary research, systems science, and a problem-based focus for population impact) to illustrate how interdisciplinary and transdisciplinary perspectives can foster the vertical integration of research among biological, behavioral, social, and population levels of analysis over the lifespan and across generations. Interdisciplinary and multilevel approaches are critical both to the OBSSR's mission of integrating behavioral and social sciences more fully into the NIH scientific enterprise and to the overall NIH mission of utilizing science in the pursuit of fundamental knowledge about the nature and behavior of living systems and the application of that knowledge to extend healthy life and reduce the burdens of illness and disability.}, } @article {pmid18716330, year = {2008}, author = {Ingvarsson, PK}, title = {Multilocus patterns of nucleotide polymorphism and the demographic history of Populus tremula.}, journal = {Genetics}, volume = {180}, number = {1}, pages = {329-340}, pmid = {18716330}, issn = {0016-6731}, mesh = {Bayes Theorem ; Computational Biology ; Gene Deletion ; Gene Frequency ; Genes, Plant ; Genetics, Population ; Linkage Disequilibrium ; Models, Genetic ; Models, Statistical ; Mutation ; Plant Proteins/metabolism ; *Polymorphism, Genetic ; Populus/*genetics ; Software ; }, abstract = {I have studied nucleotide polymorphism and linkage disequilibrium using multilocus data from 77 fragments, with an average length of fragments of 550 bp, in the deciduous tree Populus tremula (Salicaceae). The frequency spectrum across loci showed a modest excess of mutations segregating at low frequency and a marked excess of high-frequency derived mutations at silent sites, relative to neutral expectations. These excesses were also seen at replacement sites, but were not so pronounced for high-frequency derived mutations. There was a marked excess of low-frequency mutations at replacement sites, likely indicating deleterious amino acid-changing mutations that segregate at low frequencies in P. tremula. I used approximate Bayesian computation (ABC) to evaluate a number of different demographic scenarios and to estimate parameters for the best-fitting model. The data were found to be consistent with a historical reduction in the effective population size of P. tremula through a bottleneck. The timing inferred for this bottleneck is largely consistent with geological data and with data from several other long-lived plant species. The results show that P. tremula harbors substantial levels of nucleotide polymorphism with the posterior mode of the scaled mutation rate, theta = 0.0177 across loci. The ABC analyses also provided an estimate of the scaled recombination rate that indicates that recombination rates in P. tremula are likely to be 2-10 times higher than the mutation rate. This study reinforces the notion that linkage disequilibrium is low and decays to negligible levels within a few hundred base pairs in P. tremula.}, } @article {pmid18715402, year = {2008}, author = {Grosbois, V and Gimenez, O and Gaillard, JM and Pradel, R and Barbraud, C and Clobert, J and Møller, AP and Weimerskirch, H}, title = {Assessing the impact of climate variation on survival in vertebrate populations.}, journal = {Biological reviews of the Cambridge Philosophical Society}, volume = {83}, number = {3}, pages = {357-399}, doi = {10.1111/j.1469-185X.2008.00047.x}, pmid = {18715402}, issn = {1464-7931}, mesh = {Adaptation, Physiological ; Animals ; Birds/*physiology ; *Climate ; *Data Interpretation, Statistical ; Demography ; Environment ; Greenhouse Effect ; Population Density ; Population Dynamics ; Research Design ; *Survival ; }, abstract = {The impact of the ongoing rapid climate change on natural systems is a major issue for human societies. An important challenge for ecologists is to identify the climatic factors that drive temporal variation in demographic parameters, and, ultimately, the dynamics of natural populations. The analysis of long-term monitoring data at the individual scale is often the only available approach to estimate reliably demographic parameters of vertebrate populations. We review statistical procedures used in these analyses to study links between climatic factors and survival variation in vertebrate populations. We evaluated the efficiency of various statistical procedures from an analysis of survival in a population of white stork, Ciconia ciconia, a simulation study and a critical review of 78 papers published in the ecological literature. We identified six potential methodological problems: (i) the use of statistical models that are not well-suited to the analysis of long-term monitoring data collected at the individual scale; (ii) low ratios of number of statistical units to number of candidate climatic covariates; (iii) collinearity among candidate climatic covariates; (iv) the use of statistics, to assess statistical support for climatic covariates effects, that deal poorly with unexplained variation in survival; (v) spurious detection of effects due to the co-occurrence of trends in survival and the climatic covariate time series; and (vi) assessment of the magnitude of climatic effects on survival using measures that cannot be compared across case studies. The critical review of the ecological literature revealed that five of these six methodological problems were often poorly tackled. As a consequence we concluded that many of these studies generated hypotheses but only few provided solid evidence for impacts of climatic factors on survival or reliable measures of the magnitude of such impacts. We provide practical advice to solve efficiently most of the methodological problems identified. The only frequent issue that still lacks a straightforward solution was the low ratio of the number of statistical units to the number of candidate climatic covariates. In the perspective of increasing this ratio and therefore of producing more robust analyses of the links between climate and demography, we suggest leads to improve the procedures for designing field protocols and selecting a set of candidate climatic covariates. Finally, we present recent statistical methods with potential interest for assessing the impact of climatic factors on demographic parameters.}, } @article {pmid18714883, year = {2008}, author = {Sucaet, Y and Van Hemert, J and Tucker, B and Bartholomay, L}, title = {A web-based relational database for monitoring and analyzing mosquito population dynamics.}, journal = {Journal of medical entomology}, volume = {45}, number = {4}, pages = {775-784}, doi = {10.1603/0022-2585(2008)45[775:AWRDFM]2.0.CO;2}, pmid = {18714883}, issn = {0022-2585}, mesh = {Animals ; Computational Biology ; *Culicidae ; Database Management Systems ; Databases, Factual ; Databases, Genetic ; Ecosystem ; Information Systems ; Population Control ; *Population Dynamics ; }, abstract = {Mosquito population dynamics have been monitored on an annual basis in the state of Iowa since 1969. The primary goal of this project was to integrate light trap data from these efforts into a centralized back-end database and interactive website that is available through the internet at http://iowa-mosquito.ent.iastate.edu. For comparative purposes, all data were categorized according to the week of the year and normalized according to the number of traps running. Users can readily view current, weekly mosquito abundance compared with data from previous years. Additional interactive capabilities facilitate analyses of the data based on mosquito species, distribution, or a time frame of interest. All data can be viewed in graphical and tabular format and can be downloaded to a comma separated value (CSV) file for import into a spreadsheet or more specialized statistical software package. Having this long-term dataset in a centralized database/website is useful for informing mosquito and mosquito-borne disease control and for exploring the ecology of the species represented therein. In addition to mosquito population dynamics, this database is available as a standardized platform that could be modified and applied to a multitude of projects that involve repeated collection of observational data. The development and implementation of this tool provides capacity for the user to mine data from standard spreadsheets into a relational database and then view and query the data in an interactive website.}, } @article {pmid18712611, year = {2009}, author = {Wang, F and Xu, YJ}, title = {Hurricane Katrina-induced forest damage in relation to ecological factors at landscape scale.}, journal = {Environmental monitoring and assessment}, volume = {156}, number = {1-4}, pages = {491-507}, pmid = {18712611}, issn = {1573-2959}, mesh = {*Cyclonic Storms ; Ecosystem ; Environmental Monitoring/*methods ; Geographic Information Systems ; Geography ; *Trees ; United States ; }, abstract = {Forest stand stability to strong winds such as hurricanes has been found to be associated with a number of forest, soil and topography factors. In this study, through applying geographic information system (GIS) and logit regression, we assessed effects of forest characteristics and site conditions on pattern, severity and probability of Hurricane Katrina disturbance to forests in the Lower Pearl River Valley, USA. The factors included forest type, forest coverage, stand density, soil great group, elevation, slope, aspect, and stream buffer zone. Results showed that Hurricane Katrina damaged 60% of the total forested land in the region. The distribution and intensity of the hurricane disturbance varied across the landscape, with the bottomland hardwood forests on river floodplains most severely affected. All these factors had a variety of effects on vulnerability of the forests to the hurricane disturbance and thereby spatial patterns of the disturbance. Soil groups and stand factors including forest types, forest coverage and stand density contributed to 85% of accuracy in modeling the probability of the hurricane disturbance to forests in this region. Besides assessment of Katrina's damage, this study elucidates the great usefulness of remote sensing and GIS techniques combined with statistics modeling in assessment of large-scale risks of hurricane damage to coastal forests.}, } @article {pmid18709410, year = {2008}, author = {Snelder, TH and Pella, H and Wasson, JG and Lamouroux, N}, title = {Definition procedures have little effect on performance of environmental classifications of streams and rivers.}, journal = {Environmental management}, volume = {42}, number = {5}, pages = {771-788}, pmid = {18709410}, issn = {0364-152X}, mesh = {Animals ; Classification/*methods ; Ecology/*methods ; *Ecosystem ; Environmental Monitoring/*methods ; France ; Geographic Information Systems ; Invertebrates ; Rivers/*chemistry ; Water Movements ; }, abstract = {Mapped environmental classifications are defined using various procedures, but there has been little evaluation of the differences in their ability to discriminate variation in independent ecological characteristics. We tested the performance of environmental classifications of the streams and rivers of France that had been defined from the same environmental data using geographic regionalization and numerical classification of individual river valley segments. Test data comprised invertebrate assemblages, water chemistry, and hydrological indexes obtained from sites throughout France. Classification performance was measured by analysis of similarity (ANOSIM). Geometric regions defined by a regular grid and without regard to environmental variables and a posteriori classifications based on clustering the test datasets defined lower and upper bounds of performance for a given number of classes. Differences in classification performances were generally small. The ANOSIM statistics for the a posteriori classifications were around twice that of all environmental classifications, including geometrically defined regions. The hydro-ecoregions performed slightly better for the invertebrate data and the network classification performed slightly better for the chemistry and hydrological data. Our results indicate that environmental classifications that are defined using different procedures can be comparable in terms of their ability to discriminate variation of ecological characteristics and that alleged differences in performance arising from different classification procedures can be small relative to unexplained variation. We conclude that definition procedures might have little effect on the performance of large-scale environmental classifications and decisions over which procedures to use should be based primarily on pragmatic considerations.}, } @article {pmid18709143, year = {2008}, author = {Abellan, JJ and Richardson, S and Best, N}, title = {Use of space-time models to investigate the stability of patterns of disease.}, journal = {Environmental health perspectives}, volume = {116}, number = {8}, pages = {1111-1119}, pmid = {18709143}, issn = {0091-6765}, support = {//Department of Health/United Kingdom ; }, mesh = {Bayes Theorem ; Computer Simulation ; Congenital Abnormalities/*epidemiology ; England/epidemiology ; Geographic Information Systems ; Humans ; Risk Assessment/methods ; Socioeconomic Factors ; *Space-Time Clustering ; }, abstract = {BACKGROUND: The use of Bayesian hierarchical spatial models has become widespread in disease mapping and ecologic studies of health-environment associations. In this type of study, the data are typically aggregated over an extensive time period, thus neglecting the time dimension. The output of purely spatial disease mapping studies is therefore the average spatial pattern of risk over the period analyzed, but the results do not inform about, for example, whether a high average risk was sustained over time or changed over time.

OBJECTIVE: We investigated how including the time dimension in disease-mapping models strengthens the epidemiologic interpretation of the overall pattern of risk.

METHODS: We discuss a class of Bayesian hierarchical models that simultaneously characterize and estimate the stable spatial and temporal patterns as well as departures from these stable components. We show how useful rules for classifying areas as stable can be constructed based on the posterior distribution of the space-time interactions. We carry out a simulation study to investigate the sensitivity and specificity of the decision rules we propose, and we illustrate our approach in a case study of congenital anomalies in England.

RESULTS: Our results confirm that extending hierarchical disease-mapping models to models that simultaneously consider space and time leads to a number of benefits in terms of interpretation and potential for detection of localized excesses.}, } @article {pmid18704085, year = {2008}, author = {King, AA and Ionides, EL and Pascual, M and Bouma, MJ}, title = {Inapparent infections and cholera dynamics.}, journal = {Nature}, volume = {454}, number = {7206}, pages = {877-880}, doi = {10.1038/nature07084}, pmid = {18704085}, issn = {1476-4687}, mesh = {Carrier State/diagnosis/epidemiology/immunology/*transmission ; Cholera/*diagnosis/*epidemiology/immunology/transmission ; Computer Simulation ; Databases, Factual ; Humans ; Immunity, Innate ; India/epidemiology ; *Models, Biological ; Seasons ; Time Factors ; Vibrio cholerae/immunology ; }, abstract = {In many infectious diseases, an unknown fraction of infections produce symptoms mild enough to go unrecorded, a fact that can seriously compromise the interpretation of epidemiological records. This is true for cholera, a pandemic bacterial disease, where estimates of the ratio of asymptomatic to symptomatic infections have ranged from 3 to 100 (refs 1-5). In the absence of direct evidence, understanding of fundamental aspects of cholera transmission, immunology and control has been based on assumptions about this ratio and about the immunological consequences of inapparent infections. Here we show that a model incorporating high asymptomatic ratio and rapidly waning immunity, with infection both from human and environmental sources, explains 50 yr of mortality data from 26 districts of Bengal, the pathogen's endemic home. We find that the asymptomatic ratio in cholera is far higher than had been previously supposed and that the immunity derived from mild infections wanes much more rapidly than earlier analyses have indicated. We find, too, that the environmental reservoir (free-living pathogen) is directly responsible for relatively few infections but that it may be critical to the disease's endemicity. Our results demonstrate that inapparent infections can hold the key to interpreting the patterns of disease outbreaks. New statistical methods, which allow rigorous maximum likelihood inference based on dynamical models incorporating multiple sources and outcomes of infection, seasonality, process noise, hidden variables and measurement error, make it possible to test more precise hypotheses and obtain unexpected results. Our experience suggests that the confrontation of time-series data with mechanistic models is likely to revise our understanding of the ecology of many infectious diseases.}, } @article {pmid18703094, year = {2008}, author = {Morales, SE and Cosart, T and Johnson, JV and Holben, WE}, title = {Supplemental programs for enhanced recovery of data from the DOTUR application.}, journal = {Journal of microbiological methods}, volume = {75}, number = {3}, pages = {572-575}, doi = {10.1016/j.mimet.2008.07.017}, pmid = {18703094}, issn = {0167-7012}, mesh = {*Databases, Nucleic Acid ; *Software ; }, abstract = {In order to retrieve phylogenetic information from distance matrices generated from large-scale clone libraries, and to explore OTU distribution among them, we have developed downstream applications for use with the already available DOTUR program. These programs enhance and ease data extraction, providing phylogeny to the already generated distance data.}, } @article {pmid18696029, year = {2008}, author = {Townsend, JP and López-Giráldez, F and Friedman, R}, title = {The phylogenetic informativeness of nucleotide and amino acid sequences for reconstructing the vertebrate tree.}, journal = {Journal of molecular evolution}, volume = {67}, number = {5}, pages = {437-447}, pmid = {18696029}, issn = {0022-2844}, mesh = {Algorithms ; Animals ; Calmodulin/genetics ; Cytochromes b/genetics ; *Databases, Nucleic Acid ; *Databases, Protein ; *Evolution, Molecular ; Genetic Variation ; *Phylogeny ; Proto-Oncogene Proteins c-myc/genetics ; Serum Albumin/genetics ; Vertebrates/classification/*genetics ; }, abstract = {To aid in future efforts to accurately reconstruct the vertebrate tree, a quantitative measure of phylogenetic informativeness was applied to nucleotide and amino acid sequences for a set of 11 genes. We identified orthologues and assembled published fossil-calibrated divergence times between taxa that had been sequenced for each gene. Rates of molecular evolution for each site were estimated to characterize the molecular evolutionary pattern of genes and to calculate the phylogenetic informativeness. The fast-evolving gene albumin yielded the highest informativeness over the period from 60 million years ago to 500 million years ago. In contrast, calmodulin yielded the lowest informativeness, presumably because functional constraint minimized substitutions in the amino acid sequence. The gene c-myc showed an intermediate level of informativeness. The nucleotide sequence of cytochrome b showed extremely high utility for recent epochs, but low utility for times before 100 million years ago. We ranked nine other genes for their utility during the epochs of the divergence of the muroid rodents, early placental mammals, early vertebrates, and early metazoa, yielding results consistent with, but more precise than, previous studies. Interestingly, DNA sequence always exceeded amino acid sequence in informativeness over all time scales, yet support values were at best moderately higher. For epochs not subject to strong phylogenetic conflict due to convergence, we advocate gleaning the additional power of the threefold increase in number of characters that is present for DNA sequences over resorting to the less noisy but less informative amino acid sequences.}, } @article {pmid18694131, year = {2007}, author = {Lin, CP and Gennari, JH}, title = {Designing CPOE systems using an ecological approach.}, journal = {AMIA ... Annual Symposium proceedings. AMIA Symposium}, volume = {}, number = {}, pages = {1033}, pmid = {18694131}, issn = {1942-597X}, mesh = {Cognition ; Decision Support Systems, Clinical ; Humans ; *Medical Order Entry Systems ; *Software ; Systems Analysis ; Task Performance and Analysis ; }, abstract = {Medical ordering is a complex socio-technical system that contains many collaborative actors. We propose using the Cognitive Work Analysis framework to identify work environment constraints and develop software requirements for order entry systems. Our goal is to understand how to design ordering systems that support workers and help them make decisions and adapt to new situations safely and effectively.}, } @article {pmid18693864, year = {2007}, author = {Kastner, M and Straus, S and Goldsmith, CH}, title = {Estimating the Horizon of articles to decide when to stop searching in systematic reviews: an example using a systematic review of RCTs evaluating osteoporosis clinical decision support tools.}, journal = {AMIA ... Annual Symposium proceedings. AMIA Symposium}, volume = {2007}, number = {}, pages = {389-393}, pmid = {18693864}, issn = {1942-597X}, mesh = {Humans ; *Databases, Bibliographic ; *Decision Support Techniques ; *Information Storage and Retrieval/methods ; MEDLINE ; Osteoporosis/therapy ; Randomized Controlled Trials as Topic ; Retrospective Studies ; *Systematic Reviews as Topic ; }, abstract = {Researchers conducting systematic reviews need to search multiple bibliographic databases such as MEDLINE and EMBASE. However, researchers have no rational search stopping rule when looking for potentially-relevant articles. We empirically tested a stopping rule based on the concept of capture-mark-recapture (CMR), which was first pioneered in ecology. The principles of CMR can be adapted to systematic reviews and meta-analyses to estimate the Horizon of articles in the literature with its confidence interval. We retrospectively tested this Horizon Estimation using a systematic review of randomized controlled trials (RCTs) that evaluated clinical decision support tools for osteoporosis disease management. The Horizon Estimation was calculated based on 4 bibliographic databases that were included as the main data sources for the review in the following order: MEDLINE, EMBASE, CINAHL, and EBM Reviews. The systematic review captured 68% of known articles from the 4 data sources, which represented 592 articles that were estimated as missing from the Horizon.}, } @article {pmid18686255, year = {2007}, author = {Gazzinelli, A and Kloss, H}, title = {The use of spatial tools in the study of Schistosoma mansoni and its intermediate host snails in Brazil: a brief review.}, journal = {Geospatial health}, volume = {2}, number = {1}, pages = {51-58}, doi = {10.4081/gh.2007.254}, pmid = {18686255}, issn = {1970-7096}, mesh = {Animals ; Biomphalaria ; Brazil/epidemiology ; *Geographic Information Systems ; Maps as Topic ; *Population Surveillance ; *Schistosoma mansoni ; Schistosomiasis mansoni/*epidemiology/prevention & control/transmission ; }, abstract = {The rapidly increasing number of spatial studies and the complexity of schistosomiasis transmission dynamics in Brazil indicate that surveillance and control programmes can benefit from the spatial approach, not only in areas susceptible to the introduction and establishment of new transmission foci but also in areas experiencing declines in schistosomiasis transmission. Several additional areas amenable to, or requiring, spatial research are identified. This paper reviews spatial studies of schistosomiasis in Brazil with a focus on the application of spatial tools in epidemiological, disease ecological, control and several additional areas in schistosomiasis research.}, } @article {pmid18686242, year = {2007}, author = {Rizzoli, A and Neteler, M and Rosà, R and Versini, W and Cristofolini, A and Bregoli, M and Buckley, A and Gould, EA}, title = {Early detection of tick-borne encephalitis virus spatial distribution and activity in the province of Trento, northern Italy.}, journal = {Geospatial health}, volume = {1}, number = {2}, pages = {169-176}, doi = {10.4081/gh.2007.265}, pmid = {18686242}, issn = {1970-7096}, mesh = {Animals ; Animals, Domestic ; Antibodies/analysis ; Climate ; Encephalitis Viruses, Tick-Borne/immunology/*isolation & purification ; Encephalitis, Tick-Borne/*epidemiology/immunology/parasitology ; Geographic Information Systems ; Goats/immunology ; Humans ; Italy/epidemiology ; Risk Assessment ; Seasons ; Seroepidemiologic Studies ; }, abstract = {New human cases of tick-borne encephalitis (TBE) have recently been recorded outside the recognised foci of this disease, i.e. in the province of Trento in northern Italy. In order to predict the highest risk areas for increased TBE virus activity, we have combined cross-sectional serological data, obtained from 459 domestic goats, with analysis of the autumnal cooling rate based on Moderate Resolution Imaging Spectroradiometer (MODIS) land surface temperature (LST) data. A significant relationship between finding antibodies against the virus in serum (seroprevalence) in goats and the autumnal cooling rate was detected, indicating that the transmission intensity of the virus does not only vary spatially, but also in relation to climatic factors. Virus seroprevalence in goats was correlated with the occurrence of TBE in humans and also with the average number of forestry workers' tick bites, demonstrating that serological screening of domestic animals, combined with an analysis of the autumnal cooling rate, can be used as early-warning predictors of TBE risk in humans.}, } @article {pmid18686234, year = {2006}, author = {Yang, GJ and Vounatsou, P and Tanner, M and Zhou, XN and Utzinger, J}, title = {Remote sensing for predicting potential habitats of Oncomelania hupensis in Hongze, Baima and Gaoyou lakes in Jiangsu province, China.}, journal = {Geospatial health}, volume = {1}, number = {1}, pages = {85-92}, doi = {10.4081/gh.2006.283}, pmid = {18686234}, issn = {1970-7096}, mesh = {Animals ; China/epidemiology ; Disease Outbreaks ; *Ecosystem ; Environmental Monitoring ; Epidemiological Monitoring ; Fresh Water/*parasitology ; *Geographic Information Systems ; Maps as Topic ; Risk Assessment ; Schistosoma japonicum/parasitology ; Schistosomiasis japonica/epidemiology/parasitology ; Shellfish/*parasitology ; Snails/*parasitology ; Spacecraft ; }, abstract = {Political and health sector reforms, along with demographic, environmental and socio-economic transformations in the face of global warming, could cause the re-emergence of schistosomiasis in areas where transmission has been successfully interrupted and its emergence in previously non-endemic areas in China. In the present study, we used geographic information systems and remote sensing techniques to predict potential habitats of Oncomelania hupensis, the intermediate host snail of Schistosoma japonicum. Focussing on the Hongze, Baima and Gaoyou lakes in Jiangsu province in eastern China, we developed a model using the normalized difference vegetation index, a tasseled-cap transformed wetness index, and flooding areas to predict snail habitats at a small scale. Data were extracted from two Landsat images, one taken during a typical dry year and the other obtained three years later during a flooding event. An area of approximately 163.6 km2 was predicted as potential O. hupensis habitats around the three lakes, which accounts for 4.3% of the estimated snail habitats in China. In turn, these predicted snail habitats are risk areas for transmission of schistosomiasis, and hence illustrate the scale of the possible impact of climate change and other ecological transformations. The generated risk map can be used by health policy makers to guide mitigation policies targetting the possible spread of O. hupensis, and with the aim of containing the transmission of S. japonicum.}, } @article {pmid18686231, year = {2006}, author = {Rinaldi, L and Musella, V and Biggeri, A and Cringoli, G}, title = {New insights into the application of geographical information systems and remote sensing in veterinary parasitology.}, journal = {Geospatial health}, volume = {1}, number = {1}, pages = {33-47}, doi = {10.4081/gh.2006.279}, pmid = {18686231}, issn = {1970-7096}, mesh = {Animals ; Ecology ; Epidemiologic Studies ; *Geographic Information Systems ; Parasitic Diseases, Animal/*epidemiology ; Population Surveillance ; Veterinary Medicine/*methods ; }, abstract = {Over the past 10-15 years, significant advances have been made in the development and application of geographical information systems (GIS) and remote sensing (RS). In veterinary sciences, particularly in veterinary parasitology, GIS and RS offer powerful means for disease mapping, ecological analysis and epidemiological surveillance and have become indispensable tools for processing, analysing and visualising spatial data. They can also significantly assist with the assessment of the distribution of health-relevant environmental factors via interpolation and modelling. In this review, we first summarize general aspects of GIS and RS, and emphasize the most important applications of these tools in veterinary parasitology, including recent advances in territorial sampling. Disease mapping, spatial statistics, including Bayesian inference, ecological analyses and epidemiological surveillance are summarized in the next section and illustrated with a set of figures. Finally, a set of conclusions is put forward.}, } @article {pmid18686193, year = {2008}, author = {Lemmon, AR and Lemmon, EM}, title = {A likelihood framework for estimating phylogeographic history on a continuous landscape.}, journal = {Systematic biology}, volume = {57}, number = {4}, pages = {544-561}, doi = {10.1080/10635150802304761}, pmid = {18686193}, issn = {1076-836X}, mesh = {Animals ; Anura/classification/genetics ; Classification/*methods ; DNA, Mitochondrial/genetics ; Data Interpretation, Statistical ; Emigration and Immigration ; Geography ; Likelihood Functions ; Models, Genetic ; *Phylogeny ; }, abstract = {Due to lack of an adequate statistical framework, biologists studying phylogeography are abandoning traditional methods of estimating phylogeographic history in favor of statistical methods designed to test a priori hypotheses. These new methods may, however, have limited descriptive utility. Here, we develop a new statistical framework that can be used to both test a priori hypotheses and estimate phylogeographic history of a gene (and the statistical confidence in that history) in the absence of such hypotheses. The statistical approach concentrates on estimation of geographic locations of the ancestors of a set of sampled organisms. Now we use (2) to derive the likelihood of the ancestral geographic coordinates and the value of the scaled dispersal parameter, given the observed geographic coordinates (assuming known topology and branch lengths). Using a maximum likelihood approach, which is implemented in the new program PhyloMapper, we apply this statistical framework to a 246-taxon mitochondrial genealogy of North American chorus frogs, focusing in detail on one of these species. We demonstrate three lines of evidence for recent northward expansion of the mitochondrion of the coastal clade of Pseudacris feriarum: higher per-generation dispersal distance in the recently colonized region, a noncentral ancestral location, and directional migration. After illustrating one method of accommodating phylogenetic uncertainty, we conclude by discussing how extensions of this framework could function to incorporate a priori ecological and geological information into phylogeographic analyses.}, } @article {pmid18679749, year = {2008}, author = {Norman, SA}, title = {Spatial epidemiology and GIS in marine mammal conservation medicine and disease research.}, journal = {EcoHealth}, volume = {5}, number = {3}, pages = {257-267}, pmid = {18679749}, issn = {1612-9210}, mesh = {Animal Diseases/*epidemiology ; Animals ; Cluster Analysis ; Conservation of Natural Resources ; Environmental Health ; Environmental Monitoring/*methods ; Epidemiological Monitoring ; *Geographic Information Systems ; Humans ; *Mammals ; Oceans and Seas ; Risk Assessment ; }, abstract = {The use of spatial epidemiology and geographical information systems (GIS) facilitates the incorporation of spatial relationships into epidemiological investigations of marine mammal diseases and conservation medicine. Spatial epidemiology is the study of the spatial variation in disease risk or incidence and explicitly addresses spatial structures and functions that factor into disease. The GIS consists of input, management, analysis, and presentation of spatial disease data and can act as an integrative tool so that a range of varied data sources can be combined to describe different environmental aspects of wild animals and their diseases. The use of modern spatial analyses and GIS is becoming well developed in the field of marine mammal ecology and biology, but has just recently started to gain more use in disease research. The use of GIS methodology and spatial analysis in nondisease marine mammal studies is briefly discussed, while examples of the specific uses of these tools in mapping, surveillance and monitoring, disease cluster detection, identification of environmental predictors of disease in wildlife populations, risk assessment, and modeling of diseases, is presented. Marine mammal disease investigations present challenges, such as less consistent access to animals for sampling, fewer baseline data on diseases in wild populations, and less robust epidemiologic study designs, but several recommendations for future research are suggested. Since location is an integral part of investigating disease, spatial epidemiology and GIS should be incorporated as a data management and analysis tool in the study of marine mammal diseases and conservation medicine.}, } @article {pmid18678590, year = {2008}, author = {Webb, CO and Ackerly, DD and Kembel, SW}, title = {Phylocom: software for the analysis of phylogenetic community structure and trait evolution.}, journal = {Bioinformatics (Oxford, England)}, volume = {24}, number = {18}, pages = {2098-2100}, doi = {10.1093/bioinformatics/btn358}, pmid = {18678590}, issn = {1367-4811}, mesh = {*Algorithms ; Computational Biology/*methods ; *Evolution, Molecular ; Models, Genetic ; *Phylogeny ; *Software ; }, abstract = {MOTIVATION: The increasing availability of phylogenetic and trait data for communities of co-occurring species has created a need for software that integrates ecological and evolutionary analyses. Capabilities: Phylocom calculates numerous metrics of phylogenetic community structure and trait similarity within communities. Hypothesis testing is implemented using several null models. Within the same framework, it measures phylogenetic signal and correlated evolution for species traits. A range of utility functions allow community and phylogenetic data manipulation, tree and trait generation, and integration into scientific workflows.

AVAILABILITY: Open source at: http://phylodiversity.net/phylocom/.}, } @article {pmid18678479, year = {2009}, author = {Wu, JY and Tsai, M}, title = {Feasibility study of a soil-based rubberized CLSM.}, journal = {Waste management (New York, N.Y.)}, volume = {29}, number = {2}, pages = {636-642}, doi = {10.1016/j.wasman.2008.06.017}, pmid = {18678479}, issn = {0956-053X}, mesh = {Conservation of Natural Resources ; *Construction Materials ; *Materials Testing ; *Rubber ; *Soil ; }, abstract = {The development of beneficial uses of recycled scrap tires is always in great demand around the world. The disposal of on-site surplus excavated soil and the production of standard engineering aggregates have also been facing increasing environmental and ecological challenges in congested islands, such as Taiwan. This paper presents an experimental study using recycled crumb rubber and native silty sand to produce a lightweight, soil-based, rubberized controlled low strength material (CLSM) for a bridge approach repair. To assess the technical feasibility of this material, the effects of weight ratios of cement-to-water (C/W) and water-to-solid (W/S), and of rubber content on the engineering properties for different mixtures were investigated. The presented test results include flowability, unit weight, strength, settlement potential, and bearing capacity. Based on the findings, we conclude that a soil-based rubberized CLSM with 40% sand by weight and an optimal design ratio of 0.7 for C/W and 0.35 for W/S can be used for the proposed bridge approach repair. Such a mixture has demonstrated acceptable flowability, strength, and bearing capacity. Its lower unit weight, negligible compressibility, and hydrocollapse potential also help ensure that detrimental settlement is unlikely to occur. The results illustrate a novel scheme of CLSM production, and suggest a beneficial alternative for the reduction of scrap tires as well as conservation of resources and environment.}, } @article {pmid18667341, year = {2009}, author = {Calvete, C and Estrada, R and Miranda, MA and Borrás, D and Calvo, JH and Lucientes, J}, title = {Ecological correlates of bluetongue virus in Spain: predicted spatial occurrence and its relationship with the observed abundance of the potential Culicoides spp. vector.}, journal = {Veterinary journal (London, England : 1997)}, volume = {182}, number = {2}, pages = {235-243}, doi = {10.1016/j.tvjl.2008.06.010}, pmid = {18667341}, issn = {1532-2971}, mesh = {Animals ; Bluetongue/epidemiology/transmission/*virology ; Bluetongue virus/*growth & development ; Ceratopogonidae/*virology ; Disease Outbreaks/*veterinary ; Ecosystem ; Geographic Information Systems ; Insect Vectors/*virology ; Models, Biological ; Seasons ; Spain/epidemiology ; }, abstract = {Using data from bluetongue (BT) outbreaks caused by viral serotype 4 (BTV-4) in Spain during 2004-2005, a predictive model for BTV-4 occurrence in peninsular Spain was developed. An autologistic regression model was employed to estimate the relationships between BTV-4 presence and bioclimatic-related and host-availability-related variables. In addition, the observed abundances of the main potential Culicoides vectors during 2004-2005, namely Culicoides imicola, Culicoides obsoletus group, and species of the Culicoides pulicaris group, were compared between BTV-4 presence/absence areas predicted by the model. BTV-4 occurrence was mainly explained by bioclimatic variables, although a consideration of host-availability variables led to improved fit of the model. The area of BTV-4 presence predicted by the model largely resembled the core distribution area of C. imicola, and this species was the most abundant Culicoides spp. in predicted BTV-4 presence areas. The results suggest that the spatial expansion of BTV-4 took place only as far as those areas in which C. imicola populations efficiently transmitted the virus.}, } @article {pmid18665273, year = {2008}, author = {Fazekas, AJ and Burgess, KS and Kesanakurti, PR and Graham, SW and Newmaster, SG and Husband, BC and Percy, DM and Hajibabaei, M and Barrett, SC}, title = {Multiple multilocus DNA barcodes from the plastid genome discriminate plant species equally well.}, journal = {PloS one}, volume = {3}, number = {7}, pages = {e2802}, pmid = {18665273}, issn = {1932-6203}, mesh = {Computational Biology/methods ; DNA, Chloroplast/metabolism ; DNA, Mitochondrial/genetics ; DNA, Plant/chemistry ; DNA, Ribosomal/chemistry ; Genes, Plant ; Genetic Markers ; Genetic Variation ; *Genome, Plant ; *Models, Genetic ; Plants/metabolism ; Plastids/*chemistry/metabolism ; Reproducibility of Results ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {A universal barcode system for land plants would be a valuable resource, with potential utility in fields as diverse as ecology, floristics, law enforcement and industry. However, the application of plant barcoding has been constrained by a lack of consensus regarding the most variable and technically practical DNA region(s). We compared eight candidate plant barcoding regions from the plastome and one from the mitochondrial genome for how well they discriminated the monophyly of 92 species in 32 diverse genera of land plants (N = 251 samples). The plastid markers comprise portions of five coding (rpoB, rpoC1, rbcL, matK and 23S rDNA) and three non-coding (trnH-psbA, atpF-atpH, and psbK-psbI) loci. Our survey included several taxonomically complex groups, and in all cases we examined multiple populations and species. The regions differed in their ability to discriminate species, and in ease of retrieval, in terms of amplification and sequencing success. Single locus resolution ranged from 7% (23S rDNA) to 59% (trnH-psbA) of species with well-supported monophyly. Sequence recovery rates were related primarily to amplification success (85-100% for plastid loci), with matK requiring the greatest effort to achieve reasonable recovery (88% using 10 primer pairs). Several loci (matK, psbK-psbI, trnH-psbA) were problematic for generating fully bidirectional sequences. Setting aside technical issues related to amplification and sequencing, combining the more variable plastid markers provided clear benefits for resolving species, although with diminishing returns, as all combinations assessed using four to seven regions had only marginally different success rates (69-71%; values that were approached by several two- and three-region combinations). This performance plateau may indicate fundamental upper limits on the precision of species discrimination that is possible with DNA barcoding systems that include moderate numbers of plastid markers. Resolution to the contentious debate on plant barcoding should therefore involve increased attention to practical issues related to the ease of sequence recovery, global alignability, and marker redundancy in multilocus plant DNA barcoding systems.}, } @article {pmid18660959, year = {2008}, author = {Araújo, MS and Pinheiro, A and Reis, SF}, title = {Gluttonous predators: how to estimate prey size when there are too many prey.}, journal = {Brazilian journal of biology = Revista brasleira de biologia}, volume = {68}, number = {2}, pages = {315-320}, doi = {10.1590/s1519-69842008000200012}, pmid = {18660959}, issn = {1519-6984}, mesh = {Algorithms ; Animals ; Anura/*physiology ; *Body Size ; Data Interpretation, Statistical ; Feeding Behavior/*physiology ; *Food Chain ; Gastrointestinal Contents ; Predatory Behavior/*physiology ; }, abstract = {Prey size is an important factor in food consumption. In studies of feeding ecology, prey items are usually measured individually using calipers or ocular micrometers. Among amphibians and reptiles, there are species that feed on large numbers of small prey items (e.g. ants, termites). This high intake makes it difficult to estimate prey size consumed by these animals. We addressed this problem by developing and evaluating a procedure for subsampling the stomach contents of such predators in order to estimate prey size. Specifically, we developed a protocol based on a bootstrap procedure to obtain a subsample with a precision error of at the most 5%, with a confidence level of at least 95%. This guideline should reduce the sampling effort and facilitate future studies on the feeding habits of amphibians and reptiles, and also provide a means of obtaining precise estimates of prey size.}, } @article {pmid18654838, year = {2009}, author = {Pei, DS and Sun, YH and Zhu, ZY}, title = {Identification of a novel gene K23 over-expressed in fish cross-subfamily cloned embryos.}, journal = {Molecular biology reports}, volume = {36}, number = {6}, pages = {1375-1380}, pmid = {18654838}, issn = {1573-4978}, mesh = {Animals ; Base Sequence ; Clone Cells ; Computational Biology ; Embryo, Nonmammalian ; Female ; Gene Components ; *Gene Expression Regulation, Developmental ; *Genes, Developmental ; Molecular Sequence Data ; Ovum ; Phosphoproteins/*genetics/metabolism ; Phosphorylation ; Polymerase Chain Reaction ; RNA, Messenger/analysis ; Zebrafish/*genetics ; Zebrafish Proteins/*genetics/metabolism ; }, abstract = {A novel gene-K23, differentially expressed in cross-subfamily cloned embryos, was isolated by RACE-PCR technique. It had 2580 base pairs (bp) in length, with a 1,425 bp open reading frame (ORF) encoding a putative protein of 474 amino acids (aa). Bioinformatic analysis indicated that K23 had 22 phosphorylation sites, but it had no signal peptides. Developmental expression analysis in zebrafish showed that K23 transcripts were maternally expressed in ovum and the amount of K23 transcripts increased gradually from zygote to pharyngula period. Subcellular localization analysis revealed that K23 protein was homogeneously distributed both in nuclei and cytoplasm. Taken together, our findings indicate that K23 gene is a novel gene differentially expressed in fish cross-subfamily cloned embryos.}, } @article {pmid18649514, year = {2008}, author = {Liu, JC and Yan, Y and Liu, F and Ding, D and Zhao, M}, title = {[Risk assessment and safety evaluation using system normative indexes integration method for non-point source pollution on watershed scale].}, journal = {Huan jing ke xue= Huanjing kexue}, volume = {29}, number = {3}, pages = {599-606}, pmid = {18649514}, issn = {0250-3301}, mesh = {China ; Conservation of Natural Resources/economics/methods ; Geographic Information Systems ; Geologic Sediments/*analysis ; *Models, Theoretical ; Risk Assessment ; Water Pollution/economics/*prevention & control ; }, abstract = {Decision-makers take non-point source pollution under control as well as possible results from enough information of risk trend of nonpoint source pollution on watershed scale. System normative indexes integration evaluation method about system risk trend was developed when focusing on that the probability values of some elements attributing to some trend of the system were more than one, and that the system evaluation needed a formula from the system structure. On the basis of analysis on aspects and characteristics of the system risk normalization, a new valuation method, the relationship between the normalization values of the system and the factors was established. The Lugu Lake Watershed in Southwest China was selected as study area to assess the risk of non-point source loss to surface water using this method. The results indicate that 1) the wholly risk of non-point source loss to surface water in this watershed is in a high level; 2) the system indexes integration evaluation method is an universal method to evaluate a quality or a trend of any system and shows a great power in comparing several systems; 3) the method is helpful to attain an effective and integrated assessment on a system when it is combined with other methods.}, } @article {pmid18647333, year = {2008}, author = {Loy, A and Arnold, R and Tischler, P and Rattei, T and Wagner, M and Horn, M}, title = {probeCheck--a central resource for evaluating oligonucleotide probe coverage and specificity.}, journal = {Environmental microbiology}, volume = {10}, number = {10}, pages = {2894-2898}, pmid = {18647333}, issn = {1462-2920}, support = {P 18836/FWF_/Austrian Science Fund FWF/Austria ; P 20185/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {*Databases, Genetic ; Molecular Biology/*methods ; Nucleic Acid Hybridization/*methods ; Oligonucleotide Probes/*genetics ; Sensitivity and Specificity ; }, abstract = {The web server probeCheck, freely accessible at http://www.microbial-ecology.net/probecheck, provides a pivotal forum for rapid specificity and coverage evaluations of probes and primers against selected databases of phylogenetic and functional marker genes. Currently, 24 widely used sequence collections including the Ribosomal Database Project (RDP) II, Greengenes, SILVA and the Functional Gene Pipeline/Repository can be queried. For this purpose, probeCheck integrates a new online version of the popular ARB probe match tool with free energy (DeltaG) calculations for each perfectly matched and mismatched probe-target hybrid, allowing assessment of the theoretical binding stabilities of oligo-target and non-target hybrids. For each output sequence, the accession number, the GenBank taxonomy and a link to the respective entry at GenBank, EMBL and, if applicable, the query database are displayed. Filtering options allow customizing results on the output page. In addition, probeCheck is linked with probe match tools of RDP II and Greengenes, NCBI blast, the Oligonucleotide Properties Calculator, the two-state folding tool of the DINAMelt server and the rRNA-targeted probe database probeBase. Taken together, these features provide a multifunctional platform with maximal flexibility for the user in the choice of databases and options for the evaluation of published and newly developed probes and primers.}, } @article {pmid18643915, year = {2008}, author = {Baker, CS}, title = {A truer measure of the market: the molecular ecology of fisheries and wildlife trade.}, journal = {Molecular ecology}, volume = {17}, number = {18}, pages = {3985-3998}, doi = {10.1111/j.1365-294X.2008.03867.x}, pmid = {18643915}, issn = {0962-1083}, mesh = {Animals ; Animals, Wild/classification/*genetics ; Biodiversity ; *Commerce ; Conservation of Natural Resources/*methods ; Databases, Genetic ; *Fisheries ; Registries ; }, abstract = {Wildlife and fisheries markets are end-points in the supply chain of both legitimate and illegitimate or unregulated trade in species and natural products. Molecular ecology provides powerful tools for surveillance and estimation of this trade. Here, I review the application of these tools to market surveys and species in trade, including species identification and molecular taxonomy, population assignment and 'mixed-stock' analysis, genetic tracking and capture-recapture by individual identification. I consider the analogy of markets to natural populations and also the unique features that require novel analytical approaches and sampling design. In the most developed of these applications, the molecular ecology of market surveys and confiscated trade shipments has provided independent estimates of illegal, unregulated or unreported exploitation for sharks, elephants and whales. Although each study has taken advantage of information from trade records or official government reports concerning the ostensible levels of exploitation, it is telling that the truer measure of exploitation seems to arise from the market end-point of the supply chain.}, } @article {pmid18639487, year = {2008}, author = {Effken, JA and Loeb, RG and Kang, Y and Lin, ZC}, title = {Clinical information displays to improve ICU outcomes.}, journal = {International journal of medical informatics}, volume = {77}, number = {11}, pages = {765-777}, doi = {10.1016/j.ijmedinf.2008.05.004}, pmid = {18639487}, issn = {1872-8243}, mesh = {Attitude to Computers ; Audiovisual Aids/standards ; Clinical Competence ; Computer Simulation ; Computer-Assisted Instruction/methods ; Data Compression/methods/standards ; *Data Display/standards/statistics & numerical data ; Decision Support Systems, Clinical/*standards ; Efficiency ; Humans ; Intensive Care Units/*organization & administration ; Nurses/psychology ; Practice, Psychological ; Task Performance and Analysis ; *User-Computer Interface ; Workforce ; }, abstract = {PURPOSE: In a previous study, we compared a prototype ecological display (ED) that represented physiological data in a structured pictorial format with two bar graph displays [J.A. Effken, Improving clinical decision making through ecological interfaces, Ecol. Psych. 18 (2006) 283-318]. In ED and the first bar graph display, data were grouped hierarchically based on a cognitive work analysis (CWA); in the second bar graph display they were grouped as usually collected. Treatment efficiency (i.e., percentage of time seven variables in the CWA model were in target range) improved similarly with the two displays incorporating the CWA order for intensive care unit (ICU) residents, but not for novice ICU nurses. Hypothesized reasons for this result included: insufficient practice with novel displays; use of identical histories across displays; insufficient clinical knowledge; and the variables used in the efficiency analysis, which included only one of ED's four integrated design elements. In the current study we tested these hypotheses.

METHODS: We asked ICU nurses assigned to three knowledge groups based on intensive care and hemodynamic monitoring pretests to identify and treat oxygenation problems presented via ED and the first bar graph display (BGD) in an experimental laboratory simulation. We measured the impact of display, clinical scenario, data level, knowledge, presentation order, and practice extent on event recognition, treatment efficiency, cognitive workload, and user satisfaction.

RESULTS: The two displays produced little difference in recognition speed or overall cognitive workload, but user satisfaction was greater with ED. When 12 variables were included in the analysis, treatment efficiency improved with ED; when only 7 were measured, BGD prevailed. The results suggest benefits for the kind of synthesis provided in ED, but also a potential limitation. If too many different pictorial formats are used in a display, detecting critical events may be more difficult.}, } @article {pmid18632289, year = {2008}, author = {Trewick, SA and Morgan-Richards, M and Collins, LJ}, title = {Are you my mother? Phylogenetic analysis reveals orphan hybrid stick insect genus is part of a monophyletic New Zealand clade.}, journal = {Molecular phylogenetics and evolution}, volume = {48}, number = {3}, pages = {799-808}, doi = {10.1016/j.ympev.2008.05.025}, pmid = {18632289}, issn = {1095-9513}, mesh = {Algorithms ; Animals ; Biological Evolution ; Computational Biology/methods ; DNA, Ribosomal/metabolism ; Evolution, Molecular ; Female ; Insecta/*genetics/*physiology ; Likelihood Functions ; Male ; New Zealand ; Phylogeny ; }, abstract = {The hybrid stick insect genus Acanthoxyla Uvarov 1944 is unusual for an obligate parthenogen, in the extreme morphological diversity it exhibits that has led to eight species being recognised. The New Zealand sexual species Clitarchus hookeri [White, A. 1846. The zoology of the Voyage of H.M.S. Erebus and Terror. In: 1 Insects of New Zealand. E.W. Janson, London.] is the putative parental species in the hybridization that gave rise to the hybrid lineage Acanthoxyla. In an effort to identify the maternal ancestor of Acanthoxyla we sequenced nuclear 28S rDNA and/or mtDNA COI & COII of all nine endemic New Zealand stick insect genera, representing 17 of the 22 described species. We also sequenced 28S from eight non-New Zealand stick insects to supplement published 28S sequence data that provided a taxonomically and geographically broad sampling of the phasmids. We applied a novel search algorithm (SeqSSi=Sequence Similarity Sieve) to assist in selection of outgroup taxa for phylogenetic analysis prior to alignment. Phylogenetic reconstructions resolved an exclusively New Zealand clade to which the maternal lineage of Acanthoxyla belonged, but did not support existing higher level taxonomy of stick insects. We did not find a sexual maternal species for Acanthoxyla but phylogenetic relationships indicate that this species lived in New Zealand and could be classified among the New Zealand Phasmatinae. Among the available taxa, the nearest evolutionary neighbours to the New Zealand phasmid fauna as a whole were predominantly from the New Zealand region (Fiji, Australia, New Guinea, New Caledonia and South America). As it appears to be an orphan, it is interesting to speculate that a combination of parthenogenetic reproduction and/or hybrid vigour in Acanthoxyla may have contributed to the extinction of its mother.}, } @article {pmid18606794, year = {2008}, author = {Yawata, Y and Nomura, N and Uchiyama, H}, title = {Development of a novel biofilm continuous culture method for simultaneous assessment of architecture and gaseous metabolite production.}, journal = {Applied and environmental microbiology}, volume = {74}, number = {17}, pages = {5429-5435}, pmid = {18606794}, issn = {1098-5336}, mesh = {Bacteriological Techniques ; Biofilms/*growth & development ; *Bioreactors ; Chromatography, Gas ; DNA, Bacterial/genetics ; Image Interpretation, Computer-Assisted ; Microscopy, Confocal ; Nitrogen/metabolism ; Nitrous Oxide/metabolism ; Plasmids ; Pseudomonas aeruginosa/genetics/*growth & development/*metabolism ; Time Factors ; }, abstract = {The way that gaseous metabolite production changes along with biofilm architecture development is poorly understood. To address this question, we developed a novel flow reactor biofilm culture method that allows for simultaneous assessment of gaseous metabolite production and architecture visualization. In this report, we establish the utility of this method using denitrification by Pseudomonas aeruginosa biofilms as a model system. Using this method, we were able to collect and analyze gaseous metabolites produced by denitrification and also visualize biofilm architecture in a nondestructive manner. Thus, we propose that this novel method is a powerful tool to investigate potential relationships between biofilm architecture and the gas-producing metabolic activity of biofilms, providing new insights into biofilm ecology.}, } @article {pmid18605534, year = {2008}, author = {Olden, JD and Lawler, JJ and Poff, NL}, title = {Machine learning methods without tears: a primer for ecologists.}, journal = {The Quarterly review of biology}, volume = {83}, number = {2}, pages = {171-193}, doi = {10.1086/587826}, pmid = {18605534}, issn = {0033-5770}, mesh = {Algorithms ; Animals ; *Artificial Intelligence ; Biological Evolution ; Computational Biology ; Decision Trees ; Ecology/*statistics & numerical data ; Ecosystem ; Fishes/classification ; Fresh Water ; Models, Genetic ; Neural Networks, Computer ; Software ; Species Specificity ; }, abstract = {Machine learning methods, a family of statistical techniques with origins in the field of artificial intelligence, are recognized as holding great promise for the advancement of understanding and prediction about ecological phenomena. These modeling techniques are flexible enough to handle complex problems with multiple interacting elements and typically outcompete traditional approaches (e.g., generalized linear models), making them ideal for modeling ecological systems. Despite their inherent advantages, a review of the literature reveals only a modest use of these approaches in ecology as compared to other disciplines. One potential explanation for this lack of interest is that machine learning techniques do not fall neatly into the class of statistical modeling approaches with which most ecologists are familiar. In this paper, we provide an introduction to three machine learning approaches that can be broadly used by ecologists: classification and regression trees, artificial neural networks, and evolutionary computation. For each approach, we provide a brief background to the methodology, give examples of its application in ecology, describe model development and implementation, discuss strengths and weaknesses, explore the availability of statistical software, and provide an illustrative example. Although the ecological application of machine learning approaches has increased, there remains considerable skepticism with respect to the role of these techniques in ecology. Our review encourages a greater understanding of machin learning approaches and promotes their future application and utilization, while also providing a basis from which ecologists can make informed decisions about whether to select or avoid these approaches in their future modeling endeavors.}, } @article {pmid18600470, year = {2008}, author = {Kyselková, M and Kopecký, J and Felföldi, T and Cermák, L and Omelka, M and Grundmann, GL and Moënne-Loccoz, Y and Ságová-Marecková, M}, title = {Development of a 16S rRNA gene-based prototype microarray for the detection of selected actinomycetes genera.}, journal = {Antonie van Leeuwenhoek}, volume = {94}, number = {3}, pages = {439-453}, doi = {10.1007/s10482-008-9261-z}, pmid = {18600470}, issn = {0003-6072}, mesh = {Actinobacteria/classification/*genetics/isolation & purification ; Base Sequence ; Cloning, Molecular ; DNA Primers/genetics ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Databases, Genetic ; Ecosystem ; Nucleic Acid Conformation ; Oligonucleotide Array Sequence Analysis/*methods ; Polymerase Chain Reaction ; RNA, Bacterial/*genetics ; RNA, Ribosomal, 16S/*genetics ; Soil Microbiology ; Species Specificity ; }, abstract = {Actinomycetes are known for their secondary metabolites, which have been successfully used as drugs in human and veterinary medicines. However, information on the distribution of this group of Gram-positive bacteria in diverse ecosystems and a comprehension of their activities in ecosystem processes are still scarce. We have developed a 16S rRNA-based taxonomic microarray that targets key actinomycetes at the genus level. In total, 113 actinomycete 16S rRNA probes, corresponding to 55 of the 202 described genera, were designed. The microarray accuracy was evaluated by comparing signal intensities with probe/target-weighted mismatch values and the Gibbs energy of the probe/target duplex formation by hybridizing 17 non-actinomycete and 29 actinomycete strains/clones with the probe set. The validation proved that the probe set was specific, with only 1.3% of false results. The incomplete coverage of actinomycetes by a genus-specific probe was caused by the limited number of 16S rRNA gene sequences in databases or insufficient 16S rRNA gene polymorphism. The microarray enabled discrimination between actinomycete communities from three forest soil samples collected at one site. Cloning and sequencing of 16S rRNA genes from one of the soil samples confirmed the microarray results. We propose that this newly constructed microarray will be a valuable tool for genus-level comparisons of actinomycete communities in various ecological conditions.}, } @article {pmid18599787, year = {2008}, author = {Sanderson, MJ}, title = {Phylogenetic signal in the eukaryotic tree of life.}, journal = {Science (New York, N.Y.)}, volume = {321}, number = {5885}, pages = {121-123}, doi = {10.1126/science.1154449}, pmid = {18599787}, issn = {1095-9203}, mesh = {Algorithms ; Animals ; Biodiversity ; Classification ; *Databases, Nucleic Acid ; *Eukaryotic Cells ; Fungi/*classification/genetics ; Humans ; Invertebrates/*classification/genetics ; National Library of Medicine (U.S.) ; *Phylogeny ; Plants/*classification/genetics ; Sequence Alignment ; United States ; Vertebrates/*classification/genetics ; }, abstract = {Molecular sequence data have been sampled from 10% of all species known to science. Although it is not yet feasible to assemble these data into a single phylogenetic tree of life, it is possible to quantify how much phylogenetic signal is present. Analysis of 14,289 phylogenies built from 2.6 million sequences in GenBank suggests that signal is strong in vertebrates and specific groups of nonvertebrate model organisms. Across eukaryotes, however, although phylogenetic evidence is very broadly distributed, for the average species in the database it is equivalent to less than one well-supported gene tree. This analysis shows that a stronger sampling effort aimed at genomic depth, in addition to taxonomic breadth, will be required to build high-resolution phylogenetic trees at this scale.}, } @article {pmid18599780, year = {2008}, author = {Alroy, J and Aberhan, M and Bottjer, DJ and Foote, M and Fürsich, FT and Harries, PJ and Hendy, AJ and Holland, SM and Ivany, LC and Kiessling, W and Kosnik, MA and Marshall, CR and McGowan, AJ and Miller, AI and Olszewski, TD and Patzkowsky, ME and Peters, SE and Villier, L and Wagner, PJ and Bonuso, N and Borkow, PS and Brenneis, B and Clapham, ME and Fall, LM and Ferguson, CA and Hanson, VL and Krug, AZ and Layou, KM and Leckey, EH and Nürnberg, S and Powers, CM and Sessa, JA and Simpson, C and Tomasovych, A and Visaggi, CC}, title = {Phanerozoic trends in the global diversity of marine invertebrates.}, journal = {Science (New York, N.Y.)}, volume = {321}, number = {5885}, pages = {97-100}, doi = {10.1126/science.1156963}, pmid = {18599780}, issn = {1095-9203}, mesh = {Animals ; *Biodiversity ; Biological Evolution ; Databases, Factual ; Environment ; *Fossils ; Geography ; Geologic Sediments ; *Invertebrates/classification ; *Paleontology/methods ; Population Dynamics ; Sampling Studies ; Seawater ; Time Factors ; }, abstract = {It has previously been thought that there was a steep Cretaceous and Cenozoic radiation of marine invertebrates. This pattern can be replicated with a new data set of fossil occurrences representing 3.5 million specimens, but only when older analytical protocols are used. Moreover, analyses that employ sampling standardization and more robust counting methods show a modest rise in diversity with no clear trend after the mid-Cretaceous. Globally, locally, and at both high and low latitudes, diversity was less than twice as high in the Neogene as in the mid-Paleozoic. The ratio of global to local richness has changed little, and a latitudinal diversity gradient was present in the early Paleozoic.}, } @article {pmid18596914, year = {2008}, author = {Carwardine, J and Wilson, KA and Watts, M and Etter, A and Klein, CJ and Possingham, HP}, title = {Avoiding costly conservation mistakes: the importance of defining actions and costs in spatial priority setting.}, journal = {PloS one}, volume = {3}, number = {7}, pages = {e2586}, pmid = {18596914}, issn = {1932-6203}, mesh = {Australia ; Biodiversity ; Conservation of Natural Resources/*economics/methods ; Cost-Benefit Analysis ; Ecosystem ; Geographic Information Systems ; Organizational Objectives ; }, abstract = {BACKGROUND: The typical mandate in conservation planning is to identify areas that represent biodiversity targets within the smallest possible area of land or sea, despite the fact that area may be a poor surrogate for the cost of many conservation actions. It is also common for priorities for conservation investment to be identified without regard to the particular conservation action that will be implemented. This demonstrates inadequate problem specification and may lead to inefficiency: the cost of alternative conservation actions can differ throughout a landscape, and may result in dissimilar conservation priorities.

We investigate the importance of formulating conservation planning problems with objectives and cost data that relate to specific conservation actions. We identify priority areas in Australia for two alternative conservation actions: land acquisition and stewardship. Our analyses show that using the cost surrogate that most closely reflects the planned conservation action can cut the cost of achieving our biodiversity goals by half. We highlight spatial differences in relative priorities for land acquisition and stewardship in Australia, and provide a simple approach for determining which action should be undertaken where.

CONCLUSIONS/SIGNIFICANCE: Our study shows that a poorly posed conservation problem that fails to pre-specify the planned conservation action and incorporate cost a priori can lead to expensive mistakes. We can be more efficient in achieving conservation goals by clearly specifying our conservation objective and parameterising the problem with economic data that reflects this objective.}, } @article {pmid18593050, year = {2008}, author = {Wu, JZ and Li, B and Zhang, XS and Zhao, WW and Jiang, GH}, title = {[Vulnerability of eco-economy in northern slope region of Tianshan Mountains].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {19}, number = {4}, pages = {859-865}, pmid = {18593050}, issn = {1001-9332}, mesh = {Algorithms ; China ; Ecology/*economics ; *Environment Design ; Environmental Monitoring/*methods/statistics & numerical data ; Fuzzy Logic ; Geographic Information Systems/statistics & numerical data ; Geography ; Models, Theoretical ; }, abstract = {Based on the theoretical meaning of vulnerability, a vulnerability assessment of eco-econom in fifteen counties in the northern slope region of Tianshan Mountains was conducted. The ecosystem services change to land use was regarded as the impact, and based on the fourteen indices from resource holding, society development, and economy development statistic data, the adaptive ability was evaluated by using the methods of analytic hierarchy process (AHP) and fuzzy synthetic evaluation. On the basis of assessment results of impact and adaptive capacity, the fifteen counties were divided into five classes under the assessment principles, and the district with higher-class number was of more vulnerability. The first class included Usu City and Changji City, the second class included Hutubi County, Miquan County, Fukang City, Jimsar County, Qitai County and Mori Kazak Autonomous County, the third class included Karamay City and Urumqi City, the fourth class included Kuitun City and Shawan County, and the fifth class included Jinghe County, Shihezi City and Manas County. The vulnerability reflected the level of eco-environment change and socioeconomic development, and the vulnerability assessment could be a good way to ensure the sustainable development. Aiming to decrease the vulnerability, various districts belonging to different class of vulnerability should establish relevant tactics according to the vulnerability factors to accelerate the region's sustainable development.}, } @article {pmid18577087, year = {2008}, author = {Lee, H and Reusser, DA and Olden, JD and Smith, SS and Graham, J and Burkett, V and Dukes, JS and Piorkowski, RJ and McPhedran, J}, title = {Integrated monitoring and information systems for managing aquatic invasive species in a changing climate.}, journal = {Conservation biology : the journal of the Society for Conservation Biology}, volume = {22}, number = {3}, pages = {575-584}, doi = {10.1111/j.1523-1739.2008.00955.x}, pmid = {18577087}, issn = {1523-1739}, mesh = {Conservation of Natural Resources/methods ; Databases, Factual/*standards ; Demography ; *Ecosystem ; Environmental Monitoring/*methods ; Greenhouse Effect ; Models, Biological ; *Water ; }, abstract = {Changes in temperature, precipitation, and other climatic drivers and sea-level rise will affect populations of existing native and non-native aquatic species and the vulnerability of aquatic environments to new invasions. Monitoring surveys provide the foundation for assessing the combined effects of climate change and invasions by providing baseline biotic and environmental conditions, although the utility of a survey depends on whether the results are quantitative or qualitative, and other design considerations. The results from a variety of monitoring programs in the United States are available in integrated biological information systems, although many include only non-native species, not native species. Besides including natives, we suggest these systems could be improved through the development of standardized methods that capture habitat and physiological requirements and link regional and national biological databases into distributed Web portals that allow drawing information from multiple sources. Combining the outputs from these biological information systems with environmental data would allow the development of ecological-niche models that predict the potential distribution or abundance of native and non-native species on the basis of current environmental conditions. Environmental projections from climate models can be used in these niche models to project changes in species distributions or abundances under altered climatic conditions and to identify potential high-risk invaders. There are, however, a number of challenges, such as uncertainties associated with projections from climate and niche models and difficulty in integrating data with different temporal and spatial granularity. Even with these uncertainties, integration of biological and environmental information systems, niche models, and climate projections would improve management of aquatic ecosystems under the dual threats of biotic invasions and climate change.}, } @article {pmid18570031, year = {2008}, author = {Holland, BR and Clarke, AC and Meudt, HM}, title = {Optimizing automated AFLP scoring parameters to improve phylogenetic resolution.}, journal = {Systematic biology}, volume = {57}, number = {3}, pages = {347-366}, doi = {10.1080/10635150802044037}, pmid = {18570031}, issn = {1063-5157}, mesh = {Alleles ; Amplified Fragment Length Polymorphism Analysis/*methods ; Computational Biology/*methods ; Ipomoea batatas/genetics ; Phylogeny ; Plantago/anatomy & histology/genetics ; Polymorphism, Genetic ; *Software ; }, abstract = {The amplified fragment length polymorphism (AFLP) technique is an increasingly popular component of the phylogenetic toolbox, particularly for plant species. Technological advances in capillary electrophoresis now allow very precise estimates of DNA fragment mobility and amplitude, and current AFLP software allows greater control of data scoring and the production of the binary character matrix. However, for AFLP to become a useful modern tool for large data sets, improvements to automated scoring are required. We design a procedure that can be used to optimize AFLP scoring parameters to improve phylogenetic resolution and demonstrate it for two AFLP scoring programs (GeneMapper and GeneMarker). In general, we found that there was a trade-off between getting more characters of lower quality and fewer characters of high quality. Conservative settings that gave the least error did not give the best phylogenetic resolution, as too many useful characters were discarded. For example, in GeneMapper, we found that bin width was a crucial parameter, and that although reducing bin width from 1.0 to 0.5 base pairs increased the error rate, it nevertheless improved resolution due to the increased number of informative characters. For our 30-taxon data sets, moving from default to optimized parameter settings gave between 3 and 11 extra internal edges with >50% bootstrap support, in the best case increasing the number of resolved edges from 14 to 25 out of a possible 27. Nevertheless, improvements to current AFLP software packages are needed to (1) make use of replicate profiles to calibrate the data and perform error calculations and (2) perform tests to optimize scoring parameters in a rigorous and automated way. This is true not only when AFLP data are used for phylogenetics, but also for other applications, including linkage mapping and population genetics.}, } @article {pmid18570030, year = {2008}, author = {Sanderson, MJ and Boss, D and Chen, D and Cranston, KA and Wehe, A}, title = {The PhyLoTA Browser: processing GenBank for molecular phylogenetics research.}, journal = {Systematic biology}, volume = {57}, number = {3}, pages = {335-346}, doi = {10.1080/10635150802158688}, pmid = {18570030}, issn = {1063-5157}, mesh = {Cluster Analysis ; Computational Biology/methods ; *Databases, Nucleic Acid ; Internet ; *Phylogeny ; *Software ; }, abstract = {As an archive of sequence data for over 165,000 species, GenBank is an indispensable resource for phylogenetic inference. Here we describe an informatics processing pipeline and online database, the PhyLoTA Browser (http://loco.biosci.arizona.edu/pb), which offers a view of GenBank tailored for molecular phylogenetics. The first release of the Browser is computed from 2.6 million sequences representing the taxonomically enriched subset of GenBank sequences for eukaryotes (excluding most genome survey sequences, ESTs, and other high-throughput data). In addition to summarizing sequence diversity and species diversity across nodes in the NCBI taxonomy, it reports 87,000 potentially phylogenetically informative clusters of homologous sequences, which can be viewed or downloaded, along with provisional alignments and coarse phylogenetic trees. At each node in the NCBI hierarchy, the user can display a "data availability matrix" of all available sequences for entries in a subtaxa-by-clusters matrix. This matrix provides a guidepost for subsequent assembly of multigene data sets or supertrees. The database allows for comparison of results from previous GenBank releases, highlighting recent additions of either sequences or taxa to GenBank and letting investigators track progress on data availability worldwide. Although the reported alignments and trees are extremely approximate, the database reports several statistics correlated with alignment quality to help users choose from alternative data sources.}, } @article {pmid18564914, year = {2008}, author = {Field, D and Glöckner, FO and Garrity, GM and Gray, T and Sterk, P and Cochrane, G and Vaughan, R and Kolker, E and Kottmann, R and Kyrpides, N and Angiuoli, S and Dawyndt, P and Guralnick, R and Goldstein, P and Hall, N and Hirschman, L and Kravitz, S and Lister, AL and Markowitz, V and Thomson, N and Whetzel, T}, title = {Meeting report: the fourth Genomic Standards Consortium (GSC) workshop.}, journal = {Omics : a journal of integrative biology}, volume = {12}, number = {2}, pages = {101-108}, doi = {10.1089/omi.2008.0014}, pmid = {18564914}, issn = {1536-2310}, mesh = {*Databases, Genetic ; Education ; *Genomics ; Programming Languages ; Reference Standards ; }, abstract = {This meeting report summarizes the proceedings of the "eGenomics: Cataloguing our Complete Genome Collection IV" workshop held June 6-8, 2007, at the National Institute for Environmental eScience (NIEeS), Cambridge, United Kingdom. This fourth workshop of the Genomic Standards Consortium (GSC) was a mix of short presentations, strategy discussions, and technical sessions. Speakers provided progress reports on the development of the "Minimum Information about a Genome Sequence" (MIGS) specification and the closely integrated "Minimum Information about a Metagenome Sequence" (MIMS) specification. The key outcome of the workshop was consensus on the next version of the MIGS/MIMS specification (v1.2). This drove further definition and restructuring of the MIGS/MIMS XML schema (syntax). With respect to semantics, a term vetting group was established to ensure that terms are properly defined and submitted to the appropriate ontology projects. Perhaps the single most important outcome of the workshop was a proposal to move beyond the concept of "minimum" to create a far richer XML schema that would define a "Genomic Contextual Data Markup Language" (GCDML) suitable for wider semantic integration across databases. GCDML will contain not only curated information (e.g., compliant with MIGS/MIMS), but also be extended to include a variety of data processing and calculations. Further information about the Genomic Standards Consortium and its range of activities can be found at http://gensc.org.}, } @article {pmid18562677, year = {2008}, author = {Studer, RA and Penel, S and Duret, L and Robinson-Rechavi, M}, title = {Pervasive positive selection on duplicated and nonduplicated vertebrate protein coding genes.}, journal = {Genome research}, volume = {18}, number = {9}, pages = {1393-1402}, pmid = {18562677}, issn = {1088-9051}, mesh = {Animals ; *Codon ; Computational Biology ; *Gene Duplication ; *Selection, Genetic ; Vertebrates/*genetics ; }, abstract = {A stringent branch-site codon model was used to detect positive selection in vertebrate evolution. We show that the test is robust to the large evolutionary distances involved. Positive selection was detected in 77% of 884 genes studied. Most positive selection concerns a few sites on a single branch of the phylogenetic tree: Between 0.9% and 4.7% of sites are affected by positive selection depending on the branches. No functional category was overrepresented among genes under positive selection. Surprisingly, whole genome duplication had no effect on the prevalence of positive selection, whether the fish-specific genome duplication or the two rounds at the origin of vertebrates. Thus positive selection has not been limited to a few gene classes, or to specific evolutionary events such as duplication, but has been pervasive during vertebrate evolution.}, } @article {pmid18560592, year = {2008}, author = {West, JB and Sobek, A and Ehleringer, JR}, title = {A simplified GIS approach to modeling global leaf water isoscapes.}, journal = {PloS one}, volume = {3}, number = {6}, pages = {e2447}, pmid = {18560592}, issn = {1932-6203}, mesh = {*Geographic Information Systems ; Hydrogen/analysis ; Models, Theoretical ; Oxygen Isotopes/analysis ; Plant Leaves/*chemistry ; Water/*analysis ; }, abstract = {The stable hydrogen (delta(2)H) and oxygen (delta(18)O) isotope ratios of organic and inorganic materials record biological and physical processes through the effects of substrate isotopic composition and fractionations that occur as reactions proceed. At large scales, these processes can exhibit spatial predictability because of the effects of coherent climatic patterns over the Earth's surface. Attempts to model spatial variation in the stable isotope ratios of water have been made for decades. Leaf water has a particular importance for some applications, including plant organic materials that record spatial and temporal climate variability and that may be a source of food for migrating animals. It is also an important source of the variability in the isotopic composition of atmospheric gases. Although efforts to model global-scale leaf water isotope ratio spatial variation have been made (especially of delta(18)O), significant uncertainty remains in models and their execution across spatial domains. We introduce here a Geographic Information System (GIS) approach to the generation of global, spatially-explicit isotope landscapes (= isoscapes) of "climate normal" leaf water isotope ratios. We evaluate the approach and the resulting products by comparison with simulation model outputs and point measurements, where obtainable, over the Earth's surface. The isoscapes were generated using biophysical models of isotope fractionation and spatially continuous precipitation isotope and climate layers as input model drivers. Leaf water delta(18)O isoscapes produced here generally agreed with latitudinal averages from GCM/biophysical model products, as well as mean values from point measurements. These results show global-scale spatial coherence in leaf water isotope ratios, similar to that observed for precipitation and validate the GIS approach to modeling leaf water isotopes. These results demonstrate that relatively simple models of leaf water enrichment combined with spatially continuous precipitation isotope ratio and climate data layers yield accurate global leaf water estimates applicable to important questions in ecology and atmospheric science.}, } @article {pmid18548416, year = {2008}, author = {Vandenberghe, J}, title = {[Does evidence-b(i)ased psychiatry have its limitations?].}, journal = {Tijdschrift voor psychiatrie}, volume = {50}, number = {6}, pages = {377-385}, pmid = {18548416}, issn = {0303-7339}, mesh = {Algorithms ; Decision Support Techniques ; *Evidence-Based Medicine ; Humans ; Netherlands ; *Outcome and Process Assessment, Health Care ; Psychiatry/*methods/*standards ; *Research/standards/statistics & numerical data ; Treatment Outcome ; }, abstract = {Evidence-based medicine (EBM) is an algorithm that integrates information technology and the results of outcome research into clinical work. EBM, if well understood, is a valuable and critical bottom-up method that promotes a dialectical process by which the practitioner is able to arrive at an informed treatment choice; the method starts from the individual patient and involves discussion with the patient and critical reading of the relevant literature. However, there is a risk that EBM will become an ideology unless we are aware of its assumptions and epistemology. It is not valuefree, but is driven by an implicit objectivist view of man. EBM attaches greater value to biomedical sciences that to the humanities, to empiricism than to hermeneutics and to quantitative research than to qualitative research. EBM focuses on internal validity, but is in danger of neglecting factors such as qualitative changes that are difficult to measure, ecological validity and effectiveness and may hinder the generalisation of research results to clinical practice. The limitations of EBM are even more poignant in psychiatry, because psychiatry is highly sensitive to context and values. EBM is a blessing if we use it critically and remain aware of its limitations and underlying philosophy and if we supplement it with strategies such as value-based medicine (VBM). EBM, however, does not teach us what is useful or valuable, whereas VBM helps us to explain and weigh up the values that are at stake.}, } @article {pmid18547601, year = {2008}, author = {Buttemer, WA and Story, PG and Fildes, KJ and Baudinette, RV and Astheimer, LB}, title = {Fenitrothion, an organophosphate, affects running endurance but not aerobic capacity in fat-tailed dunnarts (Sminthopsis crassicaudata).}, journal = {Chemosphere}, volume = {72}, number = {9}, pages = {1315-1320}, doi = {10.1016/j.chemosphere.2008.04.054}, pmid = {18547601}, issn = {0045-6535}, mesh = {Aerobiosis/*drug effects ; Animals ; Body Temperature Regulation/drug effects ; Brain/drug effects/enzymology ; Cholinesterase Inhibitors/blood/*toxicity ; Cholinesterases/blood ; Data Interpretation, Statistical ; Fenitrothion/blood/*toxicity ; Insecticides/blood/*toxicity ; Male ; Marsupialia/*physiology ; Metabolism/drug effects ; Pesticide Residues/blood ; Physical Endurance/*drug effects ; Running/physiology ; Thermogenesis/drug effects ; }, abstract = {We measured aerobic metabolism during cold exposure and exercise performance (run duration and oxygen consumption while running at 1 m s(-1)) in the fat-tailed dunnart Sminthopsis crassicaudata, a dasyurid marsupial, before and after ingestion of 30 mg kg(-1) of fenitrothion, an organophosphate (OP) pesticide. Running endurance of OP-exposed animals was less than half that of control animals over the first 3 days after dosing and 55% of control animal endurance on day 5 post-dose. Despite these declines, peak metabolic rate at this running speed (9.3 times basal metabolic rate; BMR) was unaffected by OP exposure. Peak metabolic rate (PMR) and cumulative oxygen consumption during a 1-h exposure to conditions equivalent to -20 degrees C did not differ between OP-treated and control dunnarts, with PMR averaging 11 times BMR. We conclude that fenitrothion-induced exercise fatigue is not due to limitations in oxygen or substrate delivery to muscle or in their uptake per se, but more likely relates to decreased ability to sustain high-frequency neuromuscular function. The persistence of locomotor impairment following OP exposure in otherwise asymptomatic animals emphasizes the importance of using performance-based measures when characterising sublethal effects of pesticide exposure in an ecological context.}, } @article {pmid18541285, year = {2008}, author = {Zheng, YM and Liu, YR and Hu, HQ and He, JZ}, title = {Mercury in soils of three agricultural experimental stations with long-term fertilization in China.}, journal = {Chemosphere}, volume = {72}, number = {9}, pages = {1274-1278}, doi = {10.1016/j.chemosphere.2008.04.052}, pmid = {18541285}, issn = {0045-6535}, mesh = {Agriculture ; China ; Data Interpretation, Statistical ; Fertilizers/*analysis ; Food Contamination ; Manure/analysis ; Mercury/*analysis ; Soil Pollutants/*analysis ; }, abstract = {Mercury (Hg) in the agricultural ecosystem is a global concern because of its high potential toxicity. The objectives of this study were to determine the concentration and distribution of Hg in soils from three long-term experimental stations, i.e., Taoyuan (TY) and Qiyang (QY) in Hunan Province and Fengqiu (FQ) in Henan Province of China, and thus to assess the possible food and health risk of long-term applications of fertilizers. Soil samples at each site were collected from different fertilization plots and also from soil profiles with depths 0-100 cm. There were significant differences in soil Hg concentrations in 0-20 cm (A) or 20-40 cm (B) horizon among the three experimental stations. QY station showed significantly higher Hg concentrations than TY and FQ stations. However, there were no significant differences in soil Hg concentrations between A and B horizons at each station. It was concluded that the soil Hg concentrations at the three sites were mainly controlled by the parent materials. Moreover, chemical fertilizer, especially phosphorous fertilizers, could influence the soil Hg concentrations to some extent at the station with lower soil Hg concentrations, for example, at TY station. There were minimal amounts of Hg resulting from applications of the other chemical fertilizers and organic manure, and thus the fertilization had very low risk to the food security of the agro-ecosystems in the terms of Hg inputs and contamination.}, } @article {pmid18538000, year = {2008}, author = {Seidler, A and Hammer, GP and Husmann, G and König, J and Krtschil, A and Schmidtmann, I and Blettner, M}, title = {Cancer risk among residents of Rhineland-Palatinate winegrowing communities: a cancer-registry based ecological study.}, journal = {Journal of occupational medicine and toxicology (London, England)}, volume = {3}, number = {}, pages = {12}, pmid = {18538000}, issn = {1745-6673}, abstract = {AIM: To investigate the cancer risk among residents of Rhineland-Palatinate winegrowing communities in an ecological study.

METHODS: On the basis of the Rhineland-Palatinate cancer-registry, we calculated age-adjusted incidence rate ratios for communities with a medium area under wine cultivation (>5 to 20 percent) and a large area under wine cultivation (>20 percent) in comparison with communities with a small area under wine cultivation (>0 to 5 percent). In a side analysis, standardized cancer incidence ratios (SIR) were computed separately for winegrowing communities with small, medium and large area under wine cultivation using estimated German incidence rates as reference.

RESULTS: A statistically significant positive association with the extent of viniculture can be observed for non-melanoma skin cancer in both males and females, and additionally for prostate cancer, bladder cancer, and non-Hodgkin lymphoma in males, but not in females. Lung cancer risk is significantly reduced in communities with a large area under cultivation. In the side-analysis, elevated SIR for endocrine-related tumors of the breast, testis, prostate, and endometrium were observed.

CONCLUSION: This study points to a potentially increased risk of skin cancer, bladder cancer, and endocrine-mediated tumors in Rhineland-Palatinate winegrowing communities. However, due to the explorative ecologic study design and the problem of multiple testing, these findings are not conclusve for a causal relationship.}, } @article {pmid18537049, year = {2009}, author = {Carone, MT and Simoniello, T and Manfreda, S and Caricato, G}, title = {Watershed influence on fluvial ecosystems: an integrated methodology for river water quality management.}, journal = {Environmental monitoring and assessment}, volume = {152}, number = {1-4}, pages = {327-342}, pmid = {18537049}, issn = {1573-2959}, mesh = {Animals ; *Ecosystem ; Environmental Monitoring/*methods ; Geographic Information Systems ; Humans ; Italy ; Models, Theoretical ; *Rivers ; *Water Movements ; Water Pollutants, Chemical/analysis ; *Water Supply ; }, abstract = {The EU Water Framework Directive 2000/60 (Integrated River Basin Management for Europe) establishes the importance of preserving water quality through policies applied at watershed level given the strong links existing among ecological, hydrological, and hydrogeological systems. Therefore, monitoring campaigns of river water quality should be planned with multidisciplinary approaches starting from a landscape perspective. In this paper, the effects of the basin hydrology on the river water quality and, in particular, the impacts caused by the runoff production coming from agricultural areas are investigated. The fluvial segments receiving consistent amount of pollutant loads (due to the runoff routing over agricultural areas) are assumed more critical in terms of water quality and thus, they require more accurate controls. Starting from this perspective, to evaluate the runoff productions coming from agricultural areas, we applied a semi-distributed hydrological model that adopts satellite data, pedological and morphological information for the watershed description. Then, the river segments receiving critical amount of runoff loads from the surrounding cultivated areas were identified. Finally, in order to validate the approach, water quality for critical and non critical segment was investigated seasonally, by using river macroinvertebrates as indicators of water quality because of their effectiveness in preserving in time a memory of pollution events. Biomonitoring data showed that river water quality strongly decreases in correspondence of fluvial segments receiving critical amount of runoff coming from agricultural areas. The results highlight the usefulness of such a methodology to plan monitoring campaigns specifically devoted to non-point pollution sources and suggest the possibility to use this approach for water quality management and for planning river restoration policies.}, } @article {pmid18536367, year = {2008}, author = {Chen, J and Xie, CX and Chen, SL and Sun, CZ and Zhao, RH and Xu, R and Yu, J}, title = {[Suitability evaluation of Cistanche tubulosa based on TCMGIS-I].}, journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica}, volume = {33}, number = {5}, pages = {496-501}, pmid = {18536367}, issn = {1001-5302}, mesh = {China ; Cistanche/*growth & development ; *Geographic Information Systems ; Geography ; }, abstract = {OBJECTIVE: To analyze the appropriate producing area of Cistanche tubulosa by mean of TCMGIS-I.

METHOD: The TCMGIS-I (Suitability evaluation geographic information system of traditional Chinese medicine producing area) was used to analyze the appropriate producing area of C. tubulosa basing on the optimum ecological factors of Sorth Sinkiang municipality which is the traditional producing area of C. tubulosa.

RESULT: The suitable producing areas of C. tubulosa include 56 counties with 190952.1 km2 total areas in Sinkiang municipality, Neimongd municipality and Gansu province; Sinkiang municipality, Gansu and Qinghai provinces have the second-suitable producing areas of C. tubulosa, with 46 counties and 41217.37 km2 total areas; Sinkiang municipality, Inner Mongolia municipality, Gansu province and Ningxia municipality have the third-suitable producing areas of C. tubulosa with 56 counties and 421145.2 km2 total areas.

CONCLUSION: It is important to analyze the appropriate producing area of C. tubulosa by means of TCMGIS-I. The results are useful for development of C. tubulosa transplanting and cultivation.}, } @article {pmid18528369, year = {2008}, author = {Frood, A}, title = {Palaeobiology: the Cambrian smorgasbord.}, journal = {Nature}, volume = {453}, number = {7196}, pages = {717-718}, doi = {10.1038/453717a}, pmid = {18528369}, issn = {1476-4687}, mesh = {Animals ; Biodiversity ; Databases, Factual ; Ecology/*methods ; *Food Chain ; *Fossils ; Geologic Sediments ; *Models, Biological ; Paleontology/*methods ; Predatory Behavior ; Time Factors ; }, } @article {pmid18524932, year = {2008}, author = {Clokie, MRJ and Thalassinos, K and Boulanger, P and Slade, SE and Stoilova-McPhie, S and Cane, M and Scrivens, JH and Mann, NH}, title = {A proteomic approach to the identification of the major virion structural proteins of the marine cyanomyovirus S-PM2.}, journal = {Microbiology (Reading, England)}, volume = {154}, number = {Pt 6}, pages = {1775-1782}, doi = {10.1099/mic.0.2007/016261-0}, pmid = {18524932}, issn = {1350-0872}, mesh = {Bacteriophage T4/genetics/metabolism ; Bacteriophages/*chemistry/genetics/*metabolism ; Cryoelectron Microscopy ; Databases, Protein ; Marine Biology ; *Proteomics ; Synechococcus/virology ; Viral Structural Proteins/genetics/*metabolism ; }, abstract = {In this study, an MS-based proteomics approach to characterizing the virion structural proteins of the novel marine 'photosynthetic' phage S-PM2 is presented. The virus infects ecologically important cyanobacteria of the genus Synechococcus that make a substantial contribution to primary production in the oceans. The S-PM2 genome encodes 236 ORFs, some of which exhibit similarity to known phage virion structural proteins, but the majority (54%) show no detectable homology to known proteins from other organisms. Using public and in-house bioinformatics tools the proteome of S-PM2 was predicted and a database compatible with MS-based search engines was constructed. S-PM2 virion proteins were resolved by SDS-PAGE, excised, tryptically digested and analysed by LC-ESI-MS/MS. The resulting MS data were searched against the database. A parallel control study was undertaken on the well-characterized coliphage T4 in order to assess the sensitivity and efficiency of this approach. In total, 11 of the 15 S-PM2 proteins, predicted to be virion proteins by bioinformatics approaches, were confirmed as such, together with the identification of a further 12 novel structural proteins. In the case of T4, 24 of the 39 known virion structural proteins were identified, including the major tail-fibre proteins. This approach has wide-ranging applicability and can be applied to any novel organism whose genome encodes ORFs with few detectable homologies in the public databases.}, } @article {pmid18522986, year = {2008}, author = {Borges, RM}, title = {Commentary: The objection is sustained: a defence of the defense of beanbag genetics.}, journal = {International journal of epidemiology}, volume = {37}, number = {3}, pages = {451-454}, doi = {10.1093/ije/dyn050}, pmid = {18522986}, issn = {1464-3685}, mesh = {Biological Evolution ; Data Interpretation, Statistical ; *Genetic Variation ; Humans ; *Models, Genetic ; }, } @article {pmid18522132, year = {2008}, author = {Awkerman, JA and Raimondo, S and Barron, MG}, title = {Development of species sensitivity distributions for wildlife using interspecies toxicity correlation models.}, journal = {Environmental science & technology}, volume = {42}, number = {9}, pages = {3447-3452}, doi = {10.1021/es702861u}, pmid = {18522132}, issn = {0013-936X}, mesh = {Animals ; Birds ; Databases, Factual ; Ecosystem ; Environmental Monitoring/*methods ; Environmental Pollutants/analysis ; Models, Theoretical ; Probability ; Rats ; Risk Assessment ; Sample Size ; Sensitivity and Specificity ; Species Specificity ; Water Pollutants/analysis ; }, abstract = {Species sensitivity distributions (SSD) are probability distributions of chemical toxicity of multiple species and have had limited application in wildlife risk assessment because of relatively small data sets of wildlife toxicity values. Interspecies correlation estimation (ICE) models predict the acute toxicity to untested taxa from known toxicity of a single surrogate species. ICE models were used to predict toxicity values to wildlife species and generate SSDs for 23 chemicals using four avian surrogates. The hazard levels associated with the fifth percentile of the distribution (HD5) were compared for ICE SSDs and independent SSDs created with measured data. SSDs were composed of either avian only or avian and mammalian taxa. ICE HD5s were within 5-fold of 90% of measured HD5s and were generally higher than measured HD5s. The first percentile of the distribution (HD1) and the fifth percentile of the lower confidence limit (HDL) of ICE SSDs produced values that were not significantly different from measured HD5s. Using a bird surrogate to predicttoxicity to birds and the Norway rat to predict toxicity to mammals improved some estimates of ICE HD5s compared with those generated using only bird surrogates. These results indicate that ICE models can be used to generate SSDs comparable to those derived from measured wildlife toxicity data and provide robust estimates of the HD5.}, } @article {pmid18519293, year = {2008}, author = {Backe, SN and Andersson, R}, title = {Monitoring the "tip of the iceberg'': ambulance records as a source of injury surveillance.}, journal = {Scandinavian journal of public health}, volume = {36}, number = {3}, pages = {250-257}, doi = {10.1177/1403494807086973}, pmid = {18519293}, issn = {1403-4948}, mesh = {Adolescent ; Adult ; Aged ; Ambulances/statistics & numerical data ; Child ; Child, Preschool ; Female ; Humans ; Incidence ; Infant ; Male ; *Medical Records Systems, Computerized/statistics & numerical data ; Middle Aged ; Patient Discharge/statistics & numerical data ; Registries ; Seasons ; Sweden/epidemiology ; Wounds and Injuries/*epidemiology/etiology/prevention & control ; }, abstract = {AIMS: The aim of this study was to describe the epidemiology of moderate and severe injury morbidity in a defined population on the basis of ambulance records, and to validate ambulance records as a potential source of surveillance.

METHODS: A geographical target area was defined; the county of Värmland, Sweden. All ambulance attendances and hospitalizations for unintentional and intentional injury in 2002 were selected, analysed, and compared.

RESULTS: Ambulance data comprised 3,964 injury cases (14.5/1,000). Most injuries for which ambulance attention was sought occurred in road traffic areas (27%), followed by residential areas (20%), school and institutional areas (14%), and sports areas (8%). An ecological comparison between ambulance-based data and hospitalizations showed that ambulance services captured approximately the same amount of injury cases (3,235 ambulance reports, as compared to 3,456 hospital discharges) with a similar profile.

CONCLUSIONS: This study provides epidemiological support for ambulance services as a potential source of regular surveillance data on moderate and severe injuries. However, at a population level, our results indicate that ambulance data tend to overestimate some injury categories, and underestimate others, as compared to hospital data. The significance of these differences for preventive work, as well as other practical aspects of the feasibility of regular injury surveillance, will be analysed and discussed on the basis of general criteria for evaluation of surveillance systems in a forthcoming paper.}, } @article {pmid18516693, year = {2009}, author = {Liu, L and Jing, X and Wang, J and Zhao, C}, title = {Analysis of the changes of vegetation coverage of western Beijing mountainous areas using remote sensing and GIS.}, journal = {Environmental monitoring and assessment}, volume = {153}, number = {1-4}, pages = {339-349}, pmid = {18516693}, issn = {1573-2959}, mesh = {China ; Conservation of Natural Resources ; *Ecosystem ; Environmental Monitoring/*methods ; *Geographic Information Systems ; *Satellite Communications ; Trees/*growth & development ; }, abstract = {Mentougou District acts as a crucial component in the ecological buffer in western Beijing mountainous areas, Beijing, China. Using two Landsat MSS/TM images acquired on July 14, 1979 and July 23, 2005, the vegetation coverage of Mentougou District was calculated based on normalized difference vegetation index and spectral mixture analysis (NDVI-SMA) model. Its temporal and spatial changes were analyzed according to digital elevation model (DEM) image, social and economic data. The results showed that the vegetation coverage decreased from 76.4% in 1979 to 72.7% in 2005. Vegetation degradation was probably the result of human disturbance, such as outspreading of resident areas, and coal and stone mining activities, while vegetation restoration might be contributed by the combined effects of both natural processes and ecological construction effort. Vegetation changes were closely related to topographical characteristics. Plants at high altitude were more stable and less degraded than the plants at low altitude, while the plants on steep slope or northwest aspect were more vulnerable to degradation. During the period of 26 years, landscape appeared to become more fragmental, and ecological quality of the land seemed deteriorated sharply in that highly-covered vegetation area has been decreased by 24%.}, } @article {pmid18514576, year = {2008}, author = {Morand, S and Krasnov, B}, title = {Why apply ecological laws to epidemiology?.}, journal = {Trends in parasitology}, volume = {24}, number = {7}, pages = {304-309}, doi = {10.1016/j.pt.2008.04.003}, pmid = {18514576}, issn = {1471-4922}, mesh = {Animals ; Biodiversity ; Data Interpretation, Statistical ; *Ecosystem ; Ectoparasitic Infestations/epidemiology/parasitology/*veterinary ; Host-Parasite Interactions/*physiology ; *Models, Biological ; Population Density ; Population Dynamics ; Rodent Diseases/epidemiology/*parasitology ; Rodentia ; }, abstract = {Using ecological laws, or rules, is a useful strategy for epidemiological observations. The application of Taylor's power law to epidemiology and evolutionary ecology of parasites is exemplified here. Taylor's power law takes the form of s2=amb, where s2 is the variance in population abundance, m is the mean abundance of the population, a represents a constant parameter and b represents an index of spatial heterogeneity. Although Taylor's power law reflects the aggregation of parasite (or pathogen) individuals among host population, the values of b could reflect regulation processes in host-parasite systems. Illustrations are given showing how b value is linked to various epidemiological situations: pathogen emergence, the impact of vaccination or the level of host immune defence.}, } @article {pmid18511001, year = {2008}, author = {Ruellet, T and Dauvin, JC}, title = {[Biodiversity of the aquatic invertebrates of the eastern part of the Bay and the Estuary of the Seine River: the CISA database, two centuries of observations].}, journal = {Comptes rendus biologies}, volume = {331}, number = {6}, pages = {481-488}, doi = {10.1016/j.crvi.2008.04.004}, pmid = {18511001}, issn = {1631-0691}, mesh = {Animals ; *Biodiversity ; Databases, Factual ; France ; History, 19th Century ; History, 20th Century ; History, 21st Century ; Invertebrates/classification/*physiology ; Marine Biology/*history ; Models, Biological ; Seawater ; }, abstract = {An inventory of all aquatic invertebrates of the Estuary and the eastern part of the Bay of Seine (Normandy, France) was performed and integrated in a free-of-charge georeferenced database named CISA (Catalogue of the Invertebrates in Seine-Aval, e.g., the downstream part of the Seine from the Poses dam to the sea). One thousand four hundred eighty-five taxa of aquatic invertebrates, out of which 5% were never identified at the species level, were recorded. This inventory has been analyzed in comparison with observation efforts carried out in this zone since two centuries, by distinguishing the first inventories of the end of the 19th century, the publications of the regional naturalist societies, the scientific publications, and the grey literature, such as the scientific reports and the university works with limited diffusion. It appears that the regional naturalist societies have played an essential role for the knowledge of the biological diversity before World War II; since then, reports and university works mention approximately half of the new species for the region. Less than one quarter of these descriptions was thus the subject of a publication without restricted diffusion. Biological diversity was thus underestimated for a long time for the eastern part of the Bay and the Estuary of the Seine River. These data show that the distribution of invertebrate species in the estuary of the Seine follows a two-ecocline model.}, } @article {pmid18510999, year = {2008}, author = {Sitayeb, T and Benabdeli, K}, title = {[Contribution to the study of land-use dynamics in the plains of Macta (Algeria) with the aid of remote sensing and GIS].}, journal = {Comptes rendus biologies}, volume = {331}, number = {6}, pages = {466-474}, doi = {10.1016/j.crvi.2008.03.010}, pmid = {18510999}, issn = {1631-0691}, mesh = {Agriculture/*trends ; Algeria ; Environment ; *Geographic Information Systems ; Geography ; Plants ; }, abstract = {The plains of Macta, where the Macta marshes are located, form a wetland with particular ecological characteristics in the Maghreb and are subject to distinct land use dynamics. The plant formations are exposed to multiple forms of degradation, primarily due to climate (period of dryness) and to increasing anthropogenic activities in the area. The new methods of breeding and cultivation contribute to ongoing degradation in this natural ecosystem, with a deterioration of the wetland's biological potentialities. With the aim of safeguarding Macta's marshes, a better knowledge of vegetation distribution patterns and dynamics, together with the interpretation of the remote sensing data and GIS, makes it possible to consider programmes of natural environment restoration and sustainable management. The results of land-use dynamics analysis show a decline in agricultural land use from 33,000 ha in 1958 to 21,000 ha in 2005. Halophytic vegetation currently occupies 47,000 ha, while in 1958 it occupied only 27,000 ha. Tamarix, Inula, Joncus and Scirpus species are experiencing a decrease in surface cover, while Salicornia, Suaeda, and Atriplex are extending their area. To cite this article:}, } @article {pmid18510651, year = {2009}, author = {Xuan Mao, C and You, N}, title = {On comparison of mixture models for closed population capture-recapture studies.}, journal = {Biometrics}, volume = {65}, number = {2}, pages = {547-553}, doi = {10.1111/j.1541-0420.2008.01065.x}, pmid = {18510651}, issn = {1541-0420}, mesh = {Algorithms ; Biometry/*methods ; Computer Simulation ; *Data Interpretation, Statistical ; *Epidemiologic Research Design ; Humans ; *Models, Statistical ; Pattern Recognition, Automated ; *Population Dynamics ; *Proportional Hazards Models ; Reproducibility of Results ; Risk Assessment/methods ; *Sample Size ; Sensitivity and Specificity ; }, abstract = {A mixture model is a natural choice to deal with individual heterogeneity in capture-recapture studies. Pledger (2000, Biometrics 56, 434-442; 2005, Biometrics 61, 868-876) advertised the use of the two-point mixture model. Dorazio and Royle (2003, Biometrics 59, 351-364; 2005, Biometrics 61, 874-876) suggested that the beta-binomial model has advantages. The controversy is related to the nonidentifiability of the population size (Link, 2003, Biometrics 59, 1123-1130) and certain boundary problems. The total bias is decomposed into an intrinsic bias, an approximation bias, and an estimation bias. We propose to assess the approximation bias, the estimation bias, and the variance, with the intrinsic bias excluded when comparing different estimators. The boundary problems in both models and their impacts are investigated. Real epidemiological and ecological examples are analyzed.}, } @article {pmid18509737, year = {2009}, author = {Fancy, SG and Gross, JE and Carter, SL}, title = {Monitoring the condition of natural resources in US national parks.}, journal = {Environmental monitoring and assessment}, volume = {151}, number = {1-4}, pages = {161-174}, pmid = {18509737}, issn = {1573-2959}, mesh = {Animals ; Climate ; *Conservation of Natural Resources ; Decision Making, Organizational ; *Ecosystem ; Environment ; Environmental Monitoring/*methods ; Greenhouse Effect ; Humans ; Interinstitutional Relations ; Models, Theoretical ; United States ; }, abstract = {The National Park Service has developed a long-term ecological monitoring program for 32 ecoregional networks containing more than 270 parks with significant natural resources. The monitoring program assists park managers in developing a broad-based understanding of the status and trends of park resources as a basis for making decisions and working with other agencies and the public for the long-term protection of park ecosystems. We found that the basic steps involved in planning and designing a long-term ecological monitoring program were the same for a range of ecological systems including coral reefs, deserts, arctic tundra, prairie grasslands, caves, and tropical rainforests. These steps involve (1) clearly defining goals and objectives, (2) compiling and summarizing existing information, (3) developing conceptual models, (4) prioritizing and selecting indicators, (5) developing an overall sampling design, (6) developing monitoring protocols, and (7) establishing data management, analysis, and reporting procedures. The broad-based, scientifically sound information obtained through this systems-based monitoring program will have multiple applications for management decision-making, research, education, and promoting public understanding of park resources. When combined with an effective education program, monitoring results can contribute not only to park issues, but also to larger quality-of-life issues that affect surrounding communities and can contribute significantly to the environmental health of the nation.}, } @article {pmid18505868, year = {2008}, author = {Vasco, DA}, title = {A fast and reliable computational method for estimating population genetic parameters.}, journal = {Genetics}, volume = {179}, number = {2}, pages = {951-963}, pmid = {18505868}, issn = {0016-6731}, support = {R29 GM050428/GM/NIGMS NIH HHS/United States ; R01 HD34350-01A1/HD/NICHD NIH HHS/United States ; R29 GM50428/GM/NIGMS NIH HHS/United States ; }, mesh = {Algorithms ; Biometry ; Computational Biology/*methods ; Genetic Variation ; Genetics, Population/*statistics & numerical data ; Least-Squares Analysis ; Likelihood Functions ; Models, Genetic ; Models, Statistical ; Nonlinear Dynamics ; Population Density ; Recombination, Genetic ; Software ; Stochastic Processes ; }, abstract = {The estimation of ancestral and current effective population sizes in expanding populations is a fundamental problem in population genetics. Recently it has become possible to scan entire genomes of several individuals within a population. These genomic data sets can be used to estimate basic population parameters such as the effective population size and population growth rate. Full-data-likelihood methods potentially offer a powerful statistical framework for inferring population genetic parameters. However, for large data sets, computationally intensive methods based upon full-likelihood estimates may encounter difficulties. First, the computational method may be prohibitively slow or difficult to implement for large data. Second, estimation bias may markedly affect the accuracy and reliability of parameter estimates, as suggested from past work on coalescent methods. To address these problems, a fast and computationally efficient least-squares method for estimating population parameters from genomic data is presented here. Instead of modeling genomic data using a full likelihood, this new approach uses an analogous function, in which the full data are replaced with a vector of summary statistics. Furthermore, these least-squares estimators may show significantly less estimation bias for growth rate and genetic diversity than a corresponding maximum-likelihood estimator for the same coalescent process. The least-squares statistics also scale up to genome-sized data sets with many nucleotides and loci. These results demonstrate that least-squares statistics will likely prove useful for nonlinear parameter estimation when the underlying population genomic processes have complex evolutionary dynamics involving interactions between mutation, selection, demography, and recombination.}, } @article {pmid18492248, year = {2008}, author = {Huang, YF and Niu, DK}, title = {Evidence against the energetic cost hypothesis for the short introns in highly expressed genes.}, journal = {BMC evolutionary biology}, volume = {8}, number = {}, pages = {154}, pmid = {18492248}, issn = {1471-2148}, mesh = {Animals ; Databases, Genetic ; *Gene Expression ; Humans ; *Introns ; Mice ; *Models, Genetic ; Oligonucleotide Array Sequence Analysis ; Organ Specificity ; Species Specificity ; }, abstract = {BACKGROUND: In animals, the moss Physcomitrella patens and the pollen of Arabidopsis thaliana, highly expressed genes have shorter introns than weakly expressed genes. A popular explanation for this is selection for transcription efficiency, which includes two sub-hypotheses: to minimize the energetic cost or to minimize the time cost.

RESULTS: In an individual human, different organs may differ up to hundreds of times in cell number (for example, a liver versus a hypothalamus). Considered at the individual level, a gene specifically expressed in a large organ is actually transcribed tens or hundreds of times more than a gene with a similar expression level (a measure of mRNA abundance per cell) specifically expressed in a small organ. According to the energetic cost hypothesis, the former should have shorter introns than the latter. However, in humans and mice we have not found significant differences in intron length between large-tissue/organ-specific genes and small-tissue/organ-specific genes with similar expression levels. Qualitative estimation shows that the deleterious effect (that is, the energetic burden) of long introns in highly expressed genes is too negligible to be efficiently selected against in mammals.

CONCLUSION: The short introns in highly expressed genes should not be attributed to energy constraint. We evaluated evidence for the time cost hypothesis and other alternatives.}, } @article {pmid18489794, year = {2008}, author = {White, WT and Hendy, MD}, title = {Compressing DNA sequence databases with coil.}, journal = {BMC bioinformatics}, volume = {9}, number = {}, pages = {242}, pmid = {18489794}, issn = {1471-2105}, mesh = {Animals ; Data Compression/*methods ; *Database Management Systems ; *Databases, Nucleic Acid ; Evolution, Molecular ; Expressed Sequence Tags ; Humans ; Neural Networks, Computer ; Phylogeny ; Point Mutation ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {BACKGROUND: Publicly available DNA sequence databases such as GenBank are large, and are growing at an exponential rate. The sheer volume of data being dealt with presents serious storage and data communications problems. Currently, sequence data is usually kept in large "flat files," which are then compressed using standard Lempel-Ziv (gzip) compression - an approach which rarely achieves good compression ratios. While much research has been done on compressing individual DNA sequences, surprisingly little has focused on the compression of entire databases of such sequences. In this study we introduce the sequence database compression software coil.

RESULTS: We have designed and implemented a portable software package, coil, for compressing and decompressing DNA sequence databases based on the idea of edit-tree coding. coil is geared towards achieving high compression ratios at the expense of execution time and memory usage during compression - the compression time represents a "one-off investment" whose cost is quickly amortised if the resulting compressed file is transmitted many times. Decompression requires little memory and is extremely fast. We demonstrate a 5% improvement in compression ratio over state-of-the-art general-purpose compression tools for a large GenBank database file containing Expressed Sequence Tag (EST) data. Finally, coil can efficiently encode incremental additions to a sequence database.

CONCLUSION: coil presents a compelling alternative to conventional compression of flat files for the storage and distribution of DNA sequence databases having a narrow distribution of sequence lengths, such as EST data. Increasing compression levels for databases having a wide distribution of sequence lengths is a direction for future work.}, } @article {pmid18480817, year = {2008}, author = {Rosenzweig, C and Karoly, D and Vicarelli, M and Neofotis, P and Wu, Q and Casassa, G and Menzel, A and Root, TL and Estrella, N and Seguin, B and Tryjanowski, P and Liu, C and Rawlins, S and Imeson, A}, title = {Attributing physical and biological impacts to anthropogenic climate change.}, journal = {Nature}, volume = {453}, number = {7193}, pages = {353-357}, doi = {10.1038/nature06937}, pmid = {18480817}, issn = {1476-4687}, mesh = {Agriculture ; Databases, Factual ; *Ecosystem ; Forestry ; Geography ; *Greenhouse Effect ; History, 20th Century ; History, 21st Century ; *Human Activities ; Ice ; Internationality ; Marine Biology ; Models, Statistical ; Temperature ; }, abstract = {Significant changes in physical and biological systems are occurring on all continents and in most oceans, with a concentration of available data in Europe and North America. Most of these changes are in the direction expected with warming temperature. Here we show that these changes in natural systems since at least 1970 are occurring in regions of observed temperature increases, and that these temperature increases at continental scales cannot be explained by natural climate variations alone. Given the conclusions from the Intergovernmental Panel on Climate Change (IPCC) Fourth Assessment Report that most of the observed increase in global average temperatures since the mid-twentieth century is very likely to be due to the observed increase in anthropogenic greenhouse gas concentrations, and furthermore that it is likely that there has been significant anthropogenic warming over the past 50 years averaged over each continent except Antarctica, we conclude that anthropogenic climate change is having a significant impact on physical and biological systems globally and in some continents.}, } @article {pmid18479203, year = {2008}, author = {Field, D and Sansone, SA and Garrity, GM}, title = {Foreword to the special issue on the Fifth Genomic Standards consortium workshop.}, journal = {Omics : a journal of integrative biology}, volume = {12}, number = {2}, pages = {99}, doi = {10.1089/omi.2008.0013}, pmid = {18479203}, issn = {1536-2310}, support = {BB/E025080/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Databases, Genetic ; *Genomics ; Reference Standards ; }, } @article {pmid18478349, year = {2009}, author = {Xu, S}, title = {An approach to analyzing the intensity of the daytime surface urban heat island effect at a local scale.}, journal = {Environmental monitoring and assessment}, volume = {151}, number = {1-4}, pages = {289-300}, doi = {10.1007/s10661-008-0270-1}, pmid = {18478349}, issn = {1573-2959}, mesh = {China ; *Cities ; Environmental Monitoring/*methods ; Geographic Information Systems ; Humans ; Satellite Communications ; *Sunlight ; Surface Properties ; }, abstract = {A landscape index LI is proposed to evaluate the intensity of the daytime surface urban heat island (SUHI) effect at a local scale. Three aspects of this landscape index are crucial: the source landscape, the sink landscape, and the contribution of source and sink landscapes to the intensity of the SUHI. Source and sink landscape types are identified using the thermo-band of Landsat 7 with a spatial resolution of 60 m, along with appropriate threshold values for the Normalized Difference Vegetation Index, Modified Normalized Difference Water Index, and Normalized Difference Built-up Index. The landscape index was defined as the ratio of the contributions of the source and sink landscapes to the intensity of the SUHI. The intensity of the daytime SUHI is assessed with the help of the landscape index. Our analysis indicates the landscape index can be used to evaluate and compare the intensity of the daytime SUHI for different areas.}, } @article {pmid18469216, year = {2008}, author = {Wang, XT}, title = {Risk communication and risky choice in context: ambiguity and ambivalence hypothesis.}, journal = {Annals of the New York Academy of Sciences}, volume = {1128}, number = {}, pages = {78-89}, doi = {10.1196/annals.1399.009}, pmid = {18469216}, issn = {0077-8923}, mesh = {Adult ; Age Factors ; Biological Evolution ; Choice Behavior ; *Communication ; *Decision Making ; Decision Support Techniques ; Ecology ; Humans ; Middle Aged ; Models, Biological ; Models, Theoretical ; *Risk ; Risk Assessment ; Risk-Taking ; }, abstract = {This chapter takes a synthetic approach to six related lines of research on decision making at risk and views risky choice as a function of cue use with priorities in the context of risk communication. An evolutionary analysis of risk and risk communication is presented in which risk is defined not only as variance in monetary payoff but also as variance in biological relatedness, social relations, and ultimately in reproductive fitness. Empirical evidence of ecological and social significance embedded in risk messages is analyzed, and how these risk cues affect behavioral decision making is examined. A new explanatory framework, the ambiguity and ambivalence hypothesis, identifies two key preconditions contributing to inconsistency and biases in making risky choices as a result of cue use in the course of risk communication.}, } @article {pmid18464787, year = {2008}, author = {Field, D and Garrity, G and Gray, T and Morrison, N and Selengut, J and Sterk, P and Tatusova, T and Thomson, N and Allen, MJ and Angiuoli, SV and Ashburner, M and Axelrod, N and Baldauf, S and Ballard, S and Boore, J and Cochrane, G and Cole, J and Dawyndt, P and De Vos, P and DePamphilis, C and Edwards, R and Faruque, N and Feldman, R and Gilbert, J and Gilna, P and Glöckner, FO and Goldstein, P and Guralnick, R and Haft, D and Hancock, D and Hermjakob, H and Hertz-Fowler, C and Hugenholtz, P and Joint, I and Kagan, L and Kane, M and Kennedy, J and Kowalchuk, G and Kottmann, R and Kolker, E and Kravitz, S and Kyrpides, N and Leebens-Mack, J and Lewis, SE and Li, K and Lister, AL and Lord, P and Maltsev, N and Markowitz, V and Martiny, J and Methe, B and Mizrachi, I and Moxon, R and Nelson, K and Parkhill, J and Proctor, L and White, O and Sansone, SA and Spiers, A and Stevens, R and Swift, P and Taylor, C and Tateno, Y and Tett, A and Turner, S and Ussery, D and Vaughan, B and Ward, N and Whetzel, T and San Gil, I and Wilson, G and Wipat, A}, title = {The minimum information about a genome sequence (MIGS) specification.}, journal = {Nature biotechnology}, volume = {26}, number = {5}, pages = {541-547}, pmid = {18464787}, issn = {1546-1696}, support = {BB/E025080/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; G8225539/MRC_/Medical Research Council/United Kingdom ; U54 HG004028/HG/NHGRI NIH HHS/United States ; Z99 LM999999/ImNIH/Intramural NIH HHS/United States ; }, mesh = {Chromosome Mapping/*methods/*standards ; Databases, Factual/*standards ; Information Dissemination/*methods ; Information Storage and Retrieval/*standards ; *Information Theory ; Internationality ; }, abstract = {With the quantity of genomic data increasing at an exponential rate, it is imperative that these data be captured electronically, in a standard format. Standardization activities must proceed within the auspices of open-access and international working bodies. To tackle the issues surrounding the development of better descriptions of genomic investigations, we have formed the Genomic Standards Consortium (GSC). Here, we introduce the minimum information about a genome sequence (MIGS) specification with the intent of promoting participation in its development and discussing the resources that will be required to develop improved mechanisms of metadata capture and exchange. As part of its wider goals, the GSC also supports improving the 'transparency' of the information contained in existing genomic databases.}, } @article {pmid18460446, year = {2008}, author = {Grus, WE and Zhang, J}, title = {Distinct evolutionary patterns between chemoreceptors of 2 vertebrate olfactory systems and the differential tuning hypothesis.}, journal = {Molecular biology and evolution}, volume = {25}, number = {8}, pages = {1593-1601}, pmid = {18460446}, issn = {1537-1719}, support = {R01 GM080285/GM/NIGMS NIH HHS/United States ; T32 HG000040/HG/NHGRI NIH HHS/United States ; R01GM80285/GM/NIGMS NIH HHS/United States ; T32HG000040/HG/NHGRI NIH HHS/United States ; }, mesh = {Animals ; Chemoreceptor Cells/*cytology ; Computational Biology ; *Evolution, Molecular ; *Phylogeny ; Receptors, Pheromone/*genetics ; Smell/*genetics/physiology ; Species Specificity ; Vertebrates/*genetics ; Vomeronasal Organ/*cytology ; }, abstract = {Most tetrapod vertebrates have 2 olfactory systems, the main olfactory system (MOS) and the vomeronasal system (VNS). According to the dual olfactory hypothesis, the MOS detects environmental odorants, whereas the VNS recognizes intraspecific pheromonal cues. However, this strict functional distinction has been blurred by recent reports that both systems can perceive both types of signals. Studies of a limited number of receptors suggest that MOS receptors are broadly tuned generalists, whereas VNS receptors are narrowly tuned specialists. However, whether this distinction applies to all MOS and VNS receptors remains unknown. The differential tuning hypothesis predicts that generalist MOS receptors detect an overlapping set of ligands and thus are more likely to be conserved over evolutionary time than specialist VNS receptors, which would evolve in a more lineage-specific manner. Here we test this prediction for all olfactory chemoreceptors by examining the evolutionary patterns of MOS-expressed odorant receptors (ORs) and trace amine-associated receptors (TAARs) and VNS-expressed vomeronasal type 1 receptors (V1Rs) and vomeronasal type 2 receptors (V2Rs) in 7 tetrapods (mouse, rat, dog, opossum, platypus, chicken, and frog). The phylogenies of V1Rs and V2Rs show abundant lineage-specific gene gains/losses and virtually no one-to-one orthologs between species. Opposite patterns are found for ORs and TAARs. Analysis of functional data and ligand-binding sites of ORs confirms that paralogous chemoreceptors are more likely than orthologs to have different ligands and that functional divergence between paralogous chemoreceptors is established relatively quickly following gene duplication. Together, these results strongly suggest that the functional profile of the VNS chemoreceptor repertoire evolves much faster than that of the MOS chemoreceptor repertoire and that the differential tuning hypothesis applies to the majority, if not all, of MOS and VNS receptors.}, } @article {pmid18447932, year = {2008}, author = {Allpress, JL and Curry, RJ and Hanchette, CL and Phillips, MJ and Wilcosky, TC}, title = {A GIS-based method for household recruitment in a prospective pesticide exposure study.}, journal = {International journal of health geographics}, volume = {7}, number = {}, pages = {18}, pmid = {18447932}, issn = {1476-072X}, support = {R21 CA094717/CA/NCI NIH HHS/United States ; 5R21CA094717-02/CA/NCI NIH HHS/United States ; }, mesh = {*Atrazine ; *Crops, Agricultural ; Environmental Exposure/*analysis ; Family Characteristics ; *Geographic Information Systems ; Humans ; Illinois ; Maps as Topic ; *Patient Selection ; *Pesticides ; Photography ; Prospective Studies ; Sampling Studies ; *Zea mays ; }, abstract = {BACKGROUND: Recent advances in GIS technology and remote sensing have provided new opportunities to collect ecologic data on agricultural pesticide exposure. Many pesticide studies have used historical or records-based data on crops and their associated pesticide applications to estimate exposure by measuring residential proximity to agricultural fields. Very few of these studies collected environmental and biological samples from study participants. One of the reasons for this is the cost of identifying participants who reside near study fields and analyzing samples obtained from them. In this paper, we present a cost-effective, GIS-based method for crop field selection and household recruitment in a prospective pesticide exposure study in a remote location. For the most part, our multi-phased approach was carried out in a research facility, but involved two brief episodes of fieldwork for ground truthing purposes. This method was developed for a larger study designed to examine the validity of indirect pesticide exposure estimates by comparing measured exposures in household dust, water and urine with records-based estimates that use crop location, residential proximity and pesticide application data. The study focused on the pesticide atrazine, a broadleaf herbicide used in corn production and one of the most widely-used pesticides in the U.S.

RESULTS: We successfully used a combination of remotely-sensed data, GIS-based methods and fieldwork to select study fields and recruit participants in Illinois, a state with high corn production and heavy atrazine use. Our several-step process consisted of the identification of potential study fields and residential areas using aerial photography; verification of crop patterns and land use via site visits; development of a GIS-based algorithm to define recruitment areas around crop fields; acquisition of geocoded household-level data within each recruitment area from a commercial vendor; and confirmation of final participant household locations via ground truthing. The use of these procedures resulted in a sufficient sample of participants from 14 recruitment areas in seven Illinois counties.

CONCLUSION: One of the challenges in pesticide research is the identification and recruitment of study participants, which is time consuming and costly, especially when the study site is in a remote location. We have demonstrated how GIS-based processes can be used to recruit participants, increase efficiency and enhance accuracy. The method that we used ultimately made it possible to collect biological samples from a specific demographic group within strictly defined exposure areas, with little advance knowledge of the location or population.}, } @article {pmid18441406, year = {2008}, author = {Twumasi, YA and Merem, EC}, title = {Geospatial information systems analysis of regional environmental change along the Savannah River Basin of Georgia.}, journal = {International journal of environmental research and public health}, volume = {5}, number = {1}, pages = {54-67}, pmid = {18441406}, issn = {1660-4601}, mesh = {Agriculture ; *Conservation of Natural Resources ; *Environment ; Environmental Monitoring ; *Geographic Information Systems ; Georgia ; Human Activities ; Industry ; Rivers ; Time Factors ; Water Pollution/prevention & control ; }, abstract = {This paper uses remote sensing and geographic information systems (GIS); and descriptive statistics in the assessment of environmental change along the Savannah River Basin of Georgia. Results of the study show that Savannah River basin side of Georgia has been experiencing environmental change due to several decades of relentless pressure induced by anthropocentric activities and host of other socio-economic factors. Normalized Difference Vegetation Index (NDVI) analysis of the area also shows a decline in vegetation cover. The pace of ecological change showed some variations across time and space. Generally, the results point to a decline in water bodies, vegetation, and increase in population, loss of harvested cropland, farms and increasing threats to the environmental systems of the region.}, } @article {pmid18441115, year = {2008}, author = {Schoenfeld, T and Patterson, M and Richardson, PM and Wommack, KE and Young, M and Mead, D}, title = {Assembly of viral metagenomes from yellowstone hot springs.}, journal = {Applied and environmental microbiology}, volume = {74}, number = {13}, pages = {4164-4174}, pmid = {18441115}, issn = {1098-5336}, support = {R43 HG002714/HG/NHGRI NIH HHS/United States ; 1 R43 HG002714-01/HG/NHGRI NIH HHS/United States ; }, mesh = {Computational Biology ; DNA, Viral/analysis/isolation & purification ; Gene Library ; *Genome, Viral ; Genomics ; Hot Springs/*virology ; Microscopy, Electron, Transmission ; Pyrobaculum/virology ; Virion/isolation & purification/ultrastructure ; Viruses/*classification/genetics/*isolation & purification ; Wyoming ; }, abstract = {Thermophilic viruses were reported decades ago; however, knowledge of their diversity, biology, and ecological impact is limited. Previous research on thermophilic viruses focused on cultivated strains. This study examined metagenomic profiles of viruses directly isolated from two mildly alkaline hot springs, Bear Paw (74 degrees C) and Octopus (93 degrees C). Using a new method for constructing libraries from picograms of DNA, nearly 30 Mb of viral DNA sequence was determined. In contrast to previous studies, sequences were assembled at 50% and 95% identity, creating composite contigs up to 35 kb and facilitating analysis of the inherent heterogeneity in the populations. Lowering the assembly identity reduced the estimated number of viral types from 1,440 and 1,310 to 548 and 283, respectively. Surprisingly, the diversity of viral species in these springs approaches that in moderate-temperature environments. While most known thermophilic viruses have a chronic, nonlytic infection lifestyle, analysis of coding sequences suggests lytic viruses are more common in geothermal environments than previously thought. The 50% assembly included one contig with high similarity and perfect synteny to nine genes from Pyrobaculum spherical virus (PSV). In fact, nearly all the genes of the 28-kb genome of PSV have apparent homologs in the metagenomes. Similarities to thermoacidophilic viruses isolated on other continents were limited to specific open reading frames but were equally strong. Nearly 25% of the reads showed significant similarity between the hot springs, suggesting a common subterranean source. To our knowledge, this is the first application of metagenomics to viruses of geothermal origin.}, } @article {pmid18440951, year = {2008}, author = {Liao, BY and Zhang, J}, title = {Coexpression of linked genes in Mammalian genomes is generally disadvantageous.}, journal = {Molecular biology and evolution}, volume = {25}, number = {8}, pages = {1555-1565}, pmid = {18440951}, issn = {1537-1719}, support = {R01 GM067030/GM/NIGMS NIH HHS/United States ; R01 GM080285/GM/NIGMS NIH HHS/United States ; }, mesh = {Computational Biology ; *Evolution, Molecular ; Gene Expression Profiling ; *Gene Expression Regulation ; *Genetic Linkage ; Genome, Human/*genetics ; Humans ; Microarray Analysis ; *Models, Genetic ; }, abstract = {Similarity in gene expression pattern between closely linked genes is known in several eukaryotes. Two models have been proposed to explain the presence of such coexpression patterns. The adaptive model assumes that coexpression is advantageous and is established by relocation of initially unlinked but coexpressed genes, whereas the neutral model asserts that coexpression is a type of leaky expression due to similar expressional environments of linked genes, but is neither advantageous nor detrimental. However, these models are incompatible with several empirical observations. Here, we propose that coexpression of linked genes is a form of transcriptional interference that is disadvantageous to the organism. We show that even distantly linked genes that are tens of megabases away exhibit significant coexpression in the human genome. However, the linkage is more likely to be broken during evolution between genes of high coexpression than those of low coexpression and the breakage of linkage reduces gene coexpression. These results support our hypothesis that coexpression of linked genes in mammalian genomes is generally disadvantageous, implying that many mammalian genes may never reach their optimal expression pattern due to the interference of their genomic environment and that such transcriptional interference may be a force promoting recurrent relocation of genes in the genome.}, } @article {pmid18435233, year = {2008}, author = {Ide, R and Mizoue, T and Yamamoto, R and Tsuneoka, M}, title = {Development of a shortened Japanese version of the Oral Health Impact Profile (OHIP) for young and middle-aged adults.}, journal = {Community dental health}, volume = {25}, number = {1}, pages = {38-43}, pmid = {18435233}, issn = {0265-539X}, mesh = {Activities of Daily Living ; Adult ; Attitude to Health ; Cross-Sectional Studies ; Data Interpretation, Statistical ; Eating/physiology ; Female ; Health Status ; Humans ; Interpersonal Relations ; Japan ; Male ; Middle Aged ; *Oral Health ; Outcome Assessment, Health Care ; Pain/classification ; *Quality of Life ; Reproducibility of Results ; Social Behavior ; Speech/physiology ; Surveys and Questionnaires ; }, abstract = {OBJECTIVE: The aim of this paper is to develop a short version of the Japanese OHIP (OHIP-J) appropriate for use in young and middle-aged adults, and to evaluate its properties using cross-sectional data.

METHOD: A study population of 8,658 workers aged 20-59 years rated their oral health by means of a self-administered questionnaire. Using a factor analysis approach, a shortened version of OHIP-J was derived. Internal consistency, floor effect, and construct validity were determined.

RESULTS: We derived a subset of 18 items from OHIP-J (OHIP-JA18), grouped into four subscales: "functional limitation", "physical pain", "psychological discomfort", and "disability & handicap". All four subscales had acceptable internal consistency (Cronbach alpha > 0.79). OHIP-JA18 demonstrated an acceptable floor effect, which was determined by the proportion of subjects who obtained a 0 score (< 30%); however, the floor effect of the ordinary shortened version based on OHIP-14 (OHIP-J14) was not acceptable. We confirmed the conceptual framework of OHIP-JA18 that "disability & handicap" is affected by "functional limitation", "physical pain" and "psychological discomfort", because the model fitted the data moderately well by structural equation modeling (SEM) analysis (GFI = 0.90, RMSEA = 0.08).

CONCLUSIONS: OHIP-JA18 demonstrated acceptable measurement parameters to justify its use in outcome assessment for oral health related quality of life (OHQOL) in young and middle-aged adults in Japanese workers. Further studies will be needed to evaluate an intervention such as worksite health promotion.}, } @article {pmid18424089, year = {2008}, author = {Pleijel, F and Jondelius, U and Norlinder, E and Nygren, A and Oxelman, B and Schander, C and Sundberg, P and Thollesson, M}, title = {Phylogenies without roots? A plea for the use of vouchers in molecular phylogenetic studies.}, journal = {Molecular phylogenetics and evolution}, volume = {48}, number = {1}, pages = {369-371}, doi = {10.1016/j.ympev.2008.03.024}, pmid = {18424089}, issn = {1095-9513}, mesh = {Animals ; Classification/*methods ; Databases, Nucleic Acid/*standards ; Molecular Sequence Data ; *Phylogeny ; Plants/classification/genetics ; }, } @article {pmid18420375, year = {2008}, author = {Garcia, JA and Bartumeus, F and Roche, D and Giraldo, J and Stanley, HE and Casamayor, EO}, title = {Ecophysiological significance of scale-dependent patterns in prokaryotic genomes unveiled by a combination of statistic and genometric analyses.}, journal = {Genomics}, volume = {91}, number = {6}, pages = {538-543}, doi = {10.1016/j.ygeno.2008.03.001}, pmid = {18420375}, issn = {1089-8646}, mesh = {Archaea/genetics/*physiology ; *Bacterial Physiological Phenomena ; Chromosomes, Archaeal/genetics ; Chromosomes, Bacterial/genetics ; Data Interpretation, Statistical ; *Ecology ; Genetic Variation ; *Genome, Archaeal ; *Genome, Bacterial ; Phylogeny ; Sequence Analysis, DNA/*methods/*statistics & numerical data ; }, abstract = {We combined genometric (DNA walks) and statistical (detrended fluctuation analysis) methods on 456 prokaryotic chromosomes from 309 different bacterial and archaeal species to look for specific patterns and long-range correlations along the genome and relate them to ecological lifestyles. The position of each nucleotide along the complete genome sequence was plotted on an orthogonal plane (DNA landscape), and fluctuation analysis applied to the DNA walk series showed a long-range correlation in contrast to the lack of correlation for artificially generated genomes. Different features in the DNA landscapes among genomes from different ecological and metabolic groups of prokaryotes appeared with the combined analysis. Transition from hyperthermophilic to psychrophilic environments could have been related to more complex structural adaptations in microbial genomes, whereas for other environmental factors such as pH and salinity this effect would have been smaller. Prokaryotes with domain-specific metabolisms, such as photoautotrophy in Bacteria and methanogenesis in Archaea, showed consistent differences in genome correlation structure. Overall, we show that, beyond the relative proportion of nucleotides, correlation properties derived from their sequential position within the genome hide relevant phylogenetic and ecological information. This can be studied by combining genometric and statistical physics methods, leading to a reduction of genome complexity to a few useful descriptors.}, } @article {pmid18419657, year = {2008}, author = {Roca, E and Gamboa, G and Tàbara, JD}, title = {Assessing the multidimensionality of coastal erosion risks: public participation and multicriteria analysis in a Mediterranean coastal system.}, journal = {Risk analysis : an official publication of the Society for Risk Analysis}, volume = {28}, number = {2}, pages = {399-412}, doi = {10.1111/j.1539-6924.2008.01026.x}, pmid = {18419657}, issn = {1539-6924}, mesh = {*Community Participation ; *Decision Support Techniques ; Ecosystem ; *Environment ; Feasibility Studies ; France ; Humans ; Interviews as Topic ; Oceans and Seas ; *Policy Making ; Risk ; *Risk Assessment ; }, abstract = {The complex and multidimensional nature of coastal erosion risks makes it necessary to move away from single-perspective assessment and management methods that have conventionally predominated in coastal management. This article explores the suitability of participatory multicriteria analysis (MCA) for improving the integration of diverse expertises and values and enhancing the social-ecological robustness of the processes that lead to the definition of relevant policy options to deal with those risks. We test this approach in the Mediterranean coastal locality of Lido de Sète in France. Results show that the more adaptive alternatives such as "retreating the shoreline" were preferred by our selected stakeholders to those corresponding to "protecting the shoreline" and the business as usual proposals traditionally put forward by experts and policymakers on these matters. Participative MCA contributed to represent coastal multidimensionality, elicit and integrate different views and preferences, facilitated knowledge exchange, and allowed highlighting existing uncertainties.}, } @article {pmid18419085, year = {2008}, author = {Liu, XY and Liang, TG and Guo, ZG and Zhang, XT}, title = {[Early warning and risk assessment of snow disaster in pastoral area of northern Xinjiang].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {19}, number = {1}, pages = {133-138}, pmid = {18419085}, issn = {1001-9332}, mesh = {Animals ; Animals, Domestic ; China ; *Disasters ; Ecology/methods/trends ; Environmental Monitoring/*methods ; Forecasting ; Geographic Information Systems ; Models, Theoretical ; Poaceae/*growth & development ; Risk Assessment ; Satellite Communications ; *Snow ; }, abstract = {Based on the analysis of animal husbandry production and of distribution characteristics of snow disaster in northern Xinjiang, and by using RS and GIS techniques and field survey data, 9 early warning factors were selected from the three subsystems of grassland' s disaster-resistant capability, livestock's disaster-bearing capacity, and disaster-causing potential, and the death rate of livestock caused by snow disaster was used as a factor of risk assessment. An index system of snow disaster' s early warning and risk assessment for completely grazing grassland was established, and the early warning model of snow disaster, its distinguishing model, and risk assessment model were built by using multi-hierarchical synthetic and multi-objective linear weight function methods to predict the resistant capability of grassland and livestock against snow disaster, and to assess the potential risk loss from snow disaster in northern Xinjiang. The accuracy of the early warning model and risk assessment model was 85% and 72% , respectively.}, } @article {pmid18419084, year = {2008}, author = {Wang, H and Wang, TM and Yang, MB and Xiong, YC and Sun, TT and Shi, GJ and Ge, JP}, title = {[Quantitative monitoring of gully erosion in hilly-gully area of Loess Plateau based on aerial images].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {19}, number = {1}, pages = {127-132}, pmid = {18419084}, issn = {1001-9332}, mesh = {China ; Conservation of Natural Resources ; Ecology/*methods ; Ecosystem ; Environmental Monitoring/*methods ; *Geographic Information Systems ; Geologic Sediments/*analysis/chemistry ; Models, Theoretical ; Soil/analysis ; }, abstract = {Based on the aerial photographs in 1979 and 1993, and by using geographical information system (GIS) techniques, the digital elevation models (DEM) and digital orthophoto map (DOM) were constructed from the geomorphic changes in a chosen gully in the Loess hilly-gully area, and the spatial difference of the changes and their key affecting factors were analyzed. The results indicated that from 1979 to 1993, the gully head advanced actively (with a length of 8.5 meters and an erosion rate of 481.28 t x hm(-2) x a(-1)), and the slope tended to become steeper, exhibiting a high erosion risk. The middle part of the gully had the largest newly eroded area and the highest erosion rate, and the erosion process was quite active, with the highest erosion risk. The water outlet was primarily endowed with deposition formation, whose eroded area was smaller than its deposition area, and the gully depth and slope were becoming less, with a lower erosion risk.}, } @article {pmid18419066, year = {2008}, author = {Tang, LN and Wang, QL and Dai, LM and Shao, GF}, title = {[Ecological classification system of forest landscape in eastern mountainous region of Liaoning Province].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {19}, number = {1}, pages = {20-24}, pmid = {18419066}, issn = {1001-9332}, mesh = {Altitude ; China ; Conservation of Natural Resources/*methods ; Ecology/methods ; *Ecosystem ; *Environment Design ; Environmental Monitoring ; Geographic Information Systems ; Geography ; Satellite Communications ; Trees/classification/*growth & development ; }, abstract = {Based on Digital Elevation Models (DEM) and satellite SPOT-5 data, and by using the spatial analysis function in Geographic Information System, a hierachical Ecological Classification System of forest landscape was developed for the eastern mountainous region of Liaoning Province, and the two lowest layers in the hierachical framework, Ecological Land Types (ELTs) and Ecological Land Type Phases (ELTPs), were mapped. The results indicated that there were 5 ELTs and 34 ELTPs. The boundaries of ELTs, which presented the potential vegetation distribution and potential forestry ecosystem productivity, were determined by environmental conditions quantified by DEM. ELTPs were classified by overlaying ELTs with forest vegetation data layers which were obtained from remotely sensed data, forest inventory data, and ground data. The ELTPs represented the divisions of land in terms of both natural and human-induced forest conditions, and therefore, were reliable units for forest inventories and management. ELTPs could function as conventional forest inventory sub-compartments. By this means, forestry departments could adjust forest management planning and forest management measures from the viewpoint of forest landscape scale to realize forest ecosystem management.}, } @article {pmid18417455, year = {2008}, author = {Liow, LH and Fortelius, M and Bingham, E and Lintulaakso, K and Mannila, H and Flynn, L and Stenseth, NC}, title = {Higher origination and extinction rates in larger mammals.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {105}, number = {16}, pages = {6097-6102}, pmid = {18417455}, issn = {1091-6490}, mesh = {Animals ; *Biological Evolution ; Databases, Factual ; *Extinction, Biological ; *Fossils ; *Mammals ; }, abstract = {Do large mammals evolve faster than small mammals or vice versa? Because the answer to this question contributes to our understanding of how life-history affects long-term and large-scale evolutionary patterns, and how microevolutionary rates scale-up to macroevolutionary rates, it has received much attention. A satisfactory or consistent answer to this question is lacking, however. Here, we take a fresh look at this problem using a large fossil dataset of mammals from the Neogene of the Old World (NOW). Controlling for sampling biases, calculating per capita origination and extinction rates of boundary-crossers and estimating survival probabilities using capture-mark-recapture (CMR) methods, we found the recurring pattern that large mammal genera and species have higher origination and extinction rates, and therefore shorter durations. This pattern is surprising in the light of molecular studies, which show that smaller animals, with their shorter generation times and higher metabolic rates, have greater absolute rates of evolution. However, higher molecular rates do not necessarily translate to higher taxon rates because both the biotic and physical environments interact with phenotypic variation, in part fueled by mutations, to affect origination and extinction rates. To explain the observed pattern, we propose that the ability to evolve and maintain behavior such as hibernation, torpor and burrowing, collectively termed "sleep-or-hide" (SLOH) behavior, serves as a means of environmental buffering during expected and unexpected environmental change. SLOH behavior is more common in some small mammals, and, as a result, SLOH small mammals contribute to higher average survivorship and lower origination probabilities among small mammals.}, } @article {pmid18416713, year = {2008}, author = {Jones, OR and Clutton-Brock, T and Coulson, T and Godfray, HC}, title = {A web resource for the UK's long-term individual-based time-series (LITS) data.}, journal = {The Journal of animal ecology}, volume = {77}, number = {3}, pages = {612-615}, doi = {10.1111/j.1365-2656.2008.01382.x}, pmid = {18416713}, issn = {1365-2656}, mesh = {Animals ; *Databases, Factual/ethics ; Ecology ; Female ; *Internet ; Male ; United Kingdom ; Vertebrates ; }, } @article {pmid18413327, year = {2008}, author = {Guillot, G and Santos, F and Estoup, A}, title = {Analysing georeferenced population genetics data with Geneland: a new algorithm to deal with null alleles and a friendly graphical user interface.}, journal = {Bioinformatics (Oxford, England)}, volume = {24}, number = {11}, pages = {1406-1407}, doi = {10.1093/bioinformatics/btn136}, pmid = {18413327}, issn = {1367-4811}, mesh = {*Algorithms ; Computer Graphics ; Computer Simulation ; *Databases, Genetic ; Gene Frequency/*genetics ; Genetics, Population/*methods ; *Geographic Information Systems ; *Models, Genetic ; *Software ; *User-Computer Interface ; }, abstract = {UNLABELLED: We introduce a new algorithm to account for the presence of null alleles in inferences of populations clusters from individual multilocus genetic data. We show by simulations that the presence of null alleles can affect the accuracy of inferences if not properly accounted for and that our algorithm improve signficantly their accuracy.

AVAILABILITY: This new algorithm is implemented in the program Geneland. It is freely available under GNU public license as an R package on the Comprehensive R Archive Network. It now includes a fully clickable graphical interface. Informations on how to get the software are available on folk.uio.no/gillesg/Geneland.html}, } @article {pmid18412551, year = {2008}, author = {Dupont, CL and Neupane, K and Shearer, J and Palenik, B}, title = {Diversity, function and evolution of genes coding for putative Ni-containing superoxide dismutases.}, journal = {Environmental microbiology}, volume = {10}, number = {7}, pages = {1831-1843}, doi = {10.1111/j.1462-2920.2008.01604.x}, pmid = {18412551}, issn = {1462-2920}, mesh = {Computational Biology/*methods ; Databases, Genetic ; *Evolution, Molecular ; Marine Biology ; Molecular Sequence Data ; Nickel/chemistry/*metabolism ; Streptomyces/*enzymology/genetics ; Structural Homology, Protein ; Superoxide Dismutase/chemistry/*classification/genetics/metabolism ; }, abstract = {We examined the phylogenetic distribution, functionality and evolution of the sodN gene family, which has been shown to code for a unique Ni-containing isoform of superoxide dismutase (Ni-SOD) in Streptomyces. Many of the putative sodN sequences retrieved from public domain genomic and metagenomic databases are quite divergent from structurally and functionally characterized Ni-SOD. Structural bioinformatics studies verified that the divergent members of the sodN protein family code for similar three-dimensional structures and identified evolutionarily conserved amino acid residues. Structural and biochemical studies of the N-terminus 'Ni-hook' motif coded for by the putative sodN sequences confirmed both Ni (II) ligating and superoxide dismutase activity. Both environmental and organismal genomes expanded the previously noted phylogenetic distribution of sodN, and the sequences form four well-separated clusters, with multiple subclusters. The phylogenetic distribution of sodN suggests that the gene has been acquired via horizontal gene transfer by numerous organisms of diverse phylogenetic background, including both Eukaryotes and Prokaryotes. The presence of sodN correlates with the genomic absence of the gene coding for Fe-SOD, a structurally and evolutionarily distinct isoform of SOD. Given the low levels of Fe found in the marine environment from where many sequences were attained, we suggest that the replacement of Fe-SOD with Ni-SOD may be an evolutionary adaptation to reduce iron requirements.}, } @article {pmid18409014, year = {2009}, author = {Fang, SB and Zhang, XS and Jia, XB and An, SQ and Zhou, CF and Xu, C}, title = {Evaluation of potential habitat with an integrated analysis of a spatial conservation strategy for David's deer, Elaphurus davidians.}, journal = {Environmental monitoring and assessment}, volume = {150}, number = {1-4}, pages = {455-468}, pmid = {18409014}, issn = {1573-2959}, mesh = {Animals ; China ; *Conservation of Natural Resources ; *Deer ; *Ecosystem ; Extinction, Biological ; Geographic Information Systems ; Humans ; Risk Assessment ; Satellite Communications ; Wetlands ; }, abstract = {How to assess the potential habitat integrating landscape dynamics and population research, and how to reintroduce animals to potential habitats in environments highly human disturbed are still questions to be answered in conservation biology. According to behavioral research on Elaphurus davidians, we have developed a suitability index and a risk index to evaluate the potential habitats for the deer. With these indices, we conducted two transect assessments to evaluate the gradient change of the target region. Then, taking rivers as border lines, we tabulated the forest areas, high grassland area and total area and then compared the forest and high grassland area in each subregion. Furthermore, we computed the land use transfer matrix for the whole Yancheng coast during 1987-2000. We also computed human modified index (HMI) in six subregions. Lastly with a geographical information system support we obtained the spatial distribution of the indices and evaluation of the whole potential habitats from a neighborhood analysis. The transect assessment showed that the suitability of the coastal area was higher than that of the inland area for the deer, while the southern area was higher than the northern. Landscape metrics and HMI analysis showed that different landscape patterns and different anthropogenic disturbance existed within the region, and the increasing human disturbance was the key factor causing the pattern dynamics. The evaluation of potential habitats showed that there was an estimated carrying capacity of no more than 10,000 for David's deer reintroduction into the natural area. Also the reintroduction strategy was discussed. This integrated approach linked the population research and the landscape metrics, and the dataset with different scale; thus, it is an approach likely to be useful for the protection of other large animal in a landscape highly disturbed by humans.}, } @article {pmid18407745, year = {2008}, author = {Gil, IS and Sheldon, W and Schmidt, T and Servilla, M and Aguilar, R and Gries, C and Gray, T and Field, D and Cole, J and Pan, JY and Palanisamy, G and Henshaw, D and O'Brien, M and Kinkel, L and McMahon, K and Kottmann, R and Amaral-Zettler, L and Hobbie, J and Goldstein, P and Guralnick, RP and Brunt, J and Michener, WK}, title = {Defining linkages between the GSC and NSF's LTER program: how the Ecological Metadata Language (EML) relates to GCDML and other outcomes.}, journal = {Omics : a journal of integrative biology}, volume = {12}, number = {2}, pages = {151-156}, doi = {10.1089/omi.2008.0015}, pmid = {18407745}, issn = {1536-2310}, mesh = {*Databases, Genetic ; Genome ; *Programming Languages ; }, abstract = {The Genomic Standards Consortium (GSC) invited a representative of the Long-Term Ecological Research (LTER) to its fifth workshop to present the Ecological Metadata Language (EML) metadata standard and its relationship to the Minimum Information about a Genome/Metagenome Sequence (MIGS/MIMS) and its implementation, the Genomic Contextual Data Markup Language (GCDML). The LTER is one of the top National Science Foundation (NSF) programs in biology since 1980, representing diverse ecosystems and creating long-term, interdisciplinary research, synthesis of information, and theory. The adoption of EML as the LTER network standard has been key to build network synthesis architectures based on high-quality standardized metadata. EML is the NSF-recognized metadata standard for LTER, and EML is a criteria used to review the LTER program progress. At the workshop, a potential crosswalk between the GCDML and EML was explored. Also, collaboration between the LTER and GSC developers was proposed to join efforts toward a common metadata cataloging designer's tool. The community adoption success of a metadata standard depends, among other factors, on the tools and trainings developed to use the standard. LTER's experience in embracing EML may help GSC to achieve similar success. A possible collaboration between LTER and GSC to provide training opportunities for GCDML and the associated tools is being explored. Finally, LTER is investigating EML enhancements to better accommodate genomics data, possibly integrating the GCDML schema into EML. All these action items have been accepted by the LTER contingent, and further collaboration between the GSC and LTER is expected.}, } @article {pmid18404409, year = {2009}, author = {Gulgun, B and Yörük, I and Turkyilmaz, B and Bolca, M and Güneş, A}, title = {Determination of the effects of temporal change in urban and agricultural land uses as seen in the example of the town of Akhisar, using remote sensing techniques.}, journal = {Environmental monitoring and assessment}, volume = {150}, number = {1-4}, pages = {427-436}, doi = {10.1007/s10661-008-0241-6}, pmid = {18404409}, issn = {1573-2959}, mesh = {City Planning/*methods ; *Conservation of Natural Resources ; Female ; Geographic Information Systems ; Humans ; Photography/methods ; Population Dynamics ; Satellite Communications ; Turkey ; *Urbanization ; }, abstract = {Today, as a result of erratic and unplanned urbanization, towns are rapidly becoming a mass of concrete and town-dwellers are suffocated by their busy and stressful professional lives. They feel a need for places where they can find breathing-space in their free time. Green areas within towns are important spaces where townspeople are able to carry out recreational activities. These places form a link between townspeople and nature. The importance of urban green areas is increasing with every passing day due to their social, psychological, ecological, physical and economic functions and their impact on the quality of towns. In this study it has been attempted to demonstrate the pressures of urban development on agricultural land by determining the changing land use situation over the years in the district of Akhisar. In this research, an aerial photograph from year 1939 and satellite images of the town from the years 2000 and 2007 were used. Land use changes in the region were determined spatially. As a result of this study, which aims to determine in which direction urbanization is progressing in the district, the importance of town planning emerges. This study will be informative for the local authorities in their future town planning projects. With its flat and almost flat fertile arable land, the district of Akhisar occupies an important position within the province of Manisa. From the point of view of olive production the region is one of Turkey's important centres. Fifty-five percent of the olive production in the province of Manisa is realized in Akhisar. However, the results of the present study show that while agricultural areas comprised 2.5805 km(2) in 1939, these had diminished to 1.5146 km(2) in the year 2000 and had diminished to 1.0762 km(2) in the year 2007 and residential area (dense) 0.449 km(2) occupied in 1939, in the year 2000 this had risen to 1.9472 and 2.3238 km(2) in the year 2007. This planless urbanization in the study area has led to great losses of farmland.}, } @article {pmid18397793, year = {2008}, author = {Calenge, C and Basille, M}, title = {A general framework for the statistical exploration of the ecological niche.}, journal = {Journal of theoretical biology}, volume = {252}, number = {4}, pages = {674-685}, doi = {10.1016/j.jtbi.2008.02.036}, pmid = {18397793}, issn = {1095-8541}, mesh = {Algorithms ; Animals ; *Ecosystem ; Factor Analysis, Statistical ; Geographic Information Systems ; *Models, Biological ; Population Dynamics ; Rupicapra ; }, abstract = {We propose a new statistical framework for the exploratory analysis of the ecological niche, the "General niche-environment system factor analysis" (GNESFA). The data required for this analysis are (i) a table giving the values of the environmental variables in each environment unit (EU, e.g., the patches of habitat on a vector map), (ii) a set of weights measuring the availability of the EUs to the species (e.g., the proportion of the study area covered by a given patch), and (iii) a set of utilization weights describing the use of the EUs by the focal species (e.g., the proportion of detections of the species in each patch). Each row of the table corresponds to a point in the multidimensional space defined by the environmental variables, and each point is associated with two weights. The GNESFA searches the directions in this space where the two weight distributions differ the most, choosing one distribution as the reference, and the other one as the focus. The choice of the utilization as the reference corresponds to the MADIFA (Mahalanobis distances factor analysis), which identifies the directions on which the available EUs are in average the furthest from the optimum of the niche, allowing habitat suitability modelling. The choice of the availability as the reference corresponds to the FANTER (Factor analysis of the niche, taking the environment as the reference), which identifies the directions on which the niche is the furthest from the average environment (marginality) and those on which the niche is the narrowest compared with the environment (specialization). The commonly used ENFA (Ecological niche factor analysis) is at the middle point between the MADIFA and the FANTER, considering both distributions as the reference and the focus simultaneously. When used concurrently, these three analyses allow an extensive exploration of the system.}, } @article {pmid18393595, year = {2008}, author = {Ali, M and Clemens, JD}, title = {Ecological aspects in vaccine trials.}, journal = {Expert review of vaccines}, volume = {7}, number = {3}, pages = {279-281}, doi = {10.1586/14760584.7.3.279}, pmid = {18393595}, issn = {1744-8395}, mesh = {Animals ; Clinical Trials as Topic/*methods/trends ; *Ecology/trends ; *Geographic Information Systems/trends ; Humans ; *Vaccines ; }, } @article {pmid18393577, year = {2008}, author = {Dagnino, A and Sforzini, S and Dondero, F and Fenoglio, S and Bona, E and Jensen, J and Viarengo, A}, title = {A "weight of evidence" approach for the integration of environmental "triad" data to assess ecological risk and biological vulnerability.}, journal = {Integrated environmental assessment and management}, volume = {4}, number = {3}, pages = {314-326}, doi = {10.1897/IEAM_2007-067.1}, pmid = {18393577}, issn = {1551-3777}, mesh = {Animals ; Biomarkers/analysis ; *Decision Support Techniques ; *Environmental Pollution ; Risk Assessment ; }, abstract = {A new Expert Decision Support System (EDSS) that can integrate Triad data for assessing environmental risk and biological vulnerability at contaminated sites has been developed. Starting with ecosystem relevance, the EDSS assigns different weights to the results obtained from Triad disciplines. The following parameters have been employed: 1) chemical soil analyses (revealing the presence of potentially dangerous substances), 2) ecotoxicological bioassays (utilizing classical endpoints such as survival and reproduction rates), 3) biomarkers (showing sublethal pollutant effects), and 4) ecological parameters (assessing changes in community structure and functions). For each Triad discipline, the EDSS compares the data obtained at the studied field sites with reference values and calculates different 0-1 indexes (e.g., Chemical Risk Index, Ecotoxicological Risk Index, and Ecological Risk Index). The EDSS output consists of 3 indexes: 1) Environmental Risk index (EnvRI), quantifying the levels of biological damage at population-community level, 2) Biological Vulnerability Index (BVI), assessing the potential threats to biological equilibriums, and 3) Genotoxicity Index (GTI), screening genotoxicity effects. The EDSS has been applied in the integration of a battery of Triad data obtained during the European Union-funded Life Intervention in the Fraschetta Area (LINFA) project, which has been carried out in order to estimate the potential risk from soils of a highly anthropized area (Alessandria, Italy) mainly impacted by deposition of atmospheric pollutants. Results obtained during 4 seasonal sampling campaigns (2004-2005) show maximum values of EnvRI in sites A and B (characterized by industrial releases) and lower levels in site D (affected by vehicular traffic emissions). All 3 potentially polluted sites have shown high levels of BVI and GTI, suggesting a general change from reference conditions (site C).}, } @article {pmid18393405, year = {2008}, author = {Gutierrez-Lugo, MT and Bewley, CA}, title = {Natural products, small molecules, and genetics in tuberculosis drug development.}, journal = {Journal of medicinal chemistry}, volume = {51}, number = {9}, pages = {2606-2612}, pmid = {18393405}, issn = {0022-2623}, support = {Z01 DK031135-01/ImNIH/Intramural NIH HHS/United States ; Z01 DK031136-01/ImNIH/Intramural NIH HHS/United States ; }, mesh = {Antitubercular Agents/*chemistry/pharmacology/therapeutic use ; Biological Products/*chemistry/pharmacology/therapeutic use ; Computational Biology ; Genome, Bacterial ; Genomics ; Humans ; Mycobacterium tuberculosis/drug effects/genetics ; Small Molecule Libraries ; Tuberculosis, Pulmonary/*drug therapy ; }, abstract = {The impact of natural products on the well being of mankind has been enormous, and their study continues to influence research in the fields of chemistry, biology, and ecology. Historically, the majority of our medicines originate from natural products and their synthetic derivatives, many of which have taught us valuable lessons about biology. While advances in synthetic and combinatorial chemistry have given rise to notable successes in the development of new drugs, the perceived value of natural products has not waned when it comes to treating infectious diseases. In this Miniperspective, we review the role natural products have played in the treatment of tuberculosis (TB[a]), their value and limitations as chemical probes, the challenges associated with TB drug development, and the current status of natural product and synthetic small molecules as new TB drug leads.}, } @article {pmid18386095, year = {2008}, author = {von Schalburg, KR and Leong, J and Cooper, GA and Robb, A and Beetz-Sargent, MR and Lieph, R and Holt, RA and Moore, R and Ewart, KV and Driedzic, WR and ten Hallers, BF and Zhu, B and de Jong, PJ and Davidson, WS and Koop, BF}, title = {Rainbow smelt (Osmerus mordax) genomic library and EST resources.}, journal = {Marine biotechnology (New York, N.Y.)}, volume = {10}, number = {5}, pages = {487-491}, pmid = {18386095}, issn = {1436-2228}, mesh = {Animals ; Chromosomes, Artificial, Bacterial/genetics ; Cold Temperature ; Databases, Genetic ; *Expressed Sequence Tags ; Fish Proteins/genetics ; Gene Library ; *Genomic Library ; Molecular Sequence Data ; Osmeriformes/*genetics ; }, abstract = {Genomic resources in rainbow smelt (Osmerus mordax) enable us to examine the genome duplication process in salmonids and test hypotheses relating to the fate of duplicated genes. They further enable us to pursue physiological and ecological studies in smelt. A bacterial artificial chromosome library containing 52,410 clones with an average insert size of 146 kb was constructed. This library represents an 11-fold average coverage of the rainbow smelt (O. mordax) genome. In addition, several complementary deoxyribonucleic acid libraries were constructed, and 36,758 sequences were obtained and combined into 12,159 transcripts. Over half of these transcripts have been identified, several of which have been associated with cold adaptation. These basic resources show high levels of similarity (86%) to salmonid genes and provide initial support for genome duplication in the salmonid ancestor. They also facilitate identification of genes important to fish and direct us toward new technologies for other studies in fish biology.}, } @article {pmid18385872, year = {2008}, author = {Yang, Y and He, Z and Lin, Y and Phlips, EJ and Yang, J and Chen, G and Stoffella, PJ and Powell, CA}, title = {Temporal and spatial variations of nutrients in the Ten Mile Creek of South Florida, USA and effects on phytoplankton biomass.}, journal = {Journal of environmental monitoring : JEM}, volume = {10}, number = {4}, pages = {508-516}, doi = {10.1039/b715026a}, pmid = {18385872}, issn = {1464-0325}, mesh = {Agriculture ; Biomass ; Chlorophyll/analysis ; Eutrophication ; Florida ; Geographic Information Systems ; Nitrogen/*analysis ; Pheophytins/analysis ; Phosphorus/*analysis ; Phytoplankton/*growth & development ; Rivers/*chemistry ; Seasons ; }, abstract = {Water quality throughout south Florida has been a major concern for many years. Nutrient enrichment in the Indian River Lagoon (IRL) is a major surface water issue and is suggested as a possible cause of symptoms of ecological degradation. In 2005-06, water samples were collected weekly from seven sites along Ten Mile Creek (TMC), which drains into the Indian River Lagoon, to investigate and analyze spatial and temporal fluctuations of nutrients nitrogen (N) and phosphorus (P). The objective of this study was to understand the relationships among chlorophyll a concentration, nutrient enrichment and hydrological parameters in the surface water body. High median concentrations of total P (TP, 0.272 mg L(-1)), PO4-P (0.122 mg L(-1)), and dissolved total P (DTP, 0.179 mg L(-1)); and total N (TN, 0.988 mg L(-1)), NO3(-)-N (0.104 mg L(-1)), NH4+-N (0.103 mg L(-1)), and total Kjeldahl N (TKN, 0.829 mg L(-1)), were measured in TMC. The concentrations of TP, PO4-P, DTP, TN, NO3(-)-N, NH4+-N, and TKN were higher in summer and fall than in winter and spring. However, chlorophyll a and pheophytin concentrations during this period in TMC varied in the range of 0.000-60.7 and 0.000-17.4 microg L(-1), with their median values of 3.54 and 3.02 microg L(-1), respectively. The greatest mean chlorophyll a (10.3 microg L(-1)) and pheophytin (5.71 microg L(-1)) concentrations occurred in spring, while the lowest chlorophyll a (1.49 microg L(-1)) and pheophytin (1.97 mug L(-1)) in fall. High concentrations of PO4-P (>0.16 mg L(-1)), DTP (>0.24 mg L(-1)), NO3(-)-N (>0.15 mg L(-1)), NH4+-N (>0.12 mg L(-1)), and TKN (>0.96 mg L(-1)), occurred in the upstream of TMC, while high concentrations of chlorophyll a (>6.8 mug L(-l)) and pheophytin (>3.9 microg L(-l)) were detected in the downstream of TMC. The highest chlorophyll a (11.8 mug L(-l)) and pheophytin (6.06 microg L(-l)) concentrations, however, were associated with static and open water conditions. Hydrological parameters (total dissolved solid, electrical conductivity, salinity, pH, and water temperature) were positively correlated with chlorophyll a and pheophytin concentrations (P < 0.01) and these factors overshadowed the relationships between N and P concentrations and chlorophyll a under field conditions. Principal component analysis and the ratios of DIN/DP and TN/TP in the water suggest that N is the limiting nutrient factor for phytoplankton growth in the TMC and elevated N relative to P is beneficial to the growth of phytoplankton, which is supported by laboratory culture experiments under controlled conditions.}, } @article {pmid18380334, year = {2007}, author = {Mamikhin, SV}, title = {[The results of computerization of studies of ecological consequences of the accident on the Chernobyl Nuclear Power Plant for terrestrial ecosystems].}, journal = {Radiatsionnaia biologiia, radioecologiia}, volume = {47}, number = {6}, pages = {733-740}, pmid = {18380334}, issn = {0869-8031}, mesh = {*Chernobyl Nuclear Accident ; Computer Simulation ; Databases, Factual ; Ecology/*methods ; *Ecosystem ; Electronic Data Processing/*methods ; *Radioactive Hazard Release ; Radioisotopes/analysis/toxicity ; Soil Pollutants, Radioactive/analysis/toxicity ; Trees/radiation effects ; Ukraine ; }, abstract = {In the paper some results of application of information and calculation technologies in researches of ecological consequences of accident on Chernobyl NPP are brought. The effectiveness of a computerization of investigations is scored. Technical and information component isselected. The singularities of application of the methodology of computerization in radioecological researches are considered. The special attention is given to integration of knowledge accumulated in the form of information materials, databases, mathematical models. The browse of the series of radioecological information and of informational-prognostic systems constructed from the moment of accident is made. As an example of successful usage of a computerization in radioecological researches provided by small scientific collectives experience of MSU division of radioecology and ecotoxicology are considered.}, } @article {pmid18378949, year = {2008}, author = {Salanti, G and Kavvoura, FK and Ioannidis, JP}, title = {Exploring the geometry of treatment networks.}, journal = {Annals of internal medicine}, volume = {148}, number = {7}, pages = {544-553}, doi = {10.7326/0003-4819-148-7-200804010-00011}, pmid = {18378949}, issn = {1539-3704}, mesh = {Data Interpretation, Statistical ; Randomized Controlled Trials as Topic/*methods ; }, abstract = {BACKGROUND: Several treatment options exist for many conditions. Randomized trial evidence on the relative merits of various options may be missing or biased.

PURPOSE: To examine the patterns of trial evidence (network geometry) and explain their implications for the interpretation of the existing evidence on a treatment's relative effectiveness.

DATA SOURCES: PubMed and Thompson ISI Web of Knowledge (last search April 2007).

STUDY SELECTION: Published networks of randomized trials that included at least 4 treatments were identified.

DATA EXTRACTION: For each network, data on the number of studies per treatment comparison were extracted by one investigator and verified by a second investigator.

DATA SYNTHESIS: Indices were adopted from the ecological literature that measure diversity (number of treatments and how often they were tested) and co-occurrence (whether some treatment comparisons were preferred and others avoided). Eighteen eligible treatment networks were identified for different diseases, involving 4 to 16 alternative treatments and 10 to 84 trials. Networks in which 1 option (placebo or no treatment) was the typical comparator were star-shaped, even though several treatments might have had proven effectiveness. Other networks had different shapes. Some showed important co-occurrence that avoided specific head-to-head comparisons. Comparison choices sometimes seemed justified, such as when newer treatments were not compared with older ones already shown to be inferior, whereas other choices seemed to reflect preference bias.

LIMITATIONS: Networks evolve over time as new trials accumulate, and their geometry may change. Statistical testing for co-occurrence is underpowered when few trials exist.

CONCLUSION: Evaluation of the geometry of a treatment network can offer valuable insights for the interpretation of total evidence when many treatment options are available.}, } @article {pmid18378470, year = {2008}, author = {Weir, JT and Bermingham, E and Miller, MJ and Klicka, J and González, MA}, title = {Phylogeography of a morphologically diverse Neotropical montane species, the Common Bush-Tanager (Chlorospingus ophthalmicus).}, journal = {Molecular phylogenetics and evolution}, volume = {47}, number = {2}, pages = {650-664}, doi = {10.1016/j.ympev.2008.02.004}, pmid = {18378470}, issn = {1055-7903}, mesh = {Adenosine Triphosphatases/genetics ; Animal Migration ; Animals ; Bayes Theorem ; Databases, Nucleic Acid ; *Geography ; Passeriformes/*genetics ; Phenotype ; *Phylogeny ; }, abstract = {The Common Bush-Tanager (Chlorospingus ophthalmicus) is distributed in Neotropical cloud-forests from Mexico to Argentina and contains 25 subspecies divided into eight subspecies groups based on biogeography, eye coloration, presence of a postocular spot and chest band. All of Central America is occupied by a single subspecies group; whereas the Andes are believed to be occupied by seven additional subspecies groups. We used five mitochondrial genes to investigate the phylogeography and possible species limits of the ophthalmicus complex. A total of 14 monophyletic lineages were uncovered within the ophthalmicus complex, including three clades currently classified as separate species (C. semifuscus, inornatus and tacarcunae). Divergence estimates for these clades date between 0.8 and 5.2 million years ago (Ma). Contrary to expectations based on morphological diversity, phylogeographic structure was greatest in Mexico and Central America and weakest in the Andes. Morphological and genetic divergences were not significantly correlated and most morphologically defined subspecies groups were not supported. Our evidence suggests the ophthalmicus complex originated in Mexico ca. 6.0 Ma (million years ago) and spread south into the Andes ca. 4.7 Ma before the completion of the Isthmus of Panama. Three genetically divergent lineages of ophthalmicus that formed in the Andes possess a complex checkerboard distribution, with a single lineage represented by disjunct populations from Venezuela and the southern Andes, while intervening populations in Ecuador and Central Peru form two genetically and morphologically divergent lineages.}, } @article {pmid18374453, year = {2008}, author = {Brownstein, JS and Mandl, KD}, title = {Pediatric population size is associated with geographic patterns of acute respiratory infections among adults.}, journal = {Annals of emergency medicine}, volume = {52}, number = {1}, pages = {63-68}, pmid = {18374453}, issn = {1097-6760}, support = {R21 AI073591-01/AI/NIAID NIH HHS/United States ; R21 LM009263-01/LM/NLM NIH HHS/United States ; R21 LM009263/LM/NLM NIH HHS/United States ; R01 LM007677/LM/NLM NIH HHS/United States ; R01 LM007677-04/LM/NLM NIH HHS/United States ; R01 LM007677-01/LM/NLM NIH HHS/United States ; R21AI073591-01/AI/NIAID NIH HHS/United States ; R21 AI073591/AI/NIAID NIH HHS/United States ; R21LM009263-01/LM/NLM NIH HHS/United States ; }, mesh = {Acute Disease ; Adolescent ; Adult ; Age Distribution ; Chi-Square Distribution ; Child ; Child, Preschool ; Emergency Service, Hospital/*statistics & numerical data ; Female ; Humans ; Infant ; Infant, Newborn ; Influenza, Human/epidemiology ; Male ; Massachusetts/epidemiology ; Poisson Distribution ; Respiratory Tract Infections/*epidemiology ; }, abstract = {STUDY OBJECTIVES: We measure the association between proportion of children and specific pediatric age groups in a local population with the timing and rate of adult emergency department (ED) utilization for influenza and other acute respiratory infections.

METHODS: We performed an ecologic study on a time-series of adult patients presenting to Massachusetts EDs and residing in the greater Boston area from October 1, 2001, to September 30, 2005. Patients presenting with acute respiratory infection, used as a marker for influenza, were aggregated by home address ZIP code. We measured geographic patterns of timing and rate of adult respiratory infection-related ED utilization. We performed correlation analysis of rates and peaks identified in this analysis with pediatric population data from the US census (including specific pediatric age groups) by Poisson regression.

RESULTS: One hundred fifty seven thousand five hundred forty two adult respiratory infection-related ED visits (30 visits per 1,000 adults per year) were analyzed. Visits were distributed across 55 of ZIP codes, in which proportions of children (aged 0 to 18 years) ranged from 2.7% to 34.9% in these communities. Proportion of children in a ZIP code was directly associated with timing of seasonal onset of acute respiratory infections among adults (univariate Poisson regression rate ratio [RR] 0.985; 95% confidence interval [CI] 0.977 to 0.993). The proportion of children also explained the patterns of adult acute respiratory infection-related ED utilization rates (RR 1.035; 95% CI 1.024 to 1.047). Three- to 4-year-olds were found to be the most significant predictors of adult illness rate (RR 1.380; 95% CI 1.238 to 1.539) and timing of onset (RR 0.881; 95% CI 0.816 to 0.952).

CONCLUSION: We demonstrate a positive correlation between the timing and rate of ED utilization by adults and the proportion of children in the population. These findings add to a growing body of evidence supporting a critical role played by children in community-wide transmission of acute respiratory infections.}, } @article {pmid18372556, year = {2008}, author = {Chuvieco, E and Opazo, S and Sione, W and Del Valle, H and Anaya, J and Di Bella, C and Cruz, I and Manzo, L and López, G and Mari, N and González-Alonso, F and Morelli, F and Setzer, A and Csiszar, I and Kanpandegi, JA and Bastarrika, A and Libonati, R}, title = {Global burned-land estimation in Latin America using MODIS composite data.}, journal = {Ecological applications : a publication of the Ecological Society of America}, volume = {18}, number = {1}, pages = {64-79}, doi = {10.1890/06-2148.1}, pmid = {18372556}, issn = {1051-0761}, mesh = {*Conservation of Natural Resources ; *Geographic Information Systems ; Latin America ; }, abstract = {This paper presents results of the AQL2004 project, which has been develope within the GOFC-GOLD Latin American network of remote sensing and forest fires (RedLatif). The project intended to obtain monthly burned-land maps of the entire region, from Mexico to Patagonia, using MODIS (moderate-resolution imaging spectroradiometer) reflectance data. The project has been organized in three different phases: acquisition and preprocessing of satellite data; discrimination of burned pixels; and validation of results. In the first phase, input data consisting of 32-day composites of MODIS 500-m reflectance data generated by the Global Land Cover Facility (GLCF) of the University of Maryland (College Park, Maryland, U.S.A.) were collected and processed. The discrimination of burned areas was addressed in two steps: searching for "burned core" pixels using postfire spectral indices and multitemporal change detection and mapping of burned scars using contextual techniques. The validation phase was based on visual analysis of Landsat and CBERS (China-Brazil Earth Resources Satellite) images. Validation of the burned-land category showed an agreement ranging from 30% to 60%, depending on the ecosystem and vegetation species present. The total burned area for the entire year was estimated to be 153 215 km2. The most affected countries in relation to their territory were Cuba, Colombia, Bolivia, and Venezuela. Burned areas were found in most land covers; herbaceous vegetation (savannas and grasslands) presented the highest proportions of burned area, while perennial forest had the lowest proportions. The importance of croplands in the total burned area should be taken with reserve, since this cover presented the highest commission errors. The importance of generating systematic products of burned land areas for different ecological processes is emphasized.}, } @article {pmid18369731, year = {2009}, author = {Shi, ZH and Chen, LD and Hao, JP and Wang, TW and Cai, CF}, title = {The effects of land use change on environmental quality in the red soil hilly region, China: a case study in Xianning County.}, journal = {Environmental monitoring and assessment}, volume = {150}, number = {1-4}, pages = {295-306}, pmid = {18369731}, issn = {1573-2959}, mesh = {Agriculture/methods ; China ; *Conservation of Natural Resources ; *Environment ; Environmental Monitoring ; *Geographic Information Systems ; Humans ; Principal Component Analysis ; *Rural Population ; Satellite Communications ; Soil ; }, abstract = {Land use and land cover change is gaining recognition as a key driver of environmental change. Rapid change of land use has occurred in the red soil hilly region of southeast China in the past three decades due to rural land reform, population pressure and rapid economic growth. In this paper, land use change and its impacts on environmental quality of Xianning County were investigated using technologies of remote sensing (RS), geographic information systems (GIS), and spatial principal components analysis (SPCA). It was indicated that the area of paddy field and upland decline rapidly while the area of woodland, horticulture farm and residential land increased sharply between 1978 and 2002. The driving forces probably were land use policy of the State government, structural adjustment of agricultural sectors and implementation of environmental conservation measures. Based on the assessment of environmental implications of land use practices, the environmental quality of some land use types (i.e. Woodland, sparse woodland, and paddy field) tended to improve, while horticulture farms, water body, and residential land showed a deterioration trend of environmental quality during 1978-2002. Perhaps the most significant finding of this study is that environment appears a negative tendency in the study area from 1991 to 2002, because little attention has been paid to the status and management of agricultural lands, which account for a substantial proportion of total land area. Therefore, for further improving environment in red soil hilly region in China, urgent action is required to improve the advisory services support to farmers on new tillage practices, soil and water conservation practices, raising the efficiency of fertilizer and manure use.}, } @article {pmid18359643, year = {2008}, author = {Reid, DG and Dyal, P and Lozouet, P and Glaubrecht, M and Williams, ST}, title = {Mudwhelks and mangroves: the evolutionary history of an ecological association (Gastropoda: Potamididae).}, journal = {Molecular phylogenetics and evolution}, volume = {47}, number = {2}, pages = {680-699}, doi = {10.1016/j.ympev.2008.01.003}, pmid = {18359643}, issn = {1055-7903}, mesh = {Animals ; Bayes Theorem ; Databases, Nucleic Acid ; *Ecosystem ; *Evolution, Molecular ; Fossils ; Gastropoda/*genetics ; Phylogeny ; Rhizophoraceae/*parasitology ; }, abstract = {Most of the 29 living species of Potamididae show a close association with mangroves. The trees provide the snails with shelter, protection from predators, a solid substrate and sometimes food. Using sequences from three genes (nuclear 18S rRNA and 28S rRNA, mitochondrial COI) we derive a molecular phylogeny and recognize six living genera (Terebralia, Telescopium, Tympanotonos, Cerithidea, Cerithideopsis, Cerithideopsilla). The oldest modern genera (Terebralia, Cerithideopsis) appeared in the Tethyan realm in the Middle Eocene, shortly after the origin of mangrove trees. Whereas most potamidid genera are now restricted to either the Indo-West Pacific (IWP) or to the eastern Pacific plus Atlantic (EPA), sister clades of Cerithideopsis survive in both realms. Based on a reinterpretation of the fossil record (particularly of the monotypic Tympanotonos and extinct Potamides), and parsimonious reconstruction of ancestral habitats, we suggest that the living potamidids are an adaptive radiation that has always been closely associated with mangroves. The specialized tree-climbing groups Cerithidea and Cerithideopsis were independently derived from mud-dwelling ancestors. Cerithideopsilla cingulata (a species complex in the IWP) and 'Potamides' conicus (in the Mediterranean and Indian Ocean) form a single clade within the genus Cerithideopsilla. This refutes the hypothesis that 'P.'conicus is the sole relict of the Tethyan Potamides that has occurred in the Mediterranean region since the Palaeocene. Instead, the phylogeny and fossil record suggest that an ancestor of Cerithideopsilla conica with planktotrophic larvae dispersed from the IWP to the Mediterranean in the Middle Miocene, that its direct development evolved in the Mediterranean during the Pliocene, and that it reinvaded the Indian Ocean during the Plio-Pleistocene.}, } @article {pmid18348790, year = {2008}, author = {Prasifka, JR and Hellmich, RL and Dively, GP and Higgins, LS and Dixon, PM and Duan, JJ}, title = {Selection of nontarget arthropod taxa for field research on transgenic insecticidal crops: using empirical data and statistical power.}, journal = {Environmental entomology}, volume = {37}, number = {1}, pages = {1-10}, doi = {10.1603/0046-225x(2008)37[1:sonatf]2.0.co;2}, pmid = {18348790}, issn = {0046-225X}, mesh = {Animals ; Arthropods/*physiology ; Bacillus thuringiensis/genetics ; Crops, Agricultural/*genetics ; *Data Interpretation, Statistical ; Ecology/methods ; Insecticides ; Pest Control, Biological/methods ; Plants, Genetically Modified ; Population Density ; *Research Design ; Zea mays ; }, abstract = {One of the possible adverse effects of transgenic insecticidal crops is the unintended decline in the abundance of nontarget arthropods. Field trials designed to evaluate potential nontarget effects can be more complex than expected because decisions to conduct field trials and the selection of taxa to include are not always guided by the results of laboratory tests. Also, recent studies emphasize the potential for indirect effects (adverse impacts to nontarget arthropods without feeding directly on plant tissues), which are difficult to predict because of interactions among nontarget arthropods, target pests, and transgenic crops. As a consequence, field studies may attempt to monitor expansive lists of arthropod taxa, making the design of such broad studies more difficult and reducing the likelihood of detecting any negative effects that might be present. To improve the taxonomic focus and statistical rigor of future studies, existing field data and corresponding power analysis may provide useful guidance. Analysis of control data from several nontarget field trials using repeated-measures designs suggests that while detection of small effects may require considerable increases in replication, there are taxa from different ecological roles that are sampled effectively using standard methods. The use of statistical power to guide selection of taxa for nontarget trials reflects scientists' inability to predict the complex interactions among arthropod taxa, particularly when laboratory trials fail to provide guidance on which groups are more likely to be affected. However, scientists still may exercise judgment, including taxa that are not included in or supported by power analyses.}, } @article {pmid18336620, year = {2008}, author = {Linkie, M and Smith, RJ and Zhu, Y and Martyr, DJ and Suedmeyer, B and Pramono, J and Leader-Williams, N}, title = {Evaluating biodiversity conservation around a large Sumatran protected area.}, journal = {Conservation biology : the journal of the Society for Conservation Biology}, volume = {22}, number = {3}, pages = {683-690}, doi = {10.1111/j.1523-1739.2008.00906.x}, pmid = {18336620}, issn = {1523-1739}, mesh = {*Biodiversity ; Community Participation ; Conservation of Natural Resources/*methods ; Databases, Factual ; Developing Countries ; Geographic Information Systems ; Indonesia ; Social Planning ; Socioeconomic Factors ; Time Factors ; Trees ; }, abstract = {Many of the large, donor-funded community-based conservation projects that seek to reduce biodiversity loss in the tropics have been unsuccessful. There is, therefore, a need for empirical evaluations to identify the driving factors and to provide evidence that supports the development of context-specific conservation projects. We used a quantitative approach to measure, post hoc, the effectiveness of a US$19 million Integrated Conservation and Development Project (ICDP) that sought to reduce biodiversity loss through the development of villages bordering Kerinci Seblat National Park, a UNESCO World Heritage Site in Indonesia. We focused on the success of the ICDP component that disbursed a total of US$1.5 million through development grants to 66 villages in return for their commitment to stop illegally clearing the forest. To investigate whether the ICDP lowered deforestation rates in focal villages, we selected a subset of non-ICDP villages that had similar physical and socioeconomic features and compared their respective deforestation rates. Village participation in the ICDP and its development schemes had no effect on deforestation. Instead, accessible areas where village land-tenure had been undermined by the designation of selective-logging concessions tended to have the highest deforestation rates. Our results indicate that the goal of the ICDP was not met and, furthermore, suggest that both law enforcement inside the park and local property rights outside the park need to be strengthened. Our results also emphasize the importance of quantitative approaches in helping to inform successful and cost-effective strategies for tropical biodiversity conservation.}, } @article {pmid18335319, year = {2008}, author = {Aricò, S}, title = {Advances in concepts and methods for the marine environment: implications for policy.}, journal = {Cell biology and toxicology}, volume = {24}, number = {6}, pages = {475-481}, doi = {10.1007/s10565-008-9068-8}, pmid = {18335319}, issn = {1573-6822}, mesh = {Animals ; *Environment ; Environmental Monitoring ; Marine Biology/*methods/*trends ; *Public Policy ; Research ; }, abstract = {Science-based indicators aimed at measuring the sustainability of human activities on the environment have become of prime importance in the policy arena. At the international level, the Commission on Sustainable Development and the Convention on Biological Diversity and other Multilateral Environmental Agreements have recognised the need to develop a set of scientific indicators related to changes in biodiversity and other environmental issues able to direct policy decisions. In the marine realm, the study of the effects of both 'top-down' extractive activities such as fishing is more and more dealt with, in conjunction with 'bottom-up' activities such as nutrient loading and the effects on biogeochemical cycles, marine geochemistry and ecosystem structure and functioning of other pollutants and contaminants. 'Conventional' approaches such as the identification of taxa, model organisms and related methodologies will continue playing a key role for the monitoring of human-induced changes in the marine environment. On the other hand, newly developed disciplines such as genomics, proteomics and biodiversity informatics are increasingly looked at as a source of information and applications that can respond to questions and concerns by the policy community such as the need to adapt to global and climate change in the marine environment so as to mitigate its societal implications.}, } @article {pmid18333465, year = {2007}, author = {Kang, XW and Liu, XH and Zhang, S and Ma, X}, title = {[Regional eco-security assessment of southwest Beijing].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {18}, number = {12}, pages = {2846-2852}, pmid = {18333465}, issn = {1001-9332}, mesh = {China ; Climate ; *Ecosystem ; *Environmental Monitoring ; Fuzzy Logic ; Geographic Information Systems ; Geography ; *Plant Development ; Risk Assessment ; Soil/*analysis ; }, abstract = {Based on the zoning regulation which integrated climate, vegetation and soil as a complex, a regional eco-security index system consisting of regional physical background, ecosystem stability, landscape structure, and external interference was established, and, with the support of geographical information system technology and fuzzy mathematics, a set of regional eco-security assessment methods was constructed. By means of these methods, the eco-security index of southwest Beijing in 2004 was calculated based on the recent 30 years background data of climate and soil. The results showed that in southwest Beijing, the eco-security degree was higher in its central area and western hilly-shallow hilly areas, but lower in its southern and southeastern plain areas. The mining activity in southwest Beijing had threatened the environment, and should be stopped immediately to maintain the regional eco-security. It was proved in the case study that the assessment index system and related methods established in this paper could solve the existing problems in assessing regional eco-security, and the assessment results could reflect the regional ecological issues and the status of eco-security at different locations within the region.}, } @article {pmid18333462, year = {2007}, author = {Xu, LH and Yue, WZ and Cao, Y}, title = {[Spatial scale effect of urban land use landscape pattern in Shanghai City].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {18}, number = {12}, pages = {2827-2834}, pmid = {18333462}, issn = {1001-9332}, mesh = {China ; *City Planning ; Ecology ; *Ecosystem ; *Environment Design ; *Environmental Monitoring ; Geographic Information Systems ; Geography ; Satellite Communications ; }, abstract = {Based on geographic information system (GIS) and remote sensing (RS) techniques, the landscape classes of urban land use in Shanghai City were extracted from SPOT images with 5 m spatial resolution in 2002, and then, the classified data were applied to quantitatively explore the change patterns of several basic landscape metrics at different scales. The results indicated that landscape metrics were sensitive to grain- and extent variance. Urban landscape pattern was spatially dependent. In other words, different landscape metrics showed different responses to scale. The resolution of 40 m was an intrinsic observing scale for urban landscape in Shanghai City since landscape metrics showed random characteristics while the grain was less than 40 m. The extent of 24 km was a symbol scale in a series of extents, which was consistent with the boundary between urban built-up area and suburban area in Shanghai City. As a result, the extent of 12 km away from urban center would be an intrinsic handle scale for urban landscape in Shanghai City. However, due to the complexity of urban structure and asymmetry of urban spatial expansion, the intrinsic handle scale was not regular extent, and the square with size of 24 km was just an approximate intrinsic extent for Shanghai City.}, } @article {pmid18331983, year = {2008}, author = {Briffa, M and Rundle, SD and Fryer, A}, title = {Comparing the strength of behavioural plasticity and consistency across situations: animal personalities in the hermit crab Pagurus bernhardus.}, journal = {Proceedings. Biological sciences}, volume = {275}, number = {1640}, pages = {1305-1311}, pmid = {18331983}, issn = {0962-8452}, mesh = {Adaptation, Physiological ; Animals ; Anomura/*physiology ; Behavior, Animal/*physiology ; Data Interpretation, Statistical ; Female ; Male ; Phenotype ; Reflex, Startle/physiology ; }, abstract = {Many phenotypic traits show plasticity but behaviour is often considered the 'most plastic' aspect of phenotype as it is likely to show the quickest response to temporal changes in conditions or 'situation'. However, it has also been noted that constraints on sensory acuity, cognitive structure and physiological capacities place limits on behavioural plasticity. Such limits to plasticity may generate consistent differences in behaviour between individuals from the same population. It has recently been suggested that these consistent differences in individual behaviour may be adaptive and the term 'animal personalities' has been used to describe them. In many cases, however, a degree of both behavioural plasticity and relative consistency is probable. To understand the possible functions of animal personalities, it is necessary to determine the relative strength of each tendency and this may be achieved by comparison of statistical effect sizes for tests of difference and concordance. Here, we describe a new statistical framework for making such comparisons and investigate cross-situational plasticity and consistency in the duration of startle responses in the European hermit crab Pagurus bernhardus, in the field and the laboratory. The effect sizes of tests for behavioural consistency were greater than for tests of behavioural plasticity, indicating for the first time the presence of animal personalities in a crustacean model.}, } @article {pmid18328528, year = {2008}, author = {Stringfellow, WT}, title = {Ranking tributaries for setting remediation priorities in a TMDL context.}, journal = {Chemosphere}, volume = {71}, number = {10}, pages = {1895-1908}, doi = {10.1016/j.chemosphere.2008.01.040}, pmid = {18328528}, issn = {0045-6535}, mesh = {California ; Carbon/analysis ; Chlorophyll/analysis ; Chlorophyll A ; Environmental Monitoring ; Environmental Restoration and Remediation/*classification ; Geographic Information Systems ; Nephelometry and Turbidimetry ; Nitrates/analysis ; Phosphates/analysis ; Quaternary Ammonium Compounds/analysis ; *Rivers ; Statistics, Nonparametric ; Water Pollutants/analysis ; }, abstract = {The San Joaquin River (SJR) in the Central Valley of California has been designated an impaired waterbody based on its loss of fisheries-related beneficial uses and the river is now subject to regulation under total maximum daily load (TMDL) rules. For impaired waterbodies, numeric standards alone may not be sufficient to establish remediation priorities and priorities must be established by comparing drainages to each other. Data collected as part of regional water quality (WQ) studies in the SJR Valley were not normally distributed, so nonparametric methods based on ranking were used to compare the WQ of individual tributaries and drainages. Normalized rank means (NRMs) were calculated from ranked data and NRMs were mapped to identify priority drainages for WQ improvement activities. NRMs for individual parameters were combined into indexes that are useful for examining the relative importance of different drainages for multiple parameters simultaneously. Indexes were developed for eutrophication and overall WQ. This ranking approach is being proposed as an easily understood, transparent, and scientifically rigorous method to assess the relative WQ impact of individual drainages and set watershed remediation priorities.}, } @article {pmid18321793, year = {2008}, author = {Demuth, A and Aharonowitz, Y and Bachmann, TT and Blum-Oehler, G and Buchrieser, C and Covacci, A and Dobrindt, U and Emödy, L and van der Ende, A and Ewbank, J and Fernández, LA and Frosch, M and García-Del Portillo, F and Gilmore, MS and Glaser, P and Goebel, W and Hasnain, SE and Heesemann, J and Islam, K and Korhonen, T and Maiden, M and Meyer, TF and Montecucco, C and Oswald, E and Parkhill, J and Pucciarelli, MG and Ron, E and Svanborg, C and Uhlin, BE and Wai, SN and Wehland, J and Hacker, J}, title = {Pathogenomics: an updated European Research Agenda.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {8}, number = {3}, pages = {386-393}, doi = {10.1016/j.meegid.2008.01.005}, pmid = {18321793}, issn = {1567-1348}, mesh = {Animals ; Bacterial Infections/genetics/*microbiology ; Databases as Topic ; Europe ; Gene Transfer Techniques ; Genomics/*methods/trends ; Host-Pathogen Interactions/*genetics ; Humans ; *Research/trends ; }, abstract = {The emerging genomic technologies and bioinformatics provide novel opportunities for studying life-threatening human pathogens and to develop new applications for the improvement of human and animal health and the prevention, treatment, and diagnosis of infections. Based on the ecology and population biology of pathogens and related organisms and their connection to epidemiology, more accurate typing technologies and approaches will lead to better means of disease control. The analysis of the genome plasticity and gene pools of pathogenic bacteria including antigenic diversity and antigenic variation results in more effective vaccines and vaccine implementation programs. The study of newly identified and uncultivated microorganisms enables the identification of new threats. The scrutiny of the metabolism of the pathogen in the host allows the identification of new targets for anti-infectives and therapeutic approaches. The development of modulators of host responses and mediators of host damage will be facilitated by the research on interactions of microbes and hosts, including mechanisms of host damage, acute and chronic relationships as well as commensalisms. The study of multiple pathogenic and non-pathogenic microbes interacting in the host will improve the management of multiple infections and will allow probiotic and prebiotic interventions. Needless to iterate, the application of the results of improved prevention and treatment of infections into clinical tests will have a positive impact on the management of human and animal disease. The Pathogenomics Research Agenda draws on discussions with experts of the Network of Excellence "EuroPathoGenomics" at the management board meeting of the project held during 18-21 April 2007, in the Villa Vigoni, Menaggio, Italy. Based on a proposed European Research Agenda in the field of pathogenomics by the ERA-NET PathoGenoMics the meeting's participants updated the established list of topics as the research agenda for the future.}, } @article {pmid18321503, year = {2008}, author = {Christie, AE and Cashman, CR and Brennan, HR and Ma, M and Sousa, GL and Li, L and Stemmler, EA and Dickinson, PS}, title = {Identification of putative crustacean neuropeptides using in silico analyses of publicly accessible expressed sequence tags.}, journal = {General and comparative endocrinology}, volume = {156}, number = {2}, pages = {246-264}, doi = {10.1016/j.ygcen.2008.01.018}, pmid = {18321503}, issn = {0016-6480}, support = {P20 RR016463/RR/NCRR NIH HHS/United States ; R01 DK071801/DK/NIDDK NIH HHS/United States ; P20 RR 016463/RR/NCRR NIH HHS/United States ; 1 R01 DK 071801/DK/NIDDK NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Animals ; Brachyura ; Computer Simulation ; Crustacea/*chemistry ; Daphnia ; Databases, Genetic ; Expressed Sequence Tags ; Fourier Analysis ; Mass Spectrometry ; Molecular Sequence Data ; Nephropidae ; Neuropeptides/chemistry/*genetics/isolation & purification ; Oligopeptides/chemistry/genetics ; Penaeidae ; Pyrrolidonecarboxylic Acid/analogs & derivatives/chemistry ; Software ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ; Tachykinins/chemistry/genetics ; Transcription, Genetic ; }, abstract = {The development of expressed sequence tags (ESTs) for crustacean cDNA libraries and their deposition in publicly accessible databases has generated a rich resource for peptide discovery in this commercially and ecologically important arthropod subphylum. Here, we have conducted in silico searches of these databases for unannotated ESTs encoding putative neuropeptide precursors using the BLAST program tblastn, and have predicted the mature forms of the peptides encoded by them. The primary strategy used was to query the database with known decapod prepro-hormone sequences or, in some instances, insect precursor protein sequences. For neuropeptides for which no prepro-hormones are known, the peptides themselves were used as queries. For those peptides expected to originate from a common precursor, the individual sequences were combined, with each peptide flanked by a dibasic processing site and, if amidated, a glycine residue. Using these approaches, 13 unannotated ESTs encoding putative neuropeptide precursors were found. For example, using the first strategy, putative Marsupenaeus japonicus prepro-hormones encoding B-type allatostatins, neuropeptide F (NPF), and orcokinins were identified. Similarly, several Homarus americanus ESTs encoding putative orcokinin precursors were found. In addition to the decapod prepro-hormones, ESTs putatively encoding a NPF isoform and a red pigment concentrating hormone-like peptide were identified from the cladoceran Daphnia magna, as was one EST putatively encoding multiple tachykinin-related peptides from the isopod Eurydice pulchra. Using the second strategy, we identified a Carcinus maenas EST encoding HIGSLYRamide, a peptide recently discovered via mass spectrometry from Cancer productus. Using mass spectral methods we confirmed that this peptide is also present in Carcinus maenas. Collectively over 50 novel crustacean peptides were predicted from the identified ESTs, providing a strong foundation for future investigations of the evolution, regulation and function of these and related molecules in this arthropod taxon.}, } @article {pmid18306518, year = {2007}, author = {Murray, AG and Raynard, RS}, title = {Modelling for disease preparedness and response.}, journal = {Developments in biologicals}, volume = {129}, number = {}, pages = {41-51}, pmid = {18306518}, issn = {1424-6074}, mesh = {Animals ; Aquaculture/methods ; Civil Defense ; Communicable Disease Control ; Disease Transmission, Infectious/*veterinary ; *Models, Biological ; Models, Statistical ; Public Health Informatics/*methods ; Risk Management ; }, abstract = {Modelling is a useful tool for the understanding and hence, potentially, control of disease. In an emergency situation, obtaining data to validate detailed models may be difficult. However, modelling can be useful in aiding the management of disease, if the objectives are not too ambitious. For example, import risk analysis can use models to minimise the risk of outbreaks. Modelling can also be used to maximise the power of surveillance data to ensure that any outbreak is detected as rapidly as possible. Methods of modelling spread of disease, and measures to prevent this, including SIR-style epidemiological models, models of disease control zones and contact network models can be used to identify and minimise the potential scale of an epidemic. Finally, economic and ecological models can be used to assess the impact of outbreaks. A range of simple models is likely to be of more use than a single comprehensive model.}, } @article {pmid18296701, year = {2008}, author = {Fischer, HM and Wheat, CW and Heckel, DG and Vogel, H}, title = {Evolutionary origins of a novel host plant detoxification gene in butterflies.}, journal = {Molecular biology and evolution}, volume = {25}, number = {5}, pages = {809-820}, doi = {10.1093/molbev/msn014}, pmid = {18296701}, issn = {1537-1719}, mesh = {Animals ; Brassicaceae/parasitology/toxicity ; Butterflies/enzymology/*genetics/physiology ; Databases, Genetic ; Evolution, Molecular ; Exons ; Expressed Sequence Tags ; Gene Library ; *Genes, Insect ; Host-Parasite Interactions ; Insect Proteins/genetics ; Introns ; Multigene Family ; Phylogeny ; Protein Structure, Tertiary ; }, abstract = {Chemical interactions between plants and their insect herbivores provide an excellent opportunity to study the evolution of species interactions on a molecular level. Here, we investigate the molecular evolutionary events that gave rise to a novel detoxifying enzyme (nitrile-specifier protein [NSP]) in the butterfly family Pieridae, previously identified as a coevolutionary key innovation. By generating and sequencing expressed sequence tags, genomic libraries, and screening databases we found NSP to be a member of an insect-specific gene family, which we characterized and named the NSP-like gene family. Members consist of variable tandem repeats, are gut expressed, and are found across Insecta evolving in a dynamic, ongoing birth-death process. In the Lepidoptera, multiple copies of single-domain major allergen genes are present and originate via tandem duplications. Multiple domain genes are found solely within the brassicaceous-feeding Pieridae butterflies, one of them being NSP and another called major allergen (MA). Analyses suggest that NSP and its paralog MA have a unique single-domain evolutionary origin, being formed by intragenic domain duplication followed by tandem whole-gene duplication. Duplicates subsequently experienced a period of relaxed constraint followed by an increase in constraint, perhaps after neofunctionalization. NSP and its ortholog MA are still experiencing high rates of change, reflecting a dynamic evolution consistent with the known role of NSP in plant-insect interactions. Our results provide direct evidence to the hypothesis that gene duplication is one of the driving forces for speciation and adaptation, showing that both within- and whole-gene tandem duplications are a powerful force underlying evolutionary adaptation.}, } @article {pmid18294641, year = {2008}, author = {Yang, K and Wang, XH and Yang, GJ and Wu, XH and Qi, YL and Li, HJ and Zhou, XN}, title = {An integrated approach to identify distribution of Oncomelania hupensis, the intermediate host of Schistosoma japonicum, in a mountainous region in China.}, journal = {International journal for parasitology}, volume = {38}, number = {8-9}, pages = {1007-1016}, doi = {10.1016/j.ijpara.2007.12.007}, pmid = {18294641}, issn = {0020-7519}, mesh = {Animals ; China ; Cross-Sectional Studies ; Demography ; Ecosystem ; Geographic Information Systems ; Humans ; Satellite Communications/instrumentation ; Schistosomiasis japonica/*epidemiology/prevention & control/transmission ; Snails/growth & development/*parasitology ; }, abstract = {The aim of this study is to better understand ecological variability related to the distribution of Oncomelania hupensis, the snail intermediate host of Schistosoma japonicum, and predict the spatial distribution of O. hupensis at the local scale in order to develop a more effective control strategy for schistosomiasis in the hilly and mountainous regions of China. A two-pronged approach was applied in this study consisting of a landscape pattern analysis complemented with Bayesian spatial modelling. The parasitological data were collected by cross-sectional surveys carried out in 11 villages in 2006 and mapped based on global positioning system (GPS) coordinates. Environmental surrogates and landscape metrics were derived from remotely-sensed images and land-cover/land-use classification data. Bayesian non-spatial and spatial models were applied to investigate the variation of snail density in relation to environmental surrogates and landscape metrics at the local scale. A Bayesian spatial model, validated by the deviance information criterion (DIC), was found to be the best-fitting model. The mean shape index (MSI) and Shannon's evenness indexes (SEI) were significantly associated with snail density. These findings suggest that decreasing the heterogeneity of the landscape can reduce snail density. A prediction maps were generated by the Bayesian model together with environmental surrogates and landscape metrics. In conclusion, the risk areas of snail distribution at the local scale can be identified using an integrated approach with landscape pattern analysis supported by remote sensing and GIS technologies, as well as Bayesian modelling.}, } @article {pmid18291557, year = {2008}, author = {Kozak, KH and Graham, CH and Wiens, JJ}, title = {Integrating GIS-based environmental data into evolutionary biology.}, journal = {Trends in ecology & evolution}, volume = {23}, number = {3}, pages = {141-148}, doi = {10.1016/j.tree.2008.02.001}, pmid = {18291557}, issn = {0169-5347}, mesh = {Animals ; *Biological Evolution ; Ecology ; *Environment ; *Geographic Information Systems ; Geography ; Phylogeny ; Species Specificity ; }, abstract = {Many evolutionary processes are influenced by environmental variation over space and time, including genetic divergence among populations, speciation and evolutionary change in morphology, physiology and behaviour. Yet, evolutionary biologists have generally not taken advantage of the extensive environmental data available from geographic information systems (GIS). For example, studies of phylogeography, speciation and character evolution often ignore or use only crude proxies for environmental variation (e.g. latitude and distance between populations). Here, we describe how the integration of GIS-based environmental data, along with new spatial tools, can transform evolutionary studies and reveal new insights into the ecological causes of evolutionary patterns.}, } @article {pmid18290456, year = {2007}, author = {Mu, B and Xie, Y and Jiang, N and Cai, BF and Yu, SL}, title = {[Research on evaluation methods of road ecological effects: a case study of Lan-Hai highway].}, journal = {Huan jing ke xue= Huanjing kexue}, volume = {28}, number = {12}, pages = {2889-2895}, pmid = {18290456}, issn = {0250-3301}, mesh = {City Planning/*methods ; Ecosystem ; *Environment Design ; Environmental Monitoring/*methods ; *Geographic Information Systems ; Models, Theoretical ; Satellite Communications ; *Transportation ; }, abstract = {The ecological effects of roads are systematically and quantitatively evaluated using different methods and metrics in three scales. The small scale effects are assessed by in-situ measurement, the middle scale effects by remote sensing monitoring in different resolution and large scale effects by spatial models based on RS and GIS. The results are satisfactory when this system was applied to Lan-Hai highway. The system can be an important reference to highway ecological effects assessment.}, } @article {pmid18288193, year = {2008}, author = {Jones, KE and Patel, NG and Levy, MA and Storeygard, A and Balk, D and Gittleman, JL and Daszak, P}, title = {Global trends in emerging infectious diseases.}, journal = {Nature}, volume = {451}, number = {7181}, pages = {990-993}, pmid = {18288193}, issn = {1476-4687}, support = {R01 AI079231/AI/NIAID NIH HHS/United States ; R01 TW005869/TW/FIC NIH HHS/United States ; T32 HD007338/HD/NICHD NIH HHS/United States ; }, mesh = {Animals ; Communicable Diseases, Emerging/*epidemiology/microbiology/transmission/virology ; Databases, Factual ; Drug Resistance, Microbial ; Environment ; Geography ; Humans ; Incidence ; Risk ; Socioeconomic Factors ; Zoonoses/epidemiology/microbiology/transmission/virology ; }, abstract = {Emerging infectious diseases (EIDs) are a significant burden on global economies and public health. Their emergence is thought to be driven largely by socio-economic, environmental and ecological factors, but no comparative study has explicitly analysed these linkages to understand global temporal and spatial patterns of EIDs. Here we analyse a database of 335 EID 'events' (origins of EIDs) between 1940 and 2004, and demonstrate non-random global patterns. EID events have risen significantly over time after controlling for reporting bias, with their peak incidence (in the 1980s) concomitant with the HIV pandemic. EID events are dominated by zoonoses (60.3% of EIDs): the majority of these (71.8%) originate in wildlife (for example, severe acute respiratory virus, Ebola virus), and are increasing significantly over time. We find that 54.3% of EID events are caused by bacteria or rickettsia, reflecting a large number of drug-resistant microbes in our database. Our results confirm that EID origins are significantly correlated with socio-economic, environmental and ecological factors, and provide a basis for identifying regions where new EIDs are most likely to originate (emerging disease 'hotspots'). They also reveal a substantial risk of wildlife zoonotic and vector-borne EIDs originating at lower latitudes where reporting effort is low. We conclude that global resources to counter disease emergence are poorly allocated, with the majority of the scientific and surveillance effort focused on countries from where the next important EID is least likely to originate.}, } @article {pmid18282272, year = {2008}, author = {Ryberg, M and Nilsson, RH and Kristiansson, E and Töpel, M and Jacobsson, S and Larsson, E}, title = {Mining metadata from unidentified ITS sequences in GenBank: a case study in Inocybe (Basidiomycota).}, journal = {BMC evolutionary biology}, volume = {8}, number = {}, pages = {50}, pmid = {18282272}, issn = {1471-2148}, mesh = {Asia ; Australia ; Basidiomycota/classification/*genetics ; DNA, Fungal/chemistry/genetics ; DNA, Ribosomal Spacer/chemistry/*genetics ; *Databases, Nucleic Acid ; Europe ; Molecular Sequence Data ; North America ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: The lack of reference sequences from well-identified mycorrhizal fungi often poses a challenge to the inference of taxonomic affiliation of sequences from environmental samples, and many environmental sequences are thus left unidentified. Such unidentified sequences belonging to the widely distributed ectomycorrhizal fungal genus Inocybe (Basidiomycota) were retrieved from GenBank and divided into species that were identified in a phylogenetic context using a reference dataset from an ongoing study of the genus. The sequence metadata of the unidentified Inocybe sequences stored in GenBank, as well as data from the corresponding original papers, were compiled and used to explore the ecology and distribution of the genus. In addition, the relative occurrence of Inocybe was contrasted to that of other mycorrhizal genera.

RESULTS: Most species of Inocybe were found to have less than 3% intraspecific variability in the ITS2 region of the nuclear ribosomal DNA. This cut-off value was used jointly with phylogenetic analysis to delimit and identify unidentified Inocybe sequences to species level. A total of 177 unidentified Inocybe ITS sequences corresponding to 98 species were recovered, 32% of which were successfully identified to species level in this study. These sequences account for an unexpectedly large proportion of the publicly available unidentified fungal ITS sequences when compared with other mycorrhizal genera. Eight Inocybe species were reported from multiple hosts and some even from hosts forming arbutoid or orchid mycorrhizae. Furthermore, Inocybe sequences have been reported from four continents and in climate zones ranging from cold temperate to equatorial climate. Out of the 19 species found in more than one study, six were found in both Europe and North America and one was found in both Europe and Japan, indicating that at least many north temperate species have a wide distribution.

CONCLUSION: Although DNA-based species identification and circumscription are associated with practical and conceptual difficulties, they also offer new possibilities and avenues for research. Metadata assembly holds great potential to synthesize valuable information from community studies for use in a species and taxonomy-oriented framework.}, } @article {pmid18281313, year = {2008}, author = {Guo, J and Wu, X and Zhang, DY and Lin, K}, title = {Genome-wide inference of protein interaction sites: lessons from the yeast high-quality negative protein-protein interaction dataset.}, journal = {Nucleic acids research}, volume = {36}, number = {6}, pages = {2002-2011}, pmid = {18281313}, issn = {1362-4962}, mesh = {Data Interpretation, Statistical ; Databases, Protein ; *Genomics ; *Protein Interaction Domains and Motifs ; *Protein Interaction Mapping/standards ; Reference Standards ; Yeasts/*genetics ; }, abstract = {High-throughput studies of protein interactions may have produced, experimentally and computationally, the most comprehensive protein-protein interaction datasets in the completely sequenced genomes. It provides us an opportunity on a proteome scale, to discover the underlying protein interaction patterns. Here, we propose an approach to discovering motif pairs at interaction sites (often 3-8 residues) that are essential for understanding protein functions and helpful for the rational design of protein engineering and folding experiments. A gold standard positive (interacting) dataset and a gold standard negative (non-interacting) dataset were mined to infer the interacting motif pairs that are significantly overrepresented in the positive dataset compared to the negative dataset. Four negative datasets assembled by different strategies were evaluated and the one with the best performance was used as the gold standard negatives for further analysis. Meanwhile, to assess the efficiency of our method in detecting potential interacting motif pairs, other approaches developed previously were compared, and we found that our method achieved the highest prediction accuracy. In addition, many uncharacterized motif pairs of interest were found to be functional with experimental evidence in other species. This investigation demonstrates the important effects of a high-quality negative dataset on the performance of such statistical inference.}, } @article {pmid18270744, year = {2008}, author = {Statzner, B and Bonada, N and Dolédec, S}, title = {Predicting the abundance of European stream macroinvertebrates using biological attributes.}, journal = {Oecologia}, volume = {156}, number = {1}, pages = {65-73}, pmid = {18270744}, issn = {0029-8549}, mesh = {Animals ; Biodiversity ; Body Size ; Databases, Factual ; Europe ; Feeding Behavior ; Forecasting ; *Invertebrates/anatomy & histology/physiology ; Population Density ; *Rivers ; }, abstract = {Is there a relationship between the abundance of organisms and particular biological attributes? To assess this old, yet still acutely debated key question of ecology, we have used large databases on 312 stream macroinvertebrate genera (from 27 orders) that describe (1) invertebrate abundance at 527 least human-impacted European stream sites, (2) 11 biological traits (size, life-history, food, among others) described in 61 biological trait categories (BTCs; e.g. small, intermediate or large size) and (3) 14 attributes indicating specialization (AISs; e.g. species richness, size and food diversity). We applied interactive procedures to obtain models (for BTCs, AISs and a mixture of both descriptions) explaining as much as possible of the abundance variability of the genera with the lowest number of significant and ecologically meaningful attributes and assessed the predictive power of these models (in crosswise validations) by comparing predicted and observed abundances. Mean European invertebrate abundance increased with BTC affinities favouring viability in stream systems (e.g. attachment to the stream bottom to resist the flow, aquatic passive dispersal with the flow, exploitation of abundant food sources) and decreased with BTC affinities disfavouring this viability (e.g. drag force increase associated with larger body size, flow exposure associated with aerial respiration). Abundance consistently decreased with specialization of the genera (e.g. low species richness, oddity of their overall BTC profile from an "average" European genus). The model including a mixture of a few BTCs and AISs had the greatest predictive power: it predicted 35% of the observed abundance (ln-transformed) variability of the genera; these predictions were marginally affected by taxonomy (using orders as categorical variables). We conclude that a better appreciation of the influence of the examined taxonomic diversity, number and type of biological attributes, environmental system and spatial scale could enable abundance predictions using different sets of biological attributes for different taxonomic groups and systems.}, } @article {pmid18270370, year = {2008}, author = {Wakefield, J and Haneuse, SJ}, title = {Overcoming ecologic bias using the two-phase study design.}, journal = {American journal of epidemiology}, volume = {167}, number = {8}, pages = {908-916}, doi = {10.1093/aje/kwm386}, pmid = {18270370}, issn = {1476-6256}, support = {R01 CA095994/CA/NCI NIH HHS/United States ; R01 CA125081/CA/NCI NIH HHS/United States ; }, mesh = {*Bias ; *Birth Weight ; Case-Control Studies ; Confounding Factors, Epidemiologic ; Data Interpretation, Statistical ; *Epidemiologic Methods ; Epidemiologic Research Design ; Female ; Geography ; Humans ; Infant Mortality/*trends ; Infant, Newborn ; Models, Statistical ; North Carolina/epidemiology ; Pregnancy ; Risk Factors ; }, abstract = {Ecologic (aggregate) data are widely available and widely utilized in epidemiologic studies. However, ecologic bias, which arises because aggregate data cannot characterize within-group variability in exposure and confounder variables, can only be removed by supplementing ecologic data with individual-level data. Here the authors describe the two-phase study design as a framework for achieving this objective. In phase 1, outcomes are stratified by any combination of area, confounders, and error-prone (or discretized) versions of exposures of interest. Phase 2 data, sampled within each phase 1 stratum, provide accurate measures of exposure and possibly of additional confounders. The phase 1 aggregate-level data provide a high level of statistical power and a cross-classification by which individuals may be efficiently sampled in phase 2. The phase 2 individual-level data then provide a control for ecologic bias by characterizing the within-area variability in exposures and confounders. In this paper, the authors illustrate the two-phase study design by estimating the association between infant mortality and birth weight in several regions of North Carolina for 2000-2004, controlling for gender and race. This example shows that the two-phase design removes ecologic bias and produces gains in efficiency over the use of case-control data alone. The authors discuss the advantages and disadvantages of the approach.}, } @article {pmid18261149, year = {2008}, author = {Milbau, A and Stout, JC}, title = {Factors associated with alien plants transitioning from casual, to naturalized, to invasive.}, journal = {Conservation biology : the journal of the Society for Conservation Biology}, volume = {22}, number = {2}, pages = {308-317}, doi = {10.1111/j.1523-1739.2007.00877.x}, pmid = {18261149}, issn = {1523-1739}, mesh = {*Biodiversity ; Databases, Factual ; *Demography ; *Ecosystem ; Ireland ; Logistic Models ; *Models, Theoretical ; Odds Ratio ; Phylogeny ; *Plant Development ; Population Dynamics ; }, abstract = {To explain current plant invasions, or predict future ones, more knowledge on which factors increase the probability of alien species becoming naturalized and subsequently invasive is needed. We created a database of the alien plants in seminatural habitats in Ireland that included data on taxonomy, invasive status, invasion history, distribution, and biological and ecological plant characteristics. We used information from this database to determine the importance of these factors in increasing the ability of species to become naturalized and invasive. More specifically, we used two multiple logistic regressions to identify factors that distinguish naturalized from casual alien plant species and invasive from noninvasive, naturalized alien species. Clonal growth, moisture-indicator value, nitrogen-indicator value, native range, and date of first record affected (in order of decreasing importance) the probability of naturalization. Factors that distinguished invasive from noninvasive species were ornamental introduction, hermaphrodite flowers, pollination mode, being invasive elsewhere, onset of flowering season, moisture-indicator value, native range, and date of first record. Incorporation of phylogenetic information had little influence on the results, suggesting that the capacity of alien species to naturalize and become invasive evolved largely independently in several phylogenetic lineages. Whereas some of the variables were important for both transitions, others were only important for naturalization or for invasion. This emphasizes the importance of studying different stages of the invasion process when looking for mechanisms of becoming a successful invasive plant, instead of simply comparing invasive with noninvasive alien species. Our results also suggest that a combination of species traits and other variables is likely to produce the most accurate prediction of invasions.}, } @article {pmid18261046, year = {2008}, author = {Muirhead, JR and Gray, DK and Kelly, DW and Ellis, SM and Heath, DD and Macisaac, HJ}, title = {Identifying the source of species invasions: sampling intensity vs. genetic diversity.}, journal = {Molecular ecology}, volume = {17}, number = {4}, pages = {1020-1035}, doi = {10.1111/j.1365-294X.2008.03669.x}, pmid = {18261046}, issn = {1365-294X}, mesh = {Amphipoda/genetics ; Animals ; Computer Simulation ; DNA, Chloroplast/genetics ; DNA, Mitochondrial/genetics ; Databases, Factual ; Genetic Markers ; *Genetic Variation ; *Genetics, Population ; Plants/genetics ; Sample Size ; }, abstract = {Population geneticists and community ecologists have long recognized the importance of sampling design for uncovering patterns of diversity within and among populations and in communities. Invasion ecologists increasingly have utilized phylogeographical patterns of mitochondrial or chloroplast DNA sequence variation to link introduced populations with putative source populations. However, many studies have ignored lessons from population genetics and community ecology and are vulnerable to sampling errors owing to insufficient field collections. A review of published invasion studies that utilized mitochondrial or chloroplast DNA markers reveals that insufficient sampling could strongly influence results and interpretations. Sixty per cent of studies sampled an average of less than six individuals per source population, vs. only 45% for introduced populations. Typically, far fewer introduced than source populations were surveyed, although they were sampled more intensively. Simulations based on published data forming a comprehensive mtDNA haplotype data set highlight and quantify the impact of the number of individuals surveyed per source population and number of putative source populations surveyed for accurate assignment of introduced individuals. Errors associated with sampling a low number of individuals are most acute when rare source haplotypes are dominant or fixed in the introduced population. Accuracy of assignment of introduced individuals is also directly related to the number of source populations surveyed and to the degree of genetic differentiation among them (F(ST)). Incorrect interpretations resulting from sampling errors can be avoided if sampling design is considered before field collections are made.}, } @article {pmid18260462, year = {2007}, author = {Wang, G and Wang, L and Wu, W}, title = {[Ecological security evolvement trend of drinking water source areas along Liaohe River].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {18}, number = {11}, pages = {2548-2553}, pmid = {18260462}, issn = {1001-9332}, mesh = {China ; *Ecosystem ; Environmental Monitoring/*methods ; Geographic Information Systems ; Risk Assessment ; *Rivers ; Water Pollutants/*analysis ; Water Supply/*analysis ; }, abstract = {Based on the investigation of potential dangerous factors for the ecological security of drinking water source areas along Liaohe River, a total of 59 drinking water source counties along the River in Liaoning Province were selected, and their ecological security evolvement trend was evaluated by using the theories of safety risk assessment and the GIS grid techniques. The results indicated that among the 59 drinking water source counties, 19 counties were in high potential danger (scores < or = 0.3), with their security status having a stronger deterioration trend, 32 counties were in medium potential danger (0.3 < scores < or = 0.7), whose security status had no obvious deterioration, and 8 counties were in low potential danger (scores > 0.7), with the security status less deteriorated. Based on the evaluation, corresponding countermeasures for ecological protection of these areas were proposed.}, } @article {pmid18260457, year = {2007}, author = {Yang, M and Li, XZ and Yang, ZP and Hu, YM and Wen, QC}, title = {[Effects of sub-watershed landscape patterns at the upper reaches of Minjiang River on soil erosion].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {18}, number = {11}, pages = {2512-2519}, pmid = {18260457}, issn = {1001-9332}, mesh = {Algorithms ; China ; Conservation of Natural Resources ; Ecosystem ; Environmental Monitoring/*methods ; Geographic Information Systems ; Geologic Sediments/*analysis ; Models, Theoretical ; Rivers ; Soil/*analysis ; Water Pollutants/*analysis ; }, abstract = {Based on GIS, the spatial distribution of soil loss and sediment yield in Heishui and Zhenjiangguan sub-watersheds at the upper reaches of Minjiang River was simulated by using sediment delivery-distribution (SEDD) model, and the effects of land use/cover types on soil erosion and sediment yield were discussed, based on the simulated results and related land use maps. A landscape index named location-weighted landscape contrast index (LCI) was calculated to evaluate the effects of landscape components' spatial distribution, weight, and structure of land use/cover on soil erosion. The results showed the soil erosion modulus varied with land use pattern, and decreased in the order of bare rock > urban/village > rangeland > farmland > shrub > forest. There were no significant differences in sediment yield modules among different land use/covers. In the two sub-watersheds, the spatial distribution of land use/covers on slope tended to decrease the final sediment load at watershed outlet, hut as related to relative elevation, relative distance, and flow length, the spatial distribution tended to increase sediment yield. The two sub-watersheds had different advantages as related to landscape components' spatial distribution, but, when the land use/cover weight was considered, the advantages of Zhenjiangguan sub-watershed increased. If the land use/cover structure was considered in addition, the landscape pattern of Zhenjiangguan subwatershed was better. Therefore, only the three elements, i.e., landscape components' spatial distribution, land use/cover weight, and land use/cover structure, were considered comprehensively, can we get an overall evaluation on the effects of landscape pattern on soil erosion. The calculation of LCI related to slope suggested that this index couldn' t accurately reflect the effects of land use/cover weight and structure on soil erosion, and thus, needed to be modified.}, } @article {pmid18259802, year = {2008}, author = {Weber, TC and Blank, PJ and Sloan, A}, title = {Field validation of a conservation network on the Eastern Shore of Maryland, USA, using breeding birds as bio-indicators.}, journal = {Environmental management}, volume = {41}, number = {4}, pages = {538-550}, doi = {10.1007/s00267-008-9076-8}, pmid = {18259802}, issn = {0364-152X}, mesh = {Animals ; Biodiversity ; *Birds ; Breeding ; *Conservation of Natural Resources ; *Ecosystem ; Environmental Monitoring ; Geographic Information Systems ; Maryland ; *Models, Biological ; *Trees ; }, abstract = {Maryland's Green Infrastructure (GI) is a network of large, intact natural areas (hubs), interconnected by linear swaths of riparian or upland vegetation (corridors). The GI serves significant ecological functions and provides the bulk of the state's natural support system. This study examined whether the GI as mapped does, in fact, identify Maryland's most ecologically valuable forested lands, using forest interior dwelling birds (hereafter called "forest birds") as bio-indicators. We conducted bird point counts within forest both inside and outside of hubs on Maryland's Eastern Shore. We also collected a wide variety of habitat data. We found that both the condition of a forest and its surrounding landscape influenced the bird communities. On average, forest bird richness was significantly higher within hubs; furthermore, almost all sites with at least five forest bird species present were in hubs. Forest bird richness and abundance were highest in undisturbed, mature broadleaf forest with wetlands and streams nearby. We detected a significant relationship between forest bird richness and the ecological score of a finer-scale landscape assessment, focused on "cells" of about 0.1 ha in size. This field study also validated the Rapid Field Assessment (RFA) protocol developed in 2001 to assess, on the ground, the relative condition of individual sites or properties within the GI. Forest bird richness and abundance were positively correlated with the RFA community scores. Our results underscore the importance of maintaining regional biological diversity by retaining large blocks of forest, especially mature forest containing streams and wetlands.}, } @article {pmid18259684, year = {2008}, author = {Takeuchi, F and Ochiai, Y and Serizawa, M and Yanai, K and Kuzuya, N and Kajio, H and Honjo, S and Takeda, N and Kaburagi, Y and Yasuda, K and Shirasawa, S and Sasazuki, T and Kato, N}, title = {Search for type 2 diabetes susceptibility genes on chromosomes 1q, 3q and 12q.}, journal = {Journal of human genetics}, volume = {53}, number = {4}, pages = {314-324}, pmid = {18259684}, issn = {1434-5161}, mesh = {Asian People/*genetics ; Carrier Proteins/genetics ; Chromosomes, Human, Pair 1/*genetics ; Chromosomes, Human, Pair 12/*genetics ; Chromosomes, Human, Pair 3/*genetics ; Diabetes Mellitus, Type 2/*genetics ; Genetic Predisposition to Disease/*genetics ; Humans ; Japan ; Linkage Disequilibrium ; Lod Score ; Logistic Models ; Membrane Transport Proteins ; Nerve Tissue Proteins/genetics ; Polymorphism, Single Nucleotide ; }, abstract = {To systematically evaluate genetic susceptibility to type 2 diabetes (T2D) in "candidate" regions on chromosomes 1q, 3q and 12q, we examined disease association by using a total of 2,083 SNPs in two-step screening; a screening panel comprised 473 cases and 285 controls and an extended (or combined) panel involved 658 cases and 474 controls. For the total interval screened (40.9 Mb), suggestive evidence of association was provided for several annotated gene loci. For example, in the MCF2L2 gene on 3q, a significant association (a nominal P value of 0.00009) was observed when logistic regression analysis was performed for three associated SNPs (rs684846, rs35069869 and rs35368790) that belonged to different LD groups. Also, in the SLC15A4 gene on 12q, rs3765108 showed a marginally significant association with an overall estimated odds ratio of 0.79 (P=0.001). No significant association was found for known candidate gene loci on 3q, such as ADIPOQ and IGF2BP2. Using the available samples, we have observed disease associations of SNPs derived from two novel gene loci in the Japanese population through high-density searches of diabetes susceptibility in three chromosomal regions. Independent replication will clarify the etiological relevance of these genomic loci to T2D.}, } @article {pmid18249562, year = {2008}, author = {Near, TJ and Cheng, CH}, title = {Phylogenetics of notothenioid fishes (Teleostei: Acanthomorpha): inferences from mitochondrial and nuclear gene sequences.}, journal = {Molecular phylogenetics and evolution}, volume = {47}, number = {2}, pages = {832-840}, doi = {10.1016/j.ympev.2007.11.027}, pmid = {18249562}, issn = {1055-7903}, mesh = {Animals ; Base Sequence ; Bayes Theorem ; Cell Nucleus/*genetics ; DNA, Concatenated/genetics ; DNA, Mitochondrial/*genetics ; Databases, Nucleic Acid ; Evolution, Molecular ; Fishes/*genetics ; *Phylogeny ; Sequence Analysis, DNA ; }, abstract = {Notothenioids represent an adaptive radiation of teleost fishes in the frigid and ice-laden waters of the Southern Ocean surrounding Antarctica. Phylogenetic hypotheses for this clade have resulted primarily from analyses of mtDNA gene sequences, and studies utilizing nuclear gene DNA sequence data have focused on particular sub-clades of notothenioid fishes. In this study, we provide the first phylogenetic analysis of notothenioids using both mtDNA and nuclear gene sequences for a comprehensive sampling of all major lineages in the clade. Maximum parsimony and Bayesian analyses of aligned mtDNA genes, an aligned nuclear gene (S7 ribosomal protein intron 1), and combined dataset containing the mtDNA and nuclear genes resulted in phylogenies that contained the previously identified Antarctic and High Antarctic Clades. There were areas of agreement and disagreement between different datasets and methods of phylogenetic analysis, and the phylogenies resulting from the nuclear encoded S7 ribosomal protein intron 1 sequences were considerably less resolved than those inferred from mtDNA gene sequences. However, we anticipate increased resolution of the notothenioid phylogeny from future analyses that sample DNA sequences from several nuclear genes.}, } @article {pmid18243044, year = {2008}, author = {Seitz, N and Böttcher, M and Keiter, S and Kosmehl, T and Manz, W and Hollert, H and Braunbeck, T}, title = {A novel statistical approach for the evaluation of comet assay data.}, journal = {Mutation research}, volume = {652}, number = {1}, pages = {38-45}, doi = {10.1016/j.mrgentox.2007.12.004}, pmid = {18243044}, issn = {0027-5107}, mesh = {Animals ; Cells, Cultured ; Comet Assay/methods ; *Data Interpretation, Statistical ; Dose-Response Relationship, Drug ; Embryo, Nonmammalian ; Environmental Exposure/analysis/statistics & numerical data ; Geologic Sediments/analysis ; Germany ; Lethal Dose 50 ; Maximum Tolerated Dose ; Oncorhynchus mykiss ; Rivers ; Water Pollutants, Chemical/toxicity ; Zebrafish ; }, abstract = {The present study forms part of a weight-of-evidence framework including genotoxicological studies in the upper Danube River basin, which aim at elucidating the reasons for the decline in fish catch. The major focus of this paper is the assessment of genotoxicity of sediments from the Danube River basin by use of the comet assay with RTL-W1 cells and with embryos of zebrafish (Danio rerio). A frequently discussed question in this type of approach is how to aggregate and compare the data obtained from genotoxicity testing. There is a need to develop mathematical method combining the information from dose-response curves and level of effectiveness (maximum genotoxic effect). For comparison and ranking of the genotoxic potential of samples from different locations along the Danube River, several methods based on EC50, Lowest Observed Effect Concentration (LOEC), and maximum induction factor were compared with respect to their validity. An evaluation system termed the "3-step analysis" was developed to facilitate consideration of a maximum number of aspects of the raw data. The so-called "concentration-dependent induction factor" (CDI) introduces an index for a straightforward, precise and realistic assessment of the genotoxic potential of any kind of field sample or genotoxic agent.}, } @article {pmid18239608, year = {2008}, author = {Schloss, PD}, title = {Evaluating different approaches that test whether microbial communities have the same structure.}, journal = {The ISME journal}, volume = {2}, number = {3}, pages = {265-275}, doi = {10.1038/ismej.2008.5}, pmid = {18239608}, issn = {1751-7362}, mesh = {Cluster Analysis ; Computational Biology/*methods ; *Ecosystem ; *Environmental Microbiology ; *Monte Carlo Method ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {As microbial ecology investigations have progressed from descriptive characterizations of a community to hypothesis-driven ecological research, a number of different statistical techniques have been developed to describe and compare the structure of microbial communities. Thus far, these methods have only been evaluated using 16S rRNA gene sequence data obtained from incomplete characterizations of microbial communities. In this investigation, simulations were designed to test the statistical power of different methods to differentiate between communities with known memberships and structures. These simulations revealed three important results that affect how the results of the tests are interpreted. First, integral-LIBSHUFF, TreeClimber, UniFrac, analysis of molecular variance (AMOVA) and homogeneity of molecular variance (HOMOVA) compare the structure of communities and not just their memberships. Second, integral-LIBSHUFF is unable to detect cases when one community structure is a subset of another. Third, AMOVA determines whether the genetic diversity within two or more communities is greater than their pooled genetic diversity, and HOMOVA determines whether the amount of genetic diversity in each community is significantly different. integral-LIBSHUFF, TreeClimber and UniFrac lump these and other factors together when performing their analysis making it difficult to discern the nature of the differences that are detected between communities. These findings demonstrate that when correctly employed, the current statistical toolbox has the ability to address specific ecological questions concerning the differences between microbial communities.}, } @article {pmid18236085, year = {2008}, author = {Sparks, TH and Huber, K and Tryjanowski, P}, title = {Something for the weekend? Examining the bias in avian phenological recording.}, journal = {International journal of biometeorology}, volume = {52}, number = {6}, pages = {505-510}, doi = {10.1007/s00484-008-0146-7}, pmid = {18236085}, issn = {0020-7128}, mesh = {Animals ; Behavior, Animal ; *Birds/physiology ; Databases, Factual ; Flight, Animal ; Population Dynamics ; Seasons ; Time Factors ; United Kingdom ; }, abstract = {In this paper we examine the bias towards weekend recording (the weekend effect) in volunteer phenology, using over 14,000 bird migration phenological observations from eight locations in the UK as a data source. Data from 45 bird species were used. Overall, 44% of all records were taken at weekends in contrast to the 28.6% (i.e. two out of seven days) that would be expected if records were evenly spread throughout the week. Whilst there is documented evidence of environmental differences at weekends, particularly in large urban areas, we believe the weekend effect is mostly a consequence of greater recorder effort at weekends. Some birds, likely to be obvious by their behaviour or abundance, had fewer weekend records than the remaining species. The weekend effect, to some extent, differed between locations and between seasons. There was some evidence that, particularly in autumn, the weekend bias may be lessening. If so, this will increase the accuracy of phenological records, making the detection of changes and responses to temperature easier.}, } @article {pmid18227120, year = {2008}, author = {Smith, SA and Dunn, CW}, title = {Phyutility: a phyloinformatics tool for trees, alignments and molecular data.}, journal = {Bioinformatics (Oxford, England)}, volume = {24}, number = {5}, pages = {715-716}, doi = {10.1093/bioinformatics/btm619}, pmid = {18227120}, issn = {1367-4811}, mesh = {*Computational Biology ; *Phylogeny ; *Sequence Alignment ; User-Computer Interface ; }, abstract = {SUMMARY: Phyutility provides a set of phyloinformatics tools for summarizing and manipulating phylogenetic trees, manipulating molecular data and retrieving data from NCBI. Its simple command-line interface allows for easy integration into scripted analyses, and is able to handle large datasets with an integrated database.

AVAILABILITY: Phyutility, including source code, documentation, examples, and executables, is available at http://code.google.com/p/phyutility.}, } @article {pmid18222405, year = {2008}, author = {Mei, J and Gui, J}, title = {Bioinformatic identification of genes encoding C1q-domain-containing proteins in zebrafish.}, journal = {Journal of genetics and genomics = Yi chuan xue bao}, volume = {35}, number = {1}, pages = {17-24}, doi = {10.1016/S1673-8527(08)60003-X}, pmid = {18222405}, issn = {1673-8527}, mesh = {Amino Acid Sequence ; Animals ; Complement C1q/*chemistry ; *Computational Biology ; Evolution, Molecular ; Humans ; Molecular Sequence Data ; Phylogeny ; Protein Structure, Tertiary/genetics ; Sequence Alignment ; Zebrafish/*genetics ; Zebrafish Proteins/*chemistry/*genetics ; }, abstract = {C1q is the first subcomponent of classical pathway in the complement system and a major link between innate and acquired immunities. The globular (gC1q) domain similar with C1q was also found in many non-complement C1q-domain-containing (C1qDC) proteins which have similar crystal structure to that of the multifunctional tumor necrosis factor (TNF) ligand family, and also have diverse functions. In this study, we identified a total of 52 independent gene sequences encoding C1q-domain-containing proteins through comprehensive searches of zebrafish genome, cDNA and EST databases. In comparison to 31 orthologous genes in human and different numbers in other species, a significant selective pressure was suggested during vertebrate evolution. Domain organization of C1q-domain-containing (C1qDC) proteins mainly includes a leading signal peptide, a collagen-like region of variable length, and a C-terminal C1q domain. There are 11 highly conserved residues within the C1q domain, among which 2 are invariant within the zebrafish gene set. A more extensive database searches also revealed homologous C1qDC proteins in other vertebrates, invertebrates and even bacterium, but no homologous sequences for encoding C1qDC proteins were found in many species that have a more recent evolutionary history with zebrafish. Therefore, further studies on C1q-domain-containing genes among different species will help us understand evolutionary mechanism of innate and acquired immunities.}, } @article {pmid18218900, year = {2008}, author = {Wong, KM and Suchard, MA and Huelsenbeck, JP}, title = {Alignment uncertainty and genomic analysis.}, journal = {Science (New York, N.Y.)}, volume = {319}, number = {5862}, pages = {473-476}, doi = {10.1126/science.1151532}, pmid = {18218900}, issn = {1095-9203}, support = {R01 GM069801/GM/NIGMS NIH HHS/United States ; GM-069801/GM/NIGMS NIH HHS/United States ; }, mesh = {Algorithms ; Amino Acid Sequence ; Base Sequence ; Computational Biology ; Evolution, Molecular ; *Genome, Fungal ; *Genomics ; Models, Statistical ; Monte Carlo Method ; Open Reading Frames ; Phylogeny ; Saccharomyces/*genetics ; Selection, Genetic ; Sequence Alignment/*methods ; Software ; Uncertainty ; }, abstract = {The statistical methods applied to the analysis of genomic data do not account for uncertainty in the sequence alignment. Indeed, the alignment is treated as an observation, and all of the subsequent inferences depend on the alignment being correct. This may not have been too problematic for many phylogenetic studies, in which the gene is carefully chosen for, among other things, ease of alignment. However, in a comparative genomics study, the same statistical methods are applied repeatedly on thousands of genes, many of which will be difficult to align. Using genomic data from seven yeast species, we show that uncertainty in the alignment can lead to several problems, including different alignment methods resulting in different conclusions.}, } @article {pmid18215273, year = {2008}, author = {Schloss, PD and Handelsman, J}, title = {A statistical toolbox for metagenomics: assessing functional diversity in microbial communities.}, journal = {BMC bioinformatics}, volume = {9}, number = {}, pages = {34}, pmid = {18215273}, issn = {1471-2105}, mesh = {Animals ; Bacteria/*genetics ; Bone and Bones/microbiology ; Computational Biology/*methods ; Data Interpretation, Statistical ; *Genetic Variation ; Genomics/*methods ; Models, Genetic ; Peptide Fragments/genetics ; RNA, Ribosomal, 16S/genetics ; *Soil Microbiology ; *Water Microbiology ; Whales/*microbiology ; }, abstract = {BACKGROUND: The 99% of bacteria in the environment that are recalcitrant to culturing have spurred the development of metagenomics, a culture-independent approach to sample and characterize microbial genomes. Massive datasets of metagenomic sequences have been accumulated, but analysis of these sequences has focused primarily on the descriptive comparison of the relative abundance of proteins that belong to specific functional categories. More robust statistical methods are needed to make inferences from metagenomic data. In this study, we developed and applied a suite of tools to describe and compare the richness, membership, and structure of microbial communities using peptide fragment sequences extracted from metagenomic sequence data.

RESULTS: Application of these tools to acid mine drainage, soil, and whale fall metagenomic sequence collections revealed groups of peptide fragments with a relatively high abundance and no known function. When combined with analysis of 16S rRNA gene fragments from the same communities these tools enabled us to demonstrate that although there was no overlap in the types of 16S rRNA gene sequence observed, there was a core collection of operational protein families that was shared among the three environments.

CONCLUSION: The results of comparisons between the three habitats were surprising considering the relatively low overlap of membership and the distinctively different characteristics of the three habitats. These tools will facilitate the use of metagenomics to pursue statistically sound genome-based ecological analyses.}, } @article {pmid18212796, year = {2008}, author = {Mitchell-Olds, T and Feder, M and Wray, G}, title = {Evolutionary and ecological functional genomics.}, journal = {Heredity}, volume = {100}, number = {2}, pages = {101-102}, doi = {10.1038/sj.hdy.6801015}, pmid = {18212796}, issn = {1365-2540}, mesh = {Animals ; *Biological Evolution ; Databases, Genetic ; Ecology/*methods ; *Genomics ; Humans ; }, } @article {pmid18211546, year = {2008}, author = {van Dam, NM and Poppy, GM}, title = {Why plant volatile analysis needs bioinformatics--detecting signal from noise in increasingly complex profiles.}, journal = {Plant biology (Stuttgart, Germany)}, volume = {10}, number = {1}, pages = {29-37}, doi = {10.1055/s-2007-964961}, pmid = {18211546}, issn = {1435-8603}, support = {//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Artifacts ; *Computational Biology ; Ecosystem ; Organic Chemicals/*chemistry/*metabolism ; Plants/*metabolism ; Volatilization ; }, abstract = {Plant volatile analysis may be the oldest form of what now is called plant "metabolomic" analysis. A wide array of volatile organic compounds (VOCs), such as alkanes, alcohols, isoprenoids, and esters, can be collected simultaneously from the plant headspace, either within the laboratory or in the field. Increasingly faster and more sensitive analysis techniques allow detection of an ever-growing number of compounds in decreasing concentrations. However, the myriads of data becoming available from such experiments do not automatically increase our ecological and evolutionary understanding of the roles these VOCs play in plant-insect interactions. Herbivores and parasitoids responding to changes in VOC emissions are able to perceive minute changes within a complex VOC background. Plants modified in genes involved in VOC synthesis may be valuable for the evaluation of changes in plant-animal interactions compared to tests with synthetic compounds, as they allow changes to be made within the context of a more complex profile. We argue that bioinformatics is an essential tool to integrate statistical analysis of plant VOC profiles with insect behavioural data. The implementation of statistical techniques such as multivariate analysis (MVA) and meta-analysis is of the utmost importance to interpreting changes in plant VOC mixtures. MVA focuses on differences in volatile patterns rather than in single compounds. Therefore, it more closely resembles the information processing in insects that base their behavioural decisions on differences in VOC profiles between plants. Meta-analysis of different datasets will reveal general patterns pertaining to the ecological role of VOC in plant-insect interactions. Successful implementation of bioinformatics in VOC research also includes the development of MVA that integrate time-resolved chemical and behavioural analyses, as well as databases that link plant VOCs to their effects on insects.}, } @article {pmid18208334, year = {2008}, author = {Liang, H and Plazonic, KR and Chen, J and Li, WH and Fernández, A}, title = {Protein under-wrapping causes dosage sensitivity and decreases gene duplicability.}, journal = {PLoS genetics}, volume = {4}, number = {1}, pages = {e11}, pmid = {18208334}, issn = {1553-7404}, mesh = {Arabidopsis/genetics ; Computational Biology ; Evolution, Molecular ; Gene Dosage ; *Gene Duplication ; Genes, Bacterial ; Genes, Fungal ; Genes, Helminth ; Genes, Insect ; Genome, Human ; Humans ; Hydrogen Bonding ; Linear Models ; Protein Conformation ; Protein Structure, Tertiary ; Proteins/*chemistry/classification/metabolism ; Static Electricity ; }, abstract = {A fundamental issue in molecular evolution is how to identify the evolutionary forces that determine the fate of duplicated genes. The dosage balance hypothesis has been invoked to explain gene duplication patterns at the genomic level under the premise that a dosage imbalance among protein-complex subunits or interacting partners is often deleterious. Here we examine this hypothesis by investigating the molecular basis of dosage sensitivity. We focus on the extent of protein wrapping, which indicates how strongly the structural integrity of a protein relies on its interactive context. From this perspective, we predict that the duplicates of a highly under-wrapped protein or protein subunit should (1) be more sensitive to dosage imbalance and be less likely to be retained and (2) be more likely to survive from a whole-genome duplication (WGD) than from a non-WGD because a WGD causes little or no dosage imbalance. Our under-wrapping analysis of more than 12,000 protein structures strongly supports these predictions and further reveals that the effect of dosage sensitivity on gene duplicability decreases with increasing organismal complexity.}, } @article {pmid18206000, year = {2007}, author = {Guo, JG}, title = {[A new macro/micro area of studying snail-ecology would be initiated by the remote sensing technology].}, journal = {Zhonghua yu fang yi xue za zhi [Chinese journal of preventive medicine]}, volume = {41}, number = {5}, pages = {342-343}, pmid = {18206000}, issn = {0253-9624}, mesh = {Animals ; Environmental Monitoring/*methods ; *Geographic Information Systems ; *Snails ; }, } @article {pmid18205923, year = {2008}, author = {Robitaille, E and Herjean, P}, title = {An analysis of the accessibility of video lottery terminals: the case of Montréal.}, journal = {International journal of health geographics}, volume = {7}, number = {}, pages = {2}, pmid = {18205923}, issn = {1476-072X}, mesh = {Adolescent ; Adult ; Cluster Analysis ; Commerce/economics/standards/*statistics & numerical data ; Female ; Financing, Government ; Gambling/*psychology ; Geographic Information Systems ; Geography ; Humans ; Male ; Poverty Areas ; *Public Policy ; Quebec/epidemiology ; Residence Characteristics/*classification ; Risk Factors ; Sex Factors ; Social Environment ; *Urban Health ; Video Games/economics/psychology/*supply & distribution ; Vulnerable Populations/*psychology ; }, abstract = {BACKGROUND: Researchers and public health officials in Canada, the United States and Australia have for some time noted broader geographic accessibility to gambling establishments, above all in socioeconomically underprivileged communities. This increase in availability could lead to more and more gambling problems. This article focuses, in an ecological perspective, in particular on a spatial analysis of the geographic accessibility of sites possessing a VLT permit in the Montréal area, i.e. Montréal Island, the South Shore and Laval, from the standpoint of the development of an indicator of the vulnerability (socioeconomic components and demographic components) to gambling of populations at the level of certain neighbourhood units (dissemination areas). With the recent development of geographic information systems (GIS), it is now possible to ascertain accessibility to services much more accurately, for example by taking into account the configuration of the road network.

RESULTS: The findings of our analysis reveal widespread geographic accessibility to sites possessing a VLT permit in the downtown area and in pericentral districts. In some neighbourhood units, a site possessing a VLT permit may be within a three-minute walk. In the region studied overall, average walking time to a VLT site is nine minutes. Access to this type of service on foot is usually limited in the outskirts. However, a number of groups of sites possessing VLT permits are found along certain axial highways. According to local spatial self-correlation analyses, the findings suggest a significant link between walking accessibility to sites possessing VLT permits and the vulnerability of the communities. In a number of neighbourhood units with ready access to VLT's the populations display high vulnerability.

CONCLUSION: These findings reveal that accessibility to sites possessing a VLT permit is often linked to the vulnerability (socioeconomic and demographic components) of communities. Reliance in our analyses on neighbourhood units with fairly small areas enabled us to emphasize the rectilinear dimension of the spatial distribution of sites possessing VLT permits. This is a significant link that public health officials must consider when elaborating programs to combat pathological gambling.}, } @article {pmid18205783, year = {2008}, author = {Swenson, NG}, title = {The past and future influence of geographic information systems on hybrid zone, phylogeographic and speciation research.}, journal = {Journal of evolutionary biology}, volume = {21}, number = {2}, pages = {421-434}, doi = {10.1111/j.1420-9101.2007.01487.x}, pmid = {18205783}, issn = {1420-9101}, mesh = {Animals ; *Genetic Speciation ; *Geographic Information Systems ; Geography/*trends ; *Hybridization, Genetic ; *Phylogeny ; }, abstract = {Over the past two decades geographers have developed an increasingly sophisticated technology termed a geographic information system (GIS). A GIS has the ability to store, map and analyse spatial data. The powerful analytical capabilities of a GIS could serve to enhance our understanding of the spatial component of the evolutionary process. In particular, phylogeographers, hybrid zone and speciation researchers could benefit enormously from incorporating this sophisticated technology from the discipline of geography, as they have done so readily from other disciplines (e.g. genetics). Indeed, an increasing number of researchers in these fields are beginning to include GIS analyses into their research programmes. Some of this integration has taken the form of analysing the spatial relationship between populations and hybrid zones. Several other researchers have also begun to incorporate GIS into their work through the use of GIS-based niche models. These models estimate a multidimensional niche for a species using known geo-referenced populations and digital climate maps. Here, I review the recent integration of GIS and GIS-based predictive niche models into the above evolutionary sub-disciplines. I also describe evolutionary analyses that could be further enhanced through the implementation of GIS.}, } @article {pmid18202387, year = {2008}, author = {Mäkinen, HS and Shikano, T and Cano, JM and Merilä, J}, title = {Hitchhiking mapping reveals a candidate genomic region for natural selection in three-spined stickleback chromosome VIII.}, journal = {Genetics}, volume = {178}, number = {1}, pages = {453-465}, pmid = {18202387}, issn = {0016-6731}, mesh = {Animals ; Bayes Theorem ; Chromosomes/*genetics ; Databases, Nucleic Acid ; Fish Proteins/chemistry/genetics ; Genome/*genetics ; Geography ; *Physical Chromosome Mapping ; Population Dynamics ; *Selection, Genetic ; Sequence Homology, Amino Acid ; Smegmamorpha/*genetics ; }, abstract = {Identification of genes and genomic regions under directional natural selection has become one of the major goals in evolutionary genetics, but relatively little work to this end has been done by applying hitchhiking mapping to wild populations. Hitchhiking mapping starts from a genome scan using a randomly spaced set of molecular markers followed by a fine-scale analysis in the flanking regions of the candidate regions under selection. We used the hitchhiking mapping approach to narrow down a selective sweep in the genomic region flanking a candidate locus (Stn90) in chromosome VIII in the three-spined stickleback (Gasterosteus aculeatus). Twenty-four microsatellite markers were screened in an approximately 800-kb region around the candidate locus in three marine and four freshwater populations. The patterns of genetic diversity and differentiation in the candidate region were compared to those of a putatively neutral set of markers. The Bayesian FST-test indicated an elevated genetic differentiation, deviating significantly from neutral expectations, at a continuous region of approximately 20 kb upstream from the candidate locus. Furthermore, a method developed for an array of microsatellite markers rejected neutrality in a region of approximately 90 kb flanking the candidate locus supporting the selective sweep hypothesis. Likewise, the genomewide pattern of genetic diversity differed from the candidate region in a bottleneck analysis suggesting that selection, rather than demography, explains the reduced genetic diversity at the candidate interval. The neutrality tests suggest that the selective sweep had occurred mainly in the Lake Pulmanki population, but the results from bottleneck analyses indicate that selection might have operated in other populations as well. These results suggest that the narrow interval around locus Stn90 has likely been under directional selection, but the region contains several predicted genes, each of which can be the actual targets of selection. Understanding of the functional significance of this genomic region in an ecological context will require a more detailed sequence analysis.}, } @article {pmid18194470, year = {2008}, author = {Gosden, TP and Svensson, EI}, title = {Spatial and temporal dynamics in a sexual selection mosaic.}, journal = {Evolution; international journal of organic evolution}, volume = {62}, number = {4}, pages = {845-856}, doi = {10.1111/j.1558-5646.2008.00323.x}, pmid = {18194470}, issn = {0014-3820}, mesh = {Animals ; Body Size/*genetics ; *Ecosystem ; Female ; Geographic Information Systems ; Insecta/*genetics ; Male ; Pigmentation/genetics ; Population Density ; *Selection, Genetic ; *Sex Characteristics ; Sweden ; Time Factors ; }, abstract = {Selective regimes and phenotypic optima could either change smoothly and in a clinal fashion or be spatially organized in a more unpredictable mosaic pattern over the geographic landscape. When natural or sexual selection is driven by intra- or interspecific biotic interactions, fine-grained spatial variation in selective regimes could result in selection mosaics rather than clinal variation in selection. We investigated temporal variation and spatial organization in sexual selection on male body size along an ecological coastal-inland gradient of a polymorphic damselfly Ischnura elegans. Body size increased in a clinal fashion along this gradient: animals were smaller in size at the coast, but became larger in the inland areas. In contrast, the sexual selection regimes on male body size showed evidence of more fine-grained spatial organization with no evidence for a clinal pattern and low spatial autocorrelations between populations. These spatially fine-grained sexual selection regimes varied in sign and magnitude and were driven by a combination of the densities of heritable female color morphs and local female body sizes. We suggest that the spatial organization of the selective regimes can be interpreted as a sexual selection mosaic that is influenced by highly localized density- and frequency-dependent social interactions.}, } @article {pmid18192410, year = {2008}, author = {Geng, H and Bruhn, JB and Nielsen, KF and Gram, L and Belas, R}, title = {Genetic dissection of tropodithietic acid biosynthesis by marine roseobacters.}, journal = {Applied and environmental microbiology}, volume = {74}, number = {5}, pages = {1535-1545}, pmid = {18192410}, issn = {1098-5336}, mesh = {Animals ; Biofilms/*growth & development ; Chromatography, High Pressure Liquid ; Computational Biology ; DNA Primers/genetics ; Genomic Library ; Marine Biology ; Mutagenesis ; Pfiesteria piscicida/*metabolism ; Plasmids/genetics ; Roseobacter/*genetics ; Species Specificity ; Sulfonium Compounds/*metabolism ; *Symbiosis ; Tropolone/*analogs & derivatives/metabolism ; }, abstract = {The symbiotic association between the roseobacter Silicibacter sp. strain TM1040 and the dinoflagellate Pfiesteria piscicida involves bacterial chemotaxis to dinoflagellate-produced dimethylsulfoniopropionate (DMSP), DMSP demethylation, and ultimately a biofilm on the surface of the host. Biofilm formation is coincident with the production of an antibiotic and a yellow-brown pigment. In this report, we demonstrate that the antibiotic is a sulfur-containing compound, tropodithietic acid (TDA). Using random transposon insertion mutagenesis, 12 genes were identified as critical for TDA biosynthesis by the bacteria, and mutation in any one of these results in a loss of antibiotic activity (Tda(-)) and pigment production. Unexpectedly, six of the genes, referred to as tdaA-F, could not be found on the annotated TM1040 genome and were instead located on a previously unidentified plasmid (ca. 130 kb; pSTM3) that exhibited a low frequency of spontaneous loss. Homologs of tdaA and tdaB from Silicibacter sp. strain TM1040 were identified by mutagenesis in another TDA-producing roseobacter, Phaeobacter sp. strain 27-4, which also possesses two large plasmids (ca. 60 and ca. 70 kb, respectively), and tda genes were found by DNA-DNA hybridization in 88% of a diverse collection of nine roseobacters with known antibiotic activity. These data suggest that roseobacters may use a common pathway for TDA biosynthesis that involves plasmid-encoded proteins. Using metagenomic library databases and a bioinformatics approach, differences in the biogeographical distribution between the critical TDA synthesis genes were observed. The implications of these results to roseobacter survival and the interaction between TM1040 and its dinoflagellate host are discussed.}, } @article {pmid18176947, year = {2008}, author = {Markham, AC and Altmann, J}, title = {Remote monitoring of primates using automated GPS technology in open habitats.}, journal = {American journal of primatology}, volume = {70}, number = {5}, pages = {495-499}, doi = {10.1002/ajp.20515}, pmid = {18176947}, issn = {1098-2345}, support = {R24 HD047879/HD/NICHD NIH HHS/United States ; }, mesh = {Animals ; Body Temperature/physiology ; Ecology/methods ; *Ecosystem ; Female ; Geographic Information Systems/*standards ; Locomotion/physiology ; Papio cynocephalus/*physiology ; }, abstract = {Automated tracking using a satellite global position system (GPS) has major potential as a research tool in studies of primate ecology. However, implementation has been limited, at least partly because of technological difficulties associated with the dense forest habitat of many primates. In contrast, primates inhabiting relatively open environments may provide ideal subjects for use of GPS collars, yet no empirical tests have evaluated this proposition. Here, we used an automated GPS collar to record the locations, approximate body surface temperature, and activity for an adult female baboon during 90 days in the savannah habitat of Amboseli, Kenya. Given the GPS collar's impressive reliability, high spatial accuracy, other associated measurements, and low impact on the study animal, our results indicate the great potential of applying GPS technology to research on wild primates.}, } @article {pmid18174121, year = {2008}, author = {Zaneveld, JR and Nemergut, DR and Knight, R}, title = {Are all horizontal gene transfers created equal? Prospects for mechanism-based studies of HGT patterns.}, journal = {Microbiology (Reading, England)}, volume = {154}, number = {Pt 1}, pages = {1-15}, doi = {10.1099/mic.0.2007/011833-0}, pmid = {18174121}, issn = {1350-0872}, support = {T32 GM008759/GM/NIGMS NIH HHS/United States ; T32 GM142607/GM/NIGMS NIH HHS/United States ; T32 GM08759/GM/NIGMS NIH HHS/United States ; }, mesh = {Computational Biology/*methods ; Gene Transfer, Horizontal/*genetics ; Genomics/*methods ; *Interspersed Repetitive Sequences ; }, abstract = {Detecting patterns of horizontal gene transfer (HGT) in genomic sequences is an important problem, with implications for evolution, ecology, biotechnology and medicine. Extensive genetic, biochemical and genomic studies have provided a good understanding of sequence features that are associated with many (though not all) known mobile elements and mechanisms of gene transfer. This information, however, is not currently incorporated into automated methods for gene transfer detection in genomic data. In this review, we argue that automated annotation of sequence features associated with gene transfer mechanisms could be used both to build more sensitive, mechanism-specific compositional models for the detection of some types of HGT in genomic data, and to ask new questions about the classes of genes most frequently transferred by each mechanism. We then summarize the genes and sequence features associated with different mechanisms of horizontal transfer, emphasizing those that are most useful for distinguishing types of transfer when examining genomic data, and noting those classes of transfers that cannot be distinguished in genomic data using existing techniques. Finally, we describe software, databases and algorithms for identifying particular classes of mobile elements, and outline prospects for better detection of HGT based on specific mechanisms of transfer.}, } @article {pmid18171290, year = {2008}, author = {Kreuels, B and Kobbe, R and Adjei, S and Kreuzberg, C and von Reden, C and Bäter, K and Klug, S and Busch, W and Adjei, O and May, J}, title = {Spatial variation of malaria incidence in young children from a geographically homogeneous area with high endemicity.}, journal = {The Journal of infectious diseases}, volume = {197}, number = {1}, pages = {85-93}, doi = {10.1086/524066}, pmid = {18171290}, issn = {0022-1899}, mesh = {Animals ; Endemic Diseases ; Female ; Geographic Information Systems ; Ghana/epidemiology ; Humans ; Incidence ; Infant ; Malaria, Falciparum/*epidemiology ; Male ; Prospective Studies ; Rural Population ; *Topography, Medical ; Trees/*parasitology ; }, abstract = {BACKGROUND: In sub-Saharan Africa, malaria is a leading cause of morbidity and mortality among young children. Detailed knowledge of spatial variation of malaria epidemiology and associated risk factors is important for planning and evaluating malaria-control measures.

METHODS: The spatial variation of malaria incidences and socioeconomic factors were assessed over 21 months, from January 2003 to September 2005, in 535 children from 9 villages of a small rural area with high Plasmodium falciparum transmission in Ghana. Household positions were mapped by use of a global positioning system, and the spatial effects on malaria rates were assessed by means of ecological analyses and bivariate Poisson regression controlling for possible confounding factors.

RESULTS: Malaria incidence was surprisingly heterogeneous between villages, and ecological analyses showed strong correlations with village area (R(2) = 0.74; P = .003) and population size (R(2) = 0.68; P = .006). Malaria risk was affected by a number of socioeconomic factors. Poisson regression showed an independent linear rate reduction with increasing distance between children's households and the fringe of the forest.

CONCLUSIONS: The exact location of households in villages is an independent and important factor for the variation of malaria incidence in children from high-transmission areas. This fact should be considered in the planning of intervention trials and in spatial targeting of malaria interventions at a local level.}, } @article {pmid20037672, year = {2008}, author = {Broderick, JE}, title = {Electronic Diaries: Appraisal and Current Status.}, journal = {Pharmaceutical medicine}, volume = {22}, number = {2}, pages = {69-74}, pmid = {20037672}, issn = {1178-2595}, support = {U01 AR052170/AR/NIAMS NIH HHS/United States ; U01 AR052170-03/AR/NIAMS NIH HHS/United States ; }, abstract = {The recent explosion of technology has moved the field of patient reported outcomes (PROs) into a new era. Use of paper-and-pencil questionnaires administered before and after treatment has been eclipsed by highly sophisticated random prompts for symptom ratings at multiple points throughout the day, a method known as ecological momentary assessment (EMA). During the last 25 years, research has demonstrated that retrospective ratings are subject to a variety of cognitive heuristics that can distort the report. Initially, this was addressed by adopting paper diary protocols involving multiple ratings in a day or across a week. Technology was also advancing, and some researchers began to utilize electronic platforms for EMA assessment. A good deal of research has been conducted comparing paper and electronic formats. Issues of compliance have been particularly problematic for paper diaries. Electronic technologies can be expensive and require expertise in programming and data management. Not all research questions will require intensive momentary assessment, and end-of-day ratings may be adequate for many applications. What is required of the investigator is familiarity with the strengths and weaknesses of the methods and platforms available as well as a reasoned decision to elect a particular methodology for the study question at hand.}, } @article {pmid18163311, year = {2007}, author = {Wu, XQ and Hu, YM and He, HS and Bu, RC and Xi, FM}, title = {[Spatiotemporal pattern and its driving forces of urban growth in Shenyang City].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {18}, number = {10}, pages = {2282-2288}, pmid = {18163311}, issn = {1001-9332}, mesh = {China ; *City Planning ; Conservation of Natural Resources/methods ; *Ecosystem ; Environmental Monitoring/*methods ; Geographic Information Systems ; Geography ; Satellite Communications ; }, abstract = {By using time series Landsat TM satellite images and adopting GIS spatial analysis and landscape pattern analysis methods, this paper studied the spatiotemporal diversity of urban growth and the evolution of urban landscape pattern in Shenyang, and examined their driving forces. The results showed that in 1988-2004, the urban area in Shenyang increased persistently, and the growth intensity enhanced consistently, with the peaks occured in 2000-2004. The spatial differentiation of urban growth in the City was also distinct, with the southwest direction as the leading orientation, and the urban edges and different level economic development zones as the main growth areas. The urban landscape pattern became more and more complex, and the compactness index of urban development decreased. The evolution of urban landscape pattern was related to the characteristics of urban growth, which also showed spatiotemporal diversity. The urban growth and urban landscape pattern evolution in Shenyang were mainly attributed to the development of industrialization and the construction of different level economic development zones, the proper policies of local governments and the urban planning, as well as the development of traffic infrastructure.}, } @article {pmid18163298, year = {2007}, author = {Wen, QC and Li, XZ and He, HS and Li, LG and Li, YH and Yang, M}, title = {[Edge effects of forest landscape in upper reaches of Minjiang River].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {18}, number = {10}, pages = {2202-2208}, pmid = {18163298}, issn = {1001-9332}, mesh = {*Biomass ; China ; Conservation of Natural Resources ; *Ecosystem ; Environment Design ; Geographic Information Systems ; Poaceae/growth & development ; Rivers ; Satellite Communications ; Trees/*growth & development ; }, abstract = {By using GIS and RS techniques, the edge effects of forest landscape in the upper reaches of Minjiang River, Sichuan Province of China were studied on landscape scale. The results showed that there was a distinct boundary between forestland and farmland, with the vegetation changed significantly. The biomass at forestland edge was lower than that in forestland interior, with the edge effect width being 60 m, whereas the biomass in farmland exterior was higher than that in farmland interior, with the edge effect width being 60-90 m. Forestland-grassland boundary was naturally formed and changed gradually. The biomass at forestland edge was lower than that in forestland interior, while that at grassland edge was higher than that in grassland interior, with the edge effect being 60 m for forestland and 45-75 m for grassland. The edge effect of forestland-shrub land boundary was similar to that of forestland-grassland boundary, with the edge effect width being 60 m for forestland and 45-75 m for shrub land.}, } @article {pmid18154678, year = {2007}, author = {Shaw, JR and Colbourne, JK and Davey, JC and Glaholt, SP and Hampton, TH and Chen, CY and Folt, CL and Hamilton, JW}, title = {Gene response profiles for Daphnia pulex exposed to the environmental stressor cadmium reveals novel crustacean metallothioneins.}, journal = {BMC genomics}, volume = {8}, number = {}, pages = {477}, pmid = {18154678}, issn = {1471-2164}, support = {P42 ES007373/ES/NIEHS NIH HHS/United States ; P42 ES07373/ES/NIEHS NIH HHS/United States ; }, mesh = {Animals ; Biomarkers ; Cadmium/*toxicity ; DNA, Complementary ; Daphnia/*genetics/metabolism ; Databases, Genetic ; Dose-Response Relationship, Drug ; Environmental Monitoring ; *Gene Expression Profiling ; Gene Expression Regulation/*drug effects ; Genome/drug effects ; Metallothionein/*genetics/metabolism ; Molecular Sequence Data ; Oligonucleotide Array Sequence Analysis ; Phylogeny ; Reverse Transcriptase Polymerase Chain Reaction ; Water Pollutants, Chemical/*toxicity ; }, abstract = {BACKGROUND: Genomic research tools such as microarrays are proving to be important resources to study the complex regulation of genes that respond to environmental perturbations. A first generation cDNA microarray was developed for the environmental indicator species Daphnia pulex, to identify genes whose regulation is modulated following exposure to the metal stressor cadmium. Our experiments revealed interesting changes in gene transcription that suggest their biological roles and their potentially toxicological features in responding to this important environmental contaminant.

RESULTS: Our microarray identified genes reported in the literature to be regulated in response to cadmium exposure, suggested functional attributes for genes that share no sequence similarity to proteins in the public databases, and pointed to genes that are likely members of expanded gene families in the Daphnia genome. Genes identified on the microarray also were associated with cadmium induced phenotypes and population-level outcomes that we experimentally determined. A subset of genes regulated in response to cadmium exposure was independently validated using quantitative-realtime (Q-RT)-PCR. These microarray studies led to the discovery of three genes coding for the metal detoxication protein metallothionein (MT). The gene structures and predicted translated sequences of D. pulex MTs clearly place them in this gene family. Yet, they share little homology with previously characterized MTs.

CONCLUSION: The genomic information obtained from this study represents an important first step in characterizing microarray patterns that may be diagnostic to specific environmental contaminants and give insights into their toxicological mechanisms, while also providing a practical tool for evolutionary, ecological, and toxicological functional gene discovery studies. Advances in Daphnia genomics will enable the further development of this species as a model organism for the environmental sciences.}, } @article {pmid18093934, year = {2007}, author = {Turner, BL and Lambin, EF and Reenberg, A}, title = {The emergence of land change science for global environmental change and sustainability.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {104}, number = {52}, pages = {20666-20671}, pmid = {18093934}, issn = {1091-6490}, mesh = {Biophysical Phenomena ; Biophysics ; *Conservation of Natural Resources ; Ecology ; Ecosystem ; *Environment ; Environment Design ; *Environmental Monitoring ; Geographic Information Systems ; Geography ; Humans ; Models, Theoretical ; Science ; }, abstract = {Land change science has emerged as a fundamental component of global environmental change and sustainability research. This interdisciplinary field seeks to understand the dynamics of land cover and land use as a coupled human-environment system to address theory, concepts, models, and applications relevant to environmental and societal problems, including the intersection of the two. The major components and advances in land change are addressed: observation and monitoring; understanding the coupled system-causes, impacts, and consequences; modeling; and synthesis issues. The six articles of the special feature are introduced and situated within these components of study.}, } @article {pmid18093930, year = {2007}, author = {Irwin, EG and Bockstael, NE}, title = {The evolution of urban sprawl: evidence of spatial heterogeneity and increasing land fragmentation.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {104}, number = {52}, pages = {20672-20677}, pmid = {18093930}, issn = {1091-6490}, mesh = {Agriculture ; Biological Evolution ; City Planning ; Conservation of Natural Resources ; Demography ; Ecology ; *Ecosystem ; *Environment Design ; Environmental Monitoring ; Geographic Information Systems ; Geography ; Maryland ; *Population Density ; Population Dynamics ; Rural Population ; Urbanization ; Water Supply ; }, abstract = {We investigate the dynamics and spatial distribution of land use fragmentation in a rapidly urbanizing region of the United States to test key propositions regarding the evolution of sprawl. Using selected pattern metrics and data from 1973 and 2000 for the state of Maryland, we find significant increases in developed and undeveloped land fragmentation but substantial spatial heterogeneity as well. Estimated fragmentation gradients that describe mean fragmentation as a function of distance from urban centers confirm the hypotheses that fragmentation rises and falls with distance and that the point of maximum fragmentation shifted outward over time. However, rather than outward increases in sprawl balanced by development infill, we find substantial and significant increases in mean fragmentation values along the entire urban-rural gradient. These findings are in contrast to the results of Burchfield et al. [Burchfield M, Overman HG, Puga D, Turner MA (2006) Q J Econ 121:587-633], who conclude that the extent of sprawl remained roughly unchanged in the Unites States between 1976 and 1992. As demonstrated here, both the data and pattern measure used in their study are systematically biased against recording low-density residential development, the very land use that we find is most strongly associated with fragmentation. Other results demonstrate the association between exurban growth and increasing fragmentation and the systematic variation of fragmentation with nonurban factors. In particular, proximity to the Chesapeake Bay is negatively associated with fragmentation, suggesting that an attraction effect associated with this natural amenity has concentrated development.}, } @article {pmid18093928, year = {2007}, author = {Manson, SM and Evans, T}, title = {Agent-based modeling of deforestation in southern Yucatan, Mexico, and reforestation in the Midwest United States.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {104}, number = {52}, pages = {20678-20683}, pmid = {18093928}, issn = {1091-6490}, support = {R56 AG056046/AG/NIA NIH HHS/United States ; }, mesh = {Agriculture ; Algorithms ; Conservation of Natural Resources ; Ecosystem ; Environment ; Environment Design ; Environmental Monitoring ; *Forestry ; Geographic Information Systems ; Indiana ; Mexico ; Midwestern United States ; *Models, Theoretical ; Regression Analysis ; Software ; *Trees ; United States ; }, abstract = {We combine mixed-methods research with integrated agent-based modeling to understand land change and economic decision making in the United States and Mexico. This work demonstrates how sustainability science benefits from combining integrated agent-based modeling (which blends methods from the social, ecological, and information sciences) and mixed-methods research (which interleaves multiple approaches ranging from qualitative field research to quantitative laboratory experiments and interpretation of remotely sensed imagery). We test assumptions of utility-maximizing behavior in household-level landscape management in south-central Indiana, linking parcel data, land cover derived from aerial photography, and findings from laboratory experiments. We examine the role of uncertainty and limited information, preferences, differential demographic attributes, and past experience and future time horizons. We also use evolutionary programming to represent bounded rationality in agriculturalist households in the southern Yucatán of Mexico. This approach captures realistic rule of thumb strategies while identifying social and environmental factors in a manner similar to econometric models. These case studies highlight the role of computational models of decision making in land-change contexts and advance our understanding of decision making in general.}, } @article {pmid18083877, year = {2008}, author = {Isenbarger, TA and Finney, M and Ríos-Velázquez, C and Handelsman, J and Ruvkun, G}, title = {Miniprimer PCR, a new lens for viewing the microbial world.}, journal = {Applied and environmental microbiology}, volume = {74}, number = {3}, pages = {840-849}, pmid = {18083877}, issn = {1098-5336}, support = {F32 AI065067/AI/NIAID NIH HHS/United States ; F32AI065067/AI/NIAID NIH HHS/United States ; }, mesh = {Computational Biology ; DNA Primers/*genetics ; DNA, Archaeal/analysis/genetics ; DNA, Bacterial/analysis/genetics ; DNA-Directed DNA Polymerase/*genetics ; Escherichia coli/genetics ; Gene Library ; Geologic Sediments/*microbiology ; Halobacterium/genetics ; Molecular Sequence Data ; Polymerase Chain Reaction/*methods ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, DNA ; *Soil Microbiology ; Taq Polymerase/genetics ; }, abstract = {Molecular methods based on the 16S rRNA gene sequence are used widely in microbial ecology to reveal the diversity of microbial populations in environmental samples. Here we show that a new PCR method using an engineered polymerase and 10-nucleotide "miniprimers" expands the scope of detectable sequences beyond those detected by standard methods using longer primers and Taq polymerase. After testing the method in silico to identify divergent ribosomal genes in previously cloned environmental sequences, we applied the method to soil and microbial mat samples, which revealed novel 16S rRNA gene sequences that would not have been detected with standard primers. Deeply divergent sequences were discovered with high frequency and included representatives that define two new division-level taxa, designated CR1 and CR2, suggesting that miniprimer PCR may reveal new dimensions of microbial diversity.}, } @article {pmid18083775, year = {2008}, author = {Prachumwat, A and Li, WH}, title = {Gene number expansion and contraction in vertebrate genomes with respect to invertebrate genomes.}, journal = {Genome research}, volume = {18}, number = {2}, pages = {221-232}, pmid = {18083775}, issn = {1088-9051}, mesh = {Animals ; Base Sequence ; Computational Biology ; *Evolution, Molecular ; Gene Dosage/genetics ; Genes/*genetics ; Genome/*genetics ; Invertebrates/*genetics ; Multigene Family/*genetics ; Sequence Homology ; Species Specificity ; Vertebrates/*genetics ; }, abstract = {Where did vertebrate genes come from? Here we address this question by analyzing eight completely sequenced land vertebrate genomes and six completely sequenced invertebrate genomes. Approximately 70% of the vertebrate genes can be found in the six invertebrate genomes with the standard homology search criteria (denoted as V.MCL), another approximately 6% can be found with relaxed search criteria, and an additional approximately 2% can be found in sequenced fungal and bacterial genomes. Thus, a substantial proportion of vertebrate genes (approximately 22%) cannot be found in the nonvertebrate genomes studied (denoted as Vonly). Interestingly, genes in Vonly are predominantly singletons, while the majority of genes in the other three groups belong to gene families. The proteins of Vonly tend to evolve faster than those of V.MCL. Surprisingly, in many cases the family sizes in V.MCL are only as large as or even smaller than their counterparts in the invertebrates, contrary to the general perception of a larger family size in vertebrates. Interestingly, in comparison with the family size in invertebrates, vertebrate gene families involved in regulation, signal transduction, transcription, protein transport, and protein modification tend to be expanded, whereas those involved in metabolic processes tend to be contracted. Furthermore, for almost all of the functional categories with family size expansion in vertebrates, the number of gene types (i.e., the number of singletons plus the number of gene families) tends to be over-represented in Vonly, but under-represented in V.MCL. Our study suggests that gene function is a major determinant of gene family size.}, } @article {pmid18082395, year = {2008}, author = {Spix, C and Schmiedel, S and Kaatsch, P and Schulze-Rath, R and Blettner, M}, title = {Case-control study on childhood cancer in the vicinity of nuclear power plants in Germany 1980-2003.}, journal = {European journal of cancer (Oxford, England : 1990)}, volume = {44}, number = {2}, pages = {275-284}, doi = {10.1016/j.ejca.2007.10.024}, pmid = {18082395}, issn = {0959-8049}, mesh = {Case-Control Studies ; Child, Preschool ; Female ; Germany/epidemiology ; Humans ; Infant ; Male ; Neoplasms, Radiation-Induced/*epidemiology ; *Power Plants ; Residence Characteristics ; Risk Factors ; }, abstract = {The 1984 Windscale study raised concern about a possible association between living in the vicinity of nuclear power plants and childhood cancer. No such effect for all cancers was seen in ecological studies in Germany (1980-1995). Results from exploratory analyses led to a new study. Pre-selected areas around all 16 major nuclear power plants in Germany formed the study area. The design is a matched case-control study; cases are all cancers under five years diagnosed in 1980-2003: 1592 cases, and 4735 controls. Inverse distance of place of residence to the nearest nuclear power plant at the time of diagnosis was used as the independent variable in a conditional logistic regression model. Results show an increased risk for childhood cancer under five years when living near nuclear power plants in Germany. The inner 5-km zone shows an increased risk (odds ratio 1.47; lower one-sided 95% confidence limit 1.16). The effect was largely restricted to leukaemia. The results are compatible with the corresponding subgroups in the previous German ecological studies, with which this study shares most of the cases. They contrast with the lack of an effect observed or expected from other studies due to low doses from routine nuclear power plant operation.}, } @article {pmid18081779, year = {2008}, author = {Ferrer, M and Newton, I and Casado, E}, title = {Density dependence hypotheses and the distribution of fecundity.}, journal = {The Journal of animal ecology}, volume = {77}, number = {2}, pages = {341-345}, doi = {10.1111/j.1365-2656.2007.01338.x}, pmid = {18081779}, issn = {1365-2656}, mesh = {Animals ; Clutch Size ; *Computer Simulation ; *Data Interpretation, Statistical ; Eagles/*physiology ; Female ; Fertility/*physiology ; Male ; *Models, Biological ; Poisson Distribution ; Population Density ; Predictive Value of Tests ; }, abstract = {1. Beja & Palma (2008, Journal of Animal Ecology, 77, doi: 10.1111/j.1365-2656.2007.01312.x) attempt to provide a critical analysis of the effectiveness and limitations of a previously published method (Ferrer et al. 2006, Journal of Animal Ecology, 75, 111-117.) to discriminate between Habitat Heterogeneity Hypothesis and the Individual Adjustment Hypothesis using real data from a Bonelli's eagle Hieraaetus fasciatus population. 2. They conclude that significant and strong correlations between mean and CV or skewness are expected under a biologically plausible assumption about brood size distribution, and that the two hypotheses cannot therefore be distinguished. 3. A major concern we have with their paper centres on this biologically plausible brood-size distribution. They used the same quasi-Poisson distribution of brood sizes (typical for a saturate population under Habitat Heterogeneity Hypothesis) for both families of simulations. So, is not surprising that both groups gave similar results. 4. They argued that this approach was 'empirical', free of theoretical assumptions. But in testing between hypotheses, what we are looking for is precisely the differences among theoretical brood-size distributions predicted under the two hypotheses. 5. Summarizing, with the same mean fecundity at high densities, both hypotheses must have different brood-size distributions. So the use of a single left-skewed distribution, typical of a real saturated population (most likely under Habitat Heterogeneity Hypothesis) in attempts to distinguish between the two hypotheses by re-sampling several times on the same left-skewed distribution, as done by Beja & Palma, is clearly inappropriate.}, } @article {pmid18078526, year = {2007}, author = {Linard, C and Tersago, K and Leirs, H and Lambin, EF}, title = {Environmental conditions and Puumala virus transmission in Belgium.}, journal = {International journal of health geographics}, volume = {6}, number = {}, pages = {55}, pmid = {18078526}, issn = {1476-072X}, mesh = {Animals ; Arvicolinae/*virology ; Belgium/epidemiology ; Disease Reservoirs ; *Ecosystem ; Geographic Information Systems ; Geography ; Hemorrhagic Fever with Renal Syndrome/*epidemiology/transmission/*veterinary ; Humans ; Prevalence ; Puumala virus/*physiology ; Trees ; Zoonoses/epidemiology/transmission ; }, abstract = {BACKGROUND: Non-vector-borne zoonoses such as Puumala hantavirus (PUUV) can be transmitted directly, by physical contact between infected and susceptible hosts, or indirectly, with the environment as an intermediate. The objective of this study is to better understand the causal link between environmental features and PUUV prevalence in bank vole population in Belgium, and hence with transmission risk to humans. Our hypothesis was that environmental conditions controlling the direct and indirect transmission paths differ, such that the risk of transmission to humans is not only determined by host abundance. We explored the relationship between, on one hand, environmental variables and, on the other hand, host abundance, PUUV prevalence in the host, and human cases of nephropathia epidemica (NE). Statistical analyses were carried out on 17 field sites situated in Belgian broadleaf forests.

RESULTS: Linear regressions showed that landscape attributes, particularly landscape configuration, influence the abundance of hosts in broadleaf forests. Based on logistic regressions, we show that PUUV prevalence among bank voles is more linked to variables favouring the survival of the virus in the environment, and thus the indirect transmission: low winter temperatures are strongly linked to prevalence among bank voles, and high soil moisture is linked to the number of NE cases among humans. The transmission risk to humans therefore depends on the efficiency of the indirect transmission path. Human risk behaviours, such as the propensity for people to go in forest areas that best support the virus, also influence the number of human cases.

CONCLUSION: The transmission risk to humans of non-vector-borne zoonoses such as PUUV depends on a combination of various environmental factors. To understand the complex causal pathways between the environment and disease risk, one should distinguish between environmental factors related to the abundance of hosts such as land-surface attributes, landscape configuration, and climate - i.e., host ecology, - and environmental factors related to PUUV prevalence, mainly winter temperatures and soil moisture - i.e., virus ecology. Beyond a threshold abundance of hosts, environmental factors favouring the indirect transmission path (soil and climate) can better predict the number of NE cases among humans than factors influencing the abundance of hosts.}, } @article {pmid18078477, year = {2007}, author = {Buckland, ST and Borchers, DL and Johnston, A and Henrys, PA and Marques, TA}, title = {Line transect methods for plant surveys.}, journal = {Biometrics}, volume = {63}, number = {4}, pages = {989-998}, doi = {10.1111/j.1541-0420.2007.00798.x}, pmid = {18078477}, issn = {0006-341X}, mesh = {Agriculture/*methods ; *Algorithms ; *Biomass ; Biometry/*methods ; Computer Simulation ; *Data Interpretation, Statistical ; *Models, Statistical ; Numerical Analysis, Computer-Assisted ; *Plant Development ; }, abstract = {Interest in surveys for monitoring plant abundance is increasing, due in part to the need to quantify the rate of loss of biodiversity. Line transect sampling offers an efficient way to monitor many species. However, the method does not work well in some circumstances, for example on small survey plots, when the plant species has a strongly aggregated distribution, or when plants that are on the line are not easily detected. We develop a crossed design, together with methods that exploit the additional information from such a design, to address these problems. The methods are illustrated using data on a colony of cowslips.}, } @article {pmid18077539, year = {2008}, author = {Kunin, V and He, S and Warnecke, F and Peterson, SB and Garcia Martin, H and Haynes, M and Ivanova, N and Blackall, LL and Breitbart, M and Rohwer, F and McMahon, KD and Hugenholtz, P}, title = {A bacterial metapopulation adapts locally to phage predation despite global dispersal.}, journal = {Genome research}, volume = {18}, number = {2}, pages = {293-297}, pmid = {18077539}, issn = {1088-9051}, mesh = {Adaptation, Biological/*genetics ; Bacteria/*genetics/*virology ; Bacteriophages/*genetics ; Base Sequence ; Computational Biology/methods ; Demography ; Gene Components ; Gene Expression Profiling ; *Genetics, Population ; Microarray Analysis ; Molecular Sequence Data ; *Phylogeny ; Population Dynamics ; Queensland ; Sequence Analysis, DNA ; Sewage/*microbiology ; Wisconsin ; }, abstract = {Using a combination of bacterial and phage-targeted metagenomics, we analyzed two geographically remote sludge bioreactors enriched in a single bacterial species Candidatus Accumulibacter phosphatis (CAP). We inferred unrestricted global movement of this species and identified aquatic ecosystems as the primary environmental reservoirs facilitating dispersal. Highly related and geographically remote CAP strains differed principally in genomic regions encoding phage defense mechanisms. We found that CAP populations were high density, clonal, and nonrecombining, providing natural targets for "kill-the-winner" phage predation. Community expression analysis demonstrated that phages were consistently active in the bioreactor community. Genomic signatures linking CAP to past phage exposures were observed mostly between local phage and host. We conclude that CAP strains disperse globally but must adapt to phage predation pressure locally.}, } @article {pmid18069721, year = {2008}, author = {Riley, RD and Lambert, PC and Staessen, JA and Wang, J and Gueyffier, F and Thijs, L and Boutitie, F}, title = {Meta-analysis of continuous outcomes combining individual patient data and aggregate data.}, journal = {Statistics in medicine}, volume = {27}, number = {11}, pages = {1870-1893}, doi = {10.1002/sim.3165}, pmid = {18069721}, issn = {0277-6715}, mesh = {Adult ; Aged ; Aged, 80 and over ; *Data Interpretation, Statistical ; Female ; Humans ; Hypertension ; Male ; *Meta-Analysis as Topic ; Middle Aged ; Outcome Assessment, Health Care/*methods ; }, abstract = {Meta-analysis of individual patient data (IPD) is the gold-standard for synthesizing evidence across clinical studies. However, for some studies IPD may not be available and only aggregate data (AD), such as a treatment effect estimate and its standard error, may be obtained. In this situation, methods for combining IPD and AD are important to utilize all the available evidence. In this paper, we develop and assess a range of statistical methods for combining IPD and AD in meta-analysis of continuous outcomes from randomized controlled trials. The methods take either a one-step or a two-step approach. The latter is simple, with IPD reduced to AD so that standard AD meta-analysis techniques can be employed. The one-step approach is more complex but offers a flexible framework to include both patient-level and trial-level parameters. It uses a dummy variable to distinguish IPD trials from AD trials and to constrain which parameters the AD trials estimate. We show that this is important when assessing how patient-level covariates modify treatment effect, as aggregate-level relationships across trials are subject to ecological bias and confounding. We thus develop models to separate within-trial and across-trials treatment-covariate interactions; this ensures that only IPD trials estimate the former, whilst both IPD and AD trials estimate the latter in addition to the pooled treatment effect and any between-study heterogeneity. Extension to multiple correlated outcomes is also considered. Ten IPD trials in hypertension, with blood pressure the continuous outcome of interest, are used to assess the models and identify the benefits of utilizing AD alongside IPD.}, } @article {pmid18065616, year = {2008}, author = {Sievert, SM and Scott, KM and Klotz, MG and Chain, PS and Hauser, LJ and Hemp, J and Hügler, M and Land, M and Lapidus, A and Larimer, FW and Lucas, S and Malfatti, SA and Meyer, F and Paulsen, IT and Ren, Q and Simon, J and , }, title = {Genome of the epsilonproteobacterial chemolithoautotroph Sulfurimonas denitrificans.}, journal = {Applied and environmental microbiology}, volume = {74}, number = {4}, pages = {1145-1156}, pmid = {18065616}, issn = {1098-5336}, mesh = {Base Sequence ; Carbon/metabolism ; Carboxy-Lyases/genetics ; Chemoautotrophic Growth ; Chemotaxis/genetics ; Chromosome Mapping ; Computational Biology ; Electron Transport/physiology ; Epsilonproteobacteria/*genetics ; *Genome, Bacterial ; Models, Biological ; Molecular Sequence Data ; Nitrogen/metabolism ; Oxidative Stress/genetics ; *Phylogeny ; Sequence Analysis, DNA ; Signal Transduction/*genetics ; }, abstract = {Sulfur-oxidizing epsilonproteobacteria are common in a variety of sulfidogenic environments. These autotrophic and mixotrophic sulfur-oxidizing bacteria are believed to contribute substantially to the oxidative portion of the global sulfur cycle. In order to better understand the ecology and roles of sulfur-oxidizing epsilonproteobacteria, in particular those of the widespread genus Sulfurimonas, in biogeochemical cycles, the genome of Sulfurimonas denitrificans DSM1251 was sequenced. This genome has many features, including a larger size (2.2 Mbp), that suggest a greater degree of metabolic versatility or responsiveness to the environment than seen for most of the other sequenced epsilonproteobacteria. A branched electron transport chain is apparent, with genes encoding complexes for the oxidation of hydrogen, reduced sulfur compounds, and formate and the reduction of nitrate and oxygen. Genes are present for a complete, autotrophic reductive citric acid cycle. Many genes are present that could facilitate growth in the spatially and temporally heterogeneous sediment habitat from where Sulfurimonas denitrificans was originally isolated. Many resistance-nodulation-development family transporter genes (10 total) are present; of these, several are predicted to encode heavy metal efflux transporters. An elaborate arsenal of sensory and regulatory protein-encoding genes is in place, as are genes necessary to prevent and respond to oxidative stress.}, } @article {pmid18062311, year = {2007}, author = {Jia, KL and Chang, QR}, title = {[Dynamic changes of land desertification landscape pattern in agriculture and pasturage interlaced zone of northern Shaanxi].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {18}, number = {9}, pages = {2045-2049}, pmid = {18062311}, issn = {1001-9332}, mesh = {Agriculture/methods ; China ; Conservation of Natural Resources/*methods/trends ; Crops, Agricultural/*growth & development ; Environmental Monitoring/*methods ; Geographic Information Systems ; Geography ; Poaceae/*growth & development ; Time Factors ; }, abstract = {By using the 1986, 1993 and 2003 Landsat TM images and with the help of GIS, the dynamic changes of land desertification landscape pattern in agriculture and pasturage interlaced zone of northern Shaanxi in 1986-2003 were analyzed. The results showed that in the past 17 years, the desertification area in the zone decreased by 206,655.2 hm2, with the patches in landscape structure reduced and fragmentation abated. Fortunately, the desertification degree decreased obviously, and moderate and light desertification took the leading position. From 1986 to 2003, the spatial centroid of desertification landscape patches expanded southwestward and northeastward, giving serious threat to the ecological safety of the southeast and northeast loess gully and hilly areas.}, } @article {pmid18057786, year = {2007}, author = {Watanabe, H}, title = {[Toxicogenomics as a tool for evaluation of chemical effects].}, journal = {Yakugaku zasshi : Journal of the Pharmaceutical Society of Japan}, volume = {127}, number = {12}, pages = {1967-1974}, doi = {10.1248/yakushi.127.1967}, pmid = {18057786}, issn = {0031-6903}, mesh = {Animals ; Databases, Genetic ; *Ecotoxicology/methods ; Gene Expression Profiling ; *Genomics ; Hazardous Substances/*toxicity ; Humans ; Informatics ; Molecular Biology/methods ; Oligonucleotide Array Sequence Analysis ; *Toxicogenetics ; }, abstract = {Concern about the toxicity of chemicals released into the environment has been increasing recently. Many chemicals are suspected to have hazardous effects, but evaluation of their toxicity is still difficult and challenging. One of these difficulties is the presence of chemicals that are reported to have an adverse effect on organisms despite negative results in conventional toxicity tests. Thus, a new technique has been desired in order to evaluate the effects of chemicals, Recent advances in molecular biology have provided a technique for better understanding the responses of organisms to chemicals; this emerging field is known as toxicogenomics. Toxicogenomics is defined as an integration of genomics (transcriptomics, proteomics, metabolomics) and toxicology. For example, the DNA microarray can be used to explore the gene expression profiles (transcriptomics) of organisms in response to chemicals. Exposure to chemicals results in characteristic gene expression profiles, suggesting that the DNA microarray can be used to evaluate chemical effects. Toxicogenomics is also expected to be useful in gaining a mechanistic understanding of these effects. Although it still has some limitations, this technique can be developed to assess chemicals.}, } @article {pmid18051647, year = {2007}, author = {Cutler, DR and Edwards, TC and Beard, KH and Cutler, A and Hess, KT and Gibson, J and Lawler, JJ}, title = {Random forests for classification in ecology.}, journal = {Ecology}, volume = {88}, number = {11}, pages = {2783-2792}, doi = {10.1890/07-0539.1}, pmid = {18051647}, issn = {0012-9658}, mesh = {Algorithms ; Animals ; Birds/growth & development ; *Data Interpretation, Statistical ; Demography ; Ecology/*methods ; *Ecosystem ; Logistic Models ; *Models, Statistical ; *Models, Theoretical ; Population Density ; Population Dynamics ; Species Specificity ; Trees/growth & development ; }, abstract = {Classification procedures are some of the most widely used statistical methods in ecology. Random forests (RF) is a new and powerful statistical classifier that is well established in other disciplines but is relatively unknown in ecology. Advantages of RF compared to other statistical classifiers include (1) very high classification accuracy; (2) a novel method of determining variable importance; (3) ability to model complex interactions among predictor variables; (4) flexibility to perform several types of statistical data analysis, including regression, classification, survival analysis, and unsupervised learning; and (5) an algorithm for imputing missing values. We compared the accuracies of RF and four other commonly used statistical classifiers using data on invasive plant species presence in Lava Beds National Monument, California, USA, rare lichen species presence in the Pacific Northwest, USA, and nest sites for cavity nesting birds in the Uinta Mountains, Utah, USA. We observed high classification accuracy in all applications as measured by cross-validation and, in the case of the lichen data, by independent test data, when comparing RF to other common classification methods. We also observed that the variables that RF identified as most important for classifying invasive plant species coincided with expectations based on the literature.}, } @article {pmid18051645, year = {2007}, author = {Ver Hoef, JM and Boveng, PL}, title = {Quasi-Poisson vs. negative binomial regression: how should we model overdispersed count data?.}, journal = {Ecology}, volume = {88}, number = {11}, pages = {2766-2772}, doi = {10.1890/07-0043.1}, pmid = {18051645}, issn = {0012-9658}, mesh = {Animals ; Binomial Distribution ; Data Collection/*methods ; *Data Interpretation, Statistical ; Linear Models ; *Models, Statistical ; Phoca/*growth & development ; Poisson Distribution ; Population Density ; Population Growth ; Probability ; Regression Analysis ; Seasons ; Time Factors ; }, abstract = {Quasi-Poisson and negative binomial regression models have equal numbers of parameters, and either could be used for overdispersed count data. While they often give similar results, there can be striking differences in estimating the effects of covariates. We explain when and why such differences occur. The variance of a quasi-Poisson model is a linear function of the mean while the variance of a negative binomial model is a quadratic function of the mean. These variance relationships affect the weights in the iteratively weighted least-squares algorithm of fitting models to data. Because the variance is a function of the mean, large and small counts get weighted differently in quasi-Poisson and negative binomial regression. We provide an example using harbor seal counts from aerial surveys. These counts are affected by date, time of day, and time relative to low tide. We present results on a data set that showed a dramatic difference on estimating abundance of harbor seals when using quasi-Poisson vs. negative binomial regression. This difference is described and explained in light of the different weighting used in each regression method. A general understanding of weighting can help ecologists choose between these two methods.}, } @article {pmid18048984, year = {2007}, author = {Jin, PK and Wang, XC and Chai, H}, title = {Evaluation of floc strength by morphological analysis and PDA online monitoring.}, journal = {Water science and technology : a journal of the International Association on Water Pollution Research}, volume = {56}, number = {10}, pages = {117-124}, doi = {10.2166/wst.2007.781}, pmid = {18048984}, issn = {0273-1223}, mesh = {Alum Compounds/chemistry ; Flocculation ; Humic Substances ; *Online Systems ; Water Purification/instrumentation/*methods ; }, abstract = {This paper established a method for the evaluation of floc strength by morphological analysis and PDA online monitoring. Theoretically, the binding force of a floc can be expressed as B=k(1)d(2Df/3), where k(1) is a coefficient, d is floc size and D(f) is the fractal dimension of the floc. In order to calculate the binding force under a given flocculation condition, a jar test was conducted and d and D(f) were measured by image analysis. A shear force was exerted on the grown flocs by introducing the flocculated suspension through a transparent tube where the velocity gradient value of the flow could be accurately controlled. As the tube was connected with a particle dispersion analyzer (PDA), the condition of floc breakage was online monitored and the critical condition was identified by analyzing the PDA outputs (FI curves). The binding force coefficient k(1) could thus be determined, and the binding force B which represented the floc strength was evaluated. The validity of this method was proved by a series of experiments using aluminium sulphate as coagulant for the flocculation of humic substances.}, } @article {pmid18047529, year = {2008}, author = {Li, R and Nie, L}, title = {Efficient statistical inference procedures for partially nonlinear models and their applications.}, journal = {Biometrics}, volume = {64}, number = {3}, pages = {904-911}, pmid = {18047529}, issn = {1541-0420}, support = {P50 DA010075/DA/NIDA NIH HHS/United States ; P50 DA010075-110008/DA/NIDA NIH HHS/United States ; P50 DA10075/DA/NIDA NIH HHS/United States ; }, mesh = {Biometry/*methods ; Data Interpretation, Statistical ; Ecology/statistics & numerical data ; Ecosystem ; Finite Element Analysis ; Least-Squares Analysis ; Linear Models ; Models, Statistical ; Monte Carlo Method ; *Nonlinear Dynamics ; Photosynthesis ; Statistics, Nonparametric ; }, abstract = {Motivated by an analysis of a real data set in ecology, we consider a class of partially nonlinear models where both a nonparametric component and a parametric component are present. We develop two new estimation procedures to estimate the parameters in the parametric component. Consistency and asymptotic normality of the resulting estimators are established. We further propose an estimation procedure and a generalized F-test procedure for the nonparametric component in the partially nonlinear models. Asymptotic properties of the newly proposed estimation procedure and the test statistic are derived. Finite sample performance of the proposed inference procedures are assessed by Monte Carlo simulation studies. An application in ecology is used to illustrate the proposed methods.}, } @article {pmid18045503, year = {2007}, author = {Earnest, A and Morgan, G and Mengersen, K and Ryan, L and Summerhayes, R and Beard, J}, title = {Evaluating the effect of neighbourhood weight matrices on smoothing properties of Conditional Autoregressive (CAR) models.}, journal = {International journal of health geographics}, volume = {6}, number = {}, pages = {54}, pmid = {18045503}, issn = {1476-072X}, mesh = {Birth Rate/trends ; Congenital Abnormalities/epidemiology ; Databases, Factual/trends ; *Effect Modifier, Epidemiologic ; Humans ; *Models, Statistical ; New South Wales/epidemiology ; }, abstract = {BACKGROUND: The Conditional Autoregressive (CAR) model is widely used in many small-area ecological studies to analyse outcomes measured at an areal level. There has been little evaluation of the influence of different neighbourhood weight matrix structures on the amount of smoothing performed by the CAR model. We examined this issue in detail.

METHODS: We created several neighbourhood weight matrices and applied them to a large dataset of births and birth defects in New South Wales (NSW), Australia within 198 Statistical Local Areas. Between the years 1995-2003, there were 17,595 geocoded birth defects and 770,638 geocoded birth records with available data. Spatio-temporal models were developed with data from 1995-2000 and their fit evaluated within the following time period: 2001-2003.

RESULTS: We were able to create four adjacency-based weight matrices, seven distance-based weight matrices and one matrix based on similarity in terms of a key covariate (i.e. maternal age). In terms of agreement between observed and predicted relative risks, categorised in epidemiologically relevant groups, generally the distance-based matrices performed better than the adjacency-based neighbourhoods. In terms of recovering the underlying risk structure, the weight-7 model (smoothing by maternal-age 'Covariate model') was able to correctly classify 35/47 high-risk areas (sensitivity 74%) with a specificity of 47%, and the 'Gravity' model had sensitivity and specificity values of 74% and 39% respectively.

CONCLUSION: We found considerable differences in the smoothing properties of the CAR model, depending on the type of neighbours specified. This in turn had an effect on the models' ability to recover the observed risk in an area. Prior to risk mapping or ecological modelling, an exploratory analysis of the neighbourhood weight matrix to guide the choice of a suitable weight matrix is recommended. Alternatively, the weight matrix can be chosen a priori based on decision-theoretic considerations including loss, cost and inferential aims.}, } @article {pmid18045254, year = {2008}, author = {Collin, SP}, title = {A web-based archive for topographic maps of retinal cell distribution in vertebrates.}, journal = {Clinical & experimental optometry}, volume = {91}, number = {1}, pages = {85-95}, doi = {10.1111/j.1444-0938.2007.00228.x}, pmid = {18045254}, issn = {0816-4622}, mesh = {Animals ; Fovea Centralis/cytology ; Humans ; Information Storage and Retrieval/*methods ; *Internet ; Photoreceptor Cells, Invertebrate/cytology ; Retina/*cytology ; Retinal Ganglion Cells/cytology ; }, abstract = {Clinical and Experimental Optometry, in conjunction with Optometrists Association Australia and Professor Shaun P Collin of the University of Queensland, announce the launch of a web-based archive of previously published topographic maps of retinal cell distribution in vertebrates. At present, the archive boasts more than 770 different maps of the distribution of retinal neurons (for example, photoreceptors, bipolar cells, amacrine cells, horizontal cells and ganglion cells) in nearly 200 species within all vertebrate classes (Cephalospidomorpha, Actinopterygii, Sarcopterygii, Amphibia, Reptilia, Aves and Mammalia). The distribution of retinal neurons has been studied for more than 100 years and has become a powerful means of predicting the spatial resolving power of the eye and the retinal regions containing specialisations, such as areae centrales, horizontal streaks and foveae, where increased densities of neurons define the way in which a species visually samples its environment. The location of these retinal specialisations thereby identifies the part(s) of the visual field of critical importance for localising food and mates and for predator surveillance. The distribution of sampling elements even reflects the symmetry of a species' ecological habitat. The archive is a unique collection of most of the currently available retinal maps, which also presents relevant information, where known, about eye size, retinal cell density, retinal orientation, cell number, spatial resolving power and the type of specialisation, in addition to basic physical parameters of each species (body size, weight, sex and developmental stage). The archive is accessible at http://www.optometrists.asn.au/ceo/retinalsearch and will be updated regularly. The powerful database is interactive and freely available, providing the opportunity to upload both published and unpublished topographic maps. Following a review process, previously unpublished maps will be 'published' and available online worldwide. It is hoped that this comprehensive new resource will provide not only an up-to-date method of accessing maps of the distribution of retinal neurons in individual species but also allow broader evolutionary comparisons of the visual capabilities, ecology, development and the type(s) of retinal specialisations found in vertebrates.}, } @article {pmid18044540, year = {2007}, author = {Gloria, TP and Lippiatt, BC and Cooper, J}, title = {Life cycle impact assessment weights to support environmentally preferable purchasing in the United States.}, journal = {Environmental science & technology}, volume = {41}, number = {21}, pages = {7551-7557}, doi = {10.1021/es070750+}, pmid = {18044540}, issn = {0013-936X}, mesh = {Commerce ; *Construction Materials ; *Decision Support Techniques ; *Environment ; *Software ; United States ; }, abstract = {LCA is a quantitative method for understanding the environmental impacts of a product, yet all product purchasing decisions are ultimately subjective. Weights are the nexus between the quantitative results of LCA and the values-based, subjective choices of decision makers. In May 2007, NIST introduced a new optional weight set in Version 4.0 of the BEES software. Three key points about this new optional weight set are the basis for discussion in this paper: The new weight set was created specifically in the context of BEES. It is intended to support a practical method to assist environmentally preferable purchasing in the United States based on LCIA results. This is in contrast to the weight sets currently in BEES, which are based on generalist perspectives. The new weight set was created by a multi-stakeholder panel via the AHP method, and is a synthesis of panelists' perspectives on the relative importance of each environmental impact category in BEES. The weight set draws on each panelist's personal and professional understanding of, and value attributed to, each impact category. While the synthesized weight set may not equally satisfy each panelist's view of impact importance, it does reflect contemporary values in applying LCAto real world decisions, and represents one approach others can learn from in producing weight sets. The new weight set offers BEES users an additional option for synthesizing and comparing the environmental performance of building products and making purchasing decisions. In so doing, it strengthens the decision-making process, which is important when making product comparisons in the public domain. The Weight Set: Across all panelists and with explicit consideration of all time horizons, anthropogenic contributions to global warming, weighted at 29%, was judged most important, yet not so important that decisions can be made solely on the basis of this impact. A strong tail of other concerns include fossil fuel depletion (10%), criteria air pollutants (9%), water intake/use (8%), human health cancerous effects (8%), ecological toxicity (7%), eutrophication of water bodies (6%), land use (6%), and human health noncancerous effects (5%). Also of interest are the identified impact areas of concern assigned the lowest weights: smog formation (4%), indoor air quality (3%), acidification (3%), and ozone depletion (2%). Their low weights may indicate that there is not as much immediate concern or that the remedial actions associated with the impact for the most part are underway.}, } @article {pmid18044004, year = {2007}, author = {Lynen, G and Zeman, P and Bakuname, C and Di Giulio, G and Mtui, P and Sanka, P and Jongejan, F}, title = {Cattle ticks of the genera Rhipicephalus and Amblyomma of economic importance in Tanzania: distribution assessed with GIS based on an extensive field survey.}, journal = {Experimental & applied acarology}, volume = {43}, number = {4}, pages = {303-319}, pmid = {18044004}, issn = {0168-8162}, mesh = {Animals ; Cattle ; Cattle Diseases/epidemiology/*parasitology ; *Ecosystem ; Geographic Information Systems ; Ixodidae/*growth & development ; Tanzania/epidemiology ; Tick Infestations/epidemiology/parasitology/*veterinary ; Tick-Borne Diseases/parasitology/prevention & control/*veterinary ; }, abstract = {In order to implement a robust integrated tick and tick-borne disease control programme in Tanzania, based on ecological and epidemiological knowledge of ticks and their associated diseases, a national tick and sero-surveillance study was carried out in all 21 regions of the mainland, as well as on Mafia Island, between 1998 and 2001. The current distributions of Rhipicephalus appendiculatus, R. pravus, Amblyomma variegatum, A. gemma, and A. lepidum are illustrated and discussed. Tick distribution maps were assessed using the Weights-of-Evidence method (WofE), and employing temperature, humidity, NDVI, rainfall, and land-cover predictive data. Ground-truthing was done to check correspondence both of the data employed in prediction with land-cover characteristics discerned in the field as well as of the surveyed and predicted tick distributions. Statistical methods were used to analyse associations of the tick species with their environment, cattle density, and other ticks. Except for R. appendiculatus, no appreciable changes were demonstrated in the predicted and observed tick distributions compared to the existing maps that originated in the 1950-1960s. Cattle density influenced the distribution of A. variegatum and, to a certain extent, of A. lepidum, but had no appreciable influence on the distribution of any of the other ticks discussed in this paper, neither did livestock movement. Distinct differences for environmental requirements where observed between different tick species within the same genus. The predictive maps of R. appendiculatus and R. pravus suggest their mutually exclusive distribution in Tanzania, and simultaneous statistical analysis showed R. pravus as a greater specialist. Of the three Amblyomma species, A. variegatum is the most catholic tick species in Tanzania, while both A. gemma and A. lepidum belong to the more specialized species. Despite dissimilar habitat preferences, all three Amblyomma spp. co-exist in central Tanzania, where very heterogeneous habitats may simultaneously satisfy the environmental requirements of all three species. The current study, conducted about 4 decades after the last major survey activities, has shown that changing livestock policies, unrestricted livestock movement and a continuous change in climatic/environmental conditions in Tanzania have brought about only limited changes in the distribution patterns of R. appendiculatus, R. pravus and the three Amblyomma species investigated. Whether this observation indicates a relative indifference of these ticks to environmental and/or climate changes allows room for speculation.}, } @article {pmid18043864, year = {2008}, author = {Takeuchi, F and Serizawa, M and Kato, N}, title = {HapMap coverage for SNPs in the Japanese population.}, journal = {Journal of human genetics}, volume = {53}, number = {1}, pages = {96-99}, pmid = {18043864}, issn = {1434-5161}, mesh = {Asian People/*genetics ; Genetics, Population ; *Genome, Human ; Genotype ; Humans ; Japan ; Linkage Disequilibrium ; *Polymorphism, Single Nucleotide ; Sequence Analysis, DNA ; }, abstract = {The coverage of human genomic variations is known to substantially affect the success of genome-wide association studies. We therefore assessed the SNP coverage in the HapMap database for a total of 1,304 subjects from the Japanese population by combining resequencing and high-density genotyping approaches. First, we resequenced 48 Japanese subjects in 86 genes (572 kb in total), and we then genotyped the subset of tag SNPs and also imputed genotypes for all of the detected SNPs in an additional panel of 1,256 subjects. Subsequently, we genotyped 555,352 tag SNPs selected from the HapMap in 72 Japanese subjects (from the panel of 1,256 subjects) and further imputed genotypes for all SNPs currently included in the HapMap. Of 738 common genic SNPs (1.3 per kb) that we detected by resequencing, 58% had already been genotyped in the HapMap, and 31% were not genotyped but had a proxy SNP in the HapMap with a linkage disequilibrium coefficient r (2) > or = 0.8, whereas 11% were not represented in the current HapMap database. Thus, the HapMap coverage appears to be high although not thorough for SNPs in the Japanese population as compared to its coverage reported in Caucasians, and this needs to be considered when we interpret association results.}, } @article {pmid18040876, year = {2008}, author = {Dilek, EF and Sahin, S and Yilmazer, I}, title = {Afforestation areas defined by GIS in Gölbaşi specially protected area Ankara/Turkey.}, journal = {Environmental monitoring and assessment}, volume = {144}, number = {1-3}, pages = {251-259}, pmid = {18040876}, issn = {0167-6369}, mesh = {*Conservation of Natural Resources ; *Environment ; Environmental Monitoring/*methods ; *Geographic Information Systems ; Humans ; *Satellite Communications ; Turkey ; }, abstract = {This paper concentrates on determining the areas for afforestation and the development of conservation strategies and actions in the case where there is high demand for the conservation of a particular land area. The analysis of hydrological landscape structure and of erodibility was prerequisite in the methodological design considering the site-specific natural landscape characteristics of the study area. The Gölbaşi Specially Protected Area (SPA) being the case area has many local environmental disturbances, especially with respect to its hydrological system, and the area is beset by increasing demands for its use by the burgeoning human population. It is obviously clear that the present intensive demand for recreational use will be forecasted further increase in the future. The count of rural residences is estimated to increase by 50% over the next decade. This intensive demand shall further strain the carrying capacity of the ecological milieu, which has already suffered to a significant degree because of the present urban and rural activities. The Gölbaşi district is located only 20 km from the city center of Ankara, and its surroundings were legally designated to be a Specially Protected Area primarily for the existence of lacustral and fluvial systems where two interconnected lakes exist: Mogan and Eğmir Lakes. Essentially, the continuity of the lacustral and fluvial system of Lakes Mogan and Eğmir depends on the preservation and improvement of the water sources. However, interconnected surface water bodies of these lakes are actually quite contaminated, and a decline in the water flow from Mogan to Eğmir has been observed. For the elaboration of the present method, required conventional maps (at 1/25,000 scale) of topography (for slope analysis) and geology (for erodibility and permeability analysis) were transferred to computer media using AutoCAD R.14 software. The rectification of the transferred data was done using ERDAS Imagine 8.3. All data were then transferred into a GIS engine (Arcview 3.2). This software provided the ability to create, manipulate, analyze and display topologically correct geographic data in digital form. The method proceeded according to the following phases: 1. Analysis of the hydrologic landscape structure; 2. Permeability of the soil structure; 3. Permeability of the geological structure; 4. Conservation zones.}, } @article {pmid18036242, year = {2007}, author = {Rose, MR and Oakley, TH}, title = {The new biology: beyond the Modern Synthesis.}, journal = {Biology direct}, volume = {2}, number = {}, pages = {30}, pmid = {18036242}, issn = {1745-6150}, mesh = {Biology/*methods ; Computational Biology/*methods ; *Evolution, Molecular ; Genomics/*methods ; Models, Biological ; Molecular Biology/methods/*trends ; Phylogeny ; Proteomics/methods ; Systems Biology/methods/trends ; }, abstract = {BACKGROUND: The last third of the 20th Century featured an accumulation of research findings that severely challenged the assumptions of the "Modern Synthesis" which provided the foundations for most biological research during that century. The foundations of that "Modernist" biology had thus largely crumbled by the start of the 21st Century. This in turn raises the question of foundations for biology in the 21st Century.

CONCLUSION: Like the physical sciences in the first half of the 20th Century, biology at the start of the 21st Century is achieving a substantive maturity of theory, experimental tools, and fundamental findings thanks to relatively secure foundations in genomics. Genomics has also forced biologists to connect evolutionary and molecular biology, because these formerly Balkanized disciplines have been brought together as actors on the genomic stage. Biologists are now addressing the evolution of genetic systems using more than the concepts of population biology alone, and the problems of cell biology using more than the tools of biochemistry and molecular biology alone. It is becoming increasingly clear that solutions to such basic problems as aging, sex, development, and genome size potentially involve elements of biological science at every level of organization, from molecule to population. The new biology knits together genomics, bioinformatics, evolutionary genetics, and other such general-purpose tools to supply novel explanations for the paradoxes that undermined Modernist biology.}, } @article {pmid18035364, year = {2008}, author = {Simpson, SL and Quirino, JP and Terabe, S}, title = {On-line sample preconcentration in capillary electrophoresis. Fundamentals and applications.}, journal = {Journal of chromatography. A}, volume = {1184}, number = {1-2}, pages = {504-541}, doi = {10.1016/j.chroma.2007.11.001}, pmid = {18035364}, issn = {0021-9673}, mesh = {Animals ; Biological Products/analysis ; Ecotoxicology/methods ; Electrophoresis, Capillary/*methods ; Environmental Monitoring/methods ; Food Analysis/methods ; Forensic Toxicology/methods ; Humans ; Hydrogen-Ion Concentration ; Online Systems ; Pharmaceutical Preparations/analysis ; }, abstract = {On-line preconcentration is one of the aspects of analytical method development using capillary electrophoretic techniques. The choice of the sample matrix alone can significantly alter both method sensitivity and separation efficiency. The recent trend to detect samples in narrower separation vessels also necessitates the need to improve detection sensitivity. The desire to detect very low levels of analytes using limited amounts of sample from biological specimens and the high separation efficiency obtainable using very large injections compared to classical small size injections also adds to this list. Indeed, one of the rich areas of research in the capillary electrophoresis field is on on-line sample preconcentration. More than 400 published research articles gathered from the http://www.webofscience.com from the year 2000 described a form of on-line preconcentration in capillary electrophoresis. This review provides a comprehensive table listing the applications of on-line preconcentration in capillary electrophoresis.}, } @article {pmid18030285, year = {2007}, author = {Pickford, DB and Larroze, S and Takase, M and Mitsui, N and Tooi, O and Santo, N}, title = {Investigating potential for effects of environmental endocrine disrupters on wild populations of amphibians in UK and Japan: status of historical databases and review of methods.}, journal = {Environmental sciences : an international journal of environmental physiology and toxicology}, volume = {14}, number = {6}, pages = {297-317}, pmid = {18030285}, issn = {0915-955X}, mesh = {*Amphibians ; Animals ; Data Collection ; Databases, Factual ; Endocrine Disruptors/toxicity ; Environmental Pollutants/toxicity ; Japan ; Population Density ; United Kingdom ; }, abstract = {Concern over global declines among amphibians has resulted in increased interest in the effects of environmental contaminants on amphibian populations, and more recently, this has stimulated research on the potential adverse effects of environmental endocrine disrupters in amphibians. Laboratory studies of the effects of single chemicals on endocrine-relevant endpoints in amphibian, mainly anuran, models are valuable in characterizing sensitivity at the individual level and may yield useful bioassays for screening chemicals for endocrine toxicity (for example, thyroid disrupting activity). Nevertheless, in the UK and Japan as in many other countries, it has yet to be demonstrated unequivocally that the exposure of native amphibians to endocrine disrupting environmental contaminants results in adverse effects at the population level. Assessing the potential of such effects is likely to require an ecoepidemiological approach to investigate associations between predicted or actual exposure of amphibians to (endocrine disrupting) environmental contaminants and biologically meaningful responses at the population level. In turn, this demands recent but relatively long-term population trend data. We review two potential sources of such data for widespread UK anurans that could be used in such investigations: records for common frogs and common toads in several databases maintained by the Biological Records Centre (UK Government Centre for Ecology and Hydrology), and adult toad count data from 'Toads on Roads' schemes registered with the UK wildlife charity 'Froglife'. There were little abundance data in the BRC databases that could be used for this purpose, while count data from the Toads on Roads schemes is potentially confounded by the effects of local topology on the detection probabilities and operation of nonchemical anthropogenic stressors. For Japan, local and regional surveys of amphibians and national ecological censuses gathering amphibian data were reviewed to compile survey methodologies and these were compared with methods used in the UK and other countries. Substantial consensus exists in amphibian survey methodologies and this should be exploited in the initiation of coordinated monitoring programs for widespread and common anuran amphibians in Japan and the UK to generate long-term robust and standardized population trend data. Such data would support comparative ecoepidemiological assessments of the impact of environmental endocrine disrupters in these two cooperating countries.}, } @article {pmid18028304, year = {2008}, author = {Clark, RW and Brown, WS and Stechert, R and Zamudio, KR}, title = {Integrating individual behaviour and landscape genetics: the population structure of timber rattlesnake hibernacula.}, journal = {Molecular ecology}, volume = {17}, number = {3}, pages = {719-730}, doi = {10.1111/j.1365-294X.2007.03594.x}, pmid = {18028304}, issn = {1365-294X}, mesh = {Animal Migration ; Animals ; Crotalus/*genetics/physiology ; DNA/chemistry/genetics ; *Ecosystem ; Female ; *Gene Flow ; Genetic Variation ; Genetics, Population ; Genotype ; Geographic Information Systems ; Linkage Disequilibrium ; Male ; Microsatellite Repeats ; New York ; Polymerase Chain Reaction ; }, abstract = {Individuals of many species show high levels of fidelity to natal populations, often due to reliance on patchily distributed habitat features. In many of these species, the negative impacts of inbreeding are mitigated through specialized behaviours such as seasonal mating dispersal. Quantifying population structure for species with these characteristics can potentially elucidate social and environmental factors that interact to affect mating behaviour and population connectivity. In the northern part of their range, timber rattlesnakes are communal hibernators with high natal philopatry. Individuals generally recruit to the same hibernaculum as their mother and remain faithful to that hibernaculum throughout their lives. We examined the genetic structure of Crotalus horridus hibernacula in the northeastern USA using microsatellite loci. Sampled hibernacula exhibited only modest levels of differentiation, indicating a significant level of gene flow among them. We found no significant correlation between genetic differentiation and geographical distance, but did find significant positive correlation between genetic differentiation and a cost-based distance metric adjusted to include the amount of potential basking habitat between hibernacula. Therefore, thermoregulation sites may increase gene flow by increasing the potential for contact among individuals from different populations. Parentage analyses confirmed high levels of philopatry of both sexes to their maternal hibernaculum; however, approximately one-third of paternity assignments involved individuals between hibernacula, confirming that gene flow among hibernacula occurs largely through seasonal male mating dispersal. Our results underscore the importance of integrating individual-level behaviours and landscape features with studies of fine-scale population genetics in species with high fidelity to patchily distributed habitats.}, } @article {pmid18027752, year = {2007}, author = {Qian, SS and Shen, Z}, title = {Ecological applications of multilevel analysis of variance.}, journal = {Ecology}, volume = {88}, number = {10}, pages = {2489-2495}, doi = {10.1890/06-2041.1}, pmid = {18027752}, issn = {0012-9658}, mesh = {Analysis of Variance ; Bayes Theorem ; *Data Interpretation, Statistical ; Ecology/*methods/*statistics & numerical data ; Mathematical Computing ; *Models, Statistical ; }, abstract = {A Bayesian representation of the analysis of variance by A. Gelman is introduced with ecological examples. These examples demonstrate typical situations encountered in ecological studies. Compared to conventional methods, the multilevel approach is more flexible in model formulation, easier to set up, and easier to present. Because the emphasis is on estimation, multilevel models are more informative than the results from a significance test. The improved capacity is largely due to the changed computation methods. In our examples, we show that (1) the multilevel model is able to discern a treatment effect that is smaller than the conventional approach can detect, (2) the graphical presentation associated with the multilevel method is more informative, and (3) the multilevel model can incorporate all sources of uncertainty to accurately describe the true relationship between the outcome and potential predictors.}, } @article {pmid18022645, year = {2008}, author = {Livnat, A and Pippenger, N}, title = {Systematic mistakes are likely in bounded optimal decision-making systems.}, journal = {Journal of theoretical biology}, volume = {250}, number = {3}, pages = {410-423}, doi = {10.1016/j.jtbi.2007.09.044}, pmid = {18022645}, issn = {1095-8541}, mesh = {Animals ; Choice Behavior ; Computational Biology ; *Decision Making ; Humans ; *Models, Neurological ; Nerve Net ; }, abstract = {Systematic mistakes can be distinguished from other types of mistakes in that they are repeatable and predictable within a given organism, and are not due to uncertainty or lack of information. Here we provide a mathematical definition for the concept of systematic mistakes, which captures the way this concept has been used in the behavioral sciences. We also provide an analytical model of information processing networks that are made of large numbers of components, in analogy to the brain being made of a large number of neurons. We show that, for almost all behavioral tasks, and for a wide range of limitations on the computational complexity of the decision-making network, the best possible decision-makers will make systematic mistakes. This result, together with available empirical evidence, suggests that violations of rationality in humans and animals are consistent with natural selection, as the latter operates under constraints.}, } @article {pmid18021762, year = {2008}, author = {Lee, SJ and Hajat, S and Steer, PJ and Filippi, V}, title = {A time-series analysis of any short-term effects of meteorological and air pollution factors on preterm births in London, UK.}, journal = {Environmental research}, volume = {106}, number = {2}, pages = {185-194}, doi = {10.1016/j.envres.2007.10.003}, pmid = {18021762}, issn = {0013-9351}, mesh = {Air Pollutants/*adverse effects/chemistry ; Air Pollution/*adverse effects ; Databases, Factual ; England/epidemiology ; Environmental Exposure ; Female ; Humans ; Infant, Newborn ; Male ; Maternal Exposure ; Ozone/adverse effects/chemistry ; Particulate Matter/adverse effects/chemistry ; Premature Birth/*epidemiology/etiology/prevention & control ; Risk Factors ; Time ; Urban Health ; }, abstract = {Although much is known about the incidence and burden of preterm birth, its biological mechanisms are not well understood. While several studies have suggested that high levels of air pollution or exposure to particular climatic factors may be associated with an increased risk of preterm birth, other studies do not support such an association. To determine whether exposure to various environmental factors place a large London-based population at higher risk for preterm birth, we analyzed 482,568 births that occurred between 1988 and 2000 from the St. Mary's Maternity Information System database. Using an ecological study design, any short-term associations between preterm birth and various environmental factors were investigated using time-series regression techniques. Environmental exposures included air pollution (ambient ozone and PM(10)) and climatic factors (temperature, rainfall, sunshine, relative humidity, barometric pressure, and largest drop in barometric pressure). In addition to exposure on the day of birth, cumulative exposure up to 1 week before birth was investigated. The risk of preterm birth did not increase with exposure to the levels of ambient air pollution or meteorological factors experienced by this population. Cumulative exposure from 0 to 6 days before birth also did not show any significant effect on the risk of preterm birth. This large study, covering 13 years, suggests that there is no association between preterm births and recent exposure to ambient air pollution or recent changes in the weather.}, } @article {pmid18021129, year = {2007}, author = {Edelman, LS}, title = {Using geographic information systems in injury research.}, journal = {Journal of nursing scholarship : an official publication of Sigma Theta Tau International Honor Society of Nursing}, volume = {39}, number = {4}, pages = {306-311}, doi = {10.1111/j.1547-5069.2007.00185.x}, pmid = {18021129}, issn = {1527-6546}, mesh = {Bias ; Community Health Planning ; Confounding Factors, Epidemiologic ; Ecology ; Epidemiologic Methods ; Geographic Information Systems/*organization & administration ; Humans ; Information Services ; Internet ; Nursing Research/organization & administration ; Organizational Objectives ; Reproducibility of Results ; Research Design ; Resource Allocation ; Risk Assessment ; Risk Factors ; Software ; Technology Assessment, Biomedical ; Topography, Medical/organization & administration ; Wounds and Injuries/*epidemiology/etiology/prevention & control ; }, abstract = {PURPOSE: To provide an overview of geographic information systems (GIS) and to discuss current and future applications in injury and trauma research.

DESIGN: Literature review and discourse of GIS technology related to injury and trauma research.

METHOD: A search of scientific literature databases, text books, and online resources was undertaken to describe the current and prospective uses of GIS in injury and trauma research.

RESULTS: Geographic information systems are computerized mapping systems that link information from different data sets spatially. The advantage of GIS is the capability to graphically display different attributes of an area in a way that is easily interpretable. Geographic information systems have been used to study injury rates, describe populations at risk for injury, examine access to trauma care, and develop and assess injury prevention programs.

CONCLUSIONS: Geographic information systems are tools for injury researchers to analyze injury rates and risks and to describe their results with colorful maps and graphics that allow the public to see how injuries affect their communities.}, } @article {pmid18020808, year = {2007}, author = {Zhang, ZX and Hempel, PS and Han, YL and Tjosvold, D}, title = {Transactive memory system links work team characteristics and performance.}, journal = {The Journal of applied psychology}, volume = {92}, number = {6}, pages = {1722-1730}, doi = {10.1037/0021-9010.92.6.1722}, pmid = {18020808}, issn = {0021-9010}, mesh = {Adult ; *Cooperative Behavior ; *Employment ; Female ; Humans ; *Information Storage and Retrieval ; *Interpersonal Relations ; Male ; *Memory ; }, abstract = {Teamwork and coordination of expertise among team members with different backgrounds are increasingly recognized as important for team effectiveness. Recently, researchers have examined how team members rely on transactive memory system (TMS; D. M. Wegner, 1987) to share their distributed knowledge and expertise. To establish the ecological validity and generality of TMS research findings, this study sampled 104 work teams from a variety of organizational settings in China and examined the relationships between team characteristics, TMS, and team performance. The results suggest that task interdependence, cooperative goal interdependence, and support for innovation are positively related to work teams' TMS and that TMS is related to team performance; moreover, structural equation analysis indicates that TMS mediates the team characteristics-performance links. Findings have implications both for team leaders to manage their work teams effectively and for team members to improve their team performance.}, } @article {pmid18019961, year = {2000}, author = {Zuber, PL and Dignam, TA and Caldwell, MB and Wiesner, PJ}, title = {Disparities in hospital utilization in an urban county: use of local consumer marketing data for priority setting.}, journal = {Journal of public health management and practice : JPHMP}, volume = {6}, number = {6}, pages = {58-66}, doi = {10.1097/00124784-200006060-00009}, pmid = {18019961}, issn = {1078-4659}, mesh = {Adolescent ; Adult ; Child ; Child, Preschool ; Cross-Sectional Studies ; *Databases as Topic ; Female ; Georgia ; *Health Priorities ; Healthcare Disparities/*statistics & numerical data ; Hospitalization/*statistics & numerical data ; Humans ; Infant ; Infant, Newborn ; Male ; Middle Aged ; Racial Groups ; Social Class ; Urban Population ; }, abstract = {National data sets are often insufficient for priority setting by local public health systems and the communities they serve. We used marketing data to conduct an ecological analysis of hospital discharge rates in DeKalb County, Georgia, during 1996. Persons living in poorer areas had significantly higher discharge rates for the following conditions: hypertensive disease, blood-related conditions, pneumonia/influenza, diabetes, and chronic obstructive pulmonary diseases. Local marketing data helped identify conditions associated with higher hospital utilization in poorer areas of this urban county. This identification of priority issues informs plans for behavior modification, access to primary care and a healthy environment.}, } @article {pmid17999108, year = {2008}, author = {Dodds, WK and Oakes, RM}, title = {Headwater influences on downstream water quality.}, journal = {Environmental management}, volume = {41}, number = {3}, pages = {367-377}, pmid = {17999108}, issn = {0364-152X}, mesh = {Ecology ; *Fresh Water ; Geographic Information Systems ; Kansas ; }, abstract = {We investigated the influence of riparian and whole watershed land use as a function of stream size on surface water chemistry and assessed regional variation in these relationships. Sixty-eight watersheds in four level III U.S. EPA ecoregions in eastern Kansas were selected as study sites. Riparian land cover and watershed land use were quantified for the entire watershed, and by Strahler order. Multiple regression analyses using riparian land cover classifications as independent variables explained among-site variation in water chemistry parameters, particularly total nitrogen (41%), nitrate (61%), and total phosphorus (63%) concentrations. Whole watershed land use explained slightly less variance, but riparian and whole watershed land use were so tightly correlated that it was difficult to separate their effects. Water chemistry parameters sampled in downstream reaches were most closely correlated with riparian land cover adjacent to the smallest (first-order) streams of watersheds or land use in the entire watershed, with riparian zones immediately upstream of sampling sites offering less explanatory power as stream size increased. Interestingly, headwater effects were evident even at times when these small streams were unlikely to be flowing. Relationships were similar among ecoregions, indicating that land use characteristics were most responsible for water quality variation among watersheds. These findings suggest that nonpoint pollution control strategies should consider the influence of small upland streams and protection of downstream riparian zones alone is not sufficient to protect water quality.}, } @article {pmid17997312, year = {2007}, author = {Bull, AT and Stach, JE}, title = {Marine actinobacteria: new opportunities for natural product search and discovery.}, journal = {Trends in microbiology}, volume = {15}, number = {11}, pages = {491-499}, doi = {10.1016/j.tim.2007.10.004}, pmid = {17997312}, issn = {0966-842X}, mesh = {Actinobacteria/genetics/*isolation & purification/*physiology ; *Biological Products ; Computational Biology ; Ecosystem ; Genomics ; Geologic Sediments/microbiology ; *Marine Biology ; Phylogeny ; Seawater/*microbiology ; Symbiosis ; }, abstract = {It is widely accepted that new drugs, especially antibiotics, are urgently required, and that the most propitious source remains natural products. We argue that in exploring new sources of bioactive natural products the marine environment warrants particular attention, in view of the remarkable diversity of microorganisms and metabolic products. Recent reports of new chemical entities and first-in-class drug candidates, and confirmation of indigenous marine actinobacteria, make exciting discoveries even more likely given the unrivalled capacity of this class of bacteria to produce exploitable natural products.}, } @article {pmid17993669, year = {2007}, author = {Ghai, R and Chakraborty, T}, title = {Comparative microbial genome visualization using GenomeViz.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {395}, number = {}, pages = {97-108}, doi = {10.1007/978-1-59745-514-5_6}, pmid = {17993669}, issn = {1064-3745}, mesh = {*Databases, Genetic ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Sequence Alignment ; }, abstract = {Recent years have brought a tremendous increase in the amount of sequence data from various bacterial genome sequencing projects, an increase that is projected to accelerate over the next years. Comparative genomics of microbial strains has provided us with unprecedented information to describe a bacterial species and examine for microbial diversity. This has allowed us to define core genomes based on genes commonly present in all strains of a species or genus and to identify dispensable regions in the genome harboring genus-, species-, and even strain-specific genes. Nevertheless, the task of organizing and summarizing the data to extract the most informative features remains a challenging yet critical endeavor. Visualization is an effective way of structuring and presenting such information effectively, in a concise and eloquent fashion. The large-scale views unveil commonalities and differences between the genomes that may shed light on their evolutionary relationships and define characteristics that are typical of pathogenicity or other ecological adaptations. We describe GenomeViz, a tool for comparative visualization of bacterial genomes that allows the user to actively create, modify and query a genome plot in a visually compact, user-friendly, and interactive manner.}, } @article {pmid17993125, year = {2007}, author = {Nesatyy, VJ and Suter, MJ}, title = {Proteomics for the analysis of environmental stress responses in organisms.}, journal = {Environmental science & technology}, volume = {41}, number = {20}, pages = {6891-6900}, doi = {10.1021/es070561r}, pmid = {17993125}, issn = {0013-936X}, mesh = {Biomarkers ; Computational Biology ; Ecology ; Environmental Pollutants/*toxicity ; Proteins/analysis ; *Proteomics ; }, abstract = {Thousands of man-made chemicals are constantly released into the environment by agricultural and industrial production processes, traffic, and countless other human activities. Hence, very complex mixtures of anthropogenic chemicals and the transformation products of non-persistent compounds can be found in the aquatic environment. They reflect regional input but are also influenced by long-range transport. Thus, predicting effects on organisms and assessing the quality of a specific ecosystem based on chemical analysis is a challenge. This is not only because of the wide variety of chemicals, with far ranging physicochemical properties, but also because of the sometimes very low effect levels and concerted effects caused by concentration additivity or even synergism. The situation is further complicated by the temporal variability of the exposure concentrations caused, for example, by rain events or regular daily fluctuations as seen in wastewater treatment plant effluents. The analysis of an organism's proteome allows the detection of subtle changes in the level of individual proteins in response to environmental stressors. This potentially leads to the discovery of biomarkers of exposure and helps to gain insights into underlying mechanisms of toxicity. Today, studies using environmental proteomics have investigated many organisms, ranging from microorganisms and plants to invertebrates and vertebrates. Nevertheless, proteomics is a field of environmental research still in its infancy, due to a number of caveats, such as the limited number of organisms fully covered in the sequence databases, the high genetic variability, and the dependence on environmental factors. However, it is gradually becoming an established technology. This review article highlights recent advances in the field of proteomics, mainly focusing on experimental techniques that have the potential to help us understand toxic modes of action and identify novel ecotoxicological biomarkers.}, } @article {pmid17985307, year = {2007}, author = {Juchum, FS and Leal, JB and Santos, LM and Almeida, MP and Ahnert, D and Corrêa, RX}, title = {Evaluation of genetic diversity in a natural rosewood population (Dalbergia nigra Vell. Allemão ex Benth.) using RAPD markers.}, journal = {Genetics and molecular research : GMR}, volume = {6}, number = {3}, pages = {543-553}, pmid = {17985307}, issn = {1676-5680}, mesh = {Computational Biology/methods ; DNA Primers/chemistry/genetics ; DNA, Plant ; Dalbergia/*genetics ; *Genes, Plant ; Genetic Markers ; Genetic Variation ; Genetics, Population ; Genotype ; Models, Theoretical ; Phylogeny ; Polymerase Chain Reaction ; Polymorphism, Genetic ; Random Amplified Polymorphic DNA Technique ; }, abstract = {Dalbergia nigra (rosewood) is a long-lived leguminous species, which is endemic to the Brazilian Atlantic forest. Because of the high economic value of its wood, this species has been over-explored in recent years. Currently, rosewood is included in the IUCN Red List as vulnerable. We examined the genetic diversity of 87 specimens of D. nigra sampled from a continuous forest in the Veracel Reserve and Brazilwood Ecological Station, Porto Seguro, Bahia state, with random amplified polymorphic DNA markers. Grouping analyses were done using unweighted pair group method with arithmetic averages. Using the 16 most informative primers, 112 markers were obtained; 39% (44 bands) were polymorphic. A genetic similarity matrix was made based on the polymorphic bands. The dispersion graph and dendrogram analyses showed three distinct sub-populations. The degree of polymorphism was high, near that of other populations of similar species; however, it was considered low for the conservation of this species.}, } @article {pmid17975742, year = {2007}, author = {Huang, J and Wang, R and Zhang, H}, title = {Analysis of patterns and ecological security trend of modern oasis landscapes in Xinjiang, China.}, journal = {Environmental monitoring and assessment}, volume = {134}, number = {1-3}, pages = {411-419}, pmid = {17975742}, issn = {0167-6369}, mesh = {Agriculture ; China ; *Conservation of Natural Resources ; Desert Climate ; Ecology ; *Ecosystem ; Geographic Information Systems ; Poaceae ; Satellite Communications ; Trees ; Urbanization ; }, abstract = {Ecological security has become so important that it will affect the national security and social sustainable development. In this paper, a case study on the ecological security indexes of modern oasis landscapes in Beitun Oasis, Xinjiang, was carried out. The spatial neighbouring parameters, such as the contiguous length, measure of area and patch quantity of oasis landscape patches, affected by desert landscape patches were calculated by using GIS-based buffer analysis, the method of calculating ecological security indexes of oasis landscape was developed, and the dynamic changes of patterns and ecological security indexes of the oasis landscapes since recent 30 years were analyzed. The results showed that soil salinization or alkalization and paludification were major factors affecting the ecological security in Beitun Oasis. Therefore, measures should be taken actively to prevent and control secondary salinization and paludification. The ecological security indexes of the oasis landscape in 1972, 1990 and 2005 were 78.91, 82.28 and 83.86, respectively, which showed the degree of security is improving, and the environment was developing harmoniously between human and nature. The methods of evaluating ecological security based on the spatial neighbouring relations between landscape patches can be used to reflect preliminarily the ecological security patterns of landscapes.}, } @article {pmid17974336, year = {2007}, author = {Reich, PB and Wright, IJ and Lusk, CH}, title = {Predicting leaf physiology from simple plant and climate attributes: a global GLOPNET analysis.}, journal = {Ecological applications : a publication of the Ecological Society of America}, volume = {17}, number = {7}, pages = {1982-1988}, doi = {10.1890/06-1803.1}, pmid = {17974336}, issn = {1051-0761}, mesh = {Climate ; Databases, Factual ; Forecasting ; Nitrogen ; Phosphorus ; Photosynthesis ; Plant Development ; Plant Leaves/*physiology ; Plants/metabolism ; Rain ; Sunlight ; Temperature ; }, abstract = {Knowledge of leaf chemistry, physiology, and life span is essential for global vegetation modeling, but such data are scarce or lacking for some regions, especially in developing countries. Here we use data from 2021 species at 175 sites around the world from the GLOPNET compilation to show that key physiological traits that are difficult to measure (such as photosynthetic capacity) can be predicted from simple qualitative plant characteristics, climate information, easily measured ("soft") leaf traits, or all of these in combination. The qualitative plant functional type (PFT) attributes examined are phylogeny (angiosperm or gymnosperm), growth form (grass, herb, shrub, or tree), and leaf phenology (deciduous vs. evergreen). These three PFT attributes explain between one-third and two-thirds of the variation in each of five quantitative leaf ecophysiological traits: specific leaf area (SLA), leaf life span, mass-based net photosynthetic capacity (Amass), nitrogen content (N(mass)), and phosphorus content (P(mass)). Alternatively, the combination of four simple, widely available climate metrics (mean annual temperature, mean annual precipitation, mean vapor pressure deficit, and solar irradiance) explain only 5-20% of the variation in those same five leaf traits. Adding the climate metrics to the qualitative PFTs as independent factors in the model increases explanatory power by 3-11% for the five traits. If a single easily measured leaf trait (SLA) is also included in the model along with qualitative plant traits and climate metrics, an additional 5-25% of the variation in the other four other leaf traits is explained, with the models accounting for 62%, 65%, 66%, and 73% of global variation in N(mass), P(mass), A(mass), and leaf life span, respectively. Given the wide availability of the summary climate data and qualitative PFT data used in these analyses, they could be used to explain roughly half of global variation in the less accessible leaf traits (A(mass), leaf life span, N(mass), P(mass)); this can be augmented to two-thirds of all variation if climatic and PFT data are used in combination with the readily measured trait SLA. This shows encouraging possibilities of progress in developing general predictive equations for macro-ecology, global scaling, and global modeling.}, } @article {pmid17974242, year = {2007}, author = {Zhang, JQ and Liang, JD and Zhou, DW}, title = {[Risk assessment of ecological disasters in Jilin Province based on GIS].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {18}, number = {8}, pages = {1765-1770}, pmid = {17974242}, issn = {1001-9332}, mesh = {Algorithms ; China ; *Disasters ; *Ecosystem ; Environmental Monitoring/*methods ; *Geographic Information Systems ; Geography ; Models, Theoretical ; Risk Assessment ; Socioeconomic Factors ; }, abstract = {Based on the principles of natural disasters risk formation, and considering the natural and social features of Jilin Province, relevant indices were selected from the aspects of hazard, exposure, vulnerability and emergency responses, and recovery capability, and Natural Disaster Risk Index method, Weighted Comprehensive Analysis, and Analytic Hierarchy Process were used to build the risk assessment model of ecological disasters in this Province. The contribution of each index was assessed, and the regionalization map of the ecological disasters risk in Jilin Province was built based on GIS, which would provide scientific references in accurately understanding the risk level of ecological disasters and in decision-making of eco-environment restoration and management in Jilin Province.}, } @article {pmid17974241, year = {2007}, author = {Yang, M and Li, XZ and Hu, YM and He, XY}, title = {[Annual sediment yield in sub-watersheds at upper reaches of Minjiang River: a simulation with SEDD model].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {18}, number = {8}, pages = {1758-1764}, pmid = {17974241}, issn = {1001-9332}, mesh = {China ; Ecosystem ; Environmental Monitoring/*methods ; Geographic Information Systems ; Geography ; Geologic Sediments/*analysis ; Models, Theoretical ; *Rivers ; Water Pollutants/*analysis ; }, abstract = {Based on GIS, a sediment delivery distributed (SEDD) model was established to simulate the spatial patterns of annual soil water erosion and sediment yield in two sub-watersheds at the upper reaches of Minjiang River. The model was based on the revised universal soil loss equation (RUSLE) for calculating the annual soil water erosion, and coupled with an equation for evaluating the sediment delivery ratio of each cell. The results showed that in most regions of the two sub-watersheds, erosion intensity was below high level. Similar spatial patterns of sediment delivery ratio and sediment yield were observed, i. e., being higher along river, and approached to zero in other regions. Most parts of eroded soil were deposited in the sub-watersheds during their transportation, and less than 5% of it reached the river. Shrub land and forestland were the most important sources of sediment yield, and the sum of their sediment yield occupied 70% of the total.}, } @article {pmid17971876, year = {2007}, author = {Holloway, AK and Begun, DJ}, title = {Rampant adaptive evolution in regions of proteins with unknown function in Drosophila simulans.}, journal = {PloS one}, volume = {2}, number = {10}, pages = {e1113}, pmid = {17971876}, issn = {1932-6203}, support = {R01 GM071926/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; *Biological Evolution ; Computational Biology ; Drosophila ; Drosophila melanogaster/metabolism ; Evolution, Molecular ; Genetic Variation ; Genetics, Population ; Genome ; Models, Biological ; Models, Genetic ; Polymorphism, Genetic ; Protein Folding ; Protein Structure, Tertiary ; }, abstract = {Adaptive protein evolution is pervasive in Drosophila. Genomic studies, thus far, have analyzed each protein as a single entity. However, the targets of adaptive events may be localized to particular parts of proteins, such as protein domains or regions involved in protein folding. We compared the population genetic mechanisms driving sequence polymorphism and divergence in defined protein domains and non-domain regions. Interestingly, we find that non-domain regions of proteins are more frequent targets of directional selection. Protein domains are also evolving under directional selection, but appear to be under stronger purifying selection than non-domain regions. Non-domain regions of proteins clearly play a major role in adaptive protein evolution on a genomic scale and merit future investigations of their functional properties.}, } @article {pmid17970819, year = {2008}, author = {Hedeker, D and Mermelstein, RJ and Demirtas, H}, title = {An application of a mixed-effects location scale model for analysis of Ecological Momentary Assessment (EMA) data.}, journal = {Biometrics}, volume = {64}, number = {2}, pages = {627-634}, pmid = {17970819}, issn = {1541-0420}, support = {P01 CA098262/CA/NCI NIH HHS/United States ; P01 CA098262-03/CA/NCI NIH HHS/United States ; 5P01 CA98262/CA/NCI NIH HHS/United States ; }, mesh = {*Affect ; Bias ; Biometry/*methods ; Computer Simulation ; *Data Interpretation, Statistical ; Ecology ; *Models, Statistical ; *Research Design ; }, abstract = {For longitudinal data, mixed models include random subject effects to indicate how subjects influence their responses over repeated assessments. The error variance and the variance of the random effects are usually considered to be homogeneous. These variance terms characterize the within-subjects (i.e., error variance) and between-subjects (i.e., random-effects variance) variation in the data. In studies using ecological momentary assessment (EMA), up to 30 or 40 observations are often obtained for each subject, and interest frequently centers around changes in the variances, both within and between subjects. In this article, we focus on an adolescent smoking study using EMA where interest is on characterizing changes in mood variation. We describe how covariates can influence the mood variances, and also extend the standard mixed model by adding a subject-level random effect to the within-subject variance specification. This permits subjects to have influence on the mean, or location, and variability, or (square of the) scale, of their mood responses. Additionally, we allow the location and scale random effects to be correlated. These mixed-effects location scale models have useful applications in many research areas where interest centers on the joint modeling of the mean and variance structure.}, } @article {pmid17967071, year = {2008}, author = {Burkhard, LP and Lukasewycz, MT}, title = {Toxicity equivalency values for polychlorinated biphenyl mixtures.}, journal = {Environmental toxicology and chemistry}, volume = {27}, number = {3}, pages = {529-534}, doi = {10.1897/07-349.1}, pmid = {17967071}, issn = {0730-7268}, mesh = {Animals ; Birds ; Complex Mixtures ; Environmental Monitoring ; Environmental Pollutants/*toxicity ; Fishes ; Mammals ; Medical Informatics ; Polychlorinated Biphenyls/*toxicity ; World Health Organization ; }, abstract = {For aquatic, avian, and mammalian species, dioxin equivalency values (TEQs) were computed for Aroclor, Clophen, Kanechlor, Chlorofen, Sovol, Delor, Phenoclor, and Chinese polychlorinated biphenyl (PCB) mixtures by using World Health Organization toxicity equivalency factors (TEFs) and compound-specific compositional data for PCBs, polychlorinated dibenzo-p-dioxins (PCDDs), and polychlorinated dibenzofurans (PCDFs) for the individual mixtures. The TEQs were similar across the different PCB product lines for mixtures of similar chlorine content. Depending on the PCB mixture, the polychlorinated dibenzo-p-dioxins/dibenzofurans (PCDD/Fs) in the mixture contributed anywhere from 0 to 96% of the total TEQs, and the impact of PCDD/Fs was greatest for the fish TEQs. In comparison to the dioxin-like PCBs, few measurements have been performed for PCDD/Fs in the commercial PCB products.}, } @article {pmid17966366, year = {2007}, author = {Sun, YZ and Guo, LP and Zhu, WQ and Huang, LQ and Pan, YZ}, title = {[Remote sensing monitoring methods for medicinal plants resource in different types of ecological environment].}, journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica}, volume = {32}, number = {14}, pages = {1490-1492}, pmid = {17966366}, issn = {1001-5302}, mesh = {*Atractylodes ; China ; *Conservation of Natural Resources ; Ecosystem ; *Geographic Information Systems ; Image Processing, Computer-Assisted ; *Plants, Medicinal ; Satellite Communications ; }, abstract = {Different remote sensing monitoring methods are needed for the medicinal plant resource in different types of ecological environment. This paper explained remote sensing monitoring methods for the resource of the wild medicinal plants and cultivated plants, and analyzed the rare species, generous species and species in special ecological environment in detail. It provides a new method to all kind of medicinal plants resources' remote sensing monitoring.}, } @article {pmid17966349, year = {2007}, author = {Chen, J and Xie, CX and Chen, SL and Sun, CZ and Zhao, RH and Xu, R}, title = {[Suitability evaluation of Cistanche desertiola based on TCMGIS-I].}, journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica}, volume = {32}, number = {14}, pages = {1396-1401}, pmid = {17966349}, issn = {1001-5302}, mesh = {Breeding ; China ; Cistanche/*growth & development ; Climate ; Conservation of Natural Resources ; *Databases, Factual ; Ecosystem ; *Geographic Information Systems ; Plants, Medicinal/*growth & development ; Soil ; }, abstract = {OBJECTIVE: To analyze the appropriate producing area of Cistanche desertiola.

METHOD: The TCMGIS-I (suitability evaluation geographic information system of traditional Chinese medicine producing area) was used to analyze the appropriate producing area of C. desertiola basing on the optimum ecological factors of Aalashan, Inner-Mongolia autonomous region and North Xinjiang au-tonomous region, the traditional producing areas of C. desertiola.

RESULT: The results showed that the suitable producing areas of C. desertiola included 159 counties of 5 autonomous regions and provinces, i.e. Xinjiang, Inner Mongolia, Ningxia autonomous regions, and Gansu as well as Qinghai provinces. The total area was 675 354.9 km2 and distributed mainly in Aalashan of Inner Mongolia, eastern part of North Xinjiang, northern part of Gansu and in the middle of Ningxia.

CONCLUSION: The suitable producing areas based on TCMGIS-I covered all areas registered in the 3rd national investigation of Chinese traditional medicine resource. And the results were also corresponding to the traditional producing area of C. desertiola recorded in ancient literature and the successful cultivation areas nowadays. It suggested the rationality and reliability of TCMGIS-I.}, } @article {pmid17961001, year = {2007}, author = {Hegney, DG and Buikstra, E and Baker, P and Rogers-Clark, C and Pearce, S and Ross, H and King, C and Watson-Luke, A}, title = {Individual resilience in rural people: a Queensland study, Australia.}, journal = {Rural and remote health}, volume = {7}, number = {4}, pages = {620}, pmid = {17961001}, issn = {1445-6354}, mesh = {*Adaptation, Psychological ; Adult ; Aged ; Aged, 80 and over ; Agriculture ; Community Networks ; Environment ; Female ; Focus Groups ; Health Status ; Humans ; Interviews as Topic ; Male ; Middle Aged ; Models, Psychological ; Narration ; *Psychology, Social ; Qualitative Research ; Queensland ; *Rural Health ; *Social Support ; Socioeconomic Factors ; }, abstract = {INTRODUCTION: This article reports the results of phase 1 of a study into community and individual resilience in rural Australians. The aim of the study was to develop, implement and evaluate a model that enhances psychological wellness in rural people and communities. The study used a critical participatory action research methodology to work in partnership with key individuals and groups in a rural community in Queensland which, anecdotally, was identified by its community representatives as having confronted and responded positively to and dealt with adversities such as drought, hailstorms and bushfire. A focus in the project was to identify vulnerable as well as resilient elements in individuals and the community, with an emphasis on identifying and then using existing individual, group and community resilience as exemplars for those who are less resilient. The study recognised that not all members of the community were resilient; clearly there are more and less resilient groups within this community. Additionally, it was acknowledged that resilience was not a steady state within an individual. Rather, an individual's level of resilience could vary over their lifetime.

METHODS: A participatory action research design was chosen for this study which aimed to identify individual and community resilience factors in a community. The study is being undertaken in three phases. In phase 1 of the study (the focus of this article), 10 in-depth interviews and one focus group (with four participants) were conducted. Individuals identified by a network of community service providers as being particularly resilient were selected to participate in this phase, with the aim of identifying these individuals' perceptions of individual and community resilience. This article reports on the factors identified that impact on the individual resilience of rural people.

RESULTS: Thematic analysis of the qualitative data surrounding individual resilience revealed three themes: images of resilience; characteristics of resilient people and shapers of resilience (environmental influences that increase personal resilience).

CONCLUSIONS: The findings of this study support existing theoretical concepts of resilience, with an added dimension not previously reported. The major finding of this study is that connection to the land, which is strongly embedded in the literature on Indigenous peoples (eg human ecology) and acknowledged as part of Indigenous culture and cosmology, may also be a factor that enhances the resilience of non-Indigenous people who have built up a relationship with the land over time. The extent of this connection and its impact on individual and community resilience was, however, not established in this study, but should also be a major focus of future research.}, } @article {pmid17955469, year = {2007}, author = {Kineman, JJ}, title = {Modeling relations in nature and eco-informatics: a practical application of rosennean complexity.}, journal = {Chemistry & biodiversity}, volume = {4}, number = {10}, pages = {2436-2457}, doi = {10.1002/cbdv.200790199}, pmid = {17955469}, issn = {1612-1880}, mesh = {*Ecosystem ; *Information Management ; *Models, Theoretical ; *Nature ; }, abstract = {The purpose of eco-informatics is to communicate critical information about organisms and ecosystems. To accomplish this, it must reflect the complexity of natural systems. Present information systems are designed around mechanistic concepts that do not capture complexity. Robert Rosen's relational theory offers a way of representing complexity in terms of information entailments that are part of an ontologically implicit 'modeling relation'. This relation has corresponding epistemological components that can be captured empirically, the components being structure (associated with model encoding) and function (associated with model decoding). Relational complexity, thus, provides a long-awaited theoretical underpinning for these concepts that ecology has found indispensable. Structural information pertains to the material organization of a system, which can be represented by data. Functional information specifies potential change, which can be inferred from experiment and represented as models or descriptions of state transformations. Contextual dependency (of structure or function) implies meaning. Biological functions imply internalized or system-dependent laws. Complexity can be represented epistemologically by relating structure and function in two different ways. One expresses the phenomenal relation that exists in any present or past instance, and the other draws the ontology of a system into the empirical world in terms of multiple potentials subject to natural forms of selection and optimality. These act as system attractors. Implementing these components and their theoretical relations in an informatics system will provide more-complete ecological informatics than is possible from a strictly mechanistic point of view. This approach will enable many new possibilities for supporting science and decision making.}, } @article {pmid17955378, year = {2007}, author = {Soroko, SI and Burykh, EA and Bekshaev, SS and Sidorenko, GV and Sergeeva, EG and Khovanskikh, AE and Kormilitsyn, BN and Moralev, SN and Yagodina, OV and Dobrodeeva, LK and Maksimova, IA and Protasova, OV}, title = {Characteristics of the formation of systems activity in the brain and autonomic functions in children in conditions of the European North (discussion paper).}, journal = {Neuroscience and behavioral physiology}, volume = {37}, number = {9}, pages = {857-874}, pmid = {17955378}, issn = {0097-0549}, mesh = {Adolescent ; Alpha Rhythm ; Autonomic Nervous System/*growth & development/*physiology ; Brain/*growth & development/*physiology ; Butyrylcholinesterase/blood ; Cerebrovascular Circulation ; Child ; Child Nutritional Physiological Phenomena ; Climate ; Data Interpretation, Statistical ; Electroencephalography ; Electrophysiology ; Enzymes/metabolism ; Female ; Humans ; Immunity/physiology ; Male ; Monoamine Oxidase/blood ; Neuropsychological Tests ; Rural Population ; Russia ; Social Environment ; Trace Elements/metabolism ; Wechsler Scales ; }, abstract = {Results obtained from complex medical-physiological investigations performed during 10 scientific expeditions in the Arkhangel'sk Region in 2003-2005 are presented. The effects of climatological-geographic, biogeochemical, and social conditions of the conditions obtaining in the Far North region of Russia on sexual maturation, formation of the structural-functional organization of the brain, autonomic functions, and immunological and biochemical status of schoolchildren were studied using state-of-the-art neurophysiological methods (computerized electroencephalography, computerized rheoencephalography, computerized electric dipole origin tomography, etc.), psychophysiological and psychometric methods (assessment of the state of cognitive and memory functions, Wechsler intellectual scale), along with biochemical assay of monoamine oxidase (MAO, the key enzyme in adrenergic neurotransmitter metabolism) and the liver enzyme butyrylcholinesterase (BuChE) and physicochemical analysis of the levels of macroelements and trace elements in the body.}, } @article {pmid17949885, year = {2007}, author = {Kurland, CG and Canbäck, B and Berg, OG}, title = {The origins of modern proteomes.}, journal = {Biochimie}, volume = {89}, number = {12}, pages = {1454-1463}, doi = {10.1016/j.biochi.2007.09.004}, pmid = {17949885}, issn = {0300-9084}, mesh = {Amino Acid Sequence ; Archaea/genetics ; Archaeal Proteins/chemistry/genetics ; Bacteria/genetics ; Bacterial Proteins/chemistry/genetics ; Computational Biology ; Databases, Protein ; Eukaryotic Cells/chemistry ; *Evolution, Molecular ; Genes, Archaeal ; Genes, Bacterial ; Genome ; Humans ; Models, Biological ; Molecular Sequence Data ; Phylogeny ; Protein Structure, Tertiary ; Proteins ; *Proteome ; Proteomics ; Sequence Homology, Amino Acid ; }, abstract = {Distributions of phylogenetically related protein domains (fold superfamilies), or FSFs, among the three Superkingdoms (trichotomy) are assessed. Very nearly 900 of the 1200 FSFs of the trichotomy are shared by two or three Superkingdoms. Parsimony analysis of FSF distributions suggests that the FSF complement of the last common ancestor to the trichotomy was more like that of modern eukaryotes than that of archaea and bacteria. Studies of length distributions among members of orthologous families of proteins present in all three Superkingdoms reveal that such lengths are significantly longer among eukaryotes than among bacteria and archaea. The data also reveal that proteins lengths of eukaryotes are more broadly distributed than they are within archaeal and bacterial members of the same orthologous families. Accordingly, selective pressure for a minimal size is significantly greater for orthologous protein lengths in archaea and bacteria than in eukaryotes. Alignments of orthologous proteins of archaea, bacteria and eukaryotes are characterized by greater sequence variation at their N-terminal and C-terminal domains, than in their central cores. Length variations tend to be localized in the terminal sequences; the conserved sequences of orthologous families are localized in a central core. These data are consistent with the interpretation that the genomes of the last common ancestor (LUCA) encoded a cohort of FSFs not very different from that of modern eukaryotes. Divergence of bacterial and archaeal genomes from that common ancestor may have been accompanied by more intensive reductive evolution of proteomes than that expressed in eukaryotes. Dollo's Law suggests that the evolution of novel FSFs is a very slow process, while laboratory experiments suggests that novel protein genesis from preexisting FSFs can be relatively rapid. Reassortment of FSFs to create novel proteins may have been mediated by genetic recombination before the advent of more efficient splicing mechanisms.}, } @article {pmid17945026, year = {2007}, author = {Gilchrist, MA and Qin, H and Zaretzki, R}, title = {Modeling SAGE tag formation and its effects on data interpretation within a Bayesian framework.}, journal = {BMC bioinformatics}, volume = {8}, number = {}, pages = {403}, pmid = {17945026}, issn = {1471-2105}, mesh = {Bayes Theorem ; Computer Simulation ; Data Interpretation, Statistical ; Databases, Genetic ; *Expressed Sequence Tags ; Gene Expression Profiling/*methods ; *Models, Genetic ; Reproducibility of Results ; Sensitivity and Specificity ; Sequence Analysis, DNA/*methods ; Transcription Factors/*genetics ; }, abstract = {BACKGROUND: Serial Analysis of Gene Expression (SAGE) is a high-throughput method for inferring mRNA expression levels from the experimentally generated sequence based tags. Standard analyses of SAGE data, however, ignore the fact that the probability of generating an observable tag varies across genes and between experiments. As a consequence, these analyses result in biased estimators and posterior probability intervals for gene expression levels in the transcriptome.

RESULTS: Using the yeast Saccharomyces cerevisiae as an example, we introduce a new Bayesian method of data analysis which is based on a model of SAGE tag formation. Our approach incorporates the variation in the probability of tag formation into the interpretation of SAGE data and allows us to derive exact joint and approximate marginal posterior distributions for the mRNA frequency of genes detectable using SAGE. Our analysis of these distributions indicates that the frequency of a gene in the tag pool is influenced by its mRNA frequency, the cleavage efficiency of the anchoring enzyme (AE), and the number of informative and uninformative AE cleavage sites within its mRNA.

CONCLUSION: With a mechanistic, model based approach for SAGE data analysis, we find that inter-genic variation in SAGE tag formation is large. However, this variation can be estimated and, importantly, accounted for using the methods we develop here. As a result, SAGE based estimates of mRNA frequencies can be adjusted to remove the bias introduced by the SAGE tag formation process.}, } @article {pmid17941997, year = {2007}, author = {Eppley, JM and Tyson, GW and Getz, WM and Banfield, JF}, title = {Strainer: software for analysis of population variation in community genomic datasets.}, journal = {BMC bioinformatics}, volume = {8}, number = {}, pages = {398}, pmid = {17941997}, issn = {1471-2105}, mesh = {Base Sequence ; Chromosome Mapping/*methods ; DNA Mutational Analysis/*methods ; *Databases, Genetic ; Genetic Variation/*genetics ; Genetics, Population/methods ; Genome, Bacterial/*genetics ; Molecular Sequence Data ; Sequence Alignment/methods ; Sequence Analysis, DNA/*methods ; *Software ; Species Specificity ; }, abstract = {BACKGROUND: Metagenomic analyses of microbial communities that are comprehensive enough to provide multiple samples of most loci in the genomes of the dominant organism types will also reveal patterns of genetic variation within natural populations. New bioinformatic tools will enable visualization and comprehensive analysis of this sequence variation and inference of recent evolutionary and ecological processes.

RESULTS: We have developed a software package for analysis and visualization of genetic variation in populations and reconstruction of strain variants from otherwise co-assembled sequences. Sequencing reads can be clustered by matching patterns of single nucleotide polymorphisms to generate predicted gene and protein variant sequences, identify conserved intergenic regulatory sequences, and determine the quantity and distribution of recombination events.

CONCLUSION: The Strainer software, a first generation metagenomic bioinformatics tool, facilitates comprehension and analysis of heterogeneity intrinsic in natural communities. The program reveals the degree of clustering among closely related sequence variants and provides a rapid means to generate gene and protein sequences for functional, ecological, and evolutionary analyses.}, } @article {pmid17941840, year = {2007}, author = {McGuire, JA and Linkem, CW and Koo, MS and Hutchison, DW and Lappin, AK and Orange, DI and Lemos-Espinal, J and Riddle, BR and Jaeger, JR}, title = {Mitochondrial introgression and incomplete lineage sorting through space and time: phylogenetics of crotaphytid lizards.}, journal = {Evolution; international journal of organic evolution}, volume = {61}, number = {12}, pages = {2879-2897}, doi = {10.1111/j.1558-5646.2007.00239.x}, pmid = {17941840}, issn = {0014-3820}, mesh = {Animals ; Bayes Theorem ; DNA, Mitochondrial/*chemistry ; Geographic Information Systems ; Geography ; Hybridization, Genetic ; Lizards/*classification/genetics ; Models, Biological ; *Phylogeny ; Sequence Analysis, DNA ; }, abstract = {We investigate the roles of mitochondrial introgression and incomplete lineage sorting during the phylogenetic history of crotaphytid lizards. Our Bayesian phylogenetic estimate for Crotaphytidae is based on analysis of mitochondrial DNA sequence data for 408 individuals representing the 12 extant species of Crotaphytus and Gambelia. The mitochondrial phylogeny disagrees in several respects with a previously published morphological tree, as well as with conventional species designations, and we conclude that some of this disagreement stems from hybridization-mediated mitochondrial introgression, as well as from incomplete lineage sorting. Unidirectional introgression of Crotaphytus collaris (western collared lizard) mitochondria into C. reticulatus (reticulate collared lizard) populations in the Rio Grande Valley of Texas has resulted in the replacement of ancestral C. reticulatus mitochondria over approximately two-thirds of the total range of the species, a linear distance of approximately 270 km. Introgression of C. collaris mitochondria into C. bicinctores (Great Basin collared lizard) populations in southwestern Arizona requires a more complex scenario because at least three temporally separated and superimposed introgression events appear to have occurred in this region. We propose an "introgression conveyor" model to explain this unique pattern of mitochondrial variation in this region. We show with ecological niche modeling that the predicted geographical ranges of C. collaris, C. bicinctores, and C. reticulatus during glacial maxima could have provided enhanced opportunities for past hybridization. Our analyses suggest that incomplete lineage sorting and/or introgression has further confounded the phylogenetic placements of additional species including C. nebrius, C. vestigium, C. insularis, C. grismeri, and perhaps G. copei. Despite many independent instances of interspecific hybridization among crotaphytid lizards, the species continue to maintain morphological and geographic cohesiveness throughout their ranges.}, } @article {pmid17940870, year = {2007}, author = {Patel, MR and Mayer, JA and Slymen, DJ and Weeks, JR and Hurd, AL}, title = {Correlates of tanning facility prevalence within San Diego County, California census tracts.}, journal = {Journal of community health}, volume = {32}, number = {6}, pages = {391-400}, pmid = {17940870}, issn = {0094-5145}, support = {K05CA10051/CA/NCI NIH HHS/United States ; R01CA93532/CA/NCI NIH HHS/United States ; }, mesh = {Adolescent ; Adult ; Age Distribution ; Beauty Culture/*statistics & numerical data ; California ; Cross-Sectional Studies ; Female ; Fitness Centers/*statistics & numerical data ; Geographic Information Systems ; Humans ; Male ; Prevalence ; Sex Distribution ; Skin Neoplasms/*etiology ; Ultraviolet Rays/*adverse effects ; }, abstract = {Adolescents frequenting indoor tanning facilities may have an increased risk of skin cancer. The high level of indoor tanning by this age group may be due, in part, to the large number of tanning facilities in US cities. This study examined how facilities are distributed throughout one large county. Based on ecological models, it was predicted that tanning facilities are more likely to be located within certain neighborhoods based on the neighborhood's distributions of demographic factors, including income, educational attainment, race/ethnicity, age, and sex. We also explored whether selected aspects of the built environment, including the numbers of high schools and fitness centers, would predict the number of tanning facilities. The number of tanning facilities within 605 census tracts of San Diego County was examined through geographic information systems mapping. Results from multivariate Poisson log-linear regression indicated that higher numbers or proportions of the following variables within a census tract were significantly, positively correlated with the number of tanning facilities: fitness centers, teenagers 15-19 years, females 15-24 years, females 25-29 years, and non-Hispanic Whites. Results from additional analyses using a 1000-foot buffer zone around each census tract boundary showed that higher relative distributions of the following variables were significantly, positively correlated with the number of tanning facilities: high schools, fitness centers, females 15-24 years, females 25-29 years, and non-Hispanic Whites. These findings suggest a relationship exists between the numbers of tanning facilities and certain built-environmental and demographic characteristics within census tracts. Determining this relationship is important for developing future interventions.}, } @article {pmid17933781, year = {2008}, author = {Papanicolaou, A and Gebauer-Jung, S and Blaxter, ML and Owen McMillan, W and Jiggins, CD}, title = {ButterflyBase: a platform for lepidopteran genomics.}, journal = {Nucleic acids research}, volume = {36}, number = {Database issue}, pages = {D582-7}, pmid = {17933781}, issn = {1362-4962}, support = {BBS/B/09074/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; Chromosome Mapping ; *Databases, Genetic ; Expressed Sequence Tags ; *Genome, Insect ; Genomics ; Insect Proteins/chemistry/genetics ; Internet ; Lepidoptera/classification/*genetics ; Phylogeny ; Proteomics ; User-Computer Interface ; }, abstract = {With over 100 000 species and a large community of evolutionary biologists, population ecologists, pest biologists and genome researchers, the Lepidoptera are an important insect group. Genomic resources [expressed sequence tags (ESTs), genome sequence, genetic and physical maps, proteomic and microarray datasets] are growing, but there has up to now been no single access and analysis portal for this group. Here we present ButterflyBase (http://www.butterflybase.org), a unified resource for lepidopteran genomics. A total of 273 077 ESTs from more than 30 different species have been clustered to generate stable unigene sets, and robust protein translations derived from each unigene cluster. Clusters and their protein translations are annotated with BLAST-based similarity, gene ontology (GO), enzyme classification (EC) and Kyoto encyclopaedia of genes and genomes (KEGG) terms, and are also searchable using similarity tools such as BLAST and MS-BLAST. The database supports many needs of the lepidopteran research community, including molecular marker development, orthologue prediction for deep phylogenetics, and detection of rapidly evolving proteins likely involved in host-pathogen or other evolutionary processes. ButterflyBase is expanding to include additional genomic sequence, ecological and mapping data for key species.}, } @article {pmid20672486, year = {2005}, author = {Plack, N}, title = {Agrarian reform and ecological change during the Ancien régime: land clearance, peasants and viticulture in the province of Languedoc.}, journal = {French history}, volume = {19}, number = {2}, pages = {189-210}, doi = {10.1093/fh/cri016}, pmid = {20672486}, issn = {0269-1191}, mesh = {*Agriculture/economics/education/history/legislation & jurisprudence ; *Community Networks/economics/history/legislation & jurisprudence ; Conservation of Natural Resources/economics/history/legislation & jurisprudence ; Crops, Agricultural/economics/history ; Ecology/economics/education/history/legislation & jurisprudence ; Employment/economics/history/legislation & jurisprudence/psychology ; France/ethnology ; History, 18th Century ; Income/history ; Rural Health/history ; *Rural Population/history ; *Social Change/history ; *Socioeconomic Factors ; *Wine/economics/history ; }, abstract = {The légende noire of the French Revolution has been the underlying paradigm of much modern French environmental history. This legend contends that peasants were reckless land clearers and tree cutters who disregarded the environment and unleashed an unmitigated natural disaster in the countryside. But the legend is misconceived in many ways. The purpose of this article is to investigate Ancien Régime land-clearance legislation in a non-forested region of France: Lower Languedoc. The results of this land-clearance demonstrate that far from being culpable, the rural masses were officially encouraged to clear and cultivate land on the eve of the Revolution. The French peasantry were not as destructive as the légende noire suggests; the crops they chose to plant on their newly cleared plots reflected a sensitivity towards the environment. Vines were planted on much of the new land-viticulture was not only a sound ecological choice, well-suited to the landscape, but was also attuned to the economic realities of the day.}, } @article {pmid19492471, year = {2002}, author = {Meng, J}, title = {[Agricultural development and destruction of the ecological environment in Shanxi during the Qing dynasty].}, journal = {Shi xue yue kan}, volume = {}, number = {10}, pages = {37-40}, pmid = {19492471}, issn = {0583-0214}, mesh = {*Agriculture/economics/education/history/legislation & jurisprudence ; China/ethnology ; Community Networks/economics/history/legislation & jurisprudence ; Conservation of Natural Resources/economics/history/legislation & jurisprudence ; Crops, Agricultural/economics/history ; *Disasters/economics/history ; *Environment ; Environmental Pollutants/economics/history ; Floods/economics/history ; *Food Supply/economics/history/legislation & jurisprudence ; History, 18th Century ; Rural Health/history ; Rural Population/history ; Soil ; }, } @article {pmid17922755, year = {2007}, author = {Wegley, L and Edwards, R and Rodriguez-Brito, B and Liu, H and Rohwer, F}, title = {Metagenomic analysis of the microbial community associated with the coral Porites astreoides.}, journal = {Environmental microbiology}, volume = {9}, number = {11}, pages = {2707-2719}, doi = {10.1111/j.1462-2920.2007.01383.x}, pmid = {17922755}, issn = {1462-2912}, mesh = {Animals ; Anthozoa/genetics/*microbiology/virology ; Archaea/classification/*genetics/metabolism ; Bacteria/classification/*genetics/metabolism ; Carbon/metabolism ; Databases, Nucleic Acid ; *Ecosystem ; Eukaryotic Cells/classification/*physiology ; Fungi/classification/*genetics/metabolism ; *Genome ; Nitrogen/metabolism ; Oxidative Stress ; Sulfur/metabolism ; Virulence Factors/genetics ; }, abstract = {The coral holobiont is a dynamic assemblage of the coral animal, zooxanthellae, endolithic algae and fungi, Bacteria,Archaea and viruses. Zooxanthellae and some Bacteria form relatively stable and species-specific associations with corals. Other associations are less specific; coral-associated Archaea differ from those in the water column, but the same archaeal species may be found on different coral species. It has been hypothesized that the coral animal can adapt to differing ecological niches by 'switching' its microbial associates. In the case of corals and zooxanthellae, this has been termed adaptive bleaching and it has important implications for carbon cycling within the coral holobiont and ultimately the survival of coral reefs. However, the roles of other components of the coral holobiont are essentially unknown. To better understand these other coral associates, a fractionation procedure was used to separate the microbes, mitochondria and viruses from the coral animal cells and zooxanthellae. The resulting metagenomic DNA was sequenced using pyrosequencing. Fungi, Bacteria and phage were the most commonly identified organisms in the metagenome. Three of the four fungal phyla were represented, including a wide diversity of fungal genes involved in carbon and nitrogen metabolism, suggesting that the endolithic community is more important than previously appreciated. In particular, the data suggested that endolithic fungi could be converting nitrate and nitrite to ammonia, which would enable fixed nitrogen to cycle within the coral holobiont. The most prominent bacterial groups were Proteobacteria (68%), Firmicutes (10%), Cyanobacteria (7%) and Actinobacteria (6%). Functionally, the bacterial community was primarily heterotrophic and included a number of pathways for the degradation of aromatic compounds, the most abundant being the homogentisate pathway. The most abundant phage family was the ssDNA Microphage and most of the eukaryotic viruses were most closely related to those known to infect aquatic organisms. This study provides a metabolic and taxonomic snapshot of microbes associated with the reef-building coral Porites astreoides and presents a basis for understanding how coral-microbial interactions structure the holobiont and coral reefs.}, } @article {pmid17916574, year = {2008}, author = {Wu, GZ and Shi, QM and Niu, Y and Xing, MQ and Xue, HW}, title = {Shanghai RAPESEED Database: a resource for functional genomics studies of seed development and fatty acid metabolism of Brassica.}, journal = {Nucleic acids research}, volume = {36}, number = {Database issue}, pages = {D1044-7}, pmid = {17916574}, issn = {1362-4962}, mesh = {Brassica/embryology/*genetics/metabolism ; Brassica rapa/genetics ; *Databases, Genetic ; Expressed Sequence Tags/chemistry ; Fatty Acids/*metabolism ; Gene Expression Profiling ; *Genome, Plant ; Genomics ; Internet ; Mutagenesis ; Seeds/*genetics/growth & development/metabolism ; User-Computer Interface ; }, abstract = {The Shanghai RAPESEED Database (RAPESEED, http://rapeseed.plantsignal.cn/) was created to provide the solid platform for functional genomics studies of oilseed crops with the emphasis on seed development and fatty acid metabolism. The RAPESEED includes the resource of 8462 unique ESTs, of which 3526 clones are with full length cDNA; the expression profiles of 8095 genes and the Serial Analysis of Gene Expression (SAGE, 23,895 unique tags) and tag-to-gene data during seed development. In addition, a total of approximately 14,700 M3 mutant populations were generated by ethylmethanesulfonate (EMS) mutagenesis and related seed quality information was determined using the Foss NIR System. Further, the TILLING (Targeting Induced Local Lesions IN Genomes) platform was established based on the generated EMS mutant population. The relevant information was collected in RAPESEED database, which can be searched through keywords, nucleotide or protein sequences, or seed quality parameters, and downloaded.}, } @article {pmid17916267, year = {2007}, author = {Kenis, M and Rabitsch, W and Auger-Rozenberg, MA and Roques, A}, title = {How can alien species inventories and interception data help us prevent insect invasions?.}, journal = {Bulletin of entomological research}, volume = {97}, number = {5}, pages = {489-502}, doi = {10.1017/S0007485307005184}, pmid = {17916267}, issn = {0007-4853}, mesh = {*Animal Migration ; Animals ; Austria ; Conservation of Natural Resources ; Databases, Factual ; Environment ; Europe ; Feeding Behavior ; *Insect Control ; Insecta/classification/*physiology ; Species Specificity ; Switzerland ; }, abstract = {Information relevant to invasion processes and invasive alien insect species management in Central Europe was extracted from two databases: a compilation of two inventories of alien insects in Austria and Switzerland, and a list of interceptions of non-indigenous plant pests in Europe gathered by the European and Mediterranean Plant Protection Organisation (EPPO) for the period 1995-2004. For one-third of the insects established in Switzerland and Austria, the region of origin is unclear. Others come mainly from North America, Asia and the Mediterranean region. Among the intercepted insects, 40% were associated with commodities from Asia, 32% from Europe and only 2% from North America. Sternorrhyncha, Coleoptera and Psocoptera were particularly well represented in the alien fauna compared to the native fauna. In the interception database, Sternorrhyncha were also well represented but Diptera accounted for the highest number of records. Sap feeders and detritivores were the dominant feeding niches in the alien insect fauna. In contrast, external defoliators, stem borers, gall makers, root feeders, predators and parasitoids were underrepresented. Nearly 40% of the alien insects in Switzerland and Austria live only indoors. Another 15% live outdoors but exclusively or predominantly on exotic plants. Less than 20% are found mainly in 'natural' environments. The majority of introductions of alien insects in Europe are associated with the international trade in ornamental plants. An economic impact was found for 40% of the alien insects in Switzerland and Austria, whereas none is known to have an ecological impact. The implications of these observations for further studies and the management of alien species in Europe are discussed.}, } @article {pmid17916237, year = {2007}, author = {Irimia, M and Rukov, JL and Penny, D and Roy, SW}, title = {Functional and evolutionary analysis of alternatively spliced genes is consistent with an early eukaryotic origin of alternative splicing.}, journal = {BMC evolutionary biology}, volume = {7}, number = {}, pages = {188}, pmid = {17916237}, issn = {1471-2148}, mesh = {*Alternative Splicing ; Animals ; Databases, Genetic ; *Eukaryotic Cells ; *Evolution, Molecular ; Fungi/genetics ; *Genes ; Humans ; Introns ; Phylogeny ; Plants/genetics ; Spliceosomes ; }, abstract = {BACKGROUND: Alternative splicing has been reported in various eukaryotic groups including plants, apicomplexans, diatoms, amoebae, animals and fungi. However, whether widespread alternative splicing has evolved independently in the different eukaryotic groups or was inherited from their last common ancestor, and may therefore predate multicellularity, is still unknown. To better understand the origin and evolution of alternative splicing and its usage in diverse organisms, we studied alternative splicing in 12 eukaryotic species, comparing rates of alternative splicing across genes of different functional classes, cellular locations, intron/exon structures and evolutionary origins.

RESULTS: For each species, we find that genes from most functional categories are alternatively spliced. Ancient genes (shared between animals, fungi and plants) show high levels of alternative splicing. Genes with products expressed in the nucleus or plasma membrane are generally more alternatively spliced while those expressed in extracellular location show less alternative splicing. We find a clear correspondence between incidence of alternative splicing and intron number per gene both within and between genomes. In general, we find several similarities in patterns of alternative splicing across these diverse eukaryotes.

CONCLUSION: Along with previous studies indicating intron-rich genes with weak intron boundary consensus and complex spliceosomes in ancestral organisms, our results suggest that at least a simple form of alternative splicing may already have been present in the unicellular ancestor of plants, fungi and animals. A role for alternative splicing in the evolution of multicellularity then would largely have arisen by co-opting the preexisting process.}, } @article {pmid17914933, year = {2008}, author = {Wakefield, J}, title = {Ecologic studies revisited.}, journal = {Annual review of public health}, volume = {29}, number = {}, pages = {75-90}, doi = {10.1146/annurev.publhealth.29.020907.090821}, pmid = {17914933}, issn = {0163-7525}, support = {R01 CA 095994/CA/NCI NIH HHS/United States ; }, mesh = {Bias ; Cluster Analysis ; Confounding Factors, Epidemiologic ; *Data Interpretation, Statistical ; Ecology/*methods/standards ; *Epidemiologic Methods ; Geographic Information Systems ; Humans ; Infant ; North Carolina/epidemiology ; Sudden Infant Death/epidemiology ; }, abstract = {Ecologic studies use data aggregated over groups rather than data on individuals. Such studies are popular because they use existing databases and can offer large exposure variation if the data arise from broad geographical areas. Unfortunately, the aggregation of data that define ecologic studies results in an information loss that can lead to ecologic bias. Specifically, ecologic bias arises from the inability of ecologic data to characterize within-area variability in exposures and confounders. We describe in detail particular forms of ecologic bias so that their potential impact on any particular study may be assessed. The only way to overcome such bias, while avoiding uncheckable assumptions concerning the missing information, is to supplement the ecologic with individual-level information, and we outline a number of proposals that may achieve this aim.}, } @article {pmid17913010, year = {2007}, author = {Wagmiller, RL}, title = {Race and the spatial segregation of jobless men in urban America.}, journal = {Demography}, volume = {44}, number = {3}, pages = {539-562}, pmid = {17913010}, issn = {0070-3370}, mesh = {Adult ; Databases as Topic ; *Demography ; Humans ; Male ; Middle Aged ; Racial Groups/*ethnology ; Regression Analysis ; *Unemployment ; United States ; *Urban Population ; }, abstract = {Changes in U.S. metropolitan areas over the past 30 years are thought to have concentrated jobless men in low-income, predominantly minority neighborhoods clustered near the center of the city. Using tract-level data from the Neighborhood Change Database for 1970-2000, I examine how the residential segregation ofjobless from employed men has changed over the past three decades. I find that jobless men in U.S. metropolitan areas have become less uniformly distributed throughout the metropolis and more isolated, concentrated, and clustered since 1970; but they have also become less centralized. Racial and ethnic group differences in the spatial segregation of jobless men are large. Jobless black men occupy a uniquely disadvantaged ecological position in the metropolis: in comparison with other jobless men, they are much less uniformly distributed throughout the metropolis and much more isolated from employed men, they are concentrated in a smaller amount of physical space, and their neighborhoods are more clustered and are located closer to the center of the city. The dimensions of segregation strongly overlap for black jobless men, producing a multidimensional layering of segregation not encountered by other jobless men. Multivariate models reveal that the uniquely disadvantaged ecological position of jobless black men is less a reflection of different patterns of regional concentration and metropolitan settlement or of differences in group-status characteristics than it is an inevitable consequence of extreme levels of racial residential segregation in the United States.}, } @article {pmid17911710, year = {2007}, author = {Timpka, T and Morin, M and Jenvald, J and Gursky, E and Eriksson, H}, title = {Dealing with ecological fallacy in preparations for influenza pandemics: use of a flexible environment for adaptation of simulations to household structures in local contexts.}, journal = {Studies in health technology and informatics}, volume = {129}, number = {Pt 1}, pages = {218-222}, pmid = {17911710}, issn = {0926-9630}, mesh = {Adolescent ; Adult ; Age Distribution ; Aged ; Child ; Child, Preschool ; *Computer Simulation ; *Disease Outbreaks ; Family Characteristics ; Humans ; Influenza, Human/*epidemiology/*transmission ; Middle Aged ; *Models, Biological ; Public Health Informatics ; Socioeconomic Factors ; Sweden ; }, abstract = {Development of strategies for mitigating the severity of a new influenza pandemic is a global public health priority. The aim of this study is to examine effects on simulation outcomes caused by variations in local socio-demographic data. We used a spatially explicit geo-physical model of a virtual city as a baseline and employed an ontology-modeling tool to construct alternative population distributions and household structures. We found that adjustment for the case when single parents in practice were cohabiting led to a higher reproduction rate than that observed for a population with the highest formally recorded share of households with >2 children. When antivirals sufficient to protect 10 percent of the population were administered to schoolchildren, a preliminary effect on the reproduction rate was observed. This effect was eliminated when the household structure was adjusted for cohabiting single parents. Nations have been encouraged to develop estimates of morbidity and mortality during a possible pandemic outbreak. In order to deal with ecological fallacy, the present results suggest that this recommendation can be extended also to local communities.}, } @article {pmid17911690, year = {2007}, author = {Momtahan, KL and Burns, CM and Sherrard, H and Mesana, T and Labinaz, M}, title = {Using personal digital assistants and patient care algorithms to improve access to cardiac care best practices.}, journal = {Studies in health technology and informatics}, volume = {129}, number = {Pt 1}, pages = {117-121}, pmid = {17911690}, issn = {0926-9630}, mesh = {Algorithms ; Cardiology/instrumentation/methods/*standards ; Chest Pain/etiology/nursing/*therapy ; *Computers, Handheld ; *Decision Support Systems, Clinical ; Humans ; *Patient Care Management ; Pilot Projects ; Postoperative Complications/therapy ; *Telemedicine ; Triage/methods ; User-Computer Interface ; }, abstract = {In order to facilitate knowledge transfer between specialists and generalists and between experts and novices, and to promote interdisciplinary communication, there is a need to provide methods and tools for doing so. This interdisciplinary research team developed and evaluated a decision support tool (DST) on a personal digital assistant (PDA) for cardiac tele-triage/tele-consultation when the presenting problem was chest pain. The combined human factors methods of cognitive work analysis during the requirements-gathering phase and ecological interface design during the design phase were used to develop the DST. A pilot clinical trial was conducted at a quaternary cardiac care hospital over a 3-month period. During this time, the DST was used by the nine nursing coordinators who provide tele-triage/tele-consultation 24/7. This clinical trial validated the design and demonstrated its usefulness to advanced cardiac care nurses, its potential for use by nurses less experienced in cardiac care, and for its potential use in an interdisciplinary team environment.}, } @article {pmid17907795, year = {2007}, author = {Corney, D and Lotto, RB}, title = {What are lightness illusions and why do we see them?.}, journal = {PLoS computational biology}, volume = {3}, number = {9}, pages = {1790-1800}, pmid = {17907795}, issn = {1553-7358}, mesh = {*Artificial Intelligence ; Biomimetics/*methods ; Humans ; Image Interpretation, Computer-Assisted/*methods ; Nerve Net/*physiology ; Optical Illusions/*physiology ; Photometry/*methods ; Visual Perception/*physiology ; }, abstract = {Lightness illusions are fundamental to human perception, and yet why we see them is still the focus of much research. Here we address the question by modelling not human physiology or perception directly as is typically the case but our natural visual world and the need for robust behaviour. Artificial neural networks were trained to predict the reflectance of surfaces in a synthetic ecology consisting of 3-D "dead-leaves" scenes under non-uniform illumination. The networks learned to solve this task accurately and robustly given only ambiguous sense data. In addition--and as a direct consequence of their experience--the networks also made systematic "errors" in their behaviour commensurate with human illusions, which includes brightness contrast and assimilation--although assimilation (specifically White's illusion) only emerged when the virtual ecology included 3-D, as opposed to 2-D scenes. Subtle variations in these illusions, also found in human perception, were observed, such as the asymmetry of brightness contrast. These data suggest that "illusions" arise in humans because (i) natural stimuli are ambiguous, and (ii) this ambiguity is resolved empirically by encoding the statistical relationship between images and scenes in past visual experience. Since resolving stimulus ambiguity is a challenge faced by all visual systems, a corollary of these findings is that human illusions must be experienced by all visual animals regardless of their particular neural machinery. The data also provide a more formal definition of illusion: the condition in which the true source of a stimulus differs from what is its most likely (and thus perceived) source. As such, illusions are not fundamentally different from non-illusory percepts, all being direct manifestations of the statistical relationship between images and scenes.}, } @article {pmid17905487, year = {2008}, author = {Berthou, V and Galy, J and Magill, J and Lützenkirchen, K}, title = {Nuclides.net: a computational environment for nuclear data and applications in radioprotection and radioecology.}, journal = {Journal of environmental radioactivity}, volume = {99}, number = {4}, pages = {581-586}, doi = {10.1016/j.jenvrad.2007.08.018}, pmid = {17905487}, issn = {0265-931X}, mesh = {Conservation of Natural Resources ; Databases, Factual ; Ecology ; Environmental Monitoring/*methods ; Internet ; Models, Theoretical ; Programming Languages ; Radiation Dosage ; Radiation Protection/*instrumentation ; Radiometry ; Software ; Software Design ; Time Factors ; User-Computer Interface ; Water ; }, abstract = {An interactive multimedia tool, Nuclides.net, has been developed at the Institute for Transuranium Elements. The Nuclides.net "integrated environment" is a suite of computer programs ranging from a powerful user-friendly interface, which allows the user to navigate the nuclides chart and explore the properties of nuclides, to various computational modules for decay calculations, dosimetry and shielding calculations, etc. The product is particularly suitable for environmental radioprotection and radioecology. Detailed descriptions of Nuclides.net and some potential applications in radioprotection and radioecology are presented.}, } @article {pmid17905462, year = {2008}, author = {Fu, M and Deng, R and Wang, J and Wang, X}, title = {Detection and analysis of horizontal gene transfer in herpesvirus.}, journal = {Virus research}, volume = {131}, number = {1}, pages = {65-76}, doi = {10.1016/j.virusres.2007.08.009}, pmid = {17905462}, issn = {0168-1702}, mesh = {Computational Biology/*methods ; *Gene Transfer, Horizontal ; Genes, Viral ; Genome, Viral ; Genomics/methods ; *Herpesviridae ; Sequence Analysis, DNA ; }, abstract = {Horizontal gene transfers, where a significant proportion of the coding DNA is contributed by external sources, might give rise to extremely dynamic genomes, which brings impact on the ecological and pathogenic characters of the recipient organisms. Therefore it is important to computationally discriminate between horizontal transferred genes and normal genes. In this paper, we introduce a novel method for identifying horizontal transferred genes. This method, which relies on a gene's nucleotide composition and hence obviates the need for knowledge of codon boundaries, is able to detect the horizontal transferred genes with an accuracy of higher than 90% within a reasonable length of time by using just a common PC. With this method, 141 putative transferred genes in mammalian herpesvirus were identified. Among them, 16 genes had been predicted or reported to have cellular homologues in previous papers, including those involved in immune systems and apoptosis such as GCR in EHV-2, BCL-2 (Bcelllymphoma/leukemia-2) homologue in MuHV-4, etc., and had been suggested being acquired from other organisms. Other 125 genes were identified for the first time. Twelve of the newly identified putative transferred genes had also been reported to participate in immune response, apoptosis, cell proliferation control or virulence determinant. Moreover, 42 of the 141 putative transferred genes were found to have non-virus homologues and so were convincingly revealed as transferred genes. Nine of the 42 transferred genes were phylogenetically analyzed, the origin and the relative origin time of which were discussed.}, } @article {pmid17900339, year = {2007}, author = {Timmermans, MJ and de Boer, ME and Nota, B and de Boer, TE and Mariën, J and Klein-Lankhorst, RM and van Straalen, NM and Roelofs, D}, title = {Collembase: a repository for springtail genomics and soil quality assessment.}, journal = {BMC genomics}, volume = {8}, number = {}, pages = {341}, pmid = {17900339}, issn = {1471-2164}, mesh = {Animals ; Arthropods/*genetics ; Computational Biology/methods ; Databases as Topic ; *Databases, Nucleic Acid ; Environmental Monitoring ; Expressed Sequence Tags/*chemistry ; Gene Expression Profiling ; Genomics/*methods ; Information Storage and Retrieval/methods ; Molecular Sequence Data ; Sequence Analysis, DNA/*methods ; Soil/*analysis ; Soil Pollutants/analysis ; }, abstract = {BACKGROUND: Environmental quality assessment is traditionally based on responses of reproduction and survival of indicator organisms. For soil assessment the springtail Folsomia candida (Collembola) is an accepted standard test organism. We argue that environmental quality assessment using gene expression profiles of indicator organisms exposed to test substrates is more sensitive, more toxicant specific and significantly faster than current risk assessment methods. To apply this species as a genomic model for soil quality testing we conducted an EST sequencing project and developed an online database.

DESCRIPTION: Collembase is a web-accessible database comprising springtail (F. candida) genomic data. Presently, the database contains information on 8686 ESTs that are assembled into 5952 unique gene objects. Of those gene objects approximately 40% showed homology to other protein sequences available in GenBank (blastx analysis; non-redundant (nr) database; expect-value < 10-5). Software was applied to infer protein sequences. The putative peptides, which had an average length of 115 amino-acids (ranging between 23 and 440) were annotated with Gene Ontology (GO) terms. In total 1025 peptides (approximately 17% of the gene objects) were assigned at least one GO term (expect-value < 10-25). Within Collembase searches can be conducted based on BLAST and GO annotation, cluster name or using a BLAST server. The system furthermore enables easy sequence retrieval for functional genomic and Quantitative-PCR experiments. Sequences are submitted to GenBank (Accession numbers: EV473060 - EV481745).

CONCLUSION: Collembase http://www.collembase.org is a resource of sequence data on the springtail F. candida. The information within the database will be linked to a custom made microarray, based on the Agilent platform, which can be applied for soil quality testing. In addition, Collembase supplies information that is valuable for related scientific disciplines such as molecular ecology, ecogenomics, molecular evolution and phylogenetics.}, } @article {pmid17899413, year = {2008}, author = {Liu, H and Weng, Q}, title = {Seasonal variations in the relationship between landscape pattern and land surface temperature in Indianapolis, USA.}, journal = {Environmental monitoring and assessment}, volume = {144}, number = {1-3}, pages = {199-219}, doi = {10.1007/s10661-007-9979-5}, pmid = {17899413}, issn = {0167-6369}, mesh = {Climate ; Conservation of Natural Resources ; Environment Design ; Environmental Monitoring/methods ; Geographic Information Systems ; *Geography ; Humans ; Indiana ; Satellite Communications ; *Seasons ; *Temperature ; Urbanization ; }, abstract = {This paper intended to examine the seasonal variations in the relationship between landscape pattern and land surface temperature based on a case study of Indianapolis, United States. The integration of remote sensing, GIS, and landscape ecology methods was used in this study. Four Terra's ASTER images were used to derive the landscape patterns and land surface temperatures (LST) in four seasons in the study area. The spatial and ecological characteristics of landscape patterns and LSTs were examined by the use of landscape metrics. The impact of each land use and land cover type on LST was analyzed based on the measurements of landscape metrics. The results show that the landscape and LST patterns in the winter were unique. The rest of three seasons apparently had more agreeable landscape and LST patterns. The spatial configuration of each LST zone conformed to that of each land use and land cover type with more than 50% of overlap in area for all seasons. This paper may provide useful information for urban planners and environmental managers for assessing and monitoring urban thermal environments as result of urbanization.}, } @article {pmid17897449, year = {2007}, author = {Rivas-Ruiz, F and Perea-Milla, E and Jimenez-Puente, A}, title = {Geographic variability of fatal road traffic injuries in Spain during the period 2002-2004: an ecological study.}, journal = {BMC public health}, volume = {7}, number = {}, pages = {266}, pmid = {17897449}, issn = {1471-2458}, mesh = {Accidents, Traffic/*mortality/trends ; Adolescent ; Adult ; Aged ; Automobile Driving/*statistics & numerical data ; Data Interpretation, Statistical ; Ecology ; Environment Design ; Geography ; Humans ; Middle Aged ; Poisson Distribution ; Population Density ; Risk Factors ; Risk-Taking ; Socioeconomic Factors ; Spain/epidemiology ; }, abstract = {BACKGROUND: The aim of the present study is to describe the inter-province variability of Road Traffic Injury (RTI) mortality on Spanish roads, adjusted for vehicle-kilometres travelled, and to assess the possible role played by the following explicative variables: sociodemographic, structural, climatic and risk conducts.

METHODS: An ecological study design was employed. The mean annual rate of RTI deaths was calculated for the period 2002-2004, adjusted for vehicle-kilometres travelled, in the 50 provinces of Spain. The RTI death rate was related with the independent variables described above, using simple and multiple linear regression analysis with backward step-wise elimination. The level of statistical significance was taken as p < 0.05.

RESULTS: In the period 2002-2004 there were 12,756 RTI deaths in Spain (an average of 4,242 per year, SD = 356.6). The mean number of deaths due to RTI per 100 million vehicle-kilometres (mvk) travelled was 1.76 (SD = 0.51), with a minimum value of 0.66 (in Santa Cruz de Tenerife) and a maximum of 3.31 (in the province of Lugo). All other variables being equal, a higher proportion of kilometres available on high capacity roads, and a higher cultural and education level were associated with lower death rates due to RTI, while the opposite was true for the rate of alcohol consumers and the road traffic volume of heavy vehicles. The variables included in the model accounted for 55.4% of the variability in RTI mortality.

CONCLUSION: Adjusting RTI mortality rates for the number of vehicle-kilometres travelled enables us to identify the high variability of this cause of death, and its relation with risk factors other than those inherent to human behaviour, such as the type of roads and the type of vehicles using them.}, } @article {pmid17896128, year = {2007}, author = {Tian, G and Yang, Z and Zhang, Y}, title = {The spatio-temporal dynamic pattern of rural residential land in China in the 1990s using Landsat TM images and GIS.}, journal = {Environmental management}, volume = {40}, number = {5}, pages = {803-813}, pmid = {17896128}, issn = {0364-152X}, mesh = {China ; *Ecology ; Environmental Monitoring/*methods/statistics & numerical data ; *Geographic Information Systems ; Urbanization ; }, abstract = {Through interpreting Landsat TM images, this study analyzes the spatial distribution of rural settlements in China in 2000. It calculates rural residential land percentage for every 1-km(2) cell. The entire country is divided into 33 regions to investigate the spatio-temporal dynamic patterns of rural residential land during the 1990s. According to the remote sensing survey, the rural residential land increased by 7.88 x 10(5) ha in the 1990s. The increment of rural residential land was 0.55 million ha in 1990-1995 and 0.23 million ha in 1995-2000. In 1990-1995, rural residential land increased dramatically in the eastern regions such as the Yangtze River Delta, Pearl River Delta, and North China Plain, accounting for 80.80% of the national growth; the expansion in the western regions was much more moderate. In 1995-2000, the expansion of rural residential land in eastern regions slowed, accounting for only 58.54% of the increase at the national level, whereas the expansion in the western regions accelerated. Rapid rural residential development resulted from increasing home construction and the limited control on rural land. The great regional disparity reflected the regional economic development and land-use policy change. Our finding shows that nearly 60% of the rural residential area came from cropland.}, } @article {pmid17892477, year = {2007}, author = {Ramette, A}, title = {Multivariate analyses in microbial ecology.}, journal = {FEMS microbiology ecology}, volume = {62}, number = {2}, pages = {142-160}, pmid = {17892477}, issn = {0168-6496}, mesh = {*Data Interpretation, Statistical ; *Ecosystem ; *Environmental Microbiology ; *Multivariate Analysis ; }, abstract = {Environmental microbiology is undergoing a dramatic revolution due to the increasing accumulation of biological information and contextual environmental parameters. This will not only enable a better identification of diversity patterns, but will also shed more light on the associated environmental conditions, spatial locations, and seasonal fluctuations, which could explain such patterns. Complex ecological questions may now be addressed using multivariate statistical analyses, which represent a vast potential of techniques that are still underexploited. Here, well-established exploratory and hypothesis-driven approaches are reviewed, so as to foster their addition to the microbial ecologist toolbox. Because such tools aim at reducing data set complexity, at identifying major patterns and putative causal factors, they will certainly find many applications in microbial ecology.}, } @article {pmid17891465, year = {2008}, author = {Ouyang, W and Hao, FH and Fu, Y and Zhang, J}, title = {Desert disturbance assessments of regional oil exploitation by Aster and ETM+ images in Taklimakan Desert China.}, journal = {Environmental monitoring and assessment}, volume = {144}, number = {1-3}, pages = {159-168}, pmid = {17891465}, issn = {0167-6369}, mesh = {China ; Conservation of Natural Resources ; *Desert Climate ; Environment ; Environmental Monitoring/*methods ; *Fossil Fuels ; *Geographic Information Systems ; Humans ; *Satellite Communications ; }, abstract = {To feed its rapidly growing energy demand, oil exploitation in China has never been more intensive. The most obvious characteristics of oil exploitation are progressive and regional, which can be monitored by remote sensing, such as land use and cover change, either perpetual or temporary, during oil field development such as construction of oil well, roads, transportation systems and other facilities. In this paper, the oil field located on the north edge of Taklimakan Desert, in the Tarim River watershed in northwest of China. The disturbance effects of regional oil exploitation were the main content of regional environmental managements and monitoring. Based on Enhanced Thematic Mapper Plus (ETM+) and Aster images, analyzed regional land use and landscape change from 2001 to 2003. By the comparison, it can be concluded that the ecological quality was deteriorating in these 3 years. The woodland was degrading to grass and desert. The area of woodland dropped from 9.06 km(2) in 2001 to 3.24 km(2) in 2003 with a 64.23% decrease. At the same time, the area of shrubbery lessened 18.23%. On the other hand, the whole area of desert and Saline soils inflated from 15.08 km(2) in 2001 to 25.36 km(2) in 2003. The patch number of bare land did climb dramatically, but single patch area increased. The research demonstrated that desert and Saline soils patches were activated by the human behavior and climate change. The information from the ETM+ and Aster images was proved be an effective and efficient way to be applied in regional environmental managements.}, } @article {pmid17889371, year = {2008}, author = {Schrott, A and Kabai, P}, title = {ABCD: a functional database for the avian brain.}, journal = {Journal of neuroscience methods}, volume = {167}, number = {2}, pages = {393-395}, doi = {10.1016/j.jneumeth.2007.08.007}, pmid = {17889371}, issn = {0165-0270}, mesh = {Animals ; *Birds ; Brain/*anatomy & histology/*physiology ; Databases, Factual/*statistics & numerical data ; *Information Services ; }, abstract = {Here we present the first database developed for storing, retrieving and cross-referencing neuroscience information about the connectivity of the avian brain. The Avian Brain Circuitry Database (ABCD) contains entries about the new and old terminology of the areas and their hierarchy, data on connections between brain regions, as well as a functional keyword system linked to brain regions and connections. Data were collected from the primary literature and textbooks, and an online submission system was developed to facilitate further data collection directly from researchers. The database aims to help spread the results of avian connectivity studies, the recently revised nomenclature and also to provide data for brain network research. ABCD is freely available at http://www.behav.org/abcd.}, } @article {pmid17881844, year = {2007}, author = {Kaufmann, I and Meyer, T and Kalsch, M and Schmitt, TG and Hamacher, HW}, title = {Implementation of sustainable sanitation in existing urban areas: long-term strategies for an optimised solution.}, journal = {Water science and technology : a journal of the International Association on Water Pollution Research}, volume = {56}, number = {5}, pages = {115-124}, doi = {10.2166/wst.2007.563}, pmid = {17881844}, issn = {0273-1223}, mesh = {*Conservation of Natural Resources ; *Decision Support Techniques ; Germany ; *Models, Theoretical ; Sanitation/economics/*methods ; *Urbanization ; }, abstract = {If technologies for decentralised sanitation and reuse (DESAR) and for natural stormwater management should at least partially replace existing systems, then intensive reconstruction work becomes essential. A conversion can only be realised successively over a long period due to high construction and financial expenses and requires new strategies. This paper presents the development and practical implementation of a mathematical tool to find an optimised strategy for the realisation of alternative and more decentralised drainage and sanitation concepts in existing urban areas. The succession of construction measures (e.g. the implementation of decentralised greywater recycling) for the whole period of consideration is determined based upon a mathematical optimisation model on the condition that the favoured future state is known. The model describes the complex interdependencies of the urban water and nutrient cycle and enables the minimisation of both financial efforts and ecological impacts on the way toward the future state. The results of the implementation for a rural area in Germany show that the mathematical optimisation is an adequate instrument to support decision-making processes in finding strategies for the realisation of sustainable urban water management.}, } @article {pmid17868743, year = {2007}, author = {Ruellet, T and Dauvin, JC}, title = {Benthic indicators: analysis of the threshold values of ecological quality classifications for transitional waters.}, journal = {Marine pollution bulletin}, volume = {54}, number = {11}, pages = {1707-1714}, doi = {10.1016/j.marpolbul.2007.07.003}, pmid = {17868743}, issn = {0025-326X}, mesh = {Animals ; *Biodiversity ; *Ecology ; Environmental Monitoring/*methods ; Geographic Information Systems ; International Cooperation ; Invertebrates/*drug effects/physiology ; Quality Control ; *Water Pollutants/analysis/toxicity ; Water Supply/standards ; }, abstract = {The effect of the modifications of the threshold values generally adopted for the five EcoQ (Ecological Quality) classes recognized by the European Water Framework Directive (WFD) for the most used benthic indicators and diversity indicators (AMBI, BENTIX, BOPA, BQI, H', ITI and M-AMBI) were studied to test whether it is possible to obtain the same or similar ecological classifications for transitional waters using these different indicators, and determine whether the current classifications can be improved. The analysis included: (i) the use of indicator equations, (ii) the use of reference indicators, and (iii) the use of indicator distribution laws. These investigations demonstrated that it was impossible to obtain an exact intercalibration of the ecological classifications with the selected indicators. However, some propositions to improve the actual classification were suggested.}, } @article {pmid17868293, year = {2008}, author = {Grivet, D and Sork, VL and Westfall, RD and Davis, FW}, title = {Conserving the evolutionary potential of California valley oak (Quercus lobata Née): a multivariate genetic approach to conservation planning.}, journal = {Molecular ecology}, volume = {17}, number = {1}, pages = {139-156}, doi = {10.1111/j.1365-294X.2007.03498.x}, pmid = {17868293}, issn = {0962-1083}, mesh = {California ; Conservation of Natural Resources/*methods ; DNA, Chloroplast/genetics ; *Ecosystem ; Gene Frequency ; *Genotype ; Geographic Information Systems ; Geography ; Microsatellite Repeats/genetics ; Multivariate Analysis ; Population Dynamics ; Quercus/*genetics ; Sequence Analysis, DNA ; }, abstract = {California valley oak (Quercus lobata Née) is a seriously threatened endemic oak species in California and a keystone species for foothill oak ecosystems. Urban and agricultural development affects a significant fraction of the species' range and predicted climate change is likely to dislocate many current populations. Here, we explore spatial patterns of multivariate genotypes and genetic diversity throughout the range of valley oak to determine whether ongoing and future patterns of habitat loss could threaten the evolutionary potential of the species by eradicating populations of distinctive genetic composition. This manuscript will address three specific questions: (i) What is the spatial genetic structure of the chloroplast and nuclear genetic markers? (ii) What are the geographical trends in the distribution of chloroplast and nuclear genotypes? (iii) Is there any part of the species' range where allelic diversity in either the chloroplast or nuclear genomes is particularly high? We analysed six chloroplast and seven nuclear microsatellite genetic markers of individuals widespread across the valley oak range. We then used a multivariate approach correlating genetic markers and geographical variables through a canonical trend surface analysis, followed by GIS mapping of the significant axes. We visualized population allelic richness spatially with GIS tools to identify regions of high diversity. Our findings, based on the distribution of multivariate genotypes and allelic richness, identify areas with distinctive histories and genetic composition that should be given priority in reserve network design, especially because these areas also overlap with landscape change and little degree of protection. Thus, without a careful preservation plan, valuable evolutionary information will be lost for valley oak.}, } @article {pmid17850556, year = {2007}, author = {Joost, S and Bonin, A and Bruford, MW and Després, L and Conord, C and Erhardt, G and Taberlet, P}, title = {A spatial analysis method (SAM) to detect candidate loci for selection: towards a landscape genomics approach to adaptation.}, journal = {Molecular ecology}, volume = {16}, number = {18}, pages = {3955-3969}, doi = {10.1111/j.1365-294X.2007.03442.x}, pmid = {17850556}, issn = {0962-1083}, mesh = {*Adaptation, Biological ; Animals ; Gene Frequency ; Genetic Markers ; Genomics/*methods ; Geographic Information Systems ; Microsatellite Repeats ; Polymorphism, Genetic ; Regression Analysis ; Selection, Genetic ; Sequence Analysis, DNA ; Sheep/*genetics ; Weevils/*genetics ; }, abstract = {The detection of adaptive loci in the genome is essential as it gives the possibility of understanding what proportion of a genome or which genes are being shaped by natural selection. Several statistical methods have been developed which make use of molecular data to reveal genomic regions under selection. In this paper, we propose an approach to address this issue from the environmental angle, in order to complement results obtained by population genetics. We introduce a new method to detect signatures of natural selection based on the application of spatial analysis, with the contribution of geographical information systems (GIS), environmental variables and molecular data. Multiple univariate logistic regressions were carried out to test for association between allelic frequencies at marker loci and environmental variables. This spatial analysis method (SAM) is similar to current population genomics approaches since it is designed to scan hundreds of markers to assess a putative association with hundreds of environmental variables. Here, by application to studies of pine weevils and breeds of sheep we demonstrate a strong correspondence between SAM results and those obtained using population genetics approaches. Statistical signals were found that associate loci with environmental parameters, and these loci behave atypically in comparison with the theoretical distribution for neutral loci. The contribution of this new tool is not only to permit the identification of loci under selection but also to establish hypotheses about ecological factors that could exert the selection pressure responsible. In the future, such an approach may accelerate the process of hunting for functional genes at the population level.}, } @article {pmid17850542, year = {2007}, author = {Bonin, A and Ehrich, D and Manel, S}, title = {Statistical analysis of amplified fragment length polymorphism data: a toolbox for molecular ecologists and evolutionists.}, journal = {Molecular ecology}, volume = {16}, number = {18}, pages = {3737-3758}, doi = {10.1111/j.1365-294X.2007.03435.x}, pmid = {17850542}, issn = {0962-1083}, mesh = {Biological Evolution ; Computational Biology/methods ; Computer Simulation ; Ecology/methods ; Gene Frequency ; Genetic Markers ; *Genetic Techniques ; Hybridization, Genetic ; Phenotype ; *Polymorphism, Genetic ; Software ; }, abstract = {Recently, the amplified fragment length polymorphism (AFLP) technique has gained a lot of popularity, and is now frequently applied to a wide variety of organisms. Technical specificities of the AFLP procedure have been well documented over the years, but there is on the contrary little or scattered information about the statistical analysis of AFLPs. In this review, we describe the various methods available to handle AFLP data, focusing on four research topics at the population or individual level of analysis: (i) assessment of genetic diversity; (ii) identification of population structure; (iii) identification of hybrid individuals; and (iv) detection of markers associated with phenotypes. Two kinds of analysis methods can be distinguished, depending on whether they are based on the direct study of band presences or absences in AFLP profiles ('band-based' methods), or on allelic frequencies estimated at each locus from these profiles ('allele frequency-based' methods). We investigate the characteristics and limitations of these statistical tools; finally, we appeal for a wider adoption of methodologies borrowed from other research fields, like for example those especially designed to deal with binary data.}, } @article {pmid17847803, year = {2007}, author = {Stringer, LC and Twyman, C and Thomas, DS}, title = {Combating land degradation through participatory means: the case of Swaziland.}, journal = {Ambio}, volume = {36}, number = {5}, pages = {387-393}, doi = {10.1579/0044-7447(2007)36[387:cldtpm]2.0.co;2}, pmid = {17847803}, issn = {0044-7447}, mesh = {Animal Husbandry/methods ; Animals ; Cattle ; *Community Participation ; *Conservation of Natural Resources ; Cooperative Behavior ; Data Collection ; Databases as Topic ; Decision Making, Organizational ; Ecology ; Eswatini ; Focus Groups ; Humans ; Interviews as Topic ; Socioeconomic Factors ; Surveys and Questionnaires ; }, abstract = {This paper examines a community grazing project to rehabilitate degraded land in Swaziland. Using data from interviews, questionnaires, and focus groups, we show that the ways in which participatory, decentralized approaches to natural resource management play out at the local level are closely linked to national-level power structures. The successes and issues that emerge at different stages of the grazing project reflect local socioeconomic priorities and show how people manage their time and labor according to household livelihood goals. However, the project favored the interests of cattle owners who were already the more socially and politically powerful members of the community. We argue that for participatory natural resource management to be more meaningful to communities, projects should focus on local ecological priorities, rather than addressing the environmental concerns that are rooted within existing dominant power structures. This requires change to social and political relationships across levels and the building of new institutions.}, } @article {pmid17846830, year = {2008}, author = {Webb, TJ and Bengston, DN and Fan, DP}, title = {Forest value orientations in Australia: an application of computer content analysis.}, journal = {Environmental management}, volume = {41}, number = {1}, pages = {52-63}, doi = {10.1007/s00267-007-9011-4}, pmid = {17846830}, issn = {0364-152X}, mesh = {Australia ; *Conservation of Natural Resources ; *Databases, Factual ; Forestry/economics/methods ; Mass Media ; Policy Making ; *Public Opinion ; *Software ; Trees/*growth & development ; }, abstract = {This article explores the expression of three forest value orientations that emerged from an analysis of Australian news media discourse about the management of Australian native forests from August 1, 1997 through December 31, 2004. Computer-coded content analysis was used to measure and track the relative importance of commodity, ecological and moral/spiritual/aesthetic forest value orientations. The number of expressions of these forest value orientations followed major events in forest management and policy, with peaks corresponding to finalization of Regional Forest Agreements and conflicts over forest management. Over the time period analyzed, the relative share of commodity value orientation decreased and the shares of the ecological and moral/spiritual/aesthetic value orientations increased. The shifts in forest value orientations highlight the need for native forests to be managed for multiple values and the need for continued monitoring of forest values.}, } @article {pmid17825021, year = {2007}, author = {Storvik, G and Egeland, T}, title = {The DNA database search controversy revisited: bridging the Bayesian-frequentist gap.}, journal = {Biometrics}, volume = {63}, number = {3}, pages = {922-925}, doi = {10.1111/j.1541-0420.2007.00751.x}, pmid = {17825021}, issn = {0006-341X}, mesh = {Bayes Theorem ; DNA/*genetics ; *Data Interpretation, Statistical ; *Databases, Genetic ; Forensic Genetics/*methods ; Information Storage and Retrieval/*methods ; Reproducibility of Results ; Sensitivity and Specificity ; Sequence Analysis, DNA/*methods ; }, abstract = {Two different quantities have been suggested for quantification of evidence in cases where a suspect is found by a search through a database of DNA profiles. The likelihood ratio, typically motivated from a Bayesian setting, is preferred by most experts in the field. The so-called np rule has been suggested through frequentist arguments and has been suggested by the American National Research Council and Stockmarr (1999, Biometrics55, 671-677). The two quantities differ substantially and have given rise to the DNA database search controversy. Although several authors have criticized the different approaches, a full explanation of why these differences appear is still lacking. In this article we show that a P-value in a frequentist hypothesis setting is approximately equal to the result of the np rule. We argue, however, that a more reasonable procedure in this case is to use conditional testing, in which case a P-value directly related to posterior probabilities and the likelihood ratio is obtained. This way of viewing the problem bridges the gap between the Bayesian and frequentist approaches. At the same time it indicates that the np rule should not be used to quantify evidence.}, } @article {pmid17824429, year = {2007}, author = {Conn, PB and Diefenbach, DR}, title = {Adjusting age and stage distributions for misclassification errors.}, journal = {Ecology}, volume = {88}, number = {8}, pages = {1977-1983}, doi = {10.1890/07-0369.1}, pmid = {17824429}, issn = {0012-9658}, mesh = {Age Distribution ; Animals ; *Bias ; Causality ; *Data Interpretation, Statistical ; Female ; Male ; *Models, Biological ; *Models, Statistical ; Prevalence ; Reproducibility of Results ; Research Design ; Sensitivity and Specificity ; Ursidae/*physiology ; }, abstract = {Ecologists often use samples from the age or stage structure of a population to make inferences about population-level processes and to parameterize matrix models. Typically, researchers make a simplifying assumption that age and stage classes are determined without error, when in fact some level of misclassification often can be expected. If unaccounted for, misclassification will lead to overly optimistic levels of precision and can cause biased estimates of age or stage structure. Although several studies have used information from known-age individuals to quantify errors in age or stage distribution, the problem of estimating the age or stage structure in face of such errors has received comparably little attention. In this paper, we describe a general statistical framework for estimating the true stage distribution of a sample when misclassification rates can be estimated. The estimation process requires auxiliary information on misclassification rates, such as data from individuals of known age. We analyze age-structured harvest records from black bears in Pennsylvania to illustrate how incorporating misclassification errors leads to changes in point estimates and provides a measure of precision.}, } @article {pmid17786568, year = {2007}, author = {Wang, T and Lu, Y and Shi, Y and Giesy, JP and Luo, W}, title = {Organochlorine pesticides in soils around Guanting Reservoir, China.}, journal = {Environmental geochemistry and health}, volume = {29}, number = {6}, pages = {491-501}, pmid = {17786568}, issn = {0269-4042}, mesh = {China ; Chromatography, Gas ; Cluster Analysis ; DDT/*analysis/metabolism ; Dichlorodiphenyl Dichloroethylene/analysis ; Environmental Monitoring ; Geographic Information Systems ; Hexachlorocyclohexane/*analysis/metabolism ; Insecticides/*analysis/metabolism ; Multivariate Analysis ; Pesticide Residues/*analysis ; Principal Component Analysis ; Soil Pollutants/*analysis ; }, abstract = {Fifty-six representative samples of topsoil were collected around Guanting Reservoir, which is an important water source for Beijing. Concentrations of the insecticides HCH, DDT, and their metabolites were quantified by use of gas chromatography (GC) with electron capture detection (ECD). Organochlorine pesticides (OCPs) are still present in surface soils in the Guanting area. DDT accounts for about 93% of the total OCP content. Concentrations of alpha/gamma, beta/gamma, and DDT/DDE are the result not only of historical use, but also of more recent depositions. Statistical analyses, including principal component analysis (PCA) and cluster analysis (CA), revealed associations between concentrations of OCPs and major soil characteristics. Geographical information system (GIS) technology was used to develop maps of the distributions of OCP concentrations. The areas of greatest contamination were primarily in the central part of the study area and were correlated with greater population density, heavier traffic, and more industrial activity.}, } @article {pmid17767998, year = {2008}, author = {Lafortezza, R and Corry, RC and Sanesi, G and Brown, RD}, title = {Visual preference and ecological assessments for designed alternative brownfield rehabilitations.}, journal = {Journal of environmental management}, volume = {89}, number = {3}, pages = {257-269}, doi = {10.1016/j.jenvman.2007.01.063}, pmid = {17767998}, issn = {0301-4797}, mesh = {Conservation of Natural Resources/*methods ; *Ecosystem ; *Environment Design ; Geographic Information Systems ; Italy ; *Plant Development ; }, abstract = {This paper describes an integrative method for quantifying, analyzing, and comparing the effects of alternative rehabilitation approaches with visual preference. The method was applied to a portion of a major industrial area located in southern Italy. Four alternative approaches to rehabilitation (alternative designs) were developed and analyzed. The scenarios consisted of the cleanup of the brownfields plus: (1) the addition of ground cover species; (2) the addition of ground cover species and a few trees randomly distributed; (3) the addition of ground cover species and a few trees in small groups; and (4) the addition of ground cover species and several trees in large groups. The approaches were analyzed and compared to the baseline condition through the use of cost-surface modeling (CSM) and visual preference assessment (VPA). Statistical results showed that alternatives that were more ecologically functional for forest bird species dispersal were also more visually preferable. Some differences were identified based on user groups and location of residence. The results of the study are used to identify implications for enhancing both ecological attributes and visual preferences of rehabilitating landscapes through planning and design.}, } @article {pmid17766028, year = {2008}, author = {Lange, E and Hehl-Lange, S and Brewer, MJ}, title = {Scenario-visualization for the assessment of perceived green space qualities at the urban-rural fringe.}, journal = {Journal of environmental management}, volume = {89}, number = {3}, pages = {245-256}, doi = {10.1016/j.jenvman.2007.01.061}, pmid = {17766028}, issn = {0301-4797}, mesh = {Agriculture ; Conservation of Natural Resources/*methods ; Ecosystem ; Environment Design ; Environmental Monitoring/*methods ; Geographic Information Systems ; Plant Development ; Recreation ; Switzerland ; }, abstract = {The provision of green space is increasingly being perceived as an important factor for quality of life. However, green spaces often face high developmental pressure. The main objective of this study is to investigate a prospective approach to green space planning by combining three-dimensional (3D) visualization of green space scenarios and survey techniques to facilitate improved participation of the public. Aside from the 'Status quo', scenarios 'Agriculture', 'Recreation', 'Nature conservation' and 'Wind turbines' are visualized in three dimensions. In order to test responses, a survey was conducted both in print format and on the Internet. Overall, 49 different visualizations that belong to one of the scenarios were available in the survey and were rated according to the perceived esthetic, recreational and ecological values. The highest rated scenes include vegetation elements such as meadows with orchards, single trees, shrubs or forest. The least attractive scenes are those where buildings are highly dominant or where there are no vegetation elements. Based on the ratings for the individual images and on the corresponding scenarios, our study shows that there is high potential for improving the existing landscape. All suggested changes are either rated about equal to or considerably higher than the status quo, with the scenario 'Nature conservation' receiving the highest scores.}, } @article {pmid17763735, year = {2007}, author = {Wang, YG and Xiao, DN and Li, XY and Li, Y}, title = {[Temporal and spatial variation of land degradation in alluvial oasis at northern slope of Tianshan Mountain].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {18}, number = {6}, pages = {1311-1315}, pmid = {17763735}, issn = {1001-9332}, mesh = {Altitude ; China ; Conservation of Natural Resources/*methods/trends ; Environmental Monitoring/*methods ; Geographic Information Systems ; Satellite Communications ; Soil/*analysis ; }, abstract = {Taking the Fubei Farm, a farming oasis of Sangong River watershed at the northern slope of Tianshan Mountain as study area, and by the methods of geostatistics, GIS and RS, this paper studied the temporal and spatial variation of land degradation in topsoil (0-20 cm) and its relationship with landscape structure. The results showed that in this oasis, human activity was the key factor resulting in the increase of landscape fragmentation and diversity. From 1983 to 2005, the land degradation area decreased by 26.69%, and the degradation degree was higher in the regions adjacent to desert than in those further inside the oasis. Gray desert soil was degraded much more seriously than saline soil and aquic soil. The regions of poor land quality had an alleviated degradation, with 65.38% of land area improved, while those of good land quality had an aggravated degradation, with 33.38% of land area degraded.}, } @article {pmid17763732, year = {2007}, author = {Peng, LH and Chen, S and Liu, YX and Wang, J}, title = {[Application of Citygreen model in benefit assessment of Nanjing urban greenbelt in carbon fixation and runoff reduction].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {18}, number = {6}, pages = {1293-1298}, pmid = {17763732}, issn = {1001-9332}, mesh = {Carbon/*analysis ; China ; City Planning/methods ; Ecosystem ; Environment Design ; Environmental Monitoring/*methods ; Geographic Information Systems ; *Models, Theoretical ; *Plant Development ; }, abstract = {Based on the analysis of the framework and calculation principles of Citygreen model in assessing the benefits of urban greenbelt in carbon fixation and runoff reduction, an approach was made to obtain appropriate parameters of this model to calculate the ecological benefits of different urban land use types in the main urban district of Nanjing. The results indicated that the main urban district of Nanjing had much lower carbon fixation benefit than natural forest on per unit area base, being about 5%-60% of the latter. The ecological value of carbon fixation and runoff reduction of Nanjing urban greenbelt was about 177 million RMB in total, and the ecological benefits of different land use types were in the order of green land > public facility > residential > road and square > industrial > municipal. This research could provide references for city planning and urban greenbelt establishment, and facilitate the popularization of quantitative assessment on greenbelt ecological benefits of Chinese cities.}, } @article {pmid17763717, year = {2007}, author = {Liu, CF and He, XY and Chen, W and Zhao, GL and Xu, WD}, title = {[Estimation of Shenyang urban forest green biomass].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {18}, number = {6}, pages = {1208-1212}, pmid = {17763717}, issn = {1001-9332}, mesh = {*Biomass ; China ; *City Planning ; *Ecosystem ; Geographic Information Systems ; Humans ; Trees/*growth & development ; }, abstract = {Based on ARC/GIS and by using the method of "planar biomass estimation", the green biomass (GB) of Shenyang urban forests was measured. The results demonstrated that the GB per unit area was the highest (3.86 m2.m(-2)) in landscape and relaxation forest, and the lowest (2.27 m2.m(-2)) in ecological and public welfare forest. The GB per unit area in urban forest distribution area was 2.99 m2.m(-2), and that of the whole Shenyang urban area was 0.25 m2.m(-2). The total GB of Shenyang urban forests was about 1.13 x 10(8) m2, among which, subordinated forest, ecological and public welfare forest, landscape and relaxation forest, road forest, and production and management forest accounted for 36.64% , 23.99% , 19.38% , 16.20% and 3.79%, with their GB being 4. 15 x 10(7), 2.72 x 10(7), 2.20 x 10(7), 1.84 x 10(7) and 0.43 x 10(7) m2, respectively. The precision of the method "planar biomass estimation" was 91.81% (alpha = 0.05) by credit test.}, } @article {pmid17729408, year = {2007}, author = {Penrose, AS and Wells, EV and Aiello, AE}, title = {Infectious causation of chronic disease: examining the relationship between Giardia lamblia infection and irritable bowel syndrome.}, journal = {World journal of gastroenterology}, volume = {13}, number = {34}, pages = {4574-4578}, pmid = {17729408}, issn = {1007-9327}, mesh = {Animals ; Blue Cross Blue Shield Insurance Plans/statistics & numerical data ; Databases as Topic ; Drug Prescriptions/statistics & numerical data ; *Giardia lamblia ; Giardiasis/*complications/*epidemiology ; Humans ; Incidence ; Insurance, Pharmaceutical Services/statistics & numerical data ; Irritable Bowel Syndrome/drug therapy/*epidemiology/*parasitology ; Michigan/epidemiology ; Population Surveillance ; Prevalence ; Refugees/statistics & numerical data ; Socioeconomic Factors ; }, abstract = {AIM: To evaluate whether a higher prevalence of Giardia lamblia infection is associated with an increase in irritable bowel syndrome (IBS) prescriptions at the county level in Michigan.

METHODS: The Michigan Disease Surveillance System (MDSS) was used to ascertain both the numbers of Giardia lamblia infections as well as the total number of foodborne illnesses per population by county in Michigan during 2005. This was compared with Blue Cross Blue Shield (BCBS) of Michigan numbers of drug prescriptions for IBS per one thousand members per county in 2005. These data were also analyzed for associations with per capita income by county and the number of refugees entering each county in 2005.

RESULTS: There were a total of 786 confirmed cases of Giardia lamblia reported to MDSS in 2005. During the same time period, the number of prescriptions for IBS varied from 0.5 per 1000 members up to 6.0 per 1000 members per month. There was no trend towards higher numbers of IBS prescriptions in the counties with more Giardia lamblia infections. Per capita income was not associated with either IBS prescriptions or Giardiasis. There was a significant linear association between the number of refugees entering each county, and the number of Giardia lamblia cases per 100,000 population.

CONCLUSION: In this ecological study, there was no association found between BCBS prescriptions for IBS and Giardia lamblia infections in Michigan counties. Our findings may have been influenced by the disparate number of refugees admitted per county.}, } @article {pmid17727915, year = {2007}, author = {Hendriks, AJ and Smítková, H and Huijbregts, MA}, title = {A new twist on an old regression: transfer of chemicals to beef and milk in human and ecological risk assessment.}, journal = {Chemosphere}, volume = {70}, number = {1}, pages = {46-56}, doi = {10.1016/j.chemosphere.2007.07.030}, pmid = {17727915}, issn = {0045-6535}, mesh = {Animal Feed/analysis ; Animals ; Biomass ; Cattle ; Data Interpretation, Statistical ; Environmental Pollutants/*analysis/metabolism/toxicity ; Humans ; Meat/adverse effects/*analysis ; Milk/adverse effects/*chemistry ; Models, Biological ; Octanols/chemistry ; Regression Analysis ; Risk Assessment ; Water/chemistry ; }, abstract = {Exposure of humans to chemicals in beef or milk is part of almost all risk evaluation procedures carried out to reduce emissions or to remediate sites. Concentrations of substances in these livestock products are often estimated using log-log regressions that relate the biotransfer factor BTF to the octanol-water partition ratio K(ow). However, the correctness of these empirical correlations has been questioned. Here, we compare them to the mechanistic model OMEGA that describes the distribution of substances in organisms by integrating theory on chemical fugacity and biological allometry. OMEGA has been calibrated and validated on thousands of laboratory and field data, reflecting many chemical substances and biological species. Overall fluxes of water, food, tissue (growth), milk and stable substances calculated by OMEGA are within a factor of two from independent data obtained in experiments. Rate constants measured for elimination of individual compounds of a recalcitrant nature vary around the level expected from the model for output to faeces and milk. Both data and model suggest that biotransfer BTF of stable substances to beef and milk is independent of the octanol-water partition ratio K(ow) in the range of 10(3)-10(6). This contradicts empirical regressions including stable and labile compounds. As expected, levels of labile substances vary widely around a tentative indication derived from the model. Transformation and accumulation of labile substances remains highly specific for the chemical and organism concerned but depends weakly on the octanol-water partition ratio K(ow). Several possibilities for additional refinement are identified.}, } @article {pmid17725571, year = {2008}, author = {Davis, EB and Koo, MS and Conroy, C and Patton, JL and Moritz, C}, title = {The California Hotspots Project: identifying regions of rapid diversification of mammals.}, journal = {Molecular ecology}, volume = {17}, number = {1}, pages = {120-138}, doi = {10.1111/j.1365-294X.2007.03469.x}, pmid = {17725571}, issn = {0962-1083}, mesh = {Animals ; *Biodiversity ; *Biological Evolution ; California ; Computational Biology ; Conservation of Natural Resources/*methods ; DNA, Mitochondrial/genetics ; *Demography ; *Environment ; Gene Flow/genetics ; Geography ; Mammals/*genetics ; Models, Theoretical ; Selection, Genetic ; Species Specificity ; }, abstract = {The high rate of anthropogenic impact on natural systems mandates protection of the evolutionary processes that generate and sustain biological diversity. Environmental drivers of diversification include spatial heterogeneity of abiotic and biotic agents of divergent selection, features that suppress gene flow, and climatic or geological processes that open new niche space. To explore how well such proxies perform as surrogates for conservation planning, we need first to map areas with rapid diversification -'evolutionary hotspots'. Here we combine estimates of range size and divergence time to map spatial patterns of neo-endemism for mammals of California, a global biodiversity hotspot. Neo-endemism is explored at two scales: (i) endemic species, weighted by the inverse of range size and mtDNA sequence divergence from sisters; and (ii) as a surrogate for spatial patterns of phenotypic divergence, endemic subspecies, again using inverse-weighting of range size. The species-level analysis revealed foci of narrowly endemic, young taxa in the central Sierra Nevada, northern and central coast, and Tehachapi and Peninsular Ranges. The subspecies endemism-richness analysis supported the last four areas as hotspots for diversification, but also highlighted additional coastal areas (Monterey to north of San Francisco Bay) and the Inyo Valley to the east. We suggest these hotspots reflect the major processes shaping mammal neo-endemism: steep environmental gradients, biotic admixture areas, and areas with recent geological/climate change. Anthropogenic changes to both environment and land use will have direct impacts on regions of rapid divergence. However, despite widespread changes to land cover in California, the majority of the hotspots identified here occur in areas with relatively intact ecological landscapes. The geographical scope of conserving evolutionary process is beyond the scale of any single agency or nongovernmental organization. Choosing which land to closely protect and/or purchase will always require close coordination between agencies.}, } @article {pmid17708224, year = {2007}, author = {Ranganathan, J and Chan, KM and Daily, GC}, title = {Satellite detection of bird communities in tropical countryside.}, journal = {Ecological applications : a publication of the Ecological Society of America}, volume = {17}, number = {5}, pages = {1499-1510}, doi = {10.1890/06-0285.1}, pmid = {17708224}, issn = {1051-0761}, mesh = {Agriculture ; Animals ; Biodiversity ; Birds/*physiology ; Costa Rica ; *Ecosystem ; Environmental Monitoring/*methods ; Forestry ; *Geographic Information Systems ; Geography ; Population Dynamics ; *Satellite Communications ; Tropical Climate ; }, abstract = {The future of biodiversity hinges partly on realizing the potentially high conservation value of human-dominated countryside. The characteristics of the countryside that promote biodiversity preservation remain poorly understood, however, particularly at the fine scales at which individual farmers tend to make land use decisions. To address this problem, we explored the use of a rapid remote sensing method for estimating bird community composition in tropical countryside, using a two-step process. First, we asked how fine-grained variation in land cover affected community composition. Second, we determined whether the observed changes in community composition correlated with three easily accessible remote sensing metrics (wetness, greenness, and brightness), derived from performing a tasseled-cap transformation on a Landsat Enhanced Thematic Mapper Plus image. As a comparison, we also examined whether the most commonly used remote sensing indicator in ecology, the Normalized Difference Vegetation Index (NDVI), correlated with community composition. We worked within an agricultural landscape in southern Costa Rica, where the land comprised a complex and highly heterogeneous mosaic of remnant native vegetation, pasture, coffee cultivation, and other crops. In this region, we selected 12 study sites (each < 60 ha) that encompassed the range of available land cover possibilities in the countryside. Within each site, we surveyed bird communities within all major land cover types, and we conducted detailed field mapping of land cover. We found that the number of forest-affiliated species increased with forest cover and decreased with residential area across sites. Conversely, the number of agriculture-affiliated species using forest increased with land area devoted to agricultural and residential uses. Interestingly, we found that the wetness and brightness metrics predicted the number of forest- and agriculture-affiliated species within a site as well as did detailed field-generated maps of land cover. In contrast, NDVI and the closely correlated greenness metric did not correlate with land cover or with bird communities. Our study shows the strong potential of the tasseled-cap transformation as a tool for assessing the conservation value of countryside for biodiversity.}, } @article {pmid17704131, year = {2007}, author = {Jakó, E and Ittzés, P and Szenes, A and Kun, A and Szathmáry, E and Pál, G}, title = {In silico detection of tRNA sequence features characteristic to aminoacyl-tRNA synthetase class membership.}, journal = {Nucleic acids research}, volume = {35}, number = {16}, pages = {5593-5609}, pmid = {17704131}, issn = {1362-4962}, mesh = {Algorithms ; Amino Acyl-tRNA Synthetases/*classification ; Animals ; Computational Biology ; Humans ; RNA, Archaeal/genetics ; RNA, Bacterial/genetics ; RNA, Fungal/genetics ; RNA, Transfer/*classification/genetics ; Saccharomyces cerevisiae/genetics ; Sequence Alignment ; Sequence Analysis, DNA/*methods ; }, abstract = {Aminoacyl tRNA synthetases (aaRS) are grouped into Class I and II based on primary and tertiary structure and enzyme properties suggesting two independent phylogenetic lineages. Analogously, tRNA molecules can also form two respective classes, based on the class membership of their corresponding aaRS. Although some aaRS-tRNA interactions are not extremely specific and require editing mechanisms to avoid misaminoacylation, most aaRS-tRNA interactions are rather stereospecific. Thus, class-specific aaRS features could be mirrored by class-specific tRNA features. However, previous investigations failed to detect conserved class-specific nucleotides. Here we introduce a discrete mathematical approach that evaluates not only class-specific 'strictly present', but also 'strictly absent' nucleotides. The disjoint subsets of these elements compose a unique partition, named extended consensus partition (ECP). By analyzing the ECP for both Class I and II tDNA sets from 50 (13 archaeal, 30 bacterial and 7 eukaryotic) species, we could demonstrate that class-specific tRNA sequence features do exist, although not in terms of strictly conserved nucleotides as it had previously been anticipated. This finding demonstrates that important information was hidden in tRNA sequences inaccessible for traditional statistical methods. The ECP analysis might contribute to the understanding of tRNA evolution and could enrich the sequence analysis tool repertoire.}, } @article {pmid17704120, year = {2007}, author = {Sarkar, IN}, title = {Biodiversity informatics: organizing and linking information across the spectrum of life.}, journal = {Briefings in bioinformatics}, volume = {8}, number = {5}, pages = {347-357}, doi = {10.1093/bib/bbm037}, pmid = {17704120}, issn = {1477-4054}, mesh = {*Biodiversity ; Computational Biology/*trends ; *Databases, Genetic ; Information Dissemination/*methods ; *Population Dynamics ; }, abstract = {Biological knowledge can be inferred from three major levels of information: molecules, organisms and ecologies. Bioinformatics is an established field that has made significant advances in the development of systems and techniques to organize contemporary molecular data; biodiversity informatics is an emerging discipline that strives to develop methods to organize knowledge at the organismal level extending back to the earliest dates of recorded natural history. Furthermore, while bioinformatics studies generally focus on detailed examinations of key 'model' organisms, biodiversity informatics aims to develop over-arching hypotheses that span the entire tree of life. Biodiversity informatics is presented here as a discipline that unifies biological information from a range of contemporary and historical sources across the spectrum of life using organisms as the linking thread. The present review primarily focuses on the use of organism names as a universal metadata element to link and integrate biodiversity data across a range of data sources.}, } @article {pmid17703561, year = {2007}, author = {Doumbia, S and Chouong, H and Traore, SF and Dolo, G and Touré, AM and Coulibaly, M}, title = {Establishing an insect disease vector functional genomics training center in Africa.}, journal = {African journal of medicine and medical sciences}, volume = {36 Suppl}, number = {}, pages = {31-33}, pmid = {17703561}, issn = {0309-3913}, mesh = {Africa ; Animals ; Biomedical Research ; Computational Biology/*organization & administration ; Demography ; Genetic Vectors ; Genomics/*organization & administration ; Humans ; Insect Vectors/*genetics ; Insecta ; }, abstract = {The genome sequences for many insects vector of human diseases are now available and promise the development of a set of new, powerful tools that can be used to develop innovative approaches to control these diseases. The African continent, which is the most severely affected by vector borne diseases, lacks adequate infrastructures and personal resources required for rational use of genomic information. To fill this gap, the African Center for Training in Functional Genomics of Insect vectors of Human Disease (AFRO VECTGEN) was initiated by WHO/TDR and the Department of Medical Entomology and Vector Ecology (DMEVE) of the Malaria Research and Training Center (MRTC) in Mali. The aim of the AFRO VECTGEN program is to train young scientists in functional genomics who will ultimately use genome sequence data for research on insect vector of human disease. The program could trigger collaborative research and will benefit from an existing vector biology network in Mali, which was built around research grants funded by the National Institutes of Health, USA and WHO/TDR.}, } @article {pmid17702608, year = {2007}, author = {von Rintelen, K and von Rintelen, T and Glaubrecht, M}, title = {Molecular phylogeny and diversification of freshwater shrimps (Decapoda, Atyidae, Caridina) from ancient Lake Poso (Sulawesi, Indonesia)--the importance of being colourful.}, journal = {Molecular phylogenetics and evolution}, volume = {45}, number = {3}, pages = {1033-1041}, doi = {10.1016/j.ympev.2007.07.002}, pmid = {17702608}, issn = {1055-7903}, mesh = {Animals ; Color ; Databases, Factual ; Decapoda/anatomy & histology/*classification/*genetics ; Ecology ; *Evolution, Molecular ; *Fresh Water ; Indonesia ; *Phylogeny ; }, abstract = {Ancient Lake Poso on the Indonesian island Sulawesi hosts a highly diverse endemic fauna, including a small species flock of atyid Caridina shrimps, which are characterized by conspicuous colour patterns. We used a mtDNA based molecular phylogeny to test the assumption of a monophyletic origin and intralacustrine radiation of the species flock and to assess the species specificity of some colour morphs. Our data reveal a rapid radiation of Caridina in the entire Poso drainage system, but provide no strong evidence for a monophyletic radiation of the lake species. Nevertheless each lacustrine species shows a varying degree of substrate or trophic specialization, usually considered a hallmark of adaptive radiation. Two distinct colour forms previously attributed to a single species, C. ensifera, lack distinguishing qualitative morphological characters, but are shown to be two different species. In contrast, morphologically rather distinct lake species lacking specific colour patterns may be hybridizing with riverine taxa. These results suggest that colour may play a similar role in species recognition and possibly speciation in ancient lake Caridina as hypothesized, e.g. for some African cichlids.}, } @article {pmid17697314, year = {2007}, author = {da Cunha, SS and Pujades-Rodriguez, M and Barreto, ML and Genser, B and Rodrigues, LC}, title = {Ecological study of socio-economic indicators and prevalence of asthma in schoolchildren in urban Brazil.}, journal = {BMC public health}, volume = {7}, number = {}, pages = {205}, pmid = {17697314}, issn = {1471-2458}, support = {//Wellcome Trust/United Kingdom ; }, mesh = {Adolescent ; Asthma/economics/*epidemiology ; Brazil/epidemiology ; Child ; Data Interpretation, Statistical ; Databases, Factual ; Environmental Monitoring ; Epidemiological Monitoring ; Female ; Health Surveys ; Humans ; Male ; *Poverty ; Prevalence ; Regression Analysis ; Schools ; *Social Class ; Socioeconomic Factors ; Urban Health/*statistics & numerical data ; }, abstract = {BACKGROUND: There is evidence of higher prevalence of asthma in populations of lower socio-economic status in affluent societies, and the prevalence of asthma is also very high in some Latin American countries, where societies are characterized by a marked inequality in wealth. This study aimed to examine the relationship between estimates of asthma prevalence based on surveys conducted in children in Brazilian cities and health and socioeconomic indicators measured at the population level in the same cities.

METHODS: We searched the literature in the medical databases and in the annals of scientific meeting, retrieving population-based surveys of asthma that were conducted in Brazil using the methodology defined by the International Study of Asthma and Allergies in Childhood. We performed separate analyses for the age groups 6-7 years and 13-14 years. We examined the association between asthma prevalence rates and eleven health and socio-economic indicators by visual inspection and using linear regression models weighed by the inverse of the variance of each survey.

RESULTS: Six health and socioeconomic variables showed a clear pattern of association with asthma. The prevalence of asthma increased with poorer sanitation and with higher infant mortality at birth and at survey year, GINI index and external mortality. In contrast, asthma prevalence decreased with higher illiteracy rates.

CONCLUSION: The prevalence of asthma in urban areas of Brazil, a middle income country, appears to be higher in cities with more marked poverty or inequality.}, } @article {pmid17690990, year = {2008}, author = {Wang, Y and Xiao, D and Li, Y and Li, X}, title = {Soil salinity evolution and its relationship with dynamics of groundwater in the oasis of inland river basins: case study from the Fubei region of Xinjiang Province, China.}, journal = {Environmental monitoring and assessment}, volume = {140}, number = {1-3}, pages = {291-302}, pmid = {17690990}, issn = {0167-6369}, mesh = {China ; Fresh Water/*chemistry ; Geographic Information Systems ; Sodium Chloride/*analysis ; Soil/*analysis ; }, abstract = {Soil salinization is an important worldwide environmental problem, especially in arid and semi-arid regions. Knowledge of its temporal and spatial variability is crucial for the management of oasis agriculture. The study area has experienced dramatic change in the shallow groundwater table and soil salinization during the 20th century, especially in the past two decades. Classical statistics, geostatistics and geographic information system (GIS) were applied to estimate the spatial variability of the soil salt content in relation to the shallow groundwater table and land use from 1983 to 2005. Consumption of reservoir water for agricultural irrigation was the main cause of a rise in the shallow groundwater table under intense evapotranspiration conditions, and this led indirectly to soil salinization. The area of soil salt accumulation was greater in irrigated than in non-irrigated landscape types with an increasing of 40.04% from 1983 to 2005 in cropland at approximately 0.43 t ha(-1) year(-1), and an increase at approximately 0.68 t ha(-1) year(-1) in saline alkaline land. Maps of the shallow groundwater table in 1985 and 2000 were used to deduce maps for 1983 and 1999, respectively, and the registration accuracy was 99%.}, } @article {pmid17688507, year = {2007}, author = {Diggle, PJ and Gómez-Rubio, V and Brown, PE and Chetwynd, AG and Gooding, S}, title = {Second-order analysis of inhomogeneous spatial point processes using case-control data.}, journal = {Biometrics}, volume = {63}, number = {2}, pages = {550-557}, doi = {10.1111/j.1541-0420.2006.00683.x}, pmid = {17688507}, issn = {0006-341X}, mesh = {Biometry/*methods ; *Case-Control Studies ; Cluster Analysis ; Data Interpretation, Statistical ; Ecosystem ; Humans ; Models, Statistical ; Monte Carlo Method ; Sri Lanka ; Trees/growth & development ; Tropical Climate ; }, abstract = {Methods for the statistical analysis of stationary spatial point process data are now well established, methods for nonstationary processes less so. One of many sources of nonstationary point process data is a case-control study in environmental epidemiology. In that context, the data consist of a realization of each of two spatial point processes representing the locations, within a specified geographical region, of individual cases of a disease and of controls drawn at random from the population at risk. In this article, we extend work by Baddeley, Møller, and Waagepetersen (2000, Statistica Neerlandica54, 329-350) concerning estimation of the second-order properties of a nonstationary spatial point process. First, we show how case-control data can be used to overcome the problems encountered when using the same data to estimate both a spatially varying intensity and second-order properties. Second, we propose a semiparametric method for adjusting the estimate of intensity so as to take account of explanatory variables attached to the cases and controls. Our primary focus is estimation, but we also propose a new test for spatial clustering that we show to be competitive with existing tests. We describe an application to an ecological study in which juvenile and surviving adult trees assume the roles of controls and cases.}, } @article {pmid17683431, year = {2007}, author = {Wiens, JJ and Kuczynski, CA and Duellman, WE and Reeder, TW}, title = {Loss and re-evolution of complex life cycles in marsupial frogs: does ancestral trait reconstruction mislead?.}, journal = {Evolution; international journal of organic evolution}, volume = {61}, number = {8}, pages = {1886-1899}, doi = {10.1111/j.1558-5646.2007.00159.x}, pmid = {17683431}, issn = {0014-3820}, mesh = {Animals ; Anura/genetics/*growth & development ; Biological Evolution ; *Climate ; *DNA, Mitochondrial ; Geographic Information Systems ; Life Cycle Stages/*genetics ; *Phylogeny ; }, abstract = {Using phylogeny-based methods to identify evolutionary transitions has become an integral part of evolutionary biology. Here, we demonstrate the potential for these methods to give statistically well-supported but misleading inferences about character evolution. We also show how inferences of character evolution can be informed using GIS-based methods to reconstruct ancestral environmental regimes. We reconstruct a phylogeny for marsupial frogs (Hemiphractidae) using nuclear and mitochondrial DNA sequences and estimate patterns of life-history evolution across the resulting tree. We find that Gastrotheca species with complex life cycles (i.e., egg, tadpole, and adult stages) are phylogenetically nested among species and genera with direct development (i.e., egg and adult stages only). Assuming a single rate for gains and losses in likelihood reconstructions, there is strong statistical support for the hypothesis that the tadpole stage was lost early in the phylogeny but reappeared within Gastrotheca. Assuming different rates of gain and loss, the model with significantly higher statistical support, the tadpole stage seems to have been lost multiple times but never regained. Given that both hypotheses cannot be correct, at least one reconstruction model must be giving well-supported but misleading results. Several lines of evidence (including GIS-based reconstructions of the ancestral climatic regime) suggest that the former hypothesis is correct, and that the tadpole stage has evolved from direct development within Gastrotheca, the only known case of such a reversal in frogs.}, } @article {pmid17681351, year = {2007}, author = {Fleischer, D and Grémare, A and Labrune, C and Rumohr, H and Berghe, EV and Zettler, ML}, title = {Performance comparison of two biotic indices measuring the ecological status of water bodies in the Southern Baltic and Gulf of Lions.}, journal = {Marine pollution bulletin}, volume = {54}, number = {10}, pages = {1598-1606}, doi = {10.1016/j.marpolbul.2007.06.011}, pmid = {17681351}, issn = {0025-326X}, mesh = {Animals ; Databases, Factual ; Environmental Monitoring/*methods/*standards/statistics & numerical data ; *Invertebrates ; Linear Models ; Mediterranean Sea ; *Models, Biological ; Oceans and Seas ; Sensitivity and Specificity ; }, abstract = {Two biotic indices, ATZI Marine Biotic Index (AMBI) and Benthic Quality Index (BQI) have been recently introduced within the EC Water Framework Directive to assess the quality of marine habitats: both are based on sensitivity/tolerance classification and quantitative information on the composition of soft-bottom macrofauna. Their performance, especially with regard to sampling effort was assessed based on two data sets collected in Southern Baltic and one from the Gulf of Lions Mediterranean. AMBI was not affected by sampling effort but BQI was. Two modifications were proposed for BQI (i.e., BQI) (1) the removal of the scaling term (i.e., BQI(W)), and (2) the replacement of the scaling term by different scaling term (i.e., BQI(ES)). Both modified BQIs were largely independent of sampling effort. Variability was slightly lower for BQI(W) than for BQI(ES). BQI was highly correlated with BQI(W) and with BQI(ES) both in the Southern Baltic and in the Gulf of Lions. However, the proportions of stations, which were not attributed the same ecological quality status (EcoQ) when using BQI and its two modified forms were always high. Differences in ecological classification were mostly due to the scales used to infer EcoQ. Based on this study we recommend to use BQI(ES) in future studies because it apparently constitutes the best compromise in (1) being independent of sampling effort, (2) limiting the variability in computation in relation with sampling effort, (3) being correlated with BQI and corresponding EcoQ.}, } @article {pmid17680336, year = {2008}, author = {Pesch, R and Pehlke, H and Jerosch, K and Schröder, W and Schlüter, M}, title = {Using decision trees to predict benthic communities within and near the German Exclusive Economic Zone (EEZ) of the North Sea.}, journal = {Environmental monitoring and assessment}, volume = {136}, number = {1-3}, pages = {313-325}, pmid = {17680336}, issn = {1573-2959}, mesh = {Animals ; *Decision Trees ; *Ecosystem ; Geographic Information Systems ; *Geologic Sediments ; Germany ; *Marine Biology ; North Sea ; Seasons ; *Seawater ; }, abstract = {In this article a concept is described in order to predict and map the occurrence of benthic communities within and near the German Exclusive Economic Zone (EEZ) of the North Sea. The approach consists of two work steps: (1) geostatistical analysis of abiotic measurement data and (2) calculation of benthic provinces by means of Classification and Regression Trees (CART) and GIS-techniques. From bottom water measurements on salinity, temperature, silicate and nutrients as well as from punctual data on grain size ranges (0-20, 20-63, 63-2,000 mu) raster maps were calculated by use of geostatistical methods. At first the autocorrelation structure was examined and modelled with help of variogram analysis. The resulting variogram models were then used to calculate raster maps by applying ordinary kriging procedures. After intersecting these raster maps with punctual data on eight benthic communities a decision tree was derived to predict the occurrence of these communities within the study area. Since such a CART tree corresponds to a hierarchically ordered set of decision rules it was applied to the geostatistically estimated raster data to predict benthic habitats within and near the EEZ.}, } @article {pmid17676586, year = {2007}, author = {Pollack, KM and Agnew, J and Slade, MD and Cantley, L and Taiwo, O and Vegso, S and Sircar, K and Cullen, MR}, title = {Use of employer administrative databases to identify systematic causes of injury in aluminum manufacturing.}, journal = {American journal of industrial medicine}, volume = {50}, number = {9}, pages = {676-686}, doi = {10.1002/ajim.20493}, pmid = {17676586}, issn = {0271-3586}, support = {F31KD068940//PHS HHS/United States ; R01-OH-04040/OH/NIOSH CDC HHS/United States ; }, mesh = {Accidents, Occupational/*statistics & numerical data ; Adolescent ; Adult ; Age Factors ; Aluminum ; Databases, Factual ; Female ; Humans ; Male ; *Metallurgy ; Middle Aged ; Occupational Health/*statistics & numerical data ; Personnel Management/*statistics & numerical data ; Population Surveillance ; Sex Factors ; Task Performance and Analysis ; United States ; }, abstract = {BACKGROUND: Employer administrative files are an underutilized source of data in epidemiologic studies of occupational injuries.

METHODS: Personnel files, occupational health surveillance data, industrial hygiene data, and a real-time incident and injury management system from a large multi-site aluminum manufacturer were linked deterministically. An ecological-level measure of physical job demand was also linked. This method successfully created a database containing over 100 variables for 9,101 hourly employees from eight geographically dispersed U.S. plants.

RESULTS: Between 2002 and 2004, there were 3,563 traumatic injuries to 2,495 employees. The most common injuries were sprain/strains (32%), contusions (24%), and lacerations (14%). A multivariable logistic regression model revealed that physical job demand was the strongest predictor of injury risk, in a dose dependent fashion. Other strong predictors of injury included female gender, young age, short company tenure and short time on current job.

CONCLUSIONS: Employer administrative files are a useful source of data, as they permit the exploration of risk factors and potential confounders that are not included in many population-based surveys. The ability to link employer administrative files with injury surveillance data is a valuable analysis strategy for comprehensively studying workplace injuries, identifying salient risk factors, and targeting workforce populations disproportionately affected.}, } @article {pmid17673343, year = {2008}, author = {Schröder, W and Pesch, R and Englert, C and Harmens, H and Suchara, I and Zechmeister, HG and Thöni, L and Mankovská, B and Jeran, Z and Grodzinska, K and Alber, R}, title = {Metal accumulation in mosses across national boundaries: uncovering and ranking causes of spatial variation.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {151}, number = {2}, pages = {377-388}, doi = {10.1016/j.envpol.2007.06.025}, pmid = {17673343}, issn = {0269-7491}, mesh = {Altitude ; Bryophyta/chemistry/*metabolism ; Confounding Factors, Epidemiologic ; Environmental Monitoring/methods ; Environmental Pollutants/analysis/*metabolism ; Europe ; Geographic Information Systems ; Laboratories ; Metals/analysis/*metabolism ; Models, Statistical ; Oceans and Seas ; Rain ; Species Specificity ; }, abstract = {This study aimed at cross-border mapping metal loads in mosses in eight European countries in 1990, 1995, and 2000 and at investigating confounding factors. Geostatistics was used for mapping, indicating high local variances but clear spatial autocorrelations. Inference statistics identified differences of metal concentrations in mosses on both sides of the national borders. However, geostatistical analyses did not ascertain discontinuities of metal concentrations in mosses at national borders due to sample analysis in different laboratories applying a range of analytical techniques. Applying Classification and Regression Trees (CART) to the German moss data as an example, the local variation in metal concentrations in mosses were proved to depend mostly on different moss species, potential local emission sources, canopy drip and precipitation.}, } @article {pmid17671849, year = {2007}, author = {Schröder, W and Hornsmann, I and Pesch, R and Schmidt, G and Markert, B and Fränzle, S and Wünschmann, S and Heidenreich, H}, title = {Nitrogen and metals in two regions in Central Europe: significant differences in accumulation in mosses due to land use?.}, journal = {Environmental monitoring and assessment}, volume = {133}, number = {1-3}, pages = {495-505}, pmid = {17671849}, issn = {0167-6369}, mesh = {Bryophyta/*metabolism ; Europe ; Geographic Information Systems ; Metals/*metabolism ; Nitrogen/*metabolism ; }, abstract = {The study was conducted to test the hypothesis that the regional variability of nitrogen (N) and metal accumulations in terrestrial ecosystems are due to historical and recent ways of landuse. To this end, two regions of Central Europe were selected for investigation: the Weser-Ems Region (WER) and the Euro Region Nissa (ERN). They were assumed to have land use-specific accumulation profiles. Thus, the metal and N accumulations in both regions were examined by means of geostatistically based comparative moss analysis. The sampling and chemical analysis of mosses were conducted in accordance with the convenient guidelines and methods, respectively. The spatial representativity of the sampling sites was computed by means of a land classification which was calculated for Europe by means of classification trees and GIS-techniques. The differences of deposition loads were tested for statistical significance with regard to time and space. The measurement values corroborated the decline of metal accumulation observed since the beginning of the European Metals in Mosses Surveys in 1990. The metal loads of the mosses in the ERN exceeded those in the WER significantly. The opposite holds true for the N concentrations: those in the WER were significantly higher than those in the ERN. The reduction of emissions from power plants, factories and houses was strongly correlated with the decline of deposition and bioaccumulation of metals. As proved by the European Metals in Mosses Surveys, this tendency is due to successful environmental policies. But no such success could be verified by monitoring the accumulation of N in mosses.}, } @article {pmid17668053, year = {2007}, author = {Suga, K and Welch, DM and Tanaka, Y and Sakakura, Y and Hagiwara, A}, title = {Analysis of expressed sequence tags of the cyclically parthenogenetic rotifer Brachionus plicatilis.}, journal = {PloS one}, volume = {2}, number = {7}, pages = {e671}, pmid = {17668053}, issn = {1932-6203}, mesh = {Animals ; Contig Mapping ; DNA, Complementary/genetics/isolation & purification ; DNA, Helminth/genetics/isolation & purification ; Databases, Nucleic Acid ; *Expressed Sequence Tags ; Female ; Parthenogenesis ; RNA, Helminth/genetics/isolation & purification ; RNA, Ribosomal/genetics/isolation & purification ; Recombination, Genetic ; Reproduction ; Rotifera/anatomy & histology/*genetics/physiology ; Transcription, Genetic ; Untranslated Regions/genetics ; }, abstract = {BACKGROUND: Rotifers are among the most common non-arthropod animals and are the most experimentally tractable members of the basal assemblage of metazoan phyla known as Gnathifera. The monogonont rotifer Brachionus plicatilis is a developing model system for ecotoxicology, aquatic ecology, cryptic speciation, and the evolution of sex, and is an important food source for finfish aquaculture. However, basic knowledge of the genome and transcriptome of any rotifer species has been lacking.

We generated and partially sequenced a cDNA library from B. plicatilis and constructed a database of over 2300 expressed sequence tags corresponding to more than 450 transcripts. About 20% of the transcripts had no significant similarity to database sequences by BLAST; most of these contained open reading frames of significant length but few had recognized Pfam motifs. Sixteen transcripts accounted for 25% of the ESTs; four of these had no significant similarity to BLAST or Pfam databases. Putative up- and downstream untranslated regions are relatively short and AT rich. In contrast to bdelloid rotifers, there was no evidence of a conserved trans-spliced leader sequence among the transcripts and most genes were single-copy.

CONCLUSIONS/SIGNIFICANCE: Despite the small size of this EST project it revealed several important features of the rotifer transcriptome and of individual monogonont genes. Because there is little genomic data for Gnathifera, the transcripts we found with no known function may represent genes that are species-, class-, phylum- or even superphylum-specific; the fact that some are among the most highly expressed indicates their importance. The absence of trans-spliced leader exons in this monogonont species contrasts with their abundance in bdelloid rotifers and indicates that the presence of this phenomenon can vary at the subphylum level. Our EST database provides a relatively large quantity of transcript-level data for B. plicatilis, and more generally of rotifers and other gnathiferan phyla, and can be browsed and searched at gmod.mbl.edu.}, } @article {pmid17653929, year = {2007}, author = {Webster, DC and Chisholm, BJ and Stafslien, SJ}, title = {Mini-review: combinatorial approaches for the design of novel coating systems.}, journal = {Biofouling}, volume = {23}, number = {3-4}, pages = {179-192}, doi = {10.1080/08927010701250948}, pmid = {17653929}, issn = {0892-7014}, mesh = {Animals ; Biofilms/drug effects/growth & development ; Databases, Factual ; *Drug Design ; Marine Biology ; Polymers/*chemistry/*pharmacology ; }, abstract = {Combinatorial and high throughput experimental methods are being applied to the design and development of novel polymers and coatings used in a number of application areas. Methods have been developed for polymer synthesis and screening and for the development of polymer thin film and coating libraries and the screening of these libraries for key properties such as surface energy and modulus. Combinatorial and high throughput methods enable the efficient exploration of a large number of compositional variables over a wide range. In the development of coatings for use in the marine environment, the key challenge is in the development of screening methods that can predict good performance. A number of assays are under development that will permit the rapid screening of the interaction of coatings with representative marine organisms.}, } @article {pmid17650845, year = {2007}, author = {Peng, DL and Huang, JF and Wang, XZ}, title = {[Correlation analysis of regional vegetation seasonal fluctuation and climate factors based on MODIS-EVI].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {18}, number = {5}, pages = {983-989}, pmid = {17650845}, issn = {1001-9332}, mesh = {China ; Climate ; Crops, Agricultural/*growth & development ; Ecology ; Environmental Monitoring/*instrumentation/methods ; *Geographic Information Systems ; Seasons ; Trees/*growth & development ; }, abstract = {Taking Zhejiang Province as study area, and based on the data of MODIS-EVI, daily mean air temperature and daily precipitation from 52 weather stations, and actual land use in 2001-2004, the time lag cross-correlation analysis was made to relate the seasonal fluctuations of enhanced vegetation index (EVI) of farmland, woodland and garden plot with air temperature and precipitation. The results indicated that in most areas of Zhejiang, EVI had no time lag to air temperature, but about one month lag to precipitation. The time that air temperature or precipitation significantly influenced the seasonal fluctuation of most areas EVI lasted about 50 days. The correlation coefficients of the EVI of farmland, woodland and garden plot with air temperature and precipitation differed with time lags. When the time lag was zero, the correlation coefficient decreased in the sequence of woodland > garden plot > farmland, and when the time lag was not zero, it changed in adverse. The EVI of these three land-use types all had stronger correlation with air temperature than with precipitation, indicating that air temperature had more influence on the seasonal fluctuation of EVI.}, } @article {pmid17650843, year = {2007}, author = {Gu, XH and He, CY and Pan, YZ and Li, XB and Zhu, WQ and Zhu, XF}, title = {[Optimizing management on degraded grassland in Xilin River Basin based on ecological risk assessment].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {18}, number = {5}, pages = {968-976}, pmid = {17650843}, issn = {1001-9332}, mesh = {China ; *Conservation of Natural Resources/methods ; *Ecosystem ; Environmental Monitoring/*methods ; Geographic Information Systems ; Poaceae/*growth & development ; Risk Assessment ; Rivers ; }, abstract = {By the methods of remote sensing (RS) and geographic information system (GIS), and based on the estimations of degradation degree, risk degree and easy-restoration degree of degraded grasslands, an ecological management index (EMI) model of grassland was established to approach the practical ways of optimizing management of degraded grassland. A case study in the Xilin River Basin of Inner Mongolia showed that this model could quantitatively analyze the degradation degree, risk degree and easy-restoration degree of the grasslands under different optimizing management levels, which was of significance for applying rational measures with pertinence, and beneficial to the optimal allocation of resources during the management of degraded grassland. The EMI model could integrate most concerned information, which made it applicable widely.}, } @article {pmid17647083, year = {2008}, author = {Rodríguez-Muñoz, R and Bretman, A and Hadfield, JD and Tregenza, T}, title = {Sexual selection in the cricket Gryllus bimaculatus: no good genes?.}, journal = {Genetica}, volume = {132}, number = {3}, pages = {287-294}, doi = {10.1007/s10709-007-9172-3}, pmid = {17647083}, issn = {0016-6707}, mesh = {Animals ; Data Interpretation, Statistical ; Epistasis, Genetic ; Female ; Genetic Variation ; Gryllidae/*genetics ; Male ; Mating Preference, Animal ; Phenotype ; *Selection, Genetic ; *Sexual Behavior, Animal ; }, abstract = {Recent studies have suggested that females of the field cricket Gryllus bimaculatus exercise post-copulatory choice over the paternity of their offspring. There is evidence that these choices are made in relation to the genetic compatibility of mates rather than their absolute quality, but the magnitude of heritable differences in males has not been thoroughly examined. Using a half-sib breeding design we measured additive genetic variance and dam effects in a suite of reproductive and non-reproductive traits. Both components explained relatively little of the phenotypic variance across traits. The dam component in our design contains variance caused by both maternal effects and dominance. If maternal effects are negligible as suggested by previous studies, our data suggest that dominance variance is an important source of variation in these traits. The lack of additive genetic variation, but possible existence of large amounts of non-additive genetic variation is consistent with the idea that female mate choice and multiple mating may be driven by differences in genetic compatibility between potential mates rather than by differences in genetic quality.}, } @article {pmid17634101, year = {2007}, author = {Krupovic, M and Bamford, DH}, title = {Putative prophages related to lytic tailless marine dsDNA phage PM2 are widespread in the genomes of aquatic bacteria.}, journal = {BMC genomics}, volume = {8}, number = {}, pages = {236}, pmid = {17634101}, issn = {1471-2164}, mesh = {Bacteria/genetics/virology ; Capsid Proteins/genetics ; Corticoviridae/*genetics ; Databases, Protein ; Evolution, Molecular ; Genome, Bacterial/*genetics ; Genomics/*methods ; Prophages/*genetics ; }, abstract = {BACKGROUND: The origin and evolution of viruses is currently a heavily discussed issue. One element in this discussion is the innate viral "self" concept, which suggests that viral structures and functions can be divided into two categories. The first category consists of genetic determinants that are inherited from a viral ancestor and encode the viral "self". The second group consists of another set of structures and functions, the "nonself", which is interchangeable between different viruses and can be obtained via lateral gene transfer. Comparing the structures and sequences of the "self" elements, we have proposed that viruses can be grouped into lineages regardless of which domain of life (bacteria, archaea, eukarya) they infect. It has also been suggested that viruses are ancient and possibly predate modern cells.

RESULTS: Here we identified thirteen putative prophages (viral genomes integrated into bacterial chromosome) closely related to the virulent icosahedral tailless lipid-containing bacteriophage PM2. Using the comparative genomics approach, we present evidence to support the viral "self" hypothesis and divide genes of the bacteriophage PM2 and related prophages into "self" and "nonself" categories.

CONCLUSION: We show here that the previously proposed most conserved viral "self" determinants, the major coat protein and the packaging ATPase, were the only proteins that could be recognized in all detected corticoviral elements. We also argue here that the genes needed for viral genome replication, as well as for host cell lysis, belong to the "nonself" category of genes.Furthermore, we suggest that abundance of PM2-like viruses in the aquatic environment as well as their importance in the ecology of aquatic microorganisms might have been underestimated.}, } @article {pmid17629382, year = {2007}, author = {McNulty, SG and Cohen, EC and Moore Myers, JA and Sullivan, TJ and Li, H}, title = {Estimates of critical acid loads and exceedances for forest soils across the conterminous United States.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {149}, number = {3}, pages = {281-292}, doi = {10.1016/j.envpol.2007.05.025}, pmid = {17629382}, issn = {0269-7491}, mesh = {Acid Rain ; Acids/*analysis ; Adsorption ; Databases, Factual ; Ecology/methods/*statistics & numerical data ; Environmental Monitoring/*methods ; Environmental Pollutants/*analysis ; Humans ; Nitrogen/analysis ; Soil/analysis ; Soil Pollutants/analysis ; Sulfur/analysis ; *Trees ; United States ; }, abstract = {Concern regarding the impacts of continued nitrogen and sulfur deposition on ecosystem health has prompted the development of critical acid load assessments for forest soils. A critical acid load is a quantitative estimate of exposure to one or more pollutants at or above which harmful acidification-related effects on sensitive elements of the environment occur. A pollutant load in excess of a critical acid load is termed exceedance. This study combined a simple mass balance equation with national-scale databases to estimate critical acid load and exceedance for forest soils at a 1-km(2) spatial resolution across the conterminous US. This study estimated that about 15% of US forest soils are in exceedance of their critical acid load by more than 250eqha(-1)yr(-1), including much of New England and West Virginia. Very few areas of exceedance were predicted in the western US.}, } @article {pmid17626471, year = {2007}, author = {Jagtap, TG and Nagle, VL}, title = {Response and adaptability of mangrove habitats from the Indian subcontinent to changing climate.}, journal = {Ambio}, volume = {36}, number = {4}, pages = {328-334}, doi = {10.1579/0044-7447(2007)36[328:raaomh]2.0.co;2}, pmid = {17626471}, issn = {0044-7447}, mesh = {*Adaptation, Physiological ; Animals ; Avicennia/*growth & development ; Biodiversity ; Climate ; *Ecosystem ; Geographic Information Systems ; Geography ; Greenhouse Effect ; Indian Ocean ; Oceans and Seas ; Rhizophoraceae/*growth & development ; Water Movements ; }, abstract = {Mangroves, a predominant coastal habitat in the tropics, are constantly threatened by various anthropogenic pressures that are deteriorating the mangroves to a great extent. Global emissions of greenhouse gases are likely to raise the world temperature and the sea level at the rate of 0.3 degrees C and 6 mm 10 y(-1) by the year 2100. Mangrove habitats would be more vulnerable to climatic changes and resultant sea level rise (SLR) because of their unique location at the interface of the sea. By altering ecobiological processes, the intertidal and supratidal zones may extend further inland, resulting in changes in the existing ecological setup. The limitation of the landward margin would cause vertical rise, resulting in water-logging and ultimately killing the mangroves and dependent biota. The present document describes mangrove habitats and related issues from the Indian subcontinent in the context of climate variations and SLR, and recommends integrated long-term monitoring.}, } @article {pmid17617682, year = {2007}, author = {Twumasi, YA and Merem, EC}, title = {Using remote sensing and GIS in the analysis of ecosystem decline along the River Niger Basin: the case of Mali and Niger.}, journal = {International journal of environmental research and public health}, volume = {4}, number = {2}, pages = {173-184}, pmid = {17617682}, issn = {1661-7827}, mesh = {Ecosystem ; *Environment ; *Environmental Monitoring ; *Geographic Information Systems ; Humans ; Niger ; Pilot Projects ; Plants ; *Rivers ; Water Pollution/*adverse effects ; *Wetlands ; }, abstract = {In the Sub-Saharan African region of the River Niger Basin, where none of the major rivers is fully contained within the borders of a single nation, riverine ecosystem health monitoring is essential for survival. Even the globally proclaimed goals of sustainability and environmental security in the region are unattainable without using geospatial technologies of remote sensing and Geographic Information Systems (GIS) as conduits for environmental health within shared waters. Yet the systematic study of the nature of cooperation between states over shared water resources in troubled areas of the Middle East continues to dominate the literature with minimal coverage of the Sub- Saharan Africa experience and the role of GIS and remote sensing in monitoring the problem. Considering the intense ecosystem stress inflicted on River Niger by human activities and natural forces emanating from upstream and downstream nations. Researching the growing potential for acute riverine ecosystem decline among the nations of Niger and Mali along the River Niger Basin with the latest advances in spatial information technology as a decision support tool not only helps in ecosystem recovery and the avoidance of conflicts, but it has the potentials to bring countries much closer through information exchange. While the nature of the problem remains compounded due to the depletion of available water resources and environmental resources within shared waters, the lack of information exchange extracts ecological costs from all players. This is essential as the Niger Basin nations move towards a multinational watershed management as a conduit for sustainability. To confront these problems, some research questions with relevance to the paper have been posed. The questions include, Have there been any declines in the riverine ecosystem of the study area? What are the effects and what factors trigger the changes? What mitigation measures are in place for dealing with the problems? The first objective of the paper is to develop a new framework for analyzing the health of riverine ecosystems while the second objective seeks a contribution to the literature. The third objective is to design a geo-spatial tool for riverine ecosystem management and impact analysis. The fourth objective is to measure the nature of change in riverine environments with the latest advances in geo-spatial information technologies and methods. In terms of methodology, the paper relies on primary data sources analyzed with descriptive statistics, GIS techniques and remote sensing. The sections in the paper consist of a review of the major environmental effects and factors associated with the problem as well as mitigation measures in Mali and Niger. The paper concludes with some recommendations. The results point to growing modification along the riverine environments of the Mali and Niger portions of the River Niger Basin due to a host of factors.}, } @article {pmid17615959, year = {2007}, author = {Tachibana, J and Goto, N and Fujie, K}, title = {Estimation of cost and environmental load of fluorocarbon recovery and destruction system based on fluorocarbon stock distribution.}, journal = {Environmental technology}, volume = {28}, number = {5}, pages = {499-509}, doi = {10.1080/09593332808618811}, pmid = {17615959}, issn = {0959-3330}, mesh = {Air Conditioning ; Air Pollutants/*analysis ; *Air Pollution/economics/prevention & control ; Carbon Dioxide/*analysis ; Conservation of Energy Resources/economics/*methods ; Costs and Cost Analysis ; Fluorocarbons/*chemistry/metabolism ; Geographic Information Systems ; Refrigeration ; }, abstract = {We developed a simple method to estimate the cost and environmental load of a fluorocarbon recovery and destruction (R&D) system for commercial refrigerators (CRs) and building air conditioners (BACs). In order to estimate the fluorocarbon recovery process in detail, we also developed a method to obtain the regional fluorocarbon stock distribution with GIS (geographic information system). Then the distribution of fluorocarbon stock is visualized and the amount of fluorocarbon stock in the region can be calculated. Results show that the cost and CO2 emission of extraction, storage and destruction processes are a major part of the total cost of fluorocarbon R&D system. Also the cost and CO2 emission of a fluorocarbon R&D system of BACs is more than of CRs. This information is useful to devise a plan for the fluorocarbon R&D system and to fairly share the burden of the R&D cost.}, } @article {pmid17615873, year = {2007}, author = {Song, YT and Yu, SX and Li, N and Li, Y}, title = {[Landscape change during rapid urbanization in Shenzhen].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {18}, number = {4}, pages = {788-794}, pmid = {17615873}, issn = {1001-9332}, mesh = {China ; *City Planning ; *Conservation of Natural Resources ; *Ecosystem ; Environment Design ; Geographic Information Systems ; Humans ; Poaceae/growth & development ; Satellite Communications ; Trees/*growth & development ; }, abstract = {By using the satellite images of 4 periods of time, including the data from Thematic Mapper (TM), Enhanced Thematic Mapper Plus (ETM+), Multi Spectral Scanner (MSS) and SPOT this paper analyzed the landscape change in Shenzhen Special Economic Zone of Guangdong Province, South China in 1979-2003, aimed to study the temporal-spatial landscape change characteristics, their causes, and major driving forces in this zone. The results revealed that the characteristic of landscape change were completely different among test three periods (1979-1990, 1990-2000 and 2000-2003). During the first period (1979-1990), urbanization developed very rapidly, and the natural vegetations mainly in Futian, Luohu and Yantian districts degraded and transformed into a landscape with anthropogenic components. In the second period (1990-2000), landscape conversion mainly took place in Nanshan and Futian districts, where various types of landscape were transformed into impervious surfaces, and parts of the vegetations were transformed into anthropogenic landscapes. During this period, typical urban characteristics were formed, whereas the remaining vegetations, especially forest stand, were little disturbed. In the third period (2000-2003), subtle consolidation was observed, and the use of pervious material in certain areas counteracted the adverse ecological impacts of urbanization. The extent of urbanization still increased, but the intensity of landscape change was at lower level than that in previous periods.}, } @article {pmid17615079, year = {2007}, author = {Webster, TF}, title = {Bias magnification in ecologic studies: a methodological investigation.}, journal = {Environmental health : a global access science source}, volume = {6}, number = {}, pages = {17}, pmid = {17615079}, issn = {1476-069X}, support = {P42 ES007381/ES/NIEHS NIH HHS/United States ; 5P42ES007381/ES/NIEHS NIH HHS/United States ; }, mesh = {*Bias ; *Confounding Factors, Epidemiologic ; Data Interpretation, Statistical ; *Ecology ; Effect Modifier, Epidemiologic ; Environmental Exposure/analysis ; *Epidemiologic Research Design ; Humans ; *Observer Variation ; Regression Analysis ; Risk ; }, abstract = {BACKGROUND: As ecologic studies are often inexpensive to conduct, consideration of the magnitude and direction of ecologic biases may be useful in both study design and sensitivity analysis of results. This paper examines three types of ecologic bias: confounding by group, effect measure modification by group, and non-differential exposure misclassification.

METHODS: Bias of the risk difference on the individual and ecologic levels are compared using two-by-two tables, simple equations, and risk diagrams. Risk diagrams provide a convenient way to simultaneously display information from both levels.

RESULTS: Confounding by group and effect measure modification by group act in the same direction on the individual and group levels, but have larger impact on the latter. The reduction in exposure variance caused by aggregation magnifies the individual level bias due to ignoring groups. For some studies, the magnification factor can be calculated from the ecologic data alone. Small magnification factors indicate little bias beyond that occurring at the individual level. Aggregation is also responsible for the different impacts of non-differential exposure misclassification on individual and ecologic studies.

CONCLUSION: The analytical tools developed here are useful in analyzing ecologic bias. The concept of bias magnification may be helpful in designing ecologic studies and performing sensitivity analysis of their results.}, } @article {pmid17614217, year = {2007}, author = {Gachon, CM and Day, JG and Campbell, CN and Pröschold, T and Saxon, RJ and Küpper, FC}, title = {The Culture Collection of Algae and Protozoa (CCAP): a biological resource for protistan genomics.}, journal = {Gene}, volume = {406}, number = {1-2}, pages = {51-57}, doi = {10.1016/j.gene.2007.05.018}, pmid = {17614217}, issn = {0378-1119}, mesh = {Animals ; *Aquaculture ; Databases, Genetic ; Eukaryota/*genetics ; *Genomics ; Marine Biology ; Models, Animal ; Scotland ; }, abstract = {CCAP, the largest European protistan culture collection, is based at the Scottish Association for Marine Science near Oban, Scotland (http://www.ccap.ac.uk). The Collection comprises more than 2700 strains in the public domain, of which 1050 are marine algae, 1300 freshwater algae, and 350 protozoa. The primary mission of CCAP is to maintain and distribute defined cultures and their associated information to its customers. It also has a support and advisory function on all aspects of protistan science. In addition, it is involved in the training of students and researchers in algal identification and culture techniques. In light of the increasing number of fully sequenced protists, the CCAP is striving to provide targeted services and support to workers involved in all aspects of genomic research. At present, the Collection holds several hundred strains of genomic model taxa including: Acanthamoeba, Cafeteria, Cercomonas, Chlamydomonas, Chlorella, Cyanophora, Dictyostelium, Dunaliella, Ectocarpus, Emiliania, Euglena, Micromonas, Naegleria, Nephroselmis, Paramecium, Pavlova, Phaeodactylum, Porphyra, Pseudendoclonium, Pylaiella, Rhodomonas, Scenedesmus, Staurastrum, Tetrahymena, Thalassiosira, Volvox and Zygnema. These strains provide a defined representation of natural variation within model organisms, an increasingly useful resource for post-genomics approaches. Our aim over the next 2-5 years is to add value to the Collection by increasing the number of genome model species, and by offering an integrated, up-to-date, easy-to-use resource that would provide curated information on our strain holdings. In collaboration with other major Biological Resource Centres worldwide, we intend to build a hub providing access to both protistan cultures and their associated bioinformatics data.}, } @article {pmid17609186, year = {2007}, author = {Hamilton, MJ and Milne, BT and Walker, RS and Burger, O and Brown, JH}, title = {The complex structure of hunter-gatherer social networks.}, journal = {Proceedings. Biological sciences}, volume = {274}, number = {1622}, pages = {2195-2202}, pmid = {17609186}, issn = {0962-8452}, mesh = {*Community Networks ; Fractals ; Humans ; *Social Behavior ; }, abstract = {In nature, many different types of complex system form hierarchical, self-similar or fractal-like structures that have evolved to maximize internal efficiency. In this paper, we ask whether hunter-gatherer societies show similar structural properties. We use fractal network theory to analyse the statistical structure of 1189 social groups in 339 hunter-gatherer societies from a published compilation of ethnographies. We show that population structure is indeed self-similar or fractal-like with the number of individuals or groups belonging to each successively higher level of organization exhibiting a constant ratio close to 4. Further, despite the wide ecological, cultural and historical diversity of hunter-gatherer societies, this remarkable self-similarity holds both within and across cultures and continents. We show that the branching ratio is related to density-dependent reproduction in complex environments and hypothesize that the general pattern of hierarchical organization reflects the self-similar properties of the networks and the underlying cohesive and disruptive forces that govern the flow of material resources, genes and non-genetic information within and between social groups. Our results offer insight into the energetics of human sociality and suggest that human social networks self-organize in response to similar optimization principles found behind the formation of many complex systems in nature.}, } @article {pmid17601808, year = {2007}, author = {El Karkouri, K and Murat, C and Zampieri, E and Bonfante, P}, title = {Identification of internal transcribed spacer sequence motifs in truffles: a first step toward their DNA bar coding.}, journal = {Applied and environmental microbiology}, volume = {73}, number = {16}, pages = {5320-5330}, pmid = {17601808}, issn = {0099-2240}, mesh = {Ascomycota/classification/*genetics ; Base Sequence ; DNA, Fungal/*genetics ; DNA, Ribosomal Spacer/*genetics ; Databases, Nucleic Acid ; Phylogeny ; Species Specificity ; }, abstract = {This work presents DNA sequence motifs from the internal transcribed spacer (ITS) of the nuclear rRNA repeat unit which are useful for the identification of five European and Asiatic truffles (Tuber magnatum, T. melanosporum, T. indicum, T. aestivum, and T. mesentericum). Truffles are edible mycorrhizal ascomycetes that show similar morphological characteristics but that have distinct organoleptic and economic values. A total of 36 out of 46 ITS1 or ITS2 sequence motifs have allowed an accurate in silico distinction of the five truffles to be made (i.e., by pattern matching and/or BLAST analysis on downloaded GenBank sequences and directly against GenBank databases). The motifs considered the intraspecific genetic variability of each species, including rare haplotypes, and assigned their respective species from either the ascocarps or ectomycorrhizas. The data indicate that short ITS1 or ITS2 motifs (< or = 50 bp in size) can be considered promising tools for truffle species identification. A dot blot hybridization analysis of T. magnatum and T. melanosporum compared with other close relatives or distant lineages allowed at least one highly specific motif to be identified for each species. These results were confirmed in a blind test which included new field isolates. The current work has provided a reliable new tool for a truffle oligonucleotide bar code and identification in ecological and evolutionary studies.}, } @article {pmid17594421, year = {2007}, author = {Guralnick, RP and Hill, AW and Lane, M}, title = {Towards a collaborative, global infrastructure for biodiversity assessment.}, journal = {Ecology letters}, volume = {10}, number = {8}, pages = {663-672}, pmid = {17594421}, issn = {1461-0248}, mesh = {*Biodiversity ; Conservation of Natural Resources/methods ; *Databases, Factual ; Ecology/*methods ; Informatics/methods ; *Interdisciplinary Communication ; *Internet ; *Research Design ; }, abstract = {Biodiversity data are rapidly becoming available over the Internet in common formats that promote sharing and exchange. Currently, these data are somewhat problematic, primarily with regard to geographic and taxonomic accuracy, for use in ecological research, natural resources management and conservation decision-making. However, web-based georeferencing tools that utilize best practices and gazetteer databases can be employed to improve geographic data. Taxonomic data quality can be improved through web-enabled valid taxon names databases and services, as well as more efficient mechanisms to return systematic research results and taxonomic misidentification rates back to the biodiversity community. Both of these are under construction. A separate but related challenge will be developing web-based visualization and analysis tools for tracking biodiversity change. Our aim was to discuss how such tools, combined with data of enhanced quality, will help transform today's portals to raw biodiversity data into nexuses of collaborative creation and sharing of biodiversity knowledge.}, } @article {pmid17593532, year = {2008}, author = {Silva, TS and Costa, MP and Melack, JM and Novo, EM}, title = {Remote sensing of aquatic vegetation: theory and applications.}, journal = {Environmental monitoring and assessment}, volume = {140}, number = {1-3}, pages = {131-145}, pmid = {17593532}, issn = {0167-6369}, mesh = {*Geographic Information Systems ; *Plants ; *Water ; }, abstract = {Aquatic vegetation is an important component of wetland and coastal ecosystems, playing a key role in the ecological functions of these environments. Surveys of macrophyte communities are commonly hindered by logistic problems, and remote sensing represents a powerful alternative, allowing comprehensive assessment and monitoring. Also, many vegetation characteristics can be estimated from reflectance measurements, such as species composition, vegetation structure, biomass, and plant physiological parameters. However, proper use of these methods requires an understanding of the physical processes behind the interaction between electromagnetic radiation and vegetation, and remote sensing of aquatic plants have some particular difficulties that have to be properly addressed in order to obtain successful results. The present paper reviews the theoretical background and possible applications of remote sensing techniques to the study of aquatic vegetation.}, } @article {pmid17591309, year = {2007}, author = {Cech, I and Burau, KD and Walston, J}, title = {Spatial distribution of orofacial cleft defect births in Harris County, Texas, 1990 to 1994, and historical evidence for the presence of low-level radioactivity in tap water.}, journal = {Southern medical journal}, volume = {100}, number = {6}, pages = {560-569}, doi = {10.1097/SMJ.0b013e31802f7d38}, pmid = {17591309}, issn = {0038-4348}, mesh = {Cleft Lip/epidemiology/*etiology ; Cleft Palate/epidemiology/*etiology ; Geographic Information Systems ; Humans ; Incidence ; Infant, Newborn ; Multivariate Analysis ; Radium/*adverse effects ; Radon/*adverse effects ; Space-Time Clustering ; Texas/epidemiology ; Water Pollutants, Radioactive/*adverse effects ; Water Supply/*analysis ; }, abstract = {BACKGROUND: While both ionizing and nonionizing radiation are known to impair human reproductive capacity, the role of low-level domestic radiation continues to be an unsettled issue.

OBJECTIVES: We examined the geostatistical distribution (residential longitude and latitude) of orofacial cleft birth cases adjusted for the underlying population distribution. Furthermore, we examined the cleft birth rates enumerated by zip codes for possible associations with levels of radium and radon in drinking water.

METHODS: Cleft births and unaffected live births in Harris County, Texas, from 1990 to 1994, were geocoded by residential addresses and tested for spatial clusters using the space-time clustering program SaTScan. Historical sample data on local variations in water quality facilitated the assessment of the association of orofacial cleft defect births with low-level radiation exposure.

RESULTS: A cluster of significantly greater than expected numbers of cleft defect births was identified in northwest Harris County, (relative risk = 3.0, P = 0.043), where the presence of elevated levels of radium (> 3 pCi/L) and radon (> 300 pCi/L) in the tap water has been known since the 1980s.

CONCLUSIONS: Despite the ecological design of the study, lacking individual exposure measurements for cleft birth residences, there was strong suggestive evidence of an association between elevated radiation levels in tap water and elevated cleft birth prevalence rates by zip codes. Attention of physicians is invited to environmental causes as potential risk factors for orofacial cleft. This would aid in genetic counseling and the development of future preventive measures.}, } @article {pmid17586664, year = {2007}, author = {Wang, Q and Garrity, GM and Tiedje, JM and Cole, JR}, title = {Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy.}, journal = {Applied and environmental microbiology}, volume = {73}, number = {16}, pages = {5261-5267}, pmid = {17586664}, issn = {0099-2240}, mesh = {Algorithms ; Bacteria/*classification/*genetics ; *Bayes Theorem ; Classification/methods ; Databases, Nucleic Acid ; Phylogeny ; RNA, Ribosomal/*genetics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The Ribosomal Database Project (RDP) Classifier, a naïve Bayesian classifier, can rapidly and accurately classify bacterial 16S rRNA sequences into the new higher-order taxonomy proposed in Bergey's Taxonomic Outline of the Prokaryotes (2nd ed., release 5.0, Springer-Verlag, New York, NY, 2004). It provides taxonomic assignments from domain to genus, with confidence estimates for each assignment. The majority of classifications (98%) were of high estimated confidence (> or = 95%) and high accuracy (98%). In addition to being tested with the corpus of 5,014 type strain sequences from Bergey's outline, the RDP Classifier was tested with a corpus of 23,095 rRNA sequences as assigned by the NCBI into their alternative higher-order taxonomy. The results from leave-one-out testing on both corpora show that the overall accuracies at all levels of confidence for near-full-length and 400-base segments were 89% or above down to the genus level, and the majority of the classification errors appear to be due to anomalies in the current taxonomies. For shorter rRNA segments, such as those that might be generated by pyrosequencing, the error rate varied greatly over the length of the 16S rRNA gene, with segments around the V2 and V4 variable regions giving the lowest error rates. The RDP Classifier is suitable both for the analysis of single rRNA sequences and for the analysis of libraries of thousands of sequences. Another related tool, RDP Library Compare, was developed to facilitate microbial-community comparison based on 16S rRNA gene sequence libraries. It combines the RDP Classifier with a statistical test to flag taxa differentially represented between samples. The RDP Classifier and RDP Library Compare are available online at http://rdp.cme.msu.edu/.}, } @article {pmid17583664, year = {2007}, author = {Guis, H and Tran, A and de La Rocque, S and Baldet, T and Gerbier, G and Barragué, B and Biteau-Coroller, F and Roger, F and Viel, JF and Mauny, F}, title = {Use of high spatial resolution satellite imagery to characterize landscapes at risk for bluetongue.}, journal = {Veterinary research}, volume = {38}, number = {5}, pages = {669-683}, doi = {10.1051/vetres:2007025}, pmid = {17583664}, issn = {0928-4249}, mesh = {Animals ; Bluetongue/*epidemiology/transmission ; Ceratopogonidae/growth & development/*virology ; Disease Outbreaks ; Female ; France/epidemiology ; *Geographic Information Systems ; Insect Vectors/growth & development/*virology ; Logistic Models ; Male ; ROC Curve ; Risk Factors ; Satellite Communications ; Sentinel Surveillance/*veterinary ; Sheep ; }, abstract = {The recent and rapid spread in the Mediterranean Basin of bluetongue, a viral disease of ruminants transmitted by some species of Culicoides (biting midges), highlights the necessity of determining the conditions of its emergence. This study uses high spatial resolution satellite imagery and methods from landscape ecology science to identify environmental parameters related to bluetongue occurrence in Corsica, a French Mediterranean island where the disease occurred for the first time in 2000. A set of environmental variables recorded in the neighborhood of 80 sheep farms were related to case occurrence through a logistic regression model computed within three subsequent buffer distances of 0.5, 1 and 2 km. The results reveal the role of landscape metrics, particularly those characterizing land-use units such as prairies and woodlands, as well as farm type, latitude and sunshine to explain the presence of bluetongue. Internal and external validation both indicate that the best results are obtained with the 1 km buffer size model (area under Receiver Operating Characteristic curve = 0.9 for internal validation and 0.81 for external validation). The results show that high spatial resolution remote sensing (i.e. 10 m pixels) and landscape ecology approaches contribute to improving the understanding of bluetongue epidemiology.}, } @article {pmid17577087, year = {2007}, author = {Constantino, RE}, title = {A transdisciplinary team acting on evidence through analyses of moot malpractice cases.}, journal = {Dimensions of critical care nursing : DCCN}, volume = {26}, number = {4}, pages = {150-155}, doi = {10.1097/01.DCC.0000278766.39348.04}, pmid = {17577087}, issn = {0730-4625}, mesh = {Causality ; Data Collection ; *Data Interpretation, Statistical ; Evidence-Based Medicine/*organization & administration ; Humans ; *Malpractice/statistics & numerical data ; Organizational Culture ; Patient Care Team/*organization & administration ; Primary Prevention ; Quality of Health Care/*organization & administration ; Risk Assessment ; Safety Management/*organization & administration ; Systems Analysis ; }, abstract = {A transdiciplinary team is crucial for healthcare systems to act based on evidence in responding to the global demand of the business of caring and patient safety. The purpose of this paper is to outline a transdisciplinary team led by nurses that examines linkages between moot malpractice cases filed against a healthcare system and to the quality of the healthcare system's ecology, caregiver, and patient safety outcomes.}, } @article {pmid17575322, year = {2008}, author = {Salway, R and Wakefield, J}, title = {A hybrid model for reducing ecological bias.}, journal = {Biostatistics (Oxford, England)}, volume = {9}, number = {1}, pages = {1-17}, doi = {10.1093/biostatistics/kxm022}, pmid = {17575322}, issn = {1465-4644}, mesh = {Bayes Theorem ; *Bias ; Computer Simulation ; *Data Interpretation, Statistical ; Environmental Exposure/adverse effects ; Humans ; Lung Neoplasms/epidemiology/etiology ; Minnesota/epidemiology ; *Models, Biological ; *Models, Statistical ; Neoplasms, Radiation-Induced/epidemiology/etiology ; Radon/poisoning ; }, abstract = {A major drawback of epidemiological ecological studies, in which the association between area-level summaries of risk and exposure is used to make inference about individual risk, is the difficulty in characterizing within-area variability in exposure and confounder variables. To avoid ecological bias, samples of individual exposure/confounder data within each area are required. Unfortunately, these may be difficult or expensive to obtain, particularly if large samples are required. In this paper, we propose a new approach suitable for use with small samples. We combine a Bayesian nonparametric Dirichlet process prior with an estimating functions' approach and show that this model gives a compromise between 2 previously described methods. The method is investigated using simulated data, and a practical illustration is provided through an analysis of lung cancer mortality and residential radon exposure in counties of Minnesota. We conclude that we require good quality prior information about the exposure/confounder distributions and a large between- to within-area variability ratio for an ecological study to be feasible using only small samples of individual data.}, } @article {pmid17575003, year = {2007}, author = {Trosvik, P and Skånseng, B and Jakobsen, KS and Stenseth, NC and Naes, T and Rudi, K}, title = {Multivariate analysis of complex DNA sequence electropherograms for high-throughput quantitative analysis of mixed microbial populations.}, journal = {Applied and environmental microbiology}, volume = {73}, number = {15}, pages = {4975-4983}, pmid = {17575003}, issn = {0099-2240}, mesh = {Animals ; Bacteria/*growth & development ; Campylobacter jejuni/classification/genetics ; Cecum/microbiology ; Chickens/microbiology ; Citrate (si)-Synthase/genetics ; Computational Biology ; DNA, Bacterial/analysis/*genetics ; *Ecosystem ; Gastrointestinal Tract/*microbiology ; Humans ; *Models, Biological ; *Multivariate Analysis ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {High-throughput quantification of genetically coherent units (GCUs) is essential for deciphering population dynamics and species interactions within a community of microbes. Current techniques for microbial community analyses are, however, not suitable for this kind of high-throughput application. Here, we demonstrate the use of multivariate statistical analysis of complex DNA sequence electropherograms for the effective and accurate estimation of relative genotype abundance in cell samples from mixed microbial populations. The procedure is no more labor-intensive than standard automated DNA sequencing and provides a very effective means of quantitative data acquisition from experimental microbial communities. We present results with the Campylobacter jejuni strain-specific marker gene gltA, as well as the 16S rRNA gene, which is a universal marker across bacterial assemblages. The statistical models computed for these genes are applied to genetic data from two different experimental settings, namely, a chicken infection model and a multispecies anaerobic fermentation model, demonstrating collection of time series data from model bacterial communities. The method presented here is, however, applicable to any experimental scenario where the interest is quantification of GCUs in genetically heterogeneous DNA samples.}, } @article {pmid17567439, year = {2007}, author = {Kozlov, MV}, title = {Improper sampling design and pseudoreplicated analysis: conclusions by Velicković (2004) questioned.}, journal = {Hereditas}, volume = {144}, number = {1}, pages = {43-44}, doi = {10.1111/j.2007.0018-0661.01992.x}, pmid = {17567439}, issn = {1601-5223}, mesh = {Animals ; Data Interpretation, Statistical ; Environmental Monitoring/methods ; Environmental Pollution ; Genetic Variation ; *Genetics ; Mice/*genetics ; *Sampling Studies ; Selection Bias ; }, } @article {pmid17565672, year = {2007}, author = {Kiraga, J and Mackiewicz, P and Mackiewicz, D and Kowalczuk, M and Biecek, P and Polak, N and Smolarczyk, K and Dudek, MR and Cebrat, S}, title = {The relationships between the isoelectric point and: length of proteins, taxonomy and ecology of organisms.}, journal = {BMC genomics}, volume = {8}, number = {}, pages = {163}, pmid = {17565672}, issn = {1471-2164}, mesh = {Base Composition/genetics ; Computational Biology ; *Ecosystem ; Isoelectric Point ; Mutation/genetics ; *Phylogeny ; Proteins/*chemistry ; Proteomics/*methods ; Species Specificity ; }, abstract = {BACKGROUND: The distribution of isoelectric point (pI) of proteins in a proteome is universal for all organisms. It is bimodal dividing the proteome into two sets of acidic and basic proteins. Different species however have different abundance of acidic and basic proteins that may be correlated with taxonomy, subcellular localization, ecological niche of organisms and proteome size.

RESULTS: We have analysed 1784 proteomes encoded by chromosomes of Archaea, Bacteria, Eukaryota, and also mitochondria, plastids, prokaryotic plasmids, phages and viruses. We have found significant correlation in more than 95% of proteomes between the protein length and pI in proteomes--positive for acidic proteins and negative for the basic ones. Plastids, viruses and plasmids encode more basic proteomes while chromosomes of Archaea, Bacteria, Eukaryota, mitochondria and phages more acidic ones. Mitochondrial proteomes of Viridiplantae, Protista and Fungi are more basic than Metazoa. It results from the presence of basic proteins in the former proteomes and their absence from the latter ones and is related with reduction of metazoan genomes. Significant correlation was found between the pI bias of proteomes encoded by prokaryotic chromosomes and proteomes encoded by plasmids but there is no correlation between eukaryotic nuclear-coded proteomes and proteomes encoded by organelles. Detailed analyses of prokaryotic proteomes showed significant relationships between pI distribution and habitat, relation to the host cell and salinity of the environment, but no significant correlation with oxygen and temperature requirements. The salinity is positively correlated with acidicity of proteomes. Host-associated organisms and especially intracellular species have more basic proteomes than free-living ones. The higher rate of mutations accumulation in the intracellular parasites and endosymbionts is responsible for the basicity of their tiny proteomes that explains the observed positive correlation between the decrease of genome size and the increase of basicity of proteomes. The results indicate that even conserved proteins subjected to strong selectional constraints follow the global trend in the pI distribution.

CONCLUSION: The distribution of pI of proteins in proteomes shows clear relationships with length of proteins, subcellular localization, taxonomy and ecology of organisms. The distribution is also strongly affected by mutational pressure especially in intracellular organisms.}, } @article {pmid17562105, year = {2007}, author = {Lookingbill, TR and Gardner, RH and Townsend, PA and Carter, SL}, title = {Conceptual models as hypotheses in monitoring urban landscapes.}, journal = {Environmental management}, volume = {40}, number = {2}, pages = {171-182}, pmid = {17562105}, issn = {0364-152X}, mesh = {Animals ; *Conservation of Natural Resources ; District of Columbia ; Ecology ; *Ecosystem ; Environmental Monitoring/methods/*standards ; Geography ; Humans ; Information Systems ; Models, Theoretical ; }, abstract = {Many problems and challenges of ecosystem management currently are driven by the rapid pace and spatial extent of landscape change. Parks and reserves within areas of high human population density are especially challenged to meet the recreational needs of local populations and to preserve valued environmental resources. The complex problem of managing multiple objectives and multiple resources requires an enormous quantity of information, and conceptual models have been proposed as tools for organizing and interpreting this information. Academics generally prefer a bottom-up approach to model construction that emphasizes ecologic theory and process, whereas managers often use a top-down approach that takes advantage of existing information to address more pragmatic objectives. The authors propose a formal process for developing, applying, and testing conceptual models to be used in landscape monitoring that reconciles these seemingly opposing perspectives. The four-step process embraces the role of hypothesis testing in the development of models and evaluation of their utility. An example application of the process to a network of national parks in and around Washington, DC illustrates the ability of the approach to systematically identify monitoring data that would both advance ecologic theory and inform management decisions.}, } @article {pmid17559679, year = {2007}, author = {Quilang, J and Wang, S and Li, P and Abernathy, J and Peatman, E and Wang, Y and Wang, L and Shi, Y and Wallace, R and Guo, X and Liu, Z}, title = {Generation and analysis of ESTs from the eastern oyster, Crassostrea virginica Gmelin and identification of microsatellite and SNP markers.}, journal = {BMC genomics}, volume = {8}, number = {}, pages = {157}, pmid = {17559679}, issn = {1471-2164}, mesh = {Animals ; Computational Biology ; Contig Mapping ; DNA, Complementary/metabolism ; *Expressed Sequence Tags ; *Gene Expression Profiling ; Gene Library ; Genomics/methods ; *Microsatellite Repeats ; Models, Genetic ; Molecular Sequence Data ; Ostreidae ; *Polymorphism, Single Nucleotide ; Tissue Distribution ; }, abstract = {BACKGROUND: The eastern oyster, Crassostrea virginica (Gmelin 1791), is an economically important species cultured in many areas in North America. It is also ecologically important because of the impact of its filter feeding behaviour on water quality. Populations of C. virginica have been threatened by overfishing, habitat degradation, and diseases. Through genome research, strategies are being developed to reverse its population decline. However, large-scale expressed sequence tag (EST) resources have been lacking for this species. Efficient generation of EST resources from this species has been hindered by a high redundancy of transcripts. The objectives of this study were to construct a normalized cDNA library for efficient EST analysis, to generate thousands of ESTs, and to analyze the ESTs for microsatellites and potential single nucleotide polymorphisms (SNPs).

RESULTS: A normalized and subtracted C. virginica cDNA library was constructed from pooled RNA isolated from hemocytes, mantle, gill, gonad and digestive tract, muscle, and a whole juvenile oyster. A total of 6,528 clones were sequenced from this library generating 5,542 high-quality EST sequences. Cluster analysis indicated the presence of 635 contigs and 4,053 singletons, generating a total of 4,688 unique sequences. About 46% (2,174) of the unique ESTs had significant hits (E-value
CONCLUSION: A high quality normalized cDNA library was constructed. A total of 5,542 ESTs were generated representing 4,688 unique sequences. Putative microsatellite and SNP markers were identified. These genome resources provide the material basis for future microarray development, marker validation, and genetic linkage and QTL analysis.}, } @article {pmid17559671, year = {2007}, author = {Su, Z and Olman, V and Xu, Y}, title = {Computational prediction of Pho regulons in cyanobacteria.}, journal = {BMC genomics}, volume = {8}, number = {}, pages = {156}, pmid = {17559671}, issn = {1471-2164}, mesh = {Binding Sites/genetics ; Computational Biology/methods ; Conserved Sequence/genetics ; Cyanobacteria/*genetics/metabolism ; Genes, Bacterial/*genetics ; *Genetic Variation ; Phosphoric Monoester Hydrolases/genetics ; Phosphorus/*metabolism ; Phosphotransferases/genetics ; *Phylogeny ; Regulon/*genetics ; }, abstract = {BACKGROUND: Phosphorus is an essential element for all life forms. However, it is limiting in most ecological environments where cyanobacteria inhabit. Elucidation of the phosphorus assimilation pathways in cyanobacteria will further our understanding of the physiology and ecology of this important group of microorganisms. However, a systematic study of the Pho regulon, the core of the phosphorus assimilation pathway in a cyanobacterium, is hitherto lacking.

RESULTS: We have predicted and analyzed the Pho regulons in 19 sequenced cyanobacterial genomes using a highly effective scanning algorithm that we have previously developed. Our results show that different cyanobacterial species/ecotypes may encode diverse sets of genes responsible for the utilization of various sources of phosphorus, ranging from inorganic phosphate, phosphodiester, to phosphonates. Unlike in E. coli, some cyanobacterial genes that are directly involved in phosphorus assimilation seem to not be under the regulation of the regulator SphR (orthologue of PhoB in E coli.) in some species/ecotypes. On the other hand, SphR binding sites are found for genes known to play important roles in other biological processes. These genes might serve as bridging points to coordinate the phosphorus assimilation and other biological processes. More interestingly, in three cyanobacterial genomes where no sphR gene is encoded, our results show that there is virtually no functional SphR binding site, suggesting that transcription regulators probably play an important role in retaining their binding sites.

CONCLUSION: The Pho regulons in cyanobacteria are highly diversified to accommodate to their respective living environments. The phosphorus assimilation pathways in cyanobacteria are probably tightly coupled to a number of other important biological processes. The loss of a regulator may lead to the rapid loss of its binding sites in a genome.}, } @article {pmid17556584, year = {2007}, author = {Marvier, M and McCreedy, C and Regetz, J and Kareiva, P}, title = {A meta-analysis of effects of Bt cotton and maize on nontarget invertebrates.}, journal = {Science (New York, N.Y.)}, volume = {316}, number = {5830}, pages = {1475-1477}, doi = {10.1126/science.1139208}, pmid = {17556584}, issn = {1095-9203}, mesh = {Animals ; *Arthropods ; Bacillus thuringiensis/genetics ; Bacillus thuringiensis Toxins ; Bacterial Proteins/*genetics ; Bacterial Toxins/*genetics ; Crops, Agricultural/*genetics/growth & development ; Databases, Factual ; Endotoxins/*genetics ; Gossypium/*genetics/growth & development ; Hemolysin Proteins/*genetics ; Insecta ; Insecticides ; Pest Control, Biological ; *Plants, Genetically Modified/growth & development ; Population Dynamics ; Zea mays/*genetics ; }, abstract = {Although scores of experiments have examined the ecological consequences of transgenic Bacillus thuringiensis (Bt) crops, debates continue regarding the nontarget impacts of this technology. Quantitative reviews of existing studies are crucial for better gauging risks and improving future risk assessments. To encourage evidence-based risk analyses, we constructed a searchable database for nontarget effects of Bt crops. A meta-analysis of 42 field experiments indicates that nontarget invertebrates are generally more abundant in Bt cotton and Bt maize fields than in nontransgenic fields managed with insecticides. However, in comparison with insecticide-free control fields, certain nontarget taxa are less abundant in Bt fields.}, } @article {pmid17552195, year = {2007}, author = {Liu, M and Hu, YM and Chang, Y and Bu, RC and Zhang, W}, title = {[Landscape change and its spatial driving force of farmlands in Wenchuan County of Min-jiang River upper reach].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {18}, number = {3}, pages = {569-574}, pmid = {17552195}, issn = {1001-9332}, mesh = {China ; *Conservation of Natural Resources ; Crops, Agricultural/*growth & development ; *Ecosystem ; Environment ; Geographic Information Systems ; Logistic Models ; Poaceae/*growth & development ; Rivers ; Satellite Communications ; Soil/analysis ; Trees/*growth & development ; }, abstract = {Based on remote sensing images and geographic information system, and by using landscape metrics and Kappa coefficient, this paper studied the farmland landscape change in Wenchuan County of Minjiang River upper reach. A logistic regression model was used to analyze the driving forces of this change, with elevation, gradient, aspect, and the distances to road, river and settlement as the affecting factors. The results showed that from 1974 to 2000, the farmland area in Wenchuan County kept increasing, with the greatest increment in 1974-1986. In 1986-2000, farmland area had no evident increase, but converted with other landscape types frequently and had an evident spatial position change, especially in the period from 1994 to 2000. Such a farmland change was mainly driven by policy, and the spatial driving forces differed in different periods.}, } @article {pmid17550620, year = {2007}, author = {Jacob, BG and Muturi, EJ and Mwangangi, JM and Funes, J and Caamano, EX and Muriu, S and Shililu, J and Githure, J and Novak, RJ}, title = {Remote and field level quantification of vegetation covariates for malaria mapping in three rice agro-village complexes in Central Kenya.}, journal = {International journal of health geographics}, volume = {6}, number = {}, pages = {21}, pmid = {17550620}, issn = {1476-072X}, support = {U01A154889//PHS HHS/United States ; }, mesh = {Algorithms ; Animals ; Anopheles/*growth & development ; Crops, Agricultural ; Ecosystem ; Humans ; *Image Interpretation, Computer-Assisted ; Kenya/epidemiology ; Larva ; Logistic Models ; Malaria/epidemiology/*prevention & control ; Models, Biological ; *Mosquito Control ; *Oryza ; Reproducibility of Results ; Satellite Communications ; Sensitivity and Specificity ; Small-Area Analysis ; Topography, Medical/instrumentation/*statistics & numerical data ; Uncertainty ; }, abstract = {BACKGROUND: We examined algorithms for malaria mapping using the impact of reflectance calibration uncertainties on the accuracies of three vegetation indices (VI)'s derived from QuickBird data in three rice agro-village complexes Mwea, Kenya. We also generated inferential statistics from field sampled vegetation covariates for identifying riceland Anopheles arabiensis during the crop season. All aquatic habitats in the study sites were stratified based on levels of rice stages; flooded, land preparation, post-transplanting, tillering, flowering/maturation and post-harvest/fallow. A set of uncertainty propagation equations were designed to model the propagation of calibration uncertainties using the red channel (band 3: 0.63 to 0.69 microm) and the near infra-red (NIR) channel (band 4: 0.76 to 0.90 microm) to generate the Normalized Difference Vegetation Index (NDVI) and the Soil Adjusted Vegetation Index (SAVI). The Atmospheric Resistant Vegetation Index (ARVI) was also evaluated incorporating the QuickBird blue band (Band 1: 0.45 to 0.52 microm) to normalize atmospheric effects. In order to determine local clustering of riceland habitats Gi*(d) statistics were generated from the ground-based and remotely-sensed ecological databases. Additionally, all riceland habitats were visually examined using the spectral reflectance of vegetation land cover for identification of highly productive riceland Anopheles oviposition sites.

RESULTS: The resultant VI uncertainties did not vary from surface reflectance or atmospheric conditions. Logistic regression analyses of all field sampled covariates revealed emergent vegetation was negatively associated with mosquito larvae at the three study sites. In addition, floating vegetation (-ve) was significantly associated with immature mosquitoes in Rurumi and Kiuria (-ve); while, turbidity was also important in Kiuria. All spatial models exhibit positive autocorrelation; similar numbers of log-counts tend to cluster in geographic space. The spectral reflectance from riceland habitats, examined using the remote and field stratification, revealed post-transplanting and tillering rice stages were most frequently associated with high larval abundance and distribution.

CONCLUSION: NDVI, SAVI and ARVI generated from QuickBird data and field sampled vegetation covariates modeled cannot identify highly productive riceland An. arabiensis aquatic habitats. However, combining spectral reflectance of riceland habitats from QuickBird and field sampled data can develop and implement an Integrated Vector Management (IVM) program based on larval productivity.}, } @article {pmid17548213, year = {2007}, author = {Chakraborty, D and Ramakrishnan, U and Panor, J and Mishra, C and Sinha, A}, title = {Phylogenetic relationships and morphometric affinities of the Arunachal macaque Macaca munzala, a newly described primate from Arunachal Pradesh, northeastern India.}, journal = {Molecular phylogenetics and evolution}, volume = {44}, number = {2}, pages = {838-849}, doi = {10.1016/j.ympev.2007.04.007}, pmid = {17548213}, issn = {1055-7903}, mesh = {Animals ; Base Sequence ; Cytochromes b/genetics ; DNA, Mitochondrial/genetics ; Databases, Nucleic Acid ; India ; Macaca/*anatomy & histology/classification/*genetics ; Male ; *Phylogeny ; }, abstract = {A new species of primate, the Arunachal macaque Macaca munzala, belonging to the sinica species-group of the genus, was described from northeastern India in 2005, and, based on its appearance and distribution, hypothesised to be closely related to M. assamensis and M. thibetana. We subsequently obtained an entire adult male specimen and tissue remains from two other M. munzala individuals. Molecular analyses establish the distinct identity of the species and indicate a time of origin of c. 0.48 mya for it. The species also shows close phylogenetic affinities with the allopatric M. radiata and with the geographically closer M. assamensis and M. thibetana, possibly mediated by male introgression from an ancestral M. assamensis-M. thibetana stock into an ancestral M. munzala stock. Morphometric analyses, on the other hand, reiterate its close similarity only with M. assamensis and M. thibetana, presumably resulting from convergent evolution under similar ecological conditions and along a latitudinal gradient, as predicted by Bergmann's and Allen's rules.}, } @article {pmid17546523, year = {2007}, author = {Theobald, DM and Stevens, DL and White, D and Urquhart, NS and Olsen, AR and Norman, JB}, title = {Using GIS to generate spatially balanced random survey designs for natural resource applications.}, journal = {Environmental management}, volume = {40}, number = {1}, pages = {134-146}, doi = {10.1007/s00267-005-0199-x}, pmid = {17546523}, issn = {0364-152X}, mesh = {*Algorithms ; Computer Simulation ; *Conservation of Natural Resources ; Geographic Information Systems ; Probability ; *Research Design ; }, abstract = {Sampling of a population is frequently required to understand trends and patterns in natural resource management because financial and time constraints preclude a complete census. A rigorous probability-based survey design specifies where to sample so that inferences from the sample apply to the entire population. Probability survey designs should be used in natural resource and environmental management situations because they provide the mathematical foundation for statistical inference. Development of long-term monitoring designs demand survey designs that achieve statistical rigor and are efficient but remain flexible to inevitable logistical or practical constraints during field data collection. Here we describe an approach to probability-based survey design, called the Reversed Randomized Quadrant-Recursive Raster, based on the concept of spatially balanced sampling and implemented in a geographic information system. This provides environmental managers a practical tool to generate flexible and efficient survey designs for natural resource applications. Factors commonly used to modify sampling intensity, such as categories, gradients, or accessibility, can be readily incorporated into the spatially balanced sample design.}, } @article {pmid17544704, year = {2007}, author = {Lane, CE and Lindstrom, SC and Saunders, GW}, title = {A molecular assessment of northeast Pacific Alaria species (Laminariales, Phaeophyceae) with reference to the utility of DNA barcoding.}, journal = {Molecular phylogenetics and evolution}, volume = {44}, number = {2}, pages = {634-648}, doi = {10.1016/j.ympev.2007.03.016}, pmid = {17544704}, issn = {1055-7903}, mesh = {Base Sequence ; Chloroplasts/genetics ; Cloning, Molecular ; DNA/*classification/*genetics ; Databases, Nucleic Acid ; Genetic Markers ; Mitochondria/genetics ; Pacific Ocean ; Phaeophyceae/*classification/*genetics ; Phylogeny ; Transcription, Genetic/genetics ; }, abstract = {Despite their relatively complex morphologies, species in the genus Alaria Greville are notoriously difficult to identify with certainty. Morphological characters, often influenced by environmental factors, make individuals in similar habitats artificially appear related. Species identification would, therefore, benefit greatly from the application of molecular tools. We applied DNA barcoding, using the 5' end of the cytochrome c oxidase I (coxI-5') gene from the mitochondrial genome, to define species limits and relationships in northeast Pacific populations of Alaria. This emerging technique is being employed to catalogue species diversity worldwide, particularly among animals, and it has been shown to be sensitive enough to discriminate between closely related species. However, the utility of this marker for identifying or categorizing the majority of life remains unclear. We compared the resolution obtained with this marker to two other molecular systems commonly used in algal research: the nuclear internal transcribed spacer (ITS) of the ribosomal cistron, and the plastid Rubisco operon spacer (rbcSp). In agreement with previous results, Alaria fistulosa Postels & Ruprecht, with its distinct morphological, ecological and molecular features, stands apart from the other species in the genus and we establish Druehlia gen. nov. to accommodate it. For the remaining isolates, distinct mitochondrial haplotypes resolved with the barcode data indicate a period of genetic isolation for at least three incipient species in the northeast Pacific, whereas unexpected levels and patterns of ITS variation, as well as the extreme morphological plasticity found among these isolates, have most probably resulted from a recent collapse in species barriers. The cloning of ITS amplicons revealed multiple ITS copies in several individuals, further supporting this hypothesis.}, } @article {pmid17542934, year = {2007}, author = {Lele, SR and Dennis, B and Lutscher, F}, title = {Data cloning: easy maximum likelihood estimation for complex ecological models using Bayesian Markov chain Monte Carlo methods.}, journal = {Ecology letters}, volume = {10}, number = {7}, pages = {551-563}, doi = {10.1111/j.1461-0248.2007.01047.x}, pmid = {17542934}, issn = {1461-0248}, mesh = {Bayes Theorem ; Computational Biology/*methods ; Computer Simulation ; Ecology/*methods ; *Ecosystem ; Likelihood Functions ; Markov Chains ; *Models, Biological ; Monte Carlo Method ; *Population Dynamics ; }, abstract = {We introduce a new statistical computing method, called data cloning, to calculate maximum likelihood estimates and their standard errors for complex ecological models. Although the method uses the Bayesian framework and exploits the computational simplicity of the Markov chain Monte Carlo (MCMC) algorithms, it provides valid frequentist inferences such as the maximum likelihood estimates and their standard errors. The inferences are completely invariant to the choice of the prior distributions and therefore avoid the inherent subjectivity of the Bayesian approach. The data cloning method is easily implemented using standard MCMC software. Data cloning is particularly useful for analysing ecological situations in which hierarchical statistical models, such as state-space models and mixed effects models, are appropriate. We illustrate the method by fitting two nonlinear population dynamics models to data in the presence of process and observation noise.}, } @article {pmid17537923, year = {2007}, author = {Dediu, D and Ladd, DR}, title = {Linguistic tone is related to the population frequency of the adaptive haplogroups of two brain size genes, ASPM and Microcephalin.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {104}, number = {26}, pages = {10944-10949}, pmid = {17537923}, issn = {1091-6490}, mesh = {Cell Cycle Proteins ; Culture ; Cytoskeletal Proteins ; Databases, Factual ; *Gene Frequency ; *Genetics, Population ; *Haplotypes ; Humans ; Language ; *Linguistics ; Nerve Tissue Proteins/*genetics ; }, abstract = {The correlations between interpopulation genetic and linguistic diversities are mostly noncausal (spurious), being due to historical processes and geographical factors that shape them in similar ways. Studies of such correlations usually consider allele frequencies and linguistic groupings (dialects, languages, linguistic families or phyla), sometimes controlling for geographic, topographic, or ecological factors. Here, we consider the relation between allele frequencies and linguistic typological features. Specifically, we focus on the derived haplogroups of the brain growth and development-related genes ASPM and Microcephalin, which show signs of natural selection and a marked geographic structure, and on linguistic tone, the use of voice pitch to convey lexical or grammatical distinctions. We hypothesize that there is a relationship between the population frequency of these two alleles and the presence of linguistic tone and test this hypothesis relative to a large database (983 alleles and 26 linguistic features in 49 populations), showing that it is not due to the usual explanatory factors represented by geography and history. The relationship between genetic and linguistic diversity in this case may be causal: certain alleles can bias language acquisition or processing and thereby influence the trajectory of language change through iterated cultural transmission.}, } @article {pmid17536721, year = {2007}, author = {Fieberg, J}, title = {Kernel density estimators of home range: smoothing and the autocorrelation red herring.}, journal = {Ecology}, volume = {88}, number = {4}, pages = {1059-1066}, doi = {10.1890/06-0930}, pmid = {17536721}, issn = {0012-9658}, mesh = {Animals ; Bias ; Computer Simulation ; *Data Interpretation, Statistical ; *Ecosystem ; Fishes/*physiology ; Homing Behavior/*physiology ; *Models, Statistical ; Movement ; Sensitivity and Specificity ; }, abstract = {Two oft-cited drawbacks of kernel density estimators (KDEs) of home range are their sensitivity to the choice of smoothing parameter(s) and their need for independent data. Several simulation studies have been conducted to compare the performance of objective, data-based methods of choosing optimal smoothing parameters in the context of home range and utilization distribution (UD) estimation. Lost in this discussion of choice of smoothing parameters is the general role of smoothing in data analysis, namely, that smoothing serves to increase precision at the cost of increased bias. A primary goal of this paper is to illustrate this bias-variance trade-off by applying KDEs to sampled locations from simulated movement paths. These simulations will also be used to explore the role of autocorrelation in estimating UDs. Autocorrelation can be reduced (1) by increasing study duration (for a fixed sample size) or (2) by decreasing the sampling rate. While the first option will often be reasonable, for a fixed study duration higher sampling rates should always result in improved estimates of space use. Further, KDEs with typical data-based methods of choosing smoothing parameters should provide competitive estimates of space use for fixed study periods unless autocorrelation substantially alters the optimal level of smoothing.}, } @article {pmid17536320, year = {2007}, author = {Cousteau, JM}, title = {Time 100 scientists & thinkers. Craig Venter.}, journal = {Time}, volume = {169}, number = {20}, pages = {107}, pmid = {17536320}, issn = {0040-781X}, mesh = {Biodiversity ; Databases, Genetic ; *Ecosystem ; Expeditions ; *Genetic Research ; *Genetics, Microbial ; History, 21st Century ; *Marine Biology ; Oceans and Seas ; Ships ; *Water Microbiology ; }, } @article {pmid17526872, year = {2007}, author = {Lu, P and Su, Y and Niu, Z and Wu, J}, title = {Geostatistical analysis and risk assessment on soil total nitrogen and total soil phosphorus in the Dongting Lake plain area, China.}, journal = {Journal of environmental quality}, volume = {36}, number = {4}, pages = {935-942}, doi = {10.2134/jeq2006.0184}, pmid = {17526872}, issn = {0047-2425}, mesh = {Agriculture ; China ; Fertilizers/statistics & numerical data ; *Geographic Information Systems ; Nitrogen/*analysis ; Normal Distribution ; Phosphorus/*analysis ; Risk Assessment ; Soil/*analysis ; Water Pollution/*prevention & control ; }, abstract = {Nonpoint-source pollution and water body eutrophication have become increasing concerns for scientists and policymakers. Nitrogen and phosphorus affect environmental pollution, especially lake eutrophication. To assess the environmental risk of soil total nitrogen (TN) and total phosphorus (TP) pollution, a typical ecological unit of Dongting Lake plain was selected as the experimental site. To verify the stationary of the data, a moving windows technique was adopted. Our results showed that Box-Cox transformation achieved normality in the data set and dampened the effect of outliers. The best theoretical model for semivariogram of TN and TP was a spherical model. The ordinary kriging estimates of TN and TP concentrations were mapped. The integrative comparisons of semivariogram parameters with different trends to the kriging prediction errors of TN and TP indicated that the two-order trend is preferable. Kriging SDs provided valuable information that will increase the accuracy of TN and TP mapping. The probability kriging method is useful to assess the risk of N and P pollution by providing the conditional probability of N and P concentrations exceeding the threshold concentrations of 3.2 and 1.05 g/kg, respectively. The probability distribution of TN and TP at different levels will be helpful to conduct risk assessment, optimize fertilization, and control the pollution of N and P.}, } @article {pmid17524145, year = {2007}, author = {Swaminathan, K and Varala, K and Hudson, ME}, title = {Global repeat discovery and estimation of genomic copy number in a large, complex genome using a high-throughput 454 sequence survey.}, journal = {BMC genomics}, volume = {8}, number = {}, pages = {132}, pmid = {17524145}, issn = {1471-2164}, mesh = {Databases, Nucleic Acid ; Gene Dosage ; *Genome, Plant ; Genomics/*methods ; Methods ; Repetitive Sequences, Nucleic Acid ; Sequence Analysis, DNA ; Glycine max/*genetics ; }, abstract = {BACKGROUND: Extensive computational and database tools are available to mine genomic and genetic databases for model organisms, but little genomic data is available for many species of ecological or agricultural significance, especially those with large genomes. Genome surveys using conventional sequencing techniques are powerful, particularly for detecting sequences present in many copies per genome. However these methods are time-consuming and have potential drawbacks. High throughput 454 sequencing provides an alternative method by which much information can be gained quickly and cheaply from high-coverage surveys of genomic DNA.

RESULTS: We sequenced 78 million base-pairs of randomly sheared soybean DNA which passed our quality criteria. Computational analysis of the survey sequences provided global information on the abundant repetitive sequences in soybean. The sequence was used to determine the copy number across regions of large genomic clones or contigs and discover higher-order structures within satellite repeats. We have created an annotated, online database of sequences present in multiple copies in the soybean genome. The low bias of pyrosequencing against repeat sequences is demonstrated by the overall composition of the survey data, which matches well with past estimates of repetitive DNA content obtained by DNA re-association kinetics (Cot analysis).

CONCLUSION: This approach provides a potential aid to conventional or shotgun genome assembly, by allowing rapid assessment of copy number in any clone or clone-end sequence. In addition, we show that partial sequencing can provide access to partial protein-coding sequences.}, } @article {pmid17520926, year = {2007}, author = {Savchuk, OP and Wulff, F}, title = {Modeling the Baltic Sea eutrophication in a decision support system.}, journal = {Ambio}, volume = {36}, number = {2-3}, pages = {141-148}, doi = {10.1579/0044-7447(2007)36[141:mtbsei]2.0.co;2}, pmid = {17520926}, issn = {0044-7447}, mesh = {Animals ; Aquaculture/*methods/statistics & numerical data ; Baltic States ; *Decision Support Techniques ; Ecosystem ; Environmental Monitoring/*methods/statistics & numerical data ; Eutrophication ; Geography ; Marine Biology ; *Models, Biological ; Nitrogen/metabolism ; Oceans and Seas ; Oxygen/metabolism ; Phosphorus/metabolism ; Research ; Time Factors ; Water Movements ; Water Pollutants/metabolism/*toxicity ; }, abstract = {SANBALTS (Simple As Necessary Baltic Long-Term Large-Scale) is a model of the coupled nitrogen and phosphorus cycles. This model has been developed as an integral part of the decision support system Marine Research on Eutrophication's Nest with the overall aim to evaluate management options for reducing Baltic Sea eutrophication. Simulated nutrient and oxygen concentrations as well as transport flows and major biogeochemical fluxes can be analyzed in many different ways, including construction of detailed nutrient budgets and tracing the fate of nutrient inputs. The large amounts of data that exist for this sea makes it possible to validate model results with observations. Major biogeochemical properties of the Baltic Sea are discussed through an analyses of model sensitivity to external forcing and internal parameterizations. Model results emphasize two features that are especially important for ecosystem management: i) impacts of local measures would always be modified by the long-range transports from other regions and ii) the response to significant changes in loads would only be seen after several decades.}, } @article {pmid17520073, year = {2007}, author = {DeFur, PL and Evans, GW and Cohen Hubal, EA and Kyle, AD and Morello-Frosch, RA and Williams, DR}, title = {Vulnerability as a function of individual and group resources in cumulative risk assessment.}, journal = {Environmental health perspectives}, volume = {115}, number = {5}, pages = {817-824}, pmid = {17520073}, issn = {0091-6765}, mesh = {Age Factors ; Data Interpretation, Statistical ; *Ecosystem ; *Environmental Exposure ; Environmental Pollutants/*toxicity ; Humans ; *Models, Theoretical ; *Public Health ; Risk Assessment/*methods ; Socioeconomic Factors ; *Vulnerable Populations ; }, abstract = {BACKGROUND: The field of risk assessment has focused on protecting the health of individual people or populations of wildlife from single risks, mostly from chemical exposure. The U.S. Environmental Protection Agency recently began to address multiple risks to communities in the "Framework for Cumulative Risk Assessment" [EPA/630/P02/001F. Washington DC:Risk Assessment Forum, U.S. Environmental Protection Agency (2003)]. Simultaneously, several reports concluded that some individuals and groups are more vulnerable to environmental risks than the general population. However, vulnerability has received little specific attention in the risk assessment literature.

OBJECTIVE: Our objective is to examine the issue of vulnerability in cumulative risk assessment and present a conceptual framework rather than a comprehensive review of the literature. In this article we consider similarities between ecologic and human communities and the factors that make communities vulnerable to environmental risks.

DISCUSSION: The literature provides substantial evidence on single environmental factors and simple conditions that increase vulnerability or reduce resilience for humans and ecologic systems. This observation is especially true for individual people and populations of wildlife. Little research directly addresses the topic of vulnerability in cumulative risk situations, especially at the community level. The community level of organization has not been adequately considered as an end point in either human or ecologic risk assessment. Furthermore, current information on human risk does not completely explain the level of response in cumulative risk conditions. Ecologic risk situations are similarly more complex and unpredictable for cases of cumulative risk.

CONCLUSIONS: Psychosocial conditions and responses are the principal missing element for humans. We propose a model for including psychologic and social factors as an integral component of cumulative risk assessment.}, } @article {pmid17520072, year = {2007}, author = {Menzie, CA and MacDonell, MM and Mumtaz, M}, title = {A phased approach for assessing combined effects from multiple stressors.}, journal = {Environmental health perspectives}, volume = {115}, number = {5}, pages = {807-816}, pmid = {17520072}, issn = {0091-6765}, mesh = {Data Interpretation, Statistical ; *Ecosystem ; *Environmental Exposure ; Environmental Pollutants/*toxicity ; *Models, Theoretical ; *Public Health ; Risk Assessment/*methods ; }, abstract = {We present a phased approach for evaluating the effects of physical, biological, chemical, and psychosocial stressors that may act in combination. Although a phased concept is common to many risk-based approaches, it has not been explicitly outlined for the assessment of combined effects of multiple stressors. The approach begins with the development of appropriate conceptual models and assessment end points. The approach then proceeds through a screening stage wherein stressors are evaluated with respect to their potential importance as contributors to risk. Stressors are considered individually or as a combination of independent factors with respect to one or more common assessment end points. As necessary, the approach then proceeds to consider interactions among stressors. We make a distinction between applications that begin with effects of concern (effects based) or with specific stressors (stressor based). We describe a number of tools for use within the phased approach. The methods profiled are ones that have been applied to yield results that can be communicated to a wide audience. The latter characteristic is considered especially important because multiple stressor problems usually involve exposures to communities or to ecologic regions with many stakeholders.}, } @article {pmid17517633, year = {2007}, author = {Caputi, L and Andreakis, N and Mastrototaro, F and Cirino, P and Vassillo, M and Sordino, P}, title = {Cryptic speciation in a model invertebrate chordate.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {104}, number = {22}, pages = {9364-9369}, pmid = {17517633}, issn = {0027-8424}, support = {R24 GM075049/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Ciona intestinalis/*classification/*genetics ; Female ; Male ; *Models, Biological ; Molecular Sequence Data ; *Phylogeny ; Species Specificity ; }, abstract = {We applied independent species concepts to clarify the phylogeographic structure of the ascidian Ciona intestinalis, a powerful model system in chordate biology and for comparative genomic studies. Intensive research with this marine invertebrate is based on the assumption that natural populations globally belong to a single species. Therefore, understanding the true taxonomic classification may have implications for experimental design and data management. Phylogenies inferred from mitochondrial and nuclear DNA markers accredit the existence of two cryptic species: C. intestinalis sp. A, genetically homogeneous, distributed in the Mediterranean, northeast Atlantic, and Pacific, and C. intestinalis sp. B, geographically structured and encountered in the North Atlantic. Species-level divergence is further entailed by cross-breeding estimates. C. intestinalis A and B from allopatric populations cross-fertilize, but hybrids remain infertile because of defective gametogenesis. Although anatomy illustrates an overall interspecific similarity lacking in diagnostic features, we provide consistent tools for in-field and in-laboratory species discrimination. Finding of two cryptic taxa in C. intestinalis raises interest in a new tunicate genome as a gateway to studies in speciation and ecological adaptation of chordates.}, } @article {pmid17510172, year = {2007}, author = {Toleno, DM and Morrell, PL and Clegg, MT}, title = {Error detection in SNP data by considering the likelihood of recombinational history implied by three-site combinations.}, journal = {Bioinformatics (Oxford, England)}, volume = {23}, number = {14}, pages = {1807-1814}, doi = {10.1093/bioinformatics/btm260}, pmid = {17510172}, issn = {1367-4811}, mesh = {Algorithms ; Cloning, Molecular ; Computational Biology/*methods ; Computer Simulation ; Genotype ; Haplotypes ; Heterozygote ; Humans ; Likelihood Functions ; Models, Biological ; Models, Genetic ; Pedigree ; Polymorphism, Genetic ; *Polymorphism, Single Nucleotide ; Software ; }, abstract = {MOTIVATION: Errors in nucleotide sequence and SNP genotyping data are problematic when inferring haplotypes. Previously published methods for error detection in haplotype data make use of pedigree information; however, for many samples, individuals are not related by pedigree. This article describes a method for detecting errors in haplotypes by considering the recombinational history implied by the patterns of variation, three SNPs at a time.

RESULTS: Coalescent simulations provide evidence that the method is robust to high levels of recombination as well as homologous gene conversion, indicating that patterns produced by both proximate and distant SNPs may be useful for detecting unlikely three-site haplotypes.

AVAILABILITY: The perl script implementing the described method is called EDUT (Error Detection Using Triplets) and is available on request from the authors.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, } @article {pmid17503603, year = {2007}, author = {Kulakowski, D and Veblen, TT}, title = {Effect of prior disturbances on the extent and severity of wildfire in Colorado subalpine forests.}, journal = {Ecology}, volume = {88}, number = {3}, pages = {759-769}, doi = {10.1890/06-0124}, pmid = {17503603}, issn = {0012-9658}, mesh = {Colorado ; *Ecosystem ; *Fires ; Geographic Information Systems ; *Models, Theoretical ; *Trees ; }, abstract = {Disturbances are important in creating spatial heterogeneity of vegetation patterns that in turn may affect the spread and severity of subsequent disturbances. Between 1997 and 2002 extensive areas of subalpine forests in northwestern Colorado were affected by a blowdown of trees, bark beetle outbreaks, and salvage logging. Some of these stands were also affected by severe fires in the late 19th century. During a severe drought in 2002, fires affected extensive areas of these subalpine forests. We evaluated and modeled the extent and severity of the 2002 fires in relation to these disturbances that occurred over the five years prior to the fires and in relation to late 19th century stand-replacing fires. Occurrence of disturbances prior to 2002 was reconstructed using a combination of tree-ring methods, aerial photograph interpretation, field surveys, and geographic information systems (GIS). The extent and severity of the 2002 fires were based on the normalized difference burn ratio (NDBR) derived from satellite imagery. GIS and classification trees were used to analyze the effects of prefire conditions on the 2002 fires. Previous disturbance history had a significant influence on the severity of the 2002 fires. Stands that were severely blown down (> 66% trees down) in 1997 burned more severely than other stands, and young (approximately 120 year old) postfire stands burned less severely than older stands. In contrast, prefire disturbances were poor predictors of fire extent, except that young (approximately 120 years old) postfire stands were less extensively burned than older stands. Salvage logging and bark beetle outbreaks that followed the 1997 blowdown (within the blowdown as well as in adjacent forest that was not blown down) did not appear to affect fire extent or severity. Conclusions regarding the influence of the beetle outbreaks on fire extent and severity are limited, however, by spatial and temporal limitations associated with aerial detection surveys of beetle activity. Thus, fire extent in these forests is largely independent of prefire disturbance history and vegetation conditions. In contrast, fire severity, even during extreme fire weather and in conjunction with a multiyear drought, is influenced by prefire stand conditions, including the history of previous disturbances.}, } @article {pmid17503596, year = {2007}, author = {Collyer, ML and Adams, DC}, title = {Analysis of two-state multivariate phenotypic change in ecological studies.}, journal = {Ecology}, volume = {88}, number = {3}, pages = {683-692}, doi = {10.1890/06-0727}, pmid = {17503596}, issn = {0012-9658}, mesh = {Analysis of Variance ; Animals ; Body Weights and Measures ; Computer Simulation ; Cyprinodontiformes/anatomy & histology ; Data Interpretation, Statistical ; *Ecosystem ; *Models, Theoretical ; Multivariate Analysis ; *Phenotype ; Sex Characteristics ; Urodela/anatomy & histology ; }, abstract = {Analyses of two-state phenotypic change are common in ecological research. Some examples include phenotypic changes due to phenotypic plasticity between two environments, changes due to predator/non-predator character shifts, character displacement via competitive interactions, and patterns of sexual dimorphism. However, methods for analyzing phenotypic change for multivariate data have not been rigorously developed. Here we outline a method for testing vectors of phenotypic change in terms of two important attributes: the magnitude of change (vector length) and the direction of change described by trait covariation (angular difference between vectors). We describe a permutation procedure for testing these attributes, which allows non-targeted sources of variation to be held constant. We provide examples that illustrate the importance of considering vector attributes of phenotypic change in biological studies, and we demonstrate how greater inference can be made than by evaluating variance components with MANOVA alone. Finally, we consider how our method may be extended to more complex data.}, } @article {pmid17503585, year = {2007}, author = {Gallery, RE and Dalling, JW and Arnold, AE}, title = {Diversity, host affinity, and distribution of seed-infecting fungi: a case study with Cecropia.}, journal = {Ecology}, volume = {88}, number = {3}, pages = {582-588}, doi = {10.1890/05-1207}, pmid = {17503585}, issn = {0012-9658}, mesh = {Analysis of Variance ; Ascomycota/*genetics ; Cecropia Plant/*microbiology ; Computational Biology ; DNA, Ribosomal Spacer/genetics ; *Ecosystem ; Genotype ; Panama ; Seeds/growth & development/*microbiology ; Sequence Analysis, DNA ; Species Specificity ; Survival Analysis ; Tropical Climate ; }, abstract = {Recruitment limitation has been proposed as an important mechanism contributing to the maintenance of tropical tree diversity. For pioneer species, infection by fungi significantly reduces seed survival in soil, potentially influencing both recruitment success and adult distributions. We examined fresh seeds of four sympatric Cecropia species for evidence of fungal infection, buried seeds for five months in common gardens below four C. insignis crowns in central Panama, and measured seed survival and fungal infection of inviable seeds. Seed survival varied significantly among species and burial sites, and with regard to local (Panama) vs. foreign (Costa Rica) maternal seed sources. Fresh seeds contained few cultivable fungi, but > 80% of soil-incubated seeds were infected by diverse Ascomycota, including putative pathogens, saprophytes, and endophytes. From 220 isolates sequenced for the nuclear internal transcribed spacer region (ITS), 26 of 73 unique genotypes were encountered more than once. Based on the most common genotypes, fungal communities demonstrate host affinity and are structured at the scale of individual crowns. Similarity among fungal communities beneath a given crown was significantly greater than similarity among isolates found under different crowns. However, the frequency of rare species suggests high fungal diversity and fine-scale spatial heterogeneity. These results reveal complex plant-fungal interactions in soil and provide a first indication of how seed survival in tropical forests may be affected by fungal community composition.}, } @article {pmid17498238, year = {2007}, author = {Piñeiro, R and Fuertes Aguilar, J and Munt, DD and Nieto Feliner, G}, title = {Ecology matters: Atlantic-Mediterranean disjunction in the sand-dune shrub Armeria pungens (Plumbaginaceae).}, journal = {Molecular ecology}, volume = {16}, number = {10}, pages = {2155-2171}, doi = {10.1111/j.1365-294X.2007.03280.x}, pmid = {17498238}, issn = {0962-1083}, mesh = {Bayes Theorem ; Climate ; Cluster Analysis ; DNA Primers ; *Demography ; *Ecosystem ; *Genetic Variation ; Geographic Information Systems ; Geography ; Mediterranean Region ; Models, Theoretical ; *Phylogeny ; Plumbaginaceae/*genetics ; Polymorphism, Restriction Fragment Length ; }, abstract = {Inferring the evolutionary history of Mediterranean plant lineages from current genetic, distributional and taxonomic patterns is complex because of a number of palaeoclimatic and geological interconnected factors together with landscape heterogeneity and human influence. Therefore, choosing spatially simplified systems as study groups is a suitable approach. An amplified fragment length polymorphism (AFLP) study using two restriction enzyme combinations (EcoRI/MseI and KpnI/MseI) was carried out to estimate the structure of genetic variation throughout the range of Armeria pungens. This species has a West Iberian-Corso/Sardinian disjunct distribution on coastal sand-dune ecosystems. Bayesian, amova and genetic distance analyses of the AFLP data revealed the same distinguishable genetic groups, which do not match the main geographical disjunction. Corso-Sardinian populations were found to be genetically closer to southwest Portuguese than to those from the Gulf of Cadiz (the closest geographically). Eastwards long-distance dispersal is therefore invoked to explain this geographical disjunction. A GIS analysis based on bioclimatic envelope modelling aiming to characterize the current locations of A. pungens found strong similarities between the Portugal and Corsica-Sardinia sites and less so between these areas and the Gulf of Cadiz. This coincident pattern between AFLP and climatic data suggests that the geographical disjunction is better explained by climatic factors than by the likeliness of a stochastic dispersal event. Such a combined phylogeographical-GIS modelling approach proves to be enlightening in reconstructing the evolutionary history of plant species.}, } @article {pmid17496114, year = {2007}, author = {Hufford, KM and Canaran, P and Ware, DH and McMullen, MD and Gaut, BS}, title = {Patterns of selection and tissue-specific expression among maize domestication and crop improvement loci.}, journal = {Plant physiology}, volume = {144}, number = {3}, pages = {1642-1653}, pmid = {17496114}, issn = {0032-0889}, mesh = {*Agriculture ; Computational Biology ; Crops, Agricultural/genetics ; Gene Expression Regulation, Plant ; Genes, Plant ; Molecular Sequence Data ; Phenotype ; Plant Proteins/*genetics/metabolism ; Polymorphism, Genetic ; *Selection, Genetic ; Time Factors ; Zea mays/*genetics/metabolism ; }, abstract = {The domestication of maize (Zea mays sp. mays) from its wild progenitors represents an opportunity to investigate the timing and genetic basis of morphological divergence resulting from artificial selection on target genes. We compared sequence diversity of 30 candidate selected and 15 reference loci between the three populations of wild teosintes, maize landraces, and maize inbred lines. We inferred an approximately equal ratio of genes selected during early domestication and genes selected during modern crop breeding. Using an expanded dataset of 48 candidate selected and 658 neutral reference loci, we tested the hypothesis that candidate selected genes in maize are more likely to have transcriptional functions than neutral reference genes, but there was no overrepresentation of regulatory genes in the selected gene dataset. Electronic northern analysis revealed that candidate genes are significantly overexpressed in the maize ear relative to vegetative tissues such as maize shoot, leaf, and root tissue. The maize ear underwent dramatic morphological alteration upon domestication and has been a continuing target of selection for maize yield. Therefore, we hypothesize that genes targeted by selection are more likely to be expressed in tissues that experienced high levels of morphological divergence during domestication and crop improvement.}, } @article {pmid17494391, year = {2007}, author = {Friedlander, AM and Brown, EK and Monaco, ME}, title = {Coupling ecology and GIS to evaluate efficacy of marine protected areas in Hawaii.}, journal = {Ecological applications : a publication of the Ecological Society of America}, volume = {17}, number = {3}, pages = {715-730}, doi = {10.1890/06-0536}, pmid = {17494391}, issn = {1051-0761}, mesh = {Animals ; Conservation of Natural Resources/*methods ; Ecology ; *Ecosystem ; Fishes ; Geographic Information Systems ; Hawaii ; Seawater ; }, abstract = {In order to properly determine the efficacy of marine protected areas (MPAs), a seascape perspective that integrates ecosystem elements at the appropriate ecological scale is necessary. Over the past four decades, Hawaii has developed a system of 11 Marine Life Conservation Districts (MLCDs) to conserve and replenish marine resources around the state. Initially established to provide opportunities for public interaction with the marine environment, these MLCDs vary in size, habitat quality, and management regimes, providing an excellent opportunity to test hypotheses concerning MPA design and function using multiple discrete sampling units. Digital benthic habitat maps for all MLCDs and adjacent habitats were used to evaluate the efficacy of existing MLCDs using a spatially explicit stratified random sampling design. Analysis of benthic cover validated the a priori classification of habitat types and provided justification for using these habitat strata to conduct stratified random sampling and analyses of fish habitat utilization patterns. Results showed that a number of fish assemblage characteristics (e.g., species richness, biomass, diversity) vary among habitat types, but were significantly higher in MLCDs compared with adjacent fished areas across all habitat types. Overall fish biomass was 2.6 times greater in the MLCDs compared to open areas. In addition, apex predators and other species were more abundant and larger in the MLCDs, illustrating the effectiveness of these closures in conserving fish populations within their boundaries. Habitat type, protected area size, and level of protection from fishing were all important determinates of MLCD effectiveness with respect to their associated fish assemblages. Although size of these protected areas was positively correlated with a number of fish assemblage characteristics, all appear too small to have any measurable influence on the adjacent fished areas. These protected areas were not designed for biodiversity conservation or fisheries enhancement yet still provide varying degrees of protection for fish populations within their boundaries. Implementing this type of biogeographic process, using remote sensing technology and sampling across the range of habitats present within the seascape, provides a robust evaluation of existing MPAs and can help to define ecologically relevant boundaries for future MPA design in a range of locations.}, } @article {pmid17489454, year = {2007}, author = {Murtaugh, PA}, title = {Simplicity and complexity in ecological data analysis.}, journal = {Ecology}, volume = {88}, number = {1}, pages = {56-62}, doi = {10.1890/0012-9658(2007)88[56:sacied]2.0.co;2}, pmid = {17489454}, issn = {0012-9658}, mesh = {Analysis of Variance ; Animals ; Cypriniformes ; *Data Interpretation, Statistical ; Ecology/*methods ; Research Design ; Zooplankton ; }, abstract = {I argue that ecological data analyses are often needlessly complicated, and I present two examples of published analyses for which simpler alternatives are available. Unnecessary complexity is often introduced when analysts focus on subunits of the key experimental or observational units in a study, or use a very general framework to present an analysis that is a simple special case. Simpler analyses are easier to explain and understand; they clarify what the key units in a study are; they reduce the chances for computational mistakes; and they are more likely to lead to the same conclusions when applied by different analysts to the same data.}, } @article {pmid17488897, year = {2007}, author = {Hu, W and Tong, S and Mengersen, K and Oldenburg, B}, title = {Exploratory spatial analysis of social and environmental factors associated with the incidence of Ross River virus in Brisbane, Australia.}, journal = {The American journal of tropical medicine and hygiene}, volume = {76}, number = {5}, pages = {814-819}, pmid = {17488897}, issn = {0002-9637}, mesh = {Alphavirus Infections/*epidemiology/transmission ; *Climate ; Demography ; Geographic Information Systems ; Geography ; Humans ; Incidence ; Queensland/epidemiology ; Risk Factors ; Ross River virus/*pathogenicity ; Socioeconomic Factors ; Statistics as Topic ; }, abstract = {We used geographic information systems and a spatial analysis approach to explore the pattern of Ross River virus (RRV) incidence in Brisbane, Australia. Climate, vegetation and socioeconomic data in 2001 were obtained from the Australian Bureau of Meteorology, the Brisbane City Council and the Australian Bureau of Statistics, respectively. Information on the RRV cases was obtained from the Queensland Department of Health. Spatial and multiple negative binomial regression models were used to identify the socioeconomic and environmental determinants of RRV transmission. The results show that RRV activity was primarily concentrated in the northeastern, northwestern, and southeastern regions in Brisbane. Multiple negative binomial regression models showed that the spatial pattern of RRV disease in Brisbane seemed to be determined by a combination of local ecologic, socioeconomic, and environmental factors.}, } @article {pmid17486976, year = {2006}, author = {Suh, SO and Blackwell, M and Kurtzman, CP and Lachance, MA}, title = {Phylogenetics of Saccharomycetales, the ascomycete yeasts.}, journal = {Mycologia}, volume = {98}, number = {6}, pages = {1006-1017}, doi = {10.3852/mycologia.98.6.1006}, pmid = {17486976}, issn = {0027-5514}, mesh = {Animals ; Cluster Analysis ; Computational Biology ; DNA, Fungal/genetics ; DNA, Ribosomal/genetics ; Ecology ; Humans ; Microscopy, Electron, Scanning ; Mycoses/microbiology ; Peptide Elongation Factor 1/genetics ; *Phylogeny ; Plant Diseases/microbiology ; RNA Polymerase II/genetics ; RNA, Ribosomal, 18S/genetics ; RNA, Ribosomal, 28S/genetics ; Saccharomycetales/*classification/cytology/*genetics/physiology ; Sequence Homology ; Yeasts/classification/cytology/genetics/physiology ; }, abstract = {Ascomycete yeasts (phylum Ascomycota: subphylum Saccharomycotina: class Saccharomycetes: order Saccharomycetales) comprise a monophyletic lineage with a single order of about 1000 known species. These yeasts live as saprobes, often in association with plants, animals and their interfaces. A few species account for most human mycotic infections, and fewer than 10 species are plant pathogens. Yeasts are responsible for important industrial and biotechnological processes, including baking, brewing and synthesis of recombinant proteins. Species such as Saccharomyces cerevisiae are model organisms in research, some of which led to a Nobel Prize. Yeasts usually reproduce asexually by budding, and their sexual states are not enclosed in a fruiting body. The group also is well defined by synapomorphies visible at the ultrastructural level. Yeast identification and classification changed dramatically with the availability of DNA sequencing. Species identification now benefits from a constantly updated sequence database and no longer relies on ambiguous growth tests. A phylogeny based on single gene analyses has shown the order to be remarkably divergent despite morphological similarities among members. The limits of many previously described genera are not supported by sequence comparisons, and multigene phylogenetic studies are under way to provide a stable circumscription of genera, families and orders. One recent multigene study has resolved species of the Saccharomycetaceae into genera that differ markedly from those defined by analysis of morphology and growth responses, and similar changes are likely to occur in other branches of the yeast tree as additional sequences become available.}, } @article {pmid17486975, year = {2006}, author = {Sugiyama, J and Hosaka, K and Suh, SO}, title = {Early diverging Ascomycota: phylogenetic divergence and related evolutionary enigmas.}, journal = {Mycologia}, volume = {98}, number = {6}, pages = {996-1005}, doi = {10.3852/mycologia.98.6.996}, pmid = {17486975}, issn = {0027-5514}, mesh = {Ascomycota/*classification/cytology/*genetics/physiology ; Cluster Analysis ; Computational Biology ; DNA, Fungal/genetics ; DNA, Ribosomal/genetics ; Evolution, Molecular ; *Phylogeny ; RNA Polymerase II/genetics ; RNA, Ribosomal, 18S/genetics ; RNA, Ribosomal, 28S/genetics ; Sequence Homology ; Tubulin/genetics ; }, abstract = {The early diverging Ascomycota lineage, detected primarily from nSSU rDNA sequence-based phylogenetic analyses, includes enigmatic key taxa important to an understanding of the phylogeny and evolution of higher fungi. At the moment six representative genera of early diverging ascomycetes (i.e. Taphrina, Protomyces, Saitoella, Schizosaccharomyces, Pneumocystis and Neolecta) have been assigned to "Archiascomycetes" sensu Nishida and Sugi ama (1994) or the subphylum "Taphrinomycotina" sensu Eriksson and Winka (1997). The group includes fungi that are ecologically and morphologically diverse, and it is difficult therefore to define the group based on common phenotypic characters. Bayesian analyses of nSSU rDNA or combined nSSU and nLSU rDNA sequences supported previously published Ascomycota frameworks that consist of three major lineages (i.e. a group of early diverging Ascomycota. [Taphrinomycotina], Saccharomycotina and Pezizomycotina); Taphrinomycotina is the sister group of Saccharomycotina and Pezizomycotina. The 50% majority rule consensus of 18000 Bayesian MCMCMC-generated trees from multilocus gene sequences of nSSU rDNA, nLSU rDNA (D1/D2), RPB2 and beta-tubulin also showed the monophyly of the three subphyla and the basal position of Taphrinomycotina in Ascomycota with significantly higher statistical support. However to answer controversial questions on the origin, monophyly and evolution of the Taphrinomycotina, additional integrated phylogenetic analyses might be necessary using sequences of more genes with broader taxon sampling from the early diverging Ascomycota.}, } @article {pmid17483516, year = {2007}, author = {Zhou, Y and Landweber, LF}, title = {BLASTO: a tool for searching orthologous groups.}, journal = {Nucleic acids research}, volume = {35}, number = {Web Server issue}, pages = {W678-82}, pmid = {17483516}, issn = {1362-4962}, support = {R01 GM059708/GM/NIGMS NIH HHS/United States ; GM59708/GM/NIGMS NIH HHS/United States ; }, mesh = {Algorithms ; Animals ; Computational Biology/methods ; Databases, Genetic ; *Genome ; Genomics ; Humans ; Internet ; Pattern Recognition, Automated ; Phylogeny ; *Sequence Homology, Nucleic Acid ; *Software ; Species Specificity ; User-Computer Interface ; }, abstract = {We present BLAST on Orthologous groups (BLASTO), a modified BLAST tool for searching orthologous group data. It treats each orthologous group as a unit and outputs a ranked list of orthologous groups instead of single sequences. By filtering out redundancy and putative paralogs, sequence comparisons to orthologous groups, instead of to single sequences in the database, can improve both functional prediction and phylogenetic inference. BLASTO computes the significance score of each orthologous group based on the individual BLAST hits in the orthologous group, using the number of taxa in the group as an optional weight. This allows users to control the species diversity of the orthologous groups. BLASTO incorporates the best-known multispecies ortholog databases, including NCBI Clusters of Orthologous Group, NCBI euKaryotic Orthologous Group database, OrthoMCL, MultiParanoid and TIGR Eukaryotic Gene Orthologues database, and offers a useful platform to integrate orthology information into functional inference and evolutionary studies of individual sequences. BLASTO is accessible online at http://oxytricha.princeton.edu/BlastO.}, } @article {pmid17477288, year = {2007}, author = {van Zelm, R and Huijbregts, MA and Harbers, JV and Wintersen, A and Struijs, J and Posthuma, L and van de Meent, D}, title = {Uncertainty in msPAF-based ecotoxicological effect factors for freshwater ecosystems in life cycle impact assessment.}, journal = {Integrated environmental assessment and management}, volume = {3}, number = {2}, pages = {203-210}, doi = {10.1897/ieam_2006-013.1}, pmid = {17477288}, issn = {1551-3777}, mesh = {Acrylates/metabolism/*toxicity ; Animals ; Databases, Factual ; Ecology ; *Ecosystem ; *Environmental Exposure ; Fresh Water/*analysis ; Life Cycle Stages/*drug effects/physiology ; Risk Assessment ; Species Specificity ; Stupor/epidemiology ; *Uncertainty ; Water Pollutants, Chemical/metabolism/*toxicity ; }, abstract = {Ecotoxicological effect factors are part of the analysis of relative impacts by chemical contaminants on ecosystems. Uncertainty distributions, represented by the 90% confidence interval, belonging to ecotoxicological effect factors for freshwater ecosystems were determined. This study includes 869 high production volume chemicals, related to 7 nonspecific toxic modes of action (TMoAs). The ecotoxicological effect factors are divided into a TMoA-specific part and a chemical-specific part. The 90% confidence interval of the TMoA-specific part of the effect factor ranges from 23 orders of magnitude for acrylate toxicity to 2 orders of magnitude for nonpolar narcosis. The range in the TMoA-specific part of the effect factor is mainly caused by uncertainty in the spread in toxic sensitivity between species (sigma(j)). Average uncertainty in the chemical-specific part of the effect factors depends on the number of species tested and ranges on average from a factor of 5 for more than 3 species tested to a factor of about 1,000 for 2 species tested. Average uncertainty in the ecotoxicological effect factors ranges from a factor of 100 for more than 3 species tested to a factor of nearly 10,000 for 2 species tested. It is recommended that the ecotoxicological effect factor of a chemical is based on toxicity data of at least 4 species.}, } @article {pmid17476943, year = {2007}, author = {Comas, C and Mateu, J}, title = {Modelling forest dynamics: a perspective from point process methods.}, journal = {Biometrical journal. Biometrische Zeitschrift}, volume = {49}, number = {2}, pages = {176-196}, doi = {10.1002/bimj.200510268}, pmid = {17476943}, issn = {0323-3847}, mesh = {Computer Simulation ; *Data Interpretation, Statistical ; *Ecosystem ; *Models, Biological ; Stochastic Processes ; Trees/*growth & development ; }, abstract = {This paper reviews the main applications of (marked) point process theory in forestry including functions to analyse spatial variability and the main (marked) point process models. Although correlation functions do describe spatial variability at distinct range of scale, they are clearly restricted to the analysis of few dominant species since they are based on pairwise analysis. This has over-simplified the spatial analysis of complex forest dynamics involving "large" number of species. Moreover, although process models can reproduce, to some extent, real forest spatial patterns of trees, the biological forest-ecological interpretation of the resulting spatial structures is difficult since these models usually lack of biological realism. This problem gains in strength as usually most of these point process models are defined in terms of purely spatial relationships, though in real life, forest develop through time. We thus aim to discuss the applicability of such formulations to analyse and simulate "real" forest dynamics and unwrap their shortcomes. We present a unified approach of modern spatially explicit forest growth models. Finally, we focus on a continuous space-time stochastic process as an alternative approach to generate marked point patterns evolving through space and time.}, } @article {pmid17476324, year = {2007}, author = {Elmqvist, T and Pyykönen, M and Tengö, M and Rakotondrasoa, F and Rabakonandrianina, E and Radimilahy, C}, title = {Patterns of loss and regeneration of tropical dry forest in Madagascar: the social institutional context.}, journal = {PloS one}, volume = {2}, number = {5}, pages = {e402}, pmid = {17476324}, issn = {1932-6203}, mesh = {Geographic Information Systems ; Madagascar ; Socioeconomic Factors ; Trees/*growth & development ; *Tropical Climate ; }, abstract = {Loss of tropical forests and changes in land-use/land-cover are of growing concern worldwide. Although knowledge exists about the institutional context in which tropical forest loss is embedded, little is known about the role of social institutions in influencing regeneration of tropical forests. In the present study we used Landsat images from southern Madagascar from three different years (1984, 1993 and 2000) and covering 5500 km(2), and made a time-series analysis of three distinct large-scale patterns: 1) loss of forest cover, 2) increased forest cover, and 3) stable forest cover. Institutional characteristics underlying these three patterns were analyzed, testing the hypothesis that forest cover change is a function of strength and enforcement of local social institutions. The results showed a minor decrease of 7% total forest cover in the study area during the whole period 1984-2000, but an overall net increase of 4% during the period 1993-2000. The highest loss of forest cover occurred in a low human population density area with long distances to markets, while a stable forest cover occurred in the area with highest population density and good market access. Analyses of institutions revealed that loss of forest cover occurred mainly in areas characterized by insecure property rights, while areas with well-defined property rights showed either regenerating or stable forest cover. The results thus corroborate our hypothesis. The large-scale spontaneous regeneration dominated by native endemic species appears to be a result of a combination of changes in precipitation, migration and decreased human population and livestock grazing pressure, but under conditions of maintained and well-defined property rights. Our study emphasizes the large capacity of a semi-arid system to spontaneously regenerate, triggered by decreased pressures, but where existing social institutions mitigate other drivers of deforestation and alternative land-use.}, } @article {pmid17472910, year = {2007}, author = {Gaston, KJ and Davies, RG and Orme, CD and Olson, VA and Thomas, GH and Ding, TS and Rasmussen, PC and Lennon, JJ and Bennett, PM and Owens, IP and Blackburn, TM}, title = {Spatial turnover in the global avifauna.}, journal = {Proceedings. Biological sciences}, volume = {274}, number = {1618}, pages = {1567-1574}, pmid = {17472910}, issn = {0962-8452}, mesh = {Animals ; *Biodiversity ; Birds/*physiology ; Databases, Factual ; *Demography ; Geography ; Models, Theoretical ; Species Specificity ; }, abstract = {Despite its wide implications for many ecological issues, the global pattern of spatial turnover in the occurrence of species has been little studied, unlike the global pattern of species richness. Here, using a database on the breeding distributions of birds, we present the first global maps of variation in spatial turnover for an entire taxonomic class, a pattern that has to date remained largely a matter of conjecture, based on theoretical expectations and extrapolation of inconsistent patterns from different biogeographic realms. We use these maps to test four predictions from niche theory as to the form that this variation should take, namely that turnover should increase with species richness, towards lower latitudes, and with the steepness of environmental gradients and that variation in turnover is determined principally by rare (restricted) species. Contrary to prediction, we show that turnover is high both in areas of extremely low and high species richness, does not increase strongly towards the tropics, and is related both to average environmental conditions and spatial variation in those conditions. These results are closely associated with a further important and novel finding, namely that global patterns of spatial turnover are driven principally by widespread species rather than the restricted ones. This complements recent demonstrations that spatial patterns of species richness are also driven principally by widespread species, and thus provides an important contribution towards a unified model of how terrestrial biodiversity varies both within and between the Earth's major land masses.}, } @article {pmid17469247, year = {2005}, author = {Durán-González, A and Laguarda-Figueras, A and Solís-Marin, FA and Buitrón Sánchez, BE and Ahearn, CG and Torres-Vega, J}, title = {[Echinoderms (Echinodermata) from the Mexican waters of the Gulf of Mexico].}, journal = {Revista de biologia tropical}, volume = {53 Suppl 3}, number = {}, pages = {53-68}, pmid = {17469247}, issn = {0034-7744}, mesh = {Animals ; *Biodiversity ; Databases, Factual ; Echinodermata/*classification/physiology ; Marine Biology ; Mexico ; Population Density ; Population Dynamics ; Seawater ; }, abstract = {We present a systematic list of the echinoderms from Gulf of Mexico's Mexican waters based on specimens of the Colecci6n Nacional de Equinodermos, Instituto de Ciencias del Mar y Limnologia, Universidad Nacional Aut6noma de México and the National Museum of Natural History, Smithsonian Institution, Washington, D.C. This list reveals an important echinoderm biodiversity present in the Gulf of Mexico, where five of the six echinoderm classes are represented. A total of 209 echinoderm species is recorded, distributed in 129 genera, 63 families and 25 orders. 31 new records for the Gulf of Mexico are presented: Asteroidea (16), Ophiuroidea (nine), Echinoidea (one) and Holothuroidea (five).}, } @article {pmid17466274, year = {2007}, author = {Takeuchi, F and Yanai, K and Inomata, H and Kuzuya, N and Kajio, H and Honjo, S and Takeda, N and Kaburagi, Y and Yasuda, K and Shirasawa, S and Sasazuki, T and Kato, N}, title = {Search of type 2 diabetes susceptibility gene on chromosome 20q.}, journal = {Biochemical and biophysical research communications}, volume = {357}, number = {4}, pages = {1100-1106}, doi = {10.1016/j.bbrc.2007.04.063}, pmid = {17466274}, issn = {0006-291X}, mesh = {Acute-Phase Proteins/*genetics ; Aged ; Aged, 80 and over ; Carrier Proteins/*genetics ; Chromosomes, Human, Pair 20/*genetics ; DNA Mutational Analysis/methods ; Diabetes Mellitus, Type 2/*epidemiology/*genetics ; Female ; Genetic Predisposition to Disease/epidemiology/genetics ; Hepatocyte Nuclear Factor 4/*genetics ; Humans ; Japan/epidemiology ; Male ; Membrane Glycoproteins/*genetics ; Middle Aged ; Polymorphism, Single Nucleotide/genetics ; Prevalence ; }, abstract = {Significant evidence of linkage to type 2 diabetes (T2D) has been shown in a relatively broad region on chromosome 20q, where the hepatocyte nuclear factor-4alpha (HNF4A) has been noted as a positional candidate. To systematically evaluate genetic susceptibility to T2D in the relevant region, we examined the disease association by using 1145 SNPs in two-step screening in the Japanese population. The marker screening enabled us to identify significant disease association in the lipopolysaccharide binding protein (LBP) but not in the HNF4A locus. In a 17.7-Mb interval screened, the strongest association was identified for a SNP, rs2232592, located in the intron of LBP, with an estimated odds ratio of 1.73 (95% CI 1.30-2.31) (P=0.0002) in the whole study panel involving 675 case and 474 control subjects. Our data suggest that the LBP gene may confer genetic susceptibility to T2D and this warrants further replication study.}, } @article {pmid17465918, year = {2007}, author = {Ridley, J and Kolm, N and Freckelton, RP and Gage, MJ}, title = {An unexpected influence of widely used significance thresholds on the distribution of reported P-values.}, journal = {Journal of evolutionary biology}, volume = {20}, number = {3}, pages = {1082-1089}, doi = {10.1111/j.1420-9101.2006.01291.x}, pmid = {17465918}, issn = {1010-061X}, mesh = {Confidence Intervals ; *Data Interpretation, Statistical ; *Probability ; *Publication Bias ; }, abstract = {We consider the problematic relationship between publication success and statistical significance in the light of analyses in which we examine the distribution of published probability (P) values across the statistical 'significance' range, below the 5% probability threshold. P-values are often judged according to whether they lie beneath traditionally accepted thresholds (< 0.05, < 0.01, < 0.001, < 0.0001); we examine how these thresholds influence the distribution of reported absolute P-values in published scientific papers, the majority in biological sciences. We collected published P-values from three leading journals, and summarized their distribution using the frequencies falling across and within these four threshold values between 0.05 and 0. These published frequencies were then fitted to three complementary null models which allowed us to predict the expected proportions of P-values in the top and bottom half of each inter-threshold interval (i.e. those lying below, as opposed to above, each P-value threshold). Statistical comparison of these predicted proportions, against those actually observed, provides the first empirical evidence for a remarkable excess of probability values being cited on, or just below, each threshold relative to the smoothed theoretical distributions. The pattern is consistent across thresholds and journals, and for whichever theoretical approach used to generate our expected proportions. We discuss this novel finding and its implications for solving the problems of publication bias and selective reporting in evolutionary biology.}, } @article {pmid17465183, year = {2007}, author = {Tilt, JH and Unfried, TM and Roca, B}, title = {Using objective and subjective measures of neighborhood greenness and accessible destinations for understanding walking trips and BMI in Seattle, Washington.}, journal = {American journal of health promotion : AJHP}, volume = {21}, number = {4 Suppl}, pages = {371-379}, doi = {10.4278/0890-1171-21.4s.371}, pmid = {17465183}, issn = {0890-1171}, mesh = {Body Mass Index ; Cross-Sectional Studies ; *Environment Design ; Female ; Geographic Information Systems ; Geography ; *Health Behavior ; *Health Promotion ; Health Surveys ; Humans ; Male ; Motor Activity ; Personal Satisfaction ; *Plants ; Residence Characteristics/*classification ; Walking/*psychology ; Washington ; }, abstract = {PURPOSE: Examine the influence of destinations within walking distance of a residence and vegetation on walking trips and body mass index (BMI).

DESIGN: Cross-sectional analysis of data from residences with varying accessibility and greenness.

SETTING: Seattle, Washington.

SUBJECTS: Stratified random sample of residents, stratified by accessibility and greenness. RESPONSE RATE: 17.5 %, 529 respondents.

MEASURES: Accessibility and greenness were measured objectively by Geographic Information Systems (GIS) Network Analysis and normalized difference vegetation index (NDVI), respectively. Self-reported destinations, natural features, walking trips, BMI, and importance of destinations were measured through a postal survey.

RESULTS: Objective accessibility were related to walking trips per month (r(2) = .110, p < .0001), as was subjective greenness (r(2) = .051, p < .0001), although objective measures of actual greenness were not. In areas with high accessibility, BMI was lower in areas that had high NDVI, or more greenness (r(2) = .129428, model p < .0001; t-test of interaction p = .0257). Low NDVI areas were associated with overestimation of the number of destinations within walking distance (F1, 499 = 11.009, p = .001).

CONCLUSIONS: Objective and subjective measurements of accessibility and greenness led to an understanding of variation among walking trips and BMI in different neighborhoods.}, } @article {pmid17461003, year = {2007}, author = {Marrone, J and Fairley, CK and Chen, M and Hocking, JS}, title = {Comparisons of trends in antiretroviral use and HIV notification rates between three Australian states.}, journal = {Australian and New Zealand journal of public health}, volume = {31}, number = {2}, pages = {131-134}, doi = {10.1111/j.1753-6405.2007.00030.x}, pmid = {17461003}, issn = {1326-0200}, mesh = {Anti-HIV Agents/*administration & dosage ; Australia/epidemiology ; Databases, Factual ; HIV Infections/*drug therapy/epidemiology ; Humans ; Male ; Mandatory Reporting ; Population Surveillance/*methods ; }, abstract = {OBJECTIVE: Notification rates for HIV among men who have sex with men (MSM) have been increasing, but this increase has not been uniform across States and Territories. This paper aims to determine whether differences in the levels of antiretroviral therapy (ART) were associated with differences in HIV notification rates between Australian States.

METHODS: An ecological analysis of HIV notification and S100 drug prescribing data between 1998 and 2005.

MAIN RESULTS: HIV notification rates in 2005 per 100 individuals living with HIV were lowest in New South Wales (NSW) (4.5) and higher in Victoria (6.9) and Queensland (7.8). The proportion of individuals receiving ART in 2005 was lowest in NSW (40%) and higher in Victoria (60%) and Queensland (60%). There has been a significant decline in the proportion of individuals living with HIV receiving effective ART per year in NSW (p < 0.01) and Queensland (p < 0.01), but an increase in Victoria (p < 0.01).

CONCLUSION: Those States with the highest HIV notifications per 100 individuals living with HIV did not have the lowest proportion of individuals receiving ART.

IMPLICATIONS: These data indicate that the differences in HIV notifications between States do not appear to be due to differences in ART. However, changes in ART over time in some States may be contributing to the rise in HIV notifications.}, } @article {pmid17456282, year = {2007}, author = {Ellison, GT}, title = {Health, wealth and IQ in sub-Saharan Africa: challenges facing the 'Savanna Principle' as an explanation for global inequalities in health.}, journal = {British journal of health psychology}, volume = {12}, number = {Pt 2}, pages = {191-227}, doi = {10.1348/135910707X180972}, pmid = {17456282}, issn = {1359-107X}, mesh = {Africa South of the Sahara ; *Biological Evolution ; Data Interpretation, Statistical ; Epidemiologic Methods ; *Health Status ; Humans ; *Income ; *Intelligence ; Research Design ; Socioeconomic Factors ; }, abstract = {Kanazawa's (2006) national- and individual-level analyses seem to support his hypothesis that: IQ scores are better predictors of health than wealth or inequality, except in 'evolutionarily familiar' sub-Saharan Africa which offers limited selection for intelligence (British Journal of Health Psychology 11: 623-42). However, the present paper exposes the flawed assumptions, questionable data, inappropriate analyses and biased interpretations on which this thesis was based. It questions the assumptions that: IQ scores are markers of adaptive genetic differences in intelligence; humans evolved within a predictable 'environment of evolutionary adaptedness': and this environment characterizes contemporary sub-Saharan Africa, offering little selection for intelligence. It also demonstrates that the macro-level data on which these analyses were based were collected across a range of different years, using a range of different sources, and were significantly intercorrelated. While none of these analyses adjusted for study year or study type, all were susceptible to multicollinearity and the 'ecological fallacy'. These flaws were compounded by the selective presentation and partial interpretation of the analyses, which focused on the absence of an 'independent' relationship between 'national IQ' and health within sub-Saharan Africa, but ignored the fact that this is also true for every other region of the world. Likewise, the individual-level analyses did not explore the relationship between IQ scores, self-reported income and health by race, which would have demonstrated the impact of the ecological fallacy. Instead, Kanazawa (2006) mistook statistical associations for evidence of causality and falsely concluded that populations in sub-Saharan Africa are less healthy because they are unintelligent and not because they are poor.}, } @article {pmid17454352, year = {2007}, author = {Tranel, D and Hathaway-Nepple, J and Anderson, SW}, title = {Impaired behavior on real-world tasks following damage to the ventromedial prefrontal cortex.}, journal = {Journal of clinical and experimental neuropsychology}, volume = {29}, number = {3}, pages = {319-332}, pmid = {17454352}, issn = {1380-3395}, support = {R01 DA022549/DA/NIDA NIH HHS/United States ; NS19632/NS/NINDS NIH HHS/United States ; R01 DA022549-02/DA/NIDA NIH HHS/United States ; P01 NS019632/NS/NINDS NIH HHS/United States ; P01 NS19632/NS/NINDS NIH HHS/United States ; }, mesh = {Behavior/*physiology ; Brain Damage, Chronic/*psychology ; Data Interpretation, Statistical ; Female ; Humans ; Intelligence Tests ; Male ; Mathematics ; Memory/physiology ; Middle Aged ; Neuropsychological Tests ; Prefrontal Cortex/*physiopathology ; Psychomotor Performance/*physiology ; Verbal Behavior ; }, abstract = {Patients with damage to the ventromedial prefrontal cortices (VMPC) commonly manifest blatant behavioral navigation defects in the real world, but it has been difficult to measure these impairments in the clinic or laboratory. Using a set of "strategy application" tasks, which were designed by Shallice and Burgess (1991) to be ecologically valid for detecting executive dysfunction, we investigated the hypothesis that VMPC damage would be associated with defective performance on such tasks, whereas damage outside the VMPC region would not. A group of 9 patients with bilateral VMPC damage was contrasted with comparison groups of participants with (a) prefrontal brain damage outside the VMPC region (n = 8); (b) nonprefrontal brain damage (n = 17); and (c) no brain damage (n = 20). We found support for the hypothesis: VMPC patients had more impaired performances on the strategy application tasks, especially on a Multiple Errands Test that required patients to execute a series of unstructured tasks in a real-world setting (shopping mall). The results are consistent with the notion that efficacious behavioral navigation is dependent on the VMPC region. However, the strategy application tasks were relatively time consuming and effortful, and their diagnostic yield over and above conventional executive functioning tests may not be sufficient to warrant their inclusion in standard clinical assessment.}, } @article {pmid17453275, year = {2007}, author = {Sivanpillai, R and Latchininsky, AV}, title = {Mapping locust habitats in the Amudarya River Delta, Uzbekistan with multi-temporal MODIS imagery.}, journal = {Environmental management}, volume = {39}, number = {6}, pages = {876-886}, doi = {10.1007/s00267-006-0193-y}, pmid = {17453275}, issn = {0364-152X}, mesh = {Animals ; *Conservation of Natural Resources ; *Ecosystem ; *Geographic Information Systems ; Geography ; Locusta migratoria/*physiology ; Rivers ; *Satellite Communications ; Seasons ; Time Factors ; Uzbekistan ; }, abstract = {Reed beds of Phragmites australis in the River Amudarya delta near the Aral Sea constitute permanent breeding areas of the Asian Migratory locust, Locusta migratoria migratoria. Every year, thousands of hectares are treated with broad-spectrum insecticides to prevent locust swarms from damaging crops in adjacent areas. To devise efficient locust monitoring and management plans, accurate and updated information about the spatial distribution of reeds is necessary. Given the vast geographic extent of the delta, traditional, ground survey methods are inadequate. Remotely sensed data collected by the MODIS sensor aboard the TERRA satellite provide a useful tool to characterize the spatial distribution of reeds. Multi-temporal MODIS data, collected at different times of the growing season, were used to generate spectral-temporal signatures for reeds and other land cover classes. These spectral-temporal signatures were matched with reed phenology. MODIS information was digitally classified to generate a land cover map with an overall accuracy of 74%. MODIS data captured 87% of the ground-verified reed locations. Estimates derived from MODIS data indicate that 18% of the study area was covered by reeds. However, high commission error resulted from misclassification of reeds mixed with shrubs class and shrubs class as reeds. This could have resulted in overprediction of the area covered by reeds. Additional research is needed to minimize the overlap between reeds and other vegetation classes (shrubs, and reed and shrub mix). Nevertheless, despite its relatively low spatial resolution (250 m), multi-temporal MODIS data were able to adequately capture the distribution of reeds. Instead of blanketing the fragile wetland ecosystem of the Amudarya delta with chemical anti-locust treatments, plant protection specialists can use this information to devise ecologically sound pest management plans aimed at reducing the adverse environmental impact in the zone of the Aral Sea ecological catastrophe. MODIS methodology to identify reed stands can be applicable to the Migratory locust habitats in other geographic areas.}, } @article {pmid17453273, year = {2007}, author = {Villa, F and Ceroni, M and Krivov, S}, title = {Intelligent databases assist transparent and sound economic valuation of ecosystem services.}, journal = {Environmental management}, volume = {39}, number = {6}, pages = {887-899}, pmid = {17453273}, issn = {0364-152X}, mesh = {Animals ; Conservation of Natural Resources/*economics/methods ; *Databases as Topic ; *Ecosystem ; Environmental Pollution/*economics/legislation & jurisprudence/prevention & control ; Humans ; Models, Economic ; Policy Making ; Waste Management/*economics/methods ; Water Supply/*economics/legislation & jurisprudence ; }, abstract = {Assessment and economic valuation of services provided by ecosystems to humans has become a crucial phase in environmental management and policy-making. As primary valuation studies are out of the reach of many institutions, secondary valuation or benefit transfer, where the results of previous studies are transferred to the geographical, environmental, social, and economic context of interest, is becoming increasingly common. This has brought to light the importance of environmental valuation databases, which provide reliable valuation data to inform secondary valuation with enough detail to enable the transfer of values across contexts. This paper describes the role of next-generation, intelligent databases (IDBs) in assisting the activity of valuation. Such databases employ artificial intelligence to inform the transfer of values across contexts, enforcing comparability of values and allowing users to generate custom valuation portfolios that synthesize previous studies and provide aggregated value estimates to use as a base for secondary valuation. After a general introduction, we introduce the Ecosystem Services Database, the first IDB for environmental valuation to be made available to the public, describe its functionalities and the lessons learned from its usage, and outline the remaining needs and expected future developments in the field.}, } @article {pmid17447672, year = {2007}, author = {Watson, MO and Sanderson, P}, title = {Designing for attention with sound: challenges and extensions to ecological interface design.}, journal = {Human factors}, volume = {49}, number = {2}, pages = {331-346}, doi = {10.1518/001872007X312531}, pmid = {17447672}, issn = {0018-7208}, mesh = {Anesthesiology/*instrumentation ; Auditory Perception ; Awareness ; Data Display ; Decision Support Systems, Clinical/instrumentation ; Drug Monitoring/*instrumentation ; Ecosystem ; Equipment Design ; Humans ; Man-Machine Systems ; *Sound ; *User-Computer Interface ; }, abstract = {OBJECTIVE: We explore whether ecological interface design (EID) principles can be applied to the design of an auditory display for anesthesia monitoring.

BACKGROUND: EID examples focus almost exclusively on visual displays. In the anesthesia work environment, however, auditory displays may provide better individual and team awareness of patient state.

METHOD: Using a work domain analysis of physiological monitoring in anesthesia, we identify information to display. Using the skills, rules, and knowledge distinction we identify cognitive control needed. Using semantic mapping we map physiological variables and constraints to auditory dimensions.

RESULTS: EID principles do not address when information should be displayed and to whom. An attentional mapping stage helps to specify answers to these questions so that a workable auditory display for anesthesia monitoring is achieved.

CONCLUSION: EID principles of representing work domain functional structure and minimizing resource-demanding cognitive control are necessary but insufficient to specify requirements for an effective auditory display. Also needed are analyses of control tasks, strategies, and the social organization of work. Such analyses are an integral part of the broader cognitive work analysis framework from which EID emerged.

APPLICATION: Actual or potential uses of this research include the design of displays that support continuous peripheral awareness in collaborative multimodal work environments.}, } @article {pmid17439821, year = {2007}, author = {Critto, A and Torresan, S and Semenzin, E and Giove, S and Mesman, M and Schouten, AJ and Rutgers, M and Marcomini, A}, title = {Development of a site-specific ecological risk assessment for contaminated sites: part I. A multi-criteria based system for the selection of ecotoxicological tests and ecological observations.}, journal = {The Science of the total environment}, volume = {379}, number = {1}, pages = {16-33}, doi = {10.1016/j.scitotenv.2007.02.035}, pmid = {17439821}, issn = {0048-9697}, mesh = {Animals ; *Decision Support Techniques ; Ecology ; *Hazardous Waste ; *Risk Assessment ; Soil Pollutants/toxicity ; *Toxicity Tests ; }, abstract = {A two modules Decision Support System (DSS-ERAMANIA) was developed in order to support the site-specific Ecological Risk Assessment (ERA) for contaminated sites. Within the first module, the TRIAD and the Weight of Evidence approaches were used to develop a site-specific Ecological Risk Assessment framework including three tires of investigation. Selected ecological observations and ecotoxicological tests were compared according to Multi Criteria Decision Analysis (MCDA) methods and expert judgment, and the obtained ranking was used to identify a suitable set of tests, at each investigation tier, to be applied to the examined case study. A simplified application of the proposed methodology, implemented in the Module 1 of the DSS-ERA-MANIA, is described and discussed.}, } @article {pmid17436031, year = {2007}, author = {Field, D and Kyrpides, N}, title = {The positive role of the ecological community in the genomic revolution.}, journal = {Microbial ecology}, volume = {53}, number = {3}, pages = {507-511}, pmid = {17436031}, issn = {0095-3628}, mesh = {Base Sequence ; Computational Biology/*trends ; *Ecology/methods/trends ; Environment ; Environmental Microbiology ; Genome/genetics ; *Genomics/trends ; }, abstract = {The exponential increase of genomic and metagenomic data, fueled in part by recent advancements in sequencing technology, are greatly expanding our understanding of the phylogenetic diversity and metabolic capacity present in the environment. Two of the central challenges that bioinformaticians and ecologists alike must face are the design of bioinformatic resources that facilitate the analysis of genomic and metagenomic data in a comparative context and the efficient capture and organization of the plethora of descriptive information required to usefully describe these data sets. In this commentary, we review three initiatives presented in the "new frontiers" session of the second SCOPE meeting on Microbial Environmental Genomics (MicroEnGen-II, Shanghai, June 12-15, 2006). These are (1) the Integrated Microbial Genomes Resources (IMG), (2) the Genomic Standards Consortium (GSC), and (3) the Natural Environment Research Council (NERC) Environmental Bioinformatics Centre (NEBC). These integrative bioinformatics and data management initiatives underscore the increasingly important role ecologists have to play in the genomic (metagenomic) revolution.}, } @article {pmid17434759, year = {2007}, author = {Kjer, KM and Swigonova, Z and LaPolla, JS and Broughton, RE}, title = {Why weight?.}, journal = {Molecular phylogenetics and evolution}, volume = {43}, number = {3}, pages = {999-1004}, doi = {10.1016/j.ympev.2007.02.028}, pmid = {17434759}, issn = {1055-7903}, mesh = {Animals ; Computational Biology/methods ; DNA, Mitochondrial/*genetics ; Humans ; Mammals/classification/genetics ; *Phylogeny ; }, abstract = {Whether phylogenetic data should be differentially or equally weighted is currently debated. Further, if differential weighting is to be explored, there is no consensus among investigators as to which weighting scheme is most appropriate. Mitochondrial genome data offer a powerful tool in assessment of differential weighting schemes because taxa can be selected from which a highly corroborated phylogeny is available (so that accuracy can be assessed), and it can be assumed that different data partitions share the same history (so that gene-sorting issues are not so problematic). Using mitochondrial data from 17 mammalian genomes, we evaluated the most commonly used weighting schemes, such as successive weighting, transversion weighting, codon-based weighting, and amino acid coding, and compared them to more complex weighting schemes including a 6-parameter weighting, pseudoreplicate reweighting, and tri-level weighting. We found that the most commonly used weighting schemes perform the worst with these data. Some of the more complex schemes perform well, however, none of them is consistently superior. These results support ones biases; if one has a predilection to avoid differential weighting, these data support equally weighted parsimony and maximum likelihood. Others might be encouraged by these results to try weighting as a form of data exploration.}, } @article {pmid17434575, year = {2007}, author = {Semenzin, E and Critto, A and Carlon, C and Rutgers, M and Marcomini, A}, title = {Development of a site-specific Ecological Risk Assessment for contaminated sites: part II. A multi-criteria based system for the selection of bioavailability assessment tools.}, journal = {The Science of the total environment}, volume = {379}, number = {1}, pages = {34-45}, doi = {10.1016/j.scitotenv.2007.02.034}, pmid = {17434575}, issn = {0048-9697}, mesh = {Animals ; Biological Availability ; *Decision Support Techniques ; Ecology ; *Hazardous Waste ; *Risk Assessment ; Soil Pollutants/metabolism ; }, abstract = {A comparison procedure based on Multi-Criteria Decision Analysis (MCDA) and expert judgment was developed in order to allow the comparison of bioavailability tests to implement the chemical Line of Evidence (LoE) within a TRIAD based site-specific Ecological Risk Assessment framework including three tires of investigation. The proposed methodology was included in the Module 1 of the Decision Support System DSS-ERAMANIA and the obtained rank supported the selection of a suitable set of available tests to be applied to the case study. A simplified application of the proposed procedure is described and results obtained by the system software are discussed.}, } @article {pmid17429700, year = {2007}, author = {Dickie, IA and FitzJohn, RG}, title = {Using terminal restriction fragment length polymorphism (T-RFLP) to identify mycorrhizal fungi: a methods review.}, journal = {Mycorrhiza}, volume = {17}, number = {4}, pages = {259-270}, pmid = {17429700}, issn = {0940-6360}, mesh = {Colony Count, Microbial ; DNA Primers ; DNA Restriction Enzymes ; DNA, Fungal/genetics ; DNA, Ribosomal Spacer ; Databases, Genetic ; Mycological Typing Techniques/*methods ; Mycorrhizae/classification/*genetics ; Polymerase Chain Reaction/*methods ; *Polymorphism, Restriction Fragment Length ; Species Specificity ; }, abstract = {Terminal restriction fragment length polymorphism (T-RFLP) is an increasingly widely used technique in mycorrhizal ecology. In this paper, we review the technique as it is used to identify species of mycorrhizal fungi and distinguish two different versions of the technique: peak-profile T-RFLP (the original version) and database T-RFLP. We define database T-RFLP as the use of T-RFLP to identify individual species within samples by comparison of unknown data with a database of known T-RFLP patterns. This application of T-RFLP avoids some of the pitfalls of peak-profile T-RFLP and allows T-RFLP to be applied to polyphyletic functional groups such as ectomycorrhizal fungi. The identification of species using database T-RFLP is subject to several sources of potential error, including (1) random erroneous matches of peaks to species, (2) shared T-RFLP profiles across species, and (3) multiple T-RFLP profiles within a species. A mathematical approximation of the risk of the first type of error as a function of experimental parameters is discussed. Although potentially less accurate than some other methods such as clone libraries, the high throughput of database T-RFLP permits much greater replication and may, therefore, be preferable for many ecological questions, particularly when combined with other techniques such as cloning.}, } @article {pmid17416439, year = {2007}, author = {Mabee, PM and Ashburner, M and Cronk, Q and Gkoutos, GV and Haendel, M and Segerdell, E and Mungall, C and Westerfield, M}, title = {Phenotype ontologies: the bridge between genomics and evolution.}, journal = {Trends in ecology & evolution}, volume = {22}, number = {7}, pages = {345-350}, doi = {10.1016/j.tree.2007.03.013}, pmid = {17416439}, issn = {0169-5347}, support = {U54 HG004028/HG/NHGRI NIH HHS/United States ; 1U54 HG 004028-01/HG/NHGRI NIH HHS/United States ; HG 002659/HG/NHGRI NIH HHS/United States ; }, mesh = {Anatomy ; Animals ; *Biological Evolution ; *Databases, Factual ; *Genomics ; Genotype ; Humans ; Phenotype ; }, abstract = {Understanding the developmental and genetic underpinnings of particular evolutionary changes has been hindered by inadequate databases of evolutionary anatomy and by the lack of a computational approach to identify underlying candidate genes and regulators. By contrast, model organism studies have been enhanced by ontologies shared among genomic databases. Here, we suggest that evolutionary and genomics databases can be developed to exchange and use information through shared phenotype and anatomy ontologies. This would facilitate computing on evolutionary questions pertaining to the genetic basis of evolutionary change, the genetic and developmental bases of correlated characters and independent evolution, biomedical parallels to evolutionary change, and the ecological and paleontological correlates of particular types of change in genes, gene networks and developmental pathways.}, } @article {pmid17408790, year = {2007}, author = {Lücker, S and Steger, D and Kjeldsen, KU and MacGregor, BJ and Wagner, M and Loy, A}, title = {Improved 16S rRNA-targeted probe set for analysis of sulfate-reducing bacteria by fluorescence in situ hybridization.}, journal = {Journal of microbiological methods}, volume = {69}, number = {3}, pages = {523-528}, doi = {10.1016/j.mimet.2007.02.009}, pmid = {17408790}, issn = {0167-7012}, support = {P 18836/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Databases, Nucleic Acid ; Deltaproteobacteria/genetics/isolation & purification ; In Situ Hybridization, Fluorescence/*methods ; *Oligonucleotide Probes ; RNA, Ribosomal, 16S/*genetics ; Sensitivity and Specificity ; Species Specificity ; Sulfates/*metabolism ; Sulfur-Reducing Bacteria/genetics/*isolation & purification ; }, abstract = {An updated dataset of in silico specificities for 54 previously published 16S rRNA-targeted oligonucleotides was assembled to provide guidance for reliable fluorescence in situ hybridization (FISH) analysis of sulfate-reducing bacteria. Additionally, six new FISH probes were developed for major deltaproteobacterial taxa, including a probe trio targeting most Deltaproteobacteria and Gemmatimonadetes.}, } @article {pmid17406775, year = {2007}, author = {Shyu, C and Soule, T and Bent, SJ and Foster, JA and Forney, LJ}, title = {MiCA: a web-based tool for the analysis of microbial communities based on terminal-restriction fragment length polymorphisms of 16S and 18S rRNA genes.}, journal = {Microbial ecology}, volume = {53}, number = {4}, pages = {562-570}, pmid = {17406775}, issn = {0095-3628}, support = {IP20 RR16448/RR/NCRR NIH HHS/United States ; }, mesh = {Computational Biology ; Databases, Nucleic Acid ; Internet ; Microbiology ; Polymerase Chain Reaction ; *Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S/*genetics ; RNA, Ribosomal, 18S/*genetics ; Restriction Mapping ; Sequence Analysis, DNA ; *Software ; }, abstract = {A web-based resource, Microbial Community Analysis (MiCA), has been developed to facilitate studies on microbial community ecology that use analyses of terminal-restriction fragment length polymorphisms (T-RFLP) of 16S and 18S rRNA genes. MiCA provides an intuitive web interface to access two specialized programs and a specially formatted database of 16S ribosomal RNA sequences. The first program performs virtual polymerase chain reaction (PCR) amplification of rRNA genes and restriction of the amplicons using primer sequences and restriction enzymes chosen by the user. This program, in silico PCR and Restriction (ISPaR), uses a binary encoding of DNA sequences to rapidly scan large numbers of sequences in databases searching for primer annealing and restriction sites while permitting the user to specify the number of mismatches in primer sequences. ISPaR supports multiple digests with up to three enzymes. The number of base pairs between the 5' and 3' primers and the proximal restriction sites can be reported, printed, or exported in various formats. The second program, APLAUS, infers a plausible community structure(s) based on T-RFLP data supplied by a user. APLAUS estimates the relative abundances of populations and reports a listing of phylotypes that are consistent with the empirical data. MiCA is accessible at http://mica.ibest.uidaho.edu/.}, } @article {pmid17404314, year = {2007}, author = {Hoshino, A and Kawamura, YI and Yasuhara, M and Toyama-Sorimachi, N and Yamamoto, K and Matsukawa, A and Lira, SA and Dohi, T}, title = {Inhibition of CCL1-CCR8 interaction prevents aggregation of macrophages and development of peritoneal adhesions.}, journal = {Journal of immunology (Baltimore, Md. : 1950)}, volume = {178}, number = {8}, pages = {5296-5304}, doi = {10.4049/jimmunol.178.8.5296}, pmid = {17404314}, issn = {0022-1767}, mesh = {Animals ; Cell Aggregation ; Cell Movement ; Chemokine CCL1 ; Chemokines, CC/*antagonists & inhibitors/physiology ; Macrophages, Peritoneal/cytology/*physiology ; Male ; Mice ; Mice, Inbred C57BL ; Peritoneal Diseases/*prevention & control ; Postoperative Complications/prevention & control ; Receptors, CCR8 ; Receptors, Chemokine/*antagonists & inhibitors/physiology ; Tissue Adhesions/*prevention & control ; }, abstract = {Peritoneal adhesions are a significant complication of surgery and visceral inflammation; however, the mechanism has not been fully elucidated. The aim of this study was to clarify the mechanism of peritoneal adhesions by focusing on the cell trafficking and immune system in the peritoneal cavity. We investigated the specific recruitment of peritoneal macrophages (PMphi) and their expression of chemokine receptors in murine models of postoperative and postinflammatory peritoneal adhesions. PMphi aggregated at the site of injured peritoneum in these murine models of peritoneal adhesions. The chemokine receptor CCR8 was up-regulated in the aggregating PMphi when compared with naive PMphi. The up-regulation of CCR8 was also observed in PMphi, but not in bone marrow-derived Mphi, treated with inflammatory stimulants including bacterial components and cytokines. Importantly, CCL1, the ligand for CCR8, a product of both PMphi and peritoneal mesothelial cells (PMCs) following inflammatory stimulation, was a potent enhancer of CCR8 expression. Cell aggregation involving PMphi and PMCs was induced in vitro in the presence of CCL1. CCL1 also up-regulated mRNA levels of plasminogen activator inhibitor-1 in both PMphi and PMCs. CCR8 gene-deficient mice or mice treated with anti-CCL1-neutralizing Ab exhibited significantly reduced postoperational peritoneal adhesion. Our study now establishes a unique autocrine activation system in PMphi and the mechanism for recruitment of PMphi together with PMCs via CCL1/CCR8, as immune responses of peritoneal cavity, which triggers peritoneal adhesions.}, } @article {pmid17395734, year = {2007}, author = {Baptista-Rosas, RC and Hinojosa, A and Riquelme, M}, title = {Ecological niche modeling of Coccidioides spp. in western North American deserts.}, journal = {Annals of the New York Academy of Sciences}, volume = {1111}, number = {}, pages = {35-46}, doi = {10.1196/annals.1406.003}, pmid = {17395734}, issn = {0077-8923}, mesh = {Coccidioides/*physiology ; Coccidioidomycosis/epidemiology/*microbiology ; Databases, Factual ; Desert Climate ; Ecology/methods ; Ecosystem ; Environment ; Humans ; Mexico ; Models, Biological ; Soil ; United States ; }, abstract = {Coccidioidomycosis is an endemic infectious disease in western North American deserts caused by the dimorphic ascomycete Coccidioides spp. Even though there has been an increase in the number of reported cases in the last years, few positive isolations have been obtained from soil samples in endemic areas for the disease. This low correlation between epidemiological and environmental data prompted us to better characterize the fundamental ecological niche of this important fungal pathogen. By using a combination of environmental variables and geospatially referenced points, where positive isolations had been obtained in southern California and Arizona (USA) and Sonora (Mexico), we have applied Genetic Algorithm for Rule Set Production (GARP) and Geographical Information Systems (GIS) to characterize the most likely ecological conditions favorable for the presence of the fungus. This model, based on environmental variables, allowed us to identify hotspots for the presence of the fungus in areas of southern California, Arizona, Texas, Baja California, and northern Mexico, whereas an alternative model based on bioclimatic variables gave us much broader probable distribution areas. We have overlapped the hotspots obtained with the environmental model with the available epidemiological information and have found a high match. Our model suggests that the most probable fundamental ecological niche for Coccidioides spp. is found in the arid lands of the North American deserts and provides the methodological basis to further characterize the realized ecological niche of Coccidioides spp., which would ultimately contribute to design smart field-sampling strategies.}, } @article {pmid17391198, year = {2007}, author = {Sekercioglu, CH and Loarie, SR and Oviedo Brenes, F and Ehrlich, PR and Daily, GC}, title = {Persistence of forest birds in the Costa Rican agricultural countryside.}, journal = {Conservation biology : the journal of the Society for Conservation Biology}, volume = {21}, number = {2}, pages = {482-494}, doi = {10.1111/j.1523-1739.2007.00655.x}, pmid = {17391198}, issn = {0888-8892}, mesh = {*Agriculture ; Animals ; Appetitive Behavior/physiology ; *Conservation of Natural Resources ; Costa Rica ; Demography ; *Ecosystem ; Geographic Information Systems ; Nesting Behavior ; Passeriformes/*physiology ; Species Specificity ; Telemetry ; *Trees ; }, abstract = {Understanding the persistence mechanisms of tropical forest species in human-dominated landscapes is a fundamental challenge of tropical ecology and conservation. Many species, including more than half of Costa Rica's native land birds, use mostly deforested agricultural countryside, but how they do so is poorly known. Do they commute regularly to forest or can some species survive in this human-dominated landscape year-round? Using radiotelemetry, we detailed the habitat use, movement, foraging, and nesting patterns of three bird species, Catharus aurantiirostris, Tangara icterocephala, and Turdus assimilis, by obtaining 8101 locations from 156 individuals. We chose forest birds that varied in their vulnerability to deforestation and were representative of the species found both in forest and human-dominated landscapes. Our study species did not commute from extensive forest; rather, they fed and bred in the agricultural countryside. Nevertheless, T. icterocephala and T. assimilis, which are more habitat sensitive, were highly dependent on the remaining trees. Although trees constituted only 11% of land cover, these birds spent 69% to 85% of their time in them. Breeding success of C. aurntiirostris and T. icterocephala in deforested habitats was not different than in forest remnants, where T. assimilis experienced reduced breeding success. Although this suggests an ecological trap for T. assimilis, higher fledgling survival in forest remnants may make up for lower productivity. Tropical countryside has high potential conservation value, which can be enhanced with even modest increases in tree cover. Our findings have applicability to many human-dominated tropical areas that have the potential to conserve substantial biodiversity if appropriate restoration measures are taken.}, } @article {pmid17391189, year = {2007}, author = {Marsh, H and Dennis, A and Hines, H and Kutt, A and McDonald, K and Weber, E and Williams, S and Winter, J}, title = {Optimizing allocation of management resources for wildlife.}, journal = {Conservation biology : the journal of the Society for Conservation Biology}, volume = {21}, number = {2}, pages = {387-399}, doi = {10.1111/j.1523-1739.2006.00589.x}, pmid = {17391189}, issn = {0888-8892}, mesh = {Animals ; Australia ; Conservation of Natural Resources/*economics/*methods ; *Decision Making, Organizational ; *Decision Support Techniques ; Extinction, Biological ; *Public Policy ; *Social Values ; Species Specificity ; }, abstract = {Allocating money for species conservation on the basis of threatened species listings is not the most cost-effective way of promoting recovery or minimizing extinction rates. Using ecological and social factors in addition to threat categories, we designed a decision-support process to assist policy makers in their allocation of resources for the management of native wildlife and to clarify the considerations leading to a priority listing. Each species is scored on three criteria at the scale of the relevant jurisdiction: (1) threat category, (2) consequences of extinction, and (3) potential for successful recovery. This approach provides opportunity for independent input by policy makers and other stakeholders (who weight the relative importance of the criteria) and scientists (who score the species against the criteria). Thus the process explicitly separates societal values from the technical aspects of the decision-making process while acknowledging the legitimacy of both inputs. We applied our technique to two Australian case studies at different spatial scales: the frogs of Queensland (1,728,000 km(2); 116 species) and the mammals of the Wet Tropics bioregion (18,500 km(2); 96 species). We identified 7 frog and 10 mammal species as priorities for conservation. The frogs included 1 of the 9 species classified as endangered under Queensland legislation, 3 of the 10 species classified as vulnerable, 2 of the 22 species classified as rare, and 1 of the 75 species classified as least concern. The mammals identified included 3 of the 6 species classified as endangered, 1 of the 4 species classified as vulnerable, 5 of the 11 species classified as rare, and 1 of the 75 species classified as least concern. The methods we used to identify species were robust to comparisons across the two taxonomic groups. We concluded that (1) our process facilitates comparisons of data required to make transparent, cost-effective, and strategic management decisions across taxonomic groups and (2) the process should be used to short-list species for further discussion rather than for allocating resources per se.}, } @article {pmid17391180, year = {2007}, author = {Seddon, PJ and Armstrong, DP and Maloney, RF}, title = {Developing the science of reintroduction biology.}, journal = {Conservation biology : the journal of the Society for Conservation Biology}, volume = {21}, number = {2}, pages = {303-312}, doi = {10.1111/j.1523-1739.2006.00627.x}, pmid = {17391180}, issn = {0888-8892}, mesh = {Breeding/*methods ; Conservation of Natural Resources/*methods/*trends ; *Ecosystem ; Geographic Information Systems ; *Models, Biological ; Population Dynamics ; Species Specificity ; }, abstract = {With recent increases in the numbers of species reintroduction projects and reintroduction-related publications, there is now a recognizable field of reintroduction biology. Nevertheless, research thus far has been fragmented and ad hoc, rather than an organized attempt to gain reliable knowledge to improve reintroduction success. We reviewed 454 recent (1990-2005) peer-reviewed papers dealing with wildlife reintroductions from 101 journals. Most research has been retrospective, either opportunistic evaluations of techniques or general project summaries, and most inference is gained from post hoc interpretation of monitoring results on a species-by-species basis. Documentation of reintroduction outcomes has improved, however, and the derivation of more general principles via meta-analyses is expected to increase. The fragmentation of the reintroduction literature remains an obstacle. There is scope to improve reintroduction biology by greater application of the hypothetico-deductive method, particularly through the use of modeling approaches and well-designed experiments. Examples of fruitful approaches in reintroduction research include experimental studies to improve outcomes from the release of captive-bred animals, use of simulation modeling to identify factors affecting the viability of reintroduced populations, and the application of spatially explicit models to plan for and evaluate reintroductions. We recommend that researchers contemplating future reintroductions carefully determine a priori the specific goals, overall ecological purpose, and inherent technical and biological limitations of a given reintroduction and that evaluation processes incorporate both experimental and modeling approaches. We suggest that the best progress will be made when multidisciplinary teams of resource managers and scientists work in close collaboration and when results from comparative analyses, experiments, and modeling are combined within and among studies.}, } @article {pmid17390536, year = {2007}, author = {Booth, T and Gilbert, J and Neufeld, JD and Ball, J and Thurston, M and Chipman, K and Joint, I and Field, D}, title = {Handlebar: a flexible, web-based inventory manager for handling barcoded samples.}, journal = {BioTechniques}, volume = {42}, number = {3}, pages = {300, 302}, doi = {10.2144/000112385}, pmid = {17390536}, issn = {0736-6205}, mesh = {Computational Biology/*methods ; Computer Graphics ; Computer Systems ; Database Management Systems ; Genomics/methods ; *Internet ; Models, Genetic ; *Online Systems ; Software ; User-Computer Interface ; }, } @article {pmid17376230, year = {2007}, author = {Poptsova, MS and Gogarten, JP}, title = {The power of phylogenetic approaches to detect horizontally transferred genes.}, journal = {BMC evolutionary biology}, volume = {7}, number = {}, pages = {45}, pmid = {17376230}, issn = {1471-2148}, mesh = {Classification/*methods ; Cluster Analysis ; Computational Biology ; Gammaproteobacteria/*genetics ; Gene Transfer, Horizontal/*genetics ; *Genome, Bacterial ; Likelihood Functions ; Models, Genetic ; Multigene Family/*genetics ; *Phylogeny ; }, abstract = {BACKGROUND: Horizontal gene transfer plays an important role in evolution because it sometimes allows recipient lineages to adapt to new ecological niches. High genes transfer frequencies were inferred for prokaryotic and early eukaryotic evolution. Does horizontal gene transfer also impact phylogenetic reconstruction of the evolutionary history of genomes and organisms? The answer to this question depends at least in part on the actual gene transfer frequencies and on the ability to weed out transferred genes from further analyses. Are the detected transfers mainly false positives, or are they the tip of an iceberg of many transfer events most of which go undetected by current methods?

RESULTS: Phylogenetic detection methods appear to be the method of choice to infer gene transfers, especially for ancient transfers and those followed by orthologous replacement. Here we explore how well some of these methods perform using in silico transfers between the terminal branches of a gamma proteobacterial, genome based phylogeny. For the experiments performed here on average the AU test at a 5% significance level detects 90.3% of the transfers and 91% of the exchanges as significant. Using the Robinson-Foulds distance only 57.7% of the exchanges and 60% of the donations were identified as significant. Analyses using bipartition spectra appeared most successful in our test case. The power of detection was on average 97% using a 70% cut-off and 94.2% with 90% cut-off for identifying conflicting bipartitions, while the rate of false positives was below 4.2% and 2.1% for the two cut-offs, respectively. For all methods the detection rates improved when more intervening branches separated donor and recipient.

CONCLUSION: Rates of detected transfers should not be mistaken for the actual transfer rates; most analyses of gene transfers remain anecdotal. The method and significance level to identify potential gene transfer events represent a trade-off between the frequency of erroneous identification (false positives) and the power to detect actual transfer events.}, } @article {pmid17366282, year = {2007}, author = {Matheis, RJ and Schultheis, MT and Tiersky, LA and DeLuca, J and Millis, SR and Rizzo, A}, title = {Is learning and memory different in a virtual environment?.}, journal = {The Clinical neuropsychologist}, volume = {21}, number = {1}, pages = {146-161}, doi = {10.1080/13854040601100668}, pmid = {17366282}, issn = {1385-4046}, mesh = {Adult ; Attention ; Brain Injuries/*diagnosis/psychology/rehabilitation ; Diagnosis, Computer-Assisted/*instrumentation ; Female ; Humans ; Male ; *Memory, Short-Term ; Middle Aged ; *Neuropsychological Tests ; Orientation ; *Pattern Recognition, Visual ; Reproducibility of Results ; *Social Environment ; *User-Computer Interface ; }, abstract = {It has been suggested that virtual reality may provide a medium for producing neuropsychological measures with greater ecological validity. The present study examined the usefulness of virtual reality (VR) to assess learning and memory in individuals with traumatic brain injury (TBI). A total of 20 TBI participants were compared with 20 healthy controls on their ability to learn and recall 16 target items presented within a VR-based generic office environment. The results indicated that VR memory testing accurately distinguished the TBI group from controls. Additionally, non-memory-impaired TBI participants acquired targets at the same rate as HC participants. Finally, there was a significant relationship between the VR Office and a standard neuropsychological measure of memory, suggesting the construct validity of the task. These findings suggest that the VR Office provides a viable medium for measuring learning and memory. The present results provide preliminary support for the ecological validity of the VR Office, which ultimately can improve assessment of real-world functioning following TBI.}, } @article {pmid17363133, year = {2008}, author = {Chang, NB and Parvathinathan, G and Breeden, JB}, title = {Combining GIS with fuzzy multicriteria decision-making for landfill siting in a fast-growing urban region.}, journal = {Journal of environmental management}, volume = {87}, number = {1}, pages = {139-153}, doi = {10.1016/j.jenvman.2007.01.011}, pmid = {17363133}, issn = {0301-4797}, mesh = {*Decision Support Techniques ; Fuzzy Logic ; *Geographic Information Systems ; *Refuse Disposal ; Urbanization ; }, abstract = {Landfill siting is a difficult, complex, tedious, and protracted process requiring evaluation of many different criteria. This paper presents a fuzzy multicriteria decision analysis alongside with a geospatial analysis for the selection of landfill sites. It employs a two-stage analysis synergistically to form a spatial decision support system (SDSS) for waste management in a fast-growing urban region, south Texas. The first-stage analysis makes use of the thematic maps in Geographical information system (GIS) in conjunction with environmental, biophysical, ecological, and socioeconomic variables leading to support the second-stage analysis using the fuzzy multicriteria decision-making (FMCDM) as a tool. It differs from the conventional methods of integrating GIS with MCDM for landfill selection because the approach follows two sequential steps rather than a full-integrated scheme. The case study was made for the city of Harlingen in south Texas, which is rapidly evolving into a large urban area due to its vantage position near the US-Mexico borderlands. The purpose of GIS was to perform an initial screening process to eliminate unsuitable land followed by utilization of FMCDM method to identify the most suitable site using the information provided by the regional experts with reference to five chosen criteria. Research findings show that the proposed SDSS may aid in recognizing the pros and cons of potential areas for the localization of landfill sites in any study region. Based on initial GIS screening and final FMCDM assessment, "site 1" was selected as the most suitable site for the new landfill in the suburban area of the City of Harlingen. Sensitivity analysis was performed using Monte Carlo simulation where the decision weights associated with all criteria were varied to investigate their relative impacts on the rank ordering of the potential sites in the second stage. Despite variations of the decision weights within a range of 20%, it shows that "site 1" remains its comparative advantage in the final site selection process.}, } @article {pmid17362414, year = {2007}, author = {Carey, JM and Beilin, R and Boxshall, A and Burgman, MA and Flander, L}, title = {Risk-based approaches to deal with uncertainty in a data-poor system: stakeholder involvement in hazard identification for marine national parks and marine sanctuaries in Victoria, Australia.}, journal = {Risk analysis : an official publication of the Society for Risk Analysis}, volume = {27}, number = {1}, pages = {271-281}, doi = {10.1111/j.1539-6924.2006.00875.x}, pmid = {17362414}, issn = {0272-4332}, mesh = {*Conservation of Natural Resources ; Ecology/*methods ; Environment ; Information Systems ; *Risk Assessment ; Uncertainty ; Victoria ; }, abstract = {Management responsibilities for the system of marine national parks and sanctuaries declared in Victoria, Australia in 2002 have created imperatives for robust, scientifically defendable approaches to identifying threats to valued ecological attributes of the parks, setting management priorities, and developing monitoring systems. We are developing a protocol for ecological risk assessment in the parks that has due regard for the perception of risks by individuals, and ensures that stakeholder values are an intrinsic part of decision making. The inclusive and transparent protocol provides an opportunity for stakeholder involvement in the identification of valued attributes, as well as in the assessment of associated risks. Our approach brings together ideas about how science enters the community engagement domain in ways that promote collaboration and transparency in decision making. A series of stakeholder workshops across the state drew on the expertise of agency staff, community groups, fishers, industry representatives, academics, and knowledgeable park neighbors to identify hazards of major concern in the parks. Many hazards involved predictable, tangible threats like pollution and exotic species, but the approach also identified a number of less obvious threats related to governance issues and the knowledge-base for the parks. Importantly, the workshops with their broad range of stakeholders identified threats not previously considered by the management agency in its internal assessments, and several of these "new" threats are already the subject of action by the agency. The deliberate incorporation of local knowledge and local networks in the risk assessment process also provided opportunities for greater engagement of stakeholders with the management agency.}, } @article {pmid17362349, year = {2006}, author = {Matsuba, C and Merilä, J}, title = {Genome size variation in the common frog Rana temporaria.}, journal = {Hereditas}, volume = {143}, number = {2006}, pages = {155-158}, doi = {10.1111/j.2006.0018-0661.01919.x}, pmid = {17362349}, issn = {1601-5223}, mesh = {Animals ; Data Interpretation, Statistical ; Female ; Flow Cytometry ; *Genetic Variation ; Genetics, Population ; *Genome ; Male ; Rana temporaria/*genetics ; }, abstract = {Genome size variation in the common frog (Rana temporaria) was investigated with flow cytometry in three latitudinally separated populations in Sweden to see whether it could provide a useful tool for sex-identification in this species. Depending on the sex and population, per cell DNA content (2C value) varied from 8.823 to 11.266 pg with a mean (+/- SE) 2C value of 9.961+/-0.083 pg. Analysis of variance revealed significant differences in genome size among populations and between sexes. Females had ca 3% larger genomes (x=10.133+/-0.068 pg) than males (x=9.832+/-0.068 pg) in all of the populations (sex x population interaction: P>0.10). Individuals from the southern-most population had significantly (x=9.330+/-0.081 pg) smaller genomes than those from the more northern populations (x=10.032+/-0.085 and x=10.584+/-0.085 pg, respectively). These results are in line with the interpretation that males in the common frog are the heterogametic sex, and that there exists large (up to 12%) geographic variation in genome size in this species. However, the sex differences in the genome size are too small to be useful in individual sex identification.}, } @article {pmid17361145, year = {2007}, author = {Ledford, H}, title = {Microbes reveal extent of biodiversity.}, journal = {Nature}, volume = {446}, number = {7133}, pages = {240-241}, doi = {10.1038/446240a}, pmid = {17361145}, issn = {1476-4687}, mesh = {*Biodiversity ; Databases, Genetic ; Genomics/trends ; Marine Biology ; Microbiology ; Oceans and Seas ; Proteins/*classification/*genetics/isolation & purification ; Seawater/*microbiology ; Sequence Analysis, DNA/trends ; }, } @article {pmid17360642, year = {2007}, author = {Saunders, MA and Liang, H and Li, WH}, title = {Human polymorphism at microRNAs and microRNA target sites.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {104}, number = {9}, pages = {3300-3305}, pmid = {17360642}, issn = {0027-8424}, mesh = {Computational Biology ; Genome, Human/*genetics ; Humans ; MicroRNAs/*genetics ; Polymorphism, Single Nucleotide/*genetics ; Selection, Genetic ; }, abstract = {MicroRNAs (miRNAs) function as endogenous translational repressors of protein-coding genes in animals by binding to target sites in the 3' UTRs of mRNAs. Because a single nucleotide change in the sequence of a target site can affect miRNA regulation, naturally occurring SNPs in target sites are candidates for functional variation that may be of interest for biomedical applications and evolutionary studies. However, little is known to date about variation among humans at miRNAs and their target sites. In this study, we analyzed publicly available SNP data in context with miRNAs and their target sites throughout the human genome, and we found a relatively low level of variation in functional regions of miRNAs, but an appreciable level of variation at target sites. Approximately 400 SNPs were found at experimentally verified target sites or predicted target sites that are otherwise evolutionarily conserved across mammals. Moreover, approximately 250 SNPs potentially create novel target sites for miRNAs in humans. If some variants have functional effects, they might confer phenotypic differences among humans. Although the majority of these SNPs appear to be evolving under neutrality, interestingly, some of these SNPs are found at relatively high population frequencies even in experimentally verified targets, and a few variants are associated with atypically long-range haplotypes that may have been subject to recent positive selection.}, } @article {pmid17347106, year = {2007}, author = {Han, B and Xue, Y and Li, J and Deng, XW and Zhang, Q}, title = {Rice functional genomics research in China.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {362}, number = {1482}, pages = {1009-1021}, pmid = {17347106}, issn = {0962-8436}, mesh = {China ; Cloning, Molecular ; Databases, Genetic ; Genes, Plant ; Genetic Predisposition to Disease ; *Genome, Plant ; Genomics/*methods ; Oligonucleotide Array Sequence Analysis/methods ; Oryza/*genetics/growth & development ; Plant Diseases/genetics/microbiology ; Reproduction/genetics ; }, abstract = {Rice functional genomics is a scientific approach that seeks to identify and define the function of rice genes, and uncover when and how genes work together to produce phenotypic traits. Rapid progress in rice genome sequencing has facilitated research in rice functional genomics in China. The Ministry of Science and Technology of China has funded two major rice functional genomics research programmes for building up the infrastructures of the functional genomics study such as developing rice functional genomics tools and resources. The programmes were also aimed at cloning and functional analyses of a number of genes controlling important agronomic traits from rice. National and international collaborations on rice functional genomics study are accelerating rice gene discovery and application.}, } @article {pmid17345132, year = {2007}, author = {Kowalchuk, GA and Speksnijder, AG and Zhang, K and Goodman, RM and van Veen, JA}, title = {Finding the needles in the metagenome haystack.}, journal = {Microbial ecology}, volume = {53}, number = {3}, pages = {475-485}, pmid = {17345132}, issn = {0095-3628}, mesh = {Cloning, Molecular/methods ; Computational Biology/methods ; *Environmental Microbiology ; Environmental Monitoring/*methods ; Genetic Variation ; Genomics/*methods/trends ; Phylogeny ; }, abstract = {In the collective genomes (the metagenome) of the microorganisms inhabiting the Earth's diverse environments is written the history of life on this planet. New molecular tools developed and used for the past 15 years by microbial ecologists are facilitating the extraction, cloning, screening, and sequencing of these genomes. This approach allows microbial ecologists to access and study the full range of microbial diversity, regardless of our ability to culture organisms, and provides an unprecedented access to the breadth of natural products that these genomes encode. However, there is no way that the mere collection of sequences, no matter how expansive, can provide full coverage of the complex world of microbial metagenomes within the foreseeable future. Furthermore, although it is possible to fish out highly informative and useful genes from the sea of gene diversity in the environment, this can be a highly tedious and inefficient procedure. Microbial ecologists must be clever in their pursuit of ecologically relevant, valuable, and niche-defining genomic information within the vast haystack of microbial diversity. In this report, we seek to describe advances and prospects that will help microbial ecologists glean more knowledge from investigations into metagenomes. These include technological advances in sequencing and cloning methodologies, as well as improvements in annotation and comparative sequence analysis. More significant, however, will be ways to focus in on various subsets of the metagenome that may be of particular relevance, either by limiting the target community under study or improving the focus or speed of screening procedures. Lastly, given the cost and infrastructure necessary for large metagenome projects, and the almost inexhaustible amount of data they can produce, trends toward broader use of metagenome data across the research community coupled with the needed investment in bioinformatics infrastructure devoted to metagenomics will no doubt further increase the value of metagenomic studies in various environments.}, } @article {pmid17345010, year = {2007}, author = {Satapathy, DR and Krupadam, RJ and Kumar, LP and Wate, SR}, title = {The application of satellite data for the quantification of mangrove loss and coastal management in the Godavari estuary, East Coast of India.}, journal = {Environmental monitoring and assessment}, volume = {134}, number = {1-3}, pages = {453-469}, pmid = {17345010}, issn = {0167-6369}, mesh = {Aquaculture ; *Avicennia ; Biodiversity ; *Conservation of Natural Resources ; Extraction and Processing Industry ; Geographic Information Systems ; India ; Petroleum ; Rivers ; Satellite Communications ; Seawater ; }, abstract = {The mangrove formations of Godavari estuary are due to silting over many centuries. The estuary covers an area of 62,000 ha of which dense Coringa mangrove forest spread in 6,600 ha. Satellite sensor data was used to detect change in the mangrove cover for a period of 12 years (1992-2004). It was found that an area of about 1,250 ha of mangroves was destroyed by anthropogenic interference like aquaculture, and tree felling etc. It was found that mangrove's spectral response/digital number (DN) value is much lower than non-mangrove vegetation such as plantation and paddy fields in SWIR band. By taking this as an advantage, spectral data was utilized for clear demarcation of mangroves from nearby paddy fields and other vegetation. Simpson's diversity index, which is a measure of biodiversity, was found to be 0.09, showing mangroves dominance. Ecological parameters like mud-flats/swamps, mangrove cover alterations, and biodiversity status are studied in detail for a period of 12 years. The increase in mangrove front towards coast was delineated using remote sensing data. The major advantages of remote sensing data is monitoring of change periodically. The combination of moderate and high-resolution data provided detailed coastal land use maps for implementing coastal regulation measures. The classification accuracy has been achieved is 90%. Overall, simple and viable measures are suggested based on multi-spectral data to sustain this sensitive coastal ecology.}, } @article {pmid17345006, year = {2007}, author = {Alparslan, E and Aydöner, C and Tufekci, V and Tüfekci, H}, title = {Water quality assessment at Omerli Dam using remote sensing techniques.}, journal = {Environmental monitoring and assessment}, volume = {135}, number = {1-3}, pages = {391-398}, doi = {10.1007/s10661-007-9658-6}, pmid = {17345006}, issn = {0167-6369}, mesh = {Chlorophyll/analysis ; *Ecotoxicology ; Environmental Monitoring/*methods ; *Geographic Information Systems ; *Marine Biology ; Models, Theoretical ; Phosphates/analysis ; Satellite Communications ; Spacecraft ; Turkey ; Water Pollutants/*analysis ; Water Supply/*analysis/standards ; }, abstract = {Water quality at Omerli Dam, which is a vital potable water resource of Istanbul City, Turkey was assessed using the first four bands of Landsat 7-ETM satellite data, acquired in May 2001 and water quality parameters, such as chlorophyll-a, suspended solid matter, secchi disk and total phosphate measured at several measurement stations at Omerli Dam during satellite image acquisition time and archived at the Marine Pollution and Ecotoxicology laboratory of the Marmara Research Center, where this study was carried out. Establishing a relationship between this data, and the pixel reflectance values in the satellite image, chlorophyll-a, suspended solid matter, secchi disk and total phosphate maps were produced for the Omerli Dam.}, } @article {pmid17342432, year = {2007}, author = {Ferreira, JG and Vale, C and Soares, CV and Salas, F and Stacey, PE and Bricker, SB and Silva, MC and Marques, JC}, title = {Monitoring of coastal and transitional waters under the E.U. Water Framework Directive.}, journal = {Environmental monitoring and assessment}, volume = {135}, number = {1-3}, pages = {195-216}, pmid = {17342432}, issn = {0167-6369}, mesh = {Animals ; *Conservation of Natural Resources ; Ecosystem ; *Environmental Monitoring ; European Union ; Eutrophication/drug effects/physiology ; Fresh Water ; *Geographic Information Systems ; Humans ; *Marine Biology ; Risk Assessment ; Seawater ; Water Pollutants/*analysis/toxicity ; Water Supply ; }, abstract = {A set of guidelines are presented for the definition of monitoring plans in coastal and transitional (estuarine and lagoonal) systems subject to the European Union Water Framework Directive - WFD (2000/60/EC). General principles of best practice in monitoring are outlined, including (a) the definition of three types of broad management objectives: water quality, conservation, and human use, to which the general public may easily relate. These will define the core and research indicators (WFD quality elements) to be used for monitoring; (b) priorities and optimisation in a (financially and logistically) resource-constrained environment; (c) quality assurance; and (d) assessment of monitoring success: this should focus on the outputs, i.e. the internal audit of the monitoring activity, and on the outcomes. The latter component assesses programme effectiveness, i.e. environmental success based on a set of clearly-defined targets, and informs management action. The second part of this work discusses the approach and actions to be carried out for implementing WFD surveillance, operational and investigative monitoring. Appropriate spatial and temporal scales for surveillance monitoring of different indicators are suggested, and operational monitoring is classified into either screening or verification procedures, with an emphasis on the relationship between drivers, pressure, state and response. WFD investigative monitoring is interpreted as applied research, and thus guidelines cannot be prescriptive, except insofar as to provide examples of currently acceptable approaches. Specific case studies are presented for both operational (coastal eutrophication control) and investigative monitoring (harmful algal blooms), in order to illustrate the practical application of these monitoring guidelines. Further information is available at http://www.monae.org/ .}, } @article {pmid17337557, year = {2007}, author = {Lennon, JT}, title = {Diversity and metabolism of marine bacteria cultivated on dissolved DNA.}, journal = {Applied and environmental microbiology}, volume = {73}, number = {9}, pages = {2799-2805}, pmid = {17337557}, issn = {0099-2240}, mesh = {Bacteria/growth & development/*metabolism ; Base Sequence ; *Biodiversity ; Cloning, Molecular ; Cluster Analysis ; Computational Biology ; DNA/*metabolism ; Massachusetts ; Molecular Sequence Data ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Seawater/*chemistry/*microbiology ; Sequence Analysis, DNA ; *Water Microbiology ; }, abstract = {Dissolved DNA (dDNA) is a potentially important source of energy and nutrients in aquatic ecosystems. However, little is known about the identity, metabolism, and interactions of the microorganisms capable of consuming dDNA. Bacteria from Eel Pond (Woods Hole, MA) were cultivated on low-molecular-weight (LMW) or high-molecular-weight (HMW) dDNA, which served as the primary source of carbon, nitrogen, and phosphorus. Cloning and sequencing of 16S rRNA genes revealed that distinct bacterial assemblages with comparable levels of taxon richness developed on LMW and HMW dDNA. Since the LMW and HMW dDNA used in this study were stoichiometrically identical, the results confirm that the size alone of dissolved organic matter can influence bacterial community composition. Variation in the growth and metabolism of isolates provided insight into mechanisms that may have generated differences in bacterial community composition. For example, bacteria from LMW dDNA enrichments generally grew better on LMW dDNA than on HMW dDNA. In contrast, bacteria isolated from HMW dDNA enrichments were more effective at degrading HMW dDNA than bacteria isolated from LMW dDNA enrichments. Thus, marine bacteria may experience a trade-off between their ability to compete for LMW dDNA and their ability to access HMW dDNA via extracellular nuclease production. Together, the results of this study suggest that dDNA turnover in marine ecosystems may involve a succession of microbial assemblages with specialized ecological strategies.}, } @article {pmid17334056, year = {2006}, author = {Wijnbladh, E and Jönsson, BF and Kumblad, L}, title = {Marine ecosystem modeling beyond the box: using GIS to study carbon fluxes in a coastal ecosystem.}, journal = {Ambio}, volume = {35}, number = {8}, pages = {484-495}, doi = {10.1579/0044-7447(2006)35[486:membtb]2.0.co;2}, pmid = {17334056}, issn = {0044-7447}, mesh = {Carbon/*analysis/chemistry/metabolism ; *Ecosystem ; *Geographic Information Systems ; Marine Biology/*methods ; *Models, Theoretical ; Oceans and Seas ; Radioactive Waste ; Radioisotopes ; Safety ; Sweden ; Waste Management ; }, abstract = {Studies of carbon fluxes in marine ecosystems are often done by using box model approaches with basin size boxes, or highly resolved 3D models, and an emphasis on the pelagic component of the ecosystem. Those approaches work well in the ocean proper, but can give rise to considerable problems when applied to coastal systems, because of the scale of certain ecological niches and the fact that benthic organisms are the dominant functional group of the ecosystem. In addition, 3D models require an extensive modeling effort. In this project, an intermediate approach based on a high resolution (20x20 m) GIS data-grid has been developed for the coastal ecosystem in the Laxemar area (Baltic Sea, Sweden) based on a number of different site investigations. The model has been developed in the context of a safety assessment project for a proposed nuclear waste repository, in which the fate of hypothetically released radionuclides from the planned repository is estimated. The assessment project requires not only a good understanding of the ecosystem dynamics at the site, but also quantification of stocks and flows of matter in the system. The data-grid was then used to set up a carbon budget describing the spatial distribution of biomass, primary production, net ecosystem production and thus where carbon sinks and sources are located in the area. From these results, it was clear that there was a large variation in ecosystem characteristics within the basins and, on a larger scale, that the inner areas are net producing and the outer areas net respiring, even in shallow phytobenthic communities. Benthic processes had a similar or larger influence on carbon fluxes as advective processes in inner areas, whereas the opposite appears to be true in the outer basins. As many radionuclides are expected to follow the pathways of organic matter in the environment, these findings enhance our abilities to realistically describe and predict their fate in the ecosystem.}, } @article {pmid17327208, year = {2007}, author = {Buckley, LB and Jetz, W}, title = {Environmental and historical constraints on global patterns of amphibian richness.}, journal = {Proceedings. Biological sciences}, volume = {274}, number = {1614}, pages = {1167-1173}, pmid = {17327208}, issn = {0962-8452}, mesh = {*Amphibians ; Animals ; *Biodiversity ; *Biological Evolution ; *Climate ; *Demography ; *Environment ; Geographic Information Systems ; Geography ; *Models, Theoretical ; Species Specificity ; }, abstract = {Our knowledge of the broad-scale ecology of vertebrate ectotherms remains very limited. Despite ongoing declines and sensitivity to environmental change, amphibian distributions are particularly poorly understood. We present a global analysis of contemporary environmental and historical constraints on amphibian richness, the first for an ectotherm clade at this scale. Amphibians are presumed to experience environmental constraints distinct from those of better studied endothermic taxa due to their stringent water requirements and the temperature dependence of their energetic costs and performance. Single environmental predictors set upper bounds on, but do not exclusively determine, amphibian richness. Accounting for differing regional histories of speciation and extinction helps resolve triangular or scattered relationships between core environmental predictors and amphibian richness, as the relationships' intercepts or slopes can vary regionally. While the magnitude of richness is strongly determined by regional history, within-region patterns are consistently jointly driven by water and temperature. This confirms that ecophysiological constraints extend to the broad scale. This coupling suggests that shifts in climatic regimes will probably have dramatic consequences for amphibians. Our results illustrate how the environmental and historical explanations of species richness gradients can be reconciled and how the perspectives are complements for understanding broad-scale patterns of diversity.}, } @article {pmid17319236, year = {2006}, author = {Adams, SA and Hebert, JR and Bolick-Aldrich, S and Daguise, VG and Mosley, CM and Modayil, MV and Berger, SH and Teas, J and Mitas, M and Cunningham, JE and Steck, SE and Burch, J and Butler, WM and Horner, MJ and Brandt, HM}, title = {Breast cancer disparities in South Carolina: early detection, special programs, and descriptive epidemiology.}, journal = {Journal of the South Carolina Medical Association (1975)}, volume = {102}, number = {7}, pages = {231-239}, pmid = {17319236}, issn = {0038-3139}, support = {U01 CA114601/CA/NCI NIH HHS/United States ; U01 CA114601-01/CA/NCI NIH HHS/United States ; 1 U01 CA114601-01/CA/NCI NIH HHS/United States ; U55CCU421931/CC/ODCDC CDC HHS/United States ; }, mesh = {Black or African American/*statistics & numerical data ; Breast Neoplasms/epidemiology/ethnology/*prevention & control ; *Community Networks ; Female ; *Health Services Accessibility ; Humans ; Incidence ; Mass Screening ; *Preventive Medicine ; Socioeconomic Factors ; South Carolina/epidemiology ; White People/statistics & numerical data ; }, abstract = {A discrepancy exists between mortality and incidence rates between African-American and European-American women in South Carolina. The relationship between tumor grade and the estrogen/ progesterone receptor status is different in African-American and European-American women. African-American women with breast cancer should be encouraged to participate in clinical trials, with the goal of identifying biological factors that might facilitate the detection of tumors at an earlier stage and the development of more effective therapies. The most important of our goals is to design studies to reduce the incidence of the disease and interventions to improve survival and quality of life. The importance of participation in research cannot be overstated. Reproductive factors such as early pregnancy and multiple pregnancies are strongly related to breast cancer risk, however, promotion of these factors as a "prevention strategy," clearly does not lead to cogent, comprehensive public health messages. Data from ecological and migrant studies point clearly to other factors that may be important such as diet. Additional research around primary prevention strategies is needed. In addition, yearly mammograms (secondary prevention) are recommended for women over 50 years old or those with relatives who have developed breast cancer. The Best Chance Network, as a provider of screenings to low-income, uninsured women, has helped to narrow the racial gap in screening that otherwise might exist (see Figures 3 and 4) to a large extent. The determination for timing of surgery after diagnosis needs additional consideration. For example, factors such as effective screening in younger women, timing of screening and surgery in relationship to the ovulatory cycle, and season of screening and surgery may have a great impact on outcomes and may offer some insight into the process of carcinogenesis and therapeutic efficacy. Research into this area is so novel that the impact on possible ethnic disparities is completely unknown. The South Carolina Cancer Disparities Community Network (SCCDCN) has identified the following areas as potential research foci: Identification of small media interventions as an effective strategy to motivate targeted populations, especially those least likely to seek screening for breast cancer and those least likely to participate in research programs (African-Americans). Utilization of breast cancer survivors, self-identified as community natural helpers, can share their experiences with their church congregation. A replication of such a program in South Carolina has great potential because of the strong presence of the church, especially in rural parts of the state. Programs that closely integrate religion with screening women for breast cancer are promising in this state. Development of a mammography registry whereby information on all mammography procedures would be collected within a single database system (much like a central cancer registry). This would aid in identifying population groups that could be targeted for special programs and in the examination and exploration of the most appropriate modalities of detection. Such a resource could also be a useful tool to encourage screening. Thus, this focus area has the potential to benefit epidemiologic and health promotion research on many different levels. Additional breast cancer screening methods should not be overlooked as a potential research focus. Mammography is not the only valid screening method for breast cancer. Magnetic resonance imaging has shown some promise for screening among women with a genetic predisposition for cancer. Another promising avenue is thermography. Because detection rates may depend on age, ethnicity, and breast mammographic characteristics, women for whom regular screening methods do not detect their cancers (e.g. older age, African-American ethnicity, dense breasts) must be identified and other screening methods promoted within these populations. The above-mentioned mammography registry would support this type of research.}, } @article {pmid17319230, year = {2006}, author = {Yen, KL and Horner, MJ and Reed, SG and Daguise, VG and Bolick-Aldrich, SW and Young, MR and Day, TA and Wood, PA and Hebert, JR}, title = {Head and neck cancer disparities in South Carolina: descriptive epidemiology, early detection, and special programs.}, journal = {Journal of the South Carolina Medical Association (1975)}, volume = {102}, number = {7}, pages = {192-200}, pmid = {17319230}, issn = {0038-3139}, support = {1 U01 CA114601-01/CA/NCI NIH HHS/United States ; H75/CCH424532/CC/ODCDC CDC HHS/United States ; U55CCU421931/CC/ODCDC CDC HHS/United States ; }, mesh = {Black or African American ; *Community Networks ; Head and Neck Neoplasms/epidemiology/ethnology/*prevention & control ; *Health Services Accessibility ; Humans ; Incidence ; *Preventive Medicine ; Socioeconomic Factors ; South Carolina/epidemiology ; }, abstract = {Recognizing that relatively easily detected precancerous lesions precede many cancers, there is a need to investigate the effectiveness of early interventions on the reduction of incidence rates in well-designed large randomized control trials. If early detection can reduce mortality rates of OPCA, evaluation of the capacity of dentists and physicians to screen or detect precancerous lesions related to oral cancers may have merit. Presently, there is a paucity of research regarding ecological barriers in the healthcare system, and improving access to adequate dental and medical care among the rural minority population in South Carolina certainly deserves emphasis. Additional research, specific to South Carolina, which includes comprehensive assessment of multiple social, behavioral, and biological factors, is needed. Interdisciplinary collaboration will be particularly important to dissect key factors contributing to the racial disparities observed in South Carolina. These differences should be taken into account while recommending and implementing public health strategies for the control of these cancers.}, } @article {pmid17306022, year = {2007}, author = {Guerra, CA and Hay, SI and Lucioparedes, LS and Gikandi, PW and Tatem, AJ and Noor, AM and Snow, RW}, title = {Assembling a global database of malaria parasite prevalence for the Malaria Atlas Project.}, journal = {Malaria journal}, volume = {6}, number = {}, pages = {17}, pmid = {17306022}, issn = {1475-2875}, support = {079091/WT_/Wellcome Trust/United Kingdom ; 076951/WT_/Wellcome Trust/United Kingdom ; 079080/WT_/Wellcome Trust/United Kingdom ; 081829/WT_/Wellcome Trust/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; }, mesh = {Animals ; *Databases, Factual ; Geography ; Humans ; Malaria/*epidemiology/*parasitology ; Plasmodium/*classification/*isolation & purification ; Prevalence ; }, abstract = {BACKGROUND: Open access to databases of information generated by the research community can synergize individual efforts and are epitomized by the genome mapping projects. Open source models for outputs of scientific research funded by tax-payers and charities are becoming the norm. This has yet to be extended to malaria epidemiology and control.

METHODS: The exhaustive searches and assembly process for a global database of malaria parasite prevalence as part of the Malaria Atlas Project (MAP) are described. The different data sources visited and how productive these were in terms of availability of parasite rate (PR) data are presented, followed by a description of the methods used to assemble a relational database and an associated geographic information system. The challenges facing spatial data assembly from varied sources are described in an effort to help inform similar future applications.

RESULTS: At the time of writing, the MAP database held 3,351 spatially independent PR estimates from community surveys conducted since 1985. These include 3,036 Plasmodium falciparum and 1,347 Plasmodium vivax estimates in 74 countries derived from 671 primary sources. More than half of these data represent malaria prevalence after the year 2000.

CONCLUSION: This database will help refine maps of the global spatial limits of malaria and be the foundation for the development of global malaria endemicity models as part of MAP. A widespread application of these maps is envisaged. The data compiled and the products generated by MAP are planned to be released in June 2009 to facilitate a more informed approach to global malaria control.}, } @article {pmid17305850, year = {2007}, author = {Bouck, A and Vision, T}, title = {The molecular ecologist's guide to expressed sequence tags.}, journal = {Molecular ecology}, volume = {16}, number = {5}, pages = {907-924}, doi = {10.1111/j.1365-294X.2006.03195.x}, pmid = {17305850}, issn = {0962-1083}, mesh = {Adaptation, Biological/genetics ; Base Sequence ; Computational Biology ; Ecology/*methods ; Evolution, Molecular ; *Expressed Sequence Tags ; Gene Expression Profiling ; Genetic Markers ; Genomics ; Molecular Sequence Data ; }, abstract = {Genomics and bioinformatics have great potential to help address numerous topics in ecology and evolution. Expressed sequence tags (ESTs) can bridge genomics and molecular ecology because they can provide a means of accessing the gene space of almost any organism. We review how ESTs have been used in molecular ecology research in the last several years by providing sequence data for the design of molecular markers, genome-wide studies of gene expression and selection, the identification of candidate genes underlying adaptation, and the basis for studies of gene family and genome evolution. Given the tremendous recent advances in inexpensive sequencing technologies, we predict that molecular ecologists will increasingly be developing and using EST collections in the years to come. With this in mind, we close our review by discussing aspects of EST resource development of particular relevance for molecular ecologists.}, } @article {pmid17302838, year = {2007}, author = {Altizer, S and Nunn, CL and Lindenfors, P}, title = {Do threatened hosts have fewer parasites? A comparative study in primates.}, journal = {The Journal of animal ecology}, volume = {76}, number = {2}, pages = {304-314}, doi = {10.1111/j.1365-2656.2007.01214.x}, pmid = {17302838}, issn = {0021-8790}, mesh = {Animals ; Animals, Wild/classification/microbiology/parasitology/virology ; Biodiversity ; Databases as Topic ; Host-Parasite Interactions ; Humans ; Parasitic Diseases, Animal/*epidemiology/transmission ; Phylogeny ; Population Density ; Prevalence ; Primate Diseases/*epidemiology/transmission ; Primates/classification/*microbiology/*parasitology/virology ; Species Specificity ; }, abstract = {1. Parasites and infectious diseases have become a major concern in conservation biology, in part because they can trigger or accelerate species or population declines. Focusing on primates as a well-studied host clade, we tested whether the species richness and prevalence of parasites differed between threatened and non-threatened host species. 2. We collated data on 386 species of parasites (including viruses, bacteria, protozoa, helminths and arthropods) reported to infect wild populations of 36 threatened and 81 non-threatened primate species. Analyses controlled for uneven sampling effort and host phylogeny. 3. Results showed that total parasite species richness was lower among threatened primates, supporting the prediction that small, isolated host populations harbour fewer parasite species. This trend was consistent across three major parasite groups found in primates (helminths, protozoa and viruses). Counter to our predictions, patterns of parasite species richness were independent of parasite transmission mode and the degree of host specificity. 4. We also examined the prevalence of selected parasite genera among primate sister-taxa that differed in their ranked threat categories, but found no significant differences in prevalence between threatened and non-threatened hosts. 5. This study is the first to demonstrate differences in parasite richness relative to host threat status. Results indicate that human activities and host characteristics that increase the extinction risk of wild animal species may lead simultaneously to the loss of parasites. Lower average parasite richness in threatened host taxa also points to the need for a better understanding of the cascading effects of host biodiversity loss for affiliated parasite species.}, } @article {pmid17301914, year = {2006}, author = {Opromolla, PA and Dalben, I and Cardim, M}, title = {[Geostatistical analysis of leprosy cases in the State of São Paulo, 1991-2002].}, journal = {Revista de saude publica}, volume = {40}, number = {5}, pages = {907-913}, doi = {10.1590/s0034-89102006000600022}, pmid = {17301914}, issn = {0034-8910}, mesh = {Adult ; Analysis of Variance ; Brazil/epidemiology ; Disease Notification ; Female ; Geographic Information Systems ; Humans ; Leprosy/*epidemiology ; Male ; Middle Aged ; Models, Statistical ; Prevalence ; Residence Characteristics ; Topography, Medical/*statistics & numerical data ; }, abstract = {OBJECTIVE: To analyze the spatial pattern of leprosy case occurrences in order to identify areas with a probability of disease transmission risks.

METHODS: This was an ecological study in which the analysis units were municipalities in the State of São Paulo that were georeferenced at their centroids. The data source was the electronic database of notified leprosy cases at the Epidemiological Surveillance Center of the State of São Paulo, from 1991 to 2001. Geostatistical techniques were used for detecting areas with a probability of leprosy risk, and for quantifying the spatial dependency of cases.

RESULTS: The spatial dependence detected extended outwards to 0.55 degrees from the georeferenced coordinates, which corresponded to approximately 60 km. The main areas identified as presenting a probability of risk were the northeastern, northern and northwestern regions of the State.

CONCLUSIONS: Verification of areas with the probability of leprosy risk using spatial dependence analysis may be a useful tool for assessing health conditions and planning budget allocations.}, } @article {pmid17300727, year = {2007}, author = {Slate, J and Hale, MC and Birkhead, TR}, title = {Simple sequence repeats in zebra finch (Taeniopygia guttata) expressed sequence tags: a new resource for evolutionary genetic studies of passerines.}, journal = {BMC genomics}, volume = {8}, number = {}, pages = {52}, pmid = {17300727}, issn = {1471-2164}, support = {BB/E017509/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; Chickens/genetics ; Contig Mapping ; Databases, Protein ; *Evolution, Molecular ; *Expressed Sequence Tags ; Finches/*genetics ; Genome ; Passeriformes/*genetics ; Sequence Homology, Amino Acid ; }, abstract = {BACKGROUND: Passerines (perching birds) are widely studied across many biological disciplines including ecology, population biology, neurobiology, behavioural ecology and evolutionary biology. However, understanding the molecular basis of relevant traits is hampered by the paucity of passerine genomics tools. Efforts to address this problem are underway, and the zebra finch (Taeniopygia guttata) will be the first passerine to have its genome sequenced. Here we describe a bioinformatic analysis of zebra finch expressed sequence tag (EST) Genbank entries.

RESULTS: A total of 48,862 ESTs were downloaded from GenBank and assembled into contigs, representing an estimated 17,404 unique sequences. The unique sequence set contained 638 simple sequence repeats (SSRs) or microsatellites of length > or =20 bp and purity > or =90% and 144 simple sequence repeats of length > or =30 bp. A chromosomal location for the majority of SSRs was predicted by BLASTing against assembly 2.1 of the chicken genome sequence. The relative exonic location (5' untranslated region, coding region or 3' untranslated region) was predicted for 218 of the SSRs, by BLAST search against the ENSEMBL chicken peptide database. Ten loci were examined for polymorphism in two zebra finch populations and two populations of a distantly related passerine, the house sparrow Passer domesticus. Linkage was confirmed for four loci that were predicted to reside on the passerine homologue of chicken chromosome 7.

CONCLUSION: We show that SSRs are abundant within zebra finch ESTs, and that their genomic location can be predicted from sequence similarity with the assembled chicken genome sequence. We demonstrate that a useful proportion of zebra finch EST-SSRs are likely to be polymorphic, and that they can be used to build a linkage map. Finally, we show that many zebra finch EST-SSRs are likely to be useful in evolutionary genetic studies of other passerines.}, } @article {pmid17299587, year = {2007}, author = {Getz, WM and Fortmann-Roe, S and Cross, PC and Lyons, AJ and Ryan, SJ and Wilmers, CC}, title = {LoCoH: nonparameteric kernel methods for constructing home ranges and utilization distributions.}, journal = {PloS one}, volume = {2}, number = {2}, pages = {e207}, pmid = {17299587}, issn = {1932-6203}, mesh = {Animals ; Buffaloes ; Demography ; Ecology/*statistics & numerical data ; Geographic Information Systems ; *Homing Behavior ; South Africa ; *Statistics, Nonparametric ; }, abstract = {Parametric kernel methods currently dominate the literature regarding the construction of animal home ranges (HRs) and utilization distributions (UDs). These methods frequently fail to capture the kinds of hard boundaries common to many natural systems. Recently a local convex hull (LoCoH) nonparametric kernel method, which generalizes the minimum convex polygon (MCP) method, was shown to be more appropriate than parametric kernel methods for constructing HRs and UDs, because of its ability to identify hard boundaries (e.g., rivers, cliff edges) and convergence to the true distribution as sample size increases. Here we extend the LoCoH in two ways: "fixed sphere-of-influence," or r-LoCoH (kernels constructed from all points within a fixed radius r of each reference point), and an "adaptive sphere-of-influence," or a-LoCoH (kernels constructed from all points within a radius a such that the distances of all points within the radius to the reference point sum to a value less than or equal to a), and compare them to the original "fixed-number-of-points," or k-LoCoH (all kernels constructed from k-1 nearest neighbors of root points). We also compare these nonparametric LoCoH to parametric kernel methods using manufactured data and data collected from GPS collars on African buffalo in the Kruger National Park, South Africa. Our results demonstrate that LoCoH methods are superior to parametric kernel methods in estimating areas used by animals, excluding unused areas (holes) and, generally, in constructing UDs and HRs arising from the movement of animals influenced by hard boundaries and irregular structures (e.g., rocky outcrops). We also demonstrate that a-LoCoH is generally superior to k- and r-LoCoH (with software for all three methods available at http://locoh.cnr.berkeley.edu).}, } @article {pmid17298527, year = {2007}, author = {Winfree, R and Griswold, T and Kremen, C}, title = {Effect of human disturbance on bee communities in a forested ecosystem.}, journal = {Conservation biology : the journal of the Society for Conservation Biology}, volume = {21}, number = {1}, pages = {213-223}, doi = {10.1111/j.1523-1739.2006.00574.x}, pmid = {17298527}, issn = {0888-8892}, mesh = {Agriculture ; Animals ; Bees/*physiology ; Body Size ; Cities ; *Conservation of Natural Resources ; *Ecosystem ; Geographic Information Systems ; New Jersey ; Population Density ; *Trees ; }, abstract = {It is important for conservation biologists to understand how well species persist in human-dominated ecosystems because protected areas constitute a small fraction of the Earth's surface and because anthropogenic habitats may offer more opportunities for conservation than has been previously thought. We investigated how an important functional group, pollinators (bees; Hymenoptera: Apiformes), are affected by human land use at the landscape and local scales in southern New Jersey (U.S.A.). We established 40 sites that differed in surrounding landscape cover or local habitat type and collected 2551 bees of 130 species. The natural habitat in this ecosystem is a forested, ericaceous heath. Bee abundance and species richness within forest habitat decreased, not increased, with increasing forest cover in the surrounding landscape. Similarly, bee abundance was greater in agricultural fields and suburban and urban developments than in extensive forests, and the same trend was found for species richness. Particular species groups that might be expected to show greater sensitivity to habitat loss, such as floral specialists and bees of small or large body size, did not show strong positive associations with forest habitat. Nevertheless, 18 of the 130 bee species studied were positively associated with extensive forest. One of these species is a narrow endemic that was last seen in 1939. Our results suggest that at least in this system, moderate anthropogenic land use may be compatible with the conservation of many, but not all, bee species.}, } @article {pmid17298522, year = {2007}, author = {Semlitsch, RD and Ryan, TJ and Hamed, K and Chatfield, M and Drehman, B and Pekarek, N and Spath, M and Watland, A}, title = {Salamander abundance along road edges and within abandoned logging roads in Appalachian forests.}, journal = {Conservation biology : the journal of the Society for Conservation Biology}, volume = {21}, number = {1}, pages = {159-167}, doi = {10.1111/j.1523-1739.2006.00571.x}, pmid = {17298522}, issn = {0888-8892}, mesh = {Analysis of Variance ; Animals ; *Ecosystem ; Geographic Information Systems ; North Carolina ; Population Density ; Transportation ; *Trees ; Urodela/*physiology ; }, abstract = {Roads may be one of the most common disturbances in otherwise continuous forested habitat in the southern Appalachian Mountains. Despite their obvious presence on the landscape, there is limited data on the ecological effects along a road edge or the size of the "road-effect zone." We sampled salamanders at current and abandoned road sites within the Nantahala National Forest, North Carolina (U.S.A.) to determine the road-effect zone for an assemblage of woodland salamanders. Salamander abundance near the road was reduced significantly, and salamanders along the edges were predominantly large individuals. These results indicate that the road-effect zone for these salamanders extended 35 m on either side of the relatively narrow, low-use forest roads along which we sampled. Furthermore, salamander abundance was significantly lower on old, abandoned logging roads compared with the adjacent upslope sites. These results indicate that forest roads and abandoned logging roads have negative effects on forest-dependent species such as plethodontid salamanders. Our results may apply to other protected forests in the southern Appalachians and may exemplify a problem created by current and past land use activities in all forested regions, especially those related to road building for natural-resource extraction. Our results show that the effect of roads reached well beyond their boundary and that abandonment or the decommissioning of roads did not reverse detrimental ecological effects; rather, our results indicate that management decisions have significant repercussions for generations to come. Furthermore, the quantity of suitable forested habitat in the protected areas we studied was significantly reduced: between 28.6% and 36.9% of the area was affected by roads. Management and policy decisions must use current and historical data on land use to understand cumulative impacts on forest-dependent species and to fully protect biodiversity on national lands.}, } @article {pmid17296228, year = {2007}, author = {Chang, MX and Nie, P and Wei, LL}, title = {Short and long peptidoglycan recognition proteins (PGRPs) in zebrafish, with findings of multiple PGRP homologs in teleost fish.}, journal = {Molecular immunology}, volume = {44}, number = {11}, pages = {3005-3023}, doi = {10.1016/j.molimm.2006.12.029}, pmid = {17296228}, issn = {0161-5890}, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; *Carrier Proteins/chemistry/genetics/immunology ; Databases, Genetic ; Immunity, Innate ; *Models, Molecular ; Molecular Sequence Data ; Molecular Structure ; Phylogeny ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Sequence Alignment ; Sequence Homology ; Species Specificity ; Takifugu ; Tetraodontiformes ; Zebrafish ; }, abstract = {Peptidoglycan recognition protein (PGRP) specifically binds to peptidoglycan and is considered to be one of the pattern recognition proteins in the innate immunity of insect and mammals. Using a database mining approach and RT-PCR, multiple peptidoglycan recognition protein (PGRP) like genes have been discovered in fish including zebrafish Danio rerio, Japanese pufferfish TakiFugu rubripes and spotted green pufferfish Tetraodon nigroviridis. They share the common features of those PGRPs in arthropod and mammals, by containing a conserved PGRP domain. Based on the predicted structures, the identified zebrafish PGRP homologs resemble short and long PGRP members in arthropod and mammals. The identified PGRP genes in T. nigroviridis and TakiFugu rubripes resemble the long PGRPs, and the short PGRP genes have not been found in T. nigroviridis and TakiFugu rubripes databases. Computer modelling of these molecules revealed the presence of three alpha-helices and five or six beta-strands in all fish PGRPs reported in the present study. The long PGRP in teleost fish have multiple alternatively spliced forms, and some of the identified spliced variants, e.g., tnPGRP-L3 and tnPGRP-L4 (tn: Tetraodon nigroviridis), exhibited no characters present in the PGRP homologs domain. The coding regions of zfPGRP6 (zf: zebrafish), zfPGRP2-A, zfPGRP2-B and zfPGRP-L contain five exons and four introns; however, the other PGRP-like genes including zfPGRPSC1a, zfPGRPSC2, tnPGRP-L1-, tnPGRP-L2 and frPGRP-L (fr: Takifugu rubripes) contain four exons and three introns. In zebrafish, long and short PGRP genes identified are located in different chromosomes, and an unknown locus containing another long PGRP-like gene has also been found in zebrafish, demonstrating that multiple PGRP loci may be present in fish. In zebrafish, the constitutive expressions of zfPGRP-L, zfPGRP-6 and zfPGRP-SC during ontogeny from unfertilized eggs to larvae, in different organs of adult, and the inductive expression following stimulation by Flavobacterium columnare, were detected by real-time PCR, but the levels and patterns varied for different PGRP genes, implying that different short and long PGRPs may play different roles in innate immune response.}, } @article {pmid17295119, year = {2007}, author = {Fleming, SW and Quilty, EJ}, title = {Toward a practical method for setting screening-level, ecological risk-based water temperature criteria and monitoring compliance.}, journal = {Environmental monitoring and assessment}, volume = {131}, number = {1-3}, pages = {83-94}, doi = {10.1007/s10661-006-9458-4}, pmid = {17295119}, issn = {0167-6369}, mesh = {Animals ; British Columbia ; Environmental Monitoring/*methods ; Fisheries ; Greenhouse Effect ; Risk Assessment ; *Rivers ; *Temperature ; Trout/growth & development ; }, abstract = {We integrated basic concepts from fisheries science and toxicological risk assessment to form a potential method for setting screening-level, risk-based, site-specific water quality objectives for temperature. In summary, the proposed approach: (a) uses temperature impacts upon specific growth as a measure of chronic (cumulative) temperature effects; (b) explicitly incorporates the consequences of both magnitude and cumulative duration of exposures; (c) adjusts the result for local watershed conditions, reducing the likelihood that naturally warm systems are identified as thermally polluted while helping to ensure that naturally cool systems are closely monitored for ecologically harmful changes in thermal regime; and (d) expresses the net result both graphically and as a risk quotient, RQ, closely analogous to that used in toxicological risk assessments. The latter yields a site-specific, risk-based water quality objective and may serve as a straightforward decision rule for environmental managers. The method was applied to historical data from a small British Columbia stream subject to increasing urban development pressures. We also illustrate how the technique might be used to explore potential climatic change impacts, using coupled general circulation model predictions in conjunction with empirical downscaling. Overall, the method and results are presented as an introduction and illustration of concept, intended as a step toward the development of a logistically feasible risk-based approach to establishing screening-level, site-specific water temperature objectives, and monitoring compliance, in the context of large-scale, many-site, environmental monitoring networks. With further work, the technique offers potential to fill the gap between the temperature threshold-based targets typically specified in regulatory guidelines, which may be hydroecologically unrealistic, and detailed biophysical modelling, which typically is logistically infeasible in a day-to-day environmental monitoring and management context.}, } @article {pmid17295067, year = {2007}, author = {Aronson, RE and Wallis, AB and O'Campo, PJ and Schafer, P}, title = {Neighborhood mapping and evaluation: a methodology for participatory community health initiatives.}, journal = {Maternal and child health journal}, volume = {11}, number = {4}, pages = {373-383}, pmid = {17295067}, issn = {1092-7875}, mesh = {*Community Networks ; Humans ; Infant ; Infant Mortality ; Infant, Newborn ; *Maps as Topic ; Preventive Health Services/*organization & administration ; *Residence Characteristics ; United States ; }, abstract = {OBJECTIVES: This paper describes the use of neighborhood mapping as a key element in an ecological study of a community-based urban infant mortality prevention program. We propose the use of neighborhood mapping in evaluation research to more fully examine the local context of community health programs. Mapping can be used to study community change and to describe community assets and structural, epidemiological, and social features of neighborhoods that may influence program implementation and outcomes.

METHODS: Data on physical features were collected by community residents during street-by-street neighborhood walkthroughs. Other data sources included program records, Census, birth certificate, and state and city data. Analytic methods included geo-coding, exploratory factor analysis to create spatial density indicators of neighborhood features at the Census block group level, and analysis of associations between neighborhood features and outcomes.

RESULTS: Point and chloropleth maps provide a powerful illustration of neighborhood features (e.g., vacant buildings), client distribution and participation, health outcomes, and change over time. Factor analysis indicated two salient clusters of non-residential land use: (1) legitimate daily usage (liquor stores and other businesses) and (2) non-legitimate daily use (houses of worship and vacant buildings). A composite scale was created to indicate overall risk related to physical neighborhood features.

CONCLUSIONS: Neighborhood mapping is a powerful tool that brings participants and residents into the research process. Moreover, it can improve understanding of the role of neighborhood ecology in program implementation and outcomes.}, } @article {pmid17291165, year = {2007}, author = {Weinstein, ND}, title = {Misleading tests of health behavior theories.}, journal = {Annals of behavioral medicine : a publication of the Society of Behavioral Medicine}, volume = {33}, number = {1}, pages = {1-10}, doi = {10.1207/s15324796abm3301_1}, pmid = {17291165}, issn = {0883-6612}, mesh = {Bias ; Causality ; Culture ; Data Collection/statistics & numerical data ; Data Interpretation, Statistical ; *Health Behavior ; Health Knowledge, Attitudes, Practice ; Humans ; Intention ; Prospective Studies ; *Psychological Theory ; Reproducibility of Results ; Statistics as Topic ; }, abstract = {Most tests of cognitively oriented theories of health behavior are based on correlational data. Unfortunately, such tests are often biased, overestimating the accuracy of the theories they seek to evaluate. These biases are especially strong when studies examine health behaviors that need to be performed repeatedly, such as medication adherence, diet, exercise, and condom use. Several misleading data analysis procedures further exaggerate the theories' predictive accuracy. Because correlational designs are not adequate for deciding whether a particular construct affects behavior or for testing one theory against another, most of the literature aiming to test these theories tells us little about their validity or completeness. Neither does the existing empirical literature support decisions to use these theories to design interventions. In addition to discussing problems with correlational data, this article offers ideas for alternative testing strategies.}, } @article {pmid17284409, year = {2007}, author = {Wiens, JJ and Parra-Olea, G and García-París, M and Wake, DB}, title = {Phylogenetic history underlies elevational biodiversity patterns in tropical salamanders.}, journal = {Proceedings. Biological sciences}, volume = {274}, number = {1612}, pages = {919-928}, pmid = {17284409}, issn = {0962-8452}, mesh = {*Altitude ; Animals ; Bayes Theorem ; *Biodiversity ; Computational Biology ; Demography ; Ecosystem ; Models, Genetic ; *Phylogeny ; Time Factors ; Tropical Climate ; Urodela/*genetics ; }, abstract = {Elevational variation in species richness is ubiquitous and important for conservation, but remains poorly explained. Numerous studies have documented higher species richness at mid-elevations, but none have addressed the underlying evolutionary and biogeographic processes that ultimately explain this pattern (i.e. speciation, extinction and dispersal). Here, we address the evolutionary causes of the mid-elevational diversity hump in the most species-rich clade of salamanders, the tropical bolitoglossine plethodontids. We present a new phylogeny for the group based on DNA sequences from all 13 genera and 137 species. Using this phylogeny, we find no relationship between rates of diversification of clades and their elevational distribution, and no evidence for a rapid 'species pump' in tropical montane regions. Instead, we find a strong relationship between the number of species in each elevational zone and the estimated time when each elevational band was first colonized. Mid-elevation habitats were colonized early in the phylogenetic history of bolitoglossines, and given similar rates of diversification across elevations, more species have accumulated in the elevational zones that were inhabited the longest. This pattern may be widespread and suggests that mid-elevation habitats may not only harbour more species, but may also contain more phylogenetic diversity than other habitats within a region.}, } @article {pmid17284217, year = {2007}, author = {Pommier, T and Canbäck, B and Riemann, L and Boström, KH and Simu, K and Lundberg, P and Tunlid, A and Hagström, A}, title = {Global patterns of diversity and community structure in marine bacterioplankton.}, journal = {Molecular ecology}, volume = {16}, number = {4}, pages = {867-880}, doi = {10.1111/j.1365-294X.2006.03189.x}, pmid = {17284217}, issn = {0962-1083}, mesh = {Bacteria/classification/*genetics ; Base Sequence ; Computational Biology ; DNA Primers ; *Demography ; *Ecosystem ; Gene Library ; *Genetic Variation ; Likelihood Functions ; Models, Genetic ; Molecular Sequence Data ; Oceans and Seas ; *Phylogeny ; Plankton/*genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Because of their small size, great abundance and easy dispersal, it is often assumed that marine planktonic microorganisms have a ubiquitous distribution that prevents any structured assembly into local communities. To challenge this view, marine bacterioplankton communities from coastal waters at nine locations distributed world-wide were examined through the use of comprehensive clone libraries of 16S ribosomal RNA genes, used as operational taxonomic units (OTU). Our survey and analyses show that there were marked differences in the composition and richness of OTUs between locations. Remarkably, the global marine bacterioplankton community showed a high degree of endemism, and conversely included few cosmopolitan OTUs. Our data were consistent with a latitudinal gradient of OTU richness. We observed a positive relationship between the relative OTU abundances and their range of occupation, i.e. cosmopolitans had the largest population sizes. Although OTU richness differed among locations, the distributions of the major taxonomic groups represented in the communities were analogous, and all local communities were similarly structured and dominated by a few OTUs showing variable taxonomic affiliations. The observed patterns of OTU richness indicate that similar evolutionary and ecological processes structured the communities. We conclude that marine bacterioplankton share many of the biogeographical and macroecological features of macroscopic organisms. The general processes behind those patterns are likely to be comparable across taxa and major global biomes.}, } @article {pmid17283597, year = {2007}, author = {Suedel, BC and Bridges, TS and Kim, J and Payne, BS and Miller, AC}, title = {Application of risk assessment and decision analysis to aquatic nuisance species.}, journal = {Integrated environmental assessment and management}, volume = {3}, number = {1}, pages = {79-89}, pmid = {17283597}, issn = {1551-3777}, mesh = {Animals ; Biodiversity ; Bivalvia/physiology ; *Decision Support Techniques ; *Ecosystem ; *Models, Biological ; Plants/metabolism ; Population Dynamics ; Risk Assessment/*methods ; United States ; }, abstract = {The spread of nonindigenous (nonnative) species introduced into the United States is a significant and growing national problem and results in lost agricultural productivity, increased health problems, native species extinctions, and expensive prevention and eradication efforts. Thousands of nonindigenous species have either become established or spread, and introduction of aquatic nuisance species (ANS) into freshwater lakes threaten aquatic biodiversity. Expanding global trade is likely to increase the number of species that are spread across the globe, so the need to develop an approach to predict potential ANS invasions is great. Risk assessments currently being used to assess ANS risk rely on qualitative or semiquantitative information and expert opinion; thus, such approaches lack transparency and repeatability. A more quantitative approach is needed to augment the qualitative approaches currently in use. A quantitative approach with the use of the traditional ecological risk assessment (traditional ERA) framework combined with decision analysis tools was developed for assessing ANS risks in which the causative ecological risk agent is an organism rather than a chemical. This paper presents a systematic risk assessment framework that includes structured decision analysis to help organize and analyze pertinent data, state assumptions, address uncertainties in estimating the probability of an undesired ANS introduction, or spread and integrate these outputs with stakeholder values. This paper also describes when and how decision analysis tools can be used in such assessments for ANS. This framework and methodology will enable risk managers to systematically evaluate and compare alternatives and actions supporting ANS risk management and thus credibly prioritize resources.}, } @article {pmid17276130, year = {2007}, author = {Bogacz, R}, title = {Optimal decision-making theories: linking neurobiology with behaviour.}, journal = {Trends in cognitive sciences}, volume = {11}, number = {3}, pages = {118-125}, doi = {10.1016/j.tics.2006.12.006}, pmid = {17276130}, issn = {1364-6613}, mesh = {Basal Ganglia/physiology ; Brain/*physiology ; Cerebral Cortex/physiology ; Choice Behavior/*physiology ; Decision Making/*physiology ; Decision Support Techniques ; *Decision Theory ; Humans ; Nerve Net/physiology ; }, abstract = {This article reviews recently proposed theories postulating that, during simple choices, the brain performs statistically optimal decision making. These theories are ecologically motivated by evolutionary pressures to optimize the speed and accuracy of decisions and to maximize the rate of receiving rewards for correct choices. This article suggests that the models of decision making that are proposed on different levels of abstraction can be linked by virtue of the same optimal computation. Also reviewed here are recent observations that many aspects of the circuit that involves the cortex and basal ganglia are the same as those that are required to perform statistically optimal choice. This review illustrates how optimal-decision theories elucidate current data and provide experimental predictions that concern both neurobiology and behaviour.}, } @article {pmid17270252, year = {2007}, author = {Schroeder, W and Pesch, R}, title = {Synthesizing bioaccumulation data from the German metals in mosses surveys and relating them to ecoregions.}, journal = {The Science of the total environment}, volume = {374}, number = {2-3}, pages = {311-327}, doi = {10.1016/j.scitotenv.2006.09.015}, pmid = {17270252}, issn = {0048-9697}, mesh = {Bryophyta/*metabolism ; Ecosystem ; Environmental Monitoring/*methods ; Environmental Pollutants/history/*metabolism ; Geographic Information Systems ; Germany ; History, 20th Century ; History, 21st Century ; Metals, Heavy/history/*metabolism ; }, abstract = {The European Heavy Metals in Mosses Surveys measure and map environmental concentrations of metals at more than 7000 sites in Europe. In Germany, moss samples were taken at 592 sites in 1990, at 1026 sites in 1995, and at 1028 sites in 2000, where up to 40 metals were measured each time. This article is about how to calculate multi-metal indices from the site- and metal-specific monitoring data and how to link them with the natural regions (ecoregions) of Germany. The ecoregions were calculated with surface data on natural vegetation, elevation, soil texture and climate by means of Classification and Regression Trees (CART). The ecoregions were mapped by GIS and superimposed on a map of multi-metal bioaccumulation indices calculated by means of geostatistics and percentile statistics from the monitoring data. These indices integrate the concentrations of 8 metals measured in 1990, 1995, and 2000 or 12 metals from the 1995 and 2000 surveys, respectively, and the ecoregionalisation enables their geostatistical estimates to be grouped into 21 ecological land categories. This two-step aggregation revealed that, from 1990 to 2000, the multi-metal metal accumulation declined up to 80%, varying with the ecoregions. Based on the multi-metal accumulation index hot spots, the metal accumulation was mapped, ecoregionalised, and suggested for further ecotoxicological assessment. Thus, the approach helps to assess the metal bioaccumulation within ecoregions in a comprehensive and holistic manner over time, space, and metals. This data aggregation is of importance for the environmental reporting in Germany and within the framework of the international environmental information systems. Furthermore, ecoregions may help to plan and optimize monitoring networks. Because monitoring should measure and estimate not only the environmental concentrations of substances but also their impacts on ecoregions, the number of monitoring sites should be proportional to the areas covered by the ecoregions and located according to their spatial variation.}, } @article {pmid17267034, year = {2007}, author = {Wu, K and Li, K}, title = {Association between esophageal cancer and drought in China by using Geographic Information System.}, journal = {Environment international}, volume = {33}, number = {5}, pages = {603-608}, doi = {10.1016/j.envint.2007.01.001}, pmid = {17267034}, issn = {0160-4120}, mesh = {China/epidemiology ; Climate ; *Disasters ; Esophageal Neoplasms/etiology/*mortality ; Geographic Information Systems ; Humans ; }, abstract = {The objective of this ecological study was to discover associations between selected climate variables and esophageal cancer (EC) mortality in China using a Geographic Information System (GIS). A digital distribution map of EC mortality in China was established in GIS, which was based on one-tenth of nationwide population cause-of-death surveys conducted in mainland China in 1990-1992. Selected climate variables such as 30-year annual average precipitation and evaporation data of the sample areas were extracted from the environmental databases by zonal statistics finished in Spatial Analyst module of ArcInfo 9.0. Drought Indexes were calculated by using the precipitation and evaporation data and a digital distribution map of them was created to compare with the distribution of EC mortality. Correlation and regression analyses were applied to evaluate associations between the EC mortality rates defined at the sample areas and selected climate variables from the raster datasets. The results of the digital GIS maps of EC mortality and Drought Index show that the high EC mortality mostly occurred in areas with high Drought Index. Correlation and regression analyses also show weak negative correlation between precipitation and EC mortality (p<0.001), and weak positive correlation between Drought Index and EC mortality (p<0.001). This study presented a unique model for the link of cancer and climate using a GIS. The study suggests that drought plays a role in the occurrence and development of EC in China, however, other environmental, biological and genetic factors should not be ignored. There is need for further studies using multiple factors and more accurate and detailed environmental and health data.}, } @article {pmid17264886, year = {2007}, author = {van Gils, JA and Munster, VJ and Radersma, R and Liefhebber, D and Fouchier, RA and Klaassen, M}, title = {Hampered foraging and migratory performance in swans infected with low-pathogenic avian influenza A virus.}, journal = {PloS one}, volume = {2}, number = {1}, pages = {e184}, pmid = {17264886}, issn = {1932-6203}, mesh = {Animal Migration/*physiology ; Animals ; *Anseriformes/physiology/virology ; Feeding Behavior/*physiology ; Geographic Information Systems/instrumentation ; Influenza A virus/classification/genetics/*pathogenicity ; Influenza in Birds/epidemiology/*physiopathology ; Likelihood Functions ; Phylogeny ; }, abstract = {It is increasingly acknowledged that migratory birds, notably waterfowl, play a critical role in the maintenance and spread of influenza A viruses. In order to elucidate the epidemiology of influenza A viruses in their natural hosts, a better understanding of the pathological effects in these hosts is required. Here we report on the feeding and migratory performance of wild migratory Bewick's swans (Cygnus columbianus bewickii Yarrell) naturally infected with low-pathogenic avian influenza (LPAI) A viruses of subtypes H6N2 and H6N8. Using information on geolocation data collected from Global Positioning Systems fitted to neck-collars, we show that infected swans experienced delayed migration, leaving their wintering site more than a month after uninfected animals. This was correlated with infected birds travelling shorter distances and fuelling and feeding at reduced rates. The data suggest that LPAI virus infections in wild migratory birds may have higher clinical and ecological impacts than previously recognised.}, } @article {pmid17254831, year = {2007}, author = {Ali, M and Thiem, VD and Park, JK and Ochiai, RL and Canh, DG and Danovaro-Holliday, MC and Kaljee, LM and Clemens, JD and Acosta, CJ}, title = {Geographic analysis of vaccine uptake in a cluster-randomized controlled trial in Hue, Vietnam.}, journal = {Health & place}, volume = {13}, number = {3}, pages = {577-587}, doi = {10.1016/j.healthplace.2006.07.004}, pmid = {17254831}, issn = {1353-8292}, mesh = {Adolescent ; Child ; Child, Preschool ; Cluster Analysis ; Female ; Geographic Information Systems ; *Geography ; Hepatitis A Vaccines/economics/supply & distribution ; Humans ; Male ; Mass Vaccination/economics/*statistics & numerical data ; Patient Acceptance of Health Care/*statistics & numerical data ; Population Surveillance ; *Residence Characteristics ; School Health Services/*statistics & numerical data ; Typhoid Fever/epidemiology/*prevention & control ; Typhoid-Paratyphoid Vaccines/economics/*supply & distribution ; Vaccination/economics/*statistics & numerical data ; Vietnam/epidemiology ; }, abstract = {This paper identifies spatial patterns and predictors of vaccine uptake in a cluster-randomized controlled trial in Hue, Vietnam. Data for this study result from the integration of demographic surveillance, vaccine record, and geographic data of the study area. A multi-level cross-classified (non-hierarchical) model was used for analyzing the non-nested nature of individual's ecological data. Vaccine uptake was unevenly distributed in space and there was spatial variability among predictors of vaccine uptake. Vaccine uptake was higher among students with younger, male, or not literate family heads. Students from households with higher per-capita income were less likely to participate in the trial. Residency south of the river or further from a hospital/polyclinic was associated with higher vaccine uptake. Younger students were more likely to be vaccinated than older students in high- or low-risk areas, but not in the entire study area. The findings are important for the management of vaccine campaigns during a trial and for interpretation of disease patterns during vaccine-efficacy evaluation.}, } @article {pmid17254300, year = {2006}, author = {Wu, X and Zhu, L and Guo, J and Fu, C and Zhou, H and Dong, D and Li, Z and Zhang, DY and Lin, K}, title = {SPIDer: Saccharomyces protein-protein interaction database.}, journal = {BMC bioinformatics}, volume = {7 Suppl 5}, number = {Suppl 5}, pages = {S16}, pmid = {17254300}, issn = {1471-2105}, mesh = {Algorithms ; Computational Biology ; *Databases, Genetic ; Genome, Fungal ; Protein Interaction Mapping/*methods ; Saccharomyces/*genetics ; }, abstract = {BACKGROUND: Since proteins perform their functions by interacting with one another and with other biomolecules, reconstructing a map of the protein-protein interactions of a cell, experimentally or computationally, is an important first step toward understanding cellular function and machinery of a proteome. Solely derived from the Gene Ontology (GO), we have defined an effective method of reconstructing a yeast protein interaction network by measuring relative specificity similarity (RSS) between two GO terms.

DESCRIPTION: Based on the RSS method, here, we introduce a predicted Saccharomyces protein-protein interaction database called SPIDer. It houses a gold standard positive dataset (GSP) with high confidence level that covered 79.2% of the high-quality interaction dataset. Our predicted protein-protein interaction network reconstructed from the GSPs consists of 92,257 interactions among 3600 proteins, and forms 23 connected components. It also provides general links to connect predicted protein-protein interactions with three other databases, DIP, BIND and MIPS. An Internet-based interface provides users with fast and convenient access to protein-protein interactions based on various search features (searching by protein information, GO term information or sequence similarity). In addition, the RSS value of two GO terms in the same ontology, and the inter-member interactions in a list of proteins of interest or in a protein complex could be retrieved. Furthermore, the database presents a user-friendly graphical interface which is created dynamically for visualizing an interaction sub-network. The database is accessible at http://cmb.bnu.edu.cn/SPIDer/index.html.

CONCLUSION: SPIDer is a public database server for protein-protein interactions based on the yeast genome. It provides a variety of search options and graphical visualization of an interaction network. In particular, it will be very useful for the study of inter-member interactions among a list of proteins, especially the protein complex. In addition, based on the predicted interaction dataset, researchers could analyze the whole interaction network and associate the network topology with gene/protein properties based on a global or local topology view.}, } @article {pmid17251179, year = {2007}, author = {Touchon, M and Rocha, EP}, title = {Causes of insertion sequences abundance in prokaryotic genomes.}, journal = {Molecular biology and evolution}, volume = {24}, number = {4}, pages = {969-981}, doi = {10.1093/molbev/msm014}, pmid = {17251179}, issn = {0737-4038}, mesh = {Computational Biology ; DNA Transposable Elements/*genetics ; Databases, Nucleic Acid ; Evolution, Molecular ; Gene Transfer, Horizontal ; Genome, Archaeal/*genetics ; Genome, Bacterial/*genetics ; Humans ; Mutagenesis, Insertional ; Prokaryotic Cells/*metabolism ; RNA, Ribosomal, 16S/genetics ; Selection, Genetic ; }, abstract = {Insertion sequences (ISs) are the smallest and most frequent transposable elements in prokaryotes where they play an important evolutionary role by promoting gene inactivation and genome plasticity. Their genomic abundance varies by several orders of magnitude for reasons largely unknown and widely speculated. The current availability of hundreds of genomes renders testable many of these hypotheses, notably that IS abundance correlates positively with the frequency of horizontal gene transfer (HGT), genome size, pathogenicity, nonobligatory ecological associations, and human association. We thus reannotated ISs in 262 prokaryotic genomes and tested these hypotheses showing that when using appropriate controls, there is no empirical basis for IS family specificity, pathogenicity, or human association to influence IS abundance or density. HGT seems necessary for the presence of ISs, but cannot alone explain the absence of ISs in more than 20% of the organisms, some of which showing high rates of HGT. Gene transfer is also not a significant determinant of the abundance of IS elements in genomes, suggesting that IS abundance is controlled at the level of transposition and ensuing natural selection and not at the level of infection. Prokaryotes engaging in obligatory associations have fewer ISs when controlled for genome size, but this may be caused by some being sexually isolated. Surprisingly, genome size is the only significant predictor of IS numbers and density. Alone, it explains over 40% of the variance of IS abundance. Because we find that genome size and IS abundance correlate negatively with minimal doubling times, we conclude that selection for rapid replication cannot account for the few ISs found in small genomes. Instead, we show evidence that IS numbers are controlled by the frequency of highly deleterious insertion targets. Indeed, IS abundance increases quickly with genome size, which is the exact inverse trend found for the density of genes under strong selection such as essential genes. Hence, for ISs, the bigger the genome the better.}, } @article {pmid17243075, year = {2007}, author = {Hewitt, JE and Thrush, SF and Dayton, PK and Bonsdorff, E}, title = {The effect of spatial and temporal heterogeneity on the design and analysis of empirical studies of scale-dependent systems.}, journal = {The American naturalist}, volume = {169}, number = {3}, pages = {398-408}, doi = {10.1086/510925}, pmid = {17243075}, issn = {1537-5323}, mesh = {Data Interpretation, Statistical ; Ecological and Environmental Phenomena ; Ecology/*methods ; *Empirical Research ; *Research Design ; Spatio-Temporal Analysis ; }, abstract = {Processes interacting across scales of space and time influence emergent patterns in ecological systems, but to obtain strong inference and empirical generalities, ecologists need to balance reality with the practicalities of design and analyses. This article discusses heterogeneity, scaling, and design analysis problems and offers potential solutions to improve empirically based research. In particular, we recommend bridging the dichotomy between correlative and manipulative studies by nesting manipulative studies within a correlative framework. We suggest that building on variation, by designing studies to detect variability, rather than fighting it often leads to an increase in generality. We also emphasize the importance of natural history information for determining likely scales of spatial and temporal heterogeneity and the probable occurrence of feedback loops, indirect effects, and interacting processes. Finally, we integrate these concepts and suggest planned iterations between multiscale studies to build up natural history information and test the strength of relationships across space and time. This offers a way forward in terms of heuristically developing models and determining ecological generalities.}, } @article {pmid17238418, year = {2006}, author = {Pluye, P and Grad, RM}, title = {Cognitive impact assessment of electronic knowledge resources: a mixed methods evaluation study of a handheld prototype.}, journal = {AMIA ... Annual Symposium proceedings. AMIA Symposium}, volume = {2006}, number = {}, pages = {634-638}, pmid = {17238418}, issn = {1942-597X}, mesh = {Attitude to Computers ; Cognition ; *Computers, Handheld ; Consumer Behavior ; *Databases as Topic ; Equipment Failure ; Family Practice/education ; Humans ; *Information Storage and Retrieval ; Internship and Residency ; Longitudinal Studies ; Software ; Surveys and Questionnaires ; }, abstract = {RATIONALE: We recently proposed a new method to systematically assess the cognitive impact of knowledge resources on health professionals.

OBJECTIVE: To describe promises and shortcomings of a handheld computer prototype of this method.

BACKGROUND: We developed an impact scale, and combined this scale with a Computerized Ecological Momentary Assessment technique.

METHOD: We conducted a mixed methods evaluation study using a 7-item scale within a questionnaire linked to a commercial knowledge resource. Over two months of Family Medicine training, 17 residents assessed the impact of 1,981 information hits retrieved on handheld computer. From observations, log-reports, archives of hits and interviews, we examined issues associated with hardware, software and the questionnaire.

FINDINGS: Fifteen residents found the questionnaire clearly written, and only one pointed to the questionnaire as a major reason for their low level of use of the resource. Residents reported technical problems (e.g. screen trouble) or limitations (e.g. limited tracking function) and socio-technical issues (e.g. software dependency).

CONCLUSION: Lessons from this study suggest improvements to guide future implementation of our method for assessing the cognitive impact of knowledge resources on health professionals.}, } @article {pmid17235537, year = {2007}, author = {Studer, S and Stöckli, R and Appenzeller, C and Vidale, PL}, title = {A comparative study of satellite and ground-based phenology.}, journal = {International journal of biometeorology}, volume = {51}, number = {5}, pages = {405-414}, pmid = {17235537}, issn = {0020-7128}, mesh = {*Climate ; Databases, Factual ; Ecology/*methods ; *Ecosystem ; Greenhouse Effect ; *Plant Development ; Seasons ; Spacecraft ; Weather ; }, abstract = {Long time series of ground-based plant phenology, as well as more than two decades of satellite-derived phenological metrics, are currently available to assess the impacts of climate variability and trends on terrestrial vegetation. Traditional plant phenology provides very accurate information on individual plant species, but with limited spatial coverage. Satellite phenology allows monitoring of terrestrial vegetation on a global scale and provides an integrative view at the landscape level. Linking the strengths of both methodologies has high potential value for climate impact studies. We compared a multispecies index from ground-observed spring phases with two types (maximum slope and threshold approach) of satellite-derived start-of-season (SOS) metrics. We focus on Switzerland from 1982 to 2001 and show that temporal and spatial variability of the multispecies index correspond well with the satellite-derived metrics. All phenological metrics correlate with temperature anomalies as expected. The slope approach proved to deviate strongly from the temporal development of the ground observations as well as from the threshold-defined SOS satellite measure. The slope spring indicator is considered to indicate a different stage in vegetation development and is therefore less suited as a SOS parameter for comparative studies in relation to ground-observed phenology. Satellite-derived metrics are, however, very susceptible to snow cover, and it is suggested that this snow cover should be better accounted for by the use of newer satellite sensors.}, } @article {pmid17234866, year = {2007}, author = {Rezaeian, M and Dunn, G and St Leger, S and Appleby, L}, title = {Geographical epidemiology, spatial analysis and geographical information systems: a multidisciplinary glossary.}, journal = {Journal of epidemiology and community health}, volume = {61}, number = {2}, pages = {98-102}, pmid = {17234866}, issn = {0143-005X}, mesh = {Data Interpretation, Statistical ; Demography ; *Education, Continuing ; Epidemiology/*education ; *Geographic Information Systems ; Humans ; Topography, Medical ; }, abstract = {We provide a relatively non-technical glossary of terms and a description of the tools used in spatial or geographical epidemiology and associated geographical information systems. Statistical topics included cover adjustment and standardisation to allow for demographic and other background differences, data structures, data smoothing, spatial autocorrelation and spatial regression. We also discuss the rationale for geographical epidemiology and specific techniques such as disease clustering, disease mapping, ecological analyses, geographical information systems and global positioning systems.}, } @article {pmid17234324, year = {2007}, author = {Xu, C and Liu, M and An, S and Chen, JM and Yan, P}, title = {Assessing the impact of urbanization on regional net primary productivity in Jiangyin County, China.}, journal = {Journal of environmental management}, volume = {85}, number = {3}, pages = {597-606}, doi = {10.1016/j.jenvman.2006.08.015}, pmid = {17234324}, issn = {0301-4797}, mesh = {Biomass ; Carbon Dioxide/metabolism ; China ; Climate ; *Conservation of Natural Resources ; Crops, Agricultural/*growth & development ; Databases, Factual ; *Ecosystem ; Environmental Monitoring ; Geography ; Humans ; Models, Biological ; Risk Assessment ; Satellite Communications ; Time Factors ; Trees/*growth & development ; Urbanization/*trends ; Water Supply ; }, abstract = {Urbanization is one of the most important aspects of global change. The process of urbanization has a significant impact on the terrestrial ecosystem carbon cycle. The Yangtze Delta region has one of the highest rates of urbanization in China. In this study, carried out in Jiangyin County as a representative region within the Yangtze Delta, land use and land cover changes were estimated using Landsat TM and ETM+ imagery. With these satellite data and the BEPS process model (Boreal Ecosystem Productivity Simulator), the impacts of urbanization on regional net primary productivity (NPP) and annual net primary production were assessed for 1991 and 2002. Landsat-based land cover maps in 1991 and 2002 showed that urban development encroached large areas of cropland and forest. Expansion of residential areas and reduction of vegetated areas were the major forms of land transformation in Jiangyin County during this period. Mean NPP of the total area decreased from 818 to 699 gCm(-2)yr(-1) during the period of 1991 to 2002. NPP of cropland was only reduced by 2.7% while forest NPP was reduced by 9.3%. Regional annual primary production decreased from 808 GgC in 1991 to 691 GgC in 2002, a reduction of 14.5%. Land cover changes reduced regional NPP directly, and the increasing intensity and frequency of human-induced disturbance in the urbanized areas could be the main reason for the decrease in forest NPP.}, } @article {pmid17227406, year = {2007}, author = {Rohwer, F}, title = {Real-time microbial ecology.}, journal = {Environmental microbiology}, volume = {9}, number = {1}, pages = {10}, doi = {10.1111/j.1462-2920.2006.01222_9.x}, pmid = {17227406}, issn = {1462-2912}, mesh = {Computational Biology/methods ; Ecology/*trends ; Genomics ; Microbiological Techniques ; Microbiology/*trends ; }, } @article {pmid17227401, year = {2007}, author = {Hugenholtz, P}, title = {Riding giants.}, journal = {Environmental microbiology}, volume = {9}, number = {1}, pages = {5}, doi = {10.1111/j.1462-2920.2006.01222_4.x}, pmid = {17227401}, issn = {1462-2912}, mesh = {Computational Biology ; Databases, Genetic ; Ecology/trends ; Ecosystem ; *Environmental Microbiology ; Genomics ; Microbiological Techniques ; Microbiology/*trends ; }, } @article {pmid17222889, year = {2007}, author = {Maule, AG and Gannam, AL and Davis, JW}, title = {Chemical contaminants in fish feeds used in federal salmonid hatcheries in the USA.}, journal = {Chemosphere}, volume = {67}, number = {7}, pages = {1308-1315}, doi = {10.1016/j.chemosphere.2006.11.029}, pmid = {17222889}, issn = {0045-6535}, mesh = {Animal Feed/*analysis ; Animals ; Benzofurans/analysis ; Chromatography, Gas ; Data Interpretation, Statistical ; Electrochemistry ; Environmental Pollutants/analysis ; Fishes/*physiology ; Food Contamination/*analysis ; Hydrocarbons, Chlorinated/analysis ; Indicators and Reagents ; Pesticide Residues/analysis ; Pesticides/analysis ; Polychlorinated Biphenyls/analysis ; Polychlorinated Dibenzodioxins/analogs & derivatives/analysis ; Polymers/analysis ; *Salmonidae ; Spectrometry, Fluorescence ; Spectrophotometry, Atomic ; United States ; }, abstract = {Recent studies have demonstrated that fish feeds contain significant concentrations of contaminants, many of which can bioaccumulate and bioconcentrate in fish. Organochlorine (OC) contaminants are present in the fish oils and fish meals used in feed manufacture, and some researchers speculate that all fish feeds contain measurable levels of some contaminants. To determine the concentration of contaminants in feeds used in US Fish and Wildlife Service's National Fish Hatcheries, we systematically collected samples of feed from 11 cold-water fish hatcheries. All samples (collected from October 2001 to October 2003) contained at least one polychlorinated dibenzo-p-dioxin (PCDD), polychlorinated dibenzofuran (PCDF), polychlorinated biphenyl (PCB) congener, or dichlorodiphenyltrichloroethane (DDT) metabolite. Of the 55 samples in which they were analyzed 39 contained PCDDs, 24 contained PCDFs and 24 contained DDT or its metabolites. There were 10- to 150-fold differences in concentrations of total PCBs, PCDDs, PCDFs and DDT. Although PCBs were the most commonly detected contaminant in our study, concentrations (range: 0.07-10.46 ng g(-1) wet weight) were low compared to those reported previously. In general, we also found lower levels of OCs than reported previously in fish feed. Perhaps most notable was the near absence of OC pesticides - except for DDT or its metabolites, and two samples containing hexachlorocyclohexane (HCH). While contaminant concentrations were generally low, the ecological impacts can not be determined without a measure of the bioaccumulation of these compounds in the fish and the fate of these compounds after the fish are released.}, } @article {pmid17216626, year = {2007}, author = {Bradley, BJ and Stiller, M and Doran-Sheehy, DM and Harris, T and Chapman, CA and Vigilant, L and Poinar, H}, title = {Plant DNA sequences from feces: potential means for assessing diets of wild primates.}, journal = {American journal of primatology}, volume = {69}, number = {6}, pages = {699-705}, doi = {10.1002/ajp.20384}, pmid = {17216626}, issn = {0275-2565}, mesh = {Animals ; Base Sequence ; *Colobus ; Computational Biology ; DNA Primers ; DNA, Chloroplast/genetics ; *Diet ; Ecology/*methods ; Feces/*chemistry ; *Gorilla gorilla ; Molecular Sequence Data ; Plants/*genetics ; Ribulose-Bisphosphate Carboxylase/genetics ; Sequence Analysis, DNA ; }, abstract = {Analyses of plant DNA in feces provides a promising, yet largely unexplored, means of documenting the diets of elusive primates. Here we demonstrate the promise and pitfalls of this approach using DNA extracted from fecal samples of wild western gorillas (Gorilla gorilla) and black and white colobus monkeys (Colobus guereza). From these DNA extracts we amplified, cloned, and sequenced small segments of chloroplast DNA (part of the rbcL gene) and plant nuclear DNA (ITS-2). The obtained sequences were compared to sequences generated from known plant samples and to those in GenBank to identify plant taxa in the feces. With further optimization, this method could provide a basic evaluation of minimum primate dietary diversity even when knowledge of local flora is limited. This approach may find application in studies characterizing the diets of poorly-known, unhabituated primate species or assaying consumer-resource relationships in an ecosystem.}, } @article {pmid17210955, year = {2007}, author = {Wikelski, M and Kays, RW and Kasdin, NJ and Thorup, K and Smith, JA and Swenson, GW}, title = {Going wild: what a global small-animal tracking system could do for experimental biologists.}, journal = {The Journal of experimental biology}, volume = {210}, number = {Pt 2}, pages = {181-186}, doi = {10.1242/jeb.02629}, pmid = {17210955}, issn = {0022-0949}, mesh = {*Animal Migration ; Animals ; *Geographic Information Systems ; *Research Design ; *Spacecraft ; *Telemetry ; }, abstract = {Tracking animals over large temporal and spatial scales has revealed invaluable and spectacular biological information, particularly when the paths and fates of individuals can be monitored on a global scale. However, only large animals (greater than approximately 300 g) currently can be followed globally because of power and size constraints on the tracking devices. And yet the vast majority of animals is small. Tracking small animals is important because they are often part of evolutionary and ecological experiments, they provide important ecosystem services and they are of conservation concern or pose harm to human health. Here, we propose a small-animal satellite tracking system that would enable the global monitoring of animals down to the size of the smallest birds, mammals (bats), marine life and eventually large insects. To create the scientific framework necessary for such a global project, we formed the ICARUS initiative (www.IcarusInitiative.org), the International Cooperation for Animal Research Using Space. ICARUS also highlights how small-animal tracking could address some of the ;Grand Challenges in Environmental Sciences' identified by the US National Academy of Sciences, such as the spread of infectious diseases or the relationship between biological diversity and ecosystem functioning. Small-animal tracking would allow the quantitative assessment of dispersal and migration in natural populations and thus help solve enigmas regarding population dynamics, extinctions and invasions. Experimental biologists may find a global small-animal tracking system helpful in testing, validating and expanding laboratory-derived discoveries in wild, natural populations. We suggest that the relatively modest investment into a global small-animal tracking system will pay off by providing unprecedented insights into both basic and applied nature. Tracking small animals over large spatial and temporal scales could prove to be one of the most powerful techniques of the early 21st century, offering potential solutions to a wide range of biological and societal questions that date back two millennia to the Greek philosopher Aristotle's enigma about songbird migration. Several of the more recent Grand Challenges in Environmental Sciences, such as the regulation and functional consequences of biological diversity or the surveillance of the population ecology of zoonotic hosts, pathogens or vectors, could also be addressed by a global small-animal tracking system. Our discussion is intended to contribute to an emerging groundswell of scientific support to make such a new technological system happen.}, } @article {pmid17209996, year = {2007}, author = {Walsh, B}, title = {Escape from flatland.}, journal = {Journal of evolutionary biology}, volume = {20}, number = {1}, pages = {36-8; discussion 39-44}, doi = {10.1111/j.1420-9101.2006.01218.x}, pmid = {17209996}, issn = {1010-061X}, mesh = {*Biological Evolution ; *Data Interpretation, Statistical ; *Genetic Variation ; *Multivariate Analysis ; *Phenotype ; *Quantitative Trait, Heritable ; *Selection, Genetic ; }, } @article {pmid17209992, year = {2007}, author = {Hunt, J and Wolf, JB and Moore, AJ}, title = {The biology of multivariate evolution.}, journal = {Journal of evolutionary biology}, volume = {20}, number = {1}, pages = {24-7; discussion 39-44}, doi = {10.1111/j.1420-9101.2006.01222.x}, pmid = {17209992}, issn = {1010-061X}, mesh = {*Biological Evolution ; *Data Interpretation, Statistical ; *Genetic Variation ; *Multivariate Analysis ; *Phenotype ; *Quantitative Trait, Heritable ; *Selection, Genetic ; }, } @article {pmid17204548, year = {2007}, author = {Ingvarsson, PK}, title = {Gene expression and protein length influence codon usage and rates of sequence evolution in Populus tremula.}, journal = {Molecular biology and evolution}, volume = {24}, number = {3}, pages = {836-844}, doi = {10.1093/molbev/msl212}, pmid = {17204548}, issn = {0737-4038}, mesh = {Codon/*genetics ; Computational Biology ; *Evolution, Molecular ; Expressed Sequence Tags ; *Gene Expression ; Gene Expression Profiling ; Gene Library ; Populus/*genetics/metabolism ; Sequence Alignment ; }, abstract = {Codon bias is generally thought to be determined by a balance between mutation, genetic drift, and natural selection on translational efficiency. However, natural selection on codon usage is considered to be a weak evolutionary force and selection on codon usage is expected to be strongest in species with large effective population sizes. In this paper, I study associations between codon usage, gene expression, and molecular evolution at synonymous and nonsynonymous sites in the long-lived, woody perennial plant Populus tremula (Salicaceae). Using expression data for 558 genes derived from expressed sequence tags (EST) libraries from 19 different tissues and developmental stages, I study how gene expression levels within single tissues as well as across tissues affect codon usage and rates sequence evolution at synonymous and nonsynonymous sites. I show that gene expression have direct effects on both codon usage and the level of selective constraint of proteins in P. tremula, although in different ways. Codon usage genes is primarily determined by how highly expressed a genes is, whereas rates of sequence evolution are primarily determined by how widely expressed genes are. In addition to the effects of gene expression, protein length appear to be an important factor influencing virtually all aspects of molecular evolution in P. tremula.}, } @article {pmid17196839, year = {2007}, author = {Wang, N and Baldi, PF and Gaut, BS}, title = {Phylogenetic analysis, genome evolution and the rate of gene gain in the Herpesviridae.}, journal = {Molecular phylogenetics and evolution}, volume = {43}, number = {3}, pages = {1066-1075}, doi = {10.1016/j.ympev.2006.11.019}, pmid = {17196839}, issn = {1055-7903}, mesh = {Databases, Nucleic Acid ; *Evolution, Molecular ; Genome, Viral/genetics ; Herpesviridae/classification/*genetics ; *Phylogeny ; }, abstract = {We used complete sequence data from 30 complete Herpesviridae genomes to investigate phylogenetic relationships and patterns of genome evolution. The approach was to identify orthologous gene clusters among taxa and to generate a genomic matrix of gene content. We identified 17 genes with homologs in all 30 taxa and concatenated a subset of 10 of these genes for phylogenetic inference. We also constructed phylogenetic trees on the basis of gene content data. The amino acid and gene content phylogenies were largely concordant, but the amino acid data had much higher internal support. We mapped gene gain events onto the phylogenetic tree by assuming that genes were gained only once during the evolution of herpesviruses. Thirty genes were inferred to be present in the ancestor of all herpesvirus, a number smaller than previously hypothesized. Few genes of recent origin within herpesviruses could be identified as originating from transfer between virus and vertebrate hosts. Inferred rates of gene gain were heterogeneous, with both taxonomic and temporal biases. Nonetheless, the average rate of gene gain was approximately 3.5 x 10(-7) genes gained per year, which is an order of magnitude higher than the nucleotide mutation rate for these large DNA viruses.}, } @article {pmid17183692, year = {2006}, author = {Rzhetsky, A and Zheng, T and Weinreb, C}, title = {Self-correcting maps of molecular pathways.}, journal = {PloS one}, volume = {1}, number = {1}, pages = {e61}, pmid = {17183692}, issn = {1932-6203}, support = {R01 GM061372/GM/NIGMS NIH HHS/United States ; T15 LM007079/LM/NLM NIH HHS/United States ; R01 GM070789/GM/NIGMS NIH HHS/United States ; GM070789/GM/NIGMS NIH HHS/United States ; 5-T15-LM007079/LM/NLM NIH HHS/United States ; GM61372/GM/NIGMS NIH HHS/United States ; }, mesh = {Bayes Theorem ; *Gene Regulatory Networks ; Humans ; Metabolic Networks and Pathways ; Models, Biological ; *Models, Genetic ; Nervous System Diseases/genetics ; }, abstract = {Reliable and comprehensive maps of molecular pathways are indispensable for guiding complex biomedical experiments. Such maps are typically assembled from myriads of disparate research reports and are replete with inconsistencies due to variations in experimental conditions and/or errors. It is often an intractable task to manually verify internal consistency over a large collection of experimental statements. To automate large-scale reconciliation efforts, we propose a random-arcs-and-nodes model where both nodes (tissue-specific states of biological molecules) and arcs (interactions between them) are represented with random variables. We show how to obtain a non-contradictory model of a molecular network by computing the joint distribution for arc and node variables, and then apply our methodology to a realistic network, generating a set of experimentally testable hypotheses. This network, derived from an automated analysis of over 3,000 full-text research articles, includes genes that have been hypothetically linked to four neurological disorders: Alzheimer's disease, autism, bipolar disorder, and schizophrenia. We estimated that approximately 10% of the published molecular interactions are logically incompatible. Our approach can be directly applied to an array of diverse problems including those encountered in molecular biology, ecology, economics, politics, and sociology.}, } @article {pmid17178747, year = {2007}, author = {Ruiz-Pesini, E and Lott, MT and Procaccio, V and Poole, JC and Brandon, MC and Mishmar, D and Yi, C and Kreuziger, J and Baldi, P and Wallace, DC}, title = {An enhanced MITOMAP with a global mtDNA mutational phylogeny.}, journal = {Nucleic acids research}, volume = {35}, number = {Database issue}, pages = {D823-8}, pmid = {17178747}, issn = {1362-4962}, support = {NS213L8/NS/NINDS NIH HHS/United States ; HL64017/HL/NHLBI NIH HHS/United States ; R01 AG024373/AG/NIA NIH HHS/United States ; T15 LM007443/LM/NLM NIH HHS/United States ; R01 AG013154/AG/NIA NIH HHS/United States ; AG13154/AG/NIA NIH HHS/United States ; }, mesh = {DNA, Mitochondrial/*chemistry/classification ; *Databases, Nucleic Acid ; Genome ; Humans ; Internet ; Mitochondrial Diseases/*genetics ; *Mutation ; Phylogeny ; Pseudogenes ; User-Computer Interface ; }, abstract = {The MITOMAP (http://www.mitomap.org) data system for the human mitochondrial genome has been greatly enhanced by the addition of a navigable mutational mitochondrial DNA (mtDNA) phylogenetic tree of approximately 3000 mtDNA coding region sequences plus expanded pathogenic mutation tables and a nuclear-mtDNA pseudogene (NUMT) data base. The phylogeny reconstructs the entire mutational history of the human mtDNA, thus defining the mtDNA haplogroups and differentiating ancient from recent mtDNA mutations. Pathogenic mutations are classified by both genotype and phenotype, and the NUMT sequences permits detection of spurious inclusion of pseudogene variants during mutation analysis. These additions position MITOMAP for the implementation of our automated mtDNA sequence analysis system, Mitomaster.}, } @article {pmid17174005, year = {2007}, author = {Stephens, PA and Buskirk, SW and del Rio, CM}, title = {Inference in ecology and evolution.}, journal = {Trends in ecology & evolution}, volume = {22}, number = {4}, pages = {192-197}, doi = {10.1016/j.tree.2006.12.003}, pmid = {17174005}, issn = {0169-5347}, mesh = {Bayes Theorem ; Biological Evolution ; *Data Interpretation, Statistical ; Ecology/*statistics & numerical data ; Models, Statistical ; }, abstract = {Most ecologists and evolutionary biologists continue to rely heavily on null hypothesis significance testing, rather than on recently advocated alternatives, for inference. Here, we briefly review null hypothesis significance testing and its major alternatives. We identify major objectives of statistical analysis and suggest which analytical approaches are appropriate for each. Any well designed study can improve our understanding of biological systems, regardless of the inferential approach used. Nevertheless, an awareness of available techniques and their pitfalls could guide better approaches to data collection and broaden the range of questions that can be addressed. Although we should reduce our reliance on significance testing, it retains an important role in statistical education and is likely to remain fundamental to the falsification of scientific hypotheses.}, } @article {pmid17168023, year = {2006}, author = {DeClerck, FA and Barbour, MG and Sawyer, JO}, title = {Species richness and stand stability in conifer forests of the Sierra Nevada.}, journal = {Ecology}, volume = {87}, number = {11}, pages = {2787-2799}, doi = {10.1890/0012-9658(2006)87[2787:srassi]2.0.co;2}, pmid = {17168023}, issn = {0012-9658}, mesh = {Analysis of Variance ; *Biodiversity ; California ; *Ecosystem ; Geographic Information Systems ; Models, Biological ; Rain ; Regression Analysis ; Snow ; Species Specificity ; Statistics as Topic ; Time Factors ; Tracheophyta/growth & development/*physiology ; Trees/growth & development/*physiology ; }, abstract = {Theoretical and empirical studies have long suggested that stability and complexity are intimately related, but evidence from long-lived systems at large scales is lacking. Stability can either be driven by complex species interactions, or it can be driven by the presence/absence and abundance of a species best able to perform a specific ecosystem function. We use 64 years of stand productivity measures in forest systems composed of four dominant conifer tree species to contrast the effect of species richness and abundance on three stability measures. To perform this contrast, we measured the annual growth increments of > 900 trees in mixed and pure forest stands to test three hypotheses: increased species richness will (1) decrease stand variance, (2) increase stand resistance to drought events, and (3) increase stand resilience to drought events. In each case, the alternate hypothesis was that species richness had no effect, but that species composition and abundance within a stand drove variance, resistance, and resilience. In pure stands, the four species demonstrated significant differences in productivity, and in their resistance and resilience to drought events. The two pine species were the most drought resistant and resilient, whereas mountain hemlock was the least resistant and resilient, and red fir was intermediate. For community measures we found a moderately significant (P = 0.08) increase in the community coefficient of variation and a significant (P = 0.03) increase in resilience with increased species richness, but no significant relationship between species richness and community resistance, though the variance in community resistance to drought decreased with species richness. Community resistance to drought was significantly (P = 0.001) correlated to the relative abundance of lodgepole pine, the most resistant species. We propose that resistance is driven by competition for a single limiting resource, with negative diversity effects. In contrast resilience measures the capacity of communities to partition resources in the absence of a single limiting resource, demonstrating positive diversity effects.}, } @article {pmid17159472, year = {2007}, author = {Pierce, SJ and Miller, RL and Morales, MM and Forney, J}, title = {Identifying HIV prevention service needs of African American men who have sex with men: an application of spatial analysis techniques to service planning.}, journal = {Journal of public health management and practice : JPHMP}, volume = {Suppl}, number = {}, pages = {S72-9}, doi = {10.1097/00124784-200701001-00012}, pmid = {17159472}, issn = {1078-4659}, support = {U62/CCU513631//PHS HHS/United States ; }, mesh = {*Black or African American ; *Catchment Area, Health ; Chicago/epidemiology ; Cluster Analysis ; Community Health Planning/organization & administration ; Geographic Information Systems ; HIV Infections/ethnology/*prevention & control ; *Health Services Accessibility ; Homosexuality, Male/*ethnology ; Humans ; Male ; Maps as Topic ; Preventive Health Services/*supply & distribution ; *Public Health Administration ; Unsafe Sex/ethnology/prevention & control ; Urban Health/*statistics & numerical data ; }, abstract = {BACKGROUND: Black men who have sex with men (MSM) are a priority population for HIV prevention.

METHOD: We applied spatial analysis techniques to map the availability of HIV prevention services to young black MSM in Chicago to guide prevention planning. GIS was used to map characteristics of ZIP codes in Chicago. Choropleth maps and descriptive statistics were used to visualize and analyze the data.

RESULTS: Areas where young black MSM reside typically have low HIV service densities. HIV service density also corresponds poorly to some ZIP codes in which young black MSM who report high rates of unprotected sexual behavior reside.

CONCLUSION: Spatial analysis can show whether services are located near specific populations of interest. Data from multiple sources can be integrated to explore relationships among characteristics of geographic zones.}, } @article {pmid17148280, year = {2006}, author = {Berger, J and Cain, SL and Berger, KM}, title = {Connecting the dots: an invariant migration corridor links the Holocene to the present.}, journal = {Biology letters}, volume = {2}, number = {4}, pages = {528-531}, pmid = {17148280}, issn = {1744-9561}, mesh = {*Animal Migration ; Animals ; Conservation of Natural Resources ; Ecosystem ; Female ; Geographic Information Systems ; Geography ; Ruminants/*physiology ; Time Factors ; Wyoming ; }, abstract = {Numerous species undergo impressive movements, but due to massive changes in land use, long distance migration in terrestrial vertebrates has become a highly fragile ecological phenomenon. Uncertainty about the locations of past migrations and the importance of current corridors hampers conservation planning. Using archeological data from historic kill sites and modern methods to track migration, we document an invariant, 150 km (one-way) migration corridor used for at least 6000 years by North America's sole extant endemic ungulate. Pronghorn (Antilocapra americana) from the Greater Yellowstone Ecosystem, like other long distant migrants including Serengeti wildebeest (Connochaetes taurinus) and Arctic caribou (Rangifer tarandus), move nearly 50 km d-1, but in contrast to these other species, rely on an invariant corridor averaging only 2 km wide. Because an entire population accesses a national park (Grand Teton) by passage through bottlenecks as narrow as 121 m, any blockage to movement will result in extirpation. Based on animation of real data coupled with the loss of six historic routes, alternative pathways throughout the 60,000 km2 Yellowstone ecosystem are no longer available. Our findings have implications for developing strategies to protect long distance land migrations in Africa, Asia and North America and to prevent the disappearance of ecological phenomena that have operated for millennia.}, } @article {pmid17147178, year = {2006}, author = {Wang, H and Yuan, H and Xu, X and Liu, S}, title = {[Landscape structure of desertification grassland in source region of Yellow River].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {17}, number = {9}, pages = {1665-1670}, pmid = {17147178}, issn = {1001-9332}, mesh = {China ; *Conservation of Natural Resources ; *Ecosystem ; *Environmental Monitoring ; Geographic Information Systems ; Poaceae/growth & development ; Rivers ; Trees/growth & development ; }, abstract = {This paper analyzed the spatial pattern and its characteristics of different landscape types on the desertification grassland of Maqu County in the source region of Yellow River, based on the principles of landscape ecology, with the help of GIS techniques, and by using landscape heterogeneity indices (landscape diversity and dominance) , landscape isolation indices (patch density and fragmentation), and shape indices (elongation index and fractal dimension). The results showed that on the whole, the landscape structure of this region was simple, but varied locally. Natural landscapes such as grassland, marsh and shrubs were the main body of landscape change. The regional landscape patches had a ribbon shape spatial distribution, and the differences were significant among subregions. From fluvial terrace to low hillsides and alpine grassland, the landscape patch type, landscape diversity, and landscape fragmentation degree decreased gradually, and the landscape structure presented a simplification trend. Desertification landscape, and mobile dune in particular, had great impact on landscape structure, playing an important role in the increment of landscape heterogeneity and fragmentation. Fixed sand lands, semi-fixed sand lands, and potential sand lands had different influences on regional landscape composition and its changes. Compared with desertification landscape, artificial landscape had less effect on landscape structure, but exhibited a wider potential variation range. These two types of landscape would be the dominant factors affecting the landscape structure changes of this region in the future.}, } @article {pmid17136841, year = {2006}, author = {Denisov, AA and Zubkov, IuN and Prokazova, LM and Sobolev, AI}, title = {[Automated system of radiation monitoring in Moscow region].}, journal = {Meditsina truda i promyshlennaia ekologiia}, volume = {}, number = {10}, pages = {21-25}, pmid = {17136841}, issn = {1026-9428}, mesh = {Automation ; Computer Communication Networks ; Databases as Topic ; Environmental Monitoring ; Humans ; Moscow ; Radiation Monitoring/*instrumentation/methods ; }, abstract = {The authors consider one trend in activities of "Radon"--Center of Radiation and Ecologic Control. The article covers foundation reasons and longstanding function results of operative radiation monitoring system for large industrial city. Features of construction and functioning of the system are shown. Devices for operative radiation monitoring are subjected to comparative analysis. Prospective trends of the system development are described.}, } @article {pmid17136068, year = {2006}, author = {Whitfield, J}, title = {Plantecology: the cost of leafing.}, journal = {Nature}, volume = {444}, number = {7119}, pages = {539-241}, doi = {10.1038/444539a}, pmid = {17136068}, issn = {1476-4687}, mesh = {Biological Evolution ; Carbon/metabolism ; Databases, Factual ; Ecology ; Models, Biological ; Plant Leaves/anatomy & histology/metabolism/*physiology ; Plant Physiological Phenomena ; }, } @article {pmid17135491, year = {2006}, author = {Herbreteau, V and Demoraes, F and Hugot, JP and Kittayapong, P and Salem, G and Souris, M and Gonzalez, JP}, title = {Perspectives on applied spatial analysis to animal health: a case of rodents in Thailand.}, journal = {Annals of the New York Academy of Sciences}, volume = {1081}, number = {}, pages = {17-29}, doi = {10.1196/annals.1373.002}, pmid = {17135491}, issn = {0077-8923}, mesh = {Animals ; Female ; *Geographic Information Systems ; Humans ; Male ; *Murinae ; Rodent Diseases/*epidemiology/transmission ; *Satellite Communications/instrumentation ; Sentinel Surveillance/*veterinary ; Thailand/epidemiology ; Topography, Medical ; Zoonoses ; }, abstract = {Geographic information systems (GIS) and remote sensing have been increasingly used in ecology and epidemiology, providing a spatial approach for animal health issues. Recent development of earth environmental satellites--i.e., their growing number, improving sensor resolutions and capabilities--has offered new opportunities to delineate possible habitats and understand animals and associated parasites in their environment, by identifying the nature and structure of land use, hydrological network, soil hydromorphy, and human settlements. Integrated into GIS, remotely sensed and other geo-referenced data allow both spatial and temporal analyses of animal ecology and health. However, a review of their applications has showed the poor quality of data sources and processing used, revealing limitations between theory and practical implementations. As an example, the assessment of the expected distribution of Bandicoot rats, main agricultural pest and vector of zoonoses in Phrae province (North Thailand), illustrates a rational use of spatial analysis, with the choice of relevant data, scales, and processing. Vegetation indices are computed on a TERRA ASTER image and further classified using elevation data. The biotopes of Bandicota indica and Bandicota savilei are delimited, providing a major source of knowledge for rodent and human health analyses.}, } @article {pmid17124319, year = {2006}, author = {Wagner, PJ and Kosnik, MA and Lidgard, S}, title = {Abundance distributions imply elevated complexity of post-Paleozoic marine ecosystems.}, journal = {Science (New York, N.Y.)}, volume = {314}, number = {5803}, pages = {1289-1292}, doi = {10.1126/science.1133795}, pmid = {17124319}, issn = {1095-9203}, mesh = {Animals ; *Biodiversity ; Databases, Factual ; *Ecosystem ; Extinction, Biological ; *Fossils ; *Invertebrates ; Likelihood Functions ; Marine Biology ; Population Density ; }, abstract = {Likelihood analyses of 1176 fossil assemblages of marine organisms from Phanerozoic (i.e., Cambrian to Recent) assemblages indicate a shift in typical relative-abundance distributions after the Paleozoic. Ecological theory associated with these abundance distributions implies that complex ecosystems are far more common among Meso-Cenozoic assemblages than among the Paleozoic assemblages that preceded them. This transition coincides not with any major change in the way fossils are preserved or collected but with a shift from communities dominated by sessile epifaunal suspension feeders to communities with elevated diversities of mobile and infaunal taxa. This suggests that the end-Permian extinction permanently altered prevailing marine ecosystem structure and precipitated high levels of ecological complexity and alpha diversity in the Meso-Cenozoic.}, } @article {pmid17112587, year = {2006}, author = {Drake, B and Jonson-Reid, M and Sapokaite, L}, title = {Re-reporting of child maltreatment: does participation in other public sector services moderate the likelihood of a second maltreatment report?.}, journal = {Child abuse & neglect}, volume = {30}, number = {11}, pages = {1201-1226}, pmid = {17112587}, issn = {0145-2134}, support = {MH06173304-A1/MH/NIMH NIH HHS/United States ; R01 MH061733-01/MH/NIMH NIH HHS/United States ; R01 MH061733/MH/NIMH NIH HHS/United States ; R01 MH061733-03/MH/NIMH NIH HHS/United States ; MH06173302/MH/NIMH NIH HHS/United States ; R01 MH061733-02/MH/NIMH NIH HHS/United States ; }, mesh = {Aid to Families with Dependent Children/economics/*statistics & numerical data ; Child ; Child Abuse/*statistics & numerical data ; Child, Preschool ; Crime/*statistics & numerical data ; Databases, Factual ; *Family ; Female ; Humans ; Infant ; Male ; *Mandatory Reporting ; *Poverty ; Proportional Hazards Models ; Public Sector ; United States ; *Urban Population ; }, abstract = {OBJECTIVE: This study uses administrative data to track the first re-reports of maltreatment in a low-income, urban child welfare population (n=4957) while controlling for other public service involvement. Service system involvement is explored across the following sectors: Child Welfare, Income Maintenance, Special Education, Juvenile Court, and various forms of Medicaid-reimbursed medical or mental health care. This study builds knowledge by adding the services dimension to an ecological framework for analyses and by following recurrence for a longer period of time than prior investigations (7.5 years).

METHOD: We model the re-reporting of a child for maltreatment as a function of child, caregiver, service, and neighborhood characteristics using data from birth records, child welfare, income maintenance, Medicaid, adult corrections, juvenile court, special education, law enforcement, and census sources. Bivariate and multivariate analyses are presented, the latter using Cox regression with a robust sandwich covariance matrix estimate to account for the intracluster dependence within tracts.

RESULTS: Key results across bivariate and multivariate analyses included a lower rate of re-reporting among children with parents who were high school graduates and/or permanently exited from the first spell on AFDC (p<.0001); and for children in families that received less intensive in-home services compared to those not receiving services, receiving intensive in-home, or foster care services (p<.0001). Higher rates of re-reporting were found for children with Medicaid mental health/substance abuse treatment records (p<.0001) and special education eligibility for emotional disturbance (p<.005).

CONCLUSIONS: Caretaker characteristics and non-child welfare service use patterns had a strong association with the likelihood of a child being re-reported to the child welfare agency and should be more heavily attended to by child welfare workers. High rates of service sector overlap suggest that interagency ties and cooperation should be strengthened. The lower risk associated with less intensive in-home services compared to un-served cases may indicate under-identification of in-home service eligibility following a first report of maltreatment.}, } @article {pmid17105805, year = {2007}, author = {Carver, V and Reinert, B and Range, LM}, title = {Sustaining tobacco control coalitions amid declining resources.}, journal = {Health promotion practice}, volume = {8}, number = {3}, pages = {292-298}, doi = {10.1177/1524839906289820}, pmid = {17105805}, issn = {1524-8399}, mesh = {Community Networks ; Community Participation ; Compensation and Redress/*legislation & jurisprudence ; *Health Care Coalitions ; Health Promotion/economics/*methods ; Humans ; Leadership ; Liability, Legal/economics ; Mississippi ; *Politics ; *Public Policy ; Smoking/economics/legislation & jurisprudence ; Smoking Cessation/economics/*methods ; *Smoking Prevention ; Social Marketing ; State Government ; Tobacco Industry/economics/*legislation & jurisprudence ; Tobacco Smoke Pollution/economics/legislation & jurisprudence/prevention & control ; United States ; }, abstract = {Mississippi is unique among the 50 states in settling a lawsuit against tobacco companies earlier than the Master Settlement Agreement, devoting a relatively high amount of per capita funding on tobacco control, and avoiding tobacco-control budget cuts. Using a social-ecological approach combining insider and outsider strategies, tobacco-prevention coalitions in Mississippi succeeded in sustaining funding despite serious obstacles. Lessons learned included taking specific actions to embed themselves in the local community, wisely aligning with legislators, choosing courageous and effective champions, and ensuring that people are keenly aware of their existence and efforts. In using these strategies, tobacco-prevention coalitions in Mississippi have become an institution of the community and in so doing helped sustain their funding.}, } @article {pmid17105347, year = {2006}, author = {Guralnick, RP and Wieczorek, J and Beaman, R and Hijmans, RJ and , }, title = {BioGeomancer: automated georeferencing to map the world's biodiversity data.}, journal = {PLoS biology}, volume = {4}, number = {11}, pages = {e381}, pmid = {17105347}, issn = {1545-7885}, mesh = {Animals ; *Biodiversity ; Computational Biology/*methods ; *Conservation of Natural Resources ; *Databases, Factual ; Earth, Planet ; Environment ; Geography/*methods ; }, abstract = {The BioGeomancer Project provides a toolkit to georeference data and specimens collected for natural history collections, a crucial task if the potential of these specimens is to be fully realized.}, } @article {pmid17102485, year = {2006}, author = {Wilson, L and Gallagher Gordon, M and Cornelius, F and Rockstraw, L}, title = {National Library of Medicine and the Marine Biological Laboratory Biomedical Informatics Fellowship--one team's experience.}, journal = {Studies in health technology and informatics}, volume = {122}, number = {}, pages = {957}, pmid = {17102485}, issn = {0926-9630}, mesh = {Humans ; *Marine Biology ; Medical Informatics/*education ; *National Library of Medicine (U.S.) ; United States ; }, abstract = {Drexel University College of Nursing and Health Professions incorporates informatics in all aspects of the undergraduate and graduate curriculums. Four members of the Informatics Team completed the National Library of Medicine and the Marine Biological Laboratory's Informatics Fellowship. This presentation will describe this life changing experience for this informatics team.}, } @article {pmid17099228, year = {2007}, author = {Loy, A and Maixner, F and Wagner, M and Horn, M}, title = {probeBase--an online resource for rRNA-targeted oligonucleotide probes: new features 2007.}, journal = {Nucleic acids research}, volume = {35}, number = {Database issue}, pages = {D800-4}, pmid = {17099228}, issn = {1362-4962}, support = {P 18836/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Bacteria/classification/genetics ; *Databases, Nucleic Acid ; Internet ; Oligonucleotide Array Sequence Analysis ; *Oligonucleotide Probes ; Phylogeny ; RNA, Ribosomal/classification/*genetics ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 18S/genetics ; Software ; User-Computer Interface ; }, abstract = {probeBase is a curated database of annotated rRNA-targeted oligonucleotide probes and supporting information. Rapid access to probe, microarray and reference data is achieved by powerful search tools and via different lists that are based on selected categories such as functional or taxonomic properties of the target organism(s) or the hybridization format (fluorescence in situ hybridization or microarray) in which the probes were applied. Additional information on probe coverage and specificity is available through direct submissions of probe sequences from probeBase to RDP-II and Greengenes, two major rRNA sequence databases. A freely editable user comments field for each probe entry allows any user to add, modify or remove information or to report errors in real-time. probeBase entries increased from 700 to more than 1200 during the past three years. Several options for submission of single probes or entire probe sets, even prior to publication of newly developed probes, should further contribute to keeping probeBase an up-to-date and useful resource. probeBase is freely accessible at http://www.microbial-ecology.net/probebase. Email correspondence can be addressed to probebase@microbial-ecology.net.}, } @article {pmid17099225, year = {2007}, author = {Girard, LR and Fiedler, TJ and Harris, TW and Carvalho, F and Antoshechkin, I and Han, M and Sternberg, PW and Stein, LD and Chalfie, M}, title = {WormBook: the online review of Caenorhabditis elegans biology.}, journal = {Nucleic acids research}, volume = {35}, number = {Database issue}, pages = {D472-5}, pmid = {17099225}, issn = {1362-4962}, support = {P41 HG002223/HG/NHGRI NIH HHS/United States ; P41 HG02223/HG/NHGRI NIH HHS/United States ; }, mesh = {Animals ; Caenorhabditis elegans/genetics/*physiology ; *Databases, Factual ; Internet ; Software ; User-Computer Interface ; }, abstract = {WormBook (www.wormbook.org) is an open-access, online collection of original, peer-reviewed chapters on the biology of Caenorhabditis elegans and related nematodes. Since WormBook was launched in June 2005 with 12 chapters, it has grown to over 100 chapters, covering nearly every aspect of C.elegans research, from Cell Biology and Neurobiology to Evolution and Ecology. WormBook also serves as the text companion to WormBase, the C.elegans model organism database. Objects such as genes, proteins and cells are linked to the relevant pages in WormBase, providing easily accessible background information. Additionally, WormBook chapters contain links to other relevant topics in WormBook, and the in-text citations are linked to their abstracts in PubMed and full-text references, if available. Since WormBook is online, its chapters are able to contain movies and complex images that would not be possible in a print version. WormBook is designed to keep up with the rapid pace of discovery in the field of C.elegans research and continues to grow. WormBook represents a generic publishing infrastructure that is easily adaptable to other research communities to facilitate the dissemination of knowledge in the field.}, } @article {pmid17091004, year = {2006}, author = {Lee, SJ and Park, JM}, title = {[Evaluation of visiting nursing care using geographical information system (GIS) technology].}, journal = {Taehan Kanho Hakhoe chi}, volume = {36}, number = {6}, pages = {1042-1054}, doi = {10.4040/jkan.2006.36.6.1042}, pmid = {17091004}, issn = {1598-2874}, mesh = {Aged ; Aged, 80 and over ; *Community Health Planning ; Female ; *Geographic Information Systems ; *Health Services for the Aged ; Health Status ; *Home Care Services ; Humans ; Male ; Middle Aged ; Needs Assessment ; Socioeconomic Factors ; Task Performance and Analysis ; }, abstract = {PURPOSE: Previous evaluation studies of the visiting nursing program explained an average change of the participants' health status, without considering socio-ecological characteristics and their impacts. However, these factors must affect individual health problems and lifestyles. For effective and appropriate community based programs, the Geographical Information System (GIS) can be utilized. GIS is a computer-based tool for mapping and analyzing things that happen on earth, and integrates statistical analysis with unique visualization. The purpose of this study was to evaluate visiting nursing care and to advocate the usefulness of planning and evaluating visiting nursing programs using Exploratory Spatial Data Analysis (ESDA) with GIS technology.

METHODS: One hundred eighty-four elderly participants with cerebrovascular risk factors who lived in 13 areas of one community received visiting nursing care. The data analyzed characteristics of pre-post change and autocorrelation by ESDA using GIS technology.

RESULTS: Visiting nursing care showed an improvement in the participants' lifestyle habits, and family management ability and stress level, while the improvements were different depending on the regions. The change of family management ability and stress level correlated with neighborhoods (Morgan's I= 0.1841, 0.1675).

CONCLUSIONS: Community health providers need to consider the individual participant's health status as well as socio-ecological factors. Analysis using GIS technology will contribute to the effective monitoring, evaluation and design of a visiting nursing program.}, } @article {pmid17090583, year = {2007}, author = {Cole, JR and Chai, B and Farris, RJ and Wang, Q and Kulam-Syed-Mohideen, AS and McGarrell, DM and Bandela, AM and Cardenas, E and Garrity, GM and Tiedje, JM}, title = {The ribosomal database project (RDP-II): introducing myRDP space and quality controlled public data.}, journal = {Nucleic acids research}, volume = {35}, number = {Database issue}, pages = {D169-72}, pmid = {17090583}, issn = {1362-4962}, mesh = {*Databases, Nucleic Acid ; Internet ; Quality Control ; RNA, Ribosomal/*chemistry ; Sequence Analysis, RNA/standards ; User-Computer Interface ; }, abstract = {Substantial new features have been implemented at the Ribosomal Database Project in response to the increased importance of high-throughput rRNA sequence analysis in microbial ecology and related disciplines. The most important changes include quality analysis, including chimera detection, for all available rRNA sequences and the introduction of myRDP Space, a new web component designed to help researchers place their own data in context with the RDP's data. In addition, new video tutorials describe how to use RDP features. Details about RDP data and analytical functions can be found at the RDP-II website (http://rdp.cme.msu.edu/).}, } @article {pmid17080024, year = {2007}, author = {Storfer, A and Murphy, MA and Evans, JS and Goldberg, CS and Robinson, S and Spear, SF and Dezzani, R and Delmelle, E and Vierling, L and Waits, LP}, title = {Putting the "landscape" in landscape genetics.}, journal = {Heredity}, volume = {98}, number = {3}, pages = {128-142}, doi = {10.1038/sj.hdy.6800917}, pmid = {17080024}, issn = {0018-067X}, mesh = {Animals ; Data Interpretation, Statistical ; *Ecosystem ; Genetic Variation ; *Genetics ; Genetics, Population ; Models, Genetic ; }, abstract = {Landscape genetics has emerged as a new research area that integrates population genetics, landscape ecology and spatial statistics. Researchers in this field can combine the high resolution of genetic markers with spatial data and a variety of statistical methods to evaluate the role that landscape variables play in shaping genetic diversity and population structure. While interest in this research area is growing rapidly, our ability to fully utilize landscape data, test explicit hypotheses and truly integrate these diverse disciplines has lagged behind. Part of the current challenge in the development of the field of landscape genetics is bridging the communication and knowledge gap between these highly specific and technical disciplines. The goal of this review is to help bridge this gap by exposing geneticists to terminology, sampling methods and analysis techniques widely used in landscape ecology and spatial statistics but rarely addressed in the genetics literature. We offer a definition for the term "landscape genetics", provide an overview of the landscape genetics literature, give guidelines for appropriate sampling design and useful analysis techniques, and discuss future directions in the field. We hope, this review will stimulate increased dialog and enhance interdisciplinary collaborations advancing this exciting new field.}, } @article {pmid17078117, year = {2006}, author = {Lewis, R}, title = {A jumping off point.}, journal = {Nature}, volume = {443}, number = {7111}, pages = {600-601}, doi = {10.1038/nj7111-600a}, pmid = {17078117}, issn = {1476-4687}, mesh = {Animals ; Biodiversity ; *Biological Evolution ; Computational Biology/economics/*trends ; Ecology/economics/trends ; Genetic Speciation ; Genome/*genetics ; Genomics/economics/*trends ; Humans ; Mice ; Phylogeny ; }, } @article {pmid17074370, year = {2007}, author = {Wells, E and Wilkinson, M and Wood, P and Scanlan, C}, title = {The use of macroalgal species richness and composition on intertidal rocky seashores in the assessment of ecological quality under the European Water Framework Directive.}, journal = {Marine pollution bulletin}, volume = {55}, number = {1-6}, pages = {151-161}, doi = {10.1016/j.marpolbul.2006.08.031}, pmid = {17074370}, issn = {0025-326X}, mesh = {Databases, Factual ; *Ecosystem ; Environmental Monitoring/*methods/*standards/statistics & numerical data ; Eukaryota/*growth & development ; International Cooperation/legislation & jurisprudence ; Ireland ; Species Specificity ; United Kingdom ; }, abstract = {The EC Water Framework Directive (WFD) suggests using abundance and species composition of intertidal seaweed communities for ecological quality classification of rocky seashores. There are two difficulties with this. According to WFD all sensitive species should be present on a shore. There is no accepted list of sensitive seaweed species and those which may be sensitive in one location may not be so in another. Second, natural successions can result in very large abundance changes of common species, e.g. from almost completely fucoid-dominated shores to almost totally barnacle-dominated shores, without any change in ecological quality. Studies have shown that numerical species richness, not the list of actual species present, is broadly constant in the absence of disturbance. The ephemeral species, possibly the sensitive members of the community, change regularly in such a way as to conserve species richness. It is proposed that species richness on a defined length of shore be used as a criterion of ecological quality. A database of species found on over 300 shores in the British Isles, under strictly controlled sampling conditions, has given ranges of values of species richness to be expected and has allowed for variations in these values due to sub-habitat variability, wave exposure and turbidity to be factored in. A major problem in applying such a tool is the lack of expertise of many workers in critical identification of seaweed species. A reduced species list has been extracted from the database using species commonly present and identifiable with reasonable certainty. A numerical index of ecological quality is proposed based on scores for various aspects of the physical nature of the habitat combined with a score for species richness which may be based on the reduced species list. The scoring system also uses further aspects of community structure, such as ecological status groups and the proportions of rhodophyta, chlorophyta and opportunist species. For this system to be effective there has to be close control of the way in which sampling is carried out to ensure a uniform level of thoroughness.}, } @article {pmid17066707, year = {2006}, author = {Wang, A and Zhao, G and Wang, R and Yuan, X}, title = {[Eco-environmental evaluation and spatial-temporal collocation of regional land consolidation].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {17}, number = {8}, pages = {1481-1484}, pmid = {17066707}, issn = {1001-9332}, mesh = {China ; Crops, Agricultural/*growth & development ; Ecology/methods ; *Ecosystem ; *Environment ; Evaluation Studies as Topic ; Geographic Information Systems ; Soil/*analysis ; }, abstract = {Eco-environmental evaluation and spatial-temporal collocation of land consolidation is the basis of regional land consolidation. Taking Qingzhou County of Shandong Province as an example, this paper established the eco-environmental evaluation index system and evaluation model of land consolidation, based on the systematic analysis of land consolidation characteristics and natural and social conditions of Qingzhou County. The comprehensive score of each evaluation unit was obtained by integrated index evaluation method and GIS techniques, and the spatial-temporal collocation of regional land consolidation was proposed accordingly. The results indicated that in Qingzhou County, the total area of cultivated and un-utilized land was 1446 km2, among which, the land consolidation area in near future mainly distributed in the northwest part of plain region, occupying 15.35% of the total, mid-phase land consolidation area mainly distributed in the northwest and central parts of plain region, occupying 13.58%, land consolidation area in specified future mainly distributed in the north part of plain region, occupying 40.71%, and non-land consolidation area mainly distributed in hilly region, occupying 30.36%. These results could provide scientific instruction for the land consolidation planning and implement in Qingzhou County.}, } @article {pmid17063824, year = {2006}, author = {Hernández-Avila, JE and Rodríguez, MH and Betanzos-Reyes, AF and Danis-Lozano, R and Méndez-Galván, JF and Velázquez-Monroy, OJ and Tapia-Conyer, R}, title = {Determinant factors for malaria transmission on the coast of Oaxaca State, the main residual transmission focus in Mexico.}, journal = {Salud publica de Mexico}, volume = {48}, number = {5}, pages = {405-417}, doi = {10.1590/s0036-36342006000500007}, pmid = {17063824}, issn = {0036-3634}, mesh = {Humans ; Malaria/*epidemiology/*transmission ; Mexico/epidemiology ; Risk Factors ; Space-Time Clustering ; }, abstract = {OBJECTIVE: The purpose of this study was to investigate the influence of demographic, socioeconomic and ecological factors in malaria transmission in the most important residual transmission focus in Mexico, located in the state of Oaxaca.

MATERIAL AND METHODS: The extension of the focus was determined by a spatial and time analysis of the distribution of malaria cases in the state between 1998 and 1999 using a Geographical Information System. A malaria transmission intensity index (MTII) was constructed based on the total number of cases during the study period and the duration and frequency of transmission outbreaks within the villages. The relationship between local determinants and malaria transmission intensity was investigated using multinomial and ordered logistic models.

RESULTS: The distribution of villages according to their MTII was: 325 high, 341 medium, 142 low and 717 with no transmission. Localities of high MTII were associated with areas having a tropical climate with summer rains and low water evaporation. Most high MTII villages were located in elevations between 200 and 500 m above sea level, in the area around Pochutla City. The amount of temporary streams in the neighborhood of localities had a highly significant positive association with the MTII. Distance to roads was only significant in the high malaria MTII stratum.

CONCLUSIONS: The main factors determining malaria transmission in the focus are related to good conditions for the breeding of mosquito vectors. The existence of short-range population movements around Pochutla, the main economically active city in the area, indicates the necessity to implement a system of epidemiological surveillance to halt the dispersion of new outbreaks.}, } @article {pmid17062411, year = {2006}, author = {Hanage, WP and Fraser, C and Spratt, BG}, title = {Sequences, sequence clusters and bacterial species.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {361}, number = {1475}, pages = {1917-1927}, pmid = {17062411}, issn = {0962-8436}, support = {030662//Wellcome Trust/United Kingdom ; }, mesh = {Bacteria/*classification/*genetics ; Classification/*methods ; Cluster Analysis ; Databases, Genetic ; Genes, Bacterial/*genetics ; Genetic Speciation ; *Phylogeny ; Sequence Analysis, DNA/*methods ; }, abstract = {Whatever else they should share, strains of bacteria assigned to the same species should have house-keeping genes that are similar in sequence. Single gene sequences (or rRNA gene sequences) have very few informative sites to resolve the strains of closely related species, and relationships among similar species may be confounded by interspecies recombination. A more promising approach (multilocus sequence analysis, MLSA) is to concatenate the sequences of multiple house-keeping loci and to observe the patterns of clustering among large populations of strains of closely related named bacterial species. Recent studies have shown that large populations can be resolved into non-overlapping sequence clusters that agree well with species assigned by the standard microbiological methods. The use of clustering patterns to inform the division of closely related populations into species has many advantages for poorly studied bacteria (or to re-evaluate well-studied species), as it provides a way of recognizing natural discontinuities in the distribution of similar genotypes. Clustering patterns can be used by expert groups as the basis of a pragmatic approach to assigning species, taking into account whatever additional data are available (e.g. similarities in ecology, phenotype and gene content). The development of large MLSA Internet databases provides the ability to assign new strains to previously defined species clusters and an electronic taxonomy. The advantages and problems in using sequence clusters as the basis of species assignments are discussed.}, } @article {pmid17060202, year = {2006}, author = {McMahon, MM and Sanderson, MJ}, title = {Phylogenetic supermatrix analysis of GenBank sequences from 2228 papilionoid legumes.}, journal = {Systematic biology}, volume = {55}, number = {5}, pages = {818-836}, doi = {10.1080/10635150600999150}, pmid = {17060202}, issn = {1063-5157}, mesh = {Algorithms ; Base Sequence ; Cluster Analysis ; Computational Biology/methods ; *Databases, Nucleic Acid ; Fabaceae/*classification/genetics ; Molecular Sequence Data ; *Phylogeny ; Plant Proteins/genetics ; Sequence Alignment ; Sequence Analysis, DNA/*methods ; }, abstract = {A comprehensive phylogeny of papilionoid legumes was inferred from sequences of 2228 taxa in GenBank release 147. A semiautomated analysis pipeline was constructed to download, parse, assemble, align, combine, and build trees from a pool of 11,881 sequences. Initial steps included all-against-all BLAST similarity searches coupled with assembly, using a novel strategy for building length-homogeneous primary sequence clusters. This was followed by a combination of global and local alignment protocols to build larger secondary clusters of locally aligned sequences, thus taking into account the dramatic differences in length of the heterogeneous coding and noncoding sequence data present in GenBank. Next, clusters were checked for the presence of duplicate genes and other potentially misleading sequences and examined for combinability with other clusters on the basis of taxon overlap. Finally, two supermatrices were constructed: a "sparse" matrix based on the primary clusters alone (1794 taxa x 53,977 characters), and a somewhat more "dense" matrix based on the secondary clusters (2228 taxa x 33,168 characters). Both matrices were very sparse, with 95% of their cells containing gaps or question marks. These were subjected to extensive heuristic parsimony analyses using deterministic and stochastic heuristics, including bootstrap analyses. A "reduced consensus" bootstrap analysis was also performed to detect cryptic signal in a subtree of the data set corresponding to a "backbone" phylogeny proposed in previous studies. Overall, the dense supermatrix appeared to provide much more satisfying results, indicated by better resolution of the bootstrap tree, excellent agreement with the backbone papilionoid tree in the reduced bootstrap consensus analysis, few problematic large polytomies in the strict consensus, and less fragmentation of conventionally recognized genera. Nevertheless, at lower taxonomic levels several problems were identified and diagnosed. A large number of methodological issues in supermatrix construction at this scale are discussed, including detection of annotation errors in GenBank sequences; the shortage of effective algorithms and software for local multiple sequence alignment; the difficulty of overcoming effects of fragmentation of data into nearly disjoint blocks in sparse supermatrices; and the lack of informative tools to assess confidence limits in very large trees.}, } @article {pmid17053284, year = {2006}, author = {Rezaeian, M and Dunn, G and St Leger, S and Appleby, L}, title = {Ecological association between suicide rates and indices of deprivation in the north west region of England: the importance of the size of the administrative unit.}, journal = {Journal of epidemiology and community health}, volume = {60}, number = {11}, pages = {956-961}, pmid = {17053284}, issn = {0143-005X}, mesh = {Adolescent ; Adult ; Catchment Area, Health ; Child ; Data Interpretation, Statistical ; England ; Female ; Geography ; Humans ; Incidence ; *Linear Models ; Male ; Middle Aged ; *Psychosocial Deprivation ; Sampling Studies ; *Suicide ; }, abstract = {BACKGROUND AND OBJECTIVE: Most published research on the ecological relationship between suicide rates and indices of deprivation uses only one level of population aggregation - for example, by local authorities. These ecological associations have been studied at both the local authority and the electoral ward level.

METHODS: Data on all deaths for which suicide or an open verdict was returned between 1996 and 1998 in the North West Government Office Region (NWGOR) of England (2336 cases) were the subject of this study. These data were provided by the National Confidential Inquiry into Suicide and Homicide by People with Mental Illness. The income and employment indices of deprivation and the population counts were provided by the Department of the Environment, Transport and the Regions, and the Office for National Statistics, respectively.

RESULTS: Modelling data at the local authority and ward levels in the NWGOR showed that although at the local authorities level there are no significant associations between suicide rates and two indices, at the ward level there are significant associations. The direction of these associations is such that with an increase in the quartile ranks of each index (ie, with improving the situation of a ward in terms of that index), the rate of suicide decreases.

CONCLUSION: A lack of effect was found once we move from ward to local authority level. This may happen because of the non-homogeneous nature of the local authorities in terms of their income and employment indices. In this sense, wards are more homogeneous. This means that in examining ecological risk factors, a balance was found between large areas (diluted effects but greater power) and small areas.}, } @article {pmid17045552, year = {2007}, author = {Tsyusko, O and Yi, Y and Coughlin, D and Main, D and Podolsky, R and Hinton, TG and Glenn, TC}, title = {Radiation-induced untargeted germline mutations in Japanese medaka.}, journal = {Comparative biochemistry and physiology. Toxicology & pharmacology : CBP}, volume = {145}, number = {1}, pages = {103-110}, doi = {10.1016/j.cbpc.2006.08.010}, pmid = {17045552}, issn = {1532-0456}, mesh = {Alleles ; Animals ; DNA/genetics/radiation effects ; DNA-Directed DNA Polymerase ; Data Interpretation, Statistical ; Dose-Response Relationship, Radiation ; Female ; Fertility/radiation effects ; Genome/genetics ; Male ; Microsatellite Repeats/genetics ; Molecular Sequence Data ; Mutation/*radiation effects ; Oryzias/*genetics ; Ovum/radiation effects ; Reverse Transcriptase Polymerase Chain Reaction ; }, abstract = {Radiation has been shown to increase mutation frequencies at tandem repeat loci by indirect interactions of radiation with DNA. We studied germline mutations in chronically exposed Japanese medaka (Oryzias latipes) using microsatellite loci. After screening 26 randomly selected loci among unirradiated parents and their 200 offspring, we selected seven highly mutable loci (0.5-1.0 x 10(-2) mutants per locus per gamete) and two bonus loci for further study. To determine if radiation exposure increases mutation frequencies in these loci, medaka were chronically irradiated from subadults through maturation at relatively low dose rates of 68 mGy/d. Total doses for males and females were 10.4 and 3 Gy, respectively. The mean number of mutations for the offspring of exposed families (0.149+/-0.044) was significantly higher (P=0.018) than for control families (0.080+/-0.028), indicating induction of germline mutations from chronic irradiation. This increase in the microsatellite mutation rate is greater than expected from direct interaction of radiation with DNA, suggesting indirect, untargeted mechanism(s) for mutations. This study identified microsatellite loci with a high mutational background in medaka, variation among loci and families as important variables, and demonstrated the usefulness of this fish model for studying radiation-induced germline mutations.}, } @article {pmid17045303, year = {2007}, author = {Ballesteros, E and Torras, X and Pinedo, S and García, M and Mangialajo, L and de Torres, M}, title = {A new methodology based on littoral community cartography dominated by macroalgae for the implementation of the European Water Framework Directive.}, journal = {Marine pollution bulletin}, volume = {55}, number = {1-6}, pages = {172-180}, doi = {10.1016/j.marpolbul.2006.08.038}, pmid = {17045303}, issn = {0025-326X}, mesh = {Databases, Factual ; Environmental Monitoring/*methods/*standards ; Eukaryota/*growth & development ; *Geographic Information Systems ; Geography ; International Cooperation/legislation & jurisprudence ; Mediterranean Sea ; Population Density ; Reference Standards ; Spain ; }, abstract = {Macroalgae is a biological key element for the assessment of the ecological status in coastal waters in the frame of the European Water Framework Directive (WFD, 2000/60/EC). Here we propose a methodology for monitoring water quality based on the cartography of littoral and upper-sublittoral rocky-shore communities (CARLIT, in short). With the use of spatial databases, GIS, and available information about the value of rocky-shore communities as indicators of water quality, it is possible to obtain an environmental quality index representative of the ecological status of rocky coasts. This index, which completely fulfils the requirements of the WFD, is expressed as a ratio between the observed values in the sector of shore that is being assessed and the expected value in a reference condition zone with the same substrate and coastal morphology (Ecological Quality Ratio, EQR). The application of this index to the coast of Catalonia (North-Western Mediterranean) is presented.}, } @article {pmid17044505, year = {2006}, author = {Cao, X and Zeng, G and Zhang, S and Zhou, J and Zhu, H and Shi, L}, title = {[Ecological functional regionalization of Changsha City based on RS and GIS].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {17}, number = {7}, pages = {1269-1273}, pmid = {17044505}, issn = {1001-9332}, mesh = {China ; *City Planning ; Ecology ; *Ecosystem ; *Environment Design ; *Environmental Monitoring ; *Geographic Information Systems ; Satellite Communications ; }, abstract = {A delineation method based on the idea of regarding urban-suburban-supporting area as a system was presented in this paper, with an ecological-social-economic database created. A total of five ecological suitability regions, four ecological sensitivity regions, four ecological service regions, and five economic development regions were plotted out, and the Changsha City ecosystem was divided into five ecological functional regions, according to the heterogeneity among ecological functional units and the similarity of interior units. The areas of the five functional regions accounted for 29.47%, 32.5%, 25.95%, 9.63% and 2.45% of the total area, respectively. This research method had some advantages over traditional methods. It was flexible and efficient, because it could accept any combination of parameters organized on a polygonal base map. The variables could be added, deleted, or updated to produce new thematic map products in a short period of time. Mapping procedures were quantitative and automated. With the incorporation of remote sensing data and global position system rapid positioning, the ecological and environmental changes could be detected by monitoring the changes of regional boundary patterns. Therefore, the ecological functional regionalization of Changsha City provided a fine way of integrating remote sensing data, global position system, and geographic information system.}, } @article {pmid17043765, year = {2006}, author = {Smid, R and Kubasek, M and Klimes, D and Dusek, L and Jarkovsky, J and Marsalek, B and Hilscherova, K and Blaha, L and Cupr, P and Holoubek, I}, title = {Web portal for management of bioindication methods and ecotoxicological tests in ecological risk assessment.}, journal = {Ecotoxicology (London, England)}, volume = {15}, number = {8}, pages = {623-627}, pmid = {17043765}, issn = {0963-9292}, mesh = {*Conservation of Natural Resources ; Databases, Factual ; Decision Support Techniques ; Humans ; *Internet ; *Models, Theoretical ; Risk Assessment ; Risk Management ; Toxicity Tests/*standards/statistics & numerical data ; }, abstract = {The objective of this article is to inform about efforts to design and implement a data model that can parametrically describe and store information about a wide range of ecotoxicological tests and bioindication methods used in Ecological Risk Assessment (EcoRA). At the same time it describes comprehensive web-based portal built on this model that can be used to quickly find relevant biological assays (ecotoxicological biotests) for given situation and therefore support the decision-making process in EcoRA. The model structure, features of the corresponding website and its current content is described in detail and proposed development and possible collaboration is outlined. The portal (DATEST) is located at http://projects.cba.muni.cz/datest. The aim of this work is to complement existing EcoRA decision-support tools with a web-based engine for storing and searching biological tests and methods used in EcoRA as there is currently no similar informational source available on the Internet.}, } @article {pmid17033679, year = {2007}, author = {Portnov, BA and Dubnov, J and Barchana, M}, title = {On ecological fallacy, assessment errors stemming from misguided variable selection, and the effect of aggregation on the outcome of epidemiological study.}, journal = {Journal of exposure science & environmental epidemiology}, volume = {17}, number = {1}, pages = {106-121}, doi = {10.1038/sj.jes.7500533}, pmid = {17033679}, issn = {1559-0631}, mesh = {Child ; *Ecology ; Epidemiologic Studies ; Geographic Information Systems ; Health Status Indicators ; Humans ; Israel/epidemiology ; Respiratory Function Tests ; }, abstract = {In social and environmental sciences, ecological fallacy is an incorrect assumption about an individual based on aggregate data for a group. In the present study, the validity of this assumption was tested using both individual estimates of exposure to air pollution and aggregate data for 1,492 schoolchildren living in the in vicinity of a major coal-fired power station in the Hadera region of Israel. In 1996 and 1999, the children underwent subsequent pulmonary function tests (PFT), and their parents completed a detailed questionnaire on their health status and housing conditions. The association between children's PFT results and their exposure to air pollution was investigated in two phases. During the first phase, PFT averages were compared with average levels of air pollution detected in townships, and small census areas in which the children reside. During the second phase, individual pollution estimates were compared with individual PFT results, and pattern detection techniques (Getis-Ord statistic) were used to investigate the spatial data structure. While different levels of areal data aggregation changed the results only marginally, the choice of indices measuring the children's PFT performance had a significant influence on the outcome of the analysis. As argued, differences between individual-level and group-level effects of exposure (i.e., ecological or cross-level bias) are not necessary outcomes of data aggregation, and that seemingly unexpected results may often stem from a misguided selection of variables chosen to measure health effects. The implications of the results of the analysis for epidemiological studies are discussed, and recommendations for public health policy are formulated.}, } @article {pmid17029686, year = {2007}, author = {Rita, H and Ekholm, P}, title = {Showing similarity of results given by two methods: a commentary.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {145}, number = {2}, pages = {383-386}, doi = {10.1016/j.envpol.2006.08.007}, pmid = {17029686}, issn = {0269-7491}, mesh = {*Data Interpretation, Statistical ; Ecology/*methods ; Models, Statistical ; Software ; Therapeutic Equivalency ; }, abstract = {There is a frequent need in the environmental sciences to show the similarity of the results given by two analytical methods. This cannot, however, be done within the conventional 'there is a difference' statistical hypothesis setting of, among others, Student's t-test. We demonstrate here a more appropriate approach that originates from drug testing and that can be applied with standard statistical software. It is a challenging approach, as it requires quantification of the similarity limit. If no pre-determined value is given for similarity, a potential data-supported similarity limit can be explored from the data. The approach has numerous other potential application areas, e.g. parallelism of regression slopes, homogeneity of variances and lack of interaction.}, } @article {pmid17029557, year = {2006}, author = {Jenke-Kodama, H and Börner, T and Dittmann, E}, title = {Natural biocombinatorics in the polyketide synthase genes of the actinobacterium Streptomyces avermitilis.}, journal = {PLoS computational biology}, volume = {2}, number = {10}, pages = {e132}, pmid = {17029557}, issn = {1553-7358}, mesh = {Computational Biology ; Macrolides/chemistry/metabolism ; Molecular Structure ; Multigene Family/genetics ; Phylogeny ; Polyketide Synthases/*genetics/*metabolism ; Recombination, Genetic/*genetics ; Streptomyces/enzymology/*genetics/*metabolism ; }, abstract = {Modular polyketide synthases (PKSs) of bacteria provide an enormous reservoir of natural chemical diversity. Studying natural biocombinatorics may aid in the development of concepts for experimental design of genes for the biosynthesis of new bioactive compounds. Here we address the question of how the modularity of biosynthetic enzymes and the prevalence of multiple gene clusters in Streptomyces drive the evolution of metabolic diversity. The phylogeny of ketosynthase (KS) domains of Streptomyces PKSs revealed that the majority of modules involved in the biosynthesis of a single compound evolved by duplication of a single ancestor module. Using Streptomyces avermitilis as a model organism, we have reconstructed the evolutionary relationships of different domain types. This analysis suggests that 65% of the modules were altered by recombinational replacements that occurred within and between biosynthetic gene clusters. The natural reprogramming of the biosynthetic pathways was unambiguously confined to domains that account for the structural diversity of the polyketide products and never observed for the KS domains. We provide examples for natural acyltransferase (AT), ketoreductase (KR), and dehydratase (DH)-KR domain replacements. Potential sites of homologous recombination could be identified in interdomain regions and within domains. Our results indicate that homologous recombination facilitated by the modularity of PKS architecture is the most important mechanism underlying polyketide diversity in bacteria.}, } @article {pmid17010487, year = {2007}, author = {Luo, W and Wang, T and Lu, Y and Giesy, JP and Shi, Y and Zheng, Y and Xing, Y and Wu, G}, title = {Landscape ecology of the Guanting Reservoir, Beijing, China: multivariate and geostatistical analyses of metals in soils.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {146}, number = {2}, pages = {567-576}, doi = {10.1016/j.envpol.2006.08.001}, pmid = {17010487}, issn = {0269-7491}, mesh = {Arsenic/analysis ; Cadmium/analysis ; China ; Chromium/analysis ; Copper/analysis ; Fertilizers/analysis ; Geographic Information Systems ; Lead/analysis ; Metals, Heavy/*analysis ; Nickel/analysis ; Principal Component Analysis/methods ; Sewage ; Soil Pollutants/*analysis ; Waste Disposal, Fluid ; *Water Supply ; Zinc/analysis ; }, abstract = {Surface soil samples were collected from 52 sites around Guanting Reservoir in Beijing, China, and contents of 'total' metals (Cu, Zn, Pb, Cd, As, Ni and Cr) were determined. The results indicate that the degree of heavy metal pollution in the soils declines in the order of Cd>Cr>Zn>As>Cu>Ni>Pb. Based on the results of a combination of multivariate statistics and geostatiscal analyses, it was concluded that land application of phosphate fertilizer, wastewater and sludge were the primary sources of Cd and Zn in soils. Whereas As, Cu, Cr and Ni in some soils were due to natural rock weathering. The sources of Pb in soils only partially originated from land application of phosphate fertilizer, but mainly from vehicle exhaust. The greatest concentrations of all metals, except for Pb, were found in Huailai County and the towns of Yanghedaqiao and Guanting.}, } @article {pmid17004219, year = {2006}, author = {Börger, L and Franconi, N and Ferretti, F and Meschi, F and De Michele, G and Gantz, A and Coulson, T}, title = {An integrated approach to identify spatiotemporal and individual-level determinants of animal home range size.}, journal = {The American naturalist}, volume = {168}, number = {4}, pages = {471-485}, doi = {10.1086/507883}, pmid = {17004219}, issn = {1537-5323}, mesh = {Age Factors ; Animals ; Climate ; Deer/*physiology ; *Demography ; *Ecosystem ; Geographic Information Systems ; Homing Behavior/*physiology ; Italy ; *Models, Biological ; Photoperiod ; Sex Factors ; Telemetry ; Time Factors ; }, abstract = {Animal home range use is a central focus of ecological research. However, how and why home range size varies between individuals is not well studied or understood for most species. We develop a hierarchical analytical approach--using generalized linear mixed-effects modeling of time series of home range sizes--that allows variance in home range size to be decomposed into components due to variation in temporal, spatial, and individual-level processes, also facilitating intra- and interspecific comparative analyses. We applied the approach to data from a roe deer population radiotracked in central Italy. Over multiple timescales, temporal variation is explained by photoperiod and climate and spatial variation by the distribution of habitat types and spatial variance in radiotracking error. Differences between individuals explained a substantial amount of variance in home range size, but only a relatively minor part was explained by the individual attributes of sex and age. We conclude that the choice of temporal scale at which data are collected and the definition of home range can significantly influence biological inference. We suggest that the appropriate choice of scale and definition requires a good understanding of the ecology and life history of the study species. Our findings contrast with several common assumptions about roe deer behavior.}, } @article {pmid17002771, year = {2006}, author = {Fidler, F and Burgman, MA and Cumming, G and Buttrose, R and Thomason, N}, title = {Impact of criticism of null-hypothesis significance testing on statistical reporting practices in conservation biology.}, journal = {Conservation biology : the journal of the Society for Conservation Biology}, volume = {20}, number = {5}, pages = {1539-1544}, doi = {10.1111/j.1523-1739.2006.00525.x}, pmid = {17002771}, issn = {0888-8892}, mesh = {Conservation of Natural Resources/*methods/*statistics & numerical data ; *Data Interpretation, Statistical ; Decision Making ; Ecology/*statistics & numerical data ; Publishing ; Research Design/statistics & numerical data ; }, abstract = {Over the last decade, criticisms of null-hypothesis significance testing have grown dramatically, and several alternative practices, such as confidence intervals, information theoretic, and Bayesian methods, have been advocated. Have these calls for change had an impact on the statistical reporting practices in conservation biology? In 2000 and 2001, 92% of sampled articles in Conservation Biology and Biological Conservation reported results of null-hypothesis tests. In 2005 this figure dropped to 78%. There were corresponding increases in the use of confidence intervals, information theoretic, and Bayesian techniques. Of those articles reporting null-hypothesis testing--which still easily constitute the majority--very few report statistical power (8%) and many misinterpret statistical nonsignificance as evidence for no effect (63%). Overall, results of our survey show some improvements in statistical practice, but further efforts are clearly required to move the discipline toward improved practices.}, } @article {pmid16999580, year = {2006}, author = {Holena, M}, title = {Piecewise-linear neural networks and their relationship to rule extraction from data.}, journal = {Neural computation}, volume = {18}, number = {11}, pages = {2813-2853}, doi = {10.1162/neco.2006.18.11.2813}, pmid = {16999580}, issn = {0899-7667}, mesh = {*Algorithms ; Animals ; Artificial Intelligence ; *Data Interpretation, Statistical ; Ecology ; Fuzzy Logic ; Humans ; *Linear Models ; *Neural Networks, Computer ; Pattern Recognition, Automated/*methods ; }, abstract = {This article addresses the topic of extracting logical rules from data by means of artificial neural networks. The approach based on piecewise linear neural networks is revisited, which has already been used for the extraction of Boolean rules in the past, and it is shown that this approach can be important also for the extraction of fuzzy rules. Two important theoretical properties of piecewise-linear neural networks are proved, allowing an elaboration of the basic ideas of the approach into several variants of an algorithm for the extraction of Boolean rules. That algorithm has already been used in two real-world applications. Finally, a connection to the extraction of rules of the Łukasiewicz logic is established, relying on recent results about rational McNaughton functions. Based on one of the constructive proofs of the McNaughton theorem, an algorithm is formulated that in principle allows extracting a particular kind of formulas of the Łukasiewicz predicate logic from piecewise-linear neural networks trained with rational data.}, } @article {pmid16996198, year = {2007}, author = {Bealey, WJ and McDonald, AG and Nemitz, E and Donovan, R and Dragosits, U and Duffy, TR and Fowler, D}, title = {Estimating the reduction of urban PM10 concentrations by trees within an environmental information system for planners.}, journal = {Journal of environmental management}, volume = {85}, number = {1}, pages = {44-58}, doi = {10.1016/j.jenvman.2006.07.007}, pmid = {16996198}, issn = {0301-4797}, mesh = {Air Pollutants/analysis ; Air Pollution/*prevention & control ; Databases, Factual ; *Decision Support Techniques ; Particle Size ; *Particulate Matter/analysis ; *Trees ; United Kingdom ; }, abstract = {Trees have been widely quoted as effective scavengers of both gaseous and particulate pollutants from the atmosphere. Recent work on the deposition of urban aerosols onto woodland allows the effect of tree planting strategies on airborne aerosol concentrations to be quantified and considered within the planning process. By identifying the potential planting locations in the local authority area, and applying them within a dispersion and deposition model, the potential magnitude of reduction in the ambient concentration of PM(10), achievable through urban tree planting, has been quantified for two UK cities. As part of the Environmental Information Systems for Planners (EISP), flow diagrams, based on planning decisions, have incorporated output from the model to make decisions on land use planning ranging from development plans and strategic planning, to development control. In this way, for any new developments that contribute to the local PM(10) level, the mitigation by planting trees can be assessed, and in some cases, reductions can be sufficient to meet air quality objectives for PM(10).}, } @article {pmid16996132, year = {2007}, author = {Baird, DJ and Van den Brink, PJ}, title = {Using biological traits to predict species sensitivity to toxic substances.}, journal = {Ecotoxicology and environmental safety}, volume = {67}, number = {2}, pages = {296-301}, doi = {10.1016/j.ecoenv.2006.07.001}, pmid = {16996132}, issn = {0147-6513}, mesh = {Animals ; Databases, Factual ; Environmental Monitoring/*methods ; Environmental Pollutants/*toxicity ; *Models, Biological ; Species Specificity ; }, abstract = {Species sensitivity distributions (SSD) assume that sensitivity to toxicants within target species is random. While the SSD approach has shown promise, it is limited by the fact that data are sparse for most compounds, and that these data are largely based on the lethal responses of a small group of testing lab species. Here we present an alternative approach, based on the hypothesis that organisms' sensitivity to stress is a function of their biology, and can be predicted from species traits such as morphology, life history, physiology and feeding ecology. Using data from the US EPA's AQUIRE database, we found that four species traits explained 71% of the variability in sensitivity to toxicants within a group of 12 species exposed to 15 chemicals. Our results indicate that this approach has promise, but effort is needed to compile species trait information to increase the power, precision and taxonomic representativeness of this approach.}, } @article {pmid16989508, year = {2006}, author = {Colding, J and Lundberg, J and Folke, C}, title = {Incorporating green-area user groups in urban ecosystem management.}, journal = {Ambio}, volume = {35}, number = {5}, pages = {237-244}, doi = {10.1579/05-a-098r.1}, pmid = {16989508}, issn = {0044-7447}, mesh = {Biodiversity ; *Cities ; City Planning/*methods ; Conservation of Natural Resources/methods ; *Ecosystem ; Geographic Information Systems ; Plant Development ; Sweden ; Urban Population ; }, abstract = {We analyze the role of urban green areas managed by local user groups in their potential for supporting biodiversity and ecosystem services in growing city-regions, with focus on allotment areas, domestic gardens, and golf courses. Using Stockholm, Sweden, as an example cityregion, we compile GIS data of its spatial characteristics and relate these data to GIS data for protected areas and "green wedges" prioritized in biodiversity conservation. Results reveal that the three land uses cover 18% of the studied land area of metropolitan Stockholm, which corresponds to more than twice the land set aside as protected areas. We review the literature to identify ecosystem functions and services provided by the three green areas and discuss their potential in urban ecosystem management. We conclude that the incorporation of locally managed lands, and their stewards and institutions, into comanagement designs holds potential for improving conditions for urban biodiversity, reducing transaction costs in ecosystem management, and realizing local Agenda 21.}, } @article {pmid16987615, year = {2006}, author = {Gu, J and Li, WH}, title = {Are GC-rich isochores vanishing in mammals?.}, journal = {Gene}, volume = {385}, number = {}, pages = {50-56}, doi = {10.1016/j.gene.2006.03.026}, pmid = {16987615}, issn = {0378-1119}, mesh = {Animals ; Databases, Genetic ; Evolution, Molecular ; *GC Rich Sequence ; Isochores/*genetics ; Likelihood Functions ; Mammals/classification/*genetics ; Marsupialia/genetics ; Models, Genetic ; Phylogeny ; Rabbits ; }, abstract = {Several studies of nucleotide substitution patterns in mammalian species suggested that GC-rich isochores might be vanishing in mammalian genomes. However, the number of genes and the number of genomes included in these studies might not have given a reliable broad view of the trend in GC change in mammals. It is therefore worth exploiting this issue with a broader coverage of mammalian genomes using a reliable approach, the maximum likelihood approach. We have applied two maximum likelihood methods to infer the ancestral GC contents of 176 mammalian genes from representative eutherian species and at least one marsupial species. Except for a large GC decrease in marsupial genes, we found no general decreasing trend in GC content in GC-rich genes or in other genes among eutherian mammals; indeed, the GC content of GC-rich genes appears to have increased in recent times in some genomes, e.g., the rabbit. For the large GC decrease in marsupials, it could be mainly due to the great reduction in chromosome number, which could lead to a large reduction in recombination rate and thus also a large reduction in the rate of gene conversion. Since many eutherian mammals still maintain a fairly large number of chromosomes, it is unlikely that GC-rich isochores are vanishing in these mammals.}, } @article {pmid16972298, year = {2006}, author = {Singh, OV}, title = {Proteomics and metabolomics: the molecular make-up of toxic aromatic pollutant bioremediation.}, journal = {Proteomics}, volume = {6}, number = {20}, pages = {5481-5492}, doi = {10.1002/pmic.200600200}, pmid = {16972298}, issn = {1615-9853}, mesh = {Biodegradation, Environmental ; Computational Biology/methods ; Databases, Protein ; Electrophoresis, Gel, Two-Dimensional ; Environment ; Environmental Pollutants/*pharmacology ; *Environmental Pollution ; Magnetic Resonance Spectroscopy ; Mass Spectrometry/methods ; Metabolism ; Protein Interaction Mapping ; Proteomics/*methods ; }, abstract = {Microbial-mediated attenuation of toxic aromatic pollutants offers great potential for the restoration of contaminated environments in an ecologically acceptable manner. However, incomplete biological information regarding the regulation of growth and metabolism in many microbial communities restricts progress in the site-specific mineralization process. In the postgenomic era, recent advances in MS have allowed enormous progress in proteomics and elucidated many complex biological interactions. These research forefronts are now expanding toward the analysis of low-molecular-weight primary and secondary metabolites analysis, i.e., metabolomics. The advent of 2-DE in conjunction with MS offers a promising approach to address the molecular mechanisms of bioremediation. The two fields of proteomics and metabolomics have thus far worked separately to identify proteins and primary and secondary metabolites during bioremediation. A simultaneous study combining functional proteomics and metabolomics, i.e., proteometabolomics would create a system-wide approach to studying site-specific microorganisms during active mineralization processes. This article deals with advances in environmental proteomics and metabolomics and advocates the simultaneous study of both technologies to implement cell-free bioremediation.}, } @article {pmid16972288, year = {2006}, author = {Dowling, VA and Sheehan, D}, title = {Proteomics as a route to identification of toxicity targets in environmental toxicology.}, journal = {Proteomics}, volume = {6}, number = {20}, pages = {5597-5604}, doi = {10.1002/pmic.200600274}, pmid = {16972288}, issn = {1615-9853}, mesh = {Chromatography ; Computational Biology/methods ; Ecology ; Ecosystem ; Electrophoresis, Gel, Two-Dimensional ; Environment ; Environmental Pollutants ; Mass Spectrometry ; Oligonucleotide Array Sequence Analysis ; Oxidation-Reduction ; Proteome ; Proteomics/*methods ; Toxicogenetics/methods ; Toxicology/methods ; }, abstract = {Ecotoxicology describes a three-way relationship between ecosystems, chemical pollutants and living organisms. It is predicated on the fact that chemical pollution can exert toxic effects on organisms at the individual and population levels. These toxic effects may provide important information to supplement chemical analysis of environmental samples and aid in assessing the environmental quality of specific ecosystems. Traditionally, effects have been detected by means of biomarkers which, of necessity, were often molecules or processes known to be affected by pollutants. Proteomics provides a means of achieving high-throughput analysis of effects on protein populations and sub-populations with the potential to identify novel biomarkers. This review summarises the main approaches currently used in this area and assesses the potential of proteomics for identification of novel toxicity targets.}, } @article {pmid16969942, year = {2006}, author = {Moore, BR and Smith, SA and Donoghue, MJ}, title = {Increasing data transparency and estimating phylogenetic uncertainty in supertrees: Approaches using nonparametric bootstrapping.}, journal = {Systematic biology}, volume = {55}, number = {4}, pages = {662-676}, doi = {10.1080/10635150600920693}, pmid = {16969942}, issn = {1063-5157}, mesh = {Classification/*methods ; Computer Simulation ; *Data Interpretation, Statistical ; *Models, Statistical ; *Phylogeny ; *Uncertainty ; }, abstract = {The estimation of ever larger phylogenies requires consideration of alternative inference strategies, including divide-and-conquer approaches that decompose the global inference problem to a set of smaller, more manageable component problems. A prominent locus of research in this area is the development of supertree methods, which estimate a composite tree by combining a set of partially overlapping component topologies. Although promising, the use of component tree topologies as the primary data dissociates supertrees from complexities within the underling character data and complicates the evaluation of phylogenetic uncertainty. We address these issues by exploring three approaches that variously incorporate nonparametric bootstrapping into a common supertree estimation algorithm (matrix representation with parsimony, although any algorithm might be used), including bootstrap-weighting, source-tree bootstrapping, and hierarchical bootstrapping. We illustrate these procedures by means of hypothetical and empirical examples. Our preliminary experiments suggest that these methods have the potential to improve the correspondence of supertree estimates to those derived from simultaneous analysis of the combined data and to allow uncertainty in supertree topologies to be quantified. The ability to increase the transparency of supertrees to the underlying character data has several practical implications and sheds new light on an old debate. These methods have been implemented in the freely available program, tREeBOOT.}, } @article {pmid16964936, year = {2006}, author = {Xu, P and Zhao, D}, title = {[Ecological environmental quality assessment of Hangzhou urban area based on RS and GIS].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {17}, number = {6}, pages = {1034-1038}, pmid = {16964936}, issn = {1001-9332}, mesh = {China ; *Conservation of Natural Resources ; Ecology ; *Ecosystem ; *Environment Design ; *Environmental Monitoring ; *Geographic Information Systems ; Quality Control ; Satellite Communications ; }, abstract = {In allusion to the shortage of traditional ecological environmental quality assessment, this paper studied the spatial distribution of assessing factors at a mid-small scale, and the conversion of integer character to girding assessing cells. The main assessing factors including natural environmental condition, environmental quality, natural landscape and urbanization pressure, which were classified into four types with about eleven assessing factors, were selected from RS images and GIS-spatial analyzing environmental quality vector graph. Based on GIS, a comprehensive assessment model for the ecological environmental quality in Hangzhou urban area was established. In comparison with observed urban heat island effects, the assessment results were in good agreement with the ecological environmental quality in the urban area of Hangzhou.}, } @article {pmid16963176, year = {2006}, author = {Procter, C and Comber, L and Betson, M and Buckley, D and Frost, A and Lyons, H and Riding, A and Voyce, K}, title = {Identifying crop vulnerability to groundwater abstraction: modelling and expert knowledge in a GIS.}, journal = {Journal of environmental management}, volume = {81}, number = {3}, pages = {296-306}, doi = {10.1016/j.jenvman.2006.01.016}, pmid = {16963176}, issn = {0301-4797}, mesh = {*Crops, Agricultural ; Ecosystem ; *Environmental Monitoring ; *Geographic Information Systems ; Geological Phenomena ; Geology ; Models, Biological ; Nitrates/analysis ; Phosphorus/analysis ; Risk Assessment ; Water Pollutants, Chemical/*analysis ; *Water Supply ; }, abstract = {Water use is expected to increase and climate change scenarios indicate the need for more frequent water abstraction. Abstracting groundwater may have a detrimental effect on soil moisture availability for crop growth and yields. This work presents an elegant and robust method for identifying zones of crop vulnerability to abstraction. Archive groundwater level datasets were used to generate a composite groundwater surface that was subtracted from a digital terrain model. The result was the depth from surface to groundwater and identified areas underlain by shallow groundwater. Knowledge from an expert agronomist was used to define classes of risk in terms of their depth below ground level. Combining information on the permeability of geological drift types further refined the assessment of the risk of crop growth vulnerability. The nature of the mapped output is one that is easy to communicate to the intended farming audience because of the general familiarity of mapped information. Such Geographic Information System (GIS)-based products can play a significant role in the characterisation of catchments under the EU Water Framework Directive especially in the process of public liaison that is fundamental to the setting of priorities for management change. The creation of a baseline allows the impact of future increased water abstraction rates to be modelled and the vulnerability maps are in a format that can be readily understood by the various stakeholders. This methodology can readily be extended to encompass additional data layers and for a range of groundwater vulnerability issues including water resources, ecological impacts, nitrate and phosphorus.}, } @article {pmid16957863, year = {2006}, author = {Batzias, FA and Siontorou, CG}, title = {A knowledge-based approach to environmental biomonitoring.}, journal = {Environmental monitoring and assessment}, volume = {123}, number = {1-3}, pages = {167-197}, pmid = {16957863}, issn = {0167-6369}, mesh = {Biodiversity ; Decision Support Techniques ; Ecology ; Environmental Monitoring/*methods ; Environmental Pollutants/*toxicity ; Geographic Information Systems ; Geography ; Knowledge ; Lichens/*drug effects ; *Software ; Sulfur Dioxide/*toxicity ; }, abstract = {This paper presents the design, development and implementation of an integrated GIS-controlled knowledge-based system for environmental monitoring applications, utilizing indigenous flora for assessing quality. The system gathers and combines geographical, ecological, and physicochemical data of organisms' response to pollution within an intelligent computer program that (a) recognises groups of indigenous species suitable for long-term monitoring of a specific pollutant or a combination of pollutants, (b) estimates the ambient concentration of pollutant(s) from the population of the species comprising the bioindicator group and (c) provides biomonitoring capacity indices at national and international/transboundary levels. Significantly, a novel system in the form of a rational framework at the conceptual design level has been developed, that actually contributes towards achieving a cost-effective long-term biomonitoring program, with the flexibility to counter on-course any (anticipated or not) variations/modifications of the surveillance environment: the scheme assumes a robust dynamic cooperation between instrumental and biomonitoring systems, with a view to minimise uncertainty and monitoring costs and increase reliability of pollution control and abatement, aiming eventually at the shifting, partially or totally, from instrumental to natural monitoring. The proposed approach is presently implemented at pilot-scale for establishing a biomonitoring network at a large industrial area in Greece. The results obtained indicate that a cost-effective program can be only attained and maintained under a suitable financial/organizational scheme at the macro level, whereas the micro level viability strongly depends upon careful management of human resources and fixed assets.}, } @article {pmid16948529, year = {2006}, author = {Rizzon, C and Ponger, L and Gaut, BS}, title = {Striking similarities in the genomic distribution of tandemly arrayed genes in Arabidopsis and rice.}, journal = {PLoS computational biology}, volume = {2}, number = {9}, pages = {e115}, pmid = {16948529}, issn = {1553-7358}, mesh = {Arabidopsis/*genetics ; Chromosomes, Plant/genetics ; Computational Biology ; Computer Simulation ; Genes, Duplicate/*genetics ; Genes, Plant/*genetics ; Genome, Plant/*genetics ; *Genomics ; Oryza/*genetics ; Recombination, Genetic/genetics ; Sensitivity and Specificity ; }, abstract = {In Arabidopsis, tandemly arrayed genes (TAGs) comprise >10% of the genes in the genome. These duplicated genes represent a rich template for genetic innovation, but little is known of the evolutionary forces governing their generation and maintenance. Here we compare the organization and evolution of TAGs between Arabidopsis and rice, two plant genomes that diverged ~150 million years ago. TAGs from the two genomes are similar in a number of respects, including the proportion of genes that are tandemly arrayed, the number of genes within an array, the number of tandem arrays, and the dearth of TAGs relative to single copy genes in centromeric regions. Analysis of recombination rates along rice chromosomes confirms a positive correlation between the occurrence of TAGs and recombination rate, as found in Arabidopsis. TAGs are also biased functionally relative to duplicated, nontandemly arrayed genes. In both genomes, TAGs are enriched for genes that encode membrane proteins and function in "abiotic and biotic stress" but underrepresented for genes involved in transcription and DNA or RNA binding functions. We speculate that these observations reflect an evolutionary trend in which successful tandem duplication involves genes either at the end of biochemical pathways or in flexible steps in a pathway, for which fluctuation in copy number is unlikely to affect downstream genes. Despite differences in the age distribution of tandem arrays, the striking similarities between rice and Arabidopsis indicate similar mechanisms of TAG generation and maintenance.}, } @article {pmid16945154, year = {2006}, author = {Cooke, WH and Grala, K and Wallis, RC}, title = {Avian GIS models signal human risk for West Nile virus in Mississippi.}, journal = {International journal of health geographics}, volume = {5}, number = {}, pages = {36}, pmid = {16945154}, issn = {1476-072X}, mesh = {Animals ; Birds ; *Disease Outbreaks ; *Environment ; *Geographic Information Systems ; Humans ; Mississippi/epidemiology ; *Models, Theoretical ; Risk Factors ; West Nile Fever/*epidemiology ; West Nile virus/*isolation & purification/pathogenicity ; }, abstract = {BACKGROUND: West Nile virus (WNV) poses a significant health risk for residents of Mississippi. Physicians and state health officials are interested in new and efficient methods for monitoring disease spread and predicting future outbreaks. Geographic Information Systems (GIS) models have the potential to support these efforts. Environmental conditions favorable for mosquito habitat were modeled using GIS to derive WNV risk maps for Mississippi. Variables important to WNV dissemination were selected and classified as static and dynamic. The static variables included road density, stream density, slope, and vegetation. The dynamic variable represented seasonal water budget and was calculated using precipitation and evaporation estimates. Significance tests provided deterministic evidence of variable importance to the models.

RESULTS: Several models were developed to estimate WNV risk including a landscape-base model and seasonal climatic sub-models. P-values from t-tests guided variable importance ranking. Variables were ranked and weights assigned as follows: road density (0.4), stream density (0.3), slope (0.2) and vegetation (0.1). This landscape-base model was modified by climatic conditions to assess the importance of climate to WNV risk. Human case data at the zip code level were used to validate modeling results. All models were summarized by zip codes for interpretation and model validation. For all models, estimated risk was higher for zip codes with at least one human case than for zip codes where no human cases were recorded. Overall median measure of risk by zip code indicated that 67% of human cases occurred in the high-risk category.

CONCLUSION: Modeling results indicated that dead bird occurrences are correlated with human WNV risk and can facilitate the assessment of environmental variables that contribute to that risk. Each variable's importance in GIS-based risk predictions was assigned deterministically. Our models indicated non-uniform distribution of risk across the state and showed elevated risk in urban and as well as rural areas. Model limitations include resolution of human data, zip code aggregation issues, and quality/availability of vegetation and stream density layers. Our approach verified that WNV risk can be modeled at the state level and can be modified for risk predictions of other vector-borne diseases in varied ecological regions.}, } @article {pmid16943250, year = {2006}, author = {Roy, SW and Penny, D}, title = {Smoke without fire: most reported cases of intron gain in nematodes instead reflect intron losses.}, journal = {Molecular biology and evolution}, volume = {23}, number = {12}, pages = {2259-2262}, doi = {10.1093/molbev/msl098}, pmid = {16943250}, issn = {0737-4038}, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Caenorhabditis/genetics ; Databases, Genetic ; *Gene Deletion ; *Introns ; Molecular Sequence Data ; Nematoda/*genetics ; Phylogeny ; Sequence Homology, Nucleic Acid ; }, abstract = {Identification of recently gained spliceosomal introns would provide crucial evidence in the continuing debate concerning the age and evolutionary significance of introns. A previously published genomic analysis reported to have identified 122 introns that had been gained since the divergence of the nematodes Caenorhabidits elegans and Caenorhabditis briggsae approximately 100 MYA. However, using newly available genomic sequence from additional Caenorhabditis species, we show that 74% (60/81) of the reported gains in C. elegans are present in a C. briggsae relative. This pattern indicates that these introns represent losses in C. briggsae, not gains in C. elegans. In addition, 61% (25/41) of the reported gains in C. briggsae are present in the more distant C. briggsae relative, in a pattern suggesting that additional reported gains in C. elegans and/or C. briggsae may in fact represent unrecognized losses. These results underscore the dominance of intron loss over intron gain in recent eukaryotic evolution, the pitfalls associated with parsimony in inferring intron gains, and the importance of genomic sequencing of clusters of closely related species for drawing accurate inferences about genome evolution.}, } @article {pmid16942900, year = {2006}, author = {Field, D and Wilson, G and van der Gast, C}, title = {How do we compare hundreds of bacterial genomes?.}, journal = {Current opinion in microbiology}, volume = {9}, number = {5}, pages = {499-504}, doi = {10.1016/j.mib.2006.08.008}, pmid = {16942900}, issn = {1369-5274}, mesh = {Bacteria/classification/*genetics/isolation & purification ; Bacterial Physiological Phenomena ; Biological Evolution ; Databases, Genetic ; Ecology ; Genes, Bacterial ; *Genome, Bacterial ; Genomics/trends ; Species Specificity ; }, abstract = {The genomic revolution is fully upon us in 2006 and the pace of discovery is set to accelerate with the emergence of ultra-high-throughput sequencing technologies. Our complete genome collection of bacteria and archaea continues to grow in number and diversity, as genome sequencing is applied to an array of new problems, from the characterization of the pan-genome to the detection of mutation after experimentation and the exploration of microbial communities in unprecedented detail. The benefits of large-scale comparative genomic analyses are driving the community to think about how to manage our public collections of genomes in novel ways.}, } @article {pmid16937652, year = {2006}, author = {Hylander, K}, title = {Riparian zones increase regional species richness by harboring different, not more, species: comment.}, journal = {Ecology}, volume = {87}, number = {8}, pages = {2126-8; discussion 2128-31}, doi = {10.1890/0012-9658(2006)87[2126:rzirsr]2.0.co;2}, pmid = {16937652}, issn = {0012-9658}, mesh = {Animals ; *Biodiversity ; Data Interpretation, Statistical ; Ecosystem ; Fresh Water ; Plants ; }, } @article {pmid16937629, year = {2006}, author = {Loosmore, NB and Ford, ED}, title = {Statistical inference using the g or K point pattern spatial statistics.}, journal = {Ecology}, volume = {87}, number = {8}, pages = {1925-1931}, doi = {10.1890/0012-9658(2006)87[1925:siutgo]2.0.co;2}, pmid = {16937629}, issn = {0012-9658}, mesh = {*Data Interpretation, Statistical ; Models, Statistical ; Monte Carlo Method ; Trees ; }, abstract = {Spatial point pattern analysis provides a statistical method to compare an observed spatial pattern against a hypothesized spatial process model. The G statistic, which considers the distribution of nearest neighbor distances, and the K statistic, which evaluates the distribution of all neighbor distances, are commonly used in such analyses. One method of employing these statistics involves building a simulation envelope from the result of many simulated patterns of the hypothesized model. Specifically, a simulation envelope is created by calculating, at every distance, the minimum and maximum results computed across the simulated patterns. A statistical test is performed by evaluating where the results from an observed pattern fall with respect to the simulation envelope. However, this method, which differs from P. Diggle's suggested approach, is invalid for inference because it violates the assumptions of Monte Carlo methods and results in incorrect type I error rate performance. Similarly, using the simulation envelope to estimate the range of distances over which an observed pattern deviates from the hypothesized model is also suspect. The technical details of why the simulation envelope provides incorrect type I error rate performance are described. A valid test is then proposed, and details about how the number of simulated patterns impacts the statistical significance are explained. Finally, an example of using the proposed test within an exploratory data analysis framework is provided.}, } @article {pmid16937236, year = {2006}, author = {Caira, JN and Scholz, T and Georgiev, BB}, title = {Cestode systematics and phylogeny move forward.}, journal = {Systematic parasitology}, volume = {65}, number = {2}, pages = {171-174}, pmid = {16937236}, issn = {0165-5752}, mesh = {Animals ; Cestoda/*classification/genetics/growth & development ; Databases as Topic ; International Cooperation ; Life Cycle Stages/genetics ; Parasitology/*trends ; *Phylogeny ; }, abstract = {This paper represents a meeting report for the Fifth International Workshop on Cestode Systematics and Phylogeny held at the Institute of Parasitology, Academy of Sciences of the Czech Republic, Ceské Budejovice, 18-22 July 2005. The major topics discussed included (i) the progress in cestode systematics during 2002-2005, (ii) the use of the life-cycle data in phylogenetic studies, (iii) the utilisation of new morphological and molecular characters in cestode systematics and phylogeny, and (iv) the ongoing work on the completion of the Global Cestode Database.}, } @article {pmid16933083, year = {2006}, author = {Schlüter, M and Rüger, N and Savitsky, AG and Novikova, NM and Matthies, M and Lieth, H}, title = {TUGAI: An integrated simulation tool for ecological assessment of alternative water management strategies in a degraded river delta.}, journal = {Environmental management}, volume = {38}, number = {4}, pages = {638-653}, pmid = {16933083}, issn = {0364-152X}, mesh = {*Conservation of Natural Resources ; Ecology ; *Environment ; Environmental Monitoring ; *Geographic Information Systems ; Geologic Sediments/*analysis ; Models, Theoretical ; Rivers/*chemistry ; Water Pollution, Chemical/analysis ; }, abstract = {The development of ecologically sound water allocation strategies that account for the needs of riverine ecosystems is a pressing issue, especially in semiarid river basins. In the Aral Sea Basin, a search for strategies to mitigate ecological and socioeconomic deterioration has been in process since the early 1990s. The Geographic Information System-based simulation tool TUGAI has been developed to support the policy determination process by providing a simple, problem-oriented method to assess ecological effects of alternative water management strategies for the Amudarya River. It combines a multiobjective water allocation model with simple, spatially explicit statistical and rule-based models of landscape dynamics. Changes in environmental conditions are evaluated by a fuzzy habitat suitability index for Populus euphratica, which is the dominant species of the characteristic riverine Tugai forests. Water management scenarios can be developed by altering spatiotemporal water distribution in the delta area or the amount of water inflow into the delta. Outcomes of scenario analysis are qualitative comparisons of the ecological effects of different options for a time period of up to 28 years. The given approach utilizes different types of knowledge, from quantitative hydrological data to qualitative local expert knowledge. The main purpose of the tool is to integrate the knowledge in a comprehensive way to make it available for discussions on alternative policies in moderated workshops with stakeholders. In this article, the modules of the tool, their integration, and three hypothetical scenarios are presented. Based on the experience gained when developing the TUGAI tool, we propose that the general framework can be transferred to other areas where tradeoffs in water allocation between the environment and other water users are of major concern. The potential for a simulation tool to structure and inform a complex resource management situation by involving local experts and stakeholders in the development of possible future scenarios will become increasingly valuable for transparent and participatory resource management.}, } @article {pmid16931744, year = {2006}, author = {Kitching, RL}, title = {Ecology. Crafting the pieces of the diversity jigsaw puzzle.}, journal = {Science (New York, N.Y.)}, volume = {313}, number = {5790}, pages = {1055-1057}, doi = {10.1126/science.1131117}, pmid = {16931744}, issn = {1095-9203}, mesh = {Animals ; *Biodiversity ; Colorado ; Czech Republic ; Databases, Factual ; *Ecosystem ; Food Chain ; *Fossils ; *Insecta ; Papua New Guinea ; Phylogeny ; Plant Leaves ; *Trees ; *Tropical Climate ; }, } @article {pmid16930291, year = {2006}, author = {Vedani, A and Dobler, M and Lill, MA}, title = {The challenge of predicting drug toxicity in silico.}, journal = {Basic & clinical pharmacology & toxicology}, volume = {99}, number = {3}, pages = {195-208}, doi = {10.1111/j.1742-7843.2006.pto_471.x}, pmid = {16930291}, issn = {1742-7835}, mesh = {Computational Biology ; *Computer Simulation ; Drug Evaluation, Preclinical/*methods ; *Drug-Related Side Effects and Adverse Reactions ; Humans ; *Predictive Value of Tests ; Software ; }, abstract = {Poor pharmacokinetics, side effects and compound toxicity are frequent causes of late-stage failures in drug development. A safe in silico identification of adverse effects triggered by drugs and chemicals would be highly desirable as it not only bears economical potential but also spawns a variety of ecological benefits: sustainable resource management, reduction of animal models and possibly less risky clinical trials. In computer-aided drug discovery, both existing and hypothetical compounds may be studied; the methods are fast, reproducible, and typically based on human bioregulators, making the question of transferability obsolete. In the recent past, our laboratory contributed towards the development of in silico concepts (--> multi-dimensional QSAR) and validated a series of "virtual test kits" based on the oestrogen, androgen, thyroid, and aryl hydrocarbon receptor (endocrine disruption, receptor-mediated toxicity) as well as on the enzyme cytochrome P450 3A4 (metabolic transformations, drug-drug interactions). The test kits are based on the three-dimensional structure of their target protein (i.e. ER(alphabeta), AR, TR(alphabeta), CYP450) or a surrogate thereof (AhR) and were trained using a representative selection of 362 substances. Subsequent evaluation of 107 compounds different therefrom showed that binding affinities are predicted close to experimental uncertainty. These results suggest that our approach is suited for the in silico identification of adverse effects triggered by drugs and chemicals and encouraged us to compile an Internet Database for the virtual screening of drugs and chemicals for toxic effects.}, } @article {pmid16928418, year = {2007}, author = {Bonazountas, M and Kallidromitou, D and Kassomenos, P and Passas, N}, title = {A decision support system for managing forest fire casualties.}, journal = {Journal of environmental management}, volume = {84}, number = {4}, pages = {412-418}, doi = {10.1016/j.jenvman.2006.06.016}, pmid = {16928418}, issn = {0301-4797}, mesh = {*Decision Support Techniques ; *Disaster Planning ; *Fires ; Geographic Information Systems ; Greece ; Satellite Communications ; }, abstract = {Southern Europe is exposed to anthropogenic and natural forest fires. These result in loss of lives, goods and infrastructure, but also deteriorate the natural environment and degrade ecosystems. The early detection and combating of such catastrophes requires the use of a decision support system (DSS) for emergency management. The current literature reports on a series of efforts aimed to deliver DSSs for the management of the forest fires by utilising technologies like remote sensing and geographical information systems (GIS), yet no integrated system exists. This manuscript presents the results of scientific research aiming to the development of a DSS for managing forest fires. The system provides a series of software tools for the assessment of the propagation and combating of forest fires based on Arc/Info, ArcView, Arc Spatial Analyst, Arc Avenue, and Visual C++ technologies. The system integrates GIS technologies under the same data environment and utilises a common user interface to produce an integrated computer system based on semi-automatic satellite image processing (fuel maps), socio-economic risk modelling and probabilistic models that would serve as a useful tool for forest fire prevention, planning and management. Its performance has been demonstrated via real time up-to-date accurate information on the position and evolution of the fire. The system can assist emergency assessment, management and combating of the incident. A site demonstration and validation has been accomplished for the island of Evoia, Greece, an area particularly vulnerable to forest fires due to its ecological characteristics and prevailing wind patterns.}, } @article {pmid16922840, year = {2006}, author = {Jonsen, ID and Myers, RA and James, MC}, title = {Robust hierarchical state-space models reveal diel variation in travel rates of migrating leatherback turtles.}, journal = {The Journal of animal ecology}, volume = {75}, number = {5}, pages = {1046-1057}, doi = {10.1111/j.1365-2656.2006.01129.x}, pmid = {16922840}, issn = {0021-8790}, mesh = {*Animal Migration ; Animals ; Bayes Theorem ; Feeding Behavior/physiology ; Female ; Geographic Information Systems ; Geography ; Male ; Marine Biology/instrumentation/methods ; *Models, Statistical ; Oceans and Seas ; Satellite Communications ; Telemetry/instrumentation ; Time Factors ; Turtles/*physiology ; }, abstract = {1. Biological and statistical complexity are features common to most ecological data that hinder our ability to extract meaningful patterns using conventional tools. Recent work on implementing modern statistical methods for analysis of such ecological data has focused primarily on population dynamics but other types of data, such as animal movement pathways obtained from satellite telemetry, can also benefit from the application of modern statistical tools. 2. We develop a robust hierarchical state-space approach for analysis of multiple satellite telemetry pathways obtained via the Argos system. State-space models are time-series methods that allow unobserved states and biological parameters to be estimated from data observed with error. We show that the approach can reveal important patterns in complex, noisy data where conventional methods cannot. 3. Using the largest Atlantic satellite telemetry data set for critically endangered leatherback turtles, we show that the diel pattern in travel rates of these turtles changes over different phases of their migratory cycle. While foraging in northern waters the turtles show similar travel rates during day and night, but on their southward migration to tropical waters travel rates are markedly faster during the day. These patterns are generally consistent with diving data, and may be related to changes in foraging behaviour. Interestingly, individuals that migrate southward to breed generally show higher daytime travel rates than individuals that migrate southward in a non-breeding year. 4. Our approach is extremely flexible and can be applied to many ecological analyses that use complex, sequential data.}, } @article {pmid16922309, year = {2006}, author = {Agrawal, AA and Fishbein, M}, title = {Plant defense syndromes.}, journal = {Ecology}, volume = {87}, number = {7 Suppl}, pages = {S132-49}, doi = {10.1890/0012-9658(2006)87[132:pds]2.0.co;2}, pmid = {16922309}, issn = {0012-9658}, mesh = {Animals ; Asclepias/classification/*physiology ; *Butterflies ; Cardenolides/metabolism ; Data Interpretation, Statistical ; *Ecosystem ; Larva ; Latex/metabolism ; Phylogeny ; Plant Leaves/physiology ; }, abstract = {Given that a plant's defensive strategy against herbivory is never likely to be a single trait, we develop the concept of plant defense syndromes, where association with specific ecological interactions can result in convergence on suites of covarying defensive traits. Defense syndromes can be studied within communities of diverse plant species as well as within clades of closely related species. In either case, theory predicts that plant defense traits can consistently covary across species, due to shared evolutionary ancestry or due to adaptive convergence. We examined potential defense syndromes in 24 species of milkweeds (Asclepias spp.) in a field experiment. Employing phylogenetically independent contrasts, we found few correlations between seven defensive traits, no bivariate trade-offs, and notable positive correlations between trichome density and latex production, and between C:N ratio and leaf toughness. We then used a hierarchical cluster analysis to produce a phenogram of defense trait similarity among the 24 species. This analysis revealed three distinct clusters of species. The defense syndromes of these species clusters are associated with either low nutritional quality or a balance of higher nutritional quality coupled with physical or chemical defenses. The phenogram based on defense traits was not congruent, however, with a molecular phylogeny of the group, suggesting convergence on defense syndromes. Finally, we examined the performance of monarch butterfly caterpillars on the 24 milkweed species in the field; monarch growth and survival did not differ on plants in the three syndromes, although multiple regression revealed that leaf trichomes and toughness significantly reduced caterpillar growth. The discovery of convergent plant defense syndromes can be used as a framework to ask questions about how abiotic environments, communities of herbivores, and biogeography are associated with particular defense strategies of plants.}, } @article {pmid16922235, year = {2006}, author = {Richardson, EA and Kaiser, MJ and Edwards-Jones, G and Possingham, HP}, title = {Sensitivity of marine-reserve design to the spatial resolution of socioeconomic data.}, journal = {Conservation biology : the journal of the Society for Conservation Biology}, volume = {20}, number = {4}, pages = {1191-1202}, doi = {10.1111/j.1523-1739.2006.00426.x}, pmid = {16922235}, issn = {0888-8892}, mesh = {Animals ; Biodiversity ; Computational Biology ; Conservation of Natural Resources/*economics/methods ; Fisheries/*economics ; Geography ; Humans ; Oceans and Seas ; Socioeconomic Factors ; Software ; Wales ; }, abstract = {Socioeconomic considerations should have an important place in reserve design. Systematic reserve-selection tools allow simultaneous optimization for ecological objectives while minimizing costs but are seldom used to incorporate socioeconomic costs in the reserve-design process. The sensitivity of this process to biodiversity data resolution has been studied widely but the issue of socioeconomic data resolution has not previously been considered. We therefore designed marine reserves for biodiversity conservation with the constraint of minimizing commercial fishing revenue losses and investigated how economic data resolution affected the results. Incorporating coarse-resolution economic data from official statistics generated reserves that were only marginally less costly to the fishery than those designed with no attempt to minimize economic impacts. An intensive survey yielded fine-resolution data that, when incorporated in the design process, substantially reduced predicted fishery losses. Such an approach could help minimize fisher displacement because the least profitable grounds are selected for the reserve. Other work has shown that low-resolution biodiversity data can lead to underestimation of the conservation value of some sites, and a risk of overlooking the most valuable areas, and we have similarly shown that low-resolution economic data can cause underestimation of the profitability of some sites and a risk of inadvertently including these in the reserve. Detailed socioeconomic data are therefore an essential input for the design of cost-effective reserve networks.}, } @article {pmid16922225, year = {2006}, author = {Trakhtenbrot, A and Kadmon, R}, title = {Effectiveness of environmental cluster analysis in representing regional species diversity.}, journal = {Conservation biology : the journal of the Society for Conservation Biology}, volume = {20}, number = {4}, pages = {1087-1098}, doi = {10.1111/j.1523-1739.2006.00500.x}, pmid = {16922225}, issn = {0888-8892}, mesh = {Algorithms ; *Biodiversity ; Cluster Analysis ; Conservation of Natural Resources/*methods ; Data Interpretation, Statistical ; Geography ; Israel ; }, abstract = {A major challenge of regional conservation planning is the identification of sets of sites that together represent the overall biodiversity of the relevant region. Environmental cluster analysis (ECA) has been proposed as a potential tool for efficient selection of conservation sites, but the consequences of methodological decisions involved in its application have not been tested so far. We evaluated the performance of ECA with respect to two such decisions: the choice of the clustering algorithm (single linkage, complete linkage, unweighted arithmetic average, unweighted centroid, Ward's minimum variance, and the ALOC algorithm) and the weight given to different groups of environmental variables (rainfall, temperature, and lithology). Specifically we tested how these decisions affect the spatial configuration of clusters of sites defined by the ECA, whether and how they affect the effectiveness of the ECA (i.e., its ability to represent regional species diversity), and whether the effectiveness of alternative methods of hierarchical clustering can be predicted a priori based on the cophenetic correlation. We used an extensive database of the flora of Israel to test these questions. Differences in both the clustering algorithm and the weighting regime had considerable effects on the spatial configuration of the ECA clusters. The single-linkage algorithm produced mostly single-cell clusters plus a single large-sized cluster and was therefore found inappropriate for environmental regionalization. The effectiveness of the ECA was also sensitive to changes in the clustering algorithm and the weighting regime. Yet, most combinations of clustering algorithms and weighting regimes performed significantly better in capturing regional biodiversity than random null models. The main deviation was classifications based on Ward's minimum variance algorithm, which performed less well relative to all other algorithms. The two algorithms that showed the highest effectiveness (unweighted average and unweighted centroid clustering) also exhibited the highest values of the cophenetic correlation, suggesting that this index may serve as a potential indicator for the effectiveness of alternative ECA algorithms.}, } @article {pmid16921970, year = {2006}, author = {Zhang, KF and Li, XW and Zhang, DX and Peng, JF and Chen, J and Yu, ZR}, title = {[Spatial-temporal dynamic change of land resource degradation in China].}, journal = {Huan jing ke xue= Huanjing kexue}, volume = {27}, number = {6}, pages = {1244-1251}, pmid = {16921970}, issn = {0250-3301}, mesh = {Agriculture/*methods ; China ; Conservation of Natural Resources/*methods ; *Ecology ; Environmental Monitoring/methods ; Geographic Information Systems ; Geography ; Soil/*analysis ; Time Factors ; }, abstract = {Large scale spatial and temporal land use survey data were used to study the dynamics of land use change in China recently. With the aid of GIS, the spatial-temporal dynamic change of land resource degradation at the national level was investigated using authoritative datasets from detailed land use surveys (early 1990s approximately 2003). As a result, seven major types of land degradation processes were identified, including sandy desertification, rocky desertification, secondary salinification, non-agricultural land occupation, deforestation, natural grassland degradation and wetlands shrinking. This paper comprehensively explored the characteristics of these land degradation processes and revealed the status and trend of the holistic land resource degradation in China. Results shows that: (1) Although land degradation has been controlled in local area, but it is still continuing to spread in the whole country. The total degradation index of the holistic land resource presented fluctuating trend. Indexes of non-agricultural construction occupation and wetland shrinking process are far more than that of other process, which are two primary causes contribution to heading straight towards full-scale land resource deterioration in China. (2) Land resource degradation process of China focused on natural grass land, and non-agricultural construction land, which attained 66.27%; Land resource degradation rehabilitation mainly focused on desertification and forest restoration, which accounts for 57.5%. (3) Sandy desertification and rocky desertification process have been reversing greatly. The total net change of their quantities was decreased by 15,578km2. But most of the rehabilitation of land desertification was concentrated on the originally ecological vulnerable northwestern zone, whereas newly added desertified land has been expanding and aggravating in eastern zone, especially around river watersheds. (4) Over two-thirds of non-agriculture land expansion came from cultivated land. In addition, almost 60 percent of the loss cultivated land occupied by non-agricultural land was appeared in the Northeast, the Eastern coast and Central China where have many high productive agricultural lands of China. This kind of land degradation has threatened food security of China seriously. (5) However, large scale reclamation of ecological land transferred into cultivated land was the most dominant factor of degradation. For example, the conversion of wetland resource to croplands by reclamation accounts for over 50 percent of wetland shrinking.}, } @article {pmid16916045, year = {2006}, author = {Pfleeger, TG and Olszyk, D and Burdick, CA and King, G and Kern, J and Fletcher, J}, title = {Using a geographic information system to identify areas with potential for off-target pesticide exposure.}, journal = {Environmental toxicology and chemistry}, volume = {25}, number = {8}, pages = {2250-2259}, doi = {10.1897/05-281r.1}, pmid = {16916045}, issn = {0730-7268}, mesh = {Environmental Pollutants/*toxicity ; *Geographic Information Systems ; Pesticides/*toxicity ; }, abstract = {In many countries, numerous tests are required as part of the risk assessment process before chemical registration to protect human health and the environment from unintended effects of chemical releases. Most of these tests are not based on ecological or environmental relevance but, rather, on consistent performance in the laboratory. A conceptual approach based on Geographic Information System (GIS) technology has been developed to identify areas that are vulnerable to nontarget chemical exposure. This GIS-based approach uses wind speed, frequency of those winds, pesticide application rates, and spatial location of agricultural crops to identify areas with the highest potential for pesticide exposure. A test scenario based on an incident in Idaho (USA) was used to identify the relative magnitude of risk from off-target movement of herbicides to plants in the conterminous United States. This analysis indicated that the western portion of the Corn Belt, the central California valley, southeastern Washington, the Willamette Valley of Oregon, and agricultural areas bordering the Great Lakes are among those areas in the United States that appear to have the greatest potential for off-target movement of herbicides via drift. Agricultural areas, such as the Mississippi River Valley and the southeastern United States, appears to have less potential, possibly due to lower average wind speeds. Ecological risk assessments developed for pesticide registration would be improved by using response data from species common to high-risk areas instead of extrapolating test data from species unrelated to those areas with the highest potential for exposure.}, } @article {pmid16913141, year = {2006}, author = {Hipp, JA and Ogunseitan, O and Lejano, R and Smith, CS}, title = {Optimization of stormwater filtration at the urban/watershed interface.}, journal = {Environmental science & technology}, volume = {40}, number = {15}, pages = {4794-4801}, doi = {10.1021/es060520f}, pmid = {16913141}, issn = {0013-936X}, mesh = {California ; Cities ; Computer Simulation ; Drainage, Sanitary/methods ; Efficiency ; Enterobacteriaceae/isolation & purification ; Environmental Monitoring/methods ; Filtration/*methods ; Geographic Information Systems ; Geologic Sediments/chemistry ; Guideline Adherence ; Metals/isolation & purification ; Rain/*chemistry ; Waste Disposal, Fluid/methods ; Water Microbiology ; Water Pollutants/analysis/isolation & purification ; Water Pollutants, Chemical/isolation & purification ; Water Purification/*methods ; Water Supply/*analysis ; }, abstract = {Environmental pollution from cities is a major ecological problem attributed to contaminated runoff from nonpoint sources. The U.S. Environmental Protection Agency's guidance on implementation of total maximum daily loads (TMDL) does not adequately cover methods to improve waters impaired by nonpoint sources. To comply with TMDLs, cities may install filters in curb inlets, or use other Best Management Practices (BMPs). We tested 10 different filters and found their effectiveness in retaining pollutants ranged from 0 to >90%, depending on combinations of pollutant types (metals, pathogens, and total suspended sediments (TSS)) and filter materials. Hence, the decision to deploy filters into curb inlets must consider land use patterns associated with specific categories of pollutants generated within cities. We developed a geographic information system (GIS)-enabled model for estimating and mitigating emissions of pollutants from urban regions into watersheds. The model uses land use categories and pollutant loadings to optimize strategic placement of filters to accommodate TMDLs. For example, in a city where the landuse pattern generates 4 x 10(6) kg of TSS, 55 kg of Cd, and 2 x 10(3) kg of Zn per year into 498 curb inlets that discharge into a sensitive watershed, the optimized placement of 137, 92, and 148 filters can achieve TMDL endpoints for each pollutant, respectively. We show further that 158 strategically placed filters effectively meet the requirements simultaneously for all three pollutants, a result at least 5 times more effective than random placement of filters.}, } @article {pmid16909659, year = {2006}, author = {Halpern, BS and Pyke, CR and Fox, HE and Haney, JC and Schlaepfer, MA and Zaradic, P}, title = {Gaps and mismatches between global conservation priorities and spending.}, journal = {Conservation biology : the journal of the Society for Conservation Biology}, volume = {20}, number = {1}, pages = {56-64}, doi = {10.1111/j.1523-1739.2005.00258.x}, pmid = {16909659}, issn = {0888-8892}, mesh = {Animals ; Biodiversity ; Conservation of Natural Resources/*economics ; Costs and Cost Analysis ; Female ; *Geographic Information Systems ; *International Cooperation ; Internationality ; Male ; Regression Analysis ; }, abstract = {Several international conservation organizations have recently produced global priority maps to guide conservation activities and spending in their own and other conservation organizations. Surprisingly, it is not possible to directly evaluate the relationship between priorities and spending within a given organization because none of the organizations with global priority models tracks how they spend their money relative to their priorities. We were able, however to evaluate the spending patterns of five other large biodiversity conservation organizations without their own published global priority models and investigate the potential influence of priority models on this spending. On average, countries with priority areas received greater conservation investment; global prioritization systems, however explained between only 2 and 32% of the U.S. dollars 1.5 billion spent in 2002, depending on whether the United States was removed from analyses and whether conservation spending was adjusted by the per capita gross domestic product within each country. We also found little overlap in the spending patterns of the five conservation organizations evaluated, suggesting that informal coordination or segregation of effort may be occurring. Our results also highlight a number of potential gaps and mismatches in how limited conservation funds are spent and provide the first audit of global conservation spending patterns. More explicit presentation of conservation priorities by organizations currently withoutpriority models and better tracking of spending by those with published priorities are clearly needed to help make future conservation activities as efficient as possible.}, } @article {pmid16905225, year = {2007}, author = {Johnson, AC and Keller, V and Williams, RJ and Young, A}, title = {A practical demonstration in modelling diclofenac and propranolol river water concentrations using a GIS hydrology model in a rural UK catchment.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {146}, number = {1}, pages = {155-165}, doi = {10.1016/j.envpol.2006.05.037}, pmid = {16905225}, issn = {0269-7491}, mesh = {*Computer Simulation ; Diclofenac/*analysis ; Environmental Monitoring/*methods ; Geographic Information Systems ; *Models, Theoretical ; Propranolol/*analysis ; Rivers ; Sewage ; United Kingdom ; Water Movements ; Water Pollutants, Chemical/*analysis ; Water Purification ; }, abstract = {An existing GIS hydrology water quality model, LF2000-WQX, was applied to predict the concentrations of the pharmaceuticals diclofenac and propranalol in catchments. As a practical exercise the predominantly rural Tamar (UK) catchment was chosen. Consumption, excretion, and fate data were used to estimate the pharmaceutical input load for the model. The predicted concentrations throughout most of the catchment were 1 ng/L or less under low flow (90th percentile) conditions. However, at a few locations, downstream of small sewage treatment plants, concentrations above 25 ng/L were predicted. This exercise shows that it is relatively straightforward to predict the concentrations of new and emerging organic microcontaminants in real catchments using existing GIS hydrology water quality models. Further testing will be required to establish their accuracy.}, } @article {pmid16905167, year = {2006}, author = {Haque, M and Venturino, E}, title = {The role of transmissible diseases in the Holling-Tanner predator-prey model.}, journal = {Theoretical population biology}, volume = {70}, number = {3}, pages = {273-288}, doi = {10.1016/j.tpb.2006.06.007}, pmid = {16905167}, issn = {0040-5809}, mesh = {Animals ; *Communicable Diseases/epidemiology/transmission/veterinary ; Data Interpretation, Statistical ; Demography ; Ecology ; Endemic Diseases/statistics & numerical data ; Epidemiology ; Factor Analysis, Statistical ; Food Chain ; Humans ; Incidence ; *Models, Biological ; *Models, Statistical ; Mortality ; *Nonlinear Dynamics ; Population Density ; *Population Dynamics ; *Predatory Behavior ; }, abstract = {Transmissible diseases are known to induce remarkable major behavioral changes in predator-prey systems. However, little attention has been paid to model such situations. The latter would allow to predict useful applications in both dynamics and control. Here the Holling-Tanner model is revisited to account for the influence of a transmissible disease, under the assumption that it spreads among the prey species only. We have found the equilibria and analyzed the behavior of the system around each one of them. A threshold result determining when the disease dies out has been identified. We also investigated the parametric space under which the system enters into Hopf and transcritical bifurcations, around the disease free equilibrium. The system is shown to experience neither saddle-node nor pitch-fork bifurcation. Global stability results are obtained by constructing suitable Lyapunov functions.}, } @article {pmid16903067, year = {2006}, author = {Nams, VO}, title = {Animal movement rates as behavioural bouts.}, journal = {The Journal of animal ecology}, volume = {75}, number = {1}, pages = {298-302; discussion 303-8}, doi = {10.1111/j.1365-2656.2006.01047.x}, pmid = {16903067}, issn = {0021-8790}, mesh = {Animals ; Behavior, Animal/physiology ; Data Collection ; Data Interpretation, Statistical ; Fractals ; Geographic Information Systems ; Locomotion/*physiology ; *Models, Biological ; *Models, Statistical ; Spatial Behavior/*physiology ; }, abstract = {Johnson et al. (Journal of Animal Ecology, 2002, 71, 225-235) have proposed a new technique for identifying scales of movement in animals. Animals are located at certain time intervals, and movement rates between successive animal relocations are calculated. The null model of a nonscalar response predicts a decreasing linear relationship between log (frequency) vs. movement rate, while a scalar response predicts a monotonically decreasing curve with an inflection point at the separation between the processes. I tested this technique using three types of simulated movement paths: correlated random walks, directed walks, and movements in patchy habitat. None of the simulations showed the results expected by the technique. This occurs because the technique assumes that movement rates are exponentially distributed, which is highly unlikely. Thus before this technique can be applied to animal movement data we need to understand how spatial and temporal scale, as well as sampling interval, affect the frequency histogram of animal movement rates.}, } @article {pmid16902120, year = {2006}, author = {Kintisch, E}, title = {Migration and dispersal. As the seas warm.}, journal = {Science (New York, N.Y.)}, volume = {313}, number = {5788}, pages = {776-779}, doi = {10.1126/science.313.5788.776}, pmid = {16902120}, issn = {1095-9203}, mesh = {*Animal Migration ; Animals ; Atlantic Ocean ; Birds/*physiology ; *Climate ; Databases, Factual ; Ecosystem ; Fishes/*physiology ; Mammals/*physiology ; Marine Biology ; Oceans and Seas ; Plankton/physiology ; Seawater ; Temperature ; Turtles/*physiology ; }, } @article {pmid16901831, year = {2006}, author = {Davies, RG and Orme, CD and Olson, V and Thomas, GH and Ross, SG and Ding, TS and Rasmussen, PC and Stattersfield, AJ and Bennett, PM and Blackburn, TM and Owens, IP and Gaston, KJ}, title = {Human impacts and the global distribution of extinction risk.}, journal = {Proceedings. Biological sciences}, volume = {273}, number = {1598}, pages = {2127-2133}, pmid = {16901831}, issn = {0962-8452}, mesh = {Animals ; *Biodiversity ; *Birds ; *Conservation of Natural Resources ; Databases, Factual ; *Demography ; *Environment ; Geography ; Humans ; Models, Theoretical ; Population Dynamics ; }, abstract = {Understanding the global geographical distribution of extinction risk is a key challenge in conservation biology. It remains controversial, however, to what extent areas become threat hotspots simply because of high human impacts or due to predisposing ecological conditions. Limits to the taxonomic and geographical extent, resolution and quality of previously available data have precluded a full global assessment of the relative roles of these factors. Here, we use a new global database on the geographical distributions of birds on continents and continental islands to show that, after controlling for species richness, the best predictors of the global pattern of extinction risk are measures of human impact. Ecological gradients are of secondary importance at a global scale. The converse is true for individual biogeographic realms, within which variation in human impact is reduced and its influence on extinction risk globally is therefore underestimated. These results underline the importance of a global perspective on the mechanisms driving spatial patterns of extinction risk, and the key role of anthropogenic factors in driving the current extinction crisis.}, } @article {pmid16901232, year = {2006}, author = {Huang, WE and Spiers, AJ}, title = {Consideration of future requirements for Raman microbiology as an examplar for the ab initio development of informatics frameworks for emergent OMICS technologies.}, journal = {Omics : a journal of integrative biology}, volume = {10}, number = {2}, pages = {238-241}, doi = {10.1089/omi.2006.10.238}, pmid = {16901232}, issn = {1536-2310}, mesh = {Computational Biology/methods/*standards ; Microbiological Techniques/standards ; Microbiology/*standards ; Spectrum Analysis, Raman/*standards ; }, abstract = {Raman spectroscopy of single bacteria provides an OMIC-like view of the chemical status of individual cells, reporting on metabolism, cell stress and growth, and is likely to become a significant tool in environmental and medical microbiology. We advocate the early development of integrated data models and informatics frameworks, in parallel with the development of Raman hardware and experimental protocols, in order to maximize the benefits of this emerging OMIC technology to the research community.}, } @article {pmid16901213, year = {2006}, author = {Field, D and Morrison, N and Selengut, J and Sterk, P}, title = {Meeting report: eGenomics: Cataloguing our Complete Genome Collection II.}, journal = {Omics : a journal of integrative biology}, volume = {10}, number = {2}, pages = {100-104}, doi = {10.1089/omi.2006.10.100}, pmid = {16901213}, issn = {1536-2310}, mesh = {Animals ; Databases as Topic/*standards ; *Genome ; *Genome, Human ; Genomics/*standards ; Humans ; }, abstract = {This article summarizes the proceedings of the "eGenomics: Cataloguing our Complete Genome Collection II" workshop held November 10-11, 2005, at the European Bioinformatics Institute. This exploratory workshop, organized by members of the Genomic Standards Consortium (GSC), brought together researchers from the genomic, functional OMICS, and computational biology communities to discuss standardization activities across a range of projects. The workshop proceedings and outcomes are set to help guide the development of the GSC's Minimal Information about a Genome Sequence (MIGS) specification.}, } @article {pmid16897525, year = {2006}, author = {Peterson, EE and Merton, AA and Theobald, DM and Urquhart, NS}, title = {Patterns of spatial autocorrelation in stream water chemistry.}, journal = {Environmental monitoring and assessment}, volume = {121}, number = {1-3}, pages = {571-596}, pmid = {16897525}, issn = {0167-6369}, mesh = {Databases, Factual ; Ecology ; *Environmental Monitoring ; Geological Phenomena ; Geology ; *Models, Chemical ; *Models, Statistical ; Rivers/*chemistry ; Water/*analysis ; }, abstract = {Geostatistical models are typically based on symmetric straight-line distance, which fails to represent the spatial configuration, connectivity, directionality, and relative position of sites in a stream network. Freshwater ecologists have explored spatial patterns in stream networks using hydrologic distance measures and new geostatistical methodologies have recently been developed that enable directional hydrologic distance measures to be considered. The purpose of this study was to quantify patterns of spatial correlation in stream water chemistry using three distance measures: straight-line distance, symmetric hydrologic distance, and weighted asymmetric hydrologic distance. We used a dataset collected in Maryland, USA to develop both general linear models and geostatistical models (based on the three distance measures) for acid neutralizing capacity, conductivity, pH, nitrate, sulfate, temperature, dissolved oxygen, and dissolved organic carbon. The spatial AICC methodology allowed us to fit the autocorrelation and covariate parameters simultaneously and to select the model with the most support in the data. We used the universal kriging algorithm to generate geostatistical model predictions. We found that spatial correlation exists in stream chemistry data at a relatively coarse scale and that geostatistical models consistently improved the accuracy of model predictions. More than one distance measure performed well for most chemical response variables, but straight-line distance appears to be the most suitable distance measure for regional geostatistical modeling. It may be necessary to develop new survey designs that more fully capture spatial correlation at a variety of scales to improve the use of weighted asymmetric hydrologic distance measures in regional geostatistical models.}, } @article {pmid16897501, year = {2007}, author = {Tsuji, LJ and Manson, H and Wainman, BC and Vanspronsen, EP and Shecapio-Blacksmith, J and Rabbitskin, T}, title = {Identifying potential receptors and routes of contaminant exposure in the traditional territory of the Ouje-Bougoumou Cree: land use and a geographical information system.}, journal = {Environmental monitoring and assessment}, volume = {127}, number = {1-3}, pages = {293-306}, pmid = {16897501}, issn = {0167-6369}, mesh = {Conservation of Natural Resources ; *Environmental Exposure ; Environmental Health ; *Geographic Information Systems ; Humans ; Mining ; *Population Groups ; Quebec ; }, abstract = {Great concern has been raised with respect to the 13 traplines that constitute the traditional territory of the Ouje-Bougoumou Cree located in the James Bay region of northern Quebec, Canada, with respect to mine wastes originating from three local mines. As a result, an "Integrative Risk Assessment" was initiated consisting of three interrelated components: a comprehensive human health study, an assessment of the existing ecological/environmental database, and a land use/potential sites of concern study. In this paper, we document past and present land use in the traditional territory of the Ouje-Bougoumou Cree for 72 heads of households, including 13 tallymen, and use a Geographic Information System (GIS) to layer harvest/hunting and gathering/collecting data over known mining areas and potential sites of concern. In this way, potential receptors of contamination and routes of human exposure were identified. Areas of overlap with respect to land use activity and mining operations were relatively extensive for certain harvesting activities (e.g., beaver, Castor canadensis and various species of game birds), less so for fish harvesting (all species) and water collection, and relatively restrictive for large mammal harvesting and collection of fire wood (and other collection activities). Potential receptors of contaminants associated with mining activity (e.g., fish and small mammals) and potential routes of exposure (e.g., ingestion of contaminated game and drinking of contaminated water) were identified.}, } @article {pmid16893466, year = {2006}, author = {Lozupone, C and Hamady, M and Knight, R}, title = {UniFrac--an online tool for comparing microbial community diversity in a phylogenetic context.}, journal = {BMC bioinformatics}, volume = {7}, number = {}, pages = {371}, pmid = {16893466}, issn = {1471-2105}, support = {T32 GM008759/GM/NIGMS NIH HHS/United States ; T32 GM065103/GM/NIGMS NIH HHS/United States ; T32 GM142607/GM/NIGMS NIH HHS/United States ; T32 GM08759/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacteria/classification/*genetics ; Cluster Analysis ; Computational Biology/*methods ; Ecosystem ; Environmental Microbiology ; Genetic Variation ; *Internet ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {BACKGROUND: Moving beyond pairwise significance tests to compare many microbial communities simultaneously is critical for understanding large-scale trends in microbial ecology and community assembly. Techniques that allow microbial communities to be compared in a phylogenetic context are rapidly gaining acceptance, but the widespread application of these techniques has been hindered by the difficulty of performing the analyses.

RESULTS: We introduce UniFrac, a web application available at http://bmf.colorado.edu/unifrac, that allows several phylogenetic tests for differences among communities to be easily applied and interpreted. We demonstrate the use of UniFrac to cluster multiple environments, and to test which environments are significantly different. We show that analysis of previously published sequences from the Columbia river, its estuary, and the adjacent coastal ocean using the UniFrac interface provided insights that were not apparent from the initial data analysis, which used other commonly employed techniques to compare the communities.

CONCLUSION: UniFrac provides easy access to powerful multivariate techniques for comparing microbial communities in a phylogenetic context. We thus expect that it will provide a completely new picture of many microbial interactions and processes in both environmental and medical contexts.}, } @article {pmid16892060, year = {2006}, author = {Ruderfer, DM and Pratt, SC and Seidel, HS and Kruglyak, L}, title = {Population genomic analysis of outcrossing and recombination in yeast.}, journal = {Nature genetics}, volume = {38}, number = {9}, pages = {1077-1081}, doi = {10.1038/ng1859}, pmid = {16892060}, issn = {1061-4036}, support = {R37 MH059520/MH/NIMH NIH HHS/United States ; }, mesh = {*Crosses, Genetic ; Databases, Genetic ; *Genetics, Population ; *Genome, Fungal ; Linkage Disequilibrium ; Phylogeny ; Polymorphism, Single Nucleotide ; *Recombination, Genetic ; Saccharomyces cerevisiae/classification/*genetics ; }, abstract = {The budding yeast Saccharomyces cerevisiae has been used by humans for millennia to make wine, beer and bread. More recently, it became a key model organism for studies of eukaryotic biology and for genomic analysis. However, relatively little is known about the natural lifestyle and population genetics of yeast. One major question is whether genetically diverse yeast strains mate and recombine in the wild. We developed a method to infer the evolutionary history of a species from genome sequences of multiple individuals and applied it to whole-genome sequence data from three strains of Saccharomyces cerevisiae and the sister species Saccharomyces paradoxus. We observed a pattern of sequence variation among yeast strains in which ancestral recombination events lead to a mosaic of segments with shared genealogy. Based on sequence divergence and the inferred median size of shared segments (approximately 2,000 bp), we estimated that although any two strains have undergone approximately 16 million cell divisions since their last common ancestor, only 314 outcrossing events have occurred during this time (roughly one every 50,000 divisions). Local correlations in polymorphism rates indicate that linkage disequilibrium in yeast should extend over kilobases. Our results provide the initial foundation for population studies of association between genotype and phenotype in S. cerevisiae.}, } @article {pmid16886342, year = {2000}, author = {Morozińska-Gogol, J}, title = {Parasitofauna of the nine-spined stickleback from the Gulf of Gdańsk and the mouth of Dead Vistula.}, journal = {Wiadomosci parazytologiczne}, volume = {46}, number = {2}, pages = {231-237}, pmid = {16886342}, issn = {0043-5163}, mesh = {Animals ; Crustacea/classification ; Databases, Factual ; Ecosystem ; Eukaryota/classification/isolation & purification ; Fish Diseases/*epidemiology/*parasitology ; Helminths/classification/isolation & purification ; Larva Migrans/classification ; Microsporidia/classification/isolation & purification ; Parasites/*classification ; Parasitic Diseases, Animal/*epidemiology/*parasitology ; Poland ; Rivers/*parasitology ; Smegmamorpha/*parasitology ; Species Specificity ; Trematode Infections/classification/veterinary ; }, abstract = {Four species, one subspecies and one parasite marked to the genus were collected from the nine-spined stickleback Pungitius pungitius L. from the Gulf of Gdańsk and the mouth of Dead Vistula. Nine-spined stickleback was noted as a new host in Polish coastal water for five parasites: Glugea anomala (Microsporidia), Diplostomum spathaceum (Digenea-metacercariae) and Apatemon sp. (Digenea-incysted metacercariae), Hysterothylacium aduncum (Nematoda-third stage larvae) and Thersitina gasterostci (Copepoda). Earlier in this area have been obserwd only ciliates Tnchodina domerguei.}, } @article {pmid16883818, year = {2006}, author = {Chen, W and Zhao, X and Cui, L}, title = {[Temporal-spatial characteristics of land use in Xinjian County, Jiangxi Province].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {17}, number = {5}, pages = {873-877}, pmid = {16883818}, issn = {1001-9332}, mesh = {China ; *Conservation of Natural Resources ; Crops, Agricultural/growth & development ; Ecology ; *Ecosystem ; *Environment Design ; Environmental Monitoring/methods ; Geographic Information Systems ; Models, Theoretical ; Poaceae/*growth & development ; Satellite Communications ; Soil/*analysis ; Trees/growth & development ; }, abstract = {With the support of RS and GIS, and using a series of indices in characterizing the dynamics of land use, this paper studied the temporal-spatial characteristics of land use in Xinjian County, Jiangxi Province, between 1991 and 2000. The results indicated that among single land use types, the area for construction changed mostly. The annual change speed of comprehensive land dynamic index between 1991 and 1995 was 0.5 times higher than that between 1996 and 2000, and the utilization grade in 1991, 1996 and 2000 was 243.7, 44.1 and 244.9, respectively, being a little higher than the national average grade. The land inflow and outflow in 1996 to approximately 2000 was lower than that in 1991 to approximately 1995, and the land use change was from bilateral dynamics to unilateral unbalanced dynamics.}, } @article {pmid16881404, year = {2006}, author = {Rinaldi, L and Musella, V and Cringoli, G}, title = {Disease mapping in veterinary parasitology: an update.}, journal = {Parassitologia}, volume = {48}, number = {1-2}, pages = {85-87}, pmid = {16881404}, issn = {0048-2951}, mesh = {Animals ; Cluster Analysis ; Culicidae/parasitology ; Ecology ; Europe/epidemiology ; *Geographic Information Systems ; Insect Vectors ; Meteorological Concepts ; Parasitic Diseases, Animal/*epidemiology ; *Satellite Communications ; *Spacecraft ; }, abstract = {The development of methods for disease mapping has progressed considerably in recent years. Geographical Information Systems (GIS) and Remote Sensing (RS) represent new tools for the study of epidemiology, and their application to veterinary medicine, and in particular to veterinary parasitology, has become more and more advanced to study the spatial and temporal patterns of diseases. The present paper reports an update regarding the use of these technologies in veterinary parasitology.}, } @article {pmid16881402, year = {2006}, author = {Malone, JB and Nieto, P and Tadesse, A}, title = {Biology-based mapping of vector-borne parasites by geographic information systems and remote sensing.}, journal = {Parassitologia}, volume = {48}, number = {1-2}, pages = {77-79}, pmid = {16881402}, issn = {0048-2951}, mesh = {Aedes/parasitology ; Animals ; China/epidemiology ; *Climate ; *Disease Vectors ; Ecology ; Eritrea/epidemiology ; Ethiopia/epidemiology ; Fasciola/physiology ; Fascioliasis/epidemiology ; *Geographic Information Systems ; Humans ; Insect Vectors ; Latin America/epidemiology ; Leishmania infantum/physiology ; Leishmaniasis, Visceral/epidemiology ; Leprosy/epidemiology/transmission ; Malaria, Falciparum/epidemiology ; Parasitic Diseases/*epidemiology/transmission ; Plasmodium falciparum/physiology ; Psychodidae/parasitology ; Rain ; *Satellite Communications ; Snails/parasitology ; *Spacecraft ; Temperature ; }, abstract = {Application of growing degree day-water budget analysis and satellite climatology to vector-borne parasites will be reviewed to demonstrate the value of using the unique thermal-hydrological preferences and limits of tolerance of individual parasite-vector systems to define the environmental niche of disease agents in the landscape by modern geospatial analysis methods. Applications of geospatial modeling will be illustrated by examples on fascioliasis, malaria, leprosy and leishmaniasis.}, } @article {pmid16881400, year = {2006}, author = {Bernardi, M and Gommes, R and Grieser, J}, title = {Downscaling climate information for local disease mapping.}, journal = {Parassitologia}, volume = {48}, number = {1-2}, pages = {69-72}, pmid = {16881400}, issn = {0048-2951}, mesh = {*Climate ; *Cluster Analysis ; Cooperative Behavior ; *Databases, Factual ; Ecology ; Humans ; Information Services/organization & administration ; Meteorological Concepts ; Population Surveillance ; Satellite Communications ; Software ; Spacecraft ; United Nations ; }, abstract = {The study of the impacts of climate on human health requires the interdisciplinary efforts of health professionals, climatologists, biologists, and social scientists to analyze the relationships among physical, biological, ecological, and social systems. As the disease dynamics respond to variations in regional and local climate, climate variability affects every region of the world and the diseases are not necessarily limited to specific regions, so that vectors may become endemic in other regions. Climate data at local level are thus essential to evaluate the dynamics of vector-borne disease through health-climate models and most of the times the climatological databases are not adequate. Climate data at high spatial resolution can be derived by statistical downscaling using historical observations but the method is limited by the availability of historical data at local level. Since the 90s', the statistical interpolation of climate data has been an important priority of the Agrometeorology Group of the Food and Agriculture Organization of the United Nations (FAO), as they are required for agricultural planning and operational activities at the local level. Since 1995, date of the first FAO spatial interpolation software for climate data, more advanced applications have been developed such as SEDI (Satellite Enhanced Data Interpolation) for the downscaling of climate data, LOCCLIM (Local Climate Estimator) and the NEW_LOCCLIM in collaboration with the Deutscher Wetterdienst (German Weather Service) to estimate climatic conditions at locations for which no observations are available. In parallel, an important effort has been made to improve the FAO climate database including at present more than 30,000 stations worldwide and expanding the database from developing countries coverage to global coverage.}, } @article {pmid16881296, year = {2006}, author = {Wang, JP and Su, BL and Jia, HF and Cheng, ST and Yang, ZS and Wu, DW and Sun, F}, title = {[Integrated model of nutrients for the Miyun Reservoir and its watershed].}, journal = {Huan jing ke xue= Huanjing kexue}, volume = {27}, number = {7}, pages = {1286-1291}, pmid = {16881296}, issn = {0250-3301}, mesh = {China ; Environmental Monitoring/*methods ; *Eutrophication ; Geographic Information Systems ; Monte Carlo Method ; Water Pollutants/*analysis ; Water Supply/*analysis ; }, abstract = {In recent years, the Miyun Reservoir faces severe problems of water quality and quantity due to continuous drought. In order to simulate and predict the eutrophic status of the Miyun Reservoir and its watershed, an integrated model was developed based on GIS and RS technology, which was composed of non-point source (NPS) simulation model, aquatic ecological-hydrodynamic model, and river water quality model. Ecological-hydrodynamic model was developed through coupling water quality analysis simulation program (WASP) with environmental fluid dynamics Code (EFDC). SWAT was selected as NPS simulation model, which could also perform water quality simulation in the river. Then the integrated model was calibrated using Markov Chain Monte Carlo method and verified using observed data. Results indicated that observed water quality data laid around the mode curves of simulation distribution, and which also dropped into the confidence interval on 80 percent credibility of water quality simulation distribution. In conclusion, the results show that the integrated model can meet the need of application.}, } @article {pmid16880384, year = {2006}, author = {Sogin, ML and Morrison, HG and Huber, JA and Mark Welch, D and Huse, SM and Neal, PR and Arrieta, JM and Herndl, GJ}, title = {Microbial diversity in the deep sea and the underexplored "rare biosphere".}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {103}, number = {32}, pages = {12115-12120}, pmid = {16880384}, issn = {0027-8424}, support = {P50 ES012742/ES/NIEHS NIH HHS/United States ; 1 P50 ES012742-01/ES/NIEHS NIH HHS/United States ; }, mesh = {Biodiversity ; Databases, Genetic ; Ecosystem ; Environmental Microbiology ; Evolution, Molecular ; *Genetic Variation ; Marine Biology/*methods ; Phylogeny ; Seawater ; Sequence Analysis, DNA ; Temperature ; *Water Microbiology ; }, abstract = {The evolution of marine microbes over billions of years predicts that the composition of microbial communities should be much greater than the published estimates of a few thousand distinct kinds of microbes per liter of seawater. By adopting a massively parallel tag sequencing strategy, we show that bacterial communities of deep water masses of the North Atlantic and diffuse flow hydrothermal vents are one to two orders of magnitude more complex than previously reported for any microbial environment. A relatively small number of different populations dominate all samples, but thousands of low-abundance populations account for most of the observed phylogenetic diversity. This "rare biosphere" is very ancient and may represent a nearly inexhaustible source of genomic innovation. Members of the rare biosphere are highly divergent from each other and, at different times in earth's history, may have had a profound impact on shaping planetary processes.}, } @article {pmid16869412, year = {2006}, author = {Bell, G and Lechowicz, MJ and Waterway, MJ}, title = {The comparative evidence relating to functional and neutral interpretations of biological communities.}, journal = {Ecology}, volume = {87}, number = {6}, pages = {1378-1386}, doi = {10.1890/0012-9658(2006)87[1378:tcertf]2.0.co;2}, pmid = {16869412}, issn = {0012-9658}, mesh = {*Biodiversity ; Data Interpretation, Statistical ; *Models, Biological ; *Phylogeny ; Population Dynamics ; }, abstract = {Neutral and functional theories provide rival interpretations of community patterns involving distribution, abundance, and diversity. One group of patterns describes the overall properties of species or sites, and derives principally from the frequency distribution of abundance among species. According to neutral theory, these patterns are determined by the number of individuals of novel type appearing each generation in the community, whereas functional theory relates them to the distribution of the extent of niches. A second group of patterns describes the spatial attributes of communities, and derives principally from the decay of similarity in species composition with distance. Neutral theory interprets these patterns as consequences of local dispersal alone, whereas the functional interpretation is that more distant sites are likely to be ecologically different. Neutral theory often provides good predictions of community patterns, yet is at variance with a wide range of experimental results involving the manipulation of environments or communities. One explanation for this discrepancy is that spatially explicit models where selection is generally weak, or where selection acts strongly on only a few species at each site, have essentially the same output as neutral models with respect to the distribution of abundance and the decay of similarity. Detecting a non-neutral signal in survey data requires careful spatial or phylogenetic analysis; we emphasize the potential utility of incorporating phylogenetic information in order to detect functional processes that lead to ecological variation among clades.}, } @article {pmid16869408, year = {2006}, author = {Ellison, AM and Osterweil, LJ and Clarke, L and Hadley, JL and Wise, A and Boose, E and Foster, DR and Hanson, A and Jensen, D and Kuzeja, P and Riseman, E and Schultz, H}, title = {Analytic webs support the synthesis of ecological data sets.}, journal = {Ecology}, volume = {87}, number = {6}, pages = {1345-1358}, doi = {10.1890/0012-9658(2006)87[1345:awstso]2.0.co;2}, pmid = {16869408}, issn = {0012-9658}, mesh = {*Data Collection/methods ; *Databases, Factual ; *Ecology/methods ; *Internet ; *Software Design ; *User-Computer Interface ; }, abstract = {A wide variety of data sets produced by individual investigators are now synthesized to address ecological questions that span a range of spatial and temporal scales. It is important to facilitate such syntheses so that "consumers" of data sets can be confident that both input data sets and synthetic products are reliable. Necessary documentation to ensure the reliability and validation of data sets includes both familiar descriptive metadata and formal documentation of the scientific processes used (i.e., process metadata) to produce usable data sets from collections of raw data. Such documentation is complex and difficult to construct, so it is important to help "producers" create reliable data sets and to facilitate their creation of required metadata. We describe a formal representation, an "analytic web," that aids both producers and consumers of data sets by providing complete and precise definitions of scientific processes used to process raw and derived data sets. The formalisms used to define analytic webs are adaptations of those used in software engineering, and they provide a novel and effective support system for both the synthesis and the validation of ecological data sets. We illustrate the utility of an analytic web as an aid to producing synthetic data sets through a worked example: the synthesis of long-term measurements of whole-ecosystem carbon exchange. Analytic webs are also useful validation aids for consumers because they support the concurrent construction of a complete, Internet-accessible audit trail of the analytic processes used in the synthesis of the data sets. Finally we describe our early efforts to evaluate these ideas through the use of a prototype software tool, SciWalker. We indicate how this tool has been used to create analytic webs tailored to specific data-set synthesis and validation activities, and suggest extensions to it that will support additional forms of validation. The process metadata created by SciWalker is readily adapted for inclusion in Ecological Metadata Language (EML) files.}, } @article {pmid16855009, year = {2006}, author = {Pierson, MJ and Martinez-Arias, R and Holland, BR and Gemmell, NJ and Hurles, ME and Penny, D}, title = {Deciphering past human population movements in Oceania: provably optimal trees of 127 mtDNA genomes.}, journal = {Molecular biology and evolution}, volume = {23}, number = {10}, pages = {1966-1975}, pmid = {16855009}, issn = {0737-4038}, support = {/WT_/Wellcome Trust/United Kingdom ; 077014/WT_/Wellcome Trust/United Kingdom ; }, mesh = {DNA, Mitochondrial/*genetics ; Databases, Nucleic Acid ; *Evolution, Molecular ; Genetics, Population ; *Genome, Human ; Haplotypes ; Humans ; Molecular Sequence Data ; Oceania ; Phylogeny ; Population Dynamics ; Time Factors ; }, abstract = {The settlement of the many island groups of Remote Oceania occurred relatively late in prehistory, beginning approximately 3,000 years ago when people sailed eastwards into the Pacific from Near Oceania, where evidence of human settlement dates from as early as 40,000 years ago. Archeological and linguistic analyses have suggested the settlers of Remote Oceania had ancestry in Taiwan, as descendants of a proposed Neolithic expansion that began approximately 5,500 years ago. Other researchers have suggested that the settlers were descendants of peoples from Island Southeast Asia or the existing inhabitants of Near Oceania alone. To explore patterns of maternal descent in Oceania, we have assembled and analyzed a data set of 137 mitochondrial DNA (mtDNA) genomes from Oceania, Australia, Island Southeast Asia, and Taiwan that includes 19 sequences generated for this project. Using the MinMax Squeeze Approach (MMS), we report the consensus network of 165 most parsimonious trees for the Oceanic data set, increasing by many orders of magnitude the numbers of trees for which a provable minimal solution has been found. The new mtDNA sequences highlight the limitations of partial sequencing for assigning sequences to haplogroups and dating recent divergence events. The provably optimal trees found for the entire mtDNA sequences using the MMS method provide a reliable and robust framework for the interpretation of evolutionary relationships and confirm that the female settlers of Remote Oceania descended from both the existing inhabitants of Near Oceania and more recent migrants into the region.}, } @article {pmid16850038, year = {2006}, author = {Wittkopp, PJ}, title = {Evolution of cis-regulatory sequence and function in Diptera.}, journal = {Heredity}, volume = {97}, number = {3}, pages = {139-147}, doi = {10.1038/sj.hdy.6800869}, pmid = {16850038}, issn = {0018-067X}, mesh = {Animals ; Base Sequence ; Computational Biology ; Conserved Sequence ; Diptera/*genetics ; Enhancer Elements, Genetic/genetics/physiology ; *Evolution, Molecular ; *Regulatory Sequences, Nucleic Acid/genetics/physiology ; }, abstract = {Cis-regulatory sequences direct patterns of gene expression essential for development and physiology. Evolutionary changes in these sequences contribute to phenotypic divergence. Despite their importance, cis-regulatory regions remain one of the most enigmatic features of the genome. Patterns of sequence evolution can be used to identify cis-regulatory elements, but the power of this approach depends upon the relationship between sequence and function. Comparative studies of gene regulation among Diptera reveal that divergent sequences can underlie conserved expression, and that expression differences can evolve despite largely similar sequences. This complex structure-function relationship is the primary impediment for computational identification and interpretation of cis-regulatory sequences. Biochemical characterization and in vivo assays of cis-regulatory sequences on a genomic-scale will relieve this barrier.}, } @article {pmid16845138, year = {2006}, author = {Saitoh, T and Seiwa, K and Nishiwaki, A}, title = {Effects of resource heterogeneity on nitrogen translocation within clonal fragments of Sasa palmata: an isotopic (15N) assessment.}, journal = {Annals of botany}, volume = {98}, number = {3}, pages = {657-663}, pmid = {16845138}, issn = {0305-7364}, mesh = {Data Interpretation, Statistical ; Light ; Nitrogen/*metabolism ; Plant Leaves/metabolism ; Rhizome/metabolism ; Sasa/*metabolism ; Soil ; }, abstract = {BACKGROUND AND AIMS: Clonal fragments of the rhizomatous dwarf bamboo Sasa palmata, which widely predominates in temperate regions of Japan, were grown under heterogeneous resource conditions such as gap understories or nutrient-patchy grassland. Clonal fragments develop multiple ramets with long rhizomes and appear to be physiologically integrated by the translocation of assimilates. The glasshouse experiment reported here was designed to clarify the mechanisms of physiological integration of nitrogen more precisely.

METHODS: To assess how resource conditions influence the amount of nitrogen translocation, and which organ acts as the strongest sink, two experiments were conducted that traced movement of 15N label between interconnected pairs of ramets to compare homogeneous and heterogeneous light and soil nitrogen conditions.

KEY RESULTS: The amount of 15N translocated to leaves was between 9% and 11% greater in high-N and high-light ramets in the heterogeneous compared with homogeneous treatments. Under heterogeneous soil nitrogen conditions, translocation increased from individual ramets in resource-rich patches to ramets in resource-poor patches, while the reverse was true under heterogeneous light environments, reflecting differences in the positions of leaves that act as the strongest sinks. Neither the mass increments nor the total mass of clonal fragments was significantly affected by heterogeneity of either light or nutrients, possibly because the experimental period was too short for differences to manifest themselves.

CONCLUSIONS: This study clearly demonstrated that nitrogen is readily translocated between ramets, particularly under heterogeneous resource conditions. The translocation patterns were governed by functional 'division of labour' mechanisms that resulted in net nitrogen movement from understory sites to gaps, thereby enhancing the carbon acquisition of the whole fragment. Thus, physiological integration may provide benefits for S. palmata when it is growing under heterogeneous conditions in which there are deficits of certain environmental resources.}, } @article {pmid16844675, year = {2006}, author = {Kanchense, JH}, title = {Holistic self-management education and support: a proposed public health model for improving women's health in Zimbabwe.}, journal = {Health care for women international}, volume = {27}, number = {7}, pages = {627-645}, doi = {10.1080/07399330600803774}, pmid = {16844675}, issn = {0739-9332}, mesh = {Community Networks/*organization & administration ; Cultural Characteristics ; Female ; Health Education/*organization & administration ; *Holistic Health ; Humans ; *Models, Organizational ; Preventive Health Services/*organization & administration ; Program Evaluation ; Quality Assurance, Health Care/organization & administration ; Self Care ; Socioeconomic Factors ; *Women's Health ; Women's Health Services/*organization & administration ; Zimbabwe ; }, abstract = {The primary health care model of public health has been implemented in many countries around the globe since the Declaration of Alma Ata in 1978, without pilot testing the primary health care model. Therefore, many public health researchers have sought methods of improving primary health care by creating evidence-based models. Many of these researchers recognize the role of behavioral models in public health. These offshoots of primary health care include the ecological, care, central human capabilities, and the SPECIES models. Holistic self-management education and support is a capacity-building philosophy that ensures active involvement of consumers of health care in the planning and implementation and evaluation of health care services. It helps consumers of health care to achieve the desired improved quality of health and life in managing and sustaining their health at the grassroots level. The care model addresses disease management ideals of the in the original primary health care model. The SPECIES model addresses those aspects of the primary health care model that include the cultural and social factors, as well as individual health education and support in the original primary health care model. The ecological model offers an improvement of the socioeconomic ideal in the original primary health care model. Improving the health of individuals will prevent illness, thereby reducing health care costs and lessening the current strain on an overburdened health care system in Zimbabwe. Holistic self-management education and support links health care delivery systems with social processes. It is a best practices model that could better serve Zimbabwean girls and women by contributing positively to the national challenges in health care, thereby meeting the Zimbabwean primary health care and safe motherhood goals. It is here recommended that holistic self-management education and support must be pilot tested before being adopted as the most appropriate model for ensuring population health.}, } @article {pmid16842345, year = {2006}, author = {Fu, J and Xu, X}, title = {The functional divergence of two glgP homologues in Synechocystis sp. PCC 6803.}, journal = {FEMS microbiology letters}, volume = {260}, number = {2}, pages = {201-209}, doi = {10.1111/j.1574-6968.2006.00312.x}, pmid = {16842345}, issn = {0378-1097}, mesh = {Computational Biology ; *Gene Expression Regulation, Bacterial ; Genes, Bacterial ; Glycogen/metabolism ; Glycogen Phosphorylase/*genetics/*metabolism ; Hot Temperature ; Mutation ; Photosynthesis ; Phylogeny ; Sequence Alignment ; Sequence Homology ; Synechocystis/*enzymology/genetics/growth & development ; }, abstract = {Glycogen phosphorylase (GlgP, EC 2.4.1.1) catalyzes the cleavage of glycogen into glucose-1-phosphate (Glc-1-P), the first step in glycogen catabolism. Two glgP homologues are found in the genome of Synechocystis sp. PCC 6803, a unicellular cyanobacterium: sll1356 and slr1367. We report on the different functions of these glgP homologues. sll1356, rather than slr1367, is essential for growth at high temperatures. On the other hand, when CO2-fixation and the supply of glucose are both limited, slr1367 is the key factor in glycogen metabolism. In cells growing autotrophically, sll1356 plays a more important role in glycogen digestion than slr1367. This functional divergence is also supported by a phylogenetic analysis of glgP homologues in cyanobacteria.}, } @article {pmid16838293, year = {2006}, author = {Kamm, K and Schierwater, B}, title = {Ancient complexity of the non-Hox ANTP gene complement in the anthozoan Nematostella vectensis: implications for the evolution of the ANTP superclass.}, journal = {Journal of experimental zoology. Part B, Molecular and developmental evolution}, volume = {306}, number = {6}, pages = {589-596}, doi = {10.1002/jez.b.21123}, pmid = {16838293}, issn = {1552-5007}, mesh = {Animals ; Antennapedia Homeodomain Protein/*genetics ; Anthozoa/*genetics ; Bayes Theorem ; Cluster Analysis ; Computational Biology ; *Evolution, Molecular ; Models, Genetic ; Multigene Family/*genetics ; *Phylogeny ; }, abstract = {The origin and evolution of ANTP superclass genes has raised controversial discussions. While recent evidence suggests that a true Hox cluster emerged after the cnidarian bilaterian split, the origin of the ANTP superclass as a whole remains unclear. Based on analyses of bilaterian genomes, it seems very likely that clustering has once been a characteristic of all ANTP homeobox genes and that their ancestors have emerged through several series of cis-duplications from the same genomic region. Since the diploblastic Cnidaria possess orthologs of some non-Hox ANTP genes, at least some steps of the expansion of this hypothetical homeobox gene array must have occurred in the last common ancestor of both lineages--but it is unknown to what extent. By screening the unassembled Nematostella genome, we have identified unambiguous orthologs to almost all non-Hox ANTP genes which are present in Bilateria--with the exception of En, Tlx and (possibly) Vax. Furthermore, Nematostella possesses ANTP genes that are missing in some bilaterian lineages, like the rough gene or NK7. In addition, several ANTP homeobox gene families have been independently duplicated in Nematostella. We conclude that the last cnidarian/bilaterian ancestor already harboured the almost full complement of non-Hox ANTP genes before the Hox system evolved.}, } @article {pmid16827547, year = {2005}, author = {Cleveland, DA and Soleri, D and Cuevas, FA and Crossa, J and Gepts, P}, title = {Detecting (trans)gene flow to landraces in centers of crop origin: lessons from the case of maize in Mexico.}, journal = {Environmental biosafety research}, volume = {4}, number = {4}, pages = {197-208; discussion 209-15}, doi = {10.1051/ebr:2006006}, pmid = {16827547}, issn = {1635-7922}, mesh = {Crops, Agricultural/genetics ; Data Interpretation, Statistical ; *Gene Flow ; Mexico ; *Plants, Genetically Modified ; Population Density ; Seeds/genetics ; Zea mays/*genetics ; }, abstract = {There is much discussion of the probability of transgene flow from transgenic crop varieties to landraces and wild relatives in centers of origin or diversity, and its genetic, ecological, and social consequences. Without costly research on the variables determining gene flow, research on transgene frequencies in landrace (or wild relative) populations can be valuable for understanding transgene flow and its effects. Minimal research requirements include (1) understanding how farmer practices and seed systems affect landrace populations, (2) sampling to optimize Ne/n (effective/census population size), (3) minimizing variance at all levels sampled, and (4) using Ne to calculate binomial probabilities for transgene frequencies. A key case is maize in Mexico. Two peer-reviewed papers, based on landrace samples from the Sierra Juárez region of Oaxaca, Mexico, reached seemingly conflicting conclusions: transgenes are present (Quist and Chapela, 2001, Nature 414: 541-543; 2002, Nature 416: 602) or "detectable transgenes" are absent (Ortiz-García et al., 2005, Proc. Natl. Acad. Sci. USA 102: 12338-12343 and 18242). We analyzed these papers using information on Oaxacan maize seed systems and estimates of Ne. We conclude that if Quist and Chapela's results showing presence are accepted, Ortiz-García et al.'s conclusions of no evidence of transgenes at detectable levels or for their introgression into maize landraces in the Sierra de Juárez of Oaxaca are not scientifically justified. This is because their samples are not representative, and their statistical analysis is inconclusive due to using n instead of Ne. Using estimates of Ne based on Ortiz-García et al.'s n, we estimate that transgenes could be present in maize landraces in the Sierra Juárez region at frequencies of approximately 1-4%, and are more likely to be present in the 90% of Oaxacan landrace area that is not mountainous. Thus, we have no scientific evidence of maize transgene presence or absence in recent years in Mexico, Oaxaca State, or the Sierra Juárez region.}, } @article {pmid16817651, year = {2006}, author = {Wilhelm, FH and Pfaltz, MC and Grossman, P and Roth, WT}, title = {Distinguishing emotional from physical activation in ambulatory psychophysiological monitoring.}, journal = {Biomedical sciences instrumentation}, volume = {42}, number = {}, pages = {458-463}, pmid = {16817651}, issn = {0067-8856}, support = {MH56094/MH/NIMH NIH HHS/United States ; }, mesh = {Diagnosis, Computer-Assisted/*methods ; Diagnosis, Differential ; *Emotions ; Female ; Humans ; Monitoring, Ambulatory/*methods ; *Motor Activity ; Psychophysiologic Disorders/*diagnosis/*physiopathology/psychology ; Reproducibility of Results ; Sensitivity and Specificity ; }, abstract = {Ambulatory monitoring has gained powerful new tools due to recent electronic and computer advances. The capability simultaneously to monitor numerous physiological parameters and behavior enhances the ecological validity of field assessment, but methodological challenges abound that can compromise attempts to understand biobehavioral relations in the real world. A major obstacle is that physiological dysregulation or emotion effects can be masked by variation in physical activity. Using a multi-channel ambulatory recording system, a wide array of self-report, physiological and environmental measurements was collected from 28 participants during quiet sitting, physical exercise and an emotion induction consisting of a short commercial flight. Half of the participants were selected to respond to flying with intense anxiety, the other half, with moderate excitement. Recorded channels included ECG, EDA, calibrated respiration pattern, and skin temperature, from which 17 physiological parameters were calculated. Accelerometry and self-report in an emotion diary served as manipulation checks. Results indicate that many parameters, including heart rate, respiratory sinus arrhythmia, and skin conductance level and its fluctuation rate, were strongly and nonspecifically affected by both anxiety and exercise. However, parameters of respiratory volume were particularly responsive to exercise, while certain parameters of irregularity in breathing were to anxiety. Several respiratory timing parameters were responsive to both exercise and excitement. We conclude that physiological measures provide information helping to distinguish emotional from physical activation. However, additional context awareness is necessary for confident data interpretation in ambulatory recording. This can be achieved by specific channels such as accelerometry, items in an electronic diary, semi-structured protocols, and statistical modeling.}, } @article {pmid16813340, year = {2006}, author = {Gevrey, M and Worner, SP}, title = {Prediction of global distribution of insect pest species in relation to climate by using an ecological informatics method.}, journal = {Journal of economic entomology}, volume = {99}, number = {3}, pages = {979-986}, doi = {10.1603/0022-0493-99.3.979}, pmid = {16813340}, issn = {0022-0493}, mesh = {Animals ; *Ceratitis capitata ; *Climate ; Models, Biological ; *Moths ; }, abstract = {The aim of this work was to predict the worldwide distribution of two pest species-Ceratitis capitata (Wiedemann), the Mediterranean fruit fly, and Lymantria dispar (L.), the gypsy moth-based on climatic factors. The distribution patterns of insect pests have most often been investigated using classical statistical models or ecoclimatic assessment models such as CLIMEX. In this study, we used an artificial neural network, the multilayer perceptron, trained using the backpropagation algorithm, to model the distribution of each species. The data matrix used to model the distribution of each species was divided into three data sets to (1) develop and train the model, (2) validate the model and prevent over-fitting, and (3) test each model on novel data. The percentage of correct predictions of the global distribution of each species was high for Mediterranean fruit fly for the three data sets giving 95.8, 81.5, and 80.6% correct predictions, respectively, and 96.8, 84.3, and 81.5 for the gypsy moth. Kappa statistics used to test the level of significance of the results were highly significant (in all cases P < 0.0001). A sensitivity analysis applied to each model based on the calculation of the derivatives of each of a large number of input variables showed that the variables that contributed most to explaining the distribution of C. capitata were annual average temperature and annual potential evapotranspiration. For L. dispar, the average minimum temperature and minimum daylength range were the main explanatory variables. The ANN models and methods developed in this study offer powerful additional predictive approaches in invasive species research.}, } @article {pmid16806658, year = {2007}, author = {Geneletti, D}, title = {An approach based on spatial multicriteria analysis to map the nature conservation value of agricultural land.}, journal = {Journal of environmental management}, volume = {83}, number = {2}, pages = {228-235}, doi = {10.1016/j.jenvman.2006.03.002}, pmid = {16806658}, issn = {0301-4797}, mesh = {*Agriculture ; *Conservation of Natural Resources ; Ecosystem ; Environmental Monitoring/*methods/statistics & numerical data ; *Geographic Information Systems ; Geologic Sediments/analysis ; Italy ; Trees ; Water Pollutants/analysis ; }, abstract = {Knowledge of the nature conservation value of agricultural land provides a useful input to land-use planning. However, the scarcity of suitable data causes this component to rarely play a role. The paper proposes a methodology based on commonly available data to assess the nature conservation value of agricultural landscapes, and to generate cartographic results to be used as decision variables in planning. The approach relies on landscape ecological indicators and on the application of multicriteria analysis in a Geographical Information System (GIS) context. Four criteria were selected: the agricultural landscape type, the cover of vegetation remnants and marginal features, the length of forest-agriculture ecotones, and the proximity to nature reserves. These criteria were assessed directly or by means of specific indicators, generating maps that were subsequently aggregated through spatial multicriteria analysis. The approach was tested in an alpine area located in Trentino (northern Italy).}, } @article {pmid16794065, year = {2006}, author = {Mora, C and Andrèfouët, S and Costello, MJ and Kranenburg, C and Rollo, A and Veron, J and Gaston, KJ and Myers, RA}, title = {Ecology. Coral reefs and the global network of Marine Protected Areas.}, journal = {Science (New York, N.Y.)}, volume = {312}, number = {5781}, pages = {1750-1751}, doi = {10.1126/science.1125295}, pmid = {16794065}, issn = {1095-9203}, mesh = {Animals ; *Anthozoa ; *Biodiversity ; *Conservation of Natural Resources ; Databases, Factual ; *Ecosystem ; *Fishes ; Homing Behavior ; Marine Biology ; Population Dynamics ; }, } @article {pmid16790466, year = {2006}, author = {Coiffard, C and Gomez, B and Kvacek, J and Thevenard, F}, title = {Early angiosperm ecology: evidence from the Albian-Cenomanian of Europe.}, journal = {Annals of botany}, volume = {98}, number = {3}, pages = {495-502}, pmid = {16790466}, issn = {0305-7364}, mesh = {Biodiversity ; Biological Evolution ; Cycadopsida/genetics/physiology ; Databases as Topic ; *Ecosystem ; Europe ; *Fossils ; Magnoliopsida/classification/*genetics/physiology ; Phylogeny ; }, abstract = {BACKGROUND AND AIMS: The mid-Cretaceous is a period of sudden turnover from gymnosperm to angiosperm-dominated floras. The aim was to investigate the fossil plant ecology in order to follow the spread of angiosperm taxa.

METHODS: Floristic lists and localities from the latest Albian-Cenomanian of Europe are analysed with Wagner's Parsimony Method, a clustering method currently used in phylogeny (cladistics).

KEY RESULTS: Wagner's Parsimony Method points out that (a) gymnosperms dominated brackish water-related environments while angiosperms dominated freshwater-related environments (e.g. swamps, floodplains, levees, channels), (b) angiosperms showed the highest diversity in stable, freshwater-related environments, (c) a single angiosperm, 'Diospyros' cretacea, is restricted to brackish water-related environments and (d) the families Lauraceae and Platanaceae were exclusive to disturbed, braided river environments, implying a opportunist strategy for early tree angiosperms.

CONCLUSIONS: During the Mid-Cretaceous, European floras were characterized by (a) coastal gymnosperms, (b) highly diversified fluvial angiosperms and (c) the first European brackish water-related angiosperm.}, } @article {pmid16779112, year = {2005}, author = {Pluye, P and Grad, RM and Stephenson, R and Dunikowski, LG}, title = {A new impact assessment method to evaluate knowledge resources.}, journal = {AMIA ... Annual Symposium proceedings. AMIA Symposium}, volume = {2005}, number = {}, pages = {609-613}, pmid = {16779112}, issn = {1942-597X}, mesh = {*Databases as Topic ; *Evaluation Studies as Topic ; Feasibility Studies ; *Information Storage and Retrieval ; *Information Systems ; Textbooks as Topic ; }, abstract = {RATIONALE: Methods to systematically measure the impact of knowledge resources on health professionals would enhance evaluation of these resources in the real world.

OBJECTIVE: To propose a new impact assessment method.

BACKGROUND: We demonstrated the feasibility of combining a 4-level scale with Computerized Ecological Momentary Assessment (CEMA) for efficiently measuring the impact of a knowledge resource.

METHOD: We critically reviewed the world literature regarding the impact of clinical information-retrieval technology on trainees and doctors, and retained 26 papers for qualitative content analysis.

FINDINGS: Of those, 21 use a nominal scale (yes/no), none systematically measures the impact of searches for information outside of a laboratory setting, and none uses an ordinal scale. The literature supports the proposed levels of impact, and suggests a fifth level.

CONCLUSION: A new impact assessment method is proposed, which combines a 5-level revised scale and CEMA.}, } @article {pmid16779081, year = {2005}, author = {Lin, JL and Vahabzadeh, M and Mezghanni, M and Epstein, DH and Preston, KL}, title = {A high-level specification for adaptive ecological momentary assessment: real-time assessment of drug craving, use and abstinence.}, journal = {AMIA ... Annual Symposium proceedings. AMIA Symposium}, volume = {2005}, number = {}, pages = {455-459}, pmid = {16779081}, issn = {1942-597X}, mesh = {Behavioral Research/methods ; Computer Systems ; *Computers, Handheld ; Humans ; Medical Records ; *Medical Records Systems, Computerized ; Software ; *Software Design ; Substance-Related Disorders/*psychology ; *Surveys and Questionnaires ; }, abstract = {In psychological research, efforts to capture day-to-day human experience traditionally relied on pen-and-paper diaries and questionnaires. Some current studies, however, incorporate handheld computers, which provide researchers with many options and advantages in addition to providing more reliable data. One advantage of using handheld computers is the programmability of the electronic diary, which, compared to old-fashioned paper diaries, affords the researchers with a wealth of possibilities. An important possibility is to construct a built-in mechanism in the computer-administered questionnaires that would allow transparent branching, in which question presentation is contingent on participants' answers to previous questions. The major hurdle in implementing such an approach is the limitations of the platform used for such assessments: inexpensive "low-end" handheld devices. We propose a high-level specification which enables non-programming researchers to "branch" their questionnaires without modifications to the source code in a highly user-friendly fashion, with backtracking capability and very modest hardware requirements. A finite state automaton approach was implemented, we believe for the first time, to create an auto-trigger mechanism for the real-time evaluation of the conditions. This solution provides our investigators with the capacity to administer efficient assessments that are dynamically customized to reflect participants' behaviors without the need for any post-production programming.}, } @article {pmid16777727, year = {2006}, author = {Hall, RJ and Hastings, A and Ayres, DR}, title = {Explaining the explosion: modelling hybrid invasions.}, journal = {Proceedings. Biological sciences}, volume = {273}, number = {1592}, pages = {1385-1389}, pmid = {16777727}, issn = {0962-8452}, mesh = {Computational Biology ; *Ecosystem ; Fertility ; Genotype ; *Hybridization, Genetic ; *Models, Genetic ; Poaceae/*genetics/physiology ; Selection, Genetic ; }, abstract = {The emergence of hybrids between native and introduced species is an increasingly widespread problem which can alter entire ecosystems. We present a general model for the hybridization of two plant species to investigate the conditions under which hybrid invasions can occur, and the ecological and genetic consequences of such hybridizations. We find that parental compatibility and fecundity are important determinants of whether (and at what rate) hybrid genotypes emerge. Enhanced hybrid fitness traits affect both the population's genetic structure and total rate of increase, with rapid selection for the fittest genotype. Conversely, if different genotypes maximize different life-history characteristics, the ensuing population can be genetically very variable. The model provides a novel approach to evaluate the contributions of population dynamic and genetic processes in the study of hybrid invasions.}, } @article {pmid16770504, year = {2006}, author = {Jian-Bing, W and Du-Ning, X and Xing-Yi, Z and Xiu-Zhen, L and Xiao-Yu, L}, title = {Spatial variability of soil organic carbon in relation to environmental factors of a typical small watershed in the black soil region, northeast China.}, journal = {Environmental monitoring and assessment}, volume = {121}, number = {1-3}, pages = {597-613}, doi = {10.1007/s10661-005-9158-5}, pmid = {16770504}, issn = {0167-6369}, mesh = {Carbon/*analysis ; China ; *Conservation of Natural Resources ; Environment ; *Environmental Monitoring ; Fresh Water ; Geographic Information Systems ; Geology/methods ; Organic Chemicals/*analysis ; Soil/*analysis ; Statistics as Topic/methods ; }, abstract = {A total of 292 soil samples were taken from surface soil (0-20 cm) of a typical small watershed-Tongshuang in the black soil region of Heilongjiang province, northeast China in June 2005 for examining the concentration of soil organic carbon (SOC). Spatial variability of SOC in relation to topography and land use was evaluated using classical statistics, geostatistics and geographic information system (GIS) analyses. The objective of this study was to provide a scientific basis for land management targeting at improving soil quality in this region. Classical statistical analysis results indicated that the variability of SOC was moderate (C (V) = 0.30). Slope position and land use types were discriminating factors for its spatial variability. Geostatistics analyses showed that SOC had a strong spatial autocorrelation, which was mainly induced by structural factors. Mean concentration of SOC in surface soil was 2.27% in this watershed, which was a very low level in the northern black soil region of northeast China. In this small watershed, present soil and water conservation measures played an important role in controlling soil loss. But SOC's restoration was unsatisfactory. Nearly three-quarters of the area had worrisome productivity. How to improve SOC concentration targeting at soil fertility is a pressing need in the future.}, } @article {pmid16762374, year = {2007}, author = {Dauvin, JC and Ruellet, T and Desroy, N and Janson, AL}, title = {The ecological quality status of the Bay of Seine and the Seine estuary: use of biotic indices.}, journal = {Marine pollution bulletin}, volume = {55}, number = {1-6}, pages = {241-257}, doi = {10.1016/j.marpolbul.2006.04.010}, pmid = {16762374}, issn = {0025-326X}, mesh = {Animals ; *Biodiversity ; Databases, Factual ; Environmental Monitoring/*methods/*standards/statistics & numerical data ; France ; Geography ; Geologic Sediments/analysis ; International Cooperation/legislation & jurisprudence ; *Invertebrates ; *Marine Biology ; *Models, Biological ; Oceans and Seas ; Population Density ; Reference Standards ; Seasons ; Species Specificity ; }, abstract = {Using recent indices developed, in part, for use under the European Water Framework Directive (AMBI, BENTIX, BOPA, BQI, I2EC and the trophic index ITI), the ecological quality status of two highly contaminated environments--the Bay of Seine and the Seine estuary (Eastern English Channel)--was determined on several spatial and temporal scales. Data from 604 observations gathered over a 14-year period (1988-2002) were analyzed, and the results used to show the relationship between biotic indices, environmental variables and classic descriptors (e.g., number of species, total abundance, dominance index, ES(50) and Shannon/Brillouin diversities). Though the specific ecological quality (EcoQ) values calculated with the various indices were different, the overall trend of the results was similar. Synthesizing the values produced by the six indices used in the study allowed attribution of a high to good EcoQ status to the Bay of Seine and a moderate EcoQ to the estuary. The mesh size used when processing samples was proved to have no effect in winter on the EcoQ values for either body of water.}, } @article {pmid16758292, year = {2006}, author = {Mack, JJ}, title = {Landscape as a predictor of wetland condition: an evaluation of the Landscape Development Index (LDI) with a large reference wetland dataset from Ohio.}, journal = {Environmental monitoring and assessment}, volume = {120}, number = {1-3}, pages = {221-241}, pmid = {16758292}, issn = {0167-6369}, mesh = {Conservation of Natural Resources/*methods ; Environmental Monitoring/*methods ; *Geographic Information Systems ; Humans ; Ohio ; *Wetlands ; }, abstract = {Recent approaches to wetland assessment have advocated a multilevel approach which incorporates assessments based on landscape (remote sensing) data, on-site but "rapid" methods, and intensive methods where quantitative data is collected. Brown and Vivas (2004) recently pro- posed an assessment method that uses remote sensing information (Landscape Development Index or LDI) and propose that it may also be usable as a quantified human disturbance gradient. The LDI was evaluated using a large reference wetland data set from Ohio using land use percentages within a 1 km radius circle of the wetlands. The LDI had interpretable and significant relationships with another human disturbance gradient (the Ohio Rapid Assessment Method for Wetlands or ORAM) and with most metrics and scores from the Vegetation Index of Biotic Integrity (VIBI) developed for use in the State of Ohio. Metrics from emergent wetlands had the most significant correlations with the LDI (10 of 10 metrics), followed by forested wetlands (8 of 10 metrics) and shrub wetlands (4 of 10). Poor correlation for VIBI scores and metrics of shrub wetlands was due to differences in attainable LDI scores based on ecoregion and natural buffers shielding the wetland from otherwise intensive land uses. The ORAM and VIBI were developed for use in wetlands in Ohio completely independent of the LDI. It is an important test of the LDI concept that so many interpretable and significant relationships occurred between the VIBI scores, VIBI metric values, and the ORAM scores. For the purposes of VIBI development, the LDI is an independent, quantified disturbance gradient that has provided an additional test of the VIBI. Given its theoretical underpinnings and the fact that it uses quantified land use percentages, the LDI has many advantages over more qualitative human disturbance gradients. Using land use percentages from increasingly smaller distances from the wetland edge (100-200 m) may improve the resolution of the LDI to detect on-site disturbances to a wetland which degrade its ecological condition. The LDI should be evaluated with other large reference data sets in other regions to evaluate its validity and usefulness as an assessment tool.}, } @article {pmid16756109, year = {2006}, author = {Kozlov, MV and Hurlbert, SH}, title = {[Pseudoreplication, chatter, and the international nature of science: a response to D.V. Tatarnikov].}, journal = {Zhurnal obshchei biologii}, volume = {67}, number = {2}, pages = {145-152}, pmid = {16756109}, issn = {0044-4596}, mesh = {*Data Interpretation, Statistical ; *Ecology/education ; *Education, Continuing ; Reproducibility of Results ; *Research Design ; }, abstract = {The commentary by Tatarnikov (2005) on the design and analysis of manipulative experiments in ecology represents an obvious danger to readers with poor knowledge of modern statistics due to its erroneous interpretation of pseudoreplication and statistical independence. Here we offer clarification of those concepts--and related ones such as experimental unit and evaluation unit--by reference to studies cited by Tatarnikov (2005). We stress the necessity of learning from the accumulated experience of the international scientific community in order not to repeat the errors found in earlier publications that have already been analyzed and widely written about. (An Englisch translation of the full article is available as a pdf-file from either or the authors.)}, } @article {pmid16753077, year = {2007}, author = {Mongoh, MN and Khaitsa, ML and Dyer, NW}, title = {Environmental and ecological determinants of West Nile virus occurrence in horses in North Dakota, 2002.}, journal = {Epidemiology and infection}, volume = {135}, number = {1}, pages = {57-66}, pmid = {16753077}, issn = {0950-2688}, mesh = {Animals ; Birds/virology ; Culicidae/virology ; *Disease Outbreaks ; *Ecosystem ; *Environment ; Geographic Information Systems ; Horse Diseases/*epidemiology/virology ; Horses/virology ; Humans ; *Models, Biological ; North Dakota/epidemiology ; Principal Component Analysis ; Risk Factors ; West Nile Fever/epidemiology/*veterinary/virology ; West Nile virus/isolation & purification/*pathogenicity ; }, abstract = {West Nile virus (WNV) outbreak in North Dakota in 2002 included over 569 horse cases, clustered mainly in the eastern and northeastern parts of the state. The pattern of occurrence observed suggested existence of specific environmental and ecological factors that increased the risk for infection and illness in those locations. We developed a predictive model with factors that explained the pattern of WNV occurrence observed. Results indicated that surface elevation, temperature, precipitation, reported WNV-positive birds, reported WNV-positive humans, and reported WNV-positive mosquitoes were important predictors of occurrence in horses. However, case distance from water bodies was not significant in the model. Future predictive models of WNV occurrence in horses should take into account these factors in order to improve accuracy and reliability. Research into other potential determinants such as horse management factors are required to determine more differential risk factors associated with WNV occurrence in horses.}, } @article {pmid16751849, year = {2006}, author = {He, X and Zhang, J}, title = {Why do hubs tend to be essential in protein networks?.}, journal = {PLoS genetics}, volume = {2}, number = {6}, pages = {e88}, pmid = {16751849}, issn = {1553-7404}, mesh = {Binding Sites ; Conserved Sequence ; Databases, Protein ; Evolution, Molecular ; Genes, Essential ; Genes, Lethal ; Models, Biological ; Models, Theoretical ; Protein Binding ; Protein Interaction Mapping ; Protein Structure, Tertiary ; Proteome/*physiology ; Saccharomyces cerevisiae/*metabolism ; Saccharomyces cerevisiae Proteins/*physiology ; }, abstract = {The protein-protein interaction (PPI) network has a small number of highly connected protein nodes (known as hubs) and many poorly connected nodes. Genome-wide studies show that deletion of a hub protein is more likely to be lethal than deletion of a non-hub protein, a phenomenon known as the centrality-lethality rule. This rule is widely believed to reflect the special importance of hubs in organizing the network, which in turn suggests the biological significance of network architectures, a key notion of systems biology. Despite the popularity of this explanation, the underlying cause of the centrality-lethality rule has never been critically examined. We here propose the concept of essential PPIs, which are PPIs that are indispensable for the survival or reproduction of an organism. Our network analysis suggests that the centrality-lethality rule is unrelated to the network architecture, but is explained by the simple fact that hubs have large numbers of PPIs, therefore high probabilities of engaging in essential PPIs. We estimate that approximately 3% of PPIs are essential in the yeast, accounting for approximately 43% of essential genes. As expected, essential PPIs are evolutionarily more conserved than nonessential PPIs. Considering the role of essential PPIs in determining gene essentiality, we find the yeast PPI network functionally more robust than random networks, yet far less robust than the potential optimum. These and other findings provide new perspectives on the biological relevance of network structure and robustness.}, } @article {pmid16740589, year = {2006}, author = {Ferreira, S and Hjernø, K and Larsen, M and Wingsle, G and Larsen, P and Fey, S and Roepstorff, P and Salomé Pais, M}, title = {Proteome profiling of Populus euphratica Oliv. upon heat stress.}, journal = {Annals of botany}, volume = {98}, number = {2}, pages = {361-377}, pmid = {16740589}, issn = {0305-7364}, mesh = {Cell Membrane/physiology ; Databases, Nucleic Acid ; Electrolytes/metabolism ; Electrophoresis, Gel, Two-Dimensional ; Gene Expression Regulation, Plant ; Heat-Shock Response/physiology ; *Hot Temperature ; Plant Leaves/metabolism/physiology ; Plant Proteins/classification/genetics/*metabolism ; Populus/genetics/*metabolism/physiology ; *Proteomics ; Sequence Homology, Amino Acid ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ; }, abstract = {BACKGROUND AND AIMS: Populus euphratica is a light-demanding species ecologically characterized as a pioneer. It grows in shelter belts along riversides, being part of the natural desert forest ecosystems in China and Middle Eastern countries. It is able to survive extreme temperatures, drought and salt stress, marking itself out as an important plant species to study the mechanisms responsible for survival of woody plants under heat stress.

METHODS: Heat effects were evaluated through electrolyte leakage on leaf discs, and LT(50) was determined to occur above 50 degrees C. Protein accumulation profiles of leaves from young plants submitted to 42/37 degrees C for 3 d in a phytotron were determined through 2D-PAGE, and a total of 45 % of up- and downregulated proteins were detected. Matrix-assisted laser desorption ionization-time of flight (MALDI-TOF)/TOF analysis, combined with searches in different databases, enabled the identification of 82 % of the selected spots.

KEY RESULTS: Short-term upregulated proteins are related to membrane destabilization and cytoskeleton restructuring, sulfur assimilation, thiamine and hydrophobic amino acid biosynthesis, and protein stability. Long-term upregulated proteins are involved in redox homeostasis and photosynthesis. Late downregulated proteins are involved mainly in carbon metabolism.

CONCLUSIONS: Moderate heat response involves proteins related to lipid biogenesis, cytoskeleton structure, sulfate assimilation, thiamine and hydrophobic amino acid biosynthesis, and nuclear transport. Photostasis is achieved through carbon metabolism adjustment, a decrease of photosystem II (PSII) abundance and an increase of PSI contribution to photosynthetic linear electron flow. Thioredoxin h may have a special role in this process in P. euphratica upon moderate heat exposure.}, } @article {pmid16738815, year = {2006}, author = {Lussier, SM and Enser, RW and Dasilva, SN and Charpentier, M}, title = {Effects of habitat disturbance from residential development on breeding bird communities in riparian corridors.}, journal = {Environmental management}, volume = {38}, number = {3}, pages = {504-521}, pmid = {16738815}, issn = {0364-152X}, mesh = {Animals ; Biodiversity ; Birds/classification/*physiology ; Cities/*statistics & numerical data ; City Planning ; Conservation of Natural Resources ; *Ecosystem ; Environmental Monitoring ; Environmental Policy ; Geographic Information Systems ; Housing/*statistics & numerical data ; Humans ; Population Dynamics ; *Reproduction ; Rhode Island ; *Rivers ; }, abstract = {This study assessed the relationship among land use, riparian vegetation,and avian populations at two spatial scales. Our objective was to compare the vegetated habitat in riparian corridors with breeding bird guilds in eight Rhode Island subwatersheds along a range of increasing residential land use. Riparian habitats were characterized with fine-scale techniques (used field transects to measure riparian vegetation structure and plant species richness) at the reach spatial scale,and with coarse-scale landscape techniques (a Geographic Information System to document land-cover attributes) at the subwatershed scale. Bird surveys were conducted in the riparian zone,and the observed bird species were separated into guilds based on tolerance to human disturbance,habitat preference,foraging type, and diet preference. Bird guilds were correlated with riparian vegetation metrics,percent impervious surface,and percent residential land use,revealing patterns of breeding bird distribution. The number of intolerant species predominated below 12%residential development and 3% impervious surface,whereas tolerant species predominated above these levels.Habitat guilds of edge,forest, and wetland bird species correlated with riparian vegetation. This study showed that the application of avian guilds at both stream reach and subwatershed scales offers a comprehensive assessment of effects from disturbed habitat,but that the subwatershed scale is a more efficient method of evaluation for environmental management.}, } @article {pmid16737530, year = {2006}, author = {Beldade, P and Rudd, S and Gruber, JD and Long, AD}, title = {A wing expressed sequence tag resource for Bicyclus anynana butterflies, an evo-devo model.}, journal = {BMC genomics}, volume = {7}, number = {}, pages = {130}, pmid = {16737530}, issn = {1471-2164}, support = {T15 LM007443/LM/NLM NIH HHS/United States ; 5 T15 LM007443/LM/NLM NIH HHS/United States ; }, mesh = {Animals ; Butterflies/anatomy & histology/*genetics/growth & development ; Databases, Genetic ; Evolution, Molecular ; *Expressed Sequence Tags ; Gene Library ; Genes, Insect ; Microsatellite Repeats ; Polymorphism, Genetic ; Sequence Analysis, DNA ; Wings, Animal/*growth & development ; }, abstract = {BACKGROUND: Butterfly wing color patterns are a key model for integrating evolutionary developmental biology and the study of adaptive morphological evolution. Yet, despite the biological, economical and educational value of butterflies they are still relatively under-represented in terms of available genomic resources. Here, we describe an Expression Sequence Tag (EST) project for Bicyclus anynana that has identified the largest available collection to date of expressed genes for any butterfly.

RESULTS: By targeting cDNAs from developing wings at the stages when pattern is specified, we biased gene discovery towards genes potentially involved in pattern formation. Assembly of 9,903 ESTs from a subtracted library allowed us to identify 4,251 genes of which 2,461 were annotated based on BLAST analyses against relevant gene collections. Gene prediction software identified 2,202 peptides, of which 215 longer than 100 amino acids had no homology to any known proteins and, thus, potentially represent novel or highly diverged butterfly genes. We combined gene and Single Nucleotide Polymorphism (SNP) identification by constructing cDNA libraries from pools of outbred individuals, and by sequencing clones from the 3' end to maximize alignment depth. Alignments of multi-member contigs allowed us to identify over 14,000 putative SNPs, with 316 genes having at least one high confidence double-hit SNP. We furthermore identified 320 microsatellites in transcribed genes that can potentially be used as genetic markers.

CONCLUSION: Our project was designed to combine gene and sequence polymorphism discovery and has generated the largest gene collection available for any butterfly and many potential markers in expressed genes. These resources will be invaluable for exploring the potential of B. anynana in particular, and butterflies in general, as models in ecological, evolutionary, and developmental genetics.}, } @article {pmid16724739, year = {2006}, author = {Liu, X and Skidmore, AK and Bronsveld, MC}, title = {[Assessment of giant panda habitat based on integration of expert system and neural network].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {17}, number = {3}, pages = {438-443}, pmid = {16724739}, issn = {1001-9332}, mesh = {Animals ; Conservation of Natural Resources ; Ecology ; *Ecosystem ; *Environment ; *Expert Systems ; Geographic Information Systems ; *Neural Networks, Computer ; Ursidae/*physiology ; }, abstract = {To conserve giant panda effectively, it is important to understand the spatial pattern and temporal change of its habitat. Mapping is an effective approach for wildlife habitat evaluation and monitoring. The application of recently developed artificial intelligence tools, including expert systems and neural networks, could integrate qualitative and quantitative information for modeling complex systems, and built the information into a GIS, which could be helpful for giant panda habitat mapping. This study built a mapping approach for giant panda habitat mapping, which integrated expert system and neural network classifiers (ESNNC), and used multi-type data within GIS. The giant panda habitat types and their suitability were mapped by ESNNC. The results showed that the habitat types and their suitability in Foping Nature Reserve were assessed with a higher accuracy (> 80 %) by ESNNC, compared with non-integrated classifiers, i. e., expert system, neural network, and maximum likelihood. Z-statistic test showed that ESNNC was significantly better than the other three non-integrated classifiers. It was recommended that the integrated approach could be widely applied into wildlife habitat assessment.}, } @article {pmid16723064, year = {2006}, author = {Duarte, CM and Nascimento, VB and Akerman, M}, title = {[Adolescent pregnancy and social exclusion: analysis of intra-urban disparities].}, journal = {Revista panamericana de salud publica = Pan American journal of public health}, volume = {19}, number = {4}, pages = {236-243}, doi = {10.1590/s1020-49892006000400003}, pmid = {16723064}, issn = {1020-4989}, mesh = {Adolescent ; Birth Weight ; Brazil ; Cross-Sectional Studies ; Data Interpretation, Statistical ; Education ; Female ; Fertility ; Gestational Age ; Humans ; Infant, Newborn ; Poverty ; Pregnancy ; *Pregnancy in Adolescence/statistics & numerical data ; Social Class ; Socioeconomic Factors ; Urban Population ; }, abstract = {OBJECTIVE: To compare adolescent mothers living in four areas with different degrees of social exclusion in the city of Santo André, São Paulo, Brazil, in terms of the mothers' schooling, the birth weight and gestational age of their babies, and the specific fertility rate of each of the four areas in 1998.

METHOD: An ecological cross-sectional study was carried out with 1 314 adolescent girls. The four areas analyzed had earlier been defined in the City of Santo André Social Exclusion/Inclusion Map. Area 1 had the highest exclusion index (worst socioeconomic conditions), and Area 4 the lowest exclusion index (best socioeconomic conditions). The data relating to the adolescent mothers and their children were collected from the National Live Birth Information System, and the socioeconomic data for Santo André were obtained from the State Data Analysis System Foundation, the Brazilian Institute of Geography and Statistics, and the city's Social Exclusion/Inclusion Map.

RESULTS: Having little formal education was statistically associated with the poorest areas. Of the infants with a birthweight < 2,500 g, 76.8% of them were born in the two poorest areas of the city. The highest fertility rate (35.7 per 1,000 adolescents) was found in Area 1, the area with the worst socioeconomic conditions; the lowest fertility rate (12.1 per 1,000) was found in Area 4, the area with the best socioeconomic conditions. The proportion of births that were premature did not differ among the four areas (P = 0.81).

CONCLUSIONS: The results showed that adolescent girls with little schooling and a lower socioeconomic level were more likely to give birth. Specific actions should be promoted to prevent pregnancy in this group and to foster the social inclusion of these adolescents and their children, providing them with opportunities to improve their socioeconomic situation.}, } @article {pmid16716236, year = {2006}, author = {Nolan, JM and Petrov, V and Bertrand, C and Krisch, HM and Karam, JD}, title = {Genetic diversity among five T4-like bacteriophages.}, journal = {Virology journal}, volume = {3}, number = {}, pages = {30}, pmid = {16716236}, issn = {1743-422X}, mesh = {Aeromonas hydrophila/*virology ; Aeromonas salmonicida/*virology ; Animals ; Bacteriophage T4/*genetics ; Bacteriophages/*classification/genetics ; Base Sequence ; Coliphages/*genetics ; Computational Biology/methods ; *Genetic Variation ; Genome, Viral ; Humans ; Mice ; Molecular Sequence Data ; Open Reading Frames/genetics ; RNA, Transfer/chemistry/genetics ; Sequence Alignment ; Viral Proteins/genetics ; }, abstract = {BACKGROUND: Bacteriophages are an important repository of genetic diversity. As one of the major constituents of terrestrial biomass, they exert profound effects on the earth's ecology and microbial evolution by mediating horizontal gene transfer between bacteria and controlling their growth. Only limited genomic sequence data are currently available for phages but even this reveals an overwhelming diversity in their gene sequences and genomes. The contribution of the T4-like phages to this overall phage diversity is difficult to assess, since only a few examples of complete genome sequence exist for these phages. Our analysis of five T4-like genomes represents half of the known T4-like genomes in GenBank.

RESULTS: Here, we have examined in detail the genetic diversity of the genomes of five relatives of bacteriophage T4: the Escherichia coli phages RB43, RB49 and RB69, the Aeromonas salmonicida phage 44RR2.8t (or 44RR) and the Aeromonas hydrophila phage Aeh1. Our data define a core set of conserved genes common to these genomes as well as hundreds of additional open reading frames (ORFs) that are nonconserved. Although some of these ORFs resemble known genes from bacterial hosts or other phages, most show no significant similarity to any known sequence in the databases. The five genomes analyzed here all have similarities in gene regulation to T4. Sequence motifs resembling T4 early and late consensus promoters were observed in all five genomes. In contrast, only two of these genomes, RB69 and 44RR, showed similarities to T4 middle-mode promoter sequences and to the T4 motA gene product required for their recognition. In addition, we observed that each phage differed in the number and assortment of putative genes encoding host-like metabolic enzymes, tRNA species, and homing endonucleases.

CONCLUSION: Our observations suggest that evolution of the T4-like phages has drawn on a highly diverged pool of genes in the microbial world. The T4-like phages harbour a wealth of genetic material that has not been identified previously. The mechanisms by which these genes may have arisen may differ from those previously proposed for the evolution of other bacteriophage genomes.}, } @article {pmid16715181, year = {2006}, author = {Duell, EJ}, title = {The future of epidemiology: methodological challenges and multilevel inference.}, journal = {Bundesgesundheitsblatt, Gesundheitsforschung, Gesundheitsschutz}, volume = {49}, number = {7}, pages = {622-627}, doi = {10.1007/s00103-006-1293-9}, pmid = {16715181}, issn = {1436-9990}, support = {1 P20 RR018787/RR/NCRR NIH HHS/United States ; CA98889/CA/NCI NIH HHS/United States ; }, mesh = {*Data Interpretation, Statistical ; *Environment ; *Epidemiologic Methods ; Epidemiology/*trends ; *Forecasting ; Genetic Predisposition to Disease/epidemiology ; *Population Dynamics ; Risk Assessment/*methods ; Risk Factors ; }, abstract = {A decade ago there was considerable debate about the appropriate objectives and paradigms of modern epidemiologic research. One concern put forth in these debates was that "risk factor epidemiology" might be forcing our field to focus more on individuals and less on populations and public health. Today, most epidemiologists acknowledge that public health is influenced by both population-level and individual-level determinants. Ecologic studies are valuable tools for generating hypotheses and addressing group-level determinants of disease risk. Traditional risk factor studies and genomic studies have helped establish the multifactorial concept of disease causation. Individual-level studies also have provided the biomedical community with hypotheses that have stimulated research into disease mechanisms that have led to reductions in morbidity and mortality for diseases such as HIV/AIDS, cardiovascular disease, and cancer. Current debates about the role of genomic data in epidemiology and public health mirror the debates about risk factor epidemiology one decade ago. Genomic variation is measured at the individual level, but how this variation is maintained in human populations is a group-level (population) phenomenon that is worthy of epidemiologic investigation in its own right. Multilevel epidemiology seeks to understand multiple levels of inference, from genes to individuals to populations and could combine hypothesis-driven research with aspects of data mining. Multilevel epidemiology calls for the study of health and disease determinants defined at the population level and individual level for a more comprehensive strategy to understanding human disease etiology. With the continued development of multilevel statistical methods and the advent of data mining, the technical constraints of the past will become less relevant to the next generation of epidemiologists who wish to embrace a more multilevel epidemiology.}, } @article {pmid16705972, year = {2006}, author = {Pearman, PB and Penskar, MR and Schools, EH and Enander, HD}, title = {Identifying potential indicators of conservation value using natural heritage occurrence data.}, journal = {Ecological applications : a publication of the Ecological Society of America}, volume = {16}, number = {1}, pages = {186-201}, doi = {10.1890/04-1938}, pmid = {16705972}, issn = {1051-0761}, mesh = {Animals ; Biodiversity ; *Biological Evolution ; *Conservation of Natural Resources ; Databases, Genetic ; *Ecology ; *Environmental Monitoring ; Geography ; Great Lakes Region ; Michigan ; North America ; Population Dynamics ; Species Specificity ; }, abstract = {Conservation planning based on the occurrence of rare species has been criticized as being too limited in scope to conserve biodiversity as a whole. Conversely, planning based on indicator taxa may lack sufficient focus to conserve those species in greatest need of conservation. An alternative approach is to identify a variety of species at risk that are associated with areas of conservation value, which is defined based on species-independent characteristics. We identified potential indicators of conservation value using occurrence data on species at risk and independent information on conservation value that incorporated indices of ecosystem integrity. We propose a taxonomically diverse group of indicator species that are strongly associated with areas of exceptional ecosystem integrity, to serve as a focus for further research and in planning for biodiversity conservation. We identify potential indicator species by defining a null model in which species at risk are equally associated with areas of high ecosystem integrity, then by conducting randomization tests to identify noncompliant species in the state of Michigan, USA. Areas of high ecosystem integrity are selected using criteria to flag (1) secure biotic communities with structural integrity and few exotic species, (2) natural areas subjected to expert review, (3) contiguous relict areas of forest interior, (4) contiguous areas of unmodified wetland, and (5) all these areas combined. We determine the spatial occurrence of species at risk using data from Michigan's statewide Natural Heritage database. The potential indicators include plants, insects, and birds. Their species identity and distribution of occurrences varies with the five scenarios, and together the species broadly cover the entire state. These species at risk, many of which occur throughout the Great Lakes region, may be used to identify additional areas potentially high in conservation value and to monitor their conservation. The ecological criteria and numerical methods we employ may be broadly applicable as Heritage Program databases in North America and parts of Latin America grow to become representative of species distributions.}, } @article {pmid16705961, year = {2006}, author = {Canham, CD and Uriarte, M}, title = {Analysis of neighborhood dynamics of forest ecosystems using likelihood methods and modeling.}, journal = {Ecological applications : a publication of the Ecological Society of America}, volume = {16}, number = {1}, pages = {62-73}, doi = {10.1890/04-0657}, pmid = {16705961}, issn = {1051-0761}, mesh = {Computer Simulation ; Data Interpretation, Statistical ; *Ecosystem ; Environmental Monitoring/*methods ; *Likelihood Functions ; Models, Biological ; Numerical Analysis, Computer-Assisted ; Population Density ; Population Dynamics ; Time Factors ; *Trees ; }, abstract = {Advances in computing power in the past 20 years have led to a proliferation of spatially explicit, individual-based models of population and ecosystem dynamics. In forest ecosystems, the individual-based models encapsulate an emerging theory of "neighborhood" dynamics, in which fine-scale spatial interactions regulate the demography of component tree species. The spatial distribution of component species, in turn, regulates spatial variation in a whole host of community and ecosystem properties, with subsequent feedbacks on component species. The development of these models has been facilitated by development of new methods of analysis of field data, in which critical demographic rates and ecosystem processes are analyzed in terms of the spatial distributions of neighboring trees and physical environmental factors. The analyses are based on likelihood methods and information theory, and they allow a tight linkage between the models and explicit parameterization of the models from field data. Maximum likelihood methods have a long history of use for point and interval estimation in statistics. In contrast, likelihood principles have only more gradually emerged in ecology as the foundation for an alternative to traditional hypothesis testing. The alternative framework stresses the process of identifying and selecting among competing models, or in the simplest case, among competing point estimates of a parameter of a model. There are four general steps involved in a likelihood analysis: (1) model specification, (2) parameter estimation using maximum likelihood methods, (3) model comparison, and (4) model evaluation. Our goal in this paper is to review recent developments in the use of likelihood methods and modeling for the analysis of neighborhood processes in forest ecosystems. We will focus on a single class of processes, seed dispersal and seedling dispersion, because recent papers provide compelling evidence of the potential power of the approach, and illustrate some of the statistical challenges in applying the methods.}, } @article {pmid16705959, year = {2006}, author = {Latimer, AM and Wu, S and Gelfand, AE and Silander, JA}, title = {Building statistical models to analyze species distributions.}, journal = {Ecological applications : a publication of the Ecological Society of America}, volume = {16}, number = {1}, pages = {33-50}, doi = {10.1890/04-0609}, pmid = {16705959}, issn = {1051-0761}, mesh = {Bayes Theorem ; Computational Biology/*methods ; Computer Simulation ; Data Interpretation, Statistical ; Ecology/*methods/statistics & numerical data ; *Ecosystem ; Empirical Research ; *Environmental Monitoring ; Genetics, Population ; Humans ; *Models, Statistical ; Population Dynamics ; Probability ; Proteaceae/genetics/physiology ; Regression Analysis ; South Africa ; }, abstract = {Models of the geographic distributions of species have wide application in ecology. But the nonspatial, single-level, regression models that ecologists have often employed do not deal with problems of irregular sampling intensity or spatial dependence, and do not adequately quantify uncertainty. We show here how to build statistical models that can handle these features of spatial prediction and provide richer, more powerful inference about species niche relations, distributions, and the effects of human disturbance. We begin with a familiar generalized linear model and build in additional features, including spatial random effects and hierarchical levels. Since these models are fully specified statistical models, we show that it is possible to add complexity without sacrificing interpretability. This step-by-step approach, together with attached code that implements a simple, spatially explicit, regression model, is structured to facilitate self-teaching. All models are developed in a Bayesian framework. We assess the performance of the models by using them to predict the distributions of two plant species (Proteaceae) from South Africa's Cape Floristic Region. We demonstrate that making distribution models spatially explicit can be essential for accurately characterizing the environmental response of species, predicting their probability of occurrence, and assessing uncertainty in the model results. Adding hierarchical levels to the models has further advantages in allowing human transformation of the landscape to be taken into account, as well as additional features of the sampling process.}, } @article {pmid16705958, year = {2006}, author = {Ives, AR and Zhu, J}, title = {Statistics for correlated data: phylogenies, space, and time.}, journal = {Ecological applications : a publication of the Ecological Society of America}, volume = {16}, number = {1}, pages = {20-32}, doi = {10.1890/04-0702}, pmid = {16705958}, issn = {1051-0761}, mesh = {Animals ; Computer Simulation ; Data Interpretation, Statistical ; *Ecosystem ; Models, Statistical ; *Phylogeny ; Population Dynamics ; *Research Design ; Time ; }, abstract = {Here we give an introduction to the growing number of statistical techniques for analyzing data that are not independent realizations of the same sampling process--in other words, correlated data. We focus on regression problems, in which the value of a given variable depends linearly on the value of another variable. To illustrate different types of processes leading to correlated data, we analyze four simulated examples representing diverse problems arising in ecological studies. The first example is a comparison among species to determine the relationship between home-range area and body size; because species are phylogenetically related, they do not represent independent samples. The second example addresses spatial variation in net primary production and how this might be affected by soil nitrogen; because nearby locations are likely to have similar net primary productivity for reasons other than soil nitrogen, spatial correlation is likely. In the third example, we consider a time-series model to ask whether the decrease in density of a butterfly species is the result of decreases in its host-plant density; because the population density of a species in one generation is likely to affect the density in the following generation, time-series data are often correlated. The fourth example combines both spatial and temporal correlation in an experiment in which prey densities are manipulated to determine the response of predators to their food supply. For each of these examples, we use a different statistical approach for analyzing models of correlated data. Our goal is to give an overview of conceptual issues surrounding correlated data, rather than a detailed tutorial in how to apply different statistical techniques. By dispelling some of the mystery behind correlated data, we hope to encourage ecologists to learn about statistics that could be useful in their own work. Although at first encounter these techniques might seem complicated, they have the power to simplify ecological research by making more types of data and experimental designs open to statistical evaluation.}, } @article {pmid16705957, year = {2006}, author = {Hobbs, NT and Hilborn, R}, title = {Alternatives to statistical hypothesis testing in ecology: a guide to self teaching.}, journal = {Ecological applications : a publication of the Ecological Society of America}, volume = {16}, number = {1}, pages = {5-19}, doi = {10.1890/04-0645}, pmid = {16705957}, issn = {1051-0761}, mesh = {Algorithms ; Bayes Theorem ; Computational Biology/*methods ; Computer Simulation ; Data Interpretation, Statistical ; Ecology/*methods/*statistics & numerical data ; *Ecosystem ; *Likelihood Functions ; Meta-Analysis as Topic ; Models, Biological ; Research Design ; }, abstract = {Statistical methods emphasizing formal hypothesis testing have dominated the analyses used by ecologists to gain insight from data. Here, we review alternatives to hypothesis testing including techniques for parameter estimation and model selection using likelihood and Bayesian techniques. These methods emphasize evaluation of weight of evidence for multiple hypotheses, multimodel inference, and use of prior information in analysis. We provide a tutorial for maximum likelihood estimation of model parameters and model selection using information theoretics, including a brief treatment of procedures for model comparison, model averaging, and use of data from multiple sources. We discuss the advantages of likelihood estimation, Bayesian analysis, and meta-analysis as ways to accumulate understanding across multiple studies. These statistical methods hold promise for new insight in ecology by encouraging thoughtful model building as part of inquiry, providing a unified framework for the empirical analysis of theoretical models, and by facilitating the formal accumulation of evidence bearing on fundamental questions.}, } @article {pmid16705956, year = {2006}, author = {Hobbs, NT and Twombly, S and Schimel, DS}, title = {Deepening ecological insights using contemporary statistics.}, journal = {Ecological applications : a publication of the Ecological Society of America}, volume = {16}, number = {1}, pages = {3-4}, doi = {10.1890/05-0791}, pmid = {16705956}, issn = {1051-0761}, mesh = {Animals ; Data Interpretation, Statistical ; Ecology/*methods/*statistics & numerical data ; *Ecosystem ; Geography ; Humans ; Population Density ; Problem Solving ; Statistics as Topic/*methods ; }, } @article {pmid16705823, year = {2005}, author = {Twumasii, YA and Merem, EC}, title = {GIS applications in land management: the loss of high quality land to development in Central Mississippi from 1987-2002.}, journal = {International journal of environmental research and public health}, volume = {2}, number = {2}, pages = {234-244}, doi = {10.3390/ijerph2005020006}, pmid = {16705823}, issn = {1661-7827}, mesh = {*Agriculture ; *Conservation of Natural Resources ; Decision Making ; Geographic Information Systems ; Mississippi ; *Urbanization ; }, abstract = {The socio-economic trends and history of Central Mississippi reveal a major rural influence based upon a dependence on agricultural activities as part of the economic engine driving the state's economy. Yet, in the last several years, the amount of agricultural land in the counties continues to decline. Similar changes in other variables associated with agricultural land use and the continuity of farming in the state have also been changing. Indeed, under the pressure of urban growth, some farmers are forced to use less productive soils or have abandoned the agricultural business. Considering the gravity of the problem and the implications for sustainable development, public concern has increased in the state of Mississippi that urbanization and other factors may be eroding potential farmland. Given the effects of the current trends on the future capacity to produce food items, there are concerns that the growing incidence of farmland loss may also erode the basis for sustainable use of agricultural land, biodiversity and protection of the state's ecological treasures. Notwithstanding the gravity of these trends, no major effort in the literature has aimed at documenting the incidence of agricultural land loss and the linkages to urbanization in the region of Central Mississippi. What changes have taken place in the size of agricultural land within the counties and what factors are responsible for it? This paper examines the issue of farmland loss in Central Mississippi with a focus at the county level between 1987 and 2002 from a temporal-spatial perspective. In terms of methodology, the paper uses a mixed scale approach based upon the existing literature. Data were drawn from the United States Census databases of Population and Agriculture. This information is analyzed with basic descriptive statistics and GIS with particular attention to the spatial trends at the county level. Results indicate that the counties under consideration have experienced considerable change in the amount of agricultural land and other variables associated with the use of farmland, due to urbanization. With the types of changes occurring, instituting effective policies anchored in sustainability, community participation, and growth management will go a long way in addressing the situation. Other strategies for farmland protection based upon land information inventory and mapping in the region, are also recommended. The paper stands as an update of the existing literature and offers a valuable tool for decision makers within the domain of natural resources management.}, } @article {pmid16704737, year = {2006}, author = {Tachiiri, K and Klinkenberg, B and Mak, S and Kazmi, J}, title = {Predicting outbreaks: a spatial risk assessment of West Nile virus in British Columbia.}, journal = {International journal of health geographics}, volume = {5}, number = {}, pages = {21}, pmid = {16704737}, issn = {1476-072X}, mesh = {Animals ; Birds/virology ; British Columbia/epidemiology ; *Culicidae/virology ; Forecasting/*methods ; Geographic Information Systems ; Humans ; Models, Theoretical ; Population Density ; Population Dynamics ; Risk ; Temperature ; West Nile Fever/epidemiology/virology ; *West Nile virus ; }, abstract = {BACKGROUND: West Nile virus (WNv) has recently emerged as a health threat to the North American population. After the initial disease outbreak in New York City in 1999, WNv has spread widely and quickly across North America to every contiguous American state and Canadian province, with the exceptions of British Columbia (BC), Prince Edward Island and Newfoundland. In this study we develop models of mosquito population dynamics for Culex tarsalis and C. pipiens, and create a spatial risk assessment of WNv prior to its arrival in BC by creating a raster-based mosquito abundance model using basic geographic and temperature data. Among the parameters included in the model are spatial factors determined from the locations of BC Centre for Disease Control mosquito traps (e.g., distance of the trap from the closest wetland or lake), while other parameters were obtained from the literature. Factors not considered in the current assessment but which could influence the results are also discussed.

RESULTS: Since the model performs much better for C. tarsalis than for C. pipiens, the risk assessment is carried out using the output of C. tarsalis model. The result of the spatially-explicit mosquito abundance model indicates that the Okanagan Valley, the Thompson Region, Greater Vancouver, the Fraser Valley and southeastern Vancouver Island have the highest potential abundance of the mosquitoes. After including human population data, Greater Vancouver, due to its high population density, increases in significance relative to the other areas.

CONCLUSION: Creating a raster-based mosquito abundance map enabled us to quantitatively evaluate WNv risk throughout BC and to identify the areas of greatest potential risk, prior to WNv introduction. In producing the map important gaps in our knowledge related to mosquito ecology in BC were identified, as well, it became evident that increased efforts in bird and mosquito surveillance are required if more accurate models and maps are to be produced. Access to real time climatic data is the key for developing a real time early warning system for forecasting vector borne disease outbreaks, while including social factors is important when producing a detailed assessment in urban areas.}, } @article {pmid16701313, year = {2004}, author = {Graham, CH and Ferrier, S and Huettman, F and Moritz, C and Peterson, AT}, title = {New developments in museum-based informatics and applications in biodiversity analysis.}, journal = {Trends in ecology & evolution}, volume = {19}, number = {9}, pages = {497-503}, doi = {10.1016/j.tree.2004.07.006}, pmid = {16701313}, issn = {0169-5347}, abstract = {Information from natural history collections (NHCs) about the diversity, taxonomy and historical distributions of species worldwide is becoming increasingly available over the Internet. In light of this relatively new and rapidly increasing resource, we critically review its utility and limitations for addressing a diverse array of applications. When integrated with spatial environmental data, NHC data can be used to study a broad range of topics, from aspects of ecological and evolutionary theory, to applications in conservation, agriculture and human health. There are challenges inherent to using NHC data, such as taxonomic inaccuracies and biases in the spatial coverage of data, which require consideration. Promising research frontiers include the integration of NHC data with information from comparative genomics and phylogenetics, and stronger connections between the environmental analysis of NHC data and experimental and field-based tests of hypotheses.}, } @article {pmid16697489, year = {2006}, author = {Popelier, PL and Smith, PJ}, title = {QSAR models based on quantum topological molecular similarity.}, journal = {European journal of medicinal chemistry}, volume = {41}, number = {7}, pages = {862-873}, doi = {10.1016/j.ejmech.2006.03.004}, pmid = {16697489}, issn = {0223-5234}, mesh = {Alcohol Dehydrogenase/antagonists & inhibitors/metabolism ; Amides/chemistry/pharmacology ; Animals ; Benzimidazoles/chemistry/pharmacology ; Carbonic Anhydrases/metabolism ; Cattle ; Chlorophenols/chemistry/toxicity ; Computational Biology ; Enzyme Inhibitors/chemistry/pharmacology ; Imidazoles/chemistry/pharmacology ; Imidazolidines/chemistry/pharmacology ; Indoles/chemistry/pharmacology ; *Models, Chemical ; Molecular Structure ; Orthomyxoviridae/drug effects ; Quantitative Structure-Activity Relationship ; }, abstract = {A new method called quantum topological molecular similarity (QTMS) was fairly recently proposed [J. Chem. Inf. Comp. Sc., 41, 2001, 764] to construct a variety of medicinal, ecological and physical organic QSAR/QSPRs. QTMS method uses quantum chemical topology (QCT) to define electronic descriptors drawn from modern ab initio wave functions of geometry-optimised molecules. It was shown that the current abundance of computing power can be utilised to inject realistic descriptors into QSAR/QSPRs. In this article we study seven datasets of medicinal interest : the dissociation constants (pK(a)) for a set of substituted imidazolines , the pK(a) of imidazoles , the ability of a set of indole derivatives to displace [(3)H] flunitrazepam from binding to bovine cortical membranes , the influenza inhibition constants for a set of benzimidazoles , the interaction constants for a set of amides and the enzyme liver alcohol dehydrogenase , the natriuretic activity of sulphonamide carbonic anhydrase inhibitors and the toxicity of a series of benzyl alcohols. A partial least square analysis in conjunction with a genetic algorithm delivered excellent models. They are also able to highlight the active site, of the ligand or the molecule whose structure determines the activity. The advantages and limitations of QTMS are discussed.}, } @article {pmid16691531, year = {2006}, author = {Hayes, JP and Shonkwiler, JS}, title = {Allometry, antilog transformations, and the perils of prediction on the original scale.}, journal = {Physiological and biochemical zoology : PBZ}, volume = {79}, number = {3}, pages = {665-674}, doi = {10.1086/502814}, pmid = {16691531}, issn = {1522-2152}, mesh = {Animals ; *Bias ; *Data Interpretation, Statistical ; Statistics as Topic/*methods/standards ; }, abstract = {Biologists often use allometric equations that take the form of power functions (e.g., Y = aM(b), where M stands for mass and a and b are empirically fitted constants). Typically, these allometric equations are fitted by taking the antilog of log-log regressions. Predictions from these allometric equations are biased, and the bias my be appreciable. Methods for making predictions that correct for the bias are available, but they have rarely, if ever, been used by ecological and evolutionary physiologists. Just as physiologists would not use an instrument that was not properly calibrated, they should not use allometric equations to make predictions unless they account for the bias of those predictions. We analyzed 20 interspecific and 10 intraspecific data sets. We compared predictions from standard allometric equations with those from several alternative methods. Our analyses suggest that the bias of predictions from interspecific data sets may be substantial. For the intraspecific data sets we analyzed, the bias was likely to be small. Biologists, including ecological and evolutionary physiologists, should exercise care when using allometric equations to make predictions, particularly given that methods to adjust for bias are easily implemented.}, } @article {pmid16690862, year = {2006}, author = {Madin, JS and Alroy, J and Aberhan, M and Fürsich, FT and Kiessling, W and Kosnik, MA and Wagner, PJ}, title = {Statistical independence of escalatory ecological trends in Phanerozoic marine invertebrates.}, journal = {Science (New York, N.Y.)}, volume = {312}, number = {5775}, pages = {897-900}, doi = {10.1126/science.1123591}, pmid = {16690862}, issn = {1095-9203}, mesh = {Animals ; Biodiversity ; *Biological Evolution ; Calcium Carbonate/analysis ; Databases, Factual ; *Ecosystem ; *Fossils ; *Invertebrates/classification/physiology ; Locomotion ; Predatory Behavior ; *Seawater ; Statistics as Topic ; }, abstract = {Ecological interactions, such as predation and bioturbation, are thought to be fundamental determinants of macroevolutionary trends. A data set containing global occurrences of Phanerozoic fossils of benthic marine invertebrates shows escalatory trends in the relative frequency of ecological groups, such as carnivores and noncarnivorous infaunal or mobile organisms. Associations between these trends are either statistically insignificant or interpretable as preservational effects. Thus, there is no evidence that escalation drives macroecological trends at global and million-year time scales. We also find that taxonomic richness and occurrence data are cross-correlated, which justifies the traditional use of one as a proxy of the other.}, } @article {pmid16689242, year = {2006}, author = {Jiang, Y and Li, Q and Zhang, X and Liang, W}, title = {[Kriging prediction of soil zinc in contaminated field by using an auxiliary variable].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {17}, number = {1}, pages = {97-101}, pmid = {16689242}, issn = {1001-9332}, mesh = {*Data Interpretation, Statistical ; Environmental Monitoring/methods ; Metals, Heavy/*analysis ; Regression Analysis ; Soil/*analysis ; Soil Pollutants/*analysis ; Zinc/*analysis ; }, abstract = {In this study, two kriging methods using an auxiliary variable, i. e., ordinary cokriging (OCK) and ordinary kriging combined with regression (OKR) were used for the interpolation of soil zinc (0.1 mol x L(-1) HCl extractable Zn) in a 17.6 hm2 field at the vicinity of a metal manufacturer in southern suburb of Shenyang, China. A total of 36 measured data of soil Zn content at the depth of 10 approximately 20 cm (subsoil Zn) was selected as target variable, 72 measured data at the depth of 0 approximately 10 cm (topsoil Zn) as auxiliary variable, while other 36 measured data of subsoil for validation. The two interpolation methods were evaluated for the suitability of estimating the spatial distribution of soil Zn by using an auxiliary variable. The results showed that OKR gave better results than OCK or ordinary kriging (OK). The theoretical model obtained from OKR exhibited higher coefficient of determination and lower residual sums of squares than that from OCK or OK. The prediction accuracy of soil Zn was increased by 4% with OKR than with OK. The map of soil Zn obtained with OKR was quite similar with that obtained with OK, by using 72 measured Zn data. However, no advantages were found between OCK and OK. It was suggested that OKR was an effective way to estimate the distribution of soil heavy metals by using auxiliary variables.}, } @article {pmid16684354, year = {2006}, author = {Jacob, BG and Shililu, J and Muturi, EJ and Mwangangi, JM and Muriu, SM and Funes, J and Githure, J and Regens, JL and Novak, RJ}, title = {Spatially targeting Culex quinquefasciatus aquatic habitats on modified land cover for implementing an Integrated Vector Management (IVM) program in three villages within the Mwea Rice Scheme, Kenya.}, journal = {International journal of health geographics}, volume = {5}, number = {}, pages = {18}, pmid = {16684354}, issn = {1476-072X}, support = {U01 A154889//PHS HHS/United States ; }, mesh = {Animals ; Crops, Agricultural/growth & development ; *Culex/virology ; *Ecosystem ; *Geographic Information Systems ; Humans ; Kenya ; Mosquito Control/*methods ; Oryza/growth & development ; Population Density ; *Seasons ; Topography, Medical/methods ; }, abstract = {BACKGROUND: Continuous land cover modification is an important part of spatial epidemiology because it can help identify environmental factors and Culex mosquitoes associated with arbovirus transmission and thus guide control intervention. The aim of this study was to determine whether remotely sensed data could be used to identify rice-related Culex quinquefasciatus breeding habitats in three rice-villages within the Mwea Rice Scheme, Kenya. We examined whether a land use land cover (LULC) classification based on two scenes, IKONOS at 4 m and Landsat Thematic Mapper at 30 m could be used to map different land uses and rice planted at different times (cohorts), and to infer which LULC change were correlated to high density Cx. quinquefasciatus aquatic habitats. We performed a maximum likelihood unsupervised classification in Erdas Imagine V8.7 and generated three land cover classifications, rice field, fallow and built environment. Differentially corrected global positioning systems (DGPS) ground coordinates of Cx. quinquefasciatus aquatic habitats were overlaid onto the LULC maps generated in ArcInfo 9.1. Grid cells were stratified by levels of irrigation (well-irrigated and poorly-irrigated) and varied according to size of the paddy.

RESULTS: Total LULC change between 1988-2005 was 42.1 % in Kangichiri, 52.8 % in Kiuria and and 50.6 % Rurumi. The most frequent LULC changes was rice field to fallow and fallow to rice field. The proportion of aquatic habitats positive for Culex larvae in LULC change sites was 77.5% in Kangichiri, 72.9% in Kiuria and 73.7% in Rurumi. Poorly - irrigated grid cells displayed 63.3% of aquatic habitats among all LULC change sites.

CONCLUSION: We demonstrate that optical remote sensing can identify rice cultivation LULC sites associated with high Culex oviposition. We argue that the regions of higher Culex abundance based on oviposition surveillance sites reflect underlying differences in abundance of larval habitats which is where limited control resources could be concentrated to reduce vector larval abundance.}, } @article {pmid16684244, year = {2006}, author = {Carrer, M and Urbinati, C}, title = {Long-term change in the sensitivity of tree-ring growth to climate forcing in Larix decidua.}, journal = {The New phytologist}, volume = {170}, number = {4}, pages = {861-871}, doi = {10.1111/j.1469-8137.2006.01703.x}, pmid = {16684244}, issn = {0028-646X}, mesh = {Carbon/metabolism ; Chronology as Topic ; *Climate ; Data Interpretation, Statistical ; Geography ; Larix/anatomy & histology/*growth & development ; Temperature ; Time Factors ; Trees/growth & development ; }, abstract = {Tree rings are widely used long-term proxy data which, if combined with long-term instrumental climate records, can provide excellent information on global climate variability. This research aimed to determine whether interannual climate-growth responses in Alpine treeline forests are stationary over time. We used tree-ring width chronologies of Larix decidua (European larch) from 17 sites and monthly temperatures and precipitation data for the period 1800-1999. Climate-growth relationships were assessed with correlation and response functions, and their stationarity and consistency over time were measured using moving correlation. Tree-ring chronologies showed similar interannual variations over the last two centuries, suggesting that the same climatic factors synchronously limited growth at most sites. The most sensitive variables showed significant transient responses varying within the time period, indicating a possible deviation from the uniformitarian principle applied to dendroclimatology. If these findings are confirmed in future studies on other species and in other regions, we suggest that time-dependent variables should be taken into account to avoid overestimation of treeline advance, future forest carbon storage in temperature-limited environments and inaccurate reconstruction of past climate variability.}, } @article {pmid16684243, year = {2006}, author = {Potts, DL and Huxman, TE and Cable, JM and English, NB and Ignace, DD and Eilts, JA and Mason, MJ and Weltzin, JF and Williams, DG}, title = {Antecedent moisture and seasonal precipitation influence the response of canopy-scale carbon and water exchange to rainfall pulses in a semi-arid grassland.}, journal = {The New phytologist}, volume = {170}, number = {4}, pages = {849-860}, doi = {10.1111/j.1469-8137.2006.01732.x}, pmid = {16684243}, issn = {0028-646X}, mesh = {Arizona ; Carbon/*metabolism ; Carbon Dioxide/metabolism ; Climate ; Data Interpretation, Statistical ; *Ecosystem ; Eragrostis/metabolism ; Plant Transpiration/physiology ; Poaceae/*metabolism ; *Rain ; *Seasons ; Water/*metabolism ; }, abstract = {The influences of prior monsoon-season drought (PMSD) and the seasonal timing of episodic rainfall ('pulses') on carbon and water exchange in water-limited ecosystems are poorly quantified. *In the present study, we estimated net ecosystem exchange of CO(2) (NEE) and evapotranspiration (ET) before, and for 15 d following, experimental irrigation in a semi-arid grassland during June and August 2003. Rainout shelters near Tucson, Arizona, USA, were positioned on contrasting soils (clay and sand) and planted with native (Heteropogon contortus) or non-native invasive (Eragrostis lehmanniana) C4 bunchgrasses. Plots received increased ('wet') or decreased ('dry') monsoon-season (July-September) rainfall during 2002 and 2003. Following a June 2003 39-mm pulse, species treatments had similar NEE and ET dynamics including 15-d integrated NEE (NEE(pulse)). Contrary to predictions, PMSD increased net C uptake during June in plots of both species. Greater flux rates after an August 2003 39-mm pulse reflected biotic activity associated with the North American Monsoon. Furthermore, August NEE(pulse) and ecosystem pulse-use efficiency (PUE(e) = NEE(pulse)/ET(pulse)) was greatest in Heteropogon plots. PMSD and rainfall seasonal timing may interact with bunchgrass invasions to alter NEE and ET dynamics with consequences for PUE(e) in water-limited ecosystems.}, } @article {pmid16684242, year = {2006}, author = {He, JS and Wang, Z and Wang, X and Schmid, B and Zuo, W and Zhou, M and Zheng, C and Wang, M and Fang, J}, title = {A test of the generality of leaf trait relationships on the Tibetan Plateau.}, journal = {The New phytologist}, volume = {170}, number = {4}, pages = {835-848}, doi = {10.1111/j.1469-8137.2006.01704.x}, pmid = {16684242}, issn = {0028-646X}, mesh = {Climate ; Data Interpretation, Statistical ; Environment ; Geography ; Nitrogen/metabolism ; Photosynthesis/physiology ; Plant Leaves/anatomy & histology/*metabolism ; Rain ; Species Specificity ; Tibet ; }, abstract = {Leaf mass per area (LMA), nitrogen concentration (on mass and area bases, N(mass) and N(area), respectively), photosynthetic capacity (A(mass) and A(area)) and photosynthetic nitrogen use efficiency (PNUE) are key foliar traits, but few data are available from cold, high-altitude environments. Here, we systematically measured these leaf traits in 74 species at 49 research sites on the Tibetan Plateau to examine how these traits, measured near the extremes of plant tolerance, compare with global patterns. Overall, Tibetan species had higher leaf nitrogen concentrations and photosynthetic capacities compared with a global dataset, but they had a slightly lower A(mass) at a given N(mass). These leaf trait relationships were consistent with those reported from the global dataset, with slopes of the standardized major axes A(mass)-LMA, N(mass)-LMA and A(mass)-N(mass) identical to those from the global dataset. Climate only weakly modulated leaf traits. Our data indicate that covarying sets of leaf traits are consistent across environments and biogeographic regions. Our results demonstrate functional convergence of leaf trait relationships in an extreme environment.}, } @article {pmid16684240, year = {2006}, author = {Preston, KA and Cornwell, WK and Denoyer, JL}, title = {Wood density and vessel traits as distinct correlates of ecological strategy in 51 California coast range angiosperms.}, journal = {The New phytologist}, volume = {170}, number = {4}, pages = {807-818}, doi = {10.1111/j.1469-8137.2006.01712.x}, pmid = {16684240}, issn = {0028-646X}, mesh = {Biological Evolution ; California ; Data Interpretation, Statistical ; Ecology ; Magnoliopsida/*anatomy & histology/growth & development ; Phylogeny ; Soil ; Water/metabolism ; }, abstract = {Wood density and vessel characteristics are functionally interrelated, yet they may have distinct ecological associations. In a comparative study of 51 angiosperm species ranging from chaparral shrubs to riparian trees, we examined relationships among wood density and vessel traits and their ecological correlates. Mean vessel lumen area and vessel density (number mm(-2)) varied widely (7- to 10-fold). In multivariate analyses, both vessel traits were negatively correlated with wood density, which varied more narrowly (< 2-fold). Vessel density and lumen area were inversely related across species, allowing a broad range of vessel traits within a narrow range of wood density. Phylogenetic independent contrasts indicated correlated inverse evolutionary change in vessel traits. Each trait had a distinct pattern of ecological correlation -- wood density was most strongly associated with soil water, and vessel traits showed contrasting relationships with plant height. Within a narrow range of wood density, there was significant variation in vessel traits. Given their particular ecological associations, the results suggest that wood density and vessel traits describe two distinct ecological axes.}, } @article {pmid16680541, year = {2006}, author = {Fleury, J and Lee, SM}, title = {The social ecological model and physical activity in African American women.}, journal = {American journal of community psychology}, volume = {37}, number = {1-2}, pages = {129-140}, doi = {10.1007/s10464-005-9002-7}, pmid = {16680541}, issn = {0091-0562}, mesh = {*Black or African American ; *Community Networks ; *Exercise ; Female ; Humans ; *Models, Theoretical ; United States ; }, abstract = {Little is known about the social and contextual correlates (e.g., social norms, environment, social networks, and organizational support) influencing the adoption and maintenance of regular physical activity among minority and underserved populations. The purpose of this review was to apply the social ecological model to better understand physical activity among African American women. A review of the literature pertaining to correlates of physical activity among African American women was conducted and applied to a social ecological perspective. Understanding and addressing social and contextual correlates of physical activity behavior among African American women are necessary to establish comprehensive programs, particularly within community settings. The social ecological model provides a strong theoretical basis to guide physical activity intervention in this population.}, } @article {pmid16676712, year = {2006}, author = {Dessaigne, M}, title = {[Health practitioners' evaluation system on risks of contracting cancer due to environmental].}, journal = {Sante publique (Vandoeuvre-les-Nancy, France)}, volume = {18}, number = {1}, pages = {41-53}, doi = {10.3917/spub.061.0041}, pmid = {16676712}, issn = {0995-3914}, mesh = {*Attitude of Health Personnel ; Data Collection ; *Environment ; Humans ; Information Systems ; Neoplasms/*epidemiology ; Risk Factors ; Surveys and Questionnaires ; }, abstract = {The increase in the number of cancers sprouting from man-made environmental risk factors calls for prevention policies strictly centered on the basis of a fact-sharing and transparent, evidence-based knowledge exchange. However, the related areas which are concerned are quite diverse, and given that the risks are of a cumulative nature, they are very difficult to measure. The information system therefore is complex and infinite. A qualitative study was carried out on the representations held by a variety of specialists who have potential links to the public or groups who might be exposed or at risk, including health professionals, engineers, and NGO and association managers and supervisors. The investigation was based upon a questionnaire which was developed with the assistance and participation of those involved in the management of information regarding professional, ecological or other kinds of risks. This method allowed for the study to favour and objectively prioritise the vision of the health professionals who were interviewed. The results show that the depictions vary depending on how and to what extent the different categories of professionals are involved, and that they reflect for the most part society's fears.}, } @article {pmid16675603, year = {2006}, author = {Chung, JM and Lee, BC and Kim, JS and Park, CW and Chung, MY and Chung, MG}, title = {Fine-scale genetic structure among genetic individuals of the clone-forming monotypic genus Echinosophora koreensis (Fabaceae).}, journal = {Annals of botany}, volume = {98}, number = {1}, pages = {165-173}, pmid = {16675603}, issn = {0305-7364}, mesh = {Conservation of Natural Resources ; Data Interpretation, Statistical ; Fabaceae/*genetics/physiology ; Genetic Markers ; *Genetic Variation ; Genotype ; Korea ; Repetitive Sequences, Nucleic Acid ; Reproduction, Asexual ; }, abstract = {BACKGROUND AND AIMS: For rare endemics or endangered plant species that reproduce both sexually and vegetatively it is critical to understand the extent of clonality because assessment of clonal extent and distribution has important ecological and evolutionary consequences with conservation implications. A survey was undertaken to understand clonal effects on fine-scale genetic structure (FSGS) in two populations (one from a disturbed and the other from an undisturbed locality) of Echinosophora koreensis, an endangered small shrub belonging to a monotypic genus in central Korea that reproduces both sexually and vegetatively via rhizomes.

METHODS: Using inter-simple sequence repeats (ISSRs) as genetic markers, the spatial distribution of individuals was evaluated using Ripley's L(d)-statistics and quantified the spatial scale of clonal spread and spatial distribution of ISSR genotypes using spatial autocorrelation analysis techniques (join-count statistics and kinship coefficient, F(ij)) for total samples and samples excluding clones.

KEY RESULTS: A high degree of differentiation between populations was observed (phi(ST(g)) = 0.184, P < 0.001). Ripley's L(d)-statistics revealed a near random distribution of individuals in a disturbed population, whereas significant aggregation of individuals was found in an undisturbed site. The join-count statistics revealed that most clones significantly aggregate at < or = 6-m interplant distance. The Sp statistic reflecting patterns of correlograms revealed a strong pattern of FSGS for all four data sets (Sp = 0.072-0.154), but these patterns were not significantly different from each other. At small interplant distances (< or = 2 m), however, jackknifed 95% CIs revealed that the total samples exhibited significantly higher F(ij) values than the same samples excluding clones.

CONCLUSION: The strong FSGS from genets is consistent with two biological and ecological traits of E. koreensis: bee-pollination and limited seed dispersal. Furthermore, potential clone mates over repeated generations would contribute to the observed high F(ij) values among genets at short distance. To ensure long-term ex situ genetic variability of the endangered E. koreensis, individuals located at distances of 10-12 m should be collected across entire populations of E. koreensis.}, } @article {pmid16674576, year = {2006}, author = {Ord, TJ and Stuart-Fox, D}, title = {Ornament evolution in dragon lizards: multiple gains and widespread losses reveal a complex history of evolutionary change.}, journal = {Journal of evolutionary biology}, volume = {19}, number = {3}, pages = {797-808}, doi = {10.1111/j.1420-9101.2005.01050.x}, pmid = {16674576}, issn = {1010-061X}, mesh = {Animals ; *Biological Evolution ; Databases, Factual ; Female ; Lizards/*anatomy & histology/genetics/*physiology ; Male ; Pigmentation ; Selection, Genetic ; Sex Characteristics ; Sexual Behavior, Animal ; Skin Pigmentation/*physiology ; }, abstract = {The expression in females of ornaments thought to be the target of sexual selection in males is a long-standing puzzle. Two main hypotheses are proposed to account for the existence of conspicuous ornaments in both sexes (mutual ornamentation): genetic correlation between the sexes and sexual selection on females as well as males. We examined the pattern of ornament gains and losses in 240 species of dragon lizards (Agamidae) in order to elucidate the relative contribution of these two factors in the evolution of mutual ornamentation. In addition, we tested whether the type of shelter used by lizards to avoid predators predicts the evolutionary loss or constraint of ornament expression. We found evidence that the origin of female ornaments is broadly consistent with the predictions of the genetic correlation hypothesis. Ornaments appear congruently in both sexes with some lineages subsequently evolving male biased sexual dimorphism, apparently through the process of natural selection for reduced ornamentation in females. Nevertheless, ornaments have also frequently evolved in both sexes independently. This suggests that genetic correlations are potentially weak for several lineages and sexual selection on females is responsible for at least some evolutionary change in this group. Unexpectedly, we found that the evolutionary loss of some ornaments is concentrated more in males than females and this trend cannot be fully explained by our measures of natural selection.}, } @article {pmid16649136, year = {2006}, author = {Naito, W and Gamo, Y and Yoshida, K}, title = {Screening-level risk assessment of Di(2-ethylhexyl)phthalate for aquatic organisms using monitoring data in Japan.}, journal = {Environmental monitoring and assessment}, volume = {115}, number = {1-3}, pages = {451-471}, pmid = {16649136}, issn = {0167-6369}, mesh = {Animals ; Databases, Factual ; Environmental Monitoring/*methods ; Eukaryota/*drug effects ; Fishes/*growth & development ; Fresh Water/analysis ; Invertebrates/*drug effects ; No-Observed-Adverse-Effect Level ; Phthalic Acids/analysis/*toxicity ; Risk Assessment ; Seawater/analysis ; Water Pollutants, Chemical/analysis/*toxicity ; }, abstract = {Screening-level ecological risk assessments of di(2-ethylhexyl)phthalate (DEHP) for aquatic organisms in Japan were conducted using estimated statistical values based on surface water and sediment monitoring data and effect threshold values based on a large aquatic toxicity database. An alternative method is proposed to handle monitoring data that contain nondetects including multiple detection limits and to determine the statistical values of DEHP concentrations in Japanese surface waters. The No-Observed-Effect-Concentration (NOEC(water)) of DEHP for aquatic life of 77 micro g/L was determined giving equal importance to both physical effects probably caused by undissolved DEHP and to the intrinsic toxicity potentially caused by DEHP. The NOEC(sediment) of 615,000 micro g/kg was determined by the Equilibrium Partitioning (EqP) theory, conservatively assuming a threshold effect level in the water column as the water solubility of 3 micro g/L. The potential risks of DEHP in Japanese water environments were characterized simply by comparing the margin of exposure (MOE) with a specified uncertainty multiplier (UM). The MOE is expressed as the ratio of NOEC(water) or NOEC(sediment) to the expected environmental concentrations such as the 95th percentiles of the estimated DEHP concentration distributions for surface water or sediment. The results of risk characterization show that all MOE values calculated using the statistical values of DEHP concentrations in Japanese surface waters and sediments are above 10, indicating minimal risk. Although the DEHP concentrations of some surface water samples showed MOE values of less than 10, considering environmental chemistry such as bioavailable fractions and the form of existence of DEHP in a water environment, we conclude that the current levels of DEHP are of little concern to aquatic life in the majority of Japanese surface waters and sediments.}, } @article {pmid16647972, year = {2006}, author = {Brooker, S and Clements, AC and Bundy, DA}, title = {Global epidemiology, ecology and control of soil-transmitted helminth infections.}, journal = {Advances in parasitology}, volume = {62}, number = {}, pages = {221-261}, pmid = {16647972}, issn = {2163-6079}, support = {/WT_/Wellcome Trust/United Kingdom ; 073656/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Africa South of the Sahara ; Animals ; Child ; Ecology ; Environmental Monitoring/methods ; Epidemiological Monitoring ; Geographic Information Systems ; Geography ; Helminthiasis/*epidemiology/*prevention & control ; Helminths/*isolation & purification/physiology ; Humans ; Prevalence ; Soil/*parasitology ; Telemetry/methods ; }, abstract = {Soil-transmitted helminth (STH) infections are among the most prevalent of chronic human infections worldwide. Based on the demonstrable impact on child development, there is a global commitment to finance and implement control strategies with a focus on school-based chemotherapy programmes. The major obstacle to the implementation of cost-effective control is the lack of accurate descriptions of the geographical distribution of infection. In recent years, considerable progress has been made in the use of geographical information systems (GIS) and remote sensing (RS) to better understand helminth ecology and epidemiology, and to develop low-cost ways to identify target populations for treatment. This review explores how this information has been used practically to guide large-scale control programmes. The use of satellite-derived environmental data has yielded new insights into the ecology of infection at a geographical scale that has proven impossible to address using more traditional approaches, and has in turn allowed spatial distributions of infection prevalence to be predicted robustly by statistical approaches. GIS/RS have increasingly been used in the context of large-scale helminth control programmes, including not only STH infections but also those focusing on schistosomiasis, filariasis and onchocerciasis. The experience indicates that GIS/RS provides a cost-effective approach to designing and monitoring programmes at realistic scales. Importantly, the use of this approach has begun to transition from being a specialist approach of international vertical programmes to becoming a routine tool in developing public sector control programmes. GIS/RS is used here to describe the global distribution of STH infections and to estimate the number of infections in school-age children in sub-Saharan Africa (89.9 million) and the annual cost of providing a single anthelmintic treatment using a school-based approach (US$5.0-7.6 million). These are the first estimates at a continental scale to explicitly include the fine spatial distribution of infection prevalence and population, and suggest that traditional methods have overestimated the situation. The results suggest that continent-wide control of parasites is, from a financial perspective, an attainable goal.}, } @article {pmid16641319, year = {2006}, author = {Wu, X and Zhu, L and Guo, J and Zhang, DY and Lin, K}, title = {Prediction of yeast protein-protein interaction network: insights from the Gene Ontology and annotations.}, journal = {Nucleic acids research}, volume = {34}, number = {7}, pages = {2137-2150}, pmid = {16641319}, issn = {1362-4962}, mesh = {Databases, Genetic ; Fungal Proteins/genetics/*metabolism ; Genome, Fungal ; Models, Biological ; Protein Interaction Mapping/*methods/standards ; Vocabulary, Controlled ; }, abstract = {A map of protein-protein interactions provides valuable insight into the cellular function and machinery of a proteome. By measuring the similarity between two Gene Ontology (GO) terms with a relative specificity semantic relation, here, we proposed a new method of reconstructing a yeast protein-protein interaction map that is solely based on the GO annotations. The method was validated using high-quality interaction datasets for its effectiveness. Based on a Z-score analysis, a positive dataset and a negative dataset for protein-protein interactions were derived. Moreover, a gold standard positive (GSP) dataset with the highest level of confidence that covered 78% of the high-quality interaction dataset and a gold standard negative (GSN) dataset with the lowest level of confidence were derived. In addition, we assessed four high-throughput experimental interaction datasets using the positives and the negatives as well as GSPs and GSNs. Our predicted network reconstructed from GSPs consists of 40,753 interactions among 2259 proteins, and forms 16 connected components. We mapped all of the MIPS complexes except for homodimers onto the predicted network. As a result, approximately 35% of complexes were identified interconnected. For seven complexes, we also identified some nonmember proteins that may be functionally related to the complexes concerned. This analysis is expected to provide a new approach for predicting the protein-protein interaction maps from other completely sequenced genomes with high-quality GO-based annotations.}, } @article {pmid16639894, year = {2005}, author = {de Zwart, D}, title = {Ecological effects of pesticide use in The Netherlands: modeled and observed effects in the field ditch.}, journal = {Integrated environmental assessment and management}, volume = {1}, number = {2}, pages = {123-134}, doi = {10.1897/ieam_2004-015.1}, pmid = {16639894}, issn = {1551-3777}, mesh = {Agriculture ; Animals ; *Ecosystem ; *Geographic Information Systems ; Humans ; Netherlands ; Pesticides/*poisoning ; Population Dynamics ; Risk Assessment ; Solanum tuberosum ; }, abstract = {This study addresses the potential risks to the aquatic ecosystem posed by pesticides currently used in The Netherlands. The study used a novel method to predict aquatic exposure to pesticides based on a geographic information system (GIS) map of agricultural land use, comprising 51 crops used in open-canopy areas. Through the application of species-sensitivity distributions for aquatic organisms, in combination with rules for mixture-toxicity calculation, the modeled exposure results were transformed to risk estimates for aquatic species. The majority of the predicted risks were caused by pesticides applied to potato cropland, and approximately 95% of the predicted risk was caused by only 7 of the 261 pesticides currently used in The Netherlands. For risk verification, local toxic-risk estimates were compared with observed species composition in field ditches. The field verification study was not able to draw firm conclusions regarding the predicted impact of pesticide use on overall biodiversity. A toxicity-related shift from sensitive to more tolerant or opportunistic species could be observed for a few species.}, } @article {pmid16638000, year = {2006}, author = {Thompson, R and Townsend, C}, title = {A truce with neutral theory: local deterministic factors, species traits and dispersal limitation together determine patterns of diversity in stream invertebrates.}, journal = {The Journal of animal ecology}, volume = {75}, number = {2}, pages = {476-484}, doi = {10.1111/j.1365-2656.2006.01068.x}, pmid = {16638000}, issn = {0021-8790}, mesh = {Animals ; *Biodiversity ; Data Interpretation, Statistical ; *Ecosystem ; Environment ; Invertebrates/*physiology ; *Models, Biological ; Population Density ; Population Dynamics ; *Rivers ; Species Specificity ; }, abstract = {1. Studies seeking to explain local patterns of diversity have typically relied on niche explanations, reflected in correlations with local environmental conditions, or neutral theory, invoking dispersal processes and speciation. 2. We used macroinvertebrate community data from 10 streams that varied independently in local ecological conditions and spatial proximity. Neutral theory predicts that similarity in communities will be negatively associated with distance between sites, while niche theory suggests that community similarity will be positively associated with similarity in local ecological conditions. 3. Similarity in total invertebrate, grazer and predator assemblages showed negative relationships with distance and, for grazers and predators, positive relationships with local ecological conditions. However, the best model predicting community similarity in all three cases included aspects of both local ecological conditions and distance between sites. 4. When assemblages were analysed according to dispersal ability, high-dispersal species were shown to be freely accessing all sites and community similarity was not well predicted by either local ecology or spatial separation. Assemblages of species with low and moderate dispersal ability were best predicted by combined models, including distance between sites and local ecological factors. 5. The results suggest that the perceived dichotomy between neutral and local environmental processes in determining local patterns of diversity may not be useful. Neutral and niche processes structured these communities differentially depending on trophic level and species traits. 6. We emphasize the potential for both dispersal processes and local environmental conditions to explain local patterns of diversity.}, } @article {pmid16631936, year = {2006}, author = {Pampanin, DM and Viarengo, A and Garrigues, P and Andersen, OK}, title = {Background for the BEEP Stavanger workshops: Biological effects on marine organisms in two common, large, laboratory experiments and in a field study. Comparison of the value (sensitivity, specificity, etc.) of core and new biomarkers.}, journal = {Aquatic toxicology (Amsterdam, Netherlands)}, volume = {78 Suppl 1}, number = {}, pages = {S1-4}, doi = {10.1016/j.aquatox.2006.02.011}, pmid = {16631936}, issn = {0166-445X}, mesh = {Animals ; *Biomarkers/analysis ; *Environmental Monitoring ; Environmental Pollution/*analysis ; European Union ; Government Programs/economics/*organization & administration/standards ; Information Systems ; Marine Biology/*methods ; Oceans and Seas ; Sensitivity and Specificity ; }, } @article {pmid16629812, year = {2006}, author = {Basset, P and Yannic, G and Hausser, J}, title = {Genetic and karyotypic structure in the shrews of the Sorex araneus group: are they independent?.}, journal = {Molecular ecology}, volume = {15}, number = {6}, pages = {1577-1587}, doi = {10.1111/j.1365-294X.2006.02891.x}, pmid = {16629812}, issn = {0962-1083}, mesh = {Animals ; Biodiversity ; Data Interpretation, Statistical ; Genetic Markers ; *Genetic Variation ; Genotype ; Geography ; Karyotyping ; Microsatellite Repeats ; Shrews/*genetics ; }, abstract = {The species of the common shrew (Sorex araneus) group are morphologically very similar but exhibit high levels of karyotypic variation. Here we used genetic variation at 10 microsatellite markers in a data set of 212 individuals mostly sampled in the western Alps and composed of five karyotypic taxa (Sorex coronatus, Sorex antinorii and the S. araneus chromosome races Cordon, Bretolet and Vaud) to investigate the concordance between genetic and karyotypic structure. Bayesian analysis confirmed the taxonomic status of the three sampled species since individuals consistently grouped according to their taxonomical status. However, introgression can still be detected between S. antinorii and the race Cordon of S. araneus. This observation is consistent with the expected low karyotypic complexity of hybrids between these two taxa. Geographically based cryptic substructure was discovered within S. antinorii, a pattern consistent with the different postglaciation recolonization routes of this species. Additionally, we detected two genetic groups within S. araneus notwithstanding the presence of three chromosome races. This pattern can be explained by the probable hybrid status of the Bretolet race but also suggests a relatively low impact of chromosomal differences on genetic structure compared to historical factors. Finally, we propose that the current data set (available at http://www.unil.ch/dee/page7010_en.html#1) could be used as a reference by those wanting to identify Sorex individuals sampled in the western Alps.}, } @article {pmid16623953, year = {2006}, author = {Tress, ML and Cozzetto, D and Tramontano, A and Valencia, A}, title = {An analysis of the Sargasso Sea resource and the consequences for database composition.}, journal = {BMC bioinformatics}, volume = {7}, number = {}, pages = {213}, pmid = {16623953}, issn = {1471-2105}, mesh = {Amino Acid Sequence ; Bacterial Proteins/*genetics/*metabolism ; Base Sequence ; *Databases, Protein ; Genes, Bacterial/*genetics ; Genetic Variation ; Information Storage and Retrieval/*methods ; Marine Biology/*methods ; Molecular Sequence Data ; Oceans and Seas ; *Water Microbiology ; }, abstract = {BACKGROUND: The environmental sequencing of the Sargasso Sea has introduced a huge new resource of genomic information. Unlike the protein sequences held in the current searchable databases, the Sargasso Sea sequences originate from a single marine environment and have been sequenced from species that are not easily obtainable by laboratory cultivation. The resource also contains very many fragments of whole protein sequences, a side effect of the shotgun sequencing method.These sequences form a significant addendum to the current searchable databases but also present us with some intrinsic difficulties. While it is important to know whether it is possible to assign function to these sequences with the current methods and whether they will increase our capacity to explore sequence space, it is also interesting to know how current bioinformatics techniques will deal with the new sequences in the resource.

RESULTS: The Sargasso Sea sequences seem to introduce a bias that decreases the potential of current methods to propose structure and function for new proteins. In particular the high proportion of sequence fragments in the resource seems to result in poor quality multiple alignments.

CONCLUSION: These observations suggest that the new sequences should be used with care, especially if the information is to be used in large scale analyses. On a positive note, the results may just spark improvements in computational and experimental methods to take into account the fragments generated by environmental sequencing techniques.}, } @article {pmid16619865, year = {2006}, author = {Espinosa, C and Rojas, M and Seijas, D}, title = {[Usefulness of the geographic information system (GIS) in the identification of contributing factors to lead blood concentrations in a population of Venezuelan children].}, journal = {Salud publica de Mexico}, volume = {48}, number = {2}, pages = {84-93}, doi = {10.1590/s0036-36342006000200002}, pmid = {16619865}, issn = {0036-3634}, mesh = {Child ; Child, Preschool ; *Environmental Exposure ; Female ; *Geographic Information Systems ; Humans ; Lead/*blood ; Male ; Risk Factors ; Venezuela ; }, abstract = {OBJECTIVE: To identify environmental factors that contribute to blood lead levels (BPb) in children living in an urban area in Valencia, Venezuela, using a Geographical Information System (GIS) as an association tool.

MATERIAL AND METHODS: An analytical-ecological study was carried out.

POPULATION: 60 children.

DATA COLLECTED: Demography, potential sources of environmental lead and BPb concentrations. An association was made between environmental variables and BPb, using a buffer analysis.

RESULTS: There was a statistically significant difference between BPb in males (11.1+/-3.1 microg/dl) compared to females (9.5+/-2.7 microg/dl). Average BPb of children living within the buffer areas (10.7+/-3.2 microg/dl) was higher than that of the rest of the children (9.9+/-2.5 microg/dl). Children with BPb levels higher than the permissible limit who live in the southern region of the area studied had an average BPb significantly higher than the rest. The GIS enabled the identification of a soldering/welding shop as the nearest source of exposure to the male children's homes.

CONCLUSIONS: GIS made it possible to recognize sources of lead exposure in the area and its association with the BPb levels of children that live near such sources. It is suggested to further evaluate additional factors that could influence the risk of lead exposure.}, } @article {pmid16619628, year = {2006}, author = {Eisen, L and Eisen, RJ and Lane, RS}, title = {Geographical distribution patterns and habitat suitability models for presence of host-seeking ixodid ticks in dense woodlands of Mendocino County, California.}, journal = {Journal of medical entomology}, volume = {43}, number = {2}, pages = {415-427}, doi = {10.1603/0022-2585(2006)043[0415:gdpahs]2.0.co;2}, pmid = {16619628}, issn = {0022-2585}, support = {AI22501/AI/NIAID NIH HHS/United States ; U50/CCU906594/CC/ODCDC CDC HHS/United States ; }, mesh = {Animals ; Arachnid Vectors/*physiology ; Biodiversity ; California ; Demography ; *Ecosystem ; Geographic Information Systems ; Geography ; Ixodidae/*physiology ; Logistic Models ; Trees ; }, abstract = {We used drag sampling to examine the geographical distribution patterns of ixodid ticks engaging in open (non-nidicolous) host-seeking behavior in dense woodland habitats of the climatically and ecologically diverse Mendocino County in north coastal California. The findings based on this sampling methodology reflect risk of human exposure to host-seeking ticks rather than the true distribution of the ticks. Drag sampling in 78 sites yielded 7,860 nymphal or adult Ixodes pacificus Cooley & Kohls, 220 Dermacentor occidentalis Marx, 150 Ixodes spinipalpis Hadwen & Nuttall, 15 Hemaphysalis leporispalustris (Packard), 12 Ixodes angustus Neumann, 12 Ixodes auritulus Neumann, and a single Dermacentor variabilis (Say). I. pacificus, which is the primary vector of the Lyme disease spirochete Borrelia burgdorferi to humans in California, occurred in all 78 sites examined. D. occidentalis, another tick species commonly biting humans in California, and H. leporispalustris typically were encountered in oak-associated woodlands in the central or eastern parts of the county. In contrast, three species of Ixodes ticks (I. angustus, I. auritulus, and I. spinipalpis) most commonly were found questing openly in woodlands with redwood present in the western part of the county. I. angustus and I. spinipalpis are occasional human biters and known experimental vectors of B. burgdorferi. Our study represents the first collection of large numbers of openly host-seeking I. spinipalpis ticks. Univariate tests of associations between presence of ticks (D. occidentalis, H. leporispalustris, I. angustus, I. auritulus, or I. spinipalpis) and environmental geographical information systems-remote sensing (GIS/ RS)-based data indicated that elevation, number of growing degree-days, and tasseled cap brightness, greenness, and wetness are especially useful predictors of presence of openly hostseeking ticks. Combinations of the above-mentioned GIS/RS-based data yielded significant logistic regression models for habitat suitability of host-seeking ticks for all five above-mentioned species. The model equations were used to create spatial surfaces of predicted presence of suitable habitat for openly host-seeking ticks in Mendocino County dense woodlands.}, } @article {pmid16619139, year = {2006}, author = {Berryhill, JC and Linney, JA}, title = {On the edge of diversity: bringing African Americans and Latinos together in a neighborhood group.}, journal = {American journal of community psychology}, volume = {37}, number = {3-4}, pages = {247-255}, doi = {10.1007/s10464-006-9012-0}, pmid = {16619139}, issn = {0091-0562}, mesh = {*Black or African American ; Anthropology, Cultural ; Child ; Child Welfare ; *Community Networks ; *Hispanic or Latino ; Humans ; Power, Psychological ; Program Development ; *Race Relations ; Southeastern United States ; }, abstract = {This article describes challenges we encountered when organizing a group of African Americans and Latinos in a community where ethnic tensions had been normative. We relate how the first author, a Caucasian with a university affiliation, entered this diverse community and employed ethnographic methods in an attempt to understand it. The ethnography provides a context for the principal challenge we encountered: ensuring that the group had ethnic balance. Focusing on the group's first meeting, we describe the uncertainty of whether our work would be helpful or harmful to the community. We conclude with reflections on the gaps between science and practice in diverse communities; the utility and limits of ethnography; the multiple ecological levels of influence on the community; dilemmas around a White male taking proactive stances while trying to empower a group consisting mostly of women of color; and the influence of values we brought to the community.}, } @article {pmid16600679, year = {2006}, author = {Schröder, W}, title = {GIS, geostatistics, metadata banking, and tree-based models for data analysis and mapping in environmental monitoring and epidemiology.}, journal = {International journal of medical microbiology : IJMM}, volume = {296 Suppl 40}, number = {}, pages = {23-36}, doi = {10.1016/j.ijmm.2006.02.015}, pmid = {16600679}, issn = {1438-4221}, mesh = {Databases, Factual ; Ecosystem ; Environmental Monitoring/*methods ; *Geographic Information Systems ; *Geography/statistics & numerical data ; Marine Biology ; Metals, Heavy/chemistry ; Models, Biological ; Plant Physiological Phenomena ; Risk Assessment/*methods ; Soil/analysis ; }, abstract = {By the example of environmental monitoring, some applications of geographic information systems (GIS), geostatistics, metadata banking, and Classification and Regression Trees (CART) are presented. These tools are recommended for mapping statistically estimated hot spots of vectors and pathogens. GIS were introduced as tools for spatially modelling the real world. The modelling can be done by mapping objects according to the spatial information content of data. Additionally, this can be supported by geostatistical and multivariate statistical modelling. This is demonstrated by the example of modelling marine habitats of benthic communities and of terrestrial ecoregions. Such ecoregionalisations may be used to predict phenomena based on the statistical relation between measurements of an interesting phenomenon such as, e.g., the incidence of medically relevant species and correlated characteristics of the ecoregions. The combination of meteorological data and data on plant phenology can enhance the spatial resolution of the information on climate change. To this end, meteorological and phenological data have to be correlated. To enable this, both data sets which are from disparate monitoring networks have to be spatially connected by means of geostatistical estimation. This is demonstrated by the example of transformation of site-specific data on plant phenology into surface data. The analysis allows for spatial comparison of the phenology during the two periods 1961-1990 and 1991-2002 covering whole Germany. The changes in both plant phenology and air temperature were proved to be statistically significant. Thus, they can be combined by GIS overlay technique to enhance the spatial resolution of the information on the climate change and use them for the prediction of vector incidences at the regional scale. The localisation of such risk hot spots can be done by geometrically merging surface data on promoting factors. This is demonstrated by the example of the transfer of heavy metals through soils. The predicted hot spots of heavy metal transfer can be validated empirically by measurement data which can be inquired by a metadata base linked with a geographic information system. A corresponding strategy for the detection of vector hot spots in medical epidemiology is recommended. Data on incidences and habitats of the Anophelinae in the marsh regions of Lower Saxony (Germany) were used to calculate a habitat model by CART, which together with climate data and data on ecoregions can be further used for the prediction of habitats of medically relevant vector species. In the future, this approach should be supported by an internet-based information system consisting of three components: metadata questionnaire, metadata base, and GIS to link metadata, surface data, and measurement data on incidences and habitats of medically relevant species and related data on climate, phenology, and ecoregional characteristic conditions.}, } @article {pmid16584821, year = {2006}, author = {Pitcairn, C and Fowler, D and Leith, I and Sheppard, L and Tang, S and Sutton, M and Famulari, D}, title = {Diagnostic indicators of elevated nitrogen deposition.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {144}, number = {3}, pages = {941-950}, doi = {10.1016/j.envpol.2006.01.049}, pmid = {16584821}, issn = {0269-7491}, mesh = {Acid Rain ; Agriculture ; Air Movements ; Air Pollutants/*analysis ; Animal Husbandry ; Bryophyta/*chemistry ; Environmental Monitoring/*methods ; Geographic Information Systems ; Nitrogen/*analysis ; Trees ; United Kingdom ; }, abstract = {Tissue N content of mosses, which has been shown to be an indicator of enhanced N, was studied at a range of locations dominated either by wet or dry deposited and oxidised and reduced forms of N. Tissue N responded differently to wet and dry deposited N. For a 1 kg ha(-1) y(-1) increase in N deposition, tissue N increased by 0.01% at wet deposition sites but by 0.03% at sites dominated by dry deposited NH3. Tissue N at wet deposition sites responded more to concentrations of NO3- and NH4+ in precipitation (r(2) 0.63) than to total N deposition (r(2) 0.27), concentration explaining 66% of the variation in tissue N, wet deposition 33%. The study clearly concludes that tissue N concentration in mosses provides a good indication of N deposition at sites where deposition is dominated by NH3, and is also valuable in identifying vegetation exposed to large concentrations of NH4+ or NO3-, in wet deposition dominated areas, such as hilltops and wind exposed woodland edges.}, } @article {pmid16574306, year = {2007}, author = {Mörtberg, UM and Balfors, B and Knol, WC}, title = {Landscape ecological assessment: a tool for integrating biodiversity issues in strategic environmental assessment and planning.}, journal = {Journal of environmental management}, volume = {82}, number = {4}, pages = {457-470}, doi = {10.1016/j.jenvman.2006.01.005}, pmid = {16574306}, issn = {0301-4797}, mesh = {*Biodiversity ; Conservation of Natural Resources/*methods ; *Environment ; Environmental Monitoring/*methods ; *Geographic Information Systems ; *Models, Theoretical ; Planning Techniques ; Sweden ; *Urbanization ; }, abstract = {To achieve a sustainable development, impacts on biodiversity of urbanisation, new infrastructure projects and other land use changes must be considered on landscape and regional scales. This requires that important decisions are made after a systematic evaluation of environmental impacts. Landscape ecology can provide a conceptual framework for the assessment of consequences of long-term development processes like urbanisation on biodiversity components, and for evaluating and visualising the impacts of alternative planning scenarios. The aim of this paper was to develop methods for integrating biodiversity issues in planning and strategic environmental assessment in an urbanising environment, on landscape and regional levels. In order to test developed methods, a case study was conducted in the region of Stockholm, the capital of Sweden, and the study area embraced the city centre, suburbs and peri-urban areas. Focal species were tested as indicators of habitat quality, quantity and connectivity in the landscape. Predictive modelling of habitat distribution in geographic information systems involved the modelling of focal species occurrences based on empirical data, incorporated in a landscape ecological decision support system. When habitat models were retrieved, they were applied on future planning scenarios in order to predict and assess the impacts on focal species. The scenario involving a diffuse exploitation pattern had the greatest negative impacts on the habitat networks of focal species. The scenarios with concentrated exploitation also had negative impacts, although they were possible to mitigate quite easily. The predictions of the impacts on habitats networks of focal species made it possible to quantify, integrate and visualise the effects of urbanisation scenarios on aspects of biodiversity on a landscape level.}, } @article {pmid16571937, year = {2006}, author = {Katayama, H and Apsalikov, KN and Gusev, BI and Galich, B and Madieva, M and Koshpessova, G and Abdikarimova, A and Hoshi, M}, title = {An attempt to develop a database for epidemiological research in Semipalatinsk.}, journal = {Journal of radiation research}, volume = {47 Suppl A}, number = {}, pages = {A189-97}, doi = {10.1269/jrr.47.a189}, pmid = {16571937}, issn = {0449-3060}, mesh = {Adult ; *Databases, Factual ; *Epidemiologic Research Design ; Humans ; Information Dissemination ; Information Storage and Retrieval/*methods ; Kazakhstan/epidemiology ; Medical Records Systems, Computerized/*organization & administration ; Nuclear Warfare/*statistics & numerical data ; Radiation Injuries/*epidemiology ; *Registries ; Risk Assessment/methods/organization & administration ; Risk Factors ; }, abstract = {The present paper reports progress and problems in our development of a database for comprehensive epidemiological research in Semipalatinsk whose ultimate aim is to examine the effects of low dose radiation exposure on the human body. The database was constructed and set up at the Scientific Research Institute of Radiation Medicine Ecology in 2003, and the number of data entries into the database reached 110,000 on 31 January 2005. However, we face some problems concerning size, accuracy and reliability of data which hinder full epidemiological analysis. Firstly we need fuller bias free data. The second task is to establish a committee for a discussion of the analysis, which should be composed of statisticians and epidemiologists, to conduct a research project from a long-term perspective, and carry out the collection of data effectively, along the lines of the project. Due to the insufficiency of data collected so far, our analysis is limited to showing the trends in mortality rates in the high and low dose areas.}, } @article {pmid16569474, year = {2007}, author = {Batzias, F and Siontorou, CG}, title = {A novel system for environmental monitoring through a cooperative/synergistic scheme between bioindicators and biosensors.}, journal = {Journal of environmental management}, volume = {82}, number = {2}, pages = {221-239}, doi = {10.1016/j.jenvman.2005.12.023}, pmid = {16569474}, issn = {0301-4797}, mesh = {*Biosensing Techniques/methods ; *Conservation of Natural Resources ; *Ecosystem ; *Environmental Monitoring/instrumentation/methods ; *Geographic Information Systems ; *Software ; }, abstract = {This paper addresses environmental monitoring through a robust dynamic integration between biomonitor and biosensor systems, a strategy that has not been attempted before. The two systems are conceptually interrelated and methodologically correlated to a cooperative/synergistic scheme (CSS) with a view to minimise uncertainty and monitoring costs and increase reliability of pollution control and abatement. The structures and operations of the biosensor component (in terms of sensitivity, device and method versatility, nature-mimicking physicochemical mechanisms, prospects and technological input) are such that they reinforce or promote the structures and operations of the natural component (in terms of bio-surveillance, impact assessment, environmental quality indexing, stress responses, metabolic pathways, etc.) and vice versa. The bioindicator ontology presented herein, including concepts, relations and controlled vocabulary aiming at establishing an integrated methodology for mapping/assessing negative environmental externalities, provides a useful tool for the design/development/implementation of an environmental network for the monitoring of a variety of pollutants over time and space and the assessment of environmental quality; the collection of the available information and its classification into taxonomic and partonomic relations allows the construction of a database that links pollutants with organisms' response, at a phenomenological and in-depth level, considering ecological parameters, relations and geomorphologic characteristics. As a result, a computer program has been designed/developed as a decision support system and has been successfully tested on a representative population of species indigenous to southern Greece. Significantly, a novel system in the form of a rational framework at the conceptual design level has been developed, that actually contributes towards achieving a cost-effective long-term monitoring program, with the flexibility to counter on-course any (anticipated or not) variations/modifications of the surveillance environment. This novel and pioneering approach will further offer a dynamic system utilised in (a) environmental impact studies and risk assessment (positive/analytic approach), (b) decision-making in the short-run (normative/tactic approach), and (c) policy-making in the long-run (normative/strategic approach). The proposed CSS, based on the integration of multiple data sources, can establish a local area network, incorporated into/expanding to a wide area network, thus offering the potential of better predictive ability and greater lead-time warning at alarm conditions than that provided by separate, stand-alone surveillance modalities.}, } @article {pmid16567364, year = {2006}, author = {Ruan, Q and Steele, JA and Schwalbach, MS and Fuhrman, JA and Sun, F}, title = {A dynamic programming algorithm for binning microbial community profiles.}, journal = {Bioinformatics (Oxford, England)}, volume = {22}, number = {12}, pages = {1508-1514}, doi = {10.1093/bioinformatics/btl114}, pmid = {16567364}, issn = {1367-4803}, mesh = {Algorithms ; Biodiversity ; Cluster Analysis ; Computational Biology/*methods ; DNA, Ribosomal Spacer/*genetics ; *Genes, Bacterial ; Models, Biological ; Models, Theoretical ; Mutation ; Programming Languages ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 23S/genetics ; Seawater/*microbiology ; Software ; }, abstract = {MOTIVATION: A number of community profiling approaches have been widely used to study the microbial community composition and its variations in environmental ecology. Automated Ribosomal Intergenic Spacer Analysis (ARISA) is one such technique. ARISA has been used to study microbial communities using 16S-23S rRNA intergenic spacer length heterogeneity at different times and places. Owing to errors in sampling, random mutations in PCR amplification, and probably mostly variations in readings from the equipment used to analyze fragment sizes, the data read directly from the fragment analyzer should not be used for down stream statistical analysis. No optimal data preprocessing methods are available. A commonly used approach is to bin the reading lengths of the 16S-23S intergenic spacer. We have developed a dynamic programming algorithm based binning method for ARISA data analysis which minimizes the overall differences between replicates from the same sampling location and time.

RESULTS: In a test example from an ocean time series sampling program, data preprocessing identified several outliers which upon re-examination were found to be because of systematic errors. Clustering analysis of the ARISA from different times based on the dynamic programming algorithm binned data revealed important features of the biodiversity of the microbial communities.}, } @article {pmid16556831, year = {2006}, author = {Falkowski, PG}, title = {Evolution. Tracing oxygen's imprint on earth's metabolic evolution.}, journal = {Science (New York, N.Y.)}, volume = {311}, number = {5768}, pages = {1724-1725}, doi = {10.1126/science.1125937}, pmid = {16556831}, issn = {1095-9203}, mesh = {Animals ; *Biological Evolution ; Computational Biology ; Electron Transport ; Electrons ; Energy Metabolism ; Eukaryotic Cells/metabolism ; *Evolution, Molecular ; Gene Duplication ; Gene Transfer, Horizontal ; *Metabolism ; Oxidation-Reduction ; Oxygen/*metabolism ; Photosynthesis ; Reactive Oxygen Species/metabolism ; Selection, Genetic ; Water/metabolism ; }, } @article {pmid16549025, year = {2006}, author = {Rodriguez-Brito, B and Rohwer, F and Edwards, RA}, title = {An application of statistics to comparative metagenomics.}, journal = {BMC bioinformatics}, volume = {7}, number = {}, pages = {162}, pmid = {16549025}, issn = {1471-2105}, mesh = {*Algorithms ; Computer Simulation ; Data Interpretation, Statistical ; Genomics/*methods ; *Models, Biological ; Models, Statistical ; Proteome/*metabolism ; Sequence Analysis, DNA/*methods ; Signal Transduction/*physiology ; }, abstract = {BACKGROUND: Metagenomics, sequence analyses of genomic DNA isolated directly from the environments, can be used to identify organisms and model community dynamics of a particular ecosystem. Metagenomics also has the potential to identify significantly different metabolic potential in different environments.

RESULTS: Here we use a statistical method to compare curated subsystems, to predict the physiology, metabolism, and ecology from metagenomes. This approach can be used to identify those subsystems that are significantly different between metagenome sequences. Subsystems that were overrepresented in the Sargasso Sea and Acid Mine Drainage metagenome when compared to non-redundant databases were identified.

CONCLUSION: The methodology described herein applies statistics to the comparisons of metabolic potential in metagenomes. This analysis reveals those subsystems that are more, or less, represented in the different environments that are compared. These differences in metabolic potential lead to several testable hypotheses about physiology and metabolism of microbes from these ecosystems.}, } @article {pmid16546700, year = {2006}, author = {Young, FW}, title = {Community decline and mortality.}, journal = {Health & place}, volume = {12}, number = {3}, pages = {353-359}, doi = {10.1016/j.healthplace.2005.03.001}, pmid = {16546700}, issn = {1353-8292}, mesh = {Community Networks ; Humans ; Mortality/*trends ; New York/epidemiology ; *Poverty Areas ; }, abstract = {UNLABELLED: This study of the relation of social problems to mortality in the context of growth and decline in 50 New York counties is guided by an ecological framework that sees communities depending on their many agencies and services for maintaining and improving the well-being of residents despite external problems/threats. Two all-purpose measures of threats are community growth and decline, especially the latter. If the specialized agencies typical of more urbanized places are weak, threats generate internal social problems like crime and unemployment and these lower population health.

FINDINGS: when urbanization is held constant, growth is negatively associated with poverty-related problems while decline predicts deviance. Both poverty and deviance problems, in turn, predict mortality. The applied implications of this model are discussed.}, } @article {pmid16546420, year = {2006}, author = {Lafon, A and Han, KH and Seo, JA and Yu, JH and d'Enfert, C}, title = {G-protein and cAMP-mediated signaling in aspergilli: a genomic perspective.}, journal = {Fungal genetics and biology : FG & B}, volume = {43}, number = {7}, pages = {490-502}, doi = {10.1016/j.fgb.2006.02.001}, pmid = {16546420}, issn = {1087-1845}, mesh = {Adenylyl Cyclases/genetics ; Aspergillus/*genetics ; Aspergillus fumigatus/genetics ; Aspergillus nidulans/genetics ; Aspergillus oryzae/genetics ; Computational Biology ; Cyclic AMP-Dependent Protein Kinases/*genetics ; *Genome, Fungal ; Phosphoric Diester Hydrolases/genetics ; Phylogeny ; Protein Structure, Tertiary ; Protein Subunits/genetics ; RGS Proteins/genetics ; Receptors, G-Protein-Coupled/*genetics ; Sequence Homology, Amino Acid ; Signal Transduction/*genetics ; }, abstract = {We have carried out an in silico exploration of the genomes of Aspergillus nidulans, Aspergillus fumigatus, and Aspergillus oryzae, and identified components of G-protein/cAMP-mediated signaling. Putative G-protein coupled receptors (GPCRs) were distributed over nine classes. The GPCRs within classes were well conserved among aspergilli but varied in other ascomycetes. As previously observed in A. nidulans and other fungi, three Galpha, one Gbeta, and one Ggamma subunits of G proteins were identified in A. fumigatus, whereas an additional likely non-functional Galpha subunit was present in A. oryzae. While most fungal species had five proteins containing the regulator of G-protein signaling (RGS) domain predicted to participate in attenuation of G-protein signaling, A. fumigatus and A. oryzae had an additional RGS protein (RgsD) related to RgsA of A. nidulans. Genes encoding adenylate cyclase, a regulatory subunit and two catalytic subunits of the cAMP-dependent protein kinase, were also identified in the three aspergilli. Finally, regulators of cAMP signaling including low- and high-affinity phosphodiesterases were identified. Taken together, our data indicate a striking diversity at the GPCR level, but little diversity of components at the G-protein and cAMP-signaling level. This may reflect the abilities of these fungi to adapt to various ecological niches and to integrate diverse environmental cues into highly conserved cellular processes.}, } @article {pmid16545128, year = {2006}, author = {Yu, HL and Christakos, G}, title = {Spatiotemporal modelling and mapping of the bubonic plague epidemic in India.}, journal = {International journal of health geographics}, volume = {5}, number = {}, pages = {12}, pmid = {16545128}, issn = {1476-072X}, mesh = {Disease Outbreaks/*history/statistics & numerical data ; Geographic Information Systems ; History, 19th Century ; History, 20th Century ; Humans ; India/epidemiology ; Models, Theoretical ; Plague/epidemiology/*history ; Stochastic Processes ; }, abstract = {BACKGROUND: This work studies the spatiotemporal evolution of bubonic plague in India during 1896-1906 using stochastic concepts and geographical information science techniques. In the past, most investigations focused on selected cities to conduct different kinds of studies, such as the ecology of rats. No detailed maps existed incorporating the space-time dependence structure and uncertainty sources of the epidemic system and providing a composite space-time picture of the disease propagation characteristics.

RESULTS: Informative spatiotemporal maps were generated that represented mortality rates and geographical spread of the disease, and epidemic indicator plots were derived that offered meaningful characterizations of the spatiotemporal disease distribution. The bubonic plague in India exhibited strong seasonal and geographical features. During its entire duration, the plague continued to invade new geographical areas, while it followed a re-emergence pattern at many localities; its rate changed significantly during each year and the mortality distribution exhibited space-time heterogeneous patterns; prevalence usually occurred in the autumn and spring, whereas the plague stopped moving towards new locations during the summers.

CONCLUSION: Modern stochastic modelling and geographical information science provide powerful means to study the spatiotemporal distribution of the bubonic plague epidemic under conditions of uncertainty and multi-sourced databases; to account for various forms of interdisciplinary knowledge; and to generate informative space-time maps of mortality rates and propagation patterns. To the best of our knowledge, this kind of plague maps and plots become available for the first time, thus providing novel perspectives concerning the distribution and space-time propagation of the deadly epidemic. Furthermore, systematic maps and indicator plots make possible the comparison of the spatial-temporal propagation patterns of different diseases.}, } @article {pmid16542236, year = {2006}, author = {Kneib, T and Fahrmeir, L}, title = {Structured additive regression for categorical space-time data: a mixed model approach.}, journal = {Biometrics}, volume = {62}, number = {1}, pages = {109-118}, doi = {10.1111/j.1541-0420.2005.00392.x}, pmid = {16542236}, issn = {0006-341X}, mesh = {Bayes Theorem ; Data Interpretation, Statistical ; Ecology/methods ; Forestry/*statistics & numerical data ; Likelihood Functions ; *Models, Statistical ; Regression Analysis ; Time ; Trees ; }, abstract = {Motivated by a space-time study on forest health with damage state of trees as the response, we propose a general class of structured additive regression models for categorical responses, allowing for a flexible semiparametric predictor. Nonlinear effects of continuous covariates, time trends, and interactions between continuous covariates are modeled by penalized splines. Spatial effects can be estimated based on Markov random fields, Gaussian random fields, or two-dimensional penalized splines. We present our approach from a Bayesian perspective, with inference based on a categorical linear mixed model representation. The resulting empirical Bayes method is closely related to penalized likelihood estimation in a frequentist setting. Variance components, corresponding to inverse smoothing parameters, are estimated using (approximate) restricted maximum likelihood. In simulation studies we investigate the performance of different choices for the spatial effect, compare the empirical Bayes approach to competing methodology, and study the bias of mixed model estimates. As an application we analyze data from the forest health survey.}, } @article {pmid16533068, year = {2006}, author = {Hallam, SJ and Mincer, TJ and Schleper, C and Preston, CM and Roberts, K and Richardson, PM and DeLong, EF}, title = {Pathways of carbon assimilation and ammonia oxidation suggested by environmental genomic analyses of marine Crenarchaeota.}, journal = {PLoS biology}, volume = {4}, number = {4}, pages = {e95}, pmid = {16533068}, issn = {1545-7885}, mesh = {Acetyl-CoA Carboxylase/genetics ; Ammonia/*metabolism ; Carbon/*metabolism ; Citric Acid Cycle ; Crenarchaeota/*genetics/*metabolism ; DNA, Archaeal/genetics ; Databases, Genetic ; Genome, Archaeal/*genetics ; Isoenzymes/genetics/metabolism ; Lactic Acid/analogs & derivatives/metabolism ; Marine Biology ; Molecular Sequence Data ; Oceans and Seas ; Operon/genetics ; Oxidation-Reduction ; Oxidoreductases/genetics/metabolism ; Phylogeny ; Seawater/*microbiology ; }, abstract = {Marine Crenarchaeota represent an abundant component of oceanic microbiota with potential to significantly influence biogeochemical cycling in marine ecosystems. Prior studies using specific archaeal lipid biomarkers and isotopic analyses indicated that planktonic Crenarchaeota have the capacity for autotrophic growth, and more recent cultivation studies support an ammonia-based chemolithoautotrophic energy metabolism. We report here analysis of fosmid sequences derived from the uncultivated marine crenarchaeote, Cenarchaeum symbiosum, focused on the reconstruction of carbon and energy metabolism. Genes predicted to encode multiple components of a modified 3-hydroxypropionate cycle of autotrophic carbon assimilation were identified, consistent with utilization of carbon dioxide as a carbon source. Additionally, genes predicted to encode a near complete oxidative tricarboxylic acid cycle were also identified, consistent with the consumption of organic carbon and in the production of intermediates for amino acid and cofactor biosynthesis. Therefore, C. symbiosum has the potential to function either as a strict autotroph, or as a mixotroph utilizing both carbon dioxide and organic material as carbon sources. From the standpoint of energy metabolism, genes predicted to encode ammonia monooxygenase subunits, ammonia permease, urease, and urea transporters were identified, consistent with the use of reduced nitrogen compounds as energy sources fueling autotrophic metabolism. Homologues of these genes, recovered from ocean waters worldwide, demonstrate the conservation and ubiquity of crenarchaeal pathways for carbon assimilation and ammonia oxidation. These findings further substantiate the likely global metabolic importance of Crenarchaeota with respect to key steps in the biogeochemical transformation of carbon and nitrogen in marine ecosystems.}, } @article {pmid16529974, year = {2007}, author = {Emch, M and Ali, M and Acosta, C and Yunus, M and Sack, DA and Clemens, JD}, title = {Efficacy calculation in randomized trials: global or local measures?.}, journal = {Health & place}, volume = {13}, number = {1}, pages = {238-248}, doi = {10.1016/j.healthplace.2006.01.005}, pmid = {16529974}, issn = {1353-8292}, support = {1 R03 AI53214-01/AI/NIAID NIH HHS/United States ; }, mesh = {Adolescent ; Age Factors ; Bangladesh/epidemiology ; Child ; Child, Preschool ; Cholera/epidemiology/*prevention & control ; Cholera Vaccines/*administration & dosage ; Cluster Analysis ; Double-Blind Method ; Drug Evaluation/*methods ; Female ; Geographic Information Systems ; Humans ; Immunity, Herd ; *Immunization Programs ; Male ; Population Surveillance ; *Randomized Controlled Trials as Topic ; Residence Characteristics ; *Treatment Outcome ; }, abstract = {This study tests whether the effect of a vaccine trial varies in space and why. Analytical z-score maps identify unusually high- and low-efficacy values in a trial area. Relationships between neighborhood efficacy and ecological variables are measured to explain why efficacy varies in space. Efficacy was found to vary regardless of neighborhood size and the variation is related to several ecological determinants. Local efficacy measures can help public health practitioners make better decisions about when and where to vaccinate populations. The concepts offered in this study are pertinent for any health intervention trial, not just vaccines.}, } @article {pmid16519242, year = {2006}, author = {Ezenwa, VO and Godsey, MS and King, RJ and Guptill, SC}, title = {Avian diversity and West Nile virus: testing associations between biodiversity and infectious disease risk.}, journal = {Proceedings. Biological sciences}, volume = {273}, number = {1582}, pages = {109-117}, pmid = {16519242}, issn = {0962-8452}, mesh = {Animals ; *Biodiversity ; Birds/genetics/*physiology/virology ; Culex/virology ; Data Interpretation, Statistical ; Geography ; Humans ; Passeriformes/genetics/virology ; Risk Factors ; West Nile Fever/epidemiology/*transmission/veterinary ; *West Nile virus ; }, abstract = {The emergence of several high profile infectious diseases in recent years has focused attention on our need to understand the ecological factors contributing to the spread of infectious diseases. West Nile virus (WNV) is a mosquito-borne zoonotic disease that was first detected in the United States in 1999. The factors accounting for variation in the prevalence of WNV are poorly understood, but recentideas suggesting links between high biodiversity and reduced vector-borne disease risk may help account for distribution patterns of this disease. Since wild birds are the primary reservoir hosts for WNV, we tested associations between passerine (Passeriform) bird diversity, non-passerine (all other orders) bird diversity and virus infection rates in mosquitoes and humans to examine the extent to which bird diversity is associated with WNV infection risk. We found t h at non-passerine species richness (number of non-passerine species) was significantly negatively correlated with both mosquito and human infection rates, whereas there was no significant association between passerine species richness and any measure of infection risk. Our findings suggest that non-passerine diversity may play a role in dampening WNV amplification rates in mosquitoes, minimizing human disease risk.}, } @article {pmid16515526, year = {2006}, author = {Jones, WP and Chin, YW and Kinghorn, AD}, title = {The role of pharmacognosy in modern medicine and pharmacy.}, journal = {Current drug targets}, volume = {7}, number = {3}, pages = {247-264}, doi = {10.2174/138945006776054915}, pmid = {16515526}, issn = {1389-4501}, mesh = {Animals ; Biological Products/*pharmacology/*therapeutic use ; Humans ; *Pharmacognosy ; Pharmacology ; *Pharmacy ; Phytotherapy ; }, abstract = {This review details the contribution to modern medicine and pharmacy made by natural products and drugs derived from natural products, with an emphasis on essential medicines and new introductions to the market. Areas covered include recent advances in the development of drugs derived from marine organisms, microbes, terrestrial animals, and vascular plants, and current issues regarding botanical medicines. The role of natural products in drug discovery and development is evaluated, particularly with regard to their value as sources of drug leads with "drug-like" properties. A rationale for the success of natural products research in providing new drugs and drug prototypes is presented, drawing on lines of evidence from chemical informatics and chemical ecology. Several innovative strategies for natural products drug discovery and evaluation of botanical medicines are also reviewed.}, } @article {pmid16515174, year = {2005}, author = {Fan, W and Gong, W and Liu, D and Zhou, H and Zhu, N}, title = {[Application of 3S techniques in ecological landscape planning of Harbin suburb].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {16}, number = {12}, pages = {2291-2295}, pmid = {16515174}, issn = {1001-9332}, mesh = {China ; *City Planning ; *Ecosystem ; *Environment Design ; *Geographic Information Systems ; Satellite Communications ; }, abstract = {With the image data (SPOT), soil utilization map (1:50000) and other related materials of Harbin, and under the support of GIS, RS and GPS techniques, this paper obtained the landscape pattern of Harbin suburb and the Digital Elevation Model (DEM) of Harbin. Indices including mean patch area, landscape dominance, mean slope, mean altitude, and fragmentation degree were selected and synthetically analyzed, with the ecological landscape planning made by DEM model. The results showed that 3S techniques could help to decide typical landscape types. The landscape type database was established, and the landscape type thematic map was generated, with land use status and landscape distribution, physiognomy, and land use types combined. The ecological landscape planning was described in large scale with the image data and DEM combined, and the landscape structure of Harbin suburb was reflected directly with the ecological landscape planning and DEM combined, which improved the ecological function in this region, and provided scientific bases to the healthy development in urban-rural integration area.}, } @article {pmid16515171, year = {2005}, author = {He, X and Hu, Z and Li, Y and Hu, Y}, title = {[Dynamics of soil erosion at upper reaches of Minjiang River based on GIS].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {16}, number = {12}, pages = {2271-2278}, pmid = {16515171}, issn = {1001-9332}, mesh = {China ; *Ecosystem ; Environmental Monitoring ; *Geographic Information Systems ; Geologic Sediments/*analysis ; Models, Theoretical ; *Rivers ; Soil/*analysis ; }, abstract = {Based on TM and ETM imagines, and employing GIS technique and empirical Revised Universal Soil Loss Equation (RUSLE) model, this paper studied the dynamics of soil erosion at the upper reaches of Minjiang River during three typical periods, with the main affecting factors analyzed. The results showed that the soil erosion area was increased by 1.28%, 1.84 % and 1.70% in 1986, 1995 and 2000, respectively. The average erosion modulus was increased from 832.64 t x km(-2) x yr(-1) in 1986 to 1048.74 t x km(-2) yr(-2) in 1995 and reached 1362.11 t x km(-2) yr(-1) in 2000, and soil loss was mainly of slight and light erosion, companying with a small quantity of middling erosion. The area of soil erosion was small, and the degree was light. There was a significant correlation between slope and soil loss, which mainly happened in the regions with a slope larger than 25 degrees, and accounted for 93.65%, 93.81% and 92.71% of the total erosion in 1986, 1995 and 2000, respectively. As for the altitude, middling, semi-high and high mountains and dry valley were liable to soil erosion, which accounted for 98.21%, 97.63% and 99.27% of the total erosion in 1986, 1995 and 2000, respectively. Different vegetation had a significant effect on soil erosion, and shrub and newly restored forest were the main erosion area. Excessive depasture not only resulted in the degradation of pasture, but also led to slight soil erosion. Land use type and soil type also contributed to soil loss, among which, dry-cinnamon soil and calcic gray-cinnamon soil were the most dangerous ones needing more protection. Soil loss was also linearly increased with increasing population and households, which suggested that the increase of population and households was the driving factor for soil loss increase in this area.}, } @article {pmid16510774, year = {2006}, author = {Luo, H and Wang, Y and Poeppel, D and Simon, JZ}, title = {Concurrent encoding of frequency and amplitude modulation in human auditory cortex: MEG evidence.}, journal = {Journal of neurophysiology}, volume = {96}, number = {5}, pages = {2712-2723}, doi = {10.1152/jn.01256.2005}, pmid = {16510774}, issn = {0022-3077}, support = {R01-DC05660/DC/NIDCD NIH HHS/United States ; }, mesh = {Acoustic Stimulation ; Adult ; Algorithms ; Auditory Cortex/*physiology ; Data Interpretation, Statistical ; Female ; Humans ; Loudness Perception/*physiology ; *Magnetoencephalography ; Male ; Pitch Perception/*physiology ; }, abstract = {A natural sound can be described by dynamic changes in envelope (amplitude) and carrier (frequency), corresponding to amplitude modulation (AM) and frequency modulation (FM), respectively. Although the neural responses to both AM and FM sounds are extensively studied in both animals and humans, it is uncertain how they are corepresented when changed simultaneously but independently, as is typical for ecologically natural signals. This study elucidates the neural coding of such sounds in human auditory cortex using magnetoencephalography (MEG). Using stimuli with both sinusoidal modulated envelope (f(AM), 37 Hz) and carrier frequency (f(FM), 0.3-8 Hz), it is demonstrated that AM and FM stimulus dynamics are corepresented in the neural code of human auditory cortex. The stimulus AM dynamics are represented neurally with AM encoding, by the auditory steady-state response (aSSR) at f(AM). For sounds with slowly changing carrier frequency (f(FM) <5 Hz), it is shown that the stimulus FM dynamics are tracked by the phase of the aSSR, demonstrating neural phase modulation (PM) encoding of the stimulus carrier frequency. For sounds with faster carrier frequency change (f(FM) > or = 5 Hz), it is shown that modulation encoding of stimulus FM dynamics persists, but the neural encoding is no longer purely PM. This result is consistent with the recruitment of additional neural AM encoding over and above the original neural PM encoding, indicating that both the amplitude and phase of the aSSR at f(AM) track the stimulus FM dynamics. A neural model is suggested to account for these observations.}, } @article {pmid16505365, year = {2006}, author = {Smith, MA and Woodley, NE and Janzen, DH and Hallwachs, W and Hebert, PD}, title = {DNA barcodes reveal cryptic host-specificity within the presumed polyphagous members of a genus of parasitoid flies (Diptera: Tachinidae).}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {103}, number = {10}, pages = {3657-3662}, pmid = {16505365}, issn = {0027-8424}, mesh = {Animals ; Base Sequence ; Costa Rica ; DNA/*genetics ; Databases, Nucleic Acid ; Diptera/classification/*genetics/*pathogenicity ; Ecosystem ; Electron Transport Complex IV/genetics ; Host-Parasite Interactions ; Molecular Sequence Data ; Moths/parasitology ; Phylogeny ; }, abstract = {Insect parasitoids are a major component of global biodiversity and affect the population dynamics of their hosts. However, identification of insect parasitoids is often difficult, and they are suspected to contain many cryptic species. Here, we ask whether the cytochrome c oxidase I DNA barcode could function as a tool for species identification and discovery for the 20 morphospecies of Belvosia parasitoid flies (Diptera: Tachinidae) that have been reared from caterpillars (Lepidoptera) in Area de Conservación Guanacaste (ACG), northwestern Costa Rica. Barcoding not only discriminates among all 17 highly host-specific morphospecies of ACG Belvosia, but it also raises the species count to 32 by revealing that each of the three generalist species are actually arrays of highly host-specific cryptic species. We also identified likely hybridization among Belvosia by using a variable internal transcribed spacer region 1 nuclear rDNA sequence as a genetic covariate in addition to the strategy of overlaying barcode clusters with ecological information. If general, these results will increase estimates of global species richness and imply that tropical conservation and host-parasite interactions may be more complex than expected.}, } @article {pmid16502035, year = {2006}, author = {Sharpe, A and Conrad, C}, title = {Community based ecological monitoring in Nova Scotia: challenges and opportunities.}, journal = {Environmental monitoring and assessment}, volume = {113}, number = {1-3}, pages = {395-409}, pmid = {16502035}, issn = {0167-6369}, mesh = {*Community Networks ; *Conservation of Natural Resources ; *Ecology ; *Environmental Monitoring/economics/methods/standards ; Nova Scotia ; }, abstract = {This article examines community-based ecological monitoring in Nova Scotia, with an emphasis on watershed stewardship groups. It discusses successes to date and future challenges, drawing on examples from the Atlantic Coastal Action Program (ACAP) and other community groups. The barriers to the generation of robust monitoring datasets and effective participation in watershed management are examined. The article concludes with a discussion of issues to be addressed to ensure that community groups can both gather scientifically valid ecological data and have meaningful input into the management of their local natural resources.}, } @article {pmid16500005, year = {2006}, author = {Sazykina, T and Kryshev, II}, title = {Radiation effects in wild terrestrial vertebrates - the EPIC collection.}, journal = {Journal of environmental radioactivity}, volume = {88}, number = {1}, pages = {11-48}, doi = {10.1016/j.jenvrad.2005.12.009}, pmid = {16500005}, issn = {0265-931X}, mesh = {Adaptation, Physiological/radiation effects ; Animals ; Biodiversity ; Birds/physiology ; Cattle ; Chernobyl Nuclear Accident ; Databases, Factual ; *Ecosystem ; Environmental Monitoring ; Lizards/physiology ; Longevity/radiation effects ; Mammals/physiology ; Mice ; *Radiation Effects ; Radiation Injuries/veterinary ; Radioactive Fallout ; Radioactive Hazard Release ; Ranidae/physiology ; Reproduction/radiation effects ; Russia ; *Vertebrates ; }, abstract = {The paper presents data on radiation effects in populations of wild vertebrate animals inhabiting contaminated terrestrial ecosystems. The data were extracted from the database "Radiation effects on biota", compiled within the framework of the EC Project EPIC (2000-2003). The data collection, based on publications in Russian, demonstrates radiation effects in the areas characterized with high levels of radionuclides (Kyshtym radioactive trace; "spots" of enhanced natural radioactivity in the Komi region of Russia; territories contaminated from the Chernobyl fallout). The data covers a wide range of exposures from acute accidental irradiation to lifetime exposures at relatively low dose rates. Radiation effects include mortality, changes in reproduction, decrease of health, ecological effects, cytogenetic effects, adaptation to radiation, and others. Peculiarities of radiation effects caused by different radionuclides are described, also the severity of effects as they appear in different organisms (e.g. mice, frogs, birds, etc.).}, } @article {pmid16498611, year = {2006}, author = {MacNab, YC and Kmetic, A and Gustafson, P and Sheps, S}, title = {An innovative application of Bayesian disease mapping methods to patient safety research: a Canadian adverse medical event study.}, journal = {Statistics in medicine}, volume = {25}, number = {23}, pages = {3960-3980}, doi = {10.1002/sim.2507}, pmid = {16498611}, issn = {0277-6715}, mesh = {Adolescent ; Adult ; *Bayes Theorem ; British Columbia/epidemiology ; Child ; Child, Preschool ; *Data Interpretation, Statistical ; Female ; Humans ; Iatrogenic Disease/*epidemiology ; Infant ; Male ; *Models, Statistical ; Patient Care/*adverse effects ; }, abstract = {Recently developed disease mapping and ecological regression methods have become important techniques in studies of disease epidemiology and in health services research. This increase in importance is partially a result of the development of Bayesian statistical methodologies that make it possible to study associations between health problems and risk factors at an aggregate (i.e. areal) level while taking into account such matters as unmeasured confounding and spatial relationships. In this paper we present a demonstration of the joint use of empirical Bayes (EB) and full Bayesian inferential techniques in a small area study of adverse medical events (also known as 'iatrogenic injury') in British Columbia, Canada. In particular, we illustrate a unified Bayesian hierarchical spatial modelling framework that enables simultaneous examinations of potential associations between adverse medical event occurrence and regional characteristics, age effects, residual variation and spatial autocorrelation. We propose an analytic strategy for complementary use of EB and FB inferential techniques for risk assessment and model selection, presenting an EB-FB combined approach that draws on the strengths of each method while minimizing inherent weaknesses. The work was motivated by the need to explore relatively efficient ways to analyse regional variations of health services outcomes and resource utilization when a considerable amount of statistical modelling and inference are required.}, } @article {pmid16471340, year = {2005}, author = {Li, Z and Wang, Y and Zhang, X and Wu, J}, title = {[Spatial-temporal dynamics of landscape fragmentation in North Shannxi Loess Plateau].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {16}, number = {11}, pages = {2066-2070}, pmid = {16471340}, issn = {1001-9332}, mesh = {China ; *Conservation of Natural Resources ; *Ecosystem ; *Environmental Monitoring ; Geographic Information Systems ; Models, Theoretical ; Satellite Communications ; }, abstract = {The study of landscape fragmentation is an important means to reveal regional ecological processes. By using the remote sensing data of 1987, 1997 and 2002, and the GIS tools, some representative quantitative indices of the landscape spatial structure and landscape fragmentation in North Shannxi Loess Plateau were calculated, aimed to investigate the relationships between landscape ecological structure and landscape pattern in this area. The results showed that cropland contributed most to the extent of landscape fragmentation, but unused land lacked obvious relationship with it. To get large-area images accurately and promptly is very important for monitoring ecological process in regional scale. Moderate-Resolution Imaging Spectroradiometer (MODIS) images in 2003 were used to derive monthly landscape fragmentation information calculated with Local Index of Spatial Associations (LISA) based on Spatial Statistical Analysis (SSA). The analysis of the fragmented landscape types showed that human disturbance had a main contribution to the seasonal landscape fragmentation. Furthermore, with the increasing percentages of cropland and unused land, landscape became more fragmented, while forestland coverage had inverse effects on the fragmentation.}, } @article {pmid16471338, year = {2005}, author = {Yue, W and Xu, J and Xu, L and Tan, W and Mei, A}, title = {[Spatial variance characters of urban synthesis pattern indices at different scales].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {16}, number = {11}, pages = {2053-2059}, pmid = {16471338}, issn = {1001-9332}, mesh = {*City Planning ; Ecology ; *Ecosystem ; *Environment Design ; Geographic Information Systems ; Models, Theoretical ; Satellite Communications ; }, abstract = {Scale holds the key to understand pattern-process interactions, and indeed, becomes one of the corner-stone concepts in landscape ecology. Geographic Information System and remote sensing techniques provide an effective tool to characterize the spatial pattern and spatial heterogeneity at different scales. As an example, these techniques are applied to analyze the urban landscape diversity index, contagion index and fractal dimension on the SPOT remote sensing images at four scales. This paper modeled the semivariogram of these three landscape indices at different scales, and the results indicated that the spatial variance characters of diversity index, contagion index and fractal dimension were similar at different scales, which was spatial dependence. The spatial dependence was showed at each scale, the smaller the scale, the stronger the spatial dependence. With the scale reduced, more details of spatial variance were discovered. The contribution of spatial autocorrelation of these three indices to total spatial variance increased gradually, but when the scale was quite small, spatial variance analysis would destroy the interior structure of landscape system. The semivariogram models of different landscape indices were very different at the same scale, illuminating that these models were incomparable at different scales. According to above analyses and based on the study of urban land use structure, 1 km extent was the more perfect scale for studying the spatial variance of urban landscape pattern in Shanghai. The spatial variance of landscape indices had the character of scale-dependence, and was a function of scale. The results differed at different scales we chose, and thus, the influence of scales on pattern could not be neglected in the research of landscape ecology. The changes of these three landscape indices displayed the regularity of urban spatial structure at different scales, i. e., they were complicated and no regularity at small scale, polycentric at moderate scale, and circle-zoning at big scale.}, } @article {pmid16466373, year = {2006}, author = {Ward, N}, title = {New directions and interactions in metagenomics research.}, journal = {FEMS microbiology ecology}, volume = {55}, number = {3}, pages = {331-338}, doi = {10.1111/j.1574-6941.2005.00055.x}, pmid = {16466373}, issn = {0168-6496}, mesh = {Animals ; *Bacteria/genetics/growth & development/isolation & purification/metabolism ; Computational Biology ; *Ecosystem ; *Environmental Microbiology ; Genome, Bacterial ; Genomics/*methods ; Humans ; Mice ; Research ; }, abstract = {Metagenomics, which aims to access the genomic potential of an environmental sample directly, is a burgeoning area that is generating enormous amounts of biological information. An examination of recent metagenomics literature reveals the discipline to be heading in new and interesting directions, including the investigation of the normal flora of mammals, analysis of ancient genomes, and exploration of the distribution of novel pathways. In addition, the development of new bioinformatics approaches and tools is allowing innovative mining of both existing and new data. Finally, there are indications that the integration of metagenomics with complementary approaches in microbial ecology is beginning.}, } @article {pmid16464845, year = {2006}, author = {Mattaini, MA and McGuire, MS}, title = {Behavioral strategies for constructing nonviolent cultures with youth: a review.}, journal = {Behavior modification}, volume = {30}, number = {2}, pages = {184-224}, doi = {10.1177/0145445503259390}, pmid = {16464845}, issn = {0145-4455}, mesh = {Acculturation ; Adolescent ; Behavior Therapy/*methods ; Child ; Combined Modality Therapy ; Community Networks ; *Cultural Characteristics ; Humans ; Individuality ; Outcome and Process Assessment, Health Care ; Risk ; Social Environment ; Social Problems/*prevention & control/psychology ; *Socialization ; Violence/*prevention & control/psychology ; }, abstract = {Youth violence is widely recognized as a critical social issue in the United States, and many approaches to prevention have been developed in recent years. Emerging research suggests that only approaches that are deeply embedded in cultural, community, and organizational contexts are likely to be powerful enough to have a meaningful collective impact. No programs of this kind that are also truly practical and socially valid have yet reached a level where they can be regarded as well established, but data are beginning to appear that can guide community efforts. In this review, two classes of behavioral programming that appear promising as partial solutions to this need are identified: universal skills training and ecological strategies that focus on interlocking cultural practices. Progressive refinements in both are appearing through programs of developmental research. This paper reviews the state of the science in these efforts.}, } @article {pmid16464253, year = {2006}, author = {Yu, Y and Breitbart, M and McNairnie, P and Rohwer, F}, title = {FastGroupII: a web-based bioinformatics platform for analyses of large 16S rDNA libraries.}, journal = {BMC bioinformatics}, volume = {7}, number = {}, pages = {57}, pmid = {16464253}, issn = {1471-2105}, mesh = {Algorithms ; Computational Biology/*methods ; DNA, Bacterial/*genetics ; *Databases, Nucleic Acid ; Gene Library ; Internet ; Online Systems ; RNA, Ribosomal, 16S/*genetics ; Sequence Alignment/*methods ; Sequence Analysis, DNA/*methods ; *Software ; User-Computer Interface ; }, abstract = {BACKGROUND: High-throughput sequencing makes it possible to rapidly obtain thousands of 16S rDNA sequences from environmental samples. Bioinformatic tools for the analyses of large 16S rDNA sequence databases are needed to comprehensively describe and compare these datasets.

RESULTS: FastGroupII is a web-based bioinformatics platform to dereplicate large 16S rDNA libraries. FastGroupII provides users with the option of four different dereplication methods, performs rarefaction analysis, and automatically calculates the Shannon-Wiener Index and Chao1. FastGroupII was tested on a set of 16S rDNA sequences from coral-associated Bacteria. The different grouping algorithms produced similar, but not identical, results. This suggests that 16S rDNA datasets need to be analyzed in multiple ways when being used for community ecology studies.

CONCLUSION: FastGroupII is an effective bioinformatics tool for the trimming and dereplication of 16S rDNA sequences. Several standard diversity indices are calculated, and the raw sequences are prepared for downstream analyses.}, } @article {pmid16464126, year = {2006}, author = {Wang, X and Grus, WE and Zhang, J}, title = {Gene losses during human origins.}, journal = {PLoS biology}, volume = {4}, number = {3}, pages = {e52}, pmid = {16464126}, issn = {1545-7885}, support = {R01 GM067030/GM/NIGMS NIH HHS/United States ; T32 HG000040/HG/NHGRI NIH HHS/United States ; R01GM067030/GM/NIGMS NIH HHS/United States ; T32HG000040/HG/NHGRI NIH HHS/United States ; }, mesh = {Animals ; Caspases/genetics ; Computational Biology ; *Evolution, Molecular ; Genetic Variation/genetics ; Humans ; Pan troglodytes/*genetics ; Pseudogenes/*genetics ; Species Specificity ; }, abstract = {Pseudogenization is a widespread phenomenon in genome evolution, and it has been proposed to serve as an engine of evolutionary change, especially during human origins (the "less-is-more" hypothesis). However, there has been no comprehensive analysis of human-specific pseudogenes. Furthermore, it is unclear whether pseudogenization itself can be selectively favored and thus play an active role in human evolution. Here we conduct a comparative genomic analysis and a literature survey to identify 80 nonprocessed pseudogenes that were inactivated in the human lineage after its separation from the chimpanzee lineage. Many functions are involved among these genes, with chemoreception and immune response being outstandingly overrepresented, suggesting potential species-specific features in these aspects of human physiology. To explore the possibility of adaptive pseudogenization, we focus on CASPASE12, a cysteinyl aspartate proteinase participating in inflammatory and innate immune response to endotoxins. We provide population genetic evidence that the nearly complete fixation of a null allele at CASPASE12 has been driven by positive selection, probably because the null allele confers protection from severe sepsis. We estimate that the selective advantage of the null allele is about 0.9% and the pseudogenization started shortly before the out-of-Africa migration of modern humans. Interestingly, two other genes related to sepsis were also pseudogenized in humans, possibly by selection. These adaptive gene losses might have occurred because of changes in our environment or genetic background that altered the threat from or response to sepsis. The identification and analysis of human-specific pseudogenes open the door for understanding the roles of gene losses in human origins, and the demonstration that gene loss itself can be adaptive supports and extends the "less-is-more" hypothesis.}, } @article {pmid16462987, year = {2005}, author = {Townson, H and Nathan, MB and Zaim, M and Guillet, P and Manga, L and Bos, R and Kindhauser, M}, title = {Exploiting the potential of vector control for disease prevention.}, journal = {Bulletin of the World Health Organization}, volume = {83}, number = {12}, pages = {942-947}, pmid = {16462987}, issn = {0042-9686}, mesh = {Animals ; Communicable Disease Control/*organization & administration ; *Community Networks ; Cooperative Behavior ; Developing Countries ; Geographic Information Systems ; Global Health ; Health Care Reform ; Humans ; Insect Control/*organization & administration ; *Insect Vectors/microbiology/virology ; *Insecticides ; *Interinstitutional Relations ; Tropical Medicine ; }, abstract = {Although vector control has proven highly effective in preventing disease transmission, it is not being used to its full potential, thereby depriving disadvantaged populations of the benefits of well tried and tested methods. Following the discovery of synthetic residual insecticides in the 1940s, large-scale programmes succeeded in bringing many of the important vector-borne diseases under control. By the late 1960s, most vector-borne diseases--with the exception of malaria in Africa--were no longer considered to be of primary public health importance. The result was that control programmes lapsed, resources dwindled, and specialists in vector control disappeared from public health units. Within two decades, many important vector-borne diseases had re-emerged or spread to new areas. The time has come to restore vector control to its key role in the prevention of disease transmission, albeit with an increased emphasis on multiple measures, whether pesticide-based or involving environmental modification, and with a strengthened managerial and operational capacity. Integrated vector management provides a sound conceptual framework for deployment of cost-effective and sustainable methods of vector control. This approach allows for full consideration of the complex determinants of disease transmission, including local disease ecology, the role of human activity in increasing risks of disease transmission, and the socioeconomic conditions of affected communities.}, } @article {pmid16460763, year = {2006}, author = {Dieckmann, U and Heino, M and Parvinen, K}, title = {The adaptive dynamics of function-valued traits.}, journal = {Journal of theoretical biology}, volume = {241}, number = {2}, pages = {370-389}, doi = {10.1016/j.jtbi.2005.12.002}, pmid = {16460763}, issn = {0022-5193}, mesh = {Adaptation, Biological/*genetics ; Animals ; *Biological Evolution ; Computational Biology ; Ecosystem ; *Models, Genetic ; *Quantitative Trait, Heritable ; Seasons ; Selection, Genetic ; }, abstract = {This study extends the framework of adaptive dynamics to function-valued traits. Such adaptive traits naturally arise in a great variety of settings: variable or heterogeneous environments, age-structured populations, phenotypic plasticity, patterns of growth and form, resource gradients, and in many other areas of evolutionary ecology. Adaptive dynamics theory allows analysing the long-term evolution of such traits under the density-dependent and frequency-dependent selection pressures resulting from feedback between evolving populations and their ecological environment. Starting from individual-based considerations, we derive equations describing the expected dynamics of a function-valued trait in asexually reproducing populations under mutation-limited evolution, thus generalizing the canonical equation of adaptive dynamics to function-valued traits. We explain in detail how to account for various kinds of evolutionary constraints on the adaptive dynamics of function-valued traits. To illustrate the utility of our approach, we present applications to two specific examples that address, respectively, the evolution of metabolic investment strategies along resource gradients, and the evolution of seasonal flowering schedules in temporally varying environments.}, } @article {pmid16456624, year = {2006}, author = {Le Pichon, C and Gorges, G and Boët, P and Baudry, J and Goreaud, F and Faure, T}, title = {A spatially explicit resource-based approach for managing stream fishes in riverscapes.}, journal = {Environmental management}, volume = {37}, number = {3}, pages = {322-335}, pmid = {16456624}, issn = {0364-152X}, mesh = {Animals ; *Conservation of Natural Resources ; Diet ; Ecology ; *Fishes ; Geographic Information Systems ; Models, Theoretical ; Population Dynamics ; Reproduction ; *Rivers ; }, abstract = {The article describes a riverscape approach based on landscape ecology concepts, which aims at studying the multiscale relationships between the spatial pattern of stream fish habitat patches and processes depending on fish movements. A review of the literature shows that few operational methods are available to study this relationship due to multiple methodological and practical challenges inherent to underwater environments. We illustrated the approach with literature data on a cyprinid species (Barbus barbus) and an actual riverscape of the Seine River, France. We represented the underwater environment of fishes for different discharges using two-dimensional geographic information system-based maps of the resource habitat patches, defined according to activities (feeding, resting, and spawning). To quantify spatial patterns at nested levels (resource habitat patch, daily activities area, subpopulation area), we calculated their composition, configuration, complementation, and connectivity with multiple spatial analysis methods: patch metrics, moving-window analysis, and least cost modeling. The proximity index allowed us to evaluate habitat patches of relatively great value, depending on their spatial context, which contributes to the setting of preservation policies. The methods presented to delimit potential daily activities areas and subpopulation areas showed the potential gaps in the biological connectivity of the reach. These methods provided some space for action in restoration schemes.}, } @article {pmid16454915, year = {2006}, author = {Streibel, T and Hafner, K and Mühlberger, F and Adam, T and Zimmermann, R}, title = {Resonance-enhanced multiphoton ionization time-of-flight mass spectrometry for detection of nitrogen containing aliphatic and aromatic compounds: resonance-enhanced multiphoton ionization spectroscopic investigation and on-line analytical application.}, journal = {Applied spectroscopy}, volume = {60}, number = {1}, pages = {72-79}, doi = {10.1366/000370206775382767}, pmid = {16454915}, issn = {0003-7028}, mesh = {Air Pollutants/*analysis ; Environmental Monitoring/*instrumentation/methods ; Equipment Design ; Equipment Failure Analysis ; Flow Injection Analysis/instrumentation/methods ; Hydrocarbons, Aromatic/*analysis ; Industrial Waste/*analysis ; Microscopy, Fluorescence, Multiphoton/*instrumentation/methods ; Nitrogen Compounds/*analysis ; Online Systems ; Spectrometry, Mass, Electrospray Ionization/*instrumentation/methods ; }, abstract = {Resonance-enhanced multiphoton ionization (REMPI) combined with time-of-flight mass spectrometry (TOFMS) is an analytical method capable of on-line monitoring of trace compounds in complex matrices. A necessary prerequisite for substance selective detection is spectroscopic investigation of the target molecules. Several organic nitrogen compounds comprising aliphatic and aromatic amines, nitrogen heterocyclic compounds, and aromatic nitriles are spectroscopically investigated with a tunable narrow bandwidth optical parametric oscillator (OPO) laser system providing a scannable wavelength range between 220 and 340 nm. These species are known as possible precursors in fuel-NO formation from combustion of solid fuels such as biomass and waste. A newly conceived double inlet system was used in this study, which allows rapid change between effusive and supersonic molecular beams. The resulting REMPI spectra of the compounds are discussed with respect to electronic transitions that could be utilized for a selective ionization of these compounds in complex mixtures such as combustion and process gases. The practicability of this approach is demonstrated by wavelength selected on-line REMPI-TOFMS detection of aniline and cyanonaphthalene in the burning chamber of a waste incineration plant. REMPI mass spectra recorded at different excitation wavelengths as well as variations in time show the utilization of species-selective REMPI-TOFMS detection for on-line monitoring of crucial substances in pollutant formation.}, } @article {pmid16443385, year = {2007}, author = {Fan, Z and Lackland, DT and Lipsitz, SR and Nicholas, JS and Egan, BM and Tim Garvey, W and Hutchison, FN}, title = {Geographical patterns of end-stage renal disease incidence and risk factors in rural and urban areas of South Carolina.}, journal = {Health & place}, volume = {13}, number = {1}, pages = {179-187}, doi = {10.1016/j.healthplace.2005.12.002}, pmid = {16443385}, issn = {1353-8292}, mesh = {Adolescent ; Adult ; Black or African American/*statistics & numerical data ; Age Distribution ; Aged ; Child ; Child, Preschool ; Female ; *Geographic Information Systems ; Geography ; Health Services Accessibility ; Humans ; Incidence ; Infant ; Infant, Newborn ; Kidney Failure, Chronic/epidemiology/*ethnology ; Male ; Middle Aged ; Registries ; Risk Factors ; Rural Health/*statistics & numerical data ; South Carolina/epidemiology ; Urban Health/*statistics & numerical data ; White People/*statistics & numerical data ; }, abstract = {To assess the geographical patterns of end-stage renal disease (ESRD) incidence and to identify the risk factors on the regional differences, the authors conducted an ecological study on incidence of ESRD and related risk factors in the 46 counties of South Carolina (SC). Age and gender adjusted, race specific incidence rates for each county in SC were calculated for the 11,346 ESRD patients of all ages who registered in the United States Renal Data Systems Network 6 from 1990 to 1999. County level exposure measures on population physician density, hospitalization rates of diabetes and hypertension, per capita income, percent college degree, and percent below poverty were evaluated. There was a significant increase in mean incidence rates of ESRD from 1990 to 1999 in SC (p<0.0001). The incidence rates were consistently higher in rural than in urban counties. Population physician density (relative risk (RR) 0.49, 95% confidence interval (95%Cl, 0.41-0.58) and rural residence (adjusted RR 1.66, 95%Cl 1.59-1.74) were significantly associated with ESRD incidence. The strong relationship between ESRD and physician density suggests that access to adequate treatment of diabetes and hypertension is of paramount importance for ESRD prevention, and has important public policy implications.}, } @article {pmid16437074, year = {2006}, author = {Check, E}, title = {Treasure island: pinning down a model ecosystem.}, journal = {Nature}, volume = {439}, number = {7075}, pages = {378-379}, doi = {10.1038/439378a}, pmid = {16437074}, issn = {1476-4687}, mesh = {Animals ; Anthozoa/physiology ; *Biodiversity ; Classification/methods ; Databases, Factual ; Ecology/*methods/*trends ; Electronic Data Processing/trends ; Fishes/genetics/physiology ; *Geography ; Humans ; Insecta/genetics ; *Models, Biological ; Species Specificity ; }, } @article {pmid16430924, year = {2006}, author = {Seligmann, H and Krishnan, NM and Rao, BJ}, title = {Possible multiple origins of replication in primate mitochondria: Alternative role of tRNA sequences.}, journal = {Journal of theoretical biology}, volume = {241}, number = {2}, pages = {321-332}, doi = {10.1016/j.jtbi.2005.11.035}, pmid = {16430924}, issn = {0022-5193}, mesh = {Animals ; Computational Biology ; DNA Replication/*genetics ; DNA, Mitochondrial/*genetics ; Evolution, Molecular ; Mitochondria/*genetics ; Models, Genetic ; Multigene Family/genetics ; Mutation ; Primates/*genetics ; RNA, Transfer/*genetics ; Species Specificity ; }, abstract = {DNA replication in vertebrate mitochondria is usually directional, leaving different portions of the genome single-stranded for different periods of time. During this time, mutations resulting from deaminations of cytosines to thymines and adenines to guanines accumulate on the heavy strand. Therefore, T/C and G/A ratios increase along mitochondrial genomes, proportionally to the time spent single-stranded during replication. Such trends exist at third codon positions for base ratios averaged across genes in individual genomes as well as for gene-specific and site-specific substitution frequencies estimated using phylogenetic methods. We use multiple regressions to test for the potential functioning of all 12 tRNA clusters in 19 primate mitochondrial genomes as alternative origins of light strand replication (OL). We provide a general algorithm for calculating time spent single stranded by a given site for any possible locations of the site and OL. For codon positions 1, 2, and 3, respectively, 23%, 9% and 35% of tRNA gene clusters have significant (p < 0.05) deamination gradients originating from them. The strength of the deamination gradient originating from tRNA gene clusters varies among species, and for five clusters, correlates with the tendency of tRNA genes in each of these clusters to form secondary structures that resemble the OL's structure. This is notably true for all codon positions for tRNA-Lys, which in absence of nuclear regulation, forms secondary structures resembling the hairpin structure of OL. For two tRNA gene clusters, correlations were statistically significant, but opposite to the direction expected by the known unidirectional replication, putatively compatible with bi-directional replication. Few substitutions in tRNA sequences can be neutral at the level of cloverleaf structure and function, yet significantly alter capacities to form OL-like structures, causing sudden evolution of genome-wide nucleotide contents.}, } @article {pmid16428258, year = {2006}, author = {Wakefield, J and Shaddick, G}, title = {Health-exposure modeling and the ecological fallacy.}, journal = {Biostatistics (Oxford, England)}, volume = {7}, number = {3}, pages = {438-455}, doi = {10.1093/biostatistics/kxj017}, pmid = {16428258}, issn = {1465-4644}, support = {R01 CA095994/CA/NCI NIH HHS/United States ; }, mesh = {Aged ; Air Pollution/*adverse effects/analysis ; Bias ; Computer Simulation ; Data Interpretation, Statistical ; Environmental Exposure/adverse effects/analysis ; Geography ; Humans ; London/epidemiology ; Lung Diseases/*mortality ; Models, Statistical ; Sulfur Dioxide/*adverse effects ; }, abstract = {Recently, there has been an increased interest in modeling the association between aggregate disease counts and environmental exposures measured, for example via air pollution monitors, at point locations. This paper has two aims: first, we develop a model for such data in order to avoid ecological bias; second, we illustrate that modeling the exposure surface and estimating exposures may lead to bias in estimation of health effects. Design issues are also briefly considered, in particular the loss of information in moving from individual to ecological data, and the at-risk populations to consider in relation to the pollution monitor locations. The approach is investigated initially through simulations, and is then applied to a study of the association between mortality in those over 65 in the year 2000 and the previous year's SO2, in London. We conclude that the use of the proposed model can provide valid inference, but the use of estimated exposures should be carried out with great caution.}, } @article {pmid16426458, year = {2006}, author = {Ma, Z and Yu, J and Kang, L}, title = {LocustDB: a relational database for the transcriptome and biology of the migratory locust (Locusta migratoria).}, journal = {BMC genomics}, volume = {7}, number = {}, pages = {11}, pmid = {16426458}, issn = {1471-2164}, mesh = {Animals ; *Databases, Genetic ; Expressed Sequence Tags/chemistry ; *Genome, Insect ; Genomics ; Internet ; Locusta migratoria/*genetics/metabolism/physiology ; Transcription, Genetic ; User-Computer Interface ; }, abstract = {BACKGROUND: The migratory locust (Locusta migratoria) is an orthopteran pest and a representative member of hemimetabolous insects for biological studies. Its transcriptomic data provide invaluable information for molecular entomology and pave a way for the comparative research of other medically, agronomically, and ecologically relevant insects. We developed the first transcriptomic database of the locust (LocustDB), building necessary infrastructures to integrate, organize, and retrieve data that are either currently available or to be acquired in the future.

DESCRIPTION: LocustDB currently hosts 45,474 high-quality EST sequences from the locust, which were assembled into 12,161 unigenes. It, through user-friendly web interfaces, allows investigators to freely access sequence data, including homologous/orthologous sequences, functional annotations, and pathway analysis, based on conserved orthologous groups (COG), gene ontology (GO), protein domain (InterPro), and functional pathways (KEGG). It also provides information from comparative analysis based on data from the migratory locust and five other invertebrate species, including the silkworm, the honeybee, the fruitfly, the mosquito and the nematode. The website address of LocustDB is http://locustdb.genomics.org.cn/.

CONCLUSION: LocustDB starts with the first transcriptome information for an orthopteran and hemimetabolous insect and will be extended to provide a framework for incorporating in-coming genomic data of relevant insect groups and a workbench for cross-species comparative studies.}, } @article {pmid16412246, year = {2006}, author = {Green, CG and Krause, DO and Wylie, JL}, title = {Spatial analysis of campylobacter infection in the Canadian province of Manitoba.}, journal = {International journal of health geographics}, volume = {5}, number = {}, pages = {2}, pmid = {16412246}, issn = {1476-072X}, mesh = {Adolescent ; Adult ; Campylobacter Infections/*epidemiology ; Canada/epidemiology ; Child ; Child, Preschool ; Databases as Topic ; *Demography ; Female ; Geography ; Humans ; Incidence ; Infant ; Infant, Newborn ; Male ; Manitoba/epidemiology ; Models, Statistical ; Risk Factors ; Seasons ; Time Factors ; }, abstract = {BACKGROUND: The study describes population level variations in campylobacter incidence within the Canadian province of Manitoba, and the relationship to sociodemographic and landscape related characteristics. Using data derived from the Manitoba Health Public Health Branch communicable disease surveillance database, the study applied a number of spatial and ecological techniques to visualize, explore and model campylobacter incidence for the years 1996 to 2004. Analytical techniques used in the study included spatial smoothing, the spatial scan statistic, the Gini coefficient, and Poisson regression analysis.

RESULTS: The study demonstrated marked and statistically significant geographic variability in the rates of campylobacter incidence in Manitoba.. The incidence of campylobacter was observed to be significantly higher in populations living in rural and agricultural areas of the province, with the highest rates occurring in populations living in proximity to high densities of farm animals (cows, pigs, chickens). The study also observed that the age specific pattern of campylobacter incidence in rural Manitoba was very different than the urban pattern, with the incidence rate in the 0-4 year age group seven times higher in rural Manitoba than in the City of Winnipeg.

CONCLUSION: The study demonstrates the value of a deploying a diverse set of spatial techniques to better understand the dynamics of an enteric disease such as campylobacter infection. The study concludes that there may be three distinct mechanisms for the transmission of campylobacter in Manitoba which are operating simultaneously. These include broad population exposure to a centralized food system endemically infected with the campylobacter organism, exposure to local level factors such as farm animals or contaminated water, and exposure to campylobacter infection through foreign travel.}, } @article {pmid16410010, year = {2006}, author = {Baverstock, J and Roy, HE and Clark, SJ and Alderson, PG and Pell, JK}, title = {Effect of fungal infection on the reproductive potential of aphids and their progeny.}, journal = {Journal of invertebrate pathology}, volume = {91}, number = {2}, pages = {136-139}, doi = {10.1016/j.jip.2005.11.005}, pmid = {16410010}, issn = {0022-2011}, mesh = {Animals ; Aphids/*microbiology/*physiology ; Data Interpretation, Statistical ; Entomophthorales/*isolation & purification/physiology ; Hypocreales/*isolation & purification/physiology ; Nymph/growth & development ; Reproduction ; Time Factors ; }, abstract = {The effect of infection by Pandora neoaphidis and Beauveria bassiana on the reproductive potential of the pea aphid, Acyrthosiphon pisum, and their progeny was assessed. Infection by either P. neoaphidis or B. bassiana reduced the number of nymphs produced within 24 h of inoculation and over the entire infection period compared to uninfected aphids. However, infection by either P. neoaphidis or B. bassiana for 24 or 72 h did not alter the intrinsic rate of increase of the host aphid's progeny. Therefore, fungal infection appears to have no indirect effects on the fitness of the host's progeny.}, } @article {pmid16409639, year = {2006}, author = {Xu, Y and Glansdorff, N and Labedan, B}, title = {Bioinformatic analysis of an unusual gene-enzyme relationship in the arginine biosynthetic pathway among marine gamma proteobacteria: implications concerning the formation of N-acetylated intermediates in prokaryotes.}, journal = {BMC genomics}, volume = {7}, number = {}, pages = {4}, pmid = {16409639}, issn = {1471-2164}, mesh = {Acetylation ; Acetyltransferases/genetics/metabolism ; Amino Acid Sequence ; Arginine/*biosynthesis ; Argininosuccinate Lyase/genetics/metabolism ; Computational Biology ; Conserved Sequence ; Evolution, Molecular ; Gammaproteobacteria/classification/enzymology/*genetics/*metabolism ; Gene Fusion ; Genes, Bacterial ; Genomics ; Marine Biology ; Models, Biological ; Molecular Sequence Data ; Moritella/enzymology/genetics ; Phylogeny ; Prokaryotic Cells ; Sequence Homology, Amino Acid ; }, abstract = {BACKGROUND: The N-acetylation of L-glutamate is regarded as a universal metabolic strategy to commit glutamate towards arginine biosynthesis. Until recently, this reaction was thought to be catalyzed by either of two enzymes: (i) the classical N-acetylglutamate synthase (NAGS, gene argA) first characterized in Escherichia coli and Pseudomonas aeruginosa several decades ago and also present in vertebrates, or (ii) the bifunctional version of ornithine acetyltransferase (OAT, gene argJ) present in Bacteria, Archaea and many Eukaryotes. This paper focuses on a new and surprising aspect of glutamate acetylation. We recently showed that in Moritella abyssi and M. profunda, two marine gamma proteobacteria, the gene for the last enzyme in arginine biosynthesis (argH) is fused to a short sequence that corresponds to the C-terminal, N-acetyltransferase-encoding domain of NAGS and is able to complement an argA mutant of E. coli. Very recently, other authors identified in Mycobacterium tuberculosis an independent gene corresponding to this short C-terminal domain and coding for a new type of NAGS. We have investigated the two prokaryotic Domains for patterns of gene-enzyme relationships in the first committed step of arginine biosynthesis.

RESULTS: The argH-A fusion, designated argH(A), and discovered in Moritella was found to be present in (and confined to) marine gamma proteobacteria of the Alteromonas- and Vibrio-like group. Most of them have a classical NAGS with the exception of Idiomarina loihiensis and Pseudoalteromonas haloplanktis which nevertheless can grow in the absence of arginine and therefore appear to rely on the arg(A) sequence for arginine biosynthesis. Screening prokaryotic genomes for virtual argH-X 'fusions' where X stands for a homologue of arg(A), we retrieved a large number of Bacteria and several Archaea, all of them devoid of a classical NAGS. In the case of Thermus thermophilus and Deinococcus radiodurans, the arg(A)-like sequence clusters with argH in an operon-like fashion. In this group of sequences, we find the short novel NAGS of the type identified in M. tuberculosis. Among these organisms, at least Thermus, Mycobacterium and Streptomyces species appear to rely on this short NAGS version for arginine biosynthesis.

CONCLUSION: The gene-enzyme relationship for the first committed step of arginine biosynthesis should now be considered in a new perspective. In addition to bifunctional OAT, nature appears to implement at least three alternatives for the acetylation of glutamate. It is possible to propose evolutionary relationships between them starting from the same ancestral N-acetyltransferase domain. In M. tuberculosis and many other bacteria, this domain evolved as an independent enzyme, whereas it fused either with a carbamate kinase fold to give the classical NAGS (as in E. coli) or with argH as in marine gamma proteobacteria. Moreover, there is an urgent need to clarify the current nomenclature since the same gene name argA has been used to designate structurally different entities. Clarifying the confusion would help to prevent erroneous genomic annotation.}, } @article {pmid16404536, year = {2006}, author = {Oliveira, SV and Cortes, RM}, title = {Combining logistic models with multivariate methods for the rapid biological assessment of rivers using macroinvertebrates.}, journal = {Environmental monitoring and assessment}, volume = {112}, number = {1-3}, pages = {93-113}, pmid = {16404536}, issn = {0167-6369}, mesh = {Altitude ; Animals ; Biodiversity ; Ecosystem ; Environmental Monitoring/*methods ; Environmental Pollution/*analysis ; Geographic Information Systems ; Invertebrates/classification/*growth & development ; Logistic Models ; Multivariate Analysis ; Population Density ; Population Dynamics ; Portugal ; *Rivers ; }, abstract = {This work represents an attempt to define a simple method to classify the relative degree of disturbance of sites in lotic systems on the basis of comparison of their faunistic composition with reference sites. Two ecotypes were selected in northern Portugal where benthic invertebrates were sampled in reaches with different levels of contamination. As a first stage, previous Geographic Information System information was used to define reference sites in each ecotype. Afterwards, multivariate techniques and non linear estimation models were combined to assess biological quality. This method allowed us to quantify sites according to increasing levels of contamination, after the probabilities of occurrence of taxa along a gradient of contamination taking into account the reference condition. The results suggest that this method is sensitive to organic pollution, easy to interpret, namely the species tolerance, and could be a good framework to establish regional rankings depending on the ecological impact of river sites.}, } @article {pmid16404535, year = {2006}, author = {Wang, Z and Zhang, B and Zhang, S and Li, X and Liu, D and Song, K and Li, J and Li, F and Duan, H}, title = {Changes of land use and of ecosystem service values in Sanjiang Plain, Northeast China.}, journal = {Environmental monitoring and assessment}, volume = {112}, number = {1-3}, pages = {69-91}, pmid = {16404535}, issn = {0167-6369}, mesh = {Agriculture/*trends ; China ; *Conservation of Natural Resources ; *Ecosystem ; Environmental Monitoring ; Geographic Information Systems ; Rivers ; }, abstract = {Agricultural activities, especially reclamation, are considered major threats to the wetland ecosystems in Sanjiang Plain, the largest concentrated area of the freshwater wetlands in China. In the past decades, the area of the cultivated land and its grain production have been increased at the cost of wetlands shrinkage. The large-scale land reclamation severely affected the ecosystems in this region. However, such effects at the regional scale are seldom evaluated quantitatively. We used three datasets of LANDSAT MSS and/or TM imagery to estimate the area changes and the transition of land use types from 1980 to 2000. We also valued changes in ecosystem services delivered by each land category using value coefficients published by Costanza et al. Sensitivity analysis suggested that these estimates were relatively robust. Finally, the contribution of various ecosystem functions was ranked to the overall value of the ecosystem services in this study. According to our estimates, the total annual ecosystem service values in Sanjiang Plain have declined by about 40% between 1980 and 2000 (156284-182572.18 million US dollars in total over 20 years). This substantial decline is largely attributed to the 53.4% loss of wetlands. For individual ecosystem functions, waste treatment, water supply and disturbance regulation account for more than 60% to the total ecological values. During those two decades, the contribution of disturbance regulation, cultural and recreation decreased, while the contribution of water regulation, nutrient cycling, food production, raw materials and climate regulation increased during the same period. We also put forward a few proposals concerning the future land use policy formulation and sustainable ecosystems. They are adjusting the 'food first' agricultural policy, establishing more nature reserves for wetlands, creating systems for the rational use of water, harnessing the degraded cultivated land and encouraging eco-tourism.}, } @article {pmid16403854, year = {2006}, author = {Burgoon, LD and Boutros, PC and Dere, E and Zacharewski, TR}, title = {dbZach: A MIAME-compliant toxicogenomic supportive relational database.}, journal = {Toxicological sciences : an official journal of the Society of Toxicology}, volume = {90}, number = {2}, pages = {558-568}, doi = {10.1093/toxsci/kfj097}, pmid = {16403854}, issn = {1096-6080}, support = {ES 011271/ES/NIEHS NIH HHS/United States ; ES 011777/ES/NIEHS NIH HHS/United States ; ES 04911-12/ES/NIEHS NIH HHS/United States ; T32 ES07255/ES/NIEHS NIH HHS/United States ; }, mesh = {Animals ; *Database Management Systems ; *Databases, Factual ; Humans ; Oligonucleotide Array Sequence Analysis ; Polymerase Chain Reaction ; Risk Assessment ; *Toxicogenetics ; Toxicology ; }, abstract = {Quantitative risk assessment and the elucidation of mechanisms of toxicity requires computational infrastructure and innovative analysis approaches that systematically consider available data at all levels of biological organization. dbZach (http://dbzach.fst.msu.edu) is a modular relational database with associated data insertion, retrieval, and mining tools that manages traditional toxicology and complementary toxicogenomic data to facilitate comprehensive data integration, analysis, and sharing. It consists of four Core Subsystems (i.e., Clones, Genes, Sample Annotation, and Protocols), four Experimental Subsystems (i.e., Microarray, Affymetrix, Real-Time PCR, and Toxicology), and three Computational Subsystems (i.e., Gene Regulation, Pathways, Orthology) that comply with the Minimum Information About a Microarray Experiment (MIAME) standard. It is capable of including emerging technologies and other model systems, including ecologically relevant species. dbZach represents an enterprise toxicogenomic data management system which facilitates data integration and analysis, and reduces uncertainties in the continuum from initial exposure to toxicity while facilitating more comprehensive elucidations of mechanisms of toxicity and supporting mechanistically-based quantitative risk assessment.}, } @article {pmid16403533, year = {2006}, author = {Soyer, OS and Pfeiffer, T and Bonhoeffer, S}, title = {Simulating the evolution of signal transduction pathways.}, journal = {Journal of theoretical biology}, volume = {241}, number = {2}, pages = {223-232}, doi = {10.1016/j.jtbi.2005.11.024}, pmid = {16403533}, issn = {0022-5193}, mesh = {Animals ; Bacteria/genetics ; Chemotaxis/genetics ; Computational Biology ; *Evolution, Molecular ; *Models, Genetic ; Signal Transduction/*genetics ; }, abstract = {We use a generic model of a network of proteins that can activate or deactivate each other to explore the emergence and evolution of signal transduction networks and to gain a basic understanding of their general properties. Starting with a set of non-interacting proteins, we evolve a signal transduction network by random mutation and selection to fulfill a complex biological task. In order to validate this approach we base selection on a fitness function that captures the essential features of chemotactic behavior as seen in bacteria. We find that a system of as few as three proteins can evolve into a network mediating chemotaxis-like behavior by acting as a "derivative sensor". Furthermore, we find that the dynamics and topology of such networks show many similarities to the natural chemotaxis pathway, that the response magnitude can increase with increasing network size and that network behavior shows robustness towards variations in some of the internal parameters. We conclude that simulating the evolution of signal transduction networks to mediate a certain behavior may be a promising approach for understanding the general properties of the natural pathway for that behavior.}, } @article {pmid16393650, year = {2006}, author = {Lettieri, T}, title = {Recent applications of DNA microarray technology to toxicology and ecotoxicology.}, journal = {Environmental health perspectives}, volume = {114}, number = {1}, pages = {4-9}, pmid = {16393650}, issn = {0091-6765}, mesh = {Animals ; Databases, Genetic ; *Ecology ; *Gene Expression Profiling ; Humans ; *Oligonucleotide Array Sequence Analysis ; Toxicogenetics ; *Toxicology ; }, abstract = {Gene expression is a unique way of characterizing how cells and organisms adapt to changes in the external environment. The measurements of gene expression levels upon exposure to a chemical can be used both to provide information about the mechanism of action of the toxicant and to form a sort of "genetic signature" for the identification of toxic products. The development of high-quality, commercially available gene arrays has allowed this technology to become a standard tool in molecular toxicology. Several national and international initiatives have provided the proof-of-principle tests for the application of gene expression for the study of the toxicity of new and existing chemical compounds. In the last few years the field has progressed from evaluating the potential of the technology to illustrating the practical use of gene expression profiling in toxicology. The application of gene expression profiling to ecotoxicology is at an earlier stage, mainly because of the the many variables involved in analyzing the status of natural populations. Nevertheless, significant studies have been carried out on the response to environmental stressors both in model and in nonmodel organisms. It can be easily predicted that the development of stressor-specific signatures in gene expression profiling in ecotoxicology will have a major impact on the ecotoxicology field in the near future. International collaborations could play an important role in accelerating the application of genomic approaches in ecotoxicology.}, } @article {pmid16389922, year = {2005}, author = {Hanson, D and Hanson, J and Vardon, P and McFarlane, K and Lloyd, J and Muller, R and Durrheim, D}, title = {The injury iceberg: an ecological approach to planning sustainable community safety interventions.}, journal = {Health promotion journal of Australia : official journal of Australian Association of Health Promotion Professionals}, volume = {16}, number = {1}, pages = {5-10}, doi = {10.1071/he05005}, pmid = {16389922}, issn = {1036-1073}, mesh = {Accident Prevention ; Community Health Services/*organization & administration ; Community Networks/organization & administration ; Health Promotion/*organization & administration ; Humans ; *Safety ; Wounds and Injuries/*prevention & control ; }, abstract = {ISSUE ADDRESSED: A systematic ecological framework in which to design sustainable, community-based, safety promotion interventions is presented.

METHOD: A literature review was undertaken of English-language articles addressing the topics of 'ecological injury prevention or safety promotion', 'ecological health promotion', 'sustainable economic, health or ecological systems' and 'steady state', with 143 articles retrieved and reviewed.

RESULTS: Injury prevention is a biomedical construct, in which injury is perceived to be a physical event resulting from the sudden release of environmental energy producing tissue damage in an individual. This reductionist perspective overlooks the importance of psychological and sociological determinants of injury. Safety has physical, psychological and sociological dimensions. It is inherently an ecological concept. Interventions aiming to achieve long-term improvements in community safety must seek to develop sustainable safety promoting characteristics within the target community.

CONCLUSION: To reduce a community's risk of injury and sustain this lowered risk, the community 'ecological system' must have access to the resources necessary to maintain the desired outcome and the ability to mobilise these resources.}, } @article {pmid16385774, year = {2005}, author = {Lockhart, P and Steel, M}, title = {A tale of two processes.}, journal = {Systematic biology}, volume = {54}, number = {6}, pages = {948-951}, doi = {10.1080/10635150500234682}, pmid = {16385774}, issn = {1063-5157}, mesh = {Algorithms ; Base Sequence ; Biological Evolution ; Classification/*methods ; Data Interpretation, Statistical ; Likelihood Functions ; *Models, Biological ; *Phylogeny ; Reproducibility of Results ; }, } @article {pmid16385183, year = {2005}, author = {Lukasiewicz, M and Benyamina, A and Reynaud, M and Falissard, B}, title = {An in vivo study of the relationship between craving and reaction time during alcohol detoxification using the ecological momentary assessment.}, journal = {Alcoholism, clinical and experimental research}, volume = {29}, number = {12}, pages = {2135-2143}, doi = {10.1097/01.alc.0000191760.42980.50}, pmid = {16385183}, issn = {0145-6008}, mesh = {Adolescent ; Adult ; Affect/physiology ; Age Factors ; Aged ; Alcoholism/*psychology/*rehabilitation ; Antidepressive Agents/therapeutic use ; Anxiety/psychology ; Benzodiazepines/therapeutic use ; Cognition/physiology ; Data Interpretation, Statistical ; Female ; Humans ; Hypnotics and Sedatives/therapeutic use ; Male ; Middle Aged ; Motivation ; Pilot Projects ; Predictive Value of Tests ; Psychiatric Status Rating Scales ; Reaction Time/*physiology ; Sample Size ; Sex Factors ; Smoking/psychology ; }, abstract = {BACKGROUND: To study cognitive interference associated with craving for alcohol, the Ecological Momentary Assessment (EMA) method was used to measure the relationship between craving and reaction time. A secondary aim was the study of the predictive factors for craving during alcohol detoxification. The EMA enables both repeated measures of craving in a natural setting and the recording of reaction time without the patient being aware of this.

METHODS: Craving for alcohol, reaction time, sadness and anxiety were recorded 8 to 12 times a day, over three weeks of detoxification in 14 alcoholics (n=1767 measures), on an electronic diary issuing random prompts. Mixed models were used for statistical analysis (alpha=5%, 1-beta=88%).

RESULTS: Reaction time was significantly increased in univariate analysis when a craving episode occurred but this difference did not persist after multivariate analysis. Craving episodes were more frequent and intense than previously reported. Predictive factors of craving during detoxification were: age, gender, sadness, anxiety and the number of previous detoxifications. Antidepressants, anti-craving medications but not benzodiazepines were negatively associated to craving.}, } @article {pmid16381894, year = {2006}, author = {Lombardot, T and Kottmann, R and Pfeffer, H and Richter, M and Teeling, H and Quast, C and Glöckner, FO}, title = {Megx.net--database resources for marine ecological genomics.}, journal = {Nucleic acids research}, volume = {34}, number = {Database issue}, pages = {D390-3}, pmid = {16381894}, issn = {1362-4962}, mesh = {*Databases, Genetic ; *Ecology ; *Genome, Archaeal ; *Genome, Bacterial ; Genomics ; Internet ; Oceans and Seas ; Software ; User-Computer Interface ; }, abstract = {Marine microbial genomics and metagenomics is an emerging field in environmental research. Since the completion of the first marine bacterial genome in 2003, the number of fully sequenced marine bacteria has grown rapidly. Concurrently, marine metagenomics studies are performed on a regular basis, and the resulting number of sequences is growing exponentially. To address environmentally relevant questions like organismal adaptations to oceanic provinces and regional differences in the microbial cycling of nutrients, it is necessary to couple sequence data with geographical information and supplement them with contextual information like physical, chemical and biological data. Therefore, new specialized databases are needed to organize and standardize data storage as well as centralize data access and interpretation. We introduce Megx.net, a set of databases and tools that handle genomic and metagenomic sequences in their environmental contexts. Megx.net includes (i) a geographic information system to systematically store and analyse marine genomic and metagenomic data in conjunction with contextual information; (ii) an environmental genome browser with fast search functionalities; (iii) a database with precomputed analyses for selected complete genomes; and (iv) a database and tool to classify metagenomic fragments based on oligonucleotide signatures. These integrative databases and webserver will help researchers to generate a better understanding of the functioning of marine ecosystems. All resources are freely accessible at http://www.megx.net.}, } @article {pmid16381455, year = {2005}, author = {Guo, LP and Huang, LQ and Jiang, YX}, title = {[Application of "3S" technologies in continuous usage of traditional Chinese medicine resources].}, journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica}, volume = {30}, number = {18}, pages = {1397-1400}, pmid = {16381455}, issn = {1001-5302}, mesh = {*Conservation of Natural Resources ; *Drugs, Chinese Herbal ; Ecosystem ; *Geographic Information Systems ; Geography ; Medicine, Chinese Traditional ; Pest Control ; Plant Diseases ; *Plants, Medicinal ; Satellite Communications ; Soil ; }, abstract = {This paper introduced development of 3S technologies, i.e., remote sensing (RS), geographic information system (GIS), and global positioning system(GPS), and drew the conclusion that 3S technologies can be used widely in resources dynasty survey, ecology study, and geoherbs study and classification about traditional Chinese medicine resources.}, } @article {pmid16380750, year = {2005}, author = {Salaffi, F and Stancati, A and Procaccini, R and Cioni, F and Grassi, W}, title = {[Assessment of circadian rhythm in pain and stiffness in rheumatic diseases according the EMA (Ecologic Momentary Assessment) method: patient compliance with an electronic diary].}, journal = {Reumatismo}, volume = {57}, number = {4}, pages = {238-249}, doi = {10.4081/reumatismo.2005.238}, pmid = {16380750}, issn = {0048-7449}, mesh = {Adult ; Aged ; *Circadian Rhythm ; Cross-Sectional Studies ; Feasibility Studies ; Female ; Humans ; Male ; *Medical Records Systems, Computerized ; Middle Aged ; Pain/*physiopathology ; Pain Measurement/*instrumentation/methods ; *Patient Compliance ; Patient Satisfaction ; Rheumatic Diseases/*physiopathology ; *Self-Assessment ; Time Factors ; }, abstract = {BACKGROUND: Many researchers have used paper diaries in an attempt to capture patient experience. However, patient non-compliance with written diary protocols is a serious problem for researchers. Electronic patient experience diaries (eDiary) facilitate Ecologic Momentary Assessment (EMA) study designs by allowing the researcher to administer flexible, programmable assessments and mark each record with a time and date stamp.

OBJECTIVES: The objectives of the current study were to evaluate methodological issues associated with real-time pain reports (EMA) using electronic patient experience diaries, to quantify compliance (percentage of the total number of diary reports scheduled that were actually completed), and to examine the circadian rhythm in pain and stiffness of patients with rheumatic diseases in an ecologically valid manner.

METHODS: In this cross-sectional study we examined 49 patients with rheumatic diseases (14 patients with rheumatoid arthritis, 18 with fibromyalgia and 17 with osteoarthritis of the knee), attending the care facilities of the Department of Rheumatology of Università Politecnica delle Marche. All patients fulfilling the American College of Rheumatology (ACR) criteria. The assessment of pain and stiffness in all patients were repeated seven times a day (8 A.M., 10 A.M., 12 A.M., 2 P.M., 4 P.M., 6 P.M. and 8 P.M.) on seven consecutive days using an electronic diary (DataLogger® - Pain Level Recorder). A datalogger is newly developed electronic instrument that records measurements of pain and stiffness over time. Dataloggers are small, battery-powered devices that are equipped with a microprocessor. Specific software is then used to select logging parameters (sampling intervals, start time, etc.) and view/analyse the collected data. Compliance is based on the time and date record that was automatically recorded by the devices.

RESULTS: Using the data from the electronic diary, we determined that the average verified compliance rate for pain and stiffness were 93.8 and 93.6%, respectively. The two highest compliance rates were observed in patients with rheumatoid arthritis (95.6 and 95.2%, respectively). There were no statistically significant difference in compliance between females and males or patients above or below 60 years old. Significant circadian rhythms in patients with RA and OA of the knee were detected in pain and stiffness. No rhythm in pain or stiffness was observed in subjects with fibromyalgia.

CONCLUSIONS: We conclude that collection of subjective data using electronic diary in rheumatologic setting is a feasible method than can be adopted with high compliance rates across a range of patient demographic subgroups. The identification of diurnal cycles of self-reported pain and stiffness, using EMA method, has important implications for patients with respect to planning their daily activities and in developing individual therapeutic programs with respect to diurnal variability, which therefore may be more effective.}, } @article {pmid16377245, year = {2006}, author = {Hu, M and Gasser, RB}, title = {Mitochondrial genomes of parasitic nematodes--progress and perspectives.}, journal = {Trends in parasitology}, volume = {22}, number = {2}, pages = {78-84}, doi = {10.1016/j.pt.2005.12.003}, pmid = {16377245}, issn = {1471-4922}, mesh = {Animals ; Biological Evolution ; DNA, Helminth/genetics ; Databases, Nucleic Acid ; Genetics, Population/methods ; Genome, Helminth/*genetics ; Genomics/*trends ; Mitochondria/*genetics ; Nematoda/classification/*genetics ; Phylogeny ; }, abstract = {Mitochondria are subcellular organelles in which oxidative phosphorylation and other important biochemical functions take place within the cell. Within these organelles is a mitochondrial (mt) genome, which is distinct from, but cooperates with, the nuclear genome of the cell. Studying mt genomes has implications for various fundamental areas, including mt biochemistry, physiology and molecular biology. Importantly, the mt genome is a rich source of markers for population genetic and systematic studies. To date, more than 696 mt genomes have been sequenced for a range of metazoan organisms. However, few of these are from parasitic nematodes, despite their socioeconomic importance and the need for fundamental investigations into areas such as nematode genetics, systematics and ecology. In this article, we review knowledge and recent progress in mt genomics of parasitic nematodes, summarize applications of mt gene markers to the study of population genetics, systematics, epidemiology and evolution of key nematodes, and highlight some prospects and opportunities for future research.}, } @article {pmid16371253, year = {2006}, author = {Danson, FM and Giraudoux, P and Craig, PS}, title = {Spatial modelling and ecology of Echinococcus multilocularis transmission in China.}, journal = {Parasitology international}, volume = {55 Suppl}, number = {}, pages = {S227-31}, doi = {10.1016/j.parint.2005.11.047}, pmid = {16371253}, issn = {1383-5769}, support = {TW01565-02/TW/FIC NIH HHS/United States ; }, mesh = {Animals ; China/epidemiology ; Dog Diseases/parasitology/transmission ; Dogs ; Echinococcosis/parasitology/transmission/*veterinary ; Echinococcosis, Hepatic/parasitology/*transmission ; Echinococcus multilocularis/*physiology ; Ecology ; *Geographic Information Systems ; Host-Parasite Interactions ; Humans ; *Models, Biological ; Prevalence ; *Satellite Communications ; }, abstract = {Recent research in central China has suggested that the most likely transmission mechanism for Echinococcus multilocularis to humans is via domestic dogs which are allowed to roam freely and hunt (infected) small mammals within areas close to villages or in areas of tented pasture. This assertion has led to the hypothesis that there is a landscape control on transmission risk since the proximity of suitable habitat for susceptible small mammals appears to be the key. We have tested this hypothesis in a number of endemic areas in China, notably south Gansu Province and the Tibetan region of western Sichuan Province. The fundamental landscape control is its effect at a regional scale on small mammal species assemblages (susceptible species are not ubiquitous) and, at a local scale, the spatial distributions of small mammal populations. To date the research has examined relationships between landscape composition and patterns of human infection, landscape and small mammal distributions and recently the relationships between landscape and dog infection rates. The key tool to characterize landscape is satellite remote sensing and these data are used as inputs to drive spatial models of transmission risk. This paper reviews the progress that has been made so far in spatial modeling of the ecology of E. multilocularis with particular reference to China, outlines current research issues, and describes a framework for building a spatial-temporal model of transmission ecology.}, } @article {pmid16371242, year = {2006}, author = {McKay, JR and Franklin, TR and Patapis, N and Lynch, KG}, title = {Conceptual, methodological, and analytical issues in the study of relapse.}, journal = {Clinical psychology review}, volume = {26}, number = {2}, pages = {109-127}, doi = {10.1016/j.cpr.2005.11.002}, pmid = {16371242}, issn = {0272-7358}, support = {K01 DA015426/DA/NIDA NIH HHS/United States ; K02 DA00361/DA/NIDA NIH HHS/United States ; }, mesh = {Alcoholism/epidemiology/psychology/*rehabilitation ; Data Interpretation, Statistical ; Humans ; Medical Records/statistics & numerical data ; Microcomputers ; Outcome and Process Assessment, Health Care/statistics & numerical data ; Recurrence ; Reminder Systems ; Reproducibility of Results ; *Research Design ; Retrospective Studies ; Substance-Related Disorders/epidemiology/psychology/*rehabilitation ; }, abstract = {This article examines conceptual, methodological, and analytic issues in research on relapse to alcohol and other drug use. The review notes the continued move in relapse research from a primary reliance on retrospective assessment of factors surrounding the onset of relapse episodes to an increased focus on the use of new technologies to obtain "near real time" data on proximal factors in relapses. Recent advances in neurobiology have yielded important gains in our understanding of vulnerability to relapse in alcohol and other drug abusers. New statistical techniques are also available to analyze data on relapse. From a theoretical standpoint, there has been an increasing appreciation for the complicated and dynamic interplay of distal and proximal factors in the relapse process. At this point, the strongest and most detailed data on factors in the onset and course of relapse have been generated by studies of smoking relapses that have made use of Ecological Momentary Assessment (EMA) technology. However, there is still limited "near real" time data on proximal factors in alcohol and other drug relapses, and no such data on factors that influence the course of these relapses, once they have begun. Nevertheless, important methodological advances have been and continue to be made in the study of relapse, and our knowledge about the nature and process of relapse has increased considerably over the past 10 years.}, } @article {pmid16368872, year = {2006}, author = {Zhao, F and Zhang, X and Liang, C and Wu, J and Bao, Q and Qin, S}, title = {Genome-wide analysis of restriction-modification system in unicellular and filamentous cyanobacteria.}, journal = {Physiological genomics}, volume = {24}, number = {3}, pages = {181-190}, doi = {10.1152/physiolgenomics.00255.2005}, pmid = {16368872}, issn = {1531-2267}, mesh = {Bacterial Proteins/genetics ; Computational Biology ; Cyanobacteria/*genetics ; DNA Restriction-Modification Enzymes/*genetics ; Evolution, Molecular ; Genes, Bacterial ; Methyltransferases/genetics ; Models, Genetic ; Phylogeny ; Protein Structure, Tertiary ; Reverse Transcriptase Polymerase Chain Reaction ; Sequence Analysis, DNA ; Spirulina ; }, abstract = {Cyanobacteria are an ancient group of gram-negative bacteria with strong genome size variation ranging from 1.6 to 9.1 Mb. Here, we first retrieved all the putative restriction-modification (RM) genes in the draft genome of Spirulina and then performed a range of comparative and bioinformatic analyses on RM genes from unicellular and filamentous cyanobacterial genomes. We have identified 6 gene clusters containing putative Type I RMs and 11 putative Type II RMs or the solitary methyltransferases (MTases). RT-PCR analysis reveals that 6 of 18 MTases are not expressed in Spirulina, whereas one hsdM gene, with a mutated cognate hsdS, was detected to be expressed. Our results indicate that the number of RM genes in filamentous cyanobacteria is significantly higher than in unicellular species, and this expansion of RM systems in filamentous cyanobacteria may be related to their wide range of ecological tolerance. Furthermore, a coevolutionary pattern is found between hsdM and hsdR, with a large number of site pairs positively or negatively correlated, indicating the functional importance of these pairing interactions between their tertiary structures. No evidence for positive selection is found for the majority of RMs, e.g., hsdM, hsdS, hsdR, and Type II restriction endonuclease gene families, while a group of MTases exhibit a remarkable signature of adaptive evolution. Sites and genes identified here to have been under positive selection would provide targets for further research on their structural and functional evaluations.}, } @article {pmid16366465, year = {2005}, author = {Wang, G and Wu, W}, title = {[Assessment on ecological security spatial differences of west areas of Liaohe River based on GIS].}, journal = {Huan jing ke xue= Huanjing kexue}, volume = {26}, number = {5}, pages = {28-33}, pmid = {16366465}, issn = {0250-3301}, mesh = {China ; *Ecosystem ; Environmental Monitoring ; *Geographic Information Systems ; Rivers ; *Safety ; }, abstract = {Ecological security assessment and early warning research have spatiality; non-linearity; randomicity, it is needed to deal with much spatial information. Spatial analysis and data management are advantages of GIS, it can define distribution trend and spatial relations of environmental factors, and show ecological security pattern graphically. The paper discusses the method of ecological security spatial differences of west areas of Liaohe River based on GIS and ecosystem non-health. First, studying on pressure-state-response (P-S-R) assessment indicators system, investigating in person and gathering information; Second, digitizing the river, applying fuzzy AHP to put weight, quantizing and calculating by fuzzy comparing; Last, establishing grid data-base; expounding spatial differences of ecological security by GIS Interpolate and Assembly.}, } @article {pmid16362566, year = {2006}, author = {Chen, PY and Fedosejevs, G and Tiscareño-López, M and Arnold, JG}, title = {Assessment of MODIS-EVI, MODIS-NDVI and VEGETATION-NDVI composite data using agricultural measurements: an example at corn fields in western Mexico.}, journal = {Environmental monitoring and assessment}, volume = {119}, number = {1-3}, pages = {69-82}, doi = {10.1007/s10661-005-9006-7}, pmid = {16362566}, issn = {0167-6369}, mesh = {Crops, Agricultural/*growth & development ; Ecology ; Environmental Monitoring/*instrumentation/methods ; Geographic Information Systems/*instrumentation/statistics & numerical data ; Mexico ; Reproducibility of Results ; Satellite Communications/instrumentation/statistics & numerical data ; Zea mays/growth & development ; }, abstract = {Although several types of satellite data provide temporal information of the land use at no cost, digital satellite data applications for agricultural studies are limited compared to applications for forest management. This study assessed the suitability of vegetation indices derived from the TERRA-Moderate Resolution Imaging Spectroradiometer (MODIS) sensor and SPOT-VEGETATION (VGT) sensor for identifying corn growth in western Mexico. Overall, the Normalized Difference Vegetation Index (NDVI) composites from the VGT sensor based on bi-directional compositing method produced vegetation information most closely resembling actual crop conditions. The NDVI composites from the MODIS sensor exhibited saturated signals starting 30 days after planting, but corresponded to green leaf senescence in April. The temporal NDVI composites from the VGT sensor based on the maximum value method had a maximum plateau for 80 days, which masked the important crop transformation from vegetative stage to reproductive stage. The Enhanced Vegetation Index (EVI) composites from the MODIS sensor reached a maximum plateau 40 days earlier than the occurrence of maximum leaf area index (LAI) and maximum intercepted fraction of photosynthetic active radiation (fPAR) derived from in-situ measurements. The results of this study showed that the 250-m resolution MODIS data did not provide more accurate vegetation information for corn growth description than the 500-m and 1000-m resolution MODIS data.}, } @article {pmid16355790, year = {2005}, author = {Wang, W and Fang, C and Li, H}, title = {[Landscape ecological planning of Jiaozuo city].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {16}, number = {9}, pages = {1724-1728}, pmid = {16355790}, issn = {1001-9332}, mesh = {China ; *City Planning ; *Conservation of Natural Resources ; Ecosystem ; *Environment Design ; Geographic Information Systems ; }, abstract = {With the application of the principles of landscape ecology and the techniques of geographic information systems, the landscape of Jiaozuo city was divided into six types, i. e., farmland, garden plot, woodland, residential and industrial area, waters, and others. The landscape diversity, dominance, fragmentation, and isolation indexes were calculated by models and GIS to analyze the spatial patterns of these landscape types. Based on the optimization of landscape spatial patterns, a pattern for developing a rational and natural ecosystem in Jiaozuo city was proposed, i. e., keeping four or five large natural patches, planning small artificial green patches, linking the large and small patches by various corridors to ensure the ecosystem inside the city to circulate well, combining residential areas properly to form a urban troop with Jiaozuo town as the center and with seven surrounding towns joined through highways to form a network city pattern. After doing these, urban built-up areas could be linked each other, and inlayed in a natural ecological matrix. This pattern could strengthen the ecological connection, raise the stability of the ecosystem, and maintain the balance of urban ecological system.}, } @article {pmid16355786, year = {2005}, author = {Wei, J and Xiao, D}, title = {[Landscape pattern and its functioning after ecological reconstruction in black soil of northern China].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {16}, number = {9}, pages = {1699-1705}, pmid = {16355786}, issn = {1001-9332}, mesh = {China ; *Conservation of Natural Resources ; Crops, Agricultural/*growth & development ; *Ecosystem ; *Environment Design ; Geographic Information Systems ; Poaceae/growth & development ; Satellite Communications ; Soil/*analysis ; }, abstract = {Taken Baiquan County in Heilongjiang Province as a case, this paper studied the effects of regional ecological reconstruction on agricultural landscape pattern and its functioning in soil and water conservation, with the spatial expression and quantity identification investigated based on Geographic Information System (GIS) and field data. The landscape pattern index in class scale, transition matrix of landscape elements, macrostructure of shelter-belt networks, and spatial distribution and hydrological characteristic of reservoirs and ponds in 1989 and 2002, as well as the effects of landscape pattern and its spatial configuration change on soil and water loss were compared. The results showed that artificial ecological reconstruction changed the quantity and spatial configuration of landscape patterns in regional scale, and exerted a significant effect on soil and water conservation. From 1989 to 2002, farmland area reduced 24 731.01 hm2, while forest land, grassland and water area increased 11 728.56, 1838.97 and 1190.97 hm2, respectively. The controlled eroded land increased by 55%, and the shelterbelt-protected farmland increased by 82.2%. The number and storage capacity of reservoirs and ponds added up to 1 490 and 2.4 x 10(8) m3, respectively, and 43.7% of intercepted surface runoff of whole landscape was collected.}, } @article {pmid16354784, year = {2006}, author = {Tremblay, Y and Shaffer, SA and Fowler, SL and Kuhn, CE and McDonald, BI and Weise, MJ and Bost, CA and Weimerskirch, H and Crocker, DE and Goebel, ME and Costa, DP}, title = {Interpolation of animal tracking data in a fluid environment.}, journal = {The Journal of experimental biology}, volume = {209}, number = {Pt 1}, pages = {128-140}, doi = {10.1242/jeb.01970}, pmid = {16354784}, issn = {0022-0949}, mesh = {*Algorithms ; Animals ; Data Interpretation, Statistical ; Geography ; Linear Models ; Marine Biology/*methods ; *Models, Theoretical ; Movement/*physiology ; Species Specificity ; Vertebrates/*physiology ; }, abstract = {Interpolation of geolocation or Argos tracking data is a necessity for habitat use analyses of marine vertebrates. In a fluid marine environment, characterized by curvilinear structures, linearly interpolated track data are not realistic. Based on these two facts, we interpolated tracking data from albatrosses, penguins, boobies, sea lions, fur seals and elephant seals using six mathematical algorithms. Given their popularity in mathematical computing, we chose Bézier, hermite and cubic splines, in addition to a commonly used linear algorithm to interpolate data. Performance of interpolation methods was compared with different temporal resolutions representative of the less-precise geolocation and the more-precise Argos tracking techniques. Parameters from interpolated sub-sampled tracks were compared with those obtained from intact tracks. Average accuracy of the interpolated location was not affected by the interpolation method and was always within the precision of the tracking technique used. However, depending on the species tested, some curvilinear interpolation algorithms produced greater occurrences of more accurate locations, compared with the linear interpolation method. Total track lengths were consistently underestimated but were always more accurate using curvilinear interpolation than linear interpolation. Curvilinear algorithms are safe to use because accuracy, shape and length of the tracks are either not different or are slightly enhanced and because analyses always remain conservative. The choice of the curvilinear algorithm does not affect the resulting track dramatically so it should not preclude their use. We thus recommend using curvilinear interpolation techniques because of the more realistic fluid movements of animals. We also provide some guidelines for choosing an algorithm that is most likely to maximize track quality for different types of marine vertebrates.}, } @article {pmid16352385, year = {2006}, author = {Panter-Brick, C and Clarke, SE and Lomas, H and Pinder, M and Lindsay, SW}, title = {Culturally compelling strategies for behaviour change: a social ecology model and case study in malaria prevention.}, journal = {Social science & medicine (1982)}, volume = {62}, number = {11}, pages = {2810-2825}, doi = {10.1016/j.socscimed.2005.10.009}, pmid = {16352385}, issn = {0277-9536}, mesh = {Animals ; Bedding and Linens/statistics & numerical data ; *Community Networks ; Culicidae ; *Culture ; Gambia ; Health Promotion/*methods ; Humans ; Malaria/*prevention & control ; *Models, Theoretical ; Organizational Case Studies ; *Risk Reduction Behavior ; }, abstract = {Behaviour change is notoriously difficult to initiate and sustain, and the reasons why efforts to promote healthy behaviours fail are coming under increasing scrutiny. To be successful, health interventions should build on existing practices, skills and priorities, recognise the constraints on human behaviour, and either feature community mobilisation or target those most receptive to change. Furthermore, interventions should strive to be culturally compelling, not merely culturally appropriate: they must engage local communities and nestle within social and ecological landscapes. In this paper, we propose a social ecology perspective to make explicit the links between intention to change, actual behaviour change, and subsequent health impact, as relating to both theory-based models and practical strategies for triggering behaviour change. A social ecology model focuses attention on the contexts of behaviour when designing, implementing or critically evaluating interventions. As a case study, we reflect on a community-directed intervention in rural Gambia designed to reduce malaria by promoting a relatively simple and low-cost behaviour: repairing holes in mosquito bednets. In phase 1, contextual information on bednet usage, transactions and repairs (the 'social lives' of nets) was documented. In phase 2 (intervention), songs were composed and posters displayed by community members to encourage repairs, creating a sense of ownership and a compelling medium for the transmission of health messages. In phase 3 (evaluation), qualitative and quantitative data showed that household responses were particularly rapid and extensive, with significant increase in bednet repairs (p<0.001), despite considerable constraints on human agency. We highlight a promising approach-using songs-as a vehicle for change, and present a framework to embed the design, implementation and critical evaluation of interventions within the larger context-or social ecology-of behaviour practices that are the bedrock of health interventions.}, } @article {pmid16343983, year = {2006}, author = {Morozińska-Gogol, J}, title = {A checklist of parasites recorded on sticklebacks (Actinopterygii: Gasterosteidae) from Poland.}, journal = {Parasitology international}, volume = {55}, number = {1}, pages = {69-73}, doi = {10.1016/j.parint.2005.10.002}, pmid = {16343983}, issn = {1383-5769}, mesh = {Animals ; Biodiversity ; Databases, Factual ; Fish Diseases/*parasitology ; Parasites/*classification ; Parasitic Diseases, Animal/*parasitology ; Poland ; Smegmamorpha/*parasitology ; }, abstract = {Parasites of the three-spined stickleback, Gasterosteus aculeatus (L.), and the nine-spined stickleback, Pungitius pungitius (L.), from brackish and freshwater habitats in Poland are listed. The following list was compiled from published records and own long-term studies. Parasites are listed alphabetically in meaningful groups of parasites with notes about their location on the host and distribution in Poland with references. A total of 51 species (taxa) of parasites were recorded on G. aculeatus (3 Apicomplexa, 1 Microsporidia, 3 Peritrichia, 1 Myxozoa, 7 Digenea, 2 Monogenea, 10 Cestoda, 10 Nematoda, 7 Acanthocephala, 3 Copepoda, 1 Branchiura, 2 Hirudinea, 1 Bivalvia) and 16 parasites on P. pungitius (1 Apicomplexa, 1 Microsporidia, 2 Peritrichia, 4 Digenea, 1 Monogenea, 2 Cestoda, 2 Nematoda, 1 Copepoda, 1 Branchiura, 1 Bivalvia).}, } @article {pmid16343765, year = {2006}, author = {Liu, X and Wirtz, KW}, title = {Consensus oriented fuzzified decision support for oil spill contingency management.}, journal = {Journal of hazardous materials}, volume = {134}, number = {1-3}, pages = {27-35}, doi = {10.1016/j.jhazmat.2005.11.012}, pmid = {16343765}, issn = {0304-3894}, mesh = {*Decision Support Techniques ; *Ecosystem ; *Fuel Oils ; *Fuzzy Logic ; Germany ; Oceans and Seas ; Seawater/chemistry ; Sensitivity and Specificity ; Water Pollution/*prevention & control ; }, abstract = {Studies on multi-group multi-criteria decision-making problems for oil spill contingency management are in their infancy. This paper presents a second-order fuzzy comprehensive evaluation (FCE) model to resolve decision-making problems in the area of contingency management after environmental disasters such as oil spills. To assess the performance of different oil combat strategies, second-order FCE allows for the utilization of lexical information, the consideration of ecological and socio-economic criteria and the involvement of a variety of stakeholders. On the other hand, the new approach can be validated by using internal and external checks, which refer to sensitivity tests regarding its internal setups and comparisons with other methods, respectively. Through a case study, the Pallas oil spill in the German Bight in 1998, it is demonstrated that this approach can help decision makers who search for an optimal strategy in multi-thread contingency problems and has a wider application potential in the field of integrated coastal zone management.}, } @article {pmid16332341, year = {2005}, author = {Muresu, R and Sulas, L and Polone, E and Squartini, A}, title = {PCR primers based on different portions of insertion elements can assist genetic relatedness studies, strain fingerprinting and species identification in rhizobia.}, journal = {FEMS microbiology ecology}, volume = {54}, number = {3}, pages = {445-453}, doi = {10.1016/j.femsec.2005.05.008}, pmid = {16332341}, issn = {0168-6496}, mesh = {Base Sequence ; Classification/methods ; Cluster Analysis ; Computational Biology ; DNA Fingerprinting/methods ; DNA Primers/*genetics ; DNA Transposable Elements/*genetics ; Image Processing, Computer-Assisted ; Molecular Sequence Data ; *Phylogeny ; Polymerase Chain Reaction/*methods ; Rhizobium/*genetics ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {Using the sequence of an insertion element originally found in Rhizobium sullae, the nitrogen-fixing bacterial symbiont of the legume Hedysarum coronarium, we devised three primer pairs (inbound, outbound and internal primers) for the following applications: (a) tracing genetic relatedness within rhizobia using a method independent of ribosomal inheritance, based on the presence and conservation of IS elements; (b) achieve sensitive and reproducible bacterial fingerprinting; (c) enable a fast and unambiguous detection of rhizobia at the species level. In terms of taxonomy, while in line with part of the 16S rRNA gene- and glutamine synthetase I-based clustering, the tools appeared nonetheless more coherent with the actual geographical ranges of origin of rhizobial species, strengthening the European-Mediterranean connections and discerning them from the asian and american taxa. The fingerprinting performance of the outward-pointing primers, designed upon the inverted repeats, was shown to be at least as sensitive as BOX PCR, and to be functional on a universal basis with all 13 bacterial species tested. The primers designed on the internal part of the transposase gene instead proved highly species-specific for R. sullae, enabling selective distinction from its most related species, and testing positive on every R. sullae strain examined, fulfilling the need of PCR-mediated species identification. A general use of other IS elements for a combined approach to rhizobial taxonomy and ecology is proposed.}, } @article {pmid16316676, year = {2006}, author = {Tindall, CI and Moore, RV and Bosley, JD and Swetnam, RD and Bowie, R and De Rudder, A}, title = {Creating and using the urgent metadata catalogue and thesaurus.}, journal = {The Science of the total environment}, volume = {360}, number = {1-3}, pages = {223-232}, doi = {10.1016/j.scitotenv.2005.08.036}, pmid = {16316676}, issn = {0048-9697}, mesh = {Cataloging ; *Databases, Factual/standards ; *Environmental Monitoring ; Environmental Pollutants ; Information Storage and Retrieval/*methods ; Internet ; United Kingdom ; User-Computer Interface ; Vocabulary, Controlled ; }, abstract = {The Urban Regeneration and the Environment Research Programme (URGENT) required a system for cataloguing its datasets and enabling its scientific community to discover what data were available to it. This community was multidisciplinary in nature and therefore needed a range of facilities for searching. Of particular importance were facilities to help those unfamiliar with specialist terminology. To meet these needs, four applications were designed and developed: a Metadata Capture Tool for describing datasets in compliance with the National Geospatial Data Framework (NGDF) standard, a Term Entry Tool for creating an ISO compliant thesaurus, a Thesaurus Builder for merging thesauri and a Search Tool. To encourage users to help in cataloguing data, the capture tools were written as stand alone applications, which users could keep and use to build their own metadatabases. The tools contained export and import facilities that allowed the URGENT Data Centre to build a central database and publish it upon the web. During the development work, it was found necessary to extend the NGDF standard as it could not adequately describe time variant or 3-D atmospheric datasets. The four applications met their design objectives. However, a number of ergonomic issues will need to be addressed if the system is to meet the needs of the much larger up coming programmes. The main challenges will be moving from the NGDF standard to the ISO standard, hence bringing the work into line with the recommendations of the INSPIRE Project, and merging the metadatabase with the scientific database, which enable metadata maintenance to be semi-automated.}, } @article {pmid16313020, year = {2005}, author = {Zhou, DM and Radke, J and Tian, YQ and Xu, JC and Mu, L}, title = {A model supported by GIS for locating and quantifying PM2.5 emission originated from residential wood burning.}, journal = {Journal of environmental sciences (China)}, volume = {17}, number = {5}, pages = {861-865}, pmid = {16313020}, issn = {1001-0742}, mesh = {Air Pollutants/*analysis ; Air Pollution/*statistics & numerical data ; California ; Climate ; Demography ; *Environment ; *Geographic Information Systems ; Geography ; Linear Models ; *Models, Theoretical ; *Wood ; }, abstract = {A research method was presented for spatially quantifying and allocating the potential activity of a fine particle matter emission (PM2.5), which originated from residential wood burning (RWB) in this study. Demographic, hypsographic, climatic and topographic data were compiled and processed within a geographic information system (GIS), and as independent variables put into a linear regression model for describing spatial distribution of the potential activity of residential wood burning as primary heating source. In order to improve the estimation, the classifications of urban, suburban and rural were redefined to meet the specifications of this application. Also, several definitions of forest accessibility were tested for estimation. The results suggested that the potential activity of RWB was mostly determined by elevation of a location, forest accessibility, urban/non-urban position, climatic conditions and several demographic variables. The linear regression model could explain approximately 86% of the variation of surveyed potential activity of RWB. The analysis results were validated by employing survey data collected mainly from a WebGIS based phone interview over the study area in central California. Based on lots free public GIS data, the model provided an easy and ideal tool for geographic researchers, environmental planners and administrators to understand where and how much PM2.5 emission from RWB was contributed to air quality. With this knowledge they could identify regions of concern, and better plan mitigation strategies to improve air quality. Furthermore, it allows for future adjustment on some parameters as the spatial analysis method is implemented in the different regions or various eco-social models.}, } @article {pmid16310788, year = {2006}, author = {Poulin, R and Krasnov, BR and Shenbrot, GI and Mouillot, D and Khokhlova, IS}, title = {Evolution of host specificity in fleas: is it directional and irreversible?.}, journal = {International journal for parasitology}, volume = {36}, number = {2}, pages = {185-191}, doi = {10.1016/j.ijpara.2005.09.017}, pmid = {16310788}, issn = {0020-7519}, mesh = {Adaptation, Biological ; Animals ; *Biological Evolution ; Databases, Factual ; Ecology ; Host-Parasite Interactions ; Likelihood Functions ; Mammals/*parasitology ; Parasitic Diseases, Animal ; Phylogeny ; Siphonaptera/*physiology ; Species Specificity ; }, abstract = {Evolutionary trends in the evolution of host specificity have been the focus of much discussion but little rigorous empirical testing. On the one hand, specialization is often presumed to lead irreversibly into evolutionary dead ends and little diversification; this would mean that generalists might evolve into specialists, but not vice versa. On the other hand, low host specificity may limit the risk of extinction and provide more immediate fitness benefits to parasites, such that selection may favour evolution toward a generalist strategy. Here, we test for directionality in the evolution of host specificity using a large data set and phylogenetic information on 297 species of fleas parasitic on small mammals. The analyses determined whether host specificity, measured both as the number of host species exploited and their taxonomic diversity, was related to clade rank of the flea species, or the number of branching events between an extant species and the root of the phylogenetic tree (i.e., the total path length from the root of the tree to the species). Based on regression analyses, we found positive relationships between the number of host species used and clade rank across all 297 species, as well as within one (Hystrichopsyllidae) of four large families and one of seven large genera investigated separately; in addition, we found a positive relationship between the taxonomic diversity of host species used and clade rank in another of the seven genera. These results suggest a slight evolutionary trend of decreasing host specificity. Using a much more conservative likelihood ratio test, however, a random walk, or null model, of evolution could not be discarded in favour of the directional trends in all cases mentioned above. Still, these results suggest that host specificity may have tended to decrease in many flea lineages, a process that could have been driven by the benefits of exploiting a wide range of host species.}, } @article {pmid16309389, year = {2005}, author = {Kalyuzhnaya, MG and Nercessian, O and Lapidus, A and Chistoserdova, L}, title = {Fishing for biodiversity: novel methanopterin-linked C transfer genes deduced from the Sargasso Sea metagenome.}, journal = {Environmental microbiology}, volume = {7}, number = {12}, pages = {1909-1916}, doi = {10.1111/j.1462-2920.2005.00798.x}, pmid = {16309389}, issn = {1462-2912}, mesh = {*Biodiversity ; Biological Transport ; Carbon/*metabolism ; Computational Biology/*methods ; Formaldehyde/metabolism ; Genes, Archaeal/genetics ; Genes, Bacterial/genetics ; *Marine Biology ; Oceans and Seas ; Oxidation-Reduction ; Plankton/genetics ; Pterins/*metabolism ; *Water Microbiology ; }, abstract = {The recently generated database of microbial genes from an oligotrophic environment populated by a calculated 1800 major phylotypes (the Sargasso Sea metagenome-SSM) presents a great source for expanding local databases of genes indicative of a specific function. In this article we analyse the SSM for the presence of methanopterin-linked C1 transfer genes that are signature for methylotrophy. We conclude that more than 10 phylotypes possessing genes of interest are present in this environment. The sequences representative of these major phylotypes do not appear to belong to any known microbial group capable of methanopterin-linked C1 transfer. Instead, these sequences separate from all known sequences on phylogenetic trees, pointing toward their affiliation with novel microbial phyla. These data imply a broader distribution of methanopterin-linked functions in the microbial world than has been previously known.}, } @article {pmid16305815, year = {2006}, author = {Johnston, JM and Leung, G and Saing, H and Kwok, KO and Ho, LM and Wong, IO and Tin, KY}, title = {Non-attendance and effective equity of access at four public specialist outpatient centers in Hong Kong.}, journal = {Social science & medicine (1982)}, volume = {62}, number = {10}, pages = {2551-2564}, doi = {10.1016/j.socscimed.2005.10.036}, pmid = {16305815}, issn = {0277-9536}, mesh = {*Ambulatory Care Facilities ; Databases as Topic ; Female ; *Health Services Accessibility ; Hong Kong ; Hospital Administration ; Humans ; Interviews as Topic ; Male ; *Patient Acceptance of Health Care ; *Public Sector ; Referral and Consultation ; Social Class ; Waiting Lists ; }, abstract = {This study tests whether socio-economic status (SES), at either the individual or ecologic levels, exerts a direct impact on non-attendance or an indirect impact on attendance through longer waiting time for appointments and/or doctor-shopping behavior at four public specialist outpatient centers in Hong Kong. We collected information through three main sources, namely patients' referral letters, telephone interviews with both open- and closed-ended questions (e.g. doctor-shopping data) and hospital administrative databases from a total of 6495 attenders and non-attenders enrolled from July 2000 through October 2001. Individual-level SES was measured by education, occupation and monthly household income. Tertiary planning unit (TPU)-level SES data consisted of proportion unemployed, proportion with tertiary education, median income and Gini coefficient. Direct effects of SES on non-attendance were examined by logistic regression. Indirect contributions mediated through waiting time and doctor-shopping were analyzed by structural equation modeling. We found that SES, at the individual or ecologic level, did not exert a direct effect on non-attendance. Instead, TPU-level SES contributed positively to waiting time (beta=0.06+/-0.03, p=0.048), i.e. worse-off neighborhoods (and those with greater income inequality) had a shorter waiting time. Individual-level SES was also directly associated with the likelihood of doctor-shopping (beta=0.16+/-0.02, p<0.001), i.e. the poor were less likely to doctor-shop. Both waiting time (beta=0.12+/-0.02, p<0.001) and doctor-shopping (beta=0.37+/-0.02, p<0.001) were significantly related to non-attendance. Our findings suggest a highly equitable specialist ambulatory care public system in Hong Kong. Health care resources are appropriately targeted at the socially indigent, and the poor are not discriminated against and pushed to seek alternative sources of care by the system. These results should be confirmed using a prospective design.}, } @article {pmid16297440, year = {2006}, author = {Angold, PG and Sadler, JP and Hill, MO and Pullin, A and Rushton, S and Austin, K and Small, E and Wood, B and Wadsworth, R and Sanderson, R and Thompson, K}, title = {Biodiversity in urban habitat patches.}, journal = {The Science of the total environment}, volume = {360}, number = {1-3}, pages = {196-204}, doi = {10.1016/j.scitotenv.2005.08.035}, pmid = {16297440}, issn = {0048-9697}, mesh = {Animals ; *Biodiversity ; Butterflies/classification/genetics ; *Cities ; Coleoptera ; *Environment ; Genetic Variation ; Geographic Information Systems ; Mammals ; Models, Theoretical ; Plants ; Population Dynamics ; United Kingdom ; Urbanization ; }, abstract = {We examined the biodiversity of urban habitats in Birmingham (England) using a combination of field surveys of plants and carabid beetles, genetic studies of four species of butterflies, modelling the anthropochorous nature of the floral communities and spatially explicit modelling of selected mammal species. The aim of the project was to: (i) understand the ecological characteristics of the biota of cities model, (ii) examine the effects of habitat fragment size and connectivity upon the ecological diversity and individual species distributions, (iii) predict biodiversity in cities, and (iv) analyse the extent to which the flora and fauna utilise the 'urban greenways' both as wildlife corridors and as habitats in their own right. The results suggest that cities provide habitats for rich and diverse range of plants and animals, which occur sometimes in unlikely recombinant communities. The studies on carabids and butterflies illustrated the relative importance of habitat quality on individual sites as opposed to site location within the conurbation. This suggests that dispersal for most of our urban species is not a limiting factor in population persistence, although elements of the woodland carabid fauna did appear to have some geographical structuring. Theoretical models suggested that dormice and water voles may depend on linear habitats for dispersal. The models also indicated that other groups, such as small and medium sized mammals, may use corridors, although field-based research did not provide any evidence to suggest that plants or invertebrates use urban greenways for dispersal. This finding indicates the importance of identifying a target species or group of species for urban greenways intended as dispersal routeways rather than as habitat in their own right. Their importance for most groups is rather that greenways provide a chain of different habitats permeating the urban environment. We suggest that planners can have a positive impact on urban biodiversity by slowing the pace of redevelopment and by not hurrying to tidy up and redevelop brownfield sites.}, } @article {pmid16286085, year = {2005}, author = {Mesléard, F and Garnero, S and Beck, N and Rosecchi, E}, title = {Uselessness and indirect negative effects of an insecticide on rice field invertebrates.}, journal = {Comptes rendus biologies}, volume = {328}, number = {10-11}, pages = {955-962}, doi = {10.1016/j.crvi.2005.09.003}, pmid = {16286085}, issn = {1631-0691}, mesh = {Agriculture ; Animals ; Biomass ; Birds/*physiology ; Chironomidae ; Data Interpretation, Statistical ; Ecology ; Insecticides/*adverse effects/toxicity ; *Invertebrates/classification ; Larva ; *Oryza ; Predatory Behavior/drug effects ; Pyrazoles/toxicity ; }, abstract = {Macro-invertebrate assemblages on organic and conventional rice fields were quantitatively compared in the Camargue (Rhone delta, France). There was no major difference in family richness, but significant differences as regard to abundance. Fipronil, the insecticide used to control chironomid larvae, was one of the main factors explaining those differences. Its negative impact on predatory invertebrates appears to explain the paradoxical lack of difference in chironomid abundance between organic and conventional fields, observed during the study. Macro-invertebrate biomass estimation showed that, for some birds such as herons, conventional rice fields offered a lower value as foraging habitats than organic ones.}, } @article {pmid16285693, year = {2005}, author = {Mühlberger, F and Streibel, T and Wieser, J and Ulrich, A and Zimmermann, R}, title = {Single photon ionization time-of-flight mass spectrometry with a pulsed electron beam pumped excimer VUV lamp for on-line gas analysis: setup and first results on cigarette smoke and human breath.}, journal = {Analytical chemistry}, volume = {77}, number = {22}, pages = {7408-7414}, doi = {10.1021/ac051194+}, pmid = {16285693}, issn = {0003-2700}, mesh = {*Electrons ; Humans ; Ions/chemistry ; Mass Spectrometry/*instrumentation/*methods ; Molecular Structure ; Online Systems/*instrumentation ; Respiration ; Smoke/*analysis ; Time Factors ; *Nicotiana/chemistry ; *Ultraviolet Rays ; }, abstract = {Single-photon ionization (SPI) using vacuum ultraviolet (VUV) light produced by an electron beam pumped rare gas excimer source has been coupled to a compact and mobile time-of-flight mass spectrometer (TOFMS). The novel device enables real-time on-line monitoring of organic trace substances in complex gaseous matrixes down to the ppb range. The pulsed VUV radiation of the light source is employed for SPI in the ion source of the TOFMS. Ion extraction is also carried out in a pulsed mode with a short time delay with respect to ionization. The experimental setup of the interface VUV light source/time-of-flight mass spectrometer is described, and the novel SPI-TOFMS system is characterized by means of standard calibration gases. Limits of detection down to 50 ppb for aliphatic and aromatic hydrocarbons were achieved. First on-line applications comprised real-time measurements of aromatic and aliphatic trace compounds in mainstream cigarette smoke, which represents a highly dynamic fluctuating gaseous matrix. Time resolution was sufficient to monitor the smoking process on a puff-by-puff resolved basis. Furthermore, human breath analysis has been carried out to detect differences in the breath of a smoker and a nonsmoker, respectively. Several well-known biomarkers for smoke could be identified in the smoker's breath. The possibility for even shorter measurement times while maintaining the achieved sensitivity makes this new device a promising tool for on-line analysis of organic trace compounds in process gases or biological systems.}, } @article {pmid16284171, year = {2005}, author = {Grimm, V and Revilla, E and Berger, U and Jeltsch, F and Mooij, WM and Railsback, SF and Thulke, HH and Weiner, J and Wiegand, T and DeAngelis, DL}, title = {Pattern-oriented modeling of agent-based complex systems: lessons from ecology.}, journal = {Science (New York, N.Y.)}, volume = {310}, number = {5750}, pages = {987-991}, doi = {10.1126/science.1116681}, pmid = {16284171}, issn = {1095-9203}, mesh = {Animals ; Behavior, Animal ; Decision Support Techniques ; *Ecology ; Ecosystem ; Fishes/physiology ; *Models, Biological ; Models, Economic ; *Models, Theoretical ; Systems Theory ; Trees ; Uncertainty ; }, abstract = {Agent-based complex systems are dynamic networks of many interacting agents; examples include ecosystems, financial markets, and cities. The search for general principles underlying the internal organization of such systems often uses bottom-up simulation models such as cellular automata and agent-based models. No general framework for designing, testing, and analyzing bottom-up models has yet been established, but recent advances in ecological modeling have come together in a general strategy we call pattern-oriented modeling. This strategy provides a unifying framework for decoding the internal organization of agent-based complex systems and may lead toward unifying algorithmic theories of the relation between adaptive behavior and system complexity.}, } @article {pmid16284164, year = {2005}, author = {Ewers, RM}, title = {Illusory statistics.}, journal = {Science (New York, N.Y.)}, volume = {310}, number = {5750}, pages = {973-974}, doi = {10.1126/science.310.5750.973b}, pmid = {16284164}, issn = {1095-9203}, mesh = {*Biological Evolution ; *Biology ; *Data Interpretation, Statistical ; Ecology ; Statistics as Topic ; }, } @article {pmid16279281, year = {2004}, author = {Feaster, DJ and Robbins, MS and Horigian, V and Szapocznik, J}, title = {Statistical issues in multisite effectiveness trials: the case of brief strategic family therapy for adolescent drug abuse treatment.}, journal = {Clinical trials (London, England)}, volume = {1}, number = {5}, pages = {428-439}, pmid = {16279281}, issn = {1740-7745}, support = {U10 DA013720/DA/NIDA NIH HHS/United States ; U10 DA-13720/DA/NIDA NIH HHS/United States ; }, mesh = {Adolescent ; *Adolescent Health Services ; *Community Health Centers ; Data Interpretation, Statistical ; *Family Therapy ; Humans ; Models, Statistical ; Multicenter Studies as Topic/*methods ; Patient Selection ; Randomized Controlled Trials as Topic/methods ; Sample Size ; Substance-Related Disorders/*therapy ; *Treatment Outcome ; }, abstract = {The statistical development of the multisite Brief Strategic Family Therapy (BSFT) Trial of the National Institute on Drug Abuse's Clinical Trials Network provides a useful, real example of how an effectiveness trial can differ from an efficacy trial. In particular, two design elements distinguish this effectiveness trial from an efficacy trial. First, because the goal of the trial is to show that the use of BSFT would be an improvement on current practice, it was decided to compare BSFT to treatment as usual at each location. This decision ensures that the trial has the most ecological validity to the participating community treatment providers. Second, the desire to generalize the results to general clinical practice dictates that variability (in effect) across community treatment providers be estimated using a random effects model. These two decisions jointly influence the sample size calculations. Allowing variation in treatment as usual, will increase the variability in effect sizes across sites and estimation of this variability as a random effect necessitates a larger sample size (both number of community treatment providers and participants per community treatment provider), than is the case for a fixed site effect estimate. Details of these effects and their implications for the statistical design are presented.}, } @article {pmid16278696, year = {2006}, author = {Naska, A and Fouskakis, D and Oikonomou, E and Almeida, MD and Berg, MA and Gedrich, K and Moreiras, O and Nelson, M and Trygg, K and Turrini, A and Remaut, AM and Volatier, JL and Trichopoulou, A and , }, title = {Dietary patterns and their socio-demographic determinants in 10 European countries: data from the DAFNE databank.}, journal = {European journal of clinical nutrition}, volume = {60}, number = {2}, pages = {181-190}, doi = {10.1038/sj.ejcn.1602284}, pmid = {16278696}, issn = {0954-3007}, mesh = {Adolescent ; Adult ; Aged ; Budgets ; Child ; Child, Preschool ; Databases, Factual ; Demography ; Diet/*statistics & numerical data/*trends ; *Diet Surveys ; Europe ; Family Characteristics ; *Feeding Behavior/ethnology ; Female ; Food Supply ; Humans ; Infant ; Infant, Newborn ; Male ; Middle Aged ; Principal Component Analysis ; }, abstract = {OBJECTIVE: To describe the dietary patterns of 10 European countries and their socio-demographic determinants, using the comparable between-countries DAFNE data.

DESIGN: Analysis of standardized and postharmonized data collected through the national household budget surveys.

SETTING: Nationally representative surveys undertaken in 10 European countries, generally in the second half of the 1990s.

RESULTS: The differences in the fruit and vegetable consumption previously identified between Mediterranean and Northern European countries seem to be leveling out, particularly in relation to fruit consumption. Pulses, however, still characterize the diet of the Mediterraneans. Straying from their traditional food choices, Mediterraneans recorded high availability of unprocessed red meat, while Central and Northern Europeans preferably consumed meat products. The household availability of beverages (alcoholic and non-alcoholic) is generally higher among Central and Northern European populations. Principal component (PC) analysis led to the identification of two dietary patterns in each of the 10 countries. The first was similar in all countries and indicated 'wide-range' food buyers. The second was slightly more varied and described 'beverage and convenience' food buyers. PC1 was common among households of retired and elderly members, while PC2 was common among households located in urban or semi-urban areas and among adult Scandinavians living alone.

CONCLUSIONS: The dietary patterns identified point towards a progressive narrowing of dietary differences between North and South European countries. The comparable between-countries DAFNE data could prove useful in ecological studies, in the formulation of dietary guidelines and public health initiatives addressing specific population groups.

SPONSORSHIP: European Commission.}, } @article {pmid16276987, year = {2005}, author = {Stamova, LG and Chesnokova, EA}, title = {[Ambient air pollution and its impact on the incidence of respiratory diseases in children].}, journal = {Gigiena i sanitariia}, volume = {}, number = {5}, pages = {28-31}, pmid = {16276987}, issn = {0016-9900}, mesh = {Age Factors ; Air Pollutants/adverse effects ; Air Pollution/*adverse effects ; Bronchitis/epidemiology ; Cohort Studies ; Data Interpretation, Statistical ; Humans ; Infant ; Infant, Newborn ; Laryngitis/epidemiology ; Models, Theoretical ; Respiratory Tract Diseases/*epidemiology ; Russia/epidemiology ; Seasons ; Tracheitis/epidemiology ; Urban Population ; }, abstract = {The increased number of ecological problems in Russia has stimulated the development of methodological approaches to studying a human chemical load under the conditions of an industrial town. The data on mortality in children under 3 years of age, who lived in a developed industrial town, have been analyzed. Comparison of data on ambient air purity and those on the incidence of respiratory disease has established a correlation between environment pollution and the likelihood of diseases in children under the influence of harmful factors.}, } @article {pmid16274698, year = {2006}, author = {Olesen, JM and Bascompte, J and Dupont, YL and Jordano, P}, title = {The smallest of all worlds: pollination networks.}, journal = {Journal of theoretical biology}, volume = {240}, number = {2}, pages = {270-276}, doi = {10.1016/j.jtbi.2005.09.014}, pmid = {16274698}, issn = {0022-5193}, mesh = {Animals ; Biodiversity ; Computational Biology ; *Ecosystem ; Flowers/*physiology ; *Insecta ; Least-Squares Analysis ; Models, Biological ; Plant Physiological Phenomena ; *Pollen ; Reproduction ; }, abstract = {A pollination network may be either 2-mode, describing trophic and reproductive interactions between communities of flowering plants and pollinator species within a well-defined habitat, or 1-mode, describing interactions between either plants or pollinators. In a 1-mode pollinator network, two pollinator species are linked to each other if they both visit the same plant species, and vice versa for plants. Properties of 2-mode networks and their derived 1-mode networks are highly correlated and so are properties of 1-mode pollinator and 1-mode plant networks. Most network properties are scale-dependent, i.e. they are dependent upon network size. Pollination networks have the strongest small-world properties of any networks yet studied, i.e. all species are close to each other (short average path length) and species are highly clustered. Species in pollination networks are much more densely linked than species in traditional food webs, i.e. they have a higher density of links, a shorter distance between species, and species are more clustered.}, } @article {pmid16271138, year = {2005}, author = {Pfenninger, M and Hrabáková, M and Steinke, D and Dèpraz, A}, title = {Why do snails have hairs? A Bayesian inference of character evolution.}, journal = {BMC evolutionary biology}, volume = {5}, number = {}, pages = {59}, pmid = {16271138}, issn = {1471-2148}, mesh = {*Adaptation, Biological ; Animal Structures ; Animals ; Bayes Theorem ; *Biological Evolution ; DNA Primers/chemistry ; Data Interpretation, Statistical ; Ecosystem ; Environment ; Hair ; Humidity ; Marine Biology ; Markov Chains ; Movement ; Phylogeny ; Polymerase Chain Reaction ; Selection, Genetic ; Sequence Analysis, DNA ; Snails/*anatomy & histology/genetics/*physiology ; Species Specificity ; }, abstract = {BACKGROUND: Costly structures need to represent an adaptive advantage in order to be maintained over evolutionary times. Contrary to many other conspicuous shell ornamentations of gastropods, the haired shells of several Stylommatophoran land snails still lack a convincing adaptive explanation. In the present study, we analysed the correlation between the presence/absence of hairs and habitat conditions in the genus Trochulus in a Bayesian framework of character evolution.

RESULTS: Haired shells appeared to be the ancestral character state, a feature most probably lost three times independently. These losses were correlated with a shift from humid to dry habitats, indicating an adaptive function of hairs in moist environments. It had been previously hypothesised that these costly protein structures of the outer shell layer facilitate the locomotion in moist habitats. Our experiments, on the contrary, showed an increased adherence of haired shells to wet surfaces.

CONCLUSION: We propose the hypothesis that the possession of hairs facilitates the adherence of the snails to their herbaceous food plants during foraging when humidity levels are high. The absence of hairs in some Trochulus species could thus be explained as a loss of the potential adaptive function linked to habitat shifts.}, } @article {pmid16269252, year = {2006}, author = {Torres-Carvajal, O and Schulte, JA and Cadle, JE}, title = {Phylogenetic relationships of South American lizards of the genus Stenocercus (Squamata: Iguania): A new approach using a general mixture model for gene sequence data.}, journal = {Molecular phylogenetics and evolution}, volume = {39}, number = {1}, pages = {171-185}, doi = {10.1016/j.ympev.2005.09.007}, pmid = {16269252}, issn = {1055-7903}, mesh = {Animals ; Base Sequence ; DNA, Mitochondrial/genetics ; Databases, Nucleic Acid ; *Evolution, Molecular ; Lizards/*classification/*genetics ; Models, Genetic ; Molecular Sequence Data ; *Phylogeny ; South America ; }, abstract = {The South American iguanian lizard genus Stenocercus includes 54 species occurring mostly in the Andes and adjacent lowland areas from northern Venezuela and Colombia to central Argentina at elevations of 0-4000m. Small taxon or character sampling has characterized all phylogenetic analyses of Stenocercus, which has long been recognized as sister taxon to the Tropidurus Group. In this study, we use mtDNA sequence data to perform phylogenetic analyses that include 32 species of Stenocercus and 12 outgroup taxa. Monophyly of this genus is strongly supported by maximum parsimony and Bayesian analyses. Evolutionary relationships within Stenocercus are further analyzed with a Bayesian implementation of a general mixture model, which accommodates variability in the pattern of evolution across sites. These analyses indicate a basal split of Stenocercus into two clades, one of which receives very strong statistical support. In addition, we test previous hypotheses using non-parametric and parametric statistical methods, and provide a phylogenetic classification for Stenocercus.}, } @article {pmid16262869, year = {2005}, author = {Smith, CT and Elfstrom, CM and Seeb, LW and Seeb, JE}, title = {Use of sequence data from rainbow trout and Atlantic salmon for SNP detection in Pacific salmon.}, journal = {Molecular ecology}, volume = {14}, number = {13}, pages = {4193-4203}, doi = {10.1111/j.1365-294X.2005.02731.x}, pmid = {16262869}, issn = {0962-1083}, mesh = {Animals ; Base Sequence ; Computational Biology/*methods ; DNA Primers ; Genotype ; Molecular Sequence Data ; Polymorphism, Single Nucleotide/*genetics ; Salmon/*genetics ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {Single nucleotide polymorphisms (SNPs) are a class of genetic markers that are well suited to a broad range of research and management applications. Although advances in genotyping chemistries and analysis methods continue to increase the potential advantages of using SNPs to address molecular ecological questions, the scarcity of available DNA sequence data for most species has limited marker development. As the number and diversity of species being targeted for large-scale sequencing has increased, so has the potential for using sequence from sister taxa for marker development in species of interest. We evaluated the use of Oncorhynchus mykiss and Salmo salar sequence data to identify SNPs in three other species (Oncorhynchus tshawytscha, Oncorhynchus nerka and Oncorhynchus keta). Primers designed based on O. mykiss and S. salar alignments were more successful than primers designed based on Oncorhynchus-only alignments for sequencing target species, presumably due to the much larger number of potential targets available from the former alignments and possibly greater sequence conservation in those targets. In sequencing approximately 89 kb we observed a frequency of 4.30 x 10(-3) SNPs per base pair. Approximately half (53/101) of the subsequently designed validation assays resulted in high-throughput SNP genotyping markers. We speculate that this relatively low conversion rate may reflect the duplicated nature of the salmon genome. Our results suggest that a large number of SNPs could be developed for Pacific salmon using sequence data from other species. While the costs of DNA sequencing are still significant, these must be compared to the costs of using other marker classes for a given application.}, } @article {pmid16256228, year = {2006}, author = {Miller, GY and McNamara, PE and Singer, RS}, title = {Stakeholder position paper: economist's perspectives on antibiotic use in animals.}, journal = {Preventive veterinary medicine}, volume = {73}, number = {2-3}, pages = {163-168}, doi = {10.1016/j.prevetmed.2005.09.018}, pmid = {16256228}, issn = {0167-5877}, mesh = {Animal Husbandry/economics/methods/statistics & numerical data ; *Animal Welfare ; Animals ; *Animals, Domestic ; Anti-Bacterial Agents/*adverse effects/*therapeutic use ; Databases, Factual ; *Drug Resistance, Bacterial ; Humans ; *Public Health ; Risk Assessment ; United States ; Veterinary Medicine/economics/methods/statistics & numerical data ; }, abstract = {Economics seeks to understand and explain the allocation of resources within society and to suggest appropriate policy to achieve goals such as optimal efficiency. Relating antimicrobial use and antibiotic resistance is a complex task and requires very clear and careful analyses of many relationships. To address these relationships, antibiotic use data must be linked with other basic data. Ideally, a complex relational database needs to be developed. These must include data on: antimicrobial usage, farm-level animal productivity, basic disease, basic farm management, consumer response, and antimicrobial resistance at multiple levels (farm, during process, on a variety of both animal, vegetable and grain-derived food products, from humans, from other animal species, and from the environment) among other data. Such a complex relational database can help with the attribution and risk assessment process. Also these linked data are needed in order to develop the economic production models and other economic models, as well as control for confounding so that there is both adequate and appropriate statistical control. Antimicrobial usage data may become economically important for reasons unrelated to animal productivity and animal health. With expanding global trade of animals and animal products, there have been changes in restrictions and regulations associated with the movement of products. Future trade opportunities may be linked to antimicrobial usage. The European Union banned the use of antimicrobials for growth-promoting purposes based on perceived risk and on public opinion. Monitoring antimicrobial use, disease occurrence, and resistance patterns following changes in usage that are a result of either policy changes or response to new information will help in the understanding of the complex relationships in microbial and disease ecology. There is a lot of evidence substantiating the productivity and profitability gains to producers from the use of antimicrobials. There is also evidence for the potential gains to consumers, both from an economic perspective as well as from a health perspective. Economists can help identify the implications of these relationships both at a micro- and macro-economic level; both relative to producer and to consumer welfare. We are at a pivotal time in history with sufficient analytical expertise and tools to address this complex issue from a scientific perspective. Linking various agencies so there can be coordination of data collection and data sharing is needed to successfully address this topic.}, } @article {pmid16248202, year = {2005}, author = {Biegel, M and Schanze, J and Krebs, P}, title = {ArcEGMO-URBAN--hydrological model for point sources in river basins.}, journal = {Water science and technology : a journal of the International Association on Water Pollution Research}, volume = {52}, number = {5}, pages = {249-256}, pmid = {16248202}, issn = {0273-1223}, mesh = {*Geographic Information Systems ; *Models, Theoretical ; Nitrogen/analysis ; Phosphorus/analysis ; Rivers ; Waste Disposal, Fluid/methods ; *Water Movements ; Water Pollutants/*analysis ; }, abstract = {The new model ArcEGMO-URBAN aims at deterministic and spatiotemporal modelling of water, nitrogen and phosphorus fluxes from all urbanised areas of a river basin considering all potential sources. Pollution loads are calculated for discrete urban patches and balanced on the level of hydrological subbasins. Modelling results can be defined by the user of any level of spatial and/or temporal aggregation, e.g. matter balances for river basins or river sections and years or months, respectively. To process spatial data, a Geographic Information System is linked to the model. Information on urban land use and general characteristics of river basins is based on digital coverages, partly generated from remote-sensing data. Moreover, statistical data, e.g. on population, sewer systems, wastewater treatment plants etc. are included. Stormwater runoff from impervious surfaces is calculated as one input to the sewer network. Wastewater is considered with its main sewer system, pumping stations and treatment plants. Finally, the discharge is balanced for discrete river sections. Modelling results attest ArcEGMO-URBAN its ability to realistically quantify matter fluxes and major pollution sources as well as their seasonal variation. This makes the model an applicable tool for the analysis of scenarios with e.g. varying population distribution or climatic and technological conditions.}, } @article {pmid16243679, year = {2006}, author = {Santos, SM and Barcellos, C and Sá Carvalho, M}, title = {Ecological analysis of the distribution and socio-spatial context of homicides in Porto Alegre, Brazil.}, journal = {Health & place}, volume = {12}, number = {1}, pages = {38-47}, doi = {10.1016/j.healthplace.2004.08.009}, pmid = {16243679}, issn = {1353-8292}, mesh = {Adolescent ; Adult ; Brazil ; Censuses ; Child ; Child, Preschool ; Female ; Geographic Information Systems ; Homicide/*trends ; Humans ; Male ; *Social Conditions ; *Spatial Behavior ; }, abstract = {Over the last decade, the number of homicides in Porto Alegre has increased to the point where external causes are now the main group of causes of death in the 5-34-year age group. Preventing these deaths depends fundamentally on identifying factors related to excess violence in population groups. The overall aim of this study is to analyse the spatial distribution of homicide victims by place of residence in Porto Alegre, the capital of the southernmost Brazilian State of Rio Grande do Sul, in 1996, in order to identify and understand the socio-spatial context. Demographic and socioeconomic indicators based on the 1991 census and 1996 population count were used to build a multivariate classification characterizing the 1851 census tracts. Homicides occurring in 1996 were located using the municipality's Geographic Information System. Four socioeconomic groups were identified, mainly differentiated by housing indicators. Small areas on the urban periphery in which slums (favelas) are concentrated presented higher homicide rates. Homicide rates were lower in the two groups with higher income and educational level. The second step was to classify the census tracts according to the homicide indicator. In this case, areas were differentiated by the number of household inhabitants per room, income, schooling, and median age. We conclude that the multivariate socioeconomic classification presents a limited capacity to identify populations exposed to homicides, suggesting that socioeconomic conditions themselves do not determine violent behaviour. On the other hand, the spatial methods allowed us to identify small areas where deaths are concentrated and whose populations should receive special attention in planning measures to prevent violent deaths.}, } @article {pmid16242176, year = {2006}, author = {Keller, V and Fox, K and Rees, HG and Young, AR}, title = {Estimating population served by sewage treatment works from readily available GIS data.}, journal = {The Science of the total environment}, volume = {360}, number = {1-3}, pages = {319-327}, doi = {10.1016/j.scitotenv.2005.08.043}, pmid = {16242176}, issn = {0048-9697}, mesh = {Geographic Information Systems ; *Household Products ; Models, Theoretical ; *Population ; Risk Assessment ; Rivers ; *Waste Disposal, Fluid ; *Water Pollutants, Chemical ; Water Supply ; }, abstract = {Environmental risk assessment of household chemicals at the catchment scale requires an estimate of the load at individual Sewage Treatment Works (STWs). This can be achieved based upon population served and market consumption data. Although the population served is difficult to obtain, this paper shows that reasonable estimates can be made using readily available spatially referenced data. A new method is developed using STW data from the Exe and the Aire and Calder catchments and validated using 193 STWs within the Environment Agency's Anglian region. The estimated populations served were compared with available estimates of Population Equivalents (PEs). The population estimates were broadly similar to PEs for small works but agreement was lower for larger plants. The discrepancy for larger works is consistent with trade influent inclusion in the PE. The method is suitable for application to both rural areas and large urbanised areas, although the interpretation of corroborating data becomes increasingly difficult in very large urban areas serving more than one STW.}, } @article {pmid16235820, year = {2005}, author = {Stambuk-Giljanović, N and Stambuk, D}, title = {Information subsystem of total hardness (Ca + Mg) as a database for studying its influence on human health.}, journal = {Journal of medical systems}, volume = {29}, number = {6}, pages = {671-678}, pmid = {16235820}, issn = {0148-5598}, mesh = {Calcium/*analysis ; Croatia ; *Databases, Factual ; Environmental Monitoring/*methods ; Humans ; Magnesium/*analysis ; Water Supply/*analysis ; }, abstract = {Dalmatia (Southern Croatia) belongs to the Dinaric karst region. The permeability of karst soil allows a great quantity of dissolved organic and toxic matter rendering it hygienically unsafe. The hinterland of the Dinaric karst region is relatively scarcely populated since the largest agglomeration of population and industry is in the coastal zones. Hence, most of the surface flow have preserved their natural characteristics. The water supply authorities and health care institutions are especially interested in observing and monitoring water quality. A relational database has been developed for carrying out chemical analyses expressed by total hardness (Ca + Mg) since it is necessary to organize and integrate a large number of analytical and ecological health-data. The database can serve as a methodological platform for the study of environmental factors influencing human health. The prototype database consists of data obtained by investigations which have been conducted by the Water Examination Department of the Public Health Institute, Split-Dalmatian County (Croatia) and the University of Split Medical School. The database currently contains more than 3000 data.}, } @article {pmid16235810, year = {2005}, author = {Stambuk-Giljanović, N and Stambuk, D}, title = {Information subsystem of the Ca/Mg ratio as a database for studying its influence on human health.}, journal = {Journal of medical systems}, volume = {29}, number = {6}, pages = {581-588}, pmid = {16235810}, issn = {0148-5598}, mesh = {Calcium/*analysis ; Croatia ; *Databases, Factual ; Environmental Monitoring/statistics & numerical data ; Fresh Water/*analysis ; Humans ; Magnesium/*analysis ; Seawater/*analysis ; Water Supply/*analysis ; }, abstract = {Dalmatia is situated in the Dinaric karst in Southern Croatia. It is characterized by insufficient quantities of water during the summer months and a relatively excessive amount of rainfall during the winter and spring months. Other hydrographic characteristics of Dinaric carst include scarce and long surface streamflows with a few tributaries with changeable capacities, a small number of springs, and a relatively great number of submarine springs along the coast. The water supply and health-care institutions are especially interested in observing and monitoring water quality. A relational database has been developed for carrying out chemical analyses expressed by the Ca/Mg ratio since it is necessary to organize and integrate a large number of analytical and ecological health data. The database can serve as a methodological platform for the study of environmental factors influencing human health. The prototype database consists of data obtained by investigations which have been conducted by the water Examination Department of the Public Health Institute of the Split Dalmatian county (Croatia) University of Split Medical School. The database currently contains more than 2500 data.}, } @article {pmid16222462, year = {2005}, author = {Dai, E and Wu, S and Shi, W and Cheung, CK and Shaker, A}, title = {Modeling change-pattern-value dynamics on land use: an integrated GIS and artificial neural networks approach.}, journal = {Environmental management}, volume = {36}, number = {4}, pages = {576-591}, pmid = {16222462}, issn = {0364-152X}, mesh = {Agriculture ; China ; *Conservation of Natural Resources ; Ecosystem ; Environmental Monitoring/methods ; *Geographic Information Systems ; *Neural Networks, Computer ; Rivers ; Trees ; }, abstract = {The use of spatial methods to detect and characterize changes in land use has been attracting increasing attention from researchers. The objectives of this article were to formulate the dynamics of land use on the temporal and spatial dimensions from the perspectives of the Change-Pattern-Value (CPV) and driving mechanism, based on multitemporal remote sensing data and socioeconomic data. The Artificial Neural Networks were used to identify the factors driving changes in land use. The Pearl River Delta Region of southeast China, which was experiencing rapid economic growth and widespread land conversion, has been selected as the study region. The results show that from 1985 to 2000 in the study region (1) the most prominent characteristics of change in land use were the expansion of the urban land at the expense of farmland, forests, and grasslands, (2) the land-use pattern was being optimized during this period, (3) in an analysis of value, built-up land can yield a return of more than 30 times that of farmland, water area, and forests lands, and (4) rapid economic development, growth in population, and the development of an infrastructure were major driving factors behind ecological land loss and the nonecological land expansion.}, } @article {pmid16217847, year = {2006}, author = {Jackson, C and Best, N and Richardson, S}, title = {Improving ecological inference using individual-level data.}, journal = {Statistics in medicine}, volume = {25}, number = {12}, pages = {2136-2159}, doi = {10.1002/sim.2370}, pmid = {16217847}, issn = {0277-6715}, mesh = {*Data Interpretation, Statistical ; *Environment ; Humans ; London ; *Models, Statistical ; Multivariate Analysis ; *Social Change ; Socioeconomic Factors ; }, abstract = {In typical small-area studies of health and environment we wish to make inference on the relationship between individual-level quantities using aggregate, or ecological, data. Such ecological inference is often subject to bias and imprecision, due to the lack of individual-level information in the data. Conversely, individual-level survey data often have insufficient power to study small-area variations in health. Such problems can be reduced by supplementing the aggregate-level data with small samples of data from individuals within the areas, which directly link exposures and outcomes. We outline a hierarchical model framework for estimating individual-level associations using a combination of aggregate and individual data. We perform a comprehensive simulation study, under a variety of realistic conditions, to determine when aggregate data are sufficient for accurate inference, and when we also require individual-level information. Finally, we illustrate the methods in a case study investigating the relationship between limiting long-term illness, ethnicity and income in London.}, } @article {pmid16216286, year = {2005}, author = {Ferrari, MJ and Bjørnstad, ON and Dobson, AP}, title = {Estimation and inference of R0 of an infectious pathogen by a removal method.}, journal = {Mathematical biosciences}, volume = {198}, number = {1}, pages = {14-26}, doi = {10.1016/j.mbs.2005.08.002}, pmid = {16216286}, issn = {0025-5564}, mesh = {Animals ; Communicable Diseases/*epidemiology ; Computer Simulation ; *Data Interpretation, Statistical ; *Disease Outbreaks ; Humans ; *Models, Biological ; }, abstract = {The basic reproductive ratio, R0, is a central quantity in the investigation and management of infectious pathogens. The standard model for describing stochastic epidemics is the continuous time epidemic birth-and-death process. The incidence data used to fit this model tend to be collected in discrete units (days, weeks, etc.), which makes model fitting, and estimation of R0 difficult. Discrete time epidemic models better match the time scale of data collection but make simplistic assumptions about the stochastic epidemic process. By investigating the nature of the assumptions of a discrete time epidemic model, we derive a bias corrected maximum likelihood estimate of R0 based on the chain binomial model. The resulting 'removal' estimators provide estimates of R0 and the initial susceptible population size from time series of infectious case counts. We illustrate the performance of the estimators on both simulated data and real epidemics. Lastly, we discuss methods to address data collected with observation error.}, } @article {pmid16214749, year = {2005}, author = {Markmann, M and Tautz, D}, title = {Reverse taxonomy: an approach towards determining the diversity of meiobenthic organisms based on ribosomal RNA signature sequences.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {360}, number = {1462}, pages = {1917-1924}, pmid = {16214749}, issn = {0962-8436}, mesh = {Animals ; Base Sequence ; *Biodiversity ; Cluster Analysis ; Computational Biology ; DNA/*genetics ; DNA Primers ; Electronic Data Processing/*methods ; Eukaryota/*genetics ; Fresh Water ; *Geologic Sediments ; Germany ; Invertebrates/*genetics ; Molecular Diagnostic Techniques/*methods ; Molecular Sequence Data ; RNA, Ribosomal, 28S/genetics ; Sequence Analysis, DNA ; }, abstract = {Organisms living in or on the sediment layer of water bodies constitute the benthos fauna, which is known to harbour a large number of species of diverse taxonomic groups. The benthos plays a significant role in the nutrient cycle and it is, therefore, of high ecological relevance. Here, we have explored a DNA-taxonomic approach to access the meiobenthic organismic diversity, by focusing on obtaining signature sequences from a part of the large ribosomal subunit rRNA (28S), the D3-D5 region. To obtain a broad representation of taxa, benthos samples were taken from 12 lakes in Germany, representing different ecological conditions. In a first approach, we have extracted whole DNA from these samples, amplified the respective fragment by PCR, cloned the fragments and sequenced individual clones. However, we found a relatively large number of recombinant clones that must be considered PCR artefacts. In a second approach we have, therefore, directly sequenced PCR fragments that were obtained from DNA extracts of randomly picked individual organisms. In total, we have obtained 264 new unique sequences, which can be readily placed into taxon groups, based on phylogenetic comparison with currently available database sequences. The group with the highest taxon abundance were nematodes and protozoa, followed by chironomids. However, we find also that we have by far not exhausted the diversity of organisms in the samples. Still, our data provide a framework within which a meiobenthos DNA signature sequence database can be constructed, that will allow to develop the necessary techniques for studying taxon diversity in the context of ecological analysis. Since many taxa in our analysis are initially only identified via their signature sequences, but not yet their morphology, we propose to call this approach 'reverse taxonomy'.}, } @article {pmid16214724, year = {2005}, author = {Prilleltensky, I}, title = {Promoting well-being: time for a paradigm shift in health and human services1.}, journal = {Scandinavian journal of public health. Supplement}, volume = {66}, number = {}, pages = {53-60}, doi = {10.1080/14034950510033381}, pmid = {16214724}, issn = {1403-4956}, mesh = {*Community Networks ; Decision Making ; Environmental Health ; *Health Promotion ; Humans ; Interpersonal Relations ; Personal Satisfaction ; *Preventive Health Services ; *Public Health ; Quality of Health Care ; Social Support ; Socioeconomic Factors ; }, abstract = {The promotion of personal, relational, and collective well-being has evolved markedly in the last three decades. However positive and needed, recent developments in health promotion require further conceptual clarification and synergistic applications. To assist with conceptual clarification, this article proposes to distinguish among sites, signs, sources, and strategies of well-being. With respect to applications, progress is discussed along four domains: temporal, ecological, participation, and capabilities. The temporal domain refers to the timing of interventions and entails a continuum from reactive to proactive strategies. The ecological domain pertains to the site of interventions, ranging from person-centered to community-centered. The participation domain refers to voice and choice of citizens and consumers in delivery of services and access to resources. At one end of this continuum there is empowerment, while at the opposite end we see disempowerment and detachment. Finally, the capabilities domain refers to the concentration on either strengths or deficits. This article argues that a singular focus on strength, prevention, empowerment, or community conditions is insufficient. It presents a framework for the conceptual integration of these four approaches, while illustrating the benefits of their synergy and the risks of their fragmentation. It is high time for a paradigm shift in health and human services, and this article argues that only a new approach that focuses on strengths, prevention, empowerment, and community conditions can make considerable progress towards the achievement of well-being for all.}, } @article {pmid16212995, year = {2005}, author = {Hanlon, P and Walsh, D and Whyte, B}, title = {Meeting the information needs of the 'Health for all' challenge--lessons from Scotland.}, journal = {Public health}, volume = {119}, number = {12}, pages = {1088-1096}, doi = {10.1016/j.puhe.2005.06.002}, pmid = {16212995}, issn = {0033-3506}, mesh = {Community Participation/methods ; Humans ; Information Systems/*organization & administration ; Public Health Administration/*methods ; Scotland ; }, abstract = {OBJECTIVE: To create a public health data resource for Scotland that is based on a socio-ecological model of the determinants of health and would, therefore, meets the needs of the emerging public health agenda.

DESIGN: Action research, in which the approach moved logically through stages of action (conception, feasibility study, pilot projects, leading to a national set of integrated health and well-being profiles). Each stage built on the results of the previous research.

RESULTS: The conceptual stage identified the need for an approach to public health data that kept pace with the increasingly accepted socio-ecological models of the determinants of health. A feasibility study concluded that sufficient data were available to populate the health fields that represented the important determinants of health. At this time strengths and weakness in data were defined. This led to the articulation of a 'vision' for integrated public heath data in Scotland that was the subject of a wide consultation. Pilot studies provided local stakeholders with imaginatively presented data (on population demographics, health and function, behaviour, social environment, economy, physical environment, morbidity and mortality) for their local communities. The response to these was so positive that a demand was created for a comprehensive set of 'community profiles'. These, in addition to parliamentary constituency profiles, have now been created and widely disseminated.

CONCLUSIONS: It has been possible, despite many difficulties, to develop approaches to public health information that are informed by the socio-ecological model of health and create outputs that represent a significant advance on previous approaches to public health data. This is a work in progress and many issues remain unresolved. Interaction with others engaged in parallel tasks will facilitate the next steps.}, } @article {pmid16208357, year = {2005}, author = {Sims, DW}, title = {Ecology: stars beneath the waves.}, journal = {Nature}, volume = {437}, number = {7060}, pages = {826}, doi = {10.1038/437826a}, pmid = {16208357}, issn = {1476-4687}, mesh = {Algorithms ; Animal Identification Systems/*methods ; Animals ; Databases, Factual ; Internet ; Pattern Recognition, Automated/*methods ; Population Dynamics ; Sharks/anatomy & histology/*physiology ; }, } @article {pmid16205993, year = {2005}, author = {Buckler, DR and Mayer, FL and Ellersieck, MR and Asfaw, A}, title = {Acute toxicity value extrapolation with fish and aquatic invertebrates.}, journal = {Archives of environmental contamination and toxicology}, volume = {49}, number = {4}, pages = {546-558}, doi = {10.1007/s00244-004-0151-8}, pmid = {16205993}, issn = {0090-4341}, mesh = {Animals ; Cholinesterase Inhibitors/toxicity ; Databases, Factual ; Fishes/*physiology ; Invertebrates/*physiology ; Lethal Dose 50 ; Risk Assessment ; Software ; Species Specificity ; Toxicity Tests/*statistics & numerical data ; Water Pollutants, Chemical/*analysis/*toxicity ; }, abstract = {Assessment of risk posed by an environmental contaminant to an aquatic community requires estimation of both its magnitude of occurrence (exposure) and its ability to cause harm (effects). Our ability to estimate effects is often hindered by limited toxicological information. As a result, resource managers and environmental regulators are often faced with the need to extrapolate across taxonomic groups in order to protect the more sensitive members of the aquatic community. The goals of this effort were to 1) compile and organize an extensive body of acute toxicity data, 2) characterize the distribution of toxicant sensitivity across taxa and species, and 3) evaluate the utility of toxicity extrapolation methods based upon sensitivity relations among species and chemicals. Although the analysis encompassed a wide range of toxicants and species, pesticides and freshwater fish and invertebrates were emphasized as a reflection of available data. Although it is obviously desirable to have high-quality acute toxicity values for as many species as possible, the results of this effort allow for better use of available information for predicting the sensitivity of untested species to environmental contaminants. A software program entitled "Ecological Risk Analysis" (ERA) was developed that predicts toxicity values for sensitive members of the aquatic community using species sensitivity distributions. Of several methods evaluated, the ERA program used with minimum data sets comprising acute toxicity values for rainbow trout, bluegill, daphnia, and mysids provided the most satisfactory predictions with the least amount of data. However, if predictions must be made using data for a single species, the most satisfactory results were obtained with extrapolation factors developed for rainbow trout (0.412), bluegill (0.331), or scud (0.041). Although many specific exceptions occur, our results also support the conventional wisdom that invertebrates are generally more sensitive to contaminants than fish are.}, } @article {pmid16191619, year = {2005}, author = {Slapeta, J and Moreira, D and López-García, P}, title = {The extent of protist diversity: insights from molecular ecology of freshwater eukaryotes.}, journal = {Proceedings. Biological sciences}, volume = {272}, number = {1576}, pages = {2073-2081}, pmid = {16191619}, issn = {0962-8452}, mesh = {Animals ; Base Sequence ; Bayes Theorem ; *Biodiversity ; Computational Biology ; DNA Primers ; *Ecosystem ; France ; Fresh Water ; *Genetic Variation ; Models, Genetic ; Molecular Sequence Data ; *Phylogeny ; Plankton/*genetics ; RNA, Ribosomal/genetics ; Sequence Analysis, DNA ; }, abstract = {Classical studies on protist diversity of freshwater environments worldwide have led to the idea that most species of microbial eukaryotes are known. One exemplary case would be constituted by the ciliates, which have been claimed to encompass a few thousands of ubiquitous species, most of them already described. Recently, molecular methods have revealed an unsuspected protist diversity, especially in oceanic as well as some extreme environments, suggesting the occurrence of a hidden diversity of eukaryotic lineages. In order to test if this holds also for freshwater environments, we have carried out a molecular survey of small subunit ribosomal RNA genes in water and sediment samples of two ponds, one oxic and another suboxic, from the same geographic area. Our results show that protist diversity is very high. The majority of phylotypes affiliated within a few well established eukaryotic kingdoms or phyla, including alveolates, cryptophytes, heterokonts, Cercozoa, Centroheliozoa and haptophytes, although a few sequences did not display a clear taxonomic affiliation. The diversity of sequences within groups was very large, particularly that of ciliates, and a number of them were very divergent from known species, which could define new intra-phylum groups. This suggests that, contrary to current ideas, the diversity of freshwater protists is far from being completely described.}, } @article {pmid16180767, year = {2005}, author = {He, H and Pan, Y and Zhu, W and Liu, X and Zhang, Q and Zhu, X}, title = {[Measurement of terrestrial ecosystem service value in China].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {16}, number = {6}, pages = {1122-1127}, pmid = {16180767}, issn = {1001-9332}, mesh = {China ; Conservation of Energy Resources/*economics ; Costs and Cost Analysis ; *Ecosystem ; Environmental Monitoring ; *Geographic Information Systems ; Models, Theoretical ; *Satellite Communications/instrumentation ; }, abstract = {With the measurement of net primary productivity and vegetation coverage fraction based on remote sensing data,the terrestrial ecosystem service value of China in 2000 was quantitatively estimated as 9.17 x 10(12) yuan (RMB). The spatial distribution of the ecological service value showed a decreasing trend from southeast China to northwest China, which was consistent with the regional distribution of vegetation types. The service value varied with different vegetations, e. g., forests had the highest service value of 18 789 yuan x hm(-2), accounting for 40.80% of the total terrestrial ecosystem service value, and bushes and farmlands had a higher service value of 13 789 yuan x hm(-2) and 13054 yuan x hm(-2), which was 10.79% and 24.23% of total value, respectively. The service value was also varied with different ecosystem functions, i.e., gas regulation contributed the highest value of 45.16% to the total service value, and the contribution of soil conservation and water conservation was 28.83% and 14.44%, respectively. The integrated approach coupling ecology and remote sensing data provided a new method to measure the ecological service value, which could estimate the value objectively and spatial-explicitly. However, some uncertainties still existed in this approach, which should be improved in the future studies.}, } @article {pmid16180742, year = {2005}, author = {Luo, C and Chen, Y and Hu, H and Shen, H and Fan, S}, title = {[Neural network grade program of natural forest protection].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {16}, number = {6}, pages = {1002-1006}, pmid = {16180742}, issn = {1001-9332}, mesh = {*Conservation of Natural Resources ; *Ecosystem ; *Forestry ; Geographic Information Systems ; *Neural Networks, Computer ; Trees/*growth & development ; }, abstract = {In this paper, the implement steps of natural forest protection program grading (NFPPG) with neural network (NN) were summarized, and the concepts of program illustration, patch sign unification and regress, and inclining factor were set forth. Employing Arc/Info GIS, the tree species diversity and rarity, disturbance degree, protection of channel system, and classification management in Moershan National Forest Park were described, and, used as the input factors of NN, the relationships between NFPPG and above factors were analyzed. Through artificially determining training samples, the NFFPG of Moershan National Forest Park was built. Tested with all patches in the park, the generalization of NFFPG was satisfied. NFPPG took both the classification management and the protection of forest community types into account, as well as the ecological environments. The excitation function of NFPPG was not seriously saturated, indicating the leading effect of inclining factor on the network optimization.}, } @article {pmid16174328, year = {2005}, author = {Roux, F and Reboud, X}, title = {Is the cost of herbicide resistance expressed in the breakdown of the relationships between characters? A case study using synthetic-auxin-resistant Arabidopsis thaliana mutants.}, journal = {Genetical research}, volume = {85}, number = {2}, pages = {101-110}, doi = {10.1017/S0016672305007378}, pmid = {16174328}, mesh = {Arabidopsis/anatomy & histology/drug effects/*genetics/metabolism ; Crosses, Genetic ; Data Interpretation, Statistical ; Drug Resistance/*genetics ; Genes, Plant/*drug effects ; Herbicides/*pharmacology ; Indoleacetic Acids/metabolism/pharmacology ; Mutation ; Quantitative Trait Loci ; }, abstract = {A mutation endowing herbicide resistance is often found to induce a parallel morphological or fitness penalty. To test whether such 'cost' of resistance to herbicides is expressed through lower resource acquisition, changes in resource allocation, or both, is of ecological significance. Here, we analysed 12 morphological traits in 900 plants covering three herbicide resistance mutations at genes AUX1 , AXR1 and AXR2 in the model species Arabidopsis thaliana . Comparing these 2,4-D herbicide-resistant homozygous (RR) and heterozygous (RS) plants to homozygous susceptible (SS) plants, this analysis estimates the dominance level of the resistance allele on morphology. We also demonstrated that the herbicide resistance cost was primarily expressed as a change in resource acquisition (62.1-94% of the analysed traits). Although AUX1 , AXR1 and AXR2 genes act in the same metabolic pathway of auxin response, each resistance factor was found to have its own unique signature in the way the cost was expressed. Furthermore, no link was observed between the absolute fitness penalty and the respective modifications of resource acquisition and/or resource allocation in the resistant plants. These results and their implications for herbicide resistance spread and establishment are discussed.}, } @article {pmid16171932, year = {2006}, author = {Etter, A and McAlpine, C and Pullar, D and Possingham, H}, title = {Modelling the conversion of Colombian lowland ecosystems since 1940: drivers, patterns and rates.}, journal = {Journal of environmental management}, volume = {79}, number = {1}, pages = {74-87}, doi = {10.1016/j.jenvman.2005.05.017}, pmid = {16171932}, issn = {0301-4797}, mesh = {Agriculture ; Colombia ; *Ecosystem ; *Environmental Monitoring ; Forecasting ; *Forestry ; *Geographic Information Systems ; Humans ; Models, Biological ; Population Dynamics ; Time Factors ; Tropical Climate ; }, abstract = {In biologically mega-diverse countries that are undergoing rapid human landscape transformation, it is important to understand and model the patterns of land cover change. This problem is particularly acute in Colombia, where lowland forests are being rapidly cleared for cropping and ranching. We apply a conceptual model with a nested set of a priori predictions to analyse the spatial and temporal patterns of land cover change for six 50-100 km(2) case study areas in lowland ecosystems of Colombia. Our analysis included soil fertility, a cost-distance function, and neighbourhood of forest and secondary vegetation cover as independent variables. Deforestation and forest regrowth are tested using logistic regression analysis and an information criterion approach to rank the models and predictor variables. The results show that: (a) overall the process of deforestation is better predicted by the full model containing all variables, while for regrowth the model containing only the auto-correlated neighbourhood terms is a better predictor; (b) overall consistent patterns emerge, although there are variations across regions and time; and (c) during the transformation process, both the order of importance and significance of the drivers change. Forest cover follows a consistent logistic decline pattern across regions, with introduced pastures being the major replacement land cover type. Forest stabilizes at 2-10% of the original cover, with an average patch size of 15.4 (+/-9.2)ha. We discuss the implications of the observed patterns and rates of land cover change for conservation planning in countries with high rates of deforestation.}, } @article {pmid16171529, year = {2005}, author = {Miklós, I and Meyer, IM}, title = {A linear memory algorithm for Baum-Welch training.}, journal = {BMC bioinformatics}, volume = {6}, number = {}, pages = {231}, pmid = {16171529}, issn = {1471-2105}, mesh = {*Algorithms ; Data Interpretation, Statistical ; *Markov Chains ; Mathematical Computing ; *Models, Statistical ; Sequence Alignment/*methods ; }, abstract = {BACKGROUND: Baum-Welch training is an expectation-maximisation algorithm for training the emission and transition probabilities of hidden Markov models in a fully automated way. It can be employed as long as a training set of annotated sequences is known, and provides a rigorous way to derive parameter values which are guaranteed to be at least locally optimal. For complex hidden Markov models such as pair hidden Markov models and very long training sequences, even the most efficient algorithms for Baum-Welch training are currently too memory-consuming. This has so far effectively prevented the automatic parameter training of hidden Markov models that are currently used for biological sequence analyses.

RESULTS: We introduce the first linear space algorithm for Baum-Welch training. For a hidden Markov model with M states, T free transition and E free emission parameters, and an input sequence of length L, our new algorithm requires O(M) memory and O(LMTmax (T + E)) time for one Baum-Welch iteration, where Tmax is the maximum number of states that any state is connected to. The most memory efficient algorithm until now was the checkpointing algorithm with O(log(L)M) memory and O(log(L)LMTmax) time requirement. Our novel algorithm thus renders the memory requirement completely independent of the length of the training sequences. More generally, for an n-hidden Markov model and n input sequences of length L, the memory requirement of O(log(L)L(n-1) M) is reduced to O(L(n-1) M) memory while the running time is changed from O(log(L)Ln MTmax + Ln(T + E)) to O(Ln MTmax (T + E)). An added advantage of our new algorithm is that a reduced time requirement can be traded for an increased memory requirement and vice versa, such that for any c e {1, ..., (T + E)}, a time requirement of Ln MTmax c incurs a memory requirement of L(n-1) M(T + E - c).

CONCLUSION: For the large class of hidden Markov models used for example in gene prediction, whose number of states does not scale with the length of the input sequence, our novel algorithm can thus be both faster and more memory-efficient than any of the existing algorithms.}, } @article {pmid16168080, year = {2005}, author = {Axmann, IM and Kensche, P and Vogel, J and Kohl, S and Herzel, H and Hess, WR}, title = {Identification of cyanobacterial non-coding RNAs by comparative genome analysis.}, journal = {Genome biology}, volume = {6}, number = {9}, pages = {R73}, pmid = {16168080}, issn = {1474-760X}, mesh = {Base Sequence ; Cluster Analysis ; Computational Biology ; Cyanobacteria/*genetics ; Genes, Bacterial/genetics ; Genome, Bacterial/*genetics ; Molecular Sequence Data ; Nucleic Acid Conformation ; RNA, Untranslated/chemistry/*genetics ; Research Design ; Sequence Alignment ; }, abstract = {BACKGROUND: Whole genome sequencing of marine cyanobacteria has revealed an unprecedented degree of genomic variation and streamlining. With a size of 1.66 megabase-pairs, Prochlorococcus sp. MED4 has the most compact of these genomes and it is enigmatic how the few identified regulatory proteins efficiently sustain the lifestyle of an ecologically successful marine microorganism. Small non-coding RNAs (ncRNAs) control a plethora of processes in eukaryotes as well as in bacteria; however, systematic searches for ncRNAs are still lacking for most eubacterial phyla outside the enterobacteria.

RESULTS: Based on a computational prediction we show the presence of several ncRNAs (cyanobacterial functional RNA or Yfr) in several different cyanobacteria of the Prochlorococcus-Synechococcus lineage. Some ncRNA genes are present only in two or three of the four strains investigated, whereas the RNAs Yfr2 through Yfr5 are structurally highly related and are encoded by a rapidly evolving gene family as their genes exist in different copy numbers and at different sites in the four investigated genomes. One ncRNA, Yfr7, is present in at least seven other cyanobacteria. In addition, control elements for several ribosomal operons were predicted as well as riboswitches for thiamine pyrophosphate and cobalamin.

CONCLUSION: This is the first genome-wide and systematic screen for ncRNAs in cyanobacteria. Several ncRNAs were both computationally predicted and their presence was biochemically verified. These RNAs may have regulatory functions and each shows a distinct phylogenetic distribution. Our approach can be applied to any group of microorganisms for which more than one total genome sequence is available for comparative analysis.}, } @article {pmid16159916, year = {2005}, author = {Chung, WH and Rhee, SK and Wan, XF and Bae, JW and Quan, ZX and Park, YH}, title = {Design of long oligonucleotide probes for functional gene detection in a microbial community.}, journal = {Bioinformatics (Oxford, England)}, volume = {21}, number = {22}, pages = {4092-4100}, doi = {10.1093/bioinformatics/bti673}, pmid = {16159916}, issn = {1367-4803}, mesh = {Algorithms ; Cluster Analysis ; Computational Biology/*methods ; Conserved Sequence ; DNA Primers/*chemistry ; DNA Probes/chemistry ; Ecology/methods ; Gene Expression Profiling/*methods ; *Genes, Bacterial ; *Genetic Techniques ; Genetic Variation ; *Genome, Bacterial ; Internet ; *Models, Genetic ; Models, Theoretical ; Oligonucleotide Array Sequence Analysis/methods ; Oligonucleotide Probes/genetics ; Programming Languages ; Software ; }, abstract = {MOTIVATION: Analysis of the functions of microorganisms and their dynamics in the environment is essential for understanding microbial ecology. For analysis of highly similar sequences of a functional gene family using microarrays, the previous long oligonucleotide probe design strategies have not been useful in generating probes.

RESULTS: We developed a Hierarchical Probe Design (HPD) program that designs both sequence-specific probes and hierarchical cluster-specific probes from sequences of a conserved functional gene based on the clustering tree of the genes, specifically for analyses of functional gene diversity in environmental samples. HPD was tested on datasets for the nirS and pmoA genes. Our results showed that HPD generated more sequence-specific probes than several popular oligonucleotide design programs. With a combination of sequence-specific and cluster-specific probes, HPD generated a probe set covering all the sequences of each test set.

AVAILABILITY: http://brcapp.kribb.re.kr/HPD/}, } @article {pmid16154784, year = {2005}, author = {Druzhinina, IS and Kopchinskiy, AG and Komoń, M and Bissett, J and Szakacs, G and Kubicek, CP}, title = {An oligonucleotide barcode for species identification in Trichoderma and Hypocrea.}, journal = {Fungal genetics and biology : FG & B}, volume = {42}, number = {10}, pages = {813-828}, doi = {10.1016/j.fgb.2005.06.007}, pmid = {16154784}, issn = {1087-1845}, mesh = {Base Sequence ; Biomarkers ; *Computational Biology ; DNA, Fungal/chemistry/genetics ; DNA, Ribosomal Spacer/genetics ; Databases, Nucleic Acid ; Hypocrea/*classification/genetics ; Molecular Sequence Data ; Mycological Typing Techniques/*methods ; Oligonucleotides/*genetics ; Phylogeny ; Sequence Analysis, DNA ; Trichoderma/*classification/genetics ; }, abstract = {One of the biggest obstructions to studies on Trichoderma has been the incorrect and confused application of species names to isolates used in industry, biocontrol of plant pathogens and ecological surveys, thereby making the comparison of results questionable. Here we provide a convenient, on-line method for the quick molecular identification of Hypocrea/Trichoderma at the genus and species levels based on an oligonucleotide barcode: a diagnostic combination of several oligonucleotides (hallmarks) specifically allocated within the internal transcribed spacer 1 and 2 (ITS1 and 2) sequences of the rDNA repeat. The barcode was developed on the basis of 979 sequences of 88 vouchered species which displayed in total 135 ITS1 and 2 haplotypes. Oligonucleotide sequences which are constant in all known ITS1 and 2 of Hypocrea/Trichoderma but different in closely related fungal genera, were used to define genus-specific hallmarks. The library of species-, clade- and genus-specific hallmarks is stored in the MySQL database and integrated in the TrichOKey v. 1.0 - barcode sequence identification program with the web interface located on . TrichOKey v. 1.0 identifies 75 single species, 5 species pairs and 1 species triplet. Verification of the DNA-barcode was done by a blind test on 53 unknown isolates of Trichoderma, collected in Central and South America. The obtained results were in a total agreement with phylogenetic identification based on tef1 (large intron), NCBI BLAST of vouchered records and postum morphological analysis. We conclude that oligonucleotide barcode is a powerful tool for the routine identification of Hypocrea/Trichoderma species and should be useful as a complement to traditional methods.}, } @article {pmid16154684, year = {2006}, author = {Xu, J and Chen, L and Lu, Y and Fu, B}, title = {Local people's perceptions as decision support for protected area management in Wolong Biosphere Reserve, China.}, journal = {Journal of environmental management}, volume = {78}, number = {4}, pages = {362-372}, doi = {10.1016/j.jenvman.2005.05.003}, pmid = {16154684}, issn = {0301-4797}, mesh = {Adolescent ; Adult ; Aged ; Animals ; China ; *Conservation of Natural Resources ; Data Collection ; *Decision Support Techniques ; Female ; *Health Knowledge, Attitudes, Practice ; Humans ; Male ; Middle Aged ; Public Opinion ; }, abstract = {This paper examines local people's knowledge, attitudes and perceptions towards Wolong Biosphere Reserve (WBR) and its management policies. Pertinent data were collected through a questionnaire survey and group discussions. This study revealed that local people's perceptions were affected by many factors, including education, gender, residence location, household size and acreage of land owned. Although most respondents had limited knowledge about WBR because of their absence in WBR management, they held a positive attitude towards WBR. An in-depth analysis of their attitudes and perceptions showed that two potential conflicts might affect biodiversity conservation and protected area management. One of them was the imbalance between the limited cropland holding and the oversupply of the labor force, and the other one was the increase in electricity price versus the decrease in economic incentives for the Natural Forest Protection Project. The study also revealed that relocation was considered unacceptable to most respondents. However, those residing far from the main road were willing to relocate more than those near the main road. Based on our studies, some recommendations are given for improvement of WBR management.}, } @article {pmid16153293, year = {2005}, author = {Pushker, R and D'Auria, G and Alba-Casado, JC and Rodríguez-Valera, F}, title = {Micro-Mar: a database for dynamic representation of marine microbial biodiversity.}, journal = {BMC bioinformatics}, volume = {6}, number = {}, pages = {222}, pmid = {16153293}, issn = {1471-2105}, mesh = {Base Sequence ; *Biodiversity ; Classification ; *Databases, Factual ; *Databases, Genetic ; Ecosystem ; Information Storage and Retrieval/methods ; *Marine Biology ; Sequence Analysis, Protein ; }, abstract = {BACKGROUND: The cataloging of marine prokaryotic DNA sequences is a fundamental aspect for bioprospecting and also for the development of evolutionary and speciation models. However, large amount of DNA sequences used to quantify prokaryotic biodiversity requires proper tools for storing, managing and analyzing these data for research purposes.

DESCRIPTION: The Micro-Mar database has been created to collect DNA diversity information from marine prokaryotes for biogeographical and ecological analyses. The database currently includes 11874 sequences corresponding to high resolution taxonomic genes (16S rRNA, ITS and 23S rRNA) and many other genes including CDS of marine prokaryotes together with available biogeographical and ecological information.

CONCLUSION: The database aims to integrate molecular data and taxonomic affiliation with biogeographical and ecological features that will allow to have a dynamic representation of the marine microbial diversity embedded in a user friendly web interface. It is available online at http://egg.umh.es/micromar/.}, } @article {pmid16151181, year = {2006}, author = {He, X and Zhang, J}, title = {Higher duplicability of less important genes in yeast genomes.}, journal = {Molecular biology and evolution}, volume = {23}, number = {1}, pages = {144-151}, doi = {10.1093/molbev/msj015}, pmid = {16151181}, issn = {0737-4038}, mesh = {Computational Biology ; *Evolution, Molecular ; *Gene Duplication ; Genome, Fungal/*genetics ; Likelihood Functions ; Models, Genetic ; *Phylogeny ; Saccharomyces cerevisiae/*genetics ; Selection, Genetic ; }, abstract = {Gene duplication plays an important role in evolution because it is the primary source of new genes. Many recent studies showed that gene duplicability varies considerably among genes. Several considerations led us to hypothesize that less important genes have higher rates of successful duplications, where gene importance is measured by the fitness reduction caused by the deletion of the gene. Here, we test this hypothesis by comparing the importance of two groups of singleton genes in the yeast Saccharomyces cerevisiae (Sce). Group S genes did not duplicate in four other yeast species examined, whereas group D experienced duplication in these species. Consistent with our hypothesis, we found group D genes to be less important than group S genes. Specifically, 17% of group D genes are essential in Sce, compared to 28% for group S. Furthermore, deleting a group D gene in Sce reduces the fitness by 24% on average, compared to 38% for group S. Our subsequent analysis showed that less important genes have more cis-regulatory motifs, which could lead to a higher chance of subfunctionalization of duplicate genes and result in an enhanced rate of gene retention. Less important genes may also have weaker dosage imbalance effects and cause fewer genetic perturbations when duplicated. Regardless of the cause, our observation indicates that the previous finding of a less severe fitness consequence of deleting a duplicate gene than deleting a singleton gene is at least in part due to the fact that duplicate genes are intrinsically less important than singleton genes and suggests that the contribution of duplicate genes to genetic robustness has been overestimated.}, } @article {pmid16150155, year = {2005}, author = {Nandi, S and Mehra, N and Lynn, AM and Bhattacharya, A}, title = {Comparison of theoretical proteomes: identification of COGs with conserved and variable pI within the multimodal pI distribution.}, journal = {BMC genomics}, volume = {6}, number = {}, pages = {116}, pmid = {16150155}, issn = {1471-2164}, mesh = {Bacterial Proteins ; Cluster Analysis ; Computational Biology/*methods ; Computer Simulation ; Databases, Protein ; Electrophoresis, Gel, Two-Dimensional ; *Genome, Bacterial ; Hydrogen-Ion Concentration ; Isoelectric Point ; Models, Statistical ; Open Reading Frames ; Proteins/chemistry ; *Proteome ; Proteomics/*methods ; }, abstract = {BACKGROUND: Theoretical proteome analysis, generated by plotting theoretical isoelectric points (pI) against molecular masses of all proteins encoded by the genome show a multimodal distribution for pI. This multimodal distribution is an effect of allowed combinations of the charged amino acids, and not due to evolutionary causes. The variation in this distribution can be correlated to the organisms ecological niche. Contributions to this variation maybe mapped to individual proteins by studying the variation in pI of orthologs across microorganism genomes.

RESULTS: The distribution of ortholog pI values showed trimodal distributions for all prokaryotic genomes analyzed, similar to whole proteome plots. Pairwise analysis of pI variation show that a few COGs are conserved within, but most vary between, the acidic and basic regions of the distribution, while molecular mass is more highly conserved. At the level of functional grouping of orthologs, five groups vary significantly from the population of orthologs, which is attributed to either conservation at the level of sequences or a bias for either positively or negatively charged residues contributing to the function. Individual COGs conserved in both the acidic and basic regions of the trimodal distribution are identified, and orthologs that best represent the variation in levels of the acidic and basic regions are listed.

CONCLUSION: The analysis of pI distribution by using orthologs provides a basis for resolution of theoretical proteome comparison at the level of individual proteins. Orthologs identified that significantly vary between the major acidic and basic regions maybe used as representative of the variation of the entire proteome.}, } @article {pmid16136809, year = {2005}, author = {Rüber, L and Zardoya, R}, title = {Rapid cladogenesis in marine fishes revisited.}, journal = {Evolution; international journal of organic evolution}, volume = {59}, number = {5}, pages = {1119-1127}, pmid = {16136809}, issn = {0014-3820}, mesh = {Animals ; DNA, Ribosomal/genetics ; Databases, Nucleic Acid ; *Evolution, Molecular ; Fishes/*genetics ; Likelihood Functions ; Marine Biology ; *Models, Theoretical ; Monte Carlo Method ; *Phylogeny ; Proteins/genetics ; Sequence Alignment ; Species Specificity ; Time Factors ; }, abstract = {Lineages that underwent rapid cladogenesis are attractive systems for the study of mechanisms underlying taxonomic, ecological, morphological, and behavioral diversification. Recently developed statistical methods provide insights into historical patterns of diversity and allow distinguishing bursts of cladogenesis from stochastic background rates in the presence of confounding factors such as extinction and incomplete taxon sampling. Here, we compare the dynamics of speciation in several marine fish lineages some of which were previously proposed to have undergone significant changes of cladogenesis through time. We tested for evidence of episodes of rapid cladogenesis using the constant rate and Monte Carlo constant rate tests that are robust to incomplete taxon sampling. These tests employ the statistic gamma to measure the relative position of internal node in a chronogram. For the first time, we conducted a comparative analysis to address the behavior of the statistic under different chronogram-constructing methods (Langley-Fitch, nonparametric rate smoothing, and penalized likelihood). Although estimates of gamma sometimes differ widely among methods, acceptance or rejection of the constant rate model within a particular clade appears to be robust to the choice of method. Bursts of cladogenesis were detected in 14 of 34 studied datasets. Some of these were previously proposed to represent marine fish "radiations," whereas others are identified anew. Our results indicate that the wider application of tree shape methods that are able to detect significantly elevated rates of speciation is useful to more precisely define clades that underwent episodes of rapid cladogenesis in marine fish clades. Contrasting the patterns of phylogenetic diversification in marine fish lineages may facilitate the identification of common evolutionary trajectories versus idiosyncrasies, and ultimately help towards a better understanding of the factors and processes underlying speciation in the marine realm.}, } @article {pmid16135018, year = {2005}, author = {Zhu, J and Eickhoff, JC and Yan, P}, title = {Generalized linear latent variable models for repeated measures of spatially correlated multivariate data.}, journal = {Biometrics}, volume = {61}, number = {3}, pages = {674-683}, doi = {10.1111/j.1541-0420.2005.00343.x}, pmid = {16135018}, issn = {0006-341X}, mesh = {Algorithms ; Animals ; Coleoptera/growth & development ; *Data Interpretation, Statistical ; Longitudinal Studies ; *Models, Statistical ; Monte Carlo Method ; *Multivariate Analysis ; Pinus ; Plant Diseases/parasitology ; }, abstract = {Observations of multiple-response variables across space and over time occur often in environmental and ecological studies. Compared to purely spatial models for a single response variable in the exponential family of distributions, fewer statistical tools are available for multiple-response variables that are not necessarily Gaussian. An exception is a common-factor model developed for multivariate spatial data by Wang and Wall (2003, Biostatistics 4, 569-582). The purpose of this article is to extend this multivariate space-only model and develop a flexible class of generalized linear latent variable models for multivariate spatial-temporal data. For statistical inference, maximum likelihood estimates and their standard deviations are obtained using a Monte Carlo EM algorithm. We also use a novel way to automatically adjust the Monte Carlo sample size, which facilitates the convergence of the Monte Carlo EM algorithm. The methodology is illustrated by an ecological study of red pine trees in response to bark beetle challenges in a forest stand of Wisconsin.}, } @article {pmid16131463, year = {2006}, author = {Chen, XK and Yang, Q and Smith, G and Krewski, D and Walker, M and Wen, SW}, title = {Environmental lead level and pregnancy-induced hypertension.}, journal = {Environmental research}, volume = {100}, number = {3}, pages = {424-430}, doi = {10.1016/j.envres.2005.07.006}, pmid = {16131463}, issn = {0013-9351}, mesh = {Adult ; Age Factors ; Air Pollutants/*adverse effects ; Databases, Factual ; *Environmental Exposure ; Female ; Humans ; Hypertension, Pregnancy-Induced/epidemiology/*etiology ; Incidence ; Lead/*adverse effects ; Middle Aged ; Odds Ratio ; Parity ; Pregnancy ; Prenatal Care ; United States/epidemiology ; }, abstract = {Previous studies have suggested that environmental lead exposure increases the risk of hypertension in the general population. In this article, the authors used the 1998 linked birth/infant death database of the United States to examine the association between environmental lead level and the occurrence of pregnancy-induced hypertension (PIH). Yearly summaries of environmental lead levels were abstracted from the US Environmental Protection Agency's air pollution databases, and linked with birth/infant death records by state codes. Generalized estimating equations (GEEs) were used to evaluate the odds ratios of PIH associated with environmental lead measured at ecological levels, with adjustment for maternal age, race, education level, marital status, parity, and adequacy of prenatal care measured at individual levels, stratified by maternal cigarette smoking. A total of 2,994,072 women pregnant in 1998 were included in this study. With the first quartile of lead level as the reference group, the odds ratio for PIH among all study subjects in the second quartile of seasonal average lead level at conception was 1.07 (95% CI: 1.05-1.08), and odds ratios in the third and fourth quartiles were 1.22 (95% CI: 1.20-1.25) and 1.16 (95% CI: 1.15-1.18), respectively. The odds ratios for the second, third, and fourth quartiles of seasonal average lead level at birth were 1.07 (95% CI: 1.05-1.09), 1.21 (95% CI: 1.19-1.23), and 1.15 (95% CI: 1.13-1.17), respectively. The risk of PIH increased by 4% per 0.05 microg/m3 increase in seasonal average lead level at conception and birth, in both smokers and nonsmokers. These results suggest that higher environmental lead levels increase the risk of PIH.}, } @article {pmid16112638, year = {2005}, author = {Yang, GJ and Vounatsou, P and Zhou, XN and Utzinger, J and Tanner, M}, title = {A review of geographic information system and remote sensing with applications to the epidemiology and control of schistosomiasis in China.}, journal = {Acta tropica}, volume = {96}, number = {2-3}, pages = {117-129}, doi = {10.1016/j.actatropica.2005.07.006}, pmid = {16112638}, issn = {0001-706X}, mesh = {Animals ; China/epidemiology ; Climate ; Ecology ; *Geographic Information Systems ; Humans ; *Satellite Communications ; Schistosomiasis japonica/epidemiology/*prevention & control/transmission ; Snails/parasitology ; }, abstract = {Geographic information system (GIS) and remote sensing (RS) technologies offer new opportunities for rapid assessment of endemic areas, provision of reliable estimates of populations at risk, prediction of disease distributions in areas that lack baseline data and are difficult to access, and guidance of intervention strategies, so that scarce resources can be allocated in a cost-effective manner. Here, we focus on the epidemiology and control of schistosomiasis in China and review GIS and RS applications to date. These include mapping prevalence and intensity data of Schistosoma japonicum at a large scale, and identifying and predicting suitable habitats for Oncomelania hupensis, the intermediate host snail of S. japonicum, at a small scale. Other prominent applications have been the prediction of infection risk due to ecological transformations, particularly those induced by floods and water resource developments, and the potential impact of climate change. We also discuss the limitations of the previous work, and outline potential new applications of GIS and RS techniques, namely quantitative GIS, WebGIS, and utilization of emerging satellite information, as they hold promise to further enhance infection risk mapping and disease prediction. Finally, we stress current research needs to overcome some of the remaining challenges of GIS and RS applications for schistosomiasis, so that further and sustained progress can be made to control this disease in China and elsewhere.}, } @article {pmid16094778, year = {2005}, author = {Titov, N and Knight, RG}, title = {A computer-based procedure for assessing functional cognitive skills in patients with neurological injuries: the virtual street.}, journal = {Brain injury}, volume = {19}, number = {5}, pages = {315-322}, doi = {10.1080/02699050400013725}, pmid = {16094778}, issn = {0269-9052}, mesh = {Brain Injuries/complications/*psychology ; Cognition Disorders/etiology/*psychology ; Cues ; Diagnosis, Computer-Assisted/*methods ; *Disability Evaluation ; Humans ; Memory Disorders/etiology/psychology ; *Mental Recall ; Microcomputers ; Middle Aged ; Neuropsychological Tests ; Pilot Projects ; User-Computer Interface ; }, abstract = {PRIMARY OBJECTIVE: The aim of the present investigation was to construct and pilot test a computer-based multi-tasking procedure that could be used to assess the ability of patients with neurological damage to remember instructions in the real world.

RESEARCH DESIGN: A simulated street scene was constructed from a network of photographs and sounds that patients could move through using a touch screen. Three patients with severe, moderate or mild cognitive impairment were assessed on a range of neuropsychological tests and three multi-tasking procedures based in the street. The performance of each patient was compared with that of a matched control.

PROCEDURE: Three tests were administered, each of which involved 'walking' along the length of the street once. On the first test, participants were given up to five errands to remember while moving along the street. On the other two tests they were given three instructions to carry out repeatedly (e.g. 'Record the name of the nearest shop when you hear a dog bark'). In one condition they were given the three instructions on a sheet they could consult and in the other they had no list.

OUTCOMES AND RESULTS: In each case the patient performed more poorly on the multi-tasking test than the matched control. The patients' performance on the computer-based tests was consistent with clinical descriptions of their memory-related deficits.

CONCLUSION: The results illustrate the way in which computer presentation of naturalistic stimuli can be used to construct flexible and standardized tests of memory functioning that have enhanced ecological validity.}, } @article {pmid16089508, year = {2005}, author = {Field, D and Tiwari, B and Snape, J}, title = {Bioinformatics and data management support for environmental genomics.}, journal = {PLoS biology}, volume = {3}, number = {8}, pages = {e297}, doi = {10.1371/journal.pbio.0030297}, pmid = {16089508}, issn = {1545-7885}, mesh = {*Computational Biology ; *Database Management Systems ; *Databases, Factual ; Ecology ; *Environment ; Genomics/*methods ; Microarray Analysis ; Software ; }, abstract = {The UK Natural Environment Research Council has funded the creation of a dedicated bioinformatics centre as part of a £26m Environmental Genomics initiative.}, } @article {pmid16079603, year = {2005}, author = {Anno, S and Kudo, S and Hamasaki, K and Matsumura, K and Yamamoto, T and Ogata, K}, title = {Techniques of SNP genotyping and remote sensing applied for elucidation of the contribution of polygene and environmental factors to inter-individual variation in skin pigmentation phenotype.}, journal = {Journal of physiological anthropology and applied human science}, volume = {24}, number = {4}, pages = {483-486}, doi = {10.2114/jpa.24.483}, pmid = {16079603}, issn = {1345-3475}, mesh = {Atmosphere/analysis ; Computational Biology/*methods ; Databases, Genetic ; *Environment ; *Genetic Variation ; *Genome, Human ; Genotype ; Humans ; Polymorphism, Single Nucleotide/*genetics ; Skin Pigmentation/*genetics ; Spectrophotometry/methods ; Telemetry/methods ; }, abstract = {We present a conceptual framework for applying techniques of SNP genotyping as a molecular biological approach and remote sensing as an ecological approach to elucidation of the contribution of polygene and environmental factors to inter-individual variation in skin pigmentation phenotype. Additionally, we discuss the obstacles that frustrate our efforts to identify how the human genome encodes the complex phenotype and suggest the use of computational methods designed for knowledge discovery within hereditary database.}, } @article {pmid16079584, year = {2005}, author = {Balanovsky, O and Pocheshkhova, E and Pshenichnov, A and Solovieva, D and Kuznetsova, M and Voronko, O and Churnosov, M and Tegako, O and Atramentova, L and Lavryashina, M and Evseeva, I and Borinska, S and Boldyreva, M and Dubova, N and Balanovska, E}, title = {Is spatial distribution of the HIV-1-resistant CCR5Delta32 allele formed by ecological factors?.}, journal = {Journal of physiological anthropology and applied human science}, volume = {24}, number = {4}, pages = {375-382}, doi = {10.2114/jpa.24.375}, pmid = {16079584}, issn = {1345-3475}, mesh = {Asia ; Databases, Genetic ; *Demography ; Emigration and Immigration ; *Environment ; Europe ; Gene Frequency ; *Genetic Predisposition to Disease ; *Genetics, Population ; HIV Infections/*genetics ; *HIV-1 ; Humans ; Mutation/genetics ; Receptors, CCR5/*genetics ; }, abstract = {It has been proposed that the Delta32 mutation in the chemokine receptor gene, inducing resistance to HIV-1 and, probably, to other virus infections, has undergone selection in historical times. The frequency of this mutant allele has changed rapidly both in time (during the last two millennia) and in space (across Eurasia). We compiled a global database on Delta32 allele frequencies in 300 populations. Nearly 10 percent of them are our data on 35 East European populations analyzed here for the first time. A detailed map of Delta32 frequency distribution was constructed and statistically analysed. We found a linearly decreasing trend with a maximum in areas surrounding the Baltic and White seas. Significant correlations with ground surface temperature were revealed. However, compared with our previous results, these correlations diminished, indicating that the influence of climate on Delta32 distribution was, if anything at all, indirect. The proposed scenario includes: i) arise and initial spread of the mutation among Uralic-speaking populations; ii) a frequency increase in northeastern Europe as a result of selection and/or genetic drift; iii) secondary spread (with selection continued) due to gene flow and the migrations of northern Europeans across the globe.}, } @article {pmid16079242, year = {2005}, author = {Yamauchi, A}, title = {Rate of gene transfer from mitochondria to nucleus: effects of cytoplasmic inheritance system and intensity of intracellular competition.}, journal = {Genetics}, volume = {171}, number = {3}, pages = {1387-1396}, pmid = {16079242}, issn = {0016-6731}, mesh = {Cell Nucleus/*genetics/metabolism ; DNA, Mitochondrial/*metabolism ; Data Interpretation, Statistical ; Evolution, Molecular ; Extrachromosomal Inheritance/*genetics ; Intracellular Fluid/*metabolism ; Mitochondria/*genetics/metabolism ; Models, Genetic ; }, abstract = {Endosymbiotic theory states that mitochondria originated as bacterial intracellular symbionts, the size of the mitochondrial genome gradually reducing over a long period owing to, among other things, gene transfer from the mitochondria to the nucleus. Such gene transfer was observed in more genes in animals than in plants, implying a higher transfer rate of animals. The evolution of gene transfer may have been affected by an intensity of intracellular competition among organelle strains and the organelle inheritance system of the organism concerned. This article reveals a relationship between those factors and the gene transfer rate from organelle to nuclear genomes, using a mathematical model. Mutant mitochondria that lose a certain gene by deletion are considered to replicate more rapidly than normal ones, resulting in an advantage in intracellular competition. If the competition is intense, heteroplasmic individuals possessing both types of mitochondria change to homoplasmic individuals including mutant mitochondria only, with high probability. According to the mathematical model, it was revealed that the rate of gene transfer from mitochondria to the nucleus can be affected by three factors, the intensity of intracellular competition, the probability of paternal organelle transmission, and the effective population size. The gene transfer rate tends to increase with decreasing intracellular competition, increasing paternal organelle transmission, and decreasing effective population size. Intense intracellular competition tends to suppress gene transfer because it is likely to exclude mutant mitochondria that lose the essential gene due to the production of lethal individuals.}, } @article {pmid16079069, year = {2005}, author = {Reynolds, P and Hurley, SE and Gunier, RB and Yerabati, S and Quach, T and Hertz, A}, title = {Residential proximity to agricultural pesticide use and incidence of breast cancer in California, 1988-1997.}, journal = {Environmental health perspectives}, volume = {113}, number = {8}, pages = {993-1000}, pmid = {16079069}, issn = {0091-6765}, support = {U01 CA081789/CA/NCI NIH HHS/United States ; CA81789/CA/NCI NIH HHS/United States ; }, mesh = {Adult ; Aged ; Aged, 80 and over ; Agrochemicals/*toxicity ; Breast Neoplasms/epidemiology/*etiology ; California ; *Environmental Exposure ; Female ; Geographic Information Systems ; Housing ; Humans ; Incidence ; Middle Aged ; Pesticides/*toxicity ; }, abstract = {California is the largest agricultural state in the United States and home to some of the world's highest breast cancer rates. The objective of our study was to evaluate whether California breast cancer rates were elevated in areas with recent high agricultural pesticide use. We identified population-based invasive breast cancer cases from the California Cancer Registry for 1988-1997. We used California's pesticide use reporting data to select pesticides for analysis based on use volume, carcinogenic potential, and exposure potential. Using 1990 and 2000 U.S. Census data, we derived age- and race-specific population counts for the time period of interest. We used a geographic information system to aggregate cases, population counts, and pesticide use data for all block groups in the state. To evaluate whether breast cancer rates were related to recent agricultural pesticide use, we computed rate ratios and 95% confidence intervals using Poisson regression models, adjusting for age, race/ethnicity, and neighborhood socioeconomic status and urbanization. This ecologic (aggregative) analysis included 176,302 invasive breast cancer cases and 70,968,598 person-years of observation. The rate ratios did not significantly differ from 1 for any of the selected pesticide categories or individual agents. The results from this study provide no evidence that California women living in areas of recent, high agricultural pesticide use experience higher rates of breast cancer.}, } @article {pmid16053061, year = {2005}, author = {Burke, M}, title = {GM crop study produces major database.}, journal = {Environmental science & technology}, volume = {39}, number = {13}, pages = {280A}, doi = {10.1021/es053403d}, pmid = {16053061}, issn = {0013-936X}, mesh = {Agriculture ; Animals ; Classification ; Data Collection ; *Databases, Factual ; Ecology ; Environmental Monitoring ; *Food Chain ; Plants, Edible ; *Plants, Genetically Modified ; Risk Assessment ; }, } @article {pmid16050080, year = {2005}, author = {Stambuk-Giljanović, N and Stambuk, D}, title = {Information subsystem of the SO4/Cl ratio as database for studying its influence on human health.}, journal = {Journal of medical systems}, volume = {29}, number = {3}, pages = {251-257}, pmid = {16050080}, issn = {0148-5598}, mesh = {Chlorides/*analysis ; Croatia ; *Databases, Factual ; Environmental Monitoring/*methods ; Fresh Water/*analysis ; Sulfates/*analysis ; Water Supply/analysis ; }, abstract = {General lack of surface waters in the Dalmatian region on one hand (Croatia) and a large profusion and complexity of underground waters circulation, on the other hand, are typical phenomena of Dalmatian Karst region. Underground waters in Dalmatia belong to rift water similar to surface waters considering its hydrochemical and hygienic characteristics. Health care institutions and water authorities have become particularly interested in observing and monitoring water as well as preserving its quality. A relational database has been developed for carrying out chemical analyses expressed by the SO4/Cl ratio since it is necessary to organize and integrate a large number of analytical and ecological health-data. The database can serve as a methodological platform for the study of environmental factors influencing human health. The prototype database consists of data obtained by investigations, which have been conducted by the Water Examination Department of the Public Health Institute of Split Dalmatian County (Croatia) and University of Split Medical School. The database currently contains more than 3000 data.}, } @article {pmid16044680, year = {2005}, author = {Stensgaard, A and Jørgensen, A and Kabatereine, NB and Malone, JB and Kristensen, TK}, title = {Modeling the distribution of Schistosoma mansoni and host snails in Uganda using satellite sensor data and Geographical Information Systems.}, journal = {Parassitologia}, volume = {47}, number = {1}, pages = {115-125}, pmid = {16044680}, issn = {0048-2951}, mesh = {Animals ; Biomphalaria/*parasitology ; Child ; *Computer Simulation ; Disease Vectors ; *Ecosystem ; Endemic Diseases ; Fresh Water/parasitology ; *Geographic Information Systems ; Humans ; *Models, Theoretical ; Prevalence ; *Schistosoma mansoni ; Schistosomiasis mansoni/epidemiology/prevention & control/*transmission ; Schools ; Seasons ; Temperature ; Topography, Medical/*methods ; Uganda ; }, abstract = {The potential value of MODIS satellite sensor data on Normalized Difference Vegetation Index (NDVI) and land surface temperatures (LST) for describing the distribution of the Schistosoma mansoni-"Biomphalaria pfeifferi"/Biomphalaria sudanica parasite-snail system in inland Uganda, were tested by developing annual and seasonal composite models, and iteratively analysing for their relationship with parasite and snail distribution. The dry season composite model predicted an endemic area that produced the best fit with the distribution of schools with > or =5% prevalence. NDVI values of 151-174, day temperatures of 26-36 degrees C, and night temperatures of 15-20 degrees C were used as criteria for the prediction model. Using the same approach with host snail data indicated that most of Uganda is suitable "B. pfeifferi"/B. sudanica habitat, except for possibly the north-eastern region of the country. The parasite, however, appears to be restricted in its distribution in both the north-eastern and the south-western regions of Uganda. The absence of disease in the south-west can not be attributed to the absence of snail hosts. Results suggest a combination of satellite sensor data on temperature and standard climate data on precipitation, as the best ecological determinants of the S. mansoni-"B. pfeifferi"/B. sudanica system. Satellite composite models and logistic regression analysis, suggest low night time temperature as one of the significant factors inhibiting S. mansoni transmission in the south-western highland areas of Uganda. The developed models are, however, unique, representing species-specific ecologic preferences of the S. mansoni-"B. Pfeifferi"/B. sudanica system in inland Uganda. Further validation studies are needed to test the value of the model in other countries in East Africa.}, } @article {pmid16044678, year = {2005}, author = {de La Rocque, S and Michel, JF and Bouyer, J and De Wispelaere, G and Cuisance, D}, title = {Geographical Information Systems in parasitology: a review of potential applications using the example of animal trypanosomosis in West Africa.}, journal = {Parassitologia}, volume = {47}, number = {1}, pages = {97-104}, pmid = {16044678}, issn = {0048-2951}, mesh = {Africa, Western/epidemiology ; Agriculture ; Animals ; Cattle ; *Ecosystem ; Environment ; *Geographic Information Systems ; Host-Parasite Interactions ; Insect Vectors/parasitology ; Parasitology/*methods ; Prevalence ; Rivers ; Satellite Communications/instrumentation ; Seasons ; Trees ; Trypanosoma/physiology ; Trypanosomiasis, African/epidemiology/transmission/*veterinary ; Trypanosomiasis, Bovine/*epidemiology/transmission ; Tsetse Flies/parasitology ; }, abstract = {The epidemiology of vector-borne diseases is complex due to the variability in the ecology of the different actors involved, i.e. hosts, parasites and vectors. The transmission of African animal trypanosomosis in the West-African savannah region is an excellent example of this complexity: riverine tsetse flies have an heterogeneous distribution along the rivers, depending of suitable habitats, and transmit pathogenic trypanosomes were they use domestic animal as feeding hosts. Contrasting epidemiological situations may thus occur at the local scale, and a broad view of the overall environment is necessary to quantify the interfaces in time and space between hosts and vectors. Geographical Information Systems (GIS) can provide new insight into the study of such complex epidemiological processes. GIS is a powerful technology that has been used mainly in map-making, and an enormous amount of knowledge can be gained simply by geographical data projection. GIS also allows juxtaposition of different types of information, creation of new variables, testing of theories and correlation, and generating of predictive models. The purpose of the present paper is to exemplify the potential application of GIS using a recent study carried out on animal trypanosomosis in a cattle-raising area of Burkina Faso.}, } @article {pmid16044674, year = {2005}, author = {Malone, JB}, title = {Biology-based mapping of vector-borne parasites by Geographic Information Systems and Remote Sensing.}, journal = {Parassitologia}, volume = {47}, number = {1}, pages = {27-50}, pmid = {16044674}, issn = {0048-2951}, support = {R15-AI-28192/AI/NIAID NIH HHS/United States ; }, mesh = {Africa, Eastern/epidemiology ; Agriculture/methods ; Animals ; Anopheles/parasitology ; Budgets ; Cattle ; Cattle Diseases/*epidemiology/transmission ; *Climate ; Disease Vectors ; Ecology ; Egypt/epidemiology ; Environmental Monitoring/*instrumentation ; Epidemiological Monitoring ; Fascioliasis/epidemiology/transmission/*veterinary ; *Geographic Information Systems ; Humans ; Louisiana/epidemiology ; Malaria/*epidemiology/transmission ; Prevalence ; Risk ; *Satellite Communications ; Schistosomiasis/*epidemiology/transmission ; Snails/parasitology ; Soil ; Temperature ; Topography, Medical/instrumentation/*methods ; Water Supply/economics ; }, abstract = {Applications of growing degree day-water budget analysis and satellite climatology to vector-borne parasites are reviewed to demonstrate the value of using the unique thermal-hydrological preferences and limits of tolerance of individual parasite-vector systems to define the environmental niche of disease agents in the landscape by modern geospatial analysis methods.}, } @article {pmid16044673, year = {2005}, author = {Cringoli, G and Rinaldi, L and Veneziano, V and Musella, V}, title = {Disease mapping and risk assessment in veterinary parasitology: some case studies.}, journal = {Parassitologia}, volume = {47}, number = {1}, pages = {9-25}, pmid = {16044673}, issn = {0048-2951}, mesh = {Animals ; Cattle ; Cattle Diseases/epidemiology/parasitology ; Climate ; Coccidiosis/epidemiology/veterinary ; Cross-Sectional Studies ; Dirofilaria immitis ; Dirofilariasis/epidemiology ; Disease Reservoirs ; Dog Diseases/epidemiology/parasitology ; Dogs ; Ecology/methods ; Environmental Monitoring/instrumentation ; Epidemiological Monitoring ; Female ; Fresh Water ; Geographic Information Systems ; Helminthiasis, Animal/*epidemiology ; Italy/epidemiology ; Male ; *Maps as Topic ; Models, Theoretical ; Neospora ; Paramphistomatidae ; Parasitology/*methods ; Plants ; Risk Assessment ; Satellite Communications ; Seasons ; Sheep ; Sheep Diseases/epidemiology/parasitology ; Topography, Medical/*methods ; Trematode Infections/epidemiology/veterinary ; Veterinary Medicine/*methods ; }, abstract = {Disease mapping and risk assessment are important tasks in the area of medical and veterinary epidemiology. The development of methods for mapping diseases has progressed considerably in recent years. Geographical Information Systems (GIS), Remote Sensing (RS), and Spatial Analysis represent new tools for the study of epidemiology, and their application to parasitology has become more and more advanced, in particular to study the spatial and temporal patterns of diseases. The present review highlights the usefulness of GIS and RS in veterinary parasitology in order to better know the epidemiology of parasite organisms, causing either snail/arthropod borne diseases or direct transmissible diseases, mostly in small areas with a strong impact by man. It demonstrates the potential of these technologies to serve as effective tools for: data capture, mapping and analysis for the development of descriptive parasitological maps; studying the environmental features that influence the distribution of parasites; predicting parasite occurrence/seasonality based on their environmental requirements and as decision support for disease intervention; and surveillance and monitoring of animal diseases.}, } @article {pmid16044208, year = {2005}, author = {Hawe, P and Riley, T}, title = {Ecological theory in practice: illustrations from a community-based intervention to promote the health of recent mothers.}, journal = {Prevention science : the official journal of the Society for Prevention Research}, volume = {6}, number = {3}, pages = {227-236}, pmid = {16044208}, issn = {1389-4986}, mesh = {Community Networks/*organization & administration ; Female ; *Health Promotion ; Humans ; *Maternal Welfare ; Models, Theoretical ; Qualitative Research ; Victoria ; }, abstract = {We present a qualitative case study where we used four principles of ecological theory from community psychology as a template to assess the dynamics about how a preventive community intervention was transacted in eight communities in Victoria, Australia. The principles were cycling of resources, interdependence, adaptation, and succession. Ecological thinking focuses on key resources in communities. That is, the people, events, and settings that are the foundations of thinking about communities as systems. The data set consists of field diaries kept by and serial interviews with nine community development workers over a 2-year period. We found that the analysis highlighted a process-oriented way of representing the intervention, one that sees beyond the intervention's technical components (or packaged elements) to the complexities of the cultural and political change processes occurring beneath. The value of this is the attention focussed on likely project sustainability.}, } @article {pmid16040705, year = {2005}, author = {Sibly, RM and Barker, D and Denham, MC and Hone, J and Pagel, M}, title = {On the regulation of populations of mammals, birds, fish, and insects.}, journal = {Science (New York, N.Y.)}, volume = {309}, number = {5734}, pages = {607-610}, doi = {10.1126/science.1110760}, pmid = {16040705}, issn = {1095-9203}, mesh = {Animals ; Animals, Wild ; *Birds ; Conservation of Natural Resources ; Databases, Factual ; *Ecosystem ; Environment ; *Fishes ; *Insecta ; Logistic Models ; *Mammals ; Mathematics ; Models, Biological ; Phylogeny ; Population Density ; Population Dynamics ; Population Growth ; Regression Analysis ; }, abstract = {A key unresolved question in population ecology concerns the relationship between a population's size and its growth rate. We estimated this relationship for 1780 time series of mammals, birds, fish, and insects. We found that rates of population growth are high at low population densities but, contrary to previous predictions, decline rapidly with increasing population size and then flatten out, for all four taxa. This produces a strongly concave relationship between a population's growth rate and its size. These findings have fundamental implications for our understanding of animals' lives, suggesting in particular that many animals in these taxa will be found living at densities above the carrying capacity of their environments.}, } @article {pmid16040696, year = {2005}, author = {Reynolds, JD and Freckleton, RP}, title = {Ecology. Population dynamics: growing to extremes.}, journal = {Science (New York, N.Y.)}, volume = {309}, number = {5734}, pages = {567-568}, doi = {10.1126/science.1116268}, pmid = {16040696}, issn = {1095-9203}, mesh = {Animals ; Animals, Wild ; *Birds ; Conservation of Natural Resources ; Databases, Factual ; *Ecosystem ; Environment ; *Fishes ; *Insecta ; Logistic Models ; *Mammals ; Models, Biological ; Population Density ; Population Dynamics ; Population Growth ; }, } @article {pmid16040072, year = {2006}, author = {Opitz, R and Lutz, I and Nguyen, NH and Scanlan, TS and Kloas, W}, title = {Analysis of thyroid hormone receptor betaA mRNA expression in Xenopus laevis tadpoles as a means to detect agonism and antagonism of thyroid hormone action.}, journal = {Toxicology and applied pharmacology}, volume = {212}, number = {1}, pages = {1-13}, doi = {10.1016/j.taap.2005.06.014}, pmid = {16040072}, issn = {0041-008X}, support = {DK-52798/DK/NIDDK NIH HHS/United States ; }, mesh = {Acetates/pharmacology ; Animals ; Antithyroid Agents/*pharmacology ; Biomarkers ; Data Interpretation, Statistical ; Drug Evaluation, Preclinical ; Endocrine Disruptors/*pharmacology ; Gene Expression Regulation/drug effects ; Hindlimb/physiology ; Indicators and Reagents ; Larva ; Metamorphosis, Biological/drug effects ; Phenols/pharmacology ; RNA, Messenger/*biosynthesis/*genetics ; Reverse Transcriptase Polymerase Chain Reaction ; Thyroid Hormone Receptors alpha/genetics ; Thyroid Hormone Receptors beta/*biosynthesis/*genetics ; Thyroid Hormones/*agonists ; Xenopus laevis ; }, abstract = {Amphibian metamorphosis represents a unique biological model to study thyroid hormone (TH) action in vivo. In this study, we examined the utility of thyroid hormone receptors alpha (TRalpha) and betaA (TRbetaA) mRNA expression patterns in Xenopus laevis tadpoles as molecular markers indicating modulation of TH action. During spontaneous metamorphosis, only moderate changes were evident for TRalpha gene expression whereas a marked up-regulation of TRbetaA mRNA occurred in hind limbs (prometamorphosis), head (late prometamorphosis), and tail tissue (metamorphic climax). Treatment of premetamorphic tadpoles with 1 nM 3,5,3'-triiodothyronine (T3) caused a rapid induction of TRbetaA mRNA in head and tail tissue within 6 to 12 h which was maintained for at least 72 h after initiation of T3 treatment. Developmental stage had a strong influence on the responsiveness of tadpole tissues to induce TRbetaA mRNA during 24 h treatment with thyroxine (0, 1, 5, 10 nM T4) or T3 (0, 1, 5, 10 nM). Premetamorphic tadpoles were highly sensitive in their response to T4 and T3 treatments, whereas sensitivity to TH was decreased in early prometamorphic tadpoles and strongly diminished in late prometamorphic tadpoles. To examine the utility of TRbetaA gene expression analysis for detection of agonistic and antagonistic effects on T3 action, mRNA expression was assessed in premetamorphic tadpoles after 48 h of treatment with the synthetic agonist GC-1 (0, 10, 50, 250 nM), the synthetic antagonist NH-3 (0, 40, 200, 1000 nM), and binary combinations of NH-3 (0, 40, 200, 1000 nM) and T3 (1 nM). All tested concentrations of GC-1 as well as the highest concentration of NH-3 caused an up-regulation of TRbetaA expression. Co-treatment with NH-3 and T3 revealed strong antagonistic effects by NH-3 on T3-induced TRbetaA mRNA up-regulation. Results of this study suggest that TRbetaA mRNA expression analysis could serve as a sensitive molecular testing approach to study effects of environmental compounds on the thyroid system in X. laevis tadpoles.}, } @article {pmid16027999, year = {2005}, author = {Nietch, CT and Borst, M and Schubauer-Berigan, JP}, title = {Risk management of sediment stress: a framework for sediment risk management research.}, journal = {Environmental management}, volume = {36}, number = {2}, pages = {175-194}, pmid = {16027999}, issn = {0364-152X}, mesh = {*Conservation of Natural Resources ; *Decision Support Techniques ; *Geologic Sediments ; Models, Theoretical ; Risk ; Rivers ; *Water Supply ; }, abstract = {Research related to the ecological risk management of sediment stress in watersheds is placed under a common conceptual framework in order to help promote the timely advance of decision support methods for aquatic resource managers and watershed-level planning. The proposed risk management research program relies heavily on model development and verification, and should be applied under an adaptive management approach. The framework is centered on using best management practices (BMPs), including eco-restoration. It is designed to encourage the development of numerical representations of the performance of these management options, the integration of this information into sediment transport simulation models that account for uncertainty in both input and output, and would use strategic environmental monitoring to guide sediment-related risk management decisions for mixed land use watersheds. The goal of this project was to provide a sound scientific framework based on recent state of the practice in sediment-related risk assessment and management for research and regulatory activities. As a result, shortcomings in the extant data and measurement and modeling tools were identified that can help determine future research direction. The compilation of information is beneficial to the coordination of related work being conducted within and across entities responsible for managing watershed-scale risks to aquatic ecosystems.}, } @article {pmid16024491, year = {2005}, author = {Goldberg, MS and Burnett, RT}, title = {A new longitudinal design for identifying subgroups of the population who are susceptible to the short-term effects of ambient air pollution.}, journal = {Journal of toxicology and environmental health. Part A}, volume = {68}, number = {13-14}, pages = {1111-1125}, doi = {10.1080/15287390590935950}, pmid = {16024491}, issn = {1528-7394}, mesh = {Air Pollutants/*adverse effects ; Air Pollution/*adverse effects ; Data Interpretation, Statistical ; Humans ; *Longitudinal Studies ; *Research Design ; Risk Factors ; }, abstract = {A longitudinal design is proposed to investigate the short-term effects of air pollution on health status. The study design exploits a new statistical methodology developed by Dewanji and Moolgavkar (2000, 2002) that makes use of a Poisson counting process for the incidence of events in a longitudinal cohort study. The methodology allows for modeling of subject-specific baseline hazards of multiple events and time-dependent ecological (i.e., daily levels of air pollution and weather conditions) and individual covariates (e.g., comorbid conditions, indices of declines in health status). The study will determine the association between short-term changes in air pollution and incidence of hospitalization, emergency department visits, "intermediate health conditions" (e.g., changes in health status reflected by changes in filled prescriptions), and mortality. Data from the universal Quebec medicare system are used, including data for residents of Montreal age 65 yr and above. The cohorts include individuals who have at baseline airways disease, chronic coronary artery disease, congestive heart failure, hypertension, cerebrovascular disease, atherosclerosis, dysrhythmias, and diabetes, and these will be followed for the incidence of the already mentioned adverse outcomes, adjusting for time-dependent individual and ecological covariates. This type of study will provide findings that can be used to confirm or refute results of time series analyses. Using a different methodology that includes subject-specific information will greatly increase our understanding as to whether short-term exposures to ambient air pollution cause serious changes in health status among subgroups of the population. These results will also help in understanding mechanisms by identifying groups that are susceptible to the effects of air pollution.}, } @article {pmid16024490, year = {2005}, author = {Krewski, D and Burnett, R and Jerrett, M and Pope, CA and Rainham, D and Calle, E and Thurston, G and Thun, M}, title = {Mortality and long-term exposure to ambient air pollution: ongoing analyses based on the American Cancer Society cohort.}, journal = {Journal of toxicology and environmental health. Part A}, volume = {68}, number = {13-14}, pages = {1093-1109}, doi = {10.1080/15287390590935941}, pmid = {16024490}, issn = {1528-7394}, mesh = {Air Pollution/*adverse effects ; American Cancer Society ; Cohort Studies ; Data Collection ; Data Interpretation, Statistical ; Dose-Response Relationship, Drug ; Humans ; Mortality/*trends ; Particle Size ; Risk Assessment ; United States/epidemiology ; Urban Population ; }, abstract = {This article provides an overview of previous analysis and reanalysis of the American Cancer Society (ACS) cohort, along with an indication of current ongoing analyses of the cohort with additional follow-up information through to 2000. Results of the first analysis conducted by Pope et al. (1995) showed that higher average sulfate levels were associated with increased mortality, particularly from cardiopulmonary disease. A reanalysis of the ACS cohort, undertaken by Krewski et al. (2000), found the original risk estimates for fine-particle and sulfate air pollution to be highly robust against alternative statistical techniques and spatial modeling approaches. A detailed investigation of covariate effects found a significant modifying effect of education with risk of mortality associated with fine particles declining with increasing educational attainment. Pope et al. (2002) subsequently reported results of a subsequent study using an additional 10 yr of follow-up of the ACS cohort. This updated analysis included gaseous copollutant and new fine-particle measurements, more comprehensive information on occupational exposures, dietary variables, and the most recent developments in statistical modeling integrating random effects and nonparametric spatial smoothing into the Cox proportional hazards model. Robust associations between ambient fine particulate air pollution and elevated risks of cardiopulmonary and lung cancer mortality were clearly evident, providing the strongest evidence to date that long-term exposure to fine particles is an important health risk. Current ongoing analysis using the extended follow-up information will explore the role of ecologic, economic, and, demographic covariates in the particulate air pollution and mortality association. This analysis will also provide insight into the role of spatial autocorrelation at multiple geographic scales, and whether critical instances in time of exposure to fine particles influence the risk of mortality from cardiopulmonary and lung cancer. Information on the influence of covariates at multiple scales and of critical exposure time windows can assist policymakers in establishing timelines for regulatory interventions that maximize population health benefits.}, } @article {pmid16014867, year = {2005}, author = {Shi, T and Bibby, TS and Jiang, L and Irwin, AJ and Falkowski, PG}, title = {Protein interactions limit the rate of evolution of photosynthetic genes in cyanobacteria.}, journal = {Molecular biology and evolution}, volume = {22}, number = {11}, pages = {2179-2189}, doi = {10.1093/molbev/msi216}, pmid = {16014867}, issn = {0737-4038}, mesh = {Computational Biology ; Cyanobacteria/*genetics/metabolism ; Electron Transport/genetics ; *Evolution, Molecular ; Gene Order ; *Models, Molecular ; Multigene Family/*genetics ; Photosynthetic Reaction Center Complex Proteins/*genetics/*metabolism ; Selection, Genetic ; Sequence Alignment ; Sequence Analysis, Protein ; Species Specificity ; }, abstract = {Using a bioinformatic approach, we analyzed the correspondence in genetic distance matrices between all possible pairwise combinations of 82 photosynthetic genes in 10 species of cyanobacteria. Our analysis reveals significant correlations between proteins linked in a conserved gene order and between structurally identified interacting protein scaffolds that coordinate the binding of cofactors involved in photosynthetic electron transport. Analyses of amino acid substitution rates suggest that the tempo of evolution of genes encoding core metabolic processes in the photosynthetic apparatus is highly constrained by protein-protein, protein-lipid, and protein-cofactor interactions (collectively called "protein interactions"). These interactions are critical for energy transduction, primary charge separation, and electron transport and effectively act as an internal selection pressure governing the conservation of clusters of photosynthetic genes in oxygenic prokaryotic photoautotrophs. Consequently, although several proteins within the photosynthetic apparatus are biophysically and physiologically inefficient, selection has not significantly altered the genes encoding these essential proteins over billions of years of evolution. In effect, these core proteins have become "frozen metabolic accidents."}, } @article {pmid16012095, year = {2005}, author = {Lewis, PO and Holder, MT and Holsinger, KE}, title = {Polytomies and Bayesian phylogenetic inference.}, journal = {Systematic biology}, volume = {54}, number = {2}, pages = {241-253}, doi = {10.1080/10635150590924208}, pmid = {16012095}, issn = {1063-5157}, mesh = {*Bayes Theorem ; Chlorophyta/genetics ; Classification/*methods ; *Data Interpretation, Statistical ; Markov Chains ; Monte Carlo Method ; *Phylogeny ; Reproducibility of Results ; }, abstract = {Bayesian phylogenetic analyses are now very popular in systematics and molecular evolution because they allow the use of much more realistic models than currently possible with maximum likelihood methods. There are, however, a growing number of examples in which large Bayesian posterior clade probabilities are associated with very short branch lengths and low values for non-Bayesian measures of support such as nonparametric bootstrapping. For the four-taxon case when the true tree is the star phylogeny, Bayesian analyses become increasingly unpredictable in their preference for one of the three possible resolved tree topologies as data set size increases. This leads to the prediction that hard (or near-hard) polytomies in nature will cause unpredictable behavior in Bayesian analyses, with arbitrary resolutions of the polytomy receiving very high posterior probabilities in some cases. We present a simple solution to this problem involving a reversible-jump Markov chain Monte Carlo (MCMC) algorithm that allows exploration of all of tree space, including unresolved tree topologies with one or more polytomies. The reversible-jump MCMC approach allows prior distributions to place some weight on less-resolved tree topologies, which eliminates misleadingly high posteriors associated with arbitrary resolutions of hard polytomies. Fortunately, assigning some prior probability to polytomous tree topologies does not appear to come with a significant cost in terms of the ability to assess the level of support for edges that do exist in the true tree. Methods are discussed for applying arbitrary prior distributions to tree topologies of varying resolution, and an empirical example showing evidence of polytomies is analyzed and discussed.}, } @article {pmid16011435, year = {2005}, author = {Ward, MP and Ramsay, BH and Gallo, K}, title = {Rural cases of equine West Nile virus encephalomyelitis and the normalized difference vegetation index.}, journal = {Vector borne and zoonotic diseases (Larchmont, N.Y.)}, volume = {5}, number = {2}, pages = {181-188}, doi = {10.1089/vbz.2005.5.181}, pmid = {16011435}, issn = {1530-3667}, mesh = {Animals ; Biomass ; Cluster Analysis ; Disease Outbreaks/veterinary ; Ecology ; *Geographic Information Systems ; Horse Diseases/*epidemiology ; Horses ; Indiana/epidemiology ; Plants ; Population Surveillance ; Rural Health ; Seasons ; Topography, Medical/*methods ; West Nile Fever/epidemiology/*veterinary ; }, abstract = {Data from an outbreak (August to October, 2002) of West Nile virus (WNV) encephalomyelitis in a population of horses located in northern Indiana was scanned for clusters in time and space. One significant (p = 0.04) cluster of case premises was detected, occurring between September 4 and 10 in the south-west part of the study area (85.70 degrees N, 45.50 degrees W). It included 10 case premises (3.67 case premises expected) within a radius of 2264 m. Image data were acquired by the Advanced Very High Resolution Radiometer (AVHRR) sensor onboard a National Oceanic and Atmospheric Administration polar-orbiting satellite. The Normalized Difference Vegetation Index (NDVI) was calculated from visible and near-infrared data of daily observations, which were composited to produce a weekly-1km(2) resolution raster image product. During the epidemic, a significant (p < 0.01) decrease (0.025 per week) in estimated NDVI was observed at all case and control premise sites. The median estimated NDVI (0.659) for case premises within the cluster identified was significantly (p < 0.01) greater than the median estimated NDVI for other case (0.571) and control (0.596) premises during the same period. The difference in median estimated NDVI for case premises within this cluster, compared to cases not included in this cluster, was greatest (5.3% and 5.1%, respectively) at 1 and 5 weeks preceding occurrence of the cluster. The NDVI may be useful for identifying foci of WNV transmission.}, } @article {pmid16011160, year = {2005}, author = {Dong, Y and Quan, Z and Zhao, Y}, title = {[ComGIS-based regional landscape pattern monitoring information system].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {16}, number = {4}, pages = {647-650}, pmid = {16011160}, issn = {1001-9332}, mesh = {*Ecosystem ; Electronic Data Processing ; *Environmental Monitoring ; *Geographic Information Systems ; }, abstract = {Based on the requirement of scientifically managing landscape ecological data and dynamically monitoring regional landscape pattern, and with the Zhifanggou region in North Shaanxi Province as an example, this paper developed a regional landscape pattern monitoring information system (RLPMIS) by the combination of Delphi and MapX. The planning route and establishing method of the system were simply explained, and its basic structure and function were explicated. This system was mainly divided into four parts, i.e., data management module, query management module, landscape index analysis module, and landscape forecasting module. In this system, the graphics and the attributes of the landscape data were integrated entirely and managed effectively, and thus, the spatial information could be displayed, located and inquired in the RLPMIS. The landscape pattern could be comprehensively analyzed based on the various landscape indexes of landscape elements or whole landscape being calculated, and the landscape developing trend could be forecasted and simulated. At the same time, the statistical graph and table, which visually reflected the landscape pattern, developed and changed disciplinarian in different periods, could be dynamically generated.}, } @article {pmid16004509, year = {2005}, author = {Barnosky, AD and Carrasco, MA and Davis, EB}, title = {The impact of the species-area relationship on estimates of paleodiversity.}, journal = {PLoS biology}, volume = {3}, number = {8}, pages = {e266}, pmid = {16004509}, issn = {1545-7885}, mesh = {Animals ; *Biodiversity ; *Fossils ; Geographic Information Systems ; *Geography ; Mammals/classification ; Paleontology/methods ; Probability ; }, abstract = {Estimates of paleodiversity patterns through time have relied on datasets that lump taxonomic occurrences from geographic areas of varying size per interval of time. In essence, such estimates assume that the species-area effect, whereby more species are recorded from larger geographic areas, is negligible for fossil data. We tested this assumption by using the newly developed Miocene Mammal Mapping Project database of western North American fossil mammals and its associated analysis tools to empirically determine the geographic area that contributed to species diversity counts in successive temporal bins. The results indicate that a species-area effect markedly influences counts of fossil species, just as variable spatial sampling influences diversity counts on the modern landscape. Removing this bias suggests some traditionally recognized peaks in paleodiversity are just artifacts of the species-area effect while others stand out as meriting further attention. This discovery means that there is great potential for refining existing time-series estimates of paleodiversity, and for using species-area relationships to more reliably understand the magnitude and timing of such biotically important events as extinction, lineage diversification, and long-term trends in ecological structure.}, } @article {pmid16004372, year = {2005}, author = {Vossbrinck, CR and Debrunner-Vossbrinck, BA}, title = {Molecular phylogeny of the Microsporidia: ecological, ultrastructural and taxonomic considerations.}, journal = {Folia parasitologica}, volume = {52}, number = {1-2}, pages = {131-42; discussion 130}, doi = {10.14411/fp.2005.017}, pmid = {16004372}, issn = {0015-5683}, mesh = {Animals ; Cluster Analysis ; Databases, Nucleic Acid ; *Environment ; Microsporidia/classification/*genetics ; *Phylogeny ; RNA, Ribosomal/genetics ; }, abstract = {The Microsporidia are a group of obligate intracellular parasites, now thought to be derived fungi. Presented here is a comparative small subunit rDNA (ssrDNA) analysis of 125 species of Microsporidia (sequences obtained from GenBank). This analysis shows that groups or clades are formed based largely on habitat and host. This result is supported by comparative molecular analyses of the past decade, and indicates that structural and ultrastructural characters are unreliable for distinguishing among higher-level microsporidian taxa. Our findings indicate the presence of five major clades of Microsporidia which group according to habitat. We present three new classes of Microsporidia based on natural phylogenetic groupings as illustrated by the ssrDNA analysis: Aquasporidia, Marinosporidia and Terresporidia. The names of the proposed classes reflect the habitat of each group. The class Aquasporidia, found primarily in freshwater habitats, is a paraphyletic group consisting of three clades. The Marinosporidia are found in hosts of marine origin and the Terresporidia are primarily from terrestrial environments.}, } @article {pmid16001713, year = {2005}, author = {Leimgruber, P and Christen, CA and Laborderie, A}, title = {The impact of landsat satellite monitoring on conservation biology.}, journal = {Environmental monitoring and assessment}, volume = {106}, number = {1-3}, pages = {81-101}, pmid = {16001713}, issn = {0167-6369}, mesh = {Biology ; *Conservation of Natural Resources ; Environmental Monitoring/*methods ; *Geographic Information Systems/history/statistics & numerical data ; History, 20th Century ; History, 21st Century ; Humans ; *Satellite Communications ; }, abstract = {Landsat 7's recent malfunctioning will result in significant gaps in long-term satellite monitoring of Earth, affecting not only the research of the Earth science community but also conservation users of these data. To determine whether or how important Landsat monitoring is for conservation and natural resource management, we reviewed the Landsat program's history with special emphasis on the development of user groups. We also conducted a bibliographic search to determine the extent to which conservation research has been based on Landsat data. Conservation biologists were not an early user group of Landsat data because a) biologists lacked technical capacity--computers and software--to analyze these data; b) Landsat's 1980s commercialization rendered images too costly for biologists' budgets; and c) the broad-scale disciplines of conservation biology and landscape ecology did not develop until the mid-to-late 1980s. All these conditions had changed by the 1990s and Landsat imagery became an important tool for conservation biology. Satellite monitoring and Landsat continuity are mandated by the Land Remote Sensing Act of 1992. This legislation leaves open commercial options. However, past experiments with commercial operations were neither viable nor economical, and severely reduced the quality of monitoring, archiving and data access for academia and the public. Future satellite monitoring programs are essential for conservation and natural resource management, must provide continuity with Landsat, and should be government operated.}, } @article {pmid16000703, year = {2005}, author = {Field, D and Feil, EJ and Wilson, GA}, title = {Databases and software for the comparison of prokaryotic genomes.}, journal = {Microbiology (Reading, England)}, volume = {151}, number = {Pt 7}, pages = {2125-2132}, doi = {10.1099/mic.0.28006-0}, pmid = {16000703}, issn = {1350-0872}, mesh = {*Computational Biology ; Databases, Nucleic Acid ; Databases, Protein ; *Genome, Bacterial ; *Genomics ; Sequence Alignment ; Software ; }, abstract = {The explosion in the number of complete genomes over the past decade has spawned a new and exciting discipline, that of comparative genomics. To exploit the full potential of this approach requires the development of novel algorithms, databases and software which are sophisticated enough to draw meaningful comparisons between complete genome sequences and are widely accessible to the scientific community at large. This article reviews progress towards the development of computational tools and databases for organizing and extracting biological meaning from the comparison of large collections of genomes.}, } @article {pmid15993900, year = {2006}, author = {Zurakowski, R and Teel, AR}, title = {A model predictive control based scheduling method for HIV therapy.}, journal = {Journal of theoretical biology}, volume = {238}, number = {2}, pages = {368-382}, doi = {10.1016/j.jtbi.2005.05.004}, pmid = {15993900}, issn = {0022-5193}, support = {R21 AI057071/AI/NIAID NIH HHS/United States ; }, mesh = {AIDS Vaccines ; Anti-HIV Agents/*administration & dosage/therapeutic use ; Antiretroviral Therapy, Highly Active ; Computational Biology ; Disease Progression ; Drug Administration Schedule ; HIV Infections/*drug therapy/*immunology ; Humans ; *Models, Immunological ; T-Lymphocytes, Cytotoxic/immunology ; T-Lymphocytes, Helper-Inducer/immunology ; Viral Load ; }, abstract = {Recently developed models of the interaction of the human immune system and the human immunodeficiency virus (HIV) suggest the possibility of using interruptions of highly active anti-retroviral therapy (HAART) to simulate a therapeutic vaccine and induce cytotoxic lymphocyte (CTL) mediated control of HIV infection. We have developed a model predictive control (MPC) based method for determining optimal treatment interruption schedules for this purpose. This method provides a clinically implementable framework for calculating interruption schedules that are robust to errors due to measurement and patient variations. In this paper, we discuss the medical motivation for this work, introduce the MPC-based method, show simulation results, and discuss future work necessary to implement the method.}, } @article {pmid15993139, year = {2005}, author = {Genthner, FJ and James, JB and Yates, DF and Friedman, SD}, title = {Use of composite data sets for source-tracking enterococci in the water column and shoreline interstitial waters on Pensacola Beach, Florida.}, journal = {Marine pollution bulletin}, volume = {50}, number = {7}, pages = {724-732}, doi = {10.1016/j.marpolbul.2005.02.026}, pmid = {15993139}, issn = {0025-326X}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Birds/microbiology ; DNA Primers ; Databases, Genetic ; Drug Resistance, Bacterial ; Enterococcus faecalis/classification/drug effects/genetics/*isolation & purification ; Environmental Monitoring ; Feces/microbiology ; Florida ; Genotype ; Humans ; Microbial Sensitivity Tests ; Oceans and Seas ; Phenotype ; Polymerase Chain Reaction ; *Water Microbiology ; }, abstract = {Sources of Enterococcus faecalis isolates from Pensacola Beach, FL. were identified using a library-based approach by applying the statistical method of average similarity to single and composite data sets generated from separate analyses. Data sets included antibiotic resistance analysis (ARA), rep-fingerprints, and fatty acid methyl ester (FAME) profiles. Use of a composite data set composed of ARA and rep-fingerprints, added to the confidence of the identifications. The addition of FAME data to composite data sets did not add to the confidence of identifications. Source identification was performed to better understand risk associated with higher densities of enterococci found in swash zone interstitial water (SZIW) as compared to adjacent bathing water on Pensacola Beach, FL. The "swash zone" is that area of the beach continually washed over by waves. As the potential sources of enterococci were limited in this environment, only two library units, sea gull and human, were constructed. Identification of the beach isolates using a composite data set indicated a sea gull origin. The clonality of the beach isolates suggested that the beach environment selects certain subspecies of E. faecalis.}, } @article {pmid15984065, year = {2005}, author = {Fang, H and Liu, G and Kearney, M}, title = {Georelational analysis of soil type, soil salt content, landform, and land use in the Yellow River Delta, China.}, journal = {Environmental management}, volume = {35}, number = {1}, pages = {72-83}, doi = {10.1007/s00267-004-3066-2}, pmid = {15984065}, issn = {0364-152X}, mesh = {*Agriculture ; Animals ; Cattle ; China ; *Environment ; Environmental Monitoring ; Fisheries ; Forestry ; *Geographic Information Systems ; Guidelines as Topic ; Policy Making ; *Rivers ; *Sodium Chloride ; *Soil ; }, abstract = {The Yellow River Delta, one of China's three major river deltas, is becoming a major region for the development of agriculture and fisheries. Protecting the delicate ecology of newly formed aquatic systems as well as the evolution of soils, natural vegetation, and fauna on older upland environments in the delta is a priority in planning for the wise use of the delta's resources for future agricultural development. In this article, we use a Geographic Information System (GIS) to analyze relationships between land-use/ land-cover characteristics in the Dongying municipality, one of the most intensely developed areas of the delta, and spatial variations in soil salinity and landforms. This analysis reveals that soil salt content decreases from regionally high values in isolated depressions to relatively moderate values in embanked former back swamps, with the lowest values occurring in abandoned river courses. Comparing the present land use on this soil salinity-landform pattern shows that it is basically at odds with general concepts of land suitability for agricultural utilization of saline soils. Crop-based agriculture in the region is probably overdeveloped, whereas more appropriate agricultural development, like cattle and forest production, is underrepresented. Future development should focus on converting farmland in embanked former back swamps and abandoned river courses into grasslands and forests. Crop-based agriculture (up to 151,000 ha) could be planned at the low-salinity terrace uplands and flood plains. The article provides guidelines for decision-makers regarding agricultural land use and wetland protection in the Yellow River Delta.}, } @article {pmid15983874, year = {2005}, author = {Wagner, GP and Takahashi, K and Lynch, V and Prohaska, SJ and Fried, C and Stadler, PF and Amemiya, C}, title = {Molecular evolution of duplicated ray finned fish HoxA clusters: increased synonymous substitution rate and asymmetrical co-divergence of coding and non-coding sequences.}, journal = {Journal of molecular evolution}, volume = {60}, number = {5}, pages = {665-676}, pmid = {15983874}, issn = {0022-2844}, mesh = {Animals ; Base Sequence ; Computational Biology ; Databases, Nucleic Acid ; *Evolution, Molecular ; Fishes/*genetics ; Genes, Duplicate/*genetics ; Genes, RAG-1 ; Homeodomain Proteins/*genetics ; Molecular Sequence Data ; Mutation/genetics ; Open Reading Frames/genetics ; *Phylogeny ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {In this study the molecular evolution of duplicated HoxA genes in zebrafish and fugu has been investigated. All 18 duplicated HoxA genes studied have a higher non-synonymous substitution rate than the corresponding genes in either bichir or paddlefish, where these genes are not duplicated. The higher rate of evolution is not due solely to a higher non-synonymous-to-synonymous rate ratio but to an increase in both the non-synonymous as well as the synonymous substitution rate. The synonymous rate increase can be explained by a change in base composition, codon usage, or mutation rate. We found no changes in nucleotide composition or codon bias. Thus, we suggest that the HoxA genes may experience an increased mutation rate following cluster duplication. In the non-Hox nuclear gene RAG1 only an increase in non-synonymous substitutions could be detected, suggesting that the increased mutation rate is specific to duplicated Hox clusters and might be related to the structural instability of Hox clusters following duplication. The divergence among paralog genes tends to be asymmetric, with one paralog diverging faster than the other. In fugu, all b-paralogs diverge faster than the a-paralogs, while in zebrafish Hoxa-13a diverges faster. This asymmetry corresponds to the asymmetry in the divergence rate of conserved non-coding sequences, i.e., putative cis-regulatory elements. These results suggest that the 5' HoxA genes in the same cluster belong to a co-evolutionary unit in which genes have a tendency to diverge together.}, } @article {pmid15982673, year = {2005}, author = {McIntyre, AD}, title = {Big science in the seas.}, journal = {Marine pollution bulletin}, volume = {50}, number = {8}, pages = {791-792}, doi = {10.1016/j.marpolbul.2005.05.012}, pmid = {15982673}, issn = {0025-326X}, mesh = {*Biodiversity ; Databases, Factual ; Marine Biology/*methods/*trends ; Research/*trends ; }, } @article {pmid15953635, year = {2005}, author = {Probst, M and Berenzen, N and Lentzen-Godding, A and Schulz, R}, title = {Scenario-based simulation of runoff-related pesticide entries into small streams on a landscape level.}, journal = {Ecotoxicology and environmental safety}, volume = {62}, number = {2}, pages = {145-159}, doi = {10.1016/j.ecoenv.2005.04.012}, pmid = {15953635}, issn = {0147-6513}, mesh = {Computer Simulation ; Geographic Information Systems ; Germany ; *Models, Theoretical ; Pesticides/*analysis ; Rain ; Risk Assessment ; *Rivers ; Soil ; Water Movements ; Water Pollutants, Chemical/*analysis ; }, abstract = {The prediction of runoff-related pesticide entry into surface waters on a landscape level usually requires considerable efforts with regard to input data, time, and personnel. Therefore, the need for an easy to use simulation tool with easily accessible input data, for example from already existing public sources, is obvious. In this paper, we present a simulation tool for the simulation of pesticide entry from arable land into adjacent streams. Our aim was to develop a tool applicable on the landscape level using "real world data" from numerous sites and for the simulation of parameter case studies concerning particular parameters at single sites. We used the ratio of exposure to toxicity (REXTOX) model proposed by the OECD, which had been successfully validated in the study area as part of a previous study and which was extended to calculate pesticide concentrations in adjacent streams. We simulated the pesticide entry on the landscape level at 737 sites in small streams situated in the central lowland of Germany with winter wheat, barley, and sugar beat as the main agricultural crops. A sensitivity analysis indicated that the most significant model parameters were the width of the no-application zone and the degree of plant interception. The simulation was carried out for the 15 most frequently detected substances found in the study area using eight different environmental scenarios, covering variation of the width of the no-application zone, climate, and seasonal scenarios. The highest in-stream concentrations were predicted for a scenario using no (0m) buffer zone in conjunction with increased precipitation. According to the predicted concentrations, the risk for the aquatic communities was estimated based on standard toxicity tests and the application of a safety factor. The simulation results are presented both by means of risk maps for the study area showing the simulated pesticide concentration and the resulting ecological risk for numerous sites under varying scenarios and by case study diagrams with focus on the model behavior under the influence of single parameters. Risk maps confirmed the importance of no-application (buffer) zones for the levels of pesticide input. They also indicated the importance of the existing no-application zones for certain compounds and in some cases the need for a further evaluation of these regulations. The simulation tool was implemented as a standard PC software combining the REXTOX model with a geographical information system and can be used on any current personal computer. All input data was taken from public sources of German authorities. With little effort the tool should be applicable for other areas with similar data quality.}, } @article {pmid15952517, year = {2005}, author = {Bello-Pineda, J and Liceaga-Correa, MA and Hernández-Núñez, H and Ponce-Hernández, R}, title = {Using aerial video to train the supervised classification of Landsat TM imagery for coral reef habitats mapping.}, journal = {Environmental monitoring and assessment}, volume = {105}, number = {1-3}, pages = {145-164}, doi = {10.1007/s10661-005-3499-y}, pmid = {15952517}, issn = {0167-6369}, mesh = {Animals ; Anthozoa ; Conservation of Natural Resources ; *Environment ; Eukaryota ; Geographic Information Systems ; Geography ; Mexico ; Photography ; Satellite Communications ; Seawater ; *Spacecraft ; *Video Recording ; }, abstract = {Management of coral reef resources is a challenging task, in many cases, because of the scarcity or inexistence of accurate sources of information and maps. Remote sensing is a not intrusive, but powerful tool, which has been successfully used for the assessment and mapping of natural resources in coral reef areas. In this study we utilized GIS to combine Landsat TM imagery, aerial photography, aerial video and a digital bathymetric model, to assess and to map submerged habitats for Alacranes reef, Yucatán, México. Our main goal was testing the potential of aerial video as the source of data to produce training areas for the supervised classification of Landsat TM imagery. Submerged habitats were ecologically characterized by using a hierarchical classification of field data. Habitats were identified on an overlaid image, consisting of the three types of remote sensing products and the bathymetric model. Pixels representing those habitats were selected as training areas by using GIS tools. Training areas were used to classify the Landsat TM bands 1, 2 and 3 and the bathymetric model by using a maximum likelihood algorithm. The resulting thematic map was compared against field data classification to improve habitats definition. Contextual editing and reclassification were used to obtain the final thematic map with an overall accuracy of 77%. Analysis of aerial video by a specialist in coral reef ecology was found to be a suitable source of information to produce training areas for the supervised classification of Landsat TM imagery in coral reefs at a coarse scale.}, } @article {pmid15952429, year = {2001}, author = {Adriaenssens, V and Goethals, P and Luypaert, P and De Pauw, N}, title = {Impact of land-use on macroinvertebrate communities in the Zwalm river basin.}, journal = {Mededelingen (Rijksuniversiteit te Gent. Fakulteit van de Landbouwkundige en Toegepaste Biologische Wetenschappen)}, volume = {66}, number = {1}, pages = {51-61}, pmid = {15952429}, issn = {1373-7503}, mesh = {Animals ; Belgium ; Biodiversity ; Ecosystem ; Environmental Monitoring/*methods ; Fresh Water ; *Geographic Information Systems ; Invertebrates/growth & development/*physiology ; Rivers/*chemistry ; }, abstract = {For determining the impact of land-use on the aquatic ecosystem in a river basin, a Geographic Information System (GIS) has been used to integrate the main impact factors at different scales. The headwaters and streams of the Zwalm River basin (Flanders, Belgium), which is part of the Scheldt river basin, were selected as study site. A river ecological database was developed based on physical-chemical and biological monitoring. The research focussed on three zones within this Zwalm River basin, each characterized by different land-uses and by consequence different types of pollution, mainly of diffuse origin. The impact was measured by means of the biological diversity, the Belgian Biotic Index and a key macroinvertebrate taxon. For measuring, assessing and managing the impact of land-use on biological communities, an integrated and multidisciplinary approach will be necessary.}, } @article {pmid15943360, year = {2005}, author = {Wan, R and Yang, G}, title = {[Changes of land use and landscape pattern in Taihu Lake Basin].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {16}, number = {3}, pages = {475-480}, pmid = {15943360}, issn = {1001-9332}, mesh = {*Agriculture ; China ; *Conservation of Natural Resources ; *Ecosystem ; Environmental Monitoring/methods ; Geographic Information Systems ; *Plant Development ; }, abstract = {Based on three sets of land use data (1985, 1995 and 2000), and by means of the techniques of remote sensing, geographical information system (GIS), and landscape ecology, this paper studied the changes of land use and landscape pattern from 1985 to 2000 in Taihu Lake Basin located at Yangtse River Delta. The results showed that in past 15 years, the farmland in this Basin decreased, while the built-up areas, woodland, grassland and water body increased. The decrease of the farmland occupied 89.64% of total decrement, while the increase of the built-up areas accounted for 79.21% of total increment. Under the disturbance of human activities, the landscape structure and landscape heterogeneity in Taihu Lake Basin changed greatly. The patches density decreased from 0.996 to 0.930, diversity indices decreased from 1.127 to 1.113, evenness indices decreased from 62.891% to 62.109%; while the edge density increased from 4.408 to 4.459, dominance indices increased from 0.665 to 0.679, and shape indices increased from 1.540 to 2.796. The landscape heterogeneity varied with different kinds of landscape, indicating the complexity of landscape ecosystem. In all kinds of landscapes, farmland and grassland had the highest values of diversity indices. The diversity indices of water bodies decreased firstly and then increased, while those of built-up areas were in adverse. The evenness index was decreased in the order of woodland > farmland > grassland > water body > built-up areas. Population, economy and policies were the driving forces of the dynamic changes of landscape pattern in Lake Taihu Basin during past 15 years, and land use change in the Basin caused distinct landscape effects, such as landscape fragmenting, edge effects intensification, and environmental quality declining. The mode of land use should be adjusted in landscape scale to rehabilitate and reconstruct the landscape ecosystems in Taihu Lake Basin.}, } @article {pmid15941747, year = {2005}, author = {Dias, SF and Matos, MG and Gonçalves, AC}, title = {Preventing HIV transmission in adolescents: an analysis of the Portuguese data from the Health Behaviour School-aged Children study and focus groups.}, journal = {European journal of public health}, volume = {15}, number = {3}, pages = {300-304}, doi = {10.1093/eurpub/cki085}, pmid = {15941747}, issn = {1101-1262}, mesh = {Adolescent ; *Adolescent Behavior ; Data Interpretation, Statistical ; Female ; Focus Groups ; HIV Infections/*prevention & control/*transmission ; *Health Behavior ; Humans ; Male ; Portugal ; Sex Factors ; Sexual Behavior ; Surveys and Questionnaires ; }, abstract = {BACKGROUND: There is recognition of the need to examine psychosocial and ecological determinants contributing to both risk and protective factors related to adolescents' sexual behaviour and HIV/AIDS.

METHODS: The study utilized mixed quantitative and qualitative methods. Data were collected from the Portuguese sample of the Health Behaviour in School-aged Children (HBSC) 2002. Based on these results, 14 focus group discussions were conducted.

RESULTS: A substantial minority of young people continue to engage in high-risk practices. Thus, female gender, older age, reporting easy to talk with father, not getting drunk and not getting involved in fights are significantly associated with protected sexual behaviour (using condom during last sexual intercourse). According to these results, being female and a comprehensive grade student are both related to a significantly more positive attitude towards infected people. It was concluded that these adolescents view sexual behaviour, sexual partners and condom use as elements within a complex script that governs heterosexual interactions. Several themes related to condom used emerged. Despite HIV/AIDS knowledge, young people underestimate their own risk of becoming infected with HIV. The majority of adolescents believe that HIV-infected people experience discrimination and social exclusion. Adolescents' opinions of HIV-infected people were mostly positive. Although most participants knew that HIV cannot be transmitted through social contact, undefined fears concerning the infection exist.

CONCLUSIONS: These findings have important implications for the implementation of a comprehensive programme on HIV/AIDS education in secondary schools.}, } @article {pmid15938517, year = {2004}, author = {Daniel, M and Kolár, J and Zeman, P}, title = {GIS tools for tick and tick-borne disease occurrence.}, journal = {Parasitology}, volume = {129 Suppl}, number = {}, pages = {S329-52}, doi = {10.1017/s0031182004006080}, pmid = {15938517}, issn = {0031-1820}, mesh = {Animals ; Arachnid Vectors/*physiology ; Czech Republic/epidemiology ; Environment ; *Geographic Information Systems/instrumentation ; Humans ; Risk Factors ; Tick-Borne Diseases/*epidemiology ; Ticks/*physiology ; }, abstract = {Geographic information systems (GIS), their fundamental components and technologies are described. GIS is a computer-based system enabling the storage, integration, query, display and analysis of data using information on data location. Further, remote sensing (RS) methods and their application in landscape characterization are described. Landscape pattern analysis, combined with statistical analysis, allows the determination of landscape predictors of disease risk. This makes RS/GIS a powerful set of tools for disease surveillance, enabling the prediction of potential disease outbreaks and targeting intervention programs. The 'pre-GIS era' is briefly described including the early mapping of tick distribution, analyses and the display of biogeographical and medical data. The theory of natural focality of diseases (NFD) is explained and its significance in tick-borne diseases (TBD) research is discussed. Many problems of tick ecology and TBD epidemiology and epizootology have been addressed by means of GIS and examples of these studies are presented and discussed.}, } @article {pmid15938406, year = {2005}, author = {Medvedeva, SE and Boiandin, AN and Lankin, IuP and Kotov, DA and Kargatova, TV and Rodicheva, EK and Popova, LIu}, title = {[Database on natural and transgenic luminous microorganisms: "BiolumBase"].}, journal = {Mikrobiologiia}, volume = {74}, number = {2}, pages = {278-286}, pmid = {15938406}, issn = {0026-3656}, mesh = {Bacteria/chemistry/*genetics ; Biotechnology ; *Databases, Factual ; Ecology ; *Genes, Bacterial ; Luminescence ; Luminescent Proteins/chemistry/*genetics ; Transgenes ; }, abstract = {The database "BiolumBase" is designed for the selection and systematization of available world information on microorganisms containing bioluminescent systems; it includes two sections: "natural" and "transgenic" luminous microorganisms. At present, logic schemes of divisions, classification of the objects, presentation of characteristics, and the inputs of relative information, as well as the necessary program modules including links to the database, are developed. The database is constructed on the basis of published data and our own experimental results; the subsequent linkage of the database to the Internet is envisaged. Users will be able to obtain not only the catalogues of strains but also information concerning the properties and functions of the known species of luminous bacteria, the structure, regulatory mechanisms, and application of bioluminescent systems and genetically engineered constructions with lux genes, as well as to find references and to search strains by using any set of attributes. The database will provide information that is of interest for the development of microbial ecology and biotechnology, in particular, for the prediction of biological hazard from the application of transgenic strains.}, } @article {pmid15936897, year = {2005}, author = {Steele, HL and Streit, WR}, title = {Metagenomics: advances in ecology and biotechnology.}, journal = {FEMS microbiology letters}, volume = {247}, number = {2}, pages = {105-111}, doi = {10.1016/j.femsle.2005.05.011}, pmid = {15936897}, issn = {0378-1097}, mesh = {*Biotechnology/methods/trends ; Computational Biology ; *Ecology ; *Genomics ; *Prokaryotic Cells ; }, abstract = {This review highlights the significant advances which have been made in prokaryotic ecology and biotechnology due to the application of metagenomic techniques. It is now possible to link processes to specific microorganisms in the environment, such as the detection of a new phototrophic process in marine bacteria, and to characterise the metabolic cooperation which takes place in mixed species biofilms. The range of prokaryote derived products available for biotechnology applications is increasing rapidly. The knowledge gained from analysis of biosynthetic pathways provides valuable information about enzymology and allows engineering of biocatalysts for specific processes. The expansion of metagenomic techniques to include alternative heterologous hosts for gene expression and the development of sophisticated assays which enable screening of thousands of clones offers the possibility to find out even more valuable information about the prokaryotic world.}, } @article {pmid15936870, year = {2005}, author = {Kirzhner, V and Bolshoy, A and Volkovich, Z and Korol, A and Nevo, E}, title = {Large-scale genome clustering across life based on a linguistic approach.}, journal = {Bio Systems}, volume = {81}, number = {3}, pages = {208-222}, doi = {10.1016/j.biosystems.2005.04.003}, pmid = {15936870}, issn = {0303-2647}, mesh = {Base Composition ; Base Sequence/genetics ; Classification/*methods ; Cluster Analysis ; Computational Biology/methods ; Genome/*genetics ; Genomics/*methods ; Oligonucleotides/*genetics ; *Phylogeny ; Species Specificity ; }, abstract = {With the availability of genome sequences, the possibility of new phylogenetic reconstructions arises in order to reveal genomic relationships among organisms. According to the compositional-spectra (CS) approach proposed in our previous studies, any genomic sequence can be characterized by a distribution of frequencies of imperfect matching of words (oligonucleotides). In the current application of CS-analysis, we attempted to analyze the cluster structure of genomes across life. It appeared that compositional spectra show a clear three-group clustering of the compared prokaryotic and eukaryotic genomes. Unexpectedly, this grouping seriously differs from the classical Universal Tree of Life structure represented by common kingdoms known as Eubacteria, Archaebacteria, and Eukarya. The revealed CS-clustering displays high stability, putatively reflecting its objective nature, and still enigmatic biological significance that may result from convergent evolution driven by ecological selection. We believe that our approach provides a new and wider (compared to traditional methods) perspective of extracting genomic information of high evolutionary relevance.}, } @article {pmid15936271, year = {2005}, author = {He, X and Zhang, J}, title = {Gene complexity and gene duplicability.}, journal = {Current biology : CB}, volume = {15}, number = {11}, pages = {1016-1021}, doi = {10.1016/j.cub.2005.04.035}, pmid = {15936271}, issn = {0960-9822}, support = {GM67030/GM/NIGMS NIH HHS/United States ; }, mesh = {Chromatin Immunoprecipitation ; Computational Biology ; *Evolution, Molecular ; *Gene Duplication ; Genes, Fungal/*genetics ; *Genome, Fungal ; Protein Structure, Tertiary ; Yeasts/*genetics ; }, abstract = {Eukaryotic genes are on average more complex than prokaryotic genes in terms of expression regulation, protein length, and protein-domain structure [1-5]. Eukaryotes are also known to have a higher rate of gene duplication than prokaryotes do [6, 7]. Because gene duplication is the primary source of new genes [], the average gene complexity in a genome may have been increased by gene duplication if complex genes are preferentially duplicated. Here, we test this "gene complexity and gene duplicability" hypothesis with yeast genomic data. We show that, on average, duplicate genes from either whole-genome or individual-gene duplication have longer protein sequences, more functional domains, and more cis-regulatory motifs than singleton genes. This phenomenon is not a by-product of previously known mechanisms, such as protein function [10-13], evolutionary rate [14, 15], dosage [11], and dosage balance [16], that influence gene duplicability. Rather, it appears to have resulted from the sub-neo-functionalization process in duplicate-gene evolution [11]. Under this process, complex genes are more likely to be retained after duplication because they are prone to subfunctionalization, and gene complexity is regained via subsequent neofunctionalization. Thus, gene duplication increases both gene number and gene complexity, two important factors in the origin of genomic and organismal complexity.}, } @article {pmid15931997, year = {2005}, author = {Yue, S and Hashino, M}, title = {Statistical interpretation of the impact of forest growth on streamflow of the Sameura basin, Japan.}, journal = {Environmental monitoring and assessment}, volume = {104}, number = {1-3}, pages = {369-384}, doi = {10.1007/s10661-005-1679-4}, pmid = {15931997}, issn = {0167-6369}, mesh = {*Data Interpretation, Statistical ; Japan ; *Rivers ; Temperature ; Trees/*growth & development ; }, abstract = {A forested mountainous basin, the Sameura basin, located in Shikoku Island of Japan, experienced increased forest growth in the period from 1953 to 1994, like which occurred across the country. The impact of the forest growth on streamflow of the basin was assessed using statistical trend analysis. Annual maximum daily flow, annual minimum 5-day flow, and annual total runoff decreased by 55.8, 75.8, and 39.6%, respectively, over the period. However, the annual maximum 6-day, annual minimum 41-day, and annual total precipitation, respectively associated with annual maximum daily flow, annual minimum 5-day streamflow, and annual total runoff did not decrease. Annual and monthly temperature, which evapotranspiration positively related to, did not increase except in January. This demonstrates that the forest growth is responsible for the decrease in all these three flow regimes. The increase in evapotranspiration due to the forest growth resulted in the decrease in both total runoff and low flow. Thus, it seems that forest can hardly function to both reduce flood peaks during flood periods and increase water supply during drought periods.}, } @article {pmid15930827, year = {2005}, author = {Yasuda, T and Arai, N}, title = {Fine-scale tracking of marine turtles using GPS-Argos PTTs.}, journal = {Zoological science}, volume = {22}, number = {5}, pages = {547-553}, doi = {10.2108/zsj.22.547}, pmid = {15930827}, issn = {0289-0003}, mesh = {Animals ; *Behavior, Animal ; *Geographic Information Systems ; Marine Biology/instrumentation/methods ; *Satellite Communications ; Telemetry/instrumentation ; Turtles/*physiology ; }, abstract = {High-accuracy location data of wildlife telemetry using conventional satellite location systems are difficult to obtain. However, such data are necessary to clarify the nature of movements and home range sizes of animals. In order to measure the high-accuracy location data, we developed new GPS-Argos Platform Terminal Transmitters (PTTs) which transmit both the conventional location and GPS location simultaneously. Two experiments, one in an artificial rearing pond and the other in the open sea, were performed. First, two hawksbill turtles were tracked with the PTTs in a 5 ha breeding pond in Thailand. Their home ranges using both data were calculated and found to be 2.96 ha and 0.93 ha by the GPS data, and 156,740 ha and 184,478 ha by a conventional data. Secondly, a female green turtle attached with the GPS-Argos was released from the coast of Pangnga Province, Thailand. There was a relationship between depth and speed of travel based on the GPS data. The data from the PTT showed that the turtle moved south along the coastline at the depth of less than 20 m for 5 days, and then stayed at a depth of less than 10 m for 4 days. However, we could not find any clear relationship using conventional data. Only a meandering movement at a variety of depths was observed. The results of the two experiments indicated the PTTs have an enormous potential for enhancing our understanding of fine-scale movement patterns and home ranges of marine turtles.}, } @article {pmid15922672, year = {2006}, author = {Wiens, JJ}, title = {Missing data and the design of phylogenetic analyses.}, journal = {Journal of biomedical informatics}, volume = {39}, number = {1}, pages = {34-42}, doi = {10.1016/j.jbi.2005.04.001}, pmid = {15922672}, issn = {1532-0480}, mesh = {*Algorithms ; Animals ; Chromosome Mapping/*methods ; *Data Interpretation, Statistical ; Gene Expression Profiling/*methods ; Humans ; *Phylogeny ; *Research Design ; Sample Size ; }, abstract = {Concerns about the deleterious effects of missing data may often determine which characters and taxa are included in phylogenetic analyses. For example, researchers may exclude taxa lacking data for some genes or exclude a gene lacking data in some taxa. Yet, there may be very little evidence to support these decisions. In this paper, I review the effects of missing data on phylogenetic analyses. Recent simulations suggest that highly incomplete taxa can be accurately placed in phylogenies, as long as many characters have been sampled overall. Furthermore, adding incomplete taxa can dramatically improve results in some cases by subdividing misleading long branches. Adding characters with missing data can also improve accuracy, although there is a risk of long-branch attraction in some cases. Consideration of how missing data does (or does not) affect phylogenetic analyses may allow researchers to design studies that can reconstruct large phylogenies quickly, economically, and accurately.}, } @article {pmid15921618, year = {2005}, author = {Zhou, YB and Jiang, QW and Zhao, GM}, title = {[Study on bias and confounding in 'Spatial Epidemiology'].}, journal = {Zhonghua liu xing bing xue za zhi = Zhonghua liuxingbingxue zazhi}, volume = {26}, number = {2}, pages = {135-139}, pmid = {15921618}, issn = {0254-6450}, mesh = {*Bias ; *Confounding Factors, Epidemiologic ; Ecology ; *Epidemiology ; Geographic Information Systems ; Geography ; Humans ; Socioeconomic Factors ; Space-Time Clustering ; }, abstract = {OBJECTIVE: To explore the biases and confoundings in Spatial Epidemiological studies.

METHODS: Possible bias and confounding and their impact on study results in Spatial Epidemiology were analyzed in given examples.

RESULTS: In Spatial Epidemiology, biases related to ascertainment/numerator/denominator induced by the choice of the disease induction/latency period and mis-specification of exposure-disease model, exposure inaccuracy, spatial dependency, significance tests etc. were involved, as well as to ecological, socio-economic confoundings factors.

CONCLUSION: The sources of bias in 'Spatial Epidemiology' were both numerous and complex, that might be overestimated or underestimated on the study results. Hence, careful interpretation of such studies was needed.}, } @article {pmid15905899, year = {2005}, author = {Carvalho, MS and Souza-Santos, R}, title = {[Analysis of spatial data in public health: methods, problems, and perspectives].}, journal = {Cadernos de saude publica}, volume = {21}, number = {2}, pages = {361-378}, doi = {10.1590/s0102-311x2005000200003}, pmid = {15905899}, issn = {0102-311X}, mesh = {Epidemiologic Methods ; *Geographic Information Systems ; Humans ; Public Health/*instrumentation ; Software ; }, abstract = {Studies in which spatial distribution and geographic information systems (GIS) play a central role are becoming more common in the public health literature. However, methods and software to implement such approaches still pose serious limitations, due to unfriendliness and lack of integration. Additionally, most researchers and public health professionals are not familiar with either the techniques or the software. The aim of this work, besides presenting a systematic review of spatial analysis in health, is to discuss some representative applications of methods that deal with the analysis of spatial patterns of health events, analyzing advantages, disadvantages, and applicability of the proposed models in ecological and health services utilization studies.}, } @article {pmid15905608, year = {2005}, author = {Hoshino, A and Fujioka, K and Manabe, N and Yamaya, S and Goto, Y and Yasuhara, M and Yamamoto, K}, title = {Simultaneous multicolor detection system of the single-molecular microbial antigen with total internal reflection fluorescence microscopy.}, journal = {Microbiology and immunology}, volume = {49}, number = {5}, pages = {461-470}, doi = {10.1111/j.1348-0421.2005.tb03750.x}, pmid = {15905608}, issn = {0385-5600}, mesh = {Antigens/*analysis ; Color ; Diphtheria Toxin/*analysis ; Fluorescent Antibody Technique/*methods ; *Microscopy, Fluorescence ; Staining and Labeling/*methods ; Tetanus Toxin/*analysis ; }, abstract = {Immunological diagnostic methods have been widely performed and showed high performance in molecular and cellular biology, molecular imaging, and medical diagnostics. We have developed novel methods for the fluorescent labeling of several antibodies coupled with fluorescent nanocrystal QDs. In this study we demonstrated that two bacterial toxins, diphtheria toxin and tetanus toxin, were detected simultaneously in the same view field of a cover slip by using directly QD-conjugated antibodies. We have succeeded in detecting bacterial toxins by counting luminescent spots on the evanescent field with using primary antibody conjugated to QDs. In addition, each bacterial toxin in the mixture can be separately detected by single excitation laser with emission band pass filters, and simultaneously in situ pathogen quantification was performed by calculating the luminescent density on the surface of the cover slip. Our results demonstrate that total internal reflection fluorescence microscopy (TIRFM) enables us to distinguish each antigen from mixed samples and can simultaneously quantitate multiple antigens by QD-conjugated antibodies . Bioconjugated QDs could have great potentialities for in practical biomedical applications to develop various high-sensitivity detection systems.}, } @article {pmid15905001, year = {2005}, author = {Howard, BJ and Beresford, NA and Nisbet, A and Cox, G and Oughton, DH and Hunt, J and Alvarez, B and Andersson, KG and Liland, A and Voigt, G}, title = {The STRATEGY project: decision tools to aid sustainable restoration and long-term management of contaminated agricultural ecosystems.}, journal = {Journal of environmental radioactivity}, volume = {83}, number = {3}, pages = {275-295}, doi = {10.1016/j.jenvrad.2005.01.013}, pmid = {15905001}, issn = {0265-931X}, mesh = {Agriculture ; Animals ; Consumer Product Safety ; Cost-Benefit Analysis ; Databases, Factual ; Decision Support Systems, Management/economics/*organization & administration/trends ; *Ecosystem ; *Environmental Health ; Ethics ; Europe ; Food Contamination, Radioactive/*prevention & control ; Humans ; Policy Making ; Radiation Protection/methods ; Safety Management/economics/*organization & administration/trends ; }, abstract = {The STRATEGY project (Sustainable Restoration and Long-Term Management of Contaminated Rural, Urban and Industrial Ecosystems) aimed to provide a holistic decision framework for the selection of optimal restoration strategies for the long-term sustainable management of contaminated areas in Western Europe. A critical evaluation was carried out of countermeasures and waste disposal options, from which compendia of state-of-the-art restoration methods were compiled. A decision support system capable of optimising spatially varying restoration strategies, that considered the level of averted dose, costs (including those of waste disposal) and environmental side effects was developed. Appropriate methods of estimating indirect costs associated with side effects and of communicating with stakeholders were identified. The importance of stakeholder consultation at a local level and of ensuring that any response is site and scenario specific were emphasised. A value matrix approach was suggested as a method of addressing social and ethical issues within the decision-making process, and was designed to be compatible with both the countermeasure compendia and the decision support system. The applicability and usefulness of STRATEGY outputs for food production systems in the medium to long term is assessed.}, } @article {pmid15902506, year = {2005}, author = {Prasad, VK and Anuradha, E and Badarinath, KV}, title = {Climatic controls of vegetation vigor in four contrasting forest types of India--evaluation from National Oceanic and Atmospheric Administration's Advanced Very High Resolution Radiometer datasets (1990-2000).}, journal = {International journal of biometeorology}, volume = {50}, number = {1}, pages = {6-16}, pmid = {15902506}, issn = {0020-7128}, mesh = {Climate ; Databases, Factual ; India ; Models, Biological ; Rain ; Regression Analysis ; Temperature ; Trees/classification/*growth & development ; }, abstract = {Ten-day advanced very high resolution radiometer images from 1990 to 2000 were used to examine spatial patterns in the normalized difference vegetation index (NDVI) and their relationships with climatic variables for four contrasting forest types in India. The NDVI signal has been extracted from homogeneous vegetation patches and has been found to be distinct for deciduous and evergreen forest types, although the mixed-deciduous signal was close to the deciduous ones. To examine the decadal response of the satellite-measured vegetation phenology to climate variability, seven different NDVI metrics were calculated using the 11-year NDVI data. Results suggested strong spatial variability in forest NDVI metrics. Among the forest types studied, wet evergreen forests of north-east India had highest mean NDVI (0.692) followed by evergreen forests of the Western Ghats (0.529), mixed deciduous forests (0.519) and finally dry deciduous forests (0.421). The sum of NDVI (SNDVI) and the time-integrated NDVI followed a similar pattern, although the values for mixed deciduous forests were closer to those for evergreen forests of the Western Ghats. Dry deciduous forests had higher values of inter-annual range (RNDVI) and low mean NDVI, also coinciding with a high SD and thus a high coefficient of variation (CV) in NDVI (CVNDVI). SNDVI has been found to be high for wet evergreen forests of north-east India, followed by evergreen forests of the Western Ghats, mixed deciduous forests and dry deciduous forests. Further, the maximum NDVI values of wet evergreen forests of north-east India (0.624) coincided with relatively high annual total precipitation (2,238.9 mm). The time lags had a strong influence in the correlation coefficients between annual total rainfall and NDVI. The correlation coefficients were found to be comparatively high (R2=0.635) for dry deciduous forests than for evergreen forests and mixed deciduous forests, when the precipitation data with a lag of 30 days was correlated against NDVI. Using multiple regression approach models were developed for individual forest types using 16 different climatic indices. A high proportion of the temporal variance (>90%) has been accounted for by three of the precipitation parameters (maximum precipitation, precipitation of the wettest quarter and driest quarter) and two of the temperature parameters (annual mean temperature and temperature of the coldest quarter) for mixed deciduous forests. Similarly, in the case of deciduous forests, four precipitation parameters and three temperature parameters explained nearly 83.6% of the variance. These results suggest differences in the relationship between NDVI and climatic variables based upon the time of growing season, time interval and climatic indices over which they were summed. These results have implications for forest cover mapping and monitoring in tropical regions of India.}, } @article {pmid15891855, year = {2005}, author = {Moritz, MA and Odion, DC}, title = {Examining the strength and possible causes of the relationship between fire history and Sudden Oak Death.}, journal = {Oecologia}, volume = {144}, number = {1}, pages = {106-114}, pmid = {15891855}, issn = {0029-8549}, mesh = {California ; Databases, Factual ; *Fires ; Geographic Information Systems ; Geography ; *Models, Biological ; Phytophthora/growth & development/*pathogenicity ; Plant Diseases/*microbiology ; *Quercus ; Soil/analysis ; }, abstract = {Fire can be a dominant process in the ecology of forest vegetation and can also affect forest disease dynamics. Little is known about the relationship between fire and an emerging disease epidemic called Sudden Oak Death, which is caused by a new pathogen, Phytophthora ramorum. This disease has spread across a large, fire-prone portion of California, killing great numbers of oaks and tanoaks and infecting most associated woody plants. Suitable hosts cover a much broader geographic range, raising concern over where the disease may spread. To understand the strength and potential sensitivities of a fire-disease relationship, we examined geographic patterns of confirmed P. ramorum infections in relation to past fire history. We found these infections to be extremely rare within the perimeter of any area burned since 1950. This finding is not caused by spatial bias in sampling for the disease, and is robust to variation in host abundance scenarios and to aggregation of closely spaced sampling locations. We therefore investigated known fire-related factors that could result in significantly lower incidence of the disease in relatively recently burned landscapes. Chemical trends in post-fire environments can influence the success of pathogens like P. ramorum, either by increasing plant nutrient stress or by reducing the occurrence of chemicals antagonistic to Phytophthoras. Succession in the absence of fire leads to greater abundance of host species, which will provide increased habitat for P. ramorum; this will also increase intraspecific competition where these trees are abundant, and other density-dependent effects (e.g. shading) can reduce resource allocation to defenses. Despite these findings about a fire-disease relationship, a much deeper understanding is necessary before fire can be actively used as a tool in slowing the epidemic.}, } @article {pmid15891852, year = {2005}, author = {Schmid, I and Kazda, M}, title = {Clustered root distribution in mature stands of Fagus sylvatica and Picea abies.}, journal = {Oecologia}, volume = {144}, number = {1}, pages = {25-31}, pmid = {15891852}, issn = {0029-8549}, mesh = {Austria ; *Fagus ; Geographic Information Systems ; Models, Biological ; *Picea ; Plant Roots/anatomy & histology/*growth & development ; Species Specificity ; }, abstract = {Distribution of small roots (diameter between 2 mm and 5 mm) was studied in 19 pits with a total of 72 m(2) trench profile walls in pure stands of Fagus sylvatica and Picea abies. Root positions within the walls were marked and transformed into x-coordinates and y-coordinates. In a GIS-based evaluation, zones of potential influence around each root were calculated. The total potential influence produced isoline maps of relative root influence zones, thus indicating small root clustering. The questions studied were (1) whether there were marked clusters of small roots in the soil and (2) whether trees surrounding the pit (defined as tree density) correlate with the root abundance and distribution on the trench profile walls. Small roots of both species showed maximum abundance in the top 20 cm of the soil, where pronounced root clusters occurred next to areas with only low root accumulation. The area of root clusters did not differ significantly between the two stands. Weighted clumping, WC, calculated as a product of root class, and its area was used as an index of root clustering, which again did not differ between beech and spruce stands. However, evaluations on a single root level showed that beech achieved the same degree of clustering with lower number of roots. Regardless of soil properties related to root clusters, a significantly higher clustering acquired per root for beech than for spruce suggests beech to be more efficient in belowground acquisition of space. Because none of the parameters describing root clustering were correlated with tree density around the investigated soil profiles, clusters of small roots are inherently present within the tree stands.}, } @article {pmid15891824, year = {2005}, author = {Luyssaert, S and Staelens, J and De Schrijver, A}, title = {Does the commonly used estimator of nutrient resorption in tree foliage actually measure what it claims to?.}, journal = {Oecologia}, volume = {144}, number = {2}, pages = {177-186}, pmid = {15891824}, issn = {0029-8549}, mesh = {Betula/metabolism/*physiology ; Biomass ; Computer Simulation ; *Data Interpretation, Statistical ; *Models, Biological ; Nitrogen/metabolism ; Phosphorus/metabolism ; Reproducibility of Results ; }, abstract = {A descriptive temporal model is considered to be the best available estimator for accretion, resorption and proportional nutrient resorption. However, ecological studies rarely collect sufficient data for applying such a model. A less-demanding and commonly used estimator for proportional resorption (PR) calculates PR as the percentage of the nutrient pool that is withdrawn from mature foliage before leaf abscission. Data from an intensive sampling campaign of the aboveground nutrient pools and fluxes of two Betula pendula Roth. stands were used. We showed that the commonly used estimator is not an accurate estimator for accretion, resorption and proportional resorption. The commonly used estimator underestimated the proportional resorption of N on the average by 3-10%, and the proportional resorption of P by 20-25%. The low accuracy of the estimations was shown to be caused by a lack of selectiveness of the commonly used estimator. In other words, the commonly used estimator does not measure the underlying processes in specific nutrient accretion and resorption at the stand level. However, when a sufficiently high sampling density with several samples at a given point in time is used, then the commonly used estimator preserves the ranking relationship between the PR of different sites for N in 97% of the cases and for P in 71%. The commonly used estimator can thus be used in comparative studies as an index for proportional nutrient resorption only. The quantitative results should not be taken literally, as they are based on only two sets of observations. However, the results show that the commonly used estimator should no longer be used as a measure for accretion, resorption or PR whenever the plant accretes nutrients in the foliage as a compensation for nutrient losses due to foliar leaching and litterfall during the growing season.}, } @article {pmid15890863, year = {2005}, author = {Paraje, G and Sadana, R and Karam, G}, title = {Public health. Increasing international gaps in health-related publications.}, journal = {Science (New York, N.Y.)}, volume = {308}, number = {5724}, pages = {959-960}, doi = {10.1126/science.1108705}, pmid = {15890863}, issn = {1095-9203}, mesh = {Abstracting and Indexing ; *Biomedical Research ; China ; Databases, Bibliographic ; Developed Countries ; Developing Countries ; Ecology ; *Health ; Health Services Research ; Humans ; *Internationality ; Korea ; Public Health ; Public Policy ; *Publishing ; *Research ; Social Sciences ; United States ; }, } @article {pmid15890780, year = {2005}, author = {Gordon, LJ and Steffen, W and Jönsson, BF and Folke, C and Falkenmark, M and Johannessen, A}, title = {Human modification of global water vapor flows from the land surface.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {102}, number = {21}, pages = {7612-7617}, pmid = {15890780}, issn = {0027-8424}, mesh = {Agriculture ; Atmosphere/*chemistry ; *Conservation of Natural Resources ; *Environment ; Geographic Information Systems ; *Geography ; *Models, Theoretical ; Water/*chemistry ; *Water Movements ; }, abstract = {It is well documented that human modification of the hydrological cycle has profoundly affected the flow of liquid water across the Earth's land surface. Alteration of water vapor flows through land-use changes has received comparatively less attention, despite compelling evidence that such alteration can influence the functioning of the Earth System. We show that deforestation is as large a driving force as irrigation in terms of changes in the hydrological cycle. Deforestation has decreased global vapor flows from land by 4% (3,000 km(3)/yr), a decrease that is quantitatively as large as the increased vapor flow caused by irrigation (2,600 km(3)/yr). Although the net change in global vapor flows is close to zero, the spatial distributions of deforestation and irrigation are different, leading to major regional transformations of vapor-flow patterns. We analyze these changes in the light of future land-use-change projections that suggest widespread deforestation in sub-Saharan Africa and intensification of agricultural production in the Asian monsoon region. Furthermore, significant modification of vapor flows in the lands around the Indian Ocean basin will increase the risk for changes in the behavior of the Asian monsoon system. This analysis suggests that the need to increase food production in one region may affect the capability to increase food production in another. At the scale of the Earth as a whole, our results emphasize the need for climate models to take land-use change, in both land cover and irrigation, into account.}, } @article {pmid15883868, year = {2004}, author = {Thompson, RS and Shafer, SL and Anderson, KH and Strickland, LE and Pelltier, RT and Bartlein, PJ and Kerwin, MW}, title = {Topographic, bioclimatic, and vegetation characteristics of three ecoregion classification systems in North America: comparisons along continent-wide transects.}, journal = {Environmental management}, volume = {34 Suppl 1}, number = {}, pages = {S125-48}, doi = {10.1007/s00267-003-7200-3}, pmid = {15883868}, issn = {0364-152X}, mesh = {Classification/*methods ; *Climate ; Ecology ; *Ecosystem ; Geographic Information Systems ; *Geography ; North America ; *Plants ; }, abstract = {Ecoregion classification systems are increasingly used for policy and management decisions, particularly among conservation and natural resource managers. A number of ecoregion classification systems are currently available, with each system defining ecoregions using different classification methods and different types of data. As a result, each classification system describes a unique set of ecoregions. To help potential users choose the most appropriate ecoregion system for their particular application, we used three latitudinal transects across North America to compare the boundaries and environmental characteristics of three ecoregion classification systems [Küchler, World Wildlife Fund (WWF), and Bailey]. A variety of variables were used to evaluate the three systems, including woody plant species richness, normalized difference in vegetation index (NDVI), and bioclimatic variables (e.g., mean temperature of the coldest month) along each transect. Our results are dominated by geographic patterns in temperature, which are generally aligned north-south, and in moisture, which are generally aligned east-west. In the west, the dramatic changes in physiography, climate, and vegetation impose stronger controls on ecoregion boundaries than in the east. The Küchler system has the greatest number of ecoregions on all three transects, but does not necessarily have the highest degree of internal consistency within its ecoregions with regard to the bioclimatic and species richness data. In general, the WWF system appears to track climatic and floristic variables the best of the three systems, but not in all regions on all transects.}, } @article {pmid15883669, year = {2005}, author = {Wollin, K and Dieter, HH}, title = {Toxicological guidelines for monocyclic nitro-, amino- and aminonitroaromatics, nitramines, and nitrate esters in drinking water.}, journal = {Archives of environmental contamination and toxicology}, volume = {49}, number = {1}, pages = {18-26}, doi = {10.1007/s00244-004-0112-2}, pmid = {15883669}, issn = {0090-4341}, mesh = {Databases, Factual ; Environmental Monitoring/*methods/standards ; European Union ; Germany ; *Health Planning Guidelines ; Humans ; Nitro Compounds/*analysis/toxicity ; No-Observed-Adverse-Effect Level ; Risk Assessment ; Water Pollutants, Chemical/*analysis/toxicity ; Water Supply/*analysis/legislation & jurisprudence/standards ; }, abstract = {In order to secure a safe drinking water supply, the setting of tolerable/acceptable ceilings of drinking water hygiene is required with regard to xenobiotics resulting from several anthropogenic impacts. This is done in practice by using drinking water guidelines or standards as quantitative objectives. The list of the new EU Directive or the German drinking-water standards is limited to those parameters that have the highest relevance for drinking water quality; nitro compounds (NCs) are not regulated. Because other substances contained in water can also represent a hazard for human health, the German Drinking Water Ordinance clarifies that specific actions must be implemented if compounds other than those regulated appear at concentrations that may be a cause for concern regarding human health. NCs serve as intermediates for dyes, pharmaceuticals, and synthetic materials; they themselves are used as solvents, explosives, and pesticides. During their commercial production or from their use, they may be released to the environment and lead to a contamination of aquatic systems and thus also of drinking water resources. In practice, therefore, a need for assessment is frequently given for relevant NCs. For 19 nitro-, amino-, and aminonitroaromatics, nitramines, and nitrate esters health-based drinking water guide values have been derived. For toxicological evaluation and derivation of guideline values for the NCs of interest, the tolerable daily intake approach was used for chemicals exhibiting a threshold for toxic effects. This was done by using established tolerable body doses for humans based on an identified no-observed-adverse-effect level/low-observed-effect-level for the most sensitive indicator for toxicity. In the case of nonthreshold chemical substances, suitable estimates of excess lifetime cancer risk have been applied.}, } @article {pmid15880907, year = {2004}, author = {Biswas, G and Manders, EJ and Ramirez, J and Mahadevan, N and Abdelwahed, S}, title = {Online model-based diagnosis to support autonomous operation of an advanced life support system.}, journal = {Habitation (Elmsford, N.Y.)}, volume = {10}, number = {1}, pages = {21-37}, doi = {10.3727/154296604774808892}, pmid = {15880907}, issn = {1542-9660}, mesh = {Algorithms ; Artificial Intelligence ; Computer Simulation ; Decision Support Techniques ; *Ecological Systems, Closed ; Equipment Safety/*instrumentation ; Life Support Systems/*instrumentation ; Models, Theoretical ; *Neural Networks, Computer ; Osmosis ; Space Flight ; Systems Theory ; Water Purification/*instrumentation ; }, abstract = {This article describes methods for online model-based diagnosis of subsystems of the advanced life support system (ALS). The diagnosis methodology is tailored to detect, isolate, and identify faults in components of the system quickly so that fault-adaptive control techniques can be applied to maintain system operation without interruption. We describe the components of our hybrid modeling scheme and the diagnosis methodology, and then demonstrate the effectiveness of this methodology by building a detailed model of the reverse osmosis (RO) system of the water recovery system (WRS) of the ALS. This model is validated with real data collected from an experimental testbed at NASA JSC. A number of diagnosis experiments run on simulated faulty data are presented and the results are discussed.}, } @article {pmid15878415, year = {2005}, author = {Fesenko, SV and Voigt, G and Spiridonov, SI and Gontarenko, IA}, title = {Decision making framework for application of forest countermeasures in the long term after the Chernobyl accident.}, journal = {Journal of environmental radioactivity}, volume = {82}, number = {2}, pages = {143-166}, doi = {10.1016/j.jenvrad.2004.10.014}, pmid = {15878415}, issn = {0265-931X}, mesh = {Agaricales/chemistry ; Animals ; *Cesium Radioisotopes ; *Chernobyl Nuclear Accident ; Conservation of Natural Resources ; Decision Making ; *Decision Support Techniques ; *Forestry ; Fruit/chemistry ; Humans ; Radiation Dosage ; Radiation Monitoring ; Radioactive Hazard Release ; *Radioactive Pollutants ; Russia ; Wood ; }, abstract = {After the ChNPP accident a very large part of the territories covered by natural and artificial forests are contaminated with long-lived radionuclides, especially 137Cs. To protect people against exposure associated with forest contamination in the most affected regions of the NIS countries, countermeasures have been developed and recommended for the forest management. The paper presents a decision making framework to optimise forest countermeasures in the long term after the ChNPP accident. The approach presented is based on the analysis of the main exposure pathways and application of radiological, socio-economical and ecological criteria for the selection of optimal countermeasures strategies. Because of the diversity of these criteria modern decision support technologies based on multi-attributive analysis were applied. The results of the application of this approach are presented in a selected study area (Novozybkov district, Bryansk region, Russian Federation). The results prove and emphasize the need for a flexible technique to provide the optimised forest countermeasures taking into account radioecological, social and economic features of contaminated forests.}, } @article {pmid15875023, year = {2005}, author = {Kroymann, J and Mitchell-Olds, T}, title = {Epistasis and balanced polymorphism influencing complex trait variation.}, journal = {Nature}, volume = {435}, number = {7038}, pages = {95-98}, doi = {10.1038/nature03480}, pmid = {15875023}, issn = {1476-4687}, mesh = {Arabidopsis/*genetics/*growth & development ; Crosses, Genetic ; Databases, Nucleic Acid ; *Epistasis, Genetic ; Genotype ; Models, Genetic ; Molecular Sequence Data ; Multifactorial Inheritance/genetics ; Phenotype ; Polymorphism, Genetic/*genetics ; Quantitative Trait Loci/*genetics ; }, abstract = {Complex traits such as human disease, growth rate, or crop yield are polygenic, or determined by the contributions from numerous genes in a quantitative manner. Although progress has been made in identifying major quantitative trait loci (QTL), experimental constraints have limited our knowledge of small-effect QTL, which may be responsible for a large proportion of trait variation. Here, we identified and dissected a one-centimorgan chromosome interval in Arabidopsis thaliana without regard to its effect on growth rate, and examined the signature of historical sequence polymorphism among Arabidopsis accessions. We found that the interval contained two growth rate QTL within 210 kilobases. Both QTL showed epistasis; that is, their phenotypic effects depended on the genetic background. This amount of complexity in such a small area suggests a highly polygenic architecture of quantitative variation, much more than previously documented. One QTL was limited to a single gene. The gene in question displayed a nucleotide signature indicative of balancing selection, and its phenotypic effects are reversed depending on genetic background. If this region typifies many complex trait loci, then non-neutral epistatic polymorphism may be an important contributor to genetic variation in complex traits.}, } @article {pmid15869663, year = {2005}, author = {Kõljalg, U and Larsson, KH and Abarenkov, K and Nilsson, RH and Alexander, IJ and Eberhardt, U and Erland, S and Høiland, K and Kjøller, R and Larsson, E and Pennanen, T and Sen, R and Taylor, AF and Tedersoo, L and Vrålstad, T and Ursing, BM}, title = {UNITE: a database providing web-based methods for the molecular identification of ectomycorrhizal fungi.}, journal = {The New phytologist}, volume = {166}, number = {3}, pages = {1063-1068}, doi = {10.1111/j.1469-8137.2005.01376.x}, pmid = {15869663}, issn = {0028-646X}, mesh = {DNA, Ribosomal Spacer/chemistry ; *Databases, Nucleic Acid ; Mycorrhizae/*genetics ; }, abstract = {Identification of ectomycorrhizal (ECM) fungi is often achieved through comparisons of ribosomal DNA internal transcribed spacer (ITS) sequences with accessioned sequences deposited in public databases. A major problem encountered is that annotation of the sequences in these databases is not always complete or trustworthy. In order to overcome this deficiency, we report on UNITE, an open-access database. UNITE comprises well annotated fungal ITS sequences from well defined herbarium specimens that include full herbarium reference identification data, collector/source and ecological data. At present UNITE contains 758 ITS sequences from 455 species and 67 genera of ECM fungi. UNITE can be searched by taxon name, via sequence similarity using blastn, and via phylogenetic sequence identification using galaxie. Following implementation, galaxie performs a phylogenetic analysis of the query sequence after alignment either to pre-existing generic alignments, or to matches retrieved from a blast search on the UNITE data. It should be noted that the current version of UNITE is dedicated to the reliable identification of ECM fungi. The UNITE database is accessible through the URL http://unite.zbi.ee}, } @article {pmid15869177, year = {2005}, author = {Danz, NP and Regal, RR and Niemi, GJ and Brady, VJ and Hollenhorst, T and Johnson, LB and Host, GE and Hanowski, JM and Johnston, CA and Brown, T and Kingston, J and Kelly, JR}, title = {Environmentally stratified sampling design for the development of Great Lakes environmental indicators.}, journal = {Environmental monitoring and assessment}, volume = {102}, number = {1-3}, pages = {41-65}, pmid = {15869177}, issn = {0167-6369}, mesh = {Animals ; Cluster Analysis ; *Ecosystem ; Environmental Monitoring/*methods ; Fresh Water ; Geographic Information Systems ; Great Lakes Region ; Humans ; Principal Component Analysis ; Water Supply ; }, abstract = {Understanding the relationship between human disturbance and ecological response is essential to the process of indicator development. For large-scale observational studies, sites should be selected across gradients of anthropogenic stress, but such gradients are often unknown for apopulation of sites prior to site selection. Stress data available from public sources can be used in a geographic information system (GIS) to partially characterize environmental conditions for large geographic areas without visiting the sites. We divided the U.S. Great Lakes coastal region into 762 units consisting of a shoreline reach and drainage-shed and then summarized over 200 environmental variables in seven categories for the units using a GIS. Redundancy within the categories of environmental variables was reduced using principal components analysis. Environmental strata were generated from cluster analysis using principal component scores as input. To protect against site selection bias, sites were selected in random order from clusters. The site selection process allowed us to exclude sites that were inaccessible and was shown to successfully distribute sites across the range of environmental variation in our GIS data. This design has broad applicability when the goal is to develop ecological indicators using observational data from large-scale surveys.}, } @article {pmid15865965, year = {2005}, author = {Wolfe, AD}, title = {ISSR techniques for evolutionary biology.}, journal = {Methods in enzymology}, volume = {395}, number = {}, pages = {134-144}, doi = {10.1016/S0076-6879(05)95009-X}, pmid = {15865965}, issn = {0076-6879}, mesh = {DNA, Plant/genetics/isolation & purification ; Data Interpretation, Statistical ; *Evolution, Molecular ; Genetic Markers ; *Genetic Techniques/statistics & numerical data ; *Minisatellite Repeats ; Plants/genetics ; Polymerase Chain Reaction/methods ; }, abstract = {Inter-simple sequence repeat (ISSR) markers were originally devised for differentiating among closely related plant cultivars but have become extremely useful for studies of natural populations of plants, fungi, insects, and vertebrates. The markers are easily generated using minimal equipment and are hypervariable, yielding a large amount of data for a reasonable cost to the researcher. The methods for Miniprep DNA extraction and cleanup, polymerase chain reaction (PCR) amplification, optimization, data gathering and scoring, and data analyses are outlined.}, } @article {pmid15860611, year = {2005}, author = {Bernhardt, ES and Palmer, MA and Allan, JD and Alexander, G and Barnas, K and Brooks, S and Carr, J and Clayton, S and Dahm, C and Follstad-Shah, J and Galat, D and Gloss, S and Goodwin, P and Hart, D and Hassett, B and Jenkinson, R and Katz, S and Kondolf, GM and Lake, PS and Lave, R and Meyer, JL and O'donnell, TK and Pagano, L and Powell, B and Sudduth, E}, title = {Ecology. Synthesizing U.S. river restoration efforts.}, journal = {Science (New York, N.Y.)}, volume = {308}, number = {5722}, pages = {636-637}, doi = {10.1126/science.1109769}, pmid = {15860611}, issn = {1095-9203}, mesh = {Animals ; *Conservation of Natural Resources/economics ; Costs and Cost Analysis ; *Databases, Factual ; *Ecosystem ; Environment ; Fishes ; *Rivers ; United States ; }, } @article {pmid15860087, year = {2005}, author = {Saathoff, E and Olsen, A and Kvalsvig, JD and Appleton, CC and Sharp, B and Kleinschmidt, I}, title = {Ecological covariates of Ascaris lumbricoides infection in schoolchildren from rural KwaZulu-Natal, South Africa.}, journal = {Tropical medicine & international health : TM & IH}, volume = {10}, number = {5}, pages = {412-422}, doi = {10.1111/j.1365-3156.2005.01406.x}, pmid = {15860087}, issn = {1360-2276}, mesh = {Aluminum Silicates ; Animals ; Ascariasis/*epidemiology/prevention & control ; Ascaris lumbricoides/*physiology ; Child ; Clay ; Cluster Analysis ; *Ecosystem ; Female ; Geographic Information Systems ; Humans ; Male ; Models, Statistical ; Plants ; Prevalence ; Rural Health ; Socioeconomic Factors ; Soil/parasitology ; South Africa/epidemiology ; Sunlight ; }, abstract = {OBJECTIVES: To identify environmental factors that could serve to predict Ascaris lumbricoides infection patterns and thus guide control efforts in the absence of epidemiological information; to assess whether A. lumbricoides infection is positively associated with the soil clay content.

METHODS: Information on A. lumbricoides infection and re-infection in a cohort of primary schoolchildren and interview data on their socioeconomic background and behaviour were combined with environmental data using a geographical information system (GIS). Multivariate models served to explore the covariation of environmental and infection patterns adjusted for possible confounders.

RESULTS: Prevalence maps and spatial statistics revealed considerable spatial clustering of infection in the small study area. Logistic multivariate regression models showed strong positive associations of infection with vegetation density measured as the normalized difference vegetation index (NDVI) at baseline [odds ratio (OR) for a 10% increase: 1.82; 95% confidence interval (95% CI): 1.24-2.68; P=0.002] and after re-infection (OR: 2.22; 95% CI: 1.71-2.87; P<0.001). We also found a strong negative association of re-infection with the sun exposure of the soil surface as estimated from digital elevation models (OR: 0.78; 95% CI: 0.88; P<0.001). The soil clay content was only moderately positively associated with infection and re-infection. Socioeconomic and behavioural variables, although correlated with A. lumbricoides infection, did not appear to confound the above associations in the demographically homogeneous study area. Spatial analysis of the model residuals suggested that as the models accounted for most of the spatial pattern, the model standard errors should not be affected by spatial clustering.

CONCLUSION: NDVI seems to have a high potential for the prediction of A. lumbricoides infection as it was strongly associated with infection patterns in the study area. Further advantages are that NDVI information is easy to use, affordable and available with global coverage.}, } @article {pmid15859416, year = {2005}, author = {Yan, DH and Wang, H and Liu, Q and Wang, JH}, title = {[Spatial and temporal variation of the natural reproducible ability of water resource in the northeast part of China and its response to the land use change].}, journal = {Huan jing ke xue= Huanjing kexue}, volume = {26}, number = {1}, pages = {94-99}, pmid = {15859416}, issn = {0250-3301}, mesh = {*Agriculture ; China ; *Conservation of Natural Resources ; Ecology ; Environment ; Geographic Information Systems ; *Water Supply ; }, abstract = {With respect to the water cycling, the natural reproducible ability of water resource (NRAWR) was expressed, and the spatial and temporal differences of NRAWR in the northeast part of China were anatomized systematically with the GIS techniques. Furthermore, the response of NRAWR in the northeast part of China to land use changes was described based on land use patterns of the northeast part of China in 1986,1996 and 2000. Water resource in the northeast part of China has the distinct spatial and temporal variation during the period from 1956 to 2001 with the multi-year volume of 199.152 billion m(3), and the temporal change of NRAWR has 33-year, 11-year and 4-year cycles. In the phase from 1980 to 2001, the NRAWR in the northeast part of China has the descending trend, and the yearly variation range and intensity have marked spatial evolutional features. The coupling change of NRAWR and land use change shows that, in order to maintaining an higher NRAWR level under the condition of the acute anthropic interferes in the northeast part of China, the land use pattern should be adjusted based on the distributed eco-hydrological mechanism.}, } @article {pmid15859116, year = {2005}, author = {Chang, IC and Lu, LT and Lin, SS}, title = {Using a set of strategic indicator systems as a decision-making support implement for establishing a recycling-oriented society. A Taiwanese case study.}, journal = {Environmental science and pollution research international}, volume = {12}, number = {2}, pages = {96-108}, doi = {10.1065/espr2004.12.226}, pmid = {15859116}, issn = {0944-1344}, mesh = {Cities ; *Conservation of Natural Resources ; *Decision Support Techniques ; Environment ; Environmental Monitoring ; Policy Making ; *Refuse Disposal ; }, abstract = {UNLABELLED: BACKGROUND, SCOPE AND AIMS: To realize the vision of sustainable development (SD) originating from the 'only one earth' philosophy, and to integrate the conceptions of ecology and sustainability into the planning and decision-making criteria of urban growth management, the establishment of a recycling-oriented society (ROS) is essential. However, before the above intention can be achieved, it is indispensable to develop a system of strategic indicators for supporting a radical reformation of the urban development plan. Therefore, this study, based on the conception of the new urban development pattern ROS, attempted to carefully choose a sample city in Taiwan for launching a preliminary case study, and furthermore designed and proposed a concise and strategy-oriented assessment indicator system termed ROSAIS. ROSAIS, on the one hand, can act as a compass for understanding resource using efficiency and recycling status during city development and, on the other hand, can serve as an implement supporting decision-making for ROS construction.

METHODS: According to the definition and spirit of ROS, the structure of ROSAIS should clearly represent the relationship between resources and environment in human activities. The eco-efficiency indicator system (EEIS) and environmental symbiosis indicator system (ESIS) can be considered two key subindicator systems, and are the necessary components of ROSAIS. EEIS chooses the dominant production sectors in urban economic activities to calculate their eco-efficiency (EE). Separately, for obtaining a consensus regarding the framework of ESIS, the questionnaire approaches and expert consultation, together with the research experience and foundation of current relevant studies and indicator systems, are applied when crucial resource and environmental issues and respective indicators are selected.

RESULTS AND DISCUSSION: The calculation results of EEIS in this case study indicated that among the three dominant production activities (agricultural, fishery, and animal husbandry sector) the fishery sector has the highest EE, which indicates that the fishery activities and resources significantly influence the sustainability of the economic-environmental system of the sample city. Furthermore, according to a consensus achieved in ESIS, local green spaces, resource recovery, energy consumption pattern change, freshwater conservation and greenhouse effect abatement were considered as the five crucial issues influencing how the case study city can develop into an ES-city. The rate of local green spaces, resource recycling, freshwater conservation and the rate of reduction of nonrenewable energy use as well as carbon dioxide (CO2) emissions were used to evaluate the above five issues.

CONCLUSION: This case study is unparalleled in Taiwan. Even in Japan, where ROS legislation has been implemented, this kind of study remains in the preliminary stages. Furthermore, when communicating the indicator results, it is essential to provide the context and countermeasures of the crucial issues that are faced. The two sub-indicator systems proposed in this case study could comply completely with the above-mentioned requirements. For example, the EEIS provides information for achieving a balance between environmental burden and economic benefits among dominant production sectors; the ESIS provides information for setting strategies for overcoming the crucial issues faced.

RECOMMENDATION AND OUTLOOK: This study recommends that urban planers should consider the construction of the corresponding strategic indicator system to be indispensable, and makes further use of the indicator results related to the environmental education of residents for identifying and promoting participation with ROS, and turning them into implements for supporting urban SD decision-making. Furthermore, a successful indicator system depends on data availability and quality. This study recommends that urban planers should pay considerable attention to constructing relevant data collection channels, databases and the data quality.}, } @article {pmid15851675, year = {2005}, author = {Macdonald, SJ and Long, AD}, title = {Prospects for identifying functional variation across the genome.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {102 Suppl 1}, number = {Suppl 1}, pages = {6614-6621}, pmid = {15851675}, issn = {0027-8424}, support = {R01 GM058564/GM/NIGMS NIH HHS/United States ; GM58564/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Computational Biology ; Conserved Sequence/genetics ; DNA/genetics ; Drosophila/classification/*genetics ; Drosophila Proteins/genetics ; Evolution, Molecular ; Genetic Variation/*genetics ; *Genome ; Molecular Sequence Data ; Polymorphism, Genetic/genetics ; Selection, Genetic ; }, abstract = {The genetic factors contributing to complex trait variation may reside in regulatory, rather than protein-coding portions of the genome. Within noncoding regions, SNPs in regulatory elements are more likely to contribute to phenotypic variation than those in nonregulatory regions. Thus, it is important to be able to identify and annotate noncoding regulatory elements. DNA conservation among diverged species successfully identifies noncoding regulatory regions. However, because rapidly evolving regulatory regions will not generally be conserved across species, these will not detected by using purely conservation-based methods. Here we describe additional approaches that can be used to identify putative regulatory elements via signatures of nonneutral evolution. An examination of the pattern of polymorphism both within and between populations of Drosophila melanogaster, as well as divergence with its sibling species Drosophila simulans, across 24.2 kb of noncoding DNA identifies several nonneutrally evolving regions not identified by conservation. Because different methods tag different regions, it appears that the methods are complementary. Patterns of variation at different elements are consistent with the action of selective sweeps, balancing selection, or population differentiation. Together with regions conserved between D. melanogaster and Drosophila pseudoobscura, we tag 5.3 kb of noncoding DNA as potentially regulatory. Ninety-seven of the 408 common noncoding SNPs surveyed are within putatively regulatory regions. If these methods collectively identify the majority of functional noncoding polymorphisms, genotyping only these SNPs in an association mapping framework would reduce genotyping effort for noncoding regions 4-fold.}, } @article {pmid15840069, year = {2005}, author = {Purssell, E}, title = {Symptoms in the host: infection and treatment model.}, journal = {Journal of clinical nursing}, volume = {14}, number = {5}, pages = {555-561}, doi = {10.1111/j.1365-2702.2004.01109.x}, pmid = {15840069}, issn = {0962-1067}, mesh = {Adaptation, Physiological ; Biological Evolution ; Causality ; *Communicable Diseases/microbiology/therapy/transmission ; Cough/microbiology ; *Decision Support Techniques ; Diarrhea/microbiology ; Fever/microbiology ; Humans ; Immunity, Innate/*physiology ; Pain/microbiology ; Patient Selection ; }, abstract = {AIMS AND OBJECTIVES: The aim is to devise a decision-making model to help nurses and allied professionals treat the symptoms of infectious diseases in a logical way that maximizes the benefits of symptoms and minimizes any harm that they might do.

BACKGROUND: This paper considers the symptoms of infectious diseases from an evolutionary perspective, applying theories from ecology and evolution to nursing. Building upon evolutionary theories that suggest symptoms occur as the result of host defences, pathogen manipulations or as pure side-effects, it is suggested that those symptoms that have evolved as host defences should not always be treated because of their beneficial effects. However, clinical decision-making is more complex because of the rapid changes in environment and behaviour, which may impact upon the usefulness of symptoms to the host.

CONCLUSIONS: Although some symptoms can be identified as being beneficial adaptations, this alone is not sufficient indication to decide which symptoms should or should not be treated. Other considerations include any negative outcomes and behavioural and environmental changes that may affect the significance of any adaptation.

Nurses should aim to maximize the host defences of the patients they are caring for in order to speed recovery and to reduce transmission and the need for antibiotics. This model helps nurses to identify factors that should be considered when these decisions are made and suggests some principles that might be followed in other situations.}, } @article {pmid15839264, year = {2005}, author = {Petrov, Y}, title = {Luminance correlations define human sensitivity to contrast resolution in natural images.}, journal = {Journal of the Optical Society of America. A, Optics, image science, and vision}, volume = {22}, number = {4}, pages = {587-592}, doi = {10.1364/josaa.22.000587}, pmid = {15839264}, issn = {1084-7529}, mesh = {Artificial Intelligence ; Computer Simulation ; Discrimination, Psychological/*physiology ; Humans ; Image Interpretation, Computer-Assisted/*methods ; *Models, Biological ; Reproducibility of Results ; Sensitivity and Specificity ; Statistics as Topic ; Visual Perception/*physiology ; }, abstract = {Luminance patterns encode shape and surface structure of objects in our environment. Humans can detect gradations of 1%-2% of background luminance. Is this level of sensitivity to luminance gradations (contrast) determined by the amount of ecologically meaningful information available in natural scenes? In the first experiment, subjects discriminated natural images I from their "posterized" versions I(n), in which the number of luminance gradations was reduced to n. In the second experiment, amplified residual images I(res)(n) infinity I - I(n) were discriminated from white-noise images, which lack any luminance correlations and thus information content. Performance in the two experiments matched remarkably well. Furthermore, as a function of n, the signal detected in both experiments was well fitted by the mutual information between nearby image pixels in the residual image I(res)(n). This suggests that human sensitivity to luminance contrast is optimized to extract ecologically useful information encoded by the luminance patterns of natural scenes.}, } @article {pmid15833238, year = {2005}, author = {Gaines, KF and Boring, CS and Porter, DE}, title = {The development of a spatially explicit model to estimate radiocaesium body burdens in raccoons (Procyon lotor) for ecological risk assessment.}, journal = {The Science of the total environment}, volume = {341}, number = {1-3}, pages = {15-31}, doi = {10.1016/j.scitotenv.2004.09.017}, pmid = {15833238}, issn = {0048-9697}, mesh = {Animals ; Body Burden ; Cesium Radioisotopes/*analysis ; Environment ; Food Chain ; Geographic Information Systems ; Male ; *Models, Theoretical ; Muscles/chemistry ; Raccoons/*metabolism ; Reproducibility of Results ; Risk Assessment ; South Carolina ; Water Pollutants, Radioactive/*analysis ; }, abstract = {A spatially explicit model of raccoon (Procyon lotor) distribution for the U.S. Department of Energy's (DOE) Savannah River Site (SRS) in west-central South Carolina was developed using data from a raccoon radio-telemetry study and visualized within a Geographic Information System (GIS). An inductive approach was employed to develop three sub-models using the ecological requirements of raccoons studied in the following habitats: (1) man-made reservoirs, (2) bottomland hardwood/riverine systems, and (3) isolated wetland systems. Logistic regression was used to derive probabilistic resource selection functions using habitat compositional data and landscape metrics. The final distribution model provides a spatially explicit probability (likelihood of being in an area) surface for male raccoons. The model is a stand-alone tool consisting of algorithms independent of the specific GIS data layers to which they were derived. The model was then used to predict contaminant burdens in raccoons inhabiting a riverine system contaminated with radiocaesium (137Cs). The predicted 137Cs burdens were less than if one would assume homogeneous use of the contaminated areas. This modelling effort provides a template for DOE managed lands and other large government facilities to establish a framework for site-specific ecological assessments that use wildlife species as endpoints.}, } @article {pmid15831383, year = {2005}, author = {Oksman-Caldentey, KM and Saito, K}, title = {Integrating genomics and metabolomics for engineering plant metabolic pathways.}, journal = {Current opinion in biotechnology}, volume = {16}, number = {2}, pages = {174-179}, doi = {10.1016/j.copbio.2005.02.007}, pmid = {15831383}, issn = {0958-1669}, mesh = {Arabidopsis/genetics ; Biotechnology/methods ; Computational Biology/methods ; Crops, Agricultural/genetics ; Genetic Engineering/*methods ; Genome, Plant ; Genomics/*methods ; Models, Biological ; Plant Physiological Phenomena ; Plant Proteins/metabolism ; Plants/genetics ; Plants, Genetically Modified ; Protein Engineering/*methods ; Time Factors ; }, abstract = {Plant metabolites are characterized by an enormous chemical diversity, every plant having its own complex set of metabolites. This variety poses analytical challenges, both for profiling multiple metabolites in parallel and for the quantitative analysis of selected metabolites. We are only just starting to understand the roles of these metabolites, many of them being involved in adaptations to specific ecological niches and some finding beneficial use (e.g. as pharmaceuticals). Spectacular advances in plant metabolomics offer new possibilities, together with the aid of systems biology, to explore the extraordinary complexity of the plant biochemical capacity. State-of-the art genomics tools can be combined with metabolic profiling to identify key genes that could be engineered for the production of improved crop plants.}, } @article {pmid15827274, year = {2005}, author = {Saathoff, E and Olsen, A and Sharp, B and Kvalsvig, JD and Appleton, CC and Kleinschmidt, I}, title = {Ecologic covariates of hookworm infection and reinfection in rural Kwazulu-natal/south Africa: a geographic information system-based study.}, journal = {The American journal of tropical medicine and hygiene}, volume = {72}, number = {4}, pages = {384-391}, pmid = {15827274}, issn = {0002-9637}, mesh = {Child ; Confounding Factors, Epidemiologic ; Female ; Geographic Information Systems ; Hookworm Infections/*epidemiology ; Humans ; Male ; Recurrence ; Social Class ; South Africa/epidemiology ; }, abstract = {Information on hookworm infection and re-infection in a cohort of primary school children and interview data on their socioeconomic background and behavior were combined with environmental data using a geographic information system (GIS). Multivariate models served to explore the covariation of environmental and infection patterns adjusted for possible confounders. Our aim was to identify environmental factors that might serve to predict infection and thus guide control efforts when epidemiologic information is insufficient. Furthermore, we wanted to establish whether soil type has a genuine influence on hookworm infection. Prevalence maps and spatial statistics showed considerable spatial clustering of infection in the small (approximately 28 x 16 km) study area. The multivariate logistic regression models showed strong positive associations of infection at baseline (baseline prevalence = 83.2%) with settlement density (odds ratio [OR] = 1.24, 95% confidence interval [CI] = 1.10-1.38) and vegetation density (OR = 1.66, 95% CI = 1.25-2.22) and a strong negative association with the clay content of the soil (OR = 0.67, 95% CI = 0.62-0.73). Similar but weaker correlations were found after re-infection. Socioeconomic status and behavior did not seem to confound these associations. Spatial analysis of the model residuals suggested that because the models accounted for most of the spatial pattern, the model standard errors were not affected by spatial clustering. Our study shows that the pattern of hookworm infection is strongly influenced by several environmental factors. The GIS-aided prediction of areas in need of treatment is therefore a promising tool to guide control efforts when epidemiologic information is insufficient.}, } @article {pmid15821327, year = {2005}, author = {Gagoshidze, MV and Antelava, MO and Zedginidze, AG and Mandzhavidze, NSh}, title = {[Dependence of child health on the ecology].}, journal = {Georgian medical news}, volume = {}, number = {118}, pages = {49-52}, pmid = {15821327}, issn = {1512-0112}, mesh = {Arsenic/*toxicity ; Child ; Data Interpretation, Statistical ; Ecology ; Environmental Pollutants/*toxicity ; Georgia (Republic)/epidemiology ; Humans ; Micronuclei, Chromosome-Defective ; Micronucleus Tests ; Respiratory Tract Infections/*epidemiology ; }, abstract = {The purpose of the work was to establish correlation between detected with the help of micronuclei in exfoliation cells infringements in the genetic disorder of Acute Respiratory Infection (ARI) at children living in Lukhuni gorge. Heavy metals having mutagenous trait can cause variety of diseases and first of all influence on the genetic apparatus, which damage often reflects chromosome change. The study of micronuclei in exfoliation cells is comparatively new, easily reachable and believable informative method. From Lukhuni gorge it is indicated true lifting amount of micronuclei. In a distance this indications where far less. It is investigated 150 children: 50 from Lukhuni gorge (I group) where the maintenance of arsenic is sharply raised in environment and 100 from the regions remote from Lukhuni gorge. Amount average quantity micronuclei in 1000 cells in I group was very high 22,38+/-1,26 in. In the second was 4,36+/-0,50 (t=12,82; p<0,0001). All children, under the anamnesis and the clinical data, have been divided on frequently were ill of Acute Respiratory Infection(in one year > 4-5 times) and seldom were ill of Acute Respiratory Infection (< 4-5 times). ARI most frequently were marked in this region. It is revealed correlation between amount of micronuclei in exfoliation cells and parameters of illness respiratory diseases at children living in territories, polluted with arsenic and his derivatives (R=0,789; p<0,000001).}, } @article {pmid15817771, year = {2005}, author = {Field, D and Hughes, J}, title = {Cataloguing our current genome collection.}, journal = {Microbiology (Reading, England)}, volume = {151}, number = {Pt 4}, pages = {1016-1019}, doi = {10.1099/mic.0.27914-0}, pmid = {15817771}, issn = {1350-0872}, mesh = {Computational Biology ; *Genome ; Genomics ; Microbiology ; }, } @article {pmid15814343, year = {2005}, author = {Buckland, ST and Magurran, AE and Green, RE and Fewster, RM}, title = {Monitoring change in biodiversity through composite indices.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {360}, number = {1454}, pages = {243-254}, pmid = {15814343}, issn = {0962-8436}, mesh = {Animals ; *Biodiversity ; Birds/physiology ; Conservation of Natural Resources/*methods/*trends ; Data Interpretation, Statistical ; Population Density ; *Research Design ; Species Specificity ; United Kingdom ; }, abstract = {The need to monitor trends in biodiversity raises many technical issues. What are the features of a good biodiversity index? How should trends in abundance of individual species be estimated? How should composite indices, possibly spanning very diverse taxa, be formed? At what spatial scale should composite indices be applied? How might change-points--points at which the underlying trend changes--be identified? We address some of the technical issues underlying composite indices, including survey design, weighting of the constituent indices, identification of change-points and estimation of spatially varying time trends. We suggest some criteria that biodiversity measures for use in monitoring surveys should satisfy, and we discuss the problems of implementing rigorous methods. We illustrate the properties of different composite indices using UK farmland bird data. We conclude that no single index can capture all aspects of biodiversity change, but that a modified Shannon index and the geometric mean of relative abundance have useful properties.}, } @article {pmid15805016, year = {2005}, author = {Ané, C and Sanderson, M}, title = {Missing the forest for the trees: phylogenetic compression and its implications for inferring complex evolutionary histories.}, journal = {Systematic biology}, volume = {54}, number = {1}, pages = {146-157}, doi = {10.1080/10635150590905984}, pmid = {15805016}, issn = {1063-5157}, mesh = {*Algorithms ; Classification/*methods ; Data Interpretation, Statistical ; *Models, Genetic ; *Phylogeny ; }, abstract = {Phylogenetic tree reconstruction is difficult in the presence of lateral gene transfer and other processes generating conflicting signals. We develop a new approach to this problem using ideas borrowed from algorithmic information theory. It selects the hypothesis that simultaneously minimizes the descriptive complexity of the tree(s) plus the data when encoded using those tree(s). In practice this is the hypothesis that can compress the data the most. We show not only that phylogenetic compression is an efficient method for encoding most phylogenetic data sets and is more efficient than compression schemes designed for single sequences, but also that it provides a clear information theoretic rule for determining when a collection of conflicting trees is a better explanation of the data than a single tree. By casting the parsimony problem in this more general framework, we also conclude that the so-called total-evidence tree--the tree constructed from all the data simultaneously--is not always the most economical explanation of the data.}, } @article {pmid15803502, year = {2005}, author = {Medvedeva, SE and Boyandin, A and Lankin, Y and Kotov, D and Rodicheva, E and Popova, L}, title = {BIOLUMBASE--the database of natural and transgenic bioluminescent organisms.}, journal = {Luminescence : the journal of biological and chemical luminescence}, volume = {20}, number = {2}, pages = {90-96}, doi = {10.1002/bio.809}, pmid = {15803502}, issn = {1522-7235}, mesh = {Bacteria/genetics/*metabolism ; Bacterial Proteins/genetics/metabolism ; *Databases, Factual ; Ecology ; *Luminescence ; Luminescent Proteins/genetics/*metabolism ; Marine Biology ; Organisms, Genetically Modified/*physiology ; Photobacterium/genetics/isolation & purification ; Transgenes/physiology ; }, abstract = {The Institute of Biophysics SB RAS hosts and maintains a specialized collection of luminous bacteria (CCIBSO 836) containing over 700 strains isolated in various regions of the world's oceans. The culture collection is a source of lux genes and biologically active substances. The wide application of bioluminescence in medicine and ecology has given importance to analysing information on the structure and functioning of bioluminescence systems in natural and transgenic microorganisms, as well as on their features that are closely interrelated with bioluminescence. The aims of our BIOLUMBASE database are: gathering information on microorganisms with lux genes, their analysis and free access, and distribution of this data throughout the global network. The database includes two sections, natural and transgenic luminous microorganisms, and is updated by our own experimental results, the published literature and internet resources. For the future, a publicly available internet site for BIOLUMBASE is planned. This will list the strains and provide comprehensive information on the properties and functions of luminous bacteria, the mechanisms of regulation of bioluminescence systems, constructs with lux genes, and applications of bioluminescence in microbiology, ecology, medicine and biotechnology. It is noteworthy that this database will also be useful for evaluation of biological hazards of transgenic strains. Users will be able to carry out bibliographic and strain searches starting from any feature of interest.}, } @article {pmid15798278, year = {2005}, author = {Wilson, M and Jackson, D}, title = {Uncertainty and power at low levels of incurred radiation dose.}, journal = {Journal of radiological protection : official journal of the Society for Radiological Protection}, volume = {25}, number = {1}, pages = {51-66}, doi = {10.1088/0952-4746/25/1/003}, pmid = {15798278}, issn = {0952-4746}, mesh = {Animals ; *Data Interpretation, Statistical ; Environmental Exposure/*adverse effects ; *Fishes ; Gamma Rays ; Humans ; *Radiation Dosage ; Radiation Monitoring/methods ; United Kingdom ; Water Pollutants, Radioactive/*analysis ; }, abstract = {It is common practice when calculating dose to exposed populations to average the variables that go into the dose calculation (e.g. environmental concentrations, air kerma, consumption rates, occupancy rates). This approach is simple and can be useful where data are obtained over different periods (weekly, monthly, quarterly), where samples may be bulked for some analyses but not others and where gaps in the data are present. However, such an approach does not yield information on the degree of uncertainty around the average dose calculated. An alternative approach is to estimate the dose to each individual and to obtain an average from this data set, which can then also be used to derive a measure of uncertainty around the central dose estimate. In this study, we demonstrate the variability in dose estimates using a hypothetical data set and consider the implications for sample size to achieve fixed confidence or resolving power. We recommend calculating the dose to every individual sampled, in order both to obtain the average dose and to estimate its variability. We argue that it is best practice to obtain information as complete as possible from the available sample of individuals.}, } @article {pmid15795695, year = {2005}, author = {Geier, DA and Geier, MR}, title = {A two-phased population epidemiological study of the safety of thimerosal-containing vaccines: a follow-up analysis.}, journal = {Medical science monitor : international medical journal of experimental and clinical research}, volume = {11}, number = {4}, pages = {CR160-70}, pmid = {15795695}, issn = {1234-1010}, mesh = {Child ; Databases, Factual ; Diphtheria Toxoid/adverse effects ; Female ; Fever/epidemiology ; Humans ; Male ; Patient Selection ; Pertussis Toxin/adverse effects ; Seizures/epidemiology ; Thimerosal/*adverse effects ; Vaccines/adverse effects/*therapeutic use ; }, abstract = {BACKGROUND: Thimerosal is an ethylmercury-containing preservative in vaccines. Toxicokinetic studies have shown children received doses of mercury from thimerosal-containing vaccines (TCVs) that were in excess of safety guidelines. Previously, an ecological study showing a significant association between TCVs and neurodevelopmental disorders (NDs) in the US was published in this journal.

MATERIAL/METHODS: A two phased population-based epidemiological study was undertaken. Phase one evaluated reported NDs to the Vaccine Adverse Event Reporting System (VAERS) following thimerosal-containing Diphtheria-Tetanus-acellular-Pertussis (DTaP) vaccines in comparison to thimerosal-free DTaP vaccines administered from 1997 through 2001. Phase two evaluated the automated Vaccine Safety Datalink (VSD) for cumulative exposures to mercury from TCVs at 1-, 2-, 3-, and 6-months-of-age for infants born from 1992 through 1997 and the eventual risk of developing NDs.

RESULTS: Phase one showed significantly increased risks for autism, speech disorders, mental retardation, personality disorders, and thinking abnormalities reported to VAERS following thimerosal-containing DTaP vaccines in comparison to thimerosal-free DTaP vaccines. Phase two showed significant associations between cumulative exposures to thimerosal and the following types of NDs: unspecified developmental delay, tics, attention deficit disorder (ADD), language delay, speech delay, and neurodevelopmental delays in general.

CONCLUSIONS: This study showed that exposure to mercury from TCVs administered in the US was a consistent significant risk factor for the development of NDs. It is clear from these data and other recent publications linking TCVs with NDs that additional ND research should be undertaken in the context of evaluating mercury-associated exposures and thimerosal-free vaccines should be made available.}, } @article {pmid15774562, year = {2005}, author = {Chow, KM and Szeto, CC}, title = {Impact of enforcing the Labour Ordinance, with 1-in-7-day off for hospital doctors, on weekend hospital discharge rate.}, journal = {Journal of public health (Oxford, England)}, volume = {27}, number = {2}, pages = {189-191}, doi = {10.1093/pubmed/fdi022}, pmid = {15774562}, issn = {1741-3842}, mesh = {Aged ; Chronology as Topic ; Decision Support Systems, Clinical ; Female ; Health Services Research ; Hong Kong ; Hospitals, University/legislation & jurisprudence/*statistics & numerical data ; Humans ; *Legislation, Hospital ; Length of Stay/*statistics & numerical data ; Male ; Medical Staff, Hospital/legislation & jurisprudence/*supply & distribution ; Middle Aged ; Multivariate Analysis ; Patient Discharge/*statistics & numerical data ; Personnel Staffing and Scheduling/*legislation & jurisprudence ; Poisson Distribution ; Time Factors ; Workforce ; }, abstract = {BACKGROUND: After enforcing the Labour Ordinance, hospital doctors must have 1 day off-work every week. In this study, we aimed to evaluate its impact on the discharge pattern from an acute medical hospital.

METHODS: We undertook a hospital-based ecologic study with before-after design using the clinical management database of patient discharge records of all acute medical wards in a hospital from January to March 2002 (1 year before new system) and from January to March 2004 (1 year after restricted weekend service). The main outcome measures were the daily discharge rates for the two periods. The odds of being discharged on a Saturday were estimated by multivariate analyses.

RESULTS: The number of patient discharge on a Saturday was substantially lower in 2004 as compared to 2002 (47.5 +/- 8.5 per Saturday versus 70.5 +/- 11.1 per Saturday, respectively, p < 0.001). A statistically significant decreased trend was noted in the weekend discharge rate in 2002 and 2004 (Poisson p-value for change in discharge rate, p < 0.001). On the other hand, the number of patient discharges on weekdays did not differ between the two periods. Consistently fewer patients were being discharged on Sundays and Mondays as compared to the rest of the week days in both periods. Compared with study period 2002, patients hospitalized in 2004 (with limited weekend service) had significantly lower multivariate-adjusted odds of being discharged on a Saturday (odds ratio of 0.70; 95 percent confidence interval 0.72-0.89, p < 0.0001).

CONCLUSIONS: Length of hospital stay is influenced by the health care system delivery apart from clinical factors. Restricted weekend services in an acute medical hospital setting substantially lengthen the hospital stay, and might therefore entail a major financial burden.}, } @article {pmid15769318, year = {2004}, author = {Fang, LQ and Li, CY and Yang, H and Wu, XM and Yang, H and Chen, HX and Li, XW and Cao, WC}, title = {[Using geographic information system to study on the association between epidemic areas and main animal hosts of hemorrhagic fever with renal syndrome in China].}, journal = {Zhonghua liu xing bing xue za zhi = Zhonghua liuxingbingxue zazhi}, volume = {25}, number = {11}, pages = {929-933}, pmid = {15769318}, issn = {0254-6450}, mesh = {Animals ; China/epidemiology ; *Disease Reservoirs/virology ; Ecology ; Environmental Monitoring ; Epidemiological Monitoring ; *Geographic Information Systems ; Hantaan virus/classification/isolation & purification ; Hemorrhagic Fever with Renal Syndrome/*epidemiology ; Humans ; Mice ; Population Surveillance ; Rats ; Serotyping ; }, abstract = {OBJECTIVE: To analyze the association between types of epidemic areas and proportion of main animal hosts of hemorrhagic fever with renal syndrome (HFRS) in China.

METHODS: Data on serotype of HFRS patients from 122 regions and species as well as number of animal hosts from 41 national surveillance sites were collected and managed. The map of the types of epidemic areas from 1991-1999 in China was produced using inverse distance weighted technique in the ArcGIS 8.1 software. The map of the proportion of host animals was then overlapped on it and the surveillance sites of HFRS were clustered in terms of the proportion of host animals.

RESULTS: Variance in spatial distribution of the types of epidemic areas was observed. Two epidemic area types, namely Hantaan-dominant mixed epidemic areas and Soul-dominant mixed epidemic areas seemed to have transferred from the north-east to south-west of China in turns. There were more species of HFRS animal hosts in fields than those of in residential areas. The diversity of rodent species in fields was higher than that of the residential areas which predominant harbored rodent species of 2-3 kinds. Types of surveillance sites classified by cluster analysis of proportion of main animal hosts were consistent with the serotypes of HFRS patients.

CONCLUSION: Through employment of spatial analysis technique based on GIS databases, the HFRS types of main epidemic area in China could be well predicted by surveillance data.}, } @article {pmid15764549, year = {2003}, author = {Markwiese, JT}, title = {Collection and evaluation of existing data: an ecological risk assessment perspective.}, journal = {Quality assurance (San Diego, Calif.)}, volume = {10}, number = {3-4}, pages = {107-116}, doi = {10.1080/10529410390892043}, pmid = {15764549}, issn = {1052-9411}, mesh = {Cadmium/*toxicity ; Data Collection/*methods ; *Data Interpretation, Statistical ; *Environmental Health ; Risk Assessment/*methods ; United States ; United States Environmental Protection Agency ; }, abstract = {All scientific disciplines rely to some degree upon existing data to design new studies, test hypotheses, and make decisions. Because existing data can take many forms, a framework for addressing the quality of these data must be general and comprehensive. By nature of this inclusiveness, quality categories for existing data are necessarily broad. Effective employment of existing data requires the development of specific acceptance criteria from broad data quality categories. A framework is presented for collecting and evaluating existing data with examples of Environmental Protection Agency projects employing a tiered data review. The systematic planning inherent in a tiered review is described and attendant data quality considerations are developed in the context of an ecological risk assessment; specifically, the process is illustrated by defining an ecologically protective concentration of a chemical in soil.}, } @article {pmid15752432, year = {2005}, author = {Colbourne, JK and Singan, VR and Gilbert, DG}, title = {wFleaBase: the Daphnia genome database.}, journal = {BMC bioinformatics}, volume = {6}, number = {}, pages = {45}, pmid = {15752432}, issn = {1471-2105}, support = {R01 HG002733/HG/NHGRI NIH HHS/United States ; 1R01HG002733-01/HG/NHGRI NIH HHS/United States ; }, mesh = {Animals ; Chromosome Mapping ; Computational Biology/*methods ; Computer Graphics ; Daphnia/*genetics ; Database Management Systems ; Databases, Factual ; *Databases, Genetic ; Ecology ; Ecosystem ; Evolution, Molecular ; Genetics, Population ; *Genome ; Genomics ; Information Services ; Information Storage and Retrieval ; Internet ; Software ; }, abstract = {BACKGROUND: wFleaBase is a database with the necessary infrastructure to curate, archive and share genetic, molecular and functional genomic data and protocols for an emerging model organism, the microcrustacean Daphnia. Commonly known as the water-flea, Daphnia's ecological merit is unequaled among metazoans, largely because of its sentinel role within freshwater ecosystems and over 200 years of biological investigations. By consequence, the Daphnia Genomics Consortium (DGC) has launched an interdisciplinary research program to create the resources needed to study genes that affect ecological and evolutionary success in natural environments.

DISCUSSION: These tools include the genome database wFleaBase, which currently contains functions to search and extract information from expressed sequenced tags, genome survey sequences and full genome sequencing projects. This new database is built primarily from core components of the Generic Model Organism Database project, and related bioinformatics tools.

SUMMARY: Over the coming year, preliminary genetic maps and the nearly complete genomic sequence of Daphnia pulex will be integrated into wFleaBase, including gene predictions and ortholog assignments based on sequence similarities with eukaryote genes of known function. wFleaBase aims to serve a large ecological and evolutionary research community. Our challenge is to rapidly expand its content and to ultimately integrate genetic and functional genomic information with population-level responses to environmental challenges. URL: http://wfleabase.org/.}, } @article {pmid15747408, year = {2004}, author = {Gaines, KF and Porter, DE and Dyer, SA and Wein, GR and Pinder, JE and Brisbin, IL}, title = {Using wildlife as receptor species: a landscape approach to ecological risk assessment.}, journal = {Environmental management}, volume = {34}, number = {4}, pages = {528-545}, pmid = {15747408}, issn = {0364-152X}, mesh = {Animals ; *Animals, Wild ; *Ecology ; Environment ; *Environmental Exposure ; Environmental Pollutants ; Geographic Information Systems ; Models, Theoretical ; *Risk Assessment ; South Carolina ; United States Government Agencies ; }, abstract = {To assist risk assessors at the Department of Energy's Savannah River Site (SRS), a Geographic Information System (GIS) application was developed to provide relevant information about specific receptor species of resident wildlife that can be used for ecological risk assessment. Information was obtained from an extensive literature review of publications and reports on vertebrate- and contaminant-related research since 1954 and linked to a GIS. Although this GIS is a useful tool for risk assessors because the data quality is high, it does not describe the species' site-wide spatial distribution or life history, which may be crucial when developing a risk assessment. Specific receptor species on the SRS were modeled to provide an estimate of an overall distribution (probability of being in an area). Each model is a stand-alone tool consisting of algorithms independent of the GIS data layers to which it is applied and therefore is dynamic and will respond to changes such as habitat disturbances and natural succession. This paper describes this modeling process and demonstrates how these resource selection models can then be used to produce spatially explicit exposure estimates. This approach is a template for other large federal facilities to establish a framework for site-specific risk assessments that use wildlife species as endpoints.}, } @article {pmid15747407, year = {2004}, author = {Robertson, HA and Fitzsimons, JA}, title = {Hydrology or floristics? Mapping and classification of wetlands in Victoria, Australia, and implications for conservation planning.}, journal = {Environmental management}, volume = {34}, number = {4}, pages = {499-507}, pmid = {15747407}, issn = {0364-152X}, mesh = {*Biodiversity ; *Conservation of Natural Resources ; Ecosystem ; *Fresh Water ; Geographic Information Systems ; Geography ; Plants ; Victoria ; }, abstract = {A national approach to the conservation of biodiversity in Australia's freshwater ecosystems is a high priority. This requires a consistent and comprehensive system for the classification, inventory, and assessment of wetland ecosystems. This paper, using the State of Victoria as a case study, compares two classification systems that are commonly utilized to delineate and map wetlands--one based on hydrology (Victorian Wetland Database [VWD]) and one based on indigenous vegetation types and other natural features (Ecological Vegetation Classes [EVC]). We evaluated the extent of EVC mapping of wetlands relative to the VWD classification system using a number of datasets within a geographical information system. There were significant differences in the coverage of extant EVCs across bioregions, different-sized wetlands, and VWD wetland types. Resultant depletion levels were markedly different when examined using the two systems, with depletion levels, and therefore perceived conservation status, of EVCs being significantly higher. Although there is little doubt that many wetland ecosystems in Victoria are in fact threatened, the extent of this threat cannot accurately be determined by relying on the EVC mapping as it currently stands. The study highlighted the significant impact wetland classification methods have in determining the conservation status of freshwater ecosystems.}, } @article {pmid15742536, year = {2005}, author = {Abdelwahed, S and Wu, J and Biswas, G and Ramirez, J and Manders, EJ}, title = {Online fault adaptive control for efficient resource management in Advanced Life Support Systems.}, journal = {Habitation (Elmsford, N.Y.)}, volume = {10}, number = {2}, pages = {105-115}, doi = {10.3727/154296605774791214}, pmid = {15742536}, issn = {1542-9660}, mesh = {Algorithms ; Artificial Intelligence ; Computer Simulation ; Decision Support Techniques ; *Ecological Systems, Closed ; Equipment Safety/*instrumentation ; Life Support Systems/*instrumentation ; Models, Theoretical ; *Neural Networks, Computer ; Osmosis ; Space Flight/*instrumentation ; Systems Theory ; Water Purification/*instrumentation ; }, abstract = {This article presents the design and implementation of a controller scheme for efficient resource management in Advanced Life Support Systems. In the proposed approach, a switching hybrid system model is used to represent the dynamics of the system components and their interactions. The operational specifications for the controller are represented by utility functions, and the corresponding resource management problem is formulated as a safety control problem. The controller is designed as a limited-horizon online supervisory controller that performs a limited forward search on the state-space of the system at each time step, and uses the utility functions to decide on the best action. The feasibility and accuracy of the online algorithm can be assessed at design time. We demonstrate the effectiveness of the scheme by running a set of experiments on the Reverse Osmosis (RO) subsystem of the Water Recovery System (WRS).}, } @article {pmid15737455, year = {2005}, author = {Ierodiaconou, D and Laurenson, L and Leblanc, M and Stagnitti, F and Duff, G and Salzman, S and Versace, V}, title = {The consequences of land use change on nutrient exports: a regional scale assessment in south-west Victoria, Australia.}, journal = {Journal of environmental management}, volume = {74}, number = {4}, pages = {305-316}, doi = {10.1016/j.jenvman.2004.09.010}, pmid = {15737455}, issn = {0301-4797}, mesh = {*Environment ; Environmental Monitoring/*methods ; Environmental Pollutants/*analysis ; Geographic Information Systems ; Geography ; *Models, Theoretical ; Nitrogen/*metabolism ; Phosphorus/*metabolism ; Telemetry ; Victoria ; }, abstract = {Estimation of nutrient load production based on multi-temporal remotely sensed land use data for the Glenelg-Hopkins region in south-west Victoria, Australia, is discussed. Changes in land use were mapped using archived Landsat data and computerised classification techniques. Land use change has been rapid in recent history with 16% of the region transformed in the last 22 years. Total nitrogen and phosphorus loads were estimated using an export coefficient model. The analysis demonstrates an increase in modelled nitrogen and phosphorus loadings from 1980 to 2002. Whilst such increases were suspected from past anecdotal and ad-hoc evidence, our modelling estimated the magnitude of such increases and thus demonstrated the enormous potential of using remote sensing and GIS for monitoring regional scale environmental processes.}, } @article {pmid15736887, year = {2005}, author = {Brown, MT and Vivas, MB}, title = {Landscape development intensity index.}, journal = {Environmental monitoring and assessment}, volume = {101}, number = {1-3}, pages = {289-309}, pmid = {15736887}, issn = {0167-6369}, mesh = {Agriculture ; *Conservation of Natural Resources ; Data Collection ; *Ecology ; *Ecosystem ; Environmental Monitoring/methods ; *Geographic Information Systems ; Humans ; Residence Characteristics ; Water Supply ; }, abstract = {The condition of landscapes and the ecological communities within them is strongly related to levels of human activity. Human-dominated land uses and especially the intensity of the uses can affect adjacent ecological communities through direct, secondary, and cumulative impacts. Using land use data and a development-intensity measure derived from energy use per unit area, an index of Landscape Development Intensity (LDI) can be calculated for watersheds of varying sizes to estimate the potential impacts from human-dominated activities that are experienced by ecological systems within those watersheds. The intended use of the LDI is as an index of the human disturbance gradient (the level of human induced impacts on the biological, chemical, and physical processes of surrounding lands or waters). The LDI can be used at the scale of river, stream, or lake watersheds or at the smaller scale of individual isolated wetland watersheds. Based on land uses and land cover, the LDI can be applied using available GIS land use/land cover data, aerial photographs, or field surveys. A description of data needs and methods for calculating an LDI index and several applications of the index as a land use based ranking scheme of the human disturbance gradient for watersheds are given.}, } @article {pmid15736885, year = {2005}, author = {Seidling, W and Mues, V}, title = {Statistical and geostatistical modelling of preliminarily adjusted defoliation on an European scale.}, journal = {Environmental monitoring and assessment}, volume = {101}, number = {1-3}, pages = {223-247}, pmid = {15736885}, issn = {0167-6369}, mesh = {Conservation of Natural Resources ; Data Collection ; Environmental Monitoring/methods ; Europe ; *Geographic Information Systems ; Geological Phenomena ; Geology ; *Models, Theoretical ; *Plant Leaves ; Trees/*growth & development ; }, abstract = {Since 1987 tree crown condition is surveyed annually in large parts of Europe mainly in terms of defoliation. The plot-wise means of defoliation from 1994 to 2000 were evaluated by General Linear Models (GLM) in order to describe country-specific levels of defoliation and age-trends. Additional runs with estimates for influences of insects and fungi were performed. The amount of variance of defoliation explained by country, age and its interaction was between 35% and 59% for the main tree species, except for Quercus ilex. Additionally, up to 10% could be explained by the inclusion of estimates for infestations by insects and fungi. Residuals of the GLMs were taken as a measure of forest condition not biased by country or age effects and interpreted as 'preliminarily adjusted defoliation' (PAD). PAD values were analysed using geostatistical methods. The modelled spatial autocorrelations were used for kriging. The resulting maps give an overview on regions with elevated defoliation, which may pinpoint regional causes of defoliation. The elimination of methodologically caused variance is a precondition of any cause-effect oriented analyses. The combination of explorative modelling and geostatistics will promote the choice of further promising predictors.}, } @article {pmid15724961, year = {2004}, author = {Tittiger, C}, title = {Functional genomics and insect chemical ecology.}, journal = {Journal of chemical ecology}, volume = {30}, number = {12}, pages = {2335-2358}, doi = {10.1007/s10886-004-7940-4}, pmid = {15724961}, issn = {0098-0331}, support = {P20 RR16464/RR/NCRR NIH HHS/United States ; }, mesh = {Animals ; Chemical Phenomena ; *Chemistry ; Computational Biology ; *Ecology ; Genomics/*methods/trends ; Insecta/*chemistry/physiology ; Pheromones ; }, abstract = {High-throughput molecular techniques (i.e., genomics) are now beginning to make their way into chemical ecology research. Pioneering functional genomics studies have made significant contributions to our understanding of insect pheromone production, reception, behavior, and insect-plant interactions. Much of this research involves nonmodel organisms, including the honey bee, silkworm, and bark beetles, underscoring that researchers need not be restricted to traditional model organisms for high-throughput research. Furthermore, the technology can reveal physiological interactions that might otherwise be missed by more traditional molecular approaches. Functional genomics should become more widely used as researchers appreciate the wealth of information this potent approach can supply. This review concentrates on a summary of available technologies for functional genomics as they may be applied by chemical ecologists studying insects. Allied technologies (proteomics and metabolomics) are introduced briefly toward the end in the context of future applications.}, } @article {pmid15717925, year = {2005}, author = {Orgogozo, V and Grueber, WB}, title = {FlyPNS, a database of the Drosophila embryonic and larval peripheral nervous system.}, journal = {BMC developmental biology}, volume = {5}, number = {}, pages = {4}, pmid = {15717925}, issn = {1471-213X}, support = {F32 NS043027/NS/NINDS NIH HHS/United States ; F32 NS43027-02/NS/NINDS NIH HHS/United States ; }, mesh = {Abdomen/innervation ; Animals ; Biomarkers/analysis ; Cell Differentiation ; *Databases as Topic ; Drosophila Proteins/analysis ; Drosophila melanogaster/anatomy & histology/*embryology/growth & development ; Nerve Tissue Proteins/analysis ; Neurons/chemistry/cytology ; Peripheral Nervous System/anatomy & histology/chemistry/embryology ; Sense Organs/chemistry/cytology/embryology ; Terminology as Topic ; }, abstract = {BACKGROUND: The embryonic and larval peripheral nervous system of Drosophila melanogaster is extensively studied as a very powerful model of developmental biology. One main advantage of this system is the ability to study the origin and development of individual sensory cells. However, there remain several discrepancies regarding the organization of sensory organs in each abdominal segment A1-A7.

DESCRIPTION: We have constructed a web site called FlyPNS (for Fly Peripheral Nervous System) that consolidates a wide range of published and unpublished information about the embryonic and larval sensory organs. It communicates (1) a PNS pattern that solves the discrepancies that have been found in the recent literature, (2) the correspondence between the different nomenclatures that have been used so far, (3) a comprehensive description of each sensory organ, and (4) a list of both published and unpublished markers to reliably identify each PNS cell.

CONCLUSIONS: The FlyPNS database integrates disparate data and nomenclature and thus helps understanding the conflicting observations that have been published recently. Furthermore, it is designed to provide assistance in the identification and study of individual sensory cells. We think it will be a useful resource for any researcher with interest in Drosophila sensory organs.}, } @article {pmid15716494, year = {2005}, author = {Takeuchi, F and Yanai, K and Morii, T and Ishinaga, Y and Taniguchi-Yanai, K and Nagano, S and Kato, N}, title = {Linkage disequilibrium grouping of single nucleotide polymorphisms (SNPs) reflecting haplotype phylogeny for efficient selection of tag SNPs.}, journal = {Genetics}, volume = {170}, number = {1}, pages = {291-304}, pmid = {15716494}, issn = {0016-6731}, mesh = {Black or African American ; Chromosome Mapping ; Genetic Markers ; *Haplotypes ; Humans ; Japan ; *Linkage Disequilibrium ; *Polymorphism, Single Nucleotide ; White People ; }, abstract = {Single nucleotide polymorphisms (SNPs) have been proposed to be grouped into haplotype blocks harboring a limited number of haplotypes. Within each block, the portion of haplotypes is expected to be tagged by a selected subset of SNPs; however, none of the proposed selection algorithms have been definitive. To address this issue, we developed a tag SNP selection algorithm based on grouping of SNPs by the linkage disequilibrium (LD) coefficient r(2) and examined five genes in three ethnic populations--the Japanese, African Americans, and Caucasians. Additionally, we investigated ethnic diversity by characterizing 979 SNPs distributed throughout the genome. Our algorithm could spare 60% of SNPs required for genotyping and limit the imprecision in allele-frequency estimation of nontag SNPs to 2% on average. We discovered the presence of a mosaic pattern of LD plots within a conventionally inferred haplotype block. This emerged because multiple groups of SNPs with strong intragroup LD were mingled in their physical positions. The pattern of LD plots showed some similarity, but the details of tag SNPs were not entirely concordant among three populations. Consequently, our algorithm utilizing LD grouping allows selection of a more faithful set of tag SNPs than do previous algorithms utilizing haplotype blocks.}, } @article {pmid15716310, year = {2005}, author = {Tsirigos, A and Rigoutsos, I}, title = {A new computational method for the detection of horizontal gene transfer events.}, journal = {Nucleic acids research}, volume = {33}, number = {3}, pages = {922-933}, pmid = {15716310}, issn = {1362-4962}, mesh = {Algorithms ; Bacteriophages/genetics ; Computational Biology/*methods ; *Gene Transfer, Horizontal ; Genes, Archaeal ; Genes, Bacterial ; Genes, Viral ; Genomics/methods ; Sequence Analysis, DNA/*methods ; }, abstract = {In recent years, the increase in the amounts of available genomic data has made it easier to appreciate the extent by which organisms increase their genetic diversity through horizontally transferred genetic material. Such transfers have the potential to give rise to extremely dynamic genomes where a significant proportion of their coding DNA has been contributed by external sources. Because of the impact of these horizontal transfers on the ecological and pathogenic character of the recipient organisms, methods are continuously sought that are able to computationally determine which of the genes of a given genome are products of transfer events. In this paper, we introduce and discuss a novel computational method for identifying horizontal transfers that relies on a gene's nucleotide composition and obviates the need for knowledge of codon boundaries. In addition to being applicable to individual genes, the method can be easily extended to the case of clusters of horizontally transferred genes. With the help of an extensive and carefully designed set of experiments on 123 archaeal and bacterial genomes, we demonstrate that the new method exhibits significant improvement in sensitivity when compared to previously published approaches. In fact, it achieves an average relative improvement across genomes of between 11 and 41% compared to the Codon Adaptation Index method in distinguishing native from foreign genes. Our method's horizontal gene transfer predictions for 123 microbial genomes are available online at http://cbcsrv.watson.ibm.com/HGT/.}, } @article {pmid15682767, year = {2004}, author = {Tanjasiri, SP and Tran, JH and Kagawa-Singer, M and Foo, MA and Foong, HL and Lee, SW and Nguyen, TU and Rickles, J and Wang, JS}, title = {Exploring access to cancer control services for Asian-American and Pacific Islander communities in Southern California.}, journal = {Ethnicity & disease}, volume = {14}, number = {3 Suppl 1}, pages = {S14-9}, pmid = {15682767}, issn = {1049-510X}, mesh = {Adult ; *Asian ; Breast Neoplasms/*ethnology/*prevention & control ; California ; Cancer Care Facilities/*supply & distribution ; Catchment Area, Health ; Communication Barriers ; Community Health Planning/*organization & administration ; Female ; Geographic Information Systems ; *Health Services Accessibility ; *Healthy People Programs ; Humans ; Los Angeles ; Mass Screening/statistics & numerical data ; Multilingualism ; *Native Hawaiian or Other Pacific Islander ; Social Work/statistics & numerical data ; Uterine Cervical Neoplasms/*ethnology/*prevention & control ; }, abstract = {During the last 25 years, numerous studies have been conducted to promote breast cancer and cervical cancer screening. Most of these studies focused on individual-level factors predicting screening, but we are unaware of any that directly examined community and ecological influences. The goal of this project, Promoting Access to Health for Pacific Islander and Southeast Asian Women (PATH for Women), was to increase community capacity for breast and cervical cancer screening and follow up in Los Angeles and Orange counties. We focused on Southeast Asian and Pacific Islander women because, although they have the lowest rates for cancer, compared to all other ethnic groups, relatively few programs have specifically targeted Asian-American and Pacific Islander (AAPI) women to promote and sustain screening practices. The PATH for Women project involved a partnership between 5 community-based organizations and 2 universities, and included 7 Asian-American and Pacific Islander communities: Cambodians, Chamorros, Laotians, Thais, Tongans, Samoans, and Vietnamese. In this paper, we share our experiences in developing a Geographic Information System (GIS)-mapping evaluation component that was used to explore availability and accessibility to culturally responsive breast and cervical cancer screening services for Southeast Asian and Pacific Islander women in all 7 communities. We describe the methods used to develop the maps, and present the preliminary findings that demonstrate significant geographic and language barriers to accessing healthcare providers, services for breast and cervical cancer screening, and follow up, in each of the communities. Finally, we discuss implications for programs designed to promote breast and cervical screening and policy education.}, } @article {pmid15682640, year = {2004}, author = {Simões, LB and Marques, SA and Bagagli, E}, title = {Distribution of paracoccidioidomycosis: determination of ecologic correlates through spatial analyses.}, journal = {Medical mycology}, volume = {42}, number = {6}, pages = {517-523}, doi = {10.1080/13693780310001656795}, pmid = {15682640}, issn = {1369-3786}, mesh = {Brazil/epidemiology ; Ecology ; Endemic Diseases ; Geographic Information Systems ; Humans ; Paracoccidioidomycosis/*epidemiology/transmission ; Population Density ; Prevalence ; Rain ; Risk Factors ; Seasons ; Soil ; }, abstract = {Paracoccidioidomycosis (PCM) is endemic in Latin America and in countries like Brazil it carries a high mortality rate. The fungus' habitat has not been precisely determined. The present study aims to identify ecologic correlates based on PCM distribution in a hyper-endemic area in southeastern Brazil. The Geographic Information System (GIS) and spatial statistics were used to associate environmental attributes, human population density and, PCM distribution. By means of the Pearson r correlation coefficient, the highest statistically significant associations with prevalence density were the percent area (by county) of: basaltic rocks (r=0.63; P <0.0001), Podzolic soils (r= -0.48; P <0.001), Latosol soils (r=0.40; P <0.01), mean annual precipitation between 1500 and 1600 mm (r = 0.46; P < 0.001) and, mean precipitation during the wet season between 940 and 1040 mm (r= -0.44; P <0.01). Soil texture and precipitation analyzed together reached r=0.61 (P <0.000002) for fine-textured soils with annual precipitation above 1400 mm. Environmental correlates indicate that moisture availability plays an important role in PCM distribution.}, } @article {pmid15674290, year = {2005}, author = {Kiessling, W}, title = {Long-term relationships between ecological stability and biodiversity in Phanerozoic reefs.}, journal = {Nature}, volume = {433}, number = {7024}, pages = {410-413}, doi = {10.1038/nature03152}, pmid = {15674290}, issn = {1476-4687}, mesh = {Animals ; Anthozoa/metabolism/*physiology ; *Biodiversity ; *Biological Evolution ; Carbonates/metabolism ; Conservation of Natural Resources ; Databases, Factual ; Ecology ; *Fossils ; History, Ancient ; Population Dynamics ; Time Factors ; }, abstract = {High biodiversity has been shown to enhance ecological stability on small spatial scales and over intervals of weeks to decades. It remains unclear, however, whether this diversity-stability relationship can be scaled up to regional scales, or to longer timescales. Without empirical validation at larger scales, the implications of the diversity-stability relationship for both ecology and long-term conservation strategies cannot readily be resolved. Here I show that in biogenic reefs, ecological stability is related to taxonomic diversity on million-year timescales. The higher the mean reef diversity in a particular time interval, the smaller the change in skeletal density, style of reef building and biotic reef types in the subsequent time interval. Because the relationships apply to a wide spectrum of disturbance regimes and reef types, these results support the hypothesis that species richness itself promotes ecological stability. Carbonate production by reefs, while closely correlated with reef diversity without temporal lag, is not stabilized by reef diversity over these long timescales. This suggests that ecological stability and productivity may be decoupled in natural ecosystems.}, } @article {pmid15674276, year = {2005}, author = {Naeem, S and Baker, AC}, title = {Ecology: paradise sustained.}, journal = {Nature}, volume = {433}, number = {7024}, pages = {370-371}, doi = {10.1038/433370a}, pmid = {15674276}, issn = {1476-4687}, mesh = {Animals ; Anthozoa/*physiology ; *Biodiversity ; Biological Evolution ; Databases, Factual ; *Ecology ; *Fossils ; History, Ancient ; Population Dynamics ; Time Factors ; }, } @article {pmid15669476, year = {2004}, author = {Zhang, Z and Ou, X and Wang, C and Wu, Y}, title = {[Accuracy analysis of vegetation mapping for Meili Snow Mountain area, northwest Yunnan, China].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {15}, number = {9}, pages = {1517-1522}, pmid = {15669476}, issn = {1001-9332}, mesh = {Abies/*growth & development ; China ; *Geographic Information Systems ; Hippophae/*growth & development ; Pinus/growth & development ; *Plant Development ; *Satellite Communications/instrumentation ; }, abstract = {The Meili Snow Mountain (28 degrees 20'-28 degrees 33'N, 98 degrees 30'-8 degrees 52'E) is a very famous mountain in Northwest Yunnan of China by its rich and well protected biodiversity and Tibetan cultural diversity. By applying 3S (RS-Remote Sensing, GIS-Geography Information System, GPS-Global Position System) technology, the 1:50000 vegetation map of Meili Snow Mountain area (total about 332 km2) was drawn out. The vegetation in this area was classified into 18 vegetation types except for stone, glacier and river system. The vegetation map was rectified by applying the GPS points got from the fields. The numbers of GPS points were calculated by the formula of numbers of samples in statistics. 313 GPS points were used to rectify the vegetation map. The numbers were fit for the formula of numbers of samples in Statistics. The accuracy and verify of vegetation types distribution in the map was analyzed by building a Probability Error Matrix (PEM) and through the variance analysis. The results indicated that the overall accuracy (OA) of the vegetation map was 84.7%. The accuracy of vegetation map finished by 3S technology was lied on the area of the region and the grade of vegetation class first, but the grade of vegetation class classified by remote sensing technology disaccord with the traditional vegetation class system. The other factos deciding the accuracy of vegetation were the distinguish ability of Remote Sensing image, the accuracy of distinguish, and the numbers of the samples, including vegetation class experts knowledge.}, } @article {pmid15668157, year = {2005}, author = {Birky, CW}, title = {Sex: is giardia doing it in the dark?.}, journal = {Current biology : CB}, volume = {15}, number = {2}, pages = {R56-8}, doi = {10.1016/j.cub.2004.12.055}, pmid = {15668157}, issn = {0960-9822}, mesh = {Animals ; Computational Biology ; *Genome, Protozoan ; Genomics ; Giardia lamblia/*physiology ; Meiosis/*genetics ; *Phylogeny ; *Recombination, Genetic ; *Sex ; }, abstract = {The protist Giardia has long been considered strictly asexual. Now genes specific for meiotic recombination have been found in the Giardia genome, but their consequences for genetics, epidemiology and evolution remain unknown.}, } @article {pmid15666449, year = {2004}, author = {Tietze-Stöckinger, I and Fichtner, W and Rentz, O}, title = {A model to minimize joint total costs for industrial waste producers and waste management companies.}, journal = {Waste management & research : the journal of the International Solid Wastes and Public Cleansing Association, ISWA}, volume = {22}, number = {6}, pages = {466-476}, doi = {10.1177/0734242X04048522}, pmid = {15666449}, issn = {0734-242X}, mesh = {Decision Making, Organizational ; *Decision Support Techniques ; Germany ; *Industrial Waste ; *Models, Economic ; Refuse Disposal/*economics/methods ; *Software ; Transportation ; }, abstract = {The model LINKopt is a mixed-integer, linear programming model for mid- and long-term planning of waste management options on an inter-company level. There has been a large increase in the transportation of waste material in Germany, which has been attributed to the implementation of the European Directive 75/442/EEC on waste. Similar situations are expected to emerge in other European countries. The model LINKopt has been developed to determine a waste management system with minimal decision-relevant costs considering transportation, handling, storage and treatment of waste materials. The model can serve as a tool to evaluate various waste management strategies and to obtain the optimal combination of investment options. In addition to costs, ecological aspects are considered by determining the total mileage associated with the waste management system. The model has been applied to a German case study evaluating different investment options for a co-operation between Daimler-Chrysler AG at Rastatt, its suppliers, and the waste management company SITA P+R GmbH. The results show that the installation of waste management facilities at the premises of the waste producer would lead to significant reductions in costs and transportation.}, } @article {pmid15666346, year = {2005}, author = {Darling, JA and Reitzel, AR and Burton, PM and Mazza, ME and Ryan, JF and Sullivan, JC and Finnerty, JR}, title = {Rising starlet: the starlet sea anemone, Nematostella vectensis.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {27}, number = {2}, pages = {211-221}, doi = {10.1002/bies.20181}, pmid = {15666346}, issn = {0265-9247}, mesh = {Animals ; Biological Evolution ; Databases as Topic ; Ecology ; Gene Expression Regulation ; Genomics/methods ; Geography ; Models, Biological ; Sea Anemones/*genetics/*physiology ; }, abstract = {In recent years, a handful of model systems from the basal metazoan phylum Cnidaria have emerged to challenge long-held views on the evolution of animal complexity. The most-recent, and in many ways most-promising addition to this group is the starlet sea anemone, Nematostella vectensis. The remarkable amenability of this species to laboratory manipulation has already made it a productive system for exploring cnidarian development, and a proliferation of molecular and genomic tools, including the currently ongoing Nematostella genome project, further enhances the promise of this species. In addition, the facility with which Nematostella populations can be investigated within their natural ecological context suggests that this model may be profitably expanded to address important questions in molecular and evolutionary ecology. In this review, we explore the traits that make Nematostella exceptionally attractive as a model organism, summarize recent research demonstrating the utility of Nematostella in several different contexts, and highlight a number of developments likely to further increase that utility in the near future.}, } @article {pmid15662205, year = {2004}, author = {Ge, N and Epstein, CB}, title = {An empirical Bayesian significance test of cDNA library data.}, journal = {Journal of computational biology : a journal of computational molecular cell biology}, volume = {11}, number = {6}, pages = {1175-1188}, doi = {10.1089/cmb.2004.11.1175}, pmid = {15662205}, issn = {1066-5277}, mesh = {*Bayes Theorem ; *Computational Biology ; *DNA, Complementary ; Data Interpretation, Statistical ; *Gene Library ; }, abstract = {Automated high-throughput sequencing of cDNA clones from numerous libraries has generated a wealth of information about both genome sequence and relative transcript abundances. A common statistical challenge in the analysis of library sequences is to infer whether there is differential expression for the same transcript under two different conditions, such as normal and diseased tissue. In contrast to the continuously variable intensity measurements from microarray experiments, data from cDNA library sequencing presents itself as a discrete count of the incidence of some clone or transcript in a finite sample. In this paper, we first propose a statistical model for data generated from cDNA library sequencing efforts. The model is based on the Poisson mixed with generalized inverse Gaussian (PGIG), introduced by Sichel (1971, 1975). PGIG has been used in modeling population abundance, ecological studies, word frequencies in publications, etc. Using data from the literature, we show that the proposed model provides a good fit to the observed data. Using this new model for cDNA library data, we developed an empirical Bayesian significance test (EBST) for inferring the statistical significance of differential gene expression from discrete data.}, } @article {pmid15627228, year = {2005}, author = {Diez Roux, AV and Aiello, AE}, title = {Multilevel analysis of infectious diseases.}, journal = {The Journal of infectious diseases}, volume = {191 Suppl 1}, number = {}, pages = {S25-33}, doi = {10.1086/425288}, pmid = {15627228}, issn = {0022-1899}, mesh = {*Data Interpretation, Statistical ; Effect Modifier, Epidemiologic ; Humans ; Linear Models ; Risk Factors ; Sexually Transmitted Diseases/*epidemiology/*prevention & control ; }, abstract = {Traditional study designs, such as individual-level studies and ecological studies, are unable to simultaneously examine the effects of individual-level and group-level factors on risk of disease. Multilevel analysis overcomes this limitation by allowing the simultaneous investigation of factors defined at multiple levels. Areas in which multilevel modeling can be applied to sexually transmitted infection (STI) research include examining how both group-level and individual-level factors are related to individual-level STI outcomes, assessing interactions between individual-level and group-level constructs, and exploring how factors at multiple levels contribute to group-to-group differences in rates of disease. In this article, we review the fundamentals of multilevel modeling, the applications of multilevel models for the examination of STIs, and the key challenges associated with using multilevel modeling for infectious-disease research.}, } @article {pmid15624835, year = {2004}, author = {Ma, Q and Yu, W and Zhao, S and Zhang, L and Shen, S and Wang, Y}, title = {[Comprehensive evaluation of cultivated black soil fertility].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {15}, number = {10}, pages = {1916-1920}, pmid = {15624835}, issn = {1001-9332}, mesh = {China ; *Conservation of Natural Resources ; Crops, Agricultural/growth & development ; Ecosystem ; *Fertilizers ; Geographic Information Systems ; Soil/*analysis ; }, abstract = {Black soil is one of the main soil types in northeastern China, and is a valuable soil resource of this country. Based on the analysis of the physical and chemical properties of soil samples collected from the north-south transaction of black soil, the index system of black soil fertility was established, the fertility level was evaluated and classified by Fuzzy and Factor Analysis, and the fertility map of black soil zone was drawn with GIS software ArcInfo. It was found that the humus layer in black soil region was thick in north and thin in south, which was due to the climatic condition and soil-forming process. The soil fertility level was high in east and low in west. From north to south, it was decreased in the order of central part > northern part > south part. In most part of this region, soil fertility level was medium, and the area accounted for 73.6% of the black soil area.}, } @article {pmid15624814, year = {2004}, author = {Song, D and Xiao, D and Ma, M and Wang, J}, title = {[Impact of groundwater resource temporal-spatial change in Minqin oasis on ecological security of irrigation region landscape].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {15}, number = {10}, pages = {1815-1820}, pmid = {15624814}, issn = {1001-9332}, mesh = {China ; Conservation of Natural Resources ; Crops, Agricultural/*growth & development ; Desert Climate ; *Ecosystem ; Geographic Information Systems ; Risk Assessment ; Rivers ; Safety Management/trends ; Soil/*analysis ; Water/*analysis ; Water Pollution/prevention & control ; Water Supply ; }, abstract = {By the GIS technology, this paper studied the impact of groundwater resource temporal-spatial change in the lake area of Minqin Oasis on the ecological security of irrigation region landscape. The results showed that the depth of groundwater was descending continuously, the velocity of groundwater line change in the center of irrigation region was faster than that in the edge region, and consequently, the area of the descending funnel of groundwater line was enlarged. From 1987 to 2001, the area with a groundwater depth deeper than 3 m was increased from 81.2% to 97.4%. The descending of groundwater line due to soil water reducing was the main reason that resulted in the destruction and deadness of forests. When the depth of groundwater was deeper than 8 m and soil water content was less than 12%, the die-back rate of tree was morn than 90%, and that of shrub was more than 50%. Impacted by the descend of groundwater depth, the area of forest land, shrub land and open-canopy land was decreased by 67%, 54% and 31%, and the number of their patches was decreased by 35, 42 and 50, respectively. The mineralization degree of groundwater in northern irrigation region increased obviously, and changed the safe pattern of crop growth. The benefit of agriculture decreased, and the adjustment of planting construction was restricted seriously, which became the main impact factor on the ecological security of irrigation region. Reasonably distributing water resource between upper and lower river basin, reducing unreasonable land use, decreasing farmland area, and constructing safety landscape pattern could lead to the balance between the exploitation and replenishment of groundwater resource, prevent the descend of groundwater depth and the increase of groundwater mineralization, and improve the ecological security of the irrigation region.}, } @article {pmid15624813, year = {2004}, author = {Yu, D and Hao, Z and Jiang, P and Xiong, Z and Yang, H}, title = {[Landscape pattern variation of forest resources in typical forest zone of Changbai Mountains].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {15}, number = {10}, pages = {1809-1814}, pmid = {15624813}, issn = {1001-9332}, mesh = {Biodiversity ; China ; Climate ; *Conservation of Natural Resources ; Environment ; *Geographic Information Systems ; Satellite Communications/instrumentation ; Trees/*growth & development ; }, abstract = {Based on GIS and RS data of 1985 and 1999 and the ground information from Lushuihe Forest Bureau, this paper studied the forest landscape pattern and its changes in typical forest zone of Changbai Mountains. According to the standard variance of patch areas in 1985 and 1999, the patch area distribution of mature conifer forest, mature broad-leaved forest, middle-aged conifer forest, and middle-aged broad-leaved forest was less symmetrical, showing that these land covers had landscape diversity and species diversity. According to landscape similarity index, the mature conifer forest, mature broad-leaved forest, middle-aged conifer forest and middle-aged broad-leaved forest, which were relatively stable than other land covers, made the majority of the landscape in the study area. According to patch density, the porosity of wetland was high in 1985 and 1999, indicating that wetland had little homogenization and formed more mosaics. The fragmentation extent of farming land, due to multiple cultivating types, azimuths and shapes, was high in both phases. Attributing greatly to anthropogenic factors, the fragmentation extent of wetland was high all along. In brief, the forest landscape pattern was changed greatly in the studied phases, and human activities affected heavily on it.}, } @article {pmid15624803, year = {2004}, author = {Hao, Z and Yu, D and Xiong, Z and Ye, J}, title = {[Utilization suitability of forest resources in typical forest zone of Changbai Mountains].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {15}, number = {10}, pages = {1755-1759}, pmid = {15624803}, issn = {1001-9332}, mesh = {China ; *Conservation of Natural Resources ; *Ecosystem ; Geographic Information Systems ; Satellite Communications/instrumentation ; Trees/*growth & development ; }, abstract = {Conservation of natural forest does not simply equal to no logging. The Northeast China Forest Region has a logging quota of mature forest as part of natural forest conservation project. How to determine the logging spots rationally and scientifically is very important. Recent scientific theories of forest resources management advocate that the utilization of forest resources should stick to the principle of sustaining use, and pay attention to the ecological function of forest resources. According to the logging standards, RS and GIS techniques can be used to detect the precise location of forest resources and obtain information of forest areas and types, and thus, provide more rational and scientific support for space choice about future utilization of forest resources. In this paper, the Lushuihe Forest Bureau was selected as a typical case in Changbai Mountains Forest Region to assess the utilization conditions of forest resources, and some advices on spatial choice for future management of forest resources in the study area were offered.}, } @article {pmid15612996, year = {2005}, author = {Fadiel, A and Lithwick, S and Naftolin, F}, title = {The influence of environmental adaptation on bacterial genome structure.}, journal = {Letters in applied microbiology}, volume = {40}, number = {1}, pages = {12-18}, doi = {10.1111/j.1472-765X.2004.01619.x}, pmid = {15612996}, issn = {0266-8254}, mesh = {*Adaptation, Biological ; Amino Acid Sequence ; Base Composition ; Codon/*genetics ; Databases as Topic ; Evolution, Molecular ; *Genome, Bacterial ; Genomics ; Mycoplasma/*genetics ; Open Reading Frames/physiology ; Phylogeny ; Sequence Homology, Amino Acid ; }, abstract = {AIMS: Researchers have long been puzzled by the diversity of life. Now that the complete genomic sequence of many organisms has been determined, it is possible to evaluate the impact of organismal variation on sequence structure or vice versa. The aim of this investigation was to explore genomic changes mandated by organismal adaptation to its ecological niches.

METHODS AND RESULTS: Coding sequences from three phylogenetically related bacterial species namely Mycoplasma genitalium, M. pneumoniae and Ureaplasma urealyticum were subject to in depth sequence analyses. M. genitalium and M. pneumoniae both belong to the genus Mycoplasma while U. urealyticum is a member of the genus Ureaplasma. However, M. genitalium and U. urealyticum are urogenital pathogens while M. pneumoniae is a respiratory pathogen. Complete transcriptomes were downloaded from NCBI for each species, and were subject to in silico investigation using in-house software, and public sequence analysis tools. Clear similarities in transcriptome structure were identified among the functionally similar species M. genitalium and U. urealyticum while no such relationship was identified among the phylogenetically related species M. genitalium and M. pneumoniae.

CONCLUSIONS: It is plausible to conclude that, in these bacterial species, environmental stimuli might be more influential in shaping sequence signatures than phylogenetic relationships.

This study suggests that molecular signatures within the transcriptomes of the species examined are likely to be a product of evolutionary adaptation to diverse environmental ecological stimuli, and not a result of common phylogeny.}, } @article {pmid15612281, year = {2003}, author = {Losey, JE and Hufbauer, RA and Hartzler, RG}, title = {Enumerating lepidopteran species associated with maize as a first step in risk assessment in the USA.}, journal = {Environmental biosafety research}, volume = {2}, number = {4}, pages = {247-261}, doi = {10.1051/ebr:2003015}, pmid = {15612281}, issn = {1635-7922}, mesh = {Agriculture ; Animals ; Bacillus thuringiensis/genetics/*pathogenicity ; Databases, Factual/*statistics & numerical data ; Ecosystem ; *Insect Control ; *Lepidoptera ; *Plants, Genetically Modified ; Population Dynamics ; Risk Assessment ; Safety ; United States ; Zea mays/*genetics ; }, abstract = {Pest management can have substantial impacts on non-target species both within and outside the units being managed. Assessment of these impacts is hampered by the lack of even the most basic checklist of the species present in most systems. The maize agroecosytem is of particular interest because of the large area covered and the intensity of widely varying forms of pest management. In this study a database of lepidopteran species that occur within the maize agroecosystem in the United States was compiled. The process was initiated by developing a list of plants present in maize using published sources and the first-hand knowledge of "weed" experts. This list of plant species associated with maize was then cross-listed with lepidopteran host feeding records using published sources. Finally, phenological profiles and conservation rankings were added. Although our list is not exhaustive, we found 132 plant species in 33 families associated with maize, and 229 lepidopteran species in 21 families that feed on these plants. The database of plants and lepidopteran species can be a starting point for assessment of risk to non-target Lepidoptera in maize from chemical control, biological control, and the use of transgenic Bt maize. The lepidopteran species associated with maize were found to be significantly less imperiled, as measured by their conservation rankings, than lepidopteran species as a whole in all habitats. This finding suggests that rare or endangered lepidopteran species are unlikely to be impacted by pest management in maize. Based on the likely lack of impact of pest management in maize on individual species, future studies should focus on potential impacts on the ecological services that lepidopteran species provide.}, } @article {pmid15612280, year = {2003}, author = {Letourneau, DK and Robinson, GS and Hagen, JA}, title = {Bt crops: predicting effects of escaped transgenes on the fitness of wild plants and their herbivores.}, journal = {Environmental biosafety research}, volume = {2}, number = {4}, pages = {219-246}, doi = {10.1051/ebr:2003014}, pmid = {15612280}, issn = {1635-7922}, mesh = {Animals ; Bacillus thuringiensis/*genetics/*pathogenicity ; Bacterial Toxins/genetics ; Biological Evolution ; Databases, Factual/statistics & numerical data ; Ecology ; Forecasting ; Insect Control ; Lepidoptera/*genetics/growth & development ; *Models, Theoretical ; Plants, Edible/growth & development ; *Plants, Genetically Modified ; Risk Assessment ; *Safety ; }, abstract = {One prominent concern about genetically modified crops is the possibility of environmental impacts from the movement of fitness-enhancing traits to wild plant populations. Decisions to deregulate Bt crops in the USA have relied strongly on arguments that these crops will not interbreed with wild relatives in the permitted growing regions. Limited attention therefore has been directed to analyses of the consequences of gene flow. To provide a transparent evaluation process for risks associated with insecticidal transgene escape, we crafted a series of questions designed to guide this aspect of the risk assessment. We then explored the current knowledge base available for answering such risk-related questions for three Bt crops (cotton, rapeseed, and rice). First, we generated a list of wild relatives of these crops. A definitive list of potential transgene recipients is not yet possible for some crops. Sufficient data are not available for some crops to eliminate certain related plant species from consideration of fertile hybrid formation, thus making lists for these crops subject to speculation. Second, we queried the HOSTS database (UK) to obtain a worldwide listing of lepidopteran species that feed on these crops and their wild relatives, and to determine the host range of the larvae. To our knowledge, this list of 502 lepidopteran species is the first such list published for these crops and wild crop relatives. Third, we used a data set maintained by the Canadian Forest Service to assess Bt toxin susceptibility for these lepidopterans. Only 3% of those species have been tested for susceptibility; and the literature suggests that generalizations about susceptibility among taxa are difficult due to the variability within families. Fourth, we consulted the literature to interpret what is known about the ability of lepidopterans to regulate plant fitness or invasiveness. We could not eliminate the possibility of ecological release due to plant resistance against lepidopterans. In fact, there is strong experimental evidence that lepidopteran herbivores do limit the distribution and/or abundances of at least some wild plant species. Neither could we eliminate the possibility that non-target lepidopterans might have important functions in the ecosystem as pollinators or alternate hosts to natural enemies of pest species. This study suggests that crucial data are lacking for the development of a credible scientific basis to confirm or deny environmental risks associated with the escape of Bt transgene constructs to wild relatives. Given the absence of information on the identity, level of susceptibility, and ecological roles of lepidopterans exploiting specific wild relatives of Bt crops, we suggest that new efforts be directed to assessing possible consequences of lepidopteran mortality on resistant wild relatives.}, } @article {pmid15611617, year = {2004}, author = {Hoshino, A and Fujioka, K and Oku, T and Nakamura, S and Suga, M and Yamaguchi, Y and Suzuki, K and Yasuhara, M and Yamamoto, K}, title = {Quantum dots targeted to the assigned organelle in living cells.}, journal = {Microbiology and immunology}, volume = {48}, number = {12}, pages = {985-994}, doi = {10.1111/j.1348-0421.2004.tb03621.x}, pmid = {15611617}, issn = {0385-5600}, mesh = {Amino Acid Sequence ; Animals ; Chlorocebus aethiops ; Chromogenic Compounds/chemistry/*metabolism ; Electron Transport Complex IV/*metabolism ; Fluorescent Dyes/metabolism ; Microscopy, Confocal ; Microscopy, Fluorescence ; Mitochondria/metabolism ; Molecular Sequence Data ; Nuclear Localization Signals/*metabolism ; Organelles/*metabolism ; Protein Transport ; *Quantum Dots ; Vero Cells ; }, abstract = {Fluorescent nanocrystal quantum dots (QDs) have the potential to be applied to bioimaging since QDs emit higher and far longer fluorescence than conventional organic probes. Here we show that QDs conjugated with signal peptide obey the order to transport the assigned organelle in living cells. We designed the supermolecule of luminescent QDs conjugated with nuclear- and mitochondria-targeting ligands. When QDs with nuclear-localizing signal peptides were added to the culture media, we can visualize the movements of the QDs being delivered into the nuclear compartment of the cells with 15 min incubation. In addition, mitochondrial signal peptide can also transport QDs to the mitochondria in living cells. In conclusion, these techniques have the possibility that QDs can reveal the transduction of proteins and peptides into specific subcellular compartments as a powerful tool for studying intracellular analysis in vitro and even in vivo.}, } @article {pmid15608224, year = {2005}, author = {Cavalcanti, AR and Clarke, TH and Landweber, LF}, title = {MDS_IES_DB: a database of macronuclear and micronuclear genes in spirotrichous ciliates.}, journal = {Nucleic acids research}, volume = {33}, number = {Database issue}, pages = {D396-8}, pmid = {15608224}, issn = {1362-4962}, support = {R01 GM059708/GM/NIGMS NIH HHS/United States ; GM59708/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Ciliophora/*genetics ; *Databases, Nucleic Acid ; Genes, Protozoan ; Macronucleus/*genetics ; Micronucleus, Germline/*genetics ; *Sequence Analysis, DNA ; User-Computer Interface ; }, abstract = {Ciliated protozoa have two kinds of nuclei: Macronuclei (MAC) and Micronuclei (MIC). In some ciliate classes, such as spirotrichs, most genes undergo several layers of DNA rearrangement during macronuclear development. Because of such processes, these organisms provide ideal systems for studying mechanisms of recombination and gene rearrangement. Here, we describe a database that contains all spirotrich genes for which both MAC and MIC versions are sequenced, with consistent annotation and easy access to all the features. An interface to query the database is available at http://oxytricha.princeton.edu/dimorphism/database.htm.}, } @article {pmid15608200, year = {2005}, author = {Cole, JR and Chai, B and Farris, RJ and Wang, Q and Kulam, SA and McGarrell, DM and Garrity, GM and Tiedje, JM}, title = {The Ribosomal Database Project (RDP-II): sequences and tools for high-throughput rRNA analysis.}, journal = {Nucleic acids research}, volume = {33}, number = {Database issue}, pages = {D294-6}, pmid = {15608200}, issn = {1362-4962}, mesh = {DNA Probes ; DNA, Ribosomal/*chemistry/classification ; *Databases, Nucleic Acid ; *Genes, rRNA ; RNA, Bacterial/genetics ; RNA, Ribosomal/chemistry/classification ; Sequence Alignment ; *Sequence Analysis, DNA ; *Software ; }, abstract = {The Ribosomal Database Project (RDP-II) provides the research community with aligned and annotated rRNA gene sequences, along with analysis services and a phylogenetically consistent taxonomic framework for these data. Updated monthly, these services are made available through the RDP-II website (http://rdp.cme.msu.edu/). RDP-II release 9.21 (August 2004) contains 101,632 bacterial small subunit rRNA gene sequences in aligned and annotated format. High-throughput tools for initial taxonomic placement, identification of related sequences, probe and primer testing, data navigation and subalignment download are provided. The RDP-II email address for questions or comments is rdpstaff@msu.edu.}, } @article {pmid15604510, year = {2004}, author = {Pegram, R and Indar, L and Eddi, C and George, J}, title = {The Caribbean Amblyomma Program: some ecologic factors affecting its success.}, journal = {Annals of the New York Academy of Sciences}, volume = {1026}, number = {}, pages = {302-311}, doi = {10.1196/annals.1307.056}, pmid = {15604510}, issn = {0077-8923}, mesh = {Agriculture ; Animal Husbandry/*methods ; Animals ; *Animals, Domestic ; Caribbean Region ; *Ecology ; *Geographic Information Systems ; Humans ; Program Evaluation ; Public Health ; Tick-Borne Diseases/*prevention & control/*transmission ; }, abstract = {The Caribbean Amblyomma Program has been operational for 8 years. However, owing to funding availability, some islands did not commence eradication activities until late 1997. During the past 2 years, 6 of the 9 islands (St. Kitts, St. Lucia, Anguilla, Montserrat, Barbados, and Dominica) under the program have attained the status of provisional freedom from the tropical bont tick (TBT). There are several administrative and technical reasons why the attainment of the program goals took longer than originally anticipated. This paper examines some of the ecologic factors that necessitated the prolongation of the treatment period and the recrudescence of TBT infestation in some islands. The introduction and subsequent spread of the cattle egret, Bulbucus ibis, in the 1960s and 1970s was most likely closely associated with the dissemination of the TBT in the region. At the national or island level, variations in land use are believed to have had a major impact on the eradication efforts in the different islands. Two islands, Antigua and Nevis, both opted out of sugar production several decades ago for economic reasons. Unfortunately, however, land from former sugar estates was not developed for other agricultural purposes and it became "unimproved free-grazing" areas for livestock. Thus, in both Antigua and Nevis, large numbers of livestock tend to become feral or free-ranging, making compliance with the mandatory treatment schedules impossible. In contrast, St. Lucia has large tracts of land allocated to banana plantations and St. Kitts to sugar plantations. Thus, feral or free-ranging livestock were rarely a problem in these islands. These differences in land use management are compared and discussed in relation to their perceived profound impact on TBT eradication efforts in the region.}, } @article {pmid15604468, year = {2004}, author = {Dávila, AM and Steindel, M and Grisard, EC}, title = {Tropical diseases, pathogens, and vectors biodiversity in developing countries: need for development of genomics and bioinformatics approaches.}, journal = {Annals of the New York Academy of Sciences}, volume = {1026}, number = {}, pages = {41-46}, doi = {10.1196/annals.1307.005}, pmid = {15604468}, issn = {0077-8923}, mesh = {Animal Diseases ; Animals ; Brazil ; Computational Biology/*trends ; Conservation of Natural Resources ; *Developing Countries ; Ecology ; Genomics/*trends ; Humans ; Parasitic Diseases/epidemiology/*genetics/*transmission ; Program Development ; Public Health ; *Tropical Medicine/statistics & numerical data/trends ; *World Health Organization ; }, abstract = {The world's biodiversity, including many infectious, parasitic disease agents and their vectors whose impact on both human and animal health is significant, is largely retained in the developing countries of the tropics. Owing to the number of species involved and the relatively low-level exploration of pathogens and vectors biodiversity, several organisms are still waiting to be discovered and consequently explored in terms of genomics. Although some parasitic species of humans and animals have been studied through genomics and bioinformatics approaches, a significant number of relevant species are still to be addressed. Through the use of modern technologies, such as genomics and bioinformatics, for assessment of biodiversity and targeting tropical diseases, other relevant advantages of these initiatives for developing countries would be technology transfer and capacity building. Consequently, these initiatives could be critical to the development of the respective countries. Moreover, intra- and interhemispheric scientific collaboration should be encouraged and supported to increase the chances for success. In Brazil, the Ministry of Science and Technology has stepped forward to further such initiatives, co-supporting collaborative genomics and bioinformatics projects. The need for the establishment of working groups on genomics and bioinformatics in developing countries as well as the improvement and strengthening of collaborative research projects between developed and developing countries is discussed from our point of view. As these discussions remain open to debate, we encourage colleagues to promote further discussion on the subject.}, } @article {pmid15603165, year = {2004}, author = {Searby, A and Jouventin, P}, title = {How to measure information carried by a modulated vocal signature?.}, journal = {The Journal of the Acoustical Society of America}, volume = {116}, number = {5}, pages = {3192-3198}, doi = {10.1121/1.1775271}, pmid = {15603165}, issn = {0001-4966}, mesh = {Algorithms ; Computer Simulation ; Discriminant Analysis ; Humans ; Image Interpretation, Computer-Assisted ; Models, Theoretical ; *Recognition, Psychology ; Software ; *Voice ; }, abstract = {Acoustic signaling systems that permit individual recognition are described in an increasing number of species. Evolutionary logic predicts that the efficiency of these signatures is related to the possibilities for confusion. To test this "signature adaptation" hypothesis, one needs a standardized method to estimate and compare the efficiency of different signatures. Beecher [Am. Zool. 22, 477-490 (1989)] developed such a method by comparing scalar parameters extracted from the signals. However, vocal signatures frequently consist in the evolution of one parameter against one other, which are not comparable through Beecher's method. Here we present a method to estimate the efficiency of modulated signatures. A signature's efficiency is given by its information capacity (Hm), derived from Shannon's information theory. The measure of Hm is based on an analysis of variance and uses the Euclidian distances between the signature's contours in the population. To validate our method, simulated datasets of modulated contours were used. The predicted efficiency of those signatures, estimated from Hm, was strongly correlated to its actual efficiency given by two classification methods: a discriminant analysis and a classification by human observers. Being also untied to sample size, Hm therefore allows comparing objectively vocal, but also visual and olfactory signatures.}, } @article {pmid15601765, year = {2004}, author = {Sekercioğlu, CH and Daily, GC and Ehrlich, PR}, title = {Ecosystem consequences of bird declines.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {101}, number = {52}, pages = {18042-18047}, pmid = {15601765}, issn = {0027-8424}, mesh = {Animals ; Biodiversity ; Birds ; Conservation of Natural Resources ; Databases as Topic ; *Ecology ; Ecosystem ; Environment ; Extinction, Psychological ; Species Specificity ; Stochastic Processes ; }, abstract = {We present a general framework for characterizing the ecological and societal consequences of biodiversity loss and applying it to the global avifauna. To investigate the potential ecological consequences of avian declines, we developed comprehensive databases of the status and functional roles of birds and a stochastic model for forecasting change. Overall, 21% of bird species are currently extinction-prone and 6.5% are functionally extinct, contributing negligibly to ecosystem processes. We show that a quarter or more of frugivorous and omnivorous species and one-third or more of herbivorous, piscivorous, and scavenger species are extinction-prone. Furthermore, our projections indicate that by 2100, 6-14% of all bird species will be extinct, and 7-25% (28-56% on oceanic islands) will be functionally extinct. Important ecosystem processes, particularly decomposition, pollination, and seed dispersal, will likely decline as a result.}, } @article {pmid15599519, year = {2005}, author = {Gunasekera, AS and Sfanos, KS and Harmody, DK and Pomponi, SA and McCarthy, PJ and Lopez, JV}, title = {HBMMD: an enhanced database of the microorganisms associated with deeper water marine invertebrates.}, journal = {Applied microbiology and biotechnology}, volume = {66}, number = {4}, pages = {373-376}, doi = {10.1007/s00253-004-1763-7}, pmid = {15599519}, issn = {0175-7598}, mesh = {Animals ; *Databases, Factual ; Florida ; Internet ; Invertebrates/*microbiology ; *Marine Biology ; Seawater ; }, abstract = {The Harbor Branch Marine Microbial Database (HBMMD) provides preliminary taxonomic identifications and features of microorganisms maintained in the Harbor Branch Oceanographic Institution Marine Microbial Culture Collection. The microbes are primarily derived from marine invertebrates such as sponges (phylum Porifera) and soft corals (phylum Cnidaria) found in deep water environments [>120 feet (>35 m) seawater]. The microbes isolated from within marine invertebrates represent some unique taxa and phylogenetic signatures. The database provides a user-friendly method to systemically search or sort a desired input. The site allows a powerful search for multiple parameters of any entry. Images of the microbes are contained within the database and can be accessed from the website. The HBMMD homepage is located at http://www.hboi.edu/dbmr/dbmr_hbmmd.html.}, } @article {pmid15589984, year = {2005}, author = {Fraschetti, S and Terlizzi, A and Bussotti, S and Guarnieri, G and D'Ambrosio, P and Boero, F}, title = {Conservation of Mediterranean seascapes: analyses of existing protection schemes.}, journal = {Marine environmental research}, volume = {59}, number = {4}, pages = {309-332}, doi = {10.1016/j.marenvres.2004.05.007}, pmid = {15589984}, issn = {0141-1136}, mesh = {Animals ; *Conservation of Natural Resources ; Ecosystem ; *Environment Design ; Environmental Monitoring ; *Geographic Information Systems ; Geological Phenomena ; Geology ; Invertebrates ; Mediterranean Region ; }, abstract = {Marine protected areas (MPAs) are aimed at managing and protecting marine environments. Their design, however, often disregards both a thorough knowledge of the distribution of habitats and assemblages and the use of proper experimental evaluations of the efficacy of MPAs by comparing protected vs. unprotected zones. About 200 MPAs have been recently instituted in the Mediterranean area, but the evidence of their efficacy is scant. The MPA of Torre Guaceto (Southern Adriatic Sea, Italy) is one of the rare cases of effective protection enforcement. The reserve was instituted more than 10 years ago, a period currently considered as sufficient to show responses by organisms to protection. The MPA is divided into a C zone, the general reserve, where many activities are permitted, a B zone, the partial reserve where restrictions increase and two A zones, the integral reserve where access is prohibited. The goals of the paper were to map the distribution of benthic assemblages to assess if they were properly represented in the differently protected zones, and to test the efficacy of protection by quantifying possible differences between the assemblages in two control areas and in the two A zones, where human impact is completely excluded. The analysis of habitat and assemblage distribution within the MPA showed that the zones with total protection do not include most valuable environmental types. Most of the considered variables (i.e. cover of substratum, number of taxa, and average abundance of the most common taxa) were not significantly different in and out of the A zones, at each time of sampling. Results, however, suggested a possible effect of protection in modifying patterns of abundance of sponges under Cystoseira canopy (more abundant in the fully protected zone). In the subtidal habitat, differences were found in the structure of the whole assemblage and in the abundance of encrusting coralline red algae (more abundant outside the fully protected area). Notwithstanding the correct general methodology employed in the study, a lack of statistical power could have a role in preventing the detection of ecologically relevant effects of protection. In some instances, data pooling allowed a discrimination between cases where there was clearly no effect of protection and cases where there might be. On this basis, the optimization of this experimental design should be considered in further studies. In any case, if the goals of MPAs have not been clearly stated, efficacy of protection might prove very difficult to test even with the use of sound experimental designs.}, } @article {pmid15587950, year = {2004}, author = {Mason, M and Cheung, I and Walker, L}, title = {Substance use, social networks, and the geography of urban adolescents.}, journal = {Substance use & misuse}, volume = {39}, number = {10-12}, pages = {1751-1777}, pmid = {15587950}, issn = {1082-6084}, support = {R24 MH57909-05/MH/NIMH NIH HHS/United States ; }, mesh = {Adolescent ; *Adolescent Behavior ; Depression ; Female ; *Geographic Information Systems ; Humans ; *Interpersonal Relations ; Male ; Risk Assessment ; Stress, Psychological ; Substance-Related Disorders/*psychology ; Urban Population ; }, abstract = {This article demonstrates a research strategy and prevention methodology for substance using urban youth that incorporates individual, social, and geographical parameters to systematically understand the ecology of risk and protection for urban youth. The primary goal of this study was to describe and analyze substance using and nonusing urban adolescents' social networks; risky and protective settings where they socialize; and the relationship to health outcomes such as substance use, depression, and stress. Geographic Information Systems (GIS) derived spatial relationships and analyses between the specific locations where the teens are active, their subjective ratings of these locations, and objective environmental risk data. These social network and GIS data were merged to form a detailed description and analysis of the social ecology of urban adolescent substance use. A case study was constructed to illustrate the methodology of creating a three-dimentional ecological profile that helps explain these relationships and provides preventive applications. Linear distances were computed between the homes of the users and the risky and safe places that they identified. On average, the distance between users' homes and their identified safe places was three times the distance between their homes and their identified risky places. This study provides support for understanding urban adolescent substance use through the detailed and multiple dimensional analysis of teens' social ecologies.}, } @article {pmid15574532, year = {2005}, author = {Williams, JE and Evans, M and Kirtland, KA and Cavnar, MM and Sharpe, PA and Neet, MJ and Cook, A}, title = {Development and use of a tool for assessing sidewalk maintenance as an environmental support of physical activity.}, journal = {Health promotion practice}, volume = {6}, number = {1}, pages = {81-88}, doi = {10.1177/1524839903260595}, pmid = {15574532}, issn = {1524-8399}, support = {02T030504//PHS HHS/United States ; U48/CCU409664-06/CC/ODCDC CDC HHS/United States ; }, mesh = {Community-Institutional Relations ; Environment Design/*standards ; *Exercise ; Geographic Information Systems ; Health Promotion/*organization & administration ; Humans ; *Leisure Activities ; South Carolina ; }, abstract = {The importance of regular physical activity is well documented, yet according to epidemiological surveillance data, physical inactivity among all age groups persists. Past attempts to promote physical activity focused on individual-level changes; current approaches focus on environmental changes that will provide opportunities for whole communities to be active. The current ecological focus has led to an increase in funding and research regarding environmental supports of physical activity. As this is a new area of research, much work needs to be done to improve the ability to assess environmental features that support physical activity. This article describes a partnership between researchers and community members to develop and test an objective tool to measure sidewalk maintenance. Community members used data collected with the tool to increase awareness about sidewalk maintenance issues among local policy makers. Collaboration between researchers and community partners was critical for the success of this study.}, } @article {pmid15573996, year = {2004}, author = {Li, W and Wang, Y and Peng, J and Li, G}, title = {[Landscape spatial changes in Shenzhen and their driving factors].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {15}, number = {8}, pages = {1403-1410}, pmid = {15573996}, issn = {1001-9332}, mesh = {China ; *City Planning ; Environment Design ; *Geographic Information Systems ; Satellite Communications ; Socioeconomic Factors ; }, abstract = {Based on GIS technology, the MSS image in 1978 and the TM images in 1986, 1990, 1995 and 1999 were used to study the landscape spatial changes in Shenzhen during the past two decades. The results showed that the regional landscape in Shenzhen changed dramatically, from a typical agricultural landscape to a rapidly urbanizing landscape. The percentage of cultivated land decreased from 31.06% to 2.67%, while that of built-up area increased from 0.33% to 22.52%. The landscape diversity index showed a tendency of increase in 1978-1995, followed by a decrease in 1999. The index of landscape contagion decreased firstly and then increased, and the landscape fragmentation index increased from 0.0042 to 0.0073. Modified fractal dimension index showed the same tendency as landscape contagion index. Human activity was the main driving factor for landscape change. The change of geometry shape of landscape patches was driven by the economic interests of individual economic cells, and that of spatial configuration of landscape components was associated with the allocation of industries. The diversity of the whole landscape was mainly associated with the natural and ecological conditions such as topography and landform, while its change was strongly affected by the whole level of social and economic development.}, } @article {pmid15573990, year = {2004}, author = {Zhang, X and Chen, J and Zhang, G}, title = {[Landform-based pedodiversity of some soil chemical properties in Hainan Island, China].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {15}, number = {8}, pages = {1368-1372}, pmid = {15573990}, issn = {1001-9332}, mesh = {China ; Geographic Information Systems ; Hydrogen-Ion Concentration ; Organic Chemicals/*analysis ; Soil/*analysis ; }, abstract = {Diversity indices and abundance distribution models are the statistical tools having been applied by ecologists for decades to analyze the intrinsic regularities of various ecological entities. In this work, similar techniques were used to analyze the pedodiversity of some soil chemical properties in Hainan Island, China, and discussions were conducted on the basis of related SOTER digital databases. Through the calculation of the richness (S), diversity (H') and evenness (E) of pH value, CEC and organic matter content in surface soil of different landforms and the establishment and application of the multi-distribution models of these soil chemical properties, the pedodiversity of some soil chemical properties of different landforms in Hainan Island in the GIS environment could be expressed digitally.}, } @article {pmid15573125, year = {2004}, author = {Waters, MD and Fostel, JM}, title = {Toxicogenomics and systems toxicology: aims and prospects.}, journal = {Nature reviews. Genetics}, volume = {5}, number = {12}, pages = {936-948}, doi = {10.1038/nrg1493}, pmid = {15573125}, issn = {1471-0056}, mesh = {Animals ; Computational Biology ; Databases, Factual ; Ecology ; Forecasting ; Gene Expression Profiling ; Genetic Predisposition to Disease ; Humans ; Proteomics ; Systems Theory ; *Toxicogenetics ; *Toxicology ; }, abstract = {Toxicogenomics combines transcript, protein and metabolite profiling with conventional toxicology to investigate the interaction between genes and environmental stress in disease causation. The patterns of altered molecular expression that are caused by specific exposures or disease outcomes have revealed how several toxicants act and cause disease. Despite these success stories, the field faces noteworthy challenges in discriminating the molecular basis of toxicity. We argue that toxicology is gradually evolving into a systems toxicology that will eventually allow us to describe all the toxicological interactions that occur within a living system under stress and use our knowledge of toxicogenomic responses in one species to predict the modes-of-action of similar agents in other species.}, } @article {pmid15570047, year = {2004}, author = {Terry, PD and Terry, JB and Rohan, TE}, title = {Long-chain (n-3) fatty acid intake and risk of cancers of the breast and the prostate: recent epidemiological studies, biological mechanisms, and directions for future research.}, journal = {The Journal of nutrition}, volume = {134}, number = {12 Suppl}, pages = {3412S-3420S}, doi = {10.1093/jn/134.12.3412S}, pmid = {15570047}, issn = {0022-3166}, mesh = {Animals ; Breast Neoplasms/*epidemiology/prevention & control ; Dietary Fats, Unsaturated/*administration & dosage ; Fatty Acids, Omega-3/*administration & dosage ; Female ; Humans ; MEDLINE ; Male ; Prostatic Neoplasms/*epidemiology/prevention & control ; Risk Factors ; Seafood ; }, abstract = {The association between dietary (n-3) fatty acids and hormone-responsive cancers continues to attract considerable attention in epidemiological, clinical, and experimental studies. We previously reviewed the epidemiological literature on the association between hormone-responsive cancers and the long-chain fatty acids eicosapentaenoic acid and docosahexaenoic acid. We concluded that the compelling evidence from ecological studies, animal models, and mechanistic experiments in vitro was not supported clearly by the available epidemiological data. To various degrees, epidemiological studies published more recently attempted to address some of the methodological limitations plaguing earlier studies by using validated questionnaires, examining specific fatty acids and their interrelationships, and adjusting estimates for a wider range of potentially confounding factors than in previous studies. In this review, our aim was to update the previous review with the results of recent epidemiological studies and to discuss possible biological mechanisms and directions for future research.}, } @article {pmid15546040, year = {2004}, author = {Smith, SM and Abed, RM and Gercia-Pichel, F}, title = {Biological soil crusts of sand dunes in Cape Cod National Seashore, Massachusetts, USA.}, journal = {Microbial ecology}, volume = {48}, number = {2}, pages = {200-208}, pmid = {15546040}, issn = {0095-3628}, mesh = {Bacteria/*genetics ; Base Sequence ; *Biodiversity ; Chlorophyta/*genetics ; Cluster Analysis ; DNA, Ribosomal/genetics ; Databases, Nucleic Acid ; Electrophoresis ; Likelihood Functions ; Massachusetts ; Models, Genetic ; Molecular Sequence Data ; Phylogeny ; Sequence Analysis, DNA ; Silicon Dioxide/analysis ; *Soil Microbiology ; }, abstract = {Biological soil crusts cover hundreds of hectares of sand dunes at the northern tip of Cape Cod National Seashore (Massachusetts, USA). Although the presence of crusts in this habitat has long been recognized, neither the organisms nor their ecological roles have been described. In this study, we report on the microbial community composition of crusts from this region and describe several of their physical and chemical attributes that bear on their environmental role. Microscopic and molecular analyses revealed that eukaryotic green algae belonging to the genera Klebsormidium or Geminella formed the bulk of the material sampled. Phylogenetic reconstruction of partial 16S rDNA sequences obtained from denaturing gradient gel electrophoresis (DGGE) fingerprints also revealed the presence of bacterial populations related to the subclass of the Proteobacteria, the newly described phylum Geothrix/ Holophaga/ Acidobacterium, the Cytophaga/ Flavobacterium/ Bacteroides group, and spirochetes. The presence of these crusts had significant effects on the hydric properties and nutrient status of the natural substrate. Although biological soil crusts are known to occur in dune environments around the world, this study enhances our knowledge of their geographic distribution and suggests a potential ecological role for crust communities in this landscape.}, } @article {pmid15543149, year = {2004}, author = {Parkinson, J and Mitreva, M and Whitton, C and Thomson, M and Daub, J and Martin, J and Schmid, R and Hall, N and Barrell, B and Waterston, RH and McCarter, JP and Blaxter, ML}, title = {A transcriptomic analysis of the phylum Nematoda.}, journal = {Nature genetics}, volume = {36}, number = {12}, pages = {1259-1267}, doi = {10.1038/ng1472}, pmid = {15543149}, issn = {1061-4036}, mesh = {Animals ; Base Sequence ; Chromosome Mapping ; Computational Biology ; Conserved Sequence/genetics ; Databases, Genetic ; *Evolution, Molecular ; *Expressed Sequence Tags ; *Genetic Variation ; *Genome ; Molecular Sequence Data ; Nematoda/*genetics ; Phylogeny ; Protein Structure, Tertiary/*genetics ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {The phylum Nematoda occupies a huge range of ecological niches, from free-living microbivores to human parasites. We analyzed the genomic biology of the phylum using 265,494 expressed-sequence tag sequences, corresponding to 93,645 putative genes, from 30 species, including 28 parasites. From 35% to 70% of each species' genes had significant similarity to proteins from the model nematode Caenorhabditis elegans. More than half of the putative genes were unique to the phylum, and 23% were unique to the species from which they were derived. We have not yet come close to exhausting the genomic diversity of the phylum. We identified more than 2,600 different known protein domains, some of which had differential abundances between major taxonomic groups of nematodes. We also defined 4,228 nematode-specific protein families from nematode-restricted genes: this class of genes probably underpins species- and higher-level taxonomic disparity. Nematode-specific families are particularly interesting as drug and vaccine targets.}, } @article {pmid15539599, year = {2004}, author = {Driskell, AC and Ané, C and Burleigh, JG and McMahon, MM and O'meara, BC and Sanderson, MJ}, title = {Prospects for building the tree of life from large sequence databases.}, journal = {Science (New York, N.Y.)}, volume = {306}, number = {5699}, pages = {1172-1174}, doi = {10.1126/science.1102036}, pmid = {15539599}, issn = {1095-9203}, mesh = {Animals ; Anopheles/classification/genetics ; Biodiversity ; *Biological Evolution ; Classification ; Computational Biology ; *Databases, Nucleic Acid ; *Databases, Protein ; Multigene Family ; *Phylogeny ; Plant Proteins/genetics ; Plants/classification/genetics ; Spodoptera/classification/genetics ; }, abstract = {We assess the phylogenetic potential of approximately 300,000 protein sequences sampled from Swiss-Prot and GenBank. Although only a small subset of these data was potentially phylogenetically informative, this subset retained a substantial fraction of the original taxonomic diversity. Sampling biases in the databases necessitate building phylogenetic data sets that have large numbers of missing entries. However, an analysis of two "supermatrices" suggests that even data sets with as much as 92% missing data can provide insights into broad sections of the tree of life.}, } @article {pmid15527985, year = {2004}, author = {Zhang, P and Min, W and Li, WH}, title = {Different age distribution patterns of human, nematode, and Arabidopsis duplicate genes.}, journal = {Gene}, volume = {342}, number = {2}, pages = {263-268}, doi = {10.1016/j.gene.2004.08.001}, pmid = {15527985}, issn = {0378-1119}, mesh = {Algorithms ; Animals ; Arabidopsis/*genetics ; Caenorhabditis elegans/*genetics ; Databases, Nucleic Acid ; Drosophila melanogaster/genetics ; Genes, Duplicate/*genetics ; Genetic Variation ; Genome ; Humans ; Models, Genetic ; Time Factors ; }, abstract = {We studied the age distribution of duplicate genes in each of four eukaryotic genomes: human, Arabidopsis thaliana, Caenorhabditis elegans, and Drosophila melanogaster. The four distributions differ greatly from each other, contrary to the previous proposal of a universal L-shaped distribution in all eukaryotic genomes studied. Indeed, only the distribution in humans is L-shaped. The distribution in Arabidopsis is consistent with the hypothesis of an ancient genome duplication with no recent burst of duplication events, while the distribution in C. elegans is nearly uniform. We also applied a nonparametric method to the human distribution to show that the rate of loss of duplicate genes decreases over time, contrary to the proposal of an exponential decay. One possible explanation of the decreasing rate of loss of duplicate genes over time could be rapid functional divergence between duplicate genes, providing an advantage for the retention of both duplicates.}, } @article {pmid15520899, year = {2004}, author = {Krause, G and Bock, M and Weiers, S and Braun, G}, title = {Mapping land-cover and mangrove structures with remote sensing techniques: a contribution to a synoptic GIS in support of coastal management in North Brazil.}, journal = {Environmental management}, volume = {34}, number = {3}, pages = {429-440}, pmid = {15520899}, issn = {0364-152X}, mesh = {Brazil ; *Conservation of Natural Resources ; Ecosystem ; Environmental Monitoring/*methods ; *Geographic Information Systems ; Humans ; Social Class ; Trees ; Water Supply ; }, abstract = {This article deals with the development and application of a cartographic database for a synoptic Geographic Information System (GIS). Its purpose is the storage and evaluation of the heterogeneous datasets of the interdisciplinary scientific research program MADAM (Mangrove Dynamics and Management), which aims to develop recommendations for a tailored integrated coastal management scheme for the mangrove ecosystem at Braganca (North Brazil). The article describes the integration of remote sensing data, aerial photographs, as well as point data provided by fieldwork from different scientific fields. Using various innovative processing techniques and different scale-resolution levels, an assessment of temporal-spatial changes of the mangrove peninsula and the adjacent rural socioeconomic impact area, the type of mangrove structure, as well as a land-use cover analyses was undertaken. The definition of the spatial level of detail was found to be a major issue in the development of the GIS, as well as during the processing and analysis procedures. A division between strong and weak patterns in the mangrove ecosystem could be made, which implies different management measures and sets of specific interdisciplinary studies and monitoring at hierarchical scales.}, } @article {pmid15510230, year = {2004}, author = {Butchart, SH and Stattersfield, AJ and Bennun, LA and Shutes, SM and Akçakaya, HR and Baillie, JE and Stuart, SN and Hilton-Taylor, C and Mace, GM}, title = {Measuring global trends in the status of biodiversity: red list indices for birds.}, journal = {PLoS biology}, volume = {2}, number = {12}, pages = {e383}, pmid = {15510230}, issn = {1545-7885}, mesh = {Abstracting and Indexing ; Animals ; *Biodiversity ; Birds/*physiology ; Classification ; Conservation of Natural Resources ; Data Interpretation, Statistical ; Ecology ; Ecosystem ; Environment ; Geography ; Models, Statistical ; Models, Theoretical ; Population Density ; Population Dynamics ; Research Design ; }, abstract = {The rapid destruction of the planet's biodiversity has prompted the nations of the world to set a target of achieving a significant reduction in the rate of loss of biodiversity by 2010. However, we do not yet have an adequate way of monitoring progress towards achieving this target. Here we present a method for producing indices based on the IUCN Red List to chart the overall threat status (projected relative extinction risk) of all the world's bird species from 1988 to 2004. Red List Indices (RLIs) are based on the number of species in each Red List category, and on the number changing categories between assessments as a result of genuine improvement or deterioration in status. The RLI for all bird species shows that their overall threat status has continued to deteriorate since 1988. Disaggregated indices show that deteriorations have occurred worldwide and in all major ecosystems, but with particularly steep declines in the indices for Indo-Malayan birds (driven by intensifying deforestation of the Sundaic lowlands) and for albatrosses and petrels (driven by incidental mortality in commercial longline fisheries). RLIs complement indicators based on species population trends and habitat extent for quantifying global trends in the status of biodiversity. Their main weaknesses are that the resolution of status changes is fairly coarse and that delays may occur before some status changes are detected. Their greatest strength is that they are based on information from nearly all species in a taxonomic group worldwide, rather than a potentially biased subset. At present, suitable data are only available for birds, but indices for other taxonomic groups are in development, as is a sampled index based on a stratified sample from all major taxonomic groups.}, } @article {pmid15510132, year = {2004}, author = {Brooks, T and Kennedy, E}, title = {Conservation biology: biodiversity barometers.}, journal = {Nature}, volume = {431}, number = {7012}, pages = {1046-1047}, doi = {10.1038/4311046a}, pmid = {15510132}, issn = {1476-4687}, mesh = {Animals ; *Biodiversity ; Birds/physiology ; Conservation of Natural Resources/legislation & jurisprudence/*methods/trends ; Databases, Factual ; Ecology/*instrumentation/*methods/organization & administration ; Ecosystem ; Environment ; Geography ; International Cooperation ; Nitrogen/analysis ; Risk ; Sensitivity and Specificity ; Time Factors ; }, } @article {pmid15504492, year = {2004}, author = {Irving, P and Moncrieff, I}, title = {Managing the environmental impacts of land transport: integrating environmental analysis with urban planning.}, journal = {The Science of the total environment}, volume = {334-335}, number = {}, pages = {47-59}, doi = {10.1016/j.scitotenv.2004.04.064}, pmid = {15504492}, issn = {0048-9697}, mesh = {Cities ; Databases, Factual ; Environment ; Environmental Pollutants/*analysis ; Humans ; New Zealand ; Policy Making ; Rain ; Risk Assessment ; *Transportation ; Vehicle Emissions/*analysis ; Water Pollution/prevention & control ; }, abstract = {Ecological systems have limits or thresholds that vary by pollutant type, emissions sources and the sensitivity of a given location. Human health can also indicate sensitivity. Good environmental management requires any problem to be defined to obtain efficient and effective solutions. Cities are where transport activities, effects and resource management decisions are often most focussed. The New Zealand Ministry of Transport has developed two environmental management tools. The Vehicle Fleet Model (VFM) is a predictive database of the environmental performance of the New Zealand traffic fleet (and rail fleet). It calculates indices of local air quality, stormwater, and greenhouse gases emissions. The second is an analytical process based on Environmental Capacity Analysis (ECA). Information on local traffic is combined with environmental performance data from the Vehicle Fleet Model. This can be integrated within a live, geo-spatially defined analysis of the overall environmental effects within a defined local area. Variations in urban form and activity (traffic and other) that contribute to environmental effects can be tracked. This enables analysis of a range of mitigation strategies that may contribute, now or in the future, to maintaining environmental thresholds or meeting targets. A case study of the application of this approach was conducted within Waitakere City. The focus was on improving the understanding of the relative significance of stormwater contaminants derived from land transport.}, } @article {pmid15503759, year = {2004}, author = {Guo, LP and Huang, LQ}, title = {[Ecological research on resources of Chinese herbal medicine].}, journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica}, volume = {29}, number = {7}, pages = {615-618}, pmid = {15503759}, issn = {1001-5302}, mesh = {China ; Conservation of Natural Resources ; *Ecosystem ; Geographic Information Systems ; Pharmacognosy ; *Plants, Medicinal ; Quality Control ; }, abstract = {OBJECTIVE: To explore the status and development of the ecological research on resources of Chinese herbal medicine.

METHOD: The ecological domain related to the resources of Chinese Herbal Medicine was Analyzed.

RESULT: It was found that the weakness of the theoretical study and application were the main problems constrained the development of ecological research of Chinese Herbal Medicine.

CONCLUSION: A new subject, ecology of resources of Chinese herbal medicine, will come into being with the development of the theoretical and practical study and application of new technology and method.}, } @article {pmid15494476, year = {2004}, author = {Patil, A and Hughes, AL and Zhang, G}, title = {Rapid evolution and diversification of mammalian alpha-defensins as revealed by comparative analysis of rodent and primate genes.}, journal = {Physiological genomics}, volume = {20}, number = {1}, pages = {1-11}, doi = {10.1152/physiolgenomics.00150.2004}, pmid = {15494476}, issn = {1531-2267}, mesh = {Amino Acid Sequence ; Animals ; Antimicrobial Cationic Peptides/chemistry ; Computational Biology/methods ; Cysteine/chemistry ; DNA Primers/chemistry ; DNA, Complementary/metabolism ; Evolution, Molecular ; Exons ; Genome ; Genome, Human ; Genomics/*methods ; Humans ; Internet ; Mice ; Models, Genetic ; Molecular Sequence Data ; Multigene Family ; Pan troglodytes ; Phylogeny ; Rats ; Reverse Transcriptase Polymerase Chain Reaction ; Sequence Homology, Amino Acid ; Species Specificity ; Tissue Distribution ; alpha-Defensins/genetics ; beta-Defensins/genetics ; }, abstract = {Mammalian alpha-defensins constitute a family of cysteine-rich, cationic antimicrobial peptides produced by phagocytes and intestinal Paneth cells, playing an important role in innate host defense. Following comprehensive computational searches, here we report the discovery of complete repertoires of the alpha-defensin gene family in the human, chimpanzee, rat, and mouse with new genes identified in each species. The human genome was found to encode a cluster of 10 distinct alpha-defensin genes and pseudogenes expanding 132 kb continuously on chromosome 8p23. Such alpha-defensin loci are also conserved in the syntenic chromosomal regions of chimpanzee, rat, and mouse. Phylogenetic analyses showed formation of two distinct clusters with primate alpha-defensins forming one cluster and rodent enteric alpha-defensins forming the other cluster. Species-specific clustering of genes is evident in nonprimate species but not in the primates. Phylogenetically distinct subsets of alpha-defensins also exist in each species, with most subsets containing multiple members. In addition, natural selection appears to have acted to diversify the functionally active mature defensin region but not signal or prosegment sequences. We concluded that mammalian alpha-defensin genes may have evolved from two separate ancestors originated from beta-defensins. The current repertoires of the alpha-defensin gene family in each species are primarily a result of repeated gene duplication and positive diversifying selection after divergence of mammalian species from each other, except for the primate genes, which were evolved prior to the separation of the primate species. We argue that the presence of multiple, divergent subsets of alpha-defensins in each species may help animals to better cope with different microbial challenges in the ecological niches which they inhabit.}, } @article {pmid15493473, year = {2004}, author = {Wang, J and Li, L and Wan, X and An, L and Zhang, J}, title = {Distribution of T-DNA carrying a Ds element on rice chromosomes.}, journal = {Science in China. Series C, Life sciences}, volume = {47}, number = {4}, pages = {322-331}, doi = {10.1360/03yc0141}, pmid = {15493473}, issn = {1006-9305}, mesh = {Base Sequence ; Chromosomes, Plant/*genetics ; Computational Biology ; DNA, Bacterial/*genetics ; DNA, Intergenic/genetics ; Genetic Vectors/genetics ; Genome, Plant ; Molecular Sequence Data ; Oryza/*genetics ; Transformation, Genetic/genetics ; }, abstract = {Over 3000 rice plants with T-DNA carrying a Ds element were constructed by Agrobacterium tumefaciens mediation. Using inverse PCR methodology, 590 unique right flanking sequences of T-DNA (Ds) were retrieved from independent transformants and classified into six main types on the basis of the origin of filler DNA between the right border of T-DNA and flanking sequence of rice genome. Type I sequences were the most common and showed canonical integration that T-DNA right border was followed by rice genome sequence with or without filler DNA of no more than 50 bp, while type II sequences displayed a vector-genome combination that T-DNA right border was followed by a vector fragment and then connected with rice genome sequence. The location and distribution of 340 type I and II flanking sequences on the rice chromosome were determined using BLAST analysis. The 340 Ds insertions at an average interval of 0.8 megabase (Mb) constructed a basic framework of Ds starter points on whole rice chromosomes. The frequency of T-DNA (Ds) inserted into the exons of predicted genes on chromosome one was 21%. Knowledge of T-DNA (Ds) locations on chromosomes will prove to be a useful resource for isolating rice genes by Ds transposon tagging as these Ds insertions can be used as starting lines for further mutagenesis.}, } @article {pmid15491656, year = {2004}, author = {Simon, U and Brüggemann, R and Pudenz, S}, title = {Aspects of decision support in water management--example Berlin and Potsdam (Germany) II--improvement of management strategies.}, journal = {Water research}, volume = {38}, number = {19}, pages = {4085-4092}, doi = {10.1016/j.watres.2004.07.016}, pmid = {15491656}, issn = {0043-1354}, mesh = {*Decision Support Techniques ; Ecology ; Environment ; Germany ; *Models, Theoretical ; Waste Disposal, Fluid/*methods ; *Water Supply ; }, abstract = {Methods related to partial order theory such as the Hasse diagram technique (HDT) are increasingly used in the field of multi-criteria decision support. The HDT has the advantage of being a transparent evaluation tool, supported by several data analysis tools such as the concept of antagonistic indicators. However, the evaluation usually does not lead to a clear decision, because more than one possible solution is offered. In the example presented here, three of the nine water management strategies (scenarios) evaluated by HDT were identified as winners. However, these strategies were not comparable with each other because of the conflicting evaluation of at least two different indicators. Such antagonisms describe the advantage and disadvantage of each scenario. Based on this background information, a new innovative approach is demonstrated, enabling the stakeholders to design new, modified management strategies, with reduced negative effects. After improvement of the three potential solutions, one clear winner scenario could be identified.}, } @article {pmid15483326, year = {2005}, author = {Holland, BR and Huber, KT and Penny, D and Moulton, V}, title = {The MinMax Squeeze: guaranteeing a minimal tree for population data.}, journal = {Molecular biology and evolution}, volume = {22}, number = {2}, pages = {235-242}, doi = {10.1093/molbev/msi010}, pmid = {15483326}, issn = {0737-4038}, mesh = {Computational Biology/*methods ; DNA, Mitochondrial/*genetics ; Genetics, Population/*methods ; Humans ; *Phylogeny ; }, abstract = {We report that for population data, where sequences are very similar to one another, it is often possible to use a two-pronged (MinMax Squeeze) approach to prove that a tree is the shortest possible under the parsimony criterion. Such population data can be in a range where parsimony is a maximum likelihood estimator. This is in sharp contrast to the case with species data, where sequences are much further apart and the problem of guaranteeing an optimal phylogenetic tree is known to be computationally prohibitive for realistic numbers of species, irrespective of whether likelihood or parsimony is the optimality criterion. The Squeeze uses both an upper bound (the length of the shortest tree known) and a lower bound derived from partitions of the columns (the length of the shortest tree possible). If the two bounds meet, the shortest known tree is thus proven to be a shortest possible tree. The implementation is first tested on simulated data sets and then applied to 53 complete human mitochondrial genomes. The shortest possible trees for those data have several significant improvements from the published tree. Namely, a pair of Australian lineages comes deeper in the tree (in agreement with archaeological data), and the non-African part of the tree shows greater agreement with the geographical distribution of lineages.}, } @article {pmid15479949, year = {2004}, author = {Lerat, E and Ochman, H}, title = {Psi-Phi: exploring the outer limits of bacterial pseudogenes.}, journal = {Genome research}, volume = {14}, number = {11}, pages = {2273-2278}, pmid = {15479949}, issn = {1088-9051}, support = {R01 GM056120/GM/NIGMS NIH HHS/United States ; GM56120/GM/NIGMS NIH HHS/United States ; }, mesh = {Codon, Nonsense/genetics ; Computational Biology ; DNA Transposable Elements/genetics ; Escherichia coli/*genetics ; Evolution, Molecular ; *Genome, Bacterial ; Pseudogenes/*genetics ; Sequence Analysis, DNA/methods ; Shigella flexneri/*genetics ; Software ; }, abstract = {Because bacterial chromosomes are tightly packed with genes and were traditionally viewed as being optimized for size and replication speed, it was not surprising that the early annotations of sequenced bacterial genomes reported few, if any, pseudogenes. But because pseudogenes are generally recognized by comparisons with their functional counterparts, as more genome sequences accumulated, many bacterial pathogens were found to harbor large numbers of truncated, inactivated, and degraded genes. Because the mutational events that inactivate genes occur continuously in all genomes, we investigated whether the rarity of pseudogenes in some bacteria was attributable to properties inherent to the organism or to the failure to recognize pseudogenes. By developing a program suite (called Psi-Phi, for Psi-gene Finder) that applies a comparative method to identify pseudogenes (attributable both to misannotation and to nonrecognition), we analyzed the pseudogene inventories in the sequenced members of the Escherichia coli/Shigella clade. This approach recovered hundreds of previously unrecognized pseudogenes and showed that pseudogenes are a regular feature of bacterial genomes, even in those whose original annotations registered no truncated or otherwise inactivated genes. In Shigella flexneri 2a, large proportions of pseudogenes are generated by nonsense mutations and IS element insertions, events that seldom produce the pseudogenes present in the other genomes examined. Almost all (>95%) pseudogenes are restricted to only one of the genomes and are of relatively recent origin, suggesting that these bacteria possess active mechanisms to eliminate nonfunctional genes.}, } @article {pmid15475172, year = {2004}, author = {Grus, WE and Zhang, J}, title = {Rapid turnover and species-specificity of vomeronasal pheromone receptor genes in mice and rats.}, journal = {Gene}, volume = {340}, number = {2}, pages = {303-312}, doi = {10.1016/j.gene.2004.07.037}, pmid = {15475172}, issn = {0378-1119}, support = {GM67030/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Chromosome Mapping ; Chromosomes, Mammalian/genetics ; DNA/chemistry/genetics ; Databases, Nucleic Acid ; Evolution, Molecular ; Gene Duplication ; Mice ; Molecular Sequence Data ; Phylogeny ; Rats ; Receptors, Odorant/*genetics ; Receptors, Pheromone/*genetics ; Sequence Analysis, DNA ; Species Specificity ; Synteny ; Time Factors ; Vomeronasal Organ/metabolism ; }, abstract = {Pheromones are used by individuals of the same species to elicit behavioral or physiological changes, and they are perceived primarily by the vomeronasal organ (VNO) in terrestrial vertebrates. VNO pheromone receptors are encoded by the V1r and V2r gene superfamilies in mammals. A comparison of the V1r and V2r repertoires between closely related species can provide significant insights into the evolutionary genetic mechanisms responsible for species-specific pheromone communications. A total of 137 putatively functional V1r genes of 12 families were previously identified from the mouse genome. We report the identification of 95 putatively functional V1r genes from the draft rat genome sequence. These genes map primarily to four blocks in two chromosomes. The rat V1r genes can be phylogenetically grouped into 10 families, which are shared with mouse, and 2 new families, which are rat-specific. Even in many shared families, gene numbers differ between the two species, apparently due to frequent gene duplication and pseudogenization after the separation of the two species. Molecular dating suggests that most of the rat V1r families emerged before or during the radiation of mammalian orders, but many duplications within families occurred as recently as in the past 10 million years (MY). Our results show that the evolution of the V1r repertoire is characterized by exceptionally fast gene turnover via gains and losses of individual genes, suggesting rapid and substantial changes in pheromone communication between species.}, } @article {pmid15471740, year = {2004}, author = {Mather, FJ and White, LE and Langlois, EC and Shorter, CF and Swalm, CM and Shaffer, JG and Hartley, WR}, title = {Statistical methods for linking health, exposure, and hazards.}, journal = {Environmental health perspectives}, volume = {112}, number = {14}, pages = {1440-1445}, pmid = {15471740}, issn = {0091-6765}, support = {U50 CCU 622412/CC/ODCDC CDC HHS/United States ; }, mesh = {Case-Control Studies ; Cohort Studies ; Data Collection ; *Environmental Exposure ; Environmental Health/*statistics & numerical data ; Environmental Pollutants/*poisoning ; *Geographic Information Systems ; Humans ; *Information Systems ; *Models, Theoretical ; Monte Carlo Method ; Multivariate Analysis ; Outcome Assessment, Health Care ; Reproducibility of Results ; Risk Assessment ; United States ; }, abstract = {The Environmental Public Health Tracking Network (EPHTN) proposes to link environmental hazards and exposures to health outcomes. Statistical methods used in case-control and cohort studies to link health outcomes to individual exposure estimates are well developed. However, reliable exposure estimates for many contaminants are not available at the individual level. In these cases, exposure/hazard data are often aggregated over a geographic area, and ecologic models are used to relate health outcome and exposure/hazard. Ecologic models are not without limitations in interpretation. EPHTN data are characteristic of much information currently being collected--they are multivariate, with many predictors and response variables, often aggregated over geographic regions (small and large) and correlated in space and/or time. The methods to model trends in space and time, handle correlation structures in the data, estimate effects, test hypotheses, and predict future outcomes are relatively new and without extensive application in environmental public health. In this article we outline a tiered approach to data analysis for EPHTN and review the use of standard methods for relating exposure/hazards, disease mapping and clustering techniques, Bayesian approaches, Markov chain Monte Carlo methods for estimation of posterior parameters, and geostatistical methods. The advantages and limitations of these methods are discussed.}, } @article {pmid15471739, year = {2004}, author = {Hanrahan, LP and Anderson, HA and Busby, B and Bekkedal, M and Sieger, T and Stephenson, L and Knobeloch, L and Werner, M and Imm, P and Olson, J}, title = {Wisconsin's environmental public health tracking network: information systems design for childhood cancer surveillance.}, journal = {Environmental health perspectives}, volume = {112}, number = {14}, pages = {1434-1439}, pmid = {15471739}, issn = {0091-6765}, support = {U50 CCU 522439-01/CC/ODCDC CDC HHS/United States ; }, mesh = {Automation ; Child ; Child, Preschool ; *Community Networks ; Data Collection ; Environmental Pollutants/*poisoning ; Humans ; Infant ; Infant, Newborn ; Information Systems/*organization & administration ; Medical Informatics ; Neoplasms/*epidemiology/etiology ; *Population Surveillance ; Public Health ; Registries/*statistics & numerical data ; Risk Assessment ; Wisconsin/epidemiology ; }, abstract = {In this article we describe the development of an information system for environmental childhood cancer surveillance. The Wisconsin Cancer Registry annually receives more than 25,000 incident case reports. Approximately 269 cases per year involve children. Over time, there has been considerable community interest in understanding the role the environment plays as a cause of these cancer cases. Wisconsin's Public Health Information Network (WI-PHIN) is a robust web portal integrating both Health Alert Network and National Electronic Disease Surveillance System components. WI-PHIN is the information technology platform for all public health surveillance programs. Functions include the secure, automated exchange of cancer case data between public health-based and hospital-based cancer registrars; web-based supplemental data entry for environmental exposure confirmation and hypothesis testing; automated data analysis, visualization, and exposure-outcome record linkage; directories of public health and clinical personnel for role-based access control of sensitive surveillance information; public health information dissemination and alerting; and information technology security and critical infrastructure protection. For hypothesis generation, cancer case data are sent electronically to WI-PHIN and populate the integrated data repository. Environmental data are linked and the exposure-disease relationships are explored using statistical tools for ecologic exposure risk assessment. For hypothesis testing, case-control interviews collect exposure histories, including parental employment and residential histories. This information technology approach can thus serve as the basis for building a comprehensive system to assess environmental cancer etiology.}, } @article {pmid15470707, year = {2004}, author = {Staudt, C and Horn, H and Hempel, DC and Neu, TR}, title = {Volumetric measurements of bacterial cells and extracellular polymeric substance glycoconjugates in biofilms.}, journal = {Biotechnology and bioengineering}, volume = {88}, number = {5}, pages = {585-592}, doi = {10.1002/bit.20241}, pmid = {15470707}, issn = {0006-3592}, mesh = {Bacteria, Aerobic/*cytology/*physiology ; Biofilms/*growth & development ; Cell Size ; Colony Count, Microbial/methods ; Extracellular Fluid/metabolism ; Glycoconjugates/*metabolism ; Image Interpretation, Computer-Assisted/*methods ; Imaging, Three-Dimensional/methods ; Microscopy, Confocal/*methods ; Sewage/*microbiology ; }, abstract = {In this study an enrichment culture developed from activated sludge was used to investigate the architecture of fully hydrated multispecies biofilms. The assessment of biofilm structure and volume was carried out using confocal laser scanning microscopy (CLSM). Bacterial cell distribution was determined with the nucleic acid-specific stain SYTO 60, whereas glycoconjugates of extracellular polymeric substances (EPS) were stained with the Alexa-488-labeled lectin of Aleuria aurantia. Digital image analysis was employed for visualization and quantification of three-dimensional CLSM data sets. The specific volumes of the polymeric and cellular biofilm constituents were quantified. In addition, gravimetric measurements were done to determine dry mass and thickness of the biofilms. The data recorded by the CLSM technique and the gravimetric data were then compared. It was shown that the biofilm thicknesses determined with both methods agree well for slow-growing heterotrophic and chemoautotrophic biofilms. In addition, for slow-growing biofilms, the volumes and masses calculated from CLSM and the biomass calculated from gravimetric measurements were also comparable. For fast-growing heterotrophic biofilms cultivated with high glucose concentrations the data sets fit to a lesser degree, but still showed the same common trend. Compared with traditional gravimetric measurements, CLSM allowed differential recording of multiple biofilm parameters with subsequent three-dimensional visualization and quantification. The quantitative three-dimensional results recorded by CLSM are an important basis for understanding, controlling, exploiting, and modeling of biofilms.}, } @article {pmid15464159, year = {2004}, author = {Steinbeck, C and Kuhn, S}, title = {NMRShiftDB -- compound identification and structure elucidation support through a free community-built web database.}, journal = {Phytochemistry}, volume = {65}, number = {19}, pages = {2711-2717}, doi = {10.1016/j.phytochem.2004.08.027}, pmid = {15464159}, issn = {0031-9422}, mesh = {*Databases, Factual ; *Internet ; *Magnetic Resonance Spectroscopy ; Molecular Structure ; }, abstract = {Compound identification and support for computer-assisted structure elucidation via a free community-built web database for organic structures and their NMR data is described. The new database NMRShiftDB is available on . As the first NMR database, NMRShiftDB allows not only open access to the database but also open and peer reviewed submission of datasets, enabling the natural products community to build its first free repository of assigned 1H and 13C NMR spectra. In addition to the open access, the underlying database software is built solely from free software and is available under an open source license. This allows collaborating laboratories to fully replicate the database and to create a highly available network of NMRShiftDB mirrors. The database contains about 10,000 structures and assigned spectra, with new datasets constantly added. Its functionality includes (sub-) spectra and (sub-) structure searches as well as shift prediction of 13C spectra based on the current database material.}, } @article {pmid15461387, year = {2004}, author = {O'Connor, KA and Brindle, E and Shofer, JB and Miller, RC and Klein, NA and Soules, MR and Campbell, KL and Mar, C and Handcock, MS}, title = {Statistical correction for non-parallelism in a urinary enzyme immunoassay.}, journal = {Journal of immunoassay & immunochemistry}, volume = {25}, number = {3}, pages = {259-278}, doi = {10.1081/ias-200028078}, pmid = {15461387}, issn = {1532-1819}, support = {2 P30 HD28263/HD/NICHD NIH HHS/United States ; 5 T32 AG00208/AG/NIA NIH HHS/United States ; R01 AG14579/AG/NIA NIH HHS/United States ; R01 AG15141/AG/NIA NIH HHS/United States ; R24 HD42828/HD/NICHD NIH HHS/United States ; }, mesh = {Adult ; *Data Interpretation, Statistical ; Enzyme-Linked Immunosorbent Assay/methods/statistics & numerical data ; Estradiol/*analogs & derivatives/*blood ; Estrone/*analogs & derivatives/*urine ; Female ; Humans ; Menstrual Cycle/*blood/*urine ; Middle Aged ; Sensitivity and Specificity ; }, abstract = {Our aim was to develop a statistical method to correct for non-parallelism in an estrone-3-glucuronide (E1G) enzyme immunoassay (EIA). Non-parallelism of serially diluted urine specimens with a calibration curve was demonstrated in an EIA for E1G. A linear mixed-effects analysis of 40 urine specimens was used to model the relationship of E1G concentration with urine volume and derive a statistical correction. The model was validated on an independent sample and applied to 30 menstrual cycles from American women. Specificity, detection limit, parallelism, recovery, correlation with serum estradiol, and imprecision of the assay were determined. Intra-and inter-assay CVs were less than 14% for high- and low-urine controls. Urinary E1G across the menstrual cycle was highly correlated with serum estradiol (r= 0.94). Non-parallelism produced decreasing E1G concentration with increase in urine volume (slope = -0.210, p < 0.0001). At 50% inhibition, the assay had 100% cross-reactivity with E1G and 83% with 17beta-estradiol 3-glucuronide. The dose-response curve of the latter did not parallel that of E1G and is a possible cause of the non-parallelism. The statistical correction adjusting E1G concentration to a standardized urine volume produced parallelism in 24 independent specimens (slope = -0.043+/-0.010), and improved the average CV of E1G concentration across dilutions from 19.5%+/-5.6% before correction to 10.3%+/-5.3% after correction. A statistical method based on linear mixed effects modeling is an expedient approach for correction of non-parallelism, particularly for hormone data that will be analyzed in aggregate.}, } @article {pmid15451728, year = {2004}, author = {Shortell, SM and Weist, EM and Sow, MS and Foster, A and Tahir, R}, title = {Implementing the Institute of Medicine's recommended curriculum content in schools of public health: a baseline assessment.}, journal = {American journal of public health}, volume = {94}, number = {10}, pages = {1671-1674}, pmid = {15451728}, issn = {0090-0036}, mesh = {*Curriculum ; Humans ; National Academies of Science, Engineering, and Medicine, U.S., Health and Medicine Division ; Public Health/*education ; Surveys and Questionnaires ; United States ; }, abstract = {In September 2003, the Association of Schools of Public Health administered an online survey to representatives of all 33 accredited US schools of public health. The survey assessed the extent to which the schools were offering curriculum content in the 8 areas recommended by the Institute of Medicine: communication, community-based participatory research, cultural competence, ethics, genomics, global health, informatics, and law/policy. Findings indicated that, for the most part, schools of public health are offering content in these areas through many approaches and have incorporated various aspects of a broad-based ecological approach to public health education and training. The findings also suggested the possible need for greater content in genomics, informatics, community-based participatory research, and cultural competence.}, } @article {pmid15450203, year = {2004}, author = {Bougnoux, ME and Aanensen, DM and Morand, S and Théraud, M and Spratt, BG and d'Enfert, C}, title = {Multilocus sequence typing of Candida albicans: strategies, data exchange and applications.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {4}, number = {3}, pages = {243-252}, doi = {10.1016/j.meegid.2004.06.002}, pmid = {15450203}, issn = {1567-1348}, mesh = {Animals ; Base Sequence ; Candida albicans/*classification/*genetics ; Candidiasis/prevention & control ; Databases, Factual ; Humans ; *Mycological Typing Techniques ; Phylogeny ; Software ; }, abstract = {Multilocus sequence typing of Candida albicans: strategies, data exchange and applications. Bougnoux, M.-E., Aanensen, D.M., Morand, S., Théraud, M., Spratt, B.G., and d'Enfert, C. Infection, Genetics and Evolution. C. albicans is a commensal of humans and animals but is also the main fungal pathogen of humans, ranking fourth among the microorganisms responsible for hospital-acquired bloodstream infections. Information on the genetic diversity and dynamics of the C. albicans population and on the characteristics of C. albicans strains causing invasive infections in immunocompromised patients is important in order to adapt prevention policies. Important results in this field have been obtained using the Ca3 fingerprinting probe. Recently, multilocus sequence typing (MLST) based on the sequencing of 6-8 selected house-keeping genes and identification of polymorphic nucleotide sites has been introduced for the characterization of C. albicans isolates. Combination of the alleles at the different loci results in unique diploid sequence types (DSTs) that can be used to discriminate strains. MLST has now been successfully applied to study the epidemiology of C. albicans in the hospital as well as the diversity of C. albicans isolates obtained from diverse ecological niches including human and animal hosts. Furthermore, MLST data for C. albicans are available in a public database (http://calbicans.mlst.net) that provides a new resource to evaluate the worldwide diversity of C. albicans and the relationships of isolates identified at various locations.}, } @article {pmid15387078, year = {2004}, author = {Forbes, BC and Fresco, N and Shvidenko, A and Danell, K and Chapin, FS}, title = {Geographic variations in anthropogenic drivers that influence the vulnerability and resilience of social-ecological systems.}, journal = {Ambio}, volume = {33}, number = {6}, pages = {377-382}, doi = {10.1579/0044-7447-33.6.377}, pmid = {15387078}, issn = {0044-7447}, mesh = {Arctic Regions ; *Conservation of Natural Resources ; Ecology ; *Environment ; *Geographic Information Systems ; *Greenhouse Effect ; Humans ; Risk Assessment ; Social Conditions ; }, abstract = {Across the circumpolar North large disparities in the distribution of renewable and nonrenewable resources, human population density, capital investments, and basic residential and transportation infrastructure combine to create recognizable hotspots of recent and foreseeable change. Northern Fennoscandia exemplifies a relatively benign situation due to its current economic and political stability. Northern Russia is experiencing rapid, mostly negative changes reflecting the general state of crisis since the collapse of the Soviet Union. North America enjoys a relatively stable regulatory structure to mitigate environmental degradation associated with industry, but is on the verge of approving massive new development schemes that would significantly expand the spatial extent of potentially affected social-ecological systems. Institutional or regulatory context influences the extent to which ecosystem services are buffered against environmental change. With or without a warming climate, certain geographic areas appear especially vulnerable to damages that may threaten their ability to supply goods and services in the near future. Climate change may exacerbate this situation in some places but may offer opportunities to enhance resilience in the long term.}, } @article {pmid15387069, year = {2004}, author = {Nepal, SK and Nepal, SA}, title = {Visitor impacts on trails in the Sagarmatha (Mt. Everest) National Park, Nepal.}, journal = {Ambio}, volume = {33}, number = {6}, pages = {334-340}, doi = {10.1579/0044-7447-33.6.334}, pmid = {15387069}, issn = {0044-7447}, mesh = {Ecology ; Ecosystem ; Environmental Monitoring ; *Geographic Information Systems ; Humans ; Nepal ; *Plant Development ; *Recreation ; *Soil ; Walking ; }, abstract = {This study summarizes findings of a visitor impact study conducted in the Sagarmatha (Mt. Everest) National Park, Nepal. The effect of visitor use, and the influence of environmental characteristics on trail conditions are investigated. Seven trails divided into 208 trail segments, and with a total length of 90 kilometers were included in the assessment. A four-class rating system has been used for the assessment of trail conditions. Arc/Info and Arc/View geographic information system (GIS) are used to analyze spatial patterns of impacts. The study indicates a strong correlation between visitor use and trail degradation. However, locational and environmental factors are equally important variables. The study concludes that more systematic, and experimental studies are needed that can make a clear distinction between human-induced trail damage and the effects of natural factors.}, } @article {pmid15383875, year = {2004}, author = {Olsson, P and Folke, C and Berkes, F}, title = {Adaptive comanagement for building resilience in social-ecological systems.}, journal = {Environmental management}, volume = {34}, number = {1}, pages = {75-90}, pmid = {15383875}, issn = {0364-152X}, mesh = {Canada ; *Community Networks ; *Conservation of Natural Resources ; *Ecology ; *Ecosystem ; Humans ; Information Services ; Knowledge ; Organizational Culture ; *Social Conditions ; Sweden ; }, abstract = {Ecosystems are complex adaptive systems that require flexible governance with the ability to respond to environmental feedback. We present, through examples from Sweden and Canada, the development of adaptive comanagement systems, showing how local groups self-organize, learn, and actively adapt to and shape change with social networks that connect institutions and organizations across levels and scales and that facilitate information flows. The development took place through a sequence of responses to environmental events that widened the scope of local management from a particular issue or resource to a broad set of issues related to ecosystem processes across scales and from individual actors, to group of actors to multiple-actor processes. The results suggest that the institutional and organizational landscapes should be approached as carefully as the ecological in order to clarify features that contribute to the resilience of social-ecological systems. These include the following: vision, leadership, and trust; enabling legislation that creates social space for ecosystem management; funds for responding to environmental change and for remedial action; capacity for monitoring and responding to environmental feedback; information flow through social networks; the combination of various sources of information and knowledge; and sense-making and arenas of collaborative learning for ecosystem management. We propose that the self-organizing process of adaptive comanagement development, facilitated by rules and incentives of higher levels, has the potential to expand desirable stability domains of a region and make social-ecological systems more robust to change.}, } @article {pmid15383704, year = {2004}, author = {Shiohara, A and Hoshino, A and Hanaki, K and Suzuki, K and Yamamoto, K}, title = {On the cyto-toxicity caused by quantum dots.}, journal = {Microbiology and immunology}, volume = {48}, number = {9}, pages = {669-675}, doi = {10.1111/j.1348-0421.2004.tb03478.x}, pmid = {15383704}, issn = {0385-5600}, mesh = {Animals ; Cadmium ; *Cell Death ; *Cell Survival ; Chlorocebus aethiops ; Flow Cytometry ; Fluorescent Dyes/*toxicity ; HeLa Cells ; Hepatocytes ; Humans ; *Quantum Dots ; Selenium ; Sulfhydryl Compounds ; Vero Cells/physiology ; }, abstract = {Quantum dots (QDs) such as CdSe QDs have been introduced as new fluorophores. The QDs conjugated with antibody are starting to be widely used for immunostaining. However there is still not sufficient analysis of the toxicity of QDs in the literature. Therefore we evaluated the cell damage caused by the quantum dots for biological applications. We performed cell viability assay to determine the difference in cell damage depending on the sizes and colors of mercapto-undecanoic acid (MUA) QDs and the cell types. The results showed that the cell viability decreased with increasing concentration of MUA-QDs. But in the case of Vero cell (African green monkey's kidney cell) with red fluorescence QD (QD640), the cell damage was less than for the others. Furthermore through the flow cytometry assay we found that this cell damage caused by MUA-QD turned out to be cell death after 4-6-hr incubation. From the two assays described above, we found that there is a range of concentration of MUA-QDs where the cell viability decreased without cell death occurring and thus we conclude that attention should be given when MUAQDs are applied to living organisms even in low concentrations.}, } @article {pmid15382848, year = {2004}, author = {Whitman, RL and Nevers, MB}, title = {Escherichia coli sampling reliability at a frequently closed Chicago Beach: monitoring and management implications.}, journal = {Environmental science & technology}, volume = {38}, number = {16}, pages = {4241-4246}, doi = {10.1021/es034978i}, pmid = {15382848}, issn = {0013-936X}, mesh = {Chicago ; Databases, Factual ; Environment ; Environmental Monitoring/*standards ; Escherichia coli/*isolation & purification ; Humans ; *Recreation ; Reproducibility of Results ; Risk Assessment ; Safety ; Sample Size ; Water Microbiology ; Water Supply/standards ; }, abstract = {Monitoring beaches for recreational water quality is becoming more common, but few sampling designs or policy approaches have evaluated the efficacy of monitoring programs. The authors intensively sampled water for E. coli (N=1770) at 63rd Street Beach, Chicago for 6 months in 2000 in order to (1) characterize spatial-temporal trends, (2) determine between and within transect variation, and (3) estimate sample size requirements and determine sampling reliability. E. coli counts were highly variable within and between sampling sites but spatially and diurnally autocorrelated. Variation in counts decreased with water depth and time of day. Required number of samples was high for 70% precision around the critical closure level (i.e., 6 within or 24 between transect replicates). Since spatial replication may be cost prohibitive, composite sampling is an alternative once sources of error have been well defined. The results suggest that beach monitoring programs may be requiring too few samples to fulfill management objectives desired. As the recreational water quality national database is developed, it is important that sampling strategies are empirically derived from a thorough understanding of the sources of variation and the reliability of collected data. Greater monitoring efficacy will yield better policy decisions, risk assessments, programmatic goals, and future usefulness of the information.}, } @article {pmid15371527, year = {2005}, author = {Zhang, L and Lu, HH and Chung, WY and Yang, J and Li, WH}, title = {Patterns of segmental duplication in the human genome.}, journal = {Molecular biology and evolution}, volume = {22}, number = {1}, pages = {135-141}, doi = {10.1093/molbev/msh262}, pmid = {15371527}, issn = {0737-4038}, mesh = {Chromosome Mapping ; Chromosomes, Human/*genetics ; Computational Biology ; *Evolution, Molecular ; *Gene Duplication ; *Genome, Human ; Humans ; Telomere/genetics ; }, abstract = {We analyzed the completed human genome for recent segmental duplications (size > or = 1 kb and sequence similarity > or = 90%). We found that approximately 4% of the genome is covered by duplications and that the extent of segmental duplication varies from 1% to 14% among the 24 chromosomes. Intrachromosomal duplication is more frequent than interchromosomal duplication in 15 chromosomes. The duplication frequencies in pericentromeric and subtelomeric regions are greater than the genome average by approximately threefold and fourfold. We examined factors that may affect the frequency of duplication in a region. Within individual chromosomes, the duplication frequency shows little correlation with local gene density, repeat density, recombination rate, and GC content, except chromosomes 7 and Y. For the entire genome, the duplication frequency is correlated with each of the above factors. Based on known genes and Ensembl genes, the proportion of duplications containing complete genes is 3.4% and 10.7%, respectively. The proportion of duplications containing genes is higher in intrachromosomal than in interchromosomal duplications, and duplications containing genes have a higher sequence similarity and tend to be longer than duplications containing no genes. Our simulation suggests that many duplications containing genes have been selectively maintained in the genome.}, } @article {pmid15370344, year = {2004}, author = {Sadowski, LS and Hunter, WM and Bangdiwala, SI and Muñoz, SR}, title = {The world studies of abuse in the family environment (WorldSAFE): a model of a multi-national study of family violence.}, journal = {Injury control and safety promotion}, volume = {11}, number = {2}, pages = {81-90}, doi = {10.1080/15660970412331292306}, pmid = {15370344}, issn = {1566-0974}, mesh = {Brazil/epidemiology ; Chile/epidemiology ; Cooperative Behavior ; Cross-Sectional Studies ; Domestic Violence/*statistics & numerical data ; Egypt/epidemiology ; *Epidemiologic Research Design ; Health Surveys ; Humans ; India/epidemiology ; *International Cooperation ; Philippines/epidemiology ; }, abstract = {The World Studies of Abuse in the Family Environment (WorldSAFE) designed and implemented a study of family violence--intimate partner violence and child abuse and neglect--using standardized methods to cover over 12,000 women in eighteen communities within five lesser-developed countries. The rationale, process and methods for developing the population-based survey are described. Standardized methods included common training of investigators and field staff, sampling strategies, eligibility criteria, instruments, data collection methods, operational definitions, analysis strategies and data management. Special features of the WorldSAFE model are described--namely an ecological conceptual framework, an extensive and broad-based dissemination strategy, and community advisory boards. The World Studies of Abuse in the Family Environment (WorldSAFE) Steering Committee and principal investigators are as follows: Bhopal (India): Gandhi Medical College, S.S. Bhambal (MD) and A.K. Upadhyaya (MD). Chapel Hill (USA): University of North Carolina at Chapel Hill, Shrikant Bangdiwala (PhD); Wanda Hunter (MPH); Desmond K. Runyan (MD, DrPH); and Laura S. Sadowski (MD, MPH). Chennai (India): Chennai Medical College, Saradha Suresh (MD) and Shuba Kumar (PhD). Delhi (India): All India Institute of Medical Sciences, R.M. Pandey (PhD). Ismailia (Egypt): Suez Canal University Faculty of Medicine, Fatma Hassan (MD, PhD). Lucknow (India): King George's Medical College, M.K. Mitra (MD) and R.C. Ahuja (MD). Manila (the Philippines): University of the Philippines School of Medicine, Laurie Ramiro (PhD); M. Lourdes Amarillo (MS); Bernadette Madrid (MD). Nagpur (India): Government Medical College, Dipty Jain (MD). São Paulo (Brazil): Escola Paulista de Medicina, Isabel Bordin (MD) and Christine Silvestre De Paula. Temuco (Chile): Universidad de La Frontera, Sergio R. Muñoz (PhD) and Beatriz Vizcarra. Thiruvananthapuram (India) formerly Trivandrum: Government Medical College, M.K.C. Nair (MD) and Rajamohanan Pillai (MD). Vellore (India): Christian Medical College, L. Jeyaseelan (PhD) and Abraham Peedicayil (MD).}, } @article {pmid15363666, year = {2004}, author = {Winfree, R}, title = {Art Winfree, artist of science.}, journal = {Journal of theoretical biology}, volume = {230}, number = {4}, pages = {441-443}, doi = {10.1016/j.jtbi.2004.02.023}, pmid = {15363666}, issn = {0022-5193}, mesh = {Computational Biology/*history ; History, 20th Century ; History, 21st Century ; Humans ; Teaching ; United States ; }, } @article {pmid15357285, year = {2004}, author = {Hur, I and Chun, J}, title = {A method for comparing multiple bacterial community structures from 16S rDNA clone library sequences.}, journal = {Journal of microbiology (Seoul, Korea)}, volume = {42}, number = {1}, pages = {9-13}, pmid = {15357285}, issn = {1225-8873}, mesh = {Algorithms ; Bacteria/*genetics/*growth & development ; Cluster Analysis ; Computational Biology ; DNA, Bacterial/analysis/isolation & purification ; DNA, Ribosomal/*chemistry/isolation & purification ; Ecosystem ; *Environmental Microbiology ; *Gene Library ; Genes, rRNA ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Alignment ; *Sequence Analysis, DNA ; Software ; }, abstract = {Culture-independent approaches, based on 16S rDNA sequences, are extensively used in modern microbial ecology. Sequencing of the clone library generated from environmental DNA has advantages over fingerprint-based methods, such as denaturing gradient gel electrophoresis, as it provides precise identification and quantification of the phylotypes present in samples. However, to date, no method exists for comparing multiple bacterial community structures using clone library sequences. In this study, an automated method to achieve this has been developed, by applying pair wise alignment, hierarchical clustering and principle component analysis. The method has been demonstrated to be successful in comparing samples from various environments. The program, named CommCluster, was written in JAVA, and is now freely available, at http://chunlab.snu.ac.kr/commcluster/.}, } @article {pmid15350890, year = {2004}, author = {Davis, GA}, title = {Possible aggregation biases in road safety research and a mechanism approach to accident modeling.}, journal = {Accident; analysis and prevention}, volume = {36}, number = {6}, pages = {1119-1127}, doi = {10.1016/j.aap.2004.04.002}, pmid = {15350890}, issn = {0001-4575}, mesh = {Accidents, Traffic/*prevention & control/*statistics & numerical data ; Bias ; Causality ; Data Interpretation, Statistical ; Humans ; *Models, Theoretical ; }, abstract = {In accident reconstruction, individual road accidents are treated as essentially deterministic events, although incomplete information can leave one uncertain about how exactly an accident happened. In statistical studies, on the other hand, accidents are treated as individually random, although the parameters governing their probability distributions may be modeled deterministically. Here, a simple deterministic model of a vehicle/pedestrian encounter is used to illustrate how naïvely applying statistical methods to aggregated data could lead to an ecological fallacy and to Simpson's paradox. It is suggested that these problems occur because the statistical regularities observed in accident data have no independent status, but are simply the result of aggregating particular types and frequencies of mechanisms.}, } @article {pmid15347521, year = {2004}, author = {Leimu, R and Koricheva, J}, title = {Cumulative meta-analysis: a new tool for detection of temporal trends and publication bias in ecology.}, journal = {Proceedings. Biological sciences}, volume = {271}, number = {1551}, pages = {1961-1966}, pmid = {15347521}, issn = {0962-8452}, mesh = {Carbon/analysis ; Data Interpretation, Statistical ; Ecology/*methods/trends ; *Meta-Analysis as Topic ; Nitrogen/analysis ; Periodicals as Topic ; Plant Physiological Phenomena ; Publication Bias/*trends ; Time Factors ; }, abstract = {Temporal changes in the magnitude of research findings have recently been recognized as a general phenomenon in ecology, and have been attributed to the delayed publication of non-significant results and disconfirming evidence. Here we introduce a method of cumulative meta-analysis which allows detection of both temporal trends and publication bias in the ecological literature. To illustrate the application of the method, we used two datasets from recently conducted meta-analyses of studies testing two plant defence theories. Our results revealed three phases in the evolution of the treatment effects. Early studies strongly supported the hypothesis tested, but the magnitude of the effect decreased considerably in later studies. In the latest studies, a trend towards an increase in effect size was observed. In one of the datasets, a cumulative meta-analysis revealed publication bias against studies reporting disconfirming evidence; such studies were published in journals with a lower impact factor compared to studies with results supporting the hypothesis tested. Correlation analysis revealed neither temporal trends nor evidence of publication bias in the datasets analysed. We thus suggest that cumulative meta-analysis should be used as a visual aid to detect temporal trends and publication bias in research findings in ecology in addition to the correlative approach.}, } @article {pmid15326304, year = {2004}, author = {Guindon, S and Rodrigo, AG and Dyer, KA and Huelsenbeck, JP}, title = {Modeling the site-specific variation of selection patterns along lineages.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {101}, number = {35}, pages = {12957-12962}, pmid = {15326304}, issn = {0027-8424}, support = {R01 GM069801/GM/NIGMS NIH HHS/United States ; GM-69801/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acid Substitution ; Data Interpretation, Statistical ; Gene Products, env/genetics ; *Genetic Variation ; HIV-1/genetics ; Likelihood Functions ; Phylogeny ; *Selection, Genetic ; Sequence Analysis, Protein ; Sequence Analysis, RNA ; }, abstract = {The unambiguous footprint of positive Darwinian selection in protein-coding DNA sequences is revealed by an excess of nonsynonymous substitutions over synonymous substitutions compared with the neutral expectation. Methods for analyzing the patterns of nonsynonymous and synonymous substitutions usually rely on stochastic models in which the selection regime may vary across the sequence but remains constant across lineages for any amino acid position. Despite some work that has relaxed the constraint that selection patterns remain constant over time, no model provides a strong statistical framework to deal with switches between selection processes at individual sites during the course of evolution. This paper describes an approach that allows the site-specific selection process to vary along lineages of a phylogenetic tree. The parameters of the switching model of codon substitution are estimated by using maximum likelihood. The analysis of eight HIV-1 env homologous sequence data sets shows that this model provides a significantly better fit to the data than one that does not take into account switches between selection patterns in the phylogeny at individual sites. We also provide strong evidence that the strength and the frequency of occurrence of selection might not be estimated accurately when the site-specific variation of selection regimes is ignored.}, } @article {pmid15320385, year = {2004}, author = {Chen, W and Xiao, D and Zheng, J and Guo, F and Jiang, Y}, title = {[Forest landscape change and its driving force during past ten years in Bilahe forest region, Inner Mongolia].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {15}, number = {5}, pages = {741-747}, pmid = {15320385}, issn = {1001-9332}, mesh = {Agriculture ; Biodiversity ; China ; Conservation of Natural Resources ; *Ecosystem ; *Environmental Monitoring ; Fires ; Geographic Information Systems ; *Trees ; }, abstract = {Based on RS and GIS, this paper studied the forest landscape change during the past ten years in Bilahe forest region, Inner Mongolia, from the aspects of general landscape features, individual patch characteristics, and relationship among patches. The results showed that the forest landscape changed a lot due to the stronger human intervention on forest ecosystem. The general tendency was that the human patches (residential area and cultivated land) were! expanding quickly, whereas the natural patches (forest patches, etc.) were shrinking gradually. The results of area transformation matrix showed that in 1997, 30.87% of cultivated lands were transformed from Quercus mongolica. According to the analysis of landscape heterogeneity, the patches were increased by 68.80%, but their average area was reduced by 4.82%. In 1988, the landscape dominated by few patches changed to a landscape with comparatively even distribution of patches, due to the decrease of landscape dominance and contagion, and the increase of landscape diversity. Based on the analyses of physical geography and social economics in the study area and the regions related, this paper discovered that the most decisive driving forces of landscape changes were fire intervention, deforestation, and reclamation of virgin land.}, } @article {pmid15310087, year = {2004}, author = {Fast, J and Keating, N and Otfinowski, P and Derksen, L}, title = {Characteristics of family/friend care networks of frail seniors.}, journal = {Canadian journal on aging = La revue canadienne du vieillissement}, volume = {23}, number = {1}, pages = {5-19}, doi = {10.1353/cja.2004.0003}, pmid = {15310087}, issn = {0714-9808}, mesh = {Aged ; Aged, 80 and over ; Community Networks/*statistics & numerical data ; Data Collection ; Female ; *Frail Elderly ; Home Nursing/*statistics & numerical data ; Humans ; Male ; Middle Aged ; }, abstract = {This paper tests assumptions often made by policy makers and practitioners that networks of family, friends, and neighbours are able to provide sustained care to frail elderly Canadians. Using national survey data, we examined characteristics of the care networks of 1,104 seniors living with a long-term health problem. Care networks were found to vary considerably in size, relationship composition, gender composition, age composition, and proximity, and these network characteristics were found to help explain variations in the types and amounts of care received. As a result, network characteristics that might place seniors at risk of receiving inadequate care (including small size and higher proportions of non-kin, male, and geographically distant members) were identified. These risk factors appear to be poorly reflected in most existing policy.}, } @article {pmid15305919, year = {2004}, author = {Teeling, H and Meyerdierks, A and Bauer, M and Amann, R and Glöckner, FO}, title = {Application of tetranucleotide frequencies for the assignment of genomic fragments.}, journal = {Environmental microbiology}, volume = {6}, number = {9}, pages = {938-947}, doi = {10.1111/j.1462-2920.2004.00624.x}, pmid = {15305919}, issn = {1462-2912}, mesh = {Bacteria/*genetics ; Base Composition ; Databases, Genetic ; *Genome, Bacterial ; Genomics/*methods ; Likelihood Functions ; Nucleotides/*genetics ; Species Specificity ; }, abstract = {A basic problem of the metagenomic approach in microbial ecology is the assignment of genomic fragments to a certain species or taxonomic group, when suitable marker genes are absent. Currently, the (G + C)-content together with phylogenetic information and codon adaptation for functional genes is mostly used to assess the relationship of different fragments. These methods, however, can produce ambiguous results. In order to evaluate sequence-based methods for fragment identification, we extensively compared (G + C)-contents and tetranucleotide usage patterns of 9054 fosmid-sized genomic fragments generated in silico from 118 completely sequenced bacterial genomes (40 982 931 fragment pairs were compared in total). The results of this systematic study show that the discriminatory power of correlations of tetranucleotide-derived z-scores is by far superior to that of differences in (G + C)-content and provides reasonable assignment probabilities when applied to metagenome libraries of small diversity. Using six fully sequenced fosmid inserts from a metagenomic analysis of microbial consortia mediating the anaerobic oxidation of methane (AOM), we demonstrate that discrimination based on tetranucleotide-derived z-score correlations was consistent with corresponding data from 16S ribosomal RNA sequence analysis and allowed us to discriminate between fosmid inserts that were indistinguishable with respect to their (G + C)-contents.}, } @article {pmid15305690, year = {2004}, author = {Rinaldi, L and Cascone, C and Sibilio, G and Musella, V and Taddei, R and Cringoli, G}, title = {[Geographical Information Systems and remote sensing technologies in parasitological epidemiology].}, journal = {Parassitologia}, volume = {46}, number = {1-2}, pages = {71-74}, pmid = {15305690}, issn = {0048-2951}, mesh = {Animals ; Geographic Information Systems/instrumentation ; Humans ; Parasitic Diseases/*epidemiology ; *Satellite Communications/instrumentation ; Topography, Medical/instrumentation/*methods ; }, abstract = {Parasites have natural habitats in the same way as a species: they are found in focal areas where the spatial distribution of the parasite, host, vector and required environmental conditions coincide. The spatial distribution of parasites is, therefore, a function of the interaction between abiotic and biotic environmental factors. The boundaries of distributions are not strictly fixed in space and time and may fluctuate with climate and other components of the environment or anthropical factors. Geographic Information Systems (GIS) and remote sensing (RS) technologies are being used increasingly to study the spatial and temporal patterns of disease. GIS can be used to complement conventional ecological monitoring and modelling techniques, and provide means to portray complex relationships in the ecology of disease. In addition, the use of GIS and RS to identify environmental features allows determination of risk factors and delimitation of areas at risk, permitting more rational allocation of resources for cost-effective control. Since 1996, GIS have been used in our territorial cross-sectional and longitudinal parasitological surveys in order to experiment new applications to plan sampling protocols and to display quickly, clearly, and analytically the spatial and/or temporal distribution of parasitological data. The use of GIS allowed us to draw the following types of descriptive parasitological maps: distribution maps, distribution maps with proportioned peaks, choroplethic maps with proportioned peaks, point distribution maps and point distribution maps with proportioned peaks. In a recent study, GIS and RS technologies have been used also to identify environmental features that influence the distribution of paramphistomosis in sheep from the southern Italian Apennines and to develop a preliminary risk assessment model. A GIS was constructed using RS and landscape feature data together with paramphistome positive survey records from 197 georeferenced ovine farms with animals pasturing in an area of the southern Italian Apennines. The GIS for the study area was constructed utilizing the following environmental variables: Normalized Difference Vegetation Index (NDVI), land cover, elevation, slope, aspect, and total length of rivers. In addition, data regarding the presence of watercourses smaller than rivers, namely, streams, springs and brooks were recorded in the field. All these variables were then calculated for "buffer zones" consisting of the areas included in a circle of 3 Km diameter centred on 197 farms. The environmental data obtained were analyzed by univariate and multivariate statistical analyses using the paramphistome farm coprological status (positive/negative) as the dependent variable. A multivariate stepwise discriminant analysis model was developed that included moors and heathland, sclerophyllus and coniferous forest vegetation, autumn-winter NDVI and presence of streams, springs and brooks on pasture. The variables entered in the model are consistent with the environmental requirements of paramphistomes and their snail intermediate host. In particular, the land cover types entered in the model in this area are indicators of marginal uncultivable and sloping zones where typically there is the presence of water (permanently or temporarily). In addition, since NDVI can be used as an indicator of regional thermal-moisture regime, the distribution of farms positive for paramphistomosis corresponding to relatively high values of winter NDVI indicated the presence of adequate moisture and temperatures favourable to the rumen fluke and the snails. In conclusion, GIS and RS are useful to define the habitats of parasites, especially for those with strong environmental determinants, and to produce forecasting maps requested for the planning and the monitoring of control strategies on small and large scale.}, } @article {pmid15305689, year = {2004}, author = {Brianti, E and Malone, JB and McCarroll, JC and Bernardi, M and Drigo, M and Gruszynski, K}, title = {[A minimum medical GIS database (MMDb) for Europe].}, journal = {Parassitologia}, volume = {46}, number = {1-2}, pages = {67-70}, pmid = {15305689}, issn = {0048-2951}, mesh = {Animals ; *Databases, Factual ; Disease Outbreaks ; Disease Reservoirs ; Ecology ; Europe ; *Geographic Information Systems ; Humans ; Parasitic Diseases/epidemiology ; *Topography, Medical ; }, abstract = {Geographic information systems (GIS) and remote sensing (RS) technologies are being used increasingly to study the spatial and temporal patterns of some parasitic diseases of medical and veterinary importance. At the same time, the incorporation of GIS in this field shows the scarcity of the data and images available, which sometime discourage researchers that still look at GIS as a system too difficult and unusable for medical study. Aware of this problem and supported by success of earlier MMDb's for Africa, Asia and South America, the authors' aim is to construct and offer an MMDb for Europe. The initial MMDb is composed with vector images covering an area situated from -11 degrees-70 degrees N to 58 degrees-30 degrees E. Specifically, data layers include: a) Global Moderate-Resolution Imaging Spectroradiometer (MODIS) Normalized Difference Vegetation Index (NDVI) 16 days at 250 m spatial resolution designed to provide consistent spatial and temporal comparisons of vegetation conditions, supplied in the MMDb as seasonal and annual composite images from 2000 to 2003, b) MODIS Land Surface Temperature (LST) calculated from daytime and nighttime observations at 8 day intervals at 1 km spatial resolution, supplied in the MMDb as seasonal and annual composites images for day (maximum) temperatures, night (minimum) temperatures from 2000 to 2003, c) GTOPO30 Digital Elevation Model (DEM) at 1 km spatial resolution, d) United States Geological Survey (USGS) Land use/land cover scheme, e) USGS actual and potential evapotranspiration supplied for all 12 months as a grid at 50 km spatial resolution, f) USGS precipitation showing the amount of rainfall for all 12 months supplied as a grid at 50 km spatial resolution, g) USGS shapefiles of administrative and political boundaries, cities, towns, villages, lakes, rivers, streams, road, railroads and more. The MMDb projection will be in geographic latitude-longitude, decimal degree format. This global format is most commonly used for public access map database resources and can be readily re-projected as needed for compatibility with various national mapping systems. There is no "required" software, and end users need only common commercial GIS software packages that have mutual import-export functions. Additionally, the MMDb is meant to be a dynamic resource that end users may improve and modify with other regional data.}, } @article {pmid15305688, year = {2004}, author = {Taddei, R}, title = {[Pheno-climatic profiles of vegetation based on multitemporal analysis of satellite data].}, journal = {Parassitologia}, volume = {46}, number = {1-2}, pages = {63-66}, pmid = {15305688}, issn = {0048-2951}, mesh = {Biomass ; *Climate ; *Ecology ; Fourier Analysis ; *Geographic Information Systems/instrumentation ; Italy ; Models, Biological ; Photosynthesis ; *Plants ; Rain ; *Satellite Communications ; Seasons ; Sunlight ; Temperature ; Topography, Medical/instrumentation/methods ; }, abstract = {Satellite Remote Sensing offers numerous advantages: study of large areas in a short time, study of areas with not easy accessibility, synoptic observation of territory, multitemporal observations of the same area, monitoring land modifications and change detection studies. The effectiveness of using satellite images for studying and mapping vegetation and land use has been stressed since the early 1980s. The photosynthetically active vegetation presents a very characteristic spectral response. In fact, leaves absorb red radiation (RED) in order to do photosynthetic process and reflect almost completely near infrared (NIR) wavelengths. The most diffused index for quantifying photosynthetically active biomass is the NDVI (Normalized Difference Vegetation Index): NDVI = (NIR-RED)/(NIR+RED). The NDVI is calculated, for each pixel of the images analysed, through an appropriate software. Low values of NDVI correspond to scarcely vegetated areas, while high values indicate densely vegetated ones. In order to distinguish among vegetation typologies we need some images of the same territory, well distributed during the year, showing seasonal variations of vegetation photosynthetic activity. Then it will be e.g. very easy distinguish between evergreen species (with NDVI almost steady during the year) and deciduous ones. Several types of sensors aboard some satellites allow different investigations to be done. AVHRR sensor on NOAA and TM sensor on Landsat are among the best known sensors available. They have different characteristics as for spectral resolution (number of spectral bands), spatial resolution (size of each elementary cell) and temporal resolution (the period of the satellite passes on the same territory). Vegetation phenology (including biomass and photosynthetic activity) heavily depends on climatic factors. The most important are: solar radiance, with an annual cycle and maximum at summer solstice; air temperature, (depending on solar radiance) with an annual cycle and maximum more than one month later; water availability, which is strongly dependent on rainfalls; in the Mediterranean area they can have an annual cycle (maximum during winter) or a six-monthly one (maxima near the equinoxes). Having a set of multitemporal satellite data (e.g. 12 monthly NOAA-AVHRR images) we can use a mathematical model able to discriminate annual and six-monthly cycles. Through Fourier analysis, the mathematical model calculate, for each pixel of the image, the parameters of the annual NDVI profile and create a synthetic image (pheno-climatic map), in which the values of the three RGB components (Red, Green, Blue) are proportional to the integral of the NDVI profile for the following three periods: B=Nov-Feb G=Mar-Jun R=Jul-Oct. A similarly analysis is possible with Landsat satellite data, which have a higher spatial resolution, given that some shrewdness are taken. In fact, it is necessary to select satellite images according to the presence of cloud cover, which is--over the Italian peninsula--quite common during the March-April and October-November intervals. The purpose of carrying out pheno-climatic maps can be accomplished using 6 Landsat-TM images well-distributed during a year, every two months, even if the images have been taken during different years.}, } @article {pmid15294355, year = {2004}, author = {Van Der Perk, M and Burema, J and Vandenhove, H and Goor, F and Timofeyev, S}, title = {Spatial assessment of the economic feasibility of short rotation coppice on radioactively contaminated land in Belarus, Ukraine, and Russia. II. Monte Carlo analysis.}, journal = {Journal of environmental management}, volume = {72}, number = {4}, pages = {233-240}, doi = {10.1016/j.jenvman.2004.05.001}, pmid = {15294355}, issn = {0301-4797}, mesh = {Bioelectric Energy Sources/*statistics & numerical data ; Biomass ; Cesium Radioisotopes/analysis ; *Geographic Information Systems ; Incineration ; *Models, Theoretical ; Monte Carlo Method ; Republic of Belarus ; Russia ; Salix/*growth & development ; Ukraine ; }, abstract = {A Monte Carlo analysis of two sequential GIS-embedded submodels, which evaluate the economic feasibility of short rotation coppice (SRC) production and energy conversion in areas contaminated by Chernobyl-derived (137)Cs, was performed to allow for variability of environmental conditions that was not contained in the spatial model inputs. The results from this analysis were compared to the results from the deterministic model presented in part I of this paper. It was concluded that, although the variability in the model results due to within-gridcell variability of the model inputs was considerable, the prediction of the areas where SRC and energy conversion is potentially profitable was robust. If the additional variability in the model input that is not contained in the input maps is also taken into account, the SRC production and energy conversion appears to be potentially profitable at more locations for both the small scale and large scale production scenarios than the model predicted using the deterministic model.}, } @article {pmid15294354, year = {2004}, author = {Perk Mv, Mv and Burema, J and Vandenhove, H and Goor, F and Timofeyev, S}, title = {Spatial assessment of the economic feasibility of short rotation coppice on radioactively contaminated land in Belarus, Ukraine, and Russia. I. Model description and scenario analysis.}, journal = {Journal of environmental management}, volume = {72}, number = {4}, pages = {217-232}, doi = {10.1016/j.jenvman.2004.05.002}, pmid = {15294354}, issn = {0301-4797}, mesh = {Bioelectric Energy Sources/*economics ; Biomass ; Cesium Radioisotopes/analysis ; *Chernobyl Nuclear Accident ; Cost-Benefit Analysis ; *Geographic Information Systems ; Incineration ; *Models, Theoretical ; Republic of Belarus ; Russia ; Salix/*growth & development ; *Soil Pollutants, Radioactive ; Ukraine ; }, abstract = {The economic feasibility of short rotation coppice (SRC) production and energy conversion in areas contaminated by Chernobyl-derived (137)Cs was evaluated taking the spatial variability of environmental conditions into account. Two sequential GIS-embedded submodels were developed for a spatial assessment, which allow for spatial variation in soil contamination, soil type, and land use. These models were applied for four SRC production and four energy conversion scenarios for the entire contaminated area of Ukraine, Belarus, and Russia and for a part of the Bragin district, Belarus. It was concluded that in general medium-scale SRC production using local machines is most profitable. The areas near Chernobyl are not suitable for SRC production since the contamination levels in SRC wood exceed the intervention limit. Large scale SRC production is not profitable in areas where dry and sandy soils predominate. If the soil contamination does not exceed the intervention limit and sufficient SRC wood is available, all energy conversion scenarios are profitable.}, } @article {pmid15289485, year = {2004}, author = {Hill, JE and Penny, SL and Crowell, KG and Goh, SH and Hemmingsen, SM}, title = {cpnDB: a chaperonin sequence database.}, journal = {Genome research}, volume = {14}, number = {8}, pages = {1669-1675}, pmid = {15289485}, issn = {1088-9051}, mesh = {Animals ; Bacteria/genetics ; Base Sequence ; Chaperonin 60/*genetics ; Computational Biology ; Databases, Genetic ; Molecular Sequence Data ; Sequence Homology, Nucleic Acid ; }, abstract = {Type I chaperonins are molecular chaperones present in virtually all bacteria, some archaea and the plastids and mitochondria of eukaryotes. Sequences of cpn60 genes, encoding 60-kDa chaperonin protein subunits (CPN60, also known as GroEL or HSP60), are useful for phylogenetic studies and as targets for detection and identification of organisms. Conveniently, a 549-567-bp segment of the cpn60 coding region can be amplified with universal PCR primers. Here, we introduce cpnDB, a curated collection of cpn60 sequence data collected from public databases or generated by a network of collaborators exploiting the cpn60 target in clinical, phylogenetic, and microbial ecology studies. The growing database currently contains approximately 2000 records covering over 240 genera of bacteria, eukaryotes, and archaea. The database also contains over 60 sequences for the archaeal Type II chaperonin (thermosome, a homolog of eukaryotic cytoplasmic chaperonin) from 19 archaeal genera. As the largest curated collection of sequences available for a protein-encoding gene, cpnDB provides a resource for researchers interested in exploiting the power of cpn60 as a diagnostic or as a target for phylogenetic or microbial ecology studies, as well as those interested in broader subjects such as lateral gene transfer and codon usage. We built cpnDB from open source tools and it is available at http://cpndb.cbr.nrc.ca.}, } @article {pmid15288523, year = {2004}, author = {Burney, DA and Burney, LP and Godfrey, LR and Jungers, WL and Goodman, SM and Wright, HT and Jull, AJ}, title = {A chronology for late prehistoric Madagascar.}, journal = {Journal of human evolution}, volume = {47}, number = {1-2}, pages = {25-63}, doi = {10.1016/j.jhevol.2004.05.005}, pmid = {15288523}, issn = {0047-2484}, mesh = {Animals ; *Biological Evolution ; Birds ; Carbon Radioisotopes/analysis ; Databases, Factual ; Ecology ; *Food Chain ; *Fossils ; History, Ancient ; Humans ; Lemur ; Madagascar ; Mammals ; Population Dynamics ; Reptiles ; Tooth ; }, abstract = {A database has been assembled with 278 age determinations for Madagascar. Materials 14C dated include pretreated sediments and plant macrofossils from cores and excavations throughout the island, and bones, teeth, or eggshells of most of the extinct megafaunal taxa, including the giant lemurs, hippopotami, and ratites. Additional measurements come from uranium-series dates on speleothems and thermoluminescence dating of pottery. Changes documented include late Pleistocene climatic events and, in the late Holocene, the apparently human-caused transformation of the environment. Multiple lines of evidence point to the earliest human presence at ca. 2300 14C yr BP (350 cal yr BC). A decline in megafauna, inferred from a drastic decrease in spores of the coprophilous fungus Sporormiella spp. in sediments at 1720+/-40 14C yr BP (230-410 cal yr AD), is followed by large increases in charcoal particles in sediment cores, beginning in the SW part of the island, and spreading to other coasts and the interior over the next millennium. The record of human occupation is initially sparse, but shows large human populations throughout the island by the beginning of the Second Millennium AD. Dating of the "subfossil" megafauna, including pygmy hippos, elephant birds, giant tortoises, and large lemurs, demonstrates that most if not all the extinct taxa were still present on the island when humans arrived. Many taxa overlapped chronologically with humans for a millennium or more. The extinct lemurs Hadropithecus stenognathus, Pachylemur insignis, Mesopropithecus pithecoides, and Daubentonia robusta, and the elephant birds Aepyornis spp. and Mullerornis spp., were still present near the end of the First Millennium AD. Palaeopropithecus ingens, Megaladapis edwardsi, and Archaeolemur sp. (cf. edwardsi) may have survived until the middle of the Second Millennium A.D. One specimen of Hippopotamus of unknown provenance dates to the period of European colonization.}, } @article {pmid15285399, year = {2004}, author = {Keramitsoglou, I and Kiranoudis, CT and Sarimveis, H and Sifakis, N}, title = {A multidisciplinary decision support system for forest fire crisis management.}, journal = {Environmental management}, volume = {33}, number = {2}, pages = {212-225}, doi = {10.1007/s00267-003-0092-4}, pmid = {15285399}, issn = {0364-152X}, mesh = {Communication ; *Decision Support Techniques ; *Disaster Planning ; Environmental Monitoring ; Europe ; *Fires ; *Forestry ; *Geographic Information Systems ; Humans ; }, abstract = {A wildland fire is a serious threat for forest ecosystems in Southern Europe affecting severely and irreversibly regions of significant ecological value as well as human communities. To support decision makers during large-scale forest fire incidents, a multidisciplinary system has been developed that provides rational and quantitative information based on the site-specific circumstances and the possible consequences. The system's architecture consists of several distinct supplementary modules of near real-time satellite monitoring and fire forecast using an integrated framework of satellite Remote Sensing, GIS, and RDBMS technologies equipped with interactive communication capabilities. The system may handle multiple fire ignitions and support decisions regarding dispatching of utilities, equipment, and personnel that would appropriately attack the fire front. The operational system was developed for the region of Penteli Mountain in Attika, Greece, one of the mountain areas in the country most hit by fires. Starting from a real fire incident in August 2000, a scenario is presented to illustrate the effectiveness of the proposed approach.}, } @article {pmid15285375, year = {2004}, author = {Carlsen, TM and Coty, JD and Kercher, JR}, title = {The spatial extent of contaminants and the landscape scale: an analysis of the wildlife, conservation biology, and population modeling literature.}, journal = {Environmental toxicology and chemistry}, volume = {23}, number = {3}, pages = {798-811}, doi = {10.1897/02-202}, pmid = {15285375}, issn = {0730-7268}, mesh = {*Conservation of Natural Resources ; *Demography ; *Environment ; Environmental Pollutants/*analysis ; Geographic Information Systems ; *Models, Biological ; Models, Chemical ; }, abstract = {Many contaminant releases to the terrestrial environment are of small areal extent. Thus, rather than evaluating the ecological impact on species in the immediate vicinity of the release, it may be more ecologically meaningful to determine if population impacts occur at the landscape level. In order to do this, the cumulative impact of all releases in the landscape under consideration must be evaluated. If the release sites are viewed as localized areas that are no longer available for use by ecological receptors (i.e., no longer part of the habitat), this can be thought of as a form of habitat fragmentation. Habitat fragmentation is typically viewed as the loss of large areas of habitat within a landscape, leaving small isolated patches of intact habitat within a hostile matrix. Small-scale contaminant releases, on the other hand, result in small uninhabitable areas within a primarily intact habitat. With this consideration in mind, we analyzed the wildlife and conservation biology literature to determine if information on habitat size requirements such as home-range or critical patch size could inform us about the potential for impact at the landscape level from release sites based on the size of the release alone. We determined that evaluating the impact of release size had to be conducted within a contextual basis (considering the existing state of the landscape). Therefore, we also reviewed the population modeling literature to determine if models could be developed to further evaluate the impact of the spatial extent of chemical releases on the landscape. We identified individual-based models linked to geographic information systems to have the greatest potential in investigating the role of release size with respect to population impacts at the landscape level.}, } @article {pmid15285146, year = {2004}, author = {Rinaldi, L and Otranto, D and Veneziano, V and Milillo, P and Buono, V and Iori, A and Di Giulio, G and Cringoli, G}, title = {Cross-sectional survey of ticks (Acari: Ixodidae) in sheep from an area of the southern Italian Apennines.}, journal = {Experimental & applied acarology}, volume = {33}, number = {1-2}, pages = {145-151}, pmid = {15285146}, issn = {0168-8162}, mesh = {Animals ; Cross-Sectional Studies ; Geographic Information Systems ; Italy/epidemiology ; Ixodidae/*growth & development ; Sheep ; Sheep Diseases/epidemiology/*parasitology ; Tick Infestations/epidemiology/*veterinary ; }, abstract = {A cross-sectional survey of ticks was conducted on 197 ovine farms with animals pasturing in an area (3971 km2) of the southern Italian Apennines. The farms were selected to be uniformly distributed throughout the study area using Geographical Information System (GIS). Ticks were collected from 309 (31.4%) out of the 985 sheep sampled, belonging to 92 (46.7%) out of the 197 farms included in the study. The following tick species were found (farm prevalence): Dermacentor marginatus (37.6%), Haemaphysalis punctata (29.4%), H. sulcata (2.5%), H. parva (2.0%). H. inermis (0.5%), Ixodes gibbosus (2.0%), I. ricinus (0.5%), Rhipicephalus sanguineus group (1.0%), and R. bursa (0.5%). A point distribution map (PDM) was drawn by GIS in order to display the distribution of each tick genus in the study area. The general trends of the PDM show that Dermacentor marginatus and Haemaphysalis spp. were widely and homogeneously spread throughout the study area, whereas Rhipicephalus spp. and Ixodes spp. were present only in a few concentrated zones of the study area in accordance to their biological and ecological characteristics.}, } @article {pmid15279174, year = {2004}, author = {Cavalcanti, AR and Leite, ES and Neto, BB and Ferreira, R}, title = {On the classes of aminoacyl-tRNA synthetases, amino acids and the genetic code.}, journal = {Origins of life and evolution of the biosphere : the journal of the International Society for the Study of the Origin of Life}, volume = {34}, number = {4}, pages = {407-420}, doi = {10.1023/b:orig.0000029881.14519.42}, pmid = {15279174}, issn = {0169-6149}, mesh = {Amino Acids/chemistry/*classification ; Amino Acyl-tRNA Synthetases/*classification ; Databases as Topic ; Evolution, Molecular ; *Genetic Code ; Phylogeny ; }, abstract = {The division of the aminoacyl-tRNA synthetases in two classes is compared with a division of the amino acids in two classes, obtained from the AAIndex databank by a principal component analysis. The division of the enzymes in Classes I and II follows to a great extent a division in the chemical and biological properties of their cognate amino acids. Furthermore, the phylogenetic trees of Classes I and II enzymes are highly correlated with dendrograms obtained for their cognate amino acids by using the indices in the AAIndex database. We argue that the evolution of aminoacyl-tRNA synthetases was determined by the characteristics of their corresponding amino acids. We interpret these results considering models for the origin and evolution of the genetic code in which an initial version, containing fewer amino acids, was modified by the incorporation of new amino acids following duplication and divergence of previous synthetases and tRNA molecules.}, } @article {pmid15274745, year = {2004}, author = {Williams, CJ and Willocks, LJ and Lake, IR and Hunter, PR}, title = {Geographic correlation between deprivation and risk of meningococcal disease: an ecological study.}, journal = {BMC public health}, volume = {4}, number = {}, pages = {30}, pmid = {15274745}, issn = {1471-2458}, mesh = {Adolescent ; Age Distribution ; Censuses ; Child ; Child, Preschool ; Cluster Analysis ; England/epidemiology ; *Geographic Information Systems ; Humans ; Incidence ; Infant ; Meningococcal Infections/economics/*epidemiology/microbiology ; Neisseria meningitidis/pathogenicity ; Poisson Distribution ; *Poverty Areas ; Public Health Informatics ; Risk Factors ; Social Class ; Topography, Medical/methods ; Urban Health/statistics & numerical data ; }, abstract = {BACKGROUND: Meningitis caused by Neisseria meningitidis is a serious infection which is most common in young children and adolescents. This study investigated the relationships between the incidence and age distribution of meningococcal disease, and socioeconomic environment.

METHODS: An ecological design was used, including mapping using a Geographical Information System (GIS) at census ward level.

RESULTS: Incidence of meningococcal disease was highest in the most deprived wards, with a relative risk of 1.97 (1.55 - 2.51). Mapping revealed geographical coincidence of deprivation and meningococcal disease, particularly in urban areas. Two-thirds of the increased incidence was due to cases in the under fives.

CONCLUSIONS: The results suggest that area deprivation is a risk factor for meningococcal disease, and that its effects are seen most in young children.}, } @article {pmid15258959, year = {2004}, author = {Sherwood, CC and Cranfield, MR and Mehlman, PT and Lilly, AA and Garbe, JA and Whittier, CA and Nutter, FB and Rein, TR and Bruner, HJ and Holloway, RL and Tang, CY and Naidich, TP and Delman, BN and Steklis, HD and Erwin, JM and Hof, PR}, title = {Brain structure variation in great apes, with attention to the mountain gorilla (Gorilla beringei beringei).}, journal = {American journal of primatology}, volume = {63}, number = {3}, pages = {149-164}, doi = {10.1002/ajp.20048}, pmid = {15258959}, issn = {0275-2565}, support = {AG14308/AG/NIA NIH HHS/United States ; }, mesh = {Animals ; Autopsy/veterinary ; Biometry ; Brain/*anatomy & histology ; Databases, Factual ; Female ; Gorilla gorilla/*anatomy & histology ; Magnetic Resonance Imaging ; Male ; Pan troglodytes/anatomy & histology ; Pongo pygmaeus/anatomy & histology ; }, abstract = {This report presents data regarding the brain structure of mountain gorillas (Gorilla beringei beringei) in comparison with other great apes. Magnetic resonance (MR) images of three mountain gorilla brains were obtained with a 3T scanner, and the volume of major neuroanatomical structures (neocortical gray matter, hippocampus, thalamus, striatum, and cerebellum) was measured. These data were included with our existing database that includes 23 chimpanzees, three western lowland gorillas, and six orangutans. We defined a multidimensional space by calculating the principal components (PCs) from the correlation matrix of brain structure fractions in the well-represented sample of chimpanzees. We then plotted data from all of the taxa in this space to examine phyletic variation in neural organization. Most of the variance in mountain gorillas, as well as other great apes, was contained within the chimpanzee range along the first two PCs, which accounted for 61.73% of the total variance. Thus, the majority of interspecific variation in brain structure observed among these ape taxa was no greater than the within-species variation seen in chimpanzees. The loadings on PCs indicated that the brain structure of great apes differs among taxa mostly in the relative sizes of the striatum, cerebellum, and hippocampus. These findings suggest possible functional differences among taxa in terms of neural adaptations for ecological and locomotor capacities. Importantly, these results fill a critical gap in current knowledge regarding great ape neuroanatomical diversity.}, } @article {pmid15252969, year = {2004}, author = {Malmqvist, B and Strasevicius, D and Hellgren, O and Adler, PH and Bensch, S}, title = {Vertebrate host specificity of wild-caught blackflies revealed by mitochondrial DNA in blood.}, journal = {Proceedings. Biological sciences}, volume = {271 Suppl 4}, number = {Suppl 4}, pages = {S152-5}, pmid = {15252969}, issn = {0962-8452}, mesh = {Animals ; DNA, Mitochondrial/genetics ; Databases, Nucleic Acid ; Extremities/anatomy & histology ; Feeding Behavior/*physiology ; *Insect Bites and Stings ; Sequence Analysis, DNA ; Simuliidae/anatomy & histology/*physiology ; Species Specificity ; Sweden ; Vertebrates/*genetics ; }, abstract = {Blood-feeding blackflies (Diptera: Simuliidae) transmit pathogens, harass vertebrate hosts and may cause lethal injuries in attacked victims, but with traditional methods it has proved difficult to identify their hosts. By matching mitochondrial DNA (mtDNA) sequences in blood collected from engorged blackflies with stored sequences in the GenBank database, relationships between 17 blackfly species and 25 species of vertebrate hosts were revealed. Our results demonstrate a predominance of large hosts and marked discrimination between blackflies using either avian or mammalian hosts. Such information is of vital interest in studies of disease transmission, coevolutionary relationships, population ecology and wildlife management.}, } @article {pmid15246932, year = {2004}, author = {Graham, AJ and Danson, FM and Giraudoux, P and Craig, PS}, title = {Ecological epidemiology: landscape metrics and human alveolar echinococossis.}, journal = {Acta tropica}, volume = {91}, number = {3}, pages = {267-278}, doi = {10.1016/j.actatropica.2004.05.005}, pmid = {15246932}, issn = {0001-706X}, support = {TWO 1565-02/TW/FIC NIH HHS/United States ; }, mesh = {China/epidemiology ; Disease Transmission, Infectious ; Echinococcosis, Hepatic/*epidemiology/transmission ; Ecology ; Geographic Information Systems ; Humans ; Prevalence ; Space-Time Clustering ; }, abstract = {The larval form of the fox tapeworm Echinococcus multilocularis can cause a potentially fatal liver infection in human hosts. Globally rare, the disease has a high prevalence focus in western China. Recent research has linked landscape to the presence and prevalence of the disease. This paper discusses the epidemiology of E. multilocularis in terms of landscape and disease transmission ecology. Landscape form was defined using satellite imagery to create a land cover classification for a study site in Zhang County (Gansu Province, China). Following the analysis of many landscape metrics, mean shape index was found to be related to the prevalence of infection for 31 villages in 1975 and 1997, at two spatial intervals, suggesting that habitat form is a correlate of disease. A temporal difference shows that the landscape is no longer suitable for transmission. These results indicate the possibility of identifying future hotspots which could aid the management of the disease.}, } @article {pmid15246928, year = {2004}, author = {Graham, AJ and Atkinson, PM and Danson, FM}, title = {Spatial analysis for epidemiology.}, journal = {Acta tropica}, volume = {91}, number = {3}, pages = {219-225}, doi = {10.1016/j.actatropica.2004.05.001}, pmid = {15246928}, issn = {0001-706X}, mesh = {Animals ; Ecology ; *Epidemiology ; *Geographic Information Systems ; Humans ; Space-Time Clustering ; }, abstract = {Remote sensing, geographical information systems (GIS) and spatial analysis provide important tools that are as yet under-exploited in the fight against disease. As the use of such tools becomes more accepted and prevalent in epidemiological studies, so our understanding of the mechanisms of disease systems has the potential to increase. This paper introduces a range of techniques used in remote sensing, GIS and spatial analysis that are relevant to epidemiology. Possible future directions for the application of remote sensing, GIS and spatial analysis are also suggested.}, } @article {pmid15227993, year = {2004}, author = {Zhang, Y and Zhao, S}, title = {[Temporal and spatial change of land use in Horqin Desert and its outer area].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {15}, number = {3}, pages = {429-435}, pmid = {15227993}, issn = {1001-9332}, mesh = {*Agriculture ; Conservation of Natural Resources ; *Desert Climate ; Ecology ; Geographic Information Systems ; }, abstract = {Based on two sets of land use data (1985 and 2000), the land use change in Horqin Desert and its outer area, in both spatial and temporal aspects, was studied with the tools of geographical information system (GIS) and statistics in this paper. Conclusions of this study are drawn as follows: From 1985 to 2000, the area order of individual land use changes was grassland > plough land > forestland > unused land > water body > residential and industrial land. As to the form of changes, the swapping area was greater than its quantitative change for forestland while the quantity change was greater, with different degree, than swap for the rest 5 land use types. As a whole, the quantity change was far greater than its swap. The analysis of land use dynamics showed that the speed of individual land use changes was in order of cultivated land > water body > grassland > forestland > unused land > residential and industrial land in sequence. Meanwhile, there was notable difference of land use change among counties in the region. For plough land change, Zhalute county was the greatest. Naiman the smallest. For forest change, Naiman was the greatest, Kalaqin the smallest. For grassland change, Tongliao city was the greatest, Alukerqin the smallest. For water change, Kezuozhongqi was the greatest, Balinzuoqi the smallest. For residential and industrial land change, Naiman was the greatest, Alukerqin the smallest. Finally, the change of unused land is more obvious in Chifeng city. As to the spatial change, 9 major land use change types were identified. Wherein, the change from grassland to plough land, expanding from the center of Horqin desert towards its outer counties, was still the most important land use change for the whole study area. In addition, the construction of protective forest for grassland in Naiman, the return from plough land to forestland in Kezuozhongqi, the return from plough land to grassland in Tongliao city, the deforestation for plough land in Kukun county, the degradation of grassland in Zhaluteqi, the exploit of river beach in Kailu, the reclamation of unused land in Kezuobouqi, and the regeneration of natural vegetation in Alukerqin were all important regional characteristics of land use change during the past 15 years.}, } @article {pmid15217720, year = {2004}, author = {Huth, A and Drechsler, M and Köhler, P}, title = {Multicriteria evaluation of simulated logging scenarios in a tropical rain forest.}, journal = {Journal of environmental management}, volume = {71}, number = {4}, pages = {321-333}, doi = {10.1016/j.jenvman.2004.03.008}, pmid = {15217720}, issn = {0301-4797}, mesh = {Conservation of Natural Resources/*methods ; Decision Support Techniques ; Ecosystem ; Forestry/*methods ; Malaysia ; Models, Theoretical ; Species Specificity ; *Trees/growth & development ; }, abstract = {Forest growth models are useful tools for investigating the long-term impacts of logging. In this paper, the results of the rain forest growth model FORMIND were assessed by a multicriteria decision analysis. The main processes covered by FORMIND include tree growth, mortality, regeneration and competition. Tree growth is calculated based on a carbon balance approach. Trees compete for light and space; dying large trees fall down and create gaps in the forest. Sixty-four different logging scenarios for an initially undisturbed forest stand at Deramakot (Malaysia) were simulated. The scenarios differ regarding the logging cycle, logging method, cutting limit and logging intensity. We characterise the impacts with four criteria describing the yield, canopy opening and changes in species composition. Multicriteria decision analysis was used for the first time to evaluate the scenarios and identify the efficient ones. Our results plainly show that reduced-impact logging scenarios are more 'efficient' than the others, since in these scenarios forest damage is minimised without significantly reducing yield. Nevertheless, there is a trade-off between yield and achieving a desired ecological state of logged forest; the ecological state of the logged forests can only be improved by reducing yields and enlarging the logging cycles. Our study also demonstrates that high cutting limits or low logging intensities cannot compensate for the high level of damage caused by conventional logging techniques.}, } @article {pmid15216563, year = {2004}, author = {Glad, JA and Kotchian, SB and Barron, GM}, title = {Developing a local comprehensive environment and health tracking system: using what we know to improve health and the environment.}, journal = {Journal of environmental health}, volume = {66}, number = {10}, pages = {9-14, 28}, pmid = {15216563}, issn = {0022-0892}, mesh = {*Community Health Planning ; Databases, Factual ; Environmental Exposure/analysis/prevention & control ; *Environmental Health ; Humans ; Interprofessional Relations ; Organizational Objectives ; Pennsylvania ; Population Surveillance/*methods ; Program Development/*methods ; *Public Health Administration ; }, abstract = {Recent national reports have highlighted the absence of a coordinated local, state, and national environmental health tracking system. Local environmental health agencies are struggling to design and implement data systems that will allow them to evaluate environmental exposures ecological trends, and health outcomes in order to formulate more effective prevention strategies. This paper articulates the need for local environment and health tracking systems, discusses efforts under way around the nation, and describes the initiative being undertaken in one county health department to address this need. It provides information on attributes of indicators to be included in such a system, sources of data, criteria for evaluating the usefulness of indicators, suggestions for involving the community and staff, management strategies for implementing a data system, and recommendations for resolving common barriers to data sharing and use. This information will be useful to agencies that wish to develop their own robust environment and health tracking systems to support the three core functions of public health and the 10 essential public health services.}, } @article {pmid15212376, year = {2004}, author = {Martin, AP and Costello, EK and Meyer, AF and Nemergut, DR and Schmidt, SK}, title = {The rate and pattern of cladogenesis in microbes.}, journal = {Evolution; international journal of organic evolution}, volume = {58}, number = {5}, pages = {946-955}, doi = {10.1111/j.0014-3820.2004.tb00429.x}, pmid = {15212376}, issn = {0014-3820}, mesh = {Archaea/*genetics ; Bacteria/*genetics ; Cluster Analysis ; Databases, Genetic ; Environment ; Gene Transfer, Horizontal/*genetics ; *Genetic Variation ; Geography ; Likelihood Functions ; Models, Genetic ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Soil Microbiology ; Time Factors ; }, abstract = {Theories of macroevolution rarely have been extended to include microbes; however, because microbes represent the most ancient and diverse assemblage of organismal diversity, such oversight limits our understanding of evolutionary history. Our analysis of phylogenetic trees for microbes suggests that macroevolution may differ between prokaryotes and both micro- and macroeukaryotes (mainly plants and animals). Phylogenetic trees inferred for prokaryotes and some microbial eukaryotes conformed to expectations assuming a constant rate of cladogenesis over time and among lineages: nevertheless, microbial eukaryote trees exhibited more variation in rates of cladogenesis than prokaryote trees. We hypothesize that the contrast of macroevolutionary dynamics between prokaryotes and many eukaryotes is due, at least in part, to differences in the prevalence of lateral gene transfer (LGT) between the two groups. Inheritance is predominantly, if not wholly, vertical within eukaryotes, a feature that allows for the emergence and maintenance of heritable variation among lineages. By contrast, frequent LGT in prokaryotes may ameliorate heritable variation in rate of cladogenesis resulting from the emergence of key innovations; thus, the inferred difference in macroevolution might reflect exclusivity of key innovations in eukaryotes and their promiscuous nature in prokaryotes.}, } @article {pmid15198925, year = {2004}, author = {Ferrandiz, J and Abellan, JJ and Gomez-Rubio, V and Lopez-Quilez, A and Sanmartin, P and Abellan, C and Martinez-Beneito, MA and Melchor, I and Vanaclocha, H and Zurriaga, O and Ballester, F and Gil, JM and Perez-Hoyos, S and Ocana, R}, title = {Spatial analysis of the relationship between mortality from cardiovascular and cerebrovascular disease and drinking water hardness.}, journal = {Environmental health perspectives}, volume = {112}, number = {9}, pages = {1037-1044}, pmid = {15198925}, issn = {0091-6765}, mesh = {Adolescent ; Adult ; Aged ; Calcium/*pharmacology ; Cardiovascular Diseases/*mortality/*prevention & control ; Cerebrovascular Disorders/*mortality/*prevention & control ; Child ; Child, Preschool ; Cluster Analysis ; *Environmental Exposure ; Epidemiologic Studies ; Female ; *Geographic Information Systems ; Humans ; Infant ; Infant, Newborn ; Magnesium/*pharmacology ; Male ; Middle Aged ; Reference Values ; Risk Assessment ; Water/*chemistry ; *Water Supply ; }, abstract = {Previously published scientific papers have reported a negative correlation between drinking water hardness and cardiovascular mortality. Some ecologic and case-control studies suggest the protective effect of calcium and magnesium concentration in drinking water. In this article we present an analysis of this protective relationship in 538 municipalities of Comunidad Valenciana (Spain) from 1991-1998. We used the Spanish version of the Rapid Inquiry Facility (RIF) developed under the European Environment and Health Information System (EUROHEIS) research project. The strategy of analysis used in our study conforms to the exploratory nature of the RIF that is used as a tool to obtain quick and flexible insight into epidemiologic surveillance problems. This article describes the use of the RIF to explore possible associations between disease indicators and environmental factors. We used exposure analysis to assess the effect of both protective factors--calcium and magnesium--on mortality from cerebrovascular (ICD-9 430-438) and ischemic heart (ICD-9 410-414) diseases. This study provides statistical evidence of the relationship between mortality from cardiovascular diseases and hardness of drinking water. This relationship is stronger in cerebrovascular disease than in ischemic heart disease, is more pronounced for women than for men, and is more apparent with magnesium than with calcium concentration levels. Nevertheless, the protective nature of these two factors is not clearly established. Our results suggest the possibility of protectiveness but cannot be claimed as conclusive. The weak effects of these covariates make it difficult to separate them from the influence of socioeconomic and environmental factors. We have also performed disease mapping of standardized mortality ratios to detect clusters of municipalities with high risk. Further standardization by levels of calcium and magnesium in drinking water shows changes in the maps when we remove the effect of these covariates.}, } @article {pmid15198921, year = {2004}, author = {Nuckols, JR and Ward, MH and Jarup, L}, title = {Using geographic information systems for exposure assessment in environmental epidemiology studies.}, journal = {Environmental health perspectives}, volume = {112}, number = {9}, pages = {1007-1015}, pmid = {15198921}, issn = {0091-6765}, mesh = {Cluster Analysis ; Ecology ; *Environmental Exposure ; Environmental Pollutants/*poisoning ; *Epidemiologic Studies ; *Geographic Information Systems ; Humans ; Research Design ; Risk Assessment ; }, abstract = {Geographic information systems (GIS) are being used with increasing frequency in environmental epidemiology studies. Reported applications include locating the study population by geocoding addresses (assigning mapping coordinates), using proximity analysis of contaminant source as a surrogate for exposure, and integrating environmental monitoring data into the analysis of the health outcomes. Although most of these studies have been ecologic in design, some have used GIS in estimating environmental levels of a contaminant at the individual level and to design exposure metrics for use in epidemiologic studies. In this article we discuss fundamentals of three scientific disciplines instrumental to using GIS in exposure assessment for epidemiologic studies: geospatial science, environmental science, and epidemiology. We also explore how a GIS can be used to accomplish several steps in the exposure assessment process. These steps include defining the study population, identifying source and potential routes of exposure, estimating environmental levels of target contaminants, and estimating personal exposures. We present and discuss examples for the first three steps. We discuss potential use of GIS and global positioning systems (GPS) in the last step. On the basis of our findings, we conclude that the use of GIS in exposure assessment for environmental epidemiology studies is not only feasible but can enhance the understanding of the association between contaminants in our environment and disease.}, } @article {pmid15193096, year = {2004}, author = {Nirmalakhandan, N}, title = {Computer-aided tutorials and tests for use in distance learning.}, journal = {Water science and technology : a journal of the International Association on Water Pollution Research}, volume = {49}, number = {8}, pages = {65-71}, pmid = {15193096}, issn = {0273-1223}, mesh = {Ecology/*education ; *Educational Technology ; Engineering/*education ; Environmental Monitoring ; Humans ; Information Storage and Retrieval/methods ; Problem-Based Learning ; Programming Languages ; Sewage/analysis ; Software ; User-Computer Interface ; }, abstract = {Compared to the traditional on-campus students, remote students in distance education courses find it more difficult to develop problem-solving skills. In this paper, we propose the use of computer-aided tutorials and tests (CATTs) as convenient tools for remote students to practice and improve problem-solving and test taking skills at their own pace. Example of CATTs developed with Authorware software for use in distance education is presented.}, } @article {pmid15193095, year = {2004}, author = {Souto González, JA and Bello Bugallo, PM and Casares Long, JJ}, title = {Evaluation of air pollution modelling tools as environmental engineering courseware.}, journal = {Water science and technology : a journal of the International Association on Water Pollution Research}, volume = {49}, number = {8}, pages = {57-64}, pmid = {15193095}, issn = {0273-1223}, mesh = {*Air Pollution ; Ecology/*education ; Educational Technology ; Engineering/*education ; Environmental Monitoring ; Humans ; Information Storage and Retrieval/methods ; Models, Chemical ; Problem-Based Learning ; Program Evaluation ; Programming Languages ; User-Computer Interface ; }, abstract = {The study of phenomena related to the dispersion of pollutants usually takes advantage of the use of mathematical models based on the description of the different processes involved. This educational approach is especially important in air pollution dispersion, when the processes follow a non-linear behaviour so it is difficult to understand the relationships between inputs and outputs, and in a 3D context where it becomes hard to analyze alphanumeric results. In this work, three different software tools, as computer solvers for typical air pollution dispersion phenomena, are presented. Each software tool developed to be implemented on PCs, follows approaches that represent three generations of programming languages (Fortran 77, VisualBasic and Java), applied over three different environments: MS-DOS, MS-Windows and the world wide web. The software tools were tested by students of environmental engineering (undergraduate) and chemical engineering (postgraduate), in order to evaluate the ability of these software tools to improve both theoretical and practical knowledge of the air pollution dispersion problem, and the impact of the different environment in the learning process in terms of content, ease of use and visualization of results.}, } @article {pmid15189224, year = {2004}, author = {Kasper, ML and Reeson, AF and Cooper, SJ and Perry, KD and Austin, AD}, title = {Assessment of prey overlap between a native (Polistes humilis) and an introduced (Vespula germanica) social wasp using morphology and phylogenetic analyses of 16S rDNA.}, journal = {Molecular ecology}, volume = {13}, number = {7}, pages = {2037-2048}, doi = {10.1111/j.1365-294X.2004.02193.x}, pmid = {15189224}, issn = {0962-1083}, mesh = {Animals ; Computational Biology ; DNA Primers ; *Diet ; Gastrointestinal Contents/*chemistry ; Phylogeny ; Predatory Behavior/*physiology ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; South Australia ; Species Specificity ; Wasps/genetics/*physiology ; }, abstract = {Abstract In newly invaded communities, interspecific competition is thought to play an important role in determining the success of the invader and its impact on the native community. In southern Australia, the native Polistes humilis was the predominant social wasp prior to the arrival of the exotic Vespula germanica (Hymenoptera: Vespidae). Both species forage for similar resources (water, pulp, carbohydrate and protein prey), and concerns have arisen about potential competition between them. The aim of this study was to identify the protein foods that these wasps feed on. As many prey items are masticated by these wasps to the degree that they cannot be identified using conventional means, morphological identification was complemented by sequencing fragments of the mitochondrial 16S rRNA gene. GenBank searches using blast and phylogenetic analyses were used to identify prey items to at least order level. The results were used to construct complete prey inventories for the two species. These indicate that while P. humilis is restricted to feeding on lepidopteran larvae, V. germanica collects a variety of prey of invertebrate and vertebrate origin. Calculated values of prey overlap between the two species are used to discuss the implications of V. germanica impacting on P. humilis. Results obtained are compared to those gained by solely 'conventional' methods, and the advantages of using DNA-based taxonomy in ecological studies are emphasized.}, } @article {pmid15189000, year = {2002}, author = {Schumaker, AM}, title = {Interorganizational networks: using a theoretical model to predict effectiveness of rural health care delivery networks.}, journal = {Journal of health and human services administration}, volume = {25}, number = {3}, pages = {371-406}, pmid = {15189000}, issn = {1079-3739}, mesh = {Community Networks/*organization & administration ; Delivery of Health Care/*organization & administration ; Efficiency, Organizational ; *Interinstitutional Relations ; *Models, Organizational ; Nebraska ; Rural Health Services/*organization & administration ; }, abstract = {Interorganizational health care delivery networks have potential for sustaining health services delivery in rural areas faced with economic and demographic challenges. Four Nebraska rural health care delivery networks (Albion-Ord, Blue River Valley, Rural Partners, Inc., and Western Nebraska) were compared to an interorganizational model based on theories of interorganizational relations, exchange, population ecology, and synthesized collaboration. It assumes that outcomes, including effectiveness, are influenced by external and internal factors that are operationalized through external control, technology, structure, and operational process variables. Data were collected by a non-random, two-level cluster mail survey of network members (45/59 = 76.3% response rate). All networks received technical assistance from the Nebraska Office of Rural Health. Networks have formal organization, strategic plans, and official coordinators. Hospital administrators hold most leadership positions; few doctors or citizens are involved. Correlation and multiple regression analysis show partial fit between the research model and study networks. Effectiveness, measure by the gap between best possible and actual practice, increased with network connectivity (r=.36, p<.05), group methods of administrative decision-making (r=.52, p<.001) and sequential pattern of service delivery (r=.39, p<.05). Greater dependence on vertical funding corresponds to greater external control (r=.43, p<.01). The prediction that, as scope narrows, task intensity (r=.56, p<.001), duration (r=.41, p<.01), and task volume (r=.50, p<.01) increase is upheld. Centrality and network size decrease together (r=.43, p<.01) where there is little reliance on vertical sources of funds (r=.36, p<.05). The integrated interorganizational model demonstrates some efficacy for testing potential effectiveness of networks.}, } @article {pmid15188718, year = {2004}, author = {Kistemann, T and Zimmer, S and Vågsholm, I and Andersson, Y}, title = {GIS-supported investigation of human EHEC and cattle VTEC O157 infections in Sweden: geographical distribution, spatial variation and possible risk factors.}, journal = {Epidemiology and infection}, volume = {132}, number = {3}, pages = {495-505}, doi = {10.1017/s0950268803001729}, pmid = {15188718}, issn = {0950-2688}, mesh = {Adolescent ; Adult ; Aged ; Agriculture ; Animals ; Cattle ; Cattle Diseases/*epidemiology/etiology ; Child ; Child, Preschool ; Epidemiologic Studies ; Escherichia coli Infections/*epidemiology/etiology ; Escherichia coli O157/*pathogenicity ; Female ; *Geographic Information Systems ; Geography ; Humans ; Incidence ; Infant ; Infant, Newborn ; *Linear Models ; Male ; Middle Aged ; Population Density ; Risk Factors ; Shiga Toxins ; Sweden/epidemiology ; }, abstract = {This article describes the spatial and temporal distribution of verotoxin-producing Escherichia coli among humans (EHEC) and cattle (VTEC) in Sweden, in order to evaluate relationships between the incidence of EHEC in humans, prevalence of VTEC O157 in livestock and agricultural structure by an ecological study. The spatial patterns of the distribution of human infections were described and compared with spatial patterns of occurrence in cattle, using a Geographic Information System (GIS). The findings implicate a concentration of human infection and cattle prevalence in the southwest of Sweden. The use of probability mapping confirmed unusual patterns of infection rates. The comparison of human and cattle infection indicated a spatial and statistical association. The correlation between variables of the agricultural structure and human EHEC incidence was high, indicating a significant statistical association of cattle and farm density with human infection. The explained variation of a multiple linear regression model was 0.56.}, } @article {pmid15188681, year = {2004}, author = {Koslowsky, S and Staubach, C and Kramer, M and Wieler, LH}, title = {[Risk assessment of bluetongue disease incursion into Germany using geographic information system (GIS)].}, journal = {Berliner und Munchener tierarztliche Wochenschrift}, volume = {117}, number = {5-6}, pages = {214-225}, pmid = {15188681}, issn = {0005-9366}, mesh = {Animals ; Bluetongue/*epidemiology/transmission ; Ceratopogonidae/physiology/*virology ; *Geographic Information Systems ; Germany/epidemiology ; Insect Vectors/physiology/*virology ; Population Density ; Population Dynamics ; Risk Assessment/*methods ; Risk Factors ; Ruminants ; Seasons ; Sheep ; }, abstract = {Using a geographic information system (GIS), by analysis of the relationship between the spatial distribution of cattle density and the risk factors temperature, altitude and rainfall, we defined geographical habitats enabling optimal development and competence of Culicoides spp. to transmit Bluetongue-Virus (BTV): Risk zones (low, high, highest risk) were identified mainly in Baden-Württemberg, Hessen and Rheinland-Pfalz if persistently infected ruminants are imported into these zones in summer (June to August mainly), based on the current climatic conditions, BTD outbreaks are considered a real possibility. Overwintering of the virus seems unlikely. However, global warming will lead to a steady increase of the size of the risk zones. In addition, the possibility of primary outbreaks increases. The reason for this is not only the expected northern shift of Culicoides imicola, but in addition an increasing vector competence of domestic Culicoides species. We therefore recommend the storage of vaccines as well as conducting ecological studies analysing the presence of Culicoides vectors. Using the data from these studies, it will be possible to produce updated quantitative risk assessment via GIS.}, } @article {pmid15184669, year = {2004}, author = {Keeling, MJ and Brooks, SP and Gilligan, CA}, title = {Using conservation of pattern to estimate spatial parameters from a single snapshot.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {101}, number = {24}, pages = {9155-9160}, pmid = {15184669}, issn = {0027-8424}, support = {//Wellcome Trust/United Kingdom ; }, mesh = {Animals ; Closterovirus ; Computer Simulation ; Data Interpretation, Statistical ; *Disease Outbreaks ; *Disease Transmission, Infectious ; Foot-and-Mouth Disease/epidemiology/*transmission ; *Models, Biological ; Plant Diseases/*virology ; }, abstract = {Rapid reaction in the face of an epidemic is a key element in effective and efficient control; this is especially important when the disease has severe public health or economic consequences. Determining an appropriate level of response requires rapid estimation of the rate of spread of infection from limited disease distribution data. Generally, the techniques used to estimate such spatial parameters require detailed spatial data at multiple time points; such data are often time-consuming and expensive to collect. Here we present an alternative approach that is computationally efficient and only requires spatial data from a single time point, hence saving valuable time at the start of the epidemic. By assuming that fundamental spatial statistics are near equilibrium, parameters can be estimated by minimizing the expected rate of change of these statistics, hence conserving the general spatial pattern. Although applicable to both ecological and epidemiological data, here we focus on disease data from computer simulations and real epidemics to show that this method produces reliable results that could be used in practical situations.}, } @article {pmid15180683, year = {2004}, author = {Larsen, DR and Speckman, PL}, title = {Multivariate regression trees for analysis of abundance data.}, journal = {Biometrics}, volume = {60}, number = {2}, pages = {543-549}, doi = {10.1111/j.0006-341X.2004.00202.x}, pmid = {15180683}, issn = {0006-341X}, mesh = {*Biometry ; Cluster Analysis ; Data Interpretation, Statistical ; Ecology/statistics & numerical data ; Ecosystem ; Missouri ; *Multivariate Analysis ; Plants ; Trees ; }, abstract = {Multivariate regression tree methodology is developed and illustrated in a study predicting the abundance of several cooccurring plant species in Missouri Ozark forests. The technique is a variation of the approach of Segal (1992) for longitudinal data. It has the potential to be applied to many different types of problems in which analysts want to predict the simultaneous cooccurrence of several dependent variables. Multivariate regression trees can also be used as an alternative to cluster analysis in situations where clusters are defined by a set of independent variables and the researcher wants clusters as homogeneous as possible with respect to a group of dependent variables.}, } @article {pmid15180679, year = {2004}, author = {Krzanowski, WJ}, title = {Biplots for multifactorial analysis of distance.}, journal = {Biometrics}, volume = {60}, number = {2}, pages = {517-524}, doi = {10.1111/j.0006-341X.2004.00198.x}, pmid = {15180679}, issn = {0006-341X}, mesh = {*Biometry ; Data Interpretation, Statistical ; Ecology/statistics & numerical data ; Linear Models ; Marine Biology/statistics & numerical data ; Models, Statistical ; *Multivariate Analysis ; }, abstract = {Many data sets in practice fit a multivariate analysis of variance (MANOVA) structure, but do not accord with MANOVA assumptions for their analysis. One way forward is to calculate the matrix of dissimilarities or distances between every pair of individuals, and then to conduct an analysis of distance on the resulting data. Various metric scaling plots can be used to interpret the results of the analysis. However, developments to date of this approach have focused mainly on the individuals in the sample, and little attention has been paid to the assessment of influence of the original variables on the results. The present article attempts to rectify this omission. We discuss the inclusion of biplots on all forms of metric scaling representations in the analysis of distance. Exact biplots will often be nonlinear so we propose a simple linear approximation, and contrast it with other simple linear possibilities. An example from ecology illustrates the methodology.}, } @article {pmid15172571, year = {2004}, author = {Howard, BJ and Wright, SM and Salbu, B and Skuterud, KL and Hove, K and Loe, R}, title = {Long-term consequences for Northern Norway of a hypothetical release from the Kola nuclear power plant.}, journal = {The Science of the total environment}, volume = {327}, number = {1-3}, pages = {53-68}, doi = {10.1016/j.scitotenv.2004.01.007}, pmid = {15172571}, issn = {0048-9697}, mesh = {Cesium Radioisotopes/*analysis/pharmacokinetics ; *Environmental Exposure ; Food Contamination, Radioactive/analysis ; Forecasting ; Geographic Information Systems ; *Models, Theoretical ; Norway ; *Radioactive Hazard Release ; Radioactive Pollutants/*analysis ; Risk Assessment ; Soil Pollutants, Radioactive/analysis ; Strontium Radioisotopes/*analysis/pharmacokinetics ; Time Factors ; }, abstract = {The spatial and temporal variation in radiocaesium and (90)Sr doses to two population groups of the two Northernmost counties of Norway, Troms and Finnmark, following a hypothetical accident at the Kola nuclear power plant (KNPP) have been estimated using a model implemented within a geographical information system. The hypothetical accident assumes a severe loss of coolant accident at the KNPP coincident with meteorological conditions causing significant radionuclide deposition in the two counties. External doses are estimated from ground deposition and the behaviour of the different population groups, and internal doses from predicted food product activity concentrations and dietary consumption data. Doses are predicted for reindeer keepers and other Norwegian inhabitants, taking account of existing (137)Cs and (90)Sr deposition but not including the remedial effect of any countermeasures that might be used. The predicted doses, arising mainly from radiocaesium, confirm the Arctic Monitoring and Assessment Programme assessment that residents of the Arctic are particularly vulnerable to radiocaesium contamination, which could persist for many years. External doses are predicted to be negligible compared to ingestion doses. Ingestion doses for reindeer keepers are predicted to exceed 1 mSv y(-1) for several decades primarily due to their high consumption of reindeer meat. Other Norwegians would also be potentially exposed to doses exceeding 1 mSv y(-1) for several years, especially if they consume many local products. Whilst reindeer production is the most important exposure pathway, freshwater fish, lamb meat, dairy products, mushrooms and berries are also significant contributors to predicted ingestion doses. Radionuclide fluxes, defined as the total output of radioactivity in food from an area for a unit time, are dominated by reindeer meat. The results show the need for an effective emergency response, with appropriate countermeasures, should an accident of the scale considered in this paper occur at the KNPP.}, } @article {pmid15160893, year = {2003}, author = {Brody, SD and Carrasco, V and Highfield, W}, title = {Evaluating ecosystem management capabilities at the local level in Florida: identifying policy gaps using geographic information systems.}, journal = {Environmental management}, volume = {32}, number = {6}, pages = {661-681}, pmid = {15160893}, issn = {0364-152X}, mesh = {*Conservation of Natural Resources ; *Ecosystem ; Environment ; Environmental Monitoring/*methods ; Florida ; *Geographic Information Systems ; Policy Making ; }, abstract = {Because ecosystem approaches to management adhere to ecological systems rather than human-defined boundaries, collaboration across jurisdiction, agencies, and land ownership is often necessary to achieve effective management of transboundary resources. Local natural resource and land use planners increasingly recognize that while ecosystem management requires looking beyond specific jurisdictions and focusing on broad spatial scales, the approach will partly be implemented at the local level with the coordination of local policies across larger landscapes. This article evaluates the collective capabilities of local jurisdictions to manage large transboundary ecological systems in Florida. Specifically, it combines plan evaluation with geographic information systems (GIS) techniques to map, measure, and analyze the existing mosaic of management across selected ecosystems in the southern portion of the State. Visual and statistical results indicate significant gaps in the management framework of southern Florida that, if filled, could achieve a greater level of consistency and more complete coverage of ecosystem management policies. Based on the spatial distribution of 58 ecosystem management indicators, notable gaps persist in the southwest coast, southeast coast, and central Everglades ecosystems, particularly for wildlife corridors and collaboration with neighboring jurisdictions. We also test for spatial autocorrelation of ecosystem planning scores and find that local jurisdictions with strong ecosystem management capabilities tend to cluster within specific ecosystems. Based on the findings, we make recommendations on how and where local plans can be strengthened to more effectively attain the objectives of ecosystem approaches to management.}, } @article {pmid15156912, year = {2004}, author = {Zink, RM}, title = {The role of subspecies in obscuring avian biological diversity and misleading conservation policy.}, journal = {Proceedings. Biological sciences}, volume = {271}, number = {1539}, pages = {561-564}, pmid = {15156912}, issn = {0962-8452}, mesh = {Animals ; *Biodiversity ; Birds/*classification/*genetics ; *Conservation of Natural Resources ; DNA, Mitochondrial/genetics ; Databases, Genetic ; *Genetics, Population ; Species Specificity ; }, abstract = {Subspecies are often used in ways that require their evolutionary independence, for example as proxies for units of conservation. Mitochondrial DNA sequence data reveal that 97% of continentally distributed avian subspecies lack the population genetic structure indicative of a distinct evolutionary unit. Subspecies considered threatened or endangered, some of which have been targets of expensive restoration efforts, also generally lack genetic distinctiveness. Although sequence data show that species include 1.9 historically significant units on average, these units are not reflected by current subspecies nomenclature. Yet, it is these unnamed units and not named subspecies that should play a major role in guiding conservation efforts and in identifying biological diversity. Thus, a massive reorganization of classifications is required so that the lowest ranks, be they species or subspecies, reflect evolutionary diversity. Until such reorganization is accomplished, the subspecies rank will continue to hinder progress in taxonomy, evolutionary studies and especially conservation.}, } @article {pmid15156354, year = {2004}, author = {Brody, SD and Highfield, W and Arlikatti, S and Bierling, DH and Ismailova, RM and Lee, L and Butzler, R}, title = {Conflict on the coast: using geographic information systems to map potential environmental disputes in Matagorda Bay, Texas.}, journal = {Environmental management}, volume = {34}, number = {1}, pages = {11-25}, pmid = {15156354}, issn = {0364-152X}, mesh = {*Conflict, Psychological ; *Conservation of Natural Resources ; Ecosystem ; Environmental Monitoring ; *Geographic Information Systems ; *Problem Solving ; Texas ; }, abstract = {The sustainable management of coastal natural resources inevitably involves identifying stakeholder conflicts and developing planning processes that prevent these conflicts from becoming intractable disputes. This study links environmental conflict to specific areas within a large ecological system. Specifically, we use Geographic Information Systems (GIS) to map potentially competing stakeholder values associated with establishing protected areas in Matagorda Bay, Texas. By overlaying multiple values associated with a range of stakeholders across space, we are able to identify hotspots of potential conflict as well as areas of opportunity for maximizing joint gains. Mapping stakeholder conflict is an approach to proactively locate potential controversy in response to a specific environmental management proposal and guide decision makers in crafting planning processes that mitigate the possibility of intractable disputes and facilitate the implementation of sustainable coastal policies. Results indicate that under different management scenarios, protected area proposals will generate more conflict in specific areas. Most notably, regulated uses would produce the greatest degree of conflict on or near shore, particularly at the mouth of the Colorado River. Additionally, of all the management scenarios evaluated, the prohibition of coastal structural development would generate the overall highest level of conflict within the Bay. Based on the results, we discuss the policy implications for environmental managers and provide guidance for future research on location-based conflict management within the coastal margin.}, } @article {pmid15148423, year = {2004}, author = {Field, D and Hughes, J and Moxon, ER}, title = {Using the genome to understand pathogenicity.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {266}, number = {}, pages = {261-287}, doi = {10.1385/1-59259-763-7:261}, pmid = {15148423}, issn = {1064-3745}, mesh = {Bacteria/classification/*genetics/*pathogenicity ; Bacterial Infections/classification ; Base Sequence ; Biological Evolution ; Computational Biology ; Gene Transfer Techniques ; *Genome, Bacterial ; *Genomics ; Humans ; Virulence/*genetics ; }, abstract = {Genome sequencing, the determination of the complete complement of DNA in an organism, is revolutionizing all aspects of the biological sciences. Genome sequences make available for scientific scrutiny the complete genetic capacity of an organism. With respect to microbes, this means we now have the unprecedented opportunity to investigate the molecular basis of commensal and virulence behavior. We now have genome sequences for a wide range of bacterial pathogens (obligate, facultative, and opportunistic); this has facilitated the discovery of many previously unidentified determinants of pathogenicity and has provided novel insights into what creates a pathogen. In-depth analyses of bacterial genomes are also providing new perspectives on bacterial physiology, molecular adaptation to a preferred niche, and genomic susceptibility to the uptake of foreign DNA, three key factors that can play a significant role in determining whether a species, or a strain, will have pathogenic potential.}, } @article {pmid15146640, year = {2004}, author = {Wu, Z and Wang, J and Zhuo, M and Wan, H}, title = {[Spatial distribution and landscape ecological impact degree assessment of quarry in Zhuhai City].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {15}, number = {2}, pages = {283-286}, pmid = {15146640}, issn = {1001-9332}, mesh = {*Ecology ; Environmental Monitoring/*methods ; *Geographic Information Systems ; Satellite Communications ; }, abstract = {Artificial erosion is one of the typical artificial landscape degradation. Based on the support of GIS and RS and combined with field investigation data, the spatial distribution characteristics and landscape ecological impact degree of quarry were analyzed. There were 235 quarries in Zhuhai city, which concentrated on Sanzao town and Jingan town. According to buffer analysis, the quarries distribution had a obviously logarithm relationship with its distances from roads. 152 quarries with the area of more than 5000 m2 were assessed by landscape ecological impact degree (LEI) index. The results indicated that 9 quarries belonged to great influence level and 19 quarries belonged to strong influence on ecological environment.}, } @article {pmid15141445, year = {2004}, author = {Weber, T}, title = {Landscape ecological assessment of the Chesapeake Bay watershed.}, journal = {Environmental monitoring and assessment}, volume = {94}, number = {1-3}, pages = {39-53}, pmid = {15141445}, issn = {0167-6369}, mesh = {Animals ; *Conservation of Natural Resources ; Delaware ; *Ecology ; Environmental Monitoring ; *Food Chain ; *Geographic Information Systems ; Geologic Sediments ; Maryland ; Plants ; Risk Assessment ; Vertebrates ; Virginia ; Water Pollutants/analysis ; *Water Supply ; }, abstract = {The Chesapeake Bay Watershed, located in the Mid-Atlantic Region of the United States, is experiencing rapid habitat loss and fragmentation from sprawling low-density development. The bay itself is heavily stressed by excess sediment and nutrient runoff. Three states, the District of Columbia, and the federal government signed an agreement in 2000 to address these problems. The commitments included an assessment of the watershed's resource lands, and targeting the most valued lands for protection. As part of this task, the Resource Lands Assessment identified an ecological network comprised of large contiguous blocks (hubs) of forests, wetlands, and streams, interconnected by corridors to allow animal and plant propagule dispersal and migration. Hubs were prioritized by ecoregion, by analyzing a variety of ecological parameters, including: rare species presence, rarity and population viability; vegetation and vertebrate richness; habitat area, condition, and diversity; intactness and remoteness; connectivity potential; and the nature of the surrounding landscape. I found that much of the watershed was still fairly intact, although this varied dramatically by ecoregion. Current protection also varied, and an assessment of vulnerability will help focus protection efforts among the most valuable hubs and corridors.}, } @article {pmid15141443, year = {2004}, author = {Brooks, RP and Wardrop, DH and Bishop, JA}, title = {Assessing wetland condition on a watershed basis in the Mid-Atlantic region using synoptic land-cover maps.}, journal = {Environmental monitoring and assessment}, volume = {94}, number = {1-3}, pages = {9-22}, doi = {10.1023/b:emas.0000016876.63062.3d}, pmid = {15141443}, issn = {0167-6369}, mesh = {*Conservation of Natural Resources ; Data Collection ; *Ecosystem ; Environmental Monitoring/methods ; Environmental Pollutants/analysis ; *Geographic Information Systems ; United States ; Water Supply ; }, abstract = {We developed a series of tools to address three integrated tasks needed to effectively manage wetlands on a watershed basis: inventory, assessment, and restoration. Depending on the objectives of an assessment, availability of resources, and degree of confidence required in the results, there are three levels of effort available to address these three tasks. This paper describes the development and use of synoptic land-cover maps (Level 1) to assess wetland condition for a watershed. The other two levels are a rapid assessment using ground reconnaissance (Level 2) and intensive field assessment (Level 3). To illustrate the application of this method, seven watersheds in Pennsylvania were investigated representing a range of areas (89-777 km2), land uses, and ecoregions found in the Mid-Atlantic Region. Level 1 disturbance scores were based on land cover in 1-km radius circles centered on randomly-selected wetlands in each watershed. On a standardized, 100-point, human-disturbance scale, with 100 being severely degraded and 1 being the most ecologically intact, the range of scores for the seven watersheds was a relatively pristine score of 4 to a moderately degraded score of 66. This entire process can be conducted in a geographic information system (GIS)-capable office with readily available data and without engaging in extensive field investigations. We recommend that agencies and organizations begin the process of assessing wetlands by adopting this approach as a first step toward determining the condition of wetlands on a watershed basis.}, } @article {pmid15140359, year = {2004}, author = {Kreijns, K and Kirschner, PA and Jochems, W and Van Buuren, H}, title = {Determining sociability, social space, and social presence in (a)synchronous collaborative groups.}, journal = {Cyberpsychology & behavior : the impact of the Internet, multimedia and virtual reality on behavior and society}, volume = {7}, number = {2}, pages = {155-172}, doi = {10.1089/109493104323024429}, pmid = {15140359}, issn = {1094-9313}, mesh = {Adult ; Communication ; Computer Simulation ; Computer-Assisted Instruction/instrumentation/methods ; *Cooperative Behavior ; Education, Distance/methods ; Female ; Group Processes ; Humans ; *Interpersonal Relations ; *Learning ; Male ; Netherlands ; *Psychological Distance ; Remote Consultation/instrumentation/methods ; *Social Environment ; Software ; *User-Computer Interface ; }, abstract = {The effectiveness of group learning in asynchronous distributed learning groups depends on the social interaction that takes place. This social interaction affects both cognitive and socioemotional processes that take place during learning, group forming, establishment of group structures, and group dynamics. Though now known to be important, this aspect is often ignored, denied or forgotten by educators and researchers who tend to concentrate on cognitive processes and on-task contexts. This "one-sided" educational focus largely determines the set of requirements in the design of computer-supported collaborative learning (CSCL) environments resulting in functional CSCL environments. In contrast, our research is aimed at the design and implementation of sociable CSCL environments which may increase the likelihood that a sound social space will emerge. We use a theoretical framework that is based upon an ecological approach to social interaction, centering on the concept of social affordances, the concept of the sociability of CSCL environments, and social presence theory. The hypothesis is that the higher the sociability, the more likely that social interaction will take place or will increase, and the more likely that this will result in an emerging sound social space. In the present research, the variables of interest are sociability, social space, and social presence. This study deals with the construction and validation of three instruments to determine sociability, social space, and social presence in (a)synchronous collaborating groups. The findings suggest that the instruments have potential to be useful as measures for the respective variables. However, it must be realized that these measures are "first steps."}, } @article {pmid15139183, year = {2004}, author = {Zhou, Z and Wu, G and Shao, G}, title = {[Accuracy evaluation of land vegetative cover index by RS detection].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {15}, number = {1}, pages = {36-38}, pmid = {15139183}, issn = {1001-9332}, mesh = {*Conservation of Natural Resources ; *Ecosystem ; Geographic Information Systems ; Regression Analysis ; Satellite Communications ; }, abstract = {The accuracy of GIS data is important in GIS application. In this paper, a fictitious case and an example were used to discuss the relationship between accuracy of land vegetative cover index and accuracy of image classification, and this relationship was explained by mathematics. The accuracy of land vegetative cover index rested with the accuracy of image classification, but had no direct relations with total classification accuracy. User accuracy and producer accuracy had more direct control on the accuracy of land vegetative cover index than total classification accuracy; and hence, they could not be ignored in the image classification. To improve the accuracy of land vegetative cover index, user accuracy and producer accuracy of the same land type should be consistent to the greatest extent.}, } @article {pmid15139179, year = {2004}, author = {Chang, Y and Bu, R and Hu, Y and Xu, C and Wang, Q}, title = {[Dynamics of forest landscape boundary at Changbai Mountain].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {15}, number = {1}, pages = {15-20}, pmid = {15139179}, issn = {1001-9332}, mesh = {China ; *Ecosystem ; Geographic Information Systems ; Trees/*growth & development ; }, abstract = {By using Geographic Information System (GIS) and Remote Sensing (RS) technology combined with field investigation and correlation analysis, this study was aimed to explore the dynamics of forest landscape boundary at Changbai Mountain, and to reveal the relationships among landscape fragmentation and changes of landscape boundary indices. The results showed that in the last 20 years or so, tundra decreased by 3694.8 hm2, spruce and fir forest reduced by 130482.03 hm2, and Korean pine-hardwood and mountain birch forest increased by 41610.4 hm2 and 669.78 hm2, respectively. The forest landscapes at Changbai Mountain tended to be more fragmented, and the shape of the landscape boundary became more complicated due to timber harvesting, forest cutting for cropping, and other human activities such as tourism. The changes of landscape shape index (LSI), contrast weighted edge density (CWED), total weighted edge length (TE-WGT) and weighted landscape shape index (LSI-WGT) could be used as good indicators for the degrees of forest landscape fragmentations, which was approved by correlation analysis among landscape fragmentation and changes of landscape boundary indices. The degree of human activities on landscape could be reflected by landscape shape index.}, } @article {pmid15138040, year = {2004}, author = {Schwela, D and Hakkinen, PJ}, title = {Human exposure assessment resources on the World Wide Web.}, journal = {Toxicology}, volume = {198}, number = {1-3}, pages = {169-176}, doi = {10.1016/j.tox.2004.01.025}, pmid = {15138040}, issn = {0300-483X}, mesh = {*Databases, Factual ; Humans ; *Internet ; Risk Assessment ; *Toxicology ; United States ; }, abstract = {Human exposure assessment is frequently noted as a weak link and bottleneck in the risk assessment process. Fortunately, the World Wide Web and Internet are providing access to numerous valuable sources of human exposure assessment-related information, along with opportunities for information exchange. Internet mailing lists are available as potential online help for exposure assessment questions, e.g. RISKANAL has several hundred members from numerous countries. Various Web sites provide opportunities for training, e.g. Web sites offering general human exposure assessment training include two from the US Environmental Protection Agency (EPA) and four from the US National Library of Medicine. Numerous other Web sites offer access to a wide range of exposure assessment information. For example, the (US) Alliance for Chemical Awareness Web site addresses direct and indirect human exposures, occupational exposures and ecological exposure assessments. The US EPA's Exposure Factors Program Web site provides a focal point for current information and data on exposure factors relevant to the United States. In addition, the International Society of Exposure Analysis Web site provides information about how this society seeks to foster and advance the science of exposure analysis. A major opportunity exists for risk assessors and others to broaden the level of exposure assessment information available via Web sites. Broadening the Web's exposure information could include human exposure factors-related information about country- or region-specific ranges in body weights, drinking water consumption, etc. along with residential factors-related information on air changeovers per hour in various types of residences. Further, country- or region-specific ranges on how various tasks are performed by various types of consumers could be collected and provided. Noteworthy are that efforts are underway in Europe to develop a multi-country collection of exposure factors and the European Commission is in the early stages of planning and developing a Web-accessible information system (EIS-ChemRisks) to serve as a single gateway to all major European initiatives on human exposure to chemicals contained and released from cleaning products, textiles, toys, etc.}, } @article {pmid15137161, year = {2003}, author = {Young, AR and Grew, R and Holmes, MG}, title = {Low Flows 2000: a national water resources assessment and decision support tool.}, journal = {Water science and technology : a journal of the International Association on Water Pollution Research}, volume = {48}, number = {10}, pages = {119-126}, pmid = {15137161}, issn = {0273-1223}, mesh = {*Decision Support Techniques ; Germany ; *Models, Theoretical ; Quality Control ; Water Movements ; Water Pollution/*prevention & control ; *Water Supply ; }, abstract = {Information on the magnitude and variability of flow regimes at the river reach scale is a central component of most aspects of water resource and water quality management. However, many decisions are made within catchments for which there are no measured flow data. To meet this challenge, a suite of modelling techniques to assist in the estimation of natural and artificially influenced river-flows at ungauged sites has been developed. This paper summarises these models and how they are incorporated within the GIS framework of the Low Flows 2000 software package. The paper will also describe the implementation of Low Flows 2000 within England and Wales by the Environment Agency, and the use of the system in supporting the implementation of the Environment Agency's Catchment Abstraction Management Strategy. This strategy is focused on the delivery of sustainable abstraction licensing and will contribute to the implementation of the Water Framework Directive within England and Wales.}, } @article {pmid15134838, year = {2004}, author = {Vermeirssen, V and van der Bent, A and Van Camp, J and van Amerongen, A and Verstraete, W}, title = {A quantitative in silico analysis calculates the angiotensin I converting enzyme (ACE) inhibitory activity in pea and whey protein digests.}, journal = {Biochimie}, volume = {86}, number = {3}, pages = {231-239}, doi = {10.1016/j.biochi.2004.01.003}, pmid = {15134838}, issn = {0300-9084}, mesh = {Amino Acid Sequence ; Angiotensin-Converting Enzyme Inhibitors/chemistry/*isolation & purification/metabolism ; Animals ; Cattle ; *Computational Biology ; Milk Proteins/*chemistry ; Molecular Sequence Data ; Pisum sativum/*chemistry ; Peptide Fragments/chemistry/metabolism ; Peptidyl-Dipeptidase A/*metabolism ; Time Factors ; Whey Proteins ; }, abstract = {Angiotensin I converting enzyme (ACE) inhibitory peptides can induce antihypertensive effects after oral administration. By means of an ACE inhibitory peptide database, containing about 500 reported sequences and their IC(50) values, the different proteins in pea and whey were quantitatively evaluated as precursors for ACE inhibitory peptides. This analysis was combined with experimental data from the evolution in ACE inhibitory activity and protein degradation during in vitro gastrointestinal digestion. Pea proteins produced similar in silico scores and were degraded early in the in vitro digestion. High ACE inhibitory activity was observed after the simulated stomach phase and augmented slightly in the simulated small intestine phase. The major whey protein beta-lactoglobulin obtained the highest in silico scores, which corresponded with the fact that degradation of this protein in vitro only occurred from the simulated small intestine phase on and resulted in a 10-fold increase in the ACE inhibitory activity. Whey protein obtained total in silico scores of about 124 ml/mg, compared to 46 ml/mg for pea protein, indicating that whey protein would be a richer source of ACE inhibitory peptides than pea protein. Although beta-lactoglobulin is only partially digested, a higher ACE inhibitory activity was indeed found in the whey (IC(50) = 0.048 mg/ml) compared to the pea digest (IC(50) = 0.076 mg/ml). In silico gastrointestinal digestion of the highest scoring proteins in pea and whey, vicilin and albumin PA2, and beta-lactoglobulin, respectively, directly released a number of potent ACE inhibitory peptides. Several other ACE inhibitory sequences resisted in silico digestion by gastrointestinal proteases. Briefly, the quantitative in silico analysis will facilitate the study of precursor proteins on a large scale and the specific release of bioactive peptides.}, } @article {pmid15132867, year = {2004}, author = {Yi, BT and Xu, DZ and Zhang, ZY and Zhang, B and Xi, YZ and Fu, JG and Luo, J and Yuan, MH and Liu, SQ}, title = {[Development and application of geographic information system of Aedes vector in Chaozhou city, Guangdong province].}, journal = {Zhonghua liu xing bing xue za zhi = Zhonghua liuxingbingxue zazhi}, volume = {25}, number = {2}, pages = {134-137}, pmid = {15132867}, issn = {0254-6450}, mesh = {*Aedes ; Animals ; China ; Dengue/prevention & control ; Dengue Virus ; Ecology ; Geographic Information Systems/standards/*statistics & numerical data ; Geography ; Insect Vectors/virology ; }, abstract = {OBJECTIVE: To explore the spatial distribution character of dengue fever and the change of Aedes' population, so as to provide macroscopical decision-making evidences of prevention and supervision on dengue fever.

METHODS: (1) Collecting data on morbidity of dengue and supervision on vector's population in the corresponding period. (2) Drawing digitized map of Chaozhou in scale of 1:50,000, including elements of boundary, residential areas, road and traffic, altitude, water systems etc. (3) Measuring the latitude and longitude of center position of surveillance safes on the scene. (4) Processing spatial analysis by the ArcGIS 8.5 software.

RESULTS: Distribution of Aedes showed spatial cluster in Chaozhou, while its density was related to the distance to the watersides. The closer to the watersides, the higher the density was. Map on spatial distribution showed that although the Aedes epidemic situation changed yearly, but primarily be kept in high, middle, low regions. Cross-validation effects of the distribution maps were satisfactory.

CONCLUSION: Geographic information system was promising in analyzing data on dengue fever, and better than other routine research methods.}, } @article {pmid15128948, year = {2004}, author = {Gilbert, B and Lechowicz, MJ}, title = {Neutrality, niches, and dispersal in a temperate forest understory.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {101}, number = {20}, pages = {7651-7656}, pmid = {15128948}, issn = {0027-8424}, mesh = {Analysis of Variance ; Carex Plant ; Data Interpretation, Statistical ; *Ecology ; Environment ; *Trees ; }, abstract = {A fundamental goal of ecology is to understand what controls the distribution and abundance of species. Both environmental niches and trade-offs among species in dispersal and competitive ability have traditionally been cited as determinants of plant community composition. More recently, neutral models have shown that communities of species with identical life-history characteristics and no adaptation to environmental niches can form spatial distribution patterns similar to those found in nature, so long as the species have a limited dispersal distance. If there is a strong correlation between geographic distance and change in environmental conditions, however, such spatial patterns can arise through either neutral or niche-based processes. To test these competing theories, we developed a sampling design that decoupled distance and environment in the understory plant communities of an old-growth, temperate forest. We found strong evidence of niche-structuring but almost no support for neutral predictions. Dispersal limitation acted in conjunction with environmental gradients to determine species' distributions, and both functional and phylogenetic constraints appear to contribute to the niche differentiation that structures community assembly. Our results indicate that testing a neutral hypothesis without accounting for environmental gradients will at best cause unexplained variation in plant distributions and may well provide misleading support for neutrality because of a correlation between geographic distance and environment.}, } @article {pmid15125218, year = {2004}, author = {González-Martínez, J}, title = {The introduced free-ranging rhesus and patas monkey populations of southwestern Puerto Rico.}, journal = {Puerto Rico health sciences journal}, volume = {23}, number = {1}, pages = {39-46}, pmid = {15125218}, issn = {0738-0658}, support = {RR-03640/RR/NCRR NIH HHS/United States ; }, mesh = {Animals ; Data Interpretation, Statistical ; Ecology ; *Erythrocebus patas/physiology ; Female ; Homing Behavior ; *Macaca mulatta/physiology ; Male ; Population Density ; Population Dynamics ; Pregnancy ; Puerto Rico ; Reproduction ; Seasons ; Telemetry ; }, abstract = {Rhesus (Macaca mulatta) and patas (Erythrocebus patas) monkeys escaped to the mainland of southwestern Puerto Rico (SWPR) from research colonies on small offshore islands during the 1960s and through 1982. A three year study (1990-1993) combined radio-telemetry with visual observations to collect information on population sizes, the composition of social groups, their daily movements, and their home ranges. Two populations of rhesus monkeys were identified in SWPR: one within the study area in Sierra Bermeja and a second population located 10 km north of the study area. The size of the Sierra Bermeja rhesus population was derived from escapees from research colonies and at the time of the study was 65-85 individuals. Within their home range area (3.7 km2) the density of this population was >>18.9 individuals/km2. A second rhesus population was found in a mountainous region 10 km north of the study area. This population consisted of one (or two) heterosexual groups with a total of 40-45 individuals. Although a primary characteristic of this species in India is its ability to live as a commensal with humans, the rhesus monkey populations of SWPR are extremely shy and elusive, they avoid contact with humans. The patas monkey population consisted of >>120 individuals in four heterosexual groups and several all-male bands. There was no evidence of patas monkeys outside the study area. Within their home ranges (26.8 km2) the population density was 4.47 individuals/km2). Patas monkeys have not previously been considered a territorial species, their behavior in SWPR suggested territoriality. In contrast to studies in Africa, where the amount of home range overlap between patas monkey groups in high, in SWPR the amount of range overlap between groups is small and each group uses areas with clearly defined boundaries.}, } @article {pmid15123584, year = {2004}, author = {Zhang, J and Wang, X and Podlaha, O}, title = {Testing the chromosomal speciation hypothesis for humans and chimpanzees.}, journal = {Genome research}, volume = {14}, number = {5}, pages = {845-851}, pmid = {15123584}, issn = {1088-9051}, support = {R01 GM067030/GM/NIGMS NIH HHS/United States ; GM67030/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Chromosomes/*genetics ; Chromosomes, Human/*genetics ; Databases, Genetic ; Evolution, Molecular ; Gene Expression Regulation/genetics ; Genetic Variation/genetics ; Genome ; Genome, Human ; Gorilla gorilla/genetics ; Humans ; *Models, Genetic ; Molecular Sequence Data ; Pan troglodytes/*genetics ; Proteins/genetics ; Recombination, Genetic/genetics ; Selection, Genetic ; Species Specificity ; }, abstract = {Fixed differences of chromosomal rearrangements between isolated populations may promote speciation by preventing between-population gene flow upon secondary contact, either because hybrids suffer from lowered fitness or, more likely, because recombination is reduced in rearranged chromosomal regions. This chromosomal speciation hypothesis thus predicts more rapid genetic divergence on rearranged than on colinear chromosomes because the former are less porous to gene flow. A number of studies of fungi, plants, and animals, including limited genetic data of humans and chimpanzees, support the hypothesis. Here we reexamine the hypothesis for humans and chimpanzees with substantially more genomic data than were used previously. No difference is observed between rearranged and colinear chromosomes in the level of genomic DNA sequence divergence between species. The same is also true for protein sequences. When the gorilla is used as an outgroup, no acceleration in protein sequence evolution associated with chromosomal rearrangements is found. Furthermore, divergence in expression pattern between orthologous genes is not significantly different for rearranged and colinear chromosomes. These results, showing that chromosomal rearrangements did not affect the rate of genetic divergence between humans and chimpanzees, are expected if incipient species on the evolutionary lineages separating humans and chimpanzees did not hybridize.}, } @article {pmid15123580, year = {2004}, author = {Castillo-Davis, CI and Kondrashov, FA and Hartl, DL and Kulathinal, RJ}, title = {The functional genomic distribution of protein divergence in two animal phyla: coevolution, genomic conflict, and constraint.}, journal = {Genome research}, volume = {14}, number = {5}, pages = {802-811}, pmid = {15123580}, issn = {1088-9051}, mesh = {Amino Acid Substitution/genetics ; Animals ; Caenorhabditis/genetics ; Caenorhabditis elegans/genetics/immunology ; Caenorhabditis elegans Proteins/*physiology ; Databases, Protein ; *Evolution, Molecular ; Genes/physiology ; Genes, Helminth/genetics/immunology ; Humans ; Mice ; Mutagenesis, Insertional/genetics ; Organ Specificity/genetics ; Phylogeny ; Proteins/*physiology ; Rats ; Selection, Genetic ; Sequence Deletion/genetics ; }, abstract = {We compare the functional spectrum of protein evolution in two separate animal lineages with respect to two hypotheses: (1) rates of divergence are distributed similarly among functional classes within both lineages, indicating that selective pressure on the proteome is largely independent of organismic-level biological requirements; and (2) rates of divergence are distributed differently among functional classes within each lineage, indicating species-specific selective regimes impact genome-wide substitutional patterns. Integrating comparative genome sequence with data from tissue-specific expressed-sequence-tag (EST) libraries and detailed database annotations, we find a functional genomic signature of rapid evolution and selective constraint shared between mammalian and nematode lineages despite their extensive morphological and ecological differences and distant common ancestry. In both phyla, we find evidence of accelerated evolution among components of molecular systems involved in coevolutionary change. In mammals, lineage-specific fast evolving genes include those involved in reproduction, immunity, and possibly, maternal-fetal conflict. Likelihood ratio tests provide evidence for positive selection in these rapidly evolving functional categories in mammals. In contrast, slowly evolving genes, in terms of amino acid or insertion/deletion (indel) change, in both phyla are involved in core molecular processes such as transcription, translation, and protein transport. Thus, strong purifying selection appears to act on the same core cellular processes in both mammalian and nematode lineages, whereas positive and/or relaxed selection acts on different biological processes in each lineage.}, } @article {pmid15123438, year = {2004}, author = {Whittemore, R and Melkus, GD and Grey, M}, title = {Applying the social ecological theory to type 2 diabetes prevention and management.}, journal = {Journal of community health nursing}, volume = {21}, number = {2}, pages = {87-99}, doi = {10.1207/s15327655jchn2102_03}, pmid = {15123438}, issn = {0737-0016}, support = {F32NR07823/NR/NINR NIH HHS/United States ; }, mesh = {Community Health Nursing/*organization & administration ; Community Networks/organization & administration ; Cultural Diversity ; Diabetes Mellitus/epidemiology/*prevention & control ; Diabetes Mellitus, Type 2/epidemiology/*prevention & control ; Ecology ; Health Promotion/organization & administration ; Humans ; Nurse's Role ; *Obesity ; Patient-Centered Care/organization & administration ; Primary Prevention/organization & administration ; *Psychological Theory ; *Psychology, Social ; United States/epidemiology ; }, abstract = {Obesity and Type 2 diabetes have become major public health problems in the United States. Community health nurses, with expertise in preventive health care, have the potential to play a vital role in addressing these significant health issues. The purposes of this article are to identify current challenges related to obesity and Type 2 diabetes and to present the social ecological theory as a framework for the expansion of the reach of diabetes prevention and management that is relevant to community health nurses.}, } @article {pmid15120268, year = {2004}, author = {Ungar, P}, title = {Dental topography and diets of Australopithecus afarensis and early Homo.}, journal = {Journal of human evolution}, volume = {46}, number = {5}, pages = {605-622}, doi = {10.1016/j.jhevol.2004.03.004}, pmid = {15120268}, issn = {0047-2484}, mesh = {Animals ; *Diet ; Ecology ; *Fossils ; *Geographic Information Systems ; Hominidae/*anatomy & histology ; Humans ; Paleontology ; *Primates ; Software ; Tooth/*anatomy & histology ; }, abstract = {Diet is key to understanding the paleoecology of early hominins. We know little about the diets of these fossil taxa, however, in part because of a limited fossil record, and in part because of limitations in methods available to infer their feeding adaptations. This paper applies a new method, dental topographic analysis, to the inference of diet from fossil hominin teeth. This approach uses laser scanning to generate digital 3D models of teeth and geographic information systems software to measure surface attributes, such as slope and occlusal relief. Because it does not rely on specific landmarks that change with wear, dental topographic analysis allows measurement and comparison of variably worn teeth, greatly increasing sample sizes compared with techniques that require unworn teeth. This study involved comparison of occlusal slope and relief of the lower second molars of Australopithecus afarensis (n=15) and early Homo (n=8) with those of Gorilla gorilla gorilla (n=47) and Pan troglodytes troglodytes (n=54). Results indicate that while all groups show reduced slope and relief in progressively more worn specimens, there are consistent differences at given wear stages among the taxa. Early Homo shows steeper slopes and more relief than chimpanzees, whereas A. afarensis shows less slope and relief than any of the other groups. The differences between the two hominin taxa are on the same order as those between the extant apes, suggesting similar degrees of difference in diet. Because these chimpanzees and gorillas differ mostly in fallback foods where they are sympatric, results suggest that the early hominins may likewise have differed mostly in fallback foods, with A. afarensis emphasizing harder, more brittle foods, and early Homo relying on tougher, more elastic foods.}, } @article {pmid15094816, year = {2004}, author = {Ward, JR and Lafferty, KD}, title = {The elusive baseline of marine disease: are diseases in ocean ecosystems increasing?.}, journal = {PLoS biology}, volume = {2}, number = {4}, pages = {E120}, pmid = {15094816}, issn = {1545-7885}, mesh = {Animal Diseases/epidemiology ; Animals ; Anthozoa ; Classification ; Conservation of Natural Resources ; Databases, Bibliographic ; Ecology ; *Ecosystem ; Fish Diseases/epidemiology ; Fishes ; Marine Biology/*methods ; Oceans and Seas ; Species Specificity ; }, abstract = {Disease outbreaks alter the structure and function of marine ecosystems, directly affecting vertebrates (mammals, turtles, fish), invertebrates (corals, crustaceans, echinoderms), and plants (seagrasses). Previous studies suggest a recent increase in marine disease. However, lack of baseline data in most communities prevents a direct test of this hypothesis. We developed a proxy to evaluate a prediction of the increasing disease hypothesis: the proportion of scientific publications reporting disease increased in recent decades. This represents, to our knowledge, the first quantitative use of normalized trends in the literature to investigate an ecological hypothesis. We searched a literature database for reports of parasites and disease (hereafter "disease") in nine marine taxonomic groups from 1970 to 2001. Reports, normalized for research effort, increased in turtles, corals, mammals, urchins, and molluscs. No significant trends were detected for seagrasses, decapods, or sharks/rays (though disease occurred in these groups). Counter to the prediction, disease reports decreased in fishes. Formulating effective resource management policy requires understanding the basis and timing of marine disease events. Why disease outbreaks increased in some groups but not in others should be a priority for future investigation. The increase in several groups lends urgency to understanding disease dynamics, particularly since few viable options currently exist to mitigate disease in the oceans.}, } @article {pmid15084362, year = {2004}, author = {Swetnam, RD and Owen Mountford, J and Manchester, SJ and Broughton, RK}, title = {Agri-environmental schemes: their role in reversing floral decline in the Brue floodplain, Somerset, UK.}, journal = {Journal of environmental management}, volume = {71}, number = {1}, pages = {79-93}, doi = {10.1016/j.jenvman.2004.01.006}, pmid = {15084362}, issn = {0301-4797}, mesh = {*Agriculture ; *Conservation of Natural Resources ; England ; Environmental Monitoring ; *Geographic Information Systems ; *Plants ; Population Dynamics ; Water Pollutants ; Water Supply ; }, abstract = {This paper explores whether the introduction of an agri-environmental scheme has altered the course of long-term trends in plant species abundance in the Somerset Levels and Moors Environmentally Sensitive Area (ESA), UK. A semi-quantitative approach has been taken which integrates disparate but important historical datasets relating to flora and land management with more contemporary digital information. Species datasets from four time periods throughout the 20th century have been collated within a Geographic Information System and analysed with respect to ancillary data relating to elevation, under-drainage and ESA designation. Qualitative reconstruction of the historical ecology of this internationally important area of lowland wet grassland showed that a steady decline in abundance and extent of key components of the flora had already started by 1900. Analysis of historical under-drainage records dating from 1940s to 1980s showed a clear link between the length of time an area had been under-drained and the subsequent diversity of flora recorded in later surveys. In addition, the relative persistence of the rarer components of the wetland flora between surveys in 1980 and 1997 was related to the spatial pattern of under-drainage on the site since 1940. When overall species diversity was compared before and after ESA designation (1980-1997) there was some evidence of an increase in the number of species present and their spatial extent. The historical dataset provided useful contextual information with respect to species trends and allowed the interpretation of contemporary datasets to be placed within a longer timeframe. This pilot study using 18 species gives some evidence that long-established trends in species decline in the Somerset Levels and Moors ESA are starting to be reversed.}, } @article {pmid15078462, year = {2004}, author = {Sacks, BN and Brown, SK and Ernest, HB}, title = {Population structure of California coyotes corresponds to habitat-specific breaks and illuminates species history.}, journal = {Molecular ecology}, volume = {13}, number = {5}, pages = {1265-1275}, doi = {10.1111/j.1365-294X.2004.02110.x}, pmid = {15078462}, issn = {0962-1083}, mesh = {Animals ; California ; Coyotes/*genetics ; *Demography ; *Environment ; Gene Frequency ; *Genetics, Population ; Geographic Information Systems ; Geography ; Microsatellite Repeats/genetics ; Models, Genetic ; }, abstract = {Little is known about the relationship between animal movements and the emergent structure of populations, especially for species occupying large continuous distributions. Some such mammals disperse disproportionately into habitat similar to their natal habitat, a behavioural bias that might be expected to lead to habitat-conforming genetic structure. We hypothesized that coyotes (Canis latrans) would exhibit such natal-biased dispersal, and used 13 microsatellite loci to test, correspondingly, whether genetic structure conformed to major habitat breaks. First, we used a model-based approach to assign coyote genotypes to distinct genetic clusters irrespective of geographical location. Visualization on a geographical information system revealed a strong concordance between the locations of cluster assignments and habitat bioregions, not explainable in terms of physical dispersal barriers or intervening low-quality habitat. Next, we used a multiple Mantel test, which controlled for effects of geographical distance (itself, marginally significant; P = 0.06), to statistically determine that genetic distance was indeed higher between than within bioregions (P < 0.001). Whereas previously published examples of landscape effects on gene flow have typically been explainable in terms of species-wide habitat affinities or dispersal barriers, our finding that genetic subdivisions were associated with unobstructed boundaries between contiguous habitats suggests a role for intraspecific variability in habitat affinities as a factor underlying genetic structure. In addition, our data combined with previously published data suggest a pattern of genetic isolation-by-distance throughout western North America, consistent with independent evidence that the western half of the coyote range predates European settlement.}, } @article {pmid15067131, year = {2004}, author = {Stenseth, NC and Ehrich, D and Rueness, EK and Lingjaerde, OC and Chan, KS and Boutin, S and O'Donoghue, M and Robinson, DA and Viljugrein, H and Jakobsen, KS}, title = {The effect of climatic forcing on population synchrony and genetic structuring of the Canadian lynx.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {101}, number = {16}, pages = {6056-6061}, pmid = {15067131}, issn = {0027-8424}, mesh = {Animals ; Canada ; Carnivora/*genetics ; *Climate ; Population Dynamics ; }, abstract = {The abundance of Canadian lynx follows 10-year density fluctuations across the Canadian subcontinent. These cyclic fluctuations have earlier been shown to be geographically structured into three climatic regions: the Atlantic, Continental, and Pacific zones. Recent genetic evidence revealed an essentially similar spatial structuring. Introducing a new population model, the "climate forcing of ecological and evolutionary patterns" model, we link the observed ecological and evolutionary patterns. Specifically, we demonstrate that there is greater phase synchrony within climatic zones than between them and show that external climatic forcing may act as a synchronizer. We simulated genetic drift by using data on population dynamics generated by the climate forcing of ecological and evolutionary patterns model, and we demonstrate that the observed genetic structuring can be seen as an emerging property of the spatiotemporal ecological dynamics.}, } @article {pmid15066774, year = {2004}, author = {Falkowski, PG and de Vargas, C}, title = {Genomics and evolution. Shotgun sequencing in the sea: a blast from the past?.}, journal = {Science (New York, N.Y.)}, volume = {304}, number = {5667}, pages = {58-60}, doi = {10.1126/science.1097146}, pmid = {15066774}, issn = {1095-9203}, mesh = {Adaptation, Biological ; Archaea/*genetics ; Atlantic Ocean ; Bacteria/*genetics ; Biodiversity ; Biological Evolution ; Chromosomes, Artificial, Bacterial ; Computational Biology ; DNA, Ribosomal/genetics ; *Ecosystem ; Genetic Variation ; Genome, Archaeal ; Genome, Bacterial ; *Genomics ; Plankton/genetics ; Polymerase Chain Reaction ; Seawater/*microbiology ; *Sequence Analysis, DNA ; Water Microbiology ; }, } @article {pmid15065739, year = {2004}, author = {Rohani, P and Miramontes, O and Keeling, MJ}, title = {The colour of noise in short ecological time series data.}, journal = {Mathematical medicine and biology : a journal of the IMA}, volume = {21}, number = {1}, pages = {63-72}, doi = {10.1093/imammb/21.1.63}, pmid = {15065739}, issn = {1477-8599}, mesh = {Censuses ; *Data Interpretation, Statistical ; *Ecology ; Population Dynamics ; }, abstract = {The statistical properties of ecological time series data and general trends therein have historically been of great interest to ecologists. In recent years, there has been a focus on establishing the relative importance of 'memory' in these data. The classic study by Pimm & Redfearn (1988 Nature, 334, 613-614) has been extremely important in establishing within the ecological community the idea that population time series are generally 'red-shifted' (dominated by long-term trends). This conclusion was reached by exploring the relationship between observed variability and census length in ecological data and comparing them with those for artificially generated data. Here, we highlight some subtle problems with this approach and suggest possible alternative methods of analysis, especially when the time series of interest are short.}, } @article {pmid15062801, year = {2004}, author = {Crespi, BJ and Fulton, MJ}, title = {Molecular systematics of Salmonidae: combined nuclear data yields a robust phylogeny.}, journal = {Molecular phylogenetics and evolution}, volume = {31}, number = {2}, pages = {658-679}, doi = {10.1016/j.ympev.2003.08.012}, pmid = {15062801}, issn = {1055-7903}, mesh = {Animals ; Base Sequence ; Bayes Theorem ; Cell Nucleus/genetics ; DNA/chemistry ; DNA, Mitochondrial/chemistry ; Databases, Nucleic Acid ; Molecular Sequence Data ; *Phylogeny ; Salmonidae/*classification/genetics ; Sequence Analysis, DNA ; }, abstract = {The phylogeny of salmonid fishes has been the focus of intensive study for many years, but some of the most important relationships within this group remain unclear. We used 269 Genbank sequences of mitochondrial DNA (from 16 genes) and nuclear DNA (from nine genes) to infer phylogenies for 30 species of salmonids. We used maximum parsimony and maximum likelihood to analyze each gene separately, the mtDNA data combined, the nuclear data combined, and all of the data together. The phylogeny with the best overall resolution and support from bootstrapping and Bayesian analyses was inferred from the combined nuclear DNA data set, for which the different genes reinforced and complemented one another to a considerable degree. Addition of the mitochondrial DNA degraded the phylogenetic signal, apparently as a result of saturation, hybridization, selection, or some combination of these processes. By the nuclear-DNA phylogeny: (1) (Hucho hucho, Brachymystax lenok) form the sister group to (Salmo, Salvelinus, Oncorhynchus, H. perryi); (2) Salmo is the sister-group to (Oncorhynchus, Salvelinus); (3) Salvelinus is the sister-group to Oncorhynchus; and (4) Oncorhynchus masou forms a monophyletic group with O. mykiss and O. clarki, with these three taxa constituting the sister-group to the five other Oncorhynchus species. Species-level relationships within Oncorhynchus and Salvelinus were well supported by bootstrap levels and Bayesian analyses. These findings have important implications for understanding the evolution of behavior, ecology and life-history in Salmonidae.}, } @article {pmid15059260, year = {2004}, author = {Pushker, R and Mira, A and Rodríguez-Valera, F}, title = {Comparative genomics of gene-family size in closely related bacteria.}, journal = {Genome biology}, volume = {5}, number = {4}, pages = {R27}, pmid = {15059260}, issn = {1474-760X}, mesh = {Chlamydophila pneumoniae/genetics/pathogenicity ; Computational Biology ; Escherichia coli/*genetics/pathogenicity ; Escherichia coli O157/*genetics/pathogenicity ; Evolution, Molecular ; Gene Transfer, Horizontal/genetics ; Genes, Bacterial/genetics/physiology ; *Genome, Bacterial ; Genomics/*methods ; Multigene Family/genetics/physiology ; Staphylococcus aureus/genetics/pathogenicity ; Streptococcus pyogenes/genetics/pathogenicity ; }, abstract = {BACKGROUND: The wealth of genomic data in bacteria is helping microbiologists understand the factors involved in gene innovation. Among these, the expansion and reduction of gene families appears to have a fundamental role in this, but the factors influencing gene family size are unclear.

RESULTS: The relative content of paralogous genes in bacterial genomes increases with genome size, largely due to the expansion of gene family size in large genomes. Bacteria undergoing genome reduction display a parallel process of redundancy elimination, by which gene families are reduced to one or a few members. Gene family size is also influenced by sequence divergence and physiological function. Large gene families show wider sequence divergence, suggesting they are probably older, and certain functions (such as metabolite transport mechanisms) are overrepresented in large families. The size of a given gene family is remarkably similar in strains of the same species and in closely related species, suggesting that homologous gene families are vertically transmitted and depend little on horizontal gene transfer (HGT).

CONCLUSIONS: The remarkable preservation of copy numbers in widely different ecotypes indicates a functional role for the different copies rather than simply a back-up role. When different genera are compared, the increase in phylogenetic distance and/or ecological specialization disrupts this preservation, albeit in a gradual manner and maintaining an overall similarity, which also supports this view. HGT can have an important role, however, in nonhomologous gene families, as exemplified by a comparison between saprophytic and enterohemorrhagic strains of Escherichia coli.}, } @article {pmid15049357, year = {2003}, author = {Philipson, P and Lindell, T}, title = {Can coral reefs be monitored from space?.}, journal = {Ambio}, volume = {32}, number = {8}, pages = {586-593}, doi = {10.1579/0044-7447-32.8.586}, pmid = {15049357}, issn = {0044-7447}, mesh = {Animals ; *Anthozoa ; Ecology ; Environmental Monitoring/*methods ; *Geographic Information Systems ; Population Dynamics ; Sensitivity and Specificity ; *Spacecraft ; }, abstract = {The dramatic bleaching events on the coral reefs recently have enhanced the need for environmental monitoring. Remote sensing is an important constituent for monitoring of reefs, and an invaluable complement to field observations. This paper discusses the possibilities and limitations of present high resolution satellites for mapping and monitoring coral reefs. The sensors with the best spatial and radiometric resolution available today, e.g. IKONOS, can be useful for mapping and monitoring of reefs, but they are too costly for global surveys. However, our coral bleaching studies indicate that massive bleaching could be detected even from satellites with lower resolution, like Landsat, SPOT, and IRS. They could also be useful for coarser, from a spatial and thematic point of view, global mapping and updating purposes. A more detailed monitoring requires both better spatial resolution and spectral resolution than today's sensors. In the future, it is necessary to construct a more reef specific sensor with a few specially selected narrow bands and a good spatial, radiometric and temporal resolution.}, } @article {pmid15049353, year = {2003}, author = {Sandström, P and Pahlén, TG and Edenius, L and Tømmervik, H and Hagner, O and Hemberg, L and Olsson, H and Baer, K and Stenlund, T and Brandt, LG and Egberth, M}, title = {Conflict resolution by participatory management: remote sensing and GIS as tools for communicating land-use needs for reindeer herding in northern Sweden.}, journal = {Ambio}, volume = {32}, number = {8}, pages = {557-567}, doi = {10.1579/0044-7447-32.8.557}, pmid = {15049353}, issn = {0044-7447}, mesh = {Agriculture ; Animals ; Communication ; *Conservation of Natural Resources ; Decision Making ; Environment ; Forestry ; *Geographic Information Systems ; Humans ; *Interprofessional Relations ; Mining ; *Problem Solving ; Recreation ; *Reindeer ; Sweden ; }, abstract = {When seeking to resolve complex land-management issues, geographical assessment of resources that are in short supply or in dispute can aid the communication of knowledge and the understanding among and between different stakeholders. In this paper, we illustrate how remote sensing and GIS can be used to gather and compile information regarding land-use activities and patterns among reindeer herders and other land users (forestry, mining, tourism, etc) in northern Sweden. The project represents a novel user-oriented effort largely based on the work carried out by the principal end user, i.e. the reindeer herders themselves. The basis for development of land-use plans for reindeer husbandry, was the following: to collect and digitally systemize traditional ecological and landscape knowledge of reindeer habitat use; to integrate this information with results from field inventories and satellite-based vegetation classifications; to map activities of other land users. The resulting land-use plans provide information that can facilitate consultation between the reindeer herders and other stakeholders and can facilitate operational work in reindeer management. This project can serve as a model for participatory involvement and planning, bringing indigenous knowledge and advanced remote-sensing techniques together in an interactive process.}, } @article {pmid15040888, year = {2004}, author = {Lin, WH and Ye, R and Ma, H and Xu, ZH and Xue, HW}, title = {DNA chip-based expression profile analysis indicates involvement of the phosphatidylinositol signaling pathway in multiple plant responses to hormone and abiotic treatments.}, journal = {Cell research}, volume = {14}, number = {1}, pages = {34-45}, doi = {10.1038/sj.cr.7290200}, pmid = {15040888}, issn = {1001-0602}, mesh = {1-Phosphatidylinositol 4-Kinase/genetics/physiology ; Arabidopsis/drug effects/*genetics/physiology ; Arabidopsis Proteins ; CDP-Diacylglycerol-Inositol 3-Phosphatidyltransferase ; Calcium Channels/genetics/physiology ; Calcium Chloride/pharmacology ; Cluster Analysis ; Cold Temperature ; Databases, Genetic ; Disasters ; Down-Regulation/drug effects ; Environment ; Gene Expression/drug effects ; *Gene Expression Profiling/methods ; Gene Expression Regulation, Plant/physiology ; Inositol 1,4,5-Trisphosphate Receptors ; Membrane Proteins ; *Oligonucleotide Array Sequence Analysis ; Phosphatidylinositol 3-Kinases/genetics/physiology ; Phosphatidylinositols/*metabolism ; Phospholipases/genetics/physiology ; Phosphoric Monoester Hydrolases/genetics/physiology ; Phosphotransferases (Alcohol Group Acceptor)/genetics/physiology ; Plant Growth Regulators/pharmacology/*physiology ; Plant Structures/drug effects/genetics/physiology ; RNA, Plant/genetics/isolation & purification ; Receptors, Cytoplasmic and Nuclear/genetics/physiology ; Reproducibility of Results ; Salicylic Acid/pharmacology ; Signal Transduction/*genetics/physiology ; Sodium Chloride/pharmacology ; Transferases (Other Substituted Phosphate Groups)/genetics/physiology ; Up-Regulation/drug effects ; }, abstract = {The phosphatidylinositol (PI) metabolic pathway is considered critical in plant responses to many environmental factors, and previous studies have indicated the involvement of multiple PI-related gene families during cellular responses. Through a detailed analysis of the Arabidopsis thaliana genome, 82 polypeptides were identified as being involved in PI signaling. These could be grouped into different families including PI synthases (PIS), PI-phosphate kinases (PIPK), phospholipases (PL), inositol polyphosphate phosphatases (IPPase), inositol polyphosphate kinases (IPK), PI transfer proteins and putative inositol polyphosphate receptors. The presence of more than 10 isoforms of PIPK, PLC, PLD and IPPase suggested that these genes might be differentially expressed during plant cellular responses or growth and development. Accordingly, DNA chip technology was employed to study the expression patterns of various isoforms. In total, 79 mRNA clones were amplified and used for DNA chip generation. Expression profile analysis was performed using samples that represented multiple tissues or cellular responses. Tested samples included normal leaf, stem and flower tissues, and leaves from plants treated with various hormones (auxin, cytokinin, gibberellin, abscisic acid and brassinosteroid) or environmental factors (temperature, calcium, sodium, drought, salicylic acid and jasmonic acid). Results showed that many PI pathway-related genes were differentially expressed under these experimental conditions. In particular, the different isoforms of each family were specifically expressed in many cases, suggesting their involvement in tissue specificity and cellular responses to environmental conditions. This work provides a starting point for functional studies of the relevant PI-related proteins and may help shed light onto the role of PI pathways in development and cellular responses.}, } @article {pmid15036697, year = {2004}, author = {Xu, X and Lin, H and Fu, Z}, title = {Probe into the method of regional ecological risk assessment-a case study of wetland in the Yellow River Delta in China.}, journal = {Journal of environmental management}, volume = {70}, number = {3}, pages = {253-262}, doi = {10.1016/j.jenvman.2003.12.001}, pmid = {15036697}, issn = {0301-4797}, mesh = {China ; *Ecology ; Environmental Monitoring/methods ; Environmental Pollutants/*adverse effects ; Forecasting ; *Geographic Information Systems ; *Models, Statistical ; Risk Assessment ; *Rivers ; }, abstract = {Ecological risk assessment (ERA) is a new field of study for evaluating the risks associated with a possible eco-environmental hazard under uncertainty. Regional ERA is more complex than general ERA, as it requires that risk receptors, risk sources, risk exposure, uncertainty and especially spatial heterogeneity all be taken into account. In this paper, a five-step process of regional ERA is developed and tested through a wetland case study in the Yellow River Delta in China. First, indices and formulas are established for measuring degrees of ecological risk and damage to ecosystems. Using a combination of remote sensing data, historical records and survey data, and with the assistance of GIS techniques, the indices and formulas are then applied to the wetland in the study area. On the basis of the assessment results, we propose a number of countermeasures for the various risk zones in the Yellow River Delta.}, } @article {pmid15031939, year = {2003}, author = {Han, H and Gao, J and Liu, G}, title = {[Ecological benefit assessment of urban vegetations by remote sensing and GIS].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {14}, number = {12}, pages = {2301-2304}, pmid = {15031939}, issn = {1001-9332}, mesh = {City Planning ; *Ecology ; Environmental Monitoring/*methods ; *Geographic Information Systems ; *Plant Development ; }, abstract = {As an important part of the urban ecosystem, urban vegetation plays an important role in improving urban environmental quality. The assessment of ecological benefits of urban or regional vegetations can help us more properly plan urban green space pattern, optimize urban vegetation structure, and further strengthen ecological construction. Through the discussion of the relevant researches at home and abroad, it's indicated that remote sensing and GIS could help as better evaluate the ecological effect of urban vegetations. This article introduced the UEA method adopted by AMERICAN FORESTS and CITYgreen software working with ArcView 3.2, as to make the best use of remote sensing and GIS in evaluating urban vegetation ecological effect quantitatively, and to promote sustainable development and ecological construction.}, } @article {pmid15031899, year = {2003}, author = {Wu, Z and Wu, W and Gao, J and Zhang, S}, title = {[Analysis of urban forest landscape pattern in Hefei].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {14}, number = {12}, pages = {2117-2122}, pmid = {15031899}, issn = {1001-9332}, mesh = {China ; *Ecology ; Geographic Information Systems ; Trees/*growth & development ; Urbanization ; }, abstract = {Based on the theory and methodology of landscape ecology, the landscape pattern of the study area (17.6 km2) in the downtown of Hefei was analyzed by using the techniques of RS, GPS and GIS. The object was to provide a comprehensive method to study urban forest structure and its function in environmental improvement. The results showed that there were 5 major landscape elements, i.e., building and hard pavement surface, water, road, urban forest, and general green land in the area. The landscape matrix was building and pavement surface, occupied 73.13% of total land. Road was the typical corridor element in the city and occupied 6.89%. Green land occupied 11.44%, in which, urban forest patch occupied 9.18%. There were 408 urban forest patches, with an area of 161.16 hm2. The average area of the patch was 0.396 hm2, and the maximum area was 12 hm2. 48% of urban forest patch was identified as small scale patches with < 500 m2 of area, and only 8.6% of them was larger than 1 hm2. The number of general green land patch was 255, with an area of 39.74 hm2, which accounted for 2.26% of land area, and its average and maximum area was 0.1558 hm2 and 3.86 hm2, respectively. There were 147 water patches, with an area of 149.93 hm2, and occupied 8.54% of land, and the average and maximum area of the patch was 1.02 hm2 and 16 hm2, respectively. In the study area, both of the Shannon-Weiner landscape diversity index and evenness were low, only 0.928 and 0.576, respectively. In addition, the dominance of urban forest patch and general green land was 0.39 showing that the two landscape elements had a certain influence on the environment of the study area. The concept of interior habitat for forest was introduced in this paper, which was employed to make a scale class system of urban forest patch. The threshold area with interior habitat for urban forest patch was 9800 m2, and there was 31.69 hm2 of interior habitat of urban forest in total, which occupied 19.7% of the total area of urban forest patch. This situation was not favorable for providing more habitats to support species diversity. It's suggested that the concept of interior habitat could be employed to identify urban forest patch, and a scale system of small scale patch of urban forest-middle patch-large patch-extra large patch was build in the paper. Based on this system, the ratio of different scales of urban forest patch in the study area should be 2:2:2:3. The authors also suggested that larger pieces (1.5-3.0 hm2) of urban forest patch should be built, and more urban forests should be established in the northeastern part of the city in the future.}, } @article {pmid15031897, year = {2003}, author = {Hu, Z and He, X and Chen, W and Li, Y and Li, H}, title = {[Structure and ecological benefits of urban forest in Shenyang build-up area].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {14}, number = {12}, pages = {2108-2112}, pmid = {15031897}, issn = {1001-9332}, mesh = {China ; Ecology ; Geographic Information Systems ; Poaceae/growth & development ; Trees/*growth & development ; Urbanization ; }, abstract = {Investigations were made in the sampling plots covering 243 km2 of the Shenyang urban area, and the results were used as the input for the Urban Forest Management Information System (UFMIS), which was developed based on the model of CITY green. With this system, and using tree species, tree density, tree height grade distribution, tree DBH (diameter at beast height) grade distribution, and tree health condition as parameters, the land use and forest structure in Shenyang City were analyzed. It was found that there were 1,914,500 trees in Shenyang, belonging to 136 species. The 25 dominant species accounted for 84.78% of the total number of trees, and the forest coverage was 9.765%. Trees with DBH < 0.25 m and > 0.5 m accounted for 82.8% of the total, and the young, middle-aged and old trees occupied 27%, 58% and 15% of the total, respectively. The healthy status of 84% of the trees was above middle level. Therefore, the forest in Shenyang urban is at a stable stage. According to the statistical results from UFMIS, the ecological value of forest in Shenyang urban is as high as 26,526,955. 1 USD in terms of economy.}, } @article {pmid15031894, year = {2003}, author = {Zhu, W and He, X and Chen, W and Chen, Y and Zhang, Y and Ning, Z}, title = {[Quantitative analysis of urban forest structure: a case study on Shenyang arboretum].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {14}, number = {12}, pages = {2090-2094}, pmid = {15031894}, issn = {1001-9332}, mesh = {*City Planning ; Ecology ; Geographic Information Systems ; Trees/*growth & development ; }, abstract = {The spatial features and attribute data of urban forests in Shenyang arboretum were acquired by using aerial photographs and field investigation. After systemic and quantitative analysis of the species composition and spatial distribution pattern of urban forest community based on geographic information system (GIS), the following results were achieved: 1) the vegetation in the arboretum was rich and in a good condition. Phellodendron amurense, Robinia pseudoacacia, and Ulmus punita were the main species according to their abundant individuals and relative dominance. The spatial distribution pattern of this vegetation indicated that it was in a growing level and in the best state for ecological benefits; 2) the tree species relative dominance based on vegetation quantity had no distinct relationship with the species abundance, and the species having abundant individuals might have a low relative dominance; and 3) the curve displayed in the relationship diagram between tree individuals and tree height showed ascending and protruding. With the increment of tree height class, the individuals were unchanged nearly at the beginning, but when the height was more than 12 m, the individuals reduced distinctly, and the curve displayed a quickly declined trend. The relationship between tree individuals and tree diameter at the breast height (DBH) showed the same result.}, } @article {pmid15026235, year = {2004}, author = {Simon, U and Brüggemann, R and Pudenz, S}, title = {Aspects of decision support in water management--example Berlin and Potsdam (Germany) I--spatially differentiated evaluation.}, journal = {Water research}, volume = {38}, number = {7}, pages = {1809-1816}, doi = {10.1016/j.watres.2003.12.037}, pmid = {15026235}, issn = {0043-1354}, mesh = {Cities ; *Decision Support Techniques ; Germany ; *Models, Theoretical ; Risk Assessment ; *Waste Disposal, Fluid ; Water Pollutants/isolation & purification ; }, abstract = {Decisions about sustainable development demand spatially differentiated evaluations. As an example, we demonstrate the evaluation of water management strategies in the cities of Berlin and Potsdam (Germany) with respect to their ecological effects in 14 sections of the surface water system. Two decision support systems were compared, namely PROMETHEE, which is designed to obtain a clear decision (linear ranking), and Hasse Diagram Technique (HDT), normally providing more than one favourable solution (partial order). By PROMETHEE, the spatial differentiation had unwanted effects on the result, negating the stakeholders determined weighting of indicators. Therefore, the stakeholder can barely benefit from the convenience of obtaining a clear decision (linear ranking). In contrast, the result obtained by HDT was not influenced by spatial differentiation. Furthermore, HDT provided helpful tools to analyse the evaluation result, such as the concept of antagonistic indicators to discover conflicts in the evaluation process.}, } @article {pmid15020487, year = {2004}, author = {Turelli, M and Barton, NH}, title = {Polygenic variation maintained by balancing selection: pleiotropy, sex-dependent allelic effects and G x E interactions.}, journal = {Genetics}, volume = {166}, number = {2}, pages = {1053-1079}, pmid = {15020487}, issn = {0016-6731}, mesh = {Data Interpretation, Statistical ; *Genetic Variation ; Models, Genetic ; *Multifactorial Inheritance ; *Selection, Genetic ; }, abstract = {We investigate three alternative selection-based scenarios proposed to maintain polygenic variation: pleiotropic balancing selection, G x E interactions (with spatial or temporal variation in allelic effects), and sex-dependent allelic effects. Each analysis assumes an additive polygenic trait with n diallelic loci under stabilizing selection. We allow loci to have different effects and consider equilibria at which the population mean departs from the stabilizing-selection optimum. Under weak selection, each model produces essentially identical, approximate allele-frequency dynamics. Variation is maintained under pleiotropic balancing selection only at loci for which the strength of balancing selection exceeds the effective strength of stabilizing selection. In addition, for all models, polymorphism requires that the population mean be close enough to the optimum that directional selection does not overwhelm balancing selection. This balance allows many simultaneously stable equilibria, and we explore their properties numerically. Both spatial and temporal G x E can maintain variation at loci for which the coefficient of variation (across environments) of the effect of a substitution exceeds a critical value greater than one. The critical value depends on the correlation between substitution effects at different loci. For large positive correlations (e.g., rho(ij)2>3/4), even extreme fluctuations in allelic effects cannot maintain variation. Surprisingly, this constraint on correlations implies that sex-dependent allelic effects cannot maintain polygenic variation. We present numerical results that support our analytical approximations and discuss our results in connection to relevant data and alternative variance-maintaining mechanisms.}, } @article {pmid15017777, year = {2004}, author = {Stukalov, SE and Shchepetneva, MA and Kornienko, VN}, title = {[Clinical-immunological and ecological research in diabetic retinopathy].}, journal = {Vestnik oftalmologii}, volume = {120}, number = {1}, pages = {36-39}, pmid = {15017777}, issn = {0042-465X}, mesh = {Adjuvants, Immunologic/therapeutic use ; Adult ; Blood/radiation effects ; Data Interpretation, Statistical ; *Diabetic Retinopathy/blood/diagnosis/etiology/immunology/radiotherapy/surgery/therapy ; Ecology ; Humans ; Laser Coagulation ; Middle Aged ; Nucleic Acids/therapeutic use ; Peptides/therapeutic use ; Power Plants ; Radioactive Hazard Release ; Research ; Risk Factors ; Thymus Extracts/therapeutic use ; Ukraine ; }, abstract = {Two hundred and ninety-six patients with diabetic retinopathy (DR) were examined: conservative therapy and laser coagulation of the retina were applied in 120 and 176 of them, respectively. The ecological situation in the residence region and its impact on the morbidity and immune status of DR patients were analyzed. The comfort degree of the environment and the level of anthropogenic contamination affect the morbidity and immunogram results. Immune-correctors, i.e. T-activin, sodium nucleinate and laser blood irradiation (LBI), were used within treatment schemes in DR. Laser coagulation of the retina is advisable to assign in combination with sodium nucleinate and LBI in the aftercare of patients concurrently with complex therapy; T-activin is used, within conservative therapy, to correct the unfavorable ecological impact exerted on patient's body.}, } @article {pmid15015699, year = {2003}, author = {Hirzel, AH and Arlettaz, R}, title = {Modeling habitat suitability for complex species distributions by environmental-distance geometric mean.}, journal = {Environmental management}, volume = {32}, number = {5}, pages = {614-623}, pmid = {15015699}, issn = {0364-152X}, mesh = {Algorithms ; Animals ; *Conservation of Natural Resources ; *Ecosystem ; Environment ; Factor Analysis, Statistical ; *Geographic Information Systems ; *Models, Theoretical ; Population Dynamics ; Raptors ; Software ; }, abstract = {This paper presents a new habitat suitability modeling method whose main properties are as follows: (1) It is based on the density of observation points in the environmental space, which enables it to fit complex distributions (e.g. nongaussian, bimodal, asymmetrical, etc.). (2) This density is modeled by computing the geometric mean to all observation points, which we show to be a good trade-off between goodness of fit and prediction power. (3) It does not need any absence information, which is generally difficult to collect and of dubious reliability. (4) The environmental space is represented either by an expert-selection of standardized variables or the axes of a factor analysis [in this paper we used the Ecological Niche Factor Analysis (ENFA)]. We first explain the details of the geometric mean algorithm and then we apply it to the bearded vulture (Gypaetus barbatus) habitat in the Swiss Alps. The results are compared to those obtained by the "median algorithm" and tested by jack-knife cross-validation. We also discuss other related algorithms (BIOCLIM, HABITAT, and DOMAIN). All these analyses were implemented into and performed with the ecology-oriented GIS software BIOMAPPER 2.0.The results show the geometric mean to perform better than the median algorithm, as it produces a tighter fit to the bimodal distribution of the bearded vulture in the environmental space. However, the "median algorithm" being quicker, it could be preferred when modeling more usual distribution.}, } @article {pmid15015696, year = {2003}, author = {Griffith, JA and Stehman, SV and Loveland, TR}, title = {Landscape trends in Mid-Atlantic and Southeastern United States ecoregions.}, journal = {Environmental management}, volume = {32}, number = {5}, pages = {572-588}, pmid = {15015696}, issn = {0364-152X}, mesh = {*Conservation of Natural Resources ; *Ecosystem ; *Environment Design ; Environmental Monitoring ; Forestry ; *Geographic Information Systems ; Southeastern United States ; Trees ; }, abstract = {Landscape pattern and composition metrics are potential indicators for broad-scale monitoring of change and for relating change to human and ecological processes. We used a probability sample of 20-km x 20-km sampling blocks to characterize landscape composition and pattern in five US ecoregions: the Middle Atlantic Coastal Plain, Southeastern Plains, Northern Piedmont, Piedmont, and Blue Ridge Mountains. Land use/and cover (LULC) data for five dates between 1972 and 2000 were obtained for each sample block. Analyses focused on quantifying trends in selected landscape pattern metrics by ecoregion and comparing trends in land cover proportions and pattern metrics among ecoregions. Repeated measures analysis of the landscape pattern documented a statistically significant trend in all five ecoregions towards a more fine-grained landscape from the early 1970s through 2000. The ecologically important forest cover class also became more fine-grained with time (i.e., more numerous and smaller forest patches). Trends in LULC, forest edge, and forest percent like adjacencies differed among ecoregions. These results suggest that ecoregions provide a geographically coherent way to regionalize the story of national land use and land cover change in the United States. This study provides new information on LULC change in the southeast United States. Previous studies of the region from the 1930s to the 1980s showed a decrease in landscape fragmentation and an increase in percent forest, while this study showed an increase in forest fragmentation and a loss of forest cover.}, } @article {pmid15015256, year = {2003}, author = {Xiao, PG and Chen, SL}, title = {[Establishment of the national macro-management system on Chinese medicinal resource--base of the modernization for Chinese medicine].}, journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica}, volume = {28}, number = {1}, pages = {4-6}, pmid = {15015256}, issn = {1001-5302}, mesh = {China ; *Conservation of Natural Resources ; Databases, Factual ; *Drugs, Chinese Herbal ; Ecology ; Geographic Information Systems ; *Management Information Systems ; Medicine, Chinese Traditional ; *Plants, Medicinal ; }, abstract = {OBJECTIVE: To establish a national management system on the utilization and protection, reserves and wastes of Chinese medicinal resources, and provide a scientific basis for the national administering authorities for the macro-management.

METHOD: Many modern high technologies of community ecology, statistics, 3S technologies (remote sensing RS, geographic information system GIS, global positioning system GPS) and computer information system were based upon, and a national monitoring and protection system for the Chinese medicinal resources was set up.

RESULT AND CONCLUSION: The national Chinese medicinal macro-management system will integrate modern high technologies with administrative supervision, so as to protect Chinese medicinal resources and economy towards a sustainable utilization and development, and finally make our country and people more prosperous and powerful.}, } @article {pmid15012960, year = {2004}, author = {Tang, KL and McNyset, KM and Holcroft, NI}, title = {The phylogenetic position of five genera (Acanthochromis, Azurina, Chrysiptera, Dischistodus, and Neopomacentrus) of damselfishes (Perciformes: Pomacentridae).}, journal = {Molecular phylogenetics and evolution}, volume = {30}, number = {3}, pages = {823-828}, doi = {10.1016/S1055-7903(03)00228-8}, pmid = {15012960}, issn = {1055-7903}, mesh = {Animals ; Classification ; DNA, Mitochondrial/genetics ; DNA, Ribosomal/genetics ; Databases as Topic ; Evolution, Molecular ; Molecular Sequence Data ; Perciformes/*genetics ; Phylogeny ; RNA, Transfer, Phe/genetics ; Sequence Analysis, DNA ; Species Specificity ; }, } @article {pmid15012936, year = {2004}, author = {Thomas, GH and Wills, MA and Székely, T}, title = {Phylogeny of shorebirds, gulls, and alcids (Aves: Charadrii) from the cytochrome-b gene: parsimony, Bayesian inference, minimum evolution, and quartet puzzling.}, journal = {Molecular phylogenetics and evolution}, volume = {30}, number = {3}, pages = {516-526}, doi = {10.1016/S1055-7903(03)00222-7}, pmid = {15012936}, issn = {1055-7903}, mesh = {Animals ; Bayes Theorem ; Birds/*genetics ; Classification ; Cytochromes b/*genetics ; DNA/metabolism ; Databases as Topic ; Evolution, Molecular ; Likelihood Functions ; Nucleic Acid Hybridization ; Phylogeny ; Software ; }, abstract = {Charadrii (shorebirds, gulls, and alcids) have exceptional diversity in ecological, behavioral, and life-history traits. A phylogenetic framework is necessary to fully understand the relationships among these traits. Despite several attempts to resolve the phylogeny of the Charadrii, none have comprehensively utilized molecular sequence data. Complete and partial cytochrome-b gene sequences for 86 Charadrii and five Falconides species (as outgroup taxa) were obtained from GenBank and aligned. We analyzed the resulting matrices using parsimony, Bayesian inference, minimum evolution, and quartet puzzling methods. Posterior probabilities, decay indices, and bootstrapping provide strong support for four major lineages consisting of gulls, alcids, plovers, and sandpipers, respectively. The broad structure of the trees differ significantly from all previous hypotheses of Charadrii phylogeny in placing the plovers at the base of the tree below the sandpipers in a pectinate sequence towards a large clade of gulls and alcids. The parsimony, Bayesian, and minimum evolution models provide strong evidence for this phylogenetic hypothesis. This is further corroborated by non-tree based measures of support and conflict (Lento plots). The quartet puzzling trees are poorly resolved and inconclusive.}, } @article {pmid15012935, year = {2004}, author = {Dorchin, N and Freidberg, A and Mokady, O}, title = {Phylogeny of the Baldratiina (Diptera: Cecidomyiidae) inferred from morphological, ecological and molecular data sources, and evolutionary patterns in plant-galler relationships.}, journal = {Molecular phylogenetics and evolution}, volume = {30}, number = {3}, pages = {503-515}, doi = {10.1016/S1055-7903(03)00232-X}, pmid = {15012935}, issn = {1055-7903}, mesh = {Animals ; Classification ; DNA/metabolism ; DNA, Mitochondrial/genetics ; DNA, Ribosomal/genetics ; Databases as Topic ; Diptera/*genetics ; Ecology ; Evolution, Molecular ; Phylogeny ; Plants/*metabolism ; Species Specificity ; }, abstract = {The phylogeny of the gall-midge subtribe Baldratiina (Diptera: Cecidomyiidae) was reconstructed from molecular (partial sequence of the mitochondrial 12S rDNA), morphological and ecological data sets, using 16 representative species of most of the genera. The morphological and ecological data were combined in a single character matrix and analyzed separately from the molecular data, resulting in an eco-morphological cladogram and a molecular cladogram. Attributes of galls and host associations were superimposed on the molecular cladogram in order to detect possible trends in the evolution of these traits. The cladograms resulting from the two independent analyses were statistically incongruent, although both provide evidence for the monophyly of the genera Baldratia and Careopalpis and the paraphyly of the genera Stefaniola and Izeniola. The results suggest a minor impact of the morphological characters traditionally used in the classification of the Baldratiina, whereas ecological data had a major impact on the phylogenetic inference. Mapping of gall and host attributes on the molecular cladogram suggests that multi-chambered stem galls constitute the ancestral state in the subtribe, with several subsequent shifts to leaf galls. It is concluded that in contrast to other studied groups of gall insects, related baldratiine species induce different types of galls, attesting to speciation driven by gall-type shifts at least as often as host shifts.}, } @article {pmid15000648, year = {2004}, author = {Sáenz-de-Miera, LE and Ayala, FJ}, title = {Complex evolution of orthologous and paralogous decarboxylase genes.}, journal = {Journal of evolutionary biology}, volume = {17}, number = {1}, pages = {55-66}, doi = {10.1046/j.1420-9101.2003.00652.x}, pmid = {15000648}, issn = {1010-061X}, support = {GM42397/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Carboxy-Lyases/*genetics ; Databases, Genetic ; *Evolution, Molecular ; Likelihood Functions ; Models, Genetic ; *Phylogeny ; Sequence Alignment ; Time Factors ; }, abstract = {The decarboxylases are involved in neurotransmitter synthesis in animals, and in pathways of secondary metabolism in plants. Different decarboxylase proteins are characterized for their different substrate specificities, but are encoded by homologous genes. We study, within a maximum-likelihood framework, the evolutionary relationships among dopa decarboxylase (Ddc), histidine decarboxylase (Hdc) and alpha-methyldopa hypersensitive (amd) in animals, and tryptophan decarboxylase (Wdc) and tyrosine decarboxylase (Ydc) in plants. The evolutionary rates are heterogeneous. There are differences between paralogous genes in the same lineages: 4.13 x 10(-10) nucleotide substitutions per site per year in mammalian Ddc vs. 1.95 in Hdc; between orthologous genes in different lineages, 7.62 in dipteran Ddc vs. 4.13 in mammalian Ddc; and very large temporal variations in some lineages, from 3.7 up to 54.9 in the Drosophila Ddc lineage. Our results are inconsistent with the molecular clock hypothesis.}, } @article {pmid14997659, year = {2003}, author = {Su, F and Zhou, C and Zhang, T and Du, Y and Yao, C}, title = {[Spatial heterogeneity of pelagic fishery resources in the East China Sea].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {14}, number = {11}, pages = {1971-1975}, pmid = {14997659}, issn = {1001-9332}, mesh = {Animals ; Ecology ; *Fisheries ; *Geographic Information Systems ; }, abstract = {Quantitative description of spatial heterogeneity can help the understanding of the distribution of fishery resources and its relationship with the environment from ecological view. Based on geographic information system, the Geary index for the density distribution of pelagic fish was calculated, and the semivariograms were drawn. The Geary value c was 0.25 and Co/(Co + C) was 19.1%, indicating that the distribution of the pelagic fish had a high spatial autocorrelation with anisotropy. The sharp slope of semivariogram in the directions of 45 degrees and 135 degrees meant that there existed important dynamic environmental processes in the two directions. The annual fluctuation of fishery resource density was caused by the spatial autocorrelation, because the density had a significantly positive correlation with value C, but no correlation with Co. The fractal dimension D was negatively correlated with the density, meaning that the density increase was resulted from the increase of spatial fish centralizing.}, } @article {pmid14997655, year = {2003}, author = {Zhu, N and Wang, C and Zhou, H and Li, M}, title = {[Analysis on instantaneous spatial pattern of thermal force field in Harbin].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {14}, number = {11}, pages = {1955-1958}, pmid = {14997655}, issn = {1001-9332}, mesh = {City Planning ; *Ecology ; Geographic Information Systems ; *Hot Temperature ; Temperature ; }, abstract = {The spatial pattern of urban thermal force field is not only the dominant content in assessing city ecological environment, but also an important base for city green system planning. The status of spatial pattern of thermal force field in Harbin was analyzed with RS and GIS techniques. Based on the instantaneous radiation temperature of the land surfaces in the city when the TM image was sensed remotely, all the patches were divided into 3 levels, i.e., low radiation temperature (< 10 degrees C), middle radiation temperature (10-22 degrees C), and high radiation temperature of the land surfaces (22-31 degrees C). The patches with high radiation temperature accounted for 61%, those with low radiation temperature accounted for 17%, and those with middle radiation temperature accounted for 22%. 7018 patches (12,252 hm2 in total) with super-thermal radiation (> 28 degrees C) were uneven in their areas. The biggest area in these patches was 1489 hm2, and the smallest one was 0.72 hm2. The proportion of the patches with an area less than 1 hm2, between 1-5 hm2, and more than 5 hm2 was 95.02%, 3.46%, and 1.58%, respectively. There were 3 types of spatial patterns of the super-thermal radiation patches, i.e., round form (the average radiation temperature was 30.8 degrees C), ring form (the average radiation temperature was 27 degrees C), and pieces form (the average radiation temperature was 24.7 degrees C). Daowai District and Daoli District were round form, districts along the ring routes of railway in the city were ring form, and Nangang District and Dongli District were pieces form. Some advices to resolve the problem of 'heat island effect' influenced by the factors including greenland covering rate, greenland area and building dimension were discussed.}, } @article {pmid14996367, year = {2004}, author = {Kabatereine, NB and Brooker, S and Tukahebwa, EM and Kazibwe, F and Onapa, AW}, title = {Epidemiology and geography of Schistosoma mansoni in Uganda: implications for planning control.}, journal = {Tropical medicine & international health : TM & IH}, volume = {9}, number = {3}, pages = {372-380}, doi = {10.1046/j.1365-3156.2003.01176.x}, pmid = {14996367}, issn = {1360-2276}, mesh = {Adolescent ; Adult ; Age Distribution ; Child ; Child, Preschool ; Ecosystem ; Female ; Geographic Information Systems ; Humans ; Male ; Population Surveillance/methods ; Prevalence ; Preventive Health Services/organization & administration ; Risk Factors ; Schistosomiasis mansoni/*epidemiology ; Topography, Medical ; Uganda/epidemiology ; }, abstract = {Intestinal schistosomiasis caused by infection with Schistosoma mansoni is a widespread public health problem in Uganda. Although long known to be endemic, its current distribution within the country requires updating of parasitological data to help guide planned control. We report such data collected between 1998 and 2002 from 201 schools and 68 communities across Uganda. In accordance with epidemiological expectation, prevalence and intensity increased with age, peaking at 10-20 years and thereafter declined moderately with age, whereas intensity declined more rapidly with age, and the prevalence of infection in a school was non-linearly related to the mean intensity of infection. We used geographical information systems to map the distribution of infection and to overlay parasitological data with interpolated environmental surfaces. The derived maps indicate both a widespread occurrence of infection and a marked variability in infection prevalence, with prevalence typically highest near the lakeshore and along large rivers. No transmission occurred at altitudes >1400 m or where total annual rainfall was <900 mm; limits which can help estimate the population at risk of schistosomiasis. The results are discussed in reference to the ecology of infection and provide an epidemiological framework for the design and implementation of control efforts underway in Uganda.}, } @article {pmid14994480, year = {2003}, author = {Kalinkina, NM and Kulikova, TP and Morozov, AK and Vlasova, LI}, title = {[Causes of the technogenic changes in a freshwater zooplankton community].}, journal = {Izvestiia Akademii nauk. Seriia biologicheskaia}, volume = {}, number = {6}, pages = {747-753}, pmid = {14994480}, issn = {1026-3470}, mesh = {Animals ; Copepoda/physiology ; Crustacea/physiology ; Daphnia/physiology ; Data Interpretation, Statistical ; Ecology ; Fresh Water/analysis/*chemistry ; Ions ; Minerals/analysis ; Russia ; Zooplankton/*physiology ; }, abstract = {The situation in water bodies of northwestern Karelia in 1992-2001 was analyzed. As a result of waste discharge from the mining and ore-processing works, weakly mineralized hydrocarbonate-calcium waters changed into highly mineralized waters with the prevalence of potassium ions and sulfates. The total abundance and biomass of zooplanktonic communities decreased. Using the methods of principal components and partial correlations, differences in the responses of zooplankters to mineral pollution were revealed. Typical inhabitants of northern water bodies decreased in numbers, and the species Eudiaptomus gracilis Sars and Heterocope appendiculata Sars (Calanoida) disappeared. On the other hand, eurybiontic species prevailing in water bodies with higher mineralization manifested a positive reaction to the increase in the contents of dissolved mineral compounds. Toxicological experiments made it possible to estimate the survival threshold for E. gracilis and H. appendiculata: the populations of these crustaceans in the polluted water body perished when potassium concentration in water exceeded 50 mg/l.}, } @article {pmid14994311, year = {2004}, author = {Sokal, RR}, title = {Raymond Pearl's legacy: the proper measure of man.}, journal = {American journal of human biology : the official journal of the Human Biology Council}, volume = {16}, number = {2}, pages = {113-124}, doi = {10.1002/ajhb.20001}, pmid = {14994311}, issn = {1042-0533}, mesh = {Anthropometry/*methods ; Bias ; Data Interpretation, Statistical ; Humans ; Research Design ; Statistics as Topic/*methods ; }, abstract = {During much of his academic career, Raymond Pearl advocated the employment of quantitative and statistical methods in biology and applied them in his own voluminous research output, much of it in various aspects of human biology. If he were to return today, he would be pleased to note the fruits of his advocacy-the widespread quantification of biological and anthropological research. He would undoubtedly be impressed with the tremendous progress in statistical analysis in the 63 years since he ceased his work and with that amazing tool, the personal computer. But he would also note the dangers inherent in applying these powerful methods without sufficient regard for the experimental or observational designs they require and for their basic assumptions. Among the errors Pearl would note are: 1) the use of canned computer programs in ignorance of or inattention to their implied assumptions; 2) testing many contrasts in one dataset without making allowances for the lack of independence of these tests; 3) ignoring the effects of lack of independence (autocorrelation) when working with spatially, temporally, or phylogenetically related data; 4) presenting distorted ordination plots; and 5) using an unrealistic null distribution in computation or simulation, as when employing sample sizes too small to test the hypotheses the investigator is interested in. All of these errors are common not only in publications on physical anthropology and human biology, but also in the wider biological literature.}, } @article {pmid14992036, year = {2003}, author = {Knoors, H and Meuleman, J and Klatter-Folmer, J}, title = {Parents' and teachers' evaluations of the communicative abilities of deaf children.}, journal = {American annals of the deaf}, volume = {148}, number = {4}, pages = {287-294}, doi = {10.1353/aad.2003.0027}, pmid = {14992036}, issn = {0002-726X}, mesh = {*Communication ; Data Interpretation, Statistical ; *Faculty ; Female ; Humans ; Male ; *Mothers ; *Persons With Hearing Impairments ; Surveys and Questionnaires ; *Verbal Behavior ; }, abstract = {The authors compared evaluations by parents and teachers of the communicative abilities of deaf children. Such comparisons between parents' and professionals' assessments of the language development of children who are deaf can provide useful information on which to base ecologically valid intervention approaches. A secondary interest of the authors was to investigate the possible influences on language development of gender, the presence or absence of cochlear implantation, and communication modality (i.e., auditory-verbal or bilingual). The study included the mothers and teachers of 14 deaf children educated in auditory-verbal or bilingual programs. Two scales from a survey instrument, Profiles of the Hearing Impaired (Webster & Webster, 1995), were used. No significant differences between the teachers' and parents' evaluations were found. Gender, cochlear implantation, and communication modality were found to have no significant effect on the evaluations.}, } @article {pmid14986363, year = {2003}, author = {Jiang, Y and Zhang, Y and Liang, W and Wen, D and Chen, W}, title = {[Spatial variability of soil nutrients in cultivated surface soil of Sujiatun District, Shenyang City].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {14}, number = {10}, pages = {1673-1676}, pmid = {14986363}, issn = {1001-9332}, mesh = {Geographic Information Systems ; Nitrogen/analysis ; Organic Chemicals/analysis ; Phosphorus/analysis ; Potassium/analysis ; Soil/*analysis ; }, abstract = {The spatial variability of organic matter (OM), available nitrogen (AN), available phosphorus (AP), and available potassium (AK) in 0-20 cm horizon in cultivated soils of Sujiatun District, Shenyang City were investigated using geostatistics and geographic information system (GIS). Data of each variable fitted normal distribution or normal distribution after log transformation, and a spherical model for semivariogram fitted all the variables. Semivariograms indicated that OM content strongly spatially dependent with the ratio of nugget to sill of 24.11%. The contents of AN, AP and AK were moderately spatially dependent with the ratio of nugget to sill of 29.53%, 60.77% and 58.82%, respectively. The ranges of spatially dependent for OM, AN, AP and AK were 26.051, 28.293, 15.132 and 23.813 km, respectively. The spatial variability for OM and AN was fundamentally affected by structural factors such as soil formation factors, and that for AP and AK was by random factors such as fertilization. Kriging maps showed the spatial distributions of the four variables, which were useful in monitoring nutrient changes and providing quantitative support to decision and policy making for agriculture and environment management.}, } @article {pmid14963097, year = {2004}, author = {Shiu, SH and Li, WH}, title = {Origins, lineage-specific expansions, and multiple losses of tyrosine kinases in eukaryotes.}, journal = {Molecular biology and evolution}, volume = {21}, number = {5}, pages = {828-840}, doi = {10.1093/molbev/msh077}, pmid = {14963097}, issn = {0737-4038}, support = {5F32 GM 066554/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Cell Lineage ; Databases as Topic ; Eukaryota/*genetics ; Eukaryotic Cells ; Evolution, Molecular ; Expressed Sequence Tags ; Gene Deletion ; Gene Duplication ; Genome ; Humans ; Mutation ; Phylogeny ; Protein Kinases/metabolism ; Protein-Tyrosine Kinases/*genetics ; Signal Transduction ; Species Specificity ; Time Factors ; }, abstract = {Tyrosine kinases are important components of metazoan signaling pathways, and their mutant forms are implicated in various malignancies. Searching the sequences from the genomes of 28 eukaryotes and the GenBank, we found tyrosine kinases not only in metazoans but also in the green algae Chlamydomonas reinhardtii, the potato late blight pathogen Phytophthora infestans, and the protozoan pathogen Entamoeba histolytica, contrary to the current view that tyrosine kinases are animal-specific. Based on a phylogenetic analysis, we divided this gene family into 43 subfamilies and found that at least 19 tyrosine kinases were likely present in the common ancestor of chordates, arthropods, and nematodes. Interestingly, most of the subfamilies have conserved domain organizations among subfamily members but have undergone different degrees of expansion during the evolution of metazoans. In particular, a large number of duplications occurred in the lineage leading to the common ancestor of Tagifugu and mammals after its split from the Ciona lineage about 450 to 550 MYA. The timing of expansion coincides with proposed large-scale duplication event in the chordate lineage. Furthermore, gene losses have occurred in most subfamilies. Interestingly, different subfamilies have similar net gain rates in the chordates studied. However, the tyrosine kinases in mouse and human or in fruit fly and mosquito mostly have a one-to-one relationship between species, indicating that static periods of 90 Myr or longer in tyrosine kinase evolution have followed large expansion events.}, } @article {pmid14764866, year = {2004}, author = {May, RM}, title = {Uses and abuses of mathematics in biology.}, journal = {Science (New York, N.Y.)}, volume = {303}, number = {5659}, pages = {790-793}, doi = {10.1126/science.1094442}, pmid = {14764866}, issn = {1095-9203}, mesh = {Allergy and Immunology ; Biological Evolution ; *Biological Science Disciplines ; Computational Biology ; Computer Simulation ; Creutzfeldt-Jakob Syndrome/prevention & control ; Ecology ; Genetics, Population ; HIV Infections/epidemiology/immunology/transmission ; Humans ; *Mathematics ; *Models, Biological ; Models, Statistical ; Nonlinear Dynamics ; Statistics as Topic ; }, abstract = {In the physical sciences, mathematical theory and experimental investigation have always marched together. Mathematics has been less intrusive in the life sciences, possibly because they have until recently been largely descriptive, lacking the invariance principles and fundamental natural constants of physics. Increasingly in recent decades, however, mathematics has become pervasive in biology, taking many different forms: statistics in experimental design; pattern seeking in bioinformatics; models in evolution, ecology, and epidemiology; and much else. I offer an opinionated overview of such uses--and abuses.}, } @article {pmid14756925, year = {2003}, author = {Flynn, D and van Schaik, P and Blackman, T and Femcott, C and Hobbs, B and Calderon, C}, title = {Developing a virtual reality-based methodology for people with dementia: a feasibility study.}, journal = {Cyberpsychology & behavior : the impact of the Internet, multimedia and virtual reality on behavior and society}, volume = {6}, number = {6}, pages = {591-611}, doi = {10.1089/109493103322725379}, pmid = {14756925}, issn = {1094-9313}, mesh = {Aged ; Aged, 80 and over ; *Computer Simulation ; Dementia/*diagnosis/physiopathology/*rehabilitation ; Diagnosis, Computer-Assisted/*methods ; Feasibility Studies ; Female ; Humans ; Male ; Middle Aged ; Motion Sickness/physiopathology ; Perception ; Reality Testing ; Spatial Behavior ; Therapy, Computer-Assisted/*methods ; *User-Computer Interface ; }, abstract = {The aim of this study was to examine the feasibility of virtual reality (VR) technology for use by persons with dementia (PWD). Data were obtained directly from six PWD regarding their experiences with a virtual environment (VE) of a large outdoor park. A user-centered method was developed to assess: (a) presence; (b) user inputs; (c) display quality; (d) simulation fidelity; and (e) overall system usability. The extent to which PWD could perform four functional activities in the VE was also investigated (e.g., mailing a letter). In addition, physical and psychological well-being of PWD while interacting with the VE was assessed objectively by recording heart rate during the VR sessions and subjectively with discrete questionnaire items and real-time prompts. Symptom profiles associated with simulator sickness were assessed with an adapted version of the Simulator Sickness Questionnaire. The study found that PWD to some extent experienced presence; perceived that objects were realistic and moved naturally; generally felt in control of the interaction; and demonstrated little difficulty using a joystick for navigation. The study also demonstrated that VR is an appropriate medium for assessing functional behavior within the context of an ecologically valid VE. PWD did not experience any significant increase in symptoms associated with simulator sickness, or detriments to their psychological and physical well-being. These findings demonstrated that it is feasible to work in VEs with PWD.}, } @article {pmid14753653, year = {2003}, author = {Keramitsoglou, I and Cartalis, C and Kassomenos, P}, title = {Decision support system for managing oil spill events.}, journal = {Environmental management}, volume = {32}, number = {2}, pages = {290-298}, doi = {10.1007/s00267-003-2969-7}, pmid = {14753653}, issn = {0364-152X}, mesh = {*Accidents ; *Decision Support Techniques ; *Disaster Planning ; Environmental Monitoring ; *Geographic Information Systems ; Mediterranean Region ; Petroleum/*poisoning ; Risk Assessment ; Water Pollution/*prevention & control ; }, abstract = {The Mediterranean environment is exposed to various hazards, including oil spills, forest fires, and floods, making the development of a decision support system (DSS) for emergency management an objective of utmost importance. The present work presents a complete DSS for managing marine pollution events caused by oil spills. The system provides all the necessary tools for early detection of oil-spills from satellite images, monitoring of their evolution, estimation of the accident consequences and provision of support to responsible Public Authorities during clean-up operations. The heart of the system is an image processing-geographic information system and other assistant individual software tools that perform oil spill evolution simulation and all other necessary numerical calculations as well as cartographic and reporting tasks related to a specific management of the oil spill event. The cartographic information is derived from the extant general maps representing detailed information concerning several regional environmental and land-cover characteristics as well as financial activities of the application area. Early notification of the authorities with up-to-date accurate information on the position and evolution of the oil spill, combined with the detailed coastal maps, is of paramount importance for emergency assessment and effective clean-up operations that would prevent environmental hazard. An application was developed for the Region of Crete, an area particularly vulnerable to oil spills due to its location, ecological characteristics, and local economic activities.}, } @article {pmid14753625, year = {2003}, author = {Legleiter, CJ}, title = {Spectrally driven classification of high spatial resolution, hyperspectral imagery: a tool for mapping in-stream habitat.}, journal = {Environmental management}, volume = {32}, number = {3}, pages = {399-411}, pmid = {14753625}, issn = {0364-152X}, mesh = {Ecosystem ; Environment ; Environmental Monitoring/*methods ; *Geographic Information Systems ; Light ; *Rivers ; }, abstract = {Streams represent an essential component of functional ecosystems and serve as sensitive indicators of disturbance. Accurate mapping and monitoring of these features is therefore critical, and this study explored the potential to characterize aquatic habitat with remotely sensed data. High spatial resolution, hyperspectral imagery of the Lamar River, Wyoming, USA, was used to examine the relationship between spectrally defined classes and field-mapped habitats. Advantages of this approach included enhanced depiction of fine-scale heterogeneity and improved portrayal of gradational zones between adjacent features. Certain habitat types delineated in the field were strongly associated with specific image classes, but most included areas of diverse spectral character; spatially buffering the field map polygons strengthened this association. Canonical discriminant analysis (CDA) indicated that the ratio of the variability among groups to that within a group was an order of magnitude greater for spectrally defined image classes (20.84) than for field-mapped habitat types (1.82), suggesting that unsupervised image classification might more effectively categorize the fluvial environment. CDA results also suggested that shortwave-infrared wavelengths were valuable for distinguishing various in-stream habitats. Although hyperspectral stream classification seemed capable of identifying more features than previously recognized, the technique also suggested that the intrinsic complexity of the Lamar River would preclude its subdivision into a discrete number of classes. Establishing physically based linkages between observed spectral patterns and ecologically relevant channel characteristics will require additional research, but hyperspectral stream classification could provide novel insight into fluvial systems while emerging as a potentially powerful tool for resource management.}, } @article {pmid14749740, year = {2004}, author = {Monro, JA}, title = {Virtual food components: functional food effects expressed as food components.}, journal = {European journal of clinical nutrition}, volume = {58}, number = {2}, pages = {219-230}, doi = {10.1038/sj.ejcn.1601769}, pmid = {14749740}, issn = {0954-3007}, mesh = {*Databases, Factual ; Defecation ; Dietary Carbohydrates/administration & dosage/*analysis ; Dietary Fiber/administration & dosage/*analysis ; Feces/*chemistry ; Food Analysis/*methods ; Glycemic Index ; Health Promotion ; Health Status Indicators ; Humans ; *Nutritive Value ; }, abstract = {BACKGROUND: The ability to communicate food benefits is essential for the successful development of functional foods and their role in improving public health. However, the functional efficacy of foods often cannot be represented by food composition. The concept of virtual food components (VFCs)-food data that express health-related effects, properties or functions of foods in the format of food components-is therefore proposed.

OBJECTIVE: To develop protocols for designing VFC data sets that communicate functional efficacies of foods to end users, in order to facilitate evidence-based food choice, and allow data management systems to provide a more complete description of nutritional effects of foods than has been possible with values for actual food components alone.

METHOD: A framework within which to develop VFCs was constructed, linking food choice to health end points. It involves scientific validation, generation of relative indices, their translation into a meaningful language based on equivalents to known and understood reference foods, followed by data consolidation and ecological validation. Criteria used to evaluate VFCs were importance, independence, validity, accuracy, robustness, sensitivity, linearity/additivity, relevance, comprehensiveness, acquirability, completeness, meaningfulness, acceptability and safety. The developmental framework and evaluative criteria were applied to glycaemic glucose equivalents (GGE), a VFC representing postprandial glycaemia, and to wheat bran equivalents for faecal bulk (WBE(fb)), a VFC representing faecal bulking efficacy.

RESULTS: VFCs were used to identify foods according to health-related effects that cannot be accurately predicted from food composition data, and were used in a nutrition management system to concurrently show nutrient intake and physiological effects in the same units. The proposed evaluative criteria identified points requiring further research, and showed that lack of integrity-tested VFC data is an immediate challenge.

CONCLUSION: VFCs are a means of communicating relative functional efficacy of foods as a continuous variable, and provide end users with a more accurate and complete view of the health effects of foods than can be provided by health claims or food composition data alone.}, } @article {pmid14745111, year = {2004}, author = {Sato, JJ and Hosoda, T and Wolsan, M and Suzuki, H}, title = {Molecular phylogeny of arctoids (Mammalia: Carnivora) with emphasis on phylogenetic and taxonomic positions of the ferret-badgers and skunks.}, journal = {Zoological science}, volume = {21}, number = {1}, pages = {111-118}, doi = {10.2108/0289-0003(2004)21[111:MPOAMC]2.0.CO;2}, pmid = {14745111}, issn = {0289-0003}, mesh = {Animals ; Base Composition ; Base Sequence ; Carnivora/*classification/*genetics ; DNA Primers ; Databases, Nucleic Acid ; Genes, RAG-1/genetics ; Models, Genetic ; Molecular Sequence Data ; *Phylogeny ; Retinol-Binding Proteins/genetics ; Sequence Analysis, DNA ; }, abstract = {Phylogenetic relationships among the ferret-badger Melogale moschata, the skunk Mephitis mephitis, and 21 other arctoid carnivorans, representing Mustelidae (Mustelinae: Mustela, Martes, Gulo; Lutrinae: Enhydra; Melinae: Meles), Procyonidae (Procyon), and Ursidae (Ursus, Melursus), were evaluated through maximum-parsimony phylogenetic analysis of concatenated partial nucleotide sequences of the nuclear recombination-activating gene 1 (RAG1) and gene encoding interphotoreceptor retinoid-binding protein (IRBP). The analysis strongly supports Melogale as more closely related to a musteline-lutrine clade (containing Mustela and Enhydra) than to Meles or another musteline clade containing Martes and Gulo (causing Melinae and Mustelinae, as traditionally circumscribed, to be nonmonophyletic). This, together with known morphological and karyological evidence for nonmeline affinities of Melogale, justify the exclusion of the ferret-badgers from the monophyletic Melinae. Therefore, we recommend that Melogale be classified in a distinct mustelid subfamily, the monotypic Helictidinae. Our analysis also strongly supports an outgroup position of the skunks to a clade containing Procyonidae and the nonmephitine Mustelidae (causing Mustelidae, as traditionally circumscribed, to be paraphyletic). This position of the skunks agrees with results of most previous genetic studies. However, it is contradicted by known morphological evidence from both living and fossil taxa, as well as genetic evidence from protein electrophoresis. These consistently support the traditional placement of the skunks within the monophyletic Mustelidae (recently in a close relationship to Lutrinae). Therefore, we consider the recent elevation of the skunks to the level of family as premature, and recommend that this clade be left at the subfamily level (Mephitinae) within the family Mustelidae, pending further evidence.}, } @article {pmid14739461, year = {2004}, author = {Emerson, JJ and Kaessmann, H and Betrán, E and Long, M}, title = {Extensive gene traffic on the mammalian X chromosome.}, journal = {Science (New York, N.Y.)}, volume = {303}, number = {5657}, pages = {537-540}, doi = {10.1126/science.1090042}, pmid = {14739461}, issn = {1095-9203}, support = {GM-065429-01A1/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; *Biological Evolution ; Chromosomes, Human/genetics ; Chromosomes, Human, X/*genetics ; Chromosomes, Mammalian/genetics ; Computational Biology ; Dosage Compensation, Genetic ; Female ; Gene Expression Profiling ; Genes, Duplicate ; Genetic Linkage ; Genome ; Genome, Human ; Humans ; Introns ; Male ; Mice ; Monte Carlo Method ; Mutation ; Oligonucleotide Array Sequence Analysis ; Ovary/metabolism ; Pseudogenes/*genetics ; *Recombination, Genetic ; Retroelements/*genetics ; Selection, Genetic ; Sex Characteristics ; Testis/metabolism ; X Chromosome/*genetics ; }, abstract = {Mammalian sex chromosomes have undergone profound changes since evolving from ancestral autosomes. By examining retroposed genes in the human and mouse genomes, we demonstrate that, during evolution, the mammalian X chromosome has generated and recruited a disproportionately high number of functional retroposed genes, whereas the autosomes experienced lower gene turnover. Most autosomal copies originating from X-linked genes exhibited testis-biased expression. Such export is incompatible with mutational bias and is likely driven by natural selection to attain male germline function. However, the excess recruitment is consistent with a combination of both natural selection and mutational bias.}, } @article {pmid14739026, year = {2004}, author = {Gebre-Michael, T and Malone, JB and Balkew, M and Ali, A and Berhe, N and Hailu, A and Herzi, AA}, title = {Mapping the potential distribution of Phlebotomus martini and P. orientalis (Diptera: Psychodidae), vectors of kala-azar in East Africa by use of geographic information systems.}, journal = {Acta tropica}, volume = {90}, number = {1}, pages = {73-86}, doi = {10.1016/j.actatropica.2003.09.021}, pmid = {14739026}, issn = {0001-706X}, mesh = {Africa, Eastern ; Animals ; Databases, Factual ; Disease Vectors ; Ecology ; Logistic Models ; *Phlebotomus ; Seasons ; }, abstract = {The distribution of two principal vectors of kala-azar in East Africa, Phlebotomus martini and Phlebotomus orientalis were analysed using geographic information system (GIS) based on (1) earth observing satellite sensor data: Normalized Difference Vegetation Index (NDVI) and midday Land Surface Temperature (LST) derived from advanced very high resolution radiometer (AVHRR) of the global land 1km project of United States Geological Survey (USGS), (2) agroclimatic data from the FAO Crop Production System Zone (CPSZ) of the Intergovernmental Authority on Development (IGAD) sub-region, and (3) the FAO 1998 soils digital map for the IGAD sub-region. The aim was to produce a predictive risk model for the two vectors. Data used for the analysis were based on presence and absence of the two species from previous survey collections in the region (mainly Ethiopia, Kenya and Somalia). Annual, wet season and dry season models were constructed. Although all models resulted in more than 85% positive predictive values for both species, the best fit for the distribution of P. martini was the dry season composite (NDVI 0.07-0.38 and LST 22-33 degrees C) with a predictive value of 93.8%, and the best fit for P. orientalis was the wet season composite (NDVI -0.01 to 0.34 and LST 23-34 degrees C) with a predictive value of 96.3%. The two seasonal composites models derived from satellite data were largely similar with best fit models developed based on the CPSZ climate data: average altitude (12-1900m), average annual mean temperature (15-30 degrees C), annual rainfall (274-1212mm), average annual potential evapotranspiration (1264-1938mm) and readily available soil moisture (62-113mm) for P. martini; and average altitude (200-2200m), annual rainfall (180-1050mm), annual mean temperature (16-36 degrees C) and readily available soil moisture (67-108mm) for P. orientalis. Logistic regression analysis indicated LST dry season composite of the satellite data, average altitude, mean annual temperature and readily available soil moisture of the CPSZ data as the best ecological determinants for P. martini while LST annual composite was the only important ecological determinant for P. orientalis. Spearman's rank correlation revealed several factors to be important determinants for the distribution of the two vectors. None of the soil types analysed appeared to be important determinant for the two species in East Africa, unlike in Sudan where P. orientalis is mainly associated with eutric vertisol (black cotton clay soil).}, } @article {pmid14728428, year = {2003}, author = {Madani, S and Aronsky, D}, title = {Factors affecting the sustainability of information technology applications in health care.}, journal = {AMIA ... Annual Symposium proceedings. AMIA Symposium}, volume = {2003}, number = {}, pages = {922}, pmid = {14728428}, issn = {1942-597X}, mesh = {*Delivery of Health Care ; Humans ; *Medical Informatics ; }, abstract = {Biomedical informatics is a relatively new field; sustainability of information technology applications has not been studied in detail. We examined what factors contribute to sustainability in other fields (ecology, construction materials, business, primary health care, and environment and development). We describe some aspects of sustainability that can be applied to biomedical informatics: effectiveness, efficiency, financial viability, reproducibility, and portability.}, } @article {pmid14724647, year = {2004}, author = {Smaglik, P}, title = {Bricks & mortar: Lancaster Environment Centre.}, journal = {Nature}, volume = {427}, number = {6971}, pages = {270}, doi = {10.1038/nj6971-270b}, pmid = {14724647}, issn = {1476-4687}, mesh = {Ecology/economics/*organization & administration/*trends ; Information Storage and Retrieval ; United Kingdom ; Workforce ; }, } @article {pmid14715244, year = {2004}, author = {Hoshino, A and Hanaki, K and Suzuki, K and Yamamoto, K}, title = {Applications of T-lymphoma labeled with fluorescent quantum dots to cell tracing markers in mouse body.}, journal = {Biochemical and biophysical research communications}, volume = {314}, number = {1}, pages = {46-53}, doi = {10.1016/j.bbrc.2003.11.185}, pmid = {14715244}, issn = {0006-291X}, mesh = {Animals ; BALB 3T3 Cells ; Biomarkers, Tumor/blood/*metabolism ; Cell Line, Tumor ; Cell Transplantation/methods ; Endosomes/*metabolism/pathology ; Lymphoma, T-Cell/*metabolism/*pathology ; Male ; Mice ; Microscopy, Fluorescence/*instrumentation/*methods ; Organ Specificity ; *Quantum Dots ; Staining and Labeling/*methods ; Tissue Distribution ; }, abstract = {Photoluminescent semiconductor quantum dots (QDs) are novel nanometer-size probes that have found bioimaging. Here we imaged a cell line of mouse lymphocytes. QDs were actively taken into the target cells by endocytotic pathways. The fluorescence of QDs held in the endosomes could be studied for more than a week and remained stable luminescence against cell activation induced by concanavalin A, phytohemagglutinin, phorbol myristate acetate, and calcium ionophore A23187. These results suggested that QD-labeling was stable and did not affect either cell activation or cell function. When QD-labeled cells were intravenously injected into mouse, they remained in the peripheral blood in a concentration of approximately 10% up to 5 days after injection using both fluorescence microscopy and flow cytometry. In addition, approximately 20% of QDs were detected in the kidneys, liver, lung, and spleen and could still be observed 7 days after injection. These results suggested that fluorescent probes of QDs might be useful as bioimaging tools for tracing target cells over the period of a week in vivo.}, } @article {pmid14689511, year = {2004}, author = {Sokal, RR and Oden, NL and Rosenberg, MS and Thomson, BA}, title = {A new protocol for evaluating putative causes for multiple variables in a spatial setting, illustrated by its application to European cancer rates.}, journal = {American journal of human biology : the official journal of the Human Biology Council}, volume = {16}, number = {1}, pages = {1-16}, doi = {10.1002/ajhb.10231}, pmid = {14689511}, issn = {1042-0533}, mesh = {*Biometry ; Causality ; Cluster Analysis ; Databases, Genetic ; Demography ; Epidemiologic Research Design ; Europe/epidemiology ; Female ; Gene Frequency ; Humans ; Incidence ; Male ; Neoplasms/*epidemiology/genetics/mortality ; }, abstract = {We introduce a statistical protocol for analyzing spatially varying data, including putative explanatory variables. The procedures comprise preliminary spatial autocorrelation analysis (from an earlier study), path analysis, clustering of the resulting set of path diagrams, ordination of these diagrams, and confirmatory tests against extrinsic information. To illustrate the application of these methods, we present incidence and mortality rates of 31 organ- and sex-specific cancers in Europe; these rates vary markedly with geography and type of cancer. Additionally, we investigated three factors (ethnohistory, genetics, and geography) putatively affecting these rates. The five variables were correlated separately for the 31 cancers over European reporting stations. We analyzed the correlations by path analysis, k-means clustering, and nonmetric multidimensional scaling; coefficients of the 31 path diagrams modeling the correlations vary substantially. To simplify interpretation, we grouped the diagrams into five clusters, for which we describe the differential effects of the three putative causes on incidence and mortality. When scaled, the path coefficients intergrade without marked gaps between clusters. Ethnic differences make for differences in cancer rates, even when the populations tested are ancient and complex mixtures. Path analysis usefully decomposes a structural model involving effects and putative causes, and estimates the magnitude of the model's components. Smooth intergradation of the path coefficients suggests the putative causes are the results of multiple forces. Despite this continuity of the path diagrams of the 31 cancers, clustering offers a useful segmentation of the continuum. Etiological and other extrinsic information on the cancers map significantly into the five clusters, demonstrating their epidemiological relevance.}, } @article {pmid14674430, year = {2002}, author = {Kacira, M and Ling, PP and Short, TH}, title = {Machine vision extracted plant movement for early detection of plant water stress.}, journal = {Transactions of the ASAE. American Society of Agricultural Engineers}, volume = {45}, number = {4}, pages = {1147-1153}, doi = {10.13031/2013.9923}, pmid = {14674430}, issn = {0001-2351}, mesh = {Ecological Systems, Closed ; *Environment, Controlled ; Environmental Monitoring/instrumentation/*methods ; Expert Systems ; *Humidity ; *Image Interpretation, Computer-Assisted ; Image Processing, Computer-Assisted ; Impatiens/growth & development/metabolism/*physiology ; Life Support Systems/instrumentation ; Photography ; Plant Leaves/growth & development/metabolism/physiology ; Plant Transpiration/physiology ; Water/analysis/metabolism/*physiology ; Water Supply ; }, abstract = {A methodology was established for early, non-contact, and quantitative detection of plant water stress with machine vision extracted plant features. Top-projected canopy area (TPCA) of the plants was extracted from plant images using image-processing techniques. Water stress induced plant movement was decoupled from plant diurnal movement and plant growth using coefficient of relative variation of TPCA (CRV[TPCA)] and was found to be an effective marker for water stress detection. Threshold value of CRV(TPCA) as an indicator of water stress was determined by a parametric approach. The effectiveness of the sensing technique was evaluated against the timing of stress detection by an operator. Results of this study suggested that plant water stress detection using projected canopy area based features of the plants was feasible.}, } @article {pmid14664843, year = {2004}, author = {Wind, T and Werner, U and Jacob, M and Hauk, A}, title = {Environmental concentrations of boron, LAS, EDTA, NTA and Triclosan simulated with GREAT-ER in the river Itter.}, journal = {Chemosphere}, volume = {54}, number = {8}, pages = {1135-1144}, doi = {10.1016/j.chemosphere.2003.09.037}, pmid = {14664843}, issn = {0045-6535}, mesh = {Arylsulfonates/analysis/chemistry ; Boron/analysis ; Computer Simulation ; Databases, Factual ; Edetic Acid/analysis ; Environmental Monitoring/*methods ; Germany ; Household Products/*analysis ; Models, Theoretical ; Nitrilotriacetic Acid/analogs & derivatives/analysis ; *Rivers ; Sensitivity and Specificity ; Triclosan/analysis ; Water Pollutants, Chemical/*analysis ; }, abstract = {A computer simulation of the environmental concentrations of some typical consumer-product ingredients was performed using the geo-referenced exposure model GREAT-ER (Geo-referenced Regional Environmental Assessment Tool for European Rivers) in the river Itter. Boron and LAS were chosen as typical detergent ingredients along with EDTA, NTA and Triclosan as examples of household and cosmetic product ingredients. The simulations were based on consumption figures of the respective chemical in consumer products in the year 2000. For EDTA, the consumption figure used for the calculation had to be extended to commercial products since the EDTA-use in domestic products could not account for the measured concentrations alone. The resulting PEC (Predicted Environmental Concentration) for all investigated compounds showed very good accordance to the measured concentrations in the Itter which were monitored in the same year. The concentrations did not deviate more than by a factor of 3. GREAT-ER's calculated 90th-percentile was never exceeded by the monitoring result thus reflecting a reasonable accuracy.}, } @article {pmid14664842, year = {2004}, author = {Wind, T}, title = {Prognosis of environmental concentrations by geo-referenced and generic models: a comparison of GREAT-ER and EUSES exposure simulations for some consumer-product ingredients in the Itter.}, journal = {Chemosphere}, volume = {54}, number = {8}, pages = {1145-1153}, doi = {10.1016/j.chemosphere.2003.09.036}, pmid = {14664842}, issn = {0045-6535}, mesh = {Arylsulfonates/analysis/chemistry ; Boron/analysis ; Computer Simulation ; Databases, Factual ; Edetic Acid/analysis ; Environmental Exposure/analysis ; Environmental Monitoring/*methods ; European Union ; Household Products/*analysis ; *Models, Theoretical ; Nitrilotriacetic Acid/analogs & derivatives/analysis ; *Rivers ; Triclosan/analysis ; Water Pollutants, Chemical/*analysis ; }, abstract = {The aim of this study was the comparison between predicted environmental concentrations (PEC) derived using a generic aspacial model, European Union System for the Evaluation of Substances (EUSES), and a geo-referenced model, the Geo-referenced Regional Environmental Assessment Tool for European Rivers (GREAT-ER). The PECs of some consumer-product ingredients (boron, LAS) and professional uses (EDTA, NTA and Triclosan) were calculated for the river catchment of the Itter, a small tributary to the river Rhine. The PEClocal and PECregional for the water compartment generated by EUSES (default scenario) were subsequently refined with data that realistically reflects the region of North Rhine-Westphalia (NRW scenario) and the Itter catchment (Itter scenario). The results of the three scenarios were then compared with the PECinitial and PECcatchment calculated by GREAT-ER, that was designed as a higher-tiered exposure assessment tool, and with concrete concentrations in the Itter, measured as 24-h composite samples. While the PECregional of all scenarios was close to the lower end of the measured concentrations, the geo-referenced PECs described equally well the real spacial situation. The measured environmental concentrations confirmed the built-in conservatism of the PEClocal calculations by EUSES showing for all investigated chemicals an unrealistically high PEClocal (default). The refinement in the more realistic scenarios could not provide a straight forward general improvement of the PEClocal. In conclusion, when the EUSES prognosis is refined using more detailed substance and regional specific data, it may provide a fairly accurate modelling especially of substances that are not eliminated in the environment. However, in the case of eliminable substances, it does not match the accuracy of higher-tiered geo-referenced exposure models like GREAT-ER.}, } @article {pmid14656961, year = {2003}, author = {Zhang, L and Gaut, BS}, title = {Does recombination shape the distribution and evolution of tandemly arrayed genes (TAGs) in the Arabidopsis thaliana genome?.}, journal = {Genome research}, volume = {13}, number = {12}, pages = {2533-2540}, pmid = {14656961}, issn = {1088-9051}, mesh = {Arabidopsis/*genetics ; Chromosome Mapping ; Chromosomes, Plant/genetics ; Computational Biology/statistics & numerical data ; *Evolution, Molecular ; Genes, Plant/*genetics ; *Genome, Plant ; Physical Chromosome Mapping/methods/statistics & numerical data ; Recombination, Genetic/*genetics ; }, abstract = {Tandemly arrayed genes (TAGs) are an important genomic component. However, most previous studies have focused on individual TAG families, and a broader characterization of their genomic distribution is not yet available. In this study, we examined the distribution of TAGs in the Arabidopsis thaliana genome and examined TAG density with relation to recombination rates. Recombination rates along A. thaliana chromosomes were estimated by comparing a genetic map with the genome sequence. Average recombination rates in A. thaliana are high, and rates vary more than threefold among chromosomal regions. Comparisons between TAG density and recombination indicate a positive correlation on chromosomes 1, 2, and 3. Moreover, there is a consistent centromeric effect. Relative to single-copy genes, TAGs are proportionally less frequent in centromeres than on chromosomal arms. We also examined several factors that have been proposed to affect the sequence evolution of TAG members. Sequence divergence is related to the number of members in the TAG, but genomic location has no obvious effect on TAG sequence divergence, nor does the presence of unrelated genes within a TAG. Overall, the distribution of TAGs in the genome is not consistent with theoretical models predicting the accumulation of repeats in regions of low recombination but may be consistent with stabilizing selection models of TAG evolution.}, } @article {pmid14656379, year = {2003}, author = {Moll, C and Gessler, U and Bartsch, S and El-Sayeh, HG and Fenton, M and Adams, CE}, title = {Gross Domestic Product (GDP) and productivity of schizophrenia trials: an ecological study.}, journal = {BMC psychiatry}, volume = {3}, number = {}, pages = {18}, pmid = {14656379}, issn = {1471-244X}, mesh = {*Cross-Cultural Comparison ; Databases as Topic/statistics & numerical data ; Economics/*statistics & numerical data ; Efficiency ; Humans ; Information Dissemination ; Information Services/standards/statistics & numerical data ; Linear Models ; Probability ; Randomized Controlled Trials as Topic/*statistics & numerical data ; Schizophrenia/*drug therapy ; Socioeconomic Factors ; Software/statistics & numerical data ; }, abstract = {BACKGROUND: The 5000 randomised controlled trials (RCTs) in the Cochrane Schizophrenia Group's database affords an opportunity to research for variables related to the differences between nations of their output of schizophrenia trials.

METHODS: Ecological study--investigating the relationship between four economic/demographic variables and number of schizophrenia RCTs per country. The variable with closest correlation was used to predict the expected number of studies.

RESULTS: GDP closely correlated with schizophrenia trial output, with 76% of the total variation about the Y explained by the regression line (r = 0.87, 95% CI 0.79 to 0.92, r2 = 0.76). Many countries have a strong tradition of schizophrenia trials, exceeding their predicted output. All nations with no identified trial output had GDPs that predicted zero trial activity. Several nations with relatively small GDPs are, nevertheless, highly productive of trials. Some wealthy countries seem either not to have produced the expected number of randomised trials or not to have disseminated them to the English-speaking world.

CONCLUSIONS: This hypothesis-generating study could not investigate causal relationships, but suggests, that for those seeking all relevant studies, expending effort searching the scientific literature of Germany, Italy, France, Brazil and Japan may be a good investment.}, } @article {pmid14655377, year = {2003}, author = {Chen, C and Hu, F and Zhang, L}, title = {[Landscape pattern of Nanjing urban-rural ecotone].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {14}, number = {8}, pages = {1363-1368}, pmid = {14655377}, issn = {1001-9332}, mesh = {Agriculture ; China ; *City Planning ; *Ecosystem ; *Geographic Information Systems ; }, abstract = {Landscape ecological characteristics of the urban-rural ecotone of Nanjing City were studied by using remote sensing and geographical information system (GIS) techniques. Two representative study regions with the same area were chosen in the eastern and southern part of the city. The urban-rural fringe of both east (URFE) and south region (URFS) can be divided into three zones: fringe-paraurban zone, transition zone and pararural zone. URFE was basically characterized by low landscape diversity, dominance and fragmentation. The forest patches in URFE had larger area and average perimeter, while their average fractal dimension, average stretched index and separated degree were lower. The average area of vegetable land and paddy land was larger than that of south region. URFS showed higher landscape diversity, dominance and fragmentation, more and higher density of patches. The area and the perimeter of water and architectural patches in URFS were also larger than that of URFE. The relationship between patch area and fractal dimension, stretched index and fractal dimension, patch number and area were discussed. The function and contributing factors of each type of patches, especially forestland, and the landscape characteristics and the ecological significance of corridors including road, river, and city wall of urban-rural fringe were also analyzed.}, } @article {pmid14647493, year = {2003}, author = {Ball, P}, title = {Material witness: Towards a materials ecology.}, journal = {Nature materials}, volume = {2}, number = {12}, pages = {781}, doi = {10.1038/nmat1024}, pmid = {14647493}, issn = {1476-1122}, mesh = {Conservation of Natural Resources/*economics/legislation & jurisprudence/*methods/trends ; Decision Making ; *Decision Support Techniques ; Ecology/economics/legislation & jurisprudence/*methods/trends ; *Environment ; Environmental Pollution/*prevention & control ; Equipment Reuse/*economics/legislation & jurisprudence ; Greenhouse Effect ; Policy Making ; }, } @article {pmid14646286, year = {2003}, author = {Uehara, M and Takahashi, K and Hoshuyama, T and Tanaka, C}, title = {A proposal for topic-based impact factors and their application to occupational health literature.}, journal = {Journal of occupational health}, volume = {45}, number = {4}, pages = {248-253}, doi = {10.1539/joh.45.248}, pmid = {14646286}, issn = {1341-9145}, mesh = {*Bibliometrics ; Humans ; *MEDLINE ; *Occupational Health ; Periodicals as Topic ; }, } @article {pmid14642340, year = {2004}, author = {Loladze, I and Kuang, Y and Elser, JJ and Fagan, WF}, title = {Competition and stoichiometry: coexistence of two predators on one prey.}, journal = {Theoretical population biology}, volume = {65}, number = {1}, pages = {1-15}, doi = {10.1016/s0040-5809(03)00105-9}, pmid = {14642340}, issn = {0040-5809}, mesh = {Animals ; Data Interpretation, Statistical ; *Predatory Behavior ; United States ; }, abstract = {The competitive exclusion principle (CEP) states that no equilibrium is possible if n species exploit fewer than n resources. This principle does not appear to hold in nature, where high biodiversity is commonly observed, even in seemingly homogenous habitats. Although various mechanisms, such as spatial heterogeneity or chaotic fluctuations, have been proposed to explain this coexistence, none of them invalidates this principle. Here we evaluate whether principles of ecological stoichiometry can contribute to the stable maintenance of biodiverse communities. Stoichiometric analysis recognizes that each organism is a mixture of multiple chemical elements such as carbon (C), nitrogen (N), and phosphorus (P) that are present in various proportions in organisms. We incorporate these principles into a standard predator-prey model to analyze competition between two predators on one autotrophic prey. The model tracks two essential elements, C and P, in each species. We show that a stable equilibrium is possible with two predators on this single prey. At this equilibrium both predators can be limited by the P content of the prey. The analysis suggests that chemical heterogeneity within and among species provides new mechanisms that can support species coexistence and that may be important in maintaining biodiversity.}, } @article {pmid14632423, year = {2003}, author = {Brüggemann, R and Welzl, G and Voigt, K}, title = {Order theoretical tools for the evaluation of complex regional pollution patterns.}, journal = {Journal of chemical information and computer sciences}, volume = {43}, number = {6}, pages = {1771-1779}, doi = {10.1021/ci0300083}, pmid = {14632423}, issn = {0095-2338}, mesh = {Analysis of Variance ; Data Interpretation, Statistical ; Databases, Factual ; Environmental Pollution/*statistics & numerical data ; }, abstract = {The mathematical and statistical evaluation of environmental data gains an increasing importance in environmental chemistry as the data sets become more complex. It is inarguable that different mathematical and statistical methods should be applied in order to compare results and to enhance the possible interpretation of the data. Very often several aspects have to be considered simultaneously, for example, several chemicals entailing a data matrix with objects (rows) and variables (columns). In this paper a data set is given concerning the pollution of 58 regions in the state of Baden-Württemberg, Germany, which are polluted with metals lead, cadmium, zinc, and with sulfur. For pragmatic reasons the evaluation is performed with the dichotomized data matrix. First this dichotomized 58 x 13 data matrix is evaluated by the Hasse diagram technique, a multicriteria evaluation method which has its scientific origin in Discrete Mathematics. Then the Partially Ordered Scalogram Analysis with Coordinates (POSAC) method is applied. It reduces the data matrix in plotting it in a two-dimensional space. A small given percentage of information is lost in this method. Important priority objects, like maximal and minimal objects (high and low polluted regions), can easily be detected by Hasse diagram technique and POSAC. Two variables attained exceptional importance by the data analysis shown here: TLS, Sulfur found in Tree Layer, is difficult to interpret and needs further investigations, whereas LRPB, Lead in Lumbricus Rubellus, seems to be a satisfying result because the earthworm is commonly discussed in the ecotoxicological literature as a specific and highly sensitive bioindicator.}, } @article {pmid14630669, year = {2003}, author = {Lewis, PO}, title = {NCL: a C++ class library for interpreting data files in NEXUS format.}, journal = {Bioinformatics (Oxford, England)}, volume = {19}, number = {17}, pages = {2330-2331}, doi = {10.1093/bioinformatics/btg319}, pmid = {14630669}, issn = {1367-4803}, mesh = {Databases, Bibliographic/*standards ; Databases, Genetic/*standards ; Information Storage and Retrieval/*methods/*standards ; *Programming Languages ; Sequence Analysis/*methods/*standards ; *Software ; }, abstract = {UNLABELLED: The NEXUS Class Library (NCL) is a collection of C++ classes designed to simplify interpreting data files written in the NEXUS format used by many computer programs for phylogenetic analyses. The NEXUS format allows different programs to share the same data files, even though none of the programs can interpret all of the data stored therein. Because users are not required to reformat the data file for each program, use of the NEXUS format prevents cut-and-paste errors as well as the proliferation of copies of the original data file. The purpose of making the NCL available is to encourage the use of the NEXUS format by making it relatively easy for programmers to add the ability to interpret NEXUS files in newly developed software.

AVAILABILITY: The NCL is freely available under the GNU General Public License from http://hydrodictyon.eeb.uconn.edu/ncl/

SUPPLEMENTARY INFORMATION: Documentation for the NCL (general information and source code documentation) is available in HTML format at http://hydrodictyon.eeb.uconn.edu/ncl/}, } @article {pmid14629774, year = {2003}, author = {Cui, Y and Zhang, ZF and Froines, J and Zhao, J and Wang, H and Yu, SZ and Detels, R}, title = {Air pollution and case fatality of SARS in the People's Republic of China: an ecologic study.}, journal = {Environmental health : a global access science source}, volume = {2}, number = {1}, pages = {15}, pmid = {14629774}, issn = {1476-069X}, support = {R01 CA090833/CA/NCI NIH HHS/United States ; R21 ES011667/ES/NIEHS NIH HHS/United States ; CA90833/CA/NCI NIH HHS/United States ; ES 011667/ES/NIEHS NIH HHS/United States ; }, mesh = {Air Pollutants/*analysis ; China/epidemiology ; Disease Outbreaks/prevention & control ; Ecology ; Humans ; Public Health Informatics ; Risk Assessment ; Severe acute respiratory syndrome-related coronavirus/*pathogenicity ; Severe Acute Respiratory Syndrome/etiology/*mortality ; }, abstract = {BACKGROUND: Severe acute respiratory syndrome (SARS) has claimed 349 lives with 5,327 probable cases reported in mainland China since November 2002. SARS case fatality has varied across geographical areas, which might be partially explained by air pollution level.

METHODS: Publicly accessible data on SARS morbidity and mortality were utilized in the data analysis. Air pollution was evaluated by air pollution index (API) derived from the concentrations of particulate matter, sulfur dioxide, nitrogen dioxide, carbon monoxide and ground-level ozone. Ecologic analysis was conducted to explore the association and correlation between air pollution and SARS case fatality via model fitting. Partially ecologic studies were performed to assess the effects of long-term and short-term exposures on the risk of dying from SARS.

RESULTS: Ecologic analysis conducted among 5 regions with 100 or more SARS cases showed that case fatality rate increased with the increment of API (case fatality = - 0.063 + 0.001 * API). Partially ecologic study based on short-term exposure demonstrated that SARS patients from regions with moderate APIs had an 84% increased risk of dying from SARS compared to those from regions with low APIs (RR = 1.84, 95% CI: 1.41-2.40). Similarly, SARS patients from regions with high APIs were twice as likely to die from SARS compared to those from regions with low APIs. (RR = 2.18, 95% CI: 1.31-3.65). Partially ecologic analysis based on long-term exposure to ambient air pollution showed the similar association.

CONCLUSION: Our studies demonstrated a positive association between air pollution and SARS case fatality in Chinese population by utilizing publicly accessible data on SARS statistics and air pollution indices. Although ecologic fallacy and uncontrolled confounding effect might have biased the results, the possibility of a detrimental effect of air pollution on the prognosis of SARS patients deserves further investigation.}, } @article {pmid14620945, year = {2003}, author = {Pikula, J and Treml, F and Beklová, M and Holesovska, Z and Pikulová, J}, title = {Ecological conditions of natural foci of tularaemia in the Czech Republic.}, journal = {European journal of epidemiology}, volume = {18}, number = {11}, pages = {1091-1095}, pmid = {14620945}, issn = {0393-2990}, mesh = {Animals ; Czech Republic/epidemiology ; *Disease Reservoirs ; Disease Vectors ; *Ecosystem ; *Environment ; Francisella tularensis/isolation & purification ; Geographic Information Systems ; Prevalence ; Risk Factors ; Rodentia/*microbiology ; Trees ; Tularemia/*epidemiology/veterinary ; }, abstract = {Tularaemia, a zoonosis of veterinary and public health importance, commonly occurs in the Czech Republic as well as other countries of Northern Hemisphere. The objective of this study was to analyse the environmental conditions of distribution of natural foci of tularaemia and their long-term persistence in the Czech Republic. A geographic information system has been used for this purpose. A new variable (chi(t)), the mean number of natural foci in a specific area, has been suggested for the evaluation of diseases occurring in natural foci. Comparing two 15-year periods, a close correlation between the geographic distribution and numbers of natural foci of tularaemia in the Czech Republic in 1971-1985 and 1986-2000 (r = 0.91, n = 1814, t = 92.50, p = 0.01) was found. Natural foci of tularaemia have been persistent, but not stationary, over the period of 30 years and the geographic area of their occurrence has not been considerably growing or diminishing in the Czech Republic. The highest numbers of natural foci of tularaemia were in habitats of alluvial forests (chi(t) = 7.20), geographic areas of up to 200 m of elevation above sea (chi(t) = 9.18), 8.1-10.0 degrees C of mean annual air temperature (chi(t) = 6.24), 450-700 mm of mean annual precipitation (chi(t) = 2.84), and 2001-2200 hour of mean annual sunshine duration (chi(t) = 8.77). It was proved that tularaemia persists in specific areas of natural foci, the general environmental conditions of which can be defined and make it possible to predict the occurrence of tularaemia in other areas of suitable conditions.}, } @article {pmid14617866, year = {2003}, author = {Treskunov, K and Treskunova, O and Komarov, B and Goroshetchenko, A and Glebov, V}, title = {Medicinal herbs and phytochitodeztherapy in oncology.}, journal = {Medicina (Kaunas, Lithuania)}, volume = {39 Suppl 2}, number = {}, pages = {85-91}, pmid = {14617866}, issn = {1648-9144}, mesh = {Chitosan/administration & dosage/*therapeutic use ; Combined Modality Therapy ; Databases, Factual ; Female ; Follow-Up Studies ; Humans ; Male ; Neoplasms/*drug therapy/epidemiology/mortality/radiotherapy/surgery ; *Phytotherapy ; Plant Preparations/administration & dosage/*therapeutic use ; Quality of Life ; Russia/epidemiology ; Survival Analysis ; Time Factors ; Treatment Outcome ; }, abstract = {Application of clinical phytology in treatment of oncology diseases was limited by intensive development of chemical pharmaceuticals and surgery. The authors had set the task to develop the computer database for phytotherapy application. The database included full information on patient's clinical status (identified diseases, symptoms, syndromes) and applied phytotherapy treatment. Special attention was paid to the application of phyto preparations containing chitosan. The computer database contains information on 2335 patients. It supports reliable data on efficiency of phytotherapy in general and allows to evaluate the efficiency of some particular medicinal herbs and to develop efficient complex phyto preparations for treatment of specific diseases. The application of phytotherapy in treatment of oncology patients confirmed the positive effect on patient's quality of life. In conclusion it should be emphasized that the present situation of practical application of phytotherapy could be considered as unacceptable because of absence of necessary knowledge and practical experience in using phytotherapy in outpatient clinics, hospitals and medicinal centers.}, } @article {pmid14602639, year = {2003}, author = {Kent, AD and Smith, DJ and Benson, BJ and Triplett, EW}, title = {Web-based phylogenetic assignment tool for analysis of terminal restriction fragment length polymorphism profiles of microbial communities.}, journal = {Applied and environmental microbiology}, volume = {69}, number = {11}, pages = {6768-6776}, pmid = {14602639}, issn = {0099-2240}, mesh = {Bacteria/*classification/genetics ; Computational Biology/methods ; DNA, Bacterial/analysis/genetics/isolation & purification ; *Ecosystem ; Fresh Water/*microbiology ; Gene Library ; *Internet ; *Phylogeny ; *Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Culture-independent DNA fingerprints are commonly used to assess the diversity of a microbial community. However, relating species composition to community profiles produced by community fingerprint methods is not straightforward. Terminal restriction fragment length polymorphism (T-RFLP) is a community fingerprint method in which phylogenetic assignments may be inferred from the terminal restriction fragment (T-RF) sizes through the use of web-based resources that predict T-RF sizes for known bacteria. The process quickly becomes computationally intensive due to the need to analyze profiles produced by multiple restriction digests and the complexity of profiles generated by natural microbial communities. A web-based tool is described here that rapidly generates phylogenetic assignments from submitted community T-RFLP profiles based on a database of fragments produced by known 16S rRNA gene sequences. Users have the option of submitting a customized database generated from unpublished sequences or from a gene other than the 16S rRNA gene. This phylogenetic assignment tool allows users to employ T-RFLP to simultaneously analyze microbial community diversity and species composition. An analysis of the variability of bacterial species composition throughout the water column in a humic lake was carried out to demonstrate the functionality of the phylogenetic assignment tool. This method was validated by comparing the results generated by this program with results from a 16S rRNA gene clone library.}, } @article {pmid14595094, year = {2004}, author = {Zhang, L and Li, WH}, title = {Mammalian housekeeping genes evolve more slowly than tissue-specific genes.}, journal = {Molecular biology and evolution}, volume = {21}, number = {2}, pages = {236-239}, doi = {10.1093/molbev/msh010}, pmid = {14595094}, issn = {0737-4038}, support = {GM30998/GM/NIGMS NIH HHS/United States ; GM66104/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Databases, Nucleic Acid ; *Evolution, Molecular ; *Gene Expression Regulation ; *Genome ; Humans ; Mammals ; Mice ; Mutation ; Organ Specificity/*genetics ; }, abstract = {Do housekeeping genes, which are turned on most of the time in almost every tissue, evolve more slowly than genes that are turned on only at specific developmental times or tissues? Recent large-scale gene expression studies enable us to have a better definition of housekeeping genes and to address the above question in detail. In this study, we examined 1581 human-mouse orthologous gene pairs for their patterns of sequence evolution, contrasting housekeeping genes with tissue-specific genes. Our results show that, in comparison to tissue-specific genes, housekeeping genes on average evolve more slowly and are under stronger selective constraints as reflected by significantly smaller values of Ka/Ks. Besides stronger purifying selection, we explored several other factors that can possibly slow down nonsynonymous rates in housekeeping genes. Although mutational bias might slightly slow the nonsynonymous rates in housekeeping genes, it is unlikely to be the major cause of the rate difference between the two types of genes. The codon usage pattern of housekeeping genes does not seem to differ from that of tissue-specific genes. Moreover, contrary to the old textbook concept, we found that approximately 74% of the housekeeping genes in our study belong to multigene families, not significantly different from that of the tissue-specific genes (approximately 70%). Therefore, the stronger selective constraints on housekeeping genes are not due to a lower degree of genetic redundancy.}, } @article {pmid14593655, year = {2003}, author = {Polishchuk, TI and Muruziuk, NN}, title = {[Population analysis of the immune status of immigrants in Far North].}, journal = {Meditsina truda i promyshlennaia ekologiia}, volume = {}, number = {9}, pages = {39-42}, pmid = {14593655}, issn = {1026-9428}, mesh = {Adult ; Cold Climate ; Data Interpretation, Statistical ; Ecology ; *Emigration and Immigration ; *Health Status ; Humans ; *Immunity ; Middle Aged ; Siberia ; }, abstract = {In this article normative parameters of immune status of Nadym population of Yamalo-Nenets Autonomous Okrug are given. Type of immune status with moderate activation of cell part of immunity, humoral suppression and activation of non-specific resistance was determined.}, } @article {pmid14574143, year = {2003}, author = {Kuhnert, PM and Do, KA}, title = {Fitting genetic models to twin data with binary and ordered categorical responses: a comparison of structural equation modelling and Bayesian hierarchical models.}, journal = {Behavior genetics}, volume = {33}, number = {4}, pages = {441-454}, doi = {10.1023/a:1025325710903}, pmid = {14574143}, issn = {0001-8244}, mesh = {Bayes Theorem ; Databases, Factual ; Humans ; Middle Aged ; *Models, Genetic ; *Models, Statistical ; Monte Carlo Method ; }, abstract = {We compare Bayesian methodology utilizing free-ware BUGS (Bayesian Inference Using Gibbs Sampling) with the traditional structural equation modelling approach based on another free-ware package, Mx. Dichotomous and ordinal (three category) twin data were simulated according to different additive genetic and common environment models for phenotypic variation. Practical issues are discussed in using Gibbs sampling as implemented by BUGS to fit subject-specific Bayesian generalized linear models, where the components of variation may be estimated directly. The simulation study (based on 2000 twin pairs) indicated that there is a consistent advantage in using the Bayesian method to detect a "correct" model under certain specifications of additive genetics and common environmental effects. For binary data, both methods had difficulty in detecting the correct model when the additive genetic effect was low (between 10 and 20%) or of moderate range (between 20 and 40%). Furthermore, neither method could adequately detect a correct model that included a modest common environmental effect (20%) even when the additive genetic effect was large (50%). Power was significantly improved with ordinal data for most scenarios, except for the case of low heritability under a true ACE model. We illustrate and compare both methods using data from 1239 twin pairs over the age of 50 years, who were registered with the Australian National Health and Medical Research Council Twin Registry (ATR) and presented symptoms associated with osteoarthritis occurring in joints of the hand.}, } @article {pmid14571969, year = {2003}, author = {Baden, S and Gullström, M and Lundén, B and Pihl, L and Rosenberg, R}, title = {Vanishing seagrass (Zostera marina, L.) in Swedish coastal waters.}, journal = {Ambio}, volume = {32}, number = {5}, pages = {374-377}, doi = {10.1579/0044-7447-32.5.374}, pmid = {14571969}, issn = {0044-7447}, mesh = {*Conservation of Natural Resources ; *Ecosystem ; Environmental Monitoring ; Geographic Information Systems ; Population Dynamics ; Sweden ; *Zosteraceae ; }, abstract = {Along the Swedish Skagerrak coast eelgrass (Zostera marina) is a dominant phanerogam on shallow soft bottoms. Eelgrass meadows are important biotopes for many crustacean and fish species being either migratory or stationary. During the 1980s, inventories of the shallow coastal areas with eelgrass have been carried out along the Swedish west coast as a basis for coastal zone management. In the present study we revisited 2000 ha of eelgrass meadows in 5 coastal regions along 200 km of the Skagerrak coast. The inventory was made with the same methods (aquascope) as during the 1980s, but increasing the mapping accuracy by using a Global Positioning System (GPS). The results from this study show that the areal extension of Zostera marina has decreased 58% in 10-15 years with great regional variations. The decline was mainly restricted to the shallow parts of the meadow. The causes and ecological consequences are discussed.}, } @article {pmid14570444, year = {2003}, author = {Smith, EP and Atkins, J and Connell, CM}, title = {Family, school, and community factors and relationships to racial-ethnic attitudes and academic achievement.}, journal = {American journal of community psychology}, volume = {32}, number = {1-2}, pages = {159-173}, doi = {10.1023/a:1025663311100}, pmid = {14570444}, issn = {0091-0562}, mesh = {Adult ; *Attitude ; Child ; *Community Networks ; *Educational Status ; Ethnicity/*psychology ; Factor Analysis, Statistical ; Family/*psychology ; Female ; Humans ; Male ; *Race Relations ; *Schools ; Socialization ; }, abstract = {This study examined family, school, and community factors and the relationships to racial-ethnic attitudes and academic achievement among 98 African American fourth-grade children. It has been posited that young people who feel better about their racial-ethnic background have better behavioral and academic outcomes, yet there is a need for more empirical tests of this premise. Psychometric information is reported on measures of parent, teacher, and child racial-ethnic attitudes. Path analysis was used to investigate ecological variables potentially related to children's racial-ethnic attitudes and achievement. Parental education and level of racial-ethnic pride were correlated and both were related to children's achievement though in the final path model, only the path from parental education level was statistically significant. Children whose teachers exhibited higher levels of racial-ethnic trust and perceived fewer barriers due to race and ethnicity evidenced more trust and optimism as well. Children living in communities with higher proportions of college-educated residents also exhibited more positive racial-ethnic attitudes. For children, higher racial-ethnic pride was related to higher achievement measured by grades and standardized test scores, while racial distrust and perception of barriers due to race were related to reduced performance. This study suggests that family, school, and community are all important factors related to children's racial-ethnic attitudes and also to their academic achievement.}, } @article {pmid14570426, year = {2003}, author = {Whitelaw, G and Vaughan, H and Craig, B and Atkinson, D}, title = {Establishing the Canadian Community Monitoring Network.}, journal = {Environmental monitoring and assessment}, volume = {88}, number = {1-3}, pages = {409-418}, pmid = {14570426}, issn = {0167-6369}, mesh = {Animals ; Canada ; *Community Networks ; Conservation of Natural Resources ; Decision Making ; *Ecosystem ; Environmental Monitoring/*statistics & numerical data ; Environmental Pollution/prevention & control ; }, abstract = {Community-based ecosystem monitoring activities in Canada are increasing in response to a number of factors including: (i) the needs of decision-makers for timely information on local environmental changes; (ii) limited use of government monitoring data and information by decision makers: (iii) government cuts to monitoring programs; (iv) the increasingly recognized need to include stakeholders in planning and management processes; and (v) the desire of citizens to contribute to environmental protection. To date there has been no network coordination of community based monitoring in Canada. This paper reports on the establishment of the Canadian Community Monitoring Network by Environment Canada's Ecological Monitoring and Assessment Network Coordinating Office and the Canadian Nature Federation. Information on research prepared in support of network establishment is presented along with a discussion of the potential of the network.}, } @article {pmid14563568, year = {2003}, author = {Arbesman, S and Enthoven, L and Monteiro, A}, title = {Ancient Wings: animating the evolution of butterfly wing patterns.}, journal = {Bio Systems}, volume = {71}, number = {3}, pages = {289-295}, doi = {10.1016/s0303-2647(03)00086-8}, pmid = {14563568}, issn = {0303-2647}, mesh = {Animals ; *Biological Evolution ; Butterflies/*anatomy & histology/*genetics ; Computer Graphics ; Database Management Systems ; *Databases, Genetic ; Genetic Variation ; Information Storage and Retrieval/*methods ; Models, Genetic ; Motion ; Pattern Recognition, Automated ; Photography/methods ; *Phylogeny ; Software ; *User-Computer Interface ; Video Recording/methods ; Wings, Animal/*anatomy & histology ; }, abstract = {Character optimization methods can be used to reconstruct ancestral states at the internal nodes of phylogenetic trees. However, seldom are these ancestral states visualized collectively. Ancient Wings is a computer program that provides a novel method of visualizing the evolution of several morphological traits simultaneously. It allows users to visualize how the ventral hindwing pattern of 54 butterflies in the genus Bicyclus may have changed over time. By clicking on each of the nodes within the evolutionary tree, the user can see an animation of how wing size, eyespot size, and eyespot position relative the wing margin, have putatively evolved as a collective whole. Ancient Wings may be used as a pedagogical device as well as a research tool for hypothesis-generation in the fields of evolutionary, ecological, and developmental biology.}, } @article {pmid14557537, year = {2003}, author = {Qin, H and Lu, HH and Wu, WB and Li, WH}, title = {Evolution of the yeast protein interaction network.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {100}, number = {22}, pages = {12820-12824}, pmid = {14557537}, issn = {0027-8424}, support = {GM 66104/GM/NIGMS NIH HHS/United States ; R01 GM066104/GM/NIGMS NIH HHS/United States ; GM 30998/GM/NIGMS NIH HHS/United States ; R37 GM030998/GM/NIGMS NIH HHS/United States ; R01 GM030998/GM/NIGMS NIH HHS/United States ; }, mesh = {*Biological Evolution ; *Databases, Genetic ; Fungi/classification ; *Genome, Fungal ; Models, Biological ; Neural Networks, Computer ; Phylogeny ; Saccharomyces cerevisiae/*genetics ; Saccharomyces cerevisiae Proteins/*genetics ; }, abstract = {To study the evolution of the yeast protein interaction network, we first classified yeast proteins by their evolutionary histories into isotemporal categories, then analyzed the interaction tendencies within and between the categories, and finally reconstructed the main growth path. We found that two proteins tend to interact with each other if they are in the same or similar categories, but tended to avoid each other otherwise, and that network evolution mirrors the universal tree of life. These observations suggest synergistic selection during network evolution and provide insights into the hierarchical modularity of cellular networks.}, } @article {pmid14534174, year = {2003}, author = {Hendy, MD and Holland, BR}, title = {Upper bounds on maximum likelihood for phylogenetic trees.}, journal = {Bioinformatics (Oxford, England)}, volume = {19 Suppl 2}, number = {}, pages = {ii66-72}, doi = {10.1093/bioinformatics/btg1062}, pmid = {14534174}, issn = {1367-4811}, mesh = {*Algorithms ; Base Sequence ; Computer Simulation ; Data Interpretation, Statistical ; *Evolution, Molecular ; Likelihood Functions ; *Models, Genetic ; Models, Statistical ; Molecular Sequence Data ; *Phylogeny ; Sequence Alignment/*methods ; Sequence Analysis, DNA/*methods ; }, abstract = {We introduce a mechanism for analytically deriving upper bounds on the maximum likelihood for genetic sequence data on sets of phylogenies. A simple 'partition' bound is introduced for general models. Tighter bounds are developed for the simplest model of evolution, the two state symmetric model of nucleotide substitution under the molecular clock. This follows earlier theoretical work which has been restricted to this model by analytic complexity. A weakness of current numerical computation is that reported 'maximum likelihood' results cannot be guaranteed, both for a specified tree (because of the possibility of multiple maxima) or over the full tree space (as the computation is intractable for large sets of trees). The bounds we develop here can be used to conclusively eliminate large proportions of tree space in the search for the maximum likelihood tree. This is vital in the development of a branch and bound search strategy for identifying the maximum likelihood tree. We report the results from a simulation study of approximately 10(6) data sets generated on clock-like trees of five leaves. In each trial a likelihood value of one specific instance of a parameterised tree is compared to the bound determined for each of the 105 possible rooted binary trees. The proportion of trees that are eliminated from the search for the maximum likelihood tree ranged from 92% to almost 98%, indicating a computational speed-up factor of between 12 and 44.}, } @article {pmid14532080, year = {2003}, author = {Stach, JE and Maldonado, LA and Masson, DG and Ward, AC and Goodfellow, M and Bull, AT}, title = {Statistical approaches for estimating actinobacterial diversity in marine sediments.}, journal = {Applied and environmental microbiology}, volume = {69}, number = {10}, pages = {6189-6200}, pmid = {14532080}, issn = {0099-2240}, mesh = {Actinobacteria/*classification/genetics ; Computational Biology ; DNA, Ribosomal/analysis ; *Genetic Variation ; Geologic Sediments/*microbiology ; Molecular Sequence Data ; Nucleic Acid Hybridization ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Seawater/*microbiology ; Sequence Analysis, DNA ; Statistics as Topic/*methods ; Statistics, Nonparametric ; }, abstract = {Bacterial diversity in a deep-sea sediment was investigated by constructing actinobacterium-specific 16S ribosomal DNA (rDNA) clone libraries from sediment sections taken 5 to 12, 15 to 18, and 43 to 46 cm below the sea floor at a depth of 3,814 m. Clones were placed into operational taxonomic unit (OTU) groups with >/= 99% 16S rDNA sequence similarity; the cutoff value for an OTU was derived by comparing 16S rRNA homology with DNA-DNA reassociation values for members of the class Actinobacteria. Diversity statistics were used to determine how the level of dominance, species richness, and genetic diversity varied with sediment depth. The reciprocal of Simpson's index (1/D) indicated that the pattern of diversity shifted toward dominance from uniformity with increasing sediment depth. Nonparametric estimation of the species richness in the 5- to 12-, 15- to 18-, and 43- to 46-cm sediment sections revealed a trend of decreasing species number with depth, 1,406, 308, and 212 OTUs, respectively. Application of the LIBSHUFF program indicated that the 5- to 12-cm clone library was composed of OTUs significantly (P = 0.001) different from those of the 15- to 18- and 43- to 46-cm libraries. F(ST) and phylogenetic grouping of taxa (P tests) were both significant (P < 0.00001 and P < 0.001, respectively), indicating that genetic diversity decreased with sediment depth and that each sediment community harbored unique phylogenetic lineages. It was also shown that even nonconservative OTU definitions result in severe underestimation of species richness; unique phylogenetic clades detected in one OTU group suggest that OTUs do not correspond to real ecological groups sensu Palys (T. Palys, L. K. Nakamura, and F. M. Cohan, Int. J. Syst. Bacteriol. 47:1145-1156, 1997). Mechanisms responsible for diversity and their implications are discussed.}, } @article {pmid14530135, year = {2003}, author = {Giannini, NP}, title = {Canonical phylogenetic ordination.}, journal = {Systematic biology}, volume = {52}, number = {5}, pages = {684-695}, doi = {10.1080/10635150390238888}, pmid = {14530135}, issn = {1063-5157}, mesh = {Animals ; *Data Interpretation, Statistical ; Ecosystem ; Lizards/genetics ; *Models, Theoretical ; *Phylogeny ; }, abstract = {A phylogenetic comparative method is proposed for estimating historical effects on comparative data using the partitions that compose a cladogram, i.e., its monophyletic groups. Two basic matrices, Y and X, are defined in the context of an ordinary linear model. Y contains the comparative data measured over t taxa. X consists of an initial tree matrix that contains all the xj monophyletic groups (each coded separately as a binary indicator variable) of the phylogenetic tree available for those taxa. The method seeks to define the subset of groups, i.e., a reduced tree matrix, that best explains the patterns in Y. This definition is accomplished via regression or canonical ordination (depending on the dimensionality of Y) coupled with Monte Carlo permutations. It is argued here that unrestricted permutations (i.e., under an equiprobable model) are valid for testing this specific kind of groupwise hypothesis. Phylogeny is either partialled out or, more properly, incorporated into the analysis in the form of component variation. Direct extensions allow for testing ecomorphological data controlled by phylogeny in a variation partitioning approach. Currently available statistical techniques make this method applicable under most univariate/multivariate models and metrics; two-way phylogenetic effects can be estimated as well. The simplest case (univariate Y), tested with simulations, yielded acceptable type I error rates. Applications presented include examples from evolutionary ethology, ecology, and ecomorphology. Results showed that the new technique detected previously overlooked variation clearly associated with phylogeny and that many phylogenetic effects on comparative data may occur at particular groups rather than across the entire tree.}, } @article {pmid14524539, year = {2003}, author = {Kutz, FW and Wade, TG and Pagac, BB}, title = {A geospatial study of the potential of two exotic species of mosquitoes to impact the epidemiology of West Nile virus in Maryland.}, journal = {Journal of the American Mosquito Control Association}, volume = {19}, number = {3}, pages = {190-198}, pmid = {14524539}, issn = {8756-971X}, mesh = {Aedes/*virology ; Animals ; Environment ; Environmental Monitoring ; Epidemiological Monitoring ; *Geographic Information Systems ; Humans ; *Insect Vectors ; Maryland/epidemiology ; Population Dynamics ; West Nile Fever/*epidemiology ; West Nile virus/*pathogenicity ; }, abstract = {We used geospatial techniques to study the potential impact of 2 exotic mosquitoes, Aedes albopictus and Ochlerotatus japonicus japonicus, on the epidemiology of West Nile virus in Maryland. These 2 species have established populations in Maryland over the past 15 years. Larvae of both mosquito species are found in natural and artificial water-holding cavities and containers, particularly water in tires. Therefore, we used locations of licensed tire dealers and of tire dumps scheduled for clean up as an index for potential sources of mosquito vectors. This index was expected to underestimate the actual population of source habitats. West Nile virus activity in Maryland during 1999, 2000, and 2001 was indicated by the presence of dead, infected birds, particularly American crows and other corvids; infected pools of mosquitoes; and human and horse infections. Adult females of both mosquito species are aggressive, opportunistic feeders that have been observed to take blood meals from avian and mammalian hosts. Susceptible vertebrate hosts, particularly birds, are ubiquitously distributed throughout the developed areas of the state. This analysis demonstrated a spatial convergence of the virus, the exotic mosquito vectors, and susceptible hosts. This conjunction indicated that these 2 mosquito species have a high potential to serve as bridge vectors and thus, impact the epidemiology of West Nile virus under favorable environmental and climatic conditions. Positive mosquito pools were collected from only the Baltimore-Washington metropolitan corridor, suggesting a newly created enzootic focus for this virus. Land-cover analysis of the sites where virus activity had been detected showed predominantly developed land uses. Analyses of the environmental justice aspects (social, economic, and housing characteristics) of block groups with human West Nile fever cases or with positive mosquito pools were equivocal. Human cases seemed to occur in developed block groups with lower income levels.}, } @article {pmid14518853, year = {2003}, author = {Verdonck, FA and Janssen, CR and Jaworska, J and Vanrolleghem, PA}, title = {Geo-referencing of probabilistic risk of new chemicals in rivers.}, journal = {Water science and technology : a journal of the International Association on Water Pollution Research}, volume = {48}, number = {3}, pages = {39-46}, pmid = {14518853}, issn = {0273-1223}, mesh = {Environmental Exposure ; Environmental Pollutants/*toxicity ; *Geographic Information Systems ; *Models, Statistical ; Reference Values ; Risk Assessment ; }, abstract = {The characterisation of the risk of (new) chemicals to species/communities, when both the exposure/environmental concentration and effects (species sensitivity) are variable and uncertain, is the central issue in Probabilistic Environmental Risk Assessment. The spatial variability is one of the largest components of the total variability. This paper tries to explicitly account for this spatial variability by geo-referencing the exposure, effect and finally probabilistic risk. Geo-referencing makes the risk assessment more refined and realistic. In addition, it is also highlighted that geo-referencing the effects of chemicals (species sensitivity distribution) is still a large unexplored area but has large potential to improve probabilistic ecological risk assessments.}, } @article {pmid14511706, year = {2003}, author = {Fisher, DJ and Burton, DT and Yonkos, LT and Turley, SD and Ziegler, GP and Turley, BS}, title = {Derivation of acute ecological risk criteria for chlorite in freshwater ecosystems.}, journal = {Water research}, volume = {37}, number = {18}, pages = {4359-4368}, doi = {10.1016/S0043-1354(03)00433-0}, pmid = {14511706}, issn = {0043-1354}, mesh = {Animals ; Chlorides/*toxicity ; Chlorine Compounds/chemistry ; Databases, Factual ; *Ecosystem ; *Fishes ; Fresh Water ; Lethal Dose 50 ; *Models, Statistical ; Oxides/chemistry ; Risk Assessment ; Water Pollutants/*toxicity ; Water Purification ; }, abstract = {Chlorine dioxide has been proposed as an alternative to chlorine because it is a powerful disinfection agent that does not react with ammonia or chlorinated organics to form chloramines or trihalomethanes. The major reduction product formed when chlorine dioxide is added to water is the chlorite ion. Chlorite has been shown to be less toxic than free or combined chlorine. However, previous studies with eight freshwater families produced a US Environmental Protection Agency (USEPA) acute water quality criteria (WQC) lower than the WQC for chlorine. In the current study, an additional 12 families were added to the toxicological database to determine ecological risk criteria (ERC) using both the standard USEPA WQC methodology and the USEPA Office of Pesticide Programs (OPP) probabilistic approach. Chlorite LC50 values for the 20 family database ranged from 0.27 mg/L for the Daphnidae to 208.76 mg/L for the Salmonidae. The Daphnidae were by far the most sensitive family tested, with an LC50 44 times lower than the next most sensitive family tested, the Hyalellidae (LC50=1.19 mg/L) and 214 times lower than the most sensitive fish family tested, the Ictaluridae (LC50=5.79 mg/L). The Criteria Maximum Concentration calculated using the USEPA WQC methodology was 0.025 mg/L while the 95% ERC calculated using the USEPA OPP probabilistic methodology was 0.135 mg/L. The USEPA OPP probabilistic approach yields a criterion more consistent with the overall species sensitivity distribution and is not overly skewed by the low Daphnidae LC50 as is the USEPA WQC approach.}, } @article {pmid14499550, year = {2003}, author = {Watts, CD and Naden, PS and Cooper, DM and Gannon, B}, title = {Application of a regional procedure to assess the risk to fish from high sediment concentrations.}, journal = {The Science of the total environment}, volume = {314-316}, number = {}, pages = {551-565}, doi = {10.1016/s0048-9697(03)00073-1}, pmid = {14499550}, issn = {0048-9697}, mesh = {Agriculture ; Animals ; Databases, Factual ; *Fishes ; *Geographic Information Systems ; *Geologic Sediments ; *Models, Theoretical ; Population Dynamics ; Rain ; Risk Assessment ; Soil ; Water Movements ; Water Pollutants/*toxicity ; }, abstract = {Periods of high suspended sediment concentration in rivers can affect the behaviour, health and habitat of freshwater fish. A simple regional model relating daily mean suspended sediment concentration in rivers to flow and percentage of cropped and urban land has been applied to the Lower Swale, UK. The model uses a GIS catchment coverage of hydrological response units (HRUs) of area 5-8 km2, each of which is assumed hydrologically independent and drains to an identified river reach. The sediment delivery properties of each HRU are a function of its land use characteristics determined from existing databases, and hydrological conditions determined from effective rainfall measurements. Daily mean suspended sediment concentrations for each river reach were derived by cumulating simulated HRU flows and sediment loads down successive reaches. A map of the modelled 10% quantile sediment concentrations is presented for both HRUs and river reaches. The map is substantially different from existing erosion risk maps because the delivery model is driven by flow in addition to land use, rather than by soil type. Frequency curves showing the exceedance probability of mean simulated sediment concentrations over 1-6-day durations have been derived using peaks-over-threshold techniques. Maps of the risk of harm to fish, based on the probability of 1- and 4-day sediment concentrations exceeding 80 mg l(-1), are presented. Such maps can be used to assess the impact of sediment on fish and for setting appropriate river water quality objectives.}, } @article {pmid12975657, year = {2003}, author = {Lerat, E and Daubin, V and Moran, NA}, title = {From gene trees to organismal phylogeny in prokaryotes: the case of the gamma-Proteobacteria.}, journal = {PLoS biology}, volume = {1}, number = {1}, pages = {E19}, pmid = {12975657}, issn = {1545-7885}, mesh = {Bacteria ; Computational Biology/*methods ; Evolution, Molecular ; Gammaproteobacteria/*genetics ; Gene Expression Regulation, Bacterial ; Gene Transfer Techniques ; Gene Transfer, Horizontal ; Genome ; Genome, Bacterial ; *Models, Genetic ; Multigene Family ; Phylogeny ; Prokaryotic Cells ; }, abstract = {The rapid increase in published genomic sequences for bacteria presents the first opportunity to reconstruct evolutionary events on the scale of entire genomes. However, extensive lateral gene transfer (LGT) may thwart this goal by preventing the establishment of organismal relationships based on individual gene phylogenies. The group for which cases of LGT are most frequently documented and for which the greatest density of complete genome sequences is available is the gamma-Proteobacteria, an ecologically diverse and ancient group including free-living species as well as pathogens and intracellular symbionts of plants and animals. We propose an approach to multigene phylogeny using complete genomes and apply it to the case of the gamma-Proteobacteria. We first applied stringent criteria to identify a set of likely gene orthologs and then tested the compatibilities of the resulting protein alignments with several phylogenetic hypotheses. Our results demonstrate phylogenetic concordance among virtually all (203 of 205) of the selected gene families, with each of the exceptions consistent with a single LGT event. The concatenated sequences of the concordant families yield a fully resolved phylogeny. This topology also received strong support in analyses aimed at excluding effects of heterogeneity in nucleotide base composition across lineages. Our analysis indicates that single-copy orthologous genes are resistant to horizontal transfer, even in ancient bacterial groups subject to high rates of LGT. This gene set can be identified and used to yield robust hypotheses for organismal phylogenies, thus establishing a foundation for reconstructing the evolutionary transitions, such as gene transfer, that underlie diversity in genome content and organization.}, } @article {pmid12967088, year = {2003}, author = {Van Straalen, NM}, title = {Ecotoxicology becomes stress ecology.}, journal = {Environmental science & technology}, volume = {37}, number = {17}, pages = {324A-330A}, doi = {10.1021/es0325720}, pmid = {12967088}, issn = {0013-936X}, mesh = {Animals ; Computational Biology ; Ecology/*trends ; Environment ; Environmental Pollutants/*toxicity ; Genomics/*trends ; Humans ; Policy Making ; Risk Assessment ; Toxicology/*trends ; }, } @article {pmid12959842, year = {2003}, author = {Jerrett, M and Burnett, RT and Willis, A and Krewski, D and Goldberg, MS and DeLuca, P and Finkelstein, N}, title = {Spatial analysis of the air pollution-mortality relationship in the context of ecologic confounders.}, journal = {Journal of toxicology and environmental health. Part A}, volume = {66}, number = {16-19}, pages = {1735-1777}, doi = {10.1080/15287390306438}, pmid = {12959842}, issn = {1528-7394}, mesh = {Air Pollution/*adverse effects ; Algorithms ; Databases, Factual ; Ecology ; Epidemiologic Studies ; Health ; Heart Diseases/epidemiology/mortality ; Humans ; Income ; Lung Diseases/epidemiology/mortality ; Lung Neoplasms/epidemiology/mortality ; Models, Statistical ; Mortality/*trends ; Proportional Hazards Models ; Socioeconomic Factors ; }, abstract = {Lack of control for confounding by ecological covariates that may relate to sulfate air pollution and mortality was a key criticism of the two studies that were the focus of the Particle Reanalysis Project. To assess the validity of this criticism, we address the question: "Does sulfate air pollution exert health effects when the impact of other individual and ecologic variables thought to influence health is taken into account?" A related question arises from the possibility of autocorrelation in the mortality risks and ecologic covariates. Failure to control for autocorrelation can lead to false positive significance tests and may indicate bias resulting from a missing variable or group of variables. We control for more than 25 individual risk factors and for 20 ecologic variables representing environmental, socioeconomic, demographic, health- care, and lifestyle determinants of health in a two-stage multilevel analysis. Four modeling strategies are used to control for spatial autocorrelation. Of the 20 ecologic variables tested, only sulfate and sulfur dioxide are significant in models that incorporate spatial autocorrelation. Accounting for autocorrelation also reduces the size and certainty of the sulfate effect on mortality when compared to results generated from Cox models where independent observations are assumed. Confidence limits for the sulfate relative risk include unity in models that simultaneously control for sulfur dioxide and autocorrelation.}, } @article {pmid12959832, year = {2003}, author = {Willis, A and Jerrett, M and Burnett, RT and Krewski, D}, title = {The association between sulfate air pollution and mortality at the county scale: an exploration of the impact of scale on a long-term exposure study.}, journal = {Journal of toxicology and environmental health. Part A}, volume = {66}, number = {16-19}, pages = {1605-1624}, doi = {10.1080/15287390306432}, pmid = {12959832}, issn = {1528-7394}, mesh = {Air Pollution/*adverse effects ; American Cancer Society ; Data Interpretation, Statistical ; Environmental Monitoring ; Epidemiologic Methods ; Epidemiological Monitoring ; Heart Diseases/chemically induced/epidemiology ; Humans ; Lung Diseases/chemically induced/epidemiology ; Mortality/*trends ; Regression Analysis ; Sulfates/*adverse effects ; Sulfur Dioxide/adverse effects ; Urban Population ; }, abstract = {The American Cancer Society (ACS) Study and its reanalysis are built upon in order to examine the impact of scale on the observed relationship between sulfates and mortality. The limitations of the original ACS Study (Pope et al., 1995) and the reanalysis of this study (Krewski et al., 2000) are discussed; while the latter dealt with some issues in using ecological data, it did not address scale. Next, the article outlines the county-scale study, the methods used to aggregate data, and the two-stage analysis used to derive relative risk (RR). Finally, the results of working at the county scale are compared with those obtained by the reanalysis team using larger metropolitan areas. Less than half of the cohort used in the metropolitan study were used at the county scale because of the limited availability of sulfate monitors and because five-digit ZIP codes more accurately assigned individuals to geographical areas. Therefore, the county data should be considered as new and not as a reorganization of the original data set. The reanalysis and the county studies should be considered as two separate studies that took different scales as their basic organizing principle. The RR of all-cause mortality from sulfate exposure at the county scale was 1.50 (1.30, 1.73) compared with 1.25 (1.13, 1.37) at the metropolitan scale; for cardiopulmonary mortality, the RR was 1.75 (1.48, 2.08) at the county scale compared with 1.29 (1.15, 1.46) at the metropolitan scale. Because lung cancer mortality was low in some counties, the two-stage random effects model became unstable. At the county scale, the RR from sulfates was more robust to the inclusion of ecologic covariates. Other place-specific ecologic covariates were either insignificant or barely significant (with a lower 95% confidence limit near 0.99 or 1.00) when included in the two-stage regression model for all-cause mortality with sulfates. Moreover, no ecologic covariate changed the RR of all-cause mortality from sulfates by 25% or more. Both population change and unemployment rate affected the RR for cardiopulmonary mortality from sulfate exposure by 25% or more in the county-scale analysis. However, when these two variables were entered into a multiple covariate analysis, the RR from sulfates decreased but remained strongly significant. Sulfur dioxide was not an important covariate at the county scale. Thus, at the county scale, long-term exposure to sulfates appears to be more strongly associated with increased risk of all-cause and cardiopulmonary mortality than previously indicated by the ACS study and its reanalysis.}, } @article {pmid12952535, year = {2003}, author = {Zhang, P and Gu, Z and Li, WH}, title = {Different evolutionary patterns between young duplicate genes in the human genome.}, journal = {Genome biology}, volume = {4}, number = {9}, pages = {R56}, pmid = {12952535}, issn = {1474-760X}, mesh = {Amino Acid Substitution ; Databases, Genetic ; *Evolution, Molecular ; Genes, Duplicate/*genetics ; Genetic Variation ; *Genome, Human ; Humans ; Phylogeny ; Time Factors ; }, abstract = {BACKGROUND: Following gene duplication, two duplicate genes may experience relaxed functional constraints or acquire different mutations, and may also diverge in function. Whether the two copies will evolve in different patterns remains unclear, however, because previous studies have reached conflicting conclusions. In order to resolve this issue, by providing a general picture, we studied 250 independent pairs of young duplicate genes from the whole human genome.

RESULTS: We showed that nearly 60% of the young duplicate gene pairs have evolved at the amino-acid level at significantly different rates from each other. More than 25% of these gene pairs also showed significantly different ratios of nonsynonymous to synonymous rates (Ka/Ks ratios). Moreover, duplicate pairs with different rates of amino-acid substitution also tend to differ in the Ka/Ks ratio, with the fast-evolving copy tending to have a slightly higher Ks than the slow-evolving one. Lastly, a substantial portion of fast-evolving copies have accumulated amino-acid substitutions evenly across the protein sequences, whereas most of the slow-evolving copies exhibit uneven substitution patterns.

CONCLUSIONS: Our results suggest that duplicate genes tend to evolve in different patterns following the duplication event. One copy evolves faster than the other and accumulates amino-acid substitutions evenly across the sequence, whereas the other copy evolves more slowly and accumulates amino-acid substitutions unevenly across the sequence. Such different evolutionary patterns may be largely due to different functional constraints on the two copies.}, } @article {pmid12943263, year = {2003}, author = {Viglizzo, EF and Pordomingo, AJ and Castro, MG and Lertora, FA}, title = {Environmental assessment of agriculture at a regional scale in the Pampas of Argentina.}, journal = {Environmental monitoring and assessment}, volume = {87}, number = {2}, pages = {169-195}, pmid = {12943263}, issn = {0167-6369}, mesh = {*Agriculture ; Argentina ; Conservation of Energy Resources ; Conservation of Natural Resources ; *Environment ; *Environmental Monitoring ; Fossil Fuels ; *Geographic Information Systems ; Nitrogen ; Phosphorus ; Risk Assessment ; }, abstract = {Governments need good information to design policies. However, in the Argentine Pampas there are neither sufficient knowledge on environmental issues, nor clear perception of environmental alterations across space and time. The general objective of this work was to provide decision makers with a scientifically sound set of indicators aiming at the assessment of current status and future trends in the rural environment of this sensitive region. As driving criteria to select indicators, we assumed that they had to be sound, simple to calculate, easy to understand, and easily applicable by decision makers. They are related closely to significant ecological structures and functions. Twelve basic indicators were identified: (1) land use, (2) fossil energy use, (3) fossil energy use efficiency, (4) nitrogen (N) balance, (5) phosphorus (P) balance, (6) nitrogen contamination risk, (7) phosphorus contamination risk, (8) pesticide contamination, (9) soil erosion risk, (10) habitat intervention, (11) changes in soil carbon stock, and (12) balance of greenhouse gases. Indicators were geographically referenced using a geographic information system (GIS). The strength of this study is not in the absolute value of environmental indicators, but rather in the conceptualization of indicator and the identification of changing patterns, gradients and trends in space and time. According to our results, we can not definitely say that agriculture in the Pampas, as a whole, tends to be sustainable or not. While some indicators tend to improve, others keep stable, and the rest worsen. The relative importance among indicators must also be considered. The indicators that showed a negative net change are key to the identification of critical problems that will require special attention in the close future.}, } @article {pmid12929817, year = {2003}, author = {Barale, V}, title = {Environmental remote sensing of the Mediterranean Sea.}, journal = {Journal of environmental science and health. Part A, Toxic/hazardous substances & environmental engineering}, volume = {38}, number = {8}, pages = {1681-1688}, doi = {10.1081/ese-120021489}, pmid = {12929817}, issn = {1093-4529}, mesh = {Ecosystem ; Environmental Monitoring/*methods ; *Geographic Information Systems ; Mediterranean Sea ; Pigments, Biological/analysis ; Temperature ; Water Movements ; Wind ; }, abstract = {Remote sensing provides an overview of environmental complexities in the Mediterranean region, relating to its natural setting and to water exchanges within the basin; to typical ecological processes and their key driving forces; to environmental problems faced by the main sub-basins. Statistics of pigment concentration, surface temperature, and wind speed, derived from historical archives, differentiate between geographical provinces shaped by dynamical and bio-geochemical patterns. These are areas under the direct influence of coastal interactions, regions of enhanced characteristics linked to the impact of continental margins and/or prevailing winds, and open sea areas, characterized by frontal structures and mesoscale eddies. Features such as river plumes, filaments, and permanent gyres maintain their characteristics over time. The main trends in the provinces indicate two seasons of extreme conditions, in winter and summer, with transition periods in spring and fall, or a distinct seasonality due to local factors.}, } @article {pmid12927970, year = {2003}, author = {Sanderson, MJ and Driskell, AC}, title = {The challenge of constructing large phylogenetic trees.}, journal = {Trends in plant science}, volume = {8}, number = {8}, pages = {374-379}, doi = {10.1016/S1360-1385(03)00165-1}, pmid = {12927970}, issn = {1360-1385}, mesh = {Algorithms ; *Biological Evolution ; Computational Biology ; Databases, Genetic ; Evolution, Molecular ; Models, Genetic ; *Phylogeny ; Plants/*classification/*genetics ; Sequence Alignment ; }, abstract = {The amount of sequence data available to reconstruct the evolutionary history of genes and species has increased 20-fold in the past decade. Consequently the size of phylogenetic analyses has grown as well, and phylogenetic methods, algorithms and their implementations have struggled to keep pace. Computational and other challenges raised by this burgeoning database emerge at several stages of analysis, from the optimal assembly of large data matrices from sequence databases, to the efficient construction of trees from these large matrices and the piece-wise assembly of 'supertrees' from those trees in turn. A final challenge is posed by the difficulty of visualizing and making inferences from trees that might soon routinely contain thousands of species.}, } @article {pmid12924580, year = {2003}, author = {Russom, CL and Breton, RL and Walker, JD and Bradbury, SP}, title = {An overview of the use of quantitative structure-activity relationships for ranking and prioritizing large chemical inventories for environmental risk assessments.}, journal = {Environmental toxicology and chemistry}, volume = {22}, number = {8}, pages = {1810-1821}, doi = {10.1897/01-194}, pmid = {12924580}, issn = {0730-7268}, mesh = {*Databases, Factual ; Decision Making ; Environment ; Environmental Pollutants/*poisoning ; Forecasting ; Hazardous Substances/*poisoning ; *Models, Theoretical ; *Quantitative Structure-Activity Relationship ; Risk Assessment ; United States ; }, abstract = {Ecological risk assessments for chemical stressors are used to establish linkages between likely exposure concentrations and adverse effects to ecological receptors. At times, it is useful to conduct screening risk assessments to assist in prioritizing or ranking chemicals on the basis of potential hazard and exposure assessment parameters. Ranking of large chemical inventories can provide evidence for focusing research and/or cleanup efforts on specific chemicals of concern. Because of financial and time constraints, data gaps exist, and the risk assessor is left with decisions on which models to use to estimate the parameter of concern. In this review, several methods are presented for using quantitative structure-activity relationships (QSARs) in conducting hazard screening or screening-level risk assessments. The ranking methods described include those related to current regulatory issues associated with chemical inventories from Canada, Europe, and the United States and an example of a screening-level risk assessment conducted on chemicals associated with a watershed in the midwest region of the United States.}, } @article {pmid12924578, year = {2003}, author = {Bradbury, SP and Russom, CL and Ankley, GT and Schultz, TW and Walker, JD}, title = {Overview of data and conceptual approaches for derivation of quantitative structure-activity relationships for ecotoxicological effects of organic chemicals.}, journal = {Environmental toxicology and chemistry}, volume = {22}, number = {8}, pages = {1789-1798}, doi = {10.1897/01-234}, pmid = {12924578}, issn = {0730-7268}, mesh = {Animals ; *Databases, Factual ; Ecology ; Forecasting ; *Models, Theoretical ; Organic Chemicals/*toxicity ; *Quantitative Structure-Activity Relationship ; Risk Assessment ; Solubility ; Water Pollutants, Chemical/*toxicity ; }, abstract = {The use of quantitative structure-activity relationships (QSARs) in assessing potential toxic effects of organic chemicals on aquatic organisms continues to evolve as computational efficiency and toxicological understanding advance. With the ever-increasing production of new chemicals, and the need to optimize resources to assess thousands of existing chemicals in commerce, regulatory agencies have turned to QSARs as essential tools to help prioritize tiered risk assessments when empirical data are not available to evaluate toxicological effects. Progress in designing scientifically credible QSARs is intimately associated with the development of empirically derived databases of well-defined and quantified toxicity endpoints, which are based on a strategic evaluation of diverse sets of chemical structures, modes of toxic action, and species. This review provides a brief overview of four databases created for the purpose of developing QSARs for estimating toxicity of chemicals to aquatic organisms. The evolution of QSARs based initially on general chemical classification schemes, to models founded on modes of toxic action that range from nonspecific partitioning into hydrophobic cellular membranes to receptor-mediated mechanisms is summarized. Finally, an overview of expert systems that integrate chemical-specific mode of action classification and associated QSAR selection for estimating potential toxicological effects of organic chemicals is presented.}, } @article {pmid12924115, year = {2003}, author = {Chang, Y and Bu, R and Hu, Y and Xu, C and Wang, Q}, title = {[GIS and RS determination of abiotic range of forest landscape distribution in Changbai Mountain Natural Reserve].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {14}, number = {5}, pages = {671-675}, pmid = {12924115}, issn = {1001-9332}, mesh = {*Conservation of Natural Resources ; *Ecosystem ; *Geographic Information Systems ; Rain ; Regression Analysis ; *Satellite Communications ; Temperature ; Trees/*growth & development ; }, abstract = {Based on landscape classification of remote sensing data and spatial expression of environmental factors, the abiotic ranges of forest landscape distribution in Changbai Mountain Natural Reserve were determined by using GIS. The results showed that the optimum elevation range of tundra, mountain birch forest, evergreen coniferous forest, and broad-leaved Korean pine forest were 1780-2212 m, 1705-1956 m, 1042-1625 m, and 823-1184 m, respectively. The corresponding optimum annual average temperature ranges were -4.75(-)-2.40 degrees C, -3.42(-)-2.07 degrees C, -1.49-1.39 degrees C, and 0.71-2.37 degrees C, and the optimum ranges of annual precipitation were 1034-1110 mm, 1014-1060 mm, 883-1017 mm, and 824-925 mm, respectively. The forest landscapes in Changbai Mountain Natural Reserve were mainly distributed in flat and gentle areas. This distribution pattern was closely related to aspect. Tundra was almost evenly present in various aspects. In northern and northwestern direction, most forest landscapes were distributed, including mountain birch forest, evergreen coniferous forest, broad-leaved Korean pine forest, aspen and Betula forest. Most larch forest was in favor of northeastern direction with small amount facing eastern and northern way. Sparse forest briefly occupied west aspect with some orienting in southwest, northwest and south, while all wind-thrown areas were facing west, southwest and northwest aspects.}, } @article {pmid12924111, year = {2003}, author = {Zhang, N and Yu, G and Zhao, S and Yu, Z}, title = {[Ecosystem productivity process model for landscape based on remote sensing and surface data].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {14}, number = {5}, pages = {643-652}, pmid = {12924111}, issn = {1001-9332}, mesh = {*Conservation of Energy Resources ; *Ecosystem ; *Geographic Information Systems ; Models, Theoretical ; Plant Leaves/metabolism ; *Satellite Communications ; Seasons ; Trees/*growth & development ; }, abstract = {In this paper, the a ecosystem productivity process model for landscape (EPPML) reflecting carbon and water cycles of system was described and discussed. In EPPML, leaf area index (LAI) that greatly influenced vegetation productivity was received from remote sensing images, the spatial distribution and temporal dynamics of net primary productivity (NPP) and evapotranspiration were simulated. Geographical information system (GIS) was used to process, analyze, and display spatial data. Thus, the studies on physiological ecology could be extended, and converted from small scale to larger scale. Using EPPML, the vegetation productivity in Changbai Mountain Natural Reserve in 1995 was simulated. EPPML could well and truly simulate the NPP of main vegetations in the natural reserve. NPP was estimated to be 0.680 kg Cm.-2.yr.-1, mostly ranging from 0.105 to 1.241 kg C.m-2.yr.-1, accounting for 82.1%. The highest NPP (1.084 kg C.m-2.yr-1) appeared in mixed broad-leaved and Korean pine forests. The total NPP was estimated to be 1.332 x 10(6) t C.yr-1. The highest total NPP appeared in mixed broad-leaved and Korean pine forests and spruce-fir forest, which were 0.540 x 10(6) t C.yr.-1 and 0.428 x 10(6) t C.yr.-1, respectively. The seasonal variation of NPP appeared obvious single peak with peak value in July (6.13 g C.m-2.d-1). The most NPP accumulated in the summer, which was 0.465 kg C.m-2, secondly in the spring, and least in the winter.}, } @article {pmid12920897, year = {2003}, author = {Zang, S and Wan, L and Zhou, D}, title = {[Landscape ecological assessment and planning in the watershed of Erlong Mountain reservoir in Heilongjiang Province].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {14}, number = {4}, pages = {540-544}, pmid = {12920897}, issn = {1001-9332}, mesh = {*Conservation of Natural Resources ; *Ecology ; *Geographic Information Systems ; }, abstract = {Based on the theories of landscape ecology, the landscape eco-environment in the watershed of Erlong Mountain reservoir in Heilongjiang Province was analyzed and assessed using GIS technique and statistical model of principal component analysis and spatial cluster analysis. It was found that 100.08 km2 (36%) of total area was in good state, 85.73 km2 (31%) was in general state, and 47.26 km2 (17%) and 15.48 km2 (16%) was in relative poor and ideal states, respectively. According to the landscape ecological structure, three landscape functional areas were designed as agricultural area, the developmental direction of which was eco-agriculture, tour agriculture and high-benefit agriculture; eco-environment protection area, the development direction of which was develop soil and water conservation forest; and area for increasing vegetation cover, the developmental direction of which was rational cut and utilization of forest resources, spatial optimization disposal of forest type, and protection of wildwood.}, } @article {pmid12920896, year = {2003}, author = {Song, D and Xiao, D and Zhang, Z and Cao, Y and Ma, M and Wang, J and Wang, J}, title = {[Landscape changes of Minqin oasis in Gansu Province and its driving force].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {14}, number = {4}, pages = {535-539}, pmid = {12920896}, issn = {1001-9332}, mesh = {Agriculture ; China ; Conservation of Natural Resources ; *Desert Climate ; *Ecology ; *Geographic Information Systems ; Water Supply ; }, abstract = {Based on the technology of GIS, RS and using FRAGSTATS, studies on the landscape changes of Minqin oasis during 1987 to 2001 showed that the transitions of landscape patches were complex, and open up wasteland took place during 1994 to 1998 in the south of the oasis where the condition of water was better and desertization took place during 1998 to 2001 in the north of the oasis where the condition of water was worse. The decreasing of the Shannon's diversity index and the Shannon's evenness index and the increasing of Contagion index showed that human beings reconstructing the landscape of the oasis began stronger than before. Unreasonable land use was changed the landscape pattern, and the condition of water resource accelerated the landscape change.}, } @article {pmid12918401, year = {2001}, author = {Kondrat'ev, K and Losev, KS and Ananicheva, MD and Chesnokova, IV}, title = {Elementary structural units of the biosphere and landscapes.}, journal = {Doklady biological sciences : proceedings of the Academy of Sciences of the USSR, Biological sciences sections}, volume = {380}, number = {}, pages = {448-449}, doi = {10.1023/a:1012367203886}, pmid = {12918401}, issn = {0012-4966}, mesh = {Conservation of Natural Resources ; Databases as Topic ; Ecological Systems, Closed ; *Ecosystem ; Models, Theoretical ; Plant Physiological Phenomena ; }, } @article {pmid12907801, year = {2003}, author = {Daubin, V and Moran, NA and Ochman, H}, title = {Phylogenetics and the cohesion of bacterial genomes.}, journal = {Science (New York, N.Y.)}, volume = {301}, number = {5634}, pages = {829-832}, doi = {10.1126/science.1086568}, pmid = {12907801}, issn = {1095-9203}, mesh = {Bacteria/*classification/*genetics ; Biological Evolution ; Chlamydophila pneumoniae/genetics ; Computational Biology ; Escherichia coli/genetics ; *Gene Transfer, Horizontal ; Genes, Bacterial ; Genes, rRNA ; *Genome, Bacterial ; Likelihood Functions ; *Phylogeny ; RNA, Bacterial/genetics ; RNA, Ribosomal/genetics ; Recombination, Genetic ; Species Specificity ; }, abstract = {Gene acquisition is an ongoing process in many bacterial genomes, contributing to adaptation and ecological diversification. Lateral gene transfer is considered the primary explanation for discordance among gene phylogenies and as an obstacle to reconstructing the tree of life. We measured the extent of phylogenetic conflict and alien-gene acquisition within quartets of sequenced genomes. Although comparisons of complete gene inventories indicate appreciable gain and loss of genes, orthologs available for phylogenetic reconstruction are consistent with a single tree.}, } @article {pmid12898166, year = {2003}, author = {Pedersen, PG and Holmstrup, M}, title = {Freeze or dehydrate: only two options for the survival of subzero temperatures in the arctic enchytraeid Fridericia ratzeli.}, journal = {Journal of comparative physiology. B, Biochemical, systemic, and environmental physiology}, volume = {173}, number = {7}, pages = {601-609}, pmid = {12898166}, issn = {0174-1578}, mesh = {Adaptation, Physiological/*physiology ; Animals ; Arctic Regions ; Body Fluids/chemistry/physiology ; Body Water/metabolism/physiology ; *Cold Temperature ; Cryoprotective Agents/metabolism ; Crystallization ; Data Interpretation, Statistical ; Dehydration/metabolism ; Desiccation ; Freezing ; Glucose/analysis ; Humidity ; Oligochaeta/chemistry/growth & development/*physiology ; Soil ; Temperature ; Time Factors ; Transition Temperature ; Water/analysis/chemistry ; }, abstract = {Hygrophilic soil animals, like enchytraeids, overwintering in frozen soil are unlikely to base their cold tolerance on supercooling of body fluids. It seems more likely that they will either freeze due to inoculative freezing, or dehydrate and adjust their body fluid melting point to ambient temperature as has been shown for earthworm cocoons and Collembola. In the present study we tested this hypothesis by exposing field-collected adult Fridericia ratzeli from Disko, West Greenland, to freezing temperatures under various moisture regimes. When cooled at -1 degrees C min(-1) under dry conditions F. ratzeli had a mean temperature of crystallisation (T(c)) of -5.8 degrees C. However, when exposed to temperatures above standard T(c) for 22 h, at -4 degrees C, most individuals (90%, n= 30) remained unfrozen. Slow cooling from -1 degrees C to -6 degrees C in vials where the air was in equilibrium with the vapour pressure of ice resulted in freezing in about 65% of the individuals. These individuals maintained a normal body water content of 2.7-3.0 mg mg(-1) dry weight and had body fluid melting points of about -0.5 degrees C with little or no change due to freezing. About 35% of the individuals dehydrated drastically to below 1.1 mg mg(-1) dry weight at -6 degrees C, and consequently had lowered their body fluid melting point to ca. -6 degrees C at this time. Survival was high in both frozen and dehydrated animals at -6 degrees C, about 60%. Approximately 25% of the animals (both frozen and dehydrated individuals) had elevated glucose concentrations, but the mean glucose concentration was not increased to any great extent in any group due to cold exposure. The desiccating potential of ice was simulated using aqueous NaCl solutions at 0 degrees C. Water loss and survival in this experiment were in good agreement with results from freezing experiments. The influence of soil moisture on survival and tendency to dehydrate was also evaluated. However, soil moisture ranging between 0.74 g g(-1) and 1.15 g g(-1) dry soil did not result in any significant differences in survival or frequency of dehydrated animals even though the apparent wetness and structure of the soil was clearly different in these moisture contents.}, } @article {pmid12889578, year = {2002}, author = {Shearer, JE}, title = {The concept of protection: a dimensional analysis and critique of a theory of protection.}, journal = {ANS. Advances in nursing science}, volume = {25}, number = {1}, pages = {65-78}, doi = {10.1097/00012272-200209000-00008}, pmid = {12889578}, issn = {0161-9268}, mesh = {Adult ; Child ; Child Welfare ; Communication ; Data Interpretation, Statistical ; *Empathy ; Helping Behavior ; Humans ; Internal-External Control ; *Models, Nursing ; Models, Psychological ; Nurse's Role ; *Nurse-Patient Relations ; Nursing Care/*psychology ; Nursing Methodology Research/*methods ; Nursing Process ; *Nursing Theory ; Parent-Child Relations ; Parents/psychology ; *Philosophy, Nursing ; Risk Assessment ; Sex Education ; }, abstract = {Dimensional analysis clarifies the concept of protection, which has a commonly understood definition but is used inconsistently in research literature. Concepts such as protective factors and protective behaviors are often used interchangeably without adequately representing the phenomenon of protection itself. This article critiques a situation-specific theory of protection and presents dimensions of a model with an ecological view of protection. It uses dimensional analysis methods to derive the social construction of protection from its use in a broad range of literature; vigilant management and vigilant communication are salient dimensions of protection. The article compares conceptual literature with research literature to identify inconsistencies in use.}, } @article {pmid12878457, year = {2003}, author = {Phillips, MJ and Penny, D}, title = {The root of the mammalian tree inferred from whole mitochondrial genomes.}, journal = {Molecular phylogenetics and evolution}, volume = {28}, number = {2}, pages = {171-185}, doi = {10.1016/s1055-7903(03)00057-5}, pmid = {12878457}, issn = {1055-7903}, mesh = {Animals ; Base Composition ; Cluster Analysis ; DNA, Mitochondrial/*genetics ; Data Interpretation, Statistical ; Genetic Variation ; Likelihood Functions ; Mammals/*classification/genetics ; *Phylogeny ; Research Design ; }, abstract = {Morphological and molecular data are currently contradictory over the position of monotremes with respect to marsupial and placental mammals. As part of a re-evaluation of both forms of data we examine complete mitochondrial genomes in more detail. There is a particularly large discrepancy in the frequencies of thymine and cytosine (T-C) between mitochondrial genomes that appears to affect some deep divergences in the mammalian tree. We report that recoding nucleotides to RY-characters, and partitioning maximum-likelihood analyses among subsets of data reduces such biases, and improves the fit of models to the data, respectively. RY-coding also increases the signal on the internal branches relative to external, and thus increases the phylogenetic signal. In contrast to previous analyses of mitochondrial data, our analyses favor Theria (marsupials plus placentals) over Marsupionta (monotremes plus marsupials). However, a short therian stem lineage is inferred, which is at variance with the traditionally deep placement of monotremes on morphological data.}, } @article {pmid12877825, year = {2003}, author = {Braxton, SM and Onstad, DW and Dockter, DE and Giordano, R and Larsson, R and Humber, RA}, title = {Description and analysis of two internet-based databases of insect pathogens: EDWIP and VIDIL.}, journal = {Journal of invertebrate pathology}, volume = {83}, number = {3}, pages = {185-195}, doi = {10.1016/s0022-2011(03)00089-2}, pmid = {12877825}, issn = {0022-2011}, mesh = {Animals ; *Databases, Factual ; Insecta/*microbiology ; *Internet ; }, abstract = {In 1996, two searchable databases covering insect pathogens were posted on the World Wide Web: the Ecological Database of the World's Insect Pathogens (EDWIP) and the Viral Diseases of Insects in the Literature database (VIDIL). In this paper, we describe the format and contents of EDWIP and VIDIL on the World Wide Web. EDWIP contains over 9,400 pathogen-host association records, 677 negative test result or "no association" records, 4,454 host species, 2,285 pathogen species records, and 2,057 bibliographical references. Species of Coleoptera and Lepidoptera are the best represented groups in EDWIP. Lepidopteran species account for the most associations of any host order in EDWIP, over 2,500, or 27%. Of the pathogen groups, Protozoa (including microsporidia) accounted for nearly 66% of the pathogen species records and over 40% of the association records in EDWIP. Fungi account for only 18% of the pathogen species, but nearly 33% of the association records. Habitats dominated by human activities (e.g., crop, stored product, and human dwelling) account for most of the host habitats recorded in EDWIP. The United States and Japan are the most common locations and the Nearctic and Palearctic are the most common biogeographic regions reported in EDWIP. There are 4,801 annotated bibliographic records in VIDIL.}, } @article {pmid12872911, year = {2003}, author = {Cutter, AD and Avilés, L and Ward, S}, title = {The proximate determinants of sex ratio in C. elegans populations.}, journal = {Genetical research}, volume = {81}, number = {2}, pages = {91-102}, doi = {10.1017/s001667230300613x}, pmid = {12872911}, support = {GM 25243/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Caenorhabditis elegans/*genetics ; Data Interpretation, Statistical ; Disorders of Sex Development/genetics ; Male ; Models, Genetic ; *Sex Determination Processes ; *Sex Ratio ; }, abstract = {The soil nematode Caenorhabditis elegans is an example of a species in which self-fertilizing hermaphrodites predominate, but functional males continue to persist--allowing outcrossing to persevere at low levels. Hermaphrodites can produce male progeny as a consequence of sex chromosome non-disjunction or via outcrossing with males. Consequently, the genetics of sex determination coupled with the efficiency by which males find, inseminate and obtain fertilizations with hermaphrodites will influence the frequency at which males and outcrossing occurs in such populations. Behavioural and physiological traits with a heritable basis, as well as ecological characters, may influence male reproductive success and therefore sex ratio. Because sex ratio is tied to male reproductive success, sex ratio greatly affects outcrossing rates, patterns of genetic variation, and the ability of natural selection to act within populations. In this paper we explore the determinants of male frequency in C. elegans with a mathematical model and experimental data. We address the role of the genetic machinery of sex determination via sex chromosome non-disjunction on sex ratio and the influence of physiological components of C. elegans' life history that contribute to variation in sex ratio by way of male reproductive success. Finally, we discuss the short-term and long-term factors that are likely to affect sex ratio and breeding system evolution in species like C. elegans.}, } @article {pmid12859001, year = {2003}, author = {Dore, MH and Webb, D}, title = {Valuing biodiversity: reality or mirage?.}, journal = {Environmental monitoring and assessment}, volume = {86}, number = {1-2}, pages = {91-104}, pmid = {12859001}, issn = {0167-6369}, mesh = {Animals ; Biomass ; Conservation of Natural Resources/*economics ; Decision Support Techniques ; *Economics ; *Ecosystem ; Energy-Generating Resources ; Humans ; Population Dynamics ; *Social Values ; }, abstract = {The objective of this paper was to consider the social value of biological diversity and explore if this value could be expressed in terms of a unidimensional metric in money. Economics distinguishes between use-values and non-use-values, which are critically evaluated for valuing biodiversity. It is shown that these utility-based valuations have severe limitations as they treat species in isolation from their ecological contexts. In contrast, ecosystem ecology regards ecosystems as an integrated non-linear and nonconvex system in which ecosystem functions can be understood as a four-component cycle; exploitation, accumulation of biomass, creative destruction and renewal. Within such a cycle, ecosystems can be seen to have two properties: stability and resilience. A good proxy for resilience is the probability of extinction of species, and social value of biodiversity can be expressed as a partial ordering with this probability as an index. This approach is consistent with decision theory, of which social choice is an important component, pioneered by Arrow.}, } @article {pmid12857643, year = {2003}, author = {Wiens, JJ}, title = {Missing data, incomplete taxa, and phylogenetic accuracy.}, journal = {Systematic biology}, volume = {52}, number = {4}, pages = {528-538}, doi = {10.1080/10635150390218330}, pmid = {12857643}, issn = {1063-5157}, mesh = {Computer Simulation ; Data Interpretation, Statistical ; Fossils ; *Phylogeny ; *Research Design ; }, abstract = {The problem of missing data is often considered to be the most important obstacle in reconstructing the phylogeny of fossil taxa and in combining data from diverse characters and taxa for phylogenetic analysis. Empirical and theoretical studies show that including highly incomplete taxa can lead to multiple equally parsimonious trees, poorly resolved consensus trees, and decreased phylogenetic accuracy. However, the mechanisms that cause incomplete taxa to be problematic have remained unclear. It has been widely assumed that incomplete taxa are problematic because of the proportion or amount of missing data that they bear. In this study, I use simulations to show that the reduced accuracy associated with including incomplete taxa is caused by these taxa bearing too few complete characters rather than too many missing data cells. This seemingly subtle distinction has a number of important implications. First, the so-called missing data problem for incomplete taxa is, paradoxically, not directly related to their amount or proportion of missing data. Thus, the level of completeness alone should not guide the exclusion of taxa (contrary to common practice), and these results may explain why empirical studies have sometimes found little relationship between the completeness of a taxon and its impact on an analysis. These results also (1) suggest a more effective strategy for dealing with incomplete taxa, (2) call into question a justification of the controversial phylogenetic supertree approach, and (3) show the potential for the accurate phylogenetic placement of highly incomplete taxa, both when combining diverse data sets and when analyzing relationships of fossil taxa.}, } @article {pmid12855084, year = {2003}, author = {Lo Priore, C and Castelnuovo, G and Liccione, D and Liccione, D}, title = {Experience with V-STORE: considerations on presence in virtual environments for effective neuropsychological rehabilitation of executive functions.}, journal = {Cyberpsychology & behavior : the impact of the Internet, multimedia and virtual reality on behavior and society}, volume = {6}, number = {3}, pages = {281-287}, doi = {10.1089/109493103322011579}, pmid = {12855084}, issn = {1094-9313}, mesh = {Cognition Disorders/diagnosis/physiopathology/*rehabilitation ; Galvanic Skin Response/physiology ; Humans ; Memory, Short-Term ; Mental Recall ; Neuropsychological Tests ; Prefrontal Cortex/physiopathology ; Surveys and Questionnaires ; Therapy, Computer-Assisted/instrumentation ; *User-Computer Interface ; }, abstract = {The paper discusses the use of immersive virtual reality systems for the cognitive rehabilitation of dysexecutive syndrome, usually caused by prefrontal brain injuries. With respect to classical P&P and flat-screen computer rehabilitative tools, IVR systems might prove capable of evoking a more intense and compelling sense of presence, thanks to the highly naturalistic subject-environment interaction allowed. Within a constructivist framework applied to holistic rehabilitation, we suggest that this difference might enhance the ecological validity of cognitive training, partly overcoming the implicit limits of a lab setting, which seem to affect non-immersive procedures especially when applied to dysexecutive symptoms. We tested presence in a pilot study applied to a new VR-based rehabilitation tool for executive functions, V-Store; it allows patients to explore a virtual environment where they solve six series of tasks, ordered for complexity and designed to stimulate executive functions, programming, categorical abstraction, short-term memory and attention. We compared sense of presence experienced by unskilled normal subjects, randomly assigned to immersive or non-immersive (flat screen) sessions of V-Store, through four different indexes: self-report questionnaire, psychophysiological (GSR, skin conductance), neuropsychological (incidental recall memory test related to auditory information coming from the "real" environment) and count of breaks in presence (BIPs). Preliminary results show in the immersive group a significantly higher GSR response during tasks; neuropsychological data (fewer recalled elements from "reality") and less BIPs only show a congruent but yet non-significant advantage for the immersive condition; no differences were evident from the self-report questionnaire. A larger experimental group is currently under examination to evaluate significance of these data, which also might prove interesting with respect to the question of objective-subjective measures of presence.}, } @article {pmid12840042, year = {2003}, author = {Makova, KD and Li, WH}, title = {Divergence in the spatial pattern of gene expression between human duplicate genes.}, journal = {Genome research}, volume = {13}, number = {7}, pages = {1638-1645}, pmid = {12840042}, issn = {1088-9051}, mesh = {Computational Biology ; Databases, Genetic ; *Gene Expression Profiling/methods ; Gene Expression Regulation/*genetics/physiology ; Genes, Duplicate/*genetics/physiology ; Genetic Variation/*genetics/physiology ; Humans ; *Oligonucleotide Array Sequence Analysis/methods ; }, abstract = {Microarray gene expression data provide a wealth of information for elucidating the mode and tempo of molecular evolution. In the present study,we analyze the spatial expression pattern of human duplicate gene pairs by using oligonucleotide microarray data,and study the relationship between coding sequence divergence and expression divergence. First,we find a strong positive correlation between the proportion of duplicate gene pairs with divergent expression (as presence or absence of expression in a tissue) and both synonymous (K(S)) and nonsynonymous divergence (K(A)). The divergence of gene expression between human duplicate genes is rapid, probably faster than that between yeast duplicates in terms of generations. Second,we compute the correlation coefficient (R) between the expression levels of duplicate genes in different tissues and find a significant negative correlation between R and K(S). There is also a negative correlation between R and K(A), when K(A)
METHODS: A set of database was set up using the information collected and linked to electronic maps of China in a software ArcGIS 8.01 from 41 HFRS surveillance sites during 1995 - 1998. A HFRS spatial distribution model was developed using inverse distance weighted interpolation of ArcGIS's spatial analysis method. The normalized difference vegetation index (NDVI) in each HFRS surveillance site was extracted from SPOT4 satellite vegetation imagery. Correlation analysis was performed through SPSS 10.0 to analyze the association between NDVI and HFRS incidence, HFRS risk areas were mapped under different colors.

RESULTS: Spatial distribution model from HFRS surveillance sites showed that HFRS foci mainly presented in the Heilongjiang River drainage, the middle and lower reaches of the Yellow River, the middle and lower reaches of the Yangtze River, and the Jinghang grant Canal-Huaihe River drainage. It was consistent with HFRS distribution map derived from national infectious disease reporting system. Correlation analysis indicated that HFRS incidence rates were significantly associated with NDVI (r = 0.417, P < 0.01). The HFRS risk areas was mapped according to NDVI of each surveillance site.

CONCLUSION: It is promising to apply GIS technology in predication of the distribution of HFRS by establishing this prediction model.}, } @article {pmid12820938, year = {2003}, author = {Zhou, XN and Hu, XS and Yang, GJ and Sun, NS and Wang, TP and Malone, J and McCarroll, J and Lin, DD and Hong, QB and Sun, LP and Zhang, ZY and Xu, DZ}, title = {[Establishment of minimum medical geographic information systems database in China].}, journal = {Zhonghua liu xing bing xue za zhi = Zhonghua liuxingbingxue zazhi}, volume = {24}, number = {4}, pages = {253-256}, pmid = {12820938}, issn = {0254-6450}, mesh = {Animals ; Anopheles/parasitology ; China/epidemiology ; *Databases, Factual ; Disease Reservoirs ; Disease Vectors ; Ecology ; *Geographic Information Systems ; Humans ; Malaria/epidemiology/prevention & control/transmission ; Plasmodium vivax ; Satellite Communications ; Schistosomiasis japonica/epidemiology/prevention & control/transmission ; Snails/parasitology ; }, abstract = {OBJECTIVE: To establish a minimum medical geographic information systems (GIS) database as a spatial decision supporting system (SDSS), and to use the database into public health practice in China.

METHODS: Spatial data collected from different sources were standardized as decimal degree format, including: (1) satellite images covering areas of China; (2) digital maps of China in vector files; (3) diseases database and relevant models.

RESULTS: Necessary satellite images for the database have been collected from NOAA AVHRR, Landsat TM, etc., including the normalized difference vegetation index (NDVI) images from AVHRR, earth surface temperature images from AVHRR, GTOPO30 DEM images from USGS and landuse images from USGS. The digital vector files for GIS analysis were collected including political (county, provinces, country) boundaries file, environmental (drainage, land cover, soil type) vector file, population data and climate data; Data on diseases mainly generated from survey or case reporting. Relevant models on transmission of Schistosoma japonicum and Plasmodium vivax, and models of Oncomelania hupensis and Anophores sinansis were developed, and the relevant environmental factors related to incidence of cancers were mapped, to test and verify those database.

CONCLUSION: The database unified the data from different sources for users. Minimum medical data included in the database could be used in the practice of public health. It is expected that this database be used in a wider range.}, } @article {pmid12812774, year = {2003}, author = {Lynch, JW and Khan, MZ and Altmann, J and Njahira, MN and Rubenstein, N}, title = {Concentrations of four fecal steroids in wild baboons: short-term storage conditions and consequences for data interpretation.}, journal = {General and comparative endocrinology}, volume = {132}, number = {2}, pages = {264-271}, doi = {10.1016/s0016-6480(03)00093-5}, pmid = {12812774}, issn = {0016-6480}, support = {1 R03 MH65294/MH/NIMH NIH HHS/United States ; }, mesh = {Androgens/analysis ; Animals ; Animals, Wild ; Data Interpretation, Statistical ; Estrogens/analysis ; Feces/*chemistry ; Female ; Freeze Drying ; Glucocorticoids/analysis ; Male ; Papio ; Pregnancy ; Progestins/analysis ; Radioimmunoassay ; Reproducibility of Results ; Specimen Handling/*methods ; Steroids/*metabolism ; }, abstract = {One source of both bias and "noise" in fecal steroid analysis is temporal change in steroid concentrations resulting from duration or conditions of fecal sample storage. However, no consensus currently exists regarding correct procedures or precautions necessary for fecal sample storage, and conditions vary widely within field endocrinology literature. This study considered the effects of short-term, weeks-long, storage conditions on quantifiable fecal testosterone (fT), glucocorticoids (fGC), estrogens (fE), and progestagen (fP) metabolite concentrations in wild baboons (Papio cynocephalus). Quadruplicate subsamples of fecal samples (n=29) collected at Amboseli National Park and its environs were subjected to four different storage conditions prior to lyophilization, in order to determine the effects of storage on subsequent steroid concentrations, as assessed by 125I radioimmunoassays. As expected, the best alternative to the "initial condition" of lyophilization at three days after collection was to freeze fecal samples at -20 degrees C for two weeks prior to lyophilization. This storage method resulted in no significant change from initial steroid concentrations for fE, fT, or fP, although fGC showed a slight but significant decline. Storage for two weeks in a charcoal refrigerator caused a mean increase in all four steroid concentrations. However, the results from this storage condition were robust in terms of practical questions asked of the data: fE and fP values still reflected pregnant versus non-pregnant states in baboon females; a fGC profile constructed by age class resembled that created from the samples from the initial condition, although slightly inflated across age classes; and there were only moderate changes in relative fT concentrations across adult males. Knowledge of the effects of storage upon each steroid analyzed within one's study is a necessary component in determining the optimal compromise for storage protocol in a particular research project.}, } @article {pmid12805987, year = {2002}, author = {D'heygere, TP and Goethals, PL and De Pauw, N}, title = {Optimisation of the monitoring strategy of macroinvertebrate communities in the river Dender, in relation to the EU Water Framework Directive.}, journal = {TheScientificWorldJournal}, volume = {2}, number = {}, pages = {607-617}, doi = {10.1100/tsw.2002.121}, pmid = {12805987}, issn = {1537-744X}, mesh = {Animals ; Belgium ; Decision Support Techniques ; Decision Trees ; Ecosystem ; Environmental Monitoring/legislation & jurisprudence/*methods/statistics & numerical data ; Europe ; Fishes/classification ; *Invertebrates/classification ; Models, Statistical ; Rivers/*chemistry ; Seasons ; Water Movements ; Water Pollution/prevention & control ; }, abstract = {The Dender basin in Flanders (Belgium) was used as a case study to implement the European Union (EU) Water Framework Directive. During the last 5 years, ample research on pollution loads and ecological water quality has been done on the Dender River. In addition to biological sampling of macroinvertebrates and fish, automated measurement stations were also used to investigate the spatial-temporal variability of the physical-chemical water quality. This research revealed that the pollution of the Dender River is highly variable. The high nutrient loads result in severe algae blooms during summer, leading to very complex diurnal processes. In this paper, the monitoring strategy for the assessment of the biological water quality in the Dender basin has been reviewed in relation to the EU Water Framework Directive. For this, seasonal macroinvertebrate data were collected and assessed. General trends and hidden structures in these data were analysed by means of classification trees, using different inputs (seasons, river types, and subbasins). Validation of the results was obtained by applying statistical methods. Analysis about the presence and abundance of the macroinvertebrates revealed that there is a distinct difference between the biological water quality in the Dender stem river and its tributaries. There are also seasonal differences between the macroinvertebrate communities when the Dender and its tributaries are examined separately. An optimised monitoring strategy is proposed based on these results and the EU Water Framework Directive. This includes two monitoring campaigns in summer and winter every 3 years. Furthermore, a cyclic monitoring scheme was developed to minimise sampling efforts.}, } @article {pmid12805982, year = {2002}, author = {Adriaenssens, V and Goethals, PL and De Pauw, N}, title = {Assessment of land-use impact on macroinvertebrate communities in the Zwalm River basin (Flanders, Belgium) using multivariate analysis and geographic information systems.}, journal = {TheScientificWorldJournal}, volume = {2}, number = {}, pages = {546-557}, doi = {10.1100/tsw.2002.111}, pmid = {12805982}, issn = {1537-744X}, mesh = {*Agriculture ; Animals ; Belgium ; *Ecosystem ; *Environment ; Environmental Monitoring/*methods ; Forecasting ; Fresh Water ; *Geographic Information Systems ; Invertebrates/*physiology ; Multivariate Analysis ; Water Supply ; }, abstract = {Relationships between land-use and river water quality assessed by means of biological and physical-chemical variables and habitat characteristics were analysed for the Zwalm River basin in Flanders (Belgium). The research focussed on three zones within this river basin, each characterized by different land uses, and consequently, different types of pollution, mainly of diffuse origin. Environmental data have been integrated within a Geographic Information System. Possible relationships between aquatic ecosystem and land-use variables were searched for by means of multivariate analysis.}, } @article {pmid12805939, year = {2002}, author = {Kadvany, J}, title = {Comparing Clean Water Act Section 316(b) policy options.}, journal = {TheScientificWorldJournal}, volume = {2 Suppl 1}, number = {}, pages = {106-138}, doi = {10.1100/tsw.2002.176}, pmid = {12805939}, issn = {1537-744X}, mesh = {Animals ; Conservation of Natural Resources/*legislation & jurisprudence/*methods ; Decision Support Techniques ; *Ecosystem ; Facility Design and Construction/legislation & jurisprudence/standards ; Fishes/*physiology ; Marine Biology ; Population Dynamics ; Program Evaluation ; Risk Assessment ; United States ; United States Environmental Protection Agency/legislation & jurisprudence ; Water Purification/instrumentation/*legislation & jurisprudence/*methods ; }, abstract = {This paper develops a comparative framework for policy proposals involving fish protection and Section 316(b) of the Clean Water Act (CWA). Section 316(b) addresses the impingement and entrainment of fish by cooling-water intake structures used principally by steam electric power plants. The framework is motivated by examining the role of adverse environmental impacts (AEIs) in the context of Section 316(b) decision making. AEI is mentioned in Section 316(b), but not defined. While various AEI options have been proposed over the years, none has been formalized through environmental regulations nor universally accepted. Using a multiple values approach from decision analysis, AEIs are characterized as measurement criteria for ecological impacts. Criteria for evaluating AEI options are identified, including modeling and assessment issues, the characterization of ecological value, regulatory implementation, and the treatment of uncertainty. Motivated by the difficulties in defining AEI once and for all, a framework is introduced to compare options for 316(b) decision making. Three simplified policy options are considered, each with a different implicit or explicit AEI approach: (1) a technology-driven rule based on a strict reading of the 316(b) regulatory text, and for which any impingement and entrainment count as AEI, (2) a complementary, open-ended risk-assessment process for estimating population effects with AEI characterized on a site-specific basis, and (3) an intermediate position based on proxy measures such as specially constructed definitions of littoral zone, sensitive habitat, or water body type. The first two proposals correspond roughly to responses provided, respectively, by the Riverkeeper environmental organization and the Utility Water Act Group to the U.S. Environmental Protection Agency (EPA)'s proposed 316(b) new facilities rule of August 2000; the third example is a simplified form of the EPA's proposed August 2000 new facilities rule itself. The simplified policy positions are compared using the three dimensions of the comparative policy framework: (1) the role of CWA philosophy or vision, such as the use of technology-forcing rules, (2) regulatory policy implementation, and (3) the role for scientific information and the knowledge base. Strengths and weaknesses of all three 316(b) policy approaches are identified. The U.S. EPA's final new facilities rule of November 2001 is briefly characterized using the comparative policy framework and used to further illustrate the approach.}, } @article {pmid12803378, year = {2003}, author = {Olowokure, B and Spencer, NJ and Hawker, JI and Blair, I and Smith, RL}, title = {Invasive Haemophilus influenzae disease: an ecological study of sociodemographic risk factors before and after the introduction of Hib conjugate vaccine.}, journal = {European journal of epidemiology}, volume = {18}, number = {4}, pages = {363-367}, pmid = {12803378}, issn = {0393-2990}, mesh = {Child, Preschool ; Geographic Information Systems ; Haemophilus Infections/*epidemiology/*etiology ; Haemophilus Vaccines/*administration & dosage/*immunology ; Haemophilus influenzae/*immunology ; Hepatitis B Vaccines/*administration & dosage/*immunology ; Humans ; Incidence ; Risk Factors ; Socioeconomic Factors ; Time Factors ; United Kingdom/epidemiology ; }, abstract = {This study examines the impact of H. influenzae type b (Hib) conjugate vaccine on sociodemographic risk factors for invasive H. influenzae disease in the 2 years before and immediately after the introduction of Hib conjugate vaccine. An ecological study design was used and cases were identified using active surveillance employing several surveillance systems. The study population comprised all children aged < 5 years resident in the West Midlands, an English health region, with laboratory confirmed invasive disease 2 years before (1990-1992) and 2 years after (1992-1994) the introduction of Hib conjugate vaccine. Selected sociodemographic variables derived from the UK census were obtained for all census enumeration districts in the region. Each variable was then ranked and divided into six categories. Linear associations between disease rates and sociodemographic variables were examined. Overall, there was a significant reduction in the incidence of invasive H. influenzae disease. In the pre-conjugate vaccine era there were trends of decreasing disease incidence with increasing child population density (p = 0.012) and total population density (p = 0.0023). In the post-conjugate vaccine period, total population density (p = 0.0275) remained significant and a trend of increasing disease incidence with increasing population mobility (p = 0.0012) was seen. Although Hib conjugate vaccine has resulted in a dramatic reduction in disease incidence changes in sociodemographic risk factors were identified in the post-conjugate vaccine period, particularly population mobility. Our results may have implications for current and future vaccine strategies.}, } @article {pmid12802251, year = {2002}, author = {Schatz, P and Browndyke, J}, title = {Applications of computer-based neuropsychological assessment.}, journal = {The Journal of head trauma rehabilitation}, volume = {17}, number = {5}, pages = {395-410}, doi = {10.1097/00001199-200210000-00003}, pmid = {12802251}, issn = {0885-9701}, mesh = {Brain Injuries/*diagnosis ; Diagnosis, Computer-Assisted/*trends ; Humans ; *Neuropsychological Tests ; Neuropsychology/*trends ; }, abstract = {OBJECTIVES: To present current applications of computer-based neuropsychological assessment, including the assessment of sports-related concussion, symptom validity testing, and the remote administration of tests through the Internet.

PROBLEM AREAS: If computer-based assessment benefits are to become popularized, a few issues will need to be addressed: the development of psychometric data based on comparisons with long-standing empirically sound test measures; additional validation of measures by parties not involved in their commercial development; increased focus on ecological validity; exploration of the usefulness of remote data storage and automated posting to databases; and improved documentation of specific computer hardware and software used in experimental methods.

CONCLUSIONS: Beyond ease of administration and data collection, computer-based assessment offers benefits over paper-and-pencil measures in the form of millisecond timing accuracy, reliable and randomized presentation of stimuli over multiple trials and repeat administrations, and unobtrusive measurement of cognitive skills and response times during all aspects of the assessment process.}, } @article {pmid12801879, year = {2003}, author = {Piel, WH and Sanderson, MJ and Donoghue, MJ}, title = {The small-world dynamics of tree networks and data mining in phyloinformatics.}, journal = {Bioinformatics (Oxford, England)}, volume = {19}, number = {9}, pages = {1162-1168}, doi = {10.1093/bioinformatics/btg131}, pmid = {12801879}, issn = {1367-4803}, mesh = {*Algorithms ; Biological Evolution ; *Database Management Systems ; *Databases, Genetic ; Decision Trees ; *Evolution, Molecular ; Gene Expression Profiling/*methods ; *Genetic Variation ; Information Storage and Retrieval/*methods ; *Phylogeny ; }, abstract = {MOTIVATION: A noble and ultimate objective of phyloinformatic research is to assemble, synthesize, and explore the evolutionary history of life on earth. Data mining methods for performing these tasks are not yet well developed, but one avenue of research suggests that network connectivity dynamics will play an important role in future methods. Analysis of disordered networks, such as small-world networks, has applications as diverse as disease propagation, collaborative networks, and power grids. Here we apply similar analyses to networks of phylogenetic trees in order to understand how synthetic information can emerge from a database of phylogenies.

RESULTS: Analyses of tree network connectivity in TreeBASE show that a collection of phylogenetic trees behaves as a small-world network-while on the one hand the trees are clustered, like a non-random lattice, on the other hand they have short characteristic path lengths, like a random graph. Tree connectivities follow a dual-scale power-law distribution (first power-law exponent approximately 1.87; second approximately 4.82). This unusual pattern is due, in part, to the presence of alternative tree topologies that enter the database with each published study. As expected, small collections of trees decrease connectivity as new trees are added, while large collections of trees increase connectivity. However, the inflection point is surprisingly low: after about 600 trees the network suddenly jumps to a higher level of coherence. More stringent definitions of 'neighbour' greatly delay the threshold whence a database achieves sufficient maturity for a coherent network to emerge. However, more stringent definitions of 'neighbour' would also likely show improved focus in data mining.

AVAILABILITY: http://treebase.org}, } @article {pmid12799357, year = {2003}, author = {Schmid, KJ and Sorensen, TR and Stracke, R and Torjek, O and Altmann, T and Mitchell-Olds, T and Weisshaar, B}, title = {Large-scale identification and analysis of genome-wide single-nucleotide polymorphisms for mapping in Arabidopsis thaliana.}, journal = {Genome research}, volume = {13}, number = {6A}, pages = {1250-1257}, pmid = {12799357}, issn = {1088-9051}, mesh = {Arabidopsis/*genetics ; Computational Biology/methods ; DNA, Plant/genetics ; Databases, Genetic ; Databases, Nucleic Acid ; Genetic Variation/genetics ; *Genome, Plant ; Molecular Sequence Data ; Polymorphism, Single Nucleotide/*genetics ; Sequence Analysis, DNA/methods ; Sequence Tagged Sites ; }, abstract = {Genetic markers such as single nucleotide polymorphisms (SNPs) are essential tools for positional cloning, association, or quantitative trait locus mapping and the determination of genetic relationships between individuals. We identified and characterized a genome-wide set of SNP markers by generating 10,706 expressed sequence tags (ESTs) from cDNA libraries derived from 6 different accessions, and by analysis of 606 sequence tagged sites (STS) from up to 12 accessions of the model flowering plant Arabidopsis thaliana. The cDNA libraries for EST sequencing were made from individuals that were stressed by various means to enrich for transcripts from genes expressed under such conditions. SNPs discovered in these sequences may be useful markers for mapping genes involved in interactions with the biotic and abiotic environment. The STS loci are distributed randomly over the genome. By comparison with the Col-0 genome sequence, we identified a total of 8051 SNPs and 637 insertion/deletion polymorphisms (InDel). Analysis of STS-derived SNPs shows that most SNPs are rare, but that it is possible to identify intermediate frequency framework markers that can be used for genetic mapping in many different combinations of accessions. A substantial proportion of SNPs located in ORFs caused a change of the encoded amino acid. A comparison of the density of our SNP markers among accessions in both the EST and STS datasets, revealed that Cvi-0 is the most divergent accession from Col-0 among the 12 accessions studied. All of these markers are freely available via the internet.}, } @article {pmid12793683, year = {2003}, author = {Earle, JR}, title = {The Three Rivers Project--water quality monitoring and management systems in the Boyne, Liffey and Suir catchments in Ireland.}, journal = {Water science and technology : a journal of the International Association on Water Pollution Research}, volume = {47}, number = {7-8}, pages = {217-225}, pmid = {12793683}, issn = {0273-1223}, mesh = {Agriculture ; *Conservation of Natural Resources ; *Environment ; Environmental Monitoring ; Eutrophication ; *Geographic Information Systems ; Industrial Waste ; Ireland ; Phosphorus/isolation & purification ; Seasons ; Water Pollution/*prevention & control ; }, abstract = {The "Three Rivers Project" is a government initiative and one of a series of catchment based water quality monitoring and management systems being developed throughout Ireland since 1997. The establishment of these multi-sectoral, basin-wide and community based systems is a response to historically perceived disjointed, legalistic and non-participative approaches to water resource management and purports to transcend the restrictions of traditional local authority administrative boundaries. The new management model embodies the concepts and objectives contained in the European Union (EU) Water Framework Directive (WFD) enacted in December 2000. Ireland, in common with many EU countries, has failed to halt decades of increasing levels of eutrophication of surface waters due principally to phosphorus loading. The "Three Rivers Project" is promoting the benefits of an integrated and cooperative approach to the management of three important river systems in Ireland, namely, the Boyne, Liffey and Suir. The project objective is to protect and improve water quality to conform with "good ecological status". The implications of the Project findings for agricultural, municipal and industrial policy are grave and one of the greatest challenges now is to organise and fund Irish River Basin Management Systems as envisaged by the WFD to continue and build on the work which the "Three Rivers Project" has undertaken.}, } @article {pmid12791877, year = {2003}, author = {Jones, N and Bohnsack, JF and Takahashi, S and Oliver, KA and Chan, MS and Kunst, F and Glaser, P and Rusniok, C and Crook, DW and Harding, RM and Bisharat, N and Spratt, BG}, title = {Multilocus sequence typing system for group B streptococcus.}, journal = {Journal of clinical microbiology}, volume = {41}, number = {6}, pages = {2530-2536}, pmid = {12791877}, issn = {0095-1137}, mesh = {Adult ; *Alleles ; Bacterial Proteins/*genetics ; *Bacterial Typing Techniques ; Base Sequence ; Computational Biology ; Humans ; Infant, Newborn ; Molecular Sequence Data ; *Sequence Analysis, DNA ; Streptococcal Infections/microbiology ; Streptococcus agalactiae/*classification/genetics ; }, abstract = {A multilocus sequence typing (MLST) system was developed for group B streptococcus (GBS). The system was used to characterize a collection (n = 152) of globally and ecologically diverse human strains of GBS that included representatives of capsular serotypes Ia, Ib, II, III, V, VI, and VIII. Fragments (459 to 519 bp) of seven housekeeping genes were amplified by PCR for each strain and sequenced. The combination of alleles at the seven loci provided an allelic profile or sequence type (ST) for each strain. A subset of the strains were characterized by restriction digest patterning, and these results were highly congruent with those obtained with MLST. There were 29 STs, but 66% of isolates were assigned to four major STs. ST-1 and ST-19 were significantly associated with asymptomatic carriage, whereas ST-23 included both carried and invasive strains. All 44 isolates of ST-17 were serotype III clones, and this ST appeared to define a homogeneous clone that was strongly associated with neonatal invasive infections. The finding that isolates with different capsular serotypes had the same ST suggests that recombination occurs at the capsular locus. A web site for GBS MLST was set up and can be accessed at http://sagalactiae.mlst.net. The GBS MLST system offers investigators a valuable typing tool that will promote further investigation of the population biology of this organism.}, } @article {pmid12785598, year = {2003}, author = {Roelofs, W and Huijbregts, MA and Jager, T and Ragas, AM}, title = {Prediction of ecological no-effect concentrations for initial risk assessment: combining substance-specific data and database information.}, journal = {Environmental toxicology and chemistry}, volume = {22}, number = {6}, pages = {1387-1393}, doi = {10.1897/1551-5028(2003)022<1387:poenec>2.0.co;2}, pmid = {12785598}, issn = {0730-7268}, mesh = {Animals ; Bayes Theorem ; Daphnia/drug effects ; Databases, Factual ; Ecosystem ; Eukaryota/drug effects ; Fishes ; Forecasting ; *Models, Statistical ; No-Observed-Adverse-Effect Level ; Probability ; Risk Assessment ; Toxicity Tests, Acute ; Toxicity Tests, Chronic ; Water Pollutants/analysis/*toxicity ; }, abstract = {A new method is proposed to derive predicted no-effect concentrations (PNECs) for initial risk assessments for aquatic ecosystems from a limited set of single-species toxicity data. The method includes three steps. First, acute toxicity data are divided by an acute-to-chronic assessment factor to obtain chronic toxicity data. Subsequently, chronic toxicity data are averaged to obtain an average hazardous concentration (HC50). Finally, the HC50 is divided by an interspecies assessment factor to obtain a PNEC. Both assessment factors are derived as probability distributions from an extensive ecotoxicological database. The interspecies assessment factor is combined with substance-specific toxicity data using Bayesian statistics. The proposed method optimizes the use of the available ecotoxicological information and it produces an uncertainty estimate of the PNEC. Sample calculations indicate that the proposed method may provide a good alternative for currently applied methods for initial risk assessment, particularly if few toxicity data are available.}, } @article {pmid12785593, year = {2003}, author = {Barranguet, C and van den Ende, FP and Rutgers, M and Breure, AM and Greijdanus, M and Sinke, JJ and Admiraal, W}, title = {Copper-induced modifications of the trophic relations in riverine algal-bacterial biofilms.}, journal = {Environmental toxicology and chemistry}, volume = {22}, number = {6}, pages = {1340-1349}, pmid = {12785593}, issn = {0730-7268}, mesh = {Bacteria/drug effects/*growth & development ; Biofilms/*drug effects ; Biomass ; Colony Count, Microbial ; Copper/analysis/metabolism/*toxicity ; Data Interpretation, Statistical ; Eukaryota/drug effects/*growth & development/physiology ; Fluorescence ; Fresh Water/*microbiology ; Microbiological Techniques/methods ; Photosynthesis/drug effects/physiology ; Pigments, Biological/analysis/chemistry ; Water Microbiology ; }, abstract = {The effects of copper (Cu) on photosynthetic riverine biofilms were studied in artificial stream channels. Direct effects on the composition and functioning of the biofilms were investigated using plant pigments, community-level physiological profiles (CLPP), and pulse-amplitude-modulated (PAM) fluorescence. Copper caused a significant reduction of microalgal biomass and induced a shift in the population from diatoms to cyanobacteria. However, a decrease in biomass indicated that the replacement of species was not totally effective to counteract the toxic effects of Cu. A direct effect of Cu could also be shown in the bacterial community, and, furthermore, changes in the CLPP could be related to the Cu treatment. Copper-exposed biofilms lost the capacity to use between 11 and 15% of the substrates, but many of the remaining capacities became more robust, indicating an increased Cu tolerance due to the exposure. The change in the biofilm microbial composition points to the indirect effects of Cu on biofilms due to the close interdependence between biofilm autotrophic and heterotrophic compartments. Grazing by snails, which appeared to be an important factor structuring biofilms without any Cu addition, had a very minor effect on Cu-exposed biofilms. Although grazing changed the bacterial composition, its effects were not detected either on the algal community or on the biofilm community tolerance to Cu.}, } @article {pmid12785590, year = {2003}, author = {Hanson, ML and Sanderson, H and Solomon, KR}, title = {Variation, replication, and power analysis of Myriophyllum spp. microcosm toxicity data.}, journal = {Environmental toxicology and chemistry}, volume = {22}, number = {6}, pages = {1318-1329}, pmid = {12785590}, issn = {0730-7268}, mesh = {Acetic Acid/chemistry/*toxicity ; Analysis of Variance ; Databases, Factual ; Magnoliopsida/*drug effects/*growth & development ; Pesticides/*toxicity ; Reproducibility of Results ; Toxicity Tests/*methods ; Water Pollutants, Chemical/toxicity ; }, abstract = {Myriophyllum spp. have been proposed as a new standard laboratory aquatic macrophyte test species for the registration of pesticides. The main objectives of this investigation were to determine the power of Myriophyllum sibiricum and Myriophyllum spicatum toxicity data derived from an outdoor microcosm bioassay, to evaluate the variation of 10 different aquatic plant endpoints and to calculate the minimum detectable difference for these endpoints, to determine the replication required to detect ecologically significant changes from control for these endpoints, and to make recommendations for future field studies with Myriophyllum spp. Control data from four different studies that characterized haloacetic acid toxicity with Myriophyllum spp. for durations of three to six weeks during the summer of 1999 with five treatment levels (n = 3), including control, were examined. Endpoint coefficient of variation ranged, on average, from 6 to 28%. Node number and plant length endpoints were consistently the most statistically powerful for both plant species. It was possible to detect approximately 30% change from control in both endpoints with high statistical power (beta = 0.2, alpha = 0.05, n = 3). The range of minimum detectable differences was 40 to 60% for the other endpoints. Replication to detect a > or = 25% change from control would require an n of 2 to 21, depending on the endpoint. Myriophyllum sibiricum had slightly lower coefficients of variation and thus required fewer replicates than M. spicatum to be statistically significantly different from control values. Variation within microcosm studies was not significantly different from that of controlled laboratory studies, implying that most of the variation observed in the field is inherent in the plants. Based on statistical sensitivity, ecological relevance, and toxicological sensitivity, we recommend using plant length and root endpoints as indicators of toxicity under field conditions.}, } @article {pmid12781759, year = {2003}, author = {Pavlikakis, GE and Tsihrintzis, VA}, title = {A quantitative method for accounting human opinion, preferences and perceptions in ecosystem management.}, journal = {Journal of environmental management}, volume = {68}, number = {2}, pages = {193-205}, doi = {10.1016/s0301-4797(03)00067-7}, pmid = {12781759}, issn = {0301-4797}, mesh = {Attitude ; *Conservation of Natural Resources ; Decision Making ; *Decision Support Techniques ; *Ecosystem ; *Environment ; *Environment Design ; Humans ; Perception ; *Public Opinion ; }, abstract = {Ecosystem management (EM) is a holistic approach, in which public participation in decision-making, and incorporation of human preferences, needs and perceptions in management plans is a main element. The decision-making from human opinion method (DeMHO), presented here, can be used in EM in selecting the more suitable and socially acceptable management plan, in order to protect or restore an ecosystem. The method focuses on the quantification of the human opinion, preferences and perceptions, which are investigated after research on the local population of the ecosystem. The results of this research are the inputs of the method; multi-criteria decision-making procedures, such as the analytic hierarchy process (AHP), the expected utility method (EUM) and compromise programming (CP) are used to assign the appropriate weights and rank according to their importance the interest groups, the issues to be studied, and the alternative management plans. The alternatives are also evaluated by assessing their sustainable character. The paper presents DeMHO and its application in the National Park of Eastern Macedonia and Thrace in Greece, after a research through a questionnaire on the local population.}, } @article {pmid12777519, year = {2003}, author = {Sanderson, MJ and Driskell, AC and Ree, RH and Eulenstein, O and Langley, S}, title = {Obtaining maximal concatenated phylogenetic data sets from large sequence databases.}, journal = {Molecular biology and evolution}, volume = {20}, number = {7}, pages = {1036-1042}, doi = {10.1093/molbev/msg115}, pmid = {12777519}, issn = {0737-4038}, mesh = {*Algorithms ; *Databases, Factual ; Genes, Plant/*genetics ; *Genome, Plant ; Genomics/*methods ; Models, Genetic ; *Phylogeny ; }, abstract = {To improve the accuracy of tree reconstruction, phylogeneticists are extracting increasingly large multigene data sets from sequence databases. Determining whether a database contains at least k genes sampled from at least m species is an NP-complete problem. However, the skewed distribution of sequences in these databases permits all such data sets to be obtained in reasonable computing times even for large numbers of sequences. We developed an exact algorithm for obtaining the largest multigene data sets from a collection of sequences. The algorithm was then tested on a set of 100,000 protein sequences of green plants and used to identify the largest multigene ortholog data sets having at least 3 genes and 6 species. The distribution of sizes of these data sets forms a hollow curve, and the largest are surprisingly small, ranging from 62 genes by 6 species, to 3 genes by 65 species, with more symmetrical data sets of around 15 taxa by 15 genes. These upper bounds to sequence concatenation have important implications for building the tree of life from large sequence databases.}, } @article {pmid12774086, year = {2003}, author = {Knight, J and Abbott, A}, title = {Biologists moot daunting plan to track viruses.}, journal = {Nature}, volume = {423}, number = {6939}, pages = {471}, doi = {10.1038/423471a}, pmid = {12774086}, issn = {0028-0836}, mesh = {Blood/virology ; Communicable Diseases, Emerging/epidemiology/virology ; Databases, Genetic/*trends ; *Genome, Viral ; Genomics/*methods/trends ; Humans ; Marine Biology/methods ; Pacific Ocean ; RNA Viruses/genetics/isolation & purification ; United States ; Virus Diseases/epidemiology/*virology ; Viruses/*genetics/*isolation & purification ; }, } @article {pmid12765265, year = {2003}, author = {Guan, YN and Guo, S and Xue, Y and Li, R and Yang, QK}, title = {Landscape dynamitic change in Mu Us Desert derived from Landsat TM data.}, journal = {Journal of environmental sciences (China)}, volume = {15}, number = {2}, pages = {222-226}, pmid = {12765265}, issn = {1001-0742}, mesh = {China ; *Desert Climate ; *Environment ; Environmental Monitoring/*methods ; *Geographic Information Systems ; Humans ; *Satellite Communications ; }, abstract = {Landscape ecology emphasizes large areas and ecological effects of the spatial patterning of ecosystem. Recent developments in landscape ecology have emphasized the important relationship between spatial patterns and many ecological processes. Quantitative methods in landscape ecology link spatial patterns and ecological processes at broad spatial and temporal scales. In turn the increased attention on temporal change of ecosystem has highlighted the need for quantitative methods that can analyze patterns. This research applies quantitative methods--change detection to assess the ecosystem temporal change in the arid and semiarid area. Remote sensing offers the temporal change of ecosystem on landscape characteristics.}, } @article {pmid12765263, year = {2003}, author = {Zhao, B and Nakagoshi, N and Chen, JK and Kong, LY}, title = {The impact of urban planning on land use and land cover in Pudong of Shanghai, China.}, journal = {Journal of environmental sciences (China)}, volume = {15}, number = {2}, pages = {205-214}, pmid = {12765263}, issn = {1001-0742}, mesh = {China ; *City Planning ; *Conservation of Natural Resources ; *Ecosystem ; Environmental Monitoring/methods ; Geographic Information Systems ; Humans ; *Plants ; Satellite Communications ; }, abstract = {Functional zones in cities constitute the most conspicuous components of newly developed urban area, and have been a hot spot for domestic and foreign investors in China, which not only show the expanse of urban space accompanied by the shifts both in landscape (from rural to urban) and land use (from less extensive to extensive), but also display the transformation of regional ecological functions. By using the theories and methods of landscape ecology, the structure of landscape and landscape ecological planning can be analyzed and evaluated for studying the urban functional zones' layout. In 1990, the Central Government of China declared to develop and open up Pudong New Area so as to promote economic development in Shanghai. Benefited from the advantages of Shanghai's location and economy, the government of Pudong New Area has successively built up 7 different functional zones over the past decade according to their functions and strategic goals. Based on the multi-spectral satellite imageries taken in 1990, 1997 and 2000, a landscape ecology analysis was carried out for Pudong New Area of Shanghai, supported by GIS technology. Green space (including croplands) and built-up area are the major factors considered in developing urban landscape. This paper was mainly concerned with the different spatial patterns and dynamic of green space, built-up areas and new buildings in different functional zones, influenced by different functional layouts and development strategies. The rapid urbanization in Pudong New Area resulted in a more homogeneous landscape. Agricultural landscape and suburban landscape were gradually replaced by urban landscape as the degree of urbanization increased. As consequence of urbanization in Pudong, not only built-up patches, but also newly-built patches and green patches merged into one large patch, which should be attributed to the construction policy of extensive green space as the urban development process in Pudong New Area. The shape of green area of 7 functional zones became more and more regular because of the horticultural needs in Shanghai urban planning. Some suggestions were finally made for the study of future urban planning and layout.}, } @article {pmid12765262, year = {2003}, author = {Hong, SK and Song, IJ and Kim, HO and Lee, EK}, title = {Landscape pattern and its effect on ecosystem functions in Seoul Metropolitan area: urban ecology on distribution of the naturalized plant species.}, journal = {Journal of environmental sciences (China)}, volume = {15}, number = {2}, pages = {199-204}, pmid = {12765262}, issn = {1001-0742}, mesh = {*City Planning ; *Conservation of Natural Resources ; *Ecosystem ; Environmental Monitoring/methods ; Geographic Information Systems ; Humans ; Korea ; *Plants ; Satellite Communications ; }, abstract = {During land transformation process in the human history, naturalized plants were introduced to several land use patterns by the different ways of plant itself. Including some naturalized plants that had been contribute to land restoration, many naturalized plants have been invaded to original habitat or landscape for native plants. Once the plants were colonized, they extend their area and population size. Urban developed areas often give an important role of source habitat for naturalized plants and expanding their population size. In recent, this situation is appearing as one of environmental problem about the urban landscape management controlling the naturalized plants that invaded in the developed area and conserving the native vegetation. This paper is focusing on relationships between distribution of habitat of naturalized plants and landscape patch in urban areas in Seoul. Gangdong-Gu, one of the administrative areas in Seoul was selected for this study. We examined the recent land use change using LANDSAT TM data and spreading of the representative naturalized plants (Robinia pseudocacia and Eupatorium rugosum) by Seoul Biotope Mapping Project and field survey in 1999. As a result, these two species were often occurred in the same habitat and distributed in forest edge disturbed by man. Their distribution patterns were related to landscape indices (patch size and shape) in the forest edge.}, } @article {pmid12765261, year = {2003}, author = {Ma, MG and Wang, XM and Cheng, GD}, title = {Study on the oasis corridor landscape in the arid regions based on RS and GIS methods--application of Jinta Oasis, China.}, journal = {Journal of environmental sciences (China)}, volume = {15}, number = {2}, pages = {193-198}, pmid = {12765261}, issn = {1001-0742}, mesh = {China ; *Desert Climate ; *Ecosystem ; Environmental Monitoring/*methods ; *Geographic Information Systems ; Geography ; Humans ; Satellite Communications ; }, abstract = {The study on the oasis corridor landsape is a new hotspot in the ecological environment research in the arid regions. In oasis, main corridor landscape types include river, ditch, shelterbelt and road. This paper introduces the basic ecological effects of the corridor landscape on the transporting mass and energy and obstructing desert landscape expansion and incursion. Using Geographic Information System (GIS), we have researched the corridor distribution and its spatial relationship with other landscape types in the Jinta Oasis. Based on the dynamically monitoring on the landscape pattern change of the Jinta Oasis during the latter 10 years by using Remote Sensing (RS) and GIS, the driving functions of the corridors on this change have been analyzed in detail. The analysis results showed that all kinds of corridors' characteristics can be quantified by the indexes such as length and width, ratio of perimeter and area, density and non-heterogeneity. The total corridor length of Jinta Oasis is 1838.5 km and its density is 2.1 km/km2. The corridor density of the irrigation land, forest and resident area is maximal, which shows that affection degree of the oasis corridors on them is the most. The improvement of the corridors quality is one of the important driving factors on the irrigation land and so on. The organic combination of the RS and GIS technologies and landscape research methods would be an effective means for the corridor landscape research on arid region oasis.}, } @article {pmid12762436, year = {2003}, author = {Wakefield, J}, title = {Sensitivity analyses for ecological regression.}, journal = {Biometrics}, volume = {59}, number = {1}, pages = {9-17}, doi = {10.1111/1541-0420.00002}, pmid = {12762436}, issn = {0006-341X}, mesh = {Bias ; Confounding Factors, Epidemiologic ; Data Collection ; Data Interpretation, Statistical ; Ecology/*methods ; Environmental Exposure ; *Epidemiologic Methods ; Humans ; Magnesium/administration & dosage ; Myocardial Infarction/mortality ; *Regression Analysis ; Risk ; Sensitivity and Specificity ; Small-Area Analysis ; }, abstract = {In many ecological regression studies investigating associations between environmental exposures and health outcomes, the observed relative risks are in the range 1.0-2.0. The interpretation of such small relative risks is difficult due to a variety of biases--some of which are unique to ecological data, since they arise from within-area variability in exposures/confounders. The potential for residual spatial dependence, due to unmeasured confounders and/or data anomalies with spatial structure, must also be considered, though it often will be of secondary importance when compared to the likely effects of unmeasured confounding and within-area variability in exposures/confounders. Methods for addressing sensitivity to these issues are described, along with an approach for assessing the implications of spatial dependence. An ecological study of the association between myocardial infarction and magnesium is critically reevaluated to determine potential sources of bias. It is argued that the sophistication of the statistical analysis should not outweigh the quality of the data, and that finessing models for spatial dependence will often not be merited in the context of ecological regression.}, } @article {pmid12754926, year = {2003}, author = {Vanco, J}, title = {[The Beilstein CrossFire Information System and its use in pharmaceutical chemistry].}, journal = {Ceska a Slovenska farmacie : casopis Ceske farmaceuticke spolecnosti a Slovenske farmaceuticke spolecnosti}, volume = {52}, number = {2}, pages = {68-72}, pmid = {12754926}, issn = {1210-7816}, mesh = {Chemistry, Organic/history ; *Chemistry, Pharmaceutical/history ; *Databases, Factual/history ; History, 19th Century ; History, 20th Century ; *Information Systems ; Slovakia ; }, abstract = {The Beilstein CrossFire database system is one of the most popular, most extensive, and most accomplished systems presenting information about chemical substances, including drugs, and covering the basic identification, physico-chemical, ecological, and pharmacological data. The present article offers an overview of historical evaluation of the Beilstein CrossFire database system, beginning from its founder Prof. Friedrich Conrad Beilstein till the most recent prospects about the connection of classical data with full-text databases. The article also offers a review of the development of electronic information systems in the Slovak Republic, a definition of basic functionality of the Beilstein CrossFire database system, and an example of targeted selection of active substances structurally similar to novel COX-2 inhibitors having an approved anti-inflammatory activity.}, } @article {pmid12754811, year = {2003}, author = {Rasina, LN and Orekhova, NA}, title = {[Parameters of peroxide oxidation of lipids and the system of its regulation in the tissues of Ellobius talpinus Pall, living on the territory of the East Urals Radioactive Trace].}, journal = {Radiatsionnaia biologiia, radioecologiia}, volume = {43}, number = {2}, pages = {206-209}, pmid = {12754811}, issn = {0869-8031}, mesh = {Animals ; Arvicolinae/*metabolism ; Data Interpretation, Statistical ; Female ; Homeostasis ; *Lipid Peroxidation ; Liver/metabolism ; Male ; Myocardium/metabolism ; *Radiation Tolerance ; *Radioactive Fallout ; *Radioactive Hazard Release ; Russia ; Spleen/metabolism ; *Strontium Radioisotopes/analysis ; }, abstract = {The peroxide oxidation of lipids and the systems of its regulation was tested in Ellobius talpinus Pall, living on the territory of the East Urals Radioactive Trace with the 90Sr contamination density of 1000 Ci/km2. The degree of sensitivity of the examined tissues and organs was revealed, the most considerable parameters were defined for marking radiosensitivity of the taken species, as well as the complex of parameters, allowing classifying an animal as an inhabitant of the clean or the contaminated territory. The found changes are considered as compensatory mechanisms for forming of nonspecific resistance.}, } @article {pmid12738293, year = {2003}, author = {Dilly, O and Blume, HP and Sehy, U and Jimenez, M and Munch, JC}, title = {Variation of stabilised, microbial and biologically active carbon and nitrogen in soil under contrasting land use and agricultural management practices.}, journal = {Chemosphere}, volume = {52}, number = {3}, pages = {557-569}, doi = {10.1016/S0045-6535(03)00237-6}, pmid = {12738293}, issn = {0045-6535}, mesh = {Agriculture/methods ; Biomass ; Carbon/*chemistry/metabolism ; Climate ; Data Interpretation, Statistical ; *Ecosystem ; Minerals/chemistry/metabolism ; Nitrogen/*chemistry/metabolism ; Soil/*analysis ; Soil Microbiology ; Trees ; }, abstract = {Land use and agricultural practices modify both the amounts and properties of C and N in soil organic matter. In order to evaluate land use and management-dependent modifications of stable and labile C and N soil pools, (i). organic C and total N content, (ii). microbial (C(mic)) and N (N(mic)) content and (iii). C and N mineralisation rates, termed biologically active C and N, were estimated in arable, grassland and forest soils from northern and southern Germany. The C/N-ratios were calculated for the three levels (i)-(iii) and linked to the eco-physiological quotients of biotic-fixed C and N (C(mic)/C(org), N(mic)/N(t)) and biomass-specific C and N mineralisation rate (qCO(2), qN(min)). Correlations could mainly be determined between organic C, total N, C(mic), N(mic) and C mineralisation for the broader data set of the land use systems. Generally, the mineralisation activity rate at 22 degrees C was highly variable and ranged between 0.11 and 17.67 microg CO(2)-C g(-1) soil h(-1) and -0.12 and 3.81 microg (deltaNH(4)(+)+deltaNO(3)(-))-N g(-1) soil h(-1). Negative N data may be derived from both N immobilisation and N volatilisation during the experiments. The ratio between C and N mineralisation rate differed significantly between the soils ranging from 5 to 37, and was not correlated to the soil C/N ratio and C(mic)/N(mic) ratio. The C/N ratio in the 'biologically active' pool was significantly smaller in soils under conventional farming than those under organic farming systems. In a beech forest, it increased from the L, Of to the Ah horizon. The biologically active C and N pools refer to the current microbial eco-physiology and are related to the need for being C and N use efficient as indicated by metabolic qCO(2) and qN(min) quotients.}, } @article {pmid12726695, year = {2003}, author = {Sheppard, SC}, title = {An index of radioecology, what has been important?.}, journal = {Journal of environmental radioactivity}, volume = {68}, number = {1}, pages = {1-10}, doi = {10.1016/S0265-931X(03)00067-5}, pmid = {12726695}, issn = {0265-931X}, mesh = {Animals ; Databases, Factual ; *Ecology ; Ecosystem ; Publishing/*trends ; Radioactive Pollutants/adverse effects ; *Radioactivity ; Radiobiology/*trends ; Radioisotopes/adverse effects ; }, abstract = {The Journal of Environmental Radioactivity (JER) has been published for the last 20 years, an important time frame for the discipline of radioecology. Certainly the study of radioecology accelerated following the Chernobyl incident. As the discipline moves forward, there will be less emphasis on that incident, and scientists will find a new focus. Issues related to waste management and decommissioning may come to the fore. There is also a large effort world-wide to deal more quantitatively with the estimation of dose and consequences to non-human biota. All researchers in radioecology will have opinions on what topics are important now and will be important in the future. Indeed, Policy Board members and Associate Editors of JER have provided a number of Editorials in the Millennium Editorial Series with their perspectives. This paper explores the trends among papers published in JER since 1995, using the ScienceDirect on-line search capability to objectively categorize the papers and quantify the relative numbers of contributions. Obviously, this is somewhat imperfect, but it does provide an index of what has been important in radioecology, and provides some quantification to recent statements about the future of radioecology.}, } @article {pmid12710927, year = {2003}, author = {Bailey, N and Clements, T and Lee, JT and Thompson, S}, title = {Modelling soil series data to facilitate targeted habitat restoration: a polytomous logistic regression approach.}, journal = {Journal of environmental management}, volume = {67}, number = {4}, pages = {395-407}, doi = {10.1016/s0301-4797(02)00227-x}, pmid = {12710927}, issn = {0301-4797}, mesh = {Climate ; *Conservation of Natural Resources ; Data Collection ; Decision Making ; Ecosystem ; Environmental Monitoring ; *Geographic Information Systems ; Geography ; *Models, Theoretical ; *Soil ; }, abstract = {Habitat restoration at a landscape scale is becoming increasingly important in environmental management. In this context, geographical information systems are well suited as they can store and integrate many of the abiotic and biotic criteria used to assess the ecological worth of a site. However, this capacity can be limited by the availability or suitability of spatial data sets. A classic example of the latter case is the National Soil Map of England and Wales, which groups soils of a varied nature into associations. Consequently the national soil map has proved to be a poor predictor of habitat suitability. Using polytomous logistic regression we put forward a method for separating soil associations into their constituent soils within the Chilterns Natural Area. This approach used soil association, aspect, slope and relative height as variables for this analysis. Whilst the model's performance is likely to have been limited by the accuracy of the soil association data set, a predictive accuracy of between 47 and 65% is sufficient to facilitate better targeting of habitat restoration when combined with other abiotic factors such as climate and topography.}, } @article {pmid12695327, year = {2003}, author = {Hampson, S and McLysaght, A and Gaut, B and Baldi, P}, title = {LineUp: statistical detection of chromosomal homology with application to plant comparative genomics.}, journal = {Genome research}, volume = {13}, number = {5}, pages = {999-1010}, pmid = {12695327}, issn = {1088-9051}, mesh = {Chromosome Mapping/methods/statistics & numerical data ; Chromosomes, Plant/*genetics ; Computational Biology/methods/statistics & numerical data ; DNA, Plant/genetics ; Genomics/*methods ; *Models, Statistical ; *Sequence Homology, Nucleic Acid ; Zea mays/genetics ; }, abstract = {The identification of homologous regions between chromosomes forms the basis for studies of genome organization, comparative genomics, and evolutionary genomics. Identification of these regions can be based on either synteny or colinearity, but there are few methods to test statistically for significant evidence of homology. In the present study, we improve a preexisting method that used colinearity as the basis for statistical tests. Improvements include computational efficiency and a relaxation of the colinearity assumption. Two algorithms perform the method: FullPermutation, which searches exhaustively for runs of markers, and FastRuns, which trades faster run times for exhaustive searches. The algorithms described here are available in the LineUp package (http://www.igb.uci.edu/ approximately baldig/lineup). We explore the performance of both algorithms on simulated data and also on genetic map data from maize (Zea mays ssp. mays). The method has reasonable power to detect a homologous region; for example, in >90% of simulations, both algorithms detect a homologous region of 10 markers buried in a random background, even when the homologous regions have diverged by numerous inversion events. The methods were applied to four maize molecular maps. All maps indicate that the maize genome contains extensive regions of genomic duplication and multiplication. Nonetheless, maps differ substantially in the location of homologous regions, probably reflecting the incomplete nature of genetic map data. The variation among maps has important implications for evolutionary inference from genetic map data.}, } @article {pmid12690511, year = {2003}, author = {Tofanelli, S and Boschi, I and Bertoneri, S and Coia, V and Taglioli, L and Franceschi, MG and Destro-Bisol, G and Pascali, V and Paoli, G}, title = {Variation at 16 STR loci in Rwandans (Hutu) and implications on profile frequency estimation in Bantu-speakers.}, journal = {International journal of legal medicine}, volume = {117}, number = {2}, pages = {121-126}, pmid = {12690511}, issn = {0937-9827}, mesh = {Alleles ; Black People/genetics ; Databases, Genetic ; Eyebrows/chemistry ; Forensic Medicine ; Gene Frequency/*genetics ; *Genetic Variation ; Genetics, Population ; Genotype ; Humans ; Language ; Rwanda ; *Tandem Repeat Sequences ; }, abstract = {A data set of 16 autosomal STRs (the 13 CODIS loci plus HumCD4, HumFES, HumF13A1) was obtained in a sample of 52 unrelated Hutus from Rwanda. Genotypes at all loci met Hardy-Weinberg expectations with the exception of HumCSF1PO. No significant evidence of association across alleles at independent loci was obtained. Statistical parameters demonstrated the forensic usefulness of the analysed systems (combined PE=0.9999996, combined PD=1:2.27 x 10(18)). Pairwise comparisons showed that the Hutu gene pool differs substantially from that of other Bantu-speaking populations suggesting the use of ethnic-specific population databases in forensic casework analysis. The introduction of a non-negligible bias was confirmed by calculating the differences between multiple-locus profile frequencies of western and eastern Bantoids using local and non-local reference databases.}, } @article {pmid12683971, year = {2003}, author = {Genereux, DP and Logsdon, JM}, title = {Much ado about bacteria-to-vertebrate lateral gene transfer.}, journal = {Trends in genetics : TIG}, volume = {19}, number = {4}, pages = {191-195}, doi = {10.1016/S0168-9525(03)00055-6}, pmid = {12683971}, issn = {0168-9525}, mesh = {Animals ; Bacteria/*genetics ; Databases, Genetic ; Dictyostelium/genetics ; *Gene Transfer, Horizontal ; *Genome, Human ; Humans ; Phylogeny ; Vertebrates/*genetics ; }, abstract = {When the International Human Genome Sequencing Consortium (IHGSC) published its draft of the human genome in February 2001, several genes were identified as possible bacteria-to-vertebrate transfers (BVTs). These genes were identified by their highly significant sequence similarity to bacterial genes in BLAST searches, and by their lack of matches among non-vertebrate eukaryote genes. Many were later rejected as BVTs by several methods, including recovery of probable orthologs from the genomes of incompletely sequenced eukaryotes. Whereas the BVT issue has received considerable attention, there has been no compilation of all potential BVTs considered to date, nor any proposal of a single comprehensive method for rigorously establishing the veracity of a putative BVT. In reviewing the work to date, we list all of the proteins examined and propose systematic tests to investigate whether a vertebrate gene proposed as a BVT is indeed of bacterial origin. We use the proposed strategy to test--and reject--one of the BVTs from the original IHGSC list.}, } @article {pmid12682969, year = {2002}, author = {Ma, M and Cao, Y and Cheng, G}, title = {[Oasis corridor landscape in arid regions: a case study of Jinta Oasis].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {13}, number = {12}, pages = {1624-1628}, pmid = {12682969}, issn = {1001-9332}, mesh = {Agriculture ; *Desert Climate ; *Ecology ; Ecosystem ; *Geographic Information Systems ; Soil ; }, abstract = {In arid region oasis, the main corridor landscape types include river, ditch, shelterbelt and road. This paper introduced their basic ecological effects on transporting mass and energy and on obstructing desert landscape expansion and incursion. Using Geographic Information System (GIS), the corridor distribution and its spatial relationship with other landscape types in the Jinta Oasis were analyzed. Based on the dynamically monitoring on the landscape pattern change of the Jinta Oasis during the latter 10 years, the driving functions of the corridors on this change were analyzed in detail. The results showed that all kinds of corridors' characteristics could be quantified by the indexes such as length and width, ratio of parameter and area, density, and non-heterogeneity. The total corridor length of Jinta Oasis is 1838.5 kilometers and its density is 2.1 km.km-2. The corridor density of the irrigated land, forest and resident area is maximal, showing that the affection degree of the oasis corridors on them is the most. The improvement of the corridor quality is one of the important driving factors on the irrigated land.}, } @article {pmid12679525, year = {2003}, author = {Yang, J and Gu, Z and Li, WH}, title = {Rate of protein evolution versus fitness effect of gene deletion.}, journal = {Molecular biology and evolution}, volume = {20}, number = {5}, pages = {772-774}, doi = {10.1093/molbev/msg078}, pmid = {12679525}, issn = {0737-4038}, support = {GM30998/GM/NIGMS NIH HHS/United States ; }, mesh = {Candida albicans/*genetics ; Culture Media ; Databases, Genetic ; *Evolution, Molecular ; *Gene Deletion ; Genes, Duplicate/genetics ; *Proteins ; Saccharomyces cerevisiae/*genetics/growth & development ; Selection, Genetic ; }, abstract = {Whether nonessential genes evolve faster than essential genes has been a controversial issue. To resolve this issue, we use the data from a nearly complete set of single-gene deletions in the yeast Saccharomyces cerevisiae to assess protein dispensability. Also, instead of the nematode, which was used previously but is only distantly related to S. cerevisiae, we use another yeast, Candida albicans, as a second species to estimate the evolutionary distances between orthologous genes in two species. Our analysis reveals only a weak correlation between protein dispensability and evolutionary rate. More important, the correlation disappears when duplicate genes are removed from the analysis. And surprisingly, the average rate of nonsynonymous substitution is considerably lower than that for single-copy genes in the yeast genome. This observation suggests that structural constraints are more important in determining the rate of evolution of a protein than dispensability because duplicate genes are on average more dispensable than single-copy genes. For duplicate genes, those with only a weak effect or no effect of deletion on fitness evolve on average faster than those with a moderate or strong effect of deletion on fitness, which in turn evolve on average faster than those with a lethal effect of deletion.}, } @article {pmid12676216, year = {2003}, author = {Adams, RM and Horst, RL}, title = {Future directions in air quality research: economic issues.}, journal = {Environment international}, volume = {29}, number = {2-3}, pages = {289-302}, doi = {10.1016/S0160-4120(02)00187-3}, pmid = {12676216}, issn = {0160-4120}, mesh = {Agriculture/economics ; Air Pollutants/*economics ; Conservation of Natural Resources/economics ; *Ecosystem ; *Environment ; Forestry/economics ; Information Systems ; Policy Making ; Research/trends ; Technology Transfer ; }, abstract = {Our challenge was to address future directions in air quality research that involve economic issues. The paper outlines the role of economics in the evaluation of air pollution impacts on environmental systems and describes existing research. We identify studies that address economic effects in the agricultural sector, in the commercial forest sector, and in unmanaged natural systems. Effects related to ozone exposure are highlighted. The summary of available research is followed by a discussion of research recommendations. Several short-term recommendations are identified that can augment some of the new research being considered by scientists. A more ambitious, long-term research project is outlined for valuing air pollution impacts in unmanaged natural environments. Specifically, the paper describes possible advantages of an 'integrated assessment' framework that more formally brings together the complex relationships that exist in both ecological and economic systems. A final section contains thoughts on the importance of education (i.e., information transfer) in the research process, especially in relation to policy. It is further noted that education should be inclusive of all members of the research team, throughout all stages of the research process.}, } @article {pmid12667475, year = {2003}, author = {Black, HI and Parekh, NR and Chaplow, JS and Monson, F and Watkins, J and Creamer, R and Potter, ED and Poskitt, JM and Rowland, P and Ainsworth, G and Hornung, M}, title = {Assessing soil biodiversity across Great Britain: national trends in the occurrence of heterotrophic bacteria and invertebrates in soil.}, journal = {Journal of environmental management}, volume = {67}, number = {3}, pages = {255-266}, doi = {10.1016/s0301-4797(02)00178-0}, pmid = {12667475}, issn = {0301-4797}, mesh = {Animals ; Bacteria ; *Conservation of Natural Resources ; Data Collection ; Databases, Factual ; *Ecosystem ; Environmental Monitoring ; Geography ; *Invertebrates ; Plants ; *Soil ; *Soil Microbiology ; }, abstract = {An assessment of the biodiversity of soils was a component of the Countryside Survey 2000 (CS2000). This was the first integrated survey of soil biota and chemical properties at a national scale. A total of 1052 soil samples were collected across Great Britain during CS2000 and analysed for a range of soil microbial and invertebrate characteristics resulting in the production of a series of robust datasets. A principal objective was to use these datasets to investigate relationships between soil biota and environmental factors such as geographical location, vegetation, land use, land cover, soil type and pollutant levels as first stages in characterising the inherent biodiversity of British soils and investigating the potential of soil biodiversity as indicators of soil health at a regional or national scale. Preliminary results for culturable heterotrophic, invertebrate taxa, Acari, Collembola and Oribatid mites are presented here to illustrate the nature of the data collected and the patterns of soil biodiversity in relation to large-scale regional, vegetation and soil characteristics across the British countryside.}, } @article {pmid12667472, year = {2003}, author = {Howard, DC and Watkins, JW and Clarke, RT and Barnett, CL and Stark, GJ}, title = {Estimating the extent and change in Broad Habitats in Great Britain.}, journal = {Journal of environmental management}, volume = {67}, number = {3}, pages = {219-227}, doi = {10.1016/s0301-4797(02)00175-5}, pmid = {12667472}, issn = {0301-4797}, mesh = {*Agriculture ; Communication ; *Conservation of Natural Resources ; Databases, Factual ; Ecology ; *Ecosystem ; *Environmental Monitoring ; *Forestry ; *Geographic Information Systems ; Plants ; United Kingdom ; }, abstract = {A stratified random sample of kilometre squares in Great Britain was visited and completely mapped using four areal themes (agriculture and semi-natural vegetation, forestry, physiography and buildings and communications). The maps were digitised and the attribute information recorded to produce an electronic database. Information was summarised by square and then bootstrap re-sampling techniques were used to produce national estimates with statistical confidence intervals. The results for 1998 showed the terrestrial Broad Habitats had a range in extent covering two orders of magnitude from Montane (49000ha) to Improved Grassland (5482000ha). Just under half of Britain is covered by agricultural Broad Habitats, about 12% by woodland and just under 10% by Urban Habitats. The remaining quarter of the land area is covered by semi-natural Broad Habitats. By revisiting the same sample of squares previously visited in 1990, changes in the quantity and quality of the Broad Habitats have been determined. Significant increases in area have occurred in the Broadleaved, Mixed and Yew Woodland and Built Up and Gardens. The largest areal reduction was in Acid Grassland although that was in part balanced by a gain in Fen, Marsh and Swamp. The most significant ecological loss was in the area of Calcareous Grassland. The consequences of having different sample sizes for the different years are discussed.}, } @article {pmid12654276, year = {2003}, author = {Bayliss, J and Helyar, A and Lee, JT and Thompson, S}, title = {A multi-criteria targeting approach to neutral grassland conservation.}, journal = {Journal of environmental management}, volume = {67}, number = {2}, pages = {145-160}, doi = {10.1016/s03014797(02)00202-5}, pmid = {12654276}, issn = {0301-4797}, mesh = {Animals ; *Conservation of Natural Resources ; Decision Making ; *Ecosystem ; *Environment ; Food Chain ; *Geographic Information Systems ; *Poaceae ; Population Dynamics ; Reference Values ; }, abstract = {Resources for creating and managing rare habitats are limited, and a targeting approach aimed at identifying the most viable sites for habitat conservation is therefore desirable. This study developed a multi-criteria targeting approach to site conservation for two rare grassland types, based on a suite of biotic and abiotic factors managed within a Geographical Information System. A number of biotic and abiotic criteria were assessed to evaluate the biodiversity status of grassland sites. Biotic factors included species diversity, species richness and species rarity; and abiotic factors included patch area, position in the ecological unit and the influence of surrounding land use. Each criterion was given equal weighting and a final biodiversity value for each patch was calculated; the patch with the highest cumulative rank score was deemed the patch with the greatest biodiversity. Each site was then examined in relation to agricultural land under the existing management prescriptions of the Upper Thames Tributaries Environmentally Sensitive Area (UTTESA). Sites identified with high biodiversity potential, but currently not included under management prescriptions, were targeted for future inclusion in the ESA scheme. The targeting approach demonstrated how the national Lowland Meadows habitat action plan creation target of 500 ha could be achieved in the UTTESA. The fact that this target figure was so easily attained within this study area highlighted the possible underestimation of national habitat creation targets.}, } @article {pmid12653513, year = {2003}, author = {Steinbeck, C and Han, Y and Kuhn, S and Horlacher, O and Luttmann, E and Willighagen, E}, title = {The Chemistry Development Kit (CDK): an open-source Java library for Chemo- and Bioinformatics.}, journal = {Journal of chemical information and computer sciences}, volume = {43}, number = {2}, pages = {493-500}, pmid = {12653513}, issn = {0095-2338}, abstract = {The Chemistry Development Kit (CDK) is a freely available open-source Java library for Structural Chemo- and Bioinformatics. Its architecture and capabilities as well as the development as an open-source project by a team of international collaborators from academic and industrial institutions is described. The CDK provides methods for many common tasks in molecular informatics, including 2D and 3D rendering of chemical structures, I/O routines, SMILES parsing and generation, ring searches, isomorphism checking, structure diagram generation, etc. Application scenarios as well as access information for interested users and potential contributors are given.}, } @article {pmid12648851, year = {2003}, author = {Krivov, S and Ulanowicz, RE and Dahiya, A}, title = {Quantitative measures of organization for multiagent systems.}, journal = {Bio Systems}, volume = {69}, number = {1}, pages = {39-54}, doi = {10.1016/s0303-2647(03)00003-0}, pmid = {12648851}, issn = {0303-2647}, mesh = {*Information Systems ; Models, Theoretical ; Probability ; }, abstract = {A set of "information theoretic" measures has been developed to quantify the degree of constraint inherent in the organization of a multiagent system. Separate measures can be provided to quantify spatial organization, trophic organization and, more generally, the overall structure of interactions. The additive character of these quantities allows them to be distributed in various fashions among species and places in a way that allows one to assign an "Importance Index" to those taxa and places. In addition, a measure to gauge the degree of adaptation of a species to a particular environment is proffered. The proposed measures allow one to formulate the following hypotheses in quantitative fashion: (1). that any disturbance of an ecosystem at a location associated with a high spatial Importance Index will exert a greater impact on the population dynamics than will a similar disturbance aimed at a place where the values of these indexes are lower; (2). that any disturbance in an ecosystem affecting a particular species with high individual Importance Indexes will cause a greater impact on the overall population dynamics than will a disturbance aimed at a species with a lower values of these indexes; (3). that the ascendancy of evolving system has a propensity to increase. The precise quantitative formulation of these hypothesis would permit them to be tested via multiagent simulation. Estimating the probablities pertaining to these hypotheses presents a number of problems that merit discussion.}, } @article {pmid12647163, year = {2003}, author = {Fortin, D and Fryxell, JM and O'Brodovich, L and Frandsen, D}, title = {Foraging ecology of bison at the landscape and plant community levels: the applicability of energy maximization principles.}, journal = {Oecologia}, volume = {134}, number = {2}, pages = {219-227}, pmid = {12647163}, issn = {0029-8549}, mesh = {*Adaptation, Physiological ; Animals ; *Bison ; *Diet ; *Energy Metabolism ; Female ; Forecasting ; *Geographic Information Systems ; Plants ; Population Dynamics ; Saskatchewan ; }, abstract = {Predictions of animal distribution and resource use require multi-scale consideration because animals can use different sets of selection criteria at different scales. We investigated whether patterns of distribution and resource use by free-ranging bison (Bison bison) in Prince Albert National Park, Saskatchewan, follow rules of energy maximization that hold across multiple scales. Optimality theory predicts specialization on Carex atherodes and frequency-independent selection among plant species; that is, local variation in C. atherodes biomass should not influence diet choice but only the time spent in individual patches. The summer use of resources within meadows was closely related to energy maximization principles. C. atherodes dominated the diet of bison, was selected in all meadows, and diet choice was frequency-independent among meadows in the bison range. In winter, diet was still dominated by C. atherodes, but frequency-dependent selection of Scolochloa festucacea and the relative use of Cirsium arvense were inconsistent with theoretical predictions. At a larger spatial scale, however, the probability of meadow use was not positively related to the abundance of Carex atherodes. During summer and winter, general landscape features within the daily radius of bison (2 km in summer and 1.3 km in winter), together with abiotic characteristics of meadows, had the major influence on the probability of meadow utilization. Our study suggests that bison distribution and resource use are influenced by abiotic and biotic factors which vary in importance at different spatio-temporal scales.}, } @article {pmid12640686, year = {2003}, author = {Nyari, TA and Dickinson, HO and Parker, L}, title = {Childhood cancer in relation to infections in the community during pregnancy and around the time of birth.}, journal = {International journal of cancer}, volume = {104}, number = {6}, pages = {772-777}, doi = {10.1002/ijc.11030}, pmid = {12640686}, issn = {0020-7136}, mesh = {Adolescent ; Child ; Child, Preschool ; Cohort Studies ; Databases, Factual ; *Disease Susceptibility ; England/epidemiology ; Female ; Humans ; Infant ; Infant, Newborn ; Male ; Neoplasms/*complications/*epidemiology ; Odds Ratio ; Pregnancy ; Pregnancy Complications, Infectious/*epidemiology ; Prenatal Exposure Delayed Effects ; Retrospective Studies ; Risk Factors ; }, abstract = {In a retrospective cohort study of 404,106 live births in the northern region of England, 1975-1986, we investigated whether higher levels of community infections during the mother's pregnancy and in early life were risk factors for cancer, by diagnostic group (leukaemia and non-Hodgkin's lymphoma, Hodgkin's disease, brain/spinal tumours, neuroblastoma, other tumours), diagnosed 1975-2001 under age 15 years. Logistic regression was used to relate risk to measures of community infections (measles, respiratory and other infections) in 3 prenatal and 2 postnatal quarters. There was an increased risk of Hodgkin's disease among children exposed around birth to higher levels of measles (odds ratio for trend = 2.3, 95% confidence interval 1.3-4.2, p = 0.01). For other diagnostic groups, there was no consistent evidence of an association between risk and exposure to infections. Although the significant association observed for Hodgkin's disease may be a chance finding, consequent to multiple hypothesis testing or the ecologic nature of the study, it is consistent with other recent epidemiologic results suggesting that the risk of Hodgkin's disease may be associated with exposure to infections.}, } @article {pmid12628362, year = {2003}, author = {Livstone, MS and van Noort, D and Landweber, LF}, title = {Molecular computing revisited: a Moore's Law?.}, journal = {Trends in biotechnology}, volume = {21}, number = {3}, pages = {98-101}, doi = {10.1016/S0167-7799(03)00007-6}, pmid = {12628362}, issn = {0167-7799}, mesh = {*Algorithms ; Biopolymers/chemistry ; Computer Systems/trends ; Computers, Molecular/*trends ; *Computing Methodologies ; DNA/*chemistry ; Equipment Design ; Forecasting ; Information Storage and Retrieval/*methods ; United States ; }, abstract = {Moore's Law states that the processing power of microchips doubles every one to two years. This observation might apply to the nascent field of molecular computing, in which biomolecules carry out logical operations. Incorporation of new technologies that improve sensitivity and throughput has increased the complexity of problems that can be addressed. It is an ultimate goal for molecular computers to use the full potential of massive parallelism.}, } @article {pmid12620360, year = {2003}, author = {Brown, PD and Tokuhisa, JG and Reichelt, M and Gershenzon, J}, title = {Variation of glucosinolate accumulation among different organs and developmental stages of Arabidopsis thaliana.}, journal = {Phytochemistry}, volume = {62}, number = {3}, pages = {471-481}, doi = {10.1016/s0031-9422(02)00549-6}, pmid = {12620360}, issn = {0031-9422}, mesh = {Arabidopsis/*growth & development/metabolism ; Benzoates/chemistry/metabolism ; Chromatography, High Pressure Liquid ; Data Interpretation, Statistical ; Germination ; Glucosinolates/chemistry/*metabolism ; Indoles/chemistry/metabolism ; Plant Structures/growth & development/metabolism ; Time Factors ; }, abstract = {The glucosinolate content of various organs of the model plant Arabidopsis thaliana (L.) Heynh., Columbia (Col-0) ecotype, was analyzed at different stages during its life cycle. Significant differences were noted among organs in both glucosinolate concentration and composition. Dormant and germinating seeds had the highest concentration (2.5-3.3% by dry weight), followed by inflorescences, siliques (fruits), leaves and roots. While aliphatic glucosinolates predominated in most organs, indole glucosinolates made up nearly half of the total composition in roots and late-stage rosette leaves. Seeds had a very distinctive glucosinolate composition. They possessed much higher concentrations of several types of aliphatic glucosinolates than other organs, including methylthioalkyl and, hydroxyalkyl glucosinolates and compounds with benzoate esters than other organs. From a developmental perspective, older leaves had lower glucosinolate concentrations than younger leaves, but this was not due to decreasing concentrations in individual leaves with age (glucosinolate concentration was stable during leaf expansion). Rather, leaves initiated earlier in development simply had much lower rates of glucosinolate accumulation per dry weight gain throughout their lifetimes. During seed germination and leaf senescence, there were significant declines in glucosinolate concentration. The physiological and ecological significance of these findings is briefly discussed.}, } @article {pmid12620030, year = {2003}, author = {William, DJ and Rybicki, NB and Lombana, AV and O'Brien, TM and Gomez, RB}, title = {Preliminary investigation of submerged aquatic vegetation mapping using hyperspectral remote sensing.}, journal = {Environmental monitoring and assessment}, volume = {81}, number = {1-3}, pages = {383-392}, doi = {10.1023/a:1021318217654}, pmid = {12620030}, issn = {0167-6369}, mesh = {Algorithms ; Automation ; *Databases, Factual ; Environmental Monitoring/*methods ; Maryland ; *Plants ; Spacecraft ; Virginia ; }, abstract = {The use of airborne hyperspectral remote sensing imagery for automated mapping of submerged aquatic vegetation (SAV) in the tidal Potomac River was investigated for near to real-time resource assessment and monitoring. Airborne hyperspectral imagery and field spectrometer measurements were obtained in October of 2000. A spectral library database containing selected ground-based and airborne sensor spectra was developed for use in image processing. The spectral library is used to automate the processing of hyperspectral imagery for potential real-time material identification and mapping. Field based spectra were compared to the airborne imagery using the database to identify and map two species of SAV (Myriophyllum spicatum and Vallisneria americana). Overall accuracy of the vegetation maps derived from hyperspectral imagery was determined by comparison to a product that combined aerial photography and field based sampling at the end of the SAV growing season. The algorithms and databases developed in this study will be useful with the current and forthcoming space-based hyperspectral remote sensing systems.}, } @article {pmid12620011, year = {2003}, author = {Hale, SS and Miglarese, AH and Bradley, MP and Belton, TJ and Cooper, LD and Frame, MT and Friel, CA and Harwell, LM and King, RE and Michener, WK and Nicolson, DT and Peterjohn, BG}, title = {Managing troubled data: coastal data partnerships smooth data integration.}, journal = {Environmental monitoring and assessment}, volume = {81}, number = {1-3}, pages = {133-148}, pmid = {12620011}, issn = {0167-6369}, mesh = {*Conservation of Natural Resources ; *Databases, Factual ; Decision Making ; Ecosystem ; *Greenhouse Effect ; *Information Management ; Interinstitutional Relations ; Water Pollutants ; }, abstract = {Understanding the ecology, condition, and changes of coastal areas requires data from many sources. Broad-scale and long-term ecological questions, such as global climate change, biodiversity, and cumulative impacts of human activities, must be addressed with databases that integrate data from several different research and monitoring programs. Various barriers, including widely differing data formats, codes, directories, systems, and metadata used by individual programs, make such integration troublesome. Coastal data partnerships, by helping overcome technical, social, and organizational barriers, can lead to a better understanding of environmental issues, and may enable better management decisions. Characteristics of successful data partnerships include a common need for shared data, strong collaborative leadership, committed partners willing to invest in the partnership, and clear agreements on data standards and data policy. Emerging data and metadata standards that become widely accepted are crucial. New information technology is making it easier to exchange and integrate data. Data partnerships allow us to create broader databases than would be possible for any one organization to create by itself.}, } @article {pmid12603051, year = {2003}, author = {Comeron, JM and Kreitman, M and De La Vega, FM}, title = {On the power to detect SNP/phenotype association in candidate quantitative trait loci genomic regions: a simulation study.}, journal = {Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing}, volume = {}, number = {}, pages = {478-489}, pmid = {12603051}, issn = {2335-6928}, mesh = {Computational Biology ; Diploidy ; Genetic Variation ; Genetics, Population ; Humans ; *Models, Genetic ; Mutation ; *Phenotype ; *Polymorphism, Single Nucleotide ; Probability ; *Quantitative Trait Loci ; Recombination, Genetic ; }, abstract = {We use coalescent methods to investigate the ability of linked neutral "markers" to reveal in simulated population samples the presence of one or more single nucleotide polymorphisms that is contributing to a trait having a complex genetic basis (QTN: quantitative trait nucleotide). Realistic mutation and recombination rates in our simulations allow us to generate SNP data appropriate for analyzing human variation across short chromosomal intervals corresponding to approximately 100 kilobases. We investigate the performance of both single marker and multiple-marker (haplotype) data for several ad hoc procedures. Our results with single SNP markers indicate that (1) the density of SNP markers need not be much higher than 10% in order to achieve near-maximal detection of a QTN; (2) a higher density of markers does not improve much on the ability to localize a QTN within an interval unless the recombination rate is high. Haplotype-based tests were investigated for the case in which more than one QTN is present in the studied interval. Larger sample sizes improve both the probability of detecting the haplotype with the largest number of QTNs, as well as the ability to infer correct haplotypes from genotypic data. Testing a series of short haplotypes across a longer interval can also be beneficial. The rate of false positives (i.e., when the most significant haplotype does not contain the greatest number of QTNs in the sample) can be very high when the contribution of individual QTNs to a trait is small. The elimination of low-frequency haplotypes does not substantially reduce the probability of detecting the haplotype with the largest number of QTNs but it can reduce the rate of false positives.}, } @article {pmid12590175, year = {2003}, author = {Rodenacker, K and Bengtsson, E}, title = {A feature set for cytometry on digitized microscopic images.}, journal = {Analytical cellular pathology : the journal of the European Society for Analytical Cellular Pathology}, volume = {25}, number = {1}, pages = {1-36}, doi = {10.1155/2003/548678}, pmid = {12590175}, issn = {0921-8912}, mesh = {Algorithms ; Diagnosis, Computer-Assisted ; Humans ; *Image Cytometry/methods ; *Image Processing, Computer-Assisted/methods ; *Microscopy/methods ; Pattern Recognition, Automated ; }, abstract = {Feature extraction is a crucial step in most cytometry studies. In this paper a systematic approach to feature extraction is presented. The feature sets that have been developed and used for quantitative cytology at the Laboratory for Biomedical Image Analysis of the GSF as well as at the Center for Image Analysis in Uppsala over the last 25 years are described and illustrated. The feature sets described are divided into morphometric, densitometric, textural and structural features. The latter group is used to describe the eu- and hetero-chromatin in a way complementing the textural methods. The main goal of the paper is to bring attention to the need of a common and well defined description of features used in cyto- and histometrical studies. The application of the sets of features is shown in an overview of projects from different fields. Finally some rules of thumb for the design of studies in this field are proposed. Colour figures can be viewed on http://www.esacp.org/acp/2003/25-1/rodenacker.htm.}, } @article {pmid12578071, year = {2000}, author = {Jungk, A and Thull, B and Hoeft, A and Rau, G}, title = {Evaluation of two new ecological interface approaches for the anesthesia workplace.}, journal = {Journal of clinical monitoring and computing}, volume = {16}, number = {4}, pages = {243-258}, pmid = {12578071}, issn = {1387-1307}, mesh = {*Anesthesia, General ; Anesthesiology/*methods ; Blood Loss, Surgical ; *Data Display ; *Decision Support Systems, Clinical ; *Ergonomics ; Eye Movements ; Humans ; Monitoring, Physiologic ; *Workplace ; }, abstract = {OBJECTIVE: Currently, vital parameters are commonly displayed as trends along a timeline. However, clinical decisions are more often based upon concepts, such as the depth of anesthesia, that are derived by combining parameter relationships and additional context information. The current displays do not visualize such concepts and therefore do not optimally support the decision process. A new display should present an ecological interface (EI). The principle of EI design is to visualize all of the information necessary for decision making in one single display.

METHODS: In the first approach, we developed an EI that visualizes 35 relevant parameters for anesthesia monitoring. All of the parameters are generated by an anesthesia software simulator. Sixteen anesthetists had to administer two simulated general anesthetics: in one setting working only with the simulator's monitors ("Sim Only"), and in another setting working with the simulator's monitors in combination with the EI ("Combi1"). During each experiment, one unexpected critical incident (either blood loss or a cuff leakage) had to be identified. The control and monitoring behavior was analyzed by recording the subjects' eye movements and think-aloud protocol. With the help of the eye-tracking results, we re-designed the EI. The new EI was then tested with no eye tracking ("Combi2") on eight anesthetists under analogous conditions as in "Combi1."

RESULTS: Cuff leakage was identified significantly quicker in "Combi1" (7 of 8 cases; time (T): 65 s +/- 73 s) than in "SimOnly" (6 of 8 cases; T: 222 s +/- 187 s). Blood loss was identified in 5 of 8 cases (T: 215 s +/- 76 s) in "Combi1" as quickly as in "SimOnly" (all cases; T: 217 s +/- 72 s). In "Combi1," the EI was used as the main source of information (in 43 +/- 19% of time) and was frequently favored when identifying an evolving critical incident. In "Combi2," cuff leakage was identified in 7 of 8 cases (T: 70 s +/- 111 s) as quickly as in "Combi1." Blood loss was identified significantly quicker in all cases (T: 147 s +/- 62 s) in "Combi2" than in "Combi1" and in "SimOnly."

CONCLUSION: The results have shown that appropriately designed EIs may improve the anesthetist's decision making and focus attention on specific problems. Now, the findings have to be tested in future studies by widening the scope using other simulated scenarios and being closer to reality under real conditions in the OR. Eye tracking proved to be a useful method to analyze the anesthetists' decision making and appropriately re-design interfaces.}, } @article {pmid12576597, year = {2003}, author = {Freimoser, FM and Screen, S and Bagga, S and Hu, G and St Leger, RJ}, title = {Expressed sequence tag (EST) analysis of two subspecies of Metarhizium anisopliae reveals a plethora of secreted proteins with potential activity in insect hosts.}, journal = {Microbiology (Reading, England)}, volume = {149}, number = {Pt 1}, pages = {239-247}, doi = {10.1099/mic.0.25761-0}, pmid = {12576597}, issn = {1350-0872}, mesh = {Animals ; Culture Media ; Databases, Genetic ; *Expressed Sequence Tags ; Fungal Proteins/genetics/*metabolism ; Gene Library ; Grasshoppers/*microbiology ; Hypocreales/classification/*genetics/*pathogenicity ; Insecta/*microbiology ; Sequence Analysis, DNA ; Transcription, Genetic ; Virulence/genetics ; }, abstract = {Expressed sequence tag (EST) libraries for Metarhizium anisopliae, the causative agent of green muscardine disease, were developed from the broad host-range pathogen Metarhizium anisopliae sf. anisopliae and the specific grasshopper pathogen, M. anisopliae sf. acridum. Approximately 1,700 5' end sequences from each subspecies were generated from cDNA libraries representing fungi grown under conditions that maximize secretion of cuticle-degrading enzymes. Both subspecies had ESTs for virtually all pathogenicity-related genes cloned to date from M. anisopliae, but many novel genes encoding potential virulence factors were also tagged. Enzymes with potential targets in the insect host included proteases, chitinases, phospholipases, lipases, esterases, phosphatases and enzymes producing toxic secondary metabolites. A diverse array of proteases composed 36 % of all M. anisopliae sf. anisopliae ESTs. Eighty percent of the ESTs that could be clustered into functional groups had significant matches (E<10(-5)) in other ascomycete fungi. These included genes reported to have specific roles in pathogens with plant or vertebrate hosts. Many of the remaining ESTs had their best BLAST match among animal, plant and bacterial sequences. These include genes with plant and microbial counterparts that produce potent antimicrobials. The abundance of transcripts discovered for different functional groups varied between the two subspecies of M. anisopliae in a manner consistent with ecological adaptations of the two pathogens. By hastening gene discovery this project has enhanced development of improved mycoinsecticides. In addition, the M. anisopliae ESTs represent a significant contribution to the extensive database of sequences from ascomycetes that are saprophytes or plant and vertebrate pathogens. Comparative analyses of these sequences is providing important information about the biology and evolutionary history of this clade.}, } @article {pmid12571013, year = {2003}, author = {Blackwood, CB and Marsh, T and Kim, SH and Paul, EA}, title = {Terminal restriction fragment length polymorphism data analysis for quantitative comparison of microbial communities.}, journal = {Applied and environmental microbiology}, volume = {69}, number = {2}, pages = {926-932}, pmid = {12571013}, issn = {0099-2240}, mesh = {Bacteria/*classification/genetics ; *Bioreactors ; Cluster Analysis ; Crops, Agricultural ; *Data Interpretation, Statistical ; Medicago sativa/growth & development ; *Polymorphism, Restriction Fragment Length ; Sensitivity and Specificity ; *Soil Microbiology ; Statistics as Topic/methods ; Zea mays/growth & development ; }, abstract = {Terminal restriction fragment length polymorphism (T-RFLP) is a culture-independent method of obtaining a genetic fingerprint of the composition of a microbial community. Comparisons of the utility of different methods of (i) including peaks, (ii) computing the difference (or distance) between profiles, and (iii) performing statistical analysis were made by using replicated profiles of eubacterial communities. These samples included soil collected from three regions of the United States, soil fractions derived from three agronomic field treatments, soil samples taken from within one meter of each other in an alfalfa field, and replicate laboratory bioreactors. Cluster analysis by Ward's method and by the unweighted-pair group method using arithmetic averages (UPGMA) were compared. Ward's method was more effective at differentiating major groups within sets of profiles; UPGMA had a slightly reduced error rate in clustering of replicate profiles and was more sensitive to outliers. Most replicate profiles were clustered together when relative peak height or Hellinger-transformed peak height was used, in contrast to raw peak height. Redundancy analysis was more effective than cluster analysis at detecting differences between similar samples. Redundancy analysis using Hellinger distance was more sensitive than that using Euclidean distance between relative peak height profiles. Analysis of Jaccard distance between profiles, which considers only the presence or absence of a terminal restriction fragment, was the most sensitive in redundancy analysis, and was equally sensitive in cluster analysis, if all profiles had cumulative peak heights greater than 10,000 fluorescence units. It is concluded that T-RFLP is a sensitive method of differentiating between microbial communities when the optimal statistical method is used for the situation at hand. It is recommended that hypothesis testing be performed by redundancy analysis of Hellinger-transformed data and that exploratory data analysis be performed by cluster analysis using Ward's method to find natural groups or by UPGMA to identify potential outliers. Analyses can also be based on Jaccard distance if all profiles have cumulative peak heights greater than 10,000 fluorescence units.}, } @article {pmid12561337, year = {2002}, author = {Bulgakov, NG and Abakumov, VA and Ivanov, VIu}, title = {[Using biological, hydrochemical and hydrological data on freshwater in Russia and neighboring countries for constructing a computerized information system].}, journal = {Izvestiia Akademii nauk. Seriia biologicheskaia}, volume = {}, number = {6}, pages = {733-737}, pmid = {12561337}, issn = {1026-3470}, mesh = {Animals ; Bacteria ; Biology ; Chemistry/methods ; Computers ; Databases, Factual ; Ecology ; *Ecosystem ; Electronic Data Processing ; Environmental Monitoring/*methods ; *Fresh Water ; *Information Systems ; Internet ; Phytoplankton ; Russia ; Software ; Zooplankton ; }, abstract = {Raw hydrobiological (population, biomass, and numbers of phytoplankton, zooplankton, zoobenthos, periphyton, and bacterioplankton species) and physicochemical indices of ecosystems are integrated into information system "Ecology of Freshwater in Russia and Neighboring Countries." This system is dedicated to environmental control by biotic indices in former USSR countries. The information system is realized as an Ecograde application relying on Microsoft Access software as well as a web site.}, } @article {pmid12554441, year = {2003}, author = {Rohlf, FJ and Bookstein, FL}, title = {Computing the uniform component of shape variation.}, journal = {Systematic biology}, volume = {52}, number = {1}, pages = {66-69}, doi = {10.1080/10635150390132759}, pmid = {12554441}, issn = {1063-5157}, mesh = {*Algorithms ; Biometry/*methods ; Body Weights and Measures/methods ; *Data Interpretation, Statistical ; }, abstract = {Any change in shape of a configuration of landmark points in two or three dimensions includes a uniform component, a component that is a wholly linear (affine) transformation. The formulas for estimating this component have been standardized for two-dimensional data but not for three-dimensional data. We suggest estimating the component by way of the complementarity between the uniform component and the space of partial warps. The component can be estimated by regression in either one space or the other: regression on the partial warps, followed by their removal, or regression on a basis for the uniform component itself. Either of the new methods can be used for both two- and three-dimensional landmark data and thus generalize Bookstein's (1996, pages 153-168 in Advances in morphometrics [L. F. Marcus et al., eds.], Plenum, New York) linearized Procrustes formula for estimating the uniform component in two dimensions.}, } @article {pmid12554403, year = {2003}, author = {Casler, JG and Cook, JR}, title = {Work design and analysis for space-based manufacturing: a case analysis of initial design issues.}, journal = {Ergonomics}, volume = {46}, number = {1-3}, pages = {141-152}, doi = {10.1080/00140130303518}, pmid = {12554403}, issn = {0014-0139}, mesh = {Crystallization ; Decision Making ; Decision Support Techniques ; *Ecological Systems, Closed ; *Environment Design ; Equipment Design ; *Ergonomics ; Humans ; Man-Machine Systems ; Organizational Case Studies ; Space Flight ; Space Simulation/*instrumentation ; Task Performance and Analysis ; Workload ; }, abstract = {The purpose of the present research was to investigate the nature of potential manufacturing tasks humans may execute in a space environment. The success of space-based manufacturing (SBM) is suggested to be a precursor to permanent human presence in space. A working hypothesis for this study was that human work in the SBM environment would be substantially different from terrestrial manufacturing work. To investigate this hypothesis, a case analysis approach was developed that employed a function allocation and task analysis of a representative SBM process: the production of tailored industrial crystals. This research approach was chosen as the current state of engineering design for SBM is in the conceptual and early flow sheeting phases of a system life cycle. Results of the task analysis and function allocation process suggest response to corrective maintenance functions and to abnormal system conditions should be allocated to humans as opposed to automation. These results are discussed in relation to human factors engineering challenges associated with long-duration human presence in an SBM environment.}, } @article {pmid12554396, year = {2003}, author = {Luczak, H and Reuth, R and Schmidt, L}, title = {Development of error-compensating UI for autonomous production cells.}, journal = {Ergonomics}, volume = {46}, number = {1-3}, pages = {19-40}, doi = {10.1080/00140130303519}, pmid = {12554396}, issn = {0014-0139}, mesh = {Classification ; Computer Simulation ; Decision Support Techniques ; Efficiency ; Efficiency, Organizational ; *Ergonomics ; Humans ; Industry/*organization & administration ; Occupational Health ; Risk Management ; Software ; *Task Performance and Analysis ; Welding/*standards ; }, abstract = {This contribution deals with the impact of human error on the overall system reliability in flexible manufacturing systems (FMS). Autonomous production cells are used to illustrate an error-compensating system design on the basis of Sheridan's (1997) paradigm of supervisory control. In order to specify human errors and their effects in terms of system disturbances, a taxonomy of system disturbances is recommended. This taxonomic approach was derived by a value benefit analysis and is based on HEDOMS (Human Error and Disturbance Occurrence in Manufacturing Systems) with slight modifications and Reason's GEMS (Generic Error Modelling System). The taxonomy is used for data acquisition. Next, a risk priority equivalent to FMEA (Failure Mode and Effect Analysis) is introduced to structure the data according to their relevance. Then, Vicente's and Rasmussen's guidelines (1987) for an ecological interface design are related to the paradigm of supervisory control. On the basis of these guidelines four case studies are presented to show their successful applicability for interface design in FMS.}, } @article {pmid12539868, year = {2001}, author = {Kapustka, LA and Galbraith, H and Luxon, BM and Yocum, J}, title = {Using landscape ecology to focus ecological risk assessment and guide risk management decision-making.}, journal = {Toxicology and industrial health}, volume = {17}, number = {5-10}, pages = {236-246}, doi = {10.1191/0748233701th121oa}, pmid = {12539868}, issn = {0748-2337}, mesh = {Animals ; Animals, Wild ; *Conservation of Natural Resources ; Data Collection ; Databases, Factual ; *Decision Making ; *Ecology ; Environment ; Environmental Pollutants/*adverse effects ; *Geographic Information Systems ; Plants ; Quality Control ; Risk Assessment ; United States ; United States Environmental Protection Agency ; }, abstract = {Ecological risk assessment (EcoRA) generally suffers from limited application of ecological knowledge in the definition and characterization of real-world sites. Not surprisingly, most remediation decisions, which follow, have little or no relationship to the valued ecological resources of the site or the broader region. The practice has evolved to favor engineering-based mitigation strategies, which eliminate excess chemical concentrations at sites, or otherwise break exposure pathways, but which may not be ecologically beneficial. The heavy emphasis of EcoRA on toxicity threshold levels tends to focus dollars on clean up of small areas or volumes with high concentrations. Moreover, intrusive remediation technologies often render an area uninhabitable to the very species that were to be protected. Infusion of ecological knowledge into EcoRA has been difficult. Most professional ecologists choose not to venture into the messy applied fields, leaving their impressive knowledge untapped. Moreover, narrowly defined responsibilities within government circles can limit cooperation and coordination. The realization that land use activities often have greater adverse consequences to wildlife than do chemicals provides an opportunity to change attitudes and practices. We are developing procedures that incorporate landscape features into the environmental management process. Specifically, we are using an iterative approach to: a) identify scenarios where habitat value is important in EcoRAs; b) guide selection of appropriate assessment species, i) keyed to wildlife distribution ranges; ii) keyed to a database of habitat suitability models; iii) cross-linked with the EPA exposure handbook species; iv) referenced to wildlife distributions (e.g., breeding bird survey); c) define data collection needs for reconnaissance-, screening-, and definitive-level characterization of habitat quality for potential assessment species; d) generate spatially explicit descriptions of habitat quality for various assessment species; and e) allocate exposure estimates using both habitat quality and spatial variations in chemical concentration. These refinements in theEcoRA process are expected to improve risk estimates and provide valuable information to be used instructuring risk management options. The approach can guide the planning process so that an assessment considers the most relevant species of the area and defines the relevant parameters to be measured. In risk characterization, these data are used to calculate more realistic exposure assessments. In guiding remediation, the approach logically considers a wider range of land management options than are considered at most sites today. For example, habitat enhancement can be used to draw animals away from contaminated zones. Contaminated localities that also have poor-quality habitat may be allowed to go through a slower, less costly bioremediation process until the risk level is lowered to acceptable levels. And direct comparisons of lost resources stemming from destructive remediation options can be assessed instead of merely focusing on the lowering of contaminant concentrations. This paper presents the conceptual foundation for incorporating landscape ecology into the risk assessment process.}, } @article {pmid12539867, year = {2001}, author = {Linkov, I and Grebenkov, A and Baitchorov, VM}, title = {Spatially explicit exposure models: application to military sites.}, journal = {Toxicology and industrial health}, volume = {17}, number = {5-10}, pages = {230-235}, doi = {10.1191/0748233701th116oa}, pmid = {12539867}, issn = {0748-2337}, mesh = {Decision Support Techniques ; Ecology ; Environment ; *Environmental Exposure ; Humans ; *Military Personnel ; *Models, Theoretical ; *Occupational Exposure ; Risk Assessment ; }, abstract = {As a result of defense-related activities, large areas of valuable habitats can be physically disturbed and/or contaminated by hazardous pollutants. It is, however, important to understand that the military impact on such areas may not be wholly detrimental to the environment: their closure to the public can result in environmental conservation of large portions of habitat. Many former military ranges have been converted for civil usage; others are still actively operated for military purposes. In both cases, a major task for environmental policy- and decision-makers is to determine scientifically justified reuse and/or operation scenarios that would not result in deterioration of site habitats and that would in fact be favorable to further development of biodiversity within the areas' existing ecosystems. Ecological risk assessment is suggested as the key process to use in facilitating the assessment of the ecological value of contaminated and/or disturbed military sites and in the development of a reuse decision protocol. We are currently developing and integrating a number of risk and habitat assessment techniques into such a protocol. This paper presents our approach to one aspect of this system: the incorporation of spatial information into ecological risk assessment. We present a software prototype that calculates radionuclide accumulation by deer foraging in areas having specified contamination patterns.}, } @article {pmid12538260, year = {2003}, author = {Sanderson, MJ}, title = {r8s: inferring absolute rates of molecular evolution and divergence times in the absence of a molecular clock.}, journal = {Bioinformatics (Oxford, England)}, volume = {19}, number = {2}, pages = {301-302}, doi = {10.1093/bioinformatics/19.2.301}, pmid = {12538260}, issn = {1367-4803}, mesh = {*Algorithms ; *Database Management Systems ; Databases, Genetic ; *Evolution, Molecular ; Genetic Drift ; Genetic Variation/*genetics ; *Phylogeny ; *Sequence Analysis, DNA ; Software ; Time Factors ; }, abstract = {SUMMARY: Estimating divergence times and rates of substitution from sequence data is plagued by the problem of rate variation between lineages. R8s version 1.5 is a program which uses parametric, nonparametric and semiparametric methods to relax the assumption of constant rates of evolution to obtain better estimates of rates and times. Unlike most programs for rate inference or phylogenetics, r8s permits users to convert results to absolute rates and ages by constraining one or more node times to be fixed, minimum or maximum ages (using fossil or other evidence). Version 1.5 uses truncated Newton nonlinear optimization code with bound constraints, offering superior performance over previous versions.

AVAILABILITY: The linux executable, C source code, sample data sets and user manual are available free at http://ginger.ucdavis.edu/r8s.}, } @article {pmid12531262, year = {2003}, author = {Schauser, I and Lewandowski, J and Hupfer, M}, title = {Decision support for the selection of an appropriate in-lake measure to influence the phosphorus retention in sediments.}, journal = {Water research}, volume = {37}, number = {4}, pages = {801-812}, doi = {10.1016/s0043-1354(02)00439-6}, pmid = {12531262}, issn = {0043-1354}, mesh = {*Decision Support Techniques ; Environmental Monitoring ; Fresh Water/*chemistry ; Geologic Sediments/*chemistry ; Germany ; Phosphorus/*isolation & purification ; Time Factors ; Water Pollutants, Chemical/*isolation & purification ; }, abstract = {Many in-lake measures which aimed to influence the phosphorus retention in lake sediments have failed to improve the trophic state of the lakes. The present paper introduces a systematic approach to select an appropriate in-lake measure. Before selecting an in-lake measure the goal of the measure should be defined, the problems of the lake must be identified, and the probability of success must be estimated. The proposed decision support consists of two parts. Part A, pre-selection, excludes inappropriate measures. It uses six criteria, which are mainly based on a simple mass-balance model, and the targets of restoration. The criteria describe the magnitude of the external versus the internal phosphorus loading, the dynamics of the internal load, and the lake morphometry. Each measure is weighted differently with respect to importance and suitability by specific quantified limits. Part B, selection, uses qualitative criteria, which are specific to the measure in question. Checking these criteria will help to select a measure with a low risk of failure. The suggested decision support is illustrated in flow charts and exemplified by Lake Arendsee in Germany.}, } @article {pmid12520046, year = {2003}, author = {Cole, JR and Chai, B and Marsh, TL and Farris, RJ and Wang, Q and Kulam, SA and Chandra, S and McGarrell, DM and Schmidt, TM and Garrity, GM and Tiedje, JM and , }, title = {The Ribosomal Database Project (RDP-II): previewing a new autoaligner that allows regular updates and the new prokaryotic taxonomy.}, journal = {Nucleic acids research}, volume = {31}, number = {1}, pages = {442-443}, pmid = {12520046}, issn = {1362-4962}, mesh = {Animals ; Archaea/*classification/genetics ; Bacteria/*classification/genetics ; *Databases, Nucleic Acid ; Eukaryotic Cells/classification ; Phylogeny ; Prokaryotic Cells/classification ; RNA, Archaeal/chemistry/classification ; RNA, Bacterial/chemistry/classification ; RNA, Ribosomal/*chemistry/classification ; Sequence Alignment ; Sequence Analysis, RNA ; Software ; }, abstract = {The Ribosomal Database Project-II (RDP-II) pro-vides data, tools and services related to ribosomal RNA sequences to the research community. Through its website (http://rdp.cme.msu.edu), RDP-II offers aligned and annotated rRNA sequence data, analysis services, and phylogenetic inferences (trees) derived from these data. RDP-II release 8.1 contains 16 277 prokaryotic, 5201 eukaryotic, and 1503 mitochondrial small subunit rRNA sequences in aligned and annotated format. The current public beta release of 9.0 debuts a new regularly updated alignment of over 50 000 annotated (eu)bacterial sequences. New analysis services include a sequence search and selection tool (Hierarchy Browser) and a phylogenetic tree building and visualization tool (Phylip Interface). A new interactive tutorial guides users through the basics of rRNA sequence analysis. Other services include probe checking, phylogenetic placement of user sequences, screening of users' sequences for chimeric rRNA sequences, automated alignment, production of similarity matrices, and services to plan and analyze terminal restriction fragment polymorphism (T-RFLP) experiments. The RDP-II email address for questions or comments is rdpstaff@msu.edu.}, } @article {pmid12519972, year = {2003}, author = {Ryan, JF and Finnerty, JR}, title = {CnidBase: The Cnidarian Evolutionary Genomics Database.}, journal = {Nucleic acids research}, volume = {31}, number = {1}, pages = {159-163}, pmid = {12519972}, issn = {1362-4962}, mesh = {Animals ; Cnidaria/*genetics/growth & development/metabolism ; *Databases, Genetic ; *Evolution, Molecular ; Gene Expression ; *Genomics ; Information Storage and Retrieval ; Life Cycle Stages ; User-Computer Interface ; }, abstract = {CnidBase, the Cnidarian Evolutionary Genomics Database, is a tool for investigating the evolutionary, developmental and ecological factors that affect gene expression and gene function in cnidarians. In turn, CnidBase will help to illuminate the role of specific genes in shaping cnidarian biodiversity in the present day and in the distant past. CnidBase highlights evolutionary changes between species within the phylum Cnidaria and structures genomic and expression data to facilitate comparisons to non-cnidarian metazoans. CnidBase aims to further the progress that has already been made in the realm of cnidarian evolutionary genomics by creating a central community resource which will help drive future research and facilitate more accurate classification and comparison of new experimental data with existing data. CnidBase is available at http://cnidbase.bu.edu/.}, } @article {pmid12519970, year = {2003}, author = {Urbance, JW and Cole, J and Saxman, P and Tiedje, JM}, title = {BSD: the Biodegradative Strain Database.}, journal = {Nucleic acids research}, volume = {31}, number = {1}, pages = {152-155}, pmid = {12519970}, issn = {1362-4962}, mesh = {Bacteria/genetics/*metabolism ; Biodegradation, Environmental ; *Databases, Factual ; Hazardous Substances/*metabolism ; Information Storage and Retrieval ; Internet ; Phylogeny ; }, abstract = {The Biodegradative Strain Database (BSD) is a freely-accessible, web-based database providing detailed information on degradative bacteria and the hazardous substances that they degrade, including corresponding literature citations, relevant patents and links to additional web-based biological and chemical data. The BSD (http://bsd.cme.msu.edu) is being developed within the phylogenetic framework of the Ribosomal Database Project II (RDPII: http://rdp.cme.msu.edu/html) to provide a biological complement to the chemical and degradative pathway data of the University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD: http://umbbd.ahc.umn.edu). Data is accessible through a series of strain, chemical and reference lists or by keyword search. The web site also includes on-line data submission and user survey forms to solicit user contributions and suggestions. The current release contains information on over 250 degradative bacterial strains and 150 hazardous substances. The transformation of xenobiotics and other environmentally toxic compounds by microorganisms is central to strategies for biocatalysis and the bioremediation of contaminated environments. However, practical, comprehensive, strain-level information on biocatalytic/biodegradative microbes is not readily available and is often difficult to compile. Similarly, for any given environmental contaminant, there is no single resource that can provide comparative information on the array of identified microbes capable of degrading the chemical. A web site that consolidates and cross-references strain, chemical and reference data related to biocatalysis, biotransformation, biodegradation and bioremediation would be an invaluable tool for academic and industrial researchers and environmental engineers.}, } @article {pmid12513671, year = {2002}, author = {Botham, PA}, title = {ECVAM, ECETOC and the EU chemicals policy.}, journal = {Alternatives to laboratory animals : ATLA}, volume = {30 Suppl 2}, number = {}, pages = {185-187}, doi = {10.1177/026119290203002S28}, pmid = {12513671}, issn = {0261-1929}, mesh = {*Animal Testing Alternatives ; Animals ; Chemical Industry ; Chemistry/legislation & jurisprudence/*standards ; Databases, Factual ; *Ecology ; Ecosystem ; Environmental Monitoring ; European Union ; Hazardous Substances/*toxicity ; *Public Policy ; Reproducibility of Results ; Toxicity Tests ; }, abstract = {ECVAM's initiatives in validation have received significant support from the European Centre for Ecotoxicology and Toxicology of Chemicals (ECETOC), especially through the provision of reference chemical data banks, which contain peer-reviewed, high-quality in vivo data on commercially available chemical substances. Chemicals have been selected from these ECETOC data banks for validation studies on alternative methods for skin corrosion and irritation and for eye irritation and, in addition, an ECETOC task force peer-reviewed the selection and classification, on the basis of in vivo data, of chemicals used in the validation of three alternative methods for developmental toxicity. More recently, ECVAM and ECETOC have been pursuing parallel initiatives on the proposed new EU chemicals policy, with the common goals of ensuring that industry and European Commission resources are used to investigate only those chemicals that pose a significant risk to human health and the environment, and that the Policy requires that any testing which is required follows the Three Rs principles of reduction, refinement and replacement.}, } @article {pmid12511066, year = {2002}, author = {Loewe, L}, title = {Global computing for bioinformatics.}, journal = {Briefings in bioinformatics}, volume = {3}, number = {4}, pages = {377-388}, doi = {10.1093/bib/3.4.377}, pmid = {12511066}, issn = {1467-5463}, mesh = {*Computational Biology ; *Computer Communication Networks/economics ; Databases, Factual ; Humans ; *Information Storage and Retrieval ; Software ; Systems Integration ; User-Computer Interface ; }, abstract = {Global computing, the collaboration of idle PCs via the Internet in a SETI@home style, emerges as a new way of massive parallel multiprocessing with potentially enormous CPU power. Its relations to the broader, fast-moving field of Grid computing are discussed without attempting a review of the latter. This review (i) includes a short table of milestones in global computing history, (ii) lists opportunities global computing offers for bioinformatics, (iii) describes the structure of problems well suited for such an approach, (iv) analyses the anatomy of successful projects and (v) points to existing software frameworks. Finally, an evaluation of the various costs shows that global computing indeed has merit, if the problem to be solved is already coded appropriately and a suitable global computing framework can be found. Then, either significant amounts of computing power can be recruited from the general public, or--if employed in an enterprise-wide Intranet for security reasons--idle desktop PCs can substitute for an expensive dedicated cluster.}, } @article {pmid12503494, year = {2002}, author = {Tong, ST and Chen, W}, title = {Modeling the relationship between land use and surface water quality.}, journal = {Journal of environmental management}, volume = {66}, number = {4}, pages = {377-393}, doi = {10.1006/jema.2002.0593}, pmid = {12503494}, issn = {0301-4797}, mesh = {Agriculture ; Climate ; Ecosystem ; Environment ; Forecasting ; *Geographic Information Systems ; Industry ; *Models, Theoretical ; Policy Making ; Quality Control ; Water Movements ; Water Pollutants/*analysis ; *Water Supply ; }, abstract = {It is widely known that watershed hydrology is dependent on many factors, including land use, climate, and soil conditions. But the relative impacts of different types of land use on the surface water are yet to be ascertained and quantified. This research attempted to use a comprehensive approach to examine the hydrologic effects of land use at both a regional and a local scale. Statistical and spatial analyses were employed to examine the statistical and spatial relationships of land use and the flow and water quality in receiving waters on a regional scale in the State of Ohio. Besides, a widely accepted watershed-based water quality assessment tool, the Better Assessment Science Integrating Point and Nonpoint Sources (BASINS), was adopted to model the plausible effects of land use on water quality in a local watershed in the East Fork Little Miami River Basin. The results from the statistical analyses revealed that there was a significant relationship between land use and in-stream water quality, especially for nitrogen, phosphorus and Fecal coliform. The geographic information systems (GIS) spatial analyses identified the watersheds that have high levels of contaminants and percentages of agricultural and urban lands. Furthermore, the hydrologic and water quality modeling showed that agricultural and impervious urban lands produced a much higher level of nitrogen and phosphorus than other land surfaces. From this research, it seems that the approach adopted in this study is comprehensive, covering both the regional and local scales. It also reveals that BASINS is a very useful and reliable tool, capable of characterizing the flow and water quality conditions for the study area under different watershed scales. With little modification, these models should be able to adapt to other watersheds or to simulate other contaminants. They also can be used to study the plausible impacts of global environmental change. In addition, the information on the hydrologic effects of land use is very useful. It can provide guidelines not only for resource managers in restoring our aquatic ecosystems, but also for local planners in devising viable and ecologically-sound watershed development plans, as well as for policy makers in evaluating alternate land management decisions.}, } @article {pmid12492875, year = {2003}, author = {Llewellyn, KS and Loxdale, HD and Harrington, R and Brookes, CP and Clark, SJ and Sunnucks, P}, title = {Migration and genetic structure of the grain aphid (Sitobion avenae) in Britain related to climate and clonal fluctuation as revealed using microsatellites.}, journal = {Molecular ecology}, volume = {12}, number = {1}, pages = {21-34}, doi = {10.1046/j.1365-294x.2003.01703.x}, pmid = {12492875}, issn = {0962-1083}, mesh = {*Animal Migration ; Animals ; Aphids/*genetics/*physiology ; *Climate ; Data Interpretation, Statistical ; Genotype ; Microsatellite Repeats ; United Kingdom ; }, abstract = {Genetic structuring of populations reflects the interaction of genetic drift, mutation, migration and selection, with influences from life history. Aphids are interesting in this regard as they have the potential for unusually high levels of dispersal and natural selection, which typically counter each other. In the present study, winged grain aphids Sitobion avenae (F.) were collected in four 12.2-m high suction traps along a north-south transect in Britain in order to eliminate sampling bias from plant hosts (cereals and grasses; Poaceae), it being known that these insects show host adaptation demonstrable using molecular markers. Samples were analysed at four polymorphic microsatellite loci over two consecutive years. Population allele frequencies were similar nationally during the two years, although clonal diversity varied greatly between sites and years. In the first sampling year following a harsh winter, diversity was found to display a latitudinal clinal trend: the proportion of unique clones (genotypes) increased with latitude. However, this pattern was less apparent the following year, after a milder winter. Nonetheless, overall FST analysis showed that there was little spatial genetic structuring in either sampling year. These data support the view that the insect is highly migratory and also support a theoretical model and previous data suggesting that the reproductive mode is clinal in S. avenae. This appears to be because natural selection (reduced reproductive success of asexual genotypes under cold conditions) is sufficiently powerful to overcome the homogenizing effects of strong migration. There was no clear evidence for isolation by distance for the genetic data obtained. The data are compared with similar data from other aphid species and other insects. Only by the collection of such data sets can an accurate picture be built up relating genetic variability to flight behaviour, including migratory ambit in this group of insects since, due to their small size and rapid dilution in the air, other marking approaches are impracticable over large geographical distances.}, } @article {pmid12481811, year = {2002}, author = {Kang, S and Both, AJ}, title = {A management information system to study space diets.}, journal = {Life support & biosphere science : international journal of earth space}, volume = {8}, number = {3-4}, pages = {191-197}, pmid = {12481811}, issn = {1069-9422}, mesh = {Biomass ; *Decision Support Techniques ; Ecological Systems, Closed ; *Food, Formulated ; Humans ; Life Support Systems ; *Management Information Systems ; Menu Planning ; Minerals/analysis ; Nutritive Value ; Plants, Edible/*chemistry/growth & development ; Programming, Linear ; Software ; *Space Flight ; }, abstract = {A management information system (MIS), including a database management system (DBMS) and a decision support system (DSS), was developed to dynamically analyze the variable nutritional content of foods grown and prepared in an Advanced Life Support System (ALSS) such as required for long-duration space missions. The DBMS was designed around the known nutritional content of a list of candidate crops and their prepared foods. The DSS was designed to determine the composition of the daily crew diet based on crop and nutritional information stored in the DBMS. Each of the selected food items was assumed to be harvested from a yet-to-be designed ALSS biomass production subsystem and further prepared in accompanying food preparation subsystems. The developed DBMS allows for the analysis of the nutrient composition of a sample 20-day diet for future Advanced Life Support missions and is able to determine the required quantities of food needed to satisfy the crew's daily consumption. In addition, based on published crop growth rates, the DBMS was able to calculate the required size of the biomass production area needed to satisfy the daily food requirements for the crew. Results from this study can be used to help design future ALSS for which the integration of various subsystems (e.g., biomass production, food preparation and consumption, and waste processing) is paramount for the success of the mission.}, } @article {pmid12471398, year = {2002}, author = {Brooker, S and Beasley, M and Ndinaromtan, M and Madjiouroum, EM and Baboguel, M and Djenguinabe, E and Hay, SI and Bundy, DA}, title = {Use of remote sensing and a geographical information system in a national helminth control programme in Chad.}, journal = {Bulletin of the World Health Organization}, volume = {80}, number = {10}, pages = {783-789}, pmid = {12471398}, issn = {0042-9686}, support = {056642//Wellcome Trust/United Kingdom ; }, mesh = {Adolescent ; Animals ; Chad/epidemiology ; Child ; Communicable Disease Control ; Female ; *Geographic Information Systems ; Helminthiasis/epidemiology/parasitology/*prevention & control ; Humans ; Male ; *Satellite Communications ; }, abstract = {OBJECTIVE: To design and implement a rapid and valid epidemiological assessment of helminths among schoolchildren in Chad using ecological zones defined by remote sensing satellite sensor data and to investigate the environmental limits of helminth distribution.

METHODS: Remote sensing proxy environmental data were used to define seven ecological zones in Chad. These were combined with population data in a geographical information system (GIS) in order to define a sampling protocol. On this basis, 20 schools were surveyed. Multilevel analysis, by means of generalized estimating equations to account for clustering at the school level, was used to investigate the relationship between infection patterns and key environmental variables.

FINDINGS: In a sample of 1023 schoolchildren, 22.5% were infected with Schistosoma haematobium and 32.7% with hookworm. None were infected with Ascaris lumbricoides or Trichuris trichiura. The prevalence of S. haematobium and hookworm showed marked geographical heterogeneity and the observed patterns showed a close association with the defined ecological zones and significant relationships with environmental variables. These results contribute towards defining the thermal limits of geohelminth species. Predictions of infection prevalence were made for each school surveyed with the aid of models previously developed for Cameroon. These models correctly predicted that A. lumbricoides and T. trichiura would not occur in Chad but the predictions for S. haematobium were less reliable at the school level.

CONCLUSION: GIS and remote sensing can play an important part in the rapid planning of helminth control programmes where little information on disease burden is available. Remote sensing prediction models can indicate patterns of geohelminth infection but can only identify potential areas of high risk for S. haematobium.}, } @article {pmid12466289, year = {2002}, author = {Betrán, E and Thornton, K and Long, M}, title = {Retroposed new genes out of the X in Drosophila.}, journal = {Genome research}, volume = {12}, number = {12}, pages = {1854-1859}, pmid = {12466289}, issn = {1088-9051}, mesh = {Animals ; Databases, Genetic ; Drosophila melanogaster/*genetics ; Genes, Insect/*genetics ; Molecular Sequence Data ; Retroelements/*genetics ; X Chromosome/*genetics ; }, abstract = {New genes that originated by various molecular mechanisms are an essential component in understanding the evolution of genetic systems. We investigated the pattern of origin of the genes created by retroposition in Drosophila. We surveyed the whole Drosophila melanogaster genome for such new retrogenes and experimentally analyzed their functionality and evolutionary process. These retrogenes, functional as revealed by the analysis of expression, substitution, and population genetics, show a surprisingly asymmetric pattern in their origin. There is a significant excess of retrogenes that originate from the X chromosome and retropose to autosomes; new genes retroposed from autosomes are scarce. Further, we found that most of these X-derived autosomal retrogenes had evolved a testis expression pattern. These observations may be explained by natural selection favoring those new retrogenes that moved to autosomes and avoided the spermatogenesis X inactivation, and suggest the important role of genome position for the origin of new genes.}, } @article {pmid12460537, year = {2002}, author = {Sobecky, PA}, title = {Approaches to investigating the ecology of plasmids in marine bacterial communities.}, journal = {Plasmid}, volume = {48}, number = {3}, pages = {213-221}, doi = {10.1016/s0147-619x(02)00110-5}, pmid = {12460537}, issn = {0147-619X}, mesh = {DNA/genetics/metabolism ; Databases as Topic ; Ecology ; Ecosystem ; Escherichia coli/metabolism ; *Genetic Techniques ; Marine Biology ; Models, Genetic ; Plasmids/*genetics/metabolism ; Random Amplified Polymorphic DNA Technique ; }, abstract = {To better understand prokaryotic gene flux in marine ecosystems and to determine whether or not environmental parameters can effect the composition and structure of plasmid populations in marine bacterial communities, information on the distribution, diversity, and ecological traits of marine plasmids is necessary. This mini-review highlights recent insights gained into the molecular diversity and ecology of plasmids occurring in marine microbial communities.}, } @article {pmid12460271, year = {2002}, author = {Fromin, N and Hamelin, J and Tarnawski, S and Roesti, D and Jourdain-Miserez, K and Forestier, N and Teyssier-Cuvelle, S and Gillet, F and Aragno, M and Rossi, P}, title = {Statistical analysis of denaturing gel electrophoresis (DGE) fingerprinting patterns.}, journal = {Environmental microbiology}, volume = {4}, number = {11}, pages = {634-643}, doi = {10.1046/j.1462-2920.2002.00358.x}, pmid = {12460271}, issn = {1462-2912}, mesh = {Bacteria/*genetics ; DNA Fingerprinting/*methods ; Data Interpretation, Statistical ; Electrophoresis ; Nucleic Acid Denaturation ; }, abstract = {Technical developments in molecular biology have found extensive applications in the field of microbial ecology. Among these techniques, fingerprinting methods such as denaturing gel electrophoresis (DGE, including the three options: DGGE, TGGE and TTGE) has been applied to environmental samples over this last decade. Microbial ecologists took advantage of this technique, originally developed for the detection of single mutations, for the analysis of whole bacterial communities. However, until recently, the results of these high quality fingerprinting patterns were restricted to a visual interpretation, neglecting the analytical potential of the method in terms of statistical significance and ecological interpretation. A brief recall is presented here about the principles and limitations of DGE fingerprinting analysis, with an emphasis on the need of standardization of the whole analytical process. The main content focuses on statistical strategies for analysing the gel patterns, from single band examination to the analysis of whole fingerprinting profiles. Applying statistical method make the DGE fingerprinting technique a promising tool. Numerous samples can be analysed simultaneously, permitting the monitoring of microbial communities or simply bacterial groups for which occurrence and relative frequency are affected by any environmental parameter. As previously applied in the fields of plant and animal ecology, the use of statistics provides a significant advantage for the non-ambiguous interpretation of the spatial and temporal functioning of microbial communities.}, } @article {pmid12456784, year = {2002}, author = {Morris, CE and Bardin, M and Berge, O and Frey-Klett, P and Fromin, N and Girardin, H and Guinebretière, MH and Lebaron, P and Thiéry, JM and Troussellier, M}, title = {Microbial biodiversity: approaches to experimental design and hypothesis testing in primary scientific literature from 1975 to 1999.}, journal = {Microbiology and molecular biology reviews : MMBR}, volume = {66}, number = {4}, pages = {592-616, table of contents}, pmid = {12456784}, issn = {1092-2172}, mesh = {*Bacteria ; Databases as Topic ; Ecology ; *Ecosystem ; Publications ; *Research Design ; }, abstract = {Research interest in microbial biodiversity over the past 25 years has increased markedly as microbiologists have become interested in the significance of biodiversity for ecological processes and as the industrial, medical, and agricultural applications of this diversity have evolved. One major challenge for studies of microbial habitats is how to account for the diversity of extremely large and heterogeneous populations with samples that represent only a very small fraction of these populations. This review presents an analysis of the way in which the field of microbial biodiversity has exploited sampling, experimental design, and the process of hypothesis testing to meet this challenge. This review is based on a systematic analysis of 753 publications randomly sampled from the primary scientific literature from 1975 to 1999 concerning the microbial biodiversity of eight habitats related to water, soil, plants, and food. These publications illustrate a dominant and growing interest in questions concerning the effect of specific environmental factors on microbial biodiversity, the spatial and temporal heterogeneity of this biodiversity, and quantitative measures of population structure for most of the habitats covered here. Nevertheless, our analysis reveals that descriptions of sampling strategies or other information concerning the representativeness of the sample are often missing from publications, that there is very limited use of statistical tests of hypotheses, and that only a very few publications report the results of multiple independent tests of hypotheses. Examples are cited of different approaches and constraints to experimental design and hypothesis testing in studies of microbial biodiversity. To prompt a more rigorous approach to unambiguous evaluation of the impact of microbial biodiversity on ecological processes, we present guidelines for reporting information about experimental design, sampling strategies, and analyses of results in publications concerning microbial biodiversity.}, } @article {pmid12454089, year = {2002}, author = {Orive, ME and Barton, NH}, title = {Associations between cytoplasmic and nuclear Loci in hybridizing populations.}, journal = {Genetics}, volume = {162}, number = {3}, pages = {1469-1485}, pmid = {12454089}, issn = {0016-6731}, mesh = {Animals ; Data Interpretation, Statistical ; Emigration and Immigration ; Female ; Humans ; *Hybridization, Genetic ; *Linkage Disequilibrium ; Male ; *Models, Genetic ; Multifactorial Inheritance/*genetics ; }, abstract = {We extend current multilocus models to describe the effects of migration, recombination, selection, and nonrandom mating on sets of genes in diploids with varied modes of inheritance, allowing us to consider the patterns of nuclear and cytonuclear associations (disequilibria) under various models of migration. We show the relationship between the multilocus notation recently presented by Kirkpatrick, Johnson, and Barton (developed from previous work by Barton and Turelli) and the cytonuclear parameterization of Asmussen, Arnold, and Avise and extend this notation to describe associations between cytoplasmic elements and multiple nuclear genes. Under models with sexual symmetry, both nuclear-nuclear and cytonuclear disequilibria are equivalent. They differ, however, in cases involving some type of sexual asymmetry, which is then reflected in the asymmetric inheritance of cytoplasmic markers. An example given is the case of different migration rates in males and females; simulations using 2, 3, 4, or 5 unlinked autosomal markers with a maternally inherited cytoplasmic marker illustrate how nuclear-nuclear and cytonuclear associations can be used to separately estimate female and male migration rates. The general framework developed here allows us to investigate conditions where associations between loci with different modes of inheritance are not equivalent and to use this nonequivalence to test for deviations from simple models of admixture.}, } @article {pmid12450745, year = {2002}, author = {Jeewon, R and Liew, EC and Hyde, KD}, title = {Phylogenetic relationships of Pestalotiopsis and allied genera inferred from ribosomal DNA sequences and morphological characters.}, journal = {Molecular phylogenetics and evolution}, volume = {25}, number = {3}, pages = {378-392}, doi = {10.1016/s1055-7903(02)00422-0}, pmid = {12450745}, issn = {1055-7903}, mesh = {Ascomycota/classification/*genetics ; *DNA, Ribosomal ; Databases as Topic ; Likelihood Functions ; Models, Genetic ; Phylogeny ; Sequence Analysis, DNA ; Statistics as Topic ; }, abstract = {The taxonomy of the coelomycetous fungus Pestalotiopsis and other closely related genera based on morphological characters has been equivocal. To gain insight in the phylogenetic relationships of Pestalotiopsis and its allies, part of the large subunit (28S) ribosomal DNA region was examined and compared with existing morphological information. Phylogenetic analyses were conducted using parsimony, distance, and likelihood criteria. Results of the analyses showed that Bartalinia, Pestalotiopsis, Seimatosporium, and Seiridium represent distinct monophyletic groups with high bootstrap support. However, Truncatella species are paraphyletic with Bartalinia, sharing a common ancestor. Pestalotia species sequenced clustered together with Pestalotiopsis. These genera should be recognized as distinct natural groups except for Monochaetia and Discosia, which need to be further resolved. Tree topologies are generally in concordance with previous morphological hypotheses, most notably the placement of all Pestalotia species, except the type P. pezizoides, in Pestalotiopsis. Well-supported clades corresponding to groupings based on conidial morphology were resolved and the relative importance of morphological characters for generic delimitation is discussed. Molecular data also provide further evidence to support the association of these coelomycetes with the Amphisphaeriaceae.}, } @article {pmid12448286, year = {2002}, author = {Taylor, CS and Lerner, RM and von Eye, A and Balsano, AB and Dowling, EM and Anderson, PM and Bobek, DL and Bjelobrk, D}, title = {Individual and ecological assets and positive developmental trajectories among gang and community-based organization youth.}, journal = {New directions for youth development}, volume = {}, number = {95}, pages = {57-72}, doi = {10.1002/yd.16}, pmid = {12448286}, issn = {1533-8916}, mesh = {Achievement ; Adolescent ; Adolescent Behavior/*ethnology ; Black or African American/*psychology ; *Community Networks ; Group Processes ; *Human Development ; Humans ; Longitudinal Studies ; Male ; *Models, Organizational ; Models, Theoretical ; Program Development ; Social Problems/*ethnology ; United States ; }, abstract = {The Search Institute framework for conceptualizing developmental assets was used in a longitudinal study of African American male youth involved in gangs or in community-based organizations (CBOs) serving youth. Analyses of intraindividual change indicated that individual and ecological assets are linked to positive developmental trajectories among these youth.}, } @article {pmid12442766, year = {2002}, author = {Ciolkosz, DE and Albright, LD and Sager, JC and Langhans, RW}, title = {A model for plant lighting system selection.}, journal = {Transactions of the ASAE. American Society of Agricultural Engineers}, volume = {45}, number = {1}, pages = {215-221}, doi = {10.13031/2013.7873}, pmid = {12442766}, issn = {0001-2351}, mesh = {*Decision Making, Computer-Assisted ; Ecological Systems, Closed ; *Environment, Controlled ; Evaluation Studies as Topic ; Lactuca/growth & development/radiation effects ; Life Support Systems/instrumentation ; *Light ; Lighting/*instrumentation ; *Models, Biological ; *Plant Development ; Plants/radiation effects ; Software ; Systems Theory ; }, abstract = {A decision model is presented that compares lighting systems for a plant growth scenario and chooses the most appropriate system from a given set of possible choices. The model utilizes a Multiple Attribute Utility Theory approach, and incorporates expert input and performance simulations to calculate a utility value for each lighting system being considered. The system with the highest utility is deemed the most appropriate system. The model was applied to a greenhouse scenario, and analyses were conducted to test the model's output for validity. Parameter variation indicates that the model performed as expected. Analysis of model output indicates that differences in utility among the candidate lighting systems were sufficiently large to give confidence that the model's order of selection was valid.}, } @article {pmid12438187, year = {2002}, author = {Burgess, SK}, title = {Metabioinformatics: the ecology of an intellectual collective.}, journal = {Annals of the New York Academy of Sciences}, volume = {971}, number = {}, pages = {584}, doi = {10.1111/j.1749-6632.2002.tb04531.x}, pmid = {12438187}, issn = {0077-8923}, mesh = {Biology/*methods ; Computational Biology/*methods ; *Genome ; Internet ; Public Policy ; Software ; }, } @article {pmid12422180, year = {2002}, author = {Goodman, S}, title = {Science education: put your lab in a different class.}, journal = {Nature}, volume = {420}, number = {6911}, pages = {12-14}, doi = {10.1038/420012a}, pmid = {12422180}, issn = {0028-0836}, mesh = {Animals ; Bacillus anthracis/chemistry ; Career Choice ; Community Networks/organization & administration ; *Cooperative Behavior ; England ; Germany ; Marine Biology/education ; Models, Molecular ; Molecular Biology/education ; Physics/education ; Research Personnel/*organization & administration/psychology ; Science/*education ; *Students/psychology ; United States ; Veterinary Medicine ; Workforce ; }, } @article {pmid12421750, year = {2002}, author = {Kaessmann, H and Zöllner, S and Nekrutenko, A and Li, WH}, title = {Signatures of domain shuffling in the human genome.}, journal = {Genome research}, volume = {12}, number = {11}, pages = {1642-1650}, pmid = {12421750}, issn = {1088-9051}, support = {R01 GM065499/GM/NIGMS NIH HHS/United States ; GM30998/GM/NIGMS NIH HHS/United States ; GM65499/GM/NIGMS NIH HHS/United States ; R37 GM030998/GM/NIGMS NIH HHS/United States ; R01 GM030998/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Caenorhabditis elegans Proteins/chemistry/classification/genetics ; Databases, Protein/statistics & numerical data ; Evolution, Molecular ; Exons/genetics ; *Genome, Human ; Humans ; Introns/genetics ; Protein Structure, Tertiary/genetics ; Proteome/chemistry/classification/genetics ; }, abstract = {To elucidate the role of exon shuffling in shaping the complexity of the human genome/proteome, we have systematically analyzed intron phase distributions in the coding sequence of human protein domains. We found that introns at the boundaries of domains show high excess of symmetrical phase combinations (i.e., 0-0, 1-1, and 2-2), whereas nonboundary introns show no excess symmetry. This suggests that exon shuffling has primarily involved rearrangement of structural and functional domains as a whole. Furthermore, we found that domains flanked by phase 1 introns have dramatically expanded in the human genome due to domain shuffling and that 1-1 symmetrical domains and domain families are nonrandomly distributed with respect to their age. The predominance and extracellular location of 1-1 symmetrical domains among domains specific to metazoans suggests that they are associated with the rise of multicellularity. On the other hand, 0-0 symmetrical domains tend to be over-represented among ancient protein domains that are shared between the eukaryotic and prokaryotic kingdoms, which is compatible with the suggestion of primordial domain shuffling in the progenote. To see whether the human data reflect general genomic patterns of metazoans, similar analyses were done for the nematode Caenorhabditis elegans. Although the C. elegans data generally concur with the human patterns, we identified fewer intron-bounded domains in this organism, consistent with the lower complexity of C. elegans genes. [The following individuals kindly provided reagents, samples, or unpublished information as indicated in the paper: Z. Gu and R. Stevens.]}, } @article {pmid12420982, year = {2002}, author = {Maksimović, C and Makropoulos, CK}, title = {Integrating river basin management and the coastal zone: the (blue) Danube and the (black) sea.}, journal = {Water science and technology : a journal of the International Association on Water Pollution Research}, volume = {46}, number = {8}, pages = {187-194}, pmid = {12420982}, issn = {0273-1223}, mesh = {Baltic States ; Decision Support Techniques ; Ecology ; *Environment ; Environmental Monitoring ; *Geographic Information Systems ; International Cooperation ; Waste Disposal, Fluid/*methods ; Water Movements ; Water Pollution/*prevention & control ; *Water Supply ; }, abstract = {In order to effectively manage the wide variety of physical, chemical biological and ecological processes in a sensitive coastal environment such as the Black Sea, current environmental management objectives are no longer sufficient: a new management approach has to address the intimate functional linkage between the river basin and the costal environment. Current water quality legislation requires compliance to emission levels based on the chemical analysis of water samples taken at discharge points, such as treatment plants discharging into rivers. While such measures provide a relative indication of the water quality at the point of discharge, they fail to describe accurately and sufficiently the quality of the water received from the watershed or basin. As water flows through the catchment, rainfall run-off from urban and agricultural areas carries sediments, pesticides, and other chemicals into river systems, which lead to coastal waters. The impact of the Kosovo crisis on the Danube ecosystems provides a poignant example of the effects of such diffused pollution mechanisms and reveals a number of interesting pollution mechanisms. This paper discusses both the effects of diffused pollution on the Black Sea, drawing from state-of-the-art reports on the Danube, and proposes a framework for a decision support system based on distributed hydrological and pollution transport simulation models and GIS. The use of ecological health indicators and fuzzy inference supporting decisions on regional planning within this framework is also advocated. It is also argued that even the recently produced GEF document on Black Sea protection scenarios should benefit significantly if the concept of pollution reduction from both urban, industrial and rural areas should undergo a systematic conceptual update in the view of the recent recommendations of the UNEP IETC (2000) document.}, } @article {pmid12420965, year = {2002}, author = {Dachev, D and Zlatanova, S}, title = {Pollution sources identification in the "land-sea" system.}, journal = {Water science and technology : a journal of the International Association on Water Pollution Research}, volume = {46}, number = {8}, pages = {53-58}, pmid = {12420965}, issn = {0273-1223}, mesh = {Bulgaria ; Chemical Phenomena ; Chemistry ; Ecology ; Environmental Monitoring ; *Geographic Information Systems ; Geologic Sediments/*chemistry ; Geological Phenomena ; Geology ; Water Pollutants/*analysis ; }, abstract = {It is our opinion that the new scientific thinking and education in the 21st century will increase the significance of the multidisciplinary nature knowledge. The nature of the marine sediments as well as the biochemical features of the littoral organisms appear to be in close relation to the geochemical impact of the coastal onshore. The biogeochemical analysis of the terrestrial and marine biocenosis is still fragmental, without balance between the casual and sequential relationships. Along the Bulgarian Black Sea coast the latter necessitates the geological pattern clarification of the areas south of Bourgas. Even a superficial overview of the geological features of the region highlights the impact of the geochemical anomalies related to Rosen and Zidarovo volcanic apparatuses and intrusions, other ore deposits south and south-west as well. However, the intensive anthropogenic impact on the geochemical haloes should be pointed out in the complex of ecological damage to the coast. Through complementary geoecological studies a significant updating of the knowledge is suggested. The geoecological mapping is needed to present the ratio of the lands saturated with geonoxes, and anthropogenically polluted ones. The new methodology recommended was applied to make the distinction of such lands in the regions of Pirdop and Kardjali. Another key element appears to be the ecological-economic characteristics in the offshore-onshore balance. The marine resources will be studied in the alternative context: benefit-damage from the onshore polluters, and the biogeochemical characteristics of the littoral zone. The coastal area's environmental status should make a distinction between the environmentally undamaged, environmentally damaged by nature, anthropogenically damaged and complex damaged lands. Each ecological study or analysis presenting the ecological condition of the environment in a status quo (at a certain moment and at a certain location) is described in this work as a Status Geoecological System. For environmental management and protection of the Black Sea we refer to an indispensable Data File representing the Dynamic Geoecological System.}, } @article {pmid12418162, year = {2002}, author = {Kristensen, SP and Caspersen, OH}, title = {Analysis of changes in a shelterbelt network landscape in central Jutland, Denmark.}, journal = {Journal of environmental management}, volume = {66}, number = {2}, pages = {171-183}, doi = {10.1006/jema.2002.0582}, pmid = {12418162}, issn = {0301-4797}, mesh = {Agriculture ; Climate ; *Conservation of Natural Resources ; Denmark ; Ecology ; *Ecosystem ; Environmental Monitoring ; *Geographic Information Systems ; Trees ; }, abstract = {This paper investigates the changes in a shelterbelt network between 1950 and 1997 in a study area in central Jutland, Denmark. The analysis consists of two parts. Firstly, the changes in key parameters which are of landscape ecological importance (shelterbelt density, connectivity, node type and landscape grain size) are examined. The results of this analysis show that shelterbelt density varied considerably during the period due to changes in biophysical and socioeconomic factors. A GIS analysis shows that landscape grain size decreased in 45 percent of the area. A major change of shelterbelt type occurred in the area with landscape ecological and visual scenery implications. It appears that public-subsidised shelterbelt planting programmes were the most important factors influencing changes in the shelterbelt network in the study area while differences in soil type were less important. Secondly, data from a questionnaire survey were used to examine the driving forces behind shelterbelt activities over a 10 year period. Hobby farmers were the most active farmer group in shelterbelt planting and agronomic reasons were the most important motives for shelterbelt planting in the study area during this period. Furthermore, it appeared that microclimate effects and aesthetical considerations have become important reasons for shelterbelt planting.}, } @article {pmid12418159, year = {2002}, author = {Pearlstine, LG and Smith, SE and Brandt, LA and Allen, CR and Kitchens, WM and Stenberg, J}, title = {Assessing state-wide biodiversity in the Florida Gap analysis project.}, journal = {Journal of environmental management}, volume = {66}, number = {2}, pages = {127-144}, doi = {10.1006/jema.2002.0551}, pmid = {12418159}, issn = {0301-4797}, mesh = {Amphibians ; Animals ; *Animals, Wild ; Birds ; *Conservation of Natural Resources ; Environmental Monitoring ; Florida ; *Geographic Information Systems ; Insecta ; Mammals ; Population Dynamics ; Reptiles ; }, abstract = {The Florida Gap (Fl-Gap) project provides an assessment of the degree to which native animal species and natural communities are or are not represented in existing conservation lands. Those species and communities not adequately represented in areas being managed for native species constitute 'gaps' in the existing network of conservation lands. The United States Geological Survey Gap Analysis Program is a national effort and so, eventually, all 50 states will have completed it. The objective of Fl-Gap was to provide broad geographic information on the status of terrestrial vertebrates, butterflies, skippers and ants and their respective habitats to address the loss of biological diversity. To model the distributions and potential habitat of all terrestrial species of mammals, breeding birds, reptiles, amphibians, butterflies, skippers and ants in Florida, natural land cover was mapped to the level of dominant or co-dominant plant species. Land cover was classified from Landsat Thematic Mapper (TM) satellite imagery and auxiliary data such as the national wetlands inventory (NWI), soils maps, aerial imagery, existing land use/land cover maps, and on-the-ground surveys. Wildlife distribution models were produced by identifying suitable habitat for each species within that species' range. Mammalian models also assessed a minimum critical area required for sustainability of the species' population. Wildlife species richness was summarized against land stewardship ranked by an area's mandates for conservation protection.}, } @article {pmid12406806, year = {2002}, author = {Karpati, A and Galea, S and Awerbuch, T and Levins, R}, title = {Variability and vulnerability at the ecological level: implications for understanding the social determinants of health.}, journal = {American journal of public health}, volume = {92}, number = {11}, pages = {1768-1772}, pmid = {12406806}, issn = {0090-0036}, mesh = {Adolescent ; Adult ; Aged ; California/epidemiology ; Cause of Death ; Child ; Child, Preschool ; Data Interpretation, Statistical ; Disease/classification/economics ; Educational Status ; *Health Status Indicators ; Humans ; Infant ; Infant, Newborn ; Middle Aged ; *Mortality ; New York/epidemiology ; Poverty/statistics & numerical data ; Sensitivity and Specificity ; Social Class ; *Socioeconomic Factors ; Unemployment/statistics & numerical data ; }, abstract = {OBJECTIVES: We examined variability in disease rates to gain understanding of the complex interactions between contextual socioeconomic factors and health.

METHODS: We compared mortality rates between New York and California counties in the lowest and highest quartiles of socioeconomic status (SES), assessed rate variability between counties for various outcomes, and examined correlations between outcomes' sensitivity to SES and their variability.

RESULTS: Outcomes with mortality rates that differed most by county SES were among those whose variability across counties was high (e.g., AIDS, homicide, cirrhosis). Lower-SES counties manifested greater variability among outcome measures.

CONCLUSIONS: Differences in health outcome variability reflect differences in SES impact on health. Health variability at the ecological level might reflect the impact of stressors on vulnerable populations.}, } @article {pmid12404995, year = {2002}, author = {Schwebel, DC and Binder, SC and Plumert, JM}, title = {Using an injury diary to describe the ecology of children's daily injuries.}, journal = {Journal of safety research}, volume = {33}, number = {3}, pages = {301-319}, doi = {10.1016/s0022-4375(02)00028-2}, pmid = {12404995}, issn = {0022-4375}, mesh = {Accident Prevention ; Accidental Falls/prevention & control/statistics & numerical data ; Accidents, Home/prevention & control/*statistics & numerical data ; Analysis of Variance ; Causality ; Child ; *Child Welfare ; Data Collection/*methods ; Data Interpretation, Statistical ; Ergonomics ; Female ; Humans ; Male ; Medical Records/*standards ; Parents ; Play and Playthings ; Safety Management ; Wounds and Injuries/*etiology ; }, abstract = {PROBLEM: Two problems were addressed in this study. First, are daily injury diaries an effective means to gather information about children's unintentional injuries? Second, what are the circumstances of children's injuries as recorded through the diary method?

METHOD: Two studies were conducted with a total of 172 children to describe the ecology of children's daily unintentional injuries. Families completed a daily diary for 14 days, describing the circumstances surrounding the injuries children experienced each day.

RESULTS: Descriptive data is provided on the locations, causes, and types of injuries children incurred, as well as who was present when they were injured. Daily injury rate was modestly related to the number of major injuries children had incurred in their lifetimes.

DISCUSSION: The diary methodology was an effective means to study the ecology of children's daily injuries. Children's injuries occur in a wide range of circumstances that can be quantified through diary techniques.

IMPACT ON INDUSTRY: Data obtained from daily injury diaries may be useful in a variety of areas, including study of the etiology of childhood injury, design of interventions to prevent injury, and engineering of toys and playground equipment for children.}, } @article {pmid12389810, year = {2002}, author = {Groben, R and Medlin, LK}, title = {Meeting report: EU workshop "Analysis of Single Cells in the Marine Phytoplankton" (ASCMAP), Alfred Wegener Institute for Polar and Marine Research, Bremerhaven, Germany, April 15-21, 2002.}, journal = {Protist}, volume = {153}, number = {3}, pages = {193-195}, doi = {10.1078/1434-4610-00097}, pmid = {12389810}, issn = {1434-4610}, mesh = {Animals ; Decision Making, Computer-Assisted ; Flow Cytometry/instrumentation ; Germany ; Marine Biology/trends ; Molecular Probes ; Phytoplankton/*cytology ; Seawater/*microbiology ; }, } @article {pmid12381869, year = {2002}, author = {Winfree, AT}, title = {Chemical waves and fibrillating hearts: discovery by computation.}, journal = {Journal of biosciences}, volume = {27}, number = {5}, pages = {465-473}, pmid = {12381869}, issn = {0250-5991}, mesh = {*Computational Biology ; Heart/*physiology ; Myocardium/*chemistry ; }, } @article {pmid12380984, year = {2002}, author = {Chang, YC and Chang, NB}, title = {The design of a web-based decision support system for the sustainable management of an urban river system.}, journal = {Water science and technology : a journal of the International Association on Water Pollution Research}, volume = {46}, number = {6-7}, pages = {131-139}, pmid = {12380984}, issn = {0273-1223}, mesh = {Cities ; *Conservation of Natural Resources ; *Decision Support Techniques ; Ecosystem ; Environmental Monitoring/methods ; *Geographic Information Systems ; *Internet ; Taiwan ; *Water Supply ; }, abstract = {The effects of urbanization on the aquatic environment, and solutions to the deterioration of water quality and stream ecology in the Love River have long been the main focus of environmental management in southern Taiwan. Apart from choosing the regular strategies of installing an intercept and sewer system, coastal wastewater treatment plant, and ocean outfall pipe, a new opportunity for improving the overall managerial efficiency is to design and implement a web-based Decision Support System (DSS). This DSS must be capable of managing storm water impacts when overflow is inevitable, river water quality variations loading to influences on the ecosystem, and changing land use programs along river corridors and adjacent urban areas simultaneously. This paper presents a new design framework for building such a DSS. By using the advanced information technology in the "Internet" environment, the proposed DSS may perform normal queries and statistical analyses in a web-enabled database, spatial analysis via the use of a Geographic Information System (GIS) in the Internet environment, and essential data warehousing/data mining. Possible linkage with various analytical models is anticipated. Such a DSS must be helpful for achieving the rehabilitation of the estuarine ecosystem and satisfying the goals for sustainable management in a regional sense.}, } @article {pmid12364796, year = {2002}, author = {Ranson, H and Claudianos, C and Ortelli, F and Abgrall, C and Hemingway, J and Sharakhova, MV and Unger, MF and Collins, FH and Feyereisen, R}, title = {Evolution of supergene families associated with insecticide resistance.}, journal = {Science (New York, N.Y.)}, volume = {298}, number = {5591}, pages = {179-181}, doi = {10.1126/science.1076781}, pmid = {12364796}, issn = {1095-9203}, support = {U01 AI48846/AI/NIAID NIH HHS/United States ; U01 AI50687/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Anopheles/enzymology/*genetics ; Carboxylic Ester Hydrolases/chemistry/classification/*genetics/metabolism ; Computational Biology ; Conserved Sequence ; Cytochrome P-450 Enzyme System/chemistry/classification/*genetics/metabolism ; Drosophila melanogaster/enzymology/genetics ; *Evolution, Molecular ; Genes, Duplicate ; Genes, Insect ; Genome ; Genomics ; Glutathione Transferase/chemistry/classification/*genetics/metabolism ; Insecticide Resistance/*genetics ; Multigene Family ; Mutation ; Phylogeny ; Physical Chromosome Mapping ; Sequence Analysis, DNA ; Terminology as Topic ; }, abstract = {The emergence of insecticide resistance in the mosquito poses a serious threat to the efficacy of many malaria control programs. We have searched the Anopheles gambiae genome for members of the three major enzyme families- the carboxylesterases, glutathione transferases, and cytochrome P450s-that are primarily responsible for metabolic resistance to insecticides. A comparative genomic analysis with Drosophila melanogaster reveals that a considerable expansion of these supergene families has occurred in the mosquito. Low gene orthology and little chromosomal synteny paradoxically contrast the easily identified orthologous groups of genes presumably seeded by common ancestors. In A. gambiae, the independent expansion of paralogous genes is mainly a consequence of the formation of clusters among locally duplicated genes. These expansions may reflect the functional diversification of supergene families consistent with major differences in the life history and ecology of these organisms. These data provide a basis for identifying the resistance-associated enzymes within these families. This will enable the resistance status of mosquitoes, flies, and possibly other holometabolous insects to be monitored. The analyses also provide the means for identifying previously unknown molecules involved in fundamental biological processes such as development.}, } @article {pmid12231015, year = {2002}, author = {Galea, S and Karpati, A and Kennedy, B}, title = {Social capital and violence in the United States, 1974-1993.}, journal = {Social science & medicine (1982)}, volume = {55}, number = {8}, pages = {1373-1383}, doi = {10.1016/s0277-9536(01)00274-x}, pmid = {12231015}, issn = {0277-9536}, mesh = {Adult ; Cross-Sectional Studies ; Data Collection ; Data Interpretation, Statistical ; Ecology ; Helping Behavior ; Homicide/ethnology/*statistics & numerical data ; Humans ; Logistic Models ; Markov Chains ; *Psychology, Social ; Social Justice ; *Social Support ; Trust ; United States/epidemiology ; Violence/ethnology/*statistics & numerical data ; }, abstract = {Social capital is a characteristic of communities. Cross-sectional studies have shown that social capital is inversely associated with homicide and violent crime. We hypothesized that variations in social capital in US states over time can predict variations in regional homicide mortality both across and within time periods. We analyzed serial cross-sectional data for measures of social capital and age-adjusted homicide rates between 1974 and 1993. We used perception of social trust and per capita membership in voluntary associations, obtained from responses to the General Social Surveys, as the principal measures of social capital. We controlled for potential confounding by mean levels of income, urbanization, and region. Measures of perceived trust were strongly inversely correlated with homicide rates in an aggregate cross-sectional analysis (r=-0.51, p<0.001) and also within each time period. Social capital was an independent predictor of rates of violence when controlling for income, region, and urbanization (p<0.001). Homicide rates also predicted levels of social capital in adjusted models (p<0.001). To investigate directionality of this relationship we developed Markov transition matrices that described the change in the states' levels of social capital and homicide across time intervals. Analysis of the transitional probabilities confirmed that a simple unidirectional association between social capital and violence was not sufficient to describe this association. There is likely an impact of violence on levels of perceived trust in communities that complements the hypothesized effect of social capital on homicide. We conclude that the relationship between social capital and violence over time is non-linear and dynamic. More complex analytic models describing the relationship between violence and ecological social determinants need to be considered.}, } @article {pmid12222954, year = {2002}, author = {van Straalen, NM}, title = {Assessment of soil contamination--a functional perspective.}, journal = {Biodegradation}, volume = {13}, number = {1}, pages = {41-52}, doi = {10.1023/a:1016398018140}, pmid = {12222954}, issn = {0923-9820}, mesh = {Computational Biology ; Containment of Biohazards ; Ecosystem ; Environmental Monitoring ; Environmental Pollution/*analysis ; Hazardous Waste ; Humans ; Models, Biological ; Soil Pollutants/*analysis/toxicity ; }, abstract = {In many industrialized countries the use of land is impeded by soil pollution from a variety of sources. Decisions on clean-up, management or set-aside of contaminated land are based on various considerations, including human health risks, but ecological arguments do not have a strong position in such assessments. This paper analyses why this should be so, and what ecotoxicology and theoretical ecology can improve on the situation. It seems that soil assessment suffers from a fundamental weakness, which relates to the absence of a commonly accepted framework that may act as a reference. Soil contamination can be assessed both from a functional perspective and a structural perspective. The relationship between structure and function in ecosystems is a fundamental question of ecology which receives a lot of attention in recent literature, however, a general concept that may guide ecotoxicological assessments has not yet arisen. On the experimental side, a good deal of progress has been made in the development and standardized use of terrestrial model ecosystems (TME). In such systems, usually consisting of intact soil columns incubated in the laboratory under conditions allowing plant growth and drainage of water, a compromise is sought between field relevance and experimental manageability. A great variety of measurements can be made on such systems, including microbiological processes and activities, but also activities of the decomposer soil fauna. I propose that these TMEs can be useful instruments in ecological soil quality assessments. In addition a "bioinformatics approach" to the analysis of data obtained in TME experiments is proposed. Soil function should be considered as a multidimensional concept and the various measurements can be considered as indicators, whose combined values define the "normal operating range" of the system. Deviations from the normal operating range indicate that the system is in a condition of stress. It is hoped that more work along this line will improve the prospects for ecological arguments in soil quality assessment.}, } @article {pmid12222062, year = {2002}, author = {Zhao, Y and Yu, X and Guang, W}, title = {[Review on landscape heterogeneity].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {13}, number = {4}, pages = {495-500}, pmid = {12222062}, issn = {1001-9332}, mesh = {Data Interpretation, Statistical ; *Ecology ; Forecasting ; Methods ; }, abstract = {On the base of precedent studies, the occurring mechanism, classification, measurement methods, and the important role of landscape heterogeneity in landscape ecology were reviewed. The inner and outer uncertain factors result in landscape heterogeneity. Landscape heterogeneity has close relations with landscape stability, landscape design, architecture, management and disturbance, scale and ecological diversity in ecology. Complexity of landscape heterogeneity research, non-system of measurement indices and methods, difficulties and limitations of landscape heterogeneity modelling were all discussed respectively. In addition, it is suggested that the theory and methods of ecological complexity should be used to improve landscape heterogeneity research.}, } @article {pmid12214604, year = {2000}, author = {Guo, SS and Wang, PX and Hou, JD and Ai, WD and Chao, ZG}, title = {[Development of a ground-based experimental facility for space cultivation of higher plant].}, journal = {Hang tian yi xue yu yi xue gong cheng = Space medicine & medical engineering}, volume = {13}, number = {1}, pages = {19-24}, pmid = {12214604}, issn = {1002-0837}, mesh = {Air Conditioning ; Automation ; Carbon Dioxide ; *Ecological Systems, Closed ; *Environment, Controlled ; Equipment Design ; Humidity ; Hydroponics ; Life Support Systems/*instrumentation ; Lighting ; Oxygen ; *Plant Development ; *Space Simulation ; Temperature ; Weightlessness ; }, abstract = {A ground-based experimental facility was developed for conducting initial ground-based simulation study of Controlled Ecological Life Support System (CELSS). The facility is composed of a main chamber, O2 and CO2 composition control subsystems, plant cultivation subsystem and whole data management subsystem. The growth room, being composed of a inner wall of mirror-face stainless steel, holds a volume of 1.8 m3 and a growing area of 1.2 m2; electronic fluorescent lamps were used as lighting sources and polyvinyl formal was used for root matrixes; the environmental parameters of the growing room such as temperature, relative humidity, O2 concentration, CO2 concentration, lighting period and irradiance intensity and the nutrient parameters such as pH, electrical conductivity, dissolved oxygen concentration, liquid level of nutrient storage tank and flow rate of nutrient were all controlled automatically; all of the above-mentioned parameters can be inspected, collected, stored and printed regularly and dynamically. The results of a combined debugging and preliminary plant cultivation verified that the technical target of the facility had reached its initial design requirements, it can be used to conduct ground-based simulation studies of space cultivation of higher plants.}, } @article {pmid12213767, year = {2002}, author = {Mondragón-Palomino, M and Meyers, BC and Michelmore, RW and Gaut, BS}, title = {Patterns of positive selection in the complete NBS-LRR gene family of Arabidopsis thaliana.}, journal = {Genome research}, volume = {12}, number = {9}, pages = {1305-1315}, pmid = {12213767}, issn = {1088-9051}, mesh = {Amino Acid Sequence/genetics ; Arabidopsis/*genetics ; Binding Sites/genetics ; Computational Biology/methods ; Databases, Genetic ; Genes, Plant/*genetics ; Genetic Variation/genetics ; *Genome, Plant ; Immunity, Innate/genetics ; Leucine/*genetics/metabolism ; Leucine-Rich Repeat Proteins ; Molecular Sequence Data ; Multigene Family/*genetics ; Nucleotides/*genetics/metabolism ; Peptide Mapping ; Plant Diseases/genetics ; Protein Structure, Secondary/genetics ; Proteins/*genetics/metabolism ; Repetitive Sequences, Amino Acid/*genetics ; *Selection, Genetic ; }, abstract = {Plant disease resistance genes have been shown to be subject to positive selection, particularly in the leucine rich repeat (LRR) region that may determine resistance specificity. We performed a genome-wide analysis of positive selection in members of the nucleotide binding site (NBS)-LRR gene family of Arabidopsis thaliana. Analyses were possible for 103 of 163 NBS-LRR nucleotide sequences in the genome, and the analyses uncovered substantial evidence of positive selection. Sites under positive selection were detected and identified for 10 sequence groups representing 53 NBS-LRR sequences. Functionally characterized Arabidopsis resistance genes were in these 10 groups, but several groups with extensive evidence of positive selection contained no previously characterized resistance genes. Amino acid residues under positive selection were identified, and these residues were mapped onto protein secondary structure. Positively selected positions were disproportionately located in the LRR domain (P < 0.001), particularly a nine-amino acid beta-strand submotif that is likely to be solvent exposed. However, a substantial proportion (30%) of positively selected sites were located outside LRRs, suggesting that regions other than the LRR may function in determining resistance specificity. Because of the unusual sequence variability in the LRRs of this class of proteins, secondary-structure analysis identifies LRRs that are not identified by similarity analyses alone. LRRs also contain substantial indel variation, suggesting elasticity in LRR length could also influence resistance specificity.}, } @article {pmid12211037, year = {2002}, author = {Del Carpio-Muñoz, CA and Ichiishi, E and Yoshimori, A and Yoshikawa, T}, title = {MIAX: a new paradigm for modeling biomacromolecular interactions and complex formation in condensed phases.}, journal = {Proteins}, volume = {48}, number = {4}, pages = {696-732}, doi = {10.1002/prot.10122}, pmid = {12211037}, issn = {1097-0134}, mesh = {Algorithms ; Amino Acids/chemistry ; Animals ; Binding Sites ; Chymotrypsinogen/chemistry/metabolism ; Computational Biology/*methods ; Humans ; Hydrophobic and Hydrophilic Interactions ; Leukocyte Elastase/chemistry/metabolism ; Ligands ; Macromolecular Substances ; *Models, Molecular ; Molecular Structure ; Ovomucin/chemistry ; Protein Binding ; Proteins/*chemistry/*metabolism ; Sequence Homology, Amino Acid ; Solvents/chemistry ; Static Electricity ; Trypsin Inhibitor, Kazal Pancreatic/chemistry/metabolism ; Ubiquitins/chemistry/metabolism ; }, abstract = {A new paradigm is proposed for modeling biomacromolecular interactions and complex formation in solution (protein-protein interactions so far in this report) that constitutes the scaffold of the automatic system MIAX (acronym for Macromolecular Interaction Assessment X). It combines in a rational way a series of computational methodologies, the goal being the prediction of the most native-like protein complex that may be formed when two isolated (unbound) protein monomers interact in a liquid environment. The overall strategy consists of first inferring putative precomplex structures by identification of binding sites or epitopes on the proteins surfaces and a simultaneous rigid-body docking process using geometric instances alone. Precomplex configurations are defined here as all those decoys the interfaces of which comply substantially with the inferred binding sites and whose free energy values are lower. Retaining all those precomplex configurations with low energies leads to a reasonable number of decoys for which a flexible treatment is amenable. A novel algorithm is introduced here for automatically inferring binding sites in proteins given their 3-D structure. The procedure combines an unsupervised learning algorithm based on the self-organizing map or Kohonen network with a 2-D Fourier spectral analysis. To model interaction, the potential function proposed here plays a central role in the system and is constituted by empirical terms expressing well-characterized factors influencing biomacromolecular interaction processes, essentially electrostatic, van der Waals, and hydrophobic. Each of these procedures is validated by comparing results with observed instances. Finally, the more demanding process of flexible docking is performed in MIAX embedding the potential function in a simulated annealing optimization procedure. Whereas search of the entire configuration hyperspace is a major factor precluding hitherto systems from efficiently modeling macromolecular interaction modes and complex structures, the paradigm presented here may constitute a step forward in the field because it is shown that a rational treatment of the information available from the 3-D structure of the interacting monomers combined with conveniently selected computational techniques can assist to elude search of regions of low probability in configuration space and indeed lead to a highly efficient system oriented to solve this intriguing and fundamental biologic problem.}, } @article {pmid12209390, year = {2002}, author = {González-Martínez, SC and Alía, R and Gil, L}, title = {Population genetic structure in a Mediterranean pine (Pinus pinaster Ait.): a comparison of allozyme markers and quantitative traits.}, journal = {Heredity}, volume = {89}, number = {3}, pages = {199-206}, doi = {10.1038/sj.hdy.6800114}, pmid = {12209390}, issn = {0018-067X}, mesh = {Analysis of Variance ; Data Interpretation, Statistical ; Enzymes/*genetics ; Genetic Markers ; *Genetics, Population ; Pinus/enzymology/*genetics ; *Quantitative Trait, Heritable ; }, abstract = {F-statistics were employed to analyse quantitative and allozyme variation among 19 native populations of maritime pine (Pinus pinaster Ait.). Fourteen polymorphic allozyme loci were used to provide an empirical basis for constructing a null hypothesis to test natural selection as a determinant of quantitative evolution in stem form, total height growth and survival at 30 years old. Hidden biases, that may result in a difference between quantitative (Q(ST)) and allozyme (F(ST)) differentiation which are not because of the action of natural selection, were avoided by comparing pairs of populations using linear models. All quantitative traits showed higher differentiation than allozymes. The highest divergence was found in stem form, whereas divergences in total height and survival were significantly lower. Differential adaptation to regional and local patterns of precipitation, temperature and soil type seem to be the best explanation of the different structure found in quantitative traits and allozyme loci. Possible bias in the estimation of Q(ST) due to the level of quantitative within-population diversity and the role of adaptation of maritime pine after the last glaciation to highly diverse ecological conditions are discussed with special reference to the actual geographical structure of gene diversity in the species' native range.}, } @article {pmid12198901, year = {2002}, author = {Dykhno, IuA and Ivanova, IuD and Kas'ianov, VV and Laletina, IV and Khlebopros, RG}, title = {[Use of geoinformational systems for epidemiological studying malignant laryngeal neoplasms in Krasnoyarsk].}, journal = {Gigiena i sanitariia}, volume = {}, number = {3}, pages = {37-39}, pmid = {12198901}, issn = {0016-9900}, mesh = {Adult ; *Databases, Factual ; Female ; Geography ; Humans ; Laryngeal Neoplasms/*epidemiology/etiology ; Male ; Middle Aged ; Russia/epidemiology ; Small-Area Analysis ; }, abstract = {This paper shows it possible to use geoinformational systems for mapping and analyzing medical statistical data on those with malignant laryngeal neoplasms. The fact that the distribution of the patients can be shown on the map of a town in relation to the location of their houses (if they have an address) allows differentiation of the ecological living conditions of these patients, which in turn makes it possible to put not only high morbidity areas on the map of a town, but also to consider the characteristics of the environment in these areas.}, } @article {pmid12197081, year = {2002}, author = {Burnside, NG and Smith, RF and Waite, S}, title = {Habitat suitability modelling for calcareous grassland restoration on the South Downs, United Kingdom.}, journal = {Journal of environmental management}, volume = {65}, number = {2}, pages = {209-221}, doi = {10.1006/jema.2002.0546}, pmid = {12197081}, issn = {0301-4797}, mesh = {*Conservation of Natural Resources ; *Ecosystem ; Environmental Monitoring ; Forecasting ; *Geographic Information Systems ; Geological Phenomena ; Geology ; *Models, Theoretical ; *Poaceae ; Population Dynamics ; United Kingdom ; }, abstract = {The South Downs Area of Outstanding Natural Beauty, UK, is an internationally and nationally important landscape, which contains a significant proportion (28%) of the southeast of England's calcareous grassland resource. The traditional calcareous grassland habitats characteristic of the downland landscape have suffered significant losses since the Second World War, and the remaining sites are small, fragmented and confined to the more marginal areas, often steeper slopes. The re-creation and restoration of these species rich grasslands has become a central aim of national and regional conservation organisations, however, the methods and mechanism by which restoration sites could be identified has not been clarified. The purpose of this work was to study the landscape characteristics of the calcareous grassland systems, and by use of GIS-based modelling approaches identify those sites on the downland most suited to the re-establishment and expansion of calcareous grasslands. Using a weighted scoring approach, a GIS-based Habitat Suitability Model is developed for use as a tool to support strategic landscape evaluation and to provide a method of identifying sites for targeted restoration. The approach models the relationship between specific grassland communities and topographic variables, and is applied to the South Downs landscape in order to predict the nature of grassland communities likely to result from restoration efforts at specific sites.}, } @article {pmid12197075, year = {2002}, author = {Bunce, RG and Carey, PD and Elena-Rossello, R and Orr, J and Watkins, J and Fuller, R}, title = {A comparison of different biogeographical classifications of Europe, Great Britain and Spain.}, journal = {Journal of environmental management}, volume = {65}, number = {2}, pages = {121-134}, doi = {10.1006/jema.2002.0533}, pmid = {12197075}, issn = {0301-4797}, mesh = {*Climate ; England ; *Environment ; Europe ; *Geographic Information Systems ; *Models, Theoretical ; Reference Values ; Spain ; }, abstract = {Various biogeographical and bioclimatic classifications of a number of regions, countries and continents have been created to meet different objectives. A policy maker might ask the question 'why is there no single accepted classification and how do the different classifications compare with one another?' In order to answer these two questions three classifications created by different methods for Great Britain and two for Spain are compared using the Kappa statistic. All of the classifications were created from data on cellular grids with a set window size. Further non-statistical comparisons are made with other classifications. The biogeographic classifications studied in this paper produced three different types of zone: those that were always identified whatever the method; those that were broadly similar but where the boundaries differed; and those that were unique to a particular classification. These different types of zone are likely to exist for any comparison between classifications of a particular region. The extent of the geographic window from which data were obtained had a major effect on the classification of grid cells at the edges of the window. For example, the few grid cells in the south of England, with characteristics of continental Europe, are not detected if data from Great Britain alone are used for the classification. We conclude that the data window should always be larger than the area for which the classification is being made. The objective Kappa statistic, although useful, was not capable of discerning similarities and dissimilarities that appear obvious to the subjective human eye. Although the details of the classifications differed there were broad similarities between the classifications and these differences reflect important divisions along major environmental axes that have been inferred by earlier biogeographers. As the divisions are real there is a sound basis for their use in future land use or environmental policy.}, } @article {pmid12181913, year = {2002}, author = {Zhou, B and Yang, B and Lin, Q}, title = {[Establishment and applications of the spatial database of land resources information in Anshun, Guizhou Province].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {13}, number = {5}, pages = {632-634}, pmid = {12181913}, issn = {1001-9332}, mesh = {*Databases as Topic ; *Ecology ; *Environment ; Geography ; }, abstract = {For the purpose of managing and processing land resources and environment information, a spatial database of land information in Anshun City, Guizhou Province, which involved present data and the investigated information by remote sensing, was established under the supporting of PAMAP GIS 4.2. The spatial database could provide the functionality of querying for spatial data and its associated attributes, conversion between the different data formats, mapping the digital terrain, fast and accurate analysis on soil resources, land assessment and management application, and soil erosion risk mapping. The establishment of this spatial database was expected to play an important role in territorial planning, agricultural sustainable development, spatial assessment of ecological environment, and so on.}, } @article {pmid12173681, year = {2002}, author = {Stone, AA and Shiffman, S}, title = {Capturing momentary, self-report data: a proposal for reporting guidelines.}, journal = {Annals of behavioral medicine : a publication of the Society of Behavioral Medicine}, volume = {24}, number = {3}, pages = {236-243}, doi = {10.1207/S15324796ABM2403_09}, pmid = {12173681}, issn = {0883-6612}, mesh = {*Guidelines as Topic ; Humans ; Research/*standards ; *Self-Assessment ; }, abstract = {Self-report data are ubiquitous in behavioral and medical research. Retrospective assessment strategies are prone to recall bias and distortion. New techniques for assessing immediate experiences in respondents' natural environments (e.g., Ecological Momentary Assessment, Experience Sampling) are being used by many researchers to reduce reporting bias. This article discusses seven aspects of momentary research that are often overlooked or minimized in the presentation of momentary research reports, yet that are critical to the success of the research: (a) the rationale for the momentary sampling design, (b) the details of momentary sampling procedures, (c) the data acquisition interface, (d) rates of compliance with the sampling plan, (e) the procedures used to train and monitor participants, (f) data management procedures, and (g) the data analytic approach. Attention to these areas in both the design and reporting of momentary research studies will not only improve momentary research protocols but also allow for the successful replication of research findings by other investigators.}, } @article {pmid12149438, year = {2002}, author = {Gavrilets, S and Waxman, D}, title = {Sympatric speciation by sexual conflict.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {99}, number = {16}, pages = {10533-10538}, pmid = {12149438}, issn = {0027-8424}, mesh = {Adaptation, Physiological/*genetics ; Alleles ; Data Interpretation, Statistical ; *Evolution, Molecular ; Female ; Humans ; Male ; *Models, Genetic ; Numerical Analysis, Computer-Assisted ; *Sex Characteristics ; Species Specificity ; }, abstract = {It is well established that sexual conflict can drive an endless coevolutionary chase between the sexes potentially leading to genetic divergence of isolated populations and allopatric speciation. We present a simple mathematical model that shows that sexual conflict over mating rate can result in two other general regimes. First, rather than "running away" from males, females can diversify genetically into separate groups, effectively "trapping" the males in the middle at a state characterized by reduced mating success. Female diversification brings coevolutionary chase to the end. Second, under certain conditions, males respond to female diversification by diversifying themselves. This response results in the formation of reproductively isolated clusters of genotypes that emerge sympatrically.}, } @article {pmid12148075, year = {2002}, author = {Bojórquez-Tapia, LA and Juárez, L and Cruz-Bello, G}, title = {Integrating fuzzy logic, optimization, and GIS for ecological impact assessments.}, journal = {Environmental management}, volume = {30}, number = {3}, pages = {418-433}, doi = {10.1007/s00267-002-2655-1}, pmid = {12148075}, issn = {0364-152X}, mesh = {Decision Making ; *Ecology ; Ecosystem ; Environment ; Environmental Monitoring/*methods ; Forecasting ; *Fuzzy Logic ; *Geography ; *Information Systems ; Policy Making ; Sensitivity and Specificity ; }, abstract = {Appraisal of ecological impacts has been problematic because of the behavior of ecological system and the responses of these systems to human intervention are far from fully understood. While it has been relatively easy to itemize the potential ecological impacts, it has been difficult to arrive at accurate predictions of how these impacts affect populations, communities, or ecosystems. Furthermore, the spatial heterogeneity of ecological systems has been overlooked because its examination is practically impossible through matrix techniques, the most commonly used impact assessment approach. Besides, the public has become increasingly aware of the importance of the EIA in decision-making and thus the interpretation of impact significance is complicated further by the different value judgments of stakeholders. Moreover, impact assessments are carried out with a minimum of data, high uncertainty, and poor conceptual understanding. Hence, the evaluation of ecological impacts entails the integration of subjective and often conflicting judgments from a variety of experts and stakeholders. The purpose of this paper is to present an environmental impact assessment approach based on the integration fuzzy logic, geographical information systems and optimization techniques. This approach enables environmental analysts to deal with the intrinsic imprecision and ambiguity associated with the judgments of experts and stakeholders, the description of ecological systems, and the prediction of ecological impacts. The application of this approach is illustrated through an example, which shows how consensus about impact mitigation can be attained within a conflict resolution framework.}, } @article {pmid12144664, year = {2002}, author = {Wilke, T and Pfenninger, M}, title = {Separating historic events from recurrent processes in cryptic species: phylogeography of mud snails (Hydrobia spp.).}, journal = {Molecular ecology}, volume = {11}, number = {8}, pages = {1439-1451}, doi = {10.1046/j.1365-294x.2002.01541.x}, pmid = {12144664}, issn = {0962-1083}, mesh = {Animals ; Biological Evolution ; Data Interpretation, Statistical ; Ecosystem ; Environment ; *Genetic Variation ; Likelihood Functions ; Molecular Sequence Data ; Phylogeny ; Snails/classification/*genetics ; }, abstract = {The present study combines methods that were designed to infer intraspecific relationships (e.g. nested-clade analysis (NCA), mismatch distributions and maximum likelihood gene flow analysis) to analyse historic events and recurrent processes in the cryptic mud snail species Hydrobia acuta and H. glyca. Specifically, we test the proposed allopatry of cryptic species and whether the peculiar range-subdivision of the putative subspecies H. a. acuta and H. a. neglecta is a result of long-distance dispersal or continuous range expansion. The NCA indicates a past fragmentation of the two H. acuta subspecies as well as past fragmentations within H. glyca. Gene-flow analyses show extensive gene flow in an E-W direction (towards the Atlantic) in the Mediterranean H. a. acuta, generally low gene flow in a W-E direction in the Atlantic H. a. neglecta and complex gene-flow pattern in a N-S but also in a S-N direction (against the Gulf Stream) in H. glyca. Based on these data and supportive ecological and oceanographical data, we hypothesize that the separation of the two H. acuta subspecies was not caused by long-distance dispersal but by a range shift and/or range expansion of the closely related competitor H. glyca as a result of an interglacial warming with a subsequent range shift in H. acuta. Moreover, our data do not show evidence for a long-term, stable sympatry of Hydrobia species, supporting the concept of allopatric relationships within cryptic radiations. NCA and gene-flow analyses indicate that the only sympatric population found in our study is the result of a recent dispersal event from the nearby Mediterranean. It is assumed that allopatric relationships in ephemeral Hydrobia populations constitute an evolutionary advantage relative to competition, recruitment and re-establishment of habitats. Mechanisms that could be of relevance for maintaining allopatry are discussed.}, } @article {pmid12140334, year = {2002}, author = {Ashelford, KE and Weightman, AJ and Fry, JC}, title = {PRIMROSE: a computer program for generating and estimating the phylogenetic range of 16S rRNA oligonucleotide probes and primers in conjunction with the RDP-II database.}, journal = {Nucleic acids research}, volume = {30}, number = {15}, pages = {3481-3489}, pmid = {12140334}, issn = {1362-4962}, mesh = {Algorithms ; Bacteria/classification/genetics ; *DNA Primers ; *Databases, Nucleic Acid ; *Oligonucleotide Probes ; *Phylogeny ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/*genetics ; *Software ; Software Design ; }, abstract = {We describe PRIMROSE, a computer program for identifying 16S rRNA probes and PCR primers for use as phylogenetic and ecological tools in the identification and enumeration of bacteria. PRIMROSE is designed to use data from the Ribosomal Database Project (RDP) to find potentially useful oligonucleotides with up to two degenerate positions. The taxonomic range of these, and other existing oligonucleotides, can then be explored, allowing for the rapid identification of suitable oligonucleotides. PRIMROSE includes features to allow user-defined sequence databases to be used. An in silico trial of the program using the RDP database identified oligonucleotides that described their target taxa with a degree of accuracy far greater than that of equivalent currently used oligonucleotides. We identify oligonucleotides for subdivisions of the Proteobacteria and for the Cytophaga-Flexibacter-Bacteroides (CFB) division. These oligonucleotides describe up to 94.7% of their target taxon with fewer than 50 non-target hits, and the authors recommend that they be investigated further. A comparison with PROBE DESIGN within the ARB software package shows that PRIMROSE is capable of identifying oligonucleotides with a higher specificity. PRIMROSE has an intuitive graphical user interface and runs on the Microsoft Windows 95/NT/2000 operating systems. It is open source and is freely available from the authors.}, } @article {pmid12112556, year = {2002}, author = {Kaneko, S and Yoshimura, T and Ikemura, K and Shirasuna, K and Kusukawa, J and Ohishi, M and Shiba, R and Sunakawa, H and Tominaga, K and Sugihara, K and Shinohara, M and Katsuki, T and Yanagisawa, S and Kurokawa, H and Mimura, T and Ikeda, H and Yamabe, S and Ozeki, S}, title = {Primary neck management among patients with cancer of the oral cavity without clinical nodal metastases: A decision and sensitivity analysis.}, journal = {Head & neck}, volume = {24}, number = {6}, pages = {582-590}, doi = {10.1002/hed.10101}, pmid = {12112556}, issn = {1043-3074}, mesh = {Carcinoma, Squamous Cell/mortality/*pathology/surgery ; *Decision Support Techniques ; Decision Trees ; Humans ; *Lymph Node Excision ; Lymphatic Metastasis ; Mouth Neoplasms/mortality/*pathology/*surgery ; Palatal Neoplasms/mortality/surgery ; Tongue Neoplasms/mortality/surgery ; }, abstract = {BACKGROUND: A standardized neck management strategy for oral cancer patients without clinical nodal metastases remains to be established. Consequently, a decision and sensitivity analysis of two neck management protocols, involving either prophylactic neck dissection or careful observation, was conducted using the Oral Cancer Registry of Kyushu, Japan.

METHODS: We calculated probabilities of subclinical nodal metastases and 5-year survival using the registry data. A two-way sensitive analysis was conducted using the probabilities and parameters of the complete nodal metastasis resection rate (x) and a utility rating that describes the health state induced by dissection (y) compared with the neck condition in a careful-observation group.

RESULTS: We solved the threshold curve for y and x for the expected utility between the two groups. The results showed that prophylactic neck dissection must guarantee a complete resection of subclinical nodal metastases with no disadvantage to health state to be evaluated as equally satisfactory as careful observation.

CONCLUSIONS: Careful observation involving standardized systematic preoperative and postoperative screening of the neck seems preferable to prophylactic neck dissection for oral cancer patients without subclinical nodal metastases.}, } @article {pmid12109754, year = {2002}, author = {Grist, EP and Leung, KM and Wheeler, JR and Crane, M}, title = {Better bootstrap estimation of hazardous concentration thresholds for aquatic assemblages.}, journal = {Environmental toxicology and chemistry}, volume = {21}, number = {7}, pages = {1515-1524}, pmid = {12109754}, issn = {0730-7268}, mesh = {Data Interpretation, Statistical ; Hazardous Substances/*toxicity ; No-Observed-Adverse-Effect Level ; Regression Analysis ; Risk Assessment/statistics & numerical data ; *Statistical Distributions ; Water Pollution, Chemical/*statistics & numerical data ; }, abstract = {The introduction of species sensitivity distribution (SSD) approaches to ecological risk assessment offers the potential for a more transparent scientific basis for the derivation of predicted no-effect concentrations. However, conventional SSD methodologies have relied on standard distributions (e.g., log logistic, log normal) that are not necessarily based on sound ecological or statistical grounds. More recently, bootstrap resampling techniques that do not rely on distributional assumptions have been applied to the problem. Here we describe how a more advanced bootstrap methodology may be applied to derive better point estimates and confidence intervals for SSD estimates of safe environmental concentrations. Motivated by the fact that the true SSD may not fit any standard model category, we go on to consider a hybrid bootstrap regression approach. This can yield a substantially different estimate for the SSD when compared with both the basic bootstrap and the more frequently used parametric curve approaches. With increasing use of SSDs in ecological risk assessment, it is now imperative that the scientific community develops agreement over appropriate methods for their derivation.}, } @article {pmid12089052, year = {2002}, author = {Hagström, A and Pommier, T and Rohwer, F and Simu, K and Stolte, W and Svensson, D and Zweifel, UL}, title = {Use of 16S ribosomal DNA for delineation of marine bacterioplankton species.}, journal = {Applied and environmental microbiology}, volume = {68}, number = {7}, pages = {3628-3633}, pmid = {12089052}, issn = {0099-2240}, mesh = {Bacteria/classification/*genetics ; DNA, Bacterial/analysis ; Databases, Nucleic Acid ; Marine Biology ; RNA, Ribosomal, 16S/*genetics ; Water Microbiology ; }, abstract = {All of the marine bacterioplankton-derived 16S ribosomal DNA sequences previously deposited in GenBank were reanalyzed to determine the number of bacterial species in the oceanic surface waters. These sequences have been entered into the database since 1990. The rate of new additions reached a peak in 1999 and subsequently leveled off, suggesting that much of the marine microbial species richness has been sampled. When the GenBank sequences were dereplicated by using 97% similarity as a cutoff, 1,117 unique ribotypes were found. Of the unique sequences, 609 came from uncultured environmental clones and 508 came from cultured bacteria. We conclude that the apparent bacterioplankton species richness is relatively low.}, } @article {pmid12086536, year = {2002}, author = {Lei, J and Zhou, J}, title = {A marine natural product database.}, journal = {Journal of chemical information and computer sciences}, volume = {42}, number = {3}, pages = {742-748}, doi = {10.1021/ci010111x}, pmid = {12086536}, issn = {0095-2338}, mesh = {*Biological Factors ; *Databases as Topic ; Information Storage and Retrieval ; *Marine Biology ; }, abstract = {A database of marine natural products has been developed. The database contains approximately 6000 chemical compounds derived from over 10,000 marine-derived materials. For each compound, the structure, physical and chemical properties, marine source, and biological activities are given. A computer program for searching this database has also been developed and is described.}, } @article {pmid12082137, year = {2002}, author = {Birdsell, JA}, title = {Integrating genomics, bioinformatics, and classical genetics to study the effects of recombination on genome evolution.}, journal = {Molecular biology and evolution}, volume = {19}, number = {7}, pages = {1181-1197}, doi = {10.1093/oxfordjournals.molbev.a004176}, pmid = {12082137}, issn = {0737-4038}, mesh = {AT Rich Sequence/genetics ; Animals ; *Computational Biology ; *Evolution, Molecular ; GC Rich Sequence/*genetics ; Gene Conversion ; Genetic Variation ; *Genomics ; Humans ; Models, Genetic ; Mutation ; *Recombination, Genetic ; Selection, Genetic ; }, abstract = {This study presents compelling evidence that recombination significantly increases the silent GC content of a genome in a selectively neutral manner, resulting in a highly significant positive correlation between recombination and "GC3s" in the yeast Saccharomyces cerevisiae. Neither selection nor mutation can explain this relationship. A highly significant GC-biased mismatch repair system is documented for the first time in any member of the Kingdom Fungi. Much of the variation in the GC3s within yeast appears to result from GC-biased gene conversion. Evidence suggests that GC-biased mismatch repair exists in numerous organisms spanning six kingdoms. This transkingdom GC mismatch repair bias may have evolved in response to a ubiquitous AT mutational bias. A significant positive correlation between recombination and GC content is found in many of these same organisms, suggesting that the processes influencing the evolution of the yeast genome may be a general phenomenon. Nonrecombining regions of the genome and nonrecombining genomes would not be subject to this type of molecular drive. It is suggested that the low GC content characteristic of many nonrecombining genomes may be the result of three processes (1) a prevailing AT mutational bias, (2) random fixation of the most common types of mutation, and (3) the absence of the GC-biased gene conversion which, in recombining organisms, permits the reversal of the most common types of mutation. A model is proposed to explain the observation that introns, intergenic regions, and pseudogenes typically have lower GC content than the silent sites of corresponding open reading frames. This model is based on the observation that the greater the heterology between two sequences, the less likely it is that recombination will occur between them. According to this "Constraint" hypothesis, the formation and propagation of heteroduplex DNA is expected to occur, on average, more frequently within conserved coding and regulatory regions of the genome. In organisms possessing GC-biased mismatch repair, this would enhance the GC content of these regions through biased gene conversion. These findings have a number of important implications for the way we view genome evolution and suggest a new model for the evolution of sex.}, } @article {pmid12079659, year = {2002}, author = {Clegg, SM and Owens, IP}, title = {The 'island rule' in birds: medium body size and its ecological explanation.}, journal = {Proceedings. Biological sciences}, volume = {269}, number = {1498}, pages = {1359-1365}, pmid = {12079659}, issn = {0962-8452}, mesh = {Analysis of Variance ; Animals ; Beak/anatomy & histology ; *Biological Evolution ; Birds/*anatomy & histology ; Body Constitution ; Body Weight ; Databases, Factual ; *Ecosystem ; *Geography ; *Models, Biological ; }, abstract = {Do birds show a different pattern of insular evolution from mammals? Mammals follow the 'island rule', with large-bodied species getting smaller on islands and small-bodied species getting bigger. By contrast, the traditional view on birds is that they follow no general island rule for body size, but that there is an insular trend for large bills. Insular shifts in feeding ecology are, therefore, widely assumed to be the primary cause of divergence in island birds. We use a comparative approach to test these ideas. Contrary to the traditional view, we find no evidence for increased bill size in insular populations. Instead, changes in both bill size and body size obey the 'island rule'. The differences between our results and the traditional view arise because previous analyses were based largely on passerines. We also investigate some ecological factors that are thought to influence island evolution. As predicted by the traditional view, shifts in bill size are associated with feeding ecology. By contrast, shifts in body size are associated with the potential for intraspecific competition and thermal ecology. All these results remain qualitatively unchanged when we use different methods to score the ecological factors and restrict our analyses to taxa showing pronounced morphological divergence. Because of strong covariation between ecological factors, however, we cannot estimate the relative importance of each ecological factor. Overall, our results show that the island rule is valid for both body size and bill length in birds and that, in addition to feeding ecology, insular shifts in the level of intraspecific competition and the abiotic environment also have a role.}, } @article {pmid12067416, year = {2002}, author = {Del Carpio, CA and Hennig, T and Fickel, S and Yoshimori, A}, title = {A combined bioinformatic approach oriented to the analysis and design of peptides with high affinity to MHC class I molecules.}, journal = {Immunology and cell biology}, volume = {80}, number = {3}, pages = {286-299}, doi = {10.1046/j.1440-1711.2002.01090.x}, pmid = {12067416}, issn = {0818-9641}, mesh = {Algorithms ; Amino Acids/metabolism ; Binding Sites ; Computational Biology/*methods ; Computer-Aided Design/instrumentation ; Decision Making, Computer-Assisted ; Genes, MHC Class I ; HLA-A Antigens/analysis/classification/metabolism ; HLA-A2 Antigen/analysis/classification/metabolism ; HLA-A24 Antigen ; Histocompatibility Antigens Class I/*metabolism ; Humans ; Hydrophobic and Hydrophilic Interactions ; Peptides/*analysis/*chemistry ; Protein Binding ; Receptors, Antigen/immunology/metabolism ; Static Electricity ; }, abstract = {We report on a new method to compute the antigenic degree of peptides from available experimental data on peptide binding affinity to class I MHC molecules. The methodology is a combination of two strategies at different levels of information. The first, at the primary structure level, consists in expressing the peptides binding activity as a profile of amino acid contributions, amino acid similarity being accounted for by their characteristic physicochemical properties and their position within the sequence. The higher level of the strategy is based on a meticulous analysis of the contact interface of the peptides with the cleft constituting the receptor region of a particular class I MHC molecule. Interaction interfaces are inferred by docking the peptide onto the receptor groove of the MHC molecule; evaluation of the affinity of the peptide to the receptor is then performed by analysis of the electrostatic and hydrophobic energies on points of the interaction interface. The result is a robust system for analysis of peptide affinity to class I MHC molecules since while the first analysis dictates the composition of active sequences at the amino acid level, the second translates this information to the atomic level, where the molecular interaction can be analyzed in terms of the intrinsic interatomic forces and energies. Evaluation results for the methodology are encouraging since high affinity peptides are reflected by high scores at both levels of information, and are proportionally lower for peptides of medium and lower affinity for which interaction surfaces show relatively lower electrostatic complementarity and hydrophobic correlation than for the former.}, } @article {pmid12053238, year = {2002}, author = {Ostwald, M}, title = {GIS-based support tool system for decision-making regarding local forest protection: illustrations from Orissa, India.}, journal = {Environmental management}, volume = {30}, number = {1}, pages = {35-45}, doi = {10.1007/s00267-002-2471-7}, pmid = {12053238}, issn = {0364-152X}, mesh = {*Conservation of Natural Resources ; Ecology ; Environment ; *Environmental Monitoring ; Forecasting ; *Forestry ; *Geography ; Humans ; India ; *Information Systems ; Policy Making ; Risk Assessment ; Trees ; }, abstract = {A support tool system comprising risk and priority analyses was illustrated in a geographical information system environment and also tested with data from two forest protection areas for comparison of the system output. The system is recommended as a management monitoring tool for areas where village forest protection at a local level is taking place. The geographical area in the eastern part of India is subject to scarcity of forest resources and is representative in the context of widespread occurrence of local forest protection. Data used were topography, hectares protected, population census, distance to forest and other villages, degree of forest regeneration, presence of plantations, age of protection, surrounding forest resources, and population mix. Methods used were digitizing information for the systems' different layers, analyses of satellite information, field work, gathering of local information, and the application of five risk/priority analyses: erosion, ecological and institutional sustainability, conflict, and degree of dependency. Questions asked were how the different analyses should be interpreted and how the system could be kept updated. The results show that the system needs resource-demanding and field assistance to be kept dynamic. The system is also dependent on the interpretations of the analyses. The limits or levels of assistance for forest management depend on the resources available. The system illustrates how a tool can be utilized for decisions regarding input of resources. It can further be very useful in defining and comparing different areas in order to detect areas in need of assistance and the type of help needed.}, } @article {pmid12040915, year = {2002}, author = {Kistemann, T and Dangendorf, F and Schweikart, J}, title = {New perspectives on the use of Geographical Information Systems (GIS) in environmental health sciences.}, journal = {International journal of hygiene and environmental health}, volume = {205}, number = {3}, pages = {169-181}, doi = {10.1078/1438-4639-00145}, pmid = {12040915}, issn = {1438-4639}, mesh = {Ecology ; *Environmental Health ; Epidemiologic Studies ; *Geographic Information Systems ; Humans ; Seasons ; Spacecraft ; Time Factors ; }, abstract = {At first glance, the domain of health is no typical area to applicate Geographical Information Systems (GIS). Nevertheless, the recent development clearly shows that also within the domains of environmental health, disease ecology and public health GIS have become an indispensable tool for processing, analysing and visualising spatial data. In the field of geographical epidemiology, GIS are used for drawing up disease maps and for ecological analysis. The striking advantages of GIS for the disease mapping process are the considerably simplified generation and variation of maps as well as a broader variety in terms of determining a real units. In the frame of ecological analysis, GIS can significantly assist with the assessment of the distribution of health-relevant environmental factors via interpolation and modelling. On the other hand, the GIS-supported methods for the detection of striking spatial patterns of disease distribution need to be much improved. An important topic in this respect is the integration of the time dimension. The increasing use of remote sensing as well as the integration into internet functionalities will stimulate the application of GIS in the field of Environmental Health Sciences (EHS). In future, the integration and analysis of health-relevant data in one single data system will open up many new research opportunities.}, } @article {pmid12037565, year = {2002}, author = {Jernvall, J and Fortelius, M}, title = {Common mammals drive the evolutionary increase of hypsodonty in the Neogene.}, journal = {Nature}, volume = {417}, number = {6888}, pages = {538-540}, doi = {10.1038/417538a}, pmid = {12037565}, issn = {0028-0836}, mesh = {Animals ; *Biological Evolution ; Databases, Factual ; Diet ; Europe ; Food Chain ; *Fossils ; Mammals/*anatomy & histology/*classification ; Plants ; Species Specificity ; Tooth/*anatomy & histology/*physiology ; }, abstract = {During the past 20 million years, herbivorous mammals of numerous lineages have evolved hypsodont, or high-crowned, cheek teeth. Hypsodonty is informative ecologically because it is well developed in mammals eating fibrous and abrasive foods that are most abundant in open and generally or seasonally dry environments. Here we report that in the Neogene of Europe mammals with the greatest locality coverages showed an increase in hypsodonty. We used a data set of 209 localities to measure whether large mammals occurring in many fossil localities show a similar increase in hypsodonty to mammals occurring in single or few localities. Taxonomic and morphological groupings show a low average hypsodonty in the early Miocene epoch. From the middle Miocene onwards, only the hypsodonty of commonly found mammals shows a marked increase. Therefore, in the drying Europe of the late Miocene, only increasingly hypsodont mammals may have been able to expand their share of habitats and food resources. These results suggest that the relatively small number of species known from multiple localities are palaeoecologically informative by themselves, irrespective of the rest of the known species.}, } @article {pmid12037520, year = {2002}, author = {Murdoch, WW and Kendall, BE and Nisbet, RM and Briggs, CJ and McCauley, E and Bolser, R}, title = {Single-species models for many-species food webs.}, journal = {Nature}, volume = {417}, number = {6888}, pages = {541-543}, doi = {10.1038/417541a}, pmid = {12037520}, issn = {0028-0836}, mesh = {Animals ; Databases, Factual ; *Food Chain ; *Models, Biological ; Population Dynamics ; Predatory Behavior ; Reproducibility of Results ; Species Specificity ; }, abstract = {Most species live in species-rich food webs; yet, for a century, most mathematical models for population dynamics have included only one or two species. We ask whether such models are relevant to the real world. Two-species population models of an interacting consumer and resource collapse to one-species dynamics when recruitment to the resource population is unrelated to resource abundance, thereby weakening the coupling between consumer and resource. We predict that, in nature, generalist consumers that feed on many species should similarly show one-species dynamics. We test this prediction using cyclic populations, in which it is easier to infer underlying mechanisms, and which are widespread in nature. Here we show that one-species cycles can be distinguished from consumer resource cycles by their periods. We then analyse a large number of time series from cyclic populations in nature and show that almost all cycling, generalist consumers examined have periods that are consistent with one-species dynamics. Thus generalist consumers indeed behave as if they were one-species populations, and a one-species model is a valid representation for generalist population dynamics in many-species food webs.}, } @article {pmid12034847, year = {2002}, author = {Caetano-Anollés, G}, title = {Tracing the evolution of RNA structure in ribosomes.}, journal = {Nucleic acids research}, volume = {30}, number = {11}, pages = {2575-2587}, pmid = {12034847}, issn = {1362-4962}, mesh = {Animals ; Base Sequence ; Binding Sites ; Databases, Nucleic Acid ; *Evolution, Molecular ; Humans ; Molecular Sequence Data ; *Nucleic Acid Conformation ; Phylogeny ; RNA, Ribosomal/*chemistry/genetics/metabolism ; RNA, Transfer/chemistry/genetics/metabolism ; Ribosomes/chemistry/*genetics/metabolism ; Sequence Alignment ; }, abstract = {The elucidation of ribosomal structure has shown that the function of ribosomes is fundamentally confined to dynamic interactions established between the RNA components of the ribosomal ensemble. These findings now enable a detailed analysis of the evolution of ribosomal RNA (rRNA) structure. The origin and diversification of rRNA was studied here using phylogenetic tools directly at the structural level. A rooted universal tree was reconstructed from the combined secondary structures of large (LSU) and small (SSU) subunit rRNA using cladistic methods and considerations in statistical mechanics. The evolution of the complete repertoire of structural ribosomal characters was formally traced lineage-by-lineage in the tree, showing a tendency towards molecular simplification and a homogeneous reduction of ribosomal structural change with time. Character tracing revealed patterns of evolution in inter-subunit bridge contacts and tRNA-binding sites that were consistent with the proposed coupling of tRNA translocation and subunit movement. These patterns support the concerted evolution of tRNA-binding sites in the two subunits and the ancestral nature and common origin of certain structural ribosomal features, such as the peptidyl (P) site, the functional relay of the penultimate stem helix of SSU rRNA, and other structures participating in ribosomal dynamics. Overall results provide a rare insight into the evolution of ribosomal structure.}, } @article {pmid12029169, year = {2000}, author = {Wolfe, EW and Dozier, H}, title = {Development of a scale for measuring invasive plant environmentalism.}, journal = {Journal of applied measurement}, volume = {1}, number = {3}, pages = {219-237}, pmid = {12029169}, issn = {1529-7713}, mesh = {*Attitude ; Conservation of Natural Resources/*statistics & numerical data ; Data Collection ; *Data Interpretation, Statistical ; Humans ; Personality Tests/*statistics & numerical data ; *Plant Development ; Psychometrics/methods ; }, abstract = {The ecological impact of invasive plant species is a serious concern among environmental scientists and conservationists. Educating the public about invasive plant issues is a major hurdle, given that several invaders come into the environment through ornamental gardening. An important first step in planning an educational program concerning invasive plant issues is to assess public knowledge and attitudes concerning these issues. This paper describes the development of an instrument that measures invasive plant environmentalism. Responses from 237 nursery customers from the southeastern U.S. to a 17-item standardized interview were scaled using the partial credit model, a member of the family of Rasch (1960) measurement models. Our results indicate that the instrument adequately measures this construct. Substantive interpretations of the results are also discussed.}, } @article {pmid12028760, year = {2002}, author = {Semple, S and Cowlishaw, G and Bennett, PM}, title = {Immune system evolution among anthropoid primates: parasites, injuries and predators.}, journal = {Proceedings. Biological sciences}, volume = {269}, number = {1495}, pages = {1031-1037}, pmid = {12028760}, issn = {0962-8452}, mesh = {Animals ; *Biological Evolution ; Databases, Factual ; Ecosystem ; Environment ; Haplorhini/*immunology/parasitology ; Immune System/*physiology ; Leukocyte Count ; Male ; *Predatory Behavior ; Regression Analysis ; Species Specificity ; Wounds and Injuries ; }, abstract = {In this study we investigate whether present-day variation in a key component of the immune system (baseline leucocyte concentrations) represents evolutionary adaptation to ecological factors. In particular, we test three hypotheses, namely that leucocyte concentrations will be positively related to one of the following: risk of disease transmission between hosts, which is related to host abundance (hypothesis 1), risk of disease infection from the environment due to parasite viability and abundance (hypothesis 2), and risk of injury and subsequent infection, for example following attacks by predators (hypothesis 3). No support was found for hypothesis 1: neither population density nor group size were associated with variation in leucocyte concentrations. Hypothesis 2 was supported: for both sexes, lymphocyte and phagocyte concentrations were positively correlated with annual rainfall, as predicted if interspecific variation in the immune system is related to parasite prevalence (primates suffer higher rates of parasitism in wetter habitats). Support was also provided for hypothesis 3: for both males and females, platelet concentrations were negatively related to body mass, as predicted if injury risk affects immune system evolution, because animals with larger body mass have a relatively lower surface area available to injury. Additional support was provided for hypothesis 3 by the finding that for males, the sex which plays the active role in troop defence and retaliation against predators, concentration of platelets was positively correlated with rate of predation. In conclusion, our analysis suggests that the risk of disease infection from the environment and the risk of injury have played a key role in immune system evolution among anthropoid primates.}, } @article {pmid12028736, year = {2002}, author = {Ferrier, S}, title = {Mapping spatial pattern in biodiversity for regional conservation planning: where to from here?.}, journal = {Systematic biology}, volume = {51}, number = {2}, pages = {331-363}, doi = {10.1080/10635150252899806}, pmid = {12028736}, issn = {1063-5157}, mesh = {Algorithms ; Animals ; Computational Biology/methods ; Ecology ; *Ecosystem ; Environment ; Plants/genetics ; }, abstract = {Vast gaps in available information on the spatial distribution of biodiversity pose a major challenge for regional conservation planning in many parts of the world. This problem is often addressed by basing such planning on various biodiversity surrogates. In some situations, distributional data for selected taxa may be used as surrogates for biodiversity as a whole. However, this approach is less effective in data-poor regions, where there may be little choice but to base conservation planning on some form of remote environmental mapping, derived, for example, from interpretation of satellite imagery or from numerical classification of abiotic environmental layers. Although this alternative approach confers obvious benefits in terms of cost-effectiveness and rapidity of application, problems may arise if congruence is poor between mapped land-classes and actual biological distributions. I propose three strategies for making more effective use of available biological data and knowledge to alleviate such problems by (1) more closely integrating biological and environmental data through predictive modeling, with increased emphasis on modeling collective properties of biodiversity rather than individual entities; (2) making more rigorous use of remotely mapped surrogates in conservation planning by incorporating knowledge of heterogeneity within land-classes, and of varying levels of distinctiveness between classes, into measures of conservation priority and achievement; and (3) using relatively data-rich regions as test-beds for evaluating the performance of surrogates that can be readily applied across data-poor regions.}, } @article {pmid12028735, year = {2002}, author = {Desmet, PG and Cowling, RM and Ellis, AG and Pressey, RL}, title = {Integrating biosystematic data into conservation planning: perspectives from southern Africa's Succulent Karoo.}, journal = {Systematic biology}, volume = {51}, number = {2}, pages = {317-330}, doi = {10.1080/10635150252899798}, pmid = {12028735}, issn = {1063-5157}, mesh = {Africa ; Classification ; Computational Biology/*methods ; Ecology ; *Ecosystem ; Evolution, Molecular ; Plants/genetics ; Software ; }, abstract = {In this paper we explore the role that biosystematists can play in conservation planning. Conservation planning concerns the location and design of reserves that both represent the biodiversity of a region and enable the persistence of that biodiversity by maintaining key ecological and evolutionary processes. For conservation planning to be effective, quantitative targets are needed for the spatial components of a region that reflect evolutionary processes. Using examples from southern Africa's Succulent Karoo, we demonstrate how spatially explicit data on morphological variation within taxa provide essential information for conservation planning in that such variation represents an important surrogate for the spatial component of lineage diversification. We also provide an example of how the spatial components of evolutionary processes can be identified and targeted for conservation action. Key to this understanding are the recognition and description of taxonomic units at all spatial scales. Without the recognition of subspecific variation, it is difficult to formulate evolutionary hypotheses, let alone set quantitative targets for the conservation of this variation. Given the escalating threats to biodiversity, and the importance of planning for persistence by incorporating ecological and evolutionary processes into conservation plans, it is essential that systematists develop hypotheses on the spatial surrogates for these processes for a wide range of lineages. The important questions for systematists to be asking are (1) how is variation distributed in the landscape, and (2) how did it come about? Conservation planners too need to highlight these spatial components for conservation action.}, } @article {pmid12028734, year = {2002}, author = {Funk, VA and Richardson, KS}, title = {Systematic data in biodiversity studies: use it or lose it.}, journal = {Systematic biology}, volume = {51}, number = {2}, pages = {303-316}, doi = {10.1080/10635150252899789}, pmid = {12028734}, issn = {1063-5157}, mesh = {Computational Biology/*methods ; Ecology ; *Ecosystem ; Environment ; *Evolution, Molecular ; Guyana ; Models, Statistical ; Plants/genetics ; Software ; Species Specificity ; Statistics as Topic/methods ; Temperature ; }, abstract = {Systematic data in the form of collections data are useful in biodiversity studies in many ways, most importantly because they serve as the only direct evidence of species distributions. However, collecting bias has been demonstrated for most areas of the world and has led some to propose methods that circumvent the need for collections data. New methods that model collections data in combination with abiotic data and predict potential total species distribution are examined using 25,111 records representing 5,123 species of plants and animals from Guyana; some methods use the reduced number of 320 species. These modeled species distributions are evaluated and potential high-priority biodiversity sites are selected based on the concept of irreplaceability, a measure of uniqueness. The major impediments to using collections data are the lack of data that are available in a useful format and the reluctance of most systematists to become involved in biodiversity and conservation research.}, } @article {pmid12028730, year = {2002}, author = {Funk, VA and Sakai, AK and Richardson, K}, title = {Biodiversity: the interface between systematics and conservation.}, journal = {Systematic biology}, volume = {51}, number = {2}, pages = {235-237}, doi = {10.1080/10635150252899743}, pmid = {12028730}, issn = {1063-5157}, mesh = {Animals ; Biological Evolution ; *Computational Biology ; Ecology ; *Ecosystem ; }, } @article {pmid12028728, year = {2002}, author = {Legendre, P and Makarenkov, V}, title = {Reconstruction of biogeographic and evolutionary networks using reticulograms.}, journal = {Systematic biology}, volume = {51}, number = {2}, pages = {199-216}, doi = {10.1080/10635150252899725}, pmid = {12028728}, issn = {1063-5157}, mesh = {Algorithms ; Animals ; Arvicolinae ; *Computational Biology ; *Evolution, Molecular ; Fishes ; Models, Genetic ; Models, Statistical ; Phylogeny ; Software ; }, abstract = {A reticulogram is a general network capable of representing a reticulate evolutionary structure. It is particularly useful for portraying relationships among organisms that may be related in a nonunique way to their common ancestor - relationships that cannot be represented by a dendrogram or a phylogenetic tree. We propose a new method for constructing reticulograms that represent a given distance matrix. Reticulate evolution applies first to phylogenetic problems; it has been found in nature, for example, in the within-species microevolution of eukaryotes and in lateral gene transfer in bacteria. In this paper, we propose a new method for reconstructing reticulation networks and we develop applications of the reticulate evolution model to ecological biogeographic, population microevolutionary, and hybridization problems. The first example considers a spatially constrained reticulogram representing the postglacial dispersal of freshwater fishes in the Québec peninsula; the reticulogram provides a better model of postglacial dispersal than does a tree model. The second example depicts the morphological similarities among local populations of muskrats in a river valley in Belgium; adding supplementary branches to a tree depicting the river network leads to a better representation of the morphological distances among local populations of muskrats than does a tree structure. A third example involves hybrids between plants of the genus Aphelandra.}, } @article {pmid12020894, year = {2002}, author = {Brooker, S}, title = {Schistosomes, snails and satellites.}, journal = {Acta tropica}, volume = {82}, number = {2}, pages = {207-214}, doi = {10.1016/s0001-706x(02)00012-8}, pmid = {12020894}, issn = {0001-706X}, mesh = {Africa South of the Sahara/epidemiology ; Animals ; Child ; Databases, Factual ; *Ecology ; Humans ; Logistic Models ; Prevalence ; Preventive Health Services/*economics/organization & administration ; Risk ; *Schistosomiasis/epidemiology/prevention & control ; *Snails ; *Spacecraft ; }, abstract = {This paper gives an overview of the recent progress made in the use and application of geographical information systems (GIS) and remotely sensed (RS) satellite sensor data for the epidemiology and control of schistosomiasis in sub-Saharan Africa. Details are given of the use of GIS to collate, map and analyse available parasitological data. The use of RS data to understand better the broad scale environmental factors influencing schistosome distribution is defined and examples detailed for the prediction of schistosomiasis in unsampled areas. Finally, the current practical application of GIS and remote sensing are reviewed in the context of national control programmes.}, } @article {pmid12014416, year = {2002}, author = {Kisselev, M and Kellerer, AM}, title = {The potential for studies in other nuclear installations. On the possibility of creating medico-dosimetry registries of workers at the Siberian Chemical Industrial Complex (SCIC) and the Mountain Chemical Industrial Complex (MCIC) in Tomsk, Krasnoyarsk.}, journal = {Radiation and environmental biophysics}, volume = {41}, number = {1}, pages = {81-83}, doi = {10.1007/s00411-001-0135-2}, pmid = {12014416}, issn = {0301-634X}, mesh = {Databases as Topic ; *Environmental Exposure ; Humans ; *Nuclear Warfare ; Occupational Exposure ; Plutonium/adverse effects ; *Power Plants ; *Radioactive Fallout ; Radiometry ; *Registries ; Russia ; Siberia ; }, } @article {pmid12014414, year = {2002}, author = {Shoikhet, YN and Kiselev, VI and Algazin, AI and Kolyado, IB and Bauer, S and Grosche, B}, title = {Fallout from nuclear tests: health effects in the Altai region.}, journal = {Radiation and environmental biophysics}, volume = {41}, number = {1}, pages = {69-73}, doi = {10.1007/s00411-002-0149-4}, pmid = {12014414}, issn = {0301-634X}, mesh = {Aged ; Case-Control Studies ; Databases as Topic ; Environmental Exposure ; Female ; Humans ; Kazakhstan ; Male ; Middle Aged ; *Nuclear Warfare ; Plutonium/adverse effects ; *Radioactive Fallout ; *Radiometry ; Registries ; Risk ; Russia ; Stomach Neoplasms/epidemiology ; }, } @article {pmid12014412, year = {2002}, author = {Shoikhet, Y and Loborev, V and Sudakov, V and Kiselev, VI and Zelenov, V and Azarov, L}, title = {Fallout from nuclear tests: dosimetry in the Altai region.}, journal = {Radiation and environmental biophysics}, volume = {41}, number = {1}, pages = {57-60}, doi = {10.1007/s00411-001-0138-z}, pmid = {12014412}, issn = {0301-634X}, mesh = {Aged ; Cohort Studies ; Databases as Topic ; Dose-Response Relationship, Radiation ; Environmental Exposure ; Food Contamination, Radioactive ; Humans ; Kazakhstan ; Middle Aged ; *Nuclear Warfare ; Plutonium/adverse effects ; *Power Plants ; *Radioactive Fallout ; *Radiometry ; Russia ; Time Factors ; Water Pollutants, Radioactive ; }, } @article {pmid12008893, year = {2000}, author = {Kirchmer, CJ and Lombard, SM}, title = {Raising the curtain on the gray region.}, journal = {Quality assurance (San Diego, Calif.)}, volume = {8}, number = {3-4}, pages = {261-272}, doi = {10.1080/10529410052852402}, pmid = {12008893}, issn = {1052-9411}, mesh = {*Decision Support Techniques ; Environmental Monitoring/*standards ; Humans ; United States ; United States Environmental Protection Agency/*standards ; }, abstract = {The gray region in EPA Document QA/G-4 is defined as the range of possible parameter values near the action level where the cost of determining that the alternative condition is true outweighs the expected consequences of a decision error. The gray region is also described as a range of true parameter values within the alternative condition near the action level where it is "too close to call." EPA Document QA/G-4HW states that during the planning stage the action level is based on an ideal decision rule, while during the assessment stage an operational decision rule is used. This paper analyzes the factors that define the gray region and the action level, including the errors of the first kind (a) and second kind (beta) and the number of samples taken to determine the mean result. The relationship between the Decision Performance Curve presented in EPA QA/G-4 and the statistical power curve is also discussed. The statistically derived critical level is identified as the concentration of importance for decision-making. The action level is defined in terms of the critical level so that its value is consistent for decisions made during both planning (a priori decisions) and assessment (a posteriori decisions).}, } @article {pmid12007066, year = {2002}, author = {Swart, E}, title = {[Possibilities of utilising official statistics for health services research].}, journal = {Gesundheitswesen (Bundesverband der Arzte des Offentlichen Gesundheitsdienstes (Germany))}, volume = {64}, number = {5}, pages = {253-258}, doi = {10.1055/s-2002-28349}, pmid = {12007066}, issn = {0941-3790}, mesh = {Data Collection/statistics & numerical data ; Data Interpretation, Statistical ; Germany ; Health Services Research/*statistics & numerical data ; Humans ; National Health Programs/*statistics & numerical data ; Patient Admission/*statistics & numerical data ; }, abstract = {This report deals with the experiences and problems with using official statistics on a limited area level of Germany's 440 administrative districts. The data comprised health-related issues and were used for an ecological analysis of the determinants of hospital use. We obtained health statistics data from homepages of the German health report, the Federal statistics office, and the 16 statistics offices of the Federal states. We also made use of the data base of the joint regional statistics published by the Federal and regional statistics offices. Finally, there was a co-ordinated inquiry to the regional statistics offices about the supply of data on mortality, hospital discharges, structure of hospital care and several socio-economic indicators. The process of data collecting was mostly unproblematic. On the other hand, not all of the data were available on a limited area level in a satisfying form and quality. For reasons of data protection some information of small districts was transmitted incompletely. Additionally, there are procedural differences between regional statistics offices regarding the differentiation between some variables and in the exchange of data between the federal states. Finally, some problems were due to varying age classifications for different health indicators. For health services research the use of official statistics becomes increasingly comfortable via health reports and Internet. However, for specific questions of research some problems still remain, rising from missing standardised health indicators and deficient availability of limited area health data. Data collection is exacerbated by restrictive interpretation of data protection acts and the different handling of data inquiries in the regional statistics offices. Finally, there is a lack of data on morbidity and use of ambulatory care.}, } @article {pmid11996128, year = {2002}, author = {Rausina, GA and Wong, DC and Arnold, WR and Mancini, ER and Steen, AE}, title = {Toxicity of methyl tert-butyl ether to marine organisms: ambient water quality criteria calculation.}, journal = {Chemosphere}, volume = {47}, number = {5}, pages = {525-534}, doi = {10.1016/s0045-6535(01)00311-3}, pmid = {11996128}, issn = {0045-6535}, mesh = {Animals ; Bivalvia/drug effects ; Brachyura/drug effects ; Databases, Factual ; Decapoda/drug effects ; Ecosystem ; Eukaryota/drug effects ; Fishes/metabolism ; Fresh Water/chemistry ; Invertebrates/drug effects ; Marine Biology ; Methyl Ethers/analysis/*toxicity ; Toxicity Tests ; United States ; United States Environmental Protection Agency ; Water Pollutants, Chemical/analysis/*toxicity ; Water Supply/*standards ; }, abstract = {In response to increasing concerns over the detection of methyl tert-butyl ether (MTBE) in groundwater and surface water and its potential effects in aquatic ecosystems, industry and the United States Environmental Protection Agency (USEPA) began to collaborate in 1997 to develop aquatic toxicity databases sufficient to derive ambient water quality criteria for MTBE consistent with USEPA requirements. Acute toxicity data for seven marine species, chronic toxicity data for an invertebrate, and plant toxicity data were developed to complete the saltwater database. The species tested were Cyprinodon variegatus, Gasterosteus aculeatus, Callinectes sapidus, Mytilus galloprovincialis, Palaemonetes pugio, Rhepoxynius abronius, Americamysis bahia, and Skeletonema costatum. The toxicity tests were conducted in accordance with USEPA and American Society for Testing and Materials testing procedures and Good Laboratory Practice guidelines. Data developed from this study were consistent with existing data and showed that MTBE has low acute and chronic toxicity to the marine species tested. Based upon measured MTBE concentrations, acute effects were found to range from 166 mg MTBE/l for the grass shrimp to 1950 mg MTBE/l for marine mussel. The no-observed effect concentration for the reproduction and growth of mysids was 26 mg MTBE/l during the life cycle test. The toxicity of MTBE to saltwater organisms is comparable to its toxicity to the freshwater species tested. Reported MTBE concentrations in coastal waters are several orders of magnitude lower than concentrations observed to cause effects in marine organisms.}, } @article {pmid11990770, year = {2002}, author = {Preston, BL and Shackelford, J}, title = {Multiple stressor effects on benthic biodiversity of Chesapeake Bay: implications for ecological risk assessment.}, journal = {Ecotoxicology (London, England)}, volume = {11}, number = {2}, pages = {85-99}, pmid = {11990770}, issn = {0963-9292}, mesh = {Animals ; Data Interpretation, Statistical ; Databases, Factual ; *Ecosystem ; *Environmental Monitoring ; Geologic Sediments/chemistry ; Invertebrates ; Maryland ; Models, Statistical ; Regression Analysis ; Risk Assessment ; Seawater/*analysis ; Virginia ; Water Pollutants, Chemical/analysis ; }, abstract = {In natural aquatic systems, there is frequently overlap in the spatial distribution of both natural and anthropogenic stressors, particularly at regional geographic scales. Yet the proportional risk associated with individual stressors, their cumulative effects and the manner in which they interact to affect aquatic ecology is frequently unknown, limiting the robustness of multiple-stressor ecological risk assessments (ERA). The current study used historical environmental monitoring data (1984-1999) to identify a combination of natural and anthropogenic stressors that best accounted for observed patterns of benthic biodiversity in Chesapeake Bay. Geographic information systems (GIS) were used to geographically link spatially heterogeneous databases for benthic biodiversity, water quality and sediment toxicant concentrations. Single and multiple variable regression techniques were subsequently used to develop a statistical model to explain observed patterns of benthic biodiversity. Combinations of natural stressors alone accounted for as much as 34% of the variation in benthic biodiversity, and combinations of anthropogenic toxicants accounted for as much as 48% of the variation. The consideration of both natural and anthropogenic stressors resulted in a statistical model that accounted for approximately 73% of the observed variation in benthic biodiversity of Chesapeake Bay. These results suggest that benthic biodiversity in Chesapeake Bay is a function of complex interactions among water quality characteristics and anthropogenic toxicants. Therefore, new risk assessment methodologies are required to assess the risk of multiple stressors at regional scales.}, } @article {pmid11972025, year = {2002}, author = {Plotkin, JB and Dushoff, J and Levin, SA}, title = {Hemagglutinin sequence clusters and the antigenic evolution of influenza A virus.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {99}, number = {9}, pages = {6263-6268}, pmid = {11972025}, issn = {0027-8424}, support = {1-R01-GM60729-01/GM/NIGMS NIH HHS/United States ; }, mesh = {Antibodies/metabolism ; Binding Sites ; Databases as Topic ; Genotype ; Hemagglutinins/*genetics ; Influenza A virus/*genetics ; Influenza Vaccines/genetics ; Models, Genetic ; Multigene Family ; *Mutation ; Time Factors ; Vaccines/*genetics ; }, abstract = {Continual mutations to the hemagglutinin (HA) gene of influenza A virus generate novel antigenic strains that cause annual epidemics. Using a database of 560 viral RNA sequences, we study the structure and tempo of HA evolution over the past two decades. We detect a critical length scale, in amino acid space, at which HA sequences aggregate into clusters, or swarms. We investigate the spatio-temporal distribution of viral swarms and compare it to the time series of the influenza vaccines recommended by the World Health Organization. We introduce a method for predicting future dominant HA amino acid sequences and discuss its potential relevance to vaccine choice. We also investigate the relationship between cluster structure and the primary antibody-combining regions of the HA protein.}, } @article {pmid11955685, year = {2002}, author = {Russom, CL}, title = {Mining environmental toxicology information: web resources.}, journal = {Toxicology}, volume = {173}, number = {1-2}, pages = {75-88}, doi = {10.1016/s0300-483x(02)00023-9}, pmid = {11955685}, issn = {0300-483X}, mesh = {Animals ; *Databases as Topic ; Ecology ; *Environmental Exposure ; *Hazardous Substances ; Humans ; *Internet ; }, abstract = {Environmental toxicology is the study of the ecological effects of anthropogenic substances released into the environment. It is a relatively diverse field addressing impacts to aquatic and terrestrial organisms and communities. The determination of potential risk associated with toxic agents is of interest to government regulators, industry, researchers, private organizations and citizen groups. In assessing the ecological risk associated with a chemical stressor, it is important to establish linkages between likely exposure concentrations and adverse effects to ecological receptors. To do so requires access to reliable information resources. The proper application of such data requires familiarity with the scientific literature and keeping abreast of new and emerging issues as well as state-of-the-art research findings and methods. In addition, an understanding of government regulations as they relate to environmental issues is also of primary interest. The advent of the Web has made these tools accessible at computer desktops. This review focuses on currently available free Web resources related to environmental toxicology, specifically those which address available empirical data sources, predictive tools and publications of interest such as standard test methods, guidance documents and governmental regulations.}, } @article {pmid11928128, year = {2000}, author = {Clarke, SP and Cossette, S}, title = {Secondary analysis: theoretical, methodological, and practical considerations.}, journal = {The Canadian journal of nursing research = Revue canadienne de recherche en sciences infirmieres}, volume = {32}, number = {3}, pages = {109-129}, pmid = {11928128}, issn = {0844-5621}, support = {T32 NR07104/NR/NINR NIH HHS/United States ; }, mesh = {Bias ; *Data Interpretation, Statistical ; Humans ; Models, Statistical ; Models, Theoretical ; Nursing Research/*methods ; Reproducibility of Results ; *Research Design ; Sampling Studies ; Selection Bias ; }, abstract = {Secondary analysis, which involves the use of existing data sets to answer new research questions, is an increasingly popular methodological choice among researchers who wish to investigate particular research questions but lack the resources to undertake primary data collections. Much time loss and considerable frustration may result, however, if researchers begin secondary analyses without an awareness of the distinctive methodological and practical challenges involved. This article highlights difficulties that may arise when researchers use data from previous clinical research projects, including theoretical issues and problems involving sampling, measurement, and external and ecological validity. It also offers practical suggestions for undertaking a secondary analysis and criteria for evaluating secondary analyses.}, } @article {pmid11908957, year = {2002}, author = {Bobe, R and Behrensmeyer, AK and Chapman, RE}, title = {Faunal change, environmental variability and late Pliocene hominin evolution.}, journal = {Journal of human evolution}, volume = {42}, number = {4}, pages = {475-497}, doi = {10.1006/jhev.2001.0535}, pmid = {11908957}, issn = {0047-2484}, mesh = {Animals ; *Biological Evolution ; *Climate ; Databases, Factual ; Ethiopia ; *Fossils ; Hominidae/*classification ; Humans ; Mammals/classification ; Paleontology/methods ; Plants/classification ; Population Dynamics ; Time Factors ; }, abstract = {Global change during the late Pliocene was manifested in declining temperatures, increased amplitude of climate cycles, and shifts in the periodicity of orbital climate forcing. Linking these changes to the evolution of African continental faunas and to hominin evolution requires well-documented fossil evidence that can be examined through substantial periods of time. The Omo sequence of southern Ethiopia provides such a database, and we use it to analyze change in the abundances of mammal taxa at different levels of temporal and taxonomic resolution between 4 and 2 Ma. This study provides new evidence for shifts through time in the ecological dominance of suids, cercopithecids, and bovids, and for a trend from more forested to more open woodland habitats. Superimposed on these long-term trends are two episodes of faunal change, one involving a marked shift in the abundances of different taxa at about 2.8+/-0.1 Ma, and the second the transition at 2.5 Ma from a 200-ka interval of faunal stability to marked variability over intervals of about 100 ka. The first appearance of Homo, the earliest artefacts, and the extinction of non-robust Australopithecus in the Omo sequence coincide in time with the beginning of this period of high variability. We conclude that climate change caused significant shifts in vegetation in the Omo paleo-ecosystem and is a plausible explanation for the gradual ecological change from forest to open woodland between 3.4 and 2.0 Ma, the faunal shift at 2.8 +/-0.1 Ma, and the change in the tempo of faunal variability of 2.5 Ma. Climate forcing in the late Pliocene is more clearly indicated by population shifts within the Omo mammal community than by marked turnover at the species level.}, } @article {pmid11894065, year = {2002}, author = {Clarke, T}, title = {Formidable catalogue puts army of ants online.}, journal = {Nature}, volume = {416}, number = {6877}, pages = {115}, doi = {10.1038/416115b}, pmid = {11894065}, issn = {0028-0836}, mesh = {Animals ; Ants/*classification ; Classification/methods ; *Databases, Factual ; Ecology ; Entomology/methods ; Internet ; United States ; }, } @article {pmid11893328, year = {2002}, author = {Moran, NA}, title = {Microbial minimalism: genome reduction in bacterial pathogens.}, journal = {Cell}, volume = {108}, number = {5}, pages = {583-586}, doi = {10.1016/s0092-8674(02)00665-7}, pmid = {11893328}, issn = {0092-8674}, mesh = {Bacteria/*genetics/*pathogenicity ; Base Composition ; Biological Evolution ; Databases, Genetic ; Genes, Bacterial ; *Genome, Bacterial ; Mutation ; Open Reading Frames ; }, abstract = {When bacterial lineages make the transition from free-living or facultatively parasitic life cycles to permanent associations with hosts, they undergo a major loss of genes and DNA. Complete genome sequences are providing an understanding of how extreme genome reduction affects evolutionary directions and metabolic capabilities of obligate pathogens and symbionts.}, } @article {pmid11891342, year = {2002}, author = {Alroy, J}, title = {How many named species are valid?.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {99}, number = {6}, pages = {3706-3711}, pmid = {11891342}, issn = {0027-8424}, mesh = {Animals ; Bias ; Biological Evolution ; Classification/*methods ; Cohort Studies ; Databases, Factual ; *Ecosystem ; Fossils ; Mammals/classification ; North America ; Reproducibility of Results ; Species Specificity ; Time Factors ; }, abstract = {Estimates of biodiversity in both living and fossil groups depend on raw counts of currently recognized named species, but many of these names eventually will prove to be synonyms or otherwise invalid. This difficult bias can be resolved with a simple "flux ratio" equation that compares historical rates of invalidation and revalidation. Flux ratio analysis of a taxonomic data set of unrivalled completeness for 4,861 North American fossil mammal species shows that 24-31% of currently accepted names eventually will prove invalid, so diversity estimates are inflated by 32-44%. The estimate is conservative compared with one obtained by using an older, more basic method. Although the degree of inflation varies through both historical and evolutionary time, it has a minor impact on previously published background origination and extinction rates. Several lines of evidence suggest that the same bias probably affects more poorly studied, hyperdiverse living groups such as fungi and insects. If so, then current estimates of total global diversity could be revised downwards to as low as 3.5-10.5 million species.}, } @article {pmid11883688, year = {2002}, author = {Mumby, PJ}, title = {Statistical power of non-parametric tests: a quick guide for designing sampling strategies.}, journal = {Marine pollution bulletin}, volume = {44}, number = {1}, pages = {85-87}, doi = {10.1016/s0025-326x(01)00097-2}, pmid = {11883688}, issn = {0025-326X}, mesh = {Data Interpretation, Statistical ; Monte Carlo Method ; Reproducibility of Results ; Sample Size ; Sensitivity and Specificity ; *Statistics, Nonparametric ; }, abstract = {The importance of considering statistical power in marine pollution studies is unequivocal. However, the vast majority of ecological literature on power analysis focuses on parametric rather than non-parametric tests. This note describes a Monte Carlo simulation method for estimating the power of non-parametric tests. The method is illustrated using ordinal data.}, } @article {pmid11878481, year = {2002}, author = {Bird, SL and Perry, SG and Ray, SL and Teske, ME}, title = {Evaluation of the AgDISP aerial spray algorithms in the AgDRIFT model.}, journal = {Environmental toxicology and chemistry}, volume = {21}, number = {3}, pages = {672-681}, doi = {10.1897/1551-5028(2002)021<0672:eotaas>2.0.co;2}, pmid = {11878481}, issn = {0730-7268}, mesh = {Agriculture/*statistics & numerical data ; Air Movements ; *Algorithms ; Animals ; Animals, Domestic ; Databases, Factual ; Forecasting ; Humans ; Meteorological Concepts ; *Models, Theoretical ; Pesticides/*analysis ; Public Health ; }, abstract = {A systematic evaluation of the AgDISP algorithms, which simulate off-site drift and deposition of aerially applied pesticides, contained in the AgDRIFT model was performed by comparing model simulations to field-trial data collected by the Spray Drift Task Force. Field-trial data used for model evaluation included 161 separate trials of typical agriculture aerial applications under a wide range of application and meteorological conditions. Input for model simulations included information on the aircraft and spray equipment, spray material, meteorology, and site geometry. The model input datasets were generated independently of the field deposition results, i.e., model inputs were in no way altered or selected to improve the fit of model output to field results. AgDRIFT shows a response similar to that of the field observations for many application variables (e.g., droplet size, application height, wind speed). However, AgDRIFT is sensitive to evaporative effects, and modeled deposition in the far-field responds to wet bulb depression whereas the field observations did not. The model tended to overpredict deposition rates relative to the field data for far-field distances, particularly under evaporative conditions. AgDRIFT was in good agreement with field results for estimating near-field buffer zones needed to manage human, crop, livestock, and ecological exposure.}, } @article {pmid11876077, year = {2002}, author = {Pearson, DM}, title = {The application of local measures of spatial autocorrelation for describing pattern in north Australian landscapes.}, journal = {Journal of environmental management}, volume = {64}, number = {1}, pages = {85-95}, doi = {10.1006/jema.2001.0523}, pmid = {11876077}, issn = {0301-4797}, mesh = {Australia ; *Conservation of Natural Resources ; *Ecosystem ; Environmental Monitoring/*statistics & numerical data ; Geography/statistics & numerical data ; Information Systems/statistics & numerical data ; *Models, Theoretical ; }, abstract = {This paper tests the use of a spatial analysis technique, based on the calculation of local spatial autocorrelation, as a possible approach for modelling and quantifying structure in northern Australian savanna landscapes. Unlike many landscapes in the world, northern Australian savanna landscapes appear on the surface to be intact. They have not experienced the same large-scale land clearance and intensive land management as other landscapes across Australia. Despite this, natural resource managers are beginning to notice that processes are breaking down and declines in species are becoming more evident. With future declines of species looking more imminent it is particularly important that models are available that can help to assess landscape health, and quantify any structural change that takes place. GIS and landscape ecology provide a useful way of describing landscapes both spatially and temporally and have proved to be particularly useful for understanding vegetation structure or pattern in landscapes across the world. There are many measures that examine spatial structure in the landscape and most of these are now available in a GIS environment (e.g. FRAGSTATS* ARC, r.le, and Patch Analyst). All these methods depend on a landscape described in terms of patches, corridors and matrix. However, since landscapes in northern Australia appear to be relatively intact they tend to exist as surfaces of continuous variation rather than in clearly defined homogeneous units. As a result they cannot be easily described using entity-based models requiring patches and other essentially cartographic approaches. This means that more appropriate methods need to be developed and explored. The approach examined in this paper enables clustering and local pattern in the data to be identified and forms a generic method for conceptualising the landscape structure where patches are not obvious and where boundaries between landscape features are difficult to determine. Two sites are examined using this approach. They have been exposed to different degrees of disturbance by fire and grazing. The results show that savanna landscapes are very complex and that even where there is a high degree of disturbance the landscape is still relatively heterogeneous. This means that treating savanna landscapes as being made up of homogeneous units can limit analysis of pattern, as it can over simplify the structure present, and that methods such as the autocorrelation approach are useful tools for quantifying the variable nature of these landscapes.}, } @article {pmid11864505, year = {1999}, author = {Zhou, X and Kristensen, TK and Hong, Q and Sun, L}, title = {[Analysis for spatial distribution of Oncomelania snail in mainland China by geographic information system(GIS) database].}, journal = {Zhonghua yu fang yi xue za zhi [Chinese journal of preventive medicine]}, volume = {33}, number = {6}, pages = {343-345}, pmid = {11864505}, issn = {0253-9624}, mesh = {Animals ; China ; Demography ; *Disease Vectors ; Ecology ; Geographic Information Systems ; Polymorphism, Genetic/genetics ; Schistosomiasis japonica/*transmission ; *Snails/genetics/parasitology ; }, abstract = {OBJECTIVE: To analyze spatial distribution of Oncomelania snail populations in mainland China by geographic information system (GIS) database.

METHODS: Genetic variation experiment data and experimental data of susceptibility of 34 snail populations were collected from nine provinces in China, to set up a database. A world digital map was linked with the database in a software ArcView Release 3.0 a to be used to divide zones with ArcView spatial analyze function and GIS overlaying function. AVHRR NDVI satellite images were collected to form a new one for prevalent season, which were overlaid with distribution maps of heterozygous indices of snail populations, polymorphic locus percentage and infection rates of snail population with schistosome for classifying the images.

RESULTS: Spatial analysis showed that distribution maps of genetic heterozygous indices of snail, percentage of polymophic loci and infection rate of snail can be divided into two large zones, i.e., east zone and west zone, both with varied pictures. Analysis for overlaying three-stratum distribution map with AVHRR NDVI satellite image showed four distinctly different spatial zones, including west Sichuan zone, west Yunnan zone, middle zone of river, lake and marshland, and southeast coastal zone.

CONCLUSION: It is the first time using GIS to analyze data of Oncomelania population genetics and confirmed the population structure of Oncomelania snails presented discrete sub-population model, which supports the theory of sub-species of Oncomelania spp. Exited in mainland China.}, } @article {pmid11861885, year = {2002}, author = {Gu, Z and Cavalcanti, A and Chen, FC and Bouman, P and Li, WH}, title = {Extent of gene duplication in the genomes of Drosophila, nematode, and yeast.}, journal = {Molecular biology and evolution}, volume = {19}, number = {3}, pages = {256-262}, doi = {10.1093/oxfordjournals.molbev.a004079}, pmid = {11861885}, issn = {0737-4038}, support = {GM30998/GM/NIGMS NIH HHS/United States ; GM55759/GM/NIGMS NIH HHS/United States ; HD38287/HD/NICHD NIH HHS/United States ; }, mesh = {Animals ; Caenorhabditis elegans/*genetics ; Databases, Nucleic Acid ; Drosophila melanogaster/*genetics ; Evolution, Molecular ; *Gene Dosage ; *Gene Duplication ; Genome ; Kinetics ; Multigene Family ; Protein Isoforms/genetics ; Saccharomyces cerevisiae/*genetics ; }, abstract = {We conducted a detailed analysis of duplicate genes in three complete genomes: yeast, Drosophila, and Caenorhabditis elegans. For two proteins belonging to the same family we used the criteria: (1) their similarity is > or =I (I = 30% if L > or = 150 a.a. and I = 0.01n + 4.8L(-0.32(1 + exp(-L/1000))) if L < 150 a.a., where n = 6 and L is the length of the alignable region), and (2) the length of the alignable region between the two sequences is > or = 80% of the longer protein. We found it very important to delete isoforms (caused by alternative splicing), same genes with different names, and proteins derived from repetitive elements. We estimated that there were 530, 674, and 1,219 protein families in yeast, Drosophila, and C. elegans, respectively, so, as expected, yeast has the smallest number of duplicate genes. However, for the duplicate pairs with the number of substitutions per synonymous site (K(S)) < 0.01, Drosophila has only seven pairs, whereas yeast has 58 pairs and nematode has 153 pairs. After considering the possible effects of codon usage bias and gene conversion, these numbers became 6, 55, and 147, respectively. Thus, Drosophila appears to have much fewer young duplicate genes than do yeast and nematode. The larger numbers of duplicate pairs with K(S) < 0.01 in yeast and C. elegans were probably largely caused by block duplications. At any rate, it is clear that the genome of Drosophila melanogaster has undergone few gene duplications in the recent past and has much fewer gene families than C. elegans.}, } @article {pmid11847089, year = {2002}, author = {Hudson, RR}, title = {Generating samples under a Wright-Fisher neutral model of genetic variation.}, journal = {Bioinformatics (Oxford, England)}, volume = {18}, number = {2}, pages = {337-338}, doi = {10.1093/bioinformatics/18.2.337}, pmid = {11847089}, issn = {1367-4803}, mesh = {Computational Biology ; Gene Conversion ; *Genetic Variation ; Genetics, Population ; *Models, Genetic ; Monte Carlo Method ; Recombination, Genetic ; *Software ; }, abstract = {A Monte Carlo computer program is available to generate samples drawn from a population evolving according to a Wright-Fisher neutral model. The program assumes an infinite-sites model of mutation, and allows recombination, gene conversion, symmetric migration among subpopulations, and a variety of demographic histories. The samples produced can be used to investigate the sampling properties of any sample statistic under these neutral models.}, } @article {pmid11839197, year = {2002}, author = {Limburg, PA and Weider, LJ}, title = {'Ancient' DNA in the resting egg bank of a microcrustacean can serve as a palaeolimnological database.}, journal = {Proceedings. Biological sciences}, volume = {269}, number = {1488}, pages = {281-287}, pmid = {11839197}, issn = {0962-8452}, mesh = {Alleles ; Animals ; Crustacea/*cytology/*genetics ; DNA/genetics/*isolation & purification ; Databases, Nucleic Acid ; Ecosystem ; *Fossils ; Fresh Water/parasitology ; *Genetics, Population ; Germany ; Microsatellite Repeats/genetics ; Mutation/genetics ; Ovum/*metabolism ; Time Factors ; Zooplankton/*cytology/*genetics ; }, abstract = {Recent work on the diapausing egg banks of zooplankton, such as Daphnia (Crustacea: Anomopoda), indicates that these eggs can remain viable for decades while, theoretically, DNA can remain intact for even longer periods (i.e. centuries or millennia). We isolated diapausing eggs of Daphnia from a 30 m long sediment core taken from a hypereutrophic, northern German lake (Belauer See), with some eggs found in dated core material as old as 4500 years. Using microsatellite markers, we analysed the genetic structure of the resting eggs dated as old as ca. 200 years, and found that, although levels of heterozygosity remained remarkably stable, significant genetic differentiation (Nei's D = 0.36; F(ST) = 0.15) between recent and 'ancient' resting eggs (including allele frequency shifts and private alleles) was detected. These shifts represent either species-level changes in this complex (i.e. species-specific characters of ephippia are not always robust), or intraspecific shifts in genetic variation, or a combination of both. This study demonstrates that the egg banks of aquatic zooplankton can serve as repositories of both genetic (intrapopulational) and ecological (interspecific) information. The use of molecular markers, such as microsatellites, on diapausing egg/seed banks may open new avenues of enquiry related to tracking the long-term genetic (and/or species) shifts that are associated with long-term environmental changes.}, } @article {pmid11838769, year = {2001}, author = {Carroll, SP and Dingle, H and Famula, TR and Fox, CW}, title = {Genetic architecture of adaptive differentiation in evolving host races of the soapberry bug, Jadera haematoloma.}, journal = {Genetica}, volume = {112-113}, number = {}, pages = {257-272}, pmid = {11838769}, issn = {0016-6707}, mesh = {*Adaptation, Biological ; Animals ; *Biological Evolution ; Data Interpretation, Statistical ; Female ; Heteroptera/anatomy & histology/*genetics/growth & development ; Male ; Selection, Genetic ; Time ; }, abstract = {To explore genetic architecture and adaptive evolution, we conducted environmental and genetic experiments with two recently (ca. 100 generations) diverged, geographically adjacent races of the soapberry bug. One race occurs on a native host plant species, the other on an introduced host. We focused on three traits: length of the mouthparts, body size and development time. The first experiment was an environmental manipulation, comparing individuals of each population reared on one or the other host species ('cross-rearing') and estimating three evolutionary rates for each trait. The first rate, 'evolutionary path' compares ancestral-derived populations when both were reared on the introduced host. The second, 'current ecological contrast' compares populations with each reared on its natal host. The third, 'evolved tradeoff' compares the two races when reared on the native host. Differences among these rates are striking and informative. For example, development time, which appears to be relatively undifferentiated phenotypically, has actually evolved very rapidly via countergradient selection. The pattern differs for each trait, and clear developmental tradeoffs have evolved as quickly as adaptation to the new host in each. The second experiment was a two-generation 'line cross' study. With joint-scaling analyses, we compared purebred, hybrid and backcrossed individuals to describe genetic architecture. Additive genetic variance for mouthpart length was consistently large (ca. 60%), but the interaction of dominance, maternal effects and epistasis was important in the other traits. Rearing host strongly affected genetic architecture. There was no clear relationship between genetic architecture and rate of evolution. Selection has produced both additive and nonadditive differentiation between the host races with surprising speed, consistent with theoretical predictions about evolution in fitness-associated traits.}, } @article {pmid11836233, year = {2002}, author = {Chapman, S and Schenk, P and Kazan, K and Manners, J}, title = {Using biplots to interpret gene expression patterns in plants.}, journal = {Bioinformatics (Oxford, England)}, volume = {18}, number = {1}, pages = {202-204}, doi = {10.1093/bioinformatics/18.1.202}, pmid = {11836233}, issn = {1367-4803}, mesh = {Computational Biology ; Gene Expression Profiling/*statistics & numerical data ; *Genes, Plant ; Internet ; Multigene Family ; Oligonucleotide Array Sequence Analysis/statistics & numerical data ; Plants/*genetics ; Principal Component Analysis ; }, abstract = {Plant biologists in fields of ecology, evolution, genetics and breeding frequently use multivariate methods. This paper illustrates Principal Component Analysis (PCA) and Gabriel's biplot as applied to microarray expression data from plant pathology experiments.}, } @article {pmid11833900, year = {2002}, author = {Conant, RT and Paustian, K}, title = {Spatial variability of soil organic carbon in grasslands: implications for detecting change at different scales.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {116 Suppl 1}, number = {}, pages = {S127-35}, doi = {10.1016/s0269-7491(01)00265-2}, pmid = {11833900}, issn = {0269-7491}, mesh = {Carbon/analysis/*metabolism ; Databases, Factual ; *Ecosystem ; *Environmental Monitoring ; Organic Chemicals/analysis ; *Poaceae ; *Soil ; }, abstract = {Extensive data used to quantify broad soil C changes (without information about causation), coupled with intensive data used for attribution of changes to specific management practices, could form the basis of an efficient national grassland soil C monitoring network. Based on variability of extensive (USDA/NRCS pedon database) and intensive field-level soil C data, we evaluated the efficacy of future sample collection to detect changes in soil C in grasslands. Potential soil C changes at a range of spatial scales related to changes in grassland management can be verified (alpha=0.1) after 5 years with collection of 34, 224, 501 samples at the county, state, or national scales, respectively. Farm-level analysis indicates that equivalent numbers of cores and distinct groups of cores (microplots) results in lowest soil C coefficients of variation for a variety of ecosystems. Our results suggest that grassland soil C changes can be precisely quantified using current technology at scales ranging from farms to the entire nation.}, } @article {pmid11821909, year = {2002}, author = {Jenkins, GM and Rambaut, A and Pybus, OG and Holmes, EC}, title = {Rates of molecular evolution in RNA viruses: a quantitative phylogenetic analysis.}, journal = {Journal of molecular evolution}, volume = {54}, number = {2}, pages = {156-165}, doi = {10.1007/s00239-001-0064-3}, pmid = {11821909}, issn = {1432-1432}, support = {//Wellcome Trust/United Kingdom ; }, mesh = {Amino Acid Substitution ; Computer Simulation ; Databases, Nucleic Acid ; *Evolution, Molecular ; Genome, Viral/genetics ; Likelihood Functions ; Models, Genetic ; *Phylogeny ; RNA Viruses/*genetics ; Sequence Alignment ; }, abstract = {The study of rates of nucleotide substitution in RNA viruses is central to our understanding of their evolution. Herein we report a comprehensive analysis of substitution rates in 50 RNA viruses using a recently developed maximum likelihood phylogenetic method. This analysis revealed a significant relationship between genetic divergence and isolation time for an extensive array of RNA viruses, although more rate variation was usually present among lineages than would be expected under the constraints of a molecular clock. Despite the lack of a molecular clock, the range of statistically significant variation in overall substitution rates was surprisingly narrow for those viruses where a significant relationship between genetic divergence and time was found, as was the case when synonymous sites were considered alone, where the molecular clock was rejected less frequently. An analysis of the ecological and genetic factors that might explain this rate variation revealed some evidence of significantly lower substitution rates in vector-borne viruses, as well as a weak correlation between rate and genome length. Finally, a simulation study revealed that our maximum likelihood estimates of substitution rates are valid, even if the molecular clock is rejected, provided that sufficiently large data sets are analyzed.}, } @article {pmid11809274, year = {2002}, author = {Grimes, DA and Schulz, KF}, title = {Descriptive studies: what they can and cannot do.}, journal = {Lancet (London, England)}, volume = {359}, number = {9301}, pages = {145-149}, doi = {10.1016/S0140-6736(02)07373-7}, pmid = {11809274}, issn = {0140-6736}, mesh = {Bias ; Case-Control Studies ; Causality ; Cluster Analysis ; Cross-Sectional Studies ; Data Collection/methods/standards ; Data Interpretation, Statistical ; Environmental Exposure/adverse effects/analysis ; *Epidemiologic Research Design ; Health Planning ; Humans ; Medical Records ; Observation ; Population Surveillance ; Prevalence ; Publishing ; Reproducibility of Results ; }, abstract = {Descriptive studies often represent the first scientific toe in the water in new areas of inquiry. A fundamental element of descriptive reporting is a clear, specific, and measurable definition of the disease or condition in question. Like newspapers, good descriptive reporting answers the five basic W questions: who, what, why, when, where. and a sixth: so what? Case reports, case-series reports, cross-sectional studies, and surveillance studies deal with individuals, whereas ecological correlational studies examine populations. The case report is the least-publishable unit in medical literature. Case-series reports aggregate individual cases in one publication. Clustering of unusual cases in a short period often heralds a new epidemic, as happened with AIDS. Cross-sectional (prevalence) studies describe the health of populations. Surveillance can be thought of as watchfulness over a community; feedback to those who need to know is an integral component of surveillance. Ecological correlational studies look for associations between exposures and outcomes in populations-eg, per capita cigarette sales and rates of coronary artery disease-rather than in individuals. Three important uses of descriptive studies include trend analysis, health-care planning, and hypothesis generation. A frequent error in reports of descriptive studies is overstepping the data: studies without a comparison group allow no inferences to be drawn about associations, causal or otherwise. Hypotheses about causation from descriptive studies are often tested in rigorous analytical studies.}, } @article {pmid11804049, year = {2002}, author = {Preston, BL}, title = {Spatial patterns in benthic biodiversity of Chesapeake Bay, USA (1984-1999): association with water quality and sediment toxicity.}, journal = {Environmental toxicology and chemistry}, volume = {21}, number = {1}, pages = {151-162}, pmid = {11804049}, issn = {0730-7268}, mesh = {Animals ; Databases, Factual ; *Ecosystem ; Environmental Monitoring ; Geologic Sediments/*chemistry ; Invertebrates/*drug effects ; Quality Control ; Risk Assessment ; Seawater/*analysis ; United States ; Water Pollutants, Chemical/*toxicity ; }, abstract = {Non-point-source pollution is an increasing source of stress to aquatic, estuarine, and marine ecosystems. Such pollution may be of unknown etiology, distributed over extensive spatial scales, and comprised of multiple stressors. Current stressor-based paradigms for ecological risk assessment (ERA) may be insufficient to characterize risk from multiple stressors at regional spatial scales, necessitating the use of effects-based approaches. Historical data (1984-1999) for benthic macroinvertebrate biodiversity in Chesapeake Bay, USA, were incorporated into a geographic information system (GIS) and spatial analysis tools were used to model zones within the bay predicted to be of low or high anthropogenic impact. Data for benthic water quality and sediment toxicant concentrations from each of these zones were subsequently analyzed and compared to identify associations between benthic biodiversity and potential stressors. A number of stressors were significantly associated with high-impact zones, including increased nitrogen and phosphorus concentrations, low dissolved oxygen, heavy metals, pesticides, polycyclic aromatic hydrocarbons, and polychlorinated biphenyls. The spatial autocorrelation among multiple stressors suggests that traditional stressor-based approaches to ERA may result in the a priori exclusion of ecologically relevant stressors. Considering the effects of individual stressors rather than net effects of multiple stressors may result in underestimation of risk. The GISs are a useful tool for integrating multiple data sets in support of comprehensive regional ERA.}, } @article {pmid11793243, year = {2001}, author = {Kim, J}, title = {Descartes' fly: the geometry of genomic annotation.}, journal = {Functional & integrative genomics}, volume = {1}, number = {4}, pages = {241-249}, doi = {10.1007/s101420000025}, pmid = {11793243}, issn = {1438-793X}, mesh = {Animals ; Computational Biology/methods ; Drosophila melanogaster/*genetics ; *Genome ; Markov Chains ; Sequence Analysis, DNA ; }, abstract = {The completion of the Drosophila melanogaster genome marks another significant milestone in the growth of sequence information. But it also contributes to the ever-widening gap between sequence information and biological knowledge. One important approach to reducing this gap is theoretical inference through computational technologies. Many computer programs have been designed to annotate genomic sequence information with biologically relevant information. Here, I suggest that all of these methods have a common structure in which the sequence fragments are "coordinated" by some method of description such as Hidden Markov models. The key to the algorithms lies in constructing the most efficient set of coordinates that allow extrapolation and interpolation from existing knowledge. Efficient extrapolation and interpolation are produced if the sequence fragments acquire a natural geometrical structure in the coordinated description. Finding such a coordinate frame is an inductive problem with no algorithmic solution. The greater part of the problem of genomic annotation lies in biological modeling of the data rather than in algorithmic improvements.}, } @article {pmid11791237, year = {2001}, author = {Gorodkin, J and Lyngso, RB and Stormo, GD}, title = {A mini-greedy algorithm for faster structural RNA stem-loop search.}, journal = {Genome informatics. International Conference on Genome Informatics}, volume = {12}, number = {}, pages = {184-193}, pmid = {11791237}, issn = {0919-9454}, mesh = {*Algorithms ; Base Sequence ; Computational Biology ; Databases, Nucleic Acid ; Nucleic Acid Conformation ; RNA/*chemistry/*genetics ; Sequence Alignment/statistics & numerical data ; }, abstract = {When a set of coregulated genes share a common structural RNA motif, e.g. a hairpin, most motif search approaches fail to locate the covarying but structurally conserved motif. There do exist methods that can locate structural RNA motifs, like FOLDALIGN, but the main problem with these methods is that they are computationally expensive. In FOLDALIGN, a major contribution to this is the use of a greedy algorithm to construct the multiple alignment. To ensure good quality many redundant computations must be made. However, by applying the greedy algorithm on a carefully selected subset of sequences, near full greedy quality can be obtained. The basic idea is to estimate the order in which the sequences entered a good greedy alignment. If such a ranking, found from all pairwise alignments, is in good agreement with the order of appearance in the multiple alignment, the core structural motif can be found by performing the greedy algorithm on just the top sequences in the ranking. The ranking used in this mini-greedy algorithm is found by using two complementing approaches: 1) When interpreting the FOLDALIGN score as an inner product (kernel), the sequences can be ranked according to their distance to their center of mass; 2) We construct an algorithm that attempts to find the K closest sequences in the vector space associated with the inner product, and the remaining sequences can be ranked by their minimum distance to any of the sequences, or to the center of mass in this set. The two approaches arecompared and merged, and the results discussed. We also show that structural alignments of near full greedy quality can found in significantly reduced time, using these methods. The algorithm is being included in the SLASH (Stem-Loop Align SearcH) server available at http://www.bioinf.au.dk/slash.}, } @article {pmid11791230, year = {2001}, author = {Yoshimori, A and Del Carpio, CA}, title = {Automatic epitope recognition in proteins oriented to the system for macromolecular interaction assessment MIAX.}, journal = {Genome informatics. International Conference on Genome Informatics}, volume = {12}, number = {}, pages = {113-122}, pmid = {11791230}, issn = {0919-9454}, mesh = {*Algorithms ; Binding Sites ; Computational Biology ; Epitopes ; Macromolecular Substances ; Models, Molecular ; Proteins/*chemistry/*immunology/metabolism ; }, abstract = {In the present work we evaluate the performance of an algorithm for the automatic recognition of binding sites in proteins as well as in other macromolecules whose interactions are involved in many cellular and physiological processes. The algorithm is a combination of an unsupervised learning algorithm - based on Kohonen self organizing maps - to characterize the properties of patches of protein solvent accessible surfaces and a filtering algorithm to establish both the physical boundaries of the patches as well as the level of contribution of different and distant atoms involved in the interaction. We have found that the algorithm performs extremely well in a set of randomly selected protein complexes for which the interaction interfaces are extracted and compared with the results of the algorithm. A statistical evaluation of the algorithm is additionally performed by analysis of the degree of hydrophobicity and hydrophilicity of the output patches and comparison with that of the observed interface constituent amino acids.}, } @article {pmid11789924, year = {2001}, author = {Oksanen, E and Sober, J and Karnosky, DF}, title = {Impacts of elevated CO2 and/or O3 on leaf ultrastructure of aspen (Populus tremuloides) and birch (Betula papyrifera) in the aspen FACE experiment.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {115}, number = {3}, pages = {437-446}, doi = {10.1016/s0269-7491(01)00233-0}, pmid = {11789924}, issn = {0269-7491}, mesh = {Air Pollutants/*pharmacology ; Betula/*drug effects/metabolism/ultrastructure ; Carbon Dioxide/*pharmacology ; Chloroplasts/drug effects/metabolism/ultrastructure ; Databases as Topic ; Drug Interactions ; Ecosystem ; Forestry ; Microscopy, Electron ; Ozone/*pharmacology ; Plant Leaves/*drug effects/metabolism/ultrastructure ; Salicaceae/*drug effects/metabolism/ultrastructure ; Vacuoles/drug effects/metabolism/ultrastructure ; }, abstract = {Impacts of elevated atmospheric O3 and/or CO2 on three clones of aspen (Populus tremuloides Michx.) and birch (Betula papyrifera Marsh.) were studied to determine, whether or not elevated CO2 ameliorates O3-induced damage to leaf cells. The plants were exposed for 3 years at the Aspen FACE exposure site in Wisconsin (USA) prior to sampling for ultrastructural investigations on 19 June 1999. In the aspen clones, elevated CO2 increased chloroplast cover index, leaf and spongy mesophyll layer thickness, intercellular air space volume in mesophyll, amount of starch in chloroplasts and cytoplasmic lipids but decreased the number of plastoglobuli in chloroplasts. In contrast, elevated O3 decreased chloroplast cover index, starch content, and the proportion of cytoplasm and intercellular space in mesophyll, and increased the proportion of vacuoles, the amount of condensed vacuolar tannins and the number of plastoglobuli. Ozone also caused structural thylakoid injuries (dilation, distortion) and stromal condensation in chloroplasts, which was ameliorated by elevated CO2 by 5-66% in aspen clones and by 2-10% in birch. Birch ultrastructure was less affected by elevated CO2 or O3 stress compared to aspen. In the most O3-sensitive aspen clone, thinner leaves and cell walls, lower proportion of cell wall volume, and higher volume for vacuoles was found compared to more-tolerant clones.}, } @article {pmid11780077, year = {2002}, author = {Knight, J}, title = {Online marine resource could soon be swimming with data.}, journal = {Nature}, volume = {415}, number = {6867}, pages = {4}, doi = {10.1038/415004a}, pmid = {11780077}, issn = {0028-0836}, mesh = {Animals ; *Databases, Factual ; Diving/physiology ; *Internet ; *Marine Biology ; Swimming/*physiology ; }, } @article {pmid11779845, year = {2002}, author = {Nekrutenko, A and Makova, KD and Li, WH}, title = {The K(A)/K(S) ratio test for assessing the protein-coding potential of genomic regions: an empirical and simulation study.}, journal = {Genome research}, volume = {12}, number = {1}, pages = {198-202}, pmid = {11779845}, issn = {1088-9051}, support = {HD38287/HD/NICHD NIH HHS/United States ; GM55759/GM/NIGMS NIH HHS/United States ; GM30998/GM/NIGMS NIH HHS/United States ; R37 GM030998/GM/NIGMS NIH HHS/United States ; R01 GM030998/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Computational Biology/*methods/statistics & numerical data ; *Computer Simulation ; Exons/genetics ; False Positive Reactions ; Genes/genetics ; *Genome ; Genome, Human ; Humans ; Mice ; *Models, Genetic ; Proteins/*genetics ; Proteome/genetics ; Sequence Homology, Nucleic Acid ; }, abstract = {Comparative genomics is a simple, powerful way to increase the accuracy of gene prediction. In this study, we show the utility of a simple test for the identification of protein-coding exons using human/mouse sequence comparisons. The test takes advantage of the fact that in the vast majority of coding regions, synonymous substitutions (K(S)) occur much more frequently than nonsynonymous ones (K(A)) and uses the K(A)/K(S) ratio as the criterion. We show the following: (1) most of the human and mouse exons are sufficiently long and have a suitable degree of sequence divergence for the test to perform reliably; (2) the test is suited for the identification of long exons and single exon genes, which are difficult to predict by current methods; (3) the test has a false-negative rate, lower than most of current gene prediction methods and a false-positive rate lower than all current methods; (4) the test has been automated and can be used in combination with other existing gene-prediction methods.}, } @article {pmid11775500, year = {2001}, author = {Gustafson, EJ and Murphy, NL and Crow, TR}, title = {Using a GIS model to assess terrestrial salamander response to alternative forest management plans.}, journal = {Journal of environmental management}, volume = {63}, number = {3}, pages = {281-292}, doi = {10.1006/jema.2001.0482}, pmid = {11775500}, issn = {0301-4797}, mesh = {Animals ; *Conservation of Natural Resources ; Environment ; Environmental Monitoring ; Female ; Forecasting ; *Geography ; *Information Systems ; Male ; *Models, Theoretical ; Population Dynamics ; Risk Assessment ; *Trees ; *Urodela ; }, abstract = {A GIS model predicting the spatial distribution of terrestrial salamander abundance based on topography and forest age was developed using parameters derived from the literature. The model was tested by sampling salamander abundance across the full range of site conditions used in the model. A regression of the predictions of our GIS model against these sample data showed that the model has a modest but significant ability to predict both salamander abundance and mass per unit area. The model was used to assess the impacts of alternative management plans for the Hoosier National Forest (Indiana, USA) on salamanders. These plans differed in the spatial delineation of management areas where timber harvest was permitted, and the intensity of timber harvest within those management areas. The spatial pattern of forest openings produced by alternative forest management scenarios based on these plans was projected over 150 years using a timber-harvest simulator (HARVEST). We generated a predictive map of salamander abundance for each scenario over time, and summarized each map by calculating mean salamander abundance and the mean colonization distance (average distance from map cells with low predicted abundance to those with relatively high abundance). Projected salamander abundance was affected more by harvest rate (area harvested each decade) than by the management area boundaries. The alternatives had a varying effect on the mean distance salamanders would have to travel to colonize regenerating stands. Our GIS modeling approach is an example of a spatial analytical tool that could help resource management planners to evaluate the potential ecological impact of management alternatives.}, } @article {pmid11768661, year = {2001}, author = {Toonen, RJ and Hughes, S}, title = {Increased throughput for fragment analysis on an ABI PRISM 377 automated sequencer using a membrane comb and STRand software.}, journal = {BioTechniques}, volume = {31}, number = {6}, pages = {1320-1324}, pmid = {11768661}, issn = {0736-6205}, mesh = {Computational Biology ; Microsatellite Repeats/genetics ; Polymerase Chain Reaction ; Polymorphism, Genetic/*genetics ; Sequence Analysis, DNA/*instrumentation/*methods ; *Software ; }, abstract = {This manuscript outlines our protocol for using a freely downloadable fragment analysis software package (STRand) together with a 96+4 RapidLoad membrane comb to increase throughput of samples for fragment analysis on ABI sequencers without costly upgrades from the manufacturer. We outline how using these products allows one to score 90 lanes of sample per gel on an ABI PRISM 377XL (64-lane sequencer), saving both time and money in the processing of samples. This protocol is a major modification to those suggested by the manufacturer. This protocol gives more consistent results that are easier to score than standard protocols, and it reduces reagent costs. Interest in fragment analysis (primarily microsatellites and AFLPs) is steadily increasing among both population ecologists and geneticists, and methods that simultaneously increase sample throughput while reducing costs associated with these analyses by over 50% per gel should prove useful to anyone using an ABI, MJ Basestation, or LI-COR automated sequencer for fragment analysis.}, } @article {pmid11767574, year = {2000}, author = {Yuan, Y and Qin, Q and Lu, R}, title = {[Design and implementation of a landscape analysis system based on remote sensing data].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {11}, number = {6}, pages = {927-930}, pmid = {11767574}, issn = {1001-9332}, mesh = {Algorithms ; *Ecology ; Geography/*methods ; Image Processing, Computer-Assisted ; Information Systems ; }, abstract = {Because of the functions of Geographic Information System(GIS) being not satisfied to the requirements of landscape analysis, a landscape analysis system was designed with Visual C++ and demonstrated with remote sensing data. This system adopted the method f picking-up patch boundary pixel set, improved the patch searching speed, and supplied some landscape analysis functions, such as the calculation of the distance between patches, and the boundary length of neighboring patch, which are not provided by current GIS. It was used to analyzed the landscape of suburbs in northwest Beijing, and the shortcomings of current GIS applied in landscape analysis were overcome.}, } @article {pmid11767551, year = {2000}, author = {Guo, Z and Li, D}, title = {[Ecosystem management of settlement area in Xingshan County].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {11}, number = {6}, pages = {819-826}, pmid = {11767551}, issn = {1001-9332}, mesh = {Agriculture ; *Ecosystem ; Geography/methods ; Information Systems ; *Local Government ; }, abstract = {In the immigrant settlement area of Three-Gorges reservoir region in Xingshan County, Hubei Province, the ecological problems were the restoration of degraded ecosystem, rehabilitation of degraded crop land, and reconstruction of towns and villages. The key to the construction of the settlement area was reassigning the way of land use. The major aim of restoration of natural ecosystems should be to improve water conservation capacity of the land, because this area is located in the catchment of the Xiangxi River. The goals of management were determined as the coordinated development of both agricultural and natural forest ecosystems, the maintenance and increase of water conservation capacity of ecosystems, and the maintenance and extension of wildlife habitats. For the purpose of effective ecosystem management, the area was classified into four divisions of functional conservation region, functional rehabilitation, natural reserves and natural maintenance. The ecosystem management of the settlement area in Xingshan County was implemented in every land cell, using GIS and the typical grid-square survey method. The approach of multi-objects optimal spatial plan was developed in this paper, in which, special emphasis was put on the ecological, economic and social benefits in the construction of towns and villages. According to the scheme of management, the cover of forest in the settlement area, would increase by 30.19%, and water conservation capacity of the ecosystems would raise by 38.7%.}, } @article {pmid11767525, year = {2000}, author = {Lu, J and Wang, Z}, title = {[Qingshishan watershed agro-ecology information system and its application with the support of Geographic Information System (GIS)].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {11}, number = {5}, pages = {703-706}, pmid = {11767525}, issn = {1001-9332}, mesh = {Agriculture ; China ; Climate ; *Ecology ; *Information Systems ; Population ; Soil ; Water ; }, abstract = {Geographic Information System(GIS) is applied to establish Qingshishan Watershed Agro-Ecology Information System (QWAEIS), QWAEIS integrates spatial information such as land use, soil, water and topography with basic information such as population, climate and agricultural production. The watershed agro-ecology information was effectively analyzed and managed by QWAEIS, land suitable classes were evaluated by QWAEIS and the land evaluation result are given, QWAEIS also can support watershed planning with its spatial information.}, } @article {pmid11765993, year = {2001}, author = {Buckley, JA and Georgianna, TD}, title = {Analysis of statistical outliers with application to whole effluent toxicity testing.}, journal = {Water environment research : a research publication of the Water Environment Federation}, volume = {73}, number = {5}, pages = {575-583}, doi = {10.2175/106143001x139641}, pmid = {11765993}, issn = {1061-4303}, mesh = {Analysis of Variance ; Animals ; Crustacea/growth & development ; Data Interpretation, Statistical ; Ecology ; Environmental Monitoring/*statistics & numerical data ; Models, Statistical ; Statistics as Topic/*methods ; Toxicity Tests ; }, abstract = {In this analysis, low-value outliers were detected in five data sets obtained from laboratory records. The effect of removing the outliers by three methods data rejection (asymmetrical and symmetrical trimming and Winsorization) revealed that all three methods slightly increased the mean and reduced the variance of the data sets. These opposing effects on the results of a hypothesis test of means were examined in the context of passing or failing a regulatory requirement significant difference between effluent concentration and a control. Analysis by statistical resampling of one data set showed that while all data rejection methods reduced the level of Type II error in a hypothesis test of no difference in reproduction between a test concentration and a regulatory limit, asymmetrical trimming was the best in this regard.}, } @article {pmid11760187, year = {2001}, author = {Eisenack, K and Kropp, J}, title = {Assessment of management options in marine fisheries by qualitative modelling techniques.}, journal = {Marine pollution bulletin}, volume = {43}, number = {7-12}, pages = {215-224}, doi = {10.1016/s0025-326x(01)00076-5}, pmid = {11760187}, issn = {0025-326X}, mesh = {Animals ; *Conservation of Natural Resources ; Decision Making ; *Decision Support Techniques ; *Ecosystem ; *Fisheries/economics ; *Fishes ; Knowledge ; *Models, Theoretical ; }, abstract = {An effective management of the rapidly dwindling marine fish resources is of great ecological, economic and social importance for the future. An over-development of commercial fisheries has brought about a multitude of negative environmental impacts, such as an accelerated exploitation of stocks or a decrease of marine biodiversity, and furthermore, a profound structural change in fish industry. However, the main reason for the non-prosperous rationing of marine resources is the lack of knowledge about certain processes as well as the non-availability of adequate steering instruments. This paper addresses the lack of conceptualization in the case of uncertain knowledge. It proposes a model approach which can be used for weak but improved decision support under the premise of vague knowledge. The usage of qualitative differential equations illustrates general patterns of overcapitalization of fishing fleets. The extension of traditional model approaches by integration of additional socio-economic phenomena in this context supplies deeper insights in the dynamics of a coupled economic and ecological system. The approach provides a set of characteristic system behaviours which can be fruitfully used for the development of future management tasks.}, } @article {pmid11752186, year = {2002}, author = {Simmons, MP and Randle, CP and Freudenstein, JV and Wenzel, JW}, title = {Limitations of relative apparent synapomorphy analysis (RASA) for measuring phylogenetic signal.}, journal = {Molecular biology and evolution}, volume = {19}, number = {1}, pages = {14-23}, doi = {10.1093/oxfordjournals.molbev.a003978}, pmid = {11752186}, issn = {0737-4038}, mesh = {Algorithms ; Base Sequence ; Codon/genetics ; Computational Biology/*methods ; Computer Simulation ; *Evolution, Molecular ; Models, Genetic ; *Phylogeny ; Ribulose-Bisphosphate Carboxylase/genetics ; }, abstract = {In this paper we use hypothetical and empirical data matrices to evaluate the ability of relative apparent synapomorphy analysis (RASA) to measure phylogenetic signal, select outgroups, and identify terminals subject to long-branch attraction. In all cases, except for equal character-state frequencies, RASA indicated extraordinarily high levels of phylogenetic information for hypothetical data matrices that are uninformative regarding relationships among the terminals. Yet, regardless of the number of characters or character-state frequencies, RASA failed to detect phylogenetic signal for hypothetical matrices with strong phylogenetic signal. In our empirical example, RASA indicated increasing phylogenetic signal for matrices for which the strict consensus of the most parsimonious trees is increasingly poorly resolved, clades are increasingly poorly supported, and for which many relationships are in conflict with more widely sampled analyses. RASA is an ineffective approach to identify outgroup terminal(s) with the most plesiomorphic character states for the ingroup. Our hypothetical example demonstrated that RASA preferred outgroup terminals with increasing numbers of convergent character states with ingroup terminals, and rejected the outgroup terminal with all plesiomorphic character states. Our empirical example demonstrated that RASA, in all three cases examined, selected an ingroup terminal, rather than an outgroup terminal, as the best outgroup. In no case was one of the two outgroup terminals even close to being considered the optimal outgroup by RASA. RASA is an ineffective means of identifying problematic long-branch terminals. In our hypothetical example, RASA indicated a terminal as being a problematic long-branch terminal in spite of the terminal being on a zero-length branch and having no possibility of undergoing long-branch attraction with another terminal. RASA also failed to identify actual problematic long-branch terminals that did undergo long-branch attraction, but only after following Lyons-Weiler and Hoelzer's (1997) three-step process to identify and remove terminals subject to long-branch attraction. We conclude that RASA should not be used for any of these purposes.}, } @article {pmid11731194, year = {2001}, author = {Tofanelli, S and Taglioli, L and Varesi, L and Paoli, G}, title = {The STR-based genetic profile of the population from Corsica island (France).}, journal = {Forensic science international}, volume = {123}, number = {1}, pages = {33-38}, doi = {10.1016/s0379-0738(01)00516-3}, pmid = {11731194}, issn = {0379-0738}, mesh = {*Alleles ; DNA/*genetics ; Databases, Factual ; France ; *Genetics, Population ; Humans ; Markov Chains ; *Tandem Repeat Sequences ; }, abstract = {Short tandem repeats (STR) at loci HumFES/FPS, HumVWA, HumCSF1PO, HumTH01, HumFXIIIA01, HumTPOX, HumCD4, D3S1358 are markers of choice for population genetics and validated systems for forensic use. In this report, we analysed their allele frequency distribution in a sample of native blood donors from the two departments of Corsica island (France). Deviations from the Hardy-Weinberg rule and heterozygosity values consistently suggested a spatial differentiation of allele and genotype frequencies across the island. Pairwise comparisons showed that Corsican gene pool presents a high level of heterogeneity between departments and substantially differs from that of neighbouring and historically-related populations. The results suggest the use of local databases to calculate a priori statistics in human identity testing.}, } @article {pmid11723701, year = {2001}, author = {Boulos, MN and Roudsari, AV and Carson, ER}, title = {Health geomatics: an enabling suite of technologies in health and healthcare.}, journal = {Journal of biomedical informatics}, volume = {34}, number = {3}, pages = {195-219}, doi = {10.1006/jbin.2001.1015}, pmid = {11723701}, issn = {1532-0464}, mesh = {Delivery of Health Care ; *Geography ; *Information Management ; *Medical Laboratory Science ; }, abstract = {This Methodolical Review describes how health geomatics can improve our understanding of the important relationship between location and health, and thus assist us in Public Health tasks like disease prevention, and also in better healthcare service planning. The reader is first introduced to health geography and its two main divisions, disease ecology and healthcare delivery, followed by an overview of the basic concepts and principles of health geomatics. Topics covered include geographical information systems (GIS), GIS modeling, and GIS-related technologies (remote sensing and the global positioning system). We also present a number of real-life health geomatics applications and projects, with pointers to further studies and resources. Finally, we discuss the barriers facing the adoption of GIS technology in the health sector, including data availability/quality issues. The authors believe that we still need to combat many cultural and organizational barriers, including "spatial illiteracy" among healthcare workers, while making the tools cheaper and easier to learn and use, before health geomatics can become a mainstream technology in the health sector like today's spreadsheets and databases.}, } @article {pmid11714516, year = {2001}, author = {Ye, RW and Wang, T and Bedzyk, L and Croker, KM}, title = {Applications of DNA microarrays in microbial systems.}, journal = {Journal of microbiological methods}, volume = {47}, number = {3}, pages = {257-272}, doi = {10.1016/s0167-7012(01)00308-6}, pmid = {11714516}, issn = {0167-7012}, mesh = {DNA, Bacterial/analysis/*genetics ; Databases, Genetic ; Gene Expression Profiling ; Genome, Bacterial ; Genomics ; Oligonucleotide Array Sequence Analysis/*methods ; Phylogeny ; Polymerase Chain Reaction ; Prokaryotic Cells ; RNA/genetics ; Transcription, Genetic ; }, abstract = {DNA microarray technology allows a parallel analysis of RNA abundance and DNA homology for thousands of genes in a single experiment. Over the past few years, this powerful technology has been used to explore transcriptional profiles and genome differences for a variety of microorganisms, greatly facilitating our understanding of microbial metabolism. With the increasing availability of complete microbial genomes, DNA microarrays are becoming a common tool in many areas of microbial research, including microbial physiology, pathogenesis, epidemiology, ecology, phylogeny, pathway engineering and fermentation optimization.}, } @article {pmid11700601, year = {2000}, author = {Del Carpio, CA and Yoshimori, A}, title = {MIAX: a system for assessment of macromolecular interaction. 3) A parallel hybrid GA for flexible protein docking.}, journal = {Genome informatics. Workshop on Genome Informatics}, volume = {11}, number = {}, pages = {205-214}, pmid = {11700601}, mesh = {*Algorithms ; Biological Evolution ; Computational Biology ; Computer Simulation ; Macromolecular Substances ; Models, Genetic ; Models, Molecular ; Mutation ; Protein Binding ; Protein Conformation ; Proteins/*chemistry/genetics/metabolism ; }, abstract = {We propose a parallel hybrid genetic algorithm for flexible protein-protein docking in order to improve the conventional rigid-body models to manipulate protein-protein interactions. The proposed hybrid algorithm is a combination of an evolutionary algorithm with a simulated annealing one, yielding a powerful protein-complex conformation-searching engine. Parallelization of the procedure makes possible to reach high algorithm performance, in both, execution times and size of treated monomers and complexes. Knowledge on side chain flexibility is extracted by means of an exhaustive analysis of crystallographic data on proteins and protein complexes. Results demonstrate the competency of the algorithm since comparison of calculated and crystallographic data accounts for a maximum of 2.5A in RMS difference, including side chain conformation. The system allows routine analysis of this fundamental molecular biology problem important to elucidate bio-macromolecular function in biophysical and biochemical mechanisms involving molecular recognition and interaction, yielding simultaneously clues for designing new proteins and enzymes directed to different purposes.}, } @article {pmid11697258, year = {2001}, author = {Wulff, F and Bonsdorff, E and Gren, IM and Johansson, S and Stigebrandt, A}, title = {Giving advice on cost effective measures for a cleaner Baltic Sea: a challenge for science.}, journal = {Ambio}, volume = {30}, number = {4-5}, pages = {254-259}, pmid = {11697258}, issn = {0044-7447}, mesh = {Baltic States ; Cost-Benefit Analysis ; *Decision Support Techniques ; Ecosystem ; Environmental Monitoring ; *Eutrophication ; Interprofessional Relations ; Policy Making ; Public Policy ; Water Movements ; Water Pollution/*economics/*prevention & control ; }, abstract = {The Baltic Sea is one of the world's seas that is most severely affected by human activities. Although there is an international agreement that nutrient input to the Baltic should be reduced, the measures taken so far have not resulted in major reductions in nutrient inputs nor in environmental improvements. The reasons for this are partly due to lack of knowledge on large-scale relationships and couplings between physics, biogeochemistry and ecological properties. But there is also a lack of overall drainage basin-wide analyses on cost-effective measures. There is a danger in making the wrong decisions, e.g. implement reduction schemes that are at worst ineffective or at best, far from cost effective. Researchers from many disciplines are faced with a common challenge: To develop a decision-support system, which can be used as the scientific base for cost-effective measures for the entire Baltic Sea. Such an effort is now being made within the research program MARE (http://www.mare.su.se).}, } @article {pmid11691990, year = {2001}, author = {Kidwell, SM}, title = {Preservation of species abundance in marine death assemblages.}, journal = {Science (New York, N.Y.)}, volume = {294}, number = {5544}, pages = {1091-1094}, doi = {10.1126/science.1064539}, pmid = {11691990}, issn = {0036-8075}, mesh = {Animals ; Biomass ; Databases, Factual ; *Ecosystem ; Environment ; *Fossils ; *Geologic Sediments ; *Mollusca ; Population Dynamics ; Seawater ; Statistics as Topic ; }, abstract = {Fossil assemblages of skeletal material are thought to differ from their source live communities, particularly in relative abundance of species, owing to potential bias from postmortem transport and time-averaging of multiple generations. However, statistical meta-analysis of 85 marine molluscan data sets indicates that, although sensitive to sieve mesh-size and environment, time-averaged death assemblages retain a strong signal of species' original rank orders. Naturally accumulated death assemblages thus provide a reliable means of acquiring the abundance data that are key to a new generation of paleobiologic and macroecologic questions and to extending ecological time-series via sedimentary cores.}, } @article {pmid11657327, year = {1999}, author = {Sharp, RR and Barrett, JC}, title = {The Environmental Genome Project and bioethics.}, journal = {Kennedy Institute of Ethics journal}, volume = {9}, number = {2}, pages = {175-188}, doi = {10.1353/ken.1999.0014}, pmid = {11657327}, issn = {1054-6863}, mesh = {Confidentiality ; Databases, Factual ; Databases, Nucleic Acid ; Disclosure ; Ecology ; Genetic Determinism ; Genetic Engineering ; *Genetic Predisposition to Disease ; Genetic Privacy ; *Genetic Research ; Genetic Testing ; *Genetics ; Genetics, Behavioral ; Genetics, Population ; *Hazardous Substances ; Human Experimentation ; *Human Genome Project ; Humans ; Informed Consent ; Pedigree ; Privacy ; Research Subjects ; Risk ; Risk Assessment ; Tissue Donors ; Tissue and Organ Procurement ; United States ; }, } @article {pmid11606695, year = {2001}, author = {Ota, S and Li, WH}, title = {NJML+: an extension of the NJML method to handle protein sequence data and computer software implementation.}, journal = {Molecular biology and evolution}, volume = {18}, number = {11}, pages = {1983-1992}, doi = {10.1093/oxfordjournals.molbev.a003740}, pmid = {11606695}, issn = {0737-4038}, support = {GM30998/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Base Sequence ; Computational Biology/*methods/*statistics & numerical data ; *Computer Simulation ; Likelihood Functions ; Myosin Light Chains/chemistry/genetics ; Phylogeny ; Proteins/*chemistry/genetics ; *Software/statistics & numerical data ; Software Design ; }, abstract = {While the maximum-likelihood (ML) method of tree reconstruction is statistically rigorous, it is extremely time-consuming for reconstructing large trees. We previously developed a hybrid method (NJML) that combines the neighbor-joining (NJ) and ML methods and thus is much faster than the ML method and improves the performance of NJ. However, we considered only nucleotide sequence data, so NJML is not suitable for handling amino acid sequence data, which requires even more computer time. NJML+ is an implementation of a further improved method for practical data analyses (including protein sequence data). Our extensive simulations using nucleotide and amino acid sequences showed that NJML+ gave good results in tree reconstruction. Indeed, NJML+ showed substantial improvements over existing methods in terms of both computational times and efficiencies, especially for amino acid sequence data. We also developed a "user-friendly" interface for the NJML+ program, including a simple tree viewer.}, } @article {pmid11590753, year = {2001}, author = {Moser, A}, title = {Engineering for problem solving in future: eco-social market economy and eco-social tech.}, journal = {Journal of environmental sciences (China)}, volume = {13}, number = {3}, pages = {257-264}, pmid = {11590753}, issn = {1001-0742}, mesh = {Biotechnology/trends ; *Decision Support Techniques ; *Ecology ; Industry ; Marketing of Health Services ; Problem Solving ; *Socioeconomic Factors ; *Technology/trends ; }, abstract = {The paper differentiates approaches in technology (end-of-pipe, cleaner production, industrial ecology, zero emission and eco-social-tech) and compares them in respect to the problem solving capacity on the ecological as well as social dimension by showing the eco-impact reduction and job creation. Eco-social-tech represents the approach with highest problem solution as it is based on "eco-social market economy", which will the replace free market economy. The deep background of these innovations is "ecosophy", the wisdom of nature, which serves as guideline for eco-restructuring the world.}, } @article {pmid11584749, year = {2001}, author = {De La Rocque, S and Michel, JF and De Wispelaere, G and Cuisance, D}, title = {[New tools for the study of animal trypanosomiasis in the Sudan: model-building of dangerous epidemiological passage by remote sensing geographic information systems].}, journal = {Parasite (Paris, France)}, volume = {8}, number = {3}, pages = {171-195}, doi = {10.1051/parasite/2001083171}, pmid = {11584749}, issn = {1252-607X}, mesh = {Animals ; Burkina Faso ; Ecosystem ; Epidemiologic Methods ; Fresh Water ; Geography ; Information Systems ; Models, Biological ; Sudan ; Telecommunications ; Trypanosomiasis, African/*epidemiology/*veterinary ; Tsetse Flies/*parasitology ; }, abstract = {Recent studies in a rangeland area of Burkina Faso showed that riparian tsetse flies (Glossina tachinoides and G. palpalis gambiensis) were found along the main rivers, but depending on their location, they had different hosts and were not infected by the same trypanosomoses. There were different epidemiological situations within a distance of a few kilometres, and local assessment of the trypanosome risk thus called for a global approach taking account of the environmental and human factors involved in the interfaces between hosts and vectors. Various types of information concerning entomology, parasitology, ecology, land occupation and animal production systems were fed into a Geographical Information System. High spatial resolution remote sensing tools and original modelling methods were used to detect the valley landscapes most favourable to tsetse flies, and describe land use by herds. The impact of trypanosomes appeared to depend largely on animal movements, watering practices and the degree of contact with riparian tsetse flies. Linking these types of information revealed the most dangerous sites in epidemiological terms, which in this case represented some 18% of the network initially surveyed.}, } @article {pmid11583596, year = {2001}, author = {Hendrickx, G and Napala, A and Slingenbergh, JH and De Deken, R and Rogers, DJ}, title = {A contribution towards simplifying area-wide tsetse surveys using medium resolution meteorological satellite data.}, journal = {Bulletin of entomological research}, volume = {91}, number = {5}, pages = {333-346}, doi = {10.1079/ber2001103}, pmid = {11583596}, issn = {0007-4853}, mesh = {Animals ; Burkina Faso ; Cote d'Ivoire ; *Databases, Factual ; Meteorological Concepts ; Population Density ; Statistics as Topic ; *Tsetse Flies ; }, abstract = {A raster or grid-based Geographic Information System with data on tsetse, trypanosomiasis, animal production, agriculture and land use has recently been developed in Togo. The area-wide sampling of tsetse fly, aided by satellite imagery, is the subject of two separate papers. This paper follows on a first paper, published in this journal, describing the generation of digital tsetse distribution and abundance maps and how these accord with the local climatic and agro-ecological setting. Such maps when combined with data on the disease, the hosts and their owners, should contribute to the knowledge of the spatial epidemiology of trypanosomiasis and assist planning of integrated control operations. Here we address the problem of generating tsetse distribution and abundance maps from remotely sensed data, using a restricted amount of field data. Different discriminant analysis models have been applied using contemporary tsetse data and remotely sensed, low resolution data acquired from the National Oceanographic and Atmospheric Administration (NOAA) and Meteosat platforms. The results confirm the potential of satellite data application and multivariate analysis for the prediction of the tsetse distribution and abundance. This opens up new avenues because satellite predictions and field data may be combined to strengthen and/or substitute one another. The analysis shows how the strategic incorporation of satellite imagery may minimize field collection of data. Field surveys may be modified and conducted in two stages, first concentrating on the expected fly distribution limits and thereafter on fly abundance. The study also shows that when applying satellite data, care should be taken in selecting the optimal number of predictor variables because this number varies with the amount of training data for predicting abundance and on the homogeneity of the distribution limits for predicting fly presence. Finally, it is suggested that in addition to the use of contemporary training data and predictor variables, training and predicted data sets should refer to the same eco-geographic zone.}, } @article {pmid11577222, year = {2001}, author = {Jackson, JB and Johnson, KG}, title = {Paleoecology. Measuring past biodiversity.}, journal = {Science (New York, N.Y.)}, volume = {293}, number = {5539}, pages = {2401-2404}, doi = {10.1126/science.1063789}, pmid = {11577222}, issn = {0036-8075}, mesh = {Animals ; Biological Evolution ; Classification ; Databases, Factual ; *Ecosystem ; *Fossils ; *Invertebrates/classification ; *Marine Biology ; Oceans and Seas ; *Paleontology ; Panama ; Sampling Studies ; }, } @article {pmid11572274, year = {2001}, author = {Aldrich, TE and Andrews, KW and Liboff, AR}, title = {Brain cancer risk and electromagnetic fields (EMFs): assessing the geomagnetic component.}, journal = {Archives of environmental health}, volume = {56}, number = {4}, pages = {314-319}, doi = {10.1080/00039890109604462}, pmid = {11572274}, issn = {0003-9896}, mesh = {Aged ; Brain Neoplasms/*epidemiology/*etiology ; Case-Control Studies ; Cluster Analysis ; Confounding Factors, Epidemiologic ; Cyclotrons ; Databases, Factual ; Electromagnetic Fields/*adverse effects ; Environmental Exposure/*adverse effects/analysis ; Environmental Monitoring ; Epidemiological Monitoring ; Female ; Geography ; Humans ; Incidence ; Information Systems ; Logistic Models ; Male ; Middle Aged ; North Carolina/epidemiology ; Population Surveillance ; *Power Plants ; Predictive Value of Tests ; Residence Characteristics/statistics & numerical data ; Risk Factors ; }, abstract = {Cancer cluster studies in North Carolina identified several communities in which there existed an elevated risk of brain cancer. These findings prompted a series of case-control studies. The current article, which originated from the results of the 3rd of such studies, is focused on inclusion of the earth's own geomagnetic fields that interact with electromagnetic fields generated from distribution power lines. This article also contains an assessment of the contribution of confounding by residential (e.g., urban, rural) and case characteristics (e.g., age, race, gender). Newly diagnosed brain cancer cases were identified for a 4-county region of central North Carolina, which the authors chose on the basis of the results of earlier observations. A 3:1 matched series of cancer cases from the same hospitals in which the cases were diagnosed served as the comparison group. Extensive geographic information was collected and was based on an exact place of residence at the time of cancer diagnosis, thus providing several strategic geophysical elements for assessment. The model for this assessment was based on the effects of these two sources of electromagnetic fields for an ion cyclotron resonance mechanism of disease risk. The authors used logistic regression models that contained the predicted value for the parallel component of the earth's magnetic field; these models were somewhat erratic, and the elements were not merged productively into a single statistical model. Interpretation of these values was difficult; therefore, the modeled values for the model elements, at progressive distances from the nearest power-line segments, are provided. The results of this study demonstrate the merits of using large, population-based databases, as well as using rigorous Geographic Information System techniques, for the assessment of ecologic environmental risks. The results also suggest promise for exposure classification that is compatible with the theoretical biological mechanisms posited for electromagnetic fields.}, } @article {pmid11547246, year = {2001}, author = {Filleul, L and Zeghnoun, A and Declercq, C and Le Goaster, C and Le Tertre, A and Eilstein, D and Medina, S and Saviuc, P and Prouvost, H and Cassadou, S and Pascal, L and Quénel, P}, title = {[Short-term relationships between urban atmospheric pollution and respiratory mortality: time series studies].}, journal = {Revue des maladies respiratoires}, volume = {18}, number = {4 Pt 1}, pages = {387-395}, pmid = {11547246}, issn = {0761-8425}, mesh = {Adult ; Aged ; Air Pollution/*adverse effects ; Data Interpretation, Statistical ; Ecology ; Female ; Humans ; Male ; Meteorological Concepts ; Respiratory Tract Diseases/*mortality ; Risk Factors ; Seasons ; Smoking/adverse effects ; Time Factors ; *Urban Population ; }, abstract = {Time series studies conducted in the field of air pollution aim at testing and quantifying short-term relations which can exist between daily air pollution levels and daily health effects. The method used for this type of survey has sometimes been misunderstood mainly because individual factors and indoor exposure to air pollutants were not taken into account. The adjustment on these individual confounding factors commonly used in classic epidemiologic studies (case-control studies, cohort studies) is not adequate to times series studies which are based on aggregate data. This is different for those factors that change over time according to the levels of air pollution (meteorological conditions, influenza epidemics, trend of health cases) which, when being analysed, must be taken into account either indirectly through time modelling or directly through non-linear modelling processes. During this last decade, numerous studies using the time series method have been published and have found short-term associations between daily levels of air pollution commonly observed and daily respiratory mortality. The consistency of the numerous results published in the international literature are more arguments in favour of non-confounding short-term relations between air pollution and respiratory mortality.}, } @article {pmid11544202, year = {2001}, author = {Wiehe, T and Gebauer-Jung, S and Mitchell-Olds, T and Guigó, R}, title = {SGP-1: prediction and validation of homologous genes based on sequence alignments.}, journal = {Genome research}, volume = {11}, number = {9}, pages = {1574-1583}, pmid = {11544202}, issn = {1088-9051}, mesh = {*Algorithms ; Animals ; Brassica/genetics ; Codon/genetics ; Databases, Factual ; Evolution, Molecular ; Genes/*genetics ; Humans ; Mice ; RNA Splice Sites/genetics ; Rats ; Sequence Alignment/*methods ; *Sequence Homology, Nucleic Acid ; }, abstract = {Conventional methods of gene prediction rely on the recognition of DNA-sequence signals, the coding potential or the comparison of a genomic sequence with a cDNA, EST, or protein database. Reasons for limited accuracy in many circumstances are species-specific training and the incompleteness of reference databases. Lately, comparative genome analysis has attracted increasing attention. Several analysis tools that are based on human/mouse comparisons are already available. Here, we present a program for the prediction of protein-coding genes, termed SGP-1 (Syntenic Gene Prediction), which is based on the similarity of homologous genomic sequences. In contrast to most existing tools, the accuracy of depends little on species-specific properties such as codon usage or the nucleotide distribution. may therefore be applied to nonstandard model organisms in vertebrates as well as in plants, without the need for extensive parameter training. In addition to predicting genes in large-scale genomic sequences, the program may be useful to validate gene structure annotations from databases. To this end, SGP-1 output also contains comparisons between predicted and annotated gene structures in HTML format. The program can be accessed via a Web server at http://soft.ice.mpg.de/sgp-1. The source code, written in ANSI C, is available on request from the authors.}, } @article {pmid11544080, year = {2001}, author = {Hochachka, PW and Mommsen, TP and Walsh, PJ}, title = {Knowledge explosion in comparative physiology and biochemistry: its causes and its future.}, journal = {Comparative biochemistry and physiology. Part B, Biochemistry & molecular biology}, volume = {130}, number = {2}, pages = {125-6; discussion 133-4}, pmid = {11544080}, issn = {1096-4959}, mesh = {Allergy and Immunology/trends ; Animals ; Biochemical Phenomena ; Databases, Nucleic Acid ; Ecology ; Evolution, Molecular ; Gene Amplification/physiology ; Genome, Human ; Humans ; Molecular Biology/*trends ; Phylogeny ; Physiology, Comparative/*trends ; RNA Editing/physiology ; RNA Splicing/physiology ; Sequence Analysis, DNA ; }, } @article {pmid11536347, year = {2001}, author = {De Vreese, LP and Neri, M and Fioravanti, M and Belloi, L and Zanetti, O}, title = {Memory rehabilitation in Alzheimer's disease: a review of progress.}, journal = {International journal of geriatric psychiatry}, volume = {16}, number = {8}, pages = {794-809}, doi = {10.1002/gps.428}, pmid = {11536347}, issn = {0885-6230}, mesh = {Adaptation, Psychological ; Aged ; Aged, 80 and over ; Alzheimer Disease/classification/physiopathology/psychology/*rehabilitation ; Cues ; Evidence-Based Medicine ; Forecasting ; Geriatric Assessment ; Humans ; *Memory ; Psychomotor Performance ; Reminder Systems ; Research/trends ; Severity of Illness Index ; Treatment Outcome ; }, abstract = {BACKGROUND: Memory rehabilitation is a sadly misrepresented area of applied research in Alzheimer's disease.

OBJECTIVES: To gather and evaluate recent evidence for the clinical effectiveness or ecologically validity of memory rehabilitation for mild to moderate Alzheimer's patients.

METHODS: Computerised searches and some handsearching were conducted spanning the last five years, from 1995 to 2000, inclusively. Criteria for inclusion in this overview involved the use of a precise memory rehabilitation technique within an experimental study design applied to Alzheimer's patients with pre- and post-treatment evaluation.

FINDINGS: Three potential levels of memory rehabilitation procedures with proven clinical or pragmatic efficacy were identified. The first level bears on the facilitation of residual explicit memory with structured support both at encoding and at subsequent recall; the second level of memory rehabilitation exploits the relatively intact implicit memory system (priming and procedural memory); the last deals with finding ways of coping with the patient's limited explicit memory capacities through the use of external memory aids. A proposal of suggestions for good practice and future research in memory rehabilitation is also offered with the hope to spur further development in this rapidly expanding area of applied research.

CONCLUSION: The available evidence shows that alternative and innovative ways of memory rehabilitation for Alzheimer's patients can indeed be clinically effective or pragmatically useful with a great potential for use within the new culture of a more graded and proactive type of Alzheimer's disease care.}, } @article {pmid11534903, year = {2001}, author = {Wang, X and Sun, C and Gao, S and Wang, L and Shuokui, H}, title = {Validation of germination rate and root elongation as indicator to assess phytotoxicity with Cucumis sativus.}, journal = {Chemosphere}, volume = {44}, number = {8}, pages = {1711-1721}, doi = {10.1016/s0045-6535(00)00520-8}, pmid = {11534903}, issn = {0045-6535}, mesh = {Biomarkers ; Cucumis/*physiology ; Databases, Factual ; Environmental Monitoring/methods ; Germination/*drug effects ; Models, Theoretical ; Plant Roots/drug effects/*growth & development ; Risk Assessment ; Soil Pollutants/*toxicity ; Structure-Activity Relationship ; Toxicity Tests ; }, abstract = {Germination rate and root elongation, as a rapid phytotoxicity test method, possess several advantages, such as sensitivity, simplicity, low cost and suitability for unstable chemicals or samples. These advantages made them suitable for developing a large-scale phytotoxicity database and especially applicable for developing quantitative structure-activity relationship (QSAR) to study mechanisms of phytotoxicity. In this paper, the comparative inhibition of germination rate and root elongation of Cucumis sativus by selected halogen-substituted phenols and anilines were determined. The suitability of germination rate and root elongation as phytotoxicity endpoints was evaluated. Excellent reproducibility and stability of germination rate and root elongation in the control test, relatively greater sensitivity and similar dose-response relations for all tested compounds were observed. These results together with those of a 2-day test were used to demonstrate the suitability of this phytotoxicity test method. A QSAR was developed for the phytotoxicity mode of action of the tested compounds to C sativus seeds. Models that combined the logarithm of 1-octanol/water partition coefficient (log Kow) and the energy of the lowest unoccupied molecular orbital (Elumo) were developed for both germination rate inhibition and root elongation inhibition. The results of these studies indicate that phytotoxicity of substituted phenols and anilines to C. sativus seeds could be explained by a polar narcosis mechanism. This paper will promote the application of germination rate and root elongation method and the development of large-scale phytotoxicity database, which will provide the fundamental data for QSAR and ecological risk assessment of organic pollutants.}, } @article {pmid11505899, year = {2001}, author = {MacLeod, M and Woodfine, DG and Mackay, D and McKone, T and Bennett, D and Maddalena, R}, title = {BETR North America: a regionally segmented multimedia contaminant fate model for North America.}, journal = {Environmental science and pollution research international}, volume = {8}, number = {3}, pages = {156-163}, pmid = {11505899}, issn = {0944-1344}, mesh = {Air Movements ; Databases, Factual ; Environmental Exposure ; Environmental Monitoring ; Environmental Pollutants/*analysis ; Humans ; *Models, Theoretical ; Multimedia ; North America ; Organic Chemicals/*analysis ; Water Movements ; }, abstract = {We present the Berkeley-Trent North American contaminant fate model (BETR North America), a regionally segmented multimedia contaminant fate model based on the fugacity concept. The model is built on a framework that links contaminant fate models of individual regions, and is generally applicable to large, spatially heterogeneous areas. The North American environment is modeled as 24 ecological regions, within each region contaminant fate is described using a 7 compartment multimedia fugacity model including a vertically segmented atmosphere, freshwater, freshwater sediment, soil, coastal water and vegetation compartments. Inter-regional transport of contaminants in the atmosphere, freshwater and coastal water is described using a database of hydrological and meteorological data compiled with Geographical Information Systems (GIS) techniques. Steady-state and dynamic solutions to the 168 mass balance equations that make up the linked model for North America are discussed, and an illustrative case study of toxaphene transport from the southern United States to the Great Lakes Basin is presented. Regionally segmented models such as BETR North America can provide a critical link between evaluative models of long-range transport potential and contaminant concentrations observed in remote regions. The continent-scale mass balance calculated by the model provides a sound basis for evaluating long-range transport potential of organic pollutants, and formulation of continent-scale management and regulatory strategies for chemicals.}, } @article {pmid11505264, year = {2001}, author = {Patton, LL and Bonito, AJ and Shugars, DA}, title = {A systematic review of the effectiveness of antifungal drugs for the prevention and treatment of oropharyngeal candidiasis in HIV-positive patients.}, journal = {Oral surgery, oral medicine, oral pathology, oral radiology, and endodontics}, volume = {92}, number = {2}, pages = {170-179}, doi = {10.1067/moe.2001.116600}, pmid = {11505264}, issn = {1079-2104}, support = {290-97-0011//PHS HHS/United States ; }, mesh = {AIDS-Related Opportunistic Infections/drug therapy/*prevention & control ; Amphotericin B/therapeutic use ; Antifungal Agents/*therapeutic use ; Candidiasis/drug therapy/*prevention & control ; Candidiasis, Oral/drug therapy/*prevention & control ; Clotrimazole/therapeutic use ; Databases as Topic ; Fluconazole/therapeutic use ; HIV Seropositivity/microbiology ; Humans ; Itraconazole/therapeutic use ; Ketoconazole/therapeutic use ; Nystatin/therapeutic use ; Oropharynx/*microbiology ; Pharyngeal Diseases/*microbiology ; Randomized Controlled Trials as Topic ; Research Design ; Statistics as Topic ; Treatment Outcome ; }, abstract = {OBJECTIVE: A systematic review of randomized clinical trials published between 1966 and April 2000 was undertaken to determine the strength of evidence for the effectiveness of antifungal drugs (nystatin, clotrimazole, amphotericin B, fluconazole, ketoconazole, and itraconazole) to prevent and treat oral candidiasis in human immunodeficiency virus-positive patients.

STUDY DESIGN: An automated database search identified 366 articles. Six met inclusion and exclusion criteria with respect to prophylaxis; 12 met criteria for treatment of oral candidiasis.

RESULTS: The evidence for the prophylactic efficacy of fluconazole is good, although insufficient to draw conclusions about the other antifungals. Evidence for treatment effectiveness is insufficient for amphotericin B but good for nystatin, clotrimazole, fluconazole, ketoconazole, and itraconazole.

CONCLUSION: Suggestions for strengthening the evidence base include the following: use of larger, more well-defined groups; control for immunologic status, viral load, history of oral candidiasis, past exposure to antifungals, baseline oral Candida carriage, drug interactions, and antiretroviral therapy; and consistent use of compliance monitors, fungal speciation, and susceptibility testing.}, } @article {pmid11504856, year = {2001}, author = {Stone, JR and Wray, GA}, title = {Rapid evolution of cis-regulatory sequences via local point mutations.}, journal = {Molecular biology and evolution}, volume = {18}, number = {9}, pages = {1764-1770}, doi = {10.1093/oxfordjournals.molbev.a003964}, pmid = {11504856}, issn = {0737-4038}, mesh = {Animals ; Binding Sites/genetics ; Computer Simulation ; DNA/genetics/metabolism ; Databases, Factual ; *Evolution, Molecular ; Humans ; Point Mutation/*genetics ; Regulatory Sequences, Nucleic Acid/*genetics ; Transcription Factors/metabolism ; }, abstract = {Although the evolution of protein-coding sequences within genomes is well understood, the same cannot be said of the cis-regulatory regions that control transcription. Yet, changes in gene expression are likely to constitute an important component of phenotypic evolution. We simulated the evolution of new transcription factor binding sites via local point mutations. The results indicate that new binding sites appear and become fixed within populations on microevolutionary timescales under an assumption of neutral evolution. Even combinations of two new binding sites evolve very quickly. We predict that local point mutations continually generate considerable genetic variation that is capable of altering gene expression.}, } @article {pmid11504217, year = {2001}, author = {Berry, KH and Christopher, MM}, title = {Guidelines for the field evaluation of desert tortoise health and disease.}, journal = {Journal of wildlife diseases}, volume = {37}, number = {3}, pages = {427-450}, doi = {10.7589/0090-3558-37.3.427}, pmid = {11504217}, issn = {0090-3558}, mesh = {Animal Welfare ; Animals ; Animals, Wild ; Behavior, Animal ; Conservation of Natural Resources ; Databases, Factual ; Desert Climate ; Environmental Monitoring ; Epidemiological Monitoring ; Evaluation Studies as Topic ; Eye Diseases/epidemiology/prevention & control/*veterinary ; Female ; Guidelines as Topic/*standards ; Male ; Models, Biological ; Respiratory Tract Diseases/epidemiology/prevention & control/*veterinary ; Seasons ; Stress, Physiological ; Turtles/*physiology ; }, abstract = {Field evaluation of free-ranging wildlife requires the systematic documentation of a variety of environmental conditions and individual parameters of health and disease, particularly in the case of rare or endangered species. In addition, defined criteria are needed for the humane salvage of ill or dying animals. The purpose of this paper is to describe, in detail, the preparation, procedures, and protocols we developed and tested for the field evaluation of wild desert tortoises (Gopherus agassizii). These guidelines describe: preparations for the field, including developing familiarity with tortoise behavior and ecology, and preparation of standardized data sheets; journal notes to document background data on weather conditions, temperature, rainfall, locality, and historic and recent human activities; procedures to prevent the spread of disease and parasites; data sheets for live tortoises to record tortoise identifiation, location, sex, body measurements and activity; health profile forms for documenting and grading physical abnormalities of tortoise posture and movements, general condition (e.g., lethargy, cachexia), external parasites, and clinical abnormalities associated with shell and upper respiratory diseases; permanent photographic records for the retrospective analysis of progression and regression of upper respiratory and eye diseases, analysis of shell lesions and evaluation of growth and age; and indications and methods for salvaging ill or dying tortoises for necropsy evaluation. These guidelines, tested on 5,000 to 20,000 tortoises over a 10 to 27 yr period, were designed to maximize acquisition of data for demographic, ecological, health and disease research projects; to reduce handling and stress of individual animals; to avoid spread of infectious disease; to promote high quality and consistent data sets; and to reduce the duration and number of field trips. The field methods are adapted for desert tortoise life cycle, behavior, anatomy, physiology, and pertinent disease; however the model is applicable to other species of reptiles. Comprehesive databases of clinical signs of disease and health are crucial to research endeavors and essential to decisions on captive release, epidemiology of disease, translocation of wild tortoises, breeding programs, and euthanasia.}, } @article {pmid11494608, year = {2000}, author = {Lindstrom, RR}, title = {Towards the virtual hospital: an ecological approach to network development in health services.}, journal = {Hospital quarterly}, volume = {3}, number = {3}, pages = {18-25}, doi = {10.12927/hcq..16713}, pmid = {11494608}, issn = {1480-221X}, mesh = {British Columbia ; Community Networks/*organization & administration ; Efficiency, Organizational ; Health Planning ; *Hospital Administration ; Humans ; *Internet ; *Organizational Innovation ; User-Computer Interface ; }, } @article {pmid11484041, year = {2001}, author = {Alford, RA and Dixon, PM and Pechmann, JH}, title = {Ecology. Global amphibian population declines.}, journal = {Nature}, volume = {412}, number = {6846}, pages = {499-500}, doi = {10.1038/35087658}, pmid = {11484041}, issn = {0028-0836}, mesh = {*Amphibians ; Animals ; Data Interpretation, Statistical ; Ecology ; Population Dynamics ; }, abstract = {The decline and disappearance of relatively undisturbed populations of amphibians in several high-altitude regions since the 1970s suggests that they may have suffered a global decline, perhaps with a common cause or causes. Houlahan et al. examined means of trends for 936 amphibian populations and concluded that global declines began in the late 1950s, peaked in the 1960s, and have continued at a reduced rate since. Here we re-analyse their data using a method that accounts for the sampling of different populations over different time periods, and find evidence of a mean global decline in monitored populations only in the 1990s. However it is calculated, the global mean not only masks substantial spatial and temporal variation in population trends and sampling effort, but also fails to distinguish between a global decline with global causes and the cumulative effects of local declines with local causes.}, } @article {pmid11475761, year = {2001}, author = {Chichester, SR and Wilder, RS and Mann, GB and Neal, E}, title = {Utilization of evidence-based teaching in U.S. dental hygiene curricula.}, journal = {Journal of dental hygiene : JDH}, volume = {75}, number = {2}, pages = {156-164}, pmid = {11475761}, issn = {1043-254X}, mesh = {Attitude of Health Personnel ; Cohort Studies ; *Curriculum/trends ; Databases as Topic ; Demography ; Dental Hygienists/*education ; Educational Technology ; Evidence-Based Medicine/*education/trends ; Faculty ; Financial Support ; Forecasting ; Humans ; Internet ; Libraries ; Pilot Projects ; Statistics as Topic ; Teaching/methods ; Time Factors ; United States ; }, abstract = {PURPOSE: The purpose of this research was to survey U.S. dental hygiene program directors to determine: (1) demographic information, (2) specific Evidence-Based (EB) student instruction methods used, (3) if and how programs use an EB philosophy, (4) perceptions of faculty skills in incorporating EB instruction, and (5) opinions and attitudes regarding future need to incorporate EB philosophies in dental hygiene education.

METHODS: Data were gathered by surveying all 235 United States dental hygiene program directors in 1999. The survey included 20 closed items and 1 open-ended item. Initially, the survey was pilot tested using a convenience sample of seven U.S. dental hygiene program directors. A final, revised survey was mailed to the cohort population. A response rate of 70% (n = 164) was achieved after two mailings, and responses were analyzed using descriptive statistics.

RESULTS: The demographic results of this study revealed the majority of respondents were from associate degree/certificate dental hygiene programs (77%). Results revealed that most dental hygiene programs are beginning to include some fundamental EB concepts and skills into their curriculum, primarily by incorporating analysis of scientific literature. Most programs provide students with formal library orientation (88%), instruct students in the use of library indices or library databases (86%), and teach the use of the Internet for conducting literature searches (79%). Respondents indicated the major barriers for fully incorporating an EB approach in their dental hygiene program were: lack of faculty skills (37%), no available time (34%), lack of financial resources (33%), and lack of technical support (28%).

CONCLUSION: Findings of this study suggest dental hygiene educators have made small strides in creating an EB philosophy dental hygiene curriculum. However, the future of dental hygiene education must address the need for faculty development and training in areas such as computer utilization in core dental hygiene courses, strategies to improve the curriculum to stimulate students' critical thinking skills, and to develop educators' skills in the use of evidence for clinical decision-making.}, } @article {pmid11475045, year = {2001}, author = {Reed, DH and Frankham, R}, title = {How closely correlated are molecular and quantitative measures of genetic variation? A meta-analysis.}, journal = {Evolution; international journal of organic evolution}, volume = {55}, number = {6}, pages = {1095-1103}, doi = {10.1111/j.0014-3820.2001.tb00629.x}, pmid = {11475045}, issn = {0014-3820}, mesh = {Animals ; *Evolution, Molecular ; *Genetic Variation ; MEDLINE ; }, abstract = {The ability of populations to undergo adaptive evolution depends on the presence of quantitative genetic variation for ecologically important traits. Although molecular measures are widely used as surrogates for quantitative genetic variation, there is controversy about the strength of the relationship between the two. To resolve this issue, we carried out a meta-analysis based on 71 datasets. The mean correlation between molecular and quantitative measures of genetic variation was weak (r = 0.217). Furthermore, there was no significant relationship between the two measures for life-history traits (r = -0.11) or for the quantitative measure generally considered as the best indicator of adaptive potential, heritability (r = -0.08). Consequently, molecular measures of genetic diversity have only a very limited ability to predict quantitative genetic variability. When information about a population's short-term evolutionary potential or estimates of local adaptation and population divergence are required, quantitative genetic variation should be measured directly.}, } @article {pmid11474102, year = {2001}, author = {Inchausti, P and Halley, J}, title = {Investigating long-term ecological variability using the Global Population Dynamics Database.}, journal = {Science (New York, N.Y.)}, volume = {293}, number = {5530}, pages = {655-657}, doi = {10.1126/science.293.5530.655}, pmid = {11474102}, issn = {0036-8075}, mesh = {Animals ; *Databases, Factual ; *Ecosystem ; Internet ; Population Density ; Population Dynamics ; Population Growth ; Time Factors ; }, abstract = {The Global Population Dynamics Database (GPDD) is an important new source of information for ecologists, resource managers, and environmental scientists interested in the dynamics of natural populations. It comprises more than 4500 time series of population abundance for over 1800 animal species across many taxonomic groups and geographical locations. The GPDD offers great potential for asking comparative questions about the nature of population variability. We illustrate this by characterizing some critical features of ecological variability, variance growth, and spectral reddening.}, } @article {pmid11474094, year = {2001}, author = {Kaiser, J}, title = {An experiment for all seasons.}, journal = {Science (New York, N.Y.)}, volume = {293}, number = {5530}, pages = {624-627}, doi = {10.1126/science.293.5530.624}, pmid = {11474094}, issn = {0036-8075}, mesh = {Agriculture ; Animals ; Databases, Factual ; *Ecology ; *Ecosystem ; Government Agencies ; International Cooperation ; Internet ; Plants ; Research Support as Topic ; Software ; Time Factors ; Trees ; Weather ; }, } @article {pmid11465055, year = {2000}, author = {Wiehe, T and Guigó, R and Miller, W}, title = {Genome sequence comparisons: hurdles in the fast lane to functional genomics.}, journal = {Briefings in bioinformatics}, volume = {1}, number = {4}, pages = {381-388}, doi = {10.1093/bib/1.4.381}, pmid = {11465055}, issn = {1467-5463}, mesh = {Animals ; *Computational Biology ; Conserved Sequence ; Evolution, Molecular ; *Genome ; Genome, Human ; Genomics/*statistics & numerical data ; Humans ; Interleukin-13/genetics ; Interleukin-4/genetics ; Mice ; Sequence Alignment/*statistics & numerical data ; Software ; }, abstract = {An important computational technique for extracting the wealth of information hidden in human genomic sequence data is to compare the sequence with that from the corresponding region of the mouse genome, looking for segments that are conserved over evolutionary time. Moreover, the approach generalises to comparison of sequences from any two related species. The underlying rationale (which is abundantly confirmed by observation) is that a random mutation in a functional region is usually deleterious to the organism, and hence unlikely to become fixed in the population, whereas mutations in a non-functional region are free to accumulate over time. The potential value of this approach is so attractive that the public and private projects to sequence the human genome are now turning to sequencing the mouse, and you will soon be able to compare the human and mouse sequences of your favourite genomic region. We are currently witnessing an explosion of computer tools for comparative analysis of two genomic sequences. Here the capabilities of two new network servers for comparing genomic sequences from any pair of closely related species are sketched. The Syntenic Gene Prediction Program SGP-I utilises sequence comparisons to enhance the ability to locate protein coding segments in genomic data. PipMaker attempts to determine all conserved genomic regions, regardless of their function.}, } @article {pmid11448882, year = {2001}, author = {Gorodkin, J and Zwieb, C and Knudsen, B}, title = {Semi-automated update and cleanup of structural RNA alignment databases.}, journal = {Bioinformatics (Oxford, England)}, volume = {17}, number = {7}, pages = {642-645}, doi = {10.1093/bioinformatics/17.7.642}, pmid = {11448882}, issn = {1367-4803}, mesh = {Base Sequence ; Computational Biology ; *Databases as Topic ; Molecular Sequence Data ; RNA/*genetics ; RNA, Messenger/genetics ; Sequence Alignment/*statistics & numerical data ; Sequence Analysis, RNA/statistics & numerical data ; Sequence Homology, Nucleic Acid ; Software ; }, abstract = {UNLABELLED: We have developed a series of programs which assist in maintenance of structural RNA databases. A main program BLASTs the RNA database against GenBank and automatically extends and realigns the sequences to include the entire range of the RNA query sequences. After manual update of the database, other programs can examine base pair consistency and phylogenetic support. The output can be applied iteratively to refine the structural alignment of the RNA database. Using these tools, the number of potential misannotations per sequence was reduced from 20 to 3 in the Signal Recognition Particle RNA database.

AVAILABILITY: A quick-server and programs are available at http://www.bioinf.au.dk/rnadbtool/}, } @article {pmid11446215, year = {2001}, author = {Korine, C and Kalko, EK}, title = {Toward a global bat-signal database.}, journal = {IEEE engineering in medicine and biology magazine : the quarterly magazine of the Engineering in Medicine & Biology Society}, volume = {20}, number = {3}, pages = {81-85}, doi = {10.1109/51.932730}, pmid = {11446215}, issn = {0739-5175}, mesh = {Animals ; Chiroptera/*classification/physiology ; *Databases, Factual ; Echolocation/*classification ; Software Design ; Tape Recording ; }, abstract = {We propose a scheme for a new database using standardized protocol for recording and analysis of bat calls. The proposed database will describe and archive echolocation signals to create a reference library of bat calls. This information should be accessible to the public, thus encouraging continuous feedback from a broad audience. Because it is essential to evaluate the quality and reliability of such data, detailed information of recording and analysis procedures as well as the resulting species identification is required. A standardized and growing database on bat calls would be a potentially invaluable tool for global species identification, comparison, and distribution of microchiropterans. Currently, apart from a few websites with local call libraries, there is no "global" database established yet. We hope that researchers, amateurs, and wildlife and management authorities will adopt and further modify our suggestions for a standardized database for bat calls. We also hope that this database will stimulate new directions in bat research.}, } @article {pmid11446214, year = {2001}, author = {Nelson, DA and Gaunt, SL and Bronson, CL and Kloth, TJ}, title = {Database design for an archive of animal sounds.}, journal = {IEEE engineering in medicine and biology magazine : the quarterly magazine of the Engineering in Medicine & Biology Society}, volume = {20}, number = {3}, pages = {76-80}, doi = {10.1109/51.932729}, pmid = {11446214}, issn = {0739-5175}, mesh = {Animals ; *Databases, Factual ; *Information Storage and Retrieval ; Internet ; Tape Recording ; *Vocalization, Animal ; }, } @article {pmid11444958, year = {2001}, author = {Walsh, B}, title = {Quantitative genetics in the age of genomics.}, journal = {Theoretical population biology}, volume = {59}, number = {3}, pages = {175-184}, doi = {10.1006/tpbi.2001.1512}, pmid = {11444958}, issn = {0040-5809}, mesh = {Analysis of Variance ; Animals ; Bayes Theorem ; Breeding/methods ; Data Interpretation, Statistical ; Evolution, Molecular ; Forecasting ; Genetics/*trends ; Genetics, Medical/methods/trends ; Genomics/*methods/*trends ; Genotype ; Humans ; Models, Genetic ; Molecular Biology/*methods/*trends ; Phenotype ; }, } @article {pmid11427752, year = {2001}, author = {Yanaka, Y and Hanaki, KI and Yoshikura, H and Yamamoto, K}, title = {Further simulation on survival of mutants under non-selective condition.}, journal = {Japanese journal of infectious diseases}, volume = {54}, number = {2}, pages = {84-85}, pmid = {11427752}, issn = {1344-6304}, mesh = {Animals ; Bacteria/genetics/*growth & development ; *Computer Simulation ; Humans ; Intestines/microbiology ; Models, Theoretical ; Mutation ; }, } @article {pmid11424306, year = {2001}, author = {Appelrath, HJ and Friebe, J and Grawunder, M and Wellmann, I}, title = {The need for open geographical information systems in medicine.}, journal = {Methods of information in medicine}, volume = {40}, number = {2}, pages = {69-73}, pmid = {11424306}, issn = {0026-1270}, mesh = {Germany ; Health Services Needs and Demand ; *Health Services Research ; Humans ; *Information Systems ; *Medical Informatics Computing ; Online Systems ; Software ; *Topography, Medical ; }, abstract = {This paper presents a promising approach of using component-oriented geographical information systems (GIS) to facilitate improved medical and ecological applications. The integration of administrative geographical and medical data (map overlay) allows sophisticated and advanced analysis. This can serve as a basis to detect undiscovered relationships. We hope to increase the usage of geographical information by the creation of a general framework. This approach is mainly supported by two advances in recent years. Geographical data (e.g. administrative areas) is up-to-date, consistent and covers Germany completely. In addition, enormous technological improvements in the area of high-bandwidth networks and component-based software development have been made. These advances allowed to define our general framework for the integration of GIS functions into existing and already accepted applications.}, } @article {pmid11380887, year = {2001}, author = {De Jong, PW and De Vos, H and Nielsen, JK}, title = {Demic structure and its relation with the distribution of an adaptive trait in Danish flea beetles.}, journal = {Molecular ecology}, volume = {10}, number = {5}, pages = {1323-1332}, doi = {10.1046/j.1365-294x.2001.01268.x}, pmid = {11380887}, issn = {0962-1083}, mesh = {Adaptation, Physiological/*genetics ; Alleles ; Animals ; Coleoptera/*physiology ; Data Interpretation, Statistical ; Denmark ; *Genetics, Population ; Host-Parasite Interactions ; Isoenzymes ; Linkage Disequilibrium ; Plant Physiological Phenomena ; }, abstract = {The flea beetle Phyllotreta nemorum is an oligophagous species using crucifers as host plants. In Denmark two populations have been found which use Barbarea vulgaris ssp. arcuata (G-type) as a host plant, whereas this plant is unsuitable for the survival of the majority of P. nemorum. In the locations in which these two populations occur, alternative host plants are also present. The plants occur in patches, some of which contain a mixture of host plants. In this study of allozyme variation, genetic differentiation between P. nemorum using different host plants in patches in the two different localities was studied hierarchically to assess substructuring of the populations. Evidence was found for low, but significant, amounts of genetic differentiation between (sub)populations using spatially separated plant patches at a distance of approximately 100 m to 1 km (theta = 0.009) and between localities approximately 44 km apart (theta = 0.026), and there was an association between genetic differentiation and geographical distance. No genetic differentiation was found between beetles from different host plants with overlapping local distributions. No evidence was thus found for sympatric host race formation. The geographical distribution of genes enabling P. nemorum to use B. vulgaris as a host plant (100% 'resistant' beetles in samples from B. vulgaris, but much fewer on patches containing only alternative host plants) contrasts with the relatively low amount of genetic differentiation at the neutral allozyme loci. This distribution of 'resistant' beetles (to B. vulgaris defence) is likely to be influenced by local differences in selection and asymmetric gene flow.}, } @article {pmid11403561, year = {2001}, author = {Pertoldi, C and Kristensen, TN and Loeschcke, V}, title = {A new method for estimating environmental variability for clonal organisms, and the use of fluctuating asymmetry as an indicator of developmental Instability.}, journal = {Journal of theoretical biology}, volume = {210}, number = {4}, pages = {407-410}, doi = {10.1006/jtbi.2001.2317}, pmid = {11403561}, issn = {0022-5193}, mesh = {Animals ; Computational Biology ; *Ecosystem ; Environmental Monitoring/*methods ; }, } @article {pmid11396045, year = {1999}, author = {Caplan, DJ and Slade, GD and Gansky, SA}, title = {Complex sampling: implications for data analysis.}, journal = {Journal of public health dentistry}, volume = {59}, number = {1}, pages = {52-59}, doi = {10.1111/j.1752-7325.1999.tb03235.x}, pmid = {11396045}, issn = {0022-4006}, mesh = {Analysis of Variance ; Classification ; DMF Index ; *Data Interpretation, Statistical ; Epidemiologic Research Design ; Humans ; Probability ; *Sampling Studies ; Software ; }, abstract = {Investigators in dental public health often use strategies other than simple random sampling to identify potential subjects; however, their statistical analyses do not always take into account the complex sampling mechanism. Often it is not clear whether a given strategy requires adjustment for stratification and/or cluster sampling of observations. We propose that the need for such adjustment depends on the primary study objective. As a general rule, we recommend that if the study goal is to estimate the magnitude of either a population value of interest (e.g., prevalence), or an established exposure-outcome association, adjustment of variances to reflect complex sampling is essential because obtaining appropriate variance estimates is a priority. However, if the study goal is to establish the presence of an association, especially in a preliminary investigation of novel conditions or understudied populations, obtaining appropriate variance estimates may not be of primary importance; hence, adjustment of variances for complex sampling is not always required, but often is recommended. This paper describes several types of complex sampling designs, methods of adjusting for complex sampling strategies, examples illustrating the effect of adjustment, and alternative approaches for analysis of complex samples.}, } @article {pmid11395438, year = {2001}, author = {Xia, X and Xie, Z}, title = {AMADA: analysis of microarray data.}, journal = {Bioinformatics (Oxford, England)}, volume = {17}, number = {6}, pages = {569-570}, doi = {10.1093/bioinformatics/17.6.569}, pmid = {11395438}, issn = {1367-4803}, mesh = {Algorithms ; Cluster Analysis ; Computer Graphics ; Data Display ; *Data Interpretation, Statistical ; Oligonucleotide Array Sequence Analysis/*methods ; *Software ; User-Computer Interface ; }, abstract = {AMADA is a Windows program for identifying co-expressed genes from microarray data. It performs data transformation, principal component analysis, a variety of cluster analyses and extensive graphic functions for visualizing expression profiles.}, } @article {pmid11381941, year = {2001}, author = {Håkanson, L and Sazykina, T}, title = {A blind test of the MOIRA lake model for radiocesium for Lake Uruskul, Russia, contaminated by fallout from the Kyshtym accident in 1957.}, journal = {Journal of environmental radioactivity}, volume = {54}, number = {3}, pages = {327-344}, doi = {10.1016/s0265-931x(00)00179-x}, pmid = {11381941}, issn = {0265-931X}, mesh = {Animals ; Cesium Radioisotopes/*analysis ; Decision Support Techniques ; Environmental Monitoring ; *Fishes ; Geologic Sediments/chemistry ; *Models, Theoretical ; Radioactive Fallout ; Russia ; Strontium Radioisotopes ; Tissue Distribution ; Water Pollutants, Radioactive ; }, abstract = {This paper presents results of a model-test carried out within the framework of the COMETES project (EU). The tested model is a new lake model for radiocesium to be used within the MOIRA decision support system (DSS; MOIRA and COMETES are acronyms for EU-projects). This model has previously been validated against independent data from many lakes covering a wide domain of lake characteristics and been demonstrated to yield excellent predictive power (see Håkanson, Modelling Radiocesium in Lakes and Coastal Areas. Kluwer, Dordrecht, 2000, 215 pp). However, the model has not been tested before for cases other than those related to the Chernobyl fallout in 1986, nor for lakes from this part of the world (Southern Urals) and nor for situations with such heavy fallout as this. The aims of this work were: (1) to carry out a blind test of the model for the case of continental Lake Uruskul, heavily contaminated with 90Sr and 137Cs as a result of the Kyshtym radiation accident (29 September 1957) in the Southern Urals, Russia, and (2) if these tests gave satisfactory results to reconstruct the radiocesium dynamics for fish, water and sediments in the lake. Can the model provide meaningful predictions in a situation such as this? The answer is yes, although there are reservations due to the scarcity of reliable empirical data. From the modelling calculations, it may be noted that the maximum levels of 137Cs in fish (here 400 g ww goldfish), water and sediments were about 100,000 Bq/kg ww, 600 Bq/l and 30,000 Bq/kg dw, respectively. The values in fish are comparable to or higher than the levels in fish in the cooling pond of the Chernobyl NPP. The model also predicts an interesting seasonal pattern in 137Cs levels in sediments. There is also a characteristic "three phase" development for the 137Cs levels in fish: first an initial stage when the 137Cs concentrations in fish approach a maximum value, then a phase with relatively short ecological half-lives followed by a final phase with long ecological half-lives more or less corresponding to the physical decay of radiocesium.}, } @article {pmid11353083, year = {2001}, author = {Gorodkin, J and Stricklin, SL and Stormo, GD}, title = {Discovering common stem-loop motifs in unaligned RNA sequences.}, journal = {Nucleic acids research}, volume = {29}, number = {10}, pages = {2135-2144}, pmid = {11353083}, issn = {1362-4962}, support = {R01 HG000249/HG/NHGRI NIH HHS/United States ; HG00249/HG/NHGRI NIH HHS/United States ; }, mesh = {Algorithms ; Base Sequence ; *Computational Biology ; Databases as Topic ; Internet ; Molecular Sequence Data ; *Nucleic Acid Conformation ; RNA/*chemistry/*genetics/metabolism ; RNA, Archaeal/chemistry/genetics/metabolism ; RNA, Ribosomal/chemistry/genetics/metabolism ; Regulatory Sequences, Nucleic Acid/genetics ; Sensitivity and Specificity ; Sequence Alignment ; *Software ; Untranslated Regions/chemistry/genetics/metabolism ; }, abstract = {Post-transcriptional regulation of gene expression is often accomplished by proteins binding to specific sequence motifs in mRNA molecules, to affect their translation or stability. The motifs are often composed of a combination of sequence and structural constraints such that the overall structure is preserved even though much of the primary sequence is variable. While several methods exist to discover transcriptional regulatory sites in the DNA sequences of coregulated genes, the RNA motif discovery problem is much more difficult because of covariation in the positions. We describe the combined use of two approaches for RNA structure prediction, FOLDALIGN and COVE, that together can discover and model stem-loop RNA motifs in unaligned sequences, such as UTRs from post-transcriptionally coregulated genes. We evaluate the method on two datasets, one a section of rRNA genes with randomly truncated ends so that a global alignment is not possible, and the other a hyper-variable collection of IRE-like elements that were inserted into randomized UTR sequences. In both cases the combined method identified the motifs correctly, and in the rRNA example we show that it is capable of determining the structure, which includes bulge and internal loops as well as a variable length hairpin loop. Those automated results are quantitatively evaluated and found to agree closely with structures contained in curated databases, with correlation coefficients up to 0.9. A basic server, Stem-Loop Align SearcH (SLASH), which will perform stem-loop searches in unaligned RNA sequences, is available at http://www.bioinf.au.dk/slash/.}, } @article {pmid11359200, year = {2001}, author = {Barros, MD and Ximenes, R and de Lima, ML}, title = {[Child and adolescent mortality due to external causes: trends from 1979 to 1995].}, journal = {Revista de saude publica}, volume = {35}, number = {2}, pages = {142-149}, doi = {10.1590/s0034-89102001000200007}, pmid = {11359200}, issn = {0034-8910}, mesh = {Accidents, Traffic/statistics & numerical data ; Adolescent ; Adult ; Brazil/epidemiology ; Cause of Death/*trends ; Child ; Child, Preschool ; Female ; Firearms ; Homicide/statistics & numerical data ; Humans ; Infant ; Infant, Newborn ; Information Systems ; Male ; Suicide/statistics & numerical data ; Violence ; }, abstract = {OBJECTIVE: To analyze the magnitude and trends of mortality due to external causes in specific age groups, from 0 to 19 years old in a population living in the city of Recife, Brazil, from 1979 to 1995.

METHODS: Data from the Mortality Data System of the Ministry of Health and Health Department of Pernambuco State was used. The studied population, aged 0 to 19 years old, represented 41.8% of total city population in 1991. A time series exploratory ecological model was created to analyze trends in mortality coefficients due to external causes. Using simple linear regression these coefficients were assessed in specific age groups categorized by gender.

RESULTS AND CONCLUSIONS: In the time series, mortality coefficients due to external causes showed an increasing trend, in particular due to homicides among adolescents, where the coefficient increased on average 3.05 per year, yielding a relative increase of 601, 3% over the study period. In 1995, more than 90% of these homicides were perpetrated with fire weapons. These data reinforce the seriousness of this problem and the need to deal with it, taking into account the difficulties in determining the causes of violence.}, } @article {pmid11353852, year = {2001}, author = {Alroy, J and Marshall, CR and Bambach, RK and Bezusko, K and Foote, M and Fursich, FT and Hansen, TA and Holland, SM and Ivany, LC and Jablonski, D and Jacobs, DK and Jones, DC and Kosnik, MA and Lidgard, S and Low, S and Miller, AI and Novack-Gottshall, PM and Olszewski, TD and Patzkowsky, ME and Raup, DM and Roy, K and Sepkoski, JJ and Sommers, MG and Wagner, PJ and Webber, A}, title = {Effects of sampling standardization on estimates of Phanerozoic marine diversification.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {98}, number = {11}, pages = {6261-6266}, pmid = {11353852}, issn = {0027-8424}, mesh = {Animals ; *Biological Evolution ; Databases, Factual ; *Ecosystem ; *Fossils ; Invertebrates/*classification ; Oceans and Seas ; Paleontology ; Selection Bias ; }, abstract = {Global diversity curves reflect more than just the number of taxa that have existed through time: they also mirror variation in the nature of the fossil record and the way the record is reported. These sampling effects are best quantified by assembling and analyzing large numbers of locality-specific biotic inventories. Here, we introduce a new database of this kind for the Phanerozoic fossil record of marine invertebrates. We apply four substantially distinct analytical methods that estimate taxonomic diversity by quantifying and correcting for variation through time in the number and nature of inventories. Variation introduced by the use of two dramatically different counting protocols also is explored. We present sampling-standardized diversity estimates for two long intervals that sum to 300 Myr (Middle Ordovician-Carboniferous; Late Jurassic-Paleogene). Our new curves differ considerably from traditional, synoptic curves. For example, some of them imply unexpectedly low late Cretaceous and early Tertiary diversity levels. However, such factors as the current emphasis in the database on North America and Europe still obscure our view of the global history of marine biodiversity. These limitations will be addressed as the database and methods are refined.}, } @article {pmid11351419, year = {2001}, author = {Summers, JK}, title = {Ecological condition of the estuaries of the Atlantic and Gulf Coasts of the United States.}, journal = {Environmental toxicology and chemistry}, volume = {20}, number = {1}, pages = {99-106}, pmid = {11351419}, issn = {0730-7268}, mesh = {Data Collection ; Data Interpretation, Statistical ; *Environmental Monitoring ; Marine Biology ; Sampling Studies ; Seawater ; United States ; United States Environmental Protection Agency ; Water Pollutants, Chemical/analysis ; Water Pollution, Chemical/*analysis ; }, abstract = {Monitoring the estuaries of the Atlantic and Gulf of Mexico coastlines of the United States from Cape Cod, Massachusetts, to Brownsville, Texas, was performed annually from 1990 through 1997 to assess ecological conditions on a regional basis for four biogeographic provinces. These province estimates--Virginian, Carolinian, West Indian, and Louisianian Provinces--are combined to provide an assessment of 87% of the estuarine area of the United States and 96% of the area of the Atlantic and Gulf coasts. Combining information over the six years of monitoring showed 34 +/- 4% of the Atlantic and Gulf estuarine sediments displayed poorer than expected biological conditions, based on benthic and finfish community conditions, and 21 +/- 4% of the area was characterized by low water clarity, the presence of marine debris/noxious odors, or elevated fish tissue contaminants.}, } @article {pmid11348498, year = {2001}, author = {Moya, A and Guirao, P and Cifuentes, D and Beitia, F and Cenis, JL}, title = {Genetic diversity of Iberian populations of Bemisia tabaci (Hemiptera: Aleyrodidae) based on random amplified polymorphic DNA-polymerase chain reaction.}, journal = {Molecular ecology}, volume = {10}, number = {4}, pages = {891-897}, doi = {10.1046/j.1365-294x.2001.01221.x}, pmid = {11348498}, issn = {0962-1083}, mesh = {Animals ; Atlantic Islands ; DNA/analysis/*genetics ; Data Interpretation, Statistical ; Female ; *Genetic Variation ; Haplotypes/*genetics ; Hemiptera/*genetics ; Male ; Phylogeny ; Portugal ; *Random Amplified Polymorphic DNA Technique ; Spain ; }, abstract = {The genetic structure of six Iberian populations of the whitefly Bemisia tabaci, two of them biotype Q, one biotype B, and the other three a mixture of both, has been studied using random amplified polymorphic DNA-polymerase chain reaction (RAPD-PCR). A total of 336 individuals was completely discriminated by means of 234 scored bands. Separate analyses of molecular variance of haploid males and diploid females using the pairwise number of differences between haplotypes showed that biotypes contribute significantly more to the observed variability than populations within biotypes. On average, gene flow between two biotypes of the same population is lower than between populations of identical biotypes. On the basis of these results and the nondetection under natural conditions of a single hybrid, we consider that both biotypes are genetically isolated under the ecological conditions prevailing in the south Iberian Peninsula. All populations of biotype Q presented similar values of intrapopulational diversity, which were higher than the values shown by populations of biotype B.}, } @article {pmid11348492, year = {2001}, author = {Roslin, T}, title = {Spatial population structure in a patchily distributed beetle.}, journal = {Molecular ecology}, volume = {10}, number = {4}, pages = {823-837}, doi = {10.1046/j.1365-294x.2001.01235.x}, pmid = {11348492}, issn = {0962-1083}, mesh = {Animals ; Coleoptera/enzymology/*genetics ; DNA, Mitochondrial/analysis/*genetics ; Data Interpretation, Statistical ; Finland ; *Genetics, Population ; Haplotypes/*genetics ; Isoenzymes/*genetics ; Phylogeny ; }, abstract = {The dynamics and evolution of populations will critically depend on their spatial structure. Hence, a recent emphasis on one particular type of structure--the metapopulation concept of Levins--can only be justified by empirical assessment of spatial population structures in a wide range of organisms. This paper focuses on Aphodius fossor, a dung beetle specialized on cattle pastures. An agricultural database was used to locate nearly 50 000 local populations of A. fossor in Finland. Several independent methods were then used to quantify key processes in this vast population system. Allozyme markers and mitochondrial DNA (mtDNA) sequences were applied to examine genetic differentiation of local populations and to derive indirect estimates of gene flow. These estimates were compared to values expected on the basis of direct observations of dispersing individuals and assessments of local effective population size. Molecular markers revealed striking genetic homogeneity in A. fossor. Differentiation was only evident in mtDNA haplotype frequencies between the isolated Aland islands and the Finnish mainland. Thus, indirect estimates of gene flow agreed with direct observations that local effective population size in A. fossor is large (hundreds of individuals), and that in each generation, a substantial fraction (approximately one-fifth) of the individuals move between populations. Large local population size, extreme haplotype diversity and a high regional incidence of A. fossor all testify against recurrent population turnover. Taken together, these results provide strong evidence that the whole mainland population of A. fossor is better described as one large 'patchy population', with substantial movement between relatively persistent local populations, than as a classical metapopulation.}, } @article {pmid11324304, year = {1998}, author = {Wright, G and Smith, EP}, title = {Home, school, and community partnerships: integrating issues of race, culture, and social class.}, journal = {Clinical child and family psychology review}, volume = {1}, number = {3}, pages = {145-162}, pmid = {11324304}, issn = {1096-4037}, mesh = {Adult ; Child ; *Child Development ; *Community Networks/organization & administration ; *Community-Institutional Relations ; Ethnicity/*psychology ; Family/*ethnology/psychology ; Humans ; *Schools/organization & administration ; Social Support ; Socioeconomic Factors ; United States ; }, abstract = {The current review is an examination of home-school-community partnerships utilizing an ecological approach to understand the influences of race, culture, and social class. The ecological approach recognizes that families and schools are embedded in communities, and that these settings influence each other and the development of children. The roles of race, culture, and social class in the development of partnerships between the home, school, and community settings are explored. Race, culture, and social class may interact with parent and family attributes, teacher and school qualities, and community context. These factors are often misunderstood either through under investigation or lack of integration. The implications for future research, practice, and policy are discussed.}, } @article {pmid11318150, year = {1999}, author = {Gignoux, J and Duby, C and Barot, S}, title = {Comparing the performances of Diggle's tests of spatial randomness for small samples with and without edge-effect correction: application to ecological data.}, journal = {Biometrics}, volume = {55}, number = {1}, pages = {156-164}, doi = {10.1111/j.0006-341x.1999.00156.x}, pmid = {11318150}, issn = {0006-341X}, mesh = {Analysis of Variance ; Bias ; *Biometry ; Data Interpretation, Statistical ; *Ecology ; Ecosystem ; Models, Statistical ; Random Allocation ; Trees ; }, abstract = {Diggle's tests of spatial randomness based on empirical distributions of interpoint distances can be performed with and without edge-effect correction. We present here numerical results illustrating that tests without the edge-effect correction proposed by Diggle (1979, Biometrics 35, 87-101) have a higher power for small sample sizes than those with correction. Ignoring the correction enables detection of departure from spatial randomness with smaller samples (down to 10 points vs. 30 points for the tests with correction). These results are confirmed by an example with ecological data consisting of maps of two species of trees in a West African savanna. Tree numbers per species per map were often less than 20. For one of the species, for which maps strongly suggest an aggregated pattern, tests without edge-effect correction enabled rejection of the null hypothesis on three plots out of five vs. on only one for the tests with correction.}, } @article {pmid11298962, year = {2001}, author = {Ehrich, D and Jorde, PE and Krebs, CJ and Kenney, AJ and Stacy, JE and Stenseth, NC}, title = {Spatial structure of lemming populations (Dicrostonyx groenlandicus) fluctuating in density.}, journal = {Molecular ecology}, volume = {10}, number = {2}, pages = {481-495}, doi = {10.1046/j.1365-294x.2001.01229.x}, pmid = {11298962}, issn = {0962-1083}, mesh = {Animals ; Arvicolinae/*genetics ; Canada ; DNA, Mitochondrial/analysis/genetics ; Data Interpretation, Statistical ; Genetics, Population ; Haplotypes/genetics ; Locus Control Region/genetics ; Microsatellite Repeats/genetics ; Population Dynamics ; }, abstract = {The pattern and scale of the genetic structure of populations provides valuable information for the understanding of the spatial ecology of populations, including the spatial aspects of density fluctuations. In the present paper, the genetic structure of periodically fluctuating lemmings (Dicrostonyx groenlandicus) in the Canadian Arctic was analysed using mitochondrial DNA (mtDNA) control region sequences and four nuclear microsatellite loci. Low genetic variability was found in mtDNA, while microsatellite loci were highly variable in all localities, including localities on isolated small islands. For both genetic markers the genetic differentiation was clear among geographical regions but weaker among localities within regions. Such a pattern implies gene flow within regions. Based on theoretical calculations and population census data from a snap-trapping survey, we argue that the observed genetic variability on small islands and the low level of differentiation among these islands cannot be explained without invoking long distance dispersal of lemmings over the sea ice. Such dispersal is unlikely to occur only during population density peaks.}, } @article {pmid11298954, year = {2001}, author = {Smith, MF and Kelt, DA and Patton, JL}, title = {Testing models of diversification in mice in the Abrothrix olivaceus/xanthorhinus complex in Chile and Argentina.}, journal = {Molecular ecology}, volume = {10}, number = {2}, pages = {397-405}, doi = {10.1046/j.1365-294x.2001.01183.x}, pmid = {11298954}, issn = {0962-1083}, mesh = {Animals ; Argentina ; Chile ; Cytochrome b Group/genetics ; DNA, Mitochondrial/analysis/genetics ; Data Interpretation, Statistical ; Evolution, Molecular ; Genetic Variation ; Haplotypes/genetics ; Models, Genetic ; Muridae/classification/*genetics ; Phylogeny ; }, abstract = {Samples of the forest-dwelling mouse Abrothrix olivaceus and the steppe-dwelling A. xanthorhinus across a transect between 45 and 47 degrees S in southern Chile were analysed using the mitochondrial cytochrome b (cyt b) sequence, substantially adding to the data presented previously for these taxa from Argentina and Chile. The level of variation in the cyt b sequence throughout the entire olivaceus/xanthorhinus complex is comparable to that seen within a single species in many South American sigmodontine rodents, consistent with a previous conclusion that both taxa are sub-species of A. olivaceus. Haplotypes of xanthorhinus have not yet achieved reciprocal monophyly relative to those of olivaceus. We evaluate competing hypotheses for the morphological divergence of xanthorhinus and olivaceus by allopatry in Pleistocene refuges versus postglacial diversification across ecological gradients. Two contrasting patterns are predicted for plots of the distribution of pairwise genetic differences, depending on whether the taxa diverged in allopatric refuges or through selection across a gradient. Examples of both modes of diversification are found in this complex.}, } @article {pmid11298951, year = {2001}, author = {Stehlik, I and Schneller, JJ and Bachmann, K}, title = {Resistance or emigration: response of the high-alpine plant Eritrichium nanum (L.) Gaudin to the ice age within the Central Alps.}, journal = {Molecular ecology}, volume = {10}, number = {2}, pages = {357-370}, doi = {10.1046/j.1365-294x.2001.01179.x}, pmid = {11298951}, issn = {0962-1083}, mesh = {Altitude ; Data Interpretation, Statistical ; Environment ; Europe ; Genes, Plant ; Genetic Variation ; Genetics, Population ; Magnoliopsida/classification/*genetics ; Phylogeny ; Polymerase Chain Reaction/methods ; }, abstract = {Two main possibilities regarding glacial survival of the mountain flora of the Alps during the Quaternary have been discussed: the tabula rasa and the nunatak hypotheses. Eritrichium nanum (L.) Gaudin (Boraginaceae) is a perennial cushion plant, occurring at high elevations of the Central Alps and having a preference for extreme habitats. It belongs to a group of high-alpine plants, for which in situ glacial survival on nunataks is ecologically possible. By investigating 20 populations of E. nanum of potential nunatak and peripheral refugial regions using amplified fragment length polymorphism, considerable genetic differences between populations from the Central Alps and populations from peripheral refugia were detected; hence, the latter probably did not serve as potential sources for the re-colonization of the Central Alps after glaciation. Genetic variation was hierarchically structured (AMOVA), and three genetically distinct regions could be identified in the Central Alps. Two of these, the Penninic and Rhaetic Alps, correspond to nunatak regions proposed in the biogeographic literature. Populations from the Lepontic Alps formed a third genetic group. Genetic correlation (Mantel statistics) was highest within populations, with a modest decline among populations within specific nunatak regions and a negative correlation outside the genetic influence of specific nunatak regions. In situ glacial survival in E. nanum could be a model for the Quaternary history of other alpine plants, especially those that also occur at high elevations and in similar habitats.}, } @article {pmid11297661, year = {2001}, author = {van Ameijden, EJ and Coutinho, RA}, title = {Large decline in injecting drug use in Amsterdam, 1986-1998: explanatory mechanisms and determinants of injecting transitions.}, journal = {Journal of epidemiology and community health}, volume = {55}, number = {5}, pages = {356-363}, pmid = {11297661}, issn = {0143-005X}, mesh = {Adult ; Cohort Studies ; Data Interpretation, Statistical ; Female ; Heroin/*administration & dosage ; Humans ; Incidence ; Male ; Narcotics/*administration & dosage ; Needle-Exchange Programs ; Netherlands/epidemiology ; Prevalence ; Substance Abuse, Intravenous/*epidemiology/prevention & control ; }, abstract = {OBJECTIVES: To study community wide trends in injecting prevalence and trends in injecting transitions, and determinants.

DESIGN: Open cohort study with follow up every four months (Amsterdam Cohort Study). Generalised estimating equations were used for statistical analysis.

SETTING: Amsterdam has adopted a harm reduction approach as drug policy.

PARTICIPANTS: 996 drug users who were recruited from 1986 to 1998, mainly at methadone programmes, who paid 13620 cohort visits.

MAIN RESULTS: The prevalence of injecting decreased exponentially (66% to 36% in four to six monthly periods). Selective mortality and migration could maximally explain 33% of this decline. Instead, injecting initiation linearly decreased (4.1% to 0.7% per visit), cessation exponentially increased (10.0% to 17.1%), and relapse linearly decreased (21.3% to 11.8%). Non-injecting cocaine use (mainly pre-cooked, comparable to crack) and heroin use strongly increased. Trends were not attributable to changes in the study sample.

CONCLUSIONS: Harm reduction, including large scale needle exchange programmes, does not lead to an increase in injecting drug use. The injecting decline seems mainly attributable to ecological factors (for example, drug culture and market). Prevention of injecting is possible and peer-based interventions may be effective. The consequences of the recent upsurge in crack use requires further study.}, } @article {pmid11270169, year = {2000}, author = {Caicoya, M and Alonso, M and Natal, C and Sánchez, LM and Alonso, P and Moral, L}, title = {[Variation in medical practice. Apropos of the use of CAT and NMR in INSALUD].}, journal = {Gaceta sanitaria}, volume = {14}, number = {6}, pages = {435-441}, doi = {10.1016/s0213-9111(00)71910-8}, pmid = {11270169}, issn = {0213-9111}, mesh = {Databases, Factual ; Health Care Surveys ; Health Resources/statistics & numerical data/*supply & distribution ; Humans ; Magnetic Resonance Imaging/*statistics & numerical data ; Medical Staff, Hospital/statistics & numerical data ; Practice Patterns, Physicians' ; Regression Analysis ; Spain ; Tomography, X-Ray Computed/*statistics & numerical data ; }, abstract = {OBJECTIVE: In this study the variability on the utilization of nuclear magnetic resonance (NMR) and computerized tomography (CT) scan among hospitals and provinces in the INSALUD (Spanish National Health System) is evaluated as well as the role of the availability of resources in the variability.

METHOD: Data on availability of resources, its use and the reference population for each hospital were obtained from the Specialized Care Information System (SIAE) for the years 1996-1997. The units of analysis were the hospitals and the provinces in the INSALUD territory. The independent variables were the ratio of technologies and professional per inhabitant. Also the waiting list and the economical level of the province were used. Data analysis included the extremal quotient and multiple linear regression.

RESULTS: The ratio of the highest to lowest rate of CT and NMR use is 15 and 27 among hospitals and 3 and 4 among provinces, respectively. The number of neurosurgeons, number of CT apparatus, waiting list for CT and rate of NMR use, all standardized per population, explains 61% of CT variability among hospitals. Among provinces, the number of CT apparatus explains 31% of all variability. For NMR use among hospitals, the number of neurosurgeons, number of orthopedic surgeons and CT use, all variables standardized per population, explains 42% of variability. The amount of equipment is not associated with NMR rate among provinces.

CONCLUSIONS: The variation found in the INSALUD territory for the two procedures is high and ecologically associated to the availability of resources. It would be convenient to perform an observational study to confirm the findings and evaluate the possible contribution of inappropriate use to the variation.}, } @article {pmid11262972, year = {2001}, author = {Bininda-Emonds, OR and Brady, SG and Kim, J and Sanderson, MJ}, title = {Scaling of accuracy in extremely large phylogenetic trees.}, journal = {Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing}, volume = {}, number = {}, pages = {547-558}, doi = {10.1142/9789814447362_0053}, pmid = {11262972}, issn = {2335-6928}, mesh = {*Algorithms ; *Databases, Factual ; Models, Genetic ; *Phylogeny ; Stochastic Processes ; }, abstract = {The accuracy of phylogenetic inference was examined in simulated data sets up to nearly 10,000 taxa, the size of the largest set of homologous genes in existing molecular sequence databases. Even with a simple search algorithm (maximum parsimony without branch swapping), the number of characters needed to estimate 80% of a tree correctly can scale remarkably well at optimal substitution rates (on the order of log N, where N is the number of taxa). In other words, the number of taxa in an analysis can be doubled and only an arithmetic increase in the number of characters is required to maintain the same level of accuracy. Even substitution rates that are much higher than normally used in phylogenetic studies did not affect the scaling too adversely. However, scaling is usually worse than log N for more stringent levels of accuracy. Moreover, errors are not distributed randomly throughout the tree. Shallow nodes are remarkably easy to reconstruct and display favourable log-linear scaling. The deepest nodes are extremely difficult to reconstruct accurately, even with branch swapping, and the scaling is poor. Therefore, the strategy of sequencing large numbers of homologous genes may not always provide global solutions to extreme phylogenetic problems and alternative strategies may be required.}, } @article {pmid11254945, year = {2001}, author = {Seward, JR and Sinks, GD and Schultz, TW}, title = {Reproducibility of toxicity across mode of toxic action in the Tetrahymena population growth impairment assay.}, journal = {Aquatic toxicology (Amsterdam, Netherlands)}, volume = {53}, number = {1}, pages = {33-47}, doi = {10.1016/s0166-445x(00)00158-2}, pmid = {11254945}, issn = {0166-445X}, mesh = {Animals ; *Databases, Factual ; Narcotics/toxicity ; Reproducibility of Results ; Tetrahymena/*drug effects/growth & development ; }, abstract = {Toxicity data collected in a laboratory setting are the primary source of potency information used for regulatory, modeling, or risk assessment purposes. However, the relative reproducibility of such toxicity data is rarely discussed. This study investigated the reproducibility of growth impairment data for the freshwater ciliate Tetrahymena pyriformis exposed to a structurally diverse group of chemicals of varying hydrophobicity within different modes of toxic action, either non-covalent narcosis or covalent electro(nucleo)philicity. The proportions of chemicals representing each mode of toxic action, or mechanism of action within each mode, were not chosen to emulate the occurrence of manufactured chemicals or chemicals within the TETRATOX database. Chemicals for which prior toxicity data existed were re-tested and reproducibility was evaluated. The toxic potency values of the selected chemicals were largely reproducible after re-testing of the toxic potency, as 98% of the chemicals had re-test toxicity values within one log unit of the original potency value. To further scrutinize the reproducibility of toxicity values, differences between values were investigated by mode of toxic action. A stringent criterion for reproducibility was enforced, which dictated that the re-tested toxicity value must be encompassed by the fiducial interval (FI) of the original toxicity value and vice versa for the chemical to be considered reproducible. Toxicity values of 28 of the 50 re-tested chemicals conformed to the criterion set for reproducible values. Of the nonreproducible chemicals, seven were narcotics: four nonpolar or neutral narcotics and three other narcotics (e.g. polar narcotics). However, four of these seven narcotics did have toxicity values encompassed by one FI, but not the other FI. The remaining chemicals that did not have reproducible potency measurements were electro(nucleo)philic in nature. Certain toxicophores were highly represented among these chemicals. These included quinone derivatives, electron releasing amino and hydroxyl moieties, and electron withdrawing nitro substituents, often in tandem with strong leaving groups (i.e. halogens), and unsaturated alcohols. Lack of reproducibility was common among the chemicals that elicited toxicity after either abiotic or biotic transformation. There was no clear trend between hydrophobicity and lack of reproducibility. While data are limited, these results suggest that toxic potency values of chemicals acting via the electro(nucleo)philic mode of toxic action could be more susceptible to non-reproducibility. Ramifications of such lack of reproducibility could manifest in predictive toxicology models and their use in regulatory and risk assessment endeavors.}, } @article {pmid11541286, year = {1997}, author = {Miller, AI}, title = {Comparative diversification dynamics among palaeocontinents during the Ordovician Radiation.}, journal = {Geobios (Lyon, France). Memoire special}, volume = {20}, number = {}, pages = {397-406}, pmid = {11541286}, issn = {0293-843X}, mesh = {Animals ; *Biological Evolution ; Databases, Factual ; Earth, Planet ; *Ecosystem ; Electronic Data Processing ; Evolution, Planetary ; *Fossils ; Geologic Sediments/analysis ; Invertebrates ; Marine Biology ; Mollusca ; Paleontology/classification/*statistics & numerical data ; Phylogeny ; }, abstract = {The Ordovician Radiation was among the most extensive intervals of diversification in the history of life. However, a delineation of the proximal cause(s) of the Radiation remains elusive. Any such determination should involve an analysis of geographic overprints on diversification: did the Radiation occur randomly around the world or, alternatively, was it focused in particular geographic or depositional regimes? Here, I present a comparative evaluation of Ordovician diversification among several palaeocontinents to determine whether biotas associated with certain palaeocontinents exhibited different diversification patterns than others; in part, this involves a numerical "correction" to raw diversity trajectories. Clear disparities among palaeocontinents are indicated by the data, which appear to reflect differences in the extent of siliciclastic input partly in association with tectonic activity. Further testing will be required to fully substantiate the implication that siliciclastic influx was a predominant factor in the Ordovician Radiation, affecting a variety of higher taxa among all three Phanerozoic evolutionary faunas.}, } @article {pmid11541189, year = {1997}, author = {Miller, AI}, title = {A new look at age and area: the geographic and environmental expansion of genera during the Ordovician Radiation.}, journal = {Paleobiology}, volume = {23}, number = {4}, pages = {410-419}, doi = {10.1017/s0094837300019813}, pmid = {11541189}, issn = {0094-8373}, mesh = {Animals ; *Biological Evolution ; Databases, Factual ; Earth, Planet ; *Ecosystem ; *Fossils ; Geography ; Invertebrates ; Marine Biology ; Mollusca ; *Paleontology ; Phylogeny ; }, abstract = {Although available paleobiological data indicate that the geographic ranges of marine species are maintained throughout their entire observable durations, other evidence suggests, by contrast, that the ranges of higher taxa expand as they age, perhaps in association with increased species richness. Here, I utilize a database of Ordovician genus occurrences collected from the literature for several paleocontinents to demonstrate that a significant aging of the global biota during the Ordovician Radiation was accompanied by a geographic and environmental expansion of genus ranges. The proportion of genera occurring in two or more paleocontinents in the database, and two or more environmental zones within a six-zone onshore-offshore framework, increased significantly in the Caradocian and Ashgillian. Moreover, widespread genera tended to be significantly older than their endemic counterparts, suggesting a direct link between their ages and their environmental and geographic extents. Expansion in association with aging was corroborated further by demonstrating this pattern directly among genera that ranged from the Tremadocian through the Ashgillian. Taken together, these results are significant not only for what they reveal about the kinetics of a major, global-scale diversification, but also for what they suggest about the interpretation of relationships between diversity trends at the alpha (within-community) and beta (between-community) levels.}, } @article {pmid11541589, year = {1996}, author = {Chun, C and Mitchell, CA}, title = {Dynamic control of photosynthetic photon flux for lettuce production in CELSS.}, journal = {Acta horticulturae}, volume = {440}, number = {}, pages = {7-12}, doi = {10.17660/actahortic.1996.440.2}, pmid = {11541589}, issn = {0567-7572}, mesh = {Biomass ; Carbon Dioxide ; *Decision Making, Computer-Assisted ; *Ecological Systems, Closed ; Environment, Controlled ; Lactuca/growth & development/*radiation effects ; Life Support Systems/*instrumentation ; *Light ; Lighting ; *Photons ; Photosynthesis ; }, abstract = {A new dynamic control of photosynthetic photon flux (PPF) was tested using lettuce canopies growing in the Minitron II plant-growth/canopy gas-exchange system. Canopy photosynthetic rates (Pn) were measured in real time and fedback for further environment control. Pn can be manipulated by changing PPF, which is a good environmental parameter for dynamic control of crop production in a Controlled Ecological Life-Support Systems CELSS. Decision making that combines empirical mathematical models with rule sets developed from recent experimental data was tested. With comparable yield indices and potential for energy savings, dynamic control strategies will contribute greatly to the sustainability of space-deployed CELSS.}, } @article {pmid11539204, year = {1996}, author = {Miller, AI and Foote, M}, title = {Calibrating the Ordovician Radiation of marine life: implications for Phanerozoic diversity trends.}, journal = {Paleobiology}, volume = {22}, number = {2}, pages = {304-309}, doi = {10.1666/0094-8373-22.2.304}, pmid = {11539204}, issn = {0094-8373}, support = {DEB-9207577/DE/NIDCR NIH HHS/United States ; DEB-9496348/DE/NIDCR NIH HHS/United States ; }, mesh = {Animals ; *Biological Evolution ; Biometry ; *Databases, Factual ; *Ecosystem ; *Fossils ; Invertebrates ; Marine Biology ; Mollusca ; Paleontology/classification/*statistics & numerical data ; Sample Size ; }, abstract = {It has long been suspected that trends in global marine biodiversity calibrated for the Phanerozoic may be affected by sampling problems. However, this possibility has not been evaluated definitively, and raw diversity trends are generally accepted at face value in macroevolutionary investigations. Here, we analyze a global-scale sample of fossil occurrences that allows us to determine directly the effects of sample size on the calibration of what is generally thought to be among the most significant global biodiversity increases in the history of life: the Ordovician Radiation. Utilizing a composite database that includes trilobites, brachiopods, and three classes of molluscs, we conduct rarefaction analyses to demonstrate that the diversification trajectory for the Radiation was considerably different than suggested by raw diversity time-series. Our analyses suggest that a substantial portion of the increase recognized in raw diversity depictions for the last three Ordovician epochs (the Llandeilian, Caradocian, and Ashgillian) is a consequence of increased sample size of the preserved and catalogued fossil record. We also use biometric data for a global sample of Ordovician trilobites, along with methods of measuring morphological diversity that are not biased by sample size, to show that morphological diversification in this major clade had leveled off by the Llanvirnian. The discordance between raw diversity depictions and more robust taxonomic and morphological diversity metrics suggests that sampling effects may strongly influence our perception of biodiversity trends throughout the Phanerozoic.}, } @article {pmid11538568, year = {1996}, author = {Tosteson, JL and Marino, BD}, title = {The Biosphere 2 Global Change Testbed world wide web server: closed system research and education using the Internet.}, journal = {Life support & biosphere science : international journal of earth space}, volume = {2}, number = {3-4}, pages = {193-197}, pmid = {11538568}, issn = {1069-9422}, mesh = {*Computer Communication Networks ; Computer-Assisted Instruction ; Databases, Factual ; *Ecological Systems, Closed ; *Software ; *User-Computer Interface ; }, } @article {pmid11539503, year = {1995}, author = {Miller, AI and Mao, S}, title = {Association of orogenic activity with the Ordovician radiation of marine life.}, journal = {Geology}, volume = {23}, number = {4}, pages = {305-308}, doi = {10.1130/0091-7613(1995)023<0305:aooawt>2.3.co;2}, pmid = {11539503}, issn = {0091-7613}, mesh = {*Biological Evolution ; Carbonates ; *Databases, Factual ; Ecology ; *Fossils ; Geologic Sediments ; Geological Phenomena ; Geology ; *Marine Biology ; Paleontology ; }, abstract = {The Ordovician radiation of marine life was among the most substantial pulses of diversification in Earth history and coincided in time with a major increase in the global level of orogenic activity. To investigate a possible causal link between these two patterns, the geographic distributions of 6576 individual appearances of Ordovician vician genera around the world were evaluated with respect to their proximity to probable centers of orogeny (foreland basins). Results indicate that these genera, which belonged to an array of higher taxa that diversified in the Middle and Late Ordovician (trilobites, brachiopods, bivalves, gastropods, monoplacophorans), were far more diverse in, and adjacent to, foreland basins than they were in areas farther removed from orogenic activity (carbonate platforms). This suggests an association of orogeny with diversification at that time.}, } @article {pmid11540199, year = {1994}, author = {Drysdale, A and McRoberts, M and Sager, J and Wheeler, R}, title = {Object-oriented model-driven control.}, journal = {Advances in space research : the official journal of the Committee on Space Research (COSPAR)}, volume = {14}, number = {11}, pages = {313-322}, doi = {10.1016/0273-1177(94)90315-8}, pmid = {11540199}, issn = {0273-1177}, mesh = {Animals ; *Biomass ; Carbon Dioxide/metabolism ; *Computer Simulation ; Decision Making, Computer-Assisted ; *Ecological Systems, Closed ; Environment, Controlled ; Environmental Monitoring/instrumentation/methods ; *Expert Systems ; Humans ; Life Support Systems/*instrumentation ; *Models, Biological ; Photosynthesis/physiology ; Solanum tuberosum/growth & development/metabolism ; Systems Integration ; }, abstract = {A monitoring and control subsystem architecture has been developed that capitalizes on the use of model-driven monitoring and predictive control, knowledge-based data representation, and artificial reasoning in an operator support mode. We have developed an object-oriented model of a Controlled Ecological Life Support System (CELSS). The model, based on the NASA Kennedy Space Center CELSS breadboard data, tracks carbon, hydrogen, and oxygen, carbon dioxide, and water. It estimates and tracks resource-related parameters such as mass, energy, and manpower measurements such as growing area required for balance. We are developing an interface with the breadboard systems that is compatible with artificial reasoning. Initial work is being done on use of expert systems and user interface development. This paper presents our approach to defining universally applicable CELSS monitor and control issues, and implementing appropriate monitor and control capability for a particular instance: the KSC CELSS Breadboard Facility.}, } @article {pmid11540198, year = {1994}, author = {Guerrin, F and Bousson, K and Steyer JPh, and Trave-Massuyes, L}, title = {Qualitative Reasoning methods for CELSS modeling.}, journal = {Advances in space research : the official journal of the Committee on Space Research (COSPAR)}, volume = {14}, number = {11}, pages = {307-312}, doi = {10.1016/0273-1177(94)90314-x}, pmid = {11540198}, issn = {0273-1177}, mesh = {*Artificial Intelligence ; *Computer Simulation ; *Decision Making, Computer-Assisted ; *Ecological Systems, Closed ; Electronic Data Processing ; Eukaryota ; Life Support Systems/*instrumentation ; Mathematics ; *Models, Biological ; Phytoplankton ; }, abstract = {Qualitative Reasoning (QR) is a branch of Artificial Intelligence that arose from research on engineering problem solving. This paper describes the major QR methods and techniques, which, we believe, are capable of addressing some of the problems that are emphasized in the literature and posed by CELSS modeling, simulation, and control at the supervisory level.}, } @article {pmid11540196, year = {1994}, author = {Rauch, HE and Schaechter, DB}, title = {Neural [correction of Neutral] networks for control, identification and diagnosis.}, journal = {Advances in space research : the official journal of the Committee on Space Research (COSPAR)}, volume = {14}, number = {11}, pages = {297-305}, doi = {10.1016/0273-1177(94)90313-1}, pmid = {11540196}, issn = {0273-1177}, mesh = {Algorithms ; Artificial Intelligence ; *Computer Systems ; Decision Making, Computer-Assisted ; *Ecological Systems, Closed ; Equipment Failure ; Equipment Failure Analysis/methods ; *Neural Networks, Computer ; *Software ; Spacecraft/instrumentation ; *Systems Integration ; Task Performance and Analysis ; }, abstract = {Advances in the theory and technology of artificial neural networks provide the potential for new approaches to the problems of control, identification, and diagnosis for large, complex systems. However, these approaches must be validated for specific applications before they can be exploited effectively. Because of the unique capabilities they offer, neural networks should play an important role in space exploration systems operations. After a brief introduction to neural networks is presented, some applications of neural networks to identification and control of space systems are described and discussed. They span the spectrum of relatively straightforward to rather complex applications. An explanation of how neural networks can be applied to such important tasks as fault diagnosis and accommodation is presented. Neural networks are shown to be part of the hierarchy of intelligent control where a higher order decision element monitors and supervises lower order elements for sensing and actuation.}, } @article {pmid11540182, year = {1994}, author = {Hetzroni, A and Miles, GE and Engel, BA and Hammer, PA and Latin, RX}, title = {Machine vision monitoring of plant health.}, journal = {Advances in space research : the official journal of the Committee on Space Research (COSPAR)}, volume = {14}, number = {11}, pages = {203-212}, doi = {10.1016/0273-1177(94)90298-4}, pmid = {11540182}, issn = {0273-1177}, mesh = {*Algorithms ; Calibration ; Color ; Ecological Systems, Closed ; Equipment Design ; Hydroponics/instrumentation/methods ; *Image Interpretation, Computer-Assisted ; *Image Processing, Computer-Assisted ; Iron/metabolism ; Iron Deficiencies ; Lactuca/anatomy & histology/growth & development/metabolism/*physiology ; Life Support Systems/instrumentation ; Nitrogen/deficiency/metabolism ; Plant Diseases/classification ; *Software ; *Video Recording ; Zinc/deficiency/metabolism ; }, abstract = {Techniques and algorithms to detect and diagnose disorders in plants grown in a controlled environment have been developed. A video camera senses features of plants which are indicative of disorders. Images are calibrated for size and color variations by using calibration templates. Different image segmentation techniques for separating object from background, have been implemented. Plant size and color properties have been investigated, temporal, spectral and spatial variation of leaves were extracted from the segmented images. Neural network and statistical classifiers were used to determine plant condition.}, } @article {pmid11652281, year = {1994}, author = {McCally, M and Cassel, C and Kimball, DG}, title = {U.S. government-sponsored radiation research on humans 1945-1975.}, journal = {Medicine and global survival : M & GS}, volume = {1}, number = {1}, pages = {4-17}, pmid = {11652281}, issn = {1350-4002}, mesh = {Academies and Institutes ; Advisory Committees ; Databases, Factual ; Deception ; Disclosure ; *Ecology ; Federal Government ; Government ; Government Regulation ; *History ; History, 20th Century ; Hospitals ; *Human Experimentation ; Humans ; Informed Consent ; Military Personnel ; Motivation ; National Socialism ; Neoplasms ; Nuclear Warfare ; Occupational Exposure ; Persons with Mental Disabilities ; Political Systems ; Pregnancy ; Pregnant Women ; Prisoners ; *Public Policy ; *Radiation ; Research Personnel ; Research Subjects ; Risk ; Risk Assessment ; *Scientific Misconduct ; Social Control, Formal ; Social Justice ; Terminally Ill ; United States ; Universities ; }, } @article {pmid11538041, year = {1993}, author = {Sepkoski, JJ}, title = {Ten years in the library: new data confirm paleontological patterns.}, journal = {Paleobiology}, volume = {19}, number = {1}, pages = {43-51}, doi = {10.1017/s0094837300012306}, pmid = {11538041}, issn = {0094-8373}, mesh = {Animals ; *Biological Evolution ; *Classification ; *Databases, Factual ; Earth, Planet ; Fossils ; *Marine Biology ; *Paleontology ; Reference Books ; }, abstract = {A comparison is made between compilations of times of origination and extinction of fossil marine animal families published in 1982 and 1992. As a result of ten years of library research, half of the information in the compendia has changed: families have been added and deleted, low-resolution stratigraphic data been improved, and intervals of origination and extinction have been altered. Despite these changes, apparent macroevolutionary patterns for the entire marine fauna have remained constant. Diversity curves compiled from the two data bases are very similar, with a goodness-of-fit of 99%; the principal difference is that the 1992 curve averages 13% higher than the older curve. Both numbers and percentages of origination and extinction also match well, with fits ranging from 83% to 95%. All major events of radiation and extinction are identical. Therefore, errors in large paleontological data bases and arbitrariness of included taxa are not necessarily impediments to the analysis of pattern in the fossil record, so long as the data are sufficiently numerous.}, } @article {pmid11538007, year = {1993}, author = {Wheeler, RM and Berry, WL and Mackowiak, C and Corey, KA and Sager, JC and Heeb, MM and Knott, WM}, title = {A data base of crop nutrient use, water use, and carbon dioxide exchange in a 2O square meter growth chamber: I. Wheat as a case study.}, journal = {Journal of plant nutrition}, volume = {16}, number = {10}, pages = {1881-1915}, doi = {10.1080/01904169309364659}, pmid = {11538007}, issn = {0190-4167}, mesh = {*Biomass ; Carbon Dioxide/*metabolism ; Databases, Factual ; *Ecological Systems, Closed ; Hydroponics ; Life Support Systems/instrumentation ; Minerals/analysis ; Nutritive Value ; Oxygen Consumption/*physiology ; Photoperiod ; Photosynthesis ; Plant Roots/chemistry/growth & development/metabolism ; Time Factors ; Triticum/chemistry/*growth & development/*metabolism ; }, abstract = {A data set is given describing the daily nutrient uptake, gas exchange, environmental conditions, and carbon (C), and nutrient partitioning at harvest for the entire canopy and root system of a wheat crop (Triticum aestivum, cv. Yecora Rojo). The data were obtained from a 20 m2 stand of wheat plants grown from planting to maturity in a closed, controlled environment, and include daily nutrient uptake [macronutrients, nitrogen (N), phosphorus (P), potassium (K), calcium (Ca), magnesium (Mg), and sulfur (S); and micronutrients, iron (Fe), boron (B), manganese (Mn), zinc (Zn), copper (Cu), and molybdenum (Mo)], canopy carbon dioxide (CO2) exchange rates, and transpiration. Environmental factors such as relative humidity, air temperature, nutrient solution temperature, pH and electrical conductivity, and photoperiod were controlled in the chamber to specific set points. A detailed description of biomass yield for each of the 64 plant growth trays comprising the 20 m2 of growth area is also provided, and includes dry weights of grain, straw, chaff, and roots, along with the concentration of nutrients in different plant tissues and the percent carbohydrate, fat, and protein. To our knowledge, this information represents one of the most extensive data sets available for a canopy of wheat grown from seed to maturity under controlled environmental and nutritional conditions, and thus may provide useful information for model development and validation. A methods section is included to qualify any assumptions that might be required for the use of the data in plant growth models, along with a daily event calendar indicating when adjustments in set points and occasional equipment or sensor failures occurred.}, } @article {pmid11542147, year = {1988}, author = {Sepkoski, JJ}, title = {Alpha, beta, or gamma: where does all the diversity go?.}, journal = {Paleobiology}, volume = {14}, number = {3}, pages = {221-234}, doi = {10.1017/s0094837300011969}, pmid = {11542147}, issn = {0094-8373}, support = {DEB 81-08890/DE/NIDCR NIH HHS/United States ; }, mesh = {Animals ; *Biological Evolution ; Bryozoa ; Classification ; Databases, Factual ; *Ecosystem ; *Fossils ; Geologic Sediments/analysis ; *Marine Biology ; Models, Theoretical ; *Paleontology ; }, abstract = {Global taxonomic richness is affected by variation in three components: within-community, or alpha, diversity, between-community, or beta, diversity; and between-region, or gamma, diversity. A data set consisting of 505 faunal lists distributed among 40 stratigraphic intervals and six environmental zones was used to investigate how variation of alpha and beta diversity influenced global diversity through the Paleozoic, and especially during the Ordovician radiations. As first shown by Bambach (1977), alpha diversity increased by 50 to 70 percent in offshore marine environments during the Ordovician and then remained essentially constant of the remainder of the Paleozoic. The increase is insufficient, however, to account for the 300 percent rise observed in global generic diversity. It is shown that beta diversity among level, soft-bottom communities also increased significantly during the early Paleozoic. This change is related to enhanced habitat selection, and presumably increased overall specialization, among diversifying taxa during the Ordovician radiations. Combined with alpha diversity, the measured change in beta diversity still accounts for only about half of the increase in global diversity. Other sources of increase are probably not related to variation in gamma diversity but rather to appearance and/or expansion of organic reefs, hardground communities, bryozoan thickets, and crinoid gardens during the Ordovician.}, } @article {pmid12338372, year = {1980}, author = {Bueno Sanchez, E}, title = {[The demographic factor in the global model].}, journal = {Revista cubana de administracion de salud}, volume = {6}, number = {3}, pages = {209-229}, pmid = {12338372}, issn = {0252-1903}, mesh = {Conservation of Natural Resources ; *Demography ; *Ecology ; *Economics ; Environment ; *Food Supply ; *Industry ; *Models, Theoretical ; Population ; Population Growth ; Research ; *Social Change ; Social Sciences ; }, } @article {pmid11250811, year = {2001}, author = {Jorgenson, JL}, title = {Aldrin and dieldrin: a review of research on their production, environmental deposition and fate, bioaccumulation, toxicology, and epidemiology in the United States.}, journal = {Environmental health perspectives}, volume = {109 Suppl 1}, number = {Suppl 1}, pages = {113-139}, pmid = {11250811}, issn = {0091-6765}, mesh = {Aldrin/*adverse effects/analysis ; Animals ; Animals, Wild ; Biological Availability ; Databases, Factual ; Dieldrin/*adverse effects/analysis ; Environmental Exposure ; Environmental Monitoring ; Epidemiologic Studies ; Epidemiological Monitoring ; *Fishes ; Health Policy ; Humans ; Insecticides/*adverse effects/analysis ; Internet ; *Mammals ; Public Health ; Tissue Distribution ; United States/epidemiology ; }, abstract = {In the last decade four international agreements have focused on a group of chemical substances known as persistent organic pollutants (POPs). Global agreement on the reduction and eventual elimination of these substances by banning their production and trade is a long-term goal. Negotiations for these agreements have focused on the need to correlate data from scientists working on soil and water sampling and air pollution monitoring. Toxicologists and epidemiologists have focused on wildlife and human health effects and understanding patterns of disease requires better access to these data. In the last 20 years, substantial databases have been created and now are becoming available on the Internet. This review is a detailed examination of 2 of the 12 POPs, aldrin and dieldrin, and how scientific groups identify and measure their effects. It draws on research findings from a variety of environmental monitoring networks in the United States. An overview of the ecologic and health effects of aldrin and dieldrin provides examples of how to streamline some of the programs and improve access to mutually useful scientific data. The research groups are located in many government departments, universities, and private organizations. Identifying databases can provide an "information accelerator" useful to a larger audience and can help build better plant and animal research models across scientific fields.}, } @article {pmid11249834, year = {2001}, author = {Zaaf, A and Van Damme, R and Herrel, A and Aerts, P}, title = {Spatio-temporal gait characteristics of level and vertical locomotion in a ground-dwelling and a climbing gecko.}, journal = {The Journal of experimental biology}, volume = {204}, number = {Pt 7}, pages = {1233-1246}, doi = {10.1242/jeb.204.7.1233}, pmid = {11249834}, issn = {0022-0949}, mesh = {Adaptation, Physiological ; Animals ; Data Interpretation, Statistical ; Environment ; Forelimb/anatomy & histology/physiology ; Gait/*physiology ; Hindlimb/anatomy & histology/physiology ; Lizards/anatomy & histology/*physiology ; Locomotion/*physiology ; Time Factors ; }, abstract = {The effects of incline (vertical versus horizontal) on spatio-temporal gait characteristics (stride and step length, frequency, duty factor, degree of sprawling) were measured over a range of speeds in a ground-dwelling (Eublepharis macularius) and a climbing (Gekko gecko) species of gecko. Surprisingly, the climbing species also performs very well when moving on the horizontal substratum. In the present experiments, climbing speeds ranged from 0.6 to 1.2 m s(-1), whereas speeds for level locomotion were between 0.6 and 1.8 m s(-1). In contrast, the vertical climbing capacities of the ground-dweller are limited (speeds below 0.1 m s(-1)versus level speeds between 0.2 and 1.1 m s(-1)). In general, we demonstrate that very little adjustment in gait characteristics is made by either species when they are forced to move on their non-habitual substratum. Moreover, gait characteristics differ little between the species despite the clear differences in ecological niche. Higher level or climbing speeds are realized mainly (or exclusively in the case of level locomotion in G. gecko) by increasing stride frequency. Stride lengths and duty factors vary with speed in the ground-dweller, but not in the climbing species. Step length and the degree of sprawling are speed-independent (except for hind-limb sprawling in G. gecko on the level). It is argued that this common strategy suits climbing (fixed spatial variables, no floating phases) rather than level locomotion.}, } @article {pmid11238578, year = {2001}, author = {Benach, J and Yasui, Y and Borrell, C and Sáez, M and Pasarin, MI}, title = {Material deprivation and leading causes of death by gender: evidence from a nationwide small area study.}, journal = {Journal of epidemiology and community health}, volume = {55}, number = {4}, pages = {239-245}, pmid = {11238578}, issn = {0143-005X}, mesh = {*Cause of Death ; Cross-Sectional Studies ; Data Interpretation, Statistical ; Female ; Humans ; Male ; *Poverty ; *Sex Factors ; Small-Area Analysis ; Spain/epidemiology ; }, abstract = {STUDY OBJECTIVE: To investigate the association between material deprivation and 10 leading causes of death by gender.

DESIGN: Small area cross sectional ecological study using two dimensions of material deprivation (Index 1 and Index 2) drawn from 1991 census and cause specific mortality data aggregated for 1987-1995.

SETTING: 2218 small areas in Spain.

MAIN RESULTS: Strong detrimental associations of two deprivation indices were found with top six leading causes of death for men and top seven leading causes of death for women, except breast cancer. For men, the highest percentages of excess mortality (between 40% and 60%) were found for smoking and alcohol related causes of death such as lung cancer, chronic obstructive pulmonary diseases, and cirrhosis while for women the highest percentages of excess mortality (between 40% and 60%) were found for diet related causes such as diabetes and ischaemic heart disease.

CONCLUSIONS: Health inequality is a widespread phenomenon in the majority of the top leading causes of deaths of the nation. Increasing levels of deprivation indices are associated with mortality risk differently by both cause and gender. Results suggest that deprivation effects mainly captured by Index 2 may manifest largely as unfavourable health behaviours leading to gender specific sets of causes of deaths. Findings of this study are consistent with the idea that material deprivation determines health inequality through both an increase of general susceptibility to ill health, leading to excess mortality in a wide range of causes, and a set of specific factors, resulting in an increased risk of death from a specific set of causes in each gender.}, } @article {pmid11231894, year = {2001}, author = {Zhang, L and Pond, SK and Gaut, BS}, title = {A survey of the molecular evolutionary dynamics of twenty-five multigene families from four grass taxa.}, journal = {Journal of molecular evolution}, volume = {52}, number = {2}, pages = {144-156}, doi = {10.1007/s002390010143}, pmid = {11231894}, issn = {0022-2844}, mesh = {DNA/analysis ; Databases, Factual ; *Evolution, Molecular ; GC Rich Sequence ; Gene Conversion ; Genes, Plant/*genetics ; Hordeum/*genetics ; Multigene Family/*genetics ; Oryza/*genetics ; Phylogeny ; Triticum/*genetics ; Zea mays/*genetics ; }, abstract = {We surveyed the molecular evolutionary characteristics of 25 plant gene families, with the goal of better understanding general processes in plant gene family evolution. The survey was based on 247 GenBank sequences representing four grass species (maize, rice, wheat, and barley). For each gene family, orthology and paralogy relationships were uncertain. Recognizing this uncertainty, we characterized the molecular evolution of each gene family in four ways. First, we calculated the ratio of nonsynonymous to synonymous substitutions (d(N)/d(S)) both on branches of gene phylogenies and across codons. Our results indicated that the d(N)/d(S) ratio was statistically heterogeneous across branches in 17 of 25 (68%) gene families. The vast majority of d(N)/d(S) estimates were <<1.0, suggestive of selective constraint on amino acid replacements, and no estimates were >1.0, either across phylogenetic lineages or across codons. Second, we tested separately for nonsynonymous and synonymous molecular clocks. Sixty-eight percent of gene families rejected a nonsynonymous molecular clock, and 52% of gene families rejected a synonymous molecular clock. Thus, most gene families in this study deviated from clock-like evolution at either synonymous or nonsynonymous sites. Third, we calculated the effective number of codons and the proportion of G+C synonymous sites for each sequence in each gene family. One or both quantities vary significantly within 18 of 25 gene families. Finally, we tested for gene conversion, and only six gene families provided evidence of gene conversion events. Altogether, evolution for these 25 gene families is marked by selective constraint that varies among gene family members, a lack of molecular clock at both synonymous and nonsynonymous sites, and substantial variation in codon usage.}, } @article {pmid11212953, year = {2000}, author = {Wtorek, J}, title = {Relations between components of impedance cardiogram analyzed by means of finite element model and sensitivity theorem.}, journal = {Annals of biomedical engineering}, volume = {28}, number = {11}, pages = {1352-1361}, doi = {10.1114/1.1327596}, pmid = {11212953}, issn = {0090-6964}, mesh = {Biomechanical Phenomena ; Biomedical Engineering ; Blood Volume/physiology ; Cardiography, Impedance/*statistics & numerical data ; Heart/physiology ; Humans ; Lung/physiology ; *Models, Cardiovascular ; Models, Statistical ; Thorax/physiology ; }, abstract = {The main aim of the study is to establish a relation between different sources of Impedance cardiogram (ICG) as function of spatial distribution of conductivity. A three-dimensional model of a human thorax using the finite element method has been constructed. The model includes 35 horizontal layers consisting of up to 519 pentahedral elements that are automatically divided into tetrahedral ones before calculating the potential distribution. Electrode array configuration proposed by Kubicek et al. (Aerosp. Med. 37: 1208-1212, 1996) has been studied. A relationship proposed by Geselowitz (IEEE Trans. Biomed. Eng. 18: 38-41, 1971) has been used to calculate the sensitivity of the examined electrode array to conductivity changes inside the thorax. This relationship has allowed for the calculation of the contributions to ICG from spatially separated sources when modeling all changes in conductivity simultaneously. It has been confirmed that the main contributions to ICG signal come from ventricles, atria, aorta, and lungs. The relations between these components have been found to be dependent nonlinearly on spatial conductivity distribution. As a result, reliable and reproducible measurements of stroke volume (SV) using ICG are impossible. Nevertheless, ICG can be used to monitor relative changes of SV in all cases where the spatial distribution of conductivity and geometry of the subject, during the examination, is preserved. However, it does not mean that the accuracy of SV measurement will be the same in all these cases.}, } @article {pmid11204970, year = {2000}, author = {Zhu, Y and Strassmann, JE and Queller, DC}, title = {Insertions, substitutions, and the origin of microsatellites.}, journal = {Genetical research}, volume = {76}, number = {3}, pages = {227-236}, doi = {10.1017/s001667230000478x}, pmid = {11204970}, mesh = {Animals ; Base Sequence ; DNA Replication/*genetics ; DNA Transposable Elements/*genetics ; Databases, Factual ; Emigration and Immigration ; Humans ; Microsatellite Repeats/*genetics ; Mutation/*genetics ; Reading Frames/*genetics ; Tandem Repeat Sequences/*genetics ; Wasps/*genetics ; }, abstract = {This paper uses data from the Human Gene Mutation Database to contrast two hypotheses for the origin of short DNA repeats: substitutions and insertions that duplicate adjacent sequences. Because substitutions are much more common than insertions, they are the dominant source of new 2-repeat loci. Insertions are rarer, but over 70% of the 2-4 base insertion mutations are duplications of adjacent sequences, and over half of these generate new repeat regions. Insertions contribute fewer new repeat loci than substitutions, but their relative importance increases rapidly with repeat number so that all new 4-5-repeat mutations come from insertions, as do all 3-repeat mutations of tetranucleotide repeats. This suggests that the process of repeat duplication that dominates microsatellite evolution at high repeat numbers is also important very early in microsatellite evolution. This result sheds light on the puzzle of the origin of short tandem repeats. It also suggests that most short insertion mutations derive from a slippage-like process during replication.}, } @article {pmid11175530, year = {2000}, author = {Coeli, CM and Veras, RP and da Silva Freire Coutinho, E}, title = {[Capture-recapture methodology: an option for surveillance of non-communicable diseases in the elderly].}, journal = {Cadernos de saude publica}, volume = {16}, number = {4}, pages = {1071-1082}, doi = {10.1590/s0102-311x2000000400025}, pmid = {11175530}, issn = {0102-311X}, mesh = {Aged ; Brazil/epidemiology ; Data Collection/methods ; Data Interpretation, Statistical ; Diabetes Mellitus/*epidemiology ; Disease Notification/statistics & numerical data ; Epidemiologic Methods ; Humans ; Models, Statistical ; Population Surveillance/*methods ; }, abstract = {Capture-recapture methodology is used in Ecology to estimate the total size of wild animal populations. This method can be used in Epidemiology to estimate the incidence and prevalence of communicable and non-communicable diseases in a relatively inexpensive and quick way. Surveillance systems based on the use of this methodology are a potential alternative for monitoring non-communicable diseases in Brazil. This paper presents a brief review of fundamental capture-recapture methodology and its applications to Epidemiology. We also present a theoretical model for implementation of a diabetes mellitus surveillance system in the elderly using publicly available morbidity and mortality data sources and the capture-recapture methodology.}, } @article {pmid11160175, year = {2001}, author = {Wen, SW and Demissie, K and August, D and Rhoads, GG}, title = {Level of aggregation for optimal epidemiological analysis: the case of time to surgery and unnecessary removal of the normal appendix.}, journal = {Journal of epidemiology and community health}, volume = {55}, number = {3}, pages = {198-203}, pmid = {11160175}, issn = {0143-005X}, mesh = {Adolescent ; Adult ; Appendectomy/*statistics & numerical data ; Appendicitis/epidemiology/*surgery ; Bias ; Child ; Child, Preschool ; Cohort Studies ; Data Interpretation, Statistical ; Female ; Humans ; Infant ; Infant, Newborn ; Male ; Middle Aged ; Ontario/epidemiology ; Time Factors ; Unnecessary Procedures/*statistics & numerical data ; }, abstract = {STUDY OBJECTIVE: To illustrate the concept of "individualised fallacy", the result of improper interpretation and inference about aggregate level associations on the basis of associations at the individual level, in epidemiology.

DESIGN: Cohort study.

SETTING: Canadian province of Ontario.

PATIENTS: All patients who underwent primary appendicectomy in 175 Ontario hospitals from 1989 to 1992. The association between rate of normal appendix removal and time to surgery was analysed at two levels: (1) at individual patient level, in which, for each patient, the exact number of days to surgery was derived, and (2) at hospital level, in which hospital specific proportions of time to surgery was calculated.

MAIN RESULTS: Measured at individual level, compared with patients who had an operation on the same day of admission, the odds ratio was 2.41 (95% confidence intervals 2.28, 2.56) for patients who had an operation > 1 day after admission. Measured at hospital level, each 10% increase in the proportion of patients who had an operation > 1 day after admission resulted in a 15% reduction in the odds of normal appendix removal (odds ratio 0.85, 95% confidence intervals 0.82, 0.88)

CONCLUSIONS: In this case study, hospital level measure correctly predicted a reduction in the rate of normal appendix removal by delaying surgery, whereas individual level measure biased the direction of the relation to the opposite. This example illustrates that bias in across level inference can occur either at individual or ecological level. The preferred level of analysis is the one that minimises confounding; often, it must be selected on the basis of a priori knowledge of the subject area.}, } @article {pmid11158339, year = {2001}, author = {Spiers, AJ and Field, D and Bailey, M and Rainey, PB}, title = {Notes on designing a partial genomic database: The PfSBW25 Encyclopaedia, a sequence database for Pseudomonas fluorescens SBW25.}, journal = {Microbiology (Reading, England)}, volume = {147}, number = {Pt 2}, pages = {247-249}, doi = {10.1099/00221287-147-2-247}, pmid = {11158339}, issn = {1350-0872}, mesh = {Base Sequence ; *Databases, Factual ; *Genome, Bacterial ; Information Storage and Retrieval ; Internet ; Plasmids/genetics ; *Programming Languages ; Pseudomonas fluorescens/*genetics ; *Software Design ; }, } @article {pmid11144987, year = {2000}, author = {Araabi, BN and Kehtarnavaz, N and McKinney, T and Hillman, G and Würsig, B}, title = {A string matching computer-assisted system for dolphin photoidentification.}, journal = {Annals of biomedical engineering}, volume = {28}, number = {10}, pages = {1269-1279}, doi = {10.1114/1.1317532}, pmid = {11144987}, issn = {0090-6964}, mesh = {Animal Identification Systems/*methods/statistics & numerical data ; Animals ; Biomedical Engineering ; *Computers ; Databases, Factual ; Dolphins/*anatomy & histology ; Marine Biology/methods ; Photography ; }, abstract = {This paper presents a syntactic/semantic string representation scheme as well as a string matching method as part of a computer-assisted system to identify dolphins from photographs of their dorsal fins. A low-level string representation is constructed from the curvature function of a dolphin's fin trailing edge, consisting of positive and negative curvature primitives. A high-level string representation is then built over the low-level string via merging appropriate groupings of primitives in order to have a less sensitive representation to curvature fluctuations or noise. A family of syntactic/semantic distance measures between two strings is introduced. A composite distance measure is then defined and used as a dissimilarity measure for database search, highlighting both the syntax (structure or sequence) and semantic (attribute or feature) differences. The syntax consists of an ordered sequence of significant protrusions and intrusions on the edge, while the semantics consist of seven attributes extracted from the edge and its curvature function. The matching results are reported for a database of 624 images corresponding to 164 individual dolphins. The identification results indicate that the developed string matching method performs better than the previous matching methods including dorsal ratio, curvature, and curve matching. The developed computer-assisted system can help marine mammalogists in their identification of dolphins, since it allows them to examine only a handful of candidate images instead of the currently used manual searching of the entire database.}, } @article {pmid11142831, year = {1999}, author = {Gutiérrez, G and Reyes, H and Fernández, S and Pérez, L and Pérez-Cuevas, R and Guiscafré, H}, title = {[Impact of health services, sanitation and literacy in the mortality of children under 5 years of age]].}, journal = {Salud publica de Mexico}, volume = {41}, number = {5}, pages = {368-375}, pmid = {11142831}, issn = {0036-3634}, mesh = {Cause of Death/*trends ; Child Health Services/*organization & administration ; Child, Preschool ; Diarrhea/mortality ; Educational Status ; Humans ; Infant ; Infant, Newborn ; Measles/mortality ; Mexico/epidemiology ; Regression Analysis ; Respiratory Tract Infections/mortality ; Socioeconomic Factors ; Vaccination ; }, abstract = {OBJECTIVE: To analyze differences of the impact of health care services, sanitation and literacy on the mortality rates of children under five years of age, in two Mexican states with marked socioeconomic differences: Chiapas and Nuevo Leon.

MATERIAL AND METHODS: The study design was ecologic, based on a retrospective analysis of data published by the Health Ministry (Secretaría de Salud), National Institute of Statistics, Geography and Informatics (Instituto Nacional de Estadística, Geografía e Informática) and the National Population Council (Consejo Nacional de Población), on the tendencies of mortality among children under five years and on the changes of selected indicators corresponding to the period 1990-1997.

STUDY DESIGN: ecologic study. This was based on a retrospective analysis of data published by Secretaría de Salud, Instituto Nacional de Estadística e Informática and Consejo Nacional de Población, about the tendencies of mortality among children under five years, and about the changes of selected indicators. The analysis was carried out in the period comprised between 1990-1997. For both states the registered variations were calculated and the trends were determined through analysis of simple linear regression; the independent variable corresponded to the study years. Partial correlation analysis between the various mortality trends studies and between and the selected indicators, were calculated.

RESULTS: During the studied period there was a steady decline of children mortality, which was more marked in Chiapas. In both entities, this decrease was closely related to the decline in mortality due to acute diarrhea, and also correlated with a descent in measles and acute respiratory infections. In Chiapas, the indicators which correlated more significantly with this decline in mortality were vaccination coverage and literacy. In Nuevo Leon, the indicators with greater correlation were the increase in the number of nurses, of lodgings with piped water and vaccination coverage.

CONCLUSIONS: During the analyzed period, the mortality rate of children under five years of age decreased in the states of Chiapas and Nuevo Leon. To sustain or accelerate the decline in childhood mortality it is mandatory to continue with the currently implemented programs, and in Chiapas, and similar states, to increase the available infrastructure to provide health care.}, } @article {pmid11135713, year = {2000}, author = {Yanaka, Y and Hanaki, K and Yoshikura, H and Yamamoto, K}, title = {Computer simulation of survival of mutants under non-selective condition.}, journal = {Japanese journal of infectious diseases}, volume = {53}, number = {5}, pages = {217-218}, pmid = {11135713}, issn = {1344-6304}, mesh = {Bacteria/drug effects/*genetics/*growth & development ; *Computer Simulation ; Drug Resistance, Microbial/genetics ; Genetic Engineering ; Intestines/*microbiology ; *Models, Biological ; *Mutation ; }, } @article {pmid11125082, year = {2001}, author = {Maidak, BL and Cole, JR and Lilburn, TG and Parker, CT and Saxman, PR and Farris, RJ and Garrity, GM and Olsen, GJ and Schmidt, TM and Tiedje, JM}, title = {The RDP-II (Ribosomal Database Project).}, journal = {Nucleic acids research}, volume = {29}, number = {1}, pages = {173-174}, pmid = {11125082}, issn = {1362-4962}, mesh = {*Databases, Factual ; Information Services ; Internet ; Phylogeny ; RNA, Ribosomal/*genetics ; Ribosomes/*metabolism ; Sequence Alignment ; }, abstract = {The Ribosomal Database Project (RDP-II), previously described by Maidak et al. [Nucleic Acids Res. (2000), 28, 173-174], continued during the past year to add new rRNA sequences to the aligned data and to improve the analysis commands. Release 8.0 (June 1, 2000) consisted of 16 277 aligned prokaryotic small subunit (SSU) rRNA sequences while the number of eukaryotic and mitochondrial SSU rRNA sequences in aligned form remained at 2055 and 1503, respectively. The number of prokaryotic SSU rRNA sequences more than doubled from the previous release 14 months earlier, and approximately 75% are longer than 899 bp. An RDP-II mirror site in Japan is now available (http://wdcm.nig.ac.jp/RDP/html/index.h tml). RDP-II provides aligned and annotated rRNA sequences, derived phylogenetic trees and taxonomic hierarchies, and analysis services through its WWW server (http://rdp.cme.msu.edu/). Analysis services include rRNA probe checking, approximate phylogenetic placement of user sequences, screening user sequences for possible chimeric rRNA sequences, automated alignment, production of similarity matrices and services to plan and analyze terminal restriction fragment polymorphism experiments. The RDP-II email address for questions and comments has been changed from curator@cme.msu.edu to rdpstaff@msu.edu.}, } @article {pmid11116093, year = {2000}, author = {Nekrutenko, A and Li, WH}, title = {Assessment of compositional heterogeneity within and between eukaryotic genomes.}, journal = {Genome research}, volume = {10}, number = {12}, pages = {1986-1995}, pmid = {11116093}, issn = {1088-9051}, support = {R01 GM030998/GM/NIGMS NIH HHS/United States ; R37 GM030998/GM/NIGMS NIH HHS/United States ; GM30998/GM/NIGMS NIH HHS/United States ; GM55759/GM/NIGMS NIH HHS/United States ; }, mesh = {Algorithms ; Animals ; Base Composition ; Caenorhabditis elegans/genetics ; Centrifugation, Density Gradient ; Computational Biology ; Drosophila melanogaster/genetics ; Eukaryotic Cells/*physiology ; GC Rich Sequence/genetics ; *Genetic Heterogeneity ; *Genome ; Genome, Fungal ; Genome, Human ; Genome, Plant ; Humans ; Models, Genetic ; Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; }, abstract = {Using large amounts of long genomic sequences, we studied the compositional patterns of eukaryotic genomes. We developed a simple measure, the compositional heterogeneity (or variability) index, to compare the differences in compositional heterogeneity between long genomic sequences. The index measures the average difference in GC content between two adjacent windows normalized by the standard error expected under the assumption of random distribution of nucleotides in a window. We report the following findings: (1) The extent of the compositional heterogeneity in a genomic sequence strongly correlates with its GC content in all multicellular eukaryotes studied regardless of genome size. (2) The human genome appears to be highly compositionally heterogeneous both within and between individual chromosomes; the heterogeneity goes much beyond the predictions of the isochore model. (3) All genomes of multicellular eukaryotes examined in this study are compositionally heterogeneous, although they also contain compositionally uniform segments, or isochores. (4) The true uniqueness of the human (or mammalian) genome is the presence of very high GC regions, which exhibit unusually high compositional heterogeneity and contain few long homogeneous segments (isochores). In general, GC-poor isochores tend to be longer than GC-rich ones. These findings indicate that the genomes of multicellular organisms are much more heterogeneous in nucleotide composition than depicted by the isochore model and so lead to a looser definition of isochores.}, } @article {pmid11108699, year = {2000}, author = {Kim, J and Moriyama, EN and Warr, CG and Clyne, PJ and Carlson, JR}, title = {Identification of novel multi-transmembrane proteins from genomic databases using quasi-periodic structural properties.}, journal = {Bioinformatics (Oxford, England)}, volume = {16}, number = {9}, pages = {767-775}, doi = {10.1093/bioinformatics/16.9.767}, pmid = {11108699}, issn = {1367-4803}, support = {DC-02174/DC/NIDCD NIH HHS/United States ; }, mesh = {*Algorithms ; Amino Acid Sequence/genetics ; Animals ; Computational Biology/*methods ; Databases, Factual ; Drosophila ; Genomics/*methods ; Membrane Proteins/*genetics ; *Periodicity ; Predictive Value of Tests ; Receptors, Odorant/genetics ; Reproducibility of Results ; Sequence Alignment/methods ; }, abstract = {MOTIVATION: Identification of novel G protein-coupled receptors and other multi-transmembrane proteins from genomic databases using structural features.

RESULTS: Here we describe a new algorithm for identifying multi-transmembrane proteins from genomic databases with a specific application to identifying G protein-coupled receptors (GPCRs) that we call quasi-periodic feature classifier (QFC). The QFC algorithm uses concise statistical variables as the 'feature space' to characterize the quasi-periodic physico-chemical properties of multi-transmembrane proteins. For the case of identifying GPCRs, the variables are then used in a non-parametric linear discriminant function to separate GPCRs from non-GPCRs. The algorithm runs in time linearly proportional to the number of sequences, and performance on a test dataset shows 96% positive identification of known GPCRs. The QFC algorithm also works well with short random segments of proteins and it positively identified GPCRs at a level greater than 90% even with segments as short as 100 amino acids. The primary advantage of the algorithm is that it does not directly use primary sequence patterns which may be subject to sampling bias. The utility of the new algorithm has been demonstrated by the isolation from the Drosophila genome project database of a novel class of seven-transmembrane proteins which were shown to be the elusive olfactory receptor genes of Drosophila.}, } @article {pmid11105475, year = {2000}, author = {Skeem, JL and Mulvey, EP and Lidz, CW}, title = {Building mental health professionals' decisional models into tests of predictive validity: the accuracy of contextualized predictions of violence.}, journal = {Law and human behavior}, volume = {24}, number = {6}, pages = {607-628}, doi = {10.1023/a:1005513818748}, pmid = {11105475}, issn = {0147-7307}, support = {2 T32 MH18269-14/MH/NIMH NIH HHS/United States ; R01-MH400030/MH/NIMH NIH HHS/United States ; }, mesh = {Adolescent ; Adult ; Alcohol Drinking/psychology ; Case-Control Studies ; *Decision Support Techniques ; *Emergency Services, Psychiatric ; Female ; Humans ; Linear Models ; Male ; Matched-Pair Analysis ; Mental Disorders/*diagnosis ; Middle Aged ; Reproducibility of Results ; Risk Assessment/*methods ; *Violence/psychology ; }, abstract = {To safely manage potentially violent patients in the community, mental health professionals (MHPs) must assess when and under what conditions a patient may be involved in a violent act. This study applies a more ecologically sensitive approach than past research by building the conditions that MHPs believe make patient violence more likely into tests of their predictive validity. In specific, the accuracy of MHPs' predictions that patients were more likely to become violent when they consumed alcohol was assessed based on a sample of 714 patients. The results indicate that MHPs do not discriminate well between patients who are likely to become violent during periods in which they drink from those who are not. MHPs' predictions appear more descriptive of the drinking behavior of a high-risk group than predictive of alcohol-related violent incidents. Thus, even when their apparent decisional processes are considered in tests of accuracy, MHPs' predictions of violence are only moderately more accurate than chance. This paper analyzes the implications of these findings for risk assessment practice and for conducting further clinically relevant research.}, } @article {pmid11103669, year = {2000}, author = {Mackenbach, JP}, title = {[Roaming through methodology. XXVI. The ecological fallacy and its less well-known counterpart, the atomistic fallacy].}, journal = {Nederlands tijdschrift voor geneeskunde}, volume = {144}, number = {44}, pages = {2097-2100}, pmid = {11103669}, issn = {0028-2162}, mesh = {*Bias ; *Data Interpretation, Statistical ; *Epidemiologic Studies ; Humans ; *Research Design ; }, abstract = {Usually, individuals form the unit of observation and analysis in epidemiological studies, but such is not the case in the ecological study design in which determinants and diseases are related at the group level (school classes, companies, suburbs, countries). Ecological studies are subject to the ecological fallacy when they are used to make inferences on relationships between determinants and diseases at the individual level: the relationship on the group level may not reflect the relationship on the individual level. On the other hand, individual-level studies are subject to the atomistic fallacy, when they are used to make inferences on relationships between determinants and diseases at the group level: a relationship between a determinant and disease on group level may not be exclusively based on the relationship on the individual level.}, } @article {pmid11084525, year = {2000}, author = {Hautemanière, A and Czernichow, P and Germain, JM and Delmas, V and Falourd, JC and Zeghnoun, K and Dureuil, B}, title = {[Impact of the daily variations of the air pollution on the ambulatory emergency health services activity. Study in the urban area of Rouen (France)].}, journal = {Revue d'epidemiologie et de sante publique}, volume = {48}, number = {5}, pages = {449-458}, pmid = {11084525}, issn = {0398-7620}, mesh = {Air Pollutants/analysis ; Air Pollution/*adverse effects ; Cardiovascular Diseases/*epidemiology ; Data Interpretation, Statistical ; *Emergency Medical Services ; Environmental Monitoring ; Epidemiological Monitoring ; France ; Humans ; Nitrogen Dioxide/analysis ; Poisson Distribution ; Population Surveillance ; Respiratory Tract Diseases/*epidemiology ; Risk ; Seasons ; Sulfur Dioxide/analysis ; Urban Population ; }, abstract = {BACKGROUND: The aim of this study was to evaluate feasibility of using both the emergency phone calls (SAMU) and medical interventions (SMUR) related to ambulatory emergency services for local epidemiological surveillance of health impact of air pollution.

METHODS: A temporal ecological study was performed at Rouen area (France) (380,000 inhabitants) for 1990-1997 (SAMU) and 1990-1996 (SMUR). The pollutants tested were: Sulphur dioxide (SO(2)), Particles (PM13), and Nitrogen dioxide (NO(2)), as collected routinely by a local automated network. For each phone call (SAMU) or emergency interventions (SMUR), the date, medical reason for calling (SAMU) or diagnosis after interventions (SMUR) (classified as respiratory, cardiovascular or other diseases) have been extracted from a specific information system. A statistical analysis based on time series analysis associated to a Poisson regression was conducted, taking into account temporal trend, seasonal variations, influenza, days of the week, holiday and meteorological data.

RESULTS: An association was observed between ambulatory emergency services activity for cardiovascular diseases, and the daily variations of both SO(2) (relative risk=1.008 [1.001-1.016] for SAMU with an increase of 10 microg/m(3)) and NO(2) (relative risk=1.018 [1.008-1. 030] for SAMU, relative risk=1.016 [1.001-1.032] for SMUR with an increase of 10 microg/m(3)). No association could be observed with the respiratory diseases for these pollutants.

CONCLUSION: The ambulatory emergency services activity data could contribute to an epidemiological surveillance of the health impact of the air pollution, but a better quality of data collected (concerning both procedures and codification) is requested. The interest of an epidemiological surveillance, rather than usual pollutant monitoring, remains to evaluate.}, } @article {pmid11070058, year = {2000}, author = {Rodríguez-Trelles, F and Tarrío, R and Ayala, FJ}, title = {Evidence for a high ancestral GC content in Drosophila.}, journal = {Molecular biology and evolution}, volume = {17}, number = {11}, pages = {1710-1717}, doi = {10.1093/oxfordjournals.molbev.a026269}, pmid = {11070058}, issn = {0737-4038}, support = {GM42397/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Base Composition/*genetics ; Codon/genetics ; DNA/genetics ; Databases, Factual ; Drosophila/*genetics ; Drosophila melanogaster/genetics ; Evolution, Molecular ; Genes, Insect/genetics ; Phylogeny ; }, abstract = {Study of the nucleotide composition in Drosophila, focusing on the saltans and willistoni groups, has revealed unanticipated differences in nucleotide composition among lineages. Compositional differences are associated with an accelerated rate of nucleotide substitution in functionally less constrained regions. These observations have been set forth against the extended opinion that the pattern of point mutation has remained constant during the evolution of the genus. A crucial assumption has been that the most recent common ancestor of the subgenus Sophophora had an elevated GC content. Until now, this assumption has been supported by indirect arguments, consisting of extrapolations from closely related outgroups and limited by the robustness of mathematical descriptions concerning the extensive nucleotide composition differences among sequences. The present study seeks to test the assumption of a high ancestral GC content using realistic representations of the nucleotide substitution process to account for potential biases induced by the heterogeneous GC content of the taxa. The analysis of eight nuclear genes unambiguously corroborates that the common ancestor of Sophophora had an elevated GC content.}, } @article {pmid11027195, year = {2000}, author = {Kohli, S and Noorlind Brage, H and Löfman, O}, title = {Childhood leukaemia in areas with different radon levels: a spatial and temporal analysis using GIS.}, journal = {Journal of epidemiology and community health}, volume = {54}, number = {11}, pages = {822-826}, pmid = {11027195}, issn = {0143-005X}, mesh = {Adolescent ; Air Pollutants, Radioactive/*adverse effects ; Carcinogens, Environmental/*adverse effects ; Child ; Child, Preschool ; Female ; Humans ; Infant ; Infant, Newborn ; Leukemia, Radiation-Induced/*etiology/mortality ; Male ; Radon/*adverse effects ; Risk Assessment ; Sweden/epidemiology ; }, abstract = {OBJECTIVES: To evaluate the relation between exposure to ground radon levels and leukaemia among children using existing population and disease registers.

DESIGN: Ecological correlation study.

SETTING: The county of Ostergötland in Sweden.

METHODS: Every child born in the county between 1979 and 1992 was mapped to the property centroid coordinates by linking addresses in the population and property registers. Population maps were overlaid with radon maps and exposure at birth and each subsequent year was quantified as high, normal, low or unknown. This was analysed with data from the tumour registry. Standardised mortality ratios (SMRs) were calculated using the age and sex specific rates for Sweden for the year 1995.

RESULTS: 90 malignancies occurred among 53 146 children (498 887 person years) who formed the study population. SMRs for acute lymphatic leukaemia (ALL) among children born in high, normal and low risk areas were 1.43, 1.17 and 0.25 respectively. The relative risk for the normal risk group and high risk group as compared with the low risk group was 4.64 (95% CI 1.29, 28.26) and 5. 67 (95% CI 1.06, 42.27). The association between ALL and continued residence at normal or high risk areas showed a similar trend. No association between radon risk levels and any other malignancy was seen.

CONCLUSION: Children born in and staying at areas where the risk from ground radon has been classified as low are less likely to develop ALL than those born in areas classified as normal and high risk.}, } @article {pmid10997826, year = {2000}, author = {Corella, D and Herranz, C and Calatayud, A and Font, G and Celma, C and Laborda, R}, title = {Cancer mortality and exposure to chemical carcinogens in the work place: an ecological study in the Valencian Community, Spain (1981-1995).}, journal = {European journal of epidemiology}, volume = {16}, number = {5}, pages = {401-409}, pmid = {10997826}, issn = {0393-2990}, mesh = {Agriculture ; Carcinogens, Environmental/*adverse effects ; Data Interpretation, Statistical ; Ecology ; Female ; Humans ; Industry ; Interior Design and Furnishings ; Leukemia/chemically induced/mortality ; Lung Neoplasms/chemically induced/mortality ; Lymphoma/chemically induced/mortality ; Male ; Metallurgy ; Neoplasms/*chemically induced/*mortality ; Occupational Diseases/*chemically induced ; *Occupational Exposure ; Risk Factors ; Rubber ; Sex Factors ; Spain ; Textile Industry ; Urinary Bladder Neoplasms/chemically induced/mortality ; Wood ; }, abstract = {To evaluate the geographical distribution of the mortality from malignant tumours in relationship with exposure to chemical carcinogens in the work place, and to asses the possible association between these questions and the percentage of population employed in certain high-risk sectors, an ecological study in the Valencian Community (VC), Spain was carried out. Age-adjusted mortality rates for the total number of malignant tumours, lung, bladder, lymphomas and leukaemia during the periods 1981-1985 and 1991-1995 were calculated for the 34 geographical areas. The percentage of population in each area working in sectors in which they may be exposed to chemical carcinogens was obtained. The relationship between mortality on-the-job exposure was studied using linear regression methods. Large differences in cancer mortality were seen. In men, the geographical pattern was very stable and reveals a significant association with the distribution of certain high-risk jobs. Statistically significant positive correlations (p < 0.001) were found between cancer mortality and the percentage of the population working in metal, wood and furniture sectors. In contrast, a negative and statistically significant (p < 0.001) correlation was observed between cancer mortality and the percentage of the population working in agriculture. In conclusion, although the variability in cancer mortality in men was significantly associated with some occupational sectors in the VC, caution is needed when drawing conclusions about causation from ecological studies.}, } @article {pmid10997207, year = {2000}, author = {Hay, SI and Omumbo, JA and Craig, MH and Snow, RW}, title = {Earth observation, geographic information systems and Plasmodium falciparum malaria in sub-Saharan Africa.}, journal = {Advances in parasitology}, volume = {47}, number = {}, pages = {173-215}, pmid = {10997207}, issn = {0065-308X}, support = {/WT_/Wellcome Trust/United Kingdom ; 056642/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Africa South of the Sahara/epidemiology ; Animals ; Culicidae/parasitology/physiology ; Geography ; Humans ; *Information Systems ; Malaria, Falciparum/*epidemiology/*transmission ; Meteorological Concepts ; Plasmodium falciparum/physiology ; *Satellite Communications ; }, abstract = {This review highlights the progress and current status of remote sensing (RS) and geographical information systems (GIS) as currently applied to the problem of Plasmodium falciparum malaria in sub-Saharan Africa (SSA). The burden of P. falciparum malaria in SSA is first summarized and then contrasted with the paucity of accurate and recent information on the nature and extent of the disease. This provides perspective on both the global importance of the pathogen and the potential for contribution of RS and GIS techniques. The ecology of P. falciparum malaria and its major anopheline vectors in SSA in then outlined, to provide the epidemiological background for considering disease transmission processes and their environmental correlates. Because RS and GIS are recent techniques in epidemiology, all mosquito-borne diseases are considered in this review in order to convey the range of ideas, insights and innovation provided. To conclude, the impact of these initial studies is assessed and suggestions provided on how these advances could be best used for malaria control in an appropriate and sustainable manner, with key areas for future research highlighted.}, } @article {pmid10984869, year = {2000}, author = {Stambuk-Giljanović, N and Matoković, B and Stambuk, D and Elezović, N and Jelić, N}, title = {Information subsystem of the difference between anions sum and hardness of water and its influence on human health.}, journal = {Journal of medical systems}, volume = {24}, number = {3}, pages = {147-157}, pmid = {10984869}, issn = {0148-5598}, mesh = {Anions ; Bicarbonates/*analysis ; Calcium/*analysis ; Chlorides/*analysis ; Computer Systems ; Croatia ; Databases as Topic ; *Environmental Health ; Environmental Monitoring ; Feces/microbiology ; Humans ; *Information Systems ; Magnesium/*analysis ; Software ; Sulfates/*analysis ; Water Microbiology ; Water Pollution/adverse effects/analysis ; Water Pollution, Chemical/analysis ; Water Purification ; Water Supply/*analysis ; }, abstract = {Underground and surface waters in Dalmatia (Southern Croatia) have relatively preserved their natural characteristics since the greatest agglomeration of population and industry is located along the coast. The danger of pollution with fecal microorganism and products of biological decomposition is the most immediate problem but can be efficiently eliminated by water chlorination. The ecological need to sum up the work on water quality examination and estimation of future water quality trends resulted in water quality monitoring, i.e. in human health monitoring. It is necessary for large number of analytical and ecological health data to organize them from the informatical aspect into databases, the relational database for chemical analysis studying (the difference between anions sum and hardness) as methodological base for studying the ecological factors that influence human health defined in this paper. Results used for the prototype implementation subsystem of the chemical water analysis control are based on the investigations of Water Examination Department of the Public Health Institute of the Split-Dalmatian County (Croatia). Over 3400 data are comprised what is the sufficient examination sample. The software used included Win '95, Mo '97, and Paradox 4,5, while the hardware used included Pentium II 300 MHz, floppy, 128 MB RAM HDD 4,3 GB, CD x 24, HP DeskJet 710C.}, } @article {pmid10964574, year = {2000}, author = {Hein, J and Wiuf, C and Knudsen, B and Møller, MB and Wibling, G}, title = {Statistical alignment: computational properties, homology testing and goodness-of-fit.}, journal = {Journal of molecular biology}, volume = {302}, number = {1}, pages = {265-279}, doi = {10.1006/jmbi.2000.4061}, pmid = {10964574}, issn = {0022-2836}, mesh = {Algorithms ; Amino Acid Sequence ; Computational Biology/*methods ; Evolution, Molecular ; Globins/*chemistry ; Humans ; Likelihood Functions ; Molecular Sequence Data ; Reproducibility of Results ; Sensitivity and Specificity ; Sequence Alignment/*methods ; *Sequence Homology, Amino Acid ; Software ; Time Factors ; }, abstract = {The model of insertions and deletions in biological sequences, first formulated by Thorne, Kishino, and Felsenstein in 1991 (the TKF91 model), provides a basis for performing alignment within a statistical framework. Here we investigate this model.Firstly, we show how to accelerate the statistical alignment algorithms several orders of magnitude. The main innovations are to confine likelihood calculations to a band close to the similarity based alignment, to get good initial guesses of the evolutionary parameters and to apply an efficient numerical optimisation algorithm for finding the maximum likelihood estimate. In addition, the recursions originally presented by Thorne, Kishino and Felsenstein can be simplified. Two proteins, about 1500 amino acids long, can be analysed with this method in less than five seconds on a fast desktop computer, which makes this method practical for actual data analysis.Secondly, we propose a new homology test based on this model, where homology means that an ancestor to a sequence pair can be found finitely far back in time. This test has statistical advantages relative to the traditional shuffle test for proteins.Finally, we describe a goodness-of-fit test, that allows testing the proposed insertion-deletion (indel) process inherent to this model and find that real sequences (here globins) probably experience indels longer than one, contrary to what is assumed by the model.}, } @article {pmid10924481, year = {2000}, author = {Wall, JD and Przeworski, M}, title = {When did the human population size start increasing?.}, journal = {Genetics}, volume = {155}, number = {4}, pages = {1865-1874}, pmid = {10924481}, issn = {0016-6731}, support = {5R01H610847//PHS HHS/United States ; }, mesh = {Africa ; *DNA, Mitochondrial ; Databases, Factual ; *Evolution, Molecular ; Humans ; Models, Genetic ; Models, Statistical ; *Polymorphism, Genetic ; *Population Density ; Recombination, Genetic ; Time Factors ; }, abstract = {We analyze the frequency spectra of all available human nuclear sequence data sets by using a model of constant population size followed by exponential growth. Parameters of growth (more extreme than or) comparable to what has been suggested from mtDNA data can be rejected for 6 out of the 10 largest data sets. When the data are separated into African and non-African samples, a constant size no-growth model can be rejected for 4 out of 8 non-African samples. Long-term growth (i.e., starting 50-100 kya) can be rejected for 2 out of 8 African samples and 5 out of 8 non-African ones. Under more complex demographic models, including a bottleneck or population subdivision, more of the data are compatible with long-term growth. One problem with the data used here is that a subset of loci may reflect the action of natural selection as well as of demography. It remains possible that the correct demographic model is one of constant population size followed by long-term growth but that at several loci the demographic signature has been obscured by balancing or diversifying selection. However, it is not clear that the data at these loci are consistent with a simple model of balancing selection; more complicated selective alternatives cannot be tested unless they are made explicit. An alternative explanation is that population size growth is more recent (e.g., upper Paleolithic) and that some of the loci have experienced recent directional selection. Given the available data, the latter hypothesis seems more likely.}, } @article {pmid10919828, year = {2000}, author = {Marsh, TL and Saxman, P and Cole, J and Tiedje, J}, title = {Terminal restriction fragment length polymorphism analysis program, a web-based research tool for microbial community analysis.}, journal = {Applied and environmental microbiology}, volume = {66}, number = {8}, pages = {3616-3620}, pmid = {10919828}, issn = {0099-2240}, mesh = {Bacteria/*classification/genetics/isolation & purification ; DNA, Bacterial/analysis/genetics ; DNA, Ribosomal/analysis/genetics ; *Databases, Factual ; *Ecosystem ; *Internet ; Phylogeny ; *Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S/*genetics ; Sewage/microbiology ; Software ; Soil Microbiology ; }, abstract = {Rapid analysis of microbial communities has proven to be a difficult task. This is due, in part, to both the tremendous diversity of the microbial world and the high complexity of many microbial communities. Several techniques for community analysis have emerged over the past decade, and most take advantage of the molecular phylogeny derived from 16S rRNA comparative sequence analysis. We describe a web-based research tool located at the Ribosomal Database Project web site (http://www.cme.msu.edu/RDP/html/analyses. html) that facilitates microbial community analysis using terminal restriction fragment length polymorphism of 16S ribosomal DNA. The analysis function (designated TAP T-RFLP) permits the user to perform in silico restriction digestions of the entire 16S sequence database and derive terminal restriction fragment sizes, measured in base pairs, from the 5' terminus of the user-specified primer to the 3' terminus of the restriction endonuclease target site. The output can be sorted and viewed either phylogenetically or by size. It is anticipated that the site will guide experimental design as well as provide insight into interpreting results of community analysis with terminal restriction fragment length polymorphisms.}, } @article {pmid10908102, year = {2000}, author = {Rodenbeck, SE and Sanderson, LM and Rene, A}, title = {Maternal exposure to trichloroethylene in drinking water and birth-weight outcomes.}, journal = {Archives of environmental health}, volume = {55}, number = {3}, pages = {188-194}, doi = {10.1080/00039890009603405}, pmid = {10908102}, issn = {0003-9896}, mesh = {Arizona ; Birth Weight/*drug effects ; Epidemiologic Methods ; Female ; Humans ; Infant, Newborn ; *Infant, Very Low Birth Weight ; Logistic Models ; Maternal Exposure/*adverse effects ; Medical Records Systems, Computerized ; Solvents/*adverse effects ; Trichloroethylene/*adverse effects ; Water Pollutants, Chemical/*adverse effects ; Water Supply ; }, abstract = {An ecological epidemiological study was conducted with data obtained from an environmental dose-reconstruction study and the Arizona Birth Information Tapes. Before 1981, a portion of the city of Tucson water-distribution system was contaminated with trichloroethylene (i.e., < 5 micrograms per liter of water to 107 micrograms per liter of water). Target and comparison populations were selected with a Geographic Information System. Logistical-regression analysis revealed an association between maternal exposure to trichloroethylene via drinking water and very-low-birth-weight babies (i.e., < 1,501 grams) (odds ratio = 3.3; 95% confidence interval = 0.5, 20.6; and Wald chi-square p value = 0.2). No association was found between maternal exposure to trichloroethylene via drinking water and low birth weight or full-term low-birth-weight infants (gestational period > 35 wk and < 46 wk).}, } @article {pmid10900476, year = {2000}, author = {Kitron, U}, title = {Risk maps: transmission and burden of vector-borne diseases.}, journal = {Parasitology today (Personal ed.)}, volume = {16}, number = {8}, pages = {324-325}, doi = {10.1016/s0169-4758(00)01708-7}, pmid = {10900476}, issn = {0169-4758}, support = {AI36917/AI/NIAID NIH HHS/United States ; }, mesh = {Africa/epidemiology ; Animals ; Anopheles/physiology ; *Disease Vectors ; Ecology ; Geography ; Humans ; *Information Systems ; Lyme Disease/epidemiology/*transmission ; Malaria/epidemiology/*transmission ; Risk Factors ; Ticks/physiology ; United States/epidemiology ; }, } @article {pmid10898399, year = {2000}, author = {Kitsiou, D and Karydis, M}, title = {Categorical mapping of marine eutrophication based on ecological indices.}, journal = {The Science of the total environment}, volume = {255}, number = {1-3}, pages = {113-127}, doi = {10.1016/s0048-9697(00)00457-5}, pmid = {10898399}, issn = {0048-9697}, mesh = {Animals ; Classification/methods ; Data Interpretation, Statistical ; *Ecosystem ; Environmental Monitoring/*methods ; *Eutrophication ; Greece ; Information Systems ; *Plankton/classification/growth & development ; Seawater/*chemistry ; Water Pollution, Chemical/*analysis ; }, abstract = {The present work is concerned with the development of methodological procedures for studying the spatial distribution of eutrophication in the marine environment. Seven ecological indices (S, number of phytoplankton species; N, total number of individuals; D(Mg), Margalef's index; D(Mn), Menhinick's index; D(Od), Odum's species per thousand individuals; H', Shannon's Diversity index; E, Evenness index), based on phytoplankton community data collected from Saronicos Gulf, Greece were used for describing the eutrophication state of the sea environment. A representation of the spatial distribution for each ecological index was developed using the Inverse Distance Weighted (IDW) interpolation method. A eutrophication scale for each index was also developed for indicating four different trophic levels in the marine environment (eutrophic, upper-mesotrophic, lower-mesotrophic, oligotrophic); categorization of the interpolated values of each index resulted in a clear illustration of these trophic levels on seven thematic maps. Two methodological procedures were finally applied for synthesizing the information of these thematic maps. The purpose was the development of a final map illustrating the spatial distribution of eutrophication in the study area. The first procedure was based on the integration of unsupervised and supervised classification methods, widely used in the field of remote sensing, while the second one on the overlay technique, simply carried out within the frame of a Geographical Information System (GIS). The hybrid unsupervised/supervised classification method can assess the optimal number of classes in which data values from simultaneously considered parameters could be allocated, while the overlay technique is an additive procedure not taking into account existing trends in the dataset. The advantages and disadvantages of each procedure are further discussed.}, } @article {pmid10872721, year = {2000}, author = {Rezhnikova, ZI and Ryabko, BY}, title = {Experimental studies of the ability of ants to add and subtract small numbers.}, journal = {Neuroscience and behavioral physiology}, volume = {30}, number = {2}, pages = {123-130}, pmid = {10872721}, issn = {0097-0549}, mesh = {Animals ; Ants/*physiology ; Behavior, Animal/*physiology ; Feeding Behavior ; Mental Processes/*physiology ; Neuronal Plasticity/physiology ; }, abstract = {Ants had to communicate information to each other in an apparatus consisting of a horizontal "trunk" with "branches" in order to obtain food, the information being used to identify which of 40 branches had a feeder. The feeder was placed on two preselected branches significantly more frequently than on the other branches. The ants were able to tune their communication system such that the duration of communications was related to the frequency with which feeders were located on branches, and the ants could add and subtract small numbers during communication of information on the feeder identification number.}, } @article {pmid10870621, year = {1999}, author = {Beslagić, Z and Pasić, A}, title = {[Experience in the development of information systems at the canton level].}, journal = {Medicinski arhiv}, volume = {53}, number = {3 Suppl 3}, pages = {31-33}, pmid = {10870621}, mesh = {Bosnia and Herzegovina ; *Community Health Services ; Information Systems/*organization & administration ; }, abstract = {In the aim of need and necessity of stronger orientation and more efficient aim realization 35 Strategy SZO (health information system) country members should have the health information system able to provide information support to their National strategy "Health for All until 2005". Such a health information system should provide the information support for the planning process, monitoring and health evaluation, health care and work in public-health services sector. The experiences in the work of information system organization in Tuzla Canton Public Health Institute should be seen from two aspects: Aspect of the information system significance in the framework of the social-medical, epidemiological, hygiene-ecological and other activities of the Institute; Aspect of the information system development within the Public Health facilities of Canton in relation to the automatic data processing important for registration, tracking and recognition of success and population health care needs. From the aspect of establishing the information system in the area of Tuzla Canton and the Public Health Institute role, there is a need for adequate high technology technical equipment, with the task to enable practical realization of defined projects and in such a way, varied acceleration of work giving as a result usable information. The canton Public Health Institute needs as follows: necessary resources for free information system work; to provide free computer access to all; to ensure connection with other PHI through communications. In this way the canton Public Health Institute information system would be connected with other information systems in the field of health. In would be a base for development of integrated health information system. The information system is desirable aim for the work of Public Health Institute, method of selection and leading content of modernization. Analysing the Bill of Law on Health Care, a defectiveness has been noticed, since the information system is not regulated. Therefore, the need to be issued by Lay is of great importance. A statement that all projects on local information systems, started before war or during the war have been stooped, joins to the aforesaid, and also a series of independent information system in different health segments, which are not connected into one, unique information system. In any case, this disparaged the quality of medical decision making and therefore, providing of high-quality services at all levels of health work.}, } @article {pmid10856340, year = {2000}, author = {Donohoe, RM and Yamamoto, JT and Ricker, KE and Quinn, JF}, title = {Exposure factor and toxicity data for California wildlife: data availability and sources of uncertainty for ecological risk assessments.}, journal = {Bulletin of environmental contamination and toxicology}, volume = {64}, number = {6}, pages = {834-841}, doi = {10.1007/s0012800078}, pmid = {10856340}, issn = {0007-4861}, mesh = {Animals ; *Animals, Wild ; California ; *Databases, Factual ; *Ecology ; Ecosystem ; *Environmental Exposure/adverse effects/analysis ; Environmental Pollutants/toxicity ; Environmental Pollution/prevention & control ; Risk Assessment ; Toxicity Tests ; }, } @article {pmid10843310, year = {2000}, author = {Tengs, TO and Wallace, A}, title = {One thousand health-related quality-of-life estimates.}, journal = {Medical care}, volume = {38}, number = {6}, pages = {583-637}, doi = {10.1097/00005650-200006000-00004}, pmid = {10843310}, issn = {0025-7079}, mesh = {Attitude to Health ; Choice Behavior ; Cost-Benefit Analysis ; Data Interpretation, Statistical ; Diagnosis-Related Groups ; Health Services Research/*methods ; *Health Status ; Health Status Indicators ; Humans ; *Quality-Adjusted Life Years ; Reproducibility of Results ; }, abstract = {OBJECTIVE: Analysts performing cost-effectiveness analyses often do not have the resources to gather original quality-of-life (QOL) weights. Furthermore, variability in QOL for the same health state hampers the comparability of cost-effectiveness analyses. For these reasons, opinion leaders such as the Panel on Cost-Effectiveness in Health and Medicine have called for a national repository of QOL weights. Some authors have responded to the call by performing large primary studies of QOL. We take a different approach, amassing existing data with the hope that it will be combined responsibly in meta-analytic fashion. Toward the goal of developing a national repository of QOL weights to aid cost-effectiveness analysts, 1,000 health-related QOL estimates were gathered from publicly available source documents.

METHODS: To identify documents, we searched databases and reviewed the bibliographies of articles, books, and government reports. From each document, we extracted information on the health state, QOL weight, assessment method, respondents, and upper and lower bounds of the QOL scale. Detailed guidelines were followed to ensure consistency in data extraction.

RESULTS: We identified 154 documents yielding 1,000 original QOL weights. There was considerable variation in the weights assessed by different authors for the same health state. Methods also varied: 51% of authors used direct elicitation (standard gamble, time tradeoff, or rating scale), 32% estimated QOL based on their own expertise or that of others, and 17% used health status instruments.

CONCLUSIONS: This comprehensive review of QOL data should lead to more consistent use of QOL weights and thus more comparable cost-effectiveness analyses.}, } @article {pmid10837288, year = {2000}, author = {Harnack, LJ and Jeffery, RW and Boutelle, KN}, title = {Temporal trends in energy intake in the United States: an ecologic perspective.}, journal = {The American journal of clinical nutrition}, volume = {71}, number = {6}, pages = {1478-1484}, doi = {10.1093/ajcn/71.6.1478}, pmid = {10837288}, issn = {0002-9165}, support = {IP30-DK540456/DK/NIDDK NIH HHS/United States ; }, mesh = {Consumer Behavior ; Diet, Fat-Restricted ; Dietary Fats/administration & dosage ; *Ecology ; *Energy Intake ; Energy Metabolism ; *Feeding Behavior ; Food Preferences ; Humans ; MEDLINE ; Nutritional Physiological Phenomena ; Obesity/epidemiology ; United States ; }, abstract = {BACKGROUND: The causes of recent increases in the prevalence of overweight in the United States are perplexing because national survey data do not show clear patterns of change in energy intake or expenditure.

OBJECTIVE: Ecologic data regarding the quantities and types of foods and nutrients available in the United States between 1970 and 1998 were reviewed to provide an alternative perspective on trends in energy intake.

DESIGN: Literature searches in agriculture, business, and medical library databases were conducted to identify data regarding the quantities and types of foods and nutrients available in the United States between 1970 and 1998.

RESULTS: Per capita energy availability estimates from the US Department of Agriculture, US Food Supply Series, indicate that energy availability increased by 15% between 1970 and 1994. Data regarding trends in food purchasing and preparation suggest that Americans are eating more meals outside the home, relying more heavily on convenience foods, and consuming larger food portions. Americans appear, in some cases, to be selecting lower-fat foods over higher-fat alternatives. In addition, availability and sales of reduced-energy and reduced-fat products have increased.

CONCLUSION: Consistent with trends in overweight, most of the ecologic data reviewed suggest that energy intake has increased over the past several decades and is likely a major contributor to increases in average body weight.}, } @article {pmid10823950, year = {2000}, author = {Sokal, RR and Oden, NL and Rosenberg, MS and Thomson, BA}, title = {Cancer incidences in Europe related to mortalities, and ethnohistoric, genetic, and geographic distances.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {97}, number = {11}, pages = {6067-6072}, pmid = {10823950}, issn = {0027-8424}, mesh = {Cluster Analysis ; Data Collection ; Databases, Factual ; Ethnicity/statistics & numerical data ; Europe/epidemiology ; Female ; Genetic Predisposition to Disease ; Humans ; Incidence ; International Agencies ; Male ; Neoplasms/*epidemiology/ethnology/genetics/mortality ; Neoplastic Syndromes, Hereditary/epidemiology/genetics ; }, abstract = {We have previously shown that geographic differences in cancer mortalities in Europe are related to (in order of importance): geographic distances (reflecting environmental differences), ethnohistoric distances (encompassing cultural and genetic attributes), and genetic distances of the populations in the areas studied. In this study, we analyzed the relations of the same three factors to European incidences of 45 male and 47 female cancers. Differences in cancer incidences are correlated moderately, first with geographic distances, and then with genetic distances, but not at all with ethnohistoric distances. Comparing these findings to the earlier ones for cancer mortalities, we note the reversal in the importance of ethnohistory and genetics, and the generally lower correlations of incidence differences with the three putatively causal distance matrices. A path diagram combining both studies demonstrates the lack of cultural carcinogenic effects, but suggests cultural influences on procedures such as the registration of deaths in different political entities. Additionally, the relatively large correlation between ethnohistoric distances and mortality differences is caused by common factors behind the correlation of ethnohistoric and geographic distances. Geographic proximity results in similar ethnohistories. The direct effects of genetic distances are negligible and only their common effects with geographic distances play a role, accounting for the weak to negligible influence of genetics on incidence and mortality differences. Apparently, the genetic systems available to us do not substantially affect cancer incidence or mortality. We present indirect evidence that international differences in the quality of cancer rate data are greater in mortalities than in incidences.}, } @article {pmid10814658, year = {2000}, author = {Blakely, TA and Woodward, AJ}, title = {Ecological effects in multi-level studies.}, journal = {Journal of epidemiology and community health}, volume = {54}, number = {5}, pages = {367-374}, pmid = {10814658}, issn = {0143-005X}, mesh = {Bias ; Confounding Factors, Epidemiologic ; Data Collection/*methods ; *Data Interpretation, Statistical ; Environment ; *Epidemiologic Research Design ; Humans ; Socioeconomic Factors ; }, abstract = {Multi-level research that attempts to describe ecological effects in themselves (for example, the effect on individual health from living in deprived communities), while also including individual level effects (for example, the effect of personal socioeconomic disadvantage), is now prominent in research on the socioeconomic determinants of health and disease. Such research often involves the application of advanced statistical multi-level methods. It is hypothesised that such research is at risk of reaching beyond an epidemiological understanding of what constitutes an ecological effect, and what sources of error may be influencing any observed ecological effect. This paper aims to present such an epidemiological understanding. Three basic types of ecological effect are described: a direct cross level effect (for example, living in a deprived community directly affects individual personal health), cross level effect modification (for example, living in a deprived community modifies the effect of individual socioeconomic status on individual health), and an indirect cross level effect (for example, living in a deprived community increases the risk of smoking, which in turn affects individual health). Sources of error and weaknesses in study design that may affect estimates of ecological effects include: a lack of variation in the ecological exposure (and health outcome) in the available data; not allowing for intraclass correlation; selection bias; confounding at both the ecological and individual level; misclassification of variables; misclassification of units of analysis and assignment of individuals to those units; model mis-specification; and multicollinearity. Identification of ecological effects requires the minimisation of these sources of error, and a study design that captures sufficient variation in the ecological exposure of interest.}, } @article {pmid10813448, year = {2000}, author = {Schultz, TW and Seward, JR}, title = {Health-effects related structure-toxicity relationships: a paradigm for the first decade of the new millennium.}, journal = {The Science of the total environment}, volume = {249}, number = {1-3}, pages = {73-84}, doi = {10.1016/s0048-9697(99)00512-4}, pmid = {10813448}, issn = {0048-9697}, mesh = {Animals ; Databases, Factual ; Ecology ; Humans ; Public Health ; Software ; *Structure-Activity Relationship ; Toxicity Tests/*methods ; }, abstract = {Prediction of the effects of industrial chemicals to humans will be an area of increasing concern in the next century. The role of quantitative structure-activity relationships (QSARs) is to aid in the prediction of effects by determination of the limits of variation in structure that are consistent with the production of a specific toxic effect and define the ways in which alterations in structure influences toxicity. The paradigm followed in the development of QSARs for ecotoxic-endpoints has been successful as a direct result of the availability of in vivo toxicity data in which to build initial QSARs and validate surrogate test systems. However, the lack of quantitative in vivo toxicity data means this paradigm cannot be used in the prediction of human health-effect endpoints. Therefore, a new paradigm, which provides guidance in the use of predictive QSARs for health-effects that serves to circumvent the problems associated with the lack of whole-mammal toxicity data must be established. A scenario is given that provides for the development, standardization, and validation of health-effects related QSARs in the first decade of the 21st century. Due to the structural diversity and sheer number of industrial organic chemicals, assays used to garner health-effects data must be based on quantifiable, rapid, reliable, and inexpensive surrogate endpoints. New 'biotools' developed using modern molecular techniques will aid in the circumvention of in vivo health-effects data and provide measurable endpoints, which can be used as surrogates for health-effects endpoints. This has particular application in receptor-mediated toxicity and gene expression. The lack of whole-mammal health-effects data means that the standardization and validation, of these endpoints will be accomplished in novel ways. Databases garnered using modern biotools will allow the derivation of QSARs developed for validated surrogate health-effect endpoints. If QSARs are to be useful in bridging gaps in health-effects data, they must be based on accurate, reproducible data for a robust series of non-congeneric chemicals. The latter applies to both toxicity and descriptor values. Because health-effects are often the result of metabolic activation, if these new QSARs are to be meaningful, validated software for predicting metabolite formation must be incorporated. Lastly, once QSARs and software are developed and validated, they will need to be linked into some type of expert system.}, } @article {pmid10811901, year = {2000}, author = {Andelman, SJ and Fagan, WF}, title = {Umbrellas and flagships: efficient conservation surrogates or expensive mistakes?.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {97}, number = {11}, pages = {5954-5959}, pmid = {10811901}, issn = {0027-8424}, mesh = {Animals ; Carnivora/physiology ; Conservation of Natural Resources/economics/*statistics & numerical data ; Databases, Factual ; Ecology ; *Ecosystem ; Plants ; Population Dynamics ; United States ; }, abstract = {The use of umbrella and flagship species as surrogates for regional biota whose spatial distributions are poorly known is a popular conservation strategy. Yet many assumptions underlying the choice of surrogate species remain untested. By using biodiversity databases containing spatial incidence data for species of concern for (i) the southern California coastal sage scrub habitat, (ii) the Columbia Plateau ecoregion, and (iii) the continental United States, we evaluate the potential effectiveness of a range of conservation surrogate schemes (e.g., big carnivores, charismatic species, keystone species, wide-ranging species), asking how many species potentially are protected by each scheme and at what cost in each habitat area. For all three databases, we find that none of the surrogate schemes we evaluated performs significantly better than do a comparable number of species randomly selected from the database. Although some surrogate species may have considerable publicity value, based on the databases we analyzed, representing diverse taxa on three different geographic scales, we find that the utility of umbrella and flagship species as surrogates for regional biodiversity may be limited.}, } @article {pmid10726671, year = {2000}, author = {Groth-Marnat, G}, title = {Visions of clinical assessment: then, now, and a brief history of the future.}, journal = {Journal of clinical psychology}, volume = {56}, number = {3}, pages = {349-365}, doi = {10.1002/(sici)1097-4679(200003)56:3<349::aid-jclp11>3.0.co;2-t}, pmid = {10726671}, issn = {0021-9762}, mesh = {Diagnosis, Computer-Assisted/*trends ; Forecasting ; History, 20th Century ; Humans ; Informed Consent ; Managed Care Programs/*economics/trends ; *Psychological Tests/history ; Psychology, Clinical/economics/history/*trends ; Psychometrics ; }, abstract = {Perspectives on the discipline of psychological assessment are provided through reflections on a classic article by Hunt (1946), review of current issues, and a projection of changes likely to occur over the next fifty years. Topics covered include the place of idiosyncratic qualitative responses, test design, clinical judgment, managed care, financial efficacy, over emphasis on pathology, treatment planning, status of projectives, ecological validity, relationship between theory and tests, innovations in scale construction, and computer-assisted assessment. Future predictions relate to innovations in computer-assisted assessment, practitioner roles in an increasingly automated environment, the future of traditional tests, and human-rights issues.}, } @article {pmid10703183, year = {1999}, author = {Vena, JE and Weiner, JM}, title = {Innovative multidisciplinary research in environmental epidemiology: the challenges and needs.}, journal = {International journal of occupational medicine and environmental health}, volume = {12}, number = {4}, pages = {353-370}, pmid = {10703183}, issn = {1232-1087}, mesh = {Databases as Topic ; *Environmental Health ; *Epidemiologic Methods ; Humans ; }, abstract = {The ability of epidemiology to determine the relationships between health and environmental insults has become exceedingly difficult. The multifactorial nature of disease and the diversity of the insults, which include biologic, physical, social and cultural factors, combined with genetic susceptibility, suggest the need to develop better models of multidisciplinary epidemiologic investigation. This paper highlights the needs of an environmental epidemiologic team, discusses ways to incorporate new ideas across disciplines and to integrate constructs and paradigms of social, ecological, cultural and population determinants with individual-based exposure assessments. Innovation will be the key to the survival and increasing importance of epidemiology in addressing the public health needs of the future, but what are the ways to enhance and encourage creativity in environmental epidemiology? The process of self-renewal and continuing education will be highlighted. Additionally, the complexity of the problems and the need for clear supervision and control of multidisciplinary research efforts require a forum of communication and an 'information-processing approach' beyond those in traditional epidemiologic studies. New approaches in data management and medical informatics must be incorporated into the epidemiologic investigative framework. Methods to be included should focus on opportunities for computer-supported sharing of ideas. Such capabilities minimise the geographic distances and the disparate knowledge and training of the investigators and bring the team closer to the objectives and functions inherent in multidisciplinary investigation.}, } @article {pmid10677471, year = {2000}, author = {Faulhammer, D and Cukras, AR and Lipton, RJ and Landweber, LF}, title = {Molecular computation: RNA solutions to chess problems.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {97}, number = {4}, pages = {1385-1389}, pmid = {10677471}, issn = {0027-8424}, mesh = {Algorithms ; Combinatorial Chemistry Techniques ; *Computational Biology ; DNA/*chemistry ; Games, Experimental ; Oligodeoxyribonucleotides ; Polymerase Chain Reaction ; RNA/*chemistry ; Ribonucleases ; }, abstract = {We have expanded the field of "DNA computers" to RNA and present a general approach for the solution of satisfiability problems. As an example, we consider a variant of the "Knight problem," which asks generally what configurations of knights can one place on an n x n chess board such that no knight is attacking any other knight on the board. Using specific ribonuclease digestion to manipulate strands of a 10-bit binary RNA library, we developed a molecular algorithm and applied it to a 3 x 3 chessboard as a 9-bit instance of this problem. Here, the nine spaces on the board correspond to nine "bits" or placeholders in a combinatorial RNA library. We recovered a set of "winning" molecules that describe solutions to this problem.}, } @article {pmid10689318, year = {2000}, author = {Stothard, JR and Kristensen, TK}, title = {Medical and veterinary malacology in Africa.}, journal = {Parasitology today (Personal ed.)}, volume = {16}, number = {3}, pages = {85-86}, doi = {10.1016/s0169-4758(99)01619-1}, pmid = {10689318}, issn = {0169-4758}, mesh = {Africa ; Animals ; Ecology ; Information Systems ; *Pest Control, Biological ; Phylogeny ; Schistosomiasis haematobia/*prevention & control/transmission ; Snails/genetics/parasitology/*physiology ; }, } @article {pmid10681904, year = {1999}, author = {Tarlov, AR}, title = {Public policy frameworks for improving population health.}, journal = {Annals of the New York Academy of Sciences}, volume = {896}, number = {}, pages = {281-293}, doi = {10.1111/j.1749-6632.1999.tb08123.x}, pmid = {10681904}, issn = {0077-8923}, mesh = {Adult ; Child ; Child Development ; Community Health Planning/*organization & administration ; Community Networks ; *Developing Countries ; *Health Planning Guidelines ; *Health Policy ; Health Promotion/*organization & administration ; *Health Status ; Humans ; Linear Models ; Models, Theoretical ; Organizational Objectives ; Politics ; Public Health Practice ; *Social Class ; United Kingdom ; United States ; }, abstract = {Four conceptual frameworks provide bases for constructing comprehensive public policy strategies for improving population health within wealthy (OECD) nations. (1) Determinants of population health. There are five broad categories: genes and biology, medical care, health behaviors, the ecology of all living things, and social/societal characteristics. (2) Complex systems: Linear effects models and multiple independent effects models fail to yield results that explain satisfactorily the dynamics of population health production. A different method (complex systems modeling) is needed to select the most effective interventions to improve population health. (3) An intervention framework for population health improvement. A two-by-five grid seems useful. Most intervention strategies are either ameliorative or fundamentally corrective. The other dimension of the grid captures five general categories of interventions: child development, community development, adult self-actualization, socioeconomic well-being, and modulated hierarchical structuring. (4) Public policy development process: the process has two phases. The initial phase, in which public consensus builds and an authorizing environment evolves, progresses from values and culture to identification of the problem, knowledge development from research and experience, the unfolding of public awareness, and the setting of a national agenda. The later phase, taking policy action, begins with political engagement and progresses to interest group activation, public policy deliberation and adoption, and ultimately regulation and revision. These frameworks will be applied to help understand the 39 recommendations of the Independent Inquiry into Inequalities in Health, the Sir Donald Acheson Report from the United Kingdom, which is the most ambitious attempt to date to develop a comprehensive plan to improve population health.}, } @article {pmid10672204, year = {2000}, author = {Tanser, F and Lesueur, D and Solarsh, G and Wilkinson, D}, title = {HIV heterogeneity and proximity of homestead to roads in rural South Africa: an exploration using a geographical information system.}, journal = {Tropical medicine & international health : TM & IH}, volume = {5}, number = {1}, pages = {40-46}, doi = {10.1046/j.1365-3156.2000.00513.x}, pmid = {10672204}, issn = {1360-2276}, mesh = {Female ; HIV Antibodies/blood ; HIV Infections/*epidemiology/virology ; Housing ; Humans ; Information Systems ; Pregnancy ; Pregnancy Complications, Infectious/*epidemiology/virology ; Prevalence ; Rural Population/*statistics & numerical data ; South Africa/epidemiology ; Transportation ; }, abstract = {objective To describe heterogeneity of HIV prevalence among pregnant women in Hlabisa health district, South Africa and to correlate this with proximity of homestead to roads. methods HIV prevalence measured through anonymous surveillance among pregnant women and stratified by local village clinic. Polygons were created around each clinic, assuming women attend the clinic nearest their home. A geographical information system (GIS) calculated the mean distance from homesteads in each clinic catchment to nearest primary (1 degrees) and to nearest primary or secondary (2 degrees) road. results We found marked HIV heterogeneity by clinic catchment (range 19-31% (P < 0.001). A polygon plot demonstrated lower HIV prevalence in catchments remote from 1 degrees roads. Mean distance from homesteads to nearest 1 degrees or 2 degrees road varied by clinic catchment from 1623 to 7569 m. The mean distance from homesteads to a 1 degrees or 2 degrees road for each clinic catchment was strongly correlated with HIV prevalence (r = 0.66; P = 0.002). conclusions The substantial HIV heterogeneity in this district is closely correlated with proximity to a 1 degrees or 2 degrees road. GIS is a powerful tool to demonstrate and to start to analyse this observation. Further research is needed to better understand this relationship both at ecological and individual levels, and to develop interventions to reduce the spread of HIV infection.}, } @article {pmid10651919, year = {1999}, author = {Lu, G and Bernatchez, L}, title = {A study of fluctuating asymmetry in hybrids of dwarf and normal lake whitefish ecotypes (Coregonus clupeaformis) from different glacial races.}, journal = {Heredity}, volume = {83 (Pt 6)}, number = {}, pages = {742-747}, doi = {10.1046/j.1365-2540.1999.00625.x}, pmid = {10651919}, issn = {0018-067X}, mesh = {Animals ; Chimera/*genetics ; Data Interpretation, Statistical ; Genetics, Population ; Phenotype ; Salmonidae/anatomy & histology/genetics/*growth & development ; }, abstract = {Fish ecotypes found in north temperate lakes are increasingly used as model organisms to explore patterns and processes of population divergence that may ultimately cause speciation. Processes involved in their reproductive isolation are, however, still poorly understood. Recent experimental studies on whitefish ecotypes from different glacial races revealed that embryonic mortality of hybrids was 2.4-4.7 times higher than for parental forms. In this study, we compared fluctuating asymmetry (FA) in morphological traits of these same hybrid and pure crosses to test the hypothesis that genetic stress observed in hybrids at embryonic stages is also manifested at later developmental stages. Twelve morphological traits were used to measure asymmetry. Variable degrees of asymmetry were observed depending on traits and crosses, however there was no significant difference in FA among crosses. These results thus provided no evidence in support of the working hypothesis and indicated that genetic stress may differ among life stages. It is more likely that high hybrid embryonic mortality acts together with ecological factors at later stages to increase further the extent of reproductive isolation between sympatric whitefish ecotypes.}, } @article {pmid10651917, year = {1999}, author = {Gillies, AC and Navarro, C and Lowe, AJ and Newton, AC and Hernández, M and Wilson, J and Cornelius, JP}, title = {Genetic diversity in mesoamerican populations of mahogany (Swietenia macrophylla), assessed using RAPDs.}, journal = {Heredity}, volume = {83 (Pt 6)}, number = {}, pages = {722-732}, doi = {10.1046/j.1365-2540.1999.00626.x}, pmid = {10651917}, issn = {0018-067X}, mesh = {Central America ; Data Interpretation, Statistical ; *Genetic Variation ; Genetics, Population ; Random Amplified Polymorphic DNA Technique ; Trees/*genetics ; }, abstract = {Swietenia macrophylla King, a timber species native to tropical America, is threatened by selective logging and deforestation. To quantify genetic diversity within the species and monitor the impact of selective logging, populations were sampled across Mesoamerica, from Mexico to Panama, and analysed for RAPD DNA variation. Ten decamer primers generated 102 polymorphic RAPD bands and pairwise distances were calculated between populations according to Nei, then used to construct a radial neighbour-joining dendrogram and examine intra- and interpopulation variance coefficients, by analysis of molecular variation (AMOVA). Populations from Mexico clustered closely together in the dendrogram and were distinct from the rest of the populations. Those from Belize also clustered closely together. Populations from Panama, Guatemala, Costa Rica, Nicaragua and Honduras, however, did not cluster closely by country but were more widely scattered throughout the dendrogram. This result was also reflected by an autocorrelation analysis of genetic and geographical distance. Genetic diversity estimates indicated that 80% of detected variation was maintained within populations and regression analysis demonstrated that logging significantly decreased population diversity (P = 0.034). This study represents one of the most wide-ranging surveys of molecular variation within a tropical tree species to date. It offers practical information for the future conservation of mahogany and highlights some factors that may have influenced the partitioning of genetic diversity in this species across Mesoamerica.}, } @article {pmid10651915, year = {1999}, author = {Tas, IC and Van Dijk, PJ}, title = {Crosses between sexual and apomictic dandelions (Taraxacum). I. The inheritance of apomixis.}, journal = {Heredity}, volume = {83 (Pt 6)}, number = {}, pages = {707-714}, doi = {10.1046/j.1365-2540.1999.00619.x}, pmid = {10651915}, issn = {0018-067X}, mesh = {Asteraceae/cytology/enzymology/*genetics ; Chimera ; Crosses, Genetic ; Data Interpretation, Statistical ; Phosphogluconate Dehydrogenase/genetics ; *Ploidies ; Pollen ; Reproduction, Asexual/*genetics ; }, abstract = {Some dandelions, Taraxacum, are diplosporous gametophytic apomicts. Crosses between closely related diploid sexuals and triploid apomicts were made to study the inheritance of apomixis. Seed-set was less than one-third of that in diploid x diploid crosses, probably because of the inviability of aneuploid pollen or zygotes. Almost 90% of the viable offspring were diploid and the result of selfing, as was shown by a discriminating allozyme marker. Aneuploid outcross pollen had a mentor effect on self-pollen, causing a breakdown of the sporophytic self-incompatibility system. A similar phenomenon has been reported before in wide crosses. Of the 26 allozyme-confirmed hybrids, four were diploids, 15 were triploids and seven were tetraploids. Diploid hybrids were significantly less frequent than triploid hybrids, suggesting either low fitness of haploid pollen or more numerous formation of diploid pollen. Emasculation and bagging of flowers indicated apomictic seed-set in none of the diploid, in one-third of the triploid and in all of the tetraploid hybrids. All apomictic hybrids showed partial seed-set, but additional cross-pollination did not increase seed-set. Cytological analysis of the F2 progeny confirmed that partial apomixis was caused by semisterility and not by residual sexuality (facultative apomixis). The difference in segregation for apomixis between triploid and tetraploid hybrids may be because the triploids originated from partially reduced diploid pollen grains, whereas the tetraploids originated from unreduced triploid pollen grains.}, } @article {pmid10640335, year = {2000}, author = {Mackenzie, RG}, title = {Adolescent medicine: a model for the millennium.}, journal = {Adolescent medicine (Philadelphia, Pa.)}, volume = {11}, number = {1}, pages = {13-18}, pmid = {10640335}, issn = {1041-3499}, mesh = {Adolescent ; Adolescent Medicine/*trends ; Attitude to Health ; Counseling/trends ; Forecasting ; Health Knowledge, Attitudes, Practice ; Human Development ; Humans ; Information Systems/trends ; Medical Laboratory Science/trends ; *Models, Organizational ; Morbidity ; Physician's Role ; Social Change ; }, abstract = {This article summarizes the past decade of technological development and the past century of adolescent development in order to predict the future of adolescent medicine. The technology of communication will revolutionize behavior change approaches in the 21st century. Health will be seen as an interactive loop of connections between patients, physicians, families, institutions, peers, and support networks that may be voluntarily navigated and searched. The low-tech of counseling will be replaced with the high-tech of the interactive sensor that will be developed from our knowledge of human development. The inter-relationships between social and personal ecology-a basic premise of adolescent health care-will take on new importance in the first decade of the 21st century. The old will guide the application; the new will define the science. The major morbidities of adolescence of the 20th century will now be correctable and preventable. Models of care for all age groups will draw heavily on the experience of ephebiatrics. With application of the new science, biobehavioral issues will surface as the new technology and the practitioners of adolescent health care have the potential to lead the way.}, } @article {pmid10637535, year = {2000}, author = {Fernández, N and Tate, RB and Bonet, M and Cañizares, M and Mas, P and Yassi, A}, title = {Health-risk perception in the inner city community of Centro Habana, Cuba.}, journal = {International journal of occupational and environmental health}, volume = {6}, number = {1}, pages = {34-43}, doi = {10.1179/oeh.2000.6.1.34}, pmid = {10637535}, issn = {1077-3525}, mesh = {Adolescent ; Adult ; Child ; *Community Health Services ; Confidence Intervals ; Cuba ; Data Interpretation, Statistical ; *Environmental Health ; Female ; Health Promotion ; Housing ; Humans ; Infant ; Infant Mortality ; Infant, Newborn ; Life Style ; Male ; Mortality ; Pregnancy ; Risk Factors ; Social Environment ; Surveys and Questionnaires ; Urban Population ; }, abstract = {Perceptions of health risks were surveyed in the inner city of Centro Habana, Cuba. A questionnaire developed by community leaders and experts was administered to 348 residents to determine the level of perceived risk for each of 41 risk items. Ecologic-level data on morbidity, mortality, and environmental indicators were also gathered. Using factor analysis to reduce the dimensionality of the data, five factor groupings accounted for 60% of the variance, as follows: social environment (40.8%); infectious agents and other health-risk factors of immediate concern (6.1%); lifestyle risks (4. 9%); environmental sanitation (4.1%); and living conditions (3.3%). A relationship between the perception of risk and the ecologic data was found, with inconsistencies largely attributable to factors known to influence risk perception. The greatest concern identified throughout the municipality was housing conditions, highest in the neighborhood that had already begun to address this problem. The analysis was useful in planning targeted health promotion campaigns and prioritizing further interventions. Repeat evaluation of risk perception will be conducted following the completion of interventions.}, } @article {pmid10636045, year = {1999}, author = {Faulhammer, D and Lipton, RJ and Landweber, LF}, title = {Counting DNA: estimating the complexity of a test tube of DNA.}, journal = {Bio Systems}, volume = {52}, number = {1-3}, pages = {193-196}, doi = {10.1016/s0303-2647(99)00047-7}, pmid = {10636045}, issn = {0303-2647}, mesh = {Animals ; *Computational Biology ; *Computer Simulation ; DNA/*analysis/chemistry/genetics ; Humans ; *Models, Molecular ; }, abstract = {We consider the problem of estimation of the 'complexity' of a test tube of DNA. The complexity of a test tube is the number of different kinds of strands of DNA in the test tube. It is quite easy to estimate the number of total strands in a test tube, especially if the strands are all the same length. Estimation of the complexity is much less clear. We propose a simple kind of DNA computation that can estimate the complexity.}, } @article {pmid10636028, year = {1999}, author = {Cukras, AR and Faulhammer, D and Lipton, RJ and Landweber, LF}, title = {Chess games: a model for RNA based computation.}, journal = {Bio Systems}, volume = {52}, number = {1-3}, pages = {35-45}, doi = {10.1016/s0303-2647(99)00030-1}, pmid = {10636028}, issn = {0303-2647}, mesh = {Animals ; Computational Biology/*methods ; Computer Simulation ; Humans ; *Models, Molecular ; RNA/*analysis/*genetics ; Transcription, Genetic ; }, abstract = {Here we develop the theory of RNA computing and a method for solving the 'knight problem' as an instance of a satisfiability (SAT) problem. Using only biological molecules and enzymes as tools, we developed an algorithm for solving the knight problem (3 x 3 chess board) using a 10-bit combinatorial pool and sequential RNase H digestions. The results of preliminary experiments presented here reveal that the protocol recovers far more correct solutions than expected at random, but the persistence of errors still presents the greatest challenge.}, } @article {pmid11125088, year = {2001}, author = {van Batenburg, FH and Gultyaev, AP and Pleij, CW}, title = {PseudoBase: structural information on RNA pseudoknots.}, journal = {Nucleic acids research}, volume = {29}, number = {1}, pages = {194-195}, pmid = {11125088}, issn = {1362-4962}, mesh = {Base Sequence ; *Databases, Factual ; Information Storage and Retrieval ; Internet ; Molecular Sequence Data ; Nucleic Acid Conformation ; RNA/*chemistry ; }, abstract = {PseudoBase is a database containing structural, functional and sequence data related to RNA pseudo-knots. It can be reached at http://wwwbio.LeidenUniv.nl/ approximately Batenburg/PKB.html. For each pseudoknot, thirteen items are stored, for example the relevant sequence, the stem positions of the pseudoknot, the EMBL accession number of the sequence and the support that can be given regarding the reliability of the pseudo-knot. Since the last publication, information on sizes of the stems and the loops in the pseudoknots has been added. Also added are alternative entries that produce surveys of where the pseudoknots are, sorted according to stem size or loop size.}, } @article {pmid11125085, year = {2001}, author = {Klappenbach, JA and Saxman, PR and Cole, JR and Schmidt, TM}, title = {rrndb: the Ribosomal RNA Operon Copy Number Database.}, journal = {Nucleic acids research}, volume = {29}, number = {1}, pages = {181-184}, pmid = {11125085}, issn = {1362-4962}, mesh = {*Databases, Factual ; *Gene Dosage ; Genes, rRNA/genetics ; Internet ; Phylogeny ; rRNA Operon/*genetics ; }, abstract = {The Ribosomal RNA Operon Copy Number Database (rrndb) is an Internet-accessible database containing annotated information on rRNA operon copy number among prokaryotes. Gene redundancy is uncommon in prokaryotic genomes, yet the rRNA genes can vary from one to as many as 15 copies. Despite the widespread use of 16S rRNA gene sequences for identification of prokaryotes, information on the number and sequence of individual rRNA genes in a genome is not readily accessible. In an attempt to understand the evolutionary implications of rRNA operon redundancy, we have created a phylogenetically arranged report on rRNA gene copy number for a diverse collection of prokaryotic microorganisms. Each entry (organism) in the rrndb contains detailed information linked directly to external websites including the Ribosomal Database Project, GenBank, PubMed and several culture collections. Data contained in the rrndb will be valuable to researchers investigating microbial ecology and evolution using 16S rRNA gene sequences. The rrndb web site is directly accessible on the WWW at http://rrndb.cme. msu.edu.}, } @article {pmid11125081, year = {2001}, author = {Knudsen, B and Wower, J and Zwieb, C and Gorodkin, J}, title = {tmRDB (tmRNA database).}, journal = {Nucleic acids research}, volume = {29}, number = {1}, pages = {171-172}, pmid = {11125081}, issn = {1362-4962}, support = {R01 GM058267/GM/NIGMS NIH HHS/United States ; GM-58267/GM/NIGMS NIH HHS/United States ; }, mesh = {*Databases, Factual ; Internet ; Phylogeny ; Prokaryotic Cells/metabolism ; RNA, Messenger/*genetics ; RNA, Transfer/*genetics ; Sequence Alignment ; }, abstract = {The tmRNA database (tmRDB) is maintained at the University of Texas Health Science Center at Tyler, Texas, and accessible on the World Wide Web at the URL http://psyche.uthct.edu/dbs/tmRDB/tmRDB.++ +html. Mirror sites are located at Auburn University, Auburn, Alabama (http://www.ag.auburn.edu/mirror/tmRDB/) and the Institute of Biological Sciences, Aarhus, Denmark (http://www.bioinf.au. dk/tmRDB/). The tmRDB provides information and citation links about tmRNA, a molecule that combines functions of tRNA and mRNA in trans-translation. tmRNA is likely to be present in all bacteria and has been found in algae chloroplasts, the cyanelle of Cyanophora paradoxa and the mitochondrion of the flagellate Reclinomonas americana. This release adds 26 new sequences and corresponding predicted tmRNA-encoded tag peptides for a total of 86 tmRNAs, ordered alphabetically and phylogenetically. Secondary structures and three-dimensional models in PDB format for representative molecules are being made available. tmRNA alignments prove individual base pairs and are generated manually assisted by computational tools. The alignments with their corresponding structural annotation can be obtained in various formats, including a new column format designed to improve and simplify computational usability of the data.}, } @article {pmid11125080, year = {2001}, author = {Gorodkin, J and Knudsen, B and Zwieb, C and Samuelsson, T}, title = {SRPDB (Signal Recognition Particle Database).}, journal = {Nucleic acids research}, volume = {29}, number = {1}, pages = {169-170}, pmid = {11125080}, issn = {1362-4962}, support = {R01 GM049034/GM/NIGMS NIH HHS/United States ; GM-49034/GM/NIGMS NIH HHS/United States ; }, mesh = {*Databases, Factual ; Internet ; Proteins/genetics ; RNA/genetics ; Signal Recognition Particle/*genetics ; }, abstract = {Signal recognition particle (SRP) is a stable cytoplasmic ribonucleoprotein complex that serves to translocate secretory proteins across membranes during translation. The SRP Database (SRPDB) provides compilations of SRP components, ordered alphabetically and phylogenetically. Alignments emphasize phylogenetically-supported base pairs in SRP RNA and conserved residues in the proteins. Data are provided in various formats including a column arrangement for improved access and simplified computational usability. Included are motifs for identification of new sequences, SRP RNA secondary structure diagrams, 3-D models and links to high-resolution structures. This release includes 11 new SRP RNA sequences (total of 129), two protein SRP9 sequences (total of seven), two protein SRP14 sequences (total of 10), two protein SRP19 sequences (total of 16), 10 new SRP54 (ffh) sequences (total of 66), two protein SRP68 sequences (total of seven) and two protein SRP72 sequences (total of nine). Seven sequences of the SRP receptor alpha-subunit and its FtsY homolog (total of 51) are new. Also considered are ss-subunit of SRP receptor, Flhf, Hbsu, CaM kinase II and cpSRP43. Access to SRPDB is at http://psyche.uthct. edu/dbs/SRPDB/SRPDB.html and the European mirror http://www.medkem. gu.se/dbs/SRPDB/SRPDB.html}, } @article {pmid10623496, year = {2000}, author = {Pelletier, JD}, title = {Model assessments of the optimal design of nature reserves for maximizing species longevity.}, journal = {Journal of theoretical biology}, volume = {202}, number = {1}, pages = {25-32}, doi = {10.1006/jtbi.1999.1030}, pmid = {10623496}, issn = {0022-5193}, mesh = {Animal Population Groups/*physiology ; Animals ; Computational Biology ; *Ecology ; *Environment Design ; Longevity ; Models, Biological ; }, abstract = {Using a computational model for the population growth and dispersal of a model species in a fluctuating environment, we test three nature reserve geometries (one large, many small, and a self-similar distribution of reserve sizes) to determine which geometry maximizes species longevity. The self-similar distribution is a close approximation to the distribution of managed areas in the conterminous United States. We consider models with and without migration from or between reserve fragments and both short- and long-range dispersal mechanisms. The optimal geometry depends on the type of dispersal and on the relative probability of survival in protected and non-protected areas. When no migration is allowed from or between reserve fragments of the three geometries, many small equally sized reserves are the optimal geometry. When migration is allowed, the optimal geometry is a single large reserve when the survivability in non-protected areas is low and a self-similar distribution when the survivability is high.}, } @article {pmid10608573, year = {1999}, author = {Maciak, BJ and Guzman, R and Santiago, A and Villalobos, G and Israel, BA}, title = {Establishing LA VIDA: a community-based partnership to prevent intimate violence against Latina women.}, journal = {Health education & behavior : the official publication of the Society for Public Health Education}, volume = {26}, number = {6}, pages = {821-840}, doi = {10.1177/109019819902600606}, pmid = {10608573}, issn = {1090-1981}, mesh = {Community Health Centers/*organization & administration ; Community Networks/*organization & administration ; *Community Participation ; Female ; *Hispanic or Latino ; Humans ; Male ; Michigan ; Needs Assessment ; Organizational Objectives ; Planning Techniques ; Program Development/*methods ; Program Evaluation ; Spouse Abuse/ethnology/*prevention & control ; Urban Health ; }, abstract = {LA VIDA--the Southwest Detroit Partnership to Prevent Intimate Violence Against Latina Women--evolved in response to community concern about the problem of intimate partner violence (IPV) and the lack of culturally competent preventive and support services for Latino women and men in southwest Detroit. Since 1997, diverse organizations have mobilized as a community-academic partnership to ensure the availability, accessibility, and utilization of IPV services. This article describes and analyzes the evolution of LA VIDA within a community-based participatory research framework using a case study approach that draws on multiple data sources including group and individual interviews and field notes. The challenges and lessons learned in addressing a complex multifaceted problem such as IPV in an ethnic minority community are highlighted in an examination of the process of mobilizing diverse organizations, conducting community diagnosis and needs assessment activities, establishing goals and objectives within a social ecological framework, and integrating evaluation during the development phase.}, } @article {pmid10605117, year = {1999}, author = {Riginos, C and Nachman, MW}, title = {The origin of a Robertsonian chromosomal translocation in house mice inferred from linked microsatellite markers.}, journal = {Molecular biology and evolution}, volume = {16}, number = {12}, pages = {1763-1773}, doi = {10.1093/oxfordjournals.molbev.a026088}, pmid = {10605117}, issn = {0737-4038}, mesh = {Animals ; Data Interpretation, Statistical ; Mice/*genetics ; *Microsatellite Repeats ; Mutation ; Phylogeny ; Polymerase Chain Reaction ; *Translocation, Genetic ; }, abstract = {The western European house mouse, Mus domesticus, includes many distinct Robertsonian (Rb) chromosomal races. Two competing hypotheses may explain the distribution of Rb translocations found in different populations: they may have arisen independently multiple times, or they may have arisen once and been spread through long-distance dispersal. We investigated the origin of the Rb 5.15 translocation using six microsatellite loci linked to the centromeres of chromosomes 5 and 15 in 84 individuals from three Rb populations and four neighboring standard-karyotype populations. Microsatellite variation on the 5.15 metacentric chromosomes was significantly reduced relative to the amount of variation found on acrocentric chromosomes 5 and 15, suggesting that linked microsatellite loci can track specific mutational events. Phylogenetic analyses resulted in trees which are consistent with multiple origins of the 5.15 metacentric chromosomes found in the three Rb populations. These results suggest that cytologically indistinguishable mutations have arisen independently in natural populations of house mice.}, } @article {pmid10592225, year = {2000}, author = {van Batenburg, FH and Gultyaev, AP and Pleij, CW and Ng, J and Oliehoek, J}, title = {PseudoBase: a database with RNA pseudoknots.}, journal = {Nucleic acids research}, volume = {28}, number = {1}, pages = {201-204}, pmid = {10592225}, issn = {0305-1048}, mesh = {Base Sequence ; *Databases, Factual ; Information Storage and Retrieval ; *Nucleic Acid Conformation ; RNA/*chemistry ; }, abstract = {PseudoBase is a database containing structural, functional and sequence data related to RNA pseudo-knots. It can be reached at http://wwwbio. Leiden Univ.nl/ approximately Batenburg/PKB.html. This page will direct the user to a retrieval page from where a particular pseudoknot can be chosen, or to a submission page which enables the user to add pseudoknot information to the database or to an informative page that elaborates on the various aspects of the database. For each pseudoknot, 12 items are stored, e.g. the nucleotides of the region that contains the pseudoknot, the stem positions of the pseudoknot, the EMBL accession number of the sequence that contains this pseudoknot and the support that can be given regarding the reliability of the pseudoknot. Access is via a small number of steps, using 16 different categories. The development process was done by applying the evolutionary methodology for software development rather than by applying the methodology of the classical waterfall model or the more modern spiral model.}, } @article {pmid10592216, year = {2000}, author = {Maidak, BL and Cole, JR and Lilburn, TG and Parker, CT and Saxman, PR and Stredwick, JM and Garrity, GM and Li, B and Olsen, GJ and Pramanik, S and Schmidt, TM and Tiedje, JM}, title = {The RDP (Ribosomal Database Project) continues.}, journal = {Nucleic acids research}, volume = {28}, number = {1}, pages = {173-174}, pmid = {10592216}, issn = {0305-1048}, mesh = {*Databases, Factual ; RNA, Ribosomal/*genetics ; Ribosomes/*metabolism ; }, abstract = {The Ribosomal Database Project (RDP-II), previously described by Maidak et al., continued during the past year to add new rRNA sequences to the aligned data and to improve the analysis commands. Release 7.1 (September 17, 1999) included more than 10 700 small subunit rRNA sequences. More than 850 type strain sequences were identified and added to the prokaryotic alignment, bringing the total number of type sequences to 3324 representing 2460 different species. Availability of an RDP-II mirror site in Japan is also near completion. RDP-II provides aligned and annotated rRNA sequences, derived phylogenetic trees and taxonomic hierarchies, and analysis services through its WWW server (http://rdp.cme.msu.edu/). Analysis services include rRNA probe checking, approx-i-mate phylogenetic placement of user sequences, screening user sequences for possible chimeric rRNA sequences, automated alignment, production of similarity matrices and services to plan and analyze terminal restriction fragment length polymorphism (T-RFLP) experiments.}, } @article {pmid10583552, year = {1999}, author = {Shaw, PW and Turan, C and Wright, JM and O'Connell, M and Carvalho, GR}, title = {Microsatellite DNA analysis of population structure in Atlantic herring (Clupea harengus), with direct comparison to allozyme and mtDNA RFLP analyses.}, journal = {Heredity}, volume = {83 (Pt 4)}, number = {}, pages = {490-499}, doi = {10.1038/sj.hdy.6885860}, pmid = {10583552}, issn = {0018-067X}, mesh = {Animals ; Atlantic Ocean ; DNA, Mitochondrial/genetics ; Data Interpretation, Statistical ; Fishes/*genetics ; Genetic Variation ; Genetics, Population ; Isoenzymes/genetics ; Microsatellite Repeats ; Norway ; Polymerase Chain Reaction ; Polymorphism, Restriction Fragment Length ; }, abstract = {Previous attempts to test for small-scale stock structuring within Atlantic herring (Clupea harengus L.) with molecular markers have been hampered by uninformative levels of genetic variation. Here we report the first application of microsatellite DNA markers to investigate population subdivision in Atlantic herring from Norwegian waters and the Barents Sea, and also examine microsatellite differentiation between C. harengus and Pacific herring (C. pallasi). Results from four microsatellite loci indicate high, and informative, variation compared to molecular markers used previously: number of alleles per locus=18-41; mean expected heterozygosity within samples=0.90-0.93. Significant genetic differences were detected between almost all samples representing postulated Icelandic summer-spawner, Norwegian spring-spawner and Norwegian fjord stocks, using Fisher's exact test, FST and RST values. Levels of allele frequency differentiation between Atlantic and Pacific herring overlapped the range seen among Atlantic herring samples, indicating that microsatellites are poor indicators of the degree of species differentiation. Comparison with allozyme and mitochondrial DNA restriction fragment length polymorphism (RFLP) datasets from the same samples suggests that microsatellites may detect structuring at a finer scale, but are less informative at larger scales of divergence.}, } @article {pmid10573146, year = {1999}, author = {Bourhy, H and Kissi, B and Audry, L and Smreczak, M and Sadkowska-Todys, M and Kulonen, K and Tordo, N and Zmudzinski, JF and Holmes, EC}, title = {Ecology and evolution of rabies virus in Europe.}, journal = {The Journal of general virology}, volume = {80 (Pt 10)}, number = {}, pages = {2545-2557}, doi = {10.1099/0022-1317-80-10-2545}, pmid = {10573146}, issn = {0022-1317}, mesh = {Adaptation, Physiological ; Animals ; *Antigens, Viral ; Cats ; Cattle ; Databases, Factual ; Dogs ; Ecology ; Europe ; *Evolution, Molecular ; Glycoproteins/*genetics ; Humans ; Nucleocapsid/*genetics ; Nucleocapsid Proteins ; Phylogeny ; Rabies virus/classification/*genetics/isolation & purification ; Sequence Analysis, DNA ; Viral Envelope Proteins/*genetics ; }, abstract = {The evolution of rabies viruses of predominantly European origin was studied by comparing nucleotide sequences of the nucleoprotein and glycoprotein genes, and by typing isolates using RFLP. Phylogenetic analysis of the gene sequence data revealed a number of distinct groups, each associated with a particular geographical area. Such a pattern suggests that rabies virus has spread westwards and southwards across Europe during this century, but that physical barriers such as the Vistula river in Poland have enabled localized evolution. During this dispersal process, two species jumps took place - one into red foxes and another into raccoon dogs, although it is unclear whether virus strains are preferentially adapted to particular animal species or whether ecological forces explain the occurrence of the phylogenetic groups.}, } @article {pmid10486823, year = {1999}, author = {Aloo, PA}, title = {Ecological studies of helminth parasites of the largemouth bass, Micropterus salmoides, from Lake Naivasha and the Oloidien Bay, Kenya.}, journal = {The Onderstepoort journal of veterinary research}, volume = {66}, number = {2}, pages = {73-79}, pmid = {10486823}, issn = {0030-2465}, mesh = {Acanthocephala/*physiology ; Animals ; Bass/*parasitology ; Data Interpretation, Statistical ; Female ; Fish Diseases/*epidemiology ; Helminthiasis, Animal/*epidemiology ; Host-Parasite Interactions ; Kenya/epidemiology ; Male ; Prevalence ; }, abstract = {The parasites of 541 largemouth bass, Micropterus salmoides, were studied over a period of 12 months. The results showed that the bass from Lake Naivasha are paratenic hosts of Contracaecum sp. larva and final hosts for the acanthocephalan Polyacanthorhynchus kenyensis. The nematode occurred in large numbers in fish caught in the more saline Oloidien Bay but only in small numbers in those in the main lake. Bass in the main lake, however, were more heavily infected with acanthocephalans than those in Oloidien Bay. One of the major pathological effects of the acanthocephalan was perforation of the liver by the spiny proboscis. Seasonal variation was not apparent for either of the parasites. The intensity of infection by Contracaecum sp. larva increased with the size of the host and female fish were more heavily infected than males.}, } @article {pmid10544583, year = {1999}, author = {Skånér, Y}, title = {[Decision making--an area of expertise in health care].}, journal = {Lakartidningen}, volume = {96}, number = {39}, pages = {4189-4194}, pmid = {10544583}, issn = {0023-7205}, mesh = {*Decision Making ; Decision Support Techniques ; *Decision Theory ; Humans ; }, abstract = {Decision making is of great importance in medicine, and can be analysed according to different theories and research traditions, each with its own criteria for what is meant by a good or correct decision. In classic decision analysis, the criterion is rationality, defined as adherence to logic and probability computation. In clinical judgement analysis, the criterion is agreement with the conditions of external (ecological) reality and how well we adapt to them. According to the naturalistic decision making tradition, there is no better criterion than the opinion of experts in the field. This is discussed in the article, and some of the research traditions are presented.}, } @article {pmid10508639, year = {1999}, author = {Kuipers, OP}, title = {Genomics for food biotechnology: prospects of the use of high-throughput technologies for the improvement of food microorganisms.}, journal = {Current opinion in biotechnology}, volume = {10}, number = {5}, pages = {511-516}, doi = {10.1016/s0958-1669(99)00019-1}, pmid = {10508639}, issn = {0958-1669}, mesh = {Bacillus subtilis/genetics/metabolism ; Computational Biology ; *Food Microbiology ; Food Technology/*methods/trends ; Forecasting ; Gene Expression Regulation, Bacterial ; *Genetic Techniques ; Lactic Acid/metabolism ; Lactococcus/genetics/metabolism ; Proteins/chemistry/genetics ; Saccharomyces cerevisiae/genetics/metabolism ; Structure-Activity Relationship ; }, abstract = {Functional genomics is currently the most effective approach for increasing the knowledge at the molecular level of metabolic and adaptive processes in whole cells. High-throughput technologies, such as DNA microarrays, and improved two-dimensional electrophoresis methods combined with tandem mass-spectroscopy, supported by bioinformatics, are useful tools for food biotechnology, which depends on detailed knowledge of the properties of food microbes (and pathogens) in their industrial, food and consumer environments. Genomics of food microbes, based on rapidly emerging genome sequence information, generates valuable knowledge that can be used for metabolic engineering, improving cell factories and development of novel preservation methods. Furthermore, pre- and probiotic studies, characterization of stress responses, studies of microbial ecology and, last but not least, development of novel risk assessment procedures will be facilitated.}, } @article {pmid10485866, year = {1999}, author = {Schuessler, AA}, title = {Ecological inference.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {96}, number = {19}, pages = {10578-10581}, doi = {10.1073/pnas.96.19.10578}, pmid = {10485866}, issn = {0027-8424}, mesh = {Behavior ; *Data Interpretation, Statistical ; Diagnostic Imaging/methods ; Humans ; *Models, Statistical ; Politics ; Regression Analysis ; }, abstract = {Ecological inference is the process of drawing conclusions about individual-level behavior from aggregate-level data. Recent advances involve the combination of statistical and deterministic means to produce such inferences.}, } @article {pmid10474147, year = {1999}, author = {Wakefield, J and Elliott, P}, title = {Issues in the statistical analysis of small area health data.}, journal = {Statistics in medicine}, volume = {18}, number = {17-18}, pages = {2377-2399}, doi = {10.1002/(sici)1097-0258(19990915/30)18:17/18<2377::aid-sim263>3.0.co;2-g}, pmid = {10474147}, issn = {0277-6715}, mesh = {Bayes Theorem ; Brain Neoplasms/epidemiology ; Case-Control Studies ; Central Nervous System Neoplasms/epidemiology ; Cluster Analysis ; Confounding Factors, Epidemiologic ; *Data Interpretation, Statistical ; Female ; Heart Diseases/mortality ; Humans ; Linear Models ; Male ; Poisson Distribution ; Population Density ; Risk Factors ; *Small-Area Analysis ; United Kingdom ; Water Supply ; }, abstract = {The availability of geographically indexed health and population data, with advances in computing, geographical information systems and statistical methodology, have opened the way for serious exploration of small area health statistics based on routine data. Such analyses may be used to address specific questions concerning health in relation to sources of pollution, to investigate clustering of disease or for hypothesis generation. We distinguish four types of analysis: disease mapping; geographic correlation studies; the assessment of risk in relation to a prespecified point or line source, and cluster detection and disease clustering. A general framework for the statistical analysis of small area studies will be considered. This framework assumes that populations at risk arise from inhomogeneous Poisson processes. Disease cases are then realizations of a thinned Poisson process where the risk of disease depends on the characteristics of the person, time and spatial location. Difficulties of analysis and interpretation due to data inaccuracies and aggregation will be addressed with particular reference to ecological bias and confounding. The use of errors-in-variables modelling in small area analyses will be discussed.}, } @article {pmid10468446, year = {1999}, author = {Corvalán, CF and Kjellström, T and Smith, KR}, title = {Health, environment and sustainable development: identifying links and indicators to promote action.}, journal = {Epidemiology (Cambridge, Mass.)}, volume = {10}, number = {5}, pages = {656-660}, pmid = {10468446}, issn = {1044-3983}, mesh = {Decision Support Techniques ; *Developing Countries ; Ecology ; Environmental Exposure/prevention & control ; *Environmental Health/standards ; Global Health ; Health Promotion/*standards ; Health Status Indicators ; Health Transition ; Humans ; Risk Assessment/methods ; *Social Change ; }, abstract = {This paper discusses the links among health, environment, and sustainable development and presents a framework that extends from the epidemiological domain to the policy domain and includes the driving forces that generate environmental pressures, creating changes in the state of the environment and eventually contributing to human exposures. Health effects are the end result of this complex net of events. Environmental health interventions should not be limited to treatment of cases and directly reducing human exposures. The paper discusses the need for integrated action at all levels and, in particular, on the need to focus on long-term action directed at reducing the driving forces that generate the environmental health threats. Only this approach can achieve sustained health benefits and environmental protection in accord with the principles of sustainable development.}, } @article {pmid10466152, year = {1999}, author = {Tomberg, C and Desmedt, JE}, title = {The challenge of non-invasive cognitive physiology of the human brain: how to negotiate the irrelevant background noise without spoiling the recorded data through electronic averaging.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {354}, number = {1387}, pages = {1295-1305}, pmid = {10466152}, issn = {0962-8436}, mesh = {Attention/physiology ; Brain/blood supply/diagnostic imaging/*physiology ; Cerebrovascular Circulation ; Cognition/*physiology ; Data Interpretation, Statistical ; Evoked Potentials ; Fingers ; Humans ; Physical Stimulation ; Psychophysiology ; Regional Blood Flow ; Tomography, Emission-Computed ; }, abstract = {Brain mechanisms involved in selective attention in humans can be studied by measures of regional blood flow and metabolism (by positron emission tomography) which help identify the various locations with enhanced activities over a period of time of seconds. The physiological measures provided by scalp-recorded brain electrical potentials have a better resolution (milliseconds) and can reveal the actual sequences of distinct neural events and their precise timing. We studied selective attention to sensory inputs from fingers because the brain somatic representations are deployed over the brain convexity under the scalp thereby making it possible to assess distinct stages of cortical processing and representation through their characteristic scalp topographies. In the electrical response to a finger input attended by the subject, the well-known P300 manifests a widespread inhibitory mechanism which is released after a target stimulus has been identified. P300 is preceded by distinct cognitive electrogeneses such as P40, P100 and N140 which can be differentiated from the control (obligatory) profile by superimposition or electronic subtraction. The first cortical response N20 is stable across conditions, suggesting that the first afferent thalamocortical volley is not affected by selective attention. At the next stage of modality-specific cortex in which the sensory features are processed and represented, responses were enhanced (cognitive P40) only a very few milliseconds after arrival of the afferent volley at the cortex, thus documenting a remarkable precocity of attention gain control in the somatic modality. The physiology of selective attention also provides useful cues in relation to non-target inputs which the subject must differentiate in order to perform the task. When having to tell fingers apart, the brain strategy for non-target fingers is not to inhibit or filter them out, but rather to submit their input to several processing operations that are actually enhanced when the discrimination from targets becomes more difficult. While resolving a number of such issues, averaged data cannot disclose the flexibility of brain mechanisms nor the detailed features of cognitive electrogeneses because response variations along time have been ironed out by the bulk treatment. We attempted to address the remarkable versatility of humans in dealing with their sensory environment under ecological conditions by studying single non-averaged responses. We identified distinct cognitive P40, P100, N140 and P300 electrogeneses in spite of the noise by numerically assessing their characteristic scalp topography signatures. Single-trial data suggest reconsiderations of current psychophysiological issues. The study of non-averaged responses can clarify issues raised by averaging studies as illustrated by our recent study of cognitive brain potentials for finger stimuli which remain outside the subject's awareness. This has to do with the physiological basis of the 'cognitive unconscious', that is, current mental processes lying on the fringe or outside of phenomenal awareness and voluntary control, but which can influence ongoing behaviour. Averaged data suggest that, in selective auditory attention, the subject may not notice mild concomitant finger inputs. The study of non-averaged responses documents the optional and independent occurrence of the cognitive P40, P100 and N140 (but not P300) electrogeneses while the finger inputs remain outside phenomenal awareness. These results suggest that the subject unconsciously assigns limited cognitive resources to distinct somatic cortical areas thereby submitting finger inputs to an intermittent curtailed surveillance which can remain on the fringe or outside consciousness. The study of cognitive electrogeneses in single non-averaged responses is making possible a neurophysiology of cognition in real time.}, } @article {pmid10454621, year = {1999}, author = {Deutsch, M and Long, M}, title = {Intron-exon structures of eukaryotic model organisms.}, journal = {Nucleic acids research}, volume = {27}, number = {15}, pages = {3219-3228}, pmid = {10454621}, issn = {1362-4962}, mesh = {Animals ; Databases, Factual ; *Eukaryotic Cells ; *Evolution, Molecular ; Exons/*genetics ; Gene Frequency ; *Genes ; Genome ; Humans ; Introns/*genetics ; Invertebrates/genetics ; Molecular Weight ; Plants/genetics ; Proteins/genetics ; RNA Splicing/genetics ; RNA, Messenger/analysis/chemistry/genetics ; Rats ; Schizosaccharomyces/genetics ; Sequence Homology, Nucleic Acid ; Statistical Distributions ; Untranslated Regions/genetics ; }, abstract = {To investigate the distribution of intron-exon structures of eukaryotic genes, we have constructed a general exon database comprising all available intron-containing genes and exon databases from 10 eukaryotic model organisms: Homo sapiens, Mus musculus, Gallus gallus, Rattus norvegicus, Arabidopsis thaliana, Zea mays, Schizosaccharomyces pombe, Aspergillus, Caenorhabditis elegans and Drosophila. We purged redundant genes to avoid the possible bias brought about by redundancy in the databases. After discarding those questionable introns that do not contain correct splice sites, the final database contained 17 102 introns, 21 019 exons and 2903 independent or quasi-independent genes. On average, a eukaryotic gene contains 3.7 introns per kb protein coding region. The exon distribution peaks around 30-40 residues and most introns are 40-125 nt long. The variable intron-exon structures of the 10 model organisms reveal two interesting statistical phenomena, which cast light on some previous speculations. (i) Genome size seems to be correlated with total intron length per gene. For example, invertebrate introns are smaller than those of human genes, while yeast introns are shorter than invertebrate introns. However, this correlation is weak, suggesting that other factors besides genome size may also affect intron size. (ii) Introns smaller than 50 nt are significantly less frequent than longer introns, possibly resulting from a minimum intron size requirement for intron splicing.}, } @article {pmid10447507, year = {1999}, author = {Long, AD and Langley, CH}, title = {The power of association studies to detect the contribution of candidate genetic loci to variation in complex traits.}, journal = {Genome research}, volume = {9}, number = {8}, pages = {720-731}, pmid = {10447507}, issn = {1088-9051}, mesh = {Computational Biology/methods/statistics & numerical data ; Genetic Markers/genetics ; Genetic Variation/*genetics ; Genotype ; Humans ; Linkage Disequilibrium/genetics ; Nucleotides/genetics ; Phenotype ; Polymorphism, Genetic/genetics ; *Quantitative Trait, Heritable ; }, abstract = {The statistical power of five association study test statistics (two haplotype-based tests, two marker-based tests, and the Transmission Disequilibrium Test-Q5) to detect single nucleotide polymorphism (SNP)/phenotype associations in a linkage-disequilibrium-based candidate gene scan employing a number of SNPs is examined. Power is estimated as a function of realistic parameters expected to affect the likelihood of detecting a significant association: the number of SNPs examined, the scaled recombination size of the region examined, the proportion of variance in the trait attributable to a hidden causative polymorphism within the region, and the number of individuals or families examined. For the different combinations of parameter values, power is estimated from a large number of realizations of a simulated coalescent describing a single random mating population with mutation, random genetic drift, and recombination. This explicit population genetics model results in a distribution of DNA marker heterozygosities and linkage disequilibria that are likely to resemble those expected in actual population samples. The study concludes that (1) marker-based permutation tests are more powerful than simple haplotype-based tests, (2) there is sufficient power to detect the presence of causative polymorphisms of small effect if on the order of 500 individuals are sampled, (3) greater power is achieved by increasing the sample size than by increasing the number of polymorphisms, (4) association studies are generally more powerful than transmission disequilibrium-based tests, and (5) for the range of parameters considered association studies have a low repeatability unless sample sizes are on the order of 500 individuals. Estimates of 4Nc for a number of gene regions and human populations will be of use in determining the density of SNPs that are likely to be required for successful association studies.}, } @article {pmid10438672, year = {1999}, author = {Pascual, M and Levin, SA}, title = {Spatial scaling in a benthic population model with density-dependent disturbance.}, journal = {Theoretical population biology}, volume = {56}, number = {1}, pages = {106-122}, doi = {10.1006/tpbi.1999.1417}, pmid = {10438672}, issn = {0040-5809}, mesh = {Age Factors ; Analysis of Variance ; Animals ; Bias ; Bivalvia/physiology ; Crowding ; *Data Interpretation, Statistical ; *Marine Biology ; *Models, Statistical ; Mortality ; *Nonlinear Dynamics ; Oceans and Seas ; *Population Density ; Reproducibility of Results ; Stochastic Processes ; }, abstract = {This work investigates approaches to simplifying individual-based models in which the rate of disturbance depends on local densities. To this purpose, an individual-based model for a benthic population is developed that is both spatial and stochastic. With this model, three possible ways of approximating the dynamics of mean numbers are examined: a mean-field approximation that ignores space completely, a second-order approximation that represents spatial variation in terms of variances and covariances, and a patch-based approximation that retains information about the age structure of the patch population. Results show that space is important and that a temporal model relying on mean disturbance rates provides a poor approximation to the dynamics of mean numbers. It is possible, however, to represent relevant spatial variation with second-order moments, particularly when recruitment rates are low and/or when disturbances are large and weak. Even better approximations are obtained by retaining patch age information.}, } @article {pmid10435246, year = {1999}, author = {Stambuk-Giljanović, N and Matoković, B}, title = {Information subsystem of the chemical coefficients K1 and K2 as the base for the study of the ecological factors that influence human health.}, journal = {Journal of medical systems}, volume = {23}, number = {2}, pages = {159-169}, pmid = {10435246}, issn = {0148-5598}, mesh = {Alkalies/analysis ; Carbonates/analysis ; Chlorides/analysis ; Computer Systems ; Corrosion ; Croatia ; *Databases as Topic ; *Ecology ; *Environmental Health ; Environmental Monitoring ; Humans ; Public Health ; Seawater/analysis ; Sodium/analysis ; Software ; Sulfates/analysis ; Water Pollution, Chemical/analysis/prevention & control ; Water Supply/*analysis ; }, abstract = {With regard to the relatively limited water supply in the area of Dalmatia (Southern Croatia), water supply system and health care institutions are especially interested in observing and monitoring the waters, as well as preserving their quality. The ecological need to sum up the work on water quality investigations led us to monitor the environment. Because it is necessary, from the informatical aspect, to organize mass ecological health data into databases, the relational database for the research of chemical analyses (coefficients K1 and K2) as the methodological foundation for the study of the ecological factors that influence human health is defined in this paper. Results used for the prototype implementation subsystem of the chemical water analysis control are based on the investigations of the Water Examination Department of the Public Health Institute of the Split-Dalmatian County (Croatia). Over 2500 data comprised the examination sample. The software used included Win'95, MO'97, and Paradox 4.5, while the hardware used included Pentium II 200 MHz, floppy, 64 MB RAM, HDD 2.1 GB, CD x 24, HP Ljet 4L.}, } @article {pmid10395048, year = {1999}, author = {Shkolnikov, V and McKee, M and Leon, D and Chenet, L}, title = {Why is the death rate from lung cancer falling in the Russian Federation?.}, journal = {European journal of epidemiology}, volume = {15}, number = {3}, pages = {203-206}, pmid = {10395048}, issn = {0393-2990}, mesh = {Adolescent ; Adult ; Age Distribution ; Aged ; Child ; Child, Preschool ; Cohort Effect ; Databases, Factual/standards/trends ; Female ; *Health Transition ; Humans ; Infant ; Infant, Newborn ; Longitudinal Studies ; Lung Neoplasms/*mortality ; Male ; Middle Aged ; Regression Analysis ; Retrospective Studies ; Russia/epidemiology ; Sex Distribution ; Smoking/epidemiology ; }, abstract = {Age standardised death rates (European standard population) from lung cancer in the Russian Federation, have been rising since at least 1965, levelled out in the late 1980s and have subsequently decreased. The reasons for this decline are not apparent. This study seeks to identify the reasons for the decline in mortality from lung cancer in the Russian Federation in the 1990s. Changes in age-specific mortality from lung cancer in the Russian Federation between 1990 are described and age-cohort analysis, based on age-specific death rates for lung cancer is undertaken for the period 1965 to 1995. As other work has shown that any recent deterioration in coding of cause of death has been confined largely to the elderly, this suggests that the trend is not a coding artefact. Age-period-cohort analysis demonstrates the existence of a marked birth cohort effect, with two major peaks corresponding to those born around 1926 and 1938. These groups would have reached their early teens during the second world war and the period immediately after the death of Stalin, respectively. The present downward trend in death rates from lung cancer in the Russian Federation is partly due to a cohort effect and it is expected that this will soon reverse, with a second peak occurring in about 2003.}, } @article {pmid10391714, year = {1999}, author = {Homan, JM}, title = {The evolving digital ecology.}, journal = {Bulletin of the Medical Library Association}, volume = {87}, number = {2}, pages = {223}, pmid = {10391714}, issn = {0025-7338}, mesh = {Information Systems ; *Internet ; *Libraries, Medical ; *Library Associations ; National Library of Medicine (U.S.) ; *Periodicals as Topic ; United States ; }, } @article {pmid10384654, year = {1998}, author = {Waters, E and Rigby, M}, title = {The ethical imperative of child health population-based data a top-down/under-up analysis from the United Kingdom and Australia.}, journal = {Studies in health technology and informatics}, volume = {52 Pt 2}, number = {}, pages = {1218-1222}, pmid = {10384654}, issn = {0926-9630}, mesh = {Australia ; Child ; Child Health Services/*organization & administration/statistics & numerical data ; Child Welfare/*statistics & numerical data ; Databases, Factual ; *Ethics, Medical ; Humans ; Medical Record Linkage ; Medical Records Systems, Computerized ; Primary Health Care/organization & administration ; Quality Assurance, Health Care ; United Kingdom ; }, abstract = {The policy move in both the United Kingdom and Australia to competitive primary care child health services (including preventive services and surveillance) has many advantages, but without secure and epidemiological information systems has the potential to put children at risk. More fundamentally, it produces the perverse effect of operating directly in opposition to the desirable policies of audit, outcomes studies, and evidence-based health care. Moreover, generations of children stand to be disadvantaged if environmental and ecological risk factors, as well as adverse clinical outcomes, cannot be identified quickly. Health informatics, linked to professional duties of clinical and fiduciary accountability, provide a way out of this conundrum. Standard clinical data sets, linked to invoicing procedures, would enable the development of summary records which could underpin integrated surveillance whilst also fuelling the new public health. Appropriate professional supervision, confidentiality and security measures, and agreement of data sets, would be necessary but not difficult in informatics terms. As health policy and delivery move forward, it is important not to lose the best aspects of previous systems and opportunities of future technologies.}, } @article {pmid10383470, year = {1999}, author = {Knudsen, B and Hein, J}, title = {RNA secondary structure prediction using stochastic context-free grammars and evolutionary history.}, journal = {Bioinformatics (Oxford, England)}, volume = {15}, number = {6}, pages = {446-454}, doi = {10.1093/bioinformatics/15.6.446}, pmid = {10383470}, issn = {1367-4803}, mesh = {Algorithms ; Base Sequence ; Biological Evolution ; Computational Biology ; Computer Simulation ; Endoribonucleases/genetics ; Molecular Sequence Data ; *Nucleic Acid Conformation ; Probability ; RNA/*chemistry ; RNA, Bacterial/chemistry/genetics ; RNA, Catalytic/genetics ; Ribonuclease P ; Sequence Homology, Nucleic Acid ; Stochastic Processes ; }, abstract = {MOTIVATION: Many computerized methods for RNA secondary structure prediction have been developed. Few of these methods, however, employ an evolutionary model, thus relevant information is often left out from the structure determination. This paper introduces a method which incorporates evolutionary history into RNA secondary structure prediction. The method reported here is based on stochastic context-free grammars (SCFGs) to give a prior probability distribution of structures.

RESULTS: The phylogenetic tree relating the sequences can be found by maximum likelihood (ML) estimation from the model introduced here. The tree is shown to reveal information about the structure, due to mutation patterns. The inclusion of a prior distribution of RNA structures ensures good structure predictions even for a small number of related sequences. Prediction is carried out using maximum a posteriori estimation (MAP) estimation in a Bayesian approach. For small sequence sets, the method performs very well compared to current automated methods.}, } @article {pmid10372578, year = {1998}, author = {Tengs, TO and Winer, EP and Paddock, S and Aguilar-Chavez, O and Berry, DA}, title = {Testing for the BRCA1 and BRCA2 breast-ovarian cancer susceptibility genes: a decision analysis.}, journal = {Medical decision making : an international journal of the Society for Medical Decision Making}, volume = {18}, number = {4}, pages = {365-375}, doi = {10.1177/0272989X9801800402}, pmid = {10372578}, issn = {0272-989X}, support = {P50 CA68438/CA/NCI NIH HHS/United States ; }, mesh = {Adult ; Aged ; Breast Neoplasms/epidemiology/genetics/prevention & control ; *Decision Support Techniques ; Female ; Genes, BRCA1/*physiology ; Genes, Tumor Suppressor/*physiology ; Genetic Predisposition to Disease ; *Genetic Testing ; Humans ; Incidence ; Markov Chains ; Mastectomy ; Middle Aged ; Ovarian Neoplasms/epidemiology/genetics/prevention & control ; Ovariectomy ; Predictive Value of Tests ; Quality-Adjusted Life Years ; Risk Assessment/*methods ; Survival Analysis ; United States/epidemiology ; }, abstract = {OBJECTIVE: The authors developed a Markov decision model to evaluate the health implications of testing for mutations in the BRCA1 and BRCA2 breast-ovarian cancer susceptibility genes. Prophylactic measures considered included various combinations of immediate and delayed bilateral mastectomy and oophorectomy or taking no action.

METHODS: The model incorporated the likelihood of developing breast and/or ovarian cancer, survival, and quality of life. Parameter values were taken from public databases, the published literature, and a survey of cancer experts. Outcomes considered were additional life expectancy and quality-adjusted life years (QALYs). Results are reported for 30-year-old cancer-free women at various levels of hereditary risk.

RESULTS AND CONCLUSIONS: The vast majority of women will not benefit from testing because their pre-test risks are low and surgical prophylaxis is undesirable. However, women who have family histories of early breast and/or ovarian cancer may gain up to 2 QALYs by allowing genetic testing to inform their decisions.}, } @article {pmid10361591, year = {1999}, author = {Vasama-Neuvonen, K and Pukkala, E and Paakkulainen, H and Mutanen, P and Weiderpass, E and Boffetta, P and Shen, N and Kauppinen, T and Vainio, H and Partanen, T}, title = {Ovarian cancer and occupational exposures in Finland.}, journal = {American journal of industrial medicine}, volume = {36}, number = {1}, pages = {83-89}, doi = {10.1002/(sici)1097-0274(199907)36:1<83::aid-ajim12>3.0.co;2-q}, pmid = {10361591}, issn = {0271-3586}, mesh = {Adult ; Aged ; Aged, 80 and over ; Confidence Intervals ; Databases, Factual/statistics & numerical data ; Female ; Finland/epidemiology ; Follow-Up Studies ; Humans ; Middle Aged ; Occupational Diseases/epidemiology/*etiology ; Occupational Exposure/*adverse effects/statistics & numerical data ; *Occupations ; Odds Ratio ; Ovarian Neoplasms/epidemiology/*etiology ; Regression Analysis ; Retrospective Studies ; *Women's Health ; }, abstract = {BACKGROUND: No single occupational or environmental agent has been established as causing ovarian cancer, existing studies often being based on ecologic or proportional mortality data in which potential confounders related to reproductive history have not been taken into account.

METHODS: This study linked 324 job titles of occupationally active Finnish women (n = 892,591) at 1970 census with incidence of ovarian cancer (Finnish Cancer Registry, 5,072 cases) during 1971-1995 (over 15 million person-years). The job titles were converted into indicators of exposure to 33 agents, using a national job-exposure matrix based on measurements and surveys (FINJEM). Poisson regression analyses were performed with stratification by birth cohort, follow-up period, and socioeconomic status, and adjusted for mean number of children, mean age at first delivery, and turnover rate for each job title.

RESULTS: We found indications of elevated risks for aromatic hydrocarbon solvents (standardized incidence ratio 1.3 (95% CI 1.0-1.7), leather dust (1.4; 0.7-2.7), man-made vitreous fibers (1.3; 0.9-1.8), and high levels of asbestos (1.3; 0.9-1.8), and diesel (1.7; 0.7-4.1), and gasoline (1.5; 1.0-2.0) engine exhausts). Previously reported findings for hairdressers and women in the printing industry were supported in our data, but not for women in dry cleaning jobs.

CONCLUSIONS: Given the various drawbacks in linkage studies and job-exposure matrices, the excesses found in this study need confirmation in individual-level studies.}, } @article {pmid10339530, year = {1999}, author = {Tilman, D}, title = {Global environmental impacts of agricultural expansion: the need for sustainable and efficient practices.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {96}, number = {11}, pages = {5995-6000}, pmid = {10339530}, issn = {0027-8424}, mesh = {Agriculture/*methods/trends ; Databases as Topic ; Ecology ; Ecosystem ; Efficiency ; *Environment ; Fertilizers ; *Food Supply ; }, abstract = {The recent intensification of agriculture, and the prospects of future intensification, will have major detrimental impacts on the nonagricultural terrestrial and aquatic ecosystems of the world. The doubling of agricultural food production during the past 35 years was associated with a 6.87-fold increase in nitrogen fertilization, a 3.48-fold increase in phosphorus fertilization, a 1.68-fold increase in the amount of irrigated cropland, and a 1.1-fold increase in land in cultivation. Based on a simple linear extension of past trends, the anticipated next doubling of global food production would be associated with approximately 3-fold increases in nitrogen and phosphorus fertilization rates, a doubling of the irrigated land area, and an 18% increase in cropland. These projected changes would have dramatic impacts on the diversity, composition, and functioning of the remaining natural ecosystems of the world, and on their ability to provide society with a variety of essential ecosystem services. The largest impacts would be on freshwater and marine ecosystems, which would be greatly eutrophied by high rates of nitrogen and phosphorus release from agricultural fields. Aquatic nutrient eutrophication can lead to loss of biodiversity, outbreaks of nuisance species, shifts in the structure of food chains, and impairment of fisheries. Because of aerial redistribution of various forms of nitrogen, agricultural intensification also would eutrophy many natural terrestrial ecosystems and contribute to atmospheric accumulation of greenhouse gases. These detrimental environmental impacts of agriculture can be minimized only if there is much more efficient use and recycling of nitrogen and phosphorus in agroecosystems.}, } @article {pmid10335506, year = {1999}, author = {Popova, OB and Berezutskiĭ, NT}, title = {[Information technologies in public health to simulate the processes of decision making based on medical monitoring data].}, journal = {Meditsinskaia tekhnika}, volume = {}, number = {2}, pages = {26-28}, pmid = {10335506}, issn = {0025-8075}, mesh = {*Computer Simulation ; *Decision Making, Computer-Assisted ; Humans ; Monitoring, Physiologic ; *Public Health ; Therapy, Computer-Assisted ; }, abstract = {The paper considers how to enhance the efficiency of therapeutical-and-therapeutical procedures and to choose the strategy for arranging medical measures at different levels of public health care, which is largely determined by the corrective use of computer-aided information technologies to apply monitoring approaches to assessing and predicting medical parameters by taking into account the space position of the objects under study and the ecological situation in a region. A procedure is proposed for decision making on the basis of experts' assessments and data imaging findings in arbitrary schematic images. This procedure serves as a basis of making various management decisions.}, } @article {pmid10334659, year = {1999}, author = {Lagiou, P and Trichopoulou, A and Henderickx, HK and Kelleher, C and Leonhauser, IU and Moreiras, O and Nelson, M and Schmitt, A and Sekula, W and Trygg, K and Zajkas, G}, title = {Household budget survey nutritional data in relation to mortality from coronary heart disease, colorectal cancer and female breast cancer in European countries. DAFNE I and II projects of the European Commission. Data Food Networking.}, journal = {European journal of clinical nutrition}, volume = {53}, number = {4}, pages = {328-332}, doi = {10.1038/sj.ejcn.1600729}, pmid = {10334659}, issn = {0954-3007}, mesh = {Animals ; Breast Neoplasms/*mortality ; Budgets ; Colorectal Neoplasms/*mortality ; Coronary Disease/*mortality ; Databases as Topic ; *Diet ; Europe/epidemiology ; Female ; *Nutrition Surveys ; Statistics, Nonparametric ; }, abstract = {OBJECTIVE: We have undertaken a study to examine whether Household Budget Survey (HBS)-derived nutritional patterns are related to mortality from diseases with strong nutritional components, namely coronary heart disease, colorectal cancer and cancer of the female breast.

DESIGN: Ecological correlation study. In the context of the Data Food Networking projects of the European Union, raw data from the national HBS of 10 European countries were provided. For each of the 10 participating countries, daily food availability per capita around 1990 was calculated. Individual foods were aggregated into 12 major food groups that were linked with the diseases under consideration. Mortality data were available from a World Health Organisation database. We have used a composite score to summarise the postulated influence of diet.

SETTING: Ten European countries circa 1990.

RESULTS: The correlation coefficients between the composite score and the age-adjusted mortality from each of the studied diseases were: + 0.51 (P approximately 0.14) for colorectal cancer; +0.72 (P approximately 0.02) for female breast cancer; and +0.60 (P approximately 0.07) for coronary heart disease, after adjustment for tobacco smoking.

CONCLUSIONS: We conclude that dietary information from HBS is sufficiently reliable to reveal correlations with mortality rates from chronic diseases with fairly strong nutritional roots. HBS data could be used, with little cost, for monitoring secular trends in dietary patterns with a view to their health implications.}, } @article {pmid10212492, year = {1999}, author = {Hewzulla, D and Boulter, MC and Benton, MJ and Halley, JM}, title = {Evolutionary patterns from mass originations and mass extinctions.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {354}, number = {1382}, pages = {463-469}, pmid = {10212492}, issn = {0962-8436}, mesh = {Animals ; *Biological Evolution ; Databases, Factual ; *Ecosystem ; Fossils ; Fractals ; Marine Biology ; Models, Biological ; Time Factors ; }, abstract = {The Fossil Record 2 database gives a stratigraphic range of most known animal and plant families. We have used it to plot the number of families extant through time and argue for an exponential fit, rather than a logistic one, on the basis of power spectra of the residuals from the exponential. The times of origins and extinctions, when plotted for all families of marine and terrestrial organisms over the last 600 Myr, reveal different origination and extinction peaks. This suggests that patterns of biological evolution are driven by its own internal dynamics as well as responding to upsets from external causes. Spectral analysis shows that the residuals from the exponential model of the marine system are more consistent with 1/f noise suggesting that self-organized criticality phenomena may be involved.}, } @article {pmid10101344, year = {1999}, author = {Field, AG and Wang, E}, title = {Evaluation of the patient with nontraumatic headache: an evidence based approach.}, journal = {Emergency medicine clinics of North America}, volume = {17}, number = {1}, pages = {127-52, ix}, doi = {10.1016/s0733-8627(05)70050-x}, pmid = {10101344}, issn = {0733-8627}, mesh = {Brain Diseases/*diagnosis ; Cost-Benefit Analysis ; Decision Support Techniques ; Diagnostic Imaging/economics ; Ecological Systems, Closed ; *Evidence-Based Medicine ; Headache/diagnosis/*etiology/physiopathology/therapy ; Humans ; Risk Factors ; }, abstract = {This article reviews the literature on the diagnostic tools available to make a cost-effective yet appropriate diagnosis in the patient with an atraumatic headache in the emergency setting. The tools addressed include a good history and physical examination alone, third-generation CT, lumbar puncture, and MR imaging. The epidemiology and characteristics of the more common primary and secondary causes of headache are also reviewed, allowing the clinician to develop a better pretest probability of disease, and make a more educated decision as to when additional diagnostic testing is needed.}, } @article {pmid10097558, year = {1999}, author = {Agadzhanian, NA and Turzin, PS and Ushakov, IB}, title = {[Public and occupational health and industrial ecology].}, journal = {Meditsina truda i promyshlennaia ekologiia}, volume = {}, number = {1}, pages = {1-9}, pmid = {10097558}, issn = {1026-9428}, mesh = {*Ecology ; *Environmental Health ; Environmental Monitoring ; Humans ; Information Systems ; Man-Machine Systems ; *Occupational Health ; Power Plants ; *Public Health ; Quality of Life ; Radiation Injuries ; Radioactive Hazard Release ; Ukraine ; User-Computer Interface ; World Health Organization ; }, abstract = {The authors present results of theoretic and experimental analysis of ecologic safety in Russia. New composite discipline--"human ecology"--takes an important place in solution of medical and ecologic problems associated with correlation between natural and occupational factors influencing humans. Present medical, social and ecologic circumstances define the most vital scientific and applied directions covering medical and ecologic humanization of occupational and natural environment for humanity nowadays. Those directions are prophylaxis of ecologic stress, specification of informational technology for medical and occupational monitoring, creation of data bank on human ecology.}, } @article {pmid10095279, year = {1999}, author = {Rodríguez Ortiz de Salazar, B and Martín Galilea, MJ}, title = {[Variability in resource utilization in primary care].}, journal = {Atencion primaria}, volume = {23}, number = {3}, pages = {110-115}, pmid = {10095279}, issn = {0212-6567}, mesh = {Age Factors ; Aged ; Child, Preschool ; Data Interpretation, Statistical ; Health Resources/*statistics & numerical data ; Humans ; Infant ; Infant, Newborn ; Linear Models ; Models, Theoretical ; Physicians/supply & distribution ; *Primary Health Care ; Socioeconomic Factors ; Spain ; }, abstract = {OBJECTIVE: To measure variability in the use of primary care resources and identify factors that explain the differences.

DESIGN: An ecological observation study.

SETTING: Primary care.

PARTICIPANTS: The 1996 index of frequency of attendance was chosen as the indicator of primary care resource use throughout the territory managed by INSALUD.

INTERVENTIONS: The analysis was conducted on a provincial basis, using the statistical technique of multiple linear regression. The index of frequency of attendance was chosen as dependent variable; and demographic, social and economic, mortality, organisation, and offer and accessibility indicators were chosen as explanatory or independent variables.

MEASUREMENTS AND RESULTS: There was wide variability in frequency of attendance in the areas managed by INSALUD during 1996, with a variation coefficient of 20.5%. The simple linear regression analysis showed that the population's income explained 55% of variability. Income, the number of doctors per 1,000 inhabitants and the percentage of children under 3 explained 70% of the variability of frequency of attendance at primary care.

CONCLUSIONS: There are differences between provinces in primary care health resource use. Attendance for primary care consultation in INSALUD is more frequent in provinces with a low social and economic level, more doctors per 1000 inhabitants and more children under 3.}, } @article {pmid10082177, year = {1999}, author = {Andreassen, S and Riekehr, C and Kristensen, B and Schønheyder, HC and Leibovici, L}, title = {Using probabilistic and decision-theoretic methods in treatment and prognosis modeling.}, journal = {Artificial intelligence in medicine}, volume = {15}, number = {2}, pages = {121-134}, doi = {10.1016/s0933-3657(98)00048-7}, pmid = {10082177}, issn = {0933-3657}, mesh = {Anti-Bacterial Agents/adverse effects/economics/therapeutic use ; Bacteremia/drug therapy ; Bayes Theorem ; Databases as Topic ; Decision Support Techniques ; *Decision Theory ; Diagnosis ; Drug Costs ; Fungemia/drug therapy ; Health Care Costs ; Humans ; *Neural Networks, Computer ; *Probability ; *Prognosis ; Retrospective Studies ; Survival Rate ; *Therapeutics ; Urinary Tract Infections/drug therapy ; }, abstract = {Causal probabilistic networks, also called Bayesian networks, allow both qualitative knowledge about the structure of a problem and quantitative knowledge, derived from case databases, expert opinion and literature to be exploited in the construction of decision support systems for diagnosis, treatment and prognosis. This mixing of qualitative and quantitative knowledge will be illustrated, using the selection of antibiotics for a subset of patients with severe infections. The subset consists of patients where bacteria or fungi have been found in the blood. A simple pathophysiological model of infection is used to calculate a prognosis, dependent on the choice of antibiotics. A decision-theoretic approach is used to balance the therapeutic benefit of antibiotic treatment against the cost of antibiotics in the form of direct monetary cost, side effects and ecological cost. A retrospective trial on patients with bacteria or fungi in the blood stemming from the urinary tract indicates that with this approach, it may be possible to suggest balanced choices of antibiotics that not only achieve greater therapeutic benefit, but also reduce the cost of therapy.}, } @article {pmid10048487, year = {1998}, author = {Takanami, T and Sato, S and Ishihara, T and Katsura, I and Takahashi, H and Higashitani, A}, title = {Characterization of a Caenorhabditis elegans recA-like gene Ce-rdh-1 involved in meiotic recombination.}, journal = {DNA research : an international journal for rapid publication of reports on genes and genomes}, volume = {5}, number = {6}, pages = {373-377}, doi = {10.1093/dnares/5.6.373}, pmid = {10048487}, issn = {1340-2838}, mesh = {Animals ; Caenorhabditis elegans/*genetics ; *Caenorhabditis elegans Proteins ; Databases, Factual ; Gonads/cytology/physiology ; Meiosis/genetics ; Molecular Sequence Data ; Oogenesis/physiology ; Ovum/cytology/physiology ; Phylogeny ; Rad51 Recombinase ; Rec A Recombinases/chemical synthesis/*genetics ; *Recombination, Genetic ; }, abstract = {A recA-like gene was identified in the Caenorhabditis elegans genome project database. The putative product of the gene, termed Ce-rdh-1 (C. elegans RAD51 and DMC1/LIM15 homolog 1), consists of 357 amino acid residues. The predicted amino acid sequence of Ce-rdh-1 showed 46-60% identity to both RAD51 type and DMC1/LIM15 type genes in several eukaryote species. The results of RNAi (RNA-mediated interference) indicated that repression of Ce-rdh-1 blocked chromosome condensation of six bivalents and dissociation of chiasmata in oocytes of F1 progeny. Oogenesis did not proceed to the diakinesis stage. Accordingly, all the eggs produced (F2) died in early stages. These results suggest that Ce-rdh-1 participates in meiotic recombination.}, } @article {pmid9973068, year = {1999}, author = {Wen, SW and Kramer, MS}, title = {Uses of ecologic studies in the assessment of intended treatment effects.}, journal = {Journal of clinical epidemiology}, volume = {52}, number = {1}, pages = {7-12}, doi = {10.1016/s0895-4356(98)00136-x}, pmid = {9973068}, issn = {0895-4356}, mesh = {*Bias ; *Confounding Factors, Epidemiologic ; *Data Interpretation, Statistical ; *Effect Modifier, Epidemiologic ; Humans ; Mortality ; Practice Patterns, Physicians'/statistics & numerical data ; Randomized Controlled Trials as Topic ; Reproducibility of Results ; Research Design ; Residence Characteristics ; Severity of Illness Index ; Socioeconomic Factors ; *Treatment Outcome ; }, abstract = {Because of the potential for confounding by indication (disease severity) in individual-level observational studies of intended treatment effects, a treatment designed to prevent an adverse event may appear to cause it. We use a hypothetical example to show that despite substantial variation in the frequency of treatment among patients residing in different geographic areas, a constant area-specific mortality rate can be observed, indicating the absence of confounding by indication at the ecologic level. The advantage of ecologic over individual-level observational studies in the assessment of intended treatment effects holds even if variations in disease severity, socioeconomic status, and other unmeasured factors are taken into account, as long as treatment utilization is influenced by practice style in the local medical community independently of disease severity. Ecologic studies can suggest the need for changes in practice, help resolve ethical issues, and indicate priorities for randomized trials.}, } @article {pmid9973067, year = {1999}, author = {Naylor, CD}, title = {Ecological analysis of intended treatment effects: caveat emptor.}, journal = {Journal of clinical epidemiology}, volume = {52}, number = {1}, pages = {1-5}, doi = {10.1016/s0895-4356(98)00137-1}, pmid = {9973067}, issn = {0895-4356}, mesh = {*Bias ; Confounding Factors, Epidemiologic ; *Data Interpretation, Statistical ; *Effect Modifier, Epidemiologic ; Humans ; *Models, Statistical ; Reproducibility of Results ; *Treatment Outcome ; }, } @article {pmid9894058, year = {1998}, author = {Woolston, JL and Berkowitz, SJ and Schaefer, MC and Adnopoz, JA}, title = {Intensive, integrated, in-home psychiatric services. The catalyst to enhancing outpatient intervention.}, journal = {Child and adolescent psychiatric clinics of North America}, volume = {7}, number = {3}, pages = {615-33, x}, pmid = {9894058}, issn = {1056-4993}, mesh = {Adolescent ; Child ; Child Health Services/*organization & administration ; Child, Preschool ; Community Mental Health Services/history/*organization & administration ; Community Networks ; Female ; Financial Management ; History, 20th Century ; Home Care Services/history/*organization & administration ; Humans ; Infant ; Male ; Models, Organizational ; Referral and Consultation ; United States ; }, abstract = {The authors introduce the Yale Intensive In-Home Child and Adolescent Psychiatric Service, a model of home-based care for children with severe psychiatric disturbances. This model synthesizes the principles and method of the wrap-around paradigm and in-patient child psychiatric practice within the reality of the managed care system. A clinical team, under the direct supervision of a child psychiatrist, works directly within the family to understand and address the multilevel transactions that have affected the child's ability to function in various domains and resulted in recommendations for intensive intervention, including psychiatric hospitalization. This article suggests that if the psychiatrist is to provide the highest level of care, cognizance of and involvement in the child's ecology are as essential for the child and adolescent psychiatrist as other aspects of the child's world and life. In the days of ever shortening patient lengths of stay, this model of care offers promise for both clinical and fiscal effectiveness.}, } @article {pmid9891179, year = {1999}, author = {Tengs, TO}, title = {Radiological imaging: research on cost-effectiveness and the cost-effectiveness of research.}, journal = {Academic radiology}, volume = {6 Suppl 1}, number = {}, pages = {S120-7}, doi = {10.1016/s1076-6332(99)80106-8}, pmid = {9891179}, issn = {1076-6332}, mesh = {Attitude to Health ; Clinical Trials as Topic ; Computer Simulation ; *Cost-Benefit Analysis ; Databases as Topic ; Decision Trees ; Diagnostic Imaging/*economics ; Genetic Techniques/economics ; Health Services Research/*economics ; Humans ; Models, Theoretical ; National Institutes of Health (U.S.) ; Outcome Assessment, Health Care/*economics ; Quality-Adjusted Life Years ; Randomized Controlled Trials as Topic ; Research ; Technology Assessment, Biomedical ; Technology, Radiologic ; Treatment Outcome ; United States ; }, } @article {pmid9889450, year = {1998}, author = {O'Dwyer, LA and Burton, DL}, title = {Potential meets reality: GIS and public health research in Australia.}, journal = {Australian and New Zealand journal of public health}, volume = {22}, number = {7}, pages = {819-823}, doi = {10.1111/j.1467-842x.1998.tb01500.x}, pmid = {9889450}, issn = {1326-0200}, mesh = {Australia ; Databases as Topic ; Geography ; Humans ; *Information Systems ; *Public Health ; Research ; }, abstract = {Geographical Information Systems-computerised systems for the capture, storage, retrieval, analysis and display of spatial data-have recently been promoted as important tools for the study of public health. Attention must also be given to the issues involved in this relatively new application, especially in Australian conditions. These include the coarse spatial resolution of most health and social data, the propagation of error through the need to use estimates and concordance tables to handle data in mismatched official spatial boundaries, the inflexible analytical capacity of most GIS for the needs of epidemiology, and difficulties in access to data, which are compounded by the absence of a good metadata register. The conflict between the need for spatial precision in GIS and preserving the confidentiality of health data is a salient issue. Medical geographers and public health researchers using GIS must recognise these issues in order to work together and toward extending the use of GIS technology beyond broad ecological and accessibility studies.}, } @article {pmid9878606, year = {1998}, author = {Dewdney, AK}, title = {A general theory of the sampling process with applications to the "veil line".}, journal = {Theoretical population biology}, volume = {54}, number = {3}, pages = {294-302}, doi = {10.1006/tpbi.1997.1370}, pmid = {9878606}, issn = {0040-5809}, mesh = {Animals ; Data Interpretation, Statistical ; Ecosystem ; Logistic Models ; *Models, Biological ; *Normal Distribution ; *Poisson Distribution ; *Population Dynamics ; Reproducibility of Results ; *Sampling Studies ; }, abstract = {When a community of species is sampled, nonappearing species are not those with abundances that fall shy of some arbitrary mark, the "veil line" proposed by E. F. Preston in 1948 (Ecology 29, 254-283). Instead, they follow a hypergeometric distribution, which has no resemblance to the veil line. There is therefore no justification for the truncation of distributions proposed to describe the abundances of species in natural communities. The mistake of the veil line points to the need for a general theory of sampling. If a community has a distribution g of species abundances and if samples taken of the community tend to follow distribution f, what is the relationship of f to g? The seeds of such a theory are available in the work of E. C. Pielou. Using the Poisson distribution as a close approximation to the hypergeometric, one may immediately write and (in most cases) solve the transformation from g to f. The transformation appears to preserve distribution formulas to within constants and parameters, providing yet another reason to rule out the use of truncation. Well beyond this application, the theory provides a foundation for rethinking the sampling process and its implications for ecology.}, } @article {pmid9847171, year = {1999}, author = {Maidak, BL and Cole, JR and Parker, CT and Garrity, GM and Larsen, N and Li, B and Lilburn, TG and McCaughey, MJ and Olsen, GJ and Overbeek, R and Pramanik, S and Schmidt, TM and Tiedje, JM and Woese, CR}, title = {A new version of the RDP (Ribosomal Database Project).}, journal = {Nucleic acids research}, volume = {27}, number = {1}, pages = {171-173}, doi = {10.1093/nar/27.1.171}, pmid = {9847171}, issn = {0305-1048}, mesh = {Base Sequence ; *Databases, Factual/trends ; Information Storage and Retrieval ; Internet ; Michigan ; Phylogeny ; *RNA, Ribosomal/chemistry/genetics ; Ribosomes/*genetics ; Sequence Alignment ; Universities ; }, abstract = {The Ribosomal Database Project (RDP-II), previously described by Maidak et al. [ Nucleic Acids Res. (1997), 25, 109-111], is now hosted by the Center for Microbial Ecology at Michigan State University. RDP-II is a curated database that offers ribosomal RNA (rRNA) nucleotide sequence data in aligned and unaligned forms, analysis services, and associated computer programs. During the past two years, data alignments have been updated and now include >9700 small subunit rRNA sequences. The recent development of an ObjectStore database will provide more rapid updating of data, better data accuracy and increased user access. RDP-II includes phylogenetically ordered alignments of rRNA sequences, derived phylogenetic trees, rRNA secondary structure diagrams, and various software programs for handling, analyzing and displaying alignments and trees. The data are available via anonymous ftp (ftp.cme.msu. edu) and WWW (http://www.cme.msu.edu/RDP). The WWW server provides ribosomal probe checking, approximate phylogenetic placement of user-submitted sequences, screening for possible chimeric rRNA sequences, automated alignment, and a suggested placement of an unknown sequence on an existing phylogenetic tree. Additional utilities also exist at RDP-II, including distance matrix, T-RFLP, and a Java-based viewer of the phylogenetic trees that can be used to create subtrees.}, } @article {pmid9735915, year = {1998}, author = {Malone, JB and Gommes, R and Hansen, J and Yilma, JM and Slingenberg, J and Snijders, F and Nachtergaele, F and Ataman, E}, title = {A geographic information system on the potential distribution and abundance of Fasciola hepatica and F. gigantica in east Africa based on Food and Agriculture Organization databases.}, journal = {Veterinary parasitology}, volume = {78}, number = {2}, pages = {87-101}, doi = {10.1016/s0304-4017(98)00137-x}, pmid = {9735915}, issn = {0304-4017}, mesh = {Africa, Eastern/epidemiology ; Animals ; Animals, Domestic/*parasitology ; Climate ; *Computer Simulation ; Crops, Agricultural ; *Databases, Factual ; Ecology ; Fascioliasis/economics/epidemiology/*veterinary ; Geography ; *Models, Biological ; Prevalence ; Risk Assessment ; United Nations ; }, abstract = {An adaptation of a previously developed climate forecast computer model and digital agroecologic database resources available from FAO for developing countries were used to develop a geographic information system risk assessment model for fasciolosis in East Africa, a region where both F. hepatica and F. gigantica occur as a cause of major economic losses in livestock. Regional F. hepatica and F. gigantica forecast index maps were created. Results were compared to environmental data parameters, known life cycle micro-environment requirements and to available Fasciola prevalence survey data and distribution patterns reported in the literature for each species (F. hepatica above 1200 m elevation, F. gigantica below 1800 m, both at 1200-1800 m). The greatest risk, for both species, occurred in areas of extended high annual rainfall associated with high soil moisture and surplus water, with risk diminishing in areas of shorter wet season and/or lower temperatures. Arid areas were generally unsuitable (except where irrigation, water bodies or floods occur) due to soil moisture deficit and/or, in the case of F. hepatica, high average annual mean temperature >23 degrees C. Regions in the highlands of Ethiopia and Kenya were identified as unsuitable for F. gigantica due to inadequate thermal regime, below the 600 growing degree days required for completion of the life cycle in a single year. The combined forecast index (F. hepatica+F. gigantica) was significantly correlated to prevalence data available for 260 of the 1220 agroecologic crop production system zones (CPSZ) and to average monthly normalized difference vegetation index (NDVI) values derived from the advanced very high resolution radiometer (AVHRR) sensor on board the NOAA polar-orbiting satellites. For use in Fasciola control programs, results indicate that monthly forecast parameters, developed in a GIS with digital agroecologic zone databases and monthly climate databases, can be used to define the distribution range of the two Fasciola species, regional variations in intensity and seasonal transmission patterns at different sites. Results further indicate that many of the methods used for crop productivity models can also be used to define the potential distribution and abundance of parasites.}, } @article {pmid9726494, year = {1998}, author = {Graeber, S and Feldmann, U}, title = {Medical information processing: an interactive course for the Internet.}, journal = {International journal of medical informatics}, volume = {50}, number = {1-3}, pages = {69-76}, doi = {10.1016/s1386-5056(98)00053-7}, pmid = {9726494}, issn = {1386-5056}, mesh = {*Education, Medical ; *Internet ; Learning ; Medical Informatics/*education ; Software ; }, abstract = {Medical students in Germany have to study the basics of medical information processing within a special curriculum which is part of the ecological course. This curriculum offers an introduction to principles of medical informatics. Starting with a conventional textbook, a computer-based training (CBT) program has been developed using the technologies of the internet and the World Wide Web (WWW). Features of the program include a well structured presentation of the information within the software and a high degree of interactivity. Early experiences suggest that this program enhances the learning in the domain of medical information processing. The program may be viewed via the URL: htfp.//www.med-rz.uni-sb.de/med_fak/imbei/pro jekt.}, } @article {pmid9720272, year = {1998}, author = {Nachman, MW}, title = {Deleterious mutations in animal mitochondrial DNA.}, journal = {Genetica}, volume = {102-103}, number = {1-6}, pages = {61-69}, pmid = {9720272}, issn = {0016-6707}, mesh = {Animals ; DNA, Mitochondrial/*genetics ; Databases as Topic ; *Evolution, Molecular ; Genetic Variation ; Humans ; *Models, Genetic ; Models, Statistical ; *Mutation ; *Polymorphism, Genetic ; }, abstract = {A simple neutral model predicts that the ratio of non-synonymous to synonymous fixed differences between species will be the same as the ratio of non-synonymous to synonymous polymorphisms within species. This prediction is tested with existing mitochondrial datasets from 25 animal species. In slightly over half of the studies, the ratio of replacement to silent polymorphisms within species is significantly greater than the ratio of replacement to silent fixed differences between species. These observations are best explained by a substantial number of mildly deleterious amino acid mutations that contribute to heterozygosity but rarely become fixed.}, } @article {pmid9691493, year = {1998}, author = {Cullings, KW and Vogler, DR}, title = {A 5.8S nuclear ribosomal RNA gene sequence database: applications to ecology and evolution.}, journal = {Molecular ecology}, volume = {7}, number = {7}, pages = {919-923}, doi = {10.1046/j.1365-294x.1998.00409.x}, pmid = {9691493}, issn = {0962-1083}, mesh = {Animals ; *Biological Evolution ; *Databases, Factual ; *Ecology ; Fungi/classification/genetics ; Phylogeny ; Plants/classification/genetics ; RNA, Ribosomal, 5.8S/classification/*genetics ; Sequence Analysis, DNA ; }, abstract = {We complied a 5.8S nuclear ribosomal gene sequence database for animals, plants, and fungi using both newly generated and GenBank sequences. We demonstrate the utility of this database as an internal check to determine whether the target organism and not a contaminant has been sequenced, as a diagnostic tool for ecologists and evolutionary biologists to determine the placement of asexual fungi within larger taxonomic groups, and as a tool to help identify fungi that form ectomycorrhizae.}, } @article {pmid9668414, year = {1998}, author = {Delaney-Black, V and Covington, C and Templin, T and Ager, J and Martier, S and Compton, S and Sokol, R}, title = {Prenatal coke: what's behind the smoke? Prenatal cocaine/alcohol exposure and school-age outcomes: the SCHOO-BE experience.}, journal = {Annals of the New York Academy of Sciences}, volume = {846}, number = {}, pages = {277-288}, pmid = {9668414}, issn = {0077-8923}, mesh = {Achievement ; *Alcoholism ; Child ; *Cocaine ; Databases as Topic ; Family ; Female ; Humans ; Infant, Newborn ; Interpersonal Relations ; Longitudinal Studies ; Pregnancy ; *Prenatal Exposure Delayed Effects ; *Psychology, Child ; *Smoking ; *Substance-Related Disorders ; United States ; United States Substance Abuse and Mental Health Services Administration ; }, abstract = {Despite media reports and educators' concerns, little substantive data have been published to document or refute the emerging reports that children prenatally exposed to cocaine have serious behavioral problems in school. Recent pilot data from this institution have indeed demonstrated teacher-reported problem behaviors following prenatal cocaine exposure after controlling for the effects of prenatal alcohol use and cigarette exposure. Imperative in the study of prenatal exposure and child outcome is an acknowledgement of the influence of other control factors such as postnatal environment, secondary exposures, and parenting issues. We report preliminary evaluation from a large ongoing historical prospective study of prenatal cocaine exposure on school-age outcomes. The primary aim of this NIDA-funded study is to determine if a relationship exists between prenatal cocaine/alcohol exposures and school behavior and, if so, to determine if the relationship is characterized by a dose-response relationship. A secondary aim evaluates the relationship between prenatal cocaine/alcohol exposures and school achievement. Both relationships will be assessed in a black, urban sample of first grade students using multivariate statistical techniques for confounding as well as mediating and moderating prenatal and postnatal variables. A third aim is to evaluate the relationship between a general standardized classroom behavioral measure and a tool designed to tap the effects thought to be specific to prenatal cocaine exposure. This interdisciplinary research team can address these aims because of the existence of a unique, prospectively collected perinatal Database, funded in part by NIAAA and NICHD. The database includes repeated measures of cocaine, alcohol, and other substances for over 3,500 births since 1986. Information from this database is combined with information from the database of one of the largest public school systems in the nation. The final sample will be composed of over 600 first grade students for whom the independent variables, prenatal cocaine/alcohol exposures, were prospectively assessed and quantified at the university maternity center. After informed consent, the primary dependent variable, school behavior, is assessed, using the PROBS-14 (a teacher consensus developed instrument), the Child Behavior Check List, and the Conners' Teacher Rating Scale. The secondary dependent measure, school achievement, is measured by the Metropolitan Achievement Text and the Test of Early Reading Ability. Control variables, such as the environment and parenting, are measured by several instruments aimed at capturing the child and family ecology since birth. All analyses will be adjusted as appropriate for prospectively gathered control variables such as perinatal risk, neonatal risk, and other prenatal drug and cigarette exposures. Further adjustment will be made for postnatal social risk factors which may influence outcome. Of particular concern are characteristics of the home (adaptation of HOME), parent (depression, stress), and neighborhood (violence exposure). Finally, postnatal exposure to lead and other drugs is being considered.}, } @article {pmid9662927, year = {1998}, author = {Maĭmulov, VG and Pivovarov, AN and Lomtev, AIu and Gorbanev, SA}, title = {[Use of geographic information systems in the evaluation of medical and ecological situation in a city].}, journal = {Meditsina truda i promyshlennaia ekologiia}, volume = {}, number = {5}, pages = {10-13}, pmid = {9662927}, issn = {1026-9428}, mesh = {Adult ; Cities ; *Ecology ; Environmental Monitoring ; *Environmental Pollution ; Geography ; Humans ; Industry ; *Information Systems ; Models, Theoretical ; Mortality ; Research ; Russia ; Software ; *Urban Health ; }, abstract = {Study using geoinformational technology provides integrity and compatibility of diverse information about territories, determines "cause-effect" relationships between environmental pollution parameters and some health state parameters. Intensive technogenic pollution with cadmium, zinc, mercury, copper, chromium, lead, benzpyrene, radionuclides could be assessed through data of ecologic and social hygienic monitoring and results of research works.}, } @article {pmid9560946, year = {1998}, author = {Eremin, AL}, title = {["Information ecology" snd human health under present-day conditions].}, journal = {Gigiena i sanitariia}, volume = {}, number = {1}, pages = {58-60}, pmid = {9560946}, issn = {0016-9900}, mesh = {Computer Communication Networks ; Disease/classification ; *Ecology ; Economics ; *Health ; Humans ; *Information Systems ; International Cooperation ; Mass Media ; Mental Disorders/etiology ; Occupational Diseases/etiology ; Occupations ; Politics ; Stress, Psychological/etiology ; }, } @article {pmid9533123, year = {1998}, author = {Butlin, RK and Tregenza, T}, title = {Levels of genetic polymorphism: marker loci versus quantitative traits.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {353}, number = {1366}, pages = {187-198}, pmid = {9533123}, issn = {0962-8436}, mesh = {Alleles ; Animals ; Biological Evolution ; Databases, Factual ; Enzymes/genetics ; Female ; Genetic Markers ; Genetic Variation ; Grasshoppers/anatomy & histology/genetics/physiology ; Heterozygote ; Insecta/genetics/physiology ; Male ; *Polymorphism, Genetic ; *Quantitative Trait, Heritable ; Sexual Behavior, Animal ; }, abstract = {Species are the units used to measure ecological diversity and alleles are the units of genetic diversity. Genetic variation within and among species has been documented most extensively using allozyme electrophoresis. This reveals wide differences in genetic variability within, and genetic distances among, species, demonstrating that species are not equivalent units of diversity. The extent to which the pattern observed for allozymes can be used to infer patterns of genetic variation in quantitative traits depends on the forces generating and maintaining variability. Allozyme variation is probably not strictly neutral but, nevertheless, heterozygosity is expected to be influenced by population size and genetic distance will be affected by time since divergence. The same is true for quantitative traits influenced by many genes and under weak stabilizing selection. However, the limited data available suggest that allozyme variability is a poor predictor of genetic variation in quantitative traits within populations. It is a better predictor of general phenotypic divergence and of postzygotic isolation between populations or species, but is only weakly correlated with prezygotic isolation. Studies of grasshopper and planthopper mating signal variation and assortative mating illustrate how these characters evolve independently of general genetic and morphological variation. The role of such traits in prezygotic isolation, and hence speciation, means that they will contribute significantly to the diversity of levels of genetic variation within and among species.}, } @article {pmid9532760, year = {1998}, author = {McGuigan, K and McDonald, K and Parris, K and Moritz, C}, title = {Mitochondrial DNA diversity and historical biogeography of a wet forest-restricted frog (Litoria pearsoniana) from mid-east Australia.}, journal = {Molecular ecology}, volume = {7}, number = {2}, pages = {175-186}, doi = {10.1046/j.1365-294x.1998.00329.x}, pmid = {9532760}, issn = {0962-1083}, mesh = {Animals ; Anura/*genetics ; Behavior, Animal ; Cohort Studies ; Conservation of Natural Resources ; DNA, Mitochondrial/chemistry/*genetics ; Data Interpretation, Statistical ; *Genetic Variation ; Natural History ; New South Wales ; Phylogeny ; Population Dynamics ; Queensland ; Sequence Alignment ; Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; Tropical Climate ; }, abstract = {MtDNA sequencing was used to investigate the genetic population structure of Litoria pearsoniana, a wet forest-restricted hylid frog, endemic to southeast Queensland and northeast New South Wales, Australia. L. pearsoniana is regarded as endangered under Queensland legislation. Significant genetic divergence among populations of frogs from different rainforest isolates was identified, but the lack of reciprocal monophyly among adjacent isolates suggests this is the result of a relatively recent disruption to gene flow. A paired catchment study within a single rainforest isolate, the Conondale Range, revealed no substantial genetic structuring, indicating the occurrence of terrestrial dispersal among nearby streams either in the recent past or currently. Two major reciprocally monophyletic clades of mtDNA alleles were identified. These corresponded to two geographical regions separated by the Brisbane River valley; one consisting of the Conondale and D'Aguilar Ranges, and the other of the southern isolates in the Main, Border and Gibraltar Ranges. Sequence divergence between the two regions was more consistent with a late Miocene or Pliocene rather than late Pleistocene separation, and is similar to that found among phylogeographic divisions of rainforest reptiles and amphibians in north Queensland rainforests. The molecular evidence for long-term separation of these two regions is corroborated by the pattern of species turnover in the distributions of species of rainforest-restricted amphibians and reptiles. Bioclimatic modelling suggests that appropriate conditions for L. pearsoniana would have been restricted to isolated refugees in each phylogeographic division under cooler and drier climates, such as predicted for the last glacial maximum. Currently isolated montane areas may have been connected transiently during the past 2000 years. Identification of long-term zoogeographic divisions among southeast Queensland rainforest herpetofauna has important implications for conservation and management. Conservation management of L. pearsoniana should be applied at the scale of major rainforest isolates and the conservation status of the species should be assessed independently north and south of the historical division.}, } @article {pmid9511843, year = {1998}, author = {Slade, GD}, title = {Assessing change in quality of life using the Oral Health Impact Profile.}, journal = {Community dentistry and oral epidemiology}, volume = {26}, number = {1}, pages = {52-61}, doi = {10.1111/j.1600-0528.1998.tb02084.x}, pmid = {9511843}, issn = {0301-5661}, support = {R01-DE09588/DE/NIDCR NIH HHS/United States ; }, mesh = {Aged ; Analysis of Variance ; Data Interpretation, Statistical ; Dental Care/economics/statistics & numerical data ; *Health Transition ; Humans ; Incidence ; Middle Aged ; *Oral Health ; Poverty ; *Quality of Life ; Regression Analysis ; Risk Factors ; *Sickness Impact Profile ; South Australia/epidemiology ; Surveys and Questionnaires ; Tooth Loss/epidemiology ; }, abstract = {UNLABELLED: Traditionally, longitudinal studies of oral health have measured only disease progression and ignored improvements in health.

OBJECTIVES: This study examines methodological issues that arise in longitudinal assessment of change in oral health-related quality of life (OHRQOL).

METHODS: Baseline and 2-year follow-up data were used from an observational longitudinal study of 498 people aged 60 years or more living in South Australia. Oral health-related quality of life was measured using the Oral Health Impact Profile (OHIP). Three hypothesized risk predictors (tooth loss, problem-based dental visits and financial hardship) were selected to examine the effects of four methods of measuring change: categorical measures of improvement, deterioration and net change, and a quantitative measure of net change in OHIP scores.

RESULTS: Some 31.7% of people experienced some improvement and 32.7% experienced some deterioration in OHRQOL. All three high-risk groups had approximately twice the rate of deterioration in OHRQOL compared with their corresponding low-risk groups. Surprisingly, high-risk groups also had higher rates of improvement. When measured categorically, these effects did not cancel one another, indicating that improvement and deterioration in OHRQOL can be experienced simultaneously. However, quantitative analyses cause improvements and deteriorations to cancel, and analysis of mean OHIP scores created a spurious impression that change in OHRQOL did not differ between dental visit groups. Furthermore, changes in mean OHIP scores were masked by regression to the mean.

CONCLUSIONS: Oral health-related quality of life measures capture both improvement and deterioration in health status, creating new complexities for conceptualizing and analyzing change in longitudinal studies.}, } @article {pmid9467639, year = {1997}, author = {Lushnikova, EL and Molodykh, OP and Nepomniashchikh, LM}, title = {[Morphological study of the liver of mice-like rodents from areas of the Altai region exposed to radioactive pollution].}, journal = {Radiatsionnaia biologiia, radioecologiia}, volume = {37}, number = {6}, pages = {860-869}, pmid = {9467639}, issn = {0869-8031}, mesh = {Animals ; Arvicolinae ; Data Interpretation, Statistical ; Ecology ; Liver/metabolism/*radiation effects/ultrastructure ; Liver Glycogen/metabolism/radiation effects ; Male ; Mitochondria, Liver/metabolism/radiation effects ; *Nuclear Warfare ; Organelles/metabolism/radiation effects ; *Radioactive Fallout ; Siberia ; }, abstract = {Morphofunctional liver state of two mice-like rodents species caught at the three areas of Altai region exposed to radiation during nuclear tests at Semipalatinsk site was studied. It was shown that the stereotype morphofunctional changes in the liver of both rodent species were developed under chronic influence of low doses of radiation and chemical contamination. These changes are manifested as dystrophic disorders of hepatocytes and hemodynamic disturbances accompanied by a decrease of volume ratio of sinusoidal capillaries to hepatocytes and stroma to parenchyma. Hyperglycogenosis, redistribution of the main cytoplasmic organelles, and considerably reduction of the volume densities of mitochondria, smooth and rough endoplasmic reticulum are the leading ultrastructural changes. Moreover, character and manifestation of the changes are determined by ecological belonging and correlated with intensity of anthropogenic pollution. The role of these changes in development of long-term pathology are discussed.}, } @article {pmid9459065, year = {1998}, author = {Schwartz, JE and Stone, AA}, title = {Strategies for analyzing ecological momentary assessment data.}, journal = {Health psychology : official journal of the Division of Health Psychology, American Psychological Association}, volume = {17}, number = {1}, pages = {6-16}, doi = {10.1037//0278-6133.17.1.6}, pmid = {9459065}, issn = {0278-6133}, support = {P01 HL047540/HL/NHLBI NIH HHS/United States ; HL47540/HL/NHLBI NIH HHS/United States ; MH49490/MH/NIMH NIH HHS/United States ; }, mesh = {Analysis of Variance ; *Behavioral Medicine ; Data Interpretation, Statistical ; Effect Modifier, Epidemiologic ; Humans ; *Models, Statistical ; Psychometrics/*methods ; Regression Analysis ; Research Design ; }, abstract = {Studies incorporating repeated observations of momentary phenomena are becoming more common in behavioral and medical science. Analysis of such data requires the use of statistical techniques that are unfamiliar to many investigators. Some common ways of analyzing momentary data are reviewed--aggregation strategies, repeated measures analysis of variance, pooled within-person regression, and two-stage estimation procedures for multilevel models--and are found to be usually suboptimal, possibly leading to incorrect inferences. A broad class of statistical models for multilevel data that can address many research questions typically asked of momentary data are then described. Analytic issues that merit careful consideration include the scaling of momentary variables, allowance for serial autocorrelation of residuals, and the treatment of coefficients that vary across individuals as fixed versus random effects.}, } @article {pmid9433661, year = {1997}, author = {Kinney, A and Fitzgerald, E and Hwang, S and Bush, B and Tarbell, A}, title = {Human exposure to PCBS: modeling and assessment of environmental concentrations on the Akwesasne reservation.}, journal = {Drug and chemical toxicology}, volume = {20}, number = {4}, pages = {313-328}, doi = {10.3109/01480549709003890}, pmid = {9433661}, issn = {0148-0545}, mesh = {Animals ; Databases as Topic ; Ecology ; Environmental Exposure/*analysis ; Environmental Monitoring ; Female ; Fishes ; Humans ; Indians, North American ; Industry ; New York ; Polychlorinated Biphenyls/*analysis ; Risk Assessment ; }, abstract = {The Mohawk Nation at Akwesasne, comprised of approximately 10,000 people, is located along the St. Lawrence River in upstate New York. The Akwesasne reservation has been contaminated by local industries, which are located on the St. Lawrence River and its tributaries, and by upstream sources on the Great Lakes. The closest known source of contamination to the reservation is General Motors (GM) Foundry, which is located less than 100 feet from the reservation's border. This facility is listed on the Environmental Protection Agency's National Priority List and the New York State's Department of Environmental Conservation's (NYSDEC) inactive hazardous waste disposal site list. Contamination to the reservation arising from discharge and secondary transport mechanisms has caused concern to the Mohawk people of Akwesasne. The characterization of the environment at Akwesasne required a historical review of existing environmental data, generation of a database, review of existing data, sampling to augment existing data, data analysis, data modeling and data generation based on a chosen model for all environmental pathways of interest. The objectives this work were to: 1) assess the quality of existing data, 2) create a database which will manage the over 6000 samples recorded taken from the local area, 3) augment the existing data with additional sampling, 4) determine the degradation or attenuation of PCBs and specific congeners in various environmental media over time, and 5) create a model that estimates environmental concentrations of PCBs retro- and pro-spectively for times that sampling had not occurred. The results of this process yielded concentrations of PCBs, congener specific and total, in several environmental medium. Modeling of environmental concentrations through a thirteen-year time period was performed for a fish, wildlife and surface soil. Other media were not modeled due to limited information or non-detectable concentrations reported in past work. Additionally, the study participants activity, consumption and residential information was considered when limiting this modeling effort. The results of this work were used to estimate environmental concentrations through time and space. The results of this work were extremely valuable when determining areas of concern and provided the basis for a detailed exposure assessment of 97 women who reside at the Reservation.}, } @article {pmid9368515, year = {1997}, author = {Suissa, S and Ernst, P}, title = {Optical illusions from visual data analysis: example of the New Zealand asthma mortality epidemic.}, journal = {Journal of clinical epidemiology}, volume = {50}, number = {10}, pages = {1079-1088}, doi = {10.1016/s0895-4356(97)00158-3}, pmid = {9368515}, issn = {0895-4356}, mesh = {Administration, Inhalation ; Adolescent ; Adrenal Cortex Hormones/*adverse effects ; Adrenergic beta-Agonists/*adverse effects ; Adult ; Asthma/*epidemiology/etiology/*mortality ; Bronchodilator Agents/*adverse effects ; Child ; Child, Preschool ; Data Interpretation, Statistical ; Ecology ; Epidemiologic Methods ; Fenoterol/*adverse effects ; Humans ; New Zealand/epidemiology ; Regression Analysis ; Statistics as Topic/*methods ; }, abstract = {The abundance of health-related statistics routinely collected worldwide invites their misuse from haphazard associations between secular trends of these data. This misuse is often compounded by assessing these associations simply on the basis of a visual inspection of the data. The visual approach to data analysis, known to have several pitfalls, is particularly tempting in the context of asthma where it has often been used. For example, the epidemic of asthma deaths that occurred in New Zealand during the last two decades has been imputed to fenoterol, a medication for asthma, on the basis of a visual assessment of ecological data. The simultaneity of time trends in the asthma death rate and fenoterol market share in that country formed an important part of the statistical basis of the evidence. We verified whether the results of such visual analyses are corroborated by more objective quantitative statistical methods of analysis. We reanalyzed these same data, namely the time trend data of New Zealand asthma death rates, fenoterol market share, sales of beta-agonists and inhaled corticosteroids, measured yearly for the 16-year span 1976-1991, using Poisson weighted loglinear regression. We found that the protective effect of inhaled corticosteroids (rate ratio 0.5 per canister per month; 95% confidence interval 0.4 to 0.7; p = 0.0001) was more closely associated with changes in asthma mortality than either fenoterol (RR 2.7 per canister per month; 95% CI: 0.9 to 7.5; p = 0.06) or all beta-agonists combined (RR 1.6; 95% CI: 0.8 to 3.0; p = .19). We conclude from this quantitative analysis that these ecological asthma mortality data provide evidence of a stronger association with inhaled corticosteroids, little used in New Zealand at the onset of the epidemic but used abundantly at its termination, than with fenoterol. This conclusion is diametrically opposite to that found by the visual approach. The quantitative analysis demonstrates that the visual approach to the analysis of ecological data, although seemingly convincing, can be misleading by creating an optical illusion. This purely visual approach to data analysis may thus have serious implications when the resulting scientific information is used to make vital public health and policy decisions.}, } @article {pmid9336922, year = {1997}, author = {Palys, T and Nakamura, LK and Cohan, FM}, title = {Discovery and classification of ecological diversity in the bacterial world: the role of DNA sequence data.}, journal = {International journal of systematic bacteriology}, volume = {47}, number = {4}, pages = {1145-1156}, doi = {10.1099/00207713-47-4-1145}, pmid = {9336922}, issn = {0020-7713}, mesh = {Bacteria/*classification/*genetics ; Cluster Analysis ; DNA, Bacterial/*analysis ; Databases as Topic ; Genes, Bacterial/genetics ; *Genetic Variation ; Genetics, Population ; *Models, Genetic ; Phylogeny ; *Sequence Analysis, DNA ; }, abstract = {All living organisms fall into discrete clusters of closely related individuals on the basis of gene sequence similarity. Evolutionary genetic theory predicts that in the bacterial world, each sequence similarity cluster should correspond to an ecologically distinct population. Indeed, surveys of sequence diversity in protein-coding genes show that sequence clusters correspond to ecological populations. Future population surveys of protein-coding gene sequences can be expected to disclose many previously unknown ecological populations of bacteria. Sequence similarity clustering in protein-coding genes is recommended as a primary criterion for demarcating taxa.}, } @article {pmid9300520, year = {1997}, author = {Neeleman, J and Halpern, D and Leon, D and Lewis, G}, title = {Tolerance of suicide, religion and suicide rates: an ecological and individual study in 19 Western countries.}, journal = {Psychological medicine}, volume = {27}, number = {5}, pages = {1165-1171}, doi = {10.1017/s0033291797005357}, pmid = {9300520}, issn = {0033-2917}, support = {//Wellcome Trust/United Kingdom ; }, mesh = {Adult ; Analysis of Variance ; Attitude to Health/*ethnology ; Chi-Square Distribution ; Confidence Intervals ; *Cross-Cultural Comparison ; Data Collection ; Databases, Factual ; Europe/epidemiology ; Female ; Humans ; Likelihood Functions ; Male ; North America/epidemiology ; Odds Ratio ; Regression Analysis ; *Religion and Psychology ; Sampling Studies ; Sex Factors ; *Social Values ; Socioeconomic Factors ; *Suicide/ethnology/psychology/statistics & numerical data ; }, abstract = {BACKGROUND: Negative associations between religion and suicide, in individuals and countries, may be mediated by the degree to which suicide is tolerated.

METHODS: Linear regression was used to examine ecological associations between suicide tolerance, religion and suicide rates in 19 Western countries in 1989/90. Logistic regression was used to study associations between suicide tolerance and strength of religious belief in 28085 individuals in these countries. The concept of effect modifying function was used to examine whether the strength of the association between suicide tolerance and religious belief in individuals depended on the extent of religious belief in their country.

RESULTS: Higher female suicide rates were associated with lower aggregate levels of religious belief and, less strongly, religious attendance. These associations were mostly attributable to the association between higher tolerance of suicide and higher suicide rates. In the 28085 subjects suicide tolerance and the strength of religious belief were negatively associated even after adjustment for other religious and sociodemographic variables and general tolerance levels (odds ratios: men 0.74 (95% CI 0.58-0.94), women 0.72 (95% CI 0.60-0.86)). This negative individual-level association was more pronounced in more highly religious countries but this modifying effect of the religious context was apparent for men only.

CONCLUSIONS: Ecological associations between religious variables and suicide rates are stronger for women than men, stronger for measures of belief than observance and mediated by tolerance of suicide. In individuals, stronger religious beliefs are associated with lower tolerance of suicide. Personal religious beliefs and, for men, exposure to a religious environment, may protect against suicide by reducing its acceptability.}, } @article {pmid9208164, year = {1997}, author = {Pikhart, H and Príkazský, V and Bobák, M and Kríz, B and Celko, M and Danová, J and Pyrl, K and Pretel, J}, title = {Association between ambient air concentrations of nitrogen dioxide and respiratory symptoms in children in Prague, Czech Republic. Preliminary results from the Czech part of the SAVIAH Study. Small Area Variation in Air Pollution and Health.}, journal = {Central European journal of public health}, volume = {5}, number = {2}, pages = {82-85}, pmid = {9208164}, issn = {1210-7778}, mesh = {Air Pollution/*adverse effects/analysis ; Child ; Czech Republic/epidemiology ; Female ; Humans ; *Information Systems ; Least-Squares Analysis ; Logistic Models ; Male ; Nitrogen Dioxide/*adverse effects/analysis ; Odds Ratio ; Prevalence ; Respiratory Tract Diseases/*epidemiology ; Risk Factors ; *Small-Area Analysis ; Socioeconomic Factors ; Vehicle Emissions/adverse effects ; }, abstract = {The primary objective of the SAVIAH, a multi-centre study funded by European Union, was to assess new methodology for study of small area health statistics and to implement it in epidemiological health statistics and geography. In Prague, the study has been conducted in two city districts with large variation in air pollution. Data at individual level (health symptoms and socio-economic circumstances of the family) were collected by questionnaires completed by parents of 3680 children aged 7-10 both resident and attending schools within the area (response rate 88%). Aggregated data for geographical areas were available from census and urban planning sources for 692 enumeration districts in the study area which were aggregated into 75 medium sized areas. Outdoor concentrations of nitrogen dioxide (NO2) were monitored by passive samplers. All these data were integrated into a geographic information system (GIS). Spatial distribution of air pollution was estimated by kriging and multiple regression modelling. These models explained about 80% of the variation in air pollution measured by passive samplers. GIS was then used to assign to individuals an exposure based on place of residence and school in order to conduct individual based analyses. Association between NO2 and life-time prevalence of wheezing and/or whistling, and wheezing/whistling in the last 12 months was studied by logistic regression. For both outcomes, school levels of NO2 were positively related to symptoms but home levels of NO2 showed a negative association. Logistic regression at individual level gives similar results as ecological analysis and multilevel modelling. Hierarchical model yielded somewhat wider confidence limits. Adjustment for parental behavioural and socio-economic factors did not affect these estimates substantially. This study demonstrated the power of the GIS methodology in studying the effects of complex environmental factors on respiratory health of children.}, } @article {pmid9304225, year = {1997}, author = {Narro-Robles, J and Gutiérrez-Avila, JH}, title = {[Ecological correlation between consumption of alcoholic beverages and liver cirrhosis mortality in Mexico].}, journal = {Salud publica de Mexico}, volume = {39}, number = {3}, pages = {217-220}, pmid = {9304225}, issn = {0036-3634}, mesh = {Adolescent ; Adult ; Age Factors ; Aged ; *Alcohol Drinking ; Alcoholic Beverages ; Beer ; Child ; Data Interpretation, Statistical ; Ecology ; Female ; Humans ; Liver Cirrhosis/etiology/*mortality ; Liver Cirrhosis, Alcoholic/etiology/mortality ; Male ; Mexico ; Middle Aged ; Sex Factors ; }, abstract = {OBJECTIVE: To determine the correlation between alcohol consumption and mortality from liver cirrhosis in Mexico.

MATERIAL AND METHODS: Analysis of the ecological correlation between the patterns of alcohol consumption determined by the National Addiction Survey in 1993 and mortality by liver cirrhosis, in the period between 1971-1993, in the eight regions in which the country was divided. To determine level of correlation, the Pearson and Spearman coefficients were calculated.

RESULTS: Significant correlations were only found with the prevalence of spirits and pulque drinkers; with beer drinkers the correlation was negative.

CONCLUSIONS: The correlation with pulque is interesting, since pulque consumption is considered to be low scale in some rural areas. The negative correlation with beer may indicate that beer drinking is nor a good indicator of alcoholism. Results, though limited to the possibilities of an ecological study, reveal the necessity of effective actions in the regions where spirits and pulque are consumed in excess.}, } @article {pmid9569938, year = {1997}, author = {Haas, CN and Kersten, SP and Wright, K and Frank, MJ and Cidambi, K}, title = {Generalization of independent response model for toxic mixtures.}, journal = {Chemosphere}, volume = {34}, number = {4}, pages = {699-710}, doi = {10.1016/s0045-6535(97)00462-1}, pmid = {9569938}, issn = {0045-6535}, mesh = {Animals ; Benzofurans/toxicity ; Cleft Palate/chemically induced ; Data Interpretation, Statistical ; Drug Antagonism ; *Drug Interactions ; Drug Synergism ; *Drug-Related Side Effects and Adverse Reactions ; Humans ; Hydrocarbons, Chlorinated ; Insecticides/toxicity ; Mice ; Mice, Inbred C57BL ; Models, Theoretical ; Polychlorinated Dibenzodioxins/toxicity ; }, abstract = {Interaction between toxic compounds has long been known to researchers. Attempts to model this interaction have been based on two basic paradigms--termed additivity and independence (1, 2). Previous models based on these assumptions focused on measuring the interaction between the compounds and then classifying the type of interaction as synergism, antagonism, additivity or independence (3, 4). The aim of this work is to present a generalization of the independent action hypothesis that is quantitatively capable of describing deviations regardless of the underlying single component dose response models. The mathematical framework of copulas is employed. This approach is then tested against data sets with both human health and ecological risk applications.}, } @article {pmid9126498, year = {1997}, author = {Ness, AR and Powles, JW}, title = {Fruit and vegetables, and cardiovascular disease: a review.}, journal = {International journal of epidemiology}, volume = {26}, number = {1}, pages = {1-13}, doi = {10.1093/ije/26.1.1}, pmid = {9126498}, issn = {0300-5771}, support = {//Wellcome Trust/United Kingdom ; }, mesh = {Cardiovascular Diseases/epidemiology/*prevention & control ; Case-Control Studies ; Cerebrovascular Disorders/epidemiology/*prevention & control ; Clinical Trials as Topic ; Cohort Studies ; Female ; *Fruit ; Humans ; Incidence ; MEDLINE ; Male ; Prospective Studies ; *Vegetables ; }, abstract = {BACKGROUND: Increased interest in the potential cardio-protective effects of fruit and vegetables is currently unsupported by systematic reviews of the reported associations of these foods with risk.

METHOD: All ecological, case-control, cohort studies and unconfounded trials in humans were eligible for inclusion. Eligible outcomes were symptomatic coronary heart disease, stroke and total circulatory disease. Only studies of diet that reported on fresh fruit and vegetables or a nutrient which could serve as a proxy (reversing the usual direction of inference) were included. MEDLINE (1966-1995) and EMBASE (1980-1995) were searched using the terms cerebrovascular disorder, coronary heart disease, fruit(s) and vegetable(s) as keywords. Personal bibliographies, books and reviews were also searched, as were citations in located reports.

RESULTS: For coronary heart disease nine of ten ecological studies, two of three case-control studies and six of 16 cohort studies found a significant protective association with consumption of fruit and vegetables or surrogate nutrients. For stroke three of five ecological studies, none (of one) case-control study and six of eight cohort studies found a significant protective association with consumption of fruit and vegetables or surrogate nutrients. For total circulatory disease, one of two cohort studies reported a significant protective association. No attempt was made to arrive at a summary measure of the association because of the differences in study type, study quality and the different exposure measures used.

CONCLUSIONS: Although null findings may be underreported the results are consistent with a strong protective effect of fruit and vegetables for stroke and a weaker protective effect on coronary heart disease. Greater use of food-based hypotheses and analyses, would complement existing nutrient-based analyses and help guide the search for underlying causes.}, } @article {pmid9056395, year = {1997}, author = {Belanger, SE}, title = {Literature review and analysis of biological complexity in model stream ecosystems: influence of size and experimental design.}, journal = {Ecotoxicology and environmental safety}, volume = {36}, number = {1}, pages = {1-16}, doi = {10.1006/eesa.1996.1487}, pmid = {9056395}, issn = {0147-6513}, mesh = {Animals ; Biomass ; Databases, Factual ; *Ecosystem ; Eukaryota/drug effects/*growth & development/metabolism ; Fishes/growth & development ; Hazardous Substances/*analysis/toxicity ; Invertebrates/drug effects/*growth & development/metabolism ; Models, Biological ; Reference Values ; Research Design ; Risk Assessment ; Sample Size ; Water Pollutants, Chemical/*analysis/toxicity ; }, abstract = {A meta-analysis of more than 150 model stream ecosystem studies employed in hazard assessment was conducted to assess the effect of model ecosystem size on biological complexity and experimental design. Test system length was highly correlated to duration of colonization and chemical exposure period; however, size was generally unrelated to taxa richness, diversity, abundance, or biomass for algal, protozoan, and invertebrate assemblages. Fish were usually caged and not free-roaming, even in the relatively large (> 10 m) systems. Experimental designs, especially in recent years, have been less concerned with pseudoreplication, resulting in studies emphasizing numerous treatments with few or no replicates. Test systems have evolved that emphasize flow through exposures, use of natural source waters, and regression-style experimental designs. These factors collectively reduce problems historically associated with pseudoreplication. Larger model ecosystems (> 6 m) are advantageous for increasing the ability to sample more intensively through time and space without imposing sampling artifacts. Fish (caged and free-roaming) are also more often used in larger systems. Several model ecosystem studies that were compared with natural field-based communities demonstrated a high degree of correspondence for biological complexity attributes. Well-designed model stream ecosystems have a high degree of biological complexity and reasonable levels of variability for ecologically relevant endpoints. The use of small application factors (approximately equal to 1) is applicable to ecotoxicological results from these studies for risk assessment.}, } @article {pmid8994023, year = {1997}, author = {Levin, SA and Grenfell, B and Hastings, A and Perelson, AS}, title = {Mathematical and computational challenges in population biology and ecosystems science.}, journal = {Science (New York, N.Y.)}, volume = {275}, number = {5298}, pages = {334-343}, doi = {10.1126/science.275.5298.334}, pmid = {8994023}, issn = {0036-8075}, support = {AI28433/AI/NIAID NIH HHS/United States ; RR06555/RR/NCRR NIH HHS/United States ; }, mesh = {Acquired Immunodeficiency Syndrome/virology ; *Allergy and Immunology ; Animals ; Biological Evolution ; Communicable Diseases/transmission ; *Computational Biology ; Computer Simulation ; *Ecology ; *Epidemiology ; *Genetics ; Humans ; Models, Biological ; *Virology ; }, abstract = {Mathematical and computational approaches provide powerful tools in the study of problems in population biology and ecosystems science. The subject has a rich history intertwined with the development of statistics and dynamical systems theory, but recent analytical advances, coupled with the enhanced potential of high-speed computation, have opened up new vistas and presented new challenges. Key challenges involve ways to deal with the collective dynamics of heterogeneous ensembles of individuals, and to scale from small spatial regions to large ones. The central issues-understanding how detail at one scale makes its signature felt at other scales, and how to relate phenomena across scales-cut across scientific disciplines and go to the heart of algorithmic development of approaches to high-speed computation. Examples are given from ecology, genetics, epidemiology, and immunology.}, } @article {pmid9377045, year = {1997}, author = {Khamitov, RZ and Pavlov, SV and Gvozdev, VE}, title = {[An information support system for managing the environmental status in the Republic of Bashkortostan].}, journal = {Meditsina truda i promyshlennaia ekologiia}, volume = {}, number = {8}, pages = {1-5}, pmid = {9377045}, issn = {1026-9428}, mesh = {Bashkiria ; Computer Simulation ; *Environmental Monitoring ; Environmental Pollution/prevention & control/statistics & numerical data ; Information Systems/*organization & administration ; Models, Theoretical ; }, abstract = {The main function of informational system supporting environmental control in Bashkortostan Republic is to prevent and liquidate accidents, to provide operative and complete information on current and future state of environment. Functioning of the system is supported by geological informational structure, ecologic databases, space information processor, broad system of mathematic models incorporated into local computer network.}, } @article {pmid9150061, year = {1997}, author = {Caplan, DJ and Weintraub, JA}, title = {Factors related to loss of root canal filled teeth.}, journal = {Journal of public health dentistry}, volume = {57}, number = {1}, pages = {31-39}, doi = {10.1111/j.1752-7325.1997.tb02470.x}, pmid = {9150061}, issn = {0022-4006}, support = {5T32DE07191-05/DE/NIDCR NIH HHS/United States ; }, mesh = {Adult ; Age Factors ; Case-Control Studies ; Dental Plaque/epidemiology ; Dental Records ; Facial Injuries/epidemiology ; Female ; Health Maintenance Organizations ; Humans ; Information Systems ; Logistic Models ; Male ; Middle Aged ; Multivariate Analysis ; Odds Ratio ; Oregon/epidemiology ; Patient Care Planning ; Radiography ; Retrospective Studies ; Risk Assessment ; Risk Factors ; Root Canal Therapy/*statistics & numerical data ; Tooth/diagnostic imaging ; Tooth Loss/*epidemiology/etiology ; }, abstract = {OBJECTIVES: This case-control study characterized factors related to loss of root canal filled (RCF) teeth among members of the Kaiser Permanente Dental Care Program, a dental health maintenance organization based in Portland, Oregon.

METHODS: Individuals were identified who were enrolled continuously from January 1, 1987, through December 31, 1994, underwent initial root canal therapy on a permanent tooth (excluding third molars) in 1987 or 1988, had a clinical examination within two years after endodontic access, and were at least 21 years old at access. Patients who lost the RCF tooth by December 31, 1994, were defined as cases (n = 96); those who did not were defined as controls (n = 120). Computerized data, dental radiographs, and chart entries were reviewed to ascertain variables of interest, and multivariable logistic regression was used to describe differences between the groups.

RESULTS: RCF teeth of cases had fewer proximal contacts at access than RCF teeth of controls (odds ratio = 2.7; 95% Cl = 1.4, 5.1). Cases were older (odds ratio = 1.4; 95% Cl = 1.1, 1.9 per 10-year increase) and more likely to have had a facial injury than controls (odds ratio = 3.6; 95% Cl = 1.2, 10.5). Cases also had more missing teeth (odds ratio = 1.5; 95% Cl = 1.0, 2.1) and more plaque (odds ratio = 1.7; 95% Cl = 1.0, 2.6).

CONCLUSIONS: Conditions evident during treatment planning may help dentists assess patients' chances of losing an RCF tooth.}, } @article {pmid9072150, year = {1997}, author = {Shafran, LM and Murakhovskaia, LI}, title = {[The information-search system on industrial ecology of transport].}, journal = {Meditsina truda i promyshlennaia ekologiia}, volume = {}, number = {1}, pages = {19-23}, pmid = {9072150}, issn = {1026-9428}, mesh = {Air Pollutants, Occupational/adverse effects ; *Ecology ; *Environmental Pollution ; Humans ; *Information Systems ; Latvia ; Lithuania ; *Naval Medicine ; Occupational Diseases/chemically induced/*etiology ; Russia ; *Ships ; }, abstract = {The authors elaborated an informational search system managing some problems of industrial ecology in transport. Using ecologic survey in Baltic and Black Sea ports as an example, the authors revealed a correlation of morbidity among the workers and population with the air pollution, amounts and character of hazardous loads treated in the ports.}, } @article {pmid8997531, year = {1996}, author = {Bláha, K and Bencko, V and Cikrt, M}, title = {Exposure to lead and human health in the Czech Republic.}, journal = {Central European journal of public health}, volume = {4}, number = {4}, pages = {233-241}, pmid = {8997531}, issn = {1210-7778}, mesh = {Aged ; Biomarkers ; Central Nervous System/drug effects ; Child ; Child, Preschool ; Community Networks ; Czech Republic/epidemiology ; Environmental Exposure/analysis/*prevention & control ; Environmental Monitoring/*methods ; Epidemiological Monitoring ; Erythropoiesis/drug effects ; Female ; Health Education ; Heme/biosynthesis ; Humans ; Infant ; Infant, Newborn ; Lead/metabolism/pharmacology ; Lead Poisoning/physiopathology/*prevention & control ; Mass Screening ; Middle Aged ; Pregnancy ; Risk Factors ; }, abstract = {The aim of presented review is to address the most relevant issues related to the health effects caused by the human exposure to lead, as they have been recognized in Czech Republic in the period of 1992-1994 within the framework of the National Integrated Programme on Environment and Health (NIPEH) approved in 1992 and supported by WHO-European Centre for Environment and Health (WHO-ECEH), Bilthoven, The Netherlands and by the Government of the Netherlands. Basic sources of environment exposure to lead are identified and the fate of lead in the individual compartments of the environment is discussed. Relevant methods used for the exposure evaluation are summarized and the highest-risk group of population is defined. Attention is being paid to the effects of the long-term exposure to low lead levels, while other exposure settings are intentionally omitted. Interventional measures developed in the Czech Republic in attempt to reduce the environmental exposure are introduced. Instead of presenting specific data, current state-of-art and general trends are presented; list of references tries to combine the internationally recognized studies with those coming from national sources.}, } @article {pmid8931201, year = {1996}, author = {Gail, MH}, title = {Use of observational data, including surveillance studies, for evaluating AIDS therapies.}, journal = {Statistics in medicine}, volume = {15}, number = {21-22}, pages = {2273-2288}, doi = {10.1002/(SICI)1097-0258(19961115)15:21<2273::AID-SIM448>3.0.CO;2-3}, pmid = {8931201}, issn = {0277-6715}, mesh = {Acquired Immunodeficiency Syndrome/*drug therapy/*epidemiology/mortality ; Anti-HIV Agents/*therapeutic use ; Data Collection/methods ; Data Interpretation, Statistical ; Evaluation Studies as Topic ; Humans ; Incidence ; Male ; Observation ; Population Surveillance ; United States/epidemiology ; Zidovudine/*therapeutic use ; }, abstract = {This article discusses some of the limitations of observational data for assessing therapeutic effects and categorizes observational studies according to the strength of evidence. Ecologic studies based on AIDS surveillance registries have demonstrated improvements over time in median survival following the onset of AIDS, especially for patients with an initial diagnosis of Pneumocystis carinii pneumonia. Some of this improvement may be the result of secular changes in the stage of disease at diagnosis or in the completeness of detection of deaths in these cohorts, however. Other ecologic studies of the use of AZT in various subgroups strongly suggest that treatment had a favorable impact on US AIDS incidence rates in gay men in the year beginning July 1987. This article is reprinted with minor changes from Chapter 24 of AIDS Clinical Trials.}, } @article {pmid9036087, year = {1996}, author = {Bol'shakov, AM and Krut'ko, VN and Cherepov, EM and Skvortsova, EL}, title = {[Methodological approaches to the creation of a system of social-hygienic monitoring: aims, tasks and scenarios of the utilization of the system].}, journal = {Gigiena i sanitariia}, volume = {}, number = {6}, pages = {45-48}, pmid = {9036087}, issn = {0016-9900}, mesh = {Computer Systems ; Data Interpretation, Statistical ; Ecology ; *Environmental Health ; Environmental Monitoring ; Environmental Pollution/*prevention & control ; Health Status ; Humans ; Quality of Life ; Research ; Risk Factors ; Russia ; }, } @article {pmid8955674, year = {1996}, author = {Rudney, JD and Ji, Z and Larson, CJ}, title = {Saliva protein binding to streptococcal layers placed at different oral sites in 48 persons.}, journal = {Journal of dental research}, volume = {75}, number = {10}, pages = {1789-1797}, doi = {10.1177/00220345960750101201}, pmid = {8955674}, issn = {0022-0345}, support = {2 R01 DE 07233/DE/NIDCR NIH HHS/United States ; }, mesh = {Analysis of Variance ; Data Interpretation, Statistical ; Enzyme-Linked Immunosorbent Assay ; Humans ; Immunoglobulin A, Secretory/analysis ; Lactoferrin/analysis ; Mouth/*microbiology ; Muramidase/analysis ; Oral Health ; Protein Binding ; Saliva/enzymology/immunology ; Salivary Proteins and Peptides/*metabolism ; Streptococcus/*metabolism ; Streptococcus oralis/*metabolism ; Tooth/microbiology ; }, abstract = {Preliminary studies of 10 subjects suggested that saliva protein binding to oral bacteria might vary among oral sites. This study investigated saliva protein binding to layers of oral streptococci in an expanded sample of 48 subjects. Those persons were at opposite extremes for unstimulated whole saliva amylase, sIgA, lactoferrin, and lysozyme in an initial screening of 128 individuals. Layers of Streptococcus gordonii Blackburn or Streptococcus oralis 10557 on enamel chips were placed on buccal left and right upper premolars and molars (UL, UR), labial upper central incisors (UC), and lingual lower central incisors (LL). After a 10-minute exposure to saliva, bacterial extracts were assayed for bound amylase, sIgA, lactoferrin, and lysozyme. Those proteins also were quantified in unstimulated whole saliva collected after chip exposure. Both strains bound significantly more amylase at UL and UR, and significantly less at UC. Blackburn bound more amylase than 10557 at all sites. Significantly less sIgA was bound at UC; strain differences for sIgA were inconsistent across sites. Significantly more lactoferrin and lysozyme were bound at LL. There were no strain differences for lactoferrin; 10557 bound significantly more lysozyme at UL and UR. Subjects at opposite extremes for saliva protein concentrations differed for bound amylase and lactoferrin; those differences were smaller than site and strain differences. Bound protein levels were correlated across sites and strains. Correlations between whole saliva and bound proteins were moderate and were most consistent at LL. These findings suggest that saliva protein effects on oral ecology may vary among oral sites.}, } @article {pmid8955673, year = {1996}, author = {Schüpbach, P and Neeser, JR and Golliard, M and Rouvet, M and Guggenheim, B}, title = {Incorporation of caseinoglycomacropeptide and caseinophosphopeptide into the salivary pellicle inhibits adherence of mutans streptococci.}, journal = {Journal of dental research}, volume = {75}, number = {10}, pages = {1779-1788}, doi = {10.1177/00220345960750101101}, pmid = {8955673}, issn = {0022-0345}, mesh = {Adult ; Animals ; *Bacterial Adhesion ; Caseins/*metabolism ; Cattle ; Data Interpretation, Statistical ; Dental Caries/*etiology/prevention & control ; Dental Deposits/microbiology ; Dental Enamel/*microbiology ; Dental Pellicle ; Durapatite ; Freezing ; Humans ; In Vitro Techniques ; Mice ; Microscopy, Electron ; Microscopy, Electron, Scanning ; Microtomy ; Middle Aged ; Milk ; Peptide Fragments/*metabolism ; Phosphopeptides/*metabolism ; Saliva/*metabolism ; Salivary Proteins and Peptides/*metabolism ; Streptococcus mutans/*physiology ; Streptococcus sobrinus/*physiology ; }, abstract = {The protective effects of milk and milk products against dental caries have been demonstrated in many animal studies. We have shown that this effect was mediated by micellar casein or caseinopeptide derivatives. A reduction in the Streptococcus sobrinus population in the oral microbiota of animals fed diets supplemented with these milk components was consistently observed. A possible explanation for these findings is that milk components are incorporated into the salivary pellicle, thereby reducing the adherence of S. sobrinus. This hypothesis was tested in vitro by the incubation of bovine enamel discs with unstimulated saliva. The resulting pellicle was washed and incubated with caseinoglycomacropeptide (CGMP) and/or caseinophosphopeptide (CPP) labeled with 17- and 12-nm gold particles. All samples were prepared for electron microscopy by high-pressure freezing followed by freeze-substitution. It was demonstrated by high-resolution scanning electron microscopy with back-scattered electron imaging, as well as by transmission electron microscopy, that both peptides were incorporated into the pellicle in exchange for albumin, confirming previous findings. This protein was identified with a mouse anti-human serum albumin followed by goat anti-mouse IgG labeled with 25-nm gold particles. Incorporation of CGMP and/or CPP into salivary pellicles reduced the adherence of both S. sobrinus and S. mutans significantly. It is suggested that the calcium and phosphate-rich micellar casein or caseinopeptides are incorporated into the pellicle. The resulting ecological shifts, together with the increased remineralization potential of this biofilm, may explain its modified cariogenic potential.}, } @article {pmid8888484, year = {1996}, author = {Wittie, PS and Drane, W and Aldrich, TE}, title = {Classification methods for denominators in small areas.}, journal = {Statistics in medicine}, volume = {15}, number = {17-18}, pages = {1921-1926}, doi = {10.1002/(sici)1097-0258(19960930)15:18<1921::aid-sim403>3.0.co;2-3}, pmid = {8888484}, issn = {0277-6715}, mesh = {Black or African American ; Breast Neoplasms/epidemiology/ethnology/prevention & control ; Cluster Analysis ; *Decision Making, Computer-Assisted ; Environmental Exposure/adverse effects/*statistics & numerical data ; Female ; Humans ; Information Systems ; North Carolina/epidemiology ; Pancreatic Neoplasms/epidemiology ; Poverty ; Public Health/*statistics & numerical data ; *Small-Area Analysis ; Space-Time Clustering ; }, abstract = {Conventional methods fail to provide adequate assignments of individuals into appropriate subgroups for small area analyses, especially when studies cover only a portion of a county or use ecologic, descriptive variables. An unconventional aid to epidemiological investigations, such as a geographic information system (GIS), can aid public health investigators in determining denominators for studies of disease where overlays of environmental exposure and public health data define the geographic extent of the population being studied or where data must be analysed using a map. The basic functions of a GIS--to store, retrieve, transform and display data which have real earth-based co-ordinates--can facilitate this type of ecologic approach. In this paper, each denominator is chosen using the aid of a GIS to allow overlays of environmental elements with residential areas. A variety of methodological issues are associated with such studies, specifically the issue of thin cells (numerically). One solution is to avoid the use of denominators. Another involves careful classification rules for choosing the 'exposed' group. Each of these methods have relevance for environmental equity evaluations associated with environmental hazards.}, } @article {pmid8704865, year = {1996}, author = {Takahashi, K and Hoshuyama, T and Ikegami, K and Itoh, T and Higashi, T and Okubo, T}, title = {A bibliometric study of the trend in articles related to epidemiology published in occupational health journals.}, journal = {Occupational and environmental medicine}, volume = {53}, number = {7}, pages = {433-438}, pmid = {8704865}, issn = {1351-0711}, mesh = {Abstracting and Indexing ; *Bibliometrics ; Epidemiology/*trends ; MEDLINE ; *Occupational Health ; }, abstract = {OBJECTIVES: To study the role assumed by epidemiology in occupational health literature and characterise its change over the years.

METHODS: A bibliometric study was conducted with a MEDLINE search to evaluate 9024 articles published in eight representative occupational health journals for the period 1980-93. Articles related to epidemiology were found by descriptors indexed in the articles and their numbers and proportions among all published articles was tabulated for the study period.

RESULTS: The proportion of source items indexed by epidemiology as a descriptor increased over threefold from 7.9% (42/534) in 1980 to over 25% after 1990. Epidemiology was indexed most frequently as a subheading associated with other descriptors-for example, occupational diseases-epidemiology. Cohort studies had the largest increase in the descriptors that indicated epidemiological type of studies during the period studied.

CONCLUSION: Epidemiology is assuming increasing importance in occupational health literature. This was shown quantitatively and qualitatively by the use of descriptors in the MEDLINE database.}, } @article {pmid8804144, year = {1996}, author = {Manor, O and Kark, JD}, title = {A comparative study of four methods for analysing repeated measures data.}, journal = {Statistics in medicine}, volume = {15}, number = {11}, pages = {1143-1159}, doi = {10.1002/(SICI)1097-0258(19960615)15:11<1143::AID-SIM227>3.0.CO;2-M}, pmid = {8804144}, issn = {0277-6715}, mesh = {Analysis of Variance ; *Data Interpretation, Statistical ; Erythrocyte Membrane/chemistry ; Fatty Acids/analysis ; Female ; Humans ; *Longitudinal Studies ; Male ; Multivariate Analysis ; Myocardial Infarction/blood ; Reproducibility of Results ; Sample Size ; }, abstract = {This paper compares four alternative statistical methods for the analysis of repeated measures data. The data set involves fatty acid composition of red blood cell membrane examined after acute MI and is characterized by a moderate sample size, unbalanced repeated measures and high within-individual correlations. Two methods are based on individual curve fitting and two on the random effects model. Results yielded by the four methods differed. The advantages and disadvantages of the methods are discussed. Assumptions required for the valid application of these methods are tested.}, } @article {pmid8984442, year = {1996}, author = {Filippova, NA and Musatov, SA}, title = {[Geographic variability in the sexually mature phase of Ixodes persulcatus (Ixodidae). Experience in using databases on morphometry].}, journal = {Parazitologiia}, volume = {30}, number = {3}, pages = {205-215}, pmid = {8984442}, issn = {0031-1847}, mesh = {Animals ; *Databases, Factual ; Female ; *Genetic Variation ; Geography ; Ixodes/anatomy & histology/*physiology ; Male ; Russia ; Sex Characteristics ; *Sexual Maturation ; Species Specificity ; }, abstract = {The aim of the article is to estimate geographic variation of Ixodes persulcatus adults as a whole. Intraspecific variation of the females and males of Ixodes persulcatus Schulze, 1930 has been studied in eight geographical localities ("populations") of its distribution range (fig. 1.). The distance between western and eastern localities is more than 8700 km, between northern and southern ones it is approximately 2900 km. Twenty five to thirty specimens of each sex were studied in each geographical locality. The following eleven characters were used (fig. 2, 3): length of scutum (conscutum), width of scutum (conscutum), length of anal ring, width of anal ring, length of spiracular plate, width of spiracular plate, length of gnathosoma, width of gnathosoma, length of II-III articles of palps, length of hypostome, length of tarsus 1. The multidimensional scaling method by means of software package SYSTAT was used for estimation of relationships between populations on the basis of morphometrical data. The differences between the populations were revealed only from absolute sizes of organs, whereas their proportions (i. e. shape) were constant in all geographical localities. Fig. 4, 1 shows that females from localities G (Primorski Territory) and C (Tien Shan Mountains) occupy extreme positions. Fig. 4, 2 shows that males from localities G (Primorski Territory) and D (SW Altai Mountains) on the one hand and A, B (European) on the other one occupy extreme positions. Locality C (Tien Shan Mountains) is similar to F (Western Sayan Mountains) and to European (A, B) whereas females of locality C differ from A, B and F. Taking into account the partial discrepancy of relationships between populations in sexes we have united the data on corresponding characters of both sexes in the aggregate data base (fig. 4, 3). This was possible owing to the multidimensional scaling method. Fig. 4, 3 shows isolated position of the population G (Primorski Territory), specimens of which are the largest in sizes. The populations D (SW Altai Mountains) and H (Sakhalin Island) are morphometrically most similar to the population G. The population C (Tien-Shan Mountains) is represented of the smallest specimens. The European populations (A and B) are closer to C. The largest sizes are typical of the populations G and D associated with relict Tertiary landscapes of Primorski Territory and SW Altai with which areas of ecological optimum of I. persulcatus coincide. The smallest sizes are observed in the European populations (A, B) near the north-western boundary of the distribution range of the species, as well as in the Alpine population of Tien-Shan Mountains, near the upper vertical boundary of the distribution range (2000-3000 m above sea level). Climatic conditions of the habitat in these areas are similar to those of the northwestern part of the distribution range of I. persulcatus.}, } @article {pmid8781402, year = {1996}, author = {Schoeny, R}, title = {Use of genetic toxicology data in U.S. EPA risk assessment: the mercury study report as an example.}, journal = {Environmental health perspectives}, volume = {104 Suppl 3}, number = {Suppl 3}, pages = {663-673}, pmid = {8781402}, issn = {0091-6765}, mesh = {Animals ; Carcinogenicity Tests ; Carcinogens, Environmental/*adverse effects ; Data Interpretation, Statistical ; Female ; Germ-Line Mutation ; Guidelines as Topic ; Humans ; Male ; Mercury/*adverse effects ; Mutagenicity Tests ; Mutagens/adverse effects ; Neoplasms/chemically induced/genetics ; *Risk Assessment ; United States ; *United States Environmental Protection Agency ; }, abstract = {Assessment of human health risks of environmental agents has often been limited to consideration of the potential for the agent to cause cancer or general systemic toxicity after long-term exposure. The U.S. Environmental Protection Agency (U.S. EPA) is increasingly moving toward the development of integrated assessments, which consider all potential health end points including developmental toxicity, neurotoxicity, immunotoxicity, reproductive effects, and germ cell mutagenicity. The U.S. EPA has a responsibility to assess risks to nonhuman species or ecosystems when appropriate data are available. An example of a recent integrated human health and ecological risk assessment can be found in the U.S. EPA Mercury Study Report to Congress. This report covers the following topics in separate volumes: an inventory of anthropogenic mercury emissions in the United States; an exposure assessment using measured and predicted values and including indirect dietary exposure; an evaluation of human health risks; an assessment of ecologic risk wherein water criteria are presented for several wildlife species; an overall integrated characterization of human and nonhuman risk; and a discussion of risk management considerations. In the evaluation of human health risk, genetic toxicology data were considered for three forms of mercury: elemental, inorganic (divalent), and methylmercury. These data were used in judgments of two types of potential health effects (carcinogenicity and germ cell mutagenicity). In assessment of potential carcinogenicity of inorganic and methylmercury, genetic toxicity data were key. Data for clastogenicity in the absence of mutagenicity supported the characterization of inorganic and methylmercury as materials that produce carcinogenic effects only at high, toxic doses. The evidence for clastogenicity, coupled with information on metabolism and distribution, resulted in a judgment of a moderate degree of concern (or weight of evidence) that inorganic mercury can act as a human germ cell mutagen. For methylmercury, the degree of concern for germ cell mutagenicity is high.}, } @article {pmid8704904, year = {1996}, author = {Privalova, LI and Katsnel'son, BA and Polzik, EV and Kazantsev, VS and Terekhov, SA and Beĭkin, IaB and Kislitsina, NS and Privalov, DG}, title = {[Late changes in the body function of the inhabitants in the area of the eastern Urals radioactive trace].}, journal = {Radiatsionnaia biologiia, radioecologiia}, volume = {36}, number = {3}, pages = {323-331}, pmid = {8704904}, issn = {0869-8031}, mesh = {Adolescent ; Adult ; Air Pollution, Radioactive/*adverse effects/statistics & numerical data ; Child ; Child, Preschool ; Decision Support Techniques ; Ecology ; Environmental Exposure/*adverse effects/statistics & numerical data ; Humans ; Infant ; Middle Aged ; Pattern Recognition, Automated ; *Radiation Effects ; Radioactive Hazard Release ; Russia ; Strontium Radioisotopes/adverse effects ; Time Factors ; }, abstract = {Using a mathematical methodology based upon the theory of pattern recognition, the adequacy of this methodology being confirmed by the corroborative results obtained with neuro-net non-parametric methods of analysis, it proved possible to discriminate reliably between generalized organism's statuses, as described with a big number of laboratory indices, of the inhabitants of different areas of a big industrial city which differ in levels of radioactive and non-radioactive environmental pollution.}, } @article {pmid8652734, year = {1996}, author = {Feller, RJ and Karl, DM}, title = {The National Association of Marine Laboratories: a connected web for studying long-term changes in U.S. coastal and marine waters.}, journal = {The Biological bulletin}, volume = {190}, number = {2}, pages = {269-277}, doi = {10.2307/1542549}, pmid = {8652734}, issn = {0006-3185}, mesh = {Environmental Monitoring ; Information Services ; Interinstitutional Relations ; *Laboratories/organization & administration ; *Marine Biology ; Research ; United States ; }, abstract = {Long-term time-series measurements provide data that test specific hypotheses or suggest new avenues of study. Such studies are widely acknowledged as important for differentiating the influence of human activities from natural background variability. Several long-term research or monitoring programs are active in coastal and marine environments around the world and serve as models for development of new studies. The spatial array of U.S. coastal laboratories is suitable for resolving latitudinal trends and for many types of comparative studies. However, establishing a network of coastal laboratories focused on long-term monitoring and research problems presents special challenges in setting research priorities at appropriate scales, in data management, and in coordination of the scientific effort. The National Association of Marine Laboratories (NAML) is uniquely positioned to promote long-term studies among networks of its member institutions. The NAML can play an effective role in publicizing the importance of long-term studies, in providing access to expertise in this type of research, and in promoting its continuance for periods longer than the length of individual scientific careers.}, } @article {pmid8705870, year = {1996}, author = {Wilson, MR and Mansour, M and Ross-Degnan, D and Moukouri, E and Fobi, G and Alemayehu, W and Martone, JF and Casey, R and Bazargan, M}, title = {Prevalence and causes of low vision and blindness in the Extreme North Province of Cameroon, West Africa.}, journal = {Ophthalmic epidemiology}, volume = {3}, number = {1}, pages = {23-33}, doi = {10.3109/09286589609071598}, pmid = {8705870}, issn = {0928-6586}, mesh = {Adolescent ; Adult ; Age Distribution ; Aged ; Aged, 80 and over ; Blindness/diagnosis/*epidemiology/etiology ; Cameroon/epidemiology ; Child ; Data Interpretation, Statistical ; Female ; Humans ; Male ; Middle Aged ; Prevalence ; Retrospective Studies ; Rural Population ; Sex Distribution ; Urban Population ; Vision, Low/diagnosis/*epidemiology/etiology ; }, abstract = {A survey to determine the prevalence and causes of blindness and visual impairment in the Extreme North Province of Cameroon was conducted in the Spring of 1992. A total of 10,647 people age 6 years and older was selected from a multi-stage, clustered sample stratified by ecological zone. The subjects were examined by ophthalmologist-led teams for visual acuity and ocular diseases. Approximately 1.2% of the sample was bilaterally blind by the World Health Organization classification (Category 3) of vision less than the ability to count fingers at 3 meters. Similarly to results found in other developing countries, senile cataract was the most common diagnosis encountered and the most frequent principal cause of low vision and blindness.}, } @article {pmid8610668, year = {1996}, author = {Richardson, S and Guihenneuc-Jouyaux, C and Lasserre, V}, title = {Re: Ecologic studies--biases, misconceptions, and counterexamples.}, journal = {American journal of epidemiology}, volume = {143}, number = {5}, pages = {522-523}, doi = {10.1093/oxfordjournals.aje.a008773}, pmid = {8610668}, issn = {0002-9262}, mesh = {*Bias ; Confounding Factors, Epidemiologic ; Data Interpretation, Statistical ; *Ecology ; }, } @article {pmid8713628, year = {1996}, author = {Semenova, SK and Romanova, EA and Ryskov, AP}, title = {[Genetic differentiation of helminths on the basis of data of polymerase chain reaction using random primers].}, journal = {Genetika}, volume = {32}, number = {2}, pages = {304-309}, pmid = {8713628}, issn = {0016-6758}, mesh = {Adaptation, Physiological/genetics ; Animals ; Cestoda/*genetics ; Data Interpretation, Statistical ; *Genetic Variation ; *Genome ; Nematoda/*genetics ; *Random Amplified Polymorphic DNA Technique ; Species Specificity ; Trematoda/*genetics ; }, abstract = {The genetic variability of helminths belonging to the three classes Cestoda, Nematoda and Trematoda was analysed by means of polymerase chain reaction with randomly amplified polymorphic DNA (RAPD-PCR). Dendrograms of genetic relationships between some representatives of the genus Trichinella, Fasciola hepatica, Cysticerus ovis, Echinococcus granulosus, and Nematodirus spathiger were constructed on the basis of DNA amplification patterns. The formation of ecological and genetic adaptations in the helminth groups studied is discussed.}, } @article {pmid8712187, year = {1996}, author = {Goodman, RM and Wandersman, A and Chinman, M and Imm, P and Morrissey, E}, title = {An ecological assessment of community-based interventions for prevention and health promotion: approaches to measuring community coalitions.}, journal = {American journal of community psychology}, volume = {24}, number = {1}, pages = {33-61}, doi = {10.1007/BF02511882}, pmid = {8712187}, issn = {0091-0562}, mesh = {Alcoholism/*prevention & control ; Community Health Planning ; *Community Mental Health Services ; Community Networks ; Community Participation ; HIV Infections/prevention & control ; *Health Promotion ; Humans ; Patient Care Team ; *Preventive Health Services ; Research Support as Topic ; Risk Factors ; Sexually Transmitted Diseases/prevention & control ; *Smoking Prevention ; *Social Environment ; South Carolina ; Substance-Related Disorders/*prevention & control ; Violence/prevention & control ; }, abstract = {Presented an ecological assessment of a community coalition to prevent alcohol, tobacco, and other drug abuse, and related risks. Ecological assessment is defined as occurring at multiple social levels and along a continuum of stages of coalition readiness. The assessment is aided by the triangulation, or combining of assessment methods and strategies. Measures used to assess the coalition's formation, implementation of community initiatives, and production of community impacts are described, along with the triangulation strategies used to enhance the assessment findings.}, } @article {pmid8743696, year = {1996}, author = {Hein, J and Støvlbaek, J}, title = {Combined DNA and protein alignment.}, journal = {Methods in enzymology}, volume = {266}, number = {}, pages = {402-418}, doi = {10.1016/s0076-6879(96)66025-x}, pmid = {8743696}, issn = {0076-6879}, mesh = {Algorithms ; *Amino Acid Sequence ; *Base Sequence ; DNA/*chemistry ; *Databases, Factual ; Evolution, Molecular ; Exons ; Genes, Viral ; Genes, gag ; Genes, pol ; HIV/genetics ; Humans ; Models, Genetic ; Molecular Sequence Data ; Proteins/*chemistry ; Sequence Homology, Amino Acid ; Sequence Homology, Nucleic Acid ; *Software ; }, } @article {pmid8747300, year = {1995}, author = {Horovitz, I and Meyer, A}, title = {Systematics of New World monkeys (Platyrrhini, Primates) based on 16S mitochondrial DNA sequences: a comparative analysis of different weighting methods in cladistic analysis.}, journal = {Molecular phylogenetics and evolution}, volume = {4}, number = {4}, pages = {448-456}, doi = {10.1006/mpev.1995.1041}, pmid = {8747300}, issn = {1055-7903}, mesh = {Animals ; Base Sequence ; Cebidae/classification/*genetics ; DNA Primers/genetics ; DNA, Mitochondrial/*genetics ; Data Interpretation, Statistical ; Molecular Sequence Data ; Nucleic Acid Conformation ; *Phylogeny ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/chemistry/genetics ; Species Specificity ; }, abstract = {In order to investigate the effects of different weighting methods on a phylogeny reconstruction based on DNA sequences and to evaluate the phylogenetic information content of various secondary structures, a fragment of the large ribosomal mitochondrial gene (16S) was sequenced from 13 species of New World monkeys, three species of catarrhines, and Tarsius. The data were analyzed cladistically without weighting characters or changes, and with different weighting methods: a priori differential weights for transitions and transversions, two variants of dynamic weighting for each kind and direction of change, and successive approximations, using both the character consistency index (CI) and the rescaled consistency index (RC). The results were compared with published trees constructed from nuclear sequences of E-globins and morphological characters by different authors. The result of the analysis of the mtDNA data set with successive approximations, using the RC as weighting function, was the closest to the topology on which all molecular and morphological trees concur. Other relationships were unique to this tree. "Loops" were the type of secondary structure that showed maximum variation in sequence length and sites with the lowest character CI and RC. A large number of sites within loops showed high values for these indices, however, which suggests that uniform downweighting of these regions represents a large loss of phylogenetic information. Successive weighting, which assigns a weight for each particular character, seems to be a desirable alternative to this practice. We propose a new variant of dynamic weighting, which we call homoplasy-correcting dynamic weighting, that like dynamic weighting, is applicable to any kind of sequence, coding or noncoding.}, } @article {pmid8594139, year = {1995}, author = {Dolk, H and Mertens, B and Kleinschmidt, I and Walls, P and Shaddick, G and Elliott, P}, title = {A standardisation approach to the control of socioeconomic confounding in small area studies of environment and health.}, journal = {Journal of epidemiology and community health}, volume = {49 Suppl 2}, number = {Suppl 2}, pages = {S9-14}, pmid = {8594139}, issn = {0143-005X}, mesh = {Adolescent ; Adult ; Aged ; Child ; Child, Preschool ; *Confounding Factors, Epidemiologic ; Data Interpretation, Statistical ; *Health Status ; Humans ; Industry ; Infant ; Infant, Newborn ; Middle Aged ; Mortality ; Neoplasms/epidemiology ; Population ; Poverty/classification/statistics & numerical data ; Sample Size ; *Small-Area Analysis ; *Socioeconomic Factors ; United Kingdom/epidemiology ; }, abstract = {OBJECTIVE: To assess how effectively a routine adjustment can be made for socio-economic confounding in small area studies of environment and health using indirect standardisation and small area deprivation indices, including analysis of the appropriate size of population unit on which to base the deprivation index and the importance of region and urban/rural status as axes of stratification.

METHODS: Standardised morbidity ratios were calculated for cancers in Great Britain for 1981 and standardised mortality ratios for all cause mortality in Great Britain between 1982 and 1985. Deprivation indices were calculated for enumeration districts and wards from 1981 small area census statistics. Cancers and deaths were allocated to enumeration districts via their postcode. Standardised morbidity and mortality ratios were calculated by quintile of enumeration district according to the deprivation index. Standardised mortality ratios were further analysed by deprivation of ward, region, and urban/rural status.

RESULTS: Strong relationships were found between all cause mortality and the incidence of selected cancers and deprivation quintile-there was up to a twofold difference in lung cancer incidence between the highest and lowest quintile. The deprivation index can be used to measure gradients of deprivation according to the distance from industrial sites. The deprivation index for enumeration districts showed similar discrimination of mortality as the index forwards. There is some interaction between deprivation and region in their effect on the standardised mortality ratios, leading to a small bias in the estimation of expected numbers if this is not taken into account. The relationship between deprivation, urban/rural status, and mortality is complex and confounded by region, but mortality tends to be higher in urban than in rural areas within quintiles of deprivation.

DISCUSSION: Whether calculated for enumeration districts or wards, the main problems in the interpretation of the deprivation index may be its limited correlation with the risk factors of interest and its concentration on present rather than past socioeconomic status. Indirect standardisation based on stratification for deprivation and other variable involves a trade off between bias and precision in determining the fineness and the number of axes of stratification. Some bias may occur due to interaction between region and deprivation and the effects of urban/rural status. Complementary approaches including modeling and proportional mortality or morbidity analyses may be needed and the possibility of residual socioeconomic confounding must always be considered.

CONCLUSION: There is potential for important socioeconomic confounding in small area studies of environmental pollution and health where the health outcome under examination has a strong relationship to socioeconomic status and where the putative excess risk due to pollution may be small. One method of controlling for confounding is to use an ecological measurement of deprivation in small areas, and to adjust for deprivation by indirect standardisation. However, residual socioeconomic confounding can be expected, which may seriously complicate the interpretation of small area studies.}, } @article {pmid8594128, year = {1995}, author = {Diggle, P and Elliott, P}, title = {Disease risk near point sources: statistical issues for analyses using individual or spatially aggregated data.}, journal = {Journal of epidemiology and community health}, volume = {49 Suppl 2}, number = {Suppl 2}, pages = {S20-7}, pmid = {8594128}, issn = {0143-005X}, mesh = {Bias ; Data Collection ; *Data Interpretation, Statistical ; *Environmental Pollution ; Humans ; Models, Statistical ; Risk Factors ; *Small-Area Analysis ; United Kingdom/epidemiology ; }, abstract = {STUDY OBJECTIVE: To examine the statistical issues involved in the analysis of disease risk near point sources of environmental pollution, where data are held at both the individual and group (areal) level. To explore these issues with reference to possible socioeconomic confounding.

DESIGN: Statistical review.

SETTING: Point sources of environmental pollution.

MAIN RESULTS: Except in very specific circumstances unlikely to hold in practice, aggregation of data to the areal level will lead to bias in the estimation of disease risk.

CONCLUSIONS: There is no easy solution to the analysis of spatial data when some covariates (for example, age and sex of cases) are known at individual level, whereas others (for example, populations, age-sex distributions, small area deprivation indices) are known only at the areal (ecological) level. The underlying assumptions inherent in the analysis of these data need to be explicitly recognised in order to understand better the limitations of the available methodology as well as to inform interpretation of results. Ideally, the data should be kept as disaggregated as possible, to maximise the information available and minimise potential for bias.}, } @article {pmid8851347, year = {1995}, author = {Speer, PW and Hughey, J}, title = {Community organizing: an ecological route to empowerment and power.}, journal = {American journal of community psychology}, volume = {23}, number = {5}, pages = {729-748}, doi = {10.1007/BF02506989}, pmid = {8851347}, issn = {0091-0562}, mesh = {City Planning ; *Community Networks ; Community Participation ; *Consumer Organizations ; *Ecology ; Humans ; Interpersonal Relations ; Outcome and Process Assessment, Health Care ; *Power, Psychological ; }, abstract = {An important contribution to empowerment theory and community psychology practice can be made by examining how the concept of social power is developed and manifested in the context of community organizing. Theory and practice may be further informed through an ecological analysis of organizing processes and interventions. Lessons from a national community organizing network highlight the relationship between empowerment and power through a set of organizing principles and a cycle of organizing activity. Perhaps most important is the understanding that a reciprocal relationship exists between development of power for community organizations and individual empowerment for organization members. Implications for empowerment theory in the community organizing domain are provided in a matrix adapted from Zimmerman's description of empowerment processes and outcomes at multiple levels of analysis.}, } @article {pmid8590394, year = {1995}, author = {Bruni, V and La Ferla, R and Acosta Pomar, ML and Salomone, L}, title = {Structural differences of the microbial community in two sites of the Terra Nova Bay (Ross Sea, Antarctica): a statistical analysis.}, journal = {The new microbiologica}, volume = {18}, number = {4}, pages = {409-422}, pmid = {8590394}, issn = {1121-7138}, mesh = {Antarctic Regions ; Data Interpretation, Statistical ; *Ecosystem ; *Marine Biology ; Sample Size ; *Water Microbiology ; }, abstract = {The microbial community structure was investigated in a one month survey at two sampling stations located in the Terra Nova Bay (Antarctica). The microbial assemblage was studied by direct counts with epifluorescent microscopy (picoplankton and picophytoplankton), fractionated adenosine-triphosphate, lipopolysaccarides and bacterial growth on cultural medium. The results underwent the Spearman rank correlation and the principal component analysis together with other environmental parameters (temperature, salinity, nutrient salts and chlorophyll a) with the aim of revealing differences in the microbial community structure between the in-shore and off-shore sites.}, } @article {pmid7570660, year = {1995}, author = {Bradbury, SP}, title = {Quantitative structure-activity relationships and ecological risk assessment: an overview of predictive aquatic toxicology research.}, journal = {Toxicology letters}, volume = {79}, number = {1-3}, pages = {229-237}, doi = {10.1016/0378-4274(95)03374-t}, pmid = {7570660}, issn = {0378-4274}, mesh = {Animals ; Cyprinidae ; Databases, Factual ; Ecology ; Models, Chemical ; Risk Assessment ; *Structure-Activity Relationship ; Time Factors ; Water Pollutants/classification/*toxicity ; }, abstract = {In the field of aquatic toxicology, quantitative structure-activity relationships (QSARs) have developed as scientifically credible tools for predicting the toxicity of chemicals when little or no empirical data are available. A fundamental understanding of toxicological principles has been considered an important component to the acceptance and application of QSAR approaches as biologically relevant in ecological risk assessments. As a consequence, there has been an evolution of QSAR development and application from that of a chemical-class perspective to one that is more consistent with assumptions regarding modes of toxic action. In this review, techniques to assess modes of toxic action from chemical structure are discussed, with consideration that toxicodynamic knowledge bases must be clearly defined with regard to exposure regimes, biological models/endpoints and compounds that adequately span the diversity of chemicals anticipated for future applications. With such knowledge bases, classification systems, including rule-based expert systems, have been established for use in predictive aquatic toxicology applications. The establishment of QSAR techniques that are based on an understanding of toxic mechanisms is needed to provide a link to physiologically based toxicokinetic and toxicodynamic models, which can provide the means to extrapolate adverse effects across species and exposure regimes.}, } @article {pmid7582202, year = {1995}, author = {Elliott, P and Martuzzi, M and Shaddick, G}, title = {Spatial statistical methods in environmental epidemiology: a critique.}, journal = {Statistical methods in medical research}, volume = {4}, number = {2}, pages = {137-159}, doi = {10.1177/096228029500400204}, pmid = {7582202}, issn = {0962-2802}, mesh = {Adult ; Case-Control Studies ; Child ; *Cluster Analysis ; Contact Tracing ; *Data Collection ; *Data Interpretation, Statistical ; *Epidemiologic Methods ; Humans ; Small-Area Analysis ; }, abstract = {Despite recent advances in the available statistical methods for geographical analysis, there are many constraints to their application in environmental epidemiology. These include problems of data availability and quality, especially the lack in most situations of environmental exposure measurements. Methods for disease 'cluster' investigation, point source exposures, small-area disease mapping and ecological correlation studies are critically reviewed, with the emphasis on practical applications and epidemiological interpretation. It is shown that, unless dealing with rare diseases, high specificity exposures and high relative risks, cluster investigation is unlikely to be fruitful, and is often complicated by the post hoc nature of such studies. However, it is recognized that in these circumstances proper assessment of the available data is often required as part of the public health response. Newly available methods, particularly in Bayesian statistics, offer an appropriate framework for geographical analysis and disease mapping. Again, it is uncertain whether they will give important clues as to aetiology, although they do give valuable description. Perhaps the most satisfactory approach is to test a priori hypotheses using a geographical database, although problems of interpretation remain.}, } @article {pmid8577828, year = {1995}, author = {Bolker, B and Grenfell, B}, title = {Space, persistence and dynamics of measles epidemics.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {348}, number = {1325}, pages = {309-320}, doi = {10.1098/rstb.1995.0070}, pmid = {8577828}, issn = {0962-8436}, mesh = {Data Interpretation, Statistical ; *Disease Outbreaks ; Emigration and Immigration ; Humans ; Measles/*epidemiology ; Models, Biological ; }, abstract = {This paper explores the relations between persistence and dynamics in measles epidemics. Most current models, including the stochastic seasonally forced and age-structured models examined here, fail to capture simultaneously the observed dynamics and persistence characteristics of epidemics in large urban populations before vaccination. Summary measures of persistence and trienniality allow us to compare epidemics in England, New York and Copenhagen with results of non-spatial and spatial stochastic models. Spatial (metapopulation) structure allow persistence and triennial dynamics to coexist i this class of models. The spatial dynamics of measles, for which detailed spatiotemporal data are available, may serve as a useful test of ideas applicable to other epidemiological and ecological systems with an important spatial component.}, } @article {pmid7789827, year = {1995}, author = {Zholdakova, ZI and Zhurkov, VS and Kharchevnikova, NV and Feldt, EG and Gerasimov, IV}, title = {[Methods of development of a data bank on ecologic and hygienic characteristics of chemical environmental pollutants].}, journal = {Gigiena i sanitariia}, volume = {}, number = {2}, pages = {27-29}, pmid = {7789827}, issn = {0016-9900}, mesh = {*Databases, Factual ; Ecology ; *Environmental Pollutants ; Environmental Pollution/*analysis ; *Hazardous Substances ; Hygiene ; Maximum Allowable Concentration ; }, } @article {pmid7497343, year = {1995}, author = {Ballester Díez, F and Merino Egea, C and Pérez Hoyos, S}, title = {[Association of air pollution and mortality: a review of recent epidemiological studies].}, journal = {Revista espanola de salud publica}, volume = {69}, number = {2}, pages = {177-188}, pmid = {7497343}, issn = {1135-5727}, mesh = {Aged ; *Air Pollution ; Epidemiologic Methods ; Female ; Humans ; Information Systems ; MEDLINE ; Male ; Models, Statistical ; *Mortality ; Retrospective Studies ; Temperature ; Weather ; World Health Organization ; }, abstract = {The aim of this study is to present a review of the work published over the past few years which deals with the relationship between air pollution (AP) and mortality from the epidemiological perspective, by examining the evolution of methodology used in the analysis along with changes in values considered as threshold levels. A literature review was carried out on of articles published in the MEDLINE and IME databases. From this search some 40 articles were selected. The review has been centred on those studies which examine the association of AP indicators and short term mortality. The design of the paper is usually retrospective and, in almost all cases, these are ecological studies. Study populations are, most of times, inhabitants of cities or particular geographic areas, with the usual analysis being a combination of time series approach and multivariate regression. Also taken into account in the majority of this papers, apart from time variables, are other confounding factors, especially meteorological conditions. The results of the papers reviewed are presented along with their principle methodological characteristics. A series of recent studies indicate that the relationship between AP, especially small particles, and mortality may exist below the guidelines established at National and International level. This study finishes with a discussion on the most outstanding aspects of the results of the papers reviewed. Also mentioned is the difficulty of determining AP indicators, and their levels, which are linked to mortality.}, } @article {pmid8765904, year = {1995}, author = {Russom, CL and Bradbury, SP and Carlson, AR}, title = {Use of knowledge bases and QSARs to estimate the relative ecological risk of agrichemicals: a problem formulation exercise.}, journal = {SAR and QSAR in environmental research}, volume = {4}, number = {2-3}, pages = {83-95}, doi = {10.1080/10629369508029906}, pmid = {8765904}, issn = {1062-936X}, mesh = {Agrochemicals/chemistry/*toxicity ; Algorithms ; Animals ; Environmental Pollutants/*toxicity ; *Expert Systems ; *Information Systems ; Invertebrates/drug effects ; Plants/drug effects ; Risk Assessment ; Structure-Activity Relationship ; United States ; United States Environmental Protection Agency ; Vertebrates ; *Water Pollution, Chemical ; }, abstract = {Ecological risk assessments can be used to establish the likelihood that an adverse effect will result from exposure to one or more chemicals. When evaluating contaminated sites with many chemicals present, risk assessors must grapple with the problem of quickly identifying the chemicals that are most likely to be of concern, based on effect and exposure assessment information. Many times data gaps exist and the risk assessor is left with decisions on which models to use to estimate the parameter of concern. In the present paper, a procedure is presented for ranking agrichemicals, utilizing the ASTER (ASsessment Tools for the Evaluation of Risk) system. The procedure was employed to rank the relative ecological risk of forty-nine pesticides historically used in agricultural sites in the Walnut Creek watershed near Ames, lowa, USA. Empirical data from the ASTER system were used when available in the associated databases, and quantitative structure-activity relationships and expert systems were invoked when data were lacking. Separate rankings were conducted based on major species taxonomic groupings. Resulting toxic effects thresholds were compared to surface water concentrations.}, } @article {pmid8591596, year = {1995}, author = {Brelidze, Z and Samadashvili, Z and Khachapuridze, G and Kubaneishvili, E and Nozadze, Z and Benidze, I and Tsitskishvili, N}, title = {Psychovegetative syndrome diagnosis: an automated psychophysiological investigation and mathematical modeling approach.}, journal = {Medinfo. MEDINFO}, volume = {8 Pt 2}, number = {}, pages = {953}, pmid = {8591596}, issn = {1569-6332}, mesh = {Brain/physiopathology ; *Diagnosis, Computer-Assisted ; Electroencephalography ; Evoked Potentials, Visual ; *Expert Systems ; Homeostasis/physiology ; Humans ; *Models, Biological ; Persistent Vegetative State/*diagnosis/physiopathology ; }, abstract = {1. INTRODUCTION. The main purpose of our work was to create the informational expert system of psychovegetative syndrome diagnosis by applying clinical data and estimating the functioning of the central and peripheral part of regulatory apparatus of the human organism, taking into consideration parallel and consecutive sensory, motor, associative, emotional drive systems, and internal body state. We used automatized psychophysiological investigation and mathematical models. For this purpose the following principal tasks have been prepared: the creation of database of quantifiable estimation patient state; the definition and automation of psychophysiological investigation; mathematical modeling of vegetative functions using a non-invasive sample and its connection with real psychophysiological experiment; mathematical modeling of organisms inner medium homeostasis; and the creation of an informational-expert system of psychovegetative syndrome diagnosis. 2. DATABASE OF ESTIMATION OF PATIENTS STATE. The medical records of the DB "PATIENT" contain data on patient psychic and somatoneurological status. 3. AUTOMATED PSYCHOPHYSIOLOGICAL INVESTIGATION. Psychophysiological investigation enables estimation of the functioning of several subsystems of the human organism and establishes an interrelationship between them by means of electrophysiological data and performance parameters. The study of psychophysiological provision of behavior by psychophysiological investigation enables us to get information about adaptational mechanisms of the patient under certain environmental loads. By means of special mathematical provision, the mathematical elaboration of biosignals as performance parameters has been realized; also realized were the formation of received parameters in the database, the estimation of separated parameters in the view of informativity, and the establishment of diagnostic patterns. 4. MATHEMATICAL MODELS FOR ESTIMATION INTERNAL BODY STATE. The proposed mathematical models allow investigation of homeostatic regulation in various intensities of the metabolic processes and external load. This approach in mathematical models allows us to characterize the relations between the central and peripheral parts of the regulatory mechanisms, using non-invasive samples under psychophysiological investigation and the simulation of different surroundings for brain cells functioning. 5. INFORMATION-EXPERT SYSTEM. Proceeding from the principle of psychoneural unity, we characterized the functioning mechanisms of CNS by means of automatized EEG analysis, visually evoked potential analysis, estimated psychic status, and the characteristics of neural system biochemical processes received by mathematical modeling. By using the indices of the viscero-vegetative and somatolocomotor system (as well as parameters received by automatized analysis of ECG), the EEG respiratory signal--from mathematical models of vegetative functions decision support system applied in estimation of a peripheral block of the regulatory system--is reflected in diagnosis of certain syndromes. The informational expert system, proceeding from the functioning of the human organism's regulatory apparatus, diagnosed psychovegetative syndrome and described the mechanisms of its development. 6. CONCLUSION. The informational expert system enables estimation of the functioning of a human organism as a whole and can be introduced in the sphere of practical medicine and professional orientation as well as in laboratories of experimental psychology and neurosciences.}, } @article {pmid8591279, year = {1995}, author = {Simon, P and Ménesi, L and Fekete, A and Varga, G}, title = {Revelations from a meta database system on environmental health problems.}, journal = {Medinfo. MEDINFO}, volume = {8 Pt 1}, number = {}, pages = {610}, pmid = {8591279}, issn = {1569-6332}, mesh = {Computer Communication Networks ; Environmental Monitoring/*methods ; Environmental Pollution/prevention & control ; *Information Systems ; }, abstract = {Harmful effects of environmental pollution to the health status of population is well-known to ecologists and experts on health sciences. However, prevention and protection against such direct environmental hazards to save, or, in a worse case, re-establish the ecological balance are anything but successful. It is true, even if modern monitoring and measuring technology, adequate information systems, and related data bases are available. Precision of measurements and surveys, assessment and evaluation of the relationship between component elements of negative environmental effects on one the one hand, and general health conditions of the population on the other, could be increased by applying methods of informatics i.e., if we carry out a preliminary and professional analysis of the already existing information property. A useful tool for such activities could be the creation and maintenance of an integrated meta-type data base. It is a set sorted by a causal relations group of information that is collected from several databases of different origin, as pre-defined by the task. Our task was to systematize valuable information collected from different fields of science and research (competencies), to compare them with international standard databases, and thus, to discover new inter-relations, create new values. As an input, one could envisage a network of satellite data bases evaluating relevant results of scientists and research institutions. The main database itself could contain standard national and international information on environmental health care. The output of the system could be relational analysis produced by the meta-system on the basis of results provided by the satellite systems. Thus, frequently, even without carrying out a particular survey, one could already suspect that certain environmental health hazards exist, or plan and implement certain measurements and surveys in a more precisely targeted way. An unlimited number of local satellite workstation modules of experts and research institutions may be linked to the meta database. Information property created as a result of special analysis and annotation might create a knowledge basis for free access by participants. Thus not only would their scientific backgrounds be strengthened, but services would also be provided by the meta database which could be diversified continuously. The satellite systems, the sorting and retrieval functions of the database, and its graphical services would provide a loose but flexible micro-computer system that could be linked together by autonomous or networked workstations. Our system is written on FoxPro and uses FoxGraph. At a medium level of capacity, it requires 1 MB free RAM and 14-16 MB fixed memory. The system already shows a certain specialization: the 'PubHealth' system from general issues of environmental health care leans towards problems related to sub-toxic long term effects and correlations to health insurance risk assessment (cost-benefit, risk-benefit analysis). However, new issues are also emerging when experts wish foremost to utilize the philosophy of the system (e.g., epidemiological mental-hygienic surveys related to life style and social status).}, } @article {pmid8585237, year = {1995}, author = {Nurminen, M}, title = {Linkage failures in ecological studies.}, journal = {World health statistics quarterly. Rapport trimestriel de statistiques sanitaires mondiales}, volume = {48}, number = {2}, pages = {78-84}, pmid = {8585237}, issn = {0379-8070}, mesh = {Bias ; Data Interpretation, Statistical ; Environmental Exposure/adverse effects/prevention & control/*statistics & numerical data ; Environmental Monitoring/*statistics & numerical data ; Humans ; *Morbidity ; *Policy Making ; Risk ; }, abstract = {Ecological studies require a methodological theory distinct from that used in individual-level epidemiological studies. This article discusses the special problems that need to be considered when planning ecological studies or using the results of such studies. Ecological studies are much more sensitive to bias from model mis-specification than are results from individual-level studies. For example, deviations from linearity in the underlying individual-level regressions can lead to inability to control for confounding in ecological studies, even if no misclassification is present. Conditions for confounding differ in individual-level and ecological analyses. For ecological analyses of means, for example, a covariate will not be a confounder if its mean value in a study region is not associated with either (i) the mean exposure level across regions, or (ii) the mean outcome (disease rate) across regions. On the other hand, effect modification across areas can induce ecological bias even when the number of areas is very large and there is no confounding. In contrast to individual-level studies, independent and nondifferential misclassification of a dichotomous exposure usually leads to bias away from the null hypothesis in aggregate data studies. Failure to standardize disease, exposure and covariate data for other confounders (not included in the regression model) can lead to bias. It should be borne in mind that there is no method available to identify or measure ecological bias. While this conclusion may sound like a general criticism of ecological studies, it is not. It does, however, serve as a reminder of the problems that need to be considered when one designs, analyses, or critically evaluates ecological studies.}, } @article {pmid7639884, year = {1995}, author = {Morgenstern, H}, title = {Ecologic studies in epidemiology: concepts, principles, and methods.}, journal = {Annual review of public health}, volume = {16}, number = {}, pages = {61-81}, doi = {10.1146/annurev.pu.16.050195.000425}, pmid = {7639884}, issn = {0163-7525}, mesh = {Data Interpretation, Statistical ; *Ecology ; Environmental Exposure/*statistics & numerical data ; Epidemiologic Factors ; *Epidemiologic Methods ; Humans ; Research Design ; }, abstract = {An ecologic study focuses on the comparison of groups, rather than individuals; thus, individual-level data are missing on the joint distribution of variables within groups. Variables in an ecologic analysis may be aggregate measures, environmental measures, or global measures. The purpose of an ecologic analysis may be to make biologic inferences about effects on individual risks or to make ecologic inferences about effects on group rates. Ecologic study designs may be classified on two dimensions: (a) whether the primary group is measured (exploratory vs analytic study); and (b) whether subjects are grouped by place (multiple-group study), by time (time-trend study), or by place and time (mixed study). Despite several practical advantages of ecologic studies, there are many methodologic problems that severely limit causal inference, including ecologic and cross-level bias, problems of confounder control, within-group misclassification, lack of adequate data, temporal ambiguity, collinearity, and migration across groups.}, } @article {pmid7745367, year = {1994}, author = {Matoković, B and Stambuk-Giljanović, N}, title = {The ecological database VODE as the base for monitoring and the study of the water quality parameters correlation.}, journal = {Journal of medical systems}, volume = {18}, number = {6}, pages = {315-327}, pmid = {7745367}, issn = {0148-5598}, mesh = {Croatia ; *Databases, Factual ; *Environmental Monitoring ; *Expert Systems ; Models, Biological ; Water Supply/*standards ; }, abstract = {The ecological approach to the disease facilitates the understanding of the reasons for the multiplicity of causal factors and the finding of those on which the preventive measures will be easily and successfully directed. That is the reason why integration of space data for getting insight into the existing condition from ecological point of view is necessary. The ecological need to sum up the work of the water research and to estimate the future water quality trends by observing the relevant parameters as influential ecological factors for the health of the population resulted in relation data base VODE. Besides it integrates the data group of waters data and from the ecological standpoint is suitable for the several years study of trends of existing water supply system condition with special survey of the results of the water quality analyses in view of the recognition of the actual pollutions that are significant for the health problems of population, group and individuals. One gets informations by putting questions and than plans necessary interventions, what is the new significant contribution in the approach to the analytical and monitoring techniques, i.e., application of informatical techniques in water pollution control.}, } @article {pmid7713035, year = {1994}, author = {Colborn, T}, title = {The wildlife/human connection: modernizing risk decisions.}, journal = {Environmental health perspectives}, volume = {102 Suppl 12}, number = {Suppl 12}, pages = {55-59}, pmid = {7713035}, issn = {0091-6765}, mesh = {Animals ; *Animals, Wild ; Decision Support Techniques ; Ecology ; Environmental Monitoring ; Environmental Pollutants/*adverse effects ; Genetics, Population ; Humans ; Mutagens/*adverse effects ; Reproduction ; Risk Assessment ; Xenobiotics ; }, abstract = {This article proposes that genetic and molecular ecotoxicology can play an important role in making policy and risk assessment decisions concerning xenobiotics. It calls for a greater awareness by ecotoxicologists to the effects in wildlife and humans resulting from transgenerational exposure to synthetic chemicals that interfere with gene expression and differentiation. The difficulty of recognizing these effects on the endocrine, immune, and nervous systems in developing embryos is described and suggests why effects of this nature have traditionally not been addressed when determining risk to synthetic chemicals. Specific examples are cited of environmental effects on hormonally responsive tissue in wildlife populations which could be used as models for assessing human exposure to synthetic chemicals. Evidence is presented that the environmental load of synthetic chemicals has reached critical levels at which wildlife and human health are at risk.}, } @article {pmid7711315, year = {1994}, author = {Bram, RA}, title = {Integrated control of ectoparasites.}, journal = {Revue scientifique et technique (International Office of Epizootics)}, volume = {13}, number = {4}, pages = {1357-1365}, doi = {10.20506/rst.13.4.822}, pmid = {7711315}, issn = {0253-1933}, mesh = {Animals ; Animals, Domestic/*parasitology ; Ectoparasitic Infestations/prevention & control/*veterinary ; Integrated Advanced Information Management Systems ; Pest Control/*standards ; }, abstract = {Integrated control of ectoparasites of veterinary importance is being implemented on a limited basis at present. However, several forces are accelerating a global shift to integrated pest management (IPM). These accelerating forces include the following: reduction in new chemical compounds registered for use on livestock and poultry universal development of resistance to pesticides heightened environmental sensitivities to exclusive dependence on pesticide-based control need for strategies which increase profits for the producer while decreasing costs to the consumer. Integrated pest control requires many technologies for incorporation into specific pest management systems. Individual components include new chemicals, formulations and delivery systems, biological control, mechanical control, immunological control, genetic control, and regulatory control. Computer simulation models based on a quantitative ecological database are invaluable in devising and monitoring IPM approaches to controlling ectoparasites which affect livestock and poultry. IPM strategies have been developed for pests of veterinary importance, but eventually these must be incorporated into total livestock production systems. For implementation, a number of major impediments to IPM must be overcome. These problems can best be solved through a vigorous technology transfer programme. In addition to face-to-face meetings between producers and extension agents, the implementation of IPM can be further encouraged at producer group meetings, through education of animal health professionals, by the publication of articles in producer magazines, and by radio and television broadcasts to the agricultural sector. Research focusing on the development of cost-effective and environmentally-compatible IPM systems is necessary for future progress.}, } @article {pmid7815400, year = {1994}, author = {Duffy, DC and Clark, DD and Campbell, SR and Gurney, S and Perello, R and Simon, N}, title = {Landscape patterns of abundance of Ixodes scapularis (Acari: Ixodidae) on Shelter Island, New York.}, journal = {Journal of medical entomology}, volume = {31}, number = {6}, pages = {875-879}, doi = {10.1093/jmedent/31.6.875}, pmid = {7815400}, issn = {0022-2585}, support = {U50/CCU206621//PHS HHS/United States ; }, mesh = {Animals ; *Ecology ; Geography ; Housing ; Humans ; Information Systems ; New York ; Population Density ; Population Dynamics ; *Ticks ; }, abstract = {Nymphal Ixodes scapularis Say, the vector of Lyme borreliosis, was most common in forested areas across Shelter Island, Suffolk County, New York, and least common in xeric habitats such as beach and grassland. At the scale of individual house yards, nymphs were most common at wooded edges of property and least common on lawns. The abundance of ticks at yard edges was positively correlated with numbers on lawns and in landscaping, suggesting that tick abundance in woods affects abundances in adjacent yards. Because 57% of all yard area is adjacent to woodlands on Shelter Island, public health efforts to reduce tick populations in wooded areas should supplement efforts by individual yard owners to decrease risk. Methods of tick control for woodlands should also be evaluated for their effect on tick populations in adjacent yard habitats.}, } @article {pmid7997709, year = {1994}, author = {Frey, CM and Feuer, EJ and Timmel, MJ}, title = {Projection of incidence rates to a larger population using ecologic variables.}, journal = {Statistics in medicine}, volume = {13}, number = {17}, pages = {1755-1770}, doi = {10.1002/sim.4780131707}, pmid = {7997709}, issn = {0277-6715}, mesh = {Age Factors ; Aged ; Aged, 80 and over ; Breast Neoplasms/*epidemiology/mortality ; *Data Interpretation, Statistical ; Demography ; Ecology ; Female ; Humans ; Incidence ; Likelihood Functions ; Middle Aged ; *Models, Statistical ; Poisson Distribution ; Regression Analysis ; Reproducibility of Results ; SEER Program/statistics & numerical data ; Socioeconomic Factors ; }, abstract = {There is wide acceptance of direct standardization of vital rates to adjust for differing age distributions according to the representation within age categories of some referent population. One can use a similar process to standardize, and subsequently project vital rates with respect to continuous, or ratio scale ecologic variables. We obtained from the National Cancer Institute's Surveillance, Epidemiology and End Results (SEER) programme, a 10 per cent subset of the total U.S. population, country-level breast cancer incidence during 1987-1989 for white women aged 50 and over. We applied regression coefficients that relate ecologic factors to SEER incidence to the full national complement of county-level information to produce an age and ecologic factor adjusted rate that may be more representative of the U.S. than the simple age-adjusted SEER incidence. We conducted a validation study using breast cancer mortality data available for the entire U.S. and which supports the appropriateness of this method for projecting rates.}, } @article {pmid7949342, year = {1994}, author = {Faye, B and Calavas, D and Rosner, G}, title = {[The reliability of data in ecopathologic investigations].}, journal = {Revue scientifique et technique (International Office of Epizootics)}, volume = {13}, number = {3}, pages = {651-664}, pmid = {7949342}, issn = {0253-1933}, mesh = {Animals ; Data Collection/*standards ; Databases, Factual ; *Ecology ; Electronic Data Processing ; Humans ; Observer Variation ; *Reproducibility of Results ; Research/*standards ; Risk Factors ; }, abstract = {The reliability of information gathered during ecopathological investigations is a constant concern, requiring a rigorous strategy to limit risks of error. These risks are all the more important when there are human shortcomings (farmer or investigator) as opposed to technical shortcomings (results of laboratory tests). A dual strategy can be implemented to guarantee reliability: ensuring reliable collection of data by attention to the human element (selection of farmers, training of investigators, organisation of professional partners), and ensuring the collection of reliable data by attention to facts (quality of the questionnaire, harmonization of procedures, objective interpretation of qualitative findings, quality of data-processing support, timing of data collection, verification procedures). The argument is supported by numerous examples provided by teams of ecopathologists.}, } @article {pmid7944561, year = {1994}, author = {Davidoff, AL and Fogarty, L}, title = {Psychogenic origins of multiple chemical sensitivities syndrome: a critical review of the research literature.}, journal = {Archives of environmental health}, volume = {49}, number = {5}, pages = {316-325}, doi = {10.1080/00039896.1994.9954981}, pmid = {7944561}, issn = {0003-9896}, support = {ES03819/ES/NIEHS NIH HHS/United States ; OH07090/OH/NIOSH CDC HHS/United States ; }, mesh = {Databases, Bibliographic ; Humans ; Multiple Chemical Sensitivity/etiology/*psychology ; Psychophysiologic Disorders/*psychology ; *Research Design/standards ; Sampling Studies ; }, abstract = {The purpose of this review was to critically evaluate research on the psychogenic origins of multiple chemical sensitivities (MCS) syndrome. Using as keywords environmental illness, multiple chemical sensitivities, and clinical ecology, two databases--PsychLit and Medline--were searched by computer; reference lists of all articles located were also searched manually. Ten articles meeting three criteria were selected for review. Five sample selection problems, seven measurement problems, and three study design problems were common in all but one of the articles reviewed. Current studies investigating psychogenic hypotheses of MCS syndrome are methodologically problematic and their conclusions questionable. Studies of psychiatric profiles observed in MCS syndrome need to be designed to differentiate between competing psychogenic and biogenic hypotheses.}, } @article {pmid10134547, year = {1994}, author = {LaDuca, A}, title = {Validation of professional licensure examinations. Professions theory, test design, and construct validity.}, journal = {Evaluation & the health professions}, volume = {17}, number = {2}, pages = {178-97; discussion 236-41}, doi = {10.1177/016327879401700204}, pmid = {10134547}, issn = {0163-2787}, mesh = {Cognition ; Data Interpretation, Statistical ; Ecology ; *Educational Measurement ; Health Occupations/education/*standards ; Licensure/*standards/statistics & numerical data ; Professional Autonomy ; Reproducibility of Results ; United States ; }, abstract = {Although the unitary view of test validity has gained support recently, it has real limitations where professional licensing examinations are concerned. A strategy for validation of professional licensure tests requires modifying conventional approaches in three ways. First, a theory of professions must be incorporated into the test development process so as to acknowledge the social character of professions. Second, the importance of test design in the validation of licensing tests should be enhanced. Third, the concept of construct validation must be expanded to accommodate the special features of content that inhere to professional licensure testing. Methods for accomplishing these three things are described and the implications of these and other views discussed.}, } @article {pmid8571071, year = {1994}, author = {Kindler, E}, title = {[Concurrent engineering].}, journal = {Sbornik lekarsky}, volume = {95}, number = {1}, pages = {37-41}, pmid = {8571071}, issn = {0036-5327}, mesh = {*Computer Simulation ; Humans ; *Information Science ; *Information Systems ; }, abstract = {Concurrent engineering is a new attempt to the theoretical and practical synthesis of human activities, especially of those ones focusing to industrial production or deep to influencing human society. Although its title sound near to technology terms, concurrent engineering does not miss medicine, ecology, social security and other disciplines. From the methodological viewpoint, concurrent engineering represents a synthesis of a wide spectrum of branches of sciences and technology; that synthesis is primarily stimulated by commercial aspects, supported by the interest coming from production, control of the society and business. But that synthesis leads to a rich process of discovering interdisciplinary relations at the theoretical level, supported by the powerful tools of modern information processing, knowledge representation and exact remote transfer of symbolic, graphic and acoustic information.}, } @article {pmid8018839, year = {1994}, author = {Busenberg, SN and Velasco-Hernandez, JX}, title = {Habitat suitability and herbivore dynamics.}, journal = {Bio Systems}, volume = {32}, number = {1}, pages = {37-47}, doi = {10.1016/0303-2647(94)90017-5}, pmid = {8018839}, issn = {0303-2647}, mesh = {Animals ; Aphids ; Data Interpretation, Statistical ; *Ecosystem ; *Models, Biological ; Plants ; }, abstract = {We derive a dynamic model for a plant herbivore system describing the interaction of a gall-forming aphid and a single plant. We compare the behavior of our model with experimental observations obtained from an aphid plant system studied by Whitham (Whitham, T.G. 1978, Habitat selection of Pemphigus aphids in response to resource limitation and competition. Ecology 59, 1164-1176). A simple parameter estimation shows a close correlation between the predicted and observed results.}, } @article {pmid7624517, year = {1994}, author = {Beaton, S and Cleary, A and ten Have, J and Bradley, MP}, title = {Cloning and characterization of a fox sperm protein FSA-1.}, journal = {Reproduction, fertility, and development}, volume = {6}, number = {6}, pages = {761-770}, doi = {10.1071/rd9940761}, pmid = {7624517}, issn = {1031-3613}, mesh = {Acrosome/chemistry/metabolism ; Algorithms ; Amino Acid Sequence ; Animals ; Antibodies, Monoclonal/biosynthesis/immunology ; Base Sequence ; Blotting, Northern ; Blotting, Southern ; Cloning, Molecular ; DNA/analysis/chemistry/*genetics ; Databases, Factual ; Foxes/genetics/*metabolism ; Humans ; Hybridomas ; Immunohistochemistry ; Male ; Molecular Sequence Data ; Proteins/*analysis/*chemistry/*genetics/metabolism ; Sequence Homology, Nucleic Acid ; Species Specificity ; Spermatozoa/*chemistry ; }, abstract = {A monoclonal antibody was raised to a fox sperm protein (FSA-1) which was found to be localized to the inner acrosomal compartment of sperm fixed in methanol. Western blots of testicular germ cell membrane extracts probed with this antibody identified a major protein band with a molecular weight of 36,000. Immunofluorescent studies on fox testis sections showed that the antigen is expressed on round and elongating spermatids on a crescent-shaped structure, which probably represents the developing acrosome. An antibody specific for FSA-1 was used to screen a fox testis cDNA library for its cognate gene. An 875-bp cDNA clone was isolated and sequenced revealing an open reading frame. Searches of the GenBank and EMBL databases with the nucleic acid sequence revealed significant homology (86%) of FSA-1 with 406 bases of an unidentified RNA transcript from human fetal brain (EST02625). Northern blot analysis of fox testis RNA samples identified an RNA transcript of approximately 0.9 kb during the months when spermatogenesis is active. Zoo Northern blots (at high stringency) reveal an RNA transcript of a similar size present in testis RNA from dogs and mice. Zoo Southern analysis (high stringency) reveal genomic sequences present in dogs, mice, cattle and sheep. At present, the function of the FSA-1 gene product remains unknown, but it may play a role as a structural protein component of the acrosome.}, } @article {pmid7579528, year = {1994}, author = {Wray, GA and Bely, AE}, title = {The evolution of echinoderm development is driven by several distinct factors.}, journal = {Development (Cambridge, England). Supplement}, volume = {}, number = {}, pages = {97-106}, pmid = {7579528}, mesh = {Animals ; *Biological Evolution ; Cell Differentiation ; Cell Movement ; Databases, Factual ; Echinodermata/cytology/*embryology/genetics ; Ecology ; Gastrula/*physiology ; Gene Expression ; Models, Biological ; Morphogenesis/physiology ; }, abstract = {We analyzed a comparative data base of gene expression, cell fate specification, and morphogenetic movements from several echinoderms to determine why developmental processes do and do not evolve. Mapping this comparative data onto explicit phylogenetic frameworks revealed three distinct evolutionary patterns. First, some evolutionary differences in development correlate well with larval ecology but not with adult morphology. These associations are probably not coincidental because similar developmental changes accompany similar ecological transformations on separate occasions. This suggests that larval ecology has been a potent influence on the evolution of early development in echinoderms. Second, a few changes in early development correlate with transformations in adult morphology. Because most such changes have occurred only once, however, it is difficult to distinguish chance associations from causal relationships. And third, some changes in development have no apparent phenotypic consequences and do not correlate with obvious features of either life history or morphology. This suggests that some evolutionary changes in development may evolve in a neutral or nearly neutral mode. Importantly, these hypotheses make specific predictions that can be tested with further comparative data and by experimental manipulations. Together, our phylogenetic analyses of comparative data suggest that at least three distinct evolutionary mechanisms have shaped early development in echinoderms.}, } @article {pmid7533255, year = {1994}, author = {Yentsch, CM and Pomponi, SA}, title = {Strategies for flow cytometric analysis of marine microalgae and sponge cells.}, journal = {Methods in cell biology}, volume = {42 Pt B}, number = {}, pages = {523-538}, doi = {10.1016/s0091-679x(08)61093-6}, pmid = {7533255}, issn = {0091-679X}, support = {R01 CA55871/CA/NCI NIH HHS/United States ; }, mesh = {Animals ; Data Interpretation, Statistical ; Eukaryota/*cytology ; Flow Cytometry/instrumentation/*methods/statistics & numerical data ; Fluoresceins ; Marine Biology ; Porifera/*cytology ; Staining and Labeling/methods ; }, } @article {pmid8108458, year = {1993}, author = {Tidd, CW and Olsen, LF and Schaffer, WM}, title = {The case for chaos in childhood epidemics. II. Predicting historical epidemics from mathematical models.}, journal = {Proceedings. Biological sciences}, volume = {254}, number = {1341}, pages = {257-273}, doi = {10.1098/rspb.1993.0155}, pmid = {8108458}, issn = {0962-8452}, mesh = {Child ; Data Interpretation, Statistical ; Disease Outbreaks/history/*statistics & numerical data ; History, 20th Century ; Humans ; Measles/epidemiology/history ; *Models, Theoretical ; *Nonlinear Dynamics ; Stochastic Processes ; }, abstract = {The case for chaos in childhood epidemics rests on two observations. The first is that historical epidemics show various 'fieldmarks' of chaos, such as positive Lyapunov exponents. Second, phase portraits reconstructed from real-world epidemiological time series bear a striking resemblance to chaotic solutions obtained from certain epidemiological models. Both lines of evidence are subject to dispute: the algorithms used to look for the fieldmarks can be fooled by short, noisy time series, and the same fieldmarks can be generated by stochastic models in which there is demonstrably no chaos at all. In the present paper, we compare the predictive abilities of stochastic models with those of mechanistic scenarios that admit to chaotic solutions. The main results are as follows: (i) the mechanistic models outperform their stochastic counterparts; (ii) forecasting efficacy of the deterministic models is maximized by positing parameter values that induce chaotic behaviour; (iii) simple mechanistic models are equal if not superior to more detailed schemes that include age structure; and (iv) prediction accuracy for monthly notifications declines rapidly with time, so that, from a practical standpoint, the results are of little value. By way of contrast, next amplitude maps can successfully forecast successive changes in maximum incidence one or more years into the future.}, } @article {pmid8206041, year = {1993}, author = {Prentice, RL and Thomas, D}, title = {Methodologic research needs in environmental epidemiology: data analysis.}, journal = {Environmental health perspectives}, volume = {101 Suppl 4}, number = {Suppl 4}, pages = {39-48}, pmid = {8206041}, issn = {0091-6765}, support = {CA-53996/CA/NCI NIH HHS/United States ; }, mesh = {*Data Interpretation, Statistical ; Environmental Exposure/*analysis/statistics & numerical data ; Environmental Monitoring/*methods/statistics & numerical data ; Humans ; *Models, Biological ; *Models, Statistical ; Risk Factors ; }, abstract = {A brief review is given of data analysis methods for the identification and quantification of associations between environmental exposures and health events of interest. Data analysis methods are outlined for each of the study designs mentioned, with an emphasis on topics in need of further research. Particularly noted are the need for improved methods for accommodating exposure assessment measurement errors in analytic epidemiologic studies and for improved methods for the conduct and analysis of aggregate data (ecologic) studies.}, } @article {pmid8206029, year = {1993}, author = {Rothman, KJ}, title = {Methodologic frontiers in environmental epidemiology.}, journal = {Environmental health perspectives}, volume = {101 Suppl 4}, number = {Suppl 4}, pages = {19-21}, pmid = {8206029}, issn = {0091-6765}, mesh = {Data Interpretation, Statistical ; *Environmental Exposure/analysis ; Environmental Monitoring/*methods ; Humans ; Research Design ; Risk Factors ; }, abstract = {Environmental epidemiology comprises the epidemiologic study of those environmental factors that are outside the immediate control of the individual. Exposures of interest to environmental epidemiologists include air pollution, water pollution, occupational exposure to physical and chemical agents, as well as psychosocial elements of environmental concern. The main methodologic problem in environmental epidemiology is exposure assessment, a problem that extends through all of epidemiologic research but looms as a towering obstacle in environmental epidemiology. One of the most promising developments in improving exposure assessment in environmental epidemiology is to find exposure biomarkers, which could serve as built-in dosimeters that reflect the biologic footprint left behind by environmental exposures. Beyond exposure assessment, epidemiologists studying environmental exposures face the difficulty of studying small effects that may be distorted by confounding that eludes easy control. This challenge may prompt reliance on new study designs, such as two-stage designs in which exposure and disease information are collected in the first stage, and covariate information is collected on a subset of subjects in state two. While the analytic methods already available for environmental epidemiology are powerful, analytic methods for ecologic studies need further development. This workshop outlines the range of methodologic issues that environmental epidemiologists must address so that their work meets the goals set by scientists and society at large.}, } @article {pmid8272829, year = {1993}, author = {Borzilov, VA}, title = {Development of requirements for environmental specimen banking in ecological monitoring (exemplified by the Chernobyl NPP accident area).}, journal = {The Science of the total environment}, volume = {139-140}, number = {}, pages = {197-201}, doi = {10.1016/0048-9697(93)90019-3}, pmid = {8272829}, issn = {0048-9697}, mesh = {*Accidents ; Air Pollution, Radioactive/analysis ; Databases, Factual ; Ecology ; Environmental Monitoring/*methods ; Environmental Pollution/*analysis ; Gamma Rays ; Humans ; *Nuclear Reactors ; *Radioactive Fallout ; Soil Pollutants, Radioactive/analysis ; *Specimen Handling ; Tissue Banks/*organization & administration ; USSR ; Ukraine ; Water Pollution, Radioactive/analysis ; }, abstract = {Development of requirements for a data bank for natural media as a system of intercorrelated parameters to estimate system states are determined. The problems of functional agreement between experimental and calculation methods are analysed when organizing the ecological monitoring. The methods of forming the environmental specimen bank to estimate and forecast radioactive contamination and exposure dose are considered to be exemplified by the peculiarities of the spatial distribution of radioactive contamination in fields. Analysed is the temporal dynamics of contamination for atmospheric air, soil and water.}, } @article {pmid8224970, year = {1993}, author = {Brzhezovskiĭ, MM and Efimova, AA and Ratanova, MP}, title = {[Problems in providing medical information for ecologic research].}, journal = {Gigiena i sanitariia}, volume = {}, number = {7}, pages = {10-13}, pmid = {8224970}, issn = {0016-9900}, mesh = {Child ; *Ecology ; *Environmental Exposure ; Humans ; *Medical Informatics ; }, } @article {pmid8221493, year = {1993}, author = {Pickett, W and Davidson, JR and Brison, RJ}, title = {Suicides on Ontario farms.}, journal = {Canadian journal of public health = Revue canadienne de sante publique}, volume = {84}, number = {4}, pages = {226-230}, pmid = {8221493}, issn = {0008-4263}, mesh = {Adolescent ; Adult ; Age Factors ; Aged ; *Agriculture ; Child ; Child, Preschool ; Databases, Factual ; Death Certificates ; Female ; Humans ; Infant ; Linear Models ; Male ; Middle Aged ; Ontario/epidemiology ; Ownership ; *Population Surveillance ; *Poverty ; Regression Analysis ; Risk Factors ; Suicide/*statistics & numerical data ; }, abstract = {PURPOSE: To describe the epidemiology of suicides on Ontario farms from 1980-1989, and the ecological relationship between economic strain and farm suicide risk.

METHOD: Farm suicides were identified using a computer-assisted search of vital records. Distributions of farm suicides were examined by several demographic variables. Linear and Poisson regression were used to describe potential associations between ten economic indicators and the incidence of farm suicide.

RESULTS: 126 farm suicides were identified. After adjustment for age and under-reporting, the farm suicide rate was estimated at 7.2 per 100,000 per year. The highest suicide rate was observed among elderly farm owner-operators. Regression analyses failed to find any associations between the economic indicators and farm suicide rates.

CONCLUSION: The results do not support the notion that farmers in Ontario generally have a high rate of suicide, the ecological analysis provided no evidence for increased farm suicide risk with increasing economic strain.}, } @article {pmid8511621, year = {1993}, author = {Vigneron, E}, title = {[Geographic aspects of mortality in French Polynesia].}, journal = {Social science & medicine (1982)}, volume = {36}, number = {10}, pages = {1339-1348}, doi = {10.1016/0277-9536(93)90226-t}, pmid = {8511621}, issn = {0277-9536}, mesh = {Aged ; Cause of Death ; Data Interpretation, Statistical ; Ecology ; Female ; Humans ; Infant ; Infant Mortality/*trends ; Infant, Newborn ; Life Expectancy ; Male ; Middle Aged ; Morbidity ; Mortality/*trends ; Polynesia/epidemiology ; Population Dynamics ; Socioeconomic Factors ; }, abstract = {The fast pace of social and economic changes which have occurred in French Polynesia over the last 30 years, have made this territory a choice ground for studying trends in mortality by revealing a fast and outstanding epidemiological transition. However, the breakdown of the population in small scattered human groups raises the statistical problem of measuring mortality. The crude mortality rate has decreased steadily from 17.5/1000 in 1945-1949 to 5.3/1000 over the last five years. However, the various infant mortality rate, in spite of their decline, is still exceeding those of Metropolitan France. The contrasted trends in the causes of mortality provides a means to classify French Polynesia in the group of small fast developing countries but still ranks it far behind its 'reference models' such as Metropolitan France or the developed countries in the South Pacific, Australia and New Zealand. Moreover, there are significant regional disparities which still exist between Tahiti and the outlying archipelagoes, mainly among causes of death. As a whole, distant islands remain significantly more affected by deaths resulting from infectious and parasitic diseases, in line with the model of epidemiological transition, where as the islands of Tahiti with 70% of the total population appears as a place of cumulation of infectious and degenerative diseases, in particular of overloading and cultural problems. The centre/periphery opposition between a metropolitan country and an overseas territory repeats itself at the local level between urban and rural environments.}, } @article {pmid8511620, year = {1993}, author = {Loslier, L}, title = {The geo-systemic model and mortality in Ubon-Ratchathani.}, journal = {Social science & medicine (1982)}, volume = {36}, number = {10}, pages = {1335-1338}, doi = {10.1016/0277-9536(93)90225-s}, pmid = {8511620}, issn = {0277-9536}, mesh = {Adolescent ; Adult ; Child ; Child, Preschool ; Data Interpretation, Statistical ; Demography ; Ecology ; Health Status Indicators ; Humans ; Infant ; Infant Mortality ; Infant, Newborn ; Life Style ; Models, Statistical ; Mortality/*trends ; *Rural Population ; Socioeconomic Factors ; Thailand/epidemiology ; }, abstract = {The Thailand 'Rural Data Base' includes a number of variables in the social, economic, services, housing, agriculture and health fields. This data base comes from a survey at the village level. There are weaknesses in the data base--inaccuracies, missing data, etc ... that make it difficult to discover the structures that theoretically exist in the data using direct analysis methods, like correlation analysis for instance. The 2383 villages of the province of Ubon-Ratchathani, in Thailand, are the units of this study. The objective is to uncover the hypothetical health disparities that exist among the villages and to devise a typology of villages that will show classes of villages that have significant problems and, also, classes of villages that could suggest concrete solutions and be used as models. Some variables of the data base are considered dependent (health indicators) and others are considered independent; they are used to build a model called 'geo-systemic' that is used to expose mortality differentials in Ubon-Ratchathani.}, } @article {pmid8511615, year = {1993}, author = {Salem, G}, title = {[Geography of mortality and birth in Pikine (Senegal): value and limitations of findings of the Civil State in African villages].}, journal = {Social science & medicine (1982)}, volume = {36}, number = {10}, pages = {1297-1311}, doi = {10.1016/0277-9536(93)90220-x}, pmid = {8511615}, issn = {0277-9536}, mesh = {Adolescent ; Adult ; Aged ; Bias ; *Birth Rate ; Child ; Child, Preschool ; Data Interpretation, Statistical ; Demography ; Ecology ; Epidemiologic Methods ; Female ; Health Status Indicators ; Humans ; Infant ; Infant, Newborn ; Male ; Middle Aged ; *Mortality ; Registries ; Seasons ; Senegal/epidemiology ; }, abstract = {Research conducted in Third World towns show the heterogeneity of health population status. Among the indicators, mortality and birth are the most frequent, but the quantity of data and the classical methods in demography make the localisation of high-risk population difficult. Civil Registration Data Base are seldom studied, especially by geographers. The author analyses the interest and limits of these data in a spatial perspective, i.e. mortality and birth rates, mortality and birth volumes, seasonal variations of mortality, and relations between seasonal variations and health system activities. The author's conclusion is on the necessity to include these indicators in the health information system after complementary research on possible bias.}, } @article {pmid8502789, year = {1993}, author = {Stockwell, JR and Sorensen, JW and Eckert, JW and Carreras, EM}, title = {The U.S. EPA Geographic Information System for mapping environmental releases of Toxic Chemical Release Inventory (TRI) chemicals.}, journal = {Risk analysis : an official publication of the Society for Risk Analysis}, volume = {13}, number = {2}, pages = {155-164}, doi = {10.1111/j.1539-6924.1993.tb01065.x}, pmid = {8502789}, issn = {0272-4332}, mesh = {Animals ; Ecology ; Environmental Exposure/*statistics & numerical data ; Hazardous Substances/*adverse effects ; Humans ; *Information Systems ; Risk Factors ; Southeastern United States ; United States ; United States Environmental Protection Agency ; }, abstract = {This study characterizes the environmental releases of toxic chemicals of the Toxic Chemical Release Inventory (TRI) in the southeastern United States by using the U.S. Environmental Protection Agency (EPA) Geographic Information System (GIS) to map them. These maps show that the largest quantities of TRI releases in the Southeast are usually near densely populated areas. This GIS mapping approach takes the first steps in defining those areas in the region which may be potential exposure zones and which could be strategic targets for future risk screening efforts in this geographic area.}, } @article {pmid8143070, year = {1993}, author = {Wann, JP and Turnbull, JD}, title = {Motor skill learning in cerebral palsy: movement, action and computer-enhanced therapy.}, journal = {Bailliere's clinical neurology}, volume = {2}, number = {1}, pages = {15-28}, pmid = {8143070}, issn = {0961-0421}, mesh = {Adolescent ; Biofeedback, Psychology ; Cerebral Palsy/*rehabilitation/therapy ; Child ; Humans ; *Motor Skills ; Movement ; Physical Therapy Modalities/methods ; Physical and Rehabilitation Medicine ; *Therapy, Computer-Assisted/trends ; }, abstract = {This chapter discusses the extent to which previous research into movement control can provide key principles on which to model therapy for individuals with severe cerebral palsy. It is suggested that the movement perspective has traditionally stressed the role of implicit knowledge of the dynamic characteristics of the body and that this provides support for the principles of biofeedback training. From a more ecological 'action' perspective, however, it is concluded that previous approaches to biofeedback have been too constrained and do not translate well to functional tasks. A variation of biofeedback training is proposed that provides real-time feedback to shape the subject's action, thereby guiding them through learning contexts that are moulded to fit the individual's capabilities. A pilot study of the efficacy of such an approach in adolescents with cerebral palsy is then presented. The potential of extending computer-enhanced therapy into speculative areas such as virtual reality is also discussed.}, } @article {pmid7682504, year = {1993}, author = {Gunster, DG and Bonnevie, NL and Gillis, CA and Wenning, RJ}, title = {Assessment of chemical loadings to Newark Bay, New Jersey from petroleum and hazardous chemical accidents occurring from 1986 to 1991.}, journal = {Ecotoxicology and environmental safety}, volume = {25}, number = {2}, pages = {202-213}, doi = {10.1006/eesa.1993.1019}, pmid = {7682504}, issn = {0147-6513}, mesh = {Accidents ; Databases, Factual/statistics & numerical data ; New Jersey ; Petroleum/*analysis/statistics & numerical data ; Water Pollutants, Chemical/*analysis ; }, abstract = {Newark Bay, New Jersey, is particularly vulnerable to ecological damage from accidental petroleum and chemical spills due to the enclosed nature of the bay and the large volume of chemical and petroleum commerce within the region. A review of the New Jersey Department of Environmental Protection and Energy's database of hazardous chemical spills in New Jersey waterways was conducted to determine the frequency and volume of chemical and petroleum spills in Newark Bay and its major tributaries. Accidents reported from 1986 to 1991 were extracted from the database and summarized. The compilation of records indicated that 1400 incidents, resulting in the release of more than 18 million gallons of hazardous materials to the estuary had been reported to state officials. The bulk of the chemicals released to the aquatic environment were petroleum products, specifically No. 2 Fuel Oil (4,636,512 gallons) and No. 6 Fuel Oil (12,600,683 gallons). The majority of the reported incidents occurred in the Arthur Kill and its tributaries. The results indicate that accidental discharge of petroleum and other hazardous chemicals to Newark Bay represents a significant ongoing source of chemical pollution.}, } @article {pmid8063131, year = {1993}, author = {Koviazin, VG and Smirnov, VI and Semanov, DA and Vatnik, DM}, title = {[Information retrieval system Ecotoxicology].}, journal = {Gigiena i sanitariia}, volume = {}, number = {3}, pages = {53-55}, pmid = {8063131}, issn = {0016-9900}, mesh = {Commonwealth of Independent States ; *Ecology ; Humans ; *Information Storage and Retrieval ; International Cooperation ; *Toxicology ; United States ; }, } @article {pmid8492482, year = {1993}, author = {Sone, T and Matsuda, S and Doi, T and Kahyo, H}, title = {[Digit preference in birth weight data of obstetric facilities].}, journal = {Nihon eiseigaku zasshi. Japanese journal of hygiene}, volume = {47}, number = {6}, pages = {1050-1057}, doi = {10.1265/jjh.47.1050}, pmid = {8492482}, issn = {0021-5082}, mesh = {Biometry/instrumentation ; *Birth Weight ; Data Interpretation, Statistical ; Health Facilities ; *Health Status Indicators ; Humans ; Infant, Newborn ; Japan ; }, abstract = {An investigation on instrumentation of birth weight in obstetric facilities was made in the northern part of Fukuoka Prefecture from March 1989 to January 1991. A distribution of 3000 cases from 100 facilities was analyzed for the purpose of clarifying the reliability of the data. The following results were obtained. 1) Birth weights measured by analogue scales (1530 cases) showed digit preference in all distributions of the whole, the lower three digits and the lower two digits. But those measured by digital scales (1470 cases) did not show any distortion in these three distributions. 2) There were significant differences among mean birth weights calculated from the intact data, and 50g-, 100g- and 500g-interval frequency histograms in analogue scales (p < 0.01). But in digital scales there were no significant differences among mean birth weights. Rounding error was supposed to be one of the main causes of this discrepancy. Digital scales are superior to other types of scales because they do not show distribution distortion of the data. The reliability of the birth weight data is different among the types of scales. We have to consider which type of scale is used when we refer to annual changes or differences among areas in mean birth weights.}, } @article {pmid8436392, year = {1993}, author = {Baer, AS}, title = {Global survey of human genetic diversity: a focal point for human biology.}, journal = {Human biology}, volume = {65}, number = {1}, pages = {7-9}, pmid = {8436392}, issn = {0018-7143}, mesh = {Anthropology, Physical ; Databases, Factual/*standards ; Ecology ; *Ethnicity ; *Genetic Variation ; *Genetics, Population ; Humans ; *Population Surveillance ; }, } @article {pmid8499087, year = {1993}, author = {Kong, Z and Vanrolleghem, PA and Verstraete, W}, title = {An activated sludge-based biosensor for rapid IC50 estimation and on-line toxicity monitoring.}, journal = {Biosensors & bioelectronics}, volume = {8}, number = {1}, pages = {49-58}, doi = {10.1016/0956-5663(93)80043-o}, pmid = {8499087}, issn = {0956-5663}, mesh = {*Biosensing Techniques ; Environmental Monitoring/*instrumentation ; *Online Systems ; Oxygen Consumption/*drug effects ; Reproducibility of Results ; Sensitivity and Specificity ; *Sewage ; Time Factors ; Water Microbiology ; Water Pollutants, Chemical/*toxicity ; }, abstract = {The RODTOX (Rapid Oxygen Demand and TOXicity tester), an activated sludge-based respirographic biosensor, is a device for on-line monitoring of the short-term biochemical oxygen demand (stBOD) and potential toxicity of incoming wastewater on the basis of on-line interpretation of respirograms resulting from pulse additions of either calibration substrate or sample. The principle of toxicity detection is based on the comparison of calibration respirograms before and after receiving a potential toxicant. In this paper, the results of the RODTOX as an on-line toxicity monitor are presented. In addition, a simple and fast procedure to estimate the IC50 of a toxicant has been developed, and its validity and good repeatability demonstrated. The performance of this procedure is compared with that of the Microtox test.}, } @article {pmid8472801, year = {1993}, author = {Materia, E and Mehari, W and Mele, A and Rosmini, F and Stazi, MA and Damen, HM and Basile, G and Kifle, T and Miuccio, G and Ferrigno, L}, title = {Census in a rural area of Ethiopia: methodology and results.}, journal = {European journal of epidemiology}, volume = {9}, number = {1}, pages = {5-9}, pmid = {8472801}, issn = {0393-2990}, mesh = {Adolescent ; Adult ; Aged ; Child ; Child, Preschool ; Data Collection/methods ; Data Interpretation, Statistical ; *Demography ; Ethiopia ; Female ; Health Services Accessibility ; Humans ; Infant ; Male ; Middle Aged ; Rural Population ; }, abstract = {A census and an ecologic survey were performed in 39 villages of a rural district of Arsi Region, Ethiopia, in difficult field circumstances. Information on age, ethnic group, education and family relationship, as well as data on health facilities and availability of basic services were collected. Supervised students, working in teams, were used as interviewers. Communities were involved through plenary meetings and community health agents participated in the data collection process. A total of 64,714 people in 12,152 households were registered. The repeatability of age assessment was investigated by comparing the results from two villages with data obtained in a pilot study carried out 6 months earlier. The technical error was only 0.80 and 1.67 in the 0-5 and 6-15 age-groups, respectively. Three percent of the total population was under one year, less than previously estimated. This may, in part, be due to the family planning programme in the region. Eighteen percent of the households were headed by females. School attendance was less common among females and in the Oromo ethnic group. The availability of basic services, including safe water and basic sanitation supplies, was very poor in the area.}, } @article {pmid8421788, year = {1993}, author = {Verhasselt, Y}, title = {Geography of health: some trends and perspectives.}, journal = {Social science & medicine (1982)}, volume = {36}, number = {2}, pages = {119-123}, doi = {10.1016/0277-9536(93)90203-g}, pmid = {8421788}, issn = {0277-9536}, mesh = {Acquired Immunodeficiency Syndrome/epidemiology ; *Epidemiologic Methods ; Forecasting ; Humans ; Information Systems/*trends ; *International Cooperation ; Social Environment ; }, abstract = {The present evolution of geography of health is highlighted through a selection of recent publications. Some current research trends are listed, such as disease ecology in a changing environment, geography of AIDS, urbanization, epidemiological transition, health care delivery. The most salient future perspectives are pointed out.}, } @article {pmid1468017, year = {1992}, author = {Piepenburg, D and Piatkowski, U}, title = {A program for computer-aided analyses of ecological field data.}, journal = {Computer applications in the biosciences : CABIOS}, volume = {8}, number = {6}, pages = {587-590}, doi = {10.1093/bioinformatics/8.6.587}, pmid = {1468017}, issn = {0266-7061}, mesh = {Cluster Analysis ; *Data Interpretation, Statistical ; *Ecology ; Mathematical Computing ; Microcomputers ; Phylogeny ; *Software ; }, abstract = {A program for IBM-compatible microcomputers is introduced which combines several complementary analyses of species-station-tables generated in ecological field investigations. The scope of the program encompasses table editing functions, routines for community delimitation by cluster analysis and procedures for the analysis of properties related both to stations (e.g. diversities) and species (e.g. abundance statistics and association indices). The essential reasoning behind the application of community studies is presented briefly, as well as the multi-step analytical approach implemented in the program.}, } @article {pmid1361065, year = {1992}, author = {Stone, L}, title = {Coloured noise or low-dimensional chaos?.}, journal = {Proceedings. Biological sciences}, volume = {250}, number = {1327}, pages = {77-81}, doi = {10.1098/rspb.1992.0133}, pmid = {1361065}, issn = {0962-8452}, mesh = {Biometry ; *Data Interpretation, Statistical ; Disease Outbreaks ; Epidemiology/*statistics & numerical data ; Humans ; Measles/epidemiology ; New York City/epidemiology ; Stochastic Processes ; }, abstract = {Devising a method capable of distinguishing a low-dimensional chaotic signal that might be embedded in a noisy stochastic process has become a major challenge for those involved in time-series analysis. Here a null hypothesis approach is used in conjunction with a known nonlinear predictive test, to probe for the presence of chaos in epidemiological data. A probabilistic set of rules is used to stimulate a historic record of New York City measles outbreaks, generally understood to be governed by a chaotic attractor. The simulated runs of 'surrogate data' are carefully constructed so as to be free from any underlying low-dimensional chaotic process. They therefore serve as a useful null model against which to test the observed time series. However, despite the assumed differences between the dynamics of measles outbreaks and the null model, a nonlinear predictive scheme is found to be unable to differentiate between their characteristic time series. The methodology confirms that, if there is in fact a chaotic signal in the measles data, it is extremely difficult to detect in time series of such limited length. The results have general relevance to the analysis of physical, ecological and environmental time series.}, } @article {pmid1427045, year = {1992}, author = {Hudson, RR and Slatkin, M and Maddison, WP}, title = {Estimation of levels of gene flow from DNA sequence data.}, journal = {Genetics}, volume = {132}, number = {2}, pages = {583-589}, pmid = {1427045}, issn = {0016-6731}, support = {GM40282/GM/NIGMS NIH HHS/United States ; GM42447/GM/NIGMS NIH HHS/United States ; }, mesh = {Computer Simulation ; Data Interpretation, Statistical ; *Genetics, Population ; Models, Genetic ; Recombination, Genetic ; Sequence Analysis, DNA/*statistics & numerical data ; Software ; }, abstract = {We compare the utility of two methods for estimating the average levels of gene flow from DNA sequence data. One method is based on estimating FST from frequencies at polymorphic sites, treating each site as a separate locus. The other method is based on computing the minimum number of migration events consistent with the gene tree inferred from their sequences. We compared the performance of these two methods on data that were generated by a computer simulation program that assumed the infinite sites model of mutation and that assumed an island model of migration. We found that in general when there is no recombination, the cladistic method performed better than FST while the reverse was true for rates of recombination similar to those found in eukaryotic nuclear genes, although FST performed better for all recombination rates for very low levels of migration (Nm = 0.1).}, } @article {pmid1402775, year = {1992}, author = {Hall, CR and Hinkle, CR and Knott, WM and Summerfield, BR}, title = {Environmental monitoring and research at the John F. Kennedy Space Center.}, journal = {The Journal of the Florida Medical Association}, volume = {79}, number = {8}, pages = {545-552}, pmid = {1402775}, issn = {0015-4148}, mesh = {*Aerospace Medicine ; Air ; Animals ; Animals, Wild ; Ecology ; *Environmental Monitoring/methods ; Environmental Pollution/prevention & control ; Florida ; Government Agencies ; Information Systems ; Plants ; Rain ; Research ; Water ; }, abstract = {The Biomedical Operations and Research Office at the NASA John F. Kennedy Space Center has been supporting environmental monitoring and research since the mid-1970s. Program elements include monitoring of baseline conditions to document natural variability in the ecosystem, assessments of operations and construction of new facilities, and ecological research focusing on wildlife habitat associations. Information management is centered around development of a computerized geographic information system that incorporates remote sensing and digital image processing technologies along with traditional relational data base management capabilities. The proactive program is one in which the initiative is to anticipate potential environmental concerns before they occur and, by utilizing in-house expertise, develop impact minimization or mitigation strategies to reduce environmental risk.}, } @article {pmid1616292, year = {1992}, author = {Barrai, I and Formica, G and Scapoli, C and Beretta, M and Mamolini, E and Volinia, S and Barale, R and Ambrosino, P and Fontana, F}, title = {Microevolution in Ferrara: isonymy 1890-1990.}, journal = {Annals of human biology}, volume = {19}, number = {4}, pages = {371-385}, doi = {10.1080/03014469200002242}, pmid = {1616292}, issn = {0301-4460}, mesh = {Age Factors ; Databases, Factual/*trends ; Emigration and Immigration ; Female ; Genetics, Population/*history ; History, 19th Century ; History, 20th Century ; Humans ; Italy ; Male ; *Names ; Sex Factors ; Time Factors ; }, abstract = {The distribution of surnames in the population of the town of Ferrara, as it existed in the memory banks of the Municipality Computer in June 1990, was studied by sex, age and place of birth of residents. Random isonymy was studied separately in persons born before 1901, and in persons born in the nine decades thereafter, ending with the period 1981-90. Isonymy was higher in the older age groups studied. Also other indicators of the abundance of surnames in the distribution, the common ecological indexes derived from entropy, were calculated and compared between age groups. It was found that redundancy, as isonymy, is larger in older age classes than in younger classes. Surname effective number was defined as the inverse of isonymy corrected for sample size, and it was observed that it is practically identical with Fisher's alpha. It was then possible to separate random isonymy into two components, so that for sample size N its formulation becomes Ir = 1/alpha + 1/N It was found that in Ferrara alpha increased significantly in time, indicating enrichment of surnames in the population in the century 1890-1990.}, } @article {pmid1626879, year = {1992}, author = {Torres-Anjel, MJ}, title = {Macroepidemiology of the HIVs-AIDS (HAIDS) pandemic. Insufficiently considered zoological and geopolitical aspects.}, journal = {Annals of the New York Academy of Sciences}, volume = {653}, number = {}, pages = {257-273}, doi = {10.1111/j.1749-6632.1992.tb19655.x}, pmid = {1626879}, issn = {0077-8923}, mesh = {Acquired Immunodeficiency Syndrome/*epidemiology/transmission ; Africa/epidemiology ; African Swine Fever/epidemiology/transmission ; Animals ; Cuba/epidemiology ; *Disease Outbreaks ; HIV/*physiology ; Haiti/epidemiology ; Humans ; MEDLINE ; Portugal/epidemiology ; Warfare ; *Zoonoses ; }, abstract = {The human immunodeficiency viruses (HIVs)-acquired immunodeficiency syndrome (AIDS) or HAIDS pandemic originated from lentiviruses of nonhuman primates (thus qualifying as a zoonosis) that moved into humans in Africa. The HAIDS patients eventually die of opportunistic infections, all potentially zoonotic. The HAIDS infection remained parochial, first endemically and then epidemically, until the African urbanization that occurred in each of the countries postindependence. The latter included wars and the massive movement of soldiers (virologically naive) from the American continent to Africa and back. The HAIDS viral ecology coincided with African swine fever (ASF) in the Americas. Haiti became the focal point for both infections. Some infected Haitians also became, together with some infected drug addicts in the United States, a source of contaminated human blood for transfusions and production of plasma derivatives.}, } @article {pmid1591617, year = {1992}, author = {Byers, JA}, title = {REF-LIST: program to list references found in DOS text files of scientific manuscripts.}, journal = {Computer applications in the biosciences : CABIOS}, volume = {8}, number = {2}, pages = {196-198}, doi = {10.1093/bioinformatics/8.2.196}, pmid = {1591617}, issn = {0266-7061}, mesh = {Algorithms ; *Databases, Bibliographic ; *Software ; Software Design ; }, abstract = {A computer program, coded in QuickBASIC language, is used to make a non-redundant list of references, in alphabetical order, that are found in a scientific manuscript (formatted as a DOS text file). The program can extract either direct or indirect citations as in the following: Byers (1983a, b, 1984) and Miller and Keen, 1960; Byers et al., 1984; Byers 1984) An IBM-compatible personal computer is required to run the executable program.}, } @article {pmid1738864, year = {1992}, author = {Kennedy, KA and Chiment, J}, title = {Racial identification in the context of prehistoric-historic biological continua: examples from South Asia.}, journal = {Social science & medicine (1982)}, volume = {34}, number = {2}, pages = {119-123}, doi = {10.1016/0277-9536(92)90088-8}, pmid = {1738864}, issn = {0277-9536}, mesh = {Anthropology, Physical/*methods ; Asia, Western ; Biological Evolution ; Cephalometry/*methods ; Data Interpretation, Statistical ; Databases, Factual ; Forensic Medicine/*methods ; Genetics, Population ; Humans ; Paleontology/*methods ; Racial Groups/*classification/genetics ; }, abstract = {The practice of 'racial palaeontology' disappeared 50 years ago with the fall of the biological race concept in systematics and population genetics. However, certain ethnic minorities claim close biological affinities with extinct (sometimes Pleistocene) populations. Forensic anthropologists may be involved in this issue through analyses of prehistoric and modern populations in circumstances where a biological continuum may exist. Skeletal evidence from South Asia is discussed.}, } @article {pmid1608204, year = {1992}, author = {Petlenko, VP and Baranovskiĭ, AIu}, title = {[Methodological bases for prognosis in medicine].}, journal = {Klinicheskaia meditsina}, volume = {70}, number = {1}, pages = {3-8}, pmid = {1608204}, issn = {0023-2149}, mesh = {Diagnosis ; Diagnosis, Computer-Assisted ; Diagnostic Errors ; Humans ; Internal Medicine ; Methods ; *Prognosis ; }, abstract = {Current status of prognosis in clinical, experimental and prophylactic medicine is delineated with formulation of the purposes and feasibility of therapeutic and preventive realization of the disease onset and run prediction. Literature and first-hand experience provided the basis for grounding medical prognosis theory. Basic points in the theory are the following: utilization in the prognosis of only a complex of the most significant clinical signs of the disease, the patient's record, social and household, ecological and occupational aspects of the patient's life; comparison of the latter with leading pathogenetic mechanisms underlying the emergence and progression of the pathology; consideration of the relationships between dysfunction and morphology of the organs and systems; simultaneous analysis of the aggression factors, systemic reactivity and resistance of tissue; scrutiny of predisposition to pathological reactions. An essential aspect of medical prediction is a valid choice of mathematical methods of analysis and processing of the clinical information.}, } @article {pmid1604026, year = {1992}, author = {Richardson, S}, title = {[Statistic modeling of geographic and epidemiologic variations].}, journal = {Revue d'epidemiologie et de sante publique}, volume = {40}, number = {1}, pages = {33-45}, pmid = {1604026}, issn = {0398-7620}, mesh = {Bias ; Data Interpretation, Statistical ; Demography ; Ecology ; *Epidemiologic Factors ; Humans ; *Models, Statistical ; *Morbidity ; Mortality ; Regression Analysis ; Space-Time Clustering ; }, abstract = {In epidemiology, studies of the geographical variations of mortality or incidence rates for some chronic diseases have often given rise to etiological clues concerning those diseases. In this framework the variables concerned have a spatially autocorrelated structure which has to be taken into account in the statistical analysis. The statistical techniques used to study in the first place the spatial variations of mortality rates and then the joint geographical variations of mortality and exposure indices are reviewed. Emphasis is placed on the importance played by the geographical scale of the analysed data in the modelling process as well as on the interpretation problems of geographical correlation studies.}, } @article {pmid1576894, year = {1992}, author = {Demers, S and Kim, J and Legendre, P and Legendre, L}, title = {Analyzing multivariate flow cytometric data in aquatic sciences.}, journal = {Cytometry}, volume = {13}, number = {3}, pages = {291-298}, doi = {10.1002/cyto.990130311}, pmid = {1576894}, issn = {0196-4763}, mesh = {Data Interpretation, Statistical ; Ecology ; Flow Cytometry/*methods ; Marine Biology/*methods ; Multivariate Analysis ; }, abstract = {Flow cytometry has recently been introduced in aquatic ecology. Its unique feature is to measure several optical characteristics simultaneously on a large number of cells. Until now, these data have generally been analyzed in simple ways, e.g., frequency histograms and bivariate scatter diagrams, so that the multivariate potential of the data has not been fully exploited. This paper presents a way of answering ecologically meaningful questions, using the multivariate characteristics of the data. In order to do so, the multivariate data are reduced to a small number of classes by clustering, which reduces the data to a categorical variable. Multivariate pairwise comparisons can then be performed among samples using these new data vectors. The test case presented in the paper forms a time series of observations from which the new method enables us to study on the temporal evolution of cell types.}, } @article {pmid1536157, year = {1992}, author = {Day, R and Talbott, EO and Marsh, GM and Case, BW}, title = {A comparative ecological study of selected cancers in Kanawha County, West Virginia.}, journal = {American journal of industrial medicine}, volume = {21}, number = {2}, pages = {235-251}, doi = {10.1002/ajim.4700210213}, pmid = {1536157}, issn = {0271-3586}, mesh = {Adult ; Aged ; Cause of Death ; *Chemical Industry ; Data Interpretation, Statistical ; *Environmental Exposure ; Female ; Humans ; Leukemia/*mortality ; Lymphoma, Large B-Cell, Diffuse/*mortality ; Lymphoma, Non-Hodgkin/*mortality ; Male ; Middle Aged ; Poisson Distribution ; Sex Factors ; West Virginia/epidemiology ; }, abstract = {This study compares mortality rates for selected causes of death in Kanawha County, West Virginia, to rates reported in a number of geographically defined populations for 1950-1984. Specific conditions selected for study included cancers of the biliary passages and liver, the bladder and other urinary organs, and the central nervous system (CNS), as well as leukemia and aleukemia, lymphosarcoma and reticulosarcoma, Hodgkin's disease, and cancer of all other lymphopoietic tissue. The analysis made use of several techniques for the investigation of ecological data, including the modeling of rates using Poission regression. The primary findings of this study concern two subgroups of cancers of the lymphatic and hematopoietic tissue: (1) leukemia and aleukemia, and (2) lymphosarcoma and reticulosarcoma. For both subgroups of cancers, white male residents of Kanawha County show evidence of significantly elevated mortality rates over the 35-year period of this study.}, } @article {pmid1815380, year = {1991}, author = {Russom, CL and Anderson, EB and Greenwood, BE and Pilli, A}, title = {ASTER: an integration of the AQUIRE data base and the QSAR system for use in ecological risk assessments.}, journal = {The Science of the total environment}, volume = {109-110}, number = {}, pages = {667-670}, doi = {10.1016/0048-9697(91)90219-5}, pmid = {1815380}, issn = {0048-9697}, mesh = {Animals ; Cyprinidae ; *Databases, Bibliographic ; *Ecology ; Risk ; Structure-Activity Relationship ; United States ; United States Environmental Protection Agency ; Water Pollutants, Chemical/*toxicity ; }, abstract = {Ecological risk assessments are used by the US Environmental Protection Agency (US EPA) and other governmental agencies to assist in determining the probability and magnitude of deleterious effects of hazardous chemicals on plants and animals. These assessments are important steps in formulating regulatory decisions. The completion of an ecological risk assessment requires the gathering of ecotoxicological hazard and environmental exposure information. This information is evaluated in the risk characterization section to assist in making the final risk assessment. ASTER (ASsessment Tools for the Evaluation of Risk) was designed by the US EPA Environmental Research Laboratory-Duluth (ERL-D) to assist regulators in producing assessments. ASTER is an integration of the ACQUIRE (AQUatic toxicity Information REtrieval system) and QSAR (Quantitative Structure Activity Relationships) systems. ACQUIRE is a data base of aquatic toxicity tests and QSAR is comprised of a data base of measured physicochemical properties, and various QSAR models that estimate physicochemical and ecotoxicological endpoints. ASTER will be available to international governmental agencies through the US EPA National Computing Center.}, } @article {pmid1916736, year = {1991}, author = {Sokal, RR}, title = {Ancient movement patterns determine modern genetic variances in Europe.}, journal = {Human biology}, volume = {63}, number = {5}, pages = {589-606}, pmid = {1916736}, issn = {0018-7143}, support = {GM 28262/GM/NIGMS NIH HHS/United States ; }, mesh = {*Databases, Factual ; Emigration and Immigration/*history/statistics & numerical data ; Ethnology ; Europe ; *Gene Frequency ; *Genetic Variation ; History, Ancient ; }, abstract = {A summary ethnohistory database on population movements in Europe between 2000 B.C. and A.D. 1970 was related to genetic variances and distances based on 26 genetic systems. For the purposes of these analyses, Europe was divided into 85 terrestrial quadrats measuring 5 degrees x 5 degrees. Counts, stratified by time, were taken of the number of movements out of and into each quadrat (called source and target counts, respectively) and between each pair of quadrats. The source and target counts have distinct and different patterns in Europe and vary significantly over time. Central Europe and the Pontic area have the quadrats with the highest source counts, and the Balkans have the highest target counts. Modern genetic variances per quadrat are significantly correlated with source and target counts, somewhat more prominently with source counts. Genetic distances between pairs of quadrats are correlated strongly with geographic distances and moderately and negatively correlated with the total number of movements between these quadrats. Partial correlations of genetic distances with total number of movements, holding geographic distance constant, are small and mostly nonsignificant. These results are interpreted in light of our knowledge of the history and biology of the populations concerned.}, } @article {pmid1954943, year = {1991}, author = {Walter, SD}, title = {The ecologic method in the study of environmental health. II. Methodologic issues and feasibility.}, journal = {Environmental health perspectives}, volume = {94}, number = {}, pages = {67-73}, pmid = {1954943}, issn = {0091-6765}, mesh = {Canada/epidemiology ; Data Interpretation, Statistical ; *Ecology ; Emigration and Immigration ; Environmental Exposure ; *Environmental Health/statistics & numerical data ; Epidemiologic Methods ; Humans ; Time Factors ; United States/epidemiology ; }, abstract = {This paper reviews some methodological aspects of ecologic studies of human health, with emphasis on investigations of environmental quality. A recent census of Canadian and U.S. data sets potentially suitable for this type of study is summarized. It is concluded that despite the considerable utility of the ecologic design for this purpose, substantial practical difficulties are common in their implementation. Particular problems are the relative scarcity of relevant environmental data and complications associated with rendering them compatible with health data.}, } @article {pmid1954942, year = {1991}, author = {Walter, SD}, title = {The ecologic method in the study of environmental health. I. Overview of the method.}, journal = {Environmental health perspectives}, volume = {94}, number = {}, pages = {61-65}, pmid = {1954942}, issn = {0091-6765}, mesh = {Data Interpretation, Statistical ; *Ecology ; *Environmental Health/statistics & numerical data ; Epidemiology ; Humans ; }, abstract = {This paper summarizes the salient features of the ecologic method, with emphasis on its application in the study of environmental health. Various types of ecologic design are described, with examples. Finally, the main advantages and disadvantages are indicated. A companion paper discusses the methodology of ecologic designs in more detail and describes a census of data sets with potential suitability for the ecologic study of water quality and human health.}, } @article {pmid1994970, year = {1991}, author = {Johnston, MV and Findley, TW and DeLuca, J and Katz, RT}, title = {Research in physical medicine and rehabilitation. XII. Measurement tools with application to brain injury.}, journal = {American journal of physical medicine & rehabilitation}, volume = {70}, number = {1}, pages = {40-56}, doi = {10.1097/00002060-199102000-00008}, pmid = {1994970}, issn = {0894-9115}, mesh = {Brain Injuries/diagnosis/epidemiology/*rehabilitation ; Data Interpretation, Statistical ; Databases, Bibliographic ; Disability Evaluation ; Humans ; Outcome and Process Assessment, Health Care/methods ; *Physical and Rehabilitation Medicine/instrumentation/statistics & numerical data ; *Rehabilitation/instrumentation/statistics & numerical data ; Reproducibility of Results ; Research ; }, abstract = {There are basic principles and techniques of measurement that are relevant across biomedical disciplines. The purpose of this article is to explain some of the most important of these for medical rehabilitation, to illustrate how to use them to choose assessment instruments and to describe the nature of measurement in medical rehabilitation by examples in brain injury rehabilitation. Reliability is basic to any scientific measure. Validity, the ultimate criterion, is closely associated with the purpose of the measure. Content validity, criterion validity and construct validity are explained. Sensitivity to rehabilitative interventions and significance in patients' real lives (ecological validity) are emphasized. Measures of functional outcomes (disability) may show improvement after rehabilitation even when impairment measures do not. An extensive but selected list of measures of coma, global status, disabilities, communicative and cognitive impairments, and handicaps is presented, and their main uses are illustrated. Examples illustrate how to choose measures to study comprehensive program-level outcomes, to study learning-based interventions and to develop a general purpose database. Although there are many measures of activities of daily living and mobility, little published evidence of reliability and validity could be found even for some well-known scales. Ecologically valid and sensitive outcome measures are especially needed. Studies of the clinical utility of measures were also scarce. Many of these gaps can be spanned by clinical researchers with limited resources. Physical medicine and rehabilitation will benefit from formal studies of the reliabilities and validities of both its old and its new measurement instruments and by increased sophistication in choice of measures.}, } @article {pmid2031205, year = {1991}, author = {Pelletier, DL and Msukwa, LA}, title = {The use of national sample surveys for nutritional surveillance: lessons from Malawi's National Sample Survey of Agriculture.}, journal = {Social science & medicine (1982)}, volume = {32}, number = {8}, pages = {887-898}, doi = {10.1016/0277-9536(91)90244-7}, pmid = {2031205}, issn = {0277-9536}, mesh = {Age Factors ; Agriculture ; Body Height/physiology ; Body Weight/physiology ; Child ; Child Nutrition Disorders/*epidemiology/etiology/physiopathology ; Child, Preschool ; Data Interpretation, Statistical ; Female ; Humans ; Infant ; Malawi/epidemiology ; Male ; *Nutrition Surveys ; Sex Factors ; Socioeconomic Factors ; }, abstract = {National sample surveys, containing measurements of the weights and heights of children along with other socioeconomic modules, represent one of the important sources of information for nutritional surveillance. The potential uses of such information are political sensitization, targeting by geographic area, targeting by socioeconomic group, and identifying the most promising intervention options according to the presumed causes of malnutrition. The latter two applications depend upon the ability to detect stable associations between nutritional status and socioeconomic factors. This paper examines the extent to which these planning applications are affected by variation in the ecology of malnutrition across different segments of society, using Malawi's National Sample Survey of Agriculture (NSSA). The NSSA is nationally representative of Malawi's smallholder sector and contains information on anthropometrics of underfives and various socioeconomic characteristics of their households. This analysis is based upon 3000 households containing at least one underfive, with one child per household being selected for analysis. Height-for-age Z-scores (HAZ) are calculated using WHO standards, and analyzed using analysis of variance (ANOVA). Variation in nutritional ecology is investigated by examining statistical interactions among socioeconomic variables as they relate to HAZ and by comparing ANOVA models constructed within several sample strata. These strata are defined according to geographic region, size of cultivated area, child's sex, child's age and, for a subsample, ethnic/religious identification. The results demonstrate that significant two-way interactions exist between region, cultivated area, household labor availability and age of the child. For the total sample HAZ declines with increasing cultivated area among young children (less than 24 months) but improves with increasing cultivated area among older children (greater than or equal to 24 months). The overall trend for young children is region-specific, however, such that no generalizations can be made concerning the effects of region and cultivated area without taking the other factor and child's age into account. Similarly, cultivated area interacts with household labor availability among young children, such that more labor is associated with lower HAZ on plots less than 0.7 ha, but more labor is associated with higher HAZ on plots above 1.5 ha. The existence of variation in nutritional ecology is further borne out by the observed variation in multivariable ANOVA models constructed within various sample strata. It is concluded that significant variation in nutritional ecology does exist between various segments of society. This limits the usefulness of national sample surveys for selecting intervention options and for targeting interventions according to socioeconomic characteristics.}, } @article {pmid1754700, year = {1991}, author = {Joly, MF and Foggin, P and Pless, I}, title = {[Socioecological determinants of the risk of accidents in young pedestrians].}, journal = {Revue d'epidemiologie et de sante publique}, volume = {39}, number = {4}, pages = {345-351}, pmid = {1754700}, issn = {0398-7620}, mesh = {Accidents, Traffic/*statistics & numerical data ; Adolescent ; Child ; Child, Preschool ; Data Interpretation, Statistical ; *Ecology ; Environment ; Female ; Humans ; Male ; Prospective Studies ; Quebec/epidemiology ; Risk ; Seasons ; Time Factors ; Urban Population ; }, abstract = {We studied all traffic accidents to pedestrians under age 15 which occurred on the Island of Montreal during an eighteen months period. Data were collected from eleven hospitals and completed with accident police records. A spatial quadrat analysis, a Comparative Accident Index, and a comparative analysis of the means of different socio-ecological variables between high and low risk accident areas revealed interesting patterns. The location of traffic accidents is not random but rather presents a particular spatial structure. High risk zones are characterized by dense population, fast-moving traffic, and the absence of parks. Accidents often take place on two-way streets, far from traffic lights, on dry surfaces, in good weather, and with good visibility. The socio-economic status of the victim's family as measured by education, income, and unemployment, tends to be low. More boys than girls are victims. Children are often injured while getting out of a car or crossing unconventionally.}, } @article {pmid1981621, year = {1990}, author = {Sugihara, G and Grenfell, B and May, RM}, title = {Distinguishing error from chaos in ecological time series.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {330}, number = {1257}, pages = {235-251}, doi = {10.1098/rstb.1990.0195}, pmid = {1981621}, issn = {0962-8436}, mesh = {Chickenpox/epidemiology ; Data Interpretation, Statistical ; *Ecology ; Epidemiologic Methods ; Humans ; Measles/epidemiology ; *Population Dynamics ; }, abstract = {Over the years, there has been much discussion about the relative importance of environmental and biological factors in regulating natural populations. Often it is thought that environmental factors are associated with stochastic fluctuations in population density, and biological ones with deterministic regulation. We revisit these ideas in the light of recent work on chaos and nonlinear systems. We show that completely deterministic regulatory factors can lead to apparently random fluctuations in population density, and we then develop a new method (that can be applied to limited data sets) to make practical distinctions between apparently noisy dynamics produced by low-dimensional chaos and population variation that in fact derives from random (high-dimensional) noise, such as environmental stochasticity or sampling error. To show its practical use, the method is first applied to models where the dynamics are known. We then apply the method to several sets of real data, including newly analysed data on the incidence of measles in the United Kingdom. Here the additional problems of secular trends and spatial effects are explored. In particular, we find that on a city-by-city scale measles exhibits low-dimensional chaos (as has previously been found for measles in New York City), whereas on a larger, country-wide scale the dynamics appear as a noisy two-year cycle. In addition to shedding light on the basic dynamics of some nonlinear biological systems, this work dramatizes how the scale on which data is collected and analysed can affect the conclusions drawn.}, } @article {pmid2231769, year = {1990}, author = {Schatzkin, A and Freedman, LS and Schiffman, MH and Dawsey, SM}, title = {Validation of intermediate end points in cancer research.}, journal = {Journal of the National Cancer Institute}, volume = {82}, number = {22}, pages = {1746-1752}, doi = {10.1093/jnci/82.22.1746}, pmid = {2231769}, issn = {0027-8874}, mesh = {Biomarkers, Tumor ; Case-Control Studies ; Cohort Studies ; Data Interpretation, Statistical ; Humans ; Incidence ; Neoplasms/*epidemiology ; Reproducibility of Results ; *Research Design ; Statistics as Topic/methods ; }, abstract = {Investigations using intermediate end points as cancer surrogates are quicker, smaller, and less expensive than studies that use malignancy as the end point. We present a strategy for determining whether a given biomarker is a valid intermediate end point between an exposure and incidence of cancer. Candidate intermediate end points may be selected from case series, ecologic studies, and animal experiments. Prospective cohort and sometimes case-control studies may be used to quantify the intermediate end point-cancer association. The most appropriate measure of this association is the attributable proportion. The intermediate end point is a valid cancer surrogate if the attributable proportion is close to 1.0, but not if it is close to 0. Usually, the attributable proportion is close to neither 1.0 nor 0; in this case, valid surrogacy requires that the intermediate end point mediate an established exposure-cancer relation. This would in turn imply that the exposure effect would vanish if adjusted for the intermediate end point. We discuss the relative advantages of intervention and observational studies for the validation of intermediate end points. This validation strategy also may be applied to intermediate end points for adverse reproductive outcomes and chronic diseases other than cancer.}, } @article {pmid2120154, year = {1990}, author = {Adell, JC and Moya, A and Molina, V and González-Candelas, F}, title = {On the analysis of viability data: an example with Drosophila.}, journal = {Heredity}, volume = {65 (Pt 1)}, number = {}, pages = {39-46}, doi = {10.1038/hdy.1990.67}, pmid = {2120154}, issn = {0018-067X}, mesh = {Animals ; *Data Interpretation, Statistical ; Drosophila melanogaster ; *Ecology ; Mutation ; Phenotype ; Species Specificity ; *Survival ; }, abstract = {Larval competition experiments involving two wild type and eight mutant strains of Drosophila melanogaster have been carried out following the substitution procedure proposed by Mather and Caligari (1981). Our main goal has been to compare the competitive abilities of two phenotypically indistinguishable strains (wild and Oregon-R) by means of their responses with eight different mutants. Prior to the analyses of viability data, we have studied the normalizing effect of several transformations in order to determine which was best suited for the analyses. The differences found among the five transformations tested and the untransformed data were not very great. The folded power transformation (Mosteller and Tukey, 1977) was finally chosen. No constant pattern in the responses of the two wild type strains to the mutant competitors was detected. This leads us to conclude that the nature of the competition between the two wild type strains cannot be predicted from a knowledge of their competition with other strains.}, } @article {pmid2604905, year = {1989}, author = {Devillers, J and Zakarya, D and Chastrette, M and Doré, JC}, title = {The stochastic regression analysis as a tool in ecotoxicological QSAR studies.}, journal = {Biomedical and environmental sciences : BES}, volume = {2}, number = {4}, pages = {385-393}, pmid = {2604905}, issn = {0895-3988}, mesh = {Animals ; Benzene Derivatives/toxicity ; Cyprinidae ; *Data Interpretation, Statistical ; *Ecology ; Factor Analysis, Statistical ; Regression Analysis ; Stochastic Processes ; Structure-Activity Relationship ; Toxicology/*methods ; }, abstract = {Correspondence factor analysis (CFA) was used in conjunction with linear regression analysis to examine the structure-activity relationships of 50 benzene derivatives tested on Pimephales promelas. From nine molecular descriptions (numbers of C, H, O, N, Br, Cl, NO2, OH, and NH2 included in the molecules), CFA made it possible to define five new independent variables which were introduced in a stepwise regression analysis procedure to describe the acute toxicity (96-h LC50) of the aromatic compounds. The model log 1/C = -0.727F1 + 1.248F3 + 4.052 (r = 0.918; s = 0.270) is more relevant to describe the ecotoxicological behavior of the studied compounds on the fathead minnow than that obtained with principal components (log 1/C = 0.151 PC1 -0.271 PC2 + 4.124; r = 0.737; s = 0.460). The heuristic potency of this particular statistical analysis, which is called stochastic regression analysis, is discussed in detail.}, } @article {pmid2776577, year = {1989}, author = {Campbell, JW and Yentsch, CM and Cucci, TL}, title = {Variance within homogeneous phytoplankton populations, III: Analysis of natural populations.}, journal = {Cytometry}, volume = {10}, number = {5}, pages = {605-611}, doi = {10.1002/cyto.990100516}, pmid = {2776577}, issn = {0196-4763}, mesh = {Data Interpretation, Statistical ; Ecology ; *Flow Cytometry ; Marine Biology ; Mathematics ; Models, Theoretical ; *Phytoplankton ; *Plankton ; Population Dynamics ; }, abstract = {A theoretical framework for interpreting flow cytometric histograms from homogeneous phytoplankton populations was developed in part I of this series of articles and applied to chlorophyll fluorescence histograms from clonal cultures in part II. In this paper, we demonstrate the application of this framework to the analysis of cell volume distributions found in a natural assemblage of phytoplankton from the Gulf of California. Flow cytometric analyses of a surface water sample incubated for a period of 61 h revealed the sequential growth and decline of three distinct subpopulations. Cell volume distributions for each subpopulation measured at different times were analyzed, and the theoretical density function described in parts I and II was fitted to these distributions. The range of cell volumes within each subpopulation was similar to that predicted for asynchronous populations.}, } @article {pmid2772270, year = {1989}, author = {Beasley, VR and Schaeffer, DJ}, title = {Ecosystem health. IV. The National Animal Poison Information Network database as a tool for ecological risk assessment.}, journal = {Regulatory toxicology and pharmacology : RTP}, volume = {10}, number = {1}, pages = {63-73}, doi = {10.1016/0273-2300(89)90013-5}, pmid = {2772270}, issn = {0273-2300}, mesh = {Animals ; Animals, Wild ; *Environmental Pollution ; Epidemiology ; *Information Systems ; *Poison Control Centers ; Risk ; Toxicology ; United States ; *Veterinary Medicine ; }, abstract = {Toxicology is a unique discipline in human and veterinary medicine because there are orders of magnitude more toxicants available to man and animals than all known pathogenic microorganisms and parasites. The study of toxicologic responses of ecosystems to contaminants, ecoepidemiology, and the specific study of animal populations in this context, epizootiologic ecotoxicology, are concerned with identifying chemically induced causes and determining effects on and links among populations, communities, and ecosystems. Necessary activities implied by the term "epizootiologic ecotoxicology" are the systematic compilation and analysis of "health" data for ecosystem components. This concept paper describes the value and limitations of adapting methods used by the National Animal Poison Information Network (NAPINet) for epizootiologic ecotoxicology studies. It is concluded that NAPINet methodology, as part of an innovative use of population statistics and clinical measurements, could eventually be adapted into a valuable component of a standardized approach to epizootiologic ecotoxicology.}, } @article {pmid2721935, year = {1989}, author = {Sokal, RR and Jacquez, GM and Wooten, MC}, title = {Spatial autocorrelation analysis of migration and selection.}, journal = {Genetics}, volume = {121}, number = {4}, pages = {845-855}, pmid = {2721935}, issn = {0016-6731}, support = {GM28262/GM/NIGMS NIH HHS/United States ; }, mesh = {Computer Simulation ; *Data Interpretation, Statistical ; Gene Frequency ; *Models, Genetic ; Selection, Genetic ; }, abstract = {We test various assumptions necessary for the interpretation of spatial autocorrelation analysis of gene frequency surfaces, using simulations of Wright's isolation-by-distance model with migration or selection superimposed. Increasing neighborhood size enhances spatial autocorrelation, which is reduced again for the largest neighborhood sizes. Spatial correlograms are independent of the mean gene frequency of the surface. Migration affects surfaces and correlograms when immigrant gene frequency differentials are substantial. Multiple directions of migration are reflected in the correlograms. Selection gradients yield clinal correlograms; other selection patterns are less clearly reflected in their correlograms. Sequential migration from different directions and at different gene frequencies can be disaggregated into component migration vectors by means of principal components analysis. This encourages analysis by such methods of gene frequency surfaces in nature. The empirical results of these findings lend support to the inference structure developed earlier for spatial autocorrelation analysis.}, } @article {pmid2656561, year = {1989}, author = {Greenland, S and Morgenstern, H}, title = {Ecological bias, confounding, and effect modification.}, journal = {International journal of epidemiology}, volume = {18}, number = {1}, pages = {269-274}, doi = {10.1093/ije/18.1.269}, pmid = {2656561}, issn = {0300-5771}, mesh = {*Data Interpretation, Statistical ; *Epidemiologic Methods ; Humans ; Risk Factors ; }, abstract = {Ecological bias is sometimes attributed to confounding by the group variable (ie the variable used to define the ecological groups), or to risk factors associated with the group variable. We show that the group variable need not be a confounder (in the strict epidemiological sense) for ecological bias to occur: effect modification can lead to profound ecological bias, whether or not the group variable or the effect modifier are independent risk factors. Furthermore, an extraneous risk factor need not be associated with the study variable at the individual level in order to produce ecological bias. Thus the conditions for the production of ecological bias by a covariate are much broader than the conditions for the production of individual-level confounding by a covariate. We also show that standardization or ecological control of variables responsible for ecological bias are generally insufficient to remove such bias.}, } @article {pmid2809653, year = {1989}, author = {Feinstein, AR}, title = {Para-analysis, faute de mieux, and the perils of riding on a data barge.}, journal = {Journal of clinical epidemiology}, volume = {42}, number = {10}, pages = {929-935}, doi = {10.1016/0895-4356(89)90157-1}, pmid = {2809653}, issn = {0895-4356}, mesh = {*Data Interpretation, Statistical ; Ecology ; *Epidemiologic Methods ; Humans ; Information Systems ; Pharmacology ; Research/standards ; }, } @article {pmid3147215, year = {1988}, author = {Smit-McBride, Z and Moya, A and Ayala, FJ}, title = {Linkage disequilibrium in natural and experimental populations of Drosophila melanogaster.}, journal = {Genetics}, volume = {120}, number = {4}, pages = {1043-1051}, pmid = {3147215}, issn = {0016-6731}, mesh = {Alleles ; Animals ; Data Interpretation, Statistical ; Drosophila melanogaster/*genetics ; Gene Frequency ; *Genetic Linkage ; Heterozygote ; Isoenzymes/*genetics ; *Polymorphism, Genetic ; Selection, Genetic ; }, abstract = {We have studied linkage disequilibrium in Drosophila melanogaster in two samples from a wild population and in four large laboratory populations derived from the wild samples. We have assayed four polymorphic enzyme loci, fairly closely linked in the third chromosome: Sod Est-6, Pgm, and Odh. The assay method used allows us to identify the allele associations separately in each of the two homologous chromosomes from each male sampled. We have detected significant linkage disequilibrium between two loci in 16.7% of the cases in the wild samples and in 27.8% of the cases in the experimental populations, considerably more than would be expected by chance alone. We have also found three-locus disequilibria in more instances than would be expected by chance. Some disequilibria present in the wild samples disappear in the experimental populations derived from them, but new ones appear over the generations. The effective population sizes required to generate the observed disequilibria by randomness range from 40 to more than 60,000 individuals in the natural population, depending on which locus pair is considered, and from 100 to more than 60,000 in the experimental populations. These population sizes are unrealistic; the fact that different locus-pairs yield disparate estimates within the same population argues against the likelihood that the disequilibria may have arisen as a consequence of population bottlenecks. Migration, or population mixing, cannot be excluded as the process generating the disequilibria in the wild samples, but can in the experimental populations. We conclude that linkage disequilibrium in these populations is most likely due to natural selection acting on the allozymes, or on loci very tightly linked to them.}, } @article {pmid3201786, year = {1988}, author = {Lynch, WD and Glass, GV and Tran, ZV}, title = {Diet, tobacco, alcohol, and stress as causes of coronary artery heart disease: an ecological trend analysis of national data.}, journal = {The Yale journal of biology and medicine}, volume = {61}, number = {5}, pages = {413-426}, pmid = {3201786}, issn = {0044-0086}, mesh = {Aged ; *Alcohol Drinking ; Coronary Disease/epidemiology/*etiology/mortality ; Data Interpretation, Statistical ; *Diet, Atherogenic ; Female ; Humans ; Longitudinal Studies ; Male ; Middle Aged ; *Smoking ; Stress, Psychological/*complications ; United States ; Vital Statistics ; }, abstract = {The present investigation examined the temporal relationships between changes in coronary artery heart disease (CAHD) mortality rates from whites (1938-1980) and changes in national measures of dietary elements, tobacco consumption, alcohol consumption, and unemployment. The magnitude and latency of the causal relationships were estimated with the use of cross-lagged correlation functions (CCFs) and Granger causality tests. Preliminary CCFs showed consistent correlational patterns between CAHD and tobacco, ethanol, and dietary fats. There was little association between CAHD and dietary cholesterol. Ethanol, tobacco, and the ratio of saturated to polyunsaturated fats (S:P) were analyzed for directional causality using Granger causality tests. The S:P ratio demonstrated a unidirectional Granger causal relationship with CAHD mortality in all sex and age groups. The estimated latency of this relationship was 23 to 30 years. This finding supports a causal relationship between diet, specifically fats, and the risk of CAHD two or three decades later.}, } @article {pmid3517974, year = {1986}, author = {Strauss, H and Hattis, D and Page, G and Harrison, K and Vogel, S and Caldart, C}, title = {Genetically-engineered microorganisms: I. Identification, classification, and strain history.}, journal = {Recombinant DNA technical bulletin}, volume = {9}, number = {1}, pages = {1-15}, pmid = {3517974}, issn = {0196-0229}, mesh = {Bacteria/*classification/genetics/metabolism/pathogenicity ; Bacterial Proteins/analysis ; Containment of Biohazards ; Crosses, Genetic ; DNA, Bacterial/genetics ; DNA, Recombinant ; Ecology ; Genes, Synthetic ; *Genetic Engineering ; MEDLARS ; Phenotype ; Reference Books ; United States ; }, abstract = {We have argued that accurate identification of the microorganism will form a cornerstone of the assessment of potential hazard. Appropriate methodology for identification exists, and is continually under development and refinement. Organizations such as the American Type Culture Collection will perform certified identifications for relatively low cost. Thus there appears to be little reason that an organism should not be identified insofar as current microbiology allows prior to submission for PMN review. We suggest that a complete microbiological characterization be considered an essential element of an acceptable PMN. To accomplish this, however, current institutional arrangements for the protection of trade secret information needed in the process of identification may need to be improved. An accurate identification of the strain will often provide access to important information with which to evaluate its ecology, pathogenicity, biochemistry, and genetics. Specialized texts, the scientific literature, and professional consultation are ready sources of such information. However, a major effort should be made to establish a data base that can specifically address the needs of biohazard evaluation. This could be done, in part, by collecting information about the construction, and about the behavior in the environment of genetically-engineered microorganisms that are now under development and will soon be tested or used. Identification information may also eventually be useful for the formulation of hypotheses about possible modes of harm or about relative safety, based on phylogenetic relationships. This is a very difficult undertaking at present, however. Microbial taxonomy is currently in a process of radical reevaluation as new macromolecular sequence information reveals previously unsuspected phylogenetic relationships, and disturbs categorizations based on older types of traits such as morphology, etc. This means that both inferences about relative safety and about possible modes of harm from taxonomic relationships must be highly tentative based on current information. Regulatory authorities may wish to consider requesting confirmatory DNA hybridization data or other macromolecular sequence comparisons in cases where strong arguments related to safety must be made from taxonomic information in relatively poorly studied groups of organisms. Detailed strain histories would provide valuable information for safety evaluations.(ABSTRACT TRUNCATED AT 400 WORDS)}, } @article {pmid3516058, year = {1986}, author = {O'Rourke, DH and Suarez, BK}, title = {Patterns and correlates of genetic variation in South Amerindians.}, journal = {Annals of human biology}, volume = {13}, number = {1}, pages = {13-31}, doi = {10.1080/03014468600008171}, pmid = {3516058}, issn = {0301-4460}, support = {MH14677/MH/NIMH NIH HHS/United States ; MH31302/MH/NIMH NIH HHS/United States ; }, mesh = {Alleles ; Blood Group Antigens/genetics ; Climate ; Epidemiologic Methods ; Gene Frequency ; *Genetic Variation ; Humans ; *Indians, South American ; Information Systems ; South America ; }, abstract = {Gene frequency data from six polymorphic blood group systems in 70 South American Indian populations are used to derive synthetic gene frequency maps that document the geographical pattern of genetic variation. Additional analyses are directed toward the elucidation of mechanisms that give rise to or maintain the observed distributions. Variables of local ecology do not appear to explain gene frequency distributions in South America. Instead, local isolation and the action of stochastic forces appears to be the most parsimonious explanation of the observed geographical patterns. This is distinctly different from the geographical patterns of genetic variation seen in other continents.}, } @article {pmid4036283, year = {1985}, author = {Vorob'ev, EI}, title = {[Health and the environment].}, journal = {Vestnik Akademii meditsinskikh nauk SSSR}, volume = {}, number = {5}, pages = {84-90}, pmid = {4036283}, issn = {0002-3027}, mesh = {Ecology ; *Environmental Health ; Environmental Pollution/prevention & control ; Information Systems ; Methods ; Models, Theoretical ; Systems Analysis ; }, } @article {pmid7240350, year = {1981}, author = {Walker, CR and Menzie, CM and Bowles, WA}, title = {Evaluation of an information retrieval system for assessment of toxicological effects of chemicals on fish, wildlife, and ecosystem components.}, journal = {Journal of chemical information and computer sciences}, volume = {21}, number = {1}, pages = {29-35}, doi = {10.1021/ci00029a006}, pmid = {7240350}, issn = {0095-2338}, mesh = {*Animal Population Groups ; Animals ; *Animals, Wild ; *Ecology ; *Environmental Pollutants ; *Fishes ; *Information Systems ; *Toxicology ; }, abstract = {A user-oriented information retrieval system is needed for assessment of materials hazardous to fish, wildlife, food chain organisms, and other organisms essential to the maintenance to ecosystem processes and functions. Critical evaluation of data also requires rigorous documentation of test conditions, precision of methods used, and the sensitivity of the test organism. Particular emphasis of the evaluation was in developing practical criteria that aid in the use and interpretation of data with respect to need for further testing in a scoring exercise performed for the Toxic Substances Control Act Interagency Testing Committee. Recommendations are made for the integration of information on physical and chemical properties, health effects, ecotoxicology, and environmental concentration or exposure level.}, } @article {pmid10236960, year = {1975}, author = {Marderosian, AD}, title = {Sources of information concerning drugs from the sea.}, journal = {Drug information journal}, volume = {9}, number = {2-3}, pages = {101-106}, pmid = {10236960}, issn = {0092-8615}, mesh = {*Drug Information Services ; *Information Services ; Information Systems ; Marine Biology/*education ; Pharmacognosy/*education ; }, } @article {pmid4387193, year = {1968}, author = {Bengson, MH and Thomae, FW}, title = {Research on the effects of alteration of the indigenous microflora of the monkey. AMRL-TR-67-177.}, journal = {AMRL-TR. Aerospace Medical Research Laboratories (U.S.)}, volume = {}, number = {}, pages = {1-151}, pmid = {4387193}, mesh = {Animals ; *Bacteria ; Computers ; Ecological Systems, Closed ; *Fungi ; Germ-Free Life ; *Haplorhini ; Information Systems ; Space Flight ; }, } @article {pmid4381826, year = {1966}, author = {Harris, ES}, title = {Parts and materials data retrieval program relative to materials selection in toxicology. AMRL-TR-66-120.}, journal = {AMRL-TR. Aerospace Medical Research Laboratories (U.S.)}, volume = {}, number = {}, pages = {9-13}, pmid = {4381826}, mesh = {*Air Pollution ; *Ecological Systems, Closed ; Environmental Exposure ; Humans ; *Information Systems ; }, }